[ { "text": "Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health\n\nA pangenome and pantranscriptome of hexaploid oat.", "token_count": 42, "char_count": 160, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:26.747336", "source": { "split": "train_shard_00000", "doc_id": 0 }, "chunk_id": "train_shard_00000_0_0", "global_id": 0 }, { "text": "Aerococcus christensenii (A. christensenii) is a symbiotic bacterium that primarily colonizes the vagina. Infections caused by A. christensenii are rare but can also pose a significant health threat. In this study, two rare cases of A. christensenii bacteremia in pregnant women complicated with chorioamnionitis were investigated; and two strains KSW23 and KWL24, which were isolated from blood samples, were analyzed for their genomic characteristics and pathogenic potential. Whole-genome sequencing revealed that the genome sizes of KSW23 and KWL24 were approximately 1.6 Mb, and predicted multiple genes associated with pathogenicity (tuf, eno, plr/gapA, galU, galE, groEL, gndA, sugC, lplA1, mgtB, clpC, clpP, and lmb), antibiotic resistance (ermB and tet(M)), and mobile genetic elements (plasmid replicon repUS43 and transposon Tn6009). Correspondingly, these strains showed multidrug resistance to Macrolides, Lincosamides, and Tetracyclines. Pangenome analysis revealed close evolutionary relationships and significant genomic conservation between these two strains and the previously isolated strains, especially with respect to genes related to pathogenicity and antibiotic resistance. Notably, a mouse bacteremia model confirmed the pathogenicity and virulence of A. christensenii strains KSW23 and KWL24, which induced bacteremia and mortality, but not as strongly as Staphylococcus aureus (S. aureus) strain ATCC25923. Additionally, A. christensenii exhibited a robust survival ability in human blood comparable to those observed in S. aureus strain ATCC25923. To our knowledge, this study is the first genomic research on A. christensenii, and confirms the species' bloodstream invasive capacity and pathogenicity based on genomic studies and experimental validation. These findings underscore its role as a pathogen in the ascending genital tract in the obstetric population.", "token_count": 496, "char_count": 1892, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [ "KSW23", "ATCC25923", "KWL24" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:27.751177", "source": { "split": "train_shard_00000", "doc_id": 1 }, "chunk_id": "train_shard_00000_1_0", "global_id": 1 }, { "text": "Aerococcus christensenii: an emerging pathogen associated with infections and bacteremia in pregnancy-genomic insights and pathogenicity evaluation.", "token_count": 33, "char_count": 148, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:28.109803", "source": { "split": "train_shard_00000", "doc_id": 1 }, "chunk_id": "train_shard_00000_1_1", "global_id": 2 }, { "text": "Pediococcus pentosaceus Li05, a strain of lactic acid bacteria isolated from the faeces of healthy volunteers, exhibited potential protective effects against various diseases. This study performed third-generation sequencing and detailed characterisation of its genome. The Li05 chromosome harboured conserved genes associated with acid resistance (atp), bile salt resistance (bsh), oxidative stress resistance (hsl, dltA, and et al.), and adhesion (nrd, gap, and et al.), whereas the plasmid did not contain antibiotic resistance or virulence genes. Following intervention with Li05 in loperamide-induced constipated mice, constipation symptoms improved. Meanwhile, alterations in gut microbiota, increased BSH activity in faeces, and modifications to the faecal bile acid profile were observed. Additionally, expression levels of TGR5 and TPH1 in the colon of the mice increased, leading to elevated 5-HT levels. When the TGR5 gene was knocked out or the TPH1 inhibitor LX1606 was administered to suppress 5-HT synthesis in constipated mice, the beneficial effects of Li05 on gastrointestinal motility and mucus secretion were reversed. Culturing intestinal organoids demonstrated that increased bile acids such as DCA, Iso-LCA, and EALCA could enhance 5-HT levels through the TGR5/TPH1 axis. Therefore, we concluded that Li05 regulated bile acid metabolism, subsequently increasing 5-HT levels through the TGR5/TPH1 axis, thus alleviating constipation.\n\nProtective Effect of Pediococcus pentosaceus Li05 on Constipation via TGR5/TPH1/5-HT Activation.", "token_count": 420, "char_count": 1553, "word_count": 212, "semantic_coherence": 1, "information_density": 0.684, "quality_score": 0.842, "entities": { "genes": [ "LX1606", "TPH1", "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:28.702227", "source": { "split": "train_shard_00000", "doc_id": 2 }, "chunk_id": "train_shard_00000_2_0", "global_id": 3 }, { "text": "High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging.\n\nHigh-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons.", "token_count": 65, "char_count": 305, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:29.068283", "source": { "split": "train_shard_00000", "doc_id": 3 }, "chunk_id": "train_shard_00000_3_0", "global_id": 4 }, { "text": "The classification of living systems presents significant challenges due to the prevalence of gene transfer between genomes. Traditional taxonomic systems have been designed to describe tree-like evolution and consequently struggle to accommodate network-like evolutionary patterns. In this perspective, I consolidate and clarify terminology for describing organisms whose evolutionary history has not been strictly tree-like. I introduce two complementary concepts: epaktovars - groups (>=2) of organisms exhibiting convergent phenotypes through independent acquisition of similar functions, whether via horizontal gene transfer or independent evolution of analogous solutions; and xenotypes - organisms that share homologous genes acquired through horizontal gene transfer, regardless of whether these shared genes produce similar or different phenotypes. The epaktovar concept mirrors the previously established concept of epaktologs (independent assembly of similar protein domain architectures), while xenotypes extends the concept of xenologs (horizontally transferred homologous genes) to the genome level. Recent research on homoplastic patterns in pangenome evolution enhances our understanding of these phenomena. These concepts also have important applications in synthetic biology and de-extinction efforts, where genetically modified organisms and reconstructed extinct species can be understood as xenotypes and epaktovars of their genetic donors, providing a framework for classifying organisms whose genetic composition has been shaped by human intervention rather than natural evolutionary processes. These terms collectively provide a framework for describing both phenotypic convergence arising through any evolutionary mechanism and shared genetic material resulting specifically from gene transfer across diverse lineages.\n\nClassifying Convergences in the Light of Horizontal Gene Transfer: Epaktovars and Xenotypes.", "token_count": 372, "char_count": 1937, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:29.621124", "source": { "split": "train_shard_00000", "doc_id": 4 }, "chunk_id": "train_shard_00000_4_0", "global_id": 5 }, { "text": "Transposable elements are major components of plant genomes and major drivers of plant genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization, speciation, domestication, and crop improvement. Here, we implement genome and pangenome analyses to study in detail the dynamics of LTR-retrotransposons during the cotton evolution.\n\nDifferential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium).", "token_count": 121, "char_count": 507, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:30.046113", "source": { "split": "train_shard_00000", "doc_id": 5 }, "chunk_id": "train_shard_00000_5_0", "global_id": 6 }, { "text": "Drought poses a severe threat to the stability of crop yields. It is crucial to identify genetic resources and decipher the molecular mechanisms underlying drought resistance in crops. Here we generated high-quality genome assemblies of 25 maize germplasms exhibiting substantial variation in drought resistance. Combined with 31 additional maize genome sequences, a comprehensive pangenome analysis was performed. Rare allelic variations and extensive regulatory diversity were revealed in abscisic acid-related or drought-related genes, which may contribute to the diversity in drought resistance among germplasms. Furthermore, we identified three genes, ZmUGE2, ZmSIL2 and ZmASI3, that enhance maize drought resistance by strengthening mechanical support of the cell wall, regulating stress-responsive gene expression and coordinating male and female inflorescence development, respectively. Thus, this study provides valuable insight into the genetic control of drought resistance in maize at different growing stages. The expanded maize pangenome information serves as a valuable resource for maize genomic research.\n\nA pangenome of maize provides genetic insights into drought resistance.", "token_count": 252, "char_count": 1194, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6937, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:30.534497", "source": { "split": "train_shard_00000", "doc_id": 6 }, "chunk_id": "train_shard_00000_6_0", "global_id": 7 }, { "text": "Dietary fiber is essential for health but remains under-consumed in Western diets. Fiber types differ in their physicochemical properties, which influence gastrointestinal function, bile acid (BA) metabolism, and gut microbiota composition. C57Bl/6 mice were fed control or 10% (w/w) fiber diets containing cellulose, chitin, resistant starch, pectin, inulin, β-glucan, psyllium, dextrin, or raffinose. All fibers reduced bacterial diversity, while most increased\n\nComparative analysis of dietary fiber impact on bile acid metabolism and gut microbiota composition in mice.", "token_count": 162, "char_count": 573, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8442, "quality_score": 0.9221, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:30.970311", "source": { "split": "train_shard_00000", "doc_id": 7 }, "chunk_id": "train_shard_00000_7_0", "global_id": 8 }, { "text": "Sodium-taurocholate co-transporting polypeptide (NTCP) is a sodium-dependent transporter mediating the hepatic uptake of bile salts and serving as the receptor of hepatitis B and D viruses. While previous studies identified binding sites for sodium ions and substrates, the mechanism remains controversial. We here report a high-resolution structure of NTCP in a closed-tunnel conformation that does not feature substrate binding sites but reveals evidence of two bound sodium ions. To evaluate the functional relevance of this state and gain insight into the transport mechanism, we performed μs-scale molecular dynamics simulations of NTCP starting from distinct conformations and substrate and ion configurations. We observed that both the closed-tunnel and open-tunnel conformations are highly stable, but that the sodium ions and bile salt molecules can shift positions without substantial conformational changes. Our results suggest that the closed-tunnel conformation might represents an inactive state rather than an essential component of a productive transport cycle.\n\nStructure of nanobody-inhibited state of human bile salt transporter NTCP.", "token_count": 251, "char_count": 1153, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:31.484283", "source": { "split": "train_shard_00000", "doc_id": 8 }, "chunk_id": "train_shard_00000_8_0", "global_id": 9 }, { "text": "Campylobacter is the leading cause of bacterial foodborne gastrointestinal infection in humans, and poultry is among the most important reservoirs. Turkeys have been shown to frequently carry Campylobacter, and the isolates recovered from turkeys show high antimicrobial resistance. We studied the prevalence of Campylobacter in Finnish slaughter turkeys during 2013-2023 from the monitoring data of a Finnish turkey slaughterhouse, covering 1856 turkey flocks originating from 41 farms over the monitoring period. Additionally, we used whole-genome sequencing to identify bacterial species, resistance profiles, sequence types, and core genome allelic profiles for 103 Campylobacter isolates from turkey faecal samples collected at the slaughterhouse between 2013 and 2021. In total, 9.5 % of the flocks and 82.9 % of the farms were Campylobacter positive. The prevalence varied significantly between years, months, and farms. Campylobacter jejuni (87.6 %) was the most common species followed by Campylobacter coli (4.0 %) and Campylobacter lari (1.1 %). We obtained 34 sequence types, with ST45 being the most common (20.2 % of the isolates). Genetically closely related isolates originated mostly from the same farm with a tight temporal connection. Five antimicrobial genotypic resistance profiles were identified. Most of the isolates carried only the blaOXA gene, and only one Campylobacter isolate carried several resistance genes. We showed that Campylobacter prevalence and the occurrence of antimicrobial resistance genes in the isolates is low in Finnish slaughter turkeys. Further, we demonstrated that Campylobacter spread between the flocks on the same farm, but the same STs did not persist.\n\nDistribution and characteristics of Campylobacter spp. in turkeys at slaughter.", "token_count": 456, "char_count": 1788, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5798, "quality_score": 0.7899, "entities": { "genes": [ "ST45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:32.099005", "source": { "split": "train_shard_00000", "doc_id": 9 }, "chunk_id": "train_shard_00000_9_0", "global_id": 10 }, { "text": "The rising prevalence of metabolic dysfunction-associated steatotic liver disease (MASLD) poses a significant global public health challenge. Bile acids (BAs), synthesized in the liver and further metabolized in the gut, are essential in maintaining host metabolic homeostasis. Bile salt hydrolase (BSH), an enzyme produced by the gut microbiota, catalyzes the hydrolysis of conjugated BAs, thus regulating the balance between primary and secondary BAs. Growing evidence suggests that BSH activity is intricately linked to the pathogenesis of MASLD. This review comprehensively examines the structural and functional properties of BSH enzymes, their distribution among gut microbial communities, and current methodologies for assessing BSH expression and activity. Furthermore, it highlights the alterations in BSH observed in MASLD and explores the potential mechanistic pathways involved, offering a foundation for the development of novel diagnostic and therapeutic strategies.\n\nBile salt hydrolase: a key player in gut microbiota and its implications for metabolic dysfunction-associated steatotic liver disease.", "token_count": 254, "char_count": 1116, "word_count": 151, "semantic_coherence": 1, "information_density": 0.7086, "quality_score": 0.8543, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:32.582587", "source": { "split": "train_shard_00000", "doc_id": 10 }, "chunk_id": "train_shard_00000_10_0", "global_id": 11 }, { "text": "The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represents a limitation when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of sequencing read mapping to the current bovine genome assembly.\n\nApplication of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes.", "token_count": 103, "char_count": 567, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7467, "quality_score": 0.8733, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:32.960788", "source": { "split": "train_shard_00000", "doc_id": 11 }, "chunk_id": "train_shard_00000_11_0", "global_id": 12 }, { "text": "The aromatic compounds 2-phenylethanol (2-PE) and 2-phenylethyl acetate (2-PEA) are of high industrial relevance due to their distinctive sensory properties and extensive use in food, fragrance, and wine industries. However, their natural production is costly, motivating interest in sustainable microbial alternatives. This study examined the metabolic regulation of\n\nEndogenous pathway dysregulation in Kluyveromyces marxianus under nitrogen limitation drives 2-phenylethyl acetate and 2-phenylethanol overproduction.", "token_count": 139, "char_count": 519, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8254, "quality_score": 0.9127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:33.392237", "source": { "split": "train_shard_00000", "doc_id": 12 }, "chunk_id": "train_shard_00000_12_0", "global_id": 13 }, { "text": "This study investigated the prevalence of methicillin-resistant Staphylococcus aureus (MRSA), their antimicrobial resistance, virulence determinants, and potential zoonotic potential between pets, owners, and veterinary professionals. From July 2022 to June 2024, 213 human and 191 animal samples (nasal, pus, and wound swabs) were collected from two veterinary hospitals. Staphylococcus aureus was isolated using conventional cultural method and subsequently confirmed through Gram staining, biochemical tests, and PCR targeting the nuc gene. Methicillin resistance was confirmed using the cefoxitin disk diffusion method and PCR for the mecA gene. Antimicrobial susceptibility testing was performed using the disc diffusion method against 15 antibiotics. Additionally, whole genome sequencing (WGS) was conducted on selected MRSA isolates from pets and their owners to study clonal transmission and virulence factors. The prevalence of MRSA in humans was 15.0%, in cats was 5.8% and in dogs was 13.5%. The MRSA isolates exhibited resistance to penicillin (94.9%), azithromycin (82%), and ciprofloxacin (53.9%), in addition to their intrinsic resistance to cefoxitin. Multidrug resistance was observed in 94.9% of MRSA isolates, though all were sensitive to amikacin, clindamycin, linezolid, and vancomycin. Notably, six dogs and cats, along with their respective owners, tested positive for MRSA. WGS analysis of these six pairs (12 isolates) showed four sequence types (ST), with ST6 being the most common (66.7%). There were also four spa types identified, with t304 being the predominant (58.3%). Within four pairs, identical ST-spa patterns were observed, except for the pair C52-P52 and D88-P88", "token_count": 476, "char_count": 1701, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [ "ST6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:34.012101", "source": { "split": "train_shard_00000", "doc_id": 13 }, "chunk_id": "train_shard_00000_13_0", "global_id": 14 }, { "text": "Two pairs of isolates, C134-P134 and C185-P185, showed clonality based on whole genome and core genome SNP analysis, and other genetic parameters, suggesting clonal transmission between the pets and their respective owners. Virulence profiling revealed the presence of hemolysins, Panton-Valentine Leukocidin, and toxic shock syndrome toxin genes in selected isolates. The detection of diverse MRSA lineages, including human lineages ST80, ST88 and ST6-t304 in pets, indicates their zoonotic potential, and emphasizes the necessity for targeted MRSA surveillance and effective infection control measures. A collaborative One Health approach is therefore imperative to address the spread of MRSA between pets and their owners, thereby mitigating associated risks. The detection of diverse MRSA lineages, including human lineages ST80, ST88, and ST6-t304 in pets, underscores their zoonotic potential and emphasizes the necessity for targeted MRSA surveillance and effective infection control measures. A collaborative One Health approach is therefore imperative to address the spread of MRSA between pets and their owners, thereby mitigating associated risks.\n\nZoonotic potential of methicillin-resistant Staphylococcus aureus isolated from pets and their owners in Bangladesh.", "token_count": 302, "char_count": 1276, "word_count": 174, "semantic_coherence": 1, "information_density": 0.5287, "quality_score": 0.7644, "entities": { "genes": [ "ST88", "ST6", "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:34.554732", "source": { "split": "train_shard_00000", "doc_id": 13 }, "chunk_id": "train_shard_00000_13_1", "global_id": 15 }, { "text": "The economic feasibility of lignocellulosic ethanol production depends on obtaining high yields and productivity. This condition requires extensive research to identify strategies that maximize yield and productivity in lignocellulosic ethanol production. Self-cycling fermentation (SCF) has been shown to increase ethanol productivity. To validate whether the SCF system could enhance productivity during ethanol fermentation, we simulated the process using experimental results obtained from six cycles in a stirred bioreactor and compared the outcomes with separate hydrolysis and fermentation (SHF) and simultaneous saccharification-fermentation (SSF) for ethanol production from wheat straw using Kluyveromyces marxianus SLP1. The volumetric ethanol productivity (Q\n\nSelf-cycling fermentation strategy for efficient bioethanol production from wheat straw by Kluyveromyces marxianus.", "token_count": 201, "char_count": 887, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [ "SLP1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:35.000947", "source": { "split": "train_shard_00000", "doc_id": 14 }, "chunk_id": "train_shard_00000_14_0", "global_id": 16 }, { "text": "The sodium taurocholate cotransporting polypeptide (NTCP), the main hepatic uptake transporter of bile salts, is the docking receptor required for the HBV/HDV entry. However, the mechanism of NTCP-dependent internalization of HBV/HDV into hepatocytes is unclear. Thus, we investigated the contribution of post-translational modification of NTCP to transporter endocytosis and HBV infection.\n\nNTCP ubiquitination enables HBV infection.", "token_count": 123, "char_count": 434, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7321, "quality_score": 0.8661, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:35.380344", "source": { "split": "train_shard_00000", "doc_id": 15 }, "chunk_id": "train_shard_00000_15_0", "global_id": 17 }, { "text": "The yeast Kluyveromyces marxianus (K. marxianus), characterized by its thermotolerance and rapid growth, is emerging as a promising new platform organism for the production of recombinant proteins. In this study, we constructed an expression vector designed for the efficient expression of exogenous proteins in K. marxianus. Initially, qPCR was employed to assess the expression efficiency of endogenous promoters within the yeast. The PDC1 promoter was selected, and its ability to drive the expression of EGFP was validated. The constructed vector exhibited high stability, maintaining approximately 5.2-fold higher copy numbers than the K. marxianus genome after 72 hours of cultivation without hygromycin selection. Notably, the fluorescence signal intensity of K. marxianus harboring the vector was approximately 15.6-fold higher than that of the wild-type strain at 72 h. Subsequently, the cap gene of porcine circovirus type 3 (PCV3) was integrated into the vector, resulting in the production of soluble PCV3 cap protein. Electron microscopy analysis revealed that the PCV3 cap protein self-assembled into virus-like particles (VLPs). This study successfully established the expression vector and characterized its key elements in K. marxianus, which will facilitate further research on the expression of exogenous proteins in this yeast species. Moreover, the soluble expression of the PCV3 cap protein and its formation of VLPs provide a solid foundation for the future development of PCV3 vaccines.\n\nCharacterization of Vector Elements and Soluble Expression of Pcv3 Cap Protein in Kluyveromyces Marxianus.", "token_count": 400, "char_count": 1618, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5751, "quality_score": 0.7876, "entities": { "genes": [ "PDC1", "PCV3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:35.970181", "source": { "split": "train_shard_00000", "doc_id": 16 }, "chunk_id": "train_shard_00000_16_0", "global_id": 18 }, { "text": "The auxin response factor (ARF) is a key regulator involved in plant growth, development, and stress response. In this study, we systematically identified the ARF gene family using a pan-genomic approach based on 47 high-quality potato genomes.\n\nPan-genome identification and expression analysis of the ARF gene family in potato.", "token_count": 78, "char_count": 329, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8163, "quality_score": 0.9082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:36.342861", "source": { "split": "train_shard_00000", "doc_id": 17 }, "chunk_id": "train_shard_00000_17_0", "global_id": 19 }, { "text": "The nodD gene encodes a LysR-type transcriptional regulator critical for nodulation gene expression in rhizobia, yet its evolutionary origin, structural plasticity, and regulatory reach beyond symbiosis remain incompletely resolved. Here we investigate the genomic organization, structural variation, and functional diversification of nodD and its homologs across α-proteobacteria with selected outgroups. Using orthogroup-based pangenome clustering, dated species trees, and gene-tree-species-tree reconciliation, we reconstruct the evolutionary trajectory of nodD, indicating emergence from ancient LTTRs deep in proteobacterial history. Reconciliation reveals widespread duplication and horizontal gene transfer (HGT), with several rhizobia showing notable duplication and exchange, and marine/non-rhizobial taxa contributing to a mosaic of nodD-like genes. Gene-neighborhood and operon analyses show conserved syntenic tendencies in classical rhizobia but extensive architectural divergence in free-living lineages, including frequent monocistronic anchors with extended upstream regions and, when polycistronic, enrichment for transporters and local metabolic enzymes within compact multi-regulator cassettes. Structural comparisons with AlphaFold and PyMOL confirm the canonical LTTR fold while uncovering species-specific deviations concentrated in effector-binding loops and interfaces. Motif discovery and genome-wide scanning identify targets involved in metabolism, stress responses, and transcriptional control, and network analysis reveals modular connectivity spanning core metabolism and accessory processes such as secondary metabolism, transport, and biofilm-associated functions. These findings portray nodD as a structurally conserved yet functionally flexible regulator repeatedly reshaped by duplication, HGT, and local genome context, extending nodD-like systems beyond symbiosis and broadening the regulatory landscape of bacterial LTTRs.\n\nModular evolution and regulatory diversification of nodD-like LysR-type transcriptional regulators in α-Proteobacteria.", "token_count": 480, "char_count": 2082, "word_count": 245, "semantic_coherence": 1, "information_density": 0.7265, "quality_score": 0.8633, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:36.961846", "source": { "split": "train_shard_00000", "doc_id": 18 }, "chunk_id": "train_shard_00000_18_0", "global_id": 20 }, { "text": "In population-scale genomic variation studies based on shallow whole genome sequencing, pangenomes have become an effective tool for identifying population-specific single-nucleotide polymorphisms and indels. Extending these advantages to copy number variation (CNV), however, remains challenging due to two unresolved issues. First, current pangenome frameworks exhibit pronounced population-representation bias arising from uneven sampling across populations. As the number of samples increases, the pangenome tends to capture variations primarily from majority populations while suppressing signals from minority populations. Second, in population-scale genomic variation analyses, common but benign population-specific copy number polymorphisms (CNPs) frequently obscure pathogenic CNVs. Existing pangenome frameworks lack dedicated mechanisms for representing CNPs and CNVs, limiting their ability to distinguish pathogenic CNVs from benign, population-specific CNPs. In this study, we present PangenomeX, a graph-convolutional pangenome framework tailored for low-coverage, population-scale CNV analysis. To address CNP representation, we embed known CNPs as prior knowledge into the pangenome graph and construct a CNV relationship network guided by a phylogenetic tree. A graph convolutional network (GCN) then learns the interactions between CNV and CNP nodes. To mitigate population-representation bias, the GCN aggregates information from only one- and two-hop neighborhoods, preserving local population context while preventing majority group signals from dominating. Evaluation on simulated cohorts and 561 real samples shows that PangenomeX distinguishes pathogenic CNVs from common population CNPs markedly better than existing methods. Overall, PangenomeX offers a methodological blueprint for large-cohort variant screening and provides a practical path for bringing graph-based genomics into clinical practice.\n\nPangenomeX: a graph convolutional network-based pangenome framework for unbiased population-scale genomic variation analysis.", "token_count": 446, "char_count": 2055, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6784, "quality_score": 0.8392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:37.571538", "source": { "split": "train_shard_00000", "doc_id": 19 }, "chunk_id": "train_shard_00000_19_0", "global_id": 21 }, { "text": "Obesity and type 2 diabetes mellitus are global health challenges often associated with disrupted lipid and amino acid metabolism, as well as gut microbiota dysbiosis. Probiotic interventions offer promising potential in ameliorating metabolic disorders, yet strain-specific mechanisms remain to be elucidated. In this study, a canine-derived Pediococcus acidilactici PA-1 was subjected to in vitro evaluation for probiotic properties, and its anti-obesity effects were investigated in high-fat diet (HFD)-induced obese mice. In vitro, PA-1 exhibited safety and favorable probiotic activity including gastrointestinal tolerance, adhesion potential, bile salt hydrolase activity, α-glucosidase inhibition and fatty acid absorption. In vivo, PA-1 supplementation significantly alleviated body weight gain, hepatic steatosis, and lipid accumulation in HFD-fed mice. Multi-omics analyses of liver revealed that PA‑1 modulated hepatic amino acid metabolism at the pathway level (e.g., alanine, aspartate and glutamate metabolism), and led to significant decreases in D‑serine, glycine, and L‑proline in the targeted panel, whereas several others (e.g., L‑aspartate, L‑alanine) showed trend-level decreases. PA‑1 concomitantly suppressed pyruvate flux into the TCA cycle and reduced several TCA intermediates (e.g., fumarate, malate, citrate), eventually Limiting acetyl-CoA availability for de novo Lipogenesis. Additionally, 16S rRNA sequencing demonstrated that PA-1 reshaped the gut microbiota by reducing the Firmicutes/Bacteroidota ratio and enriching the abundance of short-chain fatty acid-producing genera, leading to elevated SCFA concentrations in the cecal contents", "token_count": 462, "char_count": 1671, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7639, "quality_score": 0.8819, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:38.185946", "source": { "split": "train_shard_00000", "doc_id": 20 }, "chunk_id": "train_shard_00000_20_0", "global_id": 22 }, { "text": "This study suggests that PA-1 ameliorates HFD-induced obesity and metabolic disturbances by modulating hepatic amino acid metabolism and gut microbiota composition, highlighting its potential as a functional probiotic for managing obesity-related metabolic disorders.\n\nPediococcus acidilactici PA-1 Alleviates Diet-Induced Obesity by Modulating Hepatic Amino Acid Metabolism and Gut Microbiota in Mice.", "token_count": 115, "char_count": 402, "word_count": 50, "semantic_coherence": 1, "information_density": 0.74, "quality_score": 0.87, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:38.562385", "source": { "split": "train_shard_00000", "doc_id": 20 }, "chunk_id": "train_shard_00000_20_1", "global_id": 23 }, { "text": "Vertical sleeve gastrectomy (VSG) is a highly effective intervention for metabolic dysfunction-associated steatotic liver disease (MASLD) and is associated with significant alterations in the gut microbiota. However, the precise mechanisms underlying its metabolic benefits remain poorly understood. In this study, we revealed that VSG mitigates MASLD by reshaping gut microbiota-mediated bile acid metabolism. Through integrated 16S rRNA sequencing, targeted metabolomics, and functional validation experiments, we demonstrated that VSG markedly enhances bile salt hydrolase (BSH) activity within the gut microbiota, resulting in elevated levels of unconjugated bile acids. These unconjugated bile acids serve as potent agonists for the intestinal farnesoid X receptor (FXR), thereby activating the intestinal FXR-fibroblast growth factor 19 signaling pathway. This activation leads to significant improvements in metabolic health, including enhanced glucose regulation and attenuated hepatic lipid accumulation. Fecal microbiota transplantation (FMT) from VSG-treated rats replicated these metabolic improvements, whereas antibiotic treatment abolished these beneficial effects, highlighting the indispensable role of the gut microbiota in mediating the anti-MASLD effects of VSG. Importantly, inhibition of intestinal FXR signaling negated the metabolic benefits of FMT, further emphasizing the critical role of the gut microbiota-BSH-FXR axis. Our findings reveal a novel mechanism by which VSG alleviates MASLD through gut microbiota-dependent activation of intestinal FXR, offering new perspectives for microbiome-targeted therapeutic strategies in MASLD.\n\nMicrobial changes resulting from VSG attenuate MASLD by modulating bile acid metabolism and the intestinal FXR-FGF19 axis.", "token_count": 454, "char_count": 1785, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6943, "quality_score": 0.8472, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:39.175070", "source": { "split": "train_shard_00000", "doc_id": 21 }, "chunk_id": "train_shard_00000_21_0", "global_id": 24 }, { "text": "Porcine deltacoronavirus (PDCoV) is a significant pathogen of swine with a global distribution, leading to severe gastrointestinal disease and substantial economic losses. Furthermore, PDCoV poses a potential threat to human health, as evidenced by the recent identification of three cases of infection in Haitian children. This study aimed to investigate the effects of PDCoV infection on host intestinal microbiota and bile acid metabolism, as well as the antiviral effects of lithocholic acid (LCA) in vitro and in vivo. Our results revealed that PDCoV infection caused microbiota dysbiosis in piglets, significantly reducing the intestinal abundance of\n\nA gut microbiota-bile acid axis inhibits the infection of an emerging coronavirus by targeting its cellular receptor aminopeptidase N.", "token_count": 197, "char_count": 792, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:39.625434", "source": { "split": "train_shard_00000", "doc_id": 23 }, "chunk_id": "train_shard_00000_23_0", "global_id": 25 }, { "text": "Oxidative stress, primarily triggered by elevated levels of reactive oxygen species (ROS) contributes to intestinal epithelial injury and apoptosis, and is closely associated with gastrointestinal disorders. In this study, we evaluated the cytoprotective effects of three", "token_count": 63, "char_count": 271, "word_count": 36, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:39.984234", "source": { "split": "train_shard_00000", "doc_id": 24 }, "chunk_id": "train_shard_00000_24_0", "global_id": 26 }, { "text": "Bile Salt Export Pump (BSEP) deficiency is a rare genetic cholestatic liver disease, often necessitating liver transplantation. The p.E297G missense mutation is associated with residual BSEP function in vitro and delayed need for transplantation in patients. We aimed to generate a p.E297G BSEP knock-in (BSEP\n\nGeneration and characterization of a mouse model for bile salt export pump deficiency with the p.E297G mutation.", "token_count": 119, "char_count": 423, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7258, "quality_score": 0.8629, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:40.363561", "source": { "split": "train_shard_00000", "doc_id": 25 }, "chunk_id": "train_shard_00000_25_0", "global_id": 27 }, { "text": "Although gut microbiota-mediated bile acid (BA) metabolism is well characterized in mammals, its mechanisms in wild birds remain largely unknown, hindering our understanding of their ecological adaptation and health. In this study, metagenomic analysis was performed on 10,455 metagenome-assembled genomes (MAGs) derived from 718 wild bird gut samples, from which 1,034 high-quality non-redundant MAGs were selected for further analysis. Functional annotation analysis identified 755 MAGs encoding genes associated with BA biotransformation pathways, primarily derived from the phyla Bacillota_A, Bacteroidota, and Bacillota, with dominant genera including Helicobacter_G and Ligilactobacillus. Subsequent genomic analysis identified 379 MAGs encoding bile salt hydrolase (BSH), with phylogenetic classification demonstrating predominant affiliation to the Bacteroidota and Bacillota_A phyla. Compared to the BSH-producing microbiota in the human and chicken gut, the phylum Bacillota exhibited a notably higher relative abundance in wild birds. Within the wild bird gut microbiome, Helicobacter_G was identified as the predominant BSH-encoding genus, whereas its relative abundance was substantially lower in both humans and chickens. Moreover, migratory birds (MB) displayed significantly higher diversity of BA biotransformation genes than resident birds (RB), with Helicobacter_G being notably enriched at the genus level in MB, potentially associated with their heightened energy and nutritional demands during migration. Notably, in addition to residency status, host species emerged as the most influential factor shaping the compositional variation of BA biotransformation genes, followed by environmental factors and dietary habits. In summary, this study systematically elucidates the potential functions of gut microbiota in BA metabolism and their close associations with host ecological traits in wild birds, not only advancing our understanding of host-microbe interactions and metabolic adaptation mechanisms but also providing a theoretical foundation for future interventions targeting gut microbiota to improve wildlife health.", "token_count": 497, "char_count": 2145, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:40.986494", "source": { "split": "train_shard_00000", "doc_id": 26 }, "chunk_id": "train_shard_00000_26_0", "global_id": 28 }, { "text": "Metagenomic analysis of bile acid biotransformation by gut microbiota in wild birds.", "token_count": 22, "char_count": 84, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:41.354284", "source": { "split": "train_shard_00000", "doc_id": 26 }, "chunk_id": "train_shard_00000_26_1", "global_id": 29 }, { "text": "As a collection of all the genetic variants in the gene pool, the pangenome is a concept that will become fundamental to conservation genomic studies. Unfortunately, most pangenomic approaches developed for humans and model organisms are financially impractical for conservation genomic studies of threatened or endangered species due to the high costs associated with deep sequencing multiple individuals using long-read platforms. Here, by integrating metagenomic and iterative map-then-assemble approaches, we (1) propose novel workflows to construct graph pangenomes from multiple low-coverage short-read datasets; (2) benchmark these short-read pangenomes (both linear and graph) against a previously published long-read graph pangenome of the barn swallow; and (3) evaluate the utility of our workflows in population and conservation genomics. Our results indicate that economical short-read graph pangenomes can recover the vast majority of the variants identified through expensive long-read graph approaches, and that these variants accurately detect important biological signals (e.g., spatial structure and independent taxonomic delineations). These results mean that researchers can utilize their limited, conservation-oriented funding to more fully characterize all the variants in a particular gene pool for population-level analyses.\n\nShort-Read Pangenomes and Their Potential Utility in Population and Conservation Genomics.", "token_count": 295, "char_count": 1440, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6492, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:41.901721", "source": { "split": "train_shard_00000", "doc_id": 27 }, "chunk_id": "train_shard_00000_27_0", "global_id": 30 }, { "text": "The human genome contains many structurally variable polymorphic loci, including several hundred disease-associated genes, almost inaccessible for accurate variant calling. Here we present Locityper, a tool capable of genotyping such challenging genes using short-read and long-read whole-genome sequencing. For each target, Locityper recruits and aligns reads to locus haplotypes, for instance, extracted from a pangenome, and finds the likeliest haplotype pair by optimizing read alignment, insert size and read depth profiles. Across 256 challenging medically relevant loci, Locityper achieves a median quality value (QV) above 35 from both long-read and short-read data, outperforming state-of-the-art Illumina and PacBio HiFi variant calling pipelines by 10.9 and 1.7 points, respectively. Furthermore, Locityper provides access to hyperpolymorphic HLA genes and other gene families, including KIR, MUC and FCGR. With its low running time of 1 h 35 m per sample at eight threads, Locityper is scalable to biobank-sized cohorts, enabling association studies for previously intractable disease-relevant genes.\n\nLocityper enables targeted genotyping of complex polymorphic genes.", "token_count": 307, "char_count": 1181, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7764, "quality_score": 0.8882, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:42.475283", "source": { "split": "train_shard_00000", "doc_id": 28 }, "chunk_id": "train_shard_00000_28_0", "global_id": 31 }, { "text": "Acinetobacter baumannii is widely recognized as a multidrug-resistant pathogen, although most public genome datasets are biased toward hospital-derived isolates. Little is known about A. baumannii isolates from healthy individuals in the community. This study analyzed genome sequences from nine A. baumannii isolates obtained from the upper respiratory tract of the indigenous Orang Asli in their rural community in Peninsular Malaysia. Genomic analysis revealed genetic diversity, including three new Pasteur sequence types (STs) and six novel Oxford STs. One isolate, A. baumannii 19064, belonged to Global Clone 8 (GC8), a lineage linked to clinical infections. Core genome phylogeny showed these community isolates interspersed with clinical isolates from a nearby hospital, indicating potential pathogenicity under suitable conditions. All isolates carried intrinsic bla\n\nThe Road Less Traveled: Exploring the Genomic Characteristics and Antimicrobial Resistance Potential of Acinetobacter baumannii From the Indigenous Orang Asli Community in Peninsular Malaysia.", "token_count": 254, "char_count": 1070, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7153, "quality_score": 0.8576, "entities": { "genes": [ "GC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:42.958527", "source": { "split": "train_shard_00000", "doc_id": 29 }, "chunk_id": "train_shard_00000_29_0", "global_id": 32 }, { "text": "Mannheimia haemolytica is an opportunistic bacterial pathogen associated with the economically costly bovine respiratory disease. Two genotypes have been described, of which genotype 2 is more strongly associated with disease. Several previous studies have investigated the genomic differences between the genotypes and/or the major serotypes (1, 2 and 6) of M. haemolytica, however we still lack a clear basis for the greater disease association of genotype 2 (serotypes 1 and 6) and demonstrations of phenotypic differences are scarce. This work builds upon previous investigations to identify genes that differentiate the two genotypes with a particular focus on genes that may play a role in virulence and fitness in the respiratory tract microbiome. We identified 422 genotype differentiating genes in a collection of 206 unique M. haemolytica genomes (61 genotype 1, 145 genotype 2). Genotype differentiating genes included genotype-associated variants of a TonB-dependent siderophore receptor homolog, transferrin binding protein B, leukotoxin A, and IgA1 proteases. We also identified a genotype 1 associated lytic transglycosylase, and a genotype 2 specific highly immunogenic outer membrane lipoprotein. Genotype 2 genomes were significantly larger in size and contained more predicted protein coding genes than genotype 1 genomes. These results expand our knowledge of what differentiates the genotypes 1 and 2 of M. haemolytica and provides information that can be used as the basis for laboratory investigations of corresponding phenotypic differences.\n\nIdentification of genes that differentiate Mannheimia haemolytica genotypes 1 and 2 using a pangenome approach.", "token_count": 419, "char_count": 1678, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5958, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:43.602938", "source": { "split": "train_shard_00000", "doc_id": 30 }, "chunk_id": "train_shard_00000_30_0", "global_id": 33 }, { "text": "Bile salt hydrolase (BSH) is a key probiotic trait, as it facilitates both host metabolism and bacterial survival into the gastrointestinal tract (GIT), through bile acid (BA) deconjugation, keeping intestinal homeostasis.\n\nGastrointestinal Survivability of a BSH-Positive", "token_count": 82, "char_count": 272, "word_count": 36, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:44.017847", "source": { "split": "train_shard_00000", "doc_id": 31 }, "chunk_id": "train_shard_00000_31_0", "global_id": 34 }, { "text": "Mycoplasma bovis, a major bacterial pathogen for cattle, is responsible for diseases such as pneumonia, mastitis, otitis, and arthritis, leading to substantial economic losses and animal welfare concerns. Despite its wide global distribution, there is limited information in South America. M. bovis has been reported as a mastitis agent in Chile, but its genetic diversity is poorly understood. Therefore, this study aimed to determine the genetic diversity of M. bovis isolates from Chilean dairy cattle (from bovine respiratory disease and mastitis cases) in the last two decades and evaluate their genetic relatedness with strains isolated in different countries using a whole genome sequencing approach. The M. bovis population in Chile was found to be highly homogeneous, with MLST and phylogenomic analysis identifying ST60 as the dominant clone, representing most of the isolates (97.8 %), while just one isolate was typed as ST12 (2.2 %). Phylogenomic analysis revealed close genetic relatedness among most Chilean isolates, showing a close genetic relationship with North American strains, forming a tight clade with Canadian ST60 strains, while the single Chilean ST12 isolate clustered with North American, Israeli, and European strains and clustered with the type strain (PG45) of this species. Moreover, the pangenome analysis confirms that M. bovis has an open pangenome, with a large range of accessory genes that remain largely unexplored and may hold key insights into its genome plasticity, thereby opening future research. The findings of this study provide the first insights into the Chilean population structure of M. bovis, contributing to the global epidemiology of this pathogen with a focus on South America. These results also open future research focused on the comprehensive characterization of this dominant clone, inspiring the scientific community to further exploration into the genetic diversity of M. bovis in Chile.\n\nGenetic diversity of Mycoplasma bovis isolated from bovine respiratory disease and bovine mastitis in Chile.", "token_count": 470, "char_count": 2061, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [ "ST12", "ST60", "PG45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:44.635158", "source": { "split": "train_shard_00000", "doc_id": 32 }, "chunk_id": "train_shard_00000_32_0", "global_id": 35 }, { "text": "Streptococcus agalactiae is a contagious pathogen responsible for bovine mastitis, leading to significant economic losses in the global dairy industry. Our objectives were to determine the population structure, to profile the antimicrobial resistance and to investigate the pathogenicity and genes associated with pathogenicity in S. agalactiae isolated from Chinese dairy herds. A total of 266 milk samples were collected on three dairy farms in Ningxia (herd A) and Hebei provinces (herds B & C) with outbreaks of bovine mastitis from September 2020 to April 2021. There were 116 isolates identified as Streptococcus agalactiae by 16S rRNA sequencing. Twenty-seven S. agalactiae isolates were randomly selected using a stratified approach from the three farms for whole genome sequencing analysis and phenotypic analyses, including antimicrobial resistance profiling, identification of adhesion, invasion and virulence genes using in vitro bovine mammary epithelial cell models and in vivo Galleria mellonella models. Multilocus sequence typing and serotyping showed that all isolates belonged to sequence type ST103 and serotype Ia. In total, 34 genes were identified as virulence genes in Streptococcus species. Isolates from herd C had significantly higher virulence than those from herd B. Genome-wide association analysis revealed 166 virulence-related genes, 221 adhesion-related genes and 218 invasion-related genes. Furthermore, 47 genes were associated with pathogenicity in infecting G. mellonella. Resistance to tetracycline and macrolides was related to the presence of antimicrobial resistance genes tetO, tetM, and ermB. Pan-genome analyses revealed that 1,421 S. agalactiae isolates (27 from our study and 1,394 from the NCBI genome database) had 20,955 genes, including 666 and 20,289 genes in the core and accessory genomes, respectively", "token_count": 516, "char_count": 1856, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [ "ST103" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T04:58:45.261276", "source": { "split": "train_shard_00000", "doc_id": 33 }, "chunk_id": "train_shard_00000_33_0", "global_id": 36 }, { "text": "This study characterized the phenotypic and genotypic profiles for S. agalactiae, and identified associations between phenotypic traits and genetic determinants of virulence and antimicrobial resistance, providing new insights into controlling S. agalactiae mastitis in Chinese dairy herds.\n\nPhenotypic and genotypic characterization of ST103 serotype Ia Streptococcus agalactiae isolated from bovine mastitis in China.", "token_count": 112, "char_count": 419, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7736, "quality_score": 0.8868, "entities": { "genes": [ "ST103" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:45.631562", "source": { "split": "train_shard_00000", "doc_id": 33 }, "chunk_id": "train_shard_00000_33_1", "global_id": 37 }, { "text": "This study aimed to isolate and evaluate a novel cellulolytic probiotic strain from the intestinal contents of yaks on the Qinghai-Tibet Plateau. A strain identified as Enterococcus faecalis JM263 exhibited strong cellulolytic activity, with CMCase, FPase, and β-glucosidase activities reaching 29.5, 23.58, and 15.62 U/mL, respectively. It exhibited strong tolerance to simulated gastric (75.3%) and intestinal (68.5%) fluids, dose-dependent bile salt resistance, and broad-spectrum antimicrobial activity-most notably, a 21.27-mm inhibition zone against Salmonella. Additionally, E. faecalis JM263 scavenged DPPH and hydroxyl radicals at rates of 41.05% and 36.54%, respectively. Additionally, E. faecalis JM263 exhibited strong degradation abilities toward cellulose, lignin, and hemicellulose in both corn straw and oatgrass. In vitro rumen fermentation experiments revealed that E. faecalis JM263 significantly increased acetate and VFAs while reducing ammonia-N levels. 16S rRNA sequencing revealed that E. faecalis JM263 altered the rumen microbial composition by increasing the abundance of beneficial taxa such as Fibrobacterota, Prevotella, and Succinivibrio. Functional prediction via PICRUSt and COG annotation suggested that E. faecalis JM263 supplementation may enhance microbial metabolism, particularly pathways involved in carbohydrate metabolism, amino acid biosynthesis, and energy production. Additionally, E. faecalis JM263 was shown to promote cooperative interactions among functional microbes, contributing to a more efficient and stable rumen microbial ecosystem. Overall, E. faecalis JM263 is a promising candidate functional probiotic for improving fiber digestibility and rumen fermentation efficiency in ruminants, offering great potential for application in sustainable animal production.", "token_count": 519, "char_count": 1818, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [ "JM263" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T04:58:46.237669", "source": { "split": "train_shard_00000", "doc_id": 34 }, "chunk_id": "train_shard_00000_34_0", "global_id": 38 }, { "text": "Characterization of Enterococcus faecalis JM263 from the Yak Gut on the Qinghai-Tibet Plateau: A Probiotic Candidate with Strong Fiber-Degrading Capacity.", "token_count": 52, "char_count": 154, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [ "JM263" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:46.598177", "source": { "split": "train_shard_00000", "doc_id": 34 }, "chunk_id": "train_shard_00000_34_1", "global_id": 39 }, { "text": "The present work aims to establish a formulation-specific, physiologically based pharmacokinetic (PBPK) model for efavirenz (EFV) nanocrystals that have shown increased dissolution and were produced following a top-down approach based on wet milling and spray drying by integrating solid-state characterization, in vitro performance, and preclinical pharmacokinetics to enable translational predictions in humans. The resulting material was thoroughly characterized using diffraction-based, spectroscopic, thermal, morphological, and particle sizing techniques, along within vitro dissolution testing and an in vivo pharmacokinetic analysis in rats. Then, a fully rat PBPK model was constructed using GastroPlus and incorporating the biopharmaceutical nanoparticle properties through the product particle size distribution (P-PSD) approach. The physiologically based biopharmaceutics model (PBBM) was validated with rat in vivo data and subsequently extrapolated to simulate human physiology. Compared with unprocessed EFV, nanocrystals exhibited superior dissolution efficiency (90.4% vs 52.6%) and a more homogeneous size distribution. Furthermore, the in vivo studies confirmed an increase in EFV exposure. The rat PBPK model accurately reproduced plasma profiles of both formulations, with all predictive error metrics falling within the acceptable 2-fold range. Extrapolation to human physiology revealed that a 350 mg EFV NC dose achieved systemic exposure comparable to that of standard 600 mg immediate-release tablet, but with faster absorption. Sensitivity analyses highlighted the critical influence of particle size and bile salt solubilization capacity on EFV oral absorption. This study pioneers the application of a fully mechanistic PBPK/PBBM model tailored to nanocrystal formulations of EFV. By bridging preclinical and human data through in silico simulation, the proposed approach supports dose optimization strategies and reinforces the role of nanotechnology in advancing nonbiological complex drug development.\n\nPhysiologically Based Pharmacokinetic Modeling of Efavirenz Nanoparticles: from Animal Model to Human Extrapolation.", "token_count": 508, "char_count": 2151, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6536, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:47.209918", "source": { "split": "train_shard_00000", "doc_id": 35 }, "chunk_id": "train_shard_00000_35_0", "global_id": 40 }, { "text": "Camelina (Camelina sativa (L.) Crantz) is an allohexaploid oilseed crop with a cultivation history of about six thousand years, yet its pan-genome was poorly studied. Moreover, Lateral Organ Boundary Domain (LBD) transcription factor family remains uninvestigated. Here, we performed a pan-genome analysis of LBD genes across 13 camelina accessions, identifying 1487 members classified into 44 Core, 2 SoftCore, 15 Dispensable, and 21 Private orthologous groups (OGGs). Camelina LBDs were classified into Class I (six subclasses) and Class II (two subclasses). Selection pressure analysis showed that compared with Core LBD genes and SoftCore genes, Dispensable genes have undergone obvious relaxed selection. Promoter analysis identified subclass-specific regulatory elements, with Class IIB significantly enriched in endosperm-specific expression motifs and Class IA1 associated with stress responses. Transcriptome profiling revealed some tissue-specific expression patterns, including potential roles of LBD40/41 in seed development. Functional validation demonstrated that AtLBD40 overexpression in Arabidopsis and camelina remodeled fatty acid composition by suppressing FAD3 and KCS18, thereby reducing the relative contents of 18:3 and 22:1. Arabidopsis lbd40-1 and lbd40-2 mutant analyses suggested a possible functional redundancy between LBD40 and LBD41. This study elucidates the dynamic evolution of the camelina LBD family and its pivotal role in regulating the fatty acid profile in seeds, establishing a foundation for targeted oil quality improvement in this versatile crop.\n\nPan-genome analysis of the LATERAL ORGAN BOUNDARIES domain family in camelina and function investigation of LATERAL ORGAN BOUNDARIES domain 40 in fatty acid synthesis.", "token_count": 452, "char_count": 1760, "word_count": 239, "semantic_coherence": 1, "information_density": 0.7029, "quality_score": 0.8515, "entities": { "genes": [ "IA1", "FAD3", "LBD40", "KCS18", "LBD41" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:47.826710", "source": { "split": "train_shard_00000", "doc_id": 36 }, "chunk_id": "train_shard_00000_36_0", "global_id": 41 }, { "text": "Transglutaminases (TGs) are crosslinking enzymes that catalyze the formation of isopeptide bonds between glutamine and lysine residues. They consist of eight isozymes: TG1-TG7 and factor XIIIa. Our previous studies have shown that TG1 and TG2 facilitate hepatic apoptosis, contributing to liver fibrosis, and that their crosslinking substrates-cytokeratin 18 (K18) and cytokeratin 8 (K8)-are also targeted by TGs in a bile-duct-ligation-induced mouse model of liver fibrosis. However, the precise mechanisms by which TGs and keratins contribute to hepatocyte damage remain unclear. This study investigates the molecular mechanisms underlying TG1- and TG2-mediated cell death in hepatocytes exposed to bile acids. HepG2 cells and primary hepatocytes were treated with glycochenodeoxycholic acid (GCDCA), a toxic bile salt elevated in cholestasis. GCDCA-reduced cell viability and induced apoptosis in a dose-dependent manner. Knockdown of K18/K8 or TG1/TG2 by siRNA significantly attenuated GCDCA-induced apoptosis, indicating their contributory roles in hepatocyte injury. GCDCA-treated cells showed increased levels of proteins crosslinked by TG1 and TG2. In vivo analysis using cholestatic model mice also showed elevated high-molecular-weight protein complexes involving K18/K8, suggesting early-stage Mallory body formation, as observed in chronic liver injury. Mass spectrometry identified cytoskeletal proteins, such as vimentin and periplakin, and regulatory proteins, such as ATP synthase subunit β and PI3K adapter protein, as K18-crosslinked partners. These results suggest that TG1/TG2-mediated aggregation of K18 sequesters essential structural and survival proteins, promoting hepatocyte apoptosis. Targeting these pathological interactions may provide a novel therapeutic strategy to mitigate liver fibrosis and improve hepatocyte survival.", "token_count": 517, "char_count": 1854, "word_count": 243, "semantic_coherence": 1, "information_density": 0.7243, "quality_score": 0.8621, "entities": { "genes": [ "PI3K", "TG2", "TG7", "TG1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T04:58:48.452470", "source": { "split": "train_shard_00000", "doc_id": 37 }, "chunk_id": "train_shard_00000_37_0", "global_id": 42 }, { "text": "Transglutaminase-mediated cytokeratin modifications implicated in bile-acid-induced hepatocyte death.", "token_count": 30, "char_count": 101, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:48.804036", "source": { "split": "train_shard_00000", "doc_id": 37 }, "chunk_id": "train_shard_00000_37_1", "global_id": 43 }, { "text": "Reliable and efficient typing methods for Staphylococcus capitis, an opportunistic pathogen of growing clinical and epidemiological concern, are urgently needed to support microbial epidemiological studies. In the study, we present a novel workflow for developing a multilocus sequence typing (MLST) scheme tailored to S. capitis. Core genome analysis of 603 high-quality S. capitis genomes revealed 2,065 core genes. A hierarchical filtering strategy, including gene, fragment, and combination filters, was applied to select loci that balance discriminatory power and cluster specificity. The final MLST scheme comprised fragments from seven genes: mntC, phoA, atpB_2, hisS, rluB, carB, and clpP. Using this approach, we assigned 39 sequence types (STs) and defined five clonal complexes. The MLST typing results were highly concordant with phylogenetic analysis and demonstrated considerable discriminatory power. Notably, the globally prevalent NRCS-A clone and the linezolid-resistant L clone were designated as ST1 and ST6, respectively. Overall, we developed a reliable, high-resolution MLST scheme for S. capitis that enables accurate characterization of its population structure and facilitates monitoring of multidrug-resistant lineages.\n\nA new approach for establishing multilocus sequence typing scheme: Staphylococcus capitis as an example.", "token_count": 330, "char_count": 1352, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7213, "quality_score": 0.8607, "entities": { "genes": [ "ST6", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:49.352837", "source": { "split": "train_shard_00000", "doc_id": 38 }, "chunk_id": "train_shard_00000_38_0", "global_id": 44 }, { "text": "Predicting probiotic strain properties that translate into beneficial effects in the host is challenging and could be considered the holy grail in developing new probiotics. One approach is to selectively evolve well-studied probiotic strains known to elicit beneficial effects in clinical studies. In this study, Limosilactobacillus reuteri DSM 17938, among the world's most studied probiotic strains, constituted the origin from which the novel strain L. reuteri BG-R46® (DSM 32846) was obtained by exposure to bile, a major stressor of the gastrointestinal tract. The bioactivity of DSM 32846 in preclinical models is documented elsewhere; this work adds crucial strain characteristics, genomic and phenotypic safety profiles, and safety and tolerability in a randomised human study. DSM 32846 was compared to DSM 17938 in terms of tolerance to bile and synthetic gastric juice, with DSM 32846 showing increased bile tolerance and slightly reduced tolerance to gastric pH. Morphological examination by scanning electron microscopy revealed high abundance of extracellular membrane vesicles on the surface of DSM 32846, a previously described bioactive feature of the strain. In addition, the activity of 5'-nucleotidase, an adenosine-producing enzyme expressed on the bacterial cell surface and membrane vesicles, was increased in large-scale production batches of DSM 32846 compared to DSM 17938. Phenotypic safety assessment showed that DSM 32846 does not produce any of the evaluated biogenic amines, produces D- and L-lactate with a ratio typical for the species, and lacks haemolytic activity. The minimum inhibitory concentration profile for antibiotics did not raise any safety concerns. A genome safety assessment revealed no antibiotic resistance and virulence genes. DSM 32846 was found safe for human consumption with no differences from the control group in any of the evaluated parameters. In conclusion, L", "token_count": 499, "char_count": 1922, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:49.971635", "source": { "split": "train_shard_00000", "doc_id": 39 }, "chunk_id": "train_shard_00000_39_0", "global_id": 45 }, { "text": "reuteri DSM 32846 is a safe strain that shows interesting differences to its parent strain DSM 17938.\n\nSelection, characterisation and safety of Limosilactobacillus reuteri DSM 32846, an evolved version of DSM 17938.", "token_count": 74, "char_count": 216, "word_count": 32, "semantic_coherence": 1, "information_density": 0.7812, "quality_score": 0.8906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:50.337285", "source": { "split": "train_shard_00000", "doc_id": 39 }, "chunk_id": "train_shard_00000_39_1", "global_id": 46 }, { "text": "Cholestatic liver diseases are a heterogeneous group of disorders characterized by impaired bile formation or flow, leading to bile salt accumulation and progressive liver injury. This term encompasses a broad spectrum of conditions, including genetic disorders, autoimmune biliary diseases, drug-induced liver injury, and mechanical or postsurgical biliary obstruction. Genetic testing has become essential in identifying hereditary cholestasis, particularly useful for conditions without clear etiologies, atypical presentations, or inadequate treatment responses. These diseases often significantly impact patient's quality of life, manifesting as chronic symptoms such as pruritus, fatigue, and impose substantial burdens on healthcare systems due to chronic management requirements and potential progression to severe complications necessitating liver transplantation. Early-onset cholestatic diseases are typically associated with genetic abnormalities, yet recent advances have revealed that genetic variants also contribute significantly to adult-onset cases. Integration of genetic testing with clinical assessments including biochemical analysis, imaging, detailed family histories, and collaboration with histopathologists and geneticists is vital for accurate diagnosis and optimized patient care. Recognizing underlying genetic causes facilitates personalized management strategies and provides opportunities for innovative therapeutic approaches, including FXR ligands and IBAT inhibitors. Although current data on genotype-phenotype correlations are limited, ongoing genetic discoveries hold promise for improving prognosis prediction and personalized treatment strategies. Consequently, the wider implementation of genetic testing in clinical practice is justified, enhancing disease understanding and patient outcomes.\n\nAdvancing the Diagnosis and Management of Genetic Cholestatic Liver Disease in Adults.", "token_count": 367, "char_count": 1923, "word_count": 232, "semantic_coherence": 1, "information_density": 0.7112, "quality_score": 0.8556, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:50.892051", "source": { "split": "train_shard_00000", "doc_id": 40 }, "chunk_id": "train_shard_00000_40_0", "global_id": 47 }, { "text": "Frequent insulin injections remain the primary method for regulating blood glucose levels in individuals with diabetes mellitus; however, patient compliance is often poor. Due to its non-invasive nature, oral insulin delivery, exploring nanomedicine strategies, is considered a highly desirable alternative as an affordable and accessible medicine. However, the physical intestinal barriers and the harsh gastrointestinal environment provide major obstacles to reaching the best possible pharmacological bioavailability of insulin. Insulin's stability, bioavailability, and targeted administration throughout the GI tract can be improved using colloidal nanocarriers, including polymeric nanoparticles, phospholipid vesicles, and lipid-based nanoparticles. These nanocarriers mimic the physiological insulin secretion and improve the pharmacokinetics of insulin by shielding it from enzymatic degradation, facilitating controlled release, and enhancing absorption across the intestinal mucosa. Key parameters such as particle size, surface charge, zeta potential, and polymer-mucin interactions are examined concerning their effects on epithelial transport and enzymatic protection. Strategies such as PEGylation, chitosan functionalization, and bile salt incorporation are discussed with an emphasis on their interfacial engineering potential. Additionally, novel strategies such as glucose-responsive formulations, cell-penetrating peptides, and enzyme inhibitors, and innovative devices like microneedle capsules and SOMA systems have been explored to enhance oral insulin efficacy. This might not, however, be helpful for translation on its own. Another deciding aspect will be the combination of that with distinct pathways. Future perspectives and innovative approaches to enhance the therapeutic potential of nano-driven systems for oral insulin administration are also discussed in this review as an affordable and accessible medicine strategy.\n\nTowards oral insulin-controlled release nanomedicine: A review.", "token_count": 439, "char_count": 2017, "word_count": 254, "semantic_coherence": 1, "information_density": 0.7165, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:51.494802", "source": { "split": "train_shard_00000", "doc_id": 41 }, "chunk_id": "train_shard_00000_41_0", "global_id": 48 }, { "text": "With the rapid advancement of sequencing technologies and bioinformatics, coupled with significant progress in sequencing efficiency and reduced costs, substantial breakthroughs have been achieved in plant functional genomics, evolutionary genetics, and molecular breeding. However, as research deepens, accumulating evidence demonstrates that reference genomes derived from a single individual fail to adequately represent the genetic diversity of entire species. This limitation has catalyzed the emergence of the pan-genome concept. Pan-genome research now stands at the forefront of plant genomics, serving as a pivotal area of focus. Its application in plant studies has unveiled extensive genetic variations, identified numerous novel genes, and significantly enhanced our understanding of genetic diversity within relevant species. This review comprehensively summarizes recent progress in plant pan-genome research, construction methodologies, current applications in plant science, and key achievements. Finally, we outline future research directions, aiming to provide a reference for theoretical and applied pan-genome studies while offering novel perspectives for deciphering the genetic basis of plant breeding, evolutionary domestication, and phenotypic diversity.\n\nFrom map to blueprint: the plant pan-genome unraveling genetic mysteries and powering precision breeding.", "token_count": 268, "char_count": 1385, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8343, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:52.024754", "source": { "split": "train_shard_00000", "doc_id": 42 }, "chunk_id": "train_shard_00000_42_0", "global_id": 49 }, { "text": "This study was to determine the spoilage microbiota of palm wine stored at room temperature in order to define appropriate strategies for shelf-life extension. For this purpose, during the storage of palm wine samples, yeast, lactic acid bacteria (LAB), and acetic acid bacteria (AAB) counts were performed. Then, species were identified by PCR-RFLP followed by sequencing and the overall bacterial community was determined by NGS (Next Generation Sequencing). The results showed that yeast, LAB and AAB counts decreased in the palm wines collected from producers after 24-48 h, while they remained constant in samples collected from resellers. Furthermore, the stored palm wine microbiota was composed of several yeast species namely Saccharomyces cerevisiae, Kluyveromyces marxianus, Hanseniaspora guilliermondii, Candida parapsilosis and Brettanomyces bruxellensis. LAB species were Enterococcus durans, Limosilactobacillus fermentum, Lactiplantibacillus plantarum, Lacticaseibacillus paracasei, Fructilactobacillus durionis, Lactobacillus parafarraginis and Lactiplantibacillus pentosus. For AAB, the species were Acetobacter oryzoeni and Acetobacter pasteurianus. The species whose proportions increased steadily during storage were B. bruxellensis, C. parapsilosis, Lc. paracasei, L. fermentum and A. oryzoeni. The NGS method confirmed that Lactobacillus was predominant during storage, followed by Zymomonas and Acetobacter. Knowledge of the microorganisms present during the spoilage of palm wine and their dynamics will enable the development of preservation methods specifically targeting the microorganisms identified.\n\nChanges in microbial communities during the spoilage of palm wine stored at room temperature.", "token_count": 448, "char_count": 1724, "word_count": 224, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:52.635221", "source": { "split": "train_shard_00000", "doc_id": 43 }, "chunk_id": "train_shard_00000_43_0", "global_id": 50 }, { "text": "Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so abundant and prevalent across a wide range of soil types and environmental conditions. Here we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium, a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. Although members of the genus Bradyrhizobium were detected in >80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.\n\nHigh strain-level diversity of Bradyrhizobium across Australian soils.", "token_count": 385, "char_count": 1877, "word_count": 257, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:53.231750", "source": { "split": "train_shard_00000", "doc_id": 44 }, "chunk_id": "train_shard_00000_44_0", "global_id": 51 }, { "text": "Oral drug delivery remains the most preferred administration route, and new oral delivery concepts continuously arise to enable oral delivery of new therapeutics. This study investigates how colloidal structures in five simulated intestinal fluids (SIFs) with varying bile salt and phospholipid compositions influence drug solubility, nanoparticle aggregation and cytotoxicity, and mucoadhesion of nanoparticles and polymers. For the poorly water-soluble drugs indomethacin and felodipine, colloidal structure size in SIFs varies with solubility, and felodipine's solubility is influenced by the lipid composition. Nanoparticles, including polymersomes and mesoporous silica nanoparticles with different surface charges, are characterized in each medium. Dynamic light scattering reveals three interaction modalities: interaction, aggregation, and combination, depending on nanoparticle type and fluid composition. Additionally, interaction patterns correlate with Caco-2 cell cytotoxicity. Quartz crystal microbalance with dissipation analysis reveals that both particle and polymer interactions with mucin are significantly altered in SIFs. For nanoparticles, mucin interactions differ depending on the type of nanoparticle. For the polymers, polyethylene oxide completely loses mucin interaction in SIFs, while chitosan retains partial mucoadhesion. These findings emphasize the importance of not only studying drug properties, but also cell compatibility and mucoadhesion of polymers and nanoparticles, in physiologically relevant conditions.\n\nColloidal Interactions in Simulated Intestinal Fluids: Implications for Oral Drug Delivery at the Nanoscale.", "token_count": 387, "char_count": 1656, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:53.832938", "source": { "split": "train_shard_00000", "doc_id": 45 }, "chunk_id": "train_shard_00000_45_0", "global_id": 52 }, { "text": "In this study, the effects of sea cucumber peptides (SCP) on hormonal regulation in male mice and their underlying mechanisms were explored. SCP was administered to mice, followed by in vivo mating experiments, serum hormone profiling, gene expression analysis, and intestinal microbiome characterization. The impact of SCP on key intestinal bacteria was further validated using in vitro antibacterial assays. In vivo, SCP effectively improved mating ability, increased serum levels of testosterone, and enhanced the expression of testosterone synthesis-related genes. Furthermore, these phenomena may be related to the significant inhibition of Alistipes in the colon of mice by SCP. In vitro, SCP demonstrated antimicrobial activities against Alistipes, characterized by disruption of its cellular membrane integrity and suppression of bile salt hydrolase (BSH) activity. Consistently, there was a significant increase in serum total conjugated bile acids, accompanied by reduced fecal BSH activity and downregulation of farnesoid X receptor (FXR) expression in the testis. Correlation analysis suggested that SCP may promote testosterone synthesis through the Alistipes-bile acid-FXR signaling pathway. Conclusively, SCP can promote testosterone synthesis in male mice through the gut-testosterone axis, providing a new perspective for the study of active peptide-regulated hormones.\n\nSea Cucumber Peptides Promote Testosterone Synthesis in Male Mice: Possibly via Alistipes-Bile Acid-FXR Signaling Pathway.", "token_count": 373, "char_count": 1510, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:54.433103", "source": { "split": "train_shard_00000", "doc_id": 46 }, "chunk_id": "train_shard_00000_46_0", "global_id": 53 }, { "text": "Evaluating clinical impacts of accessory genome elements: ETT2 in Escherichia coli and beyond!", "token_count": 26, "char_count": 94, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ETT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:54.819281", "source": { "split": "train_shard_00000", "doc_id": 47 }, "chunk_id": "train_shard_00000_47_0", "global_id": 54 }, { "text": "Nonalcoholic fatty liver disease (NAFLD), driven by liver lipid accumulation, presents a global health challenge. Bile acid metabolism critically regulates cholesterol homeostasis, but whether prebiotic stachyose can modulate it for NAFLD intervention is unknown. In NAFLD mice induced by a high-fat-high-sucrose diet, stachyose (200 mg/kg bw, 20 weeks) expanded the bile acid pool, elevating the primary bile acids (such as cholic acid and chenodeoxycholic acids) in both serum and liver while reducing secondary bile acid levels. Mechanistically, stachyose upregulated the expression of bile acid synthesis enzymes CYP7A1 and CYP27A1 by inactivating the farnesoid X receptor (FXR)-small heterodimer partner (SHP) pathway, attributed to reducing the high-affinity ligand taurodeoxycholic acid level. Concurrently, it suppressed gut bile salt hydrolase (BSH) and 7α-dehydroxylase (7α-DH) activities, along with\n\nStachyose Attenuates Hepatic Cholesterol Deposition in Nonalcoholic Fatty Liver Mice via Gut Microbiota-Driven Bile Acid Profile Remodeling.", "token_count": 319, "char_count": 1052, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7286, "quality_score": 0.8643, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:55.399860", "source": { "split": "train_shard_00000", "doc_id": 48 }, "chunk_id": "train_shard_00000_48_0", "global_id": 55 }, { "text": "Genomic medicine relies on single reference genomes that miss crucial genetic diversity, creating diagnostic gaps that disproportionately affect underrepresented populations. Pangenome graphs, collections of diverse genomes represented as interconnected genetic paths, offer a powerful alternative to the standard reference genome approach. Pangenome-based approaches capture the spectrum of human variation, dramatically improving how we detect complex structural variants, reconstruct haplotypes, and reduce bias in genetic studies. Projects like the Human Pangenome Reference Consortium have identified hundreds of megabases of missing genetic diversity, leading to remarkable improvements in variant detection across different populations. Yet, as pangenomes grow larger and computationally complex, they become more challenging to interpret clinically, creating a trade-off between comprehensiveness and usability. This review discusses the technical and conceptual advances enabling clinical applications of pangenomes in rare disease diagnosis. Realizing the future potential of pangenome graphs in genomic medicine will require innovative implementation strategies, thorough clinical testing, and user-friendly approaches.\n\nBeyond single references: pangenome graphs and the future of genomic medicine.", "token_count": 238, "char_count": 1310, "word_count": 162, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:55.899916", "source": { "split": "train_shard_00000", "doc_id": 49 }, "chunk_id": "train_shard_00000_49_0", "global_id": 56 }, { "text": "Yersinia enterocolitica is a pathogenic Yersinia species whose public health significance in China is frequently underestimated. Y. enterocolitica poses significant health risks through gastrointestinal infection and extra-intestinal complications. This study conducted systematic, whole-genome sequencing (WGS)-based surveillance of Y. enterocolitica in Jiangsu Province, China (2005-2023), to elucidate epidemiological trends, genomics and antimicrobial resistance (AMR) characteristics, and zoonotic transmission dynamics. Among 30,398 samples (from humans, animals and food), 545 Y. enterocolitica isolates were detected (1.80 %). Pigs exhibited the highest detection rate (7.29 %), followed by dogs (2.59 %) and humans (1.44 %). Serotype O:3 (78.81 % pig-derived) and sequence type (ST) 429 (25.73 % of isolates) dominated. The predominance of the highly MDR ST429-O:3 clone in pigs raises concerns about its enhanced fitness and potential virulence. Multidrug resistance (MDR) was observed in 70.07 % of isolates, with pigs exhibiting the highest rate (79.37 %). Host-specific AMR profiles revealed an escalating MDR trend in human isolates, while strains of animal origin exhibited higher resistance rates than those of human origin, particularly from pigs, dogs, and chickens. Plasmid analysis identified IncC and IncFII(Y) as the predominant replicon types, with IncC plasmids harboring 15 AMR genes (including qnrVC4 and tet(A)). WGS analysis confirmed interprovincial transmission of ST656 strains, with ≤4 core-genome single-nucleotide polymorphism (SNP) differences between isolates from Ningxia (2019) and Jiangsu (2008-2023). Notably, dogs were identified as critical zoonotic reservoirs, sharing 24 STs with humans, highlighting a possible transmission pathway for pathogenic strains to humans", "token_count": 524, "char_count": 1809, "word_count": 242, "semantic_coherence": 1, "information_density": 0.7149, "quality_score": 0.8574, "entities": { "genes": [ "ST656", "ST429" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T04:58:56.548623", "source": { "split": "train_shard_00000", "doc_id": 50 }, "chunk_id": "train_shard_00000_50_0", "global_id": 57 }, { "text": "Y. enterocolitica in Jiangsu is characterized by the clonal expansion of MDR ST429-O:3 in pigs, significant zoonotic transmission through dogs and poultry, and plasmid-driven AMR dissemination. Enhanced \"One Health\" surveillance targeting pigs, dogs, and poultry is critical for mitigating outbreaks driven by these successful MDR and potentially virulent clones.\n\nGenomic diversity and evolution of antibiotic resistance in Yersinia enterocolitica across multiple hosts in eastern China: A 19-year surveillance study.", "token_count": 133, "char_count": 518, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7971, "quality_score": 0.8986, "entities": { "genes": [ "ST429" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:56.963963", "source": { "split": "train_shard_00000", "doc_id": 50 }, "chunk_id": "train_shard_00000_50_1", "global_id": 58 }, { "text": "In this work, we report the micellization behavior of graft copolymer Soluplus that remains insufficiently explored, particularly in the presence of bile salts, which are biologically relevant surface-active agents. The unique amphiphilic architecture allows Soluplus to self-assemble into micelles above its critical micelle concentration (CMC ∼7.6 mg/L or 0.0003 mM at 25 °C), with the hydrophobic (poly(vinyl acetate) and thermoresponsive poly(vinyl caprolactam) blocks forming the core and poly(ethylene glycol) forming the hydrophilic corona, with an average hydrodynamic diameter size between ∼70 and 90 nm. The core radius is observed to be ∼14.5 nm at ambient temperature. However, its relatively low cloud point (CP) of ∼28-34 °C limits its applicability in temperature-sensitive and other formulations. To address this gap, we investigate the mixed micellar system of Soluplus in the presence of essential bile salts: sodium cholate (NaC) and sodium deoxycholate (NaDC) in an aqueous solution environment. Their influence on the micellization of the Soluplus was examined using a combined experimental and computational approach to characterize the mixed micelles formulation and explore their molecular interactions. Clouding studies demonstrated that NaC and NaDC increase the CP of Soluplus following the order: NaDC > NaC due to the former having a lower CMC (∼6 mM at 25 °C) and greater hydrophobicity, which promotes forming smaller and more compact micelles than NaC with a higher CMC (∼16 mM at 25 °C). Dynamic light scattering (DLS) data provided a concentration-dependent transition from Soluplus-rich to bile salt-rich micelles at different temperatures. Meanwhile, the analysis of small-angle neutron scattering (SANS) further confirmed their defined micellar morphologies. Additionally, density functional theory calculations at the B3LYP/3-21G level of theory were used to explore the electronic structure and energy of Soluplus, bile salts, and their mixed systems", "token_count": 506, "char_count": 1989, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:57.920883", "source": { "split": "train_shard_00000", "doc_id": 51 }, "chunk_id": "train_shard_00000_51_0", "global_id": 59 }, { "text": "At the same time, quantum mechanical descriptors provided further insights into the stability and interaction. Furthermore, noncovalent interaction and reduced density gradient analyses inferred weak intermolecular interactions within the mixed micellar systems. Fourier transform infrared spectral profile and theoretical infrared analyses assessed the compatibility between the Soluplus and the bile salts.\n\nUnderstanding Molecular-Level Interactions Between the Soluplus-Bile Salts Mixed Micellar System.", "token_count": 106, "char_count": 507, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7541, "quality_score": 0.877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:58.293009", "source": { "split": "train_shard_00000", "doc_id": 51 }, "chunk_id": "train_shard_00000_51_1", "global_id": 60 }, { "text": "Traditional fermented horsemeat and horsemeat sausages in Xinjiang are rich in microbial resources, mainly including lactic acid bacteria and yeasts. Although the probiotic effects of lactic acid bacteria have been widely studied, there is relatively little research on the probiotic properties of yeasts, which limits their application in functional food development. This study isolated 44 yeast strains from traditional fermented horsemeat products in Xinjiang, and 16 strains exhibiting strong tolerance to temperature, acidic pH, simulated gastrointestinal fluids, and high bile salt solution were screened. Molecular identification revealed that these strains belonged to Candida zeylanoides (C-5, C-8, C-13, C-15, C-21, C-22, C-24, R-8), Candida parapsilosis (R-10, R-12, R-14, R-19, R-20), Candida metapsilosis (R-18), and Rhodotorula alborubescens (R-6, R-11). Several strains demonstrated significantly higher cell surface hydrophobicity, auto-aggregation, and co-aggregation with pathogenic bacteria than the control strain Saccharomyces boulardii CNCM I-745, indicating strong intestinal adhesion and antagonistic potential. All strains have high antioxidant activity (> 60%) and certain cholesterol-lowering ability. Furthermore, extracellular metabolites from select strains exhibited antibacterial activity and potential glucose-lowering effects. Specifically, C. zeylanoides C-8 inhibited α-glucosidase by 54.14%, and C-8 inhibited angiotensin-converting enzyme (ACE) by 37.05%. Hemolysis assays confirmed that all strains were non-hemolytic, suggesting good biosafety. These findings highlight the multi-functional probiotic potential of yeast strains from traditional fermented horsemeat products and provide a scientific basis for their development as novel functional food ingredients.", "token_count": 507, "char_count": 1805, "word_count": 226, "semantic_coherence": 1, "information_density": 0.7301, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:58.890211", "source": { "split": "train_shard_00000", "doc_id": 52 }, "chunk_id": "train_shard_00000_52_0", "global_id": 61 }, { "text": "Isolation and characterization of probiotic yeasts from traditional fermented horsemeat products in Xinjiang: functional evaluation and potential application.", "token_count": 32, "char_count": 158, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:59.252473", "source": { "split": "train_shard_00000", "doc_id": 52 }, "chunk_id": "train_shard_00000_52_1", "global_id": 62 }, { "text": "Gardenia jasminoides, as a widely used traditional Chinese medicine, excessive consumption of it may lead to severe liver injury. As the main hepatotoxic component in Gardenia jasminoides, the specific mechanism by which geniposide (GE) causes liver injury remains elusive. In this study, we conducted a systematic investigation of the effects of GE on bile acid (BA) metabolism and related signal transduction and inflammatory pathways in healthy Sprague-Dawley (SD) rats after oral administration of a 13-fold clinical equivalent dose (450 mg/kg) for 5 days. It is noteworthy that GE administration altered the content and composition of BAs and disrupted BA metabolism. At the same time, the expressions of farnesoid X receptor (FXR) and its downstream proteins bile salt export pump (BSEP) and sodium taurocholate cotransporting polypeptide (NTCP) are significantly inhibited. In addition, the inhibition of FXR will increase the signal transduction of the protein kinase R-like endoplasmic reticulum kinase (PERK)-thioredoxin-interacting protein (TXNIP)-nod-like receptor family pyrin domain-containing 3 (NLRP3) inflammasome axis, thereby triggering cysteine protease-1 (caspase-1), leading to the release of inflammatory factors and worsening liver injury. The addition of the FXR agonist obeticholic acid (OCA) effectively reversed the expressions of the above proteins and mRNA, and alleviated the liver injury caused by GE by restoring BAs homeostasis and regulating the inflammatory pathway. Conclusion: GE causes severe liver injury by affecting bile acid metabolism and inflammatory pathways, and the inhibition of FXR is a crucial factor.\n\nGeniposide induces hepatotoxicity via the bile acid-induced activation of NLRP3 inflammasome and regulation of the FXR/PERK/TXNIP pathway.", "token_count": 490, "char_count": 1792, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [ "NLRP3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:58:59.873149", "source": { "split": "train_shard_00000", "doc_id": 53 }, "chunk_id": "train_shard_00000_53_0", "global_id": 63 }, { "text": "The application of pan-genomics in understanding\n\nPan- and core genome analysis of", "token_count": 20, "char_count": 82, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:00.231849", "source": { "split": "train_shard_00000", "doc_id": 54 }, "chunk_id": "train_shard_00000_54_0", "global_id": 64 }, { "text": "Aldo-keto reductase (AKR) is an important biocatalyst for the synthesis of chiral alcohols; however, its inability to catalyze bulky substrates severely limits its industrial applications. Previously, the T23V/Q213A mutant of AKR from Kluyveromyces marxianus (KmAKR) exhibited an extended substrate scope, but it still showed poor catalytic activity toward some valuable aliphatic and aromatic ketones. Here, we developed a computer-assisted strategy to virtually screen a mutation library constructed from residues 23 and 213. Guided by the binding free energy calculated from high-throughput molecular dynamics simulations, the top ten mutants with the lowest binding energies in each group were selected for testing against the corresponding substrates. It was found that most selected mutants exhibited enhanced catalytic activity, yielding the corresponding pharmaceutically important alcohols with high enantioselectivities. Structural and dynamic analyses indicated that residues 23 and 213 functioned as molecular switches to control the dynamics of the loop regions that constitute the substrate-binding pocket, thereby influencing the substrate specificity of KmAKR.\n\nMolecular Dynamics Simulation-Assisted Tuning of Key Sites to Alter the Substrate Specificity of the Aldo-Keto Reductase KmAKR.", "token_count": 317, "char_count": 1305, "word_count": 175, "semantic_coherence": 1, "information_density": 0.7029, "quality_score": 0.8514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:00.773777", "source": { "split": "train_shard_00000", "doc_id": 55 }, "chunk_id": "train_shard_00000_55_0", "global_id": 65 }, { "text": "Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequencing (SRS) samples. With the extensive growth in publicly available SRS datasets, it is now possible to calculate accurate population allele frequencies of SVs. However, reprocessing hundreds of terabytes of raw SRS data to genotype new variants is impractical for population-scale studies, a computational challenge known as the N+1 problem (i.e., the challenge of re-genotyping an entire cohort for one additional variant). Overcoming this computational bottleneck is essential for analyzing new SVs from the growing number of pangenomes, public genomic databases, and pathogenic variant discovery studies.\n\nThe Great Genotyper: a graph-based method for population genotyping of small and structural variants.", "token_count": 210, "char_count": 910, "word_count": 126, "semantic_coherence": 1, "information_density": 0.754, "quality_score": 0.877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:01.228897", "source": { "split": "train_shard_00000", "doc_id": 56 }, "chunk_id": "train_shard_00000_56_0", "global_id": 66 }, { "text": "The 17q21.31 locus in humans harbors several complex structural haplotypes including a ~970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650kb, encompasses 5 additional genes, and is ~2 million years younger than the human inversion. We further determine that gorillas exhibit an independent duplication of the\n\nRecurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes.", "token_count": 235, "char_count": 927, "word_count": 125, "semantic_coherence": 1, "information_density": 0.688, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:01.685690", "source": { "split": "train_shard_00000", "doc_id": 57 }, "chunk_id": "train_shard_00000_57_0", "global_id": 67 }, { "text": "Green synthesis of silver iodide nanoparticles (AgI-NPs) using carboxymethyl β-glucan from\n\nGreen synthesis of silver iodide nanoparticles from Kluyveromyces marxianus M59 beta-glucan: characterization and anticancer activity.", "token_count": 73, "char_count": 226, "word_count": 26, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:02.054374", "source": { "split": "train_shard_00000", "doc_id": 58 }, "chunk_id": "train_shard_00000_58_0", "global_id": 68 }, { "text": "Clostridium perfringens, a ubiquitous organism that has zoonotic potential, is associated with enteric diseases in humans and various animals, largely due to its potent toxin production and increasing antimicrobial resistance (AMR). The present study involved whole genome sequencing and comparative genomic analysis of four C. perfringens isolates (from pig, dog, and cattle) collected in Tamil Nadu, India, along with 133 global strains of animal origin. The phylogenomic analysis revealed six major clusters and no correlation associated with geographic origin or host were observed. Multilocus sequence typing (MLST) defined sequence types (STs) of two Indian isolates (ST126 and ST200) whereas the remaining two isolates were novel., Pangenome analysis indicated an open genome structure, with 18.28 % core genes and 81.72 % accessory genes. Virulent gene profiling identified widespread presence of plc, pfoA, and cpe, especially among dog isolates, suggesting potential zoonotic risks. wgMLST and MST analysis showed clustering of toxinotype F isolates from dogs and higher genetic diversity for other toxintypess. AMR gene analysis revealed tetracycline resistance as the most prevalent, with several strains harbouring multidrug resistance genes. This study underscores the genetic diversity, adaptive evolution, and One Health significance of C. perfringens in animals and highlights the importance of genomics in understanding host-specific virulence and resistance patterns for effective disease surveillance and control.\n\nGenome sequencing and comparative genome analysis of Clostridium perfringens of animal origin.", "token_count": 382, "char_count": 1629, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6933, "quality_score": 0.8467, "entities": { "genes": [ "ST200", "ST126" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:02.615696", "source": { "split": "train_shard_00000", "doc_id": 59 }, "chunk_id": "train_shard_00000_59_0", "global_id": 69 }, { "text": "Bile salts play a critical role in modulating the host gut. They possess antimicrobial properties wherein they disrupt the bacterial membrane and produce reactive oxygen species (ROS), causing DNA damage. Pathogens like\n\nThe resilience of", "token_count": 56, "char_count": 238, "word_count": 35, "semantic_coherence": 1, "information_density": 0.9143, "quality_score": 0.9571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:02.977630", "source": { "split": "train_shard_00000", "doc_id": 61 }, "chunk_id": "train_shard_00000_61_0", "global_id": 70 }, { "text": "Nuclear receptor farnesoid X receptor (FXR) acts as a key regulator of bile acid pool homeostasis and metabolism. Within the enterohepatic circulation, reabsorbed bile acids act as FXR agonists. FXR, in turn, transcriptionally controls the synthesis and transport of bile acids. Binding occurs in the ligand binding domain (LBD), favoring a conformational change to the active state in which helix 12 interacts with the LBD to form an interaction surface for nuclear co-activators. The homozygous missense variant T296I, identified in a patient with progressive familial intrahepatic cholestasis (PFIC), is located close to the critical helix 12 interaction. Here, we identified reduced transcriptional activity of the variant protein on the downstream targets bile salt export pump (BSEP) and small heterodimer partner (SHP) in vitro, within the patient's liver, and in iPSC-derived hepatic organoids. BSEP-dependent Tauro-DBD transport was impaired in T296I patient-derived organoids, but could be rescued via lipid nanoparticle-mediated FXR WT mRNA delivery, indicating the variant is responsible for the identified reduced BSEP expression. Using molecular dynamics simulations, we observed a reduced transition from the inactive to the active state for the T296I variant, indicating a molecular mechanism underlying the reduced activity. To our knowledge, this is the first study to describe the conformational change from an inactive to an active state of the FXR LBD. This might be useful for new therapeutic approaches targeting the activation of FXR.\n\nA farnesoid X receptor T296I variant disrupts ligand-induced FXR activation and thus bile acid transport in progressive familial intrahepatic cholestasis.", "token_count": 436, "char_count": 1714, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5968, "quality_score": 0.7984, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:03.580958", "source": { "split": "train_shard_00000", "doc_id": 62 }, "chunk_id": "train_shard_00000_62_0", "global_id": 71 }, { "text": "There is growing interest in probiotics due to their potential to confer health benefits. This study aimed to explore the potential probiotic characteristics, gene expression linked to biofilm formation, and anti-biofilm properties of Lacticaseibacillus casei UTMB9. L. casei UTMB9 tolerates acidic environments, with survival rates of 6.90, 7.59, and 7.96 log CFU/mL at pH 2.5, 3.5, and 4.5, respectively, and exhibits slight growth inhibition under bile concentrations up to 0.7 %. Viability declined modestly from 8.51 to 6.61 log colony forming unit (CFU)/mL under simulated gastrointestinal conditions. Surface hydrophobicity (40.89 %), auto-aggregation (30.9 %), co-aggregation (40.81 %), and adhesion (11.89 %) support its adherence potential. Antimicrobial assays showed most potent inhibition against Listeria monocytogenes (9.70 mm) versus E. coli (4.74 mm). Scanning Electron Microscopy (SEM) imaging revealed pronounced damage to L. monocytogenes cells after exposure to cell-free supernatant (CFS), accompanied by significant downregulation of prfA and flaA, and marked antibiofilm suppression. It also demonstrated antioxidant activity (2,2-diphenyl-1-picrylhydrazyl (DPPH) 43.58 %, 2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) 47.47 %, linoleic acid oxidation inhibition 30.28 %) and moderate anticancer activity (IC\n\nAnti-Listeria mechanisms, safety, and predictive modeling of Lacticaseibacillus casei UTMB9: Probiotic profiling targeting virulence gene expression and biofilm formation.", "token_count": 494, "char_count": 1521, "word_count": 195, "semantic_coherence": 1, "information_density": 0.8051, "quality_score": 0.9026, "entities": { "genes": [ "UTMB9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:04.198212", "source": { "split": "train_shard_00000", "doc_id": 63 }, "chunk_id": "train_shard_00000_63_0", "global_id": 72 }, { "text": "This study investigates the genetic, metabolic, and probiotic characteristics of Levilactobacillus brevis DY55bre, a strain isolated from the traditional Turkish fermented beverage, shalgam. Whole-genome sequencing revealed a circular genome of 2.485 Mb with a GC content of 45.72%, predicted 2791 genes, and multiple CRISPR-Cas systems. Pangenome analysis demonstrated an open structure, with 18.9% core genes and 103 strain-specific genes, highlighting its genetic diversity. The DY55bre exhibits heterofermentative carbohydrate metabolism due to the presence of the araBAD operon and the lack of 1-phosphofructokinase (pfK) and fructose-1,6-bisphosphate aldolase enzymes. Probiotic evaluation revealed firm survival under simulated gastrointestinal conditions, including resistance to acidic pH (as low as 3.0) and bile salts (up to 1%), along with significant adhesion to intestinal epithelial cell lines (HT29;59.3%, Caco-2;87%, and DLD-1;60.8%). The strain exhibited high auto-aggregation (84.55%) and cell surface hydrophobicity (56.69%), essential for gut colonization. Safety assessments confirmed its non-hemolytic nature and absence of horizontally acquired antibiotic resistance genes. Notably, GC-MS analysis identified bioactive cyclic dipeptides, Cyclo(D-Phe-L-Pro) and Cyclo(L-Leu-L-Pro), which demonstrated cytotoxic effects against colorectal cancer cell lines, with IC50 values of 7.71 mg/mL for HT29 and 3.19 mg/mL for DLD-1. The cell-free supernatant exhibited antimicrobial activity against pathogens, likely due to the synergistic effects of cyclic dipeptides, organic acids, and other metabolites. Antioxidant assays revealed significant ABTS", "token_count": 511, "char_count": 1666, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7358, "quality_score": 0.8679, "entities": { "genes": [ "HT29", "IC50" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:04.830123", "source": { "split": "train_shard_00000", "doc_id": 64 }, "chunk_id": "train_shard_00000_64_0", "global_id": 73 }, { "text": "Pangenome Analysis and Genome-Guided Probiotic Evaluation of Cyclic Dipeptides Producing Levilactobacillus brevis DY55bre Strain from a Lactic Acid Fermented Shalgam to Assess Its Metabolic, Probiotic Potentials, and Cytotoxic Effects on Colorectal Cancer Cells.", "token_count": 82, "char_count": 262, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9394, "quality_score": 0.9697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:05.195855", "source": { "split": "train_shard_00000", "doc_id": 64 }, "chunk_id": "train_shard_00000_64_1", "global_id": 74 }, { "text": "Previous studies demonstrated chitosan's ability to inhibit free fatty acid (FFA) release in emulsions, yet its structural impacts (molecular weight, MW; deacetylation degree, DD) on lipid digestion remained unclear. This study systematically evaluated chitosan variants (MW: 3.2-670 kDa; DD: 71.2-92.5 %) under simulated gastrointestinal conditions. The results revealed that all chitosan formulations suppressed corn oil digestion to varying degrees. Notably, high molecular weight chitosan (670 kDa) with elevated DD (90 %) exhibited the strongest inhibitory activity, reducing the FFA release rate by approximately 77 %. Mechanistically, this resulted from severe emulsion flocculation limiting enzyme access, coupled with enhanced bile salt adsorption (30 % binding) and lipolysis suppression (57 % inhibition). These findings highlight MW/DD as critical determinants of chitosan's lipid-modulating efficacy, offering a strategic basis for designing functional foods targeting controlled nutrient delivery or reduced caloric uptake.\n\nImpact of chitosan on lipid digestion under simulated gastro-intestinal conditions.", "token_count": 298, "char_count": 1122, "word_count": 147, "semantic_coherence": 1, "information_density": 0.8639, "quality_score": 0.932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:05.739917", "source": { "split": "train_shard_00000", "doc_id": 65 }, "chunk_id": "train_shard_00000_65_0", "global_id": 75 }, { "text": "A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows comprehensive, species-wide characterization of genetic variations and mining of variable genes that may play important roles in phenotypes of interest. Advances in DNA sequencing technologies have facilitated genome sequence assembly and have made pangenome constructions routine. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.\n\nLegume Pangenome Construction Using an Iterative Mapping and Assembly Approach.", "token_count": 122, "char_count": 609, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7412, "quality_score": 0.8706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:06.123031", "source": { "split": "train_shard_00000", "doc_id": 66 }, "chunk_id": "train_shard_00000_66_0", "global_id": 76 }, { "text": "Pursuing new probiotic targets has surged, driven by next-generation sequencing, facilitating a thorough exploration of bacterial traits. The genus Geobacillus stands out as a promising candidate for probiotics. The study explored the genetic attributes of the genus Geobacillus for their resilience to gastrointestinal conditions, nutrient production, and immunomodulatory compound creation, revealing potential probiotic traits. Predictive analyses of genomic elements like prophages, CRISPR-Cas systems, insertion sequences, genomic islands, antibiotic resistance genes, and CAZymes were conducted to assess safety. Comparative genomic analysis was performed using 18 published Geobacillus genomes and a few Lactobacillus and Bifidobacterium genomes as controls. Genes associated with probiotic traits, such as adhesion, stress tolerance (acid/bile, osmotic, oxidative), immune modulation, and molecular chaperones, were uniformly detected in Geobacillus. Mobile genetic elements (such as plasmids, prophages, and insertion sequences), virulence factors, toxins, and antibiotic resistance genes were absent, while CRISPR-Cas systems and CAZymes were present. The pan-genome comprised 25,284 protein-coding genes. Comparative genomic analysis revealed an open pan-genome for Geobacillus. Pan-genome exhibited variability, particularly in genes linked to environmental interaction and secondary metabolite synthesis. Geobacillus appears potentially safe and well-suited for the gut habitat. However, further in vitro studies are essential to confirm its probiotic potential.\n\nUnveiling the probiotic potential of the genus Geobacillus through comparative genomics and in silico analysis.", "token_count": 417, "char_count": 1688, "word_count": 211, "semantic_coherence": 1, "information_density": 0.673, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:06.745417", "source": { "split": "train_shard_00000", "doc_id": 67 }, "chunk_id": "train_shard_00000_67_0", "global_id": 77 }, { "text": "Vancomycin-resistant Enterococcus faecium (VREfm) can be detected in the intestines of humans and animals, as well as in various environments. As multidrug resistant bacteria, E. faecium causes infections that are difficult to treat and pose a significant threat to public health. In this study, we analyzed 1632 vanA or vanB-positive isolates from Homo sapiens, animals, natural environments, and hospital environments across 49 countries. MLST analysis revealed a total of 127 different sequence types, with notably higher sequence type (ST) diversity observed in the United States. ST117 and ST80 were the most common VREfm sequence types and should be continuously monitored in future surveillance programs. Phylogenetic analysis revealed a potential risk of clonal transmission in VREfm. Furthermore, genomic clustering via split k-mer and core genome SNP analyses identified cross-species, cross-border, and nosocomial transmission clusters, confirming multidirectional spread. Bioinformatics analyses revealed 68 antibiotic resistance gene (ARG) subtypes, predominantly conferring resistance to glycopeptides, aminoglycosides, and multiple classes of antibiotics. Temporal analysis revealed a 42 % increase in the average number of ARGs per isolate over three decades, along with the emergence of novel resistance genes, indicating a persistent increase in antimicrobial resistance. Geographical and source-based differences were observed in the number of antibiotic resistance gene subtypes. Specifically, H. sapiens isolates carried significantly more ARGs than did their animal or environmental counterparts (p < 0.001), whereas isolates from low-income countries presented a greater ARG burden than did those from high-income regions (p < 0.05). Mobile genetic elements, particularly plasmids, were strongly correlated with the number of ARGs (p < 0.001), as validated through explainable artificial intelligence. In conclusion, this study emphasizes the importance of monitoring and exploring the evolution of VREfm strains, particularly changes in antibiotic resistance genes and the spread of these strains, within the \"One Health\" framework. Moreover, heightened vigilance in epidemiological surveillance and infection control practices is necessary.", "token_count": 526, "char_count": 2265, "word_count": 307, "semantic_coherence": 1, "information_density": 0.6808, "quality_score": 0.8404, "entities": { "genes": [ "ST80", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T04:59:07.390460", "source": { "split": "train_shard_00000", "doc_id": 68 }, "chunk_id": "train_shard_00000_68_0", "global_id": 78 }, { "text": "Global epidemiology and genomic perspectives on vancomycin-resistant Enterococcus faecium: Rising antimicrobial resistance and transmission risks within the one health framework.", "token_count": 42, "char_count": 178, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:07.779066", "source": { "split": "train_shard_00000", "doc_id": 68 }, "chunk_id": "train_shard_00000_68_1", "global_id": 79 }, { "text": "Duck Plague Virus (DPV), an alphaherpesvirus, causes significant morbidity and mortality in waterfowl and remains a persistent threat to duck farming across Asia. This study reports the first complete genomic characterization of DPV isolates from Thailand including a commercial vaccine strain (DPVac) and two contemporary field isolates (DPV7 and DPV8). Using Oxford Nanopore Technologies (ONT) and hybrid Illumina-ONT sequencing, we successfully assembled complete genomes ranging from 160,511 to 163,789 bp. The assembled genomes showed high sequence identity to the European reference strain DEV 2085. Comparative genomic analysis revealed structural differences in the UL and US regions. Phylogenetic reconstruction based on core genome single-nucleotide polymorphisms (SNPs) placed DPV7 within a clade of recent Chinese field strains, while DPV8 clustered closely with vaccine-associated lineages from Germany, India, and Bangladesh. Notably, SNP analysis identified multiple virulence-associated mutations uniquely present in DPV7. These mutations, absent in DPVac and DPV8, were located within or near genes involved in viral replication (UL54), host immune evasion (UL41, UL14), viral entry (UL44, UL8), intracellular trafficking (US3, US8), and virulence modulation (LORF3). These findings suggest that DPV7 may be undergoing adaptive evolution under immune pressure, potentially compromising vaccine effectiveness. Our results underscore the critical need for continuous molecular surveillance and functional studies to evaluate the impact of emerging DPV variants. The complete genome sequences reported herein provide a valuable resource for future research on DPV evolution, diagnostics, and vaccine development in endemic regions.\n\nComparative genomic analysis of duck plague virus reveals evolutionary divergence between vaccine and contemporary field isolates in Thailand.", "token_count": 457, "char_count": 1889, "word_count": 252, "semantic_coherence": 1, "information_density": 0.7341, "quality_score": 0.8671, "entities": { "genes": [ "LORF3", "DPV8", "US8", "UL14", "US3", "UL41", "UL44", "UL54", "UL8", "DPV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:08.398806", "source": { "split": "train_shard_00000", "doc_id": 69 }, "chunk_id": "train_shard_00000_69_0", "global_id": 80 }, { "text": "The alarming rise of antibiotic resistance necessitates the search for novel and safe alternatives to conventional therapies. Probiotics and their metabolites, particularly bacteriocins, are increasingly recognized for maintaining gut health, combating pathogens, and alleviating oxidative stress. Bats, with their diverse and underexplored gut microbiota, represent a unique reservoir of probiotic strains and bioactive peptides. This study aimed to isolate and characterize a novel probiotic strain from the intestine of the insectivorous bat Hipposideros speoris and evaluate its probiotic attributes, antioxidant potential, safety traits, and bacteriocin production. The isolated strain was identified as Enterococcus hirae BNT6 through 16S rRNA sequencing. Probiotic properties including acid and bile tolerance, cell surface hydrophobicity, adhesion to SW480 epithelial cells, and antioxidant activities (DPPH and ABTS scavenging) were assessed. Safety traits were evaluated through hemolysis, DNase activity, and antibiotic susceptibility testing. Bacteriocin purification was carried out using ammonium sulfate precipitation, gel filtration chromatography and RP-HPLC. Antimicrobial activity was tested against pathogenic bacteria, while molecular characterization was performed by SDS-PAGE, MALDI-TOF MS, peptide mass fingerprinting, spectroscopic analysis, and 3D in silico modeling. E. hirae BNT6 survived at pH 3, tolerated 0.3% bile salts, showed high hydrophobicity (51.7%), and adhered efficiently to SW480 cells. It exhibited strong antioxidant activity (65.7% DPPH and 81.6% ABTS scavenging). Safety evaluation confirmed its non-hemolytic, DNase-negative phenotype and susceptibility to most clinically relevant antibiotics", "token_count": 464, "char_count": 1740, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7557, "quality_score": 0.8778, "entities": { "genes": [ "BNT6", "SW480" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:09.016665", "source": { "split": "train_shard_00000", "doc_id": 70 }, "chunk_id": "train_shard_00000_70_0", "global_id": 81 }, { "text": "The purified bacteriocin, Enterocin BNT6, displayed broad-spectrum antimicrobial activity against Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, and Bacillus subtilis, and remained stable under varying pH, temperature, and enzymatic conditions. Molecular analyses indicated a size of ~ 27 kDa (SDS-PAGE) and ~ 15 kDa (MALDI-TOF MS), with peptide mass fingerprinting showing 59% similarity to mammalian FAM216B protein. Structural studies revealed a predominantly α-helical conformation. Our findings establish Enterococcus hirae BNT6 as the first bat-derived probiotic strain producing a FAM216B-like bacteriocin with strong probiotic, antioxidant, and antimicrobial activities. In silico structural modeling revealed a predominantly α-helical, stable conformation with striking similarity to mammalian FAM216B, suggesting potential evolutionary mimicry. These unique attributes highlight its promise as a next-generation therapeutic and microbiome-based intervention.\n\nA Novel Bacteriocin from Insectivorous Bat (Hipposideros speoris) Intestine Mimicking Mammalian FAM216B: Probiotic, Antioxidant, and Antimicrobial Properties of Enterococcus hirae BNT6.", "token_count": 363, "char_count": 1173, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7643, "quality_score": 0.8821, "entities": { "genes": [ "FAM216B", "BNT6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:09.571133", "source": { "split": "train_shard_00000", "doc_id": 70 }, "chunk_id": "train_shard_00000_70_1", "global_id": 82 }, { "text": "Bacteriocins are ribosomally produced, proteinaceous antimicrobial biomolecules with versatile functions and are considered potential next-generation therapeutics. They are secreted by a few groups of lactic acid bacteria (LAB) that possess the ability to combat spoilage and foodborne pathogens. Given these properties, bacteriocins have generated significant interest for their potential use as natural food preservatives. This study aimed to isolate and characterize bacteriocin-producing LAB with potent antimicrobial properties and evaluate their potential use as natural food preservatives and alternative therapeutics. A total of 47 morphologically distinct LAB isolates were screened for antibacterial activity against foodborne pathogens. The isolate exhibiting the strongest antimicrobial activity, designated CW40, was selected for further study. The bacteriocin was purified from the culture supernatant using gel filtration chromatography. The isolate was identified by 16S rDNA sequencing, and optimal conditions for bacteriocin production were determined. The molecular weight of the bacteriocin was estimated, and its antimicrobial spectrum, enzyme sensitivity, bile salt tolerance, and antibiotic resistance profile were assessed. Isolate CW40 produced 8 kDa (MW) of bacteriocin from the purified supernatant of its grown culture and was identified as\n\nOptimization of bacteriocin production by", "token_count": 325, "char_count": 1411, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [ "CW40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:10.122192", "source": { "split": "train_shard_00000", "doc_id": 71 }, "chunk_id": "train_shard_00000_71_0", "global_id": 83 }, { "text": "Bile salts are key regulators of host microbe interactions and epithelial signaling in the intestine. Gut bacteria can deconjugate primary bile salts, which can be leveraged to engineer targeted therapies through bile salt hydrolase (BSH) activity. However, the interplay between bile salt signaling, microbial metabolism, and tumor-associated colonization remains poorly understood. Here, we establish an in vitro colon organoid platform to dissect bile salt driven epithelial microbe dynamics at cellular resolution. Using this system, we found that bile salts markedly modulated colonization of native Escherichia coli (EcAZ-2) and a BSH-expressing strain (EcAZ-2LsBSH) in healthy versus tumor murine organoids. Under bile salt exposure, EcAZ-2LsBSH preferentially colonized tumor organoids, though overall colonization was lower than that of the non-BSH strain. Beyond effects on bacterial colonization, bile salts also directly activated host signaling pathways. In presence of bile salts, EcAZ-2LsBSH significantly enhanced activation of bile acid receptors such as farnesoid X receptor (FXR) by 2-fold in healthy organoids. These findings reveal a mechanistic bridge between in vivo microbial function and bile salt interactions, offering potential microbiota and bile acid targeted therapeutic strategies.\n\nBile Salts and Bacterial Bile Salt Hydrolase Activity Differentially Influence Escherichia coli Colonization and FXR Signaling in Colorectal Cancer Organoids.", "token_count": 385, "char_count": 1473, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:10.710820", "source": { "split": "train_shard_00000", "doc_id": 72 }, "chunk_id": "train_shard_00000_72_0", "global_id": 84 }, { "text": "Transit time, fluid intake, diet, and overall gut health all influence stool consistency. However, the relationships between the gut microbiota, metabolome (microbial metabolites), and stool consistency in infants and young children remain poorly understood. In this study, we analyzed the microbiota and metabolome of 618 stool samples from children aged 2.5 months (n = 360), 6 months (n = 229), 14 months (n = 274), and 30 months (n = 169) from the FinnBrain Birth Cohort Study, correlating these data with stool water content and parent-reported stool consistency. We found that breastfeeding had the strongest association with both stool consistency and fecal water content. We observed that the concentrations of newly discovered microbial bile acid amidates were associated with constipation and negatively correlated with stool water content. Partial versus exclusive breastfeeding was further linked to higher levels of specific bile acid amidates through mediation by constipation. Bile salt hydrolase, an enzyme involved in deconjugating primary bile acids and generating novel microbial bile acids, was also predicted to be negatively associated with stool water content. In addition, short-chain fatty acids (SCFAs), particularly acetic acids, were positively associated with stool water content, whereas branched SCFAs showed a negative association. These findings suggest longer transit time appeared to allow more extensive bacterial metabolism of microbial metabolites, including the transformation of bile acid amidates. Here, we also observed that the relative abundances of specific genera such as\n\nEarly life gut microbial and metabolic shifts reflected in stool consistency- a gut transit time proxy.", "token_count": 409, "char_count": 1722, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:11.311884", "source": { "split": "train_shard_00000", "doc_id": 73 }, "chunk_id": "train_shard_00000_73_0", "global_id": 85 }, { "text": "Astaxanthin (Asta), a hydrophobic carotenoid, exhibits poor bioavailability due to limited water solubility and intestinal absorption. Lipid-based delivery systems enhance its uptake via mixed micelles formed by fatty acids (FFAs) and bile salts (BS). Here, we systematically investigate how the degree of FFA unsaturation-using oleic (monounsaturated), linoleic (diunsaturated), and linolenic (triunsaturated) acids-modulates Asta encapsulation. Binary (FFA-BS) and ternary (FFA-BS-Asta) micelle models reveal that FFAs expand the hydrophobic core of pure BS micelles, improving stability without altering spherical morphology. Isothermal titration calorimetry (ITC) shows electrostatic interactions dominate micellization, with polyunsaturated FFAs exhibiting higher binding affinity to BS. Spectroscopic analyses, including circular dichroism (CD) and raman spectroscopy (Raman), confirm enhanced hydrogen bonding and hydrophobic interactions between Asta and unsaturated FFAs, promoting tighter molecular packing. Quartz crystal microbalance with dissipation (QCM-D) demonstrates increased interfacial thickness and stability for polyunsaturated systems. Molecular dynamics simulations visualize faster Asta encapsulation and higher loading capacity in linolenic acid micelles, correlated with enhanced hydrogen bond formation. These results establish that FFA unsaturation governs micellar architecture and interfacial interactions, providing a mechanistic basis for designing bile salt-lipid nanocarriers to improve lipophilic nutraceutical delivery.\n\nFatty acid unsaturation regulates astaxanthin encapsulation in bile salt micelles: Insights into self-assembly mechanisms and molecular interactions.", "token_count": 427, "char_count": 1707, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7811, "quality_score": 0.8905, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:11.916474", "source": { "split": "train_shard_00000", "doc_id": 74 }, "chunk_id": "train_shard_00000_74_0", "global_id": 86 }, { "text": "The food-borne pathogen Listeria monocytogenes (L. monocytogenes, Lm) has been identified as the cause of listeriosis. In recent years, several outbreaks in Europe and the U.S. have been traced to contaminated enoki mushrooms. However, the genomic characterization of Lm from enoki mushrooms in China has not been well elucidated. In this study, 144 strains of L. monocytogenes from retail enoki mushrooms across 24 provinces of China in 2021 were characterized based on whole genome sequencing. All the isolates were classified into two lineages: lineages I (n = 54) and lineages II (n = 90) with the four most predominant clonal complexes CCs (CC8, CC87, CC14, and CC5) which are closely consistent with the ST distribution observed in Chinese clinical strains. According to WHO/FAO classification based on the LIPI-1 to 4 and inlA gene, 81.9 % were classified as hypervirulent or virulent strains. Core genome SNP analysis revealed close genetic relationships between enoki mushroom isolates and Chinese clinical strains, especially for CC8/ST8, CC87/ST87, and CC14/ST91, suggesting potential foodborne transmission. Additionally, 56.3 % harbored the SSI-1 stress survival islet, indicating adaptation to food processing environments. These findings highlight enoki mushrooms as possible reservoirs for transmitting pathogenic Lm strains to humans, emphasizing the need for strengthened surveillance and control.\n\nWhole-genome sequencing of Listeria monocytogenes isolated from retail enoki mushrooms in China highlights public health risk.", "token_count": 411, "char_count": 1543, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [ "CC8", "CC5", "CC14", "ST8", "ST91", "ST87", "CC87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:12.514237", "source": { "split": "train_shard_00000", "doc_id": 75 }, "chunk_id": "train_shard_00000_75_0", "global_id": 87 }, { "text": "Probiotics are beneficial live microorganisms that may provide secure management of several diseases, such as diarrhea. The current research aims to assess the antidiarrheal activity of potential probiotics by utilizing in vitro and in vivo approaches. Bacterial strains were isolated from dairy products and screened for probiotic characterization, with four strains, viz., Weissella confusa (ProY 5.1), Enterococcus lactis (ProY 5.3), Leuconostoc lactis (RM 2.1), and Bacillus subtilis (ProY 11.3), selected based on in vitro approaches. These strains demonstrated non-hemolytic properties, acidic resistance, tolerance to bile salt and phenol, strong adherence rate, probiotic activity, and antimicrobial activity against six enteric pathogens. Potential strains were identified by applying molecular techniques: MALDI-TOF and whole genome sequencing. In vivo experiments on castor oil-induced diarrheal Swiss albino mice showed a positive impact when compared to loperamide and bismuth subsalicylate as positive controls, whereas the PBS + MRS broth was used as a negative control. Screened ProY 5.1, ProY 5.3, and RM 2.1 significantly lengthened latency periods and reduced diarrheal symptoms (p < 0.005). Comparatively low antidiarrheal activity was found in the ProY 11.3 isolate. The combination of candidate probiotics exhibited stronger activity compared to the individual ones. In conclusion, the three strains might be potential probiotic candidates for managing diarrhea.\n\nThree Characterized Probiotics from Dairy Sources-Weissella confusa (ProY 5.1), Enterococcus lactis (ProY 5.3), and Leuconostoc lactis (RM 2.1)-Exhibit Potential for Antidiarrheal Effects.", "token_count": 480, "char_count": 1674, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:13.133771", "source": { "split": "train_shard_00000", "doc_id": 76 }, "chunk_id": "train_shard_00000_76_0", "global_id": 88 }, { "text": "Probiotic use has become more important in aquaculture for healthy and sustainable output. In particular, Bacillus spp. have emerged as effective probiotic agents, improving gut health, enhancing the immune system, promoting growth, and providing protection against pathogens in fish. Therefore, the application of Bacillus in aquaculture offers a strategic approach to increasing productivity while reducing the reliance on antibiotics. In this study, the antibacterial activities of Bacillus isolates, whose probiotic properties will be determined, against test bacteria that are fish pathogens such as Aeromonas hydrophila, Vibrio anguillarum, Lactococcus garvieae, and Yersinia ruckeri were determined by using cross-streak method and agar well diffusion methods. Then, antibiotic resistances of 75 isolates determined to have antibacterial activity were screened against 9 different antibiotics by the agar disc diffusion method. Gastric juice (pH 2.5) tolerance of 55 isolates determined to be sensitive to antibiotics was examined, and the tolerance of 13 isolates to gastric juice was determined. Optimum growth characteristics at acidic pH, surface hydrophobicity, bile tolerance, and protease, amylase, lipase, and cellulase activities, hemolytic activities, coagulase activities, bacterial adhesion abilities, and biofilm production properties of these isolates were determined. As a result, Bacillus subtilis Ö-4-68, with the best probiotic properties, was selected from the examined isolates, and production medium optimization was carried out with laboratory scale statistical experiment design (Response Surface Methodology, RSM) for high amount of biomass production. As a result of the trials, an economical cost-effective production medium content with high biomass production was determined.\n\nAn economically cost-effective production medium optimization of Bacillus subtilis Ö-4-68: A potential probiotic for aquaculture.", "token_count": 460, "char_count": 1941, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:13.747692", "source": { "split": "train_shard_00000", "doc_id": 77 }, "chunk_id": "train_shard_00000_77_0", "global_id": 89 }, { "text": "The thermotolerant yeast Ogataea polymorpha TBRC 4839 is a promising host for heterologous protein expression using sucrose and molasses as low-cost carbon sources, making it suitable for industrial applications. This study analyzed the genome and transcriptome of O. polymorpha under sucrose-induced conditions. The nuclear genome of strain TBRC 4839 measures 8.9 Mbp with a GC content of 47.87%, consistent with other Ogataea species. The genome encodes 5184 protein-coding genes, comparable to related strains. Additionally, the mitochondrial genome spans 49.4 Kbp and has a low GC content of approximately 20%. Transcriptomic analysis revealed that sucrose induction triggers a metabolic shift characterized by increased carbohydrate metabolism and decreased amino acid biosynthesis, stress signaling, and cell division, enabling efficient energy utilization in sucrose-rich environments. Among the identified genes with up-regulated expression, five were notable: FUN_000066 (hypothetical protein), FUN_001144 (maltose permease), FUN_001145 (maltase), FUN_002060 (mitochondrial NAD-dependent malic enzyme), and FUN_002263 (hypothetical protein). The promoter efficiency was evaluated by expressing the fungal xylanase gene under sucrose-inducing conditions using these promoters. The maltase (MAL) promoter exhibited the highest xylanase production efficiency, outperforming other promoters. Furthermore, the MAL promoter proved effective for xylanase production when molasses was used as the carbon source. These findings underscore the potential of O. polymorpha TBRC 4839 and the MAL promoter for industrial protein production.\n\nSucrose-Induced Transcriptomic Response in Ogataea polymorpha TBRC 4839 Reveals its Potential for Recombinant Protein Production.", "token_count": 487, "char_count": 1766, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:14.374202", "source": { "split": "train_shard_00000", "doc_id": 78 }, "chunk_id": "train_shard_00000_78_0", "global_id": 90 }, { "text": "Advancements in translational genomics have revolutionized crop breeding, driving us from traditional breeding methods towards next-generation strategies that integrate genomic, transcriptomic, and phenotypic data to expedite crop improvement. There has been a shift from single genomes to pan-genomes, which better capture intraspecific diversity, and from bulk transcriptome analyses to single-cell transcriptomics, enabling cell-specific insights into gene regulation and functional genomics. Both high throughput genopyting and phenotyping approaches are now possible due to rapid technological advancement in the field of translational genomics. Large-scale phenotyping data from multi-environment field trials is now possible due to AI-enabled digital and drone-based scanning. In the era of artificial intelligence and machine learning we have developed flexible models to handle complex genetic architecture of trait regulation using various tools and approaches. These genetic and genomic resources are the foundation for generating novel, adaptable, and high-yielding varieties, accelerating trait discovery and mapping. This review explores the comprehensive landscape of modern translational genomics, highlighting key shifts and innovations that enhance our capacity to address agricultural challenges. Integrative pipelines that unify these next-generation approaches could facilitate faster, more precise, and sustainable crop improvement, ultimately meeting the growing demands for future-ready crops.\n\nNext-generation translational genomics for developing future crops.", "token_count": 305, "char_count": 1586, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7186, "quality_score": 0.8593, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:14.923117", "source": { "split": "train_shard_00000", "doc_id": 79 }, "chunk_id": "train_shard_00000_79_0", "global_id": 91 }, { "text": "The search for the genetic basis of phenotypes has primarily focused on single nucleotide polymorphisms, often overlooking structural variants (SVs). SVs can significantly affect gene function, but detecting and characterizing them is challenging, even with long-read sequencing. Moreover, traditional single-reference methods can fail to capture many genetic variants. Using long-reads, we generated a Capuchino Seedeater (Sporophila) pangenome, including 16 individuals from seven species, to investigate how SVs contribute to species and coloration differences. Leveraging this pangenome, we mapped short-read data from 127 individuals, genotyped variants identified in the pangenome graph and subsequently perform FST scans and genome-wide association studies. Species divergence primarily arises from SNPs and indels (< 50 bp) in non-coding regions of melanin-related genes, as larger SVs rarely overlap with divergence peaks. One exception was a 55 bp deletion near the OCA2 and HERC2 genes, associated with feather pheomelanin content. These findings support the hypothesis that the reshuffling of small regulatory alleles, rather than larger species-specific mutations, accelerated plumage evolution leading to prezygotic isolation in Capuchinos.\n\nA pangenomic approach reveals the sources of genetic variation fueling the rapid radiation of Capuchino Seedeaters.", "token_count": 322, "char_count": 1371, "word_count": 184, "semantic_coherence": 1, "information_density": 0.7772, "quality_score": 0.8886, "entities": { "genes": [ "HERC2", "OCA2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:15.469240", "source": { "split": "train_shard_00000", "doc_id": 80 }, "chunk_id": "train_shard_00000_80_0", "global_id": 92 }, { "text": "After 500 million years of evolution, extant land plants compose the following two sister groups: the bryophytes and the vascular plants. Despite their small size and simple structure, bryophytes thrive in a wide variety of habitats, including extreme conditions. However, the genetic basis for their ecological adaptability and long-term survival is not well understood. A comprehensive super-pangenome analysis, incorporating 123 newly sequenced bryophyte genomes, reveals that bryophytes possess a substantially greater diversity of gene families than vascular plants. This includes a higher number of unique and lineage-specific gene families, originating from extensive new gene formation and continuous horizontal transfer of microbial genes over their long evolutionary history. The evolution of bryophytes' rich and diverse genetic toolkit, which includes new physiological innovations like unique immune receptors, likely facilitated their spread across different biomes. These newly sequenced bryophyte genomes offer a valuable resource for exploring alternative evolutionary strategies for terrestrial success.\n\nBryophytes hold a larger gene family space than vascular plants.", "token_count": 253, "char_count": 1187, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7296, "quality_score": 0.8648, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:15.950583", "source": { "split": "train_shard_00000", "doc_id": 81 }, "chunk_id": "train_shard_00000_81_0", "global_id": 93 }, { "text": "The yeast Kluyveromyces marxianus, a yeast known for its ability to ferment ethanol at high temperatures, can utilize various sugars including cellobiose, lactose and xylose. This study focused on improving cellobiose utilization by identifying and engineering a cellobiose transporter in K. marxianus. To assess cellobiose utilization capabilities, K. marxianus strains were grown in a cellobiose medium. The strains showed various growth levels, for example, the NCYC2791 strain grew well, while the DMKU3-1042 strain did not. This difference provided a basis for identifying a cellobiose transporter. Thirteen transporter candidate genes from the NCYC2791 genome were expressed in DMKU3-1042. As a result, KmSTL1 overexpression enhanced cell growth in a cellobiose medium. In addition, its disruption in NCYC2791 caused growth defects. To confirm its function, KmSTL1 was co-expressed with a β-glucosidase gene in Saccharomyces cerevisiae EBY.VW1000, which only uptake maltose. This engineered strain grew in cellobiose medium, indicating that KmSTL1 encodes a cellobiose transporter. Expression of GFP-fused KmStl1p in K. marxianus revealed that KmStl1p localized on cell membrane under cellobiose conditions, but was degraded in glucose conditions, suggesting that the transporter is regulated by available sugars. By individually disrupting seven α-arrestin genes in K. marxianus, KmRog3p was identified as a major ubiquitination mediator for KmStl1p degradation. Deletion analysis of KmStl1p revealed that its C-terminus is crucial for recognition by KmRog3p. Furthermore, expressing KmStl1p C-terminus mutants enhanced cellobiose assimilation in both K. marxianus and S. cerevisiae. These findings demonstrate that engineering KmStl1p is an effective strategy to improve cellobiose utilization in yeasts.", "token_count": 510, "char_count": 1812, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5847, "quality_score": 0.7923, "entities": { "genes": [ "NCYC2791", "VW1000", "DMKU3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:16.580174", "source": { "split": "train_shard_00000", "doc_id": 82 }, "chunk_id": "train_shard_00000_82_0", "global_id": 94 }, { "text": "Identification and engineering of a cellobiose transporter KmStl1p to enhance cellobiose utilization in Kluyveromyces marxianus and Saccharomyces cerevisiae.", "token_count": 44, "char_count": 157, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:16.935919", "source": { "split": "train_shard_00000", "doc_id": 82 }, "chunk_id": "train_shard_00000_82_1", "global_id": 95 }, { "text": "Cistanche deserticola Y. C. Ma, revered as \"desert ginseng\" in traditional Chinese medicine, has been historically prescribed for treating five strains and seven injuries, and nourishing the five zang organs. While the total glycosides from C. deserticola (GCs) demonstrate hepatoprotective potential against acute alcoholic liver disease (ALD), their efficacy in chronic ALD and mechanism remain unexplored.\n\nMulti-omics analysis reveals the mechanism of Cistanche deserticola against alcoholic liver disease via bile salt hydrolase and SCD1.", "token_count": 139, "char_count": 543, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7838, "quality_score": 0.8919, "entities": { "genes": [ "SCD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:17.362226", "source": { "split": "train_shard_00000", "doc_id": 83 }, "chunk_id": "train_shard_00000_83_0", "global_id": 96 }, { "text": "Three novel bacterial strains obtained from human fecal samples were characterized for their taxonomic classification and probiotic potential. The strains included one Gram-stain-positive (B2-R-112\n\nCoprococcus intestinalis sp. nov., Parabacteroides caecihominis sp. nov., and \"Akkermansia massiliensis\" B2-R-115 with High Probiotic Potential from the Human Gut Microbiome.", "token_count": 111, "char_count": 373, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8222, "quality_score": 0.9111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:17.737822", "source": { "split": "train_shard_00000", "doc_id": 84 }, "chunk_id": "train_shard_00000_84_0", "global_id": 97 }, { "text": "Development and validation of a core genome multilocus sequence typing scheme for", "token_count": 15, "char_count": 81, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:18.177065", "source": { "split": "train_shard_00000", "doc_id": 85 }, "chunk_id": "train_shard_00000_85_0", "global_id": 98 }, { "text": "With increasing industrialisation and human activities, heavy metal pollution has become a serious environmental concern, particularly cadmium (Cd) contamination. This study reveals significant differences in Cd tolerance between wild apple (Malus spp.) and cultivated apple (Malus domestica). Through pan-genome analysis, we identified the transcription factor WRKY17 as a key regulator of Cd stress response, with a 3355-bp insertion (P-INS) in its promoter region being the primary genetic basis for this differential tolerance. In cultivated apples, P-INS suppresses WRKY17 expression, leading to reduced Cd tolerance. In contrast, wild apples lacking P-INS exhibit activated WRKY17 expression. Further investigation demonstrated that WRKY17 enhances Cd tolerance by inducing the expression of long non-coding RNA lncRNA400. Mechanistically, lncRNA400 forms an R-loop structure that recruits the histone demethylase JMJD5 to remove H3K27me3 marks from the promoter of the Plant Cadmium Resistance gene PCR2, thereby activating PCR2 expression. Notably, WRKY17 activation also accelerates leaf senescence, explaining why P-INS was retained during apple domestication-its suppression of WRKY17 maintains better agronomic traits despite reduced Cd tolerance. In apple cultivation, grafting wild apple rootstocks with cultivated scions effectively combines the Cd-tolerant traits of wild varieties with the delayed leaf senescence characteristics of cultivated cultivars, providing a practical solution for the apple industry to address Cd contamination.\n\nDomestication-Selected Promoter Insertion in WRKY17 Increases Cadmium Sensitivity in Apple.", "token_count": 404, "char_count": 1647, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [ "WRKY17", "JMJD5", "PCR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:18.788849", "source": { "split": "train_shard_00000", "doc_id": 86 }, "chunk_id": "train_shard_00000_86_0", "global_id": 99 }, { "text": "Inflammatory bowel disease (IBD) is characterized by intestinal barrier dysfunction and bile acid (BA) dysmetabolism. BA metabolism was a pivotal regulator in the \"gut-liver axis\" to maintain intestinal homeostasis. Ovalbumin-derived peptides (OVA-Ps) exhibit potential in barrier repair; however, their systemic mechanisms within the microbiota-BA-host network remain underexplored. This study investigates the therapeutic potential of the oligomer OVA-P in a DSS-induced colitis mouse model. OVA-P administration significantly alleviated colitis symptoms, restored colon length, reduced pro-inflammatory cytokines (tumor necrosis factor-α), and enhanced antioxidant markers (SOD). Mechanistically, the OVA-P reshaped gut microbiota composition, suppressed bile salt hydrolase (BSH), and elevated conjugated BAs (e.g., taurocholic acid) levels. These changes activated the farnesoid X receptor (FXR) pathway, upregulating tight junction protein (ZO-1), and mucin (MUC-2) expression, thereby restoring intestinal barrier integrity. Metabolomic and metagenomic analyses confirmed the OVA-P-mediated modulation of the gut-liver axis through FXR-SHP/FGF15 signaling, highlighting its role in maintaining BA homeostasis. These findings provide insights into the use of OVA-P as a dietary intervention for IBD by targeting microbiota-BA-FXR interactions, offering a foundation for high-value egg protein applications in functional foods.\n\nOvalbumin Peptides Restore Intestinal Barrier Integrity via Gut-Liver Axis Modulation of Bile Salt Hydrolase and Bile Acids Crosstalk.", "token_count": 437, "char_count": 1568, "word_count": 196, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "FGF15" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:20.104103", "source": { "split": "train_shard_00000", "doc_id": 87 }, "chunk_id": "train_shard_00000_87_0", "global_id": 100 }, { "text": "High-fat diet (HFD) is positively correlated with colorectal cancer (CRC), but there are notable inter-individual differences in susceptibility to the tumor-promoting effects of HFD. A better understanding of the mechanisms that modulate the outcomes of HFD could help inform precision prevention strategies for CRC. Here, we found a key role for the gut microbiota in the individual differences observed in the tumor-promoting effects of HFD. Analysis of the gut bacteria enriched in mice resistant to HFD-induced cancer identified Lactobacillus johnsonii (L. johnsonii) as an effective protector. Colonization of L. johnsonii increased intestinal chenodeoxycholic acid (CDCA) concentrations in HFD-exposed mice, which decelerated HFD-induced CRC progression. Mechanistically, L. johnsonii converted conjugated bile acid to CDCA via bile salt hydrolase (BSH), and CDCA induced mitochondrial dysfunction and oxidative stress to promote apoptosis, effectively suppressing tumor development. These results establish the gut microbiota as a mediator of inter-individual differences in cancer susceptibility induced by HFD and reveal a probiotic strategy with the ability to inhibit tumorigenesis, suggesting a possible route to reduce HFD-induced CRC progression.\n\nLactobacillus johnsonii Synthesizes Chenodeoxycholic Acid to Reduce Susceptibility to High-Fat Diet-Induced Colorectal Cancer.", "token_count": 357, "char_count": 1388, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.8179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:20.669300", "source": { "split": "train_shard_00000", "doc_id": 88 }, "chunk_id": "train_shard_00000_88_0", "global_id": 101 }, { "text": "Candida is a common and harmless component of the vaginal microbiota, present in approximately 50% of women of reproductive age. In specific conditions like pregnancy, Candida may cause chronic or recurrent infections which significantly impair quality of life. Additionally, due to the possibility of vertical transmission, it may lead to life-threatening infections in newborns. Timely screening, suspicion and identification of the causative agent are critical determinants of patient outcomes. Candida albicans (CA) remains the most prevalent species, but other non-albicans Candida (NAC) species and other non-Candida yeast (NCY) also play an important role in vulvovaginal infections. Due to the lack of precise local epidemiological data, this study aimed to determine the 10-year prevalence of CA, NAC and NCY species (spp.) in symptomatic pregnant women in Serbia using identification Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) for species identification. The total of 2,142 cases were examined (2013-2023) and the laboratory positivity was 48.3% (n = 1,035). The prevalence of CA, NAC and NCY were 74%, 23% and 3%, respectively. Biochemical and proteomic identification methods showed 100% concordance for CA, C. krusei (Pichia kudriavzevii), C. kefyr (Kluyveromyces marxianus), C. lusitaniae (Clavispora lusitaniae), and C. zeylanoides (Pichia norvengensis). Biochemical misidentification was observed for C. tropicalis (Lodderomyces sp.), C. glabrata (Nakaseomyces glabrata), and Saccharomyces cerevisiae. A global trend highlights the importance of renamed and reclassified yeast species in vaginal infections, supporting the reconsideration of the current disease name VVC in favor of the term vulvovaginal yeast infection (VYI)", "token_count": 512, "char_count": 1791, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:21.301209", "source": { "split": "train_shard_00000", "doc_id": 89 }, "chunk_id": "train_shard_00000_89_0", "global_id": 102 }, { "text": "The prevalence of emerging NAC and NCY species is increasing but remains underestimated. There is a need for new laboratory diagnostic guidelines to enable timely and accurate identification, as this is crucial for guiding appropriate treatment and improving outcomes.\n\nPrevalence of Candida and Other Yeasts in Vulvovaginal Infections during Pregnancy: A 10-Year Serbian Survey.", "token_count": 86, "char_count": 379, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:21.673436", "source": { "split": "train_shard_00000", "doc_id": 89 }, "chunk_id": "train_shard_00000_89_1", "global_id": 103 }, { "text": "Lipopolysaccharide (LPS)-induced endotoxemia is a key pathogenic factor in metabolic diseases. Probiotics reduce LPS levels and alleviate related disorders, but the underlying mechanism remains unclear. Here, we demonstrated that Christensenella tenuis alleviated endotoxemia and metabolic disorders in Diet-Induced Obese (DIO) mice by inhibiting the LPS-TLR4 signaling pathway and modulating downstream metabolism. Omics analysis revealed increased levels of gut free bile acids (BAs) after C. tenuis treatment, while in vitro experiments confirmed that C. tenuis hydrolyzed conjugated BAs into free BAs via bile salt hydrolase (BSH) activity. Further molecular dynamics simulations showed that free BAs formed non-membrane-permeable complexes with LPS, preventing the transmembrane translocation of intestinal LPS. Experimental evidence from isothermal titration calorimetry confirmed that free bile acids bound directly with LPS in an enthalpy-driven manner, which is consistent with in silico simulations and validates specific molecular interactions. Oral administration of free BAs also reduced plasma LPS levels in DIO mice. These findings uncover a novel mechanism by which BSH-positive gut microbes and probiotics benefit host metabolism and lay the groundwork for gut-targeted biotherapies for endotoxemia and metabolic diseases.\n\nChristensenella tenuis alleviates endotoxemia and metabolic disorders via inhibition of intestinal lipopolysaccharide translocation.", "token_count": 369, "char_count": 1473, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6649, "quality_score": 0.8325, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:22.232569", "source": { "split": "train_shard_00000", "doc_id": 90 }, "chunk_id": "train_shard_00000_90_0", "global_id": 104 }, { "text": "Loss of Bsep/Abcb11 results in a hydrophilic bile acid (BA) pool consisting of tetrahydroxylated BAs (THBAs) reducing cholestasis-induced liver injury. In this study, we investigated whether loss of Bsep may protect mice from development of toxin-induced liver fibrosis by directly impacting on hepatic stellate cell (HSC) activation.\n\nLoss of Bile Salt Export Pump (Bsep/Abcb11) Ameliorates Toxin-induced Hepatic Fibrosis via Suppression of Hepatocellular Jun Amino-terminal Kinase Signaling and Hepatic Stellate Cell Activation.", "token_count": 165, "char_count": 530, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:22.669423", "source": { "split": "train_shard_00000", "doc_id": 91 }, "chunk_id": "train_shard_00000_91_0", "global_id": 105 }, { "text": "The human gut microbiome is linked to child malnutrition, yet traditional microbiome approaches lack resolution. We hypothesized that complete metagenome-assembled genomes (cMAGs), recovered through long-read (LR) DNA sequencing, would enable pangenome and microbial genome-wide association study (GWAS) analyses to identify microbial genetic associations with child linear growth. LR methods produced 44-64× more cMAGs per gigabase pair (Gbp) than short-read methods, with PacBio (PB) yielding the most accurate and cost-effective assemblies. In a Malawian longitudinal pediatric cohort, we generated 986 cMAGs (839 circular) from 47 samples and applied this database to an expanded set of 210 samples. Machine learning identified species predictive of linear growth. Pangenome analyses revealed microbial genetic associations with linear growth, while genome instability correlated with declining length-for-age Z score (LAZ). This resource demonstrates the power of comparing cMAGs with health trajectories and establishes a new standard for microbiome association studies.\n\nCulture-independent meta-pangenomics enabled by long-read metagenomics reveals associations with pediatric undernutrition.", "token_count": 292, "char_count": 1200, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:23.212122", "source": { "split": "train_shard_00000", "doc_id": 92 }, "chunk_id": "train_shard_00000_92_0", "global_id": 106 }, { "text": "Parenteral nutrition (PN) dependency in patients with intestinal failure (IF) can lead to complications including liver disease. Therefore, IF management strives to wean patients off PN. In adult IF, chronic cholestasis is predicted by the functional gut parameters citrulline (CIT) and enteroendocrine fibroblast growth factor 19 (FGF19), which inhibits hepatic bile salt synthesis. We investigated 1) whether CIT, FGF19 and a marker for enterocyte damage (urinary intestinal fatty acid-binding protein (I-FABP)) are associated with enteral autonomy within 60 days after intestinal surgery in neonates, and 2) the longitudinal patterns of CIT, FGF19, total bile salts and C4 (marker for bile salt synthesis) in subgroups of children on long-term PN (short bowel syndrome (SBS) and functional IF).\n\nDo functional gut parameters predict enteral autonomy and chronic cholestasis in pediatric intestinal failure?", "token_count": 246, "char_count": 909, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:23.688281", "source": { "split": "train_shard_00000", "doc_id": 93 }, "chunk_id": "train_shard_00000_93_0", "global_id": 107 }, { "text": "Low-coverage sequencing refers to sequencing DNA of individuals to a low depth of coverage (e.g., 0.5X) and imputing that sequence to a genomic sequence based on reference haplotypes from individuals sequenced to a high depth of coverage (e.g., ≥10X). It has been proposed as an alternative to genotyping by Single-nucleotide polymorphisms (SNP) arrays. At least one commercial product based on it is available for agricultural species. Concerns limiting adoption in its current form are: 1) the cost of storing the huge volume of data it generates and 2) whether that additional data will result in improved accuracy of genetic evaluation. This work envisions future implementation of low-coverage sequencing to reduce storage costs and enhance genetic evaluations by leveraging the additional information in the full sequence of the pangenome to account for more genetic variation. We propose addressing the storage issue by representing genomic sequence of an individual in a pair of haplotype arrays with each element pointing to an enumerated haplotype of the sequence within one of approximately 50,000 defined genome segments. Assuming 60 million genomic variants, the infrastructure required to translate the identifier of any enumerated haplotype into its genomic sequence would require less than 10 gigabytes of binary storage. Each haplotype array element would require 2 bytes, so the marginal binary storage required to represent the genomic sequence of an individual would be about 200 kilobytes (KB), similar to the genotypes from a SNP array with 200,000 markers. This assumes no pedigree and no ambiguity of the imputation, though the latter is unrealistic. Strategies to minimize, and when necessary, to manage and efficiently represent ambiguity are proposed. The genomic sequence of an individual could be stored in about 1 KB (binary) if both parents have unambiguous sequences stored as described above. The proposed system for representing the pangenome includes algorithms for read mapping and imputation intended to leverage all known genetic variation in the target population", "token_count": 469, "char_count": 2102, "word_count": 318, "semantic_coherence": 1, "information_density": 0.5881, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:24.311631", "source": { "split": "train_shard_00000", "doc_id": 94 }, "chunk_id": "train_shard_00000_94_0", "global_id": 108 }, { "text": "It is also designed to use sequencing reads generated for imputing the genomic sequence of new individuals to identify unrecognized mutations, crossovers, and structural variants, thus continuously improving the genome representation, especially if widespread use of low-coverage sequencing in livestock industries is realized. This could make improved genetic merit and management of livestock feasible without computational burden.\n\nA vision of how low-coverage sequence data should contribute to genetic evaluation in the future.", "token_count": 107, "char_count": 532, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:24.688899", "source": { "split": "train_shard_00000", "doc_id": 94 }, "chunk_id": "train_shard_00000_94_1", "global_id": 109 }, { "text": "The postweaning period is stressful for pigs due to changes in their environment and diet. The occurrence of diarrhea at this stage is high. Growth promoters such as antibiotics and zinc oxide (ZnO) have been used not only to reduce postweaning diarrhea but also to improve the growth performance of weaning pigs. It has also been shown that the growth performance of pigs is negatively associated with bile salt hydrolase (BSH) in the gut. Antibiotic growth promoters (AGP) and ZnO administration have demonstrated effective inhibition of BSH, which is linked to enhanced growth performance in pigs. Therefore, this study evaluated the effects of a plant-based supplement, green tea extract, with butyric acid, and vitamin K (GBK), on growth performance, nutrient digestibility, fecal score, blood profile, and BSH activity of the gut microbiota of weaning pigs. Here, 192 crossbred weaning pigs [(Yorkshire × Landrace) × Duroc], aged 21 d, were subjected to a 4-wk-long feeding experiment. Pigs were divided into six treatments (n = 32 per treatment, 8 pens per treatment). After feeding, the average daily gain (ADG) and gain-to-feed (G:F) ratio improved linearly with GBK supplementation. During the feeding period, diarrhea was not observed in the treatment groups, and the fecal scores of the weaned pigs were not affected. Supplementation had no negative impact on the blood profile parameters of weaned pigs, including white blood cell count, red blood cell count, lymphocyte percentage, and blood urea nitrogen. Moreover, supplementation of GBK decreased the TNF-α and IL-6, while immunoglobulins (IgA, IgG) increased. In addition, GBK reduced the abundance of gut microbiota with BSH activity, including Clostridium sensu stricto 6, the Clostridia vadinBB60 group, Marvinbryantia, Muribaculaceae, and Enterococcus", "token_count": 506, "char_count": 1823, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6558, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:25.299327", "source": { "split": "train_shard_00000", "doc_id": 95 }, "chunk_id": "train_shard_00000_95_0", "global_id": 110 }, { "text": "Correlation analysis revealed that gut microbiota function related to secondary bile acid biosynthesis had a strong negative correlation with ADG, average daily feed intake, and G:F ratio of the pigs. The combination of green tea, butyric acid, and vitamin K is an effective alternative to AGP and ZnO for improving growth performance, feed efficiency, and diarrhea score of weaned pigs. In addition, this feeding strategy had a modulatory effect on the gut microbiome, altering BSH activity associated with improved growth performance in weaning pigs.\n\nGreen tea extract complex as a phytogenic supplement to reduce bile salt hydrolase activity and enhance growth performance in weaning pigs.", "token_count": 159, "char_count": 693, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7238, "quality_score": 0.8619, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:25.738596", "source": { "split": "train_shard_00000", "doc_id": 95 }, "chunk_id": "train_shard_00000_95_1", "global_id": 111 }, { "text": "Through horizontal gene transfer, closely related bacterial strains assimilate distinct sets of genes, resulting in significantly varied lifestyles. However, it remains unclear how strains properly regulate horizontally transferred virulence genes. We hypothesized that strains may use components of the core genome to regulate diverse horizontally acquired genes. To investigate how closely related bacteria assimilate and activate horizontally acquired DNA, we used a model consisting of strains in the\n\nGacA regulates symbiosis and mediates lifestyle transitions in", "token_count": 116, "char_count": 568, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:26.117891", "source": { "split": "train_shard_00000", "doc_id": 96 }, "chunk_id": "train_shard_00000_96_0", "global_id": 112 }, { "text": "Biological nitrogen fixation converts atmospheric nitrogen into ammonia, essential to the global nitrogen cycle. While cyanobacterial diazotrophs are well characterized, recent studies have revealed a broad distribution of non-cyanobacterial diazotrophs (NCDs) in marine environments, although their study is limited by poor cultivability. Here we report a previously uncharacterized Bradyrhizobium isolated from the marine diatom Phaeodactylum tricornutum. Phylogenomic analysis places the strain within photosynthetic Bradyrhizobium, suggesting evolutionary adaptations to marine and terrestrial niches. Average nucleotide identity supports its classification as a previously undescribed species. Remarkably, inoculation experiments showed that the isolate induced nitrogen-fixing nodules in the Aeschynomene indica legume, pointing to symbiotic capabilities across ecological boundaries. Pangenome analysis and metabolic predictions indicate that this isolate shares more features with terrestrial photosynthetic Bradyrhizobium than with marine NCDs. Overall, these findings suggest that symbiotic interactions could evolve across different ecological niches, and raise questions about the evolution of nitrogen fixation and microbe-host interactions.\n\nA Bradyrhizobium isolate from a marine diatom induces nitrogen-fixing nodules in a terrestrial legume.", "token_count": 317, "char_count": 1358, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7195, "quality_score": 0.8598, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:26.665357", "source": { "split": "train_shard_00000", "doc_id": 97 }, "chunk_id": "train_shard_00000_97_0", "global_id": 113 }, { "text": "Clostridium butyricum has gained attention as a probiotic in aquaculture due to its ability to improve growth, gut health, and immune function. However, most strains currently used are derived from non-aquatic sources, which may limit their colonization and efficacy in fish. In this study, a novel strain, C. butyricum LZK-08, was isolated from the intestine of grass carp. The strain was identified based on morphological features, 16S rRNA sequencing, and whole-genome analysis. Its probiotic properties were assessed through comprehensive in vitro assays and in vivo trials in largemouth bass. LZK-08 exhibited strong acid (pH 4.0), bile salt (0.3%), and heat (up to 80 °C) tolerance, along with high auto-aggregation (92.3%) and notable surface hydrophobicity. It produced digestive enzymes (amylase, protease, lipase) and short-chain fatty acids, particularly butyrate (523.32 μg/mL). Genomic analysis revealed a 4.71 Mb genome composed of a circular chromosome and plasmid, encoding 4,207 protein-coding genes. Key genes were enriched in carbohydrate and amino acid metabolism, stress response, and adhesion. Feeding trials in largemouth bass showed that dietary supplementation with LZK-08 significantly improved growth parameters, reduced feed conversion ratio, enhanced intestinal antioxidant enzyme and digestive enzyme activities. Histological analysis revealed improved intestinal morphology, including increased villus height and muscle thickness. 16S rRNA sequencing further showed that LZK-08 modulated gut microbiota by enriching beneficial taxa such as Lactobacillus and reducing potentially unfavorable Romboutsia. These findings indicate that C. butyricum LZK-08 is a physiologically robust, and genomically safe probiotic with strong functional attributes, demonstrating high potential for use in sustainable aquaculture.", "token_count": 493, "char_count": 1842, "word_count": 250, "semantic_coherence": 1, "information_density": 0.756, "quality_score": 0.878, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:27.292068", "source": { "split": "train_shard_00000", "doc_id": 98 }, "chunk_id": "train_shard_00000_98_0", "global_id": 114 }, { "text": "Fish-Derived Clostridium butyricum LZK-08: Genomic Insights and Probiotic Evaluation in Largemouth Bass.", "token_count": 36, "char_count": 104, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:27.646837", "source": { "split": "train_shard_00000", "doc_id": 98 }, "chunk_id": "train_shard_00000_98_1", "global_id": 115 }, { "text": "While benchmarks on short-read variant calling suggest a low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher. Although multiple sets of easy regions have been identified to alleviate the issue, they fail to consider nonreference samples or are biased toward existing short-read data or aligners.\n\nFinding easy regions for short-read variant calling from pangenome data.", "token_count": 105, "char_count": 483, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7838, "quality_score": 0.8919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:28.022143", "source": { "split": "train_shard_00000", "doc_id": 99 }, "chunk_id": "train_shard_00000_99_0", "global_id": 116 }, { "text": "Phages infect bacteria and have recently re-emerged as a promising strategy to combat bacterial infections. However, there is a lack of methods to predict whether and why a particular phage can or cannot infect a bacterial strain based on their genome sequences. Understanding the complex interactions between phages and their bacterial hosts is thus of considerable interest. We recently developed Goldfinder, a phylogenetic method to discover gene co-occurrences across bacterial pangenomes. Here, we expand Goldfinder to infer which gene presences or absences influence bacterial sensitivity to phages. By integrating a bacterial pangenome with an experimentally determined host range matrix, we infer associations between phage infectivity and the presence of accessory genes in bacterial pangenomes. The presented approach can be applied to predict bacterial genes that potentially enable phage infection, bacterial genes that prevent phage infection, and potential interactions between particular bacterial and phage accessory genes. Finally, the predicted interactions are clustered and visualized with the software Cytoscape. Here, we present a method to identify candidate genes within the pool of mobile accessory genes that may contribute to phage-host interactions. This approach will help to set up follow-up experiments and to understand the complex interactions between phages and bacteria.This article is part of the discussion meeting issue 'The ecology and evolution of bacterial immune systems'.\n\nGene co-occurrence and its association with phage infectivity in bacterial pangenomes.", "token_count": 323, "char_count": 1602, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5778, "quality_score": 0.7889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:28.576280", "source": { "split": "train_shard_00000", "doc_id": 100 }, "chunk_id": "train_shard_00000_100_0", "global_id": 117 }, { "text": "Carbapenem-resistant Enterobacterales pose a critical global health threat, exemplified by increasing resistance of uropathogenic E. coli (UPEC) that cause urinary tract infections (UTIs). Here, we investigate the publicly available EnteroBase dataset and identify a signal of increasing UTI caused by phylogroup A E. coli sequence type 167 (ST167). Phylogenetic analysis of ST167 based on whole genome sequence data reveal three major clades (A, B, C), with clade C further resolving into several subclades, notably subclade C2 that possessed high carriage rates of carbapenem and cephalosporin resistance genes. Hierarchical clustering of core genome multi-locus sequence typing reveals ~77% of subclade C2 strains contain <20 allelic differences in 2,513 core genes and harbour two distinct group 1 capsule types, KL124 and KL30, likely originating from Klebsiella. Subclade C2 was predominantly sequenced in North America, and we provide evidence for clonal expansion since 2016. Analysis of UPEC virulence factors reveals complete loss of the type 1 fimbriae genes in strains from clades B and C. Two subclade C2 isolates exhibit significantly reduced capacity to colonise the bladder compared to the reference UPEC strain CFT073 in a murine UTI model. Collectively, our data identifies ST167 as an atypical UPEC clone associated with UTI.\n\nEmergence of a carbapenem-resistant atypical uropathogenic Escherichia coli clone as an increasing cause of urinary tract infection.", "token_count": 404, "char_count": 1478, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [ "ST167", "KL124", "CFT073", "KL30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:29.524390", "source": { "split": "train_shard_00000", "doc_id": 101 }, "chunk_id": "train_shard_00000_101_0", "global_id": 118 }, { "text": "Bacillus amyloliquefaciens EG025 was isolated from cheonggukjang, a traditional Korean fermented soybean paste. Among multiple isolates from diverse fermented foods, B. amyloliquefaciens EG025 uniquely exhibited potent gliadin-degrading activity, a trait with the potential to attenuate the immunogenicity of gluten peptides implicated in celiac disease. B. amyloliquefaciens EG025 maintained robust enzymatic activity across a wide pH spectrum (neutral to alkaline) and, remarkably, retained over 90.4% of its maximal activity following a 2-h exposure to pH 2. In addition to its gliadin-degrading capability, B. amyloliquefaciens EG025 demonstrated exceptional acid and bile tolerance, indicating a strong capacity to survive and function under the harsh conditions of the human gastrointestinal tract. Whole-genome sequencing and comprehensive annotation revealed biosynthetic gene clusters for secondary metabolites known to confer host benefits, alongside key probiotic functional genes involved in gliadin degradation, acid and bile resistance, stress response, mucosal adhesion, and de novo vitamin biosynthesis. Importantly, safety assessment confirmed the absence of concerning antibiotic resistance determinants or virulence factors, underscoring the strain's safety profile. Phylogenetic reconstruction further highlighted the genetic distinctiveness of EG025 relative to other B. amyloliquefaciens strains, emphasizing its novelty within the species. Collectively, these combined in vitro assay, genomic, and phylogenetic results underscore the significant probiotic potential of B. amyloliquefaciens EG025 and support its future development as a novel therapeutic candidate for improving gluten tolerance and managing celiac disease. Its safety and multifunctional attributes position it as a promising ingredient for functional foods targeted at gluten-sensitive populations.", "token_count": 478, "char_count": 1889, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6971, "quality_score": 0.8485, "entities": { "genes": [ "EG025" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:30.177300", "source": { "split": "train_shard_00000", "doc_id": 102 }, "chunk_id": "train_shard_00000_102_0", "global_id": 119 }, { "text": "Genomic and Phenotypic Evaluation of the Gliadin-Degrading Probiotic Bacillus amyloliquefaciens EG025 from Cheonggukjang for Celiac Disease Treatment.", "token_count": 55, "char_count": 150, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "EG025" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:30.548133", "source": { "split": "train_shard_00000", "doc_id": 102 }, "chunk_id": "train_shard_00000_102_1", "global_id": 120 }, { "text": "Most organismal traits result from the complex interplay of many genetic and environmental factors, making their prediction difficult. Here, we used machine learning (ML) models to explore phenotype predictions for 223 traits measured across 1011 genome-sequenced Saccharomyces cerevisiae strains isolated worldwide. We benchmarked a ML pipeline with multiple linear and non-linear models to predict phenotypes from genotypes and gene expression, and determined gradient boosting machines as the best-performing model. Gene function disruption scores and gene presence/absence emerged as best predictors, suggesting a considerable contribution of the accessory genome in controlling phenotypes. The prediction accuracy broadly varied among phenotypes, with stress resistance being easier to predict compared to growth across nutrients. ML identified relevant genomic features linked to phenotypes, including high-impact variants with established relationships to phenotypes, despite these being rare in the population. Near-perfect accuracies were achieved when other phenomics data mostly in similar conditions were used, suggesting that useful information can be conveyed across phenotypes. Overall, our study underscores the power of ML to interpret the functional outcome of genetic variants.\n\nPredicting natural variation in the yeast phenotypic landscape with machine learning.", "token_count": 280, "char_count": 1383, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7377, "quality_score": 0.8689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:31.104758", "source": { "split": "train_shard_00000", "doc_id": 103 }, "chunk_id": "train_shard_00000_103_0", "global_id": 121 }, { "text": "The soybean [Glycine max (L.) Merr.] pangenome has been studied and shown to be an invaluable resource for investigating structural variations (SVs), from which different genomic markers were successfully developed and employed for genome-wide association studies (GWAS). Among the SVs markers, gene presence-and-absence variations (PAVs) have been developed in soybean, but have not been widely utilized for association analyses. Here, we reported GWAS and haplotype analysis of seed protein and oil content for two diverse panels, comprised over 500 soybean accessions evaluated in multiple field environments using three marker datasets, whole genome sequence (WGS)-single-nucleotide polymorphisms (SNPs), 50 K-SNPs, and PAVs. The analyses identified new quantitative trait loci (QTL) for protein and oil content, along with the validation of previously reported QTL for these traits. This includes a well-studied QTL on chromosome (Chr.) 20 and another one on Chr. 05 for protein and/or oil. Importantly, this study is the first to report a new genomic locus for both protein and oil mapped to Chr. 08. Gene ontology annotations and expression profiles suggested candidate genes. Further analyses using haplotype-based markers led to the identification of multiple haplotype blocks encompassing candidate genes. Among these, Glyma.05G243400 on Chr. 05 and Glyma.08G109900 and Glyma.08G110000 on Chr. 08 were identified as promising targets. These genes can be incorporated into soybean breeding programs to enhance the selection of desirable protein and oil phenotypes through a haplotype-based breeding approach.\n\nIdentification of new genomic loci for seed protein and oil content in the soybean pangenome using genome-wide association and haplotype analyses.", "token_count": 466, "char_count": 1765, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6151, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:31.762416", "source": { "split": "train_shard_00000", "doc_id": 104 }, "chunk_id": "train_shard_00000_104_0", "global_id": 122 }, { "text": "The aging process is associated with detrimental effects on the integrity of the intestinal barrier, consequently elevating susceptibility to various diseases. Qula exhibits outstanding nutritional composition and has a characteristic taste profile, positioning it as a prime candidate for probiotic exploration given its rich reservoir of probiotic potential. In the present study, a probiotics screening strategy was developed based on the production of short-chain fatty acids (SCFA) to reverse aging-related intestinal barrier dysfunction. After screening, Limosilactobacillus fermentum TD-3 and Lactococcus lactis MQ1-1 isolated from traditional dairy product Qula were selected based on their acid and bile salt resistance, adhesion, and antibacterial properties. In the aging mice, the combination of probiotic mixture (PM) of Lb. fermentum TD-3 and Lc. lactis MQ1-1 enhanced intestinal barrier integrity by activating mitogen-activated protein kinase (AMPK) phosphorylation, which suppressed myosin light-chain kinase (MLCK) activity to increase the expression of tight junctions. Meanwhile, PM decreased colon oxidative stress (SOD, GSH-Px, and malondialdehyde) and inflammation (IL-6, IL-1β, TNFα, and IL-10), and restored the composition of the intestinal microbiota composition. Specifically, PM enriched the relative abundance of SCFAs producing bacteria, including g__norank_f__Muribaculaceae and g__Limosilactobacillus, g__Bifidobacterium, and g__Allobaculum, thereby increasing the acetic acid and butyric acid production. Thus, the combination of Lb. fermentum TD-3 and Lc. lactis MQ1-1 activated the AMPK signaling pathway by regulating the gut microbiota and metabolites. This study innovatively established a precision screening system for probiotics targeting SCFA, and isolated and identified a PM from traditional fermented dairy products (Qula) to relieve aging-associated intestinal barrier dysfunction.", "token_count": 497, "char_count": 1928, "word_count": 250, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [ "MQ1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:32.395763", "source": { "split": "train_shard_00000", "doc_id": 105 }, "chunk_id": "train_shard_00000_105_0", "global_id": 123 }, { "text": "Qula-derived Limosilactobacillus fermentum TD-3 and Lactococcus lactis MQ1-1 alleviate aging-related intestinal barrier dysfunction via microbiota-short-chain fatty acid-AMPK/MLCK-tight junction axis.", "token_count": 69, "char_count": 200, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "MQ1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:32.759629", "source": { "split": "train_shard_00000", "doc_id": 105 }, "chunk_id": "train_shard_00000_105_1", "global_id": 124 }, { "text": "Lithospermum erythrorhizon, a traditional Chinese medicinal herb and functional food ingredient, contains bioactive soluble polysaccharide with documented anti-obesity and metabolic regulatory properties. However, the precise mechanisms underlying the anti-obesity effects of Lithospermum erythrorhizon polysaccharide (LEP) fraction remain poorly characterized. In this study, diet-induced obese (DIO) mice treated with LEP exhibited significant suppression of body weight gain and hepatic lipid deposition, accompanied by improved liver function and elevated systemic energy expenditure. Mechanistic investigations revealed that LEP administration selectively suppressed the intestinal colonization of bile salt hydrolase (BSH)-producing bacterial taxa, leading to increased circulating levels of taurine-conjugated bile acids and enhanced cecal short-chain fatty acids (SCFAs) production. Concurrently, LEP activated adipose tissue thermogenesis, as evidenced by upregulated expression of thermogenic markers. Antibiotic-induced gut microbiota ablation abolished these metabolic benefits, whereas fecal microbiota transplantation from LEP-treated mice recapitulated the anti-obesity phenotype in recipient animals. These results establish that LEP ameliorates obesity through a gut microbiota-dependent mechanism involving BSH inhibition, taurine-conjugated bile acid accumulation, SCFAs elevation, and subsequent activation of adipose thermogenic pathways. These findings highlight the potential of LEP as a dietary supplement or microbiota-targeted intervention for obesity management.\n\nLithospermum erythrorhizon polysaccharide alleviates obesity via gut microbiota-mediated reprogramming of bile acid and short-chain fatty acid metabolism.", "token_count": 439, "char_count": 1745, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7291, "quality_score": 0.8645, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:33.374030", "source": { "split": "train_shard_00000", "doc_id": 106 }, "chunk_id": "train_shard_00000_106_0", "global_id": 125 }, { "text": "Water buffalo is a cornerstone livestock species in many low- and middle-income countries, yet major gaps persist in its genomic characterization-complicated by the divergent karyotypes of its two subspecies (swamp and river). Such genomic complexity makes water buffalo a particularly good candidate for the use of graph genomics, which can capture variation missed by linear reference approaches. However, the utility of this approach to improve water buffalo has been largely unexplored.\n\nA comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection.", "token_count": 130, "char_count": 625, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7674, "quality_score": 0.8837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:33.791941", "source": { "split": "train_shard_00000", "doc_id": 107 }, "chunk_id": "train_shard_00000_107_0", "global_id": 126 }, { "text": "The present study investigates the techno-functional and biosafety potential of Meyerozyma guilliermondii YB1 (OQ832654) as a novel starter culture for functional foods. M. guilliermondii YB1 exhibited xylanase and phytase activity, with an activity index (AI) of 0.66 and 0.21, respectively. Antimicrobial assays demonstrated inhibition against Escherichia coli MTCC 3222, Salmonella typhimurium MTCC 3224, and Aspergillus sp. CTS1, confirming its potential in food preservation. Furthermore, the yeast efficiently fermented a broad range of carbohydrates required for food fermentations. Auto-aggregation increased from 25% at 2 h to 96.04% at 72 h, while hydrophobicity ranged from 38.54% to 66.16%, indicating strong gut adhesion properties. Growth at 37°C followed a normal sigmoidal curve, with optimal proliferation up to 48 h. Bile salt tolerance (0.3%) and acid resistance (pH 2.5-3.5) further confirmed its survival under gastrointestinal conditions. The non-pathogenicity of M. guilliermondii YB1 was confirmed through antifungal susceptibility testing, absence of gelatinase, DNase activity, and a negative Congo red binding test, thereby supporting its use as a reliable functional food starter. Collectively, these attributes establish M. guilliermondii YB1 as a promising candidate for functional food applications, offering improved digestibility, food safety, and health benefits.\n\nUnlocking the Techno-Functional and Biosafety Potential of a Novel Yeast Meyerozyma Guilliermondii YB1 as a Fermented Functional Food Starter: A Future Vision for Probiotics.", "token_count": 460, "char_count": 1573, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [ "OQ832654", "YB1", "CTS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:34.410761", "source": { "split": "train_shard_00000", "doc_id": 108 }, "chunk_id": "train_shard_00000_108_0", "global_id": 127 }, { "text": "This study explores the potential of probiotic bacteria-yeast co-cultivation to enhance microbial growth and postbiotic production using halophyte-based media. Initial screening of six yeast strains revealed variations in nutrient utilization, with Saccharomyces cerevisiae, Kluyveromyces marxianus DSM 7238, and Cyberlindnera jadinii DSM 2361, demonstrating superior carbon source consumption and biomass production. Co-cultivation with Bacillus coagulans ATCC 7050 enhanced overall product formation, whereas Lactiplantibacillus plantarum DSM 13272 had undesirable effects on product formation. Optimization trials demonstrated that increasing the total inoculum size to 10 % (v/v) and extending cultivation to 72  h significantly enhanced product yields in selected bacteria-yeast co-cultures, enabling complete utilization of the available carbon sources. Specifically, the best performing combination of B. coagulans ATCC 7050 and K. marxianus DSM 7238 achieved 17.5 g of cell dry weight, 6.9 g of crude protein, and 42.2 mg of vitamin B12/L in halophyte-based broth. Advanced statistical analysis revealed that yeast-driven deacidification played a critical role in improving culture conditions, reducing organic acid stress, and promoting microbial growth. The findings suggest that bacteria-yeast interactions in co-cultures under non-sterile conditions contribute to enhanced fermentation efficiency, with yeast potentially acting as a detoxifier. This study underscores the viability of bacteria-yeast co-cultivation for sustainable probiotics and postbiotics production using halophyte hydrolysate as a production medium and lays the groundwork for future process optimization and industrial-scale applications in alternative protein and nutraceutical development.\n\nCo-cultivation of lactic acid bacteria and fodder yeasts for probiotics and postbiotics production on halophyte-based hydrolysate.", "token_count": 498, "char_count": 1907, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6777, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:35.040704", "source": { "split": "train_shard_00000", "doc_id": 109 }, "chunk_id": "train_shard_00000_109_0", "global_id": 128 }, { "text": "The aim of this study was to isolate and identify lactic acid bacteria (LAB) from a traditional fermented beverage, Boza, and to conduct an in-depth study on their fermentation and probiotic properties. The fermentation (acid production rate, acid tolerance, salt tolerance, amino acid decarboxylase activity) and probiotic properties (gastrointestinal tolerance, bile salt tolerance, hydrophobicity, self-aggregation, drug resistance, bacteriostatic properties) of the 16 isolated LAB were systematically analyzed by morphological, physiological, and biochemical tests and 16S rDNA molecular biology. This analysis utilized principal component analysis (PCA) to comprehensively evaluate the biological properties of the strains. The identified LAB included\n\nScreening and Phenotyping of Lactic Acid Bacteria in Boza.", "token_count": 200, "char_count": 817, "word_count": 107, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:35.484540", "source": { "split": "train_shard_00000", "doc_id": 110 }, "chunk_id": "train_shard_00000_110_0", "global_id": 129 }, { "text": "CONSTANS, CONSTANS-LIKE, TIMING OF CAB EXPRESSION1 (CCT) motif genes play a key role in barley (Hordeum vulgare L.) development and flowering, yet their genetic diversity remains underexplored. Leveraging a barley pangenome (76 genotypes) and pan-transcriptome (subset of 20 genotypes), we examined CCT gene variation and evolutionary dynamics. Motif-based searches, combined with genome assembly validation, revealed annotation limitations and novel frameshift variants (e.g., HvCO10, where Hv is Hordeum vulgare L.), indicating active diversification. Pangenome-wide phylogenetic analysis identified clade-specific domain expansions, including B-box domain additions in HvCO clades. Tissue-specific expression patterns further supported functional divergence among paralogs. Notably, VRN2, a canonical floral repressor associated with winter growth, was retained in spring genotypes, challenging its presumed exclusive role in vernalization. Discrepancies between VRN1 expression, VRN2 deletion, and growth habit implicated additional regulatory mechanisms. These findings highlight the power of pangenomes in resolving gene family complexity, refining annotations, and advancing the understanding of CCT genes to enhance barley resilience and adaptability.\n\nPangenome insights into structural variation and functional diversification of barley CCT motif genes.", "token_count": 337, "char_count": 1363, "word_count": 170, "semantic_coherence": 1, "information_density": 0.8059, "quality_score": 0.9029, "entities": { "genes": [ "EXPRESSION1", "VRN1", "VRN2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:36.049122", "source": { "split": "train_shard_00000", "doc_id": 111 }, "chunk_id": "train_shard_00000_111_0", "global_id": 130 }, { "text": "The role of the gut microbiome in respiratory infections is increasingly recognized. We have found that a gut commensal strain, Bacteroides dorei RX2020 (B. dorei) previously isolated from healthy human fecal microbiota, alleviates influenza virus infection, but the underlying mechanisms remain elusive.\n\nBacteroides dorei RX2020-derived bile acid alleviates influenza virus infection through TGR5 signaling.", "token_count": 113, "char_count": 409, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8519, "quality_score": 0.9259, "entities": { "genes": [ "TGR5", "RX2020" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:36.438321", "source": { "split": "train_shard_00000", "doc_id": 112 }, "chunk_id": "train_shard_00000_112_0", "global_id": 131 }, { "text": "Development of a core genome multilocus sequence typing scheme and life identification number code classification system for", "token_count": 20, "char_count": 124, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:36.798212", "source": { "split": "train_shard_00000", "doc_id": 113 }, "chunk_id": "train_shard_00000_113_0", "global_id": 132 }, { "text": "A Near Telomere-To-Telomere Genome Assembly and Graph-Based Pangenome of Tartary Buckwheat (Fagopyrum tataricum).", "token_count": 39, "char_count": 113, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:37.173323", "source": { "split": "train_shard_00000", "doc_id": 114 }, "chunk_id": "train_shard_00000_114_0", "global_id": 133 }, { "text": "Genome adaptation, driven by mutations, transposable elements, and structural variations, relies on plasticity and instability. This allows populations to evolve, enhance fitness, and adapt to challenges like climate change. Genomes adapt via mutations, transposable elements, DNA structural changes, and epigenetics. Genome plasticity enhances fitness by providing the genetic variation necessary for organisms to adapt their traits and survive, which is especially critical during rapid climate shifts. This plasticity often stems from genome instability, which facilitates significant genomic alterations like duplications or deletions. While potentially harmful initially, these changes increase genetic diversity, aiding adaptation. Major genome reorganizations arise from polyploidization and horizontal gene transfer, both linked to instability. Plasticity and restructuring can modify Quantitative Trait Loci (QTLs), contributing to adaptation. Tools like landscape genomics identify climate-selected regions, resurrection ecology reveals past adaptive responses, and pangenome analysis examines a species' complete gene set. Signatures of past selection include reduced diversity and allele frequency shifts. Gene expression plasticity allows environmental adaptation without genetic change through mechanisms like alternative splicing, tailoring protein function. Co-opted transposable elements also generate genetic and regulatory diversity, contributing to genome evolution. This review consolidates these findings, repositioning genome instability not as a mere source of random error but as a fundamental evolutionary engine that provides the rapid adaptive potential required for plant survival in the face of accelerating climate change.\n\nClimate change and plant genomic plasticity.", "token_count": 342, "char_count": 1799, "word_count": 227, "semantic_coherence": 1, "information_density": 0.696, "quality_score": 0.848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:37.722749", "source": { "split": "train_shard_00000", "doc_id": 115 }, "chunk_id": "train_shard_00000_115_0", "global_id": 134 }, { "text": "Pangenome indexing is a critical supporting technology in biological sequence analysis such as read alignment applications. The need to accurately identify billions of small sequencing fragments carrying sequencing errors and genomic variants drives the development of scalable and efficient pangenome indexing approach.\n\nPanaln: indexing pangenome for read alignment.", "token_count": 71, "char_count": 368, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:38.089107", "source": { "split": "train_shard_00000", "doc_id": 116 }, "chunk_id": "train_shard_00000_116_0", "global_id": 135 }, { "text": "Bile salts (BS) are antimicrobials that disrupt bacterial cell membranes and induce oxidative stress. The gut bacterium\n\nDisruptions in outer membrane-peptidoglycan interactions enhance bile salt resistance in O-antigen-producing", "token_count": 62, "char_count": 229, "word_count": 28, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:38.458949", "source": { "split": "train_shard_00000", "doc_id": 117 }, "chunk_id": "train_shard_00000_117_0", "global_id": 136 }, { "text": "White-Nose Syndrome (WNS) has devastated insectivorous bat populations, particularly in North America, leading to severe ecological and economic consequences. Despite extensive research, many aspects of the evolutionary history, mitochondrial genome organization, and metabolic adaptations of its etiological agent,\n\nBeyond White-Nose Syndrome: Mitochondrial and Functional Genomics of", "token_count": 92, "char_count": 385, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:38.829032", "source": { "split": "train_shard_00000", "doc_id": 118 }, "chunk_id": "train_shard_00000_118_0", "global_id": 137 }, { "text": "Vibrio anguillarum is a major marine fish pathogen causing high mortality and potential zoonotic risks. Understanding its genomic diversity, virulence factors, and antibiotic resistance is crucial for aquaculture disease management. In this study, a comparative pan-genomic analysis of 16 V. anguillarum strains was conducted to examine core and accessory genome diversity, virulence factors, and antibiotic resistance mechanisms. The phylogenetic analysis was conducted using six core genes and SNPs to evaluate evolutionary relationships and pathogenic traits. The core genome contained 2,038 unique ORFs, while the accessory genome had 5,197 cloud genes, confirming an open pangenome. This study identified 118 pathogenic genomic islands, antibiotic resistance genes (tetracycline, quinolone, and carbapenem), and virulence factors, including type VI secretion system (T6SS) components and RTX toxins (hcp-2, vipB/mglB, rtxC). Core genes such as ftsI uncovered substantial evolutionary divergence among species, identifying more than 150 distinct SNPs. Phylogenetic analysis showed serotype-specific clustering, with O1 strains displaying genetic homogeneity, whereas O2 and O3 exhibited divergence, suggesting distinct evolutionary adaptations influencing pathogenicity and ecological interactions. These findings provide primary insights for developing molecular markers and targeted treatments for aquaculture pathogens.\n\nMultiscale comparative pathogenomic analysis of Vibrio anguillarum linking serotype diversity, genomic plasticity and pathogenicity.", "token_count": 385, "char_count": 1560, "word_count": 196, "semantic_coherence": 1, "information_density": 0.7092, "quality_score": 0.8546, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:39.431492", "source": { "split": "train_shard_00000", "doc_id": 119 }, "chunk_id": "train_shard_00000_119_0", "global_id": 138 }, { "text": "The gut microbiome is frequently dysregulated in colorectal cancer (CRC). Gut microbiota can modify bile acids (BAs), which is a group of metabolites that have been linked to tumorigenesis and progression. Here, we observed a significant deficiency in gut bacteria with bile salt hydrolase (BSH) activity in patients with liver metastatic CRC (CRLM). These patients exhibited elevated levels of conjugated primary BAs (CPBAs) and decreased levels of unconjugated BAs (UBAs) in their circulation. The changes in bacterial BSH activity and CPBA levels were more pronounced in male CRLM patients. Microbial manipulation in mouse CRC models to create a BSH-deficient state increased CPBAs, reduced UBAs, and promoted liver metastasis. Specifically, taurocholic acid (TCA), a CPBA, promoted CRLM through a neutrophil-dependent mechanism. TCA upregulated TIMP1 in CRC cells, which in turn stimulated CXCL5/CXCR2-mediated neutrophil recruitment and CRLM. Alternatively, unconjugated primary and secondary BAs counteracted neutrophil migration induced by TCA in vitro and abolished TCA-promoted neutrophil recruitment and liver metastasis in vivo. Together, these findings elucidate a mechanistic role of the dysregulated gut microbiota-BA axis in CRLM, suggesting that manipulating the balance between conjugated and unconjugated BAs could be a potential therapeutic strategy to suppress CRC metastasis.\n\nGut Microbiota-Mediated Bile Acid Metabolism Regulates Colorectal Cancer Liver Metastasis by Altering Neutrophil Recruitment.", "token_count": 414, "char_count": 1523, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [ "CXCR2", "TIMP1", "CXCL5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:40.030526", "source": { "split": "train_shard_00000", "doc_id": 120 }, "chunk_id": "train_shard_00000_120_0", "global_id": 139 }, { "text": "Microbial whole genome sequencing (WGS)-based methods have replaced conventional methods for genomic relatedness analysis in the investigation of or surveillance for infectious outbreaks. Analysis of WGS by core genome multi-locus sequence typing (cgMLST) has been proposed for standardized strain comparisons at high resolution and for longitudinal outbreak surveillance. We compared three commercial cgMLST software pipelines, Ridom SeqSphere+, 1928 Diagnostics' platform, and Ares Genetics ARESdb, for the identification of related (clustered) strains among 255 isolates of common bacterial pathogens, including\n\nComparison of core genome multi-locus sequencing typing pipelines for hospital outbreak detection of common bacterial pathogens.", "token_count": 170, "char_count": 744, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7579, "quality_score": 0.8789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:40.472828", "source": { "split": "train_shard_00000", "doc_id": 121 }, "chunk_id": "train_shard_00000_121_0", "global_id": 140 }, { "text": "Nicotinamide riboside kinase (NRK) is an important enzyme in the nicotinamide riboside (NR) metabolic pathway, converting NR to nicotinamide mononucleotide (NMN), which has promising industrial applications. However, structural collapse in many NRKs reduces their activity and thermal stability, limiting their industrial potential. Herein, we developed an α-helix reconstruction method on a Kag-NRK from Kluyveromyces marxianus for restore its activity and stability together. First, we constructed an α-helix library and performed in silico screening using both dynamic and static evaluations. An α-helix containing 29 residues was then inserted between residues 55 and 56 of Kag-NRK, effectively repairing structural defects and significantly enhancing both enzyme activity and stability. Furthermore, semi-rational design was performed, leading to the identification of two beneficial substitutions, W171V and N214V. The resulting variant NRK\n\nRestore the Activity and Stability of Nicotinamide Riboside Kinase by α-Helix Reconstruction and Semi-Rational Design.", "token_count": 276, "char_count": 1066, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:41.009177", "source": { "split": "train_shard_00000", "doc_id": 122 }, "chunk_id": "train_shard_00000_122_0", "global_id": 141 }, { "text": "Lactobacillus helveticus is a probiotic bacterium widely used in the food industry. In this study, we evaluate the safety and probiotic properties of L. helveticus strain KM7, isolated from the gut of Apis cerana, through whole-genome sequencing and in vitro experiments. The complete genome consists of 2,164,024 bp, encoding 2192 genes with an average GC content of 36.82%. The strain lacks identifiable virulence factor genes and antibiotic resistance genes, shows no hemolytic activity, and cannot produce biogenic amines such as spermine, cadaverine, or putrescine. L. helveticus KM7 exhibited strong acid and bile salt tolerance, superior adhesion capacity, and remarkable antioxidant activity, with its genome harboring genes associated with these traits. It contains gene clusters potentially involved in the biosynthesis of bacteriocins Helveticin J and Enterolysin A, as well as encoding multiple genes of carbohydrate-active enzymes. Moreover, KM7 demonstrated excellent exopolysaccharide-producing capability, and glucose supplementation in the medium enhanced yield. These findings indicate that KM7 is a safe strain with promising probiotic properties, highlighting its potential for food applications.\n\nWhole-genome sequencing and probiotic properties of Lactobacillus helveticus KM7 isolated from the gut of the Chinese honey bee (Apis cerana): A promising exopolysaccharide-producing strain.", "token_count": 363, "char_count": 1408, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6615, "quality_score": 0.8307, "entities": { "genes": [ "KM7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:41.567274", "source": { "split": "train_shard_00000", "doc_id": 123 }, "chunk_id": "train_shard_00000_123_0", "global_id": 142 }, { "text": "The NAC transcription factor family is pivotal in regulating plant development and stress responses, yet its diversity and evolutionary dynamics in barley (\n\nThe evolution, variation, and expression patterns under development and stress responses of the NAC gene family in the barley pan-genome.", "token_count": 61, "char_count": 295, "word_count": 43, "semantic_coherence": 1, "information_density": 0.6977, "quality_score": 0.8488, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:41.946259", "source": { "split": "train_shard_00000", "doc_id": 125 }, "chunk_id": "train_shard_00000_125_0", "global_id": 143 }, { "text": "The current study aimed to isolate and characterize probiotic bacteria with potential health benefits from fermented broccoli. Sixteen bacterial strains were isolated, and two strains (MB685 and MB686) were selected based on their probiotic potential. The isolated strains showed tolerance to pH and temperature variations, and survived well in bile salt concentrations of 0.3% (68%-76%) and 0.5% (61%-71%). MB685 was resistant to gentamicin, ofloxacin, and chloramphenicol, and showed antibacterial activity. Both strains showed significant auto-aggregation (37%-66 % and 53%-43%), as well as cell surface hydrophobicity (56%-62%). MB685 inhibited pancreatic α-amylase by 41.3%, suggesting potential anti-diabetic effects. The 16S rRNA sequencing identified both strains as Lactiplantibacillus plantarum. Whole-genome sequencing of MB685 revealed a genome size of 3.38 Mb with 3181 coding sequences, including plantaricin production genes (PlnA and PlnN)  and carbohydrate-active enzymes. No virulence factors and antibiotic resistance genes were observed, confirming their safety. L. plantarum MB685 is safe, effective, and has the potential for use as a starter culture and probiotic for gut health benefits.\n\nFunctional Genomics and Probiotic Traits of Lactiplantibacillus plantarum MB685 from Fermented Broccoli: Gut Health and Metabolic Insights.", "token_count": 410, "char_count": 1352, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8407, "entities": { "genes": [ "MB686", "MB685" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:42.572754", "source": { "split": "train_shard_00000", "doc_id": 126 }, "chunk_id": "train_shard_00000_126_0", "global_id": 144 }, { "text": "The NPIP gene family is among the most positively selected gene families in humans/apes and drives independent duplication in primate lineages. These duplications promote genetic instability, leading to recurrent disease-associated microduplication and microdeletion syndromes. Despite its importance, little is known about its function or variation in humans, as short-read sequencing cannot distinguish high-identity duplications. Using long-read assemblies of 169 human haplotypes, we find extreme variation in the content and organization of NPIP loci. We identify fixed and polymorphic paralogs and observe ongoing positive selection. With long-read RNA sequencing (RNA-seq), we create paralog-specific gene models, the majority of which were not previously documented, and observe paralog-specific tissue specificity. This analysis of an exceptionally dynamic gene family provides candidates for future functional study.\n\nStructural variation, selection, and diversification of the NPIP gene family from the human pangenome.", "token_count": 223, "char_count": 1030, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:43.038573", "source": { "split": "train_shard_00000", "doc_id": 127 }, "chunk_id": "train_shard_00000_127_0", "global_id": 145 }, { "text": "The Hercules beetles have long been iconic symbols of evolutionary diversification, sexual selection, and systematics. Despite their rapid phenotypic evolution and a rich history of inspiring evolutionary biologists, genomic resources for these charismatic beetles remain limited, especially for the Giant Hercules beetles. We present the first chromosome-level genome assembly of a Giant Hercules beetle from the Lesser Antilles. The assembled genome is approximately 837 Mb in size, with a scaffold N50 of 66.68 Mb, which can be anchored to 11 pseudochromosomes with a BUSCO completeness score of 95.9%. An estimate of 55.5% of the genome can be attributed to repetitive elements. Additionally, we detected candidate sex-linked chromosomes by comparing sequencing read depths between one male and two females using Illumina short reads. The chromosome-level genome assembly of Dynastes reidi not only provides critical insights into evolutionary and functional genomics, but also supports informed conservation and management efforts. In addition, this genomic resource will enable future pangenome analyses aimed at understanding the genetic basis of species divergence and morphological innovation in beetles. Our study also marks the emergence of a new model system to investigate the origin and diversification of phenotypic novelty by leveraging genomic resources across diverse domesticated beetle breeds.\n\nChromosome Level Genome Assembly of Dynastes reidi Reveals Structural Evolution of Autosomes and the Sex Chromosomes in Hercules Beetles.", "token_count": 369, "char_count": 1552, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:43.644638", "source": { "split": "train_shard_00000", "doc_id": 128 }, "chunk_id": "train_shard_00000_128_0", "global_id": 146 }, { "text": "Chronic stress and elevated cortisol levels can compromise intestinal barrier function, potentially leading to leaky gut syndrome and associated health conditions. The probiotic potential of novel strains isolated from honey and edible flowers was evaluated in the present study. Five strains identified as Lactiplantibacillus plantarum (MP), Enterococcus lactis (PERI), Lactiplantibacillus plantarum (PARI), Lactocasiebacillus rhamnosus (M1A), and Enterococcus nangengnisis (KK) exhibited strong bile salt hydrolase (BSH) activity. Furthermore, these strains produced short-chain fatty acids, including acetic acid (8.0 to 10.0 mM), butyric acid (0.3 to 0.5 mM) and propionic acid (1.8 to 2.5 mM), known to support gut health and immune modulation. Under chronic cortisol exposure, L. rhamnosus (M1A), L. plantarum (BAN), and L. plantarum (PARI) significantly alleviated tight junction disruption, experimentally proven by FITC dextran leakage and gene expression of zona occludin-1 (≤3-fold increase) and cadherin (≤4.36-fold increase) compared to the cortisol-treated CaCo\n\nNovel Probiotic Strains From Honey and Fermented Edible Flowers Mitigate Chronic Cortisol-Induced Leaky Gut Syndrome in the CaCo", "token_count": 364, "char_count": 1205, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6894, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:44.215290", "source": { "split": "train_shard_00000", "doc_id": 129 }, "chunk_id": "train_shard_00000_129_0", "global_id": 147 }, { "text": "Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further impacting genotyping performance. Recent works highlight the advantage of haplotype-resolved pangenome graphs in addressing these challenges. Building on these developments, we propose a rigorous alignment-free genotyping method. Our optimization framework identifies a path through the pangenome graph that maximizes the matches between the path and substrings of sequencing reads (e.g.,\n\nPangenome-based genome inference using integer programming.", "token_count": 164, "char_count": 766, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8041, "quality_score": 0.9021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:44.656501", "source": { "split": "train_shard_00000", "doc_id": 130 }, "chunk_id": "train_shard_00000_130_0", "global_id": 148 }, { "text": "Bacterial species cultured from sputum change during treatment or observation for non-tuberculous mycobacterial pulmonary disease; however, strain-level changes remain unrecognized. Variable number tandem repeat typing is a standard technique for strain identification; nonetheless, its labor-intensive and time-consuming nature limits routine clinical use. Therefore, we aimed to elucidate species-subspecies and strain dynamics in non-tuberculous mycobacteria and develop a simple sequence-based strain-level determination method. We performed a single-center prospective cohort study of 112 patients with non-tuberculous mycobacterial pulmonary disease. Whole-genome sequencing was performed on two sputum samples collected at enrollment and at the end of follow-up, followed by variable number tandem repeat (VNTR) typing. We also developed a simple long-read sequencing-based digital VNTR (dVNTR) typing method and evaluated its efficacy. Our results demonstrate that core genome multi-locus sequencing typing revealed species/subspecies changes in 13 patients (11.6%); VNTR typing detected strain changes in 16 patients (14.3%) without species/subspecies changes. Overall, pathogen shifts occurred in 29 patients (shift [+] group, 25.9%), whereas 83 had no detectable pathogen shift (shift [-] group, 74.1%). Interestingly, macrolide and amikacin susceptibility changed in both groups, but resistance remained higher in shift (-) patients. dVNTR results aligned with those of conventional VNTR typing. In conclusion, since susceptibility factors remain unclear, routine species/subspecies identification and molecular typing, such as VNTR, are optimal for patient care. Core genome multi-locus sequencing typing with a dVNTR identified pathogen shifts, innovating non-tuberculous mycobacterial pulmonary disease management.\n\nMolecular epidemiological surveillance for non-tuberculous mycobacterial pulmonary disease: a single-center prospective cohort study.", "token_count": 488, "char_count": 1964, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:45.287037", "source": { "split": "train_shard_00000", "doc_id": 131 }, "chunk_id": "train_shard_00000_131_0", "global_id": 149 }, { "text": "In this study, we developed a novel 13 housekeeping gene multilocus sequence typing (MLST) scheme for Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) using whole-genome sequencing data, comprising 218 GenBank-retrieved and 29 newly isolated Turkish strains. We identified 291 distinct alleles across 13 housekeeping genes (clpX, pepX, pheS, mutL, murE, dnaA, gyrB, ddlA, pyrG, rpoB, fusA, recA, and tuf), with allele frequencies ranging from 2.7 to 10.9%, and defined 133 sequence types (STs), including 12 novel STs (ST122-ST133) unique to Turkish isolates, demonstrating superior discriminatory power compared to prior 8-gene MLST schemes (106 STs). This scheme offers a practical, standardized, and less computationally demanding alternative to core genome MLST (cgMLST) for large-scale epidemiological and industrial tracking, while maintaining high resolution. Population structure analysis revealed 17 clonal complexes (CC1-CC17) and 76 singleton STs (57.1%), with the largest complex (CC-1) containing 17 STs. Turkish isolates formed a distinct clonal complex (CC-6) or existed as singletons, underscoring their genetic uniqueness. Genetic diversity analyses showed significant differences between reference and Turkish populations, with nucleotide diversity (π) values of 0.00364 and 0.00225, respectively. The gyrB locus exhibited the highest diversity in reference strains (π = 0.00858), while pyrG and mutL showed the highest diversity in Turkish isolates. Significant linkage disequilibrium was detected in both populations (\n\nA New Multilocus Sequence Typing Scheme for Lactobacillus delbrueckii subsp. bulgaricus Based on Whole-Genome Sequencing Data.", "token_count": 493, "char_count": 1677, "word_count": 226, "semantic_coherence": 1, "information_density": 0.7345, "quality_score": 0.8673, "entities": { "genes": [ "ST122", "CC17", "CC1", "ST133" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:45.919264", "source": { "split": "train_shard_00000", "doc_id": 132 }, "chunk_id": "train_shard_00000_132_0", "global_id": 150 }, { "text": "Common oat, belonging to the genus Avena with 30 recognized species, is a nutritionally important cereal crop and high-quality forage worldwide. Here, we construct a genus-level super-pangenome of Avena comprising 35 high-quality genomes from 14 cultivated oat accessions and 21 wild species. The fully resolved phylogenomic analysis unveils the origin and evolutionary scenario of Avena species, and the super-pangenome analysis identifies 26.62% and 59.93% specific genes and haplotypes in wild species. We delineate the landscape of structural variations (SVs) and the transcriptome profile based 1,401 RNA-sequencing (RNA-seq) samples from diverse abiotic stress treatments in oat. We highlight the crucial role of SVs in modulating gene expression and shaping adaptation to diverse stresses. Further combining SV-based genome-wide association studies (GWASs), we characterize 13 candidate genes associated with drought resistance such as AsARF7, validated by transgenic oat lines. Our study provides unprecedented genomic resources to facilitate genomic, evolution and molecular breeding research in oat.\n\nSuper-pangenome analyses across 35 accessions of 23 Avena species highlight their complex evolutionary history and extensive genomic diversity.", "token_count": 316, "char_count": 1254, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7118, "quality_score": 0.8559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:46.466095", "source": { "split": "train_shard_00000", "doc_id": 133 }, "chunk_id": "train_shard_00000_133_0", "global_id": 151 }, { "text": "Variations in host species significantly impact bacterial growth traits and antibiotic resistance, making it essential to consider host origin when evaluating the zoonotic potential of pathogens. This study focuses on multiple Brucella species, which share highly similar genetic material, to explore the relationship between host origin and zoonotic potential by integrating pan-genome-wide association studies (pan-GWAS) with machine learning (ML). Our results present an open pangenome of Brucella spp. derived from the whole-genome sequencing (WGS) data of 991 strains and identify 268 genes potentially associated with the zoonotic potential of Brucella. Integrating these genes into an ML model based on the support vector machine (SVM) algorithm allows us to predict the zoonotic potential of various Brucella strains with high accuracy. Our findings reveal that zoonotic potential varies by host origin: Brucella melitensis strains isolated from humans exhibit higher zoonotic potential than those isolated from cattle, goats, and sheep, while Brucella suis biovar 2 strains isolated from domestic pigs display higher zoonotic potential than those isolated from wild boars. Our study proposes a method for predicting and quantifying the zoonotic potential of closely related bacterial pathogens from different host origins, providing valuable insights for risk assessment and public health strategy.\n\nMachine learning based on pangenome-wide association studies reveals the impact of host source on the zoonotic potential of closely related bacterial pathogens.", "token_count": 334, "char_count": 1569, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6045, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:47.017133", "source": { "split": "train_shard_00000", "doc_id": 134 }, "chunk_id": "train_shard_00000_134_0", "global_id": 152 }, { "text": "Salmonella Enteritidis infections started to appear in fox farms in Finland in 2002, but it was not until 2014 when S. Enteritidis emerged on cattle and swine farms. S. Enteritidis is also a common finding from dead hedgehogs throughout the country. In this study, we used core genome multilocus sequence typing (cgMLST) to investigate the epidemiology of S. Enteritidis infection. We analyzed 147 isolates collected from animals between 2014 and 2022, as well as two isolates from 2002. All isolates from fox and swine farms and 86 % of those from cattle farms clustered together, suggesting a diffuse and gradual spread of the infection during 2014-2020. In 2021, an outbreak of S. Enteritidis occurred on fox farms, followed by an increase in cases on cattle farms in the fox farming region in 2022. The outbreak in foxes was caused by an endemic strain that had been circulating within animal units before spreading widely in 2021. These findings suggest an endemic S. Enteritidis infection in the fox farming area. The infection is most likely transmitted from infected fox farms to cattle and swine farms via pests, such as rodents and birds. To prevent the spread of infection, better biosecurity measures and improved production hygiene should be implemented in fox farming. Isolates from hedgehogs were genetically distinct from those obtained from other animals. They were highly homogeneous and formed their own cgMLST cluster. All the Finnish isolates, including those from hedgehogs, belonged to ST11 according to classic MLST.\n\nCore genome multilocus sequence typing reveals an endemic Salmonella Enteritidis infection common to fox, cattle, and swine farms in Finland.", "token_count": 440, "char_count": 1683, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5752, "quality_score": 0.7876, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:47.630605", "source": { "split": "train_shard_00000", "doc_id": 135 }, "chunk_id": "train_shard_00000_135_0", "global_id": 153 }, { "text": "Inflammatory diseases pose a significant threat to human health, and probiotics have increasingly drawn substantial attention for their anti-inflammatory potential. In this research, a model of inflammation was constructed using J774-Dual reporter cells. Lactobacillus plantarum LPH10 with anti-inflammatory properties was screened from Yangzhou pickles. Its characteristics of acid tolerance, bile salt tolerance, bacteriostatic ability, and inhibition of the Salmonella-induced inflammation were evaluated. The results demonstrated that LPH10 exhibited excellent tolerance in simulated gastric acid (pH 3.0) and small intestinal bile salt (0.3%) environments, maintaining high survival rates at both 2 h and 4 h, indicating remarkable acid and bile salt resistance. Bacteriostatic assays demonstrated that LPH10 was effective in restraining the growth of Salmonella enteritidis and Escherichia coli. Moreover, LPH10 displayed sensitivity to a broad spectrum of antibiotics and did not notably affect the viability of RAW264.7 macrophages, which indicated its safety. LPH10 was discovered to be able to potently suppress the activation of the NF-κB and IRF signaling pathways triggered by LPS and S. enteritidis. In the LPS-induced inflammation model, LPH10 downregulated the expression of proinflammatory cytokines such as IL-1β, IL-6, and TNF-α, while upregulating the expression of the anti-inflammatory cytokine IL-10. In the Salmonella-induced inflammation model, LPH10 also regulated the expression levels of inflammatory cytokines, thereby exerting potent anti-inflammatory effects. Overall, L. plantarum LPH10 was successfully screened due to its multiple beneficial properties. This study provides a solid theoretical basis and experimental support for the screening and application of functional anti-inflammatory probiotics and will provide new approaches and probiotic candidates for the development of anti-inflammatory foods and the treatment of inflammatory diseases.", "token_count": 504, "char_count": 1983, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [ "RAW264", "LPH10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:48.261146", "source": { "split": "train_shard_00000", "doc_id": 136 }, "chunk_id": "train_shard_00000_136_0", "global_id": 154 }, { "text": "Screening of Lactobacillus plantarum LPH10 and Its Anti-inflammatory Properties: Acid and Bile Salt Tolerance, Bacteriostatic Activity and Regulation of NF-κB/IRF Pathways.", "token_count": 57, "char_count": 172, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [ "LPH10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:48.621146", "source": { "split": "train_shard_00000", "doc_id": 136 }, "chunk_id": "train_shard_00000_136_1", "global_id": 155 }, { "text": "Making sense of whole-genome polymorphism data is challenging, but it is essential for overcoming the biases in SNP data. Here we analyze 27 genomes of Arabidopsis thaliana to illustrate these issues. Genome size variation is mostly due to tandem repeat regions that are difficult to assemble. However, while the rest of the genome varies little in length, it is full of structural variants, mostly due to transposon insertions. Because of this, the pangenome coordinate system grows rapidly with sample size and ultimately becomes 70% larger than the size of any single genome, even for n = 27. Finally, we show how short-read data are biased by read mapping. SNP calling is biased by the choice of reference genome, and both transcriptome and methylome profiling results are affected by mapping reads to a reference genome rather than to the genome of the assayed individual.\n\nA comparison of 27 Arabidopsis thaliana genomes and the path toward an unbiased characterization of genetic polymorphism.", "token_count": 244, "char_count": 1000, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:49.093435", "source": { "split": "train_shard_00000", "doc_id": 137 }, "chunk_id": "train_shard_00000_137_0", "global_id": 156 }, { "text": "Designing CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) single guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we introduce ALLEGRO, a combinatorial optimization algorithm designed to compose minimal, yet highly effective sgRNA libraries targeting thousands of species at the same time. Leveraging integer linear programming, ALLEGRO identified compact sgRNA sets simultaneously targeting multiple genes of interest for over 2000 species across the fungal kingdom. We experimentally validated sgRNAs designed by ALLEGRO in Kluyveromyces marxianus, Komagataella phaffii, Yarrowia lipolytica, and Saccharomyces cerevisiae, confirming successful genome edits. Additionally, we employed a generalized Cas9-ribonucleoprotein delivery system to apply ALLEGRO's sgRNA libraries to untested fungal genomes, such as Rhodotorula araucariae. Our experimental findings, together with cross-validation, demonstrate that ALLEGRO facilitates efficient CRISPR genome editing, enabling the development of universal sgRNA libraries applicable to entire taxonomic groups.\n\nKingdom-wide CRISPR guide design with ALLEGRO.", "token_count": 354, "char_count": 1432, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:49.658239", "source": { "split": "train_shard_00000", "doc_id": 138 }, "chunk_id": "train_shard_00000_138_0", "global_id": 157 }, { "text": "In prokaryotes, lateral gene transfer (LGT) is a key mechanism leading to intraspecies variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that include Aureococcus anophagefferens-a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and within Ac. anophagefferens, we used long-read sequencing to produce high-quality genome assemblies for five strains of Ac. anophagefferens (52-54 megabase pairs [Mbp]), a telomere-to-telomere assembly for Pelagomonas calceolata (32 Mbp), and the first reference genome for Aureoumbra lagunensis (41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain-level genetic variation in Ac. anophagefferens, with a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation within Ac. anophagefferens does not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found in P. calceolata or Au. lagunensis. A total of 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5%-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.\n\nPangenome biology and evolution in harmful algal-bloom-forming pelagophytes.", "token_count": 468, "char_count": 1617, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6758, "quality_score": 0.8379, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:50.285646", "source": { "split": "train_shard_00000", "doc_id": 139 }, "chunk_id": "train_shard_00000_139_0", "global_id": 158 }, { "text": "Based on a pangenome graph platform, we simultaneously analyzed the impacts of SNPs and SVs in the population structure and phenotypic formation of global cattle using 2,409 individuals from 82 breeds. We demonstrated that SVs, like SNPs, effectively explain the population structure of global cattle. Genomic regions under strong selection, identified using both SNPs and SVs, consistently revealed footprints associated with human-mediated selection of economic traits in European improved cattle or natural selection of geographical adaptations. Notably, we detected that ∼40.14% of SVs were not tagged (LD, r2 < 0.6) by nearby SNPs. These \"orphan\" SVs may uncover new genetic signals and represent recent mutations associated with specific selection pressures or local environmental adaptation. Selected SVs tagged by SNPs also play causal or dominant roles in regions under selection. For example, our single-cell RNA sequencing has demonstrated that a notable SNP-tagged SV functions as an enhancer of the IGFBP7 gene, regulating fat deposition through IGFBP7+ cells. In conclusion, these SV-related mechanisms likely have caused some differences in economic traits and local adaptability across global cattle populations. Our integrated approaches highlight the unique and indispensable roles of SVs in shaping genetic diversity, offering novel insights into adaptation, selection, and strategies for improving cattle populations.\n\nGlobal Pangenome Analysis Highlights the Critical Role of Structural Variants in Cattle Improvement and Identifies a Unique Event as a Novel Enhancer in IGFBP7+ Cells.", "token_count": 352, "char_count": 1606, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8268, "entities": { "genes": [ "IGFBP7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:50.843635", "source": { "split": "train_shard_00000", "doc_id": 140 }, "chunk_id": "train_shard_00000_140_0", "global_id": 159 }, { "text": "Enterobacteriaceae is a diverse bacterial family that commonly colonizes the gastrointestinal tracts of humans and animals, influences host health, and also includes members adapted to colonize the phyllosphere as well as insect hosts. We lack systematic knowledge regarding the core metabolic strategy shared among Enterobacteriaceae. To address this gap, we have analyzed the pan-genome of nearly 20,000 genomes, including Citrobacter, Escherichia, Klebsiella, and Salmonella. We found that genes necessary for monosaccharide-fuelled mixed acid fermentation and (micro-)aerobic respiration are part of the Enterobacteriaceae core genome, whereas most genes involved in anaerobic respiration and carbohydrate utilization are associated to the accessory genome. Most Enterobacteriaceae possess genes enabling the utilization of D-glucose, its epimers, D-glucose-containing disaccharides, and chemically modified derivatives of D-glucose - highlighting the evolutionary adaptation of this family to efficiently exploit this simple sugar. Understanding Enterobacteriaceae's core metabolic strategy helps clarify the distinction of niche-defining nutrient sources, which can be genus-, species- or strain-specific. This study highlights the core metabolic strategy of Enterobacteriaceae, supporting the development of targeted interventions in microbiome research and infectious disease control.\n\nGene-level analysis of core carbohydrate metabolism across the Enterobacteriaceae pan-genome.", "token_count": 359, "char_count": 1487, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6973, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation", "respiration" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:51.404800", "source": { "split": "train_shard_00000", "doc_id": 141 }, "chunk_id": "train_shard_00000_141_0", "global_id": 160 }, { "text": "Pangenome analyses, which encompass the full genetic repertoire of a species, offer valuable insights into intraspecific diversity and phylogeographic gene patterns. While the taxonomic breadth and functional significance of animal pangenomes remain to be fully uncovered, recent findings (such as reports of open, bacterial-like pangenomes in bivalves) highlight the need to better understand the molecular mechanisms driving inter-haplotype structural variation. Genes affected by presence-absence variation (PAV), along with non-reference sequences (NRSs), represent evolutionary footprints that may shape genome architecture and plasticity, ultimately influencing the adaptability and long-term fitness of species. To investigate the pangenomic architecture of basal chordates, we analyzed available whole-genome resequencing data from Branchiostoma belcheri and B. floridae, examined the impact of structural genomic variation, and assessed the inheritance patterns of dispensable genes across generations. The pangenomes of both species include over a thousand of genes affected by PAV and exhibiting trans-generational Mendelian transmission from parents to offspring. We further demonstrate that 35 dispensable genes in B. belcheri are of exogenous origin, likely resulting from the integration of a malacoherpesvirus genome, thereby extending the known host range of Malacoherpesviridae from invertebrates to chordates. PAV preferentially targeted gene families involved in defense, immunity, and cell signaling, including GTPases of immunity-associated proteins (GIMAPs), caspases, toll-like receptors, and pattern recognition receptors containing apextrin C-terminal (APEC) domains. The dynamic nature of immunity genes in cephalochordates parallels patterns seen in open bacterial pangenomes, suggesting that fundamental principles of genome evolution and innovation across life domains are shaped by host-pathogen interactions.\n\nThe highly dynamic pangenome of basal chordates is enriched in defence and immunity genes and is inherited following the Mendelian law.", "token_count": 467, "char_count": 2077, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8451, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:52.033353", "source": { "split": "train_shard_00000", "doc_id": 142 }, "chunk_id": "train_shard_00000_142_0", "global_id": 161 }, { "text": "Phytate is an anti-nutrient factor that chelates micronutrients, thereby reducing their bioavailability and impairing nutrient absorption in humans and animals. This study aimed to isolate and assess potential probiotic yeast strains with phytase capability from Thai traditional fermentation starters. Three yeast isolates revealed antagonistic activity against pathogenic bacteria in preliminary probiotic screening and demonstrated phytate-degrading capabilities through phytase activity. Among the selected yeast strains, isolate NS104-STR showed the highest extracellular phytase activities (0.142 ± 0.001 U/mL and 0.126 ± 0.001 U/mg protein). Phylogenetic analysis based on 18 s rDNA and/or TSI gene regions identified this strain as closely related to Pichia kudriavzevii. Pichia kudriavzevii NS104-STR displayed several desirable probiotic attributes. This strain exhibited broad-spectrum bacteriostatic activity and tolerance to acidic conditions (≥ 10\n\nProbiotic potential and phytase-producing capacity of yeast isolated from Thai traditional fermentation starter (Look-pang).", "token_count": 305, "char_count": 1087, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7664, "quality_score": 0.8832, "entities": { "genes": [ "NS104" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:52.584809", "source": { "split": "train_shard_00000", "doc_id": 143 }, "chunk_id": "train_shard_00000_143_0", "global_id": 162 }, { "text": "Probiotic strains, defined as live microorganisms that confer health benefits to the host when administered in adequate amounts, are widely incorporated into commercial products. Therefore, assessing the safety and functional attributes of 20 commercially available probiotic strains using complete genome sequencing is of immediate importance. Our analysis revealed that 15% of the products were mislabeled, containing species different from those declared on the label. Further, 12% of the tested strains harbored transferable antimicrobial resistance genes. However, 8% Bacillus species contained virulence-associated genes. Nonetheless probiotic-related genes linked to acid and bile tolerance were consistently found in Lactobacillus strains. These findings underscore the urgent need for standardized genomic safety assessments prior to the market approval of probiotic products.\n\nComprehensive genomic assessment of available probiotics in India: A framework for safety and functionality evaluation.", "token_count": 214, "char_count": 1006, "word_count": 131, "semantic_coherence": 1, "information_density": 0.771, "quality_score": 0.8855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:53.041871", "source": { "split": "train_shard_00000", "doc_id": 144 }, "chunk_id": "train_shard_00000_144_0", "global_id": 163 }, { "text": "Transposable elements (TEs) introduce genetic and epigenetic variability, contributing to gene expression patterns that drive adaptive evolution in plants. Here, we investigate TE architecture and its effect on cold tolerance in rice. By analyzing a pangenome graph and the resequencing data of 165 rice accessions, we identify 30,316 transposable element insertion polymorphism (TIP) sites, highlighting significant diversity among polymorphic TEs (pTEs). We observe that pTEs exhibit increased H3K27me3 enrichment, suggesting a potential role in epigenetic differentiation under cold stress and in the transcriptional regulation of the cold response. We identify 26,914 TEs responsive to cold stress from transcriptome data, indicating their potential significance in regulatory networks for this response. Our TIP-GWAS analysis reveal two cold tolerance genes OsCACT and OsPTR. The biological functions of these genes are confirmed using knockout and overexpression lines. Our web tool ( https://cbi.gxu.edu.cn/RICEPTEDB/ ) makes all pTEs available to researchers for further analysis. These findings provide valuable targets for breeding cold-tolerant rice varieties, indicating the potential importance of pTEs in crop enhancement.\n\nPangenome analysis of transposable element insertion polymorphisms reveals features underlying cold tolerance in rice.", "token_count": 311, "char_count": 1356, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6906, "quality_score": 0.8453, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:53.599216", "source": { "split": "train_shard_00000", "doc_id": 145 }, "chunk_id": "train_shard_00000_145_0", "global_id": 164 }, { "text": "Vibrio parahaemolyticus (V. parahaemolyticus), a Gram-negative halophilic bacterium, is a leading seafood-borne pathogen that can cause acute gastroenteritis. Outer membrane (OM) porins are involved in exporting extracellular polymeric substances, which is essential for biofilm formation. However, the contribution of porins to the biofilm formation of V. parahaemolyticus is still obscure. We recently found that a mutation in the DHH/DHHA1 family gene vp2835 enhances biofilm formation in V. parahaemolyticus but inhibits its motility. Here, we identified an OM porin gene, vpa0810, from Δvp2835 strain. The deletion of vpa0810 in the wild type strain resulted in the inhibition of both swarming and swimming motility, while reverted the motility defect of Δvp2835. The Δvpa0810 decreased its biofilm formation capability in both the wild type and the Δvp2835 strain. Additionally, the surface hydrophobicity, auto-aggregation, OM permeability, and exopolysaccharides (EPS) content were decreased in the Δvpa0810 strain. Interestingly, qRT-PCR results demonstrated that the genes involved in EPS synthesis (cpsA, scvE, and cpsF) and the porin gene ompW were significantly up-regulated in the Δvpa0810 strain, but down-regulated in the Δvp2835-Δvpa0810 double mutant. Furthermore, the deletion of vpa0810 compromised its ability to form biofilm on silicon wafers, glass, stainless-steel plates, as well as on shrimp and crab surfaces. The vpa0810 deletion mutation also reduced its stress tolerance to bile salt, low pH, low temperature, and the antibiotics colistin. In summary, our data suggest that Vpa0810 may regulate biofilm formation through EPS biosynthesis and exportation, which might provide a new target for developing control strategies against V. parahaemolyticus.", "token_count": 526, "char_count": 1780, "word_count": 250, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [ "DHHA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T04:59:54.268186", "source": { "split": "train_shard_00000", "doc_id": 146 }, "chunk_id": "train_shard_00000_146_0", "global_id": 165 }, { "text": "Vibrio parahaemolyticus outer membrane porin Vpa0810 regulates its biofilm formation and plays a vital role in its stresses tolerance.", "token_count": 37, "char_count": 134, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:54.638307", "source": { "split": "train_shard_00000", "doc_id": 146 }, "chunk_id": "train_shard_00000_146_1", "global_id": 166 }, { "text": "Riemerella anatipestifer (R. anatipestifer) affects the duck farming industry worldwide, causing substantial economic losses. The current disease prevention and treatment strategies primarily include vaccines and antibiotics. However, the large number of serotypes and increasing resistance to R. anatipestifer make it challenging to prevent and treat the infection. This study carried out the serotyping and molecular typing of 51 R. anatipestifer strains and predicted vaccine proteins based on pan-genome analysis and cross-immune protection potential. For serotype identification, the rabbits were immunized with antigens, and 9 serotyped sera were prepared, the data revealed 6 serotypes with two unformed strains. The results for the self-made serotypes were consistent with those obtained from the externally submitted strains. Moreover, the pan-genome analysis was performed on 51 R. anatipestifer strains, and an open pan-genome set of 5094 genes was constructed. In addition, the COG annotation classification indicated that the core and non-core genomes were significantly different in gene functions. A total of 1116 core genomes that could serve as better cross-protective vaccine proteins were analyzed and revealed 5 genes of interest. In addition, the oprM-1 protein, a highly reactive protein, was expressed and purified, and the immunoreactivity with five antisera (anti-serotypes 1, 2, 5, 11, and 18) was demonstrated by Western blotting. This study fills the gaps in the existing typing systems for R. anatipestifer by combining serotyping, MLST typing, and pan-genome analysis. Furthermore, it provides valuable insights into the epidemiology, evolution, and pathogenesis of R. anatipestifer and paves the way for developing effective cross-protective vaccines.\n\nSerotyping, molecular typing, and vaccine protein screening for Riemerella anatipestifer: Overcoming challenges in prevention and treatment.", "token_count": 473, "char_count": 1924, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6241, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:55.283394", "source": { "split": "train_shard_00000", "doc_id": 147 }, "chunk_id": "train_shard_00000_147_0", "global_id": 167 }, { "text": "Kluyveromyces marxianus, formerly known as Candida kefyr, is an emerging opportunistic yeast increasingly reported in immunocompromised hosts. This review aims to summarize the clinical presentations, diagnostic approaches, treatment strategies, and outcomes of C. kefyr infections among transplantation recipients through an analysis of published case reports. A comprehensive literature search was performed using PubMed, Scopus, and Web of Science for case reports involving transplantation patients infected with C. kefyr. The review included only individual case reports describing invasive fungal infections in solid organ or hematopoietic stem cell transplant recipients. A total of seven case reports were identified. Clinical presentations included fungemia, keratitis and catheter-related bloodstream infections. Median age was 61.0. Most of the case had neutropenia and consumption of dairy products. Also, the ratio of localized organ involvement is higher. C. kefyr should be considered a potential opportunistic pathogen in transplant recipients, particularly in older or neutropenic patients with regular dairy consumption. Early diagnosis and appropriate antifungal therapy are essential for favorable outcomes.\n\nCandida kefyr as an emerging cause of invasive fungal infection in transplant patients: Case report and literature review.", "token_count": 292, "char_count": 1351, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:55.867390", "source": { "split": "train_shard_00000", "doc_id": 148 }, "chunk_id": "train_shard_00000_148_0", "global_id": 168 }, { "text": "Most genomic studies start by mapping sequencing data to a reference genome. The quality of reference genome assembly, genetic relatedness to the studied population, and the mapping method employed directly impact variant calling accuracy and subsequent genomic analyses, introducing reference bias and resulting in erroneous conclusions. However, the impacts of reference bias have gained limited attention. This study compared population genomic analyses using four different reference genomes of mango (\n\nMango pangenome reveals dramatic impacts of reference bias on population genomic analyses.", "token_count": 110, "char_count": 598, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7195, "quality_score": 0.8598, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:56.264457", "source": { "split": "train_shard_00000", "doc_id": 149 }, "chunk_id": "train_shard_00000_149_0", "global_id": 169 }, { "text": "Kluyveromyces marxianus is a traditional fermentation starter, but the effects of K. marxianus fermentation on tomato remain largely unknown. Here, K. marxianus was employed for tomato puree fermentation under sterile conditions. Sensory evaluation revealed that K. marxianus decreased the unpleasant flavor components in fermented tomato puree (FTP). GC-MS analysis demonstrated that K. marxianus fermentation improved the flavor and aroma, primarily due to increases in alcohols (48.84 %) and esters (43.31 %) and enrichment of aroma-associated metabolites in volatile organic compounds. Widely targeted metabolomics showed that the fermentation significantly increased 37 phenolic compounds, potentially enhancing the antioxidant effects of FTP. The contents of lycopene isomers including cis-lycopene significantly increased in FTP (179.52 μg/g). Notably, FTP showed enrichment of beneficial genera, including Akkermansia and Pediococcus, in fecal microbiota. Collectively, these results indicate that K. marxianus fermentation is a viable approach to improving the sensory profile and potential health benefits of fermented tomato.\n\nKluyveromyces marxianus fermenta tion improves tomato sensory profile, functional metabolites, lycopene bioaccessibility, and human fecal microbiota composition.", "token_count": 347, "char_count": 1299, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6407, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:56.828665", "source": { "split": "train_shard_00000", "doc_id": 150 }, "chunk_id": "train_shard_00000_150_0", "global_id": 170 }, { "text": "While benchmarks on short-read variant calling suggest low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher. Although multiple sets of easy regions have been identified to alleviate the issue, they fail to consider non-reference samples or are biased towards existing short-read data or aligners.\n\nFinding easy regions for short-read variant calling from pangenome data.", "token_count": 104, "char_count": 483, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7945, "quality_score": 0.8973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:57.557203", "source": { "split": "train_shard_00000", "doc_id": 151 }, "chunk_id": "train_shard_00000_151_0", "global_id": 171 }, { "text": "Structural variation causes some human haplotypes to align poorly with the linear reference genome, leading to 'reference bias'. A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a 'genetic variant.' We introduce a definition of pangenome variants and a method,\n\nDefining and cataloging variants in pangenome graphs.", "token_count": 94, "char_count": 428, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:57.931620", "source": { "split": "train_shard_00000", "doc_id": 152 }, "chunk_id": "train_shard_00000_152_0", "global_id": 172 }, { "text": "The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here we present JaSaPaGe, a pangenome graph reference for Saudi Arabian and Japanese populations, both of which have been significantly underrepresented in previous genomic studies. We constructed JaSaPaGe from high-quality phased diploid assemblies which were made utilizing PacBio high-fidelity long reads, Nanopore long reads, and Hi-C short reads of 9 Saudi and 10 Japanese individuals. Quality evaluation of the pangenome graph by variant calling showed that our pangenome outperformed earlier linear reference genomes (GRCh38 and T2T-CHM13) and showed comparable performance to the pangenome graph provided by the Human Pangenome Reference Consortium (HPRC), with more variants found in Japanese and Saudi samples using their population-specific pangenomes. This pangenome reference will serve as a valuable resource for both the research and clinical communities in Japan and Saudi Arabia.\n\nPhased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia.", "token_count": 280, "char_count": 1241, "word_count": 178, "semantic_coherence": 1, "information_density": 0.618, "quality_score": 0.809, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:58.474063", "source": { "split": "train_shard_00000", "doc_id": 153 }, "chunk_id": "train_shard_00000_153_0", "global_id": 173 }, { "text": "Pectin production by processing renewable feedstocks is an appealing and sustainable approach. However, microbial valorization of pectin remains underdeveloped and necessitates efficient expression of key enzymes. In this study, we developed a novel two-stage microbial consortium for pectin valorization through modular utilization of engineered\n\nEngineering a modular pectin-to-lipids bioconversion system using two Kluyveromyces marxianus strains.", "token_count": 110, "char_count": 450, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8364, "quality_score": 0.9182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:58.860550", "source": { "split": "train_shard_00000", "doc_id": 154 }, "chunk_id": "train_shard_00000_154_0", "global_id": 174 }, { "text": "This study investigated the effects of the inoculation of synthetic microbial communities (SynComs), including Staphylococcus carnosus, Lactiplantibacillus plantarum, Bacillus coagulans, and Kluyveromyces marxianus, on the safety, texture, taste, and flavor profiles of slightly fermented dried bonito. The results showed that all slightly fermented samples contained very low levels of total volatile base nitrogen and histamine, the fish proteins underwent acid denaturation and coagulation after fermentation, forming a dense and stable three-dimensional network structure that contributed to the appearance of the final products. A synergistic effect among S. carnosus, L. plantarum, and K. marxianus not only reduced the bitterness scores of the e-tongue, but also enhanced the umami and sweetness taste of dried bonito products by increasing the contents of pleasant tasting amino acids, with the equivalent umami concentration 1.89 times (p < 0.05) higher than control group. In addition, a linear relationship was observed between the amount of flavor compounds produced by lipid oxidation and free fatty acids. The co-inoculation of S. carnosus, L. plantarum, and B. coagulans yielded richer flavor compounds in dried bonito, the upregulation of benzaldehyde, 2, 3-dimethyl-2-cyclopentene-1-one, 1-octen-3-ol and heterocyclic compounds led to the development of intense fruity, sweet, mushroom-like and floral aromas. These findings establish a foundation for the selection of composite fermentation starter cultures, enabling the targeted formulation of SynComs with flavor enhancement and texture improvement functions.\n\nSynthetic microbial communities: A new strategy to enhance texture, taste, and flavor attributes of slightly fermented dried bonito.", "token_count": 447, "char_count": 1764, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T04:59:59.480016", "source": { "split": "train_shard_00000", "doc_id": 155 }, "chunk_id": "train_shard_00000_155_0", "global_id": 175 }, { "text": "Lactiplantibacillus plantarum, one of the lactic acid bacteria (LAB), has shown numerous probiotic properties and health benefits to humans, particularly in the fight against obesity. Identification and characterization of effective L. plantarum strains and understanding their health effects are essential for developing effective probiotic-based therapies for chronic diseases like obesity and diabetes. By screening various environmental samples, 17 L. plantarum strains were isolated. The acid and bile salt tolerance, short-chain fatty acids (SCFAs) production, cholesterol-lowering effect, and antioxidant performance of these L. plantarum strains were evaluated. The health effects of L. plantarum ZNFL-1 were assessed in high-fat diet-feeding mice by monitoring mice weight gain, adipose tissue, blood glucose, and lipid, and investigating the changes of the mice gut microbiota. The representative L. plantarum strain ZNFL-1 exhibited significant tolerance to acid and bile salts. Its supplementation significantly reduced cholesterol levels and exhibited antioxidant properties. In high-fat diet-feeding mice, L. plantarum ZNFL-1 intervention, especially at higher doses, reduced body weight gain, inhibited adipose tissue accumulation, and improved gut microbiota dysbiosis. This study identified L. plantarum ZNFL-1, which has notable anti-obesity effects in mice fed with a high-fat diet. These anti-obesity effects were achieved by increasing levels of beneficial bacteria and decreasing potentially harmful ones. Additionally, L. plantarum ZNFL-1 alleviated dysbiosis induced by a high-fat diet and improved symptoms associated with obesity by regulating lipid metabolism.\n\nAnti‑obesity Effects of Lactiplantibacillus plantarum ZNFL-1 by Modulating Gut Microbiota and Lipid Metabolism in High‑Fat Diet‑Induced Mice.", "token_count": 470, "char_count": 1830, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5958, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:00.105092", "source": { "split": "train_shard_00000", "doc_id": 156 }, "chunk_id": "train_shard_00000_156_0", "global_id": 176 }, { "text": "Rubia cordifolia L. (RCL) is a plant with both commercial and medicinal values, widely distributed worldwide. Its roots have been used to treat various diseases, including abnormal uterine bleeding, arthritis, and kidney stones. However, its stems are often overlooked and regarded as waste. This study employed response surface methodology to optimize the ultrasonic-assisted extraction (UAE) process for polysaccharides from RCL waste stems (RCLP), and compared energy consumption and carbon emissions with hot water extraction (HWE). The underlying mechanism of UAE for polysaccharide extraction was further explored. Additionally, the physicochemical properties and in vitro activities of RCLP extracted by UAE (UAE-P) and HWE (HWE-P) were evaluated and compared. The results showed that the optimal UAE conditions were as follows: temperature of 52.5 °C, extraction time of 43 min, power of 310 W, and liquid-to-solid ratio of 32 mL/g, yielding 5.97 ± 0.34 % of RCLP. Compared with HWE, UAE significantly improved extraction efficiency, with a 640.18 % increase in production rate and a 93.23 % reduction in specific energy. UAE promoted the exposure of cell wall functional groups (e.g., C=O, C-O-C) and disintegration of the crystalline structure, thereby enhancing extraction efficiency. UAE-P exhibited higher uronic acid content, smaller and more uniform particle size, and better stability than HWE-P. These structural characteristics were significantly correlated with superior in vitro antioxidant and hypoglycemic activities, as well as stronger bile salt binding capacity. In conclusion, this study highlights that UAE is a feasible method for efficiently extracting high-value polysaccharides from RCL waste stems.\n\nAdvantages of ultrasonic-assisted extraction over hot water extraction for polysaccharides from waste stems of Rubia cordifolia L.: A comprehensive comparison of efficiency, structure, and bioactivity.", "token_count": 500, "char_count": 1933, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8358, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:00.739345", "source": { "split": "train_shard_00000", "doc_id": 157 }, "chunk_id": "train_shard_00000_157_0", "global_id": 177 }, { "text": "Cardiovascular diseases remain one of the leading causes of mortality among adults worldwide, with elevated blood lipid levels serving as a key modifiable risk factor. This study aimed to investigate the probiotic potential of lactic acid bacteria (LAB) isolated from ginseng sprouts (Panax ginseng Meyer) cultivated under smart-farming conditions, with a particular emphasis on their cholesterol-lowering properties. Out of 485 isolates, five strains of Lacticaseibacillus rhamnosus were selected based on superior in vitro performance and identified through 16 S rRNA sequencing and phylogenetic analysis. The selected strains demonstrated high tolerance to simulated gastrointestinal conditions (pH 3.0, 0.3% bile salts), with survival rates ranging from 98 to 99%. In addition, they exhibited robust antibacterial activity, notable antioxidant capacity and antibiotic susceptibility to erythromycin and clindamycin, while showed resistance to tetracycline and vancomycin. The selected bacterial strains reduced cholesterol levels by 30% as compared to the reference strain Lacticaseibacillus rhamnosus GG. Moreover, the formation of white precipitates around the bacterial colonies grown on media supplemented with 0.5% (w/v) TDCA and 0.37 g/L CaCl\n\nProbiotic potential of ginseng derived Lacticaseibacillus rhamnosus strains with hypocholesterolemic, antioxidant and antibacterial activities.", "token_count": 371, "char_count": 1397, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7297, "quality_score": 0.8649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:01.315210", "source": { "split": "train_shard_00000", "doc_id": 158 }, "chunk_id": "train_shard_00000_158_0", "global_id": 178 }, { "text": "The presence of drug nanoparticles is believed to promote oral drug absorption through the particle drifting effect. These particles act as vehicles that penetrate the diffusion boundary layer adjacent to the intestinal membrane, releasing the drug near the mucosal surface, and thereby enhancing drug absorption. Despite extensive in vitro studies demonstrating the potential of this mechanism to improve drug absorption, in vivo evaluations of the particle drifting effect remain limited. In this work, we systematically evaluated the particle drifting effect in vivo in both mice and rats using enzalutamide as a model drug. To assess the impact of particle concentration, dose-escalation studies were performed to examine regions where absorption was driven by either solubilized drug or nanoparticles. The formation of amorphous drug nanoparticles was shown to significantly enhance drug absorption, confirming the role of the particle drifting effect. Nonlinear pharmacokinetics were observed in the nanoparticle absorption region, consistent with non-sink dissolution conditions in the boundary layer at high particle concentrations. Additionally, animal species-specific differences were observed, likely due to variations in bile salt concentration in the gastrointestinal fluids of mice and rats. Moreover, in vitro-in vivo relationships were established. These results provide valuable insights for early-stage formulation development, particularly for amorphous solid dispersions, before first-in-human studies where different surrogate tests and animal models are used, and should contribute to a broader understanding of how to predict the oral bioavailability of nanoparticle-containing formulations.\n\nThe particle drifting effect in vivo: impact of dose and animal species.", "token_count": 364, "char_count": 1789, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:01.883809", "source": { "split": "train_shard_00000", "doc_id": 159 }, "chunk_id": "train_shard_00000_159_0", "global_id": 179 }, { "text": "Beyond single nucleotide polymorphisms (SNPs), gene presence/absence variation (PAV) plays a crucial role in elucidating species' genetic diversity, uncovering the genetic basis of key traits, and advancing molecular marker-assisted breeding in plants. In this study, we constructed a pangenome of Liriodendron based on 24 accessions. Comparative analysis with the reference genome revealed 116 Mb of non-reference sequences and obtained 32,773 genes, including 3,558 novel genes. We subsequently employed resequencing data from 247 Liriodendron genotypes to identify PAVs, comprising 13,779 core genes and 18,179 dispensable genes. To further assess PAV applicability, a genome-wide association study (GWAS) was conducted to link gene PAVs with growth traits in hybrid Liriodendron, and identified 14 candidate genes associated with these growth traits above. Additionally, gene PAVs appeared to predominantly contribute to heterosis in growth traits, displaying a dominant expression pattern when comparing leaf, shoot, and phloem tissues of strong and weak heterotic combinations. Additionally, two key candidate genes, Litul.02G164100 and Litul.01G057400, exhibit high parental expression patterns consistent with hybrid vigor in strong heterotic combinations of leaf and shoot tissues. Altogether, this study expands the Liriodendron genomic dataset, identifies candidate genes linked to growth traits, and provides insights into their heterotic mechanisms in hybrid Liriodendron.\n\nPangenome analysis of Liriodendron reveals presence/absence variations associated with growth traits.", "token_count": 394, "char_count": 1588, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6762, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:02.484490", "source": { "split": "train_shard_00000", "doc_id": 160 }, "chunk_id": "train_shard_00000_160_0", "global_id": 180 }, { "text": "The pangenome of sulfate reducing bacteria represents a genetic reservoir that deciphers the intricate interplay of conserved and variable elements driving their ecological dominance, evolutionary adaptability, and industrial relevance. This study introduces the most comprehensive pangenome analysis of the genus Desulfovibrio till date, incorporating 63 complete and high-quality genomes using the Partitioned Pangenome Graph of Linked Neighbors (PPanGGOLiN) pipeline. The structure and dynamics of core gene families were investigated through gene ontology, KEGG pathway mapping, and gene network analyses, shedding light on the functional organization of the Desulfovibrio genomes. The analysis categorized 799, 4053, and 43,581 gene families into persistent, shell, and cloud groups, respectively. A core set of 326 gene families, conserved across Desulfovibrio genomes, highlights their essential role in community functionality. Genome plasticity analysis identified 4,576 regions of genome plasticity, with 1,322 hotspots enriched in horizontally acquired genes (89% in the cloud partition). Key gene families in these regions included glpE, fdhD, petC, and cooF, linked to sulfur metabolism. Out of 29 hypothetical genes, one was linked to actin nucleation, another contained a TRASH domain, while the other regulates filopodium assembly. Other predicted functions included lnrL, folE, RNA binding, and pyrG/pyrH involvement in CTP biosynthesis. Additionally, genomic islands revealed evolutionary events, such as cheY acquisition in Oleidesulfovibrio alaskensis G20. This study provides a genus-wide view of Desulfovibrio, emphasizing genome plasticity, hypothetical gene functions, and adaptation mechanisms.\n\nMapping the pangenome of sulfate reducing bacteria: core genes, plasticity, and novel functions in Desulfovibrio spp.", "token_count": 462, "char_count": 1838, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6762, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:03.101710", "source": { "split": "train_shard_00000", "doc_id": 161 }, "chunk_id": "train_shard_00000_161_0", "global_id": 181 }, { "text": "Cholestatic liver injury is caused by cholestasis, which is accompanied by hepatic cell dysfunction. Cellular senescence refers to a permanent arrest of cell division and a decline in metabolic activity, without a clear role in the process of cholestatic liver injury. Here, in the liver tissue of patients with cholestatic liver diseases, we found an increased proportion of hepatic cells with senescence marker P21 expression in Fibrosis stage 4 (F4) patients when compared with F1/2 patients. We also observed the colocalization of P21 with hepatocyte marker HNF4α in patients as well as in bile duct ligation (BDL)-induced cholestatic mice model. In vitro experiments also confirmed the senescence-induction effect of a classical toxic bile salt-Glycochenodeoxycholic acid (GCDCA) on AML12 cells. Importantly, the elimination of senescent hepatocytes by a new senolytic DpC improves liver function, alleviating inflammation and fibrotic changes in BDL mice. Then transcriptional analysis and target metabolomics analysis showed, in cholestatic liver injury, senescent hepatocytes were associated with SIRT3 downregulation and mitochondrial dysfunction. Subsequent experiments in vitro showed that silent SIRT3 expression aggravated GCDCA-induced AML12 cells mitochondrial dysfunction and senescence, while SIRT3 overexpression partially alleviated these changes. Furthermore, SIRT3 overexpression in hepatocytes successfully attenuates mitochondrial dysfunction and hepatocyte senescence, accompanied by the alleviation of hepatic inflammation and extracellular matrix deposition in BDL mice. These results suggest that mitochondrial dysfunction-mediated hepatocyte senescence is involved in cholestatic liver injury.\n\nMitochondrial dysfunction-mediated hepatocyte senescence is involved in cholestatic liver injury.", "token_count": 480, "char_count": 1820, "word_count": 237, "semantic_coherence": 1, "information_density": 0.557, "quality_score": 0.7785, "entities": { "genes": [ "AML12", "SIRT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:03.728262", "source": { "split": "train_shard_00000", "doc_id": 162 }, "chunk_id": "train_shard_00000_162_0", "global_id": 182 }, { "text": "Autism spectrum disorders (ASDs) are genetically and phenotypically heterogeneous and the majority of cases still remain genetically unresolved. To better understand large-effect pathogenic variation, we generated long-read sequencing data to construct phased and near-complete genome assemblies (average contig N50=43 Mbp, QV=56) for 189 individuals from 51 families with unsolved cases of autism. We applied read- and assembly-based strategies to facilitate comprehensive characterization of\n\nPangenome discovery of missing autism variants.", "token_count": 132, "char_count": 542, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:04.147021", "source": { "split": "train_shard_00000", "doc_id": 163 }, "chunk_id": "train_shard_00000_163_0", "global_id": 183 }, { "text": "Diurnal rhythmicity in the gut maintains gut integrity, circadian rhythms, and metabolic homeostasis. However, existing studies focus on microbial composition rather than transcriptional activity. To understand microbial functional dynamics, we characterize diurnal fluctuations in the mouse cecal metatranscriptome and metagenome under high-fat diet and time-restricted feeding (TRF). We show that metatranscriptomics uncover TRF-induced time-dependent microbial functional shifts that are undetectable with metagenomics alone. We also found bile salt hydrolase (\n\nMetatranscriptomics Uncover Diurnal Functional Shifts in Bacterial Transgenes with Profound Metabolic Effects.", "token_count": 173, "char_count": 676, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7561, "quality_score": 0.878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:04.580182", "source": { "split": "train_shard_00000", "doc_id": 164 }, "chunk_id": "train_shard_00000_164_0", "global_id": 184 }, { "text": "The commercial realization of hybrid wheat (Triticum aestivum L.) is a major technological challenge to sustainably increase food production for our growing population in a changing climate. Despite recent advances in cytoplasmic- and nuclear-based pollination control systems, the inefficient outcrossing of wheat's autogamous florets remains a barrier to hybrid seed production. There is a pressing need to investigate wheat floral biology and enhance the likelihood of ovaries being fertilized by airborne pollen so breeders can select and utilize male and female parents for resilient, scalable, and cost-effective hybrid seed production. Advances in understanding the wheat genomes and pangenome will aid research into the underlying floral organ development and fertility with the aim to stabilize pollination and fertilization under a changing climate. The purpose of this position paper is to highlight priority areas of research to support hybrid wheat development, including (1) structural aspects of florets that affect stigma presentation, longevity, and receptivity to airborne pollen, (2) pollen release dynamics (e.g., anther extrusion and dehiscence), and (3) the effect of heat, drought, irradiation, and humidity on these reproductive traits. A combined approach of increased understanding built on the genomic resources and advanced trait evaluation will deliver to robust measures for key floral characteristics, such that diverse germplasm can be fully exploited to realize the yield improvements and yield stability offered by hybrids.\n\nNew genomic resources to boost research in reproductive biology to enable cost-effective hybrid seed production.", "token_count": 351, "char_count": 1671, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:05.140164", "source": { "split": "train_shard_00000", "doc_id": 165 }, "chunk_id": "train_shard_00000_165_0", "global_id": 185 }, { "text": "In this study, lactic acid bacteria were isolated from traditional fermented foods in Guizhou. The fermentation supernatant and cell disruption extract were used to screen lactic acid bacteria with α-glucosidase inhibitory activity, and the active lactic acid bacteria strains with potential hypoglycemic effect were screened. The results showed that 10 strains were screened from 27 strains of lactic acid bacteria with α-glucosidase inhibitory activity, of which 5 strains had good acid and bile salt tolerance. The best acid resistance was XG01, and the survival rate was as high as 98.5%. ST01 had the strongest tolerance to bile salt, up to 77.3%. The lactic acid bacteria cell extracts of HLG01, YR01, ST01 and XG01 could better inhibit the activity of α-glucosidase, and the inhibition rates were 39.27, 38.6, 38.53, and 34.4%, respectively. The fermentation supernatant of JR01 could better inhibit the activity of α-glucosidase, and the inhibition rate reached 33.8%. Through molecular biological identification, HLG01, YR01, and ST01 were were\n\nScreening and identification of lactic acid bacteria with α-glucosidase inhibiting activity.", "token_count": 336, "char_count": 1147, "word_count": 170, "semantic_coherence": 1, "information_density": 0.5235, "quality_score": 0.7618, "entities": { "genes": [ "ST01", "XG01", "YR01", "HLG01", "JR01" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:05.691338", "source": { "split": "train_shard_00000", "doc_id": 166 }, "chunk_id": "train_shard_00000_166_0", "global_id": 186 }, { "text": "Accurate variant genotyping is crucial for genomics-assisted breeding. Graph pangenome references can address single-reference bias, thereby enhancing the performance of variant genotyping and empowering downstream applications in population genetics and quantitative genetics. However, existing pangenome-based genotyping methods are ineffective in handling large or complex pangenome graphs, particularly in polyploid genomes. Here, we introduce Varigraph, an algorithm that leverages the comparison of unique and repetitive k-mers between variant sites and short reads for genotyping both small and large variants. We evaluated Varigraph on a diverse set of representative plant genomes as well as human genomes. Varigraph outperforms current state-of-the-art linear and graph-based genotypers across non-human genomes while maintaining comparable genotyping performance in human genomes. By employing efficient data structures including counting Bloom filter and bitmap storage, as well as GPU models, Varigraph achieves improved precision and robustness in repetitive regions while managing computational costs for large datasets. Its wide applicability extends to highly repetitive or large genomes, such as those of maize and wheat. Significantly, Varigraph can handle extensive pangenome graphs, as demonstrated by its performance on a dataset containing 252 rice genomes, for which it achieved a precision exceeding 0.9 for both small and large variants. Notably, Varigraph is capable of effectively utilizing pangenome graphs for genotyping autopolyploids, enabling precise determination of allele dosage. In summary, this work provides a robust and accurate solution for genotyping plant genomes and will advance plant genomic studies and genomics-assisted breeding.\n\nVarigraph: An accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes.", "token_count": 417, "char_count": 1898, "word_count": 252, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:06.340282", "source": { "split": "train_shard_00000", "doc_id": 167 }, "chunk_id": "train_shard_00000_167_0", "global_id": 187 }, { "text": "Lettuce (Lactuca sativa L.) is among the most widely cultivated and consumed vegetables globally, valued for its phytonutrients beneficial for human health. Here, we report the high-quality reference super-pangenome for the Lactuca genus by integrating 12 chromosome-scale genomes from representative cultivated lettuce morphotypes, landrace, and wild relatives, and investigate lettuce genome evolution and domestication. These assemblies exhibit diverse genome sizes ranging from 2.1 Gb to 5.5 Gb with abundant repetitive sequences, and expansion of repetitive sequences, associated with low DNA methylation levels, likely contributes to the genome size variations. Furthermore, by constructing a graph-based lettuce pangenome reference, we explore the landscape, genomic, and epigenetic features of structural variations, and reveal their contributions to gene expression and domestication. We also identify copy number variations in FLOWERING LOCUS C in association with delayed flowering in cultivated lettuce. Overall, this comprehensive Lactuca super-pangenome assembly will expedite functional genomics studies and breeding efforts of this globally important crop.\n\nLactuca super-pangenome provides insights into lettuce genome evolution and domestication.", "token_count": 294, "char_count": 1264, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:06.916629", "source": { "split": "train_shard_00000", "doc_id": 168 }, "chunk_id": "train_shard_00000_168_0", "global_id": 188 }, { "text": "Brucellosis is among the most widespread zoonotic diseases globally, affecting multiple domestic animal species. We report the first isolation of Brucella suis from a vaginal swab collected from an aborted cow in India. The isolate (VS1) was confirmed as B. suis bv. 1 by biochemical assays and species-specific PCR. Whole genome sequencing analysis of the VS1 isolate revealed a 32,81,903 bp genome with a guanosine and cytosine (GC) content of 57.29%. Multilocus sequence typing (MLST) 9-gene, 21-gene, and core genome MLST (cgMLST) schemes identified sequence types ST14, ST75, and ST1054/1075, respectively. Comparative genomics involving publicly available B. suis genome sequences showed conservation of key virulence genes. The genome B. suis strain 1330 was used to identify the single nucleotide polymorphisms (SNP) in study genomes and 63 SNPs were identified in the virulence-associated genes. The study indicates that B. suis biovar 1 can infect cattle, and likely contributes in the epidemiology and control of bovine brucellosis in India.\n\nIsolation of Brucella suis from cattle in India: whole genome analysis unravels potential for zoonotic transmission.", "token_count": 333, "char_count": 1170, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [ "ST1054", "VS1", "ST75", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:07.514094", "source": { "split": "train_shard_00000", "doc_id": 169 }, "chunk_id": "train_shard_00000_169_0", "global_id": 189 }, { "text": "The adaptation of versatile multi-host pathogens to various hosts and various niches within hosts is often still poorly understood. The alternative Sigma factor B (SigB) is the master regulator of the general stress response of most gram-positive bacteria, which is a classic case of adaptive plasticity. In\n\nA single transcriptional regulator is crucial for the adaptation of", "token_count": 81, "char_count": 376, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:07.934068", "source": { "split": "train_shard_00000", "doc_id": 170 }, "chunk_id": "train_shard_00000_170_0", "global_id": 190 }, { "text": "Nanoplanktonic diatoms (2-20 μm) are a significant yet historically understudied component of marine ecosystems. We investigated three recently isolated nanoplanktonic diatoms from the Northwest Atlantic Ocean (NWA): Minidiscus spinulatus, Mediolabrus comicus, and Minidiscus trioculatus. Using Oxford Nanopore sequencing, we assembled and annotated their complete chloroplast and mitochondrial genomes. Pangenome analyses revealed that Minidiscus species consistently clustered more closely with select Thalassiosira species, whereas M. comicus formed a sister clade with Skeletonema. Circularized chloroplast genomes allowed us to characterize the full-length 16S ribosomal RNAs for each isolate, thereby leading to higher resolution of these taxa in preexisting 16S metabarcoding data. During our study, M. spinulatus was primarily restricted to the Bedford Basin. In contrast, both M. trioculatus and M. comicus had larger geographic ranges extending to the Labrador Sea, and in the case of M. comicus, to the Canadian Arctic Gateway. Weekly metabarcoding from the coastal Bedford Basin, N.S., Canada (2014-2022), revealed a seasonal succession of nanoplanktonic taxa, with Minidiscus trioculatus dominating in the early months, followed by M. comicus and M. spinulatus. Our results highlight the critical value of phytoplankton isolations and organelle genomics for expanding our understanding of the diversity and biogeography of nanoplanktonic diatoms.\n\nOrganellar Genomes of Three Globally Important Nanoplanktonic Diatoms Refine Their Taxon-Specific Distribution and Succession Patterns in the Northwest Atlantic.", "token_count": 449, "char_count": 1622, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6698, "quality_score": 0.8349, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:08.564333", "source": { "split": "train_shard_00000", "doc_id": 171 }, "chunk_id": "train_shard_00000_171_0", "global_id": 191 }, { "text": "Pseudomonas aeruginosa, recognized by the World Health Organization as a critical priority pathogen, exhibits significant genomic plasticity and a high potential for developing resistance to multiple antimicrobials. This study provides comprehensive genomic insights into colistin-resistant P. aeruginosa isolates obtained from cancer patients. Phenotypic assays were conducted to evaluate antibiotic susceptibility, biofilm formation, efflux pump activity, swarming motility, and pigment production. Whole genome sequencing of the collected isolates was performed using Oxford-Nanopore technology to examine sequence types, resistome profiles, virulence-associated genes, and mobile genetic elements. Our findings reveled that out of 52 isolates, 10 (19.2%) were resistant to colistin. Ceftolozane/tazobactam demonstrated full efficacy against 60% of colistin resistant P. aeruginosa isolates. Within this colistin resistant subset, high-risk clones ST308 and ST773 emerged as dominant, both harboring blaNDM-1 and exhibiting extensive resistance profiles, including resistance to colistin and, in some cases, ceftolozane/tazobactam. The first detection of ST1143 and ST1693 in Egypt carrying blaOXA-1028 and blaOXA-904, respectively was documented, neither of which had been previously reported in the country. The accessory genome, accounting for up to 34.6% of the total genome, highlights the remarkable genomic plasticity of P. aeruginosa, and its capacity for horizontal acquisition of resistance and virulence genes via mobile genetic elements, such as integrative and conjugative elements (ICEs). Virulome analysis revealed the presence of the exoU gene in high-risk clones, a marker closely linked to hypervirulence in infection models, whereas other sequence types were associated with less virulent factors, such as exoS. Despite phenotypic variability in biofilm formation, pigment production, and motility, the underlying genetic determinants of these traits were highly conserved. Mutational analysis revealed mutations in the regulatory system PhoPQ as the primary mechanism of colistin resistance, with no mcr genes detected", "token_count": 521, "char_count": 2141, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6855, "quality_score": 0.8428, "entities": { "genes": [ "ST1693", "ST1143", "ST308", "ST773" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:00:09.203671", "source": { "split": "train_shard_00000", "doc_id": 172 }, "chunk_id": "train_shard_00000_172_0", "global_id": 192 }, { "text": "In conclusion, the substantial genomic plasticity of P. aeruginosa, reflected by an extensive accessory genome facilitates horizontal gene transfer (HGT), and significantly influences antimicrobial resistance and virulence. Colistin resistance was predominantly mediated by chromosomal mutations. Virulome and resistome analyses underscores the high pathogenicity and resistance potential of high-risk clones ST773 and ST308. The detection of horizontally acquired elements, such as integrative and conjugative elements (ICEs) carrying resistance genes such as blaNDM-1, underscores their role in disseminating resistance determinants. These findings emphasize the need urgent for targeted antimicrobial stewardship and surveillance strategies within Egyptian healthcare settings.\n\nThe genomic configurations driving antimicrobial resistance and virulence in colistin resistant Pseudomonas aeruginosa from an Egyptian Tertiary Oncology Hospital.", "token_count": 216, "char_count": 945, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [ "ST308", "ST773" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:09.668706", "source": { "split": "train_shard_00000", "doc_id": 172 }, "chunk_id": "train_shard_00000_172_1", "global_id": 193 }, { "text": "Edwardsiella piscicida is a significant pathogen that poses a particular threat to Japanese flounder (Paralichthys olivaceus) aquaculture in Japan and other countries. The damage is caused by the pathogen's ability to evade host immune defences and establish intracellular infections, intensified by its genomic plasticity and capacity for horizontal gene transfer. To investigate evolutionary adaptations between one older (2019) and four recent (2023) E. piscicida strains from the same geographical locations, we performed comparative genomic analysis of five isolates using high-quality hybrid genome assemblies and compared them with 27 Edwardsiella reference genomes. Pangenome analysis identified distinct novel genomic islands (GIs) specific to the 2023 strains. These GIs (~100 kb in size) shared 85 gene clusters encoding multiple antibiotic resistance genes, phage defence systems, mobilisation genes, and mercury resistance. In addition, they encoded integrases, transposases, and conjugative transfer genes, suggesting they function as integrative and conjugative elements (ICEs), a type of mobile genetic element. Phenotypic characterisation showed the 2023 strains carrying novel GI increased antibiotic resistance, but no significant difference in virulence in Japanese flounder infection trials. These findings highlight the recent genomic diversification of E. piscicida in aquaculture and the importance of monitoring emerging GIs driving antibiotic resistance and environmental persistence.\n\nComparative Genomics of Edwardsiella piscicida in the Japanese Flounder (Paralichthys olivaceus): Discovery and Implications of a Novel Genomic Island.", "token_count": 393, "char_count": 1663, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:10.265049", "source": { "split": "train_shard_00000", "doc_id": 173 }, "chunk_id": "train_shard_00000_173_0", "global_id": 194 }, { "text": "Poly lactic acid (PLA) is one of the most promising bioplastics due to its interesting mechanical and physical properties, low carbon footprint, and biodegradability. PLA is produced from lactic acid (LA) that is either sourced from petrochemical industries or obtained through microbial fermentation using lactic acid bacteria, with the latter accounting for 90% of total LA production. While the bio-based production is more sustainable, it requires complex and expensive feedstocks and large amounts of neutralization agents for pH control during fermentation.\n\nMetabolic engineering and adaptive laboratory evolution of Kluyveromyces Marxianus for lactic acid production.", "token_count": 149, "char_count": 675, "word_count": 94, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:10.694205", "source": { "split": "train_shard_00000", "doc_id": 174 }, "chunk_id": "train_shard_00000_174_0", "global_id": 195 }, { "text": "This study investigated the preventive effects of fermented casein with Lactobacillus gasseri KML39 (FSC) on systemic inflammation through modulation of the gut-brain-microbiome axis in a dextran sulfate sodium (DSS)-induced colitis mouse model. Lactobacillus gasseri KML39 was selected based on its superior casein fermentation properties, proteolytic and antioxidant activities, and probiotic potential, including acid and bile tolerance and intestinal adhesion ability. We found that FSC significantly suppressed the expression of proinflammatory cytokines (COX-2, iNOS, TNF-α, IL-1β, and IL-6) and reduced nitric oxide (NO) production in LPS-stimulated RAW 264.7 cells. In DSS-induced colitis mice, BW loss, shortened colon length, and colonic tissue damage were observed compared with the control group. Dextran sulfate sodium also activated NF-κB signaling, leading to the upregulation of iNOS and COX-2 in both colonic and brain tissues, along with elevated serum TNF-α and corticosterone levels. Furthermore, DSS treatment compromised intestinal and blood-brain barrier integrity, as indicated by the downregulation of tight junction proteins (occludin and claudin-5). Additionally, DSS negatively regulated neurotransmitter receptors (NMDAR, GABAR, and D2DR) and neurodevelopmental markers (BAX and Bcl-2) in the brain, suggesting neuroinflammatory and neurodegenerative effects. The FSC pretreatment effectively restored tight junction integrity, attenuated neuroinflammation, and improved gut microbiota composition. Notably, Proteobacteria and Bacteroides were significantly enriched in the DSS-treated group, whereas their abundance was normalized by FSC pretreatment", "token_count": 468, "char_count": 1680, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7315, "quality_score": 0.8657, "entities": { "genes": [ "KML39" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:11.318936", "source": { "split": "train_shard_00000", "doc_id": 175 }, "chunk_id": "train_shard_00000_175_0", "global_id": 196 }, { "text": "These findings highlight systemic inflammation as a key driver of colitis-associated neuroinflammation and demonstrate the potential of FSC as a therapeutic agent for gut-brain-microbiome axis dysfunction in colitis.\n\nFermented casein with Lactobacillus gasseri KML39 alleviates systemic inflammation interacting with the gut-brain-microbiome axis in dextran sulfate sodium-induced colitis mice.", "token_count": 115, "char_count": 395, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [ "KML39" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:11.703256", "source": { "split": "train_shard_00000", "doc_id": 175 }, "chunk_id": "train_shard_00000_175_1", "global_id": 197 }, { "text": "Body weight is an important indicator of the overall health and production efficiency in broiler chickens. In broiler houses, body weight of chicks is variable despite the same genetics, hatching and feeding practices within a production system. The objective of this study was to investigate the intestinal microbiota and bile salt hydrolase (BSH) activity in slow and fast growing broiler chickens, which belonged to the 10\n\nIntestinal microbiota composition and bile salt hydrolase activity in fast and slow growing broiler chickens: implications for growth performance and production efficiency.", "token_count": 127, "char_count": 599, "word_count": 88, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:12.081505", "source": { "split": "train_shard_00000", "doc_id": 176 }, "chunk_id": "train_shard_00000_176_0", "global_id": 198 }, { "text": "Enterococcus faecium is a promising probiotic with potential antimicrobial effects. This study aimed to evaluate the probiotic and antimicrobial properties of E. faecium MBBL3, isolated from healthy cow milk, against bovine mastitis pathogens Klebsiella pneumoniae MBBL2 (Kp MBBL2) and Escherichia coli MBBL4 (Ec MBBL4), using comprehensive genomic and functional analyses. The genome assembly and functional annotations of MBBL3 unveiled many important probiotic traits, and comparative genomic analysis demonstrated its high degree of genetic similarity with other Enterococcus strains. MBBL3 exhibited the ability to ferment a diverse range of carbohydrates and possessed 76 genes linked to carbohydrate-active enzyme, including five key CAZy families with potential antimicrobial activity. Additionally, MBBL3 harbored genes essential for bile salt and acid tolerance, stress resistance, and surface adhesion. Furthermore, MBBL3 was found to harbor gene clusters encoding secondary metabolites with antimicrobial potentials. Safety evaluations revealed a low pathogenic potential, while in-vitro assays demonstrated antibiotic susceptibility and a reduction in the growth of Kp MBBL2 and Ec MBBL4, respectively. It's bacteriocin Enterolysin_A exhibited strong molecular interactions with virulence-associated proteins of the mastitis pathogens. Thus, the promising probiotic potential and antimicrobial activity of E. faecium MBBL3, particularly against mastitis-related pathogens coupled with its safety profile, render it a promising candidate for further investigation.\n\nProbiotic potential and antimicrobial efficacy of a dairy isolate, Enterococcus faecium MBBL3.", "token_count": 421, "char_count": 1672, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [ "MBBL2", "MBBL4", "MBBL3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:12.697335", "source": { "split": "train_shard_00000", "doc_id": 177 }, "chunk_id": "train_shard_00000_177_0", "global_id": 199 }, { "text": "Global climate change, particularly the increasing frequency and intensity of heat stress, poses a significant threat to crop productivity. Chickpea (Cicer arietinum L.) employs various physiological, biochemical, and molecular mechanisms to cope with elevated temperatures, including maintaining leaf chlorophyll content to preserve the functional integrity of photosystem II (PSII) and enhancing canopy temperature depression to reduce overheating. These traits are crucial for sustaining photosynthetic efficiency, plant health, and yield stability under heat stress. Recent advances in multi-omics approaches-including genomics, transcriptomics, proteomics, and metabolomics-have enhanced our understanding of the genetic basis of heat stress tolerance in chickpea. These tools have facilitated the identification of key genes and molecular pathways involved in heat stress responses. Functional characterization of these genes has provided insights into their roles within the complex metabolic and signaling networks that underpin heat resilience. This review explores integrating conventional and modern breeding technologies with high-throughput phenotyping (HTP) platforms to accelerate genetic gains in chickpea under heat stress. HTP tools enable rapid, precise screening of heat-resilient traits, facilitating early selection of superior genotypes. We also highlight recent genomic advancements, including genome-wide association studies, whole-genome resequencing, and pangenome assemblies, which have uncovered novel structural variants, candidate genes, and haplotypes associated with heat tolerance. Leveraging these resources in conjunction with functional analyses offers new opportunities for breeding climate-resilient chickpea cultivars capable of delivering stable yields and quality under adverse conditions. These developments are crucial for safeguarding chickpea productivity and ensuring global food and nutrition security amid climate change.\n\nChickpea (Cicer arietinum L.) battling against heat stress: plant breeding and genomics advances.", "token_count": 424, "char_count": 2069, "word_count": 259, "semantic_coherence": 1, "information_density": 0.7066, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:14.029348", "source": { "split": "train_shard_00000", "doc_id": 178 }, "chunk_id": "train_shard_00000_178_0", "global_id": 200 }, { "text": "Leaf thickness in rice critically influences photosynthetic efficiency and yield, yet its genetic basis remains poorly understood, with few functional genes previously characterized. In this study, we employ a pangenome-wide association study (Pan-GWAS) on 302 diverse rice accessions from southern China, identifying 49 quantitative trait loci (QTLs) associated with leaf thickness. The most significant locus, qLT9, is fine-mapped to a 79 kb region on chromosome 9. Transcriptomic and genomic sequence analyses identify LOC_Os09g33480, which encodes a protein belonging to Multiple Organellar RNA Editing Factor family, as the key candidate gene. Overexpression and complementation transgenic experiments confirm LOC_Os09g33480 (OsLT9) as the functional gene underlying qLT9, demonstrating a 24-bp Indel in its promoter correlates with the expression levels and leaf thickness. Notably, OsLT9 overexpression lines show not only thicker leaf, but also significantly enhanced photosynthetic efficiency and grain yield, establishing a link between leaf thickness modulation and yield enhancement. Population genomic analyses indicate strong selection for OsLT9 during domestication and breeding, with modern cultivars favoring thick leaf haplotype of OsLT9. This study establishes OsLT9 as a key regulator controlling leaf thickness in rice, and provides a valuable genetic resource for molecular breeding of high-yielding rice through optimization of plant architecture.\n\nFunctional characterization of OsLT9 in regulating rice leaf thickness.", "token_count": 361, "char_count": 1543, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7053, "quality_score": 0.8527, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:14.585925", "source": { "split": "train_shard_00000", "doc_id": 179 }, "chunk_id": "train_shard_00000_179_0", "global_id": 201 }, { "text": "Streptococcus infantarius, a lactic acid bacterium prevalent in Moroccan dairy products, holds significant probiotic and biotechnological potential, yet its genomic features remain poorly characterized. This study aims to provide a comprehensive genomic characterization of six S. infantarius isolates (B50-6, B50-7, B51-6, O53-2, T41-8, K85-8) from Moroccan farmhouse dairy products. Whole-genome sequencing and comparative analysis were conducted using advanced bioinformatics tools to assess their genetic diversity, functional attributes, adaptive mechanisms, probiotic properties, safety profile, and potential applications in food fermentation. All strains were confirmed as S. infantarius with average nucleotide identity (ANI) >98.2 % and digital DNA-DNA hybridization (dDDH) >85.9 %. Genomes sizes ranging from 1.81 (K85-8) to 1.91 (T41-8) Mb, with GC content ∼37.4 %. Functional profiling identified 1343, 1343, 1345, 1342, 1359 and 1345 proteins with functional assignments; 519, 521, 536, 520, 542 and 502 hypothetical proteins; and 1752, 1754, 1778, 1752, 1781 and 1740 proteins with COG (Clusters of Orthologous Groups) assignments, in B50-6, B50-7, B51-6, O53-2, T41-8 and K85-8, respectively. Gene enrichment analysis highlighted key metabolic pathways and functional categories relevant to dairy adaptation and biotechnological potential", "token_count": 452, "char_count": 1354, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7667, "quality_score": 0.8833, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:15.210685", "source": { "split": "train_shard_00000", "doc_id": 180 }, "chunk_id": "train_shard_00000_180_0", "global_id": 202 }, { "text": "The total number of genes encoding carbohydrate-active enzymes was 45 (B50-6), 45 (B50-7), 48 (B51-6), 45 (O53-2), 48 (T41-8) and 48 (K85-8). Safety assessments identified 13 (K85-8) to 16 (B51-6) virulence-associated genes per strain. However, no antimicrobial resistance genes or plasmids were detected, while the presence of CRISPR-Cas systems was detected in most strains. A total of 88 mobile genetic elements were identified ranging from 9 (B51-6) to 18 (O53-2) per strain. In addition, prophages were detected in all strains with the exception of T41-8 and K85-8. All Strains exhibited diverse biosynthetic gene clusters (BGCs), including RiPP-like, T3PKS and terpene precursor pathways. These findings position S. infantarius as a relatively stable core genome, metabolically versatile candidate for dairy fermentation, probiotic and biotechnological applications.\n\nComprehensive whole-genome analysis of Streptococcus infantarius strains from Moroccan farmhouse dairy products: Genomic insights into dairy adaptation, safety, and biotechnological potential.", "token_count": 336, "char_count": 1066, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7431, "quality_score": 0.8715, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:15.763780", "source": { "split": "train_shard_00000", "doc_id": 180 }, "chunk_id": "train_shard_00000_180_1", "global_id": 203 }, { "text": "Salmonellosis remains a globally prevalent zoonotic disease. Conventional antibiotic therapy for salmonellosis carries risks such as antimicrobial resistance and disruption of intestinal microbiota. Extensive research has demonstrated that probiotics, including lactic acid bacteria (LAB), can serve as an alternative to antibiotics. In view of the fact that host-origin probiotics possess superior functions, a canine-derived Lactiplantibacillus plantarum strain with efficacy against Salmonella was isolated, screened, and identified, and was named GHR. Biological characterization assays revealed that GHR possesses excellent acid tolerance, heat tolerance, and bile salt tolerance. Colonization assays demonstrated that GHR effectively colonizes the murine small intestine. By establishing GHR prophylactic and therapeutic mouse models of salmonellosis, followed by clinical symptom analysis, organ coefficient evaluation, and histopathological examination, we confirmed that GHR exhibits strong preventive effects against salmonellosis. This study successfully isolated and purified a canine-derived Lactiplantibacillus plantarum strain capable of effectively preventing murine salmonellosis, which provides a novel alternative approach for the prevention and treatment of salmonellosis in dogs and supports the broader application of canine-derived LAB with empirical data.\n\nIsolation and Identification of a Canine-Derived Lactic Acid Bacterium with Probiotic Potential for Salmonellosis Prevention and Treatment.", "token_count": 342, "char_count": 1520, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6862, "quality_score": 0.8431, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:16.324253", "source": { "split": "train_shard_00000", "doc_id": 181 }, "chunk_id": "train_shard_00000_181_0", "global_id": 204 }, { "text": "Kluyveromyces marxianus is an attractive chassis for microbial cell factories due to its rapid growth, thermotolerance, and wide substrate spectrum. However, gene disruption in this organism is challenging primarily due the prevalence of dominant nonhomologous recombination. AsCas12f1, a hypercompact CRISPR-associated protein consisting of 422 amino acids-approximately one-third the size of Cas9 or Cas12a-enables more efficient packaging into delivery vehicles than its larger counterparts. In this study, a gene disruption method using AsCas12f1 was established in K. marxianus through a transient targeting strategy. The integration of tRNA-gRNA into the gRNA construct increased gene disruption efficiency. Additionally, disrupting KmKU70 or KmLIG4 further increased this efficiency, achieving nearly 100%. By combining the disruption of KmKU70 with the AsCas12f1 system, the length of the homologous arm was shortened to 200 bp while maintaining a disruption efficiency of 87.5%. The implementation of the gRNA-tRNA-array system resulted in the successful generation of three single-gene knockout strains from a single transformation, resulting an overall efficiency of 86.4%. This approach leverages the transient transformation of fragments, eliminates the need for extensive time investment in constructing gRNA expression vectors and negates the requirement for the removal of the CRISPR-AsCas12f1 system after gene disruption. This study presents a novel strategy for gene disruption in K. marxianus and demonstrates the applicability of Cas12f in yeast systems.\n\nGene disruption via a transient hypercompact CRISPR-AsCas12f1 system in Kluyveromyces marxianus.", "token_count": 432, "char_count": 1673, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6283, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:16.938688", "source": { "split": "train_shard_00000", "doc_id": 182 }, "chunk_id": "train_shard_00000_182_0", "global_id": 205 }, { "text": "The role of mitochondrial dynamics in gastroesophageal reflux disease (GERD) remains unclear. We investigated how bile acid-induced mitochondrial dysfunction triggers mucosal inflammation and explored therapeutic targets.\n\nTargeting DRP1Ser637 Phosphorylation Alleviates Acidic Bile Salt-Induced NF-κB Activation via Mitochondrial Protection.", "token_count": 101, "char_count": 342, "word_count": 38, "semantic_coherence": 1, "information_density": 0.9211, "quality_score": 0.9605, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:17.318020", "source": { "split": "train_shard_00000", "doc_id": 183 }, "chunk_id": "train_shard_00000_183_0", "global_id": 206 }, { "text": "Antimicrobial resistance is increasingly recognized as one of the most significant global health threats, with profound implications for human, animal, and environmental health. Genome analysis represents a very useful tool that provides accurate and reproducible results allowing for the advancement of knowledge regarding antimicrobial resistance diagnosis, therapeutics, surveillance, transmission, and evolution. However, due to increasing complexity of bacterial genome analysis and computational power required for genomic approaches, there is a continuous need for comprehensive, user-friendly tools for data analysis. We developed Pangenome and Genomic Analysis Suite (PeGAS), to address some of these challenges by offering an all-in-one pipeline that performs a range of analyses.\n\nPeGAS: a versatile bioinformatics pipeline for antimicrobial resistance, virulence and pangenome analysis.", "token_count": 182, "char_count": 898, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7328, "quality_score": 0.8664, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:17.762503", "source": { "split": "train_shard_00000", "doc_id": 184 }, "chunk_id": "train_shard_00000_184_0", "global_id": 207 }, { "text": "Grain legumes hold great promise for advancing sustainable agriculture. Although the evolutionary history of legume species has been investigated, the conserved mechanisms that drive adaptive evolution and govern agronomic improvement remain elusive. Here we present high-quality genome assemblies for nine widely consumed pulses, including common bean, chickpea, pea, lentil, faba bean, pigeon pea, cowpea, mung bean and hyacinth bean. Pangenome analysis reveals the expansion of distinct gene sets in cool-season and warm-season legumes, highlighting the role of gene birth and duplication in the autoregulation of nodulation. Notably, hundreds of genes undergo convergent selection during the evolution of legumes, affecting agronomic traits such as seed weight. In addition, we demonstrate that tandem amplification of transposable elements in gene-depleted regions has a crucial role in driving genome enlargement and the formation of regulatory elements in cool-season legumes. Our results provide insights into the molecular mechanisms underlying the diversification of legumes and represent a valuable resource for facilitating legume breeding.\n\nPangenome analysis provides insights into legume evolution and breeding.", "token_count": 260, "char_count": 1226, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6807, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:18.327915", "source": { "split": "train_shard_00000", "doc_id": 185 }, "chunk_id": "train_shard_00000_185_0", "global_id": 208 }, { "text": "The field of comparative genomics is shifting toward pangenomics, aiming to alleviate the reference bias observed in reference-based approaches. High-quality genomes are needed as input for pangenomics, as explained by the principle of \"garbage in, garbage out\". Errors in an assembly or annotation will lead to technical variation in a pangenome, while it is meant to reveal genuine biological variation only. Achieving the required assembly and annotation quality remains challenging, particularly in plants, given the complexity in genome size, ploidy level, and repeat content present in the plant kingdom.Nevertheless, the (technical) variation uncovered by pangenomics can, in turn, guide iterative refinements that yield high-quality genomes. The comparative approach is especially powerful to identify \"abnormalities\" in a set of genomes, which cannot be detected from traditional, stand-alone quality assessment. Two use cases, on roses and chili peppers, illustrate the role of pangenomics in this iterative process leading toward meaningful pangenome analyses. Thus, we argue that high-quality genomes can be achieved through pangenomics, facilitating the convergence on real genetic variation underlying complex traits and diseases, not only in plants but also in other organisms.\n\nHigh-Quality Plant Genomes for and through Pangenomics.", "token_count": 296, "char_count": 1349, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6984, "quality_score": 0.8492, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:18.917815", "source": { "split": "train_shard_00000", "doc_id": 186 }, "chunk_id": "train_shard_00000_186_0", "global_id": 209 }, { "text": "Compared with the long history of research on Bacteria and Eukaryotes, Archaea are a young domain of study for life sciences. Before sequencing technologies, the scientific community primarily understood Archaea to be limited to extreme environments. However, it is now recognized that Archaea occupy a broad diversity of environments, including soil and marine habitats, where they play essential geochemical roles, as well as being animal and plant symbionts. Due to their late recognition as a new domain, the study of archaeal evolution has been delayed relative to Bacteria. Recent progress in high-throughput sequencing technologies has improved the accessibility of genomic data to broader phylogenetic breadths, including uncultivated clades. Here, we provide a step-by-step computational pipeline to estimate the ratio of nonsynonymous to synonymous substitution rates (dN/dS), a measure of the strength and direction of selection on protein-coding genes. We focus our chapter on the estimation of dN/dS to disentangle the evolutionary forces acting on the core genome of archaeal genomes, but this workflow is also applicable to Bacteria. Importantly, we present an overview of the biases to consider when estimating dN/dS, as well as potential strategies to circumvent technical limitations. We describe a case example of the use of dN/dS to explore differences in the evolutionary constraints acting on different archaeal species belonging to the genus Methanosarcina. We provide custom Python scripts, which are freely available and applicable to a broad diversity of questions on the evolution of Archaea.\n\nApplying the Classic Test dN/dS to Detect Selection in Archaea.", "token_count": 373, "char_count": 1684, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:19.512695", "source": { "split": "train_shard_00000", "doc_id": 187 }, "chunk_id": "train_shard_00000_187_0", "global_id": 210 }, { "text": "This study evaluated the probiotic characteristics of Lactiplantibacillus plantarum strains, revealing strong acid and bile salt tolerance and significant adhesion to HT-29 cells. In addition, the anti-melanogenic and antioxidant properties of their cell-free supernatants (CFS) were investigated in vitro. Melanogenesis assays were performed in α-melanocyte-stimulating hormone (α-MSH)-stimulated B16F10 melanoma cells, while antioxidant activity was evaluated in H\n\nAnti-melanogenic and Antioxidant Activities of Lactiplantibacillus plantarum Strains in Skin Cells via the CREB/MITF and Nrf2/HO-1 Pathways.", "token_count": 186, "char_count": 608, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:20.002346", "source": { "split": "train_shard_00000", "doc_id": 188 }, "chunk_id": "train_shard_00000_188_0", "global_id": 211 }, { "text": "The present study investigated the effect of rice protein (RP) on plasma cholesterol clearance by administering diets containing either casein or RP to growing and adult male Wistar rats over a two-week period. RP intake markedly upregulated the gene and protein expression of key regulators involved in cholesterol transport and metabolism, including ATP-binding cassette transporter G1 (ABCG1), scavenger receptor class B type I (SR-BI), ABCG5, bile salt export pump (BSEP), coactivator-associated arginine methyltransferase 1 (CARM1), and farnesoid X receptor (FXR), in both age groups. These findings indicate that RP effectively promotes cholesterol and bile acid excretion. Consequently, RP significantly reduced cholesterol concentrations in both plasma and liver (\n\nAge-Independent Hypocholesterolemic Effects of Rice Protein via FXR-Mediated Stimulation of Cholesterol Elimination.", "token_count": 241, "char_count": 890, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7833, "quality_score": 0.8917, "entities": { "genes": [ "CARM1", "ABCG1", "ABCG5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:20.482433", "source": { "split": "train_shard_00000", "doc_id": 189 }, "chunk_id": "train_shard_00000_189_0", "global_id": 212 }, { "text": "Polysaccharide-based Pickering stabilizers have been increasingly studied due to their promising potential in developing \"clean label\" emulsions. In this study, we isolated a novel type of polysaccharide particle, chitin-glucan nanofibrils (CGNFs), from I. hispidus mycelium using a combined process of mild solvent extraction and cyclic low-energy disassembly. The CGNFs are of high chitin to glucan molar ratio (1.1,1), high charge (∼ - 35 mV, which stems from carboxyl generated through H₂O₂ oxidation) and high aspect ratio (∼51). They exhibited good amphiphilicity and excellent emulsification performance, producing stable Pickering emulsions with fine oil droplets (∼8.90 μm) at 0.8 wt%. Under in vitro digestion, the emulsion was digested at a slower rate compared to the oil-water mixture without CGNFs, suggesting that CGNFs are capable of retarding lipid digestion. Cryo-SEM analysis of emulsion structure evolution revealed possible mechanism of CGNF interference in lipid digestion, including mild aggregation and fusion of oil droplets to reduce contact surface, formation of a CGNF physical barrier limiting lipase access, and inhibition of bile salt displacement. Our current study implicates that I. hispidus CGNFs could be applied as a functional ingredient not only for constructing emulsified food systems but also for offering additional health benefits in weight control.\n\nChitin-glucan nanofibrils from Inonotus hispidus mycelium as Pickering emulsion stabilizers and lipid digestion regulators.", "token_count": 396, "char_count": 1518, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7383, "quality_score": 0.8692, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:21.083798", "source": { "split": "train_shard_00000", "doc_id": 190 }, "chunk_id": "train_shard_00000_190_0", "global_id": 213 }, { "text": "With the increasing severity of bacterial drug resistance, there is a growing need for phages with well-defined genetic backgrounds to combat drug-resistant infections. Mycobacteriophages constitute the largest genome-sequenced phage group; however, the vast majority of these phage proteins have not yet been effectively annotated. In this study, we employed a structure-based similarity search approach to improve protein annotation. Through the application of this approach to 240,754 proteins from 2,169 mycobacteriophage genomes, we increased the protein annotation rate from 34% to 52.11%. Additionally, we identified a series of predicted counter-defense proteins, including anti-CRISPR proteins and antitoxins, and inferred the potential interaction network of phage-encoded proteins involved in replication, transcription, and translation with host-associated molecular machinery. This study addresses a substantial gap in the current knowledge of the potential function of phage proteins and provides key insights into the interactions between mycobacteriophages and their hosts.IMPORTANCEMycobacteriophages constitute the largest group of phages with sequenced genomes. However, a significant portion of these phage proteins have not yet been effectively annotated, seriously hindering our understanding of the basic biological processes of phage-host interactions and their practical applications. This study utilized a structure-based similarity search approach to enhance phage protein annotation. This approach led to the identification of novel predicted protein folds, structural domain fusion phenomena, and putative new enzymes. Additionally, the study identified a series of phage-encoded proteins that may play a role in hijacking host-associated replication, transcription, and translation processes, providing insights into the molecular mechanisms underlying mycobacteriophage interactions with host machinery. This study addresses a critical knowledge gap regarding the potential function of phage proteins and provides key insights into the interactions between mycobacteriophages and their hosts.\n\nPangenome-scale annotation of mycobacteriophages for dissecting phage-host interactions based on a sequence clustering and structural homology analysis strategy.", "token_count": 488, "char_count": 2286, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5171, "quality_score": 0.7586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:21.718733", "source": { "split": "train_shard_00000", "doc_id": 191 }, "chunk_id": "train_shard_00000_191_0", "global_id": 214 }, { "text": "The highly repetitive content of eukaryotic genomes, including long tandem repeats, segmental duplications, and centromeres, makes haplotype-resolved genome assembly hard. Repeat sequences introduce gaps or mis-joins in the assemblies. We introduce TRFill, a novel algorithm that can close the gaps in a draft chromosome-level assembly using exclusively PacBio HiFi and Hi-C data. Experimental results on human centromeres and tomato subtelomeres show that TRFill can improve the completeness and correctness of about two-thirds of the tandem repeats. We also show that the improved completeness of subtelomeric tandem repeats in the tomato pangenome enables a population-level analysis of these complex repeats.\n\nTRFill: synergistic use of HiFi and Hi-C sequencing enables accurate assembly of tandem repeats for population-level analysis.", "token_count": 203, "char_count": 840, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:22.178522", "source": { "split": "train_shard_00000", "doc_id": 192 }, "chunk_id": "train_shard_00000_192_0", "global_id": 215 }, { "text": "Comparisons of complete genome assemblies offer a direct procedure for characterizing all genetic differences among them. However, existing tools are often limited to specific aligners or optimized for specific organisms, narrowing their applicability, particularly for large and repetitive plant genomes. Here, we introduce Structural Variants Genotyping of Assemblies on Population scales (SVGAP), a pipeline for structural variant (SV) discovery, genotyping, and annotation from high-quality genome assemblies at the population level. Through extensive benchmarks using simulated SV datasets at individual, population, and phylogenetic contexts, we demonstrate that SVGAP performs favorably relative to existing tools in SV discovery. Additionally, SVGAP is one of the few tools to address the challenge of genotyping SVs within large assembled genome samples, and it generates fully genotyped VCF files. Applying SVGAP to 26 maize genomes revealed hidden genomic diversity in centromeres, driven by abundant insertions of centromere-specific LTR-retrotransposons. The output of SVGAP is well-suited for pangenome construction and facilitates the interpretation of previously unexplored genomic regions.\n\nAccurate, Scalable Structural Variant Genotyping in Complex Genomes at Population Scales.", "token_count": 297, "char_count": 1297, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7076, "quality_score": 0.8538, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:22.728947", "source": { "split": "train_shard_00000", "doc_id": 193 }, "chunk_id": "train_shard_00000_193_0", "global_id": 216 }, { "text": "The prokaryotic pangenome, the full complement of genes within a species, is strikingly large. To understand how ecological forces shape this diversity, it is useful to examine the variable gene pool within a single population, defined as cells of the same species coexisting in the same time and place. This single-population pangenome reflects the minimal flexible gene repertoire required in a specific environmental context. Recent long-read metagenomic studies of marine prokaryotes show that local population pangenomes remain large, often comprising thousands of genes. Specifically, cells belonging to the same species of the streamlined alfaproteobacterium Pelagibacter, coming from the same sampling site and even sample, contain more than a thousand genes. Many of these genes are related variants that collectively expand the population's metabolic potential, akin to paralogs within a single large genome. We propose for them the name 'metaparalogs' together with the idea that these data reflect cooperative, population-level strategies, where the flexible genome operates as a public good (sensu Samuelson), enhancing both adaptability and ecological resilience. A role for extracellular vesicles in facilitating resource sharing is also suggested.\n\nOn the biological meaning of the population pangenome.", "token_count": 285, "char_count": 1319, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:23.279947", "source": { "split": "train_shard_00000", "doc_id": 194 }, "chunk_id": "train_shard_00000_194_0", "global_id": 217 }, { "text": "Abiotic and biotic stresses increasingly threaten plant health and productivity, causing substantial yield losses in vital crops. In this study, 99 rhizobacteria isolated from Moroccan olive rhizospheres, OM-41 was selected as the most potent strain, exhibiting exceptional drought tolerance (thriving at Aw 0.859), thermotolerance (up to 55 °C), and halotolerance (15% NaCl), alongside plant growth-promoting (PGP) traits such as phosphate solubilization, indole-acetic acid (IAA), gibberellic acid, siderophore production, and hydrolytic enzyme secretion. The strain suppressed V. dahliae via diffusible and volatile antifungal compounds, achieving 76% and 69% inhibition rates, respectively. Whole-genome sequencing revealed a 4.2 Mbp genome (43.5% GC content) with 4362 protein-coding genes. Phylogenetic analyses confirmed its classification as B. halotolerans. Genomic annotation identified 11 secondary metabolite clusters and stress-related genes, including those linked to phosphate solubilization (phy, pho, pst family), IAA synthesis (dhaS, trp operon), siderophores (dhb cluster), nitrogen fixation (nif, suf, urt genes), ammonia production (gudB, nasD/E), biofilm formation (tasA, bsl genes), antifungal volatiles (alsD, ilv operon), hydrolytic enzymes (e.g., amyE, eglS), and vitamin biosynthesis (thiamine/riboflavin operons). Pangenome analysis of 79 B. halotolerans strains highlighted an open pangenome with 12,679 total genes (2270 core, 2382 accessory and 8027 unique); OM-41 harbored 98 unique genes", "token_count": 483, "char_count": 1520, "word_count": 197, "semantic_coherence": 1, "information_density": 0.8782, "quality_score": 0.9391, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:23.915547", "source": { "split": "train_shard_00000", "doc_id": 195 }, "chunk_id": "train_shard_00000_195_0", "global_id": 218 }, { "text": "These findings underscore potential of OM-41 as a biofertilizer and biocontrol agent, leveraging antibiosis, resource competition, and plant defense induction to mitigate pathogens and abiotic stresses. Up to our knowledge, this is the first work that evaluates the pangenome features of B. halotolerans, offering insights into its genomic plasticity and adaptive traits. The strain's multifunctional PGP capabilities and stress resilience position it as a promising solution for sustainable agriculture in challenging environments.\n\nComprehensive genomic and pan-genomic analysis of the drought-tolerant Bacillus halotolerans strain OM-41 isolated from Olive rhizosphere, reveals potential plant growth-promoting and biocontrol traits.", "token_count": 178, "char_count": 736, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:24.356121", "source": { "split": "train_shard_00000", "doc_id": 195 }, "chunk_id": "train_shard_00000_195_1", "global_id": 219 }, { "text": "The gastrointestinal tract of native animals represents a valuable reservoir of probiotic candidates. In this study, yeast strains were isolated from the feces of healthy native pigs raised in southern Thailand and evaluated for probiotic potential, safety, and extracellular enzyme production in vitro. The most promising isolate, Saccharomyces cerevisiae YH14, was selected for in vivo evaluation in a murine model. YH14 exhibited robust growth at 37 °C and demonstrated high tolerance to acidic (127.38%) and bile salt (139.94%) conditions. The strain showed strong auto-aggregation (90.09%), cell surface hydrophobicity (59.21%), and notable adhesion to Caco-2 cells (43.18%). Co-aggregation with enteric pathogens-including enterohemorrhagic E. coli (55.37%), enteropathogenic E. coli (57.91%), and Salmonella Typhimurium (56.62%)-was observed at intermediate levels. YH14 was nonhemolytic and produced beneficial feed enzymes, including xylanase and phytase. In vivo, administration of YH14 induced no mortality, behavioral changes, or adverse effects on feed intake and body weight gain. Histological examination revealed preserved tissue architecture in the intestine, liver, and spleen, with no signs of inflammation. Moreover, YH14 modulated the gut microbiota by promoting beneficial bacterial populations and suppressing potential pathogens, without significantly altering overall microbiome diversity. These findings support the potential application of S. cerevisiae YH14 as a probiotic feed additive for improving gut health and digestive efficiency in livestock.\n\nSuperior Probiotic Potential of Saccharomyces cerevisiae YH14: In Vitro and In Vivo Evaluation for Animal Nutrition and Health.", "token_count": 462, "char_count": 1707, "word_count": 228, "semantic_coherence": 1, "information_density": 0.7149, "quality_score": 0.8575, "entities": { "genes": [ "YH14" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:24.981730", "source": { "split": "train_shard_00000", "doc_id": 196 }, "chunk_id": "train_shard_00000_196_0", "global_id": 220 }, { "text": "Yeast is a promising source of alternative protein, but the low functionality limits the application of yeast protein in food industry. This paper demonstrated pH-shifting assisted ultrasonication treatment could significantly enhance the solubility of yeast protein from Kluyveromyces marxianus, with protein recovery rate increased from 7.32 % to 81.59 % at pH 12, 900 W for 120 min (pH 12-U900), and with the significant occurrence of higher-molecular-weight yeast proteins as witnessed by SDS-PAGE and SEC. The subsequent acid precipitation resulted in yeast protein with high protein content, increased hydrophobicity and higher disulfide bonds content. pH-shifting assisted ultrasonication increased the relative abundance of 60S/40S ribosomal protein, glycolytic enzymes and elongation factor revealed by proteomic analysis; and significantly improved protein functionality including higher solubility, emulsifying activity, foaming capacity, and superior oil holding capacity. Moreover, the prepared yeast protein was found to be rich in essential amino acids and had a high in vitro gastrointestinal digestibility. Peptidomics characterization further suggested the abundant proteins in yeast could release potentially bioactive peptides, especially with better ACE inhibitory activity (IC\n\nEnhancing structure, functionality, in vitro digestibility and bioactivity of yeast protein by pH-shifting assisted ultrasonication treatment.", "token_count": 351, "char_count": 1442, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6684, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:25.538222", "source": { "split": "train_shard_00000", "doc_id": 197 }, "chunk_id": "train_shard_00000_197_0", "global_id": 221 }, { "text": "Pangenomes provide a robust and comprehensive portrayal of genetic diversity in humans, but Arab populations remain underrepresented. We present a preliminary UAE-based Arab Pangenome Reference (UPR) utilizing 53 individuals of diverse Arab ethnicities residing in the United Arab Emirates. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads. This approach yielded contiguous haplotype-phased de novo assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of previously uncharacterized euchromatic sequences absent from existing human pangenomes, the T2T-CHM13 and GRCh38 reference human genomes, and other public datasets. Moreover, we identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome, not present in linear and pangenome references and public datasets. We detected 883 gene duplications, including the TATA-binding protein gene TAF11L5, which was uniquely duplicated across all Arab populations and that included 15.06% of genes associated with recessive diseases. By exploring the mitochondrial pangenome, we identified 1,436 bp of previously unreported sequences. Our study provides a valuable resource for future genetic research and genomic medicine initiatives in Arab population and other population with similar genetic backgrounds.\n\nA draft UAE-based Arab pangenome reference.", "token_count": 387, "char_count": 1491, "word_count": 200, "semantic_coherence": 1, "information_density": 0.695, "quality_score": 0.8475, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:26.134633", "source": { "split": "train_shard_00000", "doc_id": 198 }, "chunk_id": "train_shard_00000_198_0", "global_id": 222 }, { "text": "Paediatric drug development poses significant challenges due to the unique physiological and ethical considerations in children. Physiologically Based Pharmacokinetic (PBPK) modelling has emerged as a valuable tool for predicting paediatric drug absorption and optimising dosing strategies. This study aimed to refine PBPK modelling for paediatric applications by developing a customised PK-Sim-based paediatric PBPK (pPBPK) model for four drugs that are part of the Model List of Essential Medicines for Children by the World Health Organisation: paracetamol, ibuprofen, darunavir, and itraconazole. The model incorporated age-specific gastrointestinal parameters for four paediatric age groups, minimising the need for parameter interpolation or scaling. The effect of food on drug absorption was investigated by extending the absorption model to account for bile and excipient solubilisation. A literature review identified gaps in the understanding of paediatric intestinal parameters necessary for pPBPK modelling. Biorelevant in vitro dissolution and solubility data were integrated to enhance prediction accuracy. Validation with clinical pharmacokinetic data demonstrated the model's reliability across different paediatric age groups. Sensitivity analyses highlighted the influence of gastric emptying time, small intestinal transit, and bile salt concentration on drug pharmacokinetics. This research underscores the potential of pPBPK modelling to inform paediatric dosing strategies while addressing current gaps and challenges.\n\nAge-dependent oral drug absorption in children: Assessment of a bottom-up modelling approach.", "token_count": 371, "char_count": 1635, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6526, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:26.703545", "source": { "split": "train_shard_00000", "doc_id": 199 }, "chunk_id": "train_shard_00000_199_0", "global_id": 223 }, { "text": "Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (median continuity of 130 Mb), closing 92% of all previous assembly gaps\n\nComplex genetic variation in nearly complete human genomes.", "token_count": 90, "char_count": 368, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:27.075688", "source": { "split": "train_shard_00000", "doc_id": 200 }, "chunk_id": "train_shard_00000_200_0", "global_id": 224 }, { "text": "Mycobacterium abscessus (Mab) is a multidrug-resistant bacterial pathogen capable of causing widespread infections, often with a poor prognosis in susceptible populations. Mab comprises three distinct subspecies that exhibit phenotypic diversity and genetic heterogeneity.\n\nWhole-genome recombination and dynamic accessory genomes drive the phenotypic diversity of Mycobacterium abscessus subspecies.", "token_count": 103, "char_count": 400, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:27.837495", "source": { "split": "train_shard_00000", "doc_id": 201 }, "chunk_id": "train_shard_00000_201_0", "global_id": 225 }, { "text": "Understanding how a sleeve gastrectomy (SG) achieves metabolic improvement is challenging due to the complex relationship between the liver, bile acid (BA) pool, and gut microbiome. We hypothesized that SG alters the gut microbiome, which then increases the BA pool, leading to metabolic efficacy. We performed fecal material transfer (FMT) from SG or sham mice to surgically naïve mice with an intact microbiome. We evaluated the effect of surgery and FMT on BA-related liver enzymes, BA concentrations, and gut microbiome composition via 16S and metagenomic analysis. SG significantly deflected weight gain compared with sham surgery, 5 ± 2 g versus 10 ± 3 g, respectively (\n\nGut microbiome and bile acid changes after male rodent sleeve gastrectomy: what comes first?", "token_count": 210, "char_count": 770, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7583, "quality_score": 0.8792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:28.297101", "source": { "split": "train_shard_00000", "doc_id": 202 }, "chunk_id": "train_shard_00000_202_0", "global_id": 226 }, { "text": "White-nose syndrome, caused by the psychrophilic fungus Pseudogymnoascus destructans, has devastated bat populations across North America. Streptomyces albidoflavus SM254 was previously reported to exhibit antifungal activity against this pathogen, but no comprehensive genomic characterization has been performed to date. Here, we analyzed 34 S. albidoflavus genomes, including the antifungal strain SM254 and 33 publicly available references, to investigate its metabolic potential and functional distinctiveness. Using pangenome reconstruction, phylogenomics, average nucleotide identity, and KEGG pathway profiling, we found that S. albidoflavus SM254 shares high nucleotide identity (> 99%) with five closely related strains but displays a unique combination of complete ethanol fermentation capacity and asparagine biosynthesis deficiency. These traits were exclusive to SM254 and may reflect adaptation to the oxygen-limited, nutrient-variable sediment environment. Functional annotation further revealed high completeness in central energy, redox, and stress-response pathways. Although direct antifungal mechanisms remain to be experimentally validated, S. albidoflavus SM254's unique metabolic profile and ecological specialization suggest potential relevance in biocontrol contexts.\n\nGenomic insights into Streptomyces albidoflavus SM254: tracing the putative signs of anti-Pseudogymnoascus destructans properties.", "token_count": 353, "char_count": 1425, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7803, "quality_score": 0.8902, "entities": { "genes": [ "SM254" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:28.865450", "source": { "split": "train_shard_00000", "doc_id": 203 }, "chunk_id": "train_shard_00000_203_0", "global_id": 227 }, { "text": "Excess heavy metals can be toxic to plants and microbes. The application of plant growth promoting bacteria (PGPB) in agriculture has gained global attention for promising sustainable development, including in heavy metals polluted soil. However, the metal resistance and plant growth promoting determinants of strains belonging to the genus Acinetobacter remain poorly understood. Here, we characterize strain SC22, and analyzed the complete genome of strain SC22. The influence of inoculating with this strain on soybean growth by pot experiment was also analyzed. Our results showed that strain SC22 displayed high As(III) and Cu(II) resistance and high IAA production. The presence of operons such as, merRACDT, zntA and 4 znuABC, czcABCD and arsRBCH, and trpRABCDFS encode functions enabling strain SC22 to survive under extremely highly heavy metal contaminated environments and also produce plant hormones. The inoculation of strain SC22 stimulated soybean growth. Strains belonging to the genus Acinetobacter have an open pan-genome, and ArsH encoded on the core genome displayed differences to ArsH encoded on the genome of other Acinetobacter that were isolated from different habitats. These findings suggest the potential use of strain Acinetobacter junii SC22 in bioremediation and subsequent plant growth promotion in heavy metal polluted environments.\n\nIsolation and pan-genome analysis of Acinetobacter junii SC22, a heavy metal(loid)s resistant and plant growth promoting bacterium, from the Zijin Gold and Copper mine.", "token_count": 360, "char_count": 1536, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [ "SC22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:29.437106", "source": { "split": "train_shard_00000", "doc_id": 204 }, "chunk_id": "train_shard_00000_204_0", "global_id": 228 }, { "text": "The increasing use of antibiotics in shrimp aquaculture has raised concerns regarding ecological safety and the emergence of antibiotic resistance. This study aimed to isolate and characterize probiotic lactic acid bacteria (LAB) strains from the gut of Penaeus vannamei to evaluate their potential as antibiotic alternatives in aquaculture. Two strains, S1 and S2, were identified with 99.79 and 99.51% similarity to Pediococcus acidilactici DSM 20284 and Enterococcus lactis BT159, respectively. Based on minimum inhibitory concentration (MIC) assays, both strains exhibited high sensitivity to the tested antibiotics. They also demonstrated notable acid and bile salt tolerance, with S1 maintaining a survival rate of 30% at pH 5 and S2 achieving 40% survival at pH 6. Under 0.03% bile salt concentration, survival rates were approximately 60% (S1) and 45% (S2), while S1 retained 15% viability even at 0.9% bile salt. Enzymatic activity analysis indicated that both strains exhibited lower amylase activity compared to other hydrolytic enzymes, with S2 showing higher cellulase and protease activities than S1. Antimicrobial assays revealed that both strains exerted broad-spectrum inhibition against four indicator pathogens. S1 exhibited the strongest inhibitory effect against Aeromonas hydrophila (inhibition zone: 1.6-2.2 cm), whereas S2 showed the highest inhibition against Vibrio parahaemolyticus (1.5-2.4 cm). Feeding trials demonstrated that the combined application of S1 and S2 significantly enhanced shrimp body weight (6.05 ± 0.09 g vs. 9.23 ± 0.2 g, P < 0.01) and survival rate (62.49% ± 1.56 vs", "token_count": 492, "char_count": 1614, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [ "BT159" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:30.072071", "source": { "split": "train_shard_00000", "doc_id": 205 }, "chunk_id": "train_shard_00000_205_0", "global_id": 229 }, { "text": "93.78% ± 2.55, P < 0.01). These findings highlight the potential of Lactobacillus strains as probiotics in shrimp farming, offering a sustainable approach to reducing antibiotic dependency and improving shrimp health and productivity.\n\nScreening of Antibiotic-Sensitive Lactic Acid Bacteria (LAB) Associated with the Gut of Penaeus Vannamei and its Application in Shrimp Farming.", "token_count": 123, "char_count": 379, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8491, "quality_score": 0.9245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:30.501364", "source": { "split": "train_shard_00000", "doc_id": 205 }, "chunk_id": "train_shard_00000_205_1", "global_id": 230 }, { "text": "Despite rigorous safety evaluations during development, numerous drugs have been withdrawn from the market due to serious toxicities. Here we investigate the features found in drugs with these unanticipated toxicities and apply a machine learning approach to predict if a drug is likely to be withdrawn due to intolerable side effects without the need for human trial data. Our best preforming classifier was an ensemble predictor trained on protein targets, protein structure features, chemical fingerprints, and chemical features that achieved 92% accuracy and 0.845 Matthews Correlation Coefficient with 10-fold holdout test set cross validation. Analysis of features predictive of unanticipated toxicity revealed both known factors such as inhibition of cytochrome P450 as well as yet uninvestigated factors including the inhibition of bile salt export pumps. This predictor and subsequent feature analysis pave the way for the larger role of computational methods in screening potential candidates during drug development.\n\nCapturing Unanticipated Drug Toxicities Using an Ensemble Machine Learning Approach.", "token_count": 232, "char_count": 1113, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7342, "quality_score": 0.8671, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:30.988700", "source": { "split": "train_shard_00000", "doc_id": 206 }, "chunk_id": "train_shard_00000_206_0", "global_id": 231 }, { "text": "The limitations of both inorganic and organic selenium sources, such as low bioavailability and potential toxicity, have driven research towards selenium nanoparticles (SeNPs). In this study, β-glucan was extracted from the cell wall of Kluyveromyces marxianus M59 and subsequently carboxymethylated to enhance its water solubility. Carboxymethylated β-glucan was then utilized for the synthesis of selenium nanoparticles (SeNPs), and their sizes were determined using Scanning Electron Microscopy (SEM) analysis. To reduce the size of larger nanoparticles, Cold Atmospheric Plasma (CAP) treatment was applied, resulting in an approximately 82.4% decrease in particle size. The SeNPs obtained ranged in size from 180 to 83 nm. The synthesized SeNPs were characterized using UV-Vis Spectrophotometry, Fourier-Transform Infrared Spectroscopy (FTIR), and X-ray Diffraction (XRD) analysis. The absorption peak of SeNPs was detected at 330 nm, further confirming their amorphous nature. Additionally, the biological activities of SeNPs, including their antimicrobial, antibiofilm, and antioxidant properties, were investigated. When the antibiofilm activity of SeNPs was evaluated, the highest inhibition rate (43.6 ± 0.1%) was observed at a concentration of 5 mg/mL. In contrast, regarding antimicrobial activity, SeNPs exhibited limited inhibition zones at low concentrations, with a maximum inhibition diameter of 1.20 mm recorded. Antioxidant activity was evaluated through 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical scavenging, superoxide anion scavenging, and hydroxyl radical scavenging assays. The highest antioxidant activity was determined at 5 mg/mL SeNP concentration (47.7%) at DPPH method. The cytotoxic effects of SeNPs were evaluated on both healthy (L929) and lung cancer (A549) cell lines. The IC", "token_count": 521, "char_count": 1811, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:00:31.667151", "source": { "split": "train_shard_00000", "doc_id": 207 }, "chunk_id": "train_shard_00000_207_0", "global_id": 232 }, { "text": "Size reduction of selenium nanoparticles synthesized from yeast beta glucan using cold atmospheric plasma.", "token_count": 27, "char_count": 106, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:32.063749", "source": { "split": "train_shard_00000", "doc_id": 207 }, "chunk_id": "train_shard_00000_207_1", "global_id": 233 }, { "text": "Genetic introgression from Neanderthals and Denisovan has shaped modern human genomes; however, introgressed structural variants (SVs ≥50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) genomes with 94 published assemblies of diverse ancestry to infer an archaic introgressed SV map. Introgressed SVs are overall enriched in genes (44%, n=1,592), including critical genomic disorder regions, and most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping across 1,363 samples reveals 16 candidate adaptive SVs, many associated with immune-related genes and their expression, in the PNG. We hypothesize that archaic SV introgression contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution.\n\nA global map for introgressed structural variation and selection in humans.", "token_count": 255, "char_count": 1003, "word_count": 136, "semantic_coherence": 1, "information_density": 0.7721, "quality_score": 0.886, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:32.549483", "source": { "split": "train_shard_00000", "doc_id": 208 }, "chunk_id": "train_shard_00000_208_0", "global_id": 234 }, { "text": "Here, various melt-extruded formulations of the poorly soluble model drug fenofibrate based on hydrogenated phospholipid (HPL), either alone or in combination with the hydrophilic copolymer Polyvinylpyrrolidone-Polyvinylacetate (VA64), are compared with respect to their solid state and in vitro performance as an enabling formulation. The specific focus is on the spontaneous formation of micron and submicron colloids from phospholipidic versus conventional polymeric amorphous solid dispersions (ASDs), their size and FEN content, during dissolution in biomimetic media, and their impact on dissolved concentration, dissolution rate, and permeation. In order to judge the ASDs' supersaturation potential, the apparently dissolved drug concentrations of the different melt-extrudates immediately after dispersion in fasted state simulated intestinal fluid (FaSSIF) were determined. For all extrudates, the initial apparently dissolved drug concentration exceeded that of crude fenofibrate, indicating that all ASDs induced supersaturation at therapeutically relevant dose levels. Major differences were seen between the formulations upon separation of the apparently dissolved drug into size fractions. With respect to the drug content within the smallest size-fraction (filtrated through 20 nm pore size), the pure VA64 formulation performed best, followed by the ASD containing 20 % of HPL and pure HPL-based ASD, despite the fact that mean colloid sizes measured by dynamic light scattering (DLS) were essentially the same for all the ASDs. It is postulated that two alternative processes occur simultaneously: the spontaneous formation of drug-rich nanoparticles and the incorporation of FEN into small bile salt and or phospholipid micelles, which are assumed to be responsible for the different drug content in the colloidal fractions. It is presumed that some of the micelles can't easily pass the 20 nm filter pores, while the drug-rich particles being formed appear to be very small at the very beginning of the dissolution process and thus also pass these pores", "token_count": 485, "char_count": 2073, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [ "VA64" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:33.189444", "source": { "split": "train_shard_00000", "doc_id": 209 }, "chunk_id": "train_shard_00000_209_0", "global_id": 235 }, { "text": "Differentiation between drug-rich nanoparticles and drug associated with bile salt/phospholipid micelles may be important because, based on literature data, these two colloidal species are hypothesized to have a different impact on the evolution of molecularly dissolved drug concentrations during the dissolution process and thus permeability (absorption). Interestingly, the amounts of drug accumulating in the acceptor during combined dissolution/permeation experiments were rather similar, irrespective of which of the ASDs was studied.\n\nDissolution / Permeation of Amorphous Solid Dispersions of Fenofibrate & Hydrogenated Phospholipid - Spontaneous Formation of Colloids: Nanofiltration & Particle Size Analysis.", "token_count": 170, "char_count": 718, "word_count": 92, "semantic_coherence": 1, "information_density": 0.8152, "quality_score": 0.9076, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:33.628304", "source": { "split": "train_shard_00000", "doc_id": 209 }, "chunk_id": "train_shard_00000_209_1", "global_id": 236 }, { "text": "Both plastics and heavy metal(loid)s (HMs) are ubiquitous environmental contaminants, and their frequent interactions in aquatic environments are observed globally. These interactions could result in adsorption of HMs onto plastics, thereby altering the environmental behavior of both contaminants. The change of physicochemical property of plastics surfaces, due to HM adsorption, inevitably impacts the plastisphere microbiome, as well as the fate of plastics in the environment. However, our understanding of how plastisphere microbiomes respond to HMs stress, and the subsequent impacts on the fate of plastics and HMs, remain in its infancy. The current study identified keystone taxa of the plastisphere microbiome and identified their ecological roles in HM metabolism. Members of Mycobacterium were identified as the keystone taxa in the HM contaminated plastisphere. Metagenomic binning and pangenome analysis demonstrated that Mycobacterium encoded essential genes for plastics biodegradation and HM resistance. Pure isolates of Mycobacterium further confirmed that the bacteria can mineralize plastics under arsenic exposure, with plastics biodegradation rates remaining unaffected by environmentally relevant As concentrations (up to 0.5 mM). In summary, the metabolic potentials of HM detoxification as well as the mineralization of plastics by the keystone taxa of the plastisphere microbiome may play important environmental service to promote the bioremediation of the co-contamination of HMs and plastics.\n\nInvestigation of the ecological roles of the plastisphere microbiome in metal-contaminated river sediments: elucidation of their metabolic versatilities for plastics mineralization and metal resistance.", "token_count": 422, "char_count": 1726, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5451, "quality_score": 0.7725, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:34.238799", "source": { "split": "train_shard_00000", "doc_id": 210 }, "chunk_id": "train_shard_00000_210_0", "global_id": 237 }, { "text": "Parasynechococcus is one of the two essential alongside Prochlorococcus photosynthetic cyanobacteria that contribute primary productivity in the ocean. Despite its global importance its specie delimitation remains controversial. Herein, a pangenome analysis of 39 high-quality genomes was conducted to delineate Parasynechococcus species. Core-gene phylogram revealed the classification of these genomes into 18 well-defined putative genospecies, which was corroborated by ANI index and GTDB classification. Moreover, numerous interspecies and intraspecies HGT events were detected, some of which may be responsible for the inconsistencies between core-gene and pan-gene phylograms. Besides, the profiling of phycobilisome rod region in Parasynechococcus genomes unraveled intriguing diversity of their genomic organization, pigment type and genomic cluster variants. The diversification process was hypothesized to be mediated by the putative mobile elements located in these regions. Moreover, phylogeny incongruence between the genes within phycobilisome rod region and the core genome indicate distinct evolutionary history, which could be ascribed to lateral gene transfer. Conclusively, the results provide insights into the diversity and evolution of Parasynechococcus from the perspective of pangenome and pigment type, facilitating the evolutionary research and exploration of this important taxon.\n\nEvolutionary insights from the pangenome and pigment profiles of Parasynechococcus.", "token_count": 353, "char_count": 1492, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:34.809172", "source": { "split": "train_shard_00000", "doc_id": 211 }, "chunk_id": "train_shard_00000_211_0", "global_id": 238 }, { "text": "The increasing prevalence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Acinetobacter baumannii presents a major global health threat, particularly in hospital settings. Understanding the genomic landscape of A. baumannii is essential to elucidate its virulence mechanisms, resistance profiles, and evolutionary adaptations, which are critical for developing novel therapeutic strategies. This study aims to comprehensively analyze the pan-genome, antimicrobial resistance (AMR) genes, virulence factors, and clonal relationships of A. baumannii, with the goal of uncovering insights into its pathogenicity and genomic evolution. A total of 27,884 A. baumannii genomes were retrieved from GenBank for analysis. Genome annotation was carried out using Prokka, and pan-genome analysis was performed with Roary. AMR genes and virulence factors were identified through AMRFinderPlus and the Virulence Factor Database via Abricate. Temporal trends in AMR and virulence were analyzed statistically to assess changes over time. The study found that A. baumannii possesses a stable core genome and a highly diverse accessory genome, suggesting an open pan-genome structure. Temporal analysis revealed a significant increase in AMR genes, including bla\n\nUnravelling the genomic landscape of Acinetobacter baumannii: deep dive into virulence factors, resistance elements, and evolutionary adaptations.", "token_count": 339, "char_count": 1411, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6702, "quality_score": 0.8351, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:35.367266", "source": { "split": "train_shard_00000", "doc_id": 212 }, "chunk_id": "train_shard_00000_212_0", "global_id": 239 }, { "text": "The Fabaceae family, the third-largest among flowering plants, is nutritionally vital, providing rich sources of protein, dietary fiber, vitamins, and minerals. Leguminous plants, such as soybeans, peas, and chickpeas, typically contain two to three times more protein than cereals like wheat and rice, with low fat content (primarily unsaturated fats) and no cholesterol, making them essential for cardiovascular health and blood sugar management. Since the release of the soybean genome in 2010, genomic research in Fabaceae has advanced dramatically. High-quality reference genomes have been assembled for key species, including soybeans (\n\nFunctional Genomics: From Soybean to Legume.", "token_count": 167, "char_count": 688, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8557, "quality_score": 0.9278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:35.804187", "source": { "split": "train_shard_00000", "doc_id": 213 }, "chunk_id": "train_shard_00000_213_0", "global_id": 240 }, { "text": "Tan sheep outperform Dorper sheep in meat-quality traits, including muscle fiber characteristics and fatty acid composition, while Dorper sheep excel in carcass weight. However, the molecular mechanisms underlying these breed-specific traits, especially gut microbiota-bile acid (BA) interactions, remain poorly understood. As host-microbiota co-metabolites, BAs are converted by colonic microbiota via bile salt hydrolase (BSH) and dehydroxylases into secondary BAs, which activate BA receptors to regulate host lipid and glucose metabolism. This study analyzed colonic BA profiles in 8-month-old Tan and Dorper sheep, integrating microbiome and longissimus dorsi muscle transcriptome data to investigate the gut-muscle axis in meat-quality and carcass trait regulation. Results showed that Tan sheep had 1.6-fold higher secondary BA deoxycholic acid (DHCA) levels than Dorper sheep (\n\nGut Microbiota-Bile Acid Crosstalk Contributes to Meat Quality and Carcass Traits of Tan and Dorper Sheep.", "token_count": 255, "char_count": 993, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7185, "quality_score": 0.8593, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:36.286569", "source": { "split": "train_shard_00000", "doc_id": 214 }, "chunk_id": "train_shard_00000_214_0", "global_id": 241 }, { "text": "The size of ingested bolus particles and their surface area affect how accessible the substrates are to digestive enzymes and the gut microbiota. This study aimed to investigate the impact of oral breakdown of rice on the human gut microbiota in vitro. Three rice varieties with different fiber contents were chewed in vivo, then subjected to in vitro digestion and fecal batch cultures. Increasing the number of chews per bite from 5 to 40 led to higher structural breakdown and more extensive early starch hydrolysis, resulting in up to 14 % increase in the degree of starch hydrolysis during in vitro digestion, and 26-47 % smaller rice bolus particles after in vitro digestion. Higher bile salt hydrolase activity and total short-chain fatty acid levels (5-13 %) were found in less chewed rice. Untargeted lipidomics highlighted that the number of chews influenced numerous metabolites beyond SCFA.\n\nChewing behavior and bolus particle size of rice influence carbohydrate digestion and gut microbiome metabolism in vitro.", "token_count": 251, "char_count": 1025, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:36.772860", "source": { "split": "train_shard_00000", "doc_id": 215 }, "chunk_id": "train_shard_00000_215_0", "global_id": 242 }, { "text": "Understanding how foodborne pathogens adapt to changing environments is essential for improving food safety monitoring and control. Cronobacter sakazakii, a persistent opportunistic pathogen associated with powdered infant formula outbreaks, poses critical health risks to neonates and other vulnerable populations. This study tested the hypothesis that genetic variation in C. sakazakii correlates with specific isolation sources and geographic origins across the global food system. We conducted a pangenomics meta-analysis of C. sakazakii derived from food, environmental, and clinical sources spanning North America, Asia, and Europe. A robust fine-tuned Generative Pre-trained Transformer (GPT) model was developed to standardize the categorization of isolate metadata descriptors. C. sakazakii genome assemblies (n = 748) were used to build and annotate the pangenome, and genome size and accessory gene profiles were found to be significantly associated with source type and continent of origin. Isolates from powdered foods, compared to those sourced from alternative foods, had larger genomes and were enriched in functions annotated to Clusters of Orthologous Genes (COG) category L for DNA replication, recombination and repair (e.g., transposase, integrase), among other features. Random forest models using both accessory genes and the subset of virulence factor homologs accurately predicted source attributions, identifying type VI secretion system and heavy metal response genes as key indicators of isolate origins. Several antimicrobial resistance genes associated with efflux (i.e., arlR, facT, oprZ) also exhibited patterns for biogeography. Overall, this study uncovered the distribution of key accessory genetic elements of C. sakazakii throughout the food system, revealing putative adaptations for its persistence and transmission. Our reproducible and automated workflow has potential applications in molecular surveillance for emerging food safety concerns.\n\nGenomic diversity of Cronobacter sakazakii across the food system to consumers at the global scale.", "token_count": 462, "char_count": 2084, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6937, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:37.391912", "source": { "split": "train_shard_00000", "doc_id": 216 }, "chunk_id": "train_shard_00000_216_0", "global_id": 243 }, { "text": "Fluids sampled from the gastrointestinal (GI) tract are of interest for evaluating the bioequivalence of oral medications, and more generally for evaluating GI-related diseases, and for profiling the individual gut microbiome. Existing options for capturing multiple fluid samples from specific locations in the GI tract are limited and invasive, particularly for the small intestine. Here, we report the development of an ingestible capsule for the collection of multiple fluid samples along the GI tract; we additionally report the use of data from sensors within the capsule to determine the sampling regions. The capsule has an ingestible size of Φ14 × 42 mm3. Within this volume, it includes three separate cartridges that capture and retain samples within capillaries; a stepper motor for positioning the sampling cartridges at a sampling port; a 3-axis accelerometer that enables a new method of correlating sample location; a microcontroller with wireless communication and sensor data storage capabilities; and batteries to power the device. We describe in vitro characterization and in vivo tests performed with canine models that have successfully verified the capabilities of the capsule. Fluid samples from the stomach, small intestine, and colon regions of the GI tract are identified by inertial measurements taken within the capsule, and correlated to measurements of the concentration of mesalamine (a drug used for testing) and the bile salt profile in each region, respectively.\n\nAn ingestible device for automated sampling and location tracing in gastrointestinal tract.", "token_count": 347, "char_count": 1590, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:37.965517", "source": { "split": "train_shard_00000", "doc_id": 217 }, "chunk_id": "train_shard_00000_217_0", "global_id": 244 }, { "text": "Bile salt export pump (BSEP) deficiency, or progressive familial intrahepatic cholestasis type 2, is a genetic liver disease characterized by defective biliary bile acid secretion. Odevixibat, an ileal bile acid transporter inhibitor (IBATi), impairs intestinal reabsorption of conjugated bile acids, reducing serum bile acid (sBA) concentration in some patients with BSEP deficiency. We evaluated the association of pretreatment sBA levels and composition, as well as the subsequent response to odevixibat in patients with BSEP deficiency, to improve our understanding of the mechanism.\n\nPretreatment serum bile acid composition and predictability of subsequent response to odevixibat in patients with bile salt export pump (BSEP) deficiency.", "token_count": 191, "char_count": 743, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:38.411410", "source": { "split": "train_shard_00000", "doc_id": 218 }, "chunk_id": "train_shard_00000_218_0", "global_id": 245 }, { "text": "Innovations in DNA sequencing technologies have greatly boosted population-level genomic studies in plants, facilitating the identification of key genetic variations for investigating population diversity and accelerating the molecular breeding of crops. Conventional methods for genomic analysis typically rely on small variants, such as SNPs and indels, and use single linear reference genomes, which introduces biases and reduces performance in highly divergent genomic regions. By integrating the population level of sequences, pangenomes, particularly graph pangenomes, offer a promising solution to these challenges. To date, numerous algorithms have been developed for constructing pangenome graphs, aligning reads to these graphs, and performing variant genotyping based on these graphs. As demonstrated in various plant pangenomic studies, these advancements allow for the detection of previously hidden variants, especially structural variants, thereby enhancing applications such as genetic mapping of agronomically important genes. However, noteworthy challenges remain to be overcome in applying pangenome graph approaches to plants. Addressing these issues will require the development of more sophisticated algorithms tailored specifically to plants. Such improvements will contribute to the scalability of this approach, facilitating the production of super-pangenomes, in which hundreds or even thousands of de novo-assembled genomes from one species or genus can be integrated. This, in turn, will promote broader pan-omic studies, further advancing our understanding of genetic diversity and driving innovations in crop breeding.\n\nPlant graph-based pangenomics: techniques, applications, and challenges.", "token_count": 331, "char_count": 1722, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6858, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:38.978119", "source": { "split": "train_shard_00000", "doc_id": 219 }, "chunk_id": "train_shard_00000_219_0", "global_id": 246 }, { "text": "Monoterpenes are valued for their roles as flavors, fragrances, insecticides, and energy-dense fuels. Microorganisms provide sustainable biosynthesis routes for these important molecules, but production levels remain limited. Here, we introduce a biosensor-driven microbial engineering strategy to enhance monoterpene production, specifically targeting geraniol. Using mutagenized libraries of the PYR1 receptor─a versatile biosensor from plant ABA signaling pathways with a malleable binding pocket─we screened 24 monoterpenes and identified PYR1 variants responsive to eight, including geraniol. A low background, highly selective geraniol-sensitive PYR1 variant was expressed in the thermotolerant yeast\n\nPYR1 Biosensor-Driven Genome-Wide CRISPR Screens for Improved Monoterpene Production in", "token_count": 204, "char_count": 795, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8351, "quality_score": 0.9175, "entities": { "genes": [ "PYR1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:39.435024", "source": { "split": "train_shard_00000", "doc_id": 220 }, "chunk_id": "train_shard_00000_220_0", "global_id": 247 }, { "text": "Lucinid bivalves harbor environmentally acquired endosymbionts within the class Gammaproteobacteria and genus Candidatus Thiodiazotropha. Despite recent studies focused on lucinid endosymbiont genomic and functional diversity, processes influencing species diversity have been understudied. From the analysis of 333 metagenome-assembled genomes (MAGs) from 40 host species across 8 waterbodies and 77 distinct locations, 272 were high quality MAGs of Ca. Thiodiazotropha endosymbionts that represented 11 genomospecies. Of those, two new genomospecies from lucinids collected from The Bahamas and Florida (USA) were identified, Ca. Thiodiazotropha fisheri and Ca. Thiodiazotropha grosi. Metabolic specialization was evident, such as potential adaptations to diverse carbon sources based on detection of one-carbon (C1) metabolic genes in eight genomospecies. Genes associated with defense, symbiosis/pathogenesis, and horizontal gene transfer (HGT) were also distinct across genomospecies. For instance, Ca. T. taylori exhibited lower abundances of HGT-associated genes compared to other genomospecies, particularly Ca. T. endolucinida, Ca. T. lotti, and Ca. T. weberae. HGT-associated genes were linked to previously unreported retron-type reverse transcriptases, dsDNA phages, and phage resistance. Collectively, the pangenome highlights how lucinid endosymbiont diversity has been shaped by geographic and host-specific interactions linked to gene loss and HGT through time.\n\nVariation in accessory and horizontal gene transfer-associated genes drives lucinid endosymbiont diversity.", "token_count": 423, "char_count": 1586, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:40.049321", "source": { "split": "train_shard_00000", "doc_id": 221 }, "chunk_id": "train_shard_00000_221_0", "global_id": 248 }, { "text": "An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping the pangenome of a species or broader taxon, it is often unnecessary and computationally onerous to include all available genomes in studies. In addition, the over-representation of specific lineages due to sampling and sequencing bias can have undesired effects on evolutionary analyses. To assist users with\n\nskDER and CiDDER: two scalable approaches for microbial genome dereplication.", "token_count": 129, "char_count": 589, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7701, "quality_score": 0.8851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:40.467113", "source": { "split": "train_shard_00000", "doc_id": 222 }, "chunk_id": "train_shard_00000_222_0", "global_id": 249 }, { "text": "Comparative genomic analysis of two all-stage stripe rust resistance loci from Vavilov wheat landrace accession, AGG40807WHEA1, using Chinese Spring and 10 + hexaploid wheat genomes and validation of closely linked KASP markers. The ongoing occurrence and spread of wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, threatens the global food security. Cultivation of varieties with effective sources of resistance is often followed by the appearance of virulent pathotypes at various times after their introduction. This requires an ongoing search for new sources. Tests of 296 accessions from the Vavilov wheat landrace collection identified numerous lines with broadly effective all-stage stripe rust resistance. Genetic analysis of one of these accessions (Australian Grains Genebank number AGG40807WHEA1) identified two all-stage resistance genes, temporarily named YrV1 and YrV2. The YRV1 and YRV2 loci were mapped to 3.48-3.98 and 730.2-731.2 Mb intervals in the short arm of chromosome 3B and the long arm of chromosome 7B, respectively. A comparative genomic analysis of the YRV1 locus in the Chinese Spring and the 10 + wheat pangenome databases revealed genomic rearrangements and lack of sequences encoding a nucleotide-binding and leucine-rich repeat (NLR) domain protein. Sequences belonging to NLR-like genes were present in the YRV2 region. Kompetitive allele-specific PCR (KASP) markers designed from SNPs IWB71814 and IWB69562, located at 0.4 cM and 0.5 cM distal to YrV1 and YrV2, respectively, were validated for marker-assisted selection using 123 hexaploid and 15 tetraploid wheat and 14 triticale cultivars", "token_count": 494, "char_count": 1664, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6337, "quality_score": 0.8169, "entities": { "genes": [ "YRV1", "IWB69562", "IWB71814", "YRV2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:41.106485", "source": { "split": "train_shard_00000", "doc_id": 223 }, "chunk_id": "train_shard_00000_223_0", "global_id": 250 }, { "text": "YrV1 and YrV2 genes are potentially valuable resources, and use of the closely linked molecular markers will expedite their deployment in breeding.\n\nGenomic analysis of two all-stage stripe rust resistance genes in the Vavilov wheat landrace AGG40807WHEA1.", "token_count": 70, "char_count": 256, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:41.473643", "source": { "split": "train_shard_00000", "doc_id": 223 }, "chunk_id": "train_shard_00000_223_1", "global_id": 251 }, { "text": "Wild plants can contribute valuable genes to their domesticated relatives\n\nA haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum.", "token_count": 38, "char_count": 151, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:41.835294", "source": { "split": "train_shard_00000", "doc_id": 224 }, "chunk_id": "train_shard_00000_224_0", "global_id": 252 }, { "text": "Fermented foods constitute a valuable source of probiotics for both bacteria and yeasts. To date, however, there has been a limited amount of research conducted on Saccharomyces cerevisiae, Kazakhstania servazzi, Kluyveromyces marxianus and Torulaspora delbrueckii isolated from tarhana. The objective of the research is to identify additional probiotic characteristics other than the leavening activity exhibited by yeasts that were previously isolated from tarhana fermentation. In this study, yeasts were subjected to subsequent acid and bile salt tolerance, bile salt hydrolysis, antagonistic activity, aggregation activity (auto-aggregation and co-aggregation), cholesterol assimilation, folate production, biofilm production, and hemolysis activity. S. cerevisiae PCF122, S. cerevisiae PCF107, and S. cerevisiae PCF134 strains grew at pH 2 and 2,5 but remained at pH 3. Except for S. cerevisiae PCF115 and T. delbrueckii PCF150, all yeasts were found to be 0,5% and 1,0% oxalate tolerant. All yeasts hydrolyze oxalate (bile salt), but only S. cerevisiae PCF115 and T. delbrueckii PCF150 produced EPS. Yeasts also exhibited significant amounts of autoaggregation (46-87%). After 24 and 48 h incubation, all strains assimilated cholesterol at rates ranging from 10,4% to 87,5% and 10,6-91%, respectively. The highest folate production was determined at S. cerevisiae PCF108 (56 µg/mL) and the lowest was at S. cerevisiae PCF110 and K. marxianus PFC120 (18 µg/mL). In conclusion, yeasts that existed in tarhana fermentation showed cholesterol assimilation, folate production, and aggregation activity which are additional probiotic attributes that would have consumer health promotion, beside these yeast leaven the tarhana dough.", "token_count": 528, "char_count": 1733, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.8189, "entities": { "genes": [ "PCF150", "PCF115", "PCF108", "PCF107", "PCF110", "PCF122", "PFC120", "PCF134" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:00:42.476576", "source": { "split": "train_shard_00000", "doc_id": 225 }, "chunk_id": "train_shard_00000_225_0", "global_id": 253 }, { "text": "Identification of additional probiotic attributes in yeasts isolated from tarhana fermentation.", "token_count": 20, "char_count": 95, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:42.872226", "source": { "split": "train_shard_00000", "doc_id": 225 }, "chunk_id": "train_shard_00000_225_1", "global_id": 254 }, { "text": "In recent years, there has been an increase in invasive infections caused by \"'rare' Candida species\". The intrinsic resistance characteristics of these species along with their higher antifungal MIC values reduce the success of antifungal treatment. Although molecular and other sophisticated tests are reliable for the identification of many rare and newly emerging Candida species. Their implementation in routine laboratories is limited due to trained personnel, high costs, and specialized laboratory equipments. As a result, conventional methods and automated systems such as VITEK-2 and MALDI-TOF MS are still widely used in routine laboratories. This study evaluates and compares the identification capabilities of these commonly used tests for rare Candida species and provides guidance for rapid identification. A total of 201 isolates consist of 16 rare Candida species from various clinical samples were analyzed. Identification was performed using VITEK MS (as a gold standard) and results compared with VITEK-2, API ID 32 C, CHROMagar Candida, CHROMagar Candida Plus, and cornmeal agar with 1% Tween 80. VITEK MS identified all isolates and among them, the three most common species were Candida inconspicua (n:34; 16.9%), Candida lusitaniae (n:33; 16.4%), and Candida kefyr (n:31; 15.4%). Among these, a total of 107 isolates (53.2%) were correctly identified at the species level using the VITEK-2 system, whereas only 51 isolates (25.37%) were accurately identified with the API ID 32C system. However, when additional conventional methods (colony morphology and colour on chromogenic agar medium, Dalmau plate method, esculin hydrolysis test, growth at different temperatures) were applied, these identification rates increased to 81.5% (n = 164) and 54.7% (n = 110), respectively", "token_count": 472, "char_count": 1798, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8352, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:43.520455", "source": { "split": "train_shard_00000", "doc_id": 226 }, "chunk_id": "train_shard_00000_226_0", "global_id": 255 }, { "text": "Notably, even when used alone, the VITEK-2 system demonstrated a high identification success rate for Candida auris (83.3%), Candida lipolytica (85.7%), Candida lusitaniae (78.7%), Candida guilliermondii (83.8%), and Candida dubliniensis (86.4%). One of the primary reasons for misidentification was the absence of these microorganisms in the databases of the identification systems used. Additionally, all C. auris strains were correctly identified using CHROMagar Candida Plus medium, with no false-positive results observed for other Candida species. None of the identification methods, when applied alone, were able to correctly identify all 201 rare Candida species. Both VITEK-2 and API ID 32 C demonstrated limited accuracy for some rare species. However, evaluating microscopic and colony morphology on cornmeal agar and chromogenic media improved the accuracy of identification, especially for C. auris. In laboratories with limited access to MALDI-TOF MS or molecular methods, these tests should be used in combination to improve identification accuracy and provide alternative approaches for species differentiation. Also laboratories should update regular databases of their systems constantly. These organisms may be considered \"rare\" because they remain unidentified due to limitations in current identification methods and databases.\n\nIdentification of rare Candida species isolated from various clinical specimens: Comparison of different methods.", "token_count": 336, "char_count": 1463, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8266, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:44.129077", "source": { "split": "train_shard_00000", "doc_id": 226 }, "chunk_id": "train_shard_00000_226_1", "global_id": 256 }, { "text": "Barrett's esophagus (BE) is a precancerous condition closely linked to chronic gastroesophageal reflux disease, characterized by the abnormal transformation of esophageal squamous mucosa into specialized intestinal-type epithelium, significantly elevating the risk of esophageal adenocarcinoma (EAC). Recurrent acidic bile reflux promotes epithelial-mesenchymal transition (EMT), a critical event driving malignant progression. However, the underlying molecular mechanisms remain incompletely understood. Here, we identify the long non-coding RNA small nucleolar RNA host gene 1 (SNHG1) as a novel regulator of EMT in BE, mediating its effects through the UNC-52-like kinase 1 (ULK1)-Notch1 signaling axis and autophagy modulation. Using BAR-T and CP-C cell models, we demonstrate that SNHG1 expression is elevated following acidic bile salt exposure, enhancing EMT characteristics by promoting the phosphorylation of ULK1 and activating Notch1 signaling. Pharmacological interventions targeting autophagy (Rapamycin) and Notch signaling (DAPT) further confirmed that SNHG1's effects on EMT are mediated via modulation of the autophagy-Notch1 interplay. We further validated our results in vivo using the previously described IL1β-induced Lgr5-CreERT2; p16\n\nLncRNA small nucleolar RNA host gene 1 (SNHG1) mediates acidic bile salt-induced EMT via the ULK1-Notch1 axis in Barrett's esophagus.", "token_count": 403, "char_count": 1391, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7253, "quality_score": 0.8626, "entities": { "genes": [ "SNHG1", "ULK1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:44.738162", "source": { "split": "train_shard_00000", "doc_id": 227 }, "chunk_id": "train_shard_00000_227_0", "global_id": 257 }, { "text": "Cholestasis-associated pruritus is a distressing symptom. Bile salts and bilirubin are often implicated in the etiology of pruritus. We evaluated whether these compounds activate known itch receptors.\n\nThe role of bile salts in itch receptor activation.", "token_count": 72, "char_count": 253, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:45.115183", "source": { "split": "train_shard_00000", "doc_id": 228 }, "chunk_id": "train_shard_00000_228_0", "global_id": 258 }, { "text": "The structure of polyphenolic compounds plays a pivotal role in determining their functional efficacy. Moreover, the presence of bile salt surfactants can significantly impact their metabolism. Hence, this study employed multi-spectroscopic methods to explore the binding mechanism of Quercetin (Que) and Taxifolin (Tax, dihydroquercetin) with bovine hemoglobin (HB), influenced by the addition of sodium taurodeoxycholate (NaTDC). The results indicate that, through the static quenching mechanism, nearly a single Que. or Tax molecule can spontaneously form a complex on each HB chain. This process is driven by Van der Waals forces, hydrophobic interaction, and hydrogen bonds. During the interaction, the secondary structure of HB chains undergoes changes with an enhanced hydrophobicity. The hydrogenation of C2C3 double bond of flavonols increases the structural flexibility and helps to close to the active sites of HB, resulting in the stronger binding affinity of Tax on HB chains than Que. Additionally, the presence of this double bond exerts a notable influence on the physicochemical properties of polyphenols, such as solubility, antioxidant activity, and antibacterial activity. Specifically, the solubility of pure Tax in water, and its bacteriostatic effect against Klebsiella Pneumoniae (KP) and Methicillin-resistant Staphylococcus Aureus (MRSA), are superior to that of Que. The C2C3 double bond of Que. make it exhibiting better antioxidant ability than Tax. After interacting with HB, the antioxidant capacity are enhanced, and the bacteriostatic effects are either weakened or remain essentially unchanged compared to those of pure Que./Tax. The addition of NaTDC can enhance the low solubility of Que./Tax and regulate their interaction strength with HB, thereby further influencing their bioavailability. For the Tax/Que-HB mixed system, the presence of NaTDC strengthens their antioxidant capacity, but does not affect the antimicrobial activity basically. These findings hold significant practical implications for enhancing the therapeutic efficacy and bioavailability of natural products.", "token_count": 515, "char_count": 2116, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8232, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:00:45.738682", "source": { "split": "train_shard_00000", "doc_id": 229 }, "chunk_id": "train_shard_00000_229_0", "global_id": 259 }, { "text": "Effect of the C2C3 double bond and sodium taurodeoxycholate addition on the quercetin-hemoglobin and taxifolin-hemoglobin interactions.", "token_count": 44, "char_count": 135, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:46.100774", "source": { "split": "train_shard_00000", "doc_id": 229 }, "chunk_id": "train_shard_00000_229_1", "global_id": 260 }, { "text": "Considering the increasing reports of Salmonella enterica strains resistant to quinolones, antimicrobials frequently employed as therapeutic agents globally, our goal was to investigate the occurrence of plasmid-mediated quinolone resistance (PMQR) determinants in S. enterica recovered from natural surface waters in Paraíba state, Brazil. Water samples (n = 230) were collected monthly in triplicate using modified Moore swabs from 29 sampling sites belonging to 10 large dams. After conventional microbial isolation, representative isolates (n = 938) were submitted to whole genome sequencing, assembly and annotation. Antimicrobial resistance genes (ARGs) were identified, and core genome multilocus sequence typing (cgMLST) was used to infer phylogenetic relationships. Among recovered S. enterica, 130 (13.9%) isolates harboured PMQR determinants; 124 (95.4%) harboured qnrB19, while 6 (4.6%) harboured qnrS1. Multiple other ARGs associated with resistance to aminoglycosides, β-lactams, sulphonamides, tetracyclines and fosfomycin were identified. The diversity of ARGs and plasmids suggests a highly complex resistance landscape. Phylogenetic analysis revealed clustering by serovar and sequence type but not by resistance profile or geographic origin. The absence of association between phylogeny and ARGs highlights the potential role of horizontal gene transfer in disseminating resistance genes in water. Our findings reinforce the importance of antimicrobial resistance surveillance in surface waters.\n\nHigh Prevalence of Plasmid-Mediated Quinolone Resistance in Salmonella enterica Serovars Isolated From Surface Water.", "token_count": 432, "char_count": 1633, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:46.712839", "source": { "split": "train_shard_00000", "doc_id": 230 }, "chunk_id": "train_shard_00000_230_0", "global_id": 261 }, { "text": "Traditional pangenome analysis focuses on gene presence/absence variations (gene PAVs). However, the current methods for gene PAV analysis are insensitive to detect small but valuable mutations within gene regions, and they overlook variations in intergenic regions. Additionally, the visual inspection of PAVs is an important but time-consuming step for pangenome analysis and result interpretation. To address these issues, we present APAV, an advanced toolkit designed for comprehensive PAV analysis and visualization. It integrates gene element-level PAV analysis and provides PAV analysis for arbitrary given regions in a genome. The resulted PAV profile can be visualized and investigated interactively with reports in HTML format, enabling researchers to conveniently verify sequencing read depth, target region coverage, and intervals of absence for each PAV. Furthermore, APAV offers various subsequent analysis and visualization functions based on the PAV profile table, including basic statistics, sample clustering, genome size estimation, and phenotype association analysis. We demonstrated the capability of APAV with pangenome analysis of tumor genomes and rice genomes. Performing PAV analysis at the element level not only provides more accurate information about the variations but also uncovers a larger number of variations for the phenotype-genotype association studies. In the rice genome analysis, we identified over twenty thousand distributed genes and more than fifty thousand distributed genetic elements. In the tumor genome analysis, element-level analysis revealed approximately three times as many phenotype-related genes as gene-level analysis. This indicates that altering the PAV unit from genes to smaller segments or elements can lead to more biological insights.\n\nAPAV: An advanced pangenome analysis and visualization toolkit.", "token_count": 368, "char_count": 1864, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8198, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:47.285641", "source": { "split": "train_shard_00000", "doc_id": 231 }, "chunk_id": "train_shard_00000_231_0", "global_id": 262 }, { "text": "Antimicrobial-resistant ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae) have significantly restricted therapeutic alternatives for critical infections, consequently contributing to increase the severity and mortality of infectious illnesses that represent a significant global health challenge. Vaccination as a preventive measure can be crucial in substantially reducing bacterial infections and is potentially effective against antibiotic-resistant bacteria. This study shows the design of an epitope-based vaccine capable of neutralizing shared antigenic determinants present among the ESKAPE pathogens. The pangenome of the ESKAPE pathogens was analyzed to extract the core proteome. This approach facilitated reverse vaccinology analysis to identify antigenic proteins within this bacterial group. The study revealed similar structures in porins OmpA, OprD, and TolC, as well as the collagen-binding adhesins Acm and Cna. These proteins were then utilized to predict T-cell and B-cell epitopes, selecting those with their best physicochemical properties, antigenicity, non-allergenicity, and lack of toxicity. Additionally, epitopes located on the surface of the antigens and capable of coupling with HLA molecules were prioritized. In this computational approach, we engineered a construct incorporating the adjuvant RS09, a TLR4 agonist, and immunogenic epitopes connected by linkers. We assessed the stability of their interaction with pattern recognition receptors of the immune system through molecular docking and molecular dynamics simulations. The in silico immune simulation demonstrated that the vaccine could trigger humoral and cell-mediated immune responses. The resulting construct potentially represents an effective and safe vaccine candidate to prevent infections caused by the ESKAPE group.\n\nIn silico development of a broad-spectrum vaccine against ESKAPE pathogens.", "token_count": 465, "char_count": 2003, "word_count": 259, "semantic_coherence": 1, "information_density": 0.668, "quality_score": 0.834, "entities": { "genes": [ "TLR4", "RS09" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:47.915523", "source": { "split": "train_shard_00000", "doc_id": 232 }, "chunk_id": "train_shard_00000_232_0", "global_id": 263 }, { "text": "Pseudomonas syringae pathovar aesculi (E-Pae) causes bleeding canker disease in the woody tissue of European horse chestnut (HC). Comparative genomic analysis of E-Pae with a related leaf-infecting strain (I-Pae) and other P. syringae strains identified candidate virulence genes for colonisation of woody tissue, including a sucrose uptake and utilisation system (scrYABCDBR cluster) found in 162 of 206 P. syringae strains spanning the pangenome. Growth analysis using sucrose as sole carbon source showed that I-Pae (lacking the gene cluster) was unable to grow whereas E-Pae could grow. P. savastanoi pv. phaseolicola 1448A and P. syringae pv. morsprunorum R15244 were compromised in growth despite the presence of the gene cluster. Sucrose utilisation assays using scrB and scrY mutants and complemented strains confirmed the importance of the cluster for sucrose metabolism in vitro. Pathogenicity assays in HC revealed the sucrose gene cluster is important for symptom development in the woody tissue. While the scr genes contribute to disease causation, they were not essential for pathogen fitness when compared to hrpL and hopAB1 mutants. E-Pae caused disease symptoms in HC leaves, suggesting the strain has the potential to infect leaves as well. However, it was notable that the scrB mutant of E-Pae caused increased disease symptoms, possibly highlighting a niche adaptation strategy for I-Pae to cause leaf spots in HC as well as constraining E-Pae to predominantly infect the woody tissue.\n\nA Sucrose-Utilisation Gene Cluster Contributes to Colonisation of Horse Chestnut by Pseudomonas syringae pv. aesculi.", "token_count": 436, "char_count": 1624, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5868, "quality_score": 0.7934, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:48.540948", "source": { "split": "train_shard_00000", "doc_id": 233 }, "chunk_id": "train_shard_00000_233_0", "global_id": 264 }, { "text": "This manuscript introduces a novel, free and open-source physiologically based biopharmaceutics modeling (PBBM) workflow to support decision-making during oral drug product development. Developed within the Open Systems Pharmacology (OSP) framework, this workflow combines three open-source tools to predict in vivo absorption by integrating solubility, dissolution, and systemic pharmacokinetics. The PBBM workflow was successfully applied by 1) deriving solubility and dissolution parameters for vericiguat from in vitro experiments as detailed in the accompanying Part 1 publication (Vrenken et al., 2025); 2) then integrating these parameters into a physiologically based pharmacokinetic (PBPK) model. This model incorporates updates to luminal parameters, including pH and bile salt concentration, and employs a new dissolution model accounting for bile salt effects and hydrodynamics. Simulations of vericiguat pharmacokinetics in fasted, fed, and proton pump inhibitor (PPI)-treated states showed good agreement with observed clinical data. Further refinements that could enhance the PBBM workflow's capabilities were identified. However, the successful application to vericiguat highlights its potential for PBBM applications, including virtual bioequivalence assessments, formulation bridging, and dose selection. While validation across additional case studies is necessary, this free and open-source approach provides a robust foundation for advancing PBBM.\n\nDevelopment of a novel physiologically based biopharmaceutics modeling (PBBM) framework using the open systems pharmacology suite, part 2: in vivo pharmacokinetic modeling of vericiguat.", "token_count": 386, "char_count": 1656, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7042, "quality_score": 0.8521, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:49.148647", "source": { "split": "train_shard_00000", "doc_id": 234 }, "chunk_id": "train_shard_00000_234_0", "global_id": 265 }, { "text": "The production of second-generation (2 G) bioethanol, a key sector in industrial biotechnology, addresses the demand for sustainable energy by utilizing lignocellulosic biomass. Efficient fermentation of all sugars from lignocellulose hydrolysis is essential to enhance ethanol titers, improve biomass-to-biofuel yields, and lower costs. This review compares the potential of recombinant yeast strains for 2 G bioethanol production, focusing on their ability to metabolize diverse sugars, particularly xylose. Saccharomyces cerevisiae, engineered for enhanced pentose and hexose utilization, is compared with the nonconventional yeasts Scheffersomyces stipitis, Kluyveromyces marxianus, and Ogataea polymorpha. Key factors include sugar assimilation pathways, cofermentation with glucose, oxygen requirements, tolerance to hydrolysate inhibitors, and process temperature. Saccharomyces cerevisiae shows high ethanol tolerance but requires genetic modification for xylose use. Scheffersomyces stipitis ferments xylose naturally but lacks robustness. Kluyveromyces marxianus offers thermotolerance and a broad substrate range with lower ethanol yields, while O. polymorpha enables high-temperature fermentation but yields modest ethanol from xylose. The comparative analysis clarifies each yeast's advantages and limitations, supporting the development of more efficient 2 G bioethanol production strategies. Strain selection must balance ethanol yield, stress tolerance, and temperature adaptability to meet industrial requirements for cost-effective lignocellulosic bioethanol production.\n\nRecent progress in engineering yeast producers of cellulosic ethanol.", "token_count": 411, "char_count": 1659, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7376, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:49.757763", "source": { "split": "train_shard_00000", "doc_id": 235 }, "chunk_id": "train_shard_00000_235_0", "global_id": 266 }, { "text": "Hematogenous prosthetic joint infections (PJIs) are primarily associated with Staphylococcus aureus, and there is a 30%-40% risk of contracting a hematogenous PJI following an S. aureus bacteremia. The aim of this study was to investigate whether identical strains of S. aureus were present in each patient from a cohort with both bacteremia and PJI and to explore the genomic differences between paired isolates obtained from blood cultures and tissue biopsies. All patients with a PJI and a temporally concomitant bacteremia due to S. aureus from 2005 to 2020 were included. Paired isolates of S. aureus from tissue biopsies and blood cultures were subjected to whole-genome sequencing. Twenty-four episodes of PJI were identified in 23 patients. All pairwise isolates from individual patients belonged to the same multilocus sequence type, clonal complex, and core genome multilocus sequence typing (cgMLST) complex type. The median number of single nucleotide polymorphisms (SNPs) in the conserved core genomes between the pairwise isolates was 3. In conclusion, identical cgMLST complex types and low levels of SNP differences between paired isolates of S. aureus from blood cultures and tissue biopsies suggest hematogenous seeding in all cases of PJI in this cohort.\n\nStaphylococcus aureus From Prosthetic Joint Infections and Blood Cultures Display the Same Genetic Background.", "token_count": 366, "char_count": 1385, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5266, "quality_score": 0.7633, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:50.330708", "source": { "split": "train_shard_00000", "doc_id": 236 }, "chunk_id": "train_shard_00000_236_0", "global_id": 267 }, { "text": "Protein digestion is driven by interactions with enzymes and bile salts. To visualize and measure cleavage within hydrogels, fluorescent probes were developed by conjugating labeled whey protein isolate (WPI) to microbeads. These had favorable limits of detection (LOD) and range of operation. LODs were 11.3 nmol/mL Fluorescein isothiocyanate (FITC), or 26.4 nmol/mL WPI, equivalent to 5.3 ng/mL trypsin. Probes displayed bile's effect of promoting proteolysis in solution - a unique property. Protein cleavage was measured as a function of gel penetration depth, demonstrating utility for optimizing design of protein gels for digestibility or release of nutrients/drugs. Effects of gel density and bile salts were examined, and while clear density effects were observed, bile salts did not influence hydrogel digestion - suggesting an important relationship between structure and protease accessibility. Protein hydrogel interactions with bile salts were previously unknown. These tools provide new methods for characterizing food and drug delivery materials.\n\nBile salt sensitive fluorescent probes for visualization of enzymatic proteolysis of hydrogels: Development and application to whey protein digestion.", "token_count": 302, "char_count": 1214, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:50.878611", "source": { "split": "train_shard_00000", "doc_id": 237 }, "chunk_id": "train_shard_00000_237_0", "global_id": 268 }, { "text": "Eukaryotic chromosome segregation requires spindle microtubules to attach to chromosomes through kinetochores. The chromosomal locus that mediates kinetochore assembly is the centromere and is epigenetically specified in most organisms by a centromeric histone H3 variant called CENP-A. An exception to this is budding yeast, which have short, sequenced-defined point centromeres. In S. cerevisiae, a single CENP-A nucleosome is formed at the centromere and is sufficient for kinetochore assembly. The thermophilic budding yeast Kluyveromyces marxianus also has a point centromere, but its length is nearly double the S. cerevisiae centromere and the number of centromeric nucleosomes and kinetochore attachment sites is unknown. Purification of native kinetochores from K. marxianus yielded a mixed population, with one subpopulation that appeared to consist of doublets, making it unclear whether K. marxianus shares the same attachment architecture as S. cerevisiae. Here, we demonstrate that though the doublet kinetochores have a functional impact on kinetochore strength, kinetochore localization throughout the cell cycle appears conserved between these two yeasts. In addition, whole spindle electron tomography demonstrates that a single microtubule binds to each chromosome. Single-molecule nucleosome mapping analysis suggests the presence of a single centromeric nucleosome. Taken together, we propose that the K. marxianus point centromere assembles a single centromeric nucleosome that mediates attachment to one microtubule.\n\nCentromeres in the thermotolerant yeast K. marxianus mediate attachment to a single microtubule.", "token_count": 422, "char_count": 1637, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:51.498883", "source": { "split": "train_shard_00000", "doc_id": 238 }, "chunk_id": "train_shard_00000_238_0", "global_id": 269 }, { "text": "Enterococci are beneficial commensal bacteria recognized for their probiotic effects and are commonly utilized as adjunct cultures in dairy product fermentation. However, their ability to acquire antibiotic resistance and contribute to infections raises significant safety concerns. In this study, both in vitro assays and genome sequencing were conducted to evaluate the safety, functionality, and probiotic potential of Enterococcus faecium UFAS147, isolated from Moroccan goat feces. The strain tolerated acidic conditions (96.79% survival at pH 1.5) and bile salt (1-4%), with notable autoaggregation (33.66%), coaggregation with Salmonella typhymurium ATCC14028 (72.78%), and Staphylococcus aureus B1 (65.55%). Safety assays confirmed the absence of hemolytic activity, mucin degradation, and biogenic amine production. Antibiotic susceptibility testing showed sensitivity to six antibiotics. PCR analysis further confirmed the absence of vanA and vanB genes associated with vancomycin resistance. Genome analysis revealed a length of 2,606,111 bp with a GC content of 38.11% and the absence of genes linked to acquired antimicrobial resistance, cytolysins, and biogenic amine production. Genes supporting probiotic traits, such as Enterocin A, Enterocin P, and Enterolysin A, acid and bile resistance, adhesion, and colonization were identified. These findings highlight E. faecium UFAS147 as a promising candidate for probiotic applications.\n\nComprehensive Genomic Profiling and In Vitro Probiotic and Safety Assessments of Enterococcus faecium UFAS147 Isolated from Moroccan Goat Feces.", "token_count": 442, "char_count": 1594, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6542, "quality_score": 0.8271, "entities": { "genes": [ "UFAS147", "ATCC14028" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:52.117989", "source": { "split": "train_shard_00000", "doc_id": 239 }, "chunk_id": "train_shard_00000_239_0", "global_id": 270 }, { "text": "In this study, we report the draft genome sequence of strain A2. The genome size was 3.8 Mbp, the GC content was 67.4%, and it was predicted to contain 3520 protein-coding genes, 62 tRNA genes, 8 rRNA genes, and 4 snRNA genes. Phylogenetic analysis of the 16S rRNA gene in different databases suggests that strain A2 belongs to Halomonas salifodinae. Also, Multilocus Sequence Typing analysis confirms that A2 is closely related to H. salifodinae. Phylogenomic of the core genes and comparative genomic analysis using the Average Nucleotide Identity, digital DNA-DNA Hybridization, Average Amino acid Identity, the Percentage of Conserved Proteins values indicators, and the Genome Taxonomy Database indicates that strain A2 is identified as H. salifodinae and suggest that this species has a closer phylogenetic relationship with the genus Bisbaumannia than with Halomonas. The pangenomic analysis of A2 against 100 reference genomes of described Halomonas and another related genus shows 136,122 genes that comprise the pangenome with 317 core genes, 3457 shell genes, 132,332 accessory genome genes, and 691 unique genes. A2 has 261 signature genes that it shares only with Bisbaumannia and Halomonas salifodinae. For strain A2 we found 29 genes for secretion systems, 23 genes for Na\n\nDraft genome sequence and comparative genomic analysis of Halomonas salifodinae strain A2 isolated from the Zapotitlán Salinas Valley, Puebla, Mexico.", "token_count": 421, "char_count": 1439, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5753, "quality_score": 0.7877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:52.735212", "source": { "split": "train_shard_00000", "doc_id": 240 }, "chunk_id": "train_shard_00000_240_0", "global_id": 271 }, { "text": "Drug resistance (DR) of pathogens remains a global healthcare concern. In contrast to other bacteria, acquiring mutations in the core genome is the main mechanism of drug resistance for\n\nFeature selection and aggregation for antibiotic resistance GWAS in", "token_count": 54, "char_count": 254, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:53.104114", "source": { "split": "train_shard_00000", "doc_id": 241 }, "chunk_id": "train_shard_00000_241_0", "global_id": 272 }, { "text": "Egg production and performance in commercial layer flocks can be impacted by gastrointestinal health. Probiotics are considered potential alternatives to antibiotics in poultry, and have been proven to have positive impacts on gut health. The objective of this study was to isolate and characterise Lactobacillus strains isolated from high production layer flocks for probiotic properties.\n\nCharacterization of Lactobacillus spp. isolated from layer hens as probiotic candidates.", "token_count": 109, "char_count": 479, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:53.487318", "source": { "split": "train_shard_00000", "doc_id": 242 }, "chunk_id": "train_shard_00000_242_0", "global_id": 273 }, { "text": "Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in\n\nBenchmarking pangenome dynamics and horizontal gene transfer in", "token_count": 61, "char_count": 277, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:53.855931", "source": { "split": "train_shard_00000", "doc_id": 243 }, "chunk_id": "train_shard_00000_243_0", "global_id": 274 }, { "text": "Probiotic fermented milk has garnered significant attention as a functional food owing to its health-promoting effects. This study aimed to evaluate the in vitro probiotic characteristics of Lactiplantibacillus plantarum DACNJS22 (S22), a strain isolated from yak yogurt and elucidate the metabolic profile of its fermented milk and its protective effects against dextran sulfate sodium (DSS)-induced colitis. Phenotypic and whole-genome sequencing analyses confirmed that S22 possesses a favorable safety profile and exhibits a broad spectrum of probiotic properties, including strong antimicrobial activity, resilience to acidic and bile salt conditions, adhesion to intestinal epithelial cells, and potent immunomodulatory and anti-inflammatory effects. Furthermore, milk fermentation by S22 altered the metabolite profiles of the samples, which was predicted to alleviate colitis by regulating the inflammatory response through network pharmacological analysis. Notably, in vivo experiments demonstrated that S22-fermented milk effectively alleviated DSS-induced colitis, restored histopathological damage, reduced inflammatory cytokine levels, and promoted colonic expression of tight junction proteins. Additionally, S22-fermented milk ameliorated gut microbial dysbiosis by enriching beneficial microorganisms and promoting short-chain fatty acid production. Overall, these findings suggest that the targeted development of probiotic-fermented milk with prebiotic properties is a promising strategy for promoting gut health and maintaining intestinal homeostasis.\n\nProtective effect of yak yogurt derived Lactiplantibacillus plantarum DACNJS22 fermented milk on DSS-induced colitis: Insights from in vitro and in vivo studies.", "token_count": 439, "char_count": 1733, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [ "DACNJS22" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:54.506597", "source": { "split": "train_shard_00000", "doc_id": 244 }, "chunk_id": "train_shard_00000_244_0", "global_id": 275 }, { "text": "Lactobacillus crispatus, a key member of the vaginal microbiota, exhibits strain-specific diversity with important implications for host-microbe interactions and probiotic potential. This study investigates the genomic relationships and bacteriocin diversity across 95 L. crispatus strains to elucidate the mechanisms underlying strain-specific adaptation and microbial competitiveness. Using publicly available data from NCBI, we applied BAGEL4 and core genome multilocus sequence typing (cgMLST) approaches to identify and characterize bacteriocin genes, revealing a high level of conservation of major bacteriocins among strains. Analysis of nucleotide polymorphisms within bacteriocin-encoding sequences showed that these genes are generally conserved, likely due to strong purifying selection. These findings suggest that bacteriocins in L. crispatus are functionally conserved, underscoring their potential role in maintaining vaginal health through microbial competition and pathogen exclusion.\n\nComparative genomic analysis of bacteriocin genes in Lactobacillus crispatus strains.", "token_count": 240, "char_count": 1088, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7388, "quality_score": 0.8694, "entities": { "genes": [ "BAGEL4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:55.008226", "source": { "split": "train_shard_00000", "doc_id": 245 }, "chunk_id": "train_shard_00000_245_0", "global_id": 276 }, { "text": "The aim of the study was to isolate and characterize lactic acid bacteria (LAB) from traditional dairy products (tarkhineh) in Kermanshah in western Iran, with a view to their probiotic potential and antimicrobial activity (Candida albicans). A total of 60 tarkhineh samples were randomly screened to isolate the probiotic bacterial strains. Biochemical and physiological analysis confirmed that the isolates were Gram-positive, catalase-negative, and had a round or rod-shaped morphology, in accordance with the LAB classification. Out of 20 isolated strains, five (Ta12, Ta19, Ta37, Ta51, and Ta58) showed a high survival rate (> 94%) under the initial acidity and bile salt screening conditions, which led to their selection for further study. The rescreening confirmed that these strains can survive (> 54%) in enzymatic conditions of the gastrointestinal tract, including the stomach and intestinal tracts. All five strains showed significant antimicrobial activity against 12 common human pathogens, predominantly Gram-positive species, exhibiting inhibition zones ranging from 13.33 to 25.33 mm. Immunological tests revealed negative hemolysis (γ-hemolysis), which indicates that all five strains are safe. However, strains of Ta19 and Ta51 demonstrated higher susceptibility to nine common antibiotics (cefixime, azithromycin, amoxicillin, doxycycline, sulfamethoxazole, ciprofloxacin, cephalexin, amoxicillin-clavulanic acid, and vancomycin), as evidenced by susceptibility spectrum ranging from 12.00 to 39.67 mm", "token_count": 437, "char_count": 1522, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7295, "quality_score": 0.8647, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:55.652605", "source": { "split": "train_shard_00000", "doc_id": 246 }, "chunk_id": "train_shard_00000_246_0", "global_id": 277 }, { "text": "In addition, these two strains showed superior hydrophobicity (> 57%), satisfactory cell adhesion (> 41%), increased cholesterol uptake (> 37%), enhanced biofilm formation (> 26%), and improved properties of auto-aggregation (> 43%) and co-aggregation (> 36%). Antifungal tests showed that Ta19 at 10\n\nSynergistic antimicrobial and probiotic activity of lactic acid bacteria isolated from Tarkhineh against Candida albicans.", "token_count": 146, "char_count": 424, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8448, "quality_score": 0.9224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:56.128801", "source": { "split": "train_shard_00000", "doc_id": 246 }, "chunk_id": "train_shard_00000_246_1", "global_id": 278 }, { "text": "The objective of this study was to investigate the hepatotoxic effects and molecular mechanisms underlying di(2-ethylhexyl) phthalate (DEHP)-induced intrahepatic cholestasis of pregnancy (ICP) through a network toxicology approach. Utilizing liver transcriptomics in conjunction with the GeneCards, DisGeNET, and OMIM databases, we identified 151 potential targets associated with DEHP-induced ICP. Subsequent analyses employing STRING and cytoscape software revealed five core targets: EGFR, STAT3, JUN, FOS, and HSP90AA1. Functional enrichment analysis via gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) pathways indicated significant involvement in cholesterol synthesis, bile salt secretion, and the MAPK signaling pathway. Molecular docking studies conducted using AutoDock demonstrated strong binding affinities between DEHP and these core targets. In conclusion, this study offers novel insights into the molecular mechanisms of DEHP-induced hepatotoxicity during pregnancy while providing a systematic framework for assessing risks associated with DEHP exposure; thus contributing to the prevention and treatment of ICP.\n\nTranscriptomic and network toxicology approaches reveal potential mechanisms of DEHP induced intrahepatic cholestasis during pregnancy.", "token_count": 308, "char_count": 1288, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [ "STAT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:56.701641", "source": { "split": "train_shard_00000", "doc_id": 247 }, "chunk_id": "train_shard_00000_247_0", "global_id": 279 }, { "text": "Haemophilus influenza, a major contributor to respiratory infections such as pneumonia, meningitis, sinusitis, chronic bronchitis, and acute otitis, poses a significant public health challenge, driven by rising antibiotic resistance particularly among the non-typeable H. influenza (NTHi) strains given their ability to evade immune surveillance. To address this, we employed a comprehensive immunoinformatics pipeline integrated with extensive pan-genome analysis of 59 strains of H. influenzae to design a novel multiepitope vaccine (MEV) candidate targeting most virulent and clinically significant proteins. Key surface exposed and virulence associated proteins, including Protein E, PilA, Protein D, P4, TolC, YadA, and HifC were prioritized based on their roles in bacterial adhesion, immune evasion, biofilm formation, and nutrient acquisition. Advanced in silico epitope prediction and verification strategies were utilized to map highly immunogenic regions across these proteins, followed by codon optimization to enhance expression efficiency in human systems. To further stabilize the vaccine construct, we performed disulfide engineering to enhance structural integrity and resilience. Comprehensive validation through in silico immune simulations, molecular dynamics (MD) simulations and binding free energy calculations confirmed the structural stability, immunogenic potential, and strong receptor affinity of the MEV candidate. Phylogenetic and virulence factor analysis further corroborated the broad coverage of the pathogenic relevance of the selected proteins. Together, our integrative approach presents a robust pipeline for rational vaccine design, offering a promising avenue toward combating multidrug resistant and immune evasive H. influenza strains.\n\nMolecular insights into pangenome localization and constructs design for Hemophilus influenza vaccine.", "token_count": 416, "char_count": 1881, "word_count": 244, "semantic_coherence": 1, "information_density": 0.7295, "quality_score": 0.8648, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:57.320096", "source": { "split": "train_shard_00000", "doc_id": 248 }, "chunk_id": "train_shard_00000_248_0", "global_id": 280 }, { "text": "This study investigates the correlation between the expression of the sortase A gene and the probiotic characteristics of Lactiplantibacillus plantarum strains, with a focus on adhesion capabilities, acid tolerance, and bile salt resistance. Seven L. plantarum strains were isolated from traditional dairy products, including yogurt, doogh, cheese, butter, sour cream, kashk, and Lighvan cheese, and evaluated for their probiotic potential. Using real-time PCR, the expression of the sortase A gene was assessed, and the adhesion of these strains to Caco-2 cells-a model for human intestinal epithelial cells-was evaluated. Among the strains, L. plantarum MK08 exhibited the highest resistance to acidic conditions (pH 2.0) and bile salts (0.3%), along with the highest sortase A gene expression. While sortase A expression was not directly correlated with acid and bile tolerance, it was associated with enhanced adhesion capabilities, suggesting its role in probiotic colonization and persistence in the gastrointestinal tract. All L. plantarum strains demonstrated superior adhesion to Caco-2 cells compared to the non-pathogenic control strain Escherichia coli ATCC 25922. Phylogenetic analysis revealed that the sortase gene is conserved across Lactobacillus strains, with no significant differences between probiotic and non-probiotic strains. These findings provide valuable insights into the probiotic potential of L. plantarum, highlighting the functional role of sortase A in adhesion mechanisms and its evolutionary significance. This study underscores the potential of L. plantarum strains as promising probiotic candidates and lays the groundwork for further exploration of sortase-mediated adhesion in probiotic development.\n\nA Peek into the Relationship Between Probiotic Characteristics of Lactiplantibacillus plantarum Strains and Sortase A Gene Expression.", "token_count": 477, "char_count": 1874, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5486, "quality_score": 0.7743, "entities": { "genes": [ "MK08" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:57.960602", "source": { "split": "train_shard_00000", "doc_id": 249 }, "chunk_id": "train_shard_00000_249_0", "global_id": 281 }, { "text": "Unlocking the potential of genetic resources in the Pangenome era.", "token_count": 15, "char_count": 66, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:58.309875", "source": { "split": "train_shard_00000", "doc_id": 250 }, "chunk_id": "train_shard_00000_250_0", "global_id": 282 }, { "text": "Barley (\n\nGenetic resources and pangenome analysis of barley.", "token_count": 17, "char_count": 61, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:59.003428", "source": { "split": "train_shard_00000", "doc_id": 251 }, "chunk_id": "train_shard_00000_251_0", "global_id": 283 }, { "text": "Individuals across a species exhibit substantial presence-absence variation, to the extent that a reference genome from a single individual only contains a subset of the species' genome. Cataloguing genome regions absent from a reference genome can therefore reveal novel genome regions, and some of this variation can be adaptive. In this work, existing short sequencing reads for the underutilised crop lablab (\n\nNovel breeding resources for the underutilised legume, lablab, based on a pangenome approach.", "token_count": 111, "char_count": 508, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7467, "quality_score": 0.8733, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:59.381604", "source": { "split": "train_shard_00000", "doc_id": 252 }, "chunk_id": "train_shard_00000_252_0", "global_id": 284 }, { "text": "The purpose of this paper was to investigate the structural characteristics, physicochemical properties, and hypolipidemic activity of soluble dietary fiber from button mushroom (BMSDF). Our results show that BMSDF is mainly composed of galactose, glucose and mannose, has the typical spectral characteristics of dietary fiber (FT-IR), characteristic diffraction curves (XRD), and the typical characteristics of polysaccharide nuclear magnetic hydrogen spectrum, which contained both α and β glycosidic bonds. The loose and porous microstructure of BMSDF observed under scanning electron microscopy makes it has good water holding capacity, oil holding capacity, cholesterol adsorption capacity, bile salt binding capacity. The lipid metabolism-related enzymes inhibitory assay results showed that 1.2 mg/mL BMSDF reached 75.29 % of the effect of orlistat and the inhibition of cholesterol esterase reached 37.05 %. And 100 μg/mL BMSDF reduces lipid deposition, significantly decreases the content of triglyceride and serum total cholesterol in oleic acid-induced HepG2 high-fat cells, while improves abnormal liver function enzyme activity, exhibiting good hypolipidemic biological activity.\n\nStructure, physicochemical properties, and hypolipidemic activity of soluble dietary fiber obtained from button mushroom (", "token_count": 342, "char_count": 1316, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:00:59.952655", "source": { "split": "train_shard_00000", "doc_id": 253 }, "chunk_id": "train_shard_00000_253_0", "global_id": 285 }, { "text": "Genomic Islands (GEIs) are distinct DNA segments acquired through horizontal gene transfer (HGT), driving bacterial evolution and adaptation. These include Pathogenicity Islands (PAIs), Symbiosis Islands, Antibiotic Resistance Islands, Xenobiotic-Degradation Islands, and Nitrogen Fixation Islands. GEIs contribute to genetic diversity, enhancing bacterial pathogenicity, symbiosis, antibiotic resistance, and xenobiotic degradation. Characterized by variations in GC content, codon bias, and integration sites, they distinguish themselves from the core genome. Advances in genome sequencing and bioinformatics have deepened our understanding of GEIs in bacteria like Salmonella, Vibrio, E. coli, and many more, offering insights into microbial evolution, pathogenicity, and antibiotic resistance mechanisms.\n\nEmerging concept of genomic islands in bacterial adaptation and pathogenicity.", "token_count": 209, "char_count": 888, "word_count": 108, "semantic_coherence": 1, "information_density": 0.787, "quality_score": 0.8935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:00.413249", "source": { "split": "train_shard_00000", "doc_id": 254 }, "chunk_id": "train_shard_00000_254_0", "global_id": 286 }, { "text": "Current advances in next-generation sequencing (NGS) technology and assembling programs permit construct chromosome-level genome assemblies in various plants. In contrast to resequencing, the genome sequences provide comprehensive annotation data useful for plant genetics and breeding. Herein, we constructed a reference-based genome assembly of winter barley (H. vulgare ssp. vulgare) cv. 'Hayakiso 2' using long and short read NGS data and barley reference genome sequences from 'Morex'. We constructed 'Hayakiso 2' genome sequences covering 4.3 Gbp with 55,477 genes. Comparative genomics revealed that 14,106 genes had orthologs to two barley data, wheat (A, B, and D homoeologs, respectively), and rice. From the gene ontology analysis, 2,494 orthologs against wheat and rice but not two barley contained agricultural important genes, such as 'response to biotic and abiotic stress' and 'metabolic process'. Phylogenetic analysis using 76 pangenome data indicated that 'Hayakiso 2' was clustered into Japanese-type genomes with unique alleles. 'Hayakiso 2' genome sequences showed known genes related to flowering and facilitated barley breeding through the development of various markers related to agronomically important alleles such as tolerance to various types of biotic and abiotic stress. Therefore, 'Hayakiso 2' genome sequences will be used for the further barley breeding.\n\nReference-based chromosome-scale assembly of Japanese barley (Hordeum vulgare ssp. vulgare) cultivar Hayakiso 2.", "token_count": 397, "char_count": 1503, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6459, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:01.019022", "source": { "split": "train_shard_00000", "doc_id": 255 }, "chunk_id": "train_shard_00000_255_0", "global_id": 287 }, { "text": "Noni fruit phenolic-rich extract (NFE) has been confirmed to alleviate lipid metabolism disturbance, with emerging evidence implicating bile acids (BAs) metabolism in a gut microbiota-dependent manner in mediating the effect. The effect and potential mechanism of fecal microbiota transplantation from NFE intervention mouse donors (FMT-NFE) on lipid metabolism disorder were investigated. The results reveal FMT-NFE intervention regulated the body weight, lipid profile levels, and liver damage. FMT-NFE intervention upgraded the abundance of bile salt hydrolase (BSH)-expressing bacteria and short-chain fatty acid (SCFA)-producing bacteria in feces, which is accompanied by changes of BSH activity and BAs profile as well as elevation of the SCFA level. Moreover, western blotting and immunofluorescence results confirmed the intestinal FXR-FGF15 pathway was activated by FMT-NFE intervention, which was accompanied by activation of the liver FXR and inhibition of CYP7A1 expression to control cholesterol-to-BAs conversion. These findings underscore the mechanisms behind maintaining BAs and lipid metabolism homeostasis of NFE.\n\nFecal Microbiota Transplantation from Noni Fruit Phenolic-Rich Extract Intervention Mouse Donors Ameliorates Lipid Metabolism Disorder by Regulating the FXR-FGF15 Pathway in a Gut Microbiota-Dependent Manner.", "token_count": 346, "char_count": 1342, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6158, "quality_score": 0.8079, "entities": { "genes": [ "FGF15" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:01.580616", "source": { "split": "train_shard_00000", "doc_id": 256 }, "chunk_id": "train_shard_00000_256_0", "global_id": 288 }, { "text": "Numerous outbreaks of interdigital phlegmon (IP) occurred in Finnish dairy herds country-wide in the 2010s, resulting in significant but varying morbidity and severe clinical signs. These outbreaks increased antibiotic use and caused financial losses on the affected farms. During 2012-2015, we performed a study on the epidemiology, clinical presentation and bacteriology of IP outbreaks on 19 IP-affected farms. In addition, we collected Fusobacterium necrophorum isolates from IP cows for further studies. Here, we present an analysis of 25 isolates from early-stage IP from seven herds representing both moderate and high morbidity using whole genome sequencing (WGS). Our aim was to determine whether a novel contagious F. necrophorum strain had spread between the herds, causing the outbreaks, and whether the isolates possessed antibiotic resistance or known major virulence genes in silico. The Finnish F. necrophorum ssp. necrophorum isolates clustered into seven different groups, each corresponding to the herd of origin. Therefore, the isolates from high and moderate morbidity herds did not cluster together either. Our analysis revealed no known antibiotic resistance genes in the isolates, despite the clinical response to treatment being inconsistent. All isolates harboured virulence genes for leukotoxin and haemolysin but were devoid of adhesin. Instead of only one novel contagious strain, we identified herd-specific strains of F. necrophorum ssp. necrophorum in IP cows from Finnish dairy cattle herds. Therefore, the cause of IP outbreaks in Finland remains unknown and merits further research.\n\nCore genome multilocus sequence typing (cgMLST) indicates herd specificity of Fusobacterium necrophorum ssp. necrophorum isolated from dairy cattle interdigital phlegmon outbreaks in Finland.", "token_count": 449, "char_count": 1810, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5798, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:02.222800", "source": { "split": "train_shard_00000", "doc_id": 257 }, "chunk_id": "train_shard_00000_257_0", "global_id": 289 }, { "text": "Peach (Prunus persica (L.) Batsch) is one of the main agricultural stone fruit crops of the family Rosaceae. Modern breeding is aimed at improving the quality of the fruit, extending the period of its production, increasing its resistance to unfavorable environmental conditions and reducing the total cost of production of cultivated varieties. However, peach breeding is an extremely long process: it takes 10-15 years from hybridization of the parental forms to obtaining fruit-bearing trees. Research into peach varieties as donors of desirable traits began in the 1980s. The first version of the peach genome was presented in 2013, and its appearance contributed to the identification and localization of loci, followed by the identification of candidate genes that control the desired trait. The development of NGS has accelerated the development of methods based on the use of diagnostic DNA markers. Approaches that allow accelerating classical breeding processes include marker-oriented selection (MOS) and genomic selection. In order to develop DNA markers associated with the traits under investigation, it is necessary to carry out preliminary mapping of loci controlling economically desirable traits and to develop linkage maps. SNP-chip approaches and genotyping by sequencing (GBS) methods are being developed. In recent years, genome-wide association analysis (GWAS) has been actively used to identify genomic loci associated with economically important traits, which requires screening of large samples of varieties for hundreds and thousands of SNPs. Study on the pangenome has shown the need to analyze a larger number of samples, since there is still not enough data to identify polymorphic regions of the genome. The aim of this review was to systematize and summarize the major advances in peach genomic research over the last 40 years: linkage and physical map construction, development of different molecular markers, full genome sequencing for peach, and existing methods for genome-wide association studies with high-density SNP markers. This review provides a theoretical basis for future GWAS analysis in order to identify high-performance markers of economically valuable traits for peach and to develop genomic selection of this crop.\n\nModern methods in peach (Prunus persica) genome research.", "token_count": 498, "char_count": 2324, "word_count": 344, "semantic_coherence": 1, "information_density": 0.5901, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:02.863621", "source": { "split": "train_shard_00000", "doc_id": 258 }, "chunk_id": "train_shard_00000_258_0", "global_id": 290 }, { "text": "Metabolic associated fatty liver disease (MAFLD) has a high global prevalence with limited therapeutic optionsand poor efficacy. Probiotics are characterized by their safety and small side effects, making them an effective and safe option for treating chronic diseases. They help regulate gut microbiota balance, reduce inflammation, and improve liver metabolism. In this study, we isolated several strains of Lactobacillus plantarum and evaluated their potential applications in MAFLD. The results of in vitro probiotic property tests showed that L. plantarum 1-2-3 and L. plantarum D4-2 exhibited high bile salt hydrolase activity, strong stress resistance, and rapid growth advantages. Both strains were selected as candidates for lipid-lowering potential. Functional validation showed that these two strains alleviated obesity, abnormal glycolipid metabolism, liver damage, and inflammation in HFD-induced mice. Given that Lactobacillus plantarum 1-2-3 exhibited superior therapeutic effects, its regulatory mechanisms were further investigated. The strain was found to regulate the expression of liver lipid metabolism-related genes such as fas and srebp2, as well as the metabolism of free fatty acids such as petroselinic acid, tricosanoic acid, arachidonic acid, docosahexaenoic acid, and eicosapentaenoic acid. Furthermore, it boosted hepatic antioxidant capacity and suppressed ferroptosis, thereby mitigating the progression of MAFLD. Additionally, L. plantarum 1-2-3 alleviated intestinal inflammation, repaired the intestinal barrier, increased the expression of fxr and cpt1a genes, and alleviated MAFLD symptoms through the gut-liver axis. The 16S rRNA sequencing results showed that L. plantarum 1-2-3 increased the abundance of Ruminococcus and Clostridia microbial communities, while decreasing the abundance of Megamonas and Streptococcus populations, thereby improving the gut microbiota composition to some extent. Overall, the findings of this study suggest that L", "token_count": 508, "char_count": 1986, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6642, "quality_score": 0.8321, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:03.512387", "source": { "split": "train_shard_00000", "doc_id": 259 }, "chunk_id": "train_shard_00000_259_0", "global_id": 291 }, { "text": "plantarum 1-2-3 has significant potential in mitigating the adverse effects of MAFLD, improving fatty acid metabolism, and regulating the gut microbiota.\n\nLactobacillus plantarum 1-2-3 inhibits ferroptosis by regulating dysregulated fatty acid metabolism to protect mice from high-fat diet-induced MAFLD.", "token_count": 94, "char_count": 304, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:03.884239", "source": { "split": "train_shard_00000", "doc_id": 259 }, "chunk_id": "train_shard_00000_259_1", "global_id": 292 }, { "text": "During fuel ethanol production, fermenter tanks are persistently contaminated by lactic acid bacteria (LAB), lowering ethanol yields and causing costly shutdowns for cleaning. In this study, whole-genome sequencing was conducted for 156 Lactiplantibacillus plantarum, Levilactobacillus brevis, Limosilactobacillus fermentum, and Limosilactobacillus mucosae isolates previously obtained in a two-year longitudinal study at a U.S. Midwest corn dry-grind fuel ethanol production facility. Striking similarity between genomes for isolates collected during different years reveal the strong ability of LAB strains to persist in bioethanol fermentation facilities. Furthermore, comparison of bioethanol contaminant genomes and previously published genomes in the same species from other environments showed a smaller, closed pangenome for bioethanol contaminants, indicating their specialization for this niche. Additionally, 39 genomes contained a putative plasmid or transposable element encoding for resistance to the antibiotic virginiamycin, frequently used by fermentation facilities to control LAB contamination. Finally, comparison of L. fermentum isolates that strongly inhibited Saccharomyces cerevisiae fermentation and less inhibitory isolates suggest there may be genetic and metabolic changes underlying these differences. To our knowledge, this study represents the first large-scale genomic analysis for LAB contaminants of bioethanol production, providing new insights into the biology of industrial microbial contaminants that have enormous economic impact.\n\nGenomic insights into persistence, antibiotic resistance, and intraspecific diversity of lactic acid bacterial contaminants at corn dry-grind fuel ethanol facilities.", "token_count": 409, "char_count": 1737, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8417, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:04.505899", "source": { "split": "train_shard_00000", "doc_id": 260 }, "chunk_id": "train_shard_00000_260_0", "global_id": 293 }, { "text": "The increasing prevalence of Acinetobacter baumannii infections and its severity demand the acute necessity for innovative therapeutic targets against it. This study employs comprehensive pangenome analysis to investigate 124 A. baumannii multidrug-resistant strains, to determine the most promising therapeutic targets derived from its core genome. Nucleotide diversity analysis of core and variable gene clusters identified key polymorphisms, suggesting significant evolutionary adaptation. Our findings revealed significant presence/absence variation (PAV) in resistance genes across strains, with 97 antimicrobial drug resistance genes identified. Two gene clusters, cluster-288 and cluster-566, harbored resistance-related genes encoding for beta-lactamase and multidrug efflux pump, respectively, were identified from the core genome that plays a pivotal role in conferring multidrug resistance. The functional enrichment analysis of these gene clusters highlighted key proteins, such as penicillin-binding proteins and outer membrane efflux proteins, as potential targets for drug design. Furthermore, we analyzed the physicochemical properties, virulence potential, active site prediction, and predicted conserved motifs. Structural predictions via 3D modeling and molecular dynamics simulations revealed high stability of key proteins, with RMSD values of 0.52 nm for outer membrane channel subunit AdeK and 0.85 nm for beta-lactamase, suggesting these proteins' potential as novel drug targets and their structural integrity under physiological conditions. Principal component analysis (PCA) highlighted distinct motion patterns within these proteins, providing insights into their functional dynamics. This research contributes to ongoing efforts to combat antibiotic resistance through innovative approaches in drug design and therapeutic interventions.\n\nPangenome-based network analysis of Acinetobacter baumannii reveals the landscape of conserved therapeutic targets.", "token_count": 432, "char_count": 1982, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6586, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:05.137462", "source": { "split": "train_shard_00000", "doc_id": 261 }, "chunk_id": "train_shard_00000_261_0", "global_id": 294 }, { "text": "Bile acid salt (BAS) micellar structures containing phospholipids (PPLs) have many important applications in the field of drug delivery on account of their biocompatibility, but improving their structural stability is a crucial issue for further development. Combined with our previous findings, we hypothesized that coloading of drugs with different hydrophobicities can enhance the structural stability of the micelles. Puerarin (PUE) and tanshinone IIA (TSA) from the Chinese couplet medicines, Radix Puerariae-Salvia miltiorrhiza, were chosen as the model hydrophobic compound pair to be encapsulated into mixed micelles composed of BAS and PPL (BPMM), to form four mixed micellar systems, including blank BPMM, single-drug-carrying BPMM (namely, PUE-loaded BPMM (P-BPMM) and TSA-loaded BPMM (T-BPMM)), and coloaded BPMM (PT-BPMM). The hypothesis was confirmed by comparing the stability of blank BPMM with those of drug-loaded BPMM, single-drug-carrying and drug-cocarrying BPMM, by utilizing molecular dynamics (MD) simulations combined with various experimental observations. Moreover, it is found that the drug distribution preference in the system is not significant when a single drug is loaded. However, when coloaded, the distribution preference of different hydrophobic drugs in the same space is reflected, that is, a more appropriate spatial distribution of drugs in the micellar system can effectively improve the drug-loading stability of the system. The strategy to improve the stability of mixed micelles in this investigation avoids the complex processes associated with modifying the structure of micellar carrier materials and offers the advantages of the use of biosurfactants for drug delivery.\n\nInvestigation of the Enhancement Effect of Coloading of Compounds with Different Hydrophobicities on the Stability of a Phospholipid/Bile Salt Mixed Micellar System.", "token_count": 454, "char_count": 1885, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:05.767206", "source": { "split": "train_shard_00000", "doc_id": 262 }, "chunk_id": "train_shard_00000_262_0", "global_id": 295 }, { "text": "Bile salts (BS) are known to be highly important in modulating bacteria-host crosstalk in the gut, serving as essential signaling molecules governing intestinal homeostasis. However, understanding of this crosstalk is limited by challenges of analyzing the mucosal interface\n\nBacteria enable tolerance to bile salt exposure in an immune-competent human intestinal model.", "token_count": 88, "char_count": 370, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8431, "quality_score": 0.9216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:06.152884", "source": { "split": "train_shard_00000", "doc_id": 263 }, "chunk_id": "train_shard_00000_263_0", "global_id": 296 }, { "text": "Broilers farming has been suffering from multiple challenges, including extensive application of antibiotics. Probiotics-supplemented feed might serve as an efficient alternative to these growth stimulants. We designed the present study to isolate bacteria from chickens' gut and analyze their probiotic characteristics. For isolation, the serial dilution method and De Man-Rogosa-Sharpe agar (MRS) medium were used. Isolates were characterized via biochemical and ribotyping analysis, growth study, antimicrobial and antibiotic sensitivity profiling, acid and bile salt tolerance, intestinal adhesion and cholesterol degradation assays. Four isolates were identified as Enterococcus durans strain PUPro5, Lactobacillus acidophilus strain PUPro6, Enterococcus durans strain PUPro7 and Ligilactobacillus salivarius strain PUPro8. The highest growth rate was observed in E. durans strain PUPro7 with OD\n\nIn-vitro assessment of probiotic potential of bacteria isolated from chicken gastrointestinal tract.", "token_count": 255, "char_count": 1002, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7734, "quality_score": 0.8867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:06.663798", "source": { "split": "train_shard_00000", "doc_id": 264 }, "chunk_id": "train_shard_00000_264_0", "global_id": 297 }, { "text": "Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) (https://github.com/IndraGonz/CLARC) improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8000+ Streptococcus pneumoniae genomes, CLARC reduced accessory gene estimates by >30% and improved evolutionary predictions based on accessory gene frequencies. CLARC is effective across different bacterial species, making it a broadly applicable tool for comparative genomics. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.\n\nLinkage-based ortholog refinement in bacterial pangenomes with CLARC.", "token_count": 264, "char_count": 1145, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7589, "quality_score": 0.8794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:07.265604", "source": { "split": "train_shard_00000", "doc_id": 265 }, "chunk_id": "train_shard_00000_265_0", "global_id": 298 }, { "text": "Aligning genomes into common coordinates is central to pangenome construction, though computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) help to frame and solve the multiple alignment problem. We introduce Mumemto, a tool that computes multi-MUMs and other match types across large pangenomes. Mumemto allows for visualization of synteny, reveals aberrant assemblies and scaffolds, and highlights pangenome conservation and structural variation. Mumemto computes multi-MUMs across 320 human assemblies (960GB) in 25.7 h with 800 GB of memory and hundreds of fungal assemblies in minutes. Mumemto is implemented in C++ and Python and available open-source at https://github.com/vikshiv/mumemto (v1.1.1 at doi.org/10.5281/zenodo.15053447 ).\n\nMumemto: efficient maximal matching across pangenomes.", "token_count": 232, "char_count": 821, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:07.745880", "source": { "split": "train_shard_00000", "doc_id": 266 }, "chunk_id": "train_shard_00000_266_0", "global_id": 299 }, { "text": "The tomato (Solanum lycopersicum L.), a principal fruit crop, exhibits significant genetic diversity shaped by domestication and breeding. Analysis of the gene-based super-pangenome, a catalogue of all genes across diverse genome-sequenced tomatoes, has not yet been fully explored. Here, we present a comprehensive analysis of the gene-based super-pangenome across 61 genetically diverse tomato varieties, revealing 59 066 orthologous groups, thereby providing a detailed genetic framework for understanding the evolution of tomatoes. Our phylogenetic analysis recalibrates the position of S. galapagense, challenging existing paradigms of tomato evolution. Identification of genes linked to key agronomic traits such as fruit size, ripening and stress tolerance, along with their presence/absence variation among accessions, offers a rich source of genetic markers for breeding programs. The study also highlights the impact of whole-genome triplication (WGT) and tandem gene duplication (TD) events on gene family expansion, particularly in distant wild relatives. The analysis of the LRR-RLK gene family, important for plant development and defence, reveals substantial sequence diversity and conservation. Rapidly evolving genes and those under positive selection, such as HAI3, CYP711A1/MAX1, WRKY9 and CNGC15, are implicated in stress tolerance and defence mechanisms. The identification of these genes, along with specific pathogenesis-related genes in distant wild relatives, suggests potential strategies to improve fruit shelf life, fruit set and stress tolerance in elite tomato cultivar breeding. Additionally, we have developed the tomatoPangenome platform, integrating genomic and pangenomic data, gene families and tools, to support sustainable production of high-quality, climate-resilient tomatoes and advance selective breeding for future food security.\n\nPhylogenomic and super-pangenome analyses unveil the genetic landscape of tomato evolution and domestication.", "token_count": 447, "char_count": 1983, "word_count": 263, "semantic_coherence": 1, "information_density": 0.673, "quality_score": 0.8365, "entities": { "genes": [ "CNGC15", "HAI3", "WRKY9", "MAX1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:09.017260", "source": { "split": "train_shard_00000", "doc_id": 267 }, "chunk_id": "train_shard_00000_267_0", "global_id": 300 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC2) is a rare pediatric cholestatic liver disease caused by genetic deficiency in the bile salt export pump (BSEP, ABCB11). BSEP is an ATP-binding cassette transporter and the primary regulator of hepatic bile acid efflux. Loss of BSEP function in PFIC2 leads to cholestasis and intrahepatic accumulation of bile acids, the native toxicity of which drives progressive liver injury, in a manner that correlates with ABCB11 genotype. Here, to support ongoing PFIC2 research, we present two novel translational tools, 1) a codified evidence-based catalog of published disease relevant ABCB11 mutations and 2) a knockin mouse model of the PFIC2-associated missense variant E297G. Using a combination of AI-based indexing of the literature and manual review, we identified 476 nonbenign ABCB11 variants in published patients with cholestatic disease, of which 240 were associated with PFIC2. Additionally, we present phenotypic validation of a novel knockin mouse model of the cholestasis-associated ABCB11 E297G variant. Bsep\n\nAn ABCB11 variant registry and novel knockin mouse model of PFIC2 based on the clinically relevant ABCB11 E297G variant.", "token_count": 337, "char_count": 1200, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:09.577745", "source": { "split": "train_shard_00000", "doc_id": 268 }, "chunk_id": "train_shard_00000_268_0", "global_id": 301 }, { "text": "Aligning to a linear reference genome can result in a higher percentage of reads going unmapped or being incorrectly mapped owing to variations not captured by the reference, otherwise known as reference bias. Recently, in efforts to mitigate reference bias, there has been a movement to switch to using pangenomes, a collection of genomes, as the reference. In this paper, we introduce Moni-align, the first short-read pangenome aligner built on the\n\nAccurate short-read alignment through", "token_count": 108, "char_count": 489, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7733, "quality_score": 0.8867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:09.956234", "source": { "split": "train_shard_00000", "doc_id": 269 }, "chunk_id": "train_shard_00000_269_0", "global_id": 302 }, { "text": "Physiologically Based Biopharmaceutics Modeling (PBBM) links in vitro solubility and dissolution kinetics of oral drugs to Physiologically Based Pharmacokinetic (PBPK) models, enabling the prediction of drug bioavailability. This approach reduces reliance on animal experimentation during drug development. Part 1 of this series introduces a novel, open-source PBBM workflow using the Open Systems Pharmacology (OSP) Software Suite. It combines the newly developed OSP solubility toolbox to estimate drug aqueous solubility and bile salt micelle partitioning from in vitro data, with an updated MoBi® dissolution model that accounts for factors such as hydrodynamic diffusion layer thickness changes and micelle partitioning. This approach was applied to poorly soluble, highly permeable vericiguat, a first-in-class soluble guanylate cyclase (sGC) stimulator for the treatment of chronic heart failure. The solubility models effectively described the aqueous solubility-pH profile and bile salt partitioning, while the dissolution model captured the in vitro dissolution kinetics of various tablet formulations. Part 2 focuses on integrating developed PBBM sub-models into PBPK models using PK-Sim® to predict vericiguat's clinical pharmacokinetics after oral administration. This PBBM workflow demonstrates potential for diverse applications, including predictive bioavailability and bioequivalence assessments, in silico formulation optimization, formulation bridging, dose selection, and setting dissolution specifications.\n\nDevelopment of a novel physiologically based biopharmaceutics modeling (PBBM) framework using the open systems pharmacology suite, part 1: in vitro modeling of vericiguat.", "token_count": 403, "char_count": 1700, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6575, "quality_score": 0.8288, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:10.568256", "source": { "split": "train_shard_00000", "doc_id": 270 }, "chunk_id": "train_shard_00000_270_0", "global_id": 303 }, { "text": "Peroxisomes are eukaryotic oxidative organelles involved in numerous metabolic functions that include fatty acid oxidation, bile acid synthesis, and detoxification of reactive oxygen species. ATP-binding cassette transporters of the D subfamily (ABCD1-3) mediate the import of CoA thioesters of fatty acids into the peroxisome. ABCD3, the most abundant of these transporters in the peroxisomal membrane, facilitates the transport of a broad spectrum of substrates including branched-chain fatty acids, very long-chain fatty acids, bile salt intermediates, and dicarboxylic acids. Mutations in ABCD3 are associated with defects in congenital bile acid synthesis and variants of Zellweger syndrome. The structural and functional details of the human ABCD3 transporter remain unclear, despite its significance. In this study, we report the cryogenic sample electron microscopy (cryo-EM) structures of full-length human ABCD3 in its apo state and bound to one of the physiological substrates (phytanoyl-CoA) at resolutions of 3.33 Å and 3.13 Å, respectively. Our biochemical assays reveal that substrate binding induces ATPase activity in ABCD3, suggesting a substrate-dependent conformational change. Structural comparison of the apo and substrate bound states demonstrate that the substrate interaction brings nucleotide-binding domains closer, providing a mechanistic basis of substrate induced ATPase activity. These findings offer critical insights into the transport mechanism of ABCD3 and lay a structural foundation for understanding its role in peroxisomal metabolite import and related diseases.\n\nMolecular mechanism of substrate transport by human peroxisomal ABCD3.", "token_count": 421, "char_count": 1673, "word_count": 228, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [ "ABCD1", "ABCD3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:11.183804", "source": { "split": "train_shard_00000", "doc_id": 271 }, "chunk_id": "train_shard_00000_271_0", "global_id": 304 }, { "text": "Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Reference Consortium, which has been shown to improve read mapping and structural variant genotyping. In this work, we introduce pangenome-aware DeepVariant, a variant caller that uses a pangenome reference alongside sample-specific read alignments. It generates pileup images of both reads and pangenome haplotypes near potential variants and uses a Convolutional Neural Network to infer genotypes. This approach allows directly using a pangenome for distinguishing true variant signals from sequencing or alignment noise. We assessed its performance on various short-read sequencing platforms and read mappers. Across all settings, pangenome-aware DeepVariant outperformed the linear-reference-based DeepVariant, reducing errors by up to 25.5%. We also show that Element reads with pangenome-aware DeepVariant can achieve 23.6% more accurate variant calling performance compared to existing methods.\n\nPangenome-aware DeepVariant.", "token_count": 248, "char_count": 1164, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7237, "quality_score": 0.8618, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:11.664576", "source": { "split": "train_shard_00000", "doc_id": 272 }, "chunk_id": "train_shard_00000_272_0", "global_id": 305 }, { "text": "Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.\n\nLinkage of nucleotide and functional diversity varies across gut bacteria.", "token_count": 230, "char_count": 1133, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7172, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:12.134507", "source": { "split": "train_shard_00000", "doc_id": 273 }, "chunk_id": "train_shard_00000_273_0", "global_id": 306 }, { "text": "The tiny-TIM system offers an in vitro platform for the simulation of physiological processes occurring in human stomach and small intestine aiding in drug product development by predicting the bioperformance of oral formulations under fasted and fed state intake conditions. To assess this in vitro system in terms of its physiological relevance, we performed a detailed analysis of the composition as well as the solubilizing capacity of tiny-TIM intestinal fluids (TIF), and compared this to previously collected and analysed human intestinal fluids (HIF). Moreover, the impact of meal type on TIF composition and solubilising capacity was investigated by using either a liquid meal or a solid meal. In the fasted state, TIF exhibited lower lipid concentrations with a TIF/HIF ratio of 0.27, and elevated bile salt levels (TIF/HIF ratio of 1.8). Fasted state TIF generally overpredicted the solubilizing capacity of HIF, likely due to its higher bile salt concentrations. In the fed state, TIF contained biorelevant lipid concentrations but remained monophasic without phase separation, unlike HIF. This was likely due to higher bile salt levels (5.3 times that of HIF), which solubilized all lipids into the micellar phase. This resulted on average in a 3.3-fold increase in solubility of the poorly water-soluble model compounds in the micellar fraction of TIF as compared to HIF. Shifting from a liquid to a solid meal had minimal impact on TIF composition and solubilizing capacity.\n\nTiny-TIM intestinal fluids versus human intestinal fluids: A comparison of their composition and solubilizing capacity for poorly soluble drugs.", "token_count": 398, "char_count": 1635, "word_count": 250, "semantic_coherence": 1, "information_density": 0.548, "quality_score": 0.774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:12.753627", "source": { "split": "train_shard_00000", "doc_id": 274 }, "chunk_id": "train_shard_00000_274_0", "global_id": 307 }, { "text": "The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow-evolving lineage (SEL) and fast-evolving lineage (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 116 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO₂, and cold tolerance.\n\nGenetic and phenotypic diversity of wine-associated Hanseniaspora species.", "token_count": 379, "char_count": 1650, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7228, "quality_score": 0.8614, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:13.339621", "source": { "split": "train_shard_00000", "doc_id": 275 }, "chunk_id": "train_shard_00000_275_0", "global_id": 308 }, { "text": "The genomes of 39 clinical carbapenemase-producing A. baumannii (CP-Ab) and 2 A. pittii (CP-Ap) isolates from dogs and cats in Thailand (2016-2019) were analyzed for phylogenetic relationship and antimicrobial resistance gene (ARG) localization. Resistome and core genome multilocus sequence typing (cgMLST) analysis identified distinct ARG patterns within CP-Ab sequence type (ST) 2 (n = 4) and ST1575 (n = 1) of clonal complex (CC) 2, ST25 (n = 6), ST1576 (n = 1), and ST1581 (n = 2) of CC25, ST16 (n = 13), ST23 (n = 2), ST149 (n = 9), ST1093 (n = 1), along with CP-Ap (n = 2). Complete genome analysis of one CP-Ap strain and 15 representative CP-Ab strains from each clone identified strains with one to three copies of bla\n\nLocalization of AbaR4-type genomic islands and multidrug resistance plasmids in multiple Acinetobacter baumannii clones and Acinetobacter pittii from infections of dogs and cats.", "token_count": 326, "char_count": 908, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8221, "entities": { "genes": [ "ST1575", "ST23", "ST25", "ST1576", "ST149", "ST1093", "ST1581", "ST16", "CC25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:13.900536", "source": { "split": "train_shard_00000", "doc_id": 276 }, "chunk_id": "train_shard_00000_276_0", "global_id": 309 }, { "text": "The R2R3-MYB transcription factors (TFs) are pivotal regulators of plant growth, development, and stress responses. However, their genetic diversity and functional roles in\n\nPan-genome analysis of the R2R3-MYB genes family in", "token_count": 59, "char_count": 225, "word_count": 31, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:14.267373", "source": { "split": "train_shard_00000", "doc_id": 277 }, "chunk_id": "train_shard_00000_277_0", "global_id": 310 }, { "text": "Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific condition characterized by pruritus and elevated bile acids. It typically manifests in the third trimester of pregnancy and has been associated with hormonal and genetic factors. Early-onset ICP poses unique diagnostic challenges and may contribute to increased risks of adverse maternal and fetal outcomes. We present a case of severe ICP identified in the early second trimester and later attributed to a rare gene variant. A 24-year-old patient (G3P0202) was admitted at 17 weeks of gestation with pruritis, abdominal pain, and jaundice. Laboratory studies were notable for elevated total and direct bilirubin as well as elevated bile acids. The patient's medical history included early-onset ICP accompanied by jaundice in all previous pregnancies. A cholestasis gene panel revealed an autosomal recessive variant in the ABCB11 gene, which encodes a bile salt export pump and is associated with benign recurrent intrahepatic cholestasis (BRIC). Throughout the duration of her pregnancy, the patient was co-managed with the hepatobiliary service, and her symptoms were adequately controlled with ursodeoxycholic acid, rifampin, and hydroxyzine. She labored spontaneously at 34 weeks of gestation and delivered a healthy infant. This case underscores the importance of genetic evaluation in the assessment of atypical ICP, particularly in early-onset, recurrent, or treatment-refractory cases. It also highlights the need for multidisciplinary management of complex cases with obstetricians, hepatologists, and genetic counselors.\n\nEarly-onset intrahepatic cholestasis of pregnancy resulting from a genetic mutation: A case report.", "token_count": 427, "char_count": 1701, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:14.887049", "source": { "split": "train_shard_00000", "doc_id": 278 }, "chunk_id": "train_shard_00000_278_0", "global_id": 311 }, { "text": "Aspergillus oryzae is an industrially important fungus used to produce traditional fermented foods and beverages in Korea and other East Asian countries. Conversely, A. flavus, which exhibits approximately 99.5 % of genomic similarity to A. oryzae, is a species that endangers food safety due to aflatoxin production. This study involved the genome sequences of A. oryzae KBP3 and KSS2 isolated from nuruk, a traditional Korean fermentation starter, assembled at the chromosomal level. To investigate differences among closely related species concerning food safety, compartive genome analysis was conducted on 30 strains of Aspergillus section Flavi, including nuruk strains and 28 genome sequences sourced from additional sequencing and the GenBank database. A detailed interspecific diversity was compared by examining the composition and chromosomal locations of annotated genes across 30 strains. A phylogenetic tree based on whole genome sequences, orthologous genes, and single nucleotide polymorphisms of core genes across 30 strains divided A. oryzae and A. flavus into two separate clades with some exceptions. This study presents two high-quality whole genome sequences of A. oryzae, providing significant genetic insights for this species and its closely related species. Our study confirmed the wide range of enzyme-related genes in A. oryzae isolated from nuruk, and its intraspecific genomic diversity. Our findings also systematically organize the pangenome analysis data of closely related species within Aspergillus section Flavi at the chromosomal level, enhancing the understanding of the genetic information relevant to food safety-related species.\n\nComparative genome analyses of Aspergillus oryzae and Aspergillus flavus originated from a Korean fermentation starter, nuruk.", "token_count": 434, "char_count": 1797, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5929, "quality_score": 0.7964, "entities": { "genes": [ "KSS2", "KBP3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:15.512856", "source": { "split": "train_shard_00000", "doc_id": 279 }, "chunk_id": "train_shard_00000_279_0", "global_id": 312 }, { "text": "Helicobacter pylori (H. pylori) is the leading cause of infectious gastritis, and its resistance to antibiotics is becoming increasingly significant. Probiotics have been widely reported to have antagonistic effects on H. pylori. In this study, 52 strains of lactic acid bacteria (LAB) were isolated from the feces of healthy human and animal. The acid tolerance, anti-H. pylori ability, urease inhibition rate, and nickel adsorption rate of 19 LAB were determined. PCA evaluation revealed Lactiplantibacillus plantarum (L. plantarum) NCUA001057, Pediococcus pentosaceus (P. pentosaceus) NCUH006018, and L. plantarum NCUH001090 displaying the best comprehensive performance. Subsequently, the hemolytic, bile salt tolerance, antioxidant capacity, co-aggregation ability with H. pylori, and adhesion rate to AGS cells of three LAB were evaluated. Moreover, three LAB downregulated the production of IL-1β and IL-8 in H. pylori pre-treated AGS cells. We preliminarily studied the antibacterial substances of three LAB which mainly included acid, hydrogen peroxide, and protein, and the antibacterial substances are heat-tolerant. Furthermore, we found that the main modes of antibacterial action of P. pentosaceus NCUH006018 were as follows: inhibited the adhesion of H. pylori to AGS cells, made H. pylori spherical and destroyed its intact cell structure, and downregulated the metabolism genes of H. pylori flagellin and ribosome. In this study, the high potential of antagonizing H. pylori by three novel LAB was demonstrated, and their mode of antibacterial action provided a new strategy for prevention or inhibition of H. pylori infection.\n\nScreening, Characterization, and Mode of Action of Three Lactic Acid Bacteria Against Helicobacter pylori.", "token_count": 496, "char_count": 1752, "word_count": 250, "semantic_coherence": 1, "information_density": 0.616, "quality_score": 0.808, "entities": { "genes": [ "NCUA001057", "NCUH006018", "NCUH001090" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:16.157459", "source": { "split": "train_shard_00000", "doc_id": 280 }, "chunk_id": "train_shard_00000_280_0", "global_id": 313 }, { "text": "Bile salts have received considerable interest in pharmaceutical formulations for increased bioavailability of the drug. Peculiar physicochemical properties of bile salts and their interface-specific interactions with cosurfactants are believed to be crucial for such formulations. Here, we have investigated the interfacial properties of sodium deoxycholate (NaDC; bile salt) at the air/water and air/water-cetylpyridinium chloride (CPC; pharmaceutically important cosurfactant) interfaces using vibrational sum frequency generation (VSFG), Raman spectroscopy, and surface tensiometry. VSFG, being an inherently interface-selective technique, provides the vibrational spectra of interfacial molecules without interference from the bulk. To understand the peculiarity of NaDC, parallel VSFG measurements were conducted with a conventional anionic surfactant, sodium dodecyl sulfate (SDS). Surface tension measurement revealed that NaDC is more surface active than SDS. Nevertheless, the interfacial water exhibits a weaker orientational order in the presence of NaDC (0.5 mM) than with SDS (0.5 mM), suggesting a weaker interfacial electric field for the former. We propose that NaDC predominantly exists in the protonated neutral form (DC\n\nDistinct Interfacial Behavior of Bile Salts and Its Interaction with Cetylpyridinium Chloride Cosurfactant at the Air/Water Interface.", "token_count": 339, "char_count": 1375, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6983, "quality_score": 0.8492, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:16.731743", "source": { "split": "train_shard_00000", "doc_id": 281 }, "chunk_id": "train_shard_00000_281_0", "global_id": 314 }, { "text": "The gut microbiota plays a crucial role in gastrointestinal health, immune function, and overall well-being. Dysbiosis has been linked to various conditions such as colon cancer, atopic diseases, mental disorders, autoimmune disorders, obesity, and diabetes. This in vitro study aims to assess the safety and functional potential of two probiotic strains, Lactiplantibacillus (L) plantarum and Bifidobacterium (B) longum, focusing on their anti-lipidemic, anti-diabetic, antioxidant, and probiotic properties. The strains were tested for stress tolerance, including acidic, alkaline, osmotic, oxidative, thermal, detergent, bile salt, and pancreatic enzyme conditions. Both strains exhibited strong resilience, often surpassing the control strain. Their antioxidant activity, measured by radical scavenging ability, was comparable to ascorbic acid, with values of 77% for L. plantarum and 92% for B. longum. Cholesterol-lowering capacity reached 50% and 49% after 3 days, increasing to 59% and 78% after 7 days, respectively. Hydrophobicity, an indicator of adhesion potential, was approximately 78% for L. plantarum and 80% for B. longum. Additionally, both strains showed low α-amylase activity (91.65 and 92.33 U/ml), suggesting a potential role in slowing carbohydrate digestion and managing blood glucose levels. Overall, the strains demonstrated favorable safety profiles and promising functional attributes for alleviating hyperlipidemia and diabetes. PCA and heatmap analyses further highlighted L. plantarum as the most promising candidate.\n\nComparative in silico analyses between Lactiplantibacillus plantarum and Bifidobacterium longum concerning probiotic properties, anti-lipidemic, and anti-diabetic in vitro activities.", "token_count": 482, "char_count": 1734, "word_count": 229, "semantic_coherence": 1, "information_density": 0.7031, "quality_score": 0.8515, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:17.370354", "source": { "split": "train_shard_00000", "doc_id": 282 }, "chunk_id": "train_shard_00000_282_0", "global_id": 315 }, { "text": "Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We previously developed Mumemto, which computes maximal unique matches (multi-MUMs) across pangenomes using compressed indexing. In this work, we extend Mumemto by introducing two new partitioning and merging strategies. Both strategies enable highly parallel, memory efficient, and updateable computation of multi-MUMs. One of the strategies, called string-based merging, is also capable of conducting the merges in a way that follows the shape of a phylogenetic tree, naturally yielding the multi-MUM for the tree's internal nodes as well as the root. With these strategies, Mumemto now scales to 474 human haplotypes, the only multi-MUM method able to do so. It also introduces a time-memory tradeoff that allows Mumemto to be tailored to more scenarios, including in resource-limited settings.\n\nPartitioned Multi-MUM finding for scalable pangenomics.", "token_count": 247, "char_count": 1047, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7655, "quality_score": 0.8828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:17.853515", "source": { "split": "train_shard_00000", "doc_id": 283 }, "chunk_id": "train_shard_00000_283_0", "global_id": 316 }, { "text": "The equilibrium between Th17 and Treg cells plays a crucial role in the imbalance of intestinal immune homeostasis caused by a high-fat diet (HFD). SPa denotes the main component of sea buckthorn polysaccharides; its effects and potential pathways on inflammation caused by HFD-induced Th17/Treg immune imbalance are still unclear. Therefore, we conducted research on it. We discovered that SPa mitigates HFD-induced intestinal inflammation and barrier dysfunction by modulating specific pathways. Moreover, we observed that SPa significantly enriches KEGG pathways related to secondary bile acid biosynthesis and steroid degradation, especially enriching bacterial strains holding bile salt hydrolase (BSH) and 3β-hydroxysteroid dehydrogenase, such as\n\nSea Buckthorn Polysaccharides Regulate Bile Acids Synthesis and Metabolism through FXR to Improve Th17/Treg Immune Imbalance Caused by High-Fat Diet.", "token_count": 247, "char_count": 903, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7131, "quality_score": 0.8566, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:18.352573", "source": { "split": "train_shard_00000", "doc_id": 284 }, "chunk_id": "train_shard_00000_284_0", "global_id": 317 }, { "text": "Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due to the scale and complexity of pangenomic data. We present a practical and scalable indexing framework based on tag arrays, which annotate positions in the Burrows-Wheeler transform (BWT) with graph coordinates. Our method extends the FM-index with a run-length compressed tag structure that enables efficient retrieval of all unique graph locations where a query pattern appears. We introduce a novel construction algorithm that combines unique\n\nLossless Pangenome Indexing Using Tag Arrays.", "token_count": 141, "char_count": 691, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7526, "quality_score": 0.8763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:18.809343", "source": { "split": "train_shard_00000", "doc_id": 285 }, "chunk_id": "train_shard_00000_285_0", "global_id": 318 }, { "text": "The Global Panzootic Lineage (GPL) of Batrachochytrium dendrobatidis (Bd) has been described as a main driver of amphibian extinctions. Pathogen studies have benefited from three Bd-GPL strain genomes, but identifying the genetic and molecular features that distinguish the B. dendrobatidis lineages requires additional high-quality genomes from diverse lineages. We sequenced and assembled genomes with Oxford Nanopore Technologies to produce assemblies of three Bd-BRAZIL isolates and one nonpathogen outgroup species Polyrhizophydium stewartii. The Bd-BRAZIL assembly sizes ranged between 22.0 and 26.1 Mb with 8,495 to 8,620 predicted protein-coding genes. We sought to categorize the pangenome of the species by identifying homologous genes across the sampled genomes as either being core and present in all strains, or accessory and shared among strains in a lineage, an analysis that has not yet been conducted on B. dendrobatidis and its lineages. We identified a core genome consisting of 6,278 gene families, and an accessory genome of 202 Bd-BRAZIL and 172 Bd-GPL specific gene families. We discovered copy number differences in pathogenicity gene families: M36 Peptidases, Crinkler Necrosis genes, Aspartyl Peptidases, Carbohydrate-Binding Module-18 genes, and S41 Proteases, between Bd-BRAZIL and Bd-GPL strains. Comparison of B. dendrobatidis and two closely related saprophytic species identified differences in protein sequence and domain counts for M36 and CBM18 families respectively. Our pangenome analysis of lineage-specific gene content led us to explore how the selection of the reference genome affects recovery of RNAseq transcripts when comparing different strains. We tested the hypothesis that genomic variation among Bd-GPL and Bd-BRAZIL lineages can impact transcript count data by comparing results with our new Bd-BRAZIL genomes as the reference genomes", "token_count": 512, "char_count": 1885, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6292, "quality_score": 0.8146, "entities": { "genes": [ "CBM18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:19.456897", "source": { "split": "train_shard_00000", "doc_id": 286 }, "chunk_id": "train_shard_00000_286_0", "global_id": 319 }, { "text": "Our analysis examines the genomic variation between strains in Bd-BRAZIL and Bd-GPL and offers insights into the application of these high-quality reference genomes resources for future studies.\n\nComparative Genomics Reveals Intra and Inter Species Variation in the Pathogenic Fungus Batrachochytrium dendrobatidis.", "token_count": 82, "char_count": 315, "word_count": 41, "semantic_coherence": 1, "information_density": 0.8537, "quality_score": 0.9268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:19.877108", "source": { "split": "train_shard_00000", "doc_id": 286 }, "chunk_id": "train_shard_00000_286_1", "global_id": 320 }, { "text": "Candidatus Altiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of two Ca. Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high-CO\n\nDifferential Expression of Core Metabolic Functions in Candidatus Altiarchaeum Inhabiting Distinct Subsurface Ecosystems.", "token_count": 128, "char_count": 533, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7681, "quality_score": 0.8841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:20.341745", "source": { "split": "train_shard_00000", "doc_id": 287 }, "chunk_id": "train_shard_00000_287_0", "global_id": 321 }, { "text": "Three novel, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated Du54ᵀ, Du274ᵀ and P351ᵀ, were isolated from contaminated environments in Anseong, South Korea. Strains Du54ᵀ and Du274ᵀ originated from landfill soil, whilst P351ᵀ was obtained from parking lot soil. These sites are frequently exposed to pollutants such as petroleum hydrocarbons, heavy metals and industrial runoff, which exert selective pressures on microbial communities. The taxonomic positions of the strains were determined using a polyphasic approach, including 16S rRNA gene sequencing, draft genome analysis and whole-genome-based phylogenetic reconstruction. Phylogenetic trees based on both 16S rRNA genes and core genome sequences (Type Genome Server and AutoMLST) showed that the three isolates belong to the genus", "token_count": 230, "char_count": 814, "word_count": 110, "semantic_coherence": 1, "information_density": 0.8091, "quality_score": 0.9045, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:20.807818", "source": { "split": "train_shard_00000", "doc_id": 288 }, "chunk_id": "train_shard_00000_288_0", "global_id": 322 }, { "text": "Recently, microbial amino-acid-conjugated bile acids (MABAs) have been found to be prevalent in human samples. However, their physiological significance is still unclear. Here, we identify tryptophan-conjugated cholic acid (Trp-CA) as the most significantly decreased MABA in patients with type 2 diabetes (T2D), and its abundance is negatively correlated with clinical glycemic markers. We further demonstrate that Trp-CA improves glucose tolerance in diabetic mice. Mechanistically, we find that Trp-CA is a ligand of the orphan G protein-coupled receptor (GPCR) Mas-related G protein-coupled receptor family member E (MRGPRE) and determine the binding mode between the two. Both MRGPRE-Gs-cyclic AMP (cAMP) and MRGPRE-β-arrestin-1-aldolase A (ALDOA) signaling pathways contribute to the metabolic benefits of Trp-CA. Additionally, we find that the bacterial bile salt hydrolase/transferase of Bifidobacterium is responsible for the production of Trp-CA. Together, our findings pave the way for further research on MABAs and offer additional therapeutic targets for the treatment of T2D.\n\nA microbial amino-acid-conjugated bile acid, tryptophan-cholic acid, improves glucose homeostasis via the orphan receptor MRGPRE.", "token_count": 351, "char_count": 1220, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:21.382367", "source": { "split": "train_shard_00000", "doc_id": 289 }, "chunk_id": "train_shard_00000_289_0", "global_id": 323 }, { "text": "The complete telomere-to-telomere human genome assembly (T2T-CHM13) and the draft human pangenome reference provide unique opportunities to refine DNA methylation (DNAm) studies. Here, we find that T2T-CHM13 calls 7.4% more CpGs genome wide compared to GRCh38 across four widely used short-read DNAm profiling methods and improves the evaluation of probe cross-reactivity and mismatch for Illumina DNAm arrays, yielding new and more reproducible sets of unambiguous probes. The pangenome reference further expands CpG calling by 4.5% in short-read sequencing data and identifies cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity. These benefits facilitate the discovery of biologically relevant DNAm alterations in epigenome-wide association studies (EWASs). For instance, additional DNAm alterations enriched in cancer-related genes and pathways are identified in cancer EWASs. Together, this study highlights the practical applications of T2T-CHM13 and pangenome for genome biology and provides a basis for expansion of DNAm investigations.\n\nComplete reference genome and pangenome improve genome-wide detection and interpretation of DNA methylation using sequencing and array data.", "token_count": 314, "char_count": 1268, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:21.939609", "source": { "split": "train_shard_00000", "doc_id": 290 }, "chunk_id": "train_shard_00000_290_0", "global_id": 324 }, { "text": "Eucalyptus grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials, and biorefinery products. The current v2.0 genome reference for the species served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype-phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The 2 haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70-90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8 to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4 and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E", "token_count": 504, "char_count": 1571, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6926, "quality_score": 0.8463, "entities": { "genes": [ "TAG0014", "HAP1", "HAP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:22.541311", "source": { "split": "train_shard_00000", "doc_id": 291 }, "chunk_id": "train_shard_00000_291_0", "global_id": 325 }, { "text": "grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pangenome variation in the species.\n\nA haplotype-resolved reference genome for Eucalyptus grandis.", "token_count": 62, "char_count": 249, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8485, "quality_score": 0.9242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:22.906051", "source": { "split": "train_shard_00000", "doc_id": 291 }, "chunk_id": "train_shard_00000_291_1", "global_id": 326 }, { "text": "The giant panda (Ailuropoda melanoleuca) is a rare and vulnerable species facing threats from bacterial infections. The extensive use of antibiotics in disease prevention has raised concerns about antibiotic resistance, which reduces treatment efficacy and poses environmental and public health risks. This study aims to analyze the resistance profiles of Escherichia coli (E. coli) in captive pandas, providing insights into the antibiotic resistance genes within their gut microbiota. Twenty-two E. coli isolates were obtained from the feces of 22 captive giant pandas, and whole-genome sequencing was conducted. Sequence types and evolutionary relationships were determined through Multi-Locus Sequence Typing (MLST) and core genome Multi-Locus Sequence Typing (cgMLST), while virulence and resistance genes were identified. Core genome SNP analysis was performed to establish genetic relationships, and AST was conducted to evaluate antibiotic resistance profiles. Whole-genome sequencing revealed 15 distinct sequence types (STs), with ST48 (22.7%, 5 isolates) and ST212 (18.2%, 4 isolates) identified as the dominant lineages. Further resolution using cgMLST revealed that ST48 encompassed multiple cgSTs distributed across different evolutionary branches, while all ST212 isolates belonged to a single cgST. These results demonstrate the utility of cgMLST in resolving genetic diversity and isolate relationships within dominant lineages. Core genome SNP-based phylogenetic analysis grouped isolates with similar serotypes and STs, including a pathogenic cluster closely related to a panda-derived E. coli isolate (AMSHJX04). A total of 88 virulence genes (average 52 per isolate) were widespread, including those involved in iron acquisition systems (yagZ/Y), fimbriae-associated genes (fimA/H), and type II secretion systems (gspM/K)", "token_count": 460, "char_count": 1842, "word_count": 250, "semantic_coherence": 1, "information_density": 0.664, "quality_score": 0.832, "entities": { "genes": [ "ST48", "ST212", "AMSHJX04" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:23.536258", "source": { "split": "train_shard_00000", "doc_id": 292 }, "chunk_id": "train_shard_00000_292_0", "global_id": 327 }, { "text": "Antimicrobial susceptibility testing (AST) showed 59.1% resistance to ciprofloxacin, 18.2% to norfloxacin, and 13.6% to tetracycline, while all isolates remained sensitive to gentamicin and amikacin. Resistance profiling identified 78 resistance genes, primarily efflux pumps (acrB/D, emrA/B) and tetracycline-related mutations (emrK/Y). The gut microbiota of captive giant pandas harbors multiple antibiotic resistance genes, indicating a risk of resistance gene spread. Diverse sequence types, virulence genes, and phylogenetic relationships reveal the genetic complexity of E. coli in this species. Some isolates showed genetic similarities to pathogenic E. coli, emphasizing the need for continuous bacterial monitoring. This threatens antibiotic efficacy, increases infection risks, and complicates health management, underscoring the urgency of addressing resistance in panda conservation.\n\nWhole-genome analysis of escherichia coli isolated from captive giant pandas (ailuropoda melanoleuca) at the Dujiangyan base of the China conservation and research center for the giant panda, Sichuan, China.", "token_count": 297, "char_count": 1104, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7183, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:24.080756", "source": { "split": "train_shard_00000", "doc_id": 292 }, "chunk_id": "train_shard_00000_292_1", "global_id": 328 }, { "text": "Γ-aminobutyric acid (GABA), a major inhibitory neurotransmitter in the central nervous system, has been shown to alleviate various physiological disorders including insomnia, hypertension, depression, and memory loss. Lactic acid bacteria (LAB), recognized as safe GABA producers, have attracted increasing attention. This study aimed to screen GABA-producing LAB from naturally fermented dairy products and evaluate their probiotic potential, antioxidant and neuromodulatory activities, while optimizing GABA production. GABA-producing LAB were screened using the Berthelot method and thin-layer chromatography. The safety of Lactiplantibacillus plantarum SY1 was assessed through hemolysin production and drug sensitivity tests. L. plantarum SY1 demonstrated high tolerance to acidic conditions and low bile salt concentrations, along with significant antioxidant capacity (49 ± 0.2% DPPH radical scavenging rate, 86.1 ± 0.14% hydroxyl radical scavenging rate, and 32.7 ± 1.6% superoxide radical anion scavenging rate). In vivo experiments revealed that L. plantarum SY1 extended the lifespan of C. elegans N2, enhanced oxidative stress resistance, and delayed paralysis in transgenic C. elegans (CL4176) by 23.53%. Through OFAT strategy and RSM optimization, GABA production reached 1.49 g/L under optimal conditions (37℃, pH 4.44, 96 h fermentation, and 4.16% inoculum). These findings demonstrate that L. plantarum SY1 is a promising GABA-producing strain with antioxidant and neuromodulatory effects, suggesting its potential as an anti-aging and neuroprotective probiotic.", "token_count": 474, "char_count": 1579, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7536, "quality_score": 0.8768, "entities": { "genes": [ "CL4176", "SY1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:24.706533", "source": { "split": "train_shard_00000", "doc_id": 293 }, "chunk_id": "train_shard_00000_293_0", "global_id": 329 }, { "text": "Probiotic attributes, antioxidant and neuromodulatory effects of GABA-Producing Lactiplantibacillus plantarum SY1 and optimization of GABA production.", "token_count": 47, "char_count": 150, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [ "SY1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:25.069292", "source": { "split": "train_shard_00000", "doc_id": 293 }, "chunk_id": "train_shard_00000_293_1", "global_id": 330 }, { "text": "The infant gut microbiome is essential for long-term health and is linked to atopic dermatitis (AD), although the underlying mechanisms are not fully understood. This study investigated gut microbiome-host interactions in 31 infants with AD and 29 healthy controls using multi-omics approaches, including metagenomic, host transcriptomic, and metabolomic analyses. Microbial diversity was significantly altered in AD, with Bifidobacterium longum and Clostridium innocuum associated with these changes. At the strain-level, only B. longum differed significantly between groups, with pangenome analyses identifying genetic variations potentially affecting amino acid and lipid metabolites. Notably, B. longum subclade I, which was more prevalent in healthy controls, correlated with host transcriptomic pathways involved in phosphatidylinositol 3-kinase-AKT signaling and neuroactive ligand-receptor pathways, as well as specific metabolites, including tetrahydrocortisol and ornithine. These findings highlight the role of B. longum strain-level variation in infants, offering new insights into microbiome-host interactions related to AD.\n\nIntegrated multi-omics reveals different host crosstalk of atopic dermatitis-enriched Bifidobacterium longum Strains.", "token_count": 304, "char_count": 1256, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7452, "quality_score": 0.8726, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:25.626908", "source": { "split": "train_shard_00000", "doc_id": 294 }, "chunk_id": "train_shard_00000_294_0", "global_id": 331 }, { "text": "Gossypium barbadense is renowned for its superior fiber quality, particularly its extra-long fibers, although its fiber yield is lower compared to G. hirsutum. Here, to further reveal fiber-related genomic variants of G. barbadense, we de novo assemble 12 genomes of G. barbadense that span the wild-to-domesticated continuum, and construct a graph-based pangenome by integrating these assemblies and 17 publicly available tetraploid cotton genome assemblies. We uncover the divergent evolutionary trajectories and subsequent exchanges between G. barbadense and G. hirsutum through investigation of structural variants (SVs). We perform the SV-based GWAS analysis in G. barbadense and identify four, three, and seven candidate SVs for fiber length, fiber strength, and lint percentage, respectively. Furthermore, we detect the underlying candidate genes and uncover the origin and distribution of favorable alleles, and reveal the tradeoff between lint percentage and fiber quality. These pangenome and trait-associated SVs provide insights into and resources for improving cotton fiber.\n\nPangenome analysis reveals yield- and fiber-related diversity and interspecific gene flow in Gossypium barbadense L.", "token_count": 284, "char_count": 1205, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6446, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:26.182764", "source": { "split": "train_shard_00000", "doc_id": 295 }, "chunk_id": "train_shard_00000_295_0", "global_id": 332 }, { "text": "Cannabis sativa is a globally important seed oil, fibre and drug-producing plant species. However, a century of prohibition has severely restricted development of breeding and germplasm resources, leaving potential hemp-based nutritional and fibre applications unrealized. Here we present a cannabis pangenome, constructed with 181 new and 12 previously released genomes from a total of 144 biological samples including both male (XY) and female (XX) plants. We identified widespread regions of the cannabis pangenome that are surprisingly diverse for a single species, with high levels of genetic and structural variation, and propose a novel population structure and hybridization history. Across the ancient heteromorphic X and Y sex chromosomes, we observed a variable boundary at the sex-determining and pseudoautosomal regions as well as genes that exhibit male-biased expression, including genes encoding several key flowering regulators. Conversely, the cannabinoid synthase genes, which are responsible for producing cannabidiol acid and delta-9-tetrahydrocannabinolic acid, contained very low levels of diversity, despite being embedded within a variable region with multiple pseudogenized paralogues, structural variation and distinct transposable element arrangements. Additionally, we identified variants of acyl-lipid thioesterase genes that were associated with fatty acid chain length variation and the production of the rare cannabinoids, tetrahydrocannabivarin and cannabidivarin. We conclude that the C. sativa gene pool remains only partially characterized, the existence of wild relatives in Asia is likely and its potential as a crop species remains largely unrealized.\n\nDomesticated cannabinoid synthases amid a wild mosaic cannabis pangenome.", "token_count": 388, "char_count": 1766, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6946, "quality_score": 0.8473, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:26.789581", "source": { "split": "train_shard_00000", "doc_id": 296 }, "chunk_id": "train_shard_00000_296_0", "global_id": 333 }, { "text": "B. subtilis K3C was isolated from an environmental sample. Genomic analysis revealed that the GRAS strain harbors a circular chromosome of 4,120,051 bp composed of 4361 protein coding sequences with a GC content of 43.4 %, 80 tRNA, and 3 rRNA genes. Two regions containing complete assembly of prophages encoded by 83 prophage genes were present suggesting the role of bacteriophage infection in evolutionary accumulation of strain-specific genes contributing towards strain diversification. Strong recombination, repair, transfer and competence systems were identified, suggesting their role in strain fitness and evolutionary process. Pan-genomic analysis revealed 3824 protein homologs as the bacterial core genome shared among different strains and 390 singletons in the pan-genome orthologous groups. The hyaluronic acid capsule trait in the isolate seems to be acquired through selective pressure to adapt in environmentally stressed niches. Phyloproteomic analysis showed that the acquired genes responsible for HA production were phylogenetically closer to Streptococcal clade, evidencing the role of horizontal gene transfer. The bacterial genome showed the presence of multiple HA genes translating HasB and HasC proteins suggesting gene dosage in the strain. However, no gene rearrangement events seem to have taken course as the HA genes were integrated in different contigs of the genome.\n\nWhole genome sequence analysis of an environmental isolate Bacillus subtilis K3C: Genome plasticity and acquisition of hyaluronic acid capsule traits through horizontal multigene transfer.", "token_count": 375, "char_count": 1591, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6489, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:27.367819", "source": { "split": "train_shard_00000", "doc_id": 297 }, "chunk_id": "train_shard_00000_297_0", "global_id": 334 }, { "text": "Camel milk is one of the most valuable food sources in the Algerian desert. Furthermore, it is a strong candidate for use as a functional food because it contains beneficial microorganisms that promote health. The present study investigates 144 lactic acid bacteria isolated from camel milk, examining their probiotic, safety, technological, and antioxidant properties. Of these, 19 lactic acid bacteria showed very high tolerance to the simulated gastric environment and were selected for further analyses. According to the sequence analysis, 15 isolates were identified as Lactiplantibacillus plantarum, 3 as Lactobacillus gasseri, and 1 as Enterococcus faecium. The results indicated that all isolates demonstrated tolerance to bile salts, with levels ranging from 94.86 % to 102.81 %. It was established that none of the strains exhibited undesirable hemolysis, DNase and gelatinase activity, or transmissible antibiotic resistance. Furthermore, the absence of virulence or biogenic amine genes was confirmed. In particular, strain L. gasseri C1 showed remarkably high levels of auto-aggregation and hydrophobicity, which was also revealed in the principal component analysis. Furthermore, the strains exhibited potent antagonistic properties against various foodborne pathogens. Notably, several strains, including L. plantarum A5, A8, and BN2, and L. gasseri C1, showed specific antimicrobial activity against Listeria monocytogenes, potentially due to bacteriocin or other antimicrobial compounds production. Additionally, the majority of the isolates demonstrated bile salt hydrolysis activity, and all strains exhibited antioxidant activity by scavenging DPPH free radicals. Moreover, 11 L. plantarum isolates possessed the gad gene responsible for GABA production. These findings support the potential application of these isolates as probiotics in both food and therapeutic contexts.\n\nProbiotic potential, safety assessment, and functional properties of lactic acid bacteria from camel milk.", "token_count": 497, "char_count": 2002, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [ "BN2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:28.010479", "source": { "split": "train_shard_00000", "doc_id": 298 }, "chunk_id": "train_shard_00000_298_0", "global_id": 335 }, { "text": "This study investigated the influence of β-cyclodextrin (βCD) on the micellization behavior of two bile salt surfactants, sodium deoxycholate (NaDC) and sodium cholate (NaC), in aqueous solutions. Tensiometry, conductometric, and spectrofluorimetric techniques were employed to determine critical micelle concentrations (CMCs) in the presence of varying concentrations of βCD, as well as in the presence of inorganic salts (NaCl and CsCl). The results showed that βCD forms inclusion complexes with both bile salts, leading to an increase in their CMCs, consistent with a competitive interaction between micelle formation and complexation. The inclusion constants, determined graphically, revealed stronger complexation for NaDC than NaC, attributed to differences in hydrophobic surface area. Salt addition decreased the CMC of both surfactants, with CsCl having a more pronounced effect. However, salt presence also modulated the inclusion complex formation, suggesting specific ion effects influence the availability and behavior of βCD. These findings contribute to the understanding of bile salt-cyclodextrin interactions and their modulation by electrolytes, with implications for drug delivery and supramolecular chemistry.\n\nEffect of β-Cyclodextrin on the Aggregation Behavior of Sodium Deoxycholate and Sodium Cholate in Aqueous Solution.", "token_count": 319, "char_count": 1347, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:28.560566", "source": { "split": "train_shard_00000", "doc_id": 299 }, "chunk_id": "train_shard_00000_299_0", "global_id": 336 }, { "text": "The overproduction of uric acid, driven by its key precursors (inosine and guanosine), leads to hyperuricemia, a metabolic disorder associated with severe complications such as gout and renal dysfunction. Here, a promising bacterial strain YC06 with excellent biodegradation capability for inosine and guanosine was successfully isolated from healthy individual feces and identified as Bacillus paranthracis through average nucleotide identity (ANI) analysis. B. paranthracis YC06 resting cells (live but suspended in PBS buffer) and its cell-free extracts could effectively biodegrade inosine and guanosine in vitro. Whole-genome sequencing revealed a 5,535,183 bp draft genome (52 contigs, 35.22% GC content) containing 5,672 protein-coding genes. B. paranthracis YC06 demonstrated high survival rates in simulated gastrointestinal fluids, supported by the presence of stress-response genes and bile salt hydrolase genes associated with gastrointestinal tolerance. However, this strain exhibited hemolytic activity and no amino acid decarboxylase activity, while hemolysin genes, antibiotic genes and toxin-producing genes were identified, raising potential biosafety concerns for its further application. The gene functional annotation and polymerase chain reaction (PCR) amplification electrophoresis identified key genes (rihA, rihB, deoD and pnp) encoding purine nucleosidase and purine-nucleoside phosphorylase, and combined with biodegradation product analysis, elucidated the pathways of inosine and guanosine biodegradation into hypoxanthine and guanine. Comprehensive safety evaluations, including cytotoxicity assay and in vivo pathogenicity studies, must be conducted to rigorously assess its risks prior to practical utilization.\n\nWhole-genome analysis of Bacillus paranthracis YC06 isolated from healthy individual feces for biodegrading inosine and guanosine.", "token_count": 494, "char_count": 1875, "word_count": 240, "semantic_coherence": 1, "information_density": 0.7125, "quality_score": 0.8562, "entities": { "genes": [ "YC06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:29.203181", "source": { "split": "train_shard_00000", "doc_id": 300 }, "chunk_id": "train_shard_00000_300_0", "global_id": 337 }, { "text": "U1 small nuclear RNA (snRNA) mutations are recurrent non-coding alterations found in various malignancies, yet their identification has proven challenging due to their repetitive nature. We characterized the complex interindividual diversity and genomic architecture of U1 snRNA loci using sequencing data and a pangenome reference. Our analysis uncovered copy number variations and the diversity of single-nucleotide variants in regions not predicted to have significant functional impact. Compared to traditional linear reference-based analyses for mutations, the pangenome graph demonstrated the best accuracy, successfully identifying previously undetectable mutations. This underscores the utility of pangenome graph references for cancer genome research, particularly in repetitive and highly diverse genomic regions. Additionally, we developed mutation detection methods employing targeted capture sequencing, rapid quantitative polymerase chain reaction, and a machine learning approach based on splicing patterns, all exhibiting high precision in identifying U1 snRNA mutations. Our findings elucidate the structural complexity of U1 snRNA loci and establish robust methodologies for precise mutation detection in these regions.\n\nDiversity of U1 Small Nuclear RNAs and Diagnostic Methods for Their Mutations.", "token_count": 274, "char_count": 1317, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6977, "quality_score": 0.8488, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:30.091488", "source": { "split": "train_shard_00000", "doc_id": 301 }, "chunk_id": "train_shard_00000_301_0", "global_id": 338 }, { "text": "Avenanthramide (AVN), a phenolamide unique to oats, offers health benefits but is limited in application due to poor solubility, instability, and low bioavailability. This study developed bilosomes (AOE-BL) by incorporating bile salts into liposomes (AOE-LP) as a cholesterol substitute to enhance the oral delivery of AVN-enriched oat extract (AOE). AOE-BL exhibited smaller particle sizes and higher encapsulation efficiency than AOE-LP. Both formulations significantly increased AVN solubility by 2.74-fold and 2.71-fold, respectively, compared to free AOE while preventing heat-induced degradation. AOE-BL demonstrated superior stability under acidic conditions, with less pronounced changes in particle size and zeta potential than AOE-LP. After in vitro digestion, AOE-BL achieved significantly higher bioaccessibility (77.31 ± 3.31 %) than AOE-LP (67.21 ± 2.37 %) and free AOE (55.69 ± 3.43 %). Cellular uptake studies in Caco-2 enterocytes revealed that bile salts enhanced intracellular uptake compared to cholesterol. These findings highlight the potential of AOE-BL as an effective oral delivery system for AVN.\n\nDevelopment and characterization of avenanthramide-loaded bilosomes: Bile salt-incorporated liposomes as a cholesterol substitute for enhanced oral delivery.", "token_count": 375, "char_count": 1281, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:30.701406", "source": { "split": "train_shard_00000", "doc_id": 302 }, "chunk_id": "train_shard_00000_302_0", "global_id": 339 }, { "text": "Acinetobacter baumannii (A. baumannii) is a major multidrug-resistant pathogen, posing serious threats in the healthcare settings. This study provides a comprehensive genomic analysis of nosocomial A. baumannii whole-genome sequences retrieved from NCBI Genome database. Multilocus sequence typing and capsule typing were performed to investigate the clonal diversity. The genomes were characterized to identify antimicrobial resistance genes (ARGs), virulence factors, and mobile genetic elements. Further, pangenome analysis was conducted to examine the core and accessory genomes of A. baumannii. Our dataset comprised of 609 genomes deposited from diverse geographic regions worldwide between 2004 and 2024. The genomes showed high clonal heterogeneity, with sequence type ST2 being the predominant sequence type. A total of 185 unique ARGs were identified, with majority of them associated with efflux pump and β-lactamase coding genes. Over 25,000 IS elements were detected, with IS4 family being the prevalent type. High abundance of integron-mediated resistance determinants, especially for aminoglycosides and β-lactams, were identified. The open pangenome window due to its larger accessory genome suggested substantial genome plasticity. Our findings highlight A. baumannii's rapid evolution and resistance potential, emphasizing need for alternative therapeutic strategies. Enhanced surveillance, infection control measures, and antimicrobial stewardship are crucial to combat this persistent threat.\n\nGenomic landscape of nosocomial Acinetobacter baumannii: A comprehensive analysis of the resistome, virulome, and mobilome.", "token_count": 392, "char_count": 1637, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8419, "entities": { "genes": [ "ST2", "IS4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:31.336685", "source": { "split": "train_shard_00000", "doc_id": 303 }, "chunk_id": "train_shard_00000_303_0", "global_id": 340 }, { "text": "Plant-derived polyphenols such as syringic acid (SA) are promising modulators of lipid metabolism, yet their clinical utility is limited by poor aqueous solubility. Here, we report a four-step click chemistry strategy to conjugate hydrophilic sugar moieties to SA, yielding a series of sugar-SA triazole derivatives with markedly enhanced solubility and stability. Among these, the glucose conjugate (GS) exhibited the most potent pancreatic lipase (PL) inhibition, surpassing orlistat, and significantly improved cholesterol and bile salt binding. Enzyme kinetics revealed that GS acted via competitive inhibition, increasing Km without altering Vmax. Spectroscopic analyses demonstrated that GS binding induced disruption of PL's secondary and tertiary structures, diminishing thermal stability. Molecular docking confirmed strong interactions between GS and key catalytic residues, rationalizing its superior efficacy. The findings highlight the potential of GS as a novel lipid-lowering therapeutic or functional food ingredient targeting obesity and metabolic disorders.\n\nSynthesis, characterization, and in vitro hypolipidemic mechanisms of sugar-SA triazole conjugates as potent pancreatic lipase inhibitors.", "token_count": 302, "char_count": 1215, "word_count": 158, "semantic_coherence": 1, "information_density": 0.8101, "quality_score": 0.9051, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:31.926999", "source": { "split": "train_shard_00000", "doc_id": 304 }, "chunk_id": "train_shard_00000_304_0", "global_id": 341 }, { "text": "In this study, Lactiplantibacillus plantarum LPP95, a potential probiotic, was encapsulated in a sodium alginate/pectin/tea polyphenol (SA/PE/TP) complex, and its physicochemical properties, bioactivity, stability, and application potential were investigated. The results showed that tea polyphenol (TP) enriched encapsulated beads (SA/PE/TP/LP) achieved high encapsulation efficiency (96.51 %) without compromising their mechanical properties and stability. The bioactivity analysis revealed that the SA/PE/TP/LP encapsulated beads, formed through TP hydrogen bonding, exhibited good biosafety and a high DPPH radical scavenging rate. Furthermore, adding TP enhanced the enteric dissolution rate and increased the viable counts of L. plantarum with respect to in vitro digestion conditions, bile salt tolerance and refrigerated storage, compared with free-LP. When applied to fermented yogurt, SA/PE/TP/LP significantly reduced pH changes, and improved the sensory, gel structure, and rheological properties of the dairy product. These findings suggest a promising approach to preserving highly active probiotics by adding polyphenols, potentially improving yogurt quality.\n\nEncapsulation of Lactiplantibacillus plantarum in a sodium alginate/pectin/tea polyphenol complex: Enhancing stability and bioactivity for fermented milk products.", "token_count": 344, "char_count": 1339, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7321, "quality_score": 0.8661, "entities": { "genes": [ "LPP95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:32.523622", "source": { "split": "train_shard_00000", "doc_id": 305 }, "chunk_id": "train_shard_00000_305_0", "global_id": 342 }, { "text": "Campylobacter coli, a significant foodborne pathogen, has undergone extensive genetic exchange with its close relative, Campylobacter jejuni, leading to the emergence of three distinct clades. While clade 1 strains are commonly isolated from clinical and agricultural sources, clades 2 and 3 are primarily found in aquatic environments. This study aimed to enhance our understanding of C. coli clade 2 and 3 isolates through genomic and phenotypic characterization. A total of 48 surface water samples were collected from 19 different water bodies throughout Slovenia, and eleven Campylobacter isolates initially identified as C. coli from clades 2 and 3 were cultured. Whole genome sequencing was then performed on these isolates. Phylogenetic analysis was conducted using core genome multilocus sequence typing (cgMLST) and k-mer analysis. Phenotypic characterization included growth analysis, autoagglutination, biofilm formation, motility, antimicrobial susceptibility, water survival, and metabolic profiling. Genomic analysis revealed significant admixture with other Campylobacter species in the clade 2 and 3 isolates. One isolate was found to represent a new species related to C. coli. Besides C. jejuni and C. lari, this novel species appears to have contributed to introgression in the C. coli clades 2 and 3 isolates. Phenotypic characterization demonstrated diverse growth patterns, motility, autoagglutination abilities, and biofilm formation among the isolates. This study provides new insights into the genetic diversity and phenotypic characteristics of aquatic C. coli clade 2 and 3 isolates from Slovenia. The observed admixture with other Campylobacter species highlights the complex evolutionary history of these environmental strains and underscores the importance of continued surveillance and characterization of Campylobacter isolates from diverse ecological niches.\n\nCharacterization of aquatic clade 2 and 3 Campylobacter coli isolates from Slovenia reveals admixture with other Campylobacter species.", "token_count": 477, "char_count": 2029, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5484, "quality_score": 0.7742, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:33.155623", "source": { "split": "train_shard_00000", "doc_id": 306 }, "chunk_id": "train_shard_00000_306_0", "global_id": 343 }, { "text": "Corynebacterium ulcerans is an emerging zoonotic pathogen which causes diphtheria-like infections. Although C. ulcerans is found in multiple domestic and wild animal species, most human cases are linked with pets. Our ability to decipher cross-host species transmission dynamics and to understand the emergence of clinically relevant clones (e.g., diphtheria toxin-positive) is currently hampered by a limited knowledge of C. ulcerans strain diversity and genome evolution. Here, we explore the genomic population structure and evolution of C. ulcerans with 582 isolates from diverse hosts and geographical locations. A newly developed core genome genotyping scheme captures the population structure of C. ulcerans both at deep and shallow phylogenetic levels, uncovering its main sublineages and offering high strain subtyping resolution for epidemiological surveillance. Additionally, we reveal the diversity and distribution of the diphtheria toxin gene (tox), and those of its associated mobile elements. Considering the entire Corynebacterium diphtheriae Species Complex, we find four diphtheria toxin families, five tox-prophage families, and a novel tox-carrying genetic element. We show that some toxin families are shared across Corynebacterium species, revealing tox-prophage cross-species transfer. Our work enhances knowledge on the ecology and evolution of C. ulcerans and provides a genomic framework for tracking the dissemination of emerging sublineages.\n\nMicroevolution and genomic epidemiology of the diphtheria-causing zoonotic pathogen Corynebacterium ulcerans.", "token_count": 386, "char_count": 1581, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:33.759805", "source": { "split": "train_shard_00000", "doc_id": 307 }, "chunk_id": "train_shard_00000_307_0", "global_id": 344 }, { "text": "Lactic acid bacteria (LAB) possess notable functional characteristics, making them promising candidates for probiotic applications due to their ability to endure low pH and high bile salt concentrations while inhibiting enteric pathogens. This study evaluates the probiotic potential and safety of LAB strains isolated from the gastrointestinal tract of indigenous chickens of the Northwestern Himalayas. We assessed features such as antimicrobial activity, auto-aggregation, co-aggregation, haemolytic activity, antibiotic resistance, and virulence gene presence. Multivariate analysis using Principal Component Analysis (PCA) and heat mapping was conducted to evaluate variability among strains based on traits like pH and bile salt tolerance, autoaggregation and co-aggregation and antimicrobial activity. Five LAB strains were identified through 16S rDNA analysis: Lactobacillus johnsonii, Ligilactobacillus salivarius, Lactobacillus kitasatonis, Rummeliibacillus suwonensis, and Enterococcus faecalis. All strains demonstrated significant tolerance to acidic and bile salt conditions, robust aggregation abilities, and strong antibacterial activity. Safety evaluations revealed no haemolytic activity or virulence genes, except for Enterococcus faecalis, which harboured the esp gene. PCA and heat mapping identified strain NC10 as the most promising probiotic isolate due to its superior antimicrobial activity and bile tolerance. This study highlights the potential of indigenous LAB strains, particularly Ligilactobacillus salivarius NC10, as safe probiotics for enhancing poultry health. To the best of our knowledge, this study is the first to evaluate the probiotic attributes of LAB strains derived from native chickens of the Northwestern Himalayas in the Indian subcontinent. IMPORTANCE: This study underscores the potential of utilizing lactic acid bacteria (LAB) strains from indigenous chickens of the Northwestern Himalayas as safe and effective probiotics. Native breeds, such as the Kashmir Flavorella, have adapted to the region's unique environment, offering a rich source of microbiota with distinct probiotic traits", "token_count": 517, "char_count": 2139, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8067, "entities": { "genes": [ "NC10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:01:34.422050", "source": { "split": "train_shard_00000", "doc_id": 308 }, "chunk_id": "train_shard_00000_308_0", "global_id": 345 }, { "text": "The identification of LAB strains, particularly Ligilactobacillus salivarius NC10, with exceptional antimicrobial activity and bile tolerance, opens avenues for improving poultry gut health and productivity. As antibiotic resistance emerges as a global challenge, exploring natural and safe alternatives like probiotics becomes increasingly vital. Additionally, the comprehensive safety evaluation, including the absence of haemolytic activity and virulence genes in most strains, highlights their suitability for probiotic applications. This research not only contributes to sustainable poultry farming practices but also emphasizes the need to preserve and harness the microbial diversity of indigenous animal breeds, ensuring food security and environmental sustainability.\n\nProbiotic potential of LAB strains from native Kashmir Flavorella chickens of northwestern Himalayas: A focus on safety and gut health.", "token_count": 195, "char_count": 913, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7881, "quality_score": 0.8941, "entities": { "genes": [ "NC10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:34.862990", "source": { "split": "train_shard_00000", "doc_id": 308 }, "chunk_id": "train_shard_00000_308_1", "global_id": 346 }, { "text": "Wilson disease (WD) is an autosomal recessive disorder that results in excessive hepatic copper, causing hepatic steatosis, inflammation, fibrosis, cirrhosis, and liver failure. Previous studies have revealed dysregulation of many farnesoid X receptor (FXR) metabolic target genes in WD, including the bile salt exporter pump, the major determinant of bile flow.\n\nChanges in the FXR-cistrome and alterations in bile acid physiology in Wilson disease.", "token_count": 121, "char_count": 450, "word_count": 64, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:35.247297", "source": { "split": "train_shard_00000", "doc_id": 309 }, "chunk_id": "train_shard_00000_309_0", "global_id": 347 }, { "text": "A pangenome can reveal the genetic diversity across different individuals simultaneously. It offers a more comprehensive reference for genome analysis compared to a single linear genome that may introduce allele bias. Pangenomes are often represented as genome graphs, making sequence-to-graph mapping a fundamental task for pangenome construction and analysis. Numerous sequence-to-graph mapping algorithms have been developed over the past few years. Here, we provide a review of the advancements in sequence-to-graph mapping algorithms in the pangenome era. We also discuss the challenges and opportunities that arise in the context of pangenome graphs.\n\nA survey of sequence-to-graph mapping algorithms in the pangenome era.", "token_count": 148, "char_count": 728, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8284, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:35.682124", "source": { "split": "train_shard_00000", "doc_id": 310 }, "chunk_id": "train_shard_00000_310_0", "global_id": 348 }, { "text": "This study investigates how bile-salt-based edge activators (EAs) (sodium cholate, NaC; sodium deoxycholate, NaDC; and sodium taurocholate, NaTC) can influence the mechanical properties and deformability of liposomal vesicles. We have elucidated their effect on liposomes composed of l-α-phosphatidylcholine (SPC). Liposomes were formulated using thin-film hydration and characterized using scattering, spectroscopic, and atomic force microscopic (AFM) techniques. Our data show that bile salts can alter the hydrodynamic diameter (\n\nBile Salts Trigger Deformability in Liposomal Vesicles through Edge-Activating Action.", "token_count": 175, "char_count": 620, "word_count": 78, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:36.126011", "source": { "split": "train_shard_00000", "doc_id": 311 }, "chunk_id": "train_shard_00000_311_0", "global_id": 349 }, { "text": "Escherichia coli has an extensive accessory genome, though its role in impacting patient mortality is unknown.\n\nEscherichia coli Type III Secretion System 2 (ETT2) is Associated with Patient Mortality in Bloodstream Infections.", "token_count": 62, "char_count": 227, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [ "ETT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:36.494541", "source": { "split": "train_shard_00000", "doc_id": 312 }, "chunk_id": "train_shard_00000_312_0", "global_id": 350 }, { "text": "Piscine lactococcosis poses a significant threat to a wide range of cultured and wild fish populations worldwide, typically presenting as acute haemorrhagic septicemia with high morbidity and mortality. Although Lactococcus garvieae was historically considered the sole causative agent of piscine lactococcosis, recent studies have identified L. petauri and L. formosensis as additional, highly pathogenic species. In this study, we developed a novel TaqMan-based multiplex qPCR assay for the simultaneous detection and differentiation of L. garvieae, L. petauri and L. formosensis, following a pangenome analysis of the publicly available genomes of these bacterial species. The assay demonstrated high sensitivity and specificity across 156 bacterial isolates obtained from various cultured fish species and geographical locations between 2008 and 2024, as well as against a panel of non-target bacteria. It also successfully detected target pathogens in 146 field tissue samples, including tissues preserved in 70% ethanol, formalin-fixed paraffin-embedded (FFPE) tissues and tissues fixed on FTA cards. Compared to classical bacteriology, the multiplex qPCR assay yielded higher detection rates and enabled precise identification of the causative species of piscine lactococcosis. Overall, the multiplex qPCR assay developed in this study provides a reliable, rapid, highly sensitive and species-specific molecular approach for diagnosing piscine lactococcosis, contributing to better surveillance and management of the disease in aquaculture.\n\nDiving Into the Depths: Unveiling the Main Etiologies of Piscine Lactococcosis With a Novel Multiplex qPCR Assay.", "token_count": 417, "char_count": 1662, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6476, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:37.102100", "source": { "split": "train_shard_00000", "doc_id": 313 }, "chunk_id": "train_shard_00000_313_0", "global_id": 351 }, { "text": "The study focused on the evaluation of the probiotic potency of Bacillus velenzensis STPB10, isolated from the digestive tract of the hillstream fish Snow trout (Schizothorax richardsonii). Ten B. velezensis strains were identified through colony morphology, biochemical analysis, and 16 S rRNA methods. The representative laboratory strain STPB10, was subjected to various in vitro assessments including tolerance to pH, bile salt resistance, NaCl, temperature, biofilm, endospore formation, antibiotic susceptibility and antagonistic activity to determine its potential as a probiotic strain. B. velezensis STPB10 exhibited positive results for catalase, glucose, arginine, lysine, and endospore tests, while it yielded negative results for oxidative/fermentative, DNase, and urease tests. This test isolate was γ-hemolytic in nature and demonstrated growth across a temperature range of 15 to 35 °C. Moreover, it exhibited survival rates of 31, 39.7, 47, 63, and 75% at pH values of 2, 2.5, 3, 3.5, and 4, respectively, after 6 h of incubation. At a bile salt concentration of 0.3%, the bacterium exhibited a survivability of more than 99%. A strong biofilm production by B. velezensis STPB10 was detected in tryptone soya broth enriched with 0.45% glucose (p < 0.05). It also exhibited significantly greater adhesion to intestinal mucus (63.67%). Following exposure of the intestinal mucus to B. velezensis STPB10, the adhesion of A. hydrophila, A. veronii, (A) salmonicida and V. anguillarum to the mucus was notably reduced", "token_count": 477, "char_count": 1529, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7048, "quality_score": 0.8524, "entities": { "genes": [ "STPB10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:37.733244", "source": { "split": "train_shard_00000", "doc_id": 314 }, "chunk_id": "train_shard_00000_314_0", "global_id": 352 }, { "text": "It was susceptible to several antibiotics and produced an antagonistic effect against pathogenic bacteria Aeromonas salmonicida, Aeromonas veronii, Vibrio anguillarum, and Aeromonas hydrophila isolated from diseased fish. The pathogenicity of (B) velezensis STPB10 through intraperitoneal injection and immersion challenge at cell concentrations of 10\n\nProbiotic potential of Bacillus velezensis STPB10 sourced from the gut microbiota of a hillstream fish Schizothorax richardsonii (Gray, 1832) for aquaculture applications.", "token_count": 153, "char_count": 524, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [ "STPB10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:38.164290", "source": { "split": "train_shard_00000", "doc_id": 314 }, "chunk_id": "train_shard_00000_314_1", "global_id": 353 }, { "text": "The specific influence of whole gut transit time (WGTT) on microbiome dynamics and bile acid metabolism remains unclear, despite links between changes in WGTT and certain gastrointestinal disorders. Our investigation aimed to determine the impact of WGTT changes on the composition of the fecal microbiome and bile acid profile.\n\nChanging Gastrointestinal Transit Time Alters Microbiome Composition and Bile Acid Metabolism: A Cross-Over Study in Healthy Volunteers.", "token_count": 114, "char_count": 466, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:38.549052", "source": { "split": "train_shard_00000", "doc_id": 315 }, "chunk_id": "train_shard_00000_315_0", "global_id": 354 }, { "text": "Gene presence/absence variations (PAVs) have been considered as the important determinants of genome evolution and phenotypic diversity. However, studies on gene PAVs have been poorly documented, especially in fishes. In the present study, the pan-genome of rainbow trout was constructed based on 268 whole-genome re-sequencing accessions (4.38 Tb data). It recovered an additional 62 Mb sequences and 1288 protein-coding genes. Then, 9831 (22.77%) gene PAVs were genotyped across the 268 individuals. PAV-based PCA analysis, together with phylogenetic topology and STRUCTURE, revealed the clear separation among the different wild and selection populations. Additionally, a PAV-based genome-wide association study (GWAS) identified three candidate PAVs significantly associated with artificial selection. Meanwhile, fixation index analysis revealed 35 PAVs with significant frequency differences between wild and selection populations in Canada, while 15 candidate PAVs were detected between the populations in America. Their biological functions have been reported to participate in the regulation of growth performance and stress response. The present study deepens our understanding of widespread gene PAVs and facilitates the identification of key candidates that contribute to important traits.\n\nExploration of gene presence/absence variations in", "token_count": 308, "char_count": 1352, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6906, "quality_score": 0.8453, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:39.109944", "source": { "split": "train_shard_00000", "doc_id": 316 }, "chunk_id": "train_shard_00000_316_0", "global_id": 355 }, { "text": "Many gastroesophageal reflux disease (GORD) patients have heartburn symptoms despite PPI treatment, potentially via esophageal mucosa exposure to weakly acidic bile salts, leading to oxidative stress. High mobility group box 1 (HMGB1) is a nuclear protein secreted during oxidative stress that binds to receptors including TLR2, TLR4, and RAGE, inducing inflammatory signaling. We describe the release and potential downstream effects of HMGB1 in GORD.\n\nA Role for High Mobility Group Box 1 (HMGB1) Release in the Pathogenesis of Gastroesophageal Reflux Disease.", "token_count": 160, "char_count": 562, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7901, "quality_score": 0.8951, "entities": { "genes": [ "TLR4", "HMGB1", "TLR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:39.551267", "source": { "split": "train_shard_00000", "doc_id": 317 }, "chunk_id": "train_shard_00000_317_0", "global_id": 356 }, { "text": "Among potentially toxigenic cyanobacteria, Raphidiopsis raciborskii has attracted considerable attention due to its ability to produce massive blooms and its recent spread to temperate regions. In this work, we reported for the first time a taxonomic and functional assessment of a R. raciborskii strain isolated from the Mediterranean region, contributing to filling a gap in the global distribution and characteristics of this species. The strain LT_0923 was isolated from Lake Trasimeno, a large and shallow lake in central Italy. The phylogenomic analyses based on selected marker genes and the core genome obtained from a pangenomic analysis based on a selection of available high-quality genomes showed a strong correspondence of the Lake Trasimeno strain with the North American and, at a lower average nucleotide identity, with the South American genomes. The LT_0923 genome did not show the presence of gene clusters encoding legacy cyanotoxins or emerging toxigenic compounds. The open pangenome and the large fraction of distinct gene families identified in the cloud and partly shell genome, enriched with genes specialised in environmental-specific functions and defence mechanisms, are consistent with the development of Raphidiopsis in geographically distinct regions.\n\nPhylogenomic and Pangenomic Assessment of a Mediterranean Strain of Raphidiopsis raciborskii Extends Knowledge of the Global Distribution and Characteristics of a Potentially Toxigenic Cyanobacterium.", "token_count": 331, "char_count": 1485, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:40.112653", "source": { "split": "train_shard_00000", "doc_id": 318 }, "chunk_id": "train_shard_00000_318_0", "global_id": 357 }, { "text": "Accurate genome assemblies are essential for biological research, but even the highest-quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing step that uses reads aligned to the draft assembly to identify necessary edits. However, current methods struggle to find a balance between over- and underpolishing. Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacific Biosciences (PacBio) HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHAsing Reads in Areas Of Homozygosity (PHARAOH), which uses ultralong Oxford Nanopore Technologies (ONT) data to ensure alignments are accurately phased and to correctly introduce heterozygous edits in falsely homozygous regions. We demonstrate that the DeepPolisher pipeline can reduce assembly errors by approximately half, mostly driven by reductions in indel errors. We have applied our DeepPolisher-based pipeline to 180 assemblies from the next Human Pangenome Reference Consortium (HPRC) data release, producing an average predicted quality value (QV) improvement of 3.4 (54% error reduction) for the majority of the genome.\n\nHighly accurate assembly polishing with DeepPolisher.", "token_count": 312, "char_count": 1353, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7166, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:40.669732", "source": { "split": "train_shard_00000", "doc_id": 319 }, "chunk_id": "train_shard_00000_319_0", "global_id": 358 }, { "text": "Tuberculosis is a major public health threat resulting in more than one million lives lost every year. Many challenges exist to defeat this deadly infectious disease which address the importance of a thorough understanding of the biology of the causative agent Mycobacterium tuberculosis (MTB). We generated a non-redundant pangenome of 420 epidemic MTB strains from China including 344 Lineage 2 strains, 69 Lineage 4 strains, six Lineage 3 strains, and one Lineage 1 strain. We estimate that MTB strains have a pangenome of 4,278 genes encoding 4,183 proteins, of which 3,438 are core genes. However, due to 99,694 interruptions in 2,447 coding genes, we can only confidently confirm 1,651 of these genes are translated in all samples. Of these interruptions, 67,315 (67.52%) could be classified by various genetic variations detected by currently available tools, and more than half of them are due to structural variations, mostly small indels. Assuming a proportion of these interruptions are artifacts, the number of active core genes would still be much lower than 3,438. We further described differential evolutionary patterns of genes under the influences of selective pressure, population structure and purifying selection. While selective pressure is ubiquitous among these coding genes, evolutionary adaptations are concentrated in 1,310 genes. Genes involved in cell wall biogenesis are under the strongest selective pressure, while the biological process of disruption of host organelles indicates the direction of the most intensive positive selection. This study provides a comprehensive view on the genetic diversity and evolutionary patterns of coding genes in MTB which may deepen our understanding of its epidemiology and pathogenicity.\n\nUnderstanding the epidemiology and pathogenesis of Mycobacterium tuberculosis with non-redundant pangenome of epidemic strains in China.", "token_count": 459, "char_count": 1894, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6079, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:41.297666", "source": { "split": "train_shard_00000", "doc_id": 320 }, "chunk_id": "train_shard_00000_320_0", "global_id": 359 }, { "text": "Long-term geographical isolation and the different directions of domestication can cause a large number of genome variations. Population genetic analysis based on a single reference genome cannot capture all the variation information. Pan-genome construction is an effective way to overcome this problem. Resequencing data from 683 common bean landraces and breeding lines provided a pan-genome construction data resource. For the first time, for common bean pan-genome construction, 305 Mb non-reference contigs and 10,452 novel genes were identified. Among these new genes, 373 resistance gene analogs containing 372 variable genes were identified and used to narrow down the candidate genes in Pseudomonas syringae pv. phaseolicola resistance quantitative trait locus interval of the common bean. Transcriptome analysis of multiple biotic and abiotic stresses reveals that gene expression patterns are organ-, stress-, and gene conservation-specific. Core and shell genes may be co-expressed in all samples and may have functional complementarity to maintain the stability of plant growth. Within pathways, 8990 and 30,272 mutual exclusivity and co-occurrence gene presence-absence variations (PAVs) were discovered respectively, providing further insights into the functional complementarity of genes. In conclusion, our study provides a comprehensive genome resource, which will be useful for further common bean breeding and study.\n\nCommon bean pan-genome reveals abundant variation patterns and relationships of stress response genes and pathways.", "token_count": 337, "char_count": 1554, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:41.863450", "source": { "split": "train_shard_00000", "doc_id": 321 }, "chunk_id": "train_shard_00000_321_0", "global_id": 360 }, { "text": "The success of pangenome-based approaches to genomics analysis depends largely on the existence of efficient methods for constructing pangenome graphs that are applicable to large genome collections. In the current paper we present AlfaPang, a new pangenome graph building algorithm. AlfaPang is based on a novel alignment-free approach that allows to construct pangenome graphs using significantly less computational resources than state-of-the-art tools. The code of AlfaPang is freely available at https://github.com/AdamCicherski/AlfaPang .\n\nAlfaPang: alignment free algorithm for pangenome graph construction.", "token_count": 140, "char_count": 614, "word_count": 80, "semantic_coherence": 1, "information_density": 0.775, "quality_score": 0.8875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:42.290078", "source": { "split": "train_shard_00000", "doc_id": 322 }, "chunk_id": "train_shard_00000_322_0", "global_id": 361 }, { "text": "The swift emergence of antibiotic resistance genes (ARGs) across interconnected One Health compartments poses a significant global threat. Although plant growth-promoting (PGP) bacteria possess numerous attributes beneficial to host plants, many of these bacteria also harbor ARGs, necessitating a focused assessment of their negative implications. In this context, here we performed whole genome sequencing of 14 PGP endophytic strains isolated from root nodules of faba beans, belonging to three Klebsiella oxytoca species complex (KoSC): K. grimontii (n = 5), K. michiganensis (n = 5), and K. pasteurii (n = 4). We performed comparative genomics, molecular typing, and pangenome analyses on these strains. We identified significant diversity within the KoSC population, classifying the strains into five sequence types (STs), three of which are novel to this study (ST-542, ST-569, and ST-629). Phylogenomic analysis revealed that the bacterial strains clustered more closely by ST than by their source of isolation. Annotation of gene clusters indicated that all assembled genomes are enriched with genes involved in PGP activities, alongside a robust array of genes conferring tolerance to abiotic stresses. Importantly, our findings disclosed that the 14 assembled genomes harbored multiple ARGs, conferring resistance to various antibiotic classes, with 71% of the population classified as multidrug-resistant based on the in vitro antibiotic susceptibility assay. Furthermore, all genomes contained an array of virulence factors critical for survival, pathogenesis, biofilm formation, and root colonization. In conclusion, this study substantiates the hypothesis that certain PGP bacteria may serve as potential reservoirs of multidrug resistance, posing significant public health risks. Thus, the future advancement of bacteria-based biofertilizers should integrate environmental considerations and monitor their impact on antibiotic resistance dissemination in soil ecosystems.\n\nNodules-associated Klebsiella oxytoca complex: genomic insights into plant growth promotion and health risk assessment.", "token_count": 502, "char_count": 2108, "word_count": 288, "semantic_coherence": 1, "information_density": 0.684, "quality_score": 0.842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:42.960553", "source": { "split": "train_shard_00000", "doc_id": 323 }, "chunk_id": "train_shard_00000_323_0", "global_id": 362 }, { "text": "The isolation and identification of probiotic yeasts is increasing rapidly. In this context, the present study aimed to isolate and identify yeast strains from neonatal faeces in Erzurum province, Türkiye and to determine their probiotic characteristics. A total of 12 yeast strains were isolated and genotypic characterization revealed the presence of seven different species, including Kluyveromyces marxianus, Candida spp. Clavispora lusitaniae, Geotrichum candidum, Trichophyton rubrum, Pichia cactophila, and Meyerozyma guilliermondii. The non-pathogenic and potentially probiotic characteristics of the K. marxianus M2, M9, and M10 strains were further investigated. Although yeast has been isolated from neonatal faeces before, K. marxianus was isolated for the first time in this study. The results revealed that the K. marxianus strains exhibited high resistance to simulated gastric juice and bile salts. The auto-aggregation percentages of the strains ranged from 92.55 to 94.78% after 4 h, while the co-aggregation percentages with pathogens ranged from 19.70 to 53.09%. The K. marxianus M2 strain exhibited the highest degree of hydrophobicity (74.97%), and none of the strains demonstrated DN-ase or haemolytic activity. Furthermore, M2 and M9 strains displayed bile salt hydrolase activity. In conclusion, based on in vitro probiotic test results, K. marxianus strains were selected as probiotic yeast candidates for further studies, especially in patients under antibiotic therapy.\n\nSafety aspects and in vitro probiotic assessment of Kluyveromyces marxianus strains from neonatal faeces.", "token_count": 448, "char_count": 1604, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:43.595471", "source": { "split": "train_shard_00000", "doc_id": 324 }, "chunk_id": "train_shard_00000_324_0", "global_id": 363 }, { "text": "Since human genomic data produced in the 1990s are still a significant part of the reference genome, decades-old decisions pertinent to the creation of these data persist. Here, we discuss how historical documents illustrate the 1990s policy and legal environment and how they affected ethical choices in the Human Genome Project (HGP). These documents inform current controversies about informed consent and how IRBs review similar protocols today. Finally, we discuss how this informs active work in large reference pangenome efforts.\n\nEthics choices during the Human Genome Project reflected their policy world, not ours.", "token_count": 134, "char_count": 624, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7204, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:44.058005", "source": { "split": "train_shard_00000", "doc_id": 325 }, "chunk_id": "train_shard_00000_325_0", "global_id": 364 }, { "text": "Bile acids (BAs) are cholesterol derivatives synthesized by the liver, exhibit variation between different species. Researchers have long appreciated that microbiota play the roles in the biotransformation of BAs. However, relatively few studies have been reported on microbial-mediated production and transformation of BAs in amphibians. Our focus here is principally on difference of intestinal microbial diversity and BAs profiles between two common amphibians, Bufo gargarizans (B. gargarizans) and Rana chensinensis (R. chensinensis) tadpoles, through intestinal targeted BAs metabolomics and fecal metagenomic sequencing. The results demonstrated that B. gargarizans possessed higher levels of total BAs and higher ratio of unconjugated / conjugated BAs. In addition, the relative abundance of microbiota with bile salt hydrolase (BSH) activity in B. gargarizans was significantly higher than that of R. chensinensis, which may facilitate the conversion of conjugated to unconjugated BAs. Meanwhile the higher prevalence of bile-acid-induced (BAI) gene encoding microbiota in R. chensinensis may promote the synthesis of deoxycholic acid (DCA). Furthermore, discrepancies in virulence factors (VFs) and energy metabolism were observed between the two species, which may be linked to differences in the microbiota. This study revealed substantial differences in intestinal microbes and BAs across amphibian species, emphasizing the significant impact of intestinal microbes on BAs metabolism.\n\nComparative analysis of gut microbiota-mediated bile acid profiles in Bufo gargarizans and Rana chensinensis tadpoles.", "token_count": 416, "char_count": 1617, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:44.690883", "source": { "split": "train_shard_00000", "doc_id": 326 }, "chunk_id": "train_shard_00000_326_0", "global_id": 365 }, { "text": "Probiotic health benefits may be affected by decreased viability during food storage and gastrointestinal transit. Although microencapsulation is an effective protective strategy, its application to probiotics is limited. Currently, research on probiotic biofilms is expanding, with these biofilms being recognized as the fourth generation of probiotics. This study aimed to investigate the effects of biofilm formation on gastrointestinal tolerance and mucoadhesion of three different probiotics:\n\nEffects of Biofilm Formation on Gastrointestinal Tolerance, Mucoadhesion and Transcriptomic Responses of Probiotics.", "token_count": 140, "char_count": 615, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:45.117705", "source": { "split": "train_shard_00000", "doc_id": 327 }, "chunk_id": "train_shard_00000_327_0", "global_id": 366 }, { "text": "This experiment investigated the encapsulation of Lactiplantibacillus plantarum 1.0317 in a water-in-oil-in-water (W/O/W) emulsion to significantly enhance the activity of Lactiplantibacillus plantarum 1.0317 under storage conditions, during pasteurization, and in simulated in vitro gastrointestinal digestion environments. Lactiplantibacillus plantarum 1.0317 was encapsulated in emulsion using whey protein isolate (WPI) alone or non-covalent complex of whey protein isolate and konjac glucomannan (KGM). Compared with the WPI-stabilized emulsion, the WPI-KGM stabilized emulsion had smaller particle size, better rheological properties, higher embedding efficiency and markedly improved the vitality of Lactiplantibacillus plantarum 1.0317 after storage, pasteurization, low pH treatment, high concentration of bile salt treatment and simulated gastrointestinal digestion. As the mass ratio of WPI-KGM composite was 3:1, the highest embedding efficiency of W/O/W emulsion was 89.76 %. Moreover, compared with the free Lactiplantibacillus plantarum 1.0317 and its other encapsulated emulsion, when the WPI-KGM complex mass ratio is 3:1, the W/O/W emulsion containing Lactiplantibacillus plantarum 1.0317 has the highest activity of probiotics after 28 days of storage, pasteurization and simulated gastrointestinal digestion, which are 97.03 %, 74.15 % and 70.07 %, respectively. This study offers a novel idea for the emulsion system used in probiotic delivery based on WPI-KGM.\n\nEncapsulation of Lactiplantibacillus plantarum in W/O/W emulsion stabilized with whey protein isolate and konjac glucomannan complex.", "token_count": 494, "char_count": 1617, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5524, "quality_score": 0.7762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:45.755919", "source": { "split": "train_shard_00000", "doc_id": 328 }, "chunk_id": "train_shard_00000_328_0", "global_id": 367 }, { "text": "KPGD: A kiwifruit pangenome database for comprehensive mining of genetic diversity in the genus Actinidia.", "token_count": 27, "char_count": 106, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:46.118230", "source": { "split": "train_shard_00000", "doc_id": 329 }, "chunk_id": "train_shard_00000_329_0", "global_id": 368 }, { "text": "A high-fat diet leads to metabolic disturbances, which are important factors in the development of obesity. Gut microbial composition and diversity are altered by a high-fat diet. In general, a high-fat diet resulted in increased Firmicutes abundance and decreased alpha diversity. Bile acids (BAs) are involved in the digestion and absorption of fats in the small intestine and are also the metabolic substrates of microorganisms with bile salt hydrolase (BSH) activity. High-fat diets (HFDs) have been shown to alter gut microbiota composition and BA profiles in murine models. Similarly, probiotic supplementation reverses HFD-induced adverse effects. This review focuses on the energy composition characteristics of a high-fat diet and its effects on body weight, plasma lipid-related biochemical markers, changes in gut microbiome characteristics, and the important role of BAs. The regular mechanism by which a high-fat diet affects the intestinal microenvironment was attempted to be found.\n\nMicrobiota-Based Intervention Alleviates High-Fat Diet Consequences Through Host-Microbe Environment Remodeling.", "token_count": 271, "char_count": 1111, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6645, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:46.656798", "source": { "split": "train_shard_00000", "doc_id": 330 }, "chunk_id": "train_shard_00000_330_0", "global_id": 369 }, { "text": "As a member of Acinetobacter calcoaceticus-baumannii complex, Acinetobacter pittii has been an emerging concern in nosocomial infection due to its increasing prevalence and multidrug resistance (MDR). However, its population structure remains broadly unknown, hampering efficient tracing of its transmission and evolution. In this study, we developed a distributed core genome multilocus sequence typing (dcgMLST) for A. pittii based on 750 genomes and employed it to map the genetic landscape and evolution of A. pittii. The results demonstrated that two hierarchical clustering (HC) levels effectively correspond to genetic diversity from species (HC1100) to natural populations (HC450), as well as that a predominant lineage, HC1100_4, accounts for 33.9% of A. pittii strains. Subsequent analysis revealed that specific gene gain and loss events within HC1100_4 are linked to adaptations to environmental stress. Moreover, we identified a cluster of multidrug-resistant plasmids PT_712 responsible for the dissemination of bla\n\nGenetic landscape and evolution of Acinetobacter pittii, an underestimated emerging nosocomial pathogen.", "token_count": 287, "char_count": 1135, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7179, "quality_score": 0.859, "entities": { "genes": [ "HC450", "HC1100" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:47.212993", "source": { "split": "train_shard_00000", "doc_id": 331 }, "chunk_id": "train_shard_00000_331_0", "global_id": 370 }, { "text": "Murine norovirus (MNV) undergoes large conformational changes in response to the environment. The T=3 icosahedral capsid is composed of 180 copies of ~58 kDa VP1 that has N-terminal (N), shell (S), and C-terminal protruding (P) domains. In phosphate-buffered saline, the P domains are loosely tethered to the shell and float ~15 Å above the surface. At conditions found in the gut (i.e., low pH with high metal ion and bile salt concentrations), the P domain rotates and drops onto the shell with intra P domain changes that enhance receptor interactions while blocking antibody binding. Two of our monoclonal antibodies (2D3 and 4F9) have broad strain recognition, and the only escape mutants, V339I and D348E, are located on the C'D' loop and ~20 Å from the epitope. Here, we determined the cryo-EM structures of V339I and D348E at neutral pH +/-metal ions and bile salts. These allosteric escape mutants have the activated conformation in the absence of gut triggers. Since this conformation is not recognized by antibodies, it explains how these mutants evade antibody recognition. Dynamic simulations of the P domain further suggest that movement of the C'D' loop may be the rate-limiting step in the conformational change and that V339I increases the motion of the A'B'/E'F' loops compared to the wild-type (WT), facilitating the transition to the activated state. These findings have important implications for norovirus vaccine design since they uncover a form of the viral capsid that should lend superior immune protection against subsequent challenge by wild-type virus.IMPORTANCEImmune protection from norovirus infection is notoriously transient in both humans and mice. Our results strongly suggest that this is likely because the \"activated\" form of the virus found in gut conditions is not recognized by antibodies created in the circulation. By reversibly presenting one structure in the gut and a completely different antigenic structure in circulation, the gut tissue can be infected in subsequent challenges, while extraintestinal organs are protected", "token_count": 513, "char_count": 2071, "word_count": 319, "semantic_coherence": 1, "information_density": 0.5987, "quality_score": 0.7994, "entities": { "genes": [ "VP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:01:47.864217", "source": { "split": "train_shard_00000", "doc_id": 332 }, "chunk_id": "train_shard_00000_332_0", "global_id": 371 }, { "text": "We find here that allosteric escape mutants to the most broadly neutralizing antibodies thwart recognition by transitioning to the activated state without the need for gut triggers (i.e., bile, low pH, or metal ions). These findings are significant because it is now feasible to present the activated form of the virus to the immune system (for example, as a vaccine) to better protect the gut tissue for longer periods of time.\n\nMurine norovirus allosteric escape mutants mimic gut activation.", "token_count": 115, "char_count": 494, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7722, "quality_score": 0.8861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:48.249892", "source": { "split": "train_shard_00000", "doc_id": 332 }, "chunk_id": "train_shard_00000_332_1", "global_id": 372 }, { "text": "Dissemination of antimicrobial resistance (AMR) is a growing global public health burden. The aim of this study was to characterize AMR plasmid transmissions within a tertiary care hospital and identify relevant AMR plasmid transmission pathways. During an 18-month observation period, 540 clinical gram-negative multidrug-resistant bacterial (MDRB) isolates were collected during routine hospital surveillance and subjected to Pacific Biosciences long-read whole genome sequencing. Potential clonal transmissions were determined based on core genome multilocus sequence typing (cgMLST), and plasmid transmissions were detected using a novel real-time applicable tool for plasmid transmission detection. Potential transmissions were validated using epidemiological data. Among the 471 eligible MDRB isolates, we detected 1,539 plasmids; 84.41% of these were circularized. We identified 38 potential clonal transmissions in 24 clusters based on cgMLST and 121 potential plasmid transmissions in 24 clusters containing genetically related AMR plasmids. Among the latter clusters, 10 contained different multilocus sequence types (involving 2-38 isolates, median: 3 isolates), and nine contained multiple species (2-18 isolates, median: 4). Epidemiological data confirmed 19 clonal transmissions (in seven clusters) and an additional 12 plasmid transmissions (within eight plasmid clusters). Among these, we identified seven cases of intra-host and five patient-to-patient plasmid transmissions. We demonstrate that intra-host and patient-to-patient transmissions of AMR plasmids can be identified by combining long-read sequencing with real-time applicable tools during routine molecular surveillance. In addition, our study highlights that more than a decade of bacterial genomic surveillance missed at least one-third of all AMR transmission events due to plasmids.\n\nThe dark matter of bacterial genomic surveillance-antimicrobial resistance plasmid transmissions in the hospital setting.", "token_count": 481, "char_count": 1988, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:48.884519", "source": { "split": "train_shard_00000", "doc_id": 333 }, "chunk_id": "train_shard_00000_333_0", "global_id": 373 }, { "text": "Probiotics encounter colonization resistance from native gut microbiomes, affecting their effectiveness. Genetic engineering of probiotics lacks universal applicability, as gut microbiotas are highly individualized. Here, we employed probiotic\n\nGut microbiota drives structural variation of exogenous probiotics to enhance colonization.", "token_count": 72, "char_count": 336, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8718, "quality_score": 0.9359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:49.257047", "source": { "split": "train_shard_00000", "doc_id": 334 }, "chunk_id": "train_shard_00000_334_0", "global_id": 374 }, { "text": "According to the Food and Agricultural Organisation 2024 statement, developing single-cell protein technology is important to reduce the burden on conventional feed protein production sectors. In this regard, improved commercial strains rich in amino acids, especially Lys and Met, may provide a sustainable alternative source of protein in aquaculture diets. The developed and laboratory-validated methodology for creating protein-synthesizing mutants will strengthen the competitiveness of SCP production technology. The present work provides unique results on improving the protein-producing properties of wild-type Phaffia rhodozyma DSM 5626 by mutagenesis and screening on herbicide-containing medium as a selective agent for amino acid biosynthesis inhibition. Inhibitory concentrations of pure herbicide actives were determined for S-(2-aminoethyl)-L-cysteine (AEC) hydrochloride and glufosinate-ammonium (GA) for complete inhibition and strong inhibition of the DSM 5626 strain. GA at a concentration of 50 mM and 100 mM and AEC at 0.5 mM and 2.5 mM were chosen for mutant selection after chemical mutagenesis. The use of herbicides resulted in the selection of mutants with significantly improved synthesis of Met and Lys. Specifically, mutants GA6/4 and GA7/5 exhibited 37% and 26% higher Met levels, respectively, while GA6/3 had a 14% increase in Lys compared to the wild-type strain. The AEC3/9 mutant demonstrated a 35% increase in Met, 24% in Lys, 8% in Ile, and 6% in Phe, underscoring the efficacy of this screening approach in enhancing essential amino acid content. The protein quality parameters essential amino acid index and amino acid score of these mutants became higher compared with commercial strains of SCP yeast such as C. utilis, S. cerevisiae, K. marxianus, etc.\n\nEnhanced amino acid biosynthesis in Phaffia rhodozyma via herbicide-induced selection.", "token_count": 506, "char_count": 1881, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [ "AEC3", "GA7", "GA6" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:49.876507", "source": { "split": "train_shard_00000", "doc_id": 335 }, "chunk_id": "train_shard_00000_335_0", "global_id": 375 }, { "text": "Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses. The construction of a variation graph from a collection of chromosome-size genome sequences is a difficult task that is generally addressed using a number of heuristics. The question that arises is to what extent the construction method influences the resulting graph, and the characterization of variability.\n\nPairwise graph edit distance characterizes the impact of the construction method on pangenome graphs.", "token_count": 113, "char_count": 573, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:50.268662", "source": { "split": "train_shard_00000", "doc_id": 336 }, "chunk_id": "train_shard_00000_336_0", "global_id": 376 }, { "text": "Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety in methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis, a clonally evolving bacterium with a small accessory genome, as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read versus hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations.\n\nPitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.", "token_count": 257, "char_count": 1153, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:50.811789", "source": { "split": "train_shard_00000", "doc_id": 337 }, "chunk_id": "train_shard_00000_337_0", "global_id": 377 }, { "text": "Bile salts are steroids with distinctive hydroxylation patterns that are produced and excreted by vertebrates. In contrast to common human bile salts, ursodeoxycholate (UDCA) has a 7-hydroxy group in β-configuration and is used in large amounts for the treatment of diverse gastrointestinal diseases. We isolated the 7β-hydroxysteroid dehydratase Hsh3 that is involved in UDCA degradation by\n\n7β-Hydroxysteroid dehydratase Hsh3 eliminates the 7-hydroxy group of the bile salt ursodeoxycholate during degradation by", "token_count": 153, "char_count": 514, "word_count": 71, "semantic_coherence": 1, "information_density": 0.6901, "quality_score": 0.8451, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:51.252308", "source": { "split": "train_shard_00000", "doc_id": 338 }, "chunk_id": "train_shard_00000_338_0", "global_id": 378 }, { "text": "High-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, LCLs pose technical challenges for profiling immunoglobulin (IG) genes, as their IG loci contain a mixture of germline and somatically recombined haplotypes, making genotyping and assembly difficult with widely used frameworks. To address this, we introduce IGLoo, a software tool that analyzes sequence data and assemblies derived from LCLs, characterizing somatic V(D)J recombination events and identifying breakpoints and missing IG genes in the assemblies. Furthermore, IGLoo implements a reassembly framework to improve germline assembly quality by integrating information on somatic events and population structural variations in IG loci. Applying IGLoo to the assemblies from the Human Pangenome Reference Consortium, we gained valuable insights into the mechanisms, gene usage, and patterns of V(D)J recombination and the causes of assembly artifacts in the IG heavy-chain (IGH) locus, and we improved the representation of IGH assemblies.\n\nIGLoo enables comprehensive analysis and assembly of immunoglobulin heavy-chain loci in lymphoblastoid cell lines using PacBio high-fidelity reads.", "token_count": 304, "char_count": 1251, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:51.813242", "source": { "split": "train_shard_00000", "doc_id": 339 }, "chunk_id": "train_shard_00000_339_0", "global_id": 379 }, { "text": "A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of three environmentally relevant genera,\n\nPangenomic analysis of three putative hydrocarbon degrading genera", "token_count": 87, "char_count": 399, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7736, "quality_score": 0.8868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:52.198396", "source": { "split": "train_shard_00000", "doc_id": 340 }, "chunk_id": "train_shard_00000_340_0", "global_id": 380 }, { "text": "Recently, floating membrane filter cultivation was adopted to simulate solid surface and enrich surface-adapted soil ammonia-oxidizing archaea (AOA) communities from agricultural soil, as opposed to the conventional liquid medium. Here, we conducted metagenomic sequencing to recover nitrifier bins from the floating membrane filter cultures and reveal their genomic properties. Phylogenomic analysis showed that AOA bins recovered from this study, designated FF_bin01 and FF_bin02, are affiliated with the Nitrososphaeraceae family, while the third bin, FF_bin03, is a nitrite-oxidizing bacterium affiliated with the Nitrospiraceae family. Based on the ANI/AAI analysis, FF_bin01 and FF_bin02 are identified as novel species within the genera \"Candidatus Nitrosocosmicus\" and Nitrososphaera, respectively, while FF_bin03 represents a novel species within the genus Nitrospira. The pan and core genome analysis for the 29 AOA genomes considered in this study revealed 5,784 orthologous clusters, out of which 653 were core orthologous clusters. Additionally, 90 unique orthologous clusters were conserved among the Nitrososphaeraceae family, suggesting their potential role in enhancing culturability and adaptation to diverse environmental conditions. Intriguingly, FF_bin01 and FF_bin02 harbor a gene encoding manganese catalase and FF_bin03 also possesses a heme catalase gene, which might enhance their growth on the floating membrane filter. Overall, the floating membrane filter cultivation has proven to be a promising approach for isolating distinct soil AOA, and further modifications to this technique could stimulate the growth of a broader range of uncultivated nitrifiers from diverse soil environments.\n\nGenomic profiling of soil nitrifying microorganisms enriched on floating membrane filter.", "token_count": 457, "char_count": 1807, "word_count": 243, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:52.832878", "source": { "split": "train_shard_00000", "doc_id": 341 }, "chunk_id": "train_shard_00000_341_0", "global_id": 381 }, { "text": "Hepatitis E virus (HEV) infection causes acute hepatitis, chronic hepatitis, particularly in compromised hosts, and various extrahepatic manifestations. HEV infection is reportedly associated with biliary-pancreatic diseases, such as gallstones, cholangitis, choledocholithiasis, and acute pancreatitis. Severe jaundice and prolonged cholestasis are also atypical manifestations of HEV infection. The mechanism and genes involved in cholestasis, namely sinusoidal uptake of blood, bile salt synthesis and secretion from hepatocytes to the canaliculus, have been elucidated. HEV infection triggers severe jaundice and prolonged cholestasis in patients with genetic variants in adenosine triphosphatase phospholipid transporting 8B1, adenosine triphosphate-binding cassette (ABC) protein B4, ABCB11, Myosin VB, and/or farnesoid X receptor (FXR/NR1H4). Although prolonged cholestasis associated with these gene mutations does not seem to be specific to HEV infection, these mutations may be risk factors related to the severity of HEV infection. The use of the pregnane X receptor agonist rifampicin and the peroxisome proliferator-activated receptor activator bezafibrate may be useful for the treatment of cholestasis. These studies provide new insights into understanding the mechanisms of severe jaundice and prolonged cholestasis caused by HEV infection.\n\nCholestasis in hepatitis E virus infection.", "token_count": 383, "char_count": 1401, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6448, "quality_score": 0.8224, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:53.414002", "source": { "split": "train_shard_00000", "doc_id": 342 }, "chunk_id": "train_shard_00000_342_0", "global_id": 382 }, { "text": "Bacillus velezensis MFSS1 (previously known as B. subtilis FS6) was reported to have good probiotic criteria and antibacterial activity against Vibrio spp. and Aeromonas spp., through phenotypic analysis. However, whole genome sequencing is required for commercialising a new probiotic, especially due to reports on probiotics that can cause horizontal gene transfer towards the host microbiome. Therefore, this study aims to investigate the comprehensive genomic characteristics of B. velezensis MFSS1, focusing on its antimicrobial genes against aquaculture pathogens, its probiotic traits, and safety assessment. The bacterial genome was sequenced using Oxford Nanopore sequencing, resulting in 7 contigs with a total length of 3,914,361 base pairs and an average G + C content of 46.58 %. The analysis using ContEst16S and average nucleotide identity revealed that the bacterium previously reported as B. subtilis is actually B. velezensis. Additionally, secondary metabolites against pathogens were predicted using the antiSMASH website, which identified eight secondary metabolites: Bacillibactin, Bacilysin, Surfactin, Difficidin, Fengycin, Bacillaene, Macrolactin H, and Plantazolicin. Furthermore, several probiotic markers were detected, functioning in acid tolerance, bile salt tolerance, adhesion, osmotic stress, and intestinal persistence during the delivery of the bacteria to the host. Interestingly, the in silico safety assessment of the bacterium revealed a lack of 96 antibiotic resistance genes and confirmed it as non-pathogenic to humans, compared with genomic bacteria from ATCC. The study indicates that B. velezensis MFSS1 is a good probiotic through genomic analysis and can be commercialised to control aquaculture pathogens and reduce reliance on antibiotics.\n\nProbiogenomic insights into Bacillus velezensis MFSS1 for controlling aquaculture pathogens.", "token_count": 480, "char_count": 1882, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.832, "entities": { "genes": [ "FS6", "MFSS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:54.047928", "source": { "split": "train_shard_00000", "doc_id": 343 }, "chunk_id": "train_shard_00000_343_0", "global_id": 383 }, { "text": "This study aimed to identify yeast species in healthy Anatolian buffaloes and those with subclinical mastitis on smallholder farms using the Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry (MALDI-TOF MS) method and assess antifungal resistance. Milk samples from 390 udder lobes of 100 buffaloes were tested and California Mastitis Test (CMT) results showed 265 negative, 102 suspicious and 23 CMT ≥+1 lobes. A total of 76 yeast isolates (19.5%) were obtained through classical culture methods. MALDI-TOF MS identified seven genera, with the most common species being Pichia kudriavzevii (54%), Kluyveromyces marxianus (21%) and Nakaseomyces glabrata (10.5%). Antifungal resistance was determined by the disk diffusion method, showing the highest resistance to caspofungin (69.7%), followed by fluconazole (65.8%) and ketoconazole (31.6%). This study highlights the presence of diverse yeast species in buffalo milk, emphasizing the importance of understanding their role in mastitis and antifungal resistance for animal and public health. To our knowledge, this is the first study showing the identification of different yeast species isolated from Anatolian buffaloes in smallholder dairy farms in Turkey.\n\nIdentification of yeast in healthy and subclinical mastitis-diagnosed Anatolian buffaloes in smallholder dairy farms in Turkey.", "token_count": 384, "char_count": 1365, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:54.679277", "source": { "split": "train_shard_00000", "doc_id": 344 }, "chunk_id": "train_shard_00000_344_0", "global_id": 384 }, { "text": "Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, including pandemic and nonpandemic, toxigenic, and environmental variants, to investigate the diversity of mobile genetic elements (MGEs), embedded bacterial defense systems, and phage-associated signatures. Our findings include both conserved and novel MGEs across strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiphage/antiplasmid mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and suggests that nonpandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and other invading MGEs. Overall, this research offers new insights into V. cholerae's genetic complexity and potential adaptive strategies, offering a better understanding of the differences between environmental strains and their pandemic counterparts, as well as the possible evolutionary pathways that led to the emergence of pandemic strains.\n\nExploring Mobile Genetic Elements in Vibrio cholerae.", "token_count": 387, "char_count": 1749, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:55.332536", "source": { "split": "train_shard_00000", "doc_id": 345 }, "chunk_id": "train_shard_00000_345_0", "global_id": 385 }, { "text": "Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which, in turn, are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the\n\nSmall amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses.", "token_count": 200, "char_count": 904, "word_count": 125, "semantic_coherence": 1, "information_density": 0.768, "quality_score": 0.884, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:55.792186", "source": { "split": "train_shard_00000", "doc_id": 346 }, "chunk_id": "train_shard_00000_346_0", "global_id": 386 }, { "text": "Peanut (Arachis hypogaea L.) is an important oilseed and food legume crop, with seed size and weight being critical traits for domestication and breeding. However, genomic rearrangements like structural variations (SVs) underlying seed size and weight remain unclear. Here we present a comprehensive pangenome analysis utilizing eight high-quality genomes (two diploid wild, two tetraploid wild and four tetraploid cultivated peanuts) and resequencing data of 269 accessions with diverse seed sizes. We identified 22,222 core or soft-core, 22,232 distributed and 5,643 private gene families. The frequency of SVs in subgenome A is higher than in subgenome B. We identified 1,335 domestication-related SVs and 190 SVs associated with seed size or weight. Notably, a 275-bp deletion in gene AhARF2-2 results in loss of interaction with AhIAA13 and TOPLESS, reducing the inhibitory effect on AhGRF5 and promoting seed expansion. This high-quality pangenome serves as a fundamental resource for the genetic enhancement of peanuts and other legume crops.\n\nPangenome analysis reveals structural variation associated with seed size and weight traits in peanut.", "token_count": 305, "char_count": 1153, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:56.407848", "source": { "split": "train_shard_00000", "doc_id": 347 }, "chunk_id": "train_shard_00000_347_0", "global_id": 387 }, { "text": "Chromosomal rearrangements can drive adaptive evolution; however, whether the rearrangements in non-coding and non-promoter regions can lead to new phenotypes under selective pressures remains unclear. Additionally, highly producing recombinant proteins is a key industrial task but poses stress on host cells. Therefore, it is desirable to investigate the role of chromosomal rearrangement in non-coding and non-promoter regions during high-yield recombinant protein phenotype formation. In this study, we utilize the Kluyveromyces marxianus strain as the host for recombinant protein production, with the recombinant fusion protein comprising leghemoglobin (LBA) and enhanced green fluorescent protein serving as a reporter. Iterative evolution is conducted to select high-yield strains using Cre-loxP mediated chromosomal rearrangement technology and high-throughput fluorescence intensity screening. The evolved strains exhibit ~seven-fold increase in fluorescence intensity and a 1.7-fold improvement in LBA yield, identified with chromosome VIII inversion and chromosomes III and V translocation. Introducing these rearrangements into wild-type strains significantly increase recombinant protein yield to about 1.5-fold. Cascade networks are reconstructed based on RNA-seq analysis to elucidate rearrangements' impact on global metabolic processes. Our study confirms that chromosomal rearrangements in non-coding regions can establish adaptive phenotypes and provides new ways of engineering host cells to improve recombinant protein productivity.\n\nEnhancing recombinant protein production through Cre-loxP mediated chromosomal rearrangement evolution in Kluyveromyces marxianus.", "token_count": 413, "char_count": 1686, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:57.019718", "source": { "split": "train_shard_00000", "doc_id": 348 }, "chunk_id": "train_shard_00000_348_0", "global_id": 388 }, { "text": "Escherichia is a common pathogen causing diarrhea in livestock and poultry, posing a serious threat to intestinal health and leading to significant economic losses in the animal husbandry industry. While antibiotics have been used to treat Escherichia coli diarrhea, their numerous drawbacks have led to increasing attention on probiotic interventions. In this study, Lacticaseibacillus paracasei subsp. paracasei Q-1 (L. paracasei subsp. paracasei Q-1) was isolated from fresh cow dung, and its in vitro and in vivo safety and probiotic properties were evaluated. In vitro experiments demonstrated that L. paracasei subsp. paracasei Q-1 exhibited good antimicrobial activity against Escherichia coli K99, along with key probiotic characteristics such as acid production, acid and bile salt tolerance, high-temperature resistance, hydrophobicity, and cell adhesion. Furthermore, it showed no hemolytic activity, gelatinase activity, or mucin-degrading activity, and it only exhibited decarboxylase activity for histamine. While resistant to certain antibiotics, no significant resistance genes were detected, indicating favorable probiotic and safety profiles. In vivo, acute toxicity tests in mice revealed no signs of acute poisoning after 14 days of high-dose oral administration. A 28-day oral toxicity test showed that different doses did not affect organ indices, cause bacterial translocation, alter blood biochemical parameters, or damage the ileum. In the infection protection experiment, oral administration of L. paracasei subsp. paracasei Q-1 significantly increased the survival rate of Escherichia coli K99-infected mice from 50 to 80%. In conclusion, L. paracasei subsp. paracasei Q-1 demonstrated excellent safety and probiotic properties both in vitro and in vivo and showed promising potential in preventing Escherichia coli K99 infections, with possible applications in animal health management.", "token_count": 492, "char_count": 1914, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:57.663134", "source": { "split": "train_shard_00000", "doc_id": 349 }, "chunk_id": "train_shard_00000_349_0", "global_id": 389 }, { "text": "Lacticaseibacillus paracasei subsp. paracasei Q- 1 Exhibits Good Safety and Effectively Prevents Escherichia coli K99-Induced Diarrhea in Mice.", "token_count": 53, "char_count": 143, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:58.030289", "source": { "split": "train_shard_00000", "doc_id": 349 }, "chunk_id": "train_shard_00000_349_1", "global_id": 390 }, { "text": "Bloodstream infections caused by Staphylococcus epidermidis are among the most frequent and serious infections in neonatal intensive care units (NICU), being responsible for high rates of morbidity and mortality. However, how S. epidermidis prevails, disseminates and evolves to cause outbreaks in NICU is poorly understood. We aimed to understand what is the genomic basis of S. epidermidis outbreaks in NICU to provide guidelines for a better infection control. We collected all S. epidermidis isolated from newborn blood cultures admitted to a hospital NICU in Brazil over one-year and compared their genomes. The S. epidermidis infection incidence rate was 1.17 per baby-year. 83,64% of S. epidermidis were resistant to methicillin (MRSE) and 84,5% belonged to sequence type 2 (ST2) or related, carrying the staphylococcal cassette chromosome mec (SCCmec) type III or IVa. Single nucleotide polymorphisms (SNPs) analysis showed that S. epidermidis infections resulted from the co-existence of three ST2 transmission chains originating from distinct endemic sources (<50 SNPs). Each transmission chain was characterized by specific antibiotic resistance and virulence profile and content in staphylococcal cassette chromosome elements (SCCmec, SCC non-mec and ACME). During transmission, other mobile genetic elements were acquired/lost and mutations emerged in genes involved in adhesion, signal transduction, general metabolism, replication, recombination and repair. Tracking S. epidermidis transmission chains in the NICU will require a deep genomic analysis, combining bacterial genetic background and accessory genome. This study highlighted the need for the integration of whole genome sequencing as a key surveillance tool for infection control in NICUs.\n\nThe complexity of Staphylococcus epidermidis molecular epidemiology in neonatal intensive care units (NICU) as revealed by genomic approaches.", "token_count": 484, "char_count": 1909, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:58.668870", "source": { "split": "train_shard_00000", "doc_id": 350 }, "chunk_id": "train_shard_00000_350_0", "global_id": 391 }, { "text": "Leptospirosis is an emerging zoonotic and neglected disease across the world causing huge loss of life and economy. In this study, we did whole genome sequencing of one Leptospira isolate and a comparative genomic analysis with 69 other species of Leptospira available in RefSeq database provided insight into taxonomic and evolutionary relationship between species. AAI and whole genome based phylogenomic analysis established 3 clusters of Leptospira i.e. pathogenic, intermediate and saprophytic correlating with level of virulence of species. Leptospira has large closed core genome of 1038 genes and an open pan genome with 20,822 genes. The mobilome related genes were found mainly in pan-genome of pathogenic clade. A total of 498 genes have been identified as virulomes, with 329 virulent genes exhibiting presence/absence in various Leptospira species contributing to each species specific virulence profile. The hierarchical clustering of the congregated pathogenic genes yielded five groups, each with a distinct pattern of predominant genes that were either unique or common among clades, indicating lineage uniqueness. Most of the virulent gene pool identified were significantly enriched in COG functional categories of Nucleotide transport and metabolism, Intracellular trafficking, secretion and vesicular transport, cell motility and amino acid transport & metabolism. Pathogenic leptospires exhibit fewer clade-specific genes than non-pathogenic and intermediate leptospires, indicating gene loss and gain events in the evolution of pathogenic leptospires from non-pathogenic. The study's clade-specific and virulent genes can be utilised as markers for defining clade and associated virulence levels in any new Leptospira isolates. Wet-lab validation of virulent genes will help in accurately targeting pathogenic pathways of Leptospira and controlling leptospirosis.\n\nIdentification of virulence genes and clade-specific markers through pan-genomic analysis of Leptospira.", "token_count": 486, "char_count": 1992, "word_count": 274, "semantic_coherence": 1, "information_density": 0.635, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:01:59.645159", "source": { "split": "train_shard_00000", "doc_id": 351 }, "chunk_id": "train_shard_00000_351_0", "global_id": 392 }, { "text": "To assess the impact of crude oil pollution on Manila clams (Ruditapes philippinarum), we analyzed the effects of exposure to water-accommodated fraction (WAF) at different concentrations (nominal TPH concentrations of 0.5, 1.0 and 3.0 mg/L), including survival rate, histopathology observation and antioxidant enzyme detection. Results demonstrated that the activities of antioxidant enzymes-Catalase (CAT), Superoxide dismutase (SOD), Glutathione peroxidase (GSH-PX) and Malondialdehyde (MDA) in Manila clams was significantly elevated in 3.0 mg/L WAF group compared with the control group (P < 0.05). In addition, RNA-seq was performed to analyze clam hepatopancreas tissue in 0 d (control group, CG), 7 d (exposure group, O7d), 15 d (exposure group, O15d) after the exposure to WAF (3 mg/L) and recovery in clean water for 7 d after 15 d WAF exposure (recovery group, R7d). The results showed that a total of 129 differentially expressed genes (DEGs) were detected in the O7d vs CG group, 123 DEGs were detected in the O15d vs CG group, and 2113 DEGs were detected in the R7d vs CG group. Of these genes, the expression of cytochrome P450 2J2 (6.30-fold), bile salt sulfotransferase (8.06-fold), multidrug resistance-associated protein 1 (8.17-fold) was significantly induced at 15 d under the WAF exposure. DEGs were significantly enriched in pathways such as cysteine and methionine metabolism, as well as glycine, serine and threonine metabolism", "token_count": 483, "char_count": 1452, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6409, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:00.289853", "source": { "split": "train_shard_00000", "doc_id": 352 }, "chunk_id": "train_shard_00000_352_0", "global_id": 393 }, { "text": "Furthermore, eight DEGs, including metabolism-related genes (ABCC1, ABCG2, SULT2A1, CYP2J2), ion transport genes (SLC39a14, RFT2), an immune-related gene (Gvin1), and a cellular structure and signal regulatory gene (Ank3) were selected for qRT-PCR analysis. The results confirmed that DEG expression levels were consistent with RNA-seq findings. This study provides crucial molecular insights into the adaptive responses and recovery processes of marine bivalves in response to oil pollution, thereby contributing a scientific foundation for evaluating and monitoring marine environmental pollution.\n\nEffects of water-accommodated fractions of crude oil on detoxification and antioxidant mechanisms in Ruditapes philippinarum.", "token_count": 178, "char_count": 726, "word_count": 93, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [ "ABCC1", "ABCG2", "RFT2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:00.729640", "source": { "split": "train_shard_00000", "doc_id": 352 }, "chunk_id": "train_shard_00000_352_1", "global_id": 394 }, { "text": "The Cuatro Cienegas Basin (CCB) in Mexico, represents a unique ecological habitat, characterized by extreme and fluctuating conditions, providing a window into ancient evolutionary processes. This basin, characterized by hypersalinity and phosphorus scarcity, harbors diverse microbial communities that exhibit remarkable adaptations to oligotrophic conditions. Among these, Halobacterium salinarum, a halophilic archaeon known for its polyploid genome and metabolic versatility, has been extensively studied as a model for extremophile survival. However, only a limited number of H. salinarum strains have been successfully cultured and characterized to date. Here, we report the isolation and genomic analysis of a novel Halobacterium salinarum strain, AD88, from microbial mats at the Archaean Domes site in the CCB. This strain displays unique genomic features, including smaller plasmid sizes and distinctive metabolic pathways for phosphorus and sulfur utilization. Comparative analyses with other Halobacterium strains revealed genetic innovations, such as genes involved in sulfolipid biosynthesis, enabling membrane stability in phosphorus-depleted environments, and adaptations for horizontal gene transfer, which facilitate genomic flexibility in response to environmental pressures. This study reveals that H. salinarum AD88 is the first recorded diploid strain of Halobacterium, a feature previously undocumented in this genus. Phylogenomic reconstruction positioned AD88 tightly within the Halobacterium clade, reflecting its evolutionary history within the genus. Pangenome analysis further highlighted the open nature of the Halobacterium genus, with AD88 contributing novel accessory genes linked to ecological specialization. These findings emphasize the evolutionary significance of the CCB as a natural laboratory for studying microbial adaptation and expand our understanding of archaeal genomic diversity and functional innovation under extreme conditions.\n\nSalty secrets of Halobacterium salinarum AD88: a new archaeal ecotype isolated from Cuatro Cienegas Basin.", "token_count": 465, "char_count": 2086, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8297, "entities": { "genes": [ "AD88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:01.366753", "source": { "split": "train_shard_00000", "doc_id": 353 }, "chunk_id": "train_shard_00000_353_0", "global_id": 395 }, { "text": "Daily briefing: Potato pangenome reveals the complex genetics of the humble spud.", "token_count": 21, "char_count": 81, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:01.736194", "source": { "split": "train_shard_00000", "doc_id": 354 }, "chunk_id": "train_shard_00000_354_0", "global_id": 396 }, { "text": "Solanum section Petota Dumort. consists of tuber-bearing species (i.e., the cultivated potatoes and their wild relatives) that have both asexual and sexual propagation, variation in ploidy, and reproductive isolation. These species have undergone adaptation to a diversity of climates, altitudes, photoperiods, and geographical range. The section defies characterization with the biological species concept due to interspecies hybridization, allo- and auto-polyploidy, and phenotypic plasticity. Genetic studies, and more recently genome sequencing and pangenome analyses, are fostering a greater understanding of genetic processes that shape genome evolution and speciation in the section, shedding light on the phylogeny and providing insights on utilization of potato crop wild relatives in breeding for climate-resilient potato varieties.\n\nPolyploidy in potatoes: challenges and possibilities for climate resilience.", "token_count": 211, "char_count": 920, "word_count": 120, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:02.197121", "source": { "split": "train_shard_00000", "doc_id": 355 }, "chunk_id": "train_shard_00000_355_0", "global_id": 397 }, { "text": "Color and flavor are key quality traits in fruits. Using a newly constructed peach pangenome, Chen et al. demonstrated that the PbBL gene, a known regulator of peach fruit color, also contributes to malate accumulation. This finding, along with previous studies, unveils a transcriptional mechanism that co-regulates multiple traits in peaches.\n\nTranscriptional crosstalk linking color, acidity, and aroma in peach.", "token_count": 101, "char_count": 415, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:02.580120", "source": { "split": "train_shard_00000", "doc_id": 356 }, "chunk_id": "train_shard_00000_356_0", "global_id": 398 }, { "text": "Human ileal bile acid-binding protein (hI-BABP), a member of the family of intracellular lipid-binding proteins, has a key role in the enterohepatic circulation of bile salts. The two internal binding sites of hI-BABP exhibit positive cooperativity accompanied by a site preference of glycocholate (GCA) and glycochenodeoxycholate (GCDA), the two most abundant bile salts in the human body. Previous study of Q51A hI-BABP in its apo state, a mutant with lost site-selectivity, suggests that disruption of the hydrogen-bonding network in the vicinity of the C/D-turn has long-range dynamic effects. To improve our understanding of the determinants of site-selectivity in hI-BABP, a comparative NMR chemical shift and spin relaxation analysis of homo- and heterotypic bile salt complexes of wild-type and Q51A hI-BABP was carried out. The wild-type GCDA-complex shows a striking similarity with the thermodynamically most stable hI-BABP:GCDA:GCA complex in terms of both structure and dynamic behaviour, suggesting that the bound GCDA at site 1 has a decisive role in conveying key stabilizing interactions in the physiologically most abundant heterotypic complex. Destabilization of hI-BABP-GCDA by the functionally impairing mutation Q51A is indicated by both the increase of ms-timescale motions in key segments of the protein as well as by increased ps-ns local fluctuations superimposed on slow motions. Our study suggests that binding interactions in hI-BABP might be modulated by altering the dynamic behaviour of specific segments in the protein with implications for targeting the intracellular trafficking of bile salts and bile salt-induced stimulation of nuclear receptors.\n\nDeterminants of site-selectivity in human ileal bile acid-binding protein by NMR dynamic analysis of a functionally-impaired mutant.", "token_count": 485, "char_count": 1817, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5517, "quality_score": 0.7759, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:03.216736", "source": { "split": "train_shard_00000", "doc_id": 357 }, "chunk_id": "train_shard_00000_357_0", "global_id": 399 }, { "text": "Bioethanol production from non-food biomass has emerged as a sustainable alternative to satisfy future energy demands. Kluyveromyces marxianus stands out as a potential consolidated bioprocessing (CBP) strain for high-temperature ethanol production from inulin. Nevertheless, enhancing its fermentation efficiency remains crucial. Here, we characterized its glycolysis regulator KmGcr2p and demonstrated that KmGcr2p boosts the expression of target genes controlled by another glycolysis regulator, KmGcr1p, through their interaction. Furthermore, we engineered the strain Ogcr1 + 2 through co-overexpressing KmGCR1 and KmGCR2, leading to a 55.8 % increase in inulinase activity, improved growth at 37 °C to 45 °C and under 10 % ethanol, and enhanced ethanol production at 42 °C by 36.0 % from inulin and 39.5 % from Jerusalem artichoke tuber flour. Our results highlight that co-overexpression of glycolysis regulators KmGcr1p and KmGcr2p can simultaneously enhance inulin saccharification, thermotolerance, ethanol tolerance, and ethanol production, presenting a promising and feasible strategy for high-temperature CBP ethanol production from inulin and inulin-rich feedstocks.\n\nEnhanced expression of glycolysis regulators KmGcr1p and KmGcr2p in Kluyveromyces marxianus: An efficient strategy for high-temperature ethanol production from inulin.", "token_count": 382, "char_count": 1349, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:04.417425", "source": { "split": "train_shard_00000", "doc_id": 358 }, "chunk_id": "train_shard_00000_358_0", "global_id": 400 }, { "text": "Natural variations are the foundation of crop improvement. However, genomic variability remains largely understudied. Here, we present the full-spectrum integrated panvariome and pangenome of 1,020 peach accessions, including 10.5 million single-nucleotide polymorphisms, insertions, deletions, duplications, inversions, translocations, copy-number variations, transposon-insertion polymorphisms, and presence-absence variations, uncovering 70.6% novel variants and 3,289 novel genes. Analysis of the panvariome recapitulated the global evolutionary history of the peach and identified several novel trait-causally rare variants. We found that landraces and improved accessions encode more genes than the wild accessions, implying gene gains during peach domestication and improvement. Analysis of global introgression patterns revealed their value in phenotype prediction and gene mining, and suggested that the most likely wild progenitor of the domesticated peach is Prunus mira and that almond was involved in the origin of Prunus davidiana. Furthermore, we developed a novel panvariome-based one-step solution for association study, GWASPV, which was used to identify several trait-conferring genes and over 2,000 novel associations.. Collectively, our study reveals new insights into peach evolution and genomic variations, providing a novel method for plant gene mining and important targets for peach breeding.\n\nPanvariome and pangenome of 1,020 global peach accessions shed light on evolution patterns, hidden natural variations, and efficient gene discovery.", "token_count": 370, "char_count": 1568, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:04.996751", "source": { "split": "train_shard_00000", "doc_id": 359 }, "chunk_id": "train_shard_00000_359_0", "global_id": 401 }, { "text": "Listeria monocytogenes is a major foodborne pathogen associated with fresh produce contamination, posing a significant public health risk due to its adaptability and virulence. This study investigates the genomic diversity and distribution of L. monocytogenes strains isolated from imported and domestic fresh produce in Mexico between 2014 and 2018. A total of 113 L. monocytogenes strains were isolated from produce commodities and subjected to whole-genome sequencing. The analysis focused on identifying lineages, serogroups, clonal complexes (CCs), antimicrobial resistance genes, virulence factors, prophage-associated regions, and SNP clusters, while the pangenome was characterized to assess both core and accessory gene diversity. Two main lineages (I and II) were identified, with lineage I predominantly associated with imported produce. Thirty-two CCs were detected, with CC4, CC11, and CC20 being the most prevalent. The pangenome analysis revealed 2188 core genes and 3739 accessory genes. Antimicrobial resistance genes, including fosX, lin, norB, and sul, were present in all strains. Virulence analysis identified 78 virulence genes, with notable differences among serogroups. Prophage analysis revealed 189 prophage-associated regions, with common phages such as A118 and LP-101 detected predominantly in serogroup IIa. The SNP cluster analysis grouped the strains into 33 clusters, with 48 % of the strains from imported produce concentrated in only three major clusters, indicating potential common sources or similar environmental exposures. The significant genomic diversity and SNP clustering of L. monocytogenes strains underscore the pathogen's adaptability and widespread dissemination potential in the global food supply chain. The presence of virulent CCs and antimicrobial resistance genes highlights an ongoing public health risk, emphasizing the need for enhanced surveillance and targeted interventions to prevent listeriosis outbreaks.\n\nGenomic diversity and distribution of Listeria monocytogenes strains isolated from imported and national fresh produce in Mexico from 2014 to 2018.", "token_count": 513, "char_count": 2117, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5793, "quality_score": 0.7897, "entities": { "genes": [ "CC11", "CC20", "CC4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:02:05.641002", "source": { "split": "train_shard_00000", "doc_id": 360 }, "chunk_id": "train_shard_00000_360_0", "global_id": 402 }, { "text": "The supramolecular structures resulting from the complexation between the neutral-cationic block copolymer poly(ethylene oxide)-\n\nStructural interplay in block copolymer-bile salt complexes: from globules to ribbons.", "token_count": 57, "char_count": 216, "word_count": 25, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:06.011891", "source": { "split": "train_shard_00000", "doc_id": 361 }, "chunk_id": "train_shard_00000_361_0", "global_id": 403 }, { "text": "Multichromosomal mitochondrial genomes (mtDNAs) in eukaryotes exhibit remarkable structural diversity, yet intraspecific variability and the origin of the individual chromosomes remain poorly understood. We focus on a holoparasitic angiosperm with an mtDNA consisting of 65 chromosomes largely composed of foreign DNA acquired by horizontal gene transfer (HGT) from its mimosoid hosts. The frequency, timing and population dynamics of these HGT events have not been examined. Here, we sampled different individuals of the holoparasite Lophophytum mirabile, along with their host plants, to assess mtDNA intraspecific variability and capture recent events that may bring insights into the HGT process. We also gathered mitochondrial data from 43 mimosoids to identify older and recent HGT events and assess precisely the proportion of foreign DNA. Through comparative genomic and evolutionary analyses, we uncovered great intraspecific variability in chromosome content and defined the mitochondrial pangenome of L. mirabile with 105 distinct chromosomes. The estimated foreign content reaches 93.5% of the mtDNA, including 73 fully foreign chromosomes that support the circle-mediated HGT model as a key mechanism for their acquisition. We inferred recurrent DNA transfers from the host plants, leading to new mitochondrial chromosomes that replicate autonomously. Our results emphasize the importance of adopting a pangenomic approach to fully capture the genetic diversity and evolution of multichromosomal mitochondrial genomes. This study shows that HGT can strongly influence the mtDNA content and generate enormous intraspecific variability even in geographically close individuals.\n\nHighly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA.", "token_count": 420, "char_count": 1811, "word_count": 250, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:06.626076", "source": { "split": "train_shard_00000", "doc_id": 362 }, "chunk_id": "train_shard_00000_362_0", "global_id": 404 }, { "text": "Most SV studies in livestock rely on short-read sequencing, posing challenges in accurately characterizing large genomic variants due to their limited read length.\n\nLong read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.", "token_count": 62, "char_count": 304, "word_count": 41, "semantic_coherence": 1, "information_density": 0.878, "quality_score": 0.939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:07.027319", "source": { "split": "train_shard_00000", "doc_id": 363 }, "chunk_id": "train_shard_00000_363_0", "global_id": 405 }, { "text": "The reference genome plays a crucial role in uncovering genomic variations, which increase our understanding of the molecular mechanisms influencing biological traits. However, most of the sheep reference genomes derive from a single individual, which couldn't adequately represent the genetic diversity of sheep. The map-to-pan strategy was used to construct the sheep pan-genome based on 801 samples with short read whole genome sequencing data including 724 domestic individuals from 151 sheep populations/breeds and 77 wild individuals from seven genus Ovis species, and a total of 195 Mb of nonreference sequences were assembled that absent from the ARS-UI_Ramb_v2.0 reference. MAKER2 pipeline, integrating ab initio gene prediction, RNA-Seq, and protein homology was used to annotate the nonreference sequences. As a result, a total of additional 2678 genes were predicted in the nonreference sequences. We also identified 13,317 novel single nucleotide polymorphisms (SNPs) by mapping the sequences that could not be aligned to ARS1-UI_Ramb_v2.0 to the nonreference sequences. Population genetic analysis, including principal component analysis (PCA), phylogenetic tree, and ADMIXTURE based on the novel SNPs revealed a clear phylogenetic relationship of the world's domestic sheep, as well as their close wild relatives. Additionally, pangenome-wide presence and absence variations (PAVs) analysis exhibited a decreasing trend in gene number from wildto domestic populations. Several genes, including GZMH, NFE2L3, GPR146 and CALHM6 with significant changes of presence frequencies during the evolutionary history of sheep were identified by PAV selection analysis. Functional annotation revealed that these genes were primarily associated with immune responses. Our results highlight the implications of the sheep pan-genome in identifying previously unknown genetic variations.These findings broaden our knowledge about the genetic diversity in sheep genomes, and provide insight into the domestication and breeding history of sheep.\n\nSheep pan-genome retrieves the lost sequences and genes during domestication and selection.", "token_count": 485, "char_count": 2136, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8085, "entities": { "genes": [ "MAKER2", "GPR146", "CALHM6", "ARS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:07.688496", "source": { "split": "train_shard_00000", "doc_id": 364 }, "chunk_id": "train_shard_00000_364_0", "global_id": 406 }, { "text": "Variations in metabolite accumulation particularly anthocyanins have been of keen interest to the global tea industry due to their potential health benefits. Previous studies on tea genome, transcriptome, and metabolome provided an integrated spectrum of bioactive metabolites biosynthesis in tea plants. However, comprehending knowledge of anthocyanin biosynthesis and its accumulation in tea plants needed to be unified with multi-omics approaches that can build a complete depiction of the regulatory genomic machinery for improving quality characteristics in tea. Furthermore, true visualization, interpretation, and precise dissection of key traits required significant enrichment of multi-omics data for integration of machine learning. This review emphasizes the role of genetics, epigenetics, and transcriptional regulation of early (EBG) and late biosynthetic genes (LBG) involved in anthocyanin biosynthesis and accumulation in purple tea. Additionally, other factors including key transcription factors, transporters, photosynthesis, vacuole pH, and co-biosynthesis of other flavonoids were discussed. We envision an integration of pangenome and genome-wide strategies (GWAS, mGWAS, EWAS) which can offer new insights for the breeding of anthocyanin-rich tea cultivars to fetch better trade revenue and nutraceutical benefits.\n\nRevolutionizing Speciality Teas: Multi-omics prospective to breed anthocyanin-rich tea.", "token_count": 333, "char_count": 1426, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7135, "quality_score": 0.8568, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:08.294456", "source": { "split": "train_shard_00000", "doc_id": 365 }, "chunk_id": "train_shard_00000_365_0", "global_id": 407 }, { "text": "Lactiplantibacillus plantarum EA3 was isolated from traditional fermented yak milk in the Gannan Tibetan Autonomous Prefecture of Gansu Province, China. Whole-genome analysis revealed that the EA3 genome is 3.47 Mb in size, consisting of a circular chromosome and three plasmids. The circular chromosome measures 3,318,230 bp in length with a GC content of 44.48 %. Functional annotation identified at least ten regulatory pathways and 33 protein-coding genes associated with oxidative stress, whose abundance correlates with free radical scavenging rates and oxygen tolerance. Additionally, genes encoding ten acid-tolerant proteins, ten bile salt-tolerant proteins, 26 adhesive proteins, and 12 bacteriocin-related proteins were detected. In vitro experiments have confirmed that EA3 can withstand up to 4 mM H\n\nAnalysis of the antioxidant properties of Lactiplantibacillus plantarum EA3 isolated from fermented yak milk based on whole genome sequencing.", "token_count": 271, "char_count": 956, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [ "EA3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:08.860521", "source": { "split": "train_shard_00000", "doc_id": 366 }, "chunk_id": "train_shard_00000_366_0", "global_id": 408 }, { "text": "This study investigated the effects of ursodeoxycholic acid (UDCA) and bile salt (BAS) supplementation on lactation performance, health, and gut microbiota in periparturient dairy cows. Fifty-one Holstein dairy cows were selected at d -28 before parturition and blocked into 3 dietary treatments, including the control (CON; n = 17) received a basal diet, whereas the UDCA (n = 17) and BAS groups (n = 17) were supplemented with 10 g/d UDCA and 20 g/d BAS from d -21 to +21, with an observation phase until d +35. Milk yield and composition were recorded weekly, whereas the DMI were measured biweekly. Blood samples were collected at d +7 and +21, whereas rumen fluid and fecal samples were collected at d +21. Milk yield was significantly higher in the UDCA group at d +21 compared with the CON group, whereas on d +28, milk yield was significantly higher in both the UDCA and BAS groups compared with the CON group, and the DMI of the UDCA group showed an increased tendency at prepartum. Plasma nonesterified fatty acids were significantly higher in the BAS group, whereas Ala aminotransferase content were significantly lower in the UDCA group compared with the control. Furthermore, the cholesterol, malondialdehyde, oxidative stress index, serum amyloid A, and haptoglobin content were significantly lower in the UDCA and BAS groups. In total, 35, 43, and 45 plasma bile acids (BA) were detected in the control, UDCA, and BAS groups, respectively. Compared with the control, 8 key BA, including UDCA, tauroursodeoxycholic acid, glycoursodeoxycholic acid, and 5 key BA, including tauro-β-muricholic acid and hyocholic acid, were identified in the UDCA and BAS groups, respectively. The concentrations of total VFA and acetate in the UDCA and BAS groups were higher than that in the CON group, and the concentration of propionate tended to be higher", "token_count": 520, "char_count": 1854, "word_count": 301, "semantic_coherence": 1, "information_density": 0.4917, "quality_score": 0.7458, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:02:09.509174", "source": { "split": "train_shard_00000", "doc_id": 367 }, "chunk_id": "train_shard_00000_367_0", "global_id": 409 }, { "text": "The β-diversity of both rumen and gut microbiota was significantly higher in the CON, UDCA, and BAS groups, whereas no significant changes were observed in α-diversity. Key rumen VFA-production bacteria, including Prevotella_7, Succinivibrionaceae_UCG-001, and Selenomonas, were enriched in the UDCA and BAS groups, along with an increase in beneficial gut microbiota, such as Butyrivibrio, Ruminococcus, and Caproiciproducen, and a reduction in harmful bacteria, such as Stenotrophomonas and Chryseobacterium. These findings suggest that the observed improvements in production performance and health may be mediated by alterations in peripheral BA and rumen and gut microbiota, offering insights for optimizing the nutrition and health of transitional dairy cows.\n\nSupplementation with ursodeoxycholic acid and bile salt benefits lactation performance, health, and rumen and fecal microbiota of transition dairy cows.", "token_count": 242, "char_count": 919, "word_count": 125, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:09.987456", "source": { "split": "train_shard_00000", "doc_id": 367 }, "chunk_id": "train_shard_00000_367_1", "global_id": 410 }, { "text": "Staphylococcus aureus subsp. anaerobius (SAAN) causes abscesses in small ruminants, known as Morel's Disease. This study describes the presence of SAAN for the first time in Germany and Austria and examines the phylogenetic relationship among these isolates and previously described European and Sudanese ones. A total of 35 sheep and 10 goat isolates from 12 herds in Germany were available for analysis. SAAN isolates from four Polish goats and three Austrian sheep from different herds were included. Genome comparisons and phylogenetic analyses were conducted using core genome multilocus sequence typing. The comparison of the 52 SAAN core genomes revealed a close phylogenetic relationship among most German isolates (n = 38), with allelic differences ≤ 6 in two clusters associated with ST4581. In contrast, distinct clusters of the same ST included the four Polish goat isolates and two ovine isolates from Austria, respectively. A fifth cluster of ST3756 strains was identified on three German farms (six sheep, one goat) and an Austrian sheep. Tight phylogenetic relationships were observed irrespective of the host species. All isolates shared a common set of virulence genes and few known antimicrobial resistance determinants. The introduction of SAAN into herds is mostly unknown, but purchases appear to play a critical role.\n\nPresence and genetic variability of Staphylococcus aureus subsp. anaerobius isolated from small ruminants in Central Europe.", "token_count": 373, "char_count": 1466, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6409, "quality_score": 0.8205, "entities": { "genes": [ "ST4581", "ST3756" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:10.554310", "source": { "split": "train_shard_00000", "doc_id": 368 }, "chunk_id": "train_shard_00000_368_0", "global_id": 411 }, { "text": "Lactic acid bacteria (LAB) with their potential health benefits are naturally prevalent in dairy and fermented food products. This probiotic microbiota can be an alternative biological tool for controlling other pathogenic bacteria. The study aimed to isolate lactic acid bacteria (LAB) from raw cow milk and evaluate their probiotic potential. Twelve gram-positive isolates showing tolerance to bile salt, acid, and low pH were identified by 16S rRNA sequencing, which revealed the isolates belong to the genera including Lactococcus, Enterococcus, Streptococcus, Bacillus, and Weissella. In case of probiotic potential, the isolates exhibited arrays of probiotic properties: autoaggregation (33.65-84.63 %), co-aggregation (8.17-83.22 %), cell surface hydrophobicity for both polar (13.37-90.24 %) and non-polar solvents (5.52-53.58 %) and able to form biofilm (75 % weak, 16.67 % moderate and 8.33 % strong). Statistical analysis revealed the correlation pattern between the probiotic properties and showed a significant strong positive correlation between cell surface hydrophobicity and aggregation. Additionally, three isolates L. lactis, W. confusa, and E. gallinarum that were sensitive to antibiotics, able to produce biofilm, and did not contain virulence genes were able to reduce the biofilm formation of pathogen K. pneumoniae (1.3-4 log) in the co-culture assay. These Findings suggest that LAB from the raw cow milk could serve as a natural biocontrol agent for preventing and controlling K. pneumoniae biofilm formation and pave the way for innovative intervention of LAB in food safety and clinical settings.\n\nBiofilm inhibition and antagonism of Klebsiella pneumoniae by probiotic lactic acid bacteria (LAB) isolated from raw cow milk.", "token_count": 476, "char_count": 1753, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:11.188086", "source": { "split": "train_shard_00000", "doc_id": 369 }, "chunk_id": "train_shard_00000_369_0", "global_id": 412 }, { "text": "The\n\nPangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbiotic", "token_count": 26, "char_count": 125, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:11.551261", "source": { "split": "train_shard_00000", "doc_id": 370 }, "chunk_id": "train_shard_00000_370_0", "global_id": 413 }, { "text": "Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding\n\nA pangenome reference of wild and cultivated rice.", "token_count": 47, "char_count": 170, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8077, "quality_score": 0.9038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:11.912230", "source": { "split": "train_shard_00000", "doc_id": 371 }, "chunk_id": "train_shard_00000_371_0", "global_id": 414 }, { "text": "Patients with low phospholipid-associated cholelithiasis may suffer from recurrent biliary symptoms and complications despite cholecystectomy and ursodeoxycholic acid therapy. Recently, beneficial clinical effects of treatment with the potent Farnesoid X receptor (i.e. bile salt receptor) agonist obeticholic acid in combination with ursodeoxycholic acid were reported in this patient group. In contrast, other studies reported more gallstone-related events and increased cholesterol saturation indices in gallbladder biles during obeticholic acid monotherapy. We here provide an in-depth review on solubilization and crystallization of cholesterol in bile, including all relevant physico-chemical aspects of cholesterol gallstone pathogenesis. We offer an explanation that reconciles seemingly contradictory data in previous publications. We propose that, due to the well-known inhibition of intra-hepatic bile salt synthesis from cholesterol by Farnesoid X receptor stimulation, biliary bile salt concentrations decrease during obeticholic acid therapy. As a result, biliary cholesterol solubilization shifts from mixed micelles into cholesterol-phospholipid vesicles, with inhibited cholesterol crystallization despite increased cholesterol saturation index (the latter takes only micellar cholesterol solubilization into account). We suggest that obeticholic acid has a lithoprotective effect, provided that increased bile salt hydrophobicity from obeticholic acid (a quite hydrophobic bile salt that is secreted into bile) is prevented by concomitant ursodeoxycholic acid therapy. We also suggest future directions for research into the role of obeticholic acid and other Farnesoid X receptor agonists to improve the prospects of low phospholipid-associated cholelithiasis patients and other gallstone patients with persisting biliary problems after cholecystectomy. In conclusion, obeticholic acid may enhance lithoprotective effects of ursodeoxycholic acid.", "token_count": 489, "char_count": 1965, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:12.554667", "source": { "split": "train_shard_00000", "doc_id": 372 }, "chunk_id": "train_shard_00000_372_0", "global_id": 415 }, { "text": "A physico-chemical explanation for the litho-protective effects of obeticholic acid in low phospholipid-associated cholelithiasis.", "token_count": 40, "char_count": 130, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:12.912268", "source": { "split": "train_shard_00000", "doc_id": 372 }, "chunk_id": "train_shard_00000_372_1", "global_id": 416 }, { "text": "Arcobacter butzleri is a widely distributed foodborne and waterborne pathogen, increasingly recognized as an emerging enteropathogen. Understanding its survival mechanisms and interactions with probiotics is crucial for developing targeted intervention strategies. A. butzleri must withstand various hostile conditions to successfully colonize the gastrointestinal tract, including inhibition by probiotics, such as Limosilactobacillus reuteri, Lactobacillus acidophilus and Lactiplantibacillus plantarum. Thus, this study aimed to assess the survival of A. butzleri under acidic conditions and determine its minimum inhibitory concentration (MIC) for bile salts. Additionally, the antimicrobial potential of the lactobacilli strains was evaluated by analysing the effects of their culture-free supernatant (CFS) on A. butzleri growth, coculture interactions, and biofilm formation. The influence of lactobacilli on A. butzleri was further investigated through competition, displacement and exclusion assays using Caco-2 cell models. The results indicate that lactobacilli strains exhibit tolerance to acidic environments and physiological bile salt concentrations, whereas A. butzleri was more susceptible to acidic stress. The antagonistic effect of lactobacilli was evidenced by growth inhibition of A. butzleri in the presence of CFS or during coculture. However, CFS from certain lactobacilli strains was found to enhance biofilm formation, highlighting potential consequences. Furthermore, while lactobacilli did not demonstrate significant antagonistic effects in competition assays, they effectively displaced and excluded A. butzleri in the Caco-2 infection model. Overall, these findings suggest that probiotic lactobacilli can inhibit A. butzleri growth, yet their impact on its virulence remains uncertain. This underscores the need for strain-specific probiotic selection to effectively target this pathogen and emphasizes that not every probiotic contribute to the prevention of A. butzleri infections.\n\nThe dual action of probiotic lactobacilli in suppressing virulence and survival of Arcobacter butzleri.", "token_count": 511, "char_count": 2121, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:13.538739", "source": { "split": "train_shard_00000", "doc_id": 373 }, "chunk_id": "train_shard_00000_373_0", "global_id": 417 }, { "text": "This study reports the first high-quality telomere-to-telomere (T2T)\n\nT2T genome, pan-genome analysis, and heat stress response genes in", "token_count": 43, "char_count": 136, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:13.907533", "source": { "split": "train_shard_00000", "doc_id": 374 }, "chunk_id": "train_shard_00000_374_0", "global_id": 418 }, { "text": "Long-read sequencing technologies, particularly those from Pacific Biosciences and Oxford Nanopore Technologies, are revolutionizing genome research by providing high-resolution insights into complex and repetitive regions of the human genome that were previously inaccessible. These advances have been particularly enabling for the comprehensive detection of genomic structural variants (SVs), which is critical for linking genotype to phenotype in population-scale and rare disease studies, as well as in cancer. Recent developments in sequencing throughput and computational methods, such as pangenome graphs and haplotype-resolved assemblies, are paving the way for the future inclusion of long-read sequencing in clinical cohort studies and disease diagnostics. DNA methylation signals directly obtained from long reads enhance the utility of single-molecule long-read sequencing technologies by enabling molecular phenotypes to be interpreted, and by allowing the identification of the parent of origin of de novo mutations. Despite this recent progress, challenges remain in scaling long-read technologies to large populations due to cost, computational complexity, and the lack of tools to facilitate the efficient interpretation of SVs in graphs. This perspective provides a succinct review on the current state of long-read sequencing in genomics by highlighting its transformative potential and key hurdles, and emphasizing future opportunities for advancing the understanding of human genetic diversity and diseases through population-scale long-read analysis.\n\nThe impact of long-read sequencing on human population-scale genomics.", "token_count": 324, "char_count": 1644, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:14.474329", "source": { "split": "train_shard_00000", "doc_id": 375 }, "chunk_id": "train_shard_00000_375_0", "global_id": 419 }, { "text": "Over the past decade, genome sequencing and assembly approaches have been greatly improved, resulting in the assembly of many genomes for citrus, including wild, domesticated, and citrus-related genomes. Improvements in technologies have led to assembled genomes with higher completeness, contiguity, quality, and accuracy that have greatly facilitated annotation and analysis. This review summarizes the evolution of the sequencing, assembly, and annotation technologies leading to citrus genomes over the past 11 years, a comprehensive evaluation of their quality, contiguity, and completeness, and the major findings and applications. Of the 50 genomes now available, 35 have been assembled to chromosome level and 15 to draft level, and 14 were haplotype-resolved assemblies. To date there have been four pangenome-wide studies for citrus. The very recent genomes assembled with long-read sequencing have achieved >99% and >98% assembly and annotation completeness (BUSCO), respectively. However, some early genomes are not of the same high quality as more recently sequenced genomes and would benefit from re-sequencing. A more comprehensive pangenome based upon a larger set of species and genotypes assembled at the haplotype level would allow genomics to deliver the maximum benefits for citrus improvement and research.\n\nCitrus genomes: past, present and future.", "token_count": 312, "char_count": 1371, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:15.031901", "source": { "split": "train_shard_00000", "doc_id": 376 }, "chunk_id": "train_shard_00000_376_0", "global_id": 420 }, { "text": "Indian desi cattle, known for their adaptability and phenotypic diversity, represent a valuable genetic resource. However, a single reference genome often fails to capture the full extent of their genetic variation. To address this, we construct a pangenome for desi cattle by identifying and characterizing non-reference novel sequences (NRNS). We sequence 68 genomes from seven breeds, generating 48.35 billion short reads. Using the PanGenome Analysis (PanGA) pipeline, we identify 13,065 NRNS (~41 Mbp), with substantial variation across the population. Most NRNS were unique to desi cattle, with minimal overlap (4.1%) with the Chinese indicine pangenome. Approximately 40% of NRNS exhibited ancestral origins within the Bos genus and were enriched in genic regions, suggesting functional roles. These sequences are linked to quantitative trait loci for traits such as milk production. The pangenome approach enhances read mapping accuracy, reduces spurious single nucleotide polymorphism calls, and uncovers novel genetic variants, offering a deeper understanding of desi cattle genomics.\n\nConstructing a draft Indian cattle pangenome using short-read sequencing.", "token_count": 275, "char_count": 1169, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7378, "quality_score": 0.8689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:15.576940", "source": { "split": "train_shard_00000", "doc_id": 377 }, "chunk_id": "train_shard_00000_377_0", "global_id": 421 }, { "text": "The rapid progression of antimicrobial resistance, fueled by the excessive use of antibiotics, has become a major public health concern. Among the pathogens contributing to this crisis, Staphylococcus aureus stands out as a significant therapeutic challenge, especially with the rise of resistant strains like Methicillin-Resistant S. aureus (MRSA). In this context, antimicrobial peptides (AMPs) emerge as a promising alternative, thanks to their unique mechanisms of action. Exploring the genomes of species such as Staphylococcus hominis, known for producing AMPs effective against S. aureus, offers promising opportunities for discovering novel therapeutic agents. In this study, Average Nucleotide Identity (ANI) combined with phylogenetic analysis identified a potential emerging subspecies of Staphylococcus hominis. The core genome analysis led to the identification of a potential antimicrobial peptide. The peptide model simulated with the S. aureus membrane model in molecular dynamics revealed that it interacts primarily with the lipids head groups, leading to an overall rigidification of the bacterial membrane.\n\nStaphylococcus hominis as a source of antimicrobial peptides: identification of a new peptide with potential antimicrobial properties using in silico approach.", "token_count": 312, "char_count": 1287, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:16.134611", "source": { "split": "train_shard_00000", "doc_id": 378 }, "chunk_id": "train_shard_00000_378_0", "global_id": 422 }, { "text": "As sequencing costs decrease, short-read and long-read technologies are indispensable tools for uncovering the genetic drivers behind bacterial pathogen resistance. This study explores the differences between the use of short-read (Illumina) and long-read (Oxford Nanopore Technologies [ONT]) sequencing in detecting antimicrobial resistance (AMR) genes in ESKAPE pathogens (ie,\n\nInfluence of Sequencing Technology on Pangenome-Level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens.", "token_count": 134, "char_count": 511, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:16.550807", "source": { "split": "train_shard_00000", "doc_id": 379 }, "chunk_id": "train_shard_00000_379_0", "global_id": 423 }, { "text": "Conjugated bile acids (BAs) are multi-functional detergents in the gastrointestinal (GI) tract produced by the liver enzyme bile acid-CoA:amino acid N-acyltransferase (BAAT) and by the microbiome from the acyltransferase activity of bile salt hydrolase (BSH). Humans with inflammatory bowel disease (IBD) have an enrichment in both host and microbially conjugated BAs (MCBAs), but their impacts on GI inflammation are not well understood. We investigated the role of host-conjugated BAs in a mouse model of colitis using a BAAT knockout background. Baat\n\nBalance between bile acid conjugation and hydrolysis activity can alter outcomes of gut inflammation.", "token_count": 186, "char_count": 656, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7684, "quality_score": 0.8842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:16.992857", "source": { "split": "train_shard_00000", "doc_id": 380 }, "chunk_id": "train_shard_00000_380_0", "global_id": 424 }, { "text": "This study presents a dual investigation of Salmonella enterica subspecies I, focusing on serovar prediction and core genome characteristics. We utilized two large genomic datasets (panX and NCBI Pathogen Detection) to test machine learning methods for predicting Salmonella serovars based on genomic differences. Among the four tested algorithms, the Random Forest model demonstrated higher performance, achieving 90.3% accuracy with the panX dataset and 95.3% with the NCBI dataset, particularly effective when trained on >50% of available data. When combined with hierarchical clustering validation, our approach achieved 100% prediction accuracy on the simulated data. Parallel analysis of panX core genome characteristics revealed that pathogenicity-related genes (including sseA, invA, mgtC, phoP, phoQ, and sitA) exhibited similar phylogenetic topologies distinct from the core genome phylogenetic tree, suggesting shared evolutionary histories. Notably, all identified core antibiotic resistance genes and virulence factors showed evidence of negative selection, indicating their essential role in bacterial survival. This study not only presents a promising machine learning-based alternative for Salmonella serovar classification, particularly valuable when analyzing newly identified serovars alongside known reference strains but also provides insights into the evolutionary dynamics of core virulence-associated genes, contributing to our understanding of Salmonella genomic architecture and pathogenicity.\n\nUsing core genome and machine learning for serovar prediction in Salmonella enterica subspecies I strains.", "token_count": 350, "char_count": 1627, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:17.561887", "source": { "split": "train_shard_00000", "doc_id": 381 }, "chunk_id": "train_shard_00000_381_0", "global_id": 425 }, { "text": "Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two\n\nAccurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC.", "token_count": 339, "char_count": 1649, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6814, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:18.119138", "source": { "split": "train_shard_00000", "doc_id": 382 }, "chunk_id": "train_shard_00000_382_0", "global_id": 426 }, { "text": "Pangenome methods have the potential to uncover hitherto undiscovered sequences missing from established reference genomes, making them useful to study evolutionary and speciation processes in diverse organisms. The cichlid fishes of the East African Rift Lakes represent one of nature's most phenotypically diverse vertebrate radiations, but single-nucleotide polymorphism (SNP)-based studies have revealed little sequence difference, with 0.1%-0.25% pairwise divergence between Lake Malawi species. These were based on aligning short reads to a single linear reference genome and ignored the contribution of larger-scale structural variants (SVs). We constructed a pangenome graph that integrates six new and two existing long-read genome assemblies of Lake Malawi haplochromine cichlids. This graph intuitively represents complex and nested variation between the genomes and reveals that the SV landscape is dominated by large insertions, many exclusive to individual assemblies. The graph incorporates a substantial amount of extra sequence across seven species, the total size of which is 33.1% longer than that of a single cichlid genome. Approximately 4.73% to 9.86% of the assembly lengths are estimated as interspecies structural variation between cichlids, suggesting substantial genomic diversity underappreciated in SNP studies. Although coding regions remain highly conserved, our analysis uncovers a significant proportion of SV sequences as transposable element (TE) insertions, especially DNA, LINE, and LTR TEs. These findings underscore that the cichlid genome is shaped both by small-nucleotide mutations and large, TE-derived sequence alterations, both of which merit study to understand their interplay in cichlid evolution.\n\nLake Malawi cichlid pangenome graph reveals extensive structural variation driven by transposable elements.", "token_count": 431, "char_count": 1854, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:18.733517", "source": { "split": "train_shard_00000", "doc_id": 383 }, "chunk_id": "train_shard_00000_383_0", "global_id": 427 }, { "text": "Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in many tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a compelling example for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III secretion effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of type III effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.\n\nDiversification of an emerging bacterial plant pathogen; insights into the global spread of Xanthomonas euvesicatoria pv. perforans.", "token_count": 474, "char_count": 2267, "word_count": 318, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:19.395336", "source": { "split": "train_shard_00000", "doc_id": 384 }, "chunk_id": "train_shard_00000_384_0", "global_id": 428 }, { "text": "Variable Number Tandem repeats (VNTRs) refer to repeating motifs of size greater than five bp. VNTRs are an important source of genetic variation, and have been associated with multiple Mendelian and complex phenotypes. However, the highly repetitive structures require reads to span the region for accurate genotyping. Pacific Biosciences HiFi sequencing spans large regions and is highly accurate but relatively expensive. Therefore, targeted sequencing approaches coupled with long-read sequencing have been proposed to improve efficiency and throughput. In this paper, we systematically explored the trade-off between targeted and whole genome HiFi sequencing for genotyping VNTRs. We curated a set of 10 , 787 gene-proximal (G-)VNTRs, and 48 phenotype-associated (P-)VNTRs of interest. Illumina reads only spanned 46% of the G-VNTRs and 71% of P-VNTRs, motivating the use of HiFi sequencing. We performed targeted sequencing with hybridization by designing custom probes for 9,999 VNTRs and sequenced 8 samples using HiFi and Illumina sequencing, followed by adVNTR genotyping. We compared these results against HiFi whole genome sequencing (WGS) data from 28 samples in the Human Pangenome Reference Consortium (HPRC). With the targeted approach only 4,091 (41%) G-VNTRs and only 4 (8%) of P-VNTRs were spanned with at least 15 reads. A smaller subset of 3,579 (36%) G-VNTRs had higher median coverage of at least 63 spanning reads. The spanning behavior was consistent across all 8 samples. Among 5,638 VNTRs with low-coverage ( < 15), 67% were located within GC-rich regions ( > 60%). In contrast, the 40X WGS HiFi dataset spanned 98% of all VNTRs and 49 (98%) of P-VNTRs with at least 15 spanning reads, albeit with lower coverage", "token_count": 517, "char_count": 1739, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6479, "quality_score": 0.824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:02:20.068653", "source": { "split": "train_shard_00000", "doc_id": 385 }, "chunk_id": "train_shard_00000_385_0", "global_id": 429 }, { "text": "Spanning reads were sufficient for accurate genotyping in both cases. Our findings demonstrate that targeted sequencing provides consistently high coverage for a small subset of low-GC VNTRs, but WGS is more effective for broad and sufficient sampling of a large number of VNTRs.\n\nAnalysis of targeted and whole genome sequencing of PacBio HiFi reads for a comprehensive genotyping of gene-proximal and phenotype-associated Variable Number Tandem Repeats.", "token_count": 107, "char_count": 455, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:20.496302", "source": { "split": "train_shard_00000", "doc_id": 385 }, "chunk_id": "train_shard_00000_385_1", "global_id": 430 }, { "text": "Pseudomonas syringae is a soil-dwelling bacterium that exhibits remarkable niche adaptability, and it is known for its devastating impact as a plant pathogen. This bacterium has an outstanding capability to produce a wide array of biologically active natural products. P. syringae coexists with amoebal predators and fungal strains, which drives the production of secondary metabolites for predator evasion in addition to niche adaptation. In this study, we conducted a broad pangenomic analysis of 18 taxonomically distinct P. syringae strains, leading to the identification of 231 biosynthetic gene clusters (BGCs). Among these, nonribosomal peptide synthetases (NRPSs) were particularly abundant, indicating their potential significance within this ecological context. We discovered and elucidated the structures of two novel classes of bioactive compounds, the syrilipamides and chlorosecimides. Furthermore, a bioinformatic analysis enabled the identification of an undescribed halogenase, SecA, essential for the chlorination of secimide A. We observed that syrilipamides and secimides and in particular mixtures thereof, exhibit amoebicidal activities. Additionally, secimides showed selective antifungal activity. These findings provide valuable insights into the ecological roles of P. syringae natural products and highlight their potential for biotechnological and therapeutic applications.\n\nPangenome Analysis of the Plant Pathogen Pseudomonas syringae Reveals Unique Natural Products for Niche Adaptation.", "token_count": 362, "char_count": 1518, "word_count": 200, "semantic_coherence": 1, "information_density": 0.67, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:21.074428", "source": { "split": "train_shard_00000", "doc_id": 386 }, "chunk_id": "train_shard_00000_386_0", "global_id": 431 }, { "text": "Increasing number of structural variations (SVs) have been identified as causative mutations for diverse agronomic traits. However, the systematic exploration of SVs quantity, distribution, and contribution in wheat was lacking. Here, we report high-quality gene-based and SV-based pangenomes comprising 22 hexaploid wheat assemblies showing a wide range of chromosome size, gene number, and TE component, which indicates their representativeness of wheat genetic diversity. Pan-gene analyses uncover 140,261 distinct gene families, of which only 23.2 % are shared in all accessions. Moreover, we build a ∼16.15 Gb graph pangenome containing 695,897 bubbles, intersecting 5132 genes and 230,307 cis-regulatory regions. Pairwise genome comparisons identify ∼1,978,221 non-redundant SVs and 497 SV hotspots. Notably, the density of bubbles as well as SVs show remarkable aggregation in centromeres, which probably play an important role in chromosome plasticity and stability. As for functional SVs exploration, we identify 2769 SVs with absolute relative frequency differences exceeding 0.7 between spring and winter growth habit groups. Additionally, several reported functional genes in wheat display complex structural graphs, for example, PPD-A1, VRT-A2, and TaNAAT2-A. These findings deepen our understanding of wheat genetic diversity, providing valuable graphical pangenome and variation resources to improve the efficiency of genome-wide association mapping in wheat.\n\nStructural variation-based and gene-based pangenome construction reveals untapped diversity of hexaploid wheat.", "token_count": 399, "char_count": 1587, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7406, "quality_score": 0.8703, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:21.682604", "source": { "split": "train_shard_00000", "doc_id": 387 }, "chunk_id": "train_shard_00000_387_0", "global_id": 432 }, { "text": "Inflammatory bowel disease (IBD) is characterized by a chronic inflammation of the intestinal mucosa, with predominant localization in the colon in ulcerative colitis (UC) or affecting the entire length of the gastrointestinal tract in Crohn's disease (CD). Recent advances in the drug development space have been marked by a return to orally administered small molecules with novel mechanisms of action such as Janus kinase inhibitors. Additionally, the prevalence of certain chronic conditions is higher in IBD patients, many of which are treated with orally administered drugs. Given the pathophysiology and localization of IBD, altered drug absorption from the gastrointestinal tract can be expected. This review discusses several physiological differences between the small and large intestine with the potential to influence drug absorption including pathophysiology related alterations associated with IBD. The main physiological parameters which are identified include luminal fluid volume, luminal pH, transit time, bile salt concentration, microbiome, absorptive surface area, permeability and metabolizing enzymes and transporters. Literature regarding these factors in IBD patients is marked with high heterogeneity in reporting of disease severity and location leading to difficulties in interpreting data across different studies. While the influence of most of these factors has been directly assessed in healthy volunteers, this is rarely the case for IBD patients. Furthermore, studies which used PBPK modelling to describe the PK of an orally administered drug in an IBD population and were able to verify their findings using clinical data are critically examined. These models were able to incorporate the pathophysiological changes associated with IBD and partly succeeded in adequately predicting drug absorption in this population. Given the limited amount of PBPK studies performed on a limited number of drugs, the developed models are most likely not suitable to be used as a general PBPK model for the IBD population.\n\nSmall molecule drug absorption in inflammatory bowel disease and current implementation in physiologically- based pharmacokinetic models.", "token_count": 459, "char_count": 2183, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5911, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:22.318057", "source": { "split": "train_shard_00000", "doc_id": 388 }, "chunk_id": "train_shard_00000_388_0", "global_id": 433 }, { "text": "Bile salt hydrolase (BSH) is produced by gut bacteria and is responsible for deconjugating amino acids from the aliphatic side chains of conjugated bile acids (BAs), initiating the critical first step in BAs metabolism. Lead (Pb) is known to cause gut microbial dysbiosis, but whether it affects BAs profiles by reshaping the gut microbiota remains elusive. Here, using targeted BAs metabolomics and metagenomics sequencing, we found that 200 μg/L Pb treatment led to a significant increase in the abundance of BSH-producing microbiota (e.g., Eubacterium and Yersinia), thus promoting the deconjugation of taurocholic acid (TCA) and taurochenodeoxycholic acid (TCDCA). Consequently, the accumulation of relatively hydrophobic BAs cholic acid (CA) and chenodeoxycholic acid (CDCA) may cause damage to enterocytes (e.g., reduced microvilli and enterocyte heights), which attenuated tadpole digestion and ultimately led to significant reductions in morphological parameters. The inhibition of tadpole growth by Pb toxicity may negatively affect their survival and even increase their risk of death. Overall, these results revealed for the first time the toxicological mechanism by which Pb reshapes the gut microbiota and thus disrupts the BAs profile, shedding new insights into the detrimental effects of Pb toxicity on amphibian growth.\n\nLead promoted bile acid deconjugation by modulating gut bacteria encoding bile salt hydrolase (BSH) in Rana chensinensis tadpoles.", "token_count": 400, "char_count": 1468, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:22.927595", "source": { "split": "train_shard_00000", "doc_id": 389 }, "chunk_id": "train_shard_00000_389_0", "global_id": 434 }, { "text": "Modern stressors such as stress, irregular lifestyles, lack of exercise, and poor eating habits weaken immunity, thereby increasing susceptibility to infections and chronic diseases. Probiotics are functional ingredients that regulate gut microbiota, enhance immune function, and reduce oxidative stress. In this study, we identified novel probiotic candidates with antioxidant and immunostimulatory properties. Lactiplantibacillus plantarum WB4304, L. plantarum WB4305, and Levilactobacillus brevis WB4306, isolated from the traditional fermented food kimchi, exhibited acid and bile salt tolerance and strong adhesion to HT-29 cells, suggesting their suitability for intestinal colonization. Their safety was confirmed through hemolytic activity, bile salt hydrolase activity, and antibiotic susceptibility assays. Notably, L. plantarum WB4304 and L. plantarum WB4305 exhibited higher radical scavenging activities than Lacticaseibacillus rhamnosus GG. These strains significantly enhanced nitric oxide (NO) production and phagocytosis in RAW 264.7 macrophages. Immune activation was mediated by upregulation of inducible nitric oxide synthase (iNOS), cyclooxygenase-2 (COX-2), and pro-inflammatory cytokines, including interleukin (IL)-1β, IL-6, and tumor necrosis factor (TNF)-α through the nuclear factor-kappa B (NF-κB) and mitogen-activated protein kinase (MAPK) signaling pathways. Among the three strains, L. plantarum WB4304 and L. plantarum WB4305 exhibited the most pronounced immunostimulatory effects. These findings suggest the potential of L. plantarum WB4304, L. plantarum WB4305, and L. brevis WB4306 as safe and functional probiotics, with promising applications in oxidative stress management and immune health enhancement.", "token_count": 509, "char_count": 1743, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7149, "quality_score": 0.8575, "entities": { "genes": [ "WB4306", "WB4304", "WB4305" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:23.579306", "source": { "split": "train_shard_00000", "doc_id": 390 }, "chunk_id": "train_shard_00000_390_0", "global_id": 435 }, { "text": "Antioxidant and Immunostimulatory Effects of Lactobacillus Strains in RAW 264.7 Macrophages via NF-κB and MAPK Signaling Pathways.", "token_count": 51, "char_count": 130, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:23.937425", "source": { "split": "train_shard_00000", "doc_id": 390 }, "chunk_id": "train_shard_00000_390_1", "global_id": 436 }, { "text": "Pangenome graphs enable population-scale genotyping and improve expression analysis, revealing that structural variations (SVs), particularly transposable elements (TEs), significantly contribute to gene expression variation in winter oilseed rape. Structural variations (SVs) impact important traits, from yield to flowering behaviour and stress responses. Pangenome graphs capture population-level diversity, including SVs, within a single data structure and provide a robust framework for downstream applications. They have the potential to serve as unbiased references for SV genotyping, pan-transcriptomic analyses, and association studies, offering significant advantages over single reference genomes. However, their full potential for expression quantitative trait locus (eQTL) analysis is yet to be explored. We combined long and short-read whole genome sequencing data with expression profiling of Brassica napus (oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. Over 90,000 SVs were discovered from 57 long-read datasets. Pangenome graph as reference was evaluated and used for SV genotyping with short reads and transcript expression quantification. Using SVs genotyped from the graph and 100 expression datasets, we identified 267 gene proximal (cis) SV-eQTLs. Over 70% of eQTL-SVs had similarity to transposable elements (TEs), especially Helitrons. The highest proportion of cis-eQTL-SVs were found in promoter regions. About a third of transcripts whose expression was associated with SVs, had no associated SNPs, suggesting that including SVs allows capturing of relationship which would be missed in SNP-only analyses. This study demonstrated that pangenome graphs provide a unifying framework for eQTL analysis by allowing population-scale SV genotyping and gene expression quantification. We also showed that SVs make an appreciable contribution to gene expression variation in winter oilseed rape.\n\nGraphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.", "token_count": 473, "char_count": 2120, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6098, "quality_score": 0.8049, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:24.575356", "source": { "split": "train_shard_00000", "doc_id": 391 }, "chunk_id": "train_shard_00000_391_0", "global_id": 437 }, { "text": "Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when these chromosomes are missing in the reference genome. Pangenome variation graphs offer a reference-free alternative for studying these chromosomes. Here, we constructed a pangenome variation graph for 73 diverse\n\nReference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen.", "token_count": 122, "char_count": 569, "word_count": 76, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:24.960273", "source": { "split": "train_shard_00000", "doc_id": 392 }, "chunk_id": "train_shard_00000_392_0", "global_id": 438 }, { "text": "Gut microbiota and bile acid metabolism play crucial roles in the progression of nonalcoholic fatty liver disease (NAFLD). Early evidence demonstrates that Ginsenoside Re (Re) possesses pharmacological effects on NAFLD, but its mechanisms of action are not well understood. This study aimed to investigate the hepatic protective effects of Re in NAFLD and elucidate relevant mechanisms. The effects of Re treatments (10, 20, or 40 mg/kg) against high-fat diet-induced NAFLD were initially tested on male C57BL/6 mice. Then, a separate mouse group received Re with or without antibiotics to confirm the regulatory role of microbiota in the effect of Re. Finally, another group of mice received fecal microbiota transplantation (FMT) from the initial experiment of NAFLD mice to further investigate the mechanistic role of gut microbiota. Re significantly improved liver function by reducing hepatic lipid accumulation, injury and hepatocyte steatosis, and inflammation. The liver protection was mediated by the regulation of gut microbiota as evidenced by restored intestinal barrier integrity, normalized Firmicutes/Bacteroidota ratio, enhanced abundances of Adlercreutzia equolifaciens , and reduced Faecalibaculum rodentium. Following that, Re reduced total and primary bile acids and downregulated bile acid synthesis genes and proteins such as farnesoid X receptor and cytochrome P450 family 7 subfamily A member 1. The co-administration of antibiotic cocktail counteracted the effect of Re against NAFLD. Further, the results obtained from the FMT animal study confirmed that Re's liver protective effects were at least partly driven by the regulation of gut microbiota. Re modulated bile salt hydrolase-related microbial genera to alter bile acid synthesis pathways, thereby inhibiting NAFLD progression.\n\nGut Microbiota and Bile Acid Metabolism in the Mechanism of Ginsenoside Re Against Nonalcoholic Fatty Liver Disease.", "token_count": 489, "char_count": 1928, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:25.608275", "source": { "split": "train_shard_00000", "doc_id": 393 }, "chunk_id": "train_shard_00000_393_0", "global_id": 439 }, { "text": "Within a group of three captive lowland tapirs (Tapirus terrestris) suffering from clinically apparent mycobacteriosis, non-tuberculous Mycobacterium avium subsp. hominissuis (MAH) strains were isolated from the animals and the tapir's enclosure. Based on MIRU-VNTR findings, which identified two closely related INMV profiles (124 and 246), a micro-evolutionary event was assumed, and four available MAH strains were submitted to whole genome sequencing (short- and long-read technologies). Surprisingly, the differences based on single nucleotide polymorphisms (SNPs) were exceptionally high between the four strains, i.e., between 841 and 11,166 bases, due to a strong impact of homologous recombination. Thus, an ad hoc core genome multilocus sequence typing (cgMLST) scheme was created and pangenome analysis was conducted for determining the genomic similarity between the strains. The INMV246 isolate obtained from sputum on the enclosure floor and one INMV124 isolate of tapir #2 showed the highest congruence, suggesting that both originated from a shared source. The other two INMV124 isolates were genomically distinct from these strains. Nevertheless, in all four strains two plasmids were detected, which were highly conserved between the strains. The study showed that the genomic variability between MAH strains isolated from the same site within a short period of time can be exceptionally high and the influence of homologous recombination needs to be considered when determining MAH strain relationships, particularly via SNP analyses.\n\nComparative genomics of Mycobacterium avium subsp. hominissuis strains within a group of captive lowland tapirs.", "token_count": 427, "char_count": 1667, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [ "INMV246", "INMV124" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:26.229155", "source": { "split": "train_shard_00000", "doc_id": 394 }, "chunk_id": "train_shard_00000_394_0", "global_id": 440 }, { "text": "Acinetobacter baumannii, a Gram-negative bacterium, is a public health threat due to its role in nosocomial infections and increasing antibiotic resistance. In Nigeria, data on the molecular epidemiology of A. baumannii is scarce. This study investigates the genetic diversity and the presence of antimicrobial resistance determinants and virulence-related genes in whole-genome sequencing data of 189 Nigerian A. baumannii isolates deposited in public repositories. Genotypes were determined in-silico by multilocus sequence typing (MLST) and core genome MLST (cgMLST). Further, antimicrobial resistance (AMR) and virulence-related genes were analyzed.\n\nComprehensive molecular epidemiology of Acinetobacter baumannii from diverse sources in Nigeria.", "token_count": 193, "char_count": 751, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7113, "quality_score": 0.8557, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:26.682728", "source": { "split": "train_shard_00000", "doc_id": 395 }, "chunk_id": "train_shard_00000_395_0", "global_id": 441 }, { "text": "Goat milk is a superior nutritional source for human beings. It possesses probiotic, prebiotic, immunomodulatory actions and inhibits the adherence of pathogenic bacteria. The microbiota of raw goat milk is a rich source of novel bacteriocin-producing lactic acid bacteria (LAB). LAB were evaluated for their probiotic attributes, i.e. acid, bile tolerance, and safety assessment. The antimicrobial activity of LAB isolated from goat milk was assessed against the 10 most common indigenous bacterial pathogens confirmed through 16S rRNA sequencing. The strains LAB GM8 and GM121 showed high tolerance to acidic pH while GM121 showed tolerance to high bile salt concentrations. LAB GM121 showed susceptibility to eight antibiotics which meets the safety requirements regarding phenotypic resistance evaluation. Out of 10, 4 LAB GM8, GM26, GM121, GM122 displayed antibacterial activity against Pseudomonas aeruginosa and Staphylococcus aureus, demonstrating their ability to produce bioactive compounds. So, based on acid, bile tolerance, and safety requirements, it can be concluded that the GM121 has the potential to be explored as probiotic strains in the dairy industry. Bacterial isolates (n-24) were screened for exopolysaccharide production and amylase activity; Bacillus paralicheniformis GM75 showed good exopolysaccharide production and antimicrobial activity while Bacillus cereus GM56 showed maximum amylase activity.\n\nBioprospecting for probiotics and other technological aspects of the bacteria isolated from goat milk.", "token_count": 405, "char_count": 1532, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8255, "entities": { "genes": [ "GM8", "GM56", "GM75", "GM26", "GM121", "GM122" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:27.293825", "source": { "split": "train_shard_00000", "doc_id": 396 }, "chunk_id": "train_shard_00000_396_0", "global_id": 442 }, { "text": "Streptococcus thermophilus plays a pivotal role in yogurt fermentation, yet strains from traditional fermented products remain largely unexplored compared to their industrial counterparts. This study aimed to characterize the genomic diversity and functional potential of 15 S. thermophilus strains isolated from Turkish traditional yogurts, and to compare them with industrial strains. Through whole-genome sequencing and advanced bioinformatics analyses, we revealed distinct phylogenetic patterns and genetic features that differentiate these traditional strains from industrial isolates. The genomes (1.68-1.86 Mb) exhibited high genetic homogeneity (ANI > 98.69%) while maintaining significant functional diversity. Pan-genome analysis identified 1160 core genes and 5694 accessory genes, highlighting substantial genomic plasticity that enables niche adaptation. Our analysis uncovered several distinctive features: (1) unique phylogenetic clustering patterns based on both housekeeping genes and whole-genome SNPs, suggesting geographical isolation effects; (2) an extensive repertoire of carbohydrate-active enzymes (CAZymes), comprising 111 Glycoside Hydrolases, 227 Glycosyl Transferases, and 44 Carbohydrate Esterases and 13 Carbohydrate-Binding Modules, demonstrating sophisticated carbohydrate metabolism adaptation significantly enriched compared to industrial strains; (3) widespread GABA biosynthesis pathways in 8 strains, including complete gadB gene, indicating potential health-promoting properties; (4) multiple genomic islands containing genes for galactose utilization and stress response, suggesting specific adaptation to traditional fermentation environments; (5) diverse exopolysaccharide biosynthesis and bacteriocin gene clusters; and (6) widespread CRISPR-Cas systems with variable spacer content. Notably, we identified vanY glycopeptide resistance genes across all strains, with two strains additionally harboring vanT. These results reveal the genetic mechanisms behind S", "token_count": 494, "char_count": 2004, "word_count": 241, "semantic_coherence": 1, "information_density": 0.7676, "quality_score": 0.8838, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:27.951441", "source": { "split": "train_shard_00000", "doc_id": 397 }, "chunk_id": "train_shard_00000_397_0", "global_id": 443 }, { "text": "thermophilus adaptation to traditional yogurt environments, offering valuable insights for developing starter cultures and preserving the unique qualities and potential health benefits of traditional dairy products.\n\nComparative genome analysis of 15 Streptococcus thermophilus strains isolated from Turkish traditional yogurt.", "token_count": 66, "char_count": 327, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8718, "quality_score": 0.9359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:28.320721", "source": { "split": "train_shard_00000", "doc_id": 397 }, "chunk_id": "train_shard_00000_397_1", "global_id": 444 }, { "text": "Tenacibaculum dicentrarchi emerged as a major pathogen in Chilean salmon farming in early 2023, causing 32.9% of Atlantic salmon (Salmo salar) mortalities. Although recent studies have provided valuable insights into T. dicentrarchi through virulence mechanisms and genome analysis, genetic diversity based on the O-antigen gene cluster remains largely unexplored. In this study, we conducted a comparative genomic analysis of O-antigen biosynthesis genes in 30 whole-genome sequenced strains, including the T. dicentrarchi type strain. The analysis identified a single O-antigen gene cluster (O-AGC) consisting of 20 genes involved in the biosynthesis of this component of the lipopolysaccharide layer. Variations in the O-AGC revealed antigenic diversity within the species, allowing classification into four distinct groups, designated Types 1 to 4. Based on these findings, we developed a multiplex PCR-based genotyping scheme, which was successfully applied to 25 bacterial isolates from Chilean fish farms. Most isolates were identified as Type 1 and 3, while Types 2 and 4 were less common, with the same number of isolates. We also investigated whether core genome phylogeny correlated with O-AGC Types by including publicly available genomes from Chile, Norway and Canada. Notably, T. dicentrarchi isolates clustered into two groups: one comprising isolates from Norway and Canada, all belonging to Type 1. Another group consisted of Chilean isolates with diverse O-AGC Types (i.e., 1, 2, 3 and 4), including the type strain. This multiplex PCR approach provided a valuable tool for rapid and reliable typing of T. dicentrarchi, facilitating epidemiological studies and aiding in the selection of appropriate isolates for the vaccine development against tenacibaculosis in fish farms.\n\nO-Antigen Gene Cluster Reveals Genomic Variation in Chilean Tenacibaculum dicentrarchi Through Multiplex PCR-Based Genotyping Scheme.", "token_count": 486, "char_count": 1928, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:28.975496", "source": { "split": "train_shard_00000", "doc_id": 398 }, "chunk_id": "train_shard_00000_398_0", "global_id": 445 }, { "text": "The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.", "token_count": 511, "char_count": 1917, "word_count": 241, "semantic_coherence": 1, "information_density": 0.7469, "quality_score": 0.8734, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:29.621482", "source": { "split": "train_shard_00000", "doc_id": 399 }, "chunk_id": "train_shard_00000_399_0", "global_id": 446 }, { "text": "Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences.", "token_count": 36, "char_count": 124, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:29.980045", "source": { "split": "train_shard_00000", "doc_id": 399 }, "chunk_id": "train_shard_00000_399_1", "global_id": 447 }, { "text": "Breeds genetically distant from the reference genome often show considerable differences in DNA fragments, making it difficult to achieve accurate mappings. The genetic differences between pig reference genome (Sscrofa11.1) and Chinese indigenous pigs may lead to mapping bias and affect subsequent analyses.\n\nPangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.", "token_count": 95, "char_count": 425, "word_count": 57, "semantic_coherence": 1, "information_density": 0.807, "quality_score": 0.9035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:30.358405", "source": { "split": "train_shard_00000", "doc_id": 400 }, "chunk_id": "train_shard_00000_400_0", "global_id": 448 }, { "text": "Citrus is an important nutritional fruit globally; however, its yield is affected by various stresses. This study presents the draft pangenome of Citrus, developed using 11 species to examine their genetic diversity and identify members of the germin-like proteins (GLPs) gene family involved in disease responsiveness. The developed sequence-based pangenome contains 954 Mb sequence and 74,755 genes. The comparative genomics analysis revealed the presence-absence variations (PAVs) among the Citrus genomes and species-specific protein-coding genes. Gene-based pangenome analysis revealed 4,936 new genes missing in the reference genome and highlighted the core and shell genes with putative functions in stress regulation. The pangenome-wide identification of GLP gene family members indicated the intraspecies diversity among the members across 11 genomes by analyzing their gene structure, motifs, and chromosomal distribution patterns. The synteny and evolutionary constraints analyses of Citrus GLPs provide detailed evidence of their evolutionary conservation and divergence. Further, the interaction, functional enrichment, and promoter analysis revealed their involvement in abiotic-, biotic-stress, signaling, and development-related pathways. The expression patterns of C. sinensis GLPs were studied in Huanglongbing (HLB) and Citrus canker disease. Several genes including CsGLPs1-2 and CsGLPs8-4 showed changes in expression patterns under both disease conditions. The qRT-PCR analysis revealed that these two genes were highly expressed in leaves infected with HLB disease across seven HLB-tolerant and susceptible citrus species. This Citrus pangenome and pangenes family study offers a comprehensive resource and new insights into the structural and functional diversity, identifying candidate genes that are important for future research to understand the stress-responsive mechanisms in Citrus.\n\nComparative genomics profiling of Citrus species reveals the diversity and disease responsiveness of the GLP pangenes family.", "token_count": 448, "char_count": 2040, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6052, "quality_score": 0.8026, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:31.358685", "source": { "split": "train_shard_00000", "doc_id": 401 }, "chunk_id": "train_shard_00000_401_0", "global_id": 449 }, { "text": "Genetic insights into developmental variations of spiny bracts among hazels through the pangenome construction.", "token_count": 23, "char_count": 111, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:31.744734", "source": { "split": "train_shard_00000", "doc_id": 402 }, "chunk_id": "train_shard_00000_402_0", "global_id": 450 }, { "text": "Palonosetron hydrochloride [PALO (3aS, 2S)] is a highly selective second generation 5-HT3 receptor antagonist with two asymmetric carbon atoms in molecular structure. For chiral drugs, detection of the enantiomeric impurity is critical for drug safety and efficacy, because the undesired enantiomer can cause adverse effects or reduce the drug's therapeutic effect. In this work, the mechanism of online preconcentration in the analysis of PALO injection using micellar electrokinetic chromatography (MEKC) with bile salt sodium taurocholate (STC) as chiral selector was studied, based on the background difference between sample solution and background electrolyte (BGE). In addition to the field amplified sample stacking due to the conductivity difference between the sample plug and BGE, the disassociation of protonated solutes with positive charge caused by the pH increase and the distribution of solutes into STC micelles with negative charge result in a significant decrease in effective mobility, when they enter the BGE. This, combined with a reduction in field strength, causes the solutes slow down quickly and stack at the interface between sample plug and BGE. However, achieving the analysis of all three possible enantiomeric impurities in hydrodynamic injection mode is challenging due to poor separation. This is caused by the long effective capillary length consumed during online preconcentration and the wide solute band eventually focused if enough sample solution is injected. This issue was resolved by using electrokinetic injection mode, where solutes are driven into the capillary by both electric field and electroosmotic flow and stack at the interface meanwhile. As a result, a sufficient amount of solutes can be injected in a shorter sample plug compared to hydrodynamic injection mode. The method achieved a limit of detection of 0.014 μg mL\n\nEnhanced field-amplified sample injection by mobility decrease in capillary electrophoresis for the analysis of trace enantiomeric impurities in palonosetron injection.", "token_count": 473, "char_count": 2045, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7933, "entities": { "genes": [ "HT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:32.417353", "source": { "split": "train_shard_00000", "doc_id": 403 }, "chunk_id": "train_shard_00000_403_0", "global_id": 451 }, { "text": "Myosin Vb (MYO5B) deficiency, referring to the loss of protein expression or function, causes microvillus inclusion disease (MVID) and/or progressive familial intrahepatic cholestasis-type 10 (PFIC10) in humans. MYO5B plays a role in intracellular trafficking, but the mechanisms by which it contributes to cholestasis are not understood. The aim of this study was to generate a liver-specific mouse model and investigate the mechanism of MYO5B-associated cholestasis. In this study, we generated a liver-specific Myo5b cKO mice via CRISPR/Cas9 genome editing in conjunction with albumin-cre recombinase. Cholestatic stress was induced by dietary-administration of cholic acid (CA) or 3,5-diethoxycarbonyl-1,4-dihydrocollidine (DDC). To investigate the frequently recurring MYO5B variant (c.2470C > T/p.(Arg824Cys)), adenoviral vectors encoding either the missense variant or blank control sequence were delivered to wild-type and Myo5b cKO mice through tail-vein injection. Serum and liver tissues were harvested from all mice for biochemical and histological analysis. Our findings indicated that loss of Myo5b expression did not cause cholestatic liver disease and did not augment CA or DDC feeding-induced cholestatic stress. By contrast, expression of the MYO5B c.2470C > T/p. (Arg824Cys) variant induced cholestasis, evidenced by elevated levels of serum alanine aminotransferase, alkaline phosphatase and bilirubin, mild hepatocellular injury, and altered bile salt export pump (Bsep) localization, resembling that observed in human PFIC10. In summary, we have developed a mouse model of MYO5B-associated cholestasis. The expression of the MYO5B-p", "token_count": 490, "char_count": 1654, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "MYO5B", "PFIC10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:33.075869", "source": { "split": "train_shard_00000", "doc_id": 404 }, "chunk_id": "train_shard_00000_404_0", "global_id": 452 }, { "text": "(Arg824Cys) variant but not the loss of Myo5b expression caused cholestasis, indicating a toxic gain-of-function as underlying disease mechanism.\n\nA liver-specific mouse model for MYO5B-associated cholestasis reveals a toxic gain-of-function as underlying disease mechanism.", "token_count": 71, "char_count": 274, "word_count": 34, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [ "MYO5B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:33.446417", "source": { "split": "train_shard_00000", "doc_id": 404 }, "chunk_id": "train_shard_00000_404_1", "global_id": 453 }, { "text": "This review explores the advancements in drug delivery systems that incorporate bile salts since bilosomes that were developed over 20 years ago. Bile salts, recognized for their unique amphiphilic properties, have emerged as versatile agents in enhancing solubility, stability, and bioavailability of various therapeutics. We discuss the innovative formulations developed, including micelles, liposomes, and nanoparticles, that leverage bile salts to facilitate targeted and sustained release. The review also highlights the mechanisms by which bile salts improve drug absorption, particularly for hydrophobic compounds, and examines the evolving regulatory landscape surrounding these systems. Furthermore, we address challenges faced in clinical translation and future directions for research, emphasizing the potential of bile salt-based systems in personalized medicine. Our evaluation highlights the significant role of bile salts in advancing drug delivery technologies and their promise for improving therapeutic outcomes.\n\nDrug delivery systems incorporating bile salts: advancements since the conception of bilosomes.", "token_count": 226, "char_count": 1127, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6871, "quality_score": 0.8435, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:33.924376", "source": { "split": "train_shard_00000", "doc_id": 405 }, "chunk_id": "train_shard_00000_405_0", "global_id": 454 }, { "text": "Drug-induced liver injury (DILI) has increasingly become a major concern in Western countries since the late 1960s, with an estimated annual incidence of 13.9-19.1 cases per 100,000 people. DILI is a significant cause of acute liver failure, exhibiting a high mortality rate of 10-50 %. Its etiology includes medications, herbal products, and dietary supplements, exacerbated by pre-existing liver conditions, sonorities, pregnancy, and nutritional deficiencies. It is categorized into intrinsic and idiosyncratic reactions. Intrinsic DILI, dose-dependent and predictable, is primarily caused by substances like paracetamol, which leads to liver toxicity through direct metabolic pathways. In contrast, idiosyncratic DILI is less common, unpredictable, and affects susceptible individuals, with non-steroidal anti-inflammatory drugs, antibiotics, and cardiovascular agents frequently implicated in hospitals. Oxidative stress, mitochondrial dysfunction, bile salt export inhibition, and stress on the endoplasmic reticulum are some DILI-related pathophysiology. Diagnosis relies on biochemical tests, serological markers, radiological investigations, and liver biopsy. Management strategies emphasize the identification and cessation of the offending drugs, supportive care, and specific treatment options targeted to the culprit drugs. Management depends on the severity and nature of the injury.\n\nInsights into medication-induced liver injury: Understanding and management strategies.", "token_count": 373, "char_count": 1486, "word_count": 188, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:34.502952", "source": { "split": "train_shard_00000", "doc_id": 406 }, "chunk_id": "train_shard_00000_406_0", "global_id": 455 }, { "text": "Food microorganisms have been employed for centuries for the processing of fermented foods, leading to adapted populations with phenotypic traits of interest. The yeast Monosporozyma unispora (formerly Kazachstania unispora) has been identified in a wide range of fermented foods and beverages. Here, we studied the genetic and phenotypic diversity of a collection of 53 strains primarily derived from cheese, kefir, and sourdough. The 12.7-Mb genome of the type strain CLIB 234T was sequenced and assembled into near-complete chromosomes and annotated at the structural and functional levels, with 5639 coding sequences predicted. Comparison of the pangenome and core genome revealed minimal differences. From the complete yeast collection, we gathered genetic data (diversity, phylogeny, and population structure) and phenotypic data (growth capacity on solid media). Population genomic analyses revealed a low level of nucleotide diversity and strong population structure, with the presence of two major clades corresponding to ecological origins (cheese and kefir vs. plant derivatives). A high prevalence of extensive loss of heterozygosity and a slow linkage disequilibrium decay suggested a predominantly clonal mode of reproduction. Phenotypic analyses revealed growth variation under stress conditions, including high salinity and low pH, but no definitive link between phenotypic traits and environmental adaptation was established.\n\nInsights into the genomic and phenotypic diversity of Monosporozyma unispora strains isolated from anthropic environments.", "token_count": 369, "char_count": 1566, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6574, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:35.081112", "source": { "split": "train_shard_00000", "doc_id": 407 }, "chunk_id": "train_shard_00000_407_0", "global_id": 456 }, { "text": "Cholestasis arises as a clinical syndrome triggered by the accumulation and aggregation of bile acids. Currently, there are only a few treatment options available for cholestasis. Therefore, it is necessary to explore novel therapeutic strategies. β-sitosterol (SIT), the phytosterol most abundantly found in plants, exhibits diverse pharmacological activities. This study examined SIT's protective role against hepatotoxicity and cholestasis induced by lithocholic acid (LCA). LCA was administered twice a day to male C57BL/6 mice for four days to cause hepatotoxicity and cholestasis. Assessment of the improvement in cholestasis following SIT treatment used H&E staining and serum biomarkers. Mice hepatocyte culture, real-time PCR, immunofluorescence staining, and Western blot were utilized to clarify the mechanisms of SIT hepatoprotection. Furthermore, molecular docking and dual-luciferase reporter gene analysis were utilized to show that SIT would activate the farnesoid X receptor (FXR). In vivo, SIT reduced bile acid accumulation by inducing the bile salt export pump (Bsep), multidrug resistance-related protein 2 (Mrp2), and reduced hepatic uptake of bile acids by inhibiting Na+/taurocholate co-transporting polypeptide (Ntcp), and cholesterol 7α-hydroxylase (Cyp7a1) and oxysterol 12α-hydroxylase (Cyp8b1) while in vitro, it restored FXR expression and transcriptional activity. Besides, SIT decreased hepatic inflammation by suppressing the inflammatory genes NF-κB p65 and p-NF-κB p65, TNF-α, IL-6, and IL-1β. However, the hepatoprotective effects of SIT were abolished by the FXR antagonist guggulsterone in vivo and FXR siRNA in vitro, confirming FXR-dependent mechanisms. In conclusion, SIT protects against LCA-induced hepatotoxicity and cholestasis via FXR activation", "token_count": 520, "char_count": 1791, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6971, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:02:35.728456", "source": { "split": "train_shard_00000", "doc_id": 408 }, "chunk_id": "train_shard_00000_408_0", "global_id": 457 }, { "text": "These findings highlight SIT as a promising therapeutic candidate for cholestasis.\n\nβ-Sitosterol protects against lithocholic acid-induced hepatotoxicity and cholestasis via farnesoid X receptor-mediated regulation of transporters and enzymes in vitro and in vivo.", "token_count": 75, "char_count": 264, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:36.103616", "source": { "split": "train_shard_00000", "doc_id": 408 }, "chunk_id": "train_shard_00000_408_1", "global_id": 458 }, { "text": "Nonalcoholic steatohepatitis (NASH) is a significant threat to human health. Our previous study revealed that salidroside attenuated NASH and regulated the gut microbiota. However, whether the therapeutic effect of salidroside depends on gut microbiota remains to be determined. Therefore, we conducted further experiments to elucidate the essential functions of gut microbiota-associated metabolic pathways in the anti-NASH effects of salidroside. Our results showed that salidroside effectively alleviated lipid accumulation and inflammatory injury in NASH mice. 16S rRNA sequencing revealed that salidroside increased the abundance of Bacteroides. Mice receiving fecal microbiota transplantation (FMT) from salidroside-treated also presented less hepatic steatosis and higher abundance of Bacteroides. Antibiotics eliminated the effects of salidroside on hepatic steatosis and the gut microbiota. Mechanistically, salidroside and FMT from salidroside-treated altered the bile acid (BA) profile by decreasing the levels of conjugated BAs and tauro-α/β-muricholic acid and activated downstream farnesoid X receptor (FXR) and Takeda G protein-coupled receptor 5 (TGR5). Furthermore, we found that inhibitors of bile salt hydrolase (BSH) and FXR/TGR5 abolished the effects of salidroside and reduced downstream carnitine palmitoyltransferase 1α and lipoprotein lipase expression. These data demonstrate that salidroside attenuated NASH via gut microbiota-BA-FXR/TGR5 signaling pathway and reveal the underlying mechanism of salidroside on NASH.\n\nSalidroside attenuates NASH through regulating bile acid-FXR/TGR5 signaling pathway via targeting gut microbiota.", "token_count": 451, "char_count": 1658, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6291, "quality_score": 0.8146, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:36.738258", "source": { "split": "train_shard_00000", "doc_id": 409 }, "chunk_id": "train_shard_00000_409_0", "global_id": 459 }, { "text": "Nanopore sequencing is a third-generation technology known for its portability, real-time analysis and ability to generate long reads. It has great potential for use in clinical diagnostics, but thorough validation is required to address accuracy concerns and ensure reliable and reproducible results. In this study, we automated an open-source workflow (freely available at https://gitlab.com/FLI_Bioinfo/nanobacta) for the assembly of Oxford Nanopore sequencing data and used it to investigate the reproducibility of assembly results under consistent conditions. We used a benchmark dataset of five bacterial reference strains and generated eight technical sequencing replicates of the same DNA using the Ligation and Rapid Barcoding kits together with the Flongle and MinION flow cells. We assessed reproducibility by measuring discrepancies such as substitution and insertion/deletion errors, analysing plasmid recovery results and examining genetic markers and clustering information. We compared the results of genome assemblies with and without short-read polishing. Our results show an average reproducibility accuracy of 99.999955% for nanopore-only assemblies and 99.999996% when the short reads were used for polishing. The genomic analysis results were highly reproducible for the nanopore-only assemblies without short read in the following areas: identification of genetic markers for antimicrobial resistance and virulence, classical MLST, taxonomic classification, genome completeness and contamination analysis. Interestingly, the clustering information results from the core genome SNP and core genome MLST analyses were also highly reproducible for the nanopore-only assemblies, with pairwise differences of up to two allele differences in core genome MLST and two SNPs in core genome SNP across replicates. After polishing the assemblies with short reads, the pairwise differences for cgMLST were 0 and for cgSNP were 0-1 SNP across replicates. These results highlight the advances in sequencing accuracy of nanopore data without the use of short reads.", "token_count": 491, "char_count": 2073, "word_count": 287, "semantic_coherence": 1, "information_density": 0.554, "quality_score": 0.777, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:37.379654", "source": { "split": "train_shard_00000", "doc_id": 410 }, "chunk_id": "train_shard_00000_410_0", "global_id": 460 }, { "text": "High intra-laboratory reproducibility of nanopore sequencing in bacterial species underscores advances in its accuracy.", "token_count": 29, "char_count": 119, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:37.734519", "source": { "split": "train_shard_00000", "doc_id": 410 }, "chunk_id": "train_shard_00000_410_1", "global_id": 461 }, { "text": "A wheat pangenome of 17 Chinese cultivars, recently developed by Jiao et al., reveals structural variants (SVs) shaped by cultural, dietary, and environmental changes. This resource provides access to East Asian wheat genetic diversity and supports genome-driven efforts to advance wheat improvement and adaptation to changing agricultural demands.\n\nPangenome charts the genomic path for wheat improvement.", "token_count": 82, "char_count": 406, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8393, "quality_score": 0.9196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:38.113144", "source": { "split": "train_shard_00000", "doc_id": 411 }, "chunk_id": "train_shard_00000_411_0", "global_id": 462 }, { "text": "[Pangenome analysis on plasmids carried by hypervirulent", "token_count": 14, "char_count": 56, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:38.459107", "source": { "split": "train_shard_00000", "doc_id": 412 }, "chunk_id": "train_shard_00000_412_0", "global_id": 463 }, { "text": "Structural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation statuses are rarely characterized due to previous limitations in genome assembly and detection of modified nucleotides. Also, the extent to which SVs act as methylation quantitative trait loci (SV-mQTLs) is largely unknown. Here, we generated a pangenome graph summarizing SVs in 782 de novo assemblies obtained from Genomic Answers for Kids, capturing 14.6 million CpG dinucleotides that are absent from the CHM13v2 reference (SV-CpGs), thus expanding their number by 43.6%. Using 435 methylomes, we genotyped 4.06 million SV-CpGs, of which 3.93 million (96.8%) are methylated at least once. Nonrepeat sequences contribute 1.59 × 10\n\nExpanded methylome and quantitative trait loci detection by long-read profiling of personal DNA.", "token_count": 243, "char_count": 822, "word_count": 120, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:38.935168", "source": { "split": "train_shard_00000", "doc_id": 413 }, "chunk_id": "train_shard_00000_413_0", "global_id": 464 }, { "text": "Cancer is fundamentally a disease of the genome, characterized by extensive genomic, transcriptomic, and epigenomic alterations. Most current studies predominantly use short-read sequencing, gene panels, or microarrays to explore these alterations; however, these technologies can systematically miss or misrepresent certain types of alterations, especially structural variants, complex rearrangements, and alterations within repetitive regions. Long-read sequencing is rapidly emerging as a transformative technology for cancer research by providing a comprehensive view across the genome, transcriptome, and epigenome, including the ability to detect alterations that previous technologies have overlooked. In this Perspective, we explore the current applications of long-read sequencing for both germline and somatic cancer analysis. We provide an overview of the computational methodologies tailored to long-read data and highlight key discoveries and resources within cancer genomics that were previously inaccessible with prior technologies. We also address future opportunities and persistent challenges, including the experimental and computational requirements needed to scale to larger sample sizes, the hurdles in sequencing and analyzing complex cancer genomes, and opportunities for leveraging machine learning and artificial intelligence technologies for cancer informatics. We further discuss how the telomere-to-telomere genome and the emerging human pangenome could enhance the resolution of cancer genome analysis, potentially revolutionizing early detection and disease monitoring in patients. Finally, we outline strategies for transitioning long-read sequencing from research applications to routine clinical practice.\n\nUnraveling the hidden complexity of cancer through long-read sequencing.", "token_count": 343, "char_count": 1813, "word_count": 229, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:39.500014", "source": { "split": "train_shard_00000", "doc_id": 414 }, "chunk_id": "train_shard_00000_414_0", "global_id": 465 }, { "text": "Below-ground carbon transformations that contribute to healthy soils represent a natural climate change mitigation, but newly acquired traits adaptive to climate stress may alter microbial feedback mechanisms. To better define microbial evolutionary responses to long-term climate warming, we study microorganisms from an ongoing\n\nPangenomes suggest ecological-evolutionary responses to experimental soil warming.", "token_count": 81, "char_count": 413, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8431, "quality_score": 0.9216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:39.872197", "source": { "split": "train_shard_00000", "doc_id": 415 }, "chunk_id": "train_shard_00000_415_0", "global_id": 466 }, { "text": "Since novel long read sequencing technologies allow for de novo assembly of many individuals of a species, high-quality assemblies are becoming widely available. For example, the recently published draft human pangenome reference was based on assemblies composed of contigs. There is an urgent need for a software-tool that is able to generate a multiple alignment of genomes of the same species because current multiple sequence alignment programs cannot deal with such a volume of data.\n\nGenerating multiple alignments on a pangenomic scale.", "token_count": 108, "char_count": 543, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7805, "quality_score": 0.8902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:40.258689", "source": { "split": "train_shard_00000", "doc_id": 416 }, "chunk_id": "train_shard_00000_416_0", "global_id": 467 }, { "text": "Sorafenib and lenvatinib are systemic treatments for hepatocellular carcinoma. They often exhibit high intersubject pharmacokinetic variability and can cause drug-induced liver injury, yet the underlying mechanisms are poorly understood. Inhibition of some ATP-binding cassette (ABC) transporters, such as bile salt export pump (BSEP;\n\nInhibition of ABC transporters by sorafenib and lenvatinib: implications for drug-induced cholestasis.", "token_count": 118, "char_count": 438, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8545, "quality_score": 0.9273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:40.642804", "source": { "split": "train_shard_00000", "doc_id": 417 }, "chunk_id": "train_shard_00000_417_0", "global_id": 468 }, { "text": "Members of the GP63 metalloprotease family play crucial roles in parasite-host interactions, immune evasion, and pathogenesis. Although it has been widely studied in Leishmania spp., less is known about its function and diversity in Trypanosoma cruzi. This study focuses on characterizing the complete repertoire of GP63 sequences in the T. cruzi genome, refining gene annotations, and exploring the evolutionary dynamics that shape the diversity of these proteins. Eleven GP63 groups were identified, which are sharply defined and have a higher intra- than inter-group sequence identity. These GP63 groups display some distinctive features. First, two groups lack an essential amino acid in the active site, indicating that they are enzymatically inactive. Second, GP63 groups show strong preference for different genomic compartments. Moreover, genes from groups located in the core genome compartment of T. cruzi, are often arranged as tandem arrays (of larger genomic fragments that generally include a SIRE retroposon), whereas genes from groups located in the disruptive compartment tend to be surrounded by genes encoding other surface proteins (such as MASP, mucins and trans-sialidases). Transcription patterns across different life cycle stages are not homogenous. Instead, some GP63 groups have higher mRNA levels in the infective trypomastigote stage, suggesting a potential role in host invasion. To get a wider picture of the evolutionary dynamics of these proteins, a phylogenetic analysis was conducted that included species representative of kinetoplastid diversity. It was found that 10 out of 11 GP63 T. cruzi groups are specific to the Trypanosoma genus, suggesting that the diversification of these subfamilies took place before speciation of the genus, followed by other species-specific expansions. Additionally, there are other GP63 groups that are absent in T. cruzi. Notably, the processes of expansion and diversification of GP63 in Leishmania is independent of that of trypanosomes. This suggests that these proteins may have evolved under species-specific selective (functional) pressures, resulting in unique amplifications in each parasite species.", "token_count": 487, "char_count": 2179, "word_count": 315, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [ "GP63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:41.295314", "source": { "split": "train_shard_00000", "doc_id": 418 }, "chunk_id": "train_shard_00000_418_0", "global_id": 469 }, { "text": "Exploring the genomic landscape of the GP63 family in Trypanosoma cruzi: Evolutionary dynamics and functional peculiarities.", "token_count": 29, "char_count": 124, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [ "GP63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:41.649101", "source": { "split": "train_shard_00000", "doc_id": 418 }, "chunk_id": "train_shard_00000_418_1", "global_id": 470 }, { "text": "Bile salt hydrolase (BSH: EC.3.5.1.24) has been used as a biomarker for probiotics for an extended period. It is mostly present in the gut environment of vertebrates. Additionally, it influences the viability of probiotics. This biomarker is considered a promising nutritional supplement due to its unique ability to effectively address elevated blood cholesterol levels, a common issue in modern society. However, the commercialization of BSH has been limited by an incomplete understanding of the intestinal microbiota and the function of BSH. Hence, in this review, we aim to reveal the current advancements in BSH research and outline the necessary areas of investigation for future studies. The review highlights key findings related to the substrate affinity of BSH in probiotic bacteria and its BSH gene phylogeny that have been researched until today, suggesting further research regarding the differences in multiple BSH genes and corresponding differences in BSH affinity.\n\nReview on the Function, Substrate Affinity, and Potential Application of Bile Salt Hydrolase Originated from Probiotic Strains of", "token_count": 256, "char_count": 1113, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:42.192259", "source": { "split": "train_shard_00000", "doc_id": 419 }, "chunk_id": "train_shard_00000_419_0", "global_id": 471 }, { "text": "With more and more telomere-to-telomere genomes assembled, pangenomes make it possible to capture the genomic diversity of a species. Because they introduce less biases, pangenomes, represented as graphs, tend to supplant the usual linear representation of a reference genome, augmented with variations. However, this major change requires new tools adapted to this data structure. Among the numerous questions that can be addressed to a pangenome graph is the search for conserved or divergent genes.\n\nAssessing genome conservation on pangenome graphs with PanSel.", "token_count": 125, "char_count": 565, "word_count": 82, "semantic_coherence": 1, "information_density": 0.8293, "quality_score": 0.9146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:42.581597", "source": { "split": "train_shard_00000", "doc_id": 420 }, "chunk_id": "train_shard_00000_420_0", "global_id": 472 }, { "text": "Cyclodextrin formulations are crucial for enhancing the solubility of drugs. Bile salts are recognized as potential agents for displacing drugs from cyclodextrin formulations in intestinal fluids. However, the mechanism underlying this displacement remains unclear. This study aims to investigate the mechanism of competitive displacement using molecular dynamics simulations and to develop guidelines for effective cyclodextrin formulation design. The umbrella sampling method is employed to investigate the binding free energy between bile salts and cyclodextrin molecules, while metadynamics is utilized to simulate the dynamic replacement process. The results indicate that the optimal binding free energy interval between cyclodextrins and drugs ranges from -30 kJ/mol to -8 kJ/mol. Additionally, the optimal concentration ratio between drugs and cyclodextrins can be calculated based on the binding free energy. Displacement simulations showed that free single bile salt molecules are more likely to complete the displacement compared to clusters of bile salts. This suggests that the bioavailability of cyclodextrins may be higher in fasting conditions than in the fed state. This study will not only enhance our understanding of the relationships between cyclodextrin formulations and bile salts but also facilitate the rational design of more effective pharmaceutical formulations.\n\nRational cyclodextrin formulation design through insights into drug release mechanism in the gastrointestinal tract via molecular dynamics simulations.", "token_count": 317, "char_count": 1543, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:43.177140", "source": { "split": "train_shard_00000", "doc_id": 421 }, "chunk_id": "train_shard_00000_421_0", "global_id": 473 }, { "text": "Patulin (PAT) produced by genus of Penicillium spp attracted more and more concern in view of its widespread contamination in food and toxic effects, which has also promoted the research on the reduction of PAT contamination in food. The use of yeast to remove PAT in food is innovative and promising. In this study, we used the yeast Kluyveromyces marxianus XZ1 to degrade PAT, which can remove 90% of PAT (10 μg/mL) within 48 h. XZ1 exhibits high degradation effect on PAT under the conditions of pH range of 3-6, temperatures of 28-37 °C, and initial PAT concentrations below 50 μg/mL. PAT removing by XZ1 was carried out by intracellular enzymes. XZ1 or intracellular enzyme was able to remove 100% of 10 μg/mL PAT in raw apple juice or commercial apple juice within 60 h. Patulin oxidoreductase (KmPAO) was identified as a potential PTA-degrading enzymes, which degrade PAT to form ascladiol. The degradation products of PAT by XZ1 were identified as ascladiol and desoxypatulinic acid, which was then complete degraded to form unknown final degradation products. Toxic analyses on Caco-2 cells showed that the ascladiol, desoxypatulinic acid and the final degradation products were significantly less toxic compared to PAT, which was mainly manifested in less influence on cell vitality, cell integrity and reactive oxygen species accumulation compared to PAT. Finally, the results revealed the PAT degradation enzyme, as well as the safety of the degradation products, which provide basis for the future application of this yeast to decontamination of PAT in food.\n\nDegradation of patulin by a yeast strain Kluyveromyces marxianus XZ1 and its mechanism.", "token_count": 474, "char_count": 1660, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5434, "quality_score": 0.7717, "entities": { "genes": [ "XZ1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:43.832161", "source": { "split": "train_shard_00000", "doc_id": 422 }, "chunk_id": "train_shard_00000_422_0", "global_id": 474 }, { "text": "Genome-wide association studies (GWAS) are rapidly advancing due to the improved resolution and completeness provided by Telomere-to-Telomere (T2T) and pangenome assemblies. While recent advancements in GWAS methods have primarily focused on identifying genetic variants associated with discrete phenotypes, approaches for quantitative traits (QTs) remain underdeveloped. This has often led to significant variants being overlooked due to biases from genotype multicollinearity and strict p-value thresholds.\n\nImproving genetic variant identification for quantitative traits using ensemble learning-based approaches.", "token_count": 138, "char_count": 616, "word_count": 75, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:44.285278", "source": { "split": "train_shard_00000", "doc_id": 423 }, "chunk_id": "train_shard_00000_423_0", "global_id": 475 }, { "text": "Gallbladder stones alone do not explain the risk of gallbladder cancer (GBC) as the sole etiological factor. Chronic microbial infection, particularly Salmonella, has been implicated in GB carcinogenesis, but its causative role and the underlying mechanisms are largely unknown. We studied gut and gallbladder tissue microbiome through targeted metagenomics to identify pathogenic bacteria in GBC. Virulence and pathogenicity of identified Salmonella Typhimurium from GBC tissue were studied after culture by whole genome sequencing, phylogenetic analysis, mutational profiling, and pangenome analysis. Mechanistic studies for GBC carcinogenesis were carried out in a mouse model of gallstones and chronic Salmonella infection, a cellular model using GBC (NOZ) cell lines, and a xenograft tumor model. We found an increased abundance of Salmonella in the gut microbiome of patients with GBC and culturable S. Typhimurium from the gallbladder cancer tissue. Comparative genomics of S. Typhimurium isolated from the GBC tissue showed a high invasive index. S. Typhimurium isolates harbored horizontally acquired virulence functions in their accessory genome. Chronic S. Typhimurium infection caused chronic inflammation, pre-malignant changes, and tumor-promoting mechanisms in the mouse model with gallbladder stones with activation of the epigenetic modulator KDM6B both in the mouse model and human GBC. Inhibition of KDM6B reduced engrafted tumor size in SCID mice. Of the differentially regulated genes in human GBC tissue, ADAMTSL5, CX3CR1, and SPSB4 were also significantly dysregulated in NOZ cells infected with Salmonella. Chronic Salmonella infection contributes to gallbladder carcinogenesis through a host epigenetic mechanism involving KDM6B.\n\nInvasive Salmonella Typhimurium colonizes gallbladder and contributes to gallbladder carcinogenesis through activation of host epigenetic modulator KDM6B.", "token_count": 491, "char_count": 1910, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5731, "quality_score": 0.7865, "entities": { "genes": [ "KDM6B", "SPSB4", "ADAMTSL5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:44.947370", "source": { "split": "train_shard_00000", "doc_id": 424 }, "chunk_id": "train_shard_00000_424_0", "global_id": 476 }, { "text": "Allele mining of crop pangenomes can enable the identification of novel variants for trait improvement, increase crop genetic diversity, and purge deleterious mutations around fixed genomic regions. Sorghum, a C4 cereal crop domesticated in the tropics, was selected for reduced plant height and maturity to develop combine-harvestable and photoperiod-insensitive US grain sorghums. To breed semi-dwarf US grain sorghum hybrids, public and private sector programs mostly used the dw3-ref allele, which produces undesirable height revertants (frequency of 0.1-0.3%) due to uneven crossing over at the 882 bp tandem duplication region. Although the dw3-ref allele produces revertants, US sorghum breeding programs continued using this allele in the absence of identified allelic variants that suppress revertants. In this study, we leveraged a sorghum pangenome resource (resequenced sorghum association panel and a global diversity panel of 1,661 lines) to identify 7 loss-of-function variants in the Dw3 gene using the SnpEff variant calling prediction. We validated the Segaolane dw3 loss-of-function variant, resulting from a 137 bp deletion in the third exon, to suppress revertant production. Segaolane nested association mapping family recombinant inbred line (RILs) with the dw3-ref allele produced revertants while no revertants were observed in RILs with the Segaolane dw3 allele. The availability of resequencing data enabled the designing of haplotype-based markers detecting the Segaolane stable dw3 allele for marker-assisted trait introgression into elite sorghum breeding lines. This research mining new stable-dwarfing dw3 alleles demonstrated the application of sorghum pangenome for trait improvement and developing marker-assisted breeding strategies.\n\nMining sorghum pangenome enabled identification of new dw3 alleles for breeding stable-dwarfing hybrids.", "token_count": 479, "char_count": 1875, "word_count": 257, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:45.590846", "source": { "split": "train_shard_00000", "doc_id": 425 }, "chunk_id": "train_shard_00000_425_0", "global_id": 477 }, { "text": "The intestinal dysfunction plays an important role in the decreased growth performance of broiler chickens under high stocking density. Gut microbiota plays an important role in maintaining intestinal health. However, the modulation pathway of gut microbiota by regulating the intestinal barrier and histomorphology remains unknown.\n\nEffects of high stocking density on the growth performance, intestinal health and bile salts composition of broiler chickens.", "token_count": 99, "char_count": 459, "word_count": 63, "semantic_coherence": 1, "information_density": 0.6508, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:45.971561", "source": { "split": "train_shard_00000", "doc_id": 426 }, "chunk_id": "train_shard_00000_426_0", "global_id": 478 }, { "text": "Stenotrophomonas geniculata, a bacterium, has been recognized as an eco-friendly substitute for chemical fungicides in managing peanut foliar diseases, web blotch, and early leaf spot. Core genome and pan-genome analysis identified that strain MK-1 belongs to Stenotrophomonas geniculata, and nucleotide polymorphism (SNP) analysis confirmed that strain belongs to Stenotrophomonas maltophilia. The research revealed that S. geniculata MK-1 had a notable antagonistic impact on Peyronellaea arachidicola and Cercospora arachidicola and demonstrated a biocontrol efficacy of over 95% against peanut early leaf spot and web blotch disease. The nonredundant protein sequences (NR) database identified 4324 annotations related to S. geniculata, with 2682 genes similar to strain MK-1. The COG database categorized 3041 annotations into 22 functional groups, and 33 distinct metabolic pathways associated with 1851 Kyoto Encyclopedia of Genes and Genomes (KEGG) annotations. Most genes linked with metabolism are found in S. geniculata, with 380 genes related to carbohydrate metabolism and 44 genes related to secondary metabolite biosynthesis. The Carbohydrate-Active enZYmes (CAZy) database identified 194 annotations are linked to non-ribosomal synthesis of secondary metabolites. The Pathogen-Host Interactions (PHI) database showed reduced virulence in strain MK-1, while unaffected pathogenicity protein counts were 52. The MK-1 strain can produce antifungal siderophores secondary metabolites, non-ribosomal peptide synthetase (NRPS), and siderophores.\n\nGenome Mining and Antagonism of Stenotrophomonas geniculata MK-1, Against Peanut Foliage Fungus Diseases.", "token_count": 499, "char_count": 1662, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:46.619648", "source": { "split": "train_shard_00000", "doc_id": 427 }, "chunk_id": "train_shard_00000_427_0", "global_id": 479 }, { "text": "Drug-induced liver injury (DILI) is a major cause of drug development failures and postmarket drug withdrawals, posing significant challenges to public health and pharmaceutical research. The biological mechanisms leading to DILI are highly complex and the adverse reaction is often difficult to foresee. Hence, mechanistic insights into DILI, as well as machine learning models to predict molecular events that trigger adverse outcomes, pharmacokinetics and pharmacodynamics in the liver, are essential tools for understanding and preventing DILI. In this study, we collected a comprehensive data set of 28 in vitro endpoints related to liver toxicity and function, as well as data specific to DILI, to explore the potential of multi-task learning for their prediction. We demonstrate the benefits of ensemble modeling and provide an uncertainty estimation based on the standard deviation of the predictions to define an applicability domain for the models. Available assays at Bayer for two of the endpoints (Bile salt export pump (BSEP) inhibition and phospholipidosis) were run on a set of public compounds and used for further evaluation (data provided in the Supporting Information). Additionally, we conducted an in-depth data analysis of the relationships among the different endpoints, as well as with DILI. The presented models can be used to derive a \"Virtual Liver Safety Profile\" showcasing the predicted activity of a compound on the selected endpoints to support the prioritization of assays and the elucidation of modes of action.\n\nPredicting Liver-Related In Vitro Endpoints with Machine Learning to Support Early Detection of Drug-Induced Liver Injury.", "token_count": 358, "char_count": 1670, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6064, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:47.193197", "source": { "split": "train_shard_00000", "doc_id": 428 }, "chunk_id": "train_shard_00000_428_0", "global_id": 480 }, { "text": "To efficiently produce myo-inositol from glucose, the PGI1, ZWF1, ITR2, and MIOX5 genes in Kluyveromyces marxianus were knocked out to block glucose metabolism via the Embden-Meyerhof-Parnas (EMP) and pentose phosphate pathways (PPP), prevent myo-inositol oxidative degradation. The metabolically engineered KM-JC4 strain, introduced with myo-inositol synthesis genes, produced 80.7 g/L in a 5 L bioreactor using glucose and glycerol as carbon sources. Subsequently, the starch-fermenting and inositol-producing strain KM-JC5 was constructed by co-expressing BadGlA, an α-glucoamylase from Blastobotrys adeninivorans with high ability to release glucose from soluble starch, and the myo-inositol synthesis enzymes. Using 5% soluble starch and liquefied starch, the myo-inositol yields reached 32.2 g/L and 40.6 g/L, with the starch-to-myo-inositol conversion rates of 64.4% and 81.1%, respectively. This study provides an effective strategy for bioproduction by balancing glycolysis and PPP metabolism in yeast, and the metabolically engineered strain represents a promising platform for inositol production.\n\nMetabolic engineering of Kluyveromyces marxianus to produce myo-inositol from starch.", "token_count": 382, "char_count": 1195, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [ "MIOX5", "ZWF1", "PGI1", "JC4", "JC5", "ITR2" ], "proteins": [], "pathways": [ "glycolysis", "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:47.769588", "source": { "split": "train_shard_00000", "doc_id": 429 }, "chunk_id": "train_shard_00000_429_0", "global_id": 481 }, { "text": "Intrahepatic cholestasis of pregnancy (ICP) is a liver disease that manifests predominantly in the later stages of pregnancy. The primary treatment currently involves the use of ursodeoxycholic acid (UDCA). In this study, the therapeutic effectiveness of 4-phenylbutyric acid (4-PBA) in the treatment of ICP, as well as the potential mechanisms involved, are investigated to offer new references for clinical treatment decisions using ICP model. The therapeutic effect of 4-PBA on ICP was evaluated by drug therapy on ICP cells and animal models, and corresponding fluorescence immunoassay, electron microscope, WB and other experiments. In addition, the cells and animals treated with GPR30 inhibitor were treated to investigate whether 4-PBA promoted the expression of bile salt output pump (BSEP) protein through GPR30-PI3K pathway, thereby promoting bile acid excretion. Administration of 4-PBA significantly reduced the incidence of stillbirth associated with ICP. 4-PBA was effective in decreasing serum bile acid levels, reducing the activation of the GPR30-PI3K pathway, and increasing the expression of BSEP protein in hepatocytes. 4-PBA was effective in reducing bile acid levels and significantly improving fetal outcomes associated with ICP. The potential mechanism involves the promotion of BSEP localization and expression in the hepatocytes' microvilli structures via the GPR30-PI3K pathway.\n\nEfficacy and mechanism of inhibition of the GPR30-PI3K pathway by 4-phenylbutyric acid in the treatment of intrahepatic cholestasis of pregnancy.", "token_count": 396, "char_count": 1553, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5616, "quality_score": 0.7808, "entities": { "genes": [ "PI3K", "GPR30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:48.384331", "source": { "split": "train_shard_00000", "doc_id": 430 }, "chunk_id": "train_shard_00000_430_0", "global_id": 482 }, { "text": "MicroRNAs (miRNAs) are non-coding RNAs that influence gene-expression via post-transcriptional regulation of target protein-coding RNAs. With literature reports indicating survival of diet-derived miRNAs following their ingestion, it is important to study their stability and concentration during gastrointestinal digestion. The unique combination of chemicals and elevated RNAse content present in the gastrointestinal matrix may be a limiting factor for studying diet-derived miRNAs. First, chemical cross-reactivity with matrix constituents (e.g. bile salts) may interfere with the salt bridge interactions typically present during RNA extraction, reducing the efficiency of the column. Second, high RNAse content may not be fully inhibited during extraction and could continue degrading the miRNAs, as is observed for other tissues with high RNAse content. These combined issues may result in a reduced efficiency in yield and purity of RNA extracts, further limiting the study of diet-derived miRNAs (i.e. in downstream metabolism). In the present manuscript, we display a method based on silica column purification to extract and quantify diet-derived miRNAs from the bioaccessible phase of the gastrointestinal digesta. The proposed protocol provides a simple, quick (less than 2 h), reliable, and systematic method for miRNA purification from gastrointestinal digesta. The optimization showcased that the challenges caused by high RNAse activity, plant bioactive substances and bile-salt content within the gastrointestinal digesta have been overcome and the study of the miRNA fraction in a body fluid so far neglected is now available to researchers, allowing the use of miRNA as biomarkers of intake and potentially biomarkers of biological changes.\n\nA protocol for microRNA extraction from gastrointestinal digesta.", "token_count": 435, "char_count": 1827, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:49.013233", "source": { "split": "train_shard_00000", "doc_id": 431 }, "chunk_id": "train_shard_00000_431_0", "global_id": 483 }, { "text": "Aflatoxins have been reported as a significant pollutant in feed, capable of causing harm to the liver, gastrointestinal tract and kidneys of piglets. However, research on the interactions among aflatoxin B1 (AFB1), bile acid (BA) metabolism and gut microbiota is limited.\n\nGut microbiota-mediated bile acid transformations regulate the transport of aflatoxin B1 from the intestine to the liver in piglets.", "token_count": 110, "char_count": 406, "word_count": 60, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "AFB1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:49.402079", "source": { "split": "train_shard_00000", "doc_id": 432 }, "chunk_id": "train_shard_00000_432_0", "global_id": 484 }, { "text": "Human genetic diversity in today's world has been shaped by evolutionary history, demographic shifts and environmental exposures, influencing complex traits, disease susceptibility and drug responses. Capturing this diversity is essential for advancing precision medicine and promoting equitable healthcare. Despite the great progress achieved with initiatives such as the human Pangenome and large biobanks that aim for a better representation of human diversity, important challenges remain. In this Perspective, we discuss the importance of diversity in clinical genomics through an evolutionary lens. We highlight progress and challenges and outline key clinical applications of diverse genetic data. We argue that diversifying both datasets and methodologies-integrating ancestral and environmental factors-is crucial for fully understanding the genetic basis of human health and disease.\n\nEvolution, genetic diversity, and health.", "token_count": 166, "char_count": 936, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7016, "quality_score": 0.8508, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:49.849253", "source": { "split": "train_shard_00000", "doc_id": 433 }, "chunk_id": "train_shard_00000_433_0", "global_id": 485 }, { "text": "Leukocyte immunoglobulin-like receptors (LILRs), encoded on human chromosome 19q13.4, comprise a set of 11 immunoglobulin superfamily receptors known for their genetic heterogeneity. Notably, LILRB3 and LILRA6 within this cluster exhibit pronounced sequence homology in immunoglobulin-like domains involved in ligand binding and variable copy number (CN) states. However, understanding their precise role remains challenging. To address this difficulty, we developed an algorithm and tool named JoGo-LILR Caller, which jointly calls CNs of LILRB3 and LILRA6 from a population-scale whole-genome short-read sequencing dataset. This tool was applied to 2,504 international HapMap samples and yielded a global CN profile. The 100 % concordance rate corroborated this profile with the CN data obtained from 40 samples of pangenome reference assemblies provided by the Human Pangenome Reference Consortium (HPRC). The frequencies of LILRB3-LILRA6 CN haplotype structures were also estimated for five continental groups with a global CN profile. The established allele frequency profile allowed our tool to estimate LILRB3-LILRA6 CN haplotype combinations. JoGo-LILR-trio enhanced the prediction reliability for haplotype pairs within trio datasets, with trio analysis on 40 child samples demonstrating a 100 % concordance between the predicted pair of haploid CN types and the diploid reference assemblies. Its utility will extend to facilitating software advancements for imputing LILRB3-LILRA6 CN types from SNP array genotyping data, enabling subsequent association analyses that link these CN types to diverse phenotypic traits and diseases, e.g., inflammatory bowel diseases and Takayasu arteritis.\n\nJoGo-LILR caller: Unveiling and navigating the complex diversity of LILRB3-LILRA6 copy number haplotype structures with whole-genome sequencing.", "token_count": 498, "char_count": 1844, "word_count": 250, "semantic_coherence": 1, "information_density": 0.664, "quality_score": 0.832, "entities": { "genes": [ "LILRB3", "LILRA6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:50.491665", "source": { "split": "train_shard_00000", "doc_id": 434 }, "chunk_id": "train_shard_00000_434_0", "global_id": 486 }, { "text": "Tofu whey is a rich source of nutrients and can be biotransformed into functional beverages. This study assessed the fermentation of this by-product by Lactiplantibacillus plantarum BL011 and Kluyveromyces marxianus B0399, analysing cell viability, metabolite production, sugar consumption, and isoflavone concentration. Targeted metabolomics approach was employed to characterise changes in phenolic and volatile compounds during fermentation, combined with principal components analysis (PCA). Additionally, toxicological effects were evaluated in C. elegans. The co-culture's effectively metabolised sugars and increased isoflavone aglycones concentration. Fermentation also reduced the beany flavours from tofu whey and increased the diversity and concentration of fruity esters, such as ethyl acetate and 2-phenylethyl acetate. PCA revealed that fermentation influenced metabolite composition of whey. Four metabolites were selected as relevant for sample clustering: lactic acid, 2-methyl butanol, glucose, and acetic acid. The study presents a sustainable and innovative solution for the reuse of whey and generation of novel plant-based foods.\n\nTargeted metabolomics of phenolic and volatile compounds during the fermentation of a potential probiotic tofu whey beverage.", "token_count": 322, "char_count": 1278, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7006, "quality_score": 0.8503, "entities": { "genes": [ "BL011" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:51.057458", "source": { "split": "train_shard_00000", "doc_id": 435 }, "chunk_id": "train_shard_00000_435_0", "global_id": 487 }, { "text": "An outbreak of diarrheal illness related to milk cartons served in school lunches, occurred in June 2021, involving more than 1800 cases from 25 schools. A strain of Escherichia coli OUT (OgGp9):H18 was implicated in the outbreak. This strain does not possess virulence factors typical of other E. coli pathotypes. In this study, we examined the pathogenicity of the E. coli OUT (OgGp9):H18 strain using genomic analysis and animal models. A core genome-based phylogenetic analysis revealed that this strain belongs to a clade comprising ST1380 strains and is distinct from enteroaggregative E. coli 042 and uropathogenic E. coli UMN026, which were previously considered to be phylogenetically related to this strain. In addition, the strain harbors a plasmid similar to that of atypical enterotoxigenic E. coli, encoding Coli Surface antigen CS8 and a type VI secretion system (T6SS). The strain caused mortality in mice following intraperitoneal inoculation. Marmosets inoculated orally, experienced diarrhea and long-term shedding. Curing the strain of the 103 Kbp plasmid it carries reduced mortality rates and colonization in the experimental animals, indicating that the plasmid encodes virulence factors. However, the mortality of mice treated with the plasmid-cured strain was higher than that of those treated with nonvirulent E. coli K-12, indicating that the chromosome also encodes virulence factors. Identified chromosomal virulence factors include a T6SS, the second type III secretion system in E. coli, ETT2, and the capsule gene cluster kps. These findings suggest that atypical diarrheagenic E. coli, such as the strain investigated in this study, may be the cause of foodborne illness in patients with diarrhea with an unknown cause.\n\nGenomic features and pathogenicity of atypical diarrheagenic Escherichia coli from a large foodborne outbreak.", "token_count": 512, "char_count": 1864, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5576, "quality_score": 0.7788, "entities": { "genes": [ "ETT2", "ST1380", "CS8", "UMN026" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:51.712253", "source": { "split": "train_shard_00000", "doc_id": 436 }, "chunk_id": "train_shard_00000_436_0", "global_id": 488 }, { "text": "Genus-wide plant pangenome could inform next-generation crop design.", "token_count": 17, "char_count": 68, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:52.067154", "source": { "split": "train_shard_00000", "doc_id": 437 }, "chunk_id": "train_shard_00000_437_0", "global_id": 489 }, { "text": "Methylene blue (MB)-based photodynamic therapy has proven to be effective and promising for the treatment of non-melanoma skin neoplasms. However, the topical application of MB has certain challenges. MB is a cationic and water-soluble molecule. These properties limit its partition and diffusion through the layers of the skin, limiting it from reaching the neoplastic cells at therapeutic concentration. Sodium cholate (CNa), a bile salt, enables ion-pairing with cationic drugs, such as MB, through electrostatic interactions. The complex formed modifies the physicochemical properties of MB, which may enable its partition and diffusion through the layers of the skin. Thus, we proposed to investigate the interaction between CNa and MB as a function of CNa concentration and its effect on the partition coefficient, solubility, skin barrier and skin delivery of MB. Spectroscopic and thermal studies of MB/CNa dispersions suggest intermolecular interactions between MB and CNa. CNa causes an increase in the partition coefficient of MB and reduces its solubility in water. CNa at the concentrations used does not cause significant changes in electrical resistance or the profile of FTIR spectra related to the lipids and the proteins of the stratum corneum. The use of CNa at the critical micelle concentration causes a reduction in the release and cutaneous delivery of MB; and, at a concentration below the critical micelle concentration, it does not significantly influence the release, but promotes the cutaneous delivery of MB.\n\nSodium Cholate-Mediated Ion-Pairing for Skin Delivery of Methylene Blue: Physicochemical Characterization and Influence on Skin Barrier and Skin Penetration.", "token_count": 384, "char_count": 1696, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5578, "quality_score": 0.7789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:52.678325", "source": { "split": "train_shard_00000", "doc_id": 438 }, "chunk_id": "train_shard_00000_438_0", "global_id": 490 }, { "text": "The Human Pangenome Reference Consortium (HPRC) proved that pangenome graphs represent a population's genetic variability more efficiently and accurately than linear references. Graphs can intrinsically encode variations as alternative paths inside a directed set of sequence nodes connected by edges. Despite their higher complexity, graph-based genome analysis pipelines are gaining significant interest, and the first sequence-to-graph aligners have already shown improvements in semi-global alignment. However, in pangenomics studies, the global alignment of long reads is fundamental for identifying structural variations and haplotype phasing. In this context, the Graph Wavefront Alignment (GWFA) algorithm emerged as the fastest strategy for aligning long reads to genomic graphs. However, the available GWFA implementation does not support alignment backtracking, a crucial feature in real-case studies. In this paper, we propose a new open-source\n\nOn the optimization of GWFA algorithm: enabling real-case applications supporting alignment backtracking.", "token_count": 215, "char_count": 1063, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7786, "quality_score": 0.8893, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:53.146995", "source": { "split": "train_shard_00000", "doc_id": 439 }, "chunk_id": "train_shard_00000_439_0", "global_id": 491 }, { "text": "In a recent study, Hou et al. developed a high-resolution, haplotype-based pangenome for moso bamboo (Phyllostachys edulis), revealing significant genetic diversity and over 1000 climate-associated variants. Their findings highlight adaptive mechanisms for the ecological resilience of bamboo, providing crucial insights for climate-resilient breeding and conservation to ensure the long-term ecological and economic benefits of moso bamboo amid climate change.\n\nUnlocking the genetic blueprint of bamboo for climate adaption.", "token_count": 124, "char_count": 526, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:53.530657", "source": { "split": "train_shard_00000", "doc_id": 440 }, "chunk_id": "train_shard_00000_440_0", "global_id": 492 }, { "text": "The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between\n\nPangenome reconstruction in rats enhances genotype-phenotype mapping and variant discovery.", "token_count": 217, "char_count": 898, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:53.997485", "source": { "split": "train_shard_00000", "doc_id": 441 }, "chunk_id": "train_shard_00000_441_0", "global_id": 493 }, { "text": "N-glycosylation is a prevalent post-translational modification in eukaryotes, essential for regulating protein secretion. In Saccharomyces cerevisiae, glycosylation mutants have been shown to enhance the secretion of heterologous glycosylated proteins. However, whether these mutants can also increase the secretion of non-glycosylated proteins and whether the growth defects associated with glycosylation mutations can be mitigated remains unclear. This study aimed to characterize and optimize enhanced secretory expression in the promising yeast host Kluyveromyces marxianus by deleting MNN11, which encodes a subunit of the mannose polymerase II complex responsible for elongating α-1,6-linked mannose chains.\n\nCharacterization and optimization of mnn11Δ-mediated enhancement in heterologous protein production in Kluyveromyces marxianus.", "token_count": 214, "char_count": 842, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7596, "quality_score": 0.8798, "entities": { "genes": [ "MNN11" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:54.463440", "source": { "split": "train_shard_00000", "doc_id": 442 }, "chunk_id": "train_shard_00000_442_0", "global_id": 494 }, { "text": "Japanese soybeans are traditionally bred to produce soy foods such as tofu, miso and boiled soybeans. Here, to investigate their distinctive genomic features, including genomic structural variations (SVs), we constructed 11 nanopore-based genome references for Japanese and other soybean lines. Our assembly-based comparative method, designated 'Asm2sv', identified gene-level SVs comprehensively, enabling pangenome analysis of 462 worldwide cultivars and varieties. Based on these, we identified selective sweeps between Japanese and US soybeans, one of which was the pod-shattering resistance gene PDH1. Genome-wide association studies further identified several quantitative trait loci that accounted for large-seed phenotypes of Japanese soybean lines, some of which were also close to regions of the selective sweeps, including PDH1. Notably, specific combinations of alleles, including SVs, were found to increase the seed size of some Japanese landraces. In addition to the differences in cultivation environments, distinct food processing usages might result in changes in Japanese soybean genomes.\n\nThe genomic landscape of gene-level structural variations in Japanese and global soybean Glycine max cultivars.", "token_count": 274, "char_count": 1220, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [ "PDH1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:55.037195", "source": { "split": "train_shard_00000", "doc_id": 443 }, "chunk_id": "train_shard_00000_443_0", "global_id": 495 }, { "text": "Bacterial vaginosis (BV) is a prevalent condition characterized by an imbalance in the vaginal microbiota, often involving the presence of\n\nA Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species.", "token_count": 73, "char_count": 277, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8919, "quality_score": 0.9459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:55.437288", "source": { "split": "train_shard_00000", "doc_id": 444 }, "chunk_id": "train_shard_00000_444_0", "global_id": 496 }, { "text": "The complex interactions between host genetics and the gut microbiome are well documented. However, the specific impacts of gene expression patterns and microbial composition on each other remain to be further explored.\n\nDeciphering the coordinated roles of the host genome, duodenal mucosal genes, and microbiota in regulating complex traits in chickens.", "token_count": 77, "char_count": 355, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8039, "quality_score": 0.902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:55.841341", "source": { "split": "train_shard_00000", "doc_id": 445 }, "chunk_id": "train_shard_00000_445_0", "global_id": 497 }, { "text": "Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation. Indexes based on k-mers and de Bruijn graphs are limited to answering questions at a specific substring length k. We present Maximal Exact Match Ordered (MEMO), a pangenome indexing method based on maximal exact matches (MEMs) between sequences. A single MEMO index can handle arbitrary-length queries over pangenomic windows. MEMO enables both queries that test k-mer presence/absence (membership queries) and that count the number of genomes containing k-mers in a window (conservation queries). MEMO's index for a pangenome of 89 human autosomal haplotypes fits in 2.04 GB, 8.8\n\nMem-based pangenome indexing for k-mer queries.", "token_count": 235, "char_count": 978, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7338, "quality_score": 0.8669, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:56.354207", "source": { "split": "train_shard_00000", "doc_id": 446 }, "chunk_id": "train_shard_00000_446_0", "global_id": 498 }, { "text": "Cholestatic drug-induced liver injury (DILI) is caused by the aberrant excretion of bile acids (BAs) from hepatocytes via bile canaliculus-like structures (BCLSs) into the bile ducts. The precise in vitro evaluation method for cholestatic DILI has not been established due to a lack of specific markers and cell resources. We previously reported that HepG2-NIAS cells cultured on a collagen vitrigel (CV) membrane formed BCLSs with high protein expression of transporters involved in the excretion of BAs, including bile salt export pump (BSEP). In this study, the potential of connexin (Cx) 32, a component of gap junction, as a predictive marker for cholestatic DILI was investigated using a CV-culture model of HepG2-NIAS cells. The cells were treated with 7 drugs with different DILI-risk levels, and cell toxicity and Cx32 expression were evaluated. Cell toxicity was significantly increased not only by high DILI-risk drugs (troglitazone and cyclosporine A) but also by chlorpromazine with low DILI-risk. Furthermore, cell toxicity of troglitazone was not enhanced by a co-treatment with taurocholate, suggesting the low involvement of inhibition of BA excretion via BSEP in cholestatic DILI. In contrast, the total protein expression of Cx32 and co-localization of Cx32 and F-actin, which is composed of BCLSs, were significantly increased only by high DILI-risk drugs. Treatment with high DILI-risk drugs also induced the increased protein expression of zonula occludens (ZO)-1, which supports BCLSs concerted with Cx32. These results suggest that Cx32 expression in the CV-culture model of HepG2-NIAS cells may be a prominent predictive marker for cholestatic DILI.", "token_count": 478, "char_count": 1674, "word_count": 250, "semantic_coherence": 1, "information_density": 0.564, "quality_score": 0.782, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:57.024215", "source": { "split": "train_shard_00000", "doc_id": 447 }, "chunk_id": "train_shard_00000_447_0", "global_id": 499 }, { "text": "Potential of connexin 32 as a predictive marker for drug-induced cholestatic liver injury in a collagen vitrigel-culture model of HepG2-NIAS cells, a new subline of HepG2 cells, with bile canaliculus-like structures.", "token_count": 67, "char_count": 216, "word_count": 31, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:57.392011", "source": { "split": "train_shard_00000", "doc_id": 447 }, "chunk_id": "train_shard_00000_447_1", "global_id": 500 }, { "text": "Lacticaseibacillus paracasei is widely used as a probiotic supplement and food additive in the medicinal and food industries. However, its application requires careful evaluation of safety traits associated with probiotic pathogenesis, including the transfer of antibiotic-resistance genes, the presence of virulence and pathogenicity factors, and the potential disruptions of the gut microbiome and immune system. In this study, we conducted whole genome sequencing (WGS) of L. paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules and performed genome annotation to assess its probiotic and safety attributes. Our comparative genomic analysis assessed this novel strain's genetic attributes and functional diversity and unraveled its evolutionary relationships with other L. paracasei strains. The assembly yielded three contigs: one corresponding to the chromosome and two corresponding to plasmids. Genome annotation revealed the presence of 2838 DNA-coding sequences (CDS), 78 ribosomal RNAs (rRNAs), 60 transfer RNAs (tRNAs), three non-coding RNAs (ncRNAs), and 126 pseudogenes. The strain lacked antibiotic resistance genes and pathogenicity factors. Two intact prophages, one Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, and three antimicrobial peptide gene clusters were identified, highlighting the genomic stability and antimicrobial potential of the strain. Furthermore, genes linked to probiotic functions, such as mucosal colonization, stress resistance, and biofilm formation, were characterized. The pan-genome analysis identified 3358 orthologous clusters, including 1775 single-copy clusters, across all L. paracasei strains. Notably, L. paracasei FMT2 contained many unique singleton genes, potentially contributing to its distinctive probiotic properties. Our findings confirm the potential of L. paracasei FMT2 for food and therapeutic applications based on its probiotic profile and safety.", "token_count": 489, "char_count": 1965, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8236, "entities": { "genes": [ "FMT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:58.036487", "source": { "split": "train_shard_00000", "doc_id": 448 }, "chunk_id": "train_shard_00000_448_0", "global_id": 501 }, { "text": "Whole genome sequencing and In silico analysis of the safety and probiotic features of Lacticaseibacillus paracasei FMT2 isolated from fecal microbiota transplantation (FMT) capsules.", "token_count": 50, "char_count": 183, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [ "FMT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:58.396727", "source": { "split": "train_shard_00000", "doc_id": 448 }, "chunk_id": "train_shard_00000_448_1", "global_id": 502 }, { "text": "The genus Chenopodium L. is characterized by its wide geographic distribution and ecological adaptability. Species such as quinoa (Chenopodium quinoa Willd.) have served as domesticated staple crops for centuries. Wild Chenopodium species exhibit diverse niche adaptations and are important genetic reservoirs for beneficial agronomic traits, including disease resistance and climate hardiness. To harness the potential of the wild taxa for crop improvement, we developed a Chenopodium pangenome through the assembly and comparative analyses of 12 Chenopodium species that encompass the eight known genome types (A-H). Six of the species are new chromosome-scale assemblies, and many are polyploids; thus, a total of 20 genomes were included in the pangenome analyses. We show that the genomes vary dramatically in size with the D genome being the smallest (∼370 Mb) and the B genome being the largest (∼700 Mb) and that genome size was correlated with independent expansions of the Copia and Gypsy LTR retrotransposon families, suggesting that transposable elements have played a critical role in the evolution of the Chenopodium genomes. We annotated a total of 33,457 pan-Chenopodium gene families, of which ∼65% were classified as shell (2% private). Phylogenetic analysis clarified the evolutionary relationships among the genome lineages, notably resolving the taxonomic placement of the F genome while highlighting the uniqueness of the A genome in the Western Hemisphere. These genomic resources are particularly important for understanding the secondary and tertiary gene pools available for the improvement of the domesticated chenopods while furthering our understanding of the evolution and complexity within the genus.\n\nA pangenome reveals LTR repeat dynamics as a major driver of genome evolution in Chenopodium.", "token_count": 438, "char_count": 1826, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:59.023162", "source": { "split": "train_shard_00000", "doc_id": 449 }, "chunk_id": "train_shard_00000_449_0", "global_id": 503 }, { "text": "Understanding the kinetics of hepatic processes, such as bile acid (BA) handling and cellular aerobic metabolism, is crucial for advancing our knowledge of liver toxicity, particularly drug-induced cholestasis (DiCho). This article aimed to construct interpretable models with parameter estimations serving as reference values when investigating these cell metrics. Longitudinal datasets on BA disposition and oxygen consumption rates were collected using sandwich-cultured human hepatocytes. Chenodeoxycholic acid (CDCA), lithocholic acid (LCA), as well as their amidated and sulfate-conjugated metabolites were quantified with liquid chromatography-mass spectrometry. The bile salt export pump (BSEP) abundance was monitored with targeted proteomics and modelled for activity assessment. Oxygen consumption was measured using Seahorse XFp analyser. Ordinary differential equation-based models were solved in R. The basolateral uptake and efflux clearance of glycine-conjugated CDCA (GCDCA) were estimated at 1.22 µL/min/10\n\nIn Vitro-In Silico Models to Elucidate Mechanisms of Bile Acid Disposition and Cellular Aerobics in Human Hepatocytes.", "token_count": 298, "char_count": 1144, "word_count": 148, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:02:59.584696", "source": { "split": "train_shard_00000", "doc_id": 450 }, "chunk_id": "train_shard_00000_450_0", "global_id": 504 }, { "text": "Probiotics are effective for improving poultry health. Probiotic Bacillus cereus strains are widely used to improve animal health by stimulating the immune system. In this study, we obtained a B. cereus 13 (BC13) strain that functions in acid, high-temperature, and bile salt resistance. It also degrades starch, cellulose, and other proteins. To better understand the probiotic effects of BC13, we added the strain to the diet of broilers and observed its effects. We found that BC13 significantly improved the growth performance of broilers. The levels of total antioxidant capacity, superoxide dismutase, and glutathione peroxidase were increased, and the concentration of malondialdehyde was reduced by BC13. Supplementation with BC13 enhanced immune function by increasing the levels of secretory immunoglobulin A (sIgA) in the jejunum mucosa; IgA, IgM, and IgG in the serum; mRNA levels of Zo-1, claudin and occludin of the jejunal mucosa; and increased villus height/crypt depth of the jejunum. Furthermore, BC13 improved the composition of intestinal microbes, especially at the genus level of Akkermansia. The addition of BC13 increased the levels of acetic, butyric, valeric, and propionic acids. These results emphasise the potential of BC13 as a probiotic dietary supplement to improve the antioxidant capacity, intestinal barrier function, and gut microbial composition to enhance body health.\n\nIsolation of Bacillus cereus and its probiotic effect on growth performance, antioxidant capacity, and intestinal barrier protection of broilers.", "token_count": 415, "char_count": 1553, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [ "BC13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:00.546074", "source": { "split": "train_shard_00000", "doc_id": 451 }, "chunk_id": "train_shard_00000_451_0", "global_id": 505 }, { "text": "Recent advances in genetics are pushing the frontiers of health research in Africa. Notable developments include the release of the draft human pangenome reference, regulatory approval of gene editing therapies for sickle cell disease, and the announcements of major initiatives such as the Ghana Genome Project, the Personalized Medicine in North Africa Initiative, Nigeria's 100K Genome Project and South Africa's 110K Human Genomes Project. Additionally, gene-based therapies for HIV are on the horizon, with clinical trials planned in some African countries. Despite this progress, a pressing challenge remains: ensuring equitable access and delivery of genomics medicine worldwide, particularly in Africa and other low and middle income regions.\n\nScience and Society: Pathways to Equitable Access and Delivery of Genomics Medicine in Africa.", "token_count": 176, "char_count": 846, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7107, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:00.990489", "source": { "split": "train_shard_00000", "doc_id": 452 }, "chunk_id": "train_shard_00000_452_0", "global_id": 506 }, { "text": "Gut microbiota has been increasingly linked to metabolic health and diseases over the past few decades. Bile acids (BAs), the major components of bile, are bidirectionally linked to intestinal microbiota, also known as the gut microbiome-BA metabolic axis. Gut microbiota-derived bile salt hydrolase (BSH, EC 3.5.1.24), which catalyzes the \"gateway\" reaction in a wider pathway of bile acid modification, not only shapes the bile acid landscape, but also modulates the crosstalk between gut microbiota and host health. Therefore, microbial BSHs exhibit the potential to directly or indirectly influence microbial and host physiologies, and have been increasingly considered as promising targets for the modulation of gut microbiota to benefit animal and human health. However, their physiological functions in bacterial and host physiologies are still controversial and not clear. In this review, we mainly discuss the current evidence related to the physiological roles that BSHs played in gut microbiota and human health, and the possible underlying mechanisms. Meanwhile, we also present the potential applications of BSHs and BSH-producing probiotics in various fields. Finally, we describe several important questions that need to be addressed by further investigations. A detailed exploration of the physiological significance of BSHs will contribute to their future diagnostic and therapeutic applications in improving animal and human health.\n\nNew insights into microbial bile salt hydrolases: from physiological roles to potential applications.", "token_count": 348, "char_count": 1553, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6063, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:01.563024", "source": { "split": "train_shard_00000", "doc_id": 453 }, "chunk_id": "train_shard_00000_453_0", "global_id": 507 }, { "text": "Grapevine (Vitis) is one of the oldest domesticated fruit crops with great cultural and economic importance. Here we assembled and annotated haplotype-resolved genomes of 72 global Vitis accessions including 25 wild and 47 cultivated grapevines, among which genomes for 60 grapevines are newly released. Haplotype-aware phylogenomics disentangled the mysterious hybridization history of grapevines, revealing the enormous genetic diversity of the Vitis genus. Pangenomic analysis reveals that European cultivars, more susceptible to the destructive disease downy mildew (DM), have a smaller repertoire of resistance genes in the NLR family encoding the TIR-NBARC-LRR domain. Through extensive structural variation (SV) characterization, phenotyping, DM-infection transcriptome profiling of 113 Vitis accessions, and SV-expression quantitative trait loci analysis, we have identified over 63 SVs and their relevant genes significantly associated with DM resistance, exemplified by a lysine histidine transporter, VvLHT8. This haplotype-resolved super pangenome of the Vitis genus will accelerate breeding and enrich our understanding of the evolution and biology of grapevines.\n\nSuper pangenome of Vitis empowers identification of downy mildew resistance genes for grapevine improvement.", "token_count": 316, "char_count": 1286, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7412, "quality_score": 0.8706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:02.127124", "source": { "split": "train_shard_00000", "doc_id": 454 }, "chunk_id": "train_shard_00000_454_0", "global_id": 508 }, { "text": "Probiotics are living microorganisms that, when given in an adequate dose, have a healthy impact on human well-being. With global interest in self-care, dietary supplements especially probiotics is expanding rapidly due to their supported health effects. In this study, a total of twenty-two samples were collected from dairy products in Egypt's markets, firstly isolated then identified and screened for probiotic properties under stressful conditions as NaCl, acid and bile salt conditions. After evaluation of the antimicrobial effect against widespread gram negative and gram positive human infecting bacteria, besides the antiviral assessment against (SARS-CoV-2) virus which has disturbed the world, the antibiotic susceptibility test was done. Only three promising isolates were subjected for whole genome sequence with high-output next generation technology and the obtained data was subjected to a full bioinformatics analysis. The results obtained stated the advance of our isolates to tolerate the stress factors that can struggle in the human gut as well as the antimicrobial effects. All these bright characteristics were confirmed and illustrated in detail through different and reliable genome analysis tools. Our isolates were founded to have stable genome through containing mobile genetic elements like phages and CRISPR clusters that confirm the safety and quality for human health.\n\nWhole genome sequencing of promising Lactobacillus delbrueckii subsp. bulgaricus strains isolated from Egyptian dairy products for probiotic characteristics.", "token_count": 327, "char_count": 1560, "word_count": 220, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:02.698832", "source": { "split": "train_shard_00000", "doc_id": 455 }, "chunk_id": "train_shard_00000_455_0", "global_id": 509 }, { "text": "Cholestasis is defined as an impairment in the flow of bile, resulting in the accumulation of its components. Despite ursodeoxycholic acid (UDCA) being the only FDA-approved drug for cholestasis, it has little value in treating or preventing cholestasis; hence, new medications are required to treat these illnesses. The farnesoid X receptor (FXR) maintains bile acid (BA) homeostasis. It exists as heterodimers with retinoid X receptor (RXR) and responds to ligands that bind to any one of the partners and are activated synergistically in the presence of both. The hepatoprotective effect of bexarotene (Bex) against cholestasis liver injury induced by α-naphthyl isothiocyanate (ANIT) was evaluated in male Wistar albino rats. Our study demonstrates that compared to the ANIT group, Bex improves liver function tests, liver histology, and considerably reduces inflammatory mediators. Additionally, antioxidant levels increased significantly. Besides that, Bex upregulates the gene expression of FXR, bile salt export pump, hepatocyte nuclear factor 1α, and small heterodimer partner. Moreover, it enhances antioxidative nuclear factor erythroid 2-related factor gene expression and the expression of the NAD(P)H quinone oxidoreductase 1, and heme-oxygenase 1 protein targets in the rats' livers, reinforcing its hepatoprotective potential. Furthermore, Bex increases protein expressions of FXR, The bile salt export pump, and sirtuin 1 levels in the rats' livers. This study demonstrates that Bex protects against ANIT-induced cholestasis. This protective strategy involves controlling BA metabolism, inhibiting inflammatory mediators, and reducing oxidative stress.\n\nNovel insights into bexarotene's role in preventing cholestasis: mechanisms and implications.", "token_count": 468, "char_count": 1764, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6831, "quality_score": 0.8416, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:03.337553", "source": { "split": "train_shard_00000", "doc_id": 456 }, "chunk_id": "train_shard_00000_456_0", "global_id": 510 }, { "text": "Kaempferol (Kae), as a homologous flavonoid, plays a pivotal role in human nutrition and disease treatment. This study endeavors to elucidate the in vivo metabolism of Kae and its potential to modulate the interplay between bile acids (BAs) and gut microbiota (GM). After Kae administration, we analyzed pharmacokinetics, BA levels, and drug metabolic enzymes (DMEs) amount using LC-MS/MS. Subsequently, we checked the gene and protein expression with qRT-PCR and western blot and studied the changes in GM using 16S rRNA sequencing, accompanying in-depth data analysis. Finally, molecular docking was employed to explore Kae's interaction with the Farnesoid X receptor (FXR). Kae enhances its own absorption and metabolic circulation in vivo by upregulating the UDP-Glucuronosyltransferases (UGTs) expression. Furthermore, Kae significantly suppressed the expression of cholesterol 7α-hydroxylase (CYP7A1) while concurrently elevating the sterol 27-hydroxylase (CYP27A1) expression, by activating the liver FXR, a nuclear transcription factor involved in the regulation of CYPs and UGTs enzymes. For BA analysis, Kae induced the upregulation of tauro-BAs by attenuating the activity of bile salt hydrolases (BSH), which correlated with shifts in the GM composition. Specifically, Kae increased the abundance of beneficial bacteria such as\n\nThe Prebiotic Effect of Kaempferol in Regulating Bile Acid Metabolism.", "token_count": 393, "char_count": 1411, "word_count": 198, "semantic_coherence": 1, "information_density": 0.702, "quality_score": 0.851, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:03.944267", "source": { "split": "train_shard_00000", "doc_id": 457 }, "chunk_id": "train_shard_00000_457_0", "global_id": 511 }, { "text": "Mitochondria are semi-autonomous organelles that play a crucial role in the energy budget of animal cells and are closely related to the locomotor abilities of animals. Equidae is renowned for including two domesticated species with distinct purposes: the endurance-oriented donkey and the power-driven horse, making it an ideal system for studying the relationship between mitochondria and locomotor abilities. In this study, to cover the genetic diversity of donkeys, we sequenced and assembled six new mitochondrial genomes from China. Meanwhile, we downloaded the published mitochondrial genomes of all species within Equus and conducted a comprehensive pan-mitochondrial genome analysis. We found that the mitochondrial genomes of Equus are highly conserved, each encoding 37 genes, including 13 protein-coding genes (PCGs). Phylogenetic analysis based on mitochondrial genomes supports previous research, indicating that the extant species in Equus are divided into three main branches: horses, donkeys, and zebras. Specifically, 761 genetic variants were identified between donkeys and horses, 68 of which were non-synonymous mutations in PCGs, potentially linked to their different locomotor abilities. Structural protein modeling indicated that despite genetic differences, the overall protein structures between donkeys and horses remain similar. This study revealed the mitochondrial genome variation patterns of domesticated animals, offering novelty perspectives on domestication imprints. Additionally, it provides reliable candidate molecular markers for the identification of donkeys and horses.\n\nEquus mitochondrial pangenome reveals independent domestication imprints in donkeys and horses.", "token_count": 372, "char_count": 1708, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:04.520728", "source": { "split": "train_shard_00000", "doc_id": 458 }, "chunk_id": "train_shard_00000_458_0", "global_id": 512 }, { "text": "In this work, the hypolipidemic and antioxidative capacity of FSGLR (S7) and GIEWA (S10) from miiuy croaker swim bladders was explored systematically in an oleic acid (OA)-induced nonalcoholic fatty liver disease (NAFLD) model of HepG2 cells. Moreover, the hypolipidemic activity of S7 and S10 and their antioxidative abilities were preliminarily investigated in combination with molecular docking technology. The results indicated that S7 and S10 could decrease the amount of lipid accumulation and the content of triglycerides (TG) and total cholesterol (TC) in the OA-induced NAFLD cell model in a dose-dependent manner. In addition, S7 and S10 exhibited better bile salt binding, pancreatic lipase (PL) inhibition, and cholesterol esterase (CE) inhibition capacities. The hypolipidemic mechanisms of S7 and S10 were connected with the downregulation of the mRNA expression levels of adipogenic factors, including sterol-regulatory element-binding protein-1c (SREBP-1c), acetyl-CoA carboxylase (ACC), sterol-regulatory element-binding protein (SREBP)-2, hydroxymethylglutaryl-CoA reductase (HMGR), and fatty acid synthase (FAS) (\n\nAntioxidant Peptides from Miiuy Croaker Swim Bladders: Ameliorating Effect and Mechanism in NAFLD Cell Model through Regulation of Hypolipidemic and Antioxidant Capacity.", "token_count": 399, "char_count": 1304, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:05.133262", "source": { "split": "train_shard_00000", "doc_id": 459 }, "chunk_id": "train_shard_00000_459_0", "global_id": 513 }, { "text": "Probiotics are well-known therapeutic agents for managing constipation and have been used to improve chronic kidney disease (CKD) progression. However, heat-killed probiotics on CKD remain inadequately explored. This study aimed to evaluate the probiotic potential of lactic acid bacteria derived from natural sources and to investigate the effects of both live and heat-killed Leuconostoc mesenteroides (Ln.m) on renal and gastrointestinal functions in CKD mice. Ln.m was selected from acid and bile salt intolerance tests, non-hemolytic activity, and antibiotic sensitivity. CKD mice demonstrated significantly elevated blood urea nitrogen (BUN) and creatinine levels compared to control mice (p < 0.001 and p < 0.01). Treatment with live and heat-killed Ln.m significantly reduced BUN and creatinine levels in CKD mice (p < 0.01 and p < 0.05). Additionally, kidney damage observed in CKD mice compared to control mice, including glomerular necrosis, tubular dilatation, inflammation, and fibrosis, was significantly alleviated following live and heat-killed Ln.m treatments. CKD-induced gastrointestinal dysfunction was characterized by an imbalance in Firmicutes/Bacteroidota populations, increased colonic uremic toxin (p < 0.01), reduced fecal short-chain fatty acids (SCFAs) (p < 0.05), and constipation. Treatment with live and heat-killed Ln.m restored gut microbiota, decreased uremic toxin (p < 0.001), increased SCFAs (p < 0.05), and alleviated constipation. In summary, both live and heat-killed Ln.m effectively alleviated gastrointestinal dysfunction and renal damage in CKD mice, primarily through modulation of the intestinal environment", "token_count": 507, "char_count": 1654, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5877, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:05.783079", "source": { "split": "train_shard_00000", "doc_id": 460 }, "chunk_id": "train_shard_00000_460_0", "global_id": 514 }, { "text": "These findings highlight the therapeutic potential of live and heat-killed Ln.m as the gastrointestinal dysfunction treatment in CKD.\n\nLive and heat-killed Leuconostoc mesenteroides counteract the gastrointestinal dysfunction in chronic kidney disease mice through intestinal environment modulation.", "token_count": 76, "char_count": 299, "word_count": 36, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:06.145504", "source": { "split": "train_shard_00000", "doc_id": 460 }, "chunk_id": "train_shard_00000_460_1", "global_id": 515 }, { "text": "Encoded within many microbial genomes, biosynthetic gene clusters (BGCs) underlie the synthesis of various secondary metabolites that often mediate ecologically important functions. Several studies and bioinformatics methods developed over the past decade have advanced our understanding of both microbial pangenomes and BGC evolution. In this minireview, we first highlight challenges in broad evolutionary analysis of BGCs, including delineation of BGC boundaries and clustering of BGCs across genomes. We further summarize key findings from microbial comparative genomics studies on BGC conservation across taxa and habitats and discuss the potential fitness effects of BGCs in different settings. Afterward, recent research showing the importance of genomic context on the production of secondary metabolites and the evolution of BGCs is highlighted. These studies draw parallels to recent, broader, investigations on gene-to-gene associations within microbial pangenomes. Finally, we describe mechanisms by which microbial pangenomes and BGCs evolve, ranging from the acquisition or origination of entire BGCs to micro-evolutionary trends of individual biosynthetic genes. An outlook on how expansions in the biosynthetic capabilities of some taxa might support theories that open pangenomes are the result of adaptive evolution is also discussed. We conclude with remarks about how future work leveraging longitudinal metagenomics across diverse ecosystems is likely to significantly improve our understanding on the evolution of microbial genomes and BGCs.\n\nContext matters: assessing the impacts of genomic background and ecology on microbial biosynthetic gene cluster evolution.", "token_count": 366, "char_count": 1687, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:06.723425", "source": { "split": "train_shard_00000", "doc_id": 461 }, "chunk_id": "train_shard_00000_461_0", "global_id": 516 }, { "text": "Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (\n\nComparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.", "token_count": 82, "char_count": 372, "word_count": 50, "semantic_coherence": 1, "information_density": 0.94, "quality_score": 0.97, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:07.127787", "source": { "split": "train_shard_00000", "doc_id": 462 }, "chunk_id": "train_shard_00000_462_0", "global_id": 517 }, { "text": "The human genome contains numerous structurally-variable polymorphic loci, including several hundred disease-associated genes, almost inaccessible for accurate variant calling. Here we present Locityper, a tool capable of genotyping such challenging genes using short and long-read whole genome sequencing. For each target, Locityper recruits and aligns reads to locus haplotypes, for instance extracted from a pangenome, and finds the likeliest haplotype pair by optimizing read alignment, insert size and read depth profiles. Locityper accurately genotypes up to 194 of 256 challenging medically relevant loci (95% haplotypes at QV33), an 8.8-fold gain compared to 22 genes achieved with standard variant calling pipelines. Furthermore, Locityper provides access to hyperpolymorphic HLA genes and other gene families, including KIR, MUC and FCGR. With its low running time of 1h10m per sample at 8 threads, Locityper is scalable to biobank-sized cohorts, enabling association studies for previously intractable disease-relevant genes.\n\nLocityper: targeted genotyping of complex polymorphic genes.", "token_count": 279, "char_count": 1098, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7867, "quality_score": 0.8933, "entities": { "genes": [ "QV33" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:07.700389", "source": { "split": "train_shard_00000", "doc_id": 463 }, "chunk_id": "train_shard_00000_463_0", "global_id": 518 }, { "text": "Recently, there has been a growing interest in developing food-grade (F-G) microemulsions (MEMs) with potential applications in the food industry, such as a green solvent for extracting bioactive compounds or as a vehicle to solubilize low-polar bioactive compounds. Therefore, this work aimed to create F-G MEMs using a low-energy titration method, bile salt or tween 80 as surfactants, and F-G ingredients like acetic acid, olive oil, limonene, and coconut oil. For this purpose, 56 formulations were assessed, from which 14 created oil-in-water (O/W) one-phase Winsor type IV microemulsions. All the F-G MEMs were transparent (turbidity ≤ 0.17 %) with watery densities (1.00 - 1.034 g/cm\n\nFormulation and heat stability of self-assembled O/W food-grade microemulsions formulated with bile salts or tween 80 as surfactants.", "token_count": 255, "char_count": 825, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7805, "quality_score": 0.8902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:08.197455", "source": { "split": "train_shard_00000", "doc_id": 464 }, "chunk_id": "train_shard_00000_464_0", "global_id": 519 }, { "text": "Bile salts play a major role in intestinal lipid digestion. In this study, the effects of bile salts concentration on the digestive characteristics and bioaccessibility of two oils with the same fatty acid composition but different triacylglycerol structures, physical mixed oil (MO) and medium- and long- chain triacylglycerol (MLCT), were investigated under simulated gastrointestinal conditions. Results revealed that as the bile salt concentration increased from 0.0 mg/mL to 5.0 mg/mL, the free fatty acids (FFAs) release of both oils exhibited an increasing trend. MLCT presented higher free fatty acids release and more stable release rate. Furthermore, at a bile salt concentration of 5.0 mg/mL, the bioaccessibility of FAs in MLCT was significantly higher than that in MO, with respective values of 79.51 ± 1.19 % and 74.69 ± 1.02 % (p < 0.05). Notably, even in conditions of bile salts deficiency, especially at a bile salt concentration of 1.0 mg/mL, the bioaccessibility of FAs in MLCT remained superior to that in MO, reaching levels of 43.29 ± 0.89 % and 46.47 ± 1.31 %, respectively, with statistical significance (p < 0.05). Theses findings further demonstrated that MLCT exhibits superior digestion characteristics. This study provided a scientific basis for the selection of nutritional lipids in clinical nutrition support.\n\nMedium- and long-chain triacylglycerol has higher digestibility and bioaccessibility compared with physical mixed oils under conditions of bile salts secretion deficiency.", "token_count": 418, "char_count": 1515, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:08.858428", "source": { "split": "train_shard_00000", "doc_id": 465 }, "chunk_id": "train_shard_00000_465_0", "global_id": 520 }, { "text": "The current study was undertaken to isolate, characterize, and cluster lactobacilli strains of indigenous cattle (Bos indicus) and buffalo (Bubalus bubalis) calf origin to develop a species-specific multistrain potential probiotic adjunct. Bacterial strains were isolated from the feces of Bos indicus and Bubalus bubalis calves of different breeds, i.e., Sahiwal (SC), Tharparker (TP), and Gir (GC) cattle and Murrah buffalo (MB). The fecal samples were aseptically taken from five healthy calves (5-10 days old) of each breed (a total of 20 animals). Accordingly, 105 bacteria were isolated, 52 of which were catalase negative, Gram-positive, and vancomycin resistant. These isolates were presumed to be Lactobacillus species, and genus-specific PCR was used to confirm their identification. Among the 52 isolates, 22 strains demonstrated greater acid tolerance, while 29 isolates showed superior bile tolerance, with survivability greater than 90%. Fifteen isolates capable of tolerating both acid and bile were further selected, and their identities were confirmed via 16S rRNA sequencing. Cluster analysis of the phylogenetic tree revealed three different species: Ligilactobacillus salivarius (8), Ligilactobacillus agilis (1), and Limosilactobacillus reuteri (6). All lactobacilli strains showed coaggregation with Escherichia coli ATCC25922 and Salmonella arizonae ATCC13314. All the isolates were found non-hemolytic and non-mucinolytic. Principal component analysis (PCA) revealed that L. reuteri GC09, L. salivarius GC12, L. agilis MB08, L. salivarius MB14, L. reuteri SC01, and L. reuteri MB11 possessed the most desirable attributes of probiotics. Based on these findings, these strains could be used to develop multi-strain probiotic adjunct for calves.", "token_count": 519, "char_count": 1767, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [ "MB11", "ATCC25922", "GC12", "ATCC13314", "SC01", "GC09", "MB14", "MB08" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:03:09.529555", "source": { "split": "train_shard_00000", "doc_id": 466 }, "chunk_id": "train_shard_00000_466_0", "global_id": 521 }, { "text": "Evaluation of the techno-functional properties of lactobacilli strains originated from Bos indicus and Bubalus bubalis calves for probiotic potential.", "token_count": 40, "char_count": 150, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:09.891071", "source": { "split": "train_shard_00000", "doc_id": 466 }, "chunk_id": "train_shard_00000_466_1", "global_id": 522 }, { "text": "The conventional method of antigen-based serotyping for Salmonella poses challenges due to the necessity of utilizing over 150 antisera. More recently, in silico Salmonella serotyping has emerged as a predictive alternative. The purpose of this study was to predict the serovars of 62 Salmonella enterica strains isolated from Korean poultry operations and their genetic characteristics using whole genome sequencing. The analysis employed diverse methods, including ribosomal, and core genome multi-locus sequence typing (MLST), based on Salmonella In Silico Typing Resource (SISTR). Pangenome, clusters of orthologous groups (COG) analysis, and identification of virulence and antibiotic resistance genes were conducted.\n\nGenetic characterization and in silico serotyping of 62 Salmonella enterica isolated from Korean poultry operations.", "token_count": 199, "char_count": 840, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6991, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:10.344583", "source": { "split": "train_shard_00000", "doc_id": 467 }, "chunk_id": "train_shard_00000_467_0", "global_id": 523 }, { "text": "Author Correction: Pangenome graphs and their applications in biodiversity genomics.", "token_count": 19, "char_count": 84, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:10.707648", "source": { "split": "train_shard_00000", "doc_id": 468 }, "chunk_id": "train_shard_00000_468_0", "global_id": 524 }, { "text": "Eukaryotic chromosome segregation requires spindle microtubules to attach to chromosomes through kinetochores. The chromosomal locus that mediates kinetochore assembly is the centromere and is epigenetically specified in most organisms by a centromeric histone H3 variant called CENP-A. An exception to this is budding yeast which have short, sequenced-defined point centromeres. In\n\nCentromeres in the thermotolerant yeast", "token_count": 114, "char_count": 423, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8393, "quality_score": 0.9196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:11.097936", "source": { "split": "train_shard_00000", "doc_id": 469 }, "chunk_id": "train_shard_00000_469_0", "global_id": 525 }, { "text": "Traditionally, variations from a linear reference genome were used to represent large sets of haplotypes compactly. In the linear reference genome based paradigm, the positional Burrows-Wheeler transform (PBWT) has traditionally been used to perform efficient haplotype matching. Pangenome graphs have recently been proposed as an alternative to linear reference genomes for representing the full spectrum of variations in the human genome. However, haplotype matches in pangenome graph based haplotype sets are not trivially generalizable from haplotype matches in the linear reference genome based haplotype sets. Work has been done to represent large sets of haplotypes as paths through a pangenome graph. The graph Burrows-Wheeler transform (GBWT) is one such work. The GBWT essentially stores the haplotype paths in a run length compressed BWT with compressed local alphabets. Although efficient in practice count and locate queries on the GBWT were provided by the original authors, the efficient haplotype matching capabilities of the PBWT have never been shown on the GBWT. In this paper, we formally define the notion of haplotype matches in pangenome graph-based haplotype sets by generalizing from haplotype matches in linear reference genome-based haplotype sets. We also describe the relationship between set maximal matches, long matches, locally maximal matches, and text maximal matches on the GBWT, PBWT, and the BWT. We provide algorithms for outputting some of these matches by applying the data structures of the r-index (introduced by Gagie et al.) to the GBWT. We show that these structures enable set maximal match and long match queries on the GBWT in almost linear time and in space close to linear in the number of runs in the GBWT. We also provide multiple versions of the query algorithms for different combinations of the available data structures. The long match query algorithms presented here even run on the BWT in the same time complexity as the GBWT due to their similarity.\n\nHaplotype Matching with GBWT for Pangenome Graphs.", "token_count": 464, "char_count": 2061, "word_count": 318, "semantic_coherence": 1, "information_density": 0.478, "quality_score": 0.739, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:11.740724", "source": { "split": "train_shard_00000", "doc_id": 470 }, "chunk_id": "train_shard_00000_470_0", "global_id": 526 }, { "text": "Murine norovirus (MNV) undergoes large conformational changes in response to the environment. The T=3 icosahedral capsid is composed of 180 copies of ~58 kDa VP1 that has N-terminal (N), shell (S) and C-terminal protruding (P) domains. In phosphate buffered saline, the P domains are loosely tethered to the shell and float ~15Å above the surface. At conditions found in the gut (i.e. low pH with high metal ion and bile salt concentrations) the P domain rotates and drops onto the shell with intra P domain changes that enhance receptor interactions while blocking antibody binding. Two of our monoclonal antibodies (2D3 and 4F9) have broad strain recognition and the only escape mutants, V339I and D348E, are located on the C D loop and ~20 Å from the epitope. Here we determined the cryo-EM structures of V339I and D348E at neutral pH +/- metal ions and bile salts. These allosteric escape mutants are constitutively in the activated state without the addition of metal ions or bile salts, thus explaining how they escape neutralization. Dynamic simulations of the P domain further suggest that movement of the C D loop may be the rate limiting step in the conformational change and that V339I increases the motion of the A B /E F loops compared to wt, making it easier for the virus to transition to the activated state. These findings have important implications for norovirus vaccine design since they uncover a form of the viral capsid that should lend superior immune protection against subsequent challenge by wild type virus.\n\nMurine norovirus allosteric escape mutants mimic gut activation.", "token_count": 412, "char_count": 1601, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [ "VP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:12.358543", "source": { "split": "train_shard_00000", "doc_id": 471 }, "chunk_id": "train_shard_00000_471_0", "global_id": 527 }, { "text": "Various studies demonstrated that probiotics play important roles in maintaining the balance of microorganisms in the body. Some strains produce bile salt hydrolase enzyme (BSH), which is an indirect mechanism for lowering cholesterol. BSH-producing probiotics as a supplement might be an alternative way to help reducing cholesterol in the body. The aim of this study was to investigate the effects of different microcapsule formulations with selected vegetable powders on growth characteristics of 3 Thai probiotic strains,\n\nFreeze drying microencapsulation using whey protein, maltodextrin and corn powder improved survivability of probiotics during storage.", "token_count": 151, "char_count": 661, "word_count": 92, "semantic_coherence": 1, "information_density": 0.837, "quality_score": 0.9185, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:12.804185", "source": { "split": "train_shard_00000", "doc_id": 472 }, "chunk_id": "train_shard_00000_472_0", "global_id": 528 }, { "text": "Genomic diversity in prokaryotic species is largely due to the existence of extensive pangenomes, allowing different gene complements to be drawn depending on the strain. Here, we have studied the diversity of the O-chain polysaccharide biosynthesis cluster (OBC) in marine bacteria of the Pelagibacterales order as a proxy to measure such genetic diversity in a single population. The study of single-amplified genomes (SAGs) from the whole order found a pattern similar to that of other well-studied microbes, such as the Enterobacteriales or\n\nLarge diversity in the O-chain biosynthetic cluster within populations of Pelagibacterales.", "token_count": 152, "char_count": 637, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:13.243425", "source": { "split": "train_shard_00000", "doc_id": 473 }, "chunk_id": "train_shard_00000_473_0", "global_id": 529 }, { "text": "Agave spirits have gained global recognition and hold a central position within the cultural heritage of Mexico. Traditional distilleries, characterized by open fermentations driven by local microbial communities, persist despite the rise of industrial-scale counterparts. In this review, we explore the environmental conditions and production practices that make the must of cooked agave stems a unique habitat for colonizing microorganisms. Additionally, we review selected studies that have characterized yeast species within these communities, with a focus on their metabolic traits and genomic features. Over 50 fungal species, predominantly Saccharomycetales and few Basidiomycetes, along with a similar number of lactic and acetic acid bacteria, have been identified. Despite variations in the chemical composition of the agave substrates and diversity of cultural practices associated with each traditional fermentation process, yeast species such as Saccharomyces cerevisiae, Kluyveromyces marxianus, Torulaspora delbrueckii, and several Pichia species have been consistently isolated across all agave spirit-producing regions. Importantly, cooked agave must is rich in fermentable sugars, yet it also contains inhibitory compounds that influence the proliferation dynamics of the microbial community. We discuss some of the genetic traits that may enable yeasts to flourish in this challenging environment and how human practices may shape microbial diversity by promoting the selection of microbes that are well-adapted to agave fermentation environments. The increasing demand for agave spirits, combined with concerns about the preservation of natural resources and cultural practices associated with their production, underscores the need to deepen our understanding of all key players, including the yeast communities involved.\n\nThriving in Adversity: Yeasts in the Agave Fermentation Environment.", "token_count": 392, "char_count": 1912, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:13.862085", "source": { "split": "train_shard_00000", "doc_id": 474 }, "chunk_id": "train_shard_00000_474_0", "global_id": 530 }, { "text": "An extensive amount of research has been conducted on a multitude of emulsifiers regarding their effect on o/w emulsion characteristics and lipolysis kinetics. However, there is an emerging need towards the understanding of biobased emulsifier characteristics. Therefore, this research studied the effect of 6 glycolipids on interfacial tension, emulsion microstructure throughout in vitro digestion, and lipolysis kinetics. Findings showed that molecular differences between glycolipids, such as the degree of acetylation, lactonization, and symmetry, substantially affected their behavior on the oil-water (o/w) interface, lowering the interfacial tensions to values ranging between 2 and 18 mN/m. Glycolipids with a higher amount of acetyl groups, lower tendency to self-assemble, and/or smaller molecular volume on the interface, decreased the interfacial tension substantially more. Therefore, acetylated lactonic sophorolipid decreased the interfacial tension most, while non-acetylated sophoroside showed the smallest effect on the interfacial tension. While all emulsions were stable and initially had similar droplet sizes, some were unstable throughout the simulated upper digestive tract, resulting in significantly different hydrolysis behaviors. Acetylated lactonic sophorolipid and non-acetylated glucolipid were more hydrophobic than the remaining 4 glycolipids, causing this gastric instability resulting in lower lipolysis extents by the end of the small intestinal phase. The acetylated sophoroside emulsion was unstable during the small intestinal phase, attributed to bile salt interactions. Therefore, this research concludes that molecular changes between glycolipids give rise to significantly different emulsion and digestion properties. These insights can be used in future work to optimize glycolipid structure and subsequent functional properties.\n\nMolecular characteristics of glycolipids determine oil-water interfacial behavior and in vitro lipid digestion kinetics.", "token_count": 467, "char_count": 1996, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:14.500560", "source": { "split": "train_shard_00000", "doc_id": 475 }, "chunk_id": "train_shard_00000_475_0", "global_id": 531 }, { "text": "New Bacillus velezensis strains with impressive antimicrobial activities are being continuously described. Here we performed genomic comparisons of five B. velezensis strains isolated from Amazonian fish intestines with other 266 genomes from the RefSeq database through a pangenome approach. We aimed to analyze the commonalities and specificities of each strain within this clade to explore their potential as probiotics and for promoting plant growth (PGP). High-quality draft genome sequences were obtained for strains P7 and P11, with genome metrics confirming their identification as B. velezensis. The evaluation of 271 B. velezensis genome sequences revealed an open pangenome composed of 14,918 homologs, while 16% of them represented the core genome. Therefore, the majority of genes belonged to the accessory variable genome, with many strains harboring numerous unique genes, including the Amazonian strain P45. This strain also stood out as carrying the potential to produce many hydrolytic enzymes and PGP traits. Genome mining of all five Amazonian strains annotated secondary metabolites with unknown identifications. The evaluated probiotic genes are mostly conserved in all B. velezensis strains. Moreover, the investigation of the mobilome, resistome, and virulence factors showed that these strains can be considered safe for probiotic and agricultural applications, corroborating our previous studies. This data will be useful to improve our understanding and biotechnological exploration of these strains and other B. velezensis as well.\n\nPangenome analysis of Bacillus velezensis exploring the probiotic potential and plant growth promotion traits of strains isolated from fish intestines.", "token_count": 390, "char_count": 1712, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6198, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:15.114941", "source": { "split": "train_shard_00000", "doc_id": 476 }, "chunk_id": "train_shard_00000_476_0", "global_id": 532 }, { "text": "Plant adaptation to terrestrial life started 450 million years ago and has played a major role in the evolution of life on Earth. The genetic mechanisms allowing this adaptation to a diversity of terrestrial constraints have been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the model bryophyte Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, a genome-environment association study and a pangenome. We identified adaptive features, such as peroxidases or nucleotide-binding and leucine-rich repeats (NLRs), also observed in flowering plants, likely inherited from the first land plants. The M. polymorpha pangenome also harbors lineage-specific accessory genes absent from seed plants. We conclude that different land plant lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage-specific polymorphisms and gene family evolution.\n\nThe Marchantia polymorpha pangenome reveals ancient mechanisms of plant adaptation to the environment.", "token_count": 254, "char_count": 1143, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:15.599435", "source": { "split": "train_shard_00000", "doc_id": 477 }, "chunk_id": "train_shard_00000_477_0", "global_id": 533 }, { "text": "Annexins (Anns) are a family of evolutionarily conserved, calcium-dependent, phospholipid-binding proteins that play critical roles in plant growth, development, and stress responses. Utilizing the pan-genome of 26 high-quality maize genomes, we identified 12 Ann genes, comprising 9 core genes (present in all 26 lines) and 3 near-core genes (present in 24-25 lines). This highlights the limitations of studying ZmAnn genes based on a single reference genome. Evaluating the Ka/Ks values of Ann genes in 26 varieties revealed that ZmAnn10 was under positive selection in certain varieties, while the remaining genes had Ka/Ks values less than 1, indicating purifying selection. Phylogenetic analysis divided ZmAnn proteins into six groups, with group VI containing only ZmAnn12. Structural variation in certain varieties altered the conserved domains, generating many atypical genes. Transcriptome analysis showed that different Ann members have distinct expression patterns in various tissues and under different abiotic and biotic stress treatments. Weighted gene co-expression network analysis of transcriptome data from various maize tissues under cold stress identified four Ann genes (ZmAnn2, ZmAnn6, ZmAnn7, ZmAnn9) involved in co-expression modules. Overall, this study utilized high-quality maize pangenomes to perform a bioinformatic analysis of ZmAnn genes, providing a foundation for further research on ZmAnn genes.\n\nThe evolution, variation and expression patterns of the annexin gene family in the maize pan-genome.", "token_count": 367, "char_count": 1531, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6495, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:16.178249", "source": { "split": "train_shard_00000", "doc_id": 478 }, "chunk_id": "train_shard_00000_478_0", "global_id": 534 }, { "text": "This is the first study conducted in southern Spain to determine i) the population structure (PS) of carbapenem-resistant (CR) Acinetobacter baumannii isolates by multilocus sequencing typing (MLST) and core genome MLST (cgMLST) and ii) the association between the sequence type ST and the bla\n\nRegional distribution of carbapenemase-producing Acinetobacter baumannii isolates in southern Spain (Andalusia).", "token_count": 109, "char_count": 407, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7636, "quality_score": 0.8818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:16.558511", "source": { "split": "train_shard_00000", "doc_id": 479 }, "chunk_id": "train_shard_00000_479_0", "global_id": 535 }, { "text": "The complete genome of Legionella lytica PCM 2298 was sequenced and analyzed to provide insights into its genomic structure, virulence potential, and evolutionary position within the Legionella genus. The genome comprised a 3.2 Mbp chromosome and two plasmids, pLlyPCM2298_1 and pLlyPCM2298_2, contributing to a total genome size of 3.7 Mbp. Functional annotation identified 3,165 coding sequences, including genes associated with known virulence factors such as the major outer membrane protein (MOMP), the macrophage infectivity potentiator (Mip), and a comprehensive set of secretion systems (type II, type IVA, and type IVB Dot/Icm type IV secretion system). Notably, L. lytica contributed 383 unique genes to the Legionella pangenome, with 232 identified effector proteins, of which 35 were plasmid-encoded. The identification of unique genes, particularly those on plasmids, suggests an evolutionary strategy favoring horizontal gene transfer and niche adaptation. The effector repertoire included proteins with domains characteristic of host interaction strategies, such as ankyrin repeats and protein kinases. Comparative analyses showed that while L. lytica shares core virulence traits with other Legionella species, it has distinct features that may contribute to its adaptability and pathogenic potential. These findings underscore the genomic diversity within the genus and contribute to a deeper understanding of Legionella's ecological and clinical significance. A custom web application was developed using the R Shiny library, enabling users to interactively explore the expanded Legionella pangenome through UpSet plots.\n\nComparative analysis of Legionella lytica genome identifies specific metabolic traits and virulence factors.", "token_count": 421, "char_count": 1748, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6833, "quality_score": 0.8417, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:17.181177", "source": { "split": "train_shard_00000", "doc_id": 480 }, "chunk_id": "train_shard_00000_480_0", "global_id": 536 }, { "text": "This study was to examine the relationship between preexposure to salt and stress-responsive resistance to acid, bile salt, and heat in Cronobacter sakazakii, Salmonella enterica serovar Enteritidis, Bacillus cereus, and Staphylococcus aureus. Stationary phase-grown cultures of C. sakazakii, S. Enteritidis, B. cereus or St. aureus were subjected to elevated concentrations of salt (maximally 14.0%), and the cells of each bacterium were allowed to grow at 37 °C for consecutive 6 d. The 6-d habituated cells were then subjected to acid (pH 2.0), 10% bile salt, and heat (60 °C) stresses. C. sakazakii, S. Enteritidis, and St. aureus were more sensitive to acid after the habituation process than their stationary phase-grown counterparts. Although the 0.5% salt-habituated cells of B. cereus better survived at a subsequent acid challenge than did the nonhabituated cells of this bacterium, there were no significant (p< 0.05) differences in the Gompertz-derived growth kinetics between salt-habituated and nonhabituated cultures. Similarly, C. sakazakii and S. Enteritidis cells preexposed to salt was far more heat-sensitive, whereas the preexposure of B. cereus and St. aureus to 0.5 and 8.0% salt, respectively, resulted in their increased survival against heat as compared with their nonhabituated control. Nevertheless, the resultant growth parameters revealed that salt has no clear inducive effect on the acquisition of resistance responses to heterogeneous stresses. Overall, the habituation to different concentrations of salt may variably influence the ability of C. sakazakii, S. Enteritidis, B. cereus, and St. aureus to resist acid, bile salt, and heat stresses.", "token_count": 480, "char_count": 1678, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5447, "quality_score": 0.7724, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:17.827795", "source": { "split": "train_shard_00000", "doc_id": 481 }, "chunk_id": "train_shard_00000_481_0", "global_id": 537 }, { "text": "The habituation to different concentrations of salt may variably influence the ability of Cronobacter sakazakii, Salmonella enterica serovar Enteritidis, Bacillus cereus, and Staphylococcus aureus to resist acid, bile salt, and heat stresses.", "token_count": 69, "char_count": 242, "word_count": 32, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:18.191614", "source": { "split": "train_shard_00000", "doc_id": 481 }, "chunk_id": "train_shard_00000_481_1", "global_id": 538 }, { "text": "Emulsifiers in blends affect lipolysis properties such as emulsion stability, bile salt and lipase adsorption, and mixed micelle formation, influencing lipolysis kinetics. Understanding how different emulsifiers affect these roles during in vitro digestion is often lacking. This study elucidates mechanisms during emulsifier adsorption, lipolysis, and desorption affecting lipolysis kinetics. Interfacial tension kinetics and rheology of adsorbed layers containing lysolecithin (LL), monoolein (MG), or glyceryl polyethyleneglycol ricinoleate (SYN), or their mixes, were monitored during in vitro lipolysis using the OCTOPUS pendant drop technique. Results were compared with in vitro lipolysis kinetics profiles of emulsions with identical emulsifier compositions. SYN hindered bile salts and lipase adsorption, causing lag phases in lipolysis kinetics, but facilitated removal of lipid digestion products. MG had no significant effect. LL-interfaces showed similarities to the emulsifier blend, indicating its dominance in lipolysis kinetics. These findings provide insights into emulsifier effects on lipolysis processes and in vitro lipolysis kinetics.\n\nAn in-depth interfacial study uncovering the effect of emulsifier mixes on small intestinal in vitro lipid digestion kinetics.", "token_count": 329, "char_count": 1285, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:18.753286", "source": { "split": "train_shard_00000", "doc_id": 482 }, "chunk_id": "train_shard_00000_482_0", "global_id": 539 }, { "text": "Cholestasis, a condition marked by bile acid accumulation in the liver and body systems, leads to liver dysfunction and cirrhosis. Currently, ursodeoxycholic acid (UDCA) and obeticholic acid (OCA) are the only two FDA-approved drugs for Cholestasis. Thus, new therapeutic approaches need to be developed. In this study, we validated the liver-protective properties of β-sitosterol (SIT), a key bioactive element abundant in plants, against hepatic toxicity and cholestasis induced by alpha-naphthylisothiocyanate(ANIT), while elucidating its mechanisms of action both in vivo and in vitro. SIT's FXR activation was confirmed via molecular docking and dual-luciferase assays. In the mechanisms of SIT hepatoprotection, the expression levels of bile salt export pump (Bsep) and multidrug resistance protein2 (Mrp2) which are bile acid efflux transporter, and sulfate transferase 2a1 (Sult2a1) which is a bile acid metabolizing enzyme were all increased by SIT, whereas the expression of uptake transporter sodium taurocholate transporting polypeptide (Ntcp), bile acid synthesis enzyme cholesterol 7α-hydroxylase (Cyp7a1) and oxysterol 12α-hydroxylase (Cyp8b1) was decreased by SIT. In addition, SIT alleviated liver inflammation by suppressing inflammatory factor expression. However, FXR antagonist guggulsterone and FXR siRNA abolished SIT's improvements in liver histology, bile acid transporters, and enzymes. Conclusively, through activating FXR, SIT provides a protective effect against hepatotoxicity and cholestasis. SIT might serve as a new potential therapeutic strategy for the treatment of cholestatic liver diseases.\n\nβ-sitosterol protects against ANIT-induced hepatotoxicity and cholestasis via FXR activation.", "token_count": 500, "char_count": 1723, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:19.428662", "source": { "split": "train_shard_00000", "doc_id": 483 }, "chunk_id": "train_shard_00000_483_0", "global_id": 540 }, { "text": "Endosymbiotic bacteria are known to synthesize bioactive compounds which have biotechnological potentials that enhance immune responses by stimulating the production of immune cells. Horse milk is widely known to have nutraceutical and antimicrobial activities; however, there are no scientific reports on its inhibitory effects. VITAPRJS1, isolated from horse milk, showed non-hemolytic properties and was significantly tolerant to bile salt and NaCl. The isolate also exhibited potent antibacterial activity against pathogenic bacterial strains such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus, and Bacillus cereus. The bioactive antibacterial compounds were extracted using dichloromethane and were subsequently purified and identified as butanamine, 2,2-dinitro-N-methyl- through UPLC, GC-MS, and LC-MS analyses. Fourier transform infrared spectroscopy (FTIR) confirmed the presence of functional groups such as alkane, amine, and monosubstituted 1,2-disubstituted. The screened bacterial isolate was identified as Bacillus amyloliquefaciens (OR501558) upon 16S rRNA gene sequencing. To our knowledge, this study represents the first-time report on the presence of Bacillus amyloliquefaciens in horse milk having potent antibacterial activity, highlighting its unexplored potential in biotechnological and pharmaceutical applications.\n\nAntagonistic activity of butanamine 2,2-dinitro-N-methyl- synthesized by endosymbiotic Bacillus amyloliquefaciens VITAPRJS1 acquired from horse milk.", "token_count": 420, "char_count": 1512, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.8459, "entities": { "genes": [ "VITAPRJS1", "OR501558" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:20.077489", "source": { "split": "train_shard_00000", "doc_id": 484 }, "chunk_id": "train_shard_00000_484_0", "global_id": 541 }, { "text": "The release of the first draft of the human pangenome has revolutionized genomic research by enabling access to complex regions like centromeres, composed of extra-long tandem repeats (ETRs). However, a significant gap remains as current methodologies are inadequate for producing sequence alignments that effectively capture genetic events within ETRs, highlighting a pressing need for improved alignment tools. Inspired by UniAligner, we developed a rare match aligner (RaMA), using rare matches as anchors and two-piece affine gap cost to generate complete pairwise alignment that better captures genetic evolution. RaMA also employs parallel computing and the wavefront algorithm to accelerate anchor discovery and sequence alignment, achieving up to 13.66 times faster processing using only 11% of UniAligner's memory. Downstream analysis of simulated data and the CHM13 and CHM1 higher-order repeat (HOR) arrays demonstrates that RaMA achieves more accurate alignments, effectively capturing true HOR structures. RaMA also introduces two methods for defining reliable alignment regions, further refining and enhancing the accuracy of centromeric alignment statistics.\n\nFast sequence alignment for centromeres with RaMA.", "token_count": 266, "char_count": 1225, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7574, "quality_score": 0.8787, "entities": { "genes": [ "CHM13", "CHM1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:20.673549", "source": { "split": "train_shard_00000", "doc_id": 485 }, "chunk_id": "train_shard_00000_485_0", "global_id": 542 }, { "text": "Klebsiella pneumoniae is recognized as an opportunistic pathogen in pigs causing pneumonia, mastitis and diarrhoea, but can also cause mortalities due to septicaemia and meningitis in previously healthy piglets. This study aimed to identify virulence genes present in K. pneumoniae that caused outbreaks of septicaemia in neonatal pigs. The genomes of thirty-eight Australian K. pneumoniae isolates from pigs with septicaemia, meningitis, myocarditis, pneumonia, enteritis and healthy cohorts were sequenced. The presence of antimicrobial resistance, siderophore and enhanced capsule production genes were identified by sequence analysis and verified by either PCR or phenotypic tests. An additional 52 international K. pneumoniae genomes from healthy and clinically affected pigs (28), humans (16), birds (3), one rodent and environmental isolates (4) were included in a pangenome analysis. Porcine septicaemic K. pneumoniae genomes from the UK and Australia clustered together and had higher virulence scores than all other clinical and non-clinical isolates. Septicaemic isolates were predominantly ST25, had enhanced capsule polysaccharide production with K2 capsule type and contained genes for the siderophores aerobactin, salmochelin and yersiniabactin. Septicaemic K. pneumoniae were more likely to have genes encoding the assembly of LPS, fimbriae and adhesins, and enzymes needed for the integration of mobile genetic elements. No single virulence gene was solely associated with isolates causing septicaemia. These findings indicate that there may be genotypes associated with clinical disease outcomes for K. pneumoniae. In the absence of some virulence genes, K. pneumoniae was still able to cause significant disease if the pig's immune system was immature or compromised.\n\nVirulence determinants in Klebsiella pneumoniae associated with septicaemia outbreaks in neonatal pigs.", "token_count": 481, "char_count": 1891, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [ "ST25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:21.329753", "source": { "split": "train_shard_00000", "doc_id": 486 }, "chunk_id": "train_shard_00000_486_0", "global_id": 543 }, { "text": "The Western diet (WD) leads to hepatic lipid metabolism disorders. Previous studies have shown that the bile salt hydrolase 1 (bsh1) gene of Lactobacillus plantarum AR113 attenuates colitis under WD. In this study, we preliminarily explored how AR113 attenuates the hepatic inflammatory response in colitis mice on the WD. Our study suggests that the WD leads to abnormalities in hepatic lipid metabolism and dysbiosis of the gut microflora, and furthermore, there may be a correlation between abnormalities in lipid metabolism and hepatic inflammatory responses. AR113 significantly regulated lipid and bile acid metabolism in the liver of mice treated by WD and Dextran sulfate sodium (DSS), affected the structure of the mouse intestinal flora, and inhibited the expression of Sterol regulatory element-binding protein 1C (SREBP-1C) and P-NF-κB p65 at the protein level, thereby attenuating the hepatic injury phenotype. However, the bsh1 knockout strain did not exhibit the above function.\n\nThe bsh1 gene of Lactobacillus plantarum AR113 ameliorates liver injury in colitis mice.", "token_count": 312, "char_count": 1083, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6149, "quality_score": 0.8075, "entities": { "genes": [ "AR113" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:21.894193", "source": { "split": "train_shard_00000", "doc_id": 487 }, "chunk_id": "train_shard_00000_487_0", "global_id": 544 }, { "text": "A major question in infectious disease research is how bacteria have evolved into highly niche-adapted pathogens with efficient host infection strategies. The plant pathogenic bacterium Xanthomonas campestris is subdivided into pathovars that occupy two distinct niches of the same plant leaf: the vasculature and the mesophyll tissue. Using a pangenome comparison of 94 X. campestris isolates, we discovered that the vasculature-infecting pathovar emerged in one monophyletic clade, has lost its CRISPR-Cas system, and showed an increase in both genomic plasticity and acquisition of virulence factors, such as type III effector proteins, compared with the ancestral pathovar. In addition, we show that the CRISPR spacers of isolates belonging to the ancestral pathovar map to plasmids that circulate in Xanthomonas populations and encode high numbers of transposons and virulence factors, suggesting that CRISPR-Cas restricts gene flow toward this pathovar. Indeed, we demonstrate experimentally reduced plasmid uptake in a CRISPR-Cas-encoding isolate. Based on our data, we propose that the loss of the CRISPR-Cas system was a pivotal step in X. campestris evolution by facilitating increased genome dynamics and the emergence of the vasculature-adapted X. campestris pathovar campestris, a major pathogen of Brassica crops.\n\nEvolution of a vascular plant pathogen is associated with the loss of CRISPR-Cas and an increase in genome plasticity and virulence genes.", "token_count": 376, "char_count": 1467, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:22.472033", "source": { "split": "train_shard_00000", "doc_id": 488 }, "chunk_id": "train_shard_00000_488_0", "global_id": 545 }, { "text": "The main purpose of this study was to optimize the L-citrulline production process using Plackett-Burman and Box-Behnken designs. L-citrulline-producing bacterium BH-01 was isolated from raw buffalo milk. The isolate was tested for probiotic activities such as tolerance to simulated gastric and intestinal juices, antagonistic activity against six antibiotic-resistant bacteria, and temperature tolerance. L-citrulline production and arginine deiminase (ADI) activity were optimized using statistical designs. The bacterial isolate was molecularly identified as Bacillus subtilis strain AUMC B-498 (accession number PP574248.1). The strain exhibited resistance at pH 2.0 and bile salt 0.5% for a two-hour exposure period. It could inhibit the growth of Escherichia coli, Klebsiella pneumonia, Serratia sp., Staphylococcus aureus, methicillin-resistant Staphylococcus aureus (MRSA), and Streptococcus pneumoniae. From the results of statistical optimization, the Plackett-Burman design identified temperature, L-arginine, incubation period, and peptone as the most effective factors among the eight selected variables. Based on these, the Box-Behnken design was used to optimize the factors required to maximize citrulline production. The maximum L-citrulline was 632.5 µg/L, and ADI activity was 1.42 U/mL. Therefore, BH-01 isolated from Buffalo milk might be a promising candidate in food, biotechnological, and pharmaceutical applications due to its dual functionality for citrulline production and probiotic characteristics.\n\nOptimization of citrulline production from a Bacillus subtilis BH-01 isolated from raw buffalo milk.", "token_count": 455, "char_count": 1630, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [ "PP574248" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:23.108899", "source": { "split": "train_shard_00000", "doc_id": 489 }, "chunk_id": "train_shard_00000_489_0", "global_id": 546 }, { "text": "Tri-ortho-cresyl phosphate (TOCP) is an environmental toxic pollutant, belonging to the chemical class of organophosphorus flame retardants and repressing hepatic membrane drug transporter expression. The present study investigated whether the liver canalicular bile salt efflux pump (BSEP) may also be targeted by TOCP. TOCP used at a non-cytotoxic concentration of 10 μM for 48 h was demonstrated to decrease BSEP mRNA expression in cultured hepatic HepaRG cells (by a 4.4-fold factor) and primary human hepatocytes (by a 2.5-fold factor). This effect was concentration-dependent (IC\n\nRepression of bile salt efflux pump expression by tri-ortho-cresyl phosphate in cultured human hepatic cells.", "token_count": 198, "char_count": 696, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7677, "quality_score": 0.8838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:23.558456", "source": { "split": "train_shard_00000", "doc_id": 490 }, "chunk_id": "train_shard_00000_490_0", "global_id": 547 }, { "text": "Dahi, a traditional yet underexplored fermented milk product from Pakistan, harbors diverse lactic acid bacteria (LAB) that have potential as probiotics. These bacteria could be used for therapeutic purposes, beneficial modulation of gut microbiota, and in the formulation of functional foods and feeds. This study aimed to isolate and characterize probiotic LAB from dahi, assess their survival in simulated gastrointestinal conditions, and evaluate their safety and probiotic potential, both phenotypically and genotypically. A total of 143 isolates from 37 samples were evaluated for probiotic traits, including acid and bile tolerance, antibacterial activity, cholesterol-lowering capacity, and antioxidant activity. The strains were also tested for antibiotic sensitivity and safety through in vitro tests and genomic analysis. A multi-strain probiotic consortium was developed and tested for enhanced functionality. Out of 143 isolates, 62 LAB strains were identified. These strains demonstrated significant survival under acidic (pH 2) and bile conditions. Antibacterial activity against pathogens ranged from 51 to 88%. The strains exhibited high cholesterol removal (up to 98%) and antioxidant activity (up to 76%). Genomic analysis revealed the presence of key probiotic-related genes, including those for acid resistance, bile salt hydrolase, and adhesion. All strains were sensitive to EFSA-recommended antibiotics and exhibited no hemolytic or DNase activity, confirming their safety. The multi-strain consortium showed superior probiotic potential and survival in simulated gastrointestinal conditions. LAB strains isolated from dahi possess strong probiotic potential, confirmed through in vitro and genomic safety assessments. The multi-strain consortium holds promise for applications.\n\nProbiotic characteristics and survival of a multi-strain lactic acid bacteria consortium in simulated gut model.", "token_count": 471, "char_count": 1916, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5853, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:24.202062", "source": { "split": "train_shard_00000", "doc_id": 491 }, "chunk_id": "train_shard_00000_491_0", "global_id": 548 }, { "text": "India harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome.\n\nAdvancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus.", "token_count": 115, "char_count": 528, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7714, "quality_score": 0.8857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:24.589636", "source": { "split": "train_shard_00000", "doc_id": 492 }, "chunk_id": "train_shard_00000_492_0", "global_id": 549 }, { "text": "Probiotics refer to live bacteria that, when administered in a sufficiently, exert a beneficial influence on human health. Due to the probiotics' beneficial health advantages, dietary supplements are expanding rapidly as a self-care interest worldwide. It may be beneficial to administer probiotic strains resistant to antibiotics concurrently with an antibiotic treatment. Our study investigates nineteen dairy products collected from Egyptian markets, isolated, identified and underwent a characterization for probiotic features under demanding circumstances as NaCl, acid and bile salt environments. The antibiotic sensitivity test was performed later to the antimicrobial assessment against widespread both negative and positive gram-stained bacteria infecting humans, along with the antiviral evaluation against (SARS-CoV-2), the virus that has disturbed the world recently.\n\nComplete genome sequencing and probiotic characterization of promising lactic acid bacterial strains isolated from dairy products in Egyptian markets.", "token_count": 213, "char_count": 1031, "word_count": 135, "semantic_coherence": 1, "information_density": 0.763, "quality_score": 0.8815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:25.057825", "source": { "split": "train_shard_00000", "doc_id": 493 }, "chunk_id": "train_shard_00000_493_0", "global_id": 550 }, { "text": "Process and culture medium composition in bioreactor could be optimized in order to find the best conditions that improve survival of probiotic microorganism under exposure to gastric conditions such low pH and bile salts. Therefore, this study aimed to optimize agitation, yeast extract, and di-sodium phosphate (Na\n\nImproving the survival under gastric conditions of a potential multistrain probiotic produced in co-culture.", "token_count": 101, "char_count": 426, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7705, "quality_score": 0.8852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:25.435190", "source": { "split": "train_shard_00000", "doc_id": 494 }, "chunk_id": "train_shard_00000_494_0", "global_id": 551 }, { "text": "Currently, reports of the presence of emerging pathogens in cheeses are low and new outbreaks have occurred at an alarming rate, with the Vibrio and Aeromonas genera being the main causes of gastroenteritis in the world. Therefore, Multi-Omics integration has been a strategy to identify and develop detection methods for these pathogens in food. We investigated the presence of emerging pathogens in artisanal cheeses and predicted proteins with immunogenic potential, in silico, for food diagnostics. For this, multiomics integration was used: (a) metagenomics; (b) subtractive genomics; and (c) pan-genomics. Eight species of the genera Vibrio and Aeromonas were identified, the latter being the most abundant (89.7%) and identified in eight regions, with emphasis on the species A. caviae and A. veronii. Pan-genomic analyses revealed intra- and inter-species differences in both genera. Essential, non-cytoplasmic proteins were identified, without homology and with immunological potential for the species researched. Functional annotation of genes present in pan-genomic subsets reveals functionality between the core genome (transcription; amino acid transport and metabolism; and inorganic ion transport and metabolism) and the shared genome (signal transduction and carbohydrate transport and metabolism). A reinterpretation of the genomic plasticity of V. furnissii reveals the presence of mobile genetic elements critical for virulence in human isolates and the RTX toxin, also identified in this species, is present in the pathogenicity islands of V. alginolyticus and V. fluvialis. Collectively, the results provide important information for the development of a diagnostic strategy for emerging pathogens in food using immunoassays.\n\nMetagenomic analysis and proteins prediction of emerging pathogens in artisanal cheese.", "token_count": 443, "char_count": 1835, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5953, "quality_score": 0.7977, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:26.062217", "source": { "split": "train_shard_00000", "doc_id": 495 }, "chunk_id": "train_shard_00000_495_0", "global_id": 552 }, { "text": "Genomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor cost-efficiency of short-read (SR) sequencing. Oxford Nanopore long-read sequencing (ONT-LR), which allows fast on-site analysis with comparatively low costs, could provide an alternative. Despite ONT-LR raw read accuracy improvement, evidence for methylation-based errors accumulates. PCR-based library preparation, suggested as a solution, presumably poses difficulties for GC-rich bacteria. We challenged ONT-LR-based cgMLST using the highly GC-rich pathogen\n\nImproving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens like", "token_count": 201, "char_count": 855, "word_count": 107, "semantic_coherence": 1, "information_density": 0.8318, "quality_score": 0.9159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:26.520118", "source": { "split": "train_shard_00000", "doc_id": 496 }, "chunk_id": "train_shard_00000_496_0", "global_id": 553 }, { "text": "A pan-genome is a compilation of the common and unique genomes found in a given species. It incorporates the genetic information from all of the genomes sampled, producing a big and diverse set of genetic material. Pan-genomic analysis has various advantages over typical genomics research. It creates a vast and varied spectrum of genetic material by combining the genetic data from all the sampled genomes. Comparing pan-genomics analysis to conventional genomic research, there are a number of benefits. Although the most recent era of pan-genomic studies has used cutting-edge sequencing technology to shed fresh light on biological variety and improvement, the potential uses of pan-genomics in improvement have not yet been fully realized. Pan-genome research in various organisms has demonstrated that missing genetic components and the detection of significant Structural Variants (SVs) can be investigated using pan-genomic methods. Many individual-specific sequences have been linked to biological adaptability, phenotypic, and key economic attributes. This study aims to focus on how pangenome analysis uncovers genetic differences in various organisms, including human, and their effects on phenotypes, as well as how this might help us comprehend the diversity of species. The review also concentrated on potential problems and the prospects for future pangenome research.\n\nPan-genomics: Insight into the Functional Genome, Applications, Advancements, and Challenges.", "token_count": 305, "char_count": 1480, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:27.080064", "source": { "split": "train_shard_00000", "doc_id": 497 }, "chunk_id": "train_shard_00000_497_0", "global_id": 554 }, { "text": "Probiotic bacteria improve human health by secreting pro-microbial substances, balancing intestinal flora, binding to the mucous membrane and epithelium, strengthening the intestinal epithelial barrier, and creating interactions between the gastrointestinal microbiota and the immune system. This study aimed to investigate the probiotic potential, biofilm-related gene expression and anti-biofilm capabilities of\n\nExamining the impact of probiotic", "token_count": 107, "char_count": 448, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7636, "quality_score": 0.8818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:27.464669", "source": { "split": "train_shard_00000", "doc_id": 498 }, "chunk_id": "train_shard_00000_498_0", "global_id": 555 }, { "text": "The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.\n\nExtensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.", "token_count": 146, "char_count": 627, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:27.912942", "source": { "split": "train_shard_00000", "doc_id": 499 }, "chunk_id": "train_shard_00000_499_0", "global_id": 556 }, { "text": "Taylorella equigenitalis is the causative agent of contagious equine metritis, an internationally regulated sexually-transmitted infection in horses, which is of great concern as it usually results in temporary infertility. Taylorella asinigenitalis, the second member of the genus, is mainly found in donkeys and is considered non-pathogenic, although a first natural outbreak was reported in 2019 in the United Arab Emirates. Multilocus sequence typing (MLST) is currently used to study the epidemiology of Taylorella spp. but, while highly transposable and reproducible, it only focuses on < 0.5 % of the genome (seven genes). We therefore aimed to develop a robust core genome MLST (cgMLST) based on the analysis of 370 T. equigenitalis and 68 T. asinigenitalis genomes belonging to 46 and 18 sequence types (STs), respectively. Typing results based on 1333 loci (84.0 % of the genome) from T. equigenitalis genomes and 1255 loci (80.3 %) from T. asinigenitalis genomes showed that the discriminatory power of both species-specific cgMLSTs was greater than that of MLST, with 368 and 68 distinct core genome STs (cgSTs), respectively. Clustering was congruent between the cgMLST and MLST methods, with few inconsistencies for T. equigenitalis. Maximum allelic distance between epidemiologically-related strains was used to define cgMLST clustering thresholds, set at ≤ 15 and 20 allelic distances for T. equigenitalis and T. asinigenitalis, respectively. These parameters grouped the cgSTs into 47 and 11 clonal groups (CGs), respectively", "token_count": 462, "char_count": 1542, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6435, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:28.549933", "source": { "split": "train_shard_00000", "doc_id": 500 }, "chunk_id": "train_shard_00000_500_0", "global_id": 557 }, { "text": "Overall, the cgMLST method outperformed conventional MLST in distinguishing clonal strains from epidemiologically-linked strains, supporting the hypothesis that typing based on a few housekeeping genes does not always accurately reflect genomic relatedness between strains, and making cgMLST more suitable for outbreak investigations.\n\nCore genome multilocus sequence typing schemes for epidemiological investigation of Taylorella equigenitalis and Taylorella asinigenitalis.", "token_count": 104, "char_count": 475, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8772, "quality_score": 0.9386, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:28.937741", "source": { "split": "train_shard_00000", "doc_id": 500 }, "chunk_id": "train_shard_00000_500_1", "global_id": 558 }, { "text": "The safety of probiotics in aquaculture, particularly concerning the transfer of antibiotic resistance genes (ARGs), has become a significant concern. This study aims to isolate antibiotic-sensitive Bacillus strains from the gut of Penaeus vannamei and evaluate the potential for practical application in shrimp farming. The strain was tested for antibiotic sensitivity to 10 commonly used antibiotics, and the minimum inhibitory concentration (MIC) values were determined. Morphological analysis and 16S rRNA sequencing confirmed its identity. The probiotic properties, antibacterial activity, and feeding effects on P. vannamei were also assessed. The results showed that Bacillus sp. J3 and Lysinibacillus sp. R4 were generally sensitive to antibiotics but resistant to sulfapyridine and ciprofloxacin. Both strains exhibited acid and bile salt resistance in vitro and performed well in extracellular hydrolase tests. J3 demonstrated co-coagulation effects against Aeromonas veronii, Vibrio parahaemolyticus, and Vibrio alginolyticus, with coagulation rates over 35%, while R4 showed the highest co-coagulation rate (47%) against V. alginolyticus. Both strains exhibited strong antibacterial activity, with inhibition zones ranging from 20 to 22.5 mm. Preliminary shrimp farming tests showed that R4 improved shrimp growth and survival rates compared to the control, and its combination with Bacillus coagulans resulted in even greater efficacy. These findings suggest that Lysinibacillus sp. R4 holds promise as a probiotic for enhancing P. vannamei growth, and future research could explore the use of multiple probiotic combinations in aquaculture.\n\nEvaluation of Antibiotic-Sensitive Bacillus Strain as a Potential Probiotic for Enhanced Growth in Penaeus vannamei.", "token_count": 466, "char_count": 1772, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.8189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:29.922156", "source": { "split": "train_shard_00000", "doc_id": 501 }, "chunk_id": "train_shard_00000_501_0", "global_id": 559 }, { "text": "The enrichment of galactooligosaccharides (GOS), synthesized by whole cells of Kluyveromyces marxianus 3551 in a 5.0-L bioreactor, was investigated in this study. The synthesized sugar mixture containing 17.89% (w/w of total carbohydrates) of GOS with 15.57% (w/w of total carbohydrates) of lactose, and 66.54% (w/w of total carbohydrates) monosaccharides as impurities, was subjected to nanofiltration for enrichment of GOS. Three distinct spiral wound membranes, namely, NFPS-01(polysulfone), NFCA-02 (cellulose acetate), and NFPES-03 (polyethersulfone) were tested out of which the NFPES-03 performed the best for fractionation of the GOS mixture. The polyethersulphone membrane (cut-off 400-1000 Da) was evaluated at 30 ℃ and 50 ℃, at different transmembrane pressures or TMP (15, 20, 25 bar) and a combination of high temperature (50 ℃) and low pressure (15 bar) gave the greatest difference in the trisaccharide and disaccharide/monosaccharide rejection percentages, resulting in enrichment of GOS. An analysis of the sugar concentrations in the retentate samples by high-performance liquid chromatography indicated the percentage recovery of GOS in the integrated process to be 88.8%. Measurement of the growth profile of several microbes on the nano-filtered GOS demonstrated its effectiveness as a prebiotic source.\n\nNanofiltration-based purification process for whole-cell transformed prebiotic galactooligosaccharides.", "token_count": 453, "char_count": 1429, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6615, "quality_score": 0.8308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:30.561873", "source": { "split": "train_shard_00000", "doc_id": 502 }, "chunk_id": "train_shard_00000_502_0", "global_id": 560 }, { "text": "Listeria monocytogenes is a foodborne pathogen that can lead to severe pregnancy outcomes. This study reports the clinical and genomic characteristics of a Listeria-mediated stillbirth identified in January 2022 through the Child Health and Mortality Prevention Surveillance (CHAMPS) project in Bangladesh. The Lm-BD-CHAMPS-01 isolate was recovered from the blood and cerebrospinal fluid (CSF) of a male stillborn. Maternal history, clinical, and demographic data were collected by the CHAMPS surveillance platform. An expert panel evaluated all reports to determine the role of L. monocytogenes infection in the causal chain of stillbirth. Genomic characterization included multilocus sequence typing (MLST), core genome MLST (cgMLST), serotyping, and the presence or absence of virulence genes. Genetic divergence and phylogenetic analyses were conducted to determine the relationship with other reported isolates globally.\n\nA novel virulent core genome multilocus sequence type CT 11424 of Listeria monocytogenes isolate causing stillbirth in Bangladesh.", "token_count": 263, "char_count": 1057, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7153, "quality_score": 0.8576, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:31.108211", "source": { "split": "train_shard_00000", "doc_id": 503 }, "chunk_id": "train_shard_00000_503_0", "global_id": 561 }, { "text": "Milk is a rich source of probiotics, particularly lactic acid bacteria (LAB), which have been shown to promote gut health, support the immune system, enhance digestion, and prevent pathogen colonization. This study aimed to isolate and identify LAB strains from giant panda (Ailuropoda melanoleuca) milk, evaluate their probiotic properties, and analyze the genomic characteristics of a promising strain. Thirteen LAB strains were isolated from 12 samples of giant panda milk. Among all LAB strains, Lactiplantibacillus plantarum PM8 (PM8) demonstrated probiotic properties and safety features. It exhibited strong growth performance, high antipathogenic activity against four pathogens, and strong survival rates under simulated gastrointestinal conditions. PM8 also showed excellent adhesion capabilities to Caco-2 cells. Additionally, safety assessment revealed no hemolysin production and minimal antibiotic resistance, making it a promising candidate for probiotic applications. The genome of PM8 consists of 3,227,035 bp with a GC content of 44.60% and contains 3171 coding sequences, including 113 carbohydrate-active enzyme genes and genes related to exopolysaccharides synthesis, vitamin B biosynthesis, adhesion, antioxidant activity, and bile salt hydrolysis. Notably, it contains genes involved in nonribosomally synthesized secondary metabolite and bacteriocin production. The genomic safety analysis confirmed that PM8 lacks the capacity to transmit bacterial antimicrobial resistance and is non-pathogenic to both humans and animals. These findings suggest that PM8 holds considerable potential for enhancing gut health and supporting the development of safe probiotic products.\n\nProbiotic Characteristics and Whole Genome Analysis of Lactiplantibacillus plantarum PM8 from Giant Panda (Ailuropoda melanoleuca) Milk.", "token_count": 454, "char_count": 1831, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6996, "quality_score": 0.8498, "entities": { "genes": [ "PM8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:31.755026", "source": { "split": "train_shard_00000", "doc_id": 504 }, "chunk_id": "train_shard_00000_504_0", "global_id": 562 }, { "text": "Competitive exclusion is conventionally believed to prevent the establishment of a secondary strain of the same bacterial species in the gut microbiome, raising concerns for the deployment of live bacterial therapeutics (LBTs), especially if the bacterial chassis is a strain native to the gut. In this study, we investigated factors influencing competition dynamics in the murine gut using isogenic native\n\nGut Competition Dynamics of Live Bacterial Therapeutics Are Shaped by Microbiome Complexity, Diet, and Therapeutic Transgenes.", "token_count": 119, "char_count": 534, "word_count": 76, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:32.154135", "source": { "split": "train_shard_00000", "doc_id": 505 }, "chunk_id": "train_shard_00000_505_0", "global_id": 563 }, { "text": "The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations.\n\nDeveloping pangenomes for large and complex plant genomes and their representation formats.", "token_count": 124, "char_count": 711, "word_count": 87, "semantic_coherence": 1, "information_density": 0.8046, "quality_score": 0.9023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:32.564525", "source": { "split": "train_shard_00000", "doc_id": 506 }, "chunk_id": "train_shard_00000_506_0", "global_id": 564 }, { "text": "Pseudomonas aeruginosa has increasing clinical relevance and commonly occupies the cystic fibrosis (CF) airways. Its ability to colonize and persist in diverse niches is attributed to its large accessory genome, where prophages represent a common feature and may contribute to its fitness and persistence. We focused on the CF airways niche and used 197 longitudinal isolates from 12 patients persistently infected by P. aeruginosa. We computationally predicted intact prophages for each longitudinal group and scored their long-term persistence. We then confirmed prophage inducibility and mapped their location in the host chromosome with lysate sequencing. Using comparative genomics, we evaluated prophage genomic diversity, long-term persistence, and level of genomic maintenance. Our findings support previous findings that most P. aeruginosa genomes harbour prophages some of which can self-induce, and that a common CF-treating antibiotic, ciprofloxacin, can induce prophages. Induced prophage genomes displayed high diversity and even genomic novelty. Finally, all induced prophages persisted long-term with their genomes avoiding gene loss and degradation over 4 years of host replication in the stressful CF airways niche. This and our detection of phage genes, which contribute to host competitiveness and adaptation, lends support to our hypothesis that the vast majority of prophages detected as intact and inducible in this study facilitated their host fitness and persistence.\n\nPseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in cystic fibrosis lungs.", "token_count": 385, "char_count": 1627, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:33.204146", "source": { "split": "train_shard_00000", "doc_id": 507 }, "chunk_id": "train_shard_00000_507_0", "global_id": 565 }, { "text": "Ischemia-reperfusion injury (IRI) and bile salt toxicity are significant contributors to post-transplant cholangiopathy. Ferroptosis appears to play a critical role in intrahepatic bile duct injury induced by ischemia-reperfusion (I/R) and bile salt toxicity. Our study aimed to elucidate the role of ferroptosis in bile duct injuries and its potential as a therapeutic target for liver diseases. Mouse models of liver ischemia-reperfusion (I/R) and α-naphthyl isocyanate (ANIT)-induced liver cholestasis were employed to investigate the role of ferroptosis in intrahepatic bile duct injury in vivo. Hypoxia-reoxygenation (H/R) and bile salt treatment models were utilized to simulate the post-transplant bile duct injury process in vitro. In mouse models of liver I/R and cholestasis, we observed a downregulation of glutathione peroxidase 4 (GPX4) and an upregulation of lipid peroxidation levels in bile duct cells. Furthermore, the ferroptosis inhibitor Liproxstatin-1 (Lip-1) significantly attenuated intrahepatic bile duct injuries. Ferroptosis inhibitors alleviated cell death and lipid peroxide accumulation in human intrahepatic biliary epithelial cells (HiBECs) subjected to H/R or glycochenodeoxycholate (GCDCA) treatment. GCDCA treatment led to ferroptosis in HiBECs along with ferritin degradation. Inhibition of autophagy alleviated GCDCA-induced bile duct cell death. Our study suggested that ferroptosis played an important role of in the intrahepatic bile duct injury during I/R or cholestasis.\n\nInhibition of ferroptosis protects intrahepatic bile duct cells against ischemia-reperfusion and bile salt toxicity.", "token_count": 489, "char_count": 1629, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5297, "quality_score": 0.7648, "entities": { "genes": [ "GPX4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:33.851626", "source": { "split": "train_shard_00000", "doc_id": 508 }, "chunk_id": "train_shard_00000_508_0", "global_id": 566 }, { "text": "Bile salts are crucial microbe-selective inhibitors present in the intestinal tracts of humans and other animals. Environmental and clinical strains of Vibrio parahaemolyticus (V. parahaemolyticus) exhibited different biofilm-forming abilities under bile salt incubation. In order to find an effective way to eliminate biofilm, in this study, environmental strains were subjected to mouse gastrointestinal (GI) stimulation and cultured in medium containing 0.06 % bile salts. The effects of GI stimulation on V. parahaemolyticus biofilm formation were evaluated by biofilm cells assay, atomic force microscopy (AFM) assay, confocal laser scanning microscopy (CLSM) assay, extracellular polysaccharide (EPS) assay, and salmon surface biofilm formation assay. The results showed that GI stimulation diminished the ability of V. parahaemolyticus to form biofilm, significantly reduced biofilm cells, decreased the level of EPS, and destroyed the biofilm structure. For the biofilm formed by V. parahaemolyticus after GI stimulation, AFM observed that the appearance of the biofilm became inhomogeneous and rough, and CLSM observed that the 3D structure of the biofilm became dispersed and sparse. GI stimulation reduced the ability of V. parahaemolyticus to form biofilms on the surface of salmon containing 0.06 % bile salts at both 12 h and 24 h, as evidenced by a decrease in the number of adherent cells. Comparing biofilms formed by tdh-positive V. parahaemolyticus before and after undergoing GI stimulation, a total of 1169 differentially expressed genes (DEGs) were identified by RNA sequencing. And 10 of the biofilm-related genes displayed significant down-regulation after GI stimulation. Enrichment analysis of DEGs revealed that affecting the switch between succinate and fumarate in the TCA cycle could inhibit biofilm formation. This study offers new insights into strategies for preventing biofilm formation by foodborne pathogens.", "token_count": 505, "char_count": 1944, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5791, "quality_score": 0.7896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:34.506440", "source": { "split": "train_shard_00000", "doc_id": 509 }, "chunk_id": "train_shard_00000_509_0", "global_id": 567 }, { "text": "Antibiofilm mechanism of mouse gastrointestinal stimulation against Vibrio parahaemolyticus under bile salt culture.", "token_count": 30, "char_count": 116, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:34.871596", "source": { "split": "train_shard_00000", "doc_id": 509 }, "chunk_id": "train_shard_00000_509_1", "global_id": 568 }, { "text": "Meiosis is generally a fair process: each chromosome has a 50% chance of being included into each gamete. However, meiosis can become aberrant with some chromosomes having a higher chance of making it into gametes than others. Yet, why and how such systems evolve remains unclear. Here, we study the unusual reproductive genetics of mealybugs, where only maternal-origin chromosomes are included in gametes during male meiosis, while paternal chromosomes are eliminated. One species-Pseudococcus viburni-has a segregating B chromosome that drives by escaping paternal genome elimination. We present whole genome and gene expression data from lines with and without B chromosomes. We identify B-linked sequences including 204 protein-coding genes and a satellite repeat that makes up a significant proportion of the chromosome. The few paralogs between the B and the core genome are distributed throughout the genome, arguing against a simple, or at least recent, chromosomal duplication of one of the autosomes to create the B. We do, however, find one 373 kb region containing 146 genes that appears to be a recent translocation. Finally, we show that while many B-linked genes are expressed during meiosis, most of these are encoded on the recently translocated region. Only a small number of B-exclusive genes are expressed during meiosis. Of these, only one was overexpressed during male meiosis, which is when the drive occurs: an acetyltransferase involved in H3K56Ac, which has a putative role in meiosis and is, therefore, a promising candidate for further studies.\n\nThe B Chromosome of Pseudococcus viburni: A Selfish Chromosome that Exploits Whole-Genome Meiotic Drive.", "token_count": 429, "char_count": 1679, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:35.497199", "source": { "split": "train_shard_00000", "doc_id": 510 }, "chunk_id": "train_shard_00000_510_0", "global_id": 569 }, { "text": "International travel facilitates the acquisition and carriage of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E). We describe genomes of predominant ESBL-E clones detected before and after travel among subjects departing from Rio de Janeiro, Brazil, during 2015-2021, and genomes publicly available from countries visited by travelers. WGS (Illumina NovaSeq) was performed on 70 ESBL-E isolates from 66 travelers (18 pre- and 52 post-travel). Sequence type (ST), antimicrobial resistance (AMR), virulence genes, and plasmids were determined by Center for Genomic Epidemiology tools. Phylogenetic trees were constructed with each of the most frequent ST of travelers' genomes (TG) and genomes with the same ST from Enterobase (EG). Other analyses were performed with Prokka, Roary, SNP-sites, and FastTree. Trees were visualized with iTOL. Among 70 ESBL-E, the clonal composition was quite diverse, with 41 different ST, with predominance before of CC10 and CC131, and after travel, CC10, CC131, CC69, and CC38, and three ST described for the first time: ST14408 and ST14412 (CC10), and ST4411 (CC20). Core genome phylogenetic analysis revealed 17 clusters, eight of which formed by post-travel TG and EG detected in the same country visited by traveler. We observed an increased number and diversity of AMR genes, plasmids, and virulence genes in post-travel isolates, although we only found statistical significance for IncFIB plasmid. Genome clustering supported the high-risk clone acquisition and AMR during international trips. More than half of detected clones were related to ExPEC and showed an increased number and diversity of AMR and virulence-related genes, as well as plasmids in post-travel isolates.", "token_count": 487, "char_count": 1735, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8175, "entities": { "genes": [ "CC38", "ST4411", "ST14412", "CC10", "ST14408", "CC20", "CC131", "CC69" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:36.137363", "source": { "split": "train_shard_00000", "doc_id": 511 }, "chunk_id": "train_shard_00000_511_0", "global_id": 570 }, { "text": "Whole genome sequencing and phylogenetic analysis to examine acquisition of Escherichia coli clones during international travel.", "token_count": 30, "char_count": 128, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:36.491342", "source": { "split": "train_shard_00000", "doc_id": 511 }, "chunk_id": "train_shard_00000_511_1", "global_id": 571 }, { "text": "Adverse drug reactions (ADR) remain a challenge in modern healthcare, particularly given the increasing complexity of therapeutics. An anticonvulsant medicine which is frequently used in treatment of epilepsy and other neurological conditions is valproic acid (VPA), is frequently associated with hepatotoxicity, a severe ADR that complicates its clinical use, which can take two different forms: Type I, which is defined by dose-dependent and reversible liver damage, and Type II, an idiosyncratic reaction that can result in severe liver failure, frequently complicates its clinical application. Oxidative stress, the creation of reactive metabolites, mitochondrial dysfunction, carnitine shortage, immune-mediated reactions, glutathione depletion, and blockage of the bile salt export pump (BSEP) are some of the numerous underlying mechanisms of VA-induced hepatic damage. The production of reactive oxygen species and the liver's antioxidant protection are out of balance as a cause of oxidative stress, which is a significant factor in VPA intoxication. VPA can also accelerate the build-up of fatty acids, which increases the risk of steatosis, due to its interaction with the metabolism of carnitine. Immune-mediated processes have been shown to increase liver injury, implying that the immunity system may possibly be involved in VPA hepatotoxicity. Hepatocyte injury and cholestasis are caused by BSEP inhibition, which impairs bile flow. The complex interaction between biochemical and cellular mechanisms that underlie valproic acid's hepatotoxic potential calls for additional research to clarify the precise pathways implicated and create mitigation techniques for this ADR.\n\nMechanisms involved in the valproic acid-induced hepatotoxicity: a comprehensive review.", "token_count": 417, "char_count": 1778, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6599, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:37.108644", "source": { "split": "train_shard_00000", "doc_id": 512 }, "chunk_id": "train_shard_00000_512_0", "global_id": 572 }, { "text": "Potato is the world's most important nongrain crop. In this study, to assess genetic diversity within the Petota section, 29 genomes from Petota and Etuberosum sections were newly de novo assembled and 248 accessions of wild potatoes, landraces, and modern cultivars were re-sequenced at >25× depth. Subsequently, a graph-based pangenome was constructed using DM8.1 as the backbone, integrating194,330 nonredundant structural variants. To characterize the metabolome of tubers and illuminate the genomic basis of metabolic traits, LC-MS/MS was employed to obtain the metabolome of 157 accessions, and 9,321 structural variants (SVs) were detected to be significantly associated with 1,258 distinct metabolites via PAV (presence and absence variations)-based metabolomics-GWAS analysis, including metabolites of flavonoids, phenolic acids, and phospholipids. To facilitate the utilization of pangenome resources, a comprehensive platform, the Potato Pangenome Database (PPDB), was developed. Our study provides a comprehensive genomic resource for dissecting the genomic basis of agronomic and metabolic traits in potato, which will accelerate functional genomics studies and genetic improvements in potato.\n\nGraph-based pangenome provides insights into structural variations and genetic basis of metabolic traits in potato.", "token_count": 336, "char_count": 1323, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8343, "entities": { "genes": [ "DM8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:37.674995", "source": { "split": "train_shard_00000", "doc_id": 513 }, "chunk_id": "train_shard_00000_513_0", "global_id": 573 }, { "text": "A pangenome is the sum of the genetic information of all individuals in a species or a population. Genomics research has been gradually shifted to a paradigm using a pangenome as the reference. However, in disease genomics study, pangenome-based analysis is still in its infancy. In this study, we introduced a graph-based pangenome GGCPan from 185 patients with gastric cancer. We then systematically compared the cancer genomics study results using GGCPan, a linear pangenome GCPan, and the human reference genome as the reference. For small variant detection and microsatellite instability status identification, there is little difference in using three different genomes. Using GGCPan as the reference had a significant advantage in structural variant identification. A total of 24 candidate gastric cancer driver genes were detected using three different reference genomes, of which eight were common and five were detected only based on pangenomes. Our results showed that disease-specific pangenome as a reference is promising and a whole set of tools are still to be developed or improved for disease genomics study in the pangenome era.\n\nGastric cancer genomics study using reference human pangenomes.", "token_count": 266, "char_count": 1211, "word_count": 183, "semantic_coherence": 1, "information_density": 0.5738, "quality_score": 0.7869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:38.227147", "source": { "split": "train_shard_00000", "doc_id": 514 }, "chunk_id": "train_shard_00000_514_0", "global_id": 574 }, { "text": "Genome graphs, including the recently released draft human pangenome graph, can represent the breadth of genetic diversity and thus transcend the limits of traditional linear reference genomes. However, there are no genome-graph-compatible tools for analyzing whole genome bisulfite sequencing (WGBS) data. To close this gap, we introduce methylGrapher, a tool tailored for accurate DNA methylation analysis by mapping WGBS data to a genome graph. Notably, methylGrapher can reconstruct methylation patterns along haplotype paths precisely and efficiently. To demonstrate the utility of methylGrapher, we analyzed the WGBS data derived from five individuals whose genomes were included in the first Human Pangenome draft as well as WGBS data from ENCODE (EN-TEx). Along with standard performance benchmarking, we show that methylGrapher fully recapitulates DNA methylation patterns defined by classic linear genome analysis approaches. Importantly, methylGrapher captures a substantial number of CpG sites that are missed by linear methods, and improves overall genome coverage while reducing alignment reference bias. Thus, methylGrapher is a first step toward unlocking the full potential of Human Pangenome graphs in genomic DNA methylation analysis.\n\nmethylGrapher: genome-graph-based processing of DNA methylation data from whole genome bisulfite sequencing.", "token_count": 315, "char_count": 1363, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:38.781658", "source": { "split": "train_shard_00000", "doc_id": 515 }, "chunk_id": "train_shard_00000_515_0", "global_id": 575 }, { "text": "Through biochemical transformation of host-derived bile acids (BAs), gut bacteria mediate host-microbe crosstalk and sit at the interface of nutrition, the microbiome, and disease. BAs play a crucial role in human health by facilitating the absorption of dietary lipophilic nutrients, interacting with hormone receptors to regulate host physiology, and shaping gut microbiota composition through antimicrobial activity. Bile acid deconjugation by bacterial bile salt hydrolase (BSH) has long been recognized as the first necessary BA modification required before further transformations can occur. Here, we show that BSH activity is common among human gut bacterial isolates spanning seven major phyla. We observed variation in both the extent and the specificity of deconjugation of BAs among the tested taxa. Unexpectedly, we discovered that certain strains were capable of directly dehydrogenating conjugated BAs via hydroxysteroid dehydrogenases (HSD) to produce conjugated secondary BAs. These results challenge the prevailing notion that deconjugation is a prerequisite for further BA modifications and lay a foundation for new hypotheses regarding how bacteria act individually or in concert to diversify the BA pool and influence host physiology.\n\nInvestigation of Bile Salt Hydrolase Activity in Human Gut Bacteria Reveals Production of Conjugated Secondary Bile Acids.", "token_count": 331, "char_count": 1378, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:39.345382", "source": { "split": "train_shard_00000", "doc_id": 516 }, "chunk_id": "train_shard_00000_516_0", "global_id": 576 }, { "text": "Bile salt hydrolase (BSH), a probiotic-related enzyme with cholesterol-assimilating and anti-hypercholesterolemic abilities, has been isolated from intestinal bacteria; however, BSH activity of bacteria in bile-salt-free (non-intestinal) environments is largely unknown. Here, we aimed to identify BSH from non-intestinal\n\nEvidence for the Worldwide Distribution of a Bile Salt Hydrolase Gene in", "token_count": 109, "char_count": 395, "word_count": 50, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:39.731877", "source": { "split": "train_shard_00000", "doc_id": 517 }, "chunk_id": "train_shard_00000_517_0", "global_id": 577 }, { "text": "Bile salt hydrolase (BSH; EC 3.5.1.24) is the microbial enzyme that catalyzes the conversion of primary bile acids (BAs) into secondary ones, promoting microbial adaptation and modulating several host's biological functions. Probiotics with BSH activity are supposed to survive harsh intestinal conditions and exert a cholesterol-lowering effect. Here,\n\nGenome Mining and Characterization of Two Novel", "token_count": 109, "char_count": 401, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8909, "quality_score": 0.9455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:40.110588", "source": { "split": "train_shard_00000", "doc_id": 518 }, "chunk_id": "train_shard_00000_518_0", "global_id": 578 }, { "text": "We examined the evolutionary history of Phytophthora infestans and its close relatives in the 1c clade. We used whole genome sequence data from 69 isolates of Phytophthora species in the 1c clade and conducted a range of genomic analyses including nucleotide diversity evaluation, maximum likelihood trees, network assessment, time to most recent common ancestor and migration analysis. We consistently identified distinct and later divergence of the two Mexican Phytophthora species, P. mirabilis and P. ipomoeae, from P. infestans and other 1c clade species. Phytophthora infestans exhibited more recent divergence from other 1c clade species of Phytophthora from South America, P. andina and P. betacei. Speciation in the 1c clade and evolution of P. infestans occurred in the Andes. P. andina-P. betacei-P. infestans formed a species complex with indistinct species boundaries, hybridizations between the species, and short times to common ancestry. Furthermore, the distinction between modern Mexican and South American P. infestans proved less discrete, suggesting gene flow between populations over time. Admixture analysis indicated a complex relationship among these populations, hinting at potential gene flow across these regions. Historic P. infestans, collected from 1845-1889, were the first to diverge from all other P. infestans populations. Modern South American populations diverged next followed by Mexican populations which showed later ancestry. Both populations were derived from historic P. infestans. Based on the time of divergence of P. infestans from its closest relatives, P. andina and P. betacei in the Andean region, we consider the Andes to be the center of origin of P. infestans, with modern globalization contributing to admixture between P. infestans populations today from Mexico, the Andes and Europe.\n\nA pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species.", "token_count": 468, "char_count": 1963, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5017, "quality_score": 0.7509, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:40.754307", "source": { "split": "train_shard_00000", "doc_id": 519 }, "chunk_id": "train_shard_00000_519_0", "global_id": 579 }, { "text": "Cystic fibrosis (CF) is a rare genetic disorder commonly affecting multiple organs such as the lungs, pancreas, liver, kidney, and intestine. Our search focuses on the pathophysiological changes that affect the drugs' absorption, distribution, metabolism, and excretion (ADME). This review aims to identify the ADME data that compares the pharmacokinetics (PK) of different drugs in CF and healthy subjects. The published data highlight multiple factors that affect absorption, such as the bile salt precipitation and the gastrointestinal pH. Changes in CF patients' protein binding and body composition affected the drug distribution. The paper also discusses the factors affecting metabolism and renal elimination, such as drug-protein binding and metabolizing enzyme capacity. The majority of CF patients are on multidrug therapy, which increases the risk of drug-drug interactions (DDI). This is particularly true for those receiving the newly developed transmembrane conductance regulator (CFTR), as they are at a higher risk for CYP-related DDI. Our research highlights the importance of meticulously evaluating PK variations and DDIs in drug development and the therapeutic management of CF patients.\n\nThe Pharmacokinetic Changes in Cystic Fibrosis Patients Population: Narrative Review.", "token_count": 298, "char_count": 1294, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6612, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:41.317652", "source": { "split": "train_shard_00000", "doc_id": 520 }, "chunk_id": "train_shard_00000_520_0", "global_id": 580 }, { "text": "Bile salts are biosurfactants released into the intestinal lumen which play an important role in the solubilisation of fats and certain drugs. Their concentrations vary along the gastrointestinal tract (GIT). This is significant for implementation in physiologically based pharmacokinetic (PBPK) modelling to mechanistically capture drug absorption. The aims of this meta-analysis were to collate all appropriate data on intestinal bile salt concentrations in healthy adults across all GIT segments in fasted and fed states for the purpose of PBPK modelling. Terms relating to bile composition were searched in PubMed and Google Scholar from inception to May 2024. Selected studies included aspirated intestinal fluid collected via gastric tubes or colonoscopy. Results showed high variability across studies and a time-dependency for the fed state. Data were rich for the duodenum, which showed a two-fold increase for the fed state versus the fasted state within multiple studies. Peaks and troughs in bile salt concentrations along the GIT were observed for both fasted and fed states, likely due to segmental water absorption differences. The highest between subject variability was observed for the duodenum in the fasted and fed state and the fed proximal jejunum, distal ileum, and colon. The findings from this meta-analysis can be used for the purpose of PBPK modelling to capture segmental drug solubilisation and absorption in fasted and fed states. However, data are lacking under different fed conditions, especially following low-fat meals, so the impact of different fat content associated with different meals on bile salt concentrations cannot be discerned.\n\nGastrointestinal Bile Salt Concentrations in Healthy Adults Under Fasted and Fed Conditions: A Systematic Review and Meta-Analysis for Mechanistic Physiologically-Based Pharmacokinetic (PBPK) Modelling.", "token_count": 432, "char_count": 1878, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5495, "quality_score": 0.7747, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:41.943570", "source": { "split": "train_shard_00000", "doc_id": 521 }, "chunk_id": "train_shard_00000_521_0", "global_id": 581 }, { "text": "The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)\n\nLeveraging a phased pangenome for haplotype design of hybrid potato.", "token_count": 50, "char_count": 162, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:42.306028", "source": { "split": "train_shard_00000", "doc_id": 522 }, "chunk_id": "train_shard_00000_522_0", "global_id": 582 }, { "text": "The boll weevil, Anthonomus grandis grandis Boheman, and thurberia weevil, Anthonomus grandis thurberiae Pierce, together comprise a species complex that ranges throughout Mexico, the southwestern regions of the United States and parts of South America. The boll weevil is a historically damaging and contemporaneously threatening pest to commercial upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), whereas the thurberia weevil is regarded as an innocuous non-pest subspecies that is mostly found on non-cultivated Thurber's or Arizona cotton, Gossypium thurberi L., throughout its native range in western Mexico and the southwestern United States. Recent independent analyses, using mitochondrial and whole-genome markers, have suggested the independent evolution of these lineages is more attributable to geographic isolation than biotic factors. We suggest a combination of drivers after employing comparative genomic, population genetic and pangenome methodologies to identify large and small polymorphisms. By leveraging genetic differences, we determined 39,310 diagnostic loci between the subspecies, find genes under selection, and model the subspecies' shared and unique evolutionary history. Interestingly, structural variations capture a large proportion of genes at the population level and demographic reconstruction suggests a split between approximately 3,320-16,300 before present (YBP), which coincides with cotton cultivation in Mesoamerica, approximately 3,000-5,000 YBP. Observed polymorphisms are enriched for reproductive, regulatory, and metabolic genes, which may be attributed to the subspecies split and coevolution with cultivated cotton. Our results demonstrate the utility of a holistic, comparative framework utilising small and large polymorphisms to reconstruct demography and identify genetic novelty via pangenomics.\n\nPangenomics Links Boll Weevil Divergence With Ancient Mesoamerican Cotton Cultivation.", "token_count": 472, "char_count": 1949, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6969, "quality_score": 0.8484, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:42.953623", "source": { "split": "train_shard_00000", "doc_id": 523 }, "chunk_id": "train_shard_00000_523_0", "global_id": 583 }, { "text": "Traditional Turkish fermented foods like boza, pickles, and tarhana are recognized for their nutritional and health benefits, yet the probiotic potential of lactic acid bacteria (LAB) strains isolated from them remains underexplored. Sixty-six LAB strains were isolated from fermented foods using bacterial morphology, Gram staining, and catalase activity. The isolates were differentiated at strain level by RAPD-PCR (Random Amplification of Polymorphic DNA-Polymerase Chain Reaction) and twenty-five strains were selected for further evaluation of acid and bile salt tolerance. Among these, ten strains exhibited high tolerance and were subsequently assessed for adhesion to Caco-2 colorectal carcinoma cells, antimicrobial activity, exopolysaccharide (EPS) production, lysozyme resistance, and hemolytic activity. Using k-means clustering, three strains: Lactiplantibacillus plantarum ES-3, Pediococcus pentosaceus N-1, and Enterococcus faecium N-2 demonstrated superior probiotic characteristics, including significant acid (100% survival at pH3.0) and 0.3% bile salt tolerance (57%, 64%, 67%), strong adhesion to intestinal cells (65%, 88%, 91%), high lysozyme resistance (88%, 88%, 77%), and produced high amounts of EPS. These strains show promising potential as probiotics and warrant further investigation to confirm their functional properties and potential applications.\n\nHighly Potent New Probiotic Strains from Traditional Turkish Fermented Foods.", "token_count": 396, "char_count": 1460, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:43.595611", "source": { "split": "train_shard_00000", "doc_id": 524 }, "chunk_id": "train_shard_00000_524_0", "global_id": 584 }, { "text": "Urinary tract infections are a common condition affecting people globally, with multidrug-resistant (MDR) Escherichia coli (E. coli) being a major causative agent. Antimicrobial susceptibility profiling was performed using the VITEK 2 automated system for 1254 E. coli isolates, revealing that 831(66.2%) isolates were determined as MDR E. coli. A significant resistance pattern was observed for nalidixic acid (86.04%), ampicillin (74.16%), ticarcillin (70.73%), cefalotin (65.23%), cefixime (62.68%), ciprofloxacin (55.18%), ceftriaxone (53.75%), amoxicillin-clavulanic acid (22.81%), ertapenem (7.18%), and fosfomycin (2.23%). Whole Genome Sequencing of Carbapenem-resistant E. coli (CREC)-CREC 3 (ST405), CREC 4 (ST448), and CREC 5 (ST167) was performed to determine genomic characteristics. CREC 3, CREC 4, and CREC 5 belong to the phylogroup D, B1, and A, respectively. The NDM-5 gene was common in all three isolates, with CTX-M-15 being present in CREC 3 and CREC 4. Virulence factors of CREC 3 (fliC, shuA), CREC 4 (spaS), CREC 5 (iucA, papH, papG, iucB, yigF), and plasmids (IncFIA, IncFIB) were identified to be significant. The use of pangenome analysis enhances our understanding of resistance traits of isolates ST167, ST405, and ST448, offering valuable insights into comparative genomics of uropathogenic MDR E. coli.", "token_count": 499, "char_count": 1333, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7211, "quality_score": 0.8605, "entities": { "genes": [ "ST167", "ST448", "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:44.257632", "source": { "split": "train_shard_00000", "doc_id": 525 }, "chunk_id": "train_shard_00000_525_0", "global_id": 585 }, { "text": "Prevalence and genomic insights of carbapenem resistant and ESBL producing Multidrug resistant Escherichia coli in urinary tract infections.", "token_count": 37, "char_count": 140, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:44.638898", "source": { "split": "train_shard_00000", "doc_id": 525 }, "chunk_id": "train_shard_00000_525_1", "global_id": 586 }, { "text": "Chickens and ducks are vital sources of animal protein for humans. Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species, highlighting the need for more comprehensive genomes. The bird genome has more than tens of microchromosomes, but comparative genomics, annotations, and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies. We aim to complete the chicken and duck genomes, recover missing genes, and reveal common and unique chromosomal features between birds.\n\nNear telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and \"missing\" genes in birds.", "token_count": 178, "char_count": 739, "word_count": 104, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:45.132293", "source": { "split": "train_shard_00000", "doc_id": 526 }, "chunk_id": "train_shard_00000_526_0", "global_id": 587 }, { "text": "Bacterial cellulose holds significant commercial potential due to its unique structural and chemical properties, making it suitable for applications in electronics, medicine, and pharmaceuticals. However, large-scale BC production remains limited by challenges related to bacterial performance. In this study, we compared 79 microbial genomes from three genera-Komagataeibacter, Novacetimonas, and Gluconacetobacter-to investigate their pangenomes, genetic diversity, and evolutionary relationships. Through comparative genomic and phylogenetic analyses, we identified distinct genome compositions and evolutionary patterns that differ from previous reports. The role of horizontal gene transfer in shaping the genetic diversity and adaptability of these bacteria was also explored. Key determinants in BC production, such as variations in the bacterial cellulose biosynthesis (bcs) operon, carbohydrate uptake genes, and carbohydrate-active enzymes, were examined. Additionally, several biosynthetic gene clusters, including Linocin M18 and sactipeptides, which encode for antimicrobial peptides known as bacteriocins, were identified. These findings reveal new aspects of the genetic diversity in cellulose-producing bacteria and present a comprehensive genomic toolkit that will support future efforts to optimize BC production and improve microbial performance for commercial applications.\n\nPangenomic analysis of the bacterial cellulose-producing genera Komagataeibacter and Novacetimonas.", "token_count": 339, "char_count": 1494, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7268, "quality_score": 0.8634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:45.700308", "source": { "split": "train_shard_00000", "doc_id": 527 }, "chunk_id": "train_shard_00000_527_0", "global_id": 588 }, { "text": "The Human Pangenome Reference Consortium, the Chinese Pangenome Consortium, and other plant and animal pangenome projects have announced the completion of pilot work aimed at constructing high-quality, haplotype-resolved reference graph genomes representative of global ethno-linguistically different populations or different plant and animal species. These graph-based, gapless pangenome references, which are enriched in terms of genomic diversity, completeness, and contiguity, have the potential for enhancing long-read sequencing (LRS)-based genomic research, as well as improving mappability and variant genotyping on traditional short-read sequencing platforms. We comprehensively discuss the advancements in pangenome-based genomic integrative genomic discoveries across forensic-related species (humans, animals, and plants) and summarize their applications in variant identification and forensic genomics, epigenetics, transcriptomics, and microbiome research. Recent developments in multiplexed array sequencing have introduced a highly efficient and programmable technique to overcome the limitations of short forensic marker lengths in LRS platforms. This technique enables the concatenation of short RNA transcripts and DNA fragments into LRS-optimal molecules for sequencing, assembly, and genotyping. The integration of new pangenome reference coordinates and corresponding computational algorithms will benefit forensic integrative genomics by facilitating new marker identification, accurate genotyping, high-resolution panel development, and the updating of statistical algorithms. This review highlights the necessity of integrating LRS-based platforms, pangenome-based study designs, and graph-based pangenome references in short-read mapping and LRS-based innovations to achieve precision forensic science.\n\nPerspectives and opportunities in forensic human, animal, and plant integrative genomics in the Pangenome era.", "token_count": 411, "char_count": 1940, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:46.317646", "source": { "split": "train_shard_00000", "doc_id": 528 }, "chunk_id": "train_shard_00000_528_0", "global_id": 589 }, { "text": "The pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of the presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902 Salmonella enterica genomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.\n\nPersistent, Private, and Mobile Genes: A Model for Gene Dynamics in Evolving Pangenomes.", "token_count": 352, "char_count": 1633, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5551, "quality_score": 0.7776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:46.888379", "source": { "split": "train_shard_00000", "doc_id": 529 }, "chunk_id": "train_shard_00000_529_0", "global_id": 590 }, { "text": "Alpha-glucosidase inhibitors are one of the therapies used for treating type 2 diabetes by inhibiting the absorption of carbohydrates in the gastrointestinal tract. In addition to antimicrobial activity, some probiotic species show\n\nIsolation and Characterization of Lactic Acid Bacteria From \"", "token_count": 75, "char_count": 294, "word_count": 41, "semantic_coherence": 1, "information_density": 0.878, "quality_score": 0.939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:47.268900", "source": { "split": "train_shard_00000", "doc_id": 530 }, "chunk_id": "train_shard_00000_530_0", "global_id": 591 }, { "text": "Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or nearly complete Streptomyces genome sequences are now available, affording the opportunity to deeply investigate the biosynthetic potential within these organisms and to advance natural product discovery initiatives.\n\nPangenome mining of the Streptomyces genus redefines species' biosynthetic potential.", "token_count": 101, "char_count": 514, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7794, "quality_score": 0.8897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:47.645595", "source": { "split": "train_shard_00000", "doc_id": 531 }, "chunk_id": "train_shard_00000_531_0", "global_id": 592 }, { "text": "With the increasing availability of high-quality genome assemblies, pangenome graphs emerged as a new paradigm in the genomic field for identifying, encoding, and presenting genomic variation at both the population and species level. However, it remains challenging to truly dissect and interpret pangenome graphs via biologically informative visualization. To facilitate better exploration and understanding of pangenome graphs toward novel biological insights, here we present a web-based interactive visualization and interpretation framework for linear reference-projected pangenome graphs (VRPG). VRPG provides efficient and intuitive support for exploring and annotating pangenome graphs along a linear-genome-based coordinate system (e.g., that of a primary linear reference genome). Moreover, VRPG offers many unique features such as in-graph path highlighting for graph-constituent input assemblies, copy number characterization for graph-embedding nodes, and graph-based mapping for query sequences, all of which are highly valuable for researchers working with pangenome graphs. Additionally, VRPG enables side-by-side visualization between the graph-based pangenome representation and the conventional primary linear reference genome-based feature annotations, therefore seamlessly bridging the graph and linear genomic contexts. To further demonstrate its functionality and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of high-quality genome assemblies via a dedicated web portal and examined their local genome diversity in the graph contexts.\n\nInteractive visualization and interpretation of pangenome graphs by linear reference-based coordinate projection and annotation integration.", "token_count": 354, "char_count": 1768, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:48.225577", "source": { "split": "train_shard_00000", "doc_id": 532 }, "chunk_id": "train_shard_00000_532_0", "global_id": 593 }, { "text": "Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts for core genome alignments, helping to frame and solve the multiple alignment problem. We introduce Mumemto, a tool that computes multi-MUMs and other match types across large pangenomes. Mumemto allows for visualization of synteny, reveals aberrant assemblies and scaffolds, and highlights pangenome conservation and structural variation. Mumemto computes multi-MUMs across 320 human genome assemblies (960GB) in 25.7 hours with under 800 GB of memory, and over hundreds of fungal genome assemblies in minutes. Mumemto is implemented in C++ and Python and available open-source at https://github.com/vikshiv/mumemto.\n\nMumemto: efficient maximal matching across pangenomes.", "token_count": 222, "char_count": 873, "word_count": 116, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:48.689405", "source": { "split": "train_shard_00000", "doc_id": 533 }, "chunk_id": "train_shard_00000_533_0", "global_id": 594 }, { "text": "Drug-mediated inhibition of bile salt efflux transporters may cause liver injury. In vitro prediction of drug effects toward canalicular and/or sinusoidal efflux of bile salts from human hepatocytes is therefore a major issue, which can be addressed using liver cell-based assays.\n\nHuman liver cell-based assays for the prediction of hepatic bile acid efflux transporter inhibition by drugs.", "token_count": 100, "char_count": 391, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7719, "quality_score": 0.886, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:49.067301", "source": { "split": "train_shard_00000", "doc_id": 534 }, "chunk_id": "train_shard_00000_534_0", "global_id": 595 }, { "text": "This study presents the first chromosome-level genome assembly of the Korean long-tailed chicken (KLC), a unique breed of Gallus gallus known as Ginkkoridak. Our assembly achieved a super contig N50 of 5.7 Mbp and a scaffold N50 exceeding 90 Mb, with a genome completeness of 96.3% as assessed by BUSCO using the aves_odb10 set. We also constructed a comprehensive pangenome graph, incorporating 40 Gallus gallus assemblies, including the KLC genome. This graph comprises 87,934,214 nodes, 121,720,974 edges, and a total sequence length of 1,709,850,352 bp. Notably, our KLC assembly contributed 1,919,925 bp of new sequences to the pangenome, underscoring the unique genetic makeup of this breed. Furthermore, in comparison with the pangenome, we identified 36,818 structural variants in KLC, which included 2,529 insertions, 27,743 deletions, and 6,546 of either insertions or deletions shorter than 1 kb. We also successfully identified pan-genome wide non-reference sequences. Our KLC assembly and pangenome graph provide valuable genomic resources for studying G. gallus populations.\n\nChromosome-level Genome Assembly of Korean Long-tailed Chicken and Pangenome of 40 Gallus gallus Assemblies.", "token_count": 377, "char_count": 1198, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:49.652184", "source": { "split": "train_shard_00000", "doc_id": 535 }, "chunk_id": "train_shard_00000_535_0", "global_id": 596 }, { "text": "As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning. One clade that represents 24% of all currently known chimalliviruses lacks a PhuZ homolog. Here we show that Erwinia phage Asesino, one member of this PhuZ-less clade, shares a common overall replication mechanism with other characterized nucleus-forming phages despite lacking PhuZ. We show that Asesino replicates via a phage nucleus that encloses phage DNA and partitions proteins in the nuclear compartment and cytoplasm in a manner similar to previously characterized nucleus-forming phages. Consistent with a lack of PhuZ, however, we did not observe active positioning or rotation of the phage nucleus within infected cells. These data show that some nucleus-forming phages have evolved to replicate efficiently without PhuZ, providing an example of a unique variation in the nucleus-based replication pathway.\n\nErwinia phage Asesino is a nucleus-forming phage that lacks PhuZ.", "token_count": 346, "char_count": 1440, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:50.229229", "source": { "split": "train_shard_00000", "doc_id": 536 }, "chunk_id": "train_shard_00000_536_0", "global_id": 597 }, { "text": "Large genetic variants can be generated via homologous recombination (HR), such as polymerase theta-mediated end joining (TMEJ) or single-strand annealing (SSA). Given that these HR-based mechanisms leave specific genomic signatures, we developed GDBr, a genomic signature interpretation tool for DNA double-strand break repair mechanisms using high-quality genome assemblies. We applied GDBr to a draft human pangenome reference. We found that 78.1% of non-repetitive insertions and deletions and 11.0% of non-repetitive complex substitutions contained specific signatures. Of these, we interpreted that 98.7% and 1.3% of the insertions and deletions were generated via TMEJ and SSA, respectively, and all complex substitutions via TMEJ. Since population-level pangenome datasets are being dramatically accumulated, GDBr can provide mechanistic insights into how variants are formed. GDBr is available on GitHub at https://github.com/Chemical118/GDBr.\n\nGDBr: genomic signature interpretation tool for DNA double-strand break repair mechanisms.", "token_count": 271, "char_count": 1044, "word_count": 137, "semantic_coherence": 1, "information_density": 0.708, "quality_score": 0.854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:50.772771", "source": { "split": "train_shard_00000", "doc_id": 537 }, "chunk_id": "train_shard_00000_537_0", "global_id": 598 }, { "text": "Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches.\n\nGraph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors.", "token_count": 81, "char_count": 374, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8302, "quality_score": 0.9151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:51.146737", "source": { "split": "train_shard_00000", "doc_id": 538 }, "chunk_id": "train_shard_00000_538_0", "global_id": 599 }, { "text": "Gastrointestinal diseases in weaned piglets are a frequent cause of high morbidity and mortality in domestic pigs. The use of antibiotics is problematic due to increasing antibiotic resistance in bacterial populations, for which reason the use of suitable probiotics is highly recommended to maintain animal health and welfare.\n\nIn vitro characterization of lactic acid bacteria and bifidobacteria from wild and domestic pigs: probiotic potential for post-weaning piglets.", "token_count": 107, "char_count": 472, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7761, "quality_score": 0.8881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:52.156719", "source": { "split": "train_shard_00000", "doc_id": 539 }, "chunk_id": "train_shard_00000_539_0", "global_id": 600 }, { "text": "The recent emergence of bile salt hydrolase (BSH) enzyme as a therapeutic target reflects its unbound potential in mitigating hypercholesterolemia, obesity, and gastrointestinal issues. However, to bolster its industrial application, optimization of BSH assay lays the cornerstone for enhancing sensitivity, specificity, and reproducibility. The current study delved into optimizing the BSH assay parameters utilizing response surface methodology (RSM) and one-factor-at-a-time (OFAT) method for two novel, natural BSH producers, Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012. Factors such as pH, temperature, cell concentration, and substrate concentration were optimized using RSM and numerical optimization. The analysis of responses unveiled significant insights into the biochemical characteristics of BSH from both organisms. The optimal pH for BSH activity from H. coagulans ATCC 7050 and L. plantarum ATCC 10012 was determined to be 6.1 and 6.0, with their corresponding optimal temperatures being 60 °C and 40 °C, respectively. Subsequent to RSM, optimization of the remaining parameters such as buffer type, buffer molarity, cells-to-substrate ratio, etc., performed using the classical OFAT approach further enhanced BSH activity, with H. coagulans ATCC 7050 and L. plantarum ATCC 10012 exhibiting a 1.45 and 0.87-fold increase, respectively. Conventionally, even though BSH has been optimized using the OFAT approach, this is the first instance in which a hybrid model using RSM has been applied to achieve a greater performance. These findings offer valuable insights in augmenting the specificity, efficiency, and stability of BSH and broaching new avenues for industrial and therapeutic applications.", "token_count": 460, "char_count": 1747, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6461, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:52.793630", "source": { "split": "train_shard_00000", "doc_id": 540 }, "chunk_id": "train_shard_00000_540_0", "global_id": 601 }, { "text": "Targeted Assay Engineering Enhances Bile Salt Hydrolase Activity in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012.", "token_count": 54, "char_count": 146, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:53.156956", "source": { "split": "train_shard_00000", "doc_id": 540 }, "chunk_id": "train_shard_00000_540_1", "global_id": 602 }, { "text": "Lactic acid bacteria (LAB), traditionally consumed as fermented foods, are now being applied to the medical field beyond health-functional food as probiotics. Therefore, it is necessary to continuously discover and evaluate new strains with suitable probiotic characteristics, mainly focusing on safety. In this study, we isolated eight new strains from postmenopausal vaginal fluid using culturomics approaches, an emerging area of interest. Data showed that most strains possessed significant cell surface hydrophobicity (≥ 76%), auto-aggregation capacity (17 to 61%), strong adhesion activity (8 to 34%), and excellent resistance to gastric acid, bile salt, and digestive enzyme, enhancing their survival in the gastrointestinal tract. Moreover, the strains exhibited functional characteristics, including substantial antibacterial activity with a minimal inhibitory concentration (MIC) ranging from 12.5 to 50%. They also harbored bacteriocins genes, produced short-chain fatty acids (acetate and propionate), exhibited significant phagocytic activity, possessed high antioxidative properties, rapidly depleted sodium nitrite, and exhibited proteolysis and β-glucosidase activity. In addition, heat-killed LAB strains significantly reduced the gene expressions of proinflammatory cytokines such as IL-β, IL-6, and iNOS in macrophages. Safety assessment revealed no cytotoxicity in macrophage cell lines. All strains tested negative for biogenic amine or H\n\nIsolation of New Strains of Lactic Acid Bacteria from the Vaginal Microbiome of Postmenopausal Women and their Probiotic Characteristics.", "token_count": 396, "char_count": 1598, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7583, "quality_score": 0.8791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:53.765096", "source": { "split": "train_shard_00000", "doc_id": 541 }, "chunk_id": "train_shard_00000_541_0", "global_id": 603 }, { "text": "The frequency of drug-induced liver injury (DILI) in clinical trials remains a challenge for drug developers despite advances in human hepatotoxicity models and improvements in reducing liver-related attrition in preclinical species. TAK-994, an oral orexin receptor 2 agonist, was withdrawn from phase II clinical trials due to the appearance of severe DILI. Here, we investigate the likely mechanism of TAK-994 DILI in hepatic cell culture systems examined cytotoxicity, mitochondrial toxicity, impact on drug transporter proteins, and covalent binding. Hepatic liabilities were absent in rat and nonhuman primate safety studies, however, murine studies initiated during clinical trials revealed hepatic single-cell necrosis following cytochrome P450 induction at clinically relevant doses. Hepatic cell culture experiments uncovered wide margins to known mechanisms of intrinsic DILI, including cytotoxicity (>100× Cmax/IC50), mitochondrial toxicity (>100× Cmax/IC50), and bile salt efflux pump inhibition (>20× Css, avg/IC50). A potential covalent binding liability was uncovered with TAK-994 following hepatic metabolism consistent with idiosyncratic DILI and the delayed-onset clinical toxicity. Although idiosyncratic DILI is challenging to detect preclinically, reductions in total daily dose and covalent binding can reduce the covalent body binding burden and, subsequently, the clinical incidence of idiosyncratic DILI.\n\nTAK-994 mechanistic investigation into drug-induced liver injury.", "token_count": 394, "char_count": 1497, "word_count": 197, "semantic_coherence": 1, "information_density": 0.7107, "quality_score": 0.8553, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:54.382486", "source": { "split": "train_shard_00000", "doc_id": 542 }, "chunk_id": "train_shard_00000_542_0", "global_id": 604 }, { "text": "Gallstones are among the most frequent hepatobiliary conditions. Although in most cases, they remain asymptomatic, they can cause complications and, in such cases, invasive treatments like endoscopic retrograde cholangiography (ERC) or cholecystectomy are required. Here, we present the results of genetic testing of a single family with a high incidence of symptomatic gallstones and cholestatic liver phenotypes. Gallstone disease was detected among seven family members spanning three generations, and DNA samples were available from five of them. Genotyping was performed using TaqMan assays for known, selected genetic risk factors for gallstones and cholestasis, as well as next generation sequencing (NGS) of three genes involved in hepatobiliary transport. In all genotyped patients, we detected at least one copy of the gallstone-predisposing p.D19H variant in the hepatobiliary sterol transporter ABCG5/8, and in three cases, this variant was found in the rare homozygous state. In addition, the patients were all homozygous carriers of two intronic variants (c.2211+16C >T and c.3508-16T>C) and two common polymorphisms (c.504C>T and c.711A>T) in the ABCB4 gene, as well as the ATP8B1 gene variant c.696T>C. All genotyped patients also carried the predisposing variants c.1331C>T and c.3084A>G of the hepatobiliary bile salt export pump ABCB11 in either heterozygous or homozygous form. Hence, we propose that these variants taken together may have contributed to the high frequency of gallstone disease in this family, although functional studies for some variants are still lacking. In this report, we present these findings and discuss the challenges associated with interpreting sequencing data.\n\nA family with gallstone disease: defining inherited risk in the era of clinical genetic testing.", "token_count": 482, "char_count": 1808, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6183, "quality_score": 0.8092, "entities": { "genes": [ "ABCB4", "ABCB11", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:55.033377", "source": { "split": "train_shard_00000", "doc_id": 543 }, "chunk_id": "train_shard_00000_543_0", "global_id": 605 }, { "text": "Complete datasets of genetic variants are key to biodiversity genomic studies. Long-read sequencing technologies allow the routine assembly of highly contiguous, haplotype-resolved reference genomes. However, even when complete, reference genomes from a single individual may bias downstream analyses and fail to adequately represent genetic diversity within a population or species. Pangenome graphs assembled from aligned collections of high-quality genomes can overcome representation bias by integrating sequence information from multiple genomes from the same population, species or genus into a single reference. Here, we review the available tools and data structures to build, visualize and manipulate pangenome graphs while providing practical examples and discussing their applications in biodiversity and conservation genomics across the tree of life.\n\nPangenome graphs and their applications in biodiversity genomics.", "token_count": 179, "char_count": 929, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7236, "quality_score": 0.8618, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:55.512860", "source": { "split": "train_shard_00000", "doc_id": 544 }, "chunk_id": "train_shard_00000_544_0", "global_id": 606 }, { "text": "Multiple sclerosis (MS) is a devastating autoimmune disease that leads to the destruction of the myelin sheath in the human central nervous system (CNS). Infection by viruses and bacteria has been found to be strongly associated with the onset of MS or its severity. We postulated that the immune system's attack on the myelin sheath could be triggered by viruses and bacteria antigens that resemble myelin sheath components. An in-silico bioinformatics approach was undertaken in order to identify viral and bacterial antigens that resemble myelin oligodendrocyte glycoprotein (MOG) and myelin basic protein (MBP). To this end, we simultaneously analyzed both protein structures and amino acid sequences from viral and bacterial proteins and compared them to MOG and MBP. Possible associations between MBP and human parvovirus B19 (HPV-B19) and adeno-associated virus 4 (AAV-4) capsid protein structures were identified. MBP and MOG were associated with antigens from different viruses and bacteria, including Aspergillus species, Lactobacillus, Burkholderia, Clostridium, Schizosaccharomyces, SARS-CoV-2, and some gut flora metabolites. We also identified similarities between MBP and MOG proteins and bile salt hydrolase (BSH), glycosyltransferase (WcfQ), and Wzy enzymes. Identical amino acids between MBP and BSH at the active site, and protected amino acids in MOG aligning with WcfQ and Wzy enzymes were observed. Overall, our results offer valuable insights into the role of different viral and bacterial protein antigens in MS pathogenesis and suggest the possibility of identifying new therapeutic targets using in silico bioinformatics approaches. Our proposed approach could also likely be adapted for other CNS diseases in order to develop new biological insights and treatments.\n\nBioinformatics analysis of myelin-microbe interactions suggests multiple types of molecular mimicry in the pathogenesis of multiple sclerosis.", "token_count": 490, "char_count": 1936, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:56.180346", "source": { "split": "train_shard_00000", "doc_id": 545 }, "chunk_id": "train_shard_00000_545_0", "global_id": 607 }, { "text": "The oral-gut axis is a complex system linking the oral cavity and gastrointestinal tract, impacting host health and microbial composition. This study investigates genetic changes and adaptive mechanisms employed by streptococci-one of the few genera capable of colonizing oral and intestinal niches-within the same individual. We conducted whole-genome sequencing (WGS) on 218 streptococcal isolates from saliva and fecal samples of 14 inflammatory bowel disease (IBD) patients and 12 healthy controls. Our analysis identified 16 streptococcal species, with\n\nInsights into Within-Host Evolution and Dynamics of Oral and Intestinal Streptococci Unveil Niche Adaptation.", "token_count": 178, "char_count": 668, "word_count": 91, "semantic_coherence": 1, "information_density": 0.8132, "quality_score": 0.9066, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:56.660239", "source": { "split": "train_shard_00000", "doc_id": 546 }, "chunk_id": "train_shard_00000_546_0", "global_id": 608 }, { "text": "Bile salts possess innate antibacterial properties and can cause significant damage to bacteria. To survive in the mammalian gut,\n\nAcrAB Efflux Pump Plays a Crucial Role in Bile Salts Resistance and Pathogenesis of", "token_count": 56, "char_count": 214, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8485, "quality_score": 0.9242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:57.071538", "source": { "split": "train_shard_00000", "doc_id": 547 }, "chunk_id": "train_shard_00000_547_0", "global_id": 609 }, { "text": "Rocky Mountain Spotted Fever, caused by the gram-negative intracellular bacteria Rickettsia rickettsii, is a serious tick-borne infection with a fatality rate of 20-30%, if not treated. Since it is the most serious rickettsial disease in North America, modified prevention and treatment strategies are of critical importance. In order to find new therapeutic targets and create multiepitope vaccines, this study integrated subtractive proteomics with reverse vaccinology. The core genome of R. rickettsii was investigated, resulting in the identification of seven essential, human non-homologous proteins as potential drug targets, as well as four antigenic, non-allergenic proteins suitable for vaccine development. Using conserved antigenic peptides, two chimeric vaccine constructs were developed and assessed using molecular docking, molecular dynamics simulations, principal component analysis, MM-GBSA binding free energy, and dynamic cross-correlation matrix studies. The high immunogenic potential was indicated by the vaccine designs' robust and consistent interactions with human immunological receptors. Their capacity to trigger strong humoral and cellular immunological responses was further demonstrated by in silico immune simulations. The persistent interactions of vaccine V1 and V2 with human immunological receptor demonstrated that these might have high immunogenic potential. Moreover, the identified drug targets were annotated for essential biological processes, which shed light on their therapeutic potential. The vaccine constructs were cloned and expressed in suitable systems. This study displays a comprehensive strategy for managing Rocky Mountain Spotted Fever via rational vaccine development. Further experimental research is needed to confirm the immunogenicity of the vaccines and the druggability of identified targets, establishing the path toward effective RMSF management.\n\nCore-genome guided novel therapeutic targets identification and chimeric vaccine designing against Rickettsia rickettsii.", "token_count": 420, "char_count": 2034, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:57.696806", "source": { "split": "train_shard_00000", "doc_id": 548 }, "chunk_id": "train_shard_00000_548_0", "global_id": 610 }, { "text": "Pangenome indexes are promising tools for many applications, including classification of nanopore sequencing reads. Move structure is a compressed-index data structure based on the Burrows-Wheeler Transform (BWT). It offers simultaneous O(1)-time queries and O(r) space, where r is the number of BWT runs (consecutive sequence of identical characters). We developed Movi based on the move structure for indexing and querying pangenomes. Movi scales very well for repetitive text as its size grows strictly by r. Movi computes sophisticated matching queries for classification such as pseudo-matching lengths and backward search up to 30 times faster than existing methods by minimizing the number of cache misses and using memory prefetching to attain a degree of latency hiding. Movi's fast constant-time query loop makes it well suited to real-time applications like adaptive sampling for nanopore sequencing, where decisions must be made in a small and predictable time interval.\n\nMovi: A fast and cache-efficient full-text pangenome index.", "token_count": 234, "char_count": 1043, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7386, "quality_score": 0.8693, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:58.169402", "source": { "split": "train_shard_00000", "doc_id": 549 }, "chunk_id": "train_shard_00000_549_0", "global_id": 611 }, { "text": "With advances in long-read sequencing and assembly techniques, haplotype-resolved (phased) genome assemblies are becoming more common, also in the field of plant genomics. Computational tools to effectively explore these phased genomes, particularly for polyploid genomes, are currently limited. Here we describe a new strategy adopting a pangenome approach. To analyse both intra- and intergenomic variation in phased genome assemblies, we have made the software package PanTools ploidy-aware by updating the pangenome graph representation and adding several novel functionalities to assess synteny and gene retention, profile repeats and calculate synonymous and nonsynonymous mutation rates. Using PanTools, we constructed and analysed a pangenome comprising of one diploid and four tetraploid potato cultivars, and a pangenome of five diploid apple species. Both pangenomes show high intra- and intergenomic allelic diversity in terms of gene absence/presence, SNPs, indels and larger structural variants. Our findings show that the new functionalities and visualizations are useful to discover introgressions and detect likely misassemblies in phased genomes. PanTools is available at https://git.wur.nl/bioinformatics/pantools.\n\nExploring intra- and intergenomic variation in haplotype-resolved pangenomes.", "token_count": 311, "char_count": 1312, "word_count": 172, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:58.743117", "source": { "split": "train_shard_00000", "doc_id": 550 }, "chunk_id": "train_shard_00000_550_0", "global_id": 612 }, { "text": "Hawthorn leave flavonoids (HLF) are widely used as an herb or dietary supplements for cardio-cerebrovascular diseases. However, its gastrointestinal absorption behavior and mechanism have not been disclosed. In this study, gastrointestinal absorption and its regulation of 4''-O-glucosylvitexin (GLV), 2''-O-rhamnosylvitexin (RHV), vitexin (VIT), rutin (RUT) and hyperoside (HP) in HLF were investigated using in vitro, in situ and in vivo models. Apparent permeability coefficient (P\n\nGastrointestinal absorption and its regulation of hawthorn leaves flavonoids.", "token_count": 171, "char_count": 563, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7671, "quality_score": 0.8836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:03:59.547400", "source": { "split": "train_shard_00000", "doc_id": 551 }, "chunk_id": "train_shard_00000_551_0", "global_id": 613 }, { "text": "Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of Escherichia coli ST131, which likely shared a common ancestor around 100 years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6,000 core genome substitutions. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2,000 structural changes within the accessory genome, i.e. one structural change for every three core genome substitutions. Sixty-three percent of loci with structural diversity could be resolved into individual gain and loss events with 10-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in our dataset are likely deleterious and only persist for a short time before being removed by purifying selection.\n\nQuantifying the Evolutionary Dynamics of Structure and Content in Closely Related E. coli Genomes.", "token_count": 324, "char_count": 1397, "word_count": 203, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:00.111497", "source": { "split": "train_shard_00000", "doc_id": 552 }, "chunk_id": "train_shard_00000_552_0", "global_id": 614 }, { "text": "Donor-derived fecal microbiota treatments are efficacious in preventing recurrent Clostridioides difficile infection (rCDI), but they have inherently variable quality attributes, are difficult to scale and harbor the risk of pathogen transfer. In contrast, VE303 is a defined consortium of eight purified, clonal bacterial strains developed for prevention of rCDI. In the phase 2 CONSORTIUM study, high-dose VE303 was well tolerated and reduced the odds of rCDI by more than 80% compared to placebo. VE303 organisms robustly colonized the gut in the high-dose group and were among the top taxa associated with non-recurrence. Multi-omic modeling identified antibiotic history, baseline stool metabolites and serum cytokines as predictors of both on-study CDI recurrence and VE303 colonization. VE303 potentiated early recovery of the host microbiome and metabolites with increases in short-chain fatty acids, secondary bile acids and bile salt hydrolase genes after antibiotic treatment for CDI, which is considered important to prevent CDI recurrences. These results support the idea that VE303 promotes efficacy in rCDI through multiple mechanisms.\n\nMulti-omic profiling a defined bacterial consortium for treatment of recurrent Clostridioides difficile infection.", "token_count": 332, "char_count": 1266, "word_count": 177, "semantic_coherence": 1, "information_density": 0.7062, "quality_score": 0.8531, "entities": { "genes": [ "VE303" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:00.680692", "source": { "split": "train_shard_00000", "doc_id": 553 }, "chunk_id": "train_shard_00000_553_0", "global_id": 615 }, { "text": "Global food security depends heavily on a few staple crops, while orphan crops, despite being less studied, offer the potential benefits of environmental adaptation and enhanced nutritional traits, especially in a changing climate. Major crops have benefited from genomics-based breeding, initially using single genomes and later pangenomes. Recent advances in DNA sequencing have enabled pangenome construction for several orphan crops, offering a more comprehensive understanding of genetic diversity. Orphan crop research has now entered the pangenomics era and applying these pangenomes with advanced selection methods and genome editing technologies can transform these neglected species into crops of broader agricultural significance.\n\nThe role of pangenomics in orphan crop improvement.", "token_count": 150, "char_count": 794, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:01.120134", "source": { "split": "train_shard_00000", "doc_id": 554 }, "chunk_id": "train_shard_00000_554_0", "global_id": 616 }, { "text": "Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of\n\nDecomposition of the pangenome matrix reveals a structure in gene distribution in the", "token_count": 68, "char_count": 311, "word_count": 47, "semantic_coherence": 1, "information_density": 0.7234, "quality_score": 0.8617, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:01.487934", "source": { "split": "train_shard_00000", "doc_id": 555 }, "chunk_id": "train_shard_00000_555_0", "global_id": 617 }, { "text": "The development of a comprehensive pig graph pangenome assembly encompassing 27 genomes represents the most extensive collection of pig genomic data to date. Analysis of this pangenome reveals the critical role of structural variations in driving adaptation and defining breed-specific traits. Notably, the study identifies\n\nPangenome and genome variation analyses of pigs unveil genomic facets for their adaptation and agronomic characteristics.", "token_count": 92, "char_count": 446, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7705, "quality_score": 0.8852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:01.870701", "source": { "split": "train_shard_00000", "doc_id": 556 }, "chunk_id": "train_shard_00000_556_0", "global_id": 618 }, { "text": "Gut microbiome is crucial for lipid metabolism in humans and animals. However, how specific gut microbiota and their associated metabolites impact fat deposition remains unclear. In this study, we demonstrated that the colonic microbiome of lean and obese pigs differentially contributes to fat deposition, as evidenced by colonic microbiota transplantation experiments. Notably, the higher abundance of\n\nGut", "token_count": 95, "char_count": 408, "word_count": 57, "semantic_coherence": 1, "information_density": 0.807, "quality_score": 0.9035, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:02.246093", "source": { "split": "train_shard_00000", "doc_id": 557 }, "chunk_id": "train_shard_00000_557_0", "global_id": 619 }, { "text": "Foodborne bacterial enteritis is a common clinical disease, and its incidence has risen globally. To screen for functional Bacillus strains with anti-inflammatory properties, tolerance to acid and bile salts, and antagonism against Salmonella, 22 strains of Bacillus were employed as candidate strains in this study. An inflammatory cell model was established using J774-Dual NF-κB/IRF reporter macrophages to identify anti-inflammatory Bacillus. The candidate Bacillus strains were assessed through tolerance to acid and bile salts and antibacterial assays, and their inhibitory effects on the inflammatory responses triggered by S. Enteritidis infection were investigated. The findings demonstrated that B. licheniformis B410 was successfully screened, possessing a significant anti-inflammatory effect by suppressing the NF-κB and IRF signaling pathways. B410 exhibited excellent tolerance to acid and bile salts and displayed a favorable antibacterial effect against Salmonella. Co-incubation of B410 with RAW264.7 macrophages did not influence the cell viability. B. licheniformis B410 could significantly inhibit the expression of pro-inflammatory cytokines IL-1β and TNF-α induced by LPS and promote the expression of the anti-inflammatory cytokine IL-10. Additionally, B410 could markedly inhibit the activation of NF-κB and the production of inflammatory cytokines caused by S. Enteritidis infection in macrophages. This study successfully screened a new strain of B. licheniformis B410 that simultaneously had the capabilities of anti-inflammation, acid and bile salt tolerance, and antagonism against Salmonella, providing a new approach for the screening of functional anti-inflammatory probiotics and the development of anti-inflammatory probiotic therapeutic preparations.", "token_count": 467, "char_count": 1786, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5612, "quality_score": 0.7806, "entities": { "genes": [ "RAW264" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:02.887958", "source": { "split": "train_shard_00000", "doc_id": 558 }, "chunk_id": "train_shard_00000_558_0", "global_id": 620 }, { "text": "Bacillus licheniformis B410 Alleviates Inflammation Induced by Lipopolysaccharide and Salmonella by Inhibiting NF-κB and IRF Signaling Pathways in Macrophages.", "token_count": 55, "char_count": 159, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:03.251820", "source": { "split": "train_shard_00000", "doc_id": 558 }, "chunk_id": "train_shard_00000_558_1", "global_id": 621 }, { "text": "This study investigates how microbiome colonization influences the development of intestinal type 3 immunity in neonates. The results showed that reduced oxygen levels in the small intestine of neonatal rats induced by Saccharomyces boulardii accelerated microbiome colonization and type 3 immunity development, which protected against Salmonella enterica serovar Typhimurium infection. Microbiome maturation increased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and hyocholic acid (HCA) levels. Furthermore, reducing oxygen levels in the intestine increased the abundance of Limosilactobacillus reuteri, a bacterium encoding BSH, and promoted intestinal type 3 immunity. However, inhibition of BSH blocked the L. reuteri-induced development of intestinal type 3 immunity. Mechanistically, HCA promoted the development of gamma-delta T cells and type 3 innate lymphoid cells by stabilizing the mRNA expression of RAR-related orphan receptor C via the farnesoid X receptor-WT1-associated protein-N6-methyl-adenosine axis. These results reveal that gut microbiota-derived HCA plays a crucial role in promoting the development of intestinal type 3 immunity in neonates. This discovery introduces potential therapeutic avenues for strengthening intestinal immunity in early life or treating bacterial infections by targeting microbial metabolites.\n\nGut Microbiota-Derived Hyocholic Acid Enhances Type 3 Immunity and Protects Against Salmonella enterica Serovar Typhimurium in Neonatal Rats.", "token_count": 392, "char_count": 1510, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.797, "entities": { "genes": [ "WT1" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:03.869020", "source": { "split": "train_shard_00000", "doc_id": 559 }, "chunk_id": "train_shard_00000_559_0", "global_id": 622 }, { "text": "Global concern about pathogenic resistance to antibiotics is prompting interest in probiotics as a strategy to prevent or inhibit infections. Fermented beverages are promising sources of probiotic yeasts. This study aimed to evaluate the antagonistic effects of\n\nProbiotic Potential of Yeasts Isolated from Fermented Beverages: Assessment of Antagonistic Strategies Against", "token_count": 86, "char_count": 373, "word_count": 50, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:04.248098", "source": { "split": "train_shard_00000", "doc_id": 560 }, "chunk_id": "train_shard_00000_560_0", "global_id": 623 }, { "text": "Cholesterol gallstone is a disease with high incidence and quality of life. This study aimed to investigate the function of exosome-derived miRNA in gallstone formation and its related molecular mechanism. Exosomes were extracted and isolated from patients with gallbladder stones and age- and gender-matched healthy controls, and exosomal miRNA expression was compared between the two groups. The function of exosomal miR-107 in gallstone formation was evaluated using a lithogenic fed-induced gallstone mouse model. We used a dual luciferase reporter assay to identify the miR-107 target gene. Expression of BSEP and CYP7A1 were detected using Western Blot and immunohistochemical staining to ascertain the role of miR-107 in bile acid transport and cholesterol synthesis. Bile acids, phospholipids, cholesterol and triglycerides were determined with the kit, and cholesterol saturation index was calculated. Liver cholesterol transport-related genes, phospholipid transport-related genes, liver bile salt transport-related genes, sodium-dependent bile acid transporters and organic solute transporters were detected by q-PCR. Exosomal miR-107 high expression was significant in people with gallstones. Inhibitor of miR-107 reduced lithogenic diet-induced gallstone formation in mice. MiR-107 directly inhibited caveolin-1 expression. Inhibition of caveolin-1 reduced the BSEP function. After treatment of miR-107 inhibitor, the expression of BSEP and CYP7A1 was significantly increased compared with gallbladder stones model, but the concentration of bile acid in gallbladder was significantly decreased. miR-107 altered biliary and liver lipid profiles and increased biliary cholesterol saturation index (CSI). Inhibited miR-107 promoted liver homeostasis-related cholesterol and the expression of bile acid transporters. This study revealed that exosome-derived miR-107 promoted gallstone progression by regulating the hepatobiliary cholesterol secretion pathway through targeting caveolin-1.", "token_count": 521, "char_count": 1997, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5134, "quality_score": 0.7567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:04:04.877513", "source": { "split": "train_shard_00000", "doc_id": 561 }, "chunk_id": "train_shard_00000_561_0", "global_id": 624 }, { "text": "Exosome-derived miR-107 targeting caveolin-1 promotes gallstone progression by regulating the hepatobiliary cholesterol secretion pathway.", "token_count": 41, "char_count": 138, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:05.242300", "source": { "split": "train_shard_00000", "doc_id": 561 }, "chunk_id": "train_shard_00000_561_1", "global_id": 625 }, { "text": "Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota's last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature involve both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 genes with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer with other bacteria and archaea that often grow at similar temperatures, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.\n\nBacterial Growth Temperature as a Horizontally Acquired Polygenic Trait.", "token_count": 323, "char_count": 1474, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:05.809154", "source": { "split": "train_shard_00000", "doc_id": 562 }, "chunk_id": "train_shard_00000_562_0", "global_id": 626 }, { "text": "By integrating genomes from different accessions, pangenomes provide a more comprehensive and reference-bias-free representation of genetic information within a population compared to a single reference genome. With the rapid accumulation of genomic sequencing data and the expanding scope of plant research, plant pangenomics has gradually evolved from single-species to multi-species studies. This shift has given rise to the concept of a super-pangenome that covers all genomic sequences within a genus-level taxonomic group. By incorporating both cultivated and wild species, the super-pangenome has greatly enhanced the resolution of research in various areas such as plant genetic diversity, evolution, domestication, and molecular breeding. In this review, we present a comprehensive overview of the plant super-pangenome, emphasizing its development requirements, construction strategies, potential applications, and notable achievements. We also highlight the distinctive advantages and promising prospects of super-pangenomes while addressing current challenges and future directions.\n\nThe developments and prospects of plant super-pangenomes: Demands, approaches, and applications.", "token_count": 231, "char_count": 1192, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6993, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:06.283219", "source": { "split": "train_shard_00000", "doc_id": 563 }, "chunk_id": "train_shard_00000_563_0", "global_id": 627 }, { "text": "Type O8 is the most prevalent serotype of APEC isolated from Wenchang chicken embryos (Hainan, China).The isolates were more than 90% resistant to erythromycin, amoxicillin, ampicillin, and tetracycline.19.2% of the isolates were multi-resistant to more than 14 antibiotics.APEC of the same serotype isolated from Hainan Wenchang embryos have close relationships in the evolutionary tree of the core genome.\n\nEpidemiological investigation and drug resistance analysis of avian pathogenic", "token_count": 144, "char_count": 487, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7164, "quality_score": 0.8582, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:06.711996", "source": { "split": "train_shard_00000", "doc_id": 564 }, "chunk_id": "train_shard_00000_564_0", "global_id": 628 }, { "text": "The thermophilic bacterium Rhodothermus marinus has mainly been studied for its thermostable enzymes. More recently, the potential of using the species as a cell factory and in biorefinery platforms has been explored, due to the elevated growth temperature, native production of compounds such as carotenoids and exopolysaccharides, the ability to grow on a wide range of carbon sources including polysaccharides, and available genetic tools. A comprehensive understanding of the metabolism of cell factories is important. Here, we report a genome-scale metabolic model of R. marinus DSM 4252T. Moreover, the genome of the genetically amenable R. marinus ISCaR-493 was sequenced and the analysis of the core genome indicated that the model could be used for both strains. Bioreactor growth data were obtained, used for constraining the model and the predicted and experimental growth rates were compared. The model correctly predicted the growth rates of both strains. During the reconstruction process, different aspects of the R. marinus metabolism were reviewed and subsequently, both cell densities and carotenoid production were investigated for strain ISCaR-493 under different growth conditions. Additionally, the dxs gene, which was not found in the R. marinus genomes, from Thermus thermophilus was cloned on a shuttle vector into strain ISCaR-493 resulting in a higher yield of carotenoids.\n\nA genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacterium Rhodothermus marinus.", "token_count": 363, "char_count": 1530, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5676, "quality_score": 0.7838, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:07.289418", "source": { "split": "train_shard_00000", "doc_id": 565 }, "chunk_id": "train_shard_00000_565_0", "global_id": 629 }, { "text": "Bile salts enriched nanovesicles (bilosomes) have been attention worthy in the past few years due to their distinctive effect on the enhancement of drug delivery through various physiological administration routes. Oral delivery of multifunctioning phytochemical curcumin has faced a lot of difficulties due to its scarce solubility and poor oral bioavailability.\n\nIn-vivo and in-vitro assessment of curcumin loaded bile salt stabilized nanovesicles for oral delivery.", "token_count": 110, "char_count": 468, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:07.711379", "source": { "split": "train_shard_00000", "doc_id": 566 }, "chunk_id": "train_shard_00000_566_0", "global_id": 630 }, { "text": "Whole genome sequencing (WGS) marks a turning point for outbreak investigations for microorganisms related to public health matters, like Legionella pneumophila (Lp). Here, we evaluated the available Lp WGS typing tools for isolates of previously documented Belgian outbreaks, as well as small groups of related and non-related isolates. One reference strain and 77 clinical and environmental isolates were evaluated. Seven isolates belong to a Sequence Type (ST) 36 outbreak in 1999 and sixteen (ten clinical, two matching environmental and four non-related controls) belong to another ST1 outbreak in 1985-1987. The remaining isolates belong to small groups of related and non-related isolates of diverse ST's. WGS was performed and data were analysed using whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) with \"Ridom SeqSphere + \" (cgMLST), \"Applied Maths-Bionumerics\" (wgMLST) and the 50 loci cgMLST (CDC/ESGLI_ESCMID). Results of the three tools were concordant with the traditional Sequence Based Typing (SBT). The known outbreaks and small clusters could be detected and clear discrimination of ST1 non-related isolates was obtained. In addition, the 50 loci cgMLST allowed to classify the isolates into subtypes because almost all the 50 genes could be called in all the analysed isolates, which was not achieved by the other tools. This is a big advantage in terms of standardisation and comparison between laboratories for future epidemiological investigations. WGS allowed to analyse a large volume of samples and generated more accurate conclusions for outbreak investigations compared to other typing methods due to its higher discriminatory power and throughput.\n\nComparison of whole genome sequencing typing tools for the typing of Belgian Legionella pneumophila outbreaks isolates.", "token_count": 451, "char_count": 1822, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5784, "quality_score": 0.7892, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:08.364249", "source": { "split": "train_shard_00000", "doc_id": 567 }, "chunk_id": "train_shard_00000_567_0", "global_id": 631 }, { "text": "The present work focuses on the photophysical behavior of meso-N-butylcarbazole-substituted BODIPY (CBZ-BDP) in different organized media towards exploring the possible use of the dye as a molecular sensor and imaging agent. The molecule shows an appreciable change in absorption and emission spectra at 75% water-acetonitrile mixture compared to pure acetonitrile. In water-acetonitrile mixture, it displays aggregate-induced emission (AIE) bands. New emission peaks are observed at 560 nm and 630 nm, corresponding to LE (locally excited) and ICT (intramolecular charge transfer) states of CBZ-BDP aggregates. The fluorescence anisotropy studies of CBZ-BDP in glycerol medium show its better sensitivity towards the microenvironment. CBZ-BDP was used to probe various microheterogeneous systems like bile salts, pluronics, and lipid bilayer systems in aqueous medium. The dye displays sensitive variation in emission intensity and fluorescence anisotropy in sodium cholate (NaC) bile salt in aqueous medium as a function of the bile salt concentration. The molecule detects the temperature-induced phase transitions in pluronic P123 and F127, as well as 1,2-dimyristoylphosphatidylcholine (DMPC) and 1,2-dipalmitoylphosphatidylcholine (DPPC) lipid bilayer systems in aqueous medium. These studies strongly suggest that CBZ-BDP can be used as an efficient fluorescent probe in sensing the micro-environmental changes in bile salts, pluronics, and lipid bilayers in aqueous medium. The imaging studies of CBZ-BDP-embedded Giant Unilamellar Vesicles (GUVs) were carried out. The molecule stains the lipid bilayers and displays bright-green fluorescent images, suggesting its potential in lipid bilayer imaging.", "token_count": 480, "char_count": 1709, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5991, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:09.046137", "source": { "split": "train_shard_00000", "doc_id": 568 }, "chunk_id": "train_shard_00000_568_0", "global_id": 632 }, { "text": "Photophysical behavior of meso-N-butylcarbazole-substituted BODIPY in different nano-scale organized media.", "token_count": 34, "char_count": 107, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:09.440516", "source": { "split": "train_shard_00000", "doc_id": 568 }, "chunk_id": "train_shard_00000_568_1", "global_id": 633 }, { "text": "Multi-locus sequence typing (MLST) based on eight genes has become the method of choice for Borrelia typing and is extensively used for population studies. Whole-genome sequencing enables studies to scale up to genomic levels but necessitates extended schemes. We have developed a 639-loci core genome MLST (cgMLST) scheme for Borrelia burgdorferi sensu lato (s.l.) that enables unambiguous genotyping and improves the robustness of phylogenies and lineage resolution within species. Notably, all inner nodes of the cgMLST phylogenies had consistently high statistical support. Analyses of the genetically homogeneous European B. bavariensis population support the notion that cgMLST provides high discriminatory power even for closely related isolates. While isolates differed maximally in one MLST locus, there were up to 179 cgMLST loci differences. Thus, the developed cgMLST scheme for B. burgdorferi s.l. resolves lineages at a finer resolution than MLST and improves insights into the evolutionary history of the species complex.\n\nA core genome MLST scheme for Borrelia burgdorferi sensu lato improves insights into the evolutionary history of the species complex.", "token_count": 303, "char_count": 1171, "word_count": 169, "semantic_coherence": 1, "information_density": 0.645, "quality_score": 0.8225, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:10.003435", "source": { "split": "train_shard_00000", "doc_id": 569 }, "chunk_id": "train_shard_00000_569_0", "global_id": 634 }, { "text": "Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges.\n\nEvaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references.", "token_count": 173, "char_count": 805, "word_count": 98, "semantic_coherence": 1, "information_density": 0.8265, "quality_score": 0.9133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:10.448079", "source": { "split": "train_shard_00000", "doc_id": 570 }, "chunk_id": "train_shard_00000_570_0", "global_id": 635 }, { "text": "Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream of the\n\nTaurine pangenome uncovers a segmental duplication upstream of", "token_count": 88, "char_count": 392, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7885, "quality_score": 0.8942, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:10.819867", "source": { "split": "train_shard_00000", "doc_id": 571 }, "chunk_id": "train_shard_00000_571_0", "global_id": 636 }, { "text": "The study assessed the peptide production by using potent Lactiplantibacillus plantarum KGL3A (MG722814) culture to ferment the sheep milk for evaluation of α-glucosidase inhibition, ACE inhibition, α-amylase inhibition, & inhibiting lipase activities. The maximal ACE inhibitory, α-amylase, α-glucosidase, & lipase inhibiting actions were 71.69 %, 71.32 %, 67.14 %, and 64.15 %, respectively, at 37 °C after 48 h. Proteolytic activity was tested at various incubation times & inoculation rates to maximise the conditions for growth and the greatest action (9.38 mg/mL) was reported at 2.5 % rate of inoculation after incubation of 48 h. The anti-diabetic as well as ACE inhibitory properties of less than 3 kDa were maximum in contrast to >3 kDa, <10 kDa, and > 10 kDa cut-off fractions. Further, when LPS stimulation is applied to RAW 267.4 macrophage cells, the overabundance generation of IL-6, IL-1β, NO, and TNF-α is greatly reduced by using KGL3A to ferment sheep milk. 2D gel electrophoresis & SDS-PAGE were utilized in relation to protein purifications. Maximum numbers of sheep milk's fermented protein bands were present, about 10 to 124 kDa by SDS-PAGE, and 38 spots of protein were discovered using 2D gel chromatography. Ultra-filtered fractions water soluble extracts (WSEs) were employed in RP-HPLC to differentiate between various peptide fractions. The peptide sequences produced were matched using the databases of AHTPDB and BIOPEP to match hypertensive peptides & antidiabetic peptides, respectively", "token_count": 491, "char_count": 1520, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8196, "entities": { "genes": [ "KGL3A", "MG722814" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:11.466841", "source": { "split": "train_shard_00000", "doc_id": 572 }, "chunk_id": "train_shard_00000_572_0", "global_id": 637 }, { "text": "Furthermore, the discovered peptide sequences from the fermenting sheep milk was studied due to their penchant for binding against the active locations of human bile salt activated lipase (hBAL); human maltase-glucoamylase (hMGA); human pancreatic alpha-amylase (hPAM); & human angiotensin-converting enzyme (hACE) through molecular docking.\n\nPeptidomics and molecular dynamics on bioactive peptides produced and characterized from the fermented whey of \"Panchali\" sheep of West India.", "token_count": 131, "char_count": 485, "word_count": 64, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:11.887642", "source": { "split": "train_shard_00000", "doc_id": 572 }, "chunk_id": "train_shard_00000_572_1", "global_id": 638 }, { "text": "This study investigated the diversity of thermophilic Campylobacter species isolated from three New Zealand freshwater catchments affected by pastoral and urban activities. Utilising matrix-assisted laser desorption ionisation-time of flight and whole genome sequence analysis, the study identified Campylobacter jejuni (n = 46, 46.0%), C. coli (n = 39, 39%), C. lari (n = 4, 4.0%), and two novel Campylobacter species lineages (n = 11, 11%). Core genome sequence analysis provided evidence of prolonged persistence or continuous faecal shedding of closely related strains. The C. jejuni isolates displayed distinct sequence types (STs) associated with human, ruminant, and environmental sources, whereas the C. coli STs included waterborne ST3302 and ST7774. Recombination events affecting loci implicated in human pathogenesis and environmental persistence were observed, particularly in the cdtABC operon (encoding the cytolethal distending toxin) of non-human C. jejuni STs. A low diversity of antimicrobial resistance genes (aadE-Cc in C. coli), with genotype/phenotype concordance for tetracycline resistance (tetO) in three ST177 isolates, was noted. The data suggest the existence of two types of naturalised waterborne Campylobacter: environmentally persistent strains originating from waterbirds and new environmental species not linked to human campylobacteriosis. Identifying and understanding naturalised Campylobacter species is crucial for accurate waterborne public health risk assessments and the effective allocation of resources for water quality management.\n\nNew Campylobacter Lineages in New Zealand Freshwater: Pathogenesis and Public Health Implications.", "token_count": 441, "char_count": 1677, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6518, "quality_score": 0.8259, "entities": { "genes": [ "ST177", "ST3302", "ST7774" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:12.513950", "source": { "split": "train_shard_00000", "doc_id": 574 }, "chunk_id": "train_shard_00000_574_0", "global_id": 639 }, { "text": "Inflammation-induced cholestasis is a common problem in septic patients and results from cytokine-mediated inhibition of bile acid export including impaired expression of the bile salt export pump (BSEP) with a consecutive increase in intracellular bile acids mediating cell damage. The present study focuses on the mechanisms by which interleukin 1 β (IL-1β), as a critical mediator of sepsis-induced cholestasis, controls the expression of BSEP in hepatocytes. Notably, the treatment of hepatocytes with IL-1β leads to the upregulation of a broad chemokine pattern. Thereby, the IL-1β -induced expression of in particular the CXCR2 ligands CXCL1 and 2 is further enhanced by bile acids, whereas the FXR-mediated upregulation of BSEP induced by bile acids is inhibited by IL-1β. In this context, it is interesting to note that inhibitor studies indicate that IL-1β mediates its inhibitory effects on bile acid-induced expression of BSEP indirectly via CXCR2 ligands. Consistently, inhibition of CXCR2 with the inhibitor SB225002 significantly attenuated of the inhibitory effect of IL-1β on BSEP expression. These data suggest that part of the cholestasis-inducing effect of IL-1β is mediated via a CXCR2-dependent feedback mechanism.\n\nInterleukin 1 β suppresses bile acid-induced BSEP expression via a CXCR2-dependent feedback mechanism.", "token_count": 376, "char_count": 1339, "word_count": 194, "semantic_coherence": 1, "information_density": 0.567, "quality_score": 0.7835, "entities": { "genes": [ "CXCR2", "CXCL1", "SB225002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:13.092728", "source": { "split": "train_shard_00000", "doc_id": 575 }, "chunk_id": "train_shard_00000_575_0", "global_id": 640 }, { "text": "Fungal plant pathogens cause major crop losses worldwide, with many featuring compartmentalised genomes that include both core and accessory regions, which are believed to drive adaptation. The highly host-specific fungus Colletotrichum lupini greatly impacts lupin (Lupinus spp.) cultivation. This pathogen is part of clade 1 of the C. acutatum species complex and comprises four genetically uniform, presumably clonal, lineages (I-IV). Despite this, variation in virulence and morphology has been observed within these lineages. To investigate the potential sources of genetic variability in this asexual fungus, we compared the genomes of 16 C. lupini strains and 17 related Colletotrichum species. Phylogenomics confirmed the presence of four distinct lineages, but further examination based on genome size, gene content, transposable elements (TEs), and deletions revealed that lineage II could be split into two groups, II-A and II-B. TE content varied between lineages and correlated strongly with genome size variation, supporting a role for TEs in genome expansion in this species. Pangenome analysis revealed a highly variable accessory genome, including a minichromosome present in lineages II, III, and IV, but absent in lineage I. Accessory genes and effectors appeared to cluster in proximity to TEs. Presence/absence variation of putative effectors was lineage-specific, suggesting that these genes play a crucial role in determining host range. Notably, no effectors were found on the TE-rich minichromosome. Our findings shed light on the potential mechanisms generating genetic diversity in this asexual fungal pathogen that could aid future disease management.\n\nComparative Genomics Reveals Sources of Genetic Variability in the Asexual Fungal Plant Pathogen Colletotrichum lupini.", "token_count": 428, "char_count": 1800, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6836, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:13.716840", "source": { "split": "train_shard_00000", "doc_id": 576 }, "chunk_id": "train_shard_00000_576_0", "global_id": 641 }, { "text": "Pangenomes can facilitate a deeper understanding of genome complexity. Using de novo phased long-read assemblies of eight representative goat breeds, we constructed a graph-based pangenome of goats (Capra hircus) and discovered 113-Mb autosomal novel sequences. Combining this multi-assembly pangenome with low-coverage PacBio HiFi sequences, we constructed a long-read structural variations (SVs) database containing 59,325 SV deletions, 84,910 SV insertions, and 24,954 other complex SV alleles. This resource allowed reliable graph-based genotyping from short reads of 79 wild and 1,148 worldwide domestic goats. Selection signal analysis of SV captured a novel immune-related domestication locus containing the galectin-9 gene and extra copies of the ruminant-specific galectin-9-like genes (LGALS9L), which have high tissue specificity. A segmental duplication in domestic goats generates three additional LGALS9L copies. Ancient goat genome sequences show a gradual increase in frequency of this duplication from the Neolithic to the present. Two other newly detected SVs also have higher selection signals than adjacent SNPs, a truncated-LINE1 deletion in EDAR2 associated with cashmere production and a VNTR-related insertion in PAPSS2 linked to high-altitude adaptation. In summary, the multi-assembly goat pangenome and long-read SV database facilitates detecting complex variations that are important in evolution and selection.\n\nA Graph-based Goat Pangenome Reveals Structural Variations Involved in Domestication and Adaptation.", "token_count": 395, "char_count": 1541, "word_count": 206, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [ "PAPSS2", "LINE1", "LGALS9L", "EDAR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:14.338878", "source": { "split": "train_shard_00000", "doc_id": 577 }, "chunk_id": "train_shard_00000_577_0", "global_id": 642 }, { "text": "Much of prokaryotic comparative genomics currently relies on two critical computational tasks: pangenome inference and core genome inference. Pangenome inference involves clustering genes from a set of genomes into gene families, enabling genome-wide association studies and evolutionary history analysis. The core genome represents gene families present in nearly all genomes and is required to infer a high-quality phylogeny. For species-level datasets, fast pangenome inference tools have been developed. However, tools applicable to more diverse datasets are currently slow and scale poorly.\n\nSCARAP: scalable cross-species comparative genomics of prokaryotes.", "token_count": 146, "char_count": 664, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7841, "quality_score": 0.892, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:14.772359", "source": { "split": "train_shard_00000", "doc_id": 578 }, "chunk_id": "train_shard_00000_578_0", "global_id": 643 }, { "text": "Antibiotic therapy has been the most popular line of treatment for the control of mastitis worldwide during the last few decades. Alternative and sustainable treatments must be developed because pathogens are becoming more resistant to antibiotics, leading to the development and spread of antimicrobial resistance (AMR). The aim of the current investigation was to isolate lactic acid bacteria (LAB) with probiotic potential that can inhibit mastitis-causing pathogens to prevent bovine mastitis. Milk samples were collected from Sahiwal cows, and a total of 150 bacteria were isolated, of which 76 were found to be catalase negative, and resistant to vancomycin. Twenty-three isolates displayed greater acid and bile tolerance, with > 90% survivability, and were molecularly characterized by 16S rRNA partial sequencing. The autoaggregation percentages for SML7 and SML41 were greater (p<0·05) 80.38±0.19% and 80.28±0.04%, respectively. SML10 (92.04±0.26 μmol/mL) had the highest (p<0.05) ferric-reducing antioxidant power (FRAP) activity, while SML20 (52.1±0.99%) had the highest 1,1 diphenyl 2 picrylhydrazyl (DPPH) scavenging activity. All the strains were nonhemolytic or nonmucinolytic. The highest antimicrobial activity was observed in several strains (SML41, SML63, SML76, and SML60) against common mastitis-causing pathogens, namely, E. coli ATCC25922, Staphylococcus aureus ATCC25923, Enterococcus faecalis NCDC114, Streptococcus agalactiae NCDC208, and Enterococcus faecium NCDC124. The coaggregation efficacy of SML20 with S", "token_count": 501, "char_count": 1538, "word_count": 208, "semantic_coherence": 1, "information_density": 0.7404, "quality_score": 0.8702, "entities": { "genes": [ "ATCC25923", "NCDC114", "SML76", "SML41", "SML7", "SML60", "ATCC25922", "NCDC208", "SML20", "SML63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:15.425703", "source": { "split": "train_shard_00000", "doc_id": 579 }, "chunk_id": "train_shard_00000_579_0", "global_id": 644 }, { "text": "aureus was the highest (67.69±1.21%), while SML41 showed the highest (69.75±0.29%) coaggregation efficacy with E. faecalis NCDC114 and SML63 (68.078±0.26) with S. agalactiae NCDC208. Overall, seven distinct lactic acid bacterial clusters were identified by cluster analysis of the phylogenetic tree as follows: Enterococcus hirae (1), Limosilactobacillus reuteri (1), Pediococcus acidilactici (4), Weissella confusa (11), Lactobacillus helveticus (3), Limosilactobacillus balticus (2), and Lacticaseibacillus rhamnosus (1). The Lactobacillus helveticus SML41, Lactobacillus helveticus SML60, Weissella confusa SML61, Lacticaseibacillus rhamnosus SML63, Weissella confusa SML64, and Pediococcus acidilactici SML76 isolates were found to possess the most desirable characteristics of potential probiotics based on principal component analysis (PCA). Therefore, the strains chosen in the current investigation demonstrated techno-functional characteristics that rendered them appropriate for probiotic use to treat and prevent intramammary infections in dairy cattle in a sustainable manner.\n\nScreening of lactic acid bacteria from the milk of Sahiwal cows and characterization of their probiotic potential for preventing bovine mastitis.", "token_count": 386, "char_count": 1235, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [ "SML64", "NCDC114", "SML76", "SML41", "SML60", "NCDC208", "SML63", "SML61" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:16.033121", "source": { "split": "train_shard_00000", "doc_id": 579 }, "chunk_id": "train_shard_00000_579_1", "global_id": 645 }, { "text": "Morganella morganii has been recognized as an important opportunistic pathogen that is becoming increasingly prevalent worldwide. However, the current global evolutionary dynamics and emergence of ARGs remain obscure. The present study determined the global distribution, genomic classification, phylogeny, and monitor longitudinal resistome changes. During 1900-2024, a total of 1027 non-duplicate Morganella genomes have been reported from 49 countries. The countries with the highest number were China (433), the USA (143), and France (74). Through ANI distance analysis and core genome phylogeny, Morganella was reclassified into six species: M. morganii, M. sibonii, M. chanii, M. laugraudii, M. kristinii, M. psychrotolerans. Further analysis using cgMLST identified 87 distinct genetic clusters and 737 singleton strains, indicating a high level of multi-locus sequence type diversity and local clonal outbreaks. Bayesian evolutionary analysis revealed the most recent common ancestor year and potential global transmission routes. A total of 195 ARGs were carried by Morganella isolates, with each genome containing between 2 and 544 ARGs. The most common ARGs were associated with resistance to the following drug-classes: aminoglycosides, beta-lactam, chloramphenicol, sulfamides, and tetracycline. Twenty-one carbapenemase-encoding genes were identified in 22 countries, with bla\n\nGlobal phylogeography and antibiotic resistance characteristics of Morganella: An epidemiological, spatial, comparative genomic study.", "token_count": 391, "char_count": 1526, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7264, "quality_score": 0.8632, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:16.647817", "source": { "split": "train_shard_00000", "doc_id": 580 }, "chunk_id": "train_shard_00000_580_0", "global_id": 646 }, { "text": "Oral antibiotic use is both widespread and frequent in older adults and has been linked to dysbiosis of the gut microbiota, enteric infection, and chronic diseases. Diet and nutrients, particularly prebiotics, may modify the susceptibility of the gut microbiome to antibiotic-induced dysbiosis. We fed 12-month-old mice a high glycemic (HG) or low glycemic (LG) diet with or without antibiotics (ampicillin and neomycin) for an additional 11 months. The glycemic index was modulated by the ratio of rapidly digested amylopectin starch to slowly digested amylose, a type-2-resistant starch. We observed a significant decrease in survival of mice fed a HG diet containing antibiotics (HGAbx) relative to those fed a LG diet containing antibiotics (LGAbx). HGAbx mice died with an enlarged and hemorrhagic cecum, which is associated with colonic hyperplasia and goblet cell depletion. Gut microbiome analysis revealed a pronounced expansion of Proteobacteria and a near-complete loss of Bacteroidota and Firmicutes commensal bacteria in HGAbx, whereas the LGAbx group maintained a population of Bacteroides and more closely resembled the LG microbiome. The predicted functional capacity for bile salt hydrolase activity was lost in HGAbx mice but retained in LGAbx mice. An LG diet containing amylose may therefore be a potential therapeutic to prevent antibiotic-induced dysbiosis and morbidity.\n\nDietary prevention of antibiotic-induced dysbiosis and mortality upon aging in mice.", "token_count": 413, "char_count": 1479, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:17.273131", "source": { "split": "train_shard_00000", "doc_id": 581 }, "chunk_id": "train_shard_00000_581_0", "global_id": 647 }, { "text": "There is merit in investigating novel therapeutic molecules that hit vital targets during the viral infection cycle\n\nBiological and computational assessments of thiazole derivative-reinforced bile salt enriched nano carriers: a new gate in targeting SARS-CoV-2 spike protein.", "token_count": 70, "char_count": 275, "word_count": 37, "semantic_coherence": 1, "information_density": 0.973, "quality_score": 0.9865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:17.654241", "source": { "split": "train_shard_00000", "doc_id": 582 }, "chunk_id": "train_shard_00000_582_0", "global_id": 648 }, { "text": "Pangenomes are becoming a powerful framework to perform many bioinformatics analyses taking into account the genetic variability of a population, thus reducing the bias introduced by a single reference genome. With the wider diffusion of pangenomes, integrating genetic variability with transcriptome diversity is becoming a natural extension that demands specific methods for its exploration. In this work, we extend the notion of spliced pangenomes to that of annotated spliced pangenomes; this allows us to introduce a formal definition of Alternative Splicing (AS) events on a graph structure. To investigate the usage of graph pangenomes for the quantification of AS events across conditions, we developed pantas, the first pangenomic method for the detection and differential analysis of AS events from short RNA-Seq reads. A comparison with state-of-the-art linear reference-based approaches proves that pantas achieves competitive accuracy, making spliced pangenomes effective for conducting AS events quantification and opening future directions for the analysis of population-based transcriptomes.\n\nDifferential quantification of alternative splicing events on spliced pangenome graphs.", "token_count": 245, "char_count": 1196, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:18.142847", "source": { "split": "train_shard_00000", "doc_id": 583 }, "chunk_id": "train_shard_00000_583_0", "global_id": 649 }, { "text": "Brassicas are an economically important crop species that provide a source of healthy oil and vegetables. With the rising population and the impact of climate change on agriculture, there is an increasing need to improve agronomically important traits of crops such as Brassica. The genomes of plant species have significant sequence presence absence variation (PAV), which is a source of genetic variation that can be used for crop improvement, and this species variation can be captured through the construction of pangenomes. Graph pangenomes are a recent reference format that represent the genomic variation with a species or population as alternate paths in a sequence graph. Graph pangenomes contain information on alignment, PAV, and annotation. Here we present the first multi-species graph pangenome for Brassica visualized with pangenome analyzer with chromosomal exploration (Panache).\n\nBrassica Panache: A multi-species graph pangenome representing presence absence variation across forty-one Brassica genomes.", "token_count": 210, "char_count": 1023, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:18.607730", "source": { "split": "train_shard_00000", "doc_id": 584 }, "chunk_id": "train_shard_00000_584_0", "global_id": 650 }, { "text": "Weissella, a genus of lactic acid bacteria, has diverse beneficial attributes including probiotic activity and biotechnological applications. Therefore, the investigation of the Weissella genus has garnered growing interest. In this study, we sequenced the complete genome of Weissella paramesenteroides UFTM 2.6.1 isolated from unpasteurized cow's milk from the Triângulo Mineiro region and performed probiogenomic analyses. Taxonomic characterization confirmed the identity of W. paramesenteroides. The genome comprises 1926 protein-coding genes, mainly related to cell metabolism, information storage and processing, and cellular processes and signaling. Ninety-nine unique genes associated with probiotic functions were identified in the genome of W. paramesenteroides UFTM 2.6.1, including genes involved in stress response, bacterial persistence in the gastrointestinal tract, and biosynthesis of vitamins. In silico analysis of bacteriocin-related genes identified Pediocin, and subsequent in vitro testing confirmed that W. paramesenteroides UFTM 2.6.1 exhibits antimicrobial activity against Listeria spp. Genomic characterization revealed the presence of the replicon pLCK4 and four prophage regions, one of which was intact. Moreover, no CRISPR-Cas array or associated Cas proteins were found, along with an absence of resistance and virulence genes, suggesting a safety aspect of the evaluated strain. Pan-genome analysis unveiled 204 exclusive genes in the genome of W. paramesenteroides UFTM 2.6.1, which includes metabolism and stress-associated genes. In general, the results indicate probiotic potential of W. paramesenteroides UFTM 2.6.1. Further studies are required to ensure the safety and beneficial effects of this bacterium in vivo, aiming for future applications in the food industry and animal and human medicine.\n\nUnlocking Probiotic Potential: Genomic Insights into Weissella paramesenteroides UFTM 2.6.1.", "token_count": 491, "char_count": 1933, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6265, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:19.252549", "source": { "split": "train_shard_00000", "doc_id": 585 }, "chunk_id": "train_shard_00000_585_0", "global_id": 651 }, { "text": "Chicken bile is a by-product of chicken processing, rich in chenodeoxycholic acid (CDCA), an active pharmaceutical raw material. In this study, a green measure for the extraction and purification of CDCA from chicken biles by enzymatic hydrolysis and macroporous resins refining was established. For the assisted extraction of CDCA, the active bile salt hydrolase (BSH) from Bifidobacterium was heterologously expressed and applied, its activities on GCDCA and TCDCA were 4.96 ± 0.32 U/mg and 3.07 ± 0.031 U/mg and optimal catalytic conditions for the extraction of CDCA were determined as 0.04 g/g of the enzyme dosage, pH 5.0 and 38 °C. Through validation of the conditions, the yield of CDCA was up to 5.32 %, which was equivalent to that by saponification method. In order to further refine CDCA from the extract obtained by enzyme-assisted extraction, a more preferable resin, AB-8 was selected for the purification of CDCA, which had a good adsorption capacity of 61.06 ± 0.57 mg/g for CDCA. Besides, the obtained CDCA extract was purified through AB-8 resin, the purity of CDCA was improved from 51.7 % to 91.4 % and the recovery yield of CDCA was 87.8 %. The advantages of energy conservation, time saving, economy and environmental friendliness make the measure using enzyme-assisted extraction and macroporous resins refining a promising candidate for isolation of CDCA from chicken bile.\n\nAn efficient measure for the isolation of chenodeoxycholic acid from chicken biles using enzyme-assisted extraction and macroporous resins refining.", "token_count": 436, "char_count": 1548, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5372, "quality_score": 0.7686, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:19.913924", "source": { "split": "train_shard_00000", "doc_id": 586 }, "chunk_id": "train_shard_00000_586_0", "global_id": 652 }, { "text": "Parastagonospora nodorum is necrotrophic fungal pathogen of wheat with significant genomic resources. Population-level pangenome data for 173 isolates, of which 156 were from Western Australia (WA) and 17 were international, were examined for overall genomic diversity and effector gene content. A heterothallic core population occurred across all regions of WA, with asexually-reproducing clonal clusters in dryer northern regions. High potential for SNP diversity in the form of repeat-induced point mutation (RIP)-like transitions, was observed across the genome, suggesting widespread 'RIP-leakage' from transposon-rich repetitive sequences into non-repetitive regions. The strong potential for RIP-like mutations was balanced by negative selection against non-synonymous SNPs, that was observed within protein-coding regions. Protein isoform profiles of known effector loci (SnToxA, SnTox1, SnTox3, SnTox267, and SnTox5) indicated low-levels of non-synonymous and high-levels of silent RIP-like mutations. Effector predictions identified 186 candidate secreted predicted effector proteins (CSEPs), 69 of which had functional annotations and included confirmed effectors. Pangenome-based effector isoform profiles across WA were distinct from global isolates and were conserved relative to population structure, and may enable new approaches for monitoring crop disease pathotypes.\n\nRepeat-induced point mutations driving Parastagonospora nodorum genomic diversity are balanced by selection against non-synonymous mutations.", "token_count": 372, "char_count": 1528, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:20.527779", "source": { "split": "train_shard_00000", "doc_id": 587 }, "chunk_id": "train_shard_00000_587_0", "global_id": 653 }, { "text": "Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (the core genome) and measuring the extent of genomic variability as a function of sample size (pangenome growth).\n\nPanacus: fast and exact pangenome growth and core size estimation.", "token_count": 145, "char_count": 671, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7525, "quality_score": 0.8762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:20.990025", "source": { "split": "train_shard_00000", "doc_id": 588 }, "chunk_id": "train_shard_00000_588_0", "global_id": 654 }, { "text": "A single reference genome does not fully capture species diversity. By contrast, a pangenome incorporates multiple genomes to capture the entire set of nonredundant genes in a given species, along with its genome diversity. New sequencing technologies enable researchers to produce multiple high-quality genome sequences and catalog diverse genetic variations with better precision. Pangenomic studies have detected structural variants in plant genomes, dissected the genetic architecture of agronomic traits, and helped unravel molecular underpinnings and evolutionary origins of plant phenotypes. The pangenome concept has further evolved into a so-called super-pangenome that includes wild relatives within a genus or clade and shifted to graph-based reference systems. Nevertheless, building pangenomes and representing complex structural variants remain challenging in many crops. Standardized computing pipelines and common data structures are needed to compare and interpret pangenomes. The growing body of plant pangenomics data requires new algorithms, huge data storage capacity, and training to help researchers and breeders take advantage of newly discovered genes and genetic variants.\n\nWhat Are We Learning from Plant Pangenomes?", "token_count": 239, "char_count": 1243, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7219, "quality_score": 0.8609, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:21.506630", "source": { "split": "train_shard_00000", "doc_id": 589 }, "chunk_id": "train_shard_00000_589_0", "global_id": 655 }, { "text": "GCN2 is a conserved receptor kinase activating the integrated stress response (ISR) in eukaryotic cells. The ISR kinases detect accumulation of stress molecules and reprogram translation from basal tasks to preferred production of cytoprotective proteins. GCN2 stands out evolutionarily among all protein kinases due to the presence of a histidyl-tRNA synthetase-like (HRSL) domain, which arises only in GCN2 and is located next to the kinase domain (KD). How HRSL contributes to GCN2 signaling remains unknown. Here, we report a 3.2 Å cryo-EM structure of HRSL from thermotolerant yeast\n\nCryo-EM structure of histidyl-tRNA synthetase-like domain reveals activating crossed helices at the core of GCN2.", "token_count": 192, "char_count": 702, "word_count": 103, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [ "GCN2" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:21.957153", "source": { "split": "train_shard_00000", "doc_id": 590 }, "chunk_id": "train_shard_00000_590_0", "global_id": 656 }, { "text": "Hyperlipidemia is a well-known risk factor for atherosclerosis and subsequent atherosclerotic cardiovascular diseases that are associated with high morbidity and mortality in obese and diabetic patients worldwide. The current study looked on rosmarinic acid's cadioprotective effects in rats fed a high-fat diet as there was no study on this aspect. The rats were given a high-fat diet comprising of 84.3 % conventional laboratory rat chow, 5 % lard, 10 % egg yolk powder, 0.2 % cholesterol, and 0.5 % bile salt to produce hypercholesterolemia. Over a span of eight weeks. The plasma lipid profile, cardiac marker enzymes, membrane bound ATPases, lysosomal enzymes, CRP, fibrinogen, proinflammatory cytokines (IL-1β, IL-6,TNF-α, NF-κB),anti-inflammatory cytokine(IL-10) lipid peroxidation markers, enzymatic and non-enzymatic antioxidant enzymes activity were examined. The thoracic aorta's histopathology was also analyzed. It was discovered that the rats fed a high-fat diet had hypercholesterolemia and showed aberrant values in the aforementioned parameters. However, rats given rosmarinic acid (100 mg/kg b.w.) had these anomalies reversed to near-normal levels. The biochemical investigation was corroborated by enhanced histological examination of the thoracic aorta in rats suffering from hypercholestolemia. The effects of rosmarinic acid on a number of measures were similar to those of the prescription medication simvastatin. These findings revealed that rosmarinic acid is an important component in the cardiovascular system's defence against a high-fat diet induced hypercholesterolemia.", "token_count": 488, "char_count": 1601, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6742, "quality_score": 0.8371, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:22.600075", "source": { "split": "train_shard_00000", "doc_id": 591 }, "chunk_id": "train_shard_00000_591_0", "global_id": 657 }, { "text": "Rosmarinic acid alleviates the cardiac abnormalities in high fat diet induced hypercholesterolemic rats.", "token_count": 29, "char_count": 104, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:22.958762", "source": { "split": "train_shard_00000", "doc_id": 591 }, "chunk_id": "train_shard_00000_591_1", "global_id": 658 }, { "text": "Cholestatic liver diseases, accompanied by the hepatic accumulation of bile salts, frequently lead to liver fibrosis, while underlying profibrogenic mechanisms remain incompletely understood. Here, we evaluated the role of extracellular pH (pHe) on bile salt entry and hepatic stellate cell (HSC) activation and proliferation. As modulators of intracellular pH (pHi), various proton pump inhibitors (PPI) were tested for their ability to prevent bile salt entry and HSC activation. Lastly, the PPI pantoprazole was employed in the 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC)-diet model of cholestatic liver fibrosis. We found in vitro, that slightly acidic pHe (7.2-7.3) enhanced bile salt accumulation in HSC and was a prerequisite to bile salt-induced HSC activation. Pantoprazole in the DDC model exhibited antifibrotic effects. We conclude that bile salt-induced activation of HSC may depend on the slightly acidic microenvironment present in the perisinusoidal space and modulation of pHi in HSC may offer a novel pharmacological target in cholestatic disease.\n\nThe acidic microenvironment in the perisinusoidal space critically determines bile salt-induced activation of hepatic stellate cells.", "token_count": 332, "char_count": 1204, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5843, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:23.522512", "source": { "split": "train_shard_00000", "doc_id": 592 }, "chunk_id": "train_shard_00000_592_0", "global_id": 659 }, { "text": "Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction is resource intensive and hard to be parallelized, and many methods for querying large full-text indices only report exact matches or their simple extensions. These limitations have hampered the biological applications of full-text indices.\n\nBWT construction and search at the terabase scale.", "token_count": 109, "char_count": 521, "word_count": 72, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:23.906158", "source": { "split": "train_shard_00000", "doc_id": 593 }, "chunk_id": "train_shard_00000_593_0", "global_id": 660 }, { "text": "Over the past few decades, there has been increasing interest in using probiotics as an alternative to antibiotics. Researchers have conducted studies to investigate bacterial strains for their probiotic potential. Like other animals, fish also have several bacterial strains in their gut that possess probiotic properties, although this is limited to Bacillus species. Therefore, this study aimed to isolate and characterize probiotic Bacillus species from the gut of Masheer fish (Tor Puititora). Four pure bacterial isolates were selected as potential probiotic strains based on selection criteria, including survival rate in acid and bile salt. The isolates exhibited significant antimicrobial activity against pathogenic bacteria, including Escherichia coli (ATCC8739), Pseudomonas aeruginosa (ATCC9027), and Staphylococcus aureus (ATCC6538). MF2 and MF3 demonstrated clear zones, including antimicrobial activity against all three indicator pathogens. MF1 and MF4 exhibited antimicrobial activity against E. coli (ATCC8739) and P. aeruginosa (ATCC9027). Furthermore, the 16S rRNA gene sequences of all isolates exhibited a close association with Bacillus tequilensis (KCTC13622), with nucleotide similarity of 98.63%, 98.25%, 98.80%, and 98.35%, respectively. Our results demonstrate that these bacterial isolates show promise as an alternative to antibiotics in the fisheries food system. In this study, all isolates identified in the fish gut were subspecies of B. tequilensis.\n\nIdentification and molecular characterization of potential probiotic subspecies of Bacillus tequilensis isolated from the gut of Masheer fish, using 16S rRNA gene sequencing.", "token_count": 449, "char_count": 1661, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8164, "entities": { "genes": [ "MF4", "KCTC13622", "ATCC9027", "ATCC8739", "MF1", "MF2", "ATCC6538", "MF3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:24.538214", "source": { "split": "train_shard_00000", "doc_id": 594 }, "chunk_id": "train_shard_00000_594_0", "global_id": 661 }, { "text": "S-adenosylmethionine (SAM), a key molecule in plant biology, plays an essential role in stress response and growth regulation. Despite its importance, the SAM synthetase\n\nPan-genome wide identification and analysis of the", "token_count": 55, "char_count": 221, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9032, "quality_score": 0.9516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:24.910847", "source": { "split": "train_shard_00000", "doc_id": 595 }, "chunk_id": "train_shard_00000_595_0", "global_id": 662 }, { "text": "The wisent (Bison bonasus) is Europe's largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of the highly conserved single copy mammalian genes which improves contiguity a thousand-fold over an existing assembly. Extended runs of homozygosity in the wisent genome compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1580 bp deletion removing the protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 sequenced samples across the Bovinae subfamily showed that the deletion is fixed in both Bison species but absent in Bos and Bubalus. The THRSP transcript is abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus, but absent in bison. This indicates that the deletion likely inactivates THRSP in bison. We show that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also demonstrate that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing.\n\nGenome assembly of wisent (Bison bonasus) uncovers a deletion that likely inactivates the THRSP gene.", "token_count": 397, "char_count": 1467, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6449, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:25.527263", "source": { "split": "train_shard_00000", "doc_id": 596 }, "chunk_id": "train_shard_00000_596_0", "global_id": 663 }, { "text": "Pseudomonas fluorescens is commonly found in diverse environments and is well known for its metabolic and antagonistic properties. Despite its remarkable attributes, its potential role in promoting plant growth remains unexplored. This study examines these traits across 14 strains residing in diverse rhizosphere environments through pangenome and comparative genome analysis, alongside molecular docking studies against Erwinia amylovora to combat fire blight. Whole genome analysis revealed circular chromosome (6.01-7.07 Mb) with GC content averaging 59.95-63.39%. Predicted genes included 16S rRNA and protein-coding genes ranging from 4435 to 6393 bp and 1527 to 1541 bp, respectively. Pangenome analysis unveiled an open pangenome, shedding light on genetic factors influencing plant growth promotion and biocontrol, including nitrogen fixation, phosphorus solubilization, siderophore production, stress tolerance, flagella biosynthesis, and induced systemic resistance. Furthermore, pyrrolnitrin, phenazine-1-carboxylic acid, pyoluteorin, lokisin, 2,4-diacetylpholoroglucinol and pseudomonic acid were identified. Molecular docking against key proteins of E. amylovora highlighted the high binding affinities of 2,4-diacetylphloroglucinol, pseudomonic acid, and lokisin. These findings underscore the multifaceted role of P. fluorescens in plant growth promotion and biocontrol, with key biomolecules showing promising applications in plant growth and defense against pathogens.\n\nInvestigating the genomic and metabolic abilities of PGPR Pseudomonas fluorescens in promoting plant growth and fire blight management.", "token_count": 446, "char_count": 1623, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7044, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:26.157086", "source": { "split": "train_shard_00000", "doc_id": 597 }, "chunk_id": "train_shard_00000_597_0", "global_id": 664 }, { "text": "Mycotoxin contamination is a major food safety issue worldwide, posing a serious threat to animal production performance and human health. Lactic acid bacteria are generally regarded as safe fermentation potential probiotics. They have the advantages of low toxicity, small pollution, strong specificity and high safety, and can reduce the contamination of microorganisms and mycotoxins. In this study, we compared the mycotoxin degradation capacity of 15 lactic acid bacteria strains from the rumen of Qinghai yak, through comprehensive analysis, we finally identified the strains as potential probiotics because they have a fast growth speed, strong acid production capacity (pH < 4.5), and they can grow normally in an environment with a pH of 3.5, bile salt concentration of 0.1%, and good self-agglutination and hydrophobicity. It was found that the fermentation group (\n\nScreening, Identification and Application of Lactic Acid Bacteria for Degrading Mycotoxin Isolated from the Rumen of Yaks.", "token_count": 245, "char_count": 999, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:26.643452", "source": { "split": "train_shard_00000", "doc_id": 598 }, "chunk_id": "train_shard_00000_598_0", "global_id": 665 }, { "text": "Existing microbiota databases are biased toward adult samples, hampering accurate profiling of the infant gut microbiome. Here, we generated a metagenome-assembled genome inventory for children (MAGIC) from a large collection of bulk and viral-like particle-enriched metagenomes from 0 to 7 years of age, encompassing 3,299 prokaryotic and 139,624 viral species-level genomes, 8.5% and 63.9% of which are unique to MAGIC. MAGIC improves early-life microbiome profiling, with the greatest improvement in read mapping observed in Africans. We then identified 54 candidate keystone species, including several Bifidobacterium spp. and four phages, forming guilds that fluctuated in abundance with time. Their abundances were reduced in preterm infants and were associated with childhood allergies. By analyzing the B. longum pangenome, we found evidence of phage-mediated evolution and quorum sensing-related ecological adaptation. Together, the MAGIC database recovers genomes that enable characterization of the dynamics of early-life microbiomes, identification of candidate keystone species, and strain-level study of target species.\n\nA metagenome-assembled genome inventory for children reveals early-life gut bacteriome and virome dynamics.", "token_count": 317, "char_count": 1242, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7289, "quality_score": 0.8645, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:27.212806", "source": { "split": "train_shard_00000", "doc_id": 599 }, "chunk_id": "train_shard_00000_599_0", "global_id": 666 }, { "text": "The formation of a biomolecular corona on nanoparticle surfaces significantly influences their biological behaviour, particularly in drug delivery applications. Despite the prevalence of ingestion of particles (e.g, during oral drug delivery), our understanding of corona formation within the gastrointestinal (GI) tract remains limited, especially for non-protein components. The hypothesis of this work is that the exposure of nanoparticles to bile components will form a \"corona\" structure and protein corona will represent proteomes different from the original bile fluid. Two major aspects of biomolecular corona formed in GI fluid (hereby termed \"gut corona), which ultimately dictate the fate of particle-based carriers, include the composition and the surface structure of nanoparticle-corona complex.\n\nThe \"gut\" corona at the surface of nanoparticles is dependent on exposure to bile salts and phospholipids.", "token_count": 205, "char_count": 917, "word_count": 127, "semantic_coherence": 1, "information_density": 0.685, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:27.675083", "source": { "split": "train_shard_00000", "doc_id": 600 }, "chunk_id": "train_shard_00000_600_0", "global_id": 667 }, { "text": "A role of gut microbiome in pathogenesis as well as response to treatment is documented in rheumatoid arthritis. Using a novel duodenal derived Prevotella histicola strain MCI 001, we have shown that it suppresses disease progression in a collagen-induced arthritis (CIA), a model for rheumatoid arthritis (RA) using humanized mice expressing HLA-DQ8 gene in the absence of endogenous class II genes. Here we compared efficacy of P. histicola MCI 001 with tumor necrosis factor inhibitor (TNFi) for treating arthritis. DQ8 arthritic mice treated with P. histicola by oral gavage or TNFi, were compared for disease onset, incidence and severity. We demonstrate that oral treatment with P. histicola mimics treatment with TNFi in arthritic DQ8 mice. A pangenome comparison of our P. histicola MCI 001 with its closest available neighbors depicted it as a novel strain with unique gene sequences that may contribute to immune modulatory effects. Notably, it possesses a unique sequence of an outer membrane protein, BtuB, which is involved in vitamin B12 transport. Our data indicate that P. histicola MC001 is an attractive candidate to prevent the progression of disease in RA patients with ongoing disease.\n\nSmall intestinal derived Prevotella histicola simulates biologic as a therapeutic agent.", "token_count": 358, "char_count": 1296, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6181, "quality_score": 0.809, "entities": { "genes": [ "MC001", "DQ8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:28.612579", "source": { "split": "train_shard_00000", "doc_id": 601 }, "chunk_id": "train_shard_00000_601_0", "global_id": 668 }, { "text": "The clinical implication of cefepime HCl (CEF) is compromised owing to restricted oral bioavailability and harmful adverse effects without any authorized oral formulation available. The present investigation provides an innovative sustained-release oral drug delivery strategy that tackles the challenges of limited oral bioavailability and prolongs the half-life of CEF. Accordingly, CEF was loaded into a bilosome, a liposome or noisome-based vesicle employing bile salt as a permeation enhancer. Despite its hydrophilic nature, the drug was effectively loaded into bilosomes. Nine various formulas were fabricated by a reverse phase evaporation method. The resulting vesicles increased the encapsulation efficiency (EE %) from 39.31 ± 0.03 % to 63.09 ± 0.01 %, drug loading capacity (DLC %) from 6.99 ± 0.25 to 42.91 ± 0.11 %, the particle size (PS) from 264 ± 13.52 nm to 405.40 ± 8.91 nm, and the polydispersity index (PDI) values ranged from 0.243 ± 0.040 to 0.430 ± 0.050. The zeta potential (ZP) changed from - 35.67 ± 3.73 mV to - 62.21 ± 2.21 mV. Further, the release profile exhibited dual release pattern within 24 h, with the percentage of release (CR %) expanding from 42 ± 0.13 % to 69.16 ± 0.09 %", "token_count": 418, "char_count": 1212, "word_count": 198, "semantic_coherence": 1, "information_density": 0.7071, "quality_score": 0.8535, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:29.256399", "source": { "split": "train_shard_00000", "doc_id": 602 }, "chunk_id": "train_shard_00000_602_0", "global_id": 669 }, { "text": "The selected formula was found to be B3 with EE % = 56.61 ± 0.02 %, PS = 264 ± 13.52 nm, ZP = - 62.21 ± 2.21 mV, PDI = 0.430 ± 0.050, CR % = 52.94 ± 0.06 %, and IC50 of 3.4 ± 0.40 µg/ml against MCF-7 cells with scattered spherical non-agglomerated vesicles. Additionally, it exhibited higher anti-MRSA biofilm, relative bioavailability (5.1 fold), and antimicrobial capacity against P. aeruginosa, E. coli, B. subtilis, and S. aureus compared to pure CEF. Our data demonstrate that bilosome is a powerful nanocarrier for oral delivery of cefepime, boosting its biological impacts and pharmacokinetic profile.\n\nEffective tailoring of cefepime into bilosomes: A promising nanoplatform for enhancing oral absorption, extending half-life, and evaluating biocompatibility, antibacterial, anti-biofilm, anti-breast cancer activity, ex-vivo, and in-vivo studies.", "token_count": 308, "char_count": 855, "word_count": 131, "semantic_coherence": 1, "information_density": 0.8168, "quality_score": 0.9084, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:29.814388", "source": { "split": "train_shard_00000", "doc_id": 602 }, "chunk_id": "train_shard_00000_602_1", "global_id": 670 }, { "text": "Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.\n\nNiche-specific evolution and gene exchange of Salmonella in retail pork and chicken.", "token_count": 317, "char_count": 1525, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5972, "quality_score": 0.7986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:30.370872", "source": { "split": "train_shard_00000", "doc_id": 603 }, "chunk_id": "train_shard_00000_603_0", "global_id": 671 }, { "text": "The exponential growth of microbial genome data presents unprecedented opportunities for unlocking the potential of microorganisms. The burgeoning field of pangenomics offers a framework for extracting insights from this big biological data. Recent advances in microbial pangenomic research have generated substantial data and literature, yielding valuable knowledge across diverse microbial species. PanKB (pankb.org), a knowledgebase designed for microbial pangenomics research and biotechnological applications, was built to capitalize on this wealth of information. PanKB currently includes 51 pangenomes from 8 industrially relevant microbial families, comprising 8402 genomes, over 500 000 genes and over 7M mutations. To describe this data, PanKB implements four main components: (1) Interactive pangenomic analytics to facilitate exploration, intuition, and potential discoveries; (2) Alleleomic analytics, a pangenomic-scale analysis of variants, providing insights into intra-species sequence variation and potential mutations for applications; (3) A global search function enabling broad and deep investigations across pangenomes to power research and bioengineering workflows; (4) A bibliome of 833 open-access pangenomic papers and an interface with an LLM that can answer in-depth questions using its knowledge. PanKB empowers researchers and bioengineers to harness the potential of microbial pangenomics and serves as a valuable resource bridging the gap between pangenomic data and practical applications.\n\nPanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining.", "token_count": 377, "char_count": 1644, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:30.950941", "source": { "split": "train_shard_00000", "doc_id": 604 }, "chunk_id": "train_shard_00000_604_0", "global_id": 672 }, { "text": "The lactic acid bacteria are one of the sustainable ways of food production. As the native lactic acid bacteria (LAB) easily manipulate the substrate, helps in production of health essential probiotics with enhancing the bioavailability of the substrate. Here also, in present study, the native LAB isolates isolated from the millets and characterize them for the functional analysis for the human health association. In the present study, fermented millet-associated lactic acid bacteria were screened and characterized for their probiotic potential, safety evaluation and antimicrobial activity. A total of 33 isolates were purified as lactic acid bacteria based on colony shape and biochemical assays. However, only 13 isolates were found to be catalase-negative. Among the 13 isolates, 5 isolates exhibited optimum growth at 6.5% and 9.5% of salt concentrations, pH of 4.5 to 8.5 and 17 °C to 40 °C of the temperature. The probiotic properties of the five isolates exhibited that the survival rates in acid and bile salt concentration ranged from 56.2 to 73.7% and 55.3 to 70.3%, respectively. Similarly, the surface hydrophobicity of the isolates was 41-75%. Antibiotic assay revealed that all five isolates were resistant to Amoxicillin, Cloxacillin, and Penicillin-V. Interestingly, all the isolates except ME26 displayed susceptibility towards Penicillin (2 units) and Tetracycline (10 µg). Further, the four isolates (ME25, ME26, ME9, and ME2) had more antifungal activity against Aspergillus flavus. However, only three, except ME1 and ME2, showed maximum antibacterial activity and produced more antimicrobial compounds compared to reference strain L. plantarum Pb3. The potential probiotic isolates were identified as Weisella cibaria ME9, Weisella cibaria ME26, and Weisella confusa ME25.\n\nFunctional and molecular characterization of millet associated probiotic bacteria.", "token_count": 514, "char_count": 1885, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6095, "quality_score": 0.8047, "entities": { "genes": [ "ME26", "ME1", "ME9", "ME2", "ME25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:04:31.596129", "source": { "split": "train_shard_00000", "doc_id": 605 }, "chunk_id": "train_shard_00000_605_0", "global_id": 673 }, { "text": "In this study, four lactic acid bacteria (LAB) strains demonstrating ciprofloxacin, bile salt, gastric fluid, and intestinal fluid tolerance as well as adhesion ability to Caco-2 and HT-29 cells were used to improve and recover the intestinal flora disorders caused by ciprofloxacin, among which, Lactobacillus brevis 505 exhibited excellent adhesion ability to two kinds of cells and colonization ability to mouse intestinal. After ciprofloxacin treatment, certain recovery effect on cecum caused by ciprofloxacin in the mice was found during natural recovery (group 5C2), but it was challenging to fully restore the intestinal integrity to the initial level. After L. brevis 505 intervention (group 5C5), the intestinal damage to the colon and ileum caused by ciprofloxacin in mice was significantly alleviated; the recovery effect was better than that of natural recovery. Additionally, L. brevis 505 could effectively regulate INF-γ, sIgA, and RegIIIγ increase induced by ciprofloxacin. Shannon and Simpson index of the intestinal flora of mice in 5C5 group were higher than those in other group, the relative abundance of Bifidobacterium and Lactobacillus in the mice in 5C5 group was increased, indicating that LAB can better restore the structure and abundance of intestinal microflora. Consequently, L. brevis 505 shows promise as a probiotic for gut microbiota restoration and rebuilding during antibiotic therapy.\n\nImprovement and Recovery of Intestinal Flora Disorder Caused by Ciprofloxacin Using Lactic Acid Bacteria.", "token_count": 428, "char_count": 1530, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5689, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:32.246202", "source": { "split": "train_shard_00000", "doc_id": 606 }, "chunk_id": "train_shard_00000_606_0", "global_id": 674 }, { "text": "GENCODE produces comprehensive reference gene annotation for human and mouse. Entering its twentieth year, the project remains highly active as new technologies and methodologies allow us to catalog the genome at ever-increasing granularity. In particular, long-read transcriptome sequencing enables us to identify large numbers of missing transcripts and to substantially improve existing models, and our long non-coding RNA catalogs have undergone a dramatic expansion and reconfiguration as a result. Meanwhile, we are incorporating data from state-of-the-art proteomics and Ribo-seq experiments to fine-tune our annotation of translated sequences, while further insights into function can be gained from multi-genome alignments that grow richer as more species' genomes are sequenced. Such methodologies are combined into a fully integrated annotation workflow. However, the increasing complexity of our resources can present usability challenges, and we are resolving these with the creation of filtered genesets such as MANE Select and GENCODE Primary. The next challenge is to propagate annotations throughout multiple human and mouse genomes, as we enter the pangenome era. Our resources are freely available at our web portal www.gencodegenes.org, and via the Ensembl and UCSC genome browsers.\n\nGENCODE 2025: reference gene annotation for human and mouse.", "token_count": 297, "char_count": 1364, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:32.821373", "source": { "split": "train_shard_00000", "doc_id": 607 }, "chunk_id": "train_shard_00000_607_0", "global_id": 675 }, { "text": "Block copolymer micelles have been increasingly used for the solubilization and delivery of hydrophobic drugs. There exists a possibility of dissociation of micelles and formation of other association structures in contact with the gastrointestinal fluid. In this study, we demonstrated the effect of the fed-state intestinal fluid (FeSSIF) upon characteristics of bare and quercetin (QCT)-loaded pluronic 123 (P123) micelles. Characterizations were performed using dynamic light scattering (DLS),\n\nComparative Analysis of Bare and Quercetin-Loaded Nonionic Block Copolymer Micelles in an Artificial Gastrointestinal Medium.", "token_count": 153, "char_count": 624, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7561, "quality_score": 0.878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:33.305752", "source": { "split": "train_shard_00000", "doc_id": 608 }, "chunk_id": "train_shard_00000_608_0", "global_id": 676 }, { "text": "This study aimed to determine the taxonomic status of a new group of bovine strains of the genus Acinetobacter characterized by the rare ability to grow at temperatures above 44 °C. Initially, 24 strains were isolated from cattle feces collected at 11 farms in Czechia in 2022, representing a tentative new species based on preliminary whole-cell MALDI-TOF MS identification and rpoB gene sequencing. Twelve strains encompassing the within-group diversity were studied in detail, including whole genome de novo sequencing. Core genome-based phylogenetic analysis revealed that the 12 strains form a distinct clade within the genus. The genomic average nucleotide identity based on BLAST (ANIb) values within the clade were ≥ 98.2%, whereas the ANIb values between the clade and the known Acinetobacter species were < 83%. Each of the 12 genomes consisted of a circular chromosome (3.05-3.28 Mb) and 1-6 extrachromosomal elements (1.43-122.5 kb). All strains were non-glucose oxidizing, non-hemolytic, non-proteolytic, and prototrophic, and used acetate, ethanol, and DL-lactate as sole carbon and energy sources. Unrestricted growth at 47 °C was their unique diagnostic characteristic in a genus-wide comparative analysis and their growth kinetics at 37-46 °C differed from that of Acinetobacter baumannii. The studied strains were susceptible to 18 antibiotics except for sporadic resistance to streptomycin, tetracycline, and sulfonamides associated with the presence of strA/strB, tet(Y), and sul2 genes, respectively. We conclude that the studied strains represent a new species, for which we propose the name Acinetobacter thermotolerans sp. nov. The type strain is ANC 7454", "token_count": 483, "char_count": 1679, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:33.956141", "source": { "split": "train_shard_00000", "doc_id": 609 }, "chunk_id": "train_shard_00000_609_0", "global_id": 677 }, { "text": "Proposal of Acinetobacter thermotolerans sp. nov. to accommodate bovine feces-dwelling bacteria growing at 47 °C.", "token_count": 35, "char_count": 113, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:34.322130", "source": { "split": "train_shard_00000", "doc_id": 609 }, "chunk_id": "train_shard_00000_609_1", "global_id": 678 }, { "text": "Health authorities were notified of a suspected outbreak of foodborne disease in a hospital in South Africa, where staff and patients reported acute onset of abdominal cramps, diarrhoea, fever and rigours after eating a chicken pasta meal. The aim of this report is to discuss the use of whole genome sequencing (WGS) analysis of bacterial isolates to support an epidemiological investigation. An epidemiological investigation led by the Infection Control Manager of the hospital and supported by an outbreak response team was conducted. Standard microbiological procedures were used to process stool samples and culture/identify diarrhoeal pathogens. Bacterial cultures were investigated using WGS performed using Illumina NextSeq technology, and WGS data were analysed using multiple bioinformatics tools, including those available at the Center for Genomic Epidemiology and EnteroBase. Core genome multilocus sequence typing (cgMLST) was used to investigate the phylogeny of isolates. Forty-nine cases were identified, with stool samples collected from 21 cases, and nontyphoidal\n\nWhole genome sequencing assisted outbreak investigation of Salmonella enteritidis, at a hospital in South Africa, September 2022.", "token_count": 280, "char_count": 1213, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:34.877829", "source": { "split": "train_shard_00000", "doc_id": 610 }, "chunk_id": "train_shard_00000_610_0", "global_id": 679 }, { "text": "Lipids in human intestinal fluids (HIF) form various structures, resulting in phase separation in the form of a lipid fraction and a micellar aqueous fraction. Currently used fed state simulated intestinal fluids (SIF) lack phase separation, highlighting the need for a deeper understanding of the effect of these fractions on intestinal drug solubilization in HIF to improve simulation accuracy. In this study, duodenal fluids aspirated from 21 healthy volunteers in fasted, early fed, and late fed states were used to generate 7 HIF pools for each prandial state. The apparent solubility of seven lipophilic model drugs was measured across these HIF pools, differentiating between the micellar fraction and the total sample (including both micellar and lipid fractions). The solubilizing capacities of these fluids were analyzed in relation to their composition, including total lipids, bile salts, phospholipids, total cholesterol, pH, and total protein. The solubility data generated in this work demonstrated that current fed state SIF effectively predicted the average solubility in the micellar fraction of HIF but failed to discern the considerable variability between HIF pools. Furthermore, the inclusion of a lipid fraction significantly enhanced the solubility of fed state HIF pools, resulting on average in a 13.9-fold increase in solubilizing capacity across the seven model compounds. Although the average composition of the fluids was consistent with previous studies, substantial variability was observed in micellar lipid concentrations, despite relatively stable total lipid concentrations. This variability is critical, as evidenced by the strong correlations between the solubilizing capacity of the micellar fraction and its micellar lipid concentrations. Additionally, this study identified that fluctuations in bile salt concentrations and pH contributed to the observed variability in micellar lipid concentration. In summary, the influence of the lipid fraction on solubility was 2-fold: it enhanced the solubility of lipophilic drugs in the total fluid, and contributed to the variability in the solubilizing capacity of the micellar fraction.\n\nUnderstanding the Impact of Lipids on the Solubilizing Capacity of Human Intestinal Fluids.", "token_count": 514, "char_count": 2264, "word_count": 326, "semantic_coherence": 1, "information_density": 0.4816, "quality_score": 0.7408, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:04:35.530125", "source": { "split": "train_shard_00000", "doc_id": 611 }, "chunk_id": "train_shard_00000_611_0", "global_id": 680 }, { "text": "Wild species of crops serve as a valuable germplasm resource for breeding of modern cultivars. Rice (Oryza sativa L.) is a vital global staple food. However, research on genome evolution and diversity of wild rice species remains limited. Here, we present nearly complete genomes of 13 representative wild rice species. By integrating with four previously published genomes for pangenome analysis, a total of 101,723 gene families are identified across the genus, including 9834 (9.67%) core gene families. Additionally, 63,881 gene families absent in cultivated rice species but present in wild rice species are discovered. Extensive structural rearrangements, sub-genomes exchanges, widespread allelic variations, and regulatory sequence variations are observed in wild rice species. Interestingly, expanded but less diverse disease resistance genes in the genomes of cultivated rice, likely due to the loss of some resistance genes and the fixing and amplification of genes encoding resistance genes to specific diseases during domestication and artificial selection. This study not only reveals natural variations valuable for gene-level studies and breeding selection but also enhances our understanding on rice evolution and domestication.\n\nGenome evolution and diversity of wild and cultivated rice species.", "token_count": 274, "char_count": 1314, "word_count": 187, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:36.075731", "source": { "split": "train_shard_00000", "doc_id": 612 }, "chunk_id": "train_shard_00000_612_0", "global_id": 681 }, { "text": "[The pangenome integrates the vast genetic diversity of the human population].", "token_count": 16, "char_count": 78, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:36.437296", "source": { "split": "train_shard_00000", "doc_id": 613 }, "chunk_id": "train_shard_00000_613_0", "global_id": 682 }, { "text": "Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further impacting genotyping performance. Recent works highlight the advantage of haplotype-resolved pangenome graphs in addressing these challenges. Building on these developments, we propose a rigorous alignment-free genotyping framework. Our formulation seeks a path through the pangenome graph that maximizes the matches between the path and substrings of sequencing reads (e.g.,\n\nInteger programming framework for pangenome-based genome inference.", "token_count": 164, "char_count": 761, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8041, "quality_score": 0.9021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:36.878984", "source": { "split": "train_shard_00000", "doc_id": 614 }, "chunk_id": "train_shard_00000_614_0", "global_id": 683 }, { "text": "Compressed full-text indexes enable efficient sequence classification against a pangenome or tree-of-life index. Past work on compressed-index classification used matching statistics or pseudo-matching lengths to capture the fine-grained co-linearity of exact matches. But these fail to capture coarse-grained information about whether seeds appear co-linearly in the reference. We present a novel approach that additionally obtains coarse-grained co-linearity (\"chain\") statistics. We do this without using a chaining algorithm, which would require superlinear time in the number of matches. We start with a collection of strings, avoiding the multiple-alignment step required by graph approaches. We rapidly compute multi-maximal unique matches (multi-MUMs) and identify BWT sub-runs that correspond to these multi-MUMs. From these, we select those that can be \"tunneled,\" and mark these with the corresponding multi-MUM identifiers. This yields an\n\nImproved pangenomic classification accuracy with chain statistics.", "token_count": 222, "char_count": 1018, "word_count": 135, "semantic_coherence": 1, "information_density": 0.763, "quality_score": 0.8815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:37.354992", "source": { "split": "train_shard_00000", "doc_id": 615 }, "chunk_id": "train_shard_00000_615_0", "global_id": 684 }, { "text": "Pangenomes have emerged in response to limitations associated with traditional linear reference genomes. In contrast to a traditional reference that is (usually) assembled from a single individual, pangenomes aim to represent all of the genomic variation found in a group of organisms. The term 'pangenome' is currently used to describe multiple different types of genomic information, and limited language is available to differentiate between them. This is frustrating for researchers working in the field and confusing for researchers new to the field. Here, we provide an introduction to pangenomics relevant to both prokaryotic and eukaryotic organisms and propose a formalization of the language used to describe pangenomes (see the Glossary) to improve the specificity of discussion in the field.\n\nA gentle introduction to pangenomics.", "token_count": 173, "char_count": 842, "word_count": 124, "semantic_coherence": 1, "information_density": 0.621, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:37.812547", "source": { "split": "train_shard_00000", "doc_id": 616 }, "chunk_id": "train_shard_00000_616_0", "global_id": 685 }, { "text": "This study investigated the modification of highland barley bran through co-fermentation of Lactobacillus bulgaricus and Kluyveromyces marxianus, and developed a dynamic prediction model for DF content under these co-fermentation conditions using machine learning algorithms. The results showed that the XGBoost algorithm could predict changes in the DF component content (R\n\nMachine learning-enhanced modeling and characterization for optimizing dietary Fiber production from Highland barley bran.", "token_count": 110, "char_count": 498, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7969, "quality_score": 0.8984, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:38.194684", "source": { "split": "train_shard_00000", "doc_id": 617 }, "chunk_id": "train_shard_00000_617_0", "global_id": 686 }, { "text": "Bifidobacterium longum (B. longum) is a species of the core microbiome in the human gut, whose abundance is closely associated with host age and health status. B. longum has been shown to modulate host gut microecology and have the potential to alleviate various diseases. Comprehensive understanding on the colonization mechanism of B. longum and mechanism of the host-B. longum interactions, can provide us possibility to prevent and treat human diseases through B. longum-directed strategies. In this review, we summarized the gut colonization characteristics of B. longum, discussed the diet factors that have ability/potential to enrich indigenous and/or ingested B. longum strains, and reviewed the intervention mechanisms of B. longum in multiple diseases. The key findings are as follows: First, B. longum has specialized colonization mechanisms, like a wide carbohydrate utilization spectrum that allows it to adapt to the host's diet, species-level conserved genes encoding bile salt hydrolase (BSHs), and appropriate bacterial surface structures. Second, dietary intervention (e.g., anthocyanins) could effectively improve the gut colonization of B. longum, demonstrating the feasibility of diet-tuned strain colonization. Finally, we analyzed the skewed abundance of B. longum in different types of diseases and summarized the main mechanisms by which B. longum alleviates digestive (repairing the intestinal mucosal barrier by stimulating Paneth cell activity), immune (up-regulating the regulatory T cell (Treg) populations and maintaining the balance of Th1/Th2), and neurological diseases (regulating the kynurenine pathway and quinolinic acid levels in the brain through the gut-brain axis).\n\nThe gut core microbial species Bifidobacterium longum: Colonization, mechanisms, and health benefits.", "token_count": 426, "char_count": 1811, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6206, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:38.818823", "source": { "split": "train_shard_00000", "doc_id": 618 }, "chunk_id": "train_shard_00000_618_0", "global_id": 687 }, { "text": "Pangenomes are collections of annotated genome sequences of multiple individuals of a species\n\nStructural variation in the pangenome of wild and domesticated barley.", "token_count": 37, "char_count": 165, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:39.177750", "source": { "split": "train_shard_00000", "doc_id": 619 }, "chunk_id": "train_shard_00000_619_0", "global_id": 688 }, { "text": "Pigs are one of the most essential sources of high-quality proteins in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs restricts the accurate presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deeply sequenced genomes across Eurasia. Additionally, we established a section-wide gene repertoire, revealing that core genes are more evolutionarily conserved than variable genes. Furthermore, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. The constructed pig pangenome and the identified SVs in this study provide rich resources for future functional genomic research on pigs.\n\nPangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics.", "token_count": 309, "char_count": 1385, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6751, "quality_score": 0.8376, "entities": { "genes": [ "TBX19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:39.741342", "source": { "split": "train_shard_00000", "doc_id": 620 }, "chunk_id": "train_shard_00000_620_0", "global_id": 689 }, { "text": "Short tandem repeats (STRs) are widespread, repetitive elements, with a number of biological functions and are among the most rapidly mutating regions in the genome. Their distribution varies significantly between taxonomic groups in the tree of life and are highly polymorphic within the human population. Advances in sequencing technologies coupled with decreasing costs have enabled the generation of an ever-growing number of complete genomes. Additionally, the arrival of accurate long reads has facilitated the generation of Telomere-to-Telomere (T2T) assemblies of complete genomes. Nevertheless, there is no comprehensive database that encompasses the STRs found per genome across different organisms and for different human genomes across diverse ancestries. Here we introduce Microsatellites Explorer, a database of STRs found in the genomes of 117,253 organisms across all major taxonomic groups, 15 T2T genome assemblies of different organisms, and 94 human haplotypes from the human pangenome. The database currently hosts 406,758,798 STR sequences, serving as a centralized user-friendly repository to perform searches, interactive visualizations, and download existing STR data for independent analysis. Microsatellites Explorer is implemented as a web-portal for browsing, analyzing and downloading STR data. Microsatellites Explorer is publicly available at https://www.microsatellitesexplorer.com.\n\nMicrosatellites explorer: A database of short tandem repeats across genomes.", "token_count": 350, "char_count": 1493, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:40.315940", "source": { "split": "train_shard_00000", "doc_id": 621 }, "chunk_id": "train_shard_00000_621_0", "global_id": 690 }, { "text": "Salmonella remains the leading cause of foodborne infections globally. Environmental reservoirs, particularly aquatic bodies, serve as conduits for the fecal-oral transmission of this pathogen. While the gastrointestinal tract is traditionally considered the primary habitat of Salmonella, mounting evidence suggests the bacterium's capacity for survival in external environments. The application of advanced technological platforms, such as next-generation sequencing, facilitates a comprehensive analysis of Salmonella's genomic features. This study aims to characterize the genomic composition of Salmonella isolates from river water, contributing to a potential paradigm shift and advancing public health protection. A total of 25 river water samples were collected and processed, followed by microbiological isolation of Salmonella strains, which were then sequenced. Genomic characterization revealed adaptive mechanisms, including gene duplication. Furthermore, an open pangenome, predisposed to incorporating foreign genetic material, was identified. Notably, antibiotic resistance genes were found to be part of the core genome, challenging previous reports that placed them in the accessory genome.\n\nThe pangenome analysis of the environmental source Salmonella enterica highlights a diverse accessory genome and a distinct serotype clustering.", "token_count": 275, "char_count": 1354, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8764, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:40.861159", "source": { "split": "train_shard_00000", "doc_id": 622 }, "chunk_id": "train_shard_00000_622_0", "global_id": 691 }, { "text": "Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied in wild animal populations. We constructed a pangenome for House Finches (\n\nFitness consequences of structural variation inferred from a House Finch pangenome.", "token_count": 70, "char_count": 329, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8478, "quality_score": 0.9239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:41.227401", "source": { "split": "train_shard_00000", "doc_id": 623 }, "chunk_id": "train_shard_00000_623_0", "global_id": 692 }, { "text": "Interest in Saccharomyces and non-Saccharomyces yeasts as biotechnological agents is growing worldwide. Here, Kluyveromyces marxianus GBC2 and two Saccharomyces cerevisiae strains FBZ4 and FBK9 were isolated from pomegranate (Punica granatum) and fig (Ficus carica), respectively, and extensively characterized for their probiotic attributes and health benefits. Overall, these strains were found to be γ-hemolytic, non-cytotoxic against Caco-2 cells, and sensitive to therapeutic antifungals. In terms of probiotic characterization, the strains were able to survive at pH 2 and in 1% bile and had high hydrophobicity and self-aggregation properties, which could explain their ability to form biofilm on a polystyrene and adhere to Caco-2 cells. Adhesion rates of 23.52%, 14.05%, and 9.44% were recorded at 37 °C for K. marxianus GBC2, S. cerevisiae FBK9, and S. cerevisiae FBZ4, respectively. Furthermore, biological screening showed a cholesterol assimilation of 54.32% for K. marxianus GBC2 and almost 33% for both Saccharomyces, more than 73% α-amylase inhibition, and good antioxidant potential for all strains; however, only K. marxianus GBC2 showed antibacterial activity against Staphylococcus aureus ATCC 25923. In light of these findings, the strains could be potential candidates for the development of novel functional foods and for probiotic applications.\n\nCharacterization and Biological In Vitro Screening of Probiotic Yeast Strains Isolated from Algerian Fruits.", "token_count": 446, "char_count": 1478, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [ "FBK9", "FBZ4", "GBC2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:41.858199", "source": { "split": "train_shard_00000", "doc_id": 624 }, "chunk_id": "train_shard_00000_624_0", "global_id": 693 }, { "text": "Clinically important lineages in Klebsiella, especially those expressing multi-drug resistance (MDR), pose severe threats to public health worldwide. They arose from the co-evolution of the vertically inherited core genome and horizontal gene transfers by plasmids, which has not been systematically explored.\n\nKleTy: integrated typing scheme for core genome and plasmids reveals repeated emergence of multi-drug resistant epidemic lineages in Klebsiella worldwide.", "token_count": 106, "char_count": 465, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8525, "quality_score": 0.9262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:42.241347", "source": { "split": "train_shard_00000", "doc_id": 625 }, "chunk_id": "train_shard_00000_625_0", "global_id": 694 }, { "text": "Yeasts are attractive hosts for the production of heterologous products due to their genetic tractability and relative ease of growth. While the baker's yeast Saccharomyces cerevisiae is a powerful workhorse of the biotechnology industry, the species has metabolic limitations and it is critical that we develop alternative platforms that will facilitate the development of bioprocesses that rely on sustainable feedstocks. In this study, we used synthetic biology tools to construct coumaric acid-producing strains of Kluyveromyces marxianus, a yeast whose physiological traits render it attractive for biotechnology applications. Coumaric acid is a building block in the synthesis of many different families of aromatics and is a key precursor for the synthesis of complect phenylpropanoid molecules, including many flavours and aromas. The starting point for this work was a K. marxianus chassis strain that has increased flux towards the synthesis of tyrosine and phenylalanine, the aromatic amino acids that can serve as starting points for coumaric acid synthesis. Following principles of synthetic biology, a modular approach was taken to identify the best solution to different metabolic possibilities and these were then combined in different ways. For the first step, it was established that the route from phenylalanine was superior to that from tyrosine and the combined overexpression of PlPAL, AtC4H and AtCPR1 delivered the highest yield of coumaric acid. Next, it was established that while Pdc5 and Aro10 both had phenylpyruvate decarboxylase activity, inactivation of ARO10 was sufficient to prevent flux loss in the pathway. Since phenylalanine is the starting point, efforts were made to improve efficiency of its production. It was found that glutamate was a preferred nitrogen source for coumaric acid production, and this knowledge was used to engineer a strain that overexpressed S. cerevisiae GDH1 and delivered higher yields of coumaric acid. Ultimately, this strategy led to the development of strains that has yields of up to 48 mg coumaric acid /g glucose. Strains were evaluated in bioreactors to investigate the effects of different process parameters", "token_count": 509, "char_count": 2182, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5566, "quality_score": 0.7783, "entities": { "genes": [ "ARO10", "GDH1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:42.869674", "source": { "split": "train_shard_00000", "doc_id": 626 }, "chunk_id": "train_shard_00000_626_0", "global_id": 695 }, { "text": "These analyses indicated that engineered strains face some redox balance challenges and further work will be required overcome these to develop strains that can perform well under industrial conditions.\n\nOptimisation of coumaric acid production from aromatic amino acids in Kluyveromyces marxianus.", "token_count": 64, "char_count": 298, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9268, "quality_score": 0.9634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:43.241515", "source": { "split": "train_shard_00000", "doc_id": 626 }, "chunk_id": "train_shard_00000_626_1", "global_id": 696 }, { "text": "Genome-wide identification and comparative gene-family analyses have commonly been performed to investigate species-specific evolution linked to various traits and molecular pathways. However, most previous studies have been limited to gene screening in a single reference genome, failing to account for the gene presence/absence variations (gPAVs) in a species. Here, we propose an innovative pangenome-based approach for gene-family analyses based on orthologous gene groups (OGGs). Using the basic helix-loop-helix (bHLH) transcription factor family in barley as an example, we identified 161-176 bHLHs in 20 barley genomes, which can be classified into 201 OGGs. These 201 OGGs were further classified into 140 core, 12 softcore, 29 shell, and 20 line-specific/cloud bHLHs, revealing the complete profile of bHLH genes in barley. Using a genome-scanning approach, we overcame the genome annotation bias and identified an average of 1.5 un-annotated core bHLHs per barley genome. We found that whole-genome/segmental duplicates are predominant mechanisms contributing to the expansion of most core/softcore bHLHs, whereas dispensable bHLHs are more likely to result from small-scale duplication events. Interestingly, we noticed that the dispensable bHLHs tend to be enriched in the specific subfamilies SF13, SF27, and SF28, implying the potentially biased expansion of specific bHLHs in barley. We found that 50% of the bHLHs contain at least 1 intact transposon element (TE) within the 2-kb upstream-to-downstream region. bHLHs with copy-number variations (CNVs) have 1.48 TEs on average, significantly more than core bHLHs without CNVs (1.36), supporting a potential role of TEs in bHLH expansion. Analyses of selection pressure showed that dispensable bHLHs have experienced clear relaxation of selection compared with core bHLHs, consistent with their conservation patterns", "token_count": 505, "char_count": 1882, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6517, "quality_score": 0.8258, "entities": { "genes": [ "SF13", "SF27", "SF28" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:43.932840", "source": { "split": "train_shard_00000", "doc_id": 627 }, "chunk_id": "train_shard_00000_627_0", "global_id": 697 }, { "text": "We also integrated the pangenome data with recently available barley pantranscriptome data from 5 tissues and discovered apparent transcriptional divergence within and across bHLH subfamilies. We conclude that pangenome-based gene-family analyses can better describe the previously untapped, genuine evolutionary status of bHLHs and provide novel insights into bHLH evolution in barley. We expect that this study will inspire similar analyses in many other gene families and species.\n\nPangenome and pantranscriptome as the new reference for gene-family characterization: A case study of basic helix-loop-helix (bHLH) genes in barley.", "token_count": 148, "char_count": 633, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7701, "quality_score": 0.8851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:44.393935", "source": { "split": "train_shard_00000", "doc_id": 627 }, "chunk_id": "train_shard_00000_627_1", "global_id": 698 }, { "text": "In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool).\n\nUnraveling the impact of genome assembly on bacterial typing: a one health perspective.", "token_count": 102, "char_count": 476, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8615, "quality_score": 0.9308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:44.792120", "source": { "split": "train_shard_00000", "doc_id": 628 }, "chunk_id": "train_shard_00000_628_0", "global_id": 699 }, { "text": "The timing of flowering in soybean [Glycine max (L.) Merr.], a key legume crop, is influenced by many factors, including daylight length or photoperiodic sensitivity, that affect crop yield, productivity, and geographical adaptation. Despite its importance, a comprehensive understanding of the local linkage landscape and allelic diversity within regions of the genome influencing flowering and contributing to phenotypic variation in subpopulations has been limited. This study addresses these gaps by conducting an in-depth trait association and linkage analysis coupled with local haplotyping using advanced bioinformatics tools, including crosshap, to characterize genomic variation using a pangenome dataset representing 915 domesticated and wild-type individuals. The association analysis identified eight significant loci on seven chromosomes. Moving beyond traditional association analysis, local haplotyping of targeted regions on chromosomes 6 and 20 identified distinct haplotype structures, variation patterns, and genomic candidates influencing flowering in subpopulations. These results suggest the action of a network of genomic candidates influencing flowering time and an untapped reservoir of genomic variation for this trait in wild germplasm. Notably, GlymaLee.20G147200 on chromosome 20 was identified as a candidate gene that may cause delayed flowering in soybean, potentially through histone modifications of floral repressor loci as seen in Arabidopsis thaliana (L.) Heynh. These findings support future functional validation of haplotype-based alleles for marker-assisted breeding and genomic selection to enhance latitude adaptability of soybean without compromising yield.\n\nLocal haplotyping reveals insights into the genetic control of flowering time variation in wild and domesticated soybean.", "token_count": 407, "char_count": 1824, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:46.155946", "source": { "split": "train_shard_00000", "doc_id": 629 }, "chunk_id": "train_shard_00000_629_0", "global_id": 700 }, { "text": "The microbial biosynthesis of the antioxidant compound resveratrol offers an eco-friendly and sustainable alternative to chemical synthesis or plant extraction. Here, we showed that Kluyveromyces marxianus strains produce p-coumaric acid, a key precursor of resveratrol, with higher titres achieved under increased agitation conditions. Through further strain engineering, resveratrol production was achieved using glucose, xylose, and/or ethanol as substrates. Xylose emerged as the most favourable carbon source for resveratrol production, with ethanol supplementation during xylose culture resulting in increased resveratrol titres by limiting the accumulation of the by-product xylitol. At 37 ◦C, resveratrol production from corn cob hydrolysate and whole slurry substantially increased the yield of resveratrol per sugar, reaching titres of up to 69.26 mg/L. This work shows, for the first time, resveratrol production by K. marxianus and from corn cob whole slurry, establishing foundations for the development of an integrated sustainable process for resveratrol production from lignocellulosic materials.\n\nEngineering thermotolerant Kluyveromyces marxianus strains for resveratrol production by simultaneous saccharification and fermentation of whole slurry corn cob.", "token_count": 321, "char_count": 1275, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6527, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:46.726368", "source": { "split": "train_shard_00000", "doc_id": 630 }, "chunk_id": "train_shard_00000_630_0", "global_id": 701 }, { "text": "Elevated levels of cholesterol or triglycerides in the blood are one of the major risk factors for coronary heart disease, which is the foremost leading cause of death across the world. The aims of this study were to isolate and verify the potential probiotic strain and cholesterol-lowering capability from goat milk. The C03B-STR isolate had a broad-spectrum antibacterial property and exhibited remarkable bacteriostatic activity against Klebsiella pneumoniae ATCC 13883 (27.00 ± 1.73 mm), Pseudomonas aeruginosa ATCC 27853 (19.33 ± 0.57 mm) and Staphylococcus aureus ATCC 10832 (19.00 ± 1.00 mm) by agar well diffusion assay. This isolate is closely related to the 16S rDNA sequence of Acidipropionibacterium acidipropionici. Acidipropionibacterium acidipropionici C03B-STR can survive under acidic conditions (60.51 ± 0.02% of survival rate at pH 3.0 for 3 h) and was as bile-tolerant strain (> 80% of survival rate at 0.30% bile salts after 3 h of incubation). Furthermore, it showed significantly high cell surface hydrophobicity (74.36 ± 0.23%) and aggregation capability (> 83%) (p ≤ 0.05) but displayed low to moderate co-aggregation ability (44-61%). This strain can also be regarded as strongly adhesive (73.69 ± 0.74%) and inhibit pathogen attachment to the Caco-2 cell lines (39.20 ± 0.59-69.01 ± 0.29%). A", "token_count": 508, "char_count": 1320, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:47.379422", "source": { "split": "train_shard_00000", "doc_id": 631 }, "chunk_id": "train_shard_00000_631_0", "global_id": 702 }, { "text": "acidipropionici C03B-STR appeared to be safe (non-haemolytic) and controllable (sensitive to various antibiotics). Notably, it had the potential to suppress cholesterol uptake in Caco-2 cells (approximately 45%) and also reduced cholesterol level above 84% during the exponential phase under acidic conditions. Thus, A. acidipropionici C03B-STR from goat milk may be a promising novel potential cholesterol-lowering probiotic strain for application in functional foods and biotherapeutics.\n\nIsolation and assessment of probiotic potential of Acidipropionibacterium acidipropionici C03B-STR from goat milk with cholesterol-lowering capability.", "token_count": 182, "char_count": 642, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7375, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:47.823340", "source": { "split": "train_shard_00000", "doc_id": 631 }, "chunk_id": "train_shard_00000_631_1", "global_id": 703 }, { "text": "This study investigates the diverse fungal community and their probiotic functions present in ethnic fermented bamboo shoots of Arunachal Pradesh. Among 95 yeast isolates, 13 demonstrated notable probiotic attributes. These included growth at pH 3, bile tolerance, autoaggregation, co-aggregation, hydrophobicity, lysozyme tolerance and antimicrobial activity. Confirmation of some of the probiotic properties through specific primers enabled the detection of genes associated with acid and bile tolerance, antimicrobial activity, and adhesion. Probiotic yeasts were finally identified based on D1 and D2 sequences of large ribosomal subunit as\n\nProbiotic yeast characterization and fungal amplicon metagenomics analysis of fermented bamboo shoot products from Arunachal Pradesh, northeast India.", "token_count": 197, "char_count": 796, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:48.273837", "source": { "split": "train_shard_00000", "doc_id": 632 }, "chunk_id": "train_shard_00000_632_0", "global_id": 704 }, { "text": "Historically, Xanthomonas species are primarily known for their pathogenicity against plants, but recently, there have been more findings of non-pathogenic xanthomonads. In the present study, we report isolates from healthy rice seeds that belong to a new species, Xanthomonas protegens, a protector of the rice plants against a serious pathogenic counterpart, i.e. X. oryzae pv. oryzae upon leaf clip co-inoculation. The new member species is non-pathogenic to rice and lacks a type III secretion system. The pangenome investigation revealed a large number of unique genes, including a novel lipopolysaccharide biosynthetic gene cluster, that might be important in its adaptation. The phylo-taxonogenomic analysis revealed that X. protegens is a taxonomic outlier species of X. sontii, a core, vertically transmitted rice seed endophyte with numerous probiotic properties. Interestingly, X. sontii is also reported as a keystone species of healthy rice seed microbiome. The findings and resources will help in the development of unique gene markers and evolutionary studies of X. sontii as a successful symbiont and X. oryzae as a serious pathogen. Here, we propose X. protegens sp. nov. as a novel species of the genus Xanthomonas with PPL118 = MTCC 13396 = CFBP 9164 = ICMP 25181 as the type strain. PPL117, PPL124, PPL125, and PPL126 are other strains of the species.\n\nXanthomonas protegens sp. nov., a novel rice seed-associated bacterium, provides in vivo protection against X. oryzae pv. oryzae, the bacterial leaf blight pathogen.", "token_count": 434, "char_count": 1538, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5983, "quality_score": 0.7991, "entities": { "genes": [ "PPL124", "PPL126", "PPL118", "PPL125", "PPL117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:48.903267", "source": { "split": "train_shard_00000", "doc_id": 633 }, "chunk_id": "train_shard_00000_633_0", "global_id": 705 }, { "text": "The aim of this study was to determine the relative contributions of various potential food sources of human listeriosis and to identify source-specific risk factors, at exposure level, for human Listeria monocytogenes (Lm) infection. To achieve this, available Lm isolates from human cases (n = 756) and food/animal sources (n = 950) from national surveillance systems in the Netherlands (2010-2020) were whole genome sequenced. Additionally, questionnaire-based exposure data for human cases was collected. Source attribution analysis was performed using a Random Forest model based on core-genome multilocus sequence typing (cgMLST). Risk factors for human Lm infection of cattle, chicken and seafood origin were determined using beta regression analysis on the cgMLST-based attribution estimates. Results indicated that the 756 human Lm isolates were mainly attributed to cattle (62.3 %), chicken (19.4 %), and seafood (16.9 %). Specifically, fresh meat (86.2 %), including fresh bovine meat (43.7 %) and fresh chicken meat (39.3 %), accounted for most cases. These attributions stemmed from Lm contamination of either the food products or their production environments. Consumption of steak tartare and smoked salmon was associated with an increased risk of human Lm infections attributed to cattle and seafood, respectively, while no specific risk factors for chicken-borne listeriosis were identified. This study indicated that Lm isolates of cattle origin, particularly those from fresh bovine meat and associated production environments, are estimated to be the primary cause of human listeriosis in the Netherlands. This aligns with several other European source attribution studies on Lm. Moreover, the identified risk factors for human Lm infection from cattle (i.e. steak tartare) and seafood (i.e. smoked salmon) clearly indicated their attributable sources. This joint analysis of core genome and epidemiological data provided novel insights into the origins and transmission pathways of human listeriosis.\n\nSource attribution of Listeria monocytogenes in the Netherlands.", "token_count": 495, "char_count": 2087, "word_count": 300, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:49.547395", "source": { "split": "train_shard_00000", "doc_id": 634 }, "chunk_id": "train_shard_00000_634_0", "global_id": 706 }, { "text": "The study aimed to screen for the possible presence of lactic acid bacteria (LAB) in cat milk in order to evaluate their probiotic properties. The isolates were characterized by biochemical identification, morphological tests and 16S rDNA sequencing. Afterward, gastrointestinal passage,\n\nIsolation and evaluation of", "token_count": 73, "char_count": 316, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:49.923439", "source": { "split": "train_shard_00000", "doc_id": 635 }, "chunk_id": "train_shard_00000_635_0", "global_id": 707 }, { "text": "Since previous studies have suggested that the RNAs of human endogenous retrovirus (HERV) might be involved in regulating innate immunity, it is important to investigate the HERV transcriptome patterns in innate immune cell types such as CD14 + monocytes. Using single cell RNA-seq datasets from resting or stimulated PBMCs mapped to 3,220 known discrete autonomous proviral HERV loci, we found individual-specific variation in HERV transcriptomes between HERV loci in CD14 + monocytes. Analysis of paired datasets from the same individual that were cultured in vitro with LPS or without (i.e. control) revealed 36 HERV loci in CD14 + monocytes that were detected only after activation. To extend our analysis to in vivo activated CD14 + monocytes, we used two scRNA-seq datasets from studies that had demonstrated activation of circulating CD14 + monocytes in patients with physical trauma or patients hospitalized with COVID-19 infections. For direct comparison between the trauma and COVID-19 datasets, we first analyzed 1.625 billion sequence reads from a composite pangenome control of 21 normal individuals. Comparison of the sequence read depth of HERV loci in the trauma or COVID-19 samples to the pangenome control revealed that 39 loci in the COVID-19 and 11 HERV loci in the trauma samples were significantly different (Mann-Whitney U test), with 9 HERV loci shared between the COVID-19 and trauma datasets. The capacity to compare HERV loci transcriptome patterns in innate immune cells, like CD14 + monocytes, across different pathological conditions will lead to greater understanding of the physiological role of HERV expression in health and disease.\n\nShared and unique patterns of autonomous human endogenous retrovirus loci transcriptomes in CD14 + monocytes from individuals with physical trauma or infection with COVID-19.", "token_count": 503, "char_count": 1842, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5269, "quality_score": 0.7634, "entities": { "genes": [ "CD14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:50.574720", "source": { "split": "train_shard_00000", "doc_id": 636 }, "chunk_id": "train_shard_00000_636_0", "global_id": 708 }, { "text": "The construction of a pangenome graph is a fundamental task in pangenomics. A natural theoretical question is how to formalize the computational problem of building an optimal pangenome graph, making explicit the underlying optimization criterion and the set of feasible solutions. Current approaches build a pangenome graph with some heuristics, without assuming some explicit optimization criteria. Thus it is unclear how a specific optimization criterion affects the graph topology and downstream analysis, like read mapping and variant calling.\n\nPangeBlocks: customized construction of pangenome graphs via maximal blocks.", "token_count": 124, "char_count": 626, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:50.969443", "source": { "split": "train_shard_00000", "doc_id": 637 }, "chunk_id": "train_shard_00000_637_0", "global_id": 709 }, { "text": "Grapevine breeding is hindered by a limited understanding of the genetic basis of complex agronomic traits. This study constructs a graph-based pangenome reference (Grapepan v.1.0) from 18 newly generated phased telomere-to-telomere assemblies and 11 published assemblies. Using Grapepan v.1.0, we build a variation map with 9,105,787 short variations and 236,449 structural variations (SVs) from the resequencing data of 466 grapevine cultivars. Integrating SVs into a genome-wide association study, we map 148 quantitative trait loci for 29 agronomic traits (50.7% newly identified), with 12 traits significantly contributed by SVs. The estimated heritability improves by 22.78% on average when including SVs. We discovered quantitative trait locus regions under divergent artificial selection in metabolism and berry development between wine and table grapes, respectively. Moreover, significant genetic correlations were detected among the 29 traits. Under a polygenic model, we conducted genomic predictions for each trait. In general, our study facilitates the breeding of superior cultivars via the genomic selection of multiple traits.\n\nGrapevine pangenome facilitates trait genetics and genomic breeding.", "token_count": 318, "char_count": 1213, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7048, "quality_score": 0.8524, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:51.531911", "source": { "split": "train_shard_00000", "doc_id": 638 }, "chunk_id": "train_shard_00000_638_0", "global_id": 710 }, { "text": "Cutaneous burn trauma, compromise of dermal layers and immune defense system is a physical and fiscal burden on healthcare systems. Burn-wound infections are a serious complication of thermal injury and contribute significantly to care burden. After burn-induced trauma, sepsis by Pseudomonas aeruginosa impairs patient recovery and contributes to mortality and morbidity. Past studies show positive correlation between detection of Pseudomonas species and healing-impaired traumatic wounds. Pseudomonas aeruginosa is a resilient opportunistic human pathogen and a nosocomial agent involved in pathology of healing-impaired wounds, especially in burn patients. Expansive array of virulence determinants has resulted in gentamicin- and silver-resistant P. aeruginosa outbreaks. Knowledge of molecular dynamics and phylogeny of P. aeruginosa associated with burn wounds is limited. Therefore, we conducted whole-genome sequencing for genotyping and phylogenetic analysis of P. aeruginosa burn-associated strains (n = 19) isolated from 7 burn cases during hospitalization. Comparison of genetic features in P. aeruginosa strains in the core genome and mobilome detected genetic variations within some clonal infections over time. Genetic variations were observed among different burn cases, with some features identified in severe lung infections. Polyclonal infections were also observed, with differing genotypes and virulence potentials, highlighting the importance of reasoned sampling of isolates for clinical testing.\n\nPhylogenetic evaluation and genotypic identification of burn-related Pseudomonas aeruginosa strains isolated from post-burn human infections during hospitalization.", "token_count": 381, "char_count": 1686, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.8311, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:52.112588", "source": { "split": "train_shard_00000", "doc_id": 639 }, "chunk_id": "train_shard_00000_639_0", "global_id": 711 }, { "text": "CHAPS, the zwitterionic derivative of cholic acid, has garnered significant research attention owing to its biocompatibility, electro-neutrality over a wide pH range, and non-denaturing nature towards proteins. The escalating demand of CHAPS in biomedical and pharmaceutical industries mandates information on its interaction with various biological macromolecules, especially proteins. The present study involves a comprehensive investigation on the interaction of CHAPS in a wide concentration range (0.001 mM-32 mM), with two extensively used transport proteins, BSA (Bovine Serum Albumin) and HSA (Human Serum Albumin). The study suggests a concentration dependent sequential interaction of CHAPS in discreet stages with the two proteins. A detailed study using warfarin and ibuprofen as site markers provides information about the sites of interaction at different stages. The study indicates significant difference in the effect of CHAPS on these two homologous proteins in terms of their esterase-like activity and effect of chemical denaturant. Moreover, a comparison between CHAPS and its structural bile salt analogues, Sodium cholate and Sodium taurocholate, towards their interaction and effect on the two serum albumins, reveals the mildness of CHAPS towards the proteins, thus endorsing it as a more suitable drug carrier in comparison to its bile salt analogues.\n\nSpectroscopic investigation on the interaction of CHAPS, the zwitterionic steroidal surfactant, with bovine and human serum albumins: A comparative study.", "token_count": 366, "char_count": 1533, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5741, "quality_score": 0.787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:52.684942", "source": { "split": "train_shard_00000", "doc_id": 640 }, "chunk_id": "train_shard_00000_640_0", "global_id": 712 }, { "text": "The non-conventional yeast Kluyveromyces marxianus is a promising microbial host for industrial biomanufacturing. With the recent development of Cas9-based genome editing systems and other novel synthetic biology tools for K. marxianus, engineering of this yeast has become far more accessible. Enzyme colocalization is a proven approach to increase pathway flux and the synthesis of non-native products. Here, we engineer K. marxianus to enable peroxisomal surface display, an enzyme colocalization technique for displaying enzymes on the peroxisome membrane via an anchoring motif from the peroxin Pex15. The native KmPex15 anchoring motif was identified and fused to GFP, resulting in successful localization to the surface of the peroxisomes. To demonstrate the advantages for pathway localization, the Pseudomonas savastanoi IaaM and IaaH enzymes were co-displayed on the peroxisome surface; this increased production of indole-3-acetic acid 7.9-fold via substrate channeling effects. We then redirected pathway flux by displaying the violacein pathway enzymes VioE and VioD from Chromobacterium violaceum, increasing selectivity of proviolacein to prodeoxyviolacein by 2.5-fold. Finally, we improved direct access to peroxisomal acetyl-CoA and increased titers of the polyketide triacetic acid lactone (TAL) by 2-fold through concurrent display of the proteins Cat2, Acc1, and the type III PKS 2-pyrone synthase from Gerbera hybrida relative to the same three enzymes diffusing in the cytosol. We further improved TAL production by up to 2.1-fold through engineering peroxisome morphology and lifespan. Our findings demonstrate that peroxisomal surface display is an efficient enzyme colocalization strategy in K. marxianus and applicable for improving production of a wide range of non-native products.", "token_count": 484, "char_count": 1809, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:53.331458", "source": { "split": "train_shard_00000", "doc_id": 641 }, "chunk_id": "train_shard_00000_641_0", "global_id": 713 }, { "text": "Engineering peroxisomal surface display for enhanced biosynthesis in the emerging yeast Kluyveromyces marxianus.", "token_count": 30, "char_count": 112, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:53.682717", "source": { "split": "train_shard_00000", "doc_id": 641 }, "chunk_id": "train_shard_00000_641_1", "global_id": 714 }, { "text": "Low-abundance members of microbial communities are difficult to study in their native habitats, including Escherichia coli, a minor but common inhabitant of the gastrointestinal tract, and key opportunistic pathogen of the urinary tract. While multi-omic analyses have detailed interactions between uropathogenic Escherichia coli (UPEC) and the bladder mediating urinary tract infection (UTI), little is known about UPEC in its pre-infection reservoir, the gastrointestinal tract, partly due to its low relative abundance (<1%). To sensitively explore the genomes and transcriptomes of diverse gut E. coli, we develop E. coli PanSelect, which uses probes designed to specifically capture E. coli's broad pangenome. We demonstrate its ability to enrich diverse E. coli by orders of magnitude, in a mock community and in human stool from a study investigating recurrent UTI (rUTI). Comparisons of transcriptomes between gut E. coli of women with and without history of rUTI suggest rUTI gut E. coli are responding to increased oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of in vivo E. coli biology in other low-abundance environments, and the framework described here has broad applicability to other diverse, low-abundance organisms.\n\nDistinct Escherichia coli transcriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection.", "token_count": 369, "char_count": 1478, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:54.261331", "source": { "split": "train_shard_00000", "doc_id": 642 }, "chunk_id": "train_shard_00000_642_0", "global_id": 715 }, { "text": "The microorganisms colonizing the gastrointestinal tract of animals, collectively referred to as the gut microbiome, affect numerous host behaviors dependent on the central nervous system (CNS). Studies comparing germ-free mice to normally colonized mice have demonstrated influences of the microbiome on anxiety-related behaviors, voluntary activity, and gene expression in the CNS. Additionally, there is epidemiologic evidence supporting an intergenerational influence of the maternal microbiome on neurodevelopment of offspring and behavior later in life. There is limited experimental evidence however directly linking the maternal microbiome to long-term neurodevelopmental outcomes, or knowledge regarding mechanisms responsible for such effects.\n\nFetal programming by the parental microbiome of offspring behavior, and DNA methylation and gene expression within the hippocampus.", "token_count": 183, "char_count": 886, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:54.713458", "source": { "split": "train_shard_00000", "doc_id": 643 }, "chunk_id": "train_shard_00000_643_0", "global_id": 716 }, { "text": "As genomics data analysis becomes increasingly intricate, researchers face the challenge of mastering various software tools. The rise of Pangenomics analysis, which examines the complete set of genes in a group of genomes, is particularly transformative in understanding genetic diversity. Our interdisciplinary team of biologists and mathematicians developed a short Pangenomics Workshop covering Bash, Python scripting, Pangenome, and Topological Data Analysis. These skills provide deeper insights into genetic variations and their implications in Evolutionary Biology. The workshop uses a Conda environment for reproducibility and accessibility. Developed in The Carpentries Incubator infrastructure, the workshop aims to equip researchers with essential skills for Pangenomics research. By emphasizing the role of a community of practice, this work underscores its significance in empowering multidisciplinary professionals to collaboratively develop training that adheres to best practices.\n\nMeeting the challenge of genomic analysis: a collaboratively developed workshop for pangenomics and topological data analysis.", "token_count": 224, "char_count": 1125, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6781, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:55.181900", "source": { "split": "train_shard_00000", "doc_id": 644 }, "chunk_id": "train_shard_00000_644_0", "global_id": 717 }, { "text": "The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes.\n\nA stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.", "token_count": 167, "char_count": 718, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7961, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:55.657871", "source": { "split": "train_shard_00000", "doc_id": 645 }, "chunk_id": "train_shard_00000_645_0", "global_id": 718 }, { "text": "Probiotics hold great potential for treating metabolic diseases such as obesity. Given the complex and multifactorial nature of these diseases, research on probiotic combination with multiple targets has become popular. Here, we choose four obesity-related targets to perform high-throughput screening, including pancreatic lipase activity, bile salt hydrolase activity, glucagon-like peptide-1 secretion and adipocyte differentiation. Then, we obtained 649 multi-strain combinations with the requirement that each must cover all these targets in principle. After\n\nSymbiotic probiotic communities with multiple targets successfully combat obesity in high-fat-diet-fed mice.", "token_count": 159, "char_count": 673, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8471, "quality_score": 0.9235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:56.138967", "source": { "split": "train_shard_00000", "doc_id": 646 }, "chunk_id": "train_shard_00000_646_0", "global_id": 719 }, { "text": "Candidaalbicans normally colonizes the human gastrointestinal tract as a commensal. Studying fungal factors involved in colonizing the mammalian gastrointestinal tract requires mouse models with altered microbiota. We have obtained strains of C.albicans through microevolution in the mouse gut for a prolonged period (one year) that display a substantial increase in fitness in this niche. These strains show resistance to bile salts, an increase in their adhesion to the intestinal mucosa, and are unable to filament in response to serum. Genetic analysis revealed some alterations, mainly a triploidy of chr7, a whole chr6 homozygosis, and an SNP in the FLO8 gene (located in the chr6), resulting in a truncated protein version. A wild type FLO8 gene complemented filamentation and bile salt sensitivity but showed an intermediate fitness phenotype in colonization. Alterations in bile salt sensitivity were also evident in bmt mutants, defective in β-mannosylation, and transcriptional targets of Flo8, suggesting a link between the fungal cell wall and mammalian gut colonization via the Flo8 transcriptional regulator.\n\nCandida albicans strains adapted to the mouse gut are resistant to bile salts via a Flo8-dependent mechanism.", "token_count": 305, "char_count": 1234, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [ "FLO8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:56.726006", "source": { "split": "train_shard_00000", "doc_id": 647 }, "chunk_id": "train_shard_00000_647_0", "global_id": 720 }, { "text": "Ischemic-type biliary lesions (ITBL) are a major cause of graft loss and even mortality after liver transplantation (LT). The underlying cellular mechanisms for ITBL remain unclear. Gut microbiota has been found to be closely related to complications after LT. Here, using gut microbiome compositions, we found patients with ITBL had a higher abundance of bacteria associated with bile salt metabolism. These bacteria are reported to convert cholic acid (CA) into deoxycholic acid (DCA), consistent with our data that there were higher DCA concentrations and DCA/CA ratio in patients with ITBL than patients without ITBL. Using an in vitro model, human intrahepatic biliary epithelial cells (HIBEC) subjected to DCA showed a higher apoptosis rate, lower viability, and higher levels of cleaved-caspase3 than CA at the same concentration. DCA also changed the morphology of mitochondria and farnesoid X receptor (FXR) expression. Interestingly, DCA-induced apoptosis rate was significantly reduced in HIBEC when the FXR or BAX gene was knocked down, suggesting that DCA-induced apoptosis was dependent on FXR-mitochondrial pathway. Furthermore, increasing DCA/CA ratio in a bile acid-feeding mouse model resulted in cholangiocyte apoptosis and impaired liver function. The patients with ITBL also showed an increased proportion of TUNEL-positive biliary epithelial cells than those without ITBL. These suggest that changes in the gut microbiota following LT may enhance the conversion of CA to DCA, and may contribute to biliary damage via FXR-mitochondrial apoptosis pathway, providing new ideas for the early monitoring and treatment of ITBL.\n\nGut microbiota-mediated bile acid metabolism aggravates biliary injury after liver transplantation through mitochondrial apoptosis.", "token_count": 446, "char_count": 1776, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:57.409142", "source": { "split": "train_shard_00000", "doc_id": 648 }, "chunk_id": "train_shard_00000_648_0", "global_id": 721 }, { "text": "Coal, a sedimentary rock harbours a complex microbial community that plays a significant role in its formation and characteristics. However, coal metagenome sequencing and studies were less, limiting our understanding of this complex ecosystem. This study aimed to reconstruct high-quality metagenome-assembled genomes (MAGs) from the coal sample collected in the Neyveli mine to explore the unrevealed diversity of the coal microbiome. Using Illumina sequencing, we obtained high-quality raw reads in FASTQ format. Subsequently, de novo assembly and binning with metaWRAP software facilitated the reconstruction of coal MAGs. Quality assessment using CheckM identified 10 High-Quality MAGs (HQ MAGs), 7 medium-quality MAGs (MQ MAGs), and 6 low-quality MAGs (LQ MAGs). Further analysis using GTDB-Tk revealed four HQ MAGs as known species like Dermacoccus abyssi, Sphingomonas aquatilis, Acinetobacter baumannii, and Burkholderia cenocepacia. The remaining six HQ MAGs were classified as Comamonas, Arthrobacter, Noviherbaspirillum, Acidovorax, Oxalicibacterium, and Bordetella and designated as novel genomes by the validation of digital DNA-DNA hybridization (dDDH). Phylogenetic analysis and further pangenome analysis across the phylogenetic groups revealed a similar pattern with a high proportion of cloud genes. We further analysed the functional potential of these MAGs and closely related genomes using COG. The comparative functional genomics revealed that novel genomes are highly versatile, potentially reflecting adaptations to the coal environment. BlastKOALA was used to conduct a detailed analysis of the metabolic pathways associated with the MAGs. This study highlights the comparative genomic analysis of novel coal genomes with their closely related genomes to understand the evolutionary relationships and functional properties.\n\nComparative genomic analysis and characterization of novel high-quality draft genomes from the coal metagenome.", "token_count": 481, "char_count": 1962, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6113, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:58.057979", "source": { "split": "train_shard_00000", "doc_id": 649 }, "chunk_id": "train_shard_00000_649_0", "global_id": 722 }, { "text": "With the advent of advanced sequencing technologies, new insights into the genomes of pathogens, including those in the genus Curtobacterium, have emerged. This research investigates a newly isolated C. flaccumfaciens strain 208 (Cf208) from Arthrocereus glaziovii, and endemic plant from Iron Quadrangle. Previous results show that Cf208 exhibits the potential to remediate soils, facilitating the growth of tomato plants. Furthermore, Cf208 showed no virulence towards bean plants, thus, confounding its phytopathogenic origins. Using a comprehensive comparative genomics approach, we analyzed the Cf208 genome against 34 other Curtobacterium strains, aiming to discern the genomic landmarks associated with its adaptation as an endophyte and its avirulence in bean crops. This revealed a predominant core genome comprising about 2426 genes (68%). Notably, Cf208 possesses a unique plasmid, pCF208-73, which contains 84 unique genes (2.5%). However, unlike the plasmids previously described for pathogenic strains, pCF208-73 does not feature genes associated with virulence induction. In contrast, while several genes traditionally linked to virulence, like pectate lyases and proteases were identified, but the T4P apparatus emerged as new crucial factor for understanding virulence in the Curtobacterium genus. The presence or absence of this apparatus, especially in strains from different clades, may determine their virulence towards leguminous plants. In conclusion, this work highlights the significance of comparative genomics in unraveling the complexities of pathogenicity within the Curtobacterium genus. Our findings suggest that, although the limited genetic variations, specific genes, particularly those linked to the T4P apparatus, play a fundamental role in their interactions with host plants.\n\nFrom cactus to crop: genomic insights of a beneficial and non-pathogenic Curtobacterium flaccumfaciens strain and the evolution of its pathosystem.", "token_count": 492, "char_count": 1962, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6654, "quality_score": 0.8327, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:58.705051", "source": { "split": "train_shard_00000", "doc_id": 650 }, "chunk_id": "train_shard_00000_650_0", "global_id": 723 }, { "text": "Bupropion (Bpn), an FDA-approved NDRI (norepinephrine-dopamine reuptake inhibitor), poses risks of seizures and liver failure due to its stimulant properties, necessitating the development of alternative formulations. This research aims to develop a Bpn nanoformulation within bilosomal vesicles to enhance therapeutic efficacy at lower doses, using three bile salts, span 20 surfactants, and cholesterol via thin-film hydration. Optimization of bilosomal stability is achieved by trialing various ingredient concentrations, identifying a surfactant-to-cholesterol-to-bile salt ratio of 1.5:1:0.17 µM, with sodium cholate (B.SC\n\nEnhanced behavioral impact of optimized bupropion-encapsulated bilosomes over traditional niosomes treating depression.", "token_count": 215, "char_count": 748, "word_count": 91, "semantic_coherence": 1, "information_density": 0.9011, "quality_score": 0.9505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:04:59.504556", "source": { "split": "train_shard_00000", "doc_id": 651 }, "chunk_id": "train_shard_00000_651_0", "global_id": 724 }, { "text": "Milk fat globules (MFGs) are a remarkable example of nature's ingenuity. Human milk (HM) carries contains 3-5% fat, 0.8-0.9% protein, 6.9-7.2% carbohydrate calculated as lactose, and 0.2% mineral constituents. Most of these nutrients are carried in these MFGs, which are composed of an energy-rich triacylglycerol (TAG) core surrounded by a triple membrane structure. The membrane contains polar lipids, specialized proteins, glycoproteins, and cholesterol. Each of these bioactive components serves important nutritional, immunological, neurological, and digestive functions. These MFGs are designed to release energy rapidly in the upper gastrointestinal tract and then persist for some time in the gut lumen so that the protective bioactive molecules are conveyed to the colon. These properties may shape the microbial colonization and innate immune properties of the developing gastrointestinal tract. Milk fat globules in milk from humans and ruminants may resemble in structure but there are considerable differences in size, profile, composition, and specific constituents. There are possibilities to not only enhance the nutritional composition in a goal-oriented fashion to correct specific deficiencies in the infant but also to use these fat globules as a nutraceutical in infants who require specific treatments. To mention a few, there might be possibilities in enhancing neurodevelopment, in defense against gastrointestinal and respiratory tract infections, improving insulin sensitivity, treating chronic inflammation, and altering plasma lipids. This review provides an overview of the composition, structure, and biological activities of the various components of the MFGs. We have assimilated research findings from our own laboratory with an extensive review of the literature utilizing key terms in multiple databases including PubMed, EMBASE, and Science Direct. To avoid bias in the identification of studies, keywords were short-listed a priori from anecdotal experience and PubMed's Medical Subject Heading (MeSH) thesaurus.\n\nMilk Fat Globules: 2024 Updates.", "token_count": 492, "char_count": 2083, "word_count": 292, "semantic_coherence": 1, "information_density": 0.661, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:00.153383", "source": { "split": "train_shard_00000", "doc_id": 652 }, "chunk_id": "train_shard_00000_652_0", "global_id": 725 }, { "text": "Jujube (Ziziphus jujuba Mill.), belonging to the Rhamnaceae family, is gaining increasing prominence as a perennial fruit crop with significant economic and medicinal values. Here, we conduct de novo assembly of four reference-grade genomes, encompassing one wild and three cultivated jujube accessions. We present insights into the population structure, genetic diversity, and genomic variations within a diverse collection of 1059 jujube accessions. Analyzes of the jujube pan-genome, based on our four assemblies and four previously released genomes, reveal extensive genomic variations within domestication-associated regions, potentially leading to the discovery of a candidate gene that regulates flowering and fruit ripening. By leveraging the pan-genome and a large-scale resequencing population, we identify two candidate genes involved in domestication traits, including the seed-setting rate, the bearing-shoot length and the leaf size in jujube. These genomic resources will accelerate evolutionary and functional genomics studies of jujube.\n\nAnalyzes of pan-genome and resequencing atlas unveil the genetic basis of jujube domestication.", "token_count": 265, "char_count": 1150, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:00.705559", "source": { "split": "train_shard_00000", "doc_id": 653 }, "chunk_id": "train_shard_00000_653_0", "global_id": 726 }, { "text": "As a unicellular eukaryote, the budding yeast Saccharomyces cerevisiae strikes a unique balance between biological complexity and experimental tractability, serving as a long-standing classic model for both basic and applied studies. Recently, S. cerevisiae further emerged as a leading system for studying natural diversity of genome evolution and its associated functional implication at population scales. Having high-quality comparative and functional genomics data are critical for such efforts. Here, we exhaustively expanded the telomere-to-telomere (T2T) S. cerevisiae reference assembly panel (ScRAP) that we previously constructed for 142 strains to cover high-quality genome assemblies and annotations of 264 S. cerevisiae strains from diverse geographical and ecological niches and also 33 outgroup strains from all the other Saccharomyces species complex. We created a dedicated online database, ScRAPdb (https://www.evomicslab.org/db/ScRAPdb/), to host this expanded pangenome collection. Furthermore, ScRAPdb also integrates an array of population-scale pan-omics atlases (pantranscriptome, panproteome and panphenome) and extensive data exploration toolkits for intuitive genomics analyses. All curated data and downstream analysis results can be easily downloaded from ScRAPdb. We expect ScRAPdb to become a highly valuable platform for the yeast community and beyond, leading to a pan-omics understanding of the global genetic and phenotypic diversity.\n\nScRAPdb: an integrated pan-omics database for the Saccharomyces cerevisiae reference assembly panel.", "token_count": 381, "char_count": 1572, "word_count": 206, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:01.285586", "source": { "split": "train_shard_00000", "doc_id": 654 }, "chunk_id": "train_shard_00000_654_0", "global_id": 727 }, { "text": "Breeding of lettuce (Lactuca sativa L.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on four Lactuca species (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines.\n\nLactuca super-pangenome reduces bias towards reference genes in lettuce research.", "token_count": 137, "char_count": 582, "word_count": 79, "semantic_coherence": 1, "information_density": 0.8228, "quality_score": 0.9114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:01.713678", "source": { "split": "train_shard_00000", "doc_id": 655 }, "chunk_id": "train_shard_00000_655_0", "global_id": 728 }, { "text": "Melittin is a bioactive peptide and the predominant component in bee venom (BV), studied for its many medical properties, such as antibacterial, anti-inflammatory, anti-arthritis, nerve damage reduction, and muscle cell regeneration. Melittin is primarily obtained through natural extraction and chemical synthesis; however, both methods have limitations and cannot be used for mass production. This study established a heterologous melittin expression system in the probiotic yeast Kluyveromyces marxianus. This yeast was selected for its advantages in stress tolerance and high secreted protein yields, simplifying purification. A > 95% high-purity melittin (MET) and its precursor promelittin (ProMET) were successfully produced and purified at 1.68 μg/mL and 3.33 μg/mL concentrations and verified through HPLC and mass spectrum. The functional test of the NSC-34 cell regeneration revealed that MET achieved the best activity compared to ProMET and the natural-extracted BV groups. Growth-related gene expressions were evaluated, including microtubule-associated protein 2 (MAP2), microtubule-associated protein Tau (MAPT), growth-associated protein 43 (GAP-43), choline acetyltransferase (ChAT), vesicular acetylcholine transporter (VAChT), and acetylcholine esterase (AChE). The results indicated that treating MET increased MAP2, GAP-43, and VAChT expressions, in which cholinergic signaling is related to neurological functions. A heterologously expressed melittin in a probiotic yeast and its potential for promoting NSC-34 regeneration described here facilitate commercial and therapeutic use. KEY POINTS: • MET and its precursor ProMET were successfully hetero-expressed in K", "token_count": 449, "char_count": 1687, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6982, "quality_score": 0.8491, "entities": { "genes": [ "MAP2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:02.359667", "source": { "split": "train_shard_00000", "doc_id": 656 }, "chunk_id": "train_shard_00000_656_0", "global_id": 729 }, { "text": "marxianus •  > 95% high-purity MET and ProMET were purified at 1.68 μg/mL and 3.33 μg/mL • MET has no cytotoxicity toward NSC-34 and significantly promotes NSC-34 growth.\n\nHeterologous expressing melittin in a probiotic yeast to evaluate its function for promoting NSC-34 regeneration.", "token_count": 111, "char_count": 285, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:02.739637", "source": { "split": "train_shard_00000", "doc_id": 656 }, "chunk_id": "train_shard_00000_656_1", "global_id": 730 }, { "text": "The current reference genome is the backbone of diverse and rich annotations. Simple text formats, like VCF or BED, have been widely adopted and helped the critical exchange of genomic information. There is a dire need for tools and formats enabling pangenomic annotation to facilitate such enrichment of pangenomic references. The Graph Alignment Format (GAF) is a text format, tab-delimited like BED/VCF files, which was proposed to represent alignments. GAF could also be used to store paths representing annotations in a pangenome graph, but there are no tools to index and query them efficiently. Here, we present extensions to vg and HTSlib that provide efficient sorting, indexing, and querying for GAF files. With this approach, annotations overlapping a subgraph can be extracted quickly. Paths are sorted based on the IDs of traversed nodes, compressed with BGZIP, and indexed with HTSlib/tabix via our extensions for the GAF format. Compared to the binary GAM format, GAF files are easier to edit or inspect because they are plain text, and we show that they are twice as fast to sort and half as large on disk. In addition, we updated vg annotate, which takes BED or GFF3 annotation files relative to linear sequences and projects them into the pangenome. It can now produce GAF files representing these annotations' paths through the pangenome. We showcase these new tools on several applications. We projected annotations for all Human Pangenome Reference Consortium Year 1 haplotypes, including genes, segmental duplications, tandem repeats and repeats annotations, into the Minigraph-Cactus pangenome (GRCh38-based v1.1). We also projected known variants from the GWAS Catalog and expression QTLs from the GTEx project into the pangenome. Finally, we reanalyzed ATAC-seq data from ENCODE to demonstrate what a coverage track could look like in a pangenome graph. These rich annotations can be quickly queried with vg and visualized using existing tools like the Sequence Tube Map or Bandage.\n\nEfficient indexing and querying of annotations in a pangenome graph.", "token_count": 498, "char_count": 2077, "word_count": 324, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8025, "entities": { "genes": [ "GFF3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:03.395920", "source": { "split": "train_shard_00000", "doc_id": 657 }, "chunk_id": "train_shard_00000_657_0", "global_id": 731 }, { "text": "Whipple disease caused by Tropheryma whipplei a gram-positive bacterium is a systemic disorder that impacts not only the gastrointestinal tract but also the vascular system, joints, central nervous system, and cardiovascular system. Due to the lack of an approved vaccine, this study aimed to utilize immunoinformatic approaches to design multiepitope -based vaccine by utilizing the proteomes of five representative T. whipplei strains. The genomes initially comprised a total of 4,844 proteins ranging from 956 to 1012 proteins per strain. We collected 829 nonredundant lists of core proteins, that were shared among all the strains. Following subtractive proteomics, one extracellular protein, WP_033800108.1, a WhiB family transcriptional regulator, was selected for the chimeric-based multiepitope vaccine. Five immunodominant epitopes were retrieved from the WhiB family transcriptional regulator protein, indicating MHC-I and MHC-II with a global population coverage of 70.61%. The strong binding affinity, high solubility, nontoxicity, nonallergenic properties and high antigenicity scores make the selected epitopes more appropriate. Integration of the epitopes into a chimeric vaccine was carried out by applying appropriate adjuvant molecules and linkers, leading to the vaccine construct having enhanced immunogenicity and successfully eliciting both innate and adaptive immune responses. Moreover, the abilityof the vaccine to bind TLR4, a core innate immune receptor, was confirmed. Molecular dynamics simulations have also revealed the promising potential stability of the designed vaccine at 400 ns. In summary, we have designed a potential vaccine construct that has the ability not only to induce targeted immunogenicity for one strain but also for global T. whipplei strains. This study proposes a potential universal vaccine, reducing Whipple's disease risk and laying the groundwork for future research on multi-strain pathogens.\n\nPangenome analysis of five representative Tropheryma whipplei strains following multiepitope-based vaccine design via immunoinformatic approaches.", "token_count": 513, "char_count": 2098, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6307, "quality_score": 0.8153, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:05:04.049097", "source": { "split": "train_shard_00000", "doc_id": 658 }, "chunk_id": "train_shard_00000_658_0", "global_id": 732 }, { "text": "The sunflower, an important oilseed crop and food source across the world, is susceptible to several pathogens, which cause severe losses in sunflower production. The utilization of genetic resistance is the most economical, effective measure to prevent infectious diseases. Based on the sunflower pangenome, in this study, we explored the variability of resistance gene analogs (RGAs) within the species. According to a comparative analysis of RGA candidates in the sunflower pangenome using the RGAugury pipeline, a total of 1344 RGAs were identified, comprising 1107 conserved, 199 varied, and 38 rare RGAs. We also identified RGAs associated with resistance against\n\nPangenome Data Analysis Reveals Characteristics of Resistance Gene Analogs Associated with", "token_count": 184, "char_count": 761, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:04.499673", "source": { "split": "train_shard_00000", "doc_id": 659 }, "chunk_id": "train_shard_00000_659_0", "global_id": 733 }, { "text": "Research and medical genomics require comprehensive, scalable methods for the discovery of novel disease targets, evolutionary drivers and genetic markers with clinical significance. This necessitates a framework to identify all types of variants independent of their size or location. Here we present DRAGEN, which uses multigenome mapping with pangenome references, hardware acceleration and machine learning-based variant detection to provide insights into individual genomes, with ~30 min of computation time from raw reads to variant detection. DRAGEN outperforms current state-of-the-art methods in speed and accuracy across all variant types (single-nucleotide variations, insertions or deletions, short tandem repeats, structural variations and copy number variations) and incorporates specialized methods for analysis of medically relevant genes. We demonstrate the performance of DRAGEN across 3,202 whole-genome sequencing datasets by generating fully genotyped multisample variant call format files and demonstrate its scalability, accuracy and innovation to further advance the integration of comprehensive genomics. Overall, DRAGEN marks a major milestone in sequencing data analysis and will provide insights across various diseases, including Mendelian and rare diseases, with a highly comprehensive and scalable platform.\n\nComprehensive genome analysis and variant detection at scale using DRAGEN.", "token_count": 284, "char_count": 1414, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7043, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:05.058671", "source": { "split": "train_shard_00000", "doc_id": 660 }, "chunk_id": "train_shard_00000_660_0", "global_id": 734 }, { "text": "There is growing interest in the oral delivery of poorly permeable peptide drugs; however, the effect of biorelevant colloids found in the aqueous gastrointestinal environment on peptide drug solution behavior has been largely understudied. In this work, we detail the molecular level interactions between octreotide, a water-soluble macrocyclic peptide drug, and biorelevant colloids, i.e. bile salt micelles and bile salt-phospholipid mixed micelles, via dialysis membrane flux experiments and proton nuclear magnetic resonance (\n\nCharacterization of macrocyclic peptide drug interactions with bile salts and biorelevant colloids via single amino acid mutations and", "token_count": 164, "char_count": 667, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7473, "quality_score": 0.8736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:05.505251", "source": { "split": "train_shard_00000", "doc_id": 661 }, "chunk_id": "train_shard_00000_661_0", "global_id": 735 }, { "text": "Penicillium expansum (P. expansum), a widespread fungal pathogen, causes serious economic loss and public health concerns. The aim of this research is to investigate the antifungal effect of Kluyveromyces marxianus YG-4 (K. marxianus YG-4) against P. expansum and possible mechanism. The results showed that competition for nutrients and space, as well as the release of volatile organic compounds (VOCs), are the antifungal mechanisms. Citronellol may be the antifungal component of K. marxianus YG-4 VOCs based on GC-MS analysis. Further experiments had shown that citronellol inhibited the growth of P. expansum LPH9 by damaging the cell structure, disrupting the redox system, reducing antioxidant enzyme activity, and causing oxidative damage. K. marxianus YG-4, K. marxianus YG-4 VOCs and citronellol can effectively inhibit the spore germination of P. expansum on apples. The above results indicated that K. marxianus YG-4 had strong biocontrol activity and can be used as an excellent candidate strain for fruit preservation.\n\nBiocontrol activity of Kluyveromyces marxianus YG-4 against Penicillium expansum LPH9 on apples.", "token_count": 316, "char_count": 1131, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.8079, "entities": { "genes": [ "LPH9" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:06.067922", "source": { "split": "train_shard_00000", "doc_id": 662 }, "chunk_id": "train_shard_00000_662_0", "global_id": 736 }, { "text": "Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens' genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage an innovative, multi-genome method to construct and annotate the first pangenome graph of an oomycete plant pathogen. We expand on this approach by analysing the graph and creating synteny based single-copy orthogroups for all genes. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa, the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, virulence related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens.\n\nPangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew.", "token_count": 341, "char_count": 1643, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8296, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:06.644735", "source": { "split": "train_shard_00000", "doc_id": 663 }, "chunk_id": "train_shard_00000_663_0", "global_id": 737 }, { "text": "This study was performed on Micropterus salmoides to determine growth-linked gene and single nucleotide polymorphism (SNP) markers under carbohydrate diet and varying temperature through RNA-seq and whole-genome re-sequencing. The results showed that growth-related genes were primarily enriched in the fat digestion and absorption signaling pathway, playing a role in lipid transport and metabolism. Fatty acid binding protein 6, bile salt-activated lipase-like, lysophosphatidylcholine acyltransferase 2, phospholipase A2, minor isoenzyme-like, and phospholipase A2, group IB (pancreas) were identified as the crucial genes. The differentially expressed genes between high and low temperatures were enriched in the pentose phosphate pathway, with carbohydrate transport and metabolism were most affected by temperature. Major facilitator superfamily domain containing 10, phosphogluconate dehydrogenase, fructose-1,6-bisphosphatase 1a, and spinster homolog 3 transcript variant X1(spns3) were the shared genes affected by temperature. From all the common genes, 10 growth-associated SNP markers were identified. The TT genotype at rs7781 was associated with lower body weight, while AA genotype at rs31434173 and CC genotype at rs31435313 showed positive correlation with body weight. Analogously, the GG genotype at rs31436887 and AA genotype at rs31438769 also found to characterize better growth performance. At low temperature, individuals with the AA genotype at rs11506587 and rs31435313 exhibited the slowest growth. For the genotypes labeled with rs11510589, the GG individual grew faster than the AA individual, whereas the opposite phenomenon occurred in these genotypes when labeled with rs11511314. The genotypes at rs32970704 and rs32967921 showed no growth correlation", "token_count": 510, "char_count": 1784, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6653, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:07.298789", "source": { "split": "train_shard_00000", "doc_id": 664 }, "chunk_id": "train_shard_00000_664_0", "global_id": 738 }, { "text": "The AA genotype at rs31435313 in spns3 had the slowest growth under a carbohydrate-rich diet regardless of the temperature. Our study presents candidate genes and SNP markers associated with growth influenced by carbohydrate and temperature, providing basis for the development of M. salmoides strain that better accepts carbohydrate diets at varying temperature.\n\nRNA-seq and whole-genome re-sequencing reveal Micropterus salmoides growth-linked gene and selection signatures under carbohydrate-rich diet and varying temperature.", "token_count": 133, "char_count": 530, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7429, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:07.761628", "source": { "split": "train_shard_00000", "doc_id": 664 }, "chunk_id": "train_shard_00000_664_1", "global_id": 739 }, { "text": "A variety of methods exists for typing bacteria. However, guidelines for the application and interpretation of typing tools in epidemiologic investigations of Staphylococcus aureus are lacking. This study aimed to identify appropriate typing methods for S. aureus population studies and outbreak investigation. We compared pulsed-field gel electrophoresis (PFGE), seven loci multi-locus sequence typing (MLST), core genome MLST (cgMLST), core single nucleotide polymorphism (cSNP), and enterotoxin (se/SE) profiles on 351 S. aureus isolates. The discriminatory power, concordance, and congruence of typing results were assessed. cgMLST, cSNP, and PFGE yielded the highest discrimination value, followed by se/SE typing and MLST. The best concordance of results was found between cgMLST and cSNP, while the best congruence was observed for cgMLST and cSNP with all methods, followed by PFGE with MLST. The strengths and weaknesses of each method are highlighted. For population structure, cgMLST and cSNP performed better than PFGE and MLST in terms of resolution of clusters and in phylogenetic inference. Enterotoxin profiles matched with MLST groups, suggesting the use of se/SE typing to predict MLST results. For the retrospective analysis of 31 outbreaks, all methods performed almost equally to discriminate epidemiologically related strains and can be used to unambiguously distinguish outbreak strains.\n\nEpidemiology of Staphylococcus aureus food isolates: Comparison of conventional methods with whole genome sequencing typing methods.", "token_count": 384, "char_count": 1544, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:08.398656", "source": { "split": "train_shard_00000", "doc_id": 665 }, "chunk_id": "train_shard_00000_665_0", "global_id": 740 }, { "text": "Escherichia coli exhibit extensive genetic diversity at the genome level, particularly within their accessory genome. The tRNA integrated genomic islands (GIs), a part of the E. coli accessory genome, play an important role in pathogenicity. However, studies examining the evolution of GIs have been challenging due to their large size, considerable gene content variation and fragmented assembly in draft genomes. Here we examined the evolution of the GI integrated at pheV-tRNA (GI-pheV), with a primary focus on uropathogenic E. coli (UPEC) and the globally disseminated multidrug resistant ST131 clone. We show the gene content of GI-pheV is highly diverse and arranged in a modular configuration, with the P4 integrase encoding gene intP4 the only conserved gene. Despite this diversity, the GI-pheV gene content displayed conserved features among strains from the same pathotype. In ST131, GI-pheV corresponding to the reference strain EC958 (EC958_GI-pheV) was found in ~90% of strains. Phylogenetic analyses suggested that GI-pheV in ST131 has evolved together with the core genome, with the loss/gain of specific modules (or the entire GI) linked to strain specific events. Overall, we show GI-pheV exhibits a dynamic evolutionary pathway, in which modules and genes have evolved through multiple events including insertions, deletions and recombination.\n\nEvolution of the pheV-tRNA integrated genomic island in Escherichia coli.", "token_count": 379, "char_count": 1438, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6493, "quality_score": 0.8246, "entities": { "genes": [ "ST131", "EC958" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:09.015235", "source": { "split": "train_shard_00000", "doc_id": 666 }, "chunk_id": "train_shard_00000_666_0", "global_id": 741 }, { "text": "The phenolic antioxidant 2,6-Di-tert-butyl-p-cresol (BHT) has been detected in various environments and is considered a potential threat to aquatic organisms. Algal-bacterial interactions are crucial for maintaining ecosystem balance and elemental cycling, but their response to BHT remains to be investigated. This study analyzed the physiological and biochemical responses of the microalga Isochrysis galbana and the changes of associated bacterial communities under different concentrations of BHT stress. Results showed that the biomass of I. galbana exhibited a decreasing trend with increasing BHT concentrations up to 40 mg/L. The reduction in chlorophyll, carotenoid, and soluble protein content of microalgal cells was also observed under BHT stress. The production of malondialdehyde and the activities of superoxide dismutase, peroxidase, and catalase were further determined. Scanning electron microscopy analysis revealed that BHT caused surface rupture of the algal cells and loss of intracellular nutrients. Proteomic analysis demonstrated the upregulation of photosynthesis and citric acid cycle pathways as a response to BHT stress. Additionally, BHT significantly increased the relative abundance of specific bacteria in the phycosphere, including Marivita, Halomonas, Marinobacter, and Alteromonas. Further experiments confirmed that these bacteria had the ability to utilize BHT as the sole carbon resource for growth, and genes related to the degradation of phenolic compounds were detected through pangenome analysis.\n\nIntegrated proteome and pangenome analysis revealed the variation of microalga Isochrysis galbana and associated bacterial community to 2,6-Di-tert-butyl-p-cresol (BHT) stress.", "token_count": 417, "char_count": 1717, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:09.670033", "source": { "split": "train_shard_00000", "doc_id": 667 }, "chunk_id": "train_shard_00000_667_0", "global_id": 742 }, { "text": "Fungi generate a diverse array of bioactive compounds with significant pharmaceutical applications. However, the chemical diversity of natural products in fungi remains largely unexplored. Here, we present a paradigm for specifically discovering diverse and bioactive compounds from fungi by integrating genome mining with building block molecular network and coculture analysis. Through pangenome and sequence similarity network analysis, we identified a rare type I polyketide enzyme from\n\nTargeted discovery of polyketides with antioxidant activity through integrated omics and cocultivation strategies.", "token_count": 125, "char_count": 606, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7722, "quality_score": 0.8861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:10.058734", "source": { "split": "train_shard_00000", "doc_id": 668 }, "chunk_id": "train_shard_00000_668_0", "global_id": 743 }, { "text": "Aquaculture is an important component of the world food supply and a significant source of protein. However, this industry faces numerous problems. Including poor fish feed digestion and uneconomic nutrient utilization. This can result in unsatisfactory growth rates and poor stock performance. Utilizing probiotics, which are beneficial microbes that can enhance digestive systems and general fish health, is one possible way to address these issues. This study was designed to identify and evaluate a novel strain of Bacillus as a promising probiotic. The strain of Bacillus rugosus that was examined and coded NM007 showed promising probiotic characteristics that could help fish digest and utilize their feed more efficiently, reduce feed waste, and improve their digestive systems. B. rugosus NM007 exhibited the ability to produce digestive enzymes like protease, amylase, and lipase, which are the main digestive enzymes. It showed strong auto-aggregation activity and co-aggregation activity with Aeromonas sp. and Streptococcus sp. It also demonstrated tolerance to the presence of bile salt, acidic pH, and salinity up to 60 ppt. The sensitivity analysis towards antibiotics, hemolytic activity and the safety assessment on Nile tilapia fish (Oreochromis niloticus) confirmed the safety of this isolate. Based on the findings of this investigation and the isolate's characterization, Bacillus rugosus NM007 could serve as a new promising probiotic bacterium for aquaculture.\n\nIsolation, characterization, and assessment of Bacillus rugosus potential as a new probiotic for aquaculture applications.", "token_count": 378, "char_count": 1608, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6234, "quality_score": 0.8117, "entities": { "genes": [ "NM007" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:10.639634", "source": { "split": "train_shard_00000", "doc_id": 669 }, "chunk_id": "train_shard_00000_669_0", "global_id": 744 }, { "text": "Yeast-derived cell wall polysaccharides possess numerous biological activities, but their application in postharvest preservation is rarely reported. The aim of this research was to investigate the effects of Kluyveromyces marxianus soluble cell wall polysaccharide (SCWP) on preventing the infection of Penicillium expansum in pear fruit. The results showed that K. marxianus SCWP treatment could significantly improve the resistance of pear fruit to P. expansum, with respect to Saccharomyces cerevisiae-derived SCWP. Composition of both SCWPs was mannan with the main chains consisting of a → 6)-α-D-Manp-(1 → unit and the branch structure formed by → 2)-α-D-Manp-(1 except that K. marxianus SCWP took on a shorter side chain and a rougher surface than S. cerevisiae SCWP. In addition, mechanisms of K. marxianus SCWP on stimulating resistance response were associated with the apparent oxidative burst, increased gene expression and enzyme activity of antioxidant and defense systems in pear fruit. Our findings suggest that K. marxianus SCWP can be used as an innovative and promising candidate for preventing postharvest fungal decay and extending fruit shelf life.\n\nPositive effects of yeast soluble cell wall polysaccharide on fruit postharvest control through resistance response.", "token_count": 318, "char_count": 1289, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:11.198252", "source": { "split": "train_shard_00000", "doc_id": 670 }, "chunk_id": "train_shard_00000_670_0", "global_id": 745 }, { "text": "The purpose of this study was to prepare a pH-responsive microgel for co-delivering Weizmannia coagulans 99 (BC99) and procyanidins (PCs) to enhance the survival rate and tolerance of probiotics in complex micro-environment. The effects of different concentrations of PCs on the properties of microgels were optimized, and found that the spherical microgels had higher encapsulation efficiency (90.27 ± 2.51%) and smaller size when the concentration of PCs was 20 μg/mL. The interaction among PCs, pectin and protein could effectively improve the survival rate of BC99 under different pH, bile salt, digestive enzyme and temperature conditions, maintain their stability in acidic gastric fluid, and realize the release of probiotics in neutral intestinal fluid. Moreover, the microgel was able to protect BC99 against H\n\nOptimization of pH-responsive microgel for the co-delivery of Weizmannia coagulans and procyanidins to enhance survival rate and tolerance.", "token_count": 254, "char_count": 960, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8179, "entities": { "genes": [ "BC99" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:11.683880", "source": { "split": "train_shard_00000", "doc_id": 671 }, "chunk_id": "train_shard_00000_671_0", "global_id": 746 }, { "text": "Lactic acid bacteria (LAB) play a key role in regulating the balance of gut microbiota and serve as a suitable alternative to antibiotics. This study aims to evaluate the characteristics of 2 LAB isolates Lactiplantibacillus plantarum Lp71 (L. plantarum Lp71) and Enterococcus faecium Ef72 (E. faecium Ef72), and their roles in alleviating Salmonella Enteritidis infection. Sixty 1-day-old chicks were randomly divided into 4 groups which treated with or without L. plantarum Lp71 and E. faecium Ef72 mixture for 21 d, and then intestinal samples were collected for gut microbiota analysis, pathological and immunohistochemical analysis at 24 h post infection with or without Salmonella Enteritidis on the 22nd d. The results showed that L. plantarum Lp71 and E. faecium Ef72 had the ability to anti-acid and anti-bile salt. Salmonella Enteritidis infection damaged the intestinal epithelial barrier and reduced the expression level of tight junction proteins (ZO-1, Claudin-1, Occludin). Oral supplementation with L. plantarum Lp71 and E. faecium Ef72 mixture could alleviated the damages to intestinal epithelial barrier by Salmonella Enteritidis infection. Salmonella Enteritidis could cause abnormal Akkermansia muciniphila proliferation and decrease the diversity of cecal microbiota in chicks. These conditions could have further led to reduce gut microbiota health index (GMHI), and improve microbial dysbiosis index (MDI). Moreover, oral supplementation with L. plantarum Lp71 and E. faecium Ef72 mixture could effectively prevent the aforementioned infection outcomes and increase the abundance proportions of the several key functions in metabolic pathways metabolic pathways such as transcription and signal transduction mechanisms. In summary, L. plantarum Lp71 and E", "token_count": 500, "char_count": 1779, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:12.333585", "source": { "split": "train_shard_00000", "doc_id": 672 }, "chunk_id": "train_shard_00000_672_0", "global_id": 747 }, { "text": "faecium Ef72 could be the probiotics candidates that used to prevent the damage from enteric pathogens such as Salmonella Enteritidis in broiler chicks.\n\nOral supplementation with lactic acid bacteria improve the intestinal epithelial barrier and gut microbiota of broiler chicks to alleviate Salmonella Enteritidis infection.", "token_count": 85, "char_count": 326, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:12.708873", "source": { "split": "train_shard_00000", "doc_id": 672 }, "chunk_id": "train_shard_00000_672_1", "global_id": 748 }, { "text": "Erratum: Development and implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme for", "token_count": 26, "char_count": 103, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:13.072701", "source": { "split": "train_shard_00000", "doc_id": 673 }, "chunk_id": "train_shard_00000_673_0", "global_id": 749 }, { "text": "Streptococcus pneumoniae is an opportunistic human pathogen responsible for high morbidity and mortality rates. Extensive genome sequencing revealed its large pangenome, serotype diversity, and provided insight into genome dynamics. However, functional genome analysis has lagged behind, as that requires detailed and time-consuming manual curation of genome annotations and integration of genomic and phenotypic data. To remedy this, PneumoBrowse was presented in 2018, a user-friendly interactive online platform, which provided the detailed annotation of the S. pneumoniae D39V genome, alongside transcriptomic data. Since 2018, many new studies on S. pneumoniae genome biology and protein functioning have been performed. Here, we present PneumoBrowse 2 (https://veeninglab.com/pneumobrowse), fully rebuilt in JBrowse 2. We updated annotations for transcribed and transcriptional regulatory features in the D39V genome. We added genome-wide data tracks for high-resolution chromosome conformation capture (Hi-C) data, chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), ribosome profiling, CRISPRi-seq gene essentiality data and more. Additionally, we included 18 phylogenetically diverse S. pneumoniae genomes and their annotations. By providing easy access to diverse high-quality genome annotations and links to other databases (including UniProt and AlphaFold), PneumoBrowse 2 will further accelerate research and development into preventive and treatment strategies, through increased understanding of the pneumococcal genome.\n\nPneumoBrowse 2: an integrated visual platform for curated genome annotation and multiomics data analysis of Streptococcus pneumoniae.", "token_count": 433, "char_count": 1698, "word_count": 215, "semantic_coherence": 1, "information_density": 0.707, "quality_score": 0.8535, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:13.695082", "source": { "split": "train_shard_00000", "doc_id": 674 }, "chunk_id": "train_shard_00000_674_0", "global_id": 750 }, { "text": "Most DNA methylation studies have used a single reference genome with little attention paid to the bias introduced due to the reference chosen. Reference genome artifacts and genetic variation, including single nucleotide polymorphisms (SNPs) and structural variants (SVs), can lead to differences in methylation sites (CpGs) between individuals of the same species. We analyzed whole-genome bisulfite sequencing data from the fetal liver of Angus (Bos taurus taurus), Brahman (Bos taurus indicus), and reciprocally crossed samples. Using reference genomes for each breed from the Bovine Pangenome Consortium, we investigated the influence of reference genome choice on the breed and parent-of-origin effects in methylome analyses.\n\nDNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.", "token_count": 202, "char_count": 850, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:14.159606", "source": { "split": "train_shard_00000", "doc_id": 675 }, "chunk_id": "train_shard_00000_675_0", "global_id": 751 }, { "text": "Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder, a pipeline for constructing pangenome graphs without bias or exclusion. The PanGenome Graph Builder uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events and infer phylogenetic relationships.\n\nBuilding pangenome graphs.", "token_count": 110, "char_count": 542, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7703, "quality_score": 0.8851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:14.539867", "source": { "split": "train_shard_00000", "doc_id": 676 }, "chunk_id": "train_shard_00000_676_0", "global_id": 752 }, { "text": "Pangenome graphs signify a new frontier in genome representation. Recent advances in constructing and personalizing them mark progress in this area.\n\nConstructing and personalizing population pangenome graphs.", "token_count": 43, "char_count": 209, "word_count": 27, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:14.910814", "source": { "split": "train_shard_00000", "doc_id": 677 }, "chunk_id": "train_shard_00000_677_0", "global_id": 753 }, { "text": "Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This article introduces BAKIR (Biologically informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community.\n\nBiologically-informed killer cell immunoglobulin-like receptor gene annotation tool.", "token_count": 400, "char_count": 1879, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:15.529784", "source": { "split": "train_shard_00000", "doc_id": 678 }, "chunk_id": "train_shard_00000_678_0", "global_id": 754 }, { "text": "Ensuring the viability and efficacy of probiotic microorganisms during manufacturing and gastrointestinal transit remains challenging, particularly for sensitive strains such as certain lactic acid bacteria and bifidobacteria. This has led to increased interest in spore-forming bacteria, such as Heyndrickxia coagulans (formerly Bacillus coagulans), which can endure environmental stresses through their endospore forms. This study presents a comprehensive analysis of the probiotic potential of strain LMG S-24828, originally isolated from healthy human feces. The genomic analysis confirmed the strain's taxonomic placement within the species H. coagulans and revealed no extrachromosomal plasmid DNA, suggesting genetic stability. Safety assessments demonstrated that LMG S-24828 does not produce D-lactate, deconjugate bile salts, or exhibit hemolytic activity, and it lacks transmissible antibiotic resistances. Phenotypic tests showed the strain's metabolic versatility, including its ability to hydrolyze complex carbohydrates and adhere to intestinal epithelial cells. Moreover, LMG S-24828 exhibited robust survival and germination during in vitro and in vivo gastrointestinal simulations, with evidence of significant spore germination in the human gut. These findings suggest that H. coagulans LMG S-24828 possesses several advantageous traits for probiotic applications, warranting further clinical evaluation to confirm its health benefits.\n\nHeyndrickxia coagulans LMG S-24828 Is a Safe Probiotic Strain Capable of Germinating in the Human Gut.", "token_count": 396, "char_count": 1558, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:16.145932", "source": { "split": "train_shard_00000", "doc_id": 679 }, "chunk_id": "train_shard_00000_679_0", "global_id": 755 }, { "text": "Loureirin B (LB), an active component of Resina Draconis, exhibits hypoglycemic and hypolipidemic effects; however, its mode of action remains unclear. Here, ob/ob mice were utilized to investigate the effects of LB on the regulation of glucolipid metabolism disorders. Non-targeted metabolomics and 16S rDNA sequencing were performed to elucidate the potential mechanisms involved. Results indicated that LB treatment (45 mg/kg) significantly improved glucose intolerance and insulin resistance, reduced lipid levels, and alleviated hepatic steatosis. Non-targeted metabolomics analysis revealed that LB treatment regulated bile acid levels. Quantification of liver bile acids demonstrated that LB treatment significantly decreased the ratio of 12α-OH to non-12α-OH bile acids in the liver. 16S rDNA sequencing results showed that LB treatment increased the abundance of short-chain fatty acid-producing microbiota while decreasing the abundance of bile salt hydrolase (BSH) enzyme-producing microbiota. In conclusion, LB ameliorates glucolipid metabolism disorders by regulating liver bile acid levels and modulating the composition of the gut microbiota.\n\nLoureirin B Ameliorates Glycolipid Metabolism Disorders in Ob/ob Mice by Regulating Bile Acid Levels and Modulating Gut Microbiota Composition.", "token_count": 355, "char_count": 1302, "word_count": 174, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:16.724015", "source": { "split": "train_shard_00000", "doc_id": 680 }, "chunk_id": "train_shard_00000_680_0", "global_id": 756 }, { "text": "Albendazole (ABZ), an anthelmintic drug, has been repurposed to treat various types of cancers. However, poor solubility of ABZ, resulting in low bioavailability, limits its application. Nanosuspension is a versatile method for enhancing the dissolution of hydrophobic molecules, but a successful drying has been the biggest challenge in the field. The objective of this research is to formulate and optimize ABZ nanosuspension (NS) coated granules for rapid delivery of ABZ for the treatment of colorectal cancer. ABZ NS was prepared by dual centrifugation method using Kollidon® VA64 and sodium lauryl sulphate (SLS) as stabilizers. The processing method was optimized to obtain a stable nanosuspension with particle size < 300 nm. The optimized ABZ NS was coated on microcrystalline cellulose (MCC) to form the nano-coated granules (NCG) and filled in EUDRACAP® for colon targeted delivery. The ABZ NS and NCG achieved ∼ 60 % and ∼55 % drug release, respectively, in presence of bile salt at colonic pH. Half-maximal inhibitory concentration (IC\n\nAlbendazole nanosuspension coated granules for the rapid localized release and treatment of colorectal cancer.", "token_count": 329, "char_count": 1160, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [ "VA64" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:17.300320", "source": { "split": "train_shard_00000", "doc_id": 681 }, "chunk_id": "train_shard_00000_681_0", "global_id": 757 }, { "text": "High-fidelity (HiFi) sequencing has facilitated the assembly and analysis of the most repetitive region of the genome, the centromere. Nevertheless, our current understanding of human centromeres is based on a relatively small number of telomere-to-telomere assemblies, which have not yet captured its full diversity. In this study, we investigated the genomic diversity of human centromere higher order repeats (HORs) via both HiFi reads and haplotype-resolved assemblies from hundreds of samples drawn from ongoing pangenome-sequencing projects and reprocessed them via a novel HOR annotation pipeline, HiCAT-human. We used this wealth of data to provide a global survey of the centromeric HOR landscape; in particular, we found that 23 HORs presented significant copy number variability between populations. We detected three centromere genotypes with unbalanced population frequencies on chromosomes 5, 8, and 17. An inter-assembly comparison of HOR loci further revealed that while HOR array structures are diverse, they nevertheless tend to form a number of specific landscapes, each exhibiting different levels of HOR subunit expansion and possibly reflecting a cyclical evolutionary transition from homogeneous to nested structures and back.\n\nCentromere Landscapes Resolved from Hundreds of Human Genomes.", "token_count": 302, "char_count": 1313, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7297, "quality_score": 0.8649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:17.863923", "source": { "split": "train_shard_00000", "doc_id": 682 }, "chunk_id": "train_shard_00000_682_0", "global_id": 758 }, { "text": "Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA, is particularly challenging due to the short sequence length and chemical damage which creates a specific pattern of substitution (C→T and G→A) in addition to the heightened divergence between the sample and the reference genome thus exacerbating reference bias. This bias can be mitigated by aligning to pangenome graphs to incorporate documented organismic variation, but this approach still suffers from substitution patterns due to chemical damage. We introduce a novel methodology introducing the RYmer index, a variant of the commonly-used minimizer index which represents purines (A,G) and pyrimidines (C,T) as R and Y respectively. This creates an indexing scheme robust to the aforementioned chemical damage. We implemented SAFARI, an ancient DNA damage-aware version of the pangenome aligner vg giraffe which uses RYmers to rescue alignments containing deaminated seeds. We show that our approach produces more correct alignments from ancient DNA sequences than current approaches while maintaining a tolerable rate of spurious alignments. In addition, we demonstrate that our algorithm improves the estimate of the rate of ancient DNA damage, especially for highly damaged samples. Crucially, we show that this improved alignment can directly translate into better insights gained from the data by showcasing its integration with a number of extant pangenome tools.\n\nSAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings.", "token_count": 341, "char_count": 1565, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8296, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:18.433403", "source": { "split": "train_shard_00000", "doc_id": 683 }, "chunk_id": "train_shard_00000_683_0", "global_id": 759 }, { "text": "Multiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function. An alternative to the standard MSA model is partial order alignment (POA), in which aligned sequences are represented as paths in a graph rather than rows in a matrix. While the POA model has proven useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration), we lack efficient visualization tools that could highlight its advantages.\n\nSequence Flow: interactive web application for visualizing partial order alignments.", "token_count": 130, "char_count": 684, "word_count": 94, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:18.857672", "source": { "split": "train_shard_00000", "doc_id": 684 }, "chunk_id": "train_shard_00000_684_0", "global_id": 760 }, { "text": "Transposable elements are ubiquitous mobile DNA sequences generating insertion polymorphisms, contributing to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements insertions. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. Here, we demonstrate the versatility of GraffiTE by analyzing human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.\n\nA unified framework to analyze transposable element insertion polymorphisms using graph genomes.", "token_count": 253, "char_count": 1138, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7292, "quality_score": 0.8646, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:19.345548", "source": { "split": "train_shard_00000", "doc_id": 685 }, "chunk_id": "train_shard_00000_685_0", "global_id": 761 }, { "text": "The formation of a biomolecular corona on nanoparticles in blood is a well-known phenomenon influencing in vivo performance. Analogous phenomena in other biological fluids, such as the formation of a gastrointestinal (GI) corona, remain under-investigated. The ingestion of medicines leads to the generation of drug particles in the GI fluids. Consequently, an understanding of the behavior of drug particles in the gut requires determination of the adsorption of bile components onto these drug particles. This work aims to elucidate the factors affecting adsorption of bile salts onto ritonavir (RTV) particles. Crystalline RTV particles were incubated with non-micellar or micellar bile salts and bile salt depletion from solution was measured using HPLC and small angle X-ray scattering (SAXS). HPLC results show that bile salts adsorb onto RTV particles, with greater adsorption observed for more hydrophobic bile salts, following the order sodium glycodeoxycholate (SGDC)>sodium taurodeoxycholate (STDC)>sodium glycochenodeoxycholate SGCDC>sodium glycocholate (SGC)>sodium taurocholate (STC). Increasing the ionic strength of the solution led to increased adsorption of STDC, where buffer containing 300 mM NaCl resulted in greater adsorption than 150 mM NaCl. Additionally, micellar bile salts showed greater affinity for RTV particles than unimeric bile salts. In contrast, the extent of bile salt depletion was unaltered by addition of phospholipid to form mixed micelles. SAXS analysis of mixed micelles after incubation with RTV particles confirms depletion of bile salt from the supernatant, evidenced by reduced intensity of the micellar scattering feature. In conclusion, this study investigated factors influencing bile salt adsorption onto drug particles, highlighting the need to consider adsorption of bile components in forming the GI-corona.", "token_count": 496, "char_count": 1861, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:20.032418", "source": { "split": "train_shard_00000", "doc_id": 686 }, "chunk_id": "train_shard_00000_686_0", "global_id": 762 }, { "text": "Adsorption of bile salts onto crystalline ritonavir particles under simulated gastrointestinal conditions.", "token_count": 27, "char_count": 106, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:20.434050", "source": { "split": "train_shard_00000", "doc_id": 686 }, "chunk_id": "train_shard_00000_686_1", "global_id": 763 }, { "text": "Pangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGenome Graph Builder (PGGB) addresses these issues. To date, though, there is no state-of-the-art pipeline allowing for easy deployment, efficient and dynamic use of available resources, and scalable usage at the same time.\n\nCluster-efficient pangenome graph construction with nf-core/pangenome.", "token_count": 112, "char_count": 519, "word_count": 67, "semantic_coherence": 1, "information_density": 0.8955, "quality_score": 0.9478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:20.825149", "source": { "split": "train_shard_00000", "doc_id": 687 }, "chunk_id": "train_shard_00000_687_0", "global_id": 764 }, { "text": "The passion fruit peel (PFP) has a high cellulose and hemicellulose content, which can be used to produce fermentable sugars. In this context, this study aims to optimize the release of xylose and the production of xylitol from PFP. The optimized conditions were 0.71 M dilute sulfuric acid and a 21.84-minute treatment, yielding 19.03 g/L of xylose (PFP-1). Different PFP hydrolysates were evaluated to improve xylitol production by the yeast Kluyveromyces marxianus ATCC 36907: PFP-2 (PFP1 treated with Ca(OH)\n\nXylitol production from passion fruit peel hydrolysate: Optimization of hydrolysis and fermentation processes.", "token_count": 194, "char_count": 623, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [ "PFP1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:21.340691", "source": { "split": "train_shard_00000", "doc_id": 688 }, "chunk_id": "train_shard_00000_688_0", "global_id": 765 }, { "text": "The taxonomy of the Listeriaceae family has undergone substantial revisions, expanding the Listeria genus from 6 to 29 species since 2009. However, these classifications have relied on 16S rRNA gene sequences and conventional polyphasic taxonomy, with limited use of genomic approaches. This study aimed to employ genomic tools, including phylogenomics, Overall Genomic Relatedness Indices (OGRIs), and core-genome phylogenomic analyses, to reevaluate the taxonomy of the Listeriaceae family. The analyses involved the construction of phylogenetic and phylogenomic trees based on 16S rRNA gene sequences and core genomes from 34 type strain genomes belonging to Listeriaceae family. OGRIs, which encompass Average Amino acid Identity (AAI), core-proteome AAI (cAAI), and Percentage of Conserved Proteins (POCP), were calculated, and specific threshold values of 70%, 87%, and 72-73% were established, respectively, to delimitate genera in the Listeriaceae family. These newly proposed OGRI thresholds unveiled distinct evolutionary lineages. The outcomes of this taxonomic re-evaluation were: (i): the division of the Listeria genus into an emended Listeria genus regrouping only Listeria senso stricto species; (ii): the remaining Listeria senso lato species were transferred into three newly proposed genera: Murraya gen. nov., Mesolisteria gen. nov., and Paenilisteria gen. nov. within Listeriaceae; (iii): Brochothrix was transferred to the newly proposed family Brochothricaceae fam. nov. within the Caryophanales order; (iiii): Listeria ivanovii subsp. londonensis was elevated to the species level as Listeria londonensis sp. nov.; and (iiiii): Murraya murrayi comb. nov. was reclassified as a later heterotypic synonym of Murraya grayi comb. nov. This taxonomic framework enables more precise identification of pathogenic Listeriaceae species, with significant implications for important areas such as food safety, clinical diagnostics, epidemiology, and public health.", "token_count": 526, "char_count": 1977, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:05:21.998029", "source": { "split": "train_shard_00000", "doc_id": 689 }, "chunk_id": "train_shard_00000_689_0", "global_id": 766 }, { "text": "Phylogenomic analyses of the Listeriaceae family support species reclassification and proposal of a new family and new genera.", "token_count": 30, "char_count": 126, "word_count": 18, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:22.358992", "source": { "split": "train_shard_00000", "doc_id": 689 }, "chunk_id": "train_shard_00000_689_1", "global_id": 767 }, { "text": "Nocardia, a member of the Actinobacteria phylum, populates diverse habitats globally, with certain species being the cause of various clinical infections in humans. There is paucity of data regarding the population structure of this genus and of established genomic-based phylogenetic methods. We examined the whole genome sequences of 193 isolates spanning five major pathogenic Nocardia species sourced from public databases, encompassing diverse geographic regions. Using the chewBBACA pipeline, a species-specific core genome multilocus sequence typing (cgMLST) schema was created for N. cyriacigeorgica, N. farcinica, N. brasiliensis, N. wallacei, and N. abscessus. Additional genomic features that were examined included virulence factor (VF) profile, total length and open-reading frame count, the core genome length and core gene count, and GC content. Our findings indicated that: (i) N. brasiliensis diverges significantly from the other four species, underscoring its distinct evolutionary trajectory; (ii) the population structures of all species were polyclonal, with phylogenetic clustering occurring in the minority of isolates; (iii) clonal complexes were largely restricted to specific geographical locations, rather than demonstrating a global distribution, and (iv) initial evidence suggests no direct common-source transmission amongst the studied strains. Our study establishes a comprehensive genome-based phylogenetic methodology for population structure of Nocardia species.\n\nConstruction of core genome multi-locus sequence typing schemes for population structure analyses of Nocardia species.", "token_count": 376, "char_count": 1618, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:22.943152", "source": { "split": "train_shard_00000", "doc_id": 690 }, "chunk_id": "train_shard_00000_690_0", "global_id": 768 }, { "text": "Pangenomics alignment offers a solution to reduce bias in biomedical research. Traditionally, short-read aligners like Bowtie and BWA indexed a single reference genome to find approximate alignments. These methods, limited by linear-memory requirements, can only index a few genomes. Emerging pangenome aligners, such as VG, Giraffe, and Moni, address this by indexing more genomes. VG and Giraffe use a variation graph, while Moni indexes sequences accounting for repetition using prefix-free parsing to build a dictionary and parse. The main challenge is the parse's size, which becomes significantly larger than the dictionary. To scale Moni, we propose removing the parse from the construction of the run-length encoded BWT (RLBWT), suffix array, and Longest Common Prefix (LCP) by applying prefix-free parsing recursively. This approach improves construction time and memory requirements, enabling efficient construction of RLBWT, suffix array, and LCP for large pangenomes, such as those from the Human Pangenome Reference Consortium.\n\nBuilding a pangenome alignment index via recursive prefix-free parsing.", "token_count": 256, "char_count": 1113, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7278, "quality_score": 0.8639, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:23.495479", "source": { "split": "train_shard_00000", "doc_id": 691 }, "chunk_id": "train_shard_00000_691_0", "global_id": 769 }, { "text": "An elastic-degenerate (ED) string is a sequence of sets of strings. It can also be seen as a directed acyclic graph whose edges are labeled by strings. The notion of ED strings was introduced as a simple alternative to variation and sequence graphs for representing a pangenome, that is, a collection of genomic sequences to be analyzed jointly or to be used as a reference.\n\nPangenome comparison via ED strings.", "token_count": 92, "char_count": 412, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7429, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:23.875886", "source": { "split": "train_shard_00000", "doc_id": 692 }, "chunk_id": "train_shard_00000_692_0", "global_id": 770 }, { "text": "The genus Pseudomonas is characterized by its rich genetic diversity, with over 300 species been validly recognized. This reflects significant progress made through sequencing and computational methods. Pseudomonas putida group comprises highly adaptable species that thrive in diverse environments and play various ecological roles, from promoting plant growth to being pathogenic in immunocompromised individuals. By leveraging the GRUMPS computational pipeline, we scrutinized 26 363 genomes labeled as Pseudomonas in the NCBI GenBank, categorizing all Pseudomonas spp. genomes into 435 distinct species-level clusters or cliques. We identified 224 strains deposited under the taxonomic identifier \"Pseudomonas putida\" distributed within 31 of these species-level clusters, challenging prior classifications. Nine of these 31 cliques contained at least six genomes labeled as \"Pseudomonas putida\" and were analysed in depth, particularly clique_1 (P. alloputida) and clique_2 (P. putida). Pangenomic analysis of a set of 413 P. putida group strains revealed over 2.2 million proteins and more than 77 000 distinct protein families. The core genome of these 413 strains includes 2226 protein families involved in essential biological processes. Intraspecific genetic homogeneity was observed within each clique, each possessing a distinct genomic identity. These cliques exhibit distinct core genes and diverse subgroups, reflecting adaptation to specific environments. Contrary to traditional views, nosocomial infections by P. alloputida, P. putida, and P. monteilii have been reported, with strains showing varied antibiotic resistance profiles due to diverse mechanisms. This review enhances the taxonomic understanding of key P. putida group species using advanced population genomics approaches and provides a comprehensive understanding of their genetic diversity, ecological roles, interactions, and potential applications.\n\nUnraveling the genomic diversity of the Pseudomonas putida group: exploring taxonomy, core pangenome, and antibiotic resistance mechanisms.", "token_count": 493, "char_count": 2074, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6643, "quality_score": 0.8321, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:24.537875", "source": { "split": "train_shard_00000", "doc_id": 693 }, "chunk_id": "train_shard_00000_693_0", "global_id": 771 }, { "text": "In this study, probiotics with superior fermentation performance were screened, and the mixed-bacteria fermentation was carried out with Auricularia auricula treated with microwave-puffed process as fermentation substrate, and the changes in nutritional quality under different storage conditions were investigated. The results showed that the acid and bile salt resistance of Lactiplantibacillus plantarum 21,801 and 21,805 reached 95 % and 75 % respectively, and the intestinal adhesion was superior; microwave puffing treatment had the highest retention rate of A. auricula polysaccharides and the lowest loss of polyphenols, and no effect on soluble protein. Mixed bacterial fermentation significantly increased the total polyphenols and total flavonoids of A. auricula (p < 0.05), and the DPPH and ABTS radical scavenging reached 48.31 % and 73.21 % respectively. Furthermore, the viable counts, DPPH radical scavenging, color, and sensory quality of fermented A. auricula remained stable when stored at 4 °C. In contrast, when stored at 25 °C for 7 days, the taste was unfavorable, undesirable odor and spoilage occurred; by 21 days, DPPH clearance rate dropped below 40 % and color changed significantly (△E > 2). In conclusion, the probiotic mixed fermentation and storage conditions had a significant effect on the biometabolic transformation of macromolecules and other substances in A. auricula.\n\nEffect of microwave-puffed on Auricularia auricula polysaccharide and probiotic fermentation on its biotransformation and quality characteristics during storage period.", "token_count": 438, "char_count": 1576, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:25.167620", "source": { "split": "train_shard_00000", "doc_id": 695 }, "chunk_id": "train_shard_00000_695_0", "global_id": 772 }, { "text": "Language Models (LM) have been extensively utilized for learning DNA sequence patterns and generating synthetic sequences. In this paper, we present a novel approach for the generation of synthetic DNA data using pangenomes in combination with LM. We introduce three innovative pangenome-based tokenization schemes, including two that can decouple from private data, while enhance long DNA sequence generation. Our experimental results demonstrate the superiority of pangenome-based tokenization over classical methods in generating high-utility synthetic DNA sequences, highlighting a promising direction for the public sharing of genomic datasets.\n\nPangenome-Informed Language Models for Synthetic Genome Sequence Generation.", "token_count": 141, "char_count": 727, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:25.597091", "source": { "split": "train_shard_00000", "doc_id": 696 }, "chunk_id": "train_shard_00000_696_0", "global_id": 773 }, { "text": "Currently, the synthesis of compounds based on microbial cell factories is rapidly advancing, yet it encounters several challenges. During the production process, engineered strains frequently encounter disturbances in the cultivation environment or the impact of their metabolites, such as high temperature, acid-base imbalances, hypertonicity, organic solvents, toxic byproducts, and mechanical damage. These stress factors can constrain the efficiency of microbial fermentation, resulting in slow cell growth, decreased production, significantly increased energy consumption, and other issues that severely limit the application of microbial cell factories.\n\nAltered sterol composition mediates multiple tolerance of Kluyveromyces marxianus for xylitol production.", "token_count": 158, "char_count": 767, "word_count": 96, "semantic_coherence": 1, "information_density": 0.8438, "quality_score": 0.9219, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:26.031751", "source": { "split": "train_shard_00000", "doc_id": 697 }, "chunk_id": "train_shard_00000_697_0", "global_id": 774 }, { "text": "Salmonella enterica subspecies enterica serovar Abortusequi (S. Abortusequi) is a leading cause of abortion in equines that hinders the rapid growth of equine industry. S. Abortusequi infection in equids has re-emerged over last ten years. In the present study, S. Abortusequi was isolated and characterized from donkeys during an abortion storm in the southern peninsular region of India. Further, whole genome sequencing and phylogenomic analysis revealed that the present isolate was clustered among S. Abortusequi clade. The core genome MLST (cgMLST) analysis based on hierarchical clustering and single nucleotide polymorphism (SNP) core-genome dendrogram of the present isolate against 10 S. Abortusequi isolates revealed that the present isolate established a distinct clade compared to all previously reported isolates. A comparison of cgMLST and SNP analyses revealed the same clustering concordance between isolates. In addition, comparative genomics and phylogenetic analysis was carried out with six S. Abortusequi serovars showed a higher number of core genes than accessory genes. Further, comparative analysis of phenotype and genotype antimicrobial resistance revealed a concordance of 32% and discordance of 68% respectively.\n\nFirst report on whole genome sequencing and comparative genomics of Salmonella enterica serovar Abortusequi isolated from Donkey in India.", "token_count": 356, "char_count": 1382, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:26.610789", "source": { "split": "train_shard_00000", "doc_id": 698 }, "chunk_id": "train_shard_00000_698_0", "global_id": 775 }, { "text": "Gut microbial bile salt hydrolases (gmBSHs), an important class of bacteria-produced cysteine hydrolases, play a crucial role in bile acid metabolism. Modulating the total gmBSH activity is a feasible way for ameliorating some metabolic diseases including colorectal cancer, type 2 diabetes, and obesity. This study reported the discovery and characterization of a botanical compound as a covalent\n\nDiscovery of Tetrahydro Tanshinone I as a Naturally Occurring Covalent", "token_count": 130, "char_count": 469, "word_count": 67, "semantic_coherence": 1, "information_density": 0.8209, "quality_score": 0.9104, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:27.038707", "source": { "split": "train_shard_00000", "doc_id": 699 }, "chunk_id": "train_shard_00000_699_0", "global_id": 776 }, { "text": "As the largest family of dicotyledon, the Asteraceae family comprises a variety of economically important crops, ornamental plants and numerous medicinal herbs. Advancements in genomics and transcriptomic have revolutionized research in Asteraceae species, generating extensive omics data that necessitate an efficient platform for data integration and analysis. However, existing databases face challenges in mining genes with specific functions and supporting cross-species studies. To address these gaps, we introduce the Asteraceae Multi-omics Information Resource (AMIR; https://yanglab.hzau.edu.cn/AMIR/), a multi-omics hub for the Asteraceae plant community. AMIR integrates diverse omics data from 74 species, encompassing 132 genomes, 4 408 432 genes annotated across seven different perspectives, 3897 transcriptome sequencing samples spanning 131 organs, tissues and stimuli, 42 765 290 unique variants and 15 662 metabolites genes. Leveraging these data, AMIR establishes the first pan-genome, comparative genomics and transcriptome system for the Asteraceae family. Furthermore, AMIR offers user-friendly tools designed to facilitate extensive customized bioinformatics analyses. Two case studies demonstrate AMIR's capability to provide rapid, reproducible and reliable analysis results. In summary, by integrating multi-omics data of Asteraceae species and developing powerful analytical tools, AMIR significantly advances functional genomics research and contributes to breeding practices of Asteraceae.\n\nAMIR: a multi-omics data platform for Asteraceae plants genetics and breeding research.", "token_count": 390, "char_count": 1608, "word_count": 205, "semantic_coherence": 1, "information_density": 0.7171, "quality_score": 0.8585, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:27.655454", "source": { "split": "train_shard_00000", "doc_id": 700 }, "chunk_id": "train_shard_00000_700_0", "global_id": 777 }, { "text": "Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This paper introduces BAKIR (Biologically-informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community.\n\nBiologically-informed Killer cell immunoglobulin-like receptor (KIR) gene annotation tool.", "token_count": 407, "char_count": 1883, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:28.620192", "source": { "split": "train_shard_00000", "doc_id": 701 }, "chunk_id": "train_shard_00000_701_0", "global_id": 778 }, { "text": "Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps\n\nComplex genetic variation in nearly complete human genomes.", "token_count": 85, "char_count": 367, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8113, "quality_score": 0.9057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:28.994325", "source": { "split": "train_shard_00000", "doc_id": 702 }, "chunk_id": "train_shard_00000_702_0", "global_id": 779 }, { "text": "Yersinia enterocolitica, a foodborne pathogen, has emerged as a significant public health concern due to its increased prevalence and multidrug resistance. This study employed reverse vaccinology to identify novel vaccine candidates against Y. enterocolitica through comprehensive in silico analyses. The core genome's conserved protein translocase subunit SecY was selected as the target, and potential B-cell, MHC class I, and MHC class II epitopes were mapped. 3B-cell epitopes, 3 MHCI and 11 MHCII epitopes were acquired. A multi-epitope vaccine construct was designed by incorporating the identified epitopes, TLR4 Agonist was used as adjuvants to enhance the immunogenic response. EAAAK, CPGPG and AYY linkers were used to form a vaccine construct, followed by extensive computational evaluations. The vaccine exhibited desirable physicochemical properties, stable secondary and tertiary structures as evaluated by PDBSum and trRosetta. Moreover, favorable interactions with the human Toll-like receptor 4 (TLR4) was observed by ClusPro. Population coverage analysis estimated the vaccine's applicability across 99.74 % in diverse populations. In addition, molecular dynamics simulations and normal mode analysis confirmed the vaccine's structural stability and dynamics in a simulated biological environment. Furthermore, codon optimization and in silico cloning facilitated the evaluation of the vaccine's expression potential in E. coli and pET-28a was used a recombinant plasmid. This study provides a promising foundation for the development of an efficacious vaccine against Y. enterocolitica infections.\n\nIn silico vaccine design for Yersinia enterocolitica: A comprehensive approach to enhanced immunogenicity, efficacy and protection.", "token_count": 415, "char_count": 1749, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6751, "quality_score": 0.8376, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:29.615694", "source": { "split": "train_shard_00000", "doc_id": 703 }, "chunk_id": "train_shard_00000_703_0", "global_id": 780 }, { "text": "The original methodology for describing the pangenome of a prokaryotic species is based on modeling genomes as unordered sets of genes. More recent findings have underlined the importance of considering the ordering of genes along the genetic material as well, when making comparisons among genomes. To further investigate the benefits of gene order when describing genomes of a given species, we applied two distance metrics on a dataset of 84 genomes of Staphylococcus epidermidis. The first metric, GeLev, depends on the order of genes and is a derivative of the Levenshtein distance. The second, the Jaccard distance, depends on gene sets only. The application of these distances reveals information about the global structure of the genomes, and allows clustering of the genomes into classes. The main biological result is that, while genomes within the same class are structurally similar, genomes of different classes have an additional characteristic. Between genomes in different classes we can discover instances where a large segment of the first genome appears in reverse order in the second. This feature suggests that genome rearrangements in S. epidermidis happen on a large scale, while micro-rearrangements of single or a small number of genes are rare. Thus, this paper describes a straight-forward method to classify genomes into structural classes with the same order of genes and makes it possible to visualize reversed segments in pairs of genomes. The method can be readily applied to other species.\n\nChromosomal gene order defines several structural classes of Staphylococcus epidermidis genomes.", "token_count": 347, "char_count": 1620, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:30.190471", "source": { "split": "train_shard_00000", "doc_id": 704 }, "chunk_id": "train_shard_00000_704_0", "global_id": 781 }, { "text": "The non-conventional yeast Kluyveromyces marxianus has recently emerged as a promising candidate for many food, environment, and biotechnology applications. This yeast is thermotolerant and has robust growth under many adverse conditions. Here, we show that its ability to grow under potassium-limiting conditions is much better than that of Saccharomyces cerevisiae, suggesting a very efficient and high-affinity potassium uptake system(s) in this species. The K. marxianus genome contains two genes for putative potassium transporters: KmHAK1 and KmTRK1. To characterize the products of the two genes, we constructed single and double knock-out mutants in K. marxianus and also expressed both genes in an S. cerevisiae mutant, that lacks potassium importers. Our results in K. marxianus and S. cerevisiae revealed that both genes encode efficient high-affinity potassium transporters, contributing to potassium homeostasis and maintaining plasma-membrane potential and cytosolic pH. In K. marxianus, the presence of HAK1 supports growth at low K+ much better than that of TRK1, probably because the substrate affinity of KmHak1 is about 10-fold higher than that of KmTrk1, and its expression is induced ~80-fold upon potassium starvation. KmHak1 is crucial for salt stress survival in both K. marxianus and S. cerevisiae. In co-expression experiments with ScTrk1 and ScTrk2, its robustness contributes to an increased tolerance of S. cerevisiae cells to sodium and lithium salt stress.\n\nThe superior growth of Kluyveromyces marxianus at very low potassium concentrations is enabled by the high-affinity potassium transporter Hak1.", "token_count": 441, "char_count": 1632, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5745, "quality_score": 0.7872, "entities": { "genes": [ "TRK1", "HAK1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:30.818402", "source": { "split": "train_shard_00000", "doc_id": 706 }, "chunk_id": "train_shard_00000_706_0", "global_id": 782 }, { "text": "The order Crassvirales, which includes the prototypical crAssphage (p-crAssphage), is predominantly associated with humans, rendering it the most abundant and widely distributed group of DNA phages in the human gut. The reported human specificity and wide global distribution of p-crAssphage makes it a promising human fecal marker. However, the specificity for the human gut as well as the geographical distribution around the globe of other members of the order Crassvirales remains unknown. To determine this, a recruitment analysis using 91 complete, non-redundant genomes of crAss-like phages in human and animal viromes revealed that only 13 crAss-like phages among the 91 phages analyzed were highly specific to humans, and p-crAssphage was not in this group. Investigations to elucidate whether any characteristic of the phages was responsible for their prevalence in humans showed that the 13 human crAss-like phages do not share a core genome. Phylogenomic analysis placed them in three independent families, indicating that within the Crassvirales group, human specificity is likely not a feature of a common ancestor but rather was introduced on separate/independent occasions in their evolutionary history. The 13 human crAss-like phages showed variable geographical distribution across human metagenomes worldwide, with some being more prevalent in certain countries than in others, but none being universally identified. The varied geographical distribution and the absence of a phylogenetic relationship among the human crAss-like phages are attributed to the emergence and dissemination of their bacterial host, the symbiotic human strains of Bacteroides, across various human populations occupying diverse ecological niches worldwide.\n\nRecruitment of complete crAss-like phage genomes reveals their presence in chicken viromes, few human-specific phages, and lack of universal detection.", "token_count": 424, "char_count": 1905, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5889, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:31.445085", "source": { "split": "train_shard_00000", "doc_id": 707 }, "chunk_id": "train_shard_00000_707_0", "global_id": 783 }, { "text": "Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems, overcoming the limitations of conventional fossil records. However, several methodological challenges remain, particularly for classifying the DNA to species level and conducting phylogenetic analysis. Current methods, primarily tailored for modern datasets, fail to capture several idiosyncrasies of aeDNA, including species mixtures from closely related species and ancestral divergence. We introduce soibean, a novel tool that utilizes mitochondrial pangenomic graphs for identifying species from aeDNA reads. It outperforms existing methods in accurately identifying species from multiple closely related sources within a sample, enhancing phylogenetic analysis for aeDNA. soibean employs a damage-aware likelihood model for precise identification at low coverage with a high damage rate. Additionally, we reconstructed ancestral sequences for soibean's database to handle aeDNA that is highly diverged from modern references. soibean demonstrates effectiveness through simulated data tests and empirical validation. Notably, our method uncovered new empirical results in published datasets, including using porpoise whales as food in a Mesolithic community in Sweden, demonstrating its potential to reveal previously unrecognized findings in aeDNA studies.\n\nsoibean: High-Resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs.", "token_count": 315, "char_count": 1481, "word_count": 191, "semantic_coherence": 1, "information_density": 0.7173, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:32.041910", "source": { "split": "train_shard_00000", "doc_id": 708 }, "chunk_id": "train_shard_00000_708_0", "global_id": 784 }, { "text": "Brevibacillus brevis FJAT-0809-GLX has a broad spectrum of antimicrobial activity. Understanding the molecular basis of biocontrol ability of B. brevis will allow us to develop effective microbial agents for sustainable agriculture. In this study, we present the complete and annotated genome sequence of FJAT-0809-GLX. The complete genome size of B. brevis FJAT-0809-GLX was 6,137,019 bp, with 5688 predicted coding sequences (CDS). The average GC content of 47.38%, and there were 44 copies of the rRNAs operon (16S, 23S and 5S RNA), and 127 tRNA genes. A total of 11,162 genes were functionally annotated with the COG, GO, and KEGG databases, and 123 genes belonged to CAZymes. Genomic secondary metabolite analysis indicated 13 clusters encoding potential new antimicrobials. FJAT-0809-GLX was designated as B. brevis according to average nucleotide polymorphism (ANI) and phylogenetic analysis. The pangenome consisted of 7141 homologous genes, and 4469 homologous genes shared by B. brevis FJAT-0809-GLX, B. brevis NBRC100599, B. brevis DSM30, and B. brevis NCTC2611. The number of unique homologous genes of B. brevis FJAT-0809-GLX (419 genes) and B. brevis NBRC100599 (480 genes) were much more than those in B. brevis DSM30 (13 genes), and B. brevis NCTC2611 (6 genes). Nine gene clusters encoding for secondary metabolite biosynthesis were compared in the genome of B. brevis FJAT-0809-GLX with those of B. brevis NBRC100599, B. brevis DSM30 and B", "token_count": 524, "char_count": 1457, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7919, "entities": { "genes": [ "DSM30", "NCTC2611", "NBRC100599" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:05:32.725583", "source": { "split": "train_shard_00000", "doc_id": 709 }, "chunk_id": "train_shard_00000_709_0", "global_id": 785 }, { "text": "brevis NCTC2611, and the gene clusters encoding for lantipeptide and transatpks-otherks only existed in genome of B. brevis FJAT-0809-GLX. The 11 BbPks genes were included in the B. brevis FJAT-0809-GLX genome, which contained the conserved PS-DH domain. The relative expression of BbPksL, BbPksM2, BbPksM3, BbPksN3, BbPksN4 and BbPksN5 reached a maximum at 120 h and then decreased at 144 h. Our results provided detailed genomic and Pks genes information for the FJAT-0809-GLX strain, and lid a foundation for studying its biocontrol mechanisms.\n\nComplete genome sequence analysis and Pks genes identification of Brevibacillus brevis FJAT-0809-GLX with a broad inhibitory spectrum against phytopathogens.", "token_count": 244, "char_count": 706, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7129, "quality_score": 0.8564, "entities": { "genes": [ "NCTC2611" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:33.232741", "source": { "split": "train_shard_00000", "doc_id": 709 }, "chunk_id": "train_shard_00000_709_1", "global_id": 786 }, { "text": "Bile salt hydrolase (BSH), a pivotal enzyme in cholesterol management, holds significant promise in both human and animal subjects. This study investigated the effect of fermentation dynamics in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012 to enhance BSH production. Cultivation of cultures in MRS and M17 media revealed that MRS medium enhanced BSH production by 235.98 % in H. coagulans ATCC 7050 and 147.37 % in L. plantarum ATCC 10012, compared to M 17 medium. Additionally, varying oxygen concentration levels indicated that H. coagulans ATCC 7050 exhibited its minimum doubling time of 79.8 ± 0.64 min in anaerobic conditions, whereas L.plantarum ATCC 10012 demonstrated its minimum doubling time of 85.5 ± 1.2 min under microaerophilic conditions. However, their highest BSH activity was observed during the stationary phase under anaerobic conditions, yielding 17.14 ± 0.78 U/mL by H. coagulans ATCC 7050 and 19.04 ± 0.81 U/mL by L.plantarum ATCC 10012. Furthermore, it was observed that both organisms did not retain BSH within their cells. BSH activity was assessed using ninhydrin assay that detected free taurine liberated from sodium taurocholate. However, ninhydrin can yield false-positive results owing to its interaction with other free amino acids. To subjugate this limitation, the study introduced a novel and sensitive HPTLC-MS method capable of accurately detecting taurine. By comprehending fermentation dynamics and selecting appropriate conditions, BSH production increased 2.1-fold in both organisms. These findings illuminate critical insights, offering a pathway for novel strategies to enhance the BSH-producing capabilities of these LAB strains.", "token_count": 513, "char_count": 1708, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:05:33.924298", "source": { "split": "train_shard_00000", "doc_id": 710 }, "chunk_id": "train_shard_00000_710_0", "global_id": 787 }, { "text": "Fermentation dynamics of bile salt hydrolase production in Heyndrickxia coagulans ATCC 7050 and Lactiplantibacillus plantarum ATCC 10012: Addressing ninhydrin assay limitations with a novel HPTLC-MS method.", "token_count": 69, "char_count": 206, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:34.297783", "source": { "split": "train_shard_00000", "doc_id": 710 }, "chunk_id": "train_shard_00000_710_1", "global_id": 788 }, { "text": "Investigating plant genomes offers crucial foundational resources for exploring various aspects of plant biology and applications, such as functional genomics and breeding practices. With the development in sequencing and assembly technology, several\n\nRetrospect and prospect of", "token_count": 51, "char_count": 278, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8611, "quality_score": 0.9306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:34.670034", "source": { "split": "train_shard_00000", "doc_id": 711 }, "chunk_id": "train_shard_00000_711_0", "global_id": 789 }, { "text": "Currently, there is a lack of targeted medications for estrogen-induced intrahepatic cholestasis (EIC) and the primary objective in managing this condition is to safeguard liver function. Consequently, this study was conducted to examine the pharmacological efficacy of cilostazol (CTZ) in the management of EIC and explore its underlying mechanisms through the use of an animal model. Thirty female Sprague-Dawley rats were divided into five groups of six animals each: Normal group, 17-ethinylestradiol (EE)-induced intrahepatic cholestasis group, EE + ursodeoxycholic acid (UDCA)-treated group, EE + CTZ (5 mg/kg)-treated group, and EE + CTZ (10 mg/kg)-treated group. It was found that the therapeutic efficacy of UDCA and low dosage of CTZ (5 mg/kg) was comparable. Nevertheless, when CTZ was administered at a dose of 10 mg/kg, it resulted in the normalization of all liver function parameters, oxidative stress, and pro-inflammatory markers, together with improvement in the histopathological derangements and hepatocytic apoptosis. These effects were mediated through the activation of the hepatocyte nuclear factor-1 alpha (HNF1α)/Farnesoid X receptor (FXR) pathway with subsequent down-regulation of the bile acids (BAs) synthesis enzyme; cholesterol 7α-hydroxylase (CYP7A1), and up-regulation of the BAs-metabolizing enzyme; cytochrome P450 (CYP)3A1 and the bile salt export pump; BSEP. Therefore, the administration of CTZ in a dose-dependent manner can protect against EIC through regulating the HNF1α/FXR pathway and anti-apoptotic mechanisms. This implies that CTZ exhibits considerable promise as a therapeutic agent for the treatment of cholestatic liver disorders.", "token_count": 497, "char_count": 1681, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6596, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:35.323132", "source": { "split": "train_shard_00000", "doc_id": 712 }, "chunk_id": "train_shard_00000_712_0", "global_id": 790 }, { "text": "Protective effects of cilostazol via the HNF1α/FXR signalling pathway and anti-apoptotic mechanisms in a rat model of estrogen-induced intrahepatic cholestasis.", "token_count": 50, "char_count": 160, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:35.680893", "source": { "split": "train_shard_00000", "doc_id": 712 }, "chunk_id": "train_shard_00000_712_1", "global_id": 791 }, { "text": "Accurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing step that uses reads aligned to the draft assembly to identify necessary edits. However, current methods struggle to find a balance between over-and under-polishing. Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacbio HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHARAOH (Phasing Reads in Areas Of Homozygosity), which uses ultra-long ONT data to ensure alignments are accurately phased and to correctly introduce heterozygous edits in falsely homozygous regions. We demonstrate that the DeepPolisher pipeline can reduce assembly errors by half, with a greater than 70% reduction in indel errors. We have applied our DeepPolisher-based pipeline to 180 assemblies from the next Human Pangenome Reference Consortium (HPRC) data release, producing an average predicted Quality Value (QV) improvement of 3.4 (54% error reduction) for the majority of the genome.\n\nHighly accurate assembly polishing with DeepPolisher.", "token_count": 296, "char_count": 1293, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7104, "quality_score": 0.8552, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:36.240188", "source": { "split": "train_shard_00000", "doc_id": 713 }, "chunk_id": "train_shard_00000_713_0", "global_id": 792 }, { "text": "Escherichia albertii is an emerging foodborne pathogen that causes diarrhea. Although various animals, especially poultry, serve as reservoirs of E. albertii, the transmission of E. albertii among reservoirs and the associated risks to humans remain unclear. This study investigated an E. albertii-infected infant exposed to poultry, and collected samples from contact persons, poultry, and the environment to better understand the transmission dynamics of E. albertii. One E. albertii isolate from a contact person, seven isolates from poultry, and six isolates from the environment were recovered. Whole-genome sequencing analysis showed that eight strains derived from poultry or environment and classified as ST4633 shared great similarity (core genome single-nucleotide polymorphisms [cgSNPs] ≤20). However, the patient-derived strain ESA311 had a cgSNP difference of 1165 with the human strain ESA339 and differed from poultry and environmental strains (cgSNP range 2417-14997), indicating distant relatedness. The whole-genome phylogeny showed that several human-derived E. albertii strains clustered with those of animal origin. Our results suggest that family-bred poultry constitute a possible reservoir for E. albertii, with the environment acting as a crucial vector for the spread of these bacteria and posing a risk to humans. Further surveillance of poultry is required to elucidate the public health risks associated with E. albertii infections.\n\nGenetic Diversity and Potential Transmission of Escherichia albertii in a Poultry-Breeding Rural Village.", "token_count": 405, "char_count": 1568, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [ "ST4633", "ESA339", "ESA311" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:36.866554", "source": { "split": "train_shard_00000", "doc_id": 714 }, "chunk_id": "train_shard_00000_714_0", "global_id": 793 }, { "text": "Lactiplantibacillus plantarum (formerly Lactobacillus plantarum) exhibits relevant probiotic and technological features and is widely used in food industries, improving flavour, texture and organoleptic properties of fermented products. Cell-surface proteins have a key role in the molecular mechanisms responsible for healthy effects, being the first actors in the bacteria - host interactions. Proteins present on the surface of four L. plantarum strains (two isolated from vegetable matrices and two from dairy products) were identified by proteomics with the aim to gain a comprehensive picture of differences in protein profiles potentially related to the habitat of origin and specific properties of the analyzed strains. Results highlighted a more diversified pattern of surface proteins in strains from vegetable matrices compared to those from dairy matrices (>500 proteins vs about 200 proteins, respectively). The four strains shared a core of 143 proteins, while 445 were specifically present in strains from vegetable matrices and 26 were peculiar of strains from dairy origin. Sortase A, involved in adhesion, and choloylglycine hydrolase (bile salt hydrolase) were detected only in strains from vegetable matrices. The peculiar molecular functions of identified proteins suggested that these strains, and in particular L. plantarum S61, could have a significant probiotic and biotechnological potential.\n\nCatalogue of surface proteins of Lactiplantibacillus plantarum strains of dairy and vegetable niches.", "token_count": 348, "char_count": 1521, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5888, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:37.441236", "source": { "split": "train_shard_00000", "doc_id": 715 }, "chunk_id": "train_shard_00000_715_0", "global_id": 794 }, { "text": "This study highlights the agronomic potential of rare introgressions, as demonstrated by a major QTL for powdery mildew resistance on chromosome 7D. It further shows evidence for inter-homoeologue recombination in wheat. Agriculturally important genes are often introgressed into crops from closely related donor species or landraces. The gene pool of hexaploid bread wheat (Triticum aestivum) is known to contain numerous such \"alien\" introgressions. Recently established high-quality reference genome sequences allow prediction of the size, frequency and identity of introgressed chromosome regions. Here, we characterise chromosomal introgressions in bread wheat using exome capture data from the WHEALBI collection. We identified 24,981 putative introgression segments of at least 2 Mb across 434 wheat accessions. Detailed study of the most frequent introgressions identified T. timopheevii or its close relatives as a frequent donor species. Importantly, 118 introgressions of at least 10 Mb were exclusive to single wheat accessions, revealing that large populations need to be studied to assess the total diversity of the wheat pangenome. In one case, a 14 Mb introgression in chromosome 7D, exclusive to cultivar Pamukale, was shown by QTL mapping to harbour a recessive powdery mildew resistance gene. We identified multiple events where distal chromosomal segments of one subgenome were duplicated in the genome and replaced the homoeologous segment in another subgenome. We propose that these examples are the results of inter-homoeologue recombination. Our study produced an extensive catalogue of the wheat introgression landscape, providing a resource for wheat breeding. Of note, the finding that the wheat gene pool contains numerous rare, but potentially important introgressions and chromosomal rearrangements has implications for future breeding.\n\nAnalysis of a global wheat panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeologue chromosomal recombination.", "token_count": 472, "char_count": 2020, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:38.084757", "source": { "split": "train_shard_00000", "doc_id": 716 }, "chunk_id": "train_shard_00000_716_0", "global_id": 795 }, { "text": "Plant AT-rich sequence and zinc-binding proteins (PLATZs) are a novel category of plant-specific transcription factors involved in growth, development, and abiotic stress responses. However, the\n\nIdentification and Functional Characterization of Abiotic Stress Tolerance-Related", "token_count": 66, "char_count": 278, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8485, "quality_score": 0.9242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:38.456188", "source": { "split": "train_shard_00000", "doc_id": 717 }, "chunk_id": "train_shard_00000_717_0", "global_id": 796 }, { "text": "Exploring Biofilm-Related Traits and Bile Salt Efficacy as Anti-Biofilm Agents in MDR", "token_count": 27, "char_count": 85, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:38.816951", "source": { "split": "train_shard_00000", "doc_id": 718 }, "chunk_id": "train_shard_00000_718_0", "global_id": 797 }, { "text": "Porphyromonas gingivalis is a Gram-negative, anaerobic oral pathobiont, an etiological agent of periodontitis and the most commonly studied periodontal bacterium. Multiple low passage clinical isolates were sequenced, and their genomes compared to several laboratory strains. Phylogenetic distances were mapped, a gene absence-presence matrix generated, and core (present in all genomes) and accessory (absent in one or more genomes) genes delineated. Subsequently, a second pangenome delineating the prevalence of inherently essential genes was generated. The prevalence of genes conditionally essential for surviving tobacco exposure, abscess formation and epithelial invasion was also determined, in addition to genes encoding key proteolytic enzymes containing putative signal peptides. While the absolutely essential pangenome was highly conserved, significant differences in the complete and conditionally essential pangenomes were apparent. Thus, genetic plasticity appears to lie primarily in gene sets facilitating adaptation to variant disease-related environments. Those genes that are highly pervasive in the P. gingivalis absolutely essential pangenome or are highly prevalent and essential for fitness in disease-relevant models, may represent particularly attractive therapeutic targets worthy of further investigation. As mutations in absolutely essential genes are expected to be lethal, the data provided herein should also facilitate improved planning for P. gingivalis gene mutation strategies.\n\nDelineation of global, absolutely essential and conditionally essential pangenomes of Porphyromonas gingivalis.", "token_count": 344, "char_count": 1627, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:39.388238", "source": { "split": "train_shard_00000", "doc_id": 719 }, "chunk_id": "train_shard_00000_719_0", "global_id": 798 }, { "text": "The particle drifting effect, where nanosized colloidal drug particles overcome the diffusional resistance of the aqueous boundary layer adjacent to the intestinal wall and increase drug absorption rates, is drawing increasing attention in pharmaceutical research. However, mechanistic understanding and accurate prediction of the particle drifting effect remain lacking. In this study, we systematically evaluated the extent of the particle drifting effect affected by drug and colloidal properties, including the size, number, and type of the moving species using biphasic diffusion experiments combined with computational fluid dynamics simulations and mass transport analyses. The results showed that the particle drifting effect is a sequential reaction of particle dissolution/dissociation in the diffusional boundary layer, followed by absorption of the free drug. Therefore, factors affecting the rate-limiting step, which can be either process or both under different circumstances, alter the particle drifting effect. Experimental results also agree with the theory that the particle dissolution rate is dependent on particle size, concentration, and drug solubility. In addition, rapid bile micelle dissociation and bile salt absorption facilitated drug absorption by the particle drifting effect. Our findings explain the highly dynamic nature of the particle drifting effect and will contribute to rational formulation development and better bioavailability prediction for formulations containing colloidal particles.\n\nThe Particle Drifting Effect: A Combined Function of Colloidal and Drug Properties.", "token_count": 305, "char_count": 1615, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6055, "quality_score": 0.8028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:39.954903", "source": { "split": "train_shard_00000", "doc_id": 720 }, "chunk_id": "train_shard_00000_720_0", "global_id": 799 }, { "text": "Toxin-antitoxin (TA) systems are widespread in bacteria and implicated in genome stability, virulence, phage defense, and persistence. TA systems have diverse activities and cellular targets, but their physiological roles and regulatory mechanisms are often unclear. Here, we show that the NatR-NatT TA system, which is part of the core genome of the human pathogen Pseudomonas aeruginosa, generates drug-tolerant persisters by specifically depleting nicotinamide dinucleotides. While actively growing P. aeruginosa cells compensate for NatT-mediated NAD\n\nToxin-mediated depletion of NAD and NADP drives persister formation in a human pathogen.", "token_count": 170, "char_count": 644, "word_count": 87, "semantic_coherence": 1, "information_density": 0.8161, "quality_score": 0.908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:41.050915", "source": { "split": "train_shard_00000", "doc_id": 721 }, "chunk_id": "train_shard_00000_721_0", "global_id": 800 }, { "text": "The 10q11.22 chromosomal region is a duplication-rich interval of the human genome and one of the last to be fully assembled. It carries copy number-variable genes associated with intellectual disability, bipolar disorder, and obesity. In this study, we characterized the structural diversity at this locus by analyzing 64 haploid assemblies produced by the Human Pangenome Reference Consortium. We identified 11 alternative haplotypes that differ in the copy number and/or orientation of large genomic segments, ranging from hundreds of kilobase pairs (kbp) to over one megabase pair (Mbp). We uncovered a 2.4 Mbp size difference between the shortest and longest haplotypes. Breakpoint analysis revealed that genomic instability results from nonallelic homologous recombination between segmental duplication (SD) pairs with varying similarity (94.4%-99.6%). Nonetheless, these pairs generally recombine at positions where their identity is higher (>99.6%). Recurrent inversions occur with different breakpoints within the same inverted SD pair. Inversion polymorphisms shuffle the entire SD arrangement, creating new predispositions to copy-number variations. The SD architecture is associated with a catarrhine-specific subgroup of the", "token_count": 298, "char_count": 1237, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7456, "quality_score": 0.8728, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:41.608331", "source": { "split": "train_shard_00000", "doc_id": 722 }, "chunk_id": "train_shard_00000_722_0", "global_id": 801 }, { "text": "Gastrointestinal disorders originate in the gastrointestinal tract (GIT), and the therapies can benefit from direct access to the GIT achievable through the oral route. RNA molecules show great promise therapeutically but are highly susceptible to degradation and often require a carrier for cytoplasmic access. Lipid nanoparticles (LNPs) are clinically proven drug-delivery agents, primarily administered parenterally. An ideal Orally Delivered (OrD) LNP formulation should overcome the diverse GI environment, successfully delivering the drug to the site of action. A versatile OrD LNP formulation has been developed to encapsulate and deliver siRNA and mRNA in this paper. The formulations were prepared by the systematic addition of cationic lipid to the base LNP formulation, keeping the total of cationic lipid and ionizable lipid to 50 mol%. Biorelevant media stability depicted increased resistance to bile salt mediated destabilization upon the addition of the cationic lipid, however the in vitro efficacy data underscored the importance of the ionizable lipid. Based on this, OrD LNP was selected comprising of 20% cationic lipid and 30% ionizable lipid. Further investigation revealed the enhanced efficacy of OrD LNP in vitro after incubation in different dilutions of fasted gastric, fasted intestinal media, and mucin. Confocal imaging and flow cytometry confirmed uptake while in vivo studies demonstrated efficacy with siRNA and mRNA as payloads. Taken together, this research introduces OrD LNP to deliver nucleic acid locally to the GIT.\n\nOral delivery of stabilized lipid nanoparticles for nucleic acid therapeutics.", "token_count": 413, "char_count": 1636, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:42.243905", "source": { "split": "train_shard_00000", "doc_id": 723 }, "chunk_id": "train_shard_00000_723_0", "global_id": 802 }, { "text": "A novel amphiphilic guanidyl-functionalized stigmasterol hydrochloride (GFSH) was designed and synthesized as bile salt sequestrants for cholesterol reduction. GFSH exhibited a considerable in vitro capacity for bile salt binding in gastrointestinal digestion and alleviated hypercholesterolemia in vivo. GFSH spontaneously interacted with sodium cholate via synergistic electrostatic, hydrophobic, and hydrogen-bonding interactions. The effects of GFSH on serum cholesterol reduction in mice fed a high-fat-high-cholesterol diet were explored by measuring the expression of key transcription factors related to bile acid metabolism. GFSH produced a dose-dependent reduction in weight gain, hepatic fat accumulation, and fecal and blood markers. Real-time quantitative polymerase chain reaction (RT-qPCR) and western blot analyses demonstrated GFSH-induced expression of hepatic CYP7A, LXRα, and LDL-R. GFSH exerts the cholesterol-lowering activity by inducing the bile acid metabolism.\n\nNovel Guanidinium-Functionalized Stigmasterol for Bile Salt Binding and Serum Cholesterol Reduction: Synthesis, Interaction Mechanisms, and In Vivo Function.", "token_count": 317, "char_count": 1145, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6853, "quality_score": 0.8427, "entities": { "genes": [ "CYP7A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:42.807110", "source": { "split": "train_shard_00000", "doc_id": 724 }, "chunk_id": "train_shard_00000_724_0", "global_id": 803 }, { "text": "The aim of this study was to determine the impact of Kluyveromyces marxianus VM004 culture conditions on the cell wall (CW) structure and its influence on aflatoxin B\n\nImpact of Kluyveromyces marxianus VM004 culture conditions on the cell wall structure and its influence on aflatoxin B", "token_count": 78, "char_count": 286, "word_count": 46, "semantic_coherence": 1, "information_density": 0.5217, "quality_score": 0.7609, "entities": { "genes": [ "VM004" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:43.186253", "source": { "split": "train_shard_00000", "doc_id": 725 }, "chunk_id": "train_shard_00000_725_0", "global_id": 804 }, { "text": "Structural variation (SV) refers to insertions, deletions, inversions, and duplications in human genomes. SVs are present in approximately 1.5% of the human genome. Still, this small subset of genetic variation has been implicated in the pathogenesis of psoriasis, Crohn's disease and other autoimmune disorders, autism spectrum and other neurodevelopmental disorders, and schizophrenia. Since identifying structural variants is an important problem in genetics, several specialized computational techniques have been developed to detect structural variants directly from sequencing data. With advances in whole-genome sequencing (WGS) technologies, a plethora of SV detection methods have been developed. However, dissecting SVs from WGS data remains a challenge, with the majority of SV detection methods prone to a high false-positive rate, and no existing method able to precisely detect a full range of SVs present in a sample. Previous studies have shown that none of the existing SV callers can maintain high accuracy across various SV lengths and genomic coverages. Here, we report an integrated structural variant calling framework, Variant Identification and Structural Variant Analysis (VISTA), that leverages the results of individual callers using a novel and robust filtering and merging algorithm. In contrast to existing consensus-based tools which ignore the length and coverage, VISTA overcomes this limitation by executing various combinations of top-performing callers based on variant length and genomic coverage to generate SV events with high accuracy. We evaluated the performance of VISTA on comprehensive gold-standard datasets across varying organisms and coverage. We benchmarked VISTA using the Genome-in-a-Bottle gold standard SV set, haplotype-resolved de novo assemblies from the Human Pangenome Reference Consortium, along with an in-house polymerase chain reaction (PCR)-validated mouse gold standard set. VISTA maintained the highest F1 score among top consensus-based tools measured using a comprehensive gold standard across both mouse and human genomes. VISTA also has an optimized mode, where the calls can be optimized for precision or recall. VISTA-optimized can attain 100% precision and the highest sensitivity among other variant callers", "token_count": 495, "char_count": 2281, "word_count": 321, "semantic_coherence": 1, "information_density": 0.5981, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:43.838087", "source": { "split": "train_shard_00000", "doc_id": 726 }, "chunk_id": "train_shard_00000_726_0", "global_id": 805 }, { "text": "In conclusion, VISTA represents a significant advancement in structural variant calling, offering a robust and accurate framework that outperforms existing consensus-based tools and sets a new standard for SV detection in genomic research.\n\nVISTA: an integrated framework for structural variant discovery.", "token_count": 58, "char_count": 305, "word_count": 41, "semantic_coherence": 1, "information_density": 0.7805, "quality_score": 0.8902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:44.246680", "source": { "split": "train_shard_00000", "doc_id": 726 }, "chunk_id": "train_shard_00000_726_1", "global_id": 806 }, { "text": "Human Na+-taurocholate cotransporting polypeptide (hNTCP) is predominantly expressed in hepatocytes, maintaining bile salt homeostasis and serving as a receptor for hepatitis B virus (HBV). hNTCP expression is downregulated during hepatocellular carcinoma (HCC) development. In this study, we investigated the molecular mechanisms underlying hNTCP dysregulation using HCC tissues and cell lines, and primary human hepatocytes (PHHs). Firstly, we observed a significant reduction of hNTCP in HCC tumors compared to adjacent and normal tissues. Additionally, h\n\nThe loss of hepatitis B virus receptor NTCP/SLC10A1 in human liver cancer cells is due to epigenetic silencing.", "token_count": 178, "char_count": 671, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:44.709690", "source": { "split": "train_shard_00000", "doc_id": 727 }, "chunk_id": "train_shard_00000_727_0", "global_id": 807 }, { "text": "The global increase of multidrug-resistant organisms (MDROs) is one of the most urgent public health threats affecting both humans and animals. The One Health concept emphasizes the interconnectedness of human, animal and environmental health and highlights the need for integrated approaches to combat antimicrobial resistance (AMR). Although the sharing of environments and antimicrobial agents between companion animals and humans poses a risk for MDRO transmission, companion animals have been studied to a lesser extent than livestock animals. This study therefore used core genome multilocus sequence typing (cgMLST) to investigate the genetic relationships and putative transmission of MDROs between humans and pets.\n\nThe genetic relationship between human and pet isolates: a core genome multilocus sequence analysis of multidrug-resistant bacteria.", "token_count": 174, "char_count": 857, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:45.191566", "source": { "split": "train_shard_00000", "doc_id": 728 }, "chunk_id": "train_shard_00000_728_0", "global_id": 808 }, { "text": "This study isolated and characterized four indigenous lactic acid bacterial strains from naturally fermented green tender coconut water: Lactiplantibacillus plantarum CWJ3, Lacticaseibacillus casei CWM15, Lacticaseibacillus paracasei CWKu14, and Lacticaseibacillus rhamnosus CWKu-12. Notably, among the isolates, Lact. plantarum CWJ3 showed exceptional acid tolerance, with the highest survival rate of 37.34% at pH 2.0 after 1 h, indicating its higher resistance against acidic gastric conditions. However, all strains exhibited robust resistance to bile salts, phenols, and NaCl, with survival rates exceeding 80% at given concentrations. Their optimal growth at 37 °C and survival at 20 °C and 45 °C underscored adaptability to diverse environmental conditions. Additionally, all strains showed sustainable survival rates in artificial saliva and simulated gastrointestinal juices, with Lact. plantarum CWJ3 exhibiting significantly higher survival rate (70.66%) in simulated gastric juice compared to other strains. Adherence properties were particularly noteworthy, especially in Lact. rhamnosus CWKu-12, which demonstrated the highest hydrophobicity, coaggregation with pathogens and autoaggregation, among the strains. The production of exopolysaccharides, particularly by Lact. plantarum CWJ3, enhanced their potential for gut colonization and biofilm formation. Various in vitro antioxidative assays using spectrophotometric methods revealed the significant activity of Lact. plantarum CWJ3, while antimicrobial testing highlighted its efficacy against selected foodborne pathogens. Safety assessments confirmed the absence of biogenic amine production, hemolytic, DNase, and gelatinase activities, as well as the ability to hydrolase the bile salt. Furthermore, these non-dairy probiotics exhibited characteristics comparable to dairy derived probiotics, demonstrating their potential suitability in developing novel probiotic-rich foods and functional products.", "token_count": 517, "char_count": 1972, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8434, "entities": { "genes": [ "CWM15", "CWJ3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:05:45.862807", "source": { "split": "train_shard_00000", "doc_id": 729 }, "chunk_id": "train_shard_00000_729_0", "global_id": 809 }, { "text": "Evaluating the Probiotic Profile, Antioxidant Properties, and Safety of Indigenous Lactobacillus spp. Inhabiting Fermented Green Tender Coconut Water.", "token_count": 45, "char_count": 150, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:46.241120", "source": { "split": "train_shard_00000", "doc_id": 729 }, "chunk_id": "train_shard_00000_729_1", "global_id": 810 }, { "text": "Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. This presents a particular challenge for the identification of true gene frequencies within a microbial population, as core genes missing in only a few assemblies will be mischaracterized by current pangenome approaches.\n\nCELEBRIMBOR: core and accessory genes from metagenomes.", "token_count": 104, "char_count": 441, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8689, "quality_score": 0.9344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:46.623591", "source": { "split": "train_shard_00000", "doc_id": 730 }, "chunk_id": "train_shard_00000_730_0", "global_id": 811 }, { "text": "The bile salt export pump (BSEP) assay is widely used to evaluate the potential for drug-induced liver injury (DILI) early in the drug discovery process. While traditional liquid chromatography-mass spectrometry (LC-MS)-based approaches have been utilized for BSEP activity testing, they have intrinsic limitations in either throughput or the requirement for sample preparation and are difficult to scale up in order to screen drug candidates. Here we demonstrate the use of two different high-throughput MS methods based on solid-phase extraction (SPE) and desorption electrospray ionization (DESI) for high-throughput BSEP activity assessment in a label-free manner, with minimal needs for sample workup, at sampling rates of ∼11 and ∼5.5 s/sample, respectively. Both approaches were validated, compared, and successfully applied to the evaluation of 96 drug candidates for the inhibition of taurocholic acid (TCA) transport using BSEP vesicles.\n\nHigh-Throughput Assessment of Bile Salt Export Pump Inhibition Using RapidFire-MS and DESI-MS.", "token_count": 254, "char_count": 1043, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:47.116645", "source": { "split": "train_shard_00000", "doc_id": 731 }, "chunk_id": "train_shard_00000_731_0", "global_id": 812 }, { "text": "The main objective of this study was to assess cellulolytic probiotic strains from traditional fermented beverages such as palm wine in order to supplement the animal feed and strengthen the gut health of the animal for better digestibility and absorption. In the present study, different types of microbes were isolated from traditionally prepared palm wine and analyzed for their probiotic nature. For any microbe to be probiotic in nature, it has to sustain the harsh conditions of the human gastrointestinal tract such as acid tolerance, bile tolerance at the lower range of pH, and other properties like auto aggregation test, cell surface hydrophobicity test with non-polar hydrocarbons for evaluating its capabilities to adhere to the intestinal cells and antimicrobial nature against pathogens. Bacillus mycoides strain PR04 and Bacillus subtilis strain PR21 were found to be resistant to acid and bile in simulated artificial gastrointestinal tract model, found to be than 55% hydrophobic with xylene and n-hexadecane and also showed antimicrobial activity greater towards pathogenic strains like Pseudomonas aeruginosa, Staphylococcus aureus, Candida albicans, and Salmonella typhimurium respectively. The cellulolytic activity of the isolates PR04 and PR21 was evaluated in (0.2-2) % CMC (carboxymethyl cellulose) plate. Bacillus mycoides PR04 and Bacillus subtilis PR21 could degrade carboxymethyl cellulose, filter paper, and sugarcane bagasse. The degradation of sugarcane bagasse was confirmed by Scanning electron microscopy and filter paper degradation after 4 days of incubation at 37 °C. Cellulase gene of the identified Bacillus sp. strains was amplified by primers CF5'-ACAGGATCCGATGAAAACGGTCAATTTCTATTTT-3' and CR5'-ACTCTCGAGATTGGGTTCTGTTCCCAAT-3'. This study proposes potential probiotic Bacillus mycoides PR04 (Accession no", "token_count": 520, "char_count": 1847, "word_count": 258, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [ "PR04", "PR21", "CR5", "CF5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:05:47.769845", "source": { "split": "train_shard_00000", "doc_id": 732 }, "chunk_id": "train_shard_00000_732_0", "global_id": 813 }, { "text": "OR625070) and Bacillus subtilis PR21 (Accession no. OR625072) in the application as an animal feed additive to assist in its digestibility and encourage the gut health.\n\nCharacterization of probiotic strains of Bacillus sp. from fermented palm wine (Nypa fructicans sp.) and exploration of cellulolytic potential for use as an addition in animal feed.", "token_count": 103, "char_count": 351, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7925, "quality_score": 0.8962, "entities": { "genes": [ "OR625070", "PR21", "OR625072" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:48.148079", "source": { "split": "train_shard_00000", "doc_id": 732 }, "chunk_id": "train_shard_00000_732_1", "global_id": 814 }, { "text": "Powdered infant formula (PIF) is rich in nutrients that support the survival and growth of bacteria that trigger food safety disorders in deprived infants through life-threatening illnesses. The study aims to examine and identify the incidence of pathogenic bacteria of concern in PIF upon reconstitution in lukewarm water. A total of 172 samples consisting of 38 brands of PIF available in the Lagos metropolis were sampled, suspended in water (10 g in 100 mL), and bacteria strains were isolated using combinational enrichment and selective culture techniques. Pure bacterial strains were characterized and identified based on their physiology and 16S rRNA gene sequence homology. While 85 bacterial strains were isolated from the enriched culture system, 20 strains were selectively isolated based on tolerance to sodium deoxycholate. Approximately 13% of the selected bacteria were identified as Cronobacter spp., exhibiting virulence traits including extracellular protease production, coagulation and proteolysis of casein, haem-agglutination, and β-haemolysis of human blood. Approximately 82% of the Cronobacter strains tolerated NaCl (10%) and bile salt; and exhibited resistance to cefotaxime, ceftriaxone, gentamicin, and Amoxicillin-clavulanic acid antibiotics. The presence of Cronobacter spp. in 13% of the PIF brands available to infants calls for concern about the safety of deprived infants that might be fed with such PIF. Consequently, PIF safety alerts need to be activate while further studies on critical points at which the pathogens get introduced to the PIFs need to be identified.\n\nIsolation of Pathogenic Cronobacter Species as Bacteriological Risks Indicator in Powdered Infant Formula Available to Deprived Infants in Lagos Metropolis, Nigeria.", "token_count": 463, "char_count": 1773, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:48.795555", "source": { "split": "train_shard_00000", "doc_id": 733 }, "chunk_id": "train_shard_00000_733_0", "global_id": 815 }, { "text": "Individuals of Pacific ancestry suffer some of the highest rates of health disparities yet remain vastly underrepresented in genomic research, including currently available linear and pangenome references. To begin addressing this, we developed the first Pacific ancestry pangenome reference using 23 individuals with diverse Pacific ancestry. We assembled 46 haploid genomes from these 23 individuals, resulting in highly accurate and contiguous genome assemblies with an average quality value of 55.0 and an average N50 of 40.7 Mb, marking the first\n\nA Draft Pacific Ancestry Pangenome Reference.", "token_count": 141, "char_count": 598, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7326, "quality_score": 0.8663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:49.229227", "source": { "split": "train_shard_00000", "doc_id": 734 }, "chunk_id": "train_shard_00000_734_0", "global_id": 816 }, { "text": "Moso bamboo (Phyllostachys edulis), an ecologically and economically important forest species in East Asia, plays vital roles in carbon sequestration and climate change mitigation. However, intensifying climate change threatens moso bamboo survival. Here we generate high-quality haplotype-based pangenome assemblies for 16 representative moso bamboo accessions and integrated these assemblies with 427 previously resequenced accessions. Characterization of the haplotype-based pangenome reveals extensive genetic variation, predominantly between haplotypes rather than within accessions. Many genes with allele-specific expression patterns are implicated in climate responses. Integrating spatiotemporal climate data reveals more than 1050 variations associated with pivotal climate factors, including temperature and precipitation. Climate-associated variations enable the prediction of increased genetic risk across the northern and western regions of China under future emissions scenarios, underscoring the threats posed by rising temperatures. Our integrated haplotype-based pangenome elucidates moso bamboo's local climate adaptation mechanisms and provides critical genomic resources for addressing intensifying climate pressures on this essential bamboo. More broadly, this study demonstrates the power of long-read sequencing in dissecting adaptive traits in climate-sensitive species, advancing evolutionary knowledge to support conservation.\n\nHaplotype-based pangenomes reveal genetic variations and climate adaptations in moso bamboo populations.", "token_count": 326, "char_count": 1559, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7166, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:49.794522", "source": { "split": "train_shard_00000", "doc_id": 735 }, "chunk_id": "train_shard_00000_735_0", "global_id": 817 }, { "text": "The bile salt hydrolases (BSHs) are significant constituents of animal microbiomes. An evolving appreciation of their roles in health and disease has established them as targets of pharmacological inhibition. These bacterial enzymes belong to the N-terminal nucleophile superfamily and are best known to catalyze the deconjugation of glycine or taurine from bile salts to release bile acid substrates for transformation and or metabolism in the gastrointestinal tract. Here, we identify and describe the BSH from a common member of the Plains bison microbiome, Arthrobacter citreus (BSH\n\nStructural and functional analysis of a bile salt hydrolase from the bison microbiome.", "token_count": 170, "char_count": 674, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7172, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:50.238626", "source": { "split": "train_shard_00000", "doc_id": 736 }, "chunk_id": "train_shard_00000_736_0", "global_id": 818 }, { "text": "Terpene synthases (TPSs), key gatekeepers in the biosynthesis of herbivore-induced terpenes, are pivotal in the diversity of terpene chemotypes across and within plant species. Here, we constructed a gene-based pangenome of the\n\nPangenome Identification and Analysis of Terpene Synthase Gene Family Members in", "token_count": 87, "char_count": 309, "word_count": 43, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:50.613555", "source": { "split": "train_shard_00000", "doc_id": 737 }, "chunk_id": "train_shard_00000_737_0", "global_id": 819 }, { "text": "Thermophily is a trait scattered across the fungal tree of life, with its highest prevalence within three fungal families (Chaetomiaceae, Thermoascaceae, and Trichocomaceae), as well as some members of the phylum Mucoromycota. We examined 37 thermophilic and thermotolerant species and 42 mesophilic species for this study and identified thermophily as the ancestral state of all three prominent families of thermophilic fungi. Thermophilic fungal genomes were found to encode various thermostable enzymes, including carbohydrate-active enzymes such as endoxylanases, which are useful for many industrial applications. At the same time, the overall gene counts, especially in gene families responsible for microbial defense such as secondary metabolism, are reduced in thermophiles compared to mesophiles. We also found a reduction in the core genome size of thermophiles in both the Chaetomiaceae family and the Eurotiomycetes class. The Gene Ontology terms lost in thermophilic fungi include primary metabolism, transporters, UV response, and O-methyltransferases. Comparative genomics analysis also revealed higher GC content in the third base of codons (GC3) and a lower effective number of codons in fungal thermophiles than in both thermotolerant and mesophilic fungi. Furthermore, using the Support Vector Machine classifier, we identified several Pfam domains capable of discriminating between genomes of thermophiles and mesophiles with 94% accuracy. Using AlphaFold2 to predict protein structures of endoxylanases (GH10), we built a similarity network based on the structures. We found that the number of disulfide bonds appears important for protein structure, and the network clusters based on protein structures correlate with the optimal activity temperature. Thus, comparative genomics offers new insights into the biology, adaptation, and evolutionary history of thermophilic fungi while providing a parts list for bioengineering applications.\n\nComparative genomic analysis of thermophilic fungi reveals convergent evolutionary adaptations and gene losses.", "token_count": 478, "char_count": 2072, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8024, "entities": { "genes": [ "GH10", "GC3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:51.260958", "source": { "split": "train_shard_00000", "doc_id": 738 }, "chunk_id": "train_shard_00000_738_0", "global_id": 820 }, { "text": "Bile acid metabolism is partially regulated through the activity of the gut microbiota. Primary bile acids can be deconjugated and modified by bacteria expressing bile salt hydrolase and other enzymes, changing bile acid recycling by changing the interactions between enterocytes and hepatocytes. The modified bile acids can also activate signalling in cells regulating metabolism including colonic L-cells, skeletal muscle cells and brown adipocytes. In pregnancy, both bile acid metabolism and gut microbiota composition are altered. In women with intrahepatic cholestasis of pregnancy, the changes in bile acid metabolism are exacerbated and there is some evidence that the gut microbiota composition is also altered. Here we review the crosstalk between the liver and the gut especially in women with intrahepatic cholestasis of pregnancy, with a focus on the role of the gut microbiota in this crosstalk.\n\nMicrobial metabolites as a way to provide crosstalk between gut and liver.", "token_count": 244, "char_count": 985, "word_count": 147, "semantic_coherence": 1, "information_density": 0.5442, "quality_score": 0.7721, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:51.740489", "source": { "split": "train_shard_00000", "doc_id": 739 }, "chunk_id": "train_shard_00000_739_0", "global_id": 821 }, { "text": "The polysaccharides of edible mushrooms are excellent phytochemicals for adjuvant treatment of metabolic diseases, but the potential mechanisms of synergistic effects are unclear. In this work, we discovered that NAP-3 enhanced the efficiency of metformin in lipid and glucose metabolism in type 2 diabetic (T2D) mice in a gut microbiome-dependent way. NAP-3 remodeled the intestinal microbial, resulting in the decreased activity of bile salt hydrolases and upregulation of CYP27A1 and CYP7B1 functions in the alternative pathway of bile acid synthesis, which leads to accumulation of the conjugated bile acids in ileum, specifically TβMCA and TUDCA. The accumulated conjugated bile acids either blocked or stimulated the nuclear receptors Farnesoid-X-receptor and TGR5, inducing the release of GLP-1 and ultimately enhanced glucose metabolism in mice. Collectively, our research indicated that edible mushroom polysaccharide NAP-3 may serve as a promising adjunctive oral therapeutic agent for T2D.\n\nPolysaccharide NAP-3 Synergistically Enhances the Efficiency of Metformin in Type 2 Diabetes via Bile Acid/GLP-1 Axis through Gut Microbiota Remodeling.", "token_count": 327, "char_count": 1154, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:52.297574", "source": { "split": "train_shard_00000", "doc_id": 740 }, "chunk_id": "train_shard_00000_740_0", "global_id": 822 }, { "text": "Pangenomes reduce reference bias by representing genetic diversity better than a single reference sequence. Yet when comparing a sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for example, causing false read mappings. These irrelevant variants are generally rarer in terms of allele frequency, and have previously been dealt with by filtering rare variants. However, this blunt heuristic both fails to remove some irrelevant variants and removes many relevant variants. We propose a new approach that imputes a personalized pangenome subgraph by sampling local haplotypes according to k-mer counts in the reads. We implement the approach in the vg toolkit ( https://github.com/vgteam/vg ) for the Giraffe short-read aligner and compare its accuracy to state-of-the-art methods using human pangenome graphs from the Human Pangenome Reference Consortium. This reduces small variant genotyping errors by four times relative to the Genome Analysis Toolkit and makes short-read structural variant genotyping of known variants competitive with long-read variant discovery methods.\n\nPersonalized pangenome references.", "token_count": 260, "char_count": 1163, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6886, "quality_score": 0.8443, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:52.847040", "source": { "split": "train_shard_00000", "doc_id": 741 }, "chunk_id": "train_shard_00000_741_0", "global_id": 823 }, { "text": "Many factors contribute to the ability of a microbial species to persist when encountering complexly contaminated environments, including time of exposure, the nature and concentration of contaminants, availability of nutritional resources, and possession of a combination of appropriate molecular mechanisms needed for survival. Herein we sought to identify genes that are most important for survival of Gram-negative Enterobacteriaceae in contaminated groundwater environments containing high concentrations of nitrate and metals using the metal-tolerant Oak Ridge Reservation isolate, Pantoea sp. MT58 (MT58). Survival fitness experiments in which a randomly barcoded transposon insertion (RB-TnSeq) library of MT58 was exposed directly to contaminated Oak Ridge Reservation groundwater samples from across a nitrate and mixed metal contamination plume were used to identify genes important for survival with increasing exposure times and concentrations of contaminants, and availability of a carbon source. Genes involved in controlling and using carbon, encoding transcriptional regulators, and related to Gram-negative outer membrane processes were among those found to be important for survival in contaminated Oak Ridge Reservation groundwater. A comparative genomics analysis of 75 Pantoea genus strains allowed us to further separate the survival determinants into core and non-core genes in the Pantoea pangenome, revealing insights into the survival of subsurface microorganisms during contaminant plume intrusion.\n\nFitness factors impacting survival of a subsurface bacterium in contaminated groundwater.", "token_count": 338, "char_count": 1617, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6019, "quality_score": 0.8009, "entities": { "genes": [ "MT58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:53.416907", "source": { "split": "train_shard_00000", "doc_id": 742 }, "chunk_id": "train_shard_00000_742_0", "global_id": 824 }, { "text": "Increasing awareness regarding health promotion and disease prevention has driven inclusion of fermented foods and beverages in the daily diet. These are the enormous sources of beneficial microbes, probiotics. This study aims to isolate yeast strains having probiotic potential and effectivity against colitis. Initially, ninety-two yeast strains were isolated from Haria, an ethnic fermented beverage of West Bengal, India. Primary screening was done by their acid (pH 4) and bile salt (0.3%) tolerance ability. Four potent isolates were selected and found effective against Entamoeba histolytica, as this human pathogen is responsible to cause colitis. They were identified as Saccharomyces cerevisiae. They showed luxurious growth even at 37\n\nEvaluation of probiotic efficacy of indigenous yeast strain, Saccharomyces cerevisiae Y-89 isolated from a traditional fermented beverage of West Bengal, India having protective effect against DSS-induced colitis in experimental mice.", "token_count": 234, "char_count": 981, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7591, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:53.891825", "source": { "split": "train_shard_00000", "doc_id": 743 }, "chunk_id": "train_shard_00000_743_0", "global_id": 825 }, { "text": "Background Clonal complex 180 (CC180) is currently the major clone of serotype 3 Streptococcus pneumoniae (Spn). The 13-valent pneumococcal conjugate vaccine (PCV13) does not have significant efficacy against serotype 3 despite polysaccharide inclusion in the vaccine. It was hypothesized that PCV13 may effectively control Clade I of CC180 but that Clades III and IV are resistant, provoking a population shift that enables serotype 3 persistence. This has been observed in the United States, England, and Wales but not Spain. We tested this hypothesis further utilizing a dataset from Portugal. Methods We whole-genome sequenced (WGS) 501 serotype 3 strains from Portugal isolated from patients with pneumococcal infections between 1999-2020. The draft genomes underwent phylogenetic analyses, pangenome profiling, and a genome-wide association study (GWAS). We also completed antibiotic susceptibility testing and compiled over 2,600 serotype 3 multilocus sequence type 180 (MLST180) WGSs to perform global comparative genomics. Findings CC180 Clades I, II, III, IV, and VI distributions were similar when comparing non-invasive pneumonia isolates and invasive disease isolates (Fisher's exact test, P=0.29), and adult and pediatric cases (Fisher's exact test, P=0.074). The serotype 3 CCs shifted post-PCV13 (Fisher's exact test, P<0.0001) and Clade I became dominant. Clade I is largely antibiotic-sensitive and carries the phiOXC141 prophage but the pangenome is heterogenous. Strains from Portugal and Spain, where Clade I remains dominant post-PCV13, have larger pangenomes and are associated with the presence of two genes encoding hypothetical proteins. Interpretation Clade I became dominant in Portugal post-PCV13, despite the burden of the prophage and antibiotic sensitivity. The accessory genome content may mitigate these fitness costs", "token_count": 521, "char_count": 1851, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8352, "entities": { "genes": [ "MLST180", "PCV13", "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:05:54.548174", "source": { "split": "train_shard_00000", "doc_id": 744 }, "chunk_id": "train_shard_00000_744_0", "global_id": 826 }, { "text": "Regional differences in Clade I prevalence and pangenome heterogeneity suggest that clade dynamics is not a generalizable approach to understanding serotype 3 vaccine escape. Funding National Institute of Child Health and Human Development, Pfizer, and Merck Sharp & Dohme.\n\nCC180 clade dynamics do not universally explain Streptococcus pneumoniae serotype 3 persistence post-vaccine: a global comparative population genomics study.", "token_count": 103, "char_count": 432, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8448, "quality_score": 0.9224, "entities": { "genes": [ "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:54.925353", "source": { "split": "train_shard_00000", "doc_id": 744 }, "chunk_id": "train_shard_00000_744_1", "global_id": 827 }, { "text": "Much of the profound interspecific variation in genome content has been attributed to transposable elements (TEs). To explore the extent of TE variation within species, we developed an optimized open-source algorithm, panEDTA, to de novo annotate TEs in a pangenome context. We then generated a unified TE annotation for a maize pangenome derived from 26 reference-quality genomes, which reveals an excess of 35.1 Mb of TE sequences per genome in tropical maize relative to temperate maize. A small number (\n\nDifferences in activity and stability drive transposable element variation in tropical and temperate maize.", "token_count": 146, "char_count": 616, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7021, "quality_score": 0.8511, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:55.367732", "source": { "split": "train_shard_00000", "doc_id": 745 }, "chunk_id": "train_shard_00000_745_0", "global_id": 828 }, { "text": "The killer-cell immunoglobulin-like receptor (KIR) gene complex, a highly polymorphic region of the human genome that encodes proteins involved in immune responses, poses strong challenges in genotyping owing to its remarkable genetic diversity and structural intricacy. Accurate analysis of KIR alleles, including their structural variations, is crucial for understanding their roles in various immune responses. Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. In 47 HPRC-phased assemblies, SKIRT identifies a recurrent novel\n\nGenetic complexity of killer-cell immunoglobulin-like receptor genes in human pangenome assemblies.", "token_count": 206, "char_count": 830, "word_count": 108, "semantic_coherence": 1, "information_density": 0.713, "quality_score": 0.8565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:55.829729", "source": { "split": "train_shard_00000", "doc_id": 746 }, "chunk_id": "train_shard_00000_746_0", "global_id": 829 }, { "text": "Escherichia coli can colonise the urogenital tract of individuals without causing symptoms of infection, in a condition referred to as asymptomatic bacteriuria (ABU). ABU isolates can protect the host against symptomatic urinary tract infections (UTIs) by bacterial interference against uropathogenic E. coli (UPEC). The aim of this study was to investigate the genotypic and phenotypic characteristics of five ABU isolates from midstream urine samples of adults. Comparative genomic and phenotypic analysis was conducted including an antibiotic resistance profile, pangenome analysis, and a putative virulence profile. Based on the genome analysis, the isolates consisted of one from phylogroup A, three from phylogroup B2, and one from phylogroup D. Two of the isolates, PUTS 58 and SK-106-1, were noted for their lack of antibiotic resistance and virulence genes compared to the prototypic ABU strain E. coli 83,972. This study provides insights into the genotypic and phenotypic profiles of uncharacterised ABU isolates, and how relevant fitness and virulence traits can impact their potential suitability for therapeutic bacterial interference.\n\nGenotypic and phenotypic characterisation of asymptomatic bacteriuria (ABU) isolates displaying bacterial interference against multi-drug resistant uropathogenic E. Coli.", "token_count": 341, "char_count": 1321, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:56.432712", "source": { "split": "train_shard_00000", "doc_id": 747 }, "chunk_id": "train_shard_00000_747_0", "global_id": 830 }, { "text": "The underlying evolutionary mechanisms driving global expansions of pathogen strains are poorly understood. Vibrio parahaemolyticus is one of only two marine pathogens where variants have emerged in distinct climates globally. The success of a Vibrio parahaemolyticus clone (VpST3) in Latin America- the first spread identified outside its endemic region of tropical Asia- provided an invaluable opportunity to investigate mechanisms of VpST3 expansion into a distinct marine climate. A global collection of VpST3 isolates and novel Latin American isolates were used for evolutionary population genomics, pangenome analysis and combined with oceanic climate data. We found a VpST3 population (LatAm-VpST3) introduced in Latin America well before the emergence of this clone in India, previously considered the onset of the VpST3 epidemic. LatAm-VpST3 underwent successful adaptation to local conditions over its evolutionary divergence from Asian VpST3 isolates, to become dominant in Latin America. Selection signatures were found in genes providing resilience to the distinct marine climate. Core genome mutations and accessory gene presences that promoted survival over long dispersals or increased environmental fitness were associated with environmental conditions. These results provide novel insights into the global expansion of this successful V. parahaemolyticus clone into regions with different climate scenarios.\n\nEvolutionary dynamics of the successful expansion of pandemic Vibrio parahaemolyticus ST3 in Latin America.", "token_count": 326, "char_count": 1534, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [ "ST3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:57.017915", "source": { "split": "train_shard_00000", "doc_id": 748 }, "chunk_id": "train_shard_00000_748_0", "global_id": 831 }, { "text": "Identification of a toxic agent that—like a sniper—would be capable of targeting pathogenic bacteria and effectively discriminating between “good” and “evil” cells has long been the holy grail of drug discovery. The theory of magic bullet, first pioneered by Paul Ehrlich in the early 1900, has represented since then a “\n\nNext generation of \"magic bullets\", solutions from the microbial pangenome.", "token_count": 102, "char_count": 398, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8197, "quality_score": 0.9098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:57.420780", "source": { "split": "train_shard_00000", "doc_id": 749 }, "chunk_id": "train_shard_00000_749_0", "global_id": 832 }, { "text": "Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence. Whether closely related non-pathogenic species also exhibit strain heterogeneity remains unknown. Here, we comprehensively characterized the pathogenic potentials (i.e., the ability to cause morbidity and mortality) of 16 diverse strains of Aspergillus fischeri, a non-pathogenic close relative of the major pathogen Aspergillus fumigatus. In vitro immune response assays and in vivo virulence assays using a mouse model of pulmonary aspergillosis showed that A. fischeri strains varied widely in their pathogenic potential. Furthermore, pangenome analyses suggest that A. fischeri genomic and phenotypic diversity is even greater. Genomic, transcriptomic, and metabolic profiling identified several pathways and secondary metabolites associated with variation in virulence. Notably, strain virulence was associated with the simultaneous presence of the secondary metabolites hexadehydroastechrome and gliotoxin. We submit that examining the pathogenic potentials of non-pathogenic close relatives is key for understanding the origins of fungal pathogenicity.\n\nStrain heterogeneity in a non-pathogenic Aspergillus fungus highlights factors associated with virulence.", "token_count": 303, "char_count": 1257, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:58.026329", "source": { "split": "train_shard_00000", "doc_id": 750 }, "chunk_id": "train_shard_00000_750_0", "global_id": 833 }, { "text": "The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. \"Digital Microbes\" are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with > 100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.\n\nDigital Microbe: a genome-informed data integration framework for team science on emerging model organisms.", "token_count": 299, "char_count": 1357, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7582, "quality_score": 0.8791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:58.942625", "source": { "split": "train_shard_00000", "doc_id": 751 }, "chunk_id": "train_shard_00000_751_0", "global_id": 834 }, { "text": "Amiodarone is an antiarrhythmic drug which may be associated with thyroid dysfunction. Type I amiodarone-induced thyrotoxicosis (AIT) is treated with thionamides and type II AIT is treated with glucocorticoids. Combined therapy is used in mixed or indeterminate forms. When medical treatment is unsuccessful, radioiodine ablation or thyroidectomy is considered. This report reviews a case of AIT refractory to conventional treatment. Despite high doses of methimazole and prednisone, the patient remained clinically and biochemically thyrotoxic. Cholestyramine, a bile salt sequestrant, was used as an off-label adjunctive treatment resulting in significant improvement and achievement of euthyroidism that may also be in part due to the expected natural timeline of recovery from AIT after several months. The patient subsequently trended towards hypothyroidism with symptomatic weight gain and cold intolerance for which he was initiated on levothyroxine.\n\nRefractory amiodarone-induced thyrotoxicosis requiring adjunctive cholestyramine treatment.", "token_count": 261, "char_count": 1050, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7214, "quality_score": 0.8607, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:59.485628", "source": { "split": "train_shard_00000", "doc_id": 752 }, "chunk_id": "train_shard_00000_752_0", "global_id": 835 }, { "text": "Machine learning has the potential to be a powerful tool in the fight against antimicrobial resistance (AMR), a critical global health issue. Machine learning can identify resistance mechanisms from DNA sequence data without prior knowledge. The first step in building a machine learning model is a feature extraction from sequencing data. Traditional methods like single nucleotide polymorphism (SNP) calling and k-mer counting yield numerous, often redundant features, complicating prediction and analysis. In this paper, we propose PanKA, a method using the pangenome to extract a concise set of relevant features for predicting AMR. PanKA not only enables fast model training and prediction but also improves accuracy. Applied to the\n\nPanKA: Leveraging population pangenome to predict antibiotic resistance.", "token_count": 173, "char_count": 811, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7863, "quality_score": 0.8932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:05:59.945769", "source": { "split": "train_shard_00000", "doc_id": 753 }, "chunk_id": "train_shard_00000_753_0", "global_id": 836 }, { "text": "Sea buckthorn has lipid-lowering properties and is widely used in the development of functional foods. In this study, a probiotic (Lactobacillus plantarum, Lp10211) with cholesterol-lowering potential and acid and bile salt resistant was screened for the fermentation of sea buckthorn juice. Changes in the active ingredients, such as sugars and phenolics, before and after fermentation, as well as their in vitro lipid-lowering activities, were compared. The contents of reducing and total sugars decreased substantially after fermentation. Lp10211 primarily utilized fructose for growth and reproduction, with a utilization rate of 76.9%. The phenolic compound content of sea buckthorn juice increased by 37.06% after fermentation and protected the phenolic components from degradation (protocatechuic and p-coumaric acids) and produced new polyphenol (shikimic acid). Enhanced inhibition of pancreatic lipase activity (95.42%) and cholesterol micellar solubility (59.15%) was evident. The antioxidant properties of the fermentation broth were improved. Notably, Lp10211 preserved the color and reversed browning in sea buckthorn juice. The collective findings indicate that fermentation of sea buckthorn juice by Lp10211 may enhance the functional components and lipid-lowering activity of sea buckthorn, which may provide a new approach for the development of lipid-lowering foods.\n\nEffects of cholesterol-lowering probiotic fermentation on the active components and in vitro hypolipidemic activity of sea buckthorn juice.", "token_count": 408, "char_count": 1526, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:00.561841", "source": { "split": "train_shard_00000", "doc_id": 754 }, "chunk_id": "train_shard_00000_754_0", "global_id": 837 }, { "text": "Lacticaseibacillus (formerly Lactobacillus) rhamnosus is widely used in probiotics or food supplements to promote microbiome health and may also be part of the normal microbiota of the human gastrointestinal tract. However, it rarely also causes invasive or severe infections in patients. It has been postulated that these infections may originate from probiotics or from endogenous commensal reservoirs. In this report, we examine the population structure of Lacticaseibacillus rhamnosus and investigate the utility of using bacterial genomics to identify the source of invasive Lacticaseibacillus infections.\n\nThe global population stru cture of Lacticaseibacillus rhamnosus and its application to an investigation of a rare case of infective endocarditis.", "token_count": 188, "char_count": 758, "word_count": 105, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:01.013475", "source": { "split": "train_shard_00000", "doc_id": 755 }, "chunk_id": "train_shard_00000_755_0", "global_id": 838 }, { "text": "High-pressure processing (HPP) of donor human milk (DM) minimally impacts the concentration and bioactivity of some important bioactive proteins including lactoferrin, and bile salt-stimulated lipase (BSSL) compared to Holder pasteurization (HoP), yet the impact of HPP and subsequent digestion on the full array of proteins detectable by proteomics remains unclear. We investigated how HPP impacts undigested proteins in DM post-processing and across digestion by proteomic analysis. Each pool of milk (n = 3) remained raw, or was treated by HPP (500 MPa, 10 min) or HoP (62.5 °C, 30 min), and underwent dynamic in vitro digestion simulating the preterm infant. In the meal, major proteins were minimally changed post-processing. HPP-treated milk proteins better resisted proximal digestion (except for immunoglobulins, jejunum 180 min) and the extent of undigested proteins after gastric digestion of major proteins in HPP-treated milk was more similar to raw (e.g., BSSL, lactoferrin, macrophage-receptor-1, CD14, complement-c3/c4, xanthine dehydrogenase) than HoP.\n\nComparative proteomic analysis of donor human milk treated by high-pressure processing or Holder pasteurization on undigested proteins across dynamic simulated preterm infant digestion.", "token_count": 358, "char_count": 1255, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8171, "entities": { "genes": [ "CD14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:01.588821", "source": { "split": "train_shard_00000", "doc_id": 756 }, "chunk_id": "train_shard_00000_756_0", "global_id": 839 }, { "text": "Bile acids (BAs) play a crucial role in the human body's defense against infections caused by bacteria, fungi, and viruses. BAs counteract infections not only through interactions with intestinal bacteria exhibiting bile salt hydrolase (BSH) activity but they also directly combat infections. Building upon our research group's previous discoveries highlighting the role of BAs in combating infections, we have initiated an in-depth investigation into the interactions between BAs and intestinal microbiota. Leveraging the existing literature, we offer a comprehensive analysis of the relationships between BAs and 16 key microbiota. This investigation encompasses bacteria (e.g.,\n\nInterplay between Bile Acids and Intestinal Microbiota: Regulatory Mechanisms and Therapeutic Potential for Infections.", "token_count": 184, "char_count": 801, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7315, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:02.045660", "source": { "split": "train_shard_00000", "doc_id": 757 }, "chunk_id": "train_shard_00000_757_0", "global_id": 840 }, { "text": "Tauroursodeoxycholic acid (TUDCA) is a synthetic bile salt that has demonstrated efficacy in the management of hepatobiliary disorders. However, its specific mechanism of action in preventing and treating nonalcoholic fatty liver disease (NAFLD) remains incompletely understood. This research revealed that TUDCA treatment can reduce obesity and hepatic lipid buildup, enhance intestinal barrier function and microbial balance, and increase the presence of Allobaculum and Bifidobacterium in NAFLD mouse models. TUDCA can influence the activity of farnesoid X receptor (FXR) and cholesterol 7α-hydroxylase (CYP7A1), resulting in higher hepatic bile acid levels and increased expression of sodium taurocholate cotransporting polypeptide (NTCP), leading to elevated concentrations of liver-bound bile acids in mice. Furthermore, TUDCA can inhibit the expression of FXR and fatty acid transport protein 5 (FATP5), thereby reducing fatty acid absorption and hepatic lipid accumulation. This investigation provides new insights into the potential of TUDCA for preventing and treating NAFLD.\n\nTauroursodeoxycholic Acid Improves Nonalcoholic Fatty Liver Disease by Regulating Gut Microbiota and Bile Acid Metabolism.", "token_count": 316, "char_count": 1209, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6728, "quality_score": 0.8364, "entities": { "genes": [ "FATP5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:02.598118", "source": { "split": "train_shard_00000", "doc_id": 758 }, "chunk_id": "train_shard_00000_758_0", "global_id": 841 }, { "text": "The development of sequencing technology has promoted discovery of variants in the human genome. Identifying functions of these variants is important for us to link genotype to phenotype, and to diagnose diseases. However, it usually requires researchers to visit multiple databases. Here, we presented a one-stop webserver for variant function annotation tools (VCAT, https://biomed.nscc-gz.cn/zhaolab/VCAT/ ) that is the first one connecting variant to functions via the epigenome, protein, drug and RNA. VCAT is also the first one to make all annotations visualized in interactive charts or molecular structures. VCAT allows users to upload data in VCF format, and download results via a URL. Moreover, VCAT has annotated a huge number (1,262,041,068) of variants collected from dbSNP, 1000 Genomes projects, gnomAD, ICGC, TCGA, and HPRC Pangenome project. For these variants, users are able to searcher their functions, related diseases and drugs from VCAT. In summary, VCAT provides a one-stop webserver to explore the potential functions of human genomic variants including their relationship with diseases and drugs.\n\nVCAT: an integrated variant function annotation tools.", "token_count": 293, "char_count": 1179, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:03.163304", "source": { "split": "train_shard_00000", "doc_id": 759 }, "chunk_id": "train_shard_00000_759_0", "global_id": 842 }, { "text": "There is an urgent need to improve wheat for upcoming challenges, including biotic and abiotic stresses. Sustainable wheat improvement requires the introduction of new genes and alleles in high-yielding wheat cultivars. Using new approaches, tools, and technologies to identify and introduce new genes in wheat cultivars is critical. High-quality genomes, transcriptomes, and pangenomes provide essential resources and tools to examine wheat closely to identify and manipulate new and targeted genes and alleles. Wheat genomics has improved excellently in the past 5 years, generating multiple genomes, pangenomes, and transcriptomes. Leveraging these resources allows us to accelerate our crop improvement pipelines. This review summarizes the progress made in wheat genomics and trait discovery in the past 5 years.\n\nWheat genomics: genomes, pangenomes, and beyond.", "token_count": 186, "char_count": 867, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:03.607511", "source": { "split": "train_shard_00000", "doc_id": 760 }, "chunk_id": "train_shard_00000_760_0", "global_id": 843 }, { "text": "The objective of this study was to determine prevalence and perform genomic analysis of Salmonella spp. and Campylobacter spp. isolated from different stages of an integrated NAE broiler complex. Environmental samples were screened with 3M-Molecular Detection System (MDS) and MDS positive samples were further processed for confirmation of results and identification. Core genome-based phylogenies were built for both bacteria isolated from this study along with selected NCBI genomes. The odds ratios and 95% confidence limits were compared among stages and sample types (α < 0.05) using multivariable model. Based on MDS results, 4% and 18% of total samples were positive for Salmonella spp. and Campylobacter spp. respectively. The odds of Salmonella detection in hatchery samples were 2.58 times as likely as compared to its detection in production farms' samples (P = 0.151) while the odds of Campylobacter detection in production farms' samples were 32.19 times as likely as its detection in hatchery (P = 0.0015). Similarly, the odds of Campylobacter detection in boot swabs, soil, water, and miscellaneous samples were statistically significant (P < 0.05) as compared with fly paper as reference group. The serovars identified for Salmonella were Typhimurium, Barranquilla, Liverpool, Kentucky, Enteritidis, Luciana, and Rough_O:r:1,5. For Campylobacter, the species identified were Campylobacter jejuni and Campylobacter coli. Phylogeny results show close genetic relatedness among bacterial strains isolated from different locations within the same stage and between different stages. The results show possibility of multiple entry points of such bacteria entering broiler complex and can potentially contaminate the final raw product in the processing plant. It suggests the need for a comprehensive control strategy with strict biosecurity measures and best management practices to minimize or eliminate such pathogens from the poultry food chain.\n\nAssessment and genomic analysis of Salmonella and Campylobacter from different stages of an integrated no-antibiotics-ever (NAE) broiler complex: a longitudinal study.", "token_count": 509, "char_count": 2129, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5526, "quality_score": 0.7763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:04.240504", "source": { "split": "train_shard_00000", "doc_id": 761 }, "chunk_id": "train_shard_00000_761_0", "global_id": 844 }, { "text": "Gut microbiome and plasma lipidome analysis reveals a specific impact of", "token_count": 16, "char_count": 72, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:04.605506", "source": { "split": "train_shard_00000", "doc_id": 762 }, "chunk_id": "train_shard_00000_762_0", "global_id": 845 }, { "text": "The archaeal isolate J.3.6.1-F.2.7.3T was obtained from an anaerobic enrichment culture, where it may play an important role in methane production during pyrite formation. The new isolate formed a species-level clade with Methanospirillum hungatei strains GP1 and SK, which is separate from the type strain JF-1T. Cultivation-independent surveys indicate the occurrence of this phylogenetic group in sediments and anaerobic digesters. The abundance of this clade appears to be negatively affected by high nitrogen loads, indicating a sensitivity to certain nitrogen compounds that is not known in M. hungatei JF-1T. The relatively large core genome of this Methanospirillum clade is indicative of niche specialization and efficient control of horizontal gene transfer. Genes for nitrogenase and F420-dependent secondary alcohol dehydrogenase contribute to the metabolic versatility of this lineage. Characteristics of the new isolate such as the ability to utilize 2-propanol as an electron donor or the requirement for acetate as a carbon source are found also in the strains GP1 and SK, but not in the type strain M. hungatei JF-1T. Based on the genomic differences to related species, a new species within the genus Methanospirillum is proposed with the name M. purgamenti sp. nov. The determined phenotypic characteristics support this proposal and indicate a metabolic adaptation to a separate ecological niche.\n\nDescription and genome analysis of a novel archaeon isolated from a syntrophic pyrite-forming enrichment culture and reclassification of Methanospirillum hungatei strains GP1 and SK as Methanospirillum purgamenti sp. nov.", "token_count": 427, "char_count": 1639, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5858, "quality_score": 0.7929, "entities": { "genes": [ "GP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:05.228739", "source": { "split": "train_shard_00000", "doc_id": 763 }, "chunk_id": "train_shard_00000_763_0", "global_id": 846 }, { "text": "Corynebacterium pseudotuberculosis (CPS) is an important bacterial animal pathogen. CPS causes chronic, debilitating and currently incurable infectious diseases affecting a wide range of livestock and wild herbivores including camelids worldwide. Belonging to the Corynebacterium diphtheriae complex, this pathogen can also infect humans. The classical characterization of CPS is typically based on the testing of nitrate reductase activity, separating the two biovars Equi and Ovis. However, more refined resolutions are required to unravel routes of infection. This was realized in our study by generating and analyzing whole genome sequencing (WGS) data. Using newly created core genome multilocus sequence typing (cgMLST) profiles we were the first to discover isolates grouping in a cluster adjacent to clusters formed by CPS biovar Equi isolates. This novel cluster includes CPS isolates from alpacas, llamas, camels and dromedaries, which are characterized by a lack of nitrate reductase activity as encountered in biovar Ovis. This is of special interest for molecular epidemiology. Nevertheless, these isolates bear the genes of the nitrate locus, which are characteristic of biovar Equi isolates. However, sequence analysis of the genes narG and narH of the nitrate locus revealed indels leading to frameshifts and inactivity of the enzymes involved in nitrate reduction. Interestingly, one CPS isolate originating from another lama with an insertion in the MFS transporter (narT) is adjacent to a cluster formed by ovine CPS isolates biovar Equi. Based on this knowledge, the combination of biochemical and PCR based molecular biological nitrate reductase detection can be used for a fast and uncomplicated classification of isolates in routine diagnostics in order to check the origin of camelid CPS isolates. Further analysis revealed that partial sequencing of the ABC transporter substrate binding protein (CP258_RS07935) is a powerful tool to assign the biovars and the novel genomovar.\n\nCorynebacterium pseudotuberculosis: Whole genome sequencing reveals unforeseen and relevant genetic diversity in this pathogen.", "token_count": 512, "char_count": 2131, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:05.879379", "source": { "split": "train_shard_00000", "doc_id": 764 }, "chunk_id": "train_shard_00000_764_0", "global_id": 847 }, { "text": "Wild Malus species flourished in North America long before Europeans introduced domesticated apples. Malus coronaria and M. ioensis are native to the mid-western and eastern United States, while M. angustifolia and M. fusca grow in the southeast and west, respectively. They offer disease resistance, climate and soil adaptability, and horticultural traits for apple breeding. However, their utilization remains limited due to insufficient genomic resources and specific genetics. We report high-quality phased chromosome-scale assemblies of M. coronaria and M. ioensis, generated using long-read and conformation capture sequencing. Phylogenetic and synteny analysis indicated high relatedness between these 2 genomes and previously published genome of M. angustifolia, and lower relatedness with M. fusca. Gene family-based pangenome of North American Malus identified 60,211 orthogroups containing 340,087 genes. Genes involved in basic cellular and metabolic processes, growth, and development were core to the existence of these species, whereas genes involved in secondary metabolism, stress response, and interactions with other organisms were accessory and are likely associated with adaptation to specific environments. Structural variation hotspots were mostly overlapping with high gene density. This study offers novel native North American Malus genome resources that can be used to identify genes for apple breeding and understand their evolution and adaptation.\n\nAdvancing apple genetics research: Malus coronaria and Malus ioensis genomes and a gene family-based pangenome of native North American apples.", "token_count": 356, "char_count": 1621, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:06.458928", "source": { "split": "train_shard_00000", "doc_id": 765 }, "chunk_id": "train_shard_00000_765_0", "global_id": 848 }, { "text": "Characterizing probiotic features of organisms isolated from diverse environments can lead to the discovery of novel strains with promising functional features and health attributes. The present study attempts to characterize a novel probiotic strain isolated from the gut of the tribal population of Odisha, India. Based on 16S rRNA-based phylogeny, the strain was identified as a species of the Lactiplantibacillus genus and was named Lactiplantibacillus plantarum strain ILSF15. The current investigation focuses on elucidating this strain's genetic and physiological properties associated with probiotic attributes such as biosafety risk, host adaptation/survival traits, and beneficial functional features. The novel strain was observed, in vitro, exhibiting features such as acid/bile tolerance, adhesion to the host enteric epithelial cells, cholesterol assimilation, and pathogen exclusion, indicating its ability to survive the harsh environment of the human GIT and resist the growth of harmful microorganisms. Additionally, the L. plantarum ILSF15 strain was found to harbor genes associated with the metabolism and synthesis of various bioactive molecules, including amino acids, carbohydrates, lipids, and vitamins, highlighting the organism's ability to efficiently utilize diverse resources and contribute to the host's nutrition and health. Several genes involved in host adaptation/survival strategies and host-microbe interactions were also identified from the ILSF15 genome. Moreover, L. plantarum strains, in general, were found to have an open pangenome characterized by high genetic diversity and the absence of specific lineages associated with particular habitats, signifying its versatile nature and potential applications in probiotic and functional food industries.\n\nComprehensive physiological and genomic characterization of a potential probiotic strain, Lactiplantibacillus plantarum ILSF15, isolated from the gut of tribes of Odisha, India.", "token_count": 451, "char_count": 1971, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5871, "quality_score": 0.7936, "entities": { "genes": [ "ILSF15" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:07.096008", "source": { "split": "train_shard_00000", "doc_id": 766 }, "chunk_id": "train_shard_00000_766_0", "global_id": 849 }, { "text": "Lipases are used in many food, energy, and pharmaceutical processes. Thus, new systems have been sought to synthesize alternative lipases with potential biotechnological applications. Kluyveromyces marxianus is a yeast with recognized lipase activity; at least ten putative lipases/esterases in its genome have been detected, and two of them possess a signal peptide for extracellular secretion. The study of extracellular lipases becomes more relevant since they usually have higher activity rates than intracellular lipases and simpler purification mechanisms. For these reasons, this study aimed to characterize the production and lipase activity of the putative extracellular lipases of the K. marxianus L-2029 strain, encoded in the genes LIP3 and YJR107W. Both genes were heterologously expressed in Saccharomyces cerevisiae BY4742 (yeast strain without extracellular lipase activity) using a pYES2.1/V5-His-TOPO® plasmid. Herein, we show evidence that the strain transformed with the LIP3 gene did not show lipase activity during flask galactose induction. On the other hand, the strain transformed with the YJR107W gene showed a specific activity of 0.397 U/mg, with an optimum temperature of 37 °C and pH 6. For maximum cell production, glucose and yeast extract concentrations were evaluated by a 2\n\nLipase activity of recombinant KmYJR107Wp and KmLIP3p enzymes expressed in Saccharomyces cerevisiae BY4742 from Kluyveromyces marxianus L2029.", "token_count": 402, "char_count": 1452, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8237, "entities": { "genes": [ "LIP3", "YJR107W", "BY4742" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:07.713108", "source": { "split": "train_shard_00000", "doc_id": 767 }, "chunk_id": "train_shard_00000_767_0", "global_id": 850 }, { "text": "There is a critical gap in knowledge about how Gram-negative bacterial pathogens, using survival strategies developed for other niches, cause lethal bacteremia. Facultative anaerobic species of the Enterobacterales order are the most common cause of Gram-negative bacteremia, including Escherichia coli, Klebsiella pneumoniae, Serratia marcescens, Citrobacter freundii, and Enterobacter hormaechei. Bacteremia often leads to sepsis, a life-threatening organ dysfunction resulting from unregulated immune responses to infection. Despite a lack of specialization for this host environment, Gram-negative pathogens cause nearly half of bacteremia cases annually. Based on our existing Tn-Seq fitness factor data from a murine model of bacteremia combined with comparative genomics of the five Enterobacterales species above, we prioritized 18 conserved fitness genes or operons for further characterization. Mutants were constructed for all genes in all five species. Each mutant was used to cochallenge C57BL/6 mice via tail vein injection along with each respective wild-type strain to determine competitive indices for each fitness gene. Five fitness factor genes, when mutated, attenuated mutants in four or five species in the spleen and liver (tatC, ruvA, gmhB, wzxE, arcA). Five additional fitness factor genes or operons were validated as outcompeted by wild-type in three, four, or five bacterial species in the spleen (xerC, prc, apaGH, atpG, aroC). Overall, 17 of 18 fitness factor mutants were attenuated in at least one species in the spleen or liver. Together, these findings allow for the development of a model of bacteremia pathogenesis that may include future targets of therapy against bloodstream infections.\n\nFitness factor genes conserved within the multi-species core genome of Gram-negative Enterobacterales species contribute to bacteremia pathogenesis.", "token_count": 464, "char_count": 1875, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:08.384556", "source": { "split": "train_shard_00000", "doc_id": 768 }, "chunk_id": "train_shard_00000_768_0", "global_id": 851 }, { "text": "Regional analgesia based on the local anesthetic ropivacaine plays a crucial role in postoperative pain management and recovery; however, the short duration of analgesia limits its clinical potential. Various drug delivery systems such as microparticles and lipid carriers have been used to prolong the analgesic effect, yet most of them are prone to abrupt release from the site of administration or have poor analgesic effects of less than 48 h, which fail to meet the needs of postoperative analgesia. In this study, a low-molecular-weight gelator sodium deoxycholate-based hydrogel loaded with ropivacaine (DC-ROP gel) was designed for long-acting analgesia. The noncovalent interaction between ropivacaine and sodium deoxycholate helps to improve the stability and sustained release performance of the gel. This internal drug-binding hydrogel also avoids experiencing the burst release effect commonly seen in polymer hydrogels previously reported for the slow release of local anesthetics. DC-ROP gel exhibited the dual advantages of self-healing after compression and long-term controlled release. In mice with inflammatory pain, DC-ROP gel achieved peripheral nerve block for more than 1 week after a single injection. Histological and blood biochemical analyses confirmed that the DC-ROP gel did not produce systemic toxicity, and cytotoxicity experiments demonstrated that the DC-ROP gel resulted in low irritation. These results suggest that DC-ROP gel provides a promising strategy for local anesthetics in long-term postoperative pain management, broadening the potential of bile salt-based low-molecular-weight hydrogels for drug delivery.\n\nSelf-Healing Hydrogel Resulting from the Noncovalent Interaction between Ropivacaine and Low-Molecular-Weight Gelator Sodium Deoxycholate Achieves Stable and Endurable Local Analgesia in Vivo.", "token_count": 437, "char_count": 1847, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6353, "quality_score": 0.8176, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:09.036363", "source": { "split": "train_shard_00000", "doc_id": 769 }, "chunk_id": "train_shard_00000_769_0", "global_id": 852 }, { "text": "Prokaryotic genomes constantly undergo gene flux via lateral gene transfer, generating a pangenome structure consisting of a conserved core genome surrounded by a more variable accessory genome shell. Over time, flux generates change in genome content. Here, we measure and compare the rate of genome flux for 5655 prokaryotic genomes as a function of amino acid sequence divergence in 36 universally distributed proteins of the informational core (IC). We find a clock of gene content change. The long-term average rate of gene content flux is remarkably constant across all higher prokaryotic taxa sampled, whereby the size of the accessory genome-the proportion of the genome harboring gene content difference for genome pairs-varies across taxa. The proportion of species-level accessory genes per genome, varies from 0% (Chlamydia) to 30%-33% (Alphaproteobacteria, Gammaproteobacteria, and Clostridia). A clock-like rate of gene content change across all prokaryotic taxa sampled suggest that pangenome structure is a general feature of prokaryotic genomes and that it has been in existence since the divergence of bacteria and archaea.\n\nA universal and constant rate of gene content change traces pangenome flux to LUCA.", "token_count": 302, "char_count": 1226, "word_count": 182, "semantic_coherence": 1, "information_density": 0.5604, "quality_score": 0.7802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:09.623809", "source": { "split": "train_shard_00000", "doc_id": 770 }, "chunk_id": "train_shard_00000_770_0", "global_id": 853 }, { "text": "Recently, there has been an increasing interest in researching fermented food-derived yeasts as probiotics because they offer a natural and diverse source of potential strains with unique functional properties and health benefits. In this study, 13 yeast strains isolated from Zaopocu (ZPC), a traditional fermented dregs vinegar on Hainan Island, China, were evaluated for their probiotic characteristics in vitro. Yeast identification was conducted through 5.8S-ITS region sequencing, revealing Kodamaea ohmeri as the predominantly isolated species (ZPC_Y3, Y5, Y6, Y11), followed by Pichia kudriavzevii (ZPC_Y2, Y13, Y14), Rhodotorula mucilaginosa (ZPC_Y9, Y10), Pichia fermentans (ZPC_Y8, Y12), Pichia kluyveri (ZPC_Y4), and Pichia occidentalis (ZPC_Y1). Except for ZPC_Y4, ZPC_Y8, and ZPC_Y12, all isolated yeasts exhibited stable growth at 37 °C. The survival rates of all test strains exceeded 60% under challenging conditions at pH = 2 and 0.3% bile salt, along with strong antioxidant activity (> 5 6%), notable autoaggregation (> 70%), and varying levels of cell hydrophobicity with xylene (ranging from 35.32 ± 8.57% to 89.73 ± 4.84%). In addition, all isolates showed resistance to multiple antibiotics, along with antagonistic activity, and were deemed safe as none exhibited hemolytic, gelatinase, or DNase activities. Significantly, two P. kudriavzevii strains (ZPC_Y2, Y14) exhibited the production of catalase, lipase, and β-galactosidase, along with the capacity to synthesize gamma-aminobutyric acid (GABA)", "token_count": 511, "char_count": 1525, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7664, "quality_score": 0.8832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:10.316283", "source": { "split": "train_shard_00000", "doc_id": 771 }, "chunk_id": "train_shard_00000_771_0", "global_id": 854 }, { "text": "In summary, this preliminary study represents the first attempt to identify and characterize potential probiotic yeast strains isolated from Zaopocu, providing a theoretical basis for exploring their application in developing novel therapeutic probiotics.\n\nIn Vitro Characterization and Identification of Potential Probiotic Yeasts Isolated from Zaopocu, a Traditional Fermented Dregs Vinegar from Hainan Island.", "token_count": 93, "char_count": 412, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8113, "quality_score": 0.9057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:10.692422", "source": { "split": "train_shard_00000", "doc_id": 771 }, "chunk_id": "train_shard_00000_771_1", "global_id": 855 }, { "text": "Traditional cocoa bean fermentation is a spontaneous process and can result in heterogeneous sensory quality. For this reason, yeast-integrated starter cultures may be an option for creating consistent organoleptic profiles. This study proposes the mixture of Hanseniaspora opuntiae and Kluyveromyces marxianus (from non-cocoa fermentation) as starter culture candidates. The microorganisms and volatile compounds were analyzed during the cocoa fermentation process, and the most abundant were correlated with predominant microorganisms. Results showed that Kluyveromyces marxianus, isolated from mezcal fermentation, was identified as the dominant yeast by high-throughput DNA sequencing. A total of 63 volatile compounds identified by HS-SPME-GC-MS were correlated with the more abundant bacteria and yeast using Principal Component Analysis and Agglomerative Hierarchical Clustering. This study demonstrates that yeasts from other fermentative processes can be used as starter cultures in cocoa fermentation and lead to the formation of more aromatic esters, decrease the acetic acid content.\n\nExploring volatile compounds and microbial dynamics: Kluyveromyces marxianus and Hanseniaspora opuntiae reduce Forastero cocoa fermentation time.", "token_count": 305, "char_count": 1242, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:11.272452", "source": { "split": "train_shard_00000", "doc_id": 772 }, "chunk_id": "train_shard_00000_772_0", "global_id": 856 }, { "text": "Nanopore sequencing has shown the potential to democratize genomic pathogen surveillance due to its ease of use and low entry cost. However, recent genotyping studies showed discrepant results compared to gold-standard short-read sequencing. Furthermore, although essential for widespread application, the reproducibility of nanopore-only genotyping remains largely unresolved. In our multicenter performance study involving five laboratories, four public health-relevant bacterial species were sequenced with the latest R10.4.1 flow cells and V14 chemistry. Core genome MLST analysis of over 500 data sets revealed highly strain-specific typing errors in all species in each laboratory. Investigation of the methylation-related errors revealed consistent DNA motifs at error-prone sites across participants at read level. Depending on the frequency of incorrect target reads, this either leads to correct or incorrect typing, whereby only minimal frequency deviations can randomly determine the final result. PCR preamplification, recent basecalling model updates and an optimized polishing strategy notably diminished the non-reproducible typing. Our study highlights the potential for new errors to appear with each newly sequenced strain and lays the foundation for computational approaches to reduce such typing errors. In conclusion, our multicenter study shows the necessity for a new validation concept for nanopore sequencing-based, standardized bacterial typing, where single nucleotide accuracy is critical.\n\nA multicenter study on accuracy and reproducibility of nanopore sequencing-based genotyping of bacterial pathogens.", "token_count": 350, "char_count": 1635, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:11.849057", "source": { "split": "train_shard_00000", "doc_id": 773 }, "chunk_id": "train_shard_00000_773_0", "global_id": 857 }, { "text": "Different yeast strains benefit postweaning piglets by promoting intestinal health. The objective of this study was to investigate the effect of a yeast mixture containing Kluyveromyces marxianus fragilis, Pichia guilliermondii, and Saccharomyces cerevisiae (Vetoquinol italia s.r.l., Italy) on gut health parameters and growth performance traits of weaned piglets. Forty-eight postweaning castrated male piglets (27 ± 1.7 days, 7.19 ± 0.54 kg) were randomly allocated to two homogeneous experimental groups and involved in a 28-day trial. Both the groups received a basal diet with (yeast mixture, YM) or without (control, CTR) the inclusion of 0.8% yeast mixture during weeks 1 and 2, and 0.6% during weeks 3 and 4. Individual BW and box feed intake were determined on days 0, 14, and 28, and average daily gain and Gain:Feed ratio were subsequently calculated for each administration period (0-14, 14-28). Individual faecal samples were collected for microbiota analysis on days 4, 14, 21, and 28, and faecal score was evaluated on the same days. At the end of the trial, 12 piglets for each group were sacrificed, and ileal tissue was sampled for morphological analysis and the evaluation of mucins profile, using Alcian-Blue/Periodic Acid-Shiff (PAS) staining. On ileum samples, dividing and differentiated epithelial cells were also identified using proliferating cell nuclear antigen and alkaline phosphatase expression, respectively. Differences in the means between the experimental groups were determined by ANOVA, while the metataxonomics analyses were performed by sequencing for V3 and V4 hypervariable regions of the 16S rRNA gene. Growth performance traits were not different among the two experimental groups when considering the whole trial period, while treated animals showed increased faecal consistency on weeks 1 and 4 (P = 0.036 and 0.021, respectively)", "token_count": 513, "char_count": 1876, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6655, "quality_score": 0.8327, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:06:12.507313", "source": { "split": "train_shard_00000", "doc_id": 774 }, "chunk_id": "train_shard_00000_774_0", "global_id": 858 }, { "text": "Yeast mixture administration increased the abundance of Bifidobacterium (P = 0.006) and Coprococcus 2 (P = 0.015), and decreased Clostridium Sensu Stricto 1 (P = 0.019) at all the considered timepoints. Ileum villous height, villous width, and crypt depth were significantly increased by yeast mixture supplementation (P = 0.019; P = 0.013; P = 0.036, respectively), while no differences were observed for the villous:crypt ratio among the groups. The mucin profile showed no differences among experimental groups for acid and neutral glycoconjugates. However, a higher presence of PAS-positive mucins was highlighted in the villi of YM piglets (P < 0.001) compared to CTR. Overall, the administration of a yeast mixture to postweaning piglets showed positive effects on gut health when compared to piglets not receiving the tested product, improving beneficial genera and intestinal morphology.\n\nYeast mixture supplementation modulates faecal microbiota and ileum morphology of weaning pigs.", "token_count": 283, "char_count": 992, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6644, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:13.055281", "source": { "split": "train_shard_00000", "doc_id": 774 }, "chunk_id": "train_shard_00000_774_1", "global_id": 859 }, { "text": "Nanocrystals exhibit significant advantages in improving the oral bioavailability of poorly soluble drugs. However, the complicated absorption properties of nanocrystals and the differences in physiological characteristics between children and adults limit pediatric applications of nanocrystals. To elucidate the absorption differences and the underlying mechanisms between children and adults, the pharmacokinetics and tissue distribution of aprepitant crystals with different particle sizes (NC200, NC500, and MC2.5) in rats and mice at different ages were studied, and their absorption mechanisms were investigated in Caco-2 cells, mice, and rats. It was found that childhood animals demonstrated higher bioavailability compared with adolescent and adult animals, which was related to higher bile salt concentration and accelerated drug dissolution in the intestine of childhood animals. The majority of nanocrystals were dissolved and formed micelles under the influence of bile salts. Compared with intact nanocrystals, the bile salt micelle-associated aprepitant was absorbed through the chylomicron pathway, wherein Apo B assisted in the reassembling of the aprepitant micelles after endocytosis. Higher bile salt concentration and Apo B expression in the intestines of childhood animals are both responsible for the higher chylomicron transport pathways. Elucidation of the chylomicron pathway in the varied absorption of nanocrystals among children, adolescents, and adults provides strong theoretical guidance for promoting the rational and safe use of nanocrystals in pediatric populations.\n\nImpact of Physiological Characteristics on Chylomicron Pathway-Mediated Absorption of Nanocrystals in the Pediatric Population.", "token_count": 397, "char_count": 1731, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5522, "quality_score": 0.7761, "entities": { "genes": [ "NC200", "MC2", "NC500" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:13.669793", "source": { "split": "train_shard_00000", "doc_id": 775 }, "chunk_id": "train_shard_00000_775_0", "global_id": 860 }, { "text": "Solirubrobacter, though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified a pangenome consisting of 19,645 protein families, of which 2644 are shared across all studied genomes, forming the core genome. Interestingly, despite the non-motility of reported isolates, we discovered genes for flagellin and a partial flagellum assembly pathway. Examining the 16S ribosomal RNA genes of Solirubrobacter revealed substantial diversity, with 3166 operational taxonomic units identified in Mexican soils. Co-occurrence network analysis further demonstrated its significant integration within bacterial communities. Through phylogenomic scrutiny, we conclusively excluded the NCBI's GCA_009993245.1 genome from being classified as a Solirubrobacter. Our research into the metagenomic diversity of Solirubrobacter across various environments confirmed its presence in rhizospheres and certain soils, underscoring its adaptability. The geographical ubiquity of Solirubrobacter in rhizospheres raises intriguing questions regarding its potential interactions with plant hosts and the biotic and abiotic factors influencing its presence in soil. Given its ecological significance and genetic diversity, Solirubrobacter warrants further investigation as a potentially crucial yet underappreciated keystone species.\n\nUnravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter.", "token_count": 389, "char_count": 1664, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:14.294336", "source": { "split": "train_shard_00000", "doc_id": 776 }, "chunk_id": "train_shard_00000_776_0", "global_id": 861 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) is a rare childhood manifested disease associated with impaired bile secretion with severe pruritus yellow stool, and sometimes hepatosplenomegaly. PFIC is caused by mutations in ATP8B1, ABCB11, ABCB4, TJP2, NR1H4, SLC51A, USP53, KIF12, ZFYVE19, and MYO5B genes depending on its type. ABCB11 mutations lead to PFIC2 that encodes the bile salt export pump (BSEP). Different mutations of ABCB11 have been reported in different population groups but no data available in Pakistani population being a consanguineous one. We sequenced coding exons of the ABCB11 gene along with its flanking regions in 66 unrelated Pakistani children along with parents with PFIC2 phenotype. We identified 20 variations of ABCB11: 12 in homozygous form, one compound heterozygous, and seven heterozygous. These variants include 11 missenses, two frameshifts, two nonsense mutations, and five splicing variants. Seven variants are novel candidate variants and are not detected in any of the 120 chromosomes from normal ethnically matched individuals. Insilico analysis revealed that four homozygous missense variations have high pathogenic scores. Minigene analysis of splicing variants showed exon skipping and the addition of exon. This data is a useful addition to the disease variants genomic database and would be used in the future to build a diagnostic algorithm.\n\nThe spectrum of novel ABCB11 gene variations in children with progressive familial intrahepatic cholestasis type 2 in Pakistani cohorts.", "token_count": 428, "char_count": 1538, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [ "ABCB4", "USP53", "SLC51A", "PFIC2", "ABCB11", "MYO5B", "TJP2", "ZFYVE19", "KIF12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:14.923986", "source": { "split": "train_shard_00000", "doc_id": 777 }, "chunk_id": "train_shard_00000_777_0", "global_id": 862 }, { "text": "The bacterial pathogen Staphylococcus aureus employs a thick cell wall for protection against physical and chemical insults. This wall requires continuous maintenance to ensure strength and barrier integrity, but also to permit bacterial growth and division. The main cell wall component is peptidoglycan. Accordingly, the bacteria produce so-called peptidoglycan hydrolases (PGHs) that cleave glycan strands to facilitate growth, cell wall remodelling, separation of divided cells and release of exported proteins into the extracellular milieu. A special class of PGHs contains so-called 'cysteine, histidine-dependent amidohydrolase/peptidase' (CHAP) domains. In the present study, we profiled the roles of 11 CHAP PGHs encoded by the core genome of S. aureus USA300 LAC. Mutant strains lacking individual CHAP PGHs were analysed for growth, cell morphology, autolysis, and invasion and replication inside human lung epithelial cells. The results show that several investigated CHAP PGHs contribute to different extents to extracellular and intracellular growth and replication of S. aureus, septation of dividing cells, daughter cell separation once the division process is completed, autolysis and biofilm formation. In particular, the CHAP PGHs Sle1 and SAUSA300_2253 control intracellular staphylococcal replication and the resistance to β-lactam antibiotics like oxacillin. This makes the S. aureus PGHs in general, and the Sle1 and SAUSA300_2253 proteins in particular, attractive targets for future prophylactic or therapeutic anti-staphylococcal interventions. Alternatively, these cell surface-exposed enzymes, or particular domains of these enzymes, could be applied in innovative anti-staphylococcal therapies.\n\nFunctional profiling of CHAP domain-containing peptidoglycan hydrolases of Staphylococcus aureus USA300 uncovers potential targets for anti-staphylococcal therapies.", "token_count": 508, "char_count": 1890, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8092, "entities": { "genes": [ "USA300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:15.580226", "source": { "split": "train_shard_00000", "doc_id": 778 }, "chunk_id": "train_shard_00000_778_0", "global_id": 863 }, { "text": "The family Borreliaceae contains arthropod-borne spirochetes that cause two widespread human diseases, Lyme disease and relapsing fever. Lyme disease is a subacute, progressive illness with variable stage and tissue manifestations. Relapsing fever is an acute febrile illness with prominent bacteremia that may recur and disseminate, particularly to the nervous system. Clinical heterogeneity is a hallmark of both diseases. While human clinical manifestations are influenced by a wide variety of factors, including immune status and host genetic susceptibility, there is evidence that Borreliaceae microbial factors influence the clinical manifestations of human disease caused by this family of spirochetes. Despite these associations, the spirochete genes that influence the severity and manifestations of human disease are, for the most part, unknown. Recent work has identified lineage-specific expansions of lipoproteome-rich accessory genome elements in virulent clones of Borrelia burgdorferi. Using publicly available genome assemblies, it is shown that all Borreliaceae lineages for which sufficient sequence data are available harbor a similar pattern of strongly structured, lineage-specific expansions in their accessory genomes, particularly among lipoproteins, and that this pattern holds across phylogenetic scales including genera, species, and genotypes. The relationships among pangenome elements suggest that infrequent episodes of marked genomic change followed by clonal expansion in geographically and enzootically structured populations may account for the unique lineage structure of Borreliaceae. This analysis informs future genotype-phenotype studies among Borreliaceae and lays a foundation for studies of individual gene function guided by phylogenetic patterns of conservation, diversification, gain, and/or loss.\n\nAnalysis of the Borreliaceae Pangenome Reveals a Distinct Genomic Architecture Conserved Across Phylogenetic Scales.", "token_count": 427, "char_count": 1962, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:16.208097", "source": { "split": "train_shard_00000", "doc_id": 779 }, "chunk_id": "train_shard_00000_779_0", "global_id": 864 }, { "text": "Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonization, disease, antimicrobial resistance and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using the previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30 976 genomes and contextual data for carriage and disease pneumococci recovered between 1916 and 2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.\n\nDevelopment of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure.", "token_count": 357, "char_count": 1509, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:16.786795", "source": { "split": "train_shard_00000", "doc_id": 780 }, "chunk_id": "train_shard_00000_780_0", "global_id": 865 }, { "text": "Studies of bacterial adaptation and evolution are hampered by the difficulty of measuring traits such as virulence, drug resistance, and transmissibility in large populations. In contrast, it is now feasible to obtain high-quality complete assemblies of many bacterial genomes thanks to scalable high-accuracy long-read sequencing technologies. To exploit this opportunity, we introduce a phenotype- and alignment-free method for discovering coselected and epistatically interacting genomic variation from genome assemblies covering both core and accessory parts of genomes. Our approach uses a compact colored de Bruijn graph to approximate the intragenome distances between pairs of loci for a collection of bacterial genomes to account for the impacts of linkage disequilibrium (LD). We demonstrate the versatility of our approach to efficiently identify associations between loci linked with drug resistance and adaptation to the hospital niche in the major human bacterial pathogens\n\nPangenome-spanning epistasis and coselection analysis via de Bruijn graphs.", "token_count": 223, "char_count": 1064, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7007, "quality_score": 0.8503, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:17.257933", "source": { "split": "train_shard_00000", "doc_id": 781 }, "chunk_id": "train_shard_00000_781_0", "global_id": 866 }, { "text": "Eukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and there has been progress in structural studies on recombinant subassemblies. However, there is limited structural information on native kinetochore architecture. To address this, we purified functional, native kinetochores from the thermophilic yeast Kluyveromyces marxianus and examined them by electron microscopy (EM), cryoelectron tomography (cryo-ET), and atomic force microscopy (AFM). The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder, Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies and provides the foundation to study the global architecture and functions of kinetochores at a structural level.\n\nArchitecture of native kinetochores revealed by structural studies utilizing a thermophilic yeast.", "token_count": 294, "char_count": 1254, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:17.820081", "source": { "split": "train_shard_00000", "doc_id": 782 }, "chunk_id": "train_shard_00000_782_0", "global_id": 867 }, { "text": "Development and implementation of a core genome multilocus sequence typing scheme for", "token_count": 15, "char_count": 85, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:18.171244", "source": { "split": "train_shard_00000", "doc_id": 783 }, "chunk_id": "train_shard_00000_783_0", "global_id": 868 }, { "text": "Antibiotics cause collateral damage to resident microbes that is associated with various health risks. To date, studies have largely focused on the impacts of antibiotics on large intestinal and fecal microbiota. Here, we employ a gastrointestinal (GI) tract-wide integrated multiomic approach to show that amoxicillin (AMX) treatment reduces bacterial abundance, bile salt hydrolase activity, and unconjugated bile acids in the small intestine (SI). Losses of fatty acids (FAs) and increases in acylcarnitines in the large intestine (LI) correspond with spatially distinct expansions of Proteobacteria. Parasutterella excrementihominis engage in FA biosynthesis in the SI, while multiple Klebsiella species employ FA oxidation during expansion in the LI. We subsequently demonstrate that restoration of unconjugated bile acids can mitigate losses of commensals in the LI while also inhibiting the expansion of Proteobacteria during AMX treatment. These results suggest that the depletion of bile acids and lipids may contribute to AMX-induced dysbiosis in the lower GI tract.\n\nSpatial analysis of murine microbiota and bile acid metabolism during amoxicillin treatment.", "token_count": 295, "char_count": 1170, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:18.729913", "source": { "split": "train_shard_00000", "doc_id": 784 }, "chunk_id": "train_shard_00000_784_0", "global_id": 869 }, { "text": "Ocean oil pollution has a large impact on the environment and the health of living organisms. Bioremediation cleaning strategies are promising eco-friendly alternatives for tackling this problem. Previously, we designed and reported a hydrocarbon (HC) degrading microbial consortium of four marine strains belonging to the species Alloalcanivorax xenomutans, Halopseudomonas aestusnigri, Paenarthrobacter sp., and Pseudomonas aeruginosa. However, the knowledge about the metabolic potential of this bacterial consortium for HC bioremediation is not yet well understood. Here, we analyzed the complete genomes of these marine bacterial strains accompanied by a phylogenetic reconstruction along with 138 bacterial strains. Synteny between complete genomes of the same species or genus, revealed high conservation among strains of the same species, covering over 91% of their genomic sequences. Functional predictions highlighted a high abundance of genes related to HC degradation, which may result in functional redundancy within the consortium; however, unique and complete gene clusters linked to aromatic degradation were found in the four genomes, suggesting substrate specialization. Pangenome gain and loss analysis of genes involved in HC degradation provided insights into the evolutionary history of these capabilities, shedding light on the acquisition and loss of relevant genes related to alkane and aromatic degradation. Our work, including comparative genomic analyses, identification of secondary metabolites, and prediction of HC-degrading genes, enhances our understanding of the functional diversity and ecological roles of these marine bacteria in crude oil-contaminated marine environments and contributes to the applied knowledge of bioremediation.\n\nA comparative genomic study of a hydrocarbon-degrading marine bacterial consortium.", "token_count": 415, "char_count": 1854, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:19.348778", "source": { "split": "train_shard_00000", "doc_id": 785 }, "chunk_id": "train_shard_00000_785_0", "global_id": 870 }, { "text": "The international disclosure of Chinese human genetic data continues to be a contentious issue in China, generating public debates in both traditional and social media channels. Concerns have intensified after Chinese scientists' research on pangenome data was published in the prestigious journal Nature.\n\nPublic perceptions of international genetic information sharing for biomedical research in China: a case study of the social media debate on the article \"A Pangenome Reference of 36 Chinese Populations\" published in Nature.", "token_count": 104, "char_count": 530, "word_count": 76, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:19.731606", "source": { "split": "train_shard_00000", "doc_id": 786 }, "chunk_id": "train_shard_00000_786_0", "global_id": 871 }, { "text": "The study aimed to isolate and characterize lactic acid bacteria from various traditional fermented fish products from North East India, including Xindol, Hentak, and Ngari, which hold significant dietary importance for the indigenous tribes. Additionally, the study sought to examine their untargeted metabolomic profiles. A total of 43 strains of Bacillus, Priestia, Staphylococcus, Pediococcus, and Lactiplantibacillus were isolated, characterized by 16 S rRNA gene and tested for probiotic properties. Five strains passed pH and bile salt tests with strain dependent antimicrobial activity, which exhibited moderate autoaggregation and hydrophobicity properties. Lactiplantibacillus plantarum MKTJ24 exhibited the highest hydrophobicity (42 %), which was further confirmed by adhesion assay in HT-29 cell lines (100 %). Lactiplantibacillus plantarum MKTJ24 treatment in LPS-stimulated HT-29 cells up-regulated expression of mucin genes compared to LPS-treated cells. Treatment of RAW 264.7 cells with Lactiplantibacillus plantarum MKTJ24 decreased LPS-induced reactive oxygen species (ROS) and nitric oxide (NO) productions. Further, genome analysis of Lactiplantibacillus plantarum MKTJ24 revealed the presence of several probiotic markers and immunomodulatory genes. The genome was found to harbor plantaricin operon involved in bacteriocin production. A pangenome analysis using all the publicly available L. plantarum genomes specifically isolated from fermented fish products identified 120 unique genes in Lactiplantibacillus plantarum MKTJ24. Metabolomic analysis indicated dominance of ascorbic acids, pentafluropropionate, cyclopropaneacetic acid, florobenzylamine, and furanone in Xindol", "token_count": 484, "char_count": 1701, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6959, "quality_score": 0.8479, "entities": { "genes": [ "MKTJ24" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:20.409848", "source": { "split": "train_shard_00000", "doc_id": 787 }, "chunk_id": "train_shard_00000_787_0", "global_id": 872 }, { "text": "This study suggests that Lactiplantibacillus plantarum MKTJ24 has potential probiotic and immunomodulatory properties that could be used in processing traditional fermented fish products on an industrial scale to improve their quality and enhance functional properties.\n\nProbiotic and anti-inflammatory properties of Lactiplantibacillus plantarum MKTJ24 isolated from an artisanal fermented fish of North-east India.", "token_count": 106, "char_count": 416, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [ "MKTJ24" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:20.806314", "source": { "split": "train_shard_00000", "doc_id": 787 }, "chunk_id": "train_shard_00000_787_1", "global_id": 873 }, { "text": "Pangenome inference is an indispensable step in bacterial genomics, yet its scalability poses a challenge due to the rapid growth of genomic collections. This paper presents PanTA, a software package designed for constructing pangenomes of large bacterial datasets, showing unprecedented efficiency levels multiple times higher than existing tools. PanTA introduces a novel mechanism to construct the pangenome progressively without rebuilding the accumulated collection from scratch. The progressive mode is shown to consume orders of magnitude less computational resources than existing solutions in managing growing datasets. The software is open source and is publicly available at https://github.com/amromics/panta and at 10.6084/m9.figshare.23724705 .\n\nEfficient inference of large prokaryotic pangenomes with PanTA.", "token_count": 186, "char_count": 822, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7685, "quality_score": 0.8843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:21.269568", "source": { "split": "train_shard_00000", "doc_id": 788 }, "chunk_id": "train_shard_00000_788_0", "global_id": 874 }, { "text": "Clostridium septicum infections are highly predictive of certain malignancies in human patients. To initiate infections, C. septicum spores must first germinate and regain vegetative growth. Yet, what triggers the germination of C. septicum spores is still unknown. Here, we observe that C. septicum germinates in response to specific bile salts. Putative bile salt recognition genes are identified in C. septicum based on their similarity in sequence and organization to bile salt-responsive csp genes in Clostridioides difficile. Inactivating two of these csp orthologs (cspC-82 and cspC-1718) results in mutant spores that no longer germinate in the presence of their respective cognate bile salts. Additionally, inactivating the putative cspBA or sleC genes in C. septicum abrogates the germination response to all bile salt germinants, suggesting that both act at a convergent point downstream of cspC-82 and cspC-1718. Molecular dynamics simulations show that both CspC-82 and CspC-1718 bear a strong structural congruence with C. difficile's CspC. The existence of functional bile salt germination sensors in C. septicum may be relevant to the association between infection and malignancy.\n\nClostridium septicum manifests a bile salt germinant response mediated by Clostridioides difficile csp gene orthologs.", "token_count": 356, "char_count": 1316, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:21.884380", "source": { "split": "train_shard_00000", "doc_id": 789 }, "chunk_id": "train_shard_00000_789_0", "global_id": 875 }, { "text": "Previously, we demonstrated that caloric restriction (CR) stimulates the synthesis, conjugation, secretion, and deconjugation of taurine and bile acids in the intestine, as well as their reuptake. Given taurine's potent antiobesogenic properties, this study aimed to assess whether the CR-induced shift in taurine homeostasis contributes to adipose tissue loss. To verify that, male C57Bl/6 mice were subjected to 20% CR or ad libitum feeding, with variations in cage bedding and gut microbiota conditions. Additional groups received taurine supplementation or were fed a low-taurine diet (LTD). The results showed that in CR animals, taurine derived from the intestine was preferentially trafficked to epididymal white adipose tissue (eWAT) over other tested organs. Besides increased levels of taurine transporter TauT, gene expression of Cysteine dioxygenase (Cdo) involved in taurine synthesis was upregulated in CR eWAT. Taurine concentration in adipocytes was inversely correlated with fat pad weight of CR mice. Different types of cage bedding did not impact eWAT taurine levels; however, the lack of bedding and consumption of a diet high in soluble fiber did. Depleting gut microbiota with antibiotics or inhibiting bile salt hydrolase (BSH) activity reduced WAT taurine concentration in CR mice. Taurine supplementation increased taurine levels in WAT and brown adipose tissue (BAT), promoting fat loss in CR animals. LTD consumption blunted WAT loss in CR animals, with negligible impact on BAT. This study provides multiple insights into taurine's role in CR-triggered fat loss and describes a novel communication path between the liver, gut, microbiota, and WAT, with taurine acting as a messenger.\n\nGut microbiota, dietary taurine, and fiber shift taurine homeostasis in adipose tissue of calorie-restricted mice to impact fat loss.", "token_count": 487, "char_count": 1846, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5956, "quality_score": 0.7978, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:22.534557", "source": { "split": "train_shard_00000", "doc_id": 790 }, "chunk_id": "train_shard_00000_790_0", "global_id": 876 }, { "text": "This study presents the empirical findings of an in-depth genomic analysis of Enterococcus faecalis and Enterococcus lactis isolates from South Africa. It offers valuable insights into their genetic characteristics and their significant implications for public health. The study uncovers nuanced variations in the gene content of these isolates, despite their similar GC contents, providing a comprehensive view of the evolutionary diversity within the species. Genomic islands are identified, particularly in E. faecalis, emphasizing its propensity for horizontal gene transfer and genetic diversity, especially in terms of antibiotic resistance genes. Pangenome analysis reveals the existence of a core genome, accounting for a modest proportion of the total genes, with 2157 core genes, 1164 shell genes, and 4638 cloud genes out of 7959 genes in 52 South African E. faecalis genomes (2 from this study, 49 south Africa genomes downloaded from NCBI, and E. faecalis reference genome). Detecting large-scale genomic rearrangements, including chromosomal inversions, underscores the dynamic nature of bacterial genomes and their role in generating genetic diversity. The study uncovers an array of antibiotic resistance genes, with trimethoprim, tetracycline, glycopeptide, and multidrug resistance genes prevalent, raising concerns about the effectiveness of antibiotic treatment. Virulence gene profiling unveils a diverse repertoire of factors contributing to pathogenicity, encompassing adhesion, biofilm formation, stress resistance, and tissue damage. These empirical findings provide indispensable insights into these bacteria's genomic dynamics, antibiotic resistance mechanisms, and virulence potential, underlining the pressing need to address antibiotic resistance and implement robust control measures.\n\nGenomic diversity, antibiotic resistance, and virulence in South African Enterococcus faecalis and Enterococcus lactis isolates.", "token_count": 440, "char_count": 1945, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:23.161936", "source": { "split": "train_shard_00000", "doc_id": 791 }, "chunk_id": "train_shard_00000_791_0", "global_id": 877 }, { "text": "An imbalance between energy intake and energy expenditure predisposes obesity and its related metabolic diseases. Soluble dietary fiber has been shown to improve metabolic homeostasis mainly via microbiota reshaping. However, the application and metabolic effects of insoluble fiber are less understood. Herein, we employed nanotechnology to design citric acid-crosslinked carboxymethyl cellulose nanofibers (CL-CNF) with a robust capacity of expansion upon swelling. Supplementation with CL-CNF reduced food intake and delayed digestion rate in mice by occupying stomach. Besides, CL-CNF treatment mitigated diet-induced obesity and insulin resistance in mice with enhanced energy expenditure, as well as ameliorated inflammation in adipose tissue, intestine and liver and reduced hepatic steatosis, without any discernible signs of toxicity. Additionally, CL-CNF supplementation resulted in enrichment of probiotics such as Bifidobacterium and decreased in the relative abundances of deleterious microbiota expressing bile salt hydrolase, which led to increased levels of conjugated bile acids and inhibited intestinal FXR signaling to stimulate the release of GLP-1. Taken together, our findings demonstrate that CL-CNF administration protects mice from diet-induced obesity and metabolic dysfunction by reducing food intake, enhancing energy expenditure and remodeling gut microbiota, making it a potential therapeutic strategy against metabolic diseases.\n\nAn insoluble cellulose nanofiber with robust expansion capacity protects against obesity.", "token_count": 383, "char_count": 1550, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6847, "quality_score": 0.8424, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:23.737996", "source": { "split": "train_shard_00000", "doc_id": 792 }, "chunk_id": "train_shard_00000_792_0", "global_id": 878 }, { "text": "New high-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, the characteristics of LCLs pose technical challenges to profiling immunoglobulin (IG) genes. IG loci in LCLs contain a mixture of germline and somatically recombined haplotypes, making them difficult to genotype or assemble accurately. To address these challenges, we introduce IGLoo, a software tool that implements novel methods for analyzing sequence data and genome assemblies derived from LCLs. IGLoo characterizes somatic V(D)J recombination events in the sequence data and identifies the breakpoints and missing IG genes in the LCL-based assemblies. Furthermore, IGLoo implements a novel reassembly framework to improve germline assembly quality by integrating information about somatic events and population structural variantions in the IG loci. We applied IGLoo to study the assemblies from the Human Pangenome Reference Consortium, providing new insights into the mechanisms, gene usage, and patterns of V(D)J recombination, causes of assembly fragmentation in the IG heavy chain (IGH) locus, and improved representation of the IGH assemblies.\n\nIGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads.", "token_count": 328, "char_count": 1342, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:24.303703", "source": { "split": "train_shard_00000", "doc_id": 793 }, "chunk_id": "train_shard_00000_793_0", "global_id": 879 }, { "text": "Microbial aggregation mainly occurs on the intestinal epithelium, mucosal layer and undigested food particles in the gastrointestinal tract (GIT). Undigested food particles are usually insoluble dietary fiber (IDF), which can be easily obtained through daily diet, but there are few studies investigating whether the gut bacteria adhering to undigested food particles can form multi-species biofilms. In this study, we prepared mono- and multi-species biofilms using 18 core gut bacteria\n\nConstruction and characterization of stable multi-species biofilms formed by nine core gut bacteria on wheat fiber.", "token_count": 148, "char_count": 604, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7412, "quality_score": 0.8706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:24.742766", "source": { "split": "train_shard_00000", "doc_id": 794 }, "chunk_id": "train_shard_00000_794_0", "global_id": 880 }, { "text": "Shigella spp. are highly pathogenic members of the Enterobacteriaceae family, causing ∼269 million cases of bacillary dysentery and >200,000 deaths each year. Like many Gram-negative pathogens, Shigella rely on their type three secretion system (T3SS) to inject effector proteins into eukaryotic host cells, driving both cellular invasion and evasion of host immune responses. Exposure to the bile salt deoxycholate (DOC) significantly enhances Shigella virulence and is proposed to serve as a critical environmental signal present in the small intestine that prepares Shigella's T3SS for efficient infection of the colonic epithelium. Here, we uncover critical mechanistic details of the Shigella-specific DOC signaling process by describing the role of a π-helix secondary structure element within the T3SS tip protein invasion plasmid antigen D (IpaD). Biophysical characterization and high-resolution structures of IpaD mutants lacking the π-helix show that it is not required for global protein structure, but that it defines the native DOC binding site and prevents off target interactions. Additionally, Shigella strains expressing the π-helix deletion mutants illustrate the pathogenic importance of its role in guiding DOC interaction as flow cytometry and gentamycin protection assays show that the IpaD π-helix is essential for DOC-mediated apparatus maturation and enhanced invasion of eukaryotic cells. Together, these findings add to our understanding of the complex Shigella pathogenesis pathway and its evolution to respond to environmental bile salts by identifying the π-helix in IpaD as a critical structural element required for translating DOC exposure to virulence enhancement.\n\nStructural and functional characterization of the IpaD π-helix reveals critical roles in DOC interaction, T3SS apparatus maturation, and Shigella virulence.", "token_count": 457, "char_count": 1857, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:25.376818", "source": { "split": "train_shard_00000", "doc_id": 795 }, "chunk_id": "train_shard_00000_795_0", "global_id": 881 }, { "text": "Cerasomes are a modified form of liposomes containing both inorganic and organic parts and due to their strong polyorganosiloxane surface have remarkably high morphological stability and provide easier functionalization compared with conventional liposomes. To investigate the potential of these nanocarriers for oral delivery, bile salt integrated cerasomes (named bilocerasomes) encapsulating idarubicin hydrochloride (IDA) were prepared and characterized. The optimum formulation showed excellent stability in the simulated gastrointestinal fluids as well as under storage conditions. The oral pharmacokinetics of the IDA solution, empty nanocarrier + drug solution, and IDA-loaded bilocerasome were evaluated. The nanoformulation significantly increased the area under the drug concentration-time curve and the mean residence time (∼14.3- and 9-fold, respectively). The results obtained from cell uptake and chylomicron flow blocking approach revealed that bilocerasomes are absorbed into the intestinal cells via a clathrin/caveolin-independent endocytosis pathway and transported to the systemic circulation extensively via the intestinal lymphatic vessels. Considering the high stability of the prepared bilocerasome, noticeable participation of lymphatic transport in its systemic absorption and marked enhancement in the oral absorption of IDA, bilocerasomes can be introduced as a capable carrier for improving the oral bioavailability of drugs, particularly those that hepatic first-pass metabolism seriously limits their oral absorption.\n\nBile salt integrated cerasomes: A potential nanocarrier for enhancement of the oral bioavailability of idarubicin hydrochloride.", "token_count": 379, "char_count": 1679, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:25.965385", "source": { "split": "train_shard_00000", "doc_id": 796 }, "chunk_id": "train_shard_00000_796_0", "global_id": 882 }, { "text": "Pangenome Analysis Reveals Novel Contact-Dependent Growth Inhibition System and Phenazine Biosynthesis Operons in", "token_count": 31, "char_count": 113, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:26.329153", "source": { "split": "train_shard_00000", "doc_id": 797 }, "chunk_id": "train_shard_00000_797_0", "global_id": 883 }, { "text": "Antimicrobial Resistance Profile, Whole-Genome Sequencing and Core Genome Multilocus Sequence Typing of", "token_count": 28, "char_count": 103, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:26.683195", "source": { "split": "train_shard_00000", "doc_id": 798 }, "chunk_id": "train_shard_00000_798_0", "global_id": 884 }, { "text": "Myxobacteria (phylum Myxococcota) are abundant and virtually ubiquitous microbial predators. Facultatively multicellular organisms, they are able to form multicellular fruiting bodies and swarm across surfaces, cooperatively hunting for prey. Myxobacterial communities are able to kill a wide range of prey microbes, assimilating their biomass to fuel population growth. Their mechanism of predation is exobiotic - hydrolytic enzymes and toxic metabolites are secreted into the extracellular environment, killing and digesting prey cells from without. However, recent observations of single-cell predation and contact-dependent prey killing challenge the dogma of myxobacterial predation being obligately cooperative. Regardless of their predatory mechanisms, myxobacteria have a broad prey range, which includes Gram-negative bacteria, Gram-positive bacteria and fungi. Pangenome analyses have shown that their extremely large genomes are mainly composed of accessory genes, which are not shared by all members of their species. It seems that the diversity of accessory genes in different strains provides the breadth of activity required to prey upon such a smorgasbord of microbes, and also explains the considerable strain-to-strain variation in predatory efficiency against specific prey. After providing a short introduction to general features of myxobacterial biology which are relevant to predation, this review brings together a rapidly growing body of work into the molecular mechanisms and genetic basis of predation, presenting a summary of current knowledge, highlighting trends in research and suggesting strategies by which we can potentially exploit myxobacterial predation in the future.\n\nThe genetic basis of predation by myxobacteria.", "token_count": 385, "char_count": 1754, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6583, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:27.301125", "source": { "split": "train_shard_00000", "doc_id": 799 }, "chunk_id": "train_shard_00000_799_0", "global_id": 885 }, { "text": "From January 2022 to November 2022, sporadic psittacosis occurred in Lishui city, China. The patients were presented with fever, cough, and pulmonary infiltration. Their clinical symptoms were not relieved after receiving cephalosporin, penicillin, beta-lactamase inhibitors, and quinolones. Metagenomic next-generation sequencing of bronchoalveolar lavage fluid samples from the patients revealed Chlamydia psittaci infection. Then, three C. psittaci strains were isolated from the patients. Their whole genome sequences (WGSs) were obtained, and a core genome multilocus sequence typing (cgMLST) method was developed to study the population structure of C. psittaci. Using the constructed cgMLST method, 72 WGSs were divided into four related groups and ten sub-clusters. The Lishui strains formed a unique population of C. psittaci, which might represent a new variant of C. psittaci. In vitro antimicrobial susceptibility testing suggested that the Lishui strains were sensitive to tetracycline, macrolides, quinolones, and no drug-resistance was observed.\n\nA novel variant of Chlamydia psittaci causing human psittacosis in China.", "token_count": 302, "char_count": 1135, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6968, "quality_score": 0.8484, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:27.863733", "source": { "split": "train_shard_00000", "doc_id": 800 }, "chunk_id": "train_shard_00000_800_0", "global_id": 886 }, { "text": "Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing\n\nMobile genetic elements define the non-random structure of the", "token_count": 107, "char_count": 562, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8714, "quality_score": 0.9357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:28.590564", "source": { "split": "train_shard_00000", "doc_id": 801 }, "chunk_id": "train_shard_00000_801_0", "global_id": 887 }, { "text": "Yeasts are gaining increasing attention for their potential health benefits as probiotics in recent years. Researchers are actively searching for new yeast strains with probiotic properties (i.e,\n\nProbiotic Yeasts: A Developing Reality?", "token_count": 54, "char_count": 236, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9062, "quality_score": 0.9531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:28.960934", "source": { "split": "train_shard_00000", "doc_id": 802 }, "chunk_id": "train_shard_00000_802_0", "global_id": 888 }, { "text": "The lineage 4 (L4) of Mycobacterium tuberculosis (MTB) is not only globally prevalent but also locally dominant, surpassing other lineages, with lineage 2 (L2) following in prevalence. Despite its widespread occurrence, factors influencing the expansion of L4 and its sub-lineages remain poorly understood both at local and global levels. Therefore, this study aimed to conduct a pan-genome and identify genomic signatures linked to the elevated prevalence of L4 sublineages among extrapulmonary TB (EPTB) patients in western Ethiopia.\n\nPangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia.", "token_count": 186, "char_count": 712, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7172, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:29.407921", "source": { "split": "train_shard_00000", "doc_id": 803 }, "chunk_id": "train_shard_00000_803_0", "global_id": 889 }, { "text": "Structural variants (SVs) account for the majority of base pair differences both within and between primate species. However, our understanding of inter- and intra-species SV has been historically hampered by the quality of draft primate genomes and the absence of genome resources for key taxa. Recently, advances in long-read sequencing and genome assembly have begun to radically reshape our understanding of SVs. Two landmark achievements include the publication of a human telomere-to-telomere (T2T) genome as well as the development of the first human pangenome reference. In this review, we first look back to the major works laying the foundation for these projects. We then examine the ways in which T2T genome assemblies and pangenomes are transforming our understanding of and approach to primate SV. Finally, we discuss what the future of primate SV research may look like in the era of T2T genomes and pangenomics.\n\nStructural variation in humans and our primate kin in the era of telomere-to-telomere genomes and pangenomics.", "token_count": 249, "char_count": 1039, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6025, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:29.893412", "source": { "split": "train_shard_00000", "doc_id": 804 }, "chunk_id": "train_shard_00000_804_0", "global_id": 890 }, { "text": "The binding of Thioflavin T (ThT) with various bile salts, a potential host molecule, has been analyzed by steady-state and time-resolved fluorescence spectroscopy. A comparative study has been executed to investigate the influence of confinement of different bile salts, namely, sodium cholate (NaCh), sodium taurocholate (NaTC), and sodium deoxycholate (NaDC) on binding and excited state torsional motion of ThT molecules. The changes in absorption and emission properties of probe molecules were found to be sensitive to increasing bile salt concentration in aqueous 0.2 (M) NaCl solutions. The photophysics of ThT mainly depends on hydrophobicity, morphology, and size of bile salt aggregates in solution. In the presence of bile salts, the emission intensity and emission lifetime of ThT increase significantly, indicating encapsulation of dye. Moreover, we have also investigated the effect of the ionic strength of the medium by sodium chloride (NaCl) on the spectroscopic properties of ThT in the restricted surroundings of aqueous bile salts. It is observed that the fluorescence lifetime of ThT in bile salts increases significantly in the presence of NaCl. The encapsulation efficiency of ThT in bile salt aggregates has been assessed by iodide (\n\nEfficiency of Encapsulation of Thioflavin T (ThT) into Polar and Nonpolar Environments of Different Bile Salt Aggregates: A Femtosecond Fluorescence Study.", "token_count": 359, "char_count": 1415, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5476, "quality_score": 0.7738, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:30.469441", "source": { "split": "train_shard_00000", "doc_id": 805 }, "chunk_id": "train_shard_00000_805_0", "global_id": 891 }, { "text": "The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome.\n\nExploring gene content with pangene graphs.", "token_count": 75, "char_count": 351, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7925, "quality_score": 0.8962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:30.839461", "source": { "split": "train_shard_00000", "doc_id": 806 }, "chunk_id": "train_shard_00000_806_0", "global_id": 892 }, { "text": "A single strain of Candida anglica, isolated from cider, is available in international yeast collections. We present here seven new strains isolated from French PDO cheeses. For one of the cheese strains, we achieved a high-quality genome assembly of 13.7 Mb with eight near-complete telomere-to-telomere chromosomes. The genomes of two additional cheese strains and of the cider strain were also assembled and annotated, resulting in a core genome of 5966 coding sequences. Phylogenetic analysis showed that the seven cheese strains clustered together, away from the cider strain. Mating-type locus analysis revealed the presence of a MATa locus in the cider strain but a MATalpha locus in all cheese strains. The presence of LINE retrotransposons at identical genome position in the cheese strains, and two different karyotypic profiles resulting from chromosomal rearrangements were observed. Together, these findings are consistent with clonal propagation of the cheese strains. Phenotypic trait variations were observed within the cheese population under stress conditions whereas the cider strain was found to have a much greater capacity for growth in all conditions tested.\n\nDifferential adaptation of the yeast Candida anglica to fermented food.", "token_count": 296, "char_count": 1254, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6054, "quality_score": 0.8027, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:31.405842", "source": { "split": "train_shard_00000", "doc_id": 807 }, "chunk_id": "train_shard_00000_807_0", "global_id": 893 }, { "text": "Bifidobacterium animalis subsp. lactis BLa80 is a new probiotic strain with extensive applications in food products both domestically and internationally. Given the rising consumption of this probiotic, its safety assessment is increasingly crucial in the food industry. This study evaluates the safety of strain BLa80 using a combination of in vitro and in vivo assays along with genomic analysis. Methods included exposing the strain to artificial gastric and intestinal fluids, as well as a medium containing bile salts, to stimulate human digestive conditions. The strain showed high tolerance to gastric fluid at pH of 2.5 and to 0.3 % bile salts. It maintained a 99.92 % survival rate in intestinal fluid. Additional tests assessed hemolytic activity, antibiotic susceptibility (revealing sensitivity to 7 antibiotics), and biogenic amine production using HPLC-ELSD, confirming the absence of histamine, and other harmful amines. Bile salt hydrolase activity was demonstrated qualitatively, and metabolic byproducts were quantitatively analyzed using a D-/l-lactic acid assay kit, showing that BLa80 produces 1.48 mg/mL of l-lactic acid and no harmful d-lactic acid. Genomic analysis confirmed the absence of virulence or pathogenicity genes, and a 90-day oral toxicity study in rats confirmed no toxic effects at various doses. Overall, these findings support the safety classification of the strain BLa80.\n\nSafety evaluation of Bifidobacterium animalis subsp. lactis BLa80 under in vitro, and in vivo conditions.", "token_count": 396, "char_count": 1520, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:32.019266", "source": { "split": "train_shard_00000", "doc_id": 808 }, "chunk_id": "train_shard_00000_808_0", "global_id": 894 }, { "text": "Gut fungal imbalances, particularly increased Candida spp., are linked to obesity. This study explored the potential of Lactiplantibacillus plantarum cell-free extracts (postbiotics) to modulate the growth of Candida albicans and Candida kefyr, key members of the gut mycobiota. A minimal synthetic gut model was employed to evaluate the effects of Lactiplantibacillus plantarum postbiotics on fungal growth in mono- and mixed cultures. Microreactors were employed for culturing, fungal growth was quantified using CFU counting, and regression analysis was used to evaluate the effects of postbiotics on fungal growth. Postbiotics at a concentration of 12.5% significantly reduced the growth of both Candida species. At 24 h, both C. albicans and C. kefyr in monocultures exhibited a decrease in growth of 0.11 log CFU/mL. In contrast, mixed cultures showed a more pronounced antifungal effect, with C. albicans and C. kefyr reductions of 0.62 log CFU/mL and 0.64 log CFU/mL, respectively. Regression analysis using the Gompertz model supported the antifungal activity of postbiotics and revealed species-specific differences in growth parameters. These findings suggest that L. plantarum postbiotics have the potential to modulate the gut mycobiota by reducing Candida growth, potentially offering a therapeutic approach for combating fungal overgrowth associated with obesity.\n\nIn vitro analysis of postbiotic antimicrobial activity against Candida Species in a minimal synthetic model simulating the gut mycobiota in obesity.", "token_count": 403, "char_count": 1528, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5367, "quality_score": 0.7683, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:32.664374", "source": { "split": "train_shard_00000", "doc_id": 809 }, "chunk_id": "train_shard_00000_809_0", "global_id": 895 }, { "text": "Salmonella enterica serovar Typhimurium (S. Typhimurium) is a major cause of salmonellosis, and the emergence of multidrug-resistant pathovariants has become a growing concern. Here, we investigate a distinct rough colony variant exhibiting a strong biofilm-forming ability isolated in China. Whole-genome sequencing on 2,212 Chinese isolates and 1,739 publicly available genomes reveals the population structure and evolutionary history of the rough colony variants. Characterized by macro, red, dry, and rough (mrdar) colonies, these variants demonstrate enhanced biofilm formation at 28 °C and 37 °C compared to typical rdar colonies. The mrdar variants exhibit extensive multidrug resistance, with significantly higher resistance to at least five classes of antimicrobial agents compared to non-mrdar variants. This resistance is primarily conferred by an IncHI2 plasmid harboring 19 antimicrobial resistance genes. Phylogenomic analysis divides the global collections into six lineages. The majority of mrdar variants belong to sublineage L6.5, which originated from Chinese smooth colony strains and possibly emerged circa 1977. Among the mrdar variants, upregulation of the csgDEFG operons is observed, probably due to a distinct point mutation (-44G > T) in the csgD gene promoter. Pangenome and genome-wide association analyses identify 87 specific accessory genes and 72 distinct single nucleotide polymorphisms associated with the mrdar morphotype.\n\nCharacterization of a Salmonella enterica serovar Typhimurium lineage with rough colony morphology and multidrug resistance.", "token_count": 416, "char_count": 1585, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7051, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:33.309415", "source": { "split": "train_shard_00000", "doc_id": 810 }, "chunk_id": "train_shard_00000_810_0", "global_id": 896 }, { "text": "Hyperuricemia has evolved into a global public health concern, and applying probiotics fermented apple juice holds promise for alleviating this condition. This study aimed to investigate the biotransformation and metabolic features of urate-lowering probiotics sequentially fermented dealcoholized apple juice (PSFA), and assess its ameliorative effects and potential mechanisms on hyperuricemia mice. Results showed that CICC 6074 and 20,292 possessed excellent purine, nucleotide and nucleoside degradation and acid and bile salt resistance; sequential fermentation decreased the fructose in apple juice, and viable counts reached 3.76 × 10\n\nBiotransformation characteristics of urate-lowering probiotic fermented apple juice and potential regulatory mechanisms for ameliorating hyperuricemia via mediating gut microbiota and metabolic pathways.", "token_count": 215, "char_count": 847, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7315, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:33.806329", "source": { "split": "train_shard_00000", "doc_id": 811 }, "chunk_id": "train_shard_00000_811_0", "global_id": 897 }, { "text": "Oleanolic acid (OA) is a naturally occurring pentacyclic triterpene compound that has been reported to cause cholestatic liver injury. However, the regulation and pathogenic role of bile acids in OA-induced development of cholestatic liver injury remains largely unclear. Farnesoid X receptor (FXR) is a metabolic nuclear receptor that plays an important role in bile acid homeostasis in the liver by regulating efflux transporters bile salt export pump (BSEP) and multidrug resistance-associated protein 2 (MRP2). The aim of this study was to investigate the effect of OA on hepatocyte tight junction function and determine the role of FXR, BSEP, and MRP2 in the mechanism of impairment of transport of bile acids induced by OA. Both in vivo and in vitro models were used to characterize the OA-induced liver injury. The liquid chromatography-tandem mass spectrometry (LC-MS) was employed to characterize the efflux function of the transporters, and the results showed that OA caused a blockage of bile acids efflux. OA treatment resulted in decreased expression levels of the tight junction proteins zonula occludens-1 and occludin. Immunofluorescence results showed that OA treatment significantly reduced the number of bile ducts and the immunofluorescence intensity. Pretreatment with agonists of FXR and MRP2, respectively, in animal experiments attenuated OA-induced liver injury, while pretreatment with inhibitors of BSEP and MRP2 further aggravated OA-induced liver injury. These results suggest that OA inhibits FXR-mediated BSEP and MRP2, leading to impaired bile acid efflux and disruption of tight junctions between liver cells, resulting in liver damage.\n\nOleanolic acid induces hepatic injury by disrupting hepatocyte tight junction and dysregulation of farnesoid X receptor-mediated bile acid efflux transporters.", "token_count": 488, "char_count": 1830, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5489, "quality_score": 0.7744, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:34.472543", "source": { "split": "train_shard_00000", "doc_id": 812 }, "chunk_id": "train_shard_00000_812_0", "global_id": 898 }, { "text": "Numerous studies have indicated that Morocco's indigenous sheep breeds are genetically homogenous, posing a risk to their survival in the challenging harsh climate conditions where they predominantly inhabit. To understand the genetic behind genetic homogeneity through the lens of runs of homozygosity (ROH), we analyzed the whole genome sequences of five indigenous sheep breeds (Beni Guil, Ouled Djellal, D'man, Sardi, Timahdite and Admixed).The results from principal component, admixture, Fst, and neighbour joining tree analyses consistently showed a homogenous genetic structure. This structure was characterized by an average length of 1.83 Mb for runs of homozygosity (ROH) segments, with a limited number of long ROH segments (24-48 Mb and > 48 Mb). The most common ROH segments were those ranging from 1-6 Mb. The most significant regions of homozygosity (ROH Islands) were mostly observed in two chromosomes, namely Chr1 and Chr5. Specifically, ROH Islands were exclusively discovered in the Ouled Djellal breed on Chr1, whereas Chr5 exhibited ROH Islands in all breeds. The analysis of ROH Island and iHS technique was employed to detect signatures of selection on Chr1 and Chr5. The results indicate that Chr5 had a high level of homogeneity, with the same genes being discovered across all breeds. In contrast, Chr1 displays some genetic variances between breeds. Genes identified on Chr5 included SLC39A1, IL23A, CAST, IL5, IL13, and IL4 which are responsible for immune response while genes identified on Chr1 include SOD1, SLAMF9, RTP4, CLDN1, and PRKAA2. ROH segment profile and effective population sizes patterns suggests that the genetic uniformity of studied breeds is the outcome of events that transpired between 250 and 300 generations ago. This research not only contributes to the understanding of ROH distribution across breeds but helps design and implement native sheep breeding and conservation strategies in Morocco", "token_count": 504, "char_count": 1948, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6599, "quality_score": 0.8299, "entities": { "genes": [ "IL13", "RTP4", "IL5", "SLAMF9", "IL4", "PRKAA2", "SOD1", "CLDN1", "IL23A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:35.124907", "source": { "split": "train_shard_00000", "doc_id": 813 }, "chunk_id": "train_shard_00000_813_0", "global_id": 899 }, { "text": "Future research, incorporating a broader sample size and utilizing the pangenome for reference, is recommended to further elucidate these breeds' genomic landscapes and adaptive mechanisms.\n\nInsights into the genomic homogeneity of Moroccan indigenous sheep breeds though the lens of runs of homozygosity.", "token_count": 71, "char_count": 305, "word_count": 42, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:35.495161", "source": { "split": "train_shard_00000", "doc_id": 813 }, "chunk_id": "train_shard_00000_813_1", "global_id": 900 }, { "text": "Cholestasis is a hepatobiliary disorder characterized by the excessive accumulation of toxic bile acids in hepatocytes, leading to cholestatic liver injury (CLI) through multiple pathogenic inflammatory pathways. Currently, there are limited therapeutic options for the management of cholestasis and associated CLI; therefore, new options are urgently needed. Pirfenidone (PF), an oral bioavailable pyridone analog, is used for the treatment of idiopathic pulmonary fibrosis. PF has recently demonstrated diverse potential therapeutic activities against different pathologies. Accordingly, the present study adopted the α-naphthyl isothiocyanate (ANIT)-induced CLI model in mice to explore the potential protective impact of PF and investigate the underlying mechanisms of action. PF intervention markedly reduced the serum levels of ALT, AST, LDH, total bilirubin, and total bile acids, which was accompanied by a remarkable amelioration of histopathological lesions induced by ANIT. PF also protected the mice against ANIT-induced redox imbalance in the liver, represented by reduced MDA levels and elevated GSH and SOD activities. Mechanistically, PF inhibited ANIT-induced downregulated expressions of the farnesoid X receptor (FXR), as well as the bile salt export pump (BSEP) and the multidrug resistance-associated protein 2 (MRP2) bile acid efflux channels. PF further repressed ANIT-induced NF-κB activation and TNF-α and IL-6 production. These beneficial effects were associated with its ability to dose-dependently inhibit Wnt/GSK-3β/β-catenin/cyclin D1 signaling. Collectively, PF protects against ANIT-induced CLI in mice, demonstrating powerful antioxidant and anti-inflammatory activities as well as an ability to oppose BA homeostasis disorder. These protective effects are primarily mediated by modulating the interplay between FXR, NF-κB/TNF-α/IL-6, and Wnt/β-catenin signaling pathways.", "token_count": 501, "char_count": 1905, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6877, "quality_score": 0.8439, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:36.146872", "source": { "split": "train_shard_00000", "doc_id": 814 }, "chunk_id": "train_shard_00000_814_0", "global_id": 901 }, { "text": "Pirfenidone ameliorates ANIT-induced cholestatic liver injury via modulation of FXR, NF-кB/TNF-α, and Wnt/GSK-3β/β-catenin signaling pathways.", "token_count": 57, "char_count": 142, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:36.513066", "source": { "split": "train_shard_00000", "doc_id": 814 }, "chunk_id": "train_shard_00000_814_1", "global_id": 902 }, { "text": "LCPS-1, a cell wall polysaccharide (CWPS), is bound to the cell wall of the probiotic Lacticaseibacillus paracasei (formerly known as Lactobacillus casei) strain Shirota (LcS). Generally, the role of CWPS in the viability and survivability of bacteria is yet to be fully understood. This study aimed to elucidate the role of LCPS-1 in the viability and survivability of LcS. A mutant strain completely lacking LCPS-1 was constructed and evaluated for growth in bovine and soy milk and susceptibility to acid and bile. The growth of the mutant in bovine and soy milk temporarily stalled after the late logarithmic phase while wild-type LcS continued growing, resulting in a significantly lower number of viable cells for the mutant strain (p < 0.01). Significantly higher cell death relative to that of the wild-type strain was observed for the mutant strain following acid treatment at pH 3.0 (p < 0.01), with 60 and 92 % survival, respectively. The absence of LCPS-1 also reduced the survival rate of LcS cells from 3.3 to 0.8 % following 0.2 % bile treatment. The survival rate of the mutant after consecutive treatment with acid and bile was 19 %, while 73 % of the wild-type LcS survived. These results indicate that LCPS-1 leads to higher LcS growth in milk and improves tolerance to acid and bile. This study reveals the contribution of probiotic bacterial CWPS to acidic and gastrointestinal stress tolerance. Based on these findings, characterizing and modifying CWPS in probiotic strains could enhance manufacturing yields and improve gastrointestinal stress tolerance after consumption by hosts, ultimately advancing the development of more effective probiotics.\n\nCell wall polysaccharide enhances Lacticaseibacillus paracasei strain Shirota growth in milk and contributes to acid and bile tolerance.", "token_count": 485, "char_count": 1810, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5018, "quality_score": 0.7509, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:37.157621", "source": { "split": "train_shard_00000", "doc_id": 815 }, "chunk_id": "train_shard_00000_815_0", "global_id": 903 }, { "text": "In the present work, we carried out a comparative genomic analysis to trace the evolutionary trajectory of the bacterial species that make up the Liquorilactobacillus genus, from the identification of genes and speciation/adaptation mechanisms in their unique characteristics to the identification of the pattern grouping these species. We present phylogenetic relationships between Liquorilactobacillus and related taxa such as Bacillus, basal lactobacilli and Ligilactobacillus, highlighting evolutionary divergences and lifestyle transitions across different taxa. The species of this genus share a core genome of 1023 genes, distributed in all COGs, which made it possible to characterize it as Liquorilactobacillus sensu lato: few amino acid auxotrophy, low genes number for resistance to antibiotics and general and specific cellular reprogramming mechanisms for environmental responses. These species were divided into four clades, with diversity being enhanced mainly by the diversity of genes involved in sugar metabolism. Clade 1 presented lower (< 70%) average amino acid identity with the other clades, with exclusive or absent genes, and greater distance in the genome compared to clades 2, 3 and 4. The data pointed to an ancestor of clades 2, 3 and 4 as being the origin of the genus Ligilactobacillus, while the species of clade 1 being closer to the ancestral Bacillus. All these traits indicated that the species of clade 1 could be soon separated in a distinct genus.\n\nLiquorilactobacillus: A Context of the Evolutionary History and Metabolic Adaptation of a Bacterial Genus from Fermentation Liquid Environments.", "token_count": 407, "char_count": 1632, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6017, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:37.771658", "source": { "split": "train_shard_00000", "doc_id": 816 }, "chunk_id": "train_shard_00000_816_0", "global_id": 904 }, { "text": "Modern pangenome graphs are built using haplotype-resolved genome assemblies. When mapping reads to a pangenome graph, prioritizing alignments that are consistent with the known haplotypes improves genotyping accuracy. However, the existing rigorous formulations for colinear chaining and alignment problems do not consider the haplotype paths in a pangenome graph. This often leads to spurious read alignments to those paths that are unlikely recombinations of the known haplotypes. In this paper, we develop novel formulations and algorithms for sequence-to-graph alignment and chaining problems. Inspired by the genotype imputation models, we assume that a query sequence is an imperfect mosaic of reference haplotypes. Accordingly, we introduce a recombination penalty in the scoring functions for each haplotype switch. First, we solve haplotype-aware sequence-to-graph alignment in [Formula: see text] time, where\n\nHaplotype-aware sequence alignment to pangenome graphs.", "token_count": 232, "char_count": 976, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6767, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:38.244016", "source": { "split": "train_shard_00000", "doc_id": 817 }, "chunk_id": "train_shard_00000_817_0", "global_id": 905 }, { "text": "Bacterial species often consist of strains with variable gene content, collectively referred to as the pangenome. Variations in the genetic makeup of strains can alter bacterial physiology and fitness. To define biologically relevant genes of a genome, genome-wide transposon mutant libraries have been used to identify genes essential for survival or virulence in a given strain. Such phenotypic studies have been conducted in four different genotypes of the human pathogen\n\nPangenome evaluation of gene essentiality in", "token_count": 113, "char_count": 520, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:38.624965", "source": { "split": "train_shard_00000", "doc_id": 818 }, "chunk_id": "train_shard_00000_818_0", "global_id": 906 }, { "text": "We generalize a problem of finding maximum-scoring segment sets, previously studied by Csűrös (IEEE/ACM Transactions on Computational Biology and Bioinformatics, 2004, 1, 139-150), from sequences to graphs. Namely, given a vertex-weighted graph\n\nMaximum-scoring path sets on pangenome graphs of constant treewidth.", "token_count": 93, "char_count": 314, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9024, "quality_score": 0.9512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:38.998853", "source": { "split": "train_shard_00000", "doc_id": 819 }, "chunk_id": "train_shard_00000_819_0", "global_id": 907 }, { "text": "Bile salts can strongly influence energy metabolism through systemic signaling, which can be enhanced by inhibiting the hepatic bile salt transporter Na\n\nInhibition of hepatic bile salt uptake by Bulevirtide reduces atherosclerosis in Oatp1a1", "token_count": 68, "char_count": 242, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:39.369079", "source": { "split": "train_shard_00000", "doc_id": 820 }, "chunk_id": "train_shard_00000_820_0", "global_id": 908 }, { "text": "This study delves into the genomic features of 10 Vibrio strains collected from deep-sea hydrothermal vents in the Pacific Ocean, providing insights into their evolutionary history and ecological adaptations. Through sequencing and pan-genome analysis involving 141 Vibrio species, we found that deep-sea strains exhibit larger genomes with unique gene distributions, suggesting adaptation to the vent environment. The phylogenomic reconstruction of the investigated isolates revealed the presence of 2 main clades: The first is monophyletic, consisting exclusively of Vibrio alginolyticus, while the second forms a monophyletic clade comprising both Vibrio antiquarius and Vibrio diabolicus species, which were previously isolated from deep-sea vents. All strains carry virulence and antibiotic resistance genes related to those found in human pathogenic Vibrio species which may play a wider ecological role other than host infection in these environments. In addition, functional genomic analysis identified genes potentially related to deep-sea survival and stress response, alongside candidate genes encoding for novel antimicrobial agents. Ultimately, the pan-genome we generated represents a valuable resource for future studies investigating the taxonomy, evolution, and ecology of Vibrio species.\n\nPan-Genome Provides Insights into Vibrio Evolution and Adaptation to Deep-Sea Hydrothermal Vents.", "token_count": 314, "char_count": 1404, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6809, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:39.930038", "source": { "split": "train_shard_00000", "doc_id": 821 }, "chunk_id": "train_shard_00000_821_0", "global_id": 909 }, { "text": "Muskoxen are important ecosystem components and provide food, economic opportunities, and cultural well-being for Indigenous communities in the Canadian Arctic. Between 2010 and 2021, Erysipelothrix rhusiopathiae was isolated from carcasses of muskoxen, caribou, a seal, and an Arctic fox during multiple large scale mortality events in the Canadian Arctic Archipelago. A single strain ('Arctic clone') of E. rhusiopathiae was associated with the mortalities on Banks, Victoria and Prince Patrick Islands, Northwest Territories and Nunavut, Canada (2010-2017). The objectives of this study were to (i) characterize the genomes of E. rhusiopathiae isolates obtained from more recent muskox mortalities in the Canadian Arctic in 2019 and 2021; (ii) identify and compare common virulence traits associated with the core genome and mobile genetic elements (i.e. pathogenicity islands and prophages) among Arctic clone versus other E. rhusiopathiae genomes; and iii) use pan-genome wide association studies (GWAS) to determine unique genetic contents of the Arctic clone that may encode virulence traits and that could be used for diagnostic purposes.\n\nGenomic characterization and virulence gene profiling of Erysipelothrix rhusiopathiae isolated from widespread muskox mortalities in the Canadian Arctic Archipelago.", "token_count": 348, "char_count": 1313, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:40.506946", "source": { "split": "train_shard_00000", "doc_id": 822 }, "chunk_id": "train_shard_00000_822_0", "global_id": 910 }, { "text": "Membrane transporters interact not only with endogenous substrates but are also engaged in the transport of xenobiotics, including drugs. While the coordinated function of uptake (solute carrier family-SLC and SLCO) and efflux (ATP-binding cassette family-ABC, multidrug and toxic compound extrusion family-MATE) transporter system allows vectorial drug transport, efflux carriers alone achieve barrier functions. The modulation of transport functions was proved to be effective in the treatment strategies of various pathological states. Sodium-glucose cotransporter-2 (SGLT2) inhibitors are the drugs most widely applied in clinical practice, especially in the treatment of diabetes mellitus and heart failure. Sodium taurocholate co-transporting polypeptide (NTCP) serves as virus particles (HBV/HDV) carrier, and inhibition of its function is applied in the treatment of hepatitis B and hepatitis D by myrcludex B. Inherited cholestatic diseases, such as Alagille syndrome (ALGS) and progressive familial intrahepatic cholestasis (PFIC) can be treated by odevixibat and maralixibat, which inhibit activity of apical sodium-dependent bile salt transporter (ASBT). Probenecid can be considered to increase uric acid excretion in the urine mainly via the inhibition of urate transporter 1 (URAT1), and due to pharmacokinetic interactions involving organic anion transporters 1 and 3 (OAT1 and OAT3), it modifies renal excretion of penicillins or ciprofloxacin as well as nephrotoxicity of cidofovir. This review discusses clinically approved drugs that affect membrane/drug transporter function.\n\nTransporter Proteins as Therapeutic Drug Targets-With a Focus on SGLT2 Inhibitors.", "token_count": 451, "char_count": 1680, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8656, "entities": { "genes": [ "OAT1", "SGLT2", "URAT1", "OAT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:41.137941", "source": { "split": "train_shard_00000", "doc_id": 823 }, "chunk_id": "train_shard_00000_823_0", "global_id": 911 }, { "text": "The targeted depletion of potential gut pathogens is often challenging because of their intrinsic ability to thrive in harsh gut environments. Earlier, we showed that Campylobacter jejuni (C. jejuni) exclusively uses the Type-VI Secretion System (T6SS) to target its prey such as Escherichia coli (E. coli), and phenotypic differences between T6SS-negative and T6SS-positive C. jejuni isolates toward bile salt sensitivity. However, it remains unclear how the target-driven T6SS functionality prevails in a polymicrobial gut environment. Here, we investigated the fate of microbial competition in an altered gut environment via bacterial T6SS using a T6SS-negative and -positive C. jejuni or its isogenic mutant of the hemolysin-coregulated protein (hcp). We showed that in the presence of bile salt and prey bacteria (E. coli), T6SS-positive C. jejuni experiences enhanced intracellular stress leading to cell death. Intracellular tracking of fluorophore-conjugated bile salts confirmed that T6SS-mediated bile salt influx into C. jejuni can enhance intracellular oxidative stress, affecting C. jejuni viability. We further investigated whether the T6SS activity in the presence of prey (E. coli) perturbs the in vivo colonization of C. jejuni. Using chickens as primary hosts of C. jejuni and non-pathogenic E. coli as prey, we showed a marked reduction of C. jejuni load in chickens cecum when bile salt solution was administered orally. Analysis of local antibody responses and pro-inflammatory gene expression showed a reduced risk of tissue damage, indicating that T6SS activity in the complex gut environment can be exploited as a possible measure to clear the persistent colonization of C. jejuni in chickens.\n\nSelective depletion of Campylobacter jejuni via T6SS dependent functionality: an approach for improving chickens gut health.", "token_count": 467, "char_count": 1843, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5799, "quality_score": 0.79, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:41.775252", "source": { "split": "train_shard_00000", "doc_id": 824 }, "chunk_id": "train_shard_00000_824_0", "global_id": 912 }, { "text": "Enterococcus faecalis is a versatile lactic acid bacterium with a large variety of implications for humans. While some strains of this species are pathobionts being resistant against most of the common antibiotics, other strains are regarded as biological protectants or even probiotics. Accordingly, E. faecalis strains largely differ in the size and content of their accessory genome. In this study, we describe the genome-scale metabolic network reconstruction of E. faecalis ATCC 19433, a non-resistant human-associated strain. A comparison of the genome-scale metabolic model (GSM) of E. faecalis ATCC 19433 with a previously published GSM of the multi-resistant pathobiontic E. faecalis V583 reveals high similarities in the central metabolic abilities of these two human associated strains. This is reflected, e.g., in the identical amino acid auxotrophies. The ATCC 19433 strain, however, has a 14.1 % smaller genome than V583 and lacks the multiple antibiotic resistance genes and genes involved in capsule formation. Based on the measured metabolic fluxes at different growth rates, the energy demand at zero growth was calculated to be about 40 % lower for the ATCC 19433 strain compared to V583. Furthermore, the ATCC 19433 strain seems less prone to the depletion of amino acids utilizable for energy metabolism. This might hint at a lower overall energy demand of the ATCC 19433 strain as compared to V583.\n\nComparing genome-scale metabolic models of the non-resistant Enterococcus faecalis ATCC 19433 and the multi-resistant Enterococcus faecalis V583.", "token_count": 438, "char_count": 1567, "word_count": 236, "semantic_coherence": 1, "information_density": 0.572, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:42.404599", "source": { "split": "train_shard_00000", "doc_id": 825 }, "chunk_id": "train_shard_00000_825_0", "global_id": 913 }, { "text": "Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade that was originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at the genomic level among six strains (4 isolated from clam and 2 from seawater) and to determine their phylogeny. For this purpose, whole genomes of the six strains were sequenced by different technologies including Illumina and PacBio, and the resulting sequences were corrected. Genomes were annotated and compared using different online tools. Furthermore, the study of core- and pan-genomes were examined, and the phylogeny was inferred. The content of the core genome ranged from 2953 to 2766 genes and that of the pangenome ranged from 6278 to 6132, depending on the tool used. Although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI values higher than 97%, some differences were found related to motility, capsule synthesis, iron acquisition systems or mobile genetic elements. Phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle (commensal or free-living), but that of the pangenome indicated certain geographical isolation in the same growing area. This study led to the reclassification of some isolates formerly described as V. toranzoniae and demonstrated the importance of cured deposited sequences to proper phylogenetic assignment.\n\nComparative genomics of Vibrio toranzoniae strains.", "token_count": 398, "char_count": 1641, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6057, "quality_score": 0.8028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:43.027247", "source": { "split": "train_shard_00000", "doc_id": 826 }, "chunk_id": "train_shard_00000_826_0", "global_id": 914 }, { "text": "Despite the severe impact of uncommon yeast fungal infections and the pressing need for more research on the topic, there are still few studies available on the identification, epidemiology, and susceptibility profile of those pathogens. The aims of the current study were to define the profile of uncommon yeast species at Fattouma Bourguiba University Hospital using phenotypic, molecular, and proteomic methods and to study their antifungal susceptibility profile. Pre-identified uncommon yeast species were collected from 2018 to 2021. These isolates were further identified using phenotypic methods (ID32C® system and Vitek2® YST), matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS), and sequencing. The antifungal susceptibility profile was studied using the reference CLSI broth microdilution method. In total, 30 strains were collected during the study period. Referring to the sequencing, the most isolated uncommon species were Saprochaete capitata, Candida lusitaniae, Candida kefyr, Candida inconspicua, and Candida guilliermondii. A total of 90% of isolates were correctly identified by MALDI-TOF MS compared to 76.7% and 63.3% by ID32® C and VITEK® 2 YST, respectively. The isolated species showed variable responses to antifungals. Candida guilliermondii showed increased azole minimum inhibitory concentrations. Misidentification of uncommon yeast species was common using commercial phenotypic methods. The high percentage of concordance of MALDI-TOF results with sequencing highlights its high performance and usefulness as a routine diagnosis tool.\n\nIdentification and antifungal susceptibility profile of uncommon yeast species at Fattouma Bourguiba University Hospital in Tunisia.", "token_count": 440, "char_count": 1742, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8043, "entities": { "genes": [ "ID32C", "ID32" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:43.661863", "source": { "split": "train_shard_00000", "doc_id": 827 }, "chunk_id": "train_shard_00000_827_0", "global_id": 915 }, { "text": "To decipher the genetic diversity within the cucurbit genus Citrullus, we generated telomere-to-telomere (T2T) assemblies of 27 distinct genotypes, encompassing all seven Citrullus species. This T2T super-pangenome has expanded the previously published reference genome, T2T-G42, by adding 399.2 Mb and 11,225 genes. Comparative analysis has unveiled gene variants and structural variations (SVs), shedding light on watermelon evolution and domestication processes that enhanced attributes such as bitterness and sugar content while compromising disease resistance. Multidisease-resistant loci from Citrullus amarus and Citrullus mucosospermus were successfully introduced into cultivated Citrullus lanatus. The SVs identified in C. lanatus have not only been inherited from cordophanus but also from C. mucosospermus, suggesting additional ancestors beyond cordophanus in the lineage of cultivated watermelon. Our investigation substantially improves the comprehension of watermelon genome diversity, furnishing comprehensive reference genomes for all Citrullus species. This advancement aids in the exploration and genetic enhancement of watermelon using its wild relatives.\n\nTelomere-to-telomere Citrullus super-pangenome provides direction for watermelon breeding.", "token_count": 327, "char_count": 1268, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7595, "quality_score": 0.8797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:44.232477", "source": { "split": "train_shard_00000", "doc_id": 828 }, "chunk_id": "train_shard_00000_828_0", "global_id": 916 }, { "text": "Species-specific genes, also known as orphans, are ubiquitous across life's domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses followed by horizontal gene transfer, whereas the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4644 human gut microbiome species and identified more than 600,000 unique SSOGs, representing an average of 2.6% of a given species' pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most of them. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.\n\nLarge-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins.", "token_count": 410, "char_count": 1778, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:44.878186", "source": { "split": "train_shard_00000", "doc_id": 829 }, "chunk_id": "train_shard_00000_829_0", "global_id": 917 }, { "text": "There is a growing body of evidence suggesting that the composition of intestinal flora plays a significant role in regulating lipid metabolism. 2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine (IMMH007) is a new candidate compound for regulating blood cholesterol and other lipids. In this study, we conducted metagenomic and metabolomic analyses on samples from high-fat diet-fed (HFD) hamsters treated with IMMH007. Our findings revealed that IMM-H007 reversed the imbalance of gut microbiota caused by a high-fat diet. Additionally, it activated adiponectin receptor and pantothenate and CoA biosynthesis pathway-related genes, which are known to regulate lipid and glucose metabolism. Furthermore, IMM-H007 promotes cholesterol metabolism by reducing the abundance of genes and species associated with 7α-dehydroxylation and bile salt hydrolase (BSH). Metabolomics and pharmacological studies have shown that IMM-H007 effectively improved glucose and lipid metabolism disorders caused by HFD, reduced the aggregation of secondary bile acids (SBAs), significantly increased the content of hyodeoxycholic acid (HDCA), and also activated the expression of VDR in the small intestine. As a result, there was a reduction in the leakage of diamine oxidase (DAO) into the bloodstream in hamsters, accompanied by an upregulation of ZO-1 expression in the small intestine. The results suggested that IMM-H007 regulated glucose and lipid metabolism, promoted cholesterol metabolism through activating the expression of VDR, inhibiting inflammatory and improving the permeability of the intestinal barrier. Thus, our study provides new understanding of how IMM-H007 interacts with intestinal function, microbiota, and relevant targets, shedding light on its mechanism of action.", "token_count": 484, "char_count": 1778, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6516, "quality_score": 0.8258, "entities": { "genes": [ "IMMH007" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:45.539608", "source": { "split": "train_shard_00000", "doc_id": 830 }, "chunk_id": "train_shard_00000_830_0", "global_id": 918 }, { "text": "2', 3', 5'-tri-O-acetyl-N6-(3-hydroxyphenyl) adenosine alleviates diet-induced hyperlipidemia by modulating intestinal gene expression profiles and metabolic pathway.", "token_count": 64, "char_count": 166, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:45.939913", "source": { "split": "train_shard_00000", "doc_id": 830 }, "chunk_id": "train_shard_00000_830_1", "global_id": 919 }, { "text": "Bacteriophages are the most prevalent biological entities in the biosphere. However, limitations in both medical relevance and sequencing technologies have led to a systematic underestimation of the genetic diversity within phages. This underrepresentation not only creates a significant gap in our understanding of phage roles across diverse biosystems but also introduces biases in computational models reliant on these data for training and testing. In this study, we focused on publicly available genomes of bacteriophages infecting high-priority ESKAPE pathogens to show the extent and impact of this underrepresentation. First, we demonstrate a stark underrepresentation of ESKAPE phage genomes within the public genome and protein databases. Next, a pangenome analysis of these ESKAPE phages reveals extensive sharing of core genes among phages infecting the same host. Furthermore, genome analyses and clustering highlight close nucleotide-level relationships among the ESKAPE phages, raising concerns about the limited diversity within current public databases. Lastly, we uncover a scarcity of unique lytic phages and phage proteins with antimicrobial activities against ESKAPE pathogens. This comprehensive analysis of the ESKAPE phages underscores the severity of underrepresentation and its potential implications. This lack of diversity in phage genomes may restrict the resurgence of phage therapy and cause biased outcomes in data-driven computational models due to incomplete and unbalanced biological datasets.\n\nA pangenome analysis of ESKAPE bacteriophages: the underrepresentation may impact machine learning models.", "token_count": 358, "char_count": 1636, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6054, "quality_score": 0.8027, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:46.541269", "source": { "split": "train_shard_00000", "doc_id": 831 }, "chunk_id": "train_shard_00000_831_0", "global_id": 920 }, { "text": "Ohmic heating (OH), an emerging food processing technology employed in the food processing industry, raises potential food safety concerns due to the recovery of sublethally injured pathogens such as Staphylococcus aureus (S. aureus). In the present study, sensitivity to various stress conditions and the changes in cellular-related factors of OH-injured S. aureus during repair were investigated. The results indicated that liquid media differences (nutrient broth (NB), phosphate-buffered saline (PBS), milk, and cucumber juice) affected the recovery process of injured cells. Nutrient enrichment determines the bacterial repair rate, and the rates of repair for these media were milk > NB > cucumber juice > PBS. The sensitivity of injured cells to various stressors, including different acids, temperature, nisin, simulated gastric fluid, and bile salt, increased during the injury phase and subsequently diminished upon repair. Additionally, the intracellular ATP content, enzyme activities (Na\n\nChanges in stresses sensitivity of ohmic heating-induced sublethally injured Staphylococcus aureus during repair: Potential mechanisms at the cellular and molecular levels.", "token_count": 275, "char_count": 1174, "word_count": 162, "semantic_coherence": 1, "information_density": 0.679, "quality_score": 0.8395, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:47.081853", "source": { "split": "train_shard_00000", "doc_id": 832 }, "chunk_id": "train_shard_00000_832_0", "global_id": 921 }, { "text": "This study investigated the impact of dietary supplementation with hydrolyzed yeast (Kluyveromyces marxianus) on growth performance, humoral immunity, jejunal morphology, cecal microbiota and metabolic pathways in broilers raised at 45 kg/m\n\nDietary Kluyveromyces marxianus hydrolysate alters humoral immunity, jejunal morphology, cecal microbiota and metabolic pathways in broiler chickens raised under a high stocking density.", "token_count": 120, "char_count": 428, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:47.465998", "source": { "split": "train_shard_00000", "doc_id": 833 }, "chunk_id": "train_shard_00000_833_0", "global_id": 922 }, { "text": "The incidence of Pseudomonas aeruginosa infections in healthcare environments, particularly in low-and middle-income countries, is on the rise. The purpose of this study was to provide comprehensive genomic insights into thirteen P. aeruginosa isolates obtained from Egyptian healthcare settings. Phenotypic analysis of the antimicrobial resistance profile and biofilm formation were performed using minimum inhibitory concentration and microtiter plate assay, respectively. Whole genome sequencing was employed to identify sequence typing, resistome, virulome, and mobile genetic elements. Our findings indicate that 92.3% of the isolates were classified as extensively drug-resistant, with 53.85% of these demonstrating strong biofilm production capabilities. The predominant clone observed in the study was ST773, followed by ST235, both of which were associated with the O11 serotype. Core genome multi-locus sequence typing comparison of these clones with global isolates suggested their potential global expansion and adaptation. A significant portion of the isolates harbored Col plasmids and various MGEs, all of which were linked to antimicrobial resistance genes. Single nucleotide polymorphisms in different genes were associated with the development of antimicrobial resistance in these isolates. In conclusion, this pilot study underscores the prevalence of extensively drug-resistant P. aeruginosa isolates and emphasizes the role of horizontal gene transfer facilitated by a diverse array of mobile genetic elements within various clones. Furthermore, specific insertion sequences and mutations were found to be associated with antibiotic resistance.\n\nUnveiling the microevolution of antimicrobial resistance in selected Pseudomonas aeruginosa isolates from Egyptian healthcare settings: A genomic approach.", "token_count": 394, "char_count": 1822, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6224, "quality_score": 0.8112, "entities": { "genes": [ "ST235", "ST773" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:48.083948", "source": { "split": "train_shard_00000", "doc_id": 834 }, "chunk_id": "train_shard_00000_834_0", "global_id": 923 }, { "text": "A clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II/ST5 methicillin-resistant Staphylococcus aureus (MRSA) to SCCmec type IV/clonal complex (CC)1 MRSA has occurred rapidly in Japan. Our previous research in a geriatric hospital found SCCmec type IV/CC1 MRSA prevalence in long-term care wards. Due to intensive personal care requirements, frequent contact with healthcare providers can potentially cause unintentional nosocomial MRSA transmission. We performed polymerase chain reaction-based open reading frame typing (POT) and core genome multilocus sequence typing (cgMLST) to investigate the occurrence of nosocomial transmission and to compare the results of these methods.\n\nComparison of the effectiveness of core genome multilocus sequence typing and polymerase chain reaction-based open reading frame typing in tracing nosocomial methicillin-resistant Staphylococcus aureus transmission.", "token_count": 230, "char_count": 919, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8361, "entities": { "genes": [ "ST5", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:48.556500", "source": { "split": "train_shard_00000", "doc_id": 835 }, "chunk_id": "train_shard_00000_835_0", "global_id": 924 }, { "text": "The human gut microbiome plays a pivotal role in health and disease, notably through its interaction with bile acids (BAs). BAs, synthesized in the liver, undergo transformation by the gut microbiota upon excretion into the intestine, thus influencing host metabolism. However, the potential mechanisms of dicaffeoylquinic acids (DiCQAs) from Ilex kudingcha how to modulate lipid metabolism and inflammation via gut microbiota remain unclear.\n\nAnti-diabetic effect of dicaffeoylquinic acids is associated with the modulation of gut microbiota and bile acid metabolism.", "token_count": 156, "char_count": 568, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7375, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:48.995762", "source": { "split": "train_shard_00000", "doc_id": 836 }, "chunk_id": "train_shard_00000_836_0", "global_id": 925 }, { "text": "The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from\n\nBiography of", "token_count": 103, "char_count": 467, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7746, "quality_score": 0.8873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:49.380006", "source": { "split": "train_shard_00000", "doc_id": 837 }, "chunk_id": "train_shard_00000_837_0", "global_id": 926 }, { "text": "Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests", "token_count": 495, "char_count": 1913, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5539, "quality_score": 0.777, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:50.033351", "source": { "split": "train_shard_00000", "doc_id": 838 }, "chunk_id": "train_shard_00000_838_0", "global_id": 927 }, { "text": "Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.\n\nComplete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp.", "token_count": 77, "char_count": 297, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:50.405802", "source": { "split": "train_shard_00000", "doc_id": 838 }, "chunk_id": "train_shard_00000_838_1", "global_id": 928 }, { "text": "The increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human-readable graph layout: a graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph's potential excessive size, this is a significant challenge.\n\nPangenome graph layout by Path-Guided Stochastic Gradient Descent.", "token_count": 119, "char_count": 537, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:50.794230", "source": { "split": "train_shard_00000", "doc_id": 839 }, "chunk_id": "train_shard_00000_839_0", "global_id": 929 }, { "text": "The gut microbiota and diet-induced changes in microbiome composition have been linked to various liver diseases, although the specific microbes and mechanisms remain understudied. Alcohol-related liver disease (ALD) is one such disease with limited therapeutic options due to its complex pathogenesis. We demonstrate that a diet rich in soluble dietary fiber increases the abundance of Bacteroides acidifaciens (B. acidifaciens) and alleviates alcohol-induced liver injury in mice. B. acidifaciens treatment alone ameliorates liver injury through a bile salt hydrolase that generates unconjugated bile acids to activate intestinal farnesoid X receptor (FXR) and its downstream target, fibroblast growth factor-15 (FGF15). FGF15 promotes hepatocyte expression of ornithine aminotransferase (OAT), which facilitates the metabolism of accumulated ornithine in the liver into glutamate, thereby providing sufficient glutamate for ammonia detoxification via the glutamine synthesis pathway. Collectively, these findings uncover a potential therapeutic strategy for ALD involving dietary fiber supplementation and B. acidifaciens.\n\nDietary fiber alleviates alcoholic liver injury via Bacteroides acidifaciens and subsequent ammonia detoxification.", "token_count": 325, "char_count": 1242, "word_count": 160, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [ "FGF15" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:51.368612", "source": { "split": "train_shard_00000", "doc_id": 840 }, "chunk_id": "train_shard_00000_840_0", "global_id": 930 }, { "text": "The nonconventional yeast Kluyveromyces marxianus has potential for industrial production, but the lack of advanced synthetic biology tools for precise engineering hinders its rapid development. Here, we introduce a CRISPR-Cas9-mediated multilocus integration method for assembling multiple exogenous genes. Using SlugCas9-HF, a high-fidelity Cas9 nuclease, we enhance gene editing precision. Specific genomic loci predisposed to efficient integration and expression of heterologous genes are identified and combined with a set of paired CRISPR-Cas9 expression plasmids and donor plasmids to establish a CRISPR-based biosynthesis toolkit. This toolkit enables genome integration of large gene modules over 12 kb and achieves simultaneous quadruple-locus integration in a single step with 20% efficiency. As a proof-of-concept, we apply the toolkit to screen for gene combinations that promote heme production, revealing the importance of HEM4Km and HEM12Sc. This CRISPR-based toolkit simplifies the reconstruction of complex pathways in K. marxianus, broadening its application in synthetic biology.\n\nEfficient and markerless gene integration with SlugCas9-HF in Kluyveromyces marxianus.", "token_count": 304, "char_count": 1187, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:51.934368", "source": { "split": "train_shard_00000", "doc_id": 841 }, "chunk_id": "train_shard_00000_841_0", "global_id": 931 }, { "text": "We report the results of taxonomic studies on members of the family Micrococcaceae that, according to the 16S rRNA, internal transcribed spacer 1 (ITS1), average nucleotide identity (ANI), and average amino acid identity (AAI) tests, are related to Kocuria rosea strain RCAM04488, a plant-growth-promoting rhizobacterium (PGPR) isolated from the rhizosphere of potato (Solanum tuberosum L.). In these studies, we used whole-genome phylogenetic tests and pangenomic analysis. According to the ANI > 95 % criterion, several known members of K. salina, K. polaris, and K. rosea (including K. rosea type strain ATCC 186T) that are related most closely to isolate RCAM04488 in the ITS1 test should be assigned to the same species with appropriate strain verification. However, these strains were isolated from strongly contrasting ecological and geographical habitats, which could not but affect their genotypes and phenotypes and which should be taken into account in evaluation of their systematic position. This contradiction was resolved by a pangenomic analysis, which showed that the strains differed strongly in the number of accessory and strain-specific genes determining their individuality and possibly their potential for adaptation to different ecological niches. Similar results were obtained in a full-scale AAI test against the UniProt database (about 250 million records), by using the AAI-profiler program and the proteome of K. rosea strain ATCC 186T as a query. According to the AAI > 65 % criterion, members of the genus Arthrobacter and several other genera belonging to the class Actinomycetes, with a very wide geographical and ecological range of sources of isolation, should be placed into the same genus as Kocuria. Within the paradigm with vertically inherited phylogenetic markers, this could be regarded as a signal for their following taxonomic reclassification. An important factor in this case may be the detailing of the gene composition of the strains and the taxonomic ratios resulting from analysis of the pangenomes of the corresponding clades.", "token_count": 511, "char_count": 2077, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5847, "quality_score": 0.7923, "entities": { "genes": [ "RCAM04488", "ITS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:52.584430", "source": { "split": "train_shard_00000", "doc_id": 842 }, "chunk_id": "train_shard_00000_842_0", "global_id": 932 }, { "text": "Phylogenetic and pangenomic analyses of members of the family Micrococcaceae related to a plant-growth-promoting rhizobacterium isolated from the rhizosphere of potato (Solanum tuberosum L.).", "token_count": 54, "char_count": 191, "word_count": 24, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:52.949265", "source": { "split": "train_shard_00000", "doc_id": 842 }, "chunk_id": "train_shard_00000_842_1", "global_id": 933 }, { "text": "Microbial pangenome analysis identifies present or absent genes in prokaryotic genomes. However, current tools are limited when analyzing species with higher sequence diversity or higher taxonomic orders such as genera or families. The Roary ILP Bacterial core Annotation Pipeline (RIBAP) uses an integer linear programming approach to refine gene clusters predicted by Roary for identifying core genes. RIBAP successfully handles the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, outperforming other established and recent pangenome tools for identifying all-encompassing core genes at the genus level. RIBAP is a freely available Nextflow pipeline at github.com/hoelzer-lab/ribap and zenodo.org/doi/10.5281/zenodo.10890871.\n\nRIBAP: a comprehensive bacterial core genome annotation pipeline for pangenome calculation beyond the species level.", "token_count": 223, "char_count": 884, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7345, "quality_score": 0.8673, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:53.416680", "source": { "split": "train_shard_00000", "doc_id": 843 }, "chunk_id": "train_shard_00000_843_0", "global_id": 934 }, { "text": "One major conundrum of modern microbiology is the large pangenome (gene pool) present in microbes, which is much larger than those found in complex organisms such as humans. Here, we argue that this diversity of gene pools carried by different strains is maintained largely due to the control exercised by viral predation. Viruses maintain a high strain diversity through time that we describe as constant-diversity equilibrium, preventing the hoarding of resources by specific clones. Thus, viruses facilitate the release and degradation of dissolved organic matter in the ocean, which may lead to better ecosystem functioning by linking top-down to bottom-up control. By maintaining this equilibrium, viruses act as a key element of the adaptation of marine microbes to their environment and likely behave as a single evolutionary unit.\n\nHow Viruses Shape Microbial Plankton Microdiversity.", "token_count": 192, "char_count": 892, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:53.860542", "source": { "split": "train_shard_00000", "doc_id": 844 }, "chunk_id": "train_shard_00000_844_0", "global_id": 935 }, { "text": "UCYN-A (Cand. Atelocyanobacterium thalassa) has recently been recognized as a globally-distributed, early stage, nitrogen-fixing organelle (the 'nitroplast') of cyanobacterial origin present in select species of haptophyte algae (e.g., Braarudosphaera bigelowii). Although the nitroplast was recognized as the UCYN-A2 sublineage, it is yet to be confirmed in other sublineages of the algal/UCYN-A complex. We used water samples collected from Halifax Harbour (Bedford Basin, Nova Scotia, Canada) and the offshore Scotian Shelf to further our understanding of B. bigelowii and UCYN-A in the coastal Northwest Atlantic. Sequencing data revealed UCYN-A-associated haptophyte signatures and yielded near-complete metagenome-assembled genomes (MAGs) for UCYN-A1, UCYN-A4, and the plastid of the A4-associated haptophyte. Comparative genomics provided new insights into the pangenome of UCYN-A. The UCYN-A4 MAG is the first genome sequenced from this sublineage and shares ~85% identity with the UCYN-A2 nitroplast. Genes missing in the reduced genome of the nitroplast were also missing in the A4 MAG supporting its likely classification as a nitroplast as well. The UCYN-A1 MAG was found to be nearly 100% identical to the reference genome despite coming from different ocean basins. Time-series data paired with the recurrence of specific microbes in enrichment cultures gave insight into the microbes that frequently co-occur with the algal/UCYN-A complex (e.g., Pelagibacter ubique). Overall, our study expands knowledge of UCYN-A and its host across major ocean basins and investigates their co-occurring microbes in the coastal Northwest Atlantic (NWA), thereby facilitating future studies on the underpinnings of haptophyte-associated diazotrophy in the sea.", "token_count": 507, "char_count": 1760, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6735, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:54.491166", "source": { "split": "train_shard_00000", "doc_id": 845 }, "chunk_id": "train_shard_00000_845_0", "global_id": 936 }, { "text": "Targeted metagenomics reveals pangenomic diversity of the nitroplast (UCYN-A) and its algal host plastid.", "token_count": 32, "char_count": 105, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:54.853325", "source": { "split": "train_shard_00000", "doc_id": 845 }, "chunk_id": "train_shard_00000_845_1", "global_id": 937 }, { "text": "Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. In this study, we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for\n\nCofitness network connectivity determines a fuzzy essential zone in open bacterial pangenome.", "token_count": 104, "char_count": 478, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:55.236057", "source": { "split": "train_shard_00000", "doc_id": 846 }, "chunk_id": "train_shard_00000_846_0", "global_id": 938 }, { "text": "Infants have digestive environments that are more favorable for microbial proliferation and subsequent endogenous nitrite production than those of adults, but direct evidence of this has been lacking. In this study, we propose a novel epidemiology of infant methemoglobinemia by demonstrating the risk posed by nitrite-producers in the gastrointestinal tract. Nitrite-producers from vegetables (n = 323) were exposed to stress factors of the gastrointestinal environment (gastric pH, intestinal bile salts, anaerobic atmosphere) reflecting 4 different postnatal age periods (Neonate, ≤1 month; Infant A, 1-3 months; Infant B, 3-6 months; Infant C, 6-12 months). \"High-risk\" strains with a nitrate-to-nitrite conversion rate of ≥1.3 %, the minimum rate corresponding to nitrite overproduction, under the Neonate stress condition were analyzed for intestinal adhesion. Among all the phyla, Pseudomonadota achieved the highest survival (P < 0.05; survival rate of 51.3-71.8 %). Possible cross-protection against bile resistance due to acid shock was observed for all the phyla. All the high-risk strains exhibited moderate autoaggregation (14.0-36.4 %), whereas only a few exhibited satisfactory surface hydrophobicity (>40 %). The Pantoea agglomerans strain strongly adhered to Caco-2 cells (7.4 ± 1.1 %). This study showed the ability of the Pantoea, Enterobacter, and Klebsiella strains to survive under gastrointestinal stress for ≤12 months, to excessively produce nitrite under neonatal stress conditions, and to settle in the human intestine. To our knowledge, this is the first study to reveal the role of the natural flora of vegetables in the epidemiology of infant methemoglobinemia through a multilateral approach.", "token_count": 491, "char_count": 1723, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:55.879932", "source": { "split": "train_shard_00000", "doc_id": 847 }, "chunk_id": "train_shard_00000_847_0", "global_id": 939 }, { "text": "Novel hypothesis for infant methemoglobinemia: Survival and metabolism of nitrite-producers from vegetables under gastrointestinal stress and intestinal adhesion.", "token_count": 45, "char_count": 162, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:56.243170", "source": { "split": "train_shard_00000", "doc_id": 847 }, "chunk_id": "train_shard_00000_847_1", "global_id": 940 }, { "text": "Cronobacter sakazakii, an opportunity foodborne pathogen, could contaminate a broad range of food materials and cause life-threatening symptoms in infants. The bacterial envelope structure contribute to bacterial environment tolerance, biofilm formation and virulence in various in Gram-negative bacteria. DsbA and PepP are two important genes related to the biogenesis and stability of bacterial envelope. In this study, the DsbA and PepP were deleted in C. sakazakii to evaluate their contribution to stress tolerance and virulence of the pathogen. The bacterial environment resistance assays showed DsbA and PepP are essential in controlling C. sakazakii resistance to heat and desiccation in different mediums, as well as acid, osmotic, oxidation and bile salt stresses. DsbA and PepP also played an important role in regulating biofilm formation and motility. Furthermore, DsbA and PepP deletion weaken C. sakazakii adhesion and invasion in Caco-2, intracellular survival and replication in RAW 264.7. qRT-PCR results showed that DsbA and PepP of C. sakazakii played roles in regulating the expression of several genes associated with environment stress tolerance, biofilm formation, bacterial motility and cellular invasion. These findings indicate that DsbA and PepP played an important regulatory role in the environment resisitance, biofilm formation and virulence of C. sakazakii, which enrich understanding of genetic determinants of adaptability and virulence of the pathogen.\n\nThe role of DsbA and PepP genes in the environmental tolerance and virulence factors of Cronobacter sakazakii.", "token_count": 401, "char_count": 1600, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5022, "quality_score": 0.7511, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:56.886322", "source": { "split": "train_shard_00000", "doc_id": 848 }, "chunk_id": "train_shard_00000_848_0", "global_id": 941 }, { "text": "The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses.\n\nThe black honey bee genome: insights on specific structural elements and a first step towards pangenomes.", "token_count": 175, "char_count": 791, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7434, "quality_score": 0.8717, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:57.380486", "source": { "split": "train_shard_00000", "doc_id": 849 }, "chunk_id": "train_shard_00000_849_0", "global_id": 942 }, { "text": "Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.\n\nThe origins of haplotype 58 (H58) Salmonella enterica serovar Typhi.", "token_count": 448, "char_count": 1900, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:58.050151", "source": { "split": "train_shard_00000", "doc_id": 850 }, "chunk_id": "train_shard_00000_850_0", "global_id": 943 }, { "text": "Campylobacter jejuni is one of the major causes of bacterial gastrointestinal disease in humans worldwide. This foodborne pathogen colonizes the intestinal tracts of chickens, and consumption of chicken and poultry products is identified as a common route of transmission. We analyzed two C. jejuni strains after oral challenge with 10\n\nPhenotypic, genotypic and proteomic variations between poor and robust colonizing Campylobacter jejuni strains.", "token_count": 107, "char_count": 448, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:58.874514", "source": { "split": "train_shard_00000", "doc_id": 851 }, "chunk_id": "train_shard_00000_851_0", "global_id": 944 }, { "text": "Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past methods for signal-based classification do not scale efficiently to large, repetitive references like pangenomes, limiting their utility to partial references or individual genomes. We introduce Sigmoni: a rapid, multiclass classification method based on the r-index that scales to references of hundreds of Gbps. Sigmoni quantizes nanopore signal into a discrete alphabet of picoamp ranges. It performs rapid, approximate matching using matching statistics, classifying reads based on distributions of picoamp matching statistics and co-linearity statistics, all in linear query time without the need for seed-chain-extend. Sigmoni is 10-100× faster than previous methods for adaptive sampling in host depletion experiments with improved accuracy, and can query reads against large microbial or human pangenomes. Sigmoni is the first signal-based tool to scale to a complete human genome and pangenome while remaining fast enough for adaptive sampling applications.\n\nSigmoni: classification of nanopore signal with a compressed pangenome index.", "token_count": 277, "char_count": 1308, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:06:59.431886", "source": { "split": "train_shard_00000", "doc_id": 852 }, "chunk_id": "train_shard_00000_852_0", "global_id": 945 }, { "text": "The low-carbohydrate ketogenic diet (KD) has long been practiced for weight loss, but the underlying mechanisms remain elusive. Gut microbiota and metabolites have been suggested to mediate the metabolic changes caused by KD consumption, although the particular gut microbes or metabolites involved are unclear. Here, we show that KD consumption enhances serum levels of taurodeoxycholic acid (TDCA) and tauroursodeoxycholic acid (TUDCA) in mice to decrease body weight and fasting glucose levels. Mechanistically, KD feeding decreases the abundance of a bile salt hydrolase (BSH)-coding gut bacterium, Lactobacillus murinus ASF361. The reduction of L. murinus ASF361 or inhibition of BSH activity increases the circulating levels of TDCA and TUDCA, thereby reducing energy absorption by inhibiting intestinal carbonic anhydrase 1 expression, which leads to weight loss. TDCA and TUDCA treatments have been found to protect against obesity and its complications in multiple mouse models. Additionally, the associations among the abovementioned bile acids, microbial BSH and metabolic traits were consistently observed both in an observational study of healthy human participants (n = 416) and in a low-carbohydrate KD interventional study of participants who were either overweight or with obesity (n = 25). In summary, we uncover a unique host-gut microbiota metabolic interaction mechanism for KD consumption to decrease body weight and fasting glucose levels. Our findings support TDCA and TUDCA as two promising drug candidates for obesity and its complications in addition to a KD.\n\nKetogenic diet-induced bile acids protect against obesity through reduced calorie absorption.", "token_count": 441, "char_count": 1681, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "ASF361" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:00.062196", "source": { "split": "train_shard_00000", "doc_id": 853 }, "chunk_id": "train_shard_00000_853_0", "global_id": 946 }, { "text": "Enteroaggregative Escherichia coli (EAEC) strains including those of serogroup O111 are important causes of diarrhea in children. In the Czech Republic, no information is available on the etiological role of EAEC in pediatric diarrhea due to the lack of their targeted surveillance. To fill this gap, we determined the proportion of EAEC among E. coli O111 isolates from children with gastrointestinal disorders ≤ 2 years of age submitted to the National Reference Laboratory for E. coli and Shigella during 2013-2022. EAEC accounted for 177 of 384 (46.1 %) E. coli O111 isolates, being the second most frequent E. coli O111 pathotype. Most of them (75.7 %) were typical EAEC that carried aggR, usually with aaiC and aatA marker genes; the remaining 24.3 % were atypical EAEC that lacked aggR but carried aaiC and/or aatA. Whole genome sequencing of 11 typical and two atypical EAEC O111 strains demonstrated differences in serotypes, sequence types (ST), virulence gene profiles, and the core genomes between these two groups. Typical EAEC O111:H21/ST40 strains resembled by their virulence profiles including the presence of the aggregative adherence fimbriae V (AAF/V)-encoding cluster to such strains from other countries and clustered with them in the core genome multilocus sequence typing (cgMLST). Atypical EAEC O111:H12/ST10 strains lacked virulence genes of typical EAEC and differed from them in cgMLST. All tested EAEC O111 strains displayed stacked-brick aggregative adherence to human intestinal epithelial cells. The AAF/V-encoding cluster was located on a plasmid of 95,749 bp or 93,286 bp (pAA", "token_count": 513, "char_count": 1610, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [ "ST10", "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:07:00.721433", "source": { "split": "train_shard_00000", "doc_id": 854 }, "chunk_id": "train_shard_00000_854_0", "global_id": 947 }, { "text": "Enteroaggregative Escherichia coli: Frequent, yet underdiagnosed pathotype among E. coli O111 strains isolated from children with gastrointestinal disorders in the Czech Republic.", "token_count": 50, "char_count": 179, "word_count": 22, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:01.081331", "source": { "split": "train_shard_00000", "doc_id": 854 }, "chunk_id": "train_shard_00000_854_1", "global_id": 948 }, { "text": "Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility.\n\nIdentification of transposable element families from pangenome polymorphisms.", "token_count": 151, "char_count": 750, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7768, "quality_score": 0.8884, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:01.519129", "source": { "split": "train_shard_00000", "doc_id": 856 }, "chunk_id": "train_shard_00000_856_0", "global_id": 949 }, { "text": "The global landscape of Candida infections has seen a significant shift. Previously, Candida albicans was the predominant species. However, there has been an emergence of non-albicans Candida species, which are often less susceptible to antifungal treatment. Candida kefyr, in particular, has been increasingly associated with infections. This study aimed to investigate the profiles of enzymatic activity and biofilm formation in both clinical and non-clinical isolates of C. kefyr. A total of 66 C. kefyr isolates were analysed. The activities of proteinase and phospholipase were assessed using bovine serum albumin and egg yolk agar, respectively. Haemolysin, caseinolytic and esterase activities were evaluated using specific methods. Biofilm formation was investigated using crystal violet staining. The findings indicated that biofilm and proteinase activity were detected in 81.8% and 93.9% of all the isolates, respectively. Haemolysin activity was observed with the highest occurrence (95.5%) among normal microbiota isolates. Esterase activity was predominantly identified in dairy samples and was absent in hospital samples. Caseinase production was found with the highest occurrence (18.2%) in normal microbiota and hospital samples. Phospholipase activity was limited, found in only 3% of all the isolates. These findings reveal variations in enzyme activity between clinical and non-clinical C. kefyr isolates. This sheds light on their pathogenic potential and has implications for therapeutic strategies.\n\nComparative analysis of enzymatic profiles and biofilm formation in clinical and environmental Candida kefyr isolates.", "token_count": 389, "char_count": 1641, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5727, "quality_score": 0.7863, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:02.136017", "source": { "split": "train_shard_00000", "doc_id": 857 }, "chunk_id": "train_shard_00000_857_0", "global_id": 950 }, { "text": "Single-domain antibodies (sdAbs), such as V\n\nFit-for-purpose heterodivalent single-domain antibody for gastrointestinal targeting of toxin B from Clostridium difficile.", "token_count": 52, "char_count": 168, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:02.511395", "source": { "split": "train_shard_00000", "doc_id": 858 }, "chunk_id": "train_shard_00000_858_0", "global_id": 951 }, { "text": "The aim of this study was to evaluate the effectiveness of nine different biological compounds to reduce mycotoxins concentrations. The hypothesis of this study was that a static in vitro gastrointestinal tract model, as an initial screening tool, can be used to simulate the efficacy of\n\nExploring the Efficacy of Using", "token_count": 74, "char_count": 320, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7255, "quality_score": 0.8627, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:02.878513", "source": { "split": "train_shard_00000", "doc_id": 859 }, "chunk_id": "train_shard_00000_859_0", "global_id": 952 }, { "text": "Recombinant Bile Salt Hydrolase Enhances the Inhibition Efficiency of Taurodeoxycholic Acid against", "token_count": 31, "char_count": 99, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:03.240898", "source": { "split": "train_shard_00000", "doc_id": 860 }, "chunk_id": "train_shard_00000_860_0", "global_id": 953 }, { "text": "Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. Yet WGDs are hugely disruptive mutations, and we still lack a clear understanding of their fitness consequences. Here, we study whether WGDs result in greater diversity of genomic structural variants (SVs) and how they influence evolutionary dynamics in a plant genus, Cochlearia (Brassicaceae). By using long-read sequencing and a graph-based pangenome, we find both negative and positive interactions between WGDs and SVs. Masking of recessive mutations due to WGDs leads to a progressive accumulation of deleterious SVs across four ploidal levels (from diploids to octoploids), likely reducing the adaptive potential of polyploid populations. However, we also discover putative benefits arising from SV accumulation, as more ploidy-specific SVs harbor signals of local adaptation in polyploids than in diploids. Together, our results suggest that SVs play diverse and contrasting roles in the evolutionary trajectories of young polyploids.\n\nImpact of whole-genome duplications on structural variant evolution in Cochlearia.", "token_count": 270, "char_count": 1126, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7547, "quality_score": 0.8774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:03.795227", "source": { "split": "train_shard_00000", "doc_id": 862 }, "chunk_id": "train_shard_00000_862_0", "global_id": 954 }, { "text": "Leptospirosis is a zoonotic disease caused by the pathogenic spirochaetes of the genus Leptospira. It is a public health concern in the Pacific Islands and is considered endemic in Palau. However, information on the genotypes and serotypes of causative Leptospira spp. in the country is limited. In this study, we isolated leptospires and detected antileptospiral antibodies in dogs and pigs. The isolates were characterized using a serological method and whole-genome sequencing. Leptospira interrogans was isolated from five of the 20 symptomatic dogs and one of the 58 healthy pigs. Their serogroups were identified as Icterohaemorrhagiae and Pyrogenes; however, the serogroup of one isolate could not be determined. Anti-Leptospira antibodies were detected in 14.4% (26/181) of the dogs and 20% (10/50) of the pigs. The reactive serogroups in dogs and pigs were almost identical, except for the Panama serogroup. Core genome multilocus sequence typing revealed that five of the six core genome sequence types (cgSTs) were newly identified in this study. The cgSTs from the serogroup Icterohaemorrhagiae isolates belonged to the same group as the Copenhageni and Icterohaemorrhagiae serovars isolated in other countries, whereas no similar cgSTs were identified in the Pyrogenes or unidentified serogroup strains. We demonstrated a high incidence of canine and porcine leptospirosis and identified new L. interrogans genotypes (cgSTs) circulating in Palau. Further investigations are needed to determine whether dogs and pigs serve as maintenance hosts for newly identified L. interrogans genotypes and whether they pose a risk of leptospirosis transmission to humans.\n\nBacteriological and Serological Investigation of Leptospirosis in Dogs and Pigs in Palau.", "token_count": 480, "char_count": 1762, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5349, "quality_score": 0.7674, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:04.448390", "source": { "split": "train_shard_00000", "doc_id": 863 }, "chunk_id": "train_shard_00000_863_0", "global_id": 955 }, { "text": "In the context of modern aquaculture, the effort to reduce the reliance on fishmeal/marine ingredients in fish diets has led to the exploration of plant-based protein sources as potential substitutes, a dietary shift that disrupts the bile acid profile in fish. Therefore, bile salts are being sought as additives. However, artificially increased intestinal levels of bile acids may significantly impact mucosal function. Therefore, here, we explored the regulatory role in the intestine of gilthead sea bream (Sparus aurata) of (i) chenodeoxycholic acid (CDC), (ii) a mixture formed by two bile acids, 3% cholic acid and 97% deoxycholic acid (MIX), and (iii) a conjugated bile salt sodium taurocholate (TC) in Ussing chambers with the epithelial voltage clamp technique. We tested the bile salts in a 50-500 μg/ml concentration range, and all of them promoted ion absorption. Yet, clear concentration-dependent and more pronounced effects on the ion transport were observed in the posterior intestine. On the other hand, bile salts had no or minor effects on tissue resistance. However, there are indications that the MIX could have adverse effects at high concentrations (500 μg/ml), promoting a threefold increase in tissue permeability measured using FITC-dextran (4 kD) regardless of the intestinal region, thus suggesting an alteration in intestinal permeability at high bile salt concentrations. The findings from our study emphasize the importance of considering intestinal function when contemplating the possible use of a particular bile salt as a dietary supplement. It appears that bile salts, whether acting individually or in combination, play a pivotal role in orchestrating nutrient absorption by influencing the function of epithelial ion transport. However further research is needed to fully grasp the region-dependent nuances of bile salt effects on ion transport and the ultimate consequences for nutrient absorption in the context of fish aquaculture.\n\nEffect of bile salts on intestinal epithelial function in gilthead seabream (Sparus aurata).", "token_count": 510, "char_count": 2067, "word_count": 308, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:05.103257", "source": { "split": "train_shard_00000", "doc_id": 864 }, "chunk_id": "train_shard_00000_864_0", "global_id": 956 }, { "text": "The presence of intermittently dispersed insertion sequences and transposases in the\n\nPangenome-wide association study reveals the selective absence of CRISPR genes (Rv2816c-19c) in drug-resistant", "token_count": 54, "char_count": 196, "word_count": 24, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:05.475484", "source": { "split": "train_shard_00000", "doc_id": 865 }, "chunk_id": "train_shard_00000_865_0", "global_id": 957 }, { "text": "In recent years, there has been increasing interest in studying gut microbiome-derived hydrolases in relation to oral drug metabolism, particularly focusing on natural product drugs. Despite the significance of natural product drugs in the field of oral medications, there is a lack of research on the regulatory interplay between gut microbiome-derived hydrolases and these drugs. This review delves into the interaction between intestinal microbiome-derived hydrolases and natural product drugs metabolism from three key perspectives. Firstly, it examines the impact of glycoside hydrolases, amide hydrolases, carboxylesterase, bile salt hydrolases, and epoxide hydrolase on the structure of natural products. Secondly, it explores how natural product drugs influence microbiome-derived hydrolases. Lastly, it analyzes the impact of interactions between hydrolases and natural products on disease development and the challenges in developing microbial-derived enzymes. The overarching goal of this review is to lay a solid theoretical foundation for the advancement of research and development in new natural product drugs and personalized treatment.\n\nGut microbiome-derived hydrolases-an underrated target of natural product metabolism.", "token_count": 275, "char_count": 1239, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5663, "quality_score": 0.7831, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:06.023544", "source": { "split": "train_shard_00000", "doc_id": 866 }, "chunk_id": "train_shard_00000_866_0", "global_id": 958 }, { "text": "Activating the glucagon-like peptide-1 (GLP-1) receptor by oral nucleic acid delivery would be a promising treatment strategy against hyperglycemia due to its various therapeutic actions. However, GLP-1 receptor agonists are effective only in subcutaneous injections because they face multiple barriers due to harsh gastrointestinal tract (GIT) conditions before reaching the site of action. The apical sodium bile acid transporter (ASBT) pathway at the intestinal site could be an attractive target to overcome the problem. Herein, we used our previously established multimodal carrier system utilizing bile salt, protamine sulfate, and calcium phosphate as excipients (PTCA) and the GLP-1 gene as an active ingredient (GENE) to test the effects of different formulation doses against diabetes and obesity. The carrier system demonstrated the ability to protect the GLP-1 model gene encoded within the plasmid at the GIT and transport it\n\nEnhancing the Therapeutic Efficacy of GLP-1 for Hyperglycemia Treatment: Overcoming Barriers of Oral Gene Therapy with Taurocholic Acid-Conjugated Protamine Sulfate and Calcium Phosphate.", "token_count": 290, "char_count": 1127, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7125, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:06.588744", "source": { "split": "train_shard_00000", "doc_id": 867 }, "chunk_id": "train_shard_00000_867_0", "global_id": 959 }, { "text": "Taurine is a sulfur-containing amino acid found in many cell organelles that plays a wide range of biological roles, including bile salt production, osmoregulation, oxidative stress reduction, and neuromodulation. Taurine treatments have also been shown to ameliorate the onset and development of many diseases, including hypertension, fatty liver, neurodegenerative diseases and ischemia-reperfusion injury, by exerting antioxidant, anti-inflammatory, and antiapoptotic effects. The endoplasmic reticulum (ER) is a dynamic organelle involved in a wide range of cellular functions, including lipid metabolism, calcium storage and protein stabilization. Under stress, the disruption of the ER environment leads to the accumulation of misfolded proteins and a characteristic stress response called the unfolded protein response (UPR). The UPR protects cells from stress and helps to restore cellular homeostasis, but its activation promotes cell death under prolonged ER stress. Recent studies have shown that ER stress is closely related to the onset and development of many diseases. This article reviews the beneficial effects and related mechanisms of taurine by regulating the ER in different physiological and pathological states, with the aim of providing a reference for further research and clinical applications.\n\nThe role of taurine through endoplasmic reticulum in physiology and pathology.", "token_count": 317, "char_count": 1400, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:07.146686", "source": { "split": "train_shard_00000", "doc_id": 868 }, "chunk_id": "train_shard_00000_868_0", "global_id": 960 }, { "text": "Triptolide (TP) is the principal bioactive compound of Tripterygium wilfordii with significant anti-tumor, anti-inflammatory and immunosuppressive activities. However, its severe hepatotoxicity greatly limits its clinical use. The underlying mechanism of TP-induced liver damage is still poorly understood. Here, we estimate the role of the gut microbiota in TP hepatotoxicity and investigate the bile acid metabolism mechanisms involved. The results of the antibiotic cocktail (ABX) and fecal microbiota transplantation (FMT) experiment demonstrate the involvement of intestinal flora in TP hepatotoxicity. Moreover, TP treatment significantly perturbed gut microbial composition and reduced the relative abundances of Lactobacillus rhamnosus GG (LGG). Supplementation with LGG reversed TP-induced hepatotoxicity by increasing bile salt hydrolase (BSH) activity and reducing the increased conjugated bile acids (BA). LGG supplementation upregulates hepatic FXR expression and inhibits NLRP3 inflammasome activation in TP-treated mice. In summary, this study found that gut microbiota is involved in TP hepatotoxicity. LGG supplementation protects mice against TP-induced liver damage. The underlying mechanism was associated with the gut microbiota-BA-FXR axis. Therefore, LGG holds the potential to prevent and treat TP hepatotoxicity in the clinic.\n\nLactobacillus rhamnosus GG ameliorates triptolide-induced liver injury through modulation of the bile acid-FXR axis.", "token_count": 386, "char_count": 1469, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6492, "quality_score": 0.8246, "entities": { "genes": [ "NLRP3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:07.767275", "source": { "split": "train_shard_00000", "doc_id": 869 }, "chunk_id": "train_shard_00000_869_0", "global_id": 961 }, { "text": "The study focuses on the in silico genomic characterization of Sphingobium indicum B90A, revealing a wealth of genes involved in stress response, carbon monoxide oxidation, β-carotene biosynthesis, heavy metal resistance, and aromatic compound degradation, suggesting its potential as a bioremediation agent. Furthermore, genomic adaptations among nine Sphingomonad strains were explored, highlighting shared core genes via pangenome analysis, including those related to the shikimate pathway and heavy metal resistance. The majority of genes associated with aromatic compound degradation, heavy metal resistance, and stress response were found within genomic islands across all strains. Sphingobium indicum UT26S exhibited the highest number of genomic islands, while Sphingopyxis alaskensis RB2256 had the maximum fraction of its genome covered by genomic islands. The distribution of lin genes varied among the strains, indicating diverse genetic responses to environmental pressures. Additionally, in silico evidence of horizontal gene transfer (HGT) between plasmids pSRL3 and pISP3 of the Sphingobium and Sphingomonas genera, respectively, has been provided. The manuscript offers novel insights into strain B90A, highlighting its role in horizontal gene transfer and refining evolutionary relationships among Sphingomonad strains. The discovery of stress response genes and the czcABCD operon emphasizes the potential of Sphingomonads in consortia development, supported by genomic island analysis.\n\nIn Silico Analysis of the Phylogenetic and Physiological Characteristics of Sphingobium indicum B90A: A Hexachlorocyclohexane-Degrading Bacterium.", "token_count": 396, "char_count": 1653, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8157, "entities": { "genes": [ "RB2256", "UT26S" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:08.384894", "source": { "split": "train_shard_00000", "doc_id": 870 }, "chunk_id": "train_shard_00000_870_0", "global_id": 962 }, { "text": "Strangles is a globally widespread, commonly diagnosed and important infectious disease of equids caused by Streptococcus equi subsp. equi. We performed whole genome sequencing of 19 S. equi isolates collected from imported horses at the Japanese border. Of these isolates, 15 isolates were obtained from clinical cases and 4 were from subclinical cases. The 19 isolates were grouped into 3 Bayesian analysis of population structure (BAPS) groups by the core genome single nucleotide polymorphism analysis corresponding to exporting country, SeM typing, or exporter of the horses. The 19 isolates possessed same pathogenic genes regardless of clinical status in imported horses and no antimicrobial resistance genes. The disease status of the horses may rather reflect the prior exposure of animals with sub-clinical infection to S. equi.\n\nGenetic analysis based on next generation sequencing of Streptococcus equi subsp. equi isolated from horses imported into Japan.", "token_count": 227, "char_count": 968, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:08.883264", "source": { "split": "train_shard_00000", "doc_id": 871 }, "chunk_id": "train_shard_00000_871_0", "global_id": 963 }, { "text": "The gut microbiota plays a crucial role in postnatal growth, particularly in modulating the development of animals during their growth phase. In this study, we investigated the effects of antibiotic-induced dysbiosis of the gut microbiota on the growth of weaning rats by administering a non-absorbable antibiotic cocktail (ABX) in water for 4 weeks. ABX treatment significantly reduced body weight and feed intake in rats. Concurrently, ABX treatment decreased microbial abundance and diversity in rat ceca, predominantly suppressing microbes associated with bile salt hydrolase (BSH) activity. Furthermore, decreased appetite may be attributed to elevated levels of glucagon-like peptide-1 (GLP-1) in the serum, along with reduced neuropeptide Y (NPY) and increased cocaine and amphetamine-regulated transcript (CART) in the hypothalamus at the mRNA level. Importantly, concentrations of insulin-like growth factor 1 (IGF-1) and insulin-like growth factor 2 (IGF-2) were decreased in the serum and liver of antibiotic-treated rats. These alterations were associated with significant down-regulation of IGF-2 mRNA in the liver and significantly decreased farnesoid X receptor (FXR) protein expression and binding to the IGF-2 promoter. These results indicate that antibiotic-induced gut microbial dysbiosis not only impacts bile acid metabolism but also diminishes rat growth through the FXR-mediated IGF-2 pathway.\n\nAntibiotic-Induced Gut Microbial Dysbiosis Reduces the Growth of Weaning Rats via FXR-Mediated Hepatic IGF-2 Inhibition.", "token_count": 418, "char_count": 1538, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6321, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:09.530032", "source": { "split": "train_shard_00000", "doc_id": 872 }, "chunk_id": "train_shard_00000_872_0", "global_id": 964 }, { "text": "The gut microbiome possesses numerous biochemical enzymes that biosynthesize metabolites that impact human health. Bile acids comprise a diverse collection of metabolites that have important roles in metabolism and immunity. The gut microbiota-associated enzyme that is responsible for the gateway reaction in bile acid metabolism is bile salt hydrolase (BSH), which controls the host's overall bile acid pool. Despite the critical role of these enzymes, the ability to profile their activities and substrate preferences remains challenging due to the complexity of the gut microbiota, whose metaproteome includes an immense diversity of protein classes. Using a systems biochemistry approach employing activity-based probes, we have identified gut microbiota-associated BSHs that exhibit distinct substrate preferences, revealing that different microbes contribute to the diversity of the host bile acid pool. We envision that this chemoproteomic approach will reveal how secondary bile acid metabolism controlled by BSHs contributes to the etiology of various inflammatory diseases.\n\nChemoproteomic profiling of substrate specificity in gut microbiota-associated bile salt hydrolases.", "token_count": 272, "char_count": 1186, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:10.117852", "source": { "split": "train_shard_00000", "doc_id": 873 }, "chunk_id": "train_shard_00000_873_0", "global_id": 965 }, { "text": "Metabolic dysfunction-associated steatotic liver disease (MASLD) has a multifactorial and complex pathogenesis. Notably, the disorder of Bile acid (BA) metabolism and lipid metabolism-induced lipotoxicity are the main risk factors of MASLD. Lupeol, traditional regional medicine from Xinjiang, has a long history of use for its anti-inflammatory, anti-tumor, and immune-modulating properties. Recent research suggests its potential as a therapeutic option for MASLD due to its proposed binding capacity to the nuclear BA receptor, Farnesoid X receptor (FXR), hence could represent a therapeutic option for MASLD. In this study, a natural triterpenoid drug lupeol improved BA metabolism and MASLD in mice through the FXR signaling pathway and the gut-liver axis. Furthermore, lupeol effectively restored gut healthiness and improved intestinal immunity, barrier integrity, and inflammation, as indicated by the reconstructed gut flora. Compared with fenofibrate (Feno), lupeol treatment significantly reduced weight gain, fat deposition, and liver injury, decreased serum total cholesterol (TC) and triglyceride (TG) levels, and alleviated hepatic steatosis and liver inflammation. BA analysis showed that lupeol treatment accelerated BA efflux and decreased uptake of BA by increasing hepatic FXR and bile salt export pump (BSEP) expression. Gut microbiota alterations could be related to enhanced fecal BA excretion in lupeol-treated mice. Therefore, consumption of lupeol may prevent HFD-induced MASLD and BA accumulation, possibly via the FXR signaling pathway and regulating the gut microbiota.\n\nLupeol improves bile acid metabolism and metabolic dysfunction-associated steatotic liver disease in mice via FXR signaling pathway and gut-liver axis.", "token_count": 460, "char_count": 1751, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:10.768417", "source": { "split": "train_shard_00000", "doc_id": 874 }, "chunk_id": "train_shard_00000_874_0", "global_id": 966 }, { "text": "Genomics has revolutionized how we characterize and monitor infectious diseases for public health. The surveillance and characterization of Salmonella has improved drastically within the past decade. In this chapter, we discuss the prerequisites for good bacterial genomics studies and make note of advantages and disadvantages of this research approach. We discuss methods for outbreak detection and the evolutionary and epidemiological characterization of Salmonella spp. We provide an outline for determining the sequence type and serotype of isolates, building a core genome phylogenetic tree, and detecting antimicrobial resistance genes, virulence factors, and mobile genetic elements. These methods can be used to study other pathogenic bacterial species.\n\nMethods for Genomic Epidemiology of Bacterial Pathogens: Example Salmonella.", "token_count": 179, "char_count": 840, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7018, "quality_score": 0.8509, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:11.215808", "source": { "split": "train_shard_00000", "doc_id": 875 }, "chunk_id": "train_shard_00000_875_0", "global_id": 967 }, { "text": "Dusky kob (Argyrosomus japonicus) is a commercially important finfish, indigenous to South Africa, Australia, and China. Previous studies highlighted differences in genetic composition, life history, and morphology of the species across geographic regions. A draft genome sequence of 0.742 Gb (N50 = 5.49 Mb; BUSCO completeness = 97.8%) and 22,438 predicted protein-coding genes was generated for the South African (SA) conspecific. A comparison with the Chinese (CN) conspecific revealed a core set of 32,068 orthologous protein clusters across both genomes. The SA genome exhibited 440 unique clusters compared to 1928 unique clusters in the CN genome. Transportation and immune response processes were overrepresented among the SA accessory genome, whereas the CN accessory genome was enriched for immune response, DNA transposition, and sensory detection (FDR-adjusted p < 0.01). These unique clusters may represent an adaptive component of the species' pangenome that could explain population divergence due to differential environmental specialisation. Furthermore, 700 single-copy orthologues (SCOs) displayed evidence of positive selection between the SA and CN genomes, and globally these genomes shared only 92% similarity, suggesting they might be distinct species. These genes primarily play roles in metabolism and digestion, illustrating the evolutionary pathways that differentiate the species. Understanding these genomic mechanisms underlying adaptation and evolution within and between species provides valuable insights into growth and maturation of kob, traits that are particularly relevant to commercial aquaculture.\n\nComparative genomics of dusky kob (Argyrosomus japonicus, Sciaenidae) conspecifics: Evidence for speciation and the genetic mechanisms underlying traits.", "token_count": 447, "char_count": 1793, "word_count": 243, "semantic_coherence": 1, "information_density": 0.7078, "quality_score": 0.8539, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:11.845898", "source": { "split": "train_shard_00000", "doc_id": 876 }, "chunk_id": "train_shard_00000_876_0", "global_id": 968 }, { "text": "Tea, one of the most widely consumed beverages globally, exhibits remarkable genomic diversity in its underlying flavour and health-related compounds. In this study, we present the construction and analysis of a tea pangenome comprising a total of 11 genomes, with a focus on three newly sequenced genomes comprising the purple-leaved assamica cultivar \"Zijuan\", the temperature-sensitive sinensis cultivar \"Anjibaicha\" and the wild accession \"L618\" whose assemblies exhibited excellent quality scores as they profited from latest sequencing technologies. Our analysis incorporates a detailed investigation of transposon complement across the tea pangenome, revealing shared patterns of transposon distribution among the studied genomes and improved transposon resolution with long read technologies, as shown by long terminal repeat (LTR) Assembly Index analysis. Furthermore, our study encompasses a gene-centric exploration of the pangenome, exploring the genomic landscape of the catechin pathway with our study, providing insights on copy number alterations and gene-centric variants, especially for Anthocyanidin synthases. We constructed a gene-centric pangenome by structurally and functionally annotating all available genomes using an identical pipeline, which both increased gene completeness and allowed for a high functional annotation rate. This improved and consistently annotated gene set will allow for a better comparison between tea genomes. We used this improved pangenome to capture the core and dispensable gene repertoire, elucidating the functional diversity present within the tea species. This pangenome resource might serve as a valuable resource for understanding the fundamental genetic basis of traits such as flavour, stress tolerance, and disease resistance, with implications for tea breeding programmes.\n\nIn-depth exploration of the genomic diversity in tea varieties based on a newly constructed pangenome of Camellia sinensis.", "token_count": 419, "char_count": 1962, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:12.471697", "source": { "split": "train_shard_00000", "doc_id": 877 }, "chunk_id": "train_shard_00000_877_0", "global_id": 969 }, { "text": "Bile salt hydrolases (BSHs) are enzymes that are essential for the enterohepatic metabolism of bile acids (BAs). BSHs catalyze the production of unconjugated BAs and regulate the homeostasis of BA pool. This study identified\n\nTaxonomic identification of bile salt hydrolase-encoding lactobacilli: Modulation of the enterohepatic bile acid profile.", "token_count": 103, "char_count": 347, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7292, "quality_score": 0.8646, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:12.860329", "source": { "split": "train_shard_00000", "doc_id": 878 }, "chunk_id": "train_shard_00000_878_0", "global_id": 970 }, { "text": "Deciphering the activity of individual microbes within complex communities and environments remains a challenge. Here we describe the development of microbiome single-cell transcriptomics using droplet-based single-cell RNA sequencing and pangenome-based computational analysis to characterize the functional heterogeneity of the rumen microbiome. We generated a microbial genome database (the Bovine Gastro Microbial Genome Map) as a functional reference map for the construction of a single-cell transcriptomic atlas of the rumen microbiome. The atlas includes 174,531 microbial cells and 2,534 species, of which 172 are core active species grouped into 12 functional clusters. We detected single-cell-level functional roles, including a key role for Basfia succiniciproducens in the carbohydrate metabolic niche of the rumen microbiome. Furthermore, we explored functional heterogeneity and reveal metabolic niche trajectories driven by biofilm formation pathway genes within B. succiniciproducens. Our results provide a resource for studying the rumen microbiome and illustrate the diverse functions of individual microbial cells that drive their ecological niche stability or adaptation within the ecosystem.\n\nSingle-cell transcriptomics across 2,534 microbial species reveals functional heterogeneity in the rumen microbiome.", "token_count": 315, "char_count": 1331, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:13.425550", "source": { "split": "train_shard_00000", "doc_id": 879 }, "chunk_id": "train_shard_00000_879_0", "global_id": 971 }, { "text": "(1) Background: Endophytic bacteria represent an important component of plant wellness. They have been widely studied for their involvement in plant development and enhancement of stress tolerance. In this work, the endophytic communities of roots, stems, and leaves of blackberry (Rubus ulmifolius Schott) were studied in three different niches: natural, riverside, and human-impacted niches. (2) Results: The microbiome composition revealed that Sphingomonadaceae was the most abundant family in all samples, accounting for 9.4-45.8%. In contrast, other families seem to be linked to a specific tissue or niche. Families Microbacteriaceae and Hymenobacteraceae increased their presence in stem and leaf samples, while Burkholderiaceae abundance was important in riverside samples. Alpha and beta diversity analyses showed that root samples were the most diverse, and they gathered together in the same cluster, apart from the rest of the samples. (3) Conclusions: The analysis of the microbiome of R. ulmifolius plants revealed that the composition was essentially the same in different niches; the differences were primarily influenced by plant tissue factors with a core genome dominated by Sphingomonadaceae. Additionally, it was observed that R. ulmifolius can select its own microbiome, and this remains constant in all tissues evaluated regardless the niche of sampling.\n\nMetataxonomic analysis of endophytic bacteria of blackberry (Rubus ulmifolius Schott) across tissues and environmental conditions.", "token_count": 349, "char_count": 1510, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:14.001235", "source": { "split": "train_shard_00000", "doc_id": 880 }, "chunk_id": "train_shard_00000_880_0", "global_id": 972 }, { "text": "Members of the genus Lysinibacillus attract attention for their mosquitocidal, bioremediation, and plant growth-promoting abilities. Despite this interest, comprehensive studies focusing on genomic traits governing plant growth and stress resilience in this genus using whole-genome sequencing are still scarce. Therefore, we sequenced and compared the genomes of three endophytic Lysinibacillus irui strains isolated from Canary Island date palms with the ex-type strain IRB4-01. Overall, the genomes of these strains consist of a circular chromosome with an average size of 4.6 Mb and a GC content of 37.2%. Comparative analysis identified conserved gene clusters within the core genome involved in iron acquisition, phosphate solubilization, indole-3-acetic acid biosynthesis, and volatile compounds. In addition, genome analysis revealed the presence of genes encoding carbohydrate-active enzymes, and proteins that confer resistance to oxidative, osmotic, and salinity stresses. Furthermore, pathways of putative novel bacteriocins were identified in all genomes. This illustrates possible common plant growth-promoting traits shared among all strains of L. irui. Our findings highlight a rich repertoire of genes associated with plant lifestyles, suggesting significant potential for developing inoculants to enhance plant growth and resilience. This study is the first to provide insights into the overall genomic signatures and mechanisms of plant growth promotion and biocontrol in the genus Lysinibacillus. KEY POINTS: • Pioneer study in elucidating plant growth promoting in L. irui through comparative genomics. • Genome mining identified biosynthetic pathways of putative novel bacteriocins. • Future research directions to develop L. irui-based biofertilizers for sustainable agriculture.\n\nComparative genomics reveals insights into the potential of Lysinibacillus irui as a plant growth promoter.", "token_count": 453, "char_count": 1911, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6448, "quality_score": 0.8224, "entities": { "genes": [ "IRB4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:14.639096", "source": { "split": "train_shard_00000", "doc_id": 881 }, "chunk_id": "train_shard_00000_881_0", "global_id": 973 }, { "text": "Hybrid crops often exhibit increased yield and greater resilience, yet the genomic mechanism(s) underlying hybrid vigor or heterosis remain unclear, hindering our ability to predict the expression of phenotypic traits in hybrid breeding. Here, we generated haplotype-resolved T2T genome assemblies of two pear hybrid varieties, 'Yuluxiang' (YLX) and 'Hongxiangsu' (HXS), which share the same maternal parent but differ in their paternal parents. We then used these assemblies to explore the genome-scale landscape of allele-specific expression (ASE) and create a pangenome graph for pear. ASE was observed for close to 6000 genes in both hybrid cultivars. A subset of ASE genes related to aspects of fruit quality such as sugars, organic acids, and cuticular wax were identified, suggesting their important contributions to heterosis. Specifically, Ma1, a gene regulating fruit acidity, is absent in the paternal haplotypes of HXS and YLX. A pangenome graph was built based on our assemblies and seven published pear genomes. Resequencing data for 139 cultivated pear genotypes (including 97 genotypes sequenced here) were subsequently aligned to the pangenome graph, revealing numerous structural variant hotspots and selective sweeps during pear diversification. As predicted, the Ma1 allele was found to be absent in varieties with low organic acid content, and this association was functionally validated by Ma1 overexpression in pear fruit and calli. Overall, these results reveal the contributions of ASE to fruit-quality heterosis and provide a robust pangenome reference for high-resolution allele discovery and association mapping.\n\nHaplotype-resolved T2T genome assemblies and pangenome graph of pear reveal diverse patterns of allele-specific expression and the genomic basis of fruit quality traits.", "token_count": 435, "char_count": 1811, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:15.278964", "source": { "split": "train_shard_00000", "doc_id": 882 }, "chunk_id": "train_shard_00000_882_0", "global_id": 974 }, { "text": "Glanders, a highly contagious and often fatal disease affecting equids, is caused by Burkholderia mallei. Although sporadic cases of equine glanders have recently been documented in Mongolia, genome sequencing and molecular studies of the bacteria within this region are lacking. This study provided the first molecular characterization of B. mallei isolated from four native Mongolian horses from two different provinces in 2019 and 2022 by applying whole-genome sequencing with two SNP types (previously developed genotyping with 15 SNP markers that provide global coverage of the B. mallei population and the core genome coding SNP typing developed in this study). The Mongolian isolates were located within the L3B1 cluster, which was previously associated with the V-120 strain from Russia. Within the L3B1 cluster shared by neighboring countries, they were in a unique subbranch. In this study, specific SNP markers unique to the Mongolian strains were identified to track these strains using a high-resolution melting analysis (HRMA). This study revealed the unique phylogenetic background of Mongolian strains isolated from the eastern part of Mongolia. HRMA specific to the Mongolian subbranch may contribute to the molecular epidemiological monitoring of glanders in Mongolia and surrounding countries.\n\nFirst molecular characterization of Burkholderia mallei strains isolated from horses in Mongolia.", "token_count": 326, "char_count": 1411, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:15.851486", "source": { "split": "train_shard_00000", "doc_id": 883 }, "chunk_id": "train_shard_00000_883_0", "global_id": 975 }, { "text": "Streptococcus suis is a bacterium of clinical importance in diverse animal hosts including companion animals and humans. Companion animals are closely associated in the living environment of humans and are potential reservoirs for zoonotic pathogens. Given the zoonotic potential of S. suis, it is crucial to determine whether this bacterium is present among the companion animal population. This study aimed to detect Streptococcus suis in companion animals namely cats and dogs of the central west coast of Peninsular Malaysia and further characterize the positive isolates via molecular and genomic approach. The detection of S. suis was done via bacterial isolation and polymerase chain reaction assay of gdh and recN gene from oral swabs. Characterization was done by multiplex PCR serotyping, as well as muti-locus sequence typing, AMR gene prediction, MGE identification and phylogenomic analysis on whole genome sequence acquired from Illumina and Oxford Nanopore sequencing. Among the 115 samples, PCR assay detected 2/59 of the cats were positive for S. suis serotype 8 while all screened dog samples were negative. This study further described the first complete whole genome of S. suis strain SS/UPM/MY/F001 isolated from the oral cavity of a companion cat. Genomic analysis revealed a novel strain of S. suis having a unique MLST profile and antimicrobial resistance genes of mefA, msrD, patA, patB and vanY. Mobile genetic elements were described, and pathogenic determinants matched to human and swine strains were identified. Phylogenetic tree analysis on the core genome alignment revealed strain SS/UPM/MY/F001 was distinct from other S. suis strains. This study provided insight into the detection and genomic features of the S. suis isolate of a companion cat and highlighted its potential for antimicrobial resistance and pathogenicity.\n\nWhole genome sequencing of Streptococcus suis revealed potential drug resistance and zoonotic transmission in companion cat.", "token_count": 465, "char_count": 1983, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5541, "quality_score": 0.777, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:16.492947", "source": { "split": "train_shard_00000", "doc_id": 884 }, "chunk_id": "train_shard_00000_884_0", "global_id": 976 }, { "text": "The bacterium Lactobacillus kefiranofaciens OSU-BDGOA1 and yeast Kluyveromyces marxianus bdgo-ym6 were previously isolated from kefir grains and have shown probiotic traits in mono- and coculture. This research evaluates the effect of introducing probiotic kefir microorganisms in monoculture and in coculture alongside yogurt starter cultures on the physicochemical and rheological properties, volatile flavor compounds, survival of the microorganisms during simulated digestion, and sensory attributes of the final fermented products. The incorporation of L. kefiranofaciens OSU-BDGOA1 in monoculture showed promising outcomes, resulting in a final product showing more solid-like characteristics and potentially improving the texture of the product. There was also a significant increase in the concentration of desirable volatile flavor compounds in the yogurt with the monoculture, particularly 2,3-butanedione, displaying a positive correlation with buttery flavor in the sensory analysis. The inclusion of L. kefiranofaciens in monoculture also promoted better sensory attributes and was significantly better than the yogurt with the coculture with the yeast, showing promising results for the incorporation of this probiotic bacterium into functional fermented dairy products.\n\nDevelopment of probiotic yogurt products incorporated with Lactobacillus kefiranofaciens OSU-BSGOA1 in mono- and coculture with Kluyveromyces marxianus.", "token_count": 356, "char_count": 1438, "word_count": 186, "semantic_coherence": 1, "information_density": 0.543, "quality_score": 0.7715, "entities": { "genes": [ "BSGOA1", "BDGOA1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:17.078008", "source": { "split": "train_shard_00000", "doc_id": 885 }, "chunk_id": "train_shard_00000_885_0", "global_id": 977 }, { "text": "Probiotics offer health advantages when consumed in adequate quantities. As ongoing research identifies promising new strains, ensuring their viability and functionality through simple preservation methods is vital for success within the probiotic industry. This study employed a factorial design to investigate the combined effects of four cryoprotectants [C1: MRS broth + 14 % (w/v) glycerol, C2: Aqueous solution containing 4 % (w/v) trehalose, 6 % (w/v) skimmed milk, and 4 % (w/v) sodium glutamate, C3: Aqueous solution containing 10 % (w/v) skimmed milk and 4 % (w/v) sodium glutamate, C4: Aqueous solution containing 4 % (w/v) sucrose, 6 % (w/v) skimmed milk, and 4 % (w/v) sodium glutamate] and three methods of preservation (P1: -86 °C freezing, P2: -196 °C liquid nitrogen freezing, and P3: storing at 4 °C after lyophilization) on the cell viability of three potentially probiotic strains over 12 months. Pediococcus sp P15 and Weissella cibaria ml6 had the highest viability under treatments C3 and C2, after 12 months of storage, respectively. Meanwhile, Lactococcus lactis ml3 demonstrated the highest viability in both treatments C2 and C4 (P ≤ 0.05). According to the results freezing, either P1 or P2, is the most effective preservation method for P. sp P15 and W. cibaria ml6. Meanwhile, L. lactis ml3 showed the highest colony count under treatment (P1) after 12 months of storage (P ≤ 0.05). Among the tested conditions, P. sp P15 and L. lactis ml3 exhibited the highest viability and bile salt resistance when stored under P1C1. For W", "token_count": 492, "char_count": 1555, "word_count": 250, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:17.726421", "source": { "split": "train_shard_00000", "doc_id": 886 }, "chunk_id": "train_shard_00000_886_0", "global_id": 978 }, { "text": "cibaria ml6, the optimal storage condition was P2C2 (frozen in liquid nitrogen with cryoprotectant C2).\n\nImpact of protectants and the method of preservation on the stability of potentially probiotic bacteria.", "token_count": 55, "char_count": 209, "word_count": 30, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:18.099858", "source": { "split": "train_shard_00000", "doc_id": 886 }, "chunk_id": "train_shard_00000_886_1", "global_id": 979 }, { "text": "The use of animal experiments can be minimized with computational models capable of reflecting the simulated environments. One such environment is intestinal fluid and the colloids formed in it. In this study we used molecular dynamics simulations to investigate solubilization patterns for three model drugs (carvedilol, felodipine and probucol) in dog intestinal fluid, a lipid-based formulation, and a mixture of both. We observed morphological transformations that lipids undergo due to the digestion process in the intestinal environment. Further, we evaluated the effect of bile salt concentration and observed the importance of interindividual variability. We applied two methods of estimating solubility enhancement based on the simulated data, of which one was in good qualitative agreement with the experimentally observed solubility enhancement. In addition to the computational simulations, we also measured solubility in i) aspirated dog intestinal fluid samples and ii) simulated canine intestinal fluid in the fasted state, and found there was no statistical difference between the two. Hence, a simplified dissolution medium suitable for in vitro studies provided physiologically relevant data for the systems explored. The computational protocol used in this study, coupled with in vitro studies using simulated intestinal fluids, can serve as a useful prescreening tool in the process of drug delivery strategies development.\n\nDrug solubilization in dog intestinal fluids with and without administration of lipid-based formulations.", "token_count": 325, "char_count": 1550, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:18.669416", "source": { "split": "train_shard_00000", "doc_id": 887 }, "chunk_id": "train_shard_00000_887_0", "global_id": 980 }, { "text": "Shigella species are a group of highly transmissible Gram-negative pathogens. Increasing reports of infection with extensively drug-resistant varieties of this stomach bug has convinced the World Health Organization to prioritize Shigella for novel therapeutic interventions. We herein coupled the whole-genome sequencing of a natural isolate of Shigella flexneri with a pangenome ana-lysis to characterize pathogen genomics within this species, which will provide us with an insight into its existing genomic diversity and highlight the root causes behind the emergence of quick vaccine escape variants. The isolated novel strain of S. flexneri contained ~4,500 protein-coding genes, 57 of which imparted resistance to antibiotics. A comparative pan-genomic ana-lysis revealed genomic variability of ~64%, the shared conservation of core genes in central metabolic processes, and the enrichment of unique/accessory genes in virulence and defense mechanisms that contributed to much of the observed antimicrobial resistance (AMR). A pathway ana-lysis of the core genome mapped 22 genes to 2 antimicrobial resistance pathways, with the bulk coding for multidrug efflux pumps and two component regulatory systems that are considered to work synergistically towards the development of resistance phenotypes. The prospective evolvability of Shigella species as witnessed by the marked difference in genomic content, the strain-specific essentiality of unique/accessory genes, and the inclusion of a potent resistance mechanism within the core genome, strengthens the possibility of novel serotypes emerging in the near future and emphasizes the importance of tracking down genomic diversity in drug/vaccine design and AMR governance.\n\nComparative Genomics and Characterization of Shigella flexneri Isolated from Urban Wastewater.", "token_count": 415, "char_count": 1825, "word_count": 252, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:19.295959", "source": { "split": "train_shard_00000", "doc_id": 888 }, "chunk_id": "train_shard_00000_888_0", "global_id": 981 }, { "text": "Extended liver resection is the only treatment option for perihilar cholangiocarcinoma (pCCA). Bile salts and the gut hormone FGF19, both promoters of liver regeneration (LR), have not been investigated in patients undergoing resection for pCCA. We aimed to evaluate the bile salt-FGF19 axis perioperatively in pCCA and study its effects on LR.\n\nPartial liver resection alters the bile salt-FGF19 axis in patients with perihilar cholangiocarcinoma: Implications for liver regeneration.", "token_count": 135, "char_count": 485, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:19.724510", "source": { "split": "train_shard_00000", "doc_id": 889 }, "chunk_id": "train_shard_00000_889_0", "global_id": 982 }, { "text": "Salmonella enteritidis is a main pathogen responsible for sporadic outbreaks of gastroenteritis, and therefore is an important public health problem. This study investigated the drug resistance and genomic characteristics of S. enteritidis isolated from clinical and food sources in Huzhou, Zhejiang Province, China, from February 1, 2021, to December 30, 2023. In total, 43 S. enteritidis strains isolated during the study period were subjected to virulence gene, drug resistance gene, genetic correlation, antibiotic resistance, and multilocus sequence typing analyses. All 43 isolates were identified as ST11, and contained 108 virulence-related genes. Drug sensitivity analysis of the 43 isolates showed resistance rates of 100% to nalidixic acid and 90.70% to ampicillin and ampicillin/sulbactam. Multidrug resistance is a serious issue, with 81.40% of strains resistant to three or more antibacterial drugs. Genome sequencing indicated that S. enteritidis possessed 23 drug resistance genes, of which 14 were common to all 43 isolates. Phylogenetic analysis based on core genome single-nucleotide polymorphisms divided the 43 S. enteritidis strains into three clusters, with the 10 samples from an outbreak forming an independent branch located in cluster 3.\n\nAntimicrobial resistance and genome characteristics of Salmonella enteritidis from Huzhou, China.", "token_count": 371, "char_count": 1363, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:20.305359", "source": { "split": "train_shard_00000", "doc_id": 890 }, "chunk_id": "train_shard_00000_890_0", "global_id": 983 }, { "text": "Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation. Indexes based on\n\nMEM-based pangenome indexing for", "token_count": 84, "char_count": 399, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8654, "quality_score": 0.9327, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:20.701073", "source": { "split": "train_shard_00000", "doc_id": 891 }, "chunk_id": "train_shard_00000_891_0", "global_id": 984 }, { "text": "Staphylococcus aureus thrives at animal-human-environment interfaces. A large-scale work from our group indicated that antimicrobial resistance (AMR) in commensal S. aureus strains from wild ungulates is associated with agricultural land cover and livestock farming, raising the hypothesis that AMR genes in wildlife strains may originate from different hosts, namely via exchange of mobile genetic elements (MGE). In this work, we generate the largest available dataset of S. aureus draft genomes from wild ungulates in Portugal and explore their mobilome, which can determine important traits such as AMR, virulence, and host specificity, to understand MGE exchange. Core genome multi-locus sequence typing based on 98 newly generated draft genomes and 101 publicly available genomes from Portugal demonstrated that the genomic relatedness of S. aureus from wild ungulates assigned to livestock-associated sequence types (ST) is greater compared to wild ungulate isolates assigned to human-associated STs. Screening of host specificity determinants disclosed the unexpected presence in wildlife of the immune evasion cluster encoded in φSa3 prophage, described as a human-specific virulence determinant. Additionally, two plasmids, pAVX and pETB, previously associated with avian species and humans, respectively, and the Tn553 transposon were detected. Both pETB and Tn553 encode penicillin resistance through blaZ. Pangenome analysis of wild ungulate isolates shows a core genome fraction of 2133 genes, with isolates assigned to ST72 and ST3224 being distinguished from the remaining by MGEs, although there is no reported role of these in adaptation to wildlife. AMR related gene clusters found in the shell genome are directly linked to resistance against penicillin, macrolides, fosfomycin, and aminoglycosides, and they represent mobile ARGs. Altogether, our findings support epidemiological interactions of human and non-human hosts at interfaces, with MGE exchange, including AMR determinants, associated with putative indirect movements of S. aureus among human and wildlife hosts that might be bridged by livestock.", "token_count": 507, "char_count": 2128, "word_count": 300, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8267, "entities": { "genes": [ "ST72", "ST3224" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:21.351453", "source": { "split": "train_shard_00000", "doc_id": 892 }, "chunk_id": "train_shard_00000_892_0", "global_id": 985 }, { "text": "The mobilome of Staphylococcus aureus from wild ungulates reveals epidemiological links at the animal-human interface.", "token_count": 30, "char_count": 118, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:21.725851", "source": { "split": "train_shard_00000", "doc_id": 892 }, "chunk_id": "train_shard_00000_892_1", "global_id": 986 }, { "text": "Bile acids are cholesterol-derived molecules that are primarily produced in the liver. In nonruminants with fatty liver, overproduction of bile acids is associated with liver injury. During the transition period, fatty liver is a metabolic disorder that can affect up to 50% of high-producing dairy cows. The purpose of this study was to provide a comprehensive evaluation of hepatic bile acid metabolism in dairy cows with fatty liver by assessing the expression changes of genes involved in bile acid synthesis, export, and uptake. The serum activities of aspartate aminotransferase, alanine aminotransferase, and glutamate dehydrogenase and the concentration of total bile acids were all greater, whereas the serum concentration of total cholesterol was lower in cows with fatty liver than in healthy cows. The content of total bile acids was higher, but total cholesterol was slightly lower in liver tissues from fatty liver cows than from healthy cows. The hepatic mRNA abundance of cholesterol 7a-hydroxylase (CYP7A1); hydroxy-delta-5-steroid dehydrogenase, 3 β- and steroid delta-isomerase 7 (HSD3B7); and sterol 12α-hydroxylase (CYP8B1), enzymes involved in the classic pathway of bile acid synthesis, was higher in fatty liver cows than in healthy cows. Compared with healthy cows, the hepatic mRNA abundance of alternative bile acid synthesis pathway-related genes sterol 27-hydroxylase (CYP27A1) and oxysterol 7α-hydroxylase (CYP7B1) did not differ in cows with fatty liver. The protein and mRNA abundances of bile acid transporter bile salt efflux pump (BSEP) were lower in the liver of dairy cow with fatty liver", "token_count": 475, "char_count": 1625, "word_count": 243, "semantic_coherence": 1, "information_density": 0.4897, "quality_score": 0.7449, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:22.430257", "source": { "split": "train_shard_00000", "doc_id": 893 }, "chunk_id": "train_shard_00000_893_0", "global_id": 987 }, { "text": "Compared with healthy cows, the hepatic mRNA abundance of bile acid transporters solute carrier family 51 subunit α (SLC51A) and ATP binding cassette subfamily C member 1 (ABCC1) and 3 (ABCC3) was greater in cows with fatty liver, whereas the solute carrier family 51 subunit β (SLC51B) did not differ. The expression of genes involved in bile acid uptake, including solute carrier family 10 member 1 (NTCP), solute carrier organic anion transporter family member 1A2 (SLCO1A2) and 2B1 (SLCO2B1) was upregulated in dairy cows with fatty liver. Furthermore, the hepatic protein and mRNA abundance of bile acid metabolism regulators farnesoid X receptor (FXR) and small heterodimer partner (SHP) were lower in cows with fatty liver than in healthy cows. Overall, these data suggest that inhibition of the FXR signaling pathway may lead to increased bile acid synthesis and uptake and decreased secretion of bile acids from hepatocytes to the bile, which elevates hepatic bile acid content in dairy cows with fatty liver. Because the hepatotoxicity of bile acids has been demonstrated on nonruminant hepatocytes, it is likely that liver injury is induced by increased hepatic bile acid content in dairy cows with fatty liver.\n\nExpression of hepatic genes involved in bile acid metabolism in dairy cows with fatty liver.", "token_count": 379, "char_count": 1316, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [ "SLC51B", "ABCC1", "ABCC3", "SLC51A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:23.018110", "source": { "split": "train_shard_00000", "doc_id": 893 }, "chunk_id": "train_shard_00000_893_1", "global_id": 988 }, { "text": "Thanks to advancements in genome sequencing and bioinformatics, thousands of bacterial genome sequences are available in public databases. This presents an opportunity to study bacterial diversity in unprecedented detail. This chapter describes a complete bioinformatics workflow for comparative genomics of bacterial genomes, including genome annotation, pangenome reconstruction and visualization, phylogenetic analysis, and identification of sequences of interest such as antimicrobial-resistance genes, virulence factors, and phage sequences. The workflow uses state-of-the-art, open-source tools. The workflow is presented by means of a comparative analysis of Salmonella enterica serovar Typhimurium genomes. The workflow is based on Linux commands and scripts, and result visualization relies on the R environment. The chapter provides a step-by-step protocol that researchers with basic expertise in bioinformatics can easily follow to conduct investigations on their own genome datasets.\n\nStep-by-Step Bacterial Genome Comparison.", "token_count": 233, "char_count": 1039, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:23.493667", "source": { "split": "train_shard_00000", "doc_id": 894 }, "chunk_id": "train_shard_00000_894_0", "global_id": 989 }, { "text": "Computational pangenomics deals with the joint analysis of all genomic sequences of a species. It has already been successfully applied to various tasks in many research areas. Further advances in DNA sequencing technologies constantly let more and more genomic sequences become available for many species, leading to an increasing attractiveness of pangenomic studies. At the same time, larger datasets also pose new challenges for data structures and algorithms that are needed to handle the data. Efficient methods oftentimes make use of the concept of k-mers.Core detection is a common way of analyzing a pangenome. The pangenome's core is defined as the subset of genomic information shared among all individual members. Classically, it is not only determined on the abstract level of genes but can also be described on the sequence level.In this chapter, we provide an overview of k-mer-based methods in the context of pangenomics studies. We first revisit existing software solutions for k-mer counting and k-mer set representation. Afterward, we describe the usage of two k-mer-based approaches, Pangrowth and Corer, for pangenomic core detection.\n\nMethods for Pangenomic Core Detection.", "token_count": 254, "char_count": 1195, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6833, "quality_score": 0.8417, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:23.980997", "source": { "split": "train_shard_00000", "doc_id": 895 }, "chunk_id": "train_shard_00000_895_0", "global_id": 990 }, { "text": "Author Correction: Cicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.", "token_count": 31, "char_count": 140, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:24.351527", "source": { "split": "train_shard_00000", "doc_id": 896 }, "chunk_id": "train_shard_00000_896_0", "global_id": 991 }, { "text": "Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from 14 characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters or novel potential pathogenicity islands (NPPIs) within the Salmonella genome, suggesting their potential contribution to the bacterium's virulence. One of the NPPIs revealed significant overrepresentation of potentially pathogenic proteins. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied.\n\nStructure classification of the proteins from Salmonella enterica pangenome revealed novel potential pathogenicity islands.", "token_count": 472, "char_count": 2050, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5954, "quality_score": 0.7977, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:24.993357", "source": { "split": "train_shard_00000", "doc_id": 897 }, "chunk_id": "train_shard_00000_897_0", "global_id": 992 }, { "text": "Tolerance to bile stress is a crucial property for lactic acid bacteria (LAB) to survive in the gastrointestinal tract and exert their beneficial effects. Whey powder enriched with milk fat globule membrane proteins (M-WPI) as a functional component is protective for strains under stress conditions. The current study investigated the key mechanisms of action involved in\n\nProteomic Analysis of Milk Fat Globule Membrane Protein Modulation of Differently Expressed Proteins in", "token_count": 109, "char_count": 477, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7714, "quality_score": 0.8857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:25.381499", "source": { "split": "train_shard_00000", "doc_id": 898 }, "chunk_id": "train_shard_00000_898_0", "global_id": 993 }, { "text": "This study aims to screen for potential probiotic lactic acid bacteria from the intestines of meat-type pigeon squabs. Ligilactobacillus salivarius YZU37 was identified as the best comprehensive performed strain. Being acid- and bile salt-tolerant, it displayed growth-inhibition activities against Staphylococcus aureus ATCC25923, Escherichia coli ATCC25922, and Salmonella typhimurium SL1344, exhibited sensitivity to 6 commonly used antibiotics, and endowed with good cell surface hydrophobicity, auto-aggregation property, and anti-oxidant activities. Results of in vitro experiments indicated that the bacteriostatic effects of this strain were related to the production of proteinaceous substances that depend on acidic conditions. Whole-genome sequencing of L. salivarius YZU37 was performed to elucidate the genetic basis underlying its probiotic potential. Pangenome analysis of L. salivarius YZU37 and other 212 L. salivarius strains available on NCBI database revealed a pigeon-unique gene coding choloylglycine hydrolase (CGH), which had higher enzyme-substrate binding affinity than that of the common CGH shared by L. salivarius strains of other sources. Annotation of the functional genes in the genome of L. salivarius YZU37 revealed genes involved in responses to acid, bile salt, heat, cold, heavy metal, and oxidative stresses. The whole genome analysis also revealed the absence of virulence and toxin genes and the presence of 65 genes distributed under 4 CAZymes classes, 2 CRISPR-cas regions, and 3 enterolysin A clusters which may confer the acid-dependent antimicrobial potential of L. salivarius YZU37. Altogether, our results highlighted the probiotic potential of L. salivarius YZU37. Further in vivo investigations are required to elucidate its beneficial effects on pigeons.", "token_count": 489, "char_count": 1804, "word_count": 250, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [ "YZU37", "SL1344", "ATCC25923", "ATCC25922" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:26.028277", "source": { "split": "train_shard_00000", "doc_id": 899 }, "chunk_id": "train_shard_00000_899_0", "global_id": 994 }, { "text": "Putative Probiotic Ligilactobacillus salivarius Strains Isolated from the Intestines of Meat-Type Pigeon Squabs.", "token_count": 38, "char_count": 112, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:26.393836", "source": { "split": "train_shard_00000", "doc_id": 899 }, "chunk_id": "train_shard_00000_899_1", "global_id": 995 }, { "text": "HIV-1 drug resistance genotypic tests have primarily been performed by Sanger sequencing of gene segments encoding different drug target proteins. Since the number of targets has increased with the addition of a new class of antiretroviral drugs, a simple high-throughput system for assessing nucleotide sequences throughout the HIV-1 genome is required. Here, we developed a new solution using nanopore sequencing of viral pangenomes amplified by PCR. Benchmark tests using HIV-1 molecular clones demonstrated an accuracy of up to 99.9%. In addition, validation tests of our protocol in 106 clinical samples demonstrated high concordance of drug resistance and tropism genotypes (92.5% and 98.1%, respectively) between the nanopore sequencing-based results and archived clinical determinations made based on Sanger sequencing data. These results suggest that our new approach will be a powerful solution for the comprehensive survey of HIV-1 drug resistance mutations in clinical settings.\n\nPopulation-based nanopore sequencing of the HIV-1 pangenome to identify drug resistance mutations.", "token_count": 246, "char_count": 1090, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:26.877926", "source": { "split": "train_shard_00000", "doc_id": 900 }, "chunk_id": "train_shard_00000_900_0", "global_id": 996 }, { "text": "Wheat is a staple food for more than 35% of the world's population, with wheat flour used to make hundreds of baked goods. Superior end-use quality is a major breeding target; however, improving it is especially time-consuming and expensive. Furthermore, genes encoding seed-storage proteins (SSPs) form multi-gene families and are repetitive, with gaps commonplace in several genome assemblies. To overcome these barriers and efficiently identify superior wheat SSP alleles, we developed \"PanSK\" (Pan-SSP k-mer) for genotype-to-phenotype prediction based on an SSP-based pangenome resource. PanSK uses 29-mer sequences that represent each SSP gene at the pangenomic level to reveal untapped diversity across landraces and modern cultivars. Genome-wide association studies with k-mers identified 23 SSP genes associated with end-use quality that represent novel targets for improvement. We evaluated the effect of rye secalin genes on end-use quality and found that removal of ω-secalins from 1BL/1RS wheat translocation lines is associated with enhanced end-use quality. Finally, using machine-learning-based prediction inspired by PanSK, we predicted the quality phenotypes with high accuracy from genotypes alone. This study provides an effective approach for genome design based on SSP genes, enabling the breeding of wheat varieties with superior processing capabilities and improved end-use quality.\n\nA k-mer-based pangenome approach for cataloging seed-storage-protein genes in wheat to facilitate genotype-to-phenotype prediction and improvement of end-use quality.", "token_count": 368, "char_count": 1573, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:27.807901", "source": { "split": "train_shard_00000", "doc_id": 901 }, "chunk_id": "train_shard_00000_901_0", "global_id": 997 }, { "text": "The\n\nComparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among", "token_count": 32, "char_count": 115, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:28.169364", "source": { "split": "train_shard_00000", "doc_id": 902 }, "chunk_id": "train_shard_00000_902_0", "global_id": 998 }, { "text": "Obesity is associated with alterations in lipid metabolism and gut microbiota dysbiosis. This study investigated the effects of puerarin, a bioactive isoflavone, on lipid metabolism disorders and gut microbiota in high-fat diet (HFD)-induced obese mice. Supplementation with puerarin reduced plasma alanine aminotransferase, liver triglyceride, liver free fatty acid (FFA), and improved gut microbiota dysbiosis in obese mice. Puerarin's beneficial metabolic effects were attenuated when farnesoid X receptor (FXR) was antagonized, suggesting FXR-mediated mechanisms. In hepatocytes, puerarin ameliorated high FFA-induced sterol regulatory element-binding protein (SREBP) 1 signaling, inflammation, and mitochondrial dysfunction in an FXR-dependent manner. In obese mice, puerarin reduced liver damage, regulated hepatic lipogenesis, decreased inflammation, improved mitochondrial function, and modulated mitophagy and ubiquitin-proteasome pathways, but was less effective in FXR knockout mice. Puerarin upregulated hepatic expression of FXR, bile salt export pump (BSEP), and downregulated cytochrome P450 7A1 (CYP7A1) and sodium taurocholate transporter (NTCP), indicating modulation of bile acid synthesis and transport. Puerarin also restored gut microbial diversity, the\n\nPuerarin Modulates Hepatic Farnesoid X Receptor and Gut Microbiota in High-Fat Diet-Induced Obese Mice.", "token_count": 402, "char_count": 1380, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6782, "quality_score": 0.8391, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:28.782944", "source": { "split": "train_shard_00000", "doc_id": 903 }, "chunk_id": "train_shard_00000_903_0", "global_id": 999 }, { "text": "In recombinant protein-producing yeast strains, cells experience high production-related stresses similar to high temperatures. It is possible to increase recombinant protein production by enhancing thermotolerance, but few studies have focused on this topic. Here we aim to identify cellular regulators that can simultaneously activate thermotolerance and high yield of recombinant protein. Through screening at 46 °C, a heat-resistant Kluyveromyces marxianus (K. marxianus) strain FDHY23 is isolated. It also exhibits enhanced recombinant protein productivity at both 30 °C and high temperatures. The CYR1\n\nCoupling thermotolerance and high production of recombinant protein by CYR1", "token_count": 178, "char_count": 684, "word_count": 92, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "CYR1", "FDHY23" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:30.012876", "source": { "split": "train_shard_00000", "doc_id": 904 }, "chunk_id": "train_shard_00000_904_0", "global_id": 1000 }, { "text": "Chickpea (Cicer arietinum L.)-an important legume crop cultivated in arid and semiarid regions-has limited genetic diversity. Efforts are being undertaken to broaden its diversity by utilizing its wild relatives, which remain largely unexplored. Here, we present the Cicer super-pangenome based on the de novo genome assemblies of eight annual Cicer wild species. We identified 24,827 gene families, including 14,748 core, 2,958 softcore, 6,212 dispensable and 909 species-specific gene families. The dispensable genome was enriched for genes related to key agronomic traits. Structural variations between cultivated and wild genomes were used to construct a graph-based genome, revealing variations in genes affecting traits such as flowering time, vernalization and disease resistance. These variations will facilitate the transfer of valuable traits from wild Cicer species into elite chickpea varieties through marker-assisted selection or gene-editing. This study offers valuable insights into the genetic diversity and potential avenues for crop improvement in chickpea.\n\nCicer super-pangenome provides insights into species evolution and agronomic trait loci for crop improvement in chickpea.", "token_count": 285, "char_count": 1199, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7134, "quality_score": 0.8567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:30.584290", "source": { "split": "train_shard_00000", "doc_id": 905 }, "chunk_id": "train_shard_00000_905_0", "global_id": 1001 }, { "text": "The environmental bacterium\n\nCore genome multilocus sequence typing (cgMLST) applicable to the monophyletic", "token_count": 27, "char_count": 107, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:30.946009", "source": { "split": "train_shard_00000", "doc_id": 906 }, "chunk_id": "train_shard_00000_906_0", "global_id": 1002 }, { "text": "Kluyveromyces marxianus, a thermotolerant, fast-growing, Crabtree-negative yeast, is a promising chassis for the manufacture of various bioproducts. Although several genome editing tools are available for this yeast, these tools still require refinement to enable more convenient and efficient genetic modification. In this study, we engineered the K. marxianus NBRC 104275 strain by impairing the nonhomologous end joining and enhancing the homologous recombination machinery, which resulted in improved homology-directed repair effective on homology arms of up to 40 bp in length. Additionally, we simplified the CRISPR-Cas9 editing system by constructing a strain for integrative expression of Cas9 nuclease and plasmids bearing different selection markers for gRNA expression, thereby facilitating iterative genome editing without the need for plasmid curing. We demonstrated that tRNA was more effective than the hammerhead ribozyme for processing gRNA primary transcripts, and readily assembled tRNA-gRNA arrays were used for multiplexed editing of at least four targets. This editing tool was further employed for simultaneous scarless in vivo assembly of a 12-kb cassette from three fragments and marker-free integration for expressing a fusion variant of fatty acid synthase, as well as the integration of genes for starch hydrolysis. Together, the genome editing tool developed in this study makes K. marxianus more amenable to genetic modification and will facilitate more extensive engineering of this nonconventional yeast for chemical production.\n\nCRISPR-Cas9 mediated genome editing of Kluyveromyces marxianus for iterative, multiplexed gene disruption and pathway integration.", "token_count": 405, "char_count": 1692, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:31.563723", "source": { "split": "train_shard_00000", "doc_id": 907 }, "chunk_id": "train_shard_00000_907_0", "global_id": 1003 }, { "text": "Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at the species level. Here we generated and analyzed the pan-transcriptome of ~1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of transcriptome divergence. Global gene expression patterns combined with population structure showed that variation in heritable expression mainly lies within subpopulation-specific signatures, for which accessory genes are overrepresented. Genome-wide association analyses consistently highlighted that accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.\n\nPan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast.", "token_count": 211, "char_count": 1021, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6866, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:32.022309", "source": { "split": "train_shard_00000", "doc_id": 908 }, "chunk_id": "train_shard_00000_908_0", "global_id": 1004 }, { "text": "The presence of Salmonella in dry fermented sausages is source of recalls and outbreaks. The genomic diversity of 173 Salmonella isolates from the dry fermented sausage production chains (pig carcasses, pork, and sausages) from France and Spain were investigated through their core phylogenomic relationships and accessory genome profiles. Ten different serovars and thirteen sequence type profiles were identified. The most frequent serovar from sausages was the monophasic variant of S. Typhimurium (1,4,[5],12:i:-, 72%) while S. Derby was in pig carcasses (51%). Phylogenomic clusters found in S. 1,4,[5],12:i:-, S. Derby, S. Rissen and S. Typhimurium serovars identified closely related isolates, with less than 10 alleles and 20 SNPs of difference, displaying Salmonella persistence along the pork production chain. Most of the S. 1,4,[5],12:i:- contained the Salmonella genomic island-4 (SGI-4), Tn21 and IncFIB plasmid. More than half of S. Derby strains contained the SGI-1 and Tn7. S. 1,4,[5],12:i:- genomes carried the most multidrug resistance genes (91% of the strains), whereas extended-spectrum β-lactamase genes were found in Typhimurium and Derby serovars. Salmonella monitoring and characterization in the pork production chains, specially S. 1,4,[5],12:i:- serovar, is of special importance due to its multidrug resistance capacity and persistence in dry fermented sausages.\n\nGenomic insights of Salmonella isolated from dry fermented sausage production chains in Spain and France.", "token_count": 453, "char_count": 1499, "word_count": 212, "semantic_coherence": 1, "information_density": 0.566, "quality_score": 0.783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:32.660849", "source": { "split": "train_shard_00000", "doc_id": 909 }, "chunk_id": "train_shard_00000_909_0", "global_id": 1005 }, { "text": "With broad genetic diversity and as a source of key agronomic traits, wild grape species (Vitis spp.) are crucial to enhance viticulture's climatic resilience and sustainability. This review discusses how recent breakthroughs in the genome assembly and analysis of wild grape species have led to discoveries on grape evolution, from wild species' adaptation to environmental stress to grape domestication. We detail how diploid chromosome-scale genomes from wild Vitis spp. have enabled the identification of candidate disease-resistance and flower sex determination genes and the creation of the first Vitis graph-based pangenome. Finally, we explore how wild grape genomics can impact grape research and viticulture, including aspects such as data sharing, the development of functional genomics tools, and the acceleration of genetic improvement.\n\nThe wild side of grape genomics.", "token_count": 193, "char_count": 883, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6693, "quality_score": 0.8346, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:33.139143", "source": { "split": "train_shard_00000", "doc_id": 910 }, "chunk_id": "train_shard_00000_910_0", "global_id": 1006 }, { "text": "Heat stress (HS) poses a substantial challenge to livestock. Studies have demonstrated that HS reduces fertility and leads to gut microbiota dysbiosis in bulls. However, the impact of the gut microbiota on fertility in bulls during HS is still unclear. Our research revealed that HS exposure decreased semen quality in bulls, and fecal microbiota transplantation (FMT) from heat-stressed bulls to recipient mice resulted in a significant decrease in number of testicular germ cells and epididymal sperm. Untargeted metabolomics methodology and 16S rDNA sequencing conjoint analysis revealed that Akkermansia muciniphila (A. muciniphila) seemed to be a key bacterial regulator of spermatogenesis after HS exposure. Moreover, the research indicated that A. muciniphila regulated secondary bile acid metabolism by promoting the colonization of bile salt hydrolase (BSH)-metabolizing bacteria, leading to increase of retinol absorption in the host gut and subsequently elevation of testicular retinoic acid level, thereby improving spermatogenesis. This study sheds light on the relationship between HS-induced microbiota dysbiosis and spermatogenesis, offering a potential therapeutic approach for addressing bull spermatogenic dysfunction triggered by HS exposure.\n\nHeat stress-induced dysbiosis of the gut microbiota impairs spermatogenesis by regulating secondary bile acid metabolism in the gut.", "token_count": 352, "char_count": 1396, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6597, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:33.734557", "source": { "split": "train_shard_00000", "doc_id": 911 }, "chunk_id": "train_shard_00000_911_0", "global_id": 1007 }, { "text": "Increased temperatures in Arctic tundra ecosystems are leading to higher microbial respiration rates of soil organic matter, resulting in the release of carbon dioxide and methane. To understand the effects of this microbial activity, it is important to better characterize the diverse microbial communities in Arctic soil. Our goal is to refine our understanding of the phylogenetic diversity of Terriglobia, a common but elusive group within the Acidobacteriota phylum. This will help us link this diversity to variations in carbon and nitrogen usage patterns. We used long-read Oxford Nanopore MinION sequences in combination with metagenomic short-read sequences to assemble complete Acidobacteriota genomes. This allowed us to build multi-locus phylogenies and annotate pangenome markers to distinguish Acidobacteriota strains from several tundra soil isolates. We identified a phylogenetic cluster containing four new species previously associated with Edaphobacter lichenicola. We conclude that this cluster represents a new genus, which we have named Tunturibacter. We describe four new species: Tunturibacter lichenicola comb. nov., Tunturibacter empetritectus sp. nov., Tunturibacter gelidoferens sp. nov., and Tunturibacter psychrotolerans sp. nov. By uncovering new species and strains within the Terriglobia and improving the accuracy of their phylogenetic placements, we hope to enhance our understanding of this complex phylum and shed light on the mechanisms that shape microbial communities in polar soils.\n\nGenome analysis and description of Tunturibacter gen. nov. expands the diversity of Terriglobia in tundra soils.", "token_count": 402, "char_count": 1637, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:34.396976", "source": { "split": "train_shard_00000", "doc_id": 912 }, "chunk_id": "train_shard_00000_912_0", "global_id": 1008 }, { "text": "Porphyromonas gingivalis is a nonmotile, obligate anaerobic, Gram-negative bacterium known for its association with periodontal disease and its involvement in systemic diseases such as atherosclerosis, cardiovascular disease, colon cancer, and Alzheimer's disease. This bacterium produces several virulence factors, including capsules, fimbriae, lipopolysaccharides, proteolytic enzymes, and hemagglutinins. A comparative genomic analysis revealed the open pangenome of P. gingivalis and identified complete type IV secretion systems in strain KCOM2805 and almost complete type VI secretion systems in strains KCOM2798 and ATCC49417, which is a new discovery as previous studies did not find the proteins involved in secretion systems IV and VI. Conservation of some virulence factors between different strains was observed, regardless of their genetic diversity and origin. In addition, we performed for the first time a reconstruction analysis of the gene regulatory network, identifying transcription factors and proteins involved in the regulatory mechanisms of bacterial pathogenesis. In particular, QseB regulates the expression of hemagglutinin and arginine deaminase, while Rex may suppress the release of gingipain through interactions with PorV and the formatum/nitrate transporter. Our study highlights the central role of conserved virulence factors and regulatory pathways, particularly QseB and Rex, in P. gingivalis and provides insights into potential therapeutic targets.\n\nComprehensive comparative analysis of the periodontal pathogen Porphyromonas gingivalis: exploring the pan-genome, the reconstruction of the gene regulatory network and genome-scale metabolic network.", "token_count": 397, "char_count": 1690, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6441, "quality_score": 0.8221, "entities": { "genes": [ "KCOM2798", "ATCC49417", "KCOM2805" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:35.015658", "source": { "split": "train_shard_00000", "doc_id": 913 }, "chunk_id": "train_shard_00000_913_0", "global_id": 1009 }, { "text": "Author Correction: A functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome.", "token_count": 29, "char_count": 124, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:35.376789", "source": { "split": "train_shard_00000", "doc_id": 914 }, "chunk_id": "train_shard_00000_914_0", "global_id": 1010 }, { "text": "As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the proposed Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning. One clade that represents 24% of all currently known chimalliviruses lacks a PhuZ homolog. Here we show that\n\nAsesino: a nucleus-forming phage that lacks PhuZ.", "token_count": 177, "char_count": 724, "word_count": 102, "semantic_coherence": 1, "information_density": 0.8039, "quality_score": 0.902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:35.822590", "source": { "split": "train_shard_00000", "doc_id": 915 }, "chunk_id": "train_shard_00000_915_0", "global_id": 1011 }, { "text": "This study focused on the protein-stabilised triglyceride (TG)/water interfaces and oil-in-water emulsions, and explored the influence of varying molar ratios of bile salts (BSs) and phospholipids (PLs) on the intestinal lipolysis of TGs. The presence of these two major groups of biosurfactants delivered with human bile to the physiological environment of intestinal digestion was replicated in our experiments by using mixtures of individual BSs and PLs under in vitro small intestinal lipolysis conditions. Conducted initially, retrospective analysis of available scientific literature revealed that an average molar ratio of 9:4 for BSs to PLs (BS/PL) can be considered physiological in the postprandial adult human small intestine. Our experimental data showed that combining BSs and PLs synergistically enhanced interfacial activity, substantially reducing oil-water interfacial tension (IFT) during interfacial lipolysis experiments with pancreatic lipase, especially at the BS/PL-9:4 ratio. Other BS/PL molar proportions (BS/PL-6.5:6.5 and BS/PL-4:9) and an equimolar amount of BSs (BS-13) followed in IFT reduction efficiency, while using PLs alone as biosurfactants was the least efficient. In the following emulsion lipolysis experiments, BS/PL-9:4 outperformed other BS/PL mixtures in terms of enhancing the TG digestion extent. The degree of TG conversion and the desorption efficiency of interfacial material post-lipolysis correlated directly with the BS/PL ratio, decreasing as the PL proportion increased. In conclusion, this study highlights the crucial role of biliary PLs, alongside BSs, in replicating the physiological function of bile in intestinal lipolysis of emulsified TGs. Our results showed different contributions of PLs and BSs to lipolysis, strongly suggesting that any future in vitro studies aiming to simulate the human digestion conditions should take into account the impact of biliary PLs - not just BSs - to accurately mimic the physiological role of bile in intestinal lipolysis", "token_count": 513, "char_count": 2019, "word_count": 286, "semantic_coherence": 1, "information_density": 0.5804, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:07:36.457376", "source": { "split": "train_shard_00000", "doc_id": 916 }, "chunk_id": "train_shard_00000_916_0", "global_id": 1012 }, { "text": "This is particularly crucial given the fact that existing in vitro digestion protocols typically focus solely on applying specific concentrations and/or compositions of BSs to simulate the action of human bile during intestinal digestion, while overlooking the presence and concentration of biliary PLs under physiological gut conditions.\n\nThe bile salt/phospholipid ratio determines the extent of in vitro intestinal lipolysis of triglycerides: Interfacial and emulsion studies.", "token_count": 108, "char_count": 479, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:36.850898", "source": { "split": "train_shard_00000", "doc_id": 916 }, "chunk_id": "train_shard_00000_916_1", "global_id": 1013 }, { "text": "Fruit ripening is associated with the degreening process (loss of chlorophyll) that occurs in most fruit species. Kiwifruit is one of the special species whose fruits may maintain green flesh by accumulating a large amount of chlorophyll even after ripening. However, little is known about the genetic variations related to the fruit degreening process. Here, a graph-based kiwifruit pangenome by analyzing 14 chromosome-scale haplotype-resolved genome assemblies from seven representative cultivars or lines in Actinidia chinensis is built. A total of 49,770 non-redundant gene families are identified, with core genes constituting 46.6%, and dispensable genes constituting 53.4%. A total of 84,591 non-redundant structural variations (SVs) are identified. The pangenome graph integrating both reference genome sequences and variant information facilitates the identification of SVs related to fruit color. The SV in the promoter of the AcBCM gene determines its high expression in the late developmental stage of fruits, which causes chlorophyll accumulation in the green-flesh fruits by post-translationally regulating AcSGR2, a key enzyme of chlorophyll catabolism. Taken together, a high-quality pangenome is constructed, unraveled numerous genetic variations, and identified a novel SV mediating fruit coloration and fruit quality, providing valuable information for further investigating genome evolution and domestication, QTL genes function, and genomics-assisted breeding.\n\nGraph-Based Pangenome of Actinidia chinensis Reveals Structural Variations Mediating Fruit Degreening.", "token_count": 391, "char_count": 1586, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:37.471599", "source": { "split": "train_shard_00000", "doc_id": 917 }, "chunk_id": "train_shard_00000_917_0", "global_id": 1014 }, { "text": "This study focused on optimizing the production of fermented Spirulina (FS) products using a bioactivity-guided strategy with Lactobacillus helveticus B-4526 and Kluyveromyces marxianus Y-329 in a 3-L bioreactor. Various operating conditions, including aeration rates and pH modes, were tested. While both microorganisms thrived under all conditions, the \"cascade\" mode, controlling dissolved oxygen, enhanced protein hydrolysis and antioxidant activity, as confirmed by SDS-PAGE and DPPH/TEAC assays, respectively. Screening revealed that \"cascade\" FS significantly decreased viability of colon cancer cells (HT-29) in a dose-dependent manner, with up to a 72 % reduction. Doses ≤ 500 μg mL\n\nOptimizing bioreactor conditions for Spirulina fermentation by Lactobacillus helveticus and Kluyveromyces marxianus: Impact on chemical & bioactive properties.", "token_count": 244, "char_count": 852, "word_count": 113, "semantic_coherence": 1, "information_density": 0.823, "quality_score": 0.9115, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:37.953827", "source": { "split": "train_shard_00000", "doc_id": 918 }, "chunk_id": "train_shard_00000_918_0", "global_id": 1015 }, { "text": "Shigella dysenteriae, is a Gram-negative bacterium that emerged as the second most significant cause of bacillary dysentery. Antibiotic treatment is vital in lowering Shigella infection rates, yet the growing global resistance to broad-spectrum antibiotics poses a significant challenge. The persistent multidrug resistance of S. dysenteriae complicates its management and control. Hence, there is an urgent requirement to discover novel therapeutic targets and potent medications to prevent and treat this disease. Therefore, the integration of bioinformatics methods such as subtractive and comparative analysis provides a pathway to compute the pan-genome of S. dysenteriae. In our study, we analysed a dataset comprising 27 whole genomes. The S. dysenteriae strain SD197 was used as the reference for determining the core genome. Initially, our focus was directed towards the identification of the proteome of the core genome. Moreover, several filters were applied to the core genome, including assessments for non-host homology, protein essentiality, and virulence, in order to prioritize potential drug targets. Among these targets were Integration host factor subunit alpha and Tyrosine recombinase XerC. Furthermore, four drug-like compounds showing potential inhibitory effects against both target proteins were identified. Subsequently, molecular docking analysis was conducted involving these targets and the compounds. This initial study provides the list of novel targets against S. dysenteriae. Conclusively, future in vitro investigations could validate our in-silico findings and uncover potential therapeutic drugs for combating bacillary dysentery infection.\n\nAn integrated in-silico approach for drug target identification in human pathogen Shigella dysenteriae.", "token_count": 394, "char_count": 1782, "word_count": 242, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [ "SD197" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:38.563829", "source": { "split": "train_shard_00000", "doc_id": 919 }, "chunk_id": "train_shard_00000_919_0", "global_id": 1016 }, { "text": "Limosilactobacillus fermentum is an isolate obtained from oral gingival samples of healthy human individuals. The whole genome of Lb. fermentum GD5MG is composed of a circular DNA molecule containing 1,834,134 bp and exhibits a GC content of 52.80 %. The sequencing effort produced 38.6 million reads, each 150 bp in length, resulting in a sequencing depth of 2912.48x. Our examination unveiled a total of 1961 protein-coding genes, 27 rRNA genes, 24 tRNA genes, 3 non-coding RNA genes, and 63 pseudogenes with the use of gene annotations in NCBI Prokaryotic Genome Annotation tool. RAST revealed 1863 coding genes distributed across 209 subsystems, with a predominant involvement in amino acid, carbohydrate, and protein metabolism. Phylogenetic analysis infers that the Lb. fermentum GD5MG shares 281 gene clusters. Furthermore, the genome features showed a single CRISPR locus of 45 bp in length. Three genes associated with adhesion ability (strA, dltD, and dltA) and 26 genes related to acid tolerance, digestive enzyme secretion, and bile salt resistance were identified. Numerous genes associated with oral probiotic properties, comprising adhesion, acid and bile salt tolerance, oxidative stress tolerance, and sugar metabolism, were identified in the genome. Our findings shed light on the genomic characteristics of Lb. fermentum GD5MG, which are probable probiotics with functional benefits in humans.\n\nProbiotic functional gene explorations in the genome of Limosilactobacillus fermentum GD5MG.", "token_count": 433, "char_count": 1506, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6697, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:39.188819", "source": { "split": "train_shard_00000", "doc_id": 920 }, "chunk_id": "train_shard_00000_920_0", "global_id": 1017 }, { "text": "Probiotics play a significant role in enhancing health, and they are well known for bacteriocins production. Evaluating probiotics' whole-genome sequence provides insights into their consumption outcomes. Thus, genomic studies have a significant role in assessing the safety of probiotics more in-depth and offer valuable information regarding probiotics' functional diversity, metabolic pathways, and health-promoting mechanisms. Marine Pediococcus pentosaceus E3, isolated from shrimp gut, exhibited beneficial properties, indicating its potential as a probiotic candidate. Phenotypically, E3 strain was susceptible to most antibiotics assessed, tolerant to low pH and high bile salt conditions, and revealed no hemolysin activity. Interestingly, E3-neutralized CFS revealed significant antibacterial activity against pathogens under investigation. Therefore, the concentrated CFS was prepared and evaluated as a natural biopreservative and showed outstanding antimicrobial activity. Furthermore, integrated-based genome assessment has provided insight into probiotic characteristics at the genomic level. Whole-genome sequencing analysis revealed that the E3 genome possesses 1805 protein-coding genes, and the genome size was about 1.8 Mb with a G + C content of 37.28%. Moreover, the genome revealed the absence of virulence factors and clinically related antibiotic genes. Moreover, several genes consistent with probiotic microorganisms' features were estimated in the genome, including stress response, carbohydrate metabolism, and vitamin biosynthesis. In addition, several genes associated with survival and colonization within the gastrointestinal tract were also detected across the E3 genome. Therefore, the findings suggest that insights into the genetic characteristics of E3 guarantee the safety of the strain and facilitate future development of E3 isolate as a health-promoting probiotic and source of biopreservative.\n\nMarine Pediococcus pentosaceus E3 Probiotic Properties, Whole-Genome Sequence Analysis, and Safety Assessment.", "token_count": 476, "char_count": 2048, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6566, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:39.836709", "source": { "split": "train_shard_00000", "doc_id": 921 }, "chunk_id": "train_shard_00000_921_0", "global_id": 1018 }, { "text": "The cultivated apple (Malus domestica Borkh.) is a cross-pollinated perennial fruit tree of great economic importance. Earlier versions of apple reference genomes were unphased, fragmented, and lacked comprehensive insights into the apple's highly heterozygous genome, which impeded advances in genetic studies and breeding programs. In this study, we assembled a haplotype-resolved telomere-to-telomere (T2T) reference genome for the diploid apple cultivar Golden Delicious. Subsequently, we constructed a pangenome based on 12 assemblies from wild and cultivated species to investigate the dynamic changes of functional genes. Our results revealed the gene gain and loss events during apple domestication. Compared with cultivated species, more gene families in wild species were significantly enriched in oxidative phosphorylation, pentose metabolic process, responses to salt, and abscisic acid biosynthesis process. Our analyses also demonstrated a higher prevalence of different types of resistance gene analogs (RGAs) in cultivars than their wild relatives, partially attributed to segmental and tandem duplication events in certain RGAs classes. Structural variations, mainly deletions and insertions, have affected the presence and absence of TIR-NB-ARC-LRR, NB-ARC-LRR, and CC-NB-ARC-LRR genes. Additionally, hybridization/introgression from wild species has also contributed to the expansion of resistance genes in domesticated apples. Our haplotype-resolved T2T genome and pangenome provide important resources for genetic studies of apples, emphasizing the need to study the evolutionary mechanisms of resistance genes in apple breeding.\n\nPhased telomere-to-telomere reference genome and pangenome reveal an expansion of resistance genes during apple domestication.", "token_count": 421, "char_count": 1778, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:40.466191", "source": { "split": "train_shard_00000", "doc_id": 922 }, "chunk_id": "train_shard_00000_922_0", "global_id": 1019 }, { "text": "Pangenomes vary across bacteria. Some species have fluid pangenomes, with a high proportion of genes varying between individual genomes. Other species have less fluid pangenomes, with different genomes tending to contain the same genes. Two main hypotheses have been suggested to explain this variation: differences in species' bacterial lifestyle and effective population size. However, previous studies have not been able to test between these hypotheses because the different features of lifestyle and effective population size are highly correlated with each other, and phylogenetically conserved, making it hard to disentangle their relative importance. We used phylogeny-based analyses, across 126 bacterial species, to tease apart the causal role of different factors. We found that pangenome fluidity was lower in i) host-associated compared with free-living species and ii) host-associated species that are obligately dependent on a host, live inside cells, and are more pathogenic and less motile. In contrast, we found no support for the competing hypothesis that larger effective population sizes lead to more fluid pangenomes. Effective population size appears to correlate with pangenome variation because it is also driven by bacterial lifestyle, rather than because of a causal relationship.\n\nBacterial lifestyle shapes pangenomes.", "token_count": 280, "char_count": 1347, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:41.027051", "source": { "split": "train_shard_00000", "doc_id": 923 }, "chunk_id": "train_shard_00000_923_0", "global_id": 1020 }, { "text": "Deciphering the accessory genome of a novel Klebsiella pneumoniae lineage in the Brazilian Amazon region and its potential contribution to the emergence of a high-risk clone.", "token_count": 43, "char_count": 174, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:41.393939", "source": { "split": "train_shard_00000", "doc_id": 924 }, "chunk_id": "train_shard_00000_924_0", "global_id": 1021 }, { "text": "Tuberculosis (TB), caused by Mycobacterium tuberculosis, ranks among the top causes of global human mortality, as reported by the World Health Organization's 2022 TB report. The prevalence of M. tuberculosis strains that are multiple and extensive-drug resistant represents a significant barrier to TB eradication. Fortunately, having many completely sequenced M. tuberculosis genomes available has made it possible to investigate the species pangenome, conduct a pan-phylogenetic investigation, and find potential new drug targets. The 442 complete genome dataset was used to estimate the pangenome of M. tuberculosis. This study involved phylogenomic classification and in-depth analyses. Sequential filters were applied to the conserved core genome containing 2754 proteins. These filters assessed non-human homology, virulence, essentiality, physiochemical properties, and pathway analysis. Through these intensive filtering approaches, promising broad-spectrum therapeutic targets were identified. These targets were docked with FDA-approved compounds readily available on the ZINC database. Selected highly ranked ligands with inhibitory potential include dihydroergotamine and abiraterone acetate. The effectiveness of the ligands has been supported by molecular dynamics simulation of the ligand-protein complexes, instilling optimism that the identified lead compounds may serve as a robust basis for the development of safe and efficient drugs for TB treatment, subject to further lead optimization and subsequent experimental validation.\n\nExploring optimal drug targets through subtractive proteomics analysis and pangenomic insights for tailored drug design in tuberculosis.", "token_count": 379, "char_count": 1686, "word_count": 220, "semantic_coherence": 1, "information_density": 0.7227, "quality_score": 0.8614, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:41.974493", "source": { "split": "train_shard_00000", "doc_id": 925 }, "chunk_id": "train_shard_00000_925_0", "global_id": 1022 }, { "text": "Genome-wide association studies (GWAS) have been instrumental in elucidating the genetic architecture of various traits and diseases. Despite the success of GWAS, inherent limitations such as identifying rare and ultra-rare variants, the potential for spurious associations, and in pinpointing causative agents can undermine diagnostic capabilities. This review provides an overview of GWAS and highlights recent advances in genetics that employ a range of methodologies, including Whole Genome Sequencing (WGS), Mendelian Randomization (MR), the Pangenome's high-quality T2T-CHM13 panel, and the Human BioMolecular Atlas Program (HuBMAP), as potential enablers of current and future GWAS research. State of the literature demonstrate the capabilities of these techniques in enhancing the statistical power of GWAS. WGS, with its comprehensive approach, captures the entire genome, surpassing the capabilities of the traditional GWAS technique focused on predefined Single Nucleotide Polymorphism (SNP) sites. The Pangenome's T2T-CHM13 panel, with its holistic approach, aids in the analysis of regions with high sequence identity, such as segmental duplications (SDs). Mendelian Randomization has advanced causative inference, improving clinical diagnostics and facilitating definitive conclusions. Furthermore, spatial biology techniques like HuBMAP, enable 3D molecular mapping of tissues at single-cell resolution, offering insights into pathology of complex traits. This study aims to elucidate and advocate for the increased application of these technologies, highlighting their potential to shape the future of GWAS research.\n\nGWAS advancements to investigate disease associations and biological mechanisms.", "token_count": 381, "char_count": 1714, "word_count": 226, "semantic_coherence": 1, "information_density": 0.7035, "quality_score": 0.8518, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:42.552030", "source": { "split": "train_shard_00000", "doc_id": 926 }, "chunk_id": "train_shard_00000_926_0", "global_id": 1023 }, { "text": "Listeria monocytogenes exhibits varying levels of pathogenicity when entering the host through contaminated food. However, little is known regarding the stress response and environmental tolerance mechanism of different virulence strains to host gastrointestinal (GI) stimuli. This study analyzed the differences in the survival and genes of stress responses among two strains of L. monocytogenes 10403S (serotype 1/2a, highly virulent strain) and M7 (serotype 4a, low-virulence strain) during simulated gastrointestinal digestion. The results indicated that L. monocytogenes 10403S showed greater acid and bile salt tolerance than L. monocytogenes M7, with higher survival rates and less cell deformation and cell membrane permeability during the in vitro digestion. KEGG analysis of the transcriptomes indicated that L. monocytogenes 10403S displayed significant activity in amino acid metabolism, such as glutamate and arginine, associated with acid tolerance. Additionally, L. monocytogenes 10403S demonstrated a higher efficacy in promoting activities that preserve bacterial cell membrane integrity and facilitate flagellar protein synthesis. These findings will contribute valuable practical insights into the tolerance distinctions among different virulence strains of L. monocytogenes in the GI environment.\n\nDifferential mechanism between Listeria monocytogenes strains with different virulence contaminating ready-to-eat sausages during the simulated gastrointestinal tract.", "token_count": 367, "char_count": 1485, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6146, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:43.131378", "source": { "split": "train_shard_00000", "doc_id": 927 }, "chunk_id": "train_shard_00000_927_0", "global_id": 1024 }, { "text": "C. perfringens type D strains are the leading cause of enterotoxaemia in ruminants such as goats, sheep, and cattle. However, there has been no prior research on the genomic characteristics of C. perfringens type D strains from various regions in China. Here, we investigated the antibiotic resistance, genomic characteristics, and phylogenetic relationship of C. perfringens type D isolates recovered from goat farms in Shaanxi, Gansu, and Ningxia provinces. The antibiotic resistance test indicated that the isolates displayed high minimum inhibitory concentration (MIC) values to sulfafurazole, whereas the other antibiotics tested, such as penicillin, enrofloxacin, and florfenicol, worked well on them. Additionally, only tetracycline resistance genes [tetA(P) and tetB(P)] were identified from the isolates. A collective of 13 toxin genes, including etx and cpe were detected among the isolates. Sequence comparison revealed that the etx and cpe genes shared high sequence identities, and they could coexist on a pCW3-like plasmid, representing a potential risk to both animal breeding and public health. Phylogenetic analysis using core genome multi-locus sequence typing (cgMLST) and core genome single nucleotide polymorphisms (SNPs) revealed the close genetic relationship and potential regional/transregional transmission of the C. perfringens type D isolates in Shaanxi and Gansu provinces. Furthermore, pan-genomic analysis suggested the functional differences at the protein-coding gene level, although isolates from the same source shared a close genetic relationship. In conclusion, this study indicated the antibiotic resistance, virulence markers, potential transregional transmission, and genomic diversity of C. perfringens type D strains from various regions in China, which could provide references for the prevention of C. perfringens foodborne diseases and further research.\n\nGenomic analysis of Clostridium perfringens type D isolates from goat farms.", "token_count": 474, "char_count": 1976, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5824, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:43.773165", "source": { "split": "train_shard_00000", "doc_id": 928 }, "chunk_id": "train_shard_00000_928_0", "global_id": 1025 }, { "text": "Bile acids play a critical role in the emulsification of dietary lipids, a critical step in the primary function of the small intestine, which is the digestion and absorption of food. Primary bile acids delivered into the small intestine are conjugated to enhance functionality, in part, by increasing aqueous solubility and preventing passive diffusion of bile acids out of the gut lumen. Bile acid function can be disrupted by the gut microbiota via the deconjugation of primary bile acids by bile salt hydrolases (BSHs), leading to their conversion into secondary bile acids through the expression of bacterial bile acid-inducible genes, a process often observed in malabsorption due to small intestinal bacterial overgrowth. By modeling the small intestinal microbiota\n\nPreservation of conjugated primary bile acids by oxygenation of the small intestinal microbiota", "token_count": 210, "char_count": 869, "word_count": 131, "semantic_coherence": 1, "information_density": 0.542, "quality_score": 0.771, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:44.236615", "source": { "split": "train_shard_00000", "doc_id": 929 }, "chunk_id": "train_shard_00000_929_0", "global_id": 1026 }, { "text": "GCN2 is a conserved receptor kinase activating the Integrated Stress Response (ISR) in eukaryotic cells. The ISR kinases detect accumulation of stress molecules and reprogram translation from basal tasks to preferred production of cytoprotective proteins. GCN2 stands out evolutionarily among all protein kinases due to the presence of a h istidyl t R NA s ynthetase-like (HRSL) domain, which arises only in GCN2 and is located next to the kinase domain. How HRSL contributes to GCN2 signaling remains unknown. Here we report a 3.2 Å cryo-EM structure of HRSL from thermotolerant yeast\n\nCryo-EM Structure of HRSL Domain Reveals Activating Crossed Helices at the Core of GCN2.", "token_count": 187, "char_count": 675, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7264, "quality_score": 0.8632, "entities": { "genes": [ "GCN2" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:44.685695", "source": { "split": "train_shard_00000", "doc_id": 930 }, "chunk_id": "train_shard_00000_930_0", "global_id": 1027 }, { "text": "Farnesoid X receptor (FXR) was identified as an orphan nuclear receptor resembling the steroid receptor in the late '90s. Activation of FXR is a crucial step in many physiological functions of the liver. A vital role of FXR is impacting the amount of bile acids in the hepatocytes, which it performs by reducing bile acid synthesis, stimulating the bile salt export pump, and inhibiting its enterohepatic circulation, thus protecting the hepatocytes against the toxic accumulation of bile acids. Furthermore, FXR mediates bile acid biotransformation in the intestine, liver regeneration, glucose hemostasis, and lipid metabolism. In this review, we first discuss the mechanisms of the disparate pleiotropic actions of FXR agonists. We then delve into the pharmacokinetics of Obeticholic acid (OCA), the first-in-class selective, potent FXR agonist. We additionally discuss the clinical journey of OCA in humans, its current evidence in various human diseases, and its plausible roles in the future.\n\nA Short Review on Obeticholic Acid: An Effective Modulator of Farnesoid X Receptor.", "token_count": 284, "char_count": 1083, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6564, "quality_score": 0.8282, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:45.265344", "source": { "split": "train_shard_00000", "doc_id": 931 }, "chunk_id": "train_shard_00000_931_0", "global_id": 1028 }, { "text": "Pediatric pulmonary hypertension is a serious syndrome with significant morbidity and mortality. Sildenafil is widely used off-label in pediatric patients with pulmonary arterial hypertension. In this study, bile salt-stabilized nanovesicles (bilosomes) were screened for their efficacy to enhance the transdermal delivery of the phosphodiesterase type 5 inhibitor, sildenafil citrate, in an attempt to augment its therapeutic efficacy in pediatric pulmonary hypertension. A response surface methodology was implemented for fabricating and optimizing a bilosomal formulation of sildenafil (SDF-BS). The optimized SDF-BS formulation was characterized in terms of its entrapment efficiency (EE), zeta potential, vesicle size, and in vitro release profile. The optimized formula was then loaded onto hydroxypropyl methyl cellulose (HPMC) hydrogel and assessed for skin permeation, in vivo pharmacokinetics, and pharmacodynamic studies. The optimized SDF-BS showed the following characteristic features; EE of 88.7 ± 1.1%, vesicle size of 185.0 + 9.2 nm, zeta potential of -20.4 ± 1.1 mV, and efficiently sustained SDF release for 12 h. Skin permeation study revealed a remarkable improvement in SDF penetration from bilosomal gel compared to plain SDF gel. In addition, pharmacokinetic results revealed that encapsulating SDF within bilosomal vesicles significantly enhanced its systemic bioavailability (∼3 folds), compared to SDF oral suspension. In addition, pharmacodynamic investigation revealed that, compared to plain SDF gel or oral drug suspension, SDF-BS gel applied topically triggered a significant elevation (\n\nTailoring of Bilosomal Nanogel for Augmenting the Off-Label Use of Sildenafil Citrate in Pediatric Pulmonary Hypertension.", "token_count": 473, "char_count": 1743, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:45.913662", "source": { "split": "train_shard_00000", "doc_id": 932 }, "chunk_id": "train_shard_00000_932_0", "global_id": 1029 }, { "text": "The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.\n\nPangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks.", "token_count": 97, "char_count": 366, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:46.329070", "source": { "split": "train_shard_00000", "doc_id": 933 }, "chunk_id": "train_shard_00000_933_0", "global_id": 1030 }, { "text": "Potato is an important crop in the genus Solanum section Petota. Potatoes are susceptible to multiple abiotic and biotic stresses and have undergone constant improvement through breeding programs worldwide. Introgression of wild relatives from section Petota with potato is used as a strategy to enhance the diversity of potato germplasm. The current dataset contributes a phased genome assembly for diploid S. okadae, and short read sequences and de novo assemblies for the genomes of 16 additional wild diploid species in section Petota that were noted for stress resistance and were of interest to potato breeders. Genome sequence data for three additional genomes representing polyploid hybrids with cultivated potato, and an additional genome from non-tuberizing S. etuberosum, which is outside of section Petota, were also included. High quality short reads assemblies were achieved with genome sizes ranging from 575 to 795 Mbp and annotations were performed utilizing transcriptome sequence data. Genomes were compared for presence/absence of genes and phylogenetic analyses were carried out using plastome and nuclear sequences.\n\nThe phased Solanum okadae genome and Petota pangenome analysis of 23 other potato wild relatives and hybrids.", "token_count": 294, "char_count": 1248, "word_count": 184, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:46.930163", "source": { "split": "train_shard_00000", "doc_id": 934 }, "chunk_id": "train_shard_00000_934_0", "global_id": 1031 }, { "text": "Clostridium butyricum is a Gram-positive anaerobic bacterium known for its ability to produce butyate. In this study, we conducted whole-genome sequencing and assembly of 14C. butyricum industrial strains collected from various parts of China. We performed a pan-genome comparative analysis of the 14 assembled strains and 139 strains downloaded from NCBI. We found that the genes related to critical industrial production pathways were primarily present in the core and soft-core gene categories. The phylogenetic analysis revealed that strains from the same clade of the phylogenetic tree possessed similar antibiotic resistance and virulence factors, with most of these genes present in the shell and cloud gene categories. Finally, we predicted the genes producing bacteriocins and botulinum toxins as well as CRISPR systems responsible for host defense. In conclusion, our research provides a desirable pan-genome database for the industrial production, food application, and genetic research of C. butyricum.\n\nPangenome analyses of Clostridium butyricum provide insights into its genetic characteristics and industrial application.", "token_count": 259, "char_count": 1137, "word_count": 160, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:47.480476", "source": { "split": "train_shard_00000", "doc_id": 935 }, "chunk_id": "train_shard_00000_935_0", "global_id": 1032 }, { "text": "Phocaeicola dorei and Phocaeicola vulgatus are very common and abundant members of the human gut microbiome and play an important role in the infant gut microbiome. These species are closely related and often confused for one another; yet, their genome comparison, interspecific diversity, and evolutionary relationships have not been studied in detail so far. Here, we perform phylogenetic analysis and comparative genomic analyses of these two Phocaeicola species. We report that P. dorei has a larger genome yet a smaller pan-genome than P. vulgatus. We found that this is likely because P. vulgatus is more plastic than P. dorei, with a larger repertoire of genetic mobile elements and fewer anti-phage defense systems. We also found that P. dorei directly descends from a clade of P. vulgatus¸ and experienced genome expansion through genetic drift and horizontal gene transfer. Overall, P. dorei and P. vulgatus have very different functional and carbohydrate utilisation profiles, hinting at different ecological strategies, yet they present similar antimicrobial resistance profiles.\n\nGenome plasticity shapes the ecology and evolution of Phocaeicola dorei and Phocaeicola vulgatus.", "token_count": 289, "char_count": 1190, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:48.040030", "source": { "split": "train_shard_00000", "doc_id": 936 }, "chunk_id": "train_shard_00000_936_0", "global_id": 1033 }, { "text": "Streptococcus pneumoniae (pneumococcus) is a Gram-positive coccus causing both non-invasive and invasive infectious diseases. Pneumococcal diseases are vaccine preventable. Invasive pneumococcal diseases (IPD) meeting the international case definition are reported nationally and internationally and are subject to surveillance programmes in many countries, including the Czech Republic. An important part of IPD surveillance is the monitoring of causative serotypes and their frequency over time and in relation to ongoing vaccination programmes. In the world and in the Czech Republic, whole genome sequencing (WGS) is increasingly used for pneumococci, which allows for serotyping from sequencing data, precise analysis of their genetic relationships, and the study of genes present in their genome. Whole-genome sequencing enables the generation of reliable and internationally comparable data that can be easily shared. Sequencing data are analysed using bioinformatics tools that require knowledge in the field of natural sciences with an emphasis on genetics and expertise in bioinformatics. This publication presents some options for pneumococcal analysis, i.e., serotyping, multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), whole genome MLST (wgMLST), single nucleotide polymorphism (SNP) analysis, assignment to Global Pneumococcal Sequence Cluster (GPSC), and identification of virulence genes and antibiotic resistance genes. The WGS strategies and applications for Europe and WGS implementation in practice are presented. WGS analysis of pneumococci allows for improved IPD surveillance, thanks to molecular serotyping, more detailed typing, generation of internationally comparable data, and improved evaluation of the effectiveness of vaccination programmes.\n\n[Posibilities for use of whole genome sequencing (WGS) for the analysis of Streptococcus pneumoniae isolates].", "token_count": 442, "char_count": 1921, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:48.667493", "source": { "split": "train_shard_00000", "doc_id": 937 }, "chunk_id": "train_shard_00000_937_0", "global_id": 1034 }, { "text": "Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species.\n\nPangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus).", "token_count": 150, "char_count": 665, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7263, "quality_score": 0.8632, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:49.101364", "source": { "split": "train_shard_00000", "doc_id": 938 }, "chunk_id": "train_shard_00000_938_0", "global_id": 1035 }, { "text": "Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.\n\nAspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters.", "token_count": 304, "char_count": 1240, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7135, "quality_score": 0.8567, "entities": { "genes": [ "NRRL3357", "AF13", "MAT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:49.662511", "source": { "split": "train_shard_00000", "doc_id": 939 }, "chunk_id": "train_shard_00000_939_0", "global_id": 1036 }, { "text": "Pyrus (pear) is among the most nutritious fruits and contains fibers that have great health benefits to humans. It is mostly cultivated in temperate regions globally and is highly subjected to biotic and abiotic stresses which affect its yield. Pheophorbide a oxygenase (PAO) is an essential component of the chlorophyll degradation system and contributes to the senescence of leaves. It is responsible for opening the pheophorbide a porphyrin macrocycle and forming the main fluorescent chlorophyll catabolite However, this gene family and its members have not been explored in Pyrus genomes. Here we report a pangenome-wide investigation has been conducted on eight Pyrus genomes: Cuiguan, Shanxi Duli, Zhongai 1, Nijisseiki, Yunhong No.1, d'Anjou, Bartlett v2.0, and Dangshansuli v.1.1. The phylogenetic history, their gene structure, conservation patterns of motifs, their distribution on chromosomes, and gene duplication are studied in detail which shows the intraspecific structural conservation as well as evolutionary patterns of Pyrus PAOs.\n\nComparative genomics analysis of pheophorbide", "token_count": 291, "char_count": 1097, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7134, "quality_score": 0.8567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:50.221604", "source": { "split": "train_shard_00000", "doc_id": 940 }, "chunk_id": "train_shard_00000_940_0", "global_id": 1037 }, { "text": "Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as: (i) data selection, (ii) functional annotation, (iii) phylogenetic analysis, (iv) genome mining, and (v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter Notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge from the ever-growing genomic datasets of biotechnologically relevant bacterial species.\n\nBGCFlow: systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets.", "token_count": 359, "char_count": 1609, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6884, "quality_score": 0.8442, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:50.809071", "source": { "split": "train_shard_00000", "doc_id": 941 }, "chunk_id": "train_shard_00000_941_0", "global_id": 1038 }, { "text": "By decomposing genome sequences into k-mers, it is possible to estimate genome differences without alignment. Techniques such as k-mer minimisers, for example MinHash, have been developed and are often accurate approximations of distances based on full k-mer sets. These and other alignment-free methods avoid the large temporal and computational expense of alignment. However, these k-mer set comparisons are not entirely accurate within-species and can be completely inaccurate within-lineage. This is due, in part, to their inability to distinguish core polymorphism from accessory differences. Here we present a new approach, KmerAperture, which uses information on the k-mer relative genomic positions to determine the type of polymorphism causing differences in k-mer presence and absence between pairs of genomes. Single SNPs are expected to result in k unique contiguous k-mers per genome. On the other hand, contiguous series > k may be caused by accessory differences of length S-k+1; when the start and end of the sequence are contiguous with homologous sequence. Alternatively, they may be caused by multiple SNPs within k bp from each other and KmerAperture can determine whether that is the case. To demonstrate use cases KmerAperture was benchmarked using datasets including a very low diversity simulated population with accessory content independent from the number of SNPs, a simulated population where SNPs are spatially dense, a moderately diverse real cluster of genomes (Escherichia coli ST1193) with a large accessory genome and a low diversity real genome cluster (Salmonella Typhimurium ST34). We show that KmerAperture can accurately distinguish both core and accessory sequence diversity without alignment, outperforming other k-mer based tools.\n\nKmerAperture: Retaining k-mer synteny for alignment-free extraction of core and accessory differences between bacterial genomes.", "token_count": 434, "char_count": 1902, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [ "ST34", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:51.447485", "source": { "split": "train_shard_00000", "doc_id": 942 }, "chunk_id": "train_shard_00000_942_0", "global_id": 1039 }, { "text": "Recombination of short DNA fragments via horizontal gene transfer (HGT) can introduce beneficial alleles, create genomic disharmony through negative epistasis, and create adaptive gene combinations through positive epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome and are frequently observed as tightly linked cassettes with major effects. By contrast, interspecific recombination in the core genome is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma, we take advantage of an exceptional model system, the common enteric pathogens\n\nEpistasis, core-genome disharmony, and adaptation in recombining bacteria.", "token_count": 192, "char_count": 883, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7213, "quality_score": 0.8607, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:51.895510", "source": { "split": "train_shard_00000", "doc_id": 943 }, "chunk_id": "train_shard_00000_943_0", "global_id": 1040 }, { "text": "A herbal formula Tong-Xie-Yao-Fang (TXYF) is traditionally used to treat irritable bowel syndrome (IBS), modern pharmacological evidence supports that the formula efficacy is associated with altered gut microbiota. Yet, the mechanistic role of gut microbiota in the therapy of TXYF remains unclear. We previously clarified that gut microbiota-dysregulated bile acid (BA) metabolism contribute to the pathogenesis of IBS, deriving a hypothesis that microbiota-BA metabolic axis might be a potential target of TXYF.\n\nTong-Xie-Yao-Fang strengthens intestinal feedback control of bile acid synthesis to ameliorate irritable bowel syndrome by enhancing bile salt hydrolase-expressing microbiota.", "token_count": 187, "char_count": 690, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7283, "quality_score": 0.8641, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:52.351328", "source": { "split": "train_shard_00000", "doc_id": 944 }, "chunk_id": "train_shard_00000_944_0", "global_id": 1041 }, { "text": "Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated.\n\nRecGraph: recombination-aware alignment of sequences to variation graphs.", "token_count": 144, "char_count": 713, "word_count": 96, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:52.780094", "source": { "split": "train_shard_00000", "doc_id": 945 }, "chunk_id": "train_shard_00000_945_0", "global_id": 1042 }, { "text": "Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (\n\nResearch Progress and Applications of Bovine Genome in the Tribe", "token_count": 210, "char_count": 973, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6906, "quality_score": 0.8453, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:53.241301", "source": { "split": "train_shard_00000", "doc_id": 946 }, "chunk_id": "train_shard_00000_946_0", "global_id": 1043 }, { "text": "A pangenome captures the genomic diversity for a species, derived from a collection of genetic sequences of diverse populations. Advances in sequencing technologies have given rise to three primary methods for pangenome construction and analysis: de novo assembly and comparison, reference genome-based iterative assembly, and graph-based pangenome construction. Each method presents advantages and challenges in processing varying amounts and structures of DNA sequencing data. With the emergence of high-quality genome assemblies and advanced bioinformatic tools, the graph-based pangenome is emerging as an advanced reference for exploring the biological and functional implications of genetic variations.\n\nTechnological Development and Advances for Constructing and Analyzing Plant Pangenomes.", "token_count": 155, "char_count": 797, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7115, "quality_score": 0.8558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:53.674343", "source": { "split": "train_shard_00000", "doc_id": 947 }, "chunk_id": "train_shard_00000_947_0", "global_id": 1044 }, { "text": "Nearly 300 million individuals live with chronic hepatitis B virus (HBV) infection (CHB), for which no curative therapy is available. As viral diversity is associated with pathogenesis and immunological control of infection, improved methods to characterize this diversity could aid drug development efforts. Conventionally, viral sequencing data are mapped/aligned to a reference genome, and only the aligned sequences are retained for analysis. Thus, reference selection is critical, yet selecting the most representative reference a priori remains difficult. We investigate an alternative pangenome approach which can combine multiple reference sequences into a graph which can be used during alignment. Using simulated short-read sequencing data generated from publicly available HBV genomes and real sequencing data from an individual living with CHB, we demonstrate alignment to a phylogenetically representative 'genome graph' can improve alignment, avoid issues of reference ambiguity, and facilitate the construction of sample-specific consensus sequences more genetically similar to the individual's infection. Graph-based methods can, therefore, improve efforts to characterize the genetics of viral pathogens, including HBV, and have broader implications in host-pathogen research.\n\nA hepatitis B virus (HBV) sequence variation graph improves alignment and sample-specific consensus sequence construction.", "token_count": 284, "char_count": 1417, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6862, "quality_score": 0.8431, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:54.230581", "source": { "split": "train_shard_00000", "doc_id": 948 }, "chunk_id": "train_shard_00000_948_0", "global_id": 1045 }, { "text": "This study aims to utilize the microbial resources found within Laphet-so, a traditional fermented tea in Myanmar. A total of 18 isolates of thermotolerant yeasts were obtained from eight samples of Laphet-so collected from southern Shan state, Myanmar. All isolates demonstrated the tannin tolerance, and six isolates were resistant to 5% (\n\nA Thermotolerant Yeast", "token_count": 95, "char_count": 365, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7818, "quality_score": 0.8909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:54.613522", "source": { "split": "train_shard_00000", "doc_id": 949 }, "chunk_id": "train_shard_00000_949_0", "global_id": 1046 }, { "text": "During the bacterial selection, isolate PF9 demonstrated tolerance to low pH and high bile salt and an ability to extend the lifespan of\n\nFunctional evaluation of", "token_count": 38, "char_count": 162, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [ "PF9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:54.979191", "source": { "split": "train_shard_00000", "doc_id": 950 }, "chunk_id": "train_shard_00000_950_0", "global_id": 1047 }, { "text": "The Human Genome Project was an enormous accomplishment, providing a foundation for countless explorations into the genetics and genomics of the human species. Yet for many years, the human genome reference sequence remained incomplete and lacked representation of human genetic diversity. Recently, two major advances have emerged to address these shortcomings: complete gap-free human genome sequences, such as the one developed by the Telomere-to-Telomere Consortium, and high-quality pangenomes, such as the one developed by the Human Pangenome Reference Consortium. Facilitated by advances in long-read DNA sequencing and genome assembly algorithms, complete human genome sequences resolve regions that have been historically difficult to sequence, including centromeres, telomeres, and segmental duplications. In parallel, pangenomes capture the extensive genetic diversity across populations worldwide. Together, these advances usher in a new era of genomics research, enhancing the accuracy of genomic analysis, paving the path for precision medicine, and contributing to deeper insights into human biology.\n\nBeyond the Human Genome Project: The Age of Complete Human Genome Sequences and Pangenome References.", "token_count": 255, "char_count": 1218, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6265, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:55.805039", "source": { "split": "train_shard_00000", "doc_id": 951 }, "chunk_id": "train_shard_00000_951_0", "global_id": 1048 }, { "text": "Chronic pruritus is defined as an itch lasting greater than six weeks. It can manifest from a wide variety of etiologies, as many different substances can act as pruritogens, such as steroids, histamine, progesterone, endogenous opioids, and serotonin. In the setting of cholestatic liver disease, increased bile acids play a major role in chronic pruritus. The itching in cholestatic liver disease is worsened in intensity at night and localized frequently to the palms, soles, knees, and other pressure sites. It can be hard to manage, affecting the quality of sleep and causing irritability, poor attention, and, in some cases, depression. One such disease that results from chronic pruritus is progressive familial intrahepatic cholestasis (PFIC), a group of uncommon hereditary disorders that affects the formation of bile and its outflow from the liver. Previously, the drug ursodeoxycholic acid was used to help manage pruritus or surgical procedures, e.g., partial external biliary diversion or partial internal biliary diversion, to help control complications of the disease. This literature review will discuss three clinical studies covering the effectiveness of odevixibat in treating pruritus in patients with PFIC. Odevixibat (Bylvay) is an oral drug that has been FDA-approved to treat pruritus in patients three months of age and older with PFIC. Odevixibat prevents the reabsorption of bile salts in the intestines, resulting in decreased levels of bile salts via their excretion in stool. Several studies have determined that the drug is well tolerated and provides a nonsurgical, pharmacological treatment alternative for those with PFIC.\n\nOdevixibat: A Novel Bile Salt Inhibitor Treatment for Pruritus in Progressive Familial Intrahepatic Cholestasis.", "token_count": 447, "char_count": 1771, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6312, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:56.442357", "source": { "split": "train_shard_00000", "doc_id": 952 }, "chunk_id": "train_shard_00000_952_0", "global_id": 1049 }, { "text": "Graph-based pangenome is gaining more popularity than linear pangenome because it stores more comprehensive information of variations. However, traditional linear genome browser has its own advantages, especially the tremendous resources accumulated historically. With the fast-growing number of individual genomes and their annotations available, the demand for a genome browser to visualize genome annotation for many individuals together with a graph-based pangenome is getting higher and higher. Here we report a new pangenome browser PPanG, a precise pangenome browser enabling nucleotide-level comparison of individual genome annotations together with a graph-based pangenome. Nine rice genomes with annotations were provided by default as potential references, and any individual genome can be selected as the reference. Our pangenome browser provides unprecedented insights on genome variations at different levels from base to gene, and reveals how the structures of a gene could differ for individuals. PPanG can be applied to any species with multiple individual genomes available and it is available at https://cgm.sjtu.edu.cn/PPanG .\n\nPPanG: a precision pangenome browser enabling nucleotide-level analysis of genomic variations in individual genomes and their graph-based pangenome.", "token_count": 272, "char_count": 1296, "word_count": 177, "semantic_coherence": 1, "information_density": 0.5932, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:57.019444", "source": { "split": "train_shard_00000", "doc_id": 953 }, "chunk_id": "train_shard_00000_953_0", "global_id": 1050 }, { "text": "This work shows the utilization of a physiologically based biopharmaceutics model (PBBM) to mechanistically explain the impact of diverse food types on the pharmacokinetics (PK) of isoniazid (INH) and acetyl-isoniazid (Ac-INH). The model was established and validated using published PK profiles for INH along with a combination of measured and predicted values for the physico-chemical and biopharmaceutical propertied of INH and Ac-INH. A dedicated ontogeny model was developed for N-acetyltransferase 2 (NAT2) in human integrating Michaelis Menten parameters for this enzyme in the physiologically based pharmacokinetic (PBPK) model tissues and in the gut, to explain the pre-systemic and systemic metabolism of INH across different acetylator types. Additionally, a novel equation was proposed to calculate the luminal drug degradation related to the presence of reducing sugars, using individual sugar molar concentrations in the meal. By incorporating luminal degradation into the model, adjusting bile salt concentrations and gastric emptying according to food type and quantity, the PBBM was able to accurately predict the negative effect of carbohydrate-rich diets on the PK of INH.\n\nEffect of Food Composition on the PK of Isoniazid Quantitatively Explained Using Physiologically Based Biopharmaceutics Modeling.", "token_count": 330, "char_count": 1322, "word_count": 187, "semantic_coherence": 1, "information_density": 0.5989, "quality_score": 0.7995, "entities": { "genes": [ "NAT2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:57.614250", "source": { "split": "train_shard_00000", "doc_id": 954 }, "chunk_id": "train_shard_00000_954_0", "global_id": 1051 }, { "text": "Metformin is the most prescribed and recommended drug for type 2 diabetes mellitus because of its better tolerability, pleiotropic benefits, and cost-effectiveness. Metformin inhibits hepatic glucose production and increases muscle glucose uptake. Metformin is also associated with gastrointestinal side effects like abdominal bloating, flatulence, diarrhea, nausea, and vomiting. Metformin-related gastrointestinal side effects are mainly due to alteration in gut microbiota, raised intestinal glucose, and increased ileal bile salt reabsorption. We report a case of a 62-year-old diabetic patient who presented with chronic diarrhea with a weight loss of 6 kg from the last six years after initiation of metformin. He underwent multiple investigations and was finally misdiagnosed with irritable bowel syndrome for years. After discontinuation of metformin, there was a significant improvement in gastrointestinal symptoms. Our case highlights the importance of metformin-induced chronic diarrhea if no other causes for the diarrhea are obvious in patients with type 2 diabetes taking metformin. Consideration of this potential side effect of metformin must be valuable to avoid unwarranted investigations, additional drug therapy, and annoyance of the patients.\n\nMetformin-Induced Chronic Diarrhea Misdiagnosed as Irritable Bowel Syndrome for Years.", "token_count": 337, "char_count": 1352, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:58.206848", "source": { "split": "train_shard_00000", "doc_id": 955 }, "chunk_id": "train_shard_00000_955_0", "global_id": 1052 }, { "text": "Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution.\n\nPangenome analysis reveals transposon-driven genome evolution in cotton.", "token_count": 108, "char_count": 485, "word_count": 64, "semantic_coherence": 1, "information_density": 0.8594, "quality_score": 0.9297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:58.640723", "source": { "split": "train_shard_00000", "doc_id": 956 }, "chunk_id": "train_shard_00000_956_0", "global_id": 1053 }, { "text": "Probiotics are crucial components for maintaining a healthy gut microbiota in pigs, especially during the weaning period. Lactic acid bacteria (LAB) derived from the gastrointestinal tract of wild boars can serve as an abundant source of beneficial probiotic strains with suitable properties for use in pig husbandry. In this study, we analyzed and characterized 15 strains of Limosilactobacillus mucosae obtained from the gut contents of wild boars to assess their safety and suitability as probiotic candidates. The strains were compared using pan-genomic analysis with 49 L. mucosae strains obtained from the NCBI database. All isolated strains demonstrated their safety by showing an absence of transferrable antimicrobial resistance genes and hemolysin activity. Based on the presence of beneficial genes, five candidates with probiotic properties were selected and subjected to phenotypic profiling. These five selected isolates exhibited the ability to survive conditions mimicking passage through the host's digestive tract, such as low pH and the presence of bile salts. Furthermore, five selected strains demonstrated the presence of corresponding carbohydrate-active enzymes and the ability to utilize various carbohydrate substrates. These strains can enhance the digestibility of oligosaccharide or polysaccharide substrates found in food or feed, specifically resistant starch, α-galactosides, cellobiose, gentiobiose, and arabinoxylans. Based on the results obtained, the L. mucosae isolates tested in this study appear to be promising candidates for use as probiotics in pigs.\n\nComparative Genome Analysis and Characterization of the Probiotic Properties of Lactic Acid Bacteria Isolated from the Gastrointestinal Tract of Wild Boars in the Czech Republic.", "token_count": 421, "char_count": 1772, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5823, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:59.270139", "source": { "split": "train_shard_00000", "doc_id": 957 }, "chunk_id": "train_shard_00000_957_0", "global_id": 1054 }, { "text": "Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.\n\nDefence systems and horizontal gene transfer in bacteria.", "token_count": 276, "char_count": 1331, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:07:59.823699", "source": { "split": "train_shard_00000", "doc_id": 958 }, "chunk_id": "train_shard_00000_958_0", "global_id": 1055 }, { "text": "Probiotics are defined as \"live microorganisms that provide health benefits to the host when administered in adequate amounts.\" Probiotics have beneficial effects on human health, including antibacterial activity against intestinal pathogens, regulation of blood cholesterol levels, reduction of colitis and inflammation incidence, regulation of the immune system, and prevention of colon cancer. In addition to probiotic bacteria, some phenolic compounds found in foods we consume (both food and beverages) have positive effects on human health. p-coumaric acid (p-CA) is one of the most abundant phenolic compounds in nature and human diet. The interactions between these two different food components (phenolics and probiotics), resulting in more beneficial combinations called synbiotics, are not well understood in terms of how they will affect the gut microbiota by promoting the probiotic properties and growth of probiotic bacteria. Thus, this study aimed to investigate synbiotic relationship between p-CA and Lactobacillus acidophilus LA-5 (LA-5), Lacticaseibacillus rhamnosus GG (LGG). Probiotic bacteria were grown in the presence of p-CA at different concentrations, and the effects of p-CA on probiotic properties, as well as its in vitro effects on AChE and BChE activities, were investigated. Additionally, Surface analysis was conducted using FTIR. The results showed that treatment with p-CA at different concentrations did not exhibit any inhibitory effect on the growth kinetics of LA-5 and LGG probiotic bacteria. Additionally, both probiotic bacteria demonstrated high levels of antibacterial properties. It showed that it increased the auto-aggregation of both probiotics. While p-CA increased co-aggregation of LA-5 and LGG against Escherichia coli, it decreased co-aggregation against Staphylococcus aureus. Probiotics grown with p-CA were more resistant to pepsin. While p-CA increased the resistance of LA-5 to bile salt, it decreased the resistance of LGG. The combinations of bacteria and p-CA efficiently suppressed AChE and BChE with inhibition (%) 11.04-68.43 and 13.20-65.72, respectively", "token_count": 524, "char_count": 2121, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5819, "quality_score": 0.791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:08:00.480097", "source": { "split": "train_shard_00000", "doc_id": 959 }, "chunk_id": "train_shard_00000_959_0", "global_id": 1056 }, { "text": "Furthermore, surface analysis was conducted using FTIR to investigate the interaction of p-coumaric acid with LA-5 and LGG, and changes in cell components on the bacterial surface were analyzed. The results, recorded in range of 4000 -600 cm\n\nEffects of p-coumaric acid on probiotic properties of Lactobacillus acidophilus LA-5 and lacticaseibacillus rhamnosus GG.", "token_count": 107, "char_count": 364, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7547, "quality_score": 0.8774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:00.885411", "source": { "split": "train_shard_00000", "doc_id": 959 }, "chunk_id": "train_shard_00000_959_1", "global_id": 1057 }, { "text": "Epithelial-mesenchymal plasticity (EMP), the process through which epithelial cells acquire mesenchymal features, is needed for wound repair but also might contribute to cancer initiation. Earlier, in vitro studies showed that Barrett's cells exposed to acidic bile salt solutions (ABS) develop EMP. Now, we have (1) induced reflux oesophagitis in Barrett's oesophagus (BO) patients by stopping proton pump inhibitors (PPIs), (2) assessed their biopsies for EMP and (3) explored molecular pathways underlying reflux-induced EMP in BO cells and spheroids.\n\nHypoxia-inducible factor-1α mediates reflux-induced epithelial-mesenchymal plasticity in Barrett's oesophagus patients.", "token_count": 199, "char_count": 675, "word_count": 88, "semantic_coherence": 1, "information_density": 0.8295, "quality_score": 0.9148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:01.341552", "source": { "split": "train_shard_00000", "doc_id": 960 }, "chunk_id": "train_shard_00000_960_0", "global_id": 1058 }, { "text": "Kluyveromyces marxianus is a non-Saccharomyces yeast that has gained importance due to its great potential to be used in the food and biotechnology industries. In general, K. marxianus is a known yeast for its ability to assimilate hexoses and pentoses; even this yeast can grow in disaccharides such as sucrose and lactose and polysaccharides such as agave fructans. Otherwise, K. marxianus is an excellent microorganism to produce metabolites of biotechnological interest, such as enzymes, ethanol, aroma compounds, organic acids, and single-cell proteins. However, several studies highlighted the metabolic trait variations among the K. marxianus strains, suggesting genetic diversity within the species that determines its metabolic functions; this diversity can be attributed to its high adaptation capacity against stressful environments. The outstanding metabolic characteristics of K. marxianus have motivated this yeast to be a study model to evaluate its easy adaptability to several environments. This chapter will discuss overview characteristics and applications of K. marxianus and recent insights into the stress response and adaptation mechanisms used by this non-Saccharomyces yeast.\n\nStress response and adaptation mechanisms in Kluyveromyces marxianus.", "token_count": 295, "char_count": 1271, "word_count": 177, "semantic_coherence": 1, "information_density": 0.5989, "quality_score": 0.7994, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:01.914401", "source": { "split": "train_shard_00000", "doc_id": 961 }, "chunk_id": "train_shard_00000_961_0", "global_id": 1059 }, { "text": "This study isolated and identified autochthonous lactic acid bacteria (LAB) from mandacaru fruit and evaluated their potential probiotic and technological aptitudes in vitro, as well as the protective effects of freeze-dried mandacaru fruit on the most promising LAB isolate during lyophilization and refrigeration storage. Initially, 212 colonies were isolated from mandacaru fruit, and 34 were preliminarily identified as LAB. Thirteen isolates identified by 16S-rRNA sequencing as Pediococcus pentosaceus were negative for DNase, gelatinase, hemolytic, and biogenic amine production. The selected isolates showed proteolytic activity, diacetyl and exopolysaccharide production, and good tolerance to different NaCl concentrations while having low cellular hydrophobicity and antagonistic activity against pathogens. The survival of isolates sharply decreased after 3 h of exposure to pH 2 and had a good tolerance to 1 % bile salt. A principal component analysis selected P. pentosaceus 57 as the most promising isolate based on the examined technological and probiotic-related physiological properties. This isolate was lyophilized with mandacaru fruit and stored under refrigeration for 90 days. P. pentosaceus 57 lyophilized with mandacaru fruit had high viable cell counts (9.69 ± 0.03 log CFU/mL) and >50 % of physiologically active cells at 90 days of refrigeration storage. The results indicate that mandacaru fruit is a source of P. pentosaceus with aptitudes to be explored as potential probiotic and technological characteristics of interest for the food industry, besides being a good candidate for use in lyophilization processes and refrigeration storage of LAB due to its cryoprotective effects.\n\nCereus jamacaru DC. (mandacaru) fruit as a source of lactic acid bacteria with in vitro probiotic-related characteristics and its protective effects on Pediococcus pentosaceus during lyophilization and refrigeration storage.", "token_count": 487, "char_count": 1938, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5678, "quality_score": 0.7839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:02.567707", "source": { "split": "train_shard_00000", "doc_id": 962 }, "chunk_id": "train_shard_00000_962_0", "global_id": 1060 }, { "text": "Obesity is a growing epidemic worldwide. Several pharmacologic drugs are being used to treat obesity but these medicines exhibit side effects. To find out the alternatives of these drugs, we aimed to assess the probiotic properties and anti-obesity potentiality of a lactic acid bacterium E2_MCCKT, isolated from a traditional fermented rice beverage, haria. Based on the 16S rRNA sequencing, the bacterium was identified as Lactiplantibacillus plantarum E2_MCCKT. The bacterium exhibited in vitro probiotic activity in terms of high survivability in an acidic environment and 2% bile salt, moderate auto-aggregation, and hydrophobicity. Later, E2_MCCKT was applied to obese mice to prove its anti-obesity potentiality. Adult male mice (15.39 ± 0.19 g) were randomly divided into three groups (n = 5) according to the type of diet: normal diet (ND), high-fat diet (HFD), and HFD supplemented with E2_MCCKT (HFT). After four weeks of bacterial treatment on the obese mice, a significant reduction of body weight, triglyceride, and cholesterol levels, whereas, improvements in serum glucose levels were observed. The bacterial therapy led to mRNA up-regulation of lipolytic transcription factors such as peroxisome proliferator-activated receptor-α which may increase the expression of fatty acid oxidation-related genes such as acyl-CoA oxidase and carnitine palmitoyl-transferase-1. Concomitantly, both adipocytogenesis and fatty acid synthesis were arrested as reflected by the down-regulation of sterol-regulatory element-binding protein-1c, acetyl-CoA carboxylase, and fatty acid synthase genes. In protein expression study, E2_MCCKT significantly increased IL-10 expression while decreasing pro-inflammatory cytokine (IL-1Ra and TNF-α) expression. In conclusion, the probiotic Lp", "token_count": 510, "char_count": 1783, "word_count": 245, "semantic_coherence": 1, "information_density": 0.7224, "quality_score": 0.8612, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:03.224477", "source": { "split": "train_shard_00000", "doc_id": 963 }, "chunk_id": "train_shard_00000_963_0", "global_id": 1061 }, { "text": "plantarum E2_MCCKT might have significant anti-obesity effects on mice.\n\nAnti-obesity potentiality of Lactiplantibacillus plantarum E2_MCCKT isolated from a fermented beverage, haria: a high fat diet-induced obese mice model study.", "token_count": 76, "char_count": 231, "word_count": 29, "semantic_coherence": 1, "information_density": 0.8621, "quality_score": 0.931, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:03.595016", "source": { "split": "train_shard_00000", "doc_id": 963 }, "chunk_id": "train_shard_00000_963_1", "global_id": 1062 }, { "text": "Through vaginal colonization, GBS causes severe outcomes including neonatal sepsis and meningitis. Although intrapartum antibiotic prophylaxis (IAP) has reduced neonatal disease rates, persistent GBS colonization has been observed in patients following prophylaxis. To determine whether IAP selects for genomic signatures that enhance GBS survival and persistence, a pangenome analysis was performed on 97 isolates from 58 participants before (prenatal) and after (postpartum) IAP/childbirth. Thirty-one of the 34 paired strains from participants with persistent colonization clustered together in the core gene phylogeny, suggesting that the strains recovered at the postpartum sampling were highly similar to those recovered at the prenatal visit. A core-gene mutation analysis identified mutations in 74% (n=23) of the 31 postpartum genomes when compared to the prenatal strains of the same multilocus sequence type recovered from the same individuals. Several strains had acquired mutations in the same colonization-associated genes, though two postpartum strains accounted for most of the mutations. These two outliers were classified as mutators based on high mutation rates and mutations within DNA repair system genes. Increased biofilm production was observed in half of the postpartum strains relative to the prenatal strains, which is supported by the presence of point mutations in genes associated with adherence. Together, these findings suggest that antibiotics may impose a selective pressure on GBS that selects for mutations and phenotypes that promote adaptation and survival\n\nGenomic adaptation in group B", "token_count": 377, "char_count": 1625, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:04.147044", "source": { "split": "train_shard_00000", "doc_id": 964 }, "chunk_id": "train_shard_00000_964_0", "global_id": 1063 }, { "text": "The highly potent toxin cereulide is a frequent cause of foodborne intoxications. This extremely resistant toxin is produced by Bacillus cereus group strains carrying the plasmid encoded cesHPTABCD gene cluster. It is known that the capacities to produce cereulide vary greatly between different strains but the genetic background of these variations is not clear. In this study, cereulide production capacities were associated with genetic characteristics. For this, cereulide levels in cultures of 31 strains were determined after incubation in tryptic soy broth for 24 h at 24 °C, 30 °C and 37 °C. Whole genome sequencing based data were used for an in-depth characterization of gene sequences related to cereulide production. The taxonomy, population structure and phylogenetic relationships of the strains were evaluated based on average nucleotide identity, multi-locus sequence typing (MLST), core genome MLST and single nucleotide polymorphism analyses. Despite a limited strain number, the approach of a genome wide association study (GWAS) was tested to link genetic variation with cereulide quantities. Our study confirms strain-dependent differences in cereulide production. For most strains, these differences were not explainable by sequence variations in the cesHPTABCD gene cluster or the regulatory genes abrB, spo0A, codY and pagRBc. Likewise, the population structure and phylogeny of the tested strains did not comprehensively reflect the cereulide production capacities. GWAS yielded first hints for associated proteins, while their possible effect on cereulide synthesis remains to be further investigated.\n\nCereulide production capacities and genetic properties of 31 emetic Bacillus cereus group strains.", "token_count": 411, "char_count": 1728, "word_count": 246, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:04.763689", "source": { "split": "train_shard_00000", "doc_id": 965 }, "chunk_id": "train_shard_00000_965_0", "global_id": 1064 }, { "text": "Cultivating rice varieties with robust blast resistance is the most effective and economical way to manage the rice blast disease. However, rice blast disease comprises leaf and panicle blast, which are different in terms of resistance mechanisms. While many blast resistant rice cultivars were bred using genes conferring resistance to only leaf or panicle blast, mining durable and effective quantitative trait loci (QTLs) for both panicle and leaf blast resistance is of paramount importance. In this study, we conducted a pangenome-wide association study (panGWAS) on 9 blast resistance related phenotypes using 414 international diverse rice accessions from an international rice panel. This approach led to the identification of 74 QTLs associated with rice blast resistance. One notable locus, qPBR1, validated in a F\n\nPangenome-Wide Association Study and Transcriptome Analysis Reveal a Novel QTL and Candidate Genes Controlling both Panicle and Leaf Blast Resistance in Rice.", "token_count": 220, "char_count": 984, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6345, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:05.231255", "source": { "split": "train_shard_00000", "doc_id": 966 }, "chunk_id": "train_shard_00000_966_0", "global_id": 1065 }, { "text": "An Actinobacteria - Kitasatospora sp. K002 - was isolated from the soil of Cerrado, a savanna-like Brazilian biome. Herein, we conducted a phylogenetic, phenotypic and physiological characterization, revealing its potential for biotechnological applications. Kitasatospora sp. K002 is an aerobic, non-motile, Gram-positive bacteria that forms grayish-white mycelium on solid cultures and submerged spores with vegetative mycelia on liquid cultures. The strain showed antibacterial activity against Bacillus subtilis, Pseudomonas aeruginosa and Escherichia coli. Genomic analysis indicated that Kitasatospora xanthocidica JCM 4862 is the closest strain to K002, with a dDDH of 32.8-37.8% and an ANI of 86.86% and the pangenome investigations identified a high number of rare genes. A total of 60 gene clusters of 22 different types were detected by AntiSMASH, and 22 gene clusters showed low similarity (< 10%) with known compounds, which suggests the potential production of novel bioactive compounds. In addition, phylogenetic analysis and morphophysiological characterization clearly distinguished Kitasatospora sp. K002 from other related species. Therefore, we propose that Kitasatospora sp. K002 should be recognized as a new species of the genus Kitasatospora - Kitasatospora brasiliensis sp. nov. (type strains = K002).\n\nGenomic and physiological characterization of Kitasatospora sp. nov., an actinobacterium with potential for biotechnological application isolated from Cerrado soil.", "token_count": 429, "char_count": 1492, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6601, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:05.857068", "source": { "split": "train_shard_00000", "doc_id": 967 }, "chunk_id": "train_shard_00000_967_0", "global_id": 1066 }, { "text": "Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.\n\nA review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database.", "token_count": 394, "char_count": 1819, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6054, "quality_score": 0.8027, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:06.475274", "source": { "split": "train_shard_00000", "doc_id": 968 }, "chunk_id": "train_shard_00000_968_0", "global_id": 1067 }, { "text": "Kluyveromyces marxianus has become an attractive non-conventional yeast cell factory due to its advantageous properties such as high thermal tolerance and rapid growth. Succinic acid (SA) is an important platform molecule that has been applied in various industries such as food, material, cosmetics, and pharmaceuticals. SA bioproduction may be compromised by its toxicity. Besides, metabolite-responsive promoters are known to be important for dynamic control of gene transcription. Therefore, studies on global gene transcription under various SA concentrations are of great importance. Here, comparative transcriptome changes of K. marxianus exposed to various concentrations of SA were analyzed. Enrichment and analysis of gene clusters revealed repression of the tricarboxylic acid cycle and glyoxylate cycle, also activation of the glycolysis pathway and genes related to ergosterol synthesis. Based on the analyses, potential SA-responsive promoters were investigated, among which the promoter strength of IMTCP2 and KLMA_50231 increased 43.4% and 154.7% in response to 15 g/L SA. In addition, overexpression of the transcription factors Gcr1, Upc2, and Ndt80 significantly increased growth under SA stress. Our results benefit understanding SA toxicity mechanisms and the development of robust yeast for organic acid production. KEY POINTS: • Global gene transcription of K. marxianus is changed by succinic acid (SA) • Promoter activities of IMTCP2 and KLMA_50123 are regulated by SA • Overexpression of Gcr1, Upc2, and Ndt80 enhanced SA tolerance.\n\nTranscriptome analysis of Kluyveromyces marxianus under succinic acid stress and development of robust strains.", "token_count": 416, "char_count": 1671, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [ "IMTCP2" ], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:07.105529", "source": { "split": "train_shard_00000", "doc_id": 969 }, "chunk_id": "train_shard_00000_969_0", "global_id": 1068 }, { "text": "Whole-genome sequencing (WGS) is currently making its transition from research tool into routine (clinical) diagnostic practice. The workflow for WGS includes the highly labor-intensive library preparations (LP), one of the most critical steps in the WGS procedure. Here, we describe the automation of the LP on the flowbot ONE robot to minimize the risk of human error and reduce hands-on time (HOT). For this, the robot was equipped, programmed, and optimized to perform the Illumina DNA Prep automatically. Results obtained from 16 LP that were performed both manually and automatically showed comparable library DNA yields (median of 1.5-fold difference), similar assembly quality values, and 100% concordance on the final core genome multilocus sequence typing results. In addition, reproducibility of results was confirmed by re-processing eight of the 16 LPs using the automated workflow. With the automated workflow, the HOT was reduced to 25 min compared to the 125 min needed when performing eight LPs using the manual workflow. The turn-around time was 170 and 200 min for the automated and manual workflow, respectively. In summary, the automated workflow on the flowbot ONE generates consistent results in terms of reliability and reproducibility, while significantly reducing HOT as compared to manual LP.\n\nAutomating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot.", "token_count": 335, "char_count": 1454, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.8059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:07.677649", "source": { "split": "train_shard_00000", "doc_id": 970 }, "chunk_id": "train_shard_00000_970_0", "global_id": 1069 }, { "text": "Lactic acid bacteria (LAB) belong to a significant group of probiotic bacteria that provide hosts with considerable health benefits. Our previous study showed that pigs with abundant LAB had more robust immune responses in a vaccination experiment. In this study, 52 isolate strains were isolated from the pigs with superior immune responses. Out of these, 14 strains with higher antibacterial efficacy were chosen. We then assessed the probiotic features of the 14 LAB strains, including such as autoaggregation, coaggregation, acid resistance, bile salt resistance, and adhesion capability, as well as safety aspects such as antibiotic resistance, hemolytic activity, and the presence or absence of virulence factors. We also compared these properties with those of an opportunistic pathogen EB1 and two commercial probiotics (cLA and cLP). The results showed that most LAB isolates exhibited higher abilities of aggregation, acid and bile salt resistance, adhesion, and antibacterial activity than the two commercial probiotics. Out of the 14 strains, only LS1 and LS9 carried virulence genes and none had hemolytic activity. We selected three LAB strains (LA6, LR6 and LJ1) with superior probiotic properties and LS9 with a virulence gene for testing their safety\n\nMolecular identification and probiotic potential characterization of lactic acid bacteria isolated from the pigs with superior immune responses.", "token_count": 331, "char_count": 1413, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7919, "entities": { "genes": [ "EB1", "LS9", "LR6", "LJ1", "LS1", "LA6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:08.248462", "source": { "split": "train_shard_00000", "doc_id": 971 }, "chunk_id": "train_shard_00000_971_0", "global_id": 1070 }, { "text": "Nucleus-forming phages (chimalliviruses) encode numerous genes responsible for creating intricate structures for viral replication. Research on this newly appreciated family of phages has begun to reveal the mechanisms underlying the subcellular organization of the nucleus-based phage replication cycle. These discoveries include the structure of the phage nuclear shell, the identification of a membrane-bound early phage infection intermediate, the dynamic localization of phage RNA polymerases, the phylogeny and core genome of chimalliviruses, and the variation in replication mechanisms across diverse nucleus-forming phages. This research is being propelled forward through the application of fluorescence microscopy and cryo-electron microscopy and the innovative use of new tools such as proximity labeling and RNA-targeting Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems.\n\nThe intricate organizational strategy of nucleus-forming phages.", "token_count": 219, "char_count": 970, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:08.713660", "source": { "split": "train_shard_00000", "doc_id": 972 }, "chunk_id": "train_shard_00000_972_0", "global_id": 1071 }, { "text": "Bile acids regulate nutrient absorption and mitochondrial function, they establish and maintain gut microbial community composition and mediate inflammation, and they serve as signalling molecules that regulate appetite and energy homeostasis. The observation that there are hundreds of bile acids, especially many amidated bile acids, necessitates a revision of many of the classical descriptions of bile acids and bile acid enzyme functions. For example, bile salt hydrolases also have transferase activity. There are now hundreds of known modifications to bile acids and thousands of bile acid-associated genes, especially when including the microbiome, distributed throughout the human body (for example, there are >2,400 bile salt hydrolases alone). The fact that so much of our genetic and small-molecule repertoire, in both amount and diversity, is dedicated to bile acid function highlights the centrality of bile acids as key regulators of metabolism and immune homeostasis, which is, in large part, communicated via the gut microbiome.\n\nThe changing metabolic landscape of bile acids - keys to metabolism and immune regulation.", "token_count": 262, "char_count": 1137, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6145, "quality_score": 0.8072, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:09.305747", "source": { "split": "train_shard_00000", "doc_id": 973 }, "chunk_id": "train_shard_00000_973_0", "global_id": 1072 }, { "text": "Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk of patient DNA leakage. To mitigate this risk, we need near-comprehensive removal of human DNA sequences at the point of sequencing, typically involving the use of resource-constrained devices. Existing benchmarks have largely focused on the use of standardized databases and largely ignored the computational requirements of depletion pipelines as well as the impact of human genome diversity.\n\nPangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.", "token_count": 144, "char_count": 688, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7363, "quality_score": 0.8681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:09.746917", "source": { "split": "train_shard_00000", "doc_id": 974 }, "chunk_id": "train_shard_00000_974_0", "global_id": 1073 }, { "text": "Mounting evidence has shown that the gut microbiota plays a key role in human health. The homeostasis of the gut microbiota could be affected by many factors, including environmental chemicals. Aldicarb is a carbamate insecticide used to control a variety of insects and nematode pests in agriculture. Aldicarb is highly toxic and its wide existence has become a global public health concern. In our previous study, we have demonstrated that aldicarb disturbed the gut microbial community structure and composition. However, the impacts of aldicarb on gut microbiota-derived metabolites, bile acids, remain elusive. In present study, we performed targeted metabolomics analysis to explore the effects of aldicarb exposure on bile acids, as well as steroid hormones and oxylipins in the serum, feces and liver of C57BL/6 J mice. Our results showed that aldicarb exposure disturbed the level of various bile acids, steroid hormones and oxylipins in the serum and feces of C57BL/6 J mice. In the liver, the level of cortisol was decreased, meanwhile 15,16-dihydroxyoctadeca-9,12-dienoic acid was increased in aldicarb-treated mice. Metagenomic sequencing analysis showed that the relative abundance of a bile salt hydrolase, choloylglycine hydrolase (EC:3.5.1.24) and a sulfatase enzyme involved in steroid hormone metabolism, arylsulfatase, was significantly increased by aldicarb exposure. Furthermore, correlations were found between gut microbiota and various serum metabolites. The results from this study are helpful to improve the understanding of the impact of carbamate insecticides on host and microbial metabolism.\n\nAldicarb disturbed bile acid, steroid hormone and oxylipin homeostasis in C57BL/6 J mice.", "token_count": 473, "char_count": 1713, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5565, "quality_score": 0.7782, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:10.409031", "source": { "split": "train_shard_00000", "doc_id": 975 }, "chunk_id": "train_shard_00000_975_0", "global_id": 1074 }, { "text": "Bile acids are bioactive metabolites that are biotransformed into secondary bile acids by the gut microbiota, a vast consortium of microbes that inhabit the intestines. The first step in intestinal secondary bile acid metabolism is carried out by a critical enzyme, bile salt hydrolase (BSH), that catalyzes the gateway reaction that precedes all subsequent microbial metabolism of these important metabolites. As gut microbial metabolic activity is difficult to probe due to the complex nature of the gut microbiome, approaches are needed to profile gut microbiota-associated enzymes such as BSH. Here, we develop a panel of BSH activity-based probes (ABPs) to determine how changes in diurnal rhythmicity of gut microbiota-associated metabolism affects BSH activity and substrate preference. This panel of covalent probes enables determination of BSH activity and substrate specificity from multiple gut anerobic bacteria derived from the human and mouse gut microbiome. We found that both gut microbiota-associated BSH activity and substrate preference is rhythmic, likely due to feeding patterns of the mice. These results indicate that this ABP-based approach can be used to profile changes in BSH activity in physiological and disease states that are regulated by circadian rhythms.\n\nBile Salt Hydrolase Activity-Based Probes for Monitoring Gut Microbial Bile Acid Metabolism.", "token_count": 338, "char_count": 1382, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5693, "quality_score": 0.7847, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:11.019199", "source": { "split": "train_shard_00000", "doc_id": 976 }, "chunk_id": "train_shard_00000_976_0", "global_id": 1075 }, { "text": "Carbapenem-resistant Klebsiella pneumoniae (CR-KP) are a public health concern, causing infections with a high mortality rate, limited therapeutic options and challenging infection control strategies. In Portugal, the CR-KP rate has increased sharply, but the factors associated with this increase are poorly explored. In order to address this question, phylogenetic and resistome analysis were used to compare the draft genomes of 200 CR-KP isolates collected in 2017-2019 from five hospitals in the Lisbon region, Portugal. Most CR-KP belonged to sequence type (ST) 13 (29%), ST17 (15%), ST348 (13%), ST231 (12%) and ST147 (7%). Carbapenem resistance was conferred mostly by the presence of KPC-3 (74%) or OXA-181 (18%), which were associated with IncF/IncN and IncX plasmids, respectively. Almost all isolates were multi-drug resistant, harbouring resistance determinants to aminoglycosides, beta-lactams, trimethoprim, fosfomycin, quinolones and sulphonamides. In addition, 11% of isolates were resistant to colistin. Colonizing and infecting isolates were highly related, and most colonized patients (89%) reported a previous hospitalization. Moreover, among the 171 events of cross-dissemination identified by core genome multi-locus sequence typing data analysis (fewer than five allelic differences), 41 occurred between different hospitals and 130 occurred within the same hospital. The results suggest that CR-KP dissemination in the Lisbon region results from acquisition of carbapenemases in mobile genetic elements, influx of CR-KP into the hospitals by colonized ambulatory patients, and transmission of CR-KP within and between hospitals. Prudent use of carbapenems, patient screening at hospital entry, and improvement of infection control are needed to decrease the burden of CR-KP infection in Portugal.", "token_count": 490, "char_count": 1821, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [ "ST17", "ST348", "ST147", "ST231" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:11.675966", "source": { "split": "train_shard_00000", "doc_id": 977 }, "chunk_id": "train_shard_00000_977_0", "global_id": 1076 }, { "text": "Genomic insights into the expansion of carbapenem-resistant Klebsiella pneumoniae within Portuguese hospitals.", "token_count": 26, "char_count": 110, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:12.032252", "source": { "split": "train_shard_00000", "doc_id": 977 }, "chunk_id": "train_shard_00000_977_1", "global_id": 1077 }, { "text": "Precise control of gene expression is critical for optimizing cellular metabolism and improving the production of valuable biochemicals. However, hard-wired approaches to pathway engineering, such as optimizing promoters, can take time and effort. Moreover, limited tools exist for controlling gene regulation in non-conventional hosts. Here, we develop a two-channel chemically-regulated gene expression system for the multi-stress tolerant yeast Kluyveromyces marxianus and use it to tune ethyl acetate production, a native metabolite produced at high titers in this yeast. To achieve this, we repurposed the plant hormone sensing modules (PYR1\n\nRepurposing plant hormone receptors as chemically-inducible genetic switches for dynamic regulation in yeast.", "token_count": 178, "char_count": 757, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7745, "quality_score": 0.8873, "entities": { "genes": [ "PYR1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:12.478533", "source": { "split": "train_shard_00000", "doc_id": 978 }, "chunk_id": "train_shard_00000_978_0", "global_id": 1078 }, { "text": "Four isolates of the opportunistic pathogen Elizabethkingia anophelis were identified for the first time in a Vietnamese hospital and underwent antimicrobial susceptibility testing and genomic characterization by whole-genome sequencing. Complete, fully circularized genome sequences were obtained for all four isolates. Average Nucleotide Identity analysis and single nucleotide polymorphism phylogenetic analysis on the core genome showed that three of the four isolates were genetically distinct, ruling out the hypothesis of a single strain emergence. Antibiotic susceptibility testing highlighted multi-resistant phenotypes against most antimicrobial families, including beta-lactams, carbapenems, aminoglycosides, quinolones, macrolides, amphenicols, rifamycins and glycopeptides. Additionally, in silico genomic analysis was used to correlate the phenotypic susceptibility to putative resistance determinants, including resistance genes, point mutations and multidrug efflux pumps. Nine different resistance genes were located inside a single resistance pocket predicted to be a putative Integrative and Conjugative Element (ICE). This novel ICE was shared by three isolates from two different lineages and displayed similarity with ICEs previously reported in various Elizabethkingia and Chryseobacterium species. The role of such ICEs in pathogenicity, genome plasticity and antimicrobial resistance gene spread within the Flavobacteriaceae family needs to be further elucidated.\n\nWhole-genome sequence and resistance determinants of four Elizabethkingia anophelis clinical isolates collected in Hanoi, Vietnam.", "token_count": 378, "char_count": 1620, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:13.061595", "source": { "split": "train_shard_00000", "doc_id": 979 }, "chunk_id": "train_shard_00000_979_0", "global_id": 1079 }, { "text": "Pangenomes, capturing the genetic diversity of a species or genus, are essential to understanding the ecology, pathobiology and evolutionary mechanisms of fungi that cause infection in crops and humans. However, fungal pangenome databases remain unavailable. Here, we report the first fungal pangenome database, specifically for Fusarium oxysporum species complex (FOSC), a group of cross-kingdom pathogens causing devastating vascular wilt to over 100 plant species and life-threatening fusariosis to immunocompromised humans. The F. oxysporum Pangenome Database (FoPGDB) is a comprehensive resource integrating 35 high-quality FOSC genomes, coupled with robust analytical tools. FoPGDB allows for both gene-based and graph-based exploration of the F. oxysporum pangenome. It also curates a large repository of putative effector sequences, crucial for understanding the mechanisms of FOSC pathogenicity. With an assortment of functionalities including gene search, genomic variant exploration and tools for functional enrichment, FoPGDB provides a platform for in-depth investigations of the genetic diversity and adaptability of F. oxysporum. The modular and user-friendly interface ensures efficient data access and interpretation. FoPGDB promises to be a valuable resource for F. oxysporum research, contributing to our understanding of this pathogen's pangenomic landscape and aiding in the development of novel disease management strategies. Database URL: http://www.fopgdb.site.\n\nFoPGDB: a pangenome database of Fusarium oxysporum, a cross-kingdom fungal pathogen.", "token_count": 372, "char_count": 1571, "word_count": 208, "semantic_coherence": 1, "information_density": 0.649, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:13.648024", "source": { "split": "train_shard_00000", "doc_id": 980 }, "chunk_id": "train_shard_00000_980_0", "global_id": 1080 }, { "text": "Two probiotic candidates, Lactobacillus reuteri C1 (C1) and Lactobacillus acidophilus C5 (C5), which were previously isolated from canines, were evaluated in the present study. L. reuteri and L. acidophilus have anti-oxidant, anti-inflammatory, immune-enhancing, and anti-cancer properties and exhibit various probiotic effects in humans and animals. The strains C1 and C5 demonstrated good tolerance to acid and bile salt exposure, exhibited effective adhesion to HT-29 cell monolayer, and displayed sensitivity to antibiotics, thus affirming their probiotic characteristics. Moreover, C1 and C5 exhibited the ability to downregulate the expression of inducible NO synthase (iNOS), an immunomodulatory factor, leading to a reduction in NO production in lipopolysaccharide (LPS)-stimulated RAW 264.7 cells. These strains also demonstrated potent anti-inflammatory effects in LPS-stimulated RAW 264.7 cells, achieved through the augmentation of anti-inflammatory cytokine IL-10 expression and the inhibition of pro-inflammatory cytokine IL-1β expression. These anti-inflammatory effects of C1 and C5 were closely associated with the mitogen-activated protein kinase (MAPK) signaling pathway. The results of the present study suggest that the C1 and C5 probiotic candidates attenuate LPS-induced inflammation via the MAPK signaling pathway and the strains can be used as probiotics considering their anti-inflammatory potential.\n\nAnti-inflammatory potential via the MAPK signaling pathway of Lactobacillus spp. isolated from canine feces.", "token_count": 428, "char_count": 1536, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:14.277943", "source": { "split": "train_shard_00000", "doc_id": 981 }, "chunk_id": "train_shard_00000_981_0", "global_id": 1081 }, { "text": "Accurate genotyping of Killer cell Immunoglobulin-like Receptor (KIR) genes plays a pivotal role in enhancing our understanding of innate immune responses, disease correlations, and the advancement of personalized medicine. However, due to the high variability of the KIR region and high level of sequence similarity among different KIR genes, the currently available genotyping methods are unable to accurately infer copy numbers, genotypes and haplotypes of individual KIR genes from next-generation sequencing data. Here we introduce Geny, a new computational tool for precise genotyping of KIR genes. Geny utilizes available KIR haplotype databases and proposes a novel combination of expectation-maximization filtering schemes and integer linear programming-based combinatorial optimization models to resolve ambiguous reads, provide accurate copy number estimation and estimate the haplotype of each copy for the genes within the KIR region. We evaluated Geny on a large set of simulated short-read datasets covering the known validated KIR region assemblies and a set of Illumina short-read samples sequenced from 25 validated samples from the Human Pangenome Reference Consortium collection and showed that it outperforms the existing genotyping tools in terms of accuracy, precision and recall. We envision Geny becoming a valuable resource for understanding immune system response and consequently advancing the field of patient-centric medicine.\n\nGeny: A Genotyping Tool for Allelic Decomposition of Killer Cell Immunoglobulin-Like Receptor Genes.", "token_count": 354, "char_count": 1558, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:14.857748", "source": { "split": "train_shard_00000", "doc_id": 982 }, "chunk_id": "train_shard_00000_982_0", "global_id": 1082 }, { "text": "The mucus layer in the small intestine is generally regarded as a barrier to drug absorption. However, the mucus layer is a complex system, and presently, only a few studies have been conducted to elucidate its physicochemical properties. The current study hypothesizes that the mucus layer contains solubility-enhancing surfactants and thus might aid the oral absorption of poorly water-soluble drugs. Mucus was sampled from sections of the small intestine of fasted rats to analyze the rheological properties and determine the mucus pH and concentrations of proteins and endogenous surfactants, i.e., bile salts, polar lipids, and neutral lipids. The mucus layer in the two proximal sections of the small intestine exhibited different rheological properties such as higher zero-shear viscosity and lower loss tangent and higher protein concentrations compared to all subsequent sections of the small intestine. The pH of the mucus layer was stable at ~ 6.5 throughout most of the small intestine, but increased to 7.5 in the ileum. The bile salt concentrations increased from the duodenum (16.0 ± 2.2 mM) until the mid jejunum (55.1 ± 9.5 mM), whereas the concentrations of polar lipids and neutral lipids decreased from the duodenum (17.4 ± 2.2 mM and 37.8 ± 1.6 mM, respectively) until the ileum (4.8 ± 0.4 mM and 10.7 ± 1.1 mM, respectively). In conclusion, the mucus layer of the rat small intestine contains endogenous surfactants at levels that might benefit solubilization and absorption of orally administered poorly water-soluble drugs.\n\nCharacterizing interregional differences in the rheological properties and composition of rat small intestinal mucus.", "token_count": 496, "char_count": 1666, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5273, "quality_score": 0.7637, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:15.514127", "source": { "split": "train_shard_00000", "doc_id": 983 }, "chunk_id": "train_shard_00000_983_0", "global_id": 1083 }, { "text": "Probiotics with high bile salt hydrolase (BSH) activity have shown to promote cardiovascular health. However, their mechanism(s) of action remain poorly understood. Here, we performed a pilot exploratory study to investigate effects of a 4-week intervention with escalating doses of a BSH-active formula containing Lactiplantibacillus plantarum strains KABP011, KABP012, and KABP013 on bile acid (BA), lipid profile, and lipoprotein function.\n\nLactiplantibacillus plantarum strains KABP011, KABP012, and KABP013 modulate bile acids and cholesterol metabolism in humans.", "token_count": 177, "char_count": 569, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7733, "quality_score": 0.8867, "entities": { "genes": [ "KABP013", "KABP011", "KABP012" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:15.930497", "source": { "split": "train_shard_00000", "doc_id": 984 }, "chunk_id": "train_shard_00000_984_0", "global_id": 1084 }, { "text": "Overexpression of a gene with unknown function in Kluyveromyces marxianus markedly improved tolerance to lignocellulosic biomass-derived inhibitors. This overexpression also enhanced tolerance to elevated temperatures, ethanol, and high concentrations of NaCl and glucose. Inhibitor degradation and transcriptome analyses related this K. marxianusMultiple Stress Resistance (KmMSR) gene to the robustness of yeast cells. Nuclear localization and DNA-binding domain analyses indicate that KmMsr is a putative transcriptional regulator. Overexpression of a mutant protein with deletion in the flexible region between amino acids 100 and 150 further enhanced tolerance to multiple inhibitors during fermentation, with ethanol production and productivity increasing by 36.31 % and 80.22 %, respectively. In simultaneous saccharification co-fermentation of corncob without detoxification, expression of KmMSR with the deleted flexible region improved ethanol production by 5-fold at 42 °C and 2-fold at 37 °C. Overexpression of the KmMSR mutant provides a strategy for constructing robust lignocellulosic biomass using strains.\n\nEnhancing simultaneous saccharification and co-fermentation of corncob by Kluyveromyces marxianus through overexpression of putative transcription regulator.", "token_count": 334, "char_count": 1281, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:16.511082", "source": { "split": "train_shard_00000", "doc_id": 985 }, "chunk_id": "train_shard_00000_985_0", "global_id": 1085 }, { "text": "Fusarium, a member of the Ascomycota fungi, encompasses several pathogenic species significant to plants and animals. Some phytopathogenic species have received special attention due to their negative economic impact on the agricultural industry around the world. Traditionally, identification and taxonomic analysis of Fusarium have relied on morphological and phenotypic features, including the fungal host, leading to taxonomic conflicts that have been solved using molecular systematic technologies. In this work, we applied a phylogenomic approach that allowed us to resolve the evolutionary history of the species complexes of the genus and present evidence that supports the F. ventricosum species complex as the most basal lineage of the genus. Additionally, we present evidence that proposes modifications to the previous hypothesis of the evolutionary history of the F. staphyleae, F. newnesense, F. nisikadoi, F. oxysporum, and F. fujikuroi species complexes. Evolutionary analysis showed that the genome GC content tends to be lower in more modern lineages, in both, the whole-genome and core-genome coding DNA sequences. In contrast, genome size gain and losses are present during the evolution of the genus. Interestingly, core genome duplication events positively correlate with genome size. Evolutionary and genome conservation analysis supports the F3 hypothesis of Fusarium as a more compact and conserved group in terms of genome conservation. By contrast, outside of the F3 hypothesis, the most basal clades only share 8.8% of its genomic sequences with the F3 clade.\n\nAn evolutionary view of the Fusarium core genome.", "token_count": 375, "char_count": 1638, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5875, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:17.097864", "source": { "split": "train_shard_00000", "doc_id": 986 }, "chunk_id": "train_shard_00000_986_0", "global_id": 1086 }, { "text": "Bile salts of hepatic and microbial origin mediate interorgan cross talk in the gut-liver axis. Here, we assessed whether the newly discovered class of microbial bile salt conjugates (MBSCs) activate the main host bile salt receptors (Takeda G protein-coupled receptor 5 [TGR5] and farnesoid X receptor [FXR]) and enter the human systemic and enterohepatic circulation.\n\nMicrobially conjugated bile salts found in human bile activate the bile salt receptors TGR5 and FXR.", "token_count": 138, "char_count": 471, "word_count": 71, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:17.530456", "source": { "split": "train_shard_00000", "doc_id": 987 }, "chunk_id": "train_shard_00000_987_0", "global_id": 1087 }, { "text": "A core genome multi-locus sequence typing scheme for", "token_count": 12, "char_count": 52, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:17.876465", "source": { "split": "train_shard_00000", "doc_id": 988 }, "chunk_id": "train_shard_00000_988_0", "global_id": 1088 }, { "text": "Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by\n\nGenomic analysis of inter-hospital transmission of vancomycin-resistant", "token_count": 185, "char_count": 746, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:18.320609", "source": { "split": "train_shard_00000", "doc_id": 989 }, "chunk_id": "train_shard_00000_989_0", "global_id": 1089 }, { "text": "Bottle gourd (Lagenaria siceraria (Mol.) Strandl.) is an economically important vegetable crop and one of the earliest domesticated crops. However, the population history and genomic diversification of bottle gourd have not been extensively studied. We generated a comprehensive bottle gourd genome variation map from genome sequences of 197 world-wide representative accessions, which enables a genome-wide association study for identifying genomic loci associated with resistance to zucchini yellow mosaic virus, and constructed a bottle gourd pangenome that harbors 1534 protein-coding genes absent in the reference genome. Demographic analyses uncover that domesticated bottle gourd originated in Southern Africa c. 12 000 yr ago, and subsequently radiated to the New World via the Atlantic drift and to Eurasia through the efforts of early farmers in the initial Holocene. The identified highly differentiated genomic regions among different bottle gourd populations harbor many genes contributing to their local adaptations such as those related to disease resistance and stress tolerance. Presence/absence variation analysis of genes in the pangenome reveals numerous genes including those involved in abiotic/biotic stress responses that have been under selection during the world-wide expansion of bottle gourds. The bottle gourd variation map and pangenome provide valuable resources for future functional studies and genomics-assisted breeding.\n\nGenomic and pangenomic analyses provide insights into the population history and genomic diversification of bottle gourd.", "token_count": 351, "char_count": 1578, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:18.889466", "source": { "split": "train_shard_00000", "doc_id": 990 }, "chunk_id": "train_shard_00000_990_0", "global_id": 1090 }, { "text": "Evolutionary dynamics of the accessory genomes of", "token_count": 11, "char_count": 49, "word_count": 7, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:19.241170", "source": { "split": "train_shard_00000", "doc_id": 991 }, "chunk_id": "train_shard_00000_991_0", "global_id": 1091 }, { "text": "The demands of intensified aquaculture production and escalating disease prevalence underscore the need for efficacious probiotic strategies to enhance fish health. This study focused on isolating and characterising potential probiotics from the gut microbiota of the emerging aquaculture species jade perch (Scortum barcoo). Eighty-seven lactic acid bacteria and 149 other bacteria were isolated from the digestive tract of five adult jade perch. The screening revealed that 24 Enterococcus hirae isolates inhibited the freshwater pathogens Aeromonas sobria and Streptococcus iniae. Co-incubating E. hirae with the host gut suspensions demonstrated a two- to five-fold increase in the size of growth inhibition zones compared to the results when using gut suspensions from tilapia (a non-host), indicating host-specificity. Genome analysis of the lead isolate, E. hirae R44, predicted the presence of antimicrobial compounds like enterolysin A, class II lanthipeptide, and terpenes, which underlay its antibacterial attributes. Isolate R44 exhibited desirable probiotic characteristics, including survival at pH values within the range of 3 to 12, bile tolerance, antioxidant activity, ampicillin sensitivity, and absence of transferable antimicrobial resistance genes and virulence factors commonly associated with hospital Enterococcus strains (IS16, hylEfm, and esp). This study offers a foundation for sourcing host-adapted probiotics from underexplored aquaculture species. Characterisation of novel probiotics like E. hirae R44 can expedite the development of disease mitigation strategies to support aquaculture intensification.\n\nIn Vitro Profiling of Potential Fish Probiotics, Enterococcus hirae Strains, Isolated from Jade Perch, and Safety Properties Assessed Using Whole Genome Sequencing.", "token_count": 454, "char_count": 1802, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6888, "quality_score": 0.8444, "entities": { "genes": [ "IS16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:19.872344", "source": { "split": "train_shard_00000", "doc_id": 992 }, "chunk_id": "train_shard_00000_992_0", "global_id": 1092 }, { "text": "The plant microbiota is believed to be an accessory genome that extends plant functions, forming holobionts together with the host plant. Plant disease resistance, therefore, is inextricably linked with plant microbiota, which play important roles in plant growth and health. To explore the relationship between plant microbiota and disease resistance, we investigated the tobacco microbiome of two varieties with contrasting disease-resistance levels to bacterial wilt and black shank diseases. Comparative microbiome analysis indicated that the resistant variety assembled a distinct microbiota with higher network complexity and diversity. While\n\nDistinct microbiota assembly and functional patterns in disease-resistant and susceptible varieties of tobacco.", "token_count": 149, "char_count": 761, "word_count": 101, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:20.316659", "source": { "split": "train_shard_00000", "doc_id": 993 }, "chunk_id": "train_shard_00000_993_0", "global_id": 1093 }, { "text": "As different taxa evolve, gene order often changes slowly enough that chromosomal 'blocks' with conserved gene orders (synteny) are discernible. The MCScanX toolkit ( https://github.com/wyp1125/MCScanX ) was published in 2012 as freely available software for the detection of such 'colinear blocks' and subsequent synteny and evolutionary analyses based on genome-wide gene location and protein sequence information. Owing to its simplicity and high efficiency for colinear block detection, MCScanX provides a powerful tool for conducting diverse synteny and evolutionary analyses. Moreover, the detection of colinear blocks has been embraced as an integral step for pangenome graph construction. Here, new application trends of MCScanX are explored, striving to better connect this increasingly used tool to other tools and accelerate insight generation from exponentially growing sequence data. We provide a detailed protocol that covers how to install MCScanX on diverse platforms, tune parameters, prepare input files from data from the National Center for Biotechnology Information, run MCScanX and its visualization and evolutionary analysis tools, and connect MCScanX with external tools, including MCScanX-transposed, Circos and SynVisio. This protocol is easily implemented by users with minimal computational background and is adaptable to new data of interest to them. The data and utility programs for this protocol can be obtained from http://bdx-consulting.com/mcscanx-protocol .\n\nDetection of colinear blocks and synteny and evolutionary analyses based on utilization of MCScanX.", "token_count": 351, "char_count": 1594, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6516, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:20.883853", "source": { "split": "train_shard_00000", "doc_id": 994 }, "chunk_id": "train_shard_00000_994_0", "global_id": 1094 }, { "text": "To evaluate the effect of NaCl content on microbiological, biochemical, physicochemical, and sensorial characteristics, Munster cheeses were prepared from pasteurized milk seeded with 3 yeasts (Kluyveromyces marxianus, Debaryomyces hansenii, and Geotrichum candidum) and 5 ripening bacteria (Arthrobacter arilaitensis, Brevibacterium aurantiacum, Corynebacterium casei, Hafnia alvei, and Staphylococcus equorum). Experiments were performed in triplicate under 1.0%, 1.7%, and 2.4% NaCl levels in cheese. Ripening (d 2-27) was carried out at 12°C and 96% relative humidity. These kinetics were both reproducible and repeatable at a 99% confidence level. For each microbial, biochemical, and physicochemical parameter, 2 kinetic descriptors (the maximal or minimal rate and its occurrence time) were defined. On d 2, the physicochemical variables (water activity, dry matter, and water content) were strongly dependent on the salting level. From d 2 to d 27, K. lactis was insensitive to salt, whereas D. hansenii was stimulated. Geotrichum candidum growth appeared very sensitive to salt in cheese: at 1.0% NaCl, G. candidum exhibited overgrowth, negatively affecting rind appearance, underrind consistency and thickness, and off-flavor flaws. A salt concentration of 2.4% induced death of G. candidum. A total of 4 bacteria (A. arilaitensis, B. aurantiacum, C. casei, and H. alvei) were moderately sensitive to salt, but S. equorum was insensitive to it. Salt level in cheese had a significant effect on carbon substrate consumption rates. The lactate consumption rate in 1.0% salted cheeses was approximately twice higher than under 2.4% NaCl", "token_count": 483, "char_count": 1643, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:21.567049", "source": { "split": "train_shard_00000", "doc_id": 995 }, "chunk_id": "train_shard_00000_995_0", "global_id": 1095 }, { "text": "Data analysis of microorganism, biochemical, and physicochemical kinetics, as well as sensory analysis, showed that 1.7% NaCl was the best salt level in Munster-type cheeses to achieve an optimum balance between cheese characteristics, sensory qualities, and marketability.\n\nMicrobiological, physicochemical, and sensory changes throughout ripening of an experimental soft smear-ripened cheese in relation to salt concentrations.", "token_count": 107, "char_count": 429, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:21.958332", "source": { "split": "train_shard_00000", "doc_id": 995 }, "chunk_id": "train_shard_00000_995_1", "global_id": 1096 }, { "text": "Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.\n\nThe super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees.", "token_count": 387, "char_count": 1749, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8473, "entities": { "genes": [ "CUC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:22.609457", "source": { "split": "train_shard_00000", "doc_id": 996 }, "chunk_id": "train_shard_00000_996_0", "global_id": 1097 }, { "text": "Drug-induced liver injury (DILI) is a frequent cause of clinical trial failures during drug development. While inhibiting bile salt export pump (BSEP) is a well-documented DILI mechanism, interference with genes related to bile acid (BA) metabolism and transport can further complicate DILI development. Here, the effects of twenty-eight compounds on genes associated with BA metabolism and transport were evaluated, including those with discontinued development or use, boxed warnings, and clean labels for DILI. The study also included rifampicin and omeprazole, pregnane X receptor and aryl hydrocarbon receptor ligands, and four mitogen-activated protein kinase kinase (MEK1/2) inhibitors. BSEP inhibitors with more severe DILI, notably pazopanib and CP-724714, significantly upregulated the expression of 7 alpha-hydroxylase (CYP7A1), independent of small heterodimer partner (SHP) expression. CYP7A1 expression was marginally induced by omeprazole. In contrast, its expression was suppressed by mometasone (10-fold), vinblastine (18-fold), hexachlorophene (2-fold), bosentan (2.1-fold), and rifampin (2-fold). All four MEK1/2 inhibitors that show clinical DILI were not potent BSEP inhibitors but significantly induced CYP7A1 expression, accompanied by a significant SHP gene suppression. Sulfotransferase 2A1 and BSEP were marginally upregulated, but no other genes were altered by the drugs tested. Protein levels of CYP7A1 were increased with the treatment of CYP7A1 inducers and decreased with obeticholic acid, an farnesoid X receptor ligand. CYP7A1 inducers significantly increased bile acid (BA) production in hepatocytes, indicating the overall regulatory effects of BA metabolism. This study demonstrates that CYP7A1 induction via various mechanisms can pose a risk for DILI, independently or in synergy with BSEP inhibition, and it should be evaluated early in drug discovery", "token_count": 509, "char_count": 1891, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [ "MEK1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:23.279989", "source": { "split": "train_shard_00000", "doc_id": 997 }, "chunk_id": "train_shard_00000_997_0", "global_id": 1098 }, { "text": "SIGNIFICANCE STATEMENT: Kinase inhibitors, pazopanib and CP-724714, inhibit BSEP and induce CYP7A1 expression independent of small heterodimer partner (SHP) expression, leading to increased bile acid (BA) production and demonstrating clinically elevated drug-induced liver toxicity. MEK1/2 inhibitors that show BSEP-independent drug-induced liver injury (DILI) induced the CYP7A1 gene accompanied by SHP suppression. CYP7A1 induction via SHP-dependent or independent mechanisms can pose a risk for DILI, independently or in synergy with BSEP inhibition. Monitoring BA production in hepatocytes can reliably detect the total effects of BA-related gene regulation for de-risking.\n\nCYP7A1 Gene Induction via SHP-Dependent or Independent Mechanisms can Increase the Risk of Drug-Induced Liver Injury Independently or in Synergy with BSEP Inhibition.", "token_count": 238, "char_count": 845, "word_count": 111, "semantic_coherence": 1, "information_density": 0.6577, "quality_score": 0.8288, "entities": { "genes": [ "MEK1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:23.756480", "source": { "split": "train_shard_00000", "doc_id": 997 }, "chunk_id": "train_shard_00000_997_1", "global_id": 1099 }, { "text": "Metabolism-associated fatty liver disease (MAFLD), a growing health problem worldwide, is one of the major risks for the development of cirrhosis and liver cancer. Oral administration of nobiletin (NOB), a natural citrus flavonoid, modulates the gut microbes and their metabolites in mice. In the present study, we established a mouse model of MAFLD by subjecting mice to a high-fat diet (HFD) for 12 weeks. Throughout this timeframe, NOB was administered to investigate its potential benefits on gut microbial balance and bile acid (BA) metabolism using various techniques, including 16S rRNA sequencing, targeted metabolomics of BA, and biological assays. NOB effectively slowed the progression of MAFLD by reducing serum lipid levels, blood glucose levels, LPS levels, and hepatic IL-1β and TNF-α levels. Furthermore, NOB reinstated diversity within the gut microbial community, increasing the population of bacteria that produce bile salt hydrolase (BSH) to enhance BA excretion. By exploring further, we found NOB downregulated hepatic expression of the farnesoid X receptor (\n\nInvolvement of Bile Acid Metabolism and Gut Microbiota in the Amelioration of Experimental Metabolism-Associated Fatty Liver Disease by Nobiletin.", "token_count": 322, "char_count": 1229, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8464, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:25.025455", "source": { "split": "train_shard_00000", "doc_id": 998 }, "chunk_id": "train_shard_00000_998_0", "global_id": 1100 }, { "text": "The altered circulating bile acids (BAs) modulate gut microbiota, energy metabolism and various physiological functions. BA profiles in liver, serum, ileum and feces of HFD-fed mice were analyzed with normal chow diet (NCD)-fed mice after 16-week feeding. Furthermore, gut microbiota was analyzed and its correlation analysis with BA was performed. The result showed that long-term HFD feeding significantly decreased hepatic and serum BA levels, mainly attributed to the inhibition of hepatic BA synthesis and the reduced reabsorption efficiency of BAs in enterohepatic circulation. It also significantly impaired glucose and lipid homeostasis and gut microbiota in mice. We found significantly higher bile salt hydrolase activity in ileal microbes and a higher ratio of free BAs to conjugated BA content in ileal contents in HFD groups compared with NCD group mice, which might account for the activated intestinal farnesoid X receptor signaling on liver BA synthesis inhibition and reduced ileal reabsorption. The decreased circulating BAs were associated with the dysregulation of the lipid metabolism according to the decreased TGR5 signaling in the ileum and BAT. In addition, it is astonishing to find extremely high percentages of taurocholate and 12-OH BAs in liver and serum BA profiles of both groups, which was mainly attributed to the high substrate selectivity for 12-OH BAs of the intestinal BAs transporter during the ileal reabsorption of enterohepatic circulation. This study revealed a significant effect of long-term HFD feeding on the decreased circulating BA pool in mice, which impaired lipid homeostasis and gut microbiota, and collectively resulted in metabolic disorders and obesity.\n\nHigh-Fat Diet-Induced Decreased Circulating Bile Acids Contribute to Obesity Associated with Gut Microbiota in Mice.", "token_count": 465, "char_count": 1827, "word_count": 269, "semantic_coherence": 1, "information_density": 0.513, "quality_score": 0.7565, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:25.663561", "source": { "split": "train_shard_00000", "doc_id": 999 }, "chunk_id": "train_shard_00000_999_0", "global_id": 1101 }, { "text": "Pseudomonas aeruginosa (PA) is an important opportunistic pathogen that causes different infections on immunocompromised patients. Within PA accessory genome, differences in virulence, antibiotic resistance and biofilm formation have been described between strains, leading to the emergence of multidrug-resistant strains. The genome sequences of 17 strains isolated from patients with healthcare-associated infections in a Mexican hospital were genomically and phylogenetically analyzed and antibiotic resistance genes, virulence genes, and biofilm formation genes were detected. Fifteen of the 17 strains were resistant to at least two of the carbapenems meropenem, imipenem, and the monobactam aztreonam. The antibiotic resistance (mexA, mexB, and oprM) and the biofilm formation (pslA and pslD) genes were detected in all strains. Differences were found between strains in accessory genome size. The strains had different sequence types, and seven strains had sequence types associated with global high risk epidemic PA clones. All strains were represented in two groups among PA global strains. In the 17 strains, horizontally acquired resistance genes to aminoglycosides and beta-lactams were found, mainly, and between 230 and 240 genes that encode virulence factors. The strains under study were variable in terms of their accessory genome, antibiotic resistance, and virulence genes. With these characteristics, we provide information about the genomic diversity of clinically relevant PA strains.\n\nComparative genomic analysis of Pseudomonas aeruginosa strains susceptible and resistant to carbapenems and aztreonam isolated from patients with healthcare-associated infections in a Mexican hospital.", "token_count": 414, "char_count": 1709, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5322, "quality_score": 0.7661, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:26.291494", "source": { "split": "train_shard_00000", "doc_id": 1000 }, "chunk_id": "train_shard_00000_1000_0", "global_id": 1102 }, { "text": "A bioassay containing Kluyveromyces marxianus in microtiter plates was used to determine the inhibitory action of 28 antibiotics (aminoglycosides, beta-lactams, macrolides, quinolones, tetracyclines and sulfonamides) against this yeast in whey. For this purpose, the dose-response curve for each antibiotic was constructed using 16 replicates of 12 different concentrations of the antibiotic. The plates were incubated at 40°C until the negative samples exhibited their indicator (5-7h). Subsequently, the absorbances of the yeast cells in each plate were measured by the turbidimetric method (λ=600nm) and the logistic regression model was applied. The concentrations causing 10% (IC10) and 50% (IC50) of growth inhibition of the yeast were calculated. The results allowed to conclude that whey contaminated with cephalosporins, quinolones and tetracyclines at levels close to the Maximum Residue Limits inhibits the growth of K. marxianus. Therefore, previous inactivation treatments should be implemented in order to re-use this contaminated whey by fermentation with K. marxianus.\n\nInhibitory action of antibiotics on Kluyveromyces marxianus.", "token_count": 320, "char_count": 1146, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6519, "quality_score": 0.8259, "entities": { "genes": [ "IC50", "IC10" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:27.195318", "source": { "split": "train_shard_00000", "doc_id": 1001 }, "chunk_id": "train_shard_00000_1001_0", "global_id": 1103 }, { "text": "The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab).\n\nPangenome Analysis of", "token_count": 373, "char_count": 1503, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:27.778157", "source": { "split": "train_shard_00000", "doc_id": 1002 }, "chunk_id": "train_shard_00000_1002_0", "global_id": 1104 }, { "text": "Antimicrobial peptides, such as bacteriocin, produced by probiotics have become a promising novel class of therapeutic agents for treating infectious diseases. Selected lactic acid bacteria (LAB) isolated from fermented foods with probiotic potential were evaluated for various tests, including exopolysaccharide production, antibiotic susceptibility, acid and bile tolerance, antibacterial activity, and cell adhesion and cytotoxicity to gastric cell lines. Six selected LAB strains maintained their high viability under gastrointestinal conditions, produced high exopolysaccharides, showed no or less cytotoxicity, and adhered successfully to gastric cells. Furthermore, three strains, Weissella confusa CYLB30, Lactiplantibacillus plantarum CYLB47, and Limosilactobacillus fermentum CYLB55, demonstrated a strong antibacterial effect against drug-resistant Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Salmonella enterica serovar Choleraesuis, Enterococcus faecium, and Staphylococcus aureus. Whole genome sequencing was performed on these three strains using the Nanopore platform; then, the results showed that all three strains did not harbor genes related to toxins, superantigens, and acquired antimicrobial resistance, in their genome. The bacteriocin gene cluster was found in CYLB47 genome, but not in CYLB30 and CYLB55 genomes. In SDS-PAGE, the extract of CYLB30 and CYLB47 bacteriocin-like inhibitory substance (BLIS) yielded a single band with a size of less than 10 kDa. These BLIS inhibited the growth and biofilm formation of drug-resistant P. aeruginosa and methicillin-resistant S. aureus (MRSA), causing membrane disruption and inhibiting adhesion ability to human skin HaCaT cells. Moreover, CYLB30 and CYLB47 BLIS rescued the larvae after being infected with P", "token_count": 518, "char_count": 1802, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7542, "quality_score": 0.8771, "entities": { "genes": [ "CYLB30", "CYLB55", "CYLB47" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:08:28.430185", "source": { "split": "train_shard_00000", "doc_id": 1003 }, "chunk_id": "train_shard_00000_1003_0", "global_id": 1105 }, { "text": "aeruginosa and MRSA infections. In conclusion, CYLB30 and CYLB47 BLIS may be potential alternative treatment for multidrug-resistant bacteria infections.\n\nCharacterization of the broad-spectrum antibacterial activity of bacteriocin-like inhibitory substance-producing probiotics isolated from fermented foods.", "token_count": 79, "char_count": 309, "word_count": 34, "semantic_coherence": 1, "information_density": 0.9118, "quality_score": 0.9559, "entities": { "genes": [ "CYLB30", "CYLB47" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:28.800218", "source": { "split": "train_shard_00000", "doc_id": 1003 }, "chunk_id": "train_shard_00000_1003_1", "global_id": 1106 }, { "text": "Brevibacillus laterosporus is a strain of probiotic bacteria that has been widely used in pest control, cash crop, and other production areas. However, few studies have been conducted on its use as a feed additive in animals. Therefore, the probiotic potential of B. laterosporus PBC01 was evaluated by characterizing hydrophobicity, auto-aggregation activity, bile salt and simulated gastrointestinal fluid tolerance, bienzymatic, and antibacterial activity. Antibiotic susceptibility, hemolysis assays, and supplemental feeding of mice were also performed to evaluate safety features. Our results showed that B. laterosporus PBC01 had moderate hydrophobicity, high auto-agglutination ability. Meanwhile, B. laterosporus PBC01 had good tolerance to bile salt and simulated gastrointestinal fluid. It had the ability to secrete protease, cellulase, and to inhibit various pathogens. In addition, B. laterosporus PBC01 was sensitive to many antibiotics, and did not produce hemolysin. In the safety assessment of mice, it did not cause any deaths, nor did it affect the cell components of blood, antioxidant capacity, and reproductive health. The study indicated the great probiotic characteristics and safety of B. laterosporus PBC01. This may provide a theoretical basis for the clinical application and development of probiotic-based feed additives.\n\nEvaluation of probiotic properties of a Brevibacillus laterosporus strain.", "token_count": 359, "char_count": 1427, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6566, "quality_score": 0.8283, "entities": { "genes": [ "PBC01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:29.375842", "source": { "split": "train_shard_00000", "doc_id": 1004 }, "chunk_id": "train_shard_00000_1004_0", "global_id": 1107 }, { "text": "Legumes can establish a mutual association with soil-derived nitrogen-fixing bacteria called 'rhizobia' forming lateral root organs called root nodules. Rhizobia inside the root nodules get transformed into 'bacteroids' that can fix atmospheric nitrogen to ammonia for host plants in return for nutrients and shelter. A substantial 200 million tons of nitrogen is fixed annually through biological nitrogen fixation. Consequently, the symbiotic mechanism of nitrogen fixation is utilized worldwide for sustainable agriculture and plays a crucial role in the Earth's ecosystem. The development of effective nitrogen-fixing symbiosis between legumes and rhizobia is very specialized and requires coordinated signaling. A plethora of plant-derived nodule-specific cysteine-rich (NCR or NCR-like) peptides get actively involved in this complex and tightly regulated signaling process of symbiosis between some legumes of the IRLC (Inverted Repeat-Lacking Clade) and Dalbergioid clades and nitrogen-fixing rhizobia. Recent progress has been made in identifying two such peptidases that actively prevent bacterial differentiation, leading to symbiotic incompatibility. In this review, we outlined the functions of NCRs and two nitrogen-fixing blocking peptidases: HrrP (host range restriction peptidase) and SapA (symbiosis-associated peptidase A). SapA was identified through an overexpression screen from the Sinorhizobium meliloti 1021 core genome, whereas HrrP is inherited extra-chromosomally. Interestingly, both peptidases affect the symbiotic outcome by degrading the NCR peptides generated from the host plants. These NCR-degrading peptidases can shed light on symbiotic incompatibility, helping to elucidate the reasons behind the inefficiency of nitrogen fixation observed in certain groups of rhizobia with specific legumes.\n\nExploring the role of symbiotic modifier peptidases in the legume - rhizobium symbiosis.", "token_count": 499, "char_count": 1920, "word_count": 256, "semantic_coherence": 1, "information_density": 0.668, "quality_score": 0.834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:30.033152", "source": { "split": "train_shard_00000", "doc_id": 1005 }, "chunk_id": "train_shard_00000_1005_0", "global_id": 1108 }, { "text": "Di-n-butyl phthalate (DBP) is one of the most extensively used phthalic acid esters (PAEs) and is considered to be an emerging, globally concerning pollutant. The genus Streptomyces holds promise as a degrader of various organic pollutants, but PAE biodegradation mechanisms by Streptomyces species remain unsolved. In this study, a novel PAE-degrading Streptomyces sp. FZ201 isolated from natural habitats efficiently degraded various PAEs. FZ201 had strong resilience against DBP and exhibited immediate degradation, with kinetics adhering to a first-order model. The comprehensive biodegradation of DBP involves de-esterification, β-oxidation, trans-esterification, and aromatic ring cleavage. FZ201 contains numerous catabolic genes that potentially facilitate PAE biodegradation. The DBP metabolic pathway was reconstructed by genome annotation and intermediate identification. Streptomyces species have an open pangenome with substantial genome expansion events during the evolutionary process, enabling extensive genetic diversity and highly plastic genomes within the Streptomyces genus. FZ201 had a diverse array of highly expressed genes associated with the degradation of PAEs, potentially contributing significantly to its adaptive advantage and efficiency of PAE degradation. Thus, FZ201 is a promising candidate for remediating highly PAE-contaminated environments. These findings enhance our preliminary understanding of the molecular mechanisms employed by Streptomyces for the removal of PAEs.\n\nBiodegradation of phthalate acid esters and whole-genome analysis of a novel Streptomyces sp. FZ201 isolated from natural habitats.", "token_count": 401, "char_count": 1643, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [ "FZ201" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:30.647582", "source": { "split": "train_shard_00000", "doc_id": 1006 }, "chunk_id": "train_shard_00000_1006_0", "global_id": 1109 }, { "text": "The aim of this study was to compare Illumina and Oxford Nanopore Technology (ONT) sequencing data to quantify genetic variation to assess within-outbreak strain relatedness and characterise microevolutionary events in the accessory genomes of a cluster of 23 genetically and epidemiologically linked isolates related to an outbreak of Shiga toxin-producing Escherichia coli O157:H7 caused by the consumption of raw drinking milk. There were seven discrepant variants called between the two technologies, five were false-negative or false-positive variants in the Illumina data and two were false-negative calls in ONT data. After masking horizontally acquired sequences such as prophages, analysis of both short and long-read sequences revealed the 20 isolates linked to the outbreak in 2017 had a maximum SNP distance of one SNP between each other, and a maximum of five SNPs when including three additional strains identified in 2019. Analysis of the ONT data revealed a 47 kbp deletion event in a terminal compound prophage within one sample relative to the remaining samples, and a 0.65 Mbp large chromosomal rearrangement (inversion), within one sample relative to the remaining samples. Furthermore, we detected two bacteriophages encoding the highly pathogenic Shiga toxin (Stx) subtype, Stx2a. One was typical of Stx2a-phage in this sub-lineage (Ic), the other was atypical and inserted into a site usually occupied by Stx2c-encoding phage. Finally, we observed an increase in the size of the pO157 IncFIB plasmid (1.6 kbp) in isolates from 2019 compared to those from 2017, due to the duplication of insertion elements within the plasmids from the more recently isolated strains. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the genome plasticity and virulence between strains of this zoonotic, foodborne pathogen.", "token_count": 488, "char_count": 1946, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:31.301543", "source": { "split": "train_shard_00000", "doc_id": 1007 }, "chunk_id": "train_shard_00000_1007_0", "global_id": 1110 }, { "text": "Re-analysis of an outbreak of Shiga toxin-producing Escherichia coli O157:H7 associated with raw drinking milk using Nanopore sequencing.", "token_count": 42, "char_count": 137, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:31.663715", "source": { "split": "train_shard_00000", "doc_id": 1007 }, "chunk_id": "train_shard_00000_1007_1", "global_id": 1111 }, { "text": "P. aeruginosa is one of the most metabolically versatile bacteria having the ability to survive in multiple environments through its accessory genome. An important hallmark of P. aeruginosa is the high level of antibiotic resistance, which often makes eradication difficult and sometimes impossible. Evolutionary forces have led to this bacterium to develop high antimicrobial resistance with a variety of elements contributing to both intrinsic and acquired resistance. The objectives were to genetically and phenotypically characterizer P. aeruginosa strains isolated from companion animals of different species.\n\nPseudomonas aeruginosa strains isolated from animal with high virulence genes content and highly sensitive to antimicrobials.", "token_count": 155, "char_count": 741, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7327, "quality_score": 0.8663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:32.112360", "source": { "split": "train_shard_00000", "doc_id": 1008 }, "chunk_id": "train_shard_00000_1008_0", "global_id": 1112 }, { "text": "The consumption of probiotics has been extensively employed for the management or prevention of gastrointestinal disorders by modifying the gut microbiota and changing metabolites. Nevertheless, the probiotic-mediated regulation of host metabolism through the metabolism of bile acids (BAs) remains inadequately comprehended. The gut-liver axis has received more attention in recent years due to its association with BA metabolism. The objective of this research was to examine the changes in BAs and gut microbiota using an\n\nMultispecies probiotics complex improves bile acids and gut microbiota metabolism status in an", "token_count": 144, "char_count": 620, "word_count": 88, "semantic_coherence": 1, "information_density": 0.6932, "quality_score": 0.8466, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:32.538688", "source": { "split": "train_shard_00000", "doc_id": 1009 }, "chunk_id": "train_shard_00000_1009_0", "global_id": 1113 }, { "text": "Horizontal gene transfer, the exchange of genetic material through means other than reproduction, is a fundamental force in prokaryotic genome evolution. Genomic persistence of horizontally transferred genes has been shown to be influenced by both ecological and evolutionary factors. However, there is limited availability of ecological information about species other than the habitats from which they were isolated, which has prevented a deeper exploration of ecological contributions to horizontal gene transfer. Here we focus on transfers detected through comparison of individual gene trees to the species tree, assessing the distribution of gene-exchanging prokaryotes across over a million environmental sequencing samples. By analysing detected horizontal gene transfer events, we show distinct functional profiles for recent versus old events. Although most genes transferred are part of the accessory genome, genes transferred earlier in evolution tend to be more ubiquitous within present-day species. We find that co-occurring, interacting and high-abundance species tend to exchange more genes. Finally, we show that host-associated specialist species are most likely to exchange genes with other host-associated specialist species, whereas species found across different habitats have similar gene exchange rates irrespective of their preferred habitat. Our study covers an unprecedented scale of integrated horizontal gene transfer and environmental information, highlighting broad eco-evolutionary trends.\n\nA global survey of prokaryotic genomes reveals the eco-evolutionary pressures driving horizontal gene transfer.", "token_count": 310, "char_count": 1635, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:33.105284", "source": { "split": "train_shard_00000", "doc_id": 1010 }, "chunk_id": "train_shard_00000_1010_0", "global_id": 1114 }, { "text": "Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting that the knockdown of IAH1 may generate intracellular alterations in the balance of these metabolites, triggering a regulatory response. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.\n\nCRISPRi-induced transcriptional regulation of IAH1 gene and its influence on volatile compounds profile in Kluyveromyces marxianus DU3.", "token_count": 476, "char_count": 1923, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5836, "quality_score": 0.7918, "entities": { "genes": [ "ATF1", "EAT1", "ADH1", "ZWF1", "IAH1", "DU3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:33.766242", "source": { "split": "train_shard_00000", "doc_id": 1011 }, "chunk_id": "train_shard_00000_1011_0", "global_id": 1115 }, { "text": "The search for probiotics and exploration of their functions are crucial for livestock farming. Recently, porcine-derived lactic acid bacteria (LAB) have shown great potential as probiotics. However, research on the evaluation of porcine-derived LAB as potential probiotics through genomics-based analysis is relatively limited. The present study analyzed four porcine-derived LAB strains (Lactobacillus johnsonii L16, Latilactobacillus curvatus ZHA1, Ligilactobacillus salivarius ZSA5 and Ligilactobacillus animalis ZSB1) using genomic techniques and combined with in vitro tests to evaluate their potential as probiotics. The genome sizes of the four strains ranged from 1,897,301 bp to 2,318,470 bp with the GC contents from 33.03 to 41.97%. Pan-genomic analysis and collinearity analysis indicated differences among the genomes of four strains. Carbohydrate active enzymes analysis revealed that L. johnsonii L16 encoded more carbohydrate active enzymes than other strains. KEGG pathway analysis and in vitro tests confirmed that L. johnsonii L16 could utilize a wide range of carbohydrates and had good utilization capacity for each carbohydrate. The four strains had genes related to acid tolerance and were tolerant to low pH, with L. johnsonii L16 showing the greatest tolerance. The four strains contained genes related to bile salt tolerance and were able to tolerate 0.1% bile salt. Four strains had antioxidant related genes and exhibited antioxidant activity in in vitro tests. They contained the genes linked with organic acid biosynthesis and exhibited antibacterial activity against enterotoxigenic Escherichia coli K88 (ETEC K88) and Salmonella 6,7:c:1,5, wherein, L. johnsonii L16 and L. salivarius ZSA5 had gene clusters encoding bacteriocin. Results suggest that genome analysis combined with in vitro tests is an effective approach for evaluating different strains as probiotics", "token_count": 526, "char_count": 1899, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5688, "quality_score": 0.7844, "entities": { "genes": [ "ZSB1", "ZSA5", "ZHA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:08:34.443172", "source": { "split": "train_shard_00000", "doc_id": 1012 }, "chunk_id": "train_shard_00000_1012_0", "global_id": 1116 }, { "text": "The findings of this study indicate that L. johnsonii L16 has the potential as a probiotic strain among the four strains and provide theoretical basis for the development of probiotics in swine production.\n\nGenomics-based analysis of four porcine-derived lactic acid bacteria strains and their evaluation as potential probiotics.", "token_count": 77, "char_count": 329, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:34.846624", "source": { "split": "train_shard_00000", "doc_id": 1012 }, "chunk_id": "train_shard_00000_1012_1", "global_id": 1117 }, { "text": "Levilactobacillus brevis KU15006, isolated from kimchi, exhibits pathogen-antagonistic and anti-diabetic activities; however, the safety of this strain has not been assessed. In the present study, L. brevis KU15006 was evaluated to elucidate its safety as a probiotic strain using phenotypic and genotypic analyses. Its safety was assessed using a minimum inhibitory concentration test comprising nine antibiotics, 26 antibiotic resistance genes, a single conjugative element, virulence gene analysis, hemolysis, cell cytotoxicity, mucin degradation, and toxic metabolite production. L. brevis KU15006 exhibited equal or lower minimum inhibitory concentration for the nine antibiotics than the cut-off value established by the European Food Safety Authority. It did not harbor antibiotic resistance and virulence genes. L. brevis KU15006 lacked β-hemolysis, mucin degradation, cytotoxicity against Caco-2 cells, gelatin liquefaction, bile salt deconjugation, and toxic metabolite production abilities. Based on the results, L. brevis KU15006, which has antagonistic and anti-diabetic effects, could be marketed as a probiotic in the future.\n\nSafety Assessment of Levilactobacillus brevis KU15006: A Comprehensive Analysis of its Phenotypic and Genotypic Properties.", "token_count": 365, "char_count": 1265, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6548, "quality_score": 0.8274, "entities": { "genes": [ "KU15006" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:35.439753", "source": { "split": "train_shard_00000", "doc_id": 1013 }, "chunk_id": "train_shard_00000_1013_0", "global_id": 1118 }, { "text": "Microbial transformation of bile acids affects intestinal immune homoeostasis but its impact on inflammatory pathologies remains largely unknown. Using a mouse model of graft-versus-host disease (GVHD), we found that T cell-driven inflammation decreased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and reduced the levels of unconjugated and microbe-derived bile acids. Several microbe-derived bile acids attenuated farnesoid X receptor (FXR) activation, suggesting that loss of these metabolites during inflammation may increase FXR activity and exacerbate the course of disease. Indeed, mortality increased with pharmacological activation of FXR and decreased with its genetic ablation in donor T cells during mouse GVHD. Furthermore, patients with GVHD after allogeneic hematopoietic cell transplantation showed similar loss of BSH and the associated reduction in unconjugated and microbe-derived bile acids. In addition, the FXR antagonist ursodeoxycholic acid reduced the proliferation of human T cells and was associated with a lower risk of GVHD-related mortality in patients. We propose that dysbiosis and loss of microbe-derived bile acids during inflammation may be an important mechanism to amplify T cell-mediated diseases.\n\nAltered microbial bile acid metabolism exacerbates T cell-driven inflammation during graft-versus-host disease.", "token_count": 350, "char_count": 1371, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:36.018534", "source": { "split": "train_shard_00000", "doc_id": 1014 }, "chunk_id": "train_shard_00000_1014_0", "global_id": 1119 }, { "text": "To clarify the evolutionary relationships among Peptoniphilus species, whose members show association with increased risk for prostate cancer, detailed phylogenomic and comparative analyses were conducted on their genome sequences. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, Peptoniphilus species formed eight distinct clades, with Aedoeadaptatus and Anaerosphaera species branching between them. The observed clades designated as Peptoniphilus sensu stricto (encompassing its type species), Harei, Lacrimalis, Duerdenii, Mikwangii, Stercorisuis, Catoniae and Aedoeadaptatus, show genus level divergence based on 16S rRNA similarity and average amino acid identity (AAI). The Genome Taxonomy Database also assigns most of these clades to distinct taxa. Several Peptoniphilus species (viz. P. coxii, P. ivorii, P. nemausensis and some non-validly published species) grouped reliably with the type species of Aedoeadaptatus (A. acetigenes) and are affiliated to this genus based on 16S rRNA similarity, AAI, and multiple uniquely shared molecular signatures. Hence, we are proposing the transfer of these species into the emended genus Aedoeadaptatus. Our analyses on protein sequences from Peptoniphilus genomes have also identified 54 novel molecular markers consisting of conserved signature indels (CSIs), which are specific for different Peptoniphilus species clades and provide reliable means for their demarcation in molecular terms. Lastly, we also show that based on the shared presence of these CSIs in the genomes of uncharacterized Peptoniphilus spp. (cultured and uncultured), their affiliations to the specific Peptoniphilus clades can be accurately predicted. These results should prove useful in understanding the potential involvement of Peptoniphilus-related species in diseases.", "token_count": 457, "char_count": 1833, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:36.656304", "source": { "split": "train_shard_00000", "doc_id": 1015 }, "chunk_id": "train_shard_00000_1015_0", "global_id": 1120 }, { "text": "Phylogenomic and molecular markers based studies on clarifying the evolutionary relationships among Peptoniphilus species. Identification of several Genus-Level clades of Peptoniphilus species and transfer of some Peptoniphilus species to the genus Aedoeadaptatus.", "token_count": 62, "char_count": 264, "word_count": 32, "semantic_coherence": 1, "information_density": 0.7812, "quality_score": 0.8906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:37.018496", "source": { "split": "train_shard_00000", "doc_id": 1015 }, "chunk_id": "train_shard_00000_1015_1", "global_id": 1121 }, { "text": "The cultivated diploid Brassica oleracea is an important vegetable crop, but the genetic basis of its domestication remains largely unclear in the absence of high-quality reference genomes of wild B. oleracea. Here, we report the first chromosome-level assembly of the wild Brassica oleracea L. W03 genome (total genome size, 630.7 Mb; scaffold N50, 64.6 Mb). Using the newly assembled W03 genome, we constructed a gene-based B. oleracea pangenome and identified 29 744 core genes, 23 306 dispensable genes, and 1896 private genes. We re-sequenced 53 accessions, representing six potential wild B. oleracea progenitor species. The results of the population genomic analysis showed that the wild B. oleracea populations had the highest level of diversity and represents the most closely related population to modern-day horticultural B. oleracea. In addition, the WUSCHEL gene was found to play a decisive role in domestication and to be involved in cauliflower and broccoli curd formation. We also illustrate the loss of disease-resistance genes during selection for domestication. Our results provide new insights into the domestication of B. oleracea and will facilitate the future genetic improvement of Brassica crops.\n\nA new chromosome-scale genome of wild Brassica oleracea provides insights into the domestication of Brassica crops.", "token_count": 363, "char_count": 1339, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6281, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:37.594968", "source": { "split": "train_shard_00000", "doc_id": 1016 }, "chunk_id": "train_shard_00000_1016_0", "global_id": 1122 }, { "text": "A self-emulsifying drug delivery system (SEDDS) containing long chain lipid digestion products (LDP) and surfactants was developed to increase solubility of two model weakly basic drugs, cinnarizine and ritonavir, in the formulation. A 1:1.2 w/w mixture of glyceryl monooleate (Capmul GMO-50; Abitec) and oleic acid was used as the digestion product, and a 1:1 w/w mixture of Tween 80 and Cremophor EL was the surfactant used. The ratio between LDP and surfactant was 1:1 w/w. Since the commercially available Capmul GMO-50 is not pure monoglyceride and contained di-and-triglycerides, the digestion product used would provide 1:2 stoichiometric molar ratio of monoglyceride and fatty acid after complete digestion in gastrointestinal fluid. Both cinnarizine and ritonavir had much higher solubility in oleic acid (536 and 72 mg/g, respectively) than that in glyceryl monooleate and glyceryl trioleate. Therefore, by incorporating oleic acid in place of glyceryl trioleate in the formulation, the solubility of cinnarizine and ritonavir could be increased by 5-fold and 3.5-fold, respectively, as compared to a formulation without the fatty acid. The formulation dispersed readily in aqueous media, and adding 3 mM sodium taurocholate, which is generally present in GI fluid, remarkably improved the dispersibility of SEDDS and reduced particle size of dispersions. Thus, the use of digestion products of long-chain triglycerides as components of SEDDS can enhance the drug loading of weakly basic compounds and increase dispersibility in GI fluids.\n\nDevelopment of lipid-based SEDDS using digestion products of long-chain triglyceride for high drug solubility: Formulation and dispersion testing.", "token_count": 490, "char_count": 1697, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5911, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:38.246077", "source": { "split": "train_shard_00000", "doc_id": 1017 }, "chunk_id": "train_shard_00000_1017_0", "global_id": 1123 }, { "text": "An accurate, economic and green methodology for Pb(II) monitoring in bee products is proposed. Complexed metal traces were preconcentrated on Nylon membranes using the coacervation phenomenon based on room temperature reaction between the cationic surfactant hexadecyltrimethylammonium bromide and the bile salt sodium cholate. The increase in solid surface fluorescence signal of dyes 8-hydroxyquinoleine and o-phenanthroline due to Pb(II) presence was used for the metal quantification. Experimental variables that influence on preconcentration step and fluorimetric sensitivity were optimized using uni-varied assays. Pb(II) concentration was determined on membranes by solid surface fluorescence at λ\n\nDetermination of Lead in Bee Products by Solid Surface Fluorescence Using Complexation and Coacervation at Room Temperature Processes. An Environmental Friendly Methodology.", "token_count": 218, "char_count": 879, "word_count": 114, "semantic_coherence": 1, "information_density": 0.6754, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:38.716690", "source": { "split": "train_shard_00000", "doc_id": 1018 }, "chunk_id": "train_shard_00000_1018_0", "global_id": 1124 }, { "text": "Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis.\n\nPangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance.", "token_count": 108, "char_count": 510, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:39.099790", "source": { "split": "train_shard_00000", "doc_id": 1019 }, "chunk_id": "train_shard_00000_1019_0", "global_id": 1125 }, { "text": "Hibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.\n\nPan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus.", "token_count": 351, "char_count": 1301, "word_count": 166, "semantic_coherence": 1, "information_density": 0.753, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:39.673336", "source": { "split": "train_shard_00000", "doc_id": 1020 }, "chunk_id": "train_shard_00000_1020_0", "global_id": 1126 }, { "text": "The progressive escalation in the applications of bile salts in diverse fields has triggered research on their interaction with various biological macromolecules, especially with proteins. A proper understanding of the interaction process of bile salts, particularly in the lower concentrations range, with the serum albumin seems important since the normal serum concentration of bile salts is approximately in the micromolar range. The current study deals with a comprehensive and comparative analysis of the interaction of submicellar concentrations of sodium deoxycholate (NaDC) with two homologous transport proteins: bovine serum albumin (BSA) and human serum albumin (HSA). HSA and BSA with one and two tryptophans, respectively, provide the opportunity for an interesting comparison of tryptophan fluorescence behavior on interaction with NaDC. The study suggests a sequential interaction of NaDC in three discrete stages with the two proteins. A detailed study using warfarin and ibuprofen as site markers provides information about the sites of interaction, which is further confirmed by inclusive molecular dynamics simulation analysis. Moreover, the comparison of the thermodynamics and stability of the NaDC-serum albumin complexes confirms the stronger interaction of NaDC with BSA as compared to that with HSA. The differential interaction between the bile salt and the two serum albumins is further established from the difference in the extent of decrease in the esterase-like activity assay of the proteins in the presence of NaDC. Therefore, the present study provides important insight into the effect of submicellar concentrations of NaDC on the structure, stability, and activity of the two homologous serum albumins and thus can contribute not only to the general understanding of the complex nature of serum albumin-bile salt interactions but also to the design of more effective pharmaceutical formulations in the field of drug delivery and biomedical research.\n\nInsight into the Effect of Submicellar Concentrations of Sodium Deoxycholate on the Structure, Stability, and Activity of Bovine and Human Serum Albumin: An Interesting Comparison between Single and Double Tryptophan Proteins.", "token_count": 477, "char_count": 2214, "word_count": 321, "semantic_coherence": 1, "information_density": 0.4984, "quality_score": 0.7492, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:40.316271", "source": { "split": "train_shard_00000", "doc_id": 1021 }, "chunk_id": "train_shard_00000_1021_0", "global_id": 1127 }, { "text": "Previous lipase inhibitors studies mainly focus on the binding between inhibitors and lipase, ignoring the impact of inhibitors on the oil-water interface of lipid droplets. This study aimed to investigate the effect of nobiletin (NBT) from Citri Reticulatae Pericarpium on the oil-water interface properties and lipid digestion. Here, we found that NBT could destroy bile salt (BS)-stabilized lipid droplets and thus inhibited free fatty acid release, owing to the interaction between NBT and BS at the oil-water interface, and reducing the stability of the oil-water interface (the stability index decreased from 91.15 ± 2.6 % to 66.5 ± 3.6 %). Further, the molecular dynamics simulation and isothermal titration calorimetry revealed that NBT could combine with BS at oil-water interface through intermolecular interactions, including hydrogen bonds, Van der Waals force, and steric hindrance. These results suggest that the interfacial instability of NBT mediated BS emulsified oil droplets may be another pathway to inhibit lipid digestion.\n\nInhibitory effects of nobiletin-mediated interfacial instability of bile salt emulsified oil droplets on lipid digestion.", "token_count": 303, "char_count": 1167, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6213, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:40.883923", "source": { "split": "train_shard_00000", "doc_id": 1022 }, "chunk_id": "train_shard_00000_1022_0", "global_id": 1128 }, { "text": "Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.\n\nDefense systems and horizontal gene transfer in bacteria.", "token_count": 283, "char_count": 1334, "word_count": 201, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:41.442073", "source": { "split": "train_shard_00000", "doc_id": 1023 }, "chunk_id": "train_shard_00000_1023_0", "global_id": 1129 }, { "text": "Leptospirosis is a globally distributed zoonotic disease. The standard serological test, known as Microscopic Agglutination Test (MAT), requires the use of live Leptospira strains. To enhance its sensitivity and specificity, the usage of locally circulating strains is recommended. However, to date, no local strain is available from Austria. This study aimed to isolate circulating Leptospira strains from cattle in Austria to enhance the performances of the routine serological test for both humans and animals. We used a statistical approach combined with a comprehensive literature search to profile cattle with greater risk of leptospirosis infection and implemented a targeted sampling between November 2021 and October 2022. Urine and/or kidney tissue were sampled from 410 cattle considered at higher risk of infection. Samples were inoculated into EMJH-STAFF culture media within 2-6 h and a real-time PCR targeting the lipL32 gene was used to confirm the presence/absence of pathogenic Leptospira in each sample. Isolates were further characterised by core genome multilocus sequence typing (cgMLST). Nine out of 429 samples tested positive by PCR, from which three isolates were successfully cultured and identified as Leptospira borgpetersenii serogroup Sejroe serovar Hardjobovis, cgMLST cluster 40. This is the first report on the isolation and genotyping of local zoonotic Leptospira in Austria, which holds the potential for a significant improvement in diagnostic performance in the country. Although the local strain was identified as a cattle-adapted serovar, it possesses significant zoonotic implications. Furthermore, this study contributes to a better understanding of the epidemiology of leptospirosis in Europe.\n\nFirst isolation and genotyping of pathogenic Leptospira spp. from Austria.", "token_count": 437, "char_count": 1812, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:42.071419", "source": { "split": "train_shard_00000", "doc_id": 1024 }, "chunk_id": "train_shard_00000_1024_0", "global_id": 1130 }, { "text": "The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.\n\nImplications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen.", "token_count": 266, "char_count": 1174, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7233, "quality_score": 0.8616, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:42.626221", "source": { "split": "train_shard_00000", "doc_id": 1025 }, "chunk_id": "train_shard_00000_1025_0", "global_id": 1131 }, { "text": "Intestinal microbiota is a potential determinant of obesity, with probiotic bile salt hydrolase (BSH) as one of the key mechanisms in the anti-obesity effects. In this study, we present a Lactobacillus acidophilus GOLDGUT-LA100 (LA100) with high BSH activity, good gastric acid and bile salt tolerance, and a potential anti-obesity effect. LA100's anti-obesity effects were evaluated in a high-fat diet-induced, obese mouse model. LA100 administration alleviates high-fat diet-induced pathophysiological symptoms, such as body weight gain, high serum glucose and cholesterol level, hepatic lipid accumulation, and adipose inflammation. These results demonstrate concrete anti-obesity benefit in animal models and show promising applications in future clinical studies.\n\nIsolation of Lactobacillus acidophilus strain and its anti-obesity effect in a diet induced obese murine model.", "token_count": 249, "char_count": 881, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7311, "quality_score": 0.8655, "entities": { "genes": [ "LA100" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:43.112847", "source": { "split": "train_shard_00000", "doc_id": 1026 }, "chunk_id": "train_shard_00000_1026_0", "global_id": 1132 }, { "text": "As the food and pharmaceutical industry is continuously seeking new probiotic strains with unique health properties, the aim of the present study was to determine the impact of short-term dietary intervention with novel wild-type strains, isolated from various sources, on high-fat diet (HFD)-induced insulin resistance. Initially, the strains were evaluated in vitro for their ability to survive in simulated gastrointestinal (GI) conditions, for adhesion to Caco-2 cells, for bile salt hydrolase secretion, for cholesterol-lowering and cellular cholesterol-binding ability, and for growth inhibition of food-borne pathogens. In addition, safety criteria were assessed, including hemolytic activity and susceptibility to antibiotics. The in vivo test on insulin resistance showed that mice receiving the HFD supplemented with\n\nNovel Wild-Type", "token_count": 202, "char_count": 843, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7478, "quality_score": 0.8739, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:43.580235", "source": { "split": "train_shard_00000", "doc_id": 1027 }, "chunk_id": "train_shard_00000_1027_0", "global_id": 1133 }, { "text": "Bile acids, produced by the liver and secreted into the gastrointestinal tract, are dynamic molecules capable of impacting the overall health of dogs and cats in many contexts. Importantly, the gut microbiota metabolizes host primary bile acids into chemically distinct secondary bile acids. This review explores the emergence of new literature connecting microbial-derived bile acid metabolism to canine and feline health and disease. Moreover, this review highlights multi-omic methodologies for translational research as an area for continued growth in veterinary medicine aimed at accelerating microbiome science and medicine as it pertains to bile acid metabolism in dogs and cats.\n\nCollaborative Metabolism: Gut Microbes Play a Key Role in Canine and Feline Bile Acid Metabolism.", "token_count": 182, "char_count": 785, "word_count": 114, "semantic_coherence": 1, "information_density": 0.693, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:44.018092", "source": { "split": "train_shard_00000", "doc_id": 1028 }, "chunk_id": "train_shard_00000_1028_0", "global_id": 1134 }, { "text": "The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of\n\nThe intricate relationship of G-Quadruplexes and bacterial pathogenicity islands.", "token_count": 246, "char_count": 1206, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6312, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:44.502425", "source": { "split": "train_shard_00000", "doc_id": 1029 }, "chunk_id": "train_shard_00000_1029_0", "global_id": 1135 }, { "text": "The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied.\n\nPig pangenome graph reveals functional features of non-reference sequences.", "token_count": 66, "char_count": 352, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8913, "quality_score": 0.9457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:44.874040", "source": { "split": "train_shard_00000", "doc_id": 1030 }, "chunk_id": "train_shard_00000_1030_0", "global_id": 1136 }, { "text": "Campylobacter fetus comprises two closely related mammal-associated subspecies: Campylobacter fetus subsp. fetus (Cff) and Campylobacter fetus subsp. venerealis (Cfv). The latter causes bovine genital campylobacteriosis, a sexually-transmitted disease endemic in Spain that results in significant economic losses in the cattle industry. Here, 33 C. fetus Spanish isolates were whole-genome sequenced and compared with 62 publicly available C. fetus genomes from other countries. Genome-based taxonomic identification revealed high concordance with in silico PCR, confirming Spanish isolates as Cff (n = 4), Cfv (n = 9) and Cfv biovar intermedius (Cfvi, n = 20). MLST analysis assigned the Spanish isolates to 6 STs, including three novel: ST-76 and ST-77 for Cfv and ST-78 for Cff. Core genome SNP phylogenetic analysis of the 95 genomes identified multiple clusters, revealing associations at subspecies and biovar level between genomes with the same ST and separating the Cfvi genomes from Spain and other countries. A genome-wide association study identified pqqL as a Cfv-specific gene and a potential candidate for more accurate identification methods. Functionality analysis revealed variations in the accessory genome of C. fetus subspecies and biovars that deserve further studies. These results provide valuable information about the regional variants of C. fetus present in Spain and the genetic diversity and predicted functionality of the different subspecies.\n\nComparative pangenomic analysis of Campylobacter fetus isolated from Spanish bulls and other mammalian species.", "token_count": 417, "char_count": 1585, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:45.538589", "source": { "split": "train_shard_00000", "doc_id": 1031 }, "chunk_id": "train_shard_00000_1031_0", "global_id": 1137 }, { "text": "Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability, and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri. Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified 7 lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. fastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging from 43 bp to 119 kb and 36 bp to 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in genes involved in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides (LPS), flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the potential role of homologous recombination in P. parmentieri's evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.\n\nImpact of Homologous Recombination on Core Genome Evolution and Host Adaptation of Pectobacterium parmentieri.", "token_count": 489, "char_count": 1904, "word_count": 247, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:46.202517", "source": { "split": "train_shard_00000", "doc_id": 1032 }, "chunk_id": "train_shard_00000_1032_0", "global_id": 1138 }, { "text": "The field of bile acid microbiology in the gastrointestinal tract is going through a current rebirth after a peak of activity in the late 1970s and early 1980s. This renewed activity is a result of many factors, including the discovery near the turn of the century that bile acids are potent signalling molecules and technological advances in next-generation sequencing, computation, culturomics, gnotobiology, and metabolomics. We describe the current state of the field with particular emphasis on questions that have remained unanswered for many decades in both bile acid synthesis by the host and metabolism by the gut microbiota. Current knowledge of established enzymatic pathways, including bile salt hydrolase, hydroxysteroid dehydrogenases involved in the oxidation and epimerization of bile acid hydroxy groups, the Hylemon-Bjӧrkhem pathway of bile acid C7-dehydroxylation, and the formation of secondary allo-bile acids, is described. We cover aspects of bile acid conjugation and esterification as well as evidence for bile acid C3-dehydroxylation and C12-dehydroxylation that are less well understood but potentially critical for our understanding of bile acid metabolism in the human gut. The physiological consequences of bile acid metabolism for human health, important caveats and cautionary notes on experimental design and interpretation of data reflecting bile acid metabolism are also explored.\n\nAnother renaissance for bile acid gastrointestinal microbiology.", "token_count": 364, "char_count": 1481, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:46.827108", "source": { "split": "train_shard_00000", "doc_id": 1033 }, "chunk_id": "train_shard_00000_1033_0", "global_id": 1139 }, { "text": "Fourier-transform infrared (FTIR) spectroscopy using the IR Biotyper and core genome single nucleotide polymorphism (cgSNP) analysis were performed on 12 Legionella isolates associated with an outbreak at a spa house in Kanagawa Prefecture, Japan, and 3 non-outbreak isolates. The discriminative power of FTIR spectroscopy for 48-h incubation conditions of L. pneumophila in this outbreak was lower than cgSNP-based typing but higher than serogroup typing. FTIR spectroscopy could screen outbreak isolates from a group of genetically related isolates and may be useful as an initial typing method in Legionella outbreak investigations.\n\nEvaluating Fourier-transform infrared spectroscopy with IR Biotyper as a faster and simpler method for investigating the sources of an outbreak of legionellosis.", "token_count": 217, "char_count": 798, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:47.329273", "source": { "split": "train_shard_00000", "doc_id": 1034 }, "chunk_id": "train_shard_00000_1034_0", "global_id": 1140 }, { "text": "The\n\nA validated pangenome-scale metabolic model for the", "token_count": 17, "char_count": 56, "word_count": 8, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:47.685199", "source": { "split": "train_shard_00000", "doc_id": 1035 }, "chunk_id": "train_shard_00000_1035_0", "global_id": 1141 }, { "text": "The trend toward healthier food products has led to an increase in the research of in vitro gastrointestinal digestion methods. Among the most used models, static models are the simplest. Most static models have three stages: oral, gastric, and intestinal, simulating the enzymatic, electrolyte, pH, temperature, and bile salt conditions. The studies that have taken the most notice are those related to antioxidant activity, followed by those dealing with proteins and carbohydrates using most of them static in vitro digestion models. The number of these studies has increased over the years, passing from 45 to 415 in a 10-year period (2012-2023) and showing an interest in knowing the impact of food on human health. Nevertheless, published papers report different methodologies and analytical approaches. This review discusses the similarities and differences between the published static in vitro gastrointestinal digestion methods, with a focus on carbohydrates, finding that the most used protocol is Infogest, but with differences, mainly in the type of enzymes and their activity. Regarding in vitro gastrointestinal digestion of carbohydrates, many of the published studies are related to food and biomacromolecules, being the oral phase the most omitted, while the intestinal phase in the most diverse. Other methodologies to study the intestinal phase have been recommended, but the number of in vitro digestion studies using these methodologies (RSIE and BBMV) is still scarce but could represent a good alternative to analyze carbohydrates foods when combining with Infogest. More studies are required in this area.\n\nIn vitro gastrointestinal digestion methods of carbohydrate-rich foods.", "token_count": 413, "char_count": 1703, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5494, "quality_score": 0.7747, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:48.308189", "source": { "split": "train_shard_00000", "doc_id": 1036 }, "chunk_id": "train_shard_00000_1036_0", "global_id": 1142 }, { "text": "Bile salts were first used in the preparation of nanoparticles due to their stabilizing effects. As time went by, they attracted much attention and were increasingly employed in fabricating nanoparticles. It is well accepted that the physicochemical properties of nanoparticles are influential factors in their permeation, distribution, elimination and degree of effectiveness as well as toxicity. The review of articles shows that the use of bile salts in the structure of nanocarriers may cause significant changes in their physicochemical properties. Hence, having information about the effect of bile salts on the properties of nanoparticles could be valuable in the design of optimal carriers. Herein, we review studies in which bile salts were used in preparing liposomes, niosomes and other nanocarriers. Furthermore, the effects of bile salts on entrapment efficiency, particle size, polydispersity index, zeta potential, release profile and stability of nanoparticles are pointed out. Finally, we debate how to take advantage of bile salts potential for preparing desirable nanocarriers.\n\nBile salt-enriched vs. non-enriched nanoparticles: comparison of their physicochemical characteristics and release pattern.", "token_count": 276, "char_count": 1221, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:48.864778", "source": { "split": "train_shard_00000", "doc_id": 1037 }, "chunk_id": "train_shard_00000_1037_0", "global_id": 1143 }, { "text": "Delineating cohesive ecological units and determining the genetic basis for their environmental adaptation are among the most important objectives in microbiology. In the last decade, many studies have been devoted to characterizing the genetic diversity in microbial populations to address these issues. However, the impact of extreme environmental conditions, such as temperature and salinity, on microbial ecology and evolution remains unclear so far. In order to better understand the mechanisms of adaptation, we studied the (pan)genome of Exiguobacterium, a poly-extremophile bacterium able to grow in a wide range of environments, from permafrost to hot springs. To have the genome for all known Exiguobacterium type strains, we first sequenced those that were not yet available. Using a reverse-ecology approach, we showed how the integration of phylogenomic information, genomic features, gene and pathway enrichment data, regulatory element analyses, protein amino acid composition, and protein structure analyses of the entire Exiguobacterium pangenome allows to sharply delineate ecological units consisting of mesophilic, psychrophilic, halophilic-mesophilic, and halophilic-thermophilic ecotypes. This in-depth study clarified the genetic basis of the defined ecotypes and identified some key mechanisms driving the environmental adaptation to extreme environments. Our study points the way to organizing the vast microbial diversity into meaningful ecologically units, which, in turn, provides insight into how microbial communities adapt and respond to different environmental conditions in a changing world.\n\nGenomic basis of environmental adaptation in the widespread poly-extremophilic Exiguobacterium group.", "token_count": 374, "char_count": 1727, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6638, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:49.446440", "source": { "split": "train_shard_00000", "doc_id": 1038 }, "chunk_id": "train_shard_00000_1038_0", "global_id": 1144 }, { "text": "Nonreference sequences (NRSs) are DNA sequences present in global populations but absent in the current human reference genome. However, the extent and functional significance of NRSs in the human genomes and populations remains unclear. Here, we de novo assembled 539 genomes from five genetically divergent human populations using long-read sequencing technology, resulting in the identification of 5.1 million NRSs. These were merged into 45284 unique NRSs, with 29.7% being novel discoveries. Among these NRSs, 38.7% were common across the five populations, and 35.6% were population specific. The use of a graph-based pangenome approach allowed for the detection of 565 transcript expression quantitative trait loci on NRSs, with 426 of these being novel findings. Moreover, 26 NRS candidates displayed evidence of adaptive selection within human populations. Genes situated in close proximity to or intersecting with these candidates may be associated with metabolism and type 2 diabetes. Genome-wide association studies revealed 14 NRSs to be significantly associated with eight phenotypes. Additionally, 154 NRSs were found to be in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the understanding of human NRSs and provides novel insights into their functions, facilitating evolutionary and biomedical researches.\n\nHuman pangenome analysis of sequences missing from the reference genome reveals their widespread evolutionary, phenotypic, and functional roles.", "token_count": 364, "char_count": 1526, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:50.036335", "source": { "split": "train_shard_00000", "doc_id": 1039 }, "chunk_id": "train_shard_00000_1039_0", "global_id": 1145 }, { "text": "Despite Plasmodium ovale curtisi (Poc) and wallikeri (Pow) being important human-infecting malaria parasites that are widespread across Africa and Asia, little is known about their genome diversity. Morphologically identical, Poc and Pow are indistinguishable and commonly misidentified. Recent rises in the incidence of Poc/Pow infections have renewed efforts to address fundamental knowledge gaps in their biology, and to develop diagnostic tools to understand their epidemiological dynamics and malaria burden. A major roadblock has been the incompleteness of available reference assemblies (PocGH01, PowCR01; ~ 33.5 Mbp). Here, we applied multiple sequencing platforms and advanced bioinformatics tools to generate new reference genomes, Poc221 (South Sudan; 36.0 Mbp) and Pow222 (Nigeria; 34.3 Mbp), with improved nuclear genome contiguity (> 4.2 Mbp), annotation and completeness (> 99% Plasmodium spp., single copy orthologs). Subsequent sequencing of 6 Poc and 15 Pow isolates from Africa revealed a total of 22,517 and 43,855 high-quality core genome SNPs, respectively. Genome-wide levels of nucleotide diversity were determined to be 2.98 × 10\n\nNew reference genomes to distinguish the sympatric malaria parasites, Plasmodium ovale curtisi and Plasmodium ovale wallikeri.", "token_count": 374, "char_count": 1282, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7374, "quality_score": 0.8687, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:50.622419", "source": { "split": "train_shard_00000", "doc_id": 1040 }, "chunk_id": "train_shard_00000_1040_0", "global_id": 1146 }, { "text": "Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so, the genomic variation is often called from short-read alignments, which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved cattle assemblies to identify small and structural variation and genotype them with PanGenie in 307 short-read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation and confidently genotype close to 21 million small and 43,000 structural variants in the larger population. We validate 85% of these structural variants (with MAF > 0.1) directly with a subset of 25 short-read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data, and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of the top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTL for\n\nPangenome-genotyped structural variation improves molecular phenotype mapping in cattle.", "token_count": 338, "char_count": 1352, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:51.191482", "source": { "split": "train_shard_00000", "doc_id": 1041 }, "chunk_id": "train_shard_00000_1041_0", "global_id": 1147 }, { "text": "Poultry production occupies an important place in the economy of any country. High broiler production in recent years has badly affected its profitability due to bad feed quality, excessive use of chemotherapeutic agents, emergence of diverse pathogens, and the deficiencies in management practices during rearing cycle. Microbiological improvement of the meat quality using potential probiotics can be beneficial for broiler farming. Present study was initiated to isolate chicken gastrointestinal tract (GIT) bacteria with probiotic potential. To isolate probiotics from chicken gut, alimentary canal of chickens of known sizes and ages was suspended in ringers soln. Under shaking conditions for overnight followed by serial dilutions of ringers soln. Bacterial isolates were analyzed via growth curve analysis, biochemical testing using RapID™ NF Plus Panel kit, molecular characterization, antimicrobial activity assay, antibiotic sensitivity assay, GIT adherence assay, bile salt and gastric acid resistant assay, and cholesterol assimilation assay. Four bacteria isolated in present study were identified as\n\nIsolation and", "token_count": 250, "char_count": 1129, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7756, "quality_score": 0.8878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:51.676479", "source": { "split": "train_shard_00000", "doc_id": 1042 }, "chunk_id": "train_shard_00000_1042_0", "global_id": 1148 }, { "text": "Despite the importance of methicillin-resistant Staphylococcus aureus (MRSA) as a priority nosocomial pathogen, the genome sequences of Malaysian MRSA isolates are currently limited to a small pool of samples. Here, we present the genome sequence analyses of 88 clinical MRSA isolates obtained from the main tertiary hospital in Terengganu, Malaysia in 2016-2020, to obtain in-depth insights into their characteristics. The EMRSA-15 (ST22-SCCmec IV) clone of the clonal complex 22 (CC22) lineage was predominant with a total of 61 (69.3%) isolates. Earlier reports from other Malaysian hospitals indicated the predominance of the ST239 clone, but only two (2.3%) isolates were identified in this study. Two Indian-origin clones, the Bengal Bay clone ST772-SCCmec V (n = 2) and ST672 (n = 10) were also detected, with most of the ST672 isolates obtained in 2020 (n = 7). Two new STs were found, with one isolate each, and were designated ST7879 and ST7883. From the core genome phylogenetic tree, the HSNZ MRSA isolates could be grouped into seven clades. Antimicrobial phenotype-genotype concordance was high (> 95%), indicating the accuracy of WGS in predicting most resistances. Majority of the MRSA isolates were found to harbor more than 10 virulence genes, demonstrating their pathogenic nature.\n\nWhole genome sequencing of methicillin-resistant Staphylococcus aureus clinical isolates from Terengganu, Malaysia, indicates the predominance of the EMRSA-15 (ST22-SCCmec IV) clone.", "token_count": 468, "char_count": 1484, "word_count": 221, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [ "ST7883", "ST772", "ST239", "CC22", "ST22", "ST672", "ST7879" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:52.317857", "source": { "split": "train_shard_00000", "doc_id": 1043 }, "chunk_id": "train_shard_00000_1043_0", "global_id": 1149 }, { "text": "Isolation and characterization of probiotics from traditional fermented food have contributed many beneficial strains to the field of health and nutritional sciences. Handia, a traditional fermented alcoholic beverage popular in different parts of Odisha, was our source of isolation. This study characterizes one such potential bacteria, Levilactobacillus brevis ILSH3 (H3) isolated from Handia. The investigation for the probiotic attributes as per ICMR-DBT guidelines qualified the checkpoint assays like acid and bile tolerance, bile salt hydrolase activity, antimicrobial properties, and pathogen exclusion ability. The whole genome sequence of H3 (2,460,966 bp in size with GC content of 45.62%) was subjected to comparative genome analysis for its taxonomic identification and validation of probiotic potential. Various genes pertaining to its probiotic potential were identified in the genome and it showed zero matches against any pathogenic families. Metabolite profiling of cell-free supernatant using liquid chromatography-mass spectrometry revealed the presence of essential amino acids, short-chain fatty acids, antimicrobial molecules, immunomodulatory molecules, and flavor/aroma-enhancing compounds. Immunomodulatory property investigation using Bioplex and qRT-PCR showed a reduction in the levels of pro-inflammatory cytokines in L. brevis ILSH3-treated Caco-2 cells. Collectively, the results demonstrate that this Handia-origin bacteria Levilactobacillus brevis ILSH3 possesses desirable attributes of a probiotic, which is now open for nutritional and health biologists to explore. This new probiotic strain may show promising results when utilized in healthcare or functional foods.\n\nWhole Genome Mining and Characterization of a New Probiotic Strain Levilactobacillus brevis ILSH3 from Handia: An Ethnic Fermented Beverage of Odisha, India.", "token_count": 463, "char_count": 1864, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [ "ILSH3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:52.965621", "source": { "split": "train_shard_00000", "doc_id": 1044 }, "chunk_id": "train_shard_00000_1044_0", "global_id": 1150 }, { "text": "Imbalanced gut microbiota (GM) and abnormal fecal bile acid (BA) are thought to be the key factors for diarrhea-predominant irritable bowel syndrome (IBS-D), but the underlying mechanism remains unclear. Herein, we explore the influence of the GM-BA-Takeda G-protein-coupled receptor 5 (TGR5) axis on IBS-D. Twenty-five IBS-D patients and fifteen healthy controls were recruited to perform BA-related metabolic and metagenomic analyses. Further, the microbiota-humanized IBS-D rat model was established by fecal microbial transplantation (FMT) to investigate the GM-BA-TGR5 axis effects on the colonic barrier and visceral hypersensitivity (VH) in IBS-D. Finally, we used chenodeoxycholic acid (CDCA), an important BA screened out by metabolome, to evaluate whether it affected diarrhea and VH via the TGR5 pathway. Clinical research showed that GM associated with bile salt hydrolase (BSH) activity such as\n\nThe function of the gut microbiota-bile acid-TGR5 axis in diarrhea-predominant irritable bowel syndrome.", "token_count": 291, "char_count": 1013, "word_count": 141, "semantic_coherence": 1, "information_density": 0.773, "quality_score": 0.8865, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:53.522625", "source": { "split": "train_shard_00000", "doc_id": 1045 }, "chunk_id": "train_shard_00000_1045_0", "global_id": 1151 }, { "text": "The bile salt export pump (ABCB11/BSEP) is a hepatocyte plasma membrane-resident protein translocating bile salts into bile canaliculi. The sequence alignment of the four full-length transporters of the ABCB subfamily (ABCB1, ABCB4, ABCB5 and ABCB11) indicates that the NBD-NBD contact interface of ABCB11 differs from that of other members in only four residues. Notably, these are all located in the noncanonical nucleotide binding site 1 (NBS1). Substitution of all four deviant residues with canonical ones (quadruple mutant) significantly decreased the transport activity of the protein. In this study, we mutated two deviant residues in the signature sequence to generate a double mutant (R1221G/E1223Q). Furthermore, a triple mutant (E502S/R1221G/E1223Q) was generated, in which the deviant residues of the signature sequence and Q-loop were mutated concurrently to canonical residues. The double and triple mutants showed 80% and 60%, respectively, of the activity of wild-type BSEP. As expected, an increasing number of mutations gradually impair transport as an intricate network of interactions within the ABC proteins ensures proper functioning.\n\nThe noncanonical nucleotide binding site 1 of the bile salt export pump is optimized for proper function of the transporter.", "token_count": 343, "char_count": 1283, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [ "ABCB1", "ABCB5", "ABCB4", "ABCB11", "NBS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:54.098324", "source": { "split": "train_shard_00000", "doc_id": 1046 }, "chunk_id": "train_shard_00000_1046_0", "global_id": 1152 }, { "text": "Bacteria in the gastrointestinal tract produce amino acid bile acid amidates that can affect host-mediated metabolic processes\n\nBile salt hydrolase catalyses formation of amine-conjugated bile acids.", "token_count": 56, "char_count": 199, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:54.468236", "source": { "split": "train_shard_00000", "doc_id": 1047 }, "chunk_id": "train_shard_00000_1047_0", "global_id": 1153 }, { "text": "Bile acids (BAs) are steroid detergents in bile that contribute to the absorption of fats and fat-soluble vitamins while shaping the gut microbiome because of their antimicrobial properties\n\nBile salt hydrolase acyltransferase activity expands bile acid diversity.", "token_count": 71, "char_count": 264, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:54.840818", "source": { "split": "train_shard_00000", "doc_id": 1048 }, "chunk_id": "train_shard_00000_1048_0", "global_id": 1154 }, { "text": "The proportion of sodium taurolithocholate (NaTLC) is extremely low in human bile salts. NaTLC forms aggregates with other lipids in the bile and functions as an emulsifying and solubilizing agent. The molecular structure of NaTLC contains hydrophilic hydroxyl and sulfonic acid groups at both ends of the steroid ring. This molecular structure is similar to bolaform amphiphilic substance having hydrophilic groups at both ends due to the characteristics of its molecular structure. This study investigated the aggregate properties of the NaTLC using surface tension measurements, light scattering, small-angle X-ray scattering (SAXS), and cryo-transmission electron microscopy (cryo-TEM). Surface tension measurement showed that the surface tension of the NaTLC solution decreased to 54 mN m\n\nMicelle formation of sodium taurolithocholate.", "token_count": 205, "char_count": 841, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6695, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:55.310695", "source": { "split": "train_shard_00000", "doc_id": 1049 }, "chunk_id": "train_shard_00000_1049_0", "global_id": 1155 }, { "text": "The purpose of this study was to fabricate composite nanoparticles using soy protein isolate (SPI) and sorghum bran arabinoxylan (AX) for the delivery of curcumin (Cur). The influences of AX concentrations on the physicochemical characteristic, stability and bioaccessibility of curcumin were investigated. The findings showed that the encapsulation efficiency of curcumin obviously increased upon incorporating AX in comparison to SPI-Cur particles. Hydrogen bonds and hydrophobic interactions were the primary driving forces for the formation of SPI-Cur-AX nanoparticles (SCA). SCA nanoparticles with 1.00 % AX exhibited a uniform size with orderly distribution, suggesting its remarkable physical stability due to the strengthened electrostatic repulsion. However, excessive AX led to aggregation of particles, a noticeable increase in size, and subsequently, a reduction in stability. Due to the heightened free radical scavenging capacity of sorghum AX, SCA nanoparticles exhibited superior antioxidant capabilities. Compared to free curcumin, encapsulation within composite particles significantly enhanced the retention rate and bioaccessibility of curcumin. This improvement was attributed to the potent emulsification ability of AX, which coordinated with bile salt to promote the transfer of curcumin into micelles. The research provides an effective strategy for developing food-grade delivery carriers aimed at enhancing dispersibility, stability and bioaccessibility of the fat-soluble bioactives.\n\nDevelopment of sorghum arabinoxylan-soy protein isolate composite nanoparticles for delivery of curcumin: Effect of polysaccharide content on stability and in vitro digestibility.", "token_count": 389, "char_count": 1691, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:55.925625", "source": { "split": "train_shard_00000", "doc_id": 1050 }, "chunk_id": "train_shard_00000_1050_0", "global_id": 1156 }, { "text": "Regions under balancing selection are characterized by dense polymorphisms and multiple persistent haplotypes, along with other sequence complexities. Successful identification of these patterns depends on both the statistical approach and the quality of sequencing. To address this challenge, at first, a new statistical method called LD-ABF was developed, employing efficient Bayesian techniques to effectively test for balancing selection. LD-ABF demonstrated the most robust detection of selection in a variety of simulation scenarios, compared against a range of existing tests/tools (Tajima's D, HKA, Dng, BetaScan, and BalLerMix). Furthermore, the impact of the quality of sequencing on detection of balancing selection was explored, as well, using: (i) SNP genotyping and exome data, (ii) targeted high-resolution HLA genotyping (IHIW), and (iii) whole-genome long-read sequencing data (Pangenome). In the analysis of SNP genotyping and exome data, we identified known targets and 38 new selection signatures in genes not previously linked to balancing selection. To further investigate the impact of sequencing quality on detection of balancing selection, a detailed investigation of the MHC was performed with high-resolution HLA typing data. Higher quality sequencing revealed the HLA-DQ genes consistently demonstrated strong selection signatures otherwise not observed from the sparser SNP array and exome data. The HLA-DQ selection signature was also replicated in the Pangenome samples using considerably less samples but, with high-quality long-read sequence data. The improved statistical method, coupled with higher quality sequencing, leads to more consistent identification of selection and enhanced localization of variants under selection, particularly in complex regions.\n\nThe Impact of Patterns in Linkage Disequilibrium and Sequencing Quality on the Imprint of Balancing Selection.", "token_count": 413, "char_count": 1906, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5687, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:56.895289", "source": { "split": "train_shard_00000", "doc_id": 1051 }, "chunk_id": "train_shard_00000_1051_0", "global_id": 1157 }, { "text": "Cellulolytic bacteria with probiotic functions play a crucial role in promoting the intestinal health in herbivores. In this study, we aimed to correlate the 16S rRNA gene amplicon sequencing and fiber-degrading enzyme activity data from six different herbivore feces samples. By utilizing the separation and screening steps of probiotics, we targeted and screened high-efficiency fiber-degrading bacteria with probiotic functions. The animals included Maiwa Yak (MY), Holstein cow (CC), Tibetan sheep (TS), Southern Sichuan black goat (SG), Sichuan white rex rabbit (CR), and New Zealand white rabbit (ZR). The results showed that the enzymes associated with fiber degradation were higher in goat and sheep feces compared to cattle and rabbit's feces. Correlation analysis revealed that Bacillus and Fibrobacter were positively correlated with five types of fiber-degrading related enzymes. Notably, the relative abundance of Bacillus in the feces of Tibetan sheep was significantly higher than that of other five herbivores. A strain TS5 with good cellulose decomposition ability from the feces of Tibetan sheep by Congored staining, filter paper decomposition test, and enzyme activity determination was isolated. The strain was identified as Bacillus velezensis by biological characteristics, biochemical analysis, and 16S rRNA gene sequencing. To test the probiotic properties of Bacillus velezensis TS5, we evaluated its tolerance to acid and bile salt, production of digestive enzymes, antioxidants, antibacterial activity, and adhesion ability. The results showed that the strain had good tolerance to pH 2.0 and 0.3% bile salts, as well as good potential to produce cellulase, protease, amylase, and lipase. This strain also had good antioxidant capacity and the ability to antagonistic Staphylococcus aureus BJ216, Salmonella SC06, Enterotoxigenic Escherichia coli CVCC196, and Escherichia coli ATCC25922", "token_count": 509, "char_count": 1914, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6081, "quality_score": 0.804, "entities": { "genes": [ "ATCC25922", "TS5", "SC06", "BJ216", "CVCC196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:57.576454", "source": { "split": "train_shard_00000", "doc_id": 1052 }, "chunk_id": "train_shard_00000_1052_0", "global_id": 1158 }, { "text": "More importantly, the strain had good self-aggregation and Caco-2 cell adhesion rate. In addition, we tested the safety of Bacillus velezensis TS5 by hemolysis test, antimicrobial susceptibility test, and acute toxicity test in mice. The results showed that the strain had no hemolytic phenotype, did not develop resistance to 19 commonly used antibiotics, had no cytotoxicity to Caco-2, and did not have acute toxic harm to mice. In summary, this study targeted isolated and screened a strain of Bacillus velezensis TS5 with high fiber-degrading ability and probiotic potency. This strain can be used as a potential probiotic for feeding microbial preparations for ruminants.\n\nTargeted Screening of Fiber Degrading Bacteria with Probiotic Function in Herbivore Feces.", "token_count": 208, "char_count": 768, "word_count": 115, "semantic_coherence": 1, "information_density": 0.687, "quality_score": 0.8435, "entities": { "genes": [ "TS5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:58.060780", "source": { "split": "train_shard_00000", "doc_id": 1052 }, "chunk_id": "train_shard_00000_1052_1", "global_id": 1159 }, { "text": "Enterococcus mundtii AM_AQ_BC8 isolated from biofouled filtration membrane was characterised as a potential probiotic bacterium showing strong L-lactic acid-producing capability. Experimental studies revealed that E. mundtii AM_AQ_BC8 possess antibiofilm and antimicrobial ability too, as tested against strong biofilm-forming bacteria like Pseudomonas spp. The present study has evaluated the genetic potential of E. mundtii AM_AQ_BC8 through genome sequencing. Whole genome analysis revealed the presence of key genes like ldh_1 and ldh_2 responsible for lactic acid production along with genes encoding probiotic features such as acid and bile salt resistance (dnaK, dnaJ, argS), fatty acid synthesis (fabD, fabE) and lactose utilisation (lacG, lacD). The phylogenomic analysis based on OrthoANI (99.85%) and dDDH (96.8%) values revealed that the strain AM_AQ_BC8 shared the highest homology with E. mundtii. The genome sequence of strain AM_AQ_BC8 has been deposited to NCBI and released with GenBank accession no. SAMN32531201. The study primarily demonstrated the probiotic potential of E. mundtii AM_AQ_BC8 isolate, for L-lactate synthesis in high concentration (8.98 g/L/day), which also showed anti-biofilm and antimicrobial activities.\n\nGenomic and phenotypic characterisation of Enterococcus mundtii AM_AQ_BC8 for its anti-biofilm, antimicrobial and probiotic potential.", "token_count": 412, "char_count": 1381, "word_count": 184, "semantic_coherence": 1, "information_density": 0.663, "quality_score": 0.8315, "entities": { "genes": [ "SAMN32531201" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:58.699885", "source": { "split": "train_shard_00000", "doc_id": 1053 }, "chunk_id": "train_shard_00000_1053_0", "global_id": 1160 }, { "text": "Fungi use the accessory gene content of their pangenomes to adapt to their environments. While gene presence-absence variation contributes to shaping accessory gene reservoirs, the genomic contexts that shape these events remain unclear. Since pangenome studies are typically species-wide and do not analyze different populations separately, it is yet to be uncovered whether presence-absence variation patterns and mechanisms are consistent across populations. Fungal plant pathogens are useful models for studying presence-absence variation because they rely on it to adapt to their hosts, and members of a species often infect distinct hosts. We analyzed gene presence-absence variation in the blast fungus, Magnaporthe oryzae (syn. Pyricularia oryzae), and found that presence-absence variation genes involved in host-pathogen and microbe-microbe interactions may drive the adaptation of the fungus to its environment. We then analyzed genomic and epigenomic features of presence-absence variation and observed that proximity to transposable elements, gene GC content, gene length, expression level in the host, and histone H3K27me3 marks were different between presence-absence variation genes and conserved genes. We used these features to construct a model that was able to predict whether a gene is likely to experience presence-absence variation with high precision (86.06%) and recall (92.88%) in M. oryzae. Finally, we found that presence-absence variation genes in the rice and wheat pathotypes of M. oryzae differed in their number and their genomic context. Our results suggest that genomic and epigenomic features of gene presence-absence variation can be used to better understand and predict fungal pangenome evolution. We also show that substantial intra-species variation can exist in these features.\n\nDistinct genomic contexts predict gene presence-absence variation in different pathotypes of Magnaporthe oryzae.", "token_count": 433, "char_count": 1933, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5424, "quality_score": 0.7712, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:59.392327", "source": { "split": "train_shard_00000", "doc_id": 1054 }, "chunk_id": "train_shard_00000_1054_0", "global_id": 1161 }, { "text": "Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width and how incorporating gap cost in the scoring function improves alignment accuracy. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy. Implementation ( https://github.com/at-cg/PanAligner ).\n\nCo-linear chaining on pangenome graphs.", "token_count": 298, "char_count": 1479, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6456, "quality_score": 0.8228, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:08:59.962241", "source": { "split": "train_shard_00000", "doc_id": 1055 }, "chunk_id": "train_shard_00000_1055_0", "global_id": 1162 }, { "text": "Sucralose has raised concerns regarding its safety and recent studies have demonstrated that sucralose consumption can disrupt the normal gut microbiome and alter metabolic profiles in mice. However, the extent to which this perturbation affects the functional interaction between the microbiota and the host, as well as its potential impact on host health, remains largely unexplored. Here, we aimed to investigate whether chronic sucralose consumption, at levels within the Acceptable Daily Intake (ADI), could disturb key gut microbial functions and lead to adverse health effects in mice. Following six-month sucralose consumption, several bacterial genera associated with bile acid metabolism were decreased, including Lactobacillus and Ruminococcus. Consequently, the richness of secondary bile acid biosynthetic pathway and bacterial bile salt hydrolase gene were decreased in the sucralose-treated gut microbiome. Compared to controls, sucralose-consuming mice exhibited significantly lower ratios of free bile acids and taurine-conjugated bile acids in their livers. Additionally, several farnesoid X receptor (FXR) agonists were decreased in sucralose-treated mice. This reduction in hepatic FXR activation was associated with altered expression of down-stream genes, in the liver. Moreover, the expression of key lipogenic genes was up-regulated in the livers of sucralose-treated mice. Changes in hepatic lipid profiles were also observed, characterized by lower ceramide levels, a decreased PC/PE ratio, and a mildly increase in lipid accumulation. Additionally, sucralose-consumed mice exhibited higher hepatic cholesterol level compared to control mice, with up-regulation of cholesterol efflux genes and down-regulation of genes associated with reverse cholesterol transport. In conclusion, chronic sucralose consumption disrupts FXR signaling activation and perturbs hepatic lipid and cholesterol homeostasis, potentially by diminishing the bile acid metabolic capacity of the gut microbiome. These findings shed light on the complex interplay between sucralose, the gut microbiota, and host metabolism, raising important questions about the safety of its long-term consumption.", "token_count": 519, "char_count": 2195, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:09:00.622913", "source": { "split": "train_shard_00000", "doc_id": 1056 }, "chunk_id": "train_shard_00000_1056_0", "global_id": 1163 }, { "text": "Chronic sucralose consumption inhibits farnesoid X receptor signaling and perturbs lipid and cholesterol homeostasis in the mouse livers, potentially by altering gut microbiota functions.", "token_count": 47, "char_count": 187, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9583, "quality_score": 0.9792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:00.981885", "source": { "split": "train_shard_00000", "doc_id": 1056 }, "chunk_id": "train_shard_00000_1056_1", "global_id": 1164 }, { "text": "Streptococcus suis is a zoonotic pathogen that causes a major health problem in the pig production industry worldwide. Spain is one of the largest pig producers in the world. This work aimed to investigate the genetic and phenotypic features of invasive S. suis isolates recovered in Spain. A panel of 156 clinical isolates recovered from 13 Autonomous Communities, representing the major pig producers, were analysed. MLST and serotyping analysis revealed that most isolates (61.6%) were assigned to ST1 (26.3%), ST123 (18.6%), ST29 (9.6%), and ST3 (7.1%). Interestingly, 34 new STs were identified, indicating the emergence of novel genetic lineages. Serotypes 9 (27.6%) and 1 (21.8%) prevailed, followed by serotypes 7 (12.8%) and 2 (12.2%). Analysis of 13 virulence-associated genes showed significant associations between ST, serotype, virulence patterns, and clinical features, evidencing particular virulence traits associated with genetic clusters. The pangenome was generated, and the core genome was distributed in 7 Bayesian groups where each group included a variable set of over- and under-represented genes of different categories. The study provides comprehensive data and knowledge to improve the design of new vaccines, antimicrobial treatments, and bacterial typing approaches.\n\nGenomic and phenotypic analysis of invasive Streptococcus suis isolated in Spain reveals genetic diversification and associated virulence traits.", "token_count": 371, "char_count": 1442, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8341, "entities": { "genes": [ "ST3", "ST123", "ST1", "ST29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:01.567616", "source": { "split": "train_shard_00000", "doc_id": 1057 }, "chunk_id": "train_shard_00000_1057_0", "global_id": 1165 }, { "text": "Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.\n\nTranslation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast.", "token_count": 298, "char_count": 1541, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:02.118236", "source": { "split": "train_shard_00000", "doc_id": 1058 }, "chunk_id": "train_shard_00000_1058_0", "global_id": 1166 }, { "text": "The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between\n\nPangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery.", "token_count": 218, "char_count": 904, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7667, "quality_score": 0.8833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:02.581549", "source": { "split": "train_shard_00000", "doc_id": 1059 }, "chunk_id": "train_shard_00000_1059_0", "global_id": 1167 }, { "text": "The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficient colored de Bruijn graph index, arising as the combination of a k-mer dictionary with a compressed inverted index. The proposed index takes full advantage of the fact that unitigs in the colored compacted de Bruijn graph are monochromatic (i.e., all k-mers in a unitig have the same set of references of origin, or color). Specifically, the unitigs are kept in the dictionary in color order, thereby allowing for the encoding of the map from k-mers to their colors in as little as 1 + o(1) bits per unitig. Hence, one color per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for integer lists, the index achieves very small space. We implement these methods in a tool called Fulgor, and conduct an extensive experimental analysis to demonstrate the improvement of our tool over previous solutions. For example, compared to Themisto-the strongest competitor in terms of index space vs. query time trade-off-Fulgor requires significantly less space (up to 43% less space for a collection of 150,000 Salmonella enterica genomes), is at least twice as fast for color queries, and is 2-6[Formula: see text] faster to construct.\n\nFulgor: a fast and compact k-mer index for large-scale matching and color queries.", "token_count": 439, "char_count": 1989, "word_count": 313, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:03.213214", "source": { "split": "train_shard_00000", "doc_id": 1060 }, "chunk_id": "train_shard_00000_1060_0", "global_id": 1168 }, { "text": "Rare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome sequencing (HiFi-GS) detects SVs with increased sensitivity and enables assembling personal and graph genomes. We leverage standard reference genomes, public assemblies (n = 94) and a large collection of HiFi-GS data from a rare disease program (Genomic Answers for Kids, GA4K, n = 574 assemblies) to build a graph genome representing a unified SV callset in GA4K, identify common variation and prioritize SVs that are more likely to cause genetic disease (MAF < 0.01). Using graphs, we obtain a higher level of reproducibility than the standard reference approach. We observe over 200,000 SV alleles unique to GA4K, including nearly 1000 rare variants that impact coding sequence. With improved specificity for rare SVs, we isolate 30 candidate SVs in phenotypically prioritized genes, including known disease SVs. We isolate a novel diagnostic SV in KMT2E, demonstrating use of personal assemblies coupled with pangenome graphs for rare disease genomics. The community may interrogate our pangenome with additional assemblies to discover new SVs within the allele frequency spectrum relevant to genetic diseases.\n\nPangenome graphs improve the analysis of structural variants in rare genetic diseases.", "token_count": 364, "char_count": 1440, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8278, "entities": { "genes": [ "GA4K", "KMT2E" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:03.793877", "source": { "split": "train_shard_00000", "doc_id": 1061 }, "chunk_id": "train_shard_00000_1061_0", "global_id": 1169 }, { "text": "Nowadays, the bacteriocin industries have seen significant growth, supplanting chemical preservatives in its ability to improve the shelf-life and safety of food. The increasing customer desire to use natural preservatives has fueled advancing bacteriocin research. The objective of this study was to identify lactic acid bacteria (LAB) that produce bacteriocin-like inhibitory substance (BLIS) and have strong anti-listerial activity. We have identified and analyzed a LAB obtained from chhurpi samples, a popular milk-derived product in the Himalayan regions of India and Nepal. The strain was studied and identified based on its morphological, biochemical, and physiological characteristics. Furthermore, the molecular 16s-rDNA analysis suggests that the strain was Lactococcus sp. RGUAM1 (98.2% similar to Lactococcus lactis subsp. hordniae NBRC 100931T). The isolated strain can produce a potent BLIS, which has shown efficacy against three gram-positive bacteria responsible for food spoilage, such as Listeria monocytogenes (MTCC 657), Staphylococcus aureus subsp. aureus (MTCC 87), Lactobacillus plantarum (MTCC 1407), Lactobacillus paraplantarum (MTCC 12904). The scanning electron microscope (SEM) image illustrates that the crude cell-free supernatant (CFS) disrupts the cell envelope, leading to the release of cellular contents and the clustering of cells. In addition, this BLIS can easily withstand a wide range of pH (2-12), temperature (up to 100 °C for 15 min), bile salt (0.3% W/V), salinity (4% W/V), and enzyme activity of 1600 AU/ml against Listeria monocytogenes. Our research offers a robust framework and valuable insights into bio-preservation and its potential applications in diverse food products.", "token_count": 483, "char_count": 1726, "word_count": 242, "semantic_coherence": 1, "information_density": 0.7107, "quality_score": 0.8554, "entities": { "genes": [ "RGUAM1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:04.445483", "source": { "split": "train_shard_00000", "doc_id": 1062 }, "chunk_id": "train_shard_00000_1062_0", "global_id": 1170 }, { "text": "Isolation and characterization of lactic acid bacteria producing a potent anti-listerial bacteriocin-like inhibitory substance (BLIS) from chhurpi, a fermented milk product.", "token_count": 44, "char_count": 173, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:04.809204", "source": { "split": "train_shard_00000", "doc_id": 1062 }, "chunk_id": "train_shard_00000_1062_1", "global_id": 1171 }, { "text": "Recurrence of progressive familial intrahepatic cholestasis (PFIC) type II poses challenges during postoperative liver transplant care. Posttransplant patients with PFIC type II risk developing recurrent cholestasis with normal gamma-glutamyl transferase activity, which mimics the original bile salt export pump (BSEP) protein deficiency and is related to a form of immunoglobulin G antibody (anti-BSEP)-mediated rejection. Bortezomib effectively induces apoptosis of actively antibody-producing plasma cells that may have a role in antibody-mediated rejection. In this case, we used bortezomib to treat PFIC type II recurrence after liver transplantation in a child.\n\nSuccessful Use of Bortezomib for Recurrent Progressive Familial Intrahepatic Cholestasis Type II After Liver Transplantation: A Pediatric Case with a 9-Year Follow-Up.", "token_count": 225, "char_count": 837, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7117, "quality_score": 0.8559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:05.277999", "source": { "split": "train_shard_00000", "doc_id": 1063 }, "chunk_id": "train_shard_00000_1063_0", "global_id": 1172 }, { "text": "[This corrects the article DOI: 10.3389/fmicb.2023.1119226.].\n\nCorrigendum: Pangenome analysis of the genus", "token_count": 50, "char_count": 107, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:05.645158", "source": { "split": "train_shard_00000", "doc_id": 1064 }, "chunk_id": "train_shard_00000_1064_0", "global_id": 1173 }, { "text": "The health benefits of fermented fruits have attracted consumers' attention. High levels of antioxidant ability in the fermented kiwifruit extract were found at the early stage of fermentation. The co-fermention with Lactobacillus paracasei LG0260 and Kluyveromyces marxianus J2853 showed the highest ABTS radical scavenging ability (ABTS\n\nAntioxidant properties and changes in vitro digestion of the fermented kiwifruit extract prepared by lactic acid bacteria and yeasts.", "token_count": 131, "char_count": 473, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7385, "quality_score": 0.8692, "entities": { "genes": [ "LG0260" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:06.061205", "source": { "split": "train_shard_00000", "doc_id": 1065 }, "chunk_id": "train_shard_00000_1065_0", "global_id": 1174 }, { "text": "Mycoplasma (M.) hyosynoviae is a commensal of the upper respiratory tract in swine, which has the potential to spread systemically, usually resulting in arthritis in fattening pigs and gilts. To date, very little is known about the epidemiology of M. hyosynoviae, mainly due to a lack of suitable typing methods. Therefore, this study aimed to develop both a conventional multi locus sequence typing (MLST) and a core genome (cg) MLST scheme. The development of the cgMLST was based on whole genome sequences of 64 strains isolated from pigs and wild boars during routine diagnostics as well as nine publicly available genomes. A cgMLST scheme containing 390 target genes was established using the Ridom© SeqSphere+ software. Using this scheme as a foundation, seven housekeeping genes were selected for conventional MLST based on their capability to reflect genome wide relatedness and subsequently, all 73 strains were typed by applying both methods. Core genome MLST results revealed a high diversity of the studied strain population and less than 100 allele differences between epidemiologically unrelated strains were only detected for four isolates from the US. On the other hand, seven clonal clusters (≤ 12 allele differences) comprising 20 isolates were identified. Comparison of the two typing methods resulted in highly congruent phylogenetic trees and an Adjusted Rand Coefficient of 0.893, while cgMLST showed marginally higher resolution when comparing closely related isolates, indicated by a slightly higher Simpson's ID (0.992) than conventional MLST (Simpson's ID = 0.990). Overall, both methods seem well suited for epidemiological analyses for scientific as well as diagnostic purposes. While MLST is faster and cheaper, cgMLST can be used to further differentiate closely related isolates.\n\nMultilocus sequence typing schemes for the emerging swine pathogen Mycoplasma hyosynoviae.", "token_count": 463, "char_count": 1902, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6596, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:06.698662", "source": { "split": "train_shard_00000", "doc_id": 1066 }, "chunk_id": "train_shard_00000_1066_0", "global_id": 1175 }, { "text": "Malaria is endemic in the Central region of Ghana, however, the ecological and the seasonal variations of Plasmodium population structure and the intensity of malaria transmission in multiple sites in the region have not been explored. In this cross-sectional study, five districts in the region were involved. The districts were Agona Swedru, Assin Central and Gomoa East (representing the forest zone) and Abura-Asebu-Kwamankese and Cape Coast representing the coastal zone. Systematically, blood samples were collected from patients with malaria. The malaria status was screened with a rapid diagnostic test (RDT) kit (CareStart manufactured by Access Bio in Somerset, USA) and the positive ones confirmed microscopically. Approximately, 200 μL of blood was used to prepare four dried blood spots of 50μL from each microscopy positive sample. The Plasmodium genome was sequenced at the Malaria Genome Laboratory (MGL) of Wellcome Sanger Institute (WSI), Hinxton, UK. The single nucleotide polymorphisms (SNPs) in the parasite mitochondria (PfMIT:270) core genome aided the species identification of Plasmodium. Subsequently, the complexity of infection (COI) was determined using the complexity of infection likelihood (COIL) computational analysis. In all, 566 microscopy positive samples were sequenced. Of this number, Plasmodium genome was detected in 522 (92.2%). However, whole genome sequencing was successful in 409/522 (72.3%) samples. In total, 516/522 (98.8%) of the samples contained P. falciparum mono-infection while the rest (1.2%) were either P. falciparum/P. ovale (Pf/Po) (n = 4, 0.8%) or P. falciparum/P. malariae/P. vivax (Pf/Pm/Pv) mixed-infection (n = 2, 0.4%)", "token_count": 488, "char_count": 1685, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6529, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:07.349988", "source": { "split": "train_shard_00000", "doc_id": 1067 }, "chunk_id": "train_shard_00000_1067_0", "global_id": 1176 }, { "text": "All the four Pf/Po infections were identified in samples from the Assin Central municipality whilst the two Pf/Pm/Pv triple infections were identified in Abura-Asebu-Kwamankese district and Cape Coast metropolis. Analysis of the 409 successfully sequenced genome yielded between 1-6 P. falciparum clones per individual infection. The overall mean COI was 1.78±0.92 (95% CI: 1.55-2.00). Among the study districts, the differences in the mean COI between ecological zones (p = 0.0681) and seasons (p = 0.8034) were not significant. However, regression analysis indicated that the transmission of malaria was more than twice among study participants aged 15-19 years (OR = 2.16, p = 0.017) and almost twice among participants aged over 60 years (OR = 1.91, p = 0.021) compared to participants between 20-59 years. Between genders, mean COI was similar except in Gomoa East where females recorded higher values. In conclusion, the study reported, for the first time, P. vivax in Ghana. Additionally, intense malaria transmission was found to be higher in the 15-19 and > 60 years, compared to other age groups. Therefore, active surveillance for P. vivax in Ghana and enhanced malaria control measures in the 15-19 year group years and those over 60 years are recommended.\n\nMolecular speciation of Plasmodium and multiplicity of P. falciparum infection in the Central region of Ghana.", "token_count": 393, "char_count": 1380, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:07.957071", "source": { "split": "train_shard_00000", "doc_id": 1067 }, "chunk_id": "train_shard_00000_1067_1", "global_id": 1177 }, { "text": "Advances in the understanding of bile salt synthesis, transport and signalling show the potential of modulating bile salt homeostasis as a therapeutic strategy in cholestatic liver diseases. Here, recent developments in (pre)clinical research in this field is summarized and discussed.\n\nTargeting bile salt homeostasis in biliary diseases.", "token_count": 78, "char_count": 339, "word_count": 47, "semantic_coherence": 1, "information_density": 0.7234, "quality_score": 0.8617, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:08.332280", "source": { "split": "train_shard_00000", "doc_id": 1068 }, "chunk_id": "train_shard_00000_1068_0", "global_id": 1178 }, { "text": "[Analysis of gene characteristics and core genome characteristics of carbapenem-resistant Enterobacter cloacae in rural residents of Weifang City, Shandong Province].", "token_count": 38, "char_count": 166, "word_count": 20, "semantic_coherence": 1, "information_density": 0.85, "quality_score": 0.925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:08.699361", "source": { "split": "train_shard_00000", "doc_id": 1069 }, "chunk_id": "train_shard_00000_1069_0", "global_id": 1179 }, { "text": "Nanotechnology is an expanding and new technology that prompts production with nanoparticle-based (1-100 nm) organic and inorganic materials. Such a tool has an imperative function in different sectors like bioengineering, pharmaceuticals, electronics, energy, nuclear energy, and fuel, and its applications are helpful for human, animal, plant, and environmental health. In exacting, the nanoparticles are synthesized by top-down and bottom-up approaches through different techniques such as chemical, physical, and biological progress. The characterization is vital and the confirmation of nanoparticle traits is done by various instrumentation analyses like UV-Vis spectrophotometry (UV-Vis), Fourier transform infrared spectroscopy, scanning electron microscope, transmission electron microscopy, X-ray diffraction, atomic force microscopy, annular dark-field imaging, and intracranial pressure. In addition, probiotics are friendly microbes which while administered in sufficient quantity confer health advantages to the host. Characterization investigation is much more significant to the identification of good probiotics. Similarly, haemolytic activity, acid and bile salt tolerance, autoaggregation, antimicrobial compound production, inhibition of pathogens, enhance the immune system, and more health-beneficial effects on the host. The synergistic effects of nanoparticles and probiotics combined delivery applications are still limited to food, feed, and biomedical applications. However, the mechanisms by which they interact with the immune system and gut microbiota in humans and animals are largely unclear. This review discusses current research advancements to fulfil research gaps and promote the successful improvement of human and animal health.\n\nSynergistic interaction of nanoparticles and probiotic delivery: A review.", "token_count": 400, "char_count": 1843, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7034, "quality_score": 0.8517, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:09.318674", "source": { "split": "train_shard_00000", "doc_id": 1070 }, "chunk_id": "train_shard_00000_1070_0", "global_id": 1180 }, { "text": "Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.\n\nComparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity.", "token_count": 401, "char_count": 1655, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5845, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:09.975893", "source": { "split": "train_shard_00000", "doc_id": 1071 }, "chunk_id": "train_shard_00000_1071_0", "global_id": 1181 }, { "text": "Paenibacillus sonchi genomovar Riograndensis SBR5T is a plant growth-promoting rhizobacterium (PGPR) isolated in the Brazilian state of Rio Grande do Sul from the rhizosphere of Triticum aestivum. It fixes nitrogen, produces siderophores as well as the phytohormone indole-3-acetic acid, solubilizes phosphate and displays antagonist activity against Listeria monocytogenes and Pectobacterium carotovorum. Comprehensive omics analysis and the development of genetic tools are key to characterizing and engineering such non-model microorganisms. Therefore, the complete genome of SBR5T was sequenced, and shown to encode 6,705 proteins, 87 tRNAs, and 27 rRNAs and it enabled a landscape transcriptome analysis that unveiled conserved transcriptional and translational patterns and characterized operon structures and riboswitches. The pangenome of P. sonchi species is open with a stable core pangenome. At the same time, the analysis of genes coding for nitrogenases revealed that the trait of nitrogen fixation is sparse within the Paenibacillaceae family and the presence of Fe-only nitrogenase in the P. sonchi group was exclusive to SBR5T. The development of genetic tools for SBR5T enabled genetic transformation, plasmid construction for constitutive and inducible gene expression, and gene repression using the CRISPRi system. Altogether, the work with P. sonchi can guide the study of non-model bacteria with economic potential.\n\nGenome-based analyses to learn from and about Paenibacillus sonchi genomovar Riograndensis SBR5T.", "token_count": 409, "char_count": 1535, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6479, "quality_score": 0.8239, "entities": { "genes": [ "SBR5T" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:10.612182", "source": { "split": "train_shard_00000", "doc_id": 1072 }, "chunk_id": "train_shard_00000_1072_0", "global_id": 1182 }, { "text": "This paper explores how vacuum foam-drying of a protein is influenced by formulation parameters by investigating the foam structure, physical properties of the foam, and the stability of the protein. Recombinant human bile salt-stimulated lipase was used as a model of a protein drug. The stability of the lipase was evaluated through activity measurements. Two disaccharides (sucrose and trehalose), strongly tending to an amorphous form, were used as matrix formers, and the physical properties were assessed through residual water content, glass transition temperature, and crystalline state. Moreover, some formulations included surfactants with different sizes and structures of the head group. The alkyl chain length was kept constant to only investigate the impact of the surfactant head group, in the presence of the lipase, on the foamability and surface coverage of the lipase. The study demonstrated that the lipase allowed for a dry, solid foam with a foam overrun of up to 2600 %. The wall thickness of the dry, solid foam was estimated to be 20-50 µm. Clear differences between sucrose and trehalose as matrix former were identified. The lipase showed no tendency to lose activity because of the drying and rehydration, despite a proportion of the lipase covering the surfaces of the dry material.\n\nFormulation factors affecting foam properties during vacuum foam-drying.", "token_count": 307, "char_count": 1385, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:11.250575", "source": { "split": "train_shard_00000", "doc_id": 1073 }, "chunk_id": "train_shard_00000_1073_0", "global_id": 1183 }, { "text": "Whooping cough is a disease caused by Bordetella pertussis, whose morbidity has increased, motivating the improvement of current vaccines. Reverse vaccinology is a strategy that helps identify proteins with good characteristics fast and with fewer resources. In this work, we applied reverse vaccinology to study the B. pertussis proteome and pangenome with several in-silico tools. We analyzed the B. pertussis Tohama I proteome with NERVE software and compared 234 proteins with B. parapertussis, B. bronchiseptica, and B. holmessi. VaxiJen was used to calculate an antigenicity value; our threshold was 0.6, selecting 84 proteins. The candidates were depurated and grouped in eight family proteins to select representative candidates, according to bibliographic information and their immunological response predicted with ABCpred, Bcepred, IgPred, and C-ImmSim. Additionally, a pangenome study was conducted with 603 B. pertussis strains and PanRV software, identifying 3421 core proteins that were analyzed to select the best candidates. Finally, we selected 15 proteins from the proteome study and seven proteins from the pangenome analysis as good vaccine candidates.\n\nNovel vaccine candidates of Bordetella pertussis identified by reverse vaccinology.", "token_count": 314, "char_count": 1258, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6292, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:11.826659", "source": { "split": "train_shard_00000", "doc_id": 1074 }, "chunk_id": "train_shard_00000_1074_0", "global_id": 1184 }, { "text": "Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.\n\nGenomic resources for a historical collection of cultivated two-row European spring barley genotypes.", "token_count": 242, "char_count": 1113, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:12.310476", "source": { "split": "train_shard_00000", "doc_id": 1075 }, "chunk_id": "train_shard_00000_1075_0", "global_id": 1185 }, { "text": "Assessing the genomic evolution of Staphylococcus aureus can help us understand how the bacteria adapt to its environment. In this study, we aimed to assess the mutation rate within 144 methicillin-resistant Staphylococcus aureus (MRSA) carriers with a carriage time from 4 to 11 years, including some carriers who belonged to the same households. We found that 23 of the 144 individuals had completely different MRSA types over time and were therefore not long-term carriers of the same MRSA. From the remaining 121 individuals, we performed whole-genome sequencing (WGS) on 424 isolates and then compared these pairwise using core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses. We found a median within-host mutation rate in long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year and 2.7 (1.8-4.2) allelic differences/genome/year, when excluding presumed recombination. Furthermore, we stratified the cohort into subgroups and found no significant difference between the median mutation rate of members of households, individuals with presumed continued exposure, e.g., from travel and persons without known continued exposure. Finally, we found that SNPs occurred at random within the genes in our cohort. KEY POINTS: • Median mutation rate within long-term MRSA carriers of 4.9 (3.4-6.9) SNPs/genome/year • Similar median mutation rates in subgroups (households, travelers) • No hotspots for SNPs within the genome.\n\nWithin-host genomic evolution of methicillin-resistant Staphylococcus aureus in long-term carriers.", "token_count": 435, "char_count": 1570, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6126, "quality_score": 0.8063, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:12.941687", "source": { "split": "train_shard_00000", "doc_id": 1076 }, "chunk_id": "train_shard_00000_1076_0", "global_id": 1186 }, { "text": "The cholesterol-lowering effect of lactic acid bacteria with high activity of bile salt hydrolase (BSH) is unclear. We believe that distinguishing BSH substrate specificity is necessary to study the effect of various BSH enzymes. We engineered a BSH mutant enzyme recombinant strain named F67A, which exclusively hydrolyzes taurocholic acid (TCA) using site-directed mutagenesis, and a previously lab-constructed BSH recombinant strain, YB81 that exclusively hydrolyzes glycocholic acid (GCA). We also constructed the recombinant strain named NB5462, which carries the empty pSIP411 plasmid and was used as a blank control strain. The intestinal flora in pseudo-germ-free (PGF) mice in which intestinal flora were eliminated\n\nCholesterol lowering in diet-induced hypercholesterolemic mice using", "token_count": 226, "char_count": 794, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [ "YB81", "NB5462" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:13.414238", "source": { "split": "train_shard_00000", "doc_id": 1077 }, "chunk_id": "train_shard_00000_1077_0", "global_id": 1187 }, { "text": "Gut microbiota plays an important role in regulating enteric, immune and neural pathways. Many neuropsychiatric disorders such as anxiety, depression, autism and cognitive behaviour are associated with gut dysbiosis. Gamma-aminobutyric acid (GABA) and short-chain fatty acids produced by gut bacteria influence gastrointestinal and neurological functions. Ferulic acid esterase (FAE) which releases ferulic acid (FA) from feruloylated sugar ester conjugates, naturally found in grains, fruits and vegetables, is also produced by some gut bacteria and helps prevent neurodegeneration. These properties provide bacteria with the ability to maintain intestinal barrier function and prevent neuropsychiatric disorders. Therefore, this study aims to isolate GABA and FAE-producing LAB and characterize their bioactive and probiotic properties. A total of twelve cultures were isolated, of which eight bacteria positive for GABA, FAE and SCFA production were selected for further investigation. All selected bacteria were positive for bile salt hydrolase (BSH) and showed acid tolerance, resistance to bile salt, stimulated gastric and pancreatic juice, and auto- and co-aggregation properties. Furthermore, selected LAB showed mucin adhesion efficiency greater than 80% and exhibited γ-hemolytic activity. 16S rRNA sequencing identified NS0969, B1, C1, C2, M1, M2, and R2 as Limosilactobacillus fermentum and R1 as Lactiplantibacillus pentosus. This study showed that selected bacteria and/or their postbiotic preparations can be used as potential psychobiotics.\n\nGamma Amino Butyric Acid (GABA) and Ferulic Acid Esterase (FAE) Producing Psychobiotic Bacteria Isolated from Cereal-Based Fermented Food.", "token_count": 443, "char_count": 1697, "word_count": 229, "semantic_coherence": 1, "information_density": 0.7074, "quality_score": 0.8537, "entities": { "genes": [ "NS0969" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:14.046110", "source": { "split": "train_shard_00000", "doc_id": 1078 }, "chunk_id": "train_shard_00000_1078_0", "global_id": 1188 }, { "text": "Vulvovaginal candidiasis (VVC) alongside with antifungal resistance are becoming a major clinical problem in recent years. A prospective study aimed to evaluate the diversity of yeast strains associated with VVC in Tebessa city (northeastern Algeria) and investigate their susceptibility patterns. Over two months, yeasts were isolated on chromogenic medium from twenty-nine non-pregnant women with symptomatic VVC. The isolates were characterized with MALDI-TOF MS and antifungal susceptibility testing was performed for nine antifungal drugs using SensititreTM YeastOneTM YO10. Twenty-nine non-duplicate yeasts were recovered and the mass spectrometry profiles showed reliable scores of which four genera and five different species were identified. Candida albicans accounted for 65.5 % (n = 19) of the total number of isolates, followed by C. glabrata with 20.7% (n = 6). For the remaining non-albicans Candida (NCA) species, Kluyveromyces marxianus with 6.9% (n = 2), Pichia kudriavzevii and Saccharomyces cerevisiae with one isolate each. The antifungal susceptibilities showed wild type MICs of C. albicans to amphotericin B, azoles and echinocandins. In addition, four C. albicans isolates were resistant to flucytosine. For C. glabrata isolates, 100% non-WT phenotype was found for both posaconazole and itraconazole. For the very first time, the obtained outcomes bring out new data concerning the epidemiology of yeasts causing VVC in Algeria and their antimicrobial susceptibility profiles.\n\nMALDI-TOF mass spectrometry identification and antifungal susceptibility testing of yeasts causing vulvovaginal candidiasis (VVC) in Tebessa (Northeastern Algeria).", "token_count": 473, "char_count": 1667, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6407, "quality_score": 0.8203, "entities": { "genes": [ "YO10" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:14.686093", "source": { "split": "train_shard_00000", "doc_id": 1079 }, "chunk_id": "train_shard_00000_1079_0", "global_id": 1189 }, { "text": "We analyzed an outbreak of Bacillus cereus group (Bcg) at a single-center neonatal intensive care unit level IV by conducting comprehensive sampling of both patients and the environment.\n\nInvestigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing.", "token_count": 79, "char_count": 352, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:15.063818", "source": { "split": "train_shard_00000", "doc_id": 1080 }, "chunk_id": "train_shard_00000_1080_0", "global_id": 1190 }, { "text": "Bile salts have an established role in the emulsification and intestinal absorption of dietary lipids, and their homeostasis is tightly controlled by various transporters and regulators in the enterohepatic circulation. Notably, emerging evidence points toward bile salts as major modulators of cardiometabolic disease (CMD), an umbrella disease of disorders affecting the heart and blood vessels that is caused by systemic metabolic diseases such as Type 2 diabetes mellitus (T2DM) and metabolic dysfunction-associated steatotic liver disease (MASLD), the latter encompassing also metabolic dysfunction-associated steatohepatitis (MASH). The underlying mechanisms of protective effects of bile salts are their hormonal properties, enabling them to exert versatile metabolic effects by activating various bile salt-responsive signaling receptors with the nuclear farnesoid X receptor (FXR) and the Takeda G-protein-coupled receptor 5 (TGR5) as most extensively investigated. Activation of FXR and TGR5 is involved in the regulation of glucose, lipid and energy metabolism, and inflammation. Bile salt-based therapies directly targeting FXR and TGR5 signaling have been evaluated for their therapeutic potential in CMD. More recently, therapeutics targeting bile salt transporters thereby modulating bile salt localization, dynamics, and signaling, have been developed and evaluated in CMD. Here, we discuss the current knowledge on the contribution of bile salt signaling in the pathogenesis of CMD and the potential of bile salt-based therapies for the treatment of CMD.\n\nBile salt signaling and bile salt-based therapies in cardiometabolic disease.", "token_count": 405, "char_count": 1650, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.793, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:15.684093", "source": { "split": "train_shard_00000", "doc_id": 1081 }, "chunk_id": "train_shard_00000_1081_0", "global_id": 1191 }, { "text": "A long-standing question is to what degree genetic drift and selection drive the divergence in rare accessory gene content between closely related bacteria. Rare genes, including singletons, make up a large proportion of pangenomes (all genes in a set of genomes), but it remains unclear how many such genes are adaptive, deleterious or neutral to their host genome. Estimates of species' effective population sizes (N\n\nPseudogenes act as a neutral reference for detecting selection in prokaryotic pangenomes.", "token_count": 116, "char_count": 509, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8442, "quality_score": 0.9221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:16.069736", "source": { "split": "train_shard_00000", "doc_id": 1082 }, "chunk_id": "train_shard_00000_1082_0", "global_id": 1192 }, { "text": "Pandemic Pseudomonas aeruginosa clone C strains encode two inner-membrane associated ATP-dependent FtsH proteases. PaftsH1 is located on the core genome and supports cell growth and intrinsic antibiotic resistance, whereas PaftsH2, a xenolog acquired through horizontal gene transfer from a distantly related species, is unable to functionally replace PaftsH1. We show that purified PaFtsH2 degrades fewer substrates than PaFtsH1. Replacing the 31-amino acid-extended linker region of PaFtsH2 spanning from the C-terminal end of the transmembrane helix-2 to the first seven highly divergent residues of the cytosolic AAA+ ATPase module with the corresponding region of PaFtsH1 improves hybrid-enzyme substrate processing in vitro and enables PaFtsH2 to substitute for PaFtsH1 in vivo. Electron microscopy indicates that the identity of this linker sequence influences FtsH flexibility. We find membrane-cytoplasmic (MC) linker regions of PaFtsH1 characteristically glycine-rich compared to those from FtsH2. Consequently, introducing three glycines into the membrane-proximal end of PaFtsH2's MC linker is sufficient to elevate its activity in vitro and in vivo. Our findings establish that the efficiency of substrate processing by the two PaFtsH isoforms depends on MC linker identity and suggest that greater linker flexibility and/or length allows FtsH to degrade a wider spectrum of substrates. As PaFtsH2 homologs occur across bacterial phyla, we hypothesize that FtsH2 is a latent enzyme but may recognize specific substrates or is activated in specific contexts or biological niches. The identity of such linkers might thus play a more determinative role in the functionality of and physiological impact by FtsH proteases than previously thought.\n\nThe membrane-cytoplasmic linker defines activity of FtsH proteases in Pseudomonas aeruginosa clone C.", "token_count": 495, "char_count": 1857, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6388, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:16.721823", "source": { "split": "train_shard_00000", "doc_id": 1083 }, "chunk_id": "train_shard_00000_1083_0", "global_id": 1193 }, { "text": "The 5´ untranslated region (5´ UTR) plays a key role in regulating translation efficiency and mRNA stability, making it a favored target in genetic engineering and synthetic biology. A common feature found in the 5´ UTR is the poly-adenine (poly(A)) tract. However, the effect of 5´ UTR poly(A) on protein production remains controversial. Machine-learning models are powerful tools for explaining the complex contributions of features, but models incorporating features of 5´ UTR poly(A) are currently lacking. Thus, our goal is to construct such a model, using natural 5´ UTRs from Kluyveromyces marxianus, a promising cell factory for producing heterologous proteins.\n\nCharacterization and optimization of 5´ untranslated region containing poly-adenine tracts in Kluyveromyces marxianus using machine-learning model.", "token_count": 200, "char_count": 819, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7069, "quality_score": 0.8534, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:17.179849", "source": { "split": "train_shard_00000", "doc_id": 1084 }, "chunk_id": "train_shard_00000_1084_0", "global_id": 1194 }, { "text": "Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.\n\nComparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions.", "token_count": 137, "char_count": 631, "word_count": 81, "semantic_coherence": 1, "information_density": 0.8025, "quality_score": 0.9012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:17.608838", "source": { "split": "train_shard_00000", "doc_id": 1085 }, "chunk_id": "train_shard_00000_1085_0", "global_id": 1195 }, { "text": "Pangenomes, by including genetic diversity, should reduce reference bias by better representing new samples compared to them. Yet when comparing a new sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for example, causing false read mappings. These irrelevant variants are generally rarer in terms of allele frequency, and have previously been dealt with using allele frequency filters. However, this is a blunt heuristic that both fails to remove some irrelevant variants and removes many relevant variants. We propose a new approach, inspired by local ancestry inference methods, that imputes a personalized pangenome subgraph based on sampling local haplotypes according to\n\nPersonalized Pangenome References.", "token_count": 165, "char_count": 762, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7611, "quality_score": 0.8805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:18.051575", "source": { "split": "train_shard_00000", "doc_id": 1086 }, "chunk_id": "train_shard_00000_1086_0", "global_id": 1196 }, { "text": "The secretion of bile salts transported by the bile salt export pump (BSEP) is the primary driving force for the generation of bile flow; thus, it is closely related to the formation of cholesterol stones. Caveolin-1 (Cav-1), an essential player in cell signalling and endocytosis, is known to co-localize with cholesterol-rich membrane domains. This study illustrates the role of Cav-1 and BSEP in cholesterol stone formation.\n\nCav-1 regulates the bile salt export pump on the canalicular membrane of hepatocytes by PKCα-associated signalling under cholesterol stimulation.", "token_count": 157, "char_count": 574, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:18.490434", "source": { "split": "train_shard_00000", "doc_id": 1087 }, "chunk_id": "train_shard_00000_1087_0", "global_id": 1197 }, { "text": "Genomic studies with Salmonella enterica serovar Typhimurium reveal a crucial role of horizontal gene transfer (HGT) in the acquisition of accessory cellular functions involved in host-interaction. Many virulence genes are located in genomic islands, plasmids and prophages. GreA and GreB proteins, Gre factors, interact transiently with the RNA polymerase alleviating backtracked complexes during transcription elongation. The overall effect of Gre factors depletion in Salmonella expression profile was studied. Both proteins are functionally redundant since only when both Gre factors were depleted a major effect in gene expression was detected. Remarkably, the accessory gene pool is particularly sensitive to the lack of Gre factors, with 18.6% of accessory genes stimulated by the Gre factors versus 4.4% of core genome genes. Gre factors involvement is particularly relevant for the expression of genes located in genomic islands. Our data reveal that Gre factors are required for the expression of accessory genes.\n\nExpression of accessory genes in Salmonella requires the presence of the Gre factors.", "token_count": 247, "char_count": 1110, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5776, "quality_score": 0.7888, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:18.972504", "source": { "split": "train_shard_00000", "doc_id": 1088 }, "chunk_id": "train_shard_00000_1088_0", "global_id": 1198 }, { "text": "A pangenome is composed of all the genetic variability of a group of individuals, and its application to the study of neurodegenerative diseases may provide valuable insights into the underlying aspects of genetic heterogenetiy for these complex ailments, including gene expression, epigenetics, and translation mechanisms. Furthermore, a reference pangenome allows for the identification of previously undetected structural commonalities and differences among individuals, which may help in the diagnosis of a disease, support the prediction of what will happen over time (prognosis) and aid in developing novel treatments in the perspective of personalized medicine. Therefore, in the present review, the application of the pangenome concept to the study of neurodegenerative diseases will be discussed and analyzed for its potential to enable an improvement in diagnosis and prognosis for these illnesses, leading to the development of tailored treatments for individual patients from the knowledge of the genomic composition of a whole population.\n\nPangenomics: A new era in the field of neurodegenerative diseases.", "token_count": 218, "char_count": 1119, "word_count": 160, "semantic_coherence": 1, "information_density": 0.5938, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:19.438478", "source": { "split": "train_shard_00000", "doc_id": 1089 }, "chunk_id": "train_shard_00000_1089_0", "global_id": 1199 }, { "text": "The rapid increase of OXA-244-producing Escherichia coli, predominantly driven by genetically clustered isolates of sequence type (ST)38, has been observed in at least nine European countries, including Germany. However, the reasons for the spread of OXA-244-producing E. coli remain unclear. Here, we aim to evaluate the possibility of prolonged carriage. We identified a total of six different patients with repeated detection of OXA-244-producing E. coli isolates, which were subjected to both short and long-read whole-genome sequencing (WGS). Besides allelic differences using core genome multilocus sequence typing (cgMLST) analyses, we obtained numbers of single-nucleotide polymorphisms (SNPs) to calculate individual base-pair substitution (BPS) rates. To assess possible re-exposure and risk factors for prolonged carriage, case interviews were conducted. The time between detections ranged from eleven months to more than three years. Initial isolates originated in three+ out of six cases from clinical samples, whereas remaining samples were from screening, mostly in the inpatient setting. As expected, cgMLST analyses showed low numbers of allelic differences between isolates of each case ranging from 1 to 4, whereas numbers of SNPs were between 2 and 99 (mean = 36), thus clearly highlighting the discrepancy between these different bacterial typing approaches. For five out of six cases, observed BPS rates suggest that patients can be colonized with OXA-244-producing E. coli, including ST38 cluster isolates, for extensively long times. Thus, we may have previously missed the epidemiological link between cases because exposure to OXA-244-producing E. coli could have occurred in a time frame, which has not been evaluated in previous investigations. Our results may help to guide future epidemiological investigations as well as to support the interpretation of genetic diversity of OXA-244-producing E. coli, particularly among ST38 cluster isolates.", "token_count": 477, "char_count": 1974, "word_count": 282, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [ "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:20.752879", "source": { "split": "train_shard_00000", "doc_id": 1090 }, "chunk_id": "train_shard_00000_1090_0", "global_id": 1200 }, { "text": "Prolonged carriage of OXA-244-carbapenemase-producing Escherichia coli complicates epidemiological investigations.", "token_count": 37, "char_count": 114, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:21.113163", "source": { "split": "train_shard_00000", "doc_id": 1090 }, "chunk_id": "train_shard_00000_1090_1", "global_id": 1201 }, { "text": "Osteoarthritis is a bone and joint condition characterized pathologically by articular cartilage degenerative damage and can develop into a devastating and permanently disabling disorder. This investigation aimed to formulate the anti-inflammatory drug lornoxicam (LOR) into bile salt-enriched vesicles loaded in an in situ forming hydrogel as a potential local treatment of osteoarthritis. This was achieved by formulating LOR-loaded bilosomes that are also loaded with superparamagnetic iron oxide nanoparticles (SPIONs) for intra-muscular (IM) administration to improve joint targeting and localization by applying an external magnet to the joint. A 3\n\nMagnetic targeting of lornoxicam/SPION bilosomes loaded in a thermosensitive in situ hydrogel system for the management of osteoarthritis: Optimization, in vitro, ex vivo, and in vivo studies in rat model via modulation of RANKL/OPG.", "token_count": 226, "char_count": 889, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7236, "quality_score": 0.8618, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:21.596222", "source": { "split": "train_shard_00000", "doc_id": 1091 }, "chunk_id": "train_shard_00000_1091_0", "global_id": 1202 }, { "text": "This study aimed to investigate the probiotic properties of Lactic Acid Bacteria (LAB) isolates derived from various milk sources. These isolates identified based on their morphological characteristics and 16S rRNA gene sequencing. Four strains of Lactococcus lactis and two strains of Weissella confusa were identified with over 96% 16S rRNA gene similarity according to the NCBI-BLAST results. The survival of the isolates was determined in low pH, pepsin, bile salts, and pancreatin, and their adhesion ability was assessed by in vitro cell adhesion assay, hydrophobicity, auto- and co-aggregation, and safety criteria were determined by hemolytic, gelatinase activities, and DNAse production ability tests. The results showed that the LAB isolates had different levels of resistance to various stress factors. L. lactis subsp. cremoris MH31 showed the highest resistance to bile salt, while the highest pH resistance was observed in L. lactis MH31 at pH 3.0. All the isolates survived in pepsin exposure at pH 3.0 for 3 h. The auto-aggregation test results showed that all strains exhibited auto-aggregation ranging from 84.9 to 91.4%. Co-aggregation percentage ranged from 19 - 54% and 17 - 57% against Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 29213, respectively. The hydrophobicity capacity of the LAB isolated ranged from 35-61%. These isolates showed different adhesion abilities to Caco-2 cells (81.5% to 92.6%). None of the isolates exhibited DNase, gelatinase and hemolytic activity (γ-hemolysis). All results indicate that these LAB strains have the potential to be used as probiotics.\n\nIsolation, characterization of Weissella confusa and Lactococcus lactis from different milk sources and determination of probiotic features.", "token_count": 502, "char_count": 1758, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": { "genes": [ "MH31" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:22.273861", "source": { "split": "train_shard_00000", "doc_id": 1092 }, "chunk_id": "train_shard_00000_1092_0", "global_id": 1203 }, { "text": "Human pangenome: far-reaching implications in precision medicine.", "token_count": 14, "char_count": 65, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:22.646489", "source": { "split": "train_shard_00000", "doc_id": 1093 }, "chunk_id": "train_shard_00000_1093_0", "global_id": 1204 }, { "text": "Fecal bile acids (BAs) are key metabolites altered in patients with inflammatory bowel disease (IBD), therefore serving as potential targets of fecal microbial transplant (FMT). To compare changes in fecal BA composition and corresponding microbial transformation pathways in pediatric ulcerative colitis (UC) patients before and after FMT for up to 48 weeks. Fecal BAs, as well as enzymes and bacteria related to BA metabolism were measured in 28 healthy children, and 48 children with mild to moderate UC before and after FMT. Several primary BAs were higher in UC patients at baseline, and subsequently decreased over the 48 weeks following FMT. In particular, the primary BA cholic acid (CA) was higher in UC children at baseline (11.73 pg/mg) compared to healthy controls (8.47 pg/mg), decreased to 10.82 pg/mg at 4 weeks post FMT (p = 0.001) then 10.07 pg/mg at 48 weeks (p = 0.077). Following FMT, the ratio of secondary to primary BAs became more similar to healthy children. The genes coding for bile salt hydrolase, 7α/β-hydroxysteroid dehydrogenase, and bile acid induced operon enzymes were lower in UC patients at baseline, with the majority of them increasing following FMT. Similarly, many of the bacterial genera involved in bile acid metabolism had corresponding increases after FMT.\n\nFecal bile acid profiles before and after fecal microbial transplant in pediatric onset ulcerative colitis.", "token_count": 390, "char_count": 1409, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5566, "quality_score": 0.7783, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:23.308555", "source": { "split": "train_shard_00000", "doc_id": 1094 }, "chunk_id": "train_shard_00000_1094_0", "global_id": 1205 }, { "text": "The maintenance of the balance between oxidised and reduced redox cofactors is essential for the functioning of many cellular processes in all living organisms. While the electron transport chain plays a key role in maintaining this balance under respiratory conditions, its inactivity in the absence of oxygen poses a challenge that yeasts such as Saccharomyces cerevisiae overcome through the production of various metabolic end-products during alcoholic fermentation. In this study, we investigated the diversity occurring between wine yeast species in their management of redox balance and its consequences on the fermentation performances and the formation of metabolites. To this aim, we quantified the changes in NAD(H) and NADP(H) concentrations and redox status throughout the fermentation of 6 wine yeast species. While the availability of NADP and NADPH remained balanced and stable throughout the process for all the strains, important differences between species were observed in the dynamics of NAD and NADH intracellular pools. A comparative analysis of these data with the fermentation capacity and metabolic profiles of the strains revealed that Saccharomyces cerevisiae, Torulaspora delbrueckii and Lachancea thermotolerans strains were able to reoxidise NADH to NAD throughout the fermentation, mainly by the formation of glycerol. These species exhibited good fermentation capacities. Conversely, Starmerella bacillaris and Metschnikowia pulcherrima species were unable to regenerate NAD as early as one third of sugars were consumed, explaining at least in part their poor growth and fermentation performances. The Kluyveromyces marxianus strain exhibited a specific behaviour, by maintaining similar levels of NAD and NADH throughout the process. This balance between oxidised and reduced redox cofactors ensured the consumption of a large part of sugars by this species, despite a low fermentation rate. In addition, the dynamics of redox cofactors affected the production of by-products by the various strains either directly or indirectly, through the formation of precursors. Major examples are the increased formation of glycerol by S. bacillaris and M", "token_count": 494, "char_count": 2179, "word_count": 315, "semantic_coherence": 1, "information_density": 0.5429, "quality_score": 0.7714, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:23.966293", "source": { "split": "train_shard_00000", "doc_id": 1095 }, "chunk_id": "train_shard_00000_1095_0", "global_id": 1206 }, { "text": "pulcherrima strains, as a way of trying to reoxidise NADH, and the greater capacity to produce acetate and derived metabolites of yeasts capable of maintaining their redox balance. Overall, this study provided new insight into the contribution of the management of redox status to the orientation of yeast metabolism during fermentation. This information should be taken into account when developing strategies for more efficient and effective fermentation.\n\nDifferences in the management of intracellular redox state between wine yeast species dictate their fermentation performances and metabolite production.", "token_count": 130, "char_count": 611, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7326, "quality_score": 0.8663, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:24.396725", "source": { "split": "train_shard_00000", "doc_id": 1095 }, "chunk_id": "train_shard_00000_1095_1", "global_id": 1207 }, { "text": "Vesicular carriers of drugs are popular for specific targeting and delivery. The most popular vesicles among these are liposomes. However, they suffer from some inherent limitations. In this work, alternative vesicles with enhanced stability, i.e., niosomes and bilosomes have been prepared, characterized, and their delivery efficiency studied. Bilosomes have the additional advantage of being able to withstand the harsh environment of the gastrointestinal tract (GIT). The taurine-derived bile salt (NaTC) was incorporated into the bilosome bilayer. The inspiration behind NaTC insertion is the recent reports on antiaging action and immune function of taurine. Fluorescence probing was used to study the vesicle environment. The entrapment and subsequent release of the important cAMP-specific PDE4 inhibitor/drug Rolipram, which has antibreast cancer properties, was assessed on the breast cancer cell line MCF-7. Rolipram has important therapeutic applications, one of the most significant in recent times being the treatment of Covid-19-triggered pneumonia and cytokine storms. As for cancer chemotherapy, the localization of drug, targeted delivery, and sustained release are extremely important issues, and it seemed worthwhile to explore the potential of the bilosomes and niosomes to entrap and release Rolipram. The important finding is that niosomes perform much better than bilosomes in the hormone-responsive breast cancer mileau MCF-7. Moreover, there was a 4-fold decrease in the IC\n\nVesicle-Encapsulated Rolipram (PDE4 Inhibitor) and Its Anticancer Activity.", "token_count": 375, "char_count": 1576, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [ "PDE4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:24.981582", "source": { "split": "train_shard_00000", "doc_id": 1096 }, "chunk_id": "train_shard_00000_1096_0", "global_id": 1208 }, { "text": "Changes in the pharmacokinetic and resulting pharmacodynamic properties of drugs are common in many chronic liver diseases, leading to adverse effects, drug interactions and increased risk of over- or underdosing of medications. Structural and functional hepatic impairment can have major effects on drug metabolism and transport. This review summarizes research on the functional changes in phase I and II metabolic enzymes and in transport proteins in patients with metabolic diseases such as type 2 diabetes, metabolic dysfunction-associated steatotic liver disease, metabolic dysfunction-associated steatohepatitis and cirrhosis, providing a clinical perspective on how these changes affect drug uptake and metabolism. Generally, a decrease in expression and/or activity of many enzymes of the cytochrome P450 family (e.g. CYP2E1 and CYP3A4), and of influx and efflux transporters (e.g. organic anion-transporting polypeptide [OATP]1B1, OATP2B1, OAT2 and bile salt export pump), has been recently documented in patients with liver disease. Decreased enzyme levels often correlate with increased severity of chronic liver disease. In subjects with hepatic impairment, there is potential for strong alterations of drug pharmacokinetics due to reduced absorption, increased volume of distribution, metabolism and extraction. Due to the altered pharmacokinetics, specific drug-drug interactions are also a potential issue to consider in patients with liver disease. Given the huge burden of liver disease in western societies, there is a need to improve awareness among all healthcare professionals and patients with liver disease to ensure appropriate drug prescriptions.\n\nEffect of changes in metabolic enzymes and transporters on drug metabolism in the context of liver disease: Impact on pharmacokinetics and drug-drug interactions.", "token_count": 427, "char_count": 1836, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [ "OAT2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:25.608239", "source": { "split": "train_shard_00000", "doc_id": 1097 }, "chunk_id": "train_shard_00000_1097_0", "global_id": 1209 }, { "text": "Pangenomes exhibit remarkable variability in many prokaryotic species, much of which is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic backgrounds of the recipients mean that postacquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the\n\nContingency, repeatability, and predictability in the evolution of a prokaryotic pangenome.", "token_count": 145, "char_count": 712, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7629, "quality_score": 0.8814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:26.041082", "source": { "split": "train_shard_00000", "doc_id": 1098 }, "chunk_id": "train_shard_00000_1098_0", "global_id": 1210 }, { "text": "Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space are still challenging due to this high diversity. In contrast, amino acid sequences have higher similarity due to evolutionary constraints, whereby a single amino acid may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, panproteomes present an attractive alternative leveraging the higher sequence similarity while not losing much of the genome in non-coding regions.\n\nPanPA: generation and alignment of panproteome graphs.", "token_count": 171, "char_count": 826, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7759, "quality_score": 0.8879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:26.490126", "source": { "split": "train_shard_00000", "doc_id": 1099 }, "chunk_id": "train_shard_00000_1099_0", "global_id": 1211 }, { "text": "This study aims to identify lactic acid bacteria (LAB) isolates possessing physiological characteristics suitable for use as probiotics in yogurt fermentation. Following acid and bile salt tolerance tests, Lactiplantibacillus plantarum (NUC08 and NUC101), Lacticaseibacillus rhamnosus (NUC55 and NUC201), and Lacticaseibacillus paracasei (NUC159, NUC216, and NUC351) were shortlisted based on intraspecies distribution for further evaluation. Their physiological probiotic properties, including transit tolerance, adhesion, autoaggregation, surface hydrophobicity, biofilm formation, and antibacterial activity, were assessed. Principal component analysis indicated that Lactiplantibacillus plantarum NUC08 was the preferred choice among the evaluated strains. Subsequent investigations revealed that co-culturing Lactiplantibacillus plantarum NUC08 with 2 yogurt starter strains resulted in a cooperative and synergistic effect, enhancing the growth of mixed strains and increasing their tolerance to simulated gastric and intestinal conditions. Additionally, when Vibrio harveyi bioluminescent reporter strain was used, the 3 cocultured strains cooperated to induce the activity of a quorum sensing (QS) molecule autoinducer-2 (AI-2), hinting a potential connection between phenotypic traits and QS in the cocultured strains. Importantly, LAB viable counts were significantly higher in yogurt co-fermented with Lactiplantibacillus plantarum NUC08, consistently throughout the storage period. In conclusion, the study demonstrates that the probiotic strain Lactiplantibacillus plantarum NUC08 can be employed in synergy with yogurt starter strains, affirming its potential for use in the development of functional fermented dairy products.\n\nScreening of a potential probiotic Lactiplantibacillus plantarum NUC08 and its synergistic effects with yogurt starter.", "token_count": 502, "char_count": 1861, "word_count": 231, "semantic_coherence": 1, "information_density": 0.658, "quality_score": 0.829, "entities": { "genes": [ "NUC351", "NUC216", "NUC55", "NUC201", "NUC159", "NUC08", "NUC101" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:27.140405", "source": { "split": "train_shard_00000", "doc_id": 1100 }, "chunk_id": "train_shard_00000_1100_0", "global_id": 1212 }, { "text": "The poultry industry is facing continuous challenges with regard to increased feed costs and loss due to infectious disease. To overcome this challenge, several antibiotics have been used along with chicken feeds to promote growth. Nevertheless, the use of antibiotics as growth promoter has been banned in many countries, due to the concerns associated with potential risks of emerging and horizontal transfer of multidrug resistant genes to bacteria in animal tissues. The objective of this study was to identify and characterize potential probiotic bacteria strains from the gastrointestinal tract of free-range locally selected chickens. The bacterial isolates were screened, purified and characterized based on morphological, biochemical and molecular characteristics from 12 well-adopted free-range healthy young chickens. Low pH and bile salt tolerance, antagonistic activity, antibiotic activity, hemolysis activity, adhesion to the chicken intestine and carbohydrate fermentation tests was conducted to identify potential probiotic bacteria. Twelve bacterial isolates were screened based on their ability for their tolerance to low pH and bile salt. The isolates were identified by using 16S rRNA gene partial sequencing method. All screened isolates showed great survival percentage at low pH, that is (89.2 ± 0.75 to 97.1 ± 0.64) survived at 3 h and (83.6 ± 0.75 to 95.2 ± 0.63) at 6 h challenge at pH\n\nIsolation, identification, and molecular characterization of probiotic bacteria from locally selected Ethiopian free range chickens gastrointestinal tract.", "token_count": 376, "char_count": 1569, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6404, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:28.066484", "source": { "split": "train_shard_00000", "doc_id": 1101 }, "chunk_id": "train_shard_00000_1101_0", "global_id": 1213 }, { "text": "Aflatoxin B1 (AFB1) is a hazardous mycotoxin that often contaminates animal feed and may potentially induce severe liver damage if ingested. The liver is the primary organ responsible for AFB1 detoxification through enzyme-catalyzed xenobiotic metabolism and bile acid (BA)-associated excretion. In this study, we sought to investigate whether exogenous BA improves hepatic AFB1 detoxification to alleviate AFB1-induced liver injury in broiler chickens. Five-day-old broiler chicks were randomly assigned to three groups. CON and AFB1 received a basal diet; AFB1 + BA received a basal diet with 250 mg/kg BA for 20 days. After a 3-day pre-feed, AFB1 and AFB1 + BA were daily gavaged with 250 μg/kg BW AFB1, while CON received gavage solvent for AFB1 treatment. Dietary BA supplementation protected chickens from AFB1-induced hepatic inflammation and oxidative stress. The hepatic biotransformation of AFB1 to its metabolite AFBO was improved, with accelerated excretion to the gallbladder and cecum. Accordantly, AFB1-induced down-regulation of detoxification genes, including cytochrome P450 enzymes, glutathione S-transferases, and the bile salt export pump, was rescued by BA supplementation. Moreover, liver X receptor α, suppressed by AFB1, was enhanced in BA-treated broiler chickens. These results indicate that dietary BA supplementation improves hepatic AFB1 detoxification and excretion through LXRα-involved regulation of xenobiotic enzymes.\n\nBile Acids Promote Hepatic Biotransformation and Excretion of Aflatoxin B1 in Broiler Chickens.", "token_count": 459, "char_count": 1549, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6083, "quality_score": 0.8041, "entities": { "genes": [ "AFB1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:28.706204", "source": { "split": "train_shard_00000", "doc_id": 1102 }, "chunk_id": "train_shard_00000_1102_0", "global_id": 1214 }, { "text": "An important risk factor for cardiovascular disease is dyslipidemia, especially abnormal cholesterol levels. The relation between probiotics and cholesterol-lowering capability has been extensively studied. Lactobacillus acidophilus plays a significant role in affecting host health, and produces multitudinous metabolites, which have prohibitory functions against pathogenic microorganisms. In this study, we identified a cholesterol-lowering strain AM13-1, isolated from a fecal sample obtained from a healthy adult male, and performed comprehensive function analysis by whole-genome analysis and in vitro experiments. Genome analyses of L. acidophilus AM13-1 revealed that carbohydrate and amino acid transport, metabolism, translation, ribosomal structure, and biogenesis are abundant categories of functional genes. No virulence factors or toxin genes with experimentally verified were found in the genome of strain AM13-1. Besides, plenty of probiotic-related genes were predicted from the L. acidophilus AM13-1 genome, such as cbh, atpA-D, and dltD, with functions related to cholesterol-lowering and acid resistance. And strain AM13-1 showed high-efficiency of bile salt hydrolase activity and the capacity for removing cholesterol with efficiency rates of 70%. These function properties indicate that strain AM13-1 can be considered as a probiotic candidate for use in food and health care products.\n\nSafety assessment of potential probiotic Lactobacillus acidophilus AM13-1 with high cholesterol-lowering capability isolated from human gut.", "token_count": 387, "char_count": 1550, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8463, "entities": { "genes": [ "AM13" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:29.323072", "source": { "split": "train_shard_00000", "doc_id": 1103 }, "chunk_id": "train_shard_00000_1103_0", "global_id": 1215 }, { "text": "Campylobacteriosis, primarily caused by Campylobacter jejuni and C. coli, is the main bacterial zoonosis worldwide. While poultry is recognized as the main reservoir, bovines are considered another important reservoir for Campylobacter spp. found in human infections. In contrast to chicken, retail beef is seldom contaminated by Campylobacter species. However, beef liver is recognized to be frequently contaminated and has been linked to human infections via epidemiological investigations. Our aims were to evaluate the prevalence of Campylobacter spp. inside and on the surface of beef liver pieces at retail in Finland and to analyse the population in more detail using whole genome sequencing (WGS) to assess the public health relevance. A total of 90 retail beef livers were studied using both enrichment of the external peptone-saline rinse of the liver piece and direct culture from the inside after surface sterilization. Furthermore, 46 of the livers were also studied using direct culture of retail beef liver juice collected from the bottom of the consumer package to estimate the concentration of Campylobacter species. Overall, 44 (49 %) of the samples were positive for Campylobacter species, C. jejuni, C. fetus and C. lari being identified in 42 %, 8.9 % and 1.1 % of the samples, respectively. Direct culture of retail liver juice was a sensitive and convenient method for Campylobacter spp. detection, resulting in 48 % prevalence and a mean concentration of 49 cfu/ml (maximum 335 cfu/ml). Two samples (2.2 %), containing large hepatic ducts, were positive for C. jejuni internally, representing multilocus sequence typing (MLST) sequence type ST-19 and ST-21. WGS, core genome phylogeny and core genome MLST revealed that in most cases only one clearly distinct clone of clinically relevant C. jejuni or C. fetus was isolated from a single lot of samples. However, in some cases several distinct clones were identified simultaneously even from a single liver piece. In epidemiological investigations, it is thus highly advisable to genotype multiple isolates to capture the whole diversity of Campylobacter spp. from suspected food sources", "token_count": 527, "char_count": 2161, "word_count": 332, "semantic_coherence": 1, "information_density": 0.5693, "quality_score": 0.7846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:09:29.979685", "source": { "split": "train_shard_00000", "doc_id": 1104 }, "chunk_id": "train_shard_00000_1104_0", "global_id": 1216 }, { "text": "Good kitchen hygiene, avoidance of cross-contamination and thorough cooking are important for limiting the transmission of campylobacteriosis.\n\nCampylobacter species and genotype distribution in Finnish beef liver - Retail liver juice ideal for isolation and quantification.", "token_count": 58, "char_count": 274, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:30.341912", "source": { "split": "train_shard_00000", "doc_id": 1104 }, "chunk_id": "train_shard_00000_1104_1", "global_id": 1217 }, { "text": "Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.\n\nA super-pangenome of the North American wild grape species.", "token_count": 87, "char_count": 429, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7833, "quality_score": 0.8917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:30.720218", "source": { "split": "train_shard_00000", "doc_id": 1105 }, "chunk_id": "train_shard_00000_1105_0", "global_id": 1218 }, { "text": "Many inherited conditions cause hepatocellular cholestasis in infancy, including progressive familial intrahepatic cholestasis (PFIC), a heterogeneous group of diseases with highly overlapping symptoms. In our study, six unrelated Tunisian infants with PFIC suspicion were the subject of a panel-target sequencing followed by an exhaustive bioinformatic and modeling investigations. Results revealed five disease-causative variants including known ones: (the p.Asp482Gly and p.Tyr354 * in the ABCB11 gene and the p.Arg446 * in the ABCC2 gene), a novel p.Ala98Cys variant in the ATP-binding cassette subfamily G member 5 (ABCG5) gene and a first homozygous description of the p.Gln312His in the ABCB11 gene. The p.Gln312His disrupts the interaction pattern of the bile salt export pump as well as the flexibility of the second intracellular loop domain harboring this residue. As for the p.Ala98Cys, it modulates both the interactions within the first nucleotide-binding domain of the bile transporter and its accessibility. Two additional potentially modifier variants in cholestasis-associated genes were retained based on their pathogenicity (p.Gly758Val in the ABCC2 gene) and functionality (p.Asp19His in the ABCG8 gene). Molecular findings allowed a PFIC2 diagnosis in five patients and an unexpected diagnosis of sisterolemia in one case. The absence of genotype/phenotype correlation suggests the implication of environmental and epigenetic factors as well as modifier variants involved directly or indirectly in the bile composition, which could explain the cholestasis phenotypic variability.\n\nMolecular and computational characterization of ABCB11 and ABCG5 variants in Tunisian patients with neonatal/infantile low-GGT intrahepatic cholestasis: Genetic diagnosis and genotype-phenotype correlation assessment.", "token_count": 480, "char_count": 1820, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [ "PFIC2", "ABCC2", "ABCB11", "ABCG8", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:31.383979", "source": { "split": "train_shard_00000", "doc_id": 1106 }, "chunk_id": "train_shard_00000_1106_0", "global_id": 1219 }, { "text": "Lactic acid bacteria (LAB) are widely used as probiotics in poultry production due to their resilience to low pH and high bile salt concentrations, as well as their beneficial effects on growth performance and antagonistic activity against enteric pathogens. However, the efficacy of probiotics depends on strain selection and their ability to colonize the host's intestine. This study aimed to select, identify, and evaluate LAB strains isolated from chicken feces in Thailand for potential use as probiotics in the chicken industry.\n\nSelection and evaluation of lactic acid bacteria from chicken feces in Thailand as potential probiotics.", "token_count": 141, "char_count": 640, "word_count": 96, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:31.817959", "source": { "split": "train_shard_00000", "doc_id": 1107 }, "chunk_id": "train_shard_00000_1107_0", "global_id": 1220 }, { "text": "Surfactants are widely used to disperse single-walled carbon nanotubes (SWCNTs) and other nanomaterials for liquid-phase processing and characterization. Traditional techniques, however, demand high surfactant concentrations, often in the range of 1-2 wt/v% of the solution. Here, we show that optimal dispersion efficiency can be attained at substantially lower surfactant concentrations of approximately 0.08 wt/v%, near the critical micelle concentration. This unexpected observation is achieved by introducing \"bare\" nanotubes into water containing the anionic surfactant sodium deoxycholate (DOC) through a superacid-surfactant exchange process that eliminates the need for ultrasonication. Among the diverse ionic surfactants and charged biopolymers explored, DOC exhibits the highest dispersion efficiency, outperforming sodium cholate, a structurally similar bile salt surfactant containing just one additional oxygen atom compared to DOC. Employing all-atomistic molecular dynamics simulations, we unravel that the greater stabilization by DOC arises from its higher binding affinity to nanotubes and a substantially larger free energy barrier that resists nanotube rebundling. Further, we find that this barrier is nonelectrostatic in nature and does not obey the classical Derjaguin-Landau-Verwey-Overbeek (DLVO) theory of colloidal stability, underscoring the important role of nonelectrostatic dispersion and hydration interactions at the nanoscale, even in the case of ionic surfactants like DOC. These molecular insights advance our understanding of surfactant chemistry at the bare nanotube limit and suggest low-energy, surfactant-efficient solution processing of SWCNTs and potentially other nanomaterials.\n\nSurfactant-Aided Stabilization of Individual Carbon Nanotubes in Water around the Critical Micelle Concentration.", "token_count": 441, "char_count": 1839, "word_count": 236, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:32.455351", "source": { "split": "train_shard_00000", "doc_id": 1108 }, "chunk_id": "train_shard_00000_1108_0", "global_id": 1221 }, { "text": "Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkage information of the gene families of the species to resolve the contig graph of the assembly. We show that our method outperforms the current state of the arts in terms of accuracy, and at the same time, is computationally efficient to be applied to a large number of existing draft assemblies.\n\nPasa: leveraging population pangenome graph to scaffold prokaryote genome assemblies.", "token_count": 254, "char_count": 1182, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:32.944367", "source": { "split": "train_shard_00000", "doc_id": 1109 }, "chunk_id": "train_shard_00000_1109_0", "global_id": 1222 }, { "text": "Helicobacter pylori, a dominant member of the gastric microbiota, shares co-evolutionary history with humans. This has led to the development of genetically distinct H. pylori subpopulations associated with the geographic origin of the host and with differential gastric disease risk. Here, we provide insights into H. pylori population structure as a part of the Helicobacter pylori Genome Project (HpGP), a multi-disciplinary initiative aimed at elucidating H. pylori pathogenesis and identifying new therapeutic targets. We collected 1011 well-characterized clinical strains from 50 countries and generated high-quality genome sequences. We analysed core genome diversity and population structure of the HpGP dataset and 255 worldwide reference genomes to outline the ancestral contribution to Eurasian, African, and American populations. We found evidence of substantial contribution of population hpNorthAsia and subpopulation hspUral in Northern European H. pylori. The genomes of H. pylori isolated from northern and southern Indigenous Americans differed in that bacteria isolated in northern Indigenous communities were more similar to North Asian H. pylori while the southern had higher relatedness to hpEastAsia. Notably, we also found a highly clonal yet geographically dispersed North American subpopulation, which is negative for the cag pathogenicity island, and present in 7% of sequenced US genomes. We expect the HpGP dataset and the corresponding strains to become a major asset for H. pylori genomics.\n\nThe Helicobacter pylori Genome Project: insights into H. pylori population structure from analysis of a worldwide collection of complete genomes.", "token_count": 391, "char_count": 1668, "word_count": 236, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:33.562453", "source": { "split": "train_shard_00000", "doc_id": 1110 }, "chunk_id": "train_shard_00000_1110_0", "global_id": 1223 }, { "text": "Klebsiella pneumoniae is an important clinical bacterial pathogen that has hypervirulent and multidrug-resistant variants. Uniform Manifold Approximation and Projection (UMAP) was used to cluster genomes of 16 797 K. pneumoniae strains collected, based on core genome distance, in over 100 countries during the period 1937 to 2021. A total of 60 high-density genetic clusters of strains representing the major epidemic strains were identified among these strains. Using UMAP bedding, the relationship between genetic cluster, capsular polysaccharide (KL) types and sequence type (ST) of the strains was clearly demonstrated, with some important STs, such as ST11 and ST258, found to contain multiple clusters. Strains within the same cluster often exhibited significant diverse features, such as originating from different areas and being isolated in different years, as well as carriage of different resistance and virulence genes. These data enable the routes of evolution of the globally prevalent K. pneumoniae strains to be traced. Alarmingly, carbapenem-resistant K. pneumoniae strains accounted for 51.7% of the test strains and worldwide transmission was observed. Carbapenem-resistant and hypervirulent K. pneumoniae strains are mainly reported in China; however, these strains are increasingly reported in other parts of the world. Also identified in this study were several key genetic loci that facilitate development of a new K. pneumoniae typing method to differentiate between high- and low-risk strains. In particular, the acrR, ompK35 and hha genes were predicted to play a key role in expression of the resistance and virulence phenotypes.\n\nGlobal genomic profiling of Klebsiella pneumoniae: A spatio-temporal population structure analysis.", "token_count": 438, "char_count": 1758, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6389, "quality_score": 0.8194, "entities": { "genes": [ "ST11", "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:34.213814", "source": { "split": "train_shard_00000", "doc_id": 1111 }, "chunk_id": "train_shard_00000_1111_0", "global_id": 1224 }, { "text": "Pangenome indexes reduce reference bias in sequencing data analysis. However, bias can be reduced further by using a personalized reference, e.g. a diploid human reference constructed to match a donor individual's alleles. We present a novel impute-first alignment framework that combines elements of genotype imputation and pangenome alignment. It begins by genotyping the individual using only a subsample of the input reads. It next uses a reference panel and efficient imputation algorithm to impute a personalized diploid reference. Finally, it indexes the personalized reference and applies a read aligner, which could be a linear or graph aligner, to align the full read set to the personalized reference. This framework achieves higher variant-calling recall (99.54% vs. 99.37%), precision (99.36% vs. 99.18%), and F1 (99.45% vs. 99.28%) compared to a graph pangenome aligner. The personalized reference is also smaller and faster to query compared to a pangenome index, making it an overall advantageous choice for whole-genome DNA sequencing experiments.\n\nMinimizing Reference Bias with an Impute-First Approach.", "token_count": 283, "char_count": 1122, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:34.792763", "source": { "split": "train_shard_00000", "doc_id": 1112 }, "chunk_id": "train_shard_00000_1112_0", "global_id": 1225 }, { "text": "Intestine-restricted inhibitors of the apical sodium-dependent bile acid transporter (ASBT, or ileal bile acid transporter) are approved as treatment for several inheritable forms of cholestasis but are also associated with abdominal complaints and diarrhoea. Furthermore, blocking ASBT as a single therapeutic approach may be less effective in moderate to severe cholestasis. We hypothesised that interventions that lower hepatic bile salt synthesis in addition to intestinal bile salt uptake inhibition provide added therapeutic benefit in the treatment of cholestatic disorders. Here, we test combination therapies of intestinal ASBT inhibition together with obeticholic acid (OCA), cilofexor, and the non-tumorigenic fibroblast growth factor 15 (Fgf15)/fibroblast growth factor 19 (FGF19) analogue aldafermin in a mouse model of cholestasis.\n\nCombined inhibition of bile salt synthesis and intestinal uptake reduces cholestatic liver damage and colonic bile salts in mice.", "token_count": 262, "char_count": 976, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6767, "quality_score": 0.8383, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:35.370524", "source": { "split": "train_shard_00000", "doc_id": 1113 }, "chunk_id": "train_shard_00000_1113_0", "global_id": 1226 }, { "text": "Streptococcus suis is a causative agent of swine and human infections. Genomic analysis indicated that eight S. suis serotype 5 strains recovered from human patients and pigs carried many virulence-associated genes and markers defining pathogenic pathotypes. The strains were sequence types diverse and clustered within either minimum core genome group 3 (MCG-3) or MCG-7-3. Almost all the serotype 5 strains were non-susceptible to penicillin, ceftriaxone, erythromycin, and levofloxacin. Resistance to tetracycline and clindamycin was observed in all strains. The antimicrobial resistance genes tet(O), tet(O/W/32/O), tet(W), tet(44), erm(B), ant(6)-Ia, lsaE, and lnuB were found in these strains. Moderate-to-large numbers of substitutions were observed in three penicillin-binding proteins (PBP)-PBP1A, PBP2B, and PBP2X-in the penicillin-non-susceptible serotype 5 isolates that were involved in β-lactam-non-susceptibility. Comparative genomics between the serotype 5 and 2 strains revealed that only 15 genes absent from the serotype 2 strains were shared by all the serotype 5 strains. However, some additional genes were present only in some of the serotype 5 strains. This study highlighted the pathogenic potential of virulent serotype 5 strains in humans and pigs and the need for increased monitoring of penicillin-non-susceptibility in S. suis serotypes other than for serotype 2.\n\nComparative genome analysis of Streptococcus suis serotype 5 strains from humans and pigs revealed pathogenic potential of virulent, antimicrobial resistance, and genetic relationship.", "token_count": 470, "char_count": 1579, "word_count": 217, "semantic_coherence": 1, "information_density": 0.553, "quality_score": 0.7765, "entities": { "genes": [ "PBP2X", "PBP2B", "PBP1A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:36.014441", "source": { "split": "train_shard_00000", "doc_id": 1114 }, "chunk_id": "train_shard_00000_1114_0", "global_id": 1227 }, { "text": "In this study, we present the genome characterization of a novel chitin-degrading strain, KSP-S5-2, and comparative genomics of 33 strains of Cellvibrionaceae. Strain KSP-S5-2 was isolated from mangrove sediment collected in Balik Pulau, Penang, Malaysia, and its 16S rRNA gene sequence showed the highest similarity (95.09%) to Teredinibacter franksiae. Genome-wide analyses including 16S rRNA gene sequence similarity, average nucleotide identity, digital DNA-DNA hybridization, and phylogenomics, suggested that KSP-S5-2 represents a novel species in the family Cellvibrionaceae. The Cellvibrionaceae pan-genome exhibited high genomic variability, with only 1.7% representing the core genome, while the flexible genome showed a notable enrichment of genes related to carbohydrate metabolism and transport pathway. This observation sheds light on the genetic plasticity of the Cellvibrionaceae family and the gene pools that form the basis for the evolution of polysaccharide-degrading capabilities. Comparative analysis of the carbohydrate-active enzymes across Cellvibrionaceae strains revealed that the chitinolytic system is not universally present within the family, as only 18 of the 33 genomes encoded chitinases. Strain KSP-S5-2 displayed an expanded repertoire of chitinolytic enzymes (25 GH18, two GH19 chitinases, and five GH20 β-N-acetylhexosaminidases) but lacked genes for agar, xylan, and pectin degradation, indicating specialized enzymatic machinery focused primarily on chitin degradation. Further, the strain degraded 90% of chitin after 10 days of incubation", "token_count": 459, "char_count": 1580, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [ "GH18", "GH19", "GH20" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:36.651215", "source": { "split": "train_shard_00000", "doc_id": 1115 }, "chunk_id": "train_shard_00000_1115_0", "global_id": 1228 }, { "text": "In summary, our findings provided insights into strain KSP-S5-2's genomic potential, the genetics of its chitinolytic system, genomic diversity within the Cellvibrionaceae family in terms of polysaccharide degradation, and its application for chitin degradation.\n\nPolysaccharide degradation in Cellvibrionaceae: Genomic insights of the novel chitin-degrading marine bacterium, strain KSP-S5-2, and its chitinolytic activity.", "token_count": 122, "char_count": 424, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7115, "quality_score": 0.8558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:37.038043", "source": { "split": "train_shard_00000", "doc_id": 1115 }, "chunk_id": "train_shard_00000_1115_1", "global_id": 1229 }, { "text": "Commensal microbiome-based health support is gaining respect in the medical community and new human gut-associated Lactic Acid Bacteria (LAB) strains must be evaluated for their probiotic potential. Here we characterized the phenotype and genomes of human ileocecal mucosa-associated LAB strains using metagenomic sequencing and in vitro testing. The strains characterized belonged to the genus Enterococcus (Enterococcus lactis NPL1366, NPL1371, and Enterococcus mundtii NPL1379) and Lactobacillus (Lactobacillus paragasseri, NPL1369, NPL1370, and Lactiplantibacillus plantarum NPL1378). Genome annotation suggested bacterial adaptation to both human physiological and industrial manufacturing-related stressors. Genes for histidine kinases in enterococci and Na + /K + antiporters and F0F1 ATP synthases in Lactobacillus strains may support their tolerance to acid seen in vitro. The bile salt hydrolase (BSH) gene in Lp. plantarum and L. paragasseri may help explain their reported bile salt deconjugation and cholesterol-lowering behavior. Thioredoxin is the principal antioxidant system, and several oxidases and general stress-related proteins are found in lactobacilli, most notably in L. plantarum NPL1378. Multiple adhesion and biofilm-related genes were predicted in the LAB genomes. Adhesion and biofilm-related genes figured prominently in the genomes of enterococcal strains, especially E. lactis, corresponding to its biofilm formation capacity in vitro. Bacteriocin and secondary metabolite biosynthetic gene clusters in the sequenced genomes of E. lactis NPL1366 and Lp. plantarum NPL1378 may explain their in vitro pathogenic antagonism. Moreover, folate producing Lp. plantarum strain holds potential to be used in therapeutics or biofortification of food", "token_count": 525, "char_count": 1773, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": { "genes": [ "NPL1371", "NPL1379", "NPL1378", "NPL1369", "NPL1370", "NPL1366" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:09:37.667404", "source": { "split": "train_shard_00000", "doc_id": 1116 }, "chunk_id": "train_shard_00000_1116_0", "global_id": 1230 }, { "text": "All the strains were deemed safe through in vitro and in silico analysis. This basic genetic and phenotypic information supports their contention as probiotic adjuncts to conventional medical therapy.\n\nGenomic and Phenotypic Insight into the Probiotic Potential of Lactic Acid Bacterial spp. Associated with the Human Gut Mucosa.", "token_count": 83, "char_count": 329, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8542, "quality_score": 0.9271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:38.050049", "source": { "split": "train_shard_00000", "doc_id": 1116 }, "chunk_id": "train_shard_00000_1116_1", "global_id": 1231 }, { "text": "The recent global outbreak of mpox, caused by monkeypox virus (MPV) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. In this study, we analyzed 880 MPV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than single-nucleotide polymorphisms (SNPs), which do not contribute significantly to genome diversity. Although the genome contains multiple SNPs in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is amino acid position 63 of the protein encoded by the Cop-A4L gene, which is intricately related to viral maturity, which we found to be under strong positive selection. Ancestral state reconstruction indicated that the ancestral state at position 63 corresponds to the amino acid valine, which is present only in isolates of clade I. However, the isolates from the current outbreak contained threonine at position 63. Our findings contribute new information about the evolution of monkeypox virus.\n\nGenetic insights into the microevolutionary dynamics and early introductions of human monkeypox virus in Mexico.", "token_count": 356, "char_count": 1577, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6511, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:38.628218", "source": { "split": "train_shard_00000", "doc_id": 1117 }, "chunk_id": "train_shard_00000_1117_0", "global_id": 1232 }, { "text": "Garlic, originating in the mountains of Central Asia, has undergone domestication and subsequent widespread introduction to diverse regions. Human selection for adaptation to various climates has resulted in the development of numerous garlic varieties, each characterized by specific morphological and physiological traits. However, this process has led to a loss of fertility and seed production in garlic crops. In this study, we conducted morpho-physiological and transcriptome analyses, along with whole-genome resequencing of 41 garlic accessions from different regions, in order to assess the variations in reproductive traits among garlic populations. Our findings indicate that the evolution of garlic crops was associated with mutations in genes related to vernalization and the circadian clock. The decline in sexual reproduction is not solely attributed to a few mutations in specific genes, but is correlated with extensive alterations in the genetic regulation of the annual cycle, stress adaptations, and environmental requirements. The regulation of flowering ability, stress response, and metabolism occurs at both the genetic and transcriptional levels. We conclude that the migration and evolution of garlic crops involve substantial and diverse changes across the entire genome landscape. The construction of a garlic pan-genome, encompassing genetic diversity from various garlic populations, will provide further insights for research into and the improvement of garlic crops.\n\nDeprivation of Sexual Reproduction during Garlic Domestication and Crop Evolution.", "token_count": 305, "char_count": 1582, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:39.205843", "source": { "split": "train_shard_00000", "doc_id": 1118 }, "chunk_id": "train_shard_00000_1118_0", "global_id": 1233 }, { "text": "Obesity is a chronic metabolic disease worldwide and is considered a major health problem in contemporary society. Lactobacillus acidophilus have demonstrated beneficial effects on obesity, but the specific mechanism of how it exerts beneficial effects has not been elucidated. Here, we found that L. acidophilus JYLA-126 had good biological properties for intestinal health, such as antioxidation, acid tolerance, bile salt tolerance, antimicrobial activity, and gut colonization. We further identified that supplementation of L. acidophilus JYLA-126 obese mice possessed a dose-dependent amelioration of body weight, intestinal imbalance, and metabolic disorders compared to HFD-induced mice. Mechanistically, the excellent slimming effect of L. acidophilus JYLA-126 was achieved mainly by reversing HFD-induced gut dysbiosis, inhibiting inflammatory factors and balancing the homeostasis of the gut-liver axis. Specifically, L. acidophilus JYLA-126 improved hepatic glycogen synthesis, lowered oxidative stress, and facilitated lipid metabolism by regulating AMPK signaling pathway-related protein expression to restore the overall metabolic level. Accordingly, L. acidophilus JYLA-126 promoted energy uptake efficiency in obese mice, resulting in significant expression of uncoupling protein 1 (UCP1) protein in brown adipose tissue (BAT), and markedly reduced the size of adipocytes. These findings indicate that the anti-obesity activity of L. acidophilus JYLA-126 correlates with activation of the AMPK signaling pathway through improved gut-liver interactions.\n\nLactobacillus acidophilus JYLA-126 Ameliorates Obesity-Associated Metabolic Disorders by Positively Regulating the AMPK Signaling Pathway Through the Gut-Liver Axis.", "token_count": 468, "char_count": 1735, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [ "UCP1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:39.853642", "source": { "split": "train_shard_00000", "doc_id": 1119 }, "chunk_id": "train_shard_00000_1119_0", "global_id": 1234 }, { "text": "Actinomyces strains are commonly found as part of the normal microflora on human tissue surfaces, including the oropharynx, gastrointestinal tract, and female genital tract. Understanding the diversity and characterization of Actinomyces species is crucial for human health, as they play an important role in dental plaque formation and biofilm-related infections. Two Actinomyces strains ATCC 49340\n\nGenome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity.", "token_count": 137, "char_count": 556, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:40.287294", "source": { "split": "train_shard_00000", "doc_id": 1120 }, "chunk_id": "train_shard_00000_1120_0", "global_id": 1235 }, { "text": "The antifungal effect of the yeast species Kluyveromyces marxianus, Meyerozyma caribbica, and Wickerhamomyces anomalus was evaluated against two Fusarium graminearum strains (FRS 26 and FSP 27) in vitro and on corn seeds.\n\nPotential of yeasts as biocontrol agents against Fusarium graminearum in vitro and on corn.", "token_count": 102, "char_count": 314, "word_count": 46, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:40.667222", "source": { "split": "train_shard_00000", "doc_id": 1121 }, "chunk_id": "train_shard_00000_1121_0", "global_id": 1236 }, { "text": "Water caltrop (\n\nPangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization.", "token_count": 34, "char_count": 137, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:41.029948", "source": { "split": "train_shard_00000", "doc_id": 1122 }, "chunk_id": "train_shard_00000_1122_0", "global_id": 1237 }, { "text": "An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping the pangenome of a species, it is often unnecessary and computationally onerous to include all available genomes in studies. In addition, over-representation of specific lineages due to sampling and sequencing bias can have undesired effects on evolutionary analyses. To assist users with\n\nskDER & CiDDER: two scalable approaches for microbial genome dereplication.", "token_count": 124, "char_count": 566, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7831, "quality_score": 0.8916, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:41.413289", "source": { "split": "train_shard_00000", "doc_id": 1123 }, "chunk_id": "train_shard_00000_1123_0", "global_id": 1238 }, { "text": "Yinzhihuang (YZH), a traditional Chinese medicine prescription, was widely used to treat cholestasis. Cholestatic liver injury limited the use of the immunosuppressive drug cyclosporine A (CsA) in preventing organ rejection after solid organ transplantation. Clinical evidences suggested that YZH could enhance bile acids and bilirubin clearance, providing a potential therapeutic strategy against CsA-induced cholestasis. Nevertheless, it remains unclear whether YZH can effectively alleviate CsA-induced cholestatic liver injury, as well as the molecular mechanisms responsible for its hepatoprotective effects. The purpose of the present study was to investigate the hepatoprotective effects of YZH on CsA-induced cholestatic liver injury and explore its molecular mechanisms in vivo and vitro. The results demonstrated that YZH significantly improved the CsA-induced cholestatic liver injury and reduced the level of liver function markers in serum of Sprague-Dawley (SD) rats. Targeted protein and gene analysis indicated that YZH increased bile acids and bilirubin efflux into bile through the regulation of multidrug resistance-associated protein 2 (Mrp2), bile salt export pump (Bsep), sodium taurocholate cotransporting polypeptide (Ntcp) and organic anion transporting polypeptide 2 (Oatp2) transport systems, as well as upstream nuclear receptors farnesoid X receptor (Fxr). Moreover, YZH modulated enzymes involved in bile acids synthesis and bilirubin metabolism including Cyp family 7 subfamily A member 1 (Cyp7a1) and uridine 5'-diphosphate (UDP) glucuronosyltransferase family 1 member A1 (Ugt1a1). Furthermore, the active components geniposidic acid, baicalin and chlorogenic acid exerted regulated metabolic enzymes and transporters in LO2 cells", "token_count": 487, "char_count": 1763, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6695, "quality_score": 0.8347, "entities": { "genes": [ "LO2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:42.059887", "source": { "split": "train_shard_00000", "doc_id": 1124 }, "chunk_id": "train_shard_00000_1124_0", "global_id": 1239 }, { "text": "In conclusion, YZH may prevent CsA-induced cholestasis by regulating the transport systems, metabolic enzymes, and upstream nuclear receptors Fxr to restore bile acid and bilirubin homeostasis. These findings highlight the potential of YZH as a therapeutic intervention for CsA-induced cholestasis and open avenues for further research into its clinical applications.\n\nEffects of Yinzhihuang on Alleviating Cyclosporine A-Induced Cholestatic Liver Injury via Farnesoid X Receptor-Mediated Regulation of Transporters and Enzymes in Vitro and in Vivo.", "token_count": 156, "char_count": 549, "word_count": 74, "semantic_coherence": 1, "information_density": 0.8243, "quality_score": 0.9122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:42.494853", "source": { "split": "train_shard_00000", "doc_id": 1124 }, "chunk_id": "train_shard_00000_1124_1", "global_id": 1240 }, { "text": "To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate.\n\nPerformance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection.", "token_count": 104, "char_count": 377, "word_count": 46, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:42.873707", "source": { "split": "train_shard_00000", "doc_id": 1125 }, "chunk_id": "train_shard_00000_1125_0", "global_id": 1241 }, { "text": "As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses. Several data structures have been proposed for representing collections of genomes as pangenomes, in particular graphs.\n\nComparing methods for constructing and representing human pangenome graphs.", "token_count": 75, "char_count": 418, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8214, "quality_score": 0.9107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:43.249895", "source": { "split": "train_shard_00000", "doc_id": 1126 }, "chunk_id": "train_shard_00000_1126_0", "global_id": 1242 }, { "text": "Sitosterolemia is a rare genetic lipid disorder, mainly characterized by the accumulation of dietary xenosterols in plasma and tissues. It is caused by inactivating mutations in either ABCG5 or ABCG8 subunits, a subfamily-G ATP-binding cassette (ABCG) transporters. ABCG5/G8 encodes a pair of ABC half transporters that form a heterodimer (G5G8). This heterodimeric ATP-binding cassette (ABC) sterol transporter, ABCG5/G8, is responsible for the hepatobiliary and transintestinal secretion of cholesterol and dietary plant sterols to the surface of hepatocytes and enterocytes, promoting the secretion of cholesterol and xenosterols into the bile and the intestinal lumen. In this way, ABCG5/G8 function in the reverse cholesterol transport pathway and mediate the efflux of cholesterol and xenosterols to high-density lipoprotein and bile salt micelles, respectively. Here, we review the biological characteristics and function of ABCG5/G8, and how the mutations of ABCG5/G8 can cause sitosterolemia, a loss-of-function disorder characterized by plant sterol accumulation and premature atherosclerosis, among other features.\n\nAssociation of ABCG5 and ABCG8 Transporters with Sitosterolemia.", "token_count": 338, "char_count": 1191, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6025, "quality_score": 0.8012, "entities": { "genes": [ "ABCG8", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:43.817635", "source": { "split": "train_shard_00000", "doc_id": 1127 }, "chunk_id": "train_shard_00000_1127_0", "global_id": 1243 }, { "text": "Broomcorn millet (Panicum miliaceum L.) is an orphan crop with the potential to improve cereal production and quality, and ensure food security. Here we present the genetic variations, population structure and diversity of a diverse worldwide collection of 516 broomcorn millet genomes. Population analysis indicated that the domesticated broomcorn millet originated from its wild progenitor in China. We then constructed a graph-based pangenome of broomcorn millet based on long-read de novo genome assemblies of 32 representative accessions. Our analysis revealed that the structural variations were highly associated with transposable elements, which influenced gene expression when located in the coding or regulatory regions. We also identified 139 loci associated with 31 key domestication and agronomic traits, including candidate genes and superior haplotypes, such as LG1, for panicle architecture. Thus, the study's findings provide foundational resources for developing genomics-assisted breeding programs in broomcorn millet.\n\nPangenome analysis reveals genomic variations associated with domestication traits in broomcorn millet.", "token_count": 258, "char_count": 1142, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7403, "quality_score": 0.8701, "entities": { "genes": [ "LG1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:44.364772", "source": { "split": "train_shard_00000", "doc_id": 1128 }, "chunk_id": "train_shard_00000_1128_0", "global_id": 1244 }, { "text": "The aim of the current study was (1) to develop an automation-based protocol for in vitro assessment of enzymatic drug stability at fasted- and fed-state intestinal conditions, (2) to characterize the inter-individual variability of drug degradation in fasted- and fed-state human intestinal fluids, and (3) to compare the obtained in vitro results to drug degradation in human intestinal fluids by taking variability into account. In human intestinal fluids, drug degradation displayed large inter-individual variability, with coefficients of variance generally ranging between 30 and 70 %. The effect of food on the inter-individual variability was highly dependent on the type of drug. The increase of pH in the range between 5.0 and 7.0 significantly accelerated the degradation rate of the studied drugs both in the in vitro and ex vivo experiments. In contrast, the increase of bile salt and phospholipid concentrations in the in vitro screen decreased strongly the degradation rate of the hydrophobic drugs. The developed automated in vitro screen mimicked relatively well the ex vivo degradation of all drugs in the fasted state, whereas in the fed state the degradation of only one of the drugs was adequately reproduced.\n\nEnzymatic prodrug degradation in the fasted and fed small intestine: In vitro studies and interindividual variability in human aspirates.", "token_count": 333, "char_count": 1369, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5024, "quality_score": 0.7512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:44.932141", "source": { "split": "train_shard_00000", "doc_id": 1129 }, "chunk_id": "train_shard_00000_1129_0", "global_id": 1245 }, { "text": "Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease. Gut dysbiosis is considered a significant contributing factor in disease development. Increased intestinal permeability can be induced by gut dysbiosis, followed by the entry of lipopolysaccharide into circulation to reach peripheral tissue and result in chronic inflammation. We reviewed how microbial metabolites push host physiology toward MAFLD, including short-chain fatty acids (SCFAs), bile acids, and tryptophan metabolites. The effects of SCFAs are generally reported as anti-inflammatory and can improve intestinal barrier function and restore gut microbiota. Gut microbes can influence intestinal barrier function through SCFAs produced by fermentative bacteria, especially butyrate and propionate producers. This is achieved through the activation of free fatty acid sensing receptors. Bile is directly involved in lipid absorption. Gut microbes can alter bile acid composition by bile salt hydrolase-producing bacteria and bacterial hydroxysteroid dehydrogenase-producing bacteria. These bile acids can affect host physiology by activating farnesoid X receptor Takeda G protein-coupled receptor 5. Gut microbes can also induce MAFLD-associated symptoms by producing tryptophan metabolites kynurenine, serotonin, and indole-3-propionate. A summary of bacterial genera involved in SCFAs production, bile acid transformation, and tryptophan metabolism is provided. Many bacteria have demonstrated efficacy in alleviating MAFLD in animal models and are potential therapeutic candidates for MAFLD.\n\nRoles of gut microbes in metabolic-associated fatty liver disease.", "token_count": 414, "char_count": 1664, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:45.553138", "source": { "split": "train_shard_00000", "doc_id": 1130 }, "chunk_id": "train_shard_00000_1130_0", "global_id": 1246 }, { "text": "Lactic Acid Bacteria play an important role in the milk fermentation processes of traditional cheeses and have become an important target for the development of novel cheese cultures because of their ability to confer health benefits. This study aimed to evaluate the probiotic potential of 12 Lactic Acid Bacteria (LAB) strains previously isolated and molecularly identified from an artisanal Colombian Double-Cream Cheese. Probiotic properties, including safety (hemolysis and sensibility to antibiotics), pH and bile salt tolerance, auto-aggregation, cell surface hydrophobicity, antibacterial activity, and exopolysaccharide production, were examined. None of the strains were hemolytic, and\n\nAssessment of probiotic properties of lactic acid bacteria isolated from an artisanal Colombian cheese.", "token_count": 183, "char_count": 800, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6759, "quality_score": 0.838, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:46.036183", "source": { "split": "train_shard_00000", "doc_id": 1131 }, "chunk_id": "train_shard_00000_1131_0", "global_id": 1247 }, { "text": "Integrons are genetic elements, found among diverse bacteria and archaea, that capture and rearrange gene cassettes to rapidly generate genetic diversity and drive adaptation. Despite their broad taxonomic and geographic prevalence, and their role in microbial adaptation, the functions of gene cassettes remain poorly characterized. Here, using a combination of bioinformatic and experimental analyses, we examined the functional diversity of gene cassettes from different environments. We find that cassettes encode diverse antimicrobial resistance (AMR) determinants, including those conferring resistance to antibiotics currently in the developmental pipeline. Further, we find a subset of cassette functions is universally enriched relative to their broader metagenomes. These are largely involved in (a)biotic interactions, including AMR, phage defense, virulence, biodegradation, and stress tolerance. The remainder of functions are sample-specific, suggesting that they confer localised functions relevant to their microenvironment. Together, they comprise functional profiles different from bulk metagenomes, representing niche-adaptive components of the prokaryotic pangenome.\n\nFunctional enrichment of integrons: Facilitators of antimicrobial resistance and niche adaptation.", "token_count": 270, "char_count": 1286, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:46.601332", "source": { "split": "train_shard_00000", "doc_id": 1132 }, "chunk_id": "train_shard_00000_1132_0", "global_id": 1248 }, { "text": "It is necessary to explore potent therapeutic agents via regulating gut microbiota and metabolism to combat Parkinson's disease (PD). Dioscin, a bioactive steroidal saponin, shows various activities. However, its effects and mechanisms against PD are limited. In this study, dioscin dramatically alleviated neuroinflammation and oxidative stress, and restored the disorders of mice induced by 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP). 16 S rDNA sequencing assay demonstrated that dioscin reversed MPTP-induced gut dysbiosis to decrease\n\nProtective effects of dioscin against Parkinson's disease via regulating bile acid metabolism through remodeling gut microbiome/GLP-1 signaling.", "token_count": 195, "char_count": 692, "word_count": 87, "semantic_coherence": 1, "information_density": 0.8046, "quality_score": 0.9023, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:47.061491", "source": { "split": "train_shard_00000", "doc_id": 1133 }, "chunk_id": "train_shard_00000_1133_0", "global_id": 1249 }, { "text": "Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures), as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium-a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.\n\nBlueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts.", "token_count": 395, "char_count": 1838, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5946, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:47.706823", "source": { "split": "train_shard_00000", "doc_id": 1134 }, "chunk_id": "train_shard_00000_1134_0", "global_id": 1250 }, { "text": "Recent work on bile salt hydrolases (BSHs) in Gram-negative bacteria, such as Bacteroides, has primarily focused on how they can impact host physiology. However, the benefits bile acid metabolism confers to the bacterium that performs it are not well understood. In this study, we set out to define if and how\n\nLoss of", "token_count": 81, "char_count": 318, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8868, "quality_score": 0.9434, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:48.082290", "source": { "split": "train_shard_00000", "doc_id": 1135 }, "chunk_id": "train_shard_00000_1135_0", "global_id": 1251 }, { "text": "Tea is one of the world's oldest crops and is cultivated to produce beverages with various flavours. Despite advances in sequencing technologies, the genetic mechanisms underlying key agronomic traits of tea remain unclear. In this study, we present a high-quality pangenome of 22 elite cultivars, representing broad genetic diversity in the species. Our analysis reveals that a recent long terminal repeat burst contributed nearly 20% of gene copies, introducing functional genetic variants that affect phenotypes such as leaf colour. Our graphical pangenome improves the efficiency of genome-wide association studies and allows the identification of key genes controlling bud flush timing. We also identified strong correlations between allelic variants and flavour-related chemistries. These findings deepen our understanding of the genetic basis of tea quality and provide valuable genomic resources to facilitate its genomics-assisted breeding.\n\nGene mining and genomics-assisted breeding empowered by the pangenome of tea plant Camellia sinensis.", "token_count": 219, "char_count": 1052, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7347, "quality_score": 0.8673, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:48.556664", "source": { "split": "train_shard_00000", "doc_id": 1136 }, "chunk_id": "train_shard_00000_1136_0", "global_id": 1252 }, { "text": "Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a threat to global wheat production. Deployment of widely effective resistance genes underpins management of this ongoing threat. This study focused on the mapping of stripe rust resistance gene YR63 from a Portuguese hexaploid wheat landrace AUS27955 of the Watkins Collection.\n\nWheat stripe rust resistance locus YR63 is a hot spot for evolution of defence genes - a pangenome discovery.", "token_count": 122, "char_count": 461, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7465, "quality_score": 0.8732, "entities": { "genes": [ "YR63", "AUS27955" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:48.941613", "source": { "split": "train_shard_00000", "doc_id": 1137 }, "chunk_id": "train_shard_00000_1137_0", "global_id": 1253 }, { "text": "Core genome multilocus sequence typing (cgMLST) is commonly used to classify bacterial strains into different types, for taxonomical and epidemiological applications. However, cgMLST schemes require central databases for the nomenclature of new alleles and sequence types, which must be synchronized worldwide and involve increasingly intensive calculation and storage demands. Here, we describe a distributed cgMLST (dcgMLST) scheme that does not require a central database of allelic sequences and apply it to study evolutionary patterns of epidemic and endemic strains of the genus Neisseria. We classify 69,994 worldwide Neisseria strains into multi-level clusters that assign species, lineages, and local disease outbreaks. We divide Neisseria meningitidis into 168 endemic lineages and three epidemic lineages responsible for at least 9 epidemics in the past century. According to our analyses, the epidemic and endemic lineages experienced very different population dynamics in the past 100 years. Epidemic lineages repetitively emerged from endemic lineages, disseminated worldwide, and apparently disappeared rapidly afterward. We propose a stepwise model for the evolutionary trajectory of epidemic lineages in Neisseria, and expect that the development of similar dcgMLST schemes will facilitate epidemiological studies of other bacterial pathogens.\n\nDistributed genotyping and clustering of Neisseria strains reveal continual emergence of epidemic meningococcus over a century.", "token_count": 343, "char_count": 1489, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:49.514755", "source": { "split": "train_shard_00000", "doc_id": 1138 }, "chunk_id": "train_shard_00000_1138_0", "global_id": 1254 }, { "text": "Decades of antimicrobial overuse to treat respiratory disease in foals have promoted the emergence and spread of zoonotic multidrug-resistant (MDR)\n\nExploring the Accessory Genome of Multidrug-Resistant", "token_count": 57, "char_count": 202, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:49.876500", "source": { "split": "train_shard_00000", "doc_id": 1139 }, "chunk_id": "train_shard_00000_1139_0", "global_id": 1255 }, { "text": "Prokaryote diversity makes up most of the tree of life and is crucial to the functioning of the biosphere and human health. However, the patterns and mechanisms of prokaryote diversification have received relatively little attention compared to animals and plants. Adaptive radiation, the rapid diversification of an ancestor species into multiple ecologically divergent species, is a fundamental process by which macrobiological diversity is generated. Here, we discuss whether ecological opportunity could lead to similar bursts of diversification in bacteria. We explore how adaptive radiations in prokaryotes can be kickstarted by horizontally acquired key innovations allowing lineages to invade new niche space that subsequently is partitioned among diversifying specialist descendants. We discuss how novel adaptive zones are colonized and exploited after the evolution of a key innovation and whether certain types of are more prone to adaptive radiation. Radiation into niche specialists does not necessarily lead to speciation in bacteria when barriers to recombination are absent. We propose that in this scenario, niche-specific genes could accumulate within a single lineage, leading to the evolution of an open pangenome.\n\nAdaptive radiations in natural populations of prokaryotes: innovation is key.", "token_count": 264, "char_count": 1314, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:50.427900", "source": { "split": "train_shard_00000", "doc_id": 1140 }, "chunk_id": "train_shard_00000_1140_0", "global_id": 1256 }, { "text": "Pangenomics was originally defined as the problem of comparing the composition of genes into gene families within a set of bacterial isolates belonging to the same species. The problem requires the calculation of sequence homology among such genes. When combined with metagenomics, namely for human microbiome composition analysis, gene-oriented pangenome detection becomes a promising method to decipher ecosystem functions and population-level evolution. Established computational tools are able to investigate the genetic content of isolates for which a complete genomic sequence is available. However, there is a plethora of incomplete genomes that are available on public resources, which only a few tools may analyze. Incomplete means that the process for reconstructing their genomic sequence is not complete, and only fragments of their sequence are currently available. However, the information contained in these fragments may play an essential role in the analyses. Here, we present PanDelos-frags, a computational tool which exploits and extends previous results in analyzing complete genomes. It provides a new methodology for inferring missing genetic information and thus for managing incomplete genomes. PanDelos-frags outperforms state-of-the-art approaches in reconstructing gene families in synthetic benchmarks and in a real use case of metagenomics. PanDelos-frags is publicly available at https://github.com/InfOmics/PanDelos-frags.\n\nPanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies.", "token_count": 330, "char_count": 1556, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:50.992958", "source": { "split": "train_shard_00000", "doc_id": 1141 }, "chunk_id": "train_shard_00000_1141_0", "global_id": 1257 }, { "text": "The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.\n\nA pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.", "token_count": 164, "char_count": 755, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7431, "quality_score": 0.8716, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:51.436377", "source": { "split": "train_shard_00000", "doc_id": 1142 }, "chunk_id": "train_shard_00000_1142_0", "global_id": 1258 }, { "text": "Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in\n\nThe expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen", "token_count": 174, "char_count": 681, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7423, "quality_score": 0.8711, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:51.876681", "source": { "split": "train_shard_00000", "doc_id": 1143 }, "chunk_id": "train_shard_00000_1143_0", "global_id": 1259 }, { "text": "The bioconversion of porungo cheese whey to produce β-galactosidase in batch system was studied. The whey released after curd cutting and precipitation during porungo cheese production was collected in borosilicate flasks. Two strains of Kluyveromyces marxianus, CCT 4086 and CBS 6556, and whey supplementation with different nitrogen sources were evaluated. Different temperatures (30 °C and 37 °C) and pH values (5.0 to 7.0) were investigated to establish the best conditions for enzyme production. The highest enzymatic activity was obtained by K. marxianus CCT 4086 in porungo cheese whey supplemented with yeast extract (16.73 U mL-1). K. marxianus CCT 4086 produced superior β-galactosidase activity when compared to CBS 6556 for all media tested (ranging from 11.69 to 14.40 U mL-1). Highest β-galactosidase activity was reached under conditions of pH 7.0 and 30 °C using K. marxianus CCT 4086 in the better media composition. The lowest enzymatic activity was observed at 37 °C for all pH values tested (10.69 U mL-1 to 13.94 U mL-1) and a highest β-galactosidase activity was reached in pH 7.0 for both two temperatures (11.42 to 15.93 U mL-1). Porungo cheese whey shows potential for industrial β-galactosidase production by microbial fermentation.\n\nPorungo cheese whey: a new substrate to produce β-galactosidase.", "token_count": 433, "char_count": 1324, "word_count": 203, "semantic_coherence": 1, "information_density": 0.532, "quality_score": 0.766, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:52.501416", "source": { "split": "train_shard_00000", "doc_id": 1144 }, "chunk_id": "train_shard_00000_1144_0", "global_id": 1260 }, { "text": "Oral probiotic therapy has become an increasingly attractive method for treating various diseases, including intestinal barrier dysfunction, inflammatory bowel disease (IBD), and colorectal cancer due to its safety and convenience. However, only a few probiotics after oral gavage can survive the acidic and bile salt conditions of the gastrointestinal tract and colonize the colon to have a nutritional effect on the host. To address these challenges, encapsulation technology has been applied to protect probiotics from harsh gastrointestinal conditions, improve gut adhesion, and reduce immunogenicity. In addition, some of the functional polysaccharides are used to endow probiotics with exogenous functions as prebiotics. In this review, we systematically introduced the advancements of emerging single-cell modification strategies for probiotics in IBD applications. Additionally, we discussed the limitations and perspectives of single-cell modification strategies for probiotics. This review contributed to the development of probiotic delivery systems with higher therapeutic efficacy against colitis.\n\nThe single-cell modification strategies for probiotics delivery in inflammatory bowel disease: A review.", "token_count": 262, "char_count": 1216, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6894, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:53.051072", "source": { "split": "train_shard_00000", "doc_id": 1145 }, "chunk_id": "train_shard_00000_1145_0", "global_id": 1261 }, { "text": "Permeability enhancer-based formulations offer a promising approach to enhance the oral bioavailability of peptides. We used all-atom molecular dynamics simulations to investigate the interaction between two permeability enhancers (sodium caprate, and SNAC), and four different peptides (octreotide, hexarelin, degarelix, and insulin), in the presence of taurocholate, an intestinal bile salt. The permeability enhancers exhibited distinct effects on peptide release based on their properties, promoting hydrophobic peptide release while inhibiting water-soluble peptide release. Lowering peptide concentrations in the simulations reduced peptide-peptide interactions but increased their interactions with the enhancers and taurocholates. Introducing peptides randomly with enhancer and taurocholate molecules yielded dynamic molecular aggregation, and reduced peptide-peptide interactions and hydrogen bond formation compared to peptide-only systems. The simulations provided insights into molecular-level interactions, highlighting the specific contacts between peptide residues responsible for aggregation, and the interactions between peptide residues and permeability enhancers/taurocholates that are crucial within the mixed colloids. Therefore, our results can provide insights into how modifications of these critical contacts can be made to alter drug release profiles from peptide-only or mixed peptide-PE-taurocholate aggregates. To further probe the molecular nature of permeability enhancers and peptide interactions, we also analyzed insulin secondary structures using Fourier transform infrared spectroscopy. The presence of SNAC led to an increase in β-sheet formation in insulin. In contrast, both in the absence and presence of caprate, α-helices, and random structures dominated. These molecular-level insights can guide the design of improved permeability enhancer-based dosage forms, allowing for precise control of peptide release profiles near the intended absorption site.\n\nRevealing the interaction between peptide drugs and permeation enhancers in the presence of intestinal bile salts.", "token_count": 472, "char_count": 2112, "word_count": 267, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:53.697737", "source": { "split": "train_shard_00000", "doc_id": 1146 }, "chunk_id": "train_shard_00000_1146_0", "global_id": 1262 }, { "text": "The use of Nuclear Magnetic Resonance spectroscopy for studying lipid digestion in vitro most often consists of quantifying lipolysis products after they have been extracted from the reaction medium using organic solvents. However, the current sensitivity level of NMR spectrometers makes possible to avoid the extraction step and continuously quantify the lipids directly in the reaction medium. We used real-time\n\nMonitoring galactolipid digestion and simultaneous changes in lipid-bile salt micellar organization by real-time NMR spectroscopy.", "token_count": 124, "char_count": 546, "word_count": 75, "semantic_coherence": 1, "information_density": 0.8133, "quality_score": 0.9067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:54.083366", "source": { "split": "train_shard_00000", "doc_id": 1147 }, "chunk_id": "train_shard_00000_1147_0", "global_id": 1263 }, { "text": "Listeria (L.) monocytogenes is of global concern for food safety as the listeriosis-causing pathogen is widely distributed in the food processing environments, where it can survive for a long time. Frozen vegetables contaminated with L. monocytogenes were recently identified as the source of two large listeriosis outbreaks in the EU and US. So far, only a few studies have investigated the occurrence and behavior of Listeria in frozen vegetables and the associated processing environment. This study investigates the occurrence of L. monocytogenes and other Listeria spp. in a frozen vegetable processing environment and in frozen vegetable products. Using whole genome sequencing (WGS), the distribution of sequence types (MLST-STs) and core genome sequence types (cgMLST-CT) of L. monocytogenes were assessed, and in-house clones were identified. Comparative genomic analyses and phenotypical characterization of the different MLST-STs and isolates were performed, including growth ability under low temperatures, as well as survival of freeze-thaw cycles. Listeria were widely disseminated in the processing environment and five in-house clones namely ST451-CT4117, ST20-CT3737, ST8-CT1349, ST8-CT6243, ST224-CT5623 were identified among L. monocytogenes isolates present in environmental swab samples. Subsequently, the identified in-house clones were also detected in product samples. Conveyor belts were a major source of contamination in the processing environment. A wide repertoire of stress resistance markers supported the colonization and survival of L. monocytogenes in the frozen vegetable processing facility. The presence of ArgB was significantly associated with in-house clones. Significant differences were also observed in the growth rate between different MLST-STs at low temperatures (4 °C and 10 °C), but not between in-house and non-in-house isolates. All isolates harbored major virulence genes such as full length InlA and InlB and LIPI-1, yet there were differences between MLST-STs in the genomic content", "token_count": 510, "char_count": 2035, "word_count": 286, "semantic_coherence": 1, "information_density": 0.549, "quality_score": 0.7745, "entities": { "genes": [ "CT4117", "ST20", "CT6243", "ST224", "CT5623", "ST8", "CT3737", "CT1349", "ST451" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:54.722201", "source": { "split": "train_shard_00000", "doc_id": 1148 }, "chunk_id": "train_shard_00000_1148_0", "global_id": 1264 }, { "text": "The results of this study demonstrate that WGS is a strong tool for tracing contamination sources and transmission routes, and for identifying in-house clones. Further research targeting the co-occurring microbiota and the presence of biofilms is needed to fully understand the mechanism of colonization and persistence in a food processing environment.\n\nDiverse Listeria monocytogenes in-house clones are present in a dynamic frozen vegetable processing environment.", "token_count": 98, "char_count": 467, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7538, "quality_score": 0.8769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:55.102374", "source": { "split": "train_shard_00000", "doc_id": 1148 }, "chunk_id": "train_shard_00000_1148_1", "global_id": 1265 }, { "text": "Salmonella Typhi stands as the etiological agent responsible for the onset of human typhoid fever. The pressing demand for innovative therapeutic targets against S. Typhi is underscored by the escalating prevalence of this pathogen and the severe nature of its infections. Consequently, this study employs pangenome analysis to scrutinize 119 S. Typhi-resistant strains, aiming to identify the most promising therapeutic targets originating from its core genome.\n\nPangenome diversification and resistance gene characterization in Salmonella Typhi prioritized RfaJ as a significant therapeutic marker.", "token_count": 142, "char_count": 600, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7439, "quality_score": 0.872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:55.529664", "source": { "split": "train_shard_00000", "doc_id": 1149 }, "chunk_id": "train_shard_00000_1149_0", "global_id": 1266 }, { "text": "High-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs and gain an understanding of their impacts on host genomes. Such high-quality TE resources are severely lacking for species in the fungal kingdom. To facilitate future studies on the putative role of TEs in rapid adaptation observed in the fungal wheat pathogen Zymoseptoria tritici, we produced a manually curated TE library. This was generated by detecting TEs in 19 reference genome assemblies representing the global diversity of the species supplemented by multiple sister species genomes. Improvements over previous TE libraries have been made on TE boundary resolution, detection of ORFs, TE domains, terminal inverted repeats, and class-specific motifs.\n\nA pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici.", "token_count": 199, "char_count": 894, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:55.980427", "source": { "split": "train_shard_00000", "doc_id": 1150 }, "chunk_id": "train_shard_00000_1150_0", "global_id": 1267 }, { "text": "In the present study, 30 L. monocytogenes strains isolated from bivalves purchased in Poland were characterized by whole genome sequencing (WGS). The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IIa; sequence types (ST) were ST101, ST21 and ST325; and clonal complexe (CC) were CC101. Despite differential genotypic subtypes, most strains had similar antimicrobial resistance profiles. Most strains had genetic determinants of resistance to many groups of antibiotics; aminoglycosides, fluoroquinolones, lincosamides, macrolides, peptides, phosphotic acids and sulfonamides. Phenotypic resistance analyzes showed that most strains were resistant to fosfomycin, additionally, resistance to lincomycin and tetracycline was observed in some strains. Almost all L. monocytogens strains classified as biofilm producers, which is related to the presence of genetic determinants (e.g. actA, prfA, dltA, fbpA, luxS). The findings of our study emphasize the potential risk to human health posed by L. monocytogenes strains obtained from bivalve mollusks. Additional investigations, particularly focusing on biofilm, may enhance our comprehension of the underlying mechanisms responsible for the remarkable ability of L. monocytogenes to remain on the shells of bivalves.\n\nInsights into the genetic diversity of Listeria monocytogenes from bivalves.", "token_count": 370, "char_count": 1399, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8413, "entities": { "genes": [ "ST21", "CC101", "ST325", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:56.912188", "source": { "split": "train_shard_00000", "doc_id": 1151 }, "chunk_id": "train_shard_00000_1151_0", "global_id": 1268 }, { "text": "The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and bacteriophage, regulate diverse features of bacterial cell physiology and impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of a paralogous XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. crescentus. We further discovered related XRE TFs throughout the class Alphaproteobacteria and its phages, including the φCbK Caulophage, suggesting that members of this cluster impact host-phage interactions. Here we show that a closely related group of XRE transcription factors encoded by both C. crescentus and φCbK can physically interact and function to control the transcription of a common gene set, influencing processes including holdfast development and the production of φCbK virions. The φCbK-encoded XRE paralog, tgrL, is highly expressed at the earliest stages of infection and can directly inhibit transcription of host genes including hfiA, a potent holdfast inhibitor, and gafYZ, an activator of prophage-like gene transfer agents (GTAs). XRE proteins encoded from the C. crescentus chromosome also directly repress gafYZ transcription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting the C. crescentus XRE transcription factors reduced φCbK burst size, while overexpressing these host genes or φCbK tgrL rescued this burst defect. We conclude that this XRE TF gene cluster, shared by C. crescentus and φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection.\n\nXRE transcription factors conserved in Caulobacter and φCbK modulate adhesin development and phage production.", "token_count": 488, "char_count": 1992, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5936, "quality_score": 0.7968, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:57.557399", "source": { "split": "train_shard_00000", "doc_id": 1152 }, "chunk_id": "train_shard_00000_1152_0", "global_id": 1269 }, { "text": "Streptococcus mutans is commonly associated with dental caries and the ability to form biofilms is essential for its pathogenicity. We recently identified the Pgf glycosylation machinery of S. mutans, responsible for the post-translational modification of the surface-associated adhesins Cnm and WapA. Since the four-gene pgf operon (pgfS-pgfM1-pgfE-pgfM2) is part of the S. mutans core genome, we hypothesized that the scope of the Pgf system goes beyond Cnm and WapA glycosylation. In silico analyses and tunicamycin sensitivity assays suggested a functional overlap between the Pgf machinery and the rhamnose-glucose polysaccharide synthesis pathway. Phenotypic characterization of pgf mutants (ΔpgfS, ΔpgfE, ΔpgfM1, ΔpgfM2, and Δpgf) revealed that the Pgf system is important for biofilm formation, surface charge, membrane stability, and survival in human saliva. Moreover, deletion of the entire pgf operon (Δpgf strain) resulted in significantly impaired colonization in a rat oral colonization model. Using Cnm as a model, we showed that Cnm is heavily modified with N-acetyl hexosamines but it becomes heavily phosphorylated with the inactivation of the PgfS glycosyltransferase, suggesting a crosstalk between these two post-translational modification mechanisms. Our results revealed that the Pgf machinery contributes to multiple aspects of S. mutans pathobiology that may go beyond Cnm and WapA glycosylation.\n\nPost-translational modification by the Pgf glycosylation machinery modulates Streptococcus mutans OMZ175 physiology and virulence.", "token_count": 424, "char_count": 1554, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5981, "quality_score": 0.7991, "entities": { "genes": [ "OMZ175" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:58.219843", "source": { "split": "train_shard_00000", "doc_id": 1153 }, "chunk_id": "train_shard_00000_1153_0", "global_id": 1270 }, { "text": "Diploid A-genome wheat (einkorn wheat) presents a nutrition-rich option as an ancient grain crop and a resource for the improvement of bread wheat against abiotic and biotic stresses. Realizing the importance of this wheat species, reference-level assemblies of two einkorn wheat accessions were generated (wild and domesticated). This work reports an einkorn genome database that provides an interface to the cereals research community to perform comparative genomics, applied genetics and breeding research. It features queries for annotated genes, the use of a recent genome browser release, and the ability to search for sequence alignments using a modern BLAST interface. Other features include a comparison of reference einkorn assemblies with other wheat cultivars through genomic synteny visualization and an alignment visualization tool for BLAST results. Altogether, this resource will help wheat research and breeding. Database URL  https://wheat.pw.usda.gov/GG3/pangenome.\n\nAn online database for einkorn wheat to aid in gene discovery and functional genomics studies.", "token_count": 245, "char_count": 1080, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8311, "entities": { "genes": [ "GG3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:58.730288", "source": { "split": "train_shard_00000", "doc_id": 1154 }, "chunk_id": "train_shard_00000_1154_0", "global_id": 1271 }, { "text": "Core genome multilocus sequence typing (cgMLST) has gained in popularity for bacterial typing since whole-genome sequencing (WGS) has become affordable. We introduce here pyMLST, a new complete, stand-alone, free and open source pipeline for cgMLST analysis. pyMLST can create or import a core genome database. For each gene, the first allele is aligned against the bacterial genome of interest using BLAT. Incomplete genes are aligned using MAFT. All data are stored in a SQLite database. pyMLST accepts assembly genomes or raw data (with the option pyMLST-KMA) as input. To evaluate our new tool, we selected three genome collections of major bacterial pathogens (\n\nIntroduction and benchmarking of pyMLST: open-source software for assessing bacterial clonality using core genome MLST.", "token_count": 192, "char_count": 787, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7288, "quality_score": 0.8644, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:59.199069", "source": { "split": "train_shard_00000", "doc_id": 1155 }, "chunk_id": "train_shard_00000_1155_0", "global_id": 1272 }, { "text": "The nucleotide-binding site-leucine-rich repeat (NBS-LRR) gene family is the largest group of disease resistance (R) genes in plants and is active in response to viruses, bacteria, and fungi usually involved in effector-triggered immunity (ETI). Pangenome-wide studies allow researchers to analyze the genetic diversity of multiple species or their members simultaneously, providing a comprehensive understanding of the evolutionary relationships and diversity present among them. The draft pan-genome of three\n\nComparative genomics profiling revealed multi-stress responsive roles of the CC-NBS-LRR genes in three mango cultivars.", "token_count": 141, "char_count": 631, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7711, "quality_score": 0.8855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:09:59.663567", "source": { "split": "train_shard_00000", "doc_id": 1156 }, "chunk_id": "train_shard_00000_1156_0", "global_id": 1273 }, { "text": "Inversions, a type of chromosomal structural variation, significantly influence plant adaptation and gene functions by impacting gene expression and recombination rates. However, compared with other structural variations, their roles in functional biology and crop improvement remain largely unexplored. In this review, we highlight technological and methodological advancements that have allowed a comprehensive understanding of inversion variants through the pangenome framework and machine learning algorithms. Genome editing is an efficient method for inducing or reversing inversion mutations in plants, providing an effective mechanism to modify local recombination rates. Given the potential of inversions in crop breeding, we anticipate increasing attention on inversions from the scientific community in future research and breeding applications.\n\nUnravelling inversions: Technological advances, challenges, and potential impact on crop breeding.", "token_count": 176, "char_count": 955, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7705, "quality_score": 0.8852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:00.132934", "source": { "split": "train_shard_00000", "doc_id": 1157 }, "chunk_id": "train_shard_00000_1157_0", "global_id": 1274 }, { "text": "Efficient pangenome indexes are promising tools for many applications, including rapid classification of nanopore sequencing reads. Recently, a compressed-index data structure called the \"move structure\" was proposed as an alternative to other BWT-based indexes like the FM index and r-index. The move structure uniquely achieves both O(r) space and O(1)-time queries, where r is the number of runs in the pangenome BWT. We implemented Movi, an efficient tool for building and querying move-structure pangenome indexes. While the size of the Movi's index is larger than the r-index, it scales at a smaller rate for pangenome references, as its size is exactly proportional to r, the number of runs in the BWT of the reference. Movi can compute sophisticated matching queries needed for classification - such as pseudo-matching lengths and backward search - at least ten times faster than the fastest available methods, and in some cases more than 30-fold faster. Movi achieves this speed by leveraging the move structure's strong locality of reference, incurring close to the minimum possible number of cache misses for queries against large pangenomes. We achieve still further speed improvements by using memory prefetching to attain a degree of latency hiding that would be difficult with other index structures like the r-index. Movi's fast constant-time query loop makes it well suited to real-time applications like adaptive sampling for nanopore sequencing, where decisions must be made in a small and predictable time interval.\n\nMovi: a fast and cache-efficient full-text pangenome index.", "token_count": 357, "char_count": 1596, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6598, "quality_score": 0.8299, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:00.703396", "source": { "split": "train_shard_00000", "doc_id": 1158 }, "chunk_id": "train_shard_00000_1158_0", "global_id": 1275 }, { "text": "The UCSC Genome Browser (https://genome.ucsc.edu) is a web-based genomic visualization and analysis tool that serves data to over 7,000 distinct users per day worldwide. It provides annotation data on thousands of genome assemblies, ranging from human to SARS-CoV2. This year, we have introduced new data from the Human Pangenome Reference Consortium and on viral genomes including SARS-CoV2. We have added 1,200 new genomes to our GenArk genome system, increasing the overall diversity of our genomic representation. We have added support for nine new user-contributed track hubs to our public hub system. Additionally, we have released 29 new tracks on the human genome and 11 new tracks on the mouse genome. Collectively, these new features expand both the breadth and depth of the genomic knowledge that we share publicly with users worldwide.\n\nThe UCSC Genome Browser database: 2024 update.", "token_count": 231, "char_count": 895, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6232, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:01.177235", "source": { "split": "train_shard_00000", "doc_id": 1159 }, "chunk_id": "train_shard_00000_1159_0", "global_id": 1276 }, { "text": "Eudragit S100-coated bile salt-containing liposomes were prepared and optimized by experimenting with different variables, including bile salt type and concentration, and the method of incorporation into liposomes using a model hydrophilic compound, 5-aminosalicylic acid (5-ASA). After optimizing the formulation, cellular uptake, and animal pharmacokinetic experiments were performed. The inclusion of sodium glycocholate (SG) into liposomes decreased liposome particle size and entrapment efficiency significantly but had no effect on zeta potential. The method of incorporating SG into the lipid or aqueous phase of the liposome did not notably impact the characteristics of the liposomes but the hydration media had a substantial effect on the entrapment efficiency of 5-ASA. In vitro drug release in different fluids simulating distinct gastrointestinal tract sections, indicated pH-dependent disintegration of the coating layer of coated SG-containing liposomes. The majority of the drug was retained when subjected to simulated gastric fluid (SGF) and fed-state simulated intestinal fluid (FeSSIF) (≈ 37% release after 2 h in SGF pH 1.2, followed by 3 h in FeSSIF pH 5). The remaining drug was subsequently released in phosphate-buffered saline pH 7.4 (≈ 85% release within 24 h). Increasing SG concentration in the liposomes decreased the amount of drug released in FeSSIF. Similar results were observed when SG was replaced with sodium taurocholate. Cellular uptake studies in Caco-2 cells demonstrated that all liposomal formulations (conventional liposomes, bile salt-containing liposomes, and coated bile salt-containing liposomes) have shown to be equally effective at increasing the cellular uptake compared to free fluorescein solution. In the pharmacokinetic study, coated bile salt-containing liposomes showed a lower C", "token_count": 484, "char_count": 1837, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:01.827122", "source": { "split": "train_shard_00000", "doc_id": 1160 }, "chunk_id": "train_shard_00000_1160_0", "global_id": 1277 }, { "text": "Optimization, cellular uptake, and in vivo evaluation of Eudragit S100-coated bile salt-containing liposomes for oral colonic delivery of 5-aminosalicylic acid.", "token_count": 51, "char_count": 160, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:02.198697", "source": { "split": "train_shard_00000", "doc_id": 1160 }, "chunk_id": "train_shard_00000_1160_1", "global_id": 1278 }, { "text": "Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.", "token_count": 504, "char_count": 1928, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [ "SA8", "PAMP2012", "PAMP2011", "SA10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:02.847631", "source": { "split": "train_shard_00000", "doc_id": 1161 }, "chunk_id": "train_shard_00000_1161_0", "global_id": 1279 }, { "text": "The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade.", "token_count": 41, "char_count": 138, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:03.214671", "source": { "split": "train_shard_00000", "doc_id": 1161 }, "chunk_id": "train_shard_00000_1161_1", "global_id": 1280 }, { "text": "The management of inflammatory states typically involves non-steroidal anti-inflammatory drugs (NSAIDs) and opiates. Understanding the mechanisms underlying the processing of nociceptive information from potential alternatives such as some polysaccharides may enable new and meaningful therapeutic approaches. In this study, α-D-mannan isolated from the Kluyveromyces marxianus cell wall produced antinociceptive effects in models of inflammatory pain (formalin and complete Freund's adjuvant tests). Furthermore, α-D-mannan reduced paw edema and interleukin-6 (IL-6) production after carrageenan-induced inflammation. The polysaccharide α-D-mannan was characterized by gas chromatography-mass spectrometry, methylation analysis, and spectroscopic techniques. Moreover, the Doehlert experimental design was applied to find the optimal conditions for biomass production, with the best conditions being 10.8 g/L and 117 h for the glucose concentration and the fermentation time, respectively. These results indicate that α-D-mannan from K. marxianus exerts anti-inflammatory and antinociceptive effects in mice, possibly via a mechanism dependent on the inhibition of IL-6 production.\n\nAntinociceptive and anti-inflammatory properties of α-D-mannan from the yeast Kluyveromyces marxianus: evidence for a role in interleukin-6 inhibition.", "token_count": 362, "char_count": 1335, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7152, "quality_score": 0.8576, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:03.796531", "source": { "split": "train_shard_00000", "doc_id": 1162 }, "chunk_id": "train_shard_00000_1162_0", "global_id": 1281 }, { "text": "BSEP (ABCB11) is an ATP-binding cassette transporter that is expressed in hepatocytes and extrudes bile salts into the canaliculi of the liver. BSEP dysfunction, caused by mutations or induced by drugs, is frequently associated with severe cholestatic liver disease. We report the cryo-EM structure of glibenclamide-bound human BSEP in nanodiscs, revealing the basis of small-molecule inhibition. Glibenclamide binds the apex of a central binding pocket between the transmembrane domains, preventing BSEP from undergoing conformational changes, and thus rationalizing the reduced uptake of bile salts. We further report two high-resolution structures of BSEP trapped in distinct nucleotide-bound states by using a catalytically inactivated BSEP variant (BSEP\n\nStructural basis of bile salt extrusion and small-molecule inhibition in human BSEP.", "token_count": 223, "char_count": 844, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7094, "quality_score": 0.8547, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:04.271417", "source": { "split": "train_shard_00000", "doc_id": 1163 }, "chunk_id": "train_shard_00000_1163_0", "global_id": 1282 }, { "text": "Recent evidence suggests that the protective effect of gut microbiota on intestinal inflammation can be achieved through a microbe-bile acids (BAs) mechanism. Galacto-oligosaccharides (GOS) are a kind of prebiotic that alter gut microbiota composition. To verify whether GOS has a protective effect on intestinal inflammation through a microbe-BAs mechanism, this research was performed in a lipopolysaccharide (LPS) porcine model with the presence or absence of GOS. GOS prevented LPS-induced production of pro-inflammatory cytokines, the decrease of bacterial bile salt hydrolase-containing bacteria abundance, and the decrease of chendoxycholic acid (CDCA) level in piglets. Additionally, CDCA decreased LPS-induced production of pro-inflammatory cytokines, induced the expression of the takeda G-protein receptor 5 (TGR5), and its downstream cyclic adenosine monophosphate (cAMP) production in lamina propria-derived CD11b\n\nGalacto-Oligosaccharides Alleviate LPS-Induced Immune Imbalance in Small Intestine through Regulating Gut Microbe Composition and Bile Acid Pool.", "token_count": 301, "char_count": 1073, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6906, "quality_score": 0.8453, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:04.838151", "source": { "split": "train_shard_00000", "doc_id": 1164 }, "chunk_id": "train_shard_00000_1164_0", "global_id": 1283 }, { "text": "Bile acids and salts have been shown to play a role in liver carcinogenesis through DNA damage, inflammation, and tumor proliferation. However, the correlation between bile acid metabolism and hepatocellular carcinoma (HCC) prognosis remains unclear. This study aimed to identify a predictive signature of bile acid and bile salt metabolism-related long non-coding RNAs (lncRNAs) for HCC prognosis and treatment response. The study used HCC RNA-sequencing data and corresponding clinical and prognostic data from The Cancer Genome Atlas. A prognostic model consisting of five bile acid and bile salt metabolism-related lncRNAs was developed and evaluated in a training set, a validation set and an external set. The model demonstrated good performance in predicting HCC prognosis and was shown to be an independent biomarker for prognosis. Additionally, our study revealed a significant association between the signature and immune cell infiltration, as well as its predictive value for therapeutic responses to both immunotherapy and chemotherapy. Furthermore, three LncRNAs (LUCAT1, AL031985.3 and AC015908.3) expression levels in our signature were validated through qRT-PCR in a cohort of 50 pairs of HCC patient tumor samples and corresponding adjacent non-tumor samples, along with 10 samples of normal liver tissue adjacent to benign lesions. These findings suggest that this novel bile acid and bile salt metabolism-related lncRNA signature can independently predict the prognosis of patients with HCC and may be utilized as a potential predictor of response to treatment in this setting.\n\nIdentification of a bile acid and bile salt metabolism-related lncRNA signature for predicting prognosis and treatment response in hepatocellular carcinoma.", "token_count": 439, "char_count": 1754, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5551, "quality_score": 0.7776, "entities": { "genes": [ "AL031985", "AC015908", "LUCAT1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:05.472259", "source": { "split": "train_shard_00000", "doc_id": 1165 }, "chunk_id": "train_shard_00000_1165_0", "global_id": 1284 }, { "text": "Neisseria gonorrhoeae (Ngo) has emerged as a global threat leading to one of the most common sexually transmitted diseases in the world. It has also become one of the leading antimicrobial resistant organisms, resulting in fewer treatment options and an increased morbidity. Therefore, in recent years, there has been an increased focus on the development of new treatments and preventive strategies to combat its infection. In this study, we have combined the most conserved epitopes from the completely assembled strains of Ngo to develop a universal and a thermodynamically stable vaccine candidate. For our vaccine design, the epitopes were selected for their high immunogenicity, non-allergenicity and non-cytotoxicity, making them the ideal candidates for vaccine development. For the screening process, several reverse vaccinology tools were employed to rigorously extract non-homologous and immunogenic epitopes from the selected proteins. Consequently, a total number of 3 B-cell epitopes and 6 T-cell epitopes were selected and joined by multiple immune-modulating adjuvants and linkers to generate a promiscuous immune response. Additionally, the stability and flexible nature of the vaccine construct was confirmed using various molecular dynamic simulation tools. Overall, the vaccine candidate showed promising binding affinity to various HLA alleles and TLR receptors; however, further studies are needed to assess its efficacy in-vivo. In this way, we have designed a multi-subunit vaccine candidate to potentially combat and control the spread of N. gonorrhoeae.\n\nCharacterization of exclusively non-commensal Neisseria gonorrhoeae pangenome to prioritize globally conserved and thermodynamically stable vaccine candidates using immune-molecular dynamic simulations.", "token_count": 399, "char_count": 1783, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6437, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:06.091772", "source": { "split": "train_shard_00000", "doc_id": 1166 }, "chunk_id": "train_shard_00000_1166_0", "global_id": 1285 }, { "text": "The main objective of this research was to identify potential probiotic candidates belonging to the Bacillus species that could demonstrate tolerance to bile salt and acidic conditions. The study focused on isolating Bacillus strains from the intestine of marine fish-Microstomus kitt. The isolation process involved the use of selective MRS media through the pour plate method. After 24 h, one particular isolate was identified based on its morphological and biochemical traits as Bacillus species. To confirm the identity, molecular characterization of the 16S RNA from the isolated strain was performed, and the sequence analysis verified it as Bacillus subtilis strain ACL_BS 001. With the molecular confirmation, the next step was to assess the probiotic characteristics of this B. subtilis strain. Various tests were conducted to evaluate its acid/pH tolerance, NaCl tolerance, and bile salt tolerance. The results indicated that B. subtilis exhibited high viability percentages even under acidic pH, in the presence of 1.5% bile salt, and at high salt concentrations. Subsequently, we investigated the strain's ability to produce lipase, an important enzyme with potential industrial applications. B. subtilis was grown in MRS agar amended with olive oil as a lipase substrate. After incubation, the presence of lipase activity was confirmed, and the enzymatic assay revealed a significant lipase enzyme activity of 100.23 µmoles/ml of the sample. In conclusion, the study successfully isolated and identified B. subtilis from the intestine of Microstomus kitt, and the strain exhibited promising probiotic characteristics, including resistance to bile salt and acidic conditions. Furthermore, the strain was found to produce lipase, which opens up possibilities for future research focusing on isolating and purifying the lipase from this potential probiotic B. subtilis strain.\n\nUnlocking the Gut's Treasure: Lipase-Producing Bacillus subtilis Probiotic from the Intestine of Microstomus kitt (Lemon sole).", "token_count": 483, "char_count": 2015, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5529, "quality_score": 0.7765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:06.745198", "source": { "split": "train_shard_00000", "doc_id": 1167 }, "chunk_id": "train_shard_00000_1167_0", "global_id": 1286 }, { "text": "The urge of designing new safe and natural functional foods to control blood lipids and dispensable without the need of physician supervision, has increased especially after the coming into effect of the recent EU Commission regulation 2022/860, that regulates the consumption of \"red yeast rice,\" made by fermentation of rice with\n\nITC study on the interaction of some bile salts with tragacanth, Arabic, and guar gums with potential cholesterol-lowering ability.", "token_count": 109, "char_count": 464, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:07.132454", "source": { "split": "train_shard_00000", "doc_id": 1168 }, "chunk_id": "train_shard_00000_1168_0", "global_id": 1287 }, { "text": "The silkworm Bombyx mori is a domesticated insect that serves as an animal model for research and agriculture. The silkworm super-pan-genome dataset, which we published last year, is a unique resource for the study of global genomic diversity and phenotype-genotype association. Here we present SilkMeta (http://silkmeta.org.cn), a comprehensive database covering the available silkworm pan-genome and multi-omics data. The database contains 1082 short-read genomes, 546 long-read assembled genomes, 1168 transcriptomes, 294 phenotype characterizations (phenome), tens of millions of variations (variome), 7253 long non-coding RNAs (lncRNAs), 18 717 full length transcripts and a set of population statistics. We have compiled publications on functional genomics research and genetic stock deciphering (mutant map). A range of bioinformatics tools is also provided for data visualization and retrieval. The large batch of omics data and tools were integrated in twelve functional modules that provide useful strategies and data for comparative and functional genomics research. The interactive bioinformatics platform SilkMeta will benefit not only the silkworm but also the insect biology communities.\n\nSilkMeta: a comprehensive platform for sharing and exploiting pan-genomic and multi-omic silkworm data.", "token_count": 320, "char_count": 1307, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6798, "quality_score": 0.8399, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:07.699256", "source": { "split": "train_shard_00000", "doc_id": 1169 }, "chunk_id": "train_shard_00000_1169_0", "global_id": 1288 }, { "text": "Eco-friendly alternatives such as probiotics are needed to prevent economically relevant infectious diseases for a successful disease-free harvest in aquaculture. The use of antibiotics has been the favored practice, but its empirical and indiscriminate use has led to antibiotic resistance in the aquatic environment and residues in the food fish. With this rationale, a probiotic was isolated from tilapia, a commercially important cultured fish worldwide. The characteristics of the probiotic were checked against common bacterial pathogens affecting aquaculture. In vitro tests demonstrated the inhibitory effects of the isolated probiotic on the growth of Aeromonas hydrophila, Edwardsiella tarda, Vibrio anguillarum, and V. alginolyticus. The candidate probiotic, referred to as TLDK301120C24, was identified as Bacillus subtilis by a battery of biochemical tests and genotypic confirmation by 16S rDNA sequencing. The in vitro results revealed the ability of the probiotic to withstand the gut conditions that included pH range of 3-9, salt concentration of 0.5-6%, and bile salt concentration of up to 6%. The isolate could hydrolyze starch (12-14 mm clearance zone), protein (20-22 mm clearance zone), and cellulose (22-24 mm clearance zone). Further, the inhibitory ability of the probiotic against aquatic pathogens was determined in vivo using gnotobiotic zebrafish by employing a novel approach that involved tagging the probiotic with a red fluorescent protein and the pathogens with a green fluorescent protein, respectively. The colonizing ability of probiotics and its inhibitory effects against the pathogens were evaluated by fluorescence microscopy, PCR, and estimation of viable counts in LBA + Amp plates. Finally, the competitive inhibition and exclusion of fish pathogens A. hydrophila and E. tarda by B. subtilis was confirmed semi-quantitatively, through challenge experiments. This study shows the potential of B. subtilis as a probiotic and its excellent ability to inhibit major fish pathogens in vivo and in vitro", "token_count": 523, "char_count": 2043, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5724, "quality_score": 0.7862, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:10:08.368157", "source": { "split": "train_shard_00000", "doc_id": 1170 }, "chunk_id": "train_shard_00000_1170_0", "global_id": 1289 }, { "text": "It also shows promise as a potent substitute for antibiotics.\n\nIn vitro determination of probiotic efficacy of Bacillus subtilis TLDK301120C24 isolated from tilapia against warm water fish pathogens and in vivo validation using gnotobiotic zebrafish model.", "token_count": 75, "char_count": 256, "word_count": 36, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:08.736226", "source": { "split": "train_shard_00000", "doc_id": 1170 }, "chunk_id": "train_shard_00000_1170_1", "global_id": 1290 }, { "text": "Because of the heterogeneity among seedlings of outbreeding species, the use of seedling tissues as a source of DNA is unsuitable for the genomic characterization of elite germplasms. High-quality DNA, free of RNA, proteins, polysaccharides, secondary metabolites, and shearing, is mandatory for downstream molecular biology applications, especially for next-generation genome sequencing and pangenome analysis aiming to capture the complete genetic diversity within a species. The study aimed to accomplish an efficient protocol for the extraction of high-quality DNA suitable for diverse plant species/tissues. We describe a reliable, and consistent protocol suitable for the extraction of DNA from 42 difficult-to-extract plant species belonging to 33 angiosperm (monocot and dicot) families, including tissues such as seeds, roots, endosperm, and flower/fruit tissues. The protocol was first optimized for the outbreeding recalcitrant trees viz., Prosopis cineraria, Conocarpus erectus, and Phoenix dactylifera, which are rich in proteins, polysaccharides, and secondary metabolites, and the quality of the extracted DNA was confirmed by downstream applications. Nine procedures were attempted to extract high-quality, impurities-free DNA from these three plant species. Extraction of the ethanol-precipitated DNA from cetyltrimethylammonium bromide (CTAB) protocol using sodium dodecyl sulfate (SDS) buffer, i.e., the extraction using a cationic (CTAB) detergent followed by an anionic (SDS) detergent was the key for high yield and high purity (1.75-1.85 against A\n\nCationic and anionic detergent buffers in sequence yield high-quality genomic DNA from diverse plant species.", "token_count": 423, "char_count": 1681, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:09.364941", "source": { "split": "train_shard_00000", "doc_id": 1171 }, "chunk_id": "train_shard_00000_1171_0", "global_id": 1291 }, { "text": "The simulated in-vitro gastrointestinal method provides a simple way to evaluate the health risk of human body exposed to soil contaminants. Several in-vitro methods have been successfully established for soil As, Pb, and Cd. However, the method development for soil Cr failed up to now, which could be resulted from alteration in the species of Cr (e.g., Cr(VI)/Cr(III)) caused by the gastrointestinal digestion components, ultimately affecting the accessibility of Cr. This study explored the transformation and bioaccessibility of Cr in two Cr-contaminated soils during the physiologically based extraction test. The water-soluble and exchangeable Cr in soil was dissolved in gastrointestinal tract, accompanied with reduction of Cr(VI) into Cr(III), and the reduction occurred after the chemical extraction in two soils rather than during the extraction. Pepsin and organic acids in gastric phase could reduce Cr(VI) into Cr(III) and reduction efficiency were 20.4%- 53.0%, while in intestinal phase, pancreatin and bile salt had little effect on the Cr(VI) reduction, instead, more Cr(VI) was released from soil. In the gastric solution, Cr(VI) was mainly present as HCrO\n\nDigestive fluid components affect speciation and bioaccessibility and the subsequent exposure risk of soil chromium from stomach to intestinal phase in in-vitro gastrointestinal digestion.", "token_count": 339, "char_count": 1366, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:09.941188", "source": { "split": "train_shard_00000", "doc_id": 1172 }, "chunk_id": "train_shard_00000_1172_0", "global_id": 1292 }, { "text": "Virgibacillus salarius 19.PP.SC1.6 is a coral symbiont isolated from Indonesia's North Java Sea; it has the ability to produce secondary metabolites that provide survival advantages and biological functions, such as ectoine, which is synthesized by an ectoine gene cluster. Apart from being an osmoprotectant for bacteria, ectoine is also known as a chemical chaperone with numerous biological activities such as maintaining protein stability, which makes ectoine in high demand in the market industry and makes it beneficial to investigate V. salarius ectoine. However, there has been no research on genome-based secondary metabolite and ectoine gene cluster characterization from Indonesian marine V. salarius. In this study, we performed a genomic analysis and ectoine identification of V. salarius. A high-quality draft genome with total size of 4.45 Mb and 4426 coding sequence (CDS) was characterized and then mapped into the Cluster of Orthologous Groups (COG) category. The genus Virgibacillus has an \"open\" pangenome type with total of 18 genomic islands inside the V. salarius 19.PP.SC1.6 genome. There were seven clusters of secondary metabolite-producing genes found, with a total of 80 genes classified as NRPS, PKS (type III), terpenes, and ectoine biosynthetic related genes. The ectoine gene cluster forms one operon consists of ectABC gene with 2190 bp gene cluster length, and is successfully characterized. The presence of ectoine in V. salarius was confirmed using UPLC-MS/MS operated in Multiple Reaction Monitoring (MRM) mode, which indicates that V. salarius has an intact ectoine gene clusters and is capable of producing ectoine as compatible solutes.\n\nBiosynthetic gene cluster profiling from North Java Sea Virgibacillus salarius reveals hidden potential metabolites.", "token_count": 463, "char_count": 1794, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [ "SC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:10.593267", "source": { "split": "train_shard_00000", "doc_id": 1173 }, "chunk_id": "train_shard_00000_1173_0", "global_id": 1293 }, { "text": "The wide adoption of bacterial genome sequencing and encoding both core and accessory genome variation using\n\nReduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric", "token_count": 46, "char_count": 222, "word_count": 27, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:10.975432", "source": { "split": "train_shard_00000", "doc_id": 1174 }, "chunk_id": "train_shard_00000_1174_0", "global_id": 1294 }, { "text": "Chromosomal structural variation (SV) encompasses a heterogenous class of genetic variants that exerts strong influences on human health and disease. Despite their importance, many structural variants (SVs) have remained poorly characterized at even a basic level, a discrepancy predicated upon the technical limitations of prior genomic assays. However, recent advances in genomic technology can identify and localize SVs accurately, opening new questions regarding SV risk factors and their impacts in humans. Here, we first define and classify human SVs and their generative mechanisms, highlighting characteristics leveraged by various SV assays. We next examine the first-ever gapless assembly of the human genome and the technical process of assembling it, which required third-generation sequencing technologies to resolve structurally complex loci. The new portions of that \"telomere-to-telomere\" and subsequent pangenome assemblies highlight aspects of SV biology likely to develop in the near-term. We consider the strengths and limitations of the most promising new SV technologies and when they or longstanding approaches are best suited to meeting salient goals in the study of human SV in population-scale genomics research, clinical, and public health contexts. It is a watershed time in our understanding of human SV when new approaches are expected to fundamentally change genomic applications.\n\nApplications of advanced technologies for detecting genomic structural variation.", "token_count": 304, "char_count": 1494, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:11.595501", "source": { "split": "train_shard_00000", "doc_id": 1175 }, "chunk_id": "train_shard_00000_1175_0", "global_id": 1295 }, { "text": "Bulevirtide (BLV) is a small lipopeptide agent that specifically binds to the sodium taurocholate cotransporting polypeptide (NTCP) bile salt transporter and HBV/HDV receptor on the surface of human hepatocytes and inhibits HDV and HBV entry. As a satellite virus of HBV, HDV virions are formed after assembly of HDV RNA with the HBV envelope proteins (HBsAg). Because both viruses exist as eight different genotypes, this creates a potential for high diversity in the HBV/HDV combinations. To investigate the sensitivity of various combinations of HBV/HDV genotypes to BLV, clinical and laboratory strains were assessed.\n\nBroad-spectrum activity of bulevirtide against clinical isolates of HDV and recombinant pan-genotypic combinations of HBV/HDV.", "token_count": 210, "char_count": 749, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7315, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:12.083699", "source": { "split": "train_shard_00000", "doc_id": 1176 }, "chunk_id": "train_shard_00000_1176_0", "global_id": 1296 }, { "text": "Mycoplasma iowae is a worldwide spread and economically important avian pathogen that mostly infects turkeys. Currently, multi-locus sequence typing (MLST) serves as the gold standard method for strain identification in M. iowae. However, additional robust genotyping methods are required to effectively monitor M. iowae infections and conduct epidemiological investigations. The first aim of this study was to develop genotyping assays with high resolution, that specifically target M. iowae, namely a multiple-locus variable number of tandem-repeats analysis (MLVA) and a core genome multi-locus sequence typing (cgMLST) schema. The second aim was the determination of relationships among a diverse selection of M. iowae strains and clinical isolates with a previous and the newly developed assays. The MLVA was designed based on the analyses of tandem-repeat (TR) regions in the six serotype reference strains (I, J, K, N, Q and R). The cgMLST schema was developed based on the coding sequences (CDSs) common in 95% of the examined 99 isolates. The samples were submitted for a previously published MLST assay for comparison with the developed methods. Out of 94 TR regions identified, 17 alleles were selected for further evaluation by PCR. Finally, seven alleles were chosen to establish the MLVA assay. Additionally, whole genome sequence analyses identified a total of 676 CDSs shared by 95% of the isolates, all of which were included into the developed cgMLST schema. The MLVA discriminated 19 distinct genotypes (GT), while with the cgMLST assay 79 sequence types (ST) could be determined with Simpson's diversity indices of 0.810 (MLVA) and 0.989 (cgMLST). The applied assays consistently identified the same main clusters among the diverse selection of isolates, thereby demonstrating their suitability for various genetic analyses and their ability to yield congruent results.\n\nDevelopment of molecular assays for the analysis of genetic relationships of Mycoplasma iowae.", "token_count": 486, "char_count": 1985, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:12.732204", "source": { "split": "train_shard_00000", "doc_id": 1177 }, "chunk_id": "train_shard_00000_1177_0", "global_id": 1297 }, { "text": "Non-albicans Candida species, such as Candida kefyr, are emerging pathogens. Chromogenic media are highly useful for the diagnosis of urinary tract infections (UTIs). The aim was to describe the behavior of this specie on a non-specific chromogenic medium.\n\nConcerning the presumptive identification of Candida kefyr on Uriselect™4 agar.", "token_count": 90, "char_count": 337, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:13.110506", "source": { "split": "train_shard_00000", "doc_id": 1178 }, "chunk_id": "train_shard_00000_1178_0", "global_id": 1298 }, { "text": "Self-assembly with chitosan is a promising method for improving bile salt (BS) adsorption by coconut residue fiber (CRF). To study the self-assembly process, three pre-treatments were performed and investigated using microrheological analysis. The effects of the pretreatments on the self-assembly of CRF and the BS adsorption were evaluated. During self-assembly, CRFs underwent Brownian-like motion, and the addition of chitosan facilitated the formation of inter-particle interactions between CRFs in the system. These interactions were small in extent, large in number, and slow to state change, in addition to relatively high strength and longer maintenance, all of which contributed to the binding to BS. The conventional pretreatments failed to effectively improve the BS adsorption of the self-assembled CRFs and weakened the inter-particle interactions in the system. These results suggest that chitosan assists in the adsorption of self-assembled CRF to BS through a combination of H-bonds and other weak intermolecular forces.\n\nSelf-assembly of coconut residue fiber with chitosan: Effect of three pre-treatments on the self-assembly process and bile salt adsorption.", "token_count": 276, "char_count": 1178, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5449, "quality_score": 0.7725, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:13.671318", "source": { "split": "train_shard_00000", "doc_id": 1179 }, "chunk_id": "train_shard_00000_1179_0", "global_id": 1299 }, { "text": "Stenotrophomonas maltophilia is a rapidly evolving multidrug-resistant opportunistic pathogen that can cause serious infections in immunocompromised patients. Although phage therapy is one of promising strategies for dealing with MDR bacteria, the main challenges of phage therapeutics include accumulation of phage resistant mutations and acquisition of the phage defense systems. To systematically evaluate the impact of (pro)phages in shaping genetic and evolutionary diversity of S. maltophilia, we collected 166 S. maltophilia isolates from three hospitals in southern China to analyze its pangenome, virulence factors, prophage regions, and anit-viral immune systems. Pangenome analysis indicated that there are 1328 saturated core genes and 26961 unsaturated accessory genes in the pangenome, suggesting existence of highly variable parts of S. maltophilia genome. The presence of genes in relation to T3SS and T6SS mechanisms suggests the great potential to secrete toxins by the S. maltophilia population, which is contrary to the conventional notion of low-virulence of S. maltophilia. Additionally, we characterized the pan-immune system maps of these clinical isolates against phage infections and revealed the co-harboring of CBASS and anti-CBASS in some strains, suggesting a never-ending arms race and the co-evolutionary dynamic between bacteria and phages. Furthermore, our study predicted 310 prophage regions in S. maltophilia with high genetic diversity. Six viral defense systems were found to be located at specific position of the S. maltophilia prophage genomes, indicating potential evolution of certain site/region similar to bacterial 'defense islands' in prophage. Our study provides novel insights into the S. maltophilia pangenome in relation to phage-defense mechanisms, which extends our understanding of bacterial-phage interactions and might guide the application of phage therapy in combating S. maltophilia infections.\n\nGenomic insights into the phage-defense systems of Stenotrophomonas maltophilia clinical isolates.", "token_count": 492, "char_count": 2054, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:15.217596", "source": { "split": "train_shard_00000", "doc_id": 1180 }, "chunk_id": "train_shard_00000_1180_0", "global_id": 1300 }, { "text": "Streptococcus thermophilus, the only Streptococcus species considered \"Generally Recognized Safe\", has been used widely in the food industry. This bacterium is one of the most valuable industrial lactic acid bacterial species. Due to the importance of this bacterium in industrial applications, it should be stored for a long time without losing its metabolic properties. The present study aimed to investigate the cryoprotectant effect of three compatible solutes (ectoine, trehalose, and sucrose) on bacterial cells stored at different temperatures (frozen at -80 °C or freeze-dried and subsequently stored at +4, -20, and -80 °C) for three months. The bacterial cells were tested for cell viability, bile salt tolerance, and lactic acid production before and after processing. The highest cell viability, bile salt tolerance, and lactic acid production were obtained with ectoine and under frozen (storage at -80 °C) conditions. In freeze-dried and subsequently stored at various temperatures, the best preservation was obtained at -80 °C, followed by -20 °C and +4 °C. Moreover, when ectoine's preservation potential was compared to other cryoprotectants, ectoine showed the highest preservation, followed by trehalose and sucrose. Although ectoine has a variety of qualities that have been proven, in the current work, we have shown for the first time that ectoine has cryoprotectant potential in yogurt starter cultures (S. thermophilus).\n\nUsage of ectoine as a cryoprotectant for cryopreservation of lactic acid bacteria.", "token_count": 379, "char_count": 1528, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5929, "quality_score": 0.7965, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:15.805036", "source": { "split": "train_shard_00000", "doc_id": 1181 }, "chunk_id": "train_shard_00000_1181_0", "global_id": 1301 }, { "text": "Structural variations have emerged as an important driving force for genome evolution and phenotypic variation in various organisms, yet their contributions to genetic diversity and adaptation in domesticated animals remain largely unknown. Here we constructed a pangenome based on 250 sequenced individuals from 32 pig breeds in Eurasia and systematically characterized coding sequence presence/absence variations (PAVs) within pigs. We identified 308.3-Mb nonreference sequences and 3438 novel genes absent from the current reference genome. Gene PAV analysis showed that 16.8% of the genes in the pangene catalog undergo PAV. A number of newly identified dispensable genes showed close associations with adaptation. For instance, several novel swine leukocyte antigen (SLA) genes discovered in nonreference sequences potentially participate in immune responses to productive and respiratory syndrome virus (PRRSV) infection. We delineated previously unidentified features of the pig mobilome that contained 490,480 transposable element insertion polymorphisms (TIPs) resulting from recent mobilization of 970 TE families, and investigated their population dynamics along with influences on population differentiation and gene expression. In addition, several candidate adaptive TE insertions were detected to be co-opted into genes responsible for responses to hypoxia, skeletal development, regulation of heart contraction, and neuronal cell development, likely contributing to local adaptation of Tibetan wild boars. These findings enhance our understanding on hidden layers of the genetic diversity in pigs and provide novel insights into the role of SVs in the evolutionary adaptation of mammals.\n\nThe pig pangenome provides insights into the roles of coding structural variations in genetic diversity and adaptation.", "token_count": 384, "char_count": 1824, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:16.416801", "source": { "split": "train_shard_00000", "doc_id": 1182 }, "chunk_id": "train_shard_00000_1182_0", "global_id": 1302 }, { "text": "A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes.\n\nComparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.", "token_count": 167, "char_count": 797, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7476, "quality_score": 0.8738, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:16.861207", "source": { "split": "train_shard_00000", "doc_id": 1183 }, "chunk_id": "train_shard_00000_1183_0", "global_id": 1303 }, { "text": "The emergence of antimicrobial-resistant, livestock-associated Enterococcus faecalis represents a public health concern. Here, we report the isolation, molecular detection of virulence and antimicrobial resistance determinants, in addition to the phylogenetic analyses of 20 Enterococcus species using whole genome sequencing analysis of 15 Enterococcus faecalis strains including six strains of three novel sequence types, three Enterococcus faecium and two Enterococcus durans. All strains were isolated from food chain animals in South Africa. Enterococcus strains were isolated on bile aesculin azide agar, followed by identification using MALDI-TOF MS analysis. Antibiotic susceptibility testing was performed using the Kirby-Bauer disk diffusion method. The genomic DNA of the isolates was extracted and sequencing was performed using the Illumina MiSeq platform. Sequence reads were trimmed and de novo assembled. The assembled contigs were analyzed for antimicrobial resistance genes and chromosomal mutations, extra-chromosomal plasmids, and multi-locus sequence type (MLST). Multidrug antimicrobial resistance genes conferring resistance to aminoglycosides (ant(6)-Ia, aph(3')-IIIa, sat4, and spw), lincosamides (lnu(B), lsa(A), and lsa(E)), macrolides (erm(B)), trimethoprim (dfrG) and tetracyclines (tet(L) and tet(M)) were identified. Plasmid replicons were detected in seven E. faecalis and three E. faecium isolates. The sequence type (ST) of each isolate was determined using the Enterococcus PubMLST database. Ten STs were identified in the collection, three of which (ST1240, ST1241, and ST1242) have not been previously reported and are described in the present study for the first time. To compare the sequenced strains to other previously sequenced E. faecalis strains, assembled sequences of E. faecalis from livestock were downloaded from the PubMLST database. Core genome-based phylogenetic analysis was performed using ParSNP", "token_count": 528, "char_count": 1950, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [ "ST1240", "ST1241", "ST1242" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:10:17.490310", "source": { "split": "train_shard_00000", "doc_id": 1184 }, "chunk_id": "train_shard_00000_1184_0", "global_id": 1304 }, { "text": "The detection of multiple drug-resistance in Enterococcus including E. faecalis and E. faecium highlights the significance of genomic surveillance to monitor the spread of antimicrobial resistance in food chain animals. In addition, the genome sequences of Enterococcus strains reported in the present study will serve as a reference point for future molecular epidemiological studies of livestock-associated and antibiotic-resistant E. faecalis in Africa. In addition, this study enables the in-depth analysis of E. faecalis genomic structure, as well as provides valuable information on the phenotypic and genotypic antimicrobial resistance, and the pathogenesis of livestock-associated E. faecalis and E. faecium.\n\nAntimicrobial resistance and whole genome sequencing of novel sequence types of Enterococcus faecalis, Enterococcus faecium, and Enterococcus durans isolated from livestock.", "token_count": 222, "char_count": 891, "word_count": 119, "semantic_coherence": 1, "information_density": 0.5966, "quality_score": 0.7983, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:17.961367", "source": { "split": "train_shard_00000", "doc_id": 1184 }, "chunk_id": "train_shard_00000_1184_1", "global_id": 1305 }, { "text": "Gap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs.", "token_count": 22, "char_count": 72, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:18.323108", "source": { "split": "train_shard_00000", "doc_id": 1185 }, "chunk_id": "train_shard_00000_1185_0", "global_id": 1306 }, { "text": "Costunolide (COST) is a sesquiterpene lactone that belongs to the germacranolide group, and occurs mainly in Saussurea lappa Clarke. Although COST inhibits the proliferation and metastasis of cancer cells and induces their apoptosis, it suffers poor water solubility and cellular permeability. Therefore, this study aimed to enhance the anti-proliferative activity of COST in LS174T colon cancer cells through its inclusion in bilosomal nanoformulation (COST-BILs). The optimized BIL formula contained cholesterol and Span-85 in a molar ratio of 1:5 as well as bile salt at a molar concentration of 0.5 mM, with entrapment efficiency of 63.4 ± 3.59 % and particle size of 119.7 ± 3.63 nm. The optimized COST-BILs showed a potent cytotoxic effect against LS174T cells with an IC\n\nOptimized bilosome-based nanoparticles enhance cytotoxic and pro-apoptotic activity of costunolide in LS174T colon cancer cells.", "token_count": 284, "char_count": 907, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [ "LS174T" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:18.876879", "source": { "split": "train_shard_00000", "doc_id": 1186 }, "chunk_id": "train_shard_00000_1186_0", "global_id": 1307 }, { "text": "Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for genes using alternative start codons to be misreported or completely omitted. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns regions that may contain missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show this methodology recovers genes missing from canonical genome annotations. We inspect the results of the genomes of model organisms, the pangenome of Escherichia coli, and a set of 5109 prokaryotic genomes of 247 genera from the Ensembl Bacteria database. StORF-Reporter extended the core, soft-core and accessory gene collections, identified novel gene families and extended families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORFs are likely to be functional genes that should now be considered for inclusion in canonical annotations.\n\nStORF-Reporter: finding genes between genes.", "token_count": 332, "char_count": 1405, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:19.446871", "source": { "split": "train_shard_00000", "doc_id": 1187 }, "chunk_id": "train_shard_00000_1187_0", "global_id": 1308 }, { "text": "Solubility is a critical parameter controlling drug absorption after oral administration. For poorly soluble drugs, solubility is influenced by the complex composition of intestinal media and the influence of dosage form excipients, which can cause bioavailability and bioequivalence issues. This study has applied a small scale design of experiment (DoE) equilibrium solubility approach in order to investigate the impact of excipients on fenofibrate solubility in simulated fasted and fed intestinal media. Seven media parameters (bile salt (BS), phospholipid (PL), fatty acid, monoglyceride, cholesterol, pH and BS/PL ratio) were assessed in the DoE and in excipient-free media, and only pH and sodium oleate in the fasted state had a significant impact on fenofibrate solubility. The impact of excipients were studied at two concentrations, and for polyvinylpyrrolidone (PVP, K12 and K29/32) and hydroxypropylmethylcellulose (HPMC, E3 and E50), two grades were studied. Mannitol had no solubility impact in any of the DoE media. PVP significantly increased solubility in a media-, grade- and concentration-dependent manner, with the biggest change in fasted media. HPMC and chitosan significantly reduced solubility in both fasted and fed states in a media-, grade- and concentration-dependent manner. The results indicate that the impact of excipients on fenofibrate solubility is a complex interplay of media composition in combination with their physicochemical properties and concentration. The results indicate that in vitro solubility studies combining the drug of interest, proposed excipients along with suitable simulated intestinal media recipes will provide interesting information with the potential to guide formulation development.\n\nExcipient Impact on Fenofibrate Equilibrium Solubility in Fasted and Fed Simulated Intestinal Fluids Assessed Using a Design of Experiment Protocol.", "token_count": 454, "char_count": 1899, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5451, "quality_score": 0.7726, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:20.086417", "source": { "split": "train_shard_00000", "doc_id": 1188 }, "chunk_id": "train_shard_00000_1188_0", "global_id": 1309 }, { "text": "Secondary metabolites (SMs) from environmental bacteria offer viable solutions for various health and environmental challenges. Researchers are employing advanced bioinformatic tools to investigate less-explored microorganisms and unearth novel bioactive compounds. In this research area, our understanding of SMs from environmental Gram-negative bacteria lags behind that of its Gram-positive counterparts. In this regard,\n\nThe Pangenome of Gram-Negative Environmental Bacteria Hides a Promising Biotechnological Potential.", "token_count": 111, "char_count": 524, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:20.473465", "source": { "split": "train_shard_00000", "doc_id": 1189 }, "chunk_id": "train_shard_00000_1189_0", "global_id": 1310 }, { "text": "The bioluminescent symbiosis involving the urchin cardinalfish, Siphamia tubifer, and Photobacterium mandapamensis, a luminous member of the Vibrionaceae, is highly specific compared to other bioluminescent fish-bacteria associations. Despite this high degree of specificity, patterns of genetic diversity have been observed for the symbionts from hosts sampled over relatively small spatial scales. We characterized and compared sub-species, strain-level symbiont diversity within and between S. tubifer hosts sampled from the Philippines and Japan using PCR fingerprinting. We then carried out whole genome sequencing of the unique symbiont genotypes identified to characterize the genetic diversity of the symbiont community and the symbiont pangenome. We determined that an individual light organ contains six symbiont genotypes on average, but varied between 1-13. Additionally, we found that there were few genotypes shared between hosts from the same location. A phylogenetic analysis of the unique symbiont strains indicated location-specific clades, suggesting some genetic differentiation in the symbionts between host populations. We also identified symbiont genes that were variable between strains, including luxF, a member of the lux operon, which is responsible for light production. We quantified the light emission and growth rate of two strains missing luxF along with the other strains isolated from the same light organs and determined that strains lacking luxF were dimmer but grew faster than most of the other strains, suggesting a potential metabolic trade-off. This study highlights the importance of strain-level diversity in microbial associations and provides new insight into the underlying genetic architecture of intraspecific symbiont communities within a host.\n\nStrain-level diversity of symbiont communities between individuals and populations of a bioluminescent fish.", "token_count": 423, "char_count": 1903, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5779, "quality_score": 0.789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:21.098953", "source": { "split": "train_shard_00000", "doc_id": 1190 }, "chunk_id": "train_shard_00000_1190_0", "global_id": 1311 }, { "text": "The human intestines are colonized by trillions of microbes, comprising the gut microbiota, which produce diverse small molecule metabolites and modify host metabolites, such as bile acids, that regulate host physiology. Biosynthesized in the liver, bile acids are conjugated with glycine or taurine and secreted into the intestines, where gut microbial bile salt hydrolases (BSHs) deconjugate the amino acid to produce unconjugated bile acids that serve as precursors for secondary bile acid metabolites. Among these include a recently discovered class of microbially conjugated bile acids (MCBAs), wherein alternative amino acids are conjugated onto bile acids. To elucidate the metabolic potential of MCBAs, we performed detailed kinetic studies to investigate the preference of BSHs for host-conjugated bile acids and MCBAs. We identified a BSH that exhibits positive cooperativity uniquely for MCBAs containing an aromatic side chain. Further molecular modeling and phylogenetic analyses indicated that the BSH preference for aromatic MCBAs is due to a substrate-specific cation-π interaction and is predicted to be widespread among human gut microbial BSHs.\n\nElectrostatic Interactions Dictate Bile Salt Hydrolase Substrate Preference.", "token_count": 327, "char_count": 1241, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:21.663588", "source": { "split": "train_shard_00000", "doc_id": 1191 }, "chunk_id": "train_shard_00000_1191_0", "global_id": 1312 }, { "text": "The animal reservoir of Enterobacterales producing Extended-Spectrum-β-Lactamases (ESBL) and plasmid-borne cephalosporinases (pAmpC) is a global concern. Using genome data, we analyzed a population of Escherichia coli and Salmonella species resistant to third-generation cephalosporins (3GC-R) recovered from healthy food animals (HA) and diseased food animals (DA) across Europe. Among the isolates collected from HA (n = 4,498) and DA (n = 833) in up to twelve European countries, 62 (1.4%) and 45 (5.4%) were 3GC-R, respectively. The genomes of these 3GC-R 107 isolates were sequenced to identify blaESBL and blaAmpC, sequence types (STs), virulence-associated genes, and Salmonella serovars. We also assessed their population structure using core genome multilocus sequence typing. The 78 3GC-R Escherichia coli originated from poultry (n = 27), swine (n = 26), and cattle (n = 25). Almost all (n = 77; 98.7%) harbored at least one blaESBL or blaAmpC, with blaCTX-M-1 predominating. We identified 51 STs, with ST10 and ST101 being the most frequent. The population of 3GC-R E. coli was polyclonal. The 29 3GC-R Salmonella spp. were mostly retrieved from healthy broiler (96.5%). blaCMY-2 dominated in this population. We found two clusters of CMY-2-producing Salmonella spp. in Germany: one with 15 isolates of S. Heidelberg isolates and another with six S. Minnesota, all of them with blaCMY-2. Our results confirm the low prevalence of 3GC-R E. coli and Salmonella spp. in HA and DA. blaCTX-M-1 was dominating in a highly diverse population of E. coli", "token_count": 517, "char_count": 1557, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [ "ST10", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:10:22.359304", "source": { "split": "train_shard_00000", "doc_id": 1192 }, "chunk_id": "train_shard_00000_1192_0", "global_id": 1313 }, { "text": "3GC-R E.coli isolated from HA and DA were genetically unrelated, with high clonal diversity suggesting multiple origins of contamination. This contrasted with the clonal population of 3GC-R Salmonella spp. in which blaCMY-2 dominated through two dominant serovars in this collection.\n\nGenome analysis of third-generation cephalosporin-resistant Escherichia coli and Salmonella species recovered from healthy and diseased food-producing animals in Europe.", "token_count": 117, "char_count": 454, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7966, "quality_score": 0.8983, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:22.761228", "source": { "split": "train_shard_00000", "doc_id": 1192 }, "chunk_id": "train_shard_00000_1192_1", "global_id": 1314 }, { "text": "Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.\n\nDiversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes.", "token_count": 256, "char_count": 1182, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:23.334151", "source": { "split": "train_shard_00000", "doc_id": 1193 }, "chunk_id": "train_shard_00000_1193_0", "global_id": 1315 }, { "text": "Fatty liver hemorrhagic syndrome is a widespread metabolic disease in laying hens that decreases egg production and even causes death in severe cases. Many traditional Chinese medicine ingredients, such as saikosaponin a (SSa), have been shown to alleviate fatty liver, but the underlying mechanisms remain unclear. In this study, we aimed to explore the alleviation of dietary SSa on excessive hepatic lipid deposition and the interactions between intestinal microbiota and bile acid (BA) in laying hens. Fifty-four 35-wk-old laying hens were randomly allocated into 3 treatment groups with 6 replicates (3 birds per replicate) and fed with a basal diet (CON), high-energy and low-protein diet (HELP), and HELP diet with 30 mg/kg SSa (HELP + SSa). SSa reversed diet-induced egg production rate decrease (P < 0.05). SSa could potently ameliorate HELP-induced accumulation of hepatic cholesterol and liver injury via the increase (P < 0.05) of mRNA expression of BA synthesis gene, such as cholesterol 7 alpha-hydroxylase 1. SSa treatment alleviated gut dysbiosis, especially reducing (P < 0.05) the relative abundance of bile salt hydrolase (BSH)-producing bacteria such as Lactobacillus, Bifidobacterium, and Turicibacter. Ileal BA metabolomic analysis revealed that SSa increased (P < 0.05) the content of tauro-conjugated BAs, mainly taurochenodeoxycholic acid and tauro-α-muricholic acid. The mRNA expression of farnesoid X receptor (FXR) and fibroblast growth factor 19 were decreased (P < 0.05) in intestine, which was associated with increased gene expression of enzymes in the BA synthesis that reduced the levels of cholesterol", "token_count": 480, "char_count": 1636, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:24.027575", "source": { "split": "train_shard_00000", "doc_id": 1194 }, "chunk_id": "train_shard_00000_1194_0", "global_id": 1316 }, { "text": "Moreover, SSa treatment inhibited intestinal BA reabsorption via decreasing (P < 0.05) the mRNA expression of apical sodium-dependent bile acid transporter. Our findings indicated that SSa reduced liver cholesterol accumulation and alleviated fatty liver in laying hens through microbiota-BA-intestinal FXR crosstalk.\n\nSaikosaponin a ameliorates diet-induced fatty liver via regulating intestinal microbiota and bile acid profile in laying hens.", "token_count": 125, "char_count": 445, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8103, "quality_score": 0.9052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:24.419094", "source": { "split": "train_shard_00000", "doc_id": 1194 }, "chunk_id": "train_shard_00000_1194_1", "global_id": 1317 }, { "text": "Traditional epidemiological investigations of healthcare-associated Clostridioides difficile infection (HA-CDI) are often insufficient. This study aimed to evaluate a procedure that includes secondary isolation and genomic typing of single toxigenic colonies using core genome multilocus sequence typing (cgMLST) for the investigation of C. difficile transmission.\n\nCore genome multilocus sequence typing of Clostridioides difficile to investigate transmission in the hospital setting.", "token_count": 107, "char_count": 485, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7627, "quality_score": 0.8814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:24.797120", "source": { "split": "train_shard_00000", "doc_id": 1195 }, "chunk_id": "train_shard_00000_1195_0", "global_id": 1318 }, { "text": "Contamination of arsenic in drinking water and foods is a threat for human beings. To achieve the goal for the reduction of arsenic availability, besides conventional technologies, arsenic bioremediation by using some potent bacteria is one of the hot topics for researchers. In this context, bacterium, AKS4c was isolated from arsenic contaminated water of Purbasthali, West Bengal, India, and through draft genome sequence; it was identified as a strain of Micrococcus luteus that comprised of 2.4 Mb genome with 73.1% GC content and 2256 protein coding genes. As the accessory genome, about 22 genomic islands (GIs) associated with many metal-resistant genes were identified. This strain was capable to tolerate more than 46,800 mg/L arsenate and 390 mg/L arsenite salts as well as found to be tolerable to multi-metals such as Fe, Pb, Mo, Mn, and Zn up to a certain limit of concentrations. Strain AKS4c was able to oxidize arsenite to less toxic arsenate, and its arsenic adsorption property was qualitatively confirmed through X-ray fluorescence (XRF) and Fourier transform infrared spectroscopy (FTIR) analysis. Quantitative estimation of plant growth-promoting attributes like Indole acetic acid (IAA), Gibberellic acid (GA), and proline production and enhancement of rice seedling growth in laboratory condition leads to its future applicability in arsenic bioremediation as a plant growth-promoting rhizobacteria (PGPR).\n\nInsight into the genome of an arsenic loving and plant growth-promoting strain of Micrococcus luteus isolated from arsenic contaminated groundwater.", "token_count": 428, "char_count": 1580, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:25.427136", "source": { "split": "train_shard_00000", "doc_id": 1196 }, "chunk_id": "train_shard_00000_1196_0", "global_id": 1319 }, { "text": "Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the agents of pathogens. In this study, metagenomic sequencing was conducted to investigate the microbial and antibiotic resistance genes (ARGs) composition in the vitreous (intraocular body fluid) of an endophthalmitis patient, who progressed rapidly and accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome in the vitreous. This strain harbor's the ARGs mainly against beta-lactam, macrolide-lincosamide-streptogramin, and multidrug. Additionally, metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was identified. The Tetra Correlation Search (TCS) analysis uncovered that the closest relative of the Streptococcus sp. v1. nov. was Streptococcus mitis SK321. Pan/core genome analysis for Streptococcus sp. v1. nov. and TCS top 25 hits strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to ATP-binding cassette transport system, which could indicate unique virulence and pathogenic potentials of Streptococcus sp. v1. nov. In addition, a total of 7 virulence factors were identified, and the overwhelming of them were classified into \"offensive virulence factors\". The high pathogenicity of Streptococcus sp. v1. nov. could be a reason for the patient's rapid disease progression. Our study was first isolated an ocular pathogen with highly virulent based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patient in the future.\n\nGenomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis Patient.", "token_count": 496, "char_count": 1917, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5932, "quality_score": 0.7966, "entities": { "genes": [ "SK321" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:26.083438", "source": { "split": "train_shard_00000", "doc_id": 1197 }, "chunk_id": "train_shard_00000_1197_0", "global_id": 1320 }, { "text": "Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, had its genome sequenced to study the biosynthetic potential to produce novel natural products within the Brevibacterium genus. The genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium. Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs. Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. Evaluating the antibacterial activity of strain H-BE7, it exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes. Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity", "token_count": 515, "char_count": 2046, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6073, "quality_score": 0.8036, "entities": { "genes": [ "BE7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:10:26.738183", "source": { "split": "train_shard_00000", "doc_id": 1198 }, "chunk_id": "train_shard_00000_1198_0", "global_id": 1321 }, { "text": "While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.\n\nExploring the biosynthetic gene clusters in Brevibacterium: a comparative genomic analysis of diversity and distribution.", "token_count": 110, "char_count": 407, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8269, "quality_score": 0.9135, "entities": { "genes": [ "BE7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:27.120350", "source": { "split": "train_shard_00000", "doc_id": 1198 }, "chunk_id": "train_shard_00000_1198_1", "global_id": 1322 }, { "text": "Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence-absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be \"anchored\" in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias.\n\nPanKmer: k-mer-based and reference-free pangenome analysis.", "token_count": 313, "char_count": 1434, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7164, "quality_score": 0.8582, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:27.678507", "source": { "split": "train_shard_00000", "doc_id": 1199 }, "chunk_id": "train_shard_00000_1199_0", "global_id": 1323 }, { "text": "The study assessed the role of equids at slaughter as faecal carriers of Salmonella enterica and the occurrence of contaminated equid carcasses during the slaughter process in Northern Italy (Emilia-Romagna Region). From June to November 2021, 152 equids (146 horses, 5 donkeys and 1 mule) were tested for Salmonella both in caecal contents and through carcass swabs. Antimicrobial resistance (AMR) of recovered strains was tested against 15 antimicrobials. Salmonella was detected in 3/152 of the caecal contents (2.0 %), while all carcass samples were negative. S. enterica serovars Enteriditis, Typhimurium and Stanleyville were identified. The only AMR isolate was S. Typhimurium with AMR profile AmCStxT. Considering the consumption of raw horse meat (i.e., minced raw meat named \"pesto di cavallo\" and dried and smoked strips named \"sfilacci di cavallo\") in different areas of Northern Italy, we also investigated the possible link between horse meat eating and salmonellosis cases in the human population in the same area. Specifically, we compared the Salmonella strains collected during the study with those routinely processed in the laboratory surveillance system for human salmonellosis in Emilia-Romagna (a region with about 4.5 million inhabitants). The comparison was based on whole genome sequencing data through core genome multi-locus sequence typing (cgMLST) used in routine surveillance. A genomic match in cgMLST was found between the strain of S. enterica serovar Enteritidis isolated from a horse caecal content and an enduring outbreak of 17 human cases in Emilia-Romagna during the study period. The consequent epidemiological investigation highlighted that a number of cases with known food history reported the consumption of horse meat and traced different batches of the consumed meat, released weeks apart from each other, to the slaughter investigated in the study. The results of the epidemiological investigation suggested the role of horses in the S. enterica serovar Enteritidis outbreak affecting raw horse meat consumers. This study shows that, despite the low prevalence on equid carcasses, S", "token_count": 520, "char_count": 2130, "word_count": 318, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:10:28.337390", "source": { "split": "train_shard_00000", "doc_id": 1200 }, "chunk_id": "train_shard_00000_1200_0", "global_id": 1324 }, { "text": "enterica in horse meat can represent a risk to consumers. From the perspective of the slaughter activities, this highlights the need to maintain a high level of hygiene during the entire process, starting from the hygiene at lairage up to the slaughtering phase and dressing of carcasses.\n\nSalmonella in horses at slaughter and public health effects in Italy.", "token_count": 78, "char_count": 359, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7069, "quality_score": 0.8534, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:28.703205", "source": { "split": "train_shard_00000", "doc_id": 1200 }, "chunk_id": "train_shard_00000_1200_1", "global_id": 1325 }, { "text": "Exploring the effect of bile salts on the properties of emulsion carriers containing hydrophobic bioactive compounds is particularly critical to understanding the stability and bioavailability of these hydrophobic bioactive compounds in the digestive process. In this study, the effects of bile salts on the stability and digestive characteristics of the ursolic acid (UA) self-stabilized water-in-oil (W/O) emulsion were investigated via static and dynamic (with or without enzyme) in vitro simulated digestive systems. The results showed that under the static system, the basic conditions had less interference, while the bile salts had a significant effect on the appearance and microstructure of the emulsion. The primary mechanism of emulsion instability is hydrophobic binding and depletion flocculation. Under the dynamic condition, it was found that the low concentrations of bile salts can promote the release amount and the rate of free fatty acids via displacement, while high concentrations of bile salts inhibit the decomposition of lipid, which may be related to the secondary coverage formed at the interface by the bile salts. These findings provide a theoretical basis for understanding the digestive behavior of the UA emulsion and its interaction with bile salts, which are conducive to developing and designing new emulsions to improve the bioaccessibility of UA.\n\nEffect of Digestion on Ursolic Acid Self-Stabilized Water-in-Oil Emulsion: Role of Bile Salts.", "token_count": 335, "char_count": 1479, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5642, "quality_score": 0.7821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:29.610382", "source": { "split": "train_shard_00000", "doc_id": 1201 }, "chunk_id": "train_shard_00000_1201_0", "global_id": 1326 }, { "text": "Cefiderocol (CFDC) is the first-in-class siderophore-cephalosporin. Klebsiella pneumoniae strain that is extremely resistant to CFDC (MIC: 256 µg/ml) was isolated for the first time in the United Arab Emirates from a patient with pneumonia and sepsis. It belonged to sequence-type 14 (ST14), with a novel core genome ST. Resistance was driven by the co-expression of β-lactamases (bla\n\nExtreme resistance to the novel siderophore-cephalosporin cefiderocol in an extensively drug-resistant Klebsiella pneumoniae strain causing fatal pneumonia with sepsis: genomic analysis and synergistic combinations for resistance reversal.", "token_count": 188, "char_count": 625, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7381, "quality_score": 0.869, "entities": { "genes": [ "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:30.054210", "source": { "split": "train_shard_00000", "doc_id": 1202 }, "chunk_id": "train_shard_00000_1202_0", "global_id": 1327 }, { "text": "In 2019, two distinct bacterial isolates were independently isolated from the fecal samples of separate dogs in Beijing, China. These cells exhibit microaerobic, are Gram-negative, motile, and possess a characteristic spiral shape with bipolar single flagellum. They display positive results for the oxidase test while being negative for both catalase and urease. These organisms measure approximately 0.2-0.3 μm in width and 4.5-6 μm in length. The colonies are wet, flat, grey, circular, and smooth with sizes ranging from 1 to 2 mm in diameter after 2 days of growth. However, strains may exhibit variations in size and morphology following extended incubation. Phylogenetic analyses based on the 16S rRNA gene and core genome indicated that these two isolates belong to the genus", "token_count": 200, "char_count": 783, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7769, "quality_score": 0.8884, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:30.503389", "source": { "split": "train_shard_00000", "doc_id": 1203 }, "chunk_id": "train_shard_00000_1203_0", "global_id": 1328 }, { "text": "Streptococcus thermophilus FUA329, a urolithin A-producing bacterium, is isolated from human breast milk. The complete genome sequence of FUA329 did not contain any plasmids and at least 20 proteins were related to extreme environment resistance. Phenotypic assay results demonstrated that FUA329 was susceptible to 12 kinds of antibiotics and did not exhibit any hemolytic or nitrate reductase activity. Three free radical scavenging assays revealed that FUA329 have high antioxidant capability. FUA329 exhibited a cell surface hydrophobicity of 52.58 ± 1.17% and an auto-aggregation rate of 18.69 ± 2.48%. Moreover, FUA329 demonstrated a survival rate of over 60% in strong acid and bile salt environments, indicating that FUA329 may be stable colonization in the gastrointestinal tract. Additionally, we firstly found 3 potential proteins and 11 potential genes of transforming ellagic acid to urolithins in FUA329 genome. The above results indicate that FUA329 has credible safety and probiotic properties, as well as the potential to be developed as a new generation of urolithin A-producing probiotics.\n\nGenomic and phenotypic-based safety assessment and probiotic properties of Streptococcus thermophilus FUA329, a urolithin A-producing bacterium of human milk origin.", "token_count": 367, "char_count": 1275, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "FUA329" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:31.088643", "source": { "split": "train_shard_00000", "doc_id": 1204 }, "chunk_id": "train_shard_00000_1204_0", "global_id": 1329 }, { "text": "One of the most concerning characteristics of Pseudomonas aeruginosa is its low susceptibility to several antibiotics of common use in clinics, as well as its facility to acquire increased resistance levels. Consequently, the study of the antibiotic resistance mechanisms of this bacterium is of relevance for human health. For such a study, different types of resistance should be distinguished. The intrinsic resistome is composed of a set of genes, present in the core genome of P. aeruginosa, which contributes to its characteristic, species-specific, phenotype of susceptibility to antibiotics. Acquired resistance refers to those genetic events, such as the acquisition of mutations or antibiotic resistance genes that reduce antibiotic susceptibility. Finally, antibiotic resistance can be transiently acquired in the presence of specific compounds or under some growing conditions. The current article provides information on methods currently used to analyze intrinsic, mutation-driven, and transient antibiotic resistance in P. aeruginosa.\n\nThe Pseudomonas aeruginosa Resistome: Permanent and Transient Antibiotic Resistance, an Overview.", "token_count": 248, "char_count": 1148, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6392, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:31.570711", "source": { "split": "train_shard_00000", "doc_id": 1205 }, "chunk_id": "train_shard_00000_1205_0", "global_id": 1330 }, { "text": "Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class\n\nPangenome-level analysis of nucleoid-associated proteins in the", "token_count": 215, "char_count": 957, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7153, "quality_score": 0.8577, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:32.031593", "source": { "split": "train_shard_00000", "doc_id": 1206 }, "chunk_id": "train_shard_00000_1206_0", "global_id": 1331 }, { "text": "Ursolic acid (UA), a pentacyclic triterpenoid, exhibits various pharmacological actions, such as anti-inflammation, anti-tumor, anti-diabetes, heart protection, and liver protection. However, the role of nuclear factor E2-related factor 2 (NRF2)-mediated regulation of uridine diphosphate glucuronosyltransferase (UGT2B7) and bile salt export pump (BSEP)/multidrug resistance-associated protein 2 (MRP2) in UA against cholestatic liver injury has not been cleared. The purpose of this study is to explore the effect of UA on cholestatic liver injury and its potential mechanism. The results of the liver pathology sections and blood biochemical indices demonstrated that UA significantly attenuated the cholestatic liver injury induced by alpha-naphthylisothiocyanate (ANIT) in a dose-dependent manner. The mRNA and protein levels of UGT2B7 and BSEP/MRP2 were remarkably increased in the liver of ANIT rats and HepG2 cells pretreated with UA, but this activation was suppressed with NRF2 silenced. In conclusion, our findings demonstrate that UA prevents cholestasis, which may be associated with NRF2-mediated regulation of UGT2B7, BSEP/MRP2.\n\nUrsolic acid attenuates cholestasis through NRF2-mediated regulation of UGT2B7 and BSEP/MRP2.", "token_count": 353, "char_count": 1238, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8434, "entities": { "genes": [ "MRP2", "NRF2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:32.596150", "source": { "split": "train_shard_00000", "doc_id": 1207 }, "chunk_id": "train_shard_00000_1207_0", "global_id": 1332 }, { "text": "Evaluation of whole and core genome multilocus sequence typing allele schemes for", "token_count": 17, "char_count": 81, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:32.952646", "source": { "split": "train_shard_00000", "doc_id": 1208 }, "chunk_id": "train_shard_00000_1208_0", "global_id": 1333 }, { "text": "In aquaculture, probiotic yeasts have gained particular interest because of their numerous health benefits for farmed fish. Many autochthonous yeasts have been isolated and identified from fish species with potential probiotic characteristics. In the present study, four autochthonous yeast strains were identified and characterized from the intestinal tracts of 16 healthy goldfish, Carassius auratus. Their in vitro probiotic properties were examined in terms of cell surface hydrophobicity, co-aggregation, and tolerability to different pH values and bile salt concentrations. These strains were identified by culture characters and sequence analysis of ITS (Internal Transcribed Spacer) gene regions. Four strains, namely Cutaneotrichosporon jirovecii isolate jpn01, Debaryomyces nepalensis isolate jpn02, Blastobotrys proliferans isolate jpn05, and Diutina catenulata isolate jpn06, were identified and added to the NCBI GenBank with accession numbers defined as MT584874.1, MT584873.1, MT649918.1, and MT501155.1, respectively. Results demonstrated the capability of these strains to co-aggregate with several fish-associated bacterial pathogens such as Lactococcus garvieae, Vagococcus salmoninarum, Vibrio anguillarum, Yersinia ruckeri, and Aeromonas hydrophila. Only the jpn05 strain did not co-aggregate with A. hydrophila. All identified yeast isolates could grow and tolerate low pH conditions (pH 2.0) and bile salt concentrations (up to 1.5%). Of interest, the hydrophobicity (%) of the yeast isolates was 80%, 94.0%, 80.6%, and 66.4% for jpn01, jpn02, jpn05, and jpn06 isolates, respectively. In this context, our data provide important in vitro evidence for the potential probiotic features of the yeast isolates", "token_count": 501, "char_count": 1728, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8305, "entities": { "genes": [ "MT501155", "MT584874", "MT649918", "MT584873" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:33.603264", "source": { "split": "train_shard_00000", "doc_id": 1209 }, "chunk_id": "train_shard_00000_1209_0", "global_id": 1334 }, { "text": "These strains could be considered candidate probiotic yeasts; however, their application in aquaculture nutrition necessitates further in vivo assays.\n\nIdentification of four autochthonous yeasts from the intestines of goldfish, Carassius auratus with potential probiotic properties and their effects on the most common fish bacterial pathogens.", "token_count": 78, "char_count": 345, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:33.971059", "source": { "split": "train_shard_00000", "doc_id": 1209 }, "chunk_id": "train_shard_00000_1209_1", "global_id": 1335 }, { "text": "Bacteria of the Leuconostoc genus are Gram-positive bacteria that are commonly found in raw milk and persist in fermented dairy products and plant food. Studies have already explored the probiotic potential of L. mesenteroides, but not from a probiogenomic perspective, which aims to explore the molecular features responsible for their phenotypes. In the present work, probiogenomic approaches were applied in strains F-21 and F-22 of L. mesenteroides isolated from human milk to assess their biosafety at the molecular level and to correlate molecular features with their potential probiotic characteristics. The complete genome of strain F-22 is 1.99 Mb and presents one plasmid, while the draft genome of strain F-21 is 1.89 Mb and presents four plasmids. A high percentage of average nucleotide identity among other genomes of L. mesenteroides (≥ 96%) corroborated the previous taxonomic classification of these isolates. Genomic regions that influence the probiotic properties were identified and annotated. Both strains exhibited wide genome plasticity, cell adhesion ability, proteolytic activity, proinflammatory and immunomodulation capacity through interaction with TLR-NF-κB and TLR-MAPK pathway components, and no antimicrobial resistance, denoting their potential to be candidate probiotics. Further, the strains showed bacteriocin production potential and the presence of acid, thermal, osmotic, and bile salt resistance genes, indicating their ability to survive under gastrointestinal stress. Taken together, our results suggest that L. mesenteroides F-21 and F-22 are promising candidates for probiotics in the food and pharmaceutical industries.\n\nProbiogenomics of Leuconostoc Mesenteroides Strains F-21 and F-22 Isolated from Human Breast Milk Reveal Beneficial Properties.", "token_count": 453, "char_count": 1793, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6305, "quality_score": 0.8153, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:34.632491", "source": { "split": "train_shard_00000", "doc_id": 1210 }, "chunk_id": "train_shard_00000_1210_0", "global_id": 1336 }, { "text": "Consumption of high FODMAP (Fermentable Oligo-, Di-, and Monosaccharides and Polyols) diet is the leading cause of alteration in the human gut microbiome, thereby, causing irritable bowel syndrome (IBS). Therefore, sourdough technology can be exploited for reduction of FODMAPs in various foods to alleviate the symptoms of IBS. Several microorganisms viz. Pichia fermentans, Lactobacillus fetmentum, Saccharomyces cerevisiae, Torulaspora delbrueckii, Kluyveromyces marxianus etc. have been identified for the production of low FODMAP type II sourdough fermented products. However, more research on regulation of end-product and volatilome profile is required for maximal exploitation of FODMAP-reducing microorganisms. Therefore, the present review is focused on utilisation of lactic acid bacteria and yeasts, alone and in synergy, for the production of low FODMAP sourdough foods. Moreover, the microbial bioprocessing of cereal and non-cereal based low FODMAP fermented sourdough products along with their nutritional and therapeutic benefits have been elaborated. The challenges and future prospects for the production of sourdough fermented low FODMAP foods, thereby, bringing out positive alterations in gut microbiome, have also been discussed.\n\nUnlocking the potential of low FODMAPs sourdough technology for management of irritable bowel syndrome.", "token_count": 346, "char_count": 1357, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:35.219844", "source": { "split": "train_shard_00000", "doc_id": 1211 }, "chunk_id": "train_shard_00000_1211_0", "global_id": 1337 }, { "text": "This study aims to investigate the hepatotoxicity of Psoraleae Fructus water extract and the underlying mechanism in rats. Forty-eight rats were randomly assigned into four groups: a blank group and low-(BZGL, 6.25 g·kg~(-1)), medium-(BGZM, 12.5 g·kg~(-1)), and high-dose(BGZH, 25 g·kg~(-1)) Psoraleae Fructus water extract groups. The rats were treated for 28 days, and toxicity and mortality were observed daily. After 28 days, the rats were sacrificed, and the body weight, liver index, and liver-to-brain ratio were calculated. The morphological changes in the liver tissue were observed, and the serum levels of related biochemical indicators were measured. The results showed that compared with the blank group, Psoraleae Fructus water extracts of different doses decreased the body weight, increased the liver index and liver-to-brain ratio, and caused liver hypertrophy and pathological changes. Pathological examination revealed that the rats in Psoraleae Fructus water extract groups had bile duct hyperplasia, inflammatory cell infiltration, and liver cell fibrosis. Compared with the blank group, BGZL elevated the levels of alanine transaminase(ALT), α-glutathione S-transferase(α-GST), and total bile acid(TBA)(P<0.05), and BGZM and BGZH elevated the levels of ALT, TBA, α-GST, γ-glutamyl transferase(γ-GT), purine nucleoside phosphorylase(PNP), ornithine carbamoyltransferase(OCT), and arginase(ArgI)(P<0.05)", "token_count": 440, "char_count": 1429, "word_count": 191, "semantic_coherence": 1, "information_density": 0.5916, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:35.899120", "source": { "split": "train_shard_00000", "doc_id": 1212 }, "chunk_id": "train_shard_00000_1212_0", "global_id": 1338 }, { "text": "Compared with the blank group, Psoraleae Fructus water extracts of different doses down-regulated the mRNA and protein levels of bile salt export pump(BSEP) and farnesoid X receptor(FXR) and up-regulated the mRNA and protein levels of tumor necrosis factor-α(TNF-α), nuclear factor kappaB(NF-κB), and cholesterol 7 alpha-hydroxylase(CYP7A1)(P<0.05). The results suggested that Psoraleae Fructus water extract caused toxicity in rats, showing a dose-toxicity relationship. Psoraleae Fructus water extract may cause liver damage, which may be due to its effect on liver bile acid secretion and induction of inflammation.\n\n[Effect of 28-day administration of Psoraleae Fructus water extract on early liver injury in rats].", "token_count": 218, "char_count": 722, "word_count": 100, "semantic_coherence": 1, "information_density": 0.67, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:36.370492", "source": { "split": "train_shard_00000", "doc_id": 1212 }, "chunk_id": "train_shard_00000_1212_1", "global_id": 1339 }, { "text": "A chitosan-glucose derivative (ChG) with lower antimicrobial activity against whey native probiotic yeast K. marxianus VM004 was synthesized by the Maillard reaction. The ChG derivative was characterized by FT-IR,\n\nChitosan-glucose derivative as effective wall material for probiotic yeasts microencapsulation.", "token_count": 87, "char_count": 310, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8205, "quality_score": 0.9103, "entities": { "genes": [ "VM004" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:36.745266", "source": { "split": "train_shard_00000", "doc_id": 1213 }, "chunk_id": "train_shard_00000_1213_0", "global_id": 1340 }, { "text": "Lateral gene transfer (LGT) is the movement of DNA between organisms without sexual reproduction. The acquired genes represent genetic novelties that have independently evolved in the donor's genome. Phylogenetic methods have shown that LGT is widespread across the entire grass family, although we know little about the underlying dynamics. We identify laterally acquired genes in five de novo reference genomes from the same grass genus (four Alloteropsis semialata and one Alloteropsis angusta). Using additional resequencing data for a further 40 Alloteropsis individuals, we place the acquisition of each gene onto a phylogeny using stochastic character mapping, and then infer rates of gains and losses. We detect 168 laterally acquired genes in the five reference genomes (32-100 per genome). Exponential decay models indicate that the rate of LGT acquisitions (6-28 per Ma) and subsequent losses (11-24% per Ma) varied significantly among lineages. Laterally acquired genes were lost at a higher rate than vertically inherited loci (0.02-0.8% per Ma). This high turnover creates intraspecific gene content variation, with a preponderance of them occurring as accessory genes in the Alloteropsis pangenome. This rapid turnover generates standing variation that can ultimately fuel local adaptation.\n\nLateral gene transfer generates accessory genes that accumulate at different rates within a grass lineage.", "token_count": 318, "char_count": 1413, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:37.306213", "source": { "split": "train_shard_00000", "doc_id": 1214 }, "chunk_id": "train_shard_00000_1214_0", "global_id": 1341 }, { "text": "Escherichia coli K-12 is a model organism for bacteriology and has served as a workhorse for molecular biology and biochemistry for over a century since its first isolation in 1922. However, Escherichia coli K-12 strains are phenotypically devoid of an O antigen (OAg) since early reports in the scientific literature. Recent studies have reported the presence of independent mutations that abolish OAg repeating-unit (RU) biogenesis in E. coli K-12 strains from the same original source, suggesting unknown evolutionary forces have selected for inactivation of OAg biogenesis during the early propagation of K-12. Here, we show for the first time that restoration of OAg in E. coli K-12 strain MG1655 synergistically sensitises bacteria to vancomycin with bile salts (VBS). Suppressor mutants surviving lethal doses of VBS primarily contained disruptions in OAg biogenesis. We present data supporting a model where the transient presence and accumulation of lipid-linked OAg intermediates in the periplasmic leaflet of the inner membrane interfere with peptidoglycan sacculus biosynthesis, causing growth defects that are synergistically enhanced by bile salts. Lastly, we demonstrate that continuous bile salt exposure of OAg-producing MG1655 in the laboratory, can recreate a scenario where OAg disruption is selected for as an evolutionary fitness benefit. Our work thus provides a plausible explanation for the long-held mystery of the selective pressure that may have led to the loss of OAg biogenesis in E. coli K-12; this opens new avenues for exploring long-standing questions on the intricate network coordinating the synthesis of different cell envelope components in Gram-negative bacteria.\n\nO antigen biogenesis sensitises Escherichia coli K-12 to bile salts, providing a plausible explanation for its evolutionary loss.", "token_count": 473, "char_count": 1833, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [ "MG1655" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:37.949264", "source": { "split": "train_shard_00000", "doc_id": 1215 }, "chunk_id": "train_shard_00000_1215_0", "global_id": 1342 }, { "text": "The orange subfamily (Aurantioideae) contains several Citrus species cultivated worldwide, such as sweet orange and lemon. The origin of Citrus species has long been debated and less is known about the Aurantioideae. Here, we compiled the genome sequences of 314 accessions, de novo assembled the genomes of 12 species and constructed a graph-based pangenome for Aurantioideae. Our analysis indicates that the ancient Indian Plate is the ancestral area for Citrus-related genera and that South Central China is the primary center of origin of the Citrus genus. We found substantial variations in the sequence and expression of the PH4 gene in Citrus relative to Citrus-related genera. Gene editing and biochemical experiments demonstrate a central role for PH4 in the accumulation of citric acid in citrus fruits. This study provides insights into the origin and evolution of the orange subfamily and a regulatory mechanism underpinning the evolution of fruit taste.\n\nPangenome analysis provides insight into the evolution of the orange subfamily and a key gene for citric acid accumulation in citrus fruits.", "token_count": 245, "char_count": 1108, "word_count": 170, "semantic_coherence": 1, "information_density": 0.5471, "quality_score": 0.7735, "entities": { "genes": [ "PH4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:38.439651", "source": { "split": "train_shard_00000", "doc_id": 1216 }, "chunk_id": "train_shard_00000_1216_0", "global_id": 1343 }, { "text": "Pulque is a traditional Mexican non-distilled alcoholic beverage to which several beneficial functions are attributed, mainly associated with gastrointestinal health, which can be explained by the presence of probiotic bacteria in its microbiota. Therefore, the objective of this work was to evaluate the safety, probiotic activity, and functional characteristics of seven strains of lactic acid bacteria (LAB) isolated from pulque using the probiotic strain\n\nProbiotic and functional potential of lactic acid bacteria isolated from pulque and evaluation of their safety for food applications.", "token_count": 119, "char_count": 593, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7108, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:38.824032", "source": { "split": "train_shard_00000", "doc_id": 1217 }, "chunk_id": "train_shard_00000_1217_0", "global_id": 1344 }, { "text": "An in vitro model of human gastrointestinal digestion was introduced to investigate the effects of surface charge of cellulose nanoparticles on emulsion structure during gastric phase, lipase activity, bile salt diffusion, and free fatty acid (FFA) release. Four carboxymethylated cellulose nanofibrils (CNF; C\n\nModulating in vitro gastrointestinal digestion of nanocellulose-stabilized pickering emulsions by altering particle surface charge.", "token_count": 116, "char_count": 443, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:39.202998", "source": { "split": "train_shard_00000", "doc_id": 1218 }, "chunk_id": "train_shard_00000_1218_0", "global_id": 1345 }, { "text": "Traditional fermented yak milk has immense cultural and nutritional significance for Tibetan herders. In this study, we investigated the microbial community structure and flavour compounds in traditional fermented yak milk from three distinct regions of Gannan to explore the relationship between microbial composition and flavour compounds. The findings revealed significant variations in flavour compounds and the bacterial microbiota among the samples from the three regions. The dominant species identified in fermented yak milk were Streptococcus salivarius subsp. Thermophilus, Lactobacillus helveticus, and Kluyveromyces marxianus. Bidirectional orthogonal partial least-squares (O2PLS) analysis highlighted five bacterial genera and three fungal genera as contributors to the production of flavour-related compounds. Furthermore, regression analysis revealed that the Lactobacillus and Streptococcus genera were associated with the production of 2,3-pentanedione as well as eight predicted KEGG pathways. These findings provide valuable insights into the intricate relationship between flavour compounds and microbiota in traditional fermented yak milk.\n\nExploring the link between microbial community structure and flavour compounds of traditional fermented yak milk in Gannan region.", "token_count": 297, "char_count": 1293, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5542, "quality_score": 0.7771, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:39.769675", "source": { "split": "train_shard_00000", "doc_id": 1219 }, "chunk_id": "train_shard_00000_1219_0", "global_id": 1346 }, { "text": "Enteric bacteria need to adapt to endure the antibacterial activities of bile salts in the gut. Phospholipase A (PldA) is a key enzyme in the maintenance of bacterial membrane homeostasis. Bacteria respond to stress by modulating their membrane composition.", "token_count": 66, "char_count": 257, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:40.137755", "source": { "split": "train_shard_00000", "doc_id": 1220 }, "chunk_id": "train_shard_00000_1220_0", "global_id": 1347 }, { "text": "SARS-CoV-2 was the cause of the global pandemic that caused a total of 14.9 million deaths during the years 2020 and 2021, according to the WHO. The virus presents a mutation rate between 10-5 and 10-3 substitutions per nucleotide site per cell infection (s/n/c). Due to this, studies aimed at knowing the evolution of this virus could help us to foresee (through the future development of new detection strategies and vaccines that prevent the infection of this virus in human hosts) that a pandemic caused by this virus will be generated again. In this research, we performed a functional annotation and identification of changes in Nsp (non-structural proteins) domains in the coronavirus genome. The comparison of the 13 selected coronavirus pangenomes demonstrated a total of 69 protein families and 57 functions associated with the structural domain's differentials between genomes. A marked evolutionary conservation of non-structural proteins was observed. This allowed us to identify and classify highly pathogenic human coronaviruses into alpha, beta, gamma, and delta groups. The designed Nsp cluster provides insight into the trajectory of SARS-CoV-2, demonstrating that it continues to evolve rapidly. An evolutionary marker allows us to discriminate between phylogenetically divergent groups, viral genotypes, and variants between the alpha and betacoronavirus genera. These types of evolutionary studies provide a window of opportunity to use these Nsp as targets of viral therapies.\n\nNon-Structural Proteins (Nsp): A Marker for Detection of Human Coronavirus Families.", "token_count": 378, "char_count": 1584, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:40.724374", "source": { "split": "train_shard_00000", "doc_id": 1221 }, "chunk_id": "train_shard_00000_1221_0", "global_id": 1348 }, { "text": "Bile salts are biosurfactants that can induce structure transformations in supramolecular nanoassemblies with conventional surfactants owing to their unique, planar amphiphilic character and the rigidity of their hydrophobic steroid skeleton. However, structural information about the association of bile salts and amphiphilic glycosides is lacking. In this work, we investigated the micelle structure of two anionic di- and trihydroxy bile salts [sodium deoxycholate (SDC) and sodium cholate (SC)] and a conventional anionic surfactant [sodium dodecyl sulfate (SDS)] in mixtures with a nonionic steviol glycoside [α-glucosyl stevia (Stevia-G)] and studied their potential as a nanocarrier system for two poorly water-soluble drugs (clotrimazole and ketoconazole). Decreased critical micelle concentrations determined from surface tension measurements demonstrate synergistic interactions between Stevia-G and SDS/SDC/SC in a decreasing order. Small-angle X-ray and neutron scattering, interpreted by a core-shell ellipsoid model, indicate that SDS and bile salts act differently on the mixed micelle structure. Compared with SDS/Stevia-G, bile salt/Stevia-G had a core-shell structure more similar to that of pure Stevia-G micelles. SDC and SDS had an increasing and decreasing influence, respectively, on the available molecular surface area in mixtures with Stevia-G on the micelle core but a similar influence on the micelle shell solvation number relative to that of their pure micellar structures. The number of bile salt hydroxyl groups was influential in determining the micelle stoichiometry: an increasing number of hydroxyl groups corresponded to decreasing bile salt aggregation numbers and a smaller hydrophobic micellar core. The core volume was the most important structural factor in explaining the drug solubilization capacity of the nanocarrier systems", "token_count": 473, "char_count": 1870, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5953, "quality_score": 0.7977, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:41.368911", "source": { "split": "train_shard_00000", "doc_id": 1222 }, "chunk_id": "train_shard_00000_1222_0", "global_id": 1349 }, { "text": "Therefore, bile salt-steviol glycoside mixed micellar assemblies exhibit structure control mechanisms allowing the fine-tuning of their interior hydrophobic domains important for nanocarrier applications toward solubilization of poorly water-soluble drugs.\n\nTailoring the Self-Assembly of Steviol Glycoside Nanocarriers with Steroidal Amphiphiles.", "token_count": 91, "char_count": 347, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8974, "quality_score": 0.9487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:41.757525", "source": { "split": "train_shard_00000", "doc_id": 1222 }, "chunk_id": "train_shard_00000_1222_1", "global_id": 1350 }, { "text": "The aim of this study was to obtain the Lactobacillus plantarum ATCC14917 with high-level resistance to penicillin and evaluate their probiotic traits using laboratory evolution assay and whole-genome sequencing. In penicillin environment, the minimum inhibitory concentration (MIC) of L. plantarum to penicillin increased from 1 μg/mL to 16 μg/mL and remained stable after the removal of antibiotic pressure, suggesting that the resistance acquisition to penicillin was an irreversible process. Subsequently, change of probiotic characteristics was further evaluated, and the results showed that the acid tolerance, bile tolerance and adhesion ability were significantly declined in the highly resistant strains. Whole-genome sequencing indicated that genes encoding hypothetical protein, LPXTG-motif cell wall anchor domain protein and acetyltransferase were detected in highly resistant L. plantarum, and these genes were still present after the following subculture in the absence of penicillin, suggesting that these three mutants might be the main reason for the development of penicillin resistance. The homology-based analysis of surrounding DNA regions of mutant genes was further performed and indicated that no resistant genes were located on mobile elements in evolved L. plantarum strains, signifying that the spread of antibiotic resistance genes in the gut would not occur for these mutant genes. This study provided a basis for the combined use of highly resistant L. plantarum and penicillin in the treatment of pathogen induced gut diseases.\n\nEvaluation of penicillin-resistance and probiotic traits in Lactobacillus plantarum during laboratory evolution.", "token_count": 386, "char_count": 1673, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5702, "quality_score": 0.7851, "entities": { "genes": [ "ATCC14917" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:42.377437", "source": { "split": "train_shard_00000", "doc_id": 1223 }, "chunk_id": "train_shard_00000_1223_0", "global_id": 1351 }, { "text": "We conducted whole-genome sequencing to investigate the serotypes, the presence of virulence and antimicrobial resistance genes, and the genetic relationships among isolates of Actinobacillus. pleuropneumoniae derived from diseased pigs. Serotype 2 (71.2%) was the most common, but the prevalence of serotypes 6 (13.6%) and 15 (6.8%) increased. Existing vaccines are considered ineffective on the isolates belonging to serotypes 6 and 15. The phylogenetic tree based on core genome single nucleotide polymorphisms showed that the isolates were clustered by serotype. Of the isolates, 62.5% did not have an antimicrobial resistance gene, including a florfenicol resistance gene, but 32.2% had a tetracycline resistance gene. The antimicrobial resistant phenotype and genotype were almost identical. The plasmid-derived contigs harbored resistance genes of aminoglycosides, tetracyclines, β-lactams, phenicols, or sulfonamides. It has been suggested that isolates with different genetic properties from vaccine strains are circulating; however, antimicrobial resistance may not be widespread.\n\nCharacterization of Actinobacillus pleuropneumoniae isolated from pigs in Japan using whole genome sequencing.", "token_count": 328, "char_count": 1202, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7107, "quality_score": 0.8553, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:42.949685", "source": { "split": "train_shard_00000", "doc_id": 1224 }, "chunk_id": "train_shard_00000_1224_0", "global_id": 1352 }, { "text": "A serious factor hampering global maize production is gray leaf spot disease. Cercospora zeina is one of the causative pathogens, but population genomics analysis of C. zeina is lacking. We conducted whole-genome Illumina sequencing of a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe, and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the C. zeina isolates was done by (1) de novo assembly of the reads with SPAdes, (2) annotation with BRAKER, and (3) protein clustering with OrthoFinder. A published long-read assembly of C. zeina (CMW25467) from Zambia was included and annotated using the same pipeline. This analysis revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. Accessory gene content was largely shared between isolates from all countries, with a few genes unique to populations from Southern Africa (32) or East Africa (6). There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). PCA, ADMIXTURE, and phylogenetic analysis using a neighbor-net network indicated a population structure with a geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, possibly from 2 regional founder populations, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa.\n\nPopulation genomic analyses suggest recent dispersal events of the pathogen Cercospora zeina into East and Southern African maize cropping systems.", "token_count": 453, "char_count": 1829, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5963, "quality_score": 0.7981, "entities": { "genes": [ "CMW25467" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:43.582787", "source": { "split": "train_shard_00000", "doc_id": 1225 }, "chunk_id": "train_shard_00000_1225_0", "global_id": 1353 }, { "text": "Continuously increasing global temperatures present great challenges to food security. Grain size, one of the critical components determining grain yield in rice (Oryza sativa L.), is a prime target for genetic breeding. Thus, there is an immediate need for genetic improvement in rice to maintain grain yield under heat stress. However, quantitative trait loci (QTLs) endowing heat stress tolerance and grain size in rice are extremely rare. Here, we identified a novel negative regulator with pleiotropic effects, Thermo-Tolerance and grain Length 1 (TTL1), from the super pan-genomic and transcriptomic data. Loss-of-function mutations in TTL1 enhanced heat tolerance, and caused an increase in grain size by coordinating cell expansion and proliferation. TTL1 was shown to function as a transcriptional regulator and localized to the nucleus and cell membrane. Furthermore, haplotype analysis showed that hap\n\nIdentification of natural allelic variation in TTL1 controlling thermotolerance and grain size by a rice super pan-genome.", "token_count": 233, "char_count": 1036, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [ "TTL1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:44.054746", "source": { "split": "train_shard_00000", "doc_id": 1226 }, "chunk_id": "train_shard_00000_1226_0", "global_id": 1354 }, { "text": "Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like\n\nA Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other", "token_count": 262, "char_count": 907, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:44.602183", "source": { "split": "train_shard_00000", "doc_id": 1227 }, "chunk_id": "train_shard_00000_1227_0", "global_id": 1355 }, { "text": "Fine mapping of quantitative trait loci (QTL) to dissect the genetic basis of traits of interest is essential to modern breeding practice. Here, we employed a multitiered haplotypic marker system to increase fine mapping accuracy by constructing a chromosome-level, haplotype-resolved parental genome, accurate detection of recombination sites, and allele-specific characterization of the transcriptome. In the first tier of this system, we applied the preexisting panel of 2,000 rhAmpSeq core genome markers that is transferable across the entire Vitis genus and provides a genomic resolution of 200 kb to 1 Mb. The second tier consisted of high-density haplotypic markers generated from Illumina skim sequencing data for samples enriched for relevant recombinations, increasing the potential resolution to hundreds of base pairs. We used this approach to dissect a novel Resistance to Plasmopara viticola-33 (RPV33) locus conferring resistance to grapevine downy mildew, narrowing the candidate region to only 0.46 Mb. In the third tier, we used allele-specific RNA-seq analysis to identify a cluster of 3 putative disease resistance RPP13-like protein 2 genes located tandemly in a nonsyntenic insertion as candidates for the disease resistance trait. In addition, combining the rhAmpSeq core genome haplotype markers and skim sequencing-derived high-density haplotype markers enabled chromosomal-level scaffolding and phasing of the grape Vitis × doaniana 'PI 588149' assembly, initially built solely from Pacific Biosciences (PacBio) high-fidelity (HiFi) reads, leading to the correction of 16 large-scale phasing errors. Our mapping strategy integrates high-density, phased genetic information with individual reference genomes to pinpoint the genetic basis of QTLs and will likely be widely adopted in highly heterozygous species.\n\nA multitiered haplotype strategy to enhance phased assembly and fine mapping of a disease resistance locus.", "token_count": 497, "char_count": 1946, "word_count": 275, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [ "RPV33", "RPP13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:45.249503", "source": { "split": "train_shard_00000", "doc_id": 1228 }, "chunk_id": "train_shard_00000_1228_0", "global_id": 1356 }, { "text": "The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.\n\nIdentification of hidden N4-like viruses and their interactions with hosts.", "token_count": 139, "char_count": 645, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7159, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:45.681158", "source": { "split": "train_shard_00000", "doc_id": 1229 }, "chunk_id": "train_shard_00000_1229_0", "global_id": 1357 }, { "text": "Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal effectors that share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces that underlie the sequence variability of structurally-analogous effectors, we focused on MAX effectors, a structural family of effectors that are major determinants of virulence in the rice blast fungus Pyricularia oryzae. Using structure-informed gene annotation, we identified 58 to 78 MAX effector genes per genome in a set of 120 isolates representing seven host-associated lineages. The expression of MAX effector genes was primarily restricted to the early biotrophic phase of infection and strongly influenced by the host plant. Pangenome analyses of MAX effectors demonstrated extensive presence/absence polymorphism and identified gene loss events possibly involved in host range adaptation. However, gene knock-in experiments did not reveal a strong effect on virulence phenotypes suggesting that other evolutionary mechanisms are the main drivers of MAX effector losses. MAX effectors displayed high levels of standing variation and high rates of non-synonymous substitutions, pointing to widespread positive selection shaping the molecular diversity of MAX effectors. The combination of these analyses with structural data revealed that positive selection acts mostly on residues located in particular structural elements and at specific positions. By providing a comprehensive catalog of amino acid polymorphism, and by identifying the structural determinants of the sequence diversity, our work will inform future studies aimed at elucidating the function and mode of action of MAX effectors.\n\nAdaptive evolution in virulence effectors of the rice blast fungus Pyricularia oryzae.", "token_count": 400, "char_count": 1937, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6292, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:46.320475", "source": { "split": "train_shard_00000", "doc_id": 1230 }, "chunk_id": "train_shard_00000_1230_0", "global_id": 1358 }, { "text": "Gastrointestinal (GI) colonization by\n\nGenome-wide screens reveal shared and strain-specific genes that facilitate enteric colonization by", "token_count": 32, "char_count": 138, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:46.712352", "source": { "split": "train_shard_00000", "doc_id": 1231 }, "chunk_id": "train_shard_00000_1231_0", "global_id": 1359 }, { "text": "In this study, two strains of lactic acid bacteria (Lacticaseibacillus paracasei GL1 and Lactobacillus helveticus SNA12) and one yeast strain of Kluyveromyces marxianus G-Y4 (G-Y4) isolated from Tibetan kefir grains were co-cultured. It was found that the addition of G-Y4 could not only promote the growth of lactic acid bacteria, but also increase the release of metabolites (lactic acid, ethanol, and amino nitrogen). Furthermore, the addition of live cells and cell-free fermentation supernatant (CFS) of G-Y4 could increase the ability of biofilm formation. Morever, the surface characteristics results showed that the addition of G-Y4 live cells could enhance the aggregation ability and hydrophobicity of LAB. Meanwhile, adding live cells and CFS of G-Y4 could promote the release of signaling molecule AI-2 and enhance the expression of the LuxS gene related to biofilm formation. In addition, Fourier-transform infrared spectroscopy and chemical composition analysis were used to investigate the composition of the biofilm, and the results indicated that the biofilm was mainly composed of a small amount of protein but it was rich in polysaccharides including glucose, galactose, and mannose with different ratios. Finally, the formation of biofilm could delay the decline of the number of viable bacteria in storage fermented milk.\n\nThe interaction among Kluyveromyces marxianus G-Y4, Lacticaseibacillus paracasei GL1, and Lactobacillus helveticus SNA12 and signaling molecule AI-2 participate in the formation of biofilm.", "token_count": 398, "char_count": 1533, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5605, "quality_score": 0.7803, "entities": { "genes": [ "GL1", "SNA12" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:47.344800", "source": { "split": "train_shard_00000", "doc_id": 1232 }, "chunk_id": "train_shard_00000_1232_0", "global_id": 1360 }, { "text": "Industrial manufacturing of bioproducts, especially bioethanol, can benefit from high-temperature fermentation, which requires the use of thermotolerant yeast strains. Mitochondrial activity in yeast is closely related to its overall metabolism. However, the mitochondrial respiratory changes in response to adaptive thermotolerance are still poorly understood and have been rarely utilized for developing thermotolerant yeast cell factories. Here, adaptive evolution and transcriptional sequencing, as well as whole-genome-level gene knockout, were used to obtain a thermotolerant strain of\n\nElucidation and engineering mitochondrial respiratory-related genes for improving bioethanol production at high temperature in", "token_count": 165, "char_count": 719, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7978, "quality_score": 0.8989, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:47.825489", "source": { "split": "train_shard_00000", "doc_id": 1233 }, "chunk_id": "train_shard_00000_1233_0", "global_id": 1361 }, { "text": "Over the past two decades, Corynebacterium striatum has been increasingly isolated from clinical cultures with most isolates showing increased antimicrobial resistance (AMR) to last resort agents. Advances in the field of pan genomics would facilitate the understanding of the clinical significance of such bacterial species previously thought to be among commensals paving the way for identifying new drug targets and control strategies.\n\nPangenome analysis of Corynebacterium striatum: insights into a neglected multidrug-resistant pathogen.", "token_count": 117, "char_count": 543, "word_count": 73, "semantic_coherence": 1, "information_density": 0.863, "quality_score": 0.9315, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:48.249465", "source": { "split": "train_shard_00000", "doc_id": 1234 }, "chunk_id": "train_shard_00000_1234_0", "global_id": 1362 }, { "text": "The development of models for predicting hepatotoxicity is warranted, as the hepatotoxicity risk of 38-51% of compounds is undetectable in nonclinical studies. Cholestatic drug-induced liver injury (DILI) is a condition in which bile acids are abnormally excreted into the capillary bile canaliculi and are accumulated in hepatocytes, caused by the inhibition of bile salt export pump (BSEP), a transporter that is mainly associated with excretion of bile acids. Although laboratory animals are used as models, the use of human-derived cells is required owing to species differences. Unfortunately, primary human hepatocytes (PHHs) show rapid loss of function in culture and difficulties in forming bile canaliculi. Therefore, we aimed to develop an in vitro culture method for the efficient formation of bile canaliculi and for assessing the function of BSEP in PHHs. Here, PHHs were cultured from 1 h after thawing to day 2 with Z-VAD-FMK, a total caspase inhibitor, and RevitaCell™ supplement, an irreversible Rho-associated coiled-coil forming kinase (ROCK) inhibitor, in combination with RM-101. The PHHs formed bile canaliculi and showed BSEP function on day 6 of culture. Our findings suggest that cultured PHHs may improve the prediction accuracy of the risks of cholestatic DILI-contained toxicity on bile canaliculi.\n\nCulture methods focusing on bile canalicular formation using primary human hepatocytes in a short time.", "token_count": 384, "char_count": 1431, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:48.871561", "source": { "split": "train_shard_00000", "doc_id": 1235 }, "chunk_id": "train_shard_00000_1235_0", "global_id": 1363 }, { "text": "The milk fat globule membrane (MFGM) can protect probiotic bacteria from bile stress. However, its potential mechanism has not been reported. In this study, the viability, morphology and gene transcriptional response of Bifidobacterium longum ssp. infantis ATCC 15697 (BI_15697) stressed by bile salts with or without MFGM were investigated. It was shown that MFGM alleviated the reduction in BI_15697 population induced by 0.2% porcine bile stress and restored the population to the control levels. MFGM ameliorated the shrunken, fragmented appearance and irregular morphology of BI_15697 and maintained cell integrity disrupted by bile stress. RNA-sequencing results showed that MFGM increased transport of glucose and raffinose and decreased that of branched-chain amino acids (BCAA) in the presence of bile salts. MFGM stimulated the expression of genes involved in the synthesis of raffinose in galactose metabolism and the metabolism of BCAA, suggesting that MFGM stimulated the accumulation of raffinose and BCAA in the presence of bile. In addition, MFGM stimulated the expression of 2 bile efflux transporters under bile stress. Together, the multifactorial response helps BI_15697 excrete bile salts and maintain cellular integrity in response to bile stress. This study proposes a mechanism for the protection of BI_15697 against bile salt stress by MFGM, thereby providing a molecular basis for its application in incorporation of probiotics.\n\nMilk fat globule membrane protects Bifidobacterium longum ssp. infantis ATCC 15697 against bile stress by modifying global transcriptional responses.", "token_count": 437, "char_count": 1605, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5517, "quality_score": 0.7759, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:49.505205", "source": { "split": "train_shard_00000", "doc_id": 1236 }, "chunk_id": "train_shard_00000_1236_0", "global_id": 1364 }, { "text": "The thermotolerant yeast Kluyveromyces marxianus is known for its potential in high-temperature ethanol fermentation, yet it suffers from excess acetic acid production at elevated temperatures, which hinders ethanol production. To better understand how the yeast responds to acetic acid stress during high-temperature ethanol fermentation, this study investigated its transcriptomic changes under this condition. RNA sequencing (RNA-seq) was used to identify differentially expressed genes (DEGs) and enriched gene ontology (GO) terms and pathways under acetic acid stress. The results showed that 611 genes were differentially expressed, and GO and pathway enrichment analysis revealed that acetic acid stress promoted protein catabolism but repressed protein synthesis during high-temperature fermentation. Protein-protein interaction (PPI) networks were also constructed based on the interactions between proteins coded by the DEGs. Hub genes and key modules in the PPI networks were identified, providing insight into the mechanisms of this yeast's response to acetic acid stress. The findings suggest that the decrease in ethanol production is caused by the imbalance between protein catabolism and protein synthesis. Overall, this study provides valuable insights into the mechanisms of K. marxianus's response to acetic acid stress and highlights the importance of maintaining a proper balance between protein catabolism and protein synthesis for high-temperature ethanol fermentation.\n\nTranscriptomic analysis reveals hub genes and pathways in response to acetic acid stress in Kluyveromyces marxianus during high-temperature ethanol fermentation.", "token_count": 369, "char_count": 1655, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5516, "quality_score": 0.7758, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:50.092719", "source": { "split": "train_shard_00000", "doc_id": 1237 }, "chunk_id": "train_shard_00000_1237_0", "global_id": 1365 }, { "text": "Cyclospora cayetanensis is an enteric coccidian parasite responsible for gastrointestinal disease transmitted through contaminated food and water. It has been documented in several countries, mostly with low-socioeconomic levels, although major outbreaks have hit developed countries. Detection methods based on oocyst morphology, staining, and molecular testing have been developed. However, the current MLST panel offers an opportunity for enhancement, as amplification of all molecular markers remains unfeasible in the majority of samples. This study aims to address this challenge by evaluating two approaches for analyzing the genetic diversity of C. cayetanensis and identifying reliable markers for subtyping: core homologous genes and mitochondrial genome analysis. A pangenome was constructed using 36 complete genomes of C. cayetanensis, and a haplotype network and phylogenetic analysis were conducted using 33 mitochondrial genomes. Through the analysis of the pangenome, 47 potential markers were identified, emphasizing the need for more sequence data to achieve comprehensive characterization. Additionally, the analysis of mitochondrial genomes revealed 19 single-nucleotide variations that can serve as characteristic markers for subtyping this parasite. These findings not only contribute to the selection of molecular markers for C. cayetanensis subtyping, but they also drive the knowledge toward the potential development of a comprehensive genotyping method for this parasite.\n\nEvaluation of nuclear and mitochondrial phylogenetics for the subtyping of Cyclospora cayetanensis.", "token_count": 364, "char_count": 1600, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:50.672920", "source": { "split": "train_shard_00000", "doc_id": 1238 }, "chunk_id": "train_shard_00000_1238_0", "global_id": 1366 }, { "text": "The human pangenome, a new reference sequence, addresses many limitations of the current GRCh38 reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. We employed a k-mer indexing strategy for comparative analysis across multiple assemblies, including the pangenome reference, GRCh38, and CHM13, a telomere-to-telomere reference assembly. Our k-mer indexing approach enabled us to identify a valuable collection of universally conserved sequences across all assemblies, referred to as \"pan-conserved segment tags\" (PSTs). By examining intervals between these segments, we discerned highly conserved genomic segments and those with structurally related polymorphisms. We found 60,764 polymorphic intervals with unique geo-ethnic features in the pangenome reference. In this study, we utilized ultra-conserved sequences (PSTs) to forge a link between human pangenome assemblies and reference genomes. This methodology enables the examination of any sequence of interest within the pangenome, using the reference genome as a comparative framework.\n\nPan-conserved segment tags identify ultra-conserved sequences across assemblies in the human pangenome.", "token_count": 292, "char_count": 1213, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6646, "quality_score": 0.8323, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:51.239832", "source": { "split": "train_shard_00000", "doc_id": 1239 }, "chunk_id": "train_shard_00000_1239_0", "global_id": 1367 }, { "text": "In Iran, dairy-based fermented foods, like yogurt, cheese, fermented milk, buttermilk, kashk, butter, and Doogh are essential dietary components. Doogh is typically made using fermented yogurt or buttermilk. However, a literature review revealed a lack of research on extracting probiotics from Doogh during processing. As dairy products contain lactic acid bacteria, the aim was to isolate and identify them using culture and PCR-sequencing techniques. Samples of traditional Doogh were collected throughout the Chaharmahal Bakhtiari province of Iran. A specific number of strains have been isolated and among them, the strain LB12 was selected for further characterization based on its probiotic properties. Probiotic properties like adhesion capability, antagonistic activity, resistance to the simulated stomach and intestinal fluids, pH, and bile salt were assessed according to National Standard ISO 19459 of Iran. The LB12 strain was identified as Lacticaseibacillus paracasei by partial 16 rDNA sequence analysis. This L. paracasei strain demonstrated its in vitro resilience to stomach conditions with 58.04% survival at pH 3 and more than 50% resistance to different bile salt concentrations. L. paracasei LB12 showed a cell surface hydrophobicity of 38.18% and a 6.2 log CFU/ml resistance to simulated gastric and intestinal fluids, and a rate of auto- and co-aggregation of 15% and 22%, respectively. L. parasei LB12 showed also a moderate adhesion to HT-29 cell line. In conclusion, L. paracasei LB12 is considered a promising potential probiotic suitable for the development of food supplement and pharmaceutical products.\n\nLacticaseibacillus paracasei LB12, a Potential Probiotic Isolated from Traditional Iranian Fermented Milk (Doogh).", "token_count": 483, "char_count": 1752, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [ "LB12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:51.883065", "source": { "split": "train_shard_00000", "doc_id": 1240 }, "chunk_id": "train_shard_00000_1240_0", "global_id": 1368 }, { "text": "Oro-gastrointestinal stress in the digestive tract is the main stress to which orally administered probiotics are exposed. The regulation of oro-gastrointestinal transit (OGT) stress on the adhesion and survival of probiotics under continuous exposure to simulated salivary-gastric juice-intestinal juice was researched in this study.\n\nThe regulation of simulated artificial oro-gastrointestinal transit stress on the adhesion of Lactobacillus plantarum S7.", "token_count": 122, "char_count": 457, "word_count": 59, "semantic_coherence": 1, "information_density": 0.6441, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:52.280093", "source": { "split": "train_shard_00000", "doc_id": 1241 }, "chunk_id": "train_shard_00000_1241_0", "global_id": 1369 }, { "text": "Balamuthia mandrillaris is a pathogenic protozoan that causes a rare but almost always fatal infection of the central nervous system and, in some cases, cutaneous lesions. Currently, the genomic data for this free-living amoeba include the description of several complete mitochondrial genomes. In contrast, two complete genomes with draft quality are available in GenBank, but none of these have a functional annotation. In the present study, the complete genome of B. mandrillaris isolated from a freshwater artificial lagoon was sequenced and assembled, obtaining an assembled genome with better assembly quality parameter values than the currently available genomes. Afterward, the genome mentioned earlier, along with strains V039 and 2046, were subjected to functional annotation. Finally, comparative genomics analysis was performed, and it was found that homologous genes in the core genome potentially involved in the virulence of Acanthamoeba spp. and Trypanosoma cruzi. Moreover, eleven of fifteen genes were identified in the three strains described as potential target genes to develop new treatment approaches for B. mandrillaris infections. These results describe proteins in this protozoan's complete genome and help prioritize which target genes could be used to develop new treatments.\n\nFunctional annotation and comparative genomics analysis of Balamuthia mandrillaris reveals potential virulence-related genes.", "token_count": 319, "char_count": 1430, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:52.850407", "source": { "split": "train_shard_00000", "doc_id": 1242 }, "chunk_id": "train_shard_00000_1242_0", "global_id": 1370 }, { "text": "Lyme disease is the most common vector-borne disease in North America and Europe. The clinical manifestations of Lyme disease vary based on the genospecies of the infecting Borrelia burgdorferi spirochete, but the microbial genetic elements underlying these associations are not known. Here, we report the whole genome sequence (WGS) and analysis of 299 B. burgdorferi (Bb) isolates derived from patients in the Eastern and Midwestern US and Central Europe. We develop a WGS-based classification of Bb isolates, confirm and extend the findings of previous single- and multi-locus typing systems, define the plasmid profiles of human-infectious Bb isolates, annotate the core and strain-variable surface lipoproteome, and identify loci associated with disseminated infection. A core genome consisting of ~900 open reading frames and a core set of plasmids consisting of lp17, lp25, lp36, lp28-3, lp28-4, lp54, and cp26 are found in nearly all isolates. Strain-variable (accessory) plasmids and genes correlate strongly with phylogeny. Using genetic association study methods, we identify an accessory genome signature associated with dissemination in humans and define the individual plasmids and genes that make up this signature. Strains within the RST1/WGS A subgroup, particularly a subset marked by the OspC type A genotype, have increased rates of dissemination in humans. OspC type A strains possess a unique set of strongly linked genetic elements including the presence of lp56 and lp28-1 plasmids and a cluster of genes that may contribute to their enhanced virulence compared to other genotypes. These features of OspC type A strains reflect a broader paradigm across Bb isolates, in which near-clonal genotypes are defined by strain-specific clusters of linked genetic elements, particularly those encoding surface-exposed lipoproteins. These clusters of genes are maintained by strain-specific patterns of plasmid occupancy and are associated with the probability of invasive infection.", "token_count": 482, "char_count": 1998, "word_count": 292, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [ "RST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:53.497823", "source": { "split": "train_shard_00000", "doc_id": 1243 }, "chunk_id": "train_shard_00000_1243_0", "global_id": 1371 }, { "text": "Whole genome sequencing of human Borrelia burgdorferi isolates reveals linked blocks of accessory genome elements located on plasmids and associated with human dissemination.", "token_count": 41, "char_count": 174, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:53.855996", "source": { "split": "train_shard_00000", "doc_id": 1243 }, "chunk_id": "train_shard_00000_1243_1", "global_id": 1372 }, { "text": "Pangenome graphs quickly become the central data structure representing the diversity of variation we see across related genomes. Pangenome graphs have been published for some species, including plants of agronomic interest. However, visualizing these graphs is not easy as the graphs are large, and variants within these graphs are complex. Tools are needed to visualize graph data structures. Here, we present a workflow to search and visualize a wheat pangenome graph using Wheat Panache. The approach presented assists researchers interested in wheat genomics.\n\nInvestigating Pangenome Graphs Using Wheat Panache.", "token_count": 128, "char_count": 617, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6966, "quality_score": 0.8483, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:54.286067", "source": { "split": "train_shard_00000", "doc_id": 1244 }, "chunk_id": "train_shard_00000_1244_0", "global_id": 1373 }, { "text": "Upon infection, transcriptional shifts in both a host bacterium and its invading phage determine host and viral fitness. The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and phages, regulate diverse features of bacterial cell physiology and impact phage infection dynamics. Through a pangenome analysis of\n\nXRE Transcription Factors Conserved in", "token_count": 93, "char_count": 412, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8103, "quality_score": 0.9052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:54.662351", "source": { "split": "train_shard_00000", "doc_id": 1245 }, "chunk_id": "train_shard_00000_1245_0", "global_id": 1374 }, { "text": "Staphylococcus chromogenes and Staphylococcus simulans are commonly found in intramammary infections (IMI) associated with bovine subclinical mastitis, but little is known about genotypic variation and relatedness within species. This includes knowledge about genes encoding antimicrobial resistance (AMR) and potential virulence factors (pVF). The aim of this study was therefore to investigate these aspects by whole-genome sequencing of milk isolates from Swedish dairy cows with subclinical mastitis in an observational study. We also wanted to study if specific genotypes were associated with persistent IMI and the inflammatory response at udder quarter level. In total, 105 and 118 isolates of S. chromogenes and S. simulans, respectively, were included. Isolates were characterized using a 7-locus multilocus sequence typing (7-MLST), core genome analysis and in-silico analysis of AMR and pVF genes. Forty-seven sequence types (ST) and 7 core genome clusters of S. chromogenes were identified, and the most common ST were ST-6 and ST-109, both belonging to cluster VII. A 7-locus MLST scheme for S. simulans was not available, but 3 core genome clusters and 5 subclusters were described. Overall, substantial variation in ST and clusters among cows and herds were found in both species. Some ST of S. chromogenes were found in several herds, indicating spread between herds. Moreover, within-herd spread of the same genotype was observed for both species. Only a few AMR genes [blaZ, strpS194, vga(A)] were detected in a limited number of isolates, with the exception of blaZ coding for β-lactamase, which was identified in 22% of the isolates of S. chromogenes with ST-19, ST-102, and ST-103 more commonly carrying this gene compared with other ST. However, the blaZ gene was not identified in S. simulans. The average total number of pVF detected per isolate was similar in S. chromogenes (n = 30) and S", "token_count": 512, "char_count": 1914, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5898, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:55.296508", "source": { "split": "train_shard_00000", "doc_id": 1246 }, "chunk_id": "train_shard_00000_1246_0", "global_id": 1375 }, { "text": "simulans (n = 33), but some variation in total numbers and presence of specific pVF or functional groups of pVF, was shown between ST/clusters within species. Differences in inflammatory response and potentially in persistent IMI at udder quarter level were found between S. chromogenes subtypes but not between S. simulans subtypes. In conclusion, the results from the present study generates new insight into the epidemiology of bovine S. chromogenes and S. simulans IMI, which can have implications for future prevention and antimicrobial treatment of infections related to these species.\n\nGenotypic characterization of Staphylococcus chromogenes and Staphylococcus simulans from Swedish cases of bovine subclinical mastitis.", "token_count": 179, "char_count": 728, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7212, "quality_score": 0.8606, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:55.746181", "source": { "split": "train_shard_00000", "doc_id": 1246 }, "chunk_id": "train_shard_00000_1246_1", "global_id": 1376 }, { "text": "This study investigates the impact of charge and chain length of bile salts in the bilosomes on the oral bioavailability of insulin (IN) by examining their uptake via the apical sodium-dependent bile acid transporter (ASBT). Deoxycholic acid bile salt was conjugated with different amino acids to create conjugates with varying charge and chain length, which were then embedded in liposomes. The resulting bilosomes had a particle size <400 nm, a PDI of 0.121 ± 0.03, and an entrapment efficiency of ∼70 %, while maintaining the chemical and conformational integrity of the loaded IN. Bilosomes also provided superior protection in biological fluids without compromising their biophysical attributes. Quantitative studies using the Caco-2 cell line demonstrated that anionic bilosomes were taken up more efficiently through ASBT than cationic bilosomes with 4- and 1.3-fold increase, respectively. Ex-vivo permeability studies corroborated these findings. In-vivo efficacy studies revealed a 1.6-fold increase in the AUC of IN with bilosomes compared to subcutaneous IN. The developed bilosomes were able to reduce blood glucose levels by ∼65 % at 6 h, with a cumulative hypoglycemic value of 35 % and a BAR of ∼30 %. These results suggest that ASBT can be a suitable target for improving the oral bioavailability of bilosomes containing IN.\n\nEnhancing oral bioavailability of insulin through bilosomes: Implication of charge and chain length on apical sodium-dependent bile acid transporter (ASBT) uptake.", "token_count": 398, "char_count": 1506, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:56.365842", "source": { "split": "train_shard_00000", "doc_id": 1247 }, "chunk_id": "train_shard_00000_1247_0", "global_id": 1377 }, { "text": "Loganin is an iridoid with potent pharmacological effects. Loganin contains a hemiacetal structure and can convert to dialdehyde intermediates after deglycosylation. We hypothesized that the metabolites of loganin with hemiacetal can generate reactive dialdehyde intermediates. This study aims to characterize the metabolic profiling of loganin and especially for the unstable dialdehyde intermediates by using ultra-performance liquid chromatograph-quadrupole orbitrap mass spectrometry. In this study, a total of 26 stable metabolites were identified in loganin-treated rats. Loganin underwent different metabolism in the intestine and liver, which was confirmed mainly by the metabolites in the hepatic portal vein. In the intestine, the major metabolic pathways were ester hydrolysis and deglycosylation, followed by methylation and dehydrogenation. The hepatic metabolism pathways were hydrogenation, hydroxylation, glucuronidation, and sulfonation. The circulating metabolites with high abundance were mainly derived from intestinal metabolism. Importantly, 11 unstable dialdehyde intermediates of loganin were identified and described for the first time. The dialdehyde intermediates were identified by their dihydropyridine conjugates with amino acids. The dialdehyde intermediates were mainly produced in the intestine. The dialdehyde intermediates enable covalent modification of intestinal proteins. Loganin can up-regulate the activity of intestinal bile salt hydrolase (BSH), catalyzing bile acid metabolism. The level of protein adducts was positively associated with BSH activity, indicating dialdehyde intermediates played a key role in the up-regulation of BSH activities. In conclusion, this study not only demonstrates the characteristic metabolic fate of loganin but also facilitates the understanding of the pharmacologic effects of dialdehyde intermediates.", "token_count": 478, "char_count": 1879, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5597, "quality_score": 0.7798, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:57.008204", "source": { "split": "train_shard_00000", "doc_id": 1248 }, "chunk_id": "train_shard_00000_1248_0", "global_id": 1378 }, { "text": "Identification of intestinal metabolic activation of loganin generated dialdehyde reactive intermediates improves intestinal bile salt hydrolase activities.", "token_count": 37, "char_count": 156, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:57.369906", "source": { "split": "train_shard_00000", "doc_id": 1248 }, "chunk_id": "train_shard_00000_1248_1", "global_id": 1379 }, { "text": "Aspergillus flavus infection and subsequent aflatoxin contamination are considered the major constraints in senna (Cassia angustifolia Vahl.) export. Using native epiphytic yeast to control phytopathogens is a successful strategy for managing plant diseases. In the present investigation, we exploited the antagonistic potential of epiphytic yeast isolates obtained from senna against A. flavus growth and aflatoxin B\n\nInhibitory effects of epiphytic Kluyveromyces marxianus from Indian senna (Cassia angustifolia Vahl.) on growth and aflatoxin production of Aspergillus flavus.", "token_count": 152, "char_count": 578, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7237, "quality_score": 0.8618, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:57.799352", "source": { "split": "train_shard_00000", "doc_id": 1249 }, "chunk_id": "train_shard_00000_1249_0", "global_id": 1380 }, { "text": "Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen\n\nPangenome graphs in infectious disease: a comprehensive genetic variation analysis of", "token_count": 247, "char_count": 1211, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:58.281572", "source": { "split": "train_shard_00000", "doc_id": 1250 }, "chunk_id": "train_shard_00000_1250_0", "global_id": 1381 }, { "text": "In Finland, Taylorella equigenitalis, the causative agent of contagious equine metritis (CEM), was first detected in 1992. The aim of this study was to genotype Finnish T. equigenitalis isolates to investigate the epidemiology of the infection in the Finnish horse population. A total of 34 T. equigenitalis isolates from 24 horses obtained during 1992-2021 were subjected to whole genome sequencing (WGS) and subsequent local ad hoc core genome multi-locus sequence typing (cgMLST) targeting 1259 loci. Classical MLST profiles were extracted from the whole-genome sequence data. Three novel MLST types, ST81, ST82 and ST83, and four previously described sequence types, ST16, ST17, ST50 and ST63 were detected among the isolates. cgMLST minimum spanning tree analysis using 12 allele difference as threshold, resulted in five clusters and three singletons. cgMLST clusters were congruent with the MLST-defined groups, except for the ST83 isolates which were divided into two clusters. However, the high discriminatory power cgMLST allowed differentiation between isolates of the same MLST type as each isolate had a unique core genome ST. Our study suggests that cgMLST has the prospective for being a standardised typing method for T. equigenitalis in the future, and further contributes to worldwide phylogenetic and spatio-temporal analyses needed to better understand the epidemiology of the bacterium.\n\nCore genome multilocus sequence typing analysis of Finnish Taylorella equigenitalis isolates.", "token_count": 397, "char_count": 1502, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8196, "entities": { "genes": [ "ST82", "ST83", "ST81", "ST17", "ST16", "ST63", "ST50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:59.346444", "source": { "split": "train_shard_00000", "doc_id": 1251 }, "chunk_id": "train_shard_00000_1251_0", "global_id": 1382 }, { "text": "Recently the roles of gut microbiota are highly regarded in the pathogenesis of nonalcoholic fatty liver disease (NAFLD). The intestinal bacteria regulate the metabolism of bile acids depending on bile salt hydrolase (BSH), 7-dehydroxylation, hydroxysteroid dehydrogenase (HSDH), or amide conjugation reaction, thus exerting effects on NAFLD development through bile acid receptors such as farnesoid X receptor (FXR), Takeda G-protein-coupled bile acid protein 5 (TGR5), and vitamin D receptor (VDR), which modulate nutrient metabolism and insulin sensitivity via interacting with downstream molecules. Reversely, the composition of gut microbiota is also affected by the level of bile acids in turn. We summarize the mutual regulation between the specific bacteria and bile acids in NAFLD and the latest clinical research based on microbiota and bile acids, which facilitate the development of novel treatment modalities in NAFLD.\n\nThe Crosstalk between Gut Microbiota and Bile Acids Promotes the Development of Non-Alcoholic Fatty Liver Disease.", "token_count": 279, "char_count": 1047, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8221, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:10:59.931089", "source": { "split": "train_shard_00000", "doc_id": 1252 }, "chunk_id": "train_shard_00000_1252_0", "global_id": 1383 }, { "text": "Bacterial genomes differ in both gene content and sequence mutations, which underlie extensive phenotypic diversity, including variation in susceptibility to antimicrobials or vaccine-induced immunity. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated, and clustered, representing the \"pangenome.\" Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller). ggCaller combines gene prediction, functional annotation, and clustering into a single workflow using population-wide de Bruijn graphs, removing redundancy in gene annotation and resulting in more accurate gene predictions and orthologue clustering. We applied ggCaller to simulated and real-world bacterial data sets containing hundreds or thousands of genomes, comparing it to current state-of-the-art tools. ggCaller has considerable speed-ups with equivalent or greater accuracy, particularly with data sets containing complex sources of error, such as assembly contamination or fragmentation. ggCaller is also an important extension to bacterial genome-wide association studies, enabling querying of annotated graphs for functional analyses. We highlight this application by functionally annotating DNA sequences with significant associations to tetracycline and macrolide resistance in\n\nAccurate and fast graph-based pangenome annotation and clustering with ggCaller.", "token_count": 349, "char_count": 1629, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7184, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:00.516963", "source": { "split": "train_shard_00000", "doc_id": 1253 }, "chunk_id": "train_shard_00000_1253_0", "global_id": 1384 }, { "text": "This study presents the first chromosome-level genome assembly of Hanwoo, an indigenous Korean breed of Bos taurus taurus. This is the first genome assembly of Asian taurus breed. Also, we constructed a pangenome graph of 14 B. taurus genome assemblies. The contig N50 was over 55 Mb, the scaffold N50 was over 89 Mb and a genome completeness of 95.8%, as estimated by BUSCO using the mammalian set, indicated a high-quality assembly. 48.7% of the genome comprised various repetitive elements, including DNAs, tandem repeats, long interspersed nuclear elements, and simple repeats. A total of 27,314 protein-coding genes were identified, including 25,302 proteins with inferred gene names and 2,012 unknown proteins. The pangenome graph of 14 B. taurus autosomes revealed 528.47 Mb non-reference regions in total and 61.87 Mb Hanwoo-specific regions. Our Hanwoo assembly and pangenome graph provide valuable resources for studying B. taurus populations.\n\nChromosome-level genome assembly of Korean native cattle and pangenome graph of 14 Bos taurus assemblies.", "token_count": 323, "char_count": 1060, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:01.096231", "source": { "split": "train_shard_00000", "doc_id": 1254 }, "chunk_id": "train_shard_00000_1254_0", "global_id": 1385 }, { "text": "As a probiotic, enterococcus faecium (E. faecium) has the characteristics of high temperature resistance, gastric acid resistance, bile salt resistance, etc. It can also effectively improve animal performance and immunity and improve the animal's intestinal environment, so in recent years it has been more widely used in the livestock industry. However, due to the improper use of antibiotics and the growing environmental stress of strains, the drug resistance of enterococcus faecium has become more and more serious, and because some enterococcus faecium carry virulence genes, leading to the emergence of pathogenic strains, its safety issues have been widely concerned. This paper focuses on the biological characteristics of enterococcus faecium, the application of this bacterium in animal husbandry and the safety issues in its use, with a view to providing a reference for the application of enterococcus faecium in the development of animal husbandry.\n\nProgress in the application of Enterococcus faecium in animal husbandry.", "token_count": 233, "char_count": 1036, "word_count": 153, "semantic_coherence": 1, "information_density": 0.5621, "quality_score": 0.781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:01.577355", "source": { "split": "train_shard_00000", "doc_id": 1255 }, "chunk_id": "train_shard_00000_1255_0", "global_id": 1386 }, { "text": "The recently identified monkeypox virus (MPXV or mpox) is a zoonotic orthopox virus that infects humans and causes diseases with traits like smallpox. The world health organization (WHO) estimates that 3-6% of MPXV cases result in death. As it might impact everyone globally, like COVID, and become the next pandemic, the cure for this disease is important for global public health. The high incidence and disease ratio of MPXV necessitates immediate efforts to design a unique vaccine candidate capable of addressing MPXV diseases. Here, we used a computational pan-genome-based vaccine design strategy for all currently reported 19 MPXV strains acquired from different regions of the world. Thus, this study's objective was to develop a new and safe vaccine candidate against MPXV by targeting the membrane CL5 protein; identified after the pangenome analysis. Proteomics and reverse vaccinology have covered up all of the MPXV epitopes that would usually stimulate robust host immune responses. Following this, only two mapped (MHC-I, MHC-II, and B-cell) epitopes were observed to be extremely effective that can be used in the construction of CL5 protein vaccine candidates. The suggested vaccine (V5) candidate from eight vaccine models was shown to be antigenic, non-allergenic, and stable (with 213 amino acids). The vaccine's candidate efficacy was evaluated by using many\n\nDelineating multi-epitopes vaccine designing from membrane protein CL5 against all monkeypox strains: a pangenome reverse vaccinology approach.", "token_count": 360, "char_count": 1525, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [ "CL5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:02.168790", "source": { "split": "train_shard_00000", "doc_id": 1256 }, "chunk_id": "train_shard_00000_1256_0", "global_id": 1387 }, { "text": "Members of the genus\n\nPangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus", "token_count": 29, "char_count": 136, "word_count": 19, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:02.533059", "source": { "split": "train_shard_00000", "doc_id": 1257 }, "chunk_id": "train_shard_00000_1257_0", "global_id": 1388 }, { "text": "Campylobacter is a major foodborne pathogen that causes outbreaks and sporadic gastrointestinal disease, creating a serious disease burden. Campylobacter strains isolated from diarrhea cases (n = 11) and raw poultry meat products (n = 2) in Huzhou, including 11 Campylobacter jejuni and 2 Campylobacter coli strains, were subjected to virulence gene, drug resistance gene, genetic correlation, antibiotic resistance, and multilocus sequence typing (MLST) analyses. The 13 Campylobacter isolates were divided into 12 sequence types (STs), one of which was a new ST. The isolated strains contain multiple virulence-related genes. Drug sensitivity analysis showed that the resistance rate of the 13 isolates to nalidixic acid, ciprofloxacin, and tetracycline was 92.3%. Genome sequencing indicated that all 11 strains of C. jejuni carried the tet(O) and blaOXA resistance genes, and 2 strains of C. coli carried multiple drug resistance genes. Phylogenetic analysis based on core-genome single-nucleotide polymorphisms indicated that the 11 C. jejuni isolates from diarrhea patients and food sources are not closely phylogenetically related.\n\nGenomic characterization of Campylobacter isolates in Huzhou, China.", "token_count": 339, "char_count": 1208, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6294, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:03.099097", "source": { "split": "train_shard_00000", "doc_id": 1258 }, "chunk_id": "train_shard_00000_1258_0", "global_id": 1389 }, { "text": "Porcine epidemic diarrhea virus (PEDV) causes severe diarrhea diseases in piglets, which has brought huge economic losses to the pig industry. As the dominant Lactobacillus species in the piglet intestine, the antiviral effect of Limosilactobacillus reuteri (L. reuteri) has been reported. Nine L. reuteri strains were isolated and identified from swine feces in this study. The CCK-8 assay examined the anti-PEDV potential of their cell-free supernatant (CFS). Among the nine L. reuteri isolates examined, LRC8 had a higher inhibition rate to PEDV than the other strains. Thus, the biological properties of the LRC8 strain, such as growth ability, acid production ability, acid and bile salt tolerance, and adhesion to IPEC-J2 cells, were evaluated. Besides, the anti-PEDV activity of LRC8-CFS (LRC8 metabolites, LRM) was assessed using plaque reduction assays, indirect immunofluorescence assays, RT-qPCR, and western blotting. The mRNA relative expression levels of inflammatory factors including IL-1β, IL-6, IL-8, MCP1, and TNF-α were determined by RT-qPCR. The results showed that the LRC8 strain grew well, was resistant to acid, tolerated bile salts, and adhered strongly to IPEC-J2 cells. In addition, treatment with its CFS (LRM) dramatically downregulated the mRNA expression levels of inflammatory cytokines, and in the Vero cell culture, prophylactic, therapeutic, competitive, and direct-inhibitory actions were seen against PEDV. Finally, we explored the anti-PEDV effects of the LRC8 strain in piglets and found that the LRC8 strain effectively relieved the clinical symptoms and intestinal damage of piglets infected by PEDV. To sum up, we found a L. reuteri strain with an anti-PEDV effect.", "token_count": 485, "char_count": 1708, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [ "LRC8", "MCP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:03.751356", "source": { "split": "train_shard_00000", "doc_id": 1259 }, "chunk_id": "train_shard_00000_1259_0", "global_id": 1390 }, { "text": "Isolation of Limosilactobacillus reuteri Strain with Anti-porcine Epidemic Diarrhea Virus from Swine Feces.", "token_count": 38, "char_count": 107, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:04.110998", "source": { "split": "train_shard_00000", "doc_id": 1259 }, "chunk_id": "train_shard_00000_1259_1", "global_id": 1391 }, { "text": "Probiotic bacteria have capacity to bind with heavy metals. The present study was planned to assess the bioremediation potential of probiotic Lactobacillus species isolated from yogurt samples. L. acidophilus and L. plantarum were tested for acidic pH tolerance, bile salt resistance and gastric juice tolerance. The antibiotic susceptibility and antimicrobial activity was also checked. These Lactobacillus species were also evaluated for degradation of lead (Pb) and cadmium (Cd) metals. The results indicated that L. acidophilus and L. plantarum were able to tolerate high acidic pH: 3. both showed significant growth after exposure to stimulated gastric juice from 0 to 24 hours. The significant plate count was observed at different bile salt concentrations (0.1%, 0.3%). The isolates showed resistance for all the tested antibiotics except L. acidophilus showed susceptibility for gentamicin and co-amoxiclave. The isolates depicted no antimicrobial activity against the indicator bacteria. L. acidophilus and L. plantarum were capable of tolerating Cd and Pb. Maximum tolerance and removal were observed for Pb by both Lactobacillus spp. The Cd removal was 11.50 and 3.50% while Pb removal was 42.70 and 35.50% for L. plantarum and L. acidophilus, respectively. In conclusion, L. acidophilus and L. Plantarum have potential for bioremediation of heavy metals.\n\nAntibiotic susceptibility and bioremediation potential of probiotic bacteria against lead and cadmium isolated from yogurt.", "token_count": 406, "char_count": 1491, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5093, "quality_score": 0.7546, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:04.737432", "source": { "split": "train_shard_00000", "doc_id": 1260 }, "chunk_id": "train_shard_00000_1260_0", "global_id": 1392 }, { "text": "This study aimed to isolate and characterize potential probiotic yeasts from Ethiopian injera sourdough and the study was conducted by collecting samples from Gondar and Bahir Dar cities, Ethiopia. The potential yeasts were isolated and identified using morphological, physiological, biochemical and molecular based analysis. Promising isolates were selected to further investigate their in vitro probiotic properties, including survival at different temperatures (25, 30, 37, and 42 °C), acidic pH (2, 3, 4 and 5), bile salt (0.1, 0.3, and 0.5%), and osmotolerance (20, 30, 40, and 50% glucose concentration), antimicrobial activities, proteolytic and lipolytic activities as well as resistance to four antibiotics. From 20 samples, 38 isolates were obtained. Among these, 10 produced low or non-hydrogen sulfide and were selected for further work. Further screening tests revealed that five isolates (G1N1, G2N4, G3N1, G8N1, and B6N3) were able tolerate and grow at 37 °C, with harsh conditions of the human digestive tract like low pH, bile salt, and higher osmotic effect. The maximum growth OD values were recorded at 37 °C by isolate G4N1 (OD value (0.6667), while G3N1 exhibited a maximum growth OD value of 0.4227 at pH 2. On the other hand, G2N4 gave a maximum OD value of 0.8800 at 0.3% bile salt concentration. The promising isolates were sequenced and identified to species level. Based on phylogenetic tree analysis, all the five probiotic yeast isolates had one common ancestor and belonging to\n\nIsolation and characterization of potential probiotic yeasts from Ethiopian injera sourdough.", "token_count": 476, "char_count": 1603, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6626, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:05.387452", "source": { "split": "train_shard_00000", "doc_id": 1261 }, "chunk_id": "train_shard_00000_1261_0", "global_id": 1393 }, { "text": "Analysis of publicly available whole-genome sequence data from the Human Pangenome Project and the 1000 Genomes Project has identified a DNA segment of approximately 60 kb in the major histocompatibility complex (MHC) between HLA-W and HLA-J that is present in some MHC haplotypes but not others. This DNA segment is largely repeat element-rich but includes the pseudogene HLA-Y, thus pinpointing the location of this pseudogene, and a new HLA class I sequence we have called HLA-OLI. HLA-OLI clusters phylogenetically with the HLA class I pseudogenes, HLA-P and HLA-W, and appears to have a similar genetic structure. The availability of whole-genome sequence data from diverse populations enables a detailed characterization of the MHC at the population level and will have implications for understanding MHC disease associations and the non-HLA MHC factors that impact unrelated hematopoietic cell transplant outcomes.\n\nHLA-OLI: A new MHC class I pseudogene and HLA-Y are located on a 60 kb indel in the human MHC between HLA-W and HLA-J.", "token_count": 275, "char_count": 1041, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6273, "quality_score": 0.8137, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:05.938916", "source": { "split": "train_shard_00000", "doc_id": 1262 }, "chunk_id": "train_shard_00000_1262_0", "global_id": 1394 }, { "text": "A VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of", "token_count": 37, "char_count": 131, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:06.302895", "source": { "split": "train_shard_00000", "doc_id": 1263 }, "chunk_id": "train_shard_00000_1263_0", "global_id": 1395 }, { "text": "A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenome indexes. However, there are no practical tools to visualize or to check graphs that may have the Wheeler properties. Here, we present Wheelie, an algorithm that combines a\n\nWGT: Tools and algorithms for recognizing, visualizing, and generating Wheeler graphs.", "token_count": 113, "char_count": 502, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7089, "quality_score": 0.8544, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:06.690259", "source": { "split": "train_shard_00000", "doc_id": 1264 }, "chunk_id": "train_shard_00000_1264_0", "global_id": 1396 }, { "text": "Yersinia spp. vary significantly in their ability to cause diseases that threaten public health. Their pathogenicity is frequently associated with increasing antimicrobial resistance (AMR) and various virulence factors. The aim of the study was to investigate the AMR genes, virulence factors, and genetic diversity of Yersinia strains isolated from meats and fish in Wenzhou in 2020 by using whole-genome sequencing (WGS). A total of 50 isolates were collected. The phylogenetic relationships among the Yersinia species were also analyzed using multilocus sequence typing (MLST), core genome multi-locus sequence typing (cgMLST), and single nucleotide polymorphism (SNP) analysis. According to the results, all the strains could be classified into five species, with most isolated from beef, followed by poultry, pork, and fish. AMR genes were identified in 23 strains. And the qnrD1 genes were all located in the Col3M plasmid. Virulence genes, such as yaxA, ystB, pla, and yplA, were also found in the 15 Y. enterocolitica strains. And this study also found the presence of icm/dot type IVB-related genes in one Yersinia massiliensis isolate. MLST analysis identified 43 sequence types (STs), 19 of which were newly detected in Yersinia. Moreover, cgMLST analysis revealed that no dense genotype clusters were formed (cgMLST 5341, 5344, 5346-5350, 5353-5390). Instead, the strains appeared to be dispersed over large distances, except when multiple isolates shared the same ST. Isolates Y4 and Y26 were closely related to strains originating from South Korea and Denmark. This study showed considerable diversity in Yersinia spp. isolated from local areas (Wenzhou City). The data generated in our study may enrich the molecular traceability database of Yersinia and provide a basis for the development of more effective antipathogen control strategies.", "token_count": 492, "char_count": 1856, "word_count": 277, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:07.340917", "source": { "split": "train_shard_00000", "doc_id": 1265 }, "chunk_id": "train_shard_00000_1265_0", "global_id": 1397 }, { "text": "Whole-genome sequencing-based analysis of antimicrobial resistance, virulence factors, and genetic diversity in Yersinia isolated in Wenzhou, China 2020.", "token_count": 44, "char_count": 153, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:07.704760", "source": { "split": "train_shard_00000", "doc_id": 1265 }, "chunk_id": "train_shard_00000_1265_1", "global_id": 1398 }, { "text": "Back to wild relatives for future breeding through super-pangenome.", "token_count": 15, "char_count": 67, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:08.050847", "source": { "split": "train_shard_00000", "doc_id": 1266 }, "chunk_id": "train_shard_00000_1266_0", "global_id": 1399 }, { "text": "Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.\n\nPangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family.", "token_count": 359, "char_count": 1430, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:09.426374", "source": { "split": "train_shard_00000", "doc_id": 1267 }, "chunk_id": "train_shard_00000_1267_0", "global_id": 1400 }, { "text": "The bile salt-stimulated lipase (BSSL) was originally recognized as a lipolytic enzyme expressed by the exocrine pancreas and in some species, notably humans, the lactating mammary gland, being secreted into the duodenum and with the mother's milk, respectively. However, BSSL is also present in the blood and has been assigned additional functions, even beyond the gastrointestinal tract. Conventional BSSL knockout mice are protected from developing disease in animal models of arthritis, and antibodies directed towards BSSL prevent or mitigate disease in similar models. The aim of this study was to investigate the role of BSSL as a newly discovered player in inflammation and specifically in inflammatory joint disorders. As part of mechanism of action, we here show that BSSL is secreted by neutrophils, interacts with monocytes and stimulates their migration in vitro. An anti-BSSL antibody that blocks the human BSSL-monocyte interaction was shown to simultaneously prevent the signaling pathway by which BSSL induce cell migration. Moreover, in this cohort study we show that BSSL levels are significantly higher in blood samples from patients with rheumatoid arthritis and psoriatic arthritis compared to healthy controls. The BSSL levels in patients' blood also correlated with disease activity scores and established inflammatory markers. Hence, although the mode of action is not yet fully clarified, we conclude that BSSL could be considered a proinflammatory component in the innate immune system and thus a possible novel target for treatment of chronic inflammation.\n\nEffects of bile salt-stimulated lipase on blood cells and associations with disease activity in human inflammatory joint disorders.", "token_count": 394, "char_count": 1717, "word_count": 254, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:10.044767", "source": { "split": "train_shard_00000", "doc_id": 1268 }, "chunk_id": "train_shard_00000_1268_0", "global_id": 1401 }, { "text": "To contain intra-hospital transmission of third-generation cephalosporin-resistant Enterobacterales (3GCR-E), contact isolation precautions are recommended.\n\nAnalysis of transmission-related third-generation cephalosporin-resistant Enterobacterales by electronic data mining and core genome multi-locus sequence typing.", "token_count": 80, "char_count": 319, "word_count": 30, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:10.432216", "source": { "split": "train_shard_00000", "doc_id": 1269 }, "chunk_id": "train_shard_00000_1269_0", "global_id": 1402 }, { "text": "Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life.\n\nReconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.", "token_count": 113, "char_count": 506, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7971, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:10.858541", "source": { "split": "train_shard_00000", "doc_id": 1270 }, "chunk_id": "train_shard_00000_1270_0", "global_id": 1403 }, { "text": "Cholesterol is one of the hazard elements for many cardiovascular diseases, but many cholesterol-lowering drugs are expensive and unhealthy. Therefore, it is necessary to develop edible and safe biosorbents to reduce excess cholesterol and bile salts in the gastric-intestinal passage. Polysaccharide-based biosorbents offer a feasible strategy for decreasing them. This review summarized polysaccharide-based biosorbents that have been developed for adsorbing cholesterol and bile salts from the gastric-intestinal passage and analyzed common modification methods for these adsorbents. Finally, the adsorption models were also elucidated. Polysaccharides, including β-cyclodextrin, pectin, chitin/chitosan, dietary fiber extract, and cellulose, have been proposed for adsorbing cholesterol and bile salts in the gastric-intestinal passage as biosorbents. This is mainly due to the retention of pores, the capture of the viscosity network, and the help of hydrophobic interactions. In spite of this, the adsorption capacity of polysaccharides is still limited. Therefore, the modifications for them became the most popular areas in the recent studies of in vitro cholesterol adsorption. Chemical approaches namely grafting, (1) acetylation, (2) hydroxypropylation, (3) carboxymethylation, and (4) amination are considered to modify the polysaccharides for higher adsorption ability. Moreover, ultrasonic/microwave/pressure treatment and micron technology (microfluidization, micronization, and ball milling) are effective physical modification methods, while the biological approach mainly refers to enzymatic hydrolysis and microbial fermentation. The adsorption models are generally explained by two adsorption isotherms and two adsorption kinetics. In sum, it is reckoned that further food applications will follow soon.\n\nPolysaccharide-based biosorbents for cholesterol and bile salts in gastric-intestinal passage: Advances and future trends.", "token_count": 507, "char_count": 1947, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:11.505079", "source": { "split": "train_shard_00000", "doc_id": 1271 }, "chunk_id": "train_shard_00000_1271_0", "global_id": 1404 }, { "text": "Sodium taurocholate (NaT) is a hydrophobic bile salt that exhibits varying toxicity and antimicrobial activity. The accumulation of BSs during their entero-hepatic cycle causes cytotoxicity in the liver and intestine and could also alter the intestinal microbiome leading to various diseases. In this research, the acute toxicity of sodium taurocholate in different concentrations (3000 mg/L, 1500 mg/L, 750 mg/L, 375 mg/L, and 0 mg/L) was investigated on four months old zebrafish by immersion in water for 96 h. The results were determined based on the fish mortality, behavioral response, and NMR metabolomics analysis which revealed LC50 of 1760.32 mg/L and 1050.42 mg/L after 72 and 96 h treatment, respectively. However, the non-lethal NaT concentrations of 750 mg/L and 375 mg/L at 96 h exposure significantly (\n\nStudy on the acute toxicity of sodium taurocholate via zebrafish mortality, behavioral response, and NMR-metabolomics analysis.", "token_count": 338, "char_count": 947, "word_count": 142, "semantic_coherence": 1, "information_density": 0.669, "quality_score": 0.8345, "entities": { "genes": [ "LC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:12.153391", "source": { "split": "train_shard_00000", "doc_id": 1272 }, "chunk_id": "train_shard_00000_1272_0", "global_id": 1405 }, { "text": "Listeria monocytogenes is a pathogenic bacterium which can live in adverse environments (low pH, high salinity, and low temperature). Even though there are various whole genome sequencing (WGS) data on L. monocytogenes, investigations on genetic differences between stress-resistant and -sensitive L. monocytogenes grown under stress environments have been not fully examined. This study aims to investigate and compare genetic characteristics between stress-resistant and -sensitive L. monocytogenes using whole genome sequencing (WGS). A total of 47 L. monocytogenes strains (43 stress-resistant and 4 stress-sensitive) were selected based on the stress-resistance tests under pH 3, 5% salt concentration, and 1 °C. The sequencing library for WGS was prepared and sequenced using an Illumina MiSeq. Genetic characteristics of two different L. monocytogenes groups were examined to analyze the pangenome, functionality, virulence, antibiotic resistance, core, and unique genes. The functionality of unique genes in the stress-resistant L. monocytogenes was distinct compared to the stress-sensitive L. monocytogenes, such as carbohydrate and nucleotide transport and metabolism. The lisR virulence gene was detected more in the stress-resistant L. monocytogenes than in the stress-sensitive group. Five stress-resistant L. monocytogenes strains possessed tet(M) antibiotic resistance gene. This is the first study suggesting that deep genomic characteristics of L. monocytogenes may have different resistance level under stress conditions. This new insight will aid in understanding the genetic relationship between stress-resistant and -sensitive L. monocytogenes strains isolated from diverse resources. KEY POINTS: • Whole genomes of L. monocytogenes isolated from three different sources were analyzed. • Differences in two L. monocytogenes groups were identified in functionality, virulence, and antibiotic resistance genes. • This study first examines the association between resistances and whole genomes of stress-resistant and -sensitive L. monocytogenes.", "token_count": 505, "char_count": 2065, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5396, "quality_score": 0.7698, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:12.808100", "source": { "split": "train_shard_00000", "doc_id": 1273 }, "chunk_id": "train_shard_00000_1273_0", "global_id": 1406 }, { "text": "Comprehensive metagenomic analysis of stress-resistant and -sensitive Listeria monocytogenes.", "token_count": 26, "char_count": 93, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:13.166171", "source": { "split": "train_shard_00000", "doc_id": 1273 }, "chunk_id": "train_shard_00000_1273_1", "global_id": 1407 }, { "text": "A novel adsorbent β-cyclodextrin-modified pectin was synthesized for removing cholesterol and bile salts from the gastric-intestinal passage. Different amounts of β-cyclodextrin were cross-linked to pectin by aldol condensation reaction via glutaraldehyde. The prepared β-cyclodextrin-modified pectins were successfully confirmed by characterization, showing a higher specific surface area and improved thermal stability with satisfactory cellular compatibility. The introduction of β-cyclodextrins dramatically improved the cholesterol adsorption capacity of pectin due to their hydrophobic cavities. Meanwhile, the modified pectins exhibited superior adsorption for sodium cholate than β-cyclodextrin or pectin itself, which was attributed to hydrophobic interactions. P\n\nAdsorption removal properties of β-cyclodextrin-modified pectin on cholesterol and sodium cholate.", "token_count": 232, "char_count": 872, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:13.636299", "source": { "split": "train_shard_00000", "doc_id": 1274 }, "chunk_id": "train_shard_00000_1274_0", "global_id": 1408 }, { "text": "The aims of this study were to evaluate the potential of Hanseniaspora opuntiae, Meyerozyma caribbica, and Kluyveromyces marxianus for in vitro biocontrol of Aspergillus ochraceus, A. westerdijkiae, and A. carbonarius growth, the ochratoxin A (OTA) effect on yeast growth, and yeast in vitro OTA detoxification ability using an experimental design to predict the combined effects of inoculum size, incubation time, and OTA concentration.\n\nYeasts as sustainable biocontrol agents against ochratoxigenic Aspergillus species and in vitro optimization of ochratoxin A detoxification.", "token_count": 167, "char_count": 579, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:14.081425", "source": { "split": "train_shard_00000", "doc_id": 1275 }, "chunk_id": "train_shard_00000_1275_0", "global_id": 1409 }, { "text": "Fruit peels have potential as prebiotic sources thanks to their dietary fiber contents. This study aimed to determine the effects of freeze-dried banana (BPP) and watermelon (WPP) peel powders on bile salt resistance, growth kinetics, and survival of Lactobacillus acidophilus and Lactiplantibacillus plantarum. In the presence of 0.5-1% bile salt, L. plantarum counts were 0.52-1.13 log CFU/mL higher in MRS broth added with 5% peel powder than without peel powder. Lactobacillus acidophilus population was 2.47-2.79 log CFU/mL higher in MRS broth added with 5% peel powder than without peel powder in the presence of 0.5% bile salt. Both peel powders did not affect the growth kinetics of L. acidophilus in milk. Conversely, the growth of L. plantarum was promoted in milk supplemented with peel powders and yielded a shorter generation time (P < 0.05). The maximum population density of L. plantarum in milk supplemented with BPP (8.68 log CFU/mL) was higher than in milk without peel powder (7.72 log CFU/mL; P < 0.05). Survival of L. acidophilus improved during storage at 4 °C in milk added with peel powders. The results suggest that BPP and WPP can be functional ingredients in probiotic foods and may be used to improve the growth and survival of probiotic cultures.\n\nEffects of Freeze-Dried Banana and Watermelon Peel Powders on Bile Salt Resistance, Growth Kinetics, and Survival of Probiotic Bacteria.", "token_count": 440, "char_count": 1413, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5022, "quality_score": 0.7511, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:14.710625", "source": { "split": "train_shard_00000", "doc_id": 1276 }, "chunk_id": "train_shard_00000_1276_0", "global_id": 1410 }, { "text": "Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostic, prevention and treatment is still lacking. We used a collection of 912 BSI and 370 commensal E. coli isolates collected in France over a 17-year period (2000-2017). We compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity continuously increased through 1980, 2000, to 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.\n\nThe bacterial genetic determinants of Escherichia coli capacity to cause bloodstream infections in humans.", "token_count": 390, "char_count": 1638, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:15.332243", "source": { "split": "train_shard_00000", "doc_id": 1277 }, "chunk_id": "train_shard_00000_1277_0", "global_id": 1411 }, { "text": "Campylobacter spp., especially C. jejuni, is the most common zoonotic pathogen in humans worldwide. In Nordic countries, the prevalence of C. jejuni in broilers, which is an important reservoir of human infections, is generally low. Thus, other sources of domestically acquired infections besides chicken meat need to be considered. Game birds are known to carry a variety of zoonotic agents, including Campylobacter. The aim of this study was to investigate Campylobacter spp. carriage in a flock of reared pheasants at hunting in two successive samplings to better understand the dynamics of Campylobacter infections in pheasants. Overall, 72% of the intestinal samples were positive for Campylobacter spp. by direct culture on mCCDA. C. jejuni was the only species identified. The isolates were genotyped using whole genome sequencing (WGS), multilocus sequence typing (MLST), and ad hoc whole genome MLST (wgMLST). Two distinct C. jejuni clones were identified among the 18 isolates studied, representing MLST sequence types (STs) ST-45 and ST-699. The ST-45 isolates were closely related to previous human clinical isolates using core genome MLST (cgMLST). In contrast, the ST-699 isolates forming the dominant clone in the latter sampling were quite distinct from previously described cgMLST profiles from different hosts and sources worldwide. In conclusion, the intestine of reared pheasants is commonly colonized by C. jejuni and may carry genotypes relevant to infections in livestock and humans. Hygienic measures are needed to limit the spread of infection in reared flocks. Especially farmers and hunters having direct contact with pheasant offal need to be aware of the associated zoonosis risk to protect themselves and their working dogs alike. Biosecurity measures to improve the safety and reduce the zoonosis risk associated with pheasant farming should be further investigated.\n\nPrevalence and genotype diversity of Campylobacter jejuni in hunted reared pheasants (Phasianus colchicus) in Finland.", "token_count": 492, "char_count": 2017, "word_count": 299, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:15.978220", "source": { "split": "train_shard_00000", "doc_id": 1278 }, "chunk_id": "train_shard_00000_1278_0", "global_id": 1412 }, { "text": "Mannoproteins, mannose-glycosylated proteins, play an important role in biological processes and have various applications in industries. Several methods have been already used for the extraction of mannoproteins from yeast cell-wall. The aim of this study was to evaluate the extraction and deproteinization of mannan oligosaccharide from the Kluyveromyces (K.) marxianus mannoprotein.\n\nOptimal Extraction and Deproteinization Method for Mannoprotein Purification from Kluyveromyces marxianus.", "token_count": 129, "char_count": 494, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:16.412320", "source": { "split": "train_shard_00000", "doc_id": 1279 }, "chunk_id": "train_shard_00000_1279_0", "global_id": 1413 }, { "text": "Pangenomes provide access to an accurate representation of the genetic diversity of species, both in terms of sequence polymorphisms and structural variants (SVs). Here we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing the species' phylogenetic and ecological diversity. The ScRAP includes phased haplotype assemblies for several heterozygous diploid and polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that provide a broad view of the genomic diversity, including the dynamics of telomere length and transposable elements. We uncovered frequent cases of complex aneuploidies where large chromosomes underwent large deletions and translocations. We found that SVs can impact gene expression near the breakpoints and substantially contribute to gene repertoire evolution. We also discovered that horizontally acquired regions insert at chromosome ends and can generate new telomeres. Overall, the ScRAP demonstrates the benefit of a pangenome in understanding genome evolution at population scale.\n\nTelomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae.", "token_count": 294, "char_count": 1230, "word_count": 162, "semantic_coherence": 1, "information_density": 0.716, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:16.967841", "source": { "split": "train_shard_00000", "doc_id": 1280 }, "chunk_id": "train_shard_00000_1280_0", "global_id": 1414 }, { "text": "This study was conducted to develop simple methods for the extraction of chenodeoxycholic acid (CDCA) and synthesis of ursodeoxycholic acid (UDCA) from pig by-products. The enzymatic method, which uses bile salt hydrolase (BSH) enzymes to extract CDCA, was found to be more efficient than the chemical method. The chemical method, which uses pig by-products, resulted in UDCA amounts of 6.05 mg, 0.51 mg, 3.04 mg, and 1.26 mg in 100 g of the liver, stomach, small intestine, and large intestine, respectively. The amounts of UDCA synthesized/100 g through the chemical and enzymatic methods required to extract CDCA were 3.48 g and 2.22 g, respectively. The procedure developed in this study was simplified by three stages compared to the conventional chemical method of extracting CDCA. Moreover, this study provides a technique that improves the utilization of pig by-products.\n\nDeveloping a procedure to extract chenodeoxycholic acid and synthesize ursodeoxycholic acid from pig by-products.", "token_count": 281, "char_count": 994, "word_count": 151, "semantic_coherence": 1, "information_density": 0.5762, "quality_score": 0.7881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:17.517132", "source": { "split": "train_shard_00000", "doc_id": 1281 }, "chunk_id": "train_shard_00000_1281_0", "global_id": 1415 }, { "text": "Bile acid anions are steroidal biosurfactants that form primary micelles due to the hydrophobic effect. At higher concentrations of some bile acid anions, secondary micelles are formed; hydrogen bonds connect primary micelles. Monoketo derivatives of cholic acid, which have reduced membrane toxicity, are important for biopharmaceutical examinations. The main goal is to explain why the processes of formation of primary and secondary micelles are separated from each other, i.e., why secondary micelles do not form parallel to primary micelles. The association of the anion of 7-oxodeoxycholic acid (a monoketo derivative of cholic acid) is observed through the dependence of the spin-lattice relaxation time on total surfactant concentration\n\nSelf-Association of the Anion of 7-Oxodeoxycholic Acid (Bile Salt): How Secondary Micelles Are Formed.", "token_count": 205, "char_count": 848, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:17.981081", "source": { "split": "train_shard_00000", "doc_id": 1282 }, "chunk_id": "train_shard_00000_1282_0", "global_id": 1416 }, { "text": "Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Herein, we performed genomic analysis of seven S. suis serotype 4 strains belonging to clonal complex (CC) 94 that were recovered from a human patient or from diseased and clinically healthy pigs. Genomic exploration and comparisons, as well as in vitro cytotoxicity tests, indicated that S. suis CC94 serotype 4 strains are potentially virulent. Genomic analysis revealed that all seven strains clustered within minimum core genome group 3 (MCG-3) and had a high number of virulence-associated genes similar to those of virulent serotype 2 strains. Cytotoxicity assays showed that both the human lung adenocarcinoma cell line and HeLa cells rapidly lost viability following incubation for 4 h with the strains at a concentration of 106 bacterial cells. The human serotype 4 strain (ID36054) decreased cell viability profoundly and similarly to the control serotype 2 strain P1/7. In addition, strain ST1689 (ID34572), isolated from a clinically healthy pig, presented similar behaviour in an adenocarcinoma cell line and HeLa cells. The antimicrobial resistance genes tet(O) and ermB that confer resistance to tetracyclines, macrolides, and lincosamides were commonly found in the strains. However, aminoglycoside and streptothricin resistance genes were found only in certain strains in this study. Our results indicate that S. suis CC94 serotype 4 strains are potentially pathogenic and virulent and should be monitored.\n\nGenomic characterization and virulence of Streptococcus suis serotype 4 clonal complex 94 recovered from human and swine samples.", "token_count": 438, "char_count": 1648, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5633, "quality_score": 0.7816, "entities": { "genes": [ "CC94", "ID36054", "ID34572", "ST1689" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:18.608543", "source": { "split": "train_shard_00000", "doc_id": 1283 }, "chunk_id": "train_shard_00000_1283_0", "global_id": 1417 }, { "text": "For the past few years, researchers in the Human Pangenome Reference Consortium (HPRC) have been working to catalog almost all human genomic diversity. Frazer and Schork preview an article recently published in\n\nThe human pangenome reference anticipates equitable and fundamental genomic insights.", "token_count": 63, "char_count": 297, "word_count": 42, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:18.973408", "source": { "split": "train_shard_00000", "doc_id": 1284 }, "chunk_id": "train_shard_00000_1284_0", "global_id": 1418 }, { "text": "The lower female reproductive tract is notoriously dominated by Lactobacillus species, among which Lactobacillus crispatus emerges for its protective and health-promoting activities. Although previous comparative genome analyses highlighted genetic and phenotypic diversity within the L. crispatus species, most studies have focused on the presence/absence of accessory genes. Here, we investigated the variation at the single nucleotide level within protein-encoding genes shared across a human-derived L. crispatus strain selection, which includes 200 currently available human-derived L. crispatus genomes as well as 41 chromosome sequences of such taxon that have been decoded in the framework of this study. Such data clearly pointed out the presence of intra-species micro-diversities that could have evolutionary significance contributing to phenotypical diversification by affecting protein domains. Specifically, two single nucleotide variations in the type II pullulanase gene sequence led to specific amino acid substitutions, possibly explaining the substantial differences in the growth performances and competition abilities observed in a multi-strain bioreactor culture simulating the vaginal environment. Accordingly, L. crispatus strains display different growth performances, suggesting that the colonisation and stable persistence in the female reproductive tract between the members of this taxon is highly variable.\n\nThe core genome evolution of Lactobacillus crispatus as a driving force for niche competition in the human vaginal tract.", "token_count": 348, "char_count": 1559, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6812, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:19.549672", "source": { "split": "train_shard_00000", "doc_id": 1285 }, "chunk_id": "train_shard_00000_1285_0", "global_id": 1419 }, { "text": "Adsorption of gut relevant biomolecules onto particles after oral administration of solid oral dosage forms is expected to form a \"gastrointestinal corona\", which could influence solution-mediated solid-state transformations on exposure of drug particles to gastrointestinal fluids. Low-frequency Raman (LFR) spectroscopy was used in this study to investigate\n\nThe Influence of Gastrointestinal Biomolecules on Solid-State Transformations in Pharmaceutical Particulates.", "token_count": 114, "char_count": 470, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:19.932599", "source": { "split": "train_shard_00000", "doc_id": 1286 }, "chunk_id": "train_shard_00000_1286_0", "global_id": 1420 }, { "text": "A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication.", "token_count": 36, "char_count": 156, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:20.298676", "source": { "split": "train_shard_00000", "doc_id": 1287 }, "chunk_id": "train_shard_00000_1287_0", "global_id": 1421 }, { "text": "Potato (\n\nPangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species.", "token_count": 29, "char_count": 114, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:20.660211", "source": { "split": "train_shard_00000", "doc_id": 1288 }, "chunk_id": "train_shard_00000_1288_0", "global_id": 1422 }, { "text": "The indiscriminate use of antibiotics in aquaculture has led to the emergence of resistance; hence, eco-friendly, host-specific alternatives to mitigate bacterial infections have become imminent. In this study, bacteria that could possibly serve as probiotics were isolated and evaluated for their efficacy with in vitro experiments and in vivo zebrafish gut model. One isolate from each of the 23 rohu fish (Labeo rohita) was shortlisted after preliminary screening of several isolates and tested for their ability to inhibit two important warm water bacterial fish pathogens, Aeromonas hydrophila, and Edwardsiella tarda. An isolate (RODK28110C3) that showed broad-spectrum inhibitory activity against a battery of different isolates of the two fish pathogens included in this study and maintained in our repository was selected for further characterization. The culture was identified phenotypically as Bacillus subtilis and confirmed by 16S rDNA sequencing. The isolate was able to hydrolyze fish feed constituents that include starch, protein, and cellulose. Further in vitro tests ensured that the potential isolate with probiotic attributes could tolerate different gut conditions, which included a range of pH, salinity, and varying concentrations of bile salt. Exposure of 4 days post fertilization zebrafish embryos to the RFP-tagged isolate confirmed the colonization of B. subtilis in the gut of the zebrafish embryo, which is an important attribute of a probiotic. The isolate was able to inhibit both A. hydrophila and E. tarda in gnotobiotic zebrafish embryo in triplicate. The study demonstrates the probiotic characteristics of the B. subtilis isolated from L. rohita and its ability to inhibit A. hydrophila and E. tarda using in vitro conditions and in the zebrafish gut and could serve as an effective alternative to antibiotics in aquaculture.", "token_count": 468, "char_count": 1864, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5632, "quality_score": 0.7816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:21.299985", "source": { "split": "train_shard_00000", "doc_id": 1289 }, "chunk_id": "train_shard_00000_1289_0", "global_id": 1423 }, { "text": "Evaluation of Probiotic Efficacy of Bacillus subtilis RODK28110C3 Against Pathogenic Aeromonas hydrophila and Edwardsiella tarda Using In Vitro Studies and In Vivo Gnotobiotic Zebrafish Gut Model System.", "token_count": 66, "char_count": 203, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:21.666652", "source": { "split": "train_shard_00000", "doc_id": 1289 }, "chunk_id": "train_shard_00000_1289_1", "global_id": 1424 }, { "text": "We present a case of laboratory-acquired Salmonella Typhi, resulting in hospitalization of a technician. Blood and stool cultures revealed a S. Typhi strain, identical to the strain with which the employee had recently worked, confirmed using core-genome multilocus sequence typing. The incident occurred despite working in a biosafety cabinet.\n\nTyphoid fever due to laboratory-acquired Salmonella Typhi, confirmed by core genome multi-locus sequence typing.", "token_count": 107, "char_count": 458, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:22.041738", "source": { "split": "train_shard_00000", "doc_id": 1290 }, "chunk_id": "train_shard_00000_1290_0", "global_id": 1425 }, { "text": "The bacterial genus\n\nPangenome insights into the diversification and disease specificity of worldwide", "token_count": 20, "char_count": 101, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:22.400368", "source": { "split": "train_shard_00000", "doc_id": 1291 }, "chunk_id": "train_shard_00000_1291_0", "global_id": 1426 }, { "text": "Aspergillus fungi are widely used in the traditional fermentation of food products, so their safety risks and functions are worthy of investigation. In this study, one Aspergillus luchuensis YZ-1 isolated from Liubao tea was identified based on phylogenetic analyses of sequences of three genes coding for internal transcribed spacer 1 (ITS1), β-tubulin (benA), and calmodulin (CaM). The results of hemolytic activity, DNase activity, cytotoxicity assay, and antibiotic resistance assay indicated that the strain is potentially safe. The excellent gastrointestinal fluid tolerance, acid tolerance, bile tolerance, auto-aggregation, co-aggregation, cell surface hydrophobicity, and adhesion to human colon adenocarcinoma (HT29) cell line were observed on analysis of the probiotic properties. Furthermore, the results of the antibacterial activity of A. luchuensis YZ-1 indicated that the strain had strong antagonistic effects against Gram-negative and Gram-positive bacteria as well as fungi. Simultaneously, the water extracts and 80% ethanolic extracts of A. luchuensis YZ-1 cells also showed strong ABTS, DPPH, and OH\n\nProbiotic Potential, Antibacterial, and Antioxidant Capacity of Aspergillus luchuensis YZ-1 Isolated From Liubao Tea.", "token_count": 339, "char_count": 1240, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6982, "quality_score": 0.8491, "entities": { "genes": [ "HT29", "ITS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:22.998714", "source": { "split": "train_shard_00000", "doc_id": 1292 }, "chunk_id": "train_shard_00000_1292_0", "global_id": 1427 }, { "text": "Nowadays, probiotic microorganisms are given high attention due to their potential for the improvement of animal production and productivity. The natural gut microflora of poultry can serve as an excellent source of optimum probiotic strains. Therefore, this study isolated, identified and characterized potential probiotic\n\nCharacterization of potential probiotics Lactobacillus species isolated from the gastrointestinal tract of Rhode Island Red (RIR) chicken in Ethiopia.", "token_count": 104, "char_count": 475, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8254, "quality_score": 0.9127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:23.407859", "source": { "split": "train_shard_00000", "doc_id": 1293 }, "chunk_id": "train_shard_00000_1293_0", "global_id": 1428 }, { "text": "Brassica rapa is grown worldwide as economically important vegetable and oilseed crop. However, its production is challenged by yield-limiting pathogens. The sustainable control of these pathogens mainly relies on the deployment of genetic resistance primarily driven by resistance gene analogues (RGAs). While several studies have identified RGAs in B. rapa, these were mainly based on a single genome reference and do not represent the full range of RGA diversity in B. rapa. In this study, we utilized the B. rapa pangenome, constructed from 71 lines encompassing 12 morphotypes, to describe a comprehensive repertoire of RGAs in B. rapa. We show that 309 RGAs were affected by presence-absence variation (PAV) and 223 RGAs were missing from the reference genome. The transmembrane leucine-rich repeat (TM-LRR) RGA class had more core gene types than variable genes, while the opposite was observed for nucleotide-binding site leucine-rich repeats (NLRs). Comparative analysis with the B. napus pangenome revealed significant RGA conservation (93%) between the two species. We identified 138 candidate RGAs located within known B. rapa disease resistance QTL, of which the majority were under negative selection. Using blackleg gene homologues, we demonstrated how these genes in B. napus were derived from B. rapa. This further clarifies the genetic relationship of these loci, which may be useful in narrowing-down candidate blackleg resistance genes. This study provides a novel genomic resource towards the identification of candidate genes for breeding disease resistance in B. rapa and its relatives.\n\nComparative pangenome analyses provide insights into the evolution of Brassica rapa resistance gene analogues (RGAs).", "token_count": 408, "char_count": 1728, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:24.067919", "source": { "split": "train_shard_00000", "doc_id": 1295 }, "chunk_id": "train_shard_00000_1295_0", "global_id": 1429 }, { "text": "Glucose repression in yeast leads to the sequential or diauxic utilization of mixed sugars and reduces the co-utilization of glucose and xylose from lignocellulosic biomasses. Study of the glucose sensing pathway helps to construct glucose repression-released yeast strains and enhance the utilization of lignocellulosic biomasses.\n\nThe novel properties of Kluyveromyces marxianus glucose sensor/receptor repressor pathway and the construction of glucose repression-released strains.", "token_count": 134, "char_count": 483, "word_count": 62, "semantic_coherence": 1, "information_density": 0.5968, "quality_score": 0.7984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:24.526069", "source": { "split": "train_shard_00000", "doc_id": 1296 }, "chunk_id": "train_shard_00000_1296_0", "global_id": 1430 }, { "text": "Antibody-induced bile salt export pump deficiency (AIBD) is an acquired form of intrahepatic cholestasis, which may develop following orthotopic liver transplantation (OLT) for progressive familial intrahepatic cholestasis type 2 (PFIC-2). Approximately 8-33% of patients with PFIC-2 who underwent a transplant develop bile salt export pump (BSEP) antibodies, which trans-inhibit this bile salt transporter from the extracellular, biliary side. AIBD is diagnosed by demonstration of BSEP-reactive and BSEP-inhibitory antibodies in patient serum. We developed a cell-based test directly measuring BSEP trans-inhibition by antibodies in serum samples to confirm AIBD diagnosis.\n\nCell-based BSEP trans-inhibition: A novel, non-invasive test for diagnosis of antibody-induced BSEP deficiency.", "token_count": 232, "char_count": 788, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7549, "quality_score": 0.8775, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:25.007223", "source": { "split": "train_shard_00000", "doc_id": 1297 }, "chunk_id": "train_shard_00000_1297_0", "global_id": 1431 }, { "text": "Salmonella enterica serovar Derby (S. Derby) is one of the most common Salmonella serovars which can infect poultry, swine, and humans. With the reduction of the sequencing cost and the improvement of sequencing technology, whole genome sequencing (WGS) has become an important method for bacterial determination, molecular investigation, and pathogenic tracing analysis. In this study, we investigated S. Derby isolates from different sources in China using in-silico multilocus sequence typing (MLST), core genome MLST (cgMLST) and whole genome MLST (wgMLST) analysis based on WGS. The results showed that 21 S. Derby strains were divided into 3 STs using MLST analysis, including ST40 (n = 19, accounting for 90.48%), ST71 (n = 1, accounting for 4.76%) and ST8016 (n = 1, accounting for 4.76%). cgMLST and wgMLST analysis categorized the tested strains into 13 cgSTs and 21 wgSTs, respectively. The minimum spanning trees of cgMLST and wgMLST both divided these strains into 3 clusters and 4 singletons. In addition, virulence gene profiles of S. Derby isolates were also analyzed, and a total of 174 virulence genes belonged to 8 categories were identified. In summary, we studied genomic typing, phylogenetic relationship and virulence gene profiles of S. Derby strains from different sources in China. These findings were beneficial for the epidemiology and pathogenesis of Salmonella.\n\nGenomic typing and virulence gene profile analysis of Salmonella Derby from different sources.", "token_count": 412, "char_count": 1487, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7987, "entities": { "genes": [ "ST71", "ST8016", "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:25.629592", "source": { "split": "train_shard_00000", "doc_id": 1298 }, "chunk_id": "train_shard_00000_1298_0", "global_id": 1432 }, { "text": "The purpose of this study was to examine the probiotic characteristics and selenium (Se) bioaccumulation potential of five Lactobacillus strains in vitro. Lactobacillus acidophilus, L. delbrueckii subsp. lactis, L. reuteri, L. gallinarum, and L. animalis were among the strains employed. As significant aspects of probiotics, identification, and evaluation of their survival potential in the gastrointestinal system were undertaken. Although all experimental Lactobacillus strains bioaccumulated Se (IV) concentrations in media culture, three Lactobacillus strains (L. animalis, L. gallinarum, and L. acidophilus) bioaccumulated the highest Se concentrations (23.08, 8.62, and 8.51 mg/g, respectively) after culture in the presence of 1.5 mg/ml sodium selenite. By disc diffusion, all isolates were evaluated for antibiotic susceptibility against six antibiotics, including ciprofloxacin, ampicillin, methicillin, streptomycin, tetracycline, and trimethoprim-sulfamethoxazole. Many of the isolates tested positive for resistance to some of the antibiotics utilized. The L. reuteri and L. gallinarum were found to be resistant to about 50% of the antibiotics that were tested. In terms of acid tolerance, L. animalis showed significant resistance at acidic pH by 1.72 log unit reduction whereas L. delbrueckii and L. galliinarum showed significant sensitivity at acidic pH (P > 0.05). Bile tolerance was addressed as an important aspect of the safety assessment for probiotics. There were variances in acid and bile tolerance among species, although all of them tolerated stress conditions to an acceptable degree. Upon comparing the various species, it was observed that L. gallinarum exhibited a significant decline in growth, as evidenced by a decrease of 1.39 log units in cell viability. On the other hand, L. acidophilus and L. animalis demonstrated remarkable bile tolerance, with 0.09 and 0.23 log unit reduction respectively (P < 0.05)", "token_count": 537, "char_count": 1943, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5921, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:11:26.288417", "source": { "split": "train_shard_00000", "doc_id": 1299 }, "chunk_id": "train_shard_00000_1299_0", "global_id": 1433 }, { "text": "These results suggest that L. animalis, L. gallinarum, and L. acidophilus, can be good candidates to evaluate them in vivo in further investigations due to their tolerance to acid, and bile, antibiotic resistance, and strong ability to bioaccumulate Se in chickens.\n\nIn vitro evaluation of probiotic properties and selenium bioaccumulation of lactic acid bacteria isolated from poultry gastrointestinal, as an organic selenium source.", "token_count": 109, "char_count": 434, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7937, "quality_score": 0.8968, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:26.672274", "source": { "split": "train_shard_00000", "doc_id": 1299 }, "chunk_id": "train_shard_00000_1299_1", "global_id": 1434 }, { "text": "A total of 187 lactic acid bacteria were isolated from four types of grains collected in South Korea. The bacterial strains were assigned as members of Levilactobacillus brevis, Latilactobacillus curvatus, Lactiplantibacillus plantarum, Lactococcus taiwanensis, Pediococcus pentosaceus, and Weissella paramesenteroides based on the closest similarity using 16S rRNA gene sequence analysis. The strains belonging to the same species were analyzed using RAPD-PCR, and one or two among strains showing the same band pattern were selected. Finally, 25 representative strains were selected for further functional study. Inhibitory effects of lipid accumulation were observed in the strains tested. Pediococcus pentosaceus K28, Levilactobacillus brevis RP21 and Lactiplantibacillus plantarum RP12 significantly reduced lipid accumulation and did not show cytotoxicity in C3H10T1/2 cells at treatment of 1-200 μg/mL. The three LAB strains decreased significantly expression of six adipogenic marker genes, PPARγ, C/EBPα, CD36, LPL, FAS and ACC, in C3H10T1/2 adipocytes. The three strains survived under strong acidity and bile salt conditions. The three strains showed adhesion to Caco-2 cells similar to a reference strain LGG. The resistance of the three strains to several antibiotics was also assessed. Strains RP12 and K28 were confirmed not to produce harmful enzymes based on API ZYM kit results. Based on these results, strains K28, RP21 and RP12 isolated from grains had the ability to inhibit adipogenesis in adipocytes and potentially be useful as probiotics.\n\nScreening of lactic acid bacteria with anti-adipogenic effect and potential probiotic properties from grains.", "token_count": 474, "char_count": 1674, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8256, "entities": { "genes": [ "CD36", "RP12", "RP21" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:27.315985", "source": { "split": "train_shard_00000", "doc_id": 1300 }, "chunk_id": "train_shard_00000_1300_0", "global_id": 1435 }, { "text": "Polysaccharides are one of the most abundant and active components of Lysimachia christinae (L. christinae), which is widely adopted for attenuating abnormal cholesterol metabolism; however, its mechanism of action remains unclear. Therefore, we fed a natural polysaccharide (NP) purified from L. christinae to high-fat diet mice. These mice showed an altered gut microbiota and bile acid pool, which was characterized by significantly increased Lactobacillus murinus and unconjugated bile acids in the ileum. Oral administration of the NP reduced cholesterol and triglyceride levels and enhanced bile acid synthesis via cholesterol 7α-hydroxylase. Additionally, the effects of NP are microbiota-dependent, which was reconfirmed by fecal microbiota transplantation (FMT). Altered gut microbiota reshaped bile acid metabolism by modulating bile salt hydrolase (BSH) activity. Therefore, bsh genes were genetically engineered into Brevibacillus choshinensis, which was gavaged into mice to verify BSH function in vivo. Finally, adeno-associated-virus-2-mediated overexpression or inhibition of fibroblast growth factor 15 (FGF15) was used to explore the farnesoid X receptor-fibroblast growth factor 15 pathway in hyperlipidemic mice. We identified that the NP relieves hyperlipidemia by altering the gut microbiota, which is accompanied by the active conversion of cholesterol to bile acids.\n\nLysimachia christinae polysaccharide attenuates diet-induced hyperlipidemia via modulating gut microbes-mediated FXR-FGF15 signaling pathway.", "token_count": 438, "char_count": 1533, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8267, "entities": { "genes": [ "FGF15" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:28.289155", "source": { "split": "train_shard_00000", "doc_id": 1301 }, "chunk_id": "train_shard_00000_1301_0", "global_id": 1436 }, { "text": "Increasing reports on K. pneumoniae strains with antimicrobial resistance and virulence traits from food and farm animals are raising concerns about the potential role of Klebsiella spp. as a foodborne pathogen. This study aimed to report and characterize Klebsiella spp. isolates from two artisanal ready-to-eat food (soft cheese and salami) producing facilities, and to track similar genotypes in different ecological niches. Over 1170 samples were collected during the whole production chain of different food batches. The overall Klebsiella prevalence was 6%. Strains were classified into the three Klebsiella species complexes: K. pneumoniae (KpSC, n = 17), K. oxytoca (KoSC, n = 38) and K. planticola (KplaSC, n = 18). Despite high genetic diversity we found in terms of known and new sequence types (STs), core genome phylogeny revealed clonal strains persisting in the same processing setting for over 14 months, isolated from the environment, raw materials and end-products. Strains showed a natural antimicrobial resistance phenotype-genotype. K. pneumoniae strains showed the highest virulence potential, with sequence types ST4242 and ST107 strains carrying yersiniabactin ybt16 and aerobactin iuc3. The latter was detected in all K. pneumoniae from salami and was located on a large conjugative plasmid highly similar (97% identity) to iuc3\n\nGenomic features of Klebsiella isolates from artisanal ready-to-eat food production facilities.", "token_count": 409, "char_count": 1450, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6493, "quality_score": 0.8246, "entities": { "genes": [ "ST4242", "ST107" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:28.913671", "source": { "split": "train_shard_00000", "doc_id": 1302 }, "chunk_id": "train_shard_00000_1302_0", "global_id": 1437 }, { "text": "Nowadays, the increasing use of medicinal plants in the treatment and prevention of diseases has attracted the attention of researchers. The aim of this work was to investigate the probiotic properties and antibacterial and antifungal activity of silymarin-enriched Lactobacillus bacteria against several important pathogenic bacteria and also Aspergillus flavus as one of the harmful molds in the food and health industries. For this purpose, 52 g-positive and catalase-negative bacteria were isolated from 60 traditional curd samples from Ilam province. Five of the 52 bacterial strains had more than 90% viability in high bile salt and acidic conditions and were selected for further investigation. The five strains with positive results showed good hydrophobicity (≥ 50.30%), auto-aggregation (≥ 53.70%), coaggregation (≥ 28.20%), and high cholesterol removal ability (from 09.20 to 67.20%) and therefore can be considered potential probiotics. The tested strains displayed acceptable antibacterial and antifungal activity against all 12 pathogenic bacteria and A. flavus. Also, the results of the simultaneous antifungal activity of probiotic strains and silymarin showed that the combination of silymarin and probiotics has a significantly better (P < 0.05) antifungal effect than the control group or the probiotic groups alone. Interestingly, in addition to the Limosilactobacillus fermentum C3 strain, the Limosilactobacillus fermentum C18 and Lactiplantibacillus pentosus C20 strains also had significant inhibitory effects against A. flavus when used with silymarin extract in methanol. Meanwhile, silymarin extract in DMSO and PEG increased the antagonistic activity of all five potential probiotic strains.\n\nProbiotic properties and antimicrobial evaluation of silymarin-enriched Lactobacillus bacteria isolated from traditional curd.", "token_count": 490, "char_count": 1847, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5843, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:29.556908", "source": { "split": "train_shard_00000", "doc_id": 1303 }, "chunk_id": "train_shard_00000_1303_0", "global_id": 1438 }, { "text": "Saccharomyces cerevisiae is the workhorse of fermentation industry. Upon engineering for D-lactate production by a series of gene deletions, this yeast had deficiencies in cell growth and D-lactate production at high substrate concentrations. Complex nutrients or high cell density were thus required to support growth and D-lactate production with a potential to increase medium and process cost of industrial-scale D-lactate production. As an alternative microbial biocatalyst, a Crabtree-negative and thermotolerant yeast Kluyveromyces marxianus was engineered in this study to produce high titer and yield of D-lactate at a lower pH without growth defects. Only pyruvate decarboxylase 1 (PDC1) gene was replaced by a codon-optimized bacterial D-lactate dehydrogenase (ldhA). Ethanol, glycerol, or acetic acid was not produced by the resulting strain, KMΔpdc1::ldhA. Aeration rate at 1.5 vvm and culture pH 5.0 at 30 °C provided the highest D-lactate titer of 42.97 ± 0.48 g/L from glucose. Yield and productivity of D-lactate, and glucose-consumption rate were 0.85 ± 0.01 g/g, 0.90 ± 0.01 g/(L·h), and 1.06 ± 0.00 g/(L·h), respectively. Surprisingly, D-lactate titer, productivity, and glucose-consumption rate of 52.29 ± 0.68 g/L, 1.38 ± 0.05 g/(L·h), and 1.22 ± 0.00 g/(L·h), respectively, were higher at 42 °C compared to 30 °C", "token_count": 504, "char_count": 1335, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6281, "quality_score": 0.8141, "entities": { "genes": [ "PDC1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:30.210736", "source": { "split": "train_shard_00000", "doc_id": 1304 }, "chunk_id": "train_shard_00000_1304_0", "global_id": 1439 }, { "text": "Sugarcane molasses, a low-value carbon, led to the highest D-lactate titer and yield of 66.26 ± 0.81 g/L and 0.91 ± 0.01 g/g, respectively, in a medium without additional nutrients. This study is a pioneer work of engineering K. marxianus to produce D-lactate at the yield approaching theoretical maximum using simple batch process. Our results support the potential of an engineered K. marxianus for D-lactate production on an industrial scale. KEY POINTS: • K. marxianus was engineered by deleting PDC1 and expressing codon-optimized D-ldhA. • The strain allowed high D-lactate titer and yield under pH ranging from 3.5 to 5.0. • The strain produced 66 g/L D-lactate at 30 °C from molasses without any additional nutrients.\n\nGenome engineering of Kluyveromyces marxianus for high D-( -)-lactic acid production under low pH conditions.", "token_count": 274, "char_count": 836, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.8321, "entities": { "genes": [ "PDC1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:30.764298", "source": { "split": "train_shard_00000", "doc_id": 1304 }, "chunk_id": "train_shard_00000_1304_1", "global_id": 1440 }, { "text": "Microencapsulation is an optimistic method for the delivery of live microbial cells through different food products. In this study, riboflavin-producing probiotic strain Lactiplantibacillus plantarum MTCC 25,432 was encapsulated using a spray drying technique with different wall materials including Inulin, maltodextrin (MD), and MD + Inulin (1:1). The obtained spray dried powder was investigated for probiotic viability, encapsulation efficiency, particle size, water activity, moisture content, hygroscopicity, bulk and tapped densities, storage stabilities, Fourier transform infrared spectroscopy (FTIR) and thermogravimetric analysis (TGA). Besides this, the viability of the free and encapsulated probiotic cells was tested under simulated gastric and intestinal fluid conditions. In the results, microcapsules produced with the combination of MD + Inulin showed higher dry powder yield (36.5%) and viability of L. plantarum MTCC 25,432 (7.4 log CFU / g) as compared with individual coating materials. Further characterization revealed that MD + Inulin microcapsules are spherical (3.50 ± 1.61 μm in diameter) in shape with concavities, showed the highest encapsulation efficiency (82%), low water activity (0.307), moisture content (3.67%) and good survival ability at low pH (pH 2.0 and 3.0), high bile salt concentrations (1.0% and 2.0%), and long storage conditions. No differences in FTIR spectra were observed among the tested samples. However, TGA showed enhanced thermal stability of probiotic-loaded microcapsules when MD + Inulin was used together. In conclusion, MD + Inulin could be a potential encapsulation material for riboflavin-producing probiotic bacteria L. plantarum MTCC 25,432.", "token_count": 491, "char_count": 1707, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6878, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:31.413618", "source": { "split": "train_shard_00000", "doc_id": 1305 }, "chunk_id": "train_shard_00000_1305_0", "global_id": 1441 }, { "text": "Microencapsulation of riboflavin-producing Lactiplantibacillus Plantarum MTCC 25,432 and Evaluation of its Survival in Simulated Gastric and Intestinal Fluid.", "token_count": 53, "char_count": 158, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:31.774252", "source": { "split": "train_shard_00000", "doc_id": 1305 }, "chunk_id": "train_shard_00000_1305_1", "global_id": 1442 }, { "text": "Streptococcus agalactiae is one of Thailand's most important pathogens in tilapia aquaculture. Vaccination is a very effective method for protecting fish against disease in aquaculture. Oral vaccination is an interesting route for vaccine delivery as it mimics the pathogenesis of S. agalactiae and provides convenient administration for mass vaccination of fish. Moreover, gut mucosal immunity is associated with a mucus layer on the gastrointestinal tract. Therefore, this study aimed to develop a novel cationic-based nanoemulsion vaccine containing bile salts (NEB) coated by chitosan (CS) and determined its physicochemical characterization, morphology, in vitro mucoadhesive property, permeability, and acid-base tolerance. In addition, the efficacy of NEB-CS as an oral vaccination for Nile tilapia was evaluated in order to investigate the innate immune response and protection against S. agalactiae. The groups of fish consisted of: (1) deionized water as a non-vaccinated control (Control); (2) an inactivated vaccine formulated from formalin-killed bacteria (IB); and (3) a novel cationic-based nanoemulsion vaccine containing bile salts (NEB) coated by chitosan (CS). The control, IB, and NEB-CS were incorporated into commercial feed pellets and fed to Nile tilapia. In addition, we evaluated the serum bactericidal activity (SBA) for 14 days post-vaccination (dpv) and protective efficacy for 10 days post-challenge, respectively. The mucoadhesiveness, permeability, and absorption within the tilapia intestine were also assessed in vivo. The NEB-CS vaccine appeared spherical, with the nanoparticles having a size of 454.37 nm and a positive charge (+47.6 mV). The NEB-CS vaccine had higher levels of mucoadhesiveness and permeability than the NEB (p < 0.05). The relative percent survival (RPS) of IB and NEB-CS, when administered orally to fish, was 48% and 96%, respectively", "token_count": 521, "char_count": 1892, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6421, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:11:32.411682", "source": { "split": "train_shard_00000", "doc_id": 1306 }, "chunk_id": "train_shard_00000_1306_0", "global_id": 1443 }, { "text": "Enhanced SBA was noted in the NEB-CS and IB vaccine groups compared to the control group. The results demonstrate that a feed-based NEB-CS can improve the mucoadhesiveness, permeability, and protective efficacy of the vaccine, and appear to be a promising approach to protecting tilapia in aquaculture against streptococcosis.\n\nOral delivery of a Streptococcus agalactiae vaccine to Nile tilapia (Oreochromis niloticus) using a novel cationic-based nanoemulsion containing bile salts.", "token_count": 134, "char_count": 484, "word_count": 68, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:32.837331", "source": { "split": "train_shard_00000", "doc_id": 1306 }, "chunk_id": "train_shard_00000_1306_1", "global_id": 1444 }, { "text": "Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.\n\nPopulation genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador.", "token_count": 414, "char_count": 1923, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6053, "quality_score": 0.8026, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:33.461897", "source": { "split": "train_shard_00000", "doc_id": 1307 }, "chunk_id": "train_shard_00000_1307_0", "global_id": 1445 }, { "text": "This study investigated the impact of gastro-intestinal fluid volume and bile salt (BS) concentration on the dissolution of carbamazepine (CBZ) immediate release (IR) 100 mg tablets and to integrate these in vitro biorelevant dissolution profiles into physiologically based pharmacokinetic modelling (PBPK) in pediatric and adult populations to determine the biopredictive dissolution profile. Dissolution profiles of CBZ IR tablets (100 mg) were generated in 50-900 mL biorelevant adult fasted state simulated gastric and intestinal fluid (Ad-FaSSGF and Ad-FaSSIF), also in three alternative compositions of biorelevant pediatric FaSSGF and FaSSIF medias at 200 mL. This study found that CBZ dissolution was poorly sensitive to changes in the composition of the biorelevant media, where dissimilar dissolution (F2 = 46.2) was only observed when the BS concentration was changed from 3000 to 89 μM (Ad-FaSSIF vs Ped-FaSSIF 50% 14 BS). PBPK modeling demonstrated the most predictive dissolution volume and media composition to forecast the PK was 500 mL of Ad-FaSSGF/Ad-FaSSIF media for adults and 200 mL Ped-FaSSGF/FaSSIF media for pediatrics. A virtual bioequivalence simulation was conducted by using Ad-FaSSGF and/or Ad-FaSSIF 500 mL or Ped-FaSSGF and/or Ped-FaSSIF 200 mL dissolution data for CBZ 100 mg (reference and generic test) IR product. The CBZ PBPK models showed bioequivalence of the product. This study demonstrates that the integration of biorelevant dissolution data can predict the PK profile of a poorly soluble drug in both populations. Further work using more pediatric drug products is needed to verify biorelevant dissolution data to predict the in vivo performance in pediatrics.", "token_count": 504, "char_count": 1703, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:34.117136", "source": { "split": "train_shard_00000", "doc_id": 1308 }, "chunk_id": "train_shard_00000_1308_0", "global_id": 1446 }, { "text": "Integration of Biorelevant Pediatric Dissolution Methodology into PBPK Modeling to Predict In Vivo Performance and Bioequivalence of Generic Drugs in Pediatric Populations: a Carbamazepine Case Study.", "token_count": 52, "char_count": 200, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:34.477994", "source": { "split": "train_shard_00000", "doc_id": 1308 }, "chunk_id": "train_shard_00000_1308_1", "global_id": 1447 }, { "text": "As long-read sequencing technologies are becoming increasingly popular, a number of methods have been developed for the discovery and analysis of structural variants (SVs) from long reads. Long reads enable detection of SVs that could not be previously detected from short-read sequencing, but computational methods must adapt to the unique challenges and opportunities presented by long-read sequencing. Here, we summarize over 50 long-read-based methods for SV detection, genotyping and visualization, and discuss how new telomere-to-telomere genome assemblies and pangenome efforts can improve the accuracy and drive the development of SV callers in the future.\n\nA survey of algorithms for the detection of genomic structural variants from long-read sequencing data.", "token_count": 166, "char_count": 769, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7248, "quality_score": 0.8624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:34.956572", "source": { "split": "train_shard_00000", "doc_id": 1309 }, "chunk_id": "train_shard_00000_1309_0", "global_id": 1448 }, { "text": "At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined \"species\", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.\n\nExploring environmental intra-species diversity through non-redundant pangenome assemblies.", "token_count": 401, "char_count": 1876, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6459, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:35.588662", "source": { "split": "train_shard_00000", "doc_id": 1310 }, "chunk_id": "train_shard_00000_1310_0", "global_id": 1449 }, { "text": "This Medical News article discusses the Human Pangenome Project.\n\nA More Diverse and Complete Reference Human Genome Is Poised to Change Medicine.", "token_count": 32, "char_count": 146, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:35.997426", "source": { "split": "train_shard_00000", "doc_id": 1311 }, "chunk_id": "train_shard_00000_1311_0", "global_id": 1450 }, { "text": "Human life quality and expectancy have increased dramatically over the past 5 decades because of improvements in nutrition and antibiotic's usage fighting against infectious diseases. Yet, it was soon revealed that the microbes adapted to develop resistance to any of the drugs that were used. Recently, there is great concern that commensal bacteria from food and the gastrointestinal tract of humans and animals could act as a reservoir for antibiotic resistance genes.\n\nUnveiling the Antibiotic Susceptibility and Antimicrobial Potential of Bacteria from Human Breast Milk of Pakistani Women: An Exploratory Study.", "token_count": 137, "char_count": 617, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7802, "quality_score": 0.8901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:36.497008", "source": { "split": "train_shard_00000", "doc_id": 1312 }, "chunk_id": "train_shard_00000_1312_0", "global_id": 1451 }, { "text": "Hypercholesterolemia is a significant risk factor for cardiovascular disease and metabolic disorders. Probiotics are the essential constituents of the gastrointestinal microbiota that provide health-promoting effects. Cholesterol-lowering activity is a specific property of probiotics, improving the cholesterol metabolism without adverse effects. Thus, the purpose of this study was to investigate the hypocholesterolemic effect of single and mixed cholesterol-lowering probiotic strains (including\n\nBeneficial Effects of Indigenous Probiotics in High-Cholesterol Diet-Induced Hypercholesterolemic Rats.", "token_count": 153, "char_count": 604, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:36.938184", "source": { "split": "train_shard_00000", "doc_id": 1313 }, "chunk_id": "train_shard_00000_1313_0", "global_id": 1452 }, { "text": "Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by\n\nPangenome Reconstruction of", "token_count": 36, "char_count": 148, "word_count": 22, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:37.305931", "source": { "split": "train_shard_00000", "doc_id": 1314 }, "chunk_id": "train_shard_00000_1314_0", "global_id": 1453 }, { "text": "A pangenome is a collection of the common and unique genomes that are present in a given species. It combines the genetic information of all the genomes sampled, resulting in a large and diverse range of genetic material. Pangenomic analysis offers several advantages compared to traditional genomic research. For example, a pangenome is not bound by the physical constraints of a single genome, so it can capture more genetic variability. Thanks to the introduction of the concept of pangenome, it is possible to use exceedingly detailed sequence data to study the evolutionary history of two different species, or how populations within a species differ genetically. In the wake of the Human Pangenome Project, this review aims at discussing the advantages of the pangenome around human genetic variation, which are then framed around how pangenomic data can inform population genetics, phylogenetics, and public health policy by providing insights into the genetic basis of diseases or determining personalized treatments, targeting the specific genetic profile of an individual. Moreover, technical limitations, ethical concerns, and legal considerations are discussed.\n\nHuman Pangenomics: Promises and Challenges of a Distributed Genomic Reference.", "token_count": 252, "char_count": 1253, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:37.790621", "source": { "split": "train_shard_00000", "doc_id": 1315 }, "chunk_id": "train_shard_00000_1315_0", "global_id": 1454 }, { "text": "Heat stress (HS) can inhibit the growth performance of broilers and cause substantial economic losses. Alterations in bile acid (BA) pools have been reported to be correlated with chronic HS, yet the specific mechanism and whether it is related to gut microbiota remains unclear. In this study, 40 Rugao Yellow chickens were randomly selected and distributed into two groups (20 broilers in each group) when reaching 56-day age: a chronic heat stress group (HS, 36 ± 1 °C for 8 h per day in the first 7 days and 36 ± 1 °C for 24 h in the last 7 days) and a control group (CN, 24 ± 1 °C for 24 h within 14 days). Compared with the CN group, total BAs' serum content decreased, while cholic acid (CA), chenodeoxycholic acid (CDCA), and taurolithocholic acid (TLCA) increased significantly in HS broilers. Moreover, 12α-hydroxylase (CYP8B1) and bile salt export protein (BSEP) were upregulated in the liver, and the expression of fibroblast growth factor 19 (FGF19) decreased in the ileum of HS broilers. There were also significant changes in gut microbial composition, and the enrichment of\n\nChronic Heat Stress Affects Bile Acid Profile and Gut Microbiota in Broilers.", "token_count": 344, "char_count": 1168, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6497, "quality_score": 0.8249, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:38.365598", "source": { "split": "train_shard_00000", "doc_id": 1316 }, "chunk_id": "train_shard_00000_1316_0", "global_id": 1455 }, { "text": "The narrow genomic diversity of modern cultivars is a major bottleneck for enhancing the crop's salinity stress tolerance. The close relatives of modern cultivated plants, crop wild relatives (CWRs), can be a promising and sustainable resource to broaden the diversity of crops. Advances in transcriptomic technologies have revealed the untapped genetic diversity of CWRs that represents a practical gene pool for improving the plant's adaptability to salt stress. Thus, the present study emphasizes the transcriptomics of CWRs for salinity stress tolerance. In this review, the impacts of salt stress on the plant's physiological processes and development are overviewed, and the transcription factors (TFs) regulation of salinity stress tolerance is investigated. In addition to the molecular regulation, a brief discussion on the phytomorphological adaptation of plants under saline environments is provided. The study further highlights the availability and use of transcriptomic resources of CWR and their contribution to pangenome construction. Moreover, the utilization of CWRs' genetic resources in the molecular breeding of crops for salinity stress tolerance is explored. Several studies have shown that cytoplasmic components such as calcium and kinases, and ion transporter genes such as Salt Overly Sensitive 1 (\n\nInsights into the Transcriptomics of Crop Wild Relatives to Unravel the Salinity Stress Adaptive Mechanisms.", "token_count": 302, "char_count": 1435, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5874, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:38.922780", "source": { "split": "train_shard_00000", "doc_id": 1317 }, "chunk_id": "train_shard_00000_1317_0", "global_id": 1456 }, { "text": "(1) Background: Progressive familial intrahepatic cholestasis (PFIC) is a rare cause of liver failure. Surgical biliary diversion (SBD) and ileal bile salt inhibitors (IBAT) can delay or prevent liver transplantation (LTX). A comparison of the two methodologies in the literature is lacking. The combination has not been investigated. (2) Methods: We performed a literature survey on medical and surgical treatments for PFIC and reviewed the charts of our patients with PFIC of a tertiary hospital. The end points of our analysis were a decrease in serum bile acid (sBA) levels, reduction of pruritus and delay or avoidance of (LTX). (3) Results: We included 17 case series on SBD with more than 5 patients and a total of 536 patients. External or internal SBD, either conventional or minimally invasive, can reduce pruritus and sBA, but not all PFIC types are suitable for SBD. Six publications described the use of two types of IBAT in PFIC with a total of 118 patients. Treatment response was dependent on genetic type and subtype. Patients with PFIC 2 (nt-BSEP) showed the best response to treatment. Four out of eleven PFIC patients underwent SBD at our centre, with two currently receiving IBAT. (4) Conclusions: Limited data on IBAT in selected patients with PFIC show safety and effectiveness, although surgical methods should still be considered as a successful bridging procedure. Further studies to evaluate a possible combination of IBAT and SBD in PFIC are warranted and treatment decision should be discussed in an interdisciplinary board.\n\nSurgical versus Medical Management of Progressive Familial Intrahepatic Cholestasis-Case Compilation and Review of the Literature.", "token_count": 426, "char_count": 1685, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:39.546829", "source": { "split": "train_shard_00000", "doc_id": 1318 }, "chunk_id": "train_shard_00000_1318_0", "global_id": 1457 }, { "text": "The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis. Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling the identification of targets for metabolic engineering of bioproduction hosts.\n\nPopulation genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis.", "token_count": 455, "char_count": 1921, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.8169, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:40.188309", "source": { "split": "train_shard_00000", "doc_id": 1319 }, "chunk_id": "train_shard_00000_1319_0", "global_id": 1458 }, { "text": "Potential probiotic yeast strains isolated from fermented food need to meet safe and beneficial conditions for the host's health. The Pichia kudriavzevii YGM091 strain isolated from fermented goat milk has outstanding probiotic characteristics, including: the high survival percentage in digestive system conditions (reaching up 247.13 ± 0.12 and 145.03 ± 0.06% at pH 3.0 and bile salt 0.5%, respectively); good tolerance to temperature, salt, phenol, ethanol; good surface properties such as high hydrophobicity percentage (> 60%), the high auto-aggregation percentage rate (66.56 ± 1.45% after 45 min of incubation) and the high co-aggregation percentage rate with pathogenic bacteria in a short time (> 40% after 2 h of incubation); biofilm forming after 24 h of incubation on abiotic surfaces; antioxidant activity reached excellent level after only 24 h of incubation (The percentage free radical scavenging and the Trolox equivalent reaching up 79.86 ± 0.70% and 92.09 ± 0.75 µg/mL after 72 h of incubation); extracellular enzymes production protease and cellulase with high activity, amylase and pectinase with moderate activity and non-lipase activity. Simultaneously, the YGM091 strain is the in vitro safety yeast: insensitive to antibiotics and fluconazole, negative for gelatinase, phospholipase, coagulase, and non-hemolysis activities. Furthermore, this strain is in vivo safety yeast with the dosages below 10", "token_count": 461, "char_count": 1424, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8341, "entities": { "genes": [ "YGM091" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:40.829178", "source": { "split": "train_shard_00000", "doc_id": 1320 }, "chunk_id": "train_shard_00000_1320_0", "global_id": 1459 }, { "text": "Probiotic Properties and Safety Evaluation in the Invertebrate Model Host Galleria mellonella of the Pichia kudriavzevii YGM091 Strain Isolated from Fermented Goat Milk.", "token_count": 55, "char_count": 169, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [ "YGM091" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:41.191725", "source": { "split": "train_shard_00000", "doc_id": 1320 }, "chunk_id": "train_shard_00000_1320_1", "global_id": 1460 }, { "text": "Bile acid sequestrants (BASs) are non-systemic therapeutic agents used for the management of hypercholesterolemia. They are generally safe and not associated with serious systemic adverse effects. Usually, BASs are cationic polymeric gels that have the ability to bind bile salts in the small intestine and eliminate them by excretion of the non-absorbable polymer-bile salt complex. This review gives a general presentation of bile acids and the characteristics and mechanisms of action of BASs. The chemical structures and methods of synthesis are shown for commercial BASs of first- (cholestyramine, colextran, and colestipol) and second-generation (colesevelam and colestilan) and potential BASs. The latter are based on either synthetic polymers such as poly((meth)acrylates/acrylamides), poly(alkylamines), poly(allylamines) and vinyl benzyl amino polymers or biopolymers, such as cellulose, dextran, pullulan, methylan, and poly(cyclodextrins). A separate section is dedicated to molecular imprinting polymers (MIPs) because of their great selectivity and affinity for the template molecules used in the imprinting technique. Focus is given to the understanding of the relationships between the chemical structure of these cross-linked polymers and their potential to bind bile salts. The synthetic pathways used in obtaining BASs and their in vitro and in vivo hypolipidemic activities are also introduced.\n\nBile Acid Sequestrants Based on Natural and Synthetic Gels.", "token_count": 379, "char_count": 1475, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:41.769721", "source": { "split": "train_shard_00000", "doc_id": 1321 }, "chunk_id": "train_shard_00000_1321_0", "global_id": 1461 }, { "text": "Advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variation at various scales, from smaller tandem repeats to megabase rearrangements, across many human genomes. We present a PanGenome Research Tool Kit (PGR-TK) enabling analyses of complex pangenome structural and haplotype variation at multiple scales. We apply the graph decomposition methods in PGR-TK to the class II major histocompatibility complex demonstrating the importance of the human pangenome for analyzing complicated regions. Moreover, we investigate the Y-chromosome genes, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LW and OPN1MW linked to eye disorders. We further showcase PGR-TK across 395 complex repetitive medically important genes. This highlights the power of PGR-TK to resolve complex variation in regions of the genome that were previously too complex to analyze.\n\nMultiscale analysis of pangenomes enables improved representation of genomic diversity for repetitive and clinically relevant genes.", "token_count": 278, "char_count": 1210, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6832, "quality_score": 0.8416, "entities": { "genes": [ "DAZ4", "DAZ3", "DAZ2", "DAZ1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:42.336736", "source": { "split": "train_shard_00000", "doc_id": 1322 }, "chunk_id": "train_shard_00000_1322_0", "global_id": 1462 }, { "text": "Understanding the origins of variation in agricultural pathogens is of fundamental interest and practical importance, especially for diseases that threaten food security.\n\nHiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in", "token_count": 53, "char_count": 270, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:42.702369", "source": { "split": "train_shard_00000", "doc_id": 1323 }, "chunk_id": "train_shard_00000_1323_0", "global_id": 1463 }, { "text": "The bile salt export pump (BSEP) is a key transporter involved in the efflux of bile salts from hepatocytes to bile canaliculi. Inhibition of BSEP leads to the accumulation of bile salts within the hepatocytes, leading to possible cholestasis and drug-induced liver injury. Screening for and identification of chemicals that inhibit this transporter aid in understanding the safety liabilities of these chemicals. Moreover, computational approaches to identify BSEP inhibitors provide an alternative to the more resource-intensive, gold standard experimental approaches. Here, we used publicly available data to develop predictive machine learning models for the identification of potential BSEP inhibitors. Specifically, we analyzed the utility of a graph convolutional neural network (GCNN)-based approach in combination with multitask learning to identify BSEP inhibitors. Our analyses showed that the developed GCNN model performed better than the variable-nearest neighbor and Bayesian machine learning approaches, with a cross-validation receiver operating characteristic area under the curve of 0.86. In addition, we compared GCNN-based single-task and multitask models and evaluated their utility in addressing data limitation challenges commonly observed in bioactivity modeling. We found that multitask models performed better than single-task models and can be utilized to identify active molecules for targets with limited data availability. Overall, our developed multitask GCNN-based BSEP model provides a useful tool for prioritizing hits during early drug discovery and in risk assessment of chemicals.\n\nUsing a Graph Convolutional Neural Network Model to Identify Bile Salt Export Pump Inhibitors.", "token_count": 361, "char_count": 1714, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:43.282697", "source": { "split": "train_shard_00000", "doc_id": 1324 }, "chunk_id": "train_shard_00000_1324_0", "global_id": 1464 }, { "text": "The molecular basis of reduced susceptibility to amphotericin B (rs-AMB) among any yeasts is poorly defined. Genetic alterations in genes involved in ergosterol biosynthesis and total cell sterols were investigated among clinical Candida kefyr isolates. C. kefyr isolates (\n\nMolecular Characterization and Sterol Profiles Identify Nonsynonymous Mutations in", "token_count": 91, "char_count": 357, "word_count": 48, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:43.662831", "source": { "split": "train_shard_00000", "doc_id": 1325 }, "chunk_id": "train_shard_00000_1325_0", "global_id": 1465 }, { "text": "Probiotic products containing living microorganisms are gaining popularity, increasing the importance of their taxonomic status. A Bacillus-like isolate, 70 b, cultured from a probiotic feed additive, was ambiguity in taxonomic assignment and could be a novel member of Bacillus cereus group. The results of colony and cellular morphology, physiological and biochemical analysis mainly including growth performance, carbon source utilization, and rMLST and MLST were not conclusive. Fatty acids profile and molecular genetic analysis especially ANI, DDH, and core genome SNPs-based phylogenetic tree confirmed 70 b as one novel species of B. cereus group and proposed as Bacillus pfraonensis sp. nov. Comparative genomic analysis revealed the genetic differences between 70 b and other species of B. cereus group. Pseudomycoicidin was identified in 70 b. 70 b was active against multidrug-resistant pathogenic strains MRSA. The findings support 70 b is a novel species with low cytotoxicity and antimicrobial activity, and provides a better understanding of its unique characteristics and probiotic potential, and exploration of bioactive potential.\n\nBacillus pfraonensis sp. nov., a new strain isolated from a probiotic feed additive with low cytotoxicity and antimicrobial activity.", "token_count": 334, "char_count": 1284, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:44.235657", "source": { "split": "train_shard_00000", "doc_id": 1326 }, "chunk_id": "train_shard_00000_1326_0", "global_id": 1466 }, { "text": "Salmonella enterica serovar Typhimurium (S. Typhimurium) and S. 4,[5],12:i:- have become the most common serovars associated with human salmonellosis worldwide. Moreover, the emergence of mcr-carrying S. Typhimurium and S. 4,[5],12:i:- with multidrug resistance (MDR) patterns has posed a threat to public health. In this study, we retrospectively screened 2009-2022 laboratory-preserved strains for the presence of mcr genes. We obtained 16 mcr-1-positive S. Typhimurium and S. 4,[5],12:i:- strains with MDR that belonged to sequence type 34 (ST34). Whole-genome sequencing analysis revealed that the mcr-1 was located on the IncI2 or IncHI2 plasmids. The ISApl1 element downstream of mcr-1 was present in all pig-derived strains. Conjugation experiments confirmed that nine mcr-1-carrying IncHI2 plasmids could not be transferred to Escherichia coli due to loss of the conjugation region. Finally, core genome single nucleotide polymorphism (cgSNP) analyses of the 16 mcr-1-carrying strains and 77 mcr-carrying ST34-Salmonella genome sequences from the NCBI and ENA databases showed that five out of eight clusters contained strains from pig and pig products, revealing pigs and pig products as key reservoirs of mcr-1-positive ST34-Salmonella strains. The transmission of mcr-carrying ST34 Salmonella strains to humans via the pig food chain is a potential cause for public health concern in controlling human salmonellosis.\n\nPrevalence and molecular characterization of mcr-1-positive foodborne ST34-Salmonella isolates in China.", "token_count": 463, "char_count": 1533, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8286, "entities": { "genes": [ "ST34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:44.872779", "source": { "split": "train_shard_00000", "doc_id": 1327 }, "chunk_id": "train_shard_00000_1327_0", "global_id": 1467 }, { "text": "Nitrogen metabolism in the genus Citrobacter is very poorly studied despite its several implications in wastewater treatment. In the current study, Citrobacter portucalensis strain AAK_AS5 was assessed for remediation of simulated wastewater supplemented with different inorganic nitrogen sources. Combination of (NH\n\nPangenome-driven insights into nitrogen metabolic characteristics of Citrobacter portucalensis strain AAK_AS5 associated with wastewater nitrogen removal.", "token_count": 109, "char_count": 472, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:45.258423", "source": { "split": "train_shard_00000", "doc_id": 1328 }, "chunk_id": "train_shard_00000_1328_0", "global_id": 1468 }, { "text": "Seven serogroups of E. coli (Top seven E. coli) are frequently implicated in foodborne outbreaks in North America, largely due to their carriage of Shiga toxin genes (stx). This study aimed to profile resistance genes and virulence factors (VF), and their potential association with phylogeny and phenotypes of Top seven E. coli originating from cattle in Canada. 155 Top seven E. coli isolates previously characterized for heat and acid resistance and biofilm-forming ability were whole-genome sequenced and analyzed for phylogeny, VF, and stress resistance genes. The 155 E. coli strains belonged to six phylogroups: A (n = 32), B1 (n = 93), C (n = 3), D (n = 11), E (n = 15), and G (n = 1). Different phylogroups were clearly separated on the core genome tree, with strains of the same serotype closely clustered. The carriage of stx and the transmissible locus of stress tolerance (tLST), the extreme heat resistance marker, was mutually exclusive, in 33 and 15 genomes, respectively. A novel O84:H2 strain carrying stx\n\nStress Resistance and Virulence Gene Profiles Associated with Phylogeny and Phenotypes of Escherichia coli from Cattle.", "token_count": 330, "char_count": 1144, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:45.829482", "source": { "split": "train_shard_00000", "doc_id": 1329 }, "chunk_id": "train_shard_00000_1329_0", "global_id": 1469 }, { "text": "Lactic acid bacteria (LAB) in the microbiota play an important role in human and animal health and, when used as probiotics, can contribute to an increased growth performance in livestock management. Animals living in their native habitat can serve as natural sources of microorganisms, so isolation of LAB strains from wild boars could provide the opportunity to develop effective probiotics to improve production in swine industry. In this study, the probiotic potential of 56 LAB isolates, originated from the ileum, colon, caecum and faeces of 5 wild boars, were assessed in vitro in details. Their taxonomic identity at species level and their antibacterial activity against four representative strains of potentially pathogenic bacteria were determined. The ability to tolerate low pH and bile salt, antibiotic susceptibility, bile salt hydrolase activity and lack of hemolysis were tested. Draft genome sequences of ten Limosilactobacillus mucosae and three Leuconostoc suionicum strains were determined. Bioinformatic analysis excluded the presence of any known acquired antibiotic resistance genes. Three genes, encoding mesentericin B105 and two different bacteriocin-IIc class proteins, as well as two genes with possible involvement in mesentericin secretion (mesE) and transport (mesD) were identified in two L. suionicum strains. Lam29 protein, a component of an ABC transporter with proved function as mucin- and epithelial cell-adhesion factor, and a bile salt hydrolase gene were found in all ten L. mucosae genomes. Comprehensive reconsideration of all data helps to select candidate strains to assess their probiotic potential further in animal experiments.\n\nIsolation and Characterization of Lactic Acid Bacteria With Probiotic Attributes From Different Parts of the Gastrointestinal Tract of Free-living Wild Boars in Hungary.", "token_count": 451, "char_count": 1847, "word_count": 267, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:46.471657", "source": { "split": "train_shard_00000", "doc_id": 1330 }, "chunk_id": "train_shard_00000_1330_0", "global_id": 1470 }, { "text": "The human pangenome reference: the beginning of a new era for genomics.", "token_count": 17, "char_count": 71, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:46.857774", "source": { "split": "train_shard_00000", "doc_id": 1331 }, "chunk_id": "train_shard_00000_1331_0", "global_id": 1471 }, { "text": "Clostridium difficile infection (CDI) is caused by a prevalent nosocomial enteric pathogen, leading to high morbidity and mortality. CDI recurrence after antibiotic treatment is high; therefore, it is necessary to develop novel therapeutics against this enteric pathogen. Butyrate is used to treat many diseases because it provides energy, has anti-inflammatory properties, and maintains intestinal barrier function. An anti-CDI effect for butyrate has been reported; however, the specific mechanism remains elusive. This study aimed to explore the potential role and mechanism of butyrate in the treatment of CDI. Using a CDI mouse model, we found that butyrate significantly inhibited CDI development by regulating bile acid metabolism. Dysregulation of fecal bile acid was significantly higher, and levels of short-chain fatty acids were significantly lower in patients with CDI than those in controls. In CDI mice, butyrate exhibited a protective role by enhancing barrier protection, exerting anti-inflammatory effects, and regulating bile acid metabolism. Butyrate treatment also regulated the production of bile salt hydrolase (BSH) flora and activated farnesoid X receptor (FXR), and its therapeutic effects were reduced in CDI mice treated with BSH or FXR inhibitors. Thus, butyrate treatment may serve as a novel therapeutic approach for patients with CDI.\n\nButyrate Protects against Clostridium difficile Infection by Regulating Bile Acid Metabolism.", "token_count": 357, "char_count": 1461, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:47.455035", "source": { "split": "train_shard_00000", "doc_id": 1332 }, "chunk_id": "train_shard_00000_1332_0", "global_id": 1472 }, { "text": "Cholestatic liver injury is caused by toxic action or allergic reaction, resulting in abnormality of bile formation and excretion. Few effective therapies have become available for the treatment of cholestasis. Herein, we found that tectorigenin (TG), a natural isoflavone, showed definite protective effects on alpha-naphthylisothiocyanate (ANIT)-induced cholestatic liver injury, significantly reversing the abnormality of plasma alanine/aspartate aminotransferase, total/direct bilirubin and alkaline phosphatase, as well as hepatic reactive oxygen species, catalase and superoxide dismutase. Importantly, the targeted metabolomic determination found that BA homeostasis could be well maintained in TG-treated cholestatic mice, especially the levels of glycocholic acid, tauromuricholic acid, taurocholic acid, taurolithocholic acid, tauroursodeoxycholic acid and taurodeoxycholic acid. Overall, primary/secondary and amidated/unamidated bile acid (BA) levels were significantly altered upon ANIT stimulation but could be restored by TG intervention to certain extents. In addition, TG boosted the expression of farnesoid x receptor (FXR), which in turn upregulated multidrug resistance protein 2 (MRP2) and bile salt export pump (BSEP) to accelerate the excretion of BA. Meanwhile, TG enhanced the expression of Nrf2 and its upstream genes PI3K/Akt and downstream target genes HO-1, NQO1, GCLC and GCLM to strengthen the antioxidant capacity. Taken together, TG plays a vital role in maintaining BA homeostasis and ameliorating cholestatic liver injury through regulating FXR-mediated BA efflux and Nrf2-mediated antioxidative pathways.\n\nMolecular mechanisms of hepatoprotective effect of tectorigenin against ANIT-induced cholestatic liver injury: Role of FXR and Nrf2 pathways.", "token_count": 494, "char_count": 1783, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6983, "quality_score": 0.8491, "entities": { "genes": [ "MRP2", "PI3K", "NQO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:48.124712", "source": { "split": "train_shard_00000", "doc_id": 1333 }, "chunk_id": "train_shard_00000_1333_0", "global_id": 1473 }, { "text": "Numerous genotyping techniques based on different principles and with different costs and levels of resolution are currently available for understanding the transmission dynamics of brucellosis worldwide. We aimed to compare the population structure of the genomes of 53 Brazilian Brucella abortus isolates using eight different genotyping methods: multiple-locus variable-number tandem-repeat analysis (MLVA8, MLVA11, MLVA16), multilocus sequence typing (MLST9, MLST21), core genome MLST (cgMLST) and two techniques based on single nucleotide polymorphism (SNP) detection (parSNP and NASP) from whole genomes. The strains were isolated from six different Brazilian states between 1977 and 2008 and had previously been analyzed using MLVA8, MLVA11, and MLVA16. Their whole genomes were sequenced, assembled, and subjected to MLST9 MLST21, cgMLST, and SNP analyses. All the genotypes were compared by hierarchical grouping method based on the average distances between the correlation matrices of each technique. MLST9 and MLST21 had the lowest level of resolution, both revealing only four genotypes. MLVA8, MLVA11, and MLVA16 had progressively increasing levels of resolution as more loci were analyzed, identifying 6, 16, and 44 genotypes, respectively. cgMLST showed the highest level of resolution, identifying 45 genotypes, followed by the SNP-based methods, both of which had 44 genotypes. In the assessed population, MLVA was more discriminatory than MLST and was easier and cheaper to perform. SNP techniques and cgMLST provided the highest levels of resolution and the results from the two methods were in close agreement. In conclusion, the choice of genotyping technique can strongly affect one's ability to make meaningful epidemiological conclusions but is dependent on available resources: while the VNTR based techniques are more indicated to high prevalence scenarios, the WGS methods are the ones with the best discriminative power and therefore recommended for outbreaks investigation.\n\nComparison of Brucella abortus population structure based on genotyping methods with different levels of resolution.", "token_count": 506, "char_count": 2121, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5967, "quality_score": 0.7983, "entities": { "genes": [ "MLVA16", "MLST9", "MLVA11", "MLVA8", "MLST21" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:48.813158", "source": { "split": "train_shard_00000", "doc_id": 1334 }, "chunk_id": "train_shard_00000_1334_0", "global_id": 1474 }, { "text": "Lactic acid bacteria are commonly in the fermentation industry and pose potential positive effects on health. In this study, a new lactic acid bacterium was isolated from fermented vegetable extracts in Myoko, Niigata, Japan. This bacterium is fructophilic, acidophilic, and hard to grow on agar medium. The isolate is Gram-stain-positive, non-spore-forming, non-motile, rod-shaped, and catalase-negative. Growth occurred at pH 3.5-5.5, with optimal growth at pH 4.5-5.0. The cells formed colonies on a solid MRS medium with 20% (w/v) sucrose and 0.8% (w/v) gellan gum under anaerobic conditions. The bacterium was able to grow on up to 50% (w/v) sucrose but not on d-glucose. Moreover, 16S rRNA gene sequence analysis revealed that the strain was most closely related to Apilactobacillus ozensis (93.1% sequence similarity). The values of average nucleotide identity, digital DNA-DNA hybridization, average amino acid sequence identity, and amino acid identity of conserved genes were calculated between the isolated strain (type strain is WR16-4T = NBRC 115064T = DSM 112857T) and its phylogenetically closest type strains. The average nucleotide identity values (73.36-78.28%) and DNA-DNA hybridization values (16.3-32.9%) were significantly lower than the threshold values for species boundaries. The average amino acid sequence identity values (53.96-60.88%) were significantly below the threshold boundary of genus demarcation (68%)", "token_count": 427, "char_count": 1438, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [ "WR16" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:49.437680", "source": { "split": "train_shard_00000", "doc_id": 1335 }, "chunk_id": "train_shard_00000_1335_0", "global_id": 1475 }, { "text": "The amino acid identity of conserved genes values compared to strain WR16-4T were the genera Apilactobacillus, Nicoliella spurrieriana SGEP1_A5T, Acetilactobacillus jinshanensis HSLZ-75T, and Fructilactobacillus were 62.51-63.79%, 62.87%, 62.03%, and 58.00-61.04%, respectively. The 16S rRNA gene and core genome phylogenetic trees suggested that this novel strain was most closely related to the type strain of A. jinshanensis HSLZ-75T. Based on the physiological, morphological, and phenotypical characteristics of strain WR16-4T, we propose its classification as a novel genus, Philodulcilactobacillus myokoensis gen. nov., sp. nov.\n\nPhilodulcilactobacillus myokoensis gen. nov., sp. nov., a fructophilic, acidophilic, and agar-phobic lactic acid bacterium isolated from fermented vegetable extracts.", "token_count": 279, "char_count": 803, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7525, "quality_score": 0.8762, "entities": { "genes": [ "WR16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:49.981663", "source": { "split": "train_shard_00000", "doc_id": 1335 }, "chunk_id": "train_shard_00000_1335_1", "global_id": 1476 }, { "text": "Bacteria from the Turicibacter genus are prominent members of the mammalian gut microbiota and correlate with alterations in dietary fat and body weight, but the specific connections between these symbionts and host physiology are poorly understood. To address this knowledge gap, we characterize a diverse set of mouse- and human-derived Turicibacter isolates, and find they group into clades that differ in their transformations of specific bile acids. We identify Turicibacter bile salt hydrolases that confer strain-specific differences in bile deconjugation. Using male and female gnotobiotic mice, we find colonization with individual Turicibacter strains leads to changes in host bile acid profiles, generally aligning with those produced in vitro. Further, colonizing mice with another bacterium exogenously expressing bile-modifying genes from Turicibacter strains decreases serum cholesterol, triglycerides, and adipose tissue mass. This identifies genes that enable Turicibacter strains to modify host bile acids and lipid metabolism, and positions Turicibacter bacteria as modulators of host fat biology.\n\nGut microbiota Turicibacter strains differentially modify bile acids and host lipids.", "token_count": 292, "char_count": 1203, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:50.546814", "source": { "split": "train_shard_00000", "doc_id": 1336 }, "chunk_id": "train_shard_00000_1336_0", "global_id": 1477 }, { "text": "Oral delivery of probiotics has been a promising method for treatment of inflammatory bowel diseases (IBDs). However, probiotics always suffer from substantial loss of viability due to the harsh gastrointestinal conditions, especially the highly acidic environment in the stomach and bile salts in the intestine. In addition, to overcome the challenging conditions, an ideal delivery of probiotics requires the on-demand release of probiotics upon environmental response. Herein, a novel nitroreductase (NTR) labile peptidic hydrogel based on supramolecular self-assembly is demonstrated. The efficient encapsulation of typical probiotic\n\nReductase-Labile Peptidic Supramolecular Hydrogels Aided in Oral Delivery of Probiotics.", "token_count": 180, "char_count": 727, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7292, "quality_score": 0.8646, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:50.990330", "source": { "split": "train_shard_00000", "doc_id": 1337 }, "chunk_id": "train_shard_00000_1337_0", "global_id": 1478 }, { "text": "The Bovine Pangenome Consortium (BPC) is an international collaboration dedicated to the assembly of cattle genomes to develop a more complete representation of cattle genomic diversity. The goal of the BPC is to provide genome assemblies and a community-agreed pangenome representation to replace breed-specific reference assemblies for cattle genomics. The BPC invites partners sharing our vision to participate in the production of these assemblies and the development of a common, community-approved, pangenome reference as a public resource for the research community ( https://bovinepangenome.github.io/ ). This community-driven resource will provide the context for comparison between studies and the future foundation for cattle genomic selection.\n\nThe Bovine Pangenome Consortium: democratizing production and accessibility of genome assemblies for global cattle breeds and other bovine species.", "token_count": 195, "char_count": 904, "word_count": 122, "semantic_coherence": 1, "information_density": 0.582, "quality_score": 0.791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:51.445048", "source": { "split": "train_shard_00000", "doc_id": 1338 }, "chunk_id": "train_shard_00000_1338_0", "global_id": 1479 }, { "text": "The rich genetic diversity in Citrullus lanatus and the other six species in the Citrullus genus provides important sources in watermelon breeding. Here, we present the Citrullus genus pan-genome based on the 400 Citrullus genus resequencing data, showing that 477 Mb contigs and 6249 protein-coding genes were absent in the Citrullus lanatus reference genome. In the Citrullus genus pan-genome, there are a total of 8795 (30.5%) genes that exhibit presence/absence variations (PAVs). Presence/absence variation (PAV) analysis showed that a lot of gene PAV were selected during the domestication and improvement, such as 53 favorable genes and 40 unfavorable genes were identified during the C. mucosospermus to C. lanatus landrace domestication. We also identified 661 resistance gene analogs (RGAs) in the Citrullus genus pan-genome, which contains 90 RGAs (89 variable and 1 core gene) located on the pangenome additional contigs. By gene PAV-based GWAS, 8 gene presence/absence variations were found associated with flesh color. Finally, based on the results of gene PAV selection analysis between watermelon populations with different fruit colors, we identified four non-reference candidate genes associated with carotenoid accumulation, which had a significantly higher frequency in the white flesh. These results will provide an important source for watermelon breeding.\n\nPan-genome of Citrullus genus highlights the extent of presence/absence variation during domestication and selection.", "token_count": 382, "char_count": 1497, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5981, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:52.025588", "source": { "split": "train_shard_00000", "doc_id": 1339 }, "chunk_id": "train_shard_00000_1339_0", "global_id": 1480 }, { "text": "To date, the coffee industry has the second highest market value in the world and consumer behavior has transitioned from drinking coffee just for its caffeine content to reduce sleepiness into an overall experience. Instant cold brew coffee in powder form can preserve the taste of coffee well; moreover, it is easy to transport. Several consumers have increasing interests in implementing lactic acid bacteria in healthy food due to their growing awareness of the probiotic's role. Several scholars have presented stress adaptation characteristics of single probiotic strains; however, comparisons of the stress-tolerant capacities of different probiotic strains are incomplete. Five lactic acid strains are tested for adaptation under four sublethal conditions. Lactobacillus casei is the most resilient probiotic in terms of heat and cold adaptation, while Lactobacillus acidophilus is more tolerant to low acid and bile salt; Then, these probiotics are subjected to a stress challenge that stimulates drying temperature, including a heat and cold stress challenge. The results show that acid adaptation can improve Lactobacillus acidophilus TISTR 1338 tolerance to harsh drying temperatures. In addition, encapsulation using prebiotic extracts from rice bran, with pectin and resistant starch combined through crosslinking and treated by freeze-drying, provides the highest encapsulation efficiency. In summary, acid-adapted L. acidophilus TISTR 1388 at the sublethal level can be applied to high and low temperature processing techniques. Additionally, the amount of viable probiotic after in vitro digestion remains at 5 log CFU/g, which is suitable for application in the production of synbiotic cold brew coffee.\n\nRice bran as an encapsulating material to produce a healthy synbiotic product with improved gastrointestinal tolerance.", "token_count": 414, "char_count": 1842, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:52.641209", "source": { "split": "train_shard_00000", "doc_id": 1340 }, "chunk_id": "train_shard_00000_1340_0", "global_id": 1481 }, { "text": "Previous research revealed marked differences in the composition of intestinal fluids between infants and adults. To explore the impact on the solubilization of orally administered drugs, the present study assessed the solubility of five poorly water-soluble, lipophilic drugs in intestinal fluid pools from 19 infant enterostomy patients (infant HIF). For some but not all drugs, the average solubilizing capacity of infant HIF was similar to that of HIF obtained from adults (adult HIF) in fed conditions. Commonly used fed state simulated intestinal fluids (FeSSIF(-V2)) predicted fairly well drug solubility in the aqueous fraction of infant HIF, but did not account for the substantial solubilization by the lipid phase of infant HIF. Despite similarities in the average solubilities of some drugs in infant HIF and adult HIF or SIF, the underlying solubilization mechanisms likely differ, considering important compositional differences (e.g., low bile salt levels). Finally, the huge variability in composition of infant HIF pools resulted in a highly variable solubilizing capacity, potentially causing variations in drug bioavailability. The current study warrants future research focusing on (i) understanding the mechanisms underlying drug solubilization in infant HIF and (ii) evaluating the sensitivity of oral drug products to interpatient variations in drug solubilization.\n\nCharacterization of neonatal and infant enterostomy fluids - part II: Drug solubility.", "token_count": 337, "char_count": 1476, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6019, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:53.204544", "source": { "split": "train_shard_00000", "doc_id": 1341 }, "chunk_id": "train_shard_00000_1341_0", "global_id": 1482 }, { "text": "Lactobacillus contribute to maintain the human healthy and use for nutritional additives as probiotics. In this study, a cholesterol-lowering bacterium, Lactobacillus gasseri TF08-1, was isolated from the feces of a healthy adolescent, and its probiotic potentials were evaluated through genomic mining and in vitro test. The assembled draft genome comprised of 1,974,590 bp and was predicted total of 1,940 CDSs. The annotation of the genome revealed that L. gasseri TF08-1 harbored abundant categories of functional genes in metabolic and information processing. Moreover, strain TF08-1 has capacity to utilize D-Glucose, Sucrose, D-Maltose, Salicin, D-Xylose, D-Cellobiose, D-Mannose, and D-Trehalose, as the carbon source. The safety assessment showed strain TF08-1 contained few antibiotic resistance genes and virulence factors and was only resistant to 2 antibiotics detected by antimicrobial susceptibility test. A high bile salt hydrolase activity was found and a cholesterol-reducing effect was determined in vitro, which the result showed a remarkable cholesterol removal capability of L. gasseri TF08-1 with an efficiency of 84.40 %. This study demonstrated that the strain showed great capability of exopolysaccharide production, and tolerance to acid and bile salt. Therefore, these results indicate that L. gasseri TF08-1 can be considered as a safe candidate for probiotic, especially its potential in biotherapeutic for metabolic diseases.\n\nProbiotic characteristics of Lactobacillus gasseri TF08-1: A cholesterol-lowering bacterium, isolated from human gut.", "token_count": 433, "char_count": 1575, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6347, "quality_score": 0.8174, "entities": { "genes": [ "TF08" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:53.836586", "source": { "split": "train_shard_00000", "doc_id": 1342 }, "chunk_id": "train_shard_00000_1342_0", "global_id": 1483 }, { "text": "Improved understanding of the genetic basis of\n\nGenomic Insights into Pangenome and Antimicrobial Resistance in", "token_count": 27, "char_count": 111, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:54.193183", "source": { "split": "train_shard_00000", "doc_id": 1343 }, "chunk_id": "train_shard_00000_1343_0", "global_id": 1484 }, { "text": "Combining 47 human genomes into a single pangenome.", "token_count": 15, "char_count": 51, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:54.542132", "source": { "split": "train_shard_00000", "doc_id": 1344 }, "chunk_id": "train_shard_00000_1344_0", "global_id": 1485 }, { "text": "Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form, but populations of Asian ancestry are underrepresented. Here we present data from the first phase of the Chinese Pangenome Consortium, including a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With an average 30.65× high-fidelity long-read sequence coverage, an average contiguity N50 of more than 35.63 megabases and an average total size of 3.01 gigabases, the CPC core assemblies add 189 million base pairs of euchromatic polymorphic sequences and 1,367 protein-coding gene duplications to GRCh38. We identified 15.9 million small variants and 78,072 structural variants, of which 5.9 million small variants and 34,223 structural variants were not reported in a recently released pangenome reference\n\nA pangenome reference of 36 Chinese populations.", "token_count": 275, "char_count": 959, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:55.094846", "source": { "split": "train_shard_00000", "doc_id": 1345 }, "chunk_id": "train_shard_00000_1345_0", "global_id": 1486 }, { "text": "A pangenome reference representative of 36 minority Chinese ethnic groups.", "token_count": 15, "char_count": 74, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:55.444765", "source": { "split": "train_shard_00000", "doc_id": 1346 }, "chunk_id": "train_shard_00000_1346_0", "global_id": 1487 }, { "text": "Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of\n\nA sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes.", "token_count": 350, "char_count": 1281, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7584, "quality_score": 0.8792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:56.021355", "source": { "split": "train_shard_00000", "doc_id": 1347 }, "chunk_id": "train_shard_00000_1347_0", "global_id": 1488 }, { "text": "The emergence of carbapenem-resistant, hypervirulent Klebsiella pneumoniae is a new threat to health care. We studied the molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Qatar using whole-genome sequence data. We also characterized the prevalence and genetic basis of hypervirulent phenotypes and established the virulence potential using a Galleria mellonella model. Of 100 Klebsiella isolates studied, NDM and OXA-48 were the most common carbapenemases. Core genome single-nucleotide polymorphism (SNP) analysis indicated the presence of diverse sequence types and clonal lineages; isolates belonging to Klebsiella quasipneumoniae subsp.\n\nGenomic Epidemiology of Carbapenem-Resistant", "token_count": 199, "char_count": 718, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:56.473434", "source": { "split": "train_shard_00000", "doc_id": 1348 }, "chunk_id": "train_shard_00000_1348_0", "global_id": 1489 }, { "text": "Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. We apply our method to pairs of genes from the Staphylococcus aureus accessory genome of over 75,000 annotated gene families using a database of over 40,000 whole genomes. We find many pairs of genes that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of rapidly coevolving genes, primarily consisting of genes involved in virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCCmec complex. While we focus on gene gain and loss, our method can also detect genes that tend to acquire substitutions in tandem, or genotype-phenotype or phenotype-phenotype coevolution. Finally, we present the R package DeCoTUR that allows for the computation of our method.\n\nDetecting patterns of accessory genome coevolution in Staphylococcus aureus using data from thousands of genomes.", "token_count": 305, "char_count": 1319, "word_count": 199, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:57.045219", "source": { "split": "train_shard_00000", "doc_id": 1349 }, "chunk_id": "train_shard_00000_1349_0", "global_id": 1490 }, { "text": "27 strains representing eight new Prevotella species were isolated from rumen of a single sheep in eight weeks interval. One of the putative species encompassing the highest number of isolated strains which also exhibited some genetic variability in preliminary data, was then selected for description of a novel species. We examined six strains in genomic and phenotypic detail, two of which may actually be the same strain isolated nearly three weeks apart. Other strains formed clearly diverged intraspecies lineages as evidenced by core genome phylogeny and phenotypic differences. Strains of the proposed new Prevotella species are strictly saccharolytic as is usual for rumen Prevotella, and use plant cell-wall xylans and pectins for growth. However, the range of cell-wall polysaccharides utilised for growth is rather limited compared to rumen generalists such as Prevotella bryantii or Prevotella ruminicola and this extends also to the inability to utilise starch, which is unexpected for the members of the genus Prevotella. Based on the data obtained, we propose Prevotella communis sp. nov. to accommodate strain E1-9\n\nExpanding the rumen Prevotella collection: The description of Prevotella communis, sp. nov. of ovine origin.", "token_count": 304, "char_count": 1241, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:57.610848", "source": { "split": "train_shard_00000", "doc_id": 1350 }, "chunk_id": "train_shard_00000_1350_0", "global_id": 1491 }, { "text": "Inspired by the production of reference data sets in the Genome in a Bottle project, we sequenced one Charolais heifer with different technologies: Illumina paired-end, Oxford Nanopore, Pacific Biosciences (HiFi and CLR), 10X Genomics linked-reads, and Hi-C. In order to generate haplotypic assemblies, we also sequenced both parents with short reads. From these data, we built two haplotyped trio high quality reference genomes and a consensus assembly, using up-to-date software packages. The assemblies obtained using PacBio HiFi reaches a size of 3.2 Gb, which is significantly larger than the 2.7 Gb ARS-UCD1.2 reference. The BUSCO score of the consensus assembly reaches a completeness of 95.8%, among highly conserved mammal genes. We also identified 35,866 structural variants larger than 50 base pairs. This assembly is a contribution to the bovine pangenome for the \"Charolais\" breed. These datasets will prove to be useful resources enabling the community to gain additional insight on sequencing technologies for applications such as SNP, indel or structural variant calling, and de novo assembly.\n\nA Bos taurus sequencing methods benchmark for assembly, haplotyping, and variant calling.", "token_count": 316, "char_count": 1200, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7416, "quality_score": 0.8708, "entities": { "genes": [ "UCD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:58.526355", "source": { "split": "train_shard_00000", "doc_id": 1351 }, "chunk_id": "train_shard_00000_1351_0", "global_id": 1492 }, { "text": "The diverse cytochrome P450 enzymes of insects play essential physiological roles and also play important roles in the metabolism of environmental chemicals such as insecticides. We manually curated the complement of P450 (CYP) genes, or CYPome, of the black fungus gnat, Bradysia (Sciara) coprophila (Diptera, Sciaroidea), a species with a variable number of chromosomes. This CYPome carries two types of \"alien\" P450 genes. The first type of alien P450s was found among the 163 CYP genes of the core genome (autosomes and X). They consist of 28 sequences resulting from horizontal gene transfer, with closest sequences not found in insects, but in other arthropods, often Collembola. These genes are not contaminants, because they are expressed genes with introns, found in synteny with regular dipteran genes, also found in B. odoriphaga and B. hygida. Two such \"alien\" genes are representatives of CYP clans not otherwise found in insects, a CYP53 sequence related to fungal CYP53 genes, and a CYP19-like sequence similar to some collembolan sequences but of unclear origin. The second type of alien P450s are represented by 99 sequences from germline-restricted chromosomes (GRC). While most are P450 pseudogenes, 33 are apparently intact, with half being more closely related to P450s from Cecidomyiidae than from Sciaridae, thus supporting the hypothesis of a cross-family hybridization origin of the GRC.\n\nAliens in the CYPome of the black fungus gnat, Bradysia coprophila.", "token_count": 410, "char_count": 1481, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [ "CYP19", "CYP53" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:59.189793", "source": { "split": "train_shard_00000", "doc_id": 1352 }, "chunk_id": "train_shard_00000_1352_0", "global_id": 1493 }, { "text": "Type III secretion system (T3SS) effector proteins are primarily recognized for binding host proteins to subvert host immune response during infection. Besides their known host target proteins, several T3SS effectors also interact with endogenous bacterial proteins. Here we demonstrate that the Salmonella T3SS effector glycosyltransferase SseK1 glycosylates the bacterial two-component response regulator OmpR on two arginine residues, R15 and R122. Arg-glycosylation of OmpR results in reduced expression of ompF, a major outer membrane porin gene. Glycosylated OmpR has reduced affinity to the ompF promoter region, as compared to the unglycosylated form of OmpR. Additionally, the Salmonella ΔsseK1 mutant strain had higher bile salt resistance and increased capacity to form biofilms, as compared to WT Salmonella, thus linking OmpR glycosylation to several important aspects of bacterial physiology.\n\nSalmonella T3SS effector SseK1 arginine-glycosylates the two-component response regulator OmpR to alter bile salt resistance.", "token_count": 277, "char_count": 1033, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7021, "quality_score": 0.8511, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:11:59.758092", "source": { "split": "train_shard_00000", "doc_id": 1353 }, "chunk_id": "train_shard_00000_1353_0", "global_id": 1494 }, { "text": "In this study, seven strains of Limosilactobacillus fermentum were isolated from an infant fecal sample and characterized using in vitro studies. Lactobacillus rhamnosus GG was used as a comparison because it is a well-documented commercial probiotic. The isolates were tested for attributes such as acid and phenol tolerance, bile salt hydrolase (BSH) activity, and antibiotic sensitivity. One isolate, L. fermentum FS-10, displayed enhanced cell surface hydrophobicity (> 85%) and mucin adhesion. Mucin-binding helps colonization in the gut. The immunomodulatory property of L. fermentum FS-10 was evaluated by determining the modulation of pro- and anti-inflammatory factors such as tumor necrosis factor-alpha (TNF-α), interleukin (IL)-10, and nitric oxide (NO) in human acute monocytic leukemia (THP-1) cells under inflammatory conditions induced by lipopolysaccharide (LPS). L. fermentum FS-10 potently downregulated the expression of TNF-α and nitric oxide and upregulated IL-10 levels, indicating an anti-inflammatory response. Safety assessment of the strain revealed the absence of genes for virulence factors, toxin production, and antibiotic resistance, potentiating application as a probiotic strain.\n\nIn vitro adhesion and anti-inflammatory properties of Limosilactobacillus fermentum FS-10 isolated from infant fecal sample.", "token_count": 383, "char_count": 1339, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:00.367504", "source": { "split": "train_shard_00000", "doc_id": 1354 }, "chunk_id": "train_shard_00000_1354_0", "global_id": 1495 }, { "text": "Kluyveromyces marxianus yeasts represent a valuable industry alternative due to their biotechnological potential to produce aromatic compounds. 2-phenylethanol and 2-phenylethylacetate are significant aromatic compounds widely used in food and cosmetics due to their pleasant odor. Natural obtention of these compounds increases their value, and because of this, bioprocesses such as de novo synthesis has become of great significance. However, the relationship between aromatic compound production and yeast's genetic diversity has yet to be studied. In the present study, the analysis of the genetic diversity in K. marxianus isolated from the natural fermentation of Agave duranguensis for Mezcal elaboration is presented. The results of strains in a haploid and diploid state added to the direct relationship between the mating type locus MAT with metabolic characteristics are studied. Growth rate, assimilate carbohydrates (glucose, lactose, and chicory inulin), and the production of aromatic compounds such as ethyl acetate, isoamyl acetate, isoamyl alcohol, 2-phenylethyl butyrate and phenylethyl propionate and the diversity in terms of the output of 2-phenylethanol and 2-phenylethylacetate by de novo synthesis were determinate, obtaining maximum concentrations of 51.30 and 60.39 mg/L by ITD0049 and ITD 0136 yeasts respectively.\n\nCharacterization of mating type on aroma production and metabolic properties wild Kluyveromyces marxianus yeasts.", "token_count": 393, "char_count": 1457, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8085, "entities": { "genes": [ "ITD0049" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:01.009176", "source": { "split": "train_shard_00000", "doc_id": 1355 }, "chunk_id": "train_shard_00000_1355_0", "global_id": 1496 }, { "text": "BMS-932481 was designed to modulate ɣ-secretase activity to produce shorter and less amyloidogenic peptides, potentially averting liabilities associated with complete enzymatic inhibition. Although it demonstrated the intended pharmacology in the clinic, BMS-932481 unexpectedly caused drug-induced liver injury (DILI) in a multiple ascending dose study characterized by dose- and exposure-dependence, delayed onset manifestation, and a high incidence of hepatocellular damage. Retrospective studies investigating the disposition and probable mechanisms of toxicity of BMS-932481 are presented here. These included a mass balance study in bile-duct-cannulated rats and a metabolite profiling study in human hepatocytes, which together demonstrated oxidative metabolism followed by biliary elimination as the primary means of disposition. Additionally, minimal protein covalent binding in hepatocytes and lack of bioactivation products excluded reactive metabolite formation as a probable toxicological mechanism. However, BMS-932481 and 3 major oxidative metabolites were found to inhibit the bile salt export pump (BSEP) and multidrug resistance protein 4 (MRP4) in vitro. Considering human plasma concentrations, the IC50 values against these efflux transporters were clinically meaningful, particularly in the high dose cohort. Active uptake into human hepatocytes in vitro suggested the potential for hepatic levels of BMS-932481 to be elevated further above plasma concentrations, enhancing DILI risk. Conversely, measures of mitochondrial functional decline in hepatocytes treated with BMS-932481 were minimal or modest, suggesting limited contributions to DILI. Collectively, these findings suggested that repeat administration of BMS-932481 likely resulted in high hepatic concentrations of BMS-932481 and its metabolites, which disrupted bile acid transport via BSEP and MRP4, elevating serum biomarkers of liver injury.", "token_count": 487, "char_count": 1929, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [ "MRP4", "IC50" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:01.654725", "source": { "split": "train_shard_00000", "doc_id": 1356 }, "chunk_id": "train_shard_00000_1356_0", "global_id": 1497 }, { "text": "Mechanistic investigation of liver injury induced by BMS-932481, an experimental ɣ-secretase modulator.", "token_count": 28, "char_count": 103, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:02.013581", "source": { "split": "train_shard_00000", "doc_id": 1356 }, "chunk_id": "train_shard_00000_1356_1", "global_id": 1498 }, { "text": "Non-alcoholic fatty liver disease (NAFLD), the most common chronic liver disease, had no approved pharmacological agents yet. Obeticholic acid (OCA), a novel bile acid derivative, was demonstrated to ameliorate NAFLD-related manifestations. Regarding the role of gut-liver axis in liver disease development, this study aimed to explore the potential role of gut microbiota in the treatment of OCA in NAFLD mice induced by the high-fat diet (HFD). Antibiotic-induced microbiome depletion (AIMD) and fecal microbiota transplantation (FMT) confirmed the critical role of gut microbiota in OCA treatment for NAFLD by effectively alleviating histopathological lesions and restoring liver function impaired by HFD. Metagenomic analysis indicated that OCA intervention in HFD mice remarkably increased the abundance of Akkermansia muciniphila, Bifidobacterium spp., Bacteroides spp., Alistipes spp., Lactobacillus spp., Streptococcus thermophilus, and Parasutterella excrementihominis. Targeted metabolomics analysis indicated that OCA could modulate host bile acids pool by reducing levels of serum hydrophobic cholic acid (CA) and chenodeoxycholic acid (CDCA), and increasing levels of serum-conjugated bile acids, such as taurodeoxycholic acid (TDCA) and tauroursodesoxycholic acid (TUDCA) in the HFD-fed mice. Strong correlations were observed between differentially abundant microbes and the shifted bile acids. Furthermore, bacteria enriched by OCA intervention exhibited much greater potential in encoding 7alpha-hydroxysteroid dehydrogenase (7α-HSDs) producing secondary bile acids rather than bile salt hydrolases (BSHs) mainly responsible for primary bile acid deconjugation. In conclusion, this study demonstrated that OCA intervention altered gut microbiota composition with specially enriched gut microbes modulating host bile acids, thus effectively alleviating NAFLD in the mice.", "token_count": 502, "char_count": 1887, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:02.665215", "source": { "split": "train_shard_00000", "doc_id": 1357 }, "chunk_id": "train_shard_00000_1357_0", "global_id": 1499 }, { "text": "Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism.", "token_count": 27, "char_count": 97, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:03.026517", "source": { "split": "train_shard_00000", "doc_id": 1357 }, "chunk_id": "train_shard_00000_1357_1", "global_id": 1500 }, { "text": "Tools that classify sequencing reads against a database of reference sequences require efficient index data-structures. The\n\nEfficient taxa identification using a pangenome index.", "token_count": 37, "char_count": 179, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:03.396792", "source": { "split": "train_shard_00000", "doc_id": 1358 }, "chunk_id": "train_shard_00000_1358_0", "global_id": 1501 }, { "text": "In this research, yak butter (YB) microcapsule with different YB addition was successfully prepared by using maltodextrin/whey protein isolate/sodium caseinate as main wall materials. The microstructures, microencapsulation efficiency and possible sacculation mechanism was then analyzed. The in vitro intestinal digested behavior of the microcapsules affected by bile salts was monitored and investigated in details. The results indicated that microcapsules were hollow spheres with entrapped YB located in the wall materials. Higher YB addition resulted in inhomogeneous larger particles with decreased membrane thickness. H-bonding interactions between protein and carbohydrate ensured the integrity of the capsule wall. The in vitro digestion results suggested that the concentration of bile salts had significant impacts on the digestion behavior of microcapsules. The present of bile salts was necessary for pancreatin hydrolysis of wall material. Hydrolysis of pancreatin, emulsification of bile salt and its positive effect for pancreatin hydrolysis all happened during the digestion and affected the digested behavior in the end. This research would provide valuable information for the bioavailability of microcapsule in human gastrointestinal systems.\n\nImpact of Yak Butter Addition on the Performance of Microcapsule: Physical Properties and Digested Behavior.", "token_count": 307, "char_count": 1372, "word_count": 186, "semantic_coherence": 1, "information_density": 0.586, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:03.963130", "source": { "split": "train_shard_00000", "doc_id": 1359 }, "chunk_id": "train_shard_00000_1359_0", "global_id": 1502 }, { "text": "Whole genome sequencing (WGS) was introduced into Swiss antimicrobial resistance monitoring in 2022 as an additional method to phenotypic antimicrobial susceptibility testing by broth microdilution to characterize presumptive third-generation cephalosporin-resistant (3GC-R) Escherichia coli. Caecal samples from Swiss slaughter calves and fattening pigs, as well as beef and pork meat from Swiss retail taken in 2021, were analyzed for the presence of 3GC-R E. coli according to European harmonized protocols. In 2021, 3GC-R E. coli was detected in 23,8 % of slaughter calves, 5,9 % of fattening pigs, and 0 % of meat. Comparative analysis of the antimicrobial resistance results obtained by phenotypic measurement and those obtained by the detection of corresponding underlying molecular mechanisms by WGS showed very high agreement (99 %). Resistance to third-generation cephalosporins (3GCs) was mainly associated with the presence of blaCTX-M-15 in E. coli isolates from calves and blaCTX-M-1 in E. coli isolates from pigs and mutations in the ampC-promoter (g.-42 C>T) in E. coli isolates from both animal species. Moreover, WGS data were used for phylogenetic analysis based on multi locus sequence types (MLST) and core genome MLST(cgMLST) revealing that 3GC-R E. coli isolated from Swiss slaughter calves and fattening pigs were genetically diverse. In this study, it was shown that using WGS alone to monitor antimicrobial resistance could detect trends in known molecular antimicrobial resistance mechanisms while also providing other valuable information about the isolates, such as genetic relatedness. However, only by combining phenotypic susceptibility testing and WGS early detection of previously unknown resistance mechanisms will be possible.", "token_count": 479, "char_count": 1762, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:04.608340", "source": { "split": "train_shard_00000", "doc_id": 1360 }, "chunk_id": "train_shard_00000_1360_0", "global_id": 1503 }, { "text": "Characterization of third-generation cephalosporin-resistant Escherichia coli from slaughter calves and fattening pigs: A pilot study for monitoring antimicrobial resistance by whole genome sequencing in Switzerland.", "token_count": 54, "char_count": 216, "word_count": 25, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:04.967993", "source": { "split": "train_shard_00000", "doc_id": 1360 }, "chunk_id": "train_shard_00000_1360_1", "global_id": 1504 }, { "text": "This work reports on the nanostructural changes taking place during the in vitro gastrointestinal digestion of polysaccharide-casein gel-like structures through the use of small angle X-ray scattering (SAXS). The results indicated that during the gastric phase, the hydrolysis of casein led to a swelling of the micellar structure, yielding peptide clusters. The presence of sulphated polysaccharides such as agar and κ-carrageenan was seen to limit the hydrolysis of casein during the gastric phase, hence decreasing the size of the formed clusters. After the intestinal phase, the produced peptidic fragments appeared to interact with the bile salts present in the digestion medium, yielding a mixture of bile salt lamellae/micelles and vesicular structures. However, in the presence of polysaccharides, which can interact with bile salts, the formation of vesicular structures was limited. Interestingly, the inclusion of casein within hybrid gel-like structures led to the formation of strong polysaccharide-protein interactions, especially in the case of κ-carrageenan. As a result, in some of the formulations, polysaccharide-peptide complexes were released towards the liquid medium, which formed larger vesicular structures. This was related to the greater protective effect of these particular gel-like structures. Furthermore, κ-carrageenan hindered the formation of bile salt lamellae/micelles. These results are of high relevance to understand the intestinal transport mechanism of the digestion products from protein-based ingredients and will allow a rational design of novel products with optimum nutritional and functional properties.\n\nNanostructural changes in Polysaccharide-Casein Gel-Like structures upon in vitro gastrointestinal digestion.", "token_count": 423, "char_count": 1761, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5394, "quality_score": 0.7697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:05.589645", "source": { "split": "train_shard_00000", "doc_id": 1361 }, "chunk_id": "train_shard_00000_1361_0", "global_id": 1505 }, { "text": "There is an increasing interest in the use of spore-forming Bacillus spp. as probiotic ingredients on the market. However, probiotics Bacillus species are insufficient, and more safe Bacillus species were required. In the study, traditional fermented foods and soil samples were collected from more than ten provinces in China, and 506 Bacillus were selected from 109 samples. Using the optimized procedure, we screened nine strains, which successfully passed the acid, alkali, bile salt, and trypsin resistance test. Drug sensitivity test results showed that three Bacillus out of the nine isolates exhibited antibiotic sensitivity to more than 29 antibiotics. The three strains sensitive to antibiotics were identified by 16S ribosomal RNA, recA, and gyrB gene analysis, two isolates (38,327 and 38,328) belong to the species Lysinibacillus capsici and one isolate (37,326) belong to Bacillus halotolerans. Moreover, the three strains were confirmed safe through animal experiments. Finally, L. capsici 38,327 and 38,328 showed protections in the Salmonella typhimurium infection mouse model, which slowed down weight loss, reduced bacterial load, and improved antioxidant capacity. Altogether, our data demonstrated that selected L. capsici strains can be used as novel probiotics for intestinal health.\n\nLysinibacillus capsici 38,328 isolated from agricultural soils as a promising probiotic candidate for intestinal health.", "token_count": 385, "char_count": 1428, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:06.204736", "source": { "split": "train_shard_00000", "doc_id": 1362 }, "chunk_id": "train_shard_00000_1362_0", "global_id": 1506 }, { "text": "Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshape the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we developed an approach, IGTminer, that maps the evolutionary trajectories of IGTs using collinearity and gene reannotation across multiple genome assemblies. We applied IGTminer to create a nuclear organellar gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops. The resulting NOGs were verified by experiments and sequencing data sets. Our analysis revealed that most NOGs were recently transferred and lineage specific and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat (Triticum aestivum) had a higher retention rate of NOGs than maize (Zea mays) and rice (Oryza sativa), and the retained NOGs were likely involved in photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during 2 rounds of polyploidization, contributing to the genetic diversity among modern wheat accessions. We implemented an interactive web server to facilitate the exploration of NOGs in Poaceae. In summary, this study provides resources and insights into the roles of IGTs in shaping interspecies and intraspecies genome variation and driving plant genome evolution.\n\nPangenome-based trajectories of intracellular gene transfers in Poaceae unveil high cumulation in Triticeae.", "token_count": 381, "char_count": 1587, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:06.784467", "source": { "split": "train_shard_00000", "doc_id": 1363 }, "chunk_id": "train_shard_00000_1363_0", "global_id": 1507 }, { "text": "Phycodnaviridae are large double-stranded DNA viruses, which facilitate studies of host-virus interactions and co-evolution due to their prominence in algal infection and their role in the life cycle of algal blooms. However, the genomic interpretation of these viruses is hampered by a lack of functional information, stemming from the surprising number of hypothetical genes of unknown function. It is also unclear how many of these genes are widely shared within the clade. Using one of the most extensively characterized genera, Coccolithovirus, as a case study, we combined pangenome analysis, multiple functional annotation tools, AlphaFold structural modeling, and literature analysis to compare the core and accessory pangenome and assess support for novel functional predictions. We determined that the Coccolithovirus pangenome shares 30% of its genes with all 14 strains, making up the core. Notably, 34% of its genes were found in at most three strains. Core genes were enriched in early expression based on a transcriptomic dataset of Coccolithovirus EhV-201 algal infection, were more likely to be similar to host proteins than the non-core set, and were more likely to be involved in vital functions such as replication, recombination, and repair. In addition, we generated and collated annotations for the EhV representative EhV-86 from 12 different annotation sources, building up information for 142 previously hypothetical and putative membrane proteins. AlphaFold was further able to predict structures for 204 EhV-86 proteins with a modelling accuracy of good-high. These functional clues, combined with generated AlphaFold structures, provide a foundational framework for the future characterization of this model genus (and other giant viruses) and a further look into the evolution of the Coccolithovirus proteome.\n\nFunctional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome.", "token_count": 457, "char_count": 1926, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:07.428234", "source": { "split": "train_shard_00000", "doc_id": 1364 }, "chunk_id": "train_shard_00000_1364_0", "global_id": 1508 }, { "text": "Liver cancer is a public disease burden with an increasing incidence rate globally. Bile acid and bile salt's metabolic pathways participate in liver tumorigenesis and regulate the tumor microenvironment. However, there still remains a lack of systematic analysis of the genes related to bile acid and bile salt metabolic pathways in hepatocellular carcinoma (HCC). The mRNA expression data and clinical follow-up information of patients with HCC were obtained from public databases, including The Cancer Genome Atlas, Hepatocellular Carcinoma Database, Gene Expression Omnibus, and IMvigor210. The bile acid and bile salt metabolism-related genes were extracted from Molecular Signatures Database. Univariate Cox and logistic least absolute shrinkage and selection operator regression analyses were conducted to establish the risk model. Single sample gene set enrichment analysis, Estimation of STromal and Immune cells in MAlignant Tumour tissues using Expression data, and Tumor Immune Dysfunction and Exclusion were adopted to analyze immune status. The efficiency of the risk model was tested using a decision tree and a nomogram. We determined two molecular subtypes based on bile acid and bile salt metabolism-related genes, with the prognosis of the S1 subtype being markedly superior to the S2 subtype. Next, we established a risk model based on the differentially expressed genes between the two molecular subtypes. The high-risk and low-risk groups showed significant differences in the biological pathways, immune score, immunotherapy response, and drug susceptibility. Our results demonstrated the good predictive performance of the risk model in immunotherapy datasets and established that it could be an essential factor affecting the prognosis of HCC. In conclusion, we identified two molecular subtypes based on bile acid and bile salt metabolism-related genes. The risk model established in our study could effectively predict the prognosis of patients with HCC and their immunotherapeutic response, which may contribute to targeted immunotherapy in HCC.\n\nEstablishment and Validation of a Novel Risk Score for Hepatocellular Carcinoma Based on Bile Acid and Bile Salt Metabolism-Related Genes.", "token_count": 508, "char_count": 2213, "word_count": 319, "semantic_coherence": 1, "information_density": 0.5361, "quality_score": 0.768, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:08.083494", "source": { "split": "train_shard_00000", "doc_id": 1365 }, "chunk_id": "train_shard_00000_1365_0", "global_id": 1509 }, { "text": "Streptococcus mutans plays a major role in biofilm formation and pathogenic bacterial adhesion. Here we investigated the abilities of our isolates from diverse conventional sources to characterize the beneficial bacteria for inhibition of S. mutans. Enterobacter cloacae PS-74, a beneficial bacteria isolated from yoghurt, is gram negative, rod shaped, and resistant to acid, bile salt, and amylase. PS-74 cell-free supernatants (CFS) demonstrated highest zone of inhibition of 29 ± 1.7 mm. Further, the minimum inhibitory concentration (MIC) value of CFS PS-74 was recorded to be 10 μL and its minimum bactericidal concentration (MBC) value was found to be 15μL which led to 99.9% log reduction of S. mutans. Moreover, the biofilm formation was reduced by 84.91% at MIC15 of CFS PS-74 which alleviate the dental caries formation by S. mutans. This is the first report on E. cloacae PS-74, which was studied for its probiotic properties to inhibit S. mutans MTCC-890 due to the production of organic acids and employed in oral treatment.\n\nAlleviation of dental caries by use of isolated potential probiotic and its characterization.", "token_count": 313, "char_count": 1132, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6307, "quality_score": 0.8153, "entities": { "genes": [ "MIC15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:08.651231", "source": { "split": "train_shard_00000", "doc_id": 1366 }, "chunk_id": "train_shard_00000_1366_0", "global_id": 1510 }, { "text": "Chitooligosaccharides have been suggested as cholesterol reducing ingredients mostly due to their ability to sequestrate bile salts. The nature of the chitooligosaccharides-bile salts binding is usually linked with the ionic interaction. However, at physiological intestinal pH range (6.4 to 7.4) and considering chitooligosaccharides pKa, they should be mostly uncharged. This highlights that other type of interaction might be of relevance. In this work, aqueous solutions of chitooligosaccharides with an average degree of polymerization of 10 and 90 % deacetylated, were characterized regarding their effect on bile salt sequestration and cholesterol accessibility. Chitooligosaccharides were shown to bind bile salts to a similar extent as the cationic resin colestipol, both decreasing cholesterol accessibility as measured by NMR at pH 7.4. A decrease in the ionic strength leads to an increase in the binding capacity of chitooligosaccharides, in agreement with the involvement of ionic interactions. However, when the pH is decreased to 6.4, the increase in charge of chitooligosaccharides is not followed by a significant increase in bile salt sequestration. This corroborates the involvement of non-ionic interactions, which was further supported by NMR chemical shift analysis and by the negative electrophoretic mobility attained for the bile salt-chitooligosaccharide aggregates at high bile salt concentrations. These results highlight that chitooligosaccharides non-ionic character is a relevant structural feature to aid in the development of hypocholesterolemic ingredients.\n\nContribution of non-ionic interactions on bile salt sequestration by chitooligosaccharides: Potential hypocholesterolemic activity.", "token_count": 431, "char_count": 1725, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5923, "quality_score": 0.7961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:09.272883", "source": { "split": "train_shard_00000", "doc_id": 1367 }, "chunk_id": "train_shard_00000_1367_0", "global_id": 1511 }, { "text": "Grain legumes play a crucial role in human nutrition and as a staple crop for low-income farmers in developing and underdeveloped nations, contributing to overall food security and agroecosystem services. Viral diseases are major biotic stresses that severely challenge global grain legume production. In this review, we discuss how exploring naturally resistant grain legume genotypes within germplasm, landraces, and crop wild relatives could be used as promising, economically viable, and eco-environmentally friendly solution to reduce yield losses. Studies based on Mendelian and classical genetics have enhanced our understanding of key genetic determinants that govern resistance to various viral diseases in grain legumes. Recent advances in molecular marker technology and genomic resources have enabled us to identify genomic regions controlling viral disease resistance in various grain legumes using techniques such as QTL mapping, genome-wide association studies, whole-genome resequencing, pangenome and 'omics' approaches. These comprehensive genomic resources have expedited the adoption of genomics-assisted breeding for developing virus-resistant grain legumes. Concurrently, progress in functional genomics, especially transcriptomics, has helped unravel underlying candidate gene(s) and their roles in viral disease resistance in legumes. This review also examines the progress in genetic engineering-based strategies, including RNA interference, and the potential of synthetic biology techniques, such as synthetic promoters and synthetic transcription factors, for creating viral-resistant grain legumes. It also elaborates on the prospects and limitations of cutting-edge breeding technologies and emerging biotechnological tools (e.g., genomic selection, rapid generation advances, and CRISPR/Cas9-based genome editing tool) in developing virus-disease-resistant grain legumes to ensure global food security.\n\nMajor viral diseases in grain legumes: designing disease resistant legumes from plant breeding and OMICS integration.", "token_count": 424, "char_count": 2051, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6566, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:09.895195", "source": { "split": "train_shard_00000", "doc_id": 1368 }, "chunk_id": "train_shard_00000_1368_0", "global_id": 1512 }, { "text": "Horizontal gene transfer (HGT) and the resulting patterns of gene gain and loss are a fundamental part of bacterial evolution. Investigating these patterns can help us to understand the role of selection in the evolution of bacterial pangenomes and how bacteria adapt to a new niche. Predicting the presence or absence of genes can be a highly error-prone process that can confound efforts to understand the dynamics of horizontal gene transfer. This review discusses both the challenges in accurately constructing a pangenome and the potential consequences errors can have on downstream analyses. We hope that by summarizing these issues researchers will be able to avoid potential pitfalls, leading to improved bacterial pangenome analyses.\n\nChallenges in prokaryote pangenomics.", "token_count": 164, "char_count": 781, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6581, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:10.341954", "source": { "split": "train_shard_00000", "doc_id": 1369 }, "chunk_id": "train_shard_00000_1369_0", "global_id": 1513 }, { "text": "Streptococci are a predominant genera of the human milk microbiome. Among different lactic acid bacteria (LAB) a few Streptococcal strains are also considered as probiotics. Probiotic bacteria are reported to modulate immunity when consumed in adequate amount and bacterial hydrophobicity can be considered as a preliminary experiment for the adhesive capability of probiotic bacteria to the epithelial cells. The present study aimed to investigate the probiotic, hydrophobic and immune modulation property of Streptococcus lactarius MB622 and Streptococcus salivarius MB620, isolated from human milk. S. lactarius MB622 and S. salivarius MB620 displayed higher hydrophobicity (78 % and 59 % respectively) in addition to intrinsic probiotic properties such as gram positive classification, catalase negative activity, resistance to artificially stimulated gastric juice and gastrointestinal bile salt concentration. In conclusion Streptococcus lactarius MB622 and Streptococcus salivarius MB620 isolated from human milk when administered in sufficient amount and for certain duration could be used to reduce inflammation inside the colon by reducing the production of inflammatory booster (IL-8) in diseased state.\n\nStreptococcus lactarius MB622 and Streptococcus salivarius MB620 isolated from human milk reduce chemokine IL-8 production in response to TNF-α in Caco-2 cell line, an exploratory study.", "token_count": 359, "char_count": 1402, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6146, "quality_score": 0.8073, "entities": { "genes": [ "MB620", "MB622" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:10.923541", "source": { "split": "train_shard_00000", "doc_id": 1370 }, "chunk_id": "train_shard_00000_1370_0", "global_id": 1514 }, { "text": "Mycobacterium ulcerans, an environmental opportunistic pathogen, causes necrotic cutaneous and subcutaneous lesions, named Buruli ulcers, in tropical countries. PCR-derived tests used to detect M. ulcerans in environmental and clinical samples do not allow one-shot detection, identification, and typing of M. ulcerans among closely related Mycobacterium marinum complex mycobacteria. We established a 385-member M. marinum/M. ulcerans complex whole-genome sequence database by assembling and annotating 341 M. marinum/M. ulcerans complex genomes and added 44 M. marinum/M. ulcerans complex whole-genome sequences already deposited in the NCBI database. Pangenome, core genome, and single-nucleotide polymorphism (SNP) distance-based comparisons sorted the 385 strains into 10 M. ulcerans taxa and 13 M. marinum taxa, correlating with the geographic origin of strains. Aligning conserved genes identified one", "token_count": 258, "char_count": 908, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7395, "quality_score": 0.8697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:11.495664", "source": { "split": "train_shard_00000", "doc_id": 1371 }, "chunk_id": "train_shard_00000_1371_0", "global_id": 1515 }, { "text": "The present study aimed to evaluate the probiotic potential, α-amylase and α-glucosidase inhibitory effects, and β-galactosidase production of 19 non haemolytic lactic acid bacteria and bifidobacteria previously identified and isolated from honey bee gastrointestinal tract (BGIT) of Apis mellifera intermissa, honey, propolis and bee bread. The isolates were screened according to their high resistance to lysozyme and potent antibacterial activity. Our results indicated that among the 19 isolates, Limosilactobacillus fermentum BGIT\n\nAlpha-amylase and alphaglucosidase inhibitory properties, beta-galactosidase activity, and probiotic potential of lactic acid bacteria and bifidobacteria from Apis mellifera intermissa and its products.", "token_count": 211, "char_count": 739, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7128, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:11.974363", "source": { "split": "train_shard_00000", "doc_id": 1372 }, "chunk_id": "train_shard_00000_1372_0", "global_id": 1516 }, { "text": "Tuberculosis (TB) remains a major global health burden. Antitubercular drugs (ATDs) such as isoniazid (INH), rifampicin (RIF), pyrazinamide (PZA), and ethambutol are used as first-line therapy in TB patients. Drug-induced liver injury is one of the common side effects that leads to the discontinuation of ATDs in TB patients. Therefore, this review discusses the molecular pathogenesis of ATDs induced liver injury. The biotransformation of INH, RIF, and PZA in the liver liberates several reactive intermediates, leading to peroxidation of the hepatocellular membrane and oxidative stress. INH + RIF administration decreased the expression of bile acid transporters such as the bile salt export pump and multidrug resistance-associated protein 2 and induced liver injury by sirtuin 1 and farnesoid X receptor pathway. INH inhibits the nuclear translocation of Nrf2 by interfering with its nuclear importer, karyopherin β1, thereby inducing apoptosis. INF + RIF treatments alter Bcl-2 and Bax homeostasis, mitochondrial membrane potential, and cytochrome c release, thereby triggering apoptosis. RIF administration enhances the expression of genes involved in fatty acid synthesis and hepatocyte fatty acid uptake (CD36). RIF induces the expression of peroxisome proliferator-activated receptor -γ and its downstream proteins and perilipin-2 by activating the pregnane X receptor in the liver to increase fatty infiltration into the liver. ATDs administration induces oxidative stress, inflammation, apoptosis, cholestasis, and lipid accumulation in the liver. However, ATDs toxic potentials are not elaborately studied at the molecular level in clinical samples. Therefore, future studies are warranted to explore ATDs induced liver injuries at the molecular level in clinical samples whenever possible.\n\nAntitubercular drugs induced liver injury: an updated insight into molecular mechanisms.", "token_count": 504, "char_count": 1895, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6128, "quality_score": 0.8064, "entities": { "genes": [ "CD36" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:12.681013", "source": { "split": "train_shard_00000", "doc_id": 1373 }, "chunk_id": "train_shard_00000_1373_0", "global_id": 1517 }, { "text": "Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown.\n\nGraph construction method impacts variation representation and analyses in a bovine super-pangenome.", "token_count": 60, "char_count": 304, "word_count": 39, "semantic_coherence": 1, "information_density": 0.9487, "quality_score": 0.9744, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:13.071400", "source": { "split": "train_shard_00000", "doc_id": 1374 }, "chunk_id": "train_shard_00000_1374_0", "global_id": 1518 }, { "text": "Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance (AMR) genes. Despite its ongoing threat to human health, surveillance of AMR in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention strategies. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids).\n\nThe role of plasmids in carbapenem resistant E. coli in Alameda County, California.", "token_count": 292, "char_count": 1247, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6994, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:13.639313", "source": { "split": "train_shard_00000", "doc_id": 1375 }, "chunk_id": "train_shard_00000_1375_0", "global_id": 1519 }, { "text": "Combining reference genomes into a pangenome graph improves accuracy and reduces bias.", "token_count": 18, "char_count": 86, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:14.000643", "source": { "split": "train_shard_00000", "doc_id": 1376 }, "chunk_id": "train_shard_00000_1376_0", "global_id": 1520 }, { "text": "Probiotics sourced from fish intestinal microbiota have a merit over other bacterial sources due to colonization ability and effective time. This study aimed to evaluate the bacilli isolated from the Rhynchocypris lagowskii intestines and their validity as a probiotic. Three isolates were selected (LSG 2-5, LSG 3-7, and LSG 3-8) and defined by morphological and 16S rRNA analysis as Bacillus velezensis, Bacillus aryabhattai, and Bacillus mojavensis, respectively. Results showed the strain tolerant abilities to gastrointestinal fluid, bile salt, pH, and temperature expotures. Additionally, all bacterial strains showed anti-pathogenic activity against at least four strains out of six tested pathogen strains (Staphylococcus aureus, Aeromonas hydrophila, Escherichia coli, Aeromonas veronii, Edwardsiella, and Aeromonas sobria). The bacterial strains also showed a high percentage of co-aggregation activity, more than 70%, with Aer. hydrophile, Staph. epidermidis, and Klebsiella aerogenes. At the same time, the results of competition, rejection, and substitution activity with Aer. hydrophila and Aer. veronii indicated the ability of the isolated strains to reduce the adhesion of pathogens to mucin. All strains showed safety properties, non-hemolytic, and sensitivity characteristics for most of tested antibiotics. In vivo test after injecting these strains into fish at various concentrations showed no side effects in the internal or external organs of fish compared to controls, proving that this is safe for these fish. Furthermore, the three strains produced lipase, amylase, and protease enzymes. The strains also showed bile salt hydrolase activity and biofilm formation, allowing them to tolerate stressful conditions. Conclusion: Based on these strains characteristics and features, they could be considered a promising candidate probiotic and can be used as an anti-pathogenic, especially in aquaculture.", "token_count": 501, "char_count": 1926, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6654, "quality_score": 0.8327, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:14.646750", "source": { "split": "train_shard_00000", "doc_id": 1377 }, "chunk_id": "train_shard_00000_1377_0", "global_id": 1521 }, { "text": "Characterization of Bacillus spp. isolated from the intestines of Rhynchocypris lagowskii as a potential probiotic and their effects on fish pathogens.", "token_count": 42, "char_count": 151, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:15.007345", "source": { "split": "train_shard_00000", "doc_id": 1377 }, "chunk_id": "train_shard_00000_1377_1", "global_id": 1522 }, { "text": "Bacillus velezensis FS26 is a bacterium from the genus Bacillus that has been proven as a potential probiotic in aquaculture with a good antagonistic effect on Aeromonas spp. and Vibrio spp. Whole-genome sequencing (WGS) allows a comprehensive and in-depth analysis at the molecular level, and it is becoming an increasingly significant technique in aquaculture research. Although numerous probiotic genomes have been sequenced and investigated recently, there are minimal data on in silico analysis of B. velezensis as a probiotic bacterium isolated from aquaculture sources. Thus, this study aims to analyse the general genome characteristics and probiotic markers from the B. velezensis FS26 genome with secondary metabolites predicted against aquaculture pathogens. The B. velezensis FS26 genome (GenBank Accession: JAOPEO000000000) assembly proved to be of high quality, with eight contigs containing 3,926,371 bp and an average G + C content of 46.5%. According to antiSMASH analysis, five clusters of secondary metabolites from the B. velezensis FS26 genome showed 100% similarity. These clusters include Cluster 2 (bacilysin), Cluster 6 (bacillibactin), Cluster 7 (fengycin), Cluster 8 (bacillaene), and Cluster 9 (macrolactin H), which signify promising antibacterial, antifungal, and anticyanobacterial agents against pathogens in aquaculture. The probiotic markers of B. velezensis FS26 genome for adhesion capability in the hosts' intestine, as well as the acid and bile salt-tolerant genes, were also detected through the Prokaryotic Genome Annotation System (Prokka) annotation pipeline. These results are in agreement with our previous in vitro data, suggesting that the in silico investigation facilitates establishing B. velezensis FS26 as a beneficial probiotic for use in aquaculture.", "token_count": 500, "char_count": 1803, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6094, "quality_score": 0.8047, "entities": { "genes": [ "FS26", "JAOPEO000000000" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:15.651103", "source": { "split": "train_shard_00000", "doc_id": 1378 }, "chunk_id": "train_shard_00000_1378_0", "global_id": 1523 }, { "text": "Mining the genome of Bacillus velezensis FS26 for probiotic markers and secondary metabolites with antimicrobial properties against aquaculture pathogens.", "token_count": 43, "char_count": 154, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "FS26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:16.011219", "source": { "split": "train_shard_00000", "doc_id": 1378 }, "chunk_id": "train_shard_00000_1378_1", "global_id": 1524 }, { "text": "Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a novel sampled document array. By incorporating minimizers, SPUMONI 2's index is 65 times smaller than minimap2's for a mock community pangenome. SPUMONI 2 achieves a speed improvement of 3-fold compared to SPUMONI and 15-fold compared to minimap2. We show SPUMONI 2 achieves an advantageous mix of accuracy and efficiency in practical scenarios such as adaptive sampling, contamination detection and multi-class metagenomics classification.\n\nSPUMONI 2: improved classification using a pangenome index of minimizer digests.", "token_count": 188, "char_count": 758, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7358, "quality_score": 0.8679, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:16.455243", "source": { "split": "train_shard_00000", "doc_id": 1379 }, "chunk_id": "train_shard_00000_1379_0", "global_id": 1525 }, { "text": "Brucella abortus and Brucella melitensis are the primary etiological agents of brucellosis in large and small ruminants, respectively. There are limited comparative genomic studies involving Brucella strains that explore the relatedness among both species. In this study, we involved strains (n=44) representing standard, vaccine and Indian field origin for pangenome, single nucleotide polymorphism (SNP) and phylogenetic analysis. Both species shared a common gene pool representing 2884 genes out of a total 3244 genes. SNP-based phylogenetic analysis indicated higher SNP diversity among B. melitensis (3824) strains in comparison to B. abortus (540) strains, and a clear demarcation was identified between standard/vaccine and field strains. The analysis for virulence genes revealed that virB3, virB7, ricA, virB5, ipx5, wbkC, wbkB, and acpXL genes were highly conserved in most of the Brucella strains. Interestingly, virB10 gene was found to have high variability among the B. abortus strains. The cgMLST analysis revealed distinct sequence types for the standard/vaccine and field strains. B. abortus strains from north-eastern India fall within similar sequence type differing from other strains. In conclusion, the analysis revealed a highly shared core genome among two Brucella species. SNP analysis revealed B. melitensis strains exhibit high diversity as compared to B. abortus strains. Strains with absence or high polymorphism of virulence genes can be exploited for the development of novel vaccine candidates effective against both B. abortus and B. melitensis.\n\nComparative genomics of Brucella abortus and Brucella melitensis unravels the gene sharing, virulence factors and SNP diversity among the standard, vaccine and field strains.", "token_count": 446, "char_count": 1756, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5378, "quality_score": 0.7689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:17.085609", "source": { "split": "train_shard_00000", "doc_id": 1380 }, "chunk_id": "train_shard_00000_1380_0", "global_id": 1526 }, { "text": "Carbapenemase-producing bacteria (CPB) such as Klebsiella pneumoniae and Escherichia coli are causing hospital outbreaks worldwide. An important transfer route into the aquatic environment is the urban water cycle. We aimed to determine the presence of CPB in hospital wastewater, wastewater treatment plants (WWTPs) and surface waters in a German metropolitan area and to characterise these bacteria by whole-genome comparisons. During two periods in 2020, 366 samples were collected and cultivated on chromogenic screening media. Bacterial colonies were selected for species identification and PCR-based carbapenemase gene screening. Genomes of all detected CPB were sequenced and analysed for resistance gene content, followed by multilocus sequence typing (MLST) and core genome MLST (cgMLST) for K. pneumoniae and E. coli isolates. Carbapenemase genes were detected in 243 isolates, most of which belonged to genera/species Citrobacter spp. (n = 70), Klebsiella spp. (n = 57), Enterobacter spp. (n = 52) and E. coli (n = 42). Genes encoding KPC-2 carbapenemase were detected in 124 of 243 isolates. K. pneumoniae produced mainly KPC-2 and OXA-232 whereas E. coli harboured various enzymes (KPC-2, VIM-1, OXA-48, NDM-5, KPC-2 + OXA-232, GES-5, GES-5 + VIM-1, IMP-8 + OXA-48). Eight and twelve sequence types (STs) were identified for K. pneumoniae and E. coli, respectively, forming different clusters. The detection of numerous CPB species in hospital wastewater, WWTPs and river water is of concern. Genome data highlight a hospital-specific presence of distinct carbapenemase-producing K. pneumoniae and E. coli strains belonging to \"global epidemic clones\" in wastewater samples representing local epidemiology. The various detected CPB species including E", "token_count": 527, "char_count": 1764, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6172, "quality_score": 0.8086, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:12:17.739246", "source": { "split": "train_shard_00000", "doc_id": 1381 }, "chunk_id": "train_shard_00000_1381_0", "global_id": 1527 }, { "text": "coli ST635, which is not known to cause human infections, could serve as reservoirs/vectors for the spread of carbapenemase genes in the environment. Therefore, effective pretreatment of hospital wastewater prior to discharge into the municipal wastewater system may be required, although swimming lakes do not appear to be a relevant risk factor for CPB ingestion and infection.\n\nCarbapenemase-producing Gram-negative bacteria in hospital wastewater, wastewater treatment plants and surface waters in a metropolitan area in Germany, 2020.", "token_count": 126, "char_count": 539, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [ "ST635" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:18.126732", "source": { "split": "train_shard_00000", "doc_id": 1381 }, "chunk_id": "train_shard_00000_1381_1", "global_id": 1528 }, { "text": "Extracellular protein production is primarily preferred to facilitate the downstream processes in recombinant protein production. Secretion of recombinant proteins is mediated by the processing of signal peptides in their N-terminal portion by the secretory mechanism of host expression systems. These molecular elements involved in secretion are functionally interchangeable between different species and secretion sequence screening is one of the widely used approaches to improve extracellular protein production. In this study, α-mating and protein internal repeats (PIR) secretion sequences isolated from different yeasts (Kluyveromyces lactis, Kluyveromyces marxianus and Hansenula polymorpha) were tested in Pichia pastoris for the production of two different proteins (α-amylase and xylanase) and compared with the well-known secretory signals, S. cerevisiae α-mating factor (Sc-MF) and P. pastoris protein internal repeats PIR (PpPIR). The results obtained showed the potential of signal sequences tested. Among the tested peptides, the highest yields were achieved with H. polymorpha protein internal repeats (HpPIR) and K. lactis α-mating factor (Kl-MF) for xylanase and K. marxianus protein internal repeats (KmPIR) and K. lactis α-mating factor (Kl-MF) for amylase. In further studies, these sequences can be evaluated as alternatives in the production of different proteins in P. pastoris and in the production of recombinant proteins in different expression systems.\n\nAlternative secretory signal sequences for recombinant protein production in Pichia pastoris.", "token_count": 393, "char_count": 1576, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5187, "quality_score": 0.7593, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:18.741418", "source": { "split": "train_shard_00000", "doc_id": 1382 }, "chunk_id": "train_shard_00000_1382_0", "global_id": 1529 }, { "text": "Group B Streptococcus (GBS) can cause many serious infections and result in severe symptoms depending on the infected organs. To survive and initiate infection from the gastrointestinal tract, GBS must resist physiochemical factors, such as bile salts, a potent antibacterial compound in the intestine. We found that GBS isolated from diverse sources all possess the capability to defend bile salts and permit survival. By constructing the GBS A909 transposon mutant library (A909\n\nCsbD, a Novel Group B Streptococcal Stress Response Factor That Contributes to Bacterial Resistance against Environmental Bile Salts.", "token_count": 155, "char_count": 615, "word_count": 90, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:19.179335", "source": { "split": "train_shard_00000", "doc_id": 1383 }, "chunk_id": "train_shard_00000_1383_0", "global_id": 1530 }, { "text": "To investigate an outbreak of vancomycin-resistant Enterococcus faecium (VREfm) sequence type 78 (ST78) in a large tertiary Australian hospital. A collection of 63 VREfm ST78 isolates, identified during a routine genomic surveillance program, were subjected to genomic epidemiological analysis based on whole-genome sequencing (WGS) data. The population structure was reconstructed using phylogenetic analysis, and a collection of publicly available VREfm ST78 genomes were used to provide global context. Core genome single nucleotide polymorphism (SNP) distances and available clinical metadata were used to characterize outbreak clusters and reconstruct transmission events.\n\nUsing Genomics To Investigate an Outbreak of Vancomycin-Resistant Enterococcus faecium ST78 at a Large Tertiary Hospital in Queensland.", "token_count": 202, "char_count": 814, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6916, "quality_score": 0.8458, "entities": { "genes": [ "ST78" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:19.633504", "source": { "split": "train_shard_00000", "doc_id": 1384 }, "chunk_id": "train_shard_00000_1384_0", "global_id": 1531 }, { "text": "Post-transplantation evolution of progressive familial intrahepatic cholestasis type 2 patients can be complicated by antibody-induced bile salt export pump deficiency (AIBD). There is no consensus on its management. We describe a patient who presented two episodes, 9 years apart. The first episode was refractory to plasmapheresis and intravenous immunoglobulin (IVIG) started 2 months after AIBD onset, leading to graft loss. The second episode responded to plasmapheresis, IVIG and rituximab initiated less than 2 weeks after the beginning of symptoms, allowing for long-term recovery. This case suggests that intensive treatment with minimum delay after symptoms onset could sponsor a better evolution.\n\nIterative antibody-induced bile salt export pump deficiency after successive liver transplantations successfully treated with plasmapheresis and rituximab.", "token_count": 205, "char_count": 864, "word_count": 117, "semantic_coherence": 1, "information_density": 0.812, "quality_score": 0.906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:20.097268", "source": { "split": "train_shard_00000", "doc_id": 1385 }, "chunk_id": "train_shard_00000_1385_0", "global_id": 1532 }, { "text": "Intrahepatic cholestasis lacks effective therapeutic drugs. The gut microbiota-associated bile salt hydrolases (BSH) may be a potential therapeutic target. In this study, oral administration of gentamicin (GEN) decreased the serum and hepatic levels of total bile acid in 17α-ethynylestradiol (EE)-induced cholestatic male rats, significantly improved the serum levels of hepatic biomarkers and reversed the histopathological changes in the liver. In healthy male rats, the serum and hepatic levels of total bile acid were also decreased by GEN, the ratio of primary to secondary bile acids, and conjugated to unconjugated bile acids was significantly increased, and the urinary excretion of total bile acid was elevated. 16S rDNA sequencing of the ileal contents revealed that GEN treatment substantially reduced the abundance of Lactobacillus and Bacteroides both of which expressed BSH. Consistently, BSH activity analysis by the generation of d5-chenodeoxycholic acid from d5-taurochenodeoxycholic acid in situ showed BSH was significantly inhibited in the ileal contents of rats treated with GEN. This finding led to an increased proportion of hydrophilic conjugated bile acids and facilitated the urinary excretion of total bile acids, thereby decreasing serum and hepatic total bile acids and reversing liver injury related to cholestasis. Our results provide important evidence that BSH can be a potential drug target for treating cholestasis.\n\nGentamicin alleviates cholestatic liver injury by decreasing gut microbiota-associated bile salt hydrolase activity in rats.", "token_count": 412, "char_count": 1577, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5491, "quality_score": 0.7746, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:20.717062", "source": { "split": "train_shard_00000", "doc_id": 1386 }, "chunk_id": "train_shard_00000_1386_0", "global_id": 1533 }, { "text": "In this study, based on the OneKP database and through comparative genetic analysis, we found that HMT and HDM may originate from Chromista and are highly conserved in green plants, and that during the evolution from algae to land plants, histone methylation modifications gradually became complex and diverse, which is more conducive to the adaptation of plants to complex and variable environments. We also characterized the number of members, genetic similarity, and phylogeny of HMT and HDM families in barley using the barley pangenome and the Tibetan Lasa Goumang genome. The results showed that HMT and HDM were highly conserved in the domestication of barley, but there were some differences in the Lasa Goumang SDG subfamily. Expression analysis showed that\n\nMolecular Evolution of Histone Methylation Modification Families in the Plant Kingdom and Their Genome-Wide Analysis in Barley.", "token_count": 209, "char_count": 895, "word_count": 137, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:21.181685", "source": { "split": "train_shard_00000", "doc_id": 1387 }, "chunk_id": "train_shard_00000_1387_0", "global_id": 1534 }, { "text": "Poorly water-soluble weak base molecules such as cinnarizine often exhibit pH-dependent solubility within the gastrointestinal tract. This means that their solubility can be influenced by the pH of the surrounding environment, and this can affect their oral absorption. The differential pH solubility between the fasted-state stomach and intestine is an important consideration when studying the oral absorption of cinnarizine. Cinnarizine has moderate permeability and is known to exhibit supersaturation and precipitation in fasted-state simulated intestinal fluid (FaSSIF), which can significantly impact its oral absorption. The present work is aimed at studying the precipitation behavior of cinnarizine in FaSSIF using biorelevant in vitro tools and GastroPlus\n\nA Combined In-Vitro and GastroPlus® Modeling to Study the Effect of Intestinal Precipitation on Cinnarizine Plasma Profile in a Fasted State.", "token_count": 219, "char_count": 909, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:21.646652", "source": { "split": "train_shard_00000", "doc_id": 1388 }, "chunk_id": "train_shard_00000_1388_0", "global_id": 1535 }, { "text": "A pangenome represents many diverse genome sequences of the same species. In order to cope with small variations as well as structural variations, recent research focused on the development of graph-based models of pangenomes. Mapping is the process of finding the original location of a DNA read in a reference sequence, typically a genome. Using a pangenome instead of a (linear) reference genome can, e.g. reduce mapping bias, the tendency to incorrectly map sequences that differ from the reference genome. Mapping reads to a graph, however, is more complex and needs more resources than mapping to a reference genome. Reducing the complexity of the graph by encoding simple variations like SNPs in a simple way can accelerate read mapping and reduce the memory requirements at the same time.\n\nEfficient short read mapping to a pangenome that is represented by a graph of ED strings.", "token_count": 188, "char_count": 887, "word_count": 144, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:22.100683", "source": { "split": "train_shard_00000", "doc_id": 1389 }, "chunk_id": "train_shard_00000_1389_0", "global_id": 1536 }, { "text": "Cetobacterium somerae is a commensal bacterium for many fish species. However, research on C. somerae has been limited so far, and its function and beneficial potential require to be further investigated. The objective of this study was to evaluate the probiotic properties of C. somerae CPU-CS01 isolated from the intestinal contents of crucian carp (Carassius auratus). Hemolytic activity, antibiotic susceptibility, acid tolerance, bile salt tolerance, free radical scavenging, and enzyme production properties were tested for in vitro. Caenorhabditis elegans and zebrafish (Danio rerio) model were used to evaluate the antioxidant and anti-infective effects of C. somerae CPU-CS01 in vivo. Our results showed that C. somerae CPU-CS01 had no hemolytic activity, it produced cellulase, amylase, and survived at low pH (2.0-3.0) and in the presence of bile salts. The cell-free culture supernatant (CFCS) of C. somerae CPU-CS01 possessed DPPH radical, hydroxyl radical, and superoxide anion scavenging activity. C. elegans fed with C. somerae CPU-CS01 were more resistant to hydrogen peroxide-induced oxidative stress and Aeromonas hydrophila infection. In addition, zebrafish-fed diets containing C. somerae CPU-CS01 showed improved survival after A. hydrophila infection. Based on these results, the positive probiotic properties of C. somerae CPU-CS01 isolated from the intestinal contents of crucian carp make it a potential candidate for probiotic.\n\nCharacterization of Cetobacterium somerae CPU-CS01 isolated from the intestine of healthy crucian carp (Carassius auratus) as potential probiotics against Aeromonas hydrophila infection.", "token_count": 462, "char_count": 1642, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5983, "quality_score": 0.7991, "entities": { "genes": [ "CS01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:22.738217", "source": { "split": "train_shard_00000", "doc_id": 1390 }, "chunk_id": "train_shard_00000_1390_0", "global_id": 1537 }, { "text": "Given their role in lipid digestion, feed supplementation with bile salts could be an economic and sustainable solution to alterations in adiposity and intestinal inflammation generated by some strategies currently used in aquaculture. An important part of the metabolism of bile salts takes place in the intestine, where the microbiota transforms them into more toxic forms. Consequently, we aimed to evaluate the gut immune response and microbial populations in gilthead seabream (\n\nModulation of gut microbiota and intestinal immune response in gilthead seabream (", "token_count": 132, "char_count": 567, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7024, "quality_score": 0.8512, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:23.208916", "source": { "split": "train_shard_00000", "doc_id": 1391 }, "chunk_id": "train_shard_00000_1391_0", "global_id": 1538 }, { "text": "Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals\n\nA draft human pangenome reference.", "token_count": 60, "char_count": 240, "word_count": 34, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:23.598533", "source": { "split": "train_shard_00000", "doc_id": 1392 }, "chunk_id": "train_shard_00000_1392_0", "global_id": 1539 }, { "text": "Human pangenome supports analysis of complex genomic regions.", "token_count": 12, "char_count": 61, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:23.964700", "source": { "split": "train_shard_00000", "doc_id": 1393 }, "chunk_id": "train_shard_00000_1393_0", "global_id": 1540 }, { "text": "First human 'pangenome' aims to catalogue genetic diversity.", "token_count": 14, "char_count": 60, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:24.340485", "source": { "split": "train_shard_00000", "doc_id": 1394 }, "chunk_id": "train_shard_00000_1394_0", "global_id": 1541 }, { "text": "'Pangenome' aims to capture the breadth of human diversity.", "token_count": 15, "char_count": 59, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:24.734542", "source": { "split": "train_shard_00000", "doc_id": 1395 }, "chunk_id": "train_shard_00000_1395_0", "global_id": 1542 }, { "text": "Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but advances in long-read sequencing are leading to widely available, high-quality phased assemblies. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph's ability to represent variation at different scales. Here we present the Minigraph-Cactus pangenome pipeline, which creates pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium. The method builds graphs containing all forms of genetic variation while allowing use of current mapping and genotyping tools. We measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods. We also demonstrate construction of a Drosophila melanogaster pangenome.\n\nPangenome graph construction from genome alignments with Minigraph-Cactus.", "token_count": 280, "char_count": 1242, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6725, "quality_score": 0.8363, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:25.304244", "source": { "split": "train_shard_00000", "doc_id": 1396 }, "chunk_id": "train_shard_00000_1396_0", "global_id": 1543 }, { "text": "There has been tremendous progress in phased genome assembly production by combining long-read data with parental information or linked-read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than 140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 182 haploid assemblies obtained from a diversity panel of 77 unique human samples. Although trio-based approaches using HiFi are the current gold standard, chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. Importantly, the majority of assembly gaps cluster near the largest and most identical repeats (including segmental duplications [35.4%], satellite DNA [22.3%], or regions enriched in GA/AT-rich DNA [27.4%]). Consequently, 1513 protein-coding genes overlap assembly gaps in at least one haplotype, and 231 are recurrently disrupted or missing from five or more haplotypes. Furthermore, we estimate that 6-7 Mbp of DNA are misorientated per haplotype irrespective of whether trio-free or trio-based approaches are used. Of these misorientations, 81% correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large segmental duplications. We also identify large-scale alignment discontinuities consistent with 11.9 Mbp of deletions and 161.4 Mbp of insertions per haploid genome. Although 99% of this variation corresponds to satellite DNA, we identify 230 regions of euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Such variable and incompletely assembled regions are important targets for future algorithmic development and pangenome representation.\n\nGaps and complex structurally variant loci in phased genome assemblies.", "token_count": 455, "char_count": 1829, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:25.937556", "source": { "split": "train_shard_00000", "doc_id": 1397 }, "chunk_id": "train_shard_00000_1397_0", "global_id": 1544 }, { "text": "The bile acid pool has a profound impact on human health and disease. The intestinal microbiota initiates the metabolism of conjugated bile acids through a critical first step catalyzed by bacterial bile salt hydrolase (BSH) and provides unique contributions to the diversity of bile acids. There has been great interest in surveying BSH activity. We compared two substrates with either 2-(7-amino-4-methyl-coumarinyl)acetic acid or 7-amino-4-methyl-coumarin as fluorescent reporters of BSH activity. The BSH-catalyzed conversion of the natural substrate taurocholic acid was followed through an HPLC-based assay by applying 7-nitrobenzo[c][1,2,5]oxadiazole as scavenger for taurine, released in the enzymatic reaction. Hence, a new opportunity to monitor the activity of bile salt hydrolases was introduced.\n\nFluorogenic substrates and pre-column derivatization for monitoring the activity of bile salt hydrolase from Clostridium perfringens.", "token_count": 262, "char_count": 943, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6929, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:26.485210", "source": { "split": "train_shard_00000", "doc_id": 1398 }, "chunk_id": "train_shard_00000_1398_0", "global_id": 1545 }, { "text": "The bile salt hydrolase (BSH) activity is responsible for the cholesterol-lowering effect of the probiotic strains. The present study aimed to investigate the relationship between bsh gene-expression (GE) levels responsible for the BSH activity and the parameters of bile salt resistance of different Lactobacillaceae species. Accordingly, 11 Lactobacillaceae family strains with high cholesterol assimilation ratio (49.21-68.22%) determined by the o-phthalaldehyde method selected from 46 Lactobacillaceae species was evaluated for their features including acid tolerance, bile tolerance, and BSH activity. All tested strains survived at pH 2 medium and 0.3% (w/v) bile salt and showed positive BSH activity for glycocholic acid (GCA) and taurocholic acid (TCA). BSH gene expression was performed to provide clear information and to identify the key genes responsible for BSH activity. bsh3 genes were found highest GE level (P < 0.05) in Lactiplantibacillus plantarum and Lacticaseibacillus paracasei strains. The results showed that high cholesterol assimilation ratio were closely correlated with BSH activity and the parameters of bile salt resistance. The results of this study will support the development of a new approach based on phenotypic and genetic analysis to determine the bile salt parameters. The study will be useful for the selection of Lactobacillus strains with high bile salt resistance.\n\nThe Expression Levels of Genes Responsible for the Enzymatic Activity of Bile Salt Hydrolase (BSH) and the Relationship of Cholesterol Assimilation in L. plantarum and L. paracasei.", "token_count": 422, "char_count": 1593, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5261, "quality_score": 0.763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:27.108961", "source": { "split": "train_shard_00000", "doc_id": 1399 }, "chunk_id": "train_shard_00000_1399_0", "global_id": 1546 }, { "text": "Bilosomes are innovative vesicular carriers containing bile salt with a non-ionic surfactant. Being highly flexible, bilosomes can squeeze themselves through the skin carrying the drug to the action site and improving its skin penetration. The objective of this research was to encapsulate niflumic acid (NA), a non-steroidal anti-inflammatory drug into Brij® integrated bilosomes (BIBs) for effective treatment of osteoarthritis through transdermal delivery. BIBs were formulated using 100 mg of Span 20 with different amounts of sodium cholate (NaC), sodium taurocholate (NaTC), or sodium glycocholate (NaGC) as bile salt, with the addition of 5 mg of Brij-93 or Brij-35. BIBs were prepared utilizing ethanol injection method with the application of (3\n\nBrij® integrated bilosomes for improving the transdermal delivery of niflumic acid for effective treatment of osteoarthritis: In vitro characterization, ex vivo permeability assessment, and in vivo study.", "token_count": 263, "char_count": 960, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8358, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:27.656159", "source": { "split": "train_shard_00000", "doc_id": 1400 }, "chunk_id": "train_shard_00000_1400_0", "global_id": 1547 }, { "text": "Phytosterols (PS) have been shown to regulate cholesterol metabolism and alleviate hyperlipidemia (HLP), but the mechanism is still unclear. In this study, we investigated the mechanism by which PS regulates cholesterol metabolism in high-fat diet (HFD) mice. The results showed that PS treatment reduced the accumulation of total cholesterol (TC), triglycerides (TG), and low-density lipoprotein cholesterol (LDL-C) in the serum of HFD mice, while increasing the serum levels of high-density lipoprotein cholesterol (HDL-C). Compared with HFD mice, PS not only increased the antioxidant activity of the liver but also regulated the mRNA expression levels of enzymes and receptors related to cholesterol metabolism. The hypolipidemic effect of PS was abolished by antibiotic (Abx) intervention and reproduced by fecal transplantation (FMT) intervention. The results of 16S rRNA sequencing analysis showed that PS modulated the gut microbiota of mice. PS reduced the relative abundance of Lactobacillus and other bile salt hydrolase- (BSH-) producing gut microbiota in HFD mice, which are potentially related to cholesterol metabolism. These findings partially explain the mechanisms by which PS regulates cholesterol metabolism. This implies that regulation of the gut microbiota would be a potential target for the treatment of HLP.\n\nPhytosterols Alleviate Hyperlipidemia by Regulating Gut Microbiota and Cholesterol Metabolism in Mice.", "token_count": 393, "char_count": 1437, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5637, "quality_score": 0.7819, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:28.606596", "source": { "split": "train_shard_00000", "doc_id": 1401 }, "chunk_id": "train_shard_00000_1401_0", "global_id": 1548 }, { "text": "The Inulinase from Kluyveromyces marxianus ISO3 (Inu-ISO3) is an enzyme able to hydrolyze linear fructans such as chicory inulin as well as branched fructans like agavin. This enzyme was cloned and expressed in Komagataella pastoris to study the role of selected aromatic and polar residues in the catalytic pocket by Alanine scanning. Molecular dynamics (MD) simulations and enzyme kinetics analysis were performed to study the functional consequences of these amino acid substitutions. Site-directed mutagenesis was used to construct the mutants of the enzyme after carrying out the MD simulations between Inu-ISO3 and its substrates. Mutation Trp79:Ala resulted in the total loss of activity when fructans were used as substrates, while with sucrose, the activity decreased by 98 %. In contrast, the mutations Phe113:Ala and Gln236:Ala increased the invertase activity when sucrose was used as a substrate. Although these amino acids are not part of the conserved motifs where the catalytic triad is located, they are essential for the enzyme's activity. In silico and experimental approaches corroborate the relevance of these residues for substrate binding and their influence on enzymatic activity.\n\nRelevance of aromatic and polar amino acids in the specificity of Inulinase ISO3 from Kluyveromyces marxianus: A molecular dynamics approach with an experimental verification.", "token_count": 358, "char_count": 1381, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [ "ISO3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:29.185278", "source": { "split": "train_shard_00000", "doc_id": 1402 }, "chunk_id": "train_shard_00000_1402_0", "global_id": 1549 }, { "text": "Aim of this study was to investigate the prevalence and genetic environment of the oxazolidinone resistance gene optrA in Streptococcus suis (S. suis) isolates from diseased pigs in China. A total of 178 S. suis isolates were screened for the optrA gene by PCR. The phenotypes and genotypes of optrA-positive isolates were investigated by antimicrobial susceptibility testing, core genome Multilocus Sequence Typing (cgMLST), capsular serotypes determination and whole-genome sequencing (WGS). Fifty-one (28.7%) S. suis isolates were positive for optrA. Phylogenetic analysis indicated that the spread of the optrA among S. suis isolates was primarily due to horizontal transfer. Analysis of S. suis serotypes from diseased pigs revealed substantial diversity. The genetic environment of optrA was complex and diverse and could be divided into 12 different types. Interestingly, we identified a novel integrative and conjugative element ICESsu988S, carrying optrA and erm(T) genes. This is to the best of our knowledge the first report of the optrA and erm(T) co-located on an ICE in S. suis. Our results showed a high prevalence of optrA gene in S. suis isolates in China. Further research is needed to evaluate the importance of ICEs, as they horizontally propagate important clinical resistance genes.\n\nPrevalence of the optrA gene among Streptococcus suis isolates from diseased pigs and identification of a novel integrative conjugative element ICESsu988S.", "token_count": 399, "char_count": 1461, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5459, "quality_score": 0.7729, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:29.799285", "source": { "split": "train_shard_00000", "doc_id": 1403 }, "chunk_id": "train_shard_00000_1403_0", "global_id": 1550 }, { "text": "We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while reducing the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/alshai/rowbowt .\n\nPangenomic genotyping with the marker array.", "token_count": 156, "char_count": 692, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:30.243014", "source": { "split": "train_shard_00000", "doc_id": 1404 }, "chunk_id": "train_shard_00000_1404_0", "global_id": 1551 }, { "text": "Bile salts exhibit complex concentration-dependent micellization in aqueous solution, rooted in a long-standing hypothesis of increasing size in bile aggregation that has historically focused on the measurement of only one CMC detected by a given method, without resolving successive stepwise aggregates. Whether bile aggregation is continuous or discrete, at what concentration does the first aggregate form, and how many aggregation steps occur, all remain as open questions.\n\nDetermining sequential micellization steps of bile salts with multi-CMC modeling.", "token_count": 119, "char_count": 560, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:30.630268", "source": { "split": "train_shard_00000", "doc_id": 1405 }, "chunk_id": "train_shard_00000_1405_0", "global_id": 1552 }, { "text": "As large-scale genomic studies have progressed, it has been revealed that a single reference genome pattern cannot represent genetic diversity at the species level. While domestic animals tend to have complex routes of origin and migration, suggesting a possible omission of some population-specific sequences in the current reference genome. Conversely, the pangenome is a collection of all DNA sequences of a species that contains sequences shared by all individuals (core genome) and is also able to display sequence information unique to each individual (variable genome). The progress of pangenome research in humans, plants and domestic animals has proved that the missing genetic components and the identification of large structural variants (SVs) can be explored through pangenomic studies. Many individual specific sequences have been shown to be related to biological adaptability, phenotype and important economic traits. The maturity of technologies and methods such as third-generation sequencing, Telomere-to-telomere genomes, graphic genomes, and reference-free assembly will further promote the development of pangenome. In the future, pangenome combined with long-read data and multi-omics will help to resolve large SVs and their relationship with the main economic traits of interest in domesticated animals, providing better insights into animal domestication, evolution and breeding. In this review, we mainly discuss how pangenome analysis reveals genetic variations in domestic animals (sheep, cattle, pigs, chickens) and their impacts on phenotypes and how this can contribute to the understanding of species diversity. Additionally, we also go through potential issues and the future perspectives of pangenome research in livestock and poultry.\n\nA review of the pangenome: how it affects our understanding of genomic variation, selection and breeding in domestic animals?", "token_count": 380, "char_count": 1897, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6283, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:31.218821", "source": { "split": "train_shard_00000", "doc_id": 1406 }, "chunk_id": "train_shard_00000_1406_0", "global_id": 1553 }, { "text": "An outbreak involving an extensively antibiotic-resistant Acinetobacter baumannii strain in three military treatment facilities was identified. Fifty-nine isolates recovered from 30 patients over a 4-year period were found among a large collection of isolates using core genome multilocus sequence typing (MLST). They differed by only 0 to 18 single nucleotide polymorphisms (SNPs) and carried the same resistance determinants except that the\n\nIdentification of an Outbreak Cluster of Extensively Antibiotic-Resistant GC1 Acinetobacter baumannii Isolates in U.S. Military Treatment Facilities.", "token_count": 149, "char_count": 593, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7949, "quality_score": 0.8974, "entities": { "genes": [ "GC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:31.657233", "source": { "split": "train_shard_00000", "doc_id": 1407 }, "chunk_id": "train_shard_00000_1407_0", "global_id": 1554 }, { "text": "Wheat (Triticum aestivum L.) is a major source of nutrients for populations across the globe, but the amino acid composition of wheat grain does not provide optimal nutrition. The nutritional value of wheat grain is limited by low concentrations of lysine (the most limiting essential amino acid) and high concentrations of free asparagine (precursor to the processing contaminant acrylamide). There are currently few available solutions for asparagine reduction and lysine biofortification through breeding. In this study, we investigated the genetic architecture controlling grain free amino acid composition and its relationship to other traits in a Robigus × Claire doubled haploid population. Multivariate analysis of amino acids and other traits showed that the two groups are largely independent of one another, with the largest effect on amino acids being from the environment. Linkage analysis of the population allowed identification of quantitative trait loci (QTL) controlling free amino acids and other traits, and this was compared against genomic prediction methods. Following identification of a QTL controlling free lysine content, wheat pangenome resources facilitated analysis of candidate genes in this region of the genome. These findings can be used to select appropriate strategies for lysine biofortification and free asparagine reduction in wheat breeding programs.\n\nGenetic control of grain amino acid composition in a UK soft wheat mapping population.", "token_count": 306, "char_count": 1478, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:32.221913", "source": { "split": "train_shard_00000", "doc_id": 1408 }, "chunk_id": "train_shard_00000_1408_0", "global_id": 1555 }, { "text": "Soybean (Glycine max) is a major crop that contributes more than half of global oilseed production. Much research has been directed towards improvement of the fatty acid profile of soybean seeds through marker assisted breeding. Recently published soybean pangenomes, based on thousands of soybean lines, provide an opportunity to identify new alleles that may be involved in fatty acid biosynthesis. In this study, we identify fatty acid biosynthesis genes in soybean pangenomes based on sequence identity with known genes and examine their sequence diversity across diverse soybean collections. We find three possible instances of a gene missing in wild soybean, including FAD8 and FAD2-2D, which may be involved in oleic and linoleic acid desaturation, respectively, although we recommend follow-up research to verify the absence of these genes. More than half of the 53 fatty acid biosynthesis genes identified contained missense variants, including one linked with a previously identified QTL for oil quality. These variants were present in multiple studies based on either short read mappings or alignment of reference grade genomes. Missense variants were found in previously characterized genes including FAD2-1A and FAD2-1B, both of which are involved in desaturation of oleic acid, as well as uncharacterized candidate fatty acid biosynthesis genes. We find that the frequency of missense alleles in fatty acid biosynthesis genes has been reduced significantly more than the global average frequency of missense mutations during domestication, and missense variation in some genes is near absent in modern cultivars. This could be due to the selection for fatty acid profiles in seed, though future work should be conducted towards understanding the phenotypic impacts of these variants.\n\nDiversity of fatty acid biosynthesis genes across the soybean pangenome.", "token_count": 423, "char_count": 1871, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5627, "quality_score": 0.7814, "entities": { "genes": [ "FAD8", "FAD2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:32.851825", "source": { "split": "train_shard_00000", "doc_id": 1409 }, "chunk_id": "train_shard_00000_1409_0", "global_id": 1556 }, { "text": "Evaluation of core genome and whole genome multilocus sequence typing schemes for", "token_count": 17, "char_count": 81, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:33.213656", "source": { "split": "train_shard_00000", "doc_id": 1410 }, "chunk_id": "train_shard_00000_1410_0", "global_id": 1557 }, { "text": "S. 4,[5],12:i:-, a monophasic variant of S. enterica serovar Typhimurium, is an important multidrug resistant serovar. Strains of colistin-resistant S. 4,[5],12:i:- have been reported in several countries with patients occasionally had recent histories of travels to Southeast Asia. In the study herein, we investigated the genomes of S. 4,[5],12:i:- carrying mobile colistin resistance (mcr) gene in Thailand. Three isolates of mcr-3.1 carrying S. 4,[5],12:i:- in Thailand were sequenced by both Illumina and Oxford Nanopore platforms and we analyzed the sequences together with the whole genome sequences of other mcr-3 carrying S. 4,[5],12:i:- isolates available in the NCBI Pathogen Detection database. Three hundred sixty-nine core genome SNVs were identified from 27 isolates, compared to the S. Typhimurium LT2 reference genome. A maximum-likelihood phylogenetic tree was constructed and revealed that the samples could be divided into three clades, which correlated with the profiles of fljAB-hin deletions and plasmids. A couple of isolates from Denmark had the genetic profiles similar to Thai isolates, and were from the patients who had traveled to Thailand. Complete genome assembly of the three isolates revealed the insertion of a copy of IS26 at the same site near iroB, suggesting that the insertion was an initial step for the deletions of fljAB-hin regions, the hallmark of the 4,[5],12:i:- serovar. Six types of plasmid replicons were identified with the majority being IncA/C. The coexistence of mcr-3.1 and bla\n\nEvidence of international transmission of mobile colistin resistant monophasic Salmonella Typhimurium ST34.", "token_count": 459, "char_count": 1641, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5851, "quality_score": 0.7925, "entities": { "genes": [ "IS26", "ST34", "LT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:33.847355", "source": { "split": "train_shard_00000", "doc_id": 1411 }, "chunk_id": "train_shard_00000_1411_0", "global_id": 1558 }, { "text": "We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were still to be determined. Here, we show that phages encoding the major phage nucleus protein chimallin share 72 conserved genes encoded within seven gene blocks. Of these, 21 core genes are unique to nucleus-forming phage, and all but one of these genes encode proteins of unknown function. We propose that these phages comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryoelectron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication are conserved among diverse chimalliviruses and reveal variations on this replication mechanism. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.\n\nIdentifying the core genome of the nucleus-forming bacteriophage family and characterization of Erwinia phage RAY.", "token_count": 272, "char_count": 1145, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:34.403653", "source": { "split": "train_shard_00000", "doc_id": 1412 }, "chunk_id": "train_shard_00000_1412_0", "global_id": 1559 }, { "text": "Broiler cellulitis has emerged as an important cause of economic losses for farmers and slaughter plants from carcass condemnation at processing. Avian pathogenic Escherichia coli (APEC) has been identified as the main causative agent. The aim was to characterize E. coli isolated from cellulitis and organs in broilers at slaughter by whole genome sequencing analysis to study if systemic spread could be confirmed. Isolates were collected post-mortem from 101 carcasses condemned due to dermatitis/cellulitis from five commercial farms and six flocks. Forty-six isolates were characterised to determine serotypes, sequence types and virulence-associated genes. Analysis by cgMLST was performed to study the genetic similarity between isolates from the same broiler, among birds from the same flock and between flocks. Escherichia coli was isolated from 90% of birds from subcutaneous samples. In 20 broilers, E. coli was isolated from organs in pure culture or mixed with sparse growth of other bacteria. In eight of these, there were post-mortem findings suggestive of systemic bacterial spread. The majority of the isolates from the same bird and flock belonged to the same serotype and sequence type and were genetically indistinguishable, but differed when compared between flocks. Common APEC virulence genes, i.e. chuA, fyuA, hlyF, iroN, irp2, iss, ompT, sitA, TerC, TraT, were present in > 87% of the isolates. We conclude that evidence of systemic spread of E. coli from cellulitis was present in some birds at time of slaughter but cannot be reliably detected at meat inspection.\n\nCore genome multilocus sequence typing (cgMLST) confirms systemic spread of avian pathogenic Escherichia coli (APEC) in broilers with cellulitis.", "token_count": 457, "char_count": 1737, "word_count": 262, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:35.045323", "source": { "split": "train_shard_00000", "doc_id": 1413 }, "chunk_id": "train_shard_00000_1413_0", "global_id": 1560 }, { "text": "Nowadays, conventional anticancer therapy suffers many pitfalls, including drastic side effects and limited therapeutic efficacy resulting from diminished oral bioavailability. So, in an attempt to enhance their poor solubility and oral bioavailability along with the cytotoxic activity, the developed lead compounds (C1 and C2) were loaded in D-α-tocopherol polyethylene glycol 1000 succinate (TPGS) modified vesicles adopting thin film hydration technique. The formulations of the aforementioned candidates (F1 and F2, respectively) were elected as the optimum formula with desirability values of 0.701 and 0.618, respectively. Furthermore, an outstanding enhancement in the drug's cytotoxic activity against different cancer cell lines (MCF-7, HepG-2, MDA-MB-321, A375, and MGC-803) after being included in the nano-TPGS-modified optimum formula was noticed relative to the unformulated compounds. The formula F1 showed the best cytotoxic activities against HepG-2 with an IC\n\nExperimental design of D-α-tocopherol polyethylene glycol 1000 succinate stabilized bile salt based Nano-vesicles for improved cytotoxicity and bioavailability of colchicine binding site inhibitor Candidates: In Vitro, in silico, and pharmacokinetic studies.", "token_count": 344, "char_count": 1238, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7362, "quality_score": 0.8681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:35.649536", "source": { "split": "train_shard_00000", "doc_id": 1414 }, "chunk_id": "train_shard_00000_1414_0", "global_id": 1561 }, { "text": "The probiotic role of lactic acid bacteria (LAB) in regulating intestinal microbiota to promote human health has been widely reported. However, the types and quantities of probiotics used in practice are still limited. Therefore, isolating and screening LAB with potential probiotic functions from various habitats has become a hot topic. In this study, 104 strains of LAB were isolated from and identified in traditionally fermented vegetables, fresh milk, healthy infant feces, and other environments. The antibacterial properties-resistance to acid, bile salts, and digestive enzymes-and adhesion ability of the strains were determined, and the biological safety of LAB with better performance was studied. Three LAB with good comprehensive performance were obtained. These bacteria had broad-spectrum antibacterial properties and good acid resistance and adhesion ability. They exhibited some tolerance to pig bile salt, pepsin, and trypsin and showed no hemolysis. They were sensitive to the selected antibiotics, which met the required characteristics and safety evaluation criteria for probiotics. An in vitro fermentation experiment and milk fermentation performance test of\n\nScreening, Identification and Physiological Characteristics of", "token_count": 270, "char_count": 1246, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:36.210734", "source": { "split": "train_shard_00000", "doc_id": 1415 }, "chunk_id": "train_shard_00000_1415_0", "global_id": 1562 }, { "text": "A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in\n\nA Core Genome Multilocus Sequence Typing Scheme for", "token_count": 46, "char_count": 172, "word_count": 26, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:36.627220", "source": { "split": "train_shard_00000", "doc_id": 1416 }, "chunk_id": "train_shard_00000_1416_0", "global_id": 1563 }, { "text": "Campylobacter is a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies on Campylobacter generally focus on specific pathogenic species such as C. coli and C. jejuni. Currently, there are thousands of publicly available Campylobacter genomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all available Campylobacter genomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III of C. coli is in fact a novel species (referred here as Campylobacter spp12). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinct Campylobacter species. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics of Campylobacter species with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that the Campylobacter genus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.\n\nComparative genomics and phylogenomics of Campylobacter unveil potential novel species and provide insights into niche segregation.", "token_count": 298, "char_count": 1400, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6138, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:37.211479", "source": { "split": "train_shard_00000", "doc_id": 1417 }, "chunk_id": "train_shard_00000_1417_0", "global_id": 1564 }, { "text": "High-temperature ethanol fermentation (> 40 °C) can be applied as effective bioprocess technology to increase ethanol production. Thermotolerant yeast Pichia kudriavzevii 1P4 showed the ability to produce ethanol at optimum 37 °C. Thus, this study evaluated the ethanol productivity of isolate 1P4 at high-temperature ethanol fermentation (42 and 45 °C) and the identification of metabolite biomarkers using untargeted metabolomics with liquid chromatography-tandem mass spectrometry (LC-MS/MS). 1P4 showed tolerance to temperature stress up to 45 °C and thus relevant for high-temperature fermentation. As measured by gas chromatography (GC), bioethanol production of 1P4 at 30, 37, 42, and 45 °C was 5.8 g/l, 7.1 g/l, 5.1 g/l, and 2.8 g/l, respectively. The classification of biomarker compounds was based on orthogonal projection analysis to latent structure discriminant analysis (OPLS-DA), resulting in L-proline being a suspected biomarker compound for isolate 1P4 tolerance against high-temperature stress. Indeed, supplementation of L-proline on fermentation medium supported the growth of 1P4 at high temperatures (> 40 °C) than without L-proline. The bioethanol production with the addition of the L-proline resulted in the highest ethanol concentration (7.15 g/l) at 42 °C. Supplementation of L-proline as a stress-protective compound increased ethanol productivity at high-temperature fermentation of 42 and 45 °C by 36.35% and 83.33%, respectively, compared without the addition of L-proline", "token_count": 475, "char_count": 1504, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5735, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:37.855941", "source": { "split": "train_shard_00000", "doc_id": 1418 }, "chunk_id": "train_shard_00000_1418_0", "global_id": 1565 }, { "text": "Preliminary interpretation of these results indicates that bioprocess engineering through supplementation of stress-protective compounds L-proline increases the fermentation efficiency of isolate 1P4 at higher temperatures (42 °C and 45 °C).\n\nMetabolomics Study Reveals Biomarker L-Proline as Potential Stress-Protectant Compound for High-Temperature Bioethanol Fermentation by Yeast Pichia kudriavzevii 1P4.", "token_count": 117, "char_count": 408, "word_count": 48, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:38.238522", "source": { "split": "train_shard_00000", "doc_id": 1418 }, "chunk_id": "train_shard_00000_1418_1", "global_id": 1566 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) infection can cause clinical manifestations ranging from diarrhea to potentially fatal hemolytic uremic syndrome (HUS). This study is aimed at identifying STEC genetic factors associated with the development of HUS in Sweden. A total of 238 STEC genomes from STEC-infected patients with and without HUS between 1994 and 2018 in Sweden were included in this study. Serotypes, Shiga toxin gene (stx) subtypes, and virulence genes were characterized in correlation to clinical symptoms (HUS and non-HUS), and pan-genome wide association study was performed. Sixty-five strains belonged to O157:H7, and 173 belonged to non-O157 serotypes. Our study revealed that strains of O157:H7 serotype especially clade 8 were most commonly found in patients with HUS in Sweden. stx2a and stx2a + stx2c subtypes were significantly associated with HUS. Other virulence factors associated with HUS mainly included intimin (eae) and its receptor (tir), adhesion factors, toxins, and secretion system proteins. Pangenome wide-association study identified numbers of accessory genes significantly overrepresented in HUS-STEC strains, including genes encoding outer membrane proteins, transcriptional regulators, phage-related proteins, and numerous genes related to hypothetical proteins. Whole-genome phylogeny and multiple correspondence analysis of pangenomes could not differentiate HUS-STEC from non-HUS-STEC strains. In O157:H7 cluster, strains from HUS patients clustered closely; however, no significant difference in virulence genes was found in O157 strains from patients with and without HUS. These results suggest that STEC strains from different phylogenetic backgrounds may independently acquire genes determining their pathogenicity and confirm that other non-bacterial factors and/or bacteria-host interaction may affect STEC pathogenesis.", "token_count": 494, "char_count": 1880, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:38.889336", "source": { "split": "train_shard_00000", "doc_id": 1419 }, "chunk_id": "train_shard_00000_1419_0", "global_id": 1567 }, { "text": "Genome-wide association study of hemolytic uremic syndrome causing Shiga toxin-producing Escherichia coli from Sweden, 1994-2018.", "token_count": 45, "char_count": 129, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:39.250025", "source": { "split": "train_shard_00000", "doc_id": 1419 }, "chunk_id": "train_shard_00000_1419_1", "global_id": 1568 }, { "text": "Characterization of new potential probiotics is desirable in the field of research on probiotics for their extensive use in health and disease. Tribes could be an unusual source of probiotics due to their unique food habits and least dependence on medications and consumption of antibiotics. The aim of the present study is to isolate lactic acid bacteria from tribal fecal samples of Odisha, India, and characterize their genetic and probiotic attributes. In this context one of the catalase-negative and Gram-positive isolates, identified using 16S rRNA sequencing as Ligilactobacillus salivarius, was characterized in vitro for its acid and bile tolerance, cell adhesion and antimicrobial properties. The whole genome sequence was obtained and analyzed for strain level identification, presence of genomic determinants for probiotic-specific features, and safety. Genes responsible for its antimicrobial and immunomodulatory functions were detected. The secreted metabolites were analyzed using high resolution mass spectroscopy; the results indicated that the antimicrobial potential could be due to the presence of pyroglutamic acid, propionic acid, lactic acid, 2-hydroxyisocaproic acid, homoserine, and glutathione, and the immuno-modulating activity, contributed by the presence of short chain fatty acids such as acetate, propionate, and butyrate. So, to conclude we have successfully characterized a Ligilactobacillus salivarius species with potential antimicrobial and immunomodulatory ability. The health-promoting effects of this probiotic strain and/or its derivatives will be investigated in future.\n\nBiochemical, functional and genomic characterization of a new probiotic Ligilactobacillus salivarius F14 from the gut of tribes of Odisha.", "token_count": 426, "char_count": 1754, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:39.872122", "source": { "split": "train_shard_00000", "doc_id": 1420 }, "chunk_id": "train_shard_00000_1420_0", "global_id": 1569 }, { "text": "The pangenome is the set of all genes present in a prokaryotic population. Most pangenomes contain many accessory genes of low and intermediate frequencies. Different population genetics processes contribute to the shape of these pangenomes, namely selection and fitness-independent processes such as gene transfer, gene loss, and migration. However, their relative importance is unknown and highly debated. Here, we argue that the debate around prokaryotic pangenomes arose due to the imprecise application of population genetics models. Most importantly, two different processes of horizontal gene transfer act on prokaryotic populations, which are frequently confused, despite their fundamentally different behavior. Genes acquired from distantly related organisms (termed here acquiring gene transfer) are most comparable to mutation in nucleotide sequences. In contrast, gene gain within the population (termed here spreading gene transfer) has an effect on gene frequencies that is identical to the effect of positive selection on single genes. We thus show that selection and fitness-independent population genetic processes affecting pangenomes are indistinguishable at the level of single gene dynamics. Nevertheless, population genetics processes are fundamentally different when considering the joint distribution of all accessory genes across individuals of a population. We propose that, to understand to which degree the different processes shaped pangenome diversity, the development of comprehensive models and simulation tools is mandatory. Furthermore, we need to identify summary statistics and measurable features that can distinguish between the processes, where considering the joint distribution of accessory genes across individuals of a population will be particularly relevant.\n\nTackling the Pangenome Dilemma Requires the Concerted Analysis of Multiple Population Genetic Processes.", "token_count": 358, "char_count": 1909, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5637, "quality_score": 0.7819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:40.447181", "source": { "split": "train_shard_00000", "doc_id": 1421 }, "chunk_id": "train_shard_00000_1421_0", "global_id": 1570 }, { "text": "Hydrophilic phytosterol glycosyl derivatives are synthetic phytosterol analogues by coupling with the glycosyl moiety to improve the water solubility and bioaccessibility of free phytosterols. The aim of this study is to clarify the molecular interaction of phytosterol glycosyl derivatives with bile salts and the consequent impact on cholesterol solubilization. Sharp nonlinear decrease in the micellar solubility of cholesterol and accompanying changes in particle size, zeta potential and microtopography of mixed micelles were observed when phytosterol glycosyl derivatives were introduced in cholesterol-loaded bile salt micelles. These results suggested that β-sitosterol glycosyl derivatives molecules indeed participated in the formation of mixed micelles. Further, nuclear magnetic resonance showed that the structural change of mixed micelles was caused by the insertion of β-sitosterol glycosyl derivatives via hydrogen bonds with sodium taurocholate, which resulted in the low cholesterol solubilization. Moreover, the hydrogen-bond interactions were apparently influenced by the glycosyl moiety of β-sitosterol glycosyl derivatives. These molecular mechanisms may contribute to the development of cholesterol-absorption inhibitors.\n\nImpact of molecular interactions between hydrophilic phytosterol glycosyl derivatives and bile salts on the micellar solubility of cholesterol.", "token_count": 345, "char_count": 1390, "word_count": 178, "semantic_coherence": 1, "information_density": 0.5449, "quality_score": 0.7725, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:41.026113", "source": { "split": "train_shard_00000", "doc_id": 1422 }, "chunk_id": "train_shard_00000_1422_0", "global_id": 1571 }, { "text": "Through previous study, the three yeast α-mannans (MPS) from various sources of Kluyveromyces marxianus (LZ-MPS, MC-MPS, and G-MPS) were preliminarily characterized. In this study, the advanced structural characterization and the in vitro human fecal fermentation behavior of the three MPS were investigated. According to the results of this study, the polysaccharide molecules of the three MPS were aggregated in solution, supporting their branched chain structure. After in vitro fermentation, the molecular weight and pH of fermentation broth decreased significantly, indicating that the three MPS could be utilized by human gut microbiota. Meanwhile, the production of total short-chain fatty acids (SCFAs) of the three MPS was promoted, especially the production of propionic acid was 45.55, 38.23, and 38.87 mM, respectively. In particular, the three MPS have the ability to alter the composition of human gut microbiota, especially to promote the proliferation of Bacteroidetes, suggesting that the bioactivities of the three MPS can be significantly influenced by intestine Bacteroidetes. In terms of metabolism, all MPS can promote cofactors, vitamins, amino acid metabolism, and glycan biosynthesis and metabolism of bacteria. In consequence, the three MPS were confirmed to regulate the human gut microbiota, increase the level of SCFAs, promote the metabolisms of bacteria on amino acid and glycan, and improve the intestinal health.\n\nAdvanced structural characterization and in vitro fermentation prebiotic properties of cell wall polysaccharide from Kluyveromyces marxianus.", "token_count": 410, "char_count": 1588, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5398, "quality_score": 0.7699, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:41.639279", "source": { "split": "train_shard_00000", "doc_id": 1423 }, "chunk_id": "train_shard_00000_1423_0", "global_id": 1572 }, { "text": "Invasive Group B Streptococcus (GBS) can infect pregnant women, neonates, and older adults. Invasive GBS serotype VIII is infrequent in Alberta; however, cases have increased in recent years. Here, genomic analysis was used to characterize fourteen adult invasive serotype VIII isolates from 2009 to 2021. Trends in descriptive clinical data and antimicrobial susceptibility results were evaluated for invasive serotype VIII isolates from Alberta. Isolate genomes were sequenced and subjected to molecular sequence typing, virulence and antimicrobial resistance gene identification, phylogenetic analysis, and pangenome determination. Multilocus sequencing typing identified eight ST42 (Clonal Complex; CC19), four ST1 (CC1), and two ST2 (CC1) profiles. Isolates were susceptible to penicillin, erythromycin, chloramphenicol, and clindamycin, apart from one isolate that displayed erythromycin and inducible clindamycin resistance. All isolates carried genes for peptide antibiotic resistance, three isolates for tetracycline resistance, and one for macrolide, lincosamide, and streptogramin resistance. All genomes carried targets currently being considered for protein-based vaccines (e.g., pili and/or Alpha family proteins). Overall, invasive GBS serotype VIII is emerging in Alberta, primarily due to ST42. Characterization and continued surveillance of serotype VIII will be important for outbreak prevention, informing vaccine development, and contributing to our understanding of the global epidemiology of this rare serotype.\n\nGenomic characterization of emerging invasive Streptococcus agalactiae serotype VIII in Alberta, Canada.", "token_count": 411, "char_count": 1640, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6887, "quality_score": 0.8443, "entities": { "genes": [ "ST2", "ST42", "CC19", "ST1", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:42.262195", "source": { "split": "train_shard_00000", "doc_id": 1424 }, "chunk_id": "train_shard_00000_1424_0", "global_id": 1573 }, { "text": "Milk is considered one of the basic raw materials of animal origin; it must present hygienic quality and physical-chemical properties suitable for processing and human consumption. Thus, the ingestion of milk in natura when not properly treated can be characterized as an opportunistic route of transmission of possible microbial pathogens, which can offer risks to public health. The present study aimed the yeast identification, to analyze the thermo-resistance of yeasts isolated from fresh milk, and to trace the susceptibility profile of the isolates to antifungal agents. For this, 23 samples of fresh milk type B, collected by manual or mechanical milking, were stored in collective refrigeration tanks of farms located in the Metropolitan Region of Natal and nearby, State of Rio Grande do Norte (RN), Brazil. Twenty samples of fresh milk commercially traded in the city of Ceará-Mirim RN were also analyzed. The yeasts were quantified by count of colony-forming units (CFU). All isolated species were treated by slow pasteurization (62-64 °C for 30 min) and fast (72-75 °C for 20 s), as well as by boiling (100 °C). Fifty yeast strains were obtained, and the species were identified as Candida tropicalis (28%), Candida parapsilosis (14%), Candida albicans (12%), Candida glabrata (10%), Candida krusei (10%), Kluyveromyces marxianus (10%), Candida guilliermondii (8%), Candida rugosa (2%), Candida orthopsilosis (2%), Pichia manshurica (2%), and Kodamaea ohmeri (2%). Five isolates showed resistance to the antifungal agents tested. Among all the isolates submitted to heat treatment, 80% were resistant to fast pasteurization and 60% to boiling, but none of them resisted the slow pasteurization. The milk collected through mechanical milking and stored in collective cooling tanks, presented higher rates of yeast contamination, compared to milk samples collected by manual milking and kept under the same storage conditions.", "token_count": 505, "char_count": 1937, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:42.921933", "source": { "split": "train_shard_00000", "doc_id": 1425 }, "chunk_id": "train_shard_00000_1425_0", "global_id": 1574 }, { "text": "Identification and evaluation of thermotolerance of yeasts from milk in natura exposed to high temperature and slow and fast pasteurization.", "token_count": 29, "char_count": 140, "word_count": 20, "semantic_coherence": 1, "information_density": 0.85, "quality_score": 0.925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:43.278420", "source": { "split": "train_shard_00000", "doc_id": 1425 }, "chunk_id": "train_shard_00000_1425_1", "global_id": 1575 }, { "text": "Deposition of high-speed droplets on inverted surfaces is important to many fundamental scientific principles and technological applications. For example, in pesticide spraying to target pests and diseases emerging on abaxial side of leaves, the downward rebound and gravity of the droplets make the deposition exceedingly difficult on hydrophobic/superhydrophobic leaf underside, causing serious pesticide waste and environmental pollution. Here, a series of bile salt/cationic surfactant coacervates are developed to attain efficient deposition on the inverted surfaces of diverse hydrophobic/superhydrophobic characteristics. The coacervates have abundant nanoscale hydrophilic/hydrophobic domains and intrinsic network-like microstructures, which endow them with efficient encapsulation of various solutes and strong adhesion to surface micro/nanostructures. Thus, the coacervates with low viscosity achieve high-efficient deposition on superhydrophobic abaxial-side of tomato leaves and inverted artificial surfaces with a water contact angle from 170° to 124°, much better than that of commercial agricultural adjuvants. Intriguingly, the compactness of network-like structures dominantly controls adhesion force and deposition efficiency, and the most crowded one leads to the most efficient deposition. The tunable coacervates can help comprehensively understand the complex dynamic deposition, and provide innovative carriers for depositing sprayed pesticides on abaxial and adaxial sides of leaves, thereby potentially reducing pesticide use and promoting sustainable agriculture.\n\nCoacervate-Enhanced Deposition of Sprayed Pesticide on Hydrophobic/Superhydrophobic Abaxial Leaf Surfaces.", "token_count": 403, "char_count": 1698, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6476, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:43.894607", "source": { "split": "train_shard_00000", "doc_id": 1426 }, "chunk_id": "train_shard_00000_1426_0", "global_id": 1576 }, { "text": "Dolosigranulum pigrum-a lactic acid bacterium that is increasingly recognized as an important member of the nasal microbiome. Currently, there are limited rapid and low-cost options for confirming D. pigrum isolates and detecting D. pigrum in clinical specimens. Here we describe the design and validation of a novel PCR assay targeting D. pigrum that is both sensitive and specific. We designed a PCR assay targeting murJ, a single-copy core species gene identified through the analysis of 21 D. pigrum whole genome sequences. The assay achieved 100% sensitivity and 100% specificity against D. pigrum and diverse bacterial isolates and an overall 91.1% sensitivity and 100% specificity using nasal swabs, detecting D. pigrum at a threshold of 1.0 × 10\n\nDesign and validation of Dolosigranulum pigrum specific PCR primers using the bacterial core genome.", "token_count": 236, "char_count": 855, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6031, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:44.372913", "source": { "split": "train_shard_00000", "doc_id": 1427 }, "chunk_id": "train_shard_00000_1427_0", "global_id": 1577 }, { "text": "The composition of gastrointestinal (GI) fluids is crucial for the dissolution, solubilization, and absorption of orally administered drugs. Disease- or age-related changes in GI fluid composition could significantly affect the pharmacokinetics of oral drugs. However, limited studies have been conducted on the characteristics of GI fluids in neonates and infants due to practical and ethical challenges. The current study collected enterostomy fluids from 21 neonate and infant patients over an extended period of time and from different regions of the small intestine and colon. The fluids were characterized for pH, buffer capacity, osmolality, total protein, bile salts, phospholipids, cholesterol, and lipid digestion products. The study found a large variability in the fluid characteristics among the different patients, in line with the highly heterogeneous study population. Compared to adult intestinal fluids, the enterostomy fluids from neonates and infants had low bile salt concentrations, with an increasing trend as a function of age; no secondary bile salts were detected. In contrast, total protein and lipid concentrations were relatively high, even in the distal small intestine. These findings suggest marked differences in intestinal fluid composition between neonates and infants versus adults, which may affect the absorption of certain drugs.\n\nCharacterization of neonatal and infant enterostomy fluids.", "token_count": 316, "char_count": 1429, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:44.934300", "source": { "split": "train_shard_00000", "doc_id": 1428 }, "chunk_id": "train_shard_00000_1428_0", "global_id": 1578 }, { "text": "Dahi, an artisanal fermented milk product, widely consumed in Pakistan, is microbiologically diverse, and many bacterial communities await investigation. The current study is first to present probiotic assessment of Bacillus species strains isolated from dahi. Based on 49 identified strains assessed, only 6 strains, i.e., Bacillus licheniformis QAUBL19, QAUBL1901, and QAUBL1902; Bacillus mycoides QAUBM19 and QAUBM1901; and Bacillus subtilis QAUBSS1 were having prominent persistence in the simulated gastrointestinal fluids, being non-hemolytic, with no DNase activity. Probiotic characteristics, cholesterol-assimilating, and carbohydrate-fermenting capabilities were assessed for all the strains. These six strains each showed variant cholesterol assimilating abilities. B. licheniformis QAUBL19 retaining most desired probiotic traits presented both notable cholesterol assimilating and bile salt hydrolase activities. It can be used as a probiotic of choice with hypocholesterolemia ability. B. subtilis QAUBSS1 showed wide carbohydrate fermentation ability and strongest antibacterial potential. It is likely to be considered a probiotic for living beings and starter culture for fermentation of food/feed.\n\nProbiotic characterization of Bacillus species strains isolated from an artisanal fermented milk product Dahi.", "token_count": 376, "char_count": 1327, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [ "QAUBL19", "QAUBL1902", "QAUBL1901", "QAUBM19", "QAUBSS1", "QAUBM1901" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:45.514861", "source": { "split": "train_shard_00000", "doc_id": 1429 }, "chunk_id": "train_shard_00000_1429_0", "global_id": 1579 }, { "text": "The use of probiotics has been considered as a new therapy option for ulcerative colitis (UC), and yeast has recently received widespread recommendation for human health. In this study, the probiotic characteristics of four yeast strains,\n\nAnti-Inflammatory, Barrier Maintenance, and Gut Microbiome Modulation Effects of", "token_count": 78, "char_count": 320, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8444, "quality_score": 0.9222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:45.894458", "source": { "split": "train_shard_00000", "doc_id": 1430 }, "chunk_id": "train_shard_00000_1430_0", "global_id": 1580 }, { "text": "The thermotolerant yeast is beneficial in terms of efficiency improvement of processes and reduction of costs, while Saccharomyces cerevisiae does not efficiently grow and ferment at high-temperature conditions. The sterol composition alteration from ergosterol to fecosterol in the cell membrane of S. cerevisiae affects the thermotolerant capability.\n\nThermotolerance improvement of engineered Saccharomyces cerevisiae ERG5 Delta ERG4 Delta ERG3 Delta, molecular mechanism, and its application in corn ethanol production.", "token_count": 125, "char_count": 523, "word_count": 68, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "ERG4", "ERG3", "ERG5" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:46.278529", "source": { "split": "train_shard_00000", "doc_id": 1431 }, "chunk_id": "train_shard_00000_1431_0", "global_id": 1581 }, { "text": "Probiotics have been reported to influence the gut microbiota and immune system in various diseases. Now, the potential impacts of probiotics on tumor treatment still need to be investigated. In this study, three strains of probiotics, Bifidobacterium breve BBr60 (BBr60), Pediococcus pentosaceus PP06 (PP06), and Bifidobacterium longum subsp. longum BL21 (BL21) were investigated for their combination with chemotherapeutic drugs doxorubicin (DOX). Our study showed that PP06 and BL21 have good performance in gastric acid, bile salt, and intestinal fluid tolerance, antimicrobial activity to pathogenic Staphylococcus aureus, and adhesion to Caco-2 cells. Besides, the probiotics all exhibited antioxidant effect, especially BL21. In vitro cytotoxicity and in vivo animal studies revealed that probiotics used alone could not directly induce anti-tumor effects, but the combination of PP06/BL21 and DOX exhibits a higher inhibition rate than DOX alone, via recruitment and infiltration of immune cells in the tumor region. After 16S rRNA analysis of fecal samples from animal models, it was found that BL21 could increase the abundance of Akkermansia, which may also play a role in regulating the tumor microenvironment to improve immune response. In conclusion, BL21 and PP06 in this study could enhance the anti-tumor efficacy by influencing the gut microbiota and tumor immune microenvironment.\n\nProbiotics Influence Gut Microbiota and Tumor Immune Microenvironment to Enhance Anti-Tumor Efficacy of Doxorubicin.", "token_count": 422, "char_count": 1517, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [ "BL21", "PP06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:46.907105", "source": { "split": "train_shard_00000", "doc_id": 1432 }, "chunk_id": "train_shard_00000_1432_0", "global_id": 1582 }, { "text": "Probiotics have a cholesterol-lowering effect. Multi-strain probiotics (MSPs) outperformed single-strain probiotics due to the interaction of strains. Hence, we expect to develop a high-efficiency MSP for lowering cholesterol. Three strains, including Lactobacillus caseiS1, Enterococcus faeciumS4, and L. harbinensisS6, were used to develop the MSPs. To evaluate their effect, gastrointestinal tolerance, bile salt hydrolase (BSH) activity, cholesterol-lowering rate, antioxidant ability, gamma-aminobutyric acid (GABA) production, and antibiotic sensitivity were determined. The triple lactic acid bacteria probiotic (TLP) was the most efficient one. After 24 h treatment with artificial gastric fluid, 47.88% of TLP survived. TLP exhibited the highest BSH activity (149.40 U·ml-1) and cholesterol-lowering rate (75.05%) in vitro, with co-precipitation reducing the majority of cholesterol. The reducing power and superoxide radical scavenging rate of the cell-free supernatant and the hydroxyl radical scavenging rate in viable cells were 1.52, 85.03%, and 89.66%, respectively, and the GABA production was 0.67 mg·ml-1, which enhanced the health benefit effects. By fuzzy mathematical analysis, TLP was the optimal probiotic and was competitive with commercial probiotics. The three strains were susceptible to 13 antibiotics. Therefore, TLP has the potential to develop into a cholesterol-lowering probiotic preparation.\n\nDevelopment and properties evaluation of multi-strain probiotic with cholesterol-lowering potential in vitro.", "token_count": 451, "char_count": 1536, "word_count": 200, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:47.565504", "source": { "split": "train_shard_00000", "doc_id": 1433 }, "chunk_id": "train_shard_00000_1433_0", "global_id": 1583 }, { "text": "Understanding the impact of DNA variation on human traits is a fundamental question in human genetics. Variable number tandem repeats (VNTRs) make up ∼3% of the human genome but are often excluded from association analysis owing to poor read mappability or divergent repeat content. Although methods exist to estimate VNTR length from short-read data, it is known that VNTRs vary in both length and repeat (motif) composition. Here, we use a repeat-pangenome graph (RPGG) constructed on 35 haplotype-resolved assemblies to detect variation in both VNTR length and repeat composition. We align population-scale data from the Genotype-Tissue Expression (GTEx) Consortium to examine how variations in sequence composition may be linked to expression, including cases independent of overall VNTR length. We find that 9422 out of 39,125 VNTRs are associated with nearby gene expression through motif variations, of which only 23.4% are accessible from length. Fine-mapping identifies 174 genes to be likely driven by variation in certain VNTR motifs and not overall length. We highlight two genes,\n\nThe motif composition of variable number tandem repeats impacts gene expression.", "token_count": 282, "char_count": 1174, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:48.138226", "source": { "split": "train_shard_00000", "doc_id": 1434 }, "chunk_id": "train_shard_00000_1434_0", "global_id": 1584 }, { "text": "Whole-genome sequencing (WGS) has revolutionized surveillance of infectious diseases. Disease outbreaks can now be detected with high precision, and correct attribution of infection sources has been improved. Listeriosis, caused by the bacterium Listeria monocytogenes, is a foodborne disease with a high case fatality rate and a large proportion of outbreak-related cases. Timely recognition of listeriosis outbreaks and precise allocation of food sources are important to prevent further infections and to promote public health. We report the WGS-based identification of a large multinational listeriosis outbreak with 55 cases that affected Germany, Austria, Denmark, and Switzerland during 2020 and 2021. Clinical isolates formed a highly clonal cluster (called Ny9) based on core genome multilocus sequence typing (cgMLST). Routine and\n\nLarge Multicountry Outbreak of Invasive Listeriosis by a Listeria monocytogenes ST394 Clone Linked to Smoked Rainbow Trout, 2020 to 2021.", "token_count": 246, "char_count": 979, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7299, "quality_score": 0.865, "entities": { "genes": [ "ST394" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:48.653681", "source": { "split": "train_shard_00000", "doc_id": 1435 }, "chunk_id": "train_shard_00000_1435_0", "global_id": 1585 }, { "text": "Nonalcoholic fatty liver disease (NAFLD) is the most widespread chronic liver disorder globally. Unraveling the pathogenesis of simple fatty liver to nonalcoholic steatohepatitis (NASH) has important clinical significance for improving the prognosis of NAFLD. Here, we explored the role of a high-fat diet alone or combined with high cholesterol in causing NASH progression. Our results demonstrated that high dietary cholesterol intakes accelerate the progression of spontaneous NAFLD and induces liver inflammation in mice. An elevation of hydrophobic unconjugated bile acids cholic acid (CA), deoxycholic acid (DCA), muricholic acid and chenodeoxycholic acid, was observed in high-fat and high-cholesterol diet fed mice. Full-length sequencing of the 16S rDNA gene of gut microbiota revealed a significant increase in the abundance of Bacteroides, Clostridium, and Lactobacillus that possess bile salt hydrolase activity. Furthermore, the relative abundance of these bacterial species was positively correlated with content of unconjugated bile acids in liver. Moreover, the expression of genes related to bile acid reabsorption (organic anion-transporting polypeptides, Na\n\nDietary cholesterol drives the development of nonalcoholic steatohepatitis by altering gut microbiota mediated bile acid metabolism in high-fat diet fed mice.", "token_count": 354, "char_count": 1336, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:49.248872", "source": { "split": "train_shard_00000", "doc_id": 1436 }, "chunk_id": "train_shard_00000_1436_0", "global_id": 1586 }, { "text": "Aflatoxin B1 (AFB1) is one of major pollutant in food and feed worldwide. The purpose of this study is to investigate the mechanism of AFB1-induced liver injury. Our results showed that AFB1 caused hepatic bile duct proliferation, oxidative stress, inflammation and liver injury in mice. AFB1 exposure induced gut microbiota dysbiosis and reduced fecal bile salt hydrolase (BSH) activity. AFB1 exposure promoted hepatic bile acid (BA) synthesis and changed intestinal BA metabolism, especially increased intestinal conjugated bile acids levels. AFB1 exposure inhibited intestinal farnesoid X receptor (FXR)/fibroblast growth factor 15 (FGF-15) signaling. Furthermore, the mice received fecal microbiota transplantation from AFB1-treated mice induced liver injury, reduced intestinal FXR signaling and increased hepatic BA synthesis. Finally, the intestine-restricted FXR agonist treatment decreased hepatic BA synthesis, ROS level, inflammation and liver injury in AFB1-treated mice. This study suggests that modifying the gut microbiota, altering intestinal BA metabolism and/or activating intestinal FXR/FGF-15 signaling may be of value for the treatment of AFB1-induced liver disease.\n\nAflatoxin B1 induces liver injury by disturbing gut microbiota-bile acid-FXR axis in mice.", "token_count": 363, "char_count": 1279, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [ "AFB1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:49.823966", "source": { "split": "train_shard_00000", "doc_id": 1437 }, "chunk_id": "train_shard_00000_1437_0", "global_id": 1587 }, { "text": "Tomato super-pangenome highlights the potential use of wild relatives in tomato breeding.", "token_count": 20, "char_count": 89, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:50.186648", "source": { "split": "train_shard_00000", "doc_id": 1438 }, "chunk_id": "train_shard_00000_1438_0", "global_id": 1588 }, { "text": "Whole genome sequencing (WGS) has greatly improved the detection of methicillin-resistant Staphylococcus aureus (MRSA) transmission between people. We describe the transmission of two unique MRSA clones among homeless people in Copenhagen using WGS and core genome MLST (cgMLST). In 2014, an accumulation of MRSA bacteremia cases among homeless people admitted to our hospital was recognized, all having the rare MRSA spa t5147/ST88. The European Typology of Homelessness and Housing Exclusion (ETHOS) categories revealed that people who inject drugs (PWID) frequently visiting the milieu but living in private accommodation accounted for most cases. Hoping to terminate the transmission, 161 homeless people were MRSA screened in 2015, but no additional cases were found. From 2009 to 2018, 60 patients with genomically related t5147/ST88 isolates were found, of these 70% were confirmed to come from the homeless setting and 17% had bacteremia. From 2017 to 2020, cgMLST revealed a smaller MRSA outbreak including 13 PWID with a completely different clone, t1476/ST8, of which 15% had bacteremia. Our study confirms that WGS and cgMLST is excellent to reveal MRSA outbreaks. The ETHOS categorization can be useful to find the primary source of spread in the homeless community.\n\nWhole genome sequencing reveals two genetically distinct MRSA outbreaks among people who inject drugs and homeless people in Copenhagen.", "token_count": 384, "char_count": 1417, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8278, "entities": { "genes": [ "ST88", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:50.795698", "source": { "split": "train_shard_00000", "doc_id": 1439 }, "chunk_id": "train_shard_00000_1439_0", "global_id": 1589 }, { "text": "Campylobacter species are the major cause of bacterial gastroenteritis. As there is no effective vaccine, combined with the rapid increase in antimicrobial resistant strains, there is a need to identify new targets for intervention. Essential genes are those that are necessary for growth and/or survival, making these attractive targets. In this study, comprehensive transposon mutant libraries were created in six C. jejuni strains, four C. coli strains and one C. lari and C. hyointestinalis strain, allowing for those genes that cannot tolerate a transposon insertion being called as essential. Comparison of essential gene lists using core genome analysis can highlight those genes which are common across multiple strains and/or species. Comparison of C. jejuni and C. coli, the two species that cause the most disease, identified 316 essential genes. Genes of interest highlighted members of the purine pathway being essential for C. jejuni whilst also finding that a functional potassium uptake system is essential. Protein-protein interaction networks using these essential gene lists also highlighted proteins in the purine pathway being major 'hub' proteins which have a large number of interactors across the network. When adding in two more species (C. lari and C. hyointestinalis) the essential gene list reduces to 261. Within these 261 essential genes, there are many genes that have been found to be essential in other bacteria. These include htrB and PEB4, which have previously been found as core virulence genes across Campylobacter species in other studies. There were 21 genes which have no known function with eight of these being associated with the membrane. These surface-associated essential genes may provide attractive targets. The essential gene lists presented will help to prioritise targets for the development of novel therapeutic and preventative interventions.\n\nApplication of TraDIS to define the core essential genome of Campylobacter jejuni and Campylobacter coli.", "token_count": 442, "char_count": 2003, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5233, "quality_score": 0.7617, "entities": { "genes": [ "PEB4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:51.432116", "source": { "split": "train_shard_00000", "doc_id": 1440 }, "chunk_id": "train_shard_00000_1440_0", "global_id": 1590 }, { "text": "Effective utilization of wild relatives is key to overcoming challenges in genetic improvement of cultivated tomato, which has a narrow genetic basis; however, current efforts to decipher high-quality genomes for tomato wild species are insufficient. Here, we report chromosome-scale tomato genomes from nine wild species and two cultivated accessions, representative of Solanum section Lycopersicon, the tomato clade. Together with two previously released genomes, we elucidate the phylogeny of Lycopersicon and construct a section-wide gene repertoire. We reveal the landscape of structural variants and provide entry to the genomic diversity among tomato wild relatives, enabling the discovery of a wild tomato gene with the potential to increase yields of modern cultivated tomatoes. Construction of a graph-based genome enables structural-variant-based genome-wide association studies, identifying numerous signals associated with tomato flavor-related traits and fruit metabolites. The tomato super-pangenome resources will expedite biological studies and breeding of this globally important crop.\n\nSuper-pangenome analyses highlight genomic diversity and structural variation across wild and cultivated tomato species.", "token_count": 256, "char_count": 1225, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6646, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:51.982295", "source": { "split": "train_shard_00000", "doc_id": 1441 }, "chunk_id": "train_shard_00000_1441_0", "global_id": 1591 }, { "text": "Clostridioides difficile infection (CDI) is the major identifiable cause of antibiotic-associated diarrhea and has been declared an urgent threat by the CDC. C. difficile forms dormant and resistant spores that serve as infectious vehicles for CDI. To cause disease, C. difficile spores recognize taurocholate and glycine to trigger the germination process. In contrast to other sporulating bacteria, C. difficile spores are postulated to use a protease complex, CspABC, to recognize its germinants. Since spore germination is required for infection, we have developed anti-germination approaches for CDI prophylaxis. Previously, the bile salt analog CaPA (an aniline-substituted cholic acid) was shown to block spore germination and protect rodents from CDI caused by multiple C. difficile strains and isolates. In this study, we found that CaPA is an alternative substrate inhibitor of C. difficile spore germination. By competing with taurocholate for binding, CaPA delays C. difficile spore germination and reduces spore viability, thus diminishing the number of outgrowing vegetative bacteria. We hypothesize that the reduction of toxin-producing bacterial burden explains CaPA's protective activity against murine CDI. Previous data combined with our results suggests that CaPA binds tightly to C. difficile spores in a CspC-dependent manner and irreversibly traps spores in an alternative, time-delayed, and low yield germination pathway. Our results are also consistent with kinetic data suggesting the existence of at least two distinct bile salt binding sites in C. difficile spores.\n\nMechanism of germination inhibition of Clostridioides difficile spores by an aniline substituted cholate derivative (CaPA).", "token_count": 435, "char_count": 1718, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6189, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:52.608649", "source": { "split": "train_shard_00000", "doc_id": 1442 }, "chunk_id": "train_shard_00000_1442_0", "global_id": 1592 }, { "text": "Escherichia coli persistently colonizes the mammalian intestine by mechanisms that are not fully understood. Previously, we found when streptomycin-treated mice were fed E. coli MG1655, the intestine selected for\n\nOmpC-Dependent Bile Tolerance Contributes to E. coli Colonization of the Mammalian Intestine.", "token_count": 94, "char_count": 307, "word_count": 41, "semantic_coherence": 1, "information_density": 0.8293, "quality_score": 0.9146, "entities": { "genes": [ "MG1655" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:52.985883", "source": { "split": "train_shard_00000", "doc_id": 1443 }, "chunk_id": "train_shard_00000_1443_0", "global_id": 1593 }, { "text": "Liposomes composed of soy lecithin (SL) have been studied widely for drug delivery applications. The stability and elasticity of liposomal vesicles are improved by incorporating additives, including edge activators. In this study, we report the effect of sodium taurodeoxycholate (STDC, a bile salt) upon the microstructural characteristics of SL vesicles. Liposomes, prepared by the thin film hydration method, were characterized by dynamic light scattering (DLS), small-angle neutron scattering (SANS), electron microscopy, and rheological techniques. We noticed a reduction in the size of vesicles with the incremental addition of STDC. Initial changes in the size of spherical vesicles were ascribed to the edge-activating action of STDC (0.05 to 0.17 µM). At higher concentrations (0.23 to 0.27 µM), these vesicles transformed into cylindrical structures. Morphological transitions at higher STDC concentrations would have occurred due to its hydrophobic interaction with SL molecules in the bilayer. This was ascertained from nuclear magnetic resonance observations. Whereas shape transitions underscored the deformability of vesicles in the presence of STDC, the consistency of bilayer thickness ruled out any dissociative effect. It was interesting to notice that SL-STDC mixed structures could survive high thermal stress, electrolyte addition, and dilution.\n\nStructural Changes in Liposomal Vesicles in Association with Sodium Taurodeoxycholate.", "token_count": 357, "char_count": 1455, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7065, "quality_score": 0.8532, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:53.562901", "source": { "split": "train_shard_00000", "doc_id": 1444 }, "chunk_id": "train_shard_00000_1444_0", "global_id": 1594 }, { "text": "Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 strains are most prevalent worldwide, other serotypes are also occasionally detected. Herein, we investigated the genomes of two S. suis serotype 1 strains belonging to the clonal complex 1, which were recovered from a human patient and an asymptomatic pig, respectively. The genomes differed in pathotype, virulence-associated gene (VAG) profile, minimum core genome (MCG) typing, and antimicrobial resistance gene content. The porcine serotype 1 strain was sequence type (ST) 237 and MCG1, whereas the human serotype 1 strain was ST105 and MCG ungroupable. Both strains were susceptible to several antibiotics consisting of β-lactams, fluoroquinolones, and chloramphenicol. Resistance to tetracycline, macrolides, and clindamycin was observed, which was attributed to the genes tet(O) and erm(B). Analysis of 99 VAG revealed Hhly3, NisK, NisR, salK/salR, srtG, virB4, and virD4 were absent in both serotype 1. However, the porcine strain lacked sadP (Streptococcal adhesin P), whereas the human strain harbored sadP1. Phylogenetic analysis revealed that human S. suis ST105 strains from Vietnam were genetically the closest to the human serotype 1 strain, whereas porcine S. suis ST11 strains from China and Thailand were genetically the closest to the porcine strain.\n\nGenomic comparison of two Streptococcus suis serotype 1 strains recovered from porcine and human disease cases.", "token_count": 433, "char_count": 1505, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5747, "quality_score": 0.7873, "entities": { "genes": [ "ST105", "ST11", "MCG1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:54.186783", "source": { "split": "train_shard_00000", "doc_id": 1445 }, "chunk_id": "train_shard_00000_1445_0", "global_id": 1595 }, { "text": "Parabacteroides distasonis (P. distasonis) plays an important role in human health, including diabetes, colorectal cancer and inflammatory bowel disease. Here, we show that P. distasonis is decreased in patients with hepatic fibrosis, and that administration of P. distasonis to male mice improves thioacetamide (TAA)- and methionine and choline-deficient (MCD) diet-induced hepatic fibrosis. Administration of P. distasonis also leads to increased bile salt hydrolase (BSH) activity, inhibition of intestinal farnesoid X receptor (FXR) signaling and decreased taurochenodeoxycholic acid (TCDCA) levels in liver. TCDCA produces toxicity in mouse primary hepatic cells (HSCs) and induces mitochondrial permeability transition (MPT) and Caspase-11 pyroptosis in mice. The decrease of TCDCA by P. distasonis improves activation of HSCs through decreasing MPT-Caspase-11 pyroptosis in hepatocytes. Celastrol, a compound reported to increase P. distasonis abundance in mice, promotes the growth of P. distasonis with concomitant enhancement of bile acid excretion and improvement of hepatic fibrosis in male mice. These data suggest that supplementation of P. distasonis may be a promising means to ameliorate hepatic fibrosis.\n\nParabacteroides distasonis ameliorates hepatic fibrosis potentially via modulating intestinal bile acid metabolism and hepatocyte pyroptosis in male mice.", "token_count": 397, "char_count": 1378, "word_count": 185, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:54.801633", "source": { "split": "train_shard_00000", "doc_id": 1446 }, "chunk_id": "train_shard_00000_1446_0", "global_id": 1596 }, { "text": "Odevixibat Treatment Induces Biliary Bile Acid Secretion in Responsive Patients With Bile Salt Export Pump Deficiency.", "token_count": 35, "char_count": 118, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:55.164319", "source": { "split": "train_shard_00000", "doc_id": 1447 }, "chunk_id": "train_shard_00000_1447_0", "global_id": 1597 }, { "text": "Bile salt export pump (ABCB11) deficiency [Progressive familial intrahepatic cholestasis (PFIC2)] is the most common genetic cause of PFIC and is associated with pruritus and progressive liver disease. Surgical biliary diversion or pharmacological [ileal bile acid transporter inhibitor (IBATi)] approaches can be used to block the recirculation of bile acids to the liver. There is a paucity of detailed data on the natural history and, in particular, the longitudinal evolution of bile acid levels to predict treatment response. Cross-sectional data from large international consortia suggested a maximum cutoff value of bile acids after the intervention to predict a successful outcome.\n\nNative liver survival in bile salt export pump deficiency: results of a retrospective cohort study.", "token_count": 189, "char_count": 790, "word_count": 115, "semantic_coherence": 1, "information_density": 0.713, "quality_score": 0.8565, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:55.611182", "source": { "split": "train_shard_00000", "doc_id": 1448 }, "chunk_id": "train_shard_00000_1448_0", "global_id": 1598 }, { "text": "Control of hospital-associated Enterococcus faecium infection is a strenuous task due to the difficulty of identifying transmission routes and the persistence of this nosocomial pathogen despite the implementation of infection control measures that have been successful with other important nosocomial pathogens. This study provides a comprehensive analysis of over 100 E. faecium isolates collected from 66 cancer patients at the University of Arkansas for Medical Sciences (UAMS) between June 2018 and May 2019. In the top-down approach used in this study, we employed, in addition to the 106 E. faecium UAMS isolates, a filtered set of 2,167 E. faecium strains from the GenBank database to assess the current population structure of E. faecium species and, consequently, to identify the lineages associated with our clinical isolates. We then evaluated the antibiotic resistance and virulence profiles of hospital-associated strains from the species pool, focusing on antibiotics of last resort, to establish an updated classification of high-risk and multidrug-resistant nosocomial clones. Further investigation of the clinical isolates collected from UAMS patients using whole-genome sequencing analytical methodologies (core genome multilocus sequence typing [cgMLST], core single nucleotide polymorphism [coreSNP] analysis, and phylogenomics), with the addition of patient epidemiological data, revealed a polyclonal outbreak of three sequence types occurring simultaneously in different patient wards. The integration of genomic and epidemiological data collected from the patients increased our understanding of the relationships and transmission dynamics of the E. faecium isolates. Our study provides new insights into genomic surveillance of E. faecium to assist in monitoring and further limiting the spread of multidrug-resistant E. faecium.\n\nTop-Down Genomic Surveillance Approach To Investigate the Genomic Epidemiology and Antibiotic Resistance Patterns of Enterococcus faecium Detected in Cancer Patients in Arkansas.", "token_count": 464, "char_count": 2035, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5735, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:56.251280", "source": { "split": "train_shard_00000", "doc_id": 1449 }, "chunk_id": "train_shard_00000_1449_0", "global_id": 1599 }, { "text": "The basic principle for treatment of idiopathic diarrhea is to delay transit through the gut in order to promote absorption of electrolytes and water. Under mild conditions bulking agents may suffice. With increasing severity, antidiarrheal pharmaceuticals may be added in a stepwise manner. Bile salt malabsorption is a clear indication for adsorptive resins, while in idiopathic diarrhea peripherally-acting opioid receptor agonists, such as loperamide, is the first-line treatment. Second-line treatment with approved indication for severe diarrhea when other treatment options fail includes opium drops. More advanced treatments are to be used by clinicians with specialist knowledge and experience in the field.\n\n[Pharmacological treatment of idiopathic diarrhea].", "token_count": 182, "char_count": 769, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7358, "quality_score": 0.8679, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:57.527878", "source": { "split": "train_shard_00000", "doc_id": 1450 }, "chunk_id": "train_shard_00000_1450_0", "global_id": 1600 }, { "text": "Application of a core genome sequence typing (cgMLST) pipeline for surveillance of", "token_count": 17, "char_count": 82, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:58.214905", "source": { "split": "train_shard_00000", "doc_id": 1451 }, "chunk_id": "train_shard_00000_1451_0", "global_id": 1601 }, { "text": "This study was to investigate the potential mechanism of triptolide-induced hepatotoxicity. We found a novel and variable role of p53/Nrf2 crosstalk in triptolide-induced hepatotoxic process. Low doses of triptolide led to adaptive stress response without obvious toxicity, while high levels of triptolide caused severe adversity. Correspondingly, at the lower levels of triptolide treatment, nuclear translocation of Nrf2 as well as its downstream efflux transporters multidrug resistance proteins and bile salt export pump expressions were significantly enhanced, so did p53 pathways that also increased; at a toxic concentration, total and nuclear accumulations of Nrf2 decreased, while p53 showed an obvious nuclear translocation. Further studies showed the cross-regulation between p53 and Nrf2 after different concentrations of triptolide treatment. Under mild stress conditions, Nrf2 induced p53 highly expression to maintain the pro-survival outcome, while p53 showed no obvious effect on Nrf2 expression and transcriptional activity. Under high stress conditions, the remaining Nrf2 as well as the largely induced p53 mutually inhibited each other, leading to a hepatotoxic result. Nrf2 and p53 could physically and dynamically interact. Low levels of triptolide enhanced the interaction between Nrf2 and p53. Reversely, p53/Nrf2 complex dissociated at high levels of triptolide treatment. Altogether, variable p53/Nrf2 crosstalk contributes to triptolide-induced self-protection and hepatotoxicity, modulation of which may be a potential strategy for triptolide-induced hepatotoxicity intervention.\n\nVariable p53/Nrf2 crosstalk contributes to triptolide-induced hepatotoxic process.", "token_count": 434, "char_count": 1692, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5804, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:12:58.837312", "source": { "split": "train_shard_00000", "doc_id": 1452 }, "chunk_id": "train_shard_00000_1452_0", "global_id": 1602 }, { "text": "Salmonella Typhimurium (S. Typhimurium) is an important food-borne and zoonotic pathogen that causes salmonellosis. With the development of whole genome sequencing (WGS), genome-based typing has been widely applied to bacteriology. In this study, we investigated genotyping and phylogenetic clusters of S. Typhimurium isolates from humans and animals in different provinces (including Beijing, Shandong, Guangxi, Shaanxi, Henan, and Shanghai) of China during 2009-2018 using multi locus sequence typing (MLST), core genome MLST (cgMLST), whole genome MLST (wgMLST) and single nucleotide polymorphism (SNP) based on WGS. 29 S. Typhimurium isolates from chicken (n = 22), sick pigeon (n = 2), patients (n = 4) and sick swine (n = 1) were tested. MLST analysis showed S. Typhimurium strains were divided into four STs, namely ST19 (n = 14), ST34 (n = 12), ST128 (n = 2) and ST1544 (n = 1). cgMLST and wgMLST divided 29 strains into 27 cgSTs and 29 wgST, respectively. Phylogenetic clustering showed that all isolates were divided into 4 clusters and 4 singletons. SNP analysis was used to examine MLST, cgMLST, wgMLST analysis. Finally, comparisons of MLST, cgMLST, wgMLST, and SNP were analyzed and the results showed their precision increased in order. In summary, genomic typing and phylogenetic relationships of 29 S. Typhimurium strains from different sources in China were analyzed. These findings were beneficial to investigate molecular pathogenesis, bacterial diversity, and traceability analysis of Salmonella.\n\nGenomes-based MLST, cgMLST, wgMLST and SNP analysis of Salmonella Typhimurium from animals and humans.", "token_count": 513, "char_count": 1621, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [ "ST34", "ST128", "ST19", "ST1544" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:12:59.525471", "source": { "split": "train_shard_00000", "doc_id": 1453 }, "chunk_id": "train_shard_00000_1453_0", "global_id": 1603 }, { "text": "Next-generation whole-genome sequencing is essential for high-resolution surveillance of bacterial pathogens, for example, during outbreak investigations or for source tracking and escape variant analysis. However, current global sequencing and bioinformatic bottlenecks and a long time to result with standard technologies demand new approaches. In this study, we investigated whether novel nanopore Q20+ long-read chemistry enables standardized and easily accessible high-resolution typing combined with core genome multilocus sequence typing (cgMLST). We set high requirements for discriminatory power by using the slowly evolving bacterium Bordetella pertussis as a model pathogen. Our results show that the increased raw read accuracy enables the description of epidemiological scenarios and phylogenetic linkages at the level of gold-standard short reads. The same was true for our variant analysis of vaccine antigens, resistance genes, and virulence factors, demonstrating that nanopore sequencing is a legitimate competitor in the area of next-generation sequencing (NGS)-based high-resolution bacterial typing. Furthermore, we evaluated the parameters for the fastest possible analysis of the data. By combining the optimized processing pipeline with real-time basecalling, we established a workflow that allows for highly accurate and extremely fast high-resolution typing of bacterial pathogens while sequencing is still in progress. Along with advantages such as low costs and portability, the approach suggested here might democratize modern bacterial typing, enabling more efficient infection control globally.\n\nReal-Time Nanopore Q20+ Sequencing Enables Extremely Fast and Accurate Core Genome MLST Typing and Democratizes Access to High-Resolution Bacterial Pathogen Surveillance.", "token_count": 381, "char_count": 1797, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6624, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:00.117053", "source": { "split": "train_shard_00000", "doc_id": 1454 }, "chunk_id": "train_shard_00000_1454_0", "global_id": 1604 }, { "text": "Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disease associated with the pathological accumulation of lipids inside hepatocytes. Untreated NAFL can progress to non-alcoholic hepatitis (NASH), followed by fibrosis, cirrhosis, and hepatocellular carcinoma (HCC). The common denominator of the above-mentioned metabolic disorders seems to be insulin resistance, which occurs in NAFLD patients. Obesity is the greatest risk factor for lipid accumulation inside hepatocytes, but a part of the NAFLD patient population has a normal body weight according to the BMI index. Obese people with or without NAFLD have a higher incidence of small intestinal bacterial overgrowth (SIBO), and those suffering from NAFLD show increased intestinal permeability, including a more frequent presence of bacterial overgrowth in the small intestine (SIBO). The health consequences of SIBO are primarily malabsorption disorders (vitamin B12, iron, choline, fats, carbohydrates and proteins) and bile salt deconjugation. Undetected and untreated SIBO may lead to nutrient and/or energy malnutrition, thus directly impairing liver function (e.g., folic acid and choline deficiency). However, whether SIBO contributes to liver dysfunction, decreased intestinal barrier integrity, increased inflammation, endotoxemia and bacterial translocation is not yet clear. In this review, we focus on gut-liver axis and discuss critical points, novel insights and the role of nutrition, lifestyle, pre- and probiotics, medication and supplements in the therapy and prevention of both SIBO and NAFLD.\n\nSmall Intestinal Bacterial Overgrowth and Non-Alcoholic Fatty Liver Disease: What Do We Know in 2023?", "token_count": 430, "char_count": 1681, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6851, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:00.784021", "source": { "split": "train_shard_00000", "doc_id": 1455 }, "chunk_id": "train_shard_00000_1455_0", "global_id": 1605 }, { "text": "Idiosyncratic Drug-Induced Liver Injury (iDILI) represents an actual health challenge, accounting for more than 40% of hepatitis cases in adults over 50 years and more than 50% of acute fulminant hepatic failure cases. In addition, approximately 30% of iDILI are cholestatic (drug-induced cholestasis (DIC)). The liver's metabolism and clearance of lipophilic drugs depend on their emission into the bile. Therefore, many medications cause cholestasis through their interaction with hepatic transporters. The main canalicular efflux transport proteins include: 1. the bile salt export pump (BSEP) protein (\n\nMolecular and Clinical Links between Drug-Induced Cholestasis and Familial Intrahepatic Cholestasis.", "token_count": 201, "char_count": 708, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8247, "quality_score": 0.9124, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:01.270068", "source": { "split": "train_shard_00000", "doc_id": 1456 }, "chunk_id": "train_shard_00000_1456_0", "global_id": 1606 }, { "text": "Social diversification in microbes is an evolutionary process where lineages bifurcate into distinct populations that cooperate with themselves but not with other groups. In bacteria, this is frequently driven by horizontal transfer of mobile genetic elements (MGEs). Here, the resulting acquisition of new genes changes the recipient's social traits and consequently how they interact with kin. These changes include discriminating behaviors mediated by newly acquired effectors. Since the producing cell is protected by cognate immunity factors, these selfish elements benefit from selective discrimination against recent ancestors, thus facilitating their proliferation and benefiting the host. Whether social diversification benefits the population at large is less obvious. The widespread use of next-generation sequencing has recently provided new insights into population dynamics in natural habitats and the roles MGEs play. MGEs belong to accessory genomes, which often constitute the majority of the pangenome of a taxon, and contain most of the kin-discriminating loci that fuel rapid social diversification. We further discuss mechanisms of diversification and its consequences to populations and conclude with a case study involving myxobacteria.\n\nSocial Diversification Driven by Mobile Genetic Elements.", "token_count": 257, "char_count": 1318, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7127, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:01.830870", "source": { "split": "train_shard_00000", "doc_id": 1457 }, "chunk_id": "train_shard_00000_1457_0", "global_id": 1607 }, { "text": "Lactic acid bacteria (LAB) are widely used probiotics and offer promising prospects for increasing the viability of honeybees. Thus, the probiotic potential of 10 LAB strains was determined, which in our previous studies showed the most potent protective abilities. In the current study, we investigated various properties of probiotic candidates. The tested LAB strains varied in susceptibility to tested antibiotics. Isolates showed high viability in sugar syrups and gastrointestinal conditions. None of the LAB strains exhibited β-hemolytic activity, mutual antagonism, mucin degradation, hydrogen peroxide production capacity, or bile salt hydrolase (BSH) activity. Additionally, the cytotoxicity of LAB cell-free supernatants (CFS) was assessed, as well as the effect of CFS from\n\nCharacterization and Protective Properties of Lactic Acid Bacteria Intended to Be Used in Probiotic Preparation for Honeybees (", "token_count": 228, "char_count": 914, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6953, "quality_score": 0.8477, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:02.298118", "source": { "split": "train_shard_00000", "doc_id": 1458 }, "chunk_id": "train_shard_00000_1458_0", "global_id": 1608 }, { "text": "In recent years, the widespread use of antibiotics in intensive grouper mariculture has resulted in the ineffectiveness of antibiotic treatment, leading to an increasing incidence of diseases caused by bacteria, viruses, and parasites, causing serious economic losses. Hence, it is crucial to develop alternative strategies to antibiotics for healthy and sustainable development of the mariculture industry. Here, we aimed to screen host gut-derived probiotics and evaluate its effects on growth and immunity of grouper. In this study, 43 bacterial strains were isolated from the intestine of the hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂), and a potential probiotic strain G1-26, which can efficiently secrete amylase, protease, and lipase, was obtained using different screening mediums. Based on 16S rDNA sequencing, the potential probiotic strain G1-26 was identified as Vibrio fluvialis. The results of a biological characteristic evaluation showed that V. fluvialis G1-26 could grow at 25-45 °C, pH 5.5-7.5, salinity 10-40, and bile salt concentration 0-0.030%, and produce amylase, lipase, and protease under different culture conditions. Additionally, V. fluvialis G1-26 is sensitive to many antibiotics and does not exhibit aquatic biotoxicity. Subsequently, hybrid groupers were fed diets containing V. fluvialis G1-26 at different concentrations (0, 10\n\nScreening of host gut-derived probiotics and effects of feeding probiotics on growth, immunity, and antioxidant enzyme activity of hybrid grouper (Epinephelus fuscoguttatus♀ × E. lanceolatus♂).", "token_count": 437, "char_count": 1577, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6773, "quality_score": 0.8386, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:02.927060", "source": { "split": "train_shard_00000", "doc_id": 1459 }, "chunk_id": "train_shard_00000_1459_0", "global_id": 1609 }, { "text": "The genome sequence of the diploid and highly homozygous Vitis vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements to the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, being nearly homozygous, this genome contains several heterozygous regions that are yet to be resolved. Taking the opportunity of improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased with a total number decreasing from 2,059 to 640 and a reduction in N bases of 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the number of unplaced scaffolds was reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis. Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation of 35,230 genes to date. Finally, we demonstrated that PN40024 resulted from 9 selfings of cv. \"Helfensteiner\" (cross of cv. \"Pinot noir\" and \"Schiava grossa\") instead of a single \"Pinot noir\". These advances will help maintain the PN40024 genome as a gold-standard reference, also contributing toward the eventual elaboration of the grapevine pangenome.\n\nAn improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.", "token_count": 474, "char_count": 1819, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6053, "quality_score": 0.8026, "entities": { "genes": [ "PN40024", "PN12X" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:03.568414", "source": { "split": "train_shard_00000", "doc_id": 1460 }, "chunk_id": "train_shard_00000_1460_0", "global_id": 1610 }, { "text": "Rice Gene Index: A comprehensive pan-genome database for comparative and functional genomics of Asian rice.", "token_count": 22, "char_count": 107, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:03.932424", "source": { "split": "train_shard_00000", "doc_id": 1461 }, "chunk_id": "train_shard_00000_1461_0", "global_id": 1611 }, { "text": "Bile salt hydrolases (BSHs) are currently being investigated as target enzymes for metabolic regulators in humans and as growth promoters in farm animals. Understanding structural features underlying substrate specificity is necessary for inhibitor design. Here, we used a multidisciplinary workflow including mass spectrometry, mutagenesis, molecular dynamic simulations, machine learning, and crystallography to demonstrate substrate specificity in Lactobacillus salivarius BSH, the most abundant enzyme in human and farm animal intestines. We show the preference of substrates with a taurine head and a dehydroxylated sterol ring for hydrolysis. A regression model that correlates the relative rates of hydrolysis of various substrates in various enzyme mutants with the residue-substrate interaction energies guided the identification of structural determinants of substrate binding and specificity. In addition, we found T208 from another BSH protomer regulating the hydrolysis. The designed workflow can be used for fast and comprehensive characterization of enzymes with a broad range of substrates.\n\nCharacterization of the mechanism of bile salt hydrolase substrate specificity by experimental and computational analyses.", "token_count": 272, "char_count": 1230, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:04.494253", "source": { "split": "train_shard_00000", "doc_id": 1462 }, "chunk_id": "train_shard_00000_1462_0", "global_id": 1612 }, { "text": "Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is essential to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales. Isolates were collected between 2008 and 2020 from sites <60 km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared 'backbones', with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid 'backbones' were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies.\n\nEnterobacterales plasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK.", "token_count": 410, "char_count": 1744, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7195, "quality_score": 0.8597, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:05.110429", "source": { "split": "train_shard_00000", "doc_id": 1463 }, "chunk_id": "train_shard_00000_1463_0", "global_id": 1613 }, { "text": "Because nontuberculous mycobacterial pulmonary disease is a considerable health burden, a simple and clinically applicable analytical protocol enabling the identification of subspecies and drug-resistant disease is required to determine the treatment strategy. We aimed to develop a simplified workflow consisting only of direct sequencing of mycobacterial growth indicator tube cultures (MGIT-seq). In total, 138 patients were prospectively enrolled between April 2021 and May 2022, and culture-positive MGIT broths were subjected to sequencing using MinION, a portable next-generation sequencer. Sequence analysis was conducted to identify species using core genome multilocus sequence typing and to predict macrolide and amikacin (AMK) resistance based on previously reported mutations in\n\nMGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study.", "token_count": 212, "char_count": 897, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7542, "quality_score": 0.8771, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:05.573344", "source": { "split": "train_shard_00000", "doc_id": 1464 }, "chunk_id": "train_shard_00000_1464_0", "global_id": 1614 }, { "text": "Here we review two connected themes in evolutionary microbiology: (\n\nTransporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.", "token_count": 39, "char_count": 159, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:05.940447", "source": { "split": "train_shard_00000", "doc_id": 1465 }, "chunk_id": "train_shard_00000_1465_0", "global_id": 1615 }, { "text": "Recurrent cases of Clostridioides difficile infection (rCDI) remain one of the most common and serious challenges faced in the management of CDI. The accurate distinction between a relapse (caused by infection with the same strain) and reinfection (caused by a new strain) has implications for infection control and prevention, and patient therapy. Here, we used whole-genome sequencing to investigate the epidemiology of 94 C. difficile isolates from 38 patients with rCDI in Western Australia. The C. difficile strain population comprised 13 sequence types (STs) led by ST2 (PCR ribotype (RT) 014, 36.2%), ST8 (RT002, 19.1%) and ST34 (RT056, 11.7%). Among 38 patients, core genome SNP (cgSNP) typing found 27 strains (71%) from initial and recurring cases differed by ≤ 2 cgSNPs, suggesting a likely relapse of infection with the initial strain, while eight strains differed by ≥ 3 cgSNPs, suggesting reinfection. Almost half of patients with CDI relapse confirmed by WGS suffered episodes that occurred outside the widely used 8-week cut-off for defining rCDI. Several putative strain transmission events between epidemiologically unrelated patients were identified. Isolates of STs 2 and 34 from rCDI cases and environmental sources shared a recent evolutionary history, suggesting a possible common community reservoir. For some rCDI episodes caused by STs 2 and 231, within-host strain diversity was observed, characterised by loss/gain of moxifloxacin resistance. Genomics improves discrimination of relapse from reinfection and identifies putative strain transmission events among patients with rCDI. Current definitions of relapse and reinfection based on the timing of recurrence need to be reconsidered.\n\nGenomic epidemiology and transmission dynamics of recurrent Clostridioides difficile infection in Western Australia.", "token_count": 472, "char_count": 1832, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [ "ST2", "RT056", "RT002", "ST8", "ST34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:06.574878", "source": { "split": "train_shard_00000", "doc_id": 1466 }, "chunk_id": "train_shard_00000_1466_0", "global_id": 1616 }, { "text": "In 2015, an outbreak caused by OXA-48-producing Enterobacteriaceae affected a neonatal intensive care unit at a Swedish University Hospital. The aim was to explore the transmission of OXA-48-producing strains between infants and the transfer of resistance plasmids between strains during the outbreak. Twenty-four outbreak isolates from ten suspected cases were whole-genome sequenced. A complete assembly was created for the index isolate (Enterobacter cloacae) and used as a mapping reference to detect its plasmids in the remaining isolates (17 Klebsiella pneumoniae, 4 Klebsiella aerogenes, and 2 Escherichia coli). Strain typing was performed using core genome MLST and SNP analysis. As judged from sequencing and clinical epidemiological data, the outbreak involved nine cases (two developed sepsis) and four OXA-48-producing strains: E. cloacae ST1584 (index case), K. pneumoniae ST25 (eight cases), K. aerogenes ST93 (two cases), and E. coli ST453 (2 cases). Two plasmids from the index strain, pEclA2 and pEclA4, carrying bla\n\nOutbreak of OXA-48-producing Enterobacteriaceae in a neonatal intensive care unit in Western Sweden.", "token_count": 326, "char_count": 1136, "word_count": 163, "semantic_coherence": 1, "information_density": 0.681, "quality_score": 0.8405, "entities": { "genes": [ "ST25", "ST1584", "ST453", "ST93" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:07.146361", "source": { "split": "train_shard_00000", "doc_id": 1467 }, "chunk_id": "train_shard_00000_1467_0", "global_id": 1617 }, { "text": "Pangenome profiling of novel drug target against vancomycin-resistant", "token_count": 17, "char_count": 69, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:07.505657", "source": { "split": "train_shard_00000", "doc_id": 1468 }, "chunk_id": "train_shard_00000_1468_0", "global_id": 1618 }, { "text": "Despite widespread vaccination, Bordetella pertussis continues to cause pertussis infections worldwide, leaving infants at the highest risk of severe illness and death, while people around them are likely the main sources of infection and rapidly spread the disease. Rapid and less complex molecular testing for the specific and timely diagnosis of pertussis remains a challenge that could help to prevent the disease from worsening and prevent its transmission. We aimed to develop and validate a colorimetric loop-mediated isothermal amplification (LAMP) assay using a new target uvrD_2 informed by the pangenome for the specific and early detection of B. pertussis. Compared to that of multitarget quantitative polymerase chain reaction (multitarget qPCR) using a large clinical DNA specimen (n = 600), the diagnostic sensitivity and specificity of the uvrD_2 LAMP assay were 100.0% and 98.6%, respectively, with a 99.7% degree of agreement between the two assays. The novel colorimetric uvrD_2 LAMP assay is highly sensitive and specific for detecting B. pertussis DNA in nasopharyngeal swabs and showed similar diagnostic accuracy to complex and high-cost multitarget qPCR, but it is faster, simpler, and inexpensive, which makes it very helpful for the reliable and timely diagnosis of pertussis in primary health care and resource-limited settings.\n\nA pangenome approach-based loop-mediated isothermal amplification assay for the specific and early detection of Bordetella pertussis.", "token_count": 364, "char_count": 1490, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6175, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:08.081501", "source": { "split": "train_shard_00000", "doc_id": 1469 }, "chunk_id": "train_shard_00000_1469_0", "global_id": 1619 }, { "text": "Five Gram-stain-positive, aerobic, non-motile actinobacterial strains designated as CPCC 205763\n\nPangenome analysis of the genus", "token_count": 44, "char_count": 128, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:08.442354", "source": { "split": "train_shard_00000", "doc_id": 1470 }, "chunk_id": "train_shard_00000_1470_0", "global_id": 1620 }, { "text": "Bulevirtide (BLV) is an entry inhibitor blocking entry of HBsAg into hepatocytes by interfering with the bile acid transporter Na+-taurocholate co-transporting polypeptide. We here investigated if bile acid levels before or during BLV treatment would correlate with HDV RNA declines. We studied 20 patients with compensated HDV infection receiving a daily dose of 2 mg bulevirtide subcutaneously qd for at least 24 weeks. ALT levels improved in all patients including 13/20 patients showing normal ALT values at treatment Week 24. An HDV RNA drop of at least 50% was evident in 20/20 patients at Week 24 including 10 patients showing a ≥ 2 log HDV RNA decline. Elevated bile acid levels were detected already before treatment in 10 patients and further increased during BLV administration with different kinetics. Baseline bile acids were associated with higher transient elastography values (p = .0029) and evidence of portal hypertension (p = .0004). Bile acid levels before treatment were associated with HDV RNA declines throughout therapy, but not at Week 24 (rho = -0.577; p = .0078; rho = -0.635, p = .0026; rho = -0.577, p = .0077; rho = -0.519, p = .0191; rho = -0.564, p = .0119 and rho = -0.393, p = .087 at treatment Weeks 2, 8, 12, 16, 20 and 24, respectively). However, bile acid increases during treatment were not associated with HDV RNA or ALT declines at any of the time points", "token_count": 497, "char_count": 1395, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5466, "quality_score": 0.7733, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:09.102679", "source": { "split": "train_shard_00000", "doc_id": 1471 }, "chunk_id": "train_shard_00000_1471_0", "global_id": 1621 }, { "text": "BLV-induced increases in bile salts do not correlate with HDV RNA declines suggesting that the inhibitory effects of BLV on NTCP differ between blocking bile acid transport and hindering HBsAg entry. If baseline bile salt levels could be useful to predict virological response remains to be confirmed.\n\nBile acid increase during bulevirtide treatment of hepatitis D is not associated with a decline in HDV RNA.", "token_count": 99, "char_count": 410, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8308, "quality_score": 0.9154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:09.480597", "source": { "split": "train_shard_00000", "doc_id": 1471 }, "chunk_id": "train_shard_00000_1471_1", "global_id": 1622 }, { "text": "The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are currently circulating worldwide due to the fastidious nature of the bacteria and the difficulty to isolate cultures. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Our understanding of the genetic diversity of strains during human infection is therefore limited.\n\nCore genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing.", "token_count": 153, "char_count": 706, "word_count": 101, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:09.921282", "source": { "split": "train_shard_00000", "doc_id": 1472 }, "chunk_id": "train_shard_00000_1472_0", "global_id": 1623 }, { "text": "Galactolipids are the main lipids from plant photosynthetic membranes and they can be digested by pancreatic lipase related protein 2 (PLRP2), an enzyme found in the pancreatic secretion in many animal species. Here, we used transmission Fourier-transform infrared spectroscopy (FTIR) to monitor continuously the hydrolysis of galactolipids by PLRP2, in situ and in real time. The method was first developed with a model substrate, a synthetic monogalactosyl diacylglycerol with 8-carbon acyl chains (C8-MGDG), in the form of mixed micelles with a bile salt, sodium taurodeoxycholate (NaTDC). The concentrations of the residual substrate and reaction products (monogalactosylmonoglyceride, MGMG; monogalactosylglycerol, MGG; octanoic acid) were estimated from the carbonyl and carboxylate vibration bands after calibration with reference standards. The results were confirmed by thin layer chromatography analysis (TLC) and specific staining of galactosylated compounds with thymol and sulfuric acid. The method was then applied to the lipolysis of more complex substrates, a natural extract of MGDG with long acyl chains, micellized with NaTDC, and intact chloroplasts isolated from spinach leaves. After a calibration performed with α-linolenic acid, the main fatty acid (FA) found in plant galactolipids, FTIR allowed quantitative measurement of chloroplast lipolysis by PLRP2. A full release of FA from membrane galactolipids was observed, that was not dependent on the presence of bile salts. Nevertheless, the evolution of amide vibration band in FTIR spectra suggested the interaction of membrane proteins with NaTDC and lipolysis products.\n\nIn situ monitoring of galactolipid digestion by infrared spectroscopy in both model micelles and spinach chloroplasts.", "token_count": 477, "char_count": 1767, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6466, "quality_score": 0.8233, "entities": { "genes": [ "PLRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:10.565226", "source": { "split": "train_shard_00000", "doc_id": 1473 }, "chunk_id": "train_shard_00000_1473_0", "global_id": 1624 }, { "text": "A major outbreak of the globally significant Salmonella Enteritidis foodborne pathogen was identified within a large clinical data set by a program of routine WGS of clinical presentations of salmonellosis in New South Wales, Australia. Pangenome analysis helped to quantify and isolate prophage content within the accessory partition of the pangenome. A prophage similar to Gifsy-1 (henceforth GF-1L) was found to occur in all isolates of the outbreak core SNP cluster, and in three other isolates. Further analysis revealed that the GF-1L prophage carried the\n\nPangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene", "token_count": 179, "char_count": 704, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:11.011903", "source": { "split": "train_shard_00000", "doc_id": 1474 }, "chunk_id": "train_shard_00000_1474_0", "global_id": 1625 }, { "text": "Bile acids (BAs) mediate the crosstalk between human and microbial cells and influence diseases including Clostridioides difficile infection (CDI). While bile salt hydrolases (BSHs) shape the BA pool by deconjugating conjugated BAs, the basis for their substrate selectivity and impact on C. difficile remain elusive. Here we survey the diversity of BSHs in the gut commensals Lactobacillaceae, which are commonly used as probiotics, and other members of the human gut microbiome. We structurally pinpoint a loop that predicts BSH preferences for either glycine or taurine substrates. BSHs with varying specificities were shown to restrict C. difficile spore germination and growth in vitro and colonization in pre-clinical in vivo models of CDI. Furthermore, BSHs reshape the pool of microbial conjugated bile acids (MCBAs) in the murine gut, and these MCBAs can further restrict C. difficile virulence in vitro. The recognition of conjugated BAs by BSHs defines the resulting BA pool, including the expansive MCBAs. This work provides insights into the structural basis of BSH mechanisms that shape the BA landscape and promote colonization resistance against C. difficile.\n\nBile salt hydrolases shape the bile acid landscape and restrict Clostridioides difficile growth in the murine gut.", "token_count": 336, "char_count": 1291, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6166, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:11.614579", "source": { "split": "train_shard_00000", "doc_id": 1475 }, "chunk_id": "train_shard_00000_1475_0", "global_id": 1626 }, { "text": "Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.\n\nComparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus.", "token_count": 466, "char_count": 1852, "word_count": 250, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:12.280703", "source": { "split": "train_shard_00000", "doc_id": 1476 }, "chunk_id": "train_shard_00000_1476_0", "global_id": 1627 }, { "text": "Paenibacillus larvae is the causative agent of American foulbrood (AFB), a devastating disease of honeybee larvae. In the Czech Republic, two large infested regions were recognised. This study aimed to analyse P. larvae strains occurring in the Czech Republic in the years 2016-2017 and to characterise the genetic structure of their population with the use of Enterobacterial Repetitive Intergenic Consensus genotyping (ERIC), multilocus sequence typing (MLST) and whole genome sequence (WGS) analysis. The results were complemented by the analysis of isolates collected in the year 2018 in areas of Slovakia located near the Czechia-Slovakia border. ERIC genotyping revealed that 78.9% of tested isolates belonged to the ERIC II genotype and 21.1% to ERIC I genotype. MLST showed six sequence types with ST10 and ST11 being the most frequent among isolates. Within six isolates we found discrepancies in correlations between MLST and ERIC genotypes. The use of MLST and WGS analysis of isolates revealed that each of the large infested geographic regions had its own dominating P. larvae strains. We assume that these strains represented primary sources of infection in the affected areas. In addition, the sporadic presence of strains identified by core genome analysis as genetically related was unveiled in geographically distant regions suggesting possible human-mediated transmission of AFB.\n\nGenomic analysis of Paenibacillus larvae isolates from the Czech Republic and the neighbouring regions of Slovakia.", "token_count": 386, "char_count": 1515, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8044, "entities": { "genes": [ "ST10", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:12.940304", "source": { "split": "train_shard_00000", "doc_id": 1477 }, "chunk_id": "train_shard_00000_1477_0", "global_id": 1628 }, { "text": "Dextran sulfate sodium (DSS) is commonly used to induce colitis in rats. While the DSS-induced colitis rat model can be used to test new oral drug formulations for the treatment of inflammatory bowel disease, the effect of the DSS treatment on the gastrointestinal tract has not been thoroughly characterized. Additionally, the use of different markers to assess and confirm successful induction of colitis is somewhat inconsistent. This study aimed to investigate the DSS model to improve the preclinical evaluation of new oral drug formulations. The induction of colitis was evaluated based on the disease activity index (DAI) score, colon length, histological tissue evaluation, spleen weight, plasma C-reactive protein, and plasma lipocalin-2. Furthermore, the study investigated how the DSS-induced colitis affected the luminal pH, lipase activity, and concentrations of bile salts, polar lipids, and neutral lipids. For all evaluated parameters, healthy rats were used as a reference. The DAI score, colon length, and histological evaluation of the colon were effective disease indicators in DSS-induced colitis rats, while spleen weight, plasma C-reactive protein, and plasma lipocalin-2 were not. The luminal pH of the colon and bile salt- and neutral lipid concentrations in regions of the small intestine were lower in DSS-induced rats compared to healthy rats. Overall, the colitis model was deemed relevant for investigating ulcerative colitis-specific formulations.\n\nAssessing acute colitis induced by dextran sulfate sodium in rats and its impact on gastrointestinal fluids.", "token_count": 381, "char_count": 1588, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5517, "quality_score": 0.7759, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:13.539474", "source": { "split": "train_shard_00000", "doc_id": 1478 }, "chunk_id": "train_shard_00000_1478_0", "global_id": 1629 }, { "text": "The secondary and tertiary structures of myoglobin were disrupted by sodium dodecyl sulfate (SDS) but were hardly affected by the bile salt, sodium cholate (NaCho). This disruption was induced by the binding of dodecyl sulfate (DS) ions to the protein. In this study, the removal of DS ions bound to the protein was attempted using NaCho. The extent of removal of DS ions was estimated by the restoration of the secondary and tertiary structures of the protein disrupted by SDS. The secondary structural change was followed by monitoring mean residue ellipticity at 222 nm, [θ]\n\nRenaturation of Myoglobin Denatured by Sodium Dodecyl Sulfate by Removal of Dodecyl Sulfate Ions Bound to the Protein Using Sodium Cholate.", "token_count": 205, "char_count": 718, "word_count": 116, "semantic_coherence": 1, "information_density": 0.4914, "quality_score": 0.7457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:14.013653", "source": { "split": "train_shard_00000", "doc_id": 1479 }, "chunk_id": "train_shard_00000_1479_0", "global_id": 1630 }, { "text": "Marine bacterial lineages associated with algal blooms, such as the Roseobacter clade, have been well characterized in ecological and genomic contexts, yet such lineages have rarely been explored in freshwater blooms. This study performed phenotypic and genomic analyses of an alphaproteobacterial lineage 'Candidatus Phycosocius' (denoted the CaP clade), one of the few lineages ubiquitously associated with freshwater algal blooms, and described a novel species: 'Ca. Phycosocius spiralis.' Phylogenomic analyses indicated that the CaP clade is a deeply branching lineage in the Caulobacterales. Pangenome analyses revealed characteristic features of the CaP clade: aerobic anoxygenic photosynthesis and essential vitamin B auxotrophy. Genome size varies widely among members of the CaP clade (2.5-3.7 Mb), likely a result of independent genome reductions at each lineage. This includes a loss of tight adherence pilus genes (tad) in 'Ca. P. spiralis' that may reflect its adoption of a unique spiral cell shape and corkscrew-like burrowing activity at the algal surface. Notably, quorum sensing (QS) proteins showed incongruent phylogenies, suggesting that horizontal transfers of QS genes and QS-involved interactions with specific algal partners might drive CaP clade diversification. This study elucidates the ecophysiology and evolution of proteobacteria associated with freshwater algal blooms.\n\nCharacterization of a bloom-associated alphaproteobacterial lineage, 'Candidatus Phycosocius': insights into freshwater algal-bacterial interactions.", "token_count": 415, "char_count": 1553, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:14.632963", "source": { "split": "train_shard_00000", "doc_id": 1480 }, "chunk_id": "train_shard_00000_1480_0", "global_id": 1631 }, { "text": "Switzerland has one of the highest annual Legionnaires' disease (LD) notification rates in Europe (7.8 cases/100,000 population in 2021). The main sources of infection and the cause for this high rate remain largely unknown. This hampers the implementation of targeted Legionella spp. control efforts. The SwissLEGIO national case-control and molecular source attribution study investigates risk factors and infection sources for community-acquired LD in Switzerland. Over the duration of one year, the study is recruiting 205 newly diagnosed LD patients through a network of 20 university and cantonal hospitals. Healthy controls matched for age, sex, and residence at district level are recruited from the general population. Risk factors for LD are assessed in questionnaire-based interviews. Clinical and environmental Legionella spp. isolates are compared using whole genome sequencing (WGS). Direct comparison of sero- and sequence types (ST), core genome multilocus sequencing types (cgMLST), and single nucleotide polymorphisms (SNPs) between clinical and environmental isolates are used to investigate the infection sources and the prevalence and virulence of different Legionella spp. strains detected across Switzerland. The SwissLEGIO study innovates in combining case-control and molecular typing approaches for source attribution on a national level outside an outbreak setting. The study provides a unique platform for national Legionellosis and Legionella research and is conducted in an inter- and transdisciplinary, co-production approach involving various national governmental and national research stakeholders.\n\nLegionnaires' disease in Switzerland: rationale and study protocol of a prospective national case-control and molecular source attribution study (SwissLEGIO).", "token_count": 389, "char_count": 1792, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:15.254847", "source": { "split": "train_shard_00000", "doc_id": 1481 }, "chunk_id": "train_shard_00000_1481_0", "global_id": 1632 }, { "text": "The Burkholderia cepacia complex (BCC) is a Gram-negative bacterial, including Burkholderia contaminans species. Although the plain Burkholderia is pervasive from taxonomic and genetic perspectives, a common characteristic is that they may use the quorum-sensing (QS) system. In our previous study, we generated the complete genome sequence of Burkholderia contaminans SK875 isolated from the respiratory tract. To our knowledge, this is the first study to report functional genomic features of B. contaminans SK875 for understanding the pathogenic characteristics. In addition, comparative genomic analysis for five B. contaminans genomes was performed to provide comprehensive information on the disease potential of B. contaminans species. Analysis of average nucleotide identity (ANI) showed that the genome has high similarity (> 96%) with other B. contaminans strains. Five B. contaminans genomes yielded a pangenome of 8832 coding genes, a core genome of 5452 genes, the accessory genome of 2128 genes, and a unique genome of 1252 genes. The 186 genes were specific to B. contaminans SK875, including toxin higB-2, oxygen-dependent choline dehydrogenase, and hypothetical proteins. Genotypic analysis of the antimicrobial resistance of B. contaminans SK875 verified resistance to tetracycline, fluoroquinolone, and aminoglycoside. Compared with the virulence factor database, we identified 79 promising virulence genes such as adhesion system, invasions, antiphagocytic, and secretion systems. Moreover, 45 genes of 57 QS-related genes that were identified in B. contaminans SK875 indicated high sequence homology with other B. contaminans strains. Our results will help to gain insight into virulence, antibiotic resistance, and quorum sensing for B. contaminans species.\n\nComprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine.", "token_count": 513, "char_count": 1894, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5649, "quality_score": 0.7824, "entities": { "genes": [ "SK875" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:13:15.905645", "source": { "split": "train_shard_00000", "doc_id": 1482 }, "chunk_id": "train_shard_00000_1482_0", "global_id": 1633 }, { "text": "We found that the flowering time order of accessions in a genetic population considerably varied across environments, and homolog copies of essential flowering time genes played different roles in different locations. Flowering time plays a critical role in determining the life cycle length, yield, and quality of a crop. However, the allelic polymorphism of flowering time-related genes (FTRGs) in Brassica napus, an important oil crop, remains unclear. Here, we provide high-resolution graphics of FTRGs in B. napus on a pangenome-wide scale based on single nucleotide polymorphism (SNP) and structural variation (SV) analyses. A total of 1337 FTRGs in B. napus were identified by aligning their coding sequences with Arabidopsis orthologs. Overall, 46.07% of FTRGs were core genes and 53.93% were variable genes. Moreover, 1.94%, 0.74%, and 4.49% FTRGs had significant presence-frequency differences (PFDs) between the spring and semi-winter, spring and winter, and winter and semi-winter ecotypes, respectively. SNPs and SVs across 1626 accessions of 39 FTRGs underlying numerous published qualitative trait loci were analyzed. Additionally, to identify FTRGs specific to an eco-condition, genome-wide association studies (GWASs) based on SNP, presence/absence variation (PAV), and SV were performed after growing and observing the flowering time order (FTO) of plants in a collection of 292 accessions at three locations in two successive years. It was discovered that the FTO of plants in a genetic population changed a lot across various environments, and homolog copies of some key FTRGs played different roles in different locations. This study revealed the molecular basis of the genotype-by-environment (G × E) effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.\n\nStructural variations and environmental specificities of flowering time-related genes in Brassica napus.", "token_count": 490, "char_count": 1936, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6014, "quality_score": 0.8007, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:16.555956", "source": { "split": "train_shard_00000", "doc_id": 1483 }, "chunk_id": "train_shard_00000_1483_0", "global_id": 1634 }, { "text": "Bile salt hydrolases are thought to be the gatekeepers of bile acid metabolism. To study the role of BSH in colitis, we investigated the ameliorative effects of different BSH-knockout strains of\n\nBile salt hydrolase of", "token_count": 61, "char_count": 218, "word_count": 35, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:16.920685", "source": { "split": "train_shard_00000", "doc_id": 1484 }, "chunk_id": "train_shard_00000_1484_0", "global_id": 1635 }, { "text": "Core genome multilocus sequence typing (cgMLST) employs a strategy where the set of orthologous genes common to all members of a group of organisms are used for phylogenetic analysis of the group members. The Bacillus cereus group consists of species with pathogenicity towards insect species as well as warm-blooded animals including humans. While B. cereus is an opportunistic pathogen linked to a range of human disease conditions, including emesis and diarrhoea, Bacillus thuringiensis is an entomopathogenic species with toxicity toward insect larvae, and therefore used as a biological pesticide worldwide. Bacillus anthracis is a classical obligate pathogen causing anthrax, an acute lethal condition in herbivores as well as humans, and which is endemic in many parts of the world. The group also includes a range of additional species, and B. cereus group bacteria have been subject to analysis with a wide variety of phylogenetic typing systems. Here we present, based on analyses of 173 complete genomes from B. cereus group species available in public databases, the identification of a set of 1568 core genes which were used to create a core genome multilocus typing scheme for the group which is implemented in the PubMLST system as an open online database freely available to the community. The new cgMLST system provides unprecedented resolution over existing phylogenetic analysis schemes covering the B. cereus group.\n\nCore genome multilocus sequence typing scheme for Bacillus cereus group bacteria.", "token_count": 364, "char_count": 1518, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5494, "quality_score": 0.7747, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:17.501427", "source": { "split": "train_shard_00000", "doc_id": 1485 }, "chunk_id": "train_shard_00000_1485_0", "global_id": 1636 }, { "text": "Strain CAU 1641T was isolated from saltern collected in Ganghwa Island, Republic of Korea. The bacterium was an aerobic, Gram-negative, catalase-positive, oxidase-positive, motile, and rod-shaped bacterium. Cell of strain CAU 1641T could grow at 20-40°C and pH 6.0-9.0 with 1.0-3.0% (w/v) NaCl. Stain CAU 1641T shared high 16S rRNA gene sequence similarities with Defluviimonas aquaemixtae KCTC 42108T (98.0%), Defluviimonas denitrificans DSM 18921T (97.6%), and Defluviimonas aestuarii KACC 16442T (97.5%). Phylogenetic trees based on the 16S rRNA gene and the core-genome sequences indicated that strain CAU 1641T belonged to genus Defluviimonas. Strain CAU 1641T contained ubiquinone-10 (Q-10) as the sole respiratory quinone and and summed feature 8 (C18:1ω6c and/or C18:1ω7c) as the predominant fatty acid (86.1%). The pan-genome analysis indicated that the genomes of the strain CAU 1641T and 15 reference strains contain a small core genome. The Average Nucleotide Identity and digital DNA-DNA hybridization values among strain CAU 1641T and reference strains of the genus Defluviimonas were in the range of 77.6%-78.8% and 21.1-22.1%, respectively. The genome of strain CAU 1641T has several genes of benzene degradation. The genomic G + C content was 66.6%", "token_count": 486, "char_count": 1265, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6595, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:18.142952", "source": { "split": "train_shard_00000", "doc_id": 1486 }, "chunk_id": "train_shard_00000_1486_0", "global_id": 1637 }, { "text": "Based on polyphasic and genomic analyses, strain CAU 1641T represents a novel species of the genus Defluviimonas, for which the name Defluviimonas salinarum sp. nov., is proposed. The type strain is CAU 1641T ( = KCTC 92081T = MCCC 1K07180T).\n\nDescription of Defluviimonas salinarum sp. nov. with the potential of benzene-degradation isolated from saltern in the Yellow Seacoast.", "token_count": 133, "char_count": 379, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:18.564149", "source": { "split": "train_shard_00000", "doc_id": 1486 }, "chunk_id": "train_shard_00000_1486_1", "global_id": 1638 }, { "text": "Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than\n\nChallenges and opportunities of strain diversity in gut microbiome research.", "token_count": 106, "char_count": 520, "word_count": 80, "semantic_coherence": 1, "information_density": 0.775, "quality_score": 0.8875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:18.942912", "source": { "split": "train_shard_00000", "doc_id": 1487 }, "chunk_id": "train_shard_00000_1487_0", "global_id": 1639 }, { "text": "Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species' divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species' pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.\n\nEcological divergence of syntopic marine bacterial species is shaped by gene content and expression.", "token_count": 297, "char_count": 1374, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [ "NAC11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:19.511385", "source": { "split": "train_shard_00000", "doc_id": 1488 }, "chunk_id": "train_shard_00000_1488_0", "global_id": 1640 }, { "text": "As the two most widely used Kluyveromyces yeast, Kluyveromyces marxianus and K. lactis have gained increasing attention as microbial chassis in biocatalysts, biomanufacturing and the utilization of low-cost raw materials owing to their high suitability to these applications. However, due to slow progress in the development of molecular genetic manipulation tools and synthetic biology strategies, Kluyveromyces yeast cell factories as biological manufacturing platforms have not been fully developed. In this review, we provide a comprehensive overview of the attractive characteristics and applications of Kluyveromyces cell factories, with special emphasis on the development of molecular genetic manipulation tools and systems engineering strategies for synthetic biology. In addition, future avenues in the development of Kluyveromyces cell factories for the utilization of simple carbon compounds as substrates, the dynamic regulation of metabolic pathways, and for rapid directed evolution of robust strains are proposed. We expect that more synthetic systems, synthetic biology tools and metabolic engineering strategies will adapt to and optimize for Kluyveromyces cell factories to achieve green biofabrication of multiple products with higher efficiency.\n\nKluyveromyces as promising yeast cell factories for industrial bioproduction: From bio-functional design to applications.", "token_count": 289, "char_count": 1389, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:20.064334", "source": { "split": "train_shard_00000", "doc_id": 1489 }, "chunk_id": "train_shard_00000_1489_0", "global_id": 1641 }, { "text": "This paper investigates the mutual interactions between lipids and red wine polyphenols at different stages of the gastrointestinal tract by using the simgi® dynamic simulator. Three food models were tested: a Wine model, a Lipid model (olive oil + cholesterol) and a Wine + Lipid model (red wine + olive oil + cholesterol). With regard to wine polyphenols, results showed that co-digestion with lipids slightly affected the phenolic profile after gastrointestinal digestion. In relation to lipid bioaccessibility, the co-digestion with red wine tended to increase the percentage of bioaccessible monoglycerides, although significant differences were not found (p > 0.05). Furthermore, co-digestion with red wine tended to reduce cholesterol bioaccessibility (from 80 to 49 %), which could be related to the decrease in bile salt content observed in the micellar phase. For free fatty acids, almost no changes were observed. At the colonic level, the co-digestion of red wine and lipids conditioned the composition and metabolism of colonic microbiota. For instance, the growth [log (ufc/mL)] of lactic acid bacteria (6.9 ± 0.2) and bifidobacteria (6.8 ± 0.1) populations were significantly higher for the Wine + Lipid food model respect to the control colonic fermentation (5.2 ± 0.1 and 5.3 ± 0.2, respectively). Besides, the production of total SCFAs was greater for the Wine + Lipid food model. Also, the cytotoxicity of the colonic-digested samples towards human colon adenocarcinoma cells (HCT-116 and HT-29) was found to be significantly lower for the Wine and Wine + Lipid models than for the Lipid model and the control (no food addition). Overall, the results obtained using the simgi® model were consistent with those reported in vivo in the literature", "token_count": 491, "char_count": 1763, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5657, "quality_score": 0.7828, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:20.717089", "source": { "split": "train_shard_00000", "doc_id": 1490 }, "chunk_id": "train_shard_00000_1490_0", "global_id": 1642 }, { "text": "In particular, they suggest that red wine may favourably modulate lipid bioaccessibility - a fact that could explain the hypocholesterolemic effects of red wine and red wine polyphenols observed in humans.\n\nDeciphering the interactions between lipids and red wine polyphenols through the gastrointestinal tract.", "token_count": 72, "char_count": 311, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:21.084767", "source": { "split": "train_shard_00000", "doc_id": 1490 }, "chunk_id": "train_shard_00000_1490_1", "global_id": 1643 }, { "text": "In this study, hypolipidemic peptides were obtained from tea protein by enzymatic hydrolysis, ultrafiltration and high-performance liquid chromatography. Subsequently, the hypolipidemic peptides were identified by mass spectrometry and screened through molecular docking technology, and the hypolipidemic activities and mechanisms of the active peptides were explored. The results showed that the hydrolysate of hypolipidemic peptides obtained by pepsin hydrolysis for 3 h had good bile salt binding ability. After purification, identification and molecular docking screening, three novel hypolipidemic peptides FLF, IYF and QIF were obtained. FLF, IYF and QIF can interact with the receptor proteins 1LPB and 1F6W through hydrogen bonds, π-π bonds, hydrophobic interactions and van der Waals forces, thus exerting hypolipidemic activities. Activity studies showed that, compared with the positive controls, FLF, IYF and QIF had excellent sodium taurocholate binding abilities, pancreatic lipase inhibitory activities and cholesterol esterase inhibitory activities. Moreover, FLF, IYF and QIF can effectively inhibit lipogenic differentiation of 3T3-L1 preadipocytes, reduce intracellular lipid and low-density lipoprotein content and increase high-density lipoprotein content. These results indicated that the three novel hypolipidemic peptides screened in this study had excellent hypolipidemic activities and were expected to be used as natural-derived hypolipidemic active ingredients for the development and application in functional foods.\n\nPurification, identification and hypolipidemic activities of three novel hypolipidemic peptides from tea protein.", "token_count": 417, "char_count": 1660, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:21.715571", "source": { "split": "train_shard_00000", "doc_id": 1491 }, "chunk_id": "train_shard_00000_1491_0", "global_id": 1644 }, { "text": "We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of\n\nIdentifying the core genome of the nucleus-forming bacteriophage family and characterization of", "token_count": 202, "char_count": 874, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6885, "quality_score": 0.8443, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:22.181581", "source": { "split": "train_shard_00000", "doc_id": 1492 }, "chunk_id": "train_shard_00000_1492_0", "global_id": 1645 }, { "text": "High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. Several ongoing pangenome projects are producing collections of high-quality assemblies of various species. Each project has already generated assemblies of hundreds of gigabytes on disk, greatly impeding the distribution of and access to such rich datasets.\n\nAGC: compact representation of assembled genomes with fast queries and updates.", "token_count": 84, "char_count": 451, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8033, "quality_score": 0.9016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:22.565153", "source": { "split": "train_shard_00000", "doc_id": 1493 }, "chunk_id": "train_shard_00000_1493_0", "global_id": 1646 }, { "text": "We tested the hypothesis that Campylobacter isolated from chicken ceca and river water in an overlapping geographic area would share genetic information. Isolates of C. jejuni from chicken ceca were collected from a commercial slaughter plant and isolates of C. jejuni were also collected from rivers and creeks in the same watershed. Isolates were subjected to whole-genome sequencing and the data were used for core genome multilocus sequence typing (cgMLST). Cluster analysis showed that there were four distinct subpopulations, two from chickens and two from water. Calculation of fixation statistic (Fst) showed that all four subpopulations were significantly distinct. Greater than 90% of the loci were differentiated by subpopulation. Only two genes showed clear differentiation of both chicken subpopulations from both water subpopulations. Sequence fragments of the CJIE4 bacteriophage family were found frequently in the main chicken subpopulation and the water outgroup subpopulation but were sparsely found in the main water population and not at all in the chicken outgroup. CRISPR spacers that targeted the phage sequences were common in the main water subpopulation, only once in the main chicken subpopulation, and not at all in the chicken or water outgroups. Restriction enzyme genes also showed a biased distribution. These data suggest that there is little transfer of C. jejuni genetic material between chickens and nearby river water. Campylobacter differentiation according to these two sources does not show clear evidence of evolutionary selection; the differentiation is probably due to geospatial isolation, genetic drift, and the action of CRISPRs and restriction enzymes.\n\nDespite Shared Geography, Campylobacter Isolated from Surface Water Are Genetically Distinct from Campylobacter Isolated from Chickens.", "token_count": 411, "char_count": 1837, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5243, "quality_score": 0.7622, "entities": { "genes": [ "CJIE4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:23.186518", "source": { "split": "train_shard_00000", "doc_id": 1494 }, "chunk_id": "train_shard_00000_1494_0", "global_id": 1647 }, { "text": "Long-read sequencing (LRS) facilitates both the genome assembly and the discovery of structural variants (SVs). Here, we built a graph-based pig pangenome by incorporating 11 LRS genomes with an average of 94.01% BUSCO completeness score, revealing 206-Mb novel sequences. We discovered 183,352 nonredundant SVs (63% novel), representing 12.12% of the reference genome. By genotyping SVs in an additional 196 short-read sequencing samples, we identified thousands of population stratified SVs. Particularly, we detected 7,568 Tibetan specific SVs, some of which demonstrate significant population differentiation between Tibetan and low-altitude pigs, which might be associated with the high-altitude hypoxia adaptation in Tibetan pigs. Further integrating functional genomic data, the most promising candidate genes within the SVs that might contribute to the high-altitude hypoxia adaptation were discovered. Overall, our study generates a benchmark pangenome resource for illustrating the important roles of SVs in adaptive evolution, domestication, and genetic improvement of agronomic traits in pigs.\n\nPangenome obtained by long-read sequencing of 11 genomes reveal hidden functional structural variants in pigs.", "token_count": 307, "char_count": 1217, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6909, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:23.784854", "source": { "split": "train_shard_00000", "doc_id": 1495 }, "chunk_id": "train_shard_00000_1495_0", "global_id": 1648 }, { "text": "Nile tilapia is one of the most consumed farmed fish in the world. The outbreak of pathogenic bacterial diseases causes high mortality rates and economic losses in Nile tilapia farming. Antibiotic administrations are commonly utilized to inhibit and prevent bacterial infections. However, antibiotics are expensive and cause serious concerns for antibiotic resistance in fish that can be potentially transferred to humans. As an alternative solution, probiotics can be used to prevent infection of pathogenic bacteria in fish. In this work, both bacteria and yeast were isolated from fish gastrointestinal tracts and their inhibitory activity against Nile tilapia pathogenic bacteria was evaluated, as well as other probiotic properties. In this study, 66 bacteria and 176 acid tolerant yeasts were isolated from fish gastrointestinal tracts. Of all isolated microorganisms, 39 bacterial and 15 yeast isolates with inhibitory effect against pathogens were then examined for their probiotic properties (acidic and bile salt resistance, adhesion potential, and biofilm formation), formation of antibacterial factor survival rate under simulated gastrointestinal fluid, and safety evaluation. AT8/5 bacterial isolate demonstrated probiotic properties and the highest inhibition against all 54 tested pathogens while YON3/2 yeast isolate outperformed the inhibitory effect among all yeast isolates. These two probiotic isolates were further identified by 16S rDNA and the D1/D2 domain of 26S rDNA sequence analysis for bacterial and yeast identification, respectively. AT8/5 and YON3/2 showed the highest similarity to", "token_count": 379, "char_count": 1614, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [ "AT8", "YON3" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:24.394558", "source": { "split": "train_shard_00000", "doc_id": 1496 }, "chunk_id": "train_shard_00000_1496_0", "global_id": 1649 }, { "text": "In this study, biodelignification and enzymatic hydrolysis of elephant grass were performed by recombinant and native strain of Trichoderma reesei, respectively. Initially, rT. reesei displaying Lip8H and MnP1 gene was used for biodelignification with NiO nanoparticles. Saccharification was performed by combining hydrolytic enzyme produced with NiO nanoparticles. Elephant grass hydrolysate was used for bioethanol production using Kluyveromyces marxianus. Maximum lignolytic enzyme production was obtained with 15 µg/L of NiO nanoparticles and initial pH of 5 at 32 °C. Subsequently, about 54% of lignin degradation was achieved after 192 h. Hydrolytic enzymes showed elevated enzyme activity and resulted in 84.52 ± 3.5 g/L of total reducing sugar at 15 µg/mL NiO NPs. About 14.65 ± 1.75 g/L of ethanol was produced using K. marxianus after 24 h. Thus, dual strategy employed for conversion of elephant grass biomass into fermentable sugar and subsequent biofuel production could become potential platform for commercialization.\n\nDual strategy for bioconversion of elephant grass biomass into fermentable sugars using Trichoderma reesei towards bioethanol production.", "token_count": 356, "char_count": 1171, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6205, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:25.007309", "source": { "split": "train_shard_00000", "doc_id": 1497 }, "chunk_id": "train_shard_00000_1497_0", "global_id": 1650 }, { "text": "Adding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of", "token_count": 27, "char_count": 105, "word_count": 15, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:25.408321", "source": { "split": "train_shard_00000", "doc_id": 1498 }, "chunk_id": "train_shard_00000_1498_0", "global_id": 1651 }, { "text": "Cholestasis refers to impaired bile flow from the liver to the intestine. In neonates, cholestasis causes poor growth and may progress to liver failure and death. Normal bile flow requires an intact liver-gut-microbiome axis, whereby liver-derived primary bile acids are transformed into secondary bile acids. Microbial bile salt hydrolase (BSH) enzymes are responsible for the first step, deconjugating glycine- and taurine-conjugated primary bile acids. Cholestatic neonates often are treated with the potent choleretic bile acid ursodeoxycholic acid (UDCA), although interactions between UDCA, gut microbes, and other bile acids are poorly understood. To gain insight into how the liver-gut-microbiome axis develops in extreme prematurity and how cholestasis alters this maturation, we conducted a nested case-control study collecting 124 stool samples longitudinally from 24 preterm infants born at mean 27.2 ± 1.8 weeks gestation and 946 ± 249.6 g, half of whom developed physiologic cholestasis. Samples were analyzed by whole metagenomic sequencing,\n\nCholestasis impairs gut microbiota development and bile salt hydrolase activity in preterm neonates.", "token_count": 338, "char_count": 1158, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7239, "quality_score": 0.862, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:25.980034", "source": { "split": "train_shard_00000", "doc_id": 1499 }, "chunk_id": "train_shard_00000_1499_0", "global_id": 1652 }, { "text": "The mobile tigecycline-resistant gene tet(X4), which confers resistance to all tetracyclines, has been identified in bacterial isolates from various sources. However, there are no reports on the occurrence of tet(X4) in bacterial isolates of ready-to-eat fresh vegetables. In this study, 113 vegetable samples from farmers' markets were screened for tigecycline-resistant strains. Ten Escherichia coli (two ST195, two ST48, and one ST10, ST58, ST88, ST394, ST641, and ST101) and one Klebsiella pneumoniae (ST327) recovered from nine vegetable samples (7.96 %) were identified as carrying tet(X4). The core genome sequences of the two E. coli ST195 isolates showed a close relationship (14-41 single-nucleotide polymorphisms) with 31 tet(X4)-bearing E. coli ST195 isolates from humans, pigs, pork, and bird in China and Thailand, and the 33 E. coli ST195 isolates producing Tet(X4) shared similar resistance genes and plasmid replicons. Nanopore sequencing and conjugation experiments confirmed that the tet(X4) genes were located on the hybrid plasmids IncFIA-HI1A-HI1B (n = 6), IncX1 (n = 3), and IncFII2 (n = 1) in E. coli, and IncFII plasmid in K. pneumoniae. IncFIA-HI1A-HI1B and IncX1 plasmids shared highly similar structures with plasmids from various sources in the GenBank database. This is the first study to report the observation of tet(X4)-positive bacteria in retail vegetables. The epidemic clones and plasmids contribute to tet(X4) dissemination in vegetables. The clonal spread of Tet(X4)-producing E. coli ST195 across multiple niches and countries could pose a potential threat to public health.", "token_count": 511, "char_count": 1614, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8101, "entities": { "genes": [ "HI1B", "ST641", "ST48", "ST88", "HI1A", "ST394", "ST10", "ST327", "ST101", "ST195" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:26.636531", "source": { "split": "train_shard_00000", "doc_id": 1500 }, "chunk_id": "train_shard_00000_1500_0", "global_id": 1653 }, { "text": "First detection of tet(X4)-positive Enterobacterales in retail vegetables and clonal spread of Escherichia coli ST195 producing Tet(X4) in animals, foods, and humans across China and Thailand.", "token_count": 53, "char_count": 192, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [ "ST195" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:27.000473", "source": { "split": "train_shard_00000", "doc_id": 1500 }, "chunk_id": "train_shard_00000_1500_1", "global_id": 1654 }, { "text": "Traditional probiotics comprise mainly lactic acid bacteria that are safe for human use, tolerate acid and bile, and adhere to the epithelial lining and mucosal surfaces. In this study, one hundred commercial and non-commercial strains that were isolated from human feces or vaginal samples were tested with regards to overall growth in culture media, tolerance to acid and bile, hydrogen peroxide (H\n\nIn Vitro Screen of Lactobacilli Strains for Gastrointestinal and Vaginal Benefits.", "token_count": 122, "char_count": 484, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7534, "quality_score": 0.8767, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:27.731878", "source": { "split": "train_shard_00000", "doc_id": 1501 }, "chunk_id": "train_shard_00000_1501_0", "global_id": 1655 }, { "text": "Based on the postulate that glioblastoma (GBM) tumors generate anti-inflammatory prostaglandins and bile salts to gain immune privilege, we analyzed 712 tumors in-silico from three GBM transcriptome databases for prostaglandin and bile synthesis/signaling enzyme-transcript markers. A pan-database correlation analysis was performed to identify cell-specific signal generation and downstream effects. The tumors were stratified by their ability to generate prostaglandins, their competency in bile salt synthesis, and the presence of bile acid receptors nuclear receptor subfamily 1, group H, member 4 (NR1H4) and G protein-coupled bile acid receptor 1 (GPBAR1). The survival analysis indicates that tumors capable of prostaglandin and/or bile salt synthesis are linked to poor outcomes. Tumor prostaglandin D\n\nAcquisition of Immune Privilege in GBM Tumors: Role of Prostaglandins and Bile Salts.", "token_count": 241, "char_count": 896, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [ "GPBAR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:28.215600", "source": { "split": "train_shard_00000", "doc_id": 1502 }, "chunk_id": "train_shard_00000_1502_0", "global_id": 1656 }, { "text": "The study aimed to investigate the effects of guar gum on the growth performance, gut microbiota composition, and hepatic lipid metabolism of largemouth bass (Micropterus salmoides) fed high-fat diets. Experimental fish were fed a normal-fat diet (Control), high-fat diet (HF), or HF diets supplemented with 0.3 %, 1 %, and 3 % guar gum (GG0.3, GG1, and GG3, respectively) for eight weeks. The results showed that HF significantly decreased fish growth performance, increased hepatic lipid accumulation, upregulated the expression of sterol regulatory element binding proteins 1 (SREBP1), and downregulated the expression of liver X receptor alpha (LXRα), cytochrome P450 7A1 (CYP7A1), and CYP8B1, compared to Control. However, these problems of high-fat diets were significantly alleviated by GG 0.3. The intestinal microbial communities of the GG0.3 and Control were similar but distinctly different from that of the HF group. Compared to HF, GG0.3 significantly increased the relative abundances of Firmicutes and Lactococcus and decreased the relative abundance of Tenericutes, Mesomycoplasma, and Phenylobacterium. In addition, the GG0.3 and GG1 treatments significantly enhanced the bile salt hydrolase (BSH) activity in the digesta compared to HF. In conclusion, 0.3 % guar gum supplementation can improve growth performance, intestinal health, and hepatic lipid metabolism in fish fed high-fat diets.\n\nGuar gum improves growth performance, intestinal microbiota homeostasis, and hepatic lipid metabolism in juvenile largemouth bass (Micropterus salmoides) fed high-fat diets.", "token_count": 461, "char_count": 1583, "word_count": 225, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [ "SREBP1", "GG0", "GG3", "GG1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:28.852101", "source": { "split": "train_shard_00000", "doc_id": 1503 }, "chunk_id": "train_shard_00000_1503_0", "global_id": 1657 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) clonal-complex 398 (CC398) is the dominant livestock-associated (LA) MRSA lineage in European livestock and an increasing cause of difficult-to-treat human disease. LA-CC398 MRSA evolved from a diverse human-associated methicillin-sensitive population, and this transition from humans to livestock was associated with three mobile genetic elements (MGEs). In this study, we apply transposon-directed insertion site sequencing (TraDIS), a high-throughput transposon mutagenesis approach, to investigate genetic signatures that contribute to LA-CC398 causing disease in humans. We identified 26 genes associated with LA-CC398 survival in human blood and 47 genes in porcine blood. We carried out phylogenetic reconstruction on 1,180 CC398 isolates to investigate the genetic context of all identified genes. We found that all genes associated with survival in human blood were part of the CC398 core genome, while 2/47 genes essential for survival in porcine blood were located on MGEs. Gene\n\nHigh-Throughput Mutagenesis Reveals a Role for Antimicrobial Resistance- and Virulence-Associated Mobile Genetic Elements in Staphylococcus aureus Host Adaptation.", "token_count": 327, "char_count": 1205, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8168, "entities": { "genes": [ "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:29.413224", "source": { "split": "train_shard_00000", "doc_id": 1504 }, "chunk_id": "train_shard_00000_1504_0", "global_id": 1658 }, { "text": "We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1 306 676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2 kb span. We annotated in addition 3252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.\n\nFrangiPANe, a tool for creating a panreference using left behind reads.", "token_count": 358, "char_count": 1343, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [ "TOG5681", "CG14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:30.000784", "source": { "split": "train_shard_00000", "doc_id": 1505 }, "chunk_id": "train_shard_00000_1505_0", "global_id": 1659 }, { "text": "Diurnal rhythmicity of cellular function is key to survival for most organisms on Earth. Many circadian functions are driven by the brain, but regulation of a separate set of peripheral rhythms remains poorly understood. The gut microbiome is a potential candidate for regulation of host peripheral rhythms, and this study sought to specifically examine the process of microbial bile salt biotransformation. To enable this work, an assay for bile salt hydrolase (BSH) that could work with small quantities of stool samples was necessary. Using a turn-on fluorescence probe, we developed a rapid and inexpensive assay to detect BSH enzyme activity with concentrations as low as 6-25 μM, which is considerably more robust than prior approaches. We successfully applied this rhodamine-based assay to detect BSH activity in a wide range of biological samples such as recombinant protein, whole cells, fecal samples, and gut lumen content from mice. We were able to detect significant BSH activity in small amounts of mouse fecal/gut content (20-50 mg) within 2 h, which illustrates its potential for use in various biological/clinical applications. Using this assay, we investigated the diurnal fluctuations of BSH activity in the large intestine of mice. By using time restricted feeding conditions, we provided direct evidence of 24 h rhythmicity in microbiome BSH activity levels and showed that this rhythmicity is influenced by feeding patterns. Our novel function-centric approach has potential to aid in the discovery of therapeutic, diet, or lifestyle interventions for correction of circadian perturbations linked to bile metabolism.\n\nProfiling rhythmicity of bile salt hydrolase activity in the gut lumen with a rapid fluorescence assay.", "token_count": 406, "char_count": 1743, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:30.621173", "source": { "split": "train_shard_00000", "doc_id": 1506 }, "chunk_id": "train_shard_00000_1506_0", "global_id": 1660 }, { "text": "Probiotic fermented foods are perceived as contributing to human health; however, solid evidence for their presumptive therapeutic systemic benefits is generally lacking. Here we report that tryptophol acetate and tyrosol acetate, small-molecule metabolites secreted by the probiotic milk-fermented yeast Kluyveromyces marxianus, inhibit hyperinflammation (e.g., \"cytokine storm\"). Comprehensive in vivo and in vitro analyses, employing LPS-induced hyperinflammation models, reveal dramatic effects of the molecules, added in tandem, on mice morbidity, laboratory parameters, and mortality. Specifically, we observed attenuated levels of the proinflammatory cytokines IL-6, IL-1α, IL-1β, and TNF-α and reduced reactive oxygen species. Importantly, tryptophol acetate and tyrosol acetate did not completely suppress proinflammatory cytokine generation, rather brought their concentrations back to baseline levels, thus maintaining core immune functions, including phagocytosis. The anti-inflammatory effects of tryptophol acetate and tyrosol acetate were mediated through downregulation of TLR4, IL-1R, and TNFR signaling pathways and increased A20 expression, leading to NF-kB inhibition. Overall, this work illuminates phenomenological and molecular details underscoring anti-inflammatory properties of small molecules identified in a probiotic mixture, pointing to potential therapeutic avenues against severe inflammation.\n\nTryptophol Acetate and Tyrosol Acetate, Small-Molecule Metabolites Identified in a Probiotic Mixture, Inhibit Hyperinflammation.", "token_count": 415, "char_count": 1555, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7249, "quality_score": 0.8624, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:31.247454", "source": { "split": "train_shard_00000", "doc_id": 1507 }, "chunk_id": "train_shard_00000_1507_0", "global_id": 1661 }, { "text": "The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high-resolution assembly graph built from long, accurate PacBio high-fidelity reads. We have improved and automated this strategy in Verkko, an iterative, graph-based pipeline for assembling complete, diploid genomes. Verkko begins with a multiplex de Bruijn graph built from long, accurate reads and progressively simplifies this graph by integrating ultra-long reads and haplotype-specific markers. The result is a phased, diploid assembly of both haplotypes, with many chromosomes automatically assembled from telomere to telomere. Running Verkko on the HG002 human genome resulted in 20 of 46 diploid chromosomes assembled without gaps at 99.9997% accuracy. The complete assembly of diploid genomes is a critical step towards the construction of comprehensive pangenome databases and chromosome-scale comparative genomics.\n\nTelomere-to-telomere assembly of diploid chromosomes with Verkko.", "token_count": 289, "char_count": 1134, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6558, "quality_score": 0.8279, "entities": { "genes": [ "HG002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:31.802546", "source": { "split": "train_shard_00000", "doc_id": 1508 }, "chunk_id": "train_shard_00000_1508_0", "global_id": 1662 }, { "text": "The Fructobacillus genus is a group of obligately fructophilic lactic acid bacteria (FLAB) that requires the use of fructose or another electron acceptor for their growth. In this work, we performed a comparative genomic analysis within the genus Fructobacillus by using 24 available genomes to evaluate genomic and metabolic differences among these organisms. In the genome of these strains, which varies between 1.15- and 1.75-Mbp, nineteen intact prophage regions, and seven complete CRISPR-Cas type II systems were found. Phylogenetic analyses located the studied genomes in two different clades. A pangenome analysis and a functional classification of their genes revealed that genomes of the first clade presented fewer genes involved in the synthesis of amino acids and other nitrogen compounds. Moreover, the presence of genes strictly related to the use of fructose and electron acceptors was variable within the genus, although these variations were not always related to the phylogeny.\n\nGenomic diversity in Fructobacillus spp. isolated from fructose-rich niches.", "token_count": 261, "char_count": 1074, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6772, "quality_score": 0.8386, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:32.345956", "source": { "split": "train_shard_00000", "doc_id": 1509 }, "chunk_id": "train_shard_00000_1509_0", "global_id": 1663 }, { "text": "Capturing haplotype variation in populations using pangenome references.", "token_count": 15, "char_count": 72, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:32.694174", "source": { "split": "train_shard_00000", "doc_id": 1510 }, "chunk_id": "train_shard_00000_1510_0", "global_id": 1664 }, { "text": "It is known that the reduction of blood cholesterol can be accomplished through foods containing a large number of dietary fibers; this process is partially related to the binding of bile salt to fibers. To gain new insights into the interactions between dietary fibers and bile salts, this study investigates the interactions between cationic hydroxyethyl cellulose (catHEC) and sodium deoxycholate (NaDC) or sodium cholate (NaC), which have a similar structure. Turbidity measurements reveal strong interactions between catHEC and NaDC, and under some conditions, macroscopic phase separation occurs. In contrast, the interactions with NaC are weak. At a catHEC concentration of 2 wt %, incipient phase separation is approached at concentrations of NaC and NaDC of 32.5 and 19.3 mM, respectively. The rheological results show strong interactions and a prominent viscosification effect for the catHEC/NaDC system but only moderate interactions for the catHEC/NaC system. Both cryogenic transmission electron microscopy and small-angle X-ray scattering results display fundamental structural differences between the two systems, which may explain the stronger interactions in the presence of NaDC. The surmise is that the extended structures formed in the presence of NaDC can easily form connections and entanglements in the network.\n\nInteractions in Aqueous Mixtures of Cationic Hydroxyethyl Cellulose and Different Anionic Bile Salts.", "token_count": 331, "char_count": 1437, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8213, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:33.276634", "source": { "split": "train_shard_00000", "doc_id": 1511 }, "chunk_id": "train_shard_00000_1511_0", "global_id": 1665 }, { "text": "Ethyl acetate is an important organic solvent and currently produced from fossil carbon resources. Microbial synthesis of this ester from sugar-rich waste could be an interesting alternative. Therefore, synthesis of ethyl acetate by Kluyveromyces marxinanus DSM 5422 from delactosed whey permeate (DWP) was studied in an aerated stirred bioreactor at 40 °C. DWP is mainly composed of residual lactose and minerals. The minerals inhibited yeast growth, as witnessed by an increased lag period, a reduced growth rate, and an extended process duration. All experiments were therefore carried out with diluted DWP. In a series of batch experiments, the pH of iron-deficient DWP medium varied between 4.8 and 5.9. The pH of the cultivation medium significantly influenced cell growth and product syntheses, with the highest ethyl acetate yield of 0.347 g g\n\nUtilization of delactosed whey permeate for the synthesis of ethyl acetate with Kluyveromyces marxianus.", "token_count": 258, "char_count": 957, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:33.826124", "source": { "split": "train_shard_00000", "doc_id": 1512 }, "chunk_id": "train_shard_00000_1512_0", "global_id": 1666 }, { "text": "In the post-genomic era, data management and development of bioinformatic tools are critical for the adequate exploitation of genomics data. In this review, we address the actual situation for the subset of crops represented by the perennial fruit species. The agronomical singularity of these species compared to plant and crop model species provides significant challenges on the implementation of good practices generally not addressed in other species. Studies are usually performed over several years in non-controlled environments, usage of rootstock is common, and breeders heavily rely on vegetative propagation. A reference genome is now available for all the major species as well as many members of the economically important genera for breeding purposes. Development of pangenome for these species is beginning to gain momentum which will require a substantial effort in term of bioinformatic tool development. The available tools for genome annotation and functional analysis will also be presented.\n\nGenomic and Bioinformatic Resources for Perennial Fruit Species.", "token_count": 209, "char_count": 1078, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6624, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:34.292040", "source": { "split": "train_shard_00000", "doc_id": 1513 }, "chunk_id": "train_shard_00000_1513_0", "global_id": 1667 }, { "text": "Farnesoid X receptor (FXR) and Takeda G protein-coupled Receptor 5 (TGR5), the intestinal bile acid (BA) receptors, regulate the gut-derived hormones including fibroblast growth factor 15/19 (FGF15/19) and serotonin (5-hydrooxytryptamine, 5-HT). Here we show that ingestion of whey protein isolate, a milk protein, significantly decreased expression of heteromeric organic solute transporter Ostα and Ostβ, which is the basolateral BA transporter in the enterocyte, and increased the expression of FXR and FGF15 in C57BL6J mouse ileum and plasma FGF15 levels. In addition, the ingestion of whey protein isolate significantly suppressed expression of hepatic cholesterol-7α hydroxylase (CYP7A1), which induces the primary BA synthesis, bile salt export pump (BSEP) and sodium-taurocholate cotransporting polypeptide (NTCP), which are the key transporters for the BA excretion and uptake in the liver, and genes involved in gluconeogenesis, and decreased the primary BAs including cholic acid, taurocholic acid, glycocholic acid, and taurochenodeoxycholic acid in the liver compared with controls. Moreover, ingestion of whey protein isolate significantly decreased the expression of TGR5, glucagon-like peptide 1 (GLP-1), and tryptophan hydroxylase1 (Tph1) in the small intestine, leading to decreases in plasma 5-HT and insulin levels. On the other hand, ingestion of the soy protein β-conglycinin significantly increased the expression of Ostα and Ostβ, and decreased the expression of FGF15 in the ileum and plasma FGF15 levels, leading to the increases in expression of hepatic CYP7A1, BSEP, NTCP, and genes involved in gluconeogenesis, and the primary BAs in the liver", "token_count": 500, "char_count": 1672, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5336, "quality_score": 0.7668, "entities": { "genes": [ "FGF15", "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:34.950487", "source": { "split": "train_shard_00000", "doc_id": 1514 }, "chunk_id": "train_shard_00000_1514_0", "global_id": 1668 }, { "text": "Moreover, ingestion of β-conglycinin significantly increased the expression of intestinal TGR5, GLP-1, and Tph1, leading to increases in plasma 5-HT and insulin levels. These findings suggest that whey protein and β-conglycinin have opposite effects on intestinal FGF15 and 5-HT secretion in mice.\n\nIngestion of whey protein and β-conglycinin exerts opposite effects on intestinal FGF15 and serotonin secretion in mice.", "token_count": 125, "char_count": 419, "word_count": 59, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [ "FGF15", "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:35.333723", "source": { "split": "train_shard_00000", "doc_id": 1514 }, "chunk_id": "train_shard_00000_1514_1", "global_id": 1669 }, { "text": "[This corrects the article DOI: 10.3389/fmed.2018.00059.].\n\nCorrigendum: Compositional quality and potential gastrointestinal behavior of probiotic products commercialized in Italy.", "token_count": 62, "char_count": 181, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:35.736759", "source": { "split": "train_shard_00000", "doc_id": 1515 }, "chunk_id": "train_shard_00000_1515_0", "global_id": 1670 }, { "text": "Recombinant proteins (RP) are widely used as biopharmaceuticals, industrial enzymes, or sustainable food source. Yeasts, with their ability to produce complex proteins through a broad variety of cheap carbon sources, have emerged as promising eukaryotic production hosts. As such, the prevalence of yeasts as favourable production organisms in commercial RP production is expected to increase. Yet, with the selection of a robust production host on the one hand, successful scale-up is dependent on a thorough understanding of the challenging environment and limitations of large-scale bioreactors on the other hand. In the present work, several prominent yeast species, including Saccharomyces cerevisiae, Pichia pastoris, Yarrowia lipolytica, Kluyveromyces lactis and Kluyveromyces marxianus are reviewed for their current state and performance in commercial RP production. Thereafter, the impact of principal process control parameters, including dissolved oxygen, pH, substrate concentration, and temperature, on large-scale RP production are discussed. Finally, technical challenges of process scale-up are identified. To that end, process intensification strategies to enhance industrial feasibility are summarized, specifically highlighting fermentation strategies to ensure sufficient cooling capacity, overcome oxygen limitation, and increase protein quality and productivity. As such, this review aims to contribute to the pursuit of sustainable yeast-based RP production.\n\nChallenges and progress towards industrial recombinant protein production in yeasts: A review.", "token_count": 330, "char_count": 1578, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:36.331924", "source": { "split": "train_shard_00000", "doc_id": 1516 }, "chunk_id": "train_shard_00000_1516_0", "global_id": 1671 }, { "text": "Simvastatin (SMV), a cholesterol-lowering agent, has antioxidant and anti-inflammatory effects. Nevertheless, the oral use of SMV is linked with poor systemic bioavailability owing to its limited aqueous solubility and extensive first-pass metabolism. The aim of this study was to evaluate the feasibility of transdermal delivery of SMV using bile salt stabilized vesicles (bilosomes) for enhancing the anti-inflammatory potential of SMV. SMV-loaded bilosomes (SMV-BS) were prepared by the thin film hydration technique and optimized by 3\n\nTailoring of Novel Bile Salt Stabilized Vesicles for Enhanced Transdermal Delivery of Simvastatin: A New Therapeutic Approach against Inflammation.", "token_count": 192, "char_count": 687, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7447, "quality_score": 0.8723, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:36.793183", "source": { "split": "train_shard_00000", "doc_id": 1517 }, "chunk_id": "train_shard_00000_1517_0", "global_id": 1672 }, { "text": "Over the past decades the potential role of the gut microbiome and bile acids in type 2 diabetes mellitus (T2DM) has been revealed, with a special reference to low bacterial alpha diversity. Certain bile acid effects on gut bacteria concern cytotoxicity, or in the case of the microbiome, bacteriotoxicity. Reciprocally, the gut microbiome plays a key role in regulating the bile acid pool by influencing the conversion and (de)conjugation of primary bile acids into secondary bile acids. Three main groups of bacterial enzymes responsible for the conversion of bile acids are bile salt hydrolases (BSHs), hydroxysteroid dehydrogenases (HSDHs) and enzymes encoded in the bile acid inducible (Bai) operon genes. Interventions such as probiotics, antibiotics and fecal microbiome transplantation can impact bile acids levels. Further evidence of the reciprocal interaction between gut microbiota and bile acids comes from a multitude of nutritional interventions including macronutrients, fibers, prebiotics, specific individual products or diets. Finally, anatomical changes after bariatric surgery are important because of their metabolic effects. The heterogeneity of studies, diseases, bacterial species and (epi)genetic influences such as nutrition may challenge establishing specific and detailed interventions that aim to tackle the gut microbiome and bile acids.\n\nThe Black Box Orchestra of Gut Bacteria and Bile Acids: Who Is the Conductor?", "token_count": 362, "char_count": 1447, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:37.413915", "source": { "split": "train_shard_00000", "doc_id": 1518 }, "chunk_id": "train_shard_00000_1518_0", "global_id": 1673 }, { "text": "Bile salt hydrolase (BSH) in Bacteroides is considered a potential drug target for obesity-related metabolic diseases, but its involvement in colon tumorigenesis has not been explored. BSH-expressing Bacteroides is found at high abundance in the stools of colorectal cancer (CRC) patients  with overweight and in the feces of a high-fat diet (HFD)-induced CRC mouse model. Colonization of B. fragilis 638R, a strain with low BSH activity, overexpressing a recombinant bsh gene from B. fragilis NCTC9343 strain, results in increased unconjugated bile acids in the colon and accelerated progression of CRC under HFD treatment. In the presence of high BSH activity, the resultant elevation of unconjugated deoxycholic acid and lithocholic acid activates the G-protein-coupled bile acid receptor, resulting in increased β-catenin-regulated chemokine (C-C motif) ligand 28 (CCL28) expression in colon tumors. Activation of the β-catenin/CCL28 axis leads to elevated intra-tumoral immunosuppressive CD25\n\nBile salt hydrolase in non-enterotoxigenic Bacteroides potentiates colorectal cancer.", "token_count": 340, "char_count": 1084, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6733, "quality_score": 0.8367, "entities": { "genes": [ "CCL28", "CD25", "NCTC9343" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:37.982536", "source": { "split": "train_shard_00000", "doc_id": 1519 }, "chunk_id": "train_shard_00000_1519_0", "global_id": 1674 }, { "text": "Mutations with deleterious consequences in nature may be conditionally deleterious in crop plants. That is, while some genetic variants may reduce fitness under wild conditions and be subject to purifying selection, they can be under positive selection in domesticates. Such deleterious alleles can be plant breeding targets, particularly for complex traits. The difficulty of distinguishing favorable from unfavorable variants reduces the power of selection, while favorable trait variation and heterosis may be attributable to deleterious alleles. Here, we review the roles of deleterious mutations in crop breeding and discuss how they can be used as a new avenue for crop improvement with emerging genomic tools, including HapMaps and pangenome analysis, aiding the identification, removal, or exploitation of deleterious mutations.\n\nEvolutionary dynamics and adaptive benefits of deleterious mutations in crop gene pools.", "token_count": 202, "char_count": 926, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6565, "quality_score": 0.8282, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:38.451895", "source": { "split": "train_shard_00000", "doc_id": 1520 }, "chunk_id": "train_shard_00000_1520_0", "global_id": 1675 }, { "text": "Irc3 is one of the six mitochondrial helicases described in Saccharomyces cerevisiae. Physiological functions of Irc3 are not completely understood as both DNA metabolic processes and mRNA translation have been suggested to be direct targets of the helicase. In vitro analysis of Irc3 has been hampered by the modest thermostability of the S. cerevisiae protein. Here, we purified a homologous helicase (Irc3\n\nMitochondrial Irc3 helicase of the thermotolerant yeast Ogataea polymorpha displays dual DNA- and RNA-stimulated ATPase activity.", "token_count": 148, "char_count": 539, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7821, "quality_score": 0.891, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:38.886514", "source": { "split": "train_shard_00000", "doc_id": 1521 }, "chunk_id": "train_shard_00000_1521_0", "global_id": 1676 }, { "text": "Probiotics are known to possess strain- and species-specific functional properties, of which hypocholesteremia is of major interest. Bile salt hydrolase (BSH) activity is one of the key mechanisms involved in the hypocholesterolemic effect. The study was designed to genetically characterize probiotics obtained from human milk on the basis of simple sequence repeat (SSR), isolate potent hypocholesterolemic strains, and detect BSH activity, deconjugation of bile salts, and bsh polymorphism. This study, for the first time, linked genetic diversity with cholesterol reduction potential and proved the presence of conserved bsh of Levilactobacillus brevis in genetically diverse species. The strains displayed 2.78%-42.23% cholesterol reduction, which was not influenced by prebiotics. In this study, data obtained from SSR markers indicated 93.3% diversity, and based on cluster analysis, they were distributed into XI clades; out of five potent cholesterol-reducing strains, three belonged to clade I. The strains could deconjugate both sodium glycocholate and sodium taurocholate, but we preferred using sodium glycocholate. The variation in cholesterol reduction potential and BSH activity pointed toward the presence of more than one bsh in the strains. Weissella confusa MW051433 displayed highest cholesterol reduction (42.23%) and specific BSH activity (2.64 U ml -1). Search for other bsh and in vivo assessments of cholesterol reduction by W. confusa MW051433 have been proposed.\n\nGenetic diversity, cholesterol reduction, and presence of conserved bile salt hydrolase gene in probiotic strains from human milk.", "token_count": 434, "char_count": 1622, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [ "MW051433" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:39.517295", "source": { "split": "train_shard_00000", "doc_id": 1522 }, "chunk_id": "train_shard_00000_1522_0", "global_id": 1677 }, { "text": "Astaxanthin (AST), a super antioxidant with coloring and medical properties, renders it a beneficial feed additive for shrimp. This study conducted a white shrimp feeding trial of 3S, 3'S isoform AST, which was derived from metabolic-engineered Kluyveromyces marxianus fermented broth (TB) and its extract (TE) compared to sources from two chemically synthetic ASTs (Carophyll Pink [CP] and Lucantin Pink [LP]), which contain 3S, 3'S, 3R, 3'S (3S, 3'R) and 3R, 3'R isoforms ratio of 1:2:1. The effects on red coloration, immune parameters and resistance to Vibrio infection were evaluated. Four AST sources were incorporated into the diets at concentrations of 0 (control), 100 mg kg\n\nImproving red-color performance, immune response and resistance to Vibrio parahaemolyticus on white shrimp Penaeus vannamei by an engineered astaxanthin yeast.", "token_count": 263, "char_count": 844, "word_count": 125, "semantic_coherence": 1, "information_density": 0.784, "quality_score": 0.892, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:40.055616", "source": { "split": "train_shard_00000", "doc_id": 1523 }, "chunk_id": "train_shard_00000_1523_0", "global_id": 1678 }, { "text": "The cholesterol-lowering and immunomodulatory effects and probiotic properties of 25 lactic acid bacteria (LAB) isolated from fermented fish (pla-paeng-daeng) in Thailand were examined in the present study. Based on their phenotypic and genetic characteristics, LAB were identified as Lactiplantibacillus pentosus (Group I, 6 isolates), Lactiplantibacillus argentoratensis (Group II, 1 isolate), Limosilactobacillus fermentum (Group III, 2 isolates), Companilactobacillus pabuli (Group IV, 4 isolates), Companilactobacillus farciminis (Group V, 5 isolates), Companilactobacillus futsaii (Group VI, 6 isolates), and Enterococcus lactis (Group VII, 1 isolate). Lactiplantibacillus pentosus PD3-1 and PD9-2 and Enterococcus lactis PD3-2 exhibited bile salt hydrolase (BSH) activities. The percentage of cholesterol assimilated by all isolates ranged between 21.40 and 54.07%. Bile salt hydrolase-producing isolates tolerated acidic and bile conditions and possessed adhesion properties. They also exerted immunomodulatory effects that affected the production of interleukin-12 (IL-12), interferon-γ (IFN-γ), human β-defensin-2 (hBD-2), and nitric oxide (NO). These isolates meet standard probiotic requirements and exert beneficial effects.\n\nCharacterization of Lactic Acid Bacteria from Fermented Fish (pla-paeng-daeng) and Their Cholesterol-lowering and Immunomodulatory Effects.", "token_count": 439, "char_count": 1378, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6548, "quality_score": 0.8274, "entities": { "genes": [ "PD3", "PD9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:40.680198", "source": { "split": "train_shard_00000", "doc_id": 1524 }, "chunk_id": "train_shard_00000_1524_0", "global_id": 1679 }, { "text": "A novel methylotrophic bacterium designated as NMS14P was isolated from the root of an organic coffee plant (Coffea arabica) in Thailand. The 16S rRNA sequence analysis revealed that this new isolate belongs to the genus Methylobacterium, and its novelty was clarified by genomic and comparative genomic analyses, in which NMS14P exhibited low levels of relatedness with other Methylobacterium-type strains. NMS14P genome consists of a 6,268,579 bp chromosome, accompanied by a 542,519 bp megaplasmid and a 66,590 bp plasmid, namely pNMS14P1 and pNMS14P2, respectively. Several genes conferring plant growth promotion are aggregated on both chromosome and plasmids, including phosphate solubilization, indole-3-acetic acid (IAA) biosynthesis, cytokinins (CKs) production, 1-aminocyclopropane-1-carboxylate (ACC) deaminase activity, sulfur-oxidizing activity, trehalose synthesis, and urea metabolism. Furthermore, pangenome analysis showed that NMS14P possessed the highest number of strain-specific genes accounting for 1408 genes, particularly those that are essential for colonization and survival in a wide array of host environments, such as ABC transporter, chemotaxis, quorum sensing, biofilm formation, and biosynthesis of secondary metabolites. In vivo tests have supported that NMS14P significantly promoted the growth and development of maize, chili, and sugarcane. Collectively, NMS14P is proposed as a novel plant growth-promoting Methylobacterium that could potentially be applied to a broad range of host plants as Methylobacterium-based biofertilizers to reduce and ultimately substitute the use of synthetic agrochemicals for sustainable agriculture.\n\nInsights into the genome of Methylobacterium sp. NMS14P, a novel bacterium for growth promotion of maize, chili, and sugarcane.", "token_count": 509, "char_count": 1796, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6778, "quality_score": 0.8389, "entities": { "genes": [ "NMS14P" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:41.339605", "source": { "split": "train_shard_00000", "doc_id": 1525 }, "chunk_id": "train_shard_00000_1525_0", "global_id": 1680 }, { "text": "The increase of Vancomycin-resistant\n\nSplit k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany.", "token_count": 66, "char_count": 285, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:41.711112", "source": { "split": "train_shard_00000", "doc_id": 1526 }, "chunk_id": "train_shard_00000_1526_0", "global_id": 1681 }, { "text": "Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date.\n\nComparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication.", "token_count": 118, "char_count": 606, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7262, "quality_score": 0.8631, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:42.092597", "source": { "split": "train_shard_00000", "doc_id": 1527 }, "chunk_id": "train_shard_00000_1527_0", "global_id": 1682 }, { "text": "Taurine, a sulfur-containing amino acid, has a wide range of biological effects, such as bile salt formation, osmotic regulation, oxidative stress inhibition, immunomodulation and neuromodulation. Taurine has been proved to be synthesized and abundant in male reproductive organs. Recently, accumulating data showed that taurine has a potential protective effect on reproductive function of male animals. In physiology, taurine can promote the endocrine function of the hypothalamus-pituitary-testis (HPT) axis, testicular tissue development, spermatogenesis and maturation, delay the aging of testicular structure and function, maintain the homeostasis of the testicular environment, and enhance sexual ability. In pathology, taurine supplement may be beneficial to alleviate pathological damage of male reproductive system, including oxidative damage of sperm preservation\n\nThe role of taurine in male reproduction: Physiology, pathology and toxicology.", "token_count": 231, "char_count": 955, "word_count": 125, "semantic_coherence": 1, "information_density": 0.672, "quality_score": 0.836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:42.574217", "source": { "split": "train_shard_00000", "doc_id": 1528 }, "chunk_id": "train_shard_00000_1528_0", "global_id": 1683 }, { "text": "β-carotene is a carotenoid with provitamin A activity and other health benefits, which needs to become bioavailable upon oral intake to exert its biological activity. A better understanding of its behaviour and stability in the gastrointestinal tract and means to increase its bioavailability are highly needed. Using an in vitro gastrointestinal digestion method coupled to an intestinal cell model, we explored the stability, gastrointestinal bioaccessibility and cellular uptake of β-carotene from microparticles containing carotenoid extracts derived from mango by-products. Three types of microparticles were tested: one with the carotenoid extract as such, one with added inulin and one with added fructooligosaccharides. Overall, β-carotene was relatively stable during the in vitro digestion, as total recoveries were above 68 %. Prebiotics in the encapsulating material, especially inulin, enhanced the bioaccessibility of β-carotene almost 2-fold compared to microparticles without prebiotics. Likewise, β-carotene bioaccessibility increased proportionally with bile salt concentrations during digestion. Yet, a bile salts level above 10 mM did not contribute markedly to β-carotene bioaccessibility of prebiotic containing microparticles. Cellular uptake experiments with non-filtered gastrointestinal digests yielded higher absolute levels of β-carotene taken up in the epithelial cells as compared to uptake assays with filtered digests. However, the proportional uptake of β-carotene was higher for filtered digests (24 - 31 %) than for non-filtered digests (2 - 8 %). Matrix-dependent carotenoid uptake was only visible in the unfiltered medium, thereby pointing to possible other cellular transport mechanisms of non-micellarized carotenoids, besides the concentration effect. Regardless of a filtration step, inulin-amended microparticles consistently resulted in a higher β-carotene uptake than regular microparticles or FOS-amended microparticles", "token_count": 505, "char_count": 1965, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:43.232145", "source": { "split": "train_shard_00000", "doc_id": 1529 }, "chunk_id": "train_shard_00000_1529_0", "global_id": 1684 }, { "text": "In conclusion, encapsulation of carotenoid extracts from mango by-products displayed chemical stability and release of a bioaccessible β-carotene fraction upon gastrointestinal digestion. This indicates the potential of the microparticles to be incorporated into functional foods with provitamin A activity.\n\nIn vitro bioaccessibility and uptake of β-carotene from encapsulated carotenoids from mango by-products in a coupled gastrointestinal digestion/Caco-2 cell model.", "token_count": 119, "char_count": 471, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7458, "quality_score": 0.8729, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:43.618247", "source": { "split": "train_shard_00000", "doc_id": 1529 }, "chunk_id": "train_shard_00000_1529_1", "global_id": 1685 }, { "text": "The effect of konjac glucomannan (KGM) on the stability and digestion characteristics of xanthan gum/lysozyme nanoparticles (XG/Ly NPs) stabilized Pickering emulsions was investigated. Results indicated that the high viscosity of KGM prompted the particles to be adsorbed toward the interface, which decreased the particle size and increased the stability of emulsions. As the concentration of KGM increased, the G' and G″ of emulsions became larger and approached a \"solid-like\" state. When the KGM concentration was ≥0.2 %, the large amplitude sweeps of the emulsion exhibited a \"weak strain overshoot\". The network structure formed by KGM molecular chain and particles was intertwined around the droplets to form a polysaccharide layer and fibrous network structure. Emulsions containing KGM showed a \"spider web\" epidermal network pattern. It was found by illumination for 4 h that samples with 0.2 % KGM concentration increased the retention of β-carotene by 18.74 %. KGM decreased the release rate of fatty acids and bioaccessibility by hindering bile salt and lipase adsorption.\n\nPickering emulsions synergistic stabilized with konjac glucomannan and xanthan gum/lysozyme nanoparticles: Structure, protection and gastrointestinal digestion.", "token_count": 335, "char_count": 1247, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6257, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:44.187468", "source": { "split": "train_shard_00000", "doc_id": 1530 }, "chunk_id": "train_shard_00000_1530_0", "global_id": 1686 }, { "text": "The present communication offers a comprehensive overview of the self-assembly of bile salts emphasizing their mixed smart aggregates with a variety of amphiphiles. Using an updated literature survey, we have explored the dissimilar interactions of bile salts with different types of surfactants, phospholipids, ionic liquids, drugs, and a variety of natural and synthetic polymers. While assembling this review, special attention was also provided to the potency of bile salts to alter the size/shape of aggregates formed by several amphiphiles to use these aggregates for solubility improvement of medicinally important compounds, active pharmaceutical ingredients, and also to develop their smart delivery vehicles. A fundamental understanding of bile salt mixed aggregates will enable the development of new strategies for improving the bioavailability of drugs solubilized in newly developed potential hosts and to formulate smart aggregates of desired morphology for specific targeted applications. It enriches our existing knowledge of the distinct interactions exerted in mixed systems of bile salts with variety of amphiphiles. By virtue of this, researchers can get innovative ideas to construct novel nanoaggregates from bile salts by incorporating various amphiphiles that serve as a building block for smart aggregates for their numerous industrial applications.\n\nSelf-assembly of bile salts and their mixed aggregates as building blocks for smart aggregates.", "token_count": 304, "char_count": 1472, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:44.754859", "source": { "split": "train_shard_00000", "doc_id": 1531 }, "chunk_id": "train_shard_00000_1531_0", "global_id": 1687 }, { "text": "Untreated wastewater emanating from healthcare facilities are risk factors for the spread of antimicrobial resistance (AMR) at the human-environment interface. In this study, we investigated the determinants of resistance in three multidrug resistant strains of Proteus mirabilis isolated from untreated wastewater collected from three government owned hospitals in Ibadan, Nigeria. Despite showing low-level resistance to ciprofloxacin, whole genome sequencing revealed the transferable mechanism of quinolone resistance (TMQR) gene qnrD3 carried on Col3M plasmids in all the isolates. Core genome phylogenetic analysis showed the isolates are closely related differing from each other by ≤ 23 single nucleotide polymorphisms (SNP). Further, they shared the closest evolutionary relationship with isolates from China. Similarly, the Col3M plasmids is most closely related to p3M-2A found in P. vulgaris 3 M isolated from the intestine of shrimps in China. This to the best of our knowledge is the first report of Col3M plasmids carrying qnrD3 in environmental bacterial isolates. Our results indicate a possible silent spread of this important plasmid associated with the dissemination of qnrD3 in Nigeria, and further highlights the important role played by untreated wastewater from healthcare facilities in the spread of AMR in low- and middle-income countries.\n\nProteus mirabilis isolated from untreated hospital wastewater, Ibadan, Southwestern Nigeria showed low-level resistance to fluoroquinolone and carried qnrD3 on Col3M plasmids.", "token_count": 377, "char_count": 1542, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:45.344294", "source": { "split": "train_shard_00000", "doc_id": 1532 }, "chunk_id": "train_shard_00000_1532_0", "global_id": 1688 }, { "text": "Probiotics and prebiotics together work synergistically as synbiotics and confer various health benefits. Many studies on synbiotic foods only focus on the survival of probiotics but fail to evaluate their functional properties. The impact on functional properties should be explored to better understand its therapeutic efficacy. In this work, probiotics (Lactiplantibacillus plantarum NCIM 2083) were encapsulated with prebiotics (fructooligosaccharide + whey protein + maltodextrin) using spray-drying (SD), freeze-drying (FD), spray-freeze-drying (SFD), and refractance window-drying (RWD) techniques. Aggregation, intestinal adhesion, antagonistic activity, and bile salt hydrolase (BSH) activity of probiotics were studied before and after the encapsulation process. The SFD probiotics showed better aggregation ability (79% at 24-h incubation), on par with free cells (FC) (81% at 24-h incubation). The co-aggregation ability of encapsulated probiotics has drastic variations with each pathogenic strain. The adhesion ability of probiotics in chicken intestinal mucus was assessed by the crystal violet method, indicating no significant variations between FC and SFD probiotics. Also, encapsulated probiotics exhibit antagonistic activity (zone of inhibition in mm) against gut pathogens E. coli (11.33 to 17.34), S. faecalis (8.83 to 15.32), L. monocytogenes (13.67 to 18), S. boydii (12.17 to 15.5), and S. typhi (2.17 to 6.86). Overall, these studies confirm the significance and impact of various drying techniques on the functionality of encapsulated probiotics in synbiotic powders. KEY POINTS: • Understanding the relevance of processing effects on the functionality of probiotics. • Spray-freeze-dried probiotics showed superior functional properties", "token_count": 514, "char_count": 1765, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:13:45.989417", "source": { "split": "train_shard_00000", "doc_id": 1533 }, "chunk_id": "train_shard_00000_1533_0", "global_id": 1689 }, { "text": "• The encapsulation process had no significant impact on bile salt hydrolase activity.\n\nEffect of different drying methods on the functional properties of probiotics encapsulated using prebiotic substances.", "token_count": 45, "char_count": 206, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:46.348512", "source": { "split": "train_shard_00000", "doc_id": 1533 }, "chunk_id": "train_shard_00000_1533_1", "global_id": 1690 }, { "text": "The Penicillia are known to produce a wide range natural products-some with devastating outcome for the agricultural industry and others with unexploited potential in different applications. However, a large-scale overview of the biosynthetic potential of different species has been lacking. In this study, we sequenced 93 Penicillium isolates and, together with eleven published genomes that hold similar assembly characteristics, we established a species phylogeny as well as defining a Penicillium pangenome. A total of 5612 genes were shared between ≥ 98 isolates corresponding to approximately half of the average number of genes a Penicillium genome holds. We further identified 15 lateral gene transfer events that have occurred in this collection of Penicillium isolates, which might have played an important role, such as niche adaption, in the evolution of these fungi. The comprehensive characterization of the genomic diversity in the Penicillium genus supersedes single-reference genomes, which do not necessarily capture the entire genetic variation.\n\nComparative genomic study of the Penicillium genus elucidates a diverse pangenome and 15 lateral gene transfer events.", "token_count": 266, "char_count": 1184, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:46.893221", "source": { "split": "train_shard_00000", "doc_id": 1534 }, "chunk_id": "train_shard_00000_1534_0", "global_id": 1691 }, { "text": "While the association between colorectal cancer (CRC) features and Fusobacterium has been extensively studied, less is known of other intratumoral bacteria. Here, we leverage whole transcriptomes from 807 CRC samples to dually characterize tumor gene expression and 74 intratumoral bacteria. Seventeen of these species, including 4 Fusobacterium spp., are classified as orally derived and are enriched among right-sided, microsatellite instability-high (MSI-H), and BRAF-mutant tumors. Across consensus molecular subtypes (CMSs), integration of Fusobacterium animalis (Fa) presence and tumor expression reveals that Fa has the most significant associations in mesenchymal CMS4 tumors despite a lower prevalence than in immune CMS1. Within CMS4, the prevalence of Fa is uniquely associated with collagen- and immune-related pathways. Additional Fa pangenome analysis reveals that stress response genes and the adhesion FadA are commonly expressed intratumorally. Overall, this study identifies oral-derived bacteria as enriched in inflamed tumors, and the associations of bacteria and tumor expression are context and species specific.\n\nEnrichment of oral-derived bacteria in inflamed colorectal tumors and distinct associations of Fusobacterium in the mesenchymal subtype.", "token_count": 319, "char_count": 1272, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [ "CMS1", "CMS4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:47.447676", "source": { "split": "train_shard_00000", "doc_id": 1535 }, "chunk_id": "train_shard_00000_1535_0", "global_id": 1692 }, { "text": "A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking.\n\nA pangenome analysis pipeline provides insights into functional gene identification in rice.", "token_count": 97, "char_count": 522, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7568, "quality_score": 0.8784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:47.860781", "source": { "split": "train_shard_00000", "doc_id": 1536 }, "chunk_id": "train_shard_00000_1536_0", "global_id": 1693 }, { "text": "Lytic enzymes secreted by Kluyveromyces marxianus can lyse Saccharomyces cerevisiae cells. Their ability to hydrolyze yeast cell walls can be used in biotechnological applications, such as the production of glucans and protoplasts, as well as a biological control agent against plant pathogenic fungi. Herein, 27 proteins secreted by K. marxianus were identified by mass spectrometry analyses. Importantly, 14 out of the 27 proteins were classified as hydrolases. Indeed, the enzyme extract secreted by K. marxianus caused damage to S. cerevisiae cells and reduced yeast cell viability. Moreover, K marxianus inhibited spore germination and mycelial growth of the phytopathogenic fungus Botrytis cinerea in simultaneous cocultivation assays. We suggest that this inhibition may be partially related to the yeast's ability to secrete lytic enzymes. Consistent with the in vitro antagonistic tests, K. marxianus was able to protect strawberry fruits inoculated with B. cinerea. Therefore, these findings suggest that K. marxianus possesses potential as a biocontrol agent against strawberry gray mold during the postharvest stage and may also have potential against other phytopathogenic fungi by means of its lytic enzymatic arsenal.\n\nIdentification of the main proteins secreted by Kluyveromyces marxianus and their possible roles in antagonistic activity against fungi.", "token_count": 365, "char_count": 1370, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:48.460944", "source": { "split": "train_shard_00000", "doc_id": 1537 }, "chunk_id": "train_shard_00000_1537_0", "global_id": 1694 }, { "text": "Humans are exposed to per- and polyfluoroalkyl substances (PFASs) mainly through oral exposure route, while little is known about their bioaccessibility (BC) in oral matrices. Here, the BC of 13 PFASs in simulated vegetable (VFs) and animal foods (AFs) as well as indoor dust was investigated using a physiology-based extraction test. The BC of PFASs in the AFs (78.5 ± 13.6 %) was distinctly higher than that in the VFs (60.6 ± 13.4 %), because high-saturated and long-chain fatty acids in the animal fat favored formation of more stable micelles. The BC of most long-chain PFASs was positively correlated with the protein content while negatively correlated with the carbohydrate content in the foods. The BC of polyfluoroalkyl phosphate diesters was negatively correlated with the lipid content. The BC of the very long-chain PFASs in the foods was 2.42-6.02 times higher than that in the dust, which might be attributed to their strong sequestration in dust. With the increase in bile salt concentration, the BC of PFASs in food increased and then remained constant, which was related to the changes in fatty acids and stability of the formed micelles. Comparing with the previous results obtained from animal study, the BC obtained in this study has the potential to predict PFAS bioavailability in food.\n\nBioaccessibility of per- and polyfluoroalkyl substances in food and dust: Implication for more accurate risk assessment.", "token_count": 375, "char_count": 1431, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5614, "quality_score": 0.7807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:49.068252", "source": { "split": "train_shard_00000", "doc_id": 1538 }, "chunk_id": "train_shard_00000_1538_0", "global_id": 1695 }, { "text": "Bile salt export pump (BSEP) deficiency frequently necessitates liver transplantation in childhood. In contrast to two predicted protein truncating mutations (PPTMs), homozygous p.D482G or p.E297G mutations are associated with relatively mild phenotypes, responsive to surgical interruption of the enterohepatic circulation (siEHC). The phenotype of patients with a compound heterozygous genotype of one p.D482G or p.E297G mutation and one PPTM has remained unclear. We aimed to assess their genotype-phenotype relationship.\n\nGenotype-phenotype relationships of truncating mutations, p.E297G and p.D482G in bile salt export pump deficiency.", "token_count": 185, "char_count": 640, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7229, "quality_score": 0.8614, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:49.550598", "source": { "split": "train_shard_00000", "doc_id": 1539 }, "chunk_id": "train_shard_00000_1539_0", "global_id": 1696 }, { "text": "In vitro digestion studies demonstrate large potential to gain more and quicker insights into the underlying mechanisms of feed additives, allowing the optimization of feed design. Unfortunately, current in vitro digestion models relevant for broiler chickens lack sufficient description in terms of protocols and standardisation used. Furthermore, no distinction is made between the different life phases of these animals (starter, grower, and finisher). Hence, our research aimed to establish adapted in vitro digestion conditions, corresponding to the 3 life phases in broilers, with specific focus on lipid digestion. The effect of 3 different bile salt concentrations of 2, 10, and 20 mM, and 3 different lipase activities of 5, 20, and 100 U/mL, on in vitro lipid digestion kinetics were evaluated using a full factorial design. These values were selected to represent starter, grower, and finisher birds, respectively. Our findings showed that the extent of lipid digestion was mainly influenced by lipase activity. The rate of lipid digestion was affected by an interplay between bile salt concentration and lipase activity, due to possible lipase inhibition at certain bile salt concentrations. Overall, this work resulted in 3 in vitro lipid digestion models representative for starter, grower, and finisher birds. In conclusion, this research showed the impact of adapted in vitro digestion conditions on lipid digestion kinetics and thus the need for these conditions relevant for each life phase of broilers.\n\nImportance of adapted digestion conditions to simulate in vitro lipid digestion of broilers in different life stages.", "token_count": 379, "char_count": 1640, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5447, "quality_score": 0.7724, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:50.132111", "source": { "split": "train_shard_00000", "doc_id": 1540 }, "chunk_id": "train_shard_00000_1540_0", "global_id": 1697 }, { "text": "Typhoid fever is transmitted by ingestion of polluted water, contaminated food, and stool of typhoid-infected individuals, mostly in developing countries with poor hygienic environments. To find novel therapeutic targets and inhibitors, We employed a subtractive genomics strategy towards Salmonella Typhi and the complete genomes of eight strains were primarily subjected to the EDGAR tool to predict the core genome (n = 3207). Human non-homology (n = 2450) was followed by essential genes identification (n = 37). The STRING database predicted maximum protein-protein interactions, followed by cellular localization. The virulent/immunogenic ability of predicted genes were checked to differentiate drug and vaccine targets. Furthermore, the 3D models of the identified putative proteins encoded by the respective genes were constructed and subjected to druggability analyses where only \"highly druggable\" proteins were selected for molecular docking and simulation analyses. The putative targets ATP-dependent CLP protease proteolytic subunit, Imidazole glycerol phosphate synthase hisH, 7,8-dihydropteroate synthase folP and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmI were screened against a drug-like library (n = 12,000) and top hits were selected based on H-bonds, RMSD and energy scores. Finally, the ADMET properties for novel inhibitors ZINC19340748, ZINC09319798, ZINC00494142, ZINC32918650 were optimized followed by binding free energy (MM/PBSA) calculation for ligand-receptor complexes. The findings of this work are expected to aid in expediting the identification of novel protein targets and inhibitors in combating typhoid Salmonellosis, in addition to the already existing therapies.", "token_count": 489, "char_count": 1726, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6826, "quality_score": 0.8413, "entities": { "genes": [ "ZINC00494142", "ZINC32918650", "ZINC09319798", "ZINC19340748" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:50.781516", "source": { "split": "train_shard_00000", "doc_id": 1541 }, "chunk_id": "train_shard_00000_1541_0", "global_id": 1698 }, { "text": "Genomic landscape of the emerging XDR Salmonella Typhi for mining druggable targets clpP, hisH, folP and gpmI and screening of novel TCM inhibitors, molecular docking and simulation analyses.", "token_count": 49, "char_count": 191, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:51.145360", "source": { "split": "train_shard_00000", "doc_id": 1541 }, "chunk_id": "train_shard_00000_1541_1", "global_id": 1699 }, { "text": "In the pre-clinical setting, hepatocellular bile salt accumulation impairs liver regeneration following partial hepatectomy. Here, we study the impact of cholestasis on portal vein embolization (PVE)-induced hypertrophy of the future liver remnant (FLR).\n\nInfluence of cholestasis on portal vein embolization-induced hypertrophy of the future liver remnant.", "token_count": 101, "char_count": 357, "word_count": 46, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:52.240534", "source": { "split": "train_shard_00000", "doc_id": 1542 }, "chunk_id": "train_shard_00000_1542_0", "global_id": 1700 }, { "text": "Basmisanil, is a lipophilic drug substance, exhibiting poor solubility and good permeability (BCS class 2). A validated physiologically based biopharmaceutics model (PBBM) has been previously described for tablets dosed in the fed state. The PBBM captured the less than proportional increases in exposure at higher doses well and indicated that absorption was dissolution rate-limited below 200 mg while solubility was limiting for higher doses. In this study, a model for dosing in the fasted state is described and is verified for simulation of the food effect where exposures were ~1.5 fold higher when a 660 mg tablet was given with food. The model is then applied to simulate the food effect for a granules formulation given at a lower dose (120 mg). The food effect at the lower dose was reasonably simulated with a ratio of simulated/observed food effect of 1.35 for Cmax and 0.83 for AUC. Sensitivity analysis was carried out for uncertain model parameters to confirm that the model could predict the magnitude of the positive food effect with moderate to high confidence. This study suggests that a verified PBBM can provide a useful alternative to a repeat food effect study when formulation changes are minor. However, there is need for further evaluation of the approach and a definition of what formulation changes are minor in this context. In addition, this work highlights some uncertainties in the handling of solubility in PBBM, in particular around temperature dependency of solubility and the parameterization of bile salt solubilization using measurements in biorelevant media.\n\nPhysiologically Based Biopharmaceutics Modeling of Food Effect for Basmisanil: A Retrospective Case Study of the Utility for Formulation Bridging.", "token_count": 400, "char_count": 1746, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:52.868174", "source": { "split": "train_shard_00000", "doc_id": 1543 }, "chunk_id": "train_shard_00000_1543_0", "global_id": 1701 }, { "text": "Early intervention in rheumatoid arthritis (RA) is critical for optimal treatment, but initiation of pharmacotherapy to prevent damage remains unsatisfactory currently. Manipulation of the gut microbiome and microbial metabolites can be effective in protecting against RA. Thus, probiotics can be utilized to explore new strategies for preventing joint damage. The aim of this study was to explore the metabolites and mechanisms by which", "token_count": 95, "char_count": 437, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7937, "quality_score": 0.8968, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:53.248077", "source": { "split": "train_shard_00000", "doc_id": 1544 }, "chunk_id": "train_shard_00000_1544_0", "global_id": 1702 }, { "text": "In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil.\n\nHybrid Genomic Analysis of", "token_count": 311, "char_count": 1227, "word_count": 179, "semantic_coherence": 1, "information_density": 0.5922, "quality_score": 0.7961, "entities": { "genes": [ "SE3", "SE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:53.831069", "source": { "split": "train_shard_00000", "doc_id": 1545 }, "chunk_id": "train_shard_00000_1545_0", "global_id": 1703 }, { "text": "The production and consumption of pineapple creates large quantities of residues. Ensiling these residues might help to minimize the waste burden and meet the intensive feed demand for ruminants. Proper lactic acid bacteria (LAB) are not only responsible for pineapple residual silage fermentation, but might also deliver probiotics. The aim of this study was to isolate LAB strains with probiotic functions, and to enhance intestinal antioxidant capacity from naturally fermented pineapple residues. A total of 47 LAB isolates with gram-positive, catalase-negative, nonhemolytic properties were used for probiotic screening. Lactiplantibacillus plantarum (L. plantarum) A1, C1 and C10 were susceptible to rifampicin, gentamicin and erythromycin, did not contain virulence factor-coding genes and showed good tolerance to acid (pH 3.0), 0.5% bile salt and simulated gastric and intestinal fluid. Their hydrophobicity indices were 71.92%, 45.50% and 66.90%, respectively. All of them were able to adhere to bovine jejunum epithelial cells (BJECs) and to antagonize Escherichia coli F5 and Salmonella Dublin. These three LAB strains tolerated hydrogen peroxide and significantly decreased (p < 0.05) reactive oxygen species levels in BJECs. In addition, L. plantarum C1 and C10 significantly increased (p < 0.05) the total antioxidant capacity in BJECs in the presence of 200 μmol/L hydrogen peroxide condition. L. plantarum A1, C1 and C10 are potential probiotics isolated from pineapple residual silage. This study aims to promote pineapple residue’s utilization in the feed industry.", "token_count": 458, "char_count": 1584, "word_count": 229, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:54.465208", "source": { "split": "train_shard_00000", "doc_id": 1546 }, "chunk_id": "train_shard_00000_1546_0", "global_id": 1704 }, { "text": "Lben is a dairy fermented food that is largely consumed in Tunisia for its numerous health benefits that are related to the existence of probiotics. Lactic Acid Bacteria (LAB) are well known for their beneficial probiotic properties for humans, especially when administered in adequate amounts. The aim of this study was to isolate and investigate the probiotics properties of Lacticaseibacillus paracasei L2 from Lben. The isolated strain was identified by 16S r-RNA gene sequences and MALDI- TOF MS. To evaluate the probiotic potential of the isolated bacterium, in vitro tests were performed, including adhesion ability to HCT-116 cells, survival in acid and bile salt conditions, lysozyme resistance, biofilm formation, hemolytic activity, antioxidant activity, and antimicrobial activity. Our results revealed that the selected Lacticaseibacillus paracasei L2 strain expressed a high adherence to HCT-116 cells (45.03%), survived under acidic conditions (pH3), and showed a resistance to bile salts. The strain was considered as safe (α-hemolysis). L. paracasei L2 showed a high biofilm-formation ability (OD 570 > 1.7) after 24 h of incubation. It also demonstrated an important antioxidant activity in the range of 85.31% for the intact cells. However, an antimicrobial activity against pathogens, namely Staphylococcus aureus, was detected with an IZ that was above 19 mm. In conjunction with the results obtained and the technological properties of Lacticaseibacillus paracasei L2 (proteolytic property, autolytic activity, acidifying activity, and EPS production), this strain may be used as a probiotic for manufacturing fermented foods.\n\nCharacterization of Probiotic Properties of", "token_count": 451, "char_count": 1693, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:55.107919", "source": { "split": "train_shard_00000", "doc_id": 1547 }, "chunk_id": "train_shard_00000_1547_0", "global_id": 1705 }, { "text": "Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on generalized linear regression that is robust to population structure, sampling bias, and errors in the predicted presence/absence of genes. We show using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analyzing several diverse bacterial genome data sets representing major human pathogens.\n\nRobust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe.", "token_count": 246, "char_count": 1236, "word_count": 181, "semantic_coherence": 1, "information_density": 0.674, "quality_score": 0.837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:55.592325", "source": { "split": "train_shard_00000", "doc_id": 1548 }, "chunk_id": "train_shard_00000_1548_0", "global_id": 1706 }, { "text": "Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.\n\nA chromosome-level reference genome and pangenome for barn swallow population genomics.", "token_count": 217, "char_count": 1017, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:56.057279", "source": { "split": "train_shard_00000", "doc_id": 1549 }, "chunk_id": "train_shard_00000_1549_0", "global_id": 1707 }, { "text": "Probiotic-based oral therapy can potentially prevent and treat diseases by regulating the balance of intestinal flora. However, significant loss of viability and bioactivity of probiotics before reaching the colon results in low delivery efficiency and therapeutic effects, which limits their clinical applications. Here, this work proposes a multishell colloidosome (MSC) platform with sequential gastrointestinal resistance for on-demand probiotic delivery based on biomimetic mineralization and microfluidic technology. Notably, the viability of the decorated probiotics increases 280-fold compared to that of free bacteria during preservation. Because of the sequential gastrointestinal resistance of MSC, encapsulated probiotics exhibit high viability (61%) under continuous exposure to extreme acidity, bile salt erosion, and enzymatic action, whereas free bacteria have a viability of 0%. Moreover, in vitro and in vivo studies reveal that MSC mainly releases probiotics in the colon and improves colonic colonization by probiotics to maintain the integrity of the intestinal barrier and regulate the balance of intestinal flora. Consequently, MSC significantly improves the therapeutic effect on colitis in mice. The MSC platform provides a promising delivery strategy to enhance the efficacy of orally administered probiotics.\n\nMultishell Colloidosome Platform with Sequential Gastrointestinal Resistance for On-Demand Probiotic Delivery.", "token_count": 332, "char_count": 1447, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6146, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:56.633849", "source": { "split": "train_shard_00000", "doc_id": 1550 }, "chunk_id": "train_shard_00000_1550_0", "global_id": 1708 }, { "text": "Kluyveromyces marxianus is a non-conventional yeast with outstanding physiological characteristics and a high potential for lignocellulosic ethanol production. However, achieving high ethanol productivity requires overcoming several biotechnological challenges due to the cellular inhibition caused by the inhibitors present in the medium. In this work, K. marxianus SLP1 was adapted to increase its tolerance to a mix of inhibitory compounds using the adaptive laboratory evolution strategy to study the adaptation and stress response mechanisms used by this non-Saccharomyces yeast. The fermentative and physiological parameters demonstrated that the adapted K. marxianus P8 had a better response against the synergistic effects of multiple inhibitors because it reduced the lag phase from 12 to 4 h, increasing the biomass by 40% and improving the volumetric ethanol productivity 16-fold than the parental K. marxianus SLP1. To reveal the effect of adaptation process in P8, transcriptome analysis was carried out; the result showed that the basal gene expression in P8 changed, suggesting the biological capability of K. marxianus to activate the adaptative prediction mechanism. Similarly, we carried out physiologic and transcriptome analyses to reveal the mechanisms involved in the stress response triggered by furfural, the most potent inhibitor in K. marxianus. Stress response studies demonstrated that P8 had a better physiologic response than SLP1, since key genes related to furfural transformation (ALD4 and ALD6) and stress response (STL1) were upregulated. Our study demonstrates the rapid adaptability of K. marxianus to stressful environments, making this yeast a promising candidate to produce lignocellulosic ethanol. KEY POINTS: • K. marxianus was adapted to increase its tolerance to a mix of inhibitory compounds • The basal gene expression of K. marxianus changed after the adaptation process • Adapted K. marxianus showed a better physiological response to stress by inhibitors • Transcriptome analyses revealed key genes involved in the stress response.", "token_count": 486, "char_count": 2080, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5133, "quality_score": 0.7567, "entities": { "genes": [ "ALD4", "ALD6", "STL1", "SLP1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:57.617278", "source": { "split": "train_shard_00000", "doc_id": 1551 }, "chunk_id": "train_shard_00000_1551_0", "global_id": 1709 }, { "text": "Physiological and transcriptome analyses of Kluyveromyces marxianus reveal adaptive traits in stress response.", "token_count": 27, "char_count": 110, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:57.973731", "source": { "split": "train_shard_00000", "doc_id": 1551 }, "chunk_id": "train_shard_00000_1551_1", "global_id": 1710 }, { "text": "Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were challenging with previous reference-based methods. In this work, we extend these methods into transcriptomics to analyze sequencing data using the pantranscriptome: a population-level transcriptomic reference. Our toolchain, which consists of additions to the VG toolkit and a standalone tool, RPVG, can construct spliced pangenome graphs, map RNA sequencing data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. We show that this workflow improves accuracy over state-of-the-art RNA sequencing mapping methods, and that it can efficiently quantify haplotype-specific transcript expression without needing to characterize the haplotypes of a sample beforehand.\n\nHaplotype-aware pantranscriptome analyses using spliced pangenome graphs.", "token_count": 238, "char_count": 1040, "word_count": 133, "semantic_coherence": 1, "information_density": 0.7068, "quality_score": 0.8534, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:58.443428", "source": { "split": "train_shard_00000", "doc_id": 1552 }, "chunk_id": "train_shard_00000_1552_0", "global_id": 1711 }, { "text": "For oral drug delivery the stability of liposomes against intestinal bile salts is of key importance. Here, asymmetric flow field-flow fractionation (AF4) coupled to multi-angle laser light scattering (MALLS) and a differential refractive index (dRI) detector was employed to monitor structural re-arrangement of liposomes upon exposure to the model bile salt taurocholate. For comparison, a conventional stability assay was employed using a hydrophilic marker and size exclusion chromatography (SEC) to separate released from liposome-entrapped dye. Calcein-containing liposomes with and without cholesterol were compared in terms of their in vitro stability upon exposure to bile salts by separating liposomes from co-existing colloidal species emerging after stress test using AF4/MALLS/dRI. Dynamic light scattering (DLS) was utilized in parallel. Our AF4/MALLS/dRI results suggested that exposure of egg-phospholipid liposomes to bile salts at physiological concentrations led to the formation of two new species of colloidal associates, likely (mixed) micelles. Subjecting cholesterol-containing liposomes to the same bile media did not lead to any new colloidal structures, indicating increased stability of these liposomes. Our SEC-based release assay largely confirmed these findings, indicating that AF4/MALLS/dRI is a suitable technique for prediction of in vitro oral stability of liposomal formulations. Moreover, the powerful AF4/MALLS/dRI technique appears promising to improve the understanding of the underlying mechanisms during bile salt-induced liposomal breakdown.\n\nInteraction of liposomes with bile salts investigated by asymmetric flow field-flow fractionation (AF4): A novel approach for stability assessment of oral drug carriers.", "token_count": 421, "char_count": 1756, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6043, "quality_score": 0.8021, "entities": { "genes": [ "AF4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:59.069259", "source": { "split": "train_shard_00000", "doc_id": 1553 }, "chunk_id": "train_shard_00000_1553_0", "global_id": 1712 }, { "text": "Open burning of agricultural residues causes numerous complications including particulate matter pollution in the air, soil degradation, global warming and many more. Since they possess bio-conversion potential, agro-industrial residues including sugarcane bagasse (SCB), rice straw (RS), corncob (CC) and sweet sorghum bagasse (SSB) were chosen for the study. Yeast strains, Candida tropicalis, C. shehatae, Saccharomyces cerevisiae, and Kluyveromyces marxianus var. marxianus were compared for their production potential of bioethanol and phenylacetylcarbinol (PAC), an intermediate in the manufacture of crucial pharmaceuticals, namely, ephedrine, and pseudoephedrine. Among the substrates and yeasts evaluated, RS cultivated with C. tropicalis produced significantly (p ≤ 0.05) higher ethanol concentration at 15.3 g L\n\nValorization of rice straw, sugarcane bagasse and sweet sorghum bagasse for the production of bioethanol and phenylacetylcarbinol.", "token_count": 265, "char_count": 954, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:13:59.610637", "source": { "split": "train_shard_00000", "doc_id": 1554 }, "chunk_id": "train_shard_00000_1554_0", "global_id": 1713 }, { "text": "The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of Kluyveromyces lactis, a yeast species well known for its involvement in dairy processes and also present in natural environments. Using a combination of short- and long-read sequencing strategies, we investigated the genomic variability of 41 K. lactis isolates and found that the overall genetic diversity of this species is very high (θw = 3.3 × 10-2) compared with other species such as Saccharomyces cerevisiae (θw = 1.6 × 10-2). However, the domesticated dairy population shows a reduced level of diversity (θw = 1 × 10-3), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus, as previously described. Our results highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation, and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.\n\nContrasting Genomic Evolution Between Domesticated and Wild Kluyveromyces lactis Yeast Populations.", "token_count": 409, "char_count": 1740, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6211, "quality_score": 0.8105, "entities": { "genes": [ "LAC12", "LAC4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:00.259439", "source": { "split": "train_shard_00000", "doc_id": 1555 }, "chunk_id": "train_shard_00000_1555_0", "global_id": 1714 }, { "text": "Kluyveromyces marxianus' high production of 2-phenylethyl acetate (2-PEA) via L-phenylalanine (Phe) catabolism makes it relevant for industries relying on the production of aroma compounds through fermentation processes. This study assessed the physiological impact of exogenous supplementation of Phe on cell viability, fermentation performance, and, by extension, on lipid and amino acid metabolism in a wine isolate of this yeast.\n\nComparative impact of exogenous phenylalanine on oenological isolates of Kluyveromyces marxianus and Saccharomyces cerevisiae.", "token_count": 160, "char_count": 561, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7671, "quality_score": 0.8836, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:00.725743", "source": { "split": "train_shard_00000", "doc_id": 1556 }, "chunk_id": "train_shard_00000_1556_0", "global_id": 1715 }, { "text": "Hyperlipidemia is a risk factor and key indicator for cardiovascular diseases, and the gut microbiota is highly associated with hyperlipidemia. Bacteroides vulgatus is a prevalent mutualist across human populations and confers multiple health benefits such as immunoregulation, antiobesity, and coronary artery disease intervention. However, its role in antihyperlipidemia has not been systematically characterized. This study sought to identify the effect of B. vulgatus Bv46 on hyperlipidemia. Hyperlipidemic rats were modeled by feeding them a high-fat diet for 6 weeks. The effect of B. vulgatus Bv46 supplementation was evaluated by measuring anthropometric parameters, lipid and inflammation markers, and the liver pathology. Multi-omics was used to explore the underlying mechanisms. The ability of B. vulgatus Bv46 to produce bile salt hydrolase was confirmed by gene annotation and\n\nBacteroides vulgatus Ameliorates Lipid Metabolic Disorders and Modulates Gut Microbial Composition in Hyperlipidemic Rats.", "token_count": 272, "char_count": 1014, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7122, "quality_score": 0.8561, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:01.325881", "source": { "split": "train_shard_00000", "doc_id": 1557 }, "chunk_id": "train_shard_00000_1557_0", "global_id": 1716 }, { "text": "Sideroxydans sp. CL21 is a microaerobic, acid-tolerant Fe(II)-oxidizer, isolated from the Schlöppnerbrunnen fen. Since the genome size of Sideroxydans sp. CL21 is 21% larger than that of the neutrophilic Sideroxydans lithotrophicus ES-1, we hypothesized that strain CL21 contains additional metabolic traits to thrive in the fen. The common genomic content of both strains contains homologs of the putative Fe(II) oxidation genes, mtoAB and cyc2. A large part of the accessory genome in strain CL21 contains genes linked to utilization of alternative electron donors, including NiFe uptake hydrogenases, and genes encoding lactate uptake and utilization proteins, motility and biofilm formation, transposable elements, and pH homeostasis mechanisms. Next, we incubated the strain in different combinations of electron donors and characterized the fen microbial communities. Sideroxydans spp. comprised 3.33% and 3.94% of the total relative abundance in the peatland soil and peatland water, respectively. Incubation results indicate Sideroxydans sp. CL21 uses H2 and thiosulfate, while lactate only enhances growth when combined with Fe, H2, or thiosulfate. Rates of H2 utilization were highest in combination with other substrates. Thus, Sideroxydans sp. CL21 is a mixotroph, growing best by simultaneously using substrate combinations, which helps to thrive in dynamic and complex habitats.\n\nMixotrophy broadens the ecological niche range of the iron oxidizer Sideroxydans sp. CL21 isolated from an iron-rich peatland.", "token_count": 423, "char_count": 1520, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [ "CL21" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:01.971308", "source": { "split": "train_shard_00000", "doc_id": 1558 }, "chunk_id": "train_shard_00000_1558_0", "global_id": 1717 }, { "text": "Ochratoxin A (OTA) is a potent mycotoxin found in foods and feeds, posing a health risk to animals and humans. Biological detoxification of OTA is considered a promising method, and some bacteria and fungi which can degrade OTA are isolated. However, research on safety and alleviating toxic effects are scarce. This study aims to isolate OTA-detoxification probiotics from natural samples and evaluate their safety and protective effects in mice. Here, a new OTA-detoxification strain named Pediococcus acidilactici NJB421 (P. acidilactici NJB421) was isolated from cow manure, which exhibited a removal rate of OTA at 48.53% for 48 h. P. acidilactici NJB421 exhibited high temperature resistance, acid tolerance, 0.3% bile salt and 1.4% trypsin resistance. The safety evaluation showed that P. acidilactici NJB421 at 2 × 10\n\nIsolation, identification and safety evaluation of OTA-detoxification strain Pediococcus acidilactici NJB421 and its effects on OTA-induced toxicity in mice.", "token_count": 292, "char_count": 984, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6759, "quality_score": 0.8379, "entities": { "genes": [ "NJB421" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:02.530917", "source": { "split": "train_shard_00000", "doc_id": 1559 }, "chunk_id": "train_shard_00000_1559_0", "global_id": 1718 }, { "text": "Oxidative damage to DNA is a significant source of mutations in living organisms. While DNA damage must be repaired to maintain the integrity of the genome and cell survival, errors made during DNA repair may contribute to evolution. Previous work has revealed that\n\nThe bile salt deoxycholate induces", "token_count": 65, "char_count": 301, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:02.897261", "source": { "split": "train_shard_00000", "doc_id": 1560 }, "chunk_id": "train_shard_00000_1560_0", "global_id": 1719 }, { "text": "Evolutionary dynamics of AP2/ERF and WRKY genes, the major components of defense response were studied extensively in the sesame pan-genome. Massive variation was observed for gene copy numbers, genome location, domain structure, exon-intron structure and protein parameters. In the pan-genome, 63% of AP2/ERF members were devoid of introns whereas >99% of WRKY genes contained multiple introns. AP2 subfamily was found to be micro-exon rich with the adjoining intronic sequences sharing sequence similarity to many stress-responsive and fatty acid metabolism genes. WRKY family included extensive multi-domain gene fusions where the additional domains significantly enhanced gene and exonic sizes as well as gene copy numbers. The fusion genes were found to have roles in acquired immunity, stress response, cell and membrane integrity as well as ROS signaling. The individual genomes shared extensive synteny and collinearity although ecological adaptation was evident among the Chinese and Indian accessions. Significant positive selection effects were noticed for both micro-exon and multi-domain genes. Splice variants with changes in acceptor, donor and branch sites were common and 6-7 splice variants were detected per gene. The study ascertained vital roles of lipid metabolism and chlorophyll biosynthesis in the defense response and stress signaling pathways. 60% of the studied genes localized in the nucleus while 20% preferred chloroplast. Unique cis-element distribution was noticed in the upstream promoter region with MYB and STRE in WRKY genes while MYC was present in the AP2/ERF genes. Intron-less genes exhibited great diversity in the promoter sequences wherein the predominance of dosage effect indicated variable gene expression levels. Mimicking the NBS-LRR genes, a chloroplast localized WRKY gene, Swetha_24868, with additional domains of chorismate mutase, cAMP and voltage-dependent potassium channel was found to act as a master regulator of defense signaling, triggering immunity and reducing ROS levels.", "token_count": 485, "char_count": 2035, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6151, "quality_score": 0.8076, "entities": { "genes": [ "AP2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:03.559967", "source": { "split": "train_shard_00000", "doc_id": 1561 }, "chunk_id": "train_shard_00000_1561_0", "global_id": 1720 }, { "text": "Gene fusions, micro-exons and splice variants define stress signaling by AP2/ERF and WRKY transcription factors in the sesame pan-genome.", "token_count": 39, "char_count": 137, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [ "AP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:03.917670", "source": { "split": "train_shard_00000", "doc_id": 1561 }, "chunk_id": "train_shard_00000_1561_1", "global_id": 1721 }, { "text": "Yersiniosis of cultured Atlantic salmon is a recurrent fish health management challenge in many continents. The causative organism, Yersinia ruckeri, can reside latently in the gut and lead to acute infection and disease during hatchery and sea-transfer stages. One potential prevention approach is the administration of probiotic bacteria to suppress gut colonization of Y. ruckeri. Our study aimed to isolate and identify anti-Yersinia activity among lactic acid bacteria (LAB) isolated from the gastrointestinal tract (GIT) of aquatic animals. Of the 186 aquatic GIT isolates examined, three strains showed diffusible antimicrobial activity towards Y. ruckeri O1b. Analysis of 16 s rRNA gene sequences indicated the three bacterial strains were Enterococci, related to Enterococcus sp. (99%), Enterococcus thailandicus (99%), and Enterococcus durans (99%). Anti-Yersinia activity was maintained at neutral pH (~6.5-7.0), and in-vitro environmental tolerance assays showed the three strains could withstand simulated salmonids gastrointestinal tract conditions of: low pH (3.4) and 3% bile salt content. All three Enterococci strains showed higher adhesion to the intestinal mucus of Atlantic salmon than Y. ruckeri O1b (E. durans 24%, E. enterococcus sp. 25% and E. thailandicus 98%, compared to Y. ruckeri O1b 5%). However, only Enterococcus sp. and E. thailandicus were able to grow in the salmon intestinal mucus broth while E. durans showed no growth. Anti-Yersinia activity was completely inactivated by proteinase-K treatment, suggesting that the active compound/s are proteinaceous and may be bacteriocin-like inhibitory substances (BLIS). Our data indicate that Enterococcus sp. MA176 and E. thailandicus MA122 are potential probionts for the prevention of yersiniosis in salmonids", "token_count": 509, "char_count": 1792, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8137, "entities": { "genes": [ "MA122", "MA176" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:04.549551", "source": { "split": "train_shard_00000", "doc_id": 1562 }, "chunk_id": "train_shard_00000_1562_0", "global_id": 1722 }, { "text": "Further in-vivo studies are required to determine whether these bacteria reduce the incidence of yersiniosis in Atlantic salmon.\n\nScreening and activity of potential gastrointestinal probiotic lactic acid bacteria against Yersinia ruckeri O1b.", "token_count": 61, "char_count": 243, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:04.919757", "source": { "split": "train_shard_00000", "doc_id": 1562 }, "chunk_id": "train_shard_00000_1562_1", "global_id": 1723 }, { "text": "Trueperella pyogenes, an opportunistic pathogen causes various ailments in different animals. Different strains from different animals have distinct characters phenotypically and genotypically. Hence understanding the strains in a particular geographical location helps in framing the preventive measures. Comparative genomics of all the available T. pyogenes genome in the NCBI was conducted to understand the relatedness among strains. Whole genome phylogeny showed host associated clustering of strains recovered from swine lungs. Core genome phylogeny also showed host associated clustering mimicking whole genome phylogeny results. MLST analysis showed that there was higher diversity among cattle strains. Multidimensional scaling revealed five swine clusters, two cattle and buffalo clusters. Pangenome analysis also showed that T. pyogenes had an open genome with 57.09% accessory genome. Host specific genes were identified by pangenome analysis, and (R)-citramalate synthase was specific for swine strains of Asian origin. Host specifc genes identified by pangenome analysis can be exploited for developing a molecular assay to specifically identify the strains. The study shows that MLST having higher discriminatory power can be used as an epidemiological tool for strain discrimination of T. pyogenes.\n\nComparative phylogenomics of Trueperella pyogenes reveals host-based distinction of strains.", "token_count": 318, "char_count": 1408, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:05.483424", "source": { "split": "train_shard_00000", "doc_id": 1563 }, "chunk_id": "train_shard_00000_1563_0", "global_id": 1724 }, { "text": "Forty-eight lactic acid bacteria (LAB) isolated from fermented mussels in Thailand were evaluated for their probiotic properties, bile salt hydrolase (BSH), cholesterol assimilation and immunomodulatory effects. They were identified as\n\nDistribution, cholesterol-lowering and immunomodulation effects of lactic acid bacteria from fermented mussel (", "token_count": 92, "char_count": 348, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:05.861186", "source": { "split": "train_shard_00000", "doc_id": 1564 }, "chunk_id": "train_shard_00000_1564_0", "global_id": 1725 }, { "text": "The worldwide emergence and diffusion of extended-spectrum β-lactamase-\n\nIntestinal colonization with ESBL-producing", "token_count": 32, "char_count": 116, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:06.227560", "source": { "split": "train_shard_00000", "doc_id": 1565 }, "chunk_id": "train_shard_00000_1565_0", "global_id": 1726 }, { "text": "Chiglitazar, a pan agonist of non-thiazolidinedione peroxisome proliferator-activated receptor, has the potential to regulate blood sugar, improve lipid metabolism, and reduce cardiovascular complications. This study aimed to examine the effect of cytochrome P450 (CYP) 3A4 inhibitors/inducers on the in vivo metabolism of chiglitazar and provide a reference for the clinical combination use of chiglitazar. A single-center, open-label, sequential crossover, and self-control study was carried out in 24 healthy subjects to determine the pharmacokinetics of chiglitazar dosed with and without CYP3A4 inhibitors and inducers. The findings showed that the CYP3A4 inhibitor itraconazole had no apparent pharmacokinetic drug interaction with chiglitazar, whereas rifampicin did. When combined with rifampicin after continuous dosing, chiglitazar exposure was not theoretically reduced but increased compared to a single dose of chiglitazar. The possible explanation may be the transporters of bile salt export pump, but this needs to be confirmed. The safety of chiglitazar in single or combination doses was well tolerated. The findings of this study provide a basis for clinical combinations of chiglitazar with CYP3A4 inhibitors or inducers.\n\nPharmacokinetic Interaction of Chiglitazar with CYP3A4 Inducer or Inhibitor: An Open-Label, Sequential Crossover, Self-Control, 3-Period Study in Healthy Chinese Volunteers.", "token_count": 375, "char_count": 1415, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6094, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:06.804444", "source": { "split": "train_shard_00000", "doc_id": 1566 }, "chunk_id": "train_shard_00000_1566_0", "global_id": 1727 }, { "text": "Management of late blight of potato incited by Phytophthora infestans remains a major challenge. Coevolution of pathogen with resistant strains and the rise of fungicide resistance have made it more challenging to prevent the spread of P. infestans. Here, the anti-oomycete potential of Bacillus velezensis VB7 against P. infestans through pan-genome analysis and molecular docking were explored. The Biocontrol potential of VB7 against P. infestans was assessed using a confrontational assay. The biomolecules from the inhibition zone were identified and subjected to in silico analysis against P. infestans target proteins. Nucleotide sequences for 54 B. velezensis strains from different geographical locations were used for pan-genome analysis. The confrontational assay revealed the anti-oomycetes potential of VB7 against P. infestans. Molecular docking confirmed that the penicillamine disulfide had the maximum binding energy with eight effector proteins of P. infestans. Besides, scanning electron microscopic observations of P. infestans interaction with VB7 revealed structural changes in hypha and sporangia. Pan-genome analysis between 54 strains of B. velezensis confirmed that the core genome had 2226 genes, and it has an open pan-genome. The present study confirmed the anti-oomycete potential of B. velezensis VB7 against P. infestans and paved the way to explore the genetic potential of VB7.\n\nPan-genome analysis and molecular docking unveil the biocontrol potential of Bacillus velezensis VB7 against Phytophthora infestans.", "token_count": 397, "char_count": 1545, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5229, "quality_score": 0.7615, "entities": { "genes": [ "VB7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:07.432204", "source": { "split": "train_shard_00000", "doc_id": 1567 }, "chunk_id": "train_shard_00000_1567_0", "global_id": 1728 }, { "text": "The effect of Lactiplantibacillus plantarum PGB02 isolated from buttermilk on serum cholesterol profile of normal and hypercholesterolemic mice was evaluated. Further changes in the expression of mice genes were determined. The hypercholesterolemia was induced in experimental mice by feeding high cholesterol and fat diet. Serum cholesterol parameters, physical parameters, cholic acid excretion, and cholesterol metabolism related gene expression analysis was carried out. L. plantarum PGB02 efficiently reduced total cholesterol, triglycerides, and LDL-cholesterol and improved HDL-cholesterol in hypercholesterolaemic mice. Body weight was reduced and fecal cholic acid increased in probiotic treatment groups. Gene expression analysis revealed that L. plantarum PGB02 up-regulated the expression of LDL receptors, CYP7A1, ABCA1, ABCG5, ABCG8, and down-regulated the expression of FXR and NPC1L1 genes. Summarizing the mechanism, L. plantarum PGB02 improved hypercholesterolemia by increasing bile acid synthesis and excretion, reducing exogeneous cholesterol absorption from the intestine, and increased LDL clearance through upregulation of LDL-receptors. The present study has given insight into the mechanism of serum cholesterol reduction by bile salt hydrolase positive L. plantarum PGB02 in mice. L. plantarum PGB02 reduced the serum cholesterol level through increased bile acid synthesis and deconjugation and reduced absorption of cholesterol in the intestine. Isolate PGB02 shown cholesterol removal potential as good as statin.\n\nLactiplantibacillus plantarum PGB02 Improved Serum Cholesterol Profile by Tweaking Genes Involved in Cholesterol Homeostasis in Male Swiss Albino Mice.", "token_count": 468, "char_count": 1696, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5202, "quality_score": 0.7601, "entities": { "genes": [ "ABCG8", "PGB02", "ABCA1", "ABCG5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:08.069730", "source": { "split": "train_shard_00000", "doc_id": 1568 }, "chunk_id": "train_shard_00000_1568_0", "global_id": 1729 }, { "text": "Trimethoprim-sulfamethoxazole (SXT) is the preferable treatment option of the infections caused by Achromobacter spp. Our study aimed to analyze the SXT resistance of 98 Achromobacter spp. isolates from pediatric patients, among which 33 isolates were SXT-resistant. The presence of intI1 was screened by PCR and genome sequence analyses. The intI1 gene was detected in 10 of SXT-resistant isolates that had shorter intI1 PCR fragments named intI1S. Structural changes in intI1S were confirmed by genome sequencing and analyses which revealed 86 amino acids deletion in IntI1S protein compared to canonical IntI1 protein. All IntI1S isolates were of non-CF origin. Pan-genome analysis of intI1S bearing A. xylosoxidans isolates comprised 9052 genes, with the core genome consisting of 5455 protein-coding genes. Results in this study indicate that IntI1S isolates were derived from clinical settings and that cystic fibrosis (CF) patients were potential reservoirs for healthcare-associated infections that occurred in non-CF patients.\n\nComparative genomics of trimethoprim-sulfamethoxazole-resistant Achromobacter xylosoxidans clinical isolates from Serbia reveals shortened variant of class 1 integron integrase gene.", "token_count": 336, "char_count": 1219, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:08.642658", "source": { "split": "train_shard_00000", "doc_id": 1569 }, "chunk_id": "train_shard_00000_1569_0", "global_id": 1730 }, { "text": "Methicillin-resistant Staphylococcus aureus bloodstream infections (MRSA-BSI) are a significant cause of mortality. We analysed the evolution of the molecular and clinical epidemiology of MRSA-BSI (n = 784) in adult patients (Barcelona, 1990−2019). Isolates were tested for antimicrobial susceptibility and genotyped (PFGE), and a selection was sequenced (WGS) to characterise the pangenome and mechanisms underlying antimicrobial resistance. Increases in patient age (60 to 71 years), comorbidities (Charlson’s index > 2, 10% to 94%), community-onset healthcare-associated acquisition (9% to 60%), and 30-day mortality (28% to 36%) were observed during the 1990−1995 and 2014−2019 periods. The proportion of catheter-related BSIs fell from 57% to 20%. Current MRSA-BSIs are caused by CC5-IV and an upward trend of CC8-IV and CC22-IV clones. CC5 and CC8 had the lowest core genome proportions. Antimicrobial resistance rates fell, and only ciprofloxacin, tobramycin, and erythromycin remained high (>50%) due to GyrA/GrlA changes, the presence of aminoglycoside-modifying enzymes (AAC(6′)-Ie-APH(2″)-Ia and ANT(4′)-Ia), and mph(C)/msr(A) or erm (C) genes. Two CC22-IV strains showed daptomycin resistance (MprF substitutions). MRSA-BSI has become healthcare-associated, affecting elderly patients with comorbidities and causing high mortality rates. Clonal replacement with CC5-IV and CC8-IV clones resulted in lower antimicrobial resistance rates. The increased frequency of the successful CC22-IV, associated with daptomycin resistance, should be monitored.", "token_count": 511, "char_count": 1559, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7282, "quality_score": 0.8641, "entities": { "genes": [ "CC5", "CC22", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:09.294060", "source": { "split": "train_shard_00000", "doc_id": 1570 }, "chunk_id": "train_shard_00000_1570_0", "global_id": 1731 }, { "text": "Molecular Epidemiology, Antimicrobial Susceptibility, and Clinical Features of Methicillin-Resistant", "token_count": 30, "char_count": 100, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:09.651418", "source": { "split": "train_shard_00000", "doc_id": 1570 }, "chunk_id": "train_shard_00000_1570_1", "global_id": 1732 }, { "text": "Under bile salt treatment, strains display significant differences in their tolerance ability, suggesting the existence of diverse resistance mechanisms in\n\nIdentification of Novel Bile Salt-Tolerant Genes in", "token_count": 41, "char_count": 208, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8519, "quality_score": 0.9259, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:10.012446", "source": { "split": "train_shard_00000", "doc_id": 1571 }, "chunk_id": "train_shard_00000_1571_0", "global_id": 1733 }, { "text": "Patients with psoriasis are at a higher risk of developing nonalcoholic fatty liver disease. We previously identified an oxidized derivative of cholesterol, 7-ketocholesterol (7KC), in diet-induced steatohepatitic mice. Here, we investigated whether 7KC exacerbates psoriasis-like dermatitis by accelerating steatohepatitis in mice. A high-fat/high-cholesterol/high-sucrose/bile salt diet (nonalcoholic steatohepatitis (NASH) diet) with or without 0.0125% 7KC was fed to C57BL/6 mice (7KC or control group) for three weeks to induce steatohepatitis. A 5% imiquimod cream was then applied to the ears and dorsal skin for four days to induce psoriasis-like dermatitis. Hepatic lipid accumulation and inflammatory cell infiltration were exacerbated in the 7KC group compared with the control group after three weeks. Serum tumor necrosis factor-α (TNF-α) levels were also elevated in the 7KC group (108.5 ± 9.8 vs. 83.1 ± 13.1 pg/mL, p < 0.005). Imiquimod cream increased the psoriasis area severity index (PASI) score in mice in the 7KC group (9.14 ± 0.75 vs. 5.17 ± 1.17, p < 0.0001). Additionally, Tnfa, Il23a, Il17a, and Il22 mRNA levels in the dorsal lesion were significantly upregulated. Finally, Th17 cell differentiation and the TNF signaling pathway were enhanced in the dorsal lesions and liver of mice in the 7KC group. These data suggest that steatohepatitis and psoriasis are linked by a potent, diet-related factor.", "token_count": 493, "char_count": 1427, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:10.662397", "source": { "split": "train_shard_00000", "doc_id": 1572 }, "chunk_id": "train_shard_00000_1572_0", "global_id": 1734 }, { "text": "A Dietary Oxysterol, 7-Ketocholesterol, Exacerbates Imiquimod-Induced Psoriasis-like Dermatitis in Steatohepatitic Mice.", "token_count": 48, "char_count": 120, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:11.017022", "source": { "split": "train_shard_00000", "doc_id": 1572 }, "chunk_id": "train_shard_00000_1572_1", "global_id": 1735 }, { "text": "Colorectal cancer (CRC) ranks third among all cancers in terms of prevalence. There is growing evidence that gut microbiota has a role in the development of colorectal cancer. Fusobacterium nucleatum is overrepresented in the gastrointestinal tract and tumor microenvironment of patients with CRC. This suggests the role of F. nucleatum as a potential risk factor in the development of CRC. Hence, we aimed to explore whole genomes of F. nucleatum strains related to CRC to predict potential therapeutic markers through a pan-genome integrated subtractive genomics approach. In the current study, we identified 538 proteins as essential for F. nucleatum survival, 209 non-homologous to a human host, and 12 as drug targets. Eventually, riboflavin synthase (RiS) was selected as a therapeutic target for further processing. Three different inhibitor libraries of lead-like natural products, i.e., cyanobactins (n = 237), streptomycins (n = 607), and marine bacterial secondary metabolites (n = 1226) were screened against it. After the structure-based study, three compounds, i.e., CMNPD3609 (−7.63) > Malyngamide V (−7.03) > ZINC06804365 (−7.01) were prioritized as potential inhibitors of F. nucleatum. Additionally, the stability and flexibility of these compounds bound to RiS were determined via a molecular dynamics simulation of 50 ns. Results revealed the stability of these compounds within the binding pocket, after 5 ns. ADMET profiling showed compounds as drug-like, non-permeable to the blood brain barrier, non-toxic, and HIA permeable. Pan-genomics mediated drug target identification and the virtual screening of inhibitors is the preliminary step towards inhibition of this pathogenic oncobacterium and we suggest mouse model experiments to validate our findings.\n\nTherapeutic Target Identification and Inhibitor Screening against Riboflavin Synthase of Colorectal Cancer Associated", "token_count": 510, "char_count": 1898, "word_count": 272, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [ "ZINC06804365", "CMNPD3609" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:11.642885", "source": { "split": "train_shard_00000", "doc_id": 1573 }, "chunk_id": "train_shard_00000_1573_0", "global_id": 1736 }, { "text": "The marketed oral solution of itraconazole (Sporanox®) contains 40% (259.2 mM) of 2-hydroxypropyl-β-cyclodextrin (HP-β-CD). The obvious role of HP-β-CD is to solubilize itraconazole and to overcome its poor aqueous solubility that restricts its absorption. In this study, we investigated the biorelevance of in vitro experiments by the influence of biomimetic media (containing bile salts and phospholipids) on the predicted itraconazole absorption from the commercial HP-β-CD-based Sporanox® solution. We performed phase-solubility studies of itraconazole and dynamic 2-step-dissolution/permeation studies using a biomimetic artificial barrier, Sporanox® solution, and fasted state simulated intestinal fluid (FaSSIF_V1). Both FaSSIF_V1 and HP-β-CD increased the apparent solubility of itraconazole when used individually. In combination, their solubility-enhancing effects were not additive probably due to the competition of bile salts with itraconazole for the hydrophobic cavity of HP-β-CD. Our combined dissolution/permeation experiments indicated the occurrence of a transient supersaturation from Sporanox® upon two-step dissolution. Through systematic variation of bile salt concentrations in the biomimetic media, it was observed that the extent and the duration of supersaturation depend on the concentrations of bile salts: supersaturation was rather stable in the absence of bile salts and phospholipids. The higher the bile salt concentration, the faster the collapse of the transient supersaturation occurred, an effect which is nicely mirrored by reduced in vitro permeation across the barrier. This is an indication of a negative food effect, which in fact correlates well with what earlier had been observed in clinical studies for Sporanox® solution", "token_count": 467, "char_count": 1768, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5958, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:12.313632", "source": { "split": "train_shard_00000", "doc_id": 1574 }, "chunk_id": "train_shard_00000_1574_0", "global_id": 1737 }, { "text": "In essence, we could demonstrate that in vitro two-stage dissolution/permeation experiments using an artificial barrier and selected biomimetic media may predict the negative effects of the latter on cyclodextrin-based drug formulations like Sporanox® Oral Solution and, at the same time, provide a deeper mechanistic insight.\n\nWhen Interactions Between Bile Salts and Cyclodextrin Cause a Negative Food Effect: Dynamic Dissolution/Permeation Studies with Itraconazole (Sporanox®) and Biomimetic Media.", "token_count": 127, "char_count": 502, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:12.730586", "source": { "split": "train_shard_00000", "doc_id": 1574 }, "chunk_id": "train_shard_00000_1574_1", "global_id": 1738 }, { "text": "Corynebacterium striatum has recently received increasing attention due to its multiple antimicrobial resistances and its role as an invasive infection/outbreak agent. Recently, whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) has been used in epidemiological studies of specific human pathogens. However, this method has not been reported in studies of C. striatum. In this work, we aim to propose a cgMLST scheme for C. striatum. All publicly available C. striatum genomes, 30 C. striatum strains isolated from the same hospital, and 1 epidemiologically unrelated outgroup C. striatum strain were used to establish a cgMLST scheme targeting 1,795 genes (hereinafter referred to as 1,795-cgMLST). The genotyping results of cgMLST showed good congruence with core genome-based single-nucleotide polymorphism typing in terms of tree topology. In addition, the cgMLST provided a greater discrimination than the MLST method based on 6 housekeeping genes (\n\nEpidemiological Investigation of Hospital Transmission of Corynebacterium striatum Infection by Core Genome Multilocus Sequence Typing Approach.", "token_count": 301, "char_count": 1133, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6815, "quality_score": 0.8408, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:13.337231", "source": { "split": "train_shard_00000", "doc_id": 1575 }, "chunk_id": "train_shard_00000_1575_0", "global_id": 1739 }, { "text": "The Tibetan livestock sector is now ailing from many infectious ailments brought on by harmful microorganisms. Therefore, this research aimed to assess the probiotic potential and safety of Bacillus amyloliquefaciens isolated from yaks in the Tibet area to provide upper-edge strain resources for probiotics development. The four strains isolated from the intestine of yaks had been identified as Bacillus amyloliquefaciens after the 16S rRNA sequence. The ethanol, bile salt, and acid tolerance revealed that the isolates had significant tolerance levels. The antibiotics susceptibility assay showed that the strains were sensitive to commonly used antibiotics, while the antibacterial assay prevented the isolates from outperforming five harmful bacteria in terms of antibacterial potency. Moreover, it was evident that strain BA5 had the strongest activity to scavenge hydroxyl radical and reduce power. According to the animal experiment, no apparent pathological change was observed in intestinal tissue sections. Furthermore, the strain had a positive effect on promoting the development of jejunal villi referred to its safety. Therefore, more research is required into the bacteriostatic and antioxidant capabilities of isolates in animal production.\n\nProbiotic Potential of Bacillus amyloliquefaciens Isolated from Tibetan Yaks.", "token_count": 307, "char_count": 1337, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "BA5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:13.936564", "source": { "split": "train_shard_00000", "doc_id": 1576 }, "chunk_id": "train_shard_00000_1576_0", "global_id": 1740 }, { "text": "Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from \"normal skin microbiome\" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.\n\nThe pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum.", "token_count": 452, "char_count": 1761, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [ "ATCC6940" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:14.574148", "source": { "split": "train_shard_00000", "doc_id": 1577 }, "chunk_id": "train_shard_00000_1577_0", "global_id": 1741 }, { "text": "Deep sequencing is a term that has become embedded in the plant genomic literature in recent years and with good reason. A torrent of (largely) high-quality genomic and transcriptomic data has been collected and most of this has been publicly released. Indeed, almost 1000 plant genomes have been reported (www.plabipd.de) and the 2000 Plant Transcriptomes Project has long been completed. The EarthBioGenome project will dwarf even these milestones. That said, massive progress in understanding plant physiology, evolution, and crop domestication has been made by sequencing broadly (across a species) as well as deeply (within a single individual). We will outline the current state of the art in genome and transcriptome sequencing before we briefly review the most visible of these broad approaches, namely genome-wide association and transcriptome-wide association studies, as well as the compilation of pangenomes. This will include both (i) the most commonly used methods reliant on single nucleotide polymorphisms and short InDels and (ii) more recent examples which consider structural variants. We will subsequently present case studies exemplifying how their application has brought insight into either plant physiology or evolution and crop domestication. Finally, we will provide conclusions and an outlook as to the perspective for the extension of such approaches to different species, tissues, and biological processes.\n\nGoing broad and deep: sequencing-driven insights into plant physiology, evolution, and crop domestication.", "token_count": 337, "char_count": 1543, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:15.142304", "source": { "split": "train_shard_00000", "doc_id": 1578 }, "chunk_id": "train_shard_00000_1578_0", "global_id": 1742 }, { "text": "Avian pathogenic Escherichia coli, a causative agent of avian colibacillosis, has been causing serious economic losses in the poultry industry. The increase in multidrug-resistant isolates and the complexity of the serotypes of this pathogen, especially the recently reported emergence of a newly predominant serogroup of O145, make the control of this disease difficult. To address this challenge, a high-throughput screening approach, called Pan-RV (Reverse vaccinology based on pangenome analysis), is proposed to search for universal protective antigens against the three traditional serogroups and the newly emerged O145. Using this approach, a total of 61 proteins regarded as probable antigens against the four important serogroups were screened from the core genome of 127 Avian pathogenic Escherichia coli (APEC) genomes, and six were verified by Western blots using antisera. Overall, our research will provide a foundation for the development of an APEC subunit vaccine against avian colibacillosis. Given the exponential growth of whole-genome sequencing (WGS) data, our Pan-RV pipeline will make screening of bacterial vaccine candidates inexpensive, rapid, and efficient.\n\nIdentification of Subunits for Novel Universal Vaccines against Three Predominant Serogroups and the Emerging O145 among Avian Pathogenic Escherichia coli by Pan-RV Pipeline.", "token_count": 337, "char_count": 1361, "word_count": 191, "semantic_coherence": 1, "information_density": 0.644, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:15.710822", "source": { "split": "train_shard_00000", "doc_id": 1579 }, "chunk_id": "train_shard_00000_1579_0", "global_id": 1743 }, { "text": "Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato, respectively. The latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenome versus a single reference dramatically improves heritability in tomato.", "token_count": 65, "char_count": 305, "word_count": 43, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:16.078909", "source": { "split": "train_shard_00000", "doc_id": 1580 }, "chunk_id": "train_shard_00000_1580_0", "global_id": 1744 }, { "text": "Akkermansia muciniphila is a human intestinal tract bacterium that plays an important role in the mucus layer renewal. Several studies have demonstrated that it is a modulator for gut homeostasis and a probiotic for human health. The Akkermansia genus contains two species with standing in nomenclature but their genomic diversity remains unclear. In this study, eight new Akkermansia sp. strains were isolated from the human gut. Using the digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analysis applied to 104 A. muciniphila whole genomes sequences, strains were reclassified into three clusters. Cluster I groups A. muciniphila strains (including strain ATCC BAA-835\n\nReclassification of eight Akkermansia muciniphila strains and description of Akkermansia massiliensis sp. nov. and Candidatus Akkermansia timonensis, isolated from human feces.", "token_count": 246, "char_count": 907, "word_count": 126, "semantic_coherence": 1, "information_density": 0.7302, "quality_score": 0.8651, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:16.565334", "source": { "split": "train_shard_00000", "doc_id": 1581 }, "chunk_id": "train_shard_00000_1581_0", "global_id": 1745 }, { "text": "Probiotic microorganisms are incorporated in foods due to their numerous health benefits. We investigated lactic acid bacteria (LAB) and yeasts isolated from goat milk in Nigeria for novel probiotic strains. In this study, a total of 27 LAB and 23 yeast strains were assessed for their probiotic potentials. Only six LAB strains (Weissella cibaria GM 93m3, Weissella confusa GM 92m1, Pediococcus acidilactici GM 18a, Pediococcus pentosaceus GM 23d, Lactiplantibacillus pentosus GM 102s4, Limosilactobacillus fermentum GM 30m1) and four yeast strains (Candida tropicalis 12a, C. tropicalis 33d, Diutina rugosa 53b, and D. rugosa 77a) identified using partial 16S and 26S rDNA sequencing, respectively, showed survival at pH 2.5, 0.3% bile salt, and simulated gastrointestinal conditions and possessed auto-aggregative and hydrophobic properties, thus satisfying key in vitro criteria as probiotics. All LAB strains showed coaggregation properties and antimicrobial activities against pathogens. Pediococcus pentosaceus GM 23d recorded the strongest coaggregation percentage (34-94%) against 14 pathogens, while W. cibaria GM 93m3 showed the least (6-57%) against eight of the 14 pathogens. The whole cell and extracellular extracts of LAB and yeast strains, with the exception of D. rugosa 77a, had either 2,2-diphenyl-1-picryl-hydrazyl and/or hydroxyl radical scavenging activity. In conclusion, all six LAB and four yeast strains are important probiotic candidates that can be further investigated for use as functional starter cultures.\n\nProbiotic Potentials of Lactic Acid Bacteria and Yeasts from Raw Goat Milk in Nigeria.", "token_count": 507, "char_count": 1626, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:17.210424", "source": { "split": "train_shard_00000", "doc_id": 1582 }, "chunk_id": "train_shard_00000_1582_0", "global_id": 1746 }, { "text": "What makes a good reference? First steps toward a Chlamydomonas pangenome.", "token_count": 20, "char_count": 74, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:17.569417", "source": { "split": "train_shard_00000", "doc_id": 1583 }, "chunk_id": "train_shard_00000_1583_0", "global_id": 1747 }, { "text": "The human gut acts as a habitat for diverse microbial communities, including mucin utilizers that play a significant role in host health and diseases. In this study, a gram-positive, rod-shaped mucin degrading bacterium was isolated from human faeces that belonged to the Priestia flexa species. Priestia isolate was analyzed for mucin-degrading ability and found that the KS1 strain could grow on mucin as the sole carbon source. The experimental results of the mucolytic zone around the colony and a 58% decrease in carbohydrate concentration confirmed the ability of Priestia to degrade mucin. The intracellular and extracellular glycosidase assay data supported the above results suggesting the ability of P. flexa to produce glycan hydrolysis enzymes that convert complex mucin oligosaccharide chains into simple glycans. The survival ability of the KS1 strain in simulated gastrointestinal conditions revealed that it could tolerate low pH (≥ 50% cell viability at pH 1.0) and 0.5% bile salt concentration (≥ 85% cell viability). The strain showed low hydrophobicity towards n-hexadecane (26.51 ± 0.92%) and xylene (21.71 ± 0.54%). Moreover, the KS1 culture was resistant to cefixime, clavulanic acid/ceftazidime, nafallin, methicillin, trimethoprim, kanamycin, and nalidixic antibiotic. Our results highlight the isolation of P. flexa KS1 strain that degrade mucin under in vitro conditions and show its better acclimatization within the GI environment. Further studies are required to unearth the molecular mechanisms involved in the degradation of mucin oligosaccharides in the human gut, advancing our understanding of health and disease.\n\nPriestia flexa KS1: A new bacterial strain isolated from human faeces implicated in mucin degradation.", "token_count": 501, "char_count": 1752, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [ "KS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:18.215515", "source": { "split": "train_shard_00000", "doc_id": 1584 }, "chunk_id": "train_shard_00000_1584_0", "global_id": 1748 }, { "text": "Cholestasis is characterized by impaired bile flow which results in inflammation, cirrhosis, and ultimately liver failure. The current study is aimed to evaluate the anti-cholestatic effect of silymarin against α-naphthylisothiocyanate (ANIT) induced cholestasis. Mice were gavaged with various doses of silymarin or ursodeoxycholic acid (UDCA) for 19 days. Then they were challenged with α-naphthylisothiocyanate (ANIT) and after 48 hours the animals were sacrificed to obtain blood and liver sections. Serum levels of bilirubin, aspartate transaminase (AST), alanine transaminase (ALP), and liver histology were analyzed. mRNA expression of selected transporters (Bile salt export pump (BSEP) and sodium taurocholate cotransporting polypeptide (NTCP)) and proteins (farnesoid x receptor (FXR) and Cytochrome P450 Family 7 Subfamily A Member 1 (Cyp7a1)) involved in bile acids biosynthesis, excretion and uptake were also evaluated by quantitative PCR. The results indicated that the serum levels of bilirubin, AST, and ALP were significantly higher in a cholestatic model group as compared to an untreated control group. However, in silymarin groups, the serum level of these parameters is significantly lower than in a cholestatic model group. Liver histology also showed that silymarin prevents ANIT-induced hepatic injury. mRNA expression of FXR, BSEP, and NTCP was downregulated and expression of Cyp7a1 was upregulated in a cholestatic model group as compared to an untreated control group. However, in silymarin treatment groups, the expression of FXR, BSEP and NTCP was upregulated and the expression of Cyp7a1 was downregulated as compared to the cholestatic model group. In conclusion, silymarin could alleviate hepatic injury by modulating the expression of genes involved in bile acid homeostasis.", "token_count": 499, "char_count": 1810, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5598, "quality_score": 0.7799, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:18.883317", "source": { "split": "train_shard_00000", "doc_id": 1585 }, "chunk_id": "train_shard_00000_1585_0", "global_id": 1749 }, { "text": "Silymarin protects the liver from α-naphthylisothiocyanate-induced cholestasis by modulating the expression of genes involved in bile acid homeostasis.", "token_count": 43, "char_count": 151, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:19.243611", "source": { "split": "train_shard_00000", "doc_id": 1585 }, "chunk_id": "train_shard_00000_1585_1", "global_id": 1750 }, { "text": "Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains with different lifestyles in foods.\n\nPangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum.", "token_count": 181, "char_count": 689, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:19.683615", "source": { "split": "train_shard_00000", "doc_id": 1586 }, "chunk_id": "train_shard_00000_1586_0", "global_id": 1751 }, { "text": "The genus Rhodopseudomonas comprises purple non-sulfur bacteria with extremely versatile metabolisms. Characterization of several strains revealed that each is a distinct ecotype highly adapted to its specific micro-habitat. Here we present the sequencing, genomic comparison and functional annotation of AZUL, a Rhodopseudomonas strain isolated from a high altitude Andean lagoon dominated by extreme conditions and fluctuating levels of chemicals. Average nucleotide identity (ANI) analysis of 39 strains of this genus showed that the genome of AZUL is 96.2% identical to that of strain AAP120, which suggests that they belong to the same species. ANI values also show clear separation at the species level with the rest of the strains, being more closely related to R. palustris. Pangenomic analyses revealed that the genus Rhodopseudomonas has an open pangenome and that its core genome represents roughly 5 to 12% of the total gene repertoire of the genus. Functional annotation showed that AZUL has genes that participate in conferring genome plasticity and that, in addition to sharing the basal metabolic complexity of the genus, it is also specialized in metal and multidrug resistance and in responding to nutrient limitation. Our results also indicate that AZUL might have evolved to use some of the mechanisms involved in resistance as redox reactions for bioenergetic purposes. Most of those features are shared with strain AAP120, and mainly involve the presence of additional orthologs responsible for the mentioned processes. Altogether, our results suggest that AZUL, one of the few bacteria from its habitat with a sequenced genome, is highly adapted to the extreme and changing conditions that constitute its niche.\n\nThe draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis.", "token_count": 433, "char_count": 1862, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "AAP120" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:20.313674", "source": { "split": "train_shard_00000", "doc_id": 1587 }, "chunk_id": "train_shard_00000_1587_0", "global_id": 1752 }, { "text": "Campylobacter jejuni is a pervasive pathogen of major public health concern with a complex ecology requiring accurate and informative approaches to define pathogen diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic diversity of a C. jejuni population is not adequately captured in a single specimen. The aim of this study was to determine the genomic diversity of C. jejuni within individual stool specimens from four campylobacteriosis patients. Direct plating and pre-culture filtration of one stool specimen per patient was used to culture multiple isolates per stool specimen. Whole genome sequencing and pangenome level analysis were used to investigate genomic diversity of C. jejuni within a patient.\n\nComparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens.", "token_count": 192, "char_count": 855, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6612, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:20.763819", "source": { "split": "train_shard_00000", "doc_id": 1588 }, "chunk_id": "train_shard_00000_1588_0", "global_id": 1753 }, { "text": "Simultaneous saccharification and fermentation (SSF) is effective for minimizing sugar inhibition during high solids fermentation of biomass solids to ethanol. However, fungal enzymes used during SSF are optimal between 50 and 60 °C, whereas most fermentative yeast, such as Saccharomyces cerevisiae, do not tolerate temperatures above 37 °C. Kluyveromyces marxianus variant CBS 6556 is a thermotolerant eukaryote that thrives at 43 °C, thus potentially serving as a promising new host for SSF operation in biorefineries. Here, we attempt to leverage the thermotolerance of the strain to demonstrate the application of CBS 6556 in a high solids (up to 20 wt% insoluble solid loading) SSF configuration to understand its capabilities and limitations as compared to a proven SSF strain, S. cerevisiae D5A. For this study, we first pretreated hardwood poplar chips using Co-Solvent Enhanced Lignocellulosic Fractionation (CELF) to remove lignin and hemicellulose and to produce cellulose-enriched pretreated solids for SSF. Our results demonstrate that although CBS 6556 could not directly outperform D5A, it demonstrated similar tolerance to high gravity sugar solutions, superior growth rates at higher temperatures and higher early stage ethanol productivity. We discovered that CBS 6556's membrane was particularly sensitive to higher ethanol concentrations causing it to suffer earlier fermentation arrest than D5A. Cross-examination of metabolite data between CBS 6556 and D5A and cell surface imaging suggests that the combined stresses of high ethanol concentrations and temperature to CBS 6556's cell membrane was a primary factor limiting its ethanol productivity. Hence, we believe K. marxianus to be an excellent host for future genetic engineering efforts to improve membrane robustness especially at high temperatures in order to achieve higher ethanol productivity and titers, serving as a viable alternative to D5A.", "token_count": 492, "char_count": 1928, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:21.408373", "source": { "split": "train_shard_00000", "doc_id": 1589 }, "chunk_id": "train_shard_00000_1589_0", "global_id": 1754 }, { "text": "Prospects of thermotolerant Kluyveromyces marxianus for high solids ethanol fermentation of lignocellulosic biomass.", "token_count": 38, "char_count": 116, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:21.765940", "source": { "split": "train_shard_00000", "doc_id": 1589 }, "chunk_id": "train_shard_00000_1589_1", "global_id": 1755 }, { "text": "This study was conducted to determine the phylogenies of Salmonella strains isolated from cross-sectional studies conducted at hatcheries, broiler farms, processing plants, and retail outlets (broiler production chain) in Trinidad and Tobago over 4 yr (2016-2019). Whole-genome sequencing (WGS) was used to characterize Salmonella isolates. Core genome phylogenies of 8 serovars of public health significance were analyzed for similarities in origin and relatedness. In addition, Salmonella strains isolated from human salmonellosis cases in Trinidad were analyzed for their relatedness to the isolates detected along the broiler production chain. The common source of these isolates of diverse serovars within farms, within processing plants, between processing plants and retail outlets, and among farm-processing plant-retail outlet continuum was well-supported (bootstrap value >70%) by the core genome phylogenies for the respective serovars. Also, genome analyses revealed clustering of Salmonella serovars of regional (intra-Caribbean) and international (extra-Caribbean) origin. Similarly, strains of S. Enteritidis and S. Infantis isolated from human clinical salmonellosis in 2019 from Trinidad and Tobago clustered with our processing plant isolates recovered in 2018. This study is the first phylogenetic analysis of Salmonella isolates using WGS from the broiler industry in the Caribbean region. The use of WGS confirmed the genetic relatedness and transmission of Salmonella serovars contaminating chickens in broiler processing, and retailing in the country, with zoonotic and food safety implications for humans.\n\nPhylogenetic analyses of Salmonella detected along the broiler production chain in Trinidad and Tobago.", "token_count": 426, "char_count": 1734, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5466, "quality_score": 0.7733, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:22.387379", "source": { "split": "train_shard_00000", "doc_id": 1590 }, "chunk_id": "train_shard_00000_1590_0", "global_id": 1756 }, { "text": "Over the past two decades, livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has become widely prevalent in pig production in Europe. The carriage status of LA-MRSA is known to vary among individual pigs, but bacterial load in pigs has rarely been studied. We assessed the quantity of LA-MRSA in nasal and skin samples of pigs and investigated the genetic diversity of the strains together with sequenced strains from national surveillance and pathology samples from the Finnish Food Authority. On two farms with assumed MRSA-positive status, farm 1 and farm 2, 10 healthy pigs were sampled three times during 2 weeks from the nares and skin (study A). On farm 1, 54 additional pigs were sampled and from confirmed MRSA-positive animals, 10 were randomly selected and transported to a clean, controlled environment for further sampling (study B). From the samples taken on farms 1 and 2 and in the controlled environment, MRSA was isolated both by direct plating and enrichment on selective media. spa types, multilocus sequence types, staphylococcal cassette chromosome mec types, resistance and virulence genes were determined. Core genome multilocus sequence typing (cgMLST) analysis was performed, including the sequences deriving from the surveillance/pathology samples from the Finnish Food Authority.\n\nLow-level colonization of methicillin-resistant Staphylococcus aureus in pigs is maintained by slowly evolving, closely related strains in Finnish pig farms.", "token_count": 369, "char_count": 1491, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6193, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:22.969880", "source": { "split": "train_shard_00000", "doc_id": 1591 }, "chunk_id": "train_shard_00000_1591_0", "global_id": 1757 }, { "text": "As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects.\n\nA technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes.", "token_count": 80, "char_count": 372, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:23.346942", "source": { "split": "train_shard_00000", "doc_id": 1592 }, "chunk_id": "train_shard_00000_1592_0", "global_id": 1758 }, { "text": "Temperature is a key variable in biological processes. However, a complete understanding of biological temperature adaptation is lacking, in part because of the unique constraints among different evolutionary lineages and physiological groups. Here we compared the genomes of cultivated psychrotolerant and thermotolerant methanogens, which are physiologically related and span growth temperatures from -2.5°C to 122°C. Despite being phylogenetically distributed amongst three phyla in the archaea, the genomic core of cultivated methanogens comprises about one-third of a given genome, while the genome fraction shared by any two organisms decreases with increasing phylogenetic distance between them. Increased methanogenic growth temperature is associated with reduced genome size, and thermotolerant organisms-which are distributed across the archaeal tree-have larger core genome fractions, suggesting that genome size is governed by temperature rather than phylogeny. Thermotolerant methanogens are enriched in metal and other transporters, and psychrotolerant methanogens are enriched in proteins related to structure and motility. Observed amino acid compositional differences between temperature groups include proteome charge, polarity and unfolding entropy. Our results suggest that in the methanogens, shared physiology maintains a large, conserved genomic core even across large phylogenetic distances and biology's temperature extremes.\n\nThe methanogen core and pangenome: conservation and variability across biology's growth temperature extremes.", "token_count": 349, "char_count": 1561, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:23.935023", "source": { "split": "train_shard_00000", "doc_id": 1593 }, "chunk_id": "train_shard_00000_1593_0", "global_id": 1759 }, { "text": "The Clostridioides difficile pathogen is responsible for nosocomial infections. Germination is an essential step for the establishment of C. difficile infection (CDI) because toxins that are secreted by vegetative cells are responsible for the symptoms of CDI. Germination can be stimulated by the combinatorial actions of certain amino acids and either conjugated or deconjugated cholic acid-derived bile salts. During synthesis in the liver, cholic acid- and chenodeoxycholic acid-class bile salts are conjugated with either taurine or glycine at the C24 carboxyl. During GI transit, these conjugated bile salts are deconjugated by microbes that express bile salt hydrolases (BSHs). Here, we surprisingly find that several C. difficile strains have BSH activity. We observed this activity in both C. difficile vegetative cells and in spores and that the observed BSH activity was specific to taurine-derived bile salts. Additionally, we find that this BSH activity can produce cholate for metabolic conversion to deoxycholate by C. scindens. The C. scindens-produced deoxycholate signals to C. difficile to initiate biofilm formation. Our results show that C. difficile BSH activity has the potential to influence the interactions between microbes, and this could extend to the GI setting.\n\nClostridioides difficile bile salt hydrolase activity has substrate specificity and affects biofilm formation.", "token_count": 360, "char_count": 1403, "word_count": 203, "semantic_coherence": 1, "information_density": 0.5567, "quality_score": 0.7783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:24.532943", "source": { "split": "train_shard_00000", "doc_id": 1594 }, "chunk_id": "train_shard_00000_1594_0", "global_id": 1760 }, { "text": "Pangenome graphs are flexible data structures that contain the genetic variation that exists in a population of genomes and describe the sequences of the many possible ensuing haplotypes. Here, we use such a pangenome graph to represent and genotype transposable element (TE) polymorphisms. By combining the transposable element annotation (Alus, L1s, and SVAs) of the human genome reference with novel transposable element insertions observed in two high-quality assemblies (HG002 and HG00733), we show how to create a transposable element pangenome that consists of ~1.2 million reference and 2939 non-reference transposable elements. We then demonstrate this approach by aligning short-read sequencing data and genotyping transposable element deletions and insertions with reasonable specificity and sensitivity (0.85 F1-score).\n\nA Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms.", "token_count": 225, "char_count": 904, "word_count": 125, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [ "HG00733", "HG002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:25.013337", "source": { "split": "train_shard_00000", "doc_id": 1595 }, "chunk_id": "train_shard_00000_1595_0", "global_id": 1761 }, { "text": "Pangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments. Existing related approaches depend on a single reference, a specific ordering of genomes or a de Bruijn model based on a fixed k-mer length. A scalable, self-contained method to build pangenome graphs without such limitations would be a key step in pangenome construction and manipulation pipelines.\n\nUnbiased pangenome graphs.", "token_count": 119, "char_count": 552, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:25.446904", "source": { "split": "train_shard_00000", "doc_id": 1596 }, "chunk_id": "train_shard_00000_1596_0", "global_id": 1762 }, { "text": "It is unknown whether bacterial bloodstream infections (BSIs) are commonly caused by single organisms or mixed microbial populations. We hypothesized that contemporaneous carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from blood cultures of individual patients are genetically and phenotypically distinct. We determined short-read whole-genome sequences of 10 sequence type 258 (ST258) CRKP strains from blood cultures in each of 6 patients (Illumina HiSeq). Strains clustered by patient by core genome and pan-genome phylogeny. In 5 patients, there was within-host strain diversity by gene mutations, presence/absence of antibiotic resistance or virulence genes, and/or plasmid content. Accessory gene phylogeny revealed strain diversity in all 6 patients. Strains from 3 patients underwent long-read sequencing for genome completion (Oxford Nanopore) and phenotypic testing. Genetically distinct strains within individuals exhibited significant differences in carbapenem and other antibiotic responses, capsular polysaccharide (CPS) production, mucoviscosity, and/or serum killing. In 2 patients, strains differed significantly in virulence during mouse BSIs. Genetic or phenotypic diversity was not observed among strains recovered from blood culture bottles seeded with index strains from the 3 patients and incubated\n\nWithin-Host Genotypic and Phenotypic Diversity of Contemporaneous Carbapenem-Resistant Klebsiella pneumoniae from Blood Cultures of Patients with Bacteremia.", "token_count": 388, "char_count": 1491, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6597, "quality_score": 0.8298, "entities": { "genes": [ "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:26.082719", "source": { "split": "train_shard_00000", "doc_id": 1597 }, "chunk_id": "train_shard_00000_1597_0", "global_id": 1763 }, { "text": "The concomitant increase in cultivation of fish and decrease in supply of marine ingredients, have greatly increased the demand for new nutrient sources. This also regards so-called functional ingredients which may benefit health and welfare of the fish. In vitro cell line-based intestinal epithelial barrier models may serve as tools for narrowing down the broad range of ingredient options, to identify the most promising candidates before in vivo feeding trials are run. In vivo, differentiation of the various epithelial cells in the fish intestine, from the multipotent stem cells, takes place in the presence of a variety of substances from dietary and endogenous origin. Among these, bile salts have recently received attention as regulators of epithelial function in health and disease but have not, until now, been included in the medium when culturing fish gut epithelial cells in vitro. As bile salts are present at high levels in the chyme of the fish intestine, in particular in salmon and rainbow trout, mostly as taurocholate (>90%), their role for effects of diet ingredients on the in vitro gut cell model should be understood. With this study, we wanted to investigate whether inclusion of bile from rainbow trout or pure taurocholate in the culture media would modulate functions of the RTgutGC epithelial cells. Here, we demonstrated that the rainbow trout intestinal epithelial cell line RTgutGC responded significantly to the presence of bile components. Treatment with rainbow trout bile taken from the gall bladder (RTbile) or pure taurocholate (TC) at taurocholate concentrations of ≤0.5 mg/mL retained normal cell morphology, cell viability as in cell oxidation-reduction metabolic activity and membrane integrity, and barrier features, while high concentrations of bile salts (≥1 mg/mL) were cytotoxic to the cells. After long-term (4 days) bile treatment, transcriptome responses showed how bile salts play important roles in intestinal epithelial cell metabolism. qPCR data demonstrated that barrier function genes, brush border enzyme genes and immune genes were significantly affected", "token_count": 503, "char_count": 2116, "word_count": 320, "semantic_coherence": 1, "information_density": 0.5906, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:26.739164", "source": { "split": "train_shard_00000", "doc_id": 1598 }, "chunk_id": "train_shard_00000_1598_0", "global_id": 1764 }, { "text": "Although similar trends were seen, treatment with bile salt as a component of rainbow trout bile or pure taurocholate, induced somewhat different effects. In conclusion, this study clearly indicates that bile salts should be included in the cell medium when running in vitro studies of gut cell functions, not at least immune functions, preferably at the level of ∼0.5 mg/mL supplemented as pure taurocholate to ensure reproducibility.\n\nBile components affect the functions and transcriptome of the rainbow trout intestinal epithelial cell line RTgutGC.", "token_count": 134, "char_count": 553, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7711, "quality_score": 0.8855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:27.158215", "source": { "split": "train_shard_00000", "doc_id": 1598 }, "chunk_id": "train_shard_00000_1598_1", "global_id": 1765 }, { "text": "The Reference Human Genome remains the single most important resource for mapping genetic variations and assessing their impact. However, it is monophasic, incomplete and not representative of the variation that exists in the population. Given the extent of ethno-geographic diversity and the consequent diversity in clinical manifestations of these variations, population specific references were developed overtime. The dramatically plummeting cost of sequencing whole genomes and the advent of third generation long range sequencers allowing accurate, error free, telomere-to-telomere assemblies of human genomes present us with a unique and unprecedented opportunity to develop a more composite standard reference consisting of a collection of multiple genomes that capture the maximal variation existing in the population, with the deepest annotation possible, enabling a realistic, reliable and actionable estimation of clinical significance of specific variations. The Human Pangenome Project thus is a logical next step promising a more accurate and global representation of genomic variations. The pangenome effort must be reciprocally complemented with precise variant discovery tools and exhaustive annotation to ensure unambiguous clinical assessment of the variant in ethno-geographical context. Here we discuss a broad roadmap, the challenges and way forward in developing a universal pangenome reference including data visualization techniques and integration of prior knowledge base in the new graph based architecture and tools to submit, compare, query, annotate and retrieve relevant information from the pangenomes. The biggest challenge, however, will be the ethical, legal and social implications and the training of human resource to the new reference paradigm.\n\nFrom the reference human genome to human pangenome: Premise, promise and challenge.", "token_count": 355, "char_count": 1869, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:27.734611", "source": { "split": "train_shard_00000", "doc_id": 1599 }, "chunk_id": "train_shard_00000_1599_0", "global_id": 1766 }, { "text": "Formulating poorly soluble drugs with polymers in the form of solid dispersions has been widely used for improving drug dissolution. Endogenous surface-active species present in the gut, such as bile salts, lecithin and other phospholipids, have been shown to play a key role in facilitating lipids and poorly soluble drugs solubilisation in the gut. In this study, we examined the possible occurrence of interactions between a model bile salt, sodium taurocholate (NaTC), and model spray dried solid dispersions comprising piroxicam and Hydroxypropyl Methylcellulose (HPMC), a commonly used hydrophilic polymer for solid dispersion preparation. Solubility measurements revealed the good solubilisation effect of NaTC on the crystalline drug, which was enhanced by the addition of HPMC, and further boosted by the drug formulation into solid dispersion. The colloidal behaviour of the solid dispersions upon dissolution in biorelevant media, with and without NaTC, revealed the formation of NaTC-HPMC complexes and other mixed colloidal species. Cellular level drug absorption studies obtained using Caco-2 monolayers confirmed that the combination of drug being delivered by solid dispersion and the presence of bile salt and lecithin significantly contributed to the improved drug absorption. Together with the role of NaTC-HPMC complexes in assisting the drug solubilisation, our results also highlight the complex interplay between bile salts, excipients and drug absorption.\n\nInteraction of polymers with bile salts - Impact on solubilisation and absorption of poorly water-soluble drugs.", "token_count": 373, "char_count": 1593, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:28.320675", "source": { "split": "train_shard_00000", "doc_id": 1600 }, "chunk_id": "train_shard_00000_1600_0", "global_id": 1767 }, { "text": "Strain Marseille-Q6994 was isolated from a 72-year-old patient with pneumonia from Bouches-du-Rhône department, in France. Cells were Gram positive, non-motile, catalase and oxidase-negative cocci. The major fatty acids were hexadecanoic (47.4%) and tetradecanoic acids (28.3%). 16S rRNA gene sequence comparison suggested that strain Marseille-Q6994 was affiliated to the Streptococcus genus. GroEL phylogenetic analysis separated strain Marseille-Q6994 in a distinct branch from the closely related Streptococcus-type strains with standing in nomenclature. Whole genome sequencing-based methods (OrthoAverage Nucleotide Identity, digital DNA-DNA hybridization and pangenome analysis) supported the classification of the strain into a novel species. Therefore, based on the phenotypic, genomic, and phylogenetic analyses, we propose the name Streptococcus bouchesdurhonensis sp. nov for which strain Marseille-Q6994\n\nStreptococcus bouchesdurhonensis sp. nov. isolated from a bronchoalveolar lavage of a patient with pneumonia.", "token_count": 310, "char_count": 1027, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7031, "quality_score": 0.8516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:29.225747", "source": { "split": "train_shard_00000", "doc_id": 1601 }, "chunk_id": "train_shard_00000_1601_0", "global_id": 1768 }, { "text": "In the last decade, legume genomics research has seen a paradigm shift due to advances in genome sequencing technologies, assembly algorithms, and computational genomics that enabled the construction of high-quality reference genome assemblies of major legume crops. These advances have certainly facilitated the identification of novel genetic variants underlying the traits of agronomic importance in many legume crops. Furthermore, these robust sequencing technologies have allowed us to study structural variations across the whole genome in multiple individuals and at the species level using 'pangenome analysis.' This review updates the progress of constructing pangenome assemblies for various legume crops and discusses the prospects for these pangenomes and how to harness the information to improve various traits of economic importance through molecular breeding to increase genetic gain in legumes and tackle the increasing global food crisis.\n\nLegume Pangenome: Status and Scope for Crop Improvement.", "token_count": 196, "char_count": 1014, "word_count": 142, "semantic_coherence": 1, "information_density": 0.669, "quality_score": 0.8345, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:29.676651", "source": { "split": "train_shard_00000", "doc_id": 1602 }, "chunk_id": "train_shard_00000_1602_0", "global_id": 1769 }, { "text": "Integrated Pangenome Analysis and Pharmacophore Modeling Revealed Potential Novel Inhibitors against", "token_count": 25, "char_count": 100, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:30.033390", "source": { "split": "train_shard_00000", "doc_id": 1603 }, "chunk_id": "train_shard_00000_1603_0", "global_id": 1770 }, { "text": "The present study reports the first genome of Nitrosopumilus extracted from the marine sponge Thoosa mismalolli. The genomic study of Nitrosopumilus genus using seven genomes type strains (N. maritimus, N. piranensis, N. zosterae, N. ureiphilus, N. adriaticus, N. oxyclinae and N. cobalaminigenes), four genomes Candidatus species (Ca. N. koreensis, Ca. N. sp. AR2, Ca. N. salaria BD31, and SZUA-335), and six reference genomes (SI075, SI0036, SI0060, SI0034, SI0048, and bin36o) isolated from marine sponge, a tropical marine fish tank, dimly lit deep coastal waters, the lower euphotic zone of coastal waters, near-surface sediment, and MAG N. sp NMAG03 isolated from Thoosa mismalolli was performed. These genomes were characterized by means of a polyphasic approach comprising multilocus sequence analysis (MLSA) of 139 single-copy genes (SCG), core-pangenome, ANI, and in silico phenotypic characterization. We found that the genomes of the Nitrosopumilus genus formed three separate clusters (A, B, and C) based in 139 SCG sequence similarity. The genomes showed values between 75.2 and 99.5% for ANI, the core genome consisted of 168 gene families and the pangenome of 6,011 gene families. Based on the genomic analyses performed, the cluster A may contain a potential new species (NMAG03), and the cluster C could be represented by three new species of the genus. Finally, based on the results shown in this polyphasic approach, we support the use of the integrated approach for genomic analysis of poorly studied genera.\n\nGenomics, Phylogeny, and in Silico Phenotyping of Nitrosopumilus Genus.", "token_count": 497, "char_count": 1602, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6132, "quality_score": 0.8066, "entities": { "genes": [ "SI0036", "SI0034", "BD31", "NMAG03", "SI075", "SI0060", "AR2", "SI0048" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:30.678221", "source": { "split": "train_shard_00000", "doc_id": 1604 }, "chunk_id": "train_shard_00000_1604_0", "global_id": 1771 }, { "text": "Members of the bacterial genus Pseudomonas form mutualistic, commensal, and pathogenic associations with diverse hosts. The prevalence of host association across the genus suggests that symbiosis may be a conserved ancestral trait and that distinct symbiotic lifestyles may be more recently evolved. Here we show that the ColR/S two-component system, part of the Pseudomonas core genome, is functionally conserved between Pseudomonas aeruginosa and Pseudomonas fluorescens. Using plant rhizosphere colonization and virulence in a murine abscess model, we show that colR is required for commensalism with plants and virulence in animals. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not host-specific, requirements for ColR-dependent genes. Collectively, our results suggest that ColR/S allows Pseudomonas to sense and respond to a host, but that the ColR-regulon has diverged between Pseudomonas strains with distinct lifestyles. This suggests that conservation of two-component systems, coupled with life-style dependent diversification of the regulon, may play a role in host association and lifestyle transitions.\n\nThe ColR/S two-component system is a conserved determinant of host association across Pseudomonas species.", "token_count": 330, "char_count": 1366, "word_count": 187, "semantic_coherence": 1, "information_density": 0.5722, "quality_score": 0.7861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:31.246739", "source": { "split": "train_shard_00000", "doc_id": 1605 }, "chunk_id": "train_shard_00000_1605_0", "global_id": 1772 }, { "text": "Previous reviews have already explored the safety and bioavailability of astaxanthin, as well as its beneficial effects on human body. The great commercial potential in a variety of industries, such as the pharmaceutical and health supplement industries, has led to a skyrocketing demand for natural astaxanthin. In this study, we have successfully optimized the astaxanthin yield up to 12.8 mg/g DCW in a probiotic yeast and purity to 97%. We also verified that it is the desired free-form 3S, 3'S configurational stereoisomer by NMR and FITR that can significantly increase the bioavailability of astaxanthin. In addition, we have proven that our extracted astaxanthin crystals have higher antioxidant capabilities compared with natural esterified astaxanthin from\n\nSafety Assessment of 3S, 3'S Astaxanthin Derived from Metabolically Engineered", "token_count": 213, "char_count": 846, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:31.704145", "source": { "split": "train_shard_00000", "doc_id": 1606 }, "chunk_id": "train_shard_00000_1606_0", "global_id": 1773 }, { "text": "The mechanisms by which early microbial colonizers of the neonate influence gut development are poorly understood. Bacterial bile salt hydrolase (BSH) acts as a putative colonization factor that influences bile acid signatures and microbe-host signaling pathways and we considered whether this activity can influence infant gut development.\n\nMicrobial bile salt hydrolase activity influences gene expression profiles and gastrointestinal maturation in infant mice.", "token_count": 101, "char_count": 464, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7903, "quality_score": 0.8952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:32.078372", "source": { "split": "train_shard_00000", "doc_id": 1607 }, "chunk_id": "train_shard_00000_1607_0", "global_id": 1774 }, { "text": "Potato peel waste (PPW) is a starchy by-product generated in great amounts during the industrial processing of potatoes. It can be used as a low cost alternative, and renewable feedstock for the production of second generation bioethanol. In order to intensify this process, Saccharomyces cerevisiae Ethanol Red®, a robust and thermotolerant yeast strain, was selected and two experimental designs and response surfaces assessment were conducted to enable very high gravity fermentations (VHGF) using PPW as feedstock. The first one focused on the optimization of the liquefaction and enzymatic hydrolysis stages, enabling a maximum ethanol concentration of 116.5 g/L and a yield of 80.4 % at 72 h of fermentation; whereas, the second one, focus on the optimization of the pre-saccharification and fermentation stages, which further increased process productivity, leading to a maximum ethanol concentration of 108.8 g/L and a yield of 75.1 % after 54 h of fermentation. These results allowed the definition of an intensified pre-saccharification and simultaneous saccharification and fermentation (PSSF) process for ethanol production from PPW, resorting to short liquefaction and pre-saccharification times, 2 h and 10 h respectively, at an enzyme loading of 80 U/g PPW of Viscozyme and 5 UE/g PPW of SAN Super and a higher fermentation temperature of 34 °C due to the use of a thermotolerant yeast. Overall, with these conditions and solely from PPW without any supplementation, the outlined PSSF process allowed reaching a high ethanol concentration and yield (104.1 g/L and 71.9 %, respectively) standing at high productivities with only 54 h of fermentation.\n\nPotato peels waste as a sustainable source for biotechnological production of biofuels: Process optimization.", "token_count": 470, "char_count": 1775, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:32.717831", "source": { "split": "train_shard_00000", "doc_id": 1608 }, "chunk_id": "train_shard_00000_1608_0", "global_id": 1775 }, { "text": "Acinetobacter baumannii is one of the most problematic nosocomial pathogens that can efficiently thrive within hospital settings, mainly due to resistances toward antibiotics, desiccation, disinfectants, human serum and oxidative stress. Recently, increased resistance against last-resort antibiotics earns this bacterium the highest priority concern classified by the Centers for Disease Control and Prevention and the World Health Organization. An obvious hallmark of this bacterium is the high heterogeneity observed among A. baumannii isolates, with a limited core genome. This feature complexifies the study of A. baumannii bacteria as an entity, subsequently reflected in a diversity of phenotypes of not only antimicrobial and environmental resistance but also virulence. A high degree of genome plasticity, along with the use of a limited subset of established strains, can lead to strain-specific observations, decreasing the global understanding of this pathogenic agent. Phenotypic variability of A. baumannii strains is easily observable such as with the macrocolony morphologies, in vitro and in vivo virulence, natural competence level, production of different capsular polysaccharide structures and cellular densities. Some strains encode an extensive amount of virulence factors, while others, including the established strains, lack several key ones. The lack/excess of genes or specific physiological processes might interfere with in vivo and in vitro experiments, thus providing a limited impact on the global understanding of Acinetobacter bacteria. As an answer to the high heterogeneity among A. baumannii strains, we propose a first comprehensive database that includes the bacterial strains and the associated phenotypic and genetic data. This new repository, freely accessible to the entire scientific community, allows selecting the best bacterial isolate(s) related to any biological question, using an efficient and fast exchange platform. Database URL: https://acinetobase.vib.be/.\n\nAcinetobase: the comprehensive database and repository of Acinetobacter strains.", "token_count": 463, "char_count": 2093, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:33.354500", "source": { "split": "train_shard_00000", "doc_id": 1609 }, "chunk_id": "train_shard_00000_1609_0", "global_id": 1776 }, { "text": "Bacterial pathogens are fostered in and transmitted through wastewater. Hence, monitoring their impact on sanitation and hygiene is imperative. As part of the monitoring process, culture-based methodologies are primarily used, which centre on the use of selective and differential media. Media available today are, at best, difficult to formulate and, at worst, prohibitively expensive. To address this lacuna, the study proposes a selective and differential medium for Klebsiella spp. Klebsiella blue agar (KBA) is completely selective against selected gram-positive bacteria (Bacillus spp., Staphylococcus aureus) and a few gram-negative bacteria (Acinetobacter baumanii, Serratia marcescens). On the other hand, it supports the growth of the chosen members of the Klebsiella pneumoniae species-complex with a characteristic green colouration. Methylene blue, tryptophan, and bile salt make up the selective components of KBA. Moreover, methylene blue, 0.6% NaCl, and glycerol render it differential. KBA was more selective than HiCrome™ Klebsiella Selective Agar Base (KSA) in replica plating experiments. KBA promoted only 157 CFUs against 209 CFUs in KSA when stamped with 253 CFUs grown on LB. The colonies so isolated were predominantly Klebsiella spp., on identification through colony polymerase chain reaction. Moreover, the differential nature of KBA distinguished Klebsiella aerogenes from other species. On the contrary, KSA lodged colonies indistinguishable from each other and Klebsiella spp. Due to its ease of formulation, high selectivity, differential nature, and cost-effective composition, KBA is a viable option for the routine culture of Klebsiella spp. in environmental and clinical settings. KEY POINTS: • Formulated a novel selective and differential media for Klebsiella spp., named Klebsiella Blue agar • Facile formulation methodology • Can be employed to isolate Klebsiella spp. from complex sources such as wastewater.", "token_count": 496, "char_count": 1949, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:34.010528", "source": { "split": "train_shard_00000", "doc_id": 1610 }, "chunk_id": "train_shard_00000_1610_0", "global_id": 1777 }, { "text": "A novel and improved selective media for the isolation and enumeration of Klebsiella species.", "token_count": 20, "char_count": 93, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:34.366023", "source": { "split": "train_shard_00000", "doc_id": 1610 }, "chunk_id": "train_shard_00000_1610_1", "global_id": 1778 }, { "text": "Foodborne botulism is a rare but life-threatening illness resulting from the action of a potent toxin mainly produced by Clostridium botulinum. It grows in an oxygen-deficient environment and is extremely viable in meat and soy products, making it one of the most virulent bacteria. How to track foodborne botulism events quickly and accurately has become a key issue. Here, we investigated two foodborne botulism events that occurred in Xinjiang in 2019 based on whole-genome sequencing and also successfully traced the relationship between clinical and food C. botulinum isolates using whole-genome core gene markers. All 59 isolates were classified as group I strains. Of the strains isolated in this study, 44 were found to be botulinum toxin A(B), and 15 isolates contained only the toxin B locus. Both the toxin A and B gene segments were located on the chromosome and organized in an ha cluster. Antibiotic resistance and virulence factors were also investigated. A set of 329 universal core gene markers were established using C. botulinum strains from a public database. These core gene markers were applied to the published C. botulinum genomes, and three outbreaks were identified. This work demonstrates that universal core gene markers can be used to trace foodborne botulism events, and we hope that our work will facilitate this effort in future.\n\nTracing Foodborne Botulism Events Caused by Clostridium botulinum in Xinjiang Province, China, Using a Core Genome Sequence Typing Scheme.", "token_count": 368, "char_count": 1501, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5957, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:34.946222", "source": { "split": "train_shard_00000", "doc_id": 1611 }, "chunk_id": "train_shard_00000_1611_0", "global_id": 1779 }, { "text": "The advent of the pangenome era has unraveled previously unknown genetic variation existing within diverse crop plants, including rice. This untapped genetic variation is believed to account for a major portion of phenotypic variation existing in crop plants. However, the use of conventional single reference-guided genotyping often fails to capture a large portion of this genetic variation leading to a reference bias. This makes it difficult to identify and utilize novel population/cultivar-specific genes for crop improvement. Thus, we developed a Rice Pangenome Genotyping Array (RPGA) harboring probes assaying 80K single-nucleotide polymorphisms (SNPs) and presence-absence variants spanning the entire 3K rice pangenome. This array provides a simple, user-friendly and cost-effective (60-80 USD per sample) solution for rapid pangenome-based genotyping in rice. The genome-wide association study (GWAS) conducted using RPGA-SNP genotyping data of a rice diversity panel detected a total of 42 loci, including previously known as well as novel genomic loci regulating grain size/weight traits in rice. Eight of these identified trait-associated loci (dispensable loci) could not be detected with conventional single reference genome-based GWAS. A WD repeat-containing PROTEIN 12 gene underlying one of such dispensable locus on chromosome 7 (qLWR7) along with other non-dispensable loci were subsequently detected using high-resolution quantitative trait loci mapping confirming authenticity of RPGA-led GWAS. This demonstrates the potential of RPGA-based genotyping to overcome reference bias. The application of RPGA-based genotyping for population structure analysis, hybridity testing, ultra-high-density genetic map construction and chromosome-level genome assembly, and marker-assisted selection was also demonstrated. A web application (http://www.rpgaweb.com) was further developed to provide an easy to use platform for the imputation of RPGA-based genotyping data using 3K rice reference panel and subsequent GWAS.", "token_count": 495, "char_count": 2033, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:35.597510", "source": { "split": "train_shard_00000", "doc_id": 1612 }, "chunk_id": "train_shard_00000_1612_0", "global_id": 1780 }, { "text": "Rice Pangenome Genotyping Array: an efficient genotyping solution for pangenome-based accelerated genetic improvement in rice.", "token_count": 30, "char_count": 126, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:35.962855", "source": { "split": "train_shard_00000", "doc_id": 1612 }, "chunk_id": "train_shard_00000_1612_1", "global_id": 1781 }, { "text": "Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.\n\nNGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.", "token_count": 260, "char_count": 1286, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6045, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:36.531651", "source": { "split": "train_shard_00000", "doc_id": 1613 }, "chunk_id": "train_shard_00000_1613_0", "global_id": 1782 }, { "text": "Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth's microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform ( http://www.kbase.us/ ). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).\n\nMetagenome-assembled genome extraction and analysis from microbiomes using KBase.", "token_count": 390, "char_count": 1810, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:37.164364", "source": { "split": "train_shard_00000", "doc_id": 1614 }, "chunk_id": "train_shard_00000_1614_0", "global_id": 1783 }, { "text": "Dietzia strains are widely distributed in the environment, presenting an opportunistic role, and some species have undetermined taxonomic characteristics. Here, we propose the existence of errors in the classification of species in this genus using comparative genomics. We performed ANI, dDDH, pangenome and genomic plasticity analyses better to elucidate the phylogenomic relationships between Dietzia strains. For this, we used 55 genomes of Dietzia downloaded from public databases that were combined with a newly sequenced. Sequence analysis of a phylogenetic tree based on genome similarity comparisons and dDDH, ANI analyses supported grouping different Dietzia species into four distinct groups. The pangenome analysis corroborated the classification of these groups, supporting the idea that some species of Dietzia could be reassigned in a possible classification into three distinct species, each containing less variability than that found within the global pangenome of all strains. Additionally, analysis of genomic plasticity based on groups containing Dietzia strains found differences in the presence and absence of symbiotic Islands and pathogenic islands related to their isolation site. We propose that the comparison of pangenome subsets together with phylogenomic approaches can be used as an alternative for the classification and differentiation of new species of the genus Dietzia.\n\nComparative genomic analysis of the Dietzia genus: an insight into genomic diversity, and adaptation.", "token_count": 324, "char_count": 1509, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5822, "quality_score": 0.7911, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:37.779283", "source": { "split": "train_shard_00000", "doc_id": 1615 }, "chunk_id": "train_shard_00000_1615_0", "global_id": 1784 }, { "text": "This study investigated the interaction among Kluyveromyces marxianus G-Y4 (G-Y4), Lacticaseibacillus paracasei GL1 (GL1) and Lactobacillus helveticus SNA12 (SNA12) that isolated from Tibetan kefir grains. Additionally, the effects of G-Y4 on the growth and biofilm formation of GL1 and SNA12 were determined. The results indicated that G-Y4 promoted the growth of GL1 and SNA12 and improved their biofilm-forming ability. Furthermore, the dead cells of G-Y4 were found that could enhance bacterial biofilm formation, and the cell wall polysaccharide (CWPS) produced by G-Y4 was performed to be key substances that promote the formation of bacterial biofilms. Moreover, the structure of soluble cell wall polysaccharides (SCWP) and insoluble cell wall polysaccharide (NCWP) of G-Y4 were studied to determine their contribution to biofilm formation. Results showed that G-Y4-SCWP was α-mannan with the main chain of a →6)-α-d-Manp-(1→ unit and the branch structure of →2)-α-d-Manp-(1. At the same time, G-Y4-NCWP was a glucan rich in β-(1→3), β-(1→2), or β-(1→4) linkages.\n\nYeast cell wall polysaccharides in Tibetan kefir grains are key substances promoting the formation of bacterial biofilm.", "token_count": 366, "char_count": 1193, "word_count": 173, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [ "GL1", "SNA12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:38.365021", "source": { "split": "train_shard_00000", "doc_id": 1616 }, "chunk_id": "train_shard_00000_1616_0", "global_id": 1785 }, { "text": "Global climate change and the urgency to transform crops require an exhaustive genetic evaluation. The large polyploid genomes of food crops, such as cereals, make it difficult to identify candidate genes with confirmed hereditary. Although genome-wide association studies (GWAS) have been proficient in identifying genetic variants that are associated with complex traits, the resolution of acquired heritability faces several significant bottlenecks such as incomplete detection of structural variants (SV), genetic heterogeneity, and/or locus heterogeneity. Consequently, a biased estimate is generated with respect to agronomically complex traits. The graph pangenomes have resolved this missing heritability and provide significant details in terms of specific loci segregating among individuals and evolving to variations. The graph pangenome approach facilitates crop improvements through genome-linked fast breeding.\n\nGraph Pangenomes Track Genetic Variants for Crop Improvement.", "token_count": 202, "char_count": 987, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7674, "quality_score": 0.8837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:38.829242", "source": { "split": "train_shard_00000", "doc_id": 1617 }, "chunk_id": "train_shard_00000_1617_0", "global_id": 1786 }, { "text": "Most probiotics possess bile salt hydrolase enzymes and may increase bile acid excretion and negatively affect fat digestion and absorption. Therefore, the study objective was to determine the time course effects of a commercial probiotic (P) FloraMax-B11 (FM) supplementation on bile acid neosynthesis and enterohepatic circulation in broiler chickens. Fertile Ross 708 eggs were incubated under standard commercial conditions. At hatch, chicks (n = 550) were randomly assigned to 5 treatment groups (n = 5 replicates per treatment group) with 22 birds per pen. The 5 treatment groups consisted of: control group (C, normal water from hatch to 35 days of age without supplements); P3, water supplemented with FM for the first 3 days post-hatch followed by normal water until day 35; P10, water supplemented with FM for the first 10 days post-hatch followed by normal water until day 35; P35, water supplemented with FM from hatch to day 35; and AGP, water supplemented with antibiotic growth promoter (AGP) from hatch until day 35. Ileum, liver, and plasma were collected at hatch, days 3, 10, 21, and 35 post-hatch. The relative mRNA expression of genes involved in bile acid synthesis (CYP7A1, CYP8B1, FXR, FGFR4, and FGF19) and transport (ASBT, I-BABP, OSTα, OSTβ, and BSEP) as well as ileal deoxycholic acid and plasma cholic acid were determined. There was no FM and AGP interaction for any of the response criteria. No FM or AGP effects were observed (p > 0.05) for any genes, except FGF19, which expression was increased (p < 0.0001) in AGP compared to P35. No FM or AGP effects were observed (p > 0.05) for levels of deoxycholic and cholic acids", "token_count": 496, "char_count": 1654, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5788, "quality_score": 0.7894, "entities": { "genes": [ "FGF19", "FGFR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:39.483216", "source": { "split": "train_shard_00000", "doc_id": 1618 }, "chunk_id": "train_shard_00000_1618_0", "global_id": 1787 }, { "text": "However, all the genes, deoxycholic acid, and plasma cholic acid were affected by age (p < 0.0001). In general, the data indicate that FM did not negatively impact bile acid metabolism and enterohepatic circulation, which appeared to be age dependent. However, more research should be conducted to confirm these results and investigate the effects of FM on bile acid metabolism, fat digestion, and intestinal microbiota in broiler chickens.\n\nThe Supplementation of FloraMax-B11 Did Not Affect the Bile Acid Neosynthesis and the Enterohepatic Circulation in Broiler Chickens.", "token_count": 153, "char_count": 574, "word_count": 86, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:39.921023", "source": { "split": "train_shard_00000", "doc_id": 1618 }, "chunk_id": "train_shard_00000_1618_1", "global_id": 1788 }, { "text": "Conventional eye drops are most commonly employed topically in the eye for the management of bacterial conjunctivitis. Eye drops have a low corneal residence time and 90−95% of the administered dose is eliminated from the eye by blinking and the nasolacrimal drainage system. This problem can be minimized by formulating a mucoadhesive ocular in-situ gel system that undergoes sol-gel transition upon stimulation by temperature, pH, and ions. The goal of this study was to develop ciprofloxacin (CIP) loaded bilosomes (BLO) in-situ gel for the improvement of therapeutic efficacy. The BLO was prepared by the thin-film hydration method and optimized by the Box−Behnken design. Cholesterol (CHO), surfactant (Span 60), and bile salt (sodium deoxycholate/SDC) were used as formulation factors. The vesicle size (nm) and entrapment efficiency (%) were selected as responses (dependent factors). The optimized CIP-BLO (CIP-BLO-opt) formulation displayed a vesicle size of 182.4 ± 9.2 nm, a polydispersity index of 0.274, a zeta potential of −34,461.51 mV, and an entrapment efficiency of 90.14 ± 1.24%. Both x-ray diffraction and differential scanning calorimetry spectra did not exhibit extensive peaks of CIP in CIP-BLO-opt, revealing that CIP is encapsulated in the BLO matrix. The CIP-BLO-opt formulation was successfully incorporated into an in-situ gel system using a gelling agent, i.e., Carbopol 934P and hydroxyl propyl methyl cellulose (HPMC K100 M). CIP-BLO-opt in-situ gel formulation (CIP-BLO-opt-IG3) was evaluated for gelling capacity, clarity, pH, viscosity, in-vitro CIP release, bio-adhesive, ex-vivo permeation, toxicity, and antimicrobial study", "token_count": 517, "char_count": 1660, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [ "IG3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:14:40.546497", "source": { "split": "train_shard_00000", "doc_id": 1619 }, "chunk_id": "train_shard_00000_1619_0", "global_id": 1789 }, { "text": "The CIP-BLO-opt-IG3 exhibited satisfactory gelling properties with a viscosity of 145.85 ± 9.48 cP in the gelling state. CIP-BLO-opt-IG3 displayed sustained CIP release (83.87 ± 5.24%) with Korsmeyer−Peppas kinetic as a best-fitted model (R2 = 0.9667). CIP-BLO-opt-IG3 exhibited a 1.16-fold than CIP-IG and a 2.08-fold higher permeability than pure CIP. CIP-BLO-opt-IG3 displayed a significantly greater bio-adhesion property (924.52 ± 12.37 dyne/cm2) than tear film. Further, CIP-BLO-opt-IG3 does not display any toxicity as confirmed by corneal hydration (76.15%), histology, and the HET-CAM test (zero scores). CIP-BLO-opt-IG3 shows significantly higher (p < 0.05) antimicrobial activity against P. aeruginosa and S. aureus than pure CIP. From all these findings, it could be concluded that CIP-BLO-opt-IG3 might be an effective strategy for the increment of corneal residence time and therapeutic activity of CIP.\n\nDevelopment of Ciprofloxacin-Loaded Bilosomes In-Situ Gel for Ocular Delivery: Optimization, In-Vitro Characterization, Ex-Vivo Permeation, and Antimicrobial Study.", "token_count": 386, "char_count": 1083, "word_count": 146, "semantic_coherence": 1, "information_density": 0.726, "quality_score": 0.863, "entities": { "genes": [ "IG3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:41.162050", "source": { "split": "train_shard_00000", "doc_id": 1619 }, "chunk_id": "train_shard_00000_1619_1", "global_id": 1790 }, { "text": "Over the past decade, whole-genome sequencing (WGS) has overtaken traditional bacterial typing methods for studies of genetic relatedness. Further, WGS data generated during epidemiologic studies can be used in other clinically relevant bioinformatic applications, such as antibiotic resistance prediction. Using commercially available software tools, the relatedness of 38 clinical isolates of multidrug-resistant Pseudomonas aeruginosa was defined by two core genome multilocus sequence typing (cgMLST) methods, and the WGS data of each isolate was analyzed to predict antibiotic susceptibility to nine antibacterial agents. The WGS typing and resistance prediction data were compared with pulsed-field gel electrophoresis (PFGE) and phenotypic antibiotic susceptibility results, respectively. Simpson's Diversity Index and adjusted Wallace pairwise assessments of the three typing methods showed nearly identical discriminatory power. Antibiotic resistance prediction using a trained analytical pipeline examined 342 bacterial-drug combinations with an overall categorical agreement of 92.4% and very major, major, and minor error rates of 3.6, 4.1, and 4.1%, respectively.\n\nCore Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates.", "token_count": 323, "char_count": 1345, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:41.728501", "source": { "split": "train_shard_00000", "doc_id": 1620 }, "chunk_id": "train_shard_00000_1620_0", "global_id": 1791 }, { "text": "Streptomycetes are highly metabolically gifted bacteria with the abilities to produce bioproducts that have profound economic and societal importance. These bioproducts are produced by metabolic pathways including those for the biosynthesis of secondary metabolites and catabolism of plant biomass constituents. Advancements in genome sequencing technologies have revealed a wealth of untapped metabolic potential from Streptomyces genomes. Here, we report the largest Streptomyces pangenome generated by using 205 complete genomes. Metabolic potentials of the pangenome and individual genomes were analyzed, revealing degrees of conservation of individual metabolic pathways and strains potentially suitable for metabolic engineering. Of them, Streptomyces bingchenggensis was identified as a potent degrader of plant biomass. Polyketide, non-ribosomal peptide, and gamma-butyrolactone biosynthetic enzymes are primarily strain specific while ectoine and some terpene biosynthetic pathways are highly conserved. A large number of transcription factors associated with secondary metabolism are strain-specific while those controlling basic biological processes are highly conserved. Although the majority of genes involved in morphological development are highly conserved, there are strain-specific varieties which may contribute to fine tuning the timing of cellular differentiation. Overall, these results provide insights into the metabolic potential, regulation and physiology of streptomycetes, which will facilitate further exploitation of these important bacteria.\n\nComparative and pangenomic analysis of the genus Streptomyces.", "token_count": 363, "char_count": 1636, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:42.305901", "source": { "split": "train_shard_00000", "doc_id": 1621 }, "chunk_id": "train_shard_00000_1621_0", "global_id": 1792 }, { "text": "This study includes the utilization of sweet lemon peel (SLP) and sugarcane bagasse (SB) in solid-state fermentation using Kluyveromyces marxianus for bioflavor compounds production adopting response surface methodology. The major flavor compounds, 2-phenylethanol (2-PE) and 2-phenylethyl acetate (2-PEA) were quantified using gas chromatography-mass spectrometry with and without adding any supplements. Quantification of flavor compounds indicated that without adding any accessory in the substrate, the concentration of 2-PE using SLP and SB was 0.15 ± 0.003 mg/g and 0.14 ± 0.002 mg/g, respectively. Whereas 2-PEA concentration using SLP and SB was observed as 0.01 ± 0.008 mg/g and 0.02 ± 0.001 mg/g, respectively. The addition of l-phenylalanine (l-phe) in the substrates showed 30%-75% enhancement in the production of 2-PE and 2-PEA. The present study indicates that the K. marxianus is a potential microbial cell factory for the production of 2-PE and 2-PEA with the addition of synthetic l-phe having a plethora of applications in food and pharmaceutical industries.\n\nEnhancing bioflavor production by solid-state fermentation using Kluyveromyces marxianus and l-phenylalanine.", "token_count": 405, "char_count": 1188, "word_count": 168, "semantic_coherence": 1, "information_density": 0.5952, "quality_score": 0.7976, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:42.931020", "source": { "split": "train_shard_00000", "doc_id": 1622 }, "chunk_id": "train_shard_00000_1622_0", "global_id": 1793 }, { "text": "The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.\n\nInvestigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes.", "token_count": 400, "char_count": 1740, "word_count": 250, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [ "PET6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:43.551202", "source": { "split": "train_shard_00000", "doc_id": 1623 }, "chunk_id": "train_shard_00000_1623_0", "global_id": 1794 }, { "text": "Error correction is the canonical first step in long-read sequencing data analysis. Current self-correction methods, however, are affected by consensus sequence induced biases that mask true variants in haplotypes of lower frequency showing in mixed samples. Unlike consensus sequence templates, graph-based reference systems are not affected by such biases, so do not mistakenly mask true variants as errors. We present VeChat, as an approach to implement this idea: VeChat is based on variation graphs, as a popular type of data structure for pangenome reference systems. Extensive benchmarking experiments demonstrate that long reads corrected by VeChat contain 4 to 15 (Pacific Biosciences) and 1 to 10 times (Oxford Nanopore Technologies) less errors than when being corrected by state of the art approaches. Further, using VeChat prior to long-read assembly significantly improves the haplotype awareness of the assemblies. VeChat is an easy-to-use open-source tool and publicly available at https://github.com/HaploKit/vechat .\n\nVeChat: correcting errors in long reads using variation graphs.", "token_count": 251, "char_count": 1099, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7325, "quality_score": 0.8662, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:44.047683", "source": { "split": "train_shard_00000", "doc_id": 1624 }, "chunk_id": "train_shard_00000_1624_0", "global_id": 1795 }, { "text": "This research aimed to investigate the effect of N-acetylglucosamine (GlcNAc) on the biocontrol activity of Kluyveromyces marxianus and involved possible mechanisms. The results indicated that 0.5% GlcNAc significantly improved the antagonistic efficacy of K. marxianus against Penicillium expansum. GlcNAc supplementation led to increases of biocontrol-related enzymes and stress-resistant substances in K. marxianus including chitinase, β-1,3-glucanase, trehalose and proline, being beneficial for yeasts vigor maintenance under adverse circumstances. The antioxidative-related enzyme activities in K. marxianus, such as superoxide dismutase (SOD), catalase (CAT) and others, were increased by GlcNAc along with more quickly excess reactive oxygen species (ROS) scavenging. GlcNAc resulted in an enhancement of proliferative capacity in K. marxianus according to the transcriptomic analysis. Consequently, GlcNAc contributed to improvements of K. marxianus in the environmental adaptability and stress resistance. Our study demonstrated that both GlcNAc and K. marxianus could be regarded as potential candidates for postharvest technology application.\n\nEnhancement of biocontrol efficacy of Kluyveromyces marxianus induced by N-acetylglucosamine against Penicillium expansum.", "token_count": 345, "char_count": 1278, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:44.623231", "source": { "split": "train_shard_00000", "doc_id": 1625 }, "chunk_id": "train_shard_00000_1625_0", "global_id": 1796 }, { "text": "Ensembl (https://www.ensembl.org) has produced high-quality genomic resources for vertebrates and model organisms for more than twenty years. During that time, our resources, services and tools have continually evolved in line with both the publicly available genome data and the downstream research and applications that utilise the Ensembl platform. In recent years we have witnessed a dramatic shift in the genomic landscape. There has been a large increase in the number of high-quality reference genomes through global biodiversity initiatives. In parallel, there have been major advances towards pangenome representations of higher species, where many alternative genome assemblies representing different breeds, cultivars, strains and haplotypes are now available. In order to support these efforts and accelerate downstream research, it is our goal at Ensembl to create high-quality annotations, tools and services for species across the tree of life. Here, we report our resources for popular reference genomes, the dramatic growth of our annotations (including haplotypes from the first human pangenome graphs), updates to the Ensembl Variant Effect Predictor (VEP), interactive protein structure predictions from AlphaFold DB, and the beta release of our new website.\n\nEnsembl 2023.", "token_count": 274, "char_count": 1293, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6793, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:45.175967", "source": { "split": "train_shard_00000", "doc_id": 1626 }, "chunk_id": "train_shard_00000_1626_0", "global_id": 1797 }, { "text": "Campylobacter jejuni is a major foodborne pathogen transmitted to humans primarily via contaminated poultry meat. Since poultry meat is generally processed, distributed, and stored in the cold chain, the survival of C. jejuni at refrigeration temperatures crucially affects human exposure to C. jejuni. Here, we investigated genetic factors associated with cold stress tolerance in C. jejuni. Seventy-nine C. jejuni strains isolated from retail raw chicken exhibited different survival levels at 4°C for 21 days. Multilocus sequence typing (MLST) clonal complex 21 (CC-21) and CC-443 were dominant among cold stress-tolerant strains, whereas CC-45 was common among cold stress-sensitive strains. Genome-wide average nucleotide identity (ANI) analysis identified a phylogenetic cluster associated with cold stress tolerance. Moreover, a pangenome analysis revealed 58 genes distinctively present in the cold stress-tolerant phylogenetic cluster. Among these 58 genes,\n\nPhylogenetic Association and Genetic Factors in Cold Stress Tolerance in Campylobacter jejuni.", "token_count": 270, "char_count": 1062, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:45.718830", "source": { "split": "train_shard_00000", "doc_id": 1627 }, "chunk_id": "train_shard_00000_1627_0", "global_id": 1798 }, { "text": "Kluyveromyces marxianus has a promising enological potential because of strong extracellular pectinase activity and the copious production of specific higher alcohols and esters. However, K. marxianus is unable to complete alcoholic fermentation on its own. For this reason it is only used in co- or sequential fermentation in conjunction with Saccharomyces spp. Here we applied the protoplast fusion technique to two commercial Saccharomyces cerevisiae strains (Lalvin EC1118\n\nNew Saccharomyces cerevisiae-Kluyveromyces marxianus fusant shows enhanced alcoholic fermentation performance.", "token_count": 153, "char_count": 588, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8312, "quality_score": 0.9156, "entities": { "genes": [ "EC1118" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:46.161442", "source": { "split": "train_shard_00000", "doc_id": 1628 }, "chunk_id": "train_shard_00000_1628_0", "global_id": 1799 }, { "text": "Cyclic nucleotide-gated channels (CNGC) gene family has been found to be involved in physiological processes including signaling pathways, environmental stresses, plant growth, and development. This gene family of non-selective cation channels is known to regulate the uptake of calcium and is reported in several plant species. The pangenome-wide studies enable researchers to understand the genetic diversity comprehensively; as a comparative analysis of multiple plant species or member of a species at once helps to better understand the evolutionary relationships and diversity present among them. In the current study, pangenome-wide analysis of the CNGC gene family has been performed on five Citrus species\n\nPangenome-wide analysis of cyclic nucleotide-gated channel (CNGC) gene family in citrus", "token_count": 173, "char_count": 803, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8097, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:47.099822", "source": { "split": "train_shard_00000", "doc_id": 1629 }, "chunk_id": "train_shard_00000_1629_0", "global_id": 1800 }, { "text": "Salinity severely affects crop yield by hindering nitrogen uptake and reducing plant growth. Plant growth-promoting bacteria (PGPB) are capable of providing cross-protection against biotic/abiotic stresses and facilitating plant growth. Genome-level knowledge of PGPB is necessary to translate the knowledge into a product as efficient biofertilizers and biocontrol agents. The current study aimed to isolate and characterize indigenous plant growth-promoting strains with the potential to promote plant growth under various stress conditions. In this regard, 72 bacterial strains were isolated from various saline-sodic soil/lakes; 19 exhibited multiple in vitro plant growth-promoting traits, including indole 3 acetic acid production, phosphate solubilization, siderophore synthesis, lytic enzymes production, biofilm formation, and antibacterial activities. To get an in-depth insight into genome composition and diversity, whole-genome sequence and genome mining of one promising Bacillus paralicheniformis strain ES-1 were performed. The strain ES-1 genome carries 12 biosynthetic gene clusters, at least six genomic islands, and four prophage regions. Genome mining identified plant growth-promoting conferring genes such as phosphate solubilization, nitrogen fixation, tryptophan production, siderophore, acetoin, butanediol, chitinase, hydrogen sulfate synthesis, chemotaxis, and motility. Comparative genome analysis indicates the region of genome plasticity which shapes the structure and function of B. paralicheniformis and plays a crucial role in habitat adaptation. The strain ES-1 has a relatively large accessory genome of 649 genes (~ 19%) and 180 unique genes. Overall, these results provide valuable insight into the bioactivity and genomic insight into B. paralicheniformis strain ES-1 with its potential use in sustainable agriculture.\n\nGenome mining, antimicrobial and plant growth-promoting potentials of halotolerant Bacillus paralicheniformis ES-1 isolated from salt mine.", "token_count": 488, "char_count": 1998, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6615, "quality_score": 0.8308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:47.740302", "source": { "split": "train_shard_00000", "doc_id": 1630 }, "chunk_id": "train_shard_00000_1630_0", "global_id": 1801 }, { "text": "Various countries and organizations call for banning the use of antibiotic growth promoters (AGPs) as prophylaxis and for growth promotion in the livestock industry. Hence, seeking a substitute for antibiotics is strongly required by the livestock industry to maintain the productivity level and profits. Probiotics could represent one viable solution because of their beneficial effects on host health and maintaining the intestinal microbiota balance. In the present study, we aimed to isolate bacterial strains with probiotics properties from JinHua pig (a Chinese native pig breed) gastrointestinal tract that have antagonistic activity against to common disease-causing bacteria on farms. The four most potent strains were isolated (PP31, BA11, BA40, BV5) by the agar well diffusion method and further characterized by acid, bile salt, trypsin tolerance, whole genome sequencing (WGS), and suppressing\n\nScreening of Bacteria Inhibiting", "token_count": 219, "char_count": 940, "word_count": 134, "semantic_coherence": 1, "information_density": 0.791, "quality_score": 0.8955, "entities": { "genes": [ "BA11", "BA40", "BV5", "PP31" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:48.254688", "source": { "split": "train_shard_00000", "doc_id": 1631 }, "chunk_id": "train_shard_00000_1631_0", "global_id": 1802 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) is a debilitating disease manifest by severe cholestasis, intractable pruritus and growth delay that ultimately leads to liver failure or transplantation. Maralixibat (MRX) was recently approved for the treatment of cholestatic pruritus in patients with Alagille syndrome. The aim of this study was to determine whether specific changes in the composition of the serum bile acid metabolome could predict pruritus response to treatment. Serum BAs (sBA) and 7α-hydroxy-4-cholesten-3-one (7α-C4), a surrogate marker of BA synthesis, were monitored by ultrahigh-performance liquid chromatography coupled with tandem mass spectrometry over 72 weeks in PFIC patients with mild to moderate non-truncating bile salt export pump (BSEP) mutations (n = 19) treated with MRX. The weekly itch reported outcome observer (ItchRO[Obs]) score measured pruritus severity. Linear mixed models (LMM) were applied to explore the effects of individual sBA profiles and their relationship to pruritus response. Changes in the composition of sBA correlated with pruritus improvement. Notably, the trajectory of serum total and individual BA species and 7α-C4 were significantly associated with ItchRO[Obs] score (p < 0.05). These results reveal that beyond simple total sBA concentrations, specific changes to the BA metabolome are associated with pruritus reduction in patients with BSEP deficiency, thus providing further insight into causal relationship of bile acids and pruritus.\n\nSerum Bile Acid Profiling and Mixed Model Analysis Reveal Biomarkers Associated with Pruritus Reduction in Maralixibat-Treated Patients with BSEP Deficiency.", "token_count": 446, "char_count": 1672, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:48.906551", "source": { "split": "train_shard_00000", "doc_id": 1632 }, "chunk_id": "train_shard_00000_1632_0", "global_id": 1803 }, { "text": "Triazole fungicides such as propiconazole (Pi) or tebuconazole (Te) show hepatotoxicity in vivo, e.g., hypertrophy and vacuolization of liver cells following interaction with nuclear receptors such as PXR (pregnane-X-receptor) and CAR (constitutive androstane receptor). Accordingly, azoles affect gene expression associated with these adverse outcomes in vivo but also in human liver cells in vitro. Additionally, genes indicative of liver cholestasis are affected in vivo and in vitro. We therefore analyzed the capability of Pi and Te to cause cholestasis in an adverse outcome pathway (AOP)-driven approach in hepatic cells of human origin in vitro, considering also previous in vivo studies. Bile salt export pump (BSEP) activity assays confirmed that both azoles are weak inhibitors of BSEP. They alternate the expression of various cholestasis-associated target genes and proteins as well as the mitochondrial membrane function. Published in vivo data, however, demonstrate that neither Pi nor Te cause cholestasis in rodent bioassays. This discrepancy can be explained by the in vivo concentrations of both azoles being well below their EC50 for BSEP inhibition. From a regulatory perspective, this illustrates that toxicogenomics and human in vitro models are valuable tools to detect the potential of a substance to cause a specific type of toxicity. To come to a sound regulatory conclusion on the in vivo relevance of such a finding, results will have to be considered in a broader context also including toxicokinetics in a weight-of-evidence approach.\n\nNew Approach Methods for Hazard Identification: A Case Study with Azole Fungicides Affecting Molecular Targets Associated with the Adverse Outcome Pathway for Cholestasis.", "token_count": 427, "char_count": 1738, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6187, "quality_score": 0.8093, "entities": { "genes": [ "EC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:49.556736", "source": { "split": "train_shard_00000", "doc_id": 1633 }, "chunk_id": "train_shard_00000_1633_0", "global_id": 1804 }, { "text": "The aim of this study was to select potential probiotic yeasts from dry-cured Xuanwei ham and investigate yeast-derived antioxidant peptides. The results showed that two strains (XHY69 and XHY79) were selected as potential probiotic yeasts and identified as Yamadazyma triangularis. The two yeasts showed tolerance under pH 2.5 and 1% bile salt, in addition to protease activity, auto-aggregation, antibacterial, and antioxidant activities. The peptide fraction (MW < 3 kDa) isolated from XHY69 fermentation broth, named XHY69AP, showed higher radical scavenging activities than glutathione at a concentration of 4.5 mg/mL (p < 0.05). The fraction (AP-D10) was purified from XHY69AP by gel filtration chromatography and reversed-phase high performance liquid chromatography, and then further identified by a UHPLC-LTQ-Orbitrap mass spectrometer. The molecular weight of all 55 purified sequences was distributed between 0.370 and 0.735 kDa. Among these seven novel peptides, Tyr-Pro-Leu-Pro (YPLP), Ala-Gly-Pro-Leu (AGPL), Gly-Pro-Phe-Pro (GPFP), and Ala-Pro-Gly-Gly-Phe (APGGF) were identified. All sequences were abundant in hydrophobic amino acids, especially proline residue. Among these novel peptides, YPLP possessed the highest ABTS scavenging rate (75.48%). The present work selects two new probiotic potential yeasts from dry-cured Xuanwei ham that are effective to yield novel antioxidant peptides.\n\nSelection of Potential Probiotic Yeasts from Dry-Cured Xuanwei Ham and Identification of Yeast-Derived Antioxidant Peptides.", "token_count": 474, "char_count": 1534, "word_count": 208, "semantic_coherence": 1, "information_density": 0.649, "quality_score": 0.8245, "entities": { "genes": [ "XHY69", "XHY79" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:50.233774", "source": { "split": "train_shard_00000", "doc_id": 1634 }, "chunk_id": "train_shard_00000_1634_0", "global_id": 1805 }, { "text": "Esophageal adenocarcinoma (EAC), the predominant type of esophageal cancer in the United States, develops through Barrett's esophagus (BE)-dysplasia-carcinoma cascade. Gastroesophageal reflux disease, where acidic bile salts refluxate into the esophagus, is the main risk factor for the development of BE and its progression to EAC. The NFE2-related factor 2 (NRF2) is the master cellular antioxidant regulator. We detected high NRF2 protein levels in the EAC cell lines and primary tissues. Knockdown of NRF2 significantly enhanced acidic bile salt-induced oxidative stress, DNA damage, and inhibited EAC cell growth. Brusatol, an NRF2 inhibitor, significantly inhibited NRF2 transcriptional activity and downregulated the NRF2 target genes. We discovered that in addition to inducing apoptosis, Brusatol alone or in combination with cisplatin (CDDP) induced significant lipid peroxidation and ferroptosis, as evidenced by reduced xCT and GPX4 expression, two known ferroptosis markers. The combination of Brusatol and CDDP significantly inhibited EAC tumor xenograft growth in vivo and confirmed the in vitro data showing ferroptosis as an important mechanism in the tumors treated with Brusatol or Brusatol and CDDP combination. Our data support the role of NRF2 in protecting against stress-induced apoptosis and ferroptosis in EACs. Targeting NRF2 in combination with platinum therapy can be an effective strategy for eliminating cancer cells in EAC.\n\nTargeting NRF2 Sensitizes Esophageal Adenocarcinoma Cells to Cisplatin through Induction of Ferroptosis and Apoptosis.", "token_count": 439, "char_count": 1575, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [ "GPX4", "NFE2", "NRF2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:50.870736", "source": { "split": "train_shard_00000", "doc_id": 1635 }, "chunk_id": "train_shard_00000_1635_0", "global_id": 1806 }, { "text": "Glycerol is an ideal co-substrate for xylitol production with Kluyveromyces marxianus. This study demonstrated that K. marxianus catabolizes glycerol through the Gut1-Gut2 pathway instead of the previously speculated NADPH-dependent Gcy1-Dak1 pathway using the transient clustered regularly interspaced short palindromic repeats/ CRISPR-associated protein 9 (CRISPR/Cas9) system. Additionally, Utr1p was demonstrated to mediate NADPH generation through NADH phosphorylation. YZB392, which was constructed by integrating Utr1 into the Ypr1 site in the strain overexpressing NcXyl1 and CiGxf1 and harboring disrupted Xyl2, exhibited enhanced glycerol utilization for xylitol production (from 2.50- to 3.30- g/L after consuming 1 g/L glycerol). Fed-batch fermentation at 42 °C with YZB392 yielded 322.07 g/L xylitol, which is the highest known xylitol titer obtained via biological method. Feeding crude glycerol, xylose mother liquor, and corn steep liquor powder into a bioreactor resulted in the production of 235.69 g/L xylitol. This study developed a platform for xylitol production from industrial by-products.\n\nImproving glycerol utilization during high-temperature xylitol production with Kluyveromyces marxianus using a transient clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 system.", "token_count": 411, "char_count": 1338, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6936, "quality_score": 0.8468, "entities": { "genes": [ "YZB392" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "gut", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:51.503295", "source": { "split": "train_shard_00000", "doc_id": 1636 }, "chunk_id": "train_shard_00000_1636_0", "global_id": 1807 }, { "text": "In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements.\n\nThe pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB.", "token_count": 184, "char_count": 749, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:51.956595", "source": { "split": "train_shard_00000", "doc_id": 1637 }, "chunk_id": "train_shard_00000_1637_0", "global_id": 1808 }, { "text": "Orthopoxviruses comprise several relevant pathogens, including the causative agent of smallpox and monkeypox virus. Analysis of orthopoxvirus genome evolution mainly focused on gene gains/losses. We instead analyzed core genes, which are conserved in all orthopoxviruses. We show that, despite their strong constraint, some genes involved in viral morphogenesis and transcription/replication were targets of pervasive positive selection, which was relatively uncommon in immunomodulatory genes. However at least three of the positively selected genes, E3L, A24R, and H3L, might have evolved in response to immune selection. Episodic positive selection was particularly common on the internal branches of the orthopox phylogeny and on the monkeypox virus lineage. The latter showed evidence of episodic positive selection at the D14L gene, which encodes a modulator of complement activation (MOPICE). Notably, two genes (B1R and A33R) targeted by episodic selection on more than one branch are involved in forms of intra-genomic conflict. Finally, we found that, in orthopoxvirus proteomes, intrinsically disordered regions (IDRs) tend to be less constrained and are common targets of positive selection. Extension of our analysis to all poxviruses showed no evidence that the IDR fraction differs with host range. Conversely, we found a strong effect of base composition, which was however not sufficient to explain IDR fraction. We thus suggest that, in poxviruses, the IDR fraction is maintained by modulating GC content to accommodate disorder-promoting codons. Overall, our data provide novel insight in orthopoxvirus evolution and provide a list of genes and sites that are expected to modulate viral phenotypes.\n\nEvolution of the orthopoxvirus core genome.", "token_count": 418, "char_count": 1762, "word_count": 254, "semantic_coherence": 1, "information_density": 0.622, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:52.580573", "source": { "split": "train_shard_00000", "doc_id": 1638 }, "chunk_id": "train_shard_00000_1638_0", "global_id": 1809 }, { "text": "The human microbiome is a reservoir of potential bacteriocins that can counteract multidrug resistant bacterial pathogens. Unlike antibiotics, bacteriocins selectively inhibit a spectrum of competent bacteria and are said to safeguard gut commensals, reducing the chance of dysbiosis. Bacteriocinogenic probiotics or bacteriocins of human origin will be more pertinent in human physiological conditions for therapeutic applications to act against invading pathogens. Recent advancement in the omics approach enables the mining of diverse and novel bacteriocins by identifying biosynthetic gene clusters from the human microbial genome, pangenome or shotgun metagenome, which is a breakthrough in the discovery line of novel bacteriocins. This review summarizes the most recent trends and therapeutic potential of bacteriocins of human microbial origin, the advancement in the in silico algorithms and databases in the discovery of novel bacteriocin, and how to bridge the gap between the discovery of bacteriocin genes from big datasets and their in vitro production. Besides, the later part of the review discussed the various impediments in their clinical applications and possible solution to bring them into the frontline therapeutics to control infections, thereby meeting the challenges of global antimicrobial resistance.\n\nDemystifying Bacteriocins of Human Microbiota by Genome Guided Prospects: An Impetus to Rekindle the Antimicrobial Research.", "token_count": 327, "char_count": 1454, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:53.148298", "source": { "split": "train_shard_00000", "doc_id": 1639 }, "chunk_id": "train_shard_00000_1639_0", "global_id": 1810 }, { "text": "Salmonella enterica serotype Oranienburg is a multi-host, ubiquitous, and prevalent Non-typhoidal Salmonella (NTS) in subtropical rivers, particularly in sediments; little studied so far possible the adaptation and establishment of this microorganism based on its genetic content. This study was focused on the first five genomes of S. Oranienburg in sediments through whole-genome sequencing (WGS) and 61 river water genomes isolated in previous studies. Results showed an open pangenome with 5,594 gene clusters (GCs), and the division of their categories showed; 3,303 core genes, 741 persistent genes, 1,282 accessory genes, and 268 unique genes. Additionally, it showed three main subclades within the same serotype and showed a conserved genetic content, suggesting the display of different adaptation strategies to its establishment. Nine genes for antimicrobial resistance were detected: aac (6') - Iy, H-NS, golS, marA, mdsABC, mdtK, and sdiA, and a mutation in the parC gene p. T57S generating a resistance. In addition, virulence genes and pathogenicity islands (SPI's) were analyzed, finding 92 genes and an identity above 80 % in the SPI's 1 to 5, and the centisomes 54 and 63. The environmental strains of S. Oranienburg do not represent a concern as multidrug resistance (MDR) bacterium; however, virulence genes remain a potential health risk. This study contributes to understanding its adaptation to aquatic environments in Mexico.\n\nPopulation structure of the Salmonella enterica serotype Oranienburg reveals similar virulence, regardless of isolation years and sources.", "token_count": 418, "char_count": 1589, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:53.771671", "source": { "split": "train_shard_00000", "doc_id": 1640 }, "chunk_id": "train_shard_00000_1640_0", "global_id": 1811 }, { "text": "The honeybee gut microbiome is thought to be important for bee health, but the role of the individual members is poorly understood. Here, we present closed genomes and associated mobilomes of 102 Apilactobacillus kunkeei isolates obtained from the honey crop (foregut) of honeybees sampled from beehives in Helsingborg in the south of Sweden and from the islands Gotland and Åland in the Baltic Sea. Each beehive contained a unique composition of isolates and repeated sampling of similar isolates from two beehives in Helsingborg suggests that the bacterial community is stably maintained across bee generations during the summer months. The sampled bacterial population contained an open pan-genome structure with a high genomic density of transposons. A subset of strains affiliated with phylogroup A inhibited growth of the bee pathogen Melissococcus plutonius, all of which contained a 19.5 kb plasmid for the synthesis of the antimicrobial compound kunkecin A, while a subset of phylogroups B and C strains contained a 32.9 kb plasmid for the synthesis of a putative polyketide antibiotic. This study suggests that the mobile gene pool of A. kunkeei plays a key role in pathogen defense in honeybees, providing new insights into the evolutionary dynamics of defensive symbiont populations.\n\nGenome Evolution of a Symbiont Population for Pathogen Defense in Honeybees.", "token_count": 348, "char_count": 1373, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:54.354831", "source": { "split": "train_shard_00000", "doc_id": 1641 }, "chunk_id": "train_shard_00000_1641_0", "global_id": 1812 }, { "text": "Although the importance of bile acid (BA)-related microbial strains and enzymes is increasingly recognized for monogastric animals, a lack of knowledge about BA metabolism in dairy cows limits functional applications aimed at the targeted modulation of microbe-host interactions for animal production and health. In the present study, 108 content samples from six intestinal regions of dairy cows were used for shotgun metagenomic sequencing. Overall, 372 high-quality metagenome-assembled genomes (MAGs) were involved in BA deconjugation, oxidation, and dehydroxylation pathways. Furthermore, the BA-metabolizing microbiome predominately occurred in the large intestine, resulting in the accumulation of secondary unconjugated BAs. Comparative genomic analysis revealed that the bile salt hydrolase (BSH)-carrying microbial populations managed with the selective environment of the dairy cow intestine by adopting numerous host mucin glycan-degrading abilities. A sequence similarity network analysis classified 439 BSH homologs into 12 clusters and identified different clusters with diverse evolution, taxonomy, signal peptides, and ecological niches. Our omics data further revealed that the strains of Firmicutes bacterium CAG-110 processed the increased abundance of BSHs from Cluster 1, coinciding with the changes in the colon cholic acid concentration after grain introduction, and were intricately related to intestinal inflammation. This study is the first to use a genome-centric approach and whole intestine-targeted metabolomics to reveal microbial BA metabolism and its diet-induced functional implications in dairy cows. These findings provide insight into the manipulation of intestinal microorganisms for improving host health.\n\nGenome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications.", "token_count": 445, "char_count": 1879, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:54.986773", "source": { "split": "train_shard_00000", "doc_id": 1642 }, "chunk_id": "train_shard_00000_1642_0", "global_id": 1813 }, { "text": "Pseudomonas is a bacterial genus, with a bona fide environmental habitat that comprises different species, some of them causing diseases in humans and plants, as well as some strains with biotechnological potential. Amongst them, Pseudomonas aeruginosa is currently one of the most important nosocomial pathogens. In addition, this microorganism is a prevalent cause of chronic infections in cystic fibrosis patients and in people suffering from chronic obstructive pulmonary disease. The success of P. aeruginosa in colonising different habitats largely relies on its metabolic versatility and robustness. Besides, this bacterial pathogen harbours in its core genome a large set of virulence determinants that allows it to colonise/infect a variety of hosts, from unicellular organisms to humans. Nevertheless, these are not just the only conditions needed for infecting patients at hospitals. Taking into consideration that infected patients are regularly under antibiotic treatment, the ability to avoid antibiotics' action is also needed. In this sense, P. aeruginosa displays a characteristic low susceptibility to several antibiotics currently used in therapy. This is due to the reduced permeability of its cellular envelopes and the presence in its genome of an arrangement of genes encoding multidrug efflux pumps and antibiotic-inactivating enzymes that contribute to its resilience to antibiotics. Besides intrinsic resistance, P. aeruginosa is able to evolve towards antibiotic resistance through mutations (particularly relevant in the case of chronic infections) and via acquisition of antibiotic resistance genes. It is worth mentioning that acquired resistance is not the only venue that P. aeruginosa has for avoiding the action of antibiotics. Transient resistance can also confer this phenotype. Indeed, the induction of the expression of intrinsic resistance genes by conditions or compounds that P. aeruginosa could face during infection can compromise the effectiveness of antibiotics for treating such infections. In addition, tolerant cells able to survive during the exposure to bactericidal antibiotics without an increase in their antibiotic resistance phenotype are found as well in these patients, and they are the prelude of the evolution towards antibiotic resistance. Finally, P", "token_count": 508, "char_count": 2310, "word_count": 332, "semantic_coherence": 1, "information_density": 0.5843, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:55.642464", "source": { "split": "train_shard_00000", "doc_id": 1643 }, "chunk_id": "train_shard_00000_1643_0", "global_id": 1814 }, { "text": "aeruginosa biofilms, frequently encountered in the lungs of cystic fibrosis patients, in prostheses, or in catheters, present low antibiotic susceptibility and are associated with recalcitrance and disease worsening.\n\nAntibiotic Resistance in Pseudomonas.", "token_count": 69, "char_count": 255, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8438, "quality_score": 0.9219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:56.010745", "source": { "split": "train_shard_00000", "doc_id": 1643 }, "chunk_id": "train_shard_00000_1643_1", "global_id": 1815 }, { "text": "In this chapter, we leverage a novel approach to assess the seamless population structure of Pseudomonas aeruginosa, using the full repertoire of genomes sequenced to date (GenBank, April 6, 2020). In order to assess the set of core functions that represents the species as well as the differences in these core functions among the phylogroups observed in the population structure analysis, we performed pangenome analyses at the species level and at the phylogroup level. The existence of the phylogroups described in the population structure analyses was supported by their different profiles of antibiotic-resistant determinants. Finally, we utilized a presence/absence matrix of protein families from the entire species to evaluate if P. aeruginosa phylogroups can be differentiated according to their accessory genomic content. Our analysis shows that the core genome of P. aeruginosa is approximately 62% of the average gene content for the species, and it is highly enriched with pathways related to the metabolism of carbohydrates and amino acids as well as cellular processes and cell maintenance. The analysis of the accessory genome of P. aeruginosa performed in this chapter confirmed not only the existence of the three phylogroups previously described in the population structure analysis, but also of 29 genetic substructures (subgroups) within the main phylogroups. Our work illustrates the utility of populations genomics pipelines to better understand highly complex bacterial species such as P. aeruginosa.\n\nPseudomonas aeruginosa Pangenome: Core and Accessory Genes of a Highly Resourceful Opportunistic Pathogen.", "token_count": 366, "char_count": 1633, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5708, "quality_score": 0.7854, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:56.596224", "source": { "split": "train_shard_00000", "doc_id": 1644 }, "chunk_id": "train_shard_00000_1644_0", "global_id": 1816 }, { "text": "Bicelles, composed of a mixture of long and short chain lipids, form nanostructured molecular assemblies that are attractive lipid-membrane mimics for\n\nChange in Morphology of Dimyristoylphosphatidylcholine/Bile Salt Derivative Bicelle Assemblies with Dodecylmaltoside in the Disk and Ribbon Phases.", "token_count": 89, "char_count": 299, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8684, "quality_score": 0.9342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:56.974237", "source": { "split": "train_shard_00000", "doc_id": 1645 }, "chunk_id": "train_shard_00000_1645_0", "global_id": 1817 }, { "text": "Gut microbiota and their metabolites like bile acid (BA) have been investigated as causes of irritable bowel syndrome (IBS) symptoms. Primary BAs are synthesized and conjugated in the liver and released into the duodenum. BA biotransformation by gut microbiota begins in the intestine and results in production of a broad range of secondary BAs. Deconjugation is considered the gateway reaction for further modification and is mediated by bile salt hydrolase, which is widely expressed by the gut microbiota. However, gut bacteria that convert primary BAs to secondary BAs belong to a limited number of species, mainly Clostridiales. Like gut microbiota modify BA profile, BAs can shape gut microbiota via direct and indirect actions. BAs have prosecretory effects and regulates gut motility. BAs can also affect gut sensitivity. Because of the vital role of the gut microbiota and BAs in gut function, their bidirectional relationship may contribute to the pathophysiology of IBS. Individuals with IBS have been reported to have altered microbial profiles and modified BA profiles. A significant increase in fecal primary BA and a corresponding decrease in secondary BA have been observed in IBS with predominant diarrhea. In addition, primary BA was positively correlated with IBS symptoms. In IBS with predominant diarrhea, bacteria with reduced abundance mainly belonged to the genera in Ruminococcaceae and exhibited a negative correlation with primary BAs. Integrating the analysis of the gut microbiota and BAs could better understanding of IBS pathophysiology. The gap in this field needs to be further filled in the future.\n\nBile Acid and Gut Microbiota in Irritable Bowel Syndrome.", "token_count": 395, "char_count": 1691, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5328, "quality_score": 0.7664, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:57.594944", "source": { "split": "train_shard_00000", "doc_id": 1646 }, "chunk_id": "train_shard_00000_1646_0", "global_id": 1818 }, { "text": "The human gut microbiome is composed of a diverse consortium of microorganisms. Relatively little is known about the diversity of the bacteriophage population and their interactions with microbial organisms in the human microbiome. Due to the persistent rivalry between microbial organisms (hosts) and phages (invaders), genetic traces of phages are found in the hosts' CRISPR-Cas adaptive immune system. Mobile genetic elements (MGEs) found in bacteria include genetic material from phage and plasmids, often resultant from invasion events. We developed a computational pipeline (BacMGEnet), which can be used for inference and exploratory analysis of putative interactions between microbial organisms and MGEs (phages and plasmids) and their interaction network. Given a collection of genomes as the input, BacMGEnet utilizes computational tools we have previously developed to characterize CRISPR-Cas systems in the genomes, which are then used to identify putative invaders from publicly available collections of phage/prophage sequences. In addition, BacMGEnet uses a greedy algorithm to summarize identified putative interactions to produce a bacteria-MGE network in a standard network format. Inferred networks can be utilized to assist further examination of the putative interactions and for discovery of interaction patterns. Here we apply the BacMGEnet pipeline to a few collections of genomic/metagenomic datasets to demonstrate its utilities. BacMGEnet revealed a complex interaction network of the\n\nRevealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systems.", "token_count": 360, "char_count": 1609, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5811, "quality_score": 0.7905, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:58.178000", "source": { "split": "train_shard_00000", "doc_id": 1647 }, "chunk_id": "train_shard_00000_1647_0", "global_id": 1819 }, { "text": "The thermotolerant yeast\n\nRNA polymerase II-driven CRISPR-Cas9 system for efficient non-growth-biased metabolic engineering of", "token_count": 39, "char_count": 126, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:58.543444", "source": { "split": "train_shard_00000", "doc_id": 1648 }, "chunk_id": "train_shard_00000_1648_0", "global_id": 1820 }, { "text": "Reducing high blood cholesterol is an important strategy to decrease the chances of a cardiovascular disease occurrence, the main cause of mortality in western developed countries. Therefore, the search for an alternative therapeutic or preventive approach being natural, biocompatible, and not toxic is still more relevant than ever. This need is particularly felt in Pediatrics for treating childhood hypercholesterolemia, due to statins interference in the production of steroid hormones in prepuberal children. Notwithstanding the general acceptance of the healthy role of the fibers in the diet, the mechanism underlying the cholesterol-lowering ability of soluble fibers is still under discussion. Therefore, we started a systematic study of the binding ability of some soluble dietary fibers (SDF) originated from different natural sources toward selected bile salts (BS) by isothermal titration calorimetry (ITC). Here we report the results of our ITC studies on the interaction of alginate, pectin and chitosan with sodium cholate (NaC), sodium deoxycholate (NaDC), sodium taurocholate (NaTC) and sodium taurodeoxycholate (NaTDC). Thermodynamic data on the micelle formation process of the above bile salts, as a premise to the study of their binding ability to the SDF, are also reported. Alginate does not show specific binding interaction with BS, while pectin shows a strong exothermic bond with NaDC in monomeric form. Chitosan, positively charged and soluble only at low pH, shows strong exothermic interactions with NaTC and NaTDC (soluble at pH = 3 in acetate buffer) with precipitate formation. For NaTC, the exothermic peak starts at about 5 mM. At this concentration NaTC bound on the fiber reaches locally the cmc value and micelles start forming on the fiber inducing its conformational change. For NaTDC the same process occurs at much lower concentrations, due to lower cmc, and with a greater quantity of heat involved. The first set of results here presented shows that for some SDF the binding of BS could be an important mechanism in cholesterol lowering but not the only one", "token_count": 504, "char_count": 2103, "word_count": 323, "semantic_coherence": 1, "information_density": 0.6285, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:59.197119", "source": { "split": "train_shard_00000", "doc_id": 1649 }, "chunk_id": "train_shard_00000_1649_0", "global_id": 1821 }, { "text": "The information here presented could be a starting point for the design of optimized functional foods with high cholesterol lowering ability.\n\nOn the mechanism of the cholesterol lowering ability of soluble dietary fibers: Interaction of some bile salts with pectin, alginate, and chitosan studied by isothermal titration calorimetry.", "token_count": 83, "char_count": 334, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:59.569198", "source": { "split": "train_shard_00000", "doc_id": 1649 }, "chunk_id": "train_shard_00000_1649_1", "global_id": 1822 }, { "text": "Several individuals reported gastrointestinal symptoms following meals consumed in late January 2021 at a restaurant in western Finland. We conducted a retrospective cohort study and defined a case as a person who ate at the lunch restaurant between 27 and 29 January 2021 and had stomach pain, vomiting or diarrhoea and/or a laboratory-confirmed", "token_count": 84, "char_count": 346, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7925, "quality_score": 0.8962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:14:59.938781", "source": { "split": "train_shard_00000", "doc_id": 1650 }, "chunk_id": "train_shard_00000_1650_0", "global_id": 1823 }, { "text": "The burden of public health challenges associated with the western dietary and living style is growing. Nutraceuticals have been paid increasing attentions due to their effects in promotion of health. However, in the gastrointestinal (GI) tract, the nutraceuticals suffer from not only the harsh acidic environment of the stomach and a variety of digestive enzymes, but also the antibacterial activity of intestinal bile salts and the action of protease from the gut microbiota. The amount of the nutraceuticals arriving at the sites in GI tract for absorption or exerting the bioactivities is always unfortunately limited, which puts forward high requirements for protection of nutraceuticals in a certain high contents during oral consumption. Hydrogels are three-dimensional polymeric porous networks formed by the cross-linking of polymer chains, which can hold huge amounts of water. Compared with other carries with the size in microscopic scale such as nanoparticle and microcapsules, hydrogels could be considered to be more suitable delivery systems in food due to their macroscopic bulk properties, adjustable viscoelasticity and large spatial structure for embedding nutraceuticals. Regarding to the applications in food, natural polymer-based hydrogels are commonly safe and popular due to their source with the appealing characteristics of affordability, biodegradability and biocompatibility. Although chemical crosslinking has been widely utilized in preparation of hydrogels, it prefers the physical crosslinking in the researches in food. The reasonable design for the structure of natural polymeric hydrogels is essential for seeking the favorable functionalities to apply in the delivery system, and it could be possible to obtain the enhanced adhesive property, acid stability, resistant to bile salt, and the controlled release behavior. The hydrogels prepared with proteins, polysaccharides or the mix of them to deliver the functional ingredients, mainly the phenolic components, vitamins, probiotics are discussed to obtain inspiration for the wide applications in delivery systems. Further efforts might be made in the\n\nHydrogels as promising carriers for the delivery of food bioactive ingredients.", "token_count": 470, "char_count": 2224, "word_count": 319, "semantic_coherence": 1, "information_density": 0.6144, "quality_score": 0.8072, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:00.996776", "source": { "split": "train_shard_00000", "doc_id": 1651 }, "chunk_id": "train_shard_00000_1651_0", "global_id": 1824 }, { "text": "Human ileal bile acid-binding protein (hI-BABP) has a key role in the enterohepatic circulation of bile salts. Its two internal binding sites exhibit positive cooperativity accompanied by a site-selectivity of glycocholate (GCA) and glycochenodeoxycholate (GCDA), the two most abundant bile salts in humans. To improve our understanding of the role of dynamics in ligand binding, we introduced functionally impairing single-residue mutations at two key regions of the protein and subjected the mutants to NMR relaxation analysis and MD simulations. According to our results, mutation in both the vicinity of the C/D (Q51A) and the G/H (Q99A) turns results in a redistribution of motional freedom in\n\nMultiple Timescale Dynamic Analysis of Functionally-Impairing Mutations in Human Ileal Bile Acid-Binding Protein.", "token_count": 216, "char_count": 813, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:01.512869", "source": { "split": "train_shard_00000", "doc_id": 1652 }, "chunk_id": "train_shard_00000_1652_0", "global_id": 1825 }, { "text": "Antimicrobial resistance (AMR) is a public health issue attributed to the misuse of antibiotics in human and veterinary medicine. Since AMR surveillance requires a One Health approach, we sampled nine interconnected compartments at a hydrological open-air lab (HOAL) in Austria to obtain six bacterial species included in the WHO priority list of antibiotic-resistant bacteria (ARB). Whole genome sequencing-based typing included core genome multilocus sequence typing (cgMLST). Genetic and phenotypic characterization of AMR was performed for all isolates. Eighty-nine clinically-relevant bacteria were obtained from eight compartments including 49\n\nCharacterizing Antimicrobial Resistance in Clinically Relevant Bacteria Isolated at the Human/Animal/Environment Interface Using Whole-Genome Sequencing in Austria.", "token_count": 196, "char_count": 815, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7788, "quality_score": 0.8894, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:02.020690", "source": { "split": "train_shard_00000", "doc_id": 1653 }, "chunk_id": "train_shard_00000_1653_0", "global_id": 1826 }, { "text": "Current market trends point at increasing demand for functional foods, namely those carrying probiotics. In the case of table olives, presence of probiotics would convey a competitive advantage to Mediterranean-based diets, already established for their cultural heritage and gastronomic character. This work assessed the safety and resistance to gastrointestinal digestion of 19 native LAB strains from Cobrançosa table olives. Strains were identified via molecular sequencing (4 fingerprints/10 strains for Lactiplantibacillus pentosus, and 2 fingerprints/9 strains for L. paraplantarum), and exposed to simulated gastrointestinal fluids, as per the INFOGEST in vitro protocol with modifications. None of those strains proved dangerous for human consumption. Survivability to the gastrointestinal resistance test ranged from 29% to 70%, with strain-dependent variability. L. paraplantarum i18, i27, and i102, and L. pentosus i10 and i11 exhibited statistically lower survival rates (29−35%) than probiotic the Greek table olive reference strain L. pentosus B281 (53%). Among the other strains, L. paraplantarum i101 and L. pentosus i53 and i106 showed the highest survival rates but were not significantly different from the strain of Lacticaseibacillus casei isolated from commercial probiotic yoghurt (65−70%). In vitro results proved that strains retrieved from fermenting cultivar Cobrançosa possess the potential to be claimed as probiotics—thus deserving further attention toward the development of a specific starter culture.\n\nStudy of Lactic Acid Bacteria Biodiversity in Fermented", "token_count": 421, "char_count": 1591, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6849, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:02.646723", "source": { "split": "train_shard_00000", "doc_id": 1654 }, "chunk_id": "train_shard_00000_1654_0", "global_id": 1827 }, { "text": "Budesonide (BUD), a glucocorticoids drug, inhibits all steps in the inflammatory response. It can reduce and treat inflammation and other symptoms associated with acute lung injury such as COVID-19. Loading BUD into bilosomes could boost its therapeutic activity, and lessen its frequent administration and side effects. Different bilosomal formulations were prepared where the independent variables were lipid type (Cholesterol, Phospholipon 80H, L-alpha phosphatidylcholine, and Lipoid S45), bile salt type (Na cholate and Na deoxycholate), and drug concentration (10, 20 mg). The measured responses were: vesicle size, entrapment efficiency, and release efficiency. One optimum formulation (composed of cholesterol, Na cholate, and 10 mg of BUD) was selected and investigated for its anti-inflammatory efficacy in vivo using Wistar albino male rats. Randomly allocated rats were distributed into four groups: The first: normal control group and received intranasal saline, the second one acted as the acute lung injury model received intranasal single dose of 2 mg/kg potassium dichromate (PD). Whereas the third and fourth groups received the market product (Pulmicort® nebulising suspension 0.5 mg/ml) and the optimized formulation (0.5 mg/kg; intranasal) for 7 days after PD instillation, respectively. Results showed that the optimized formulation decreased the pro-inflammatory cytokines TNF-α, and TGF-β contents as well as reduced PKC content in lung. These findings suggest the potentiality of BUD-loaded bilosomes for the treatment of acute lung injury with the ability of inhibiting the pro-inflammatory cytokines induced COVID-19.\n\nBudesonide-Loaded Bilosomes as a Targeted Delivery Therapeutic Approach Against Acute Lung Injury in Rats.", "token_count": 469, "char_count": 1752, "word_count": 246, "semantic_coherence": 1, "information_density": 0.7033, "quality_score": 0.8516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:03.289893", "source": { "split": "train_shard_00000", "doc_id": 1655 }, "chunk_id": "train_shard_00000_1655_0", "global_id": 1828 }, { "text": "Being some of the most efficient agents to individually solubilize single-wall carbon nanotubes (SWCNTs), bile salt surfactants (BSS) represent the foundation for the surfactant-based structure sorting and spectroscopic characterization of SWCNTs. In this work, we investigate three BSS in their ability to separate different SWCNT chiral structures by aqueous two-phase extraction (ATPE): sodium deoxycholate (DOC), sodium cholate (SC) and sodium chenodeoxycholate (CDOC). The small difference in their chemical structure (just one hydroxyl group) leads to significant differences in their stacking behavior on SWCNT walls with different diameter and chiral structure that, in turn, has direct consequences for the chiral sorting of SWCNTs using these BSS. By performing several series of systematic ATPE experiments, we reveal that, in general, the stacking of DOC and CDOC is more enantioselective than the stacking of SC on the SWCNT walls, while SC has a clear diameter preference for efficiently solubilizing the SWCNTs in comparison to DOC and CDOC. Moreover, combining sodium dodecylsulfate with SC allows for resolving the ATPE sorting transitions of empty and water-filled SWCNTs for a number of SWCNT chiralities. We also show that addition of SC to combinations of DOC and sodium dodecylbenzenesulfonate can enhance separations of particular chiralities.\n\nVariations in bile salt surfactant structure allow tuning of the sorting of single-wall carbon nanotubes by aqueous two-phase extraction.", "token_count": 379, "char_count": 1505, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:03.900314", "source": { "split": "train_shard_00000", "doc_id": 1656 }, "chunk_id": "train_shard_00000_1656_0", "global_id": 1829 }, { "text": "Carotenoids are widely utilized in the food, pharmaceutical and nutraceutical industries. Here, Kluyveromyces marxianus was engineered to overproduce carotenoids from corncob hydrolysate or xylose mother liquid (XML, a byproduct of commercial xylose purification). First, the toxicity of fat-soluble carotenoids to cells was reduced by employing xylose inducible promoters using with a two-temperature strategy to separate cell growth and product accumulation. Then, through further engineering and optimization of the carotenoid biosynthesis pathway, 1506.7 mg/L lycopene, 988.5 mg/L β-carotene or 142.9 mg/L astaxanthin were produced with glucose and xylose by K. marxianus. Finally, 397.7 mg/L and 279.7 mg/L lycopene, 297.3 mg/L and 108.8 mg/L β-carotene, and 86.4 mg/L and 56.8 mg/L astaxanthin were produced with nonsterilized andnondetoxified XML or corncob hydrolysate after nitrogen source optimization. To our knowledge, the produced amounts of lycopene, β-carotene and astaxanthin from lignocellulose biomass by yeast in this study were higher than those in previous reports.\n\nCarotenoid production from nondetoxified xylose mother liquid or corncob hydrolysate with engineered Kluyveromyces marxianus.", "token_count": 396, "char_count": 1213, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:04.516050", "source": { "split": "train_shard_00000", "doc_id": 1657 }, "chunk_id": "train_shard_00000_1657_0", "global_id": 1830 }, { "text": "The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, consisting of core and accessory genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for\n\nA global pangenome for the wheat fungal pathogen", "token_count": 81, "char_count": 365, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7321, "quality_score": 0.8661, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:04.896327", "source": { "split": "train_shard_00000", "doc_id": 1658 }, "chunk_id": "train_shard_00000_1658_0", "global_id": 1831 }, { "text": "Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of a S. marcescens cgMLST scheme is reported with the goal of enabling a standardized methodology and typing nomenclature. Four hundred ninety-one high-quality S. marcescens WGS data sets were extracted from public databases and-using the genomic sequence of NCBI reference strain S. marcescens Db11 (NZ_HG326223.1) as a starting point-all Db11 genes present in ≥97% data sets used to create a cgMLST scheme. The novel scheme was evaluated using WGS data from 24 outbreak investigations (\n\nDevelopment and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations.", "token_count": 275, "char_count": 1029, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:05.455176", "source": { "split": "train_shard_00000", "doc_id": 1659 }, "chunk_id": "train_shard_00000_1659_0", "global_id": 1832 }, { "text": "Inflammatory bowel disease (IBD) is characterized by chronic and relapsing inflammation of gastrointestinal tract, with steadily increased incidence and prevalence worldwide. Although the precise pathogenesis remains unclear, gut microbiota, bile acids (BAs), and aberrant immune response play essential roles in the development of IBD. Lately, gut dysbiosis including certain decreased beneficial bacteria and increased pathogens and aberrant BAs metabolism have been reported in IBD. The bacteria inhabited in human gut have critical functions in BA biotransformation. Patients with active IBD have elevated primary and conjugated BAs and decreased secondary BAs, accompanied by the impaired transformation activities (mainly deconjugation and 7α-dehydroxylation) of gut microbiota. Probiotics have exhibited certain positive effects by different mechanisms in the therapy of IBD. This review discussed the effectiveness of probiotics in certain clinical and animal model studies that might involve in gut microbiota-BAs axis. More importantly, the possible mechanisms of probiotics on regulating gut microbiota-BAs axis in IBD were elucidated, which we focused on the elevated gut bacteria containing bile salt hydrolase or BA-inducible enzymes at genus/species level that might participate in the BA biotransformation. Furthermore, beneficial effects exerted by activation of BA-activated receptors on intestinal immunity were also summarized, which might partially explain the protect effects and mechanisms of probiotics on IBD. Therefore, this review will provide new insights into a better understanding of probiotics in the therapy targeting gut microbiota-BAs axis of IBD.\n\nRegulation of gut microbiota-bile acids axis by probiotics in inflammatory bowel disease.", "token_count": 417, "char_count": 1773, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5851, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:06.084785", "source": { "split": "train_shard_00000", "doc_id": 1660 }, "chunk_id": "train_shard_00000_1660_0", "global_id": 1833 }, { "text": "Lipid-based formulations (LBFs) are used by the pharmaceutical industry in oral delivery systems for both poorly water-soluble drugs and biologics. Digestibility is key for the performance of LBFs and in vitro lipolysis is commonly used to compare the digestibility of LBFs. Results from in vitro lipolysis experiments depend highly on the experimental conditions and formulation characteristics, such as droplet size (which defines the surface area available for digestion) and interfacial structure. This study introduced the intrinsic lipolysis rate (ILR) as a surface area-independent approach to compare lipid digestibility. Pure acylglycerol nanoemulsions, stabilized with polysorbate 80 at low concentration, were formulated and digested according to a standardized pH-stat lipolysis protocol. A methodology originally developed to calculate the intrinsic dissolution rate of poorly water-soluble drugs was adapted for the rapid calculation of ILR from lipolysis data. The impact of surfactant concentration on the apparent lipolysis rate and lipid structure on ILR was systematically investigated. The surfactant polysorbate 80 inhibited lipolysis of tricaprylin nanoemulsions in a concentration-dependent manner. Coarse-grained molecular dynamics simulations supported these experimental observations. In the absence of bile and phospholipids, tricaprylin was shielded from lipase at 0.25% polysorbate 80. In contrast, the inclusion of bile salt and phospholipid increased the surfactant-free area and improved the colloidal presentation of the lipids to the enzyme, especially at 0.125% polysorbate 80. At a constant and low surfactant content, acylglycerol digestibility increased with decreasing acyl chain length, decreased esterification, and increasing unsaturation. The calculated ILR of pure acylglycerols was successfully used to accurately predict the IRL of binary lipid mixtures. The ILR measurements hold great promise as an efficient method supporting pharmaceutical formulation scientists in the design of LBFs with specific digestion profiles.\n\nIntrinsic lipolysis rate for systematic design of lipid-based formulations.", "token_count": 508, "char_count": 2145, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:06.740450", "source": { "split": "train_shard_00000", "doc_id": 1661 }, "chunk_id": "train_shard_00000_1661_0", "global_id": 1834 }, { "text": "The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation.\n\nA graph-based approach for the visualisation and analysis of bacterial pangenomes.", "token_count": 79, "char_count": 399, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7414, "quality_score": 0.8707, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:07.123215", "source": { "split": "train_shard_00000", "doc_id": 1662 }, "chunk_id": "train_shard_00000_1662_0", "global_id": 1835 }, { "text": "Despite vaccination, outbreaks of vibriosis still occur in sea-reared rainbow trout in Denmark. Vibriosis outbreaks are caused mainly by V. anguillarum serotypes O1 and O2a, and bacterins of both serotypes are included in the commonly used vaccine against this disease in Danish aquaculture. However, while the strains belonging to serotype O1 are genetically similar, the strains belonging to serotype O2a are highly diverse. This work aimed first at examining how the antibody response and protection induced by bacterin-based vaccines were affected by the antigenic variability within V. anguillarum serotype O2a strains. Following vaccination of rainbow trout with either a commercial or an experimental vaccine, specific antibody reactivity in serum from vaccinated fish was examined by ELISA against 23 strains of V. anguillarum serotype O2a (VaO2a). The strains were divided into 4 distinct subgroups according to the observed detection pattern. Seven strains were strongly recognized only by sera from fish vaccinated with the experimental vaccine (EV-I antisera), while 13 other strains were primarily recognized by sera from fish vaccinated with the commercial vaccine (CV antisera). Two strains were recognized by both EV-I and CV antisera, but with intermediate reactivity, while one strain was not recognized at all. A partly similar recognition pattern was observed when purified lipopolysaccharide (LPS) was used as antigen in the examination of antibody reactivity in Western blotting. The level of protection was highly dependent on both the vaccine and the strain used for challenge and showed no consistent correlation with antibody reactivity. Secondly, we attempted to use a bacterin vaccine based on one of the V. anguillarum O2a strains intermediately recognized by both EV-I and CV antisera to investigate whether that could potentially provide protection across strain variability. The immunized fish did mount a cross-reactive antibody response, but protection still varied depending on the strain used for challenge", "token_count": 466, "char_count": 2042, "word_count": 301, "semantic_coherence": 1, "information_density": 0.5382, "quality_score": 0.7691, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:07.766355", "source": { "split": "train_shard_00000", "doc_id": 1663 }, "chunk_id": "train_shard_00000_1663_0", "global_id": 1836 }, { "text": "Interestingly, the grouping of strains according to antibody reactivity correlated not only with genotyping based on single nucleotides polymorphisms analysis (SNP) but also with variability in the accessory genome, indicating that presence or absence of protein antigens or proteins associated with the biosynthesis of antigenic epitopes may explain the observed distinct serological subgrouping within VaO2a strains by trout immune sera. In terms of vaccination against VaO2a, our results demonstrate that it is important to take (local) antigen variations into account when using bacterin-based vaccines but also that alternatives to traditional bacterin-based vaccines might be needed to induce protection against the highly virulent Vibrio anguillarum serotype O2a strains.\n\nAntigenic variability of Vibrio anguillarum serotype O2a: A hurdle for vaccine efficacy against vibriosis in rainbow trout (Oncorhynchus mykiss).", "token_count": 230, "char_count": 925, "word_count": 126, "semantic_coherence": 1, "information_density": 0.754, "quality_score": 0.877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:08.243593", "source": { "split": "train_shard_00000", "doc_id": 1663 }, "chunk_id": "train_shard_00000_1663_1", "global_id": 1837 }, { "text": "Moraxella bovoculi has been isolated frequently from cattle with Infectious bovine keratoconjunctivitis (IBK). Two diverse genotypes of M. bovoculi, 1 and 2 were identified based on whole genome sequence analysis. It is essential to discriminate between the two genotypes to frame prevention and control measures. The whole genome of M. bovoculi TN7 was sequenced and compared to other M. bovoculi strains available in the NCBI database. M. bovoculi TN7 was found to be genotype 1, had an RTX toxin operon and pilA gene that are the known virulence factors in related Moraxella sp., but lacked antimicrobial resistance genes. M. bovoculi was found to have an open pangenome with 4051 (75.31%) accessory genes, and the addition of each new genome adds 18 genes to the pangenome. Comparison of pilin protein amino acid sequences revealed three new sequence types. Furthermore, the presence of linx, nagL, swrC and mdtA genes was found to be genotype 1 specific, whereas hyaD, garR, gbsA, yhdG, gabT, iclR, higB2, hmuU, hmuT and hemS were found only in genotype 2. Polymerase Chain Reaction (PCR) primers were designed and evaluated on strain TN7 plus seven additional strains accessible to us that had not been whole genome sequenced. This initial evaluation of the designed primers for the linX and hyaD genes produced the expected banding patterns on PCR gels for genotypes 1 and 2, respectively, among the 8 strains. The genotype-specific genes identified in this study can be used as markers for accurate diagnosis of genotype 1 isolates and this can aid in the development of autogenous or other molecular vaccines for treatment of infectious bovine keratoconjunctivitis (IBK) in resource-limited research settings.\n\nFirst report of the whole genome of Moraxella bovoculi genotype 1 from India and comparative genomics of Moraxella bovoculi to identify genotype-specific markers.", "token_count": 512, "char_count": 1882, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5966, "quality_score": 0.7983, "entities": { "genes": [ "TN7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:08.895467", "source": { "split": "train_shard_00000", "doc_id": 1664 }, "chunk_id": "train_shard_00000_1664_0", "global_id": 1838 }, { "text": "High-resolution and efficient typing for the bacterial pathogen is essential for tracking the sources, detecting or diagnosing variants, and conducting a risk assessment. However, a systematic in-field investigation of Salmonella along the food chain has not been documented. This study assessed 12 typing methods, such as antimicrobial-resistance (AMR) gene profile typing, Core Genome Multilocus Sequence Typing (cgMLST), and CRISPR multi-virulence locus sequence typing (CRISPR-MVLST), to evaluate their effectiveness for use in routine monitoring of foodborne Salmonella transmission along the poultry production chain. During 2015-16, a total of 1,064 samples were collected from poultry production chain, starting from breeding farms and slaughterhouses to the markets of Zhejiang province in China. A total of 61 consecutive unique Salmonella isolates recovered from these samples were selected for genome sequencing and further comparative typing analysis. Traditional typing methods, including serotyping, AMR phenotype-based typing, as well as modern genotyping approaches, were evaluated and compared by their discrimination index (DI). The results showed that the serotyping method identified nine serovars. The gold standard cgMLST method indicated only 18 different types (DI = 0.8541), while the CRISPR-MVLST method detected 30 types (DI = 0.9628), with a higher DI than all examined medium-resolution WGS-based genotyping methods. We demonstrate that the CRISPR-MVLST might be used as a tool with high discriminatory power, comparable ease of use, ability of tracking the source of Salmonella strains along the food chain and indication of genetic features especially virulence genes. The available methods with different purposes and laboratory expertise were also illustrated to assist in rational implementation.\n\nComprehensive Assessment of Subtyping Methods for Improved Surveillance of Foodborne Salmonella.", "token_count": 464, "char_count": 1929, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6792, "quality_score": 0.8396, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:09.533904", "source": { "split": "train_shard_00000", "doc_id": 1665 }, "chunk_id": "train_shard_00000_1665_0", "global_id": 1839 }, { "text": "Lactiplantibacillus plantarum PMO 08 has been used as a probiotic starter culture for plant-based fermented beverages, with various health-promoting effects such as cholesterol-lowering and anti-inflammatory activities. This study aimed to analyze the genome sequence of Lp. plantarum PMO 08 and identify its safety and probiotic characteristics at the genomic level. For this, complete genome sequencing was conducted to investigate the genes associated with risk and probiotic characteristics by using Pacbio combined with Illumina HiSeq. This bacterial strain has one circular chromosome of 3,247,789 bp with 44.5% G + C content and two plasmids of 50,296 bp with 39.0% G + C content and 19,592 bp with 40.5% G + C content. Orthologous average nucleotide identity analysis showed that PMO 08 belongs to the Lp. plantarum group with 99.14% similarity to Lp. plantarum WCFS1. No deleterious genes were determined in the virulence factor analysis, and no hemolysin activity or secondary bile salt synthesis were detected in vitro test. In the case of antibiotic resistance analysis, PMO 08 was resistant to ampicillin in vitro test, but these genes were not transferable. In addition, the strain showed same carbohydrate utilization with Lp. plantarum WCFS1, except for mannopyranoside, which only our strain can metabolize. The strain also harbors a gene for inositol monophosphatase family protein related with phytate hydrolysis and have several genes for metabolizing various carbohydrate which were rich in plant environment. Furthermore, in probiotic characteristics several genes involved in phenotypes such as acid/bile tolerance, adhesion ability, and oxidative stress response were detected in genome analysis. This study demonstrates that Lp. plantarum PMO 08 harbors several probiotic-related genes (with no deleterious genes) and is a suitable probiotic starter for plant-based fermentation.", "token_count": 518, "char_count": 1904, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5827, "quality_score": 0.7914, "entities": { "genes": [ "WCFS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:15:10.195572", "source": { "split": "train_shard_00000", "doc_id": 1666 }, "chunk_id": "train_shard_00000_1666_0", "global_id": 1840 }, { "text": "Integrated genome-based assessment of safety and probiotic characteristics of Lactiplantibacillus plantarum PMO 08 isolated from kimchi.", "token_count": 37, "char_count": 136, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:10.553593", "source": { "split": "train_shard_00000", "doc_id": 1666 }, "chunk_id": "train_shard_00000_1666_1", "global_id": 1841 }, { "text": "Staphylococcus aureus is a Gram-positive pathogen that causes various infections in humans and domestic animals. In China, S. aureus is the most common Gram-positive pathogen that causes clinical infections. However, there are few comprehensive genome-based molecular epidemiology studies to investigate the genotypic background of the major S. aureus clones that are epidemic in China. Here, four S. aureus isolates that were recovered from hospital personnel were sequenced. In combination with whole-genome sequencing (WGS) data of 328 S. aureus strains as references, we performed a comprehensive molecular epidemiology study to reveal the molecular epidemic characterization of S. aureus that is epidemic in China. It was found that 332 S. aureus isolates were phylogenetically categorized into 4 major epidemic groups with different epidemiology phenotypes. Each group has exclusive features in virulence genotypic profiles, antimicrobial resistance genotypic profiles, core and pangenome features representing the differences involved in genetic features, evolutionary processes, and potential future evolutionary directions. Moreover, a comparative core genome analysis of 332 S. aureus isolates indicated several key genes that contributed to differences in molecular epidemic characterization and promoted the adaptive evolutionary process of each group. This study provides a comprehensive understanding of molecular epidemiological characteristics and adaptive evolutionary directions of major S. aureus clones that are epidemic in China.\n\nMolecular Epidemiology of Staphylococcus aureus in China Reveals the Key Gene Features Involved in Epidemic Transmission and Adaptive Evolution.", "token_count": 388, "char_count": 1696, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5263, "quality_score": 0.7632, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:11.174184", "source": { "split": "train_shard_00000", "doc_id": 1667 }, "chunk_id": "train_shard_00000_1667_0", "global_id": 1842 }, { "text": "Biofilm production is responsible for persistent food contamination by Listeria monocytogenes, threatening food safety and public health. Human infection and food contamination with L. monocytogenes are caused primarily by serotypes 1/2a, 1/2b, and 4b. However, the association of biofilm production with phylogenic lineage and serotype has not yet been fully understood. In this study, we measured the levels of biofilm production in 98 clinical strains of L. monocytogenes at 37°C, 25°C, and 4°C. The phylogenetic clusters grouped by core genome multilocus sequence typing (cgMLST) exhibited association between biofilm production and phylogenetic lineage and serotype. Whereas clusters 1 and 3 consisting of serotype 4b strains exhibited weak biofilm production, clusters 2 (serotype 1/2b) and 4 (serotype 1/2a) were composed of strong biofilm formers. Particularly, cluster 2 (serotype 1/2b) strains exhibited the highest levels of biofilm production at 37°C, and the levels of biofilm production of cluster 4 (serotype 1/2a) strains were significantly elevated at all tested temperatures. Pan-genome analysis identified 22 genes unique to strong biofilm producers, most of which are related to the synthesis and modification of teichoic acids. Notably, a knockout mutation of the\n\nSugar Modification of Wall Teichoic Acids Determines Serotype-Dependent Strong Biofilm Production in Listeria monocytogenes.", "token_count": 383, "char_count": 1410, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5779, "quality_score": 0.7889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:11.754676", "source": { "split": "train_shard_00000", "doc_id": 1668 }, "chunk_id": "train_shard_00000_1668_0", "global_id": 1843 }, { "text": "Obesity is a risk factor for cerebrovascular diseases. Accumulating evidence has revealed that gut dysbiosis plays an important role in the pathophysiology of cerebrovascular diseases. However, little is known about the role of gut dysbiosis in stroke in obesity. In this study, we established a rodent middle cerebral artery occlusion (MCAO) model to investigate whether obesity-induced gut dysbiosis exacerbates cerebral ischemic injury and the role of the bile salt sequestrant cholestyramine resin (CR) in gut microbiota and stroke outcome in obese mice. Long-term 45% high-fat diet (HFD) diet (8 weeks) induced an obesity phenotype and caused gut dysbiosis, resulting in a larger infarct volume and higher serum levels of inflammatory cytokines after stroke, compared to those in the lean counterparts. LC-MS/MS and GC analysis revealed that obese mice with stroke developed an obviously perturbed bile acid (BA) profile characterized by higher levels of deoxycholic acid and its conjugated forms, and lower levels of butyrate in the cecal content. CR administration improved the obesity-induced dysbiotic microbiome, attenuated ischemic brain injury and modulated the stroke-perturbed BA profile. Furthermore, fecal microbiota transplantation (FMT) experiments revealed that the impact of obesity on stroke and the neuroprotective effects of CR were mediated by gut microbiota. In conclusion, Obesity induces gut dysbiosis, worsens stroke outcomes, and perturbs the BA profile. The dysbiotic microbiome is an important linkage between obesity and stroke. CR confers metabolic benefits and neuroprotective effects in obesity, perhaps by modulating gut microbial composition and BA metabolism.\n\nCholestyramine resin administration alleviated cerebral ischemic injury in obese mice by improving gut dysbiosis and modulating the bile acid profile.", "token_count": 479, "char_count": 1849, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5627, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:12.425568", "source": { "split": "train_shard_00000", "doc_id": 1669 }, "chunk_id": "train_shard_00000_1669_0", "global_id": 1844 }, { "text": "Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space efficiently.\n\nGBZ file format for pangenome graphs.", "token_count": 66, "char_count": 295, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8222, "quality_score": 0.9111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:12.833480", "source": { "split": "train_shard_00000", "doc_id": 1670 }, "chunk_id": "train_shard_00000_1670_0", "global_id": 1845 }, { "text": "The availability of multiple gene sequences, and in particular full genome sequence data, for microbial strains has changed how taxonomists delineate subspecies belonging to the Archaea and Bacteria. Well-defined phylogenetic lineages that share higher genome similarity values compared to the widely used species thresholds are often described as subspecies, despite clear evidence of genetic isolation between them. These well-defined lineages, reflecting notable genetic isolation of the core genome represent more recently evolved, unique and\n\nRelevance of prokaryotic subspecies in the age of genomics.", "token_count": 133, "char_count": 607, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7831, "quality_score": 0.8916, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:13.291939", "source": { "split": "train_shard_00000", "doc_id": 1671 }, "chunk_id": "train_shard_00000_1671_0", "global_id": 1846 }, { "text": "Deserts represent extreme environments for microorganisms, and conditions such as high soil salinity, nutrient deficiency, and increased levels of UV radiation make desert soil communities of high biotechnological potential. In this study, we isolated, sequenced, and assembled the genomes of Bacillus safensis strains BcP62 and Bcs93, to which we performed comparative genome analyses. Using the DDH and ANI of both strains with the available B. safensis genomes, we identified three potential subspecies within this group. Intra-species core genome phylogenetic analysis did not result in clustering genomes by niche type, with some exceptions. This study also revealed that the genomes of the analyzed strains possessed plant growth-promoting characteristics, most of which were conserved in all B. safensis strains. Furthermore, we highlight the genetic features of B. safensis BcP62 and Bcs93 related to survival in the Merzouga desert in Morocco. These strains could be potentially used in agriculture as PGPB in extreme environments, given their high tolerability to unfavorable conditions.\n\nGenomic analysis of two Bacillus safensis isolated from Merzouga desert reveals desert adaptive and potential plant growth-promoting traits.", "token_count": 287, "char_count": 1239, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6534, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:13.887005", "source": { "split": "train_shard_00000", "doc_id": 1672 }, "chunk_id": "train_shard_00000_1672_0", "global_id": 1847 }, { "text": "Berberine (BBR) is an effective cholesterol-lowering drug. Although gut microbiota has been implicated in the pharmacological activities of BBR, little evidence exists on the specific species of gut microbiota involved in its therapeutic effects, nor on linking gut bacteria to its recognized hypercholesterolemia-alleviating mechanism-upregulation of the low-density lipoprotein receptor (LDLR) in the liver. The present study was performed to identify the specific species of gut microbiota involved in the anti-hyperlipdemic effect of BBR, and interpret its mechanism through linking the gut microbiota and LDLR. The BBR-enriched gut bacterial species were identified by whole genome shotgun sequencing. Pure cultured B. producta was orally administered to C57BL/6 mice to evaluate its anti-hyperlipdemic effect. The LDLR-upregulating effect of B. producta was evaluated both in vitro and in vivo. Orally administration of BBR (200 mg/kg) decreased serum and liver lipid levels in HFD-induced hyperlipidemic mice. Microbiome analysis indicated that Blautia was closely associated with BBR's lipid-modulating activities. Further analysis revealed that BBR selectively promoted the growth of Blautia producta. Orally treatment of HFD mice with live B. producta reduced obesity and alleviated hyperlipidemia. Notably, the B. producta significantly increased LDLR expression in the liver, and its spent culture supernatant upregulated the LDLR level and promoted LDL uptake by HepG2 cells. Simultaneously, B. producta also linked butyrate-producing and bile salt hydrolase (BSH)-inhibiting effect of BBR. The gut microbiota, especially B. producta, may confers the hypercholesterolemia-alleviating effects of berberine. B. producta represents a novel probiotic that may be used for the treatment of dyslipidemia.", "token_count": 482, "char_count": 1811, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:14.545003", "source": { "split": "train_shard_00000", "doc_id": 1673 }, "chunk_id": "train_shard_00000_1673_0", "global_id": 1848 }, { "text": "The berberine-enriched gut commensal Blautia producta ameliorates high-fat diet (HFD)-induced hyperlipidemia and stimulates liver LDLR expression.", "token_count": 47, "char_count": 146, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:14.903294", "source": { "split": "train_shard_00000", "doc_id": 1673 }, "chunk_id": "train_shard_00000_1673_1", "global_id": 1849 }, { "text": "Surfactants are applied in several industrial processes when the modification of interface activity and the stability of colloidal systems are required. Lipopeptides are a class of microbial biosurfactants produced by species of the Bacillus genus. The present study aimed at assembling and analyzing the genome of a new Bacillus vallismortis strain, TIM68, that was shown to produce surfactant lipopeptides. The draft genome was also screened for common virulence factors and antibiotics resistance genes to investigate the strain biosafety. Comparative genomics analyses, i.e., synteny, average nucleotide identity (ANI), and pangenome, were also carried out using strain TIM68 and publicly available B. vallismortis complete and partial genomes. Three peptide synthetase operons were found in TIM68 genome, and they were surfactin A, mojavensin, and a novel plipastatin-like lipopeptide named vallisin. No virulence factors that render pathogenicity to the strain have been identified, but a region of prophage, that may contain unknown pathogenic factors, has been predicted. The pangenome of the species was characterized as closed, with 57% of genes integrating the core genome. The results obtained here on the genetic potential of TIM68 strain should contribute to its exploration in biotechnological applications.\n\nGenomic Analysis of Surfactant-Producing Bacillus vallismortis TIM68: First Glimpse at Species Pangenome and Prediction of New Plipastatin-Like Lipopeptide.", "token_count": 375, "char_count": 1480, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8382, "entities": { "genes": [ "TIM68" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:15.489301", "source": { "split": "train_shard_00000", "doc_id": 1674 }, "chunk_id": "train_shard_00000_1674_0", "global_id": 1850 }, { "text": "Promoter choice is an important step in recombinant protein production, which directly determines the expression manner as constitutive or inducible and the expression level of the recombinant protein. This study aims to investigate the applicability of heterologous yeast promoters (Kluyveromyces marxianus TPI, Hansenula polymorpha PMA, Candida tropicalis ICL, and Saccharomyces cerevisiae CUP) in Pichia pastoris. The regulation mode of the CtICL and ScCUP promoters in P. pastoris was found to be inducible and that of the KmTPI and HpPMA was constitutive. The carbon sources in which the promoters exhibited the highest activity were determined as glycerol for PMA and TPI, glucose for CUP, and ethanol for ICL. The DNA region showing the highest activity was determined as 1000 bp for all promoters by promoter deletion analysis. Results from the study demonstrate the potential of inducible and constitutive heterologous promoters allowing expression under different conditions in the P. pastoris expression system and offers alternatives to frequently used promoters. KEY POINTS: • Heterologous promoters exhibited similar expression pattern in P. pastoris with its native host. • HpPMA has the highest promoter activity among the heterologous promoters tested. • Reporter gene expression with ScCUP is responsive to elevating Cu\n\nApplicability of the heterologous yeast promoters for recombinant protein production in Pichia pastoris.", "token_count": 360, "char_count": 1443, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5502, "quality_score": 0.7751, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:16.065582", "source": { "split": "train_shard_00000", "doc_id": 1675 }, "chunk_id": "train_shard_00000_1675_0", "global_id": 1851 }, { "text": "Non-absorbable inhibitors of the apical sodium-dependent bile acid transporter (ASBT; also called ileal bile acid transporter [IBAT]) are recently approved or in clinical development for multiple cholestatic liver disorders and lead to a reduction in pruritus and (markers for) liver injury. Unfortunately, non-absorbable ASBT inhibitors (ASBTi) can induce diarrhoea or may be ineffective if cholestasis is extensive and largely precludes intestinal excretion of bile acids. Systemically acting ASBTi that divert bile salts towards renal excretion may alleviate these issues.\n\nSystemic ASBT inactivation protects against liver damage in obstructive cholestasis in mice.", "token_count": 176, "char_count": 669, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7802, "quality_score": 0.8901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:16.515272", "source": { "split": "train_shard_00000", "doc_id": 1676 }, "chunk_id": "train_shard_00000_1676_0", "global_id": 1852 }, { "text": "The silkworm Bombyx mori is an important economic insect for producing silk, the \"queen of fabrics\". The currently available genomes limit the understanding of its genetic diversity and the discovery of valuable alleles for breeding. Here, we deeply re-sequence 1,078 silkworms and assemble long-read genomes for 545 representatives. We construct a high-resolution pan-genome dataset representing almost the entire genomic content in the silkworm. We find that the silkworm population harbors a high density of genomic variants and identify 7308 new genes, 4260 (22%) core genes, and 3,432,266 non-redundant structure variations (SVs). We reveal hundreds of genes and SVs that may contribute to the artificial selection (domestication and breeding) of silkworm. Further, we focus on four genes responsible, respectively, for two economic (silk yield and silk fineness) and two ecologically adaptive traits (egg diapause and aposematic coloration). Taken together, our population-scale genomic resources will promote functional genomics studies and breeding improvement for silkworm.\n\nHigh-resolution silkworm pan-genome provides genetic insights into artificial selection and ecological adaptation.", "token_count": 291, "char_count": 1198, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7012, "quality_score": 0.8506, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:17.072364", "source": { "split": "train_shard_00000", "doc_id": 1677 }, "chunk_id": "train_shard_00000_1677_0", "global_id": 1853 }, { "text": "The goal of this study was to determine the unique characteristics of Enterococcus faecium MC-5, a probiotic bacteria isolated from the intestine of a fish, Cyprinus carpio specularis, collected from Dal Lake in Srinagar, Kashmir, India. For this, the important valuable probiotic attributes, some functional properties, and safety assessments were analyzed in-vitro for the strain MC-5. The strain E. faecium MC-5 exhibited high resistance to low pH, high bile salt, lysozyme, and phenol. The strain MC-5 showed excellent auto- and co-aggregation properties and displayed remarkable hydrophobicity towards various tested hydrocarbons which suggested that the strain possesses venerable adhesion properties. Apart from these, the cell-free supernatant (CFS) of strain MC-5 exhibited phenomenal antimicrobial activity against the tested pathogens. A scanning electron microscope (SEM) image revealed strain MC-5 finely adhered to human colon adenocarcinoma cells (HCT-15 cells). The strain MC-5 showed high bile salt hydrolase activity and excellent cholesterol removal ability of 70.27%. The intact cells of strain MC-5 also showed strong DPPH scavenging activity. The EPS produced by E. faecium MC-5 inhibited the adhesion of Listeria monocytogenes, Staphylococcus aureus, and Salmonella enterica on HCT-15 cells with maximum inhibition rates of 41.82, 40.34, and 55.51%, respectively for displacement assay, which was higher as compared to exclusion (26.06, 26.11, and 39.23%) and competition assays (30.06, 26.7, and 41.20%). Strain MC-5 did not exhibit hemolysis and was also found susceptible to vancomycin and other clinically important antibiotics", "token_count": 476, "char_count": 1654, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6695, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:17.723111", "source": { "split": "train_shard_00000", "doc_id": 1678 }, "chunk_id": "train_shard_00000_1678_0", "global_id": 1854 }, { "text": "When evaluating all the results from the present study, it is propounded that strain MC-5 has enviable probiotic characteristics and thus can be used as bio-protective cultures and/or bio-shield in food and pharmaceutical industries.\n\nCharacterization of potential probiotic bacteria Enterococcus faecium MC-5 isolated from the gut content of Cyprinus carpio specularis.", "token_count": 90, "char_count": 370, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8627, "quality_score": 0.9314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:18.095595", "source": { "split": "train_shard_00000", "doc_id": 1678 }, "chunk_id": "train_shard_00000_1678_1", "global_id": 1855 }, { "text": "Correction to: Development of a ribosome profiling protocol to study translation in Kluyveromyces marxianus.", "token_count": 27, "char_count": 108, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:18.465685", "source": { "split": "train_shard_00000", "doc_id": 1679 }, "chunk_id": "train_shard_00000_1679_0", "global_id": 1856 }, { "text": "Metformin is widely used to surmount insulin resistance (IR) and type 2 diabetes. Accumulating evidence suggests that metformin may improve IR through regulating gut microbiota and bile acids. However, the underlying mechanisms remain unclear. Our metabolomic analysis showed that metformin significantly increased the accumulation of tauroursodeoxycholic acid (TUDCA) in intestine and liver from high-fat diet (HFD)-induced IR mice. TUDCA also alleviated IR, and reduced oxidative stress and intestinal inflammation in ob/ob mice. TUDCA blocked KEAP1 to bind with Nrf2, resulting in Nrf2 translocation into nuclear and initiating the transcription of antioxidant genes, which eventually reduced intracellular ROS accumulation and improved insulin signaling. Analysis of gut microbiota further revealed that metformin reduced the relative abundance of Bifidobacterium, which produces bile salt hydrolase (BSH). The reduction in BSH was probably crucial for the accumulation of TUDCA. Metformin also increased the proportion of Akkermanisia muciniphlia in gut microbiota of ob/ob mice via TUDCA. These beneficial effects of metformin in remodeling gut microbiota, reducing oxidative stress and improving insulin sensitivity were partly due to the accumulation of TUDCA, suggesting that TUDCA may be a potential therapy for metabolic syndrome.\n\nTauroursodeoxycholic acid functions as a critical effector mediating insulin sensitization of metformin in obese mice.", "token_count": 365, "char_count": 1461, "word_count": 200, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [ "KEAP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:19.042693", "source": { "split": "train_shard_00000", "doc_id": 1680 }, "chunk_id": "train_shard_00000_1680_0", "global_id": 1857 }, { "text": "The oral delivery of diclofenac sodium (DNa), a non-steroidal analgesic, anti-inflammatory drug, is associated with various gastrointestinal side effects. The aim of the research was to appraise the potential of transdermal delivery of DNa using bilosomes as a vesicular carrier (BSVC) in inflamed paw edema. DNa-BSVCs were elaborated using a thin-film hydration technique and optimized using a 3\n\nNovel Bile Salt Stabilized Vesicles-Mediated Effective Topical Delivery of Diclofenac Sodium: A New Therapeutic Approach for Pain and Inflammation.", "token_count": 159, "char_count": 545, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7792, "quality_score": 0.8896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:19.487486", "source": { "split": "train_shard_00000", "doc_id": 1681 }, "chunk_id": "train_shard_00000_1681_0", "global_id": 1858 }, { "text": "The bile resistance of intestinal bacteria is among the key factors responsible for their successful colonization of and survival in the mammalian gastrointestinal tract. In this study, we demonstrated that lactate-producing Atopobiaceae bacteria (\n\nBile Salt Hydrolases with Extended Substrate Specificity Confer a High Level of Resistance to Bile Toxicity on Atopobiaceae Bacteria.", "token_count": 94, "char_count": 383, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8113, "quality_score": 0.9057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:19.863744", "source": { "split": "train_shard_00000", "doc_id": 1682 }, "chunk_id": "train_shard_00000_1682_0", "global_id": 1859 }, { "text": "Subepithelial human esophageal myofibroblasts (HEMFs) in gastroesophageal reflux disease (GERD) are exposed to luminal contents via impaired squamous epithelium barrier integrity. The supernatant of HEMFs treated with acidic bile salts reflective of in vivo reflux increases squamous epithelial thickness. We aimed to identify the involved mechanisms using an unbiased approach. Acidic-bile-salt-treated primary HEMF cultures (n = 4) were submitted for RNA-Seq and analyzed with Partek Flow followed by Ingenuity Pathway Analysis (IPA). A total of 1165 molecules (579 downregulated, 586 upregulated) were differentially expressed, with most top regulated molecules either extracellular or in the plasma membrane. Increases in HEMF CXCL-8, IL-6, AREG, and EREG mRNA, and protein secretion were confirmed. Top identified canonical pathways were agranulocyte and granulocyte adhesion and diapedesis, PI3K/AKT signaling, CCR5 signaling in macrophages, and the STAT3 pathway. Top diseases and biological functions were cellular growth and development, hematopoiesis, immune cell trafficking, and cell-mediated response. The targets of the top upstream regulator ErbB2 included CXCL-8, IL-6, and AREG and the inhibition of CXCL-8 in the HEMF supernatant decreased squamous epithelial proliferation. Our work shows an inflammatory/immune cell and proliferative pathways activation in HEMFs in the GERD environment and identifies CXCL-8 as a HEMF-derived chemokine with paracrine proliferative effects on squamous epithelium.\n\nInflammatory and Proliferative Pathway Activation in Human Esophageal Myofibroblasts Treated with Acidic Bile Salts.", "token_count": 478, "char_count": 1635, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [ "PI3K", "STAT3", "CCR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:20.504378", "source": { "split": "train_shard_00000", "doc_id": 1683 }, "chunk_id": "train_shard_00000_1683_0", "global_id": 1860 }, { "text": "Complete and accurate reference genomes and annotations provide fundamental resources for functional genomics and crop breeding. Here we report a de novo assembly and annotation of a pea cultivar ZW6 with contig N50 of 8.98 Mb, which features a 243-fold increase in contig length and evident improvements in the continuity and quality of sequence in complex repeat regions compared with the existing one. Genome diversity of 118 cultivated and wild pea demonstrated that Pisum abyssinicum is a separate species different from P. fulvum and P. sativum within Pisum. Quantitative trait locus analyses uncovered two known Mendel's genes related to stem length (Le/le) and seed shape (R/r) as well as some candidate genes for pod form studied by Mendel. A pan-genome of 116 pea accessions was constructed, and pan-genes preferred in P. abyssinicum and P. fulvum showed distinct functional enrichment, indicating the potential value of them as pea breeding resources in the future.\n\nImproved pea reference genome and pan-genome highlight genomic features and evolutionary characteristics.", "token_count": 273, "char_count": 1083, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [ "ZW6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:21.055941", "source": { "split": "train_shard_00000", "doc_id": 1684 }, "chunk_id": "train_shard_00000_1684_0", "global_id": 1861 }, { "text": "Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.\n\nCritical assessment of pan-genomic analysis of metagenome-assembled genomes.", "token_count": 350, "char_count": 1395, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6127, "quality_score": 0.8064, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:21.638476", "source": { "split": "train_shard_00000", "doc_id": 1685 }, "chunk_id": "train_shard_00000_1685_0", "global_id": 1862 }, { "text": "The ancient, ongoing coevolutionary battle between bacteria and their viruses, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Many additional anti-phage systems have been identified using computational approaches based on genomic co-location within defence islands, but these screens may not be exhaustive. Here we developed an experimental selection scheme agnostic to genomic context to identify defence systems in 71 diverse E. coli strains. Our results unveil 21 conserved defence systems, none of which were previously detected as enriched in defence islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defence systems in E. coli, with defence systems typically carried in specific locations or hotspots. These hotspots encode dozens of additional uncharacterized defence system candidates. Our findings reveal an extended landscape of antiviral immunity in E. coli and provide an approach for mapping defence systems in other species.\n\nA functional selection reveals previously undetected anti-phage defence systems in the E. coli pangenome.", "token_count": 246, "char_count": 1197, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7256, "quality_score": 0.8628, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:22.118984", "source": { "split": "train_shard_00000", "doc_id": 1686 }, "chunk_id": "train_shard_00000_1686_0", "global_id": 1863 }, { "text": "Within-host evolution produces genetic diversity in bacterial strains that cause chronic human infections. However, the lack of facile methods to measure bacterial allelic variation in clinical samples has limited understanding of intrastrain diversity's effects on disease. Here, we report a new method termed genome capture sequencing (GenCap-Seq) in which users inexpensively make hybridization probes from genomic DNA or PCR amplicons to selectively enrich and sequence targeted bacterial DNA from clinical samples containing abundant human or nontarget bacterial DNA. GenCap-Seq enables accurate measurement of allele frequencies over targeted regions and is scalable from specific genes to entire genomes, including the strain-specific accessory genome. The method is effective with samples in which target DNA is rare and inhibitory and DNA-degrading substances are abundant, including human sputum and feces. In proof-of-principle experiments, we used GenCap-Seq to investigate the responses of diversified Pseudomonas aeruginosa populations chronically infecting the lungs of people with cystic fibrosis to\n\nGenome Capture Sequencing Selectively Enriches Bacterial DNA and Enables Genome-Wide Measurement of Intrastrain Genetic Diversity in Human Infections.", "token_count": 282, "char_count": 1267, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6568, "quality_score": 0.8284, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:22.687216", "source": { "split": "train_shard_00000", "doc_id": 1687 }, "chunk_id": "train_shard_00000_1687_0", "global_id": 1864 }, { "text": "Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Transposon insertion sequencing (Tn-seq), whole-genome sequencing and RNA-seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species' pan-genome, we identify a species-wide 'essentialome' that can be subdivided into universal, core strain-specific and accessory essential genes. By employing 'forced-evolution experiments', we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms, we show that gene essentiality can be highly influenced by and/or be dependent on: (1) the composition of the accessory genome, (2) the accumulation of toxic intermediates, (3) functional redundancy, (4) efficient recycling of critical metabolites and (5) pathway rewiring. While this functional characterization underscores the evolvability potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo.\n\nA bacterial pan-genome makes gene essentiality strain-dependent and evolvable.", "token_count": 342, "char_count": 1476, "word_count": 200, "semantic_coherence": 1, "information_density": 0.685, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:23.259617", "source": { "split": "train_shard_00000", "doc_id": 1688 }, "chunk_id": "train_shard_00000_1688_0", "global_id": 1865 }, { "text": "Chrysobacterium indologenes is an emerging MDR pathogen that belongs to the family Flavobacteriaceae. The genome of the C. indologenes, isolated from the nephrotic patient, was sequenced through Illumina MiSeq. The pangenomics of available 56 C. indologenes strains using BPGA revealed an open pangenome (n=5553 CDS), core genome (2141), and accessory genome (2013). The CEG/DEG database identified 662 essential genes that drastically reduced to 68 genes after non-homology analyses towards human and gut microbiome. Further filtering the data for other drug target prioritizing parameters resulted in 32 putative targets. Keeping in view the crucial role played in cell wall biosynthesis, dacB was selected as the final target that encodes D-alanyl-d-alanine carboxypeptidase/endopeptidase (DD-peptidase). The 3D structure of dacB was modelled and rendered to docking analyses against two compound libraries of African plants (n=6842) and Tibetan medicines (n=52). The ADMET profiling exhibited the physicochemical properties of final compounds. The MD simulations showed the stability of inhibitor-DD-peptidase complex and interactions in terms of RMSD, RMSF, binding free energy calculation and H-bonding. We propose that the novel compounds Leptopene and ZINC95486338 from our findings might be potent DD-peptidase inhibitors that could aid in the development of new antibiotic-resistant therapy for the emerging MDR C. indologenes.\n\nGenomic analysis of Chryseobacterium indologenes and conformational dynamics of the selected DD-peptidase.", "token_count": 438, "char_count": 1545, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7075, "quality_score": 0.8538, "entities": { "genes": [ "ZINC95486338" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:23.894890", "source": { "split": "train_shard_00000", "doc_id": 1690 }, "chunk_id": "train_shard_00000_1690_0", "global_id": 1866 }, { "text": "Paenibacillus sonchi genomovar Riograndensis is a nitrogen-fixing bacteria isolated from wheat that displays diverse plant growth-promoting abilities. Beyond conventional Mo-nitrogenase, this organism also harbors an alternative Fe-nitrogenase, whose many aspects related to regulation, physiology, and evolution remain to be elucidated. In this work, the origins of this alternative system were investigated, exploring the distribution and diversification of nitrogenases in the Panibacillaceae family. Our analysis showed that diazotrophs represent 17% of Paenibacillaceae genomes, of these, only 14.4% (2.5% of all Paenibacillaceae genomes) also contained Fe or V- nitrogenases. Diverse nif-like sequences were also described, occurring mainly in genomes that also harbor the alternative systems. The analysis of genomes containing Fe-nitrogenase showed a conserved cluster of nifEN anfHDGK across three genera: Gorillibacterium, Fontibacillus, and Paenibacillus. A phylogeny of anfHDGK separated the Fe-nitrogenases into three main groups. Our analysis suggested that Fe-nitrogenase was acquired by the ancestral lineage of Fontibacillus, Gorillibacterium, and Paenibacillus genera via horizontal gene transfer (HGT), and further events of transfer and gene loss marked the evolution of this alternative nitrogenase in these groups. The species phylogeny of N-fixing Paenibacillaceae separated the diazotrophs into five clades, one of these containing all occurrences of strains harboring alternative nitrogenases in the Paenibacillus genus. The pangenome of this clade is open and composed of more than 96% of accessory genes. Diverse functional categories were enriched in the flexible genome, including functions related to replication and repair. The latter involved diverse genes related to HGT, suggesting that such events may have an important role in the evolution of diazotrophic Paenibacillus. This study provided an insight into the organization, distribution, and evolution of alternative nitrogenase genes in Paenibacillaceae, considering different genomic aspects.", "token_count": 513, "char_count": 2082, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5921, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:15:24.578867", "source": { "split": "train_shard_00000", "doc_id": 1691 }, "chunk_id": "train_shard_00000_1691_0", "global_id": 1867 }, { "text": "Alternative nitrogenase of Paenibacillus sonchi genomovar Riograndensis: An insight in the origin of Fe-nitrogenase in the Paenibacillaceae family.", "token_count": 44, "char_count": 147, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:24.959216", "source": { "split": "train_shard_00000", "doc_id": 1691 }, "chunk_id": "train_shard_00000_1691_1", "global_id": 1868 }, { "text": "Bacillus subtilis is a versatile bacterial species able to produce surfactin, a lipopeptide biosurfactant. We carried out the phylogenomic characterization and pangenomic analyses using available B. subtilis complete genomes. Also, we report the whole genome of the biosurfactant-producing B. subtilis strain RI4914 that was isolated from effluent water from an oil exploration field. We applied a hybrid sequencing approach using both long- and short-read sequencing technologies to generate a highly accurate, single-chromosome genome. The pangenomics analysis of 153 complete genomes classified as B. subtilis retrieved from the NCBI shows an open pangenome composed of 28,511 accessory genes, which agrees with the high genetic plasticity of the species. Also, this analysis suggests that surfactin production is a common trait shared by members of this species since the srfA operon is highly conserved among the B. subtilis strains found in most of the assemblies available. Finally, increased surfactin production corroborates the higher srfAA gene expression in B. subtilis strain RI4914.\n\nPhylogenomic characterization and pangenomic insights into the surfactin-producing bacteria Bacillus subtilis strain RI4914.", "token_count": 315, "char_count": 1222, "word_count": 171, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "RI4914" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:25.532478", "source": { "split": "train_shard_00000", "doc_id": 1692 }, "chunk_id": "train_shard_00000_1692_0", "global_id": 1869 }, { "text": "The major drawbacks of biofuel production at the commercial level are its low yield, nonavailability of feedstock, feedback inhibition, presence of inhibitory pathways in various organisms, and biofuel intolerance of organisms. The present review focuses on the implications of the CRISPRCas9 mediated gene editing tool to alter the genome of bacteria, algae, fungi, and higher plants for efficient biofuel production. Gene knockout and gene cassette insertions employing CRISPR-Cas9 in Saccharomyces cerevisiae and Kluyveromyces marxianus have resulted in enhanced production of bioethanol and 2-Phenyl ethanol in these organisms, respectively. Genomes of several bacterial strains were also modified to enhance ethanol and butanol production in them. CRISPR-Cas9 modification of microalgae has demonstrated improved total lipid content, a prerequisite for biofuel production. All over, CRISPR-Cas9 has emerged as a tool of choice for engineering the genome and metabolic pathways of organisms for producing industrial biofuel. In plant-based biofuel production, the biosynthetic pathways of lignin interfere with the satisfactory release of fermentable sugars thus hampering efficient biofuel production. CRISPR-Cas9 has shown a promising role in reducing lignin content in various plants including barley, switchgrass, and rice straw.\n\nImplications of CRISPR-Cas9 in Developing Next Generation Biofuel: A Mini-review.", "token_count": 359, "char_count": 1420, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6321, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:26.165049", "source": { "split": "train_shard_00000", "doc_id": 1693 }, "chunk_id": "train_shard_00000_1693_0", "global_id": 1870 }, { "text": "Dietary polyphenol ellagic acid has anti-cancer and anti-inflammatory activities, and these biological activities require the conversion of ellagic acid to urolithins by intestinal microbes. However, few gut microbes are capable of metabolizing ellagic acid to produce urolithins, limiting the beneficial effects of ellagic acid on health. Here, we describe an intestinal bacterium Lactococcus garvieae FUA009 isolated from the feces of a healthy volunteer. It was demonstrated via HPLC and UPLC-MS analysis that the end product of ellagic acid metabolism of FUA009 was urolithin A. In addition, we also examined the whole genome sequence of FUA009 and then assessed the safety and probiotic properties of FUA009 based on a complete genome and phenotype analysis. We indicated that FUA009 was safe, which was confirmed by FUA009 being sensitive to multiple antibiotics, having no hemolytic activity, and being free of aggressive putative virulence factors. Moreover, 19 stress-responsive protein genes and 8 adhesion-related genes were predicted in the FUA009 genome. Furthermore, we demonstrated that FUA009 was tolerant to acid and bile salt by determining the cell viability in a stress environment. In summary, Lactococcus garvieae FUA009, as a novel UA-producing bacterium, not only contributes to the study of the metabolic pathway of ellagic acid but is also expected to be a novel probiotic candidate.", "token_count": 372, "char_count": 1409, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6238, "quality_score": 0.8119, "entities": { "genes": [ "FUA009" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:26.747843", "source": { "split": "train_shard_00000", "doc_id": 1695 }, "chunk_id": "train_shard_00000_1695_0", "global_id": 1871 }, { "text": "The potential probiotic function of Latilactobacills curvatus has attracted the attention of researchers. To explore the differences in the genomes of L. curvatus, nine strains were isolated from various sources, including feces and fermented vegetables and compared with 25 strains from the NCBI database. The findings indicated that the average genome size, GC content, and CDS of L. curvatus were 1.94 MB, 41.9%, and 1825, respectively. Its core genome is associated with transcription, translation, carbohydrate transport and metabolism, and defense functions. The pan-genome of L. curvatus was in a closed state. The genetic diversity of L. curatus is mainly manifested in its ability to use carbohydrates, antibiotic resistance, bacteriocin operon, and polymeric regularly interspaced short palindromic repeats (CRISPR)-Cas for bacterial immunity. The CRISPR system of 34 strains of L. curvatus was predominantly found to be of the IIA type with a few IIC and IE types. These findings will contribute to a better understanding of this species.\n\nPhenotype-genotype analysis of Latilactobacills curvatus from different niches: Carbohydrate metabolism, antibiotic resistance, bacteriocin, phage fragments and linkages with CRISPR-Cas systems.", "token_count": 322, "char_count": 1245, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6554, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:27.318317", "source": { "split": "train_shard_00000", "doc_id": 1696 }, "chunk_id": "train_shard_00000_1696_0", "global_id": 1872 }, { "text": "Although probiotics have been isolated from different sources, few were isolated from traditional Chinese medicine. The current study firstly isolates Pulsatilla Radix-utilising Pediococcus pentosaceus PR-1 from human faeces. Subsequently, the tolerance of PR-1 to low pH, bile salts, simulated gastric juice and succus entericus, antioxidant activity, antimicrobial activity, cholesterol assimilation and antibiotics susceptibility were investigated. After 2 h of incubation at pH 2.0, over 80% of PR-1 survived. The cell viability of PR-1 at 2 h under 0.1% bile salt condition was 99.2%. The survival rate of PR-1 in gastric juice and succus entericus was 64.48% and 81.86%, respectively. Cell-free supernatant of PR-1 culture also showed antimicrobial activity against Escherichia coli, Staphylococcus aureus and Salmonella typhimurium. Besides, antioxidant activity of PR-1 CFS was significantly greater than cell pellet. PR-1 was shown to be resistant to kanamycin, streptomycin, vancomycin and norfloxacin and was able to lower the cholesterol level to 72.5±1.5%. In addition, PR-1 displayed γ-haemolysis and was non-pathogenic.\n\nIsolation and characterisation of Pulsatilla Radix-utilising bacteria Pediococcus pentosaceus PR-1 from human faeces.", "token_count": 384, "char_count": 1253, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6374, "quality_score": 0.8187, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:27.936654", "source": { "split": "train_shard_00000", "doc_id": 1697 }, "chunk_id": "train_shard_00000_1697_0", "global_id": 1873 }, { "text": "Phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) using whole-genome sequencing (WGS) is increasingly used in epidemiological investigations of bacteria. The approach, however, is both resource intensive and time-consuming. Oxford Nanopore Technologies (ONT) sequencing is capable of real-time data analysis but the high error rate hampers its application in cgSNP-based phylogenetic analysis. Here, we developed a cgSNP-independent phylogenetic analysis method using ONT read assemblies by focusing on open reading frame (ORF) content patterns.\n\nRapid phylogenetic analysis using open reading frame content patterns acquired by Oxford nanopore sequencing.", "token_count": 172, "char_count": 690, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7528, "quality_score": 0.8764, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:28.385672", "source": { "split": "train_shard_00000", "doc_id": 1698 }, "chunk_id": "train_shard_00000_1698_0", "global_id": 1874 }, { "text": "The genus Prevotella comprises 55 species with validly published, and correct, names (at June 2021) that are phenotypically, ecologically and functionally diverse. This study used a range of comparative genome approaches (marker gene-based genome phylogeny, core genome phylogeny, average amino acid identity, percentage of conserved proteins and clade-specific marker genes) to identify large differences between the 53 species for which genomes are available, as well as two effectively published yet not validly named species and four novel species. These differences were consistent between the various analysis methods and justify the separation of Prevotella into multiple genera. While the distribution across 19 ecosystem types was unique for each species and inconsistent within clades, the functional repertoire based on the presence/absence of both PFAMs and CAZy families revealed distinct clustering based on the proposed genera. Based on the integration of all results, we propose the reclassification of species previously assigned to the genus Prevotella into seven genera, including four novel genera for which the names Segatella, Hoylesella, Leyella and Palleniella are proposed. In addition to the reclassification of Prevotella, this work describes four novel species, Hallella faecis, Xylanibacter rodentium, Xylanibacter muris, and Palleniella intestinalis.\n\nA taxonomic note on the genus Prevotella: Description of four novel genera and emended description of the genera Hallella and Xylanibacter.", "token_count": 357, "char_count": 1521, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6385, "quality_score": 0.8192, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:28.961688", "source": { "split": "train_shard_00000", "doc_id": 1699 }, "chunk_id": "train_shard_00000_1699_0", "global_id": 1875 }, { "text": "The second messenger c-di-AMP contributes to various homeostatic and stress responses in bacteria. In this issue of\n\nRounding out cyclic dinucleotide signaling in", "token_count": 41, "char_count": 162, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:29.331289", "source": { "split": "train_shard_00000", "doc_id": 1700 }, "chunk_id": "train_shard_00000_1700_0", "global_id": 1876 }, { "text": "To colonize the host and cause disease, the human enteropathogen\n\nc-di-AMP signaling is required for bile salt resistance, osmotolerance, and long-term host colonization by", "token_count": 45, "char_count": 172, "word_count": 24, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:30.037746", "source": { "split": "train_shard_00000", "doc_id": 1701 }, "chunk_id": "train_shard_00000_1701_0", "global_id": 1877 }, { "text": "The CDC's Emerging Infections Program (EIP) conducted population- and laboratory-based surveillance of US carbapenem-resistant Pseudomonas aeruginosa (CRPA) from 2016 through 2018. To characterize the pathotype, 1,019 isolates collected through this project underwent antimicrobial susceptibility testing and whole-genome sequencing. Sequenced genomes were classified using the seven-gene multilocus sequence typing (MLST) scheme and a core genome (cg)MLST scheme was used to determine phylogeny. Both chromosomal and horizontally transmitted mechanisms of carbapenem resistance were assessed. There were 336 sequence types (STs) among the 1,019 sequenced genomes, and the genomes varied by an average of 84.7% of the cgMLST alleles used. Mutations associated with dysfunction of the porin OprD were found in 888 (87.1%) of the genomes and were correlated with carbapenem resistance, and a machine learning model incorporating hundreds of genetic variations among the chromosomal mechanisms of resistance was able to classify resistant genomes. While only 7 (0.1%) isolates harbored carbapenemase genes, 66 (6.5%) had acquired non-carbapenemase β-lactamase genes, and these were more likely to have OprD dysfunction and be resistant to all carbapenems tested. The genetic diversity demonstrates that the pathotype includes a variety of strains, and clones previously identified as high-risk make up only a minority of CRPA strains in the United States. The increased carbapenem resistance in isolates with acquired non-carbapenemase β-lactamase genes suggests that horizontally transmitted mechanisms aside from carbapenemases themselves may be important drivers of the spread of carbapenem resistance in P. aeruginosa.\n\nWhole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant", "token_count": 480, "char_count": 1786, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8174, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:30.682468", "source": { "split": "train_shard_00000", "doc_id": 1702 }, "chunk_id": "train_shard_00000_1702_0", "global_id": 1878 }, { "text": "One of the most important livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) genetic lineages is the clonal complex (CC) 398, which can cause typical S. aureus-associated infections in people. In this work, whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics were applied to study the genetic characteristics of three MRSA CC398 isolates recovered from humans (strains C5621 and C9017), and from an animal (strain OR418). Of the three strains, C9017 presented the broadest resistance genotype, including resistance to fluroquinolone, clindamycin, tiamulin, macrolide and aminoglycoside antimicrobial classes. The scn, sak, and chp genes of the immune evasion cluster system were solely detected in OR418. Pangenome analysis showed a total of 288 strain-specific genes, most of which are hypothetical or phage-related proteins. OR418 had the most pronounced genetic differences. RNAIII (δ-hemolysin) gene was clearly the most expressed gene in OR418 and C5621, but it was not detected in C9017. Significant differences in the proteome profiles were found between strains. For example, the immunoglobulin-binding protein Sbi was more abundant in OR418. Considering that Sbi is a multifunctional immune evasion factor in S. aureus, the results point to OR418 strain having high zoonotic potential. Overall, multiomics biomarker signatures can assume an important role to advance precision medicine in the years to come. SIGNIFICANCE: MRSA is one of the most representative drug-resistant pathogens and its dissemination is increasing due to MRSA capability of establishing new reservoirs. LA-MRSA is considered an emerging problem worldwide and CC398 is one of the most important genetic lineages", "token_count": 473, "char_count": 1743, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [ "OR418", "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:31.330993", "source": { "split": "train_shard_00000", "doc_id": 1703 }, "chunk_id": "train_shard_00000_1703_0", "global_id": 1879 }, { "text": "In this study, three MRSA CC398 isolates recovered from humans and from a wild animal were analyzed through whole-genome sequencing, RNA-sequencing, and gel-based comparative proteomics in order to gather systems-wide omics data and better understand the genetic characteristics of this lineage to identify distinctive markers and genomic features of relevance to public health.\n\nBioinformatics study of expression from genomes of epidemiologically related MRSA CC398 isolates from human and wild animal samples.", "token_count": 115, "char_count": 512, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7324, "quality_score": 0.8662, "entities": { "genes": [ "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:31.711447", "source": { "split": "train_shard_00000", "doc_id": 1703 }, "chunk_id": "train_shard_00000_1703_1", "global_id": 1880 }, { "text": "Ergosterol is an important precursor in the pharmaceutical industry for the production of numerous drugs. In this study, Kluyveromyces marxianus that showed more potential for ergosterol production than some other yeasts was reported. The effects of transcription factors UPC2, MOT3, and ROX1 of K. marxianus on ergosterol synthesis were explored, and a Upc2-overexpressing strain produced 1.78 times more ergosterol (167.33 mg/L) than the wild-type strain (60.04 mg/L). A total of 239.98 mg/L ergosterol was produced when glucose was replaced with fructose to limit ethanol production. Enhanced aeration increased ergosterol titer from 63.09 mg/L to 128.46 mg/L at 42 °C. The ergosterol titer reached 304.37 mg/L in a shake flask at 37 °C, or 1124.38 and 948.32 mg/L at 37 °C and 42 °C, respectively, in a 5 L bioreactor, using Jerusalem artichoke tubers as the sole carbon source. This study establishes a platform for ergosterol biosynthesis using inexpensive materials.\n\nErgosterol production at elevated temperatures by Upc2-overexpressing Kluyveromyces marxianus using Jerusalem artichoke tubers as feedstock.", "token_count": 373, "char_count": 1115, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [ "MOT3", "ROX1", "UPC2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:32.295056", "source": { "split": "train_shard_00000", "doc_id": 1704 }, "chunk_id": "train_shard_00000_1704_0", "global_id": 1881 }, { "text": "At the beginning of the SARS-CoV-2 pandemic, developing of new treatments to control the spread of infection and decrease morbidity and mortality are necessary. This prospective, open-label, case-control intervention study evaluates the impact of the oral intake of the probiotic yeast\n\nOral intake of Kluyveromyces marxianus B0399 plus Lactobacillus rhamnosus CECT 30579 to mitigate symptoms in COVID-19 patients: A randomized open label clinical trial.", "token_count": 124, "char_count": 454, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7812, "quality_score": 0.8906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:32.680888", "source": { "split": "train_shard_00000", "doc_id": 1706 }, "chunk_id": "train_shard_00000_1706_0", "global_id": 1882 }, { "text": "The ability to regulate B cell development has long been recognized to have therapeutic potential in a variety of autoimmune diseases. However, despite the presence of a classic autoantibody in primary biliary cholangitis (PBC), B cell depleting therapy and indeed therapy with other biologic agents has been disappointing. Unsuccessful treatment using Rituximab is associated with elevation of B-cell activating factor (BAFF) level. Indeed, therapies for PBC remain directed at modulating bile salt biology, rather than targeting effector pathways. With these data in mind, we proposed that targeting two major stages of B cell development, namely long-lived memory B cells and short-lived peripheral autoreactive plasma cells would have therapeutic potential.\n\nDual B-cell targeting therapy ameliorates autoimmune cholangitis.", "token_count": 193, "char_count": 828, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7672, "quality_score": 0.8836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:33.139538", "source": { "split": "train_shard_00000", "doc_id": 1707 }, "chunk_id": "train_shard_00000_1707_0", "global_id": 1883 }, { "text": "Beneficial effects of Lactiplantibacillus plantarum strains have been widely reported. Knowing that the effects of probiotic bacteria are strain-dependent, this study aimed to characterize the probiotic properties and investigate the gastrointestinal protective effects of nine novel L. plantarum strains isolated from Bahia, Brazil. The probiotic functionality was first evaluated in vitro by characterizing bile salt and acidic tolerance, antibacterial activity, and adhesion to Caco-2 cells. Antibiotic resistance profile, mucin degradation, and hemolytic activity assays were also performed to evaluate safety features. In vivo analyses were conducted to investigate the anti-inflammatory effects of the strains on a mouse model of 5-Fluorouracil-induced mucositis. Our results suggest that the used L. plantarum strains have good tolerance to bile salts and low pH and can inhibit commonly gastrointestinal pathogens. Lp2 and Lpl1 strains also exhibited high adhesion rates to Caco-2 cells (13.64 and 9.05%, respectively). Phenotypical resistance to aminoglycosides, vancomycin, and tetracycline was observed for most strains. No strain showed hemolytic or mucolytic activity. Seven strains had a protective effect against histopathological and inflammatory damage induced by 5-FU. Gene expression analysis of inflammatory markers showed that five strains upregulated interleukin 10 (Il10), while four downregulated both interleukin 6 (Il6) and interleukin 1b (Il1b). Additionally, all strains reduced eosinophilic and neutrophilic infiltration; however, they could not prevent weight loss or reduced liquid/ food intake. Altogether, our study suggests these Brazilian L. plantarum strains present good probiotic characteristics and safety levels for future applications and can be therapeutically adjuvant alternatives to prevent/treat intestinal mucositis.\n\nEvaluation of Probiotic Properties of Novel Brazilian Lactiplantibacillus plantarum Strains.", "token_count": 511, "char_count": 1957, "word_count": 258, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:33.777362", "source": { "split": "train_shard_00000", "doc_id": 1708 }, "chunk_id": "train_shard_00000_1708_0", "global_id": 1884 }, { "text": "Candidemia is a pervasive problem associated with significant morbidity and mortality in health care settings. This study aimed to determine the changing distribution of Candida species and the emergence of uncommon species.\n\nPrevalence and species distribution of Candida bloodstream infection in children and adults in two teaching university hospitals in Egypt: first report of Candida kefyr.", "token_count": 80, "char_count": 395, "word_count": 56, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:34.184312", "source": { "split": "train_shard_00000", "doc_id": 1709 }, "chunk_id": "train_shard_00000_1709_0", "global_id": 1885 }, { "text": "Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E", "token_count": 524, "char_count": 2054, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8466, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:15:34.813524", "source": { "split": "train_shard_00000", "doc_id": 1710 }, "chunk_id": "train_shard_00000_1710_0", "global_id": 1886 }, { "text": "coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.\n\nDesign of Multi-Epitope Vaccine for", "token_count": 101, "char_count": 374, "word_count": 52, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:35.200313", "source": { "split": "train_shard_00000", "doc_id": 1710 }, "chunk_id": "train_shard_00000_1710_1", "global_id": 1887 }, { "text": "Nattokinase is a potential new thrombolytic drug because of its strong thrombolytic effect, high safety, and low cost. However, there is no research reporting on bile salt-tolerant nattokinase-producing probiotics. In this study, the bile salt-tolerant nattokinase-producing strain\n\nCharacterization of a Nattokinase from the Newly Isolated Bile Salt-Resistant", "token_count": 105, "char_count": 360, "word_count": 47, "semantic_coherence": 1, "information_density": 0.7872, "quality_score": 0.8936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:35.579354", "source": { "split": "train_shard_00000", "doc_id": 1711 }, "chunk_id": "train_shard_00000_1711_0", "global_id": 1888 }, { "text": "Nonalcoholic beers are becoming increasingly popular, in part due to consumers' awareness of a healthier lifestyle. Additionally, consumers are demanding diversification in the product range, which can be offered by producing nonalcoholic beers using non-Saccharomyces yeasts for fermentation to create a wide variety of flavors. So far, little is known about the nutritionally relevant byproducts that these yeasts release during wort fermentation and whether these yeasts can be considered safe for food fermentations. To gain insights into this, the B vitamins of four different nonalcoholic beers fermented with the yeast species Saccharomycodes ludwigii, Cyberlindnera saturnus (two strains), and Kluyveromyces marxianus were analyzed. Furthermore, a total of 16 beers fermented with different non-Saccharomyces yeast strains were analyzed for biogenic amines. Additionally, stress tolerance tests were performed at 37°C and in synthetic human gastric juice in vitro. B vitamins were found in the four nonalcoholic beers in nutritionally relevant amounts so they could serve as a supplement for a balanced diet. Biogenic amines remained below the limit of determination in all 16 beers, and thus likely had no influence, while the stress tolerance tests gave a first indication that seven yeast strains could possibly tolerate the human gastric juice milieu.\n\nInvestigations into metabolic properties and selected nutritional metabolic byproducts of different non-Saccharomyces yeast strains when producing nonalcoholic beer.", "token_count": 364, "char_count": 1530, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6204, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:36.156702", "source": { "split": "train_shard_00000", "doc_id": 1712 }, "chunk_id": "train_shard_00000_1712_0", "global_id": 1889 }, { "text": "The triazole fungicide prothioconazole (PTC) can cause adverse effects in animals, and its main metabolite prothioconazole-desthio (PTC-d) is even much more harmful. However, the toxic effects of PTC and PTC-d on the liver-gut axis of mice are still unknown. In the present experiment, we found that oral exposure to PTC and PTC-d increased total bile acids (TBAs) levels in the serum, liver, and feces. Correspondingly, the transcription of genes involved in bile acids (BAs) disposition was significantly influenced by PTC or PTC-d exposure. Furthermore, the BAs composition of serum BAs was analyzed by LC-MS, and the results indicated that PTC and PTC-d exposure changed the BAs composition, lowered the ratio of conjugated/unconjugated BAs, elevated the ratio of CA/b-MCA, and enhanced the hydrophobicity of BAs pool. 16s RNA gene sequencing of the DNA from colonic contents uncovered that PTC and PTC-d exposure altered the relative abundance and constitution of intestinal microbiota, increasing the relative level of Lactobacillus with bile salt hydrolase (BSH) activity. Furthermore, PTC and PTC-d exposure impaired the gut barrier function, causing an increase in mucus secretion. In particular, the effects of PTC-d on some endpoints in the BAs metabolism and gut barrier function had been proven to be more significant than the parent compound PTC. All these findings draw attention to the health risk of PTC and PTC-d exposure in regulating BAs metabolism, which might lead to some metabolic disorders and occur of related diseases in animals.\n\nThe fungicide prothioconazole and its metabolite prothioconazole-desthio disturbed the liver-gut axis in mice.", "token_count": 448, "char_count": 1668, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5873, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:36.817294", "source": { "split": "train_shard_00000", "doc_id": 1713 }, "chunk_id": "train_shard_00000_1713_0", "global_id": 1890 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is a common bacterial pathogen that frequently colonizes healthy individuals, with potential to cause invasive infection. In Denmark, to keep the prevalence low, MRSA carriers are recommended to undergo decolonization treatments, but achieving decolonization is challenging. Knowledge about the factors contributing to decolonization is scarce. We aimed to identify bacterial genome and clinical factors influencing MRSA decolonization. We identified all new MRSA patients above 2 years of age within the Hvidovre catchment area, Copenhagen, Denmark, in 2017 and 2018. Carriers were defined as chronic carriers (cases) if they were MRSA positive after two or more treatments and as nonchronic carriers (controls) if they were MRSA free after the first or second treatment. Using whole-genome sequencing (WGS), we constructed a pangenome of bacterial strains. With the incorporation of bacterial genome and clinical patient data, machine learning and multivariate analyses were performed to determine the factors associated with decolonization. A total of 477 MRSA carriers were included. An age of ≥13 years was significantly associated with nonchronic carriage. We identified 278 bacterial genetic features that were statistically significantly associated with chronic carriage (\n\nEstimated Roles of the Carrier and the Bacterial Strain When Methicillin-Resistant Staphylococcus aureus Decolonization Fails: a Case-Control Study.", "token_count": 366, "char_count": 1481, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:37.418489", "source": { "split": "train_shard_00000", "doc_id": 1714 }, "chunk_id": "train_shard_00000_1714_0", "global_id": 1891 }, { "text": "Mycobacterium abscessus is an emerging multidrug-resistant non-tuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Whole genome sequencing data of 1991 isolates were employed to validate the scheme, re-analyze global population structure and set genetic distance thresholds for cluster detection and taxonomic identification. We confirmed and amended the nomenclature of the main dominant circulating clones and found that these also correlate well with traditional 7-loci MLST. Dominant circulating clones could be linked to a corresponding reference genome with less than 250 alleles while 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.\n\nDelineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing.", "token_count": 293, "char_count": 1277, "word_count": 169, "semantic_coherence": 1, "information_density": 0.716, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:38.013248", "source": { "split": "train_shard_00000", "doc_id": 1715 }, "chunk_id": "train_shard_00000_1715_0", "global_id": 1892 }, { "text": "Hepatic cell lines serve as economical and reproducible alternatives for primary human hepatocytes. However, the utility of hepatic cell lines to examine bile acid homeostasis and cholestatic toxicity is limited due to abnormal expression and function of bile acid-metabolizing enzymes, transporters, and the absence of canalicular formation. We discovered that culturing HuH-7 human hepatoma cells with dexamethasone (DEX) and 0.5% dimethyl sulfoxide (DMSO) for two weeks, with Matrigel overlay after one week, resulted in a shorter and improved differentiation process. These culture conditions increased the expression and function of the major bile acid uptake and efflux transporters, sodium taurocholate co-transporting polypeptide (NTCP) and the bile salt export pump (BSEP), respectively, in two-week cultures of HuH-7 cells. This in vitro model was further characterized for expression and function of bile acid-metabolizing enzymes, transporters, and cellular bile acids. Differentiated HuH-7 cells displayed a marked shift in bile acid composition and induction of cytochrome P450 (CYP) 7A1, CYP8B1, CYP3A4, and bile acid-CoA: amino acid N-acyltransferase (BAAT) mRNAs compared to control. Inhibition of taurocholate uptake and excretion after a 24-h treatment with prototypical cholestatic drugs suggests that differentiated HuH-7 cells are a suitable model to examine cholestatic hepatotoxicity.\n\nA novel differentiated HuH-7 cell model to examine bile acid metabolism, transport and cholestatic hepatotoxicity.", "token_count": 423, "char_count": 1524, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7967, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:38.654324", "source": { "split": "train_shard_00000", "doc_id": 1716 }, "chunk_id": "train_shard_00000_1716_0", "global_id": 1893 }, { "text": "The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase (http://enterobase.warwick.ac.uk) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short-read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC's ability to correctly assign 100 000s of genomes to the species/subspecies and population levels for\n\nEnteroBase: hierarchical clustering of 100 000s of bacterial genomes into species/subspecies and populations.", "token_count": 234, "char_count": 1016, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:39.130458", "source": { "split": "train_shard_00000", "doc_id": 1717 }, "chunk_id": "train_shard_00000_1717_0", "global_id": 1894 }, { "text": "Lactiplantibacillus sp. LM14-2, isolated from Thai-fermented mussel (Hoi-dong), showed attractive probiotic properties. This strain was identified as Lactiplantibacillus plantarum based on its phenotypic, chemotaxonomic, and genetic characteristics including whole-genome sequencing (WGS). The draft genome sequence was analyzed and annotated for the molecular mechanisms involved in the safety assessment, the adaptation and adhesion of L. plantarum LM14-2 to the gastrointestinal tract (GIT), and the beneficial genes involved in bacteria-host interactions. The L. plantarum LM14-2 exhibited bile salt hydrolase (BSH) activity, assimilated cholesterol at 86.07 ± 5.03%, stimulated the secretion of interleukin-12, interferon-gamma, and human beta defensin-2, and induced nitric oxide production. In addition, L. plantarum LM14-2 showed excellent gastrointestinal tolerance and adhesion ability to Caco-2 cells. Furthermore, the in silico analysis showed that L. plantarum LM14-2 was a non-human pathogen and did not contain antibiotic resistance genes or plasmids. L. plantarum LM14-2 also contained potential genes associated with various probiotic characteristics and health-promoting effects. Consequently, this study suggested that L. plantarum LM14-2 could be considered safe, with potential probiotic properties and health-promoting impacts, which could facilitate its probiotic application.\n\nProbiogenomic Analysis of Lactiplantibacillus sp. LM14-2 from Fermented Mussel (Hoi-dong), and Evaluation of its Cholesterol-lowering and Immunomodulation Effects.", "token_count": 440, "char_count": 1564, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": { "genes": [ "LM14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:39.757023", "source": { "split": "train_shard_00000", "doc_id": 1718 }, "chunk_id": "train_shard_00000_1718_0", "global_id": 1895 }, { "text": "Mycoplasma bovis (M. bovis) is an emerging major bovine pathogen, causing economic losses worldwide in the dairy and beef industry. Whole-genome sequencing (WGS) now allows high resolution for tracing clonal populations. Based on WGS, we developed the core genome multilocus sequence typing (cgMLST) scheme and applied it onto 151 genomes of clonal and non-clonal strains of M. bovis isolated from China, Australia, Israel, Denmark, Canada, and the USA. We used the complete genome of M. bovis PG45 as the reference genome. The pairwise genome comparison of these 151 genome sequences resulted in 478 cgMLST gene targets present in > 99.0 % clonal and non-clonal isolates with 100 % overlap and > 90 % sequence similarity. A total of 478 core genes were retained as cgMLST target genes of which an average of 90.4-99 % were present in 151 M. bovis genomes, while M. agalactiae (PG2) had 17.0 % and M. mycoides subsp. capri (PG3), M. ovipneumoniae (Y98), and M. arginine resulted in 0.0 % of good targets. When tested against the clonal and non-clonal strains, we found cgMLST clusters were congruent with the MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish between clonal and epidemiologically unrelated strains of the same clonal group, which could not be achieved using traditional MLST schemes. Our results showed that ninety-two M. bovis genomes from clonal group isolates had > 10 allele differences and unambiguously differentiated from unrelated outgroup strains. Additionally, cgMLST revealed that there might be several sub-clones of the emerging ST-52 clone. The cgMLST phylogenetic analysis results showed substantial agreement with geographical and temporal information. cgMLST enables the use of next-generation sequencing technology to bovine mycoplasma epidemiology at both the local and global levels", "token_count": 526, "char_count": 1896, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8052, "entities": { "genes": [ "PG2", "PG45", "PG3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:15:40.408589", "source": { "split": "train_shard_00000", "doc_id": 1719 }, "chunk_id": "train_shard_00000_1719_0", "global_id": 1896 }, { "text": "In conclusion, the novel cgMLST scheme not only showed discrimination resolution highly as compared with MLST and SNP cgMLST in sub-typing but also indicated the capability to reveal more population structure characteristics than MLST.\n\nA core genome multilocus sequence typing (cgMLST) analysis of Mycoplasma bovis isolates.", "token_count": 76, "char_count": 325, "word_count": 46, "semantic_coherence": 1, "information_density": 0.9348, "quality_score": 0.9674, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:40.774725", "source": { "split": "train_shard_00000", "doc_id": 1719 }, "chunk_id": "train_shard_00000_1719_1", "global_id": 1897 }, { "text": "Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe.\n\nGenomic features of Mycoplasma bovis subtypes currently circulating in France.", "token_count": 207, "char_count": 922, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:41.243433", "source": { "split": "train_shard_00000", "doc_id": 1720 }, "chunk_id": "train_shard_00000_1720_0", "global_id": 1898 }, { "text": "Metagenomic next-generation sequencing (mNGS) is useful for difficult to cultivate pathogens. Here, we use cerebrospinal fluid mNGS to diagnose invasive meningococcal disease. The complete genome sequences of Neisseria meningitidis were assembled using N. meningitidis of ST4821-serotype C isolated from four patients. To investigate the phylogeny, 165 CC4821 N. meningitidis genomes from 1972 to 2017 were also included. The core genome accumulated variation at a rate of 4.84×10\n\nMetagenomic data from cerebrospinal fluid permits tracing the origin and spread of Neisseria meningitidis CC4821 in China.", "token_count": 187, "char_count": 604, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7381, "quality_score": 0.869, "entities": { "genes": [ "ST4821", "CC4821" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:41.692797", "source": { "split": "train_shard_00000", "doc_id": 1721 }, "chunk_id": "train_shard_00000_1721_0", "global_id": 1899 }, { "text": "Streptococcus pneumoniae (S. pneumoniae), the major etiological agent of community-acquired pneumonia (CAP) contributes significantly to the global burden of infectious diseases which is getting resistant day by day. Nearly 30% of the S. pneumoniae genomes encode hypothetical proteins (HPs), and better understandings of these HPs in virulence and pathogenicity plausibly decipher new treatments. Some of the HPs are present across many Streptococcus species, systematic assessment of these unexplored HPs will disclose prospective drug targets. In this study, through a stringent bioinformatics analysis of the core genome and proteome of S. pneumoniae PCS8235, we identified and analyzed 28 HPs that are common in many Streptococcus species and might have a potential role in the virulence or pathogenesis of the bacteria. Functional annotations of the proteins were conducted based on the physicochemical properties, subcellular localization, virulence prediction, protein-protein interactions, and identification of essential genes, to find potentially druggable proteins among 28 HPs. The majority of the HPs are involved in bacterial transcription and translation. Besides, some of them were homologs of enzymes, binding proteins, transporters, and regulators. Protein-protein interactions revealed HP PCS8235_RS05845 made the highest interactions with other HPs and also has TRP structural motif along with virulent and pathogenic properties indicating it has critical cellular functions and might go under unconventional protein secretions. The second highest interacting protein HP PCS8235_RS02595 interacts with the Regulator of chromosomal segregation (RocS) which participates in chromosome segregation and nucleoid protection in S. pneumoniae. In this interacting network, 54% of protein members have virulent properties and 40% contain pathogenic properties. Among them, most of these proteins circulate in the cytoplasmic area and have hydrophilic properties", "token_count": 491, "char_count": 1974, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [ "PCS8235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:42.985051", "source": { "split": "train_shard_00000", "doc_id": 1722 }, "chunk_id": "train_shard_00000_1722_0", "global_id": 1900 }, { "text": "Finally, molecular docking and dynamics simulation demonstrated that the antimalarial drug Artenimol can act as a drug repurposing candidate against HP PCS8235_RS 04650 of S. pneumoniae. Hence, the present study could aid in drugs against S. pneumoniae.\n\nExploration of Streptococcus core genome to reveal druggable targets and novel therapeutics against S. pneumoniae.", "token_count": 103, "char_count": 369, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8077, "quality_score": 0.9038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:43.365414", "source": { "split": "train_shard_00000", "doc_id": 1722 }, "chunk_id": "train_shard_00000_1722_1", "global_id": 1901 }, { "text": "Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled genomes or through single-cell genomes. While this expanded diversity can provide novel insights into microbial population structure, most tools available for core-genome estimation are sensitive to genome completeness. Consequently, a major portion of the huge phylogenetic diversity uncovered by environmental genomic approaches remains excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core genome for sets of genomes of highly diverse completeness range. The likelihood for each gene cluster to belong to core or accessory genome is estimated by computing the probability of its presence/absence pattern in the target genome set. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates to state-of-the-art tools Roary and PPanGGOLiN for high-quality genomes and is capable of using genomes at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.\n\nmOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation.", "token_count": 368, "char_count": 1621, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:43.947001", "source": { "split": "train_shard_00000", "doc_id": 1723 }, "chunk_id": "train_shard_00000_1723_0", "global_id": 1902 }, { "text": "High-temperature ethanol fermentation by thermotolerant yeast is considered a promising technology for ethanol production, especially in tropical and subtropical regions. In this study, optimization conditions for high-temperature ethanol fermentation of pineapple waste hydrolysate (PWH) using a newly isolated thermotolerant yeast, Saccharomyces cerevisiae HG1.1, and the expression of genes during ethanol fermentation at 40 °C were carried out. Three independent variables, including cell concentration, pH, and yeast extract, positively affected ethanol production from PWH at 40 °C. The optimum levels of these significant factors evaluated using response surface methodology (RSM) based on central composite design (CCD) were a cell concentration of 8.0 × 10\n\nHigh-temperature ethanol fermentation from pineapple waste hydrolysate and gene expression analysis of thermotolerant yeast Saccharomyces cerevisiae.", "token_count": 237, "char_count": 916, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8445, "entities": { "genes": [ "HG1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:44.422442", "source": { "split": "train_shard_00000", "doc_id": 1724 }, "chunk_id": "train_shard_00000_1724_0", "global_id": 1903 }, { "text": "A cattle pangenome representation was created based on the genome sequences of 898 cattle representing 57 breeds. The pangenome identified 83 Mb of sequence not found in the cattle reference genome, representing 3.1% novel sequence compared with the 2.71-Gb reference. A catalog of structural variants developed from this cattle population identified 3.3 million deletions, 0.12 million inversions, and 0.18 million duplications. Estimates of breed ancestry and hybridization between cattle breeds using insertion/deletions as markers were similar to those produced by single nucleotide polymorphism-based analysis. Hundreds of deletions were observed to have stratification based on subspecies and breed. For example, an insertion of a Bov-tA1 repeat element was identified in the first intron of the\n\nAssembly of a pangenome for global cattle reveals missing sequences and novel structural variations, providing new insights into their diversity and evolutionary history.", "token_count": 225, "char_count": 973, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6934, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:44.898201", "source": { "split": "train_shard_00000", "doc_id": 1725 }, "chunk_id": "train_shard_00000_1725_0", "global_id": 1904 }, { "text": "Natural populations are characterized by abundant genetic diversity driven by a range of different types of mutation. The tractability of sequencing complete genomes has allowed new insights into the variable composition of genomes, summarized as a species pan-genome. These analyses demonstrate that many genes are absent from the first reference genomes, whose analysis dominated the initial years of the genomic era. Our field now turns towards understanding the functional consequence of these highly variable genomes. Here, we analysed weighted gene coexpression networks from leaf transcriptome data for drought response in the purple false brome Brachypodium distachyon and the differential expression of genes putatively involved in adaptation to this stressor. We specifically asked whether genes with variable \"occupancy\" in the pan-genome - genes which are either present in all studied genotypes or missing in some genotypes - show different distributions among coexpression modules. Coexpression analysis united genes expressed in drought-stressed plants into nine modules covering 72 hub genes (87 hub isoforms), and genes expressed under controlled water conditions into 13 modules, covering 190 hub genes (251 hub isoforms). We find that low occupancy pan-genes are under-represented among several modules, while other modules are over-enriched for low-occupancy pan-genes. We also provide new insight into the regulation of drought response in B. distachyon, specifically identifying one module with an apparent role in primary metabolism that is strongly responsive to drought. Our work shows the power of integrating pan-genomic analysis with transcriptomic data using factorial experiments to understand the functional genomics of environmental response.\n\nPatterns of pan-genome occupancy and gene coexpression under water-deficit in Brachypodium distachyon.", "token_count": 396, "char_count": 1878, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6565, "quality_score": 0.8282, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:45.514128", "source": { "split": "train_shard_00000", "doc_id": 1726 }, "chunk_id": "train_shard_00000_1726_0", "global_id": 1905 }, { "text": "Maifan stone is a kind of mineral medicine in Chinese medicine, which has good adsorption, dissolution, mineralization and biological activity. It has an excellent therapeutic effect on livestock, poultry and aquatic animals suffering from intestinal diseases. This study explored the effect of Maifan stone on the growth ability of Lacticaseibacillus rhamnosus GG (L. rhamnosus GG) and the effect of Maifan stone-L. rhamnosus GG-fermented product on the intestinal inflammation and gut microbiota. We find that Maifan stone can adsorb L. rhamnosus GG to form a carrier bacteria. Maifan stone has the characteristics of acid tolerance and bile salt tolerance and can also improve the activity of L. rhamnosus GG in artificial gastrointestinal juice. The fermented product can reduce the degree of diarrhoea and colon pathology in rats to a certain extent and significantly improve intestinal inflammatory factors and gut microbiota. This study improves the application effect of L. rhamnosus GG in the prevention and treatment of diarrhoea animals and provides a scientific basis for the rational development of Maifan stone resources.\n\nEffect of maifan stone on the growth of probiotics and regulation of gut microbiota.", "token_count": 303, "char_count": 1221, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5272, "quality_score": 0.7636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:46.073805", "source": { "split": "train_shard_00000", "doc_id": 1727 }, "chunk_id": "train_shard_00000_1727_0", "global_id": 1906 }, { "text": "Bovine mastitis, a major infectious disease affecting milking cows, leads to reduced milk yield and quality, reduced animal welfare, and an increased need for culling. Although its major causative agents are bacteria, yeast species and achlorophyllous algae of the Prototheca genus are well known as causative agents of bovine refractory mastitis. Nevertheless, few studies have analyzed specific yeasts and Prototheca in this context. Herein, we present survey data of yeast species and Prototheca species isolated from bulk tank milk in the Tokachi district of Japan from April 2020 through March 2021. The species of 276 isolates were determined. Yeast species accounted for 184 isolates, of which Pichia kudriavzevii was the most prevalent species. Regarding Prototheca species, only Prototheca bovis was isolated (92 isolates). Prototheca bovis and Pichia kudriavzevii were detected throughout the year and were detected repeatedly on the same farm. Kluyveromyces marxianus was the second most frequently isolated yeast species after Pichia kudriavzevii. Candida parapsilosis, the fourth most frequently isolated yeast species, was found discontinuously. Analysis of monthly data indicated that Kluyveromyces marxianus and Candida parapsilosis were mainly found during the winter and summer months, respectively. Candida akabanensis and Pichia cactophila were the third and fifth most frequently isolated yeast species, respectively. They were detected repeatedly in bulk tank milk samples from the same farms. Results obtained from bulk tank milk underscore the prevalence of these species. These study results are expected to contribute to the elucidation of problematic yeast and Prototheca species.\n\nAnalysis of Prototheca and yeast species isolated from bulk tank milk collected in Tokachi District, Japan.", "token_count": 439, "char_count": 1816, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5308, "quality_score": 0.7654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:46.705112", "source": { "split": "train_shard_00000", "doc_id": 1728 }, "chunk_id": "train_shard_00000_1728_0", "global_id": 1907 }, { "text": "Fuel ethanol from lignocellulose could be important source of renewable energy. However, to make the process feasible, more efficient microbial fermentation of pentose sugars, mainly xylose, should be achieved. The native xylose-fermenting thermotolerant yeast Ogataea polymorpha is a promising organism for further development. Efficacy of xylose alcoholic fermentation by O. polymorpha was significantly improved by metabolic engineering. Still, genes involved in regulation of xylose fermentation are insufficiently studied.\n\nThe role of hexose transporter-like sensor hxs1 and transcription activator involved in carbohydrate sensing azf1 in xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha.", "token_count": 190, "char_count": 725, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7553, "quality_score": 0.8777, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:47.157559", "source": { "split": "train_shard_00000", "doc_id": 1729 }, "chunk_id": "train_shard_00000_1729_0", "global_id": 1908 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is the leading cause of infection in hospitalized patients and can be prevalent in humans and various animal species. In European countries, MRSA isolates belonging to clonal complex 398 have been detected at high rates in pigs. However, the prevalence of MRSA in pigs and farm environments in Japan remains unclear. MRSA isolates were obtained from pigs in slaughterhouses, diseased pigs on farms, imported breeding pigs, and farm dust. We conducted whole-genome sequencing (WGS) and analyzed the molecular epidemiological relationship between these MRSA isolates using core genome multilocus sequence typing (cgMLST). The prevalence rates of MRSA among pigs in slaughterhouses, diseased pigs on farms, imported breeding pigs, and farm dust were 5.2 %, 3.4 %, 28.8 %, and 0.06 %, respectively. ST 398 isolates that classified as ST398/t034 were isolated from pigs from all sources. The results of cgMLST showed that ST398/t034 isolates originating from domestic pigs clustered into the same cluster as the isolates from imported breeding pigs. However, some clusters only included isolates of domestic pig origin. Most MRSA isolates in this study carried resistance genes for aminoglycosides, β-lactams, macrolides, tetracyclines, and zinc. None of the MRSA isolates in this study harbored Panton-Valentine leukocidin toxin genes. Molecular epidemiological analysis suggested a relationship between isolates from slaughter pigs and imported breeding pigs and the presence of MRSA isolates of domestic origin. However, more data are needed for elucidation of the origin of these MRSA variants in the pig industry in Japan.\n\nMolecular epidemiology of methicillin-resistant Staphylococcus aureus isolated from pigs in Japan.", "token_count": 470, "char_count": 1773, "word_count": 257, "semantic_coherence": 1, "information_density": 0.537, "quality_score": 0.7685, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:47.799711", "source": { "split": "train_shard_00000", "doc_id": 1730 }, "chunk_id": "train_shard_00000_1730_0", "global_id": 1909 }, { "text": "The incidence of fungal infections particularly Candida species, is increasing gradually as a result of the increased life expectancy associated with the advances in the diagnosis and treatment of diseases, and increased number of patients in the risk group over the years. In addition, the incidence of fungal infection types that are resistant to antifungal drugs has been increasing, and rare fungal species have been reported to be isolated more frequently. For this reason, it is indicated that identification to the species level will contribute to the early initiation of an accurate and effective treatment. In this study, it was aimed to define the Candida species isolated from various clinical specimens and to document the performance of antifungal sensitivity tests. The Candida isolates sent to the central mycology laboratory in 2019 for identification and antifungal susceptibility tests were included in the study. The definition of the fungi to the species level was carried out using matrix-assisted laser desorption ionization-time of fl ight mass spectrometry (MALDI-TOF MS) and conventional methods. In vitro antifungal drug susceptibilities were analyzed using the The Clinical and Laboratory Standarts Institute (CLSI, M27-A3) reference broth microdilution method. The minimum inhibitory concentration (MIC) results were interpreted in accordance with the species-specific clinical breakpoints (CBPs) cited in the CLSI-M60 guidelines, and according to the epidemiological cut-off value (ECV) when no CBP was mentioned", "token_count": 333, "char_count": 1541, "word_count": 224, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:48.376096", "source": { "split": "train_shard_00000", "doc_id": 1731 }, "chunk_id": "train_shard_00000_1731_0", "global_id": 1910 }, { "text": "The distribution of the species of the total 813 Candida isolates included in the study were as follows: Candida albicans (n= 312 ), Candida parapsilosis (n= 202), Candida tropicalis (n= 92), Candida glabrata (n= 71), Candida dubliniensis (n=28), Candida lusitaniae (n= 26), Candida kefyr (n= 22), Candida utilis (n= 17), Candida krusei (n= 14), Candida orthopsilosis (n= 7), Candida inconspicua (n= 7), Candida guilliermondii (n= 5), Candida metapsilosis (n= 4), Candida norvegensis (n= 4), Candida lambica (n= 1) and Candida lipolytica (n= 1). The evaluation of the results of the antifungal susceptibility tests according to the CBPs revealed that one C.albicans isolate and 60 C.parapsilosis (29.7%) isolates were resistant, and seven C.parapsilosis (3.5%) isolates were dose-dependent susceptible to fluconazole; 32 C.parapsilosis (15.8%) isolates were intermediately susceptible to voriconazole; one C.parapsilosis (0.5%) was resistant and one C.krusei (7.1%) was intermediately susceptible to anidulafungin; and one C.parapsilosis (0.5%) was resistant and one C.krusei (7.1%) isolate was intermediately susceptible to micafungin. In terms of ECVs, one C.lusitaniae isolate for fluconazole and one of each C.lusitaniae and C.kefyr isolates were evaluated as a non-wild type", "token_count": 465, "char_count": 1279, "word_count": 181, "semantic_coherence": 1, "information_density": 0.5028, "quality_score": 0.7514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:49.036457", "source": { "split": "train_shard_00000", "doc_id": 1731 }, "chunk_id": "train_shard_00000_1731_1", "global_id": 1911 }, { "text": "In the present study, 61 of 813 isolates were found to be resistant to fluconazole and seven were dose dependently susceptible, 32 were intermediately susceptible to voriconazole, one was resistant to anidulafungin, one was intermediately susceptible, and one was resistant to micafungin and one was intermediately susceptible to micafungin. In conclusion, the increased number of non- albicans Candida species and increased levels of resistance to antifungal drugs further establish the importance of early diagnosis at a species level alongside antifungal susceptibility tests.\n\n[One-Year Candida Data of the Central Mycology Laboratory: Which Sample, Which Species, How Resistant?].", "token_count": 172, "char_count": 685, "word_count": 96, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:49.490407", "source": { "split": "train_shard_00000", "doc_id": 1731 }, "chunk_id": "train_shard_00000_1731_2", "global_id": 1912 }, { "text": "During crop domestication and breeding, wild plant species have been shaped into modern high-yield crops and adapted to the main agro-ecological regions. However, climate change will impact crop productivity in these regions, and agriculture needs to adapt to support future food production. On a global scale, crop wild relatives grow in more diverse environments than crop species, and so may host genes that could support the adaptation of crops to new and variable environments. Through identification of individuals with increased climate resilience we may gain a greater understanding of the genomic basis for this resilience and transfer this to crops. Pangenome analysis can help to identify the genes underlying stress responses in individuals harbouring untapped genomic diversity in crop wild relatives. The information gained from the analysis of these pangenomes can then be applied towards breeding climate resilience into existing crops or to re-domesticating crops, combining environmental adaptation traits with crop productivity.\n\nPangenomics and Crop Genome Adaptation in a Changing Climate.", "token_count": 215, "char_count": 1110, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:49.992457", "source": { "split": "train_shard_00000", "doc_id": 1732 }, "chunk_id": "train_shard_00000_1732_0", "global_id": 1913 }, { "text": "Bile acid (BA) species and the gut microbiota (GM) contribute to intestinal mucosa homeostasis. BAs shape the GM and, conversely, intestinal bacteria with bile salt hydrolase (BSH) activity modulate the BA pool composition. The mutual interaction between BAs and intestinal microorganisms also influences mucosal barrier integrity, which is important for inflammatory bowel disease (IBD) pathogenesis, prevention and therapy. High levels of secondary BAs are detrimental for the intestinal barrier and increase the intestinal inflammatory response and dysbiosis. Additionally, a lack of BSH-active bacteria plays a role in intestinal inflammation and BA dysmetabolism. Thus, BSH-competent bacteria in probiotic formulations are being actively studied in IBD. At the same time, studies exploring the modulation of the master regulator of BA homeostasis, the Farnesoid X Receptor (FXR), in intestinal inflammation and how this impacts the GM are gaining significant momentum. Overall, the choice of probiotic supplementation should be a peculiar issue of personalized medicine, considering not only the disease but also the specific BA and metabolic signatures of a given patient.\n\nBile Salt Hydrolase-Competent Probiotics in the Management of IBD: Unlocking the \"Bile Acid Code\".", "token_count": 315, "char_count": 1278, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:50.573679", "source": { "split": "train_shard_00000", "doc_id": 1733 }, "chunk_id": "train_shard_00000_1733_0", "global_id": 1914 }, { "text": "Bile salts accumulating during cholestatic liver disease are believed to promote liver fibrosis. We have recently shown that chenodeoxycholate (CDC) induces expansion of hepatic stellate cells (HSCs) in vivo, thereby promoting liver fibrosis. Mechanisms underlying bile salt-induced fibrogenesis remain elusive. We aimed to characterize the effects of different bile salts on HSC biology and investigated underlying signaling pathways. Murine HSCs (mHSCs) were stimulated with hydrophilic and hydrophobic bile salts. Proliferation, cell mass, collagen deposition, and activation of signaling pathways were determined. Activation of the human HSC cell line LX 2 was assessed by quantification of α-smooth muscle actin (αSMA) expression. Phosphatidyl-inositol-3-kinase (PI3K)-dependent signaling was inhibited both pharmacologically and by siRNA. CDC, the most abundant bile salt accumulating in human cholestasis, but no other bile salt tested, induced Protein kinase B (PKB) phosphorylation and promoted HSC proliferation and subsequent collagen deposition. Pharmacological inhibition of the upstream target PI3K-inhibited activation of PKB and pro-fibrogenic proliferation of HSCs. The PI3K p110α-specific inhibitor Alpelisib and siRNA-mediated knockdown of p110α ameliorated pro-fibrogenic activation of mHSC and LX 2 cells, respectively. In summary, pro-fibrogenic signaling in mHSCs is selectively induced by CDC. PI3K p110α may be a potential therapeutic target for the inhibition of bile salt-induced fibrogenesis in cholestasis.\n\nHydrophobic Bile Salts Induce Pro-Fibrogenic Proliferation of Hepatic Stellate Cells through PI3K p110 Alpha Signaling.", "token_count": 476, "char_count": 1656, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [ "PI3K" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:51.218662", "source": { "split": "train_shard_00000", "doc_id": 1734 }, "chunk_id": "train_shard_00000_1734_0", "global_id": 1915 }, { "text": "Eighteen strains of lactic acid bacteria were isolated from spontaneously fermented sour porridge with broomcorn millet in Northwestern Shanxi Province of China, and their probiotic characteristics were investigated in vitro. Survival rates under gastrointestinal conditions, cholesterol reduction, antibacterial capabilities, antioxidant activities, and safety assessments were examined. Results showed that five strains were selected as probiotics and identified as\n\nFunctional Characteristics of Lactic Acid Bacteria In Vitro Isolated from Spontaneously Fermented Sour Porridge with Broomcorn Millet in Northwestern Shanxi Province of China.", "token_count": 149, "char_count": 644, "word_count": 81, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:51.656760", "source": { "split": "train_shard_00000", "doc_id": 1735 }, "chunk_id": "train_shard_00000_1735_0", "global_id": 1916 }, { "text": "The majority of Klebsiella pneumoniae (Kp) infections are nosocomial, but a growing number of community-acquired infections are caused by hypervirulent strains (hvKp) characterised by liver invasion and rapid metastasis. Unlike nosocomial Kp infections, hvKp are generally susceptible to antibiotics. Due to the rapid progression of hvKp infections, timely and accurate diagnosis is required for effective treatment. To identify potential drivers of the hypervirulent phenotype, we performed a genome-wide association study (GWAS) analysis on single nucleotide variants and accessory genome loci across 79 publicly available Kp isolates collected from patients' liver and a diverse global Kp dataset (n = 646). The GWAS analysis revealed 29 putative genes (P < 10\n\nGenomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains.", "token_count": 235, "char_count": 898, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7339, "quality_score": 0.8669, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:52.138871", "source": { "split": "train_shard_00000", "doc_id": 1736 }, "chunk_id": "train_shard_00000_1736_0", "global_id": 1917 }, { "text": "The non-conventional yeast Kluyveromyces marxianus is widely used for several biotechnological applications, mainly due to its thermotolerance, high growth rate, and ability to metabolise a wide range of sugars. These cell traits are strategic for lignocellulosic biomass valorisation and strain diversity prompts the development of robust chassis, either with improved tolerance to lignocellulosic inhibitors or ethanol. This review summarises bioethanol and value-added chemicals production by K. marxianus from different lignocellulosic biomasses. Moreover, metabolic engineering and process optimization strategies developed to expand K. marxianus potential are also compiled, as well as studies reporting cell mechanisms to cope with lignocellulosic-derived inhibitors. The main lignocellulosic-based products are bioethanol, representing 71% of the reports, and xylitol, representing 17% of the reports. K. marxianus also proved to be a good chassis for lactic acid and volatile compounds production from lignocellulosic biomass, although the literature on this matter is still scarce. The increasing advances in genome editing tools and process optimization strategies will widen the K. marxianus-based portfolio products.\n\nKluyveromyces marxianus as a microbial cell factory for lignocellulosic biomass valorisation.", "token_count": 327, "char_count": 1324, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:52.702590", "source": { "split": "train_shard_00000", "doc_id": 1737 }, "chunk_id": "train_shard_00000_1737_0", "global_id": 1918 }, { "text": "Avian pathogenic Escherichia coli (APEC) is recognized as a primary source of foodborne extraintestinal pathogenic E. coli (ExPEC), which poses a significant risk of extraintestinal infections in humans. The potential of human infection with ST117 lineage APEC/ExPEC from poultry is particularly concerning. However, relatively few whole-genome studies have focused on ST117 as an emerging ExPEC lineage. In this study, the complete genomes of 11 avian ST117 isolates and the draft genomes of 20 ST117 isolates in China were sequenced to reveal the genomic islands and large plasmid composition of ST117 APEC. With reference to the extensive E. coli genomes available in public databases, large-scale comprehensive genomic analysis of the ST117 lineage APEC/ExPEC was performed to reveal the features of the ST117 pan-genome and population. The high variability of the accessory genome emphasized the diversity and dynamic traits of the ST117 pan-genome. ST117 isolates recovered from different hosts and geographic sources were randomly located on a phylogeny tree, suggesting that ST117 E. coli lacked host specificity. A time-scaled phylogeny tree showed that ST117 was a recent E. coli lineage with a relatively short evolutionary period. Further characterization of a wide diversity of ExPEC-related virulence genes, pathogenicity islands (PAIs), and resistance genes of the ST117 pan-genome provided insights into the virulence and resistance of ST117 APEC/ExPEC. The results suggested zoonotic potential of ST117 APEC/ExPEC between birds and humans. Moreover, genomic analysis showed that a pool of diverse plasmids drove the virulence and multidrug resistance of ST117 APEC/ExPEC. Several types of large plasmids were scattered across the ST117 isolates, but there was no strong plasmid-clade adaptation", "token_count": 483, "char_count": 1811, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5551, "quality_score": 0.7776, "entities": { "genes": [ "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:53.354143", "source": { "split": "train_shard_00000", "doc_id": 1738 }, "chunk_id": "train_shard_00000_1738_0", "global_id": 1919 }, { "text": "Combined with the pan-genome analysis, a double polymerase chain reaction (PCR) method was designed for rapid and cost-effective detection of ST117 isolates from various avian and human APEC/ExPEC isolates. Overall, this study addressed a gap in current knowledge about the ST117 APEC/ExPEC genome, with significant implications to understand the success and spread of ST117 APEC/ExPEC.\n\nComplete genomic analysis of ST117 lineage extraintestinal pathogenic Escherichia coli (ExPEC) to reveal multiple genetic determinants to drive its global transmission: ST117 E. coli as an emerging multidrug-resistant foodborne ExPEC with zoonotic potential.", "token_count": 174, "char_count": 646, "word_count": 88, "semantic_coherence": 1, "information_density": 0.8068, "quality_score": 0.9034, "entities": { "genes": [ "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:53.797939", "source": { "split": "train_shard_00000", "doc_id": 1738 }, "chunk_id": "train_shard_00000_1738_1", "global_id": 1920 }, { "text": "The universal ancestor at the root of the species tree of life depicts a population of organisms with a surprising degree of complexity, posessing genomes and translation systems much like that of microbial life today. As the first life forms were most likely to have been simple replicators, considerable evolutionary change must have taken place prior to the last universal common ancestor. It is often assumed that the lack of earlier branches on the tree of life is due to a prevalence of random horizontal gene transfer that obscured the delineations between lineages and hindered their divergence. Therefore, principles of microbial evolution and ecology may give us some insight into these early stages in the history of life. Here, we synthesize the current understanding of organismal and genome evolution from the perspective of microbial ecology and apply these evolutionary principles to the earliest stages of life on Earth. We focus especially on broad evolutionary modes pertaining to horizontal gene transfer, pangenome structure, and microbial mat communities.\n\nVery early evolution from the perspective of microbial ecology.", "token_count": 234, "char_count": 1142, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6229, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:54.277357", "source": { "split": "train_shard_00000", "doc_id": 1739 }, "chunk_id": "train_shard_00000_1739_0", "global_id": 1921 }, { "text": "In this study, we describe a case report of gonococcal arthritis in a Systemic Lupus Erythematosus patient. Although several mechanisms favor disseminated gonococcal infection (DGI) in patients immunosuppressed by SLE, this association is rarely reported in literature. We performed whole genome sequencing (WGS) of the etiologic agent involved and molecular analysis using a global collection of Neisseria gonorrhoeae strains. Ours is the only sample derived from synovial fluid identified in this collection, the others being from the usual anatomical sites. Antimicrobial susceptibility was determined by disk diffusion and Etest, and WGS was conducted to determine multilocus sequence typing profiles, group isolates based on core genome single nucleotide polymorphisms (SNP), and identify virulence genes and antimicrobial resistance determinants. The N. gonorrhoeae samples in the global collection were highly heterogeneous. The SNP tree had a total 19,532 SNPs in 320 samples. Our sample displayed resistance to ciprofloxacin (MIC = 2 μg/mL) and tetracycline (zone diameter = 0 mm) belonged to ST 1588 and was not closely related to any isolate in the global collection of N. gonorrhoeae strains. The isolate had genetic features related to beta-lactam, tetracycline and quinolone resistance. Seventy-one virulence genes were identified in our sample, belonging to the following classes: adherence, efflux pump, immune modulator, invasion, iron uptake, protease and stress adaptation. Moreover, no virulence genes for immune evasion and toxin were identified.\n\nNeisseria gonorrhoeae arthritis in a patient with systemic lupus: resistance and virulence profiles.", "token_count": 446, "char_count": 1669, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:54.908830", "source": { "split": "train_shard_00000", "doc_id": 1740 }, "chunk_id": "train_shard_00000_1740_0", "global_id": 1922 }, { "text": "Cadmium (Cd) is a widely prevalent environmental pollutant that accumulates in the liver and induces liver injury. The mechanism of Cd-induced liver injury remains elusive. Our study aimed to clarify the mechanism by which changes in the gut microbiota contribute to Cd-induced liver injury. Here, a murine model of liver injury induced by chronic Cd exposure was used. Liver injury was assessed by biochemistry and histopathology. Expression profiles of genes involved in bile acid (BA) homeostasis, inflammation and injury were assessed via Realtime-PCR and Western-blot. 16S rRNA gene sequencing and mass spectrometry-based metabolomics were used to investigate changes in the gut microbiota and its metabolites in the regulation of Cd-induced liver injury. Here, we showed that Cd exposure induced hepatic ductular proliferation, hepatocellular damage and inflammatory infiltration in mice. Cd exposure induced gut microbiota dysbiosis and reduced the fecal bile salt hydrolase activity leading to an increase of tauro-β-muricholic acid levels in the intestine. Cd exposure decreased intestine FXR/FGF-15 signaling and promoted hepatic BA synthesis. Furthermore, the mice receiving fecal microbiota transplantation from Cd-treated mice showed reduced intestinal FXR/FGF-15 signaling, increased hepatic BA synthesis, and liver injury. However, the depletion of the commensal microbiota by antibiotics failed to change these indices in Cd-treated mice. Finally, the administration of the intestine-restricted FXR agonist fexaramine attenuated the liver injury, improved the intestinal barrier, and decreased hepatic BA synthesis in the Cd-treated mice. Our study identified a new mechanism of Cd-induced liver injury", "token_count": 449, "char_count": 1718, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5417, "quality_score": 0.7708, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:55.544998", "source": { "split": "train_shard_00000", "doc_id": 1741 }, "chunk_id": "train_shard_00000_1741_0", "global_id": 1923 }, { "text": "Cd-induced gut microbiota dysbiosis, decreased feces BSH activity, and increased intestinal T-βMCA levels led to an inhibition of intestinal FXR/FGF-15 signaling and an increase in hepatic BA synthesis, ultimately facilitating the development of hepatic ductular proliferation, inflammation, and injury in mice. This study expands our understanding of the health hazards caused by environmental Cd pollution.\n\nGut microbiota-bile acid-intestinal Farnesoid X receptor signaling axis orchestrates cadmium-induced liver injury.", "token_count": 144, "char_count": 524, "word_count": 67, "semantic_coherence": 1, "information_density": 0.8358, "quality_score": 0.9179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:55.973678", "source": { "split": "train_shard_00000", "doc_id": 1741 }, "chunk_id": "train_shard_00000_1741_1", "global_id": 1924 }, { "text": "The genus Herbaspirillum gained the spotlight due to the several reports of diazotrophic strains and promising results in plant-growth field assays. However, as diversity exploration of Herbaspirillum species gained momentum, it became clearer that the plant beneficial lifestyle was not the only form of ecological interaction in this genus, due to reports of phytopathogenesis and nosocomial infections. Here we performed a deep search across all publicly available Herbaspirillum genomes. Using a robust core genome phylogeny, we have found that all described species are well delineated, being the only exception H. aquaticum and H. huttiense clade. We also uncovered that the nif genes are only highly prevalent in H. rubrisubalbicans; however, irrespective to the species, all nif genes share the same gene arrangement with high protein identity, and are present in only two main types, in inverted strands. By means of a NifHDKENB phylogenetic tree, we have further revealed that the Herbaspirillum nif sequences may have been acquired from the same last common ancestor belonging to the Nitrosomonadales order.\n\nComparative Genomics Reveal the High Conservation and Scarce Distribution of Nitrogen Fixation nif Genes in the Plant-Associated Genus Herbaspirillum.", "token_count": 313, "char_count": 1270, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:56.528072", "source": { "split": "train_shard_00000", "doc_id": 1742 }, "chunk_id": "train_shard_00000_1742_0", "global_id": 1925 }, { "text": "Streptococcus dysgalactiae (SD) is capable of infecting both humans and animals and causing a wide range of invasive and non-invasive infections. With two subspecies, the taxonomic status of subspecies of SD remains controversial. Subspecies\n\nPhylogenetic analysis and accessory genome diversity reveal insight into the evolutionary history of", "token_count": 84, "char_count": 343, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:56.896989", "source": { "split": "train_shard_00000", "doc_id": 1743 }, "chunk_id": "train_shard_00000_1743_0", "global_id": 1926 }, { "text": "Porcine rotavirus (PoRV) is an important pathogen, leading to the occurrence of viral diarrhoea . As the infection displays obvious enterotropism, intestinal mucosal immunity is the significant line of defence against pathogen invasion. Moreover, as lactic acid bacteria (LAB) show acid resistance, bile salt resistance and immune regulation, it is of great significance to develop an oral vaccine. Most traditional plasmid delivery vectors use antibiotic genes as selective markers, easily leading to antibiotic accumulation. Therefore, to select a food-grade marker in genetically engineering food-grade microorganisms is vital. Based on the CRISPR-Cas9D10A system, we constructed a stable auxotrophic\n\nEvaluation of the immunogenicity of auxotrophic", "token_count": 182, "char_count": 752, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7767, "quality_score": 0.8883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:57.347530", "source": { "split": "train_shard_00000", "doc_id": 1744 }, "chunk_id": "train_shard_00000_1744_0", "global_id": 1927 }, { "text": "Bacterial extracellular vesicles (BEVs) released from both Gram-negative and Gram-positive bacteria provide an effective means of communication and trafficking of cell signaling molecules. In the gastrointestinal tract (GIT) BEVs produced by members of the intestinal microbiota can impact host health by mediating microbe-host cell interactions. A major unresolved question, however, is what factors influence the composition of BEV proteins and whether the host influences protein packaging into BEVs and secretion into the GIT. To address this, we have analyzed the proteome of BEVs produced by the major human gut symbiont Bacteroides thetaiotaomicron both\n\nThe Proteome of Extracellular Vesicles Produced by the Human Gut Bacteria Bacteroides thetaiotaomicron", "token_count": 190, "char_count": 764, "word_count": 106, "semantic_coherence": 1, "information_density": 0.6604, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:57.787881", "source": { "split": "train_shard_00000", "doc_id": 1745 }, "chunk_id": "train_shard_00000_1745_0", "global_id": 1928 }, { "text": "The discovery that biomechanical forces regulate microbial virulence was established with the finding that physiological low fluid shear (LFS) forces altered gene expression, stress responses, and virulence of the enteric pathogen Salmonella enterica serovar Typhimurium during the log phase. These log phase LFS-induced phenotypes were independent of the master stress response regulator, RpoS (σ\n\nRole of RpoS in Regulating Stationary Phase Salmonella Typhimurium Pathogenesis-Related Stress Responses under Physiological Low Fluid Shear Force Conditions.", "token_count": 140, "char_count": 557, "word_count": 73, "semantic_coherence": 1, "information_density": 0.726, "quality_score": 0.863, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:58.217892", "source": { "split": "train_shard_00000", "doc_id": 1746 }, "chunk_id": "train_shard_00000_1746_0", "global_id": 1929 }, { "text": "Microbial strains of variable functional capacities coexist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data. Here we present\n\nStrainPanDA: Linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data.", "token_count": 77, "char_count": 388, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:58.586009", "source": { "split": "train_shard_00000", "doc_id": 1747 }, "chunk_id": "train_shard_00000_1747_0", "global_id": 1930 }, { "text": "Fusobacterium necrophorum causes a range of mild to life threatening infections and there is uncertainty in terms of diagnosis and treatment due to the lack of knowledge on their pathogenic mechanisms. This study characterised genomes of F. necrophorum to compare their virulence factors and investigate potential infection markers. 27 isolates of F. necrophorum from patients with pharyngotonsillitis were subjected to whole genome sequencing and compared with 42 genomes published in the NCBI database. Phylogenomics, pangemome, pan-GWAS and virulome were analysed to study strain variations with reference to virulence factors. Core genome based phylogenomic tree exhibited three clades of which Clade A belonged to F. necrophorum subsp necrophorum, clades B and C were F. necrophorum subsp funduliforme. Pan-GWAS and Pan-Virulome suggest some marker genes associated with clinical sources of isolation that needs further validation. Our study highlights some interesting features of the pathogenesis of F. necrophorum infections. Although the animal isolate genomes had some marker genes, the genomes of human isolates did not exhibit clear correlation to their clinical sources of isolation. This prompts to think of other mechanisms such as co-infections or host factors that can be involved in the pathogenesis.\n\nA genome-led study on the pathogenesis of Fusobacterium necrophorum infections.", "token_count": 337, "char_count": 1399, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:59.156248", "source": { "split": "train_shard_00000", "doc_id": 1748 }, "chunk_id": "train_shard_00000_1748_0", "global_id": 1931 }, { "text": "Probiotics encounter various stresses during food processing and digestion. This study evaluated the differential proteomic responses of a newly identified potential probiotic lactic acid bacteria, Lactococcus garvieae, isolated from camel milk. Lc. garvieae C47 was exposed to heat, cold, acid, and bile conditions, and stress-responsive proteins were identified. The proteomic analysis was done using 2D-IEF SDS PAGE and nano-LC-MS/MS. Out of 91 differentially expressed proteins, 20 upregulated and 27 downregulated proteins were shared among the stresses. The multivariate data analysis revealed abundance of elongation factor Ts (spot C42), uridine phosphorylase, fructose-bisphosphate aldolase, peptidase T, cobalt ECF transporter T component CbiQ, UDP-N-acetylmuramate-l-alanine ligase, uncharacterized protein, aspartokinase, chaperone protein DnaK, IGP synthase cyclase subunit, probable nicotinate-nucleotide adenylyltransferase, NADH-quinone oxidoreductase, holo-[acyl-carrier-protein] synthase, l-lactate dehydrogenase, and uncharacterized protein. The maximum number of differentially expressed proteins belonged to carbohydrate and protein metabolism, which indicates Lc. garvieae shifts towards growth and energy metabolism for resistance against stress conditions.\n\nHeat, cold, acid, and bile salt induced differential proteomic responses of a novel potential probiotic Lactococcus garvieae C47 isolated from camel milk.", "token_count": 408, "char_count": 1436, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7356, "quality_score": 0.8678, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:15:59.771086", "source": { "split": "train_shard_00000", "doc_id": 1749 }, "chunk_id": "train_shard_00000_1749_0", "global_id": 1932 }, { "text": "Silybin, an active component in the plant Silybum marianum (L.) Gaertn., is commonly used to protect against liver disease. We investigated silybin's protective potential in rat liver against emodin-induced liver injury 4 weeks. It was found that aspartate aminotransferase and direct bilirubin serum biomarkers for liver toxicity significantly increased, and liver histopathology revealed cholestasis and necrosis in rats administered emodin alone, whereas aspartate aminotransferase and total bile acid levels in rats administered emodin and silybin simultaneously were changed compared to rats administered emodin alone. Liver mRNA and protein levels of Cyp7a1-which plays roles in cholesterol metabolism and bile acid synthesis-and Abcb11 (Bsep)-which facilitates bile salt secretion in hepatocyte canaliculi-were significantly altered with emodin, whereas cotreatment with silybin attenuated emodin's adverse effect. Metabolomic analysis using ultra-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry determined eight potential metabolite biomarkers in serum, urine, and liver tissue. Network analysis was conducted to conceptualize the interplay of genes, metabolites, and metabolic pathways for cholesterol metabolism and bile acid synthesis for liver injury. Overall, rats administered only emodin were shown to be a sound model to investigate fat-associated drug-induced hepatoxicity or liver injury and cotreatment of emodin with silybin prevents fatty liver injury. This metabolomic study revealed that emodin-induced fatty liver injury disrupted bile acid synthesis, vitamin B\n\nMetabolic profiling of emodin drug-induced liver injury and silybin treatment in rats using ultra-performance liquid chromatography-quadrupole-time-of-flight-mass spectrometry: A metabolomic and mechanistic approach.", "token_count": 477, "char_count": 1833, "word_count": 230, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:00.415159", "source": { "split": "train_shard_00000", "doc_id": 1750 }, "chunk_id": "train_shard_00000_1750_0", "global_id": 1933 }, { "text": "Metformin has been shown to repress transcription of the bile salt export pump (BSEP) in human primary hepatocytes. The primary objective of this study was to assess the effect of oral metformin on the human pharmacokinetics (PKs) of two BSEP probe substrates: pravastatin and chenodeoxycholic acid (CDCA; also known as chenodiol). Endogenous bile acid levels were assessed as a secondary measure of metformin impact. An open-label, randomized, single-dose, placebo-controlled, fasted, crossover PK study was conducted in 12 healthy adult volunteers. Metformin (500 mg b.i.d.) or placebo (b.i.d.) was administered orally for 6 days. On day 7, a single dose of the BSEP substrates pravastatin (80 mg) and CDCA (250 mg) were administered orally. Plasma samples were quantified for pravastatin, CDCA, and endogenous bile acids. Compared to placebo, metformin increased pravastatin plasma exposure, did not impact CDCA plasma exposure, and reduced conjugated primary bile acid levels in the blood. These results are consistent with metformin repressing BSEP expression. This differential effect reflects the degree of enterohepatic recirculation of victim substrates.\n\nDifferential effects of metformin-mediated BSEP repression on pravastatin and bile acid pharmacokinetics in humans: A randomized controlled trial.", "token_count": 376, "char_count": 1311, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:01.409484", "source": { "split": "train_shard_00000", "doc_id": 1751 }, "chunk_id": "train_shard_00000_1751_0", "global_id": 1934 }, { "text": "Globally dominant marine bacterioplankton lineages are often limited in metabolic versatility, owing to their extensive genome reductions, and thus cannot take advantage of transient nutrient patches. It is therefore perplexing how the nutrient-poor bulk seawater sustains the pelagic streamlined lineages, each containing numerous populations. Here, we sequenced the genomes of 33 isolates of the recently discovered CHUG lineage (~2.6 Mbp), which have some of the smallest genomes in the globally abundant Roseobacter group (commonly over 4 Mbp). These genome-reduced bacteria were isolated from a transient habitat: seawater surrounding the brown alga, Sargassum hemiphyllum. Population genomic analyses showed that: (i) these isolates, despite sharing identical 16S rRNA genes, were differentiated into several genetically isolated populations through successive speciation events; (ii) only the first speciation event led to the genetic separation of both core and accessory genomes; and (iii) populations resulting from this event are differentiated at many loci involved in carbon utilization and oxygen respiration, corroborated by BiOLOG phenotype microarray assays and oxygen uptake kinetics experiments, respectively. These differentiated traits match well with the dynamic nature of the macroalgal seawater, in which the quantity and quality of carbon sources and the concentration of oxygen likely vary spatially and temporally, though other habitats, like fresh organic aggregates, cannot be ruled out. Our study implies that transient habitats in the overall nutrient-poor ocean can shape the microdiversity and population structure of genome-reduced bacterioplankton lineages.\n\nCoastal Transient Niches Shape the Microdiversity Pattern of a Bacterioplankton Population with Reduced Genomes.", "token_count": 420, "char_count": 1806, "word_count": 245, "semantic_coherence": 1, "information_density": 0.7184, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:02.061830", "source": { "split": "train_shard_00000", "doc_id": 1752 }, "chunk_id": "train_shard_00000_1752_0", "global_id": 1935 }, { "text": "Milk kefir is a fermented dairy product with numerous attributed health benefits due to the presence of a complex eukaryotic and prokaryotic microbiota. In this study, a total number of 26 yeast isolates were obtained from eight kefir samples from three different cities of Iran. The isolates belonged to Kluyveromyces marxianus, Saccharomyces cerevisiae, Pichia fermentans and P. kudriavzevii. The potential probiotic characteristics of the isolates were evaluated based on their ability to tolerate the stimulated condition of the gastrointestinal tract. In addition, hemolytic activity, adherence to different solvents, auto-aggregation, adhesion to the epithelial intestine-derived cells and antimicrobial activity of the selected isolates were evaluated. Overall, four yeast strains (three strains of S. cerevisiae and one strain of P. fermentans) showed resistance and survival ability against the gastrointestinal physiological conditions including acidic pH, presence of bile salt and digestive enzymes. They were able to grow at 37°C and had the capacity to adhere to epithelial intestine-derived cells. These results suggest that the selected strains can be proper candidates as probiotic yeast strains for the development of novel functional foods.\n\nYeasts from Iranian traditional milk kefir samples: isolation, molecular identification and their potential probiotic properties.", "token_count": 343, "char_count": 1390, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:02.680036", "source": { "split": "train_shard_00000", "doc_id": 1753 }, "chunk_id": "train_shard_00000_1753_0", "global_id": 1936 }, { "text": "Ralstonia pseudosolanacearum causes bacterial wilt in ginger, reducing ginger production worldwide. We sequenced the whole genome of a highly virulent phylotype I, race 4, biovar 3 Ralstonia pseudosolanacearum strain GRsMep isolated from a severely infected ginger field in India. R. pseudosolanacearum GRsMep genome is organised into two replicons: chromosome and megaplasmid with a total genome size of 5,810,605 bp. This strain encodes approximately 72 effectors which include a combination of core effectors as well as highly variable, diverse repertoire of type III effectors. Comparative genome analysis with GMI1000 identified conservation in the genes involved in the general virulence mechanism. Our analysis identified type III effectors, RipBJ and RipBO as present in GRsMep but absent in the reported genomes of other strains infecting Zingiberaceae family. GRsMep contains 126 unique genes when compared to the pangenome of the Ralstonia strains that infect the Zingiberaceae family. The whole-genome data of R. pseudosolanacearum strain will serve as a resource for exploring the evolutionary processes that structure and regulate the virulence determinants of the strain. Pathogenicity testing of the transposon insertional mutant library of GRsMep through virulence assay on ginger plants identified a few candidate virulence determinants specific to bacterial wilt in ginger.\n\nGenome-wide identification of type III effectors and other virulence factors in Ralstonia pseudosolanacearum causing bacterial wilt in ginger (Zingiber officinale).", "token_count": 403, "char_count": 1558, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8005, "entities": { "genes": [ "GMI1000" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:03.300151", "source": { "split": "train_shard_00000", "doc_id": 1754 }, "chunk_id": "train_shard_00000_1754_0", "global_id": 1937 }, { "text": "Key genes controlling flowering and interactions of different photoperiod alleles with various environments were identified in a barley MAGIC population. A new candidate gene for vernalisation requirements was also detected. Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions.\n\nMulti-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population.", "token_count": 476, "char_count": 2371, "word_count": 318, "semantic_coherence": 1, "information_density": 0.6132, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:03.945068", "source": { "split": "train_shard_00000", "doc_id": 1755 }, "chunk_id": "train_shard_00000_1755_0", "global_id": 1938 }, { "text": "In this study, moxifloxacin (MX)-loaded bilosome (BS) in situ gel was prepared to improve ocular residence time. MX-BSs were prepared using the thin-film hydration method. They were optimized using a Box−Behnken design (BBD) with bile salt (A, sodium deoxycholate), an edge activator (B, Cremophor EL), and a surfactant (C, Span 60) as process variables. Their effects were assessed based on hydrodynamic diameter (Y1), entrapment efficacy (Y2), and polydispersity index (Y3). The optimized formulation (MX-BSop) depicted a low hydrodynamic diameter (192 ± 4 nm) and high entrapment efficiency (76 ± 1%). Further, MX-BSop was successfully transformed into an in situ gel using chitosan and sodium alginate as carriers. The optimized MX-BSop in situ gel (MX-BSop-Ig4) was further evaluated for gelling capacity, clarity, pH, viscosity, in vitro release, bio-adhesiveness, ex vivo permeation, toxicity, and antimicrobial properties. MX-BSop-Ig4 exhibited an optimum viscosity of 65.4 ± 5.3 cps in sol and 287.5 ± 10.5 cps in gel states. The sustained release profile (82 ± 4% in 24 h) was achieved with a Korsmeyer−Peppas kinetic release model (R2 = 0.9466). Significant bio-adhesion (967.9 dyne/cm2) was achieved in tear film. It also exhibited 1.2-fold and 2.8-fold higher permeation than MX-Ig and a pure MX solution, respectively. It did not show any toxicity to the tested tissue, confirmed by corneal hydration (77.3%), cornea histopathology (no internal changes), and a HET-CAM test (zero score)", "token_count": 489, "char_count": 1500, "word_count": 226, "semantic_coherence": 1, "information_density": 0.7301, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:04.603291", "source": { "split": "train_shard_00000", "doc_id": 1756 }, "chunk_id": "train_shard_00000_1756_0", "global_id": 1939 }, { "text": "MX-BSop-Ig4 exhibited a significantly (p < 0.05) higher antimicrobial effect than pure MX against Staphylococcus aureus and Escherichia coli. The findings suggest that bilosome in situ gel is a good alternative to increase corneal residence time, as well as to improve therapeutic activity.\n\nFormulation and Evaluation of Moxifloxacin Loaded Bilosomes In-Situ Gel: Optimization to Antibacterial Evaluation.", "token_count": 120, "char_count": 406, "word_count": 56, "semantic_coherence": 1, "information_density": 0.9107, "quality_score": 0.9554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:04.984426", "source": { "split": "train_shard_00000", "doc_id": 1756 }, "chunk_id": "train_shard_00000_1756_1", "global_id": 1940 }, { "text": "Bile acids (BA) fulfill a wide range of physiological functions, but are also involved in pathologies, such as cholestasis. Cholestasis is characterized by an intrahepatic accumulation of BAs and subsequent spillage to the systemic circulation. The aim of the present study was to develop physiologically based kinetic (PBK) models that would provide a tool to predict dose-dependent BA accumulation in humans upon treatment with a Bile Salt Export Pump (BSEP) inhibitor. We developed a PBK model describing the BA homeostasis using glycochenodeoxycholic acid as an exemplary BA. Population wide distributions of BSEP abundances were incorporated in the PBK model using Markov Chain Monte Carlo simulations, and alternatively the total amount of BAs was scaled empirically to describe interindividual differences in plasma BA levels. Next, the effects of the BSEP inhibitor bosentan on the BA levels were simulated. The PBK model developed adequately predicted the in vivo BA dynamics. Both the Markov Chain Monte Carlo simulations based on a distribution of BSEP abundances and empirical scaling of the total BA pool readily described the variations within and between data in human volunteers. Bosentan treatment disproportionally increased the maximum BA concentration in individuals with a large total BA pool or low BSEP abundance. Especially individuals having a large total BA pool size and a low BSEP abundance were predicted to be at risk for rapid saturation of BSEP and subsequent intrahepatic BA accumulation. This model provides a first estimate of personalized safe therapeutic external dose levels of compounds with BSEP-inhibitory properties.\n\nPopulation pharmacokinetic model to generate mechanistic insights in bile acid homeostasis and drug-induced cholestasis.", "token_count": 408, "char_count": 1780, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5856, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:05.610429", "source": { "split": "train_shard_00000", "doc_id": 1757 }, "chunk_id": "train_shard_00000_1757_0", "global_id": 1941 }, { "text": "Staphylococcus capitis, which causes bloodstream infections in neonatal intensive care units, is a common cause of healthcare-associated infections. Thus, a standardized high-resolution typing method to document the transmission and dissemination of multidrug-resistant S. capitis isolates is required. We aimed to establish a core genome multilocus sequence typing (cgMLST) scheme to surveil S. capitis. The cgMLST scheme was defined based on primary and validation genome sets and tested with outbreaks of linezolid-resistant isolates and a validation set. Phylogenetic analysis was performed to investigate the population structure and compare it with the result of cgMLST analysis. The S. capitis population consists of 1 dominant, NRCS-A, and 4 less common clones. In this work, a multidrug-resistant clone (L clone) with linezolid resistance is identified. With the features of type III SCCmec and multiple copies of mutations of G2576T and C2104T in the 23S rRNA, the L clone has been spreading silently across China.\n\nDevelopment of a novel core genome MLST scheme for tracing multidrug resistant Staphylococcus capitis.", "token_count": 290, "char_count": 1128, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:06.171187", "source": { "split": "train_shard_00000", "doc_id": 1758 }, "chunk_id": "train_shard_00000_1758_0", "global_id": 1942 }, { "text": "Bacillus licheniformis is a well-known probiotic that can be found in a variety of foods. The strain Bacillus licheniformis MCC 2514 was previously characterized by our group for its bio-physiological capabilities establishing it as a promising probiotic, but information on the genetic evidence for its attributes was lacking. In the current study, whole genome analysis identified the underlying molecular determinants responsible for its probiotic potential. The circular genome of MCC 2514 was 4,230,480 bp with 46.2% GC content, 24 rRNA, and 83 tRNA genes. The pangenome analysis between B. licheniformis MCC 2514 and 12 other B. licheniformis strains revealed a pangenome of 6008 genes and core genome of 3775 genes. Genome mining revealed NRPS and bacteriocins producing gene clusters indicating its biocontrol properties. Several genes encoding carbohydrate degrading enzymes, which aid in proper food degradation in the intestine, were also observed. Stress tolerance, vitamin, and essential amino acids biosynthesis related genes were found, which are important characteristics of a probiotic strain. Additionally, vital genes responsible for gut adhesion and biofilm formation were observed in its genome. The bacterium has been shown to improve the shelf life of idli batter by preventing whey separation, CO\n\nBacillus licheniformis MCC 2514 genome sequencing and functional annotation for providing genetic evidence for probiotic gut adhesion properties and its applicability as a bio-preservative agent.", "token_count": 391, "char_count": 1517, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:06.790186", "source": { "split": "train_shard_00000", "doc_id": 1759 }, "chunk_id": "train_shard_00000_1759_0", "global_id": 1943 }, { "text": "Limosilactobacillus fermentum KUB-D18 is a heterofermentative lactic acid bacterium that its potential probiotic relevance originally isolated from the chicken intestine. This study sequenced a whole-genome of L. fermentum KUB-D18 and annotated its genes and functions in relation to probiotic properties. As a result, the genome sequence of L. fermentum KUB-D18 approximately contained 2.02 Mbps with GC content of51.7%. After annotating the genome by integrated protein and pathway databases, 2,158 protein-encoding genes were majorly annotated for metabolisms of amino acids, carbohydrates and cofactors as well as vitamins which showed a versatile metabolic capability to gastrointestinal microhabitats. According to the comparative genome analysis of L. fermentum KUB-D18 and the other related strains, L. fermentum KUB-D18 showed common characteristics e.g., folate biosynthesis and bile salt hydrolase enzymes-related cholesterol lowering effect as well as a unique gene cluster involved in metabolism of l-ascorbic acid of L. fermentum KUB-D18. Taken together, L. fermentum KUB-D18 genome provides the genetic basis towards cellular capability for further elucidating the functional mechanisms of its probiotic properties. This study serves for designing desirable targets for the development of probiotic foods and feeds.\n\nComparative genomics-based probiotic relevance of Limosilactobacillus fermentum KUB-D18.", "token_count": 395, "char_count": 1420, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6105, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:07.405553", "source": { "split": "train_shard_00000", "doc_id": 1760 }, "chunk_id": "train_shard_00000_1760_0", "global_id": 1944 }, { "text": "Yersinia pseudotuberculosis is an enteric pathogen causing mild enteritis that can lead to mesenteric adenitis in children and septicemia in elderly patients. Most cases are sporadic, but outbreaks have already been described in different countries. We report for the first time a Y. pseudotuberculosis clonal outbreak in France, that occurred in 2020. An epidemiological investigation based on food queries pointed toward the consumption of tomatoes as the suspected source of infection. The\n\nFirst Description of a Yersinia pseudotuberculosis Clonal Outbreak in France, Confirmed Using a New Core Genome Multilocus Sequence Typing Method.", "token_count": 151, "char_count": 640, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7717, "quality_score": 0.8859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:07.846809", "source": { "split": "train_shard_00000", "doc_id": 1761 }, "chunk_id": "train_shard_00000_1761_0", "global_id": 1945 }, { "text": "Klebsiella pneumoniae is an opportunistic Gram-negative bacterium that has become a leading causative agent of nosocomial infections, mainly infecting patients with immunosuppressive diseases. Capsular (K) serotypes K1, K2, K47, and K64 are commonly associated with higher virulence (hypervirulent Klebsiella pneumoniae), and more threateningly, isolates belonging to the last two K serotypes are also frequently associated with resistance to carbapenem (hypervirulent carbapenem-resistant Klebsiella pneumoniae). The prevalence of these isolates has posed significant threats to human health, and there are no appropriate therapies available against them. Therefore, in this study, a method combining immunoinformatics and pangenome analysis was applied for contriving a multiepitope subunit vaccine against these four threatening serotypes. To obtain cross-protection, 12 predicted conserved antigens were screened from the core genome of 274 complete Klebsiella pneumoniae genomes (KL1, KL2, KL47, and KL64), from which the epitopes of T and B cells were extracted for vaccine construction. In addition, the immunological properties, the interaction with Toll-like receptors, and the stability in a simulative humoral environment were evaluated by immunoinformatics methods, molecular docking, and molecular dynamics simulation. All of these evaluations indicated the potency of this constructed vaccine to be an effective therapeutic agent. Lastly, the cDNA of the designed vaccine was optimized and ligated to pET-28a(+) for expression vector construction. Overall, our research provides a newly cross-protective control strategy against these troublesome pathogens and paves the way for the development of a safe and effective vaccine.\n\nCombing Immunoinformatics with Pangenome Analysis To Design a Multiepitope Subunit Vaccine against Klebsiella pneumoniae K1, K2, K47, and K64.", "token_count": 469, "char_count": 1885, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8209, "entities": { "genes": [ "KL1", "KL2", "KL64", "KL47" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:08.488125", "source": { "split": "train_shard_00000", "doc_id": 1762 }, "chunk_id": "train_shard_00000_1762_0", "global_id": 1946 }, { "text": "We present the demographic features of invasive meningococcal disease (IMD) in Taiwan between 1993 and 2020 and the genetic characteristics of Neisseria meningitidis isolates recovered from 2003 to 2020. IMD was rare in Taiwan between 1993 and 2020, with an annual incidence ranging from 0.009 to 0.204 per 100,000 people. The case fatality rate (CFR) declined from 18.1% for patients in 1993 to 2002 to 9.8% in 2003 to 2020. Infants less than 12 months were most susceptible to the disease. N. meningitidis serogroup B (NmB) was most predominant, responsible for 81.2% (134/165) of the IMD cases in 2003 to 2020. The majority of the isolates recovered from 2003 to 2020 belonged to 4 worldwide-spread hyperinvasive clonal complexes (cc), cc4821 (30.3%), cc32 (19.4%), cc41/44 (12.7%), cc23 (7.3%), and also a newly assigned clonal complex, cc3439 (10.3%). Core genome multilocus sequence typing (cgMLST) profile comparisons revealed that the cc4821 isolates with a T-to-I substitution at position 91 in\n\nDemographic Features of Invasive Meningococcal Disease in Taiwan, 1993 to 2020, and Genetic Characteristics of Neisseria meningitidis Isolates, 2003 to 2020.", "token_count": 445, "char_count": 1162, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6067, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:09.115540", "source": { "split": "train_shard_00000", "doc_id": 1763 }, "chunk_id": "train_shard_00000_1763_0", "global_id": 1947 }, { "text": "Staphylococcus aureus is a major human and animal pathogen, colonizing diverse ecological niches within its hosts. Predicting whether an isolate will infect a specific host and its subsequent clinical fate remains unknown. In this study, we investigated the S. aureus pangenome using a curated set of 356 strains, spanning a wide range of hosts, origins, and clinical display and antibiotic resistance profiles. We used genome-wide association study (GWAS) and random forest (RF) algorithms to discriminate strains based on their origins and clinical sources. Here, we show that the presence of\n\nForecasting Staphylococcus aureus Infections Using Genome-Wide Association Studies, Machine Learning, and Transcriptomic Approaches.", "token_count": 173, "char_count": 728, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7767, "quality_score": 0.8883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:09.557316", "source": { "split": "train_shard_00000", "doc_id": 1764 }, "chunk_id": "train_shard_00000_1764_0", "global_id": 1948 }, { "text": "Whole-genome sequencing (WGS) is rapidly replacing traditional typing methods for the investigation of infectious disease outbreaks. Additionally, WGS data are being used to predict phenotypic antimicrobial susceptibility. Acinetobacter baumannii, which is often multidrug-resistant, is a significant culprit in outbreaks in health care settings. A well-characterized collection of A. baumannii was studied using core genome multilocus sequence typing (cgMLST). Seventy-two isolates previously typed by PCR-electrospray ionization mass spectrometry (PCR/ESI-MS) provided by the Antimicrobial Resistance Leadership Group (ARLG) were analyzed using a clinical microbiology laboratory developed workflow for cgMLST with genomic susceptibility prediction performed using the ARESdb platform. Previously performed PCR/ESI-MS correlated with cgMLST using relatedness thresholds of allelic differences of ≤9 and ≤200 allelic differences in 78 and 94% of isolates, respectively. Categorical agreement between genotypic and phenotypic antimicrobial susceptibility across a panel of 11 commonly used drugs was 89%, with minor, major, and very major error rates of 8%, 11%, and 1%, respectively.\n\nAcinetobacter baumannii Genomic Sequence-Based Core Genome Multilocus Sequence Typing Using Ridom SeqSphere+ and Antimicrobial Susceptibility Prediction in ARESdb.", "token_count": 357, "char_count": 1349, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6901, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:10.134579", "source": { "split": "train_shard_00000", "doc_id": 1765 }, "chunk_id": "train_shard_00000_1765_0", "global_id": 1949 }, { "text": "The ever-increasing number of sequenced genomes necessitates the development of pangenomic approaches for comparative genomics. Introduced in 2016, PanTools is a platform that allows pangenome construction, homology grouping and pangenomic read mapping. The use of graph database technology makes PanTools versatile, applicable from small viral genomes like SARS-CoV-2 up to large plant or animal genomes like tomato or human. Here, we present our third major update to PanTools that enables the integration of functional annotations and provides both gene-level analyses and phylogenetics.\n\nPanTools v3: functional annotation, classification and phylogenomics.", "token_count": 157, "char_count": 661, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7753, "quality_score": 0.8876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:10.575570", "source": { "split": "train_shard_00000", "doc_id": 1766 }, "chunk_id": "train_shard_00000_1766_0", "global_id": 1950 }, { "text": "Brucellosis poses a significant burden to human and animal health worldwide. Robust and harmonized molecular epidemiological approaches and population studies that include routine disease screening are needed to efficiently track the origin and spread of Brucella strains. Core genome multilocus sequence typing (cgMLST) is a powerful genotyping system commonly used to delineate pathogen transmission routes for disease surveillance and control. Except for Brucella melitensis, cgMLST schemes for Brucella species are currently not established. Here, we describe a novel cgMLST scheme that covers multiple Brucella species. We first determined the phylogenetic breadth of the genus using 612 Brucella genomes. We selected 1,764 genes that were particularly well conserved and typeable in at least 98% of these genomes. We tested the new scheme on 600 genomes and found high agreement with the whole-genome-based single nucleotide polymorphism (SNP) analysis. Next, we applied the scheme to reanalyze the genome of Brucella strains from epidemiologically linked outbreaks. We demonstrated the applicability of the new scheme for high-resolution typing required in outbreak investigations as previously reported with whole-genome SNP methods. We also used the novel scheme to define the global population structure of the genus using 1,322 Brucella genomes. Finally, we demonstrated the possibility of tracing distribution of Brucella strains by performing cluster analysis of cgMLST profiles and found nearly identical cgMLST profiles in different countries. Our results show that sequencing depth of more than 40-fold is optimal for allele calling with this scheme. In summary, this study describes a novel Brucella-wide cgMLST scheme that is applicable in Brucella molecular epidemiology and helps in accurately tracking and thus controlling the sources of infection. The scheme is publicly accessible and should represent a valuable resource for laboratories with limited computational resources and bioinformatics expertise.\n\nCore Genome Multilocus Sequence Typing Scheme for Improved Characterization and Epidemiological Surveillance of Pathogenic Brucella.", "token_count": 476, "char_count": 2162, "word_count": 302, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:11.216818", "source": { "split": "train_shard_00000", "doc_id": 1767 }, "chunk_id": "train_shard_00000_1767_0", "global_id": 1951 }, { "text": "The goal of this study is to improve the adhesion and survival of yogurt bacteria with probiotic traits by using polysorbate 80, a food additive emulsifier commonly found in milk derivative products. Polysorbate 80 was used at 1% (w/v), and its effects on yogurt bacteria's survival under simulated digestive conditions, cholesterol uptake activities, bile salt hydrolase (BSH) activity, and adhesion to HT-29 culture were studied. In the presence of 1% polysorbate 80, both starters demonstrated better cholesterol uptake and BSH activities, as well as higher bacterial survival at pH 2.5, particularly in associated cultures. In the presence of 0.3 % bile or cholic acid, polysorbate 80 reduced the drop in\n\nPolysorbate 80 improves the adhesion and survival of yogurt starters with cholesterol uptake abilities.", "token_count": 230, "char_count": 813, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:11.688960", "source": { "split": "train_shard_00000", "doc_id": 1768 }, "chunk_id": "train_shard_00000_1768_0", "global_id": 1952 }, { "text": "Metagenomic sequencing data provide a rich resource from which to expand our understanding of differential protein functions involved in human health. Here, we outline a pipeline that combines microbial whole genome sequencing with protein structure data to yield a structural metagenomics-informed atlas of microbial enzyme families of interest. Visualizing metagenomics data through a structural lens facilitates downstream studies including targeted inhibition and probe-based proteomics to define at the molecular level how different enzyme orthologs impact in vivo function. Application of this pipeline to gut microbial enzymes like glucuronidases, TMA lyases, and bile salt hydrolases is expected to pinpoint their involvement in health and disease and may aid in the development of therapeutics that target specific enzymes within the microbiome.\n\nA structural metagenomics pipeline for examining the gut microbiome.", "token_count": 202, "char_count": 924, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7109, "quality_score": 0.8555, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:12.153621", "source": { "split": "train_shard_00000", "doc_id": 1769 }, "chunk_id": "train_shard_00000_1769_0", "global_id": 1953 }, { "text": "Studies on the control of lipid digestion by food-derived active substances have prioritized the direct inhibition of lipase, ignoring the influence of these substances on the stability of bile salt (BS)-stabilized oil emulsions, which are essential for the hydrolysis of triglycerides by lipase. This study aimed to demonstrate the inhibitory potential of oat peptides (OPs) on lipolysis due to lipase inhibition, in particular, the physicochemical destruction of BS-stabilized emulsions. OPs were characterized by an enterostatin-like X-Pro-Y-Pro-Arg terminal sequence, competitively and/or noncompetitively inhibited lipase, and even caused lipase conformational changes. Interestingly, OPs destabilized BS-stabilized emulsions by weakening the rheological cross-linking structure of the emulsions through competitive hydrophobic binding to BS. Further analysis revealed that the H-bond binding of OP to BS significantly destroyed the hydrophilic and lipophilic balance of BS by increasing the surface hydrophobicity. These findings provided novel insights into the action mechanism of bioactive peptides on lipid digestion.\n\nInhibitory effects of oat peptides on lipolysis: A physicochemical perspective.", "token_count": 297, "char_count": 1208, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6855, "quality_score": 0.8428, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:12.715495", "source": { "split": "train_shard_00000", "doc_id": 1770 }, "chunk_id": "train_shard_00000_1770_0", "global_id": 1954 }, { "text": "Abnormal cervicovaginal microbiota play an important role in HPV persistence and progression to cervical cancer. The present study aimed at isolating and identifying potential probiotics from vaginal swabs of healthy women and evaluating their activity against vaginal pathogens isolated from cervical cancer patients. Based on probiotic, acid-bile tolerance and antimicrobial properties, 13 lactic acid bacteria (LAB) from the healthy group were identified by MALDI TOF MS (Matrix Assisted Laser Desorption and Ionisation, Time Of Flight Mass Spectrometry). Among these, four strains, Lactobacillus gasseri P36Mops, Limosilactobacillus fermentum P37Mws, Lactobacillus delbrueckii P31Mcs and Enterococcus faecium P26Mcm, exhibited significant antimicrobial activity against 8 vaginal pathogens (Staphylococcus haemolyticus P41Tcs, Escherichia coli P30Tcs, E. coli P79Bcm, Enterococus faecalis P29Mops, E. faecalis P50Tws, E. faecalis P68Tcb, S. haemolyticus P48Bcb and S. haemolyticus P58Bcb) isolated from precancerous and cervical cancer patients. 16S rRNA sequencing of four potential probiotics revealed congruency with the MALDI-TOF MS identification and phylogenetic analysis showed genetic relationship with previously reported LAB strains. The selected LAB showed strain specific hydrophobicity (35.88-56.70%), auto-aggregation (35.26-61.39%) and antibiotic susceptibility. Interestingly, L. gasseri P36Mops was resistant to five standard antibiotics routinely used against urogenital or vaginal infections", "token_count": 462, "char_count": 1514, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7407, "quality_score": 0.8704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:13.390394", "source": { "split": "train_shard_00000", "doc_id": 1771 }, "chunk_id": "train_shard_00000_1771_0", "global_id": 1955 }, { "text": "LCMS (Liquid Chromatography Mass Spectrometry) analyses of the CFS (cell-free supernatant) of the four potential probiotics revealed the presence of metabolites such as N-(1-deoxy-1-fructosyl)valine, hygroline, acetoxy-2-hydroxy-16-heptadecen-4-one, avocadyne 4-acetate, avocadyne 2-acetate, taraxinic acid glucosyl ester, 6-hydroxypentadecanedioic acid, with reported antimicrobial activity. The overall data suggest the bio-therapeutic potential of the identified vaginal probiotics against cervical cancer-associated pathogens.\n\nCervicovaginal microbiota isolated from healthy women exhibit probiotic properties and antimicrobial activity against pathogens isolated from cervical cancer patients.", "token_count": 218, "char_count": 699, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7867, "quality_score": 0.8933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:13.860650", "source": { "split": "train_shard_00000", "doc_id": 1771 }, "chunk_id": "train_shard_00000_1771_1", "global_id": 1956 }, { "text": "Bile stress tolerance is a crucial characteristic of probiotics for surviving in the human gastrointestinal tract. The mechanism underlying the effect of l-malic acid on enhancing the glycodeoxycholic acid (GDCA) tolerance of\n\nL-Malic Acid Protects", "token_count": 63, "char_count": 248, "word_count": 35, "semantic_coherence": 1, "information_density": 0.7429, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:14.246216", "source": { "split": "train_shard_00000", "doc_id": 1772 }, "chunk_id": "train_shard_00000_1772_0", "global_id": 1957 }, { "text": "Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on\n\nGenomic Characterization of", "token_count": 87, "char_count": 380, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7547, "quality_score": 0.8774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:14.655342", "source": { "split": "train_shard_00000", "doc_id": 1773 }, "chunk_id": "train_shard_00000_1773_0", "global_id": 1958 }, { "text": "Cyp2a12-/-Cyp2c70-/- double knockout (DKO) mice have a human-like hydrophobic bile acid (BA) composition and show reduced fertility and liver injury. Ursodeoxycholic acid (UDCA) is a hydrophilic and cytoprotective BA used to treat various liver injuries in humans. This study investigated the effects of orally administered UDCA on fertility and liver injury in DKO mice. UDCA treatment prevented abnormal delivery (miscarriage and preterm birth) in pregnant DKO mice, presumably by increasing the hydrophilicity of serum BAs. UDCA also prevented liver damage in six-week-old DKO mice, however liver injury emerged in UDCA-treated 20-week-old female, but not male, DKO mice. In 20-week-old male UDCA-treated DKO mice, conjugated plus unconjugated UDCA proportions in serum, liver, and bile were 71, 64, and 71% of the total BAs, respectively. In contrast, conjugated plus unconjugated UDCA proportions in serum, liver, and bile of females were 56, 34, and 58% of the total BAs, respectively. The UDCA proportion was considerably low in female liver only and was compensated by highly hydrophobic lithocholic acid (LCA). Therefore, UDCA treatment markedly reduced the BA hydrophobicity index in the male liver but not in females. This appears to be why UDCA treatment causes liver injury in 20-week-old female mice. To explore the cause of LCA accumulation in the female liver, we evaluated the hepatic activity of CYP3A11 and SULT2A1, which metabolize LCAs to more hydrophilic BAs. However, there was no evidence to suggest that either enzyme activity was lower in females than in males", "token_count": 468, "char_count": 1586, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5537, "quality_score": 0.7769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:15.309355", "source": { "split": "train_shard_00000", "doc_id": 1775 }, "chunk_id": "train_shard_00000_1775_0", "global_id": 1959 }, { "text": "As female mice have a larger BA pool than males, excessive loading of LCAs on the hepatic bile salt export pump (BSEP) may be the reason for the hepatic accumulation of LCAs in female DKO mice with prolonged UDCA treatment. Our results suggest that the improvement of BA hydrophobicity in DKO mice by UDCA administration is sex-, age-, and organ-dependent.\n\nSex-, age-, and organ-dependent improvement of bile acid hydrophobicity by ursodeoxycholic acid treatment: A study using a mouse model with human-like bile acid composition.", "token_count": 141, "char_count": 531, "word_count": 84, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:15.737499", "source": { "split": "train_shard_00000", "doc_id": 1775 }, "chunk_id": "train_shard_00000_1775_1", "global_id": 1960 }, { "text": "The pangenome of a species is the sum of the genomes of its individuals. As coding sequences often represent only a small fraction of each genome, analyzing the pangene set can be a cost-effective strategy for plants with large genomes or highly heterozygous species. Here, we describe a step-by-step protocol to analyze plant pangene sets with the software GET_HOMOLOGUES-EST . After a short introduction, where the main concepts are illustrated, the remaining sections cover the installation and typical operations required to analyze and annotate pantranscriptomes and gene sets of plants. The recipes include instructions on how to call core and accessory genes, how to compute a presence-absence pangenome matrix, and how to identify and analyze private genes, present only in some genotypes. Downstream phylogenetic analyses are also discussed.\n\nPangenome Analysis of Plant Transcripts and Coding Sequences.", "token_count": 203, "char_count": 913, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6838, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:16.207344", "source": { "split": "train_shard_00000", "doc_id": 1776 }, "chunk_id": "train_shard_00000_1776_0", "global_id": 1961 }, { "text": "Presence-absence variants (PAV) are genomic regions present in some individuals of a species, but not others. PAVs have been shown to contribute to genomic diversity, especially in bacteria and plants. These structural variations have been linked to traits and can be used to track a species' evolutionary history. PAVs are usually called by aligning short read sequence data from one or more individuals to a reference genome or pangenome assembly, and then comparing coverage. Regions where reads do not align define absence in that individual, and the regions are classified as PAVs. The method below details how to align sequence reads to a reference and how to use the sequencing-coverage calculator Mosdepth to identify PAVs and construct a PAV table for use in downstream comparative genome analysis.\n\nAn SGSGeneloss-Based Method for Constructing a Gene Presence-Absence Table Using Mosdepth.", "token_count": 198, "char_count": 899, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:16.660937", "source": { "split": "train_shard_00000", "doc_id": 1777 }, "chunk_id": "train_shard_00000_1777_0", "global_id": 1962 }, { "text": "The aim of this study was to prepare a liposomal formulation of a model drug (budesonide) for colonic delivery by incorporating a bile salt (sodium glycocholate, SGC) into liposomes followed by coating with a pH-responsive polymer (Eudragit S100, ES100). The role of the SGC is to protect the liposome from the emulsifying effect of physiological bile salts, while that of ES100 is to protect the liposomes from regions of high acidity and enzymatic activity in the stomach and small intestine. Vesicles containing SGC were prepared by two preparation methods (sonication and extrusion), and then coated by ES100 (ES100-SGC-Lip). ES100-SGC-Lip showed a high entrapment efficiency (>90%) and a narrow size distribution (particle size = 275 nm, polydispersity index < 0.130). The characteristics of liposomes were highly influenced by the concentration of incorporated SGC. The lipid/polymer weight ratio, liposome charge, liposome addition, and mixing rate were critical factors for efficient and uniform coating. In vitro drug release studies in various simulated fluids indicate a pH-dependent dissolution of the coating layer, and the disintegration process of ES100-SGC-Lip was evaluated. In conclusion, the bile salt-containing ES100-coated liposomal formulation has potential for effective oral colonic drug delivery.\n\nPreparation, Characterization and In Vitro Evaluation of Eudragit S100-Coated Bile Salt-Containing Liposomes for Oral Colonic Delivery of Budesonide.", "token_count": 411, "char_count": 1473, "word_count": 210, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [ "ES100" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:17.286148", "source": { "split": "train_shard_00000", "doc_id": 1778 }, "chunk_id": "train_shard_00000_1778_0", "global_id": 1963 }, { "text": "Recombination is essential to microbial evolution, and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche. However, assessing the impact of homologous recombination on accessory genes which are only present in a subset of strains of a given species remains challenging due to their complex phylogenetic relationships. Quantifying homologous recombination for accessory genes (which are important for niche-specific adaptations) in comparison to core genes (which are present in all strains and have essential functions) is critical to understanding how selection acts on variation to shape species diversity and genome structures of bacteria. Here, we apply a computationally efficient, non-phylogenetic approach to measure homologous recombination rates in the core and accessory genome using >100,000 whole genome sequences from\n\nCore genes can have higher recombination rates than accessory genes within global microbial populations.", "token_count": 211, "char_count": 991, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:17.758547", "source": { "split": "train_shard_00000", "doc_id": 1779 }, "chunk_id": "train_shard_00000_1779_0", "global_id": 1964 }, { "text": "The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].\n\nPhylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.", "token_count": 297, "char_count": 889, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:18.324897", "source": { "split": "train_shard_00000", "doc_id": 1780 }, "chunk_id": "train_shard_00000_1780_0", "global_id": 1965 }, { "text": "Bacillus coagulans is Gram positive, spore forming and high lactic acid producing bacteria; however, probiotic and safety assessment of the isolated strain need to be investigated for commercial applications. Current study aimed to screen SKB LAB-19 for potential probiotic characteristics viz. enzyme production, antimicrobial properties, pH/bile salt tolerance, temperature stability, antidiarrheal activity in Swiss albino mice and Wistar rats; and acute oral toxicity in mice. The results showed that, SKB LAB-19 produces eight potential enzymes, effective against E. coli and C. perfringensis, tolerant to bile salt (0.3%w/v)/gastric pH (2.5), stable at 40-90 °C and nontoxic to cells. SKB LAB-19 was found to be safe and displayed promising results to reverse E. coli and castor oil induced diarrhoea. Histopathological studies showed repair to damaged mucosal epithelium cells and improves integrity of the goblet cells of colon. SKB LAB-19 showed immunomodulatory effects with increased immunoglobulins in blood and augmented weight of spleen and thymus. In addition, SKB LAB-19 showed significant in-vitro antioxidant activity (82.93%), reducing capacity and ascorbate auto-oxidation inhibition effect (94.62%). These preliminary results suggested that, SKB LAB-19 was found to be safe and has the potential to be used as effective probiotic and anti-diarrhoeal agent in humans and animal healthcare.\n\nIn vitro and in vivo evaluation of probiotic potential and safety assessment of Bacillus coagulans SKB LAB-19 (MCC 0554) in humans and animal healthcare.", "token_count": 441, "char_count": 1564, "word_count": 224, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:18.953269", "source": { "split": "train_shard_00000", "doc_id": 1781 }, "chunk_id": "train_shard_00000_1781_0", "global_id": 1966 }, { "text": "Burkholderia mallei is the etiological agent of glanders, a highly contagious and often fatal disease in equids. Due to the high genetic clonality of B. mallei, high-resolution typing assays are necessary to differentiate between individual strains. Here we report on the development and validation of a robust and reproducible core genome-based Multi Locus Sequence Typing Assay (cgMLST) for B. mallei, which is based on 3328 gene targets and enables high-resolution typing at the strain level. The assay was validated using a set of 120 B. mallei genomes from public databases and 23 newly sequenced outbreak strains from in-house strain collections. In this cgMLST analysis, strains from different geographic regions were clearly distinguished by at least 70 allele differences, allowing spatial clustering while closely related and epidemiologically related strains were separated by only zero to three alleles. Neither the different sequencing technologies nor the assembly strategies had an influence on the cgMLST results. The developed cgMLST is highly robust, reproducible and can be used for outbreak investigations, source tracking and molecular characterization of new B. mallei isolates.\n\nGenetic diversity and spatial distribution of Burkholderia mallei by core genome-based multilocus sequence typing analysis.", "token_count": 312, "char_count": 1325, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6597, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:19.512276", "source": { "split": "train_shard_00000", "doc_id": 1782 }, "chunk_id": "train_shard_00000_1782_0", "global_id": 1967 }, { "text": "Clostridioides difficile infection (CDI) results in significant morbidity and mortality in hospitalised patients. The pathogenesis of CDI is intrinsically related to the ability of C. difficile to shuffle between active vegetative cells and dormant endospores through the processes of germination and sporulation. Here, we hypothesise that dysregulation of microbiome-mediated bile salt metabolism contributes to CDI and that its alleviation can limit the pathogenesis of CDI. We engineer a genetic circuit harbouring a genetically encoded sensor, amplifier and actuator in probiotics to restore intestinal bile salt metabolism in response to antibiotic-induced microbiome dysbiosis. We demonstrate that the engineered probiotics limited the germination of endospores and the growth of vegetative cells of C. difficile in vitro and further significantly reduced CDI in model mice, as evidenced by a 100% survival rate and improved clinical outcomes. Our work presents an antimicrobial strategy that harnesses the host-pathogen microenvironment as the intervention target to limit the pathogenesis of infection.\n\nEngineering probiotics to inhibit Clostridioides difficile infection by dynamic regulation of intestinal metabolism.", "token_count": 297, "char_count": 1228, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6048, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:20.071105", "source": { "split": "train_shard_00000", "doc_id": 1783 }, "chunk_id": "train_shard_00000_1783_0", "global_id": 1968 }, { "text": "Hydrophilic β-sitosterol sugar esters were synthesized by a two-step biocatalytic approach using β-sitosterol vinyl adipate as an intermediate. The maximum conversion (above 90%) of β-sitosterol vinyl adipate was achieved using the saccharides glucose, sucrose, and raffinose. The chemical structure of the synthesized esters was confirmed by various techniques. The investigation of physical properties revealed that β-sitosterol sugar esters had enhanced water solubility (3.0-8.0 mM at 35 °C), reduced crystallinity, and high wettability. Their lyotropic liquid crystal properties were observed by polarized light microscopy. Furthermore, β-sitosterol sugar esters could be hydrolyzed into β-sitosterol adipate under simulated intestinal conditions at a low rate (2.83-18.14%). Most β-sitosterol sugar esters probably entered into intestinal bile salt micelles with ester bonds intact and showed up to 10-fold higher in vitro bioaccessibility than free β-sitosterol in non-fat systems. The excellent physical and functional characteristics of β-sitosterol sugar esters suggested their great potential application in the food industry.\n\nSynthesis, Physical Properties, and In Vitro-Simulated Gastrointestinal Digestion of Hydrophilic β-Sitosterol Sugar Esters.", "token_count": 353, "char_count": 1262, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:20.646773", "source": { "split": "train_shard_00000", "doc_id": 1784 }, "chunk_id": "train_shard_00000_1784_0", "global_id": 1969 }, { "text": "Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into such models was first enabled by the GECKO toolbox, allowing the study of phenotypes constrained by protein limitations. Here, we upgrade the toolbox in order to enhance models with enzyme and proteomics constraints for any organism with a compatible GEM reconstruction. With this, enzyme-constrained models for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus are generated to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions reveal that upregulation and high saturation of enzymes in amino acid metabolism are common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO is expanded with an automated framework for continuous and version-controlled update of enzyme-constrained GEMs, also producing such models for Escherichia coli and Homo sapiens. In this work, we facilitate the utilization of enzyme-constrained GEMs in basic science, metabolic engineering and synthetic biology purposes.\n\nReconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0.", "token_count": 352, "char_count": 1501, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:21.229240", "source": { "split": "train_shard_00000", "doc_id": 1785 }, "chunk_id": "train_shard_00000_1785_0", "global_id": 1970 }, { "text": "Vibrio vulnificus is an opportunistic pathogen that naturally inhabits sea water globally and is responsible for most vibriosis-related deaths. The consumption of V. vulnificus contaminated seafood and exposure of wounds to Vibrio can result in systemic infection, with increased risks of amputation and extremely high rates of mortality. However, the pathogenicity and virulence factors of V. vulnificus are not fully understood. The genomic characterization of V. vulnificus will be helpful to extend our understanding on V. vulnificus at a genomic level. In this manuscript, the genome of V. vulnificus strain MCCC 1A08743 isolated from contaminated prawns from Zhanjiang, China, was sequenced using Illumina HiSeq X Ten system and annotated through multiple databases. The strain MCCC 1A08743 genome included 4371 protein-coding genes and 117 RNA genes. Average nucleotide identity analysis and core genome phylogenetic analysis revealed that MCCC 1A08743 was most closely related to strains from clinical samples from the United States. Pathogenicity annotation of the MCCC 1A08743 genome, using Virulence Factor Database and Pathogen-Host Interactions database, predicted the pathogenicity of the strain, and this was confirmed using mice infection experiments, which indicated that V. vulnificus strain MCCC 1A08743 could infect C57BL/6J mice and cause liver lesions. This article has an associated First Person interview with the first author of the paper.\n\nGenome sequence and pathogenicity of Vibrio vulnificus strain MCCC 1A08743 isolated from contaminated prawns.", "token_count": 423, "char_count": 1575, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:21.851128", "source": { "split": "train_shard_00000", "doc_id": 1786 }, "chunk_id": "train_shard_00000_1786_0", "global_id": 1971 }, { "text": "The gut microbiome is increasingly recognized as a vital organ that participates in nutrient acquisition, energy regulation and maintenance of human health. Targeted manipulation of the gut microbiota by dietary supplements has been validated as an effective approach to improve human health. Among various gut microbiome-host interactions, bile acids (BAs) are intensively metabolized by the gut microbes and control a variety of metabolic processes such as energy homeostasis, glucose and lipid metabolism by activation of farnesoid X receptor (FXR). How dietary supplements regulate FXR signaling and promote human health is thus attracting broad interest and well-reviewed. However, the exact effects of BAs on FXR activity and host metabolism are compound-specific. Different BAs are metabolized by the gut microbes into varied BA derivatives and then impose distinct modulation of FXR activity and host health. As the gateway enzymes, bile salt hydrolases (BSHs), produced by the gut microbiota, control the first step of BA transformation in the gut. Therefore, BSH is a key mediator linking the food supplements' modulation to the gut microbiota and BAs-FXR signaling. In this review, we generalized the relationship between BAs, gut microbial BSHs and FXR, and summarized the dietary regulators of BSH and FXR activities, aiming to rationalize the dietary management of human health\n\nTargeting gut microbial bile salt hydrolase (BSH) by diet supplements: new insights into dietary modulation of human health.", "token_count": 362, "char_count": 1517, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7933, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:22.435839", "source": { "split": "train_shard_00000", "doc_id": 1787 }, "chunk_id": "train_shard_00000_1787_0", "global_id": 1972 }, { "text": "The growth and tolerance of Kluyveromyces marxianus at high temperatures decreased significantly in the synthetic medium (SM), which is commonly used in industrial fermentations. After 100 days of adaptive laboratory evolution, a strain named KM234 exhibited excellent tolerance at a high temperature, without loss of its growth ability at a moderate temperature. Transcriptomic analysis revealed that the KM234 strain decreased the expression of the ammonium (NH\n\nDownregulation of ammonium uptake improves the growth and tolerance of Kluyveromyces marxianus at high temperature.", "token_count": 134, "char_count": 580, "word_count": 81, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [ "KM234" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:22.860476", "source": { "split": "train_shard_00000", "doc_id": 1788 }, "chunk_id": "train_shard_00000_1788_0", "global_id": 1973 }, { "text": "The increased accessibility of next generation sequencing has allowed enough genomes from a given bacterial species to be sequenced to describe the distribution of genes in the pangenome, without limiting analyses to genes present in reference strains. Although some taxa have thousands of whole genome sequences available on public databases, most genomes were sequenced with short read technology, resulting in incomplete assemblies. Studying pangenomes could lead to important insights into adaptation, pathogenicity, or molecular epidemiology, however given the known information loss inherent in analyzing contig-level assemblies, these inferences may be biased or inaccurate. In this study we describe the pangenome of a clonally evolving pathogen,\n\nA critical evaluation of", "token_count": 163, "char_count": 780, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7798, "quality_score": 0.8899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:23.308318", "source": { "split": "train_shard_00000", "doc_id": 1789 }, "chunk_id": "train_shard_00000_1789_0", "global_id": 1974 }, { "text": "Honeybee products have been among important consumer products throughout history. Microbiota has attracted attention in recent years due to both their probiotic value and industrial potential. Fructophilic lactic acid bacteria (FLAB), whose field of study has been expanding rapidly in the last 20 years, are among the groups that can be isolated from the bee gut. This study aimed to isolate FLAB from the honeybees of two different geographic regions in Turkey and investigate their probiotic, metabolic and anti-quorum sensing (anti-QS) potential. Metabolic properties were investigated based on fructose toleration and acid and diacetyl production while the probiotic properties of the isolates were determined by examining pH, pepsin, pancreatin resistance, antimicrobial susceptibility, and antimicrobial activity. Anti-QS activities were also evaluated with the Chromobacterium violaceum biosensor strain. Two FLAB members were isolated and identified by the 16S rRNA analysis as Fructobacillus tropaeoli and Apilactobacillus kunkeei, which were found to be tolerant to high fructose, low pH, pepsin, pancreatin, and bile salt environments. Both isolates showed anti-QS activity against the C. violaceum biosensor strain and no diacetyl production. The daily supernatants of the isolates inhibited the growth of Enterococcus faecalis ATCC 29212 among the selected pathogens. The isolates were found resistant to kanamycin, streptomycin, erythromycin, and clindamycin. In the evaluation of the probiotic potential of these species, the negative effect of antibiotics and other chemicals to which honeybees are directly or indirectly exposed draws attention within the scope of the \"One Health\" approach.\n\nInvestigation of the probiotic and metabolic potential of Fructobacillus tropaeoli and Apilactobacillus kunkeei from apiaries.", "token_count": 464, "char_count": 1837, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6211, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:23.941412", "source": { "split": "train_shard_00000", "doc_id": 1790 }, "chunk_id": "train_shard_00000_1790_0", "global_id": 1975 }, { "text": "The gut microbiome has significant effects on healthy aging and aging-related diseases, whether in humans or nonhuman primates. However, little is known about the divergence and convergence of gut microbial diversity between humans and nonhuman primates during aging, which limits their applicability for studying the gut microbiome's role in human health and aging. Here, we performed 16S rRNA gene sequencing analysis for captive rhesus macaques (Macaca mulatta) and compared this data set with other freely available gut microbial data sets containing four human populations (Chinese, Japanese, Italian, and British) and two nonhuman primates (wild lemurs [Lemur catta] and wild chimpanzees [Pan troglodytes]). Based on the consistent V4 region of the 16S rRNA gene, beta diversity analysis suggested significantly separated gut microbial communities associated with host backgrounds of seven host groups, but within each group, significant gut microbial divergences were observed, and indicator bacterial genera were identified as associated with aging. We further discovered six common anti-inflammatory gut bacteria (\n\nConvergent and Divergent Age Patterning of Gut Microbiota Diversity in Humans and Nonhuman Primates.", "token_count": 279, "char_count": 1225, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6936, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:24.491998", "source": { "split": "train_shard_00000", "doc_id": 1791 }, "chunk_id": "train_shard_00000_1791_0", "global_id": 1976 }, { "text": "Mycoplasma bovis (M. bovis) in cattle causes pneumonia, arthritis, otitis media, and mastitis. In addition, multiple outbreaks have been recorded in North American bison. The genomic data on Canadian M. bovis in bison and cattle to date is limited. Whole-genome sequencing (WGS) was used to assess the degree of genome conservation across four Canadian M. bovis strains recovered from bison and cattle. Whole-genome sequences of four M. bovis isolates (Mb1, Mb160, Mb300, Mb304) and the PG45 reference genome were utilized to identify the M. bovis genomic similarity, whole-genome single nucleotide polymorphism (WGS-SNP), virulence determinants, and genomic islands. The pan-genome analysis showed that M. bovis encodes a minimum of 971 genes, while the core genome contained 637 genes. Comparative genomics revealed limited diversity in gene content between bison and cattle isolates. Whole-genome SNP analysis showed that the four M. bovis isolates differed from each other and to PG45. A total of 40 putative virulence genes associated with adhesion, colonization, and destruction of tissues were found in the bison and cattle isolates using the virulence factors database (VFDB). These putative virulence factors were equally distributed among isolates. Genomic Islands (GIs) ranging from 4 to 9 and associated with transposases, restriction-modification, ribosomal hypothetical proteins, variable surface lipoproteins, and unknowns were also identified. Overall, the genomic characterization of these isolates may provide new insights into the mechanisms of pathogenicity in M. bovis.\n\nComparative genomic analysis of Canadian Mycoplasma bovis strains isolated from Bison and Cattle.", "token_count": 450, "char_count": 1689, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5892, "quality_score": 0.7946, "entities": { "genes": [ "PG45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:25.163638", "source": { "split": "train_shard_00000", "doc_id": 1792 }, "chunk_id": "train_shard_00000_1792_0", "global_id": 1977 }, { "text": "Psychobiotics are a novel class of probiotics with potential to confer mental wellness via production of neuroactive compounds such as gamma-aminobutyric acid (GABA). The demand for new biological sources of GABA has increased steadily. Therefore, the current study reports the isolation of 17 presumptive lactic acid bacteria (LAB) from marine samples and their screening for GABA synthesis from monosodium glutamate (MSG) using thin-layer chromatography (TLC). The isolate SH9 was selected as a high GABA producing strain. The GABA content of SH9 cell free supernatant (CFS) was quantitatively determined by high performance liquid chromatography (HPLC) to be 0.97 g/L. SH9 was identified biochemically and molecularly as Enterococcus faecium (identity 99%). Moreover, SH9 demonstrated promising probiotic potentials; it gave no signs of hemolysis and could survive at low pH values and high bile salt concentrations. It also exhibited antimicrobial activity against highly pathogenic strains and the ability to grow at 6.5% NaCl. In addition, SH9 CFS showed anti-inflammatory and antioxidant properties. The glutamate decarboxylase (GAD) gene was detected in SH9 by using specific primers. Product of 540 bp was obtained, sequenced, and analyzed (accession number: MW713382). The inferred amino acid sequence was 99.3% identical to Lactobacillus plantarum M-6 gadB gene. The findings of this study suggest that the marine isolate E. faecium SH9 could be used as a novel psychobiotics in the development of GABA rich healthy products.\n\nPsychobiotic Potential of Gamma-Aminobutyric Acid-Producing Marine Enterococcus faecium SH9 from Marine Shrimp.", "token_count": 457, "char_count": 1649, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8361, "entities": { "genes": [ "SH9", "MW713382" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:25.822438", "source": { "split": "train_shard_00000", "doc_id": 1793 }, "chunk_id": "train_shard_00000_1793_0", "global_id": 1978 }, { "text": "Pseudoacini are generally a morphologic feature of hepatocellular carcinoma (HCC), being absent or rare in benign hepatocytic tumors, such as hepatocellular adenoma. However, rarely these can be seen in focal nodular hyperplasia (FNH) and may pose diagnostic challenges, especially when prominent. The study was aimed to evaluate the occurrence of pseudoacini in FNH and their clinicopathologic correlations. A total of 95 FNH cases diagnosed from 2005 to 2020 were included in the study. A pseudoacinus was defined as a circular arrangement of hepatocytes around a central dilated lumen present within the lobular parenchyma of the lesion with or without inspissated bile. Among the 95 FNH cases, 28 (29.5%) showed pseudoacini, which were prominent in 12 (12.6%) cases. Of these 3 occurred in patients above 50 years old. The pseudoacini were numerous in 3 cases, leading to an initial consideration of HCC in the differential diagnosis, and 1 case was diagnosed as well-differentiated hepatocellular neoplasm on initial biopsy. All 12 cases showed map-like staining pattern for glutamine synthetase. The hepatocytes forming the pseudoacini were positive for CK7 and HepPar1, while the inner lumina were highlighted by CD10 and bile salt export pump immunostains similar to adjacent canaliculi. The presence of prominent pseudoacini was not significantly associated with any clinical or pathologic features. The findings suggest that pseudoacini are likely manifestation of hepatocyte biliary transdifferentiation associated with chronic cholestasis in the lesion. This feature may pose a potential diagnostic pitfall especially on needle biopsies and awareness is needed to avoid misdiagnosing this as HCC.\n\nProminent Pseudoacini in Focal Nodular Hyperplasia: A Potential Diagnostic Pitfall.", "token_count": 467, "char_count": 1793, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6374, "quality_score": 0.8187, "entities": { "genes": [ "CK7", "CD10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:26.511283", "source": { "split": "train_shard_00000", "doc_id": 1794 }, "chunk_id": "train_shard_00000_1794_0", "global_id": 1979 }, { "text": "Escherichia coli is the most researched microbial organism in the world. Its varied impact on human health, consisting of commensalism, gastrointestinal disease, or extraintestinal pathologies, has generated a separation of the species into at least eleven pathotypes (also known as pathovars). These are broadly split into two groups, intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC). However, components of E. coli's infinite open accessory genome are horizontally transferred with substantial frequency, creating pathogenic hybrid strains that defy a clear pathotype designation. Here, we take a birds-eye view of the E. coli species, characterizing it from historical, clinical, and genetic perspectives. We examine the wide spectrum of human disease caused by E. coli, the genome content of the bacterium, and its propensity to acquire, exchange, and maintain antibiotic resistance genes and virulence traits. Our portrayal of the species also discusses elements that have shaped its overall population structure and summarizes the current state of vaccine development targeted at the most frequent E. coli pathovars. In our conclusions, we advocate streamlining efforts for clinical reporting of ExPEC, and emphasize the pathogenic potential that exists throughout the entire species.\n\nGenomics and pathotypes of the many faces of Escherichia coli.", "token_count": 329, "char_count": 1390, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:27.102730", "source": { "split": "train_shard_00000", "doc_id": 1795 }, "chunk_id": "train_shard_00000_1795_0", "global_id": 1980 }, { "text": "Pangenomes provide novel insights for population and quantitative genetics, genomics and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.\n\nThe Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.", "token_count": 133, "char_count": 651, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7473, "quality_score": 0.8736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:27.531677", "source": { "split": "train_shard_00000", "doc_id": 1796 }, "chunk_id": "train_shard_00000_1796_0", "global_id": 1981 }, { "text": "Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.", "token_count": 502, "char_count": 2024, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [ "ST150" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:28.184448", "source": { "split": "train_shard_00000", "doc_id": 1797 }, "chunk_id": "train_shard_00000_1797_0", "global_id": 1982 }, { "text": "Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes.", "token_count": 66, "char_count": 233, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9032, "quality_score": 0.9516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:28.565648", "source": { "split": "train_shard_00000", "doc_id": 1797 }, "chunk_id": "train_shard_00000_1797_1", "global_id": 1983 }, { "text": "Bile salt hydrolase (BSH) is a well-characterized probiotic enzyme associated with bile detoxification and colonization of lactic acid bacteria in the human gastrointestinal tract. Here, we isolated a putative BSH (LpBSH) from the probiotic bacterium\n\nBile Salt Hydrolase Degrades β-Lactam Antibiotics and Confers Antibiotic Resistance on", "token_count": 101, "char_count": 338, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:28.943856", "source": { "split": "train_shard_00000", "doc_id": 1798 }, "chunk_id": "train_shard_00000_1798_0", "global_id": 1984 }, { "text": "Whole genome sequencing (WGS) of methicillin-resistant Staphylococcus aureus (MRSA) provides high-resolution typing, facilitating surveillance and outbreak investigations. The aim of this study was to evaluate the genomic variation rate in MRSA, by comparing commonly used core genome multilocus sequencing (cgMLST) against single nucleotide polymorphism (SNP) analyses. WGS was performed on 95 MRSA isolates, collected from 20 carriers during years 2003-2019. To assess variation and methodological-related differences, two different cgMLST schemes were obtained using Ridom SeqSphere+ and the cloud-based 1928 platform. In addition, two SNP methods, 1928 platform and Northern Arizona SNP Pipeline (NASP) were used. The cgMLST using Ridom SeqSphere+ and 1928 showed a median of 5.0 and 2.0 allele variants/year, respectively. In the SNP analysis, performed with two reference genomes COL and Newman, 1928 showed a median of 13 and 24 SNPs (including presumed recombination) and 3.8 respectively 4.0 SNPs (without recombination) per individual/year. Accordantly, NASP showed a median of 5.5 and 5.8 SNPs per individual/year. In conclusion, an estimated genomic variation rate of 2.0-5.8 genetic events per year (without recombination), is suggested as a general guideline to be used at clinical laboratories for surveillance and outbreak investigations independently of analysis approach used.\n\nEvaluation of within-host evolution of methicillin-resistant Staphylococcus aureus (MRSA) by comparing cgMLST and SNP analysis approaches.", "token_count": 435, "char_count": 1534, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:29.575966", "source": { "split": "train_shard_00000", "doc_id": 1799 }, "chunk_id": "train_shard_00000_1799_0", "global_id": 1985 }, { "text": "Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared with core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent HGT between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.\n\nPangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance.", "token_count": 442, "char_count": 1902, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5923, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:30.207185", "source": { "split": "train_shard_00000", "doc_id": 1800 }, "chunk_id": "train_shard_00000_1800_0", "global_id": 1986 }, { "text": "Tenacibaculum maritimum is a devastating bacterial pathogen affecting a large variety of marine fish species. It is responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyse bacterial diversity and population structure. Serological heterogeneity has been observed and up to four different serotypes have been described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping and genome-wide association study, we identified the genomic loci likely involved in the O-antigen biosynthesis. This finding allowed the development of a robust multiplex PCR-based serotyping scheme able to detect subgroups within each serotype and therefore performs better than conventional serotyping. This scheme was successfully applied to a large number of isolates from worldwide origin and retrieved from a large variety of fish species. No obvious correlations were observed between the mPCR-based serotype and the host species or the geographic origin of the isolates. Strikingly, the distribution of mPCR-based serotypes does not follow the core genome phylogeny. Nevertheless, this simple and cost-effective mPCR-based serotyping method could be useful for different applications such as population structure analysis, disease surveillance, vaccine formulation and efficacy follow-up.\n\nGenomic characterization of Tenacibaculum maritimum O-antigen gene cluster and development of a multiplex PCR-based serotyping scheme.", "token_count": 324, "char_count": 1528, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:31.114385", "source": { "split": "train_shard_00000", "doc_id": 1801 }, "chunk_id": "train_shard_00000_1801_0", "global_id": 1987 }, { "text": "The Klebsiella pneumoniae complex is comprised of ubiquitous bacteria that can be found in soils, plants or water, and as humans' opportunistic pathogens. This study aimed at inferring common and distinctive features in clinical and environmental K. pneumoniae. Whole genome sequences of members of the K. pneumoniae complex (including K. variicola, n = 6; and K. quasipneumoniae, n = 7), of clinical (n = 78) and environmental (n = 61) origin from 21 countries were accessed from the GenBank. These genomes were compared based on phylogeny, pangenome and selected clinically relevant traits. Phylogenetic analysis based on 2704 genes of the core genome showed close relatedness between clinical and environmental strains, in agreement with the multi-locus sequence typing. Eight out of the 62 sequence types (STs) identified, included both clinical and environmental genomes (ST11, ST14, ST15, ST37, ST45, ST147, ST348, ST437). Pangenome-wide association studies did not evidence significant differences between clinical and environmental genomes. However, the genomes of clinical isolates presented significantly more exclusive genes related to antibiotic resistance/plasmids, while the environmental isolates yielded significantly higher allelic diversity of genes related with functions such as efflux or oxidative stress. The study suggests that K. pneumoniae can circulate among the natural environment and clinical settings, probably under distinct adaptation pressures.\n\nCommon and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings.", "token_count": 406, "char_count": 1604, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6267, "quality_score": 0.8133, "entities": { "genes": [ "ST45", "ST37", "ST348", "ST11", "ST14", "ST15", "ST147", "ST437" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:31.737212", "source": { "split": "train_shard_00000", "doc_id": 1802 }, "chunk_id": "train_shard_00000_1802_0", "global_id": 1988 }, { "text": "The genus Streptococcus, a member of family Streptococcaceae, is known for its wide range of industrial, clinical and human relevance. Among the species of genus Streptococcus two members, namely Streptococcus koreensis and Streptococcus ilei, were isolated from subgingival dental plaque and human small intestinal fluid, respectively. The 16S rRNA gene sequence similarity of the type strains of these members shows a similarity of 99.87%. In this study, we performed a systematic study to clarify the taxonomic assignment of these two species. Genome similarity assessment based on whole-genome sequence information such as average nucleotide identity using orthoANI and fastANI, digital DNA-DNA hybridization value between S. koreensis and S. ilei were 96.31, 96.60, 86.4 and 97.63, respectively. All these genome similarity values clearly exceeded the species delineation cutoffs. Phylogenetic assessment using 16S rRNA gene and whole-genome information using PhyloPhlAn, which uses around 400 conserved genes across bacterial phyla, provides additional evidence for these members forming a monophyletic clade in the phylogenetic tree. Pan genome analysis suggests a very large core genome (n = 1374) and the presence of no unique gene between the genomes of S. koreensis and S. ilei. Additionally, we found highly syntenic genomes of type strains of these two species. Based on these evidences, we propose S. ilei should be reclassified as a later heterotypic synonym of S. koreensis.\n\nReclassification of Streptococcus ilei as a later heterotypic synonym of Streptococcus koreensis based on whole-genome sequence analysis.", "token_count": 450, "char_count": 1629, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5823, "quality_score": 0.7911, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:32.376265", "source": { "split": "train_shard_00000", "doc_id": 1803 }, "chunk_id": "train_shard_00000_1803_0", "global_id": 1989 }, { "text": "Crystallization inhibitors in amorphous solid dispersions (ASD) enable metastable supersaturated drug solutions that persist for a physiologically relevant time. Olefin cross-metathesis (CM) has successfully provided multifunctional cellulose-based derivatives as candidate ASD matrix polymers. In proof of concept studies, we prepared hydrophobic bile salt/cellulose adducts by CM with naturally occurring bile salts. We hypothesized that increased hydrophilicity would enhance the ability of these conjugates to maximize bioactive supersaturation. Their selective preparation presents a significant synthetic challenge, given polysaccharide reactivity and polysaccharide and bile salt complexity. We prepared such derivatives using a more hydrophilic hydroxypropyl cellulose (HPC) backbone, employing a pent-4-enyl tether (Pen) for appending bile acids. We probed structure-property relationships by varying the nature and degree of substitution of the bile acid substituent (lithocholic or deoxycholic acid). These conjugates are indeed synergistic inhibitors, as demonstrated with the fast-crystallizing prostate cancer drug, enzalutamide. The lithocholic acid methyl ester derivative, AcrMLC-PenHHPCPen (0.64), increased induction time 68 fold vs. drug alone.\n\nDesigning synergistic crystallization inhibitors: Bile salt derivatives of cellulose with enhanced hydrophilicity.", "token_count": 350, "char_count": 1380, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7574, "quality_score": 0.8787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:32.952965", "source": { "split": "train_shard_00000", "doc_id": 1804 }, "chunk_id": "train_shard_00000_1804_0", "global_id": 1990 }, { "text": "Reliable hepatic in vitro systems are crucial for the safety assessment of xenobiotics. Certain xenobiotics decrease the hepatic bile efflux, which can ultimately result in cholestasis. Preclinical animal models and the currently available in vitro systems poorly predict a xenobiotic's cholestatic potential. Here, we compared the phenotype and capacity of three liver derived in vitro systems to emulate human functionality to synthesize and secrete bile acids (BAs). To this end, basal BA production of sandwich cultured human hepatocytes (SCHHs), HepaRG cells (HepaRGs) and hepatocyte-like intrahepatic cholangiocyte organoids (ICO-heps) were analysed, and the effect of the known BSEP (Bile Salt Export Pump)-inhibitors bosentan and lopinavir on BA disposition in SCHHs and HepaRGs was quantified. RT-qPCR of selected target genes involved in maturation status, synthesis, transport and conjugation of BAs was performed to mechanistically underpin the observed differences in BA homeostasis. ICO-heps produced a (very) low amount of BAs. SCHHs are a powerful tool in cholestasis-testing due to their high basal BA production and high transporter expression compared to the other models tested. HepaRGs were responsive to both selected BSEP-inhibitors and produced a BA profile that is most similar to the human in vivo situation, making them a suitable and practical candidate for cholestasis-testing.\n\nHepatic bile acid synthesis and secretion: Comparison of in vitro methods.", "token_count": 395, "char_count": 1482, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6526, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:33.565517", "source": { "split": "train_shard_00000", "doc_id": 1805 }, "chunk_id": "train_shard_00000_1805_0", "global_id": 1991 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC2) is a rare autosomal recessive disorder caused by mutations in the ABCB11 gene. Clinical manifestations include cholestasis with low γ-glutamyltransferase (GGT), hepatosplenomegaly, and severe pruritus. Liver transplantation is required for individuals with progressive liver disease or failure of the bypass procedure and has been considered curative. However, in the case of PFIC2, although bile salt excretory pump (BSEP) deficiency is a liver-specific condition rather than a systemic disease, evidence of recurrent BSEP disease has been shown in a small proportion of allografts. We describe an unusual case of a 21-year-old individual with PFIC2 and evidence of recurrent BSEP disease after liver transplantation, with clinical and laboratory improvement after pulse therapy with methylprednisolone for 3 days and adjustment of oral immunosuppression. This case report highlights the recurrence of PFIC2 in patients post liver transplant. It also emphasizes the importance of clinical suspicion, which should be considered in cases of posttransplant cholestasis in PFIC2 patients, especially those with low γ-glutamyltransferase (GGT) and without signs of acute graft rejection. Having knowledge of the condition favors a targeted diagnostic approach and contributes to early therapeutic management and a higher success rate.\n\nProgressive Familial Intrahepatic Cholestasis Type 2 and Recurrence After Liver Transplantation: A Case Report.", "token_count": 371, "char_count": 1504, "word_count": 208, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:34.142685", "source": { "split": "train_shard_00000", "doc_id": 1806 }, "chunk_id": "train_shard_00000_1806_0", "global_id": 1992 }, { "text": "Probiotics have attracted much attention due to their ability to modulate host intestinal microbe, participate in nutrient metabolism or immunomodulatory. Both inflammatory bowel disease (IBD) and bowel cancer are digestive system disease, which have become a global public health problem due to their unclear etiology, difficult to cure, and repeated attacks. Disturbed gut microbiota and abnormal lipid metabolism would increase the risk of intestinal inflammation. However, the link between lipid metabolism, probiotics, and IBD is unclear. In this review, we found that different lipids and their derivatives have different effects on IBD and gut microbes. ω-3 polyunsaturated fatty acids (PUFAs) docosahexaenoic acid, eicosapentaenoic acid, and their derivatives resolvin E1, resolvin D can inhibit oxidative stress and reactive oxygen species activate NFκB and MAPk pathway. While ω-6 PUFAs linoleic acid and arachidonic acid can be derived into leukotrienes and prostaglandins, which will aggravate IBD. Cholesterol can be converted into bile acids to promote lipid absorption and affect microbial survival and colonization. At the same time, it is affected by microbial bile salt hydrolase to regulate blood lipids. Low denstiy lipoprotein (LDL) is easily converted into oxidized LDL, thereby promoting inflammation, while high denstiy lipoprotein (HDL) has the opposite effect. Probiotics compete with intestinal microorganisms for nutrients or ecological sites and thus affect the structure of intestinal microbiota. Moreover, microbial short chain fatty acids, bile salt hydrolase, superoxide dismutase, glutathione, etc. can affect lipid metabolism and IBD. In conclusion, probiotics are directly or indirectly involved in lipids metabolism and their impact on IBD, which provides the possibility to explore the role of probiotics in improving gut health.\n\nProbiotics Interact With Lipids Metabolism and Affect Gut Health.", "token_count": 508, "char_count": 1934, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:34.789169", "source": { "split": "train_shard_00000", "doc_id": 1807 }, "chunk_id": "train_shard_00000_1807_0", "global_id": 1993 }, { "text": "Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile.\n\nTo kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131.", "token_count": 135, "char_count": 558, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8765, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:35.211795", "source": { "split": "train_shard_00000", "doc_id": 1808 }, "chunk_id": "train_shard_00000_1808_0", "global_id": 1994 }, { "text": "This study was conducted to assess the effects of the dietary supplementation of riboflavin (as a bile salt hydrolase [BSH] inhibitor) and\n\nRiboflavin and", "token_count": 44, "char_count": 154, "word_count": 24, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:35.570102", "source": { "split": "train_shard_00000", "doc_id": 1809 }, "chunk_id": "train_shard_00000_1809_0", "global_id": 1995 }, { "text": "Drugs are often withdrawn from the market due to the manifestation of drug-induced liver injury (DILI) in patients. Drug-induced cholestasis (DIC), defined as obstruction of hepatic bile flow due to medication, is one form of DILI. Because DILI is idiosyncratic, and the resulting cholestasis complex, there is no suitable in vitro model for early DIC detection during drug development. Our goal was to develop a mouse precision-cut liver slice (mPCLS) model to study DIC and to assess cholestasis development using conventional molecular biology and analytical chemistry methods. Cholestasis was induced in mPCLS through a 48-h-incubation with three drugs known to induce cholestasis in humans, namely chlorpromazine (15, 20, and 30 µM), cyclosporin A (1, 3, and 6 µM) or glibenclamide (25, 50, and 65 µM). A bile-acid mixture (16 µM) that is physiologically representative of the human bile-acid pool was added to the incubation medium with drug, and results were compared to incubations with no added bile acids. Treatment of PCLS with cholestatic drugs increased the intracellular bile-acid concentration of deoxycholic acid and modulated bile-transporter genes. Chlorpromazine led to the most pronounced cholestasis in 48 h, observed as increased toxicity; decreased protein and gene expression of the bile salt export pump; increased gene expression of multidrug resistance-associated protein 4; and accumulation of intracellular bile acids. Moreover, chlorpromazine-induced cholestasis exhibited some transition into fibrosis, evidenced by increased gene expression of collagen 1A1 and heatshock protein 47. In conclusion, we demonstrate that mPCLS can be used to study human DIC onset and progression in a 48 h period. We thus propose this model is suited for other similar studies of human DIC.", "token_count": 497, "char_count": 1803, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:36.214398", "source": { "split": "train_shard_00000", "doc_id": 1810 }, "chunk_id": "train_shard_00000_1810_0", "global_id": 1996 }, { "text": "Mouse precision-cut liver slices as an ex vivo model to study drug-induced cholestasis.", "token_count": 24, "char_count": 87, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:36.568221", "source": { "split": "train_shard_00000", "doc_id": 1810 }, "chunk_id": "train_shard_00000_1810_1", "global_id": 1997 }, { "text": "Dyslipidemia, specifically abnormal levels of low-density lipoprotein cholesterol (LDL-C), is an important risk factor of cardiovascular disease. Evidence showing the promising abilities of probiotics to lower total cholesterol or LDL-C has, however, not yet convinced experts to recommend probiotic bacteria as treatment for blood lipid management. Therefore, there are opportunities for the development of new efficient cholesterol-lowering probiotics. Bile salt hydrolase (BSH) and feruloyl esterase (FAE) are bacterial enzymes proposed to explain the cholesterol-lowering capacity of some bacteria and have both been shown to be responsible for lipid reduction in vivo. Here, in order to select for cholesterol-lowering bacteria, 70 strains related to Lactobacillaceae were screened for BSH and FAE activities. Based on this two-way screening approach, two bacteria were selected and assessed for their capacity to assimilate cholesterol in vitro, another suggested mechanism. Lactobacillus acidophilus CL1285 showed BSH and FAE activity as well as capacity to assimilate cholesterol in vitro. Lactiplantibacillus plantarum CHOL-200 exhibited BSH activity and ability to assimilate cholesterol. These properties observed in vitro make both strains good probiotic candidates for the management of dyslipidemia. Further investigation is needed to assess their ability to reduce blood cholesterol in human trial.\n\nScreening and Characterization of Some Lactobacillaceae for Detection of Cholesterol-Lowering Activities.", "token_count": 387, "char_count": 1520, "word_count": 204, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [ "CL1285" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:37.213579", "source": { "split": "train_shard_00000", "doc_id": 1811 }, "chunk_id": "train_shard_00000_1811_0", "global_id": 1998 }, { "text": "The present study aimed to isolate and identify the potential probiotic, pathobiont, and pathogenic microorganisms in the stool samples of 12 healthy individuals and evaluate their in vitro effects on cancer formation. A total of 83 strains were isolated from the stool samples and identified using MALDI-Biotyper. Fourteen of the isolates were identified as Candida spp., three isolates were identified as Cryptococcus neoformans, 55 isolates were identified as lactic acid bacteria, and the remaining isolates belonged to different 11 bacterial genera. Important microbial properties for cancer prevention and some probiotic properties were examined. All strains maintained their viability under acidic conditions and in media containing bile salts. Of the bacterial strains, 62.5% were resistant to ampicillin, chloramphenicol, gentamicin, erythromycin, kanamycin, penicillin, streptomycin, tetracycline, and vancomycin. All yeast strains were resistant to ketoconazole and susceptible to nystatin. The susceptibility of the strains to fluconazole, voriconazole, amphotericin B, and itraconazole varied. Fifty-nine percent of the strains produced EPS and 21.7% showed proteolytic activity (PA). Of the strains, 15.7% both produced exopolysaccharides (EPS) and had PA. The antioxidant activity (AOA) varied depending on the strains. The pathobiont and pathogenic microorganisms promoted tumor formation, while potential probiotic microorganisms had a suppressive effect on tumor formation (P > 0.01). One yeast (Candida kefyr MK17) and three lactic acid bacteria strains (Lacticaseibacillus paracasei MK73, Lactiplantibacillus plantarum MK55, Limosilactobacillus mucosae MK45) have superior potential thanks to their anticarcinogenic properties as well as tolerance to gastrointestinal tract conditions", "token_count": 514, "char_count": 1804, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6208, "quality_score": 0.8104, "entities": { "genes": [ "MK55", "MK17", "MK45", "MK73" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:16:37.894214", "source": { "split": "train_shard_00000", "doc_id": 1812 }, "chunk_id": "train_shard_00000_1812_0", "global_id": 1999 }, { "text": "Stool samples of each individual contain various potential probiotic, pathobiont, and pathogenic microorganisms.\n\nCharacterization of Some Microorganisms from Human Stool Samples and Determination of Their Effects on CT26 Colorectal Carcinoma Cell Line.", "token_count": 63, "char_count": 253, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8438, "quality_score": 0.9219, "entities": { "genes": [ "CT26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:38.268404", "source": { "split": "train_shard_00000", "doc_id": 1812 }, "chunk_id": "train_shard_00000_1812_1", "global_id": 2000 }, { "text": "Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users' genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.\n\nA Dual Barcoding Approach to Bacterial Strain Nomenclature: Genomic Taxonomy of Klebsiella pneumoniae Strains.", "token_count": 462, "char_count": 1910, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:38.955596", "source": { "split": "train_shard_00000", "doc_id": 1813 }, "chunk_id": "train_shard_00000_1813_0", "global_id": 2001 }, { "text": "Campylobacter coli resides in the intestine of several commonly consumed animals, as well as water and soil. It leads to campylobacteriosis when humans eat raw/undercooked meat or come into contact with infected animals. A common manifestation of the infection is fever, nausea, headache, and diarrhea. Increasing antibiotic resistance is being observed in this pathogen. The increased incidence of C. coli infection, and post-infection complications like Guillain-Barré syndrome, make it an important pathogen. It is essential to find novel therapeutic targets and drugs against it, especially with the emergence of antibiotic-resistant strains. In the current study, genomes of 89 antibiotic-resistant strains of C. coli were downloaded from the PATRIC database. Potent drug targets (n = 36) were prioritized from the core genome (n = 1,337 genes) of this species. Riboflavin synthase was selected as a drug target and pharmacophore-based virtual screening was performed to predict its inhibitors from the NPASS (n =  ~ 30,000 compounds) natural product library. The top three docked compounds (NPC115144, NPC307895, and NPC470462) were selected for dynamics simulation (for 50 ns) and ADMET profiling. These identified compounds appear safe for targeting this pathogen and can be further validated by experimental analysis before clinical trials.\n\nMining therapeutic targets from the antibiotic-resistant Campylobacter coli and virtual screening of natural product inhibitors against its riboflavin synthase.", "token_count": 422, "char_count": 1511, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6713, "quality_score": 0.8356, "entities": { "genes": [ "NPC307895", "NPC115144", "NPC470462" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:39.580567", "source": { "split": "train_shard_00000", "doc_id": 1814 }, "chunk_id": "train_shard_00000_1814_0", "global_id": 2002 }, { "text": "The mutualistic interactions between Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone (short Endoriftia) have been extensively researched. However, the closed Endoriftia genome is still lacking. Here, by employing single-molecule real-time sequencing we present the closed chromosomal sequence of Endoriftia. In contrast to theoretical predictions of enlarged and mobile genetic element-rich genomes related to facultative endosymbionts, the closed Endoriftia genome is streamlined with fewer than expected coding sequence regions, insertion-, prophage-sequences and transposase-coding sequences. Automated and manually curated functional analyses indicated that Endoriftia is more versatile regarding sulphur metabolism than previously reported. We identified the presence of two identical rRNA operons and two long CRISPR regions in the closed genome. Additionally, pangenome analyses revealed the presence of three types of secretion systems (II, IV and VI) in the different Endoriftia populations indicating lineage-specific adaptations. The in depth mobilome characterization identified the presence of shared genomic islands in the different Endoriftia drafts and in the closed genome, suggesting that the acquisition of foreign DNA predates the geographical dispersal of the different endosymbiont populations. Finally, we found no evidence of epigenetic regulation in Endoriftia, as revealed by gene screenings and absence of methylated modified base motifs in the genome. As a matter of fact, the restriction-modification system seems to be dysfunctional in Endoriftia, pointing to a higher importance of molecular memory-based immunity against phages via spacer incorporation into CRISPR system. The Endoriftia genome is the first closed tubeworm endosymbiont to date and will be valuable for future gene oriented and evolutionary comparative studies.\n\nThe complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep-sea hydrothermal vents.", "token_count": 469, "char_count": 2013, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6292, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:40.223790", "source": { "split": "train_shard_00000", "doc_id": 1815 }, "chunk_id": "train_shard_00000_1815_0", "global_id": 2003 }, { "text": "As a new feed additive, bile acid (BA) can promote the absorption and transport of lipids and fat-soluble vitamins. In recent years, BAs have been widely used in animal feed to promote fat absorption. Therefore, this study aimed to investigate the effect of bile salt supplementation in the diet of yellow-feathered broilers on messenger RNA (mRNA) expression of sterol regulatory element-binding protein 1 (SREBF1), fatty acid synthase (FAS), acetyl-coenzyme A carboxylase (ACC), and fatty acid transport protein 4 (FATP4).\n\nThe effect of bile salt diet supplementation on genes related to fat metabolism in yellow-feathered broilers.", "token_count": 170, "char_count": 635, "word_count": 95, "semantic_coherence": 1, "information_density": 0.6737, "quality_score": 0.8368, "entities": { "genes": [ "SREBF1", "FATP4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:40.664012", "source": { "split": "train_shard_00000", "doc_id": 1816 }, "chunk_id": "train_shard_00000_1816_0", "global_id": 2004 }, { "text": "Healthcare-associated infections (HAIs) cause mortality, morbidity, and waste of health care resources. HAIs are also an important driver of antimicrobial resistance, which is increasing around the world. Beginning in November 2016, we instituted an initiative to detect outbreaks of HAIs using prospective whole-genome sequencing-based surveillance of bacterial pathogens collected from hospitalized patients. Here, we describe the diversity of bacteria sampled from hospitalized patients at a single center, as revealed through systematic analysis of bacterial isolate genomes. We sequenced the genomes of 3,004 bacterial isolates from hospitalized patients collected over a 25-month period. We identified bacteria belonging to 97 distinct species, which were distributed among 14 groups of related species. Within these groups, isolates could be distinguished from one another by both average nucleotide identity (ANI) and principal-component analysis of accessory genes (PCA-A). Core genome genetic distances and rates of evolution varied among species, which has practical implications for defining shared ancestry during outbreaks and for our broader understanding of the origins of bacterial strains and species. Finally, antimicrobial resistance genes and putative mobile genetic elements were frequently observed, and our systematic analysis revealed patterns of occurrence across the different species sampled from our hospital. Overall, this study shows how understanding the population structure of diverse pathogens circulating in a single health care setting can improve the discriminatory power of genomic epidemiology studies and can help define the processes leading to strain and species differentiation.\n\nGenomic Diversity of Hospital-Acquired Infections Revealed through Prospective Whole-Genome Sequencing-Based Surveillance.", "token_count": 383, "char_count": 1846, "word_count": 245, "semantic_coherence": 1, "information_density": 0.649, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:41.252836", "source": { "split": "train_shard_00000", "doc_id": 1817 }, "chunk_id": "train_shard_00000_1817_0", "global_id": 2005 }, { "text": "Bile salt export pump (Bsep) (Abcb11)\n\nTetrahydroxylated bile acids improve cholestatic liver and bile duct injury in the Mdr2", "token_count": 45, "char_count": 126, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:41.617419", "source": { "split": "train_shard_00000", "doc_id": 1818 }, "chunk_id": "train_shard_00000_1818_0", "global_id": 2006 }, { "text": "In response to the massive use of biocides for controlling Listeria monocytogenes (hereafter Lm) contaminations along the food chain, strains showing biocide tolerance emerged. Here, accessory genomic elements were associated with biocide tolerance through pangenome-wide associations performed on 197 Lm strains from different lineages, ecological, geographical and temporal origins. Mobile elements, including prophage-related loci, the Tn6188_qacH transposon and pLMST6_emrC plasmid, were widespread across lineage I and II food strains and associated with tolerance to benzalkonium-chloride (BC), a quaternary ammonium compound (QAC) widely used in food processing. The pLMST6_emrC was also associated with tolerance to another QAC, the didecyldimethylammonium-chloride, displaying a pleiotropic effect. While no associations were detected for chemically reactive biocides (alcohols and chlorines), genes encoding for cell-surface proteins were associated with BC or polymeric biguanide tolerance. The latter was restricted to lineage I strains from animal and the environment. In conclusion, different genetic markers, with polygenic nature or not, appear to have driven the Lm adaptation to biocide, especially in food strains but also from animal and the environment. These markers could aid to monitor and predict the spread of biocide tolerant Lm genotypes across different ecological niches, finally reducing the risk of such strains in food industrial settings.\n\nGenomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches.", "token_count": 397, "char_count": 1627, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7977, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:42.239197", "source": { "split": "train_shard_00000", "doc_id": 1819 }, "chunk_id": "train_shard_00000_1819_0", "global_id": 2007 }, { "text": "This study evaluates the in vitro probiotic characteristics of P. konkukensis sp. nov. SK-3146, which was isolated from animal feed, and its dietary effects on growth performance, intestinal characteristics, intestinal microbiota, and meat quality in broilers. In vitro experiments revealed that P. konkukensis was non-hemolytic with variable antibiotic susceptibility, and acid as well as bile tolerance. To assess the effect of P. konkukensis on broilers, a total of four hundred eighty 1-day-old Ross 308 broiler chicks were allocated to 3 treatment groups with 4 replicates of 40 birds each; the negative control group was fed a basal diet without any feed additives (NC), the positive control group was fed a basal diet containing 0.01% enramycin (PC), and the experimental group was fed a basal diet containing P. konkukensis bacterial culture (PK) at 104 CFU/g of the diet based on bacterial count. The experiment lasted for 35 days. Results indicated that there were no significant differences in any growth performance parameters among the dietary treatments (p > 0.05). In addition, the inclusion of P. konkukensis in the broilers’ diet did not affect meat cooking loss, color, and pH but increased the relative weight of breast meat (p < 0.05). The PK group showed heavier intestinal weight and shorter intestinal length than the NC group (p < 0.05). The ratio of the intestinal weight to length of jejunum was the highest in the PK group (p < 0.05). The PK group showed increased counts of Streptococcus thermophilus (p < 0.05) with no adverse effects of P. konkukensis on other intestinal microbiota in the jejunum. This study implies that P. konkukensis might have the potential to be applied as a probiotic feed additive in poultry.\n\nPotential Probiotic Acceptability of a Novel Strain of", "token_count": 482, "char_count": 1803, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5448, "quality_score": 0.7724, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:42.887272", "source": { "split": "train_shard_00000", "doc_id": 1820 }, "chunk_id": "train_shard_00000_1820_0", "global_id": 2008 }, { "text": "Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits\n\nGraph pangenome captures missing heritability and empowers tomato breeding.", "token_count": 45, "char_count": 205, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:43.256712", "source": { "split": "train_shard_00000", "doc_id": 1821 }, "chunk_id": "train_shard_00000_1821_0", "global_id": 2009 }, { "text": "Staphylococcus aureus is an important human and livestock pathogen that is well-protected against environmental insults by a thick cell wall. Accordingly, the wall is a major target of present-day antimicrobial therapy. Unfortunately, S. aureus has mastered the art of antimicrobial resistance, as underscored by the global spread of methicillin-resistant S. aureus (MRSA). The major cell wall component is peptidoglycan. Importantly, the peptidoglycan network is not only vital for cell wall function, but it also represents a bacterial Achilles' heel. In particular, this network is continuously opened by no less than 18 different peptidoglycan hydrolases (PGHs) encoded by the S. aureus core genome, which facilitate bacterial growth and division. This focuses attention on the specific functions executed by these enzymes, their subcellular localization, their control at the transcriptional and post-transcriptional levels, their contributions to staphylococcal virulence and their overall importance in bacterial homeostasis. As highlighted in the present review, our understanding of the different aspects of PGH function in S. aureus has been substantially increased over recent years. This is important because it opens up new possibilities to exploit PGHs as innovative targets for next-generation antimicrobials, passive or active immunization strategies, or even to engineer them into effective antimicrobial agents.\n\nStaphylococcus aureus cell wall maintenance - the multifaceted roles of peptidoglycan hydrolases in bacterial growth, fitness, and virulence.", "token_count": 380, "char_count": 1572, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6544, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:43.839381", "source": { "split": "train_shard_00000", "doc_id": 1822 }, "chunk_id": "train_shard_00000_1822_0", "global_id": 2010 }, { "text": "Some Weissella species are used in probiotic products because of their beneficial effects in humans, whereas some species are considered as opportunistic pathogens that cause infections in humans. Therefore, an accurate and rapid identification of Weissella species is essential to control pathogenic Weissella species or isolate new functional strains with probiotic effects from their habitat. The objective of our study was to extract novel molecular targets using pangenome analysis for the identification of major Weissella species present in food. With 50 genomes representing 11 Weissella species, novel molecular targets were mined based on their 100% presence in the respective strains of the target species and absence in the strains of non-target bacteria. Primers based on molecular targets showed positive results for the corresponding species, whereas 79 non-target strains showed negative results. Standard curves revealed good linearity in the range of 10\n\nIdentification of novel molecular targets for Weissella species-specific real-time PCR based on pangenome analysis.", "token_count": 224, "char_count": 1088, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:44.317271", "source": { "split": "train_shard_00000", "doc_id": 1823 }, "chunk_id": "train_shard_00000_1823_0", "global_id": 2011 }, { "text": "Cadmium (Cd) directly endangers poultry health and indirectly causes harm to human health by food chain. Numerous studies have focused on removing Cd using lactic acid bacteria (LAB). However, there is still a lack of in vivo studies to validate whether Cd can be absorbed successfully by LAB to alleviate Cd toxicity. Here, we aimed to isolated and screened poultry-derived Cd-tolerant LAB with the strongest adsorption capacity in vitro and investigate the protective effect of which on sub-chronic Cd toxicity in chickens. First, nine Cd-tolerant LAB strains were selected preliminarily by isolating, screening, and identifying from poultry farms. Next, four strains with the strongest adsorption capacity were used to explore the influence of different physical and chemical factors on the ability of LAB to adsorb Cd as well as its probiotic properties in terms of acid tolerance, bile salt tolerance, drug resistance, and antibacterial effects. Resultantly, the CLF9-1 strain with the best comprehensive ability was selected for further animal protection test. The Cd-tolerant LAB treatment promoted the growth performance of chickens and reduced the Cd-elevated liver and kidney coefficients. Moreover, Cd-induced liver, kidney, and duodenum injuries were alleviated significantly by high-dose LAB treatment. Furthermore, LAB treatment also increased the elimination of Cd in feces and markedly reduced the Cd buildup in the liver and kidney. In summary, these findings determine that screened Cd-tolerant LAB strain exerts a protective effect on chickens against sub-chronic cadmium poisoning, thus providing an essential guideline for the public health and safety of livestock and poultry.\n\nProtective effects of fowl-origin cadmium-tolerant lactobacillus against sub-chronic cadmium-induced toxicity in chickens.", "token_count": 445, "char_count": 1822, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6145, "quality_score": 0.8073, "entities": { "genes": [ "CLF9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:44.943760", "source": { "split": "train_shard_00000", "doc_id": 1824 }, "chunk_id": "train_shard_00000_1824_0", "global_id": 2012 }, { "text": "One of the most basic kinds of analysis to be performed on a pangenome is the detection of its core, i.e., the information shared among all members. Pangenomic core detection is classically done on the gene level and many tools focus exclusively on core detection in prokaryotes. Here, we present a new method for sequence-based pangenomic core detection. Our model generalizes from a strict core definition allowing us to flexibly determine suitable core properties depending on the research question and the dataset under consideration. We propose an algorithm based on a colored de Bruijn graph that runs in linear time with respect to the number of\n\nSequence-based pangenomic core detection.", "token_count": 141, "char_count": 695, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:45.377587", "source": { "split": "train_shard_00000", "doc_id": 1825 }, "chunk_id": "train_shard_00000_1825_0", "global_id": 2013 }, { "text": "The beany flavor adversely influences consumer acceptance of soymilk (SM) products. Thus, in this work, the co-fermentation of isolated new yeasts (Kluyveromyces marxianus SP-1, Candida ethanolica ATW-1, and Pichia amenthionina Y) and Kluyveromyces marxianus K (a commercial yeast) along with an XPL-1 starter (including five strains of lactic acid bacteria (LAB)) was utilized to mend the beany flavor of fermented SM (FSM) beverages. Probiotic count, pH, titratable acidity, syneresis, water holding capacity, rheological characteristics, and sensory attributes were investigated. Furthermore, the free amino acids, nucleotides, and volatile compounds (VCs) were analyzed, also presenting the collected VC data by exploiting a principal component analysis (PCA) and a heatmap with a hierarchical cluster analysis. The co-fermentation with Kluyveromyces marxianus SP-1 and K remarkably enhanced the LAB strain growth and acid production, improving the rheological attributes, whereas that of yeast along with XPL-1 as a mullite starter could reduce the beany odor. PCA chart displayed that higher amounts of alcohols, ketones, acids, and esters that significantly improved the flavor quality of FSM beverages were generated throughout the co-fermentation process. The co-fermentation with Pichia amenthionina Y generated the highest acetoin (36.19%) and diacetyl (2.02%), thus improving the overall acceptance of FSM, as well as the sensory characteristics of FSM beverages with the highest umami, sweet, odorless amino acids, and umami nucleotides, and the lowest content of alcohol and inosine. Taken together, the co-fermentation of Pichia amenthionina Y along with XPL-1 within SM provides novel insights regarding the development of FSM and fermented beverages.", "token_count": 474, "char_count": 1767, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:46.016629", "source": { "split": "train_shard_00000", "doc_id": 1826 }, "chunk_id": "train_shard_00000_1826_0", "global_id": 2014 }, { "text": "Effect of co-fermentation system with isolated new yeasts on soymilk: microbiological, physicochemical, rheological, aromatic, and sensory characterizations.", "token_count": 42, "char_count": 157, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:46.381964", "source": { "split": "train_shard_00000", "doc_id": 1826 }, "chunk_id": "train_shard_00000_1826_1", "global_id": 2015 }, { "text": "Complications of short bowel syndrome (SBS) include malabsorption and bacterial overgrowth, requiring prolonged dependence on parenteral nutrition (PN). We hypothesized that the intolerance of whole food in some SBS patients might be due to the effect of dietary fiber on the gut microbiome. Shotgun metagenomic sequencing and targeted metabolomics were performed using biospecimens collected from 55 children with SBS and a murine dietary fiber model. Bioinformatic analyses were performed on these datasets as well as from a healthy human dietary intervention study. Compared to healthy controls, the gut microbiota in SBS had lower diversity and increased Proteobacteria, a pattern most pronounced in children on PN and inversely correlated with whole food consumption. Whole food intake correlated with increased glycoside hydrolases (GH) and bile salt hydrolases (BSH) with reduced fecal conjugated bile acids suggesting that dietary fiber regulates BSH activity via GHs. Mechanistic evidence supporting this notion was generated via fecal and plasma bile acid profiling in a healthy human fiber-free dietary intervention study as well as in a dietary fiber mouse experiment. Gaussian mixture modeling of fecal bile acids was used to identify three clinically relevant SBS phenotypes. Dietary fiber is associated with bile acid deconjugation likely via an interaction between gut microbiota BSHs and GHs in the small intestine, which may lead to whole food intolerance in patients with SBS. This mechanism not only has potential utility in clinical phenotyping and targeted therapeutics in SBS based on bile acid metabolism but may have relevance to other intestinal disease states.\n\nDietary fiber-based regulation of bile salt hydrolase activity in the gut microbiota and its relevance to human disease.", "token_count": 422, "char_count": 1809, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:47.002170", "source": { "split": "train_shard_00000", "doc_id": 1827 }, "chunk_id": "train_shard_00000_1827_0", "global_id": 2016 }, { "text": "Propolis is commonly used in traditional Chinese medicine. Studies have demonstrated the therapeutic effects of propolis extracts and its major bioactive compound caffeic acid phenethyl ester (CAPE) on obesity and diabetes. Herein, CAPE was found to have pharmacological activity against nonalcoholic fatty liver disease (NAFLD) in diet-induced obese mice. CAPE, previously reported as an inhibitor of bacterial bile salt hydrolase (BSH), inhibited BSH enzymatic activity in the gut microbiota when administered to mice. Upon BSH inhibition by CAPE, levels of tauro-β-muricholic acid were increased in the intestine and selectively suppressed intestinal farnesoid X receptor (FXR) signaling. This resulted in lowering of the ceramides in the intestine that resulted from increased diet-induced obesity. Elevated intestinal ceramides are transported to the liver where they promoted fat production. Lowering FXR signaling was also accompanied by increased GLP-1 secretion. In support of this pathway, the therapeutic effects of CAPE on NAFLD were absent in intestinal FXR-deficient mice, and supplementation of mice with C16-ceramide significantly exacerbated hepatic steatosis. Treatment of mice with an antibiotic cocktail to deplete BSH-producing bacteria also abrogated the therapeutic activity of CAPE against NAFLD. These findings demonstrate that CAPE ameliorates obesity-related steatosis at least partly through the gut microbiota-bile acid-FXR pathway via inhibiting bacterial BSH activity and suggests that propolis enriched with CAPE might serve as a promising therapeutic agent for the treatment of NAFLD.\n\nCaffeic acid phenethyl ester suppresses intestinal FXR signaling and ameliorates nonalcoholic fatty liver disease by inhibiting bacterial bile salt hydrolase activity.", "token_count": 466, "char_count": 1786, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:47.644461", "source": { "split": "train_shard_00000", "doc_id": 1828 }, "chunk_id": "train_shard_00000_1828_0", "global_id": 2017 }, { "text": "Gut microbiota comprise microorganisms residing in the gastrointestinal tract. Some of these microbiota are implicated in the progression of colorectal cancer (CRC). Here, we highlight studies on the effects of meat intake and fermented foods on characteristics of gut microbiota that can influence colitis-associated factors underlying CRC. Gut microbiota can influence the development and progression of CRC, through influencing factors such as secretion of toxins; enzymes for activating carcinogenesis (including β-glucuronidase, β-glucosidase, azoreductase, nitroreductase, and alcohol dehydrogenase); hydrogen sulfide generation; generation of reactive oxygen species and inflammation; secondary bile salt transformation; and products of protein fermentation. Additionally, some studies that the composition of gut microbiota (probiotics) or prebiotics plays an important role in the production of short chain fatty acids, inactivation enzymes for carcinogenesis, antioxidant activities, and inhibition of pathogen colonization. In this review, we discuss various explanatory mechanisms of the relationship between the multifactorial role of the gut microbiota and the development of CRC. Moreover, this review provides fundamental information on dietary fermented food and the gut microbiota, which is helpful for healthy people and those with CRC alike.\n\nRelationship between gut microbiota and colorectal cancer: Probiotics as a potential strategy for prevention.", "token_count": 348, "char_count": 1472, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6392, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:48.217161", "source": { "split": "train_shard_00000", "doc_id": 1829 }, "chunk_id": "train_shard_00000_1829_0", "global_id": 2018 }, { "text": "In this work, a multireactor system to study digestion (MuReDi) kinetics is introduced. For this, a custom-made automated system with four independent syringe pumps (BioXplorer 100, H.E.L Group) was acquired. This system consists of multiple, small-scale reactors allowing to study digestion as a function of time and thus to determine digestion kinetics. The different digestion conditions used in the oral, gastric, and small intestinal phase were based on the digestion protocols published by the INFOGEST consortium. We showed that the minimum working volume of a reactor is 30 mL. Besides, repeatability of the digestion kinetics was shown for two food systems: a liquid Ensure® Plus Vanilla drink, and a solid, cooked lentil sample. When comparing static digestion kinetics with semi-dynamic ones, a significantly different digestion pattern was observed. In the static case, a relatively fast hydrolysis rate was observed until a clear plateau was reached. Oppositely, for the semi-dynamic case, a delayed start of the hydrolysis process was noticed. In the gastric phase, this was explained by the decreasing pH and the large pH dependency of pepsin activity. In the small intestine, the lag phase was relatively shorter, yet clearly present. Here we related it to the gradual enzyme (and bile salt) secretion that had to diffuse towards the substrate before hydrolysis could start. Generally, this work showed that the MuReDi system could be used to perform a semi-dynamic digestion approach which largely impacted the overall digestion kinetics. This is important to consider in future in vitro food digestion simulation work to come closer to physiologically relevant digestion kinetics.\n\nStudying semi-dynamic digestion kinetics of food: Establishing a computer-controlled multireactor approach.", "token_count": 429, "char_count": 1807, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:48.845261", "source": { "split": "train_shard_00000", "doc_id": 1830 }, "chunk_id": "train_shard_00000_1830_0", "global_id": 2019 }, { "text": "In silico genome mining provides easy access to secondary metabolite biosynthetic gene clusters (BGCs) encoding the biosynthesis of many bioactive compounds, which are the basis for many important drugs used in human medicine. However, the association between BGCs and other functions encoded in the genomes of producers have remained elusive. Here, we present a systems biology workflow that integrates genome mining with a detailed pangenome analysis for detecting genes associated with a particular BGC. We analyzed 3,889 enterobacterial genomes and found 13,266 BGCs, represented by 252 distinct BGC families and 347 additional singletons. A pangenome analysis revealed 88 genes putatively associated with a specific BGC coding for the colon cancer-related colibactin that code for diverse metabolic and regulatory functions\n\nPangenome analysis of Enterobacteria reveals richness of secondary metabolite gene clusters and their associated gene sets.", "token_count": 223, "char_count": 953, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:49.342599", "source": { "split": "train_shard_00000", "doc_id": 1831 }, "chunk_id": "train_shard_00000_1831_0", "global_id": 2020 }, { "text": "Bread wheat (Triticum aestivum L.) is one of humanity's most important staple crops, characterized by a large and complex genome with a high level of gene presence-absence variation (PAV) between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate because of the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess PAV between bread wheat genomes.\n\nWheat Panache: A pangenome graph database representing presence-absence variation across sixteen bread wheat genomes.", "token_count": 254, "char_count": 1219, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:49.843965", "source": { "split": "train_shard_00000", "doc_id": 1832 }, "chunk_id": "train_shard_00000_1832_0", "global_id": 2021 }, { "text": "Bile acid (BA) homeostasis is mainly regulated by bile salt excretory pump (BSEP), a hepatocyte transporter that transfers BAs to the bile. BSEP expression is regulated by BA levels through activation of farnesoid X receptor transcription factor, which binds to the inverted repeat (IR-1) element in the BSEP promoter. Gene therapy of cholestatic diseases could benefit from using vectors carrying endogenous promoters physiologically regulated by BAs, however their large size limits this approach, especially when using adeno-associated viral vector (AAV) vectors.\n\nA minimal bile salt excretory pump promoter allows bile acid-driven physiological regulation of transgene expression from a gene therapy vector.", "token_count": 178, "char_count": 712, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7624, "quality_score": 0.8812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:50.314174", "source": { "split": "train_shard_00000", "doc_id": 1833 }, "chunk_id": "train_shard_00000_1833_0", "global_id": 2022 }, { "text": "Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. Here we generate haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT is sufficient to produce two haplotype-resolved assemblies meeting standards set by the Vertebrate Genomes Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrate significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identifies 90 thousand structural variants including 931 overlapping with coding sequences; this approach reveals variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46, and GC that have potential to affect phenotype.\n\nStructural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies.", "token_count": 295, "char_count": 1292, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7117, "quality_score": 0.8558, "entities": { "genes": [ "QRICH2", "PRDM9", "HSPA1A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:50.912984", "source": { "split": "train_shard_00000", "doc_id": 1834 }, "chunk_id": "train_shard_00000_1834_0", "global_id": 2023 }, { "text": "For all the promise of and need for clinical drug-induced liver injury (DILI) risk screening systems, demonstrating the predictive value of these systems versus readily available physicochemical properties and inherent dosing information has not been thoroughly evaluated. Therefore, we utilized a systematic approach to evaluate the predictive value of in vitro safety assays including bile salt export pump transporter inhibition and cytotoxicity in HepG2 and transformed human liver epithelial along with physicochemical properties. We also evaluated the predictive value of in vitro ADME assays including hepatic partition coefficient (Kp) and its unbound counterpart because they provide insight on hepatic accumulation potential. The datasets comprised of 569 marketed drugs with FDA DILIrank annotation (most vs less/none), dose and physicochemical information, 384 drugs with Kp and plasma protein binding data, and 279 drugs with safety assay data. For each dataset and combination of input parameters, we developed random forest machine learning models and measured model performance using the receiver operator characteristic area under the curve (ROC AUC). The median ROC AUC across the various data and parameters sets ranged from 0.67 to 0.77 with little evidence of additive predictivity when including safety or ADME assay data. Subsequent machine learning models consistently demonstrated daily dose, fraction sp3 or ionization, and cLogP/D inputs produced the best, simplest model for predicting clinical DILI risk with an ROC AUC of 0.75. This systematic framework should be used for future assay predictive value assessments and highlights the need for continued improvements to clinical DILI risk annotation.\n\nEarly Drug-Induced Liver Injury Risk Screening: \"Free,\" as Good as It Gets.", "token_count": 407, "char_count": 1806, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8352, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:51.538738", "source": { "split": "train_shard_00000", "doc_id": 1835 }, "chunk_id": "train_shard_00000_1835_0", "global_id": 2024 }, { "text": "Since its introduction in 2011 the variant call format (VCF) has been widely adopted for processing DNA and RNA variants in practically all population studies-as well as in somatic and germline mutation studies. The VCF format can represent single nucleotide variants, multi-nucleotide variants, insertions and deletions, and simple structural variants called and anchored against a reference genome. Here we present a spectrum of over 125 useful, complimentary free and open source software tools and libraries, we wrote and made available through the multiple vcflib, bio-vcf, cyvcf2, hts-nim and slivar projects. These tools are applied for comparison, filtering, normalisation, smoothing and annotation of VCF, as well as output of statistics, visualisation, and transformations of files variants. These tools run everyday in critical biomedical pipelines and countless shell scripts. Our tools are part of the wider bioinformatics ecosystem and we highlight best practices. We shortly discuss the design of VCF, lessons learnt, and how we can address more complex variation through pangenome graph formats, variation that can not easily be represented by the VCF format.\n\nA spectrum of free software tools for processing the VCF variant call format: vcflib, bio-vcf, cyvcf2, hts-nim and slivar.", "token_count": 306, "char_count": 1299, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:52.112188", "source": { "split": "train_shard_00000", "doc_id": 1836 }, "chunk_id": "train_shard_00000_1836_0", "global_id": 2025 }, { "text": "Allergic inflammation refers to a hyperimmune reaction that causes hypersensitivity responses such as hives, itchiness, runny nose, and cough due to specific allergens. Allergic diseases are known to be influenced by the diversity and distribution of intestinal microbiota, and Lactobacill is known to relieve allergic symptoms by modulating cytokines secreted by T helper type 1 (Th1)/Th2 cells. This study was designed to investigate the effects of Lactobacillus gasseri MG4247 and Lacticaseibacillus paracasei MG4272, MG4577, and MG4657 on levels of pro-inflammatory cytokines and proteins associated with allergic symptoms in RAW 264.7 macrophages, and RBL-2H3 mast cells, as well as their probiotic properties. MG4247, MG4272, and MG4577 significantly reduced tumor necrosis factor-α and interleukin (IL)-6 levels in LPS-induced RAW 264.7 macrophages, and markedly decreased IL-4, IL-5, and IL-13 levels and STAT6 phosphorylation in DNP-IgE/HSA sensitized RBL-2H3 mast cells. Furthermore, MG4247, MG4272, and MG4577 tolerated the acidic condition with pepsin and basic condition with bile salt, and showed a high adhesion rate (≥ 73.9%). In safety evaluation, MG4247, MG4272, and MG4577 showed no hemolytic or bile salt hydrolase activity and no cytotoxicity to HT-29 cells (≥ 96.7%). Hence, MG4272, MG4272, and MG4577 can be used as candidate probiotic strains to relieve cytokines associated with allergic inflammation.", "token_count": 488, "char_count": 1426, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8177, "entities": { "genes": [ "MG4247", "MG4272", "MG4657", "MG4577", "STAT6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:52.765224", "source": { "split": "train_shard_00000", "doc_id": 1837 }, "chunk_id": "train_shard_00000_1837_0", "global_id": 2026 }, { "text": "Lactobacillus gasseri MG4247 and Lacticaseibacillus paracasei MG4272 and MG4577 Modulate Allergic Inflammatory Response in RAW 264.7 and RBL-2H3 cells.", "token_count": 69, "char_count": 151, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [ "MG4247", "MG4272", "MG4577" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:53.135620", "source": { "split": "train_shard_00000", "doc_id": 1837 }, "chunk_id": "train_shard_00000_1837_1", "global_id": 2027 }, { "text": "This study aimed to investigate genomic traits underlying the antimicrobial resistance and virulence of multidrug-resistant (MDR) group B streptococci with reduced penicillin susceptibility (PRGBS) recovered from elderly patients with bloodstream infections, which remain poorly characterized. The pangenome was found to be open, with the predicted pan- and core genome sizes being 3,531 and 1,694 genes, respectively. Accessory and unique genes were enriched for the Clusters of Orthologous Groups (COG) categories L, Replication, recombination, and repair, and K, Transcription. All MDR PRGBS isolates retained a core virulence gene repertoire (\n\nGenomic Traits Associated with Virulence and Antimicrobial Resistance of Invasive Group B Streptococcus Isolates with Reduced Penicillin Susceptibility from Elderly Adults.", "token_count": 216, "char_count": 821, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:53.610476", "source": { "split": "train_shard_00000", "doc_id": 1838 }, "chunk_id": "train_shard_00000_1838_0", "global_id": 2028 }, { "text": "We announce the complete genomes of nine Streptococcus pneumoniae strains belonging to serotype 3 clonal complex 180 (CC180). The genomes consist of a single circularized contig with an average length of 2.033 Mbp. Pangenome analysis identified 1,762 core genes and 412 accessory genes. These genomes are the basis for future population genomic studies.\n\nComplete Genome Sequences of Nine Streptococcus pneumoniae Serotype 3 Clonal Complex 180 Strains.", "token_count": 131, "char_count": 452, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [ "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:54.034676", "source": { "split": "train_shard_00000", "doc_id": 1839 }, "chunk_id": "train_shard_00000_1839_0", "global_id": 2029 }, { "text": "Staphylococcus aureus is an important opportunistic pathogen of both humans and animals. It can cause several diseases, including mastitis, as well as food poisoning by production of heat-stable enterotoxins in food. The aim of this study was to determine the prevalence of S. aureus and the diversity of strains circulating in the Zambian dairy value chain, which have not been studied in detail before. Three provinces were covered by the study (Lusaka, Southern, and Western) and almost 2000 samples along the dairy value chain, covering both the informal and formal market sectors, were taken at two time points (dry and wet season), with a special focus on raw milk. Nearly 300 presumptive S. aureus isolates were confirmed by MALDI-TOF MS and real-time PCR. Raw milk from traditional and smallholder farms was widely contaminated with S. aureus; prevalence was 33-46% depending on the study province. Raw milk from milk collection centres, informal traders, traditional market sellers, and processors were also frequently contaminated with S. aureus. In addition, S. aureus was detected in several milk bucket swabs and nasal and hand swabs of milkers. From industrially processed (heat-treated) milk and dairy products, no S. aureus was isolated. Methicillin-resistant S. aureus (MRSA) were not detected, but around 10% of the S. aureus isolates carried lukS-PV, a marker gene for the virulence factor Pantone-Valentine leucocidin (PVL), which has been associated with severe diseases in human. Molecular typing identified a total of 44 spa types including 13 novel types: t18396, t18397, t18398, t18399, t18400, t18402, t18416, t20459, t20460, t20461, t20462, t20463, and t20464", "token_count": 506, "char_count": 1686, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:54.668858", "source": { "split": "train_shard_00000", "doc_id": 1840 }, "chunk_id": "train_shard_00000_1840_0", "global_id": 2030 }, { "text": "Furthermore, 12 novel multi-locus sequence types were identified: ST7012, ST7100, ST7101, ST7177, ST7291, ST7304, ST7305, ST7344, ST7596, ST7597, ST7598, and ST7599, of which ST7012, ST7177, and ST7596 fall into the bovine-associated clonal linage CC97. The spa types t084, t267, t355, and the novel type t20464 were common in all three study provinces. The predominant spa type varied depending on the province. Whole genome sequencing (WGS) and core genome multi-locus sequence typing (cgMLST) indicates transmission of strains along the Zambian dairy chain with possible persistence in the chain over time. cgMLST also revealed a very close relatedness between some isolates from milkers and from raw milk or milk buckets. The high prevalence and wide spa type diversity of S. aureus, as well as possible direct or indirect transmission of (potentially highly virulent) S. aureus to humans along the Zambian dairy value chain, are of public health concern, particularly as milk and milk products are often consumed raw by the Zambian population.\n\nPrevalence and diversity of Staphylococcus aureus in the Zambian dairy value chain: A public health concern.", "token_count": 355, "char_count": 1158, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6477, "quality_score": 0.8239, "entities": { "genes": [ "ST7012", "ST7344", "ST7599", "ST7597", "ST7177", "ST7291", "ST7304", "ST7101", "ST7305", "ST7598" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:55.239617", "source": { "split": "train_shard_00000", "doc_id": 1840 }, "chunk_id": "train_shard_00000_1840_1", "global_id": 2031 }, { "text": "The present study aimed to evaluate the probiotic potential of lactic acid bacteria (LAB) isolated from Chinese traditional fermented buffalo milk. Out of 22 isolates, 11 were putatively identified as LAB preliminarily. A total of six LAB strains displayed strong adhesion to HT-29 cells and all these strains showed preferable tolerance to artificially simulated gastrointestinal juices. WDS-4, WDS-7, and WDS-18 exhibited excellent antioxidant capacities, including DPPH radical, ABTS\n\nEvaluation of the Probiotic Potential of", "token_count": 142, "char_count": 528, "word_count": 74, "semantic_coherence": 1, "information_density": 0.8243, "quality_score": 0.9122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:55.667104", "source": { "split": "train_shard_00000", "doc_id": 1841 }, "chunk_id": "train_shard_00000_1841_0", "global_id": 2032 }, { "text": "Toxin-antitoxin (TA) systems are prevalent adaptive genetic elements in bacterial genomes, which can respond to environmental stress. While, few studies have addressed TA systems in probiotics and their roles in the adaptation to gastrointestinal transit (GIT) environments.\n\nHigBA toxin-antitoxin system of Weissella cibaria is involved in response to the bile salt stress.", "token_count": 96, "char_count": 374, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8269, "quality_score": 0.9135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:56.041213", "source": { "split": "train_shard_00000", "doc_id": 1842 }, "chunk_id": "train_shard_00000_1842_0", "global_id": 2033 }, { "text": "The demand of functional foods is on the rise, and researchers are trying to develop nutritious dairy products by using well-characterized strains of bacteria. In this study, we identified locally isolated strains of Lactobacillus fermentum from Bubalus bubalis (Nilli Ravi buffalo) milk and evaluated their potential as probiotics in food products like fermented milk. Fifteen Lactobacillus strains were initially isolated, and only four strains (NMCC-2, NMCC-14, NMCC-17, and NMCC-27) were examined for morphological and biochemical characterizations due to their ability of gas production in Durham tubes. Moreover, these strains were selected for further probiotic characterizations due to their extreme morphological resemblance with lactic acid bacteria for their antimicrobial activity, enzymatic potential, autoaggregation capability, hydrophobicity, and acid and bile tolerance. All selected isolates showed significant probiotic potential. However, NMCC-14 and NMCC-17 strains showed maximum probiotic potential. The isolates (NMCC-2, NMCC-14, NMCC-17, and NMCC-27) were identified as Lactobacillus fermentum utilizing 16S rRNA gene sequencing. The in vivo safety study of NMCC-14 (dose: 1010 CFU/day/mice; 21 days, orally) showed no histological dysfunctions in a mouse model. Pathogenic bacterial enzymes reduced the beneficial bacterial load in the host gastrointestinal tract. These results suggest that the NMCC-14 strain is safe and can be potentially used as a probiotic. Moreover, fermented milk was prepared by using the NMCC-14 strain. The results revealed that NMCC-14 strain-based fermented milk had significantly (p < 0.05) higher protein content (4.4 ± 0.06), water-holding capacity (WHC), and dynamic viscosity as compared to non-fermented milk. The results suggest that L", "token_count": 496, "char_count": 1797, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:56.699569", "source": { "split": "train_shard_00000", "doc_id": 1843 }, "chunk_id": "train_shard_00000_1843_0", "global_id": 2034 }, { "text": "fermentum NMCC-14 is safe and nontoxic; hence, it can be a beneficial supplement to be used for the development of dairy products to be subjected to further clinical testing.\n\nIdentification, Biochemical Characterization, and Safety Attributes of Locally Isolated", "token_count": 65, "char_count": 263, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:57.062369", "source": { "split": "train_shard_00000", "doc_id": 1843 }, "chunk_id": "train_shard_00000_1843_1", "global_id": 2035 }, { "text": "This study is about the isolation of yeast from fermented dairy and non-dairy products as well as the characterization of their survival in in vitro digestion conditions and tolerance to bile salts. Promising strains were selected to further investigate their probiotic properties, including cell surface properties (autoaggregation, hydrophobicity and coaggregation), physiological properties (adhesion to the HT-29 cell line and cholesterol lowering), antimicrobial activities, bile salt hydrolysis, exopolysaccharide (EPS) producing capability, heat resistance and resistance to six antibiotics. The selected yeast isolates demonstrated remarkable survivability in an acidic environment. The reduction caused by in vitro digestion conditions ranged from 0.7 to 2.1 Log\n\nIn Vitro Characterization and Identification of Potential Probiotic Yeasts Isolated from Fermented Dairy and Non-Dairy Food Products.", "token_count": 213, "char_count": 906, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8361, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:57.526776", "source": { "split": "train_shard_00000", "doc_id": 1844 }, "chunk_id": "train_shard_00000_1844_0", "global_id": 2036 }, { "text": "The global utilization of single-use, non-biodegradable plastics, such as bottles made of polyethylene terephthalate (PET), has contributed to catastrophic levels of plastic pollution. Fortunately, microbial communities are adapting to assimilate plastic waste. Previously, our work showed a full consortium of five bacteria capable of synergistically degrading PET. Using omics approaches, we identified the key genes implicated in PET degradation within the consortium's pangenome and transcriptome. This analysis led to the discovery of a novel PETase, EstB, which has been observed to hydrolyze the oligomer BHET and the polymer PET. Besides the genes implicated in PET degradation, many other biodegradation genes were discovered. Over 200 plastic and plasticizer degradation-related genes were discovered through the Plastic Microbial Biodegradation Database (PMBD). Diverse carbon source utilization was observed by a microbial community-based assay, which, paired with an abundant number of plastic- and plasticizer-degrading enzymes, indicates a promising possibility for mixed plastic degradation. Using RNAseq differential analysis, several genes were predicted to be involved in PET degradation, including aldehyde dehydrogenases and several classes of hydrolases. Active transcription of PET monomer metabolism was also observed, including the generation of polyhydroxyalkanoate (PHA)/polyhydroxybutyrate (PHB) biopolymers. These results present an exciting opportunity for the bio-recycling of mixed plastic waste with upcycling potential.\n\nMicrobial Consortia and Mixed Plastic Waste: Pangenomic Analysis Reveals Potential for Degradation of Multiple Plastic Types via Previously Identified PET Degrading Bacteria.", "token_count": 429, "char_count": 1729, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:58.145640", "source": { "split": "train_shard_00000", "doc_id": 1845 }, "chunk_id": "train_shard_00000_1845_0", "global_id": 2037 }, { "text": "The gene family protein phosphatase 2C (PP2C) is related to developmental processes and stress responses in plants. Barley (\n\nGenome-Wide Identification and Transcriptional Expression Profiles of", "token_count": 48, "char_count": 195, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [ "PP2C" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:58.505376", "source": { "split": "train_shard_00000", "doc_id": 1846 }, "chunk_id": "train_shard_00000_1846_0", "global_id": 2038 }, { "text": "The current environmental challenge is pushing food systems towards more sustainable models of production that require reorganizing of processes by re-using side products still containing nutrients. This work aimed at valorising a mix of bovine sweet whey and sunflower press cake, through targeted fermentation. After preliminary screening based on growth rate, final pH, lactose/galactose assimilation, phytase activity, six Lactic Acid Bacteria strains (Lacticaseibacillus casei, L. paracasei (2), Lactococcus lactis, Lentilactobacillus parakefiri and Leuconostoc pseudomesenteroides) and three yeasts (Kluyveromyces lactis, K. marxianus and Torulaspora delbrueckii) were co-cultivated in pairs in microcosms (1-part ground press cake: 4-parts whey). All tested microorganisms were able to grow and acidify the blend: the LAB counts increased during the incubation (26 °C for 48 h) of +2.80 log CFU/g, whereas yeasts counts were of +1.98 log CFU/g, with significant differences among the different associations (p < 0.01). Mould counts were always <3 log CFU/g. Interestingly, the bacterial contaminants count significantly varied in samples with different pairs of strains (p < 0.001). Acidification level, acetic acid and ethanol contents were the limiting factors affecting the growth of spoilage micro-organisms. Best performances were attained in microcosms inoculated with L. lactis or L. paracasei and K. lactis or K. marxianus.\n\nValorisation of Bovine Sweet Whey and Sunflower Press Cake Blend through Controlled Fermentation as Platform for Innovative Food Materials.", "token_count": 441, "char_count": 1579, "word_count": 220, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:59.130739", "source": { "split": "train_shard_00000", "doc_id": 1847 }, "chunk_id": "train_shard_00000_1847_0", "global_id": 2039 }, { "text": "Identification of Therapeutic Targets in an Emerging Gastrointestinal Pathogen", "token_count": 19, "char_count": 78, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:16:59.486995", "source": { "split": "train_shard_00000", "doc_id": 1848 }, "chunk_id": "train_shard_00000_1848_0", "global_id": 2040 }, { "text": "Leptospirosis is one of the most prevalent zoonotic diseases caused by pathogenic spirochetes of Leptospira spp. The disease has become a public health concern in urban localities in the tropics, where rats serve as significant reservoir animals for leptospirosis transmission. In Indonesia, the occurrence of leptospirosis is underestimated, and information on the causative Leptospira genotypes and serotypes is limited. This study reports the isolation of Leptospira spp. from rats captured in urban areas of Bogor, Indonesia. Serogroups and genotypes, sequence types (STs), or multiple-locus variable-number tandem repeat analysis (MLVA) types using 11 loci, were determined for the isolates. Furthermore, whole genome sequencing (WGS) was performed on 11 Indonesian isolates and 24 isolates from other Asian countries. Ninety small mammals, including 80 Rattus norvegicus and ten Suncus murinus, were captured and, 25 Leptospira spp. were isolated solely from R. norvegicus (31.3%). The isolates were identified as Leptospira borgpetersenii serogroup Javanica with ST 143 (four strains) and Leptospira interrogans serogroup Bataviae with the same MLVA type as isolates from other Asian countries (19); the serogroup of the two L. interrogans with ST252 could not be identified. The core genome SNP-based phylogenetic tree revealed that Indonesian isolates were genetically related to L. borgpetersenii serogroup Javanica strains widely distributed in Asian countries but formed a different cluster from other strains. The phylogenetic tree of L. interrogans serogroup Bataviae isolates from Indonesia, the Philippines, Taiwan, and Vietnam revealed that isolates were grouped into five clusters based on their geographic locations. This study discovered a high carriage rate of Leptospira spp. among R. norvegicus in Bogor, Indonesia, indicating a potential risk of rat-borne leptospirosis in the area. Besides L. borgpetersenii serogroup Javanica, WGS on L", "token_count": 520, "char_count": 1961, "word_count": 279, "semantic_coherence": 1, "information_density": 0.595, "quality_score": 0.7975, "entities": { "genes": [ "ST252" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:17:00.121400", "source": { "split": "train_shard_00000", "doc_id": 1849 }, "chunk_id": "train_shard_00000_1849_0", "global_id": 2041 }, { "text": "interrogans serogroup Bataviae illustrated the geographical structuring of genetic diversity in Leptospira spp.\n\nComparative genomic analysis of Leptospira spp. isolated from Rattus norvegicus in Indonesia.", "token_count": 52, "char_count": 206, "word_count": 25, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:00.491222", "source": { "split": "train_shard_00000", "doc_id": 1849 }, "chunk_id": "train_shard_00000_1849_1", "global_id": 2042 }, { "text": "As one of the US Department of Agriculture-Agricultural Research Service flagship databases, GrainGenes (https://wheat.pw.usda.gov) serves the data and community needs of globally distributed small grains researchers for the genetic improvement of the Triticeae family and Avena species that include wheat, barley, rye and oat. GrainGenes accomplishes its mission by continually enriching its cross-linked data content following the findable, accessible, interoperable and reusable principles, enhancing and maintaining an intuitive web interface, creating tools to enable easy data access and establishing data connections within and between GrainGenes and other biological databases to facilitate knowledge discovery. GrainGenes operates within the biological database community, collaborates with curators and genome sequencing groups and contributes to the AgBioData Consortium and the International Wheat Initiative through the Wheat Information System (WheatIS). Interactive and linked content is paramount for successful biological databases and GrainGenes now has 2917 manually curated gene records, including 289 genes and 254 alleles from the Wheat Gene Catalogue (WGC). There are >4.8 million gene models in 51 genome browser assemblies, 6273 quantitative trait loci and >1.4 million genetic loci on 4756 genetic and physical maps contained within 443 mapping sets, complete with standardized metadata. Most notably, 50 new genome browsers that include outputs from the Wheat and Barley PanGenome projects have been created. We provide an example of an expression quantitative trait loci track on the International Wheat Genome Sequencing Consortium Chinese Spring wheat browser to demonstrate how genome browser tracks can be adapted for different data types. To help users benefit more from its data, GrainGenes created four tutorials available on YouTube. GrainGenes is executing its vision of service by continuously responding to the needs of the global small grains community by creating a centralized, long-term, interconnected data repository. Database URL:https://wheat.pw.usda.gov.\n\nGrainGenes: a data-rich repository for small grains genetics and genomics.", "token_count": 494, "char_count": 2178, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6342, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:01.141813", "source": { "split": "train_shard_00000", "doc_id": 1850 }, "chunk_id": "train_shard_00000_1850_0", "global_id": 2043 }, { "text": "Previous genome mining of the strains Bacillus pumilus 7PB, Bacillus safensis 1TAz, 8Taz, and 32PB, and Priestia megaterium 16PB isolated from canola revealed differences in the profile of antimicrobial biosynthetic genes when compared to the species type strains. To evaluate not only the similarities among B. pumilus, B. safensis, and P. megaterium genomes but also the specificities found in the canola bacilli, we performed comparative genomic analyses through the pangenome evaluation of each species. Besides that, other genome features were explored, especially focusing on plant-associated and biotechnological characteristics. The combination of the genome metrics Average Nucleotide Identity and digital DNA-DNA hybridization formulas 1 and 3 adopting the universal thresholds of 95 and 70%, respectively, was suitable to verify the identification of strains from these groups. On average, core genes corresponded to 45%, 52%, and 34% of B. pumilus, B. safensis, and P. megaterium open pangenomes, respectively. Many genes related to adaptations to plant-associated lifestyles were predicted, especially in the Bacillus genomes. These included genes for acetoin production, polyamines utilization, root exudate chemoreceptors, biofilm formation, and plant cell-wall degrading enzymes. Overall, we could observe that strains of these species exhibit many features in common, whereas most of their variable genome portions have features yet to be uncovered. The observed antifungal activity of canola bacilli might be a result of the synergistic action of secondary metabolites, siderophores, and chitinases. Genome analysis confirmed that these species and strains have biotechnological potential to be used both as agricultural inoculants or hydrolases producers. Up to our knowledge, this is the first work that evaluates the pangenome features of P. megaterium.", "token_count": 476, "char_count": 1874, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:02.261252", "source": { "split": "train_shard_00000", "doc_id": 1851 }, "chunk_id": "train_shard_00000_1851_0", "global_id": 2044 }, { "text": "Pangenome analyses of Bacillus pumilus, Bacillus safensis, and Priestia megaterium exploring the plant-associated features of bacilli strains isolated from canola.", "token_count": 48, "char_count": 163, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:02.638468", "source": { "split": "train_shard_00000", "doc_id": 1851 }, "chunk_id": "train_shard_00000_1851_1", "global_id": 2045 }, { "text": "Saccharomyces boulardii (S. boulardii) is a probiotic and is widely used to improve the nutritional and functional value of food. This study aimed to compare the probiotic properties of S. boulardii and Saccharomyces cerevisiae. A series of in vitro probiotic experiments was performed, including simulated gastrointestinal digestion, bile salt tolerance, hydrophobicity, self-aggregation, and antioxidant and antibacterial properties. Self-aggregation and hydrophobic properties of S. boulardii were relatively poor, but they showed high tolerance, antioxidant properties, and broad antibacterial properties. In addition, non-targeted metabolomics was used to comprehensively analyze the active metabolites of S. boulardii and the metabolic differences between S. boulardii and S. cerevisiae were compared. Saccharomyces boulardii produced many bioactive metabolites, which generally showed antioxidant, antibacterial, antitumor, anti-inflammatory, and other properties. In contrast to S. cerevisiae, S. boulardii produced phenyllactic acid and 2-hydroxyisocaproic acid. There were also significant differences in their metabolic pathways. These results may be of great significance in the medical and food industries and provide a basis for understanding the metabolism of S. boulardii. It also shows that metabolomics is an effective and novel method for screening microbial functional metabolites and identifying functional differences between similar microorganisms.\n\nUnique Probiotic Properties and Bioactive Metabolites of Saccharomyces boulardii.", "token_count": 388, "char_count": 1554, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:03.287924", "source": { "split": "train_shard_00000", "doc_id": 1852 }, "chunk_id": "train_shard_00000_1852_0", "global_id": 2046 }, { "text": "Renibacterium salmoninarum, a Gram-positive intracellular pathogen, is the causative agent of bacterial kidney disease (BKD), the impacts of which are high mortalities and economic losses for the salmon industry. This study provides novel analyses for the whole-genome sequences of 50 R. salmoninarum isolates and the reference strain ATCC 33209 using a pan-genomic approach to elucidate phylogenomic relationships and identify unique and shared genes associated with pathogenicity and infection mechanisms. Genome size varied from 3,061,638 to 3,155,332 bp; gene count from 3452 to 3580; and predicted coding sequences from 3402 to 3527. Comparative analyses revealed an open, but approaching closed, pan-genome. The pan-genome analysis recovered 4064 genes, with a core genome containing 3306 genes. Phylogenetic analysis of R. salmoninarum showed high genomic homogeneity, apart from one isolate obtained from Salmo trutta in Norway. All genomes presented the 57-kDa protein (p57). Strain ATCC 33209 and the Chilean isolates H-2 and DJ2R presented two copies of the msa gene, while the remaining isolates had one copy. The pan-genome analysis further identified differences in the number of copies and length of the signalling peptide for p57, the principal virulence factor reported for this bacterium. This heterogeneity could be associated with the secretion levels of p57, potentially influencing virulence. Additionally identified were numerous common genes related to iron uptake, the stress response and regulation, and cell signalling-all of which constitute the pathogenic repertoire of R. salmoninarum. This investigation provides information that is applicable in future studies for identifying therapeutic targets and/or for designing new strategies (e.g., vaccines) to prevent BKD infections in salmon farming.", "token_count": 477, "char_count": 1826, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [ "DJ2R" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:03.926805", "source": { "split": "train_shard_00000", "doc_id": 1853 }, "chunk_id": "train_shard_00000_1853_0", "global_id": 2047 }, { "text": "Comparative pan-genomic analysis of 51 Renibacterium salmoninarum indicates heterogeneity in the principal virulence factor, the 57 kDa protein.", "token_count": 40, "char_count": 144, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:04.283415", "source": { "split": "train_shard_00000", "doc_id": 1853 }, "chunk_id": "train_shard_00000_1853_1", "global_id": 2048 }, { "text": "The bacterial accessory genome provides the genetic flexibility needed to facilitate environment and host adaptation. In Neisseria gonorrhoeae, known accessory elements include plasmids which can transfer and mediate antimicrobial resistance (AMR); however, chromosomal accessory genes could also play a role in AMR. Here, the gonococcal accessory genome was characterized using gene-by-gene approaches and its association with the core genome and AMR were assessed. The gonococcal accessory gene pool consisted of 247 genes, which were mainly genes located on large mobile genetic elements, phage associated genes, or genes encoding putative secretion systems. Accessory elements showed similar synteny across genomes, indicating either a predisposition for particular genomic locations or ancestral inheritance that are conserved during strain expansion. Significant associations were found between the prevalence of accessory elements and core genome multi-locus sequence types (cgMLST), consistent with a structured gonococcal population despite frequent horizontal gene transfer (HGT). Increased prevalence of putative DNA exchange regulators was significantly associated with AMR, which included a putative secretion system, methyltransferases and a toxin-antitoxin system. Although frequent HGT results in high genetic diversity in the gonococcus, we found that this is mediated by a small gene pool. In fact, a highly organized genome composition was identified with a strong association between the accessory and core genome. Increased prevalence of DNA exchange regulators in antimicrobial resistant isolates suggests that genetic material exchange plays a role in the development or maintenance of AMR. These findings enhance our understanding of gonococcal genome architecture and have important implications for gonococcal population biology.\n\nThe Neisseria gonorrhoeae Accessory Genome and Its Association with the Core Genome and Antimicrobial Resistance.", "token_count": 431, "char_count": 1970, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7943, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:04.912182", "source": { "split": "train_shard_00000", "doc_id": 1854 }, "chunk_id": "train_shard_00000_1854_0", "global_id": 2049 }, { "text": "During the development of a melanocortin (MC) peptide drug to treat the condition of cachexia (a hypermetabolic state producing lean body mass wasting), we were confronted with the need for peptide transport across the blood-brain barrier (BBB): the MC-4 receptors (MC4Rs) for metabolic rate control are located in the hypothalamus, i.e., behind the BBB. Using the term \"peptides with BBB transport\", we screened the medical literature like a peptide library. This revealed numerous \"hits\"-peptides with BBB transport and/or oral activity. We noted several features common to most peptides in this class, including a dipeptide sequence of nonpolar residues, primary structure cyclization (whole or partial), and a Pro-aromatic motif usually within the cyclized region. Based on this, we designed an MC4R antagonist peptide, TCMCB07, that successfully treated many forms of cachexia. As part of our pharmacokinetic characterization of TCMCB07, we discovered that hepatobiliary extraction from blood accounted for a majority of the circulating peptide's excretion. Further screening of the literature revealed that TCMCB07 is a member of a long-forgotten peptide class, showing active transport by a multi-specific bile salt carrier. Bile salt transport peptides have predictable pharmacokinetics, including BBB transport, but rapid hepatic clearance inhibited their development as drugs. TCMCB07 shares the general characteristics of the bile salt peptide class but with a much longer half-life of hours, not minutes. A change in its C-terminal amino acid sequence slows hepatic clearance. This modification is transferable to other peptides in this class, suggesting a platform approach for producing drug-like peptides.\n\nDevelopment of a Therapeutic Peptide for Cachexia Suggests a Platform Approach for Drug-like Peptides.", "token_count": 471, "char_count": 1824, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6412, "quality_score": 0.8206, "entities": { "genes": [ "TCMCB07", "MC4R" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:05.552936", "source": { "split": "train_shard_00000", "doc_id": 1855 }, "chunk_id": "train_shard_00000_1855_0", "global_id": 2050 }, { "text": "Gamma-aminobutyric acid (GABA) improves various physiological illnesses, including diabetes, hypertension, depression, memory lapse, and insomnia in humans. Therefore, interest in the commercial production of GABA is steadily increasing. Lactic acid bacteria (LAB) have widely been reported as a GABA producer and are safe for human consumption. In this study, GABA-producing LAB were preliminarily identified and quantified via GABase assay. The acid and bile tolerance of the\n\nProbiotic Properties and Optimization of Gamma-Aminobutyric Acid Production by", "token_count": 140, "char_count": 557, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7867, "quality_score": 0.8933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:05.978937", "source": { "split": "train_shard_00000", "doc_id": 1856 }, "chunk_id": "train_shard_00000_1856_0", "global_id": 2051 }, { "text": "Congenital bile acid synthesis defect type 3 is a rare metabolic liver disease with only eight patients reported in literature. We describe clinical, pathological and molecular features for a ninth patient. A 4-month-old infant presented to us with conjugated hyperbilirubinemia. His liver biopsy revealed giant cell change, steatosis, and activity with diffuse fibrosis. Immunostaining with bile salt export pump showed preserved canalicular pattern and γ-glutamyl transferase 1 staining showed unusual complete membranous pattern. Genetic workup revealed homozygous single base pair duplication in exon 3 of the\n\nCongenital Bile Acid Synthesis Defect Type 3 With Severe Neonatal Cholestasis.", "token_count": 177, "char_count": 693, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7835, "quality_score": 0.8918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:06.421648", "source": { "split": "train_shard_00000", "doc_id": 1857 }, "chunk_id": "train_shard_00000_1857_0", "global_id": 2052 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is a serious public health concern in the United States. Patients colonized and/or infected can transmit MRSA to healthcare workers and subsequent patients However, the components of this transmission chain are just becoming evident, including certain patient factors, specific patient-healthcare worker interactions, and microbial factors. We conducted a comparative genomic analysis of 388 isolates from four hospitals in three states: Maryland, California, and New York. Isolates from nasal surveillance or clinical cultures were categorized as high, moderate, or low transmission surrogate outcomes based on the number of times the species was identified on the gloves or gowns of healthcare providers. The comparative analyses included a single gene, multigene, and core genome phylogenetic analysis, as well as a genome-wide association analysis to identify molecular signatures associated with the observed transmission surrogate outcomes, geographic origin, or sample source of isolation. Based on the phylogenetic analysis, 95% (\n\nComparative Genomics Identifies Features Associated with Methicillin-Resistant Staphylococcus aureus (MRSA) Transmission in Hospital Settings.", "token_count": 272, "char_count": 1233, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7117, "quality_score": 0.8558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:06.973484", "source": { "split": "train_shard_00000", "doc_id": 1858 }, "chunk_id": "train_shard_00000_1858_0", "global_id": 2053 }, { "text": "The Streptococcus pneumoniae Rgg144/SHP144 regulator-peptide quorum sensing (QS) system is critical for nutrient utilization, oxidative stress response, and virulence. Here, we characterized this system by assessing the importance of each residue within the active short hydrophobic peptide (SHP) by alanine-scanning mutagenesis and testing the resulting peptides for receptor binding and activation of the receptor. Interestingly, several of the mutations had little effect on binding to Rgg144 but reduced transcriptional activation appreciably. In particular, a proline substitution (P21A) reduced transcriptional activation by 29-fold but bound with a 3-fold higher affinity than the wild-type SHP. Consistent with the function of Rgg144, the mutant peptide led to decreased utilization of mannose and increased susceptibility to superoxide generator paraquat. Pangenome comparison showed full conservation of P21 across SHP144 allelic variants. Crystallization of Rgg144 in the absence of peptide revealed a comparable structure to the DNA bound and free forms of its homologs suggesting similar mechanisms of activation. Together, these analyses identify key interactions in a critical pneumococcal QS system. Further manipulation of the SHP has the potential to facilitate the development of inhibitors that are functional across strains. The approach described here is likely to be effective across QS systems in multiple species.\n\nStructure-function analysis for the development of peptide inhibitors for a Gram-positive quorum sensing system.", "token_count": 375, "char_count": 1552, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "SHP144" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:07.557829", "source": { "split": "train_shard_00000", "doc_id": 1859 }, "chunk_id": "train_shard_00000_1859_0", "global_id": 2054 }, { "text": "The commensal microbes of the gut microbiota make important contributions to host defense against gastrointestinal pathogens, including\n\nMicrobiota-Associated Biofilm Regulation Leads to", "token_count": 45, "char_count": 186, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:07.922938", "source": { "split": "train_shard_00000", "doc_id": 1860 }, "chunk_id": "train_shard_00000_1860_0", "global_id": 2055 }, { "text": "Streptococcus suis, the leading causative agent of swine streptococcosis, is considered as a severe zoonotic and foodborne pathogen for humans. Characteristics of population structure and pathogenicity of S. suis vary significantly by serotypes. As one of the main pathogenic serotypes causing clinical disease in pigs, very little is known about the pathogenicity, population structure, and antimicrobial resistance of S. suis serotype 8 (SS8). In this study, the genome of 26 SS8 strains isolated from healthy and diseased pigs was sequenced. Together with 38 sequences from NCBI, we found that SS8 population was clustered into 12 sequence types (ST) and 4 minimum core genome (MCG) groups, linked to the geographical distribution. Noteworthily, 10 strains belonged to MCG group 1 which was defined to possess the capacity to cause global outbreaks in our previous study. We found that 75% (9/12) of representative SS8 strains were virulent in mice and zebrafish, including all ST1241 strains. No virulence indicators were identified from 67 putative virulence-associated genes mainly identified among pathogenic serotype 2 strains. Instead, we found that the genotype of some of these genes was correlated to their evolution. All 26 isolates were classified as multidrug-resistant strains by antimicrobial susceptibility testing. The high carrying rate of tetO and ermB, mainly disseminated by integrative mobilizable elements, contributed to the prevalent resistance phenotypes to macrolides, lincosamides and tetracyclines. These findings indicated that the pathogenic potential of SS8 cannot be ignored and provided valuable information for SS8 surveillance.\n\nThe characteristics of population structure and antimicrobial resistance of Streptococcus suis serotype 8, a non-negligible pathotype.", "token_count": 453, "char_count": 1801, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.8191, "entities": { "genes": [ "ST1241", "SS8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:08.557086", "source": { "split": "train_shard_00000", "doc_id": 1861 }, "chunk_id": "train_shard_00000_1861_0", "global_id": 2056 }, { "text": "The present work describes the synthesis and characterization of pyrene derivatives, N-(1-Pyrenoylmethyl) pyridinium bromide (PM-PB) and N-(1-Pyrenoylmethyl)-N,N,N-triethylammonium bromide (PM-TAB). The photophysical behavior of these molecules has been studied in various protic and aprotic solvents. Using steady state fluorescence intensity, fluorescence anisotropy and dynamic fluorescence lifetime studies, the sensitivity of these molecules towards the micellization process of bile salts has been monitored. These derivatives have been effectively used in estimating critical micellar concentration (CMC) of bile salt, sodium deoxycholate (NaDC).\n\nPhotophysical Behaviour of Novel Quaternary Pyrenoyl Salts and Their Sensitivity Towards Bile Salt Micellization.", "token_count": 217, "char_count": 768, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:09.016511", "source": { "split": "train_shard_00000", "doc_id": 1862 }, "chunk_id": "train_shard_00000_1862_0", "global_id": 2057 }, { "text": "Pangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions. Nevertheless, analyzing hundreds of gigabase-scale genomes using pangenome graphs is difficult as it is not well-supported by existing tools. Hence, fast and versatile software is required to ask advanced questions to such data in an efficient way.\n\nODGI: understanding pangenome graphs.", "token_count": 103, "char_count": 519, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8082, "quality_score": 0.9041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:09.399027", "source": { "split": "train_shard_00000", "doc_id": 1863 }, "chunk_id": "train_shard_00000_1863_0", "global_id": 2058 }, { "text": "Members of the bacterial genus Rickettsia were originally identified as causative agents of vector-borne diseases in mammals. However, many Rickettsia species are arthropod symbionts and close relatives of 'Candidatus Megaira', which are symbiotic associates of microeukaryotes. Here, we clarify the evolutionary relationships between these organisms by assembling 26 genomes of Rickettsia species from understudied groups, including the Torix group, and two genomes of 'Ca. Megaira' from various insects and microeukaryotes. Our analyses of the new genomes, in comparison with previously described ones, indicate that the accessory genome diversity and broad host range of Torix Rickettsia are comparable to those of all other Rickettsia combined. Therefore, the Torix clade may play unrecognized roles in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose the name 'Candidatus Tisiphia'.\n\nGenomic diversity across the Rickettsia and 'Candidatus Megaira' genera and proposal of genus status for the Torix group.", "token_count": 268, "char_count": 1077, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:09.957240", "source": { "split": "train_shard_00000", "doc_id": 1864 }, "chunk_id": "train_shard_00000_1864_0", "global_id": 2059 }, { "text": "While previous research on zoonotic transmission of community-acquired Clostridioides difficile infection (CA-CDI) focused on food-producing animals, the present study aimed to investigate whether dogs are carriers of resistant and/or virulent C. difficile strains. Rectal swabs were collected from 323 dogs and 38 C. difficile isolates (11.8%) were obtained. Isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing (WGS) and a DNA hybridization assay. Multilocus sequence typing (MLST), core genome MLST (cgMLST) and screening for virulence and antimicrobial resistance genes were performed based on WGS. Minimum inhibitory concentrations for erythromycin, clindamycin, tetracycline, vancomycin and metronidazole were determined by E-test. Out of 38 C. difficile isolates, 28 (73.7%) carried genes for toxins. The majority of isolates belonged to MLST sequence types (STs) of clade I and one to clade V. Several isolates belonged to STs previously associated with human CA-CDI. However, cgMLST showed low genetic relatedness between the isolates of this study and C. difficile strains isolated from humans in Austria for which genome sequences were publicly available. Four isolates (10.5%) displayed resistance to three of the tested antimicrobial agents. Isolates exhibited resistance to erythromycin, clindamycin, tetracycline and metronidazole. These phenotypic resistances were supported by the presence of the resistance genes erm(B), cfr(C) and tet(M). All isolates were susceptible to vancomycin. Our results indicate that dogs may carry virulent and antimicrobial-resistant C. difficile strains.\n\nDogs as carriers of virulent and resistant genotypes of Clostridioides difficile.", "token_count": 477, "char_count": 1725, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6309, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:10.599909", "source": { "split": "train_shard_00000", "doc_id": 1866 }, "chunk_id": "train_shard_00000_1866_0", "global_id": 2060 }, { "text": "The liver takes up bile salts from blood to generate bile, enabling absorption of lipophilic nutrients and excretion of metabolites and drugs\n\nStructural basis of sodium-dependent bile salt uptake into the liver.", "token_count": 55, "char_count": 212, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8438, "quality_score": 0.9219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:10.964580", "source": { "split": "train_shard_00000", "doc_id": 1867 }, "chunk_id": "train_shard_00000_1867_0", "global_id": 2061 }, { "text": "Tanshinone IIA alleviate rifampicin-induced cholestasis by regulating the expression and function of bile salt export pump.", "token_count": 34, "char_count": 123, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:11.329963", "source": { "split": "train_shard_00000", "doc_id": 1868 }, "chunk_id": "train_shard_00000_1868_0", "global_id": 2062 }, { "text": "The lipolysis-mediated postprandial small intestinal environment is known to influence the solubilisation and subsequent absorption of lipophilic drugs. In a previously performed small-scale clinical study in healthy volunteers, co-administration of the lipase inhibitor orlistat increased jejunal solubilisation and systemic absorption of fenofibrate after intake of the lipid-based formulation Fenogal. In the present study, the jejunal disposition of the locally acting orlistat was assessed and linked to fenofibrate solubilisation. In addition, the effect of orlistat-induced lipolysis inhibition on bile salt concentrations and composition was evaluated. Orlistat was distributed predominantly in the lipid layer, as indicated by a 5- to 14-fold higher AUC\n\nOrlistat disposition in the human jejunum and the effect of lipolysis inhibition on bile salt concentrations and composition.", "token_count": 212, "char_count": 889, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6134, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:11.786802", "source": { "split": "train_shard_00000", "doc_id": 1869 }, "chunk_id": "train_shard_00000_1869_0", "global_id": 2063 }, { "text": "The Crabtree effect molecular regulation comprehension could help to improve ethanol production with biotechnological purposes and a better understanding of cancer etiology due to its similarity with the Warburg effect. Snf1p/Hxk2p/Mig1p pathway has been linked with the transcriptional regulation of the hexose transporters and phenotypes associated with the Crabtree effect. Nevertheless, direct evidence linking the genetic control of the hexose transporters with modulation of the Crabtree effect phenotypes by the Snf1p/Hxk2p/Mig1p pathway is still lacking. In this sense, we provide evidence that SNF1 and HXK2 genes deletion affects exponential growth, mitochondrial respiration, and transcript levels of hexose transporters in a glucose-dependent manner. The Vmax of the hexose transporters with the high transcript levels was correlated positively with the exponential growth and negatively with the mitochondrial respiration. HXT2 gene transcript levels were the most affected by the deletion of the SNF1/HXK2/MIG1 pathway. Deleting the orthologous genes SNF1 and HXK2 in Kluyveromyces marxianus (Crabtree negative yeast) has an opposite effect compared to Saccharomyces cerevisiae in growth and mitochondrial respiration. Overall, these results indicate that the SNF1/HXK2/MIG1 pathway regulates transcript levels of the hexose transporters, which shows an association with the exponential growth and mitochondrial respiration in a glucose-dependent manner.\n\nSnf1p/Hxk2p/Mig1p pathway regulates hexose transporters transcript levels, affecting the exponential growth and mitochondrial respiration of Saccharomyces cerevisiae.", "token_count": 428, "char_count": 1636, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [ "SNF1", "HXT2", "HXK2", "MIG1" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:12.428520", "source": { "split": "train_shard_00000", "doc_id": 1870 }, "chunk_id": "train_shard_00000_1870_0", "global_id": 2064 }, { "text": "Kluyveromyces marxianus is an interesting and important yeast because of particular traits such as thermotolerance and rapid growth, and for applications in food and industrial biotechnology. For both understanding its biology and developing bioprocesses, it is important to understand how K. marxianus responds and adapts to changing environments. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. We report here the development of a ribosome profiling method for K. marxianus, which allows codon resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs. To aid in the analysis and sharing of ribosome profiling data, we added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. We also provide a set of step-by-step protocols for the experimental and bioinformatic methods that we developed.\n\nDevelopment of a ribosome profiling protocol to study translation in Kluyveromyces marxianus.", "token_count": 297, "char_count": 1235, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:12.989895", "source": { "split": "train_shard_00000", "doc_id": 1871 }, "chunk_id": "train_shard_00000_1871_0", "global_id": 2065 }, { "text": "As a halophilic food-borne pathogen, Vibrio parahaemolyticus continueo be a major health issue worldwide. The pathogenic mechanisms of V. parahaemolyticus are still not fully understood. One of the most abundant and widely distributed groups of helix-turn-helix transcription factors is the GntR family of regulators, which are involved in the regulation of various biological processes in bacteria, but little is known about their functions in V. parahaemolyticus. Here, we identified a gene designated as hutC in V. parahaemolyticus SH112 that encodes a member belongs to the HutC subfamily of the large GntR transcriptional regulator family. Compared to the wild type, the hutC mutant strain was significantly more sensitive to acid, bile salt, Triton X-100, and sodium dodecyl sulfate stresses. Our results showed that HutC is required for optimal swimming motility but not necessary for the swarming of V. parahaemolyticus. In addition, inactivation of hutC in V. parahaemolyticus SH112 led to decreased biofilm formation, reduced cytotoxicity in Coca-2 cells, and defective virulence in vivo compared to the wild-type strain. Furthermore, transcriptome sequencing (RNA-Seq) analysis and real-time PCR indicated 4 upregulated and 14 downregulated genes in the hutC mutant strain. Functional analysis revealed that 4 upregulated genes were related to the histidine metabolism pathway. The 14 downregulated genes were mostly related to the cellular metabolic process, binding, and membrane part. This study presents evidence that HutC is involved in bacterial survival under conditions of stress, swimming motility, biofilm formation, cytotoxicity, virulence, and gene regulation of V. parahaemolyticus during infection.\n\nThe GntR-like transcriptional regulator HutC involved in motility, biofilm-forming ability, and virulence in Vibrio parahaemolyticus.", "token_count": 489, "char_count": 1858, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7989, "entities": { "genes": [ "SH112" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:13.677701", "source": { "split": "train_shard_00000", "doc_id": 1872 }, "chunk_id": "train_shard_00000_1872_0", "global_id": 2066 }, { "text": "Children with progressive familial intrahepatic cholestasis, including bile salt export pump (BSEP) and familial intrahepatic cholestasis-associated protein 1 (FIC1) deficiencies, suffer debilitating cholestatic pruritus that adversely affects growth and quality of life (QoL). Reliance on surgical interventions, including liver transplantation, highlights the unmet therapeutic need. INDIGO was an open-label, Phase 2, international, long-term study to assess the efficacy and safety of maralixibat in children with FIC1 or BSEP deficiencies. Thirty-three patients, ranging from 12 months to 18 years of age, were enrolled. Eight had FIC1 deficiency and 25 had BSEP deficiency. Of the latter, 6 had biallelic, protein truncating mutations (t)-BSEP, and 19 had ≥ 1 nontruncating mutation (nt)-BSEP. Patients received maralixibat 266 μg/kg orally, once daily, from baseline to Week 72, with twice-daily dosing permitted from Week 72. Long-term efficacy was determined at Week 240. Serum bile acid (sBA) response (reduction in sBAs of > 75% from baseline or concentrations <102.0 μmol/L) was achieved in 7 patients with nt-BSEP, 6 during once-daily dosing, and 1 after switching to twice-daily dosing. sBA responders also demonstrated marked reductions in sBAs and pruritus, and increases in height, weight, and QoL. All sBA responders remained liver transplant-free after > 5 years. No patients with FIC1 deficiency or t-BSEP deficiency met the sBA responder criteria during the study. Maralixibat was generally well-tolerated throughout the study", "token_count": 488, "char_count": 1547, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6742, "quality_score": 0.8371, "entities": { "genes": [ "FIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:14.358299", "source": { "split": "train_shard_00000", "doc_id": 1873 }, "chunk_id": "train_shard_00000_1873_0", "global_id": 2067 }, { "text": "Conclusion: Response to maralixibat was dependent on progressive familial intrahepatic cholestasis subtype, and 6 of 19 patients with nt-BSEP experienced rapid and sustained reductions in sBA levels. The 7 responders survived with native liver and experienced clinically significant reductions in pruritus and meaningful improvements in growth and QoL. Maralixibat may represent a well-tolerated alternative to surgical intervention.\n\nMaralixibat for the treatment of PFIC: Long-term, IBAT inhibition in an open-label, Phase 2 study.", "token_count": 139, "char_count": 533, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:14.810058", "source": { "split": "train_shard_00000", "doc_id": 1873 }, "chunk_id": "train_shard_00000_1873_1", "global_id": 2068 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC2) is a rare disorder caused by variants in the ABCB11 gene encoding the bile salt export pump (BSEP). We investigated the molecular defect in a PFIC2 infant and rescued the splicing defect with antisense oligonucleotides (ASOs).\n\nAntisense oligonucleotides rescue an intronic splicing variant in the ABCB11 gene that causes progressive familial intrahepatic cholestasis type 2.", "token_count": 128, "char_count": 436, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:15.267715", "source": { "split": "train_shard_00000", "doc_id": 1874 }, "chunk_id": "train_shard_00000_1874_0", "global_id": 2069 }, { "text": "The aim of this study was to evaluate the biosynthesis of flavor compounds from rice bran by fermentation facilitated by Kluyveromyces marxianus and Debaryomyces hansenii. The growth of both yeasts was assessed by specific growth rates and doubling time. The biosynthesis of flavor compounds was evaluated by gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS), and Spectrum™ sensory analysis. The specific growth rate (µ) and doubling time (t\n\nProduction of flavor compounds from rice bran by yeasts metabolisms of Kluyveromyces marxianus and Debaryomyces hansenii.", "token_count": 163, "char_count": 599, "word_count": 83, "semantic_coherence": 1, "information_density": 0.5542, "quality_score": 0.7771, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:15.718265", "source": { "split": "train_shard_00000", "doc_id": 1875 }, "chunk_id": "train_shard_00000_1875_0", "global_id": 2070 }, { "text": "Methods that use a linear genome reference for genome sequencing data analysis are reference-biased. In the field of clinical genetics for rare diseases, a resulting reduction in genotyping accuracy in some regions has likely prevented the resolution of some cases. Pangenome graphs embed population variation into a reference structure. Although pangenome graphs have helped to reduce reference mapping bias, further performance improvements are possible. We introduce VG-Pedigree, a pedigree-aware workflow based on the pangenome-mapping tool of Giraffe and the variant calling tool DeepTrio using a specially trained model for Giraffe-based alignments. We demonstrate mapping and variant calling improvements in both single-nucleotide variants (SNVs) and insertion and deletion (indel) variants over those produced by alignments created using BWA-MEM to a linear-reference and Giraffe mapping to a pangenome graph containing data from the 1000 Genomes Project. We have also adapted and upgraded deleterious-variant (DV) detecting methods and programs into a streamlined workflow. We used these workflows in combination to detect small lists of candidate DVs among 15 family quartets and quintets of the Undiagnosed Diseases Program (UDP). All candidate DVs that were previously diagnosed using the Mendelian models covered by the previously published methods were recapitulated by these workflows. The results of these experiments indicate that a slightly greater absolute count of DVs are detected in the proband population than in their matched unaffected siblings.\n\nA complete pedigree-based graph workflow for rare candidate variant analysis.", "token_count": 364, "char_count": 1649, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:16.297888", "source": { "split": "train_shard_00000", "doc_id": 1876 }, "chunk_id": "train_shard_00000_1876_0", "global_id": 2071 }, { "text": "In this study, three yeast α-mannans (LZ-MPS, MC-MPS, and G-MPS) were extracted from different sources of Kluyveromyces marxianus. The total sugar content of the three α-mannans ranged from 91.13-97.10%, whereas no proteins were detected. A structural arrangement was proposed using ultraviolet spectroscopy, Fourier-transform infrared spectroscopy, and one-dimensional and two-dimensional nuclear magnetic resonance. The main chain of the three yeast α-mannans was formed by a →6)-α-D-Manp-(1→ unit, which was slightly different from the repeating unit of the branch structure. The prebiotic potential of LZ-MPS, MC-MPS, and G-MPS was assessed using in vitro fermentation with pure and faecal cultures. The three yeast α-mannans could be utilised as substrates for the growth of Lactobacillus and Lactococcus strains. In addition, the three yeast α-mannans markedly regulated the intestinal microbiota composition by increasing the relative abundances of Bacteroides, Parabacteroides, and Phascolarctobacterium and decreasing the abundance of pathogenic bacteria.\n\nExtraction, isolation, structural characterization and prebiotic activity of cell wall polysaccharide from Kluyveromyces marxianus.", "token_count": 338, "char_count": 1197, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6306, "quality_score": 0.8153, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:16.866966", "source": { "split": "train_shard_00000", "doc_id": 1877 }, "chunk_id": "train_shard_00000_1877_0", "global_id": 2072 }, { "text": "Enterococcus faecium is regarded as fourth most emerging common pathogen causing hospital acquired infections (HAIs), with high mortality rate, especially in children, elderly and immunocompromised patients. Recently, due to the emergence of E. faecium resistant strains especially vancomycin resistance (VRE) and their continuously growing resistivity to antibiotics, design of safe vaccine remains a choice for its control. Alternative control through vaccination has received much attention, but there is no clinically approved vaccine against this pathogen. Therefore, in current study we have applied a triple helix approach i.e., Pan-genome, subtractive genome and reverse vaccinology to identify and design potential vaccine candidates and multiepitope-based vaccine (MEV) construct against E. faecium (via core genome analysis from 216 strains). In this study, only 2 outer membrane proteins were identified through genome subtraction of resistant strains genes against human and essential proteins. Subsequently, phosphate ABC transporter substrate binding protein (Psts) was selected as a promiscuous vaccine candidate to develop a potent vaccine model. A final of four epitopes from CD8 + T-cell, CD4 + T-cell epitopes, and B-cell were shortlisted from outer membrane protein with highly antigenic, IFN-γ inducer, and overlapping characteristics for the construction of twelve vaccine models. The V3 construct was found to be highly immunogenic, non-toxic, non-allergenic, highly antigenic and most stable in terms of molecular docking and simulation studies against six HLAs, TLR2, and TLR4 complex. So far, this protein and multiepitope have never been characterized as vaccine targets against E. faecium. The current study proposed V3 as a significant vaccine candidate that could help the scientific community to treat E. faecium infections.\n\nPan genome based reverse vaccinology approach to explore Enterococcus faecium (VRE) strains for identification of novel multi-epitopes vaccine candidate.", "token_count": 469, "char_count": 2011, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [ "TLR4", "TLR2", "CD4", "CD8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:17.502113", "source": { "split": "train_shard_00000", "doc_id": 1878 }, "chunk_id": "train_shard_00000_1878_0", "global_id": 2073 }, { "text": "To understand the molecular mechanisms that contribute to the stress responses of the important foodborne pathogen Listeria monocytogenes, we collected 139 strains (meat,\n\nPhylogenetic and Phenotypic Analyses of a Collection of Food and Clinical Listeria monocytogenes Isolates Reveal Loss of Function of Sigma B from Several Clonal Complexes.", "token_count": 91, "char_count": 343, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:17.876805", "source": { "split": "train_shard_00000", "doc_id": 1879 }, "chunk_id": "train_shard_00000_1879_0", "global_id": 2074 }, { "text": "The PAN2HGENE is a computational tool that enables two main analyses. First, the tool can identify gene products absent from the original prokaryotic genome sequence. Second, it enables automated comparative analysis for both complete and draft genomes. All analyses are performed through a simple and intuitive graphical user interface without the need for extensive and complex command lines. For complete details on the use and execution of this protocol, please refer to Silva de Oliveira (2021).\n\nProtocol to analyze the bacterial pangenome using PAN2HGENE software.", "token_count": 126, "char_count": 571, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8118, "quality_score": 0.9059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:18.261501", "source": { "split": "train_shard_00000", "doc_id": 1880 }, "chunk_id": "train_shard_00000_1880_0", "global_id": 2075 }, { "text": "Combatting Clostridioides difficile infections, a dominant cause of hospital-associated infections with incidence and resulting deaths increasing worldwide, is complicated by the frequent emergence of new virulent strains. Here, we employ whole-genome sequencing, high-throughput phenotypic screenings, and genome-scale models of metabolism to evaluate the genetic diversity of 451 strains of C. difficile. Constructing the C. difficile pangenome based on this set revealed 9,924 distinct gene clusters, of which 2,899 (29%) are defined as core, 2,968 (30%) are defined as unique, and the remaining 4,057 (41%) are defined as accessory. We develop a strain typing method, sequence typing by accessory genome (STAG), that identifies 176 genetically distinct groups of strains and allows for explicit interrogation of accessory gene content. Thirty-five strains representative of the overall set were experimentally profiled on 95 different nutrient sources, revealing 26 distinct growth profiles and unique nutrient preferences; 451 strain-specific genome scale models of metabolism were constructed, allowing us to computationally probe phenotypic diversity in 28,864 unique conditions. The models create a mechanistic link between the observed phenotypes and strain-specific genetic differences and exhibit an ability to correctly predict growth in 76% of measured cases. The typing and model predictions are used to identify and contextualize discriminating genetic features and phenotypes that may contribute to the emergence of new problematic strains.\n\nSystems biology approach to functionally assess the", "token_count": 380, "char_count": 1609, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6516, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:18.850501", "source": { "split": "train_shard_00000", "doc_id": 1881 }, "chunk_id": "train_shard_00000_1881_0", "global_id": 2076 }, { "text": "Strains of the freshwater cyanobacterium Synechococcus elongatus were first isolated approximately 60 years ago, and PCC 7942 is well established as a model for photosynthesis, circadian biology, and biotechnology research. The recent isolation of UTEX 3055 and subsequent discoveries in biofilm and phototaxis phenotypes suggest that lab strains of S. elongatus are highly domesticated. We performed a comprehensive genome comparison among the available genomes of S. elongatus and sequenced two additional laboratory strains to trace the loss of native phenotypes from the standard lab strains and determine the genetic basis of useful phenotypes. The genome comparison analysis provides a pangenome description of S. elongatus, as well as correction of extensive errors in the published sequence for the type strain PCC 6301. The comparison of gene sets and single nucleotide polymorphisms (SNPs) among strains clarifies strain isolation histories and, together with large-scale genome differences, supports a hypothesis of laboratory domestication. Prophage genes in laboratory strains, but not UTEX 3055, affect pigmentation, while unique genes in UTEX 3055 are necessary for phototaxis. The genomic differences identified in this study include previously reported SNPs that are, in reality, sequencing errors, as well as SNPs and genome differences that have phenotypic consequences. One SNP in the circadian response regulator\n\nComparative Genomics of Synechococcus elongatus Explains the Phenotypic Diversity of the Strains.", "token_count": 378, "char_count": 1532, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:19.433315", "source": { "split": "train_shard_00000", "doc_id": 1882 }, "chunk_id": "train_shard_00000_1882_0", "global_id": 2077 }, { "text": "Pangenome analysis is fundamental to explore molecular evolution occurring in bacterial populations. Here, we introduce Pagoo, an R framework that enables straightforward handling of pangenome data. The encapsulated nature of Pagoo allows the storage of complex molecular and phenotypic information using an object-oriented approach. This facilitates to go back and forward to the data using a single programming environment and saving any stage of analysis (including the raw data) in a single file, making it sharable and reproducible. Pagoo provides tools to query, subset, compare, visualize, and perform statistical analyses, in concert with other microbial genomics packages available in the R ecosystem. As working examples, we used 1,000\n\nAn object-oriented framework for evolutionary pangenome analysis.", "token_count": 173, "char_count": 812, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7304, "quality_score": 0.8652, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:19.878327", "source": { "split": "train_shard_00000", "doc_id": 1883 }, "chunk_id": "train_shard_00000_1883_0", "global_id": 2078 }, { "text": "Microorganisms contribute to the biology and physiology of eukaryotic hosts and affect other organisms through natural products. Xenorhabdus and Photorhabdus (XP) living in mutualistic symbiosis with entomopathogenic nematodes generate natural products to mediate bacteria-nematode-insect interactions. However, a lack of systematic analysis of the XP biosynthetic gene clusters (BGCs) has limited the understanding of how natural products affect interactions between the organisms. Here we combine pangenome and sequence similarity networks to analyse BGCs from 45 XP strains that cover all sequenced strains in our collection and represent almost all XP taxonomy. The identified 1,000 BGCs belong to 176 families. The most conserved families are denoted by 11 BGC classes. We homologously (over)express the ubiquitous and unique BGCs and identify compounds featuring unusual architectures. The bioactivity evaluation demonstrates that the prevalent compounds are eukaryotic proteasome inhibitors, virulence factors against insects, metallophores and insect immunosuppressants. These findings explain the functional basis of bacterial natural products in this tripartite relationship.\n\nGlobal analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria.", "token_count": 315, "char_count": 1327, "word_count": 172, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:20.436407", "source": { "split": "train_shard_00000", "doc_id": 1884 }, "chunk_id": "train_shard_00000_1884_0", "global_id": 2079 }, { "text": "Knowledge of within-host genetic variation informs studies on transmission dynamics. We studied within-host genetic variation in Neisseria gonorrhoeae over the course of infection and across different anatomical locations. Isolates were obtained during a clinical trial, and isolates from consecutive time points reflected persistent infections after treatment failure. We compared sequence types (STs) and recombination unfiltered- and filtered core genome single nucleotide polymorphism (SNP) distances in 65 within-host isolate pairs from the same anatomical location over time-obtained with a median interval of 7 days-and 65 isolate pairs across different anatomical locations at one time point. Isolates with different Multi-Locus Sequence Types (MLST), NG-Sequence Types for Antimicrobial Resistance (NG-STAR) and NG-Multi Antigen Sequence Types (NG-MAST) had a median of 1466 recombination filtered SNPs, whereas a median of 1 SNP was found between isolates with identical STs or a different NG-MAST only. The threshold for differentiating between strains was set at 10 recombination filtered SNPs, showing that isolates from persistent infections could have different NG-MASTs. Antibiotic pressure applied through treatment did not lead to an increase in genetic variation in specific genes or in overall extent of variation, compared to variation across anatomical locations. Instead, within-host genetic variation was proposedly driven by the host immune response, as it was concentrated in genomic regions encoding surface exposed proteins involved in host-microbe interaction. Ultimately, 15/228 (6.5%) between-host pairs contained a single strain, suggesting between-host transmission. However, patient reported data are needed to differentiate within-host persistence from between-host transmission.\n\nWithin-Host Genetic Variation in Neisseria gonorrhoeae over the Course of Infection.", "token_count": 446, "char_count": 1900, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:21.068830", "source": { "split": "train_shard_00000", "doc_id": 1885 }, "chunk_id": "train_shard_00000_1885_0", "global_id": 2080 }, { "text": "Six different yeasts were used to study their metabolism of glucose and xylose, and mainly their capacity to produce ethanol and xylitol. The strains used were Candida guilliermondii, Debaryomyces hansenii, Saccharomyces cerevisiae, Kluyveromyces marxianus, Meyerozyma guilliermondii and Clavispora lusitaniae, four isolated from a rural mezcal fermentation facility. All of them produced ethanol when the substrate was glucose. When incubated in a medium containing xylose instead of glucose, only K. marxianus and M. guilliermondii were able to produce ethanol from xylose. On the other hand, all of them could produce some xylitol from xylose, but the most active in this regard were K. marxianus, M. guilliermondii, C. lusitaniae, and C. guilliermondii with the highest amount of xylitol produced. The capacity of all strains to take up glucose and xylose was also studied. Xylose, in different degrees, produced a redox imbalance in all yeasts. Respiration capacity was also studied with glucose or xylose, where C. guilliermondii, D. hansenii, K. marxianus and M. guilliermondii showed higher cyanide resistant respiration when grown in xylose. Neither xylose transport nor xylitol production were enhanced by an acidic environment (pH 4), which can be interpreted as the absence of a proton/sugar symporter mechanism for xylose transport, except for C. lusitaniae. The effects produced by xylose and their magnitude depend on the background of the studied yeast and the conditions in which these are studied.\n\nXylose and yeasts: A story beyond xylitol production.", "token_count": 437, "char_count": 1570, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5532, "quality_score": 0.7766, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:21.702448", "source": { "split": "train_shard_00000", "doc_id": 1886 }, "chunk_id": "train_shard_00000_1886_0", "global_id": 2081 }, { "text": "Performance and efficiency of feed utilization in poultry is highly influenced by gut health, which is dependent on intestinal microbial balance. Probiotics are live microbial feed supplements or viable microorganisms that beneficially affect the host animal by improving its gastrointestinal tract (GIT) microbial balance. However, their mode of action and suitable GIT environment favoring their colonization of the GIT is obscure. The probiotic properties of Lactobacillus plantarum, Bifidobacterium longum, and Saccharomyces boulardii were evaluated. These microbes were tested in vitro against gastrointestinal conditions for survivability and their ability to attach to the intestinal mucosa. The ability of the microbes to tolerate and survive varying pH levels and bile concentrations was assessed. The microbes were challenged with a pH of 2 to 7 for 5 h and bile concentrations of 1 to 3% for 6 hrs. The microbes were sampled hourly to evaluate growth or decline in colony-forming units (CFU). B. longum, L. Plantarum, and S. boulardii exhibited significantly higher CFU (p < 0.05) at a pH range of 5 to 7, 4 to 7, and 2 to 7, respectively, when compared with other pH levels. L. plantarum had much higher colony-forming units per mL within each pH level, except at pH 2 where S. boulardii was the only microbe to survive over time. While L. plantarum and S. boulardii were able to tolerate the various bile concentrations, B. longum and L. plantarum showed remarkable ability to attach to the intestinal mucosa and to inhibit pathogenic microbes.\n\nEvaluation of Selected Bacteria and Yeast for Probiotic Potential in Poultry Production.", "token_count": 444, "char_count": 1647, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5736, "quality_score": 0.7868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:22.335745", "source": { "split": "train_shard_00000", "doc_id": 1887 }, "chunk_id": "train_shard_00000_1887_0", "global_id": 2082 }, { "text": "Advances in sequencing technologies and bioinformatics tools have fueled a renewed interest in whole genome sequencing efforts in many organisms. The growing availability of multiple genome sequences has advanced our understanding of the within-species diversity, in the form of a pangenome. Pangenomics has opened new avenues for future research such as allowing dissection of complex molecular mechanisms and increased confidence in genome mapping. To comprehensively capture the genetic diversity for improving plant performance, the pangenome concept is further extended from species to genus level by the inclusion of wild species, constituting a super-pangenome. Characterization of pangenome has implications for both basic and applied research. The concept of pangenome has transformed the way biological questions are addressed. From understanding evolution and adaptation to elucidating host-pathogen interactions, finding novel genes or breeding targets to aid crop improvement to design effective vaccines for human prophylaxis, the increasing availability of the pangenome has revolutionized several aspects of biological research. The future availability of high-resolution pangenomes based on reference-level near-complete genome assemblies would greatly improve our ability to address complex biological problems.\n\nPangenomics in Microbial and Crop Research: Progress, Applications, and Perspectives.", "token_count": 277, "char_count": 1416, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6631, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:22.888380", "source": { "split": "train_shard_00000", "doc_id": 1888 }, "chunk_id": "train_shard_00000_1888_0", "global_id": 2083 }, { "text": "Yak (Bos grunniens) inhabit an oxygen-deficient environment at the altitude of 3000 m on the Tibetan Plateau, with a distinctive gut micro-ecosystem. This study evaluated the probiotic potential and physiological property of Bacillus licheniformis and Bacillus pumilus isolated from the gut of yaks. Four strains, two Bacillus licheniformis (named D1 and D2) and two Bacillus pumilus (named X1 and X2), were isolated and identified by 16S rRNA sequencing. All strains had potential antibacterial ability against three indicator pathogens: Escherichia coli C83902, Staphylococcus aureus BNCC186335, and Salmonella enteritidis NTNC13349. The antioxidant activity test showed that D2 sample showed the highest antioxidant activity. Furthermore, all four strains had a higher hydrophobicity, auto-aggregation, acid tolerance, bile tolerance, and antibiotic sensitivity, which all contribute to their survival in the gastrointestinal tract and clinical utility. The animal experimentation (40 KM mice, equally divided into five groups of eight mice each) showed that the strain supplementation not only increased daily weight gain and reduced feed conversion ratio, but also increased the length of the jejunum villi and the value of the V/C (Villi/Crypt). In conclusion, this is the first study demonstrated the probiotic potential of Bacillus licheniformis and Bacillus pumilus isolated from yaks, providing a theoretical basis for the clinical application and development of new feed additives.\n\nProbiotic Potential of Bacillus licheniformis and Bacillus pumilus Isolated from Tibetan Yaks, China.", "token_count": 438, "char_count": 1595, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.817, "entities": { "genes": [ "NTNC13349", "BNCC186335" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:23.523090", "source": { "split": "train_shard_00000", "doc_id": 1889 }, "chunk_id": "train_shard_00000_1889_0", "global_id": 2084 }, { "text": "The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation. A high-quality reference with global representation of common variants, including single-nucleotide variants, structural variants and functional elements, is needed. The Human Pangenome Reference Consortium aims to create a more sophisticated and complete human reference genome with a graph-based, telomere-to-telomere representation of global genomic diversity. Here we leverage innovations in technology, study design and global partnerships with the goal of constructing the highest-possible quality human pangenome reference. Our goal is to improve data representation and streamline analyses to enable routine assembly of complete diploid genomes. With attention to ethical frameworks, the human pangenome reference will contain a more accurate and diverse representation of global genomic variation, improve gene-disease association studies across populations, expand the scope of genomics research to the most repetitive and polymorphic regions of the genome, and serve as the ultimate genetic resource for future biomedical research and precision medicine.\n\nThe Human Pangenome Project: a global resource to map genomic diversity.", "token_count": 307, "char_count": 1502, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:24.087108", "source": { "split": "train_shard_00000", "doc_id": 1890 }, "chunk_id": "train_shard_00000_1890_0", "global_id": 2085 }, { "text": "The life cycle of Yersinia pestis has changed a lot to adapt to flea-borne transmission since it evolved from an enteric pathogen, Yersinia pseudotuberculosis. Small insertions and deletions (indels), especially frameshift mutations, can have major effects on phenotypes and contribute to virulence and host adaptation through gene disruption and inactivation. Here, we analyzed 365 Y. pestis genomes and identified 2,092 genome-wide indels on the core genome. As recently reported in Mycobacterium tuberculosis, we also detected \"indel pockets\" in Y. pestis, with average complexity scores declining around indel positions, which we speculate might also exist in other prokaryotes. Phylogenic analysis showed that indel-based phylogenic tree could basically reflect the phylogenetic relationships of major phylogroups in Y. pestis, except some inconsistency around the Big Bang polytomy. We observed 83 indels arising in the trunk of the phylogeny, which played a role in accumulation of pseudogenes related to key metabolism and putatively pathogenicity. We also discovered 32 homoplasies at the level of phylogroups and 7 frameshift scars (i.e., disrupted reading frame being rescued by a second frameshift). Additionally, our analysis showed evidence of parallel evolution at the level of genes, with\n\nSmall Insertions and Deletions Drive Genomic Plasticity during Adaptive Evolution of Yersinia pestis.", "token_count": 363, "char_count": 1407, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7015, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:24.658330", "source": { "split": "train_shard_00000", "doc_id": 1891 }, "chunk_id": "train_shard_00000_1891_0", "global_id": 2086 }, { "text": "Endophytic strains belonging to the Bacillus cereus group were isolated from the halophytes Atriplex halimus L. (Amaranthaceae) and Tamarix aphylla L. (Tamaricaceae) from costal and continental regions in Algeria. Based on their salt tolerance (up to 5%), the strains were tested for their ability to alleviate salt stress in tomato and wheat. Bacillus sp. strain BH32 showed the highest potential to reduce salinity stress (up to + 50% and + 58% of dry weight improvement, in tomato and wheat, respectively, compared to the control). To determine putative mechanisms involved in salt tolerance and plant growth promotion, the whole genome of Bacillus sp. BH32 was sequenced, annotated, and used for comparative genomics against the genomes of closely related strains. The pangenome of Bacillus sp. BH32 and its closest relative was further analyzed. The phylogenomic analyses confirmed its taxonomic position, a member of the Bacillus cereus group, with intergenomic distances (GBDP analysis) pinpointing to a new taxon (digital DNA-DNA hybridization, dDDH < 70%). Genome mining unveiled several genes involved in stress tolerance, production of anti-oxidants and genes involved in plant growth promotion as well as in the production of secondary metabolites. KEY POINTS : • Bacillus sp. BH32 and other bacterial endophytes were isolated from halophytes, to be tested on tomato and wheat and to limit salt stress adverse effects. • The strain with the highest potential was then studied at the genomic level to highlight numerous genes linked to plant growth promotion and stress tolerance. • Pangenome approaches suggest that the strain belongs to a new taxon within the Bacillus cereus group.\n\nIn-depth genome analysis of Bacillus sp. BH32, a salt stress-tolerant endophyte obtained from a halophyte in a semiarid region.", "token_count": 491, "char_count": 1824, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5536, "quality_score": 0.7768, "entities": { "genes": [ "BH32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:25.310435", "source": { "split": "train_shard_00000", "doc_id": 1892 }, "chunk_id": "train_shard_00000_1892_0", "global_id": 2087 }, { "text": "The objective was to evaluate the effect of two probiotic yeast strains (\n\nRespiratory tract clinometry, fat thickness, haematology and productive parameters associated with direct-fed microbials used as growth promoter antibiotic alternative in weaned piglets.", "token_count": 59, "char_count": 261, "word_count": 35, "semantic_coherence": 1, "information_density": 0.9714, "quality_score": 0.9857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:25.707640", "source": { "split": "train_shard_00000", "doc_id": 1893 }, "chunk_id": "train_shard_00000_1893_0", "global_id": 2088 }, { "text": "A Yersinia pseudotuberculosis outbreak was diagnosed in a male turkey flock in Finland. Y. pseudotuberculosis is a quite rare zoonotic bacterium, which typically causes enteritis in humans and sudden death in animals. In this study, osteomyelitis was diagnosed in small, lame, 11- to 12-wk-old male turkeys. Lameness and slower growth among the turkeys was observed on the farm. During pathological examination, multiple lesions were found in the metaphyseal and physeal areas of the femurs, tibiotarsi, and tarsometatarsi, with multifocal to coalescing mixed heterophilic/granulomatous necrotizing osteomyelitis. Y. pseudotuberculosis was isolated from the femoral and tibiotarsal bones or from the joints of six lame turkeys sent for necropsy. The isolation required homogenizing of lesion tissue in phosphate-mannitol-peptone broth, which was cultured directly - and, if needed, after cold enrichment - on selective cefsulodin-irgasan-novobiocin agar. Whole-genome sequencing was used for identification and typing. All isolates belonged to bio/serotype 1/O:1a and sequence type ST42 (Achtman scheme), which is commonly reported in both human and animal Y. pseudotuberculosis infections in Europe. The isolates from all six turkeys showed only one to two allele differences in the core genome comparison, indicating a common source of infection. All asymptomatic turkeys were slaughtered at the age of 17 weeks. Whole and partial carcass condemnation rates at the slaughterhouse were high, but no macroscopic changes in the skeletal system were found, showing that food chain information is essential. This study confirms earlier findings that Y. pseudotuberculosis can cause osteomyelitis in fattening turkeys, leading to lameness. Food chain information is essential for slaughterhouse operations, to protect the workers and emphasize good working hygiene during slaughter.", "token_count": 484, "char_count": 1878, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6642, "quality_score": 0.8321, "entities": { "genes": [ "ST42" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:26.381025", "source": { "split": "train_shard_00000", "doc_id": 1894 }, "chunk_id": "train_shard_00000_1894_0", "global_id": 2089 }, { "text": "Osteomyelitis in a slaughter turkey flock caused by Yersinia pseudotuberculosis sequence type ST42.", "token_count": 29, "char_count": 99, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST42" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:26.745779", "source": { "split": "train_shard_00000", "doc_id": 1894 }, "chunk_id": "train_shard_00000_1894_1", "global_id": 2090 }, { "text": "Root nodulating rhizobia are nearly ubiquitous in soils and provide the critical service of nitrogen fixation to thousands of legume species, including staple crops. However, the magnitude of fixed nitrogen provided to hosts varies markedly among rhizobia strains, despite host legumes having mechanisms to selectively reward beneficial strains and to punish ones that do not fix sufficient nitrogen. Variation in the services of microbial mutualists is considered paradoxical given host mechanisms to select beneficial genotypes. Moreover, the recurrent evolution of non-fixing symbiont genotypes is predicted to destabilize symbiosis, but breakdown has rarely been observed. Here, we deconstructed hundreds of genome sequences from genotypically and phenotypically diverse\n\nPangenome Evolution Reconciles Robustness and Instability of Rhizobial Symbiosis.", "token_count": 197, "char_count": 857, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7826, "quality_score": 0.8913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:27.255836", "source": { "split": "train_shard_00000", "doc_id": 1895 }, "chunk_id": "train_shard_00000_1895_0", "global_id": 2091 }, { "text": "Typical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions, which are particularly challenging for fast k-mer-based genotypers. In the present study, we propose a new algorithm, PanGenie, that leverages a haplotype-resolved pangenome reference together with k-mer counts from short-read sequencing data to genotype a wide spectrum of genetic variation-a process we refer to as genome inference. Compared with mapping-based approaches, PanGenie is more than 4 times faster at 30-fold coverage and achieves better genotype concordances for almost all variant types and coverages tested. Improvements are especially pronounced for large insertions (≥50 bp) and variants in repetitive regions, enabling the inclusion of these classes of variants in genome-wide association studies. PanGenie efficiently leverages the increasing amount of haplotype-resolved assemblies to unravel the functional impact of previously inaccessible variants while being faster compared with alignment-based workflows.\n\nPangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes.", "token_count": 297, "char_count": 1346, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7159, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:27.819421", "source": { "split": "train_shard_00000", "doc_id": 1896 }, "chunk_id": "train_shard_00000_1896_0", "global_id": 2092 }, { "text": "Probiotics are increasingly used as functional food ingredients. The objectives of this study were to isolate and characterise probiotic bacteria from dairy and fermented foods and to use a selected strain for the production of probiotic chèvre cheese. Tolerance to acid (pH 2.0) and bile salt (0.4% (w/v)) were first investigated, and then other probiotic properties were determined. Out of 241 isolates, 35 showed high tolerance to acid and bile salt, and 6 were chosen for further characterisation. They were Lactobacillus plantarum and L. fermentum, and possessed antibacterial activities against foodborne pathogens such as Bacillus cereus, Staphylococcus aureus, Salmonella enterica and Escherichia coli O157:H7. L. plantarum (isolate AD73) showed the highest percentage of adhesion (81.74 ± 0.16%) and was nontoxic to Caco-2 cells at a concentration of 108 CFU/mL. This isolate was therefore selected for the production of probiotic chèvre cheese from goat’s milk and was prepared in a lyophilised form with a concentration of probiotic culture of 8.6 log CFU/g. The cheese had a shelf life of 8 days. On the expiry date, the probiotic, the starter and the yeast contents were 7.56 ± 0.05, 7.81 ± 0.03 and 5.64 log CFU/g, respectively. The level of the probiotics in this chèvre cheese was still sufficiently high to warrant its being a probiotic cheese.\n\nCharacterisation of", "token_count": 408, "char_count": 1382, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [ "AD73" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:28.436041", "source": { "split": "train_shard_00000", "doc_id": 1897 }, "chunk_id": "train_shard_00000_1897_0", "global_id": 2093 }, { "text": "Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of\n\nPangenome Analysis of the Soilborne Fungal Phytopathogen", "token_count": 90, "char_count": 377, "word_count": 50, "semantic_coherence": 1, "information_density": 0.88, "quality_score": 0.94, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:28.810882", "source": { "split": "train_shard_00000", "doc_id": 1898 }, "chunk_id": "train_shard_00000_1898_0", "global_id": 2094 }, { "text": "Oltipraz, a synthetic dithiolethione, has chemopreventive effect through nuclear factor erythroid 2-related factor 2 (Nrf2) activation. Nrf2 is known to be involved in the development of experimental steatohepatitis in rodents. In this study, to evaluate the effect of oltipraz on lipid and bile acid metabolism, wild-type and Nrf2-null mice were fed the standard diet (containing 4% soybean oil) with or without oltipraz. Based on these results, we examined the effect of oltipraz on the experimental steatohepatitis in high-fat diet (containing 4% soybean oil and 20% lard) fed Nrf2-null mice. Oltipraz induced hepatic mRNA expression of peroxisome proliferator-activated receptor α, carnitine palmityl transferase 1, and bile salt export pump by Nrf2 independent mechanisms. In Nrf2-null mice fed a high-fat diet for 12 weeks, moderate to severe inflammation and fibrosis were observed. Oral administration of oltipraz suppressed the degree of inflammation and fibrosis in Nrf2-null mouse liver fed a high-fat diet. These histopathological findings approximately corresponded to the data of mRNA expression of tumor necrosis factor α, monocyte chemoattractant protein-1, Timp-1, and collagen type 1α1. These results indicated that oltipraz administration ameliorated liver injury by Nrf2 independent manner in a model of steatohepatitis generated by Nrf2-null mice with high-fat diet.\n\nOltipraz ameliorates the progression of steatohepatitis in Nrf2-null mice fed a high-fat diet.", "token_count": 434, "char_count": 1483, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5687, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:29.442670", "source": { "split": "train_shard_00000", "doc_id": 1899 }, "chunk_id": "train_shard_00000_1899_0", "global_id": 2095 }, { "text": "Agar and κ-carrageenan emulsion gels and oil-filled aerogels were investigated as curcumin carriers and their structure and mechanical properties, as well as their structural changes upon in vitro gastrointestinal digestion were characterized. Agar emulsion gels presented stiffer behaviour, with smaller and more homogeneous oil droplets (ϕ ∼ 12 µm) than those from κ-carrageenan (ϕ ∼ 243 µm). The structure of κ-carrageenan gels was characterized by the presence of rigid swollen linear chains, while agar produced more branched networks. After simulated gastrointestinal digestion bile salt lamellae/micelles (∼5 nm) and larger vesicles of partially digested oil (R\n\nEmulsion gels and oil-filled aerogels as curcumin carriers: Nanostructural characterization of gastrointestinal digestion products.", "token_count": 224, "char_count": 801, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6697, "quality_score": 0.8349, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:29.911583", "source": { "split": "train_shard_00000", "doc_id": 1900 }, "chunk_id": "train_shard_00000_1900_0", "global_id": 2096 }, { "text": "Enterococcus faecalis (E. faecalis) belongs to lactic acid bacteria which can be used as a probiotic additive and feed, bringing practical value to the health of humans and animals. The prebiotic function of tea polyphenols lays a foundation for green tea polyphenols (GTP) to repair the adverse changes of E. faecalis under stress conditions. In this study, RNA-sequence analysis was used to explore the protective effect of GTP on E. faecalis under bile salt stress. A total of 50 genes were found to respond to GTP under bile salts stress, containing 18 up-regulated and 32 down-regulated genes. The results showed that multiple genes associated with cell wall and membrane, transmembrane transport, nucleotide transport and metabolism were significantly differentially expressed (P < 0.05), while GTP intervention can partly alleviate the detrimental effects of bile salt on amino acid metabolism and transport. The present study provides the whole genome transcriptomics of E. faecalis under bile salt stress and GTP intervention which help us understand the growth and mechanism of continuous adaptation of E. faecalis under stress conditions.\n\nRNA-Seq Transcriptomic Analysis of Green Tea Polyphenols Modulation of Differently Expressed Genes in Enterococcus faecalis Under Bile Salt Stress.", "token_count": 323, "char_count": 1298, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:30.828846", "source": { "split": "train_shard_00000", "doc_id": 1901 }, "chunk_id": "train_shard_00000_1901_0", "global_id": 2097 }, { "text": "Persistent Organic Pollutants (POPs) have become immensely prevalent in the environment as a result of their unique chemical properties (persistent, semi-volatile and bioaccumulative nature). Their occurrence in the soil, water and subsequently in food has become a matter of concern. With food being one of the major sources of exposure, the detrimental impact of these chemicals on the gut microbiome is inevitable. The gut microbiome is considered as an important integrant for human health. It participates in various physiological, biochemical and immunological activities; thus, affects the metabolism and physiology of the host. A myriad of studies have corroborated an association between POP-induced gut microbial dysbiosis and prevalence of disorders. For instance, ingestion of polychlorinated biphenyls, polybrominated diphenyl ethers or organochlorine pesticides influenced bile acid metabolism via alteration of bile salt hydrolase activity of Lactobacillus, Clostridium or Bacteroides genus. At the same time, some chemicals such as DDE have the potential to elevate Proteobacteria and Firmicutes/Bacteriodetes ratio influencing their metabolic activity leading to enhanced short-chain fatty acid synthesis, ensuing obesity or a pre-diabetic state. This review highlights the impact of POPs exposure on the gut microbiota composition and metabolic activity, along with an account of its corresponding consequences on the host physiology. The critical role of gut microbiota in impeding the POPs excretion out of the body resulting in their prolonged exposure and consequently, enhanced degree of toxicity is also emphasized.\n\nPersistent organic pollutants in foods, their interplay with gut microbiota and resultant toxicity.", "token_count": 417, "char_count": 1740, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:31.452769", "source": { "split": "train_shard_00000", "doc_id": 1902 }, "chunk_id": "train_shard_00000_1902_0", "global_id": 2098 }, { "text": "Penthorum chinense Pursh. is a traditional herbal medicine of Miao, and its extracts (PCPE) have been used for treatment of liver diseases in the clinic including nonalcoholic fatty liver disease (NAFLD). However, the active components and pharmacological mechanisms of PCPE for treating NAFLD remain unclear. This study aimed to explore potential mechanisms of action through network pharmacology, molecular docking combined with experimental in vitro. A total of five dihydroflavonoids (1-5) with the same parent nucleus of pinocembrin (PCB) from PCPE, were selected as bioactive ingredients and 109 potential targets related to NAFLD were obtained from public databases and literature mining. The core targets related to the bile secretion signaling were selected based on PPI network and KEGG enrichment analysis for exploring the mechanism of PCPE against NAFLD. Molecular docking results showed good interaction between the core targets in bile secretion signaling pathway and the five compounds predicted to be bioactive. With the strong binding activity to retinoid X receptor-alpha (RXRA) and farnesoid X receptor (FXR) protein, pinocembrin-7-O-β-D-glucoside (PCBG, the highest content in PCPE) and its metabolite PCB, could significantly increase the expression of RXRA, FXR and bile salt export pump (BSEP) in L02 cells, and significantly decrease the expression of cholesterol 7α-hydroxylase (CYP7A1) at mRNA and protein levels. This study provided favorable evidence for mechanism of the main dihydroflavonoids of PCPE against NAFLD, and presented a paradigm for the study of ethnomedicine.\n\nDihydroflavonoids as Bioactive Components of Penthorum chinense, a Miao Ethnomedicine, against NAFLD through Bile Acid Metabolism Pathway.", "token_count": 459, "char_count": 1743, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:32.094355", "source": { "split": "train_shard_00000", "doc_id": 1903 }, "chunk_id": "train_shard_00000_1903_0", "global_id": 2099 }, { "text": "Holder pasteurization (HoP) is the current recommended treatment for donor human milk. Although this method inactivates microbial contaminants, it also negatively affects various milk components. High-pressure processing (HPP, 400, 500, and 600 MPa), ultraviolet-C irradiation (UV-C, 2,430, 3,645, and 4,863 J/L) and thermoultrasonication (TUS, 1,080 and 1,620 kJ/L) were investigated as alternatives to thermal pasteurization (HoP). We assessed the effects of these methods on microbiological safety, and on concentration and functionality of immunoglobulin A, lactoferrin, lysozyme and bile salt-stimulated lipase, with LC-MS/MS-based proteomics and activity assays. HoP, HPP, TUS, and UV-C at 4863 J/L, achieved >5-log\n\nEffects of High-Pressure Processing, UV-C Irradiation and Thermoultrasonication on Donor Human Milk Safety and Quality.", "token_count": 280, "char_count": 842, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7838, "quality_score": 0.8919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:33.439968", "source": { "split": "train_shard_00000", "doc_id": 1904 }, "chunk_id": "train_shard_00000_1904_0", "global_id": 2100 }, { "text": "Pseudomonas amygdali is a hemibiotrophic phytopathogen that causes disease in woody and herbaceous plants. Complete genomes of four P. amygdali pathovars were comparatively analyzed to decipher the impact of genomic diversity on host colonization. The pan-genome indicated that 3,928 core genes are conserved among pathovars, while 504-1,009 are unique to specific pathovars. The unique genome contained many mobile elements and exhibited a functional distribution different from the core genome. Genes involved in O-antigen biosynthesis and antimicrobial peptide resistance were significantly enriched for adaptation to hostile environments. While the type III secretion system was distributed in the core genome, unique genomes revealed a different organization of secretion systems as follows: type I in pv. tabaci, type II in pv. japonicus, type IV in pv. morsprunorum, and type VI in pv. lachrymans. These findings provide genetic insight into the dynamic interactions of the bacteria with plant hosts.\n\nComparative Analyses of Four Complete Genomes in Pseudomonas amygdali Revealed Differential Adaptation to Hostile Environments and Secretion Systems.", "token_count": 294, "char_count": 1158, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6564, "quality_score": 0.8282, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:34.003723", "source": { "split": "train_shard_00000", "doc_id": 1905 }, "chunk_id": "train_shard_00000_1905_0", "global_id": 2101 }, { "text": "Development of new pan-genome analysis tools is important, as the pangenome of a microbial species has become an important method to define the diversity of a selected taxon, most commonly a species, in the last years. This enables comparison of strains from different ecological niches and can be used to define the functional potential in a bacterial population. It gives us a much better view of microbial genomics than can be gained from singular genomes which after all are just single representatives of a much more varied population.\n\nPanakeia - a universal tool for bacterial pangenome analysis.", "token_count": 127, "char_count": 603, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7423, "quality_score": 0.8711, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:34.402285", "source": { "split": "train_shard_00000", "doc_id": 1906 }, "chunk_id": "train_shard_00000_1906_0", "global_id": 2102 }, { "text": "To combat the shortage of single agro-residue and overcome the problem of seasonal availability, it is beneficial to use mixture of lignocellulosic biomasses. In the present study, efforts were made to use mixed lignocellulosic biomass for production of bioethanol, along with microbial lipids and lactic acid. Upon enzymatic hydrolysis of mixed biomass at varied proportions it was observed that mixture of paddy straw and jute in the ratio 3:1 resulted in best sugar yield (41.50 g/L) at 10% substrate loading. Ethanolic fermentation of mixed substrate hydrolysate by thermotolerant yeast,\n\nProduction of ethanol, lipid and lactic acid from mixed agrowastes hydrolysate.", "token_count": 190, "char_count": 672, "word_count": 100, "semantic_coherence": 1, "information_density": 0.71, "quality_score": 0.855, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:34.866877", "source": { "split": "train_shard_00000", "doc_id": 1907 }, "chunk_id": "train_shard_00000_1907_0", "global_id": 2103 }, { "text": "The potential and modes of action of novel human colostrum probiotics were investigated with the aim of studying their application as an alternative in the bioprophylactic and biotherapy of colon cancer. A total of 218 isolates of Gram-positive rod and cocci bacteria obtained from the colostrum of 50 healthy lactating females were collected. Beneficial probiotic criteria from these isolates, which included growth inhibition against seven foodborne pathogens (Helicobacter pylori, Escherichia coli, Salmonella Enteritidis, Salmonella Typhimurium, Staphylococcus aureus, Bacillus cereus and Listeria monocytogenes), no blood haemolysis and tolerance to acid and bile salt conditions, resulted in only eight probiotic bacteria successfully inhibiting the proliferation of colon cancer cells at rates of 32.47-61.21%. Two probiotic bacteria with higher anticancer efficacy (Streptococcus salivarius CP163 and S. salivarius CP208) were identified using 16S rRNA sequences. High rates of cell surface hydrophobicity, autoaggregation and coaggregation were obtained from both probiotics. The probiotic mode of action involved synergic probiotic adhesion to colon cancer cells that triggered SCFA bioproduction. Apoptotic induction of colon cancer cell death through caspase-2 activity, DNA fragmentation and morphological change as assessed by AO/PI staining were also observed. Immune stimulation by S. salivarius CP163 and S. salivarius CP208 resulted in B and T-cell lymphocyte activation. This study suggests that these novel human colostrum probiotics could be applied as a functional food to facilitate a bioprophylactic strategy in colon cancer.\n\nBioprophylactic potential of novel human colostrum probiotics via apoptotic induction of colon cancer cells and cell immune activation.", "token_count": 461, "char_count": 1786, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [ "CP208", "CP163" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:35.505984", "source": { "split": "train_shard_00000", "doc_id": 1908 }, "chunk_id": "train_shard_00000_1908_0", "global_id": 2104 }, { "text": "Carbapenem-resistant Klebsiella pneumoniae (CR\n\nAccessory Genomes Drive Independent Spread of Carbapenem-Resistant Klebsiella pneumoniae Clonal Groups 258 and 307 in Houston, TX.", "token_count": 63, "char_count": 178, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:35.870125", "source": { "split": "train_shard_00000", "doc_id": 1909 }, "chunk_id": "train_shard_00000_1909_0", "global_id": 2105 }, { "text": "While Klebsiella pneumoniae is a common cause of nosocomial and community-acquired infections, including pneumonia and pyogenic liver abscess, little is known about the population structure of this bacterium. In this study, we investigated the prevalence and molecular characteristics of K. pneumoniae isolates from carriers, pyogenic liver abscess patients, and pneumonia patients, and genomic and phenotypic assays were used to determine the differences among the isolates. A total of 232 K. pneumoniae isolates were subtyped into 74 sequence types (STs). The isolates from different sources had their own STs, and the predominant subtypes in liver abscess and pneumonia patients were ST23 and ST11, respectively. Pangenome analysis also distinguished three phylogroups that were consistent with the isolate sources. The isolates collected from liver abscess patients carried significantly more virulence factors, and those from pneumonia patients harbored significantly more resistance genes and replicons. Almost all isolate STs (93/97 [95.88%]) from liver abscesses strongly correlated with the virulence factor salmochelin, while most pneumonia isolate STs (52/53 [98.11%]) from pneumonia did not correlate with salmochelin. The isolates collected from liver abscesses showed higher virulence in the cytotoxicity and mouse models. These data provide genomic support for the proposal that isolates collected from carriers, liver abscess patients, and pneumonia patients have distinct genomic features. Isolates from the different sources are largely nonoverlapping, suggesting that different patients may be infected via different sources. Further studies on the pathogenic mechanisms of salmochelin and other virulence factors will be required.\n\nGenetic Diversity and Pathogenic Features in Klebsiella pneumoniae Isolates from Patients with Pyogenic Liver Abscess and Pneumonia.", "token_count": 461, "char_count": 1884, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5543, "quality_score": 0.7771, "entities": { "genes": [ "ST23", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:36.514335", "source": { "split": "train_shard_00000", "doc_id": 1910 }, "chunk_id": "train_shard_00000_1910_0", "global_id": 2106 }, { "text": "Niche environmental conditions influence both the structure and function of microbial communities and the cellular function of individual strains. The terrestrial subsurface is a dynamic and diverse environment that exhibits specific biogeochemical conditions associated with depth, resulting in distinct environmental niches. Here, we present the characterization of seven distinct strains belonging to the genus Arthrobacter isolated from varying depths of a single sediment core and associated groundwater from an adjacent well. We characterized genotype and phenotype of each isolate to connect specific cellular functions and metabolisms to ecotype. Arthrobacter isolates from each ecotype demonstrated functional and genomic capacities specific to their biogeochemical conditions of origin, including laboratory-demonstrated characterization of salinity tolerance and optimal pH, and genes for utilization of carbohydrates and other carbon substrates. Analysis of the Arthrobacter pangenome revealed that it is notably open with a volatile accessory genome compared to previous pangenome studies on other genera, suggesting a high potential for adaptability to environmental niches.\n\nGenotype to ecotype in niche environments: adaptation of Arthrobacter to carbon availability and environmental conditions.", "token_count": 259, "char_count": 1312, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:37.062525", "source": { "split": "train_shard_00000", "doc_id": 1911 }, "chunk_id": "train_shard_00000_1911_0", "global_id": 2107 }, { "text": "Bifidobacterium animalis CP-9 was a commensal strain isolated from human breast milk. In this study, genetic and 90-day oral toxicity were assessed in rodents for its safety. Ames test as well as in vivo bone marrow micronucleus and spermatocyte chromosomal aberration were surveyed in mice. B. animalis CP-9 exhibited no mutagenic activity in the Ames test at the highest tested dosage (5000 µg/plate) with or without metabolic activation. No evidence of in vivo genetic toxicity was observed at the maximum tested dosage of 10 g/kg body weight (BW). Furthermore, there was no statistically significant difference of the biochemical and histological parameters in the rats administrated with B. animalis CP-9 at dosages of 0, 0.25, 0.5, or 1.5 g/kg BW/day. No indication of concern for pathogenicity was exhibited during evaluation of Bifidobacterium ssp. generally, or B. animalis specifically. It was noted that B. animalis CP-9 was able to survive in gastric acid-like and high bile salt environment, and showed strong adhesion to the intestinal epithelial cells, Caco-2. Intriguingly, B. animalis CP-9 decreased olic acid-induced triglyceral (TG) accumulation in the Caco-2 cells, and viable B. animalis CP-9 had a better bacteriostatic activity compared to another well-documented B. animalis ssp. lactis, BB-12. Based on the present study, B. animalis CP-9 can be a safe probiotic supplement and may improve the health of host. PRACTICAL APPLICATION: Although the health benefits of probiotics are well known, the safety of a probiotic product is acquired particularly for a long-term consumption. We conduct the safety of B. animalis CP-9 isolated from human breast milk, and demonstrate no toxicity concern in vitro and in vivo. Hence, B. animalis CP-9 powder can be used as a commercial and safe probiotic supplement with some health benefits.\n\nSafety and the probiotic potential of Bifidobacterium animalis CP-9.", "token_count": 537, "char_count": 1923, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5593, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:17:37.749758", "source": { "split": "train_shard_00000", "doc_id": 1912 }, "chunk_id": "train_shard_00000_1912_0", "global_id": 2108 }, { "text": "Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles.\n\nIn vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.", "token_count": 107, "char_count": 419, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7414, "quality_score": 0.8707, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:38.152675", "source": { "split": "train_shard_00000", "doc_id": 1913 }, "chunk_id": "train_shard_00000_1913_0", "global_id": 2109 }, { "text": "In this study, we aimed to analyse the spoilage potential of the isolated yeast, LAB and AAB species. Thus, 11 strains were inoculated at 0·3% (v/v) into a sterile filtered tchapalo and stored for 3 days at ambient temperature (27-30°C). All the tested strains grew well or remained stable except for Limosilactobacillus fermentum and Pediococcus acidilactici, which decreased throughout the storage time. A significant decrease of total soluble solids was observed only for Saccharomyces cerevisiae (from 7·8 to 5·8 °Brix) and Meyerozyma guilliermondii (from 7·8 to 5·5 °Brix). The tchapalo samples inoculated with the LAB strains Weissella paramesenteroides, P. acidilactici, L. fermentum and the yeast strain Candida tropicalis were judged similar to the control by the panellists. However, the strains of Lacticaseibacillus paracasei and Latilactobacillus curvatus (LAB), S. cerevisiae, M. guilliermondii and Kluyveromyces marxianus (yeasts) and Acetobacter pasteurianus and A. cerevisiae (AAB) induced the spoilage of the tchapalo appearance, smell and/or taste. In the spoiled tchapalo quantitative and qualitative modification of some volatile compounds (VOCs), such as lilac aldehyde, ethyl acetate, ethyl hexanoate, ethyl octanoate and phenethyl acetate, were observed. These results provide information about the microorganisms that need to be removed to extend the shelf life of tchapalo.\n\nDetection of spoilage-causing yeasts and bacteria in tchapalo, the Ivorian traditional sorghum beer.", "token_count": 451, "char_count": 1501, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7028, "quality_score": 0.8514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:38.814757", "source": { "split": "train_shard_00000", "doc_id": 1914 }, "chunk_id": "train_shard_00000_1914_0", "global_id": 2110 }, { "text": "The health-promoting effects of probiotics are species-specific, and hence it is important to declare the correct information in products. However, some studies have identified issues related to the accuracy of labeling commercial probiotic products. In this study, we developed a high-resolution real-time PCR method based on pangenome analysis for a more affordable, rapid, and accurate identification of commercial probiotic products than sequencing methods. We selected 25 species or subspecies primarily used for probiotic strains and are closely related to them as targets. To extract molecular markers, 354 whole-genome sequences present in the target genomes but not in the pangenome of other genomes were compared, which resulted in the identification of molecular marker genes. The marker genes exhibited 100% specificity for 100 strains as assessed by the real-time PCR method. Fifty probiotic and dairy products were investigated to verify the information claimed on the label. Real-time PCR results showed that most products reflected the bacterial species declared in the label claim, whereas 12 products showed the presence of undeclared species or missing species. Our method for accurately verifying the labeling of probiotic products would be useful for quality control and safety.\n\nValidation of probiotic species or subspecies identity in commercial probiotic products using high-resolution PCR method based on large-scale genomic analysis.", "token_count": 313, "char_count": 1460, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:39.411580", "source": { "split": "train_shard_00000", "doc_id": 1915 }, "chunk_id": "train_shard_00000_1915_0", "global_id": 2111 }, { "text": "Salmonella enterica serovar Rissen is recognized as one of the most common serotypes in pigs and pig products in many countries and can be transmitted to human through the consumption of contaminated food. To reveal the genetic characteristics of S. Rissen, 39 isolates from human and animal food were subjected to whole-genome sequencing analysis combined with 337 genome sequences downloaded from the NCBI Assembly database. Core genome single nucleotide polymorphism (cgSNP) divided these S. Rissen isolates into two clusters, of which cluster A included 78.3% of American isolates, while cluster B was mainly composed of isolates from China, Asia, and the UK. The 39 S. Rissen isolates located in cluster B were further divided into two subclusters with cluster B-1 of 26 isolates from both humans and food, while cluster B-2 consisted of 13 isolates from animal food, mainly pork. CRISPR typing and cgMLST of the 39 isolates showed perfect correspondence to cgSNP results of their phylogenetic relationship. Virulence factors analysis revealed that ABZJ_0085 and ABZJ_0086 genes presenting in cluster B-2 were lost in cluster B-1. Additionally, antimicrobial resistance gene profiles showed qnrS1, cmlA1, and tet(M) could be detected in cluster B-2 other than cluster B-1. The findings of the divergent difference between cluster B-1 and cluster B-2 demonstrated that S. Rissen was continuously evolved through the pork production chain. In conclusion, pigs are the main reservoir for S. Rissen capable of causing human nontyphoid salmonellosis.\n\nWhole-genome sequencing analysis reveals pig as the main reservoir for persistent evolution of Salmonella enterica serovar Rissen causing human salmonellosis.", "token_count": 432, "char_count": 1710, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5664, "quality_score": 0.7832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:40.041829", "source": { "split": "train_shard_00000", "doc_id": 1916 }, "chunk_id": "train_shard_00000_1916_0", "global_id": 2112 }, { "text": "In the present research study, we formulate bilosomes (BMs) of diclofenac (DC) for oral delivery for enhancement of therapeutic efficacy (anti-inflammatory disease). The BMS were prepared by thin film hydration method and optimized by Box−Behnken design (BBD) using cholesterol (A), lipid (B), surfactant (C), and bile salt (D) as formulation factors. Their effects were evaluated on vesicle size (Y1) and entrapment efficacy (Y2). The optimized DC-BMs-opt showed a vesicle size of 270.21 ± 3.76 nm, PDI of 0.265 ± 0.03, and entrapment efficiency of 79.01 ± 2.54%. DSC study result revealed that DC-BMs-opt exhibited complete entrapment of DC in BM matrix. It also depicted significant enhancement (p < 0.05) in release (91.82 ± 4.65%) as compared to pure DC (36.32 ± 4.23%) and DC-liposomes (74.54 ± 4.76%). A higher apparent permeability coefficient (2.08 × 10−3 cm/s) was also achieved compared to pure DC (6.6 × 10−4 cm/s) and DC-liposomes (1.33 × 10−3 cm/s). A 5.21-fold and 1.43-fold enhancement in relative bioavailability was found relative to pure DC and DC liposomes (DC-LP). The anti-inflammatory activity result showed a significant (p < 0.05) reduction of paw edema swelling compared to pure DC and DC-LP. Our findings revealed that encapsulation of DC in BMs matrix is a good alternative for improvement of therapeutic efficacy.\n\nDevelopment and Optimization of Nanolipid-Based Formulation of Diclofenac Sodium: In Vitro Characterization and Preclinical Evaluation.", "token_count": 495, "char_count": 1479, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:40.695243", "source": { "split": "train_shard_00000", "doc_id": 1917 }, "chunk_id": "train_shard_00000_1917_0", "global_id": 2113 }, { "text": "It is important to understand the basis of thermotolerance in yeasts to broaden their application in industrial biotechnology. The capacity to run bioprocesses at temperatures above 40 °C is of great interest but this is beyond the growth range of most of the commonly used yeast species. In contrast, some industrial yeasts such as\n\nIdentification of a novel gene required for competitive growth at high temperature in the thermotolerant yeast", "token_count": 100, "char_count": 444, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:41.077110", "source": { "split": "train_shard_00000", "doc_id": 1918 }, "chunk_id": "train_shard_00000_1918_0", "global_id": 2114 }, { "text": "Bile acids are important molecules that participate in digestion and regulate many host physiological processes, including metabolism and inflammation. Primary bile acids are biosynthesized from cholesterol in the liver, where they are conjugated to glycine and taurine before secretion into the intestines. A small fraction of these molecules remain in the gut, where they are modified by a microbial enzyme, bile salt hydrolase (BSH), which deconjugates the glycine and taurine groups. This deconjugation precedes all subsequent biotransformation in the intestines, including regioselective dehydroxylation and epimerization reactions, to produce numerous secondary bile acids. Thus, BSH is considered the gatekeeper enzyme of secondary bile acid metabolism, and, as a result, it controls the overall bile acid composition in the host. Despite the critical role that BSH plays in bile acid metabolism, there exist few tools to probe its activity in complex biological mixtures. In this chapter, we describe a chemoproteomic approach termed BSH-TRAP (bile salt hydrolase tagging and retrieval with activity-based probes) that enables visualization and identification of BSH activity in bacteria. Here, we describe application of BSH-TRAP to cultured bacterial strains and the gut microbes derived from mice. We envision that BSH-TRAP could be used to profile changes in BSH activity and identify novel BSH enzymes in complex biological samples, such as the gut microbiome.\n\nBSH-TRAP: Bile salt hydrolase tagging and retrieval with activity-based probes.", "token_count": 390, "char_count": 1554, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:41.701262", "source": { "split": "train_shard_00000", "doc_id": 1919 }, "chunk_id": "train_shard_00000_1919_0", "global_id": 2115 }, { "text": "Bile is a digestive fluid produced in the liver and stored in the gallbladder. It participates in absorption of fatty nutrients and vitamins, and aids in elimination of metabolic waste and toxins. The major chemical components of bile are bile salts that, apart from their function in digestion, are also known to participate in cell signaling by binding host farnesoid X (FXR), vitamin D (VDR), and G-protein coupled bile acid (TGR5) receptors. Microbial bile salt hydrolases (BSHs) catalyze bile salt deconjugation, a gatekeeper reaction that is a prerequisite for all subsequent microbial transformations of bile acids. As a result, BSH determines the composition of the bile salt and acid pools, which in turn affects its nutrient absorption and signaling capabilities. BSH profiling remains a challenge due to a paucity of tools that enable scientists to study its function. In this chapter, we discuss current BSH profiling approaches and demonstrate a novel fluorogenic probe-based assay that circumvents laborious and resource intensive BSH quantification methods. Alongside our assay protocol, we provide the reader with a detailed method for microbial cell extraction from fecal matter. We also cover probe validation protocols that can be adapted for Michaelis-Menten analysis with any BSH expressing strain.\n\nBile salt hydrolase profiling by fluorogenic probes in the human gut microbiome.", "token_count": 346, "char_count": 1401, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6462, "quality_score": 0.8231, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:42.275464", "source": { "split": "train_shard_00000", "doc_id": 1920 }, "chunk_id": "train_shard_00000_1920_0", "global_id": 2116 }, { "text": "Metformin hydrochloride (metformin HCL), a first-line drug treating diabetes type II, was known to cause severe gastritis, so seeking a non-oral dosage form was the new trend. Bilosomes are bilayer nano-vesicles of non-ionic surfactants embodying bile salts. In our study, bilosomes were investigated as an acceptable novel carrier for active targeting transdermal delivery of metformin HCL, circumventing its side effects.\n\nEvaluation of Metformin Hydrochloride Tailoring Bilosomes as an Effective Transdermal Nanocarrier.", "token_count": 142, "char_count": 523, "word_count": 71, "semantic_coherence": 1, "information_density": 0.831, "quality_score": 0.9155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:42.704957", "source": { "split": "train_shard_00000", "doc_id": 1921 }, "chunk_id": "train_shard_00000_1921_0", "global_id": 2117 }, { "text": "The family of Ustilaginaceae belongs to the order of Basidiomycetes. Despite their plant pathogenicity causing, e.g., corn smut disease, they are also known as natural producers of value-added chemicals such as extracellular glycolipids, organic acids, and polyols. Here, we present 17 high-quality draft genome sequences (N50 > 1 Mb) combining third-generation nanopore and second-generation Illumina sequencing. The data were analyzed with taxonomical genome-based bioinformatics methods such as Percentage of Conserved Proteins (POCP), Average Nucleotide Identity (ANI), and Average Amino Acid Identity (AAI) analyses indicating that a reclassification of the Ustilaginaceae family might be required. Further, conserved core genes were determined to calculate a phylogenomic core genome tree of the Ustilaginaceae that also supported the results of the other phylogenomic analysis. In addition, to genomic comparisons, secondary metabolite clusters (e.g., itaconic acid, mannosylerythritol lipids, and ustilagic acid) of biotechnological interest were analyzed, whereas the sheer number of clusters did not differ much between species.\n\nSeventeen Ustilaginaceae High-Quality Genome Sequences Allow Phylogenomic Analysis and Provide Insights into Secondary Metabolite Synthesis.", "token_count": 335, "char_count": 1280, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7262, "quality_score": 0.8631, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:43.270200", "source": { "split": "train_shard_00000", "doc_id": 1922 }, "chunk_id": "train_shard_00000_1922_0", "global_id": 2118 }, { "text": "The Lactobacillus acidophilus group consists of seven closely related species. Among these, Lb. acidophilus, Lb. gallinarum, and Lb. helveticus help maintain gut health and are used as a starter for fermented food. However, these species are difficult to differentiate using conventional methods due to the high similarity between the 16S rRNA and housekeeping genes. Thus, in this study, we selected biomarker genes to identify and discriminate the three species via pangenome analysis, and a multiplex SYBR Green real-time PCR that can be detected simultaneously in a single tube was developed. Pangenome analysis revealed three specific target genes: mucus-binding protein precursor to detect Lb. acidophilus, an amino acid ABC superfamily ATP binding cassette transporter carrier protein to detect Lb. gallinarum, and selenocysteine lyase to detect Lb. helveticus. The specificity was robustly verified using 26 Lb. acidophilus group strains and 62 other strains. The detection limits were 10\n\nMultiplex SYBR Green real-time PCR for Lactobacillus acidophilus group species targeting biomarker genes revealed by a pangenome approach.", "token_count": 293, "char_count": 1136, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6768, "quality_score": 0.8384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:43.829761", "source": { "split": "train_shard_00000", "doc_id": 1923 }, "chunk_id": "train_shard_00000_1923_0", "global_id": 2119 }, { "text": "Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.\n\nLandscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes.", "token_count": 375, "char_count": 1540, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6338, "quality_score": 0.8169, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:44.413404", "source": { "split": "train_shard_00000", "doc_id": 1924 }, "chunk_id": "train_shard_00000_1924_0", "global_id": 2120 }, { "text": "Klebsiella pneumoniae is a leading cause of highly drug-resistant infections in hospitals worldwide. Strain-level bacterial identification on the genetic determinants of multidrug resistance and high pathogenicity is critical for the surveillance and treatment of this clinically relevant pathogen. In this study, metagenomic next-generation sequencing was performed for specimens collected from August 2020 to May 2021 in Ruijin Hospital, Ningbo Women and Children's Hospital, and the Second Affiliated Hospital of Harbin Medical University. Genome biology of K. pneumoniae prevalent in China was characterized based on metagenomic data. Thirty K. pneumoniae strains derived from 14 sequence types were identified by multilocus sequence typing. The hypervirulent ST11 K. pneumoniae strains carrying the KL64 capsular locus were the most prevalent in the hospital population. The phylogenomic analyses revealed that the metagenome-reconstructed strains and public isolate genomes belonging to the same STs were closely related in the phylogenetic tree. Furthermore, the pangenome structure of the detected K. pneumoniae strains was analyzed, particularly focusing on the distribution of antimicrobial resistance genes and virulence genes across the strains. The genes encoding carbapenemases and extended-spectrum beta-lactamases were frequently detected in the strains of ST11 and ST15. The highest numbers of virulence genes were identified in the well-known hypervirulent strains affiliated to ST23 bearing the K1 capsule. In comparison to traditional cultivation and identification, strain-level metagenomics is advantageous to understand the mechanisms underlying resistance and virulence of K. pneumoniae directly from clinical specimens. Our findings should provide novel clues for future research into culture-independent metagenomic surveillance for bacterial pathogens.\n\nMetagenomic Approaches Reveal Strain Profiling and Genotyping of Klebsiella pneumoniae from Hospitalized Patients in China.", "token_count": 471, "char_count": 2004, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5925, "quality_score": 0.7962, "entities": { "genes": [ "ST15", "ST23", "KL64", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:45.062597", "source": { "split": "train_shard_00000", "doc_id": 1925 }, "chunk_id": "train_shard_00000_1925_0", "global_id": 2121 }, { "text": "Underutilized crops are, by definition, under-researched compared to staple crops yet come with traits that may be especially important given climate change and the need to feed a globally increasing population. These crops are often stress-tolerant, and this combined with unique and beneficial nutritional profiles. Whilst progress is being made by generating reference genome sequences, in this Tansley Review, we show how this is only the very first step. We advocate that going 'beyond a reference genome' should be a priority, as it is only at this stage one can identify the specific genes and the adaptive alleles that underpin the valuable traits. We sum up how population genomic and pangenomic approaches have led to the identification of stress- and disease-tolerant alleles in staple crops and compare this to the small number of examples from underutilized crops. We also demonstrate how previously underutilized crops have benefitted from genomic advances and that many breeding targets in underutilized crops are often well studied in staple crops. This cross-crop population-level resequencing could lead to an understanding of the genetic basis of adaptive traits in underutilized crops. This level of investment may be crucial for fully understanding the value of these crops before they are lost.\n\nBeyond a reference genome: pangenomes and population genomics of underutilized and orphan crops for future food and nutrition security.", "token_count": 307, "char_count": 1453, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6018, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:45.628655", "source": { "split": "train_shard_00000", "doc_id": 1926 }, "chunk_id": "train_shard_00000_1926_0", "global_id": 2122 }, { "text": "Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in-depth whole-genome study of V. cholerae El Tor strains isolated during endemic cholera in Bangladesh (1991 to 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera during 2004 to 2017. Genome-wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely, heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICE\n\nGenomic Characteristics of Recently Recognized Vibrio cholerae El Tor Lineages Associated with Cholera in Bangladesh, 1991 to 2017.", "token_count": 465, "char_count": 1624, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [ "PLE1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:46.269592", "source": { "split": "train_shard_00000", "doc_id": 1927 }, "chunk_id": "train_shard_00000_1927_0", "global_id": 2123 }, { "text": "Thermotolerant ethanol fermenting yeasts have been extensively used in industrial bioethanol production. However, little is known about yeast physiology under stress during bioethanol processing. This study investigated the physiological characteristics of the thermotolerant yeast Pichia kudriavzevii, strains NUNS-4, NUNS-5 and NUNS-6, under the multiple stresses of heat, ethanol and sodium chloride. Results showed that NUNS-4, NUNS-5 and NUNS-6 displayed higher growth rates under each stress condition than the reference strain, Saccharomyces cerevisiae TISTR5606. Maximum specific growth rates under stresses of heat (45°C), 15% v/v ethanol and 1·0 M sodium chloride were 0·23 ± 0·04 (NUNS-4), 0·11 ± 0·01 (NUNS-5) and 0·15 ± 0·01 h\n\nThe ability of Pichia kudriavzevii to tolerate multiple stresses makes it promising for developing improved bioethanol production processes.", "token_count": 302, "char_count": 881, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7295, "quality_score": 0.8648, "entities": { "genes": [ "TISTR5606" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:46.838679", "source": { "split": "train_shard_00000", "doc_id": 1928 }, "chunk_id": "train_shard_00000_1928_0", "global_id": 2124 }, { "text": "Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirmed human cases. Clustering studies by single nucleotide polymorphism (SNP) core-genome phylogenetic analysis of outbreaks due to these major serovars are simplified by the availability of many complete genomes in the free access databases. This is not the case for outbreaks due to less common serovars, such as Welikade, for which no reference genomes are available. In this study, we propose a method to solve this problem. We propose to perform a core genome MLST (cgMLST) analysis based on hierarchical clustering using the free-access EnteroBase to select the most suitable genome to use as a reference for SNP phylogenetic analysis. In this study, we applied this protocol to a retrospective analysis of a Salmonella enterica serovar Welikade (S. Welikade) foodborne outbreak that occurred in France in 2016. Finally, we compared the cgMLST and SNP analyses. SNP phylogenetic reconstruction was carried out considering the effect of recombination events identified by the ClonalFrameML tool. The accessory genome was also explored by phage content and virulome analyses.\n\nSalmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks.", "token_count": 354, "char_count": 1422, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:47.415011", "source": { "split": "train_shard_00000", "doc_id": 1929 }, "chunk_id": "train_shard_00000_1929_0", "global_id": 2125 }, { "text": "A FEFEFKFK (FEK, F, phenylalaninyl; E, glutamyl; K, lysinyl)-based self-assembling peptide hydrogel (FEK-SAPH) was developed to replace sandwich culture (SC) for improved culture of primary hepatocytes in vitro. Under neutral conditions, FEK self-assembles to form β-sheet nanofibers, which in turn form FEK-SAPH. For the culture of rat primary hepatocytes (RPH), the use of FEK-SAPH simplified operation steps and promoted excellent cell-cell interactions while maintaining the SC-related RPH polarity trend. Compared with SC, FEK-SAPH cultured RPH for 14 days, the bile duct network was formed, the secretion of albumin and urea was improved, and the metabolic clearance rate based on cytochrome P450 (CYPs) was comparable. In FEK-SAPH culture, the expression level of the biliary efflux transporter bile salt export pump increased by 230.7%, while the biliary excretion index value of deuterium-labeled sodium taurocholate (d8-TCA) differed slightly from the SC value (72% and 77%, respectively, p = .0195). The inhibitory effect of cholestasis drugs on FEK-SAPH was significantly higher than that of SC. In FEK-SAPH, hepatoprotective drugs were more effective in antagonizing hepatotoxicity induced by lithocholic acid (LCA). FEK-SAPH cultured RPH with hepatoprotective drugs can better recover from LCA-induced damage. In summary, FEK-SAPH can be used as a substitute for SC for pharmacokinetic screening to evaluate the drug absorption, disposition, metabolism, excretion, and toxicity (ADMET) in hepatocytes.\n\nFEK self-assembled peptide hydrogels facilitate primary hepatocytes culture and pharmacokinetics screening.", "token_count": 493, "char_count": 1624, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6858, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:48.068410", "source": { "split": "train_shard_00000", "doc_id": 1930 }, "chunk_id": "train_shard_00000_1930_0", "global_id": 2126 }, { "text": "Microbe domestication has a major applied relevance but is still poorly understood from an evolutionary perspective. The yeast Torulaspora delbrueckii is gaining importance for biotechnology but little is known about its population structure, variation in gene content or possible domestication routes. Here, we show that T. delbrueckii is composed of five major clades. Among the three European clades, a lineage associated with the wild arboreal niche is sister to the two other lineages that are linked to anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix-Anthropic clade). Using 64 genomes we assembled the pangenome and the variable genome of T. delbrueckii. A comparison with Saccharomyces cerevisiae indicated that the weight of the variable genome in the pangenome of T. delbrueckii is considerably smaller. An association of gene content and ecology supported the hypothesis that the Mix-Anthropic clade has the most specialized genome and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. In contrast to S. cerevisiae, domestication in T. delbrueckii is not primarily driven by alcoholic fermentation but rather by adaptation to dairy and bread-production niches. This study expands our views on the processes of microbe domestication and on the trajectories leading to adaptation to anthropic niches.\n\nA glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast.", "token_count": 418, "char_count": 1795, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5768, "quality_score": 0.7884, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:48.690247", "source": { "split": "train_shard_00000", "doc_id": 1931 }, "chunk_id": "train_shard_00000_1931_0", "global_id": 2127 }, { "text": "Polyploidy and life-strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and the genetic bases of such transitions remain elusive. We assembled chromosome-level genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. These perennial diploids exhibit greater genome stability and possess fewer centromere repeats than the annuals. Biased subgenomic fractionation occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with pre-existing local subgenomic differentiation. Two genes annotated to modulate vegetative-reproductive phase transition and lateral shoot outgrowth were postulated as candidates underlying the perenniality-annuality transition. Our study provides insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.\n\nPhylogenomics of the genus Glycine sheds light on polyploid evolution and life-strategy transition.", "token_count": 285, "char_count": 1261, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7342, "quality_score": 0.8671, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:49.248020", "source": { "split": "train_shard_00000", "doc_id": 1932 }, "chunk_id": "train_shard_00000_1932_0", "global_id": 2128 }, { "text": "Microcystis is a cyanobacteria that is widely distributed across the world. It has attracted great attention because it produces the hepatotoxin microcystin (MC) that can inhibit eukaryotic protein phosphatases and pose a great risk to animal and human health. Due to the high diversity of morphospecies and genomes, it is still difficult to classify Microcystis species. In this study, we investigated the pangenome of 23 Microcystis strains to detect the genetic diversity and evolutionary dynamics. Microcystis revealed an open pangenome containing 22,009 gene families and exhibited different functional constraints. The core-genome phylogenetic analysis accurately differentiated the toxic and nontoxic strains and could be used as a taxonomic standard at the genetic level. We also investigated the functions of HGT events, of which were mostly conferred from cyanobacteria and closely related species. In order to detect the potential toxicity of Microcystis, we searched and characterized MC biosynthetic gene clusters and other secondary metabolite gene clusters. Our work provides insights into the genetic diversity, evolutionary dynamics, and potential toxicity of Microcystis, which could benefit the species classification and development of new methods for drinking water quality control and management of bloom formation in the future.\n\nComprehensive and functional analyses reveal the genomic diversity and potential toxicity of Microcystis.", "token_count": 321, "char_count": 1458, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:49.849997", "source": { "split": "train_shard_00000", "doc_id": 1933 }, "chunk_id": "train_shard_00000_1933_0", "global_id": 2129 }, { "text": "Synechococcus cyanobacteria are ubiquitous and abundant in the marine environment and contribute to an estimated 16% of the ocean net primary productivity. Their light-harvesting complexes, called phycobilisomes (PBS), are composed of a conserved allophycocyanin core, from which radiates six to eight rods with variable phycobiliprotein and chromophore content. This variability allows Synechococcus cells to optimally exploit the wide variety of spectral niches existing in marine ecosystems. Seven distinct pigment types or subtypes have been identified so far in this taxon based on the phycobiliprotein composition and/or the proportion of the different chromophores in PBS rods. Most genes involved in their biosynthesis and regulation are located in a dedicated genomic region called the PBS rod region. Here, we examine the variability of gene content and organization of this genomic region in a large set of sequenced isolates and natural populations of Synechococcus representative of all known pigment types. All regions start with a tRNA-PheGAA and some possess mobile elements for DNA integration and site-specific recombination, suggesting that their genomic variability relies in part on a \"tycheposon\"-like mechanism. Comparison of the phylogenies obtained for PBS and core genes revealed that the evolutionary history of PBS rod genes differs from the core genome and is characterized by the co-existence of different alleles and frequent allelic exchange. We propose a scenario for the evolution of the different pigment types and highlight the importance of incomplete lineage sorting in maintaining a wide diversity of pigment types in different Synechococcus lineages despite multiple speciation events.\n\nDiversity and Evolution of Pigment Types in Marine Synechococcus Cyanobacteria.", "token_count": 421, "char_count": 1806, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:50.496694", "source": { "split": "train_shard_00000", "doc_id": 1934 }, "chunk_id": "train_shard_00000_1934_0", "global_id": 2130 }, { "text": "Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.\n\nPlant genome sequence assembly in the era of long reads: Progress, challenges and future directions.", "token_count": 194, "char_count": 1029, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6809, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:50.984319", "source": { "split": "train_shard_00000", "doc_id": 1935 }, "chunk_id": "train_shard_00000_1935_0", "global_id": 2131 }, { "text": "Pangenomes are a rich resource to examine the genomic variation observed within a species or genera, supporting population genetics studies, with applications for the improvement of crop traits. Major crop species such as maize (\n\nPangenomes as a Resource to Accelerate Breeding of Under-Utilised Crop Species.", "token_count": 69, "char_count": 310, "word_count": 46, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:51.395759", "source": { "split": "train_shard_00000", "doc_id": 1936 }, "chunk_id": "train_shard_00000_1936_0", "global_id": 2132 }, { "text": "Dietary fat and oil could aid in reaching the high-energy requirements of fast-growing birds; however, these inclusions could lead to nutrient waste. This is because young birds have limited lipid digestion due to the low secretion of lipase and bile salt. Sophorolipid (SPL), a glycolipid emulsifier with lower toxicity and higher biodegradability, can upregulate fat utilization by increasing digestibility. Accordingly, a five-week-long experiment was conducted with 720 one-day-old chicks (Ross 308) to investigate the effects of dietary SPL on growth, organ characteristics, and gut health. The allotment was partitioned into four treatment groups according to their body weight with six replications (30 chick/pen). The three treatment diets comprised a basal diet with a formulation that met the Ross 308 standard and 5, 10, and 15 ppm SPL in the basal diet. During the experiment, the birds had free access to feed, and body weight and feed intake were measured at the end of each phase. Chickens were put down at the end of the growing and finishing phases, and jejunum and cecal samples were obtained to investigate organ characteristics and gut environments. The data were analyzed using the generalized linear model procedures of SAS 9.4, and all data were assessed for linear, quadratic, and cubic effects of dietary SPL-supplemented dosages. Body weight was significantly increased with 10 ppm of SPL supplementation in the grower phase without affecting feed efficiency. The relative weights of the intestine and the bursa of Fabricius were quadratically decreased by SPL supplementation with a lower population of\n\nEffects of Sophorolipid on Growth Performance, Organ Characteristics, Lipid Digestion Markers, and Gut Functionality and Integrity in Broiler Chickens.", "token_count": 434, "char_count": 1782, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:52.036276", "source": { "split": "train_shard_00000", "doc_id": 1937 }, "chunk_id": "train_shard_00000_1937_0", "global_id": 2133 }, { "text": "Bile salt hydrolases (BSHs), a group of cysteine-hydrolases produced by gut microbes, play a crucial role in the hydrolysis of glycine- or taurine-conjugated bile acids and have been validated as key targets to modulate bile acid metabolism. This study aims to discover one or more efficacious inhibitors against a BSH produced by\n\nDiscovery and characterization of amentoflavone as a naturally occurring inhibitor against the bile salt hydrolase produced by", "token_count": 123, "char_count": 458, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:52.424838", "source": { "split": "train_shard_00000", "doc_id": 1938 }, "chunk_id": "train_shard_00000_1938_0", "global_id": 2134 }, { "text": "Pharmacological activation of the xenobiotic-sensing nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) is well-known to increase drug metabolism and reduce inflammation. Little is known regarding their physiological functions on the gut microbiome. In this study, we discovered bivalent hormetic functions of PXR/CAR modulating the richness of the gut microbiome using genetically engineered mice. The absence of\n\nUnderstanding the physiological functions of the host xenobiotic-sensing nuclear receptors PXR and CAR on the gut microbiome using genetically modified mice.", "token_count": 154, "char_count": 608, "word_count": 81, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:52.865332", "source": { "split": "train_shard_00000", "doc_id": 1939 }, "chunk_id": "train_shard_00000_1939_0", "global_id": 2135 }, { "text": "The prevalence of vancomycin-resistant Enterococcus faecium has increased rapidly, and in Denmark, we are facing an endemic outbreak situation in hospitals. The aim of this study was to use whole-genome sequencing (WGS) and core genome multilocus sequencing typing (cgMLST) to determine the duration of VREfm outbreaks and thereby evaluate the effect of our infection control strategies. We included all VREfm isolates from six hospitals in the Capital Region of Denmark that were sequenced between 2012 and 2020. Ward data were collected from our laboratory information system. A ward outbreak was defined as two patient samples from the same ward within a period of 30 days belonging to the same cgMLST cluster. cgMLST complex types were determined using Ridom SeqSphere v7.2.3, where a maximum of 20 allelic differences between isolates defines a cluster. We included 1690 patient isolates between 2012 and 2020. Our collection consisted of 45 unique clusters and 227 ward outbreaks. The median duration of outbreaks was 20 days. We reported a median outbreak duration of VREfm outbreaks based on WGS data to be 20 days, and thus concluded that our infection control precautions are adequate.\n\nThe use of core genome multilocus sequence typing to determine the duration of vancomycin-resistant Enterococcus faecium outbreaks.", "token_count": 340, "char_count": 1328, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5588, "quality_score": 0.7794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:53.434397", "source": { "split": "train_shard_00000", "doc_id": 1940 }, "chunk_id": "train_shard_00000_1940_0", "global_id": 2136 }, { "text": "Bile salt hydrolase (BSH) enzymes produced by intestinal\n\nIsolation of a Highly Thermostable Bile Salt Hydrolase With Broad Substrate Specificity From", "token_count": 45, "char_count": 150, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:53.796204", "source": { "split": "train_shard_00000", "doc_id": 1941 }, "chunk_id": "train_shard_00000_1941_0", "global_id": 2137 }, { "text": "Probiotics are living microorganisms that confer health benefits to host when administered in adequate amounts. To develop novel host-specific probiotic for their application as feed additive, the present study was undertaken to isolate and characterize probiotic strains of indigenous cattle-calves origin. A total of 55 colonies were isolated from 12 healthy calves, with 34 of the isolates being Gram-positive, catalase-negative and vancomycin-resistant. Furthermore, eleven isolates showed tolerance to acid (pH 2.0) and thirteen isolates tolerated bile salts (0.3%). Seven common acid and bile tolerance strains were further investigated for other probiotic attributes and displayed higher (\n\nScreening and characterization of Sahiwal cattle calves-origin lactic acid bacteria based on desired probiotic attributes for potential application.", "token_count": 198, "char_count": 846, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7719, "quality_score": 0.886, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:54.259050", "source": { "split": "train_shard_00000", "doc_id": 1942 }, "chunk_id": "train_shard_00000_1942_0", "global_id": 2138 }, { "text": "Gut microbiota exerts a fundamental role in human health and increased evidence supports the beneficial role of probiotic microorganisms in the maintenance of intestinal health. Enterococcus durans LAB18S was previously isolated from soft cheese and showed some desirable in vitro probiotic properties, for that reason its genome was sequenced and evaluated for genes that can be relevant for probiotic activity and are involved in selenium metabolism. Genome sequencing was performed using the Illumina MiSeq System. A variety of genes potentially associated with probiotic properties, including adhesion capability, viability at low pH, bile salt resistance, antimicrobial activity, and utilization of prebiotic fructooligosaccharides (FOS) were identified. The strain showed tolerance to acid pH and bile salts, exhibited antimicrobial activity and thrived on prebiotic oligosaccharides. Six genes involved in selenium metabolism were predicted. Analysis of the SECIS element showed twelve known selenoprotein candidates. E. durans LAB18S was the only food isolate showing absence of plasmids, virulence and antimicrobial resistance genes, when compared with other 30 E. durans genomes. The results of this study provide evidence supporting the potential of E. durans LAB18S as alternative for probiotic formulations.\n\nGenomic analysis of Enterococcus durans LAB18S, a potential probiotic strain isolated from cheese.", "token_count": 342, "char_count": 1420, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6396, "quality_score": 0.8198, "entities": { "genes": [ "LAB18S" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:54.835950", "source": { "split": "train_shard_00000", "doc_id": 1943 }, "chunk_id": "train_shard_00000_1943_0", "global_id": 2139 }, { "text": "Kluyveromyces marxianus is the most suitable fungus for inulinase industrial production. However, the underlying transcriptional activation mechanism of the inulinase gene (INU1) is hitherto unclear. Here, we undertook genetic and biochemical analyses to elucidate that a glycolysis regulator KmGcr1p with unique Q-rich repeats is the key transcriptional activator of INU1. We determined that INU1 and glycolytic genes share similar transcriptional activation patterns and that inulinase activity is induced by fermentable carbon sources including the hydrolysis products of inulin (fructose and glucose), which suggests a novel model of product feedback activation. Furthermore, all four CT-boxes in the INU1 promoter are important for KmGcr1p DNA-binding in vitro, but the most downstream CT-box 1 primarily confers upstream activating sequence activity in vivo. More intriguingly, the use of artificial and natural GCR1 mutants suggests that the Q-rich repeats act as a functional module to maintain KmGcr1p transcriptional activity by contributing to its solubility and DNA-binding affinity. Altogether, this study uncovers a novel transcriptional activation mechanism for the inulinase gene, that is different from the previous understanding for filamentous fungi, but might have universal significance among inulinase-producing yeasts, thereby leading to a better understanding of the regulation mechanism of yeast inulinase genes.\n\nA novel transcriptional activation mechanism of inulinase gene in Kluyveromyces marxianus involving a glycolysis regulator KmGcr1p with unique and functional Q-rich repeats.", "token_count": 390, "char_count": 1612, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5936, "quality_score": 0.7968, "entities": { "genes": [ "GCR1", "INU1" ], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:55.454744", "source": { "split": "train_shard_00000", "doc_id": 1945 }, "chunk_id": "train_shard_00000_1945_0", "global_id": 2140 }, { "text": "With increase in the number of sequenced genomes, it is now recognized that graph-based pangenomes can provide a comprehensive platform to study diversity in a population or species, from point mutations to large chromosomal rearrangements. By incorporating concepts from graph theory, a graph-pangenome can be studied directly to identify genomic regions and genes that underlie important evolutionary processes and traits. Here, I discuss how basic concepts in graph theory can be implemented to address questions in evolutionary genomics and guide future breeding efforts. Despite its compelling versatility, a graph-pangenome assembly is still challenging especially in species with large complex genomes. As technology is rapidly improving, the graph-pangenome is expected to become a central platform in genomics studies and applications. Thus, development of tools and methods that exploit the graph structure are urged to pave the route to evolutionary graph-pangenomics.\n\nAre we there yet? Driving the road to evolutionary graph-pangenomics.", "token_count": 217, "char_count": 1050, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6779, "quality_score": 0.8389, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:55.919926", "source": { "split": "train_shard_00000", "doc_id": 1946 }, "chunk_id": "train_shard_00000_1946_0", "global_id": 2141 }, { "text": "Extraintestinal pathogenic Escherichia coli (ExPEC) is a globally distributed pathogen, with uropathogenic E. coli (UPEC) and sepsis-associated E. coli (SEPEC) pathotypes particularly involved in human and companion animal disease, while avian pathogenic pathotype (APEC) severely impact poultry health and production. Similarities between APEC from poultry/meat and human ExPEC suggest that some APEC lineages may have zoonotic potential. ExPEC sequence type 73 (ST73) and its clonal complex (CC) are increasing causes of urinary tract infections and sepsis, but its role in zoonotic disease is less well understood. Here, we analyzed the genome sequences of 25 E. coli isolates from Brazil (11 APEC and 14 UPEC) from two time periods, from poultry producing areas and hospitals in the same geographical regions. Isolates were compared to 558 publicly available ST73/CC73 global sequences. Brazilian APEC harbored virulence factors associated with UPEC/SEPEC such as sfa, cnf1, vat, usp, hlyA, iron acquisition and protectins/serum resistance systems, while lacking some common APEC markers and widespread multidrug resistance. Analysis of core genome MLST and SNP phylogenetic trees indicated evolutionary relationships between subgroups of the Brazilian APEC to two contemporary Brazilian UPEC isolates from the same region, and one Brazilian UPEC available from another study. Phylogenies showed a non-host, geographical, or pathotype specificity, with APEC isolates clustering closely with international human UPEC, SEPEC. The remaining Brazilian UPEC grouped within human clusters. Collectively, this suggests a zoonotic potential for subgroups of Brazilian APEC from the ST73 lineage that could contaminate poultry products and subsequently cause human infection.\n\nGenomic analysis of the zoonotic ST73 lineage containing avian and human extraintestinal pathogenic Escherichia coli (ExPEC).", "token_count": 507, "char_count": 1897, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [ "ST73", "CC73" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:56.573163", "source": { "split": "train_shard_00000", "doc_id": 1947 }, "chunk_id": "train_shard_00000_1947_0", "global_id": 2142 }, { "text": "This study aimed to evaluate the occurrence and diversity of yeasts in frozen concentrated orange juice (FCOJ) and assess the resistance of yeasts to peracetic acid. One thousand five hundred (n = 1500) samples of frozen concentrated orange juice (FCOJ) were analyzed, and 280 yeast strains were isolated and identified. Candida represented 37% of all isolates, and the main species identified were Candida pseudointermedia and C. orthopsilosis. Other yeasts identified were Starmerella, Wickerhamiella, Wickerhamiella, Clavispora, Kodamaea, Meyerozyma, Rhodotorula, Trichosporon, Wickerhamomyces, Kluyveromyces, Hanseniaspora, Saccharomyces, Torulaspora, and Zygosaccharomyces. The exogenous origin of the contamination in FCOJ samples analyzed was shown by the high diversity, corroborated by the Simpson (D) and Shannon (H') indices. From a total of 227 yeasts strains tested, more than 20% were able to withstand peracetic acid concentrations >200 ppm, with emphasis on W. anomalus (300 ppm), W. sergipensis (350 ppm), C. rugopelliculosa (350 ppm), K. marxianus (450 ppm), C. parapsilosis (500 ppm), C. pseudointermedia (500 ppm), W. sorbosivorans (500 ppm), C. boleticola (600 ppm), S. cerevisiae (700 ppm) and C. orthopsilosis (750 ppm). This study adds novel data regarding the occurrence and diversity of yeasts present in FCOJ and their resistance to a chemical compound commonly employed in the sanitization of processing and distribution premises and vehicles", "token_count": 486, "char_count": 1470, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:57.225096", "source": { "split": "train_shard_00000", "doc_id": 1948 }, "chunk_id": "train_shard_00000_1948_0", "global_id": 2143 }, { "text": "These findings are essential to support the development of measures for proper mitigation of contamination of orange juice towards reducing the risks of spoilage by yeasts during FCOJ transportation/storage or when FCOJ is used as an ingredient.\n\nLarge scale survey of yeasts in frozen concentrated orange juice (FCOJ): Occurrence, diversity, and resistance to peracetic acid.", "token_count": 82, "char_count": 376, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:57.595000", "source": { "split": "train_shard_00000", "doc_id": 1948 }, "chunk_id": "train_shard_00000_1948_1", "global_id": 2144 }, { "text": "Pangenomes aim to represent the complete repertoire of the genome diversity present within a species or cohort of species, capturing the genomic structural variance between individuals. This genomic information coupled with phenotypic data can be applied to identify genes and alleles involved with abiotic stress tolerance, disease resistance, and other desirable traits. The characterisation of novel structural variants from pangenomes can support genome editing approaches such as Clustered Regularly Interspaced Short Palindromic Repeats and CRISPR associated protein Cas (CRISPR-Cas), providing functional information on gene sequences and new target sites in variant-specific genes with increased efficiency. This review discusses the application of pangenomes in genome editing and crop improvement, focusing on the potential of pangenomes to accurately identify target genes for CRISPR-Cas editing of plant genomes while avoiding adverse off-target effects. We consider the limitations of applying CRISPR-Cas editing with pangenome references and potential solutions to overcome these limitations.\n\nExpanding Gene-Editing Potential in Crop Improvement with Pangenomes.", "token_count": 243, "char_count": 1177, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:58.079440", "source": { "split": "train_shard_00000", "doc_id": 1949 }, "chunk_id": "train_shard_00000_1949_0", "global_id": 2145 }, { "text": "Haemophilus influenzae is an opportunistic pathogen adapted to the human respiratory tract. Non-typeable H. influenzae are highly heterogeneous, but few studies have analysed the genomic variability of capsulated strains. This study aims to examine the genetic diversity of 37 serotype f isolates from the Netherlands, Portugal, and Spain, and to compare all capsulated genomes available on public databases. Serotype f isolates belonged to CC124 and shared few single nucleotide polymorphisms (SNPs) (n = 10,999), but a high core genome (> 80%). Three main clades were identified by the presence of 75, 60 and 41 exclusive genes for each clade, respectively. Multi-locus sequence type analysis of all capsulated genomes revealed a reduced number of clonal complexes associated with each serotype. Pangenome analysis showed a large pool of genes (n = 6360), many of which were accessory genome (n = 5323). Phylogenetic analysis revealed that serotypes a, b, and f had greater diversity. The total number of SNPs in serotype f was significantly lower than in serotypes a, b, and e (p < 0.0001), indicating low variability within the serotype f clonal complexes. Capsulated H. influenzae are genetically homogeneous, with few lineages in each serotype. Serotype f has high genetic stability regardless of time and country of isolation.\n\nComparative pangenome analysis of capsulated Haemophilus influenzae serotype f highlights their high genomic stability.", "token_count": 398, "char_count": 1454, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6273, "quality_score": 0.8136, "entities": { "genes": [ "CC124" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:58.693606", "source": { "split": "train_shard_00000", "doc_id": 1950 }, "chunk_id": "train_shard_00000_1950_0", "global_id": 2146 }, { "text": "The ability to perform effectively in the gastrointestinal tract (GIT) is one of the most significant criteria in the selection of potential probiotic bacteria. Thus, the present study aimed to investigate the potential probiotic characteristics of some selected lactic acid bacteria (LAB) isolated from vegetable products. Probiotic characteristics included tolerance to acid and bile, cholesterol-removing ability, bile salt hydrolysis, resistance against lysozyme and antibiotics, production of exopolysaccharides (EPS), antimicrobial and hemolytic activities, and cell surface characteristics (auto-aggregation, co-aggregation, and hydrophobicity). The survival rate of isolates after G120 ranged from 8.0 to 8.6 Log\n\nLactic Acid Bacteria Isolated from Fresh Vegetable Products: Potential Probiotic and Postbiotic Characteristics Including Immunomodulatory Effects.", "token_count": 213, "char_count": 869, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:17:59.499343", "source": { "split": "train_shard_00000", "doc_id": 1951 }, "chunk_id": "train_shard_00000_1951_0", "global_id": 2147 }, { "text": "The aim of the current study was to isolate indigenous lactic acid bacteria (LAB) from traditional Greek cheeses and assess their biochemical, technological, and functional characteristics, so as to develop novel cultures with multi-functional properties. Hence, 109 LAB isolates were recovered from traditional fresh cheeses and were evaluated in vitro for their gas production; proteolytic, lipolytic, and haemolytic activity; exopolysaccharide production (EPS); enzymatic potential; and ability to grow at 6.5% NaCl and at different pH, temperature, and anaerobic conditions. Consequently, 48 selected isolates were further evaluated for their survival under simulated gastrointestinal tract conditions, partial bile salt hydrolase activity, antibiotic resistance, and antimicrobial activity against pathogens. These isolates were also incorporated as co-cultures in yogurt production to examine their sensory characteristics and their survival in the product. Some prominent isolates that showed favorable technological and functional characteristics (good survival rates at low pH and bile salts, ability to produce\n\nMapping the Key Technological and Functional Characteristics of Indigenous Lactic Acid Bacteria Isolated from Greek Traditional Dairy Products.", "token_count": 287, "char_count": 1265, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:00.054465", "source": { "split": "train_shard_00000", "doc_id": 1952 }, "chunk_id": "train_shard_00000_1952_0", "global_id": 2148 }, { "text": "Biotransformation of host bile salts by gut microbes results in generation of secondary bile salt species that have biological and physicochemical properties that are distinct from the parent compounds. There is increased awareness that a bile salt-gut microbiome axis modulates various processes in the host, including innate and adaptive immunity, by interaction of microbial bile salt metabolites with host receptors. Omics and targeted approaches have vastly expanded the number and repertoire of secondary bile salt species. A new class of microbial bile salt metabolites was reported in 2020 and comprises bile salts that are conjugated by microbial enzymes. Amino acids other than those employed by host enzymes (glycine and taurine) are used as substrates in the formation of these microbial bile salt conjugates (MBSCs). Leucocholic acid, phenylalanocholic acid and tyrosocholic acid were the first MBSCs identified in mice and humans. The number of distinct MBSCs is now approaching 50, with variation both at the level of bile salt and amino acid employed for conjugation. Evidence is emerging that MBSC generation is a common feature of human gut bacteria, and initial links with disease states have been reported. In this review, we discuss this intriguing new class of secondary bile salts, with yet enigmatic function.\n\nNew Kids on the Block: Bile Salt Conjugates of Microbial Origin.", "token_count": 346, "char_count": 1399, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:00.632683", "source": { "split": "train_shard_00000", "doc_id": 1953 }, "chunk_id": "train_shard_00000_1953_0", "global_id": 2149 }, { "text": "Human milk is critical for the survival and development of infants. This source of nutrition contains components that protect against infections while stimulating immune maturation. In cases where the mother's own milk is unavailable, pasteurized donor milk is the preferred option. Although pasteurization has been shown to have minimal impact on the lipid and FA composition before digestion, no correlation has been made between the impact of pasteurization on the FFA composition and the self-assembly of lipids during digestion, which could act as delivery mechanisms for poorly water-soluble components. Pooled nonpasteurized and pasteurized human milk from a single donor was used in this study. The evolving FFA composition during digestion was determined using GC coupled to a flame ionization detector. In vitro digestion coupled to small-angle X-ray scattering was utilized to investigate the influence of different calcium levels, fat content, and the presence of bile salts on the extent of digestion and structural behavior of human milk lipids. Almost complete digestion was achieved when bile salts were added to the systems containing high calcium to milk fat ratio, with similar structural behavior of lipids during digestion of both types of human milk being apparent. In contrast, differences in the colloidal structures were formed during digestion in the absence of bile salt because of a greater amount of FFAs being released from the nonpasteurized than pasteurized milks. This difference in FFAs released from both types of human milk could result in varying nutritional implications for infants.\n\nImpact of pasteurization on the self-assembly of human milk lipids during digestion.", "token_count": 358, "char_count": 1707, "word_count": 257, "semantic_coherence": 1, "information_density": 0.537, "quality_score": 0.7685, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:01.214429", "source": { "split": "train_shard_00000", "doc_id": 1954 }, "chunk_id": "train_shard_00000_1954_0", "global_id": 2150 }, { "text": "γ-Aminobutyric acid (GABA) is a non-protein amino acid with a variety of physiological functions. Recently, yeast Kluyveromyces marxianus strains involved in the catabolism and anabolism of GABA can be used as a microbial platform for GABA production. Okara, rich in nutrients, can be used as a low-cost fermentation substrate for the production of functional materials. This study first proved the advantages of the okara medium to produce GABA by K. marxianus C21 when L-glutamate (L-Glu) or monosodium glutamate (MSG) is the substrate. The highest production of GABA was obtained with 4.31 g/L at optimization condition of culture temperature 35 °C, fermentation time 60 h, and initial pH 4.0. Furthermore, adding peptone significantly increased the GABA production while glucose and vitamin B6 had no positive impact on GABA production. This research provided a powerful new strategy of GABA production by K. marxianus C21 fermentation and is expected to be widely utilized in the functional foods industry to increase GABA content for consumers as a daily supplement as suggested.\n\nOptimization of fermentation for γ-aminobutyric acid (GABA) production by yeast Kluyveromyces marxianus C21 in okara (soybean residue).", "token_count": 345, "char_count": 1222, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6033, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:01.807586", "source": { "split": "train_shard_00000", "doc_id": 1955 }, "chunk_id": "train_shard_00000_1955_0", "global_id": 2151 }, { "text": "We describe the genomic characteristics of Vibrio cholerae strain PS-4 that is unable to ferment sucrose on a thiosulfate citrate bile salt sucrose (TCBS) agar medium. This bacterium was isolated from the skin mucus of a freshwater pufferfish. The genome of strain PS-4 was sequenced to understand the sucrose nonfermenting phenotype. The gene encoding the sucrose-specific phosphotransferase system IIB (sucR) was absent, resulting in the defective sucrose fermenting phenotype. In contrast, genes encoding the glucose-specific transport system IIB (ptsG) and fructose-specific transport system IIB (fruA) showed acid production while growing with respective sugars. The overall genome relatedness indices (OGRI), such as\n\nPufferfish (Tetraodon cutcutia) Sampled from a Freshwater River Serves as an Intermediate Reservoir of a Sucrose Nonfermenting Variant of Vibrio cholerae PS-4.", "token_count": 240, "char_count": 883, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:02.316543", "source": { "split": "train_shard_00000", "doc_id": 1956 }, "chunk_id": "train_shard_00000_1956_0", "global_id": 2152 }, { "text": "Brachyspira (B.) hyodysenteriae is a fastidious anaerobe spirochete that can cause swine dysentery, a severe mucohaemorragic colitis that affects pig production and animal welfare worldwide. In Switzerland, the population of B. hyodysenteriae is characterized by the predominance of macrolide-lincosamide-resistant B. hyodysenteriae isolates of sequence type (ST) ST196, prompting us to obtain deeper insights into the genomic structure and variability of ST196 using pangenome and whole genome variant analyses.\n\nWhole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196.", "token_count": 184, "char_count": 627, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [ "ST196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:02.775152", "source": { "split": "train_shard_00000", "doc_id": 1957 }, "chunk_id": "train_shard_00000_1957_0", "global_id": 2153 }, { "text": "Streptococcus mutans (S. mutans) is the most important oral pathogenic bacterial cause of dental caries. Here we investigated the abilities of probiotic lactobacillus strains of Lactobacillus curvatus (L. curvatus) BSF206 and Pediococcus pentosaceus (P. pentosaceus) AC1-2 to control S. mutans. Both probiotic strains are acid and bile salt tolerant and are resistant to hydrogen peroxide and lysozyme to promote their survival within the oral environment. In addition, both strains are highly hydrophobic and are also capable of engaging in electrostatic interactions. These properties enhance abilities of both strains to adhere to gingival epithelial cells and HT-29 for improved colonization of oral tissues, while also enabling these probiotics auto-aggregate and to form aggregates with S. mutans that both may prevent S. mutans from colonizing oral tissues and facilitate the clearance of the cariogenic bacteria from the mouth during swallowing of food and saliva. Furthermore, results presented herein revealed that L. curvatus BSF206 and P. pentosaceus AC1-2 effectively inhibited S. mutans activities (biofilm formation, secretion of extracellular matrix components, synthesis of water-insoluble glucans) and led to downregulation of expression of key S. mutans genes involved in biofilm production (gtfA, gtfB, ftf, brpA). Taken together, these results indicate that L. curvatus BSF206 and P. pentosaceus AC1-2 can inhibit S. mutans biofilm formation as a new strategy for preventing dental caries.\n\nAntibacterial and anti-biofilm activities of probiotic Lactobacillus curvatus BSF206 and Pediococcus pentosaceus AC1-2 against Streptococcus mutans.", "token_count": 447, "char_count": 1660, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5966, "quality_score": 0.7983, "entities": { "genes": [ "BSF206", "AC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:03.447341", "source": { "split": "train_shard_00000", "doc_id": 1958 }, "chunk_id": "train_shard_00000_1958_0", "global_id": 2154 }, { "text": "In the present study, thirty two lactic acid bacteria (LAB) were isolated from fermented Indian herbal medicine. In comparison to other strains, MNL5 had stronger bile salt hydrolase (BSH) and cholesterol-lowering properties. Furthermore, it can withstand the extreme conditions found in the GI tract, due to, e.g., pepsin, bile salts, pancreatin, and acids.\n\nAnti-Obesity Efficacy of", "token_count": 110, "char_count": 384, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [ "MNL5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:03.866048", "source": { "split": "train_shard_00000", "doc_id": 1959 }, "chunk_id": "train_shard_00000_1959_0", "global_id": 2155 }, { "text": "The use of non-Saccharomyces yeasts in the winemaking process may have several positive outcomes. Kluyveromyces marxianus has recently been revealed as a promising species for this industry. While the majority of studies mention the use of K. marxianus in various industries including food production (e.g. dairy and cocoa), recent studies have also shown that its aroma and pectinase production make it a suitable yeast for the wine industry. Nevertheless, only particular strain, IWBT Y885, was investigated. In this study, five different K. marxianus strains as well as one protoplast fusant (BF2020) were compared to strain Y885. These comparisons focused on various oenological traits such as fermentation performance, fermentation metabolites, hydrogen sulfide, and pectinase production. Throughout the study, variations were found between the K. marxianus strains investigated. Indeed, although common traits such as high pectinase activity appeared conserved among K. marxianus strains, a fairly large phenotypic diversity was also evident. Using cluster analysis, strain groupings emerged with strains L01, L05, Y885, and BF2020 grouping together. Similarly, strains L02 and L04 grouped together while strain L03 appearing to show the most variation between the strains investigated. Variation between strains was observed regardless of the original source of isolation.\n\nExploring the phenotypic diversity of oenological traits in Kluyveromyces marxianus strains.", "token_count": 364, "char_count": 1473, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8213, "entities": { "genes": [ "BF2020" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:04.453568", "source": { "split": "train_shard_00000", "doc_id": 1960 }, "chunk_id": "train_shard_00000_1960_0", "global_id": 2156 }, { "text": "Lactobacillus rhamnosus GG (LGG) microcapsules prepared using the complex coacervation method were dried through spray and vacuum freeze drying. Physical properties, resistance to simulated gastrointestinal and bile salt conditions, and the stability of the LGG microcapsules during storage and heat treatment were estimated. Spray and vacuum freeze drying are suitable for LGG microcapsule preparation because of lower than 2.80% of the water content, and higher than 93.21% of the encapsulation efficiency. Under the simulated gastrointestinal condition, the survival rates of two kinds of microencapsulated LGG were over 96%. At 0.6% bile salt concentration, the survival rate of microencapsulated LGG subjected to spray drying was 110.89% higher than that of LGG subjected to vacuum freeze drying. In addition, the stability of the former was better than that of the latter during storage under low water activity condition (0.11). However, under high water activity condition (0.75), the two showed opposite results. The two kinds of microencapsulated LGG were completely inactivated after 4 weeks in 0.75 of water activity. The survival counts of microencapsulated LGG had no significant difference at -18°C after 8 weeks. After 8 weeks at 25°C and 4°C, the survival loss of microencapsulated LGG through drying and vacuum freeze drying was approximately 2 and 1 log CFU/g, respectively. PRACTICAL APPLICATION: LGG is a kind of microorganism beneficial to the human body, but it is easy to inactivate and lose its physiological value. LGG microcapsules can improve the stability of LGG, prolong the release time, and expand its application range. The drying method will affect the properties of LGG microcapsules. So, the characteristics analysis of LGG microcapsules with different drying methods can provide a reference for the preparation and application of LGG microcapsules.\n\nEffect of drying methods on Lactobacillus Rhamnosus GG microcapsules prepared using the complex coacervation method.", "token_count": 498, "char_count": 2003, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5017, "quality_score": 0.7508, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:05.120774", "source": { "split": "train_shard_00000", "doc_id": 1961 }, "chunk_id": "train_shard_00000_1961_0", "global_id": 2157 }, { "text": "Kluyveromyces marxianus is expected to be used in the production of yeast extracts due to its good fermentation ability and nutritional properties. Yeast autolysis is a key process to produce yeast extract and vacuum negative pressure stress can be used as an effective way to assist autolysis. However, the molecular mechanism of initiating Kluyveromyces marxianus autolysis induced by vacuum negative pressure and the higher temperature is still unclear. In this study, RNA-seq technology was performed mainly to analyze autolytic processes in Kluyveromyces marxianus strains. Considerable differentially expressed genes (DEGs) of downregulation were significantly enriched in 7 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways related to synthesis and transport of RNA and ribosome, which indicated that abnormal protein translations had already occurred in autolytic process. Interestingly, due to obvious change of related DEGs, endoplasmic reticulum-associated degradation (ERAD) and autophagy were activated and cell wall integrity pathway was hindered. Under the continuous influence of the external stress environment, the long-term changes of the above pathways triggered a vicious circle of gradual damage to yeast cells, which is the main cause of yeast autolysis. These results may provide important clues for the in-depth interpretation of the yeast autolytic mechanism.\n\nTranscriptomic analysis reveals process of autolysis of Kluyveromyces marxianus in vacuum negative pressure and the higher temperature.", "token_count": 353, "char_count": 1528, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6262, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:05.701732", "source": { "split": "train_shard_00000", "doc_id": 1962 }, "chunk_id": "train_shard_00000_1962_0", "global_id": 2158 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC2) is a rare inherited disorder caused by mutation in the ATP-binding cassette subfamily B member 11 gene (ABCB11) that encodes the bile salt export pump (BSEP), which is the main transporter of bile acids from hepatocytes to the canalicular lumen. Defects in BSEP synthesis and/or function lead to reduced bile salt secretion followed by accumulation of bile salts in hepatocytes and hepatocellular damage. This study aimed to detect variations in exons 14, 15, and 24 of the ABCB11 gene in patients with suspected PFIC2 among a group of Egyptian infants and children with normal gamma-glutamyl transpeptidase (GGT) cholestasis.\n\nA study of exons 14, 15, and 24 of the ABCB11 gene in Egyptian children with normal GGT cholestasis.", "token_count": 239, "char_count": 789, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:06.175696", "source": { "split": "train_shard_00000", "doc_id": 1963 }, "chunk_id": "train_shard_00000_1963_0", "global_id": 2159 }, { "text": "Pangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (~ 38%), high recombination rates (ρ = 0.044), and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion may be controlled by frequent recombination. We additionally identified that within the ergoline biosynthetic cluster the lpsA1 and lpsA2 were the result of a recombination event. However, the high recombination rates observed in C. purpurea may be influencing an overall trend of purifying selection across the genome. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.\n\nA large accessory genome and high recombination rates may influence global distribution and broad host range of the fungal plant pathogen Claviceps purpurea.", "token_count": 353, "char_count": 1548, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:06.753428", "source": { "split": "train_shard_00000", "doc_id": 1964 }, "chunk_id": "train_shard_00000_1964_0", "global_id": 2160 }, { "text": "Burkholderia pseudomallei is a soil-dwelling bacterium endemic to Southeast Asia and northern Australia that causes the disease, melioidosis. Although the global genomic diversity of clinical B. pseudomallei isolates has been investigated, there is limited understanding of its genomic diversity across small geographic scales, especially in soil. In this study, we obtained 288 B. pseudomallei isolates from a single soil sample (~100g; intensive site 2, INT2) collected at a depth of 30cm from a site in Ubon Ratchathani Province, Thailand. We sequenced the genomes of 169 of these isolates that represent 7 distinct sequence types (STs), including a new ST (ST1820), based on multi-locus sequence typing (MLST) analysis. A core genome SNP phylogeny demonstrated that all identified STs share a recent common ancestor that diverged an estimated 796-1260 years ago. A pan-genomics analysis demonstrated recombination between clades and intra-MLST phylogenetic and gene differences. To identify potential differential virulence between STs, groups of BALB/c mice (5 mice/isolate) were challenged via subcutaneous injection (500 CFUs) with 30 INT2 isolates representing 5 different STs; over the 21-day experiment, eight isolates killed all mice, 2 isolates killed an intermediate number of mice (1-2), and 20 isolates killed no mice. Although the virulence results were largely stratified by ST, one virulent isolate and six attenuated isolates were from the same ST (ST1005), suggesting that variably conserved genomic regions may contribute to virulence. Genomes from the animal-challenged isolates were subjected to a bacterial genome-wide association study to identify genomic regions associated with differential virulence. One associated region is a unique variant of Hcp1, a component of the type VI secretion system, which may result in attenuation. The results of this study have implications for comprehensive sampling strategies, environmental exposure risk assessment, and understanding recombination and differential virulence in B. pseudomallei.", "token_count": 511, "char_count": 2059, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6655, "quality_score": 0.8328, "entities": { "genes": [ "ST1005", "ST1820", "INT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:07.415087", "source": { "split": "train_shard_00000", "doc_id": 1965 }, "chunk_id": "train_shard_00000_1965_0", "global_id": 2161 }, { "text": "Multiple phylogenetically-diverse, differentially-virulent Burkholderia pseudomallei isolated from a single soil sample collected in Thailand.", "token_count": 35, "char_count": 142, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:07.774376", "source": { "split": "train_shard_00000", "doc_id": 1965 }, "chunk_id": "train_shard_00000_1965_1", "global_id": 2162 }, { "text": "Lactococcus spp. are industrially crucial lactic acid bacteria (LAB) used to manufacture lactic acid, pickled vegetables, buttermilk, cheese, and many kinds of delicious dairy foods and drinks. In addition to these, they are also being used as probiotics in specific formulations. However, their uses as probiotics are comparatively less than the other LAB genera. The present communication hypothesizes to validate the probiotic potentiality of two new Lactococcus lactis subsp. lactis strains for their future uses. These native food fermenting strains were characterized for in vitro acid tolerance, tolerance to simulated gastric and pancreatic juices, autoaggregation and co-aggregation, hydrophobicity, haemolytic activity, bile salt deconjugation, cholesterol removal, antimicrobial spectrum, and antibiotic sensitivity. The in vivo live bacterial feeding of these strains for 30 days was done in Swiss albino mice either singly or in combination with prebiotic inulin and evaluated for hypocholesterolemic activity, immune enhancement, and gut colonization efficiency and compared with the commercial probiotic consortia. The study revealed that the strains could survive in human gut bile concentration, gastric pH conditions at pH 2.0, 3.0, and 8.0 for 6 h, had a broad antibacterial spectrum, and cholesterol binding efficacy. The strains could survive with higher colony-forming units (CFU/mL) when amended with sodium caseinate. The strains had autoaggregation ranges from 15 to 25% over 24 h and had a significant co-aggregation with both lactic acid and Gram-positive and Gram-negative bacterial strains related to human illness. The strains also showed solvent and media-specific hydrophobicity against n-hexane and xylene", "token_count": 449, "char_count": 1738, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:08.412462", "source": { "split": "train_shard_00000", "doc_id": 1966 }, "chunk_id": "train_shard_00000_1966_0", "global_id": 2163 }, { "text": "The live bacterial feeding either singly or in combination with prebiotic inulin resulted in a significant reduction of LDL (low-density lipoprotein), VLDL (very low-density lipoprotein) cholesterol and triglyceride (TG), and a significant increase in HDL (high-density lipoprotein) cholesterol level, and improved gut colonization and gut immunomodulation. The results prove that these non-haemolytic, non-toxic strains had significant health benefits than the commercial probiotics consortium with the recommended prebiotics mix. Thus, these new Lactococcus lactis subsp. lactis strains could be trialled as a new probiotic combination for human and animal feeds.\n\nCharacterization of two new strains of Lactococcus lactis for their probiotic efficacy over commercial synbiotics consortia.", "token_count": 211, "char_count": 791, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7048, "quality_score": 0.8524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:08.872078", "source": { "split": "train_shard_00000", "doc_id": 1966 }, "chunk_id": "train_shard_00000_1966_1", "global_id": 2164 }, { "text": "While thermotolerance is an attractive trait for yeasts used in industrial ethanol production, oxygen requirements of known thermotolerant species are incompatible with process requirements. Analysis of oxygen-sufficient and oxygen-limited chemostat cultures of the facultatively fermentative, thermotolerant species Ogataea parapolymorpha showed its minimum oxygen requirements to be an order of magnitude larger than those reported for the thermotolerant yeast Kluyveromyces marxianus. High oxygen requirements of O. parapolymorpha coincided with a near absence of glycerol, a key NADH/NAD+ redox-cofactor-balancing product in many other yeasts, in oxygen-limited cultures. Genome analysis indicated absence of orthologs of the Saccharomyces cerevisiae glycerol-3-phosphate-phosphatase genes GPP1 and GPP2. Co-feeding of acetoin, whose conversion to 2,3-butanediol enables reoxidation of cytosolic NADH, supported a 2.5-fold increase of the biomass concentration in oxygen-limited cultures. An O. parapolymorpha strain in which key genes involved in mitochondrial reoxidation of NADH were inactivated did produce glycerol, but transcriptome analysis did not reveal a clear candidate for a responsible phosphatase. Expression of S. cerevisiae GPD2, which encodes NAD+-dependent glycerol-3-phosphate dehydrogenase, and GPP1 supported increased glycerol production by oxygen-limited chemostat cultures of O. parapolymorpha. These results identify dependence on respiration for NADH reoxidation as a key contributor to unexpectedly high oxygen requirements of O. parapolymorpha.\n\nRespiratory reoxidation of NADH is a key contributor to high oxygen requirements of oxygen-limited cultures of Ogataea parapolymorpha.", "token_count": 449, "char_count": 1712, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [ "GPP1", "GPP2", "GPD2" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:09.507678", "source": { "split": "train_shard_00000", "doc_id": 1967 }, "chunk_id": "train_shard_00000_1967_0", "global_id": 2165 }, { "text": "Human listeriosis outbreaks are often associated with food products, which could be contaminated, at the same time, also by different clones of Listeria monocytogenes. This emphasize the need to type more than one L.monocytogenes isolate found in a single food or environmental sample. The purpose of the present study was to evaluate the presence of different L.monocytogenes strains in food and food production environment in order to understand if there is need to type more isolates from the same sample in case of presence of L.monocytogenes. Between 2011 and 2015, at the Italian National Reference Laboratory for L.monocytogenes, for each positive sample, from two to twenty-three isolates of L.monocytogenes were collected. All the isolates were characterized by conventional serotyping and pulsed field gel electrophoresis (PFGE). Moreover, isolates from the same sample, having indistinguishable PFGE profile, were subjected to whole genome sequencing in order to perform core genome Multi Locus Sequence Typing (cgMLST). Within each sample, more than one serotype and one pulsotype were found in 11.9% and 27.5%, respectively. For indistinguishable PFGE patterns the cgMLST analysis showed 96.2% of concordance demonstrating the added value of new sequencing technologies. This study has demonstrated the need to select and type more than one L.monocytogenes colony in one food or food environmental sample to detect the diversity of L.monocytogenes strains and facilitate downstream investigations and effective source attribution in foodborne outbreak inquiry.\n\nGenetic diversity of Listeria monocytogenes strains contaminating food and food producing environment as single based sample in Italy (retrospective study).", "token_count": 418, "char_count": 1731, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5743, "quality_score": 0.7871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:10.132673", "source": { "split": "train_shard_00000", "doc_id": 1968 }, "chunk_id": "train_shard_00000_1968_0", "global_id": 2166 }, { "text": "FGF19/FGF15 is an endocrine regulator of hepatic bile salt and lipid metabolism, which has shown promising effects in the treatment of NASH in clinical trials. FGF19/15 is transcribed and released from enterocytes of the small intestine into enterohepatic circulation in response to bile-induced FXR activation. Previously, the TSS of FGF19 was identified to bind Wnt-regulated TCF7L2/encoded transcription factor TCF4 in colorectal cancer cells. Impaired Wnt signaling and specifical loss of function of its coreceptor LRP6 have been associated with NASH. We, therefore, examined if TCF7L2/TCF4 upregulates Fgf19 in the small intestine and restrains NASH through gut-liver crosstalk. We examined the mice globally overexpressing, haploinsufficient, and conditional knockout models of TCF7L2 in the intestinal epithelium. The TCF7L2\n\nTCF7L2 transcriptionally regulates Fgf15 to maintain bile acid and lipid homeostasis through gut-liver crosstalk.", "token_count": 281, "char_count": 947, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7154, "quality_score": 0.8577, "entities": { "genes": [ "TCF4", "LRP6", "FGF15", "FGF19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:10.684243", "source": { "split": "train_shard_00000", "doc_id": 1969 }, "chunk_id": "train_shard_00000_1969_0", "global_id": 2167 }, { "text": "Donor human milk is generally processed by holder pasteurization (HoP) at 62. 5°C for 30 min. This temperature-time combination is sufficient for eliminating pathogens in donor milk, but also negatively affects several bioactive milk components. Long heating up times may further affect the bioactive properties of pasteurized milk. High-Temperature-Short-Time (HTST), a treatment with shorter processing times (72°C for 15 sec), was investigated as a suitable alternative to HoP. In addition, pasteurization methods that follow the same temperature regime but with varying heating up times were compared. Human milk samples from four different donors were combined into one pool, which was then used to perform all analyses. The effects of these methods on the levels and functionality of immunoglobulin A, lactoferrin, lysozyme and bile salt-stimulated lipase, were evaluated with LC-MS/MS-based proteomics and activity assays, while the pasteurization efficacy was evaluated with an alkaline phosphatase test. HoP, a treatment with long processing times, times, caused the highest reduction in all proteins studied (reduced by 50-98%). Compounds such as lactoferrin and bile salt-stimulated lipase that are more sensitive to heat treatments were better retained with HTST, but their levels and functionality were still significantly lower than those of untreated donor milk (52 and 81% reduction of lactoferrin and bile salt-stimulated lipase activity, respectively). Our findings showed that a treatment with considerably shorter processing times, such as HTST, may reduce the thermal damage caused to the bioactive proteins compared to HoP, without affecting pasteurization efficacy. Since the vast majority of the donor human milk banks that are currently operating on a global level apply HoP to donor milk, our findings may provide relevant information for the optimization of donor milk processing.\n\nHigh-Temperature Short-Time Preserves Human Milk's Bioactive Proteins and Their Function Better Than Pasteurization Techniques With Long Processing Times.", "token_count": 478, "char_count": 2063, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5898, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:11.330885", "source": { "split": "train_shard_00000", "doc_id": 1970 }, "chunk_id": "train_shard_00000_1970_0", "global_id": 2168 }, { "text": "Recent evidence points towards the role of genotype to understand the phenotype, predict the natural course and long term outcome of patients with progressive familial intrahepatic cholestasis (PFIC). Expanded role of the heterozygous transporter defects presenting late needs to be suspected and identified. Treatment of pruritus, nutritional rehabilitation, prevention of fibrosis progression and liver transplantation (LT) in those with end stage liver disease form the crux of the treatment. LT in PFIC has its own unique issues like high rates of intractable diarrhoea, growth failure; steatohepatitis and graft failure in PFIC1 and antibody-mediated bile salt export pump deficiency in PFIC2. Drugs inhibiting apical sodium-dependent bile transporter and adenovirus-associated vector mediated gene therapy hold promise for future.\n\nRecent updates on progressive familial intrahepatic cholestasis types 1, 2 and 3: Outcome and therapeutic strategies.", "token_count": 237, "char_count": 955, "word_count": 132, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "PFIC1", "PFIC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:11.807203", "source": { "split": "train_shard_00000", "doc_id": 1971 }, "chunk_id": "train_shard_00000_1971_0", "global_id": 2169 }, { "text": "Among the numerous serotypes of Avian pathogenic Escherichia coli (APEC), O1, O2 and O78 have long been considered the predominant serogroups. O145, a pivotal serogroup in non-O157 Shiga toxin-producing Escherichia coli, has never been considered an important serogroup among APEC. The prevalence of APEC O145 was determined from the results of molecular serogrouping based on 42 sequenced isolates from Jiangsu and Guangxi Provinces in China. After realizing the potential importance of O145, 224 APEC isolates isolated from Jiangsu, Guangxi, Anhui, Shandong, Henan, Yunnan and Fujian provinces were screened using PCR amplification. The results showed that the proportion of O145 detected was 37.9 % (85/224), which was higher than those of the three traditional APEC serogroups. The virulence evaluation experiment showed that this serogroup may have stronger pathogenicity. Here, we report for the first time that O145 may be emerging as a predominant serogroup of APEC in China. The possible reasons for its prevalence and oversight were analyzed through genomic analysis. Furthermore, pangenome analysis with STEC O145 was performed to assess the potential threat to humans. The discovery of the ubiquity of O145 may not be coincidental, which may also account for the failure of vaccines that target the three major serogroups. Therefore, this newly predominant serogroup should be paid more attention and the focus should not be limited to the so-called three major APEC serogroups.\n\nO145 may be emerging as a predominant serogroup of Avian pathogenic Escherichia coli (APEC) in China.", "token_count": 437, "char_count": 1593, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:12.434869", "source": { "split": "train_shard_00000", "doc_id": 1972 }, "chunk_id": "train_shard_00000_1972_0", "global_id": 2170 }, { "text": "Lactiplantibacillus plantarum is one of the most diverse species of lactic acid bacteria found in various habitats. The aim of this work was to perform preliminary phenotypic and genomic characterization of two novel and potentially probiotic L. plantarum strains isolated from Indian foods, viz., dhokla batter and jaggery. Both the strains were bile and acid tolerant, utilized various sugars, adhered to intestinal epithelial cells, produced exopolysaccharides and folate, were susceptible for tetracycline, erythromycin, and chloramphenicol, did not cause hemolysis, and exhibited antimicrobial and plant phenolics metabolizing activities. The genetic determinants of bile tolerance, cell-adhesion, bacteriocins production, riboflavin and folate biosynthesis, plant polyphenols utilization, and exopolysaccharide production were found in both the strains. One of the strains contained a large number of unique genes while the other had a simultaneous presence of glucansucrase and fructansucrase genes which is a rare trait in L. plantarum. Comparative genome analysis of 149 L. plantarum strains highlighted high variation in the cell-adhesion and sugar metabolism genes while the genomic regions for some other properties were relatively conserved. This work highlights the unique properties of our strains along with the probiotic and technically important genomic features of a large number of L. plantarum strains.\n\nIsolation, characterization and comparative genomics of potentially probiotic Lactiplantibacillus plantarum strains from Indian foods.", "token_count": 389, "char_count": 1559, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:13.060740", "source": { "split": "train_shard_00000", "doc_id": 1973 }, "chunk_id": "train_shard_00000_1973_0", "global_id": 2171 }, { "text": "The human gut microbiota resides within a diverse chemical environment challenging our ability to understand the forces shaping this ecosystem. Here, we reveal that fitness of the Bacteroidales, the dominant order of bacteria in the human gut, is an emergent property of glycans and one specific metabolite, butyrate. Distinct sugars serve as strain-variable fitness switches activating context-dependent inhibitory functions of butyrate. Differential fitness effects of butyrate within the Bacteroides are mediated by species-level variation in Acyl-CoA thioesterase activity and nucleotide polymorphisms regulating an Acyl-CoA transferase. Using in vivo multi-omic profiles, we demonstrate Bacteroides fitness in the human gut is associated together, but not independently, with Acyl-CoA transferase expression and butyrate. Our data reveal that each strain of the Bacteroides exists within a unique fitness landscape based on the interaction of chemical components unpredictable by the effect of each part alone mediated by flexibility in the core genome.\n\nStrain-level fitness in the gut microbiome is an emergent property of glycans and a single metabolite.", "token_count": 268, "char_count": 1162, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6196, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:13.616235", "source": { "split": "train_shard_00000", "doc_id": 1974 }, "chunk_id": "train_shard_00000_1974_0", "global_id": 2172 }, { "text": "Escherichia coli ST58 has recently emerged as a globally disseminated uropathogen that often progresses to sepsis. Unlike most pandemic extra-intestinal pathogenic E. coli (ExPEC), which belong to pathogenic phylogroup B2, ST58 belongs to the environmental/commensal phylogroup B1. Here, we present a pan-genomic analysis of a global collection of 752 ST58 isolates from diverse sources. We identify a large ST58 sub-lineage characterized by near ubiquitous carriage of ColV plasmids, which carry genes encoding virulence factors, and by a distinct accessory genome including genes typical of the Yersiniabactin High Pathogenicity Island. This sub-lineage includes three-quarters of all ExPEC sequences in our study and has a broad host range, although poultry and porcine sources predominate. By contrast, strains isolated from cattle often lack ColV plasmids. Our data indicate that ColV plasmid acquisition contributed to the divergence of the major ST58 sub-lineage, and different sub-lineages inhabit poultry, swine and cattle.\n\nA role for ColV plasmids in the evolution of pathogenic Escherichia coli ST58.", "token_count": 296, "char_count": 1112, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6981, "quality_score": 0.8491, "entities": { "genes": [ "ST58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:14.221432", "source": { "split": "train_shard_00000", "doc_id": 1975 }, "chunk_id": "train_shard_00000_1975_0", "global_id": 2173 }, { "text": "Effective crop improvement, whether through selective breeding or biotech strategies, is largely dependent on the cumulative knowledge of a species' pangenome and its containing genes. Acquiring this knowledge is specially challenging in grapevine, one of the oldest fruit crops grown worldwide, which is known to have more than 30,000 genes. Well-established research communities studying model organisms have created and maintained, through public and private funds, a diverse range of online tools and databases serving as repositories of genomes and gene function data. The lack of such resources for the non-model, but economically important,\n\nThe Grape Gene Reference Catalogue as a Standard Resource for Gene Selection and Genetic Improvement.", "token_count": 158, "char_count": 750, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7685, "quality_score": 0.8843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:14.689317", "source": { "split": "train_shard_00000", "doc_id": 1976 }, "chunk_id": "train_shard_00000_1976_0", "global_id": 2174 }, { "text": "To enhance monitoring of high-burden foodborne pathogens, there is opportunity to combine pangenome data with network analysis.\n\nGenome-wide networks reveal emergence of epidemic strains of Salmonella Enteritidis.", "token_count": 51, "char_count": 213, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:15.067407", "source": { "split": "train_shard_00000", "doc_id": 1977 }, "chunk_id": "train_shard_00000_1977_0", "global_id": 2175 }, { "text": "Bacterial genomes are massively sequenced, and they provide valuable data to better know the complete set of genes of a species. The analysis of thousands of bacterial strains can identify both shared genes and those appearing only in the pathogenic ones. Current computational gene finders facilitate this task but often miss some existing genes. However, the present availability of different genomes from the same species is useful to estimate the selective pressure applied on genes of complete pangenomes. It may assist in evaluating gene predictions either by checking the certainty of a new gene or annotating it as a gene under positive selection. Here, we estimated the selective pressure of 19 271 genes that are part of the pangenome of the human opportunistic pathogen Acinetobacter baumannii and found that most genes in this bacterium are subject to negative selection. However, 23% of them showed values compatible with positive selection. These latter were mainly uncharacterized proteins or genes required to evade the host defence system including genes related to resistance and virulence whose changes may be favoured to acquire new functions. Finally, we evaluated the utility of measuring selection pressure in the detection of sequencing errors and the validation of gene prediction.\n\nAssessment of selection pressure exerted on genes from complete pangenomes helps to improve the accuracy in the prediction of new genes.", "token_count": 291, "char_count": 1444, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:15.667660", "source": { "split": "train_shard_00000", "doc_id": 1978 }, "chunk_id": "train_shard_00000_1978_0", "global_id": 2176 }, { "text": "Bacillus velezensis HNA3, a potential plant growth promoter and biocontrol rhizobacterium, was isolated from plant rhizosphere soils in our previous work. Here, we sequenced the entire genome of the HNA3 strain and performed a comparative genome analysis. We found that HNA3 has a 3,929-kb chromosome with 46.5% GC content and 4,080 CDSs. We reclassified HNA3 as a Bacillus velezensis strain by core genome analysis between HNA3 and 74 previously defined\n\nComparative Genome Analysis Reveals Phylogenetic Identity of Bacillus velezensis HNA3 and Genomic Insights into Its Plant Growth Promotion and Biocontrol Effects.", "token_count": 185, "char_count": 618, "word_count": 91, "semantic_coherence": 1, "information_density": 0.6703, "quality_score": 0.8352, "entities": { "genes": [ "HNA3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:16.131366", "source": { "split": "train_shard_00000", "doc_id": 1979 }, "chunk_id": "train_shard_00000_1979_0", "global_id": 2177 }, { "text": "Prokaryote pangenomes are influenced heavily by environmental factors and the opportunity for gene gain and loss events. As the field of pangenome analysis has expanded, so has the need to fully understand the complexity of how eco-evolutionary dynamics shape pangenomes. Here, we describe current models of pangenome evolution and discuss their suitability and accuracy. We suggest that pangenomes are dynamic entities under constant flux, highlighting the influence of two-way interactions between pangenome and environment. New classifications of core and accessory genes are also considered, underscoring the need for continuous evaluation of nomenclature in a fast-moving field. We conclude that future models of pangenome evolution should incorporate eco-evolutionary dynamics to fully encompass their dynamic, changeable nature.\n\nProkaryote pangenomes are dynamic entities.", "token_count": 182, "char_count": 880, "word_count": 120, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:16.577774", "source": { "split": "train_shard_00000", "doc_id": 1980 }, "chunk_id": "train_shard_00000_1980_0", "global_id": 2178 }, { "text": "Shigella flexneri is the main causative agent of the communicable diarrheal disease, shigellosis. It is estimated that about 80-165 million cases and > 1 million deaths occur every year due to this disease. S. flexneri causes dysentery mostly in young children, elderly and immunocompromised patients, all over the globe. Recently, due to the emergence of S. flexneri antibiotic resistance strains, it is a dire need to predict novel therapeutic drug targets in the bacterium and screen natural products against it, which could eliminate the curse of antibiotic resistance. Therefore, in current study, available antibiotic-resistant genomes (n = 179) of S. flexneri were downloaded from PATRIC database and a pan-genome and resistome analysis was conducted. Around 5059 genes made up the accessory, 2469 genes made up the core, and 1558 genes made up the unique genome fraction, with 44, 34, and 13 antibiotic-resistant genes in each fraction, respectively. Core genome fraction (27% of the pan-genome), which was common to all strains, was used for subtractive genomics and resulted in 384 non-homologous, and 85 druggable targets. Dihydroorotase was chosen for further analysis and docked with natural product libraries (Ayurvedic and Streptomycin compounds), while the control was orotic acid or vitamin B13 (which is a natural binder of this protein). Dynamics simulation of 50 ns was carried out to validate findings for top-scored inhibitors. The current study proposed dihydroorotase as a significant drug target in S. flexneri and 4-tritriacontanone & patupilone compounds as potent drugs against shigellosis. Further experiments are required to ascertain validity of our findings.\n\nAn in silico hierarchal approach for drug candidate mining and validation of natural product inhibitors against pyrimidine biosynthesis enzyme in the antibiotic-resistant Shigella flexneri.", "token_count": 501, "char_count": 1881, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:17.234252", "source": { "split": "train_shard_00000", "doc_id": 1981 }, "chunk_id": "train_shard_00000_1981_0", "global_id": 2179 }, { "text": "In this study, the inhibitory effect of components from Chinese Herb Medicine (CHMs) with potential hepatotoxicity was assessed by human bile salt export pump (hBSEP) vesicles with and without S9 metabolism. Sixty-three compounds from 22 hepatoxicity CHMs were selected as the test articles. In hBSEP vesicles, eighteen of them were found to have moderate or strong inhibitory effect towards BSEP. Further studies were performed to determine the IC\n\nClarify the potential cholestatic hepatotoxicity components from Chinese Herb Medicine and metabolism's role via hBSEP vesicles and S9/hBSEP vesicles.", "token_count": 162, "char_count": 600, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7356, "quality_score": 0.8678, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:17.676089", "source": { "split": "train_shard_00000", "doc_id": 1982 }, "chunk_id": "train_shard_00000_1982_0", "global_id": 2180 }, { "text": "Cranberry extract (CBE) is a major source of the antioxidant polyphenolics but suffers from limited bioavailability. The goal of this research was to encapsulate the nutraceutical (CBE), into bile salt augmented liposomes (BSALs) as a promising oral delivery system to potentiate its hepatoprotective impact against dimethylnitrosamine (DMN) induced liver injury in rats. The inclusion of bile salt in the liposomal structure can enhance their stability within the gastrointestinal tract and promote CBE permeability. CBE loaded BSALs formulations were fabricated utilizing a (2\n\nDesign and optimization of cranberry extract loaded bile salt augmented liposomes for targeting of MCP-1/STAT3/VEGF signaling pathway in DMN-intoxicated liver in rats.", "token_count": 199, "char_count": 747, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [ "STAT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:18.139774", "source": { "split": "train_shard_00000", "doc_id": 1983 }, "chunk_id": "train_shard_00000_1983_0", "global_id": 2181 }, { "text": "Pathogenic Escherichia coli (E. coli) is an important causative agent for infectious diseases in pigs and causes significant economic loss. The global concern of antimicrobial resistance of bacteria raises awareness of the alternative ways of using antimicrobial peptides (AMPs). The study was aimed to identify and test the efficacy of AMPs from Lactobacillus spp. against the growth of pathogenic E. coli isolated from pigs in Thailand. Briefly, cell-free culture supernatants (CFCS) from 3 strains of lactic acid bacteria (LAB) consisting of Lactobacillus acidophilus (strain KMP), Lactobacillus plantarum (strain KMP), and Pediococcus pentosaceus (strain KMP) were tested against pathogenic E. coli via agar well diffusion assay in quadruplicates. The presence of a zone of inhibition (ZOI) around wells was evaluated at different incubation time. Acid and bile tolerance test was performed for bacterial viability in acid and bile salt conditions. In addition, LAB cross-streaking assay was evaluated for antagonist activity.\n\nCell-free culture supernatants of Lactobacillus spp. and Pediococcus spp. inhibit growth of pathogenic Escherichia coli isolated from pigs in Thailand.", "token_count": 326, "char_count": 1183, "word_count": 169, "semantic_coherence": 1, "information_density": 0.5976, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:18.699682", "source": { "split": "train_shard_00000", "doc_id": 1984 }, "chunk_id": "train_shard_00000_1984_0", "global_id": 2182 }, { "text": "The rising concern with the emission of greenhouse gases has boosted new incentives for biofuels production, which are less polluting than fossil fuels. Special attention has been given to the second-generation ethanol, as it is produced from abundant feedstocks which do not compete with food production, such as lignocellulosic biomass and whey. Kluyveromyces marxianus stands out in second-generation ethanol production due to its capacity of assimilating lactose, the sugar found in whey, and tolerating high temperatures used in simultaneous saccharification processes. Nonetheless, contrary to Saccharomyces cerevisiae, K. marxianus does not tolerate high ethanol concentrations. Ethanol causes a broad range of toxic effects on yeasts, acting on cell membrane and proteins, as well as inducing the generation of reactive oxygen species (ROS). The ethanol stress responses are not fully understood, mainly in non-conventional yeasts such as K. marxianus. Indeed, many molecular responses to ethanol stress are still inferred from S. cerevisiae. As such, a better understanding of the ethanol stress responses in K. marxianus may provide the basis for improving its use in the biofuel industry. Additionally, the selection of ethanol-tolerant strains by metabolic engineering is useful to provide strains with improved capacity to withstand stressful conditions, as well as to obtain new insights about the ethanol stress responses. Key points • It is still not totally clear why K. marxianus is less tolerant to ethanol than S. cerevisiae. • Understanding the ethanol stress response in K. marxianus is pivotal for improving its application in the biofuel industry. • The Metabolic engineering is expected to improve the ethanol tolerance in K. marxianus.\n\nEthanol stress responses in Kluyveromyces marxianus: current knowledge and perspectives.", "token_count": 452, "char_count": 1851, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5609, "quality_score": 0.7804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:19.337632", "source": { "split": "train_shard_00000", "doc_id": 1985 }, "chunk_id": "train_shard_00000_1985_0", "global_id": 2183 }, { "text": "Klebsiella variicola is generally known as endophyte as well as lignocellulose-degrading strain. However, their roles in goat omasum along with lignocellulolytic genetic repertoire are not yet explored. In this study, five different pectin-degrading bacteria were isolated from a healthy goat omasum. Among them, a new Klebsiella variicola strain HSTU-AAM51 was identified to degrade lignocellulose. The genome of the HSTU-AAM51 strain comprised 5,564,045 bp with a GC content of 57.2% and 5312 coding sequences. The comparison of housekeeping genes (16S rRNA, TonB, gyrase B, RecA) and whole-genome sequence (ANI, pangenome, synteny, DNA-DNA hybridization) revealed that the strain HSTU-AAM51 was clustered with Klebsiella variicola strains, but the HSTU-AAM51 strain was markedly deviated. It consisted of seventeen cellulases (GH1, GH3, GH4, GH5, GH13), fourteen beta-glucosidase (2GH3, 7GH4, 4GH1), two glucosidase, and one pullulanase genes. The strain secreted cellulase, pectinase, and xylanase, lignin peroxidase approximately 76-78 U/mL and 57-60 U/mL, respectively, when it was cultured on banana pseudostem for 96 h. The catalytically important residues of extracellular cellulase, xylanase, mannanase, pectinase, chitinase, and tannase proteins (validated 3D model) were bound to their specific ligands. Besides, genes involved in the benzoate and phenylacetate catabolic pathways as well as laccase and DiP-type peroxidase were annotated, which indicated the strain lignin-degrading potentiality. This study revealed a new K", "token_count": 512, "char_count": 1537, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7156, "quality_score": 0.8578, "entities": { "genes": [ "GH5", "GH4", "AAM51", "GH3", "GH1", "GH13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:19.990215", "source": { "split": "train_shard_00000", "doc_id": 1986 }, "chunk_id": "train_shard_00000_1986_0", "global_id": 2184 }, { "text": "variicola bacterium from goat omasum which harbored lignin and cellulolytic enzymes that could be utilized for the production of bioethanol from lignocelluloses.\n\nUnveiling lignocellulolytic trait of a goat omasum inhabitant Klebsiella variicola strain HSTU-AAM51 in light of biochemical and genome analyses.", "token_count": 99, "char_count": 308, "word_count": 41, "semantic_coherence": 1, "information_density": 0.8293, "quality_score": 0.9146, "entities": { "genes": [ "AAM51" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:20.372145", "source": { "split": "train_shard_00000", "doc_id": 1986 }, "chunk_id": "train_shard_00000_1986_1", "global_id": 2185 }, { "text": "Streptococcus consists of ecologically diverse species, some of which are important pathogens of humans and animals. We sought to quantify and compare the frequencies and characteristics of within-species recombination in the pan-genomes of Streptococcus agalactiae, Streptococcus pyogenes and Streptococcus suis. We used 1081, 1813 and 1204 publicly available genome sequences of each species, respectively. Based on their core genomes, S. agalactiae had the highest relative rate of recombination to mutation (11.5743) compared to S. pyogenes (1.03) and S. suis (0.57). The proportion of the species pan-genome that have had a history of recombination was 12.85%, 24.18% and 20.50% of the pan-genomes of each species, respectively. The composition of recombining genes varied among the three species, and some of the most frequently recombining genes are implicated in adhesion, colonization, oxidative stress response and biofilm formation. For each species, a total of 22.75%, 29.28% and 18.75% of the recombining genes were associated with prophages. The cargo genes of integrative conjugative elements and integrative and mobilizable elements contained genes associated with antimicrobial resistance and virulence. Homologous recombination and mobilizable pan-genomes enable the creation of novel combinations of genes and sequence variants, and the potential for high-risk clones to emerge.\n\nFrequencies and characteristics of genome-wide recombination in Streptococcus agalactiae, Streptococcus pyogenes, and Streptococcus suis.", "token_count": 423, "char_count": 1536, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5429, "quality_score": 0.7714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:20.994747", "source": { "split": "train_shard_00000", "doc_id": 1987 }, "chunk_id": "train_shard_00000_1987_0", "global_id": 2186 }, { "text": "Pathogens from the Vibrio and Aeromonas genera often cause detrimental effects to the aquaculture sector. Previously, antibiotics was used to resolve the infections, but this caused the spread of antibiotic resistant bacteria and antibiotic resistance genes into the environment. As an approach to address this issue, probiotic bacteria were introduced to improve the hosts' microbiome, disease protection, health condition, growth efficiency, feed consumption, stress response and general vigour. However, reports showed that some commercially available probiotics were restricted to a small number of microbial species and there are inconsistencies concerning its effectiveness. Hence, the aim of this study was to isolate and evaluate new Bacillus spp. from the gut of giant freshwater prawn as potential probiotics. Three Bacillus spp. isolates, Bacillus subtilis FS6 (MZ960135), Bacillus velezensis FS26 (MZ960133) and Bacillus pumilus FS97 (MZ960136) were characterised, and in vitro testing showed good probiotic properties which can help in dealing with diseases in aquaculture. Among the Bacillus spp., Bacillus velezensis FS26 showed higher antimicrobial activity towards Aeromonas hydrophila LMG 13658 and Aeromonas veronii clone DK-A. veronii-27 at 23.7 mm and 25 mm, respectively. Bacillus subtilis FS6 and Bacillus velezensis FS26 resulted in good adherence to both xylene and chloroform hydrocarbons. The Bacillus spp. isolated displayed high survivability towards 0.3% bile salt and exhibited amylase, protease, and lipase activities. Thus, the isolated Bacillus spp. are considered safe based on the sensitivity analysis towards antibiotics and γ-haemolytic activity.", "token_count": 473, "char_count": 1684, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [ "MZ960135", "FS97", "MZ960133", "FS26", "FS6", "MZ960136" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:21.637723", "source": { "split": "train_shard_00000", "doc_id": 1988 }, "chunk_id": "train_shard_00000_1988_0", "global_id": 2187 }, { "text": "Evaluation of three Bacillus spp. isolated from the gut of giant freshwater prawn as potential probiotics against pathogens causing Vibriosis and Aeromonosis.", "token_count": 41, "char_count": 158, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:21.994309", "source": { "split": "train_shard_00000", "doc_id": 1988 }, "chunk_id": "train_shard_00000_1988_1", "global_id": 2188 }, { "text": "Lactic acid bacteria (LABs) are known to secrete species-specific secondary metabolites that could be utilized as novel therapeutics against multi-drug resistant pathogens. This study aimed to investigate the antagonistic and probiotic properties of LABs isolated from the vaginal ecosystem of healthy women and to assess the stability of their antagonistic metabolites. Among 43 strains isolated from healthy women, eight LAB strains exhibited detectable BLISs (bacteriocin-like substances) producing ability against E. faecalis (JH-86), S. aureus (JH-68), Streptococcus sp. (JH-80), and E. coli (JH-101), with zone of inhibition (ZI) ranging from 9.00 to 20.33 mm and minimum inhibitory concentrations (MICs) from 62.5 to 500 μL/mL, respectively. The partially purified compounds extracted from cell free supernatant (CFS) displayed an increase in antagonistic activity based on ZI, 9.67-30.17 mm and MICs, 3.91-15.63 mg/mL, respectively. In a time-kill study, both crude and partially purified compounds of Limosilactobacillus reuteri (MT180537), Pediococcus pentosaceus (MT176555), Limosilactobacillus pontis (MW362838), and Levilactobacillus brevis (MW362790) exhibited significant bactericidal action against E. faecalis (MW051601), the most frequent etiological agent of aerobic vaginitis (AV). The active secondary metabolites from L. reuteri (MT180537), P. pentosaceus (MT176555), and L. pontis (MW362838) were protein in nature and remained stable under different physicochemical conditions", "token_count": 491, "char_count": 1500, "word_count": 197, "semantic_coherence": 1, "information_density": 0.7259, "quality_score": 0.8629, "entities": { "genes": [ "MW362790", "MW051601", "MT180537", "MT176555", "MW362838" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:22.638725", "source": { "split": "train_shard_00000", "doc_id": 1989 }, "chunk_id": "train_shard_00000_1989_0", "global_id": 2189 }, { "text": "Regarding probiotic properties, the strains presented probiotic characteristics, i.e., good acid, bile salt tolerance, aggregation properties, and biofilm formation. The strains were susceptible to most of the commonly used antibiotics and had no hemolytic activity. In conclusion, antagonistic compounds or BLIS produced by L. reuteri (MT180537) could be investigated further for preparation of ointments to treat AV.\n\nEvaluation of inhibitory and probiotic properties of lactic acid bacteria isolated from vaginal microflora.", "token_count": 127, "char_count": 527, "word_count": 71, "semantic_coherence": 1, "information_density": 0.831, "quality_score": 0.9155, "entities": { "genes": [ "MT180537" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:23.021038", "source": { "split": "train_shard_00000", "doc_id": 1989 }, "chunk_id": "train_shard_00000_1989_1", "global_id": 2190 }, { "text": "Vancomycin-resistant Enterococcus faecium (VREfm) is a major nosocomial pathogen. Identifying VREfm transmission dynamics permits targeted interventions, and while genomics is increasingly being utilised, methods are not yet standardised or optimised for accuracy. We aimed to develop a standardized genomic method for identifying putative VREfm transmission links. Using comprehensive genomic and epidemiological data from a cohort of 308 VREfm infection or colonization cases, we compared multiple approaches for quantifying genetic relatedness. We showed that clustering by core genome multilocus sequence type (cgMLST) was more informative of population structure than traditional MLST. Pairwise genome comparisons using split k-mer analysis (SKA) provided the high-level resolution needed to infer patient-to-patient transmission. The more common mapping to a reference genome was not sufficiently discriminatory, defining more than three times more genomic transmission events than SKA (3729 compared to 1079 events). Here, we show a standardized genomic framework for inferring VREfm transmission that can be the basis for global deployment of VREfm genomics into routine outbreak detection and investigation.\n\nOptimising genomic approaches for identifying vancomycin-resistant Enterococcus faecium transmission in healthcare settings.", "token_count": 297, "char_count": 1342, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:23.582535", "source": { "split": "train_shard_00000", "doc_id": 1990 }, "chunk_id": "train_shard_00000_1990_0", "global_id": 2191 }, { "text": "Table olive brines, inoculated with six different starters of lactic acid bacteria (LAB) or spontaneously fermented, have been used as isolating source of killer yeasts throughout the fermentation process (120 d). Killer yeast isolates were identified and evaluated for technological and probiotic traits. Although the count of yeast population did not markedly vary among the different vessels and over time, the killer yeast phenotype was mainly present in yeast strains isolated from spontaneous fermentation; the number of killer isolates decreased over fermentation time. Killer phenotype was found in species identified as Pichia kluyveri, Zygoascus hellenicus, Wickerhamomyces anomalus, Pichia membranifaciens, Candida boidinii, Candida diddensiae and Saccharomyces cerevisiae. Among all tested isolates, W. anomalus strains evidenced the widest spectrum of enzymatic activities and the highest β-glucosidase and phtytase activity. These strains evidenced also the best growth at low pH and increasing bile salt concentration, when grown at 37 °C, as well as the most constant viability index (%) during in vitro digestion.\n\nKiller yeasts isolated from olive brines: Technological and probiotic aptitudes.", "token_count": 309, "char_count": 1212, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6941, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:24.145213", "source": { "split": "train_shard_00000", "doc_id": 1991 }, "chunk_id": "train_shard_00000_1991_0", "global_id": 2192 }, { "text": "The intrinsic mechanism of the thermotolerance of Kluyveromyces marxianus was investigated by comparison of its physiological and metabolic properties at high and low temperatures. After glucose consumption, the conversion of ethanol to acetic acid became gradually prominent only at a high temperature (45°C) and eventually caused a decline in viability, which was prevented by exogenous glutathione. Distinct levels of reactive oxygen species (ROS), glutathione, and NADPH suggest a greater accumulation of ROS and enhanced ROS-scavenging activity at a high temperature. Fusion and fission forms of mitochondria were dominantly observed at 30°C and 45°C, respectively. Consistent results were obtained by temperature upshift experiments, including transcriptomic and enzymatic analyses, suggesting a change of metabolic flow from glycolysis to the pentose phosphate pathway. The results of this study suggest that K. marxianus survives at a high temperature by scavenging ROS via metabolic change for a period until a critical concentration of acetate is reached.\n\nDistinct Metabolic Flow in Response to Temperature in Thermotolerant Kluyveromyces marxianus.", "token_count": 285, "char_count": 1160, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:24.700923", "source": { "split": "train_shard_00000", "doc_id": 1992 }, "chunk_id": "train_shard_00000_1992_0", "global_id": 2193 }, { "text": "Bacillus amyloliquefaciens is a nonpathogenic microorganism whose highly active amylase is widely isolated from soil and plants. TL106 is an isolate of Bacillus amyloliquefaciens isolated from cold- and disease-resistant Tibetan pigs in Linzhi, Tibet. Here, we report that TL106 not only could survive in acidic environments, high bile salt concentrations, and high-temperature conditions but also was resistant to antibiotics. It significantly improved the growth performance of weaned piglets, especially in the prevention of diarrhea. The crude fiber and crude ash digestibility in weaned piglets after TL106 administration was considerably higher than that in other groups. The results of 16S rRNA sequencing conveyed that TL106 stabilized gut microbiota that was disturbed by the weaning process with an increased level of\n\nEffects of Bacillus amyloliquefaciens TL106 Isolated from Tibetan Pigs on Probiotic Potential and Intestinal Microbes in Weaned Piglets.", "token_count": 252, "char_count": 965, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6861, "quality_score": 0.8431, "entities": { "genes": [ "TL106" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:25.181170", "source": { "split": "train_shard_00000", "doc_id": 1993 }, "chunk_id": "train_shard_00000_1993_0", "global_id": 2194 }, { "text": "Escherichia coli sequence type 95 (ST95) is an extraintestinal pathogenic E. coli (ExPEC) renowned for its ability to cause significant morbidity and mortality in humans and poultry. A core genome analysis of 668 ST95 isolates generated 10 clades (A to J), 5 of which are reported here for the first time. F plasmid replicon sequence typing showed that almost a third (178/668 [27%]) of the collection carry pUTI89 (F29:B10) and were restricted to clade A and a sublineage of clade B. In contrast, almost half (328/668 [49%]) of the collection across multiple clades harbor ColV plasmids (multiple F types). Strikingly, ST95 lineages with pUTI89 were almost exclusively from humans, while ColV\n\nF Plasmid Lineages in Escherichia coli ST95: Implications for Host Range, Antibiotic Resistance, and Zoonoses.", "token_count": 255, "char_count": 805, "word_count": 126, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "ST95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:25.670793", "source": { "split": "train_shard_00000", "doc_id": 1994 }, "chunk_id": "train_shard_00000_1994_0", "global_id": 2195 }, { "text": "Edema disease is an often fatal enterotoxemia caused by specific strains of Shiga toxin-producing Escherichia coli (STEC) that affect primarily healthy, rapidly growing nursery pigs. Recently, outbreaks of edema disease have also emerged in France in wild boars. Analysis of STEC strains isolated from wild boars during 2013-2019 showed that they belonged to the serotype O139:H1 and were positive for both Stx2e and F18 fimbriae. However, in contrast to classical STEC O139:H1 strains circulating in pigs, they also possessed enterotoxin genes sta1 and stb, typical of enterotoxigenic E. coli. In addition, the strains contained a unique accessory genome composition and did not harbor antimicrobial-resistance genes, in contrast to domestic pig isolates. These data thus reveal that the emergence of edema disease in wild boars was caused by atypical hybrid of STEC and enterotoxigenic E. coli O139:H1, which so far has been restricted to the wildlife environment.\n\nWild Boars as Reservoir of Highly Virulent Clone of Hybrid Shiga Toxigenic and Enterotoxigenic Escherichia coli Responsible for Edema Disease, France.", "token_count": 314, "char_count": 1118, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:26.271621", "source": { "split": "train_shard_00000", "doc_id": 1995 }, "chunk_id": "train_shard_00000_1995_0", "global_id": 2196 }, { "text": "Antibiotics used to be supplemented to animal feeds as growth promoter and as an effective strategy to reduce the burden of pathogenic bacteria present in the gastro-intestinal tract. However, in-feed antibiotics also kill bacteria that may be beneficial to the animal. Secondly, unrestricted use of antibiotics enhanced the antibiotic resistance in pathogenic bacteria. To overcome above problems, scientists are taking a great deal of measures to develop alternatives of antibiotics. There is convincing evidence that probiotics could replace in-feed antibiotics in poultry production. Because they have beneficial effects on growth performance, meat quality, bone health and eggshell quality in poultry. Better immune responses, healthier intestinal microflora and morphology which help the birds to resist against disease attack were also identified with the supplementation of probiotics. Probiotics establish cross-feeding between different bacterial strains of gut ecosystem and reduce the blood cholesterol level via bile salt hydrolase activity. The action mode of probiotics was also updated according to recently published literatures, i.e antimicrobial substances generation or toxin reduction. This comprehensive review of probiotics is aimed to highlight the beneficial effects of probiotics as a potential alternative strategy to replace the antibiotics in poultry.\n\nAn updated review on probiotics as an alternative of antibiotics in poultry - A review.", "token_count": 315, "char_count": 1469, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6456, "quality_score": 0.8228, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:26.854609", "source": { "split": "train_shard_00000", "doc_id": 1996 }, "chunk_id": "train_shard_00000_1996_0", "global_id": 2197 }, { "text": "Biofilm formation of staphylococci has been an emerging field of research for many years. However, the underlying molecular mechanisms are still not fully understood and vary widely between species and strains. The aim of this study was to identify new effectors impacting biofilm formation of two Staphylococcus xylosus strains. We identified a novel surface protein conferring cell aggregation, adherence to abiotic surfaces, and biofilm formation. The S. xylosus surface protein A (SxsA) is a large protein occurring in variable sizes. It lacks sequence similarity to other staphylococcal surface proteins but shows similar structural domain organization and functional features. Upon deletion of sxsA, adherence of S. xylosus strain TMW 2.1523 to abiotic surfaces was completely abolished and significantly reduced in TMW 2.1023. Macro- and microscopic aggregation assays further showed that TMW 2.1523 sxsA mutants exhibit reduced cell aggregation compared with the wildtype. Comparative genomic analysis revealed that sxsA is part of the core genome of S. xylosus, Staphylococcus paraxylosus, and Staphylococcus nepalensis and additionally encoded in a small group of Staphylococcus cohnii and Staphylococcus saprophyticus strains. This study provides insights into protein-mediated biofilm formation of S. xylosus and identifies a new cell wall-associated protein influencing cell aggregation and biofilm formation.\n\nSxsA, a novel surface protein mediating cell aggregation and adhesive biofilm formation of Staphylococcus xylosus.", "token_count": 395, "char_count": 1538, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5981, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:27.506156", "source": { "split": "train_shard_00000", "doc_id": 1997 }, "chunk_id": "train_shard_00000_1997_0", "global_id": 2198 }, { "text": "Previously, our group showed that a quadruple coating of probiotics resulted in higher survivability of probiotics under high acid, bile salt, and thermal stresses. In this study, we evaluated the effect of the quadruple coating of probiotics on adhesive properties as well as on competitive exclusion of\n\nA Quadruple Coating of Probiotics for Enhancing Intestinal Adhesion and Competitive Exclusion of", "token_count": 101, "char_count": 402, "word_count": 60, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:27.938240", "source": { "split": "train_shard_00000", "doc_id": 1998 }, "chunk_id": "train_shard_00000_1998_0", "global_id": 2199 }, { "text": "Kluyveromyces marxianus is a promising cell factory for producing heterologous proteins. Essential components including partition element, copy number control element, promoter, and terminator in multicopy plasmids applicable for K. marxianus are not extensively characterized. The pKD1 is an endogenous multicopy plasmid identified in K. lactis, and the pKD1-based plasmid is the only multicopy plasmid successfully applied in K. marxianus. The circular plasmid pKD1 contains three major open reading frames, namely A, B, and C. Here, we showed that the A gene was responsible for maintaining the high-copy number of pKD1-based plasmid in K. marxianus. Deletion of the B or C gene impaired the stable propagation of pKD1-based plasmid in K. marxianus, and this defect could not be rescued by the trans expression of B and C genes. In a quantitative analysis of a series of promoters and terminators, AFT1 promoter from Pichia pastoris, OM45 promoter and INU1 terminator from K. marxianus, and a set of synthetic terminators, supported high-level expressions. A combination of AFT1 or OM45 promoter with INU1 terminator in a pKD1-based plasmid achieved high-level expressions of four different heterologous proteins. Our study provides valuable elements for high-level episomal expressions in K. marxianus.\n\nCharacterization of essential elements for improved episomal expressions in Kluyveromyces marxianus.", "token_count": 376, "char_count": 1408, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5463, "quality_score": 0.7732, "entities": { "genes": [ "OM45", "INU1", "AFT1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:29.375429", "source": { "split": "train_shard_00000", "doc_id": 1999 }, "chunk_id": "train_shard_00000_1999_0", "global_id": 2200 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) is a heterogeneous group of disorders characterized by defects in bile secretion and presentation with intrahepatic cholestasis in infancy or childhood. The most common types include PFIC 1 (deficiency of FIC1 protein, ATP8B1 gene mutation), PFIC 2 (bile salt export pump deficiency, ABCB11 gene mutation), and PFIC 3 (multidrug resistance protein-3 deficiency, ABCB4 gene mutation). Mutational analysis of subjects with normal gamma-glutamyl transferase cholestasis of unknown etiology has led to the identification of newer variants of PFIC, known as PFIC 4, 5, and MYO5B related (sometimes known as PFIC 6). PFIC 4 is caused by the loss of function of tight junction protein 2 (TJP2) and PFIC 5 is due to NR1H4 mutation causing Farnesoid X receptor deficiency. MYO5B gene mutation causes microvillous inclusion disease (MVID) and is also associated with isolated cholestasis. Children with TJP2 related cholestasis (PFIC-4) have a variable spectrum of presentation. Some have a self-limiting disease, while others have progressive liver disease with an increased risk of hepatocellular carcinoma. Hence, frequent surveillance for hepatocellular carcinoma is recommended from infancy. PFIC-5 patients usually have rapidly progressive liver disease with early onset coagulopathy, high alpha-fetoprotein and ultimately require a liver transplant. Subjects with MYO5 B-related disease can present with isolated cholestasis or cholestasis with intractable diarrhea (MVID). These children are at risk of worsening cholestasis post intestinal transplant (IT) for MVID, hence combined intestinal and liver transplant or IT with biliary diversion is preferred. Immunohistochemistry can differentiate most of the variants of PFIC but confirmation requires genetic analysis.\n\nNewer variants of progressive familial intrahepatic cholestasis.", "token_count": 508, "char_count": 1885, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [ "ABCB4", "MYO5", "ABCB11", "MYO5B", "TJP2", "FIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:30.021061", "source": { "split": "train_shard_00000", "doc_id": 2000 }, "chunk_id": "train_shard_00000_2000_0", "global_id": 2201 }, { "text": "Chronic liver disease (CLD) is one of the leading causes of disability-adjusted life years in many countries. A recent understanding of nuclear bile acid receptor pathways has increased focus on the impact of crosstalk between the gut, bile acids, and liver on liver pathology. While conventionally used in cholestatic disorders and to dissolve gallstones, the discovery of bile acids' influence on the gut microbiome and human metabolism offers a unique potential for their utility in early and advanced liver diseases because of diverse etiologies. Based on these findings, preclinical studies using bile acid-based molecules have shown encouraging results at addressing liver inflammation and fibrosis. Emerging data also suggest that bile acid profiles change distinctively across various causes of liver disease. We summarize the current knowledge and evidence related to bile acids in health and disease and discuss culminated and ongoing therapeutic trials of bile acid derivatives in CLD. In the near future, further evidence in this area might help clinicians better detect and manage liver diseases.\n\nA Current Understanding of Bile Acids in Chronic Liver Disease.", "token_count": 253, "char_count": 1174, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:30.852382", "source": { "split": "train_shard_00000", "doc_id": 2001 }, "chunk_id": "train_shard_00000_2001_0", "global_id": 2202 }, { "text": "Vitis has two subgenera: Euvitis, which includes commercially important Vitis vinifera and interspecific hybrid cultivars, and Muscadinia. Of note, the market for Muscadinia grapes remains small, and only Muscadinia rotundifolia is cultivated as a commercial crop. To establish a basis for the study of Muscadinia species, we generated chromosome-level whole-genome sequences of Muscadinia rotundifolia cv. Noble. A total of 393.8 Mb of sequences were assembled from 20 haploid chromosomes, and 26 394 coding genes were identified from the sequences. Comparative analysis with the genome sequence of V. vinifera revealed a smaller size of the M. rotundifolia genome but highly conserved gene synteny. A genome-wide association study of 12 Muscadinia berry-related traits was performed among 356 individuals from breeding populations of M. rotundifolia. For the transferability of markers between Euvitis and Muscadinia, we used 2000 core genome rhAmpSeq markers developed to allow marker transferability across Euvitis species. A total of 1599 (80%) rhAmpSeq markers returned data in Muscadinia. From the GWAS analyses, we identified a total of 52 quantitative trait nucleotides (QTNs) associated with the 12 berry-related traits. The transferable markers enabled the direct comparison of the QTNs with previously reported results. The whole-genome sequences along with the GWAS results provide a new basis for the extensive study of Muscadinia species.\n\nChromosome-level genome sequence assembly and genome-wide association study of Muscadinia rotundifolia reveal the genetics of 12 berry-related traits.", "token_count": 440, "char_count": 1605, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5746, "quality_score": 0.7873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:31.487326", "source": { "split": "train_shard_00000", "doc_id": 2002 }, "chunk_id": "train_shard_00000_2002_0", "global_id": 2203 }, { "text": "Phage therapy has been proposed as a possible alternative treatment for infections caused by the ubiquitous bacterial pathogen Staphylococcus aureus. However, successful therapy requires understanding the genetic basis of host range-the subset of strains in a species that could be killed by a particular phage. We searched diverse sets of S. aureus public genome sequences against a database of genes suggested from prior studies to influence host range to look for patterns of variation across the species. We found that genes encoding biosynthesis of molecules that were targets of S. aureus phage adsorption to the outer surface of the cell were the most conserved in the pangenome. Putative phage resistance genes that were core components of the pangenome genes had similar nucleotide diversity, ratio of nonsynonymous to synonymous substitutions, and functionality (measured by delta-bitscore) to other core genes. However, phage resistance genes that were not part of the core genome were significantly less consistent with the core genome phylogeny than all noncore genes in this set, suggesting more frequent movement between strains by horizontal gene transfer. Only superinfection immunity genes encoded by temperate phages inserted in the genome correlated with experimentally determined temperate phage resistance. Taken together, these results suggested that, while phage adsorption genes are heavily conserved in the S. aureus species, HGT may play a significant role in strain-specific evolution of host range patterns.\n\nSpecies-Scale Genomic Analysis of Staphylococcus aureus Genes Influencing Phage Host Range and Their Relationships to Virulence and Antibiotic Resistance Genes.", "token_count": 372, "char_count": 1698, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6138, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:32.066146", "source": { "split": "train_shard_00000", "doc_id": 2003 }, "chunk_id": "train_shard_00000_2003_0", "global_id": 2204 }, { "text": "Recently, probiotics have gained much attention for their roles against various clinical conditions. Obesity is a worldwide health problem that triggers various other major complications like type 2 diabetes (T2D) and cancers, including colorectal cancer (CRC). Earlier, Kluyveromyces marxianus PCH397 isolated from yak (Bos grunniens) milk has been characterised by us for its efficient β-galactosidase-producing ability, an important probiotic property. In the present study, yeast PCH397 has been evaluated for various parameters for its probiotic use. PCH397 exhibited tolerance to GI tract conditions (low pH, pancreatin, pepsin, and bile salts) with 78 to 99% survivability, possessed around 81% cell surface hydrophobicity, and 96% autoaggregation ability. The cell-free extract (CFE) and cell-free supernatant (CFS) from PCH397 improved insulin sensitisation by enhancing 2-NBDG (a glucose analogue) uptake in 3T3-L1 adipocytes, an approach useful in T2D treatment. They also exhibited lower intracellular lipid accumulation, triglyceride storage, and reactive oxygen species in differentiated adipocytes, indicating their anti-adipogenic ability. Also, CFE and intact cells (ICs) exhibited 73.33 ± 1.11% and 34.88 ± 2.80% DPPH radical scavenging activity, respectively. Furthermore, CFS showed a cytotoxic effect on SW-480 colorectal cancer (CRC) cells and induced the cell cycle phase arrest after 24 h of treatment. In conclusion, these results demonstrate that K. marxianus PCH397 could be used as a potential probiotic yeast and presents a therapeutic potential against obesity, T2D, and colon cancer.", "token_count": 481, "char_count": 1614, "word_count": 225, "semantic_coherence": 1, "information_density": 0.7644, "quality_score": 0.8822, "entities": { "genes": [ "PCH397" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:32.714315", "source": { "split": "train_shard_00000", "doc_id": 2004 }, "chunk_id": "train_shard_00000_2004_0", "global_id": 2205 }, { "text": "In Vitro Characterisation Revealed Himalayan Dairy Kluyveromyces marxianus PCH397 as Potential Probiotic with Therapeutic Properties.", "token_count": 40, "char_count": 133, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "PCH397" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:33.072133", "source": { "split": "train_shard_00000", "doc_id": 2004 }, "chunk_id": "train_shard_00000_2004_1", "global_id": 2206 }, { "text": "Exposure of lactic acid bacteria (LAB) and yeasts to adverse fluctuations during fermentation causes stress; consequently, microbes develop adaptive responses. In this study, we investigated the physiological and proteomic responses of LAB and yeast to acid stress and their application in food fermentation. The physiological and proteomic responses of\n\nAcid stress responses of", "token_count": 83, "char_count": 379, "word_count": 53, "semantic_coherence": 1, "information_density": 0.6792, "quality_score": 0.8396, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:33.450902", "source": { "split": "train_shard_00000", "doc_id": 2005 }, "chunk_id": "train_shard_00000_2005_0", "global_id": 2207 }, { "text": "Pangenomes have replaced single reference genomes as genetic references, as they contain a better scope of the diversity found in a single species. This protocol outlines the iterative mapping approach in constructing a pangenome, including how to check the raw data, align the data to a reference, how to assemble the data, and how to remove potential contaminants from the final assembly.\n\nMaking a Pangenome Using the Iterative Mapping Approach.", "token_count": 97, "char_count": 448, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:33.836534", "source": { "split": "train_shard_00000", "doc_id": 2006 }, "chunk_id": "train_shard_00000_2006_0", "global_id": 2208 }, { "text": "Kefir is a traditional fermented milk containing beneficial bacteria and yeasts. Despite Kluyveromyces marxianus, isolated from kefir, gaining increasing attention as a potential probiotic yeast owing to its biological function, Saccharomyces boulardii is the only species considered as a probiotic yeast. We evaluated the safety of K. marxianus strains A4 and A5, isolated from Korean kefir, in comparison with that of S. boulardii. Virulence attributes were preliminarily assessed in vitro including their ability of gelatin hydrolysis, pseudohyphae formation, and hemolysis. To evaluate in vivo safety, the strains were challenged in a healthy animal model, four-week-old female BALB/c mice. Mice were orally administered 0.2 mL of 0.9% sterilized saline (NC_S; n = 6), S. boulardii ATCC MYA-796 (high concentration, S.b_H; low concentration, S.b_L; n = 6 for each), K. marxianus A4 (high concentration, A4_H; low concentration, A4_L; n = 6 for each), or K. marxianus A5 (high concentration, A5_H; low concentration, A5_L; n = 6 for each) for 2 weeks. At study end, body weight, spleen and liver weights, and blood parameters were assessed. K. marxianus A4 and A5 were tested negative for gelatinase and hemolysis. Overall, hematological, plasma biochemical, and cytokine (interleukin-1β and tumor necrosis factor-α) parameters were comparable between the experimental and negative control (NC) groups. Notably, the interleukin-6 level of the A5_H group was significantly lower than that of the NC group (p < 0.05), suggesting anti-inflammatory potential of K. marxianus A5.", "token_count": 499, "char_count": 1577, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:34.492049", "source": { "split": "train_shard_00000", "doc_id": 2007 }, "chunk_id": "train_shard_00000_2007_0", "global_id": 2209 }, { "text": "A Combined In Vitro and In Vivo Assessment of the Safety of the Yeast Strains Kluyveromyces marxianus A4 and A5 Isolated from Korean Kefir.", "token_count": 44, "char_count": 139, "word_count": 24, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:34.859419", "source": { "split": "train_shard_00000", "doc_id": 2007 }, "chunk_id": "train_shard_00000_2007_1", "global_id": 2210 }, { "text": "Intestinal microflora can influence abnormal adipocyte growth. Therefore, this study was aimed to investigate the probiotic properties and antioxidant and antiobesity effects of isolated strains from homemade kimchi. Among the isolated strains, Lactiplantibacillus plantarum KU15120 showed high tolerance to artificial gastric juice and bile salt conditions, high adhesion to HT-29 cells, nonproduction of β-glucuronidase, nonhemolysis, and acceptable resistance to antibiotics. It showed high antioxidant activity, including DPPH and ABTS radical scavenging and antioxidant activity, as determined by the β-carotene bleaching assay. Oil red O staining and intracellular triglyceride levels revealed reduced lipid accumulation, which confirmed the anti-adipogenic activity of L. plantarum KU15120. In addition, the expression levels of fatty acid synthase, CCAAT/enhance-binding protein α, and peroxisome proliferator-activated receptor γ, were significantly lower in the probiotic-treated group than in the control group. These results suggest that L. plantarum KU15120 has probiotic properties, antioxidant, and antiobesity effects and could be used as a therapeutic probiotics.\n\nEffects of the Probiotic Lactiplantibacillus plantarum KU15120 Derived from Korean Homemade Diced-Radish Kimchi Against Oxidation and Adipogenesis.", "token_count": 377, "char_count": 1329, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7118, "quality_score": 0.8559, "entities": { "genes": [ "KU15120" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:35.458369", "source": { "split": "train_shard_00000", "doc_id": 2008 }, "chunk_id": "train_shard_00000_2008_0", "global_id": 2211 }, { "text": "This study investigated the prevalence of Salmonella in 210 retail meat samples (105 raw chicken and 105 raw pork) collected from supermarkets and wet markets in 13 areas of Hebei Province, China, from June to October 2018. Whole-genome sequencing was performed on all 125 Salmonella isolates to investigate their genetic relationship. Core genome multilocus sequence typing of 77 representative isolates was used to further elucidate the genetic relatedness among the Salmonella isolated from retail meat. The mean detection rate of Salmonella in all samples was 59.5% (125/210). The prevalence of Salmonella was 53.3% (56/105) in chicken and 65.7% (69/105) in pork. Chicken and pork samples collected in July had the highest detection rate of Salmonella among the sampling months. The isolates were assigned to 19 serotypes, with S. Derby, S. London, and S. Thompson being the most frequent serotypes. Resistance to tetracycline (primarily used for the treatment of bacterial infections) was observed in 89.6% of the isolates, and 84.0% were resistant to doxycycline (also a tetracycline antibiotic) or gemifloxacin (commonly used for clinical treatment of human acute bronchitis). More than 80% of the isolates were multidrug resistant. A total of 21 sequence types were identified. Sequence type 40 (ST-40), the predominant genotype among all isolates, was found only in pork; the sequence types of chicken isolates were more diverse. A total of 58 different antibiotic resistance genes (ARGs) were detected in the 125 isolates. Most types of ARGs were associated with aminoglycoside and β-lactam resistance. Nevertheless, the tetracycline resistance gene tet(A) was the most frequently occurring ARG in all isolates at 78.4%. Multiple isolates of ST-26 contained 20 ARGs", "token_count": 507, "char_count": 1775, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5651, "quality_score": 0.7825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:36.112370", "source": { "split": "train_shard_00000", "doc_id": 2009 }, "chunk_id": "train_shard_00000_2009_0", "global_id": 2212 }, { "text": "All isolates of ST-40 were divided into two clusters, with at least 160 allelic differences between them. The findings highlight the need to continually monitor ARGs in foodborne Salmonella with particular emphasis on ST-40 and ST-26; the monitoring should include as many retail meat types as possible in the study area.\n\nPrevalence, antimicrobial resistance, and genotype diversity of Salmonella isolates recovered from retail meat in Hebei Province, China.", "token_count": 109, "char_count": 459, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7941, "quality_score": 0.8971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:36.494493", "source": { "split": "train_shard_00000", "doc_id": 2009 }, "chunk_id": "train_shard_00000_2009_1", "global_id": 2213 }, { "text": "BackgroundEvidence supporting the effectiveness of single-room contact precautions (SCP) in preventing in-hospital acquisition of vancomycin-resistant enterococci (haVRE) is limited.AimWe assessed the impact of SCP on haVRE and their transmission.MethodsWe conducted a prospective, multicentre cohort study in German haematological/oncological departments during 2016. Two sites performed SCP for VRE patients and two did not (NCP). We defined a 5% haVRE-risk difference as non-inferiority margin, screened patients for VRE, and characterised isolates by whole genome sequencing and core genome MLST (cgMLST). Potential confounders were assessed by competing risk regression analysis.ResultsWe included 1,397 patients at NCP and 1,531 patients at SCP sites. Not performing SCP was associated with a significantly higher proportion of haVRE; 12.2% (170/1,397) patients at NCP and 7.4% (113/1,531) patients at SCP sites (relative risk (RR) 1.74; 95% confidence interval (CI): 1.35-2.23). The difference (4.8%) was below the non-inferiority margin. Competing risk regression analysis indicated a stronger impact of antimicrobial exposure (subdistribution hazard ratio (SHR) 7.46; 95% CI: 4.59-12.12) and underlying disease (SHR for acute leukaemia 2.34; 95% CI: 1.46-3.75) on haVRE than NCP (SHR 1.60; 95% CI: 1.14-2.25)", "token_count": 437, "char_count": 1317, "word_count": 178, "semantic_coherence": 1, "information_density": 0.691, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:37.123333", "source": { "split": "train_shard_00000", "doc_id": 2010 }, "chunk_id": "train_shard_00000_2010_0", "global_id": 2214 }, { "text": "Based on cgMLST and patient movement data, we observed 131 patient-to-patient VRE transmissions at NCP and 85 at SCP sites (RR 1.76; 95% CI: 1.33-2.34).ConclusionsWe show a positive impact of SCP on haVRE in a high-risk population, although the observed difference was below the pre-specified non-inferiority margin. Importantly, other factors including antimicrobial exposure seem to be more influential.\n\nImpact of single-room contact precautions on acquisition and transmission of vancomycin-resistant enterococci on haematological and oncological wards, multicentre cohort-study, Germany, January-December 2016.", "token_count": 184, "char_count": 615, "word_count": 80, "semantic_coherence": 1, "information_density": 0.825, "quality_score": 0.9125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:37.567998", "source": { "split": "train_shard_00000", "doc_id": 2010 }, "chunk_id": "train_shard_00000_2010_1", "global_id": 2215 }, { "text": "Bile acids (BAs) are amphipathic molecules important for metabolism of cholesterol, absorption of lipids and lipid soluble vitamins, bile flow, and regulation of gut microbiome. There are over 30 different BA species known to exist in humans and mice, which are endogenous modulators of at least 6 different membrane or nuclear receptors. This diversity of ligands and receptors play important roles in health and disease; however, the full functions of each individual BA\n\nBile acid homeostasis in female mice deficient in", "token_count": 134, "char_count": 523, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7654, "quality_score": 0.8827, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:37.993860", "source": { "split": "train_shard_00000", "doc_id": 2011 }, "chunk_id": "train_shard_00000_2011_0", "global_id": 2216 }, { "text": "This study aimed to isolate lactic acid bacteria (LAB) from the digestive tract, meat and slime of edible snails (Helix lucorum, Helix aspersa and Eobania vermiculata) and investigate their antagonistic activity against Penicillium expansum. They were then characterized for their probiotic potential. Among 900 bacterial isolates, 47 LAB exhibiting anti-P. expansum activity were identified through matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) as Levilactobacillus brevis (25), Lactococcus lactis (3), Enterococcus faecium (12), Enterococcus faecalis (4), Enterococcus casseliflavus (1), and Enterococcus mundtii (2). Sixty-two percent of the strains were tolerant to 100 mg/L of lysozyme. Seventy two percent of the isolates were able to survive at pH 3 and most of them tolerate 2.5% bile salt concentration. Moreover, 23% of the strains displayed bile salt hydrolase activity. Interestingly, all strains were biofilm strong producers. However, their auto- and co-aggregation properties were time and pH dependent with high aggregative potentiality at pH 4.5 after 24 h. Remarkably, 48.94% of the strains showed high affinity to chloroform. The safety assessment revealed that the 47 LAB had no hemolytic activity and 64% of them lacked mucin degradation activity. All isolated strains were susceptible to gentamycin, streptomycin, tetracycline, chloramphenicol, and trimethoprim-sulfamethoxazole. Overall, 43 LAB strains showed inhibitory activity against a broad spectrum of pathogenic Gram-positive and gram-negative bacteria, fungi, and yeast. Our findings suggest that L. brevis (EVM12 and EVM14) and Ent. faecium HAS34 strains could be potential candidates for probiotics with interesting antibacterial and anti-P. expansum activities.", "token_count": 525, "char_count": 1791, "word_count": 244, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [ "EVM14", "EVM12", "HAS34" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:18:38.636799", "source": { "split": "train_shard_00000", "doc_id": 2012 }, "chunk_id": "train_shard_00000_2012_0", "global_id": 2217 }, { "text": "Potential Probiotic Lactic Acid Bacteria with Anti-Penicillium expansum Activity from Different Species of Tunisian Edible Snails.", "token_count": 35, "char_count": 130, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:39.025488", "source": { "split": "train_shard_00000", "doc_id": 2012 }, "chunk_id": "train_shard_00000_2012_1", "global_id": 2218 }, { "text": "Streptococcus equi subsp.\n\nDifferences in the Accessory Genomes and Methylomes of Strains of Streptococcus equi subsp.", "token_count": 40, "char_count": 118, "word_count": 16, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:39.410050", "source": { "split": "train_shard_00000", "doc_id": 2013 }, "chunk_id": "train_shard_00000_2013_0", "global_id": 2219 }, { "text": "Mycoplasma agalactiae, causing agent of contagious agalactia, infects domestic small ruminants such as sheep and goats but also wild Caprinae. M. agalactiae is highly contagious and transmitted through oral, respiratory, and mammary routes spreading rapidly in an infected herd.\n\nMycoplasma agalactiae ST35: a new sequence type with a minimal accessory genome primarily affecting goats.", "token_count": 108, "char_count": 386, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [ "ST35" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:39.861419", "source": { "split": "train_shard_00000", "doc_id": 2014 }, "chunk_id": "train_shard_00000_2014_0", "global_id": 2220 }, { "text": "Disorders in bile acid transport and metabolism have been related to a number of metabolic disease states, atherosclerosis, type-II diabetes, and cancer. Bile acid-binding proteins (BABPs), a subfamily of intracellular lipid-binding proteins (iLBPs), have a key role in the cellular trafficking and metabolic targeting of bile salts. Within the family of iLBPs, BABPs exhibit unique binding properties including positive binding cooperativity and site-selectivity, which in different tissues and organisms appears to be tailored to the local bile salt pool. Structural and biophysical studies of the past two decades have shed light on the mechanism of bile salt binding at the atomic level, providing us with a mechanistic picture of ligand entry and release, and the communication between the binding sites. In this review, we discuss the emerging view of bile salt recognition in intestinal- and liver-BABPs, with examples from both mammalian and non-mammalian species. The structural and dynamic determinants of the BABP-bile-salt interaction reviewed herein set the basis for the design and development of drug candidates targeting the transcellular traffic of bile salts in enterocytes and hepatocytes.\n\nStructural and Dynamic Determinants of Molecular Recognition in Bile Acid-Binding Proteins.", "token_count": 316, "char_count": 1301, "word_count": 188, "semantic_coherence": 1, "information_density": 0.617, "quality_score": 0.8085, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:40.430364", "source": { "split": "train_shard_00000", "doc_id": 2015 }, "chunk_id": "train_shard_00000_2015_0", "global_id": 2221 }, { "text": "The human bile salt sodium deoxycholate induces metabolic and cell envelope changes in", "token_count": 21, "char_count": 86, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:40.790902", "source": { "split": "train_shard_00000", "doc_id": 2016 }, "chunk_id": "train_shard_00000_2016_0", "global_id": 2222 }, { "text": "Introduction The removal of the terminal ileum may interfere with gut-associated lymphoid tissue function, reduce bile salt reabsorption, and change intraluminal pH, which may contribute to the development of\n\nAnalysis of Perioperative Risk Factors for Clostridium difficile Infection After a Colectomy.", "token_count": 79, "char_count": 303, "word_count": 41, "semantic_coherence": 1, "information_density": 0.878, "quality_score": 0.939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:41.171989", "source": { "split": "train_shard_00000", "doc_id": 2017 }, "chunk_id": "train_shard_00000_2017_0", "global_id": 2223 }, { "text": "Skin conditions associated with Tenacibaculum spp. constitute a significant threat to the health and welfare of sea-farmed Atlantic salmon (Salmo salar L.) in Norway. Fifteen presumptive tenacibaculosis outbreaks distributed along the Norwegian coast during the late winter and spring of 2018 were investigated. Bacteriological culture confirmed the presence of Tenacibaculum spp. Seventy-six isolates cultured from individual fish were selected and subjected to whole-genome sequencing and MALDI-TOF MS analysis. Average nucleotide identity and MALDI-TOF analyses confirmed the presence of T. finnmarkense and T. dicentrarchi, with further division of T. finnmarkense into genomovars (gv.) finnmarkense and ulcerans. Core genome multilocus sequence typing (cgMLST) and single-nucleotide polymorphism (SNP) analyses identified the presence of a genetically conserved cluster of gv. finnmarkense isolates against a background of relatively genetically diverse gv. finnmarkense and gv. ulcerans isolates in 13 of the 15 studied cases. This clustering strongly suggests a link between T. finnmarkense gv. finnmarkense and development of clinical tenacibaculosis in sea-farmed Norwegian salmon in the late winter and spring. Analysis of 25 Tenacibaculum isolates collected during the spring of 2019 from similar cases identified a similar distribution of genotypes. Low water temperatures were common to all cases, and most incidences involved relatively small fish shortly after sea transfer, suggesting that these fish are particularly predisposed to Tenacibaculum infection.\n\nTenacibaculosis in Norwegian Atlantic salmon (Salmo salar) cage-farmed in cold sea water is primarily associated with Tenacibaculum finnmarkense genomovar finnmarkense.", "token_count": 445, "char_count": 1743, "word_count": 233, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:41.802415", "source": { "split": "train_shard_00000", "doc_id": 2018 }, "chunk_id": "train_shard_00000_2018_0", "global_id": 2224 }, { "text": "The current investigation aimed at characterizing the cause of multiple disease outbreaks in the same broiler production unit during a course of 18 months. The outbreaks had mortality rates of up to 22%. Escherichia coli was diagnosed as the responsible agent. Multiple-locus variable-number tandem-repeat analysis showed that all chicken isolates had identical band patterns. Core genome comparisons demonstrated that the 36 chicken isolates differed with maximum of nine nucleotides indicating that the same E. coli clone was responsible for all seven disease outbreaks despite adherence to the all-in-all production principle and rigorous cleaning and disinfection procedures.\n\nRecurring outbreaks by the same Escherichia coli ST10 clone in a broiler unit during 18 months.", "token_count": 181, "char_count": 776, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6518, "quality_score": 0.8259, "entities": { "genes": [ "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:42.253468", "source": { "split": "train_shard_00000", "doc_id": 2019 }, "chunk_id": "train_shard_00000_2019_0", "global_id": 2225 }, { "text": "Bacillus species isolated from honeybee Apis mellifera gut, honey and bee bread samples were characterized for their in vitro probiotic and safety attributes. Alpha and γ haemolytic cultures were tested for their antibiotic resistance, antibacterial spectrum, acid and bile tolerance, adhesion ability (auto-aggregation, co-aggregation and hydrophobicity) and phenol tolerance. Safety criteria included evaluation of virulence genes and cytotoxicity percentages. Bacillus isolates inhibited both Gram-positive and Gram-negative pathogens including Staphylococcus aureus, Pseudomonas aeruginosa, Enterococcus faecalis and Streptococcus mutans, while none could inhibit Listeria monocytogenes. Among the isolates, Bacillus subtilis ZH05, ZB03 and ZG025 showed resistance to most of the tested antibiotics and were considered unsafe. B. subtilis (4) and B. licheniformis (1) tolerated acidic pH and bile conditions, never the less were more tolerant in simulated intestinal conditions vis-a-vis gastric conditions. In 0·5% phenol concentrations, B. licheniformis ZH02 showed highest growth, while, B. subtilis ZG029 demonstrated highest auto-aggregation (65 ± 4·6) and hydrophobicity (23 ± 3·6) percentages (P < 0·05). The isolates lacked virulence genes (hblA, hblC, hblD, nhe, cytK and ces), and their cytotoxic percentage on Caco-2 cell lines was ˂15%. Overall, honeybees appear to be a good source of Bacillus species exhibiting typical in vitro probiotic properties, which could be of commercial interest.\n\nIn vitro probiotic and safety attributes of Bacillus spp. isolated from beebread, honey samples and digestive tract of honeybees Apis mellifera.", "token_count": 499, "char_count": 1653, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [ "ZB03", "ZH02", "ZH05", "ZG025", "ZG029" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:42.903173", "source": { "split": "train_shard_00000", "doc_id": 2020 }, "chunk_id": "train_shard_00000_2020_0", "global_id": 2226 }, { "text": "Wolbachia, a gram-negative [Formula: see text]-proteobacterium, is an endosymbiont found in some arthropods and nematodes. Diaphorina citri Kuwayama, the vector of 'Candidatus Liberibacter asiaticus' (CLas), are naturally infected with a strain of Wolbachia (wDi), which has been shown to colocalize with the bacteria pathogens CLas, the pathogen associated with huanglongbing (HLB) disease of citrus. The relationship between wDi and CLas is poorly understood in part because the complete genome of wDi has not been available. Using high-quality long-read PacBio circular consensus sequences, we present the largest complete circular wDi genome among supergroup-B members. The assembled circular chromosome is 1.52 megabases with 95.7% genome completeness with contamination of 1.45%, as assessed by checkM. We identified Insertion Sequences (ISs) and prophage genes scattered throughout the genomes. The proteins were annotated using Pfam, eggNOG, and COG that assigned unique domains and functions. The wDi genome was compared with previously sequenced Wolbachia genomes using pangenome and phylogenetic analyses. The availability of a complete circular chromosome of wDi will facilitate understanding of its role within the insect vector, which may assist in developing tools for disease management. This information also provides a baseline for understanding phylogenetic relationships among Wolbachia of other insect vectors.\n\nComplete de novo assembly of Wolbachia endosymbiont of Diaphorina citri Kuwayama (Hemiptera: Liviidae) using long-read genome sequencing.", "token_count": 411, "char_count": 1570, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:43.525186", "source": { "split": "train_shard_00000", "doc_id": 2021 }, "chunk_id": "train_shard_00000_2021_0", "global_id": 2227 }, { "text": "Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome.\n\nCharacterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation.", "token_count": 179, "char_count": 775, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:43.972175", "source": { "split": "train_shard_00000", "doc_id": 2022 }, "chunk_id": "train_shard_00000_2022_0", "global_id": 2228 }, { "text": "A total of 272 isolates of lactic acid bacteria (LAB) were isolated from 22 samples of naturally fermented milk products of Sikkim in India viz. dahi, soft-variety chhurpi, hard-variety chhurpi, mohi and philu, out of which, 68 LAB isolates were randomly grouped on the basis of phenotypic characteristics, and were identified by 16S rRNA gene sequence analysis. Leuconostoc mesenteroides was the most dominant genus, followed by Leuc. mesenteroides subsp. jonggajibkimchii, Lactococcus lactis subsp. cremoris, Lc. lactis, Lc. lactis subsp. hordniae, Lc. lactis subsp. tructae, Enterococcus faecalis, E. italicus and E. pseudoavium. LAB strains were tested for probiotics attributes by in vitro and genetic screening, based on marker genes. LAB strains showed tolerance to pH 3.0, bile salt, resistance to lysozyme and β-galactosidase activity. Enterococcus faecalis YS4-11 and YS4-14 and Lactococcus lactis subsp. cremoris SC3 showed more than 85% of hydrophobicity. Genes clp L and tdc encoding for low pH tolerance, agu A and Ir1516 encoding for bile tolerance, LBA1446 gene encoding for BSH activity, map A, apf, mub 1 and msa encoding for mucosal binding property were detected. Gene mesY for bacteriocin production was detected only in Leuconostoc spp. Based on the in vitro and genetic screening of probiotic attributes, Leuc. mesenteroides; Leuc. mesenteroides subsp. jonggajibkimchii and Lc. lactis subsp. cremoris were tentatively selected for possible probiotic candidates.", "token_count": 474, "char_count": 1484, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [ "SC3", "LBA1446", "YS4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:44.615463", "source": { "split": "train_shard_00000", "doc_id": 2023 }, "chunk_id": "train_shard_00000_2023_0", "global_id": 2229 }, { "text": "In vitro and genetic screening of probiotic properties of lactic acid bacteria isolated from naturally fermented cow-milk and yak-milk products of Sikkim, India.", "token_count": 40, "char_count": 161, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:44.976555", "source": { "split": "train_shard_00000", "doc_id": 2023 }, "chunk_id": "train_shard_00000_2023_1", "global_id": 2230 }, { "text": "With the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few studies have scaled beyond single pangenomes to compare global genetic diversity both within and across different species. We present here several methods for \"comparative pangenomics\" that can be used to contextualize multi-pangenome scale genetic diversity with gene function for multiple species at multiple resolutions: pangenome shape, genes, sequence variants, and positions within variants.\n\nComparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity.", "token_count": 148, "char_count": 746, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7708, "quality_score": 0.8854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:45.423048", "source": { "split": "train_shard_00000", "doc_id": 2024 }, "chunk_id": "train_shard_00000_2024_0", "global_id": 2231 }, { "text": "Breast milk is well known as the abundant source of beneficial bacteria. A new alternative source of human probiotic origin from breast milk is in demand and currently of interest for both the functional food industry and biopharmaceuticals. The aim in this study was to investigate the anticancer and antioxidant efficacies of the new potential probiotics isolated from human breast milk. Three strains of lactic acid bacteria (LAB) have shown their potential probiotic criteria including antimicrobial activity, non-hemolytic property, and survival in acid and bile salt conditions. These strains showed high abilities on cell surface hydrophobicity, auto-aggregation, and co-aggregation. The genera identification by 16S rRNA sequencing and comparison revealed that they were\n\nCharacterization of", "token_count": 177, "char_count": 799, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:45.870939", "source": { "split": "train_shard_00000", "doc_id": 2025 }, "chunk_id": "train_shard_00000_2025_0", "global_id": 2232 }, { "text": "Candida kefyr (Kluyveromyces marxianus), an ascomycetous environmental yeast, occasionally isolated from dairy products, represents an uncommon but emerging pathogen in immunocompromised patients. Herein, we present a case of C. kefyr pyelonephritis in a 41-year-old, previously immunocompetent, patient who was hospitalized in an COVID-19 ICU. Pyelonephritis was associated with caliectasis and obstruction due to possible fungus ball formation. Predisposing factors included ICU stay, use of broad spectrum antibiotics and steroids, central venous catheterization, mechanical ventilation and urologic manipulation. Susceptibility testing revealed high MIC values to amphotericin B. Infection was effectively controlled by prolonged administration of fluconazole without further surgical intervention. COVID-19 complicated with invasive candidiasis is an increasingly observed clinical situation that warrants high suspicion index and careful evaluation of laboratory data.\n\nInvasive Candida kefyr infection presenting as pyelonephritis in an ICU hospitalized COVID-19 patient: Case report and review of the literature.", "token_count": 271, "char_count": 1120, "word_count": 141, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:46.424323", "source": { "split": "train_shard_00000", "doc_id": 2026 }, "chunk_id": "train_shard_00000_2026_0", "global_id": 2233 }, { "text": "Orientia tsutsugamushi (Ott) is a causative agent of scrub typhus, and one of the emerging pathogens that could affect a large human population. It is one of the misdiagnosed and under-reported, febrile illnesses that infects various body organs (skin, heart, lung, kidney, and brain). The control of this infection is hampered due to the lack of drugs or vaccine against it. This study was undertaken to identify potential drug targets from the core genome of Ott and investigate novel natural product inhibitors against them. Hence, the available genomes for 22 strains of Ott were downloaded from the PATRIC database, and pan-genomic analysis was performed. Only 202 genes were present in the core region. Among these, 94 were identified as essential, 32 non-homologous to humans, nine non-homologous to useful gut flora and a single gene dapD as a drug target. Product of this gene (2,3,4,5-tetrahydropyridine-2-carboxylate N-succinyltransferase) was modeled and docked against traditional Indian (Ayurvedic) and Chinese phytochemical libraries, with best hits selected for docking, based on multiple target-drug/s interactions and minimum energy scores. ADMET profiling and molecular dynamics simulation was performed for top three compounds from each library to assess the toxicity and stability, respectively. We presume that these compounds (ZINC8214635, ZINC32793028, ZINC08101133, ZINC85625167, ZINC06018678, and ZINC13377938) could be successful inhibitors of Ott. However, in-depth experimental and clinical research is needed for further validation.\n\nDifferential analysis of Orientia tsutsugamushi genomes for therapeutic target identification and possible intervention through natural product inhibitor screening.", "token_count": 469, "char_count": 1728, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6929, "quality_score": 0.8465, "entities": { "genes": [ "ZINC8214635", "ZINC13377938", "ZINC32793028", "ZINC06018678", "ZINC08101133", "ZINC85625167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:47.061413", "source": { "split": "train_shard_00000", "doc_id": 2027 }, "chunk_id": "train_shard_00000_2027_0", "global_id": 2234 }, { "text": "Biliary atresia (BA) is the most serious type of obstructive cholangiopathy that occurs in infants. BA can be the cause of death in children under 2 years if untreated early. However, the etiology of the disease is not known. BA is considered to be the result of the destruction of the bile duct system including the accumulation of bile acids. The bile salt export pump, a transporter protein encoded by the ABCB11 gene, plays the main role in the exportation and accumulation of bile acids. The p.Val444Ala variant in this gene is known to be associated with many cholestatic diseases. However, to date no study have been performed to evaluate the association of this variant with susceptibility to the risk of BA. In this study, we aimed to identify the frequency of p.Val444Ala variant and the risk of BA in Vietnamese patients.The polymerase chain reaction (PCR)- restriction fragment length polymorphism method was used to determine the frequency of alleles c.1331T>C (p.Val444Ala, rs2287622) in the ABCB11 gene in 266 Vietnamese patients with BA and 150 healthy people. The gene segment containing the variant was amplified by PCR with specific primers, after that the PCR products were cut by HaeIII restriction enzyme and analyzed on agarose gel to determine the genotypes. The frequency of alleles was assessed statistically to determine the association between these alleles and the risk of disease in patients.In our study, the frequency of alleles c.1331T>C (p.Val444Ala, rs2287622) in the ABCB11 gene was investigated the first time in the patients with BA. The results showed that CC and TC genotypes were significantly different between BA patients and healthy people (P < .01), and the C allele was associated with an increased risk of BA (odds ratio = 2.47; 95% confidence interval: 1.84-3.32; P < .01)", "token_count": 495, "char_count": 1820, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5304, "quality_score": 0.7652, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:47.709275", "source": { "split": "train_shard_00000", "doc_id": 2028 }, "chunk_id": "train_shard_00000_2028_0", "global_id": 2235 }, { "text": "The initial results of clinical, biochemical, and genetic analysis in our study suggested that the p.Val444Ala variant in the ABCB11 gene may be a susceptibility factor for the disease in Vietnamese patients with BA. These results provided new insights into the role of this ABCB11 variant in the pathogenesis of BA.\n\nThe role of p.Val444Ala variant in the ABCB11 gene and susceptibility to biliary atresia in Vietnamese patients.", "token_count": 112, "char_count": 430, "word_count": 68, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:48.084936", "source": { "split": "train_shard_00000", "doc_id": 2028 }, "chunk_id": "train_shard_00000_2028_1", "global_id": 2236 }, { "text": "Campylobacter fetus can cause intestinal and systemic disease in humans and are well-established veterinary and economic pathogens. We report the complete genomic sequences of two C. fetus subsp. fetus (Cff) isolates recovered in 2017 (CITCf01) and 2018 (CITCf02) from a case of recurrent prosthetic valve endocarditis. Both were capable of growth aerobically. Their genomes were found to be highly conserved and syntenic with 99.97% average nucleotide identity (ANI) while differences in their respective sap loci defined the temporal separation of their genomes. Based on core genome phylogeny and ANI of 83 Cff genomes belonging to the previously described human-associated Cff lineage, CITCf01 and CITCf02 grouped in a clade of 11 sequence type (ST)3 Cff (including the Cff type strain NCTC 10842T). CITCf01 and CITCf02 were marked for their lack of unique genomic features when compared to isolates within the subspecies and the type strain in particular. We identified point mutations in oxidative stress response genes, among others, that may contribute to aerobiosis. We report a case of Cff causing relapsed prosthetic valve endocarditis and we highlight the sap island as a polymorphic site within the genetically stable ST3 lineage, central to pathogenicity.\n\nPhenotypic and genetic analyses of two Campylobacter fetus isolates from a patient with relapsed prosthetic valve endocarditis.", "token_count": 389, "char_count": 1398, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "ST3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:48.700220", "source": { "split": "train_shard_00000", "doc_id": 2029 }, "chunk_id": "train_shard_00000_2029_0", "global_id": 2237 }, { "text": "Soybean is one of the most important legume crops worldwide. However, soybean yield is dramatically affected by fungal diseases, leading to economic losses of billions of dollars yearly. Here, we integrated publicly available genome-wide association studies and transcriptomic data to prioritize candidate genes associated with resistance to Cadophora gregata, Fusarium graminearum, Fusarium virguliforme, Macrophomina phaseolina, and Phakopsora pachyrhizi. We identified 188, 56, 11, 8, and 3 high-confidence candidates for resistance to F. virguliforme, F. graminearum, C. gregata, M. phaseolina and P. pachyrhizi, respectively. The prioritized candidate genes are highly conserved in the pangenome of cultivated soybeans and are heavily biased towards fungal species-specific defense responses. The vast majority of the prioritized candidate resistance genes are related to plant immunity processes, such as recognition, signaling, oxidative stress, systemic acquired resistance, and physical defense. Based on the number of resistance alleles, we selected the five most resistant accessions against each fungal species in the soybean USDA germplasm. Interestingly, the most resistant accessions do not reach the maximum theoretical resistance potential. Hence, they can be further improved to increase resistance in breeding programs or through genetic engineering. Finally, the coexpression network generated here is available in a user-friendly web application ( https://soyfungigcn.venanciogroup.uenf.br/ ) and an R/Shiny package ( https://github.com/almeidasilvaf/SoyFungiGCN ) that serve as a public resource to explore soybean-pathogenic fungi interactions at the transcriptional level.\n\nIntegration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens.", "token_count": 449, "char_count": 1856, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6805, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:49.342537", "source": { "split": "train_shard_00000", "doc_id": 2030 }, "chunk_id": "train_shard_00000_2030_0", "global_id": 2238 }, { "text": "Routine and systematic use of bacterial whole-genome sequencing (WGS) is enhancing the accuracy and resolution of epidemiological investigations carried out by Public Health laboratories and regulatory agencies. Large volumes of publicly available WGS data can be used to study pathogenic populations at a large scale. Recently, a freely available computational platform called ProkEvo was published to enable reproducible, automated, and scalable hierarchical-based population genomic analyses using bacterial WGS data. This implementation of ProkEvo demonstrated the importance of combining standard genotypic mapping of populations with mining of accessory genomic content for ecological inference. In particular, the work highlighted here used ProkEvo-derived outputs for population-scaled hierarchical analyses using the R programming language. The main objective was to provide a practical guide for microbiologists, ecologists, and epidemiologists by showing how to: i) use a phylogeny-guided mapping of hierarchical genotypes; ii) assess frequency distributions of genotypes as a proxy for ecological fitness; iii) determine kinship relationships and genetic diversity using specific genotypic classifications; and iv) map lineage differentiating accessory loci. To enhance reproducibility and portability, R markdown files were used to demonstrate the entire analytical approach. The example dataset contained genomic data from 2,365 isolates of the zoonotic foodborne pathogen Salmonella Newport. Phylogeny-anchored mapping of hierarchical genotypes (Serovar -> BAPS1 -> ST -> cgMLST) revealed the population genetic structure, highlighting sequence types (STs) as the keystone differentiating genotype. Across the three most dominant lineages, ST5 and ST118 shared a common ancestor more recently than with the highly clonal ST45 phylotype. ST-based differences were further highlighted by the distribution of accessory antimicrobial resistance (AMR) loci. Lastly, a phylogeny-anchored visualization was used to combine hierarchical genotypes and AMR content to reveal the kinship structure and lineage-specific genomic signatures. Combined, this analytical approach provides some guidelines for conducting heuristic bacterial population genomic analyses using pan-genomic information.", "token_count": 517, "char_count": 2296, "word_count": 299, "semantic_coherence": 1, "information_density": 0.6555, "quality_score": 0.8278, "entities": { "genes": [ "BAPS1", "ST5", "ST45", "ST118" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:18:49.994548", "source": { "split": "train_shard_00000", "doc_id": 2031 }, "chunk_id": "train_shard_00000_2031_0", "global_id": 2239 }, { "text": "Heuristic Mining of Hierarchical Genotypes and Accessory Genome Loci in Bacterial Populations.", "token_count": 26, "char_count": 94, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:50.415893", "source": { "split": "train_shard_00000", "doc_id": 2031 }, "chunk_id": "train_shard_00000_2031_1", "global_id": 2240 }, { "text": "Polymyxin resistance is an emerging health issue aggravated by mcr dissemination among Enterobacterales recovered from various sources. Commensal Escherichia coli plays a key role in the spread of antimicrobial resistance in community settings and is likely to spread silently. It may transfer resistance genes to pathogenic bacteria in the gastrointestinal tract and the environment, and may cause difficult-to-treat infections, especially in immunocompromised patients. Unraveling actors disseminating resistance to last-resort antimicrobials might support the future development of control measures. Here we report the occurrence of a commensal ST683/CC155 colistin-resistant mcr-1.1-harboring E. coli (JP24) obtained from touristic coastal water. JP24's genome was sequenced and comparatively analyzed with other genomes from ST683/CC155 isolated worldwide and with mcr-carrying isolates recovered from various sources in Brazil. Besides mcr-1, JP24 carried bla\n\nDescription and comparative genomic analysis of a mcr-1-carrying Escherichia coli ST683/CC155 recovered from touristic coastal water in Northeastern Brazil.", "token_count": 294, "char_count": 1123, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6966, "quality_score": 0.8483, "entities": { "genes": [ "CC155", "JP24", "ST683" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:50.989852", "source": { "split": "train_shard_00000", "doc_id": 2032 }, "chunk_id": "train_shard_00000_2032_0", "global_id": 2241 }, { "text": "The present study improved the effectiveness of a poorly water-soluble drug, luteolin (LUT), by encapsulating it in lecithin-bile salt-integrated system called bilosomes (BLs). Such a delivery system offers the benefits of mimicking the skin's biological structure and being a prominent tool to circumvent skin delivery obstacles. The prepared BLs underwent complete in vitro assessment. The developed BLs showed enhanced characteristics compared to free luteolin suspension (P < 0.05). Optimized BLs attained good entrapment efficiency (78.60% ± 0.88%), small particle size (226.1 ± 2.45 nm), and sustained drug-release pattern. The study also showed that both blank and LUT-loaded BLs preparations were safe to the skin with a primary irritancy index of < 2 based on the Draize test. In vivo tests were conducted to study the effect of the bile salt-based nanovesicles compared with the free LUT suspension. The photoprotective effect was evaluated according to the visual examination and biochemical analyses of antioxidant, anti-inflammatory, and anti-wrinkling markers after ultraviolet B irradiation. Results of biochemical markers and histopathological examination demonstrated that the LUT-BLs effect was superior than the LUT suspension (P < 0.05). Consequently, the current study proves that novel LUT-loaded BLs is a promising nanoplatform that overcome LUT delivery obstacles and, hence, alleviate UV-induced skin damage.\n\nIntegrated lecithin-bile salt nanovesicles as a promising approach for effective skin delivery of luteolin to improve UV-induced skin damage in Wistar Albino rats.", "token_count": 413, "char_count": 1598, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:51.643024", "source": { "split": "train_shard_00000", "doc_id": 2033 }, "chunk_id": "train_shard_00000_2033_0", "global_id": 2242 }, { "text": "In order to investigate the hypolipidaemic and antioxidant effects of various dark teas produced from different post-fermentation using the same raw material, a hyperlipidaemia zebrafish model combined with binding bile salts assay and antioxidant assays were performed in this study. Results showed that the hypolipidaemic effect of dark tea extracts increased significantly (p < 0.05) while the antioxidant ability decreased sharply compared with raw material. Particularly, Liupao tea (50%) and Pu-erh tea (48%) showed promising hypolipidaemic potential; however, the antioxidant capacity of Pu-erh tea decreased (31-49%) most dramatically. Besides, the levels of total polyphenols and catechins decreased sharply, but theabrownin, gallic acid, and caffeine increased significantly after post-fermentation. Moreover, the potential mechanisms of regulating hyperlipidaemia by dark tea extracts were discussed. These results suggest that microbial fermentation significantly affects the bioactivity of dark teas, and provide theoretical basis for processing and improving of dark tea products for hyperlipidaemia therapy.\n\nHypolipidaemic and antioxidant effects of various Chinese dark tea extracts obtained from the same raw material and their main chemical components.", "token_count": 309, "char_count": 1271, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:52.251075", "source": { "split": "train_shard_00000", "doc_id": 2034 }, "chunk_id": "train_shard_00000_2034_0", "global_id": 2243 }, { "text": "Enterococcus faecalis is one of the probiotic groups in the intestinal tract which has varieties of functional effects in the host, such as a protective barrier, nutritional efficacy and antibacterial effects. Stress conditions such as low pH, bile salts, and hypertonicity are inevitable negative factors for the normal survival of E. faecalis in the gastrointestinal tract. Under the stress and inhibition of bile salt, E. faecalis needs specific adaptation and coping style if it wants to successfully colonize the intestine stably. The appropriate concentration of flavonoids can assist probiotics to serve a beneficial role and help them resist the stress of external irresistible environmental factors. In the present research, RNA-sequence (RNA-seq) technology was employed to investigate the influence of Cyclocarya paliurus flavonoids (CPF) on E. faecalis 131-2 (E. faecalis 131-2) exposed to bile salt stress. Analysis results revealed that under bile salt stress, many genes related to cellular process, catalytic activity and transport activity were significantly differentially expressed (P < 0·05), and some not expected variations of which could be partly alleviated by supplementation of CPF, indicating its capacity to improve the bile salt tolerances of E. faecalis 131-2. Additionally, CPF alleviated the obvious inhibitory effects of bile salt stress on the exponential growth of E. faecalis 131-2. An overall view of the physiological and transcriptomic changes of E. faecalis 131-2 under bile salt stresses with or without CPF will further deepen our understanding of the mechanism by which CPF assists E. faecalis 131-2 to perform beneficial functions in the gastrointestinal environment.\n\nAnalysis of Cyclocarya paliurus flavonoids modulation on the physiology and gene expression in Enterococcus faecalis under bile salt stress.", "token_count": 466, "char_count": 1853, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:52.892422", "source": { "split": "train_shard_00000", "doc_id": 2035 }, "chunk_id": "train_shard_00000_2035_0", "global_id": 2244 }, { "text": "Much attention has been recently paid to the health benefits of synbiotics, a combination of probiotics and prebiotics. In this study, synbiotics were prepared by combining lactic acid bacteria with potential as probiotics and purified glucooligosaccharides, and their immunostimulatory activity was evaluated using RAW 264.7 macrophage cells. A lactic acid bacteria strain with high antioxidant activity, acid and bile salt tolerance, adhesion to Caco-2 cells, and nitric oxide (NO) production was selected as a potential probiotic strain. The selected strain, isolated from forsythia, was identified as\n\nImmunostimulatory Activity of Synbiotics Using", "token_count": 166, "char_count": 652, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:53.336507", "source": { "split": "train_shard_00000", "doc_id": 2036 }, "chunk_id": "train_shard_00000_2036_0", "global_id": 2245 }, { "text": "Urinary tract infection (UTI) develops after a pathogen adheres to the inner lining of the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and account for high morbidity in the clinical and community settings. Of greater concern are the strains carrying antimicrobial resistance (AMR)-conferring genes. The gravity of a UTI is also determined by a spectrum of other virulence factors. This study represents a pilot project to investigate the burden of AMR among uropathogens in East Africa. We examined bacterial samples isolated in 2017-2018 from in- and out-patients in Kenya (KY) and Uganda (UG) that presented with clinical symptoms of UTI. We reconstructed the evolutionary history of the strains, investigated their population structure, and performed comparative analysis their pangenome contents. We found 55\n\nPan-Resistome Characterization of Uropathogenic", "token_count": 219, "char_count": 905, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7481, "quality_score": 0.874, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:53.801740", "source": { "split": "train_shard_00000", "doc_id": 2037 }, "chunk_id": "train_shard_00000_2037_0", "global_id": 2246 }, { "text": "Gram-negative Tripartite Resistance Nodulation and cell Division (RND) superfamily efflux pumps confer various functions, including multidrug and bile salt resistance, quorum-sensing, virulence and can influence the rate of mutations on the chromosome. Multidrug RND efflux systems are often characterized by a wide substrate specificity. Similarly to many other RND efflux pump systems, AcrAD-TolC confers resistance toward SDS, novobiocin and deoxycholate. In contrast to the other pumps, however, it in addition confers resistance against aminoglycosides and dianionic β-lactams, such as sulbenicillin, aztreonam and carbenicillin. Here, we could show that AcrD from\n\nCharacterization and Molecular Determinants for β-Lactam Specificity of the Multidrug Efflux Pump AcrD from", "token_count": 218, "char_count": 778, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7596, "quality_score": 0.8798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:54.261791", "source": { "split": "train_shard_00000", "doc_id": 2038 }, "chunk_id": "train_shard_00000_2038_0", "global_id": 2247 }, { "text": "When harmful bacteria are detected in the final product at a food manufacturing plant, it is necessary to identify and eliminate the source of contamination so that it does not occur again. In the current study, the source of contamination was tracked using core genome multilocus sequence typing (cgMLST) analysis in cases where Escherichia coli was detected in the final product at a food manufacturing plant. cgMLST analysis was performed on 40 strains of E. coli collected from the environment [floor (26 strains), drainage ditch (5 strains), container (4 strains), post-heating production line (1 strain)] and products [final product (3 strains) and intermediate product (1 strain)]. In total, 40 E. coli isolates were classified into 17 genogroups by cgMLST analysis. The 4 E. coli strains isolated from the intermediate and final products were classified into two genogroups (I and II). Certain isolates collected from the environment also belonged to those genogroups, it was possible to estimate the transmission of E. coli in the manufacturing plant. Thus, the dynamics of E. coli in the food manufacturing location were clarified by using cgMLST analysis. In conclusion, our results indicate that cgMLST analysis can be effectively used for hygiene management at food manufacturing locations.\n\nMolecular subtyping for source tracking of Escherichia coli using core genome multilocus sequence typing at a food manufacturing plant.", "token_count": 331, "char_count": 1440, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5273, "quality_score": 0.7636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:54.826592", "source": { "split": "train_shard_00000", "doc_id": 2039 }, "chunk_id": "train_shard_00000_2039_0", "global_id": 2248 }, { "text": "Hypercholesterolemia is a major risk factor for cardiovascular diseases worldwide. Healthy intestinal microbiota can contribute to reducing the high cholesterol symptoms by producing bile salt hydrolase (BSH). In this study, recombinant BSH from the strain\n\nCholesterol-lowering effect of bile salt hydrolase from a", "token_count": 83, "char_count": 315, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8605, "quality_score": 0.9302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:55.201321", "source": { "split": "train_shard_00000", "doc_id": 2040 }, "chunk_id": "train_shard_00000_2040_0", "global_id": 2249 }, { "text": "There is increased interest in strain engineering in the food and industrial yeast Kluyveromyces marxianus and a number of CRISPR/Cas9 systems have been described and used by different groups. The methods that we developed allow for very rapid and efficient inactivation of target genes using the endogenous DNA repair mechanisms of the cell. The strains and plasmids that we use are freely available, and here we provide a set of integrated protocols to easily inactivate genes and to precisely integrate DNA fragments into the genome, for example for promoter replacement, allelic swaps or introduction of point mutations. The protocols use the Cas9/gRNA expression plasmid pUCC001 and Golden Gate assembly for molecular cloning of targeting sequences. A genome-wide set of target sequences is provided. Using these plasmids in wild-type strains or in strains lacking non-homologous end-joining (NHEJ) DNA repair, the first set of protocols explain how to introduce indels (NHEJ-mediated) or precise deletions (homology-dependent repair (HDR)-mediated) at precise targets. The second set of protocols describe how to swap a promoter or coding sequence to yield a reprogrammed gene. The methods do not require the use of dominant or auxotrophic marker genes and thus the strains generated are marker-free. The protocols have been tested in multiple K. marxianus strains, are straightforward and can be carried out in any molecular biology laboratory without specialized equipment.\n\nProtocols for marker-free gene knock-out and knock-down in Kluyveromyces marxianus using CRISPR/Cas9.", "token_count": 372, "char_count": 1584, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6068, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:55.786938", "source": { "split": "train_shard_00000", "doc_id": 2041 }, "chunk_id": "train_shard_00000_2041_0", "global_id": 2250 }, { "text": "Lipopolysaccharide (LPS) clearance is delayed in cholestatic liver diseases. While compromised clearance by Kupffer cells (KCs) is involved, the role of LPS uptake into hepatocytes and canalicular excretion remains unclear.\n\nLoss of bile salt export pump aggravates lipopolysaccharide-induced liver injury in mice due to impaired hepatic endotoxin clearance.", "token_count": 105, "char_count": 358, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8958, "quality_score": 0.9479, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:56.171504", "source": { "split": "train_shard_00000", "doc_id": 2042 }, "chunk_id": "train_shard_00000_2042_0", "global_id": 2251 }, { "text": "Functional bowel disorders such as irritable bowel syndrome (IBS) are common, multifactorial and have a major impact on the quality of life of individuals diagnosed with the condition. Heterogeneity in symptom manifestation, which includes changes in bowel habit and visceral pain sensitivity, are an indication of the complexity of the underlying pathophysiology. It is accepted that dysfunctional gut-brain communication, which incorporates efferent and afferent branches of the peripheral nervous system, circulating endocrine hormones and local paracrine and neurocrine factors, such as host and microbially-derived signaling molecules, underpins symptom manifestation. This review will focus on the potential role of hepatic bile acids in modulating gut-to-brain signaling in IBS patients. Bile acids are amphipathic molecules synthesized in the liver, which facilitate digestion and absorption of dietary lipids. They are also important bioactive signaling molecules however, binding to bile acid receptors which are expressed on many different cell types. Bile acids have potent anti-microbial actions and thereby shape intestinal bacterial profiles. In turn, bacteria with bile salt hydrolase activity initiate the critical first step in transforming primary bile acids into secondary bile acids. Individuals with IBS are reported to have altered microbial profiles and modified bile acid pools. We have assessed the evidence to support a role for bile acids in the pathophysiology underlying the manifestation of IBS symptoms.\n\nAberrant Gut-To-Brain Signaling in Irritable Bowel Syndrome - The Role of Bile Acids.", "token_count": 386, "char_count": 1622, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6201, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:56.792048", "source": { "split": "train_shard_00000", "doc_id": 2043 }, "chunk_id": "train_shard_00000_2043_0", "global_id": 2252 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) is one of the most frequent bacterial agents associated with food-borne outbreaks in Europe. In humans, the infection can lead to life-threatening diseases. Domestic and wild animals can harbor STEC, and ruminants are the main STEC reservoirs, although asymptomatic. In the present study we have characterized STEC from wildlife (wild boar (n = 56), red deer (n = 101), red fox (n = 37) and otter (n = 92)). Cultivable STEC (n = 52) were isolated from 17% (n = 49) of the faecal samples. All the isolates were non-O157 STEC encoding stx1 (n = 2; 4%) and/or stx2 genes (n = 51; 98%). Only one strain (2%) isolated from red fox had an antibiotic resistant phenotype. However, when the normalized resistance interpretation of epidemiological cutoffs (NRI ECOFFs) were used, 23% (n = 12) of the strains were non-wildtype to at least one of the antibiotics tested. After analysis by pulsed-field gel electrophoresis (PFGE), 20 strains were selected for whole genome sequencing and belonged to the following serotypes: O27:H30 (n = 15), O146:H28 (n = 2), O146:H21 (n = 1), O178:H19 (n = 1), and O103:H2 (n = 1). In addition to stx, all strains encode several virulence factors such as toxins, adhesins, fimbriae and secretion systems, among others. All sequenced genomes carried several mobile genetic elements (MGEs), such as prophages and/or plasmids. The core genome and the phylogenetic analysis showed close evolutionary relationships between some of the STEC recovered from wildlife and strains of clinical origin, highlighting their pathogenic potential", "token_count": 516, "char_count": 1600, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:18:57.445343", "source": { "split": "train_shard_00000", "doc_id": 2044 }, "chunk_id": "train_shard_00000_2044_0", "global_id": 2253 }, { "text": "Overall, our results show the zoonotic potential of STEC strains originating from wildlife, highlighting the importance of monitoring their genomic characteristics following a One Health perspective, in which the health of humans is related to the health of animals, and the environment.\n\nPathogenicity of Shiga toxin-producing Escherichia coli (STEC) from wildlife: Should we care?", "token_count": 86, "char_count": 382, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:57.824067", "source": { "split": "train_shard_00000", "doc_id": 2044 }, "chunk_id": "train_shard_00000_2044_1", "global_id": 2254 }, { "text": "We introduce Giraffe, a pangenome short-read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe maps sequencing reads to thousands of human genomes at a speed comparable to that of standard methods mapping to a single reference genome. The increased mapping accuracy enables downstream improvements in genome-wide genotyping pipelines for both small variants and larger structural variants. We used Giraffe to genotype 167,000 structural variants, discovered in long-read studies, in 5202 diverse human genomes that were sequenced using short reads. We conclude that pangenomics facilitates a more comprehensive characterization of variation and, as a result, has the potential to improve many genomic analyses.\n\nPangenomics enables genotyping of known structural variants in 5202 diverse genomes.", "token_count": 196, "char_count": 851, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7025, "quality_score": 0.8512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:58.277840", "source": { "split": "train_shard_00000", "doc_id": 2045 }, "chunk_id": "train_shard_00000_2045_0", "global_id": 2255 }, { "text": "Clostridioides difficile is the most common cause of antibiotic-associated gastrointestinal infections. Capillary electrophoresis (CE)-PCR ribotyping is currently the gold standard for C. difficile typing but lacks the discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better and provide standardized and interlaboratory exchangeable data. Using a well-characterized collection of diverse strains (N = 630; 100 unique ribotypes [RTs]), we compared the discriminatory power of core genome multilocus sequence typing (cgMLST) (SeqSphere and EnteroBase), whole-genome MLST (wgMLST) (EnteroBase), and single-nucleotide polymorphism (SNP) analysis. A unique cgMLST profile (more than six allele differences) was observed in 82 of 100 RTs, indicating that cgMLST could distinguish most, but not all, RTs. Application of cgMLST in two outbreak settings with RT078 and RT181 (known to have low intra-RT allele differences) showed no distinction between outbreak and nonoutbreak strains in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize, and offers higher discrimination. However, adjusted cutoff thresholds and epidemiological data are necessary to recognize outbreaks of some specific RTs. We propose to use an allelic threshold of three alleles to identify outbreaks.\n\nComparison of Whole-Genome Sequence-Based Methods and PCR Ribotyping for Subtyping of Clostridioides difficile.", "token_count": 420, "char_count": 1572, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [ "RT078", "RT181" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:58.900789", "source": { "split": "train_shard_00000", "doc_id": 2046 }, "chunk_id": "train_shard_00000_2046_0", "global_id": 2256 }, { "text": "Kluyveromyces marxianus is a promising cell factory for producing bioethanol and that raised a demand for a high yield of heterologous proteins in this species. Expressions of heterologous proteins usually lead to the accumulation of misfolded or unfolded proteins in the lumen of the endoplasmic reticulum (ER) and then cause ER stress. To cope with this problem, a group of ER stress response target genes (ESRTs) are induced, mainly through a signaling network called unfolded protein response (UPR). Characterization and modulation of ESRTs direct the optimization of heterologous expressions. However, ESRTs in K. marxianus have not been identified so far.\n\nCharacterization and modulation of endoplasmic reticulum stress response target genes in Kluyveromyces marxianus to improve secretory expressions of heterologous proteins.", "token_count": 201, "char_count": 834, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:59.361254", "source": { "split": "train_shard_00000", "doc_id": 2047 }, "chunk_id": "train_shard_00000_2047_0", "global_id": 2257 }, { "text": "Kluyveromyces marxianus is a potentially excellent host for microbial cell factories using lignocellulosic biomass, due to its thermotolerance, high growth rate, and wide substrate spectrum. However, its tolerance to inhibitors derived from lignocellulosic biomass pretreatment needs to be improved. The prefoldin complex assists the folding of cytoskeleton which relates to the stress tolerance, moreover, several subunits of prefoldin have been verified to be involved in gene expression regulation. With the presence of inhibitors, the expression of a gene coding the subunit 4 of prefoldin (KmPFD4), a possible transcription factor, was significantly changed. Therefore, KmPFD4 was selected to evaluate its functions in inhibitors tolerance.\n\nInfluence of prefoldin subunit 4 on the tolerance of Kluyveromyces marxianus to lignocellulosic biomass-derived inhibitors.", "token_count": 220, "char_count": 870, "word_count": 118, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:18:59.830429", "source": { "split": "train_shard_00000", "doc_id": 2048 }, "chunk_id": "train_shard_00000_2048_0", "global_id": 2258 }, { "text": "Since the first reported crop pangenome in 2014, advances in high-throughput and cost-effective DNA sequencing technologies facilitated multiple such studies including the pangenomes of oilseed rape (Brassica napus L.), soybean [Glycine max (L.) Merr.], rice (Oryza sativa L.), wheat (Triticum aestivum L.), and barley (Hordeum vulgare L.). Compared with single-reference genomes, pangenomes provide a more accurate representation of the genetic variation present in a species. By combining the genomic data of multiple accessions, pangenomes allow for the detection and annotation of complex DNA polymorphisms such as structural variations (SVs), one of the major determinants of genetic diversity within a species. In this review we summarize the current literature on crop pangenomics, focusing on their application to find candidate SVs involved in traits of agronomic interest. We then highlight the potential of pangenomes in the discovery and functional characterization of noncoding regulatory sequences and their variations. We conclude with a summary and outlook on innovative data structures representing the complete content of plant pangenomes including annotations of coding and noncoding elements and outcomes of transcriptomic and epigenomic experiments.\n\nPangenomics in crop improvement-from coding structural variations to finding regulatory variants with pangenome graphs.", "token_count": 302, "char_count": 1391, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:00.393408", "source": { "split": "train_shard_00000", "doc_id": 2049 }, "chunk_id": "train_shard_00000_2049_0", "global_id": 2259 }, { "text": "Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants' chromosome structures, gene identification and annotation. The published genomes of agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specific for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants' pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described.\n\nCrop pangenomes.", "token_count": 281, "char_count": 1443, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5941, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:00.961160", "source": { "split": "train_shard_00000", "doc_id": 2050 }, "chunk_id": "train_shard_00000_2050_0", "global_id": 2260 }, { "text": "Until 2019, the human genome was available in only one fully annotated version, GRCh38, which was the result of 18 years of continuous improvement and revision. Despite dramatic improvements in sequencing technology, no other genome was available as an annotated reference until 2019, when the genome of an Ashkenazi individual, Ash1, was released. In this study, we describe the assembly and annotation of a second individual genome, from a Puerto Rican individual whose DNA was collected as part of the Human Pangenome project. The new genome, called PR1, is the first true reference genome created from an individual of African descent. Due to recent improvements in both sequencing and assembly technology, and particularly to the use of the recently completed CHM13 human genome as a guide to assembly, PR1 is more complete and more contiguous than either GRCh38 or Ash1. Annotation revealed 37,755 genes (of which 19,999 are protein coding), including 12 additional gene copies that are present in PR1 and missing from CHM13. Fifty-seven genes have fewer copies in PR1 than in CHM13, 9 map only partially, and 3 genes (all noncoding) from CHM13 are entirely missing from PR1.\n\nA reference-quality, fully annotated genome from a Puerto Rican individual.", "token_count": 318, "char_count": 1258, "word_count": 200, "semantic_coherence": 1, "information_density": 0.585, "quality_score": 0.7925, "entities": { "genes": [ "CHM13", "PR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:01.862366", "source": { "split": "train_shard_00000", "doc_id": 2051 }, "chunk_id": "train_shard_00000_2051_0", "global_id": 2261 }, { "text": "Citrus pectins were studied by enzymatic fingerprinting using a simultaneous enzyme treatment with endo-polygalacturonase (endo-PG) from Kluyveromyces fragilis and pectin lyase (PL) from Aspergillus niger to reveal the methyl-ester distribution patterns over the pectin backbone. Using HILIC-MS combined with HPAEC enabled the separation and identification of the diagnostic oligomers released. Structural information on the pectins was provided by using novel descriptive parameters such as degree of blockiness of methyl-esterified oligomers by PG (DB\n\nRevealing methyl-esterification patterns of pectins by enzymatic fingerprinting: Beyond the degree of blockiness.", "token_count": 171, "char_count": 668, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:02.312598", "source": { "split": "train_shard_00000", "doc_id": 2052 }, "chunk_id": "train_shard_00000_2052_0", "global_id": 2262 }, { "text": "[This corrects the article DOI: 10.1371/journal.pcbi.1007732.].\n\nCorrection: PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.", "token_count": 61, "char_count": 153, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:02.714050", "source": { "split": "train_shard_00000", "doc_id": 2053 }, "chunk_id": "train_shard_00000_2053_0", "global_id": 2263 }, { "text": "Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological processes that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of this ecosystem. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (~15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (noncore) genes were isolate-specific and showed low in situ abundances based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or transient, 3.5% of them became abundant when salinity (but not light) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results provide an explanation for how this immense intrapopulation gene diversity is maintained, which has implications for the prokaryotic species concept.\n\nToward quantifying the adaptive role of bacterial pangenomes during environmental perturbations.", "token_count": 333, "char_count": 1556, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7251, "quality_score": 0.8626, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:03.292031", "source": { "split": "train_shard_00000", "doc_id": 2054 }, "chunk_id": "train_shard_00000_2054_0", "global_id": 2264 }, { "text": "Developing an effective method to improve the quality of Pu-erh tea is of great scientific and commercial interest. In this work, Penicillium chrysogenum P1 isolated from Pu-erh tea was inoculated in sterilized or unsterilized sun-dreid green tea leaves to develop pure-culture fermentation (PF) and enhanced fermentation (EF) of Pu-erh tea. Spectrophotometry and high performance liquid chromatography determined that contents of free amino acids (FAA), total tea polyphenols and eight polyphenolic compounds in PF were significantly lower than these in non-inoculation control test (CK) (P < 0.05), whereas the contents of soluble sugars and theabrownins (TB) in PF were significantly higher (P < 0.05) than in CK. A total of 416 volatile compounds were detected by headspace solid-phase micro-extraction combined with gas chromatography-mass spectrometry. Comparison to CK, 124 compounds in PF were degraded or decreased significantly [Variable importance in projection [(VIP) > 1.0, P < 0.05, fold change (FC) < 0.5], whereas 110 compounds in PF were formed or increased significantly (VIP > 1.0, P < 0.05, FC > 2). Compared with normal fermentation (NF), the levels of gallic acid, (+)-catechin, (-)-epicatechin and 64 volatile compounds in EF were significantly lower (VIP > 1.0, P < 0.05, FC < 0.5), whereas the levels of FAA and 39 volatile compounds were significantly higher (VIP > 1.0, P < 0.05, FC > 2). Amplicon sequencing of fungal internal transcribed spacer 1 (ITS1) revealed that P", "token_count": 466, "char_count": 1498, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:03.967688", "source": { "split": "train_shard_00000", "doc_id": 2055 }, "chunk_id": "train_shard_00000_2055_0", "global_id": 2265 }, { "text": "chrysogenum P1 didn't become the dominant fungus in EF; while the fungal communities in EF were different from those in NF, in that the relative abundances of Blastobotrys bambusae and P. chrysogenum in EF were higher, and the relative abundances of Aspergillus niger and Kluyveromyces marxianus in EF were lower. Overall, inoculation of P. chrysogenum in unsterilized sun-dreid green tea leaves changed the the fungal communities in fermentation of Pu-erh tea, and chemical compounds in fermented tea leaves, i.e., the levels of TB and the compounds responsible for the stale flavor, e.g., 2-amino-4-methoxybenzothiazole were increased, resulting in improvement of the sensory quality, including mellower taste and stronger stale flavor.\n\nEffect of inoculation with Penicillium chrysogenum on chemical components and fungal communities in fermentation of Pu-erh tea.", "token_count": 242, "char_count": 867, "word_count": 126, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:04.473433", "source": { "split": "train_shard_00000", "doc_id": 2055 }, "chunk_id": "train_shard_00000_2055_1", "global_id": 2266 }, { "text": "Probiotics are considered as functional food as they provide health benefits along with traditional nutrition. Spore forming probiotic Bacillus are of commercial interest than Lactic Acid Bacillus due to their relatively lower cost of production and higher survivability. In the present study we identified the bacterial strain SDG14 isolated from Indian oil Sardine by Average Nucleotide Identity of whole genome sequence. The whole genome of SDG14 was also explored for pathogenicity, the presence of genes responsible for probiotic traits such as spore formation, resistance to host gastrointestinal tract conditions, adhesion to intestinal mucosa, interference in pathogen survival, expression of bacteriocins, oxidative and other stress responses, absorption of nutrition, production of essential amino acids and vitamins. Wet lab experiments for probiotic characterization were also conducted. The organism was confirmed to be Bacillus safensis SDG14. The possible pathogenicity of the organism was also ruled out by in silico analysis. Bacillus safensis SDG14 was able to survive at pH 3 and bile salt concentration of 0.5% (w/v). The adhesion index of Bacillus safensis SDG14 on HEp-2 was 36.82 ± 5.93 and 45.54 ± 9.55 respectively after 60 and 90 min of incubation and self aggregation percentage was 18.4 ± 0.48% after 3 h. Bacillus safensis SDG14 produced bacteriocin and co-aggregated with E. coli, Salmonella Typhimurium and Pseudomonas aeruginosa. The genomic data supported the findings of wet lab study and vice versa. Bacillus safensis SDG14 was proved to be a non-pathogenic, spore forming, pH and bile salt resistant, bacteriocin, amino acid and vitamin producing probiotic with proposed food and feed applications.\n\nIndian oil sardine (Sardinella longiceps) gut derived Bacillus safensis SDG14 with enhanced probiotic competence for food and feed applications.", "token_count": 513, "char_count": 1880, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [ "SDG14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:19:05.133911", "source": { "split": "train_shard_00000", "doc_id": 2056 }, "chunk_id": "train_shard_00000_2056_0", "global_id": 2267 }, { "text": "The aim of this study is the consolidated bioprocessing of lactose into lactic acid and ethanol using non-engineered Cell Factories (CFs). Therefore, two different types of composite biocatalysts (CF1-CF2) based on Saccharomyces cerevisiae with immobilized microorganism or enzyme on starch gel (SG) were prepared for 5% w/v lactose fermentation. In CF1, S. cerevisiae was covered with SG containing Lactobacillus casei, Lactobacillus bulgaricus, Kluyveromyces marxianus CF1a-c. S. cerevisiae/SG-β-galactosidase (CF1d) was also used for simultaneous saccharification and fermentation (SSF) of lactose. In CF2, S. cerevisiae immobilized on tubular cellulose (TC) was covered with SG containing the aforementioned microorganisms (CF2a-c). The wet CF1d resulted in 96% of the theoretical ethanol yield while the wet CF1b and freeze-dried CF2b resulted in 89% of the theoretical lactic acid yield. The repeated batches using the CF2a-c exhibited better results than using CF1a-c. Subsequently, the freeze-dried CF2 as preservative and more manageable were verified for future exploitation of whey.\n\nConsolidated bioprocessing of lactose into lactic acid and ethanol using non-engineered cell factories.", "token_count": 365, "char_count": 1198, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6242, "quality_score": 0.8121, "entities": { "genes": [ "CF2", "CF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:05.723052", "source": { "split": "train_shard_00000", "doc_id": 2057 }, "chunk_id": "train_shard_00000_2057_0", "global_id": 2268 }, { "text": "To understand the reasons of successful spread of carbapenem-resistant Klebsiella pneumoniae ST14 (CRKP-ST14) in countries of the Arabian Peninsula, the resistome, capsular locus, carbapenemase carrying plasmid types, and core genome of isolates from the region were compared to global isolates. Thirty-nine CRKP-ST14 strains isolated from 13 hospitals in the United Arab Emirates, Bahrain, and Saudi Arabia were selected for whole genome sequencing on Illumina MiSeq platform based on the variety of carbapenemase genes carried and plasmids bearing these genes. Their resistome, capsular locus, and core genome MLST were compared to 173 CRKP-ST14 genomes available in public databases. The selected 39 CRKP-ST14 produced either NDM-1, OXA-48, OXA-162, OXA-232, KPC-2, or co-produced NDM-1 and an OXA-48-like carbapenemase. cgMLST revealed three clusters: 16 isolates from five UAE cities (C1), 11 isolates from three UAE cities and Bahrain (C2), and 5 isolates from Saudi Arabia (C3), respectively, and seven singletons. Resistance gene profile, carbapenemase genes, and their plasmid types were variable in both C1 and C2 clusters. The majority of CRKP-ST14 had KL2, but members of the C2 cluster and two further singletons possessed KL64 capsular locus. Based on cgMLST comparison of regional and global isolates, CRKP-ST14 with KL64 from four continents formed a distinct cluster, suggesting a recent emergence and spread of this variant. Our findings confirmed clonal transmission coupled with likely horizontal gene transfer in carbapenem-resistant Klebsiella pneumoniae ST14. Dissemination of this genetically flexible, highly resistant clone warrants further monitoring.", "token_count": 486, "char_count": 1678, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "KL2", "KL64", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:06.373423", "source": { "split": "train_shard_00000", "doc_id": 2058 }, "chunk_id": "train_shard_00000_2058_0", "global_id": 2269 }, { "text": "Diversity of carbapenem-resistant Klebsiella pneumoniae ST14 and emergence of a subgroup with KL64 capsular locus in the Arabian Peninsula.", "token_count": 45, "char_count": 139, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [ "KL64", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:06.733163", "source": { "split": "train_shard_00000", "doc_id": 2058 }, "chunk_id": "train_shard_00000_2058_1", "global_id": 2270 }, { "text": "The increase of concentrations of total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) in the serum of postmenopausal women is the important risk factor of the high morbidity of cardiovascular diseases of old women worldwide. To test the anti-hypercholesterolemia function of dihydroartemisinin (DHA) in postmenopausal women, ovariectomized (OVX) mice were generated, and DHA were administrated to OVX mice for 4 weeks. The blood and liver tissues were collected for biochemical and histological tests respectively. The mRNA and protein expression levels of genes related to metabolism and transport of cholesterol, bile acid and fatty acid in the liver or ileum were checked through qPCR and western blot. DHA could significantly reduce the high concentrations of TC and LDL-C in the serum and the lipid accumulation in the liver of ovariectomized mice. The expression of ABCG5/8 was reduced in liver of OVX mice, and DHA could up-regulate the expression of them. Genes of transport proteins for bile salt transport from blood to bile, including Slc10a1, Slco1b2 and Abcb11, were also significantly up-regulated by DHA. DHA also down-regulated the expression of Slc10a2 in the ileum of OVX mice to reduce the absorption of bile salts. Genes required for fatty acid synthesis and uptake, such as Fasn and CD36, were reduced in the liver of OVX mice, and DHA administration could significantly up-regulate the expression of them. These results demonstrated that DHA could improve hypercholesterolemia in OVX mice through enhancing the vectorial transport of cholesterol and bile acid from blood to bile.\n\nDihydroartemisinin improves hypercholesterolemia in ovariectomized mice via enhancing vectorial transport of cholesterol and bile acids from blood to bile.", "token_count": 500, "char_count": 1777, "word_count": 267, "semantic_coherence": 1, "information_density": 0.4494, "quality_score": 0.7247, "entities": { "genes": [ "CD36", "ABCG5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:07.384742", "source": { "split": "train_shard_00000", "doc_id": 2059 }, "chunk_id": "train_shard_00000_2059_0", "global_id": 2271 }, { "text": "RESEARCH HIGHLIGHTSPan-RV analysis was used for the first time in the discovery of APEC-protective proteins.A total of 53 potential protective proteins were screened out.Four proteins were verified as potential vaccine candidates using western blotting.\n\nCombining pangenome analysis to identify potential cross-protective antigens against avian pathogenic", "token_count": 88, "char_count": 356, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8444, "quality_score": 0.9222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:07.758701", "source": { "split": "train_shard_00000", "doc_id": 2060 }, "chunk_id": "train_shard_00000_2060_0", "global_id": 2272 }, { "text": "In this study, hydrostatic high-pressure processing (HHP), a non-thermal pasteurisation method, was used to achieve the microbiological safety of donor human milk. After HHP, no bacteria were detected in human milk processed at 400 MPa for 5 min. Activities of a selection of bioactive components, including lysozyme, xanthine oxidase, lactoperoxidase, immunoglobulin A, lactoferrin, lipoprotein lipase and bile salt-stimulated lipase, did not decrease significantly. This study further investigated the gastrointestinal digestion kinetics of HoP and HHP milk compared with raw human milk, using an in vitro static infant digestion model. After 60 min of 'gastric digestion', the microstructure and protein profile of HHP milk samples were more similar to raw milk samples than HoP milk samples. Overall, HPP showed a better retention in milk nutrients and closer digestion behavior than that of HoP.\n\nComparing the effects of hydrostatic high-pressure processing vs holder pasteurisation on the microbial, biochemical and digestion properties of donor human milk.", "token_count": 273, "char_count": 1064, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6928, "quality_score": 0.8464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:08.319163", "source": { "split": "train_shard_00000", "doc_id": 2061 }, "chunk_id": "train_shard_00000_2061_0", "global_id": 2273 }, { "text": "To explore the reparative effects of DHA on the gut microbiome disturbance and dysfunctional lipid metabolism caused by long-term antibiotic therapy, it was tested on an azithromycin (AZI) mouse antibiotic model. Thirty specific-pathogen-free BALB/c mice (SPF grade, half male and half female) were randomly separated into three groups (n = 10, 5 male and 5 female): control group (CK), azithromycin natural recovery group (AZI) and DHA group (DHA). High-throughput sequencing and bioinformatics methods were used to analyze the gut microbiome. ELASE kits were used to measure blood lipid, lipids in the liver, and bile salt hydrolase (BSH) levels in feces. Gas chromatography and UPLC-MS/MS were employed to detect DHA and bile acids contents in liver, respectively. Real-time polymerase chain reaction (RT-PCR) was used to measure the expression of key enzymes involved in lipid metabolism. Long-term AZI treatment led to dyslipidemia, gut microbiome disturbance and anxious behaviors in the mouse model. DHA was found to significantly improve the dyslipidemia and anxiety-like behaviors induced by AZI. DHA had no effect on the structure of gut microbiome and bile acids contents but increased the content of the metabolic enzyme BSH in gut microbiota and normalized the expression of enzymes involved in lipid metabolism.\n\nEvaluating the reparative effects and the mechanism of action of docosahexaenoic acid on azithromycin-induced lipid metabolism dysfunction.", "token_count": 400, "char_count": 1466, "word_count": 217, "semantic_coherence": 1, "information_density": 0.576, "quality_score": 0.788, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:08.932320", "source": { "split": "train_shard_00000", "doc_id": 2062 }, "chunk_id": "train_shard_00000_2062_0", "global_id": 2274 }, { "text": "We studied whether probiotics were beneficial for hormonal change-associated dysbiosis, which may influence the enteric nervous system and GI function during early pregnancy. The study was 16 days consisting of two cycles of six daily probiotics mainly\n\nProbiotics Improve Gastrointestinal Function and Life Quality in Pregnancy.", "token_count": 77, "char_count": 329, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8478, "quality_score": 0.9239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:09.309042", "source": { "split": "train_shard_00000", "doc_id": 2063 }, "chunk_id": "train_shard_00000_2063_0", "global_id": 2275 }, { "text": "Whey is the main byproduct of the dairy industry and contains sugars (lactose) and proteins (especially serum proteins and, at lesser extent, residual caseins), which can be valorized by the fermentative action of yeasts. In the present study, we characterized the spoilage yeast population inhabiting natural whey starter (NWS), the undefined starter culture of thermophilic lactic acid bacteria used in Parmigiano Reggiano (PR) cheesemaking, and evaluated thermotolerance, mating type, and the aptitude to produce ethanol and bioactive peptides from whey lactose and proteins, respectively, in a selected pool of strains. PCR-RFLP assay of ribosomal ITS regions and phylogenetic analysis of 26S rDNA D1/D2 domains showed that PR NWS yeast population consists of the well-documented\n\nCharacterization of Yeasts Isolated from Parmigiano Reggiano Cheese Natural Whey Starter: From Spoilage Agents to Potential Cell Factories for Whey Valorization.", "token_count": 257, "char_count": 946, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7259, "quality_score": 0.863, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:09.857809", "source": { "split": "train_shard_00000", "doc_id": 2064 }, "chunk_id": "train_shard_00000_2064_0", "global_id": 2276 }, { "text": "The quality control of probiotic products is the focus of numerous organizations worldwide. Several studies have highlighted the poor microbiological quality of many commercial probiotic formulations in terms of the identity of the contained microorganisms, viability, and purity, thus precluding the expected health benefits and representing a potential health risk for consumers. In this paper, we analyzed the contents of two probiotic formulations, one composed of an encapsulated mixture of lactobacilli and bifidobacteria, and one by a lyophilized yeast. The microorganisms contained in the products were quantified and identified using up-to-date methodologies, such as MALDI-TOF MS and metagenomic analysis. Moreover, as acid and bile tolerance is included among the criteria used to select probiotic microorganisms, in vitro tests were performed to evaluate the behavior of the formulations in conditions mimicking the harsh gastric environment and the intestinal fluids. Our results indicate the high quality of the formulations in terms of the enumeration and identification of the contained organisms, as well as the absence of contaminants. Moreover, both products tolerated the acidic conditions well, with encapsulation providing further protection for the microorganisms. A good tolerance to the simulated artificial intestinal conditions was also evidenced for both preparations.\n\nMicrobiological Quality and Resistance to an Artificial Gut Environment of Two Probiotic Formulations.", "token_count": 318, "char_count": 1500, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:10.419554", "source": { "split": "train_shard_00000", "doc_id": 2065 }, "chunk_id": "train_shard_00000_2065_0", "global_id": 2277 }, { "text": "1. OATP1A2 overexpressed is involved in chemotherapy disposition, indicating its role in tumour development and progression.2. CHIP and siRNA were used to evaluate the status of histone acetylation at the OATP1A2 promoter. The role of OATP1A2 was analysed by gene-set enrichment and overall survival analysis.3. OATP1A2 expression levels in ESCC was notably higher than that in para-cancer tissues. OATP1A2 high expression are associated with bile salt metabolic pathway and poor prognosis. Furthermore, HDAC6 was repressed in ESCC, increasing the levels of H3K9Ac catalysed by GCN5/PCAF at the OATP1A2 promoter region.4. Abnormal histone hyperacetylation mediated by the HDAC6-GCN5/PCAF-H3K9Ac axis resulted in increased OATP1A2 expression in ESCC, and OATP1A2 may serve as a promising prognostic biomarker for ESCC.5. In conclusion, this study indicated that suppression of OATP1A2 would inhibit the progression and prognosis in ESCC.\n\nUpregulation of OATP1A2 in human oesophageal squamous cell carcinoma cells via the HDAC6-GCN5/PCAF-H3K9Ac axis.", "token_count": 332, "char_count": 1049, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6803, "quality_score": 0.8401, "entities": { "genes": [ "HDAC6", "GCN5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:10.982112", "source": { "split": "train_shard_00000", "doc_id": 2066 }, "chunk_id": "train_shard_00000_2066_0", "global_id": 2278 }, { "text": "Acetobacter senegalensis belongs to the group of acetic acid bacteria (AAB) that present potential biotechnological applications, for production of D-gluconate, cellulose and acetic acid. AAB can overcome heat and acid stresses by using strategies involving the overexpression of heat-shock proteins and enzymes from the complex pyrroquinoline-ADH, besides alcohol dehydrogenases (ADH). Nonetheless, the isolation of A. senegalensis and other AAB from food may be challenging due to presence of viable but non-culturable (VBNC) cells and due to uncertainties about nutritional requirements. To contribute for a better understanding of the ecology of AAB, this paper reports on the pangenome analysis of five strains of A. senegalensis recently isolated from a Brazilian spontaneous cocoa fermentation. The results showed biosynthetic clusters exclusively found in some cocoa-related AAB, such as those related to terpene pathways, which are important for flavour development. Genes related to oxidative stress were conserved in all the genomes, with multiple clusters. Moreover, there were genes coding for ADH and putative ABC transporters distributed in core, shell and cloud genomes, while chaperonin-encoding genes were present only in the core and soft-core genomes. Regarding quorum sensing, a response regulator gene was in the shell genome, and the gene encoding for acyl-homoserine lactone efflux protein was in the soft-core genome. There were quorum quenching-related genes, mainly encoding for lactonases, but also for acylases. Moreover, A. senegalensis did not have determinants of virulence or antibiotic resistance, which are good traits for strains intended to be applied in food fermentation.\n\nComparative pangenomic analyses and biotechnological potential of cocoa-related Acetobacter senegalensis strains.", "token_count": 450, "char_count": 1825, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6431, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:11.621679", "source": { "split": "train_shard_00000", "doc_id": 2067 }, "chunk_id": "train_shard_00000_2067_0", "global_id": 2279 }, { "text": "Polycyclic aromatic hydrocarbons (PAHs) are hazardous pollutants that are ubiquitous in the environment. Numerous bacteria have evolved to have degrading genes or pathways to degrade PAHs. Stenotrophomonas maltophilia strain W18 was found to be able to degrade PAHs. Including 43 other complete genome sequences of S. maltophilia strains, we performed a comparative genomic analysis of 44 S. maltophilia strains by running OrthoFinder. A KEGG pathway enrichment analysis of environmental and clinical isolates of S. maltophilia revealed that environmental isolates tended to enhance gene functions such as \"energy metabolism,\" \"amino acid metabolism,\" \"xenobiotic biodegradation and metabolism,\" and \"folding, sorting, and degradation.\" The pangenome of the 44 S. maltophilia strains was open, while the core genome was estimated to reach a steady plateau. Based on gene annotations, we inferred that most of the degradation potential came from the core genome of S. maltophilia, while character genes and accessory genes also contributed to the degradation ability of S. maltophilia W18. The genes expression level of core genes, character genes and accessory genes were proved by RT-qPCR experiment, and accessory genes encoding alcohol dehydrogenase were upregulated most compared with genes with similar functions. We performed a credible comparative genomic analysis of S. maltophilia strains. S. maltophilia W18 was set as a model PAH-degrading bacterium of this species in this study, which would provide guidance for understanding and predicting the degradation mechanisms of other PAH-degrading S. maltophilia strains lacking complete genome data or waiting to be determined.\n\nComparative Genomic Analysis of Stenotrophomonas maltophilia Strain W18 Reveals Its Adaptative Genomic Features for Degrading Polycyclic Aromatic Hydrocarbons.", "token_count": 481, "char_count": 1845, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5346, "quality_score": 0.7673, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:12.271472", "source": { "split": "train_shard_00000", "doc_id": 2068 }, "chunk_id": "train_shard_00000_2068_0", "global_id": 2280 }, { "text": "Pseudomonas aeruginosa is an opportunistic human pathogen and a major cause of nosocomial infections. The global spread of carbapenem-resistant strains is growing rapidly and has become a major public health challenge. Imipenem-relebactam (I/R) is a novel carbapenem-beta-lactamase inhibitor combination that can overcome carbapenem resistance. In this study, we aimed to understand the mechanism underlying resistance to imipenem and imipenem-relebactam. For this purpose, we performed a genomic comparison of 40 new clinical P. aeruginosa strains with different antibiotic sensitivity patterns as well as the presence/absence of carbapenemases. Results indicated the presence of a reduced flexible genome (15% total) mostly represented by phages and defense mechanisms against them, showing an important role in evolution and pathogenicity. We found a high diversity of antibiotic resistance genes grouped in small clusters mobilized via integrative and conjugative elements and facilitated by the high homologous recombination detected. Ortholog genes were found in several pathogenic strains from distantly related taxa in different mobile elements with a global distribution. The microdiversity found in those strains without carbapenemases did not reveal a clear pattern that could be associated with carbapenem resistance, suggesting multiple mechanisms of resistance in the core genome. Our results provide new insight into the dynamics and high genomic plasticity by which clinical strains of P. aeruginosa acquire resistance. This knowledge can be applied to other multidrug-resistant microbes to create predictive frameworks for assessing common molecular mechanisms of antibiotic resistance and integrated into new strategies for their prevention.\n\nGenomic Characterization of Imipenem- and Imipenem-Relebactam-Resistant Clinical Isolates of Pseudomonas aeruginosa.", "token_count": 424, "char_count": 1877, "word_count": 252, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:12.896396", "source": { "split": "train_shard_00000", "doc_id": 2069 }, "chunk_id": "train_shard_00000_2069_0", "global_id": 2281 }, { "text": "With the release of high-quality reference genomes assembled by long reads from the third-generation sequencing technology, as well as extensive re-sequencing and population genetic analysis, researchers found that a single reference genome does not represent the diversity within a species. The missing sequences on the reference genome result in an incomplete population genetic polymorphism map. The emergence of pan-genome can well repair the deficiency of single reference genome, which include core genome (responsible for basic biological functions and the main phenotypic characteristics within a species) and the variable genome (related to the genetic diversity or biological characteristics). According to the core and variable genome proportion, the types of pan-genomes can be either open or closed. Here, we review the current exploring of pan-genome for a range of species, to discuss the characteristics of pan-genome in various biological groups. The pan-genome of mammals are more likely closed, while the pan-genomes of microbes, angiosperms, and some invertebrates are likely non-closed. It is possible to complete the reference genome and obtain complete variation information through the pan-genomic study, which will contribute to the study of molecular mechanism for genetic diversity and phenotypic evolution.\n\nPan-genome: setting a new standard for high-quality reference genomes.", "token_count": 291, "char_count": 1406, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5879, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:13.463909", "source": { "split": "train_shard_00000", "doc_id": 2070 }, "chunk_id": "train_shard_00000_2070_0", "global_id": 2282 }, { "text": "Hemicellulose acts as one factor contributing to the recalcitrance of lignocellulose that prevents cellulases to degrade the cellulose efficiently even in low quantities. Supplement of hemicellulases can enhance the performance of commercial cellulases in the enzymatic hydrolyses of lignocellulose. Kluyveromyce marxianus is an attractive yeast for cellulosic ethanol fermentation, as well as a promising host for heterologous protein production, since it has remarkable thermotolerance, high growth rate, and broad substrate spectrum etc. In this study, we attempted to coordinately express multiple hemicellulases in K. marxianus through a 2A-mediated ribosome skipping to self-cleave polyproteins, and investigated their capabilities for saccharification and ethanol production from corncobs.\n\nCoordinately express hemicellulolytic enzymes in Kluyveromyces marxianus to improve the saccharification and ethanol production from corncobs.", "token_count": 239, "char_count": 940, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:13.930454", "source": { "split": "train_shard_00000", "doc_id": 2071 }, "chunk_id": "train_shard_00000_2071_0", "global_id": 2283 }, { "text": "miRNA-223 has been previously reported to play an essential role in hepatic cholesterol homeostasis. However, its role in regulation of biliary cholesterol secretion and gallstone formation remains unknown. Hence, mice with conventional knockout (KO), hepatocyte-specific knockout (ΔHepa) / knockdown (KD) or gain expression of miRNA-223 were included in the study and were subjected to lithogenic diet (LD) for various weeks. The gall bladders and liver tissues were harvested for cholesterol crystal imaging, gallstone mass measurement and molecular analysis. Levels of cholesterol, bile salt, phospholipids, and triglyceride were determined in serum, liver tissues, and bile by enzyme color reactive assays. A 3' UTR reporter gene assay was used to verify the direct target genes for miRNA-223. LD-induced gallstone formation was remarkably accelerated in miRNA-223 KO, ΔHepa, and KD mice with concurrent enhancement in total cholesterol levels in liver tissues and bile. Key biliary cholesterol transporters ABCG5 and ABCG8 were identified as direct targets of miRNA-223. Reversely, AAV-mediated hepatocyte-specific miRNA-223 overexpression prevented gallstone progression with reduced targets expression. Therefore, the present study demonstrates a novel role of miRNA-223 in the gallstone formation by targeting ABCG5 and ABCG8 and elevating miRNA-223 would be a potentially novel approach to overcome the sternness of cholesterol gallstone disease.\n\nmiRNA-223 Suppresses Mouse Gallstone Formation by Targeting Key Transporters in Hepatobiliary Cholesterol Secretion Pathway.", "token_count": 440, "char_count": 1581, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5972, "quality_score": 0.7986, "entities": { "genes": [ "ABCG8", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:14.617787", "source": { "split": "train_shard_00000", "doc_id": 2072 }, "chunk_id": "train_shard_00000_2072_0", "global_id": 2284 }, { "text": "Due to their unique breeding pattern, aquatic bird farms are increasingly considered as hotspots in the development and spread of antimicrobial resistance. However, comprehensive studies addressing the whole-genomic features of colistin-resistant bacteria in aquatic bird farms are scarce. Over a 2-year period, we conducted surveillance to determine the whole-genome epidemiology and characterisation of mcr-1-positive Escherichia coli in aquatic bird farms in southeastern coastal China. A total of 100 mcr-1-producing isolates among 654 E. coli strains were recovered from 781 samples collected in 11 aquatic bird farms and 1 veterinary clinic in the Pearl River Delta area. Higher resistance phenotypes to 17 antibiotics were found in mcr-1-positive isolates compared with other isolates. Subsequently, 20 mcr-1-carrying isolates were sequenced to analyse the whole-genomic features. Molecular typing as well as antimicrobial resistance gene and virulence factor profiles of the isolates showed considerable diversity. Three types of genetic backbones of mcr-1 in the isolates were assembled and were identified in diverse broad-host-range plasmids and bacterial species. Pangenome analyses revealed a large genetic pool composed of the isolates. Furthermore, phylogenetic trees both of the isolates in this study and a global data set were built, indicating the spread of the three mcr-1 backbones and the mcr-1-positive isolates among different habitats, farms and even countries. This study highlights that aquatic bird farms may act as an important reservoir for mcr-1-producing E. coli, from which colistin resistance may be spread to diverse habitats, different geographical locations and even across bacterial species.\n\nWhole-genome epidemiology and characterisation of mcr-1-encoding Escherichia coli in aquatic bird farms from the Pearl River Delta, China, 2019-2020.", "token_count": 469, "char_count": 1880, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5627, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:15.282996", "source": { "split": "train_shard_00000", "doc_id": 2073 }, "chunk_id": "train_shard_00000_2073_0", "global_id": 2285 }, { "text": "Colistin is used against multi-drug resistant pathogens, yet resistance emerges through dissemination of plasmid-mediated genes (mcr) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challenging due to poor diffusion of colistin in agar media, leading to an underestimation of resistance. Performance of five phenotypic approaches was compared in the context of different molecular mechanisms of resistance. We evaluated Vitek 2® (bioMérieux, AST N242), Colistin MIC Test Strip (Liofilchem Diagnostici), UMIC (Biocentric), and Rapid Polymyxin™ NP test (ELITechGroup) against the standard broth microdilution (BMD) method. We used whole genome sequencing (WGS) to infer molecular resistance mechanisms. We analysed 97 Enterobacterales and non-fermenting bacterial isolates, largely clinical isolates collected up to 2018. Data was analysed by comparing susceptibility categories (susceptible or resistant) and minimal inhibitory concentrations (MIC). Susceptibility category concordance is the percentage of test results sharing the same category to BMD. MIC concordance was calculated similarly but considering ±1 MIC titre error range. We determined genomic diversity by core genome multi locus sequencing typing (cgMLST) and identified putative antimicrobial resistance genes using NCBI and CARD databases, and manual annotation.\n\nColistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms.", "token_count": 399, "char_count": 1555, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:15.929764", "source": { "split": "train_shard_00000", "doc_id": 2074 }, "chunk_id": "train_shard_00000_2074_0", "global_id": 2286 }, { "text": "A cluster of five human Salmonella Guinea cases was identified among Ohio residents through core genome multilocus sequence typing of clinical isolates. An investigation was conducted to characterize illnesses and identify common exposures. Four patients were aged ≤5 years and three of four patients with information available regarding exposure to animals reported prior exposure to bearded dragons. Practices that potentially increased the risk for Salmonella transmission from reptiles to humans included allowing pet reptiles to roam freely in the home, cleaning reptile habitats indoors, and kissing reptiles. These findings prompted a multistate investigation that resulted in the identification of additional closely related Salmonella Guinea isolates from patients across multiple states. The investigation of cases in Ohio and information shared by other states indicated the potential association between human Salmonella Guinea infections and reptiles, particularly bearded dragons. To prevent Salmonella transmission from reptiles, continued educational efforts should address pet owners and focus on specific reptile ownership practices.\n\nCluster of human Salmonella Guinea infections: Reported reptile exposures and associated opportunities for infection prevention - Ohio, 2019-2020.", "token_count": 258, "char_count": 1299, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6724, "quality_score": 0.8362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:16.514149", "source": { "split": "train_shard_00000", "doc_id": 2075 }, "chunk_id": "train_shard_00000_2075_0", "global_id": 2287 }, { "text": "As whole-genome sequencing for pathogen genomes becomes increasingly popular, the typing methods of gene-by-gene comparison, such as core genome multilocus sequence typing (cgMLST) and whole-genome multilocus sequence typing (wgMLST), are being routinely implemented in molecular epidemiology. However, some intrinsic problems remain. For example, genomic sequences with varying read depths, read lengths, and assemblers influence the genome assemblies, introducing error or missing alleles into the generated allelic profiles. These errors and missing alleles might create \"specious discrepancy\" among closely related isolates, thus making accurate epidemiological interpretation challenging. In addition, the rapid growth of the cgMLST allelic profile database can cause problems related to storage and maintenance as well as long query search times.\n\nA machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking.", "token_count": 220, "char_count": 1037, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7481, "quality_score": 0.8741, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:16.987070", "source": { "split": "train_shard_00000", "doc_id": 2076 }, "chunk_id": "train_shard_00000_2076_0", "global_id": 2288 }, { "text": "Staphylococcus pseudintermedius is the main aetiological agent of canine pyoderma. Whole genome sequencing is the most comprehensive way of obtaining relevant genomic information about micro-organisms.\n\nWhole genome sequencing and de novo assembly of Staphylococcus pseudintermedius: a pangenome approach to unravelling pathogenesis of canine pyoderma.", "token_count": 91, "char_count": 352, "word_count": 44, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:17.364162", "source": { "split": "train_shard_00000", "doc_id": 2077 }, "chunk_id": "train_shard_00000_2077_0", "global_id": 2289 }, { "text": "Drug-induced liver injury (DILI) is the leading cause of acute liver failure and a major concern in drug development. Altered bile acid homeostasis via inhibition of the bile salt export pump (BSEP) is one mechanism of DILI. Dasatinib, pazopanib, and sorafenib are tyrosine kinase inhibitors (TKIs) that competitively inhibit BSEP and increase serum biomarkers for hepatotoxicity in ∼25-50% of patients. However, the mechanism(s) of hepatotoxicity beyond competitive inhibition of BSEP are poorly understood. This study examined mechanisms of TKI-mediated hepatotoxicity associated with altered bile acid homeostasis. Dasatinib, pazopanib, and sorafenib showed bile acid-dependent toxicity at clinically relevant concentrations, based on the C-DILI assay using sandwich-cultured human hepatocytes (SCHH). Among several bile acid-relevant genes, cytochrome P450 (CYP) 7A1 mRNA was specifically upregulated by 6.2- to 7.8-fold (dasatinib) and 5.7- to 9.3-fold (pazopanib), compared with control, within 8 hours. This was consistent with increased total bile acid concentrations in culture medium up to 2.3-fold, and in SCHH up to 1.4-fold, compared with control, within 24 hours. Additionally, protein abundance of sodium taurocholate co-transporting polypeptide (NTCP) was increased up to 2.0-fold by these three TKIs. The increase in NTCP protein abundance correlated with increased function; dasatinib and pazopanib increased hepatocyte uptake clearance (CL\n\nNovel Bile Acid-Dependent Mechanisms of Hepatotoxicity Associated with Tyrosine Kinase Inhibitors.", "token_count": 464, "char_count": 1558, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:18.004433", "source": { "split": "train_shard_00000", "doc_id": 2078 }, "chunk_id": "train_shard_00000_2078_0", "global_id": 2290 }, { "text": "All genomes include gene families with very limited taxonomic distributions that potentially represent new genes and innovations in protein-coding sequence, raising questions on the origins of such genes. Some of these genes are hypothesized to have formed de novo, from noncoding sequences, and recent work has begun to elucidate the processes by which de novo gene formation can occur. A special case of de novo gene formation, overprinting, describes the origin of new genes from noncoding alternative reading frames of existing open reading frames (ORFs). We argue that additionally, out-of-frame gene fission/fusion events of alternative reading frames of ORFs and out-of-frame lateral gene transfers could contribute to the origin of new gene families. To demonstrate this, we developed an original pattern-search in sequence similarity networks, enhancing the use of these graphs, commonly used to detect in-frame remodeled genes. We applied this approach to gene families in 524 complete genomes of Escherichia coli. We identified 767 gene families whose evolutionary history likely included at least one out-of-frame remodeling event. These genes with out-of-frame components represent ∼2.5% of all genes in the E. coli pangenome, suggesting that alternative reading frames of existing ORFs can contribute to a significant proportion of de novo genes in bacteria.\n\nHundreds of Out-of-Frame Remodeled Gene Families in the Escherichia coli Pangenome.", "token_count": 333, "char_count": 1457, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5794, "quality_score": 0.7897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:18.573305", "source": { "split": "train_shard_00000", "doc_id": 2079 }, "chunk_id": "train_shard_00000_2079_0", "global_id": 2291 }, { "text": "Kluyveromyces marxianus is a promising host for the production of heterologous proteins, chemicals, and bioethanol. One superior feature of this species is its capacity to assimilate lactose, which is rendered by the LAC12-LAC4 gene pair encoding a lactose permease and a β-galactosidase enzyme. Little is known about the regulation of LAC4 in K. marxianus. In this study, we showed the presence of weak glucose repression in the regulation of LAC4 and that might contribute to the leaky expression of LAC4 in the glucose medium. In a mutagenesis screen of 1000-bp LAC4 upstream region, one mutant region, named H1, drove low-leakage expression of a URA3 reporter gene in glucose medium. Two mutations inside a polyadenosine stretch (poly(A)) of 5' UTR were major contributors to the low-leakage phenotype of H1. H1 directed low-leakage expression of GFP on a plasmid and that of LAC4 in situ in the glucose medium, which was not due to the reduction of mRNA levels. Meanwhile, H1 did not affect the induction of GFP or LAC4 by lactose. Cre recombinase expressed by H1 caused lower toxicity in the repressive condition and achieved higher yield after induction, compared with that expressed by a wild-type LAC4 upstream region or a strong INU1 promoter. Our study suggested that poly(A) inside 5' UTR played a role in regulating the expression of LAC4 in the repressive condition. Meanwhile, H1 provided a base for the development of a strict inducible system for expressing industrial proteins, especially toxic proteins.\n\nCharacterization and optimization of the LAC4 upstream region for low-leakage expression in Kluyveromyces marxianus.", "token_count": 445, "char_count": 1640, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5504, "quality_score": 0.7752, "entities": { "genes": [ "URA3", "LAC12", "INU1", "LAC4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:19.197959", "source": { "split": "train_shard_00000", "doc_id": 2080 }, "chunk_id": "train_shard_00000_2080_0", "global_id": 2292 }, { "text": "Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.ensembl.org). The two resources collectively present genome annotation through a consistent set of interfaces spanning the tree of life presenting genome sequence, annotation, variation, transcriptomic data and comparative analysis. Here, we present our largest increase in plant, metazoan and fungal genomes since the project's inception creating one of the world's most comprehensive genomic resources and describe our efforts to reduce genome redundancy in our Bacteria portal. We detail our new efforts in gene annotation, our emerging support for pangenome analysis, our efforts to accelerate data dissemination through the Ensembl Rapid Release resource and our new AlphaFold visualization. Finally, we present details of our future plans including updates on our integration with Ensembl, and how we plan to improve our support for the microbial research community. Software and data are made available without restriction via our website, online tools platform and programmatic interfaces (available under an Apache 2.0 license). Data updates are synchronised with Ensembl's release cycle.\n\nEnsembl Genomes 2022: an expanding genome resource for non-vertebrates.", "token_count": 300, "char_count": 1355, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6448, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:19.763499", "source": { "split": "train_shard_00000", "doc_id": 2081 }, "chunk_id": "train_shard_00000_2081_0", "global_id": 2293 }, { "text": "Aspergillus terreus is an industrial microorganism used in the brewing and sauce industries. It produces monacolin K, a natural statin. The study conducted an 8-week randomized controlled trial with hypercholesterolemic subjects to examine the hypocholesterolemic effects and mechanisms of supplementation with yellow yeast rice (YYR) prepared by growing Aspergillus fungi on steamed rice.\n\nYellow Yeast Rice Prepared Using Aspergillus terreus DSMK01 Lowers Cholesterol Levels by Stimulating Bile Salt Export Pump in Subjects with Mild-to-Moderate Hypercholesterolemia: A Randomized Controlled Trial.", "token_count": 165, "char_count": 600, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7595, "quality_score": 0.8797, "entities": { "genes": [ "DSMK01" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:20.210209", "source": { "split": "train_shard_00000", "doc_id": 2082 }, "chunk_id": "train_shard_00000_2082_0", "global_id": 2294 }, { "text": "Here the pangenome analysis of Burkholderia sensu lato (s.l.) was performed for the first time, together with an updated analysis of the pangenome of Burkholderia sensu stricto, and Burkholderia cepacia complex (Bcc) focusing on the Bcc B. catarinensis specific features of its re-sequenced genome. The pangenome of Burkholderia s.l., Burkholderia s.s., and of the Bcc was open, composed of more than 96% of accessory genes, and more than 62% of unknown genes. Functional annotations showed that secondary metabolism genes belonged to the variable portion of genomes, which might explain their production of several compounds with varied bioactivities. Taken together, this work showed the great variability and uniqueness of these genomes and revealed an underexplored unknown potential in poorly characterized genes. Regarding B. catarinensis 89\n\nPangenome inventory of Burkholderia sensu lato, Burkholderia sensu stricto, and the Burkholderia cepacia complex reveals the uniqueness of Burkholderia catarinensis.", "token_count": 262, "char_count": 1014, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:20.754292", "source": { "split": "train_shard_00000", "doc_id": 2083 }, "chunk_id": "train_shard_00000_2083_0", "global_id": 2295 }, { "text": "In order to develop microbial additives for rabbit feed, a spore-forming bacteria was isolated from the feces of Hyla rabbit using reinforced clostridium medium (RCM). The 16S rDNA sequence of the bacterium was subjected to pairwise sequence alignment using BLAST; the colony morphology, and physiological, biochemical, and stress resistance were studied. The results showed that the bacterium was Clostridium sartagoforme, a gram positive anaerobe, which can produce spores. The colony diameter was 0.5 mm-2.5 mm, the diameter of the bacteria was 0.5 μm-1.0 μm × 2.0 μm-6.3 μm, and the spore diameter was 1 μm-1.2 μm × 1 μm-1.2 μm. C. sartagoforme can utilize various sugars and alcohols such as fructose, galactose, sorbitol, and inositol. It secreted cellulase into the extracellular environment to form a transparent hydrolysis circle in Congo red medium, it could not liquify gelatin, and the lysine decarboxylase reaction was positive. In liquid medium it entered the stable growth period after 9 h of inoculation. Additionally, it had good stress resistance with a survival rate that exceeded 53% after gastric juice (pH 2.5) treatment for 3 h, it grew in a medium with a bile salt concentration of 0.3%, and the survival rate exceeded 85% after 10 minutes at 80°C. Moreover, animal testing indicated that this strain has no adverse effects on the morbidity and mortality of rabbits. In summary, C. sartagoforme XN-T4 was isolated from rabbit feces. This bacterium has good resistance to stress, can decompose a variety of monosaccharides and polysaccharides including cellulose, which is relatively harmless for animal health.\n\nIsolation, identification, and biological characteristics of Clostridium sartagoforme from rabbit.", "token_count": 495, "char_count": 1734, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:21.397266", "source": { "split": "train_shard_00000", "doc_id": 2084 }, "chunk_id": "train_shard_00000_2084_0", "global_id": 2296 }, { "text": "Clostridioides difficile infection (CDI) is the major identifiable cause of antibiotic-associated diarrhea. The emergence of hypervirulent C. difficile strains has led to increases in both hospital- and community-acquired CDI. Furthermore, the rate of CDI relapse from hypervirulent strains can reach up to 25%. Thus, standard treatments are rendered less effective, making new methods of prevention and treatment more critical. Previously, the bile salt analog CamSA (cholic acid substituted with\n\nAn Aniline-Substituted Bile Salt Analog Protects both Mice and Hamsters from Multiple Clostridioides difficile Strains.", "token_count": 159, "char_count": 618, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7738, "quality_score": 0.8869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:21.843343", "source": { "split": "train_shard_00000", "doc_id": 2085 }, "chunk_id": "train_shard_00000_2085_0", "global_id": 2297 }, { "text": "Enzymes, the natural catalysts, replace catalysts of chemical origin in a wide spectrum of reactions and generally work under environment friendly conditions. Various strategies are adopted to modify catalytic activities of enzymes further, of which one is application of novel reaction medium. This work reviews applicability of novel media like mixed micelles and bicontinuous microemulsions in enzymatic reactions and points out their capability to play bigger roles in enzyme catalysis. Ionic reverse micelles reduced catalytic activities of enzymes through denaturation. Addition of nonionic surfactant to these reverse micelles led to corresponding mixed micelles and thus restored or sometimes enhanced catalytic abilities of enzymes. Mixed micelles comprising of two nonionic surfactants, bicontinuous microemulsion containing two anionic surfactants also acted as efficient reaction media for enzymes. Even a cationic/anionic/nonionic mixed micelle was found to increase activity of enzyme. Mixed micelles and bicontinuous microemulsions comprising of anionic and zwitterionic surfactants augmented enzyme catalysis. Mixed micelles and bicontinuous microemulsions containing ionic liquid and surfactant also had critical impact on enzyme catalysis. Catalytic abilities of enzymes altered significantly in substrate/surfactant and bile salt/surfactant mixed micelles. Concentrations of individual surfactant, molar ratio of surfactants, and molar ratio of water to total surfactants had notable impacts on enzyme catalysis in those media.\n\nMixed micelles and bicontinuous microemulsions: Promising media for enzymatic reactions.", "token_count": 389, "char_count": 1636, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:22.460939", "source": { "split": "train_shard_00000", "doc_id": 2086 }, "chunk_id": "train_shard_00000_2086_0", "global_id": 2298 }, { "text": "Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is becoming more and more important to accurately and swiftly identify AMR pathogenic strains. Pangenome-wide association studies (e.g. Scoary) identified numerous putative AMR genes. However, only a tiny proportion of the putative resistance genes are annotated by AMR databases or Gene Ontology. In addition, many putative resistance genes are of unknown function (termed hypothetical proteins). An annotation tool is crucially needed in order to reveal the functional organization of the resistome and expand our knowledge of the AMR gene repertoire.\n\nPangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains.", "token_count": 179, "char_count": 749, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7157, "quality_score": 0.8578, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:22.925180", "source": { "split": "train_shard_00000", "doc_id": 2087 }, "chunk_id": "train_shard_00000_2087_0", "global_id": 2299 }, { "text": "Condensation of DNA helices into hexagonally packed bundles and toroids represents an intriguing example of functional organization of biological macromolecules at the nanoscale. The condensation models are based on the unique polyelectrolyte features of DNA, however here we could reproduce a DNA-like condensation with supramolecular helices of small chiral molecules, thereby demonstrating that it is a more general phenomenon. We show that the bile salt sodium deoxycholate can form supramolecular helices upon interaction with oppositely charged polyelectrolytes of homopolymer or block copolymers. At higher order, a controlled hexagonal packing of the helices into DNA-like bundles and toroids could be accomplished. The results disclose unknown similarities between covalent and supramolecular non-covalent helical polyelectrolytes, which inspire visionary ideas of constructing supramolecular versions of biological macromolecules. As drug nanocarriers the polymer-bile salt superstructures would get advantage of a complex chirality at molecular and supramolecular levels, whose effect on the nanocarrier assisted drug efficiency is a still unexplored fascinating issue.\n\nCondensed Supramolecular Helices: The Twisted Sisters of DNA.", "token_count": 297, "char_count": 1243, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:24.120021", "source": { "split": "train_shard_00000", "doc_id": 2088 }, "chunk_id": "train_shard_00000_2088_0", "global_id": 2300 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) belonging to the serogroup O91 are among the most common non-O157 STEC serogroups associated with human illness in Europe. This study aimed to analyse the virulence factors, antimicrobial resistance genes and phylogenetic relatedness among 48 clinical STEC O91 isolates collected during 2003-2019 in Switzerland. The isolates were subjected to whole genome sequencing using short-read sequencing technologies and a subset of isolates additionally to long-read sequencing. They belonged to O91:H10 (n=6), O91:H14 (n=40), and O91:H21 (n=2). Multilocus sequence typing showed that the O91:H10 isolates all belonged to sequence type (ST)641, while the O91:H14 isolates were assigned to ST33, ST9700, or were non-typeable. Both O91:H21 isolates belonged to ST442. Shiga toxin gene stx1a was the most common Shiga toxin gene subtype among the isolates, followed by stx2b, stx2d and stx2a. All isolates were LEE-negative and carried one or two copies of the IrgA adhesin gene iha. In a subset of long-read sequenced isolates, modules of the Locus of Adhesion and Autoaggregation pathogenicity island (LAA-PAI) carrying iha and other genes such as hes, lesP or agn43 were identified. A large proportion of STEC O91:H14 carried the subtilase cytotoxin gene subA, colicin genes (cba, cea, cib and cma) or microcin genes (mcmA, mchB, mchC and mchF). STEC O91:H14 were further distinguished from STEC O91:H10/H21 by one or more virulence factors found in extraintestinal pathogenic E. coli (ExPEC), including hlyF, iucC/iutA, kpsE and traT", "token_count": 517, "char_count": 1573, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6282, "quality_score": 0.8141, "entities": { "genes": [ "ST9700", "ST442", "ST33" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:19:24.774273", "source": { "split": "train_shard_00000", "doc_id": 2089 }, "chunk_id": "train_shard_00000_2089_0", "global_id": 2301 }, { "text": "The hlyF gene was identified on a novel mosaic plasmid that was unrelated to hlyF+ plasmids described previously in STEC. Core genome phylogenetic analysis revealed that STEC O91:H10 and STEC O91:H21 were clonally conserved, whereas STEC O91:H14 were clonally diverse. Among three STEC O91:H14 isolates, a number of resistance genes were identified, including genes that mediate resistance to aminoglycosides (aadA, aadA2, aadA9, aadA23, aph(3'')-Ib and aph(6)-Id), chloramphenicol (cmlA), sulphonamides (sul2 and sul3), and trimethoprim (drfA12). Our data contribute to understanding the genetic diversity and differing levels of virulence potential within the STEC O91 serogroup.\n\nDistribution of virulence factors, antimicrobial resistance genes and phylogenetic relatedness among Shiga toxin-producing Escherichia coli serogroup O91 from human infections.", "token_count": 275, "char_count": 859, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7281, "quality_score": 0.864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:25.327048", "source": { "split": "train_shard_00000", "doc_id": 2089 }, "chunk_id": "train_shard_00000_2089_1", "global_id": 2302 }, { "text": "In this study, the survival capacity (acid and bile salt tolerance, and adhesion to gut epithelial cells) and probiotic properties (enzyme activity-inhibition and anti-inflammatory activities, inhibition of adipogenesis, and stress hormone level reduction) of\n\nMultifunctional Probiotic and Functional Properties of", "token_count": 80, "char_count": 315, "word_count": 40, "semantic_coherence": 1, "information_density": 0.775, "quality_score": 0.8875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:25.703789", "source": { "split": "train_shard_00000", "doc_id": 2090 }, "chunk_id": "train_shard_00000_2090_0", "global_id": 2303 }, { "text": "Campylobacter coli and Campylobacter Jejuni are highly resistant to most therapeutic antimicrobials in Taiwan; rapid diagnostics of resistance in bacterial isolates is crucial for the treatment of campylobacteriosis. We characterized 219 (40 C. coli and 179 C. jejuni) isolates recovered from humans from 2016 to 2019 using whole-genome sequencing to investigate the genetic diversity among isolates and the genetic resistance determinants associated with antimicrobial resistance. Susceptibility testing with 8 antimicrobials was conducted to assess the concordance between phenotypic resistance and genetic determinants. The conventional and core genome multilocus sequence typing analysis revealed diverse clonality among the isolates. Mutations in\n\nAntimicrobial Resistance in Campylobacter coli and Campylobacter jejuni from Human Campylobacteriosis in Taiwan, 2016 to 2019.", "token_count": 226, "char_count": 879, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:26.181186", "source": { "split": "train_shard_00000", "doc_id": 2091 }, "chunk_id": "train_shard_00000_2091_0", "global_id": 2304 }, { "text": "The present research work aimed at developing robust yeast cell factory via adaptive laboratory evolution (ALE) for improved cellulosic bioethanol production. Kluyveromyces marxianus JKH5, a newly isolated thermotolerant ethanologenic yeast, was engineered by serial passaging for 60 generations in medium supplemented with gradually higher concentration of inhibitors (acetic acid, furfural, and vanillin) that are generated during dilute acid pretreatment. The improved strain K. marxianus JKH5 C60, showed 3.3-fold higher specific growth rate, 56% reduced lag phase and 80% enhanced fermentation efficiency at 42 °C in comparison to parent strain in inhibitor cocktail comprising medium. Bioethanol production by simultaneous saccharification and fermentation of sequential dilute acid-alkali pretreated sugarcane bagasse in presence of inhibitors, resulted in ethanol titre and yield, respectively, 54.8 ± 0.9 g/L and 0.40 g/g. The adapted yeast can be used to ferment unwashed pretreated biomass, thereby, reducing overall cost, time, and wastewater generation, hence making bioethanol production sustainable.\n\nDevelopment of multiple inhibitor tolerant yeast via adaptive laboratory evolution for sustainable bioethanol production.", "token_count": 318, "char_count": 1237, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7683, "quality_score": 0.8841, "entities": { "genes": [ "JKH5" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:26.776728", "source": { "split": "train_shard_00000", "doc_id": 2092 }, "chunk_id": "train_shard_00000_2092_0", "global_id": 2305 }, { "text": "Whole genome sequencing (WGS) has become the reference standard for bacterial outbreak investigation and pathogen typing, providing a resolution unattainable with conventional molecular methods. Data generated with Illumina sequencers can however only be analysed after the sequencing run has finished, thereby losing valuable time during emergency situations. We evaluated both the effect of decreasing overall run time, and also a protocol to transfer and convert intermediary files generated by Illumina sequencers enabling real-time data analysis for multiple samples part of the same ongoing sequencing run, as soon as the forward reads have been sequenced. To facilitate implementation for laboratories operating under strict quality systems, extensive validation of several bioinformatics assays (16S rRNA species confirmation, gene detection against virulence factor and antimicrobial resistance databases, SNP-based antimicrobial resistance detection, serotype determination, and core genome multilocus sequence typing) for three bacterial pathogens (\n\nEvaluation of WGS performance for bacterial pathogen characterization with the Illumina technology optimized for time-critical situations.", "token_count": 243, "char_count": 1200, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7564, "quality_score": 0.8782, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:27.316705", "source": { "split": "train_shard_00000", "doc_id": 2093 }, "chunk_id": "train_shard_00000_2093_0", "global_id": 2306 }, { "text": "Many public health laboratories across the world have implemented whole-genome sequencing (WGS) for the surveillance and outbreak detection of foodborne pathogens. PulseNet-affiliated laboratories have determined that most single-strain foodborne outbreaks are contained within 0–10 multi-locus sequence typing (MLST)-based allele differences and/or core genome single-nucleotide variants (SNVs). In addition to being a food- and travel-associated outbreak pathogen, most\n\nEvaluation of whole-genome sequencing-based subtyping methods for the surveillance of", "token_count": 136, "char_count": 558, "word_count": 67, "semantic_coherence": 1, "information_density": 0.806, "quality_score": 0.903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:27.755749", "source": { "split": "train_shard_00000", "doc_id": 2094 }, "chunk_id": "train_shard_00000_2094_0", "global_id": 2307 }, { "text": "Pseudomonas aeruginosa possesses one of the most complex bacterial regulatory networks, which largely contributes to its success as a pathogen. However, most of its transcription factors (TFs) are still uncharacterized and the potential intra-species variability in regulatory networks has been mostly ignored so far. Here, we used DAP-seq to map the genome-wide binding sites of all 55 DNA-binding two-component systems (TCSs) response regulators (RRs) across the three major P. aeruginosa lineages. The resulting networks encompass about 40% of all genes in each strain and contain numerous new regulatory interactions across most major physiological processes. Strikingly, about half of the detected targets are specific to only one or two strains, revealing a previously unknown large functional diversity of TFs within a single species. Three main mechanisms were found to drive this diversity, including differences in accessory genome content, as exemplified by the strain-specific plasmid in IHMA87 outlier strain which harbors numerous binding sites of conserved chromosomally-encoded RRs. Additionally, most RRs display potential auto-regulation or RR-RR cross-regulation, bringing to light the vast complexity of this network. Overall, we provide the first complete delineation of the TCSs regulatory network in P. aeruginosa that will represent an important resource for future studies on this pathogen.\n\nDetermination of the two-component systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages.", "token_count": 354, "char_count": 1557, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "IHMA87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:28.388618", "source": { "split": "train_shard_00000", "doc_id": 2095 }, "chunk_id": "train_shard_00000_2095_0", "global_id": 2308 }, { "text": "The yeast Kluyveromyces marxianus SLP1 has the potential for application in biotechnological processes because it can metabolize several sugars and produce high-value metabolites. K. marxianus SLP1 is a thermotolerant yeast isolated from the mezcal process, and it is tolerant to several cell growth inhibitors such as saponins, furan aldehydes, weak acids, and phenolics compounds. The genomic differences between dairy and nondairy strains related to K. marxianus variability are a focus of research attention, particularly the pathways leading this species toward polyploidy. We report the diploid genome assembly of K. marxianus SLP1 nonlactide strain into 32 contigs to reach a size of ∼12 Mb (N50 = 1.3 Mb) and a ∼39% GC content. Genome size is consistent with the k-mer frequency results. Genome annotation by Funannotate estimated 5000 genes in haplotype A and 4910 in haplotype B. The enriched annotated genes by ontology show differences between alleles in biological processes and cellular component. The analysis of variants related to DMKU3 and between haplotypes shows changes in LAC12 and INU1, which we hypothesize can impact carbon source performance. This report presents the first polyploid K. marxianus strain recovered from nonlactic fermenting medium.\n\nDiploid genome assembly of Kluyveromyces marxianus NRRL Y-50883 (SLP1).", "token_count": 390, "char_count": 1346, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6583, "quality_score": 0.8291, "entities": { "genes": [ "LAC12", "INU1", "DMKU3", "SLP1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:29.002857", "source": { "split": "train_shard_00000", "doc_id": 2096 }, "chunk_id": "train_shard_00000_2096_0", "global_id": 2309 }, { "text": "Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter by 13,8% and 88,6% respectively, as well as root dry matter by 61,4%, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.", "token_count": 479, "char_count": 1812, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:29.645495", "source": { "split": "train_shard_00000", "doc_id": 2097 }, "chunk_id": "train_shard_00000_2097_0", "global_id": 2310 }, { "text": "Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacterium Azospirillum sp. UENF-412522, a novel member of the Azospirillum genus.", "token_count": 59, "char_count": 187, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:30.006345", "source": { "split": "train_shard_00000", "doc_id": 2097 }, "chunk_id": "train_shard_00000_2097_1", "global_id": 2311 }, { "text": "Ten Bifidobacterium strains, i.e., 6T3, 64T4, 79T10, 80T4, 81T8, 82T1, 82T10, 82T18, 82T24, and 82T25, were isolated from mantled guereza (Colobus guereza), Sumatran orangutan (Pongo abeli), silvery marmoset (Mico argentatus), golden lion tamarin (Leontopithecus rosalia), pied tamarin (Saguinus bicolor), and common pheasant (Phaisanus colchinus). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic, and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on the core genome sequences revealed that isolated strains exhibit close phylogenetic relatedness with Bifidobacterium genus members belonging to the Bifidobacterium bifidum, Bifidobacterium longum, Bifidobacterium pullorum, and Bifidobacterium tissieri phylogenetic groups. Phenotypic characterization and genotyping based on the genome sequences clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, B. phasiani sp. nov. (6T3 = LMG 32224\n\nPhylogenetic classification of ten novel species belonging to the genus Bifidobacterium comprising B. phasiani sp. nov., B. pongonis sp. nov., B. saguinibicoloris sp. nov., B. colobi sp. nov., B. simiiventris sp. nov., B. santillanense sp. nov., B. miconis sp. nov., B. amazonense sp. nov., B. pluvialisilvae sp. nov., and B. miconisargentati sp. nov.", "token_count": 497, "char_count": 1375, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:30.653716", "source": { "split": "train_shard_00000", "doc_id": 2098 }, "chunk_id": "train_shard_00000_2098_0", "global_id": 2312 }, { "text": "Efficient bioethanol production from lignocellulosic biomass requires thermotolerant yeasts capable of utilizing multiple sugars, tolerating inhibitors and fermenting at high temperatures. In this study, 98 thermotolerant yeasts were isolated from nine compost samples. We selected 37 yeasts that belonged to 11 species; 31 grew at 45°C; 6 strains grew at 47°C, while 9 yeasts could utilize multiple sugars. Many yeast isolates showed high ethanol production in the range of 12-24 g l\n\nCompost as an untapped niche for thermotolerant yeasts capable of high-temperature ethanol production.", "token_count": 170, "char_count": 588, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7765, "quality_score": 0.8882, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:31.100327", "source": { "split": "train_shard_00000", "doc_id": 2099 }, "chunk_id": "train_shard_00000_2099_0", "global_id": 2313 }, { "text": "Whole-genome sequencing (WGS) has recently been used to investigate acquisition of Mycobacterium abscessus. Investigators have reached conflicting conclusions about the meaning of genetic distances for interpretation of person-to-person transmission. Existing genomic studies were limited by a lack of WGS from environmental M. abscessus isolates. In this study, we retrospectively analyzed the core and accessory genomes of 26 M. abscessus subsp.\n\nGenomic Analysis of a Hospital-Associated Outbreak of Mycobacterium abscessus: Implications on Transmission.", "token_count": 137, "char_count": 557, "word_count": 72, "semantic_coherence": 1, "information_density": 0.8194, "quality_score": 0.9097, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:31.523007", "source": { "split": "train_shard_00000", "doc_id": 2100 }, "chunk_id": "train_shard_00000_2100_0", "global_id": 2314 }, { "text": "Clostridium perfringens is a spore-forming anaerobic pathogen responsible for a variety of histotoxic and intestinal infections in humans and animals. High-resolution genotyping aiming to identify bacteria at strain level has become increasingly important in modern microbiology to understand pathogen transmission pathways and to tackle infection sources. This study aimed at establishing a publicly available genome-wide multilocus sequence-typing (MLST) scheme for C. perfringens. A total of 1,431 highly conserved core genes (1.34 megabases; 50% of the reference genome genes) were indexed for a core genome-based MLST (cgMLST) scheme for C. perfringens. The scheme was applied to 282 ecologically and geographically diverse genomes, showing that the genotyping results of cgMLST were highly congruent with the core genome-based single-nucleotide-polymorphism typing in terms of resolution and tree topology. In addition, the cgMLST provided a greater discrimination than classical MLST methods for C. perfringens. The usability of the scheme for outbreak analysis was confirmed by reinvestigating published outbreaks of C. perfringens-associated infections in the United States and the United Kingdom. In summary, a publicly available scheme and an allele nomenclature database for genomic typing of C. perfringens have been established and can be used for broad-based and standardized epidemiological studies.\n\nEstablishment of a Publicly Available Core Genome Multilocus Sequence Typing Scheme for Clostridium perfringens.", "token_count": 372, "char_count": 1529, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:32.441296", "source": { "split": "train_shard_00000", "doc_id": 2101 }, "chunk_id": "train_shard_00000_2101_0", "global_id": 2315 }, { "text": "The entry inhibitor bulevirtide (BLV) received conditional approval from the EMA in July 2020 for the treatment of adult patients with compensated chronic hepatitis delta. However, the effectiveness and safety of BLV administered as monotherapy beyond 48 weeks in difficult-to-treat patients with HDV-related cirrhosis is presently unknown. Herein, we describe the first patients with HDV-related compensated cirrhosis who were treated with BLV (10 mg/day as a starting dose) for up to 3 years on a compassionate use program. Patients were also monitored for HBcrAg and HBV RNA levels, and HDV- and HBV-specific T-cell markers. In the patient who stopped BLV at week 48, after achieving a virological and biochemical response, the initial virological and biochemical rebound was followed by alanine aminotransferase normalization coupled with low HDV RNA and HBsAg levels. In the 2 patients treated continuously for 3 years, virological and biochemical responses were maintained throughout the treatment period even after dose reduction. In a patient with advanced compensated cirrhosis, liver function tests significantly improved, esophageal varices disappeared, and histological/laboratory features of autoimmune hepatitis resolved. Overall, no safety issues were recorded, as bile salt increase was asymptomatic. While serum HBV RNA levels remained undetectable in all patients, HBV core-related antigen levels showed a progressive, yet modest decline during long-term BLV treatment. No HDV-specific interferon-γ-producing T cells were detected, neither after HDV reactivation (after BLV withdrawn in Patient 1) nor during 3 years of BLV treatment. In conclusion, this report shows that continuous administration of BLV monotherapy for 3 years leads to excellent virological and clinical responses in patients with HDV-related cirrhosis who had contraindications to interferon-based therapies.\n\nSafety and effectiveness of up to 3 years' bulevirtide monotherapy in patients with HDV-related cirrhosis.", "token_count": 497, "char_count": 2005, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:33.092324", "source": { "split": "train_shard_00000", "doc_id": 2102 }, "chunk_id": "train_shard_00000_2102_0", "global_id": 2316 }, { "text": "The Gram-positive Lacticaseibacillus rhamnosus has been broadly reported as capable of exerting beneficial health effects. Bacterial genomic diversity may promote niche specialization, thus creating subpatterns within populations. As L. rhamnosus advantageous effects have been widely reported at strain level and few is known regarding the distribution of beneficial genes among L. rhamnosus strains, we investigated all publicly available genomes of Lactobacillus and Lacticaseibacillus genera to study the pangenome and general population structure of L. rhamnosus. Core genome multilocus sequence typing detected eight L. rhamnosus phylogroups (PG1 to PG8). L. rhamnosus harbors an open pangenome; PG1, PG3, PG4, and PG5 exhibited highly conserved gene distribution patterns. Genes significantly associated to the PG1, which comprises L. rhamnosus GG, are mainly phage-related. The adhesion operon spaCBA-srtC1 was found in 44 (24.7%) genomes; however, considering only the PG1, the prevalence was of 65%. In PG2 the spaCBA-srtC1 prevalence was of 43%. Nevertheless, both human and milk-derived strains harbored this operon. Further, two main types of bacteriocin clusters were found (Bact1 and Bact2). Bact1 predictions indicate the presence of garQ, encoding the class II bacteriocin garvieacin Q, that is mainly present in the closely related PG8A and a PG2 subcluster. PG2 harbors two distinct subclusters, harboring either spaCBA-srtC1 or Bact1. Our findings provide novel insights on the distribution of biotechnological relevant genes across L. rhamnosus population, uncovering intra-species patterns that may bring forth the development of more efficient probiotic products.\n\nDistribution of Genes Related to Probiotic Effects Across Lacticaseibacillus rhamnosus Revealed by Population Structure.", "token_count": 484, "char_count": 1808, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6787, "quality_score": 0.8394, "entities": { "genes": [ "PG8", "PG5", "PG8A", "PG3", "PG1", "PG2", "PG4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:33.745083", "source": { "split": "train_shard_00000", "doc_id": 2103 }, "chunk_id": "train_shard_00000_2103_0", "global_id": 2317 }, { "text": "In this experiment, laying hens were divided into a high productive group (group H) and a low productive group (group L). The purpose of this experiment was to screen and isolate a potential probiotic associated with the laying rate from group H by comparing the results via 16S rDNA high-throughput sequencing. The high-throughput sequencing analysis results showed that there were some differences in the composition of the gut microbiome between groups H and L on the Phylum and Genus levels. Through isolation and identification, we screened 16 lactobacilli strains. Among the 16 strains, S5 showed good acid tolerance, bile salt tolerance, and cholesterol degradation. Therefore, we chose strain S5 (identified as Limosilactobacillus oris, named Limosilactobacillus oris BSLO 1801) as a potential probiotic to promote the productivity of ordinary laying hens. During the animal experiment, 288 Hy-line white hens (30 weeks old) were divided into four groups, with six replications (n = 12) per group. The control group received the basic diet, and the treatment groups received the same basic diet supplemented with 10\n\nPromotion of Egg Production Rate and Quality Using Limosilactobacillus oris BSLO 1801, a Potential Probiotic Screened from Feces of Laying Hens with Higher Egg Productive Performance.", "token_count": 342, "char_count": 1308, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6281, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:34.317692", "source": { "split": "train_shard_00000", "doc_id": 2104 }, "chunk_id": "train_shard_00000_2104_0", "global_id": 2318 }, { "text": "The emergence of 16S rRNA methyltransferases (RMTs) in Gram-negative pathogens bearing other clinically relevant resistance mechanisms, such as carbapenemase-producing Enterobacterales (CPE), is becoming an alarming concern. We investigated the prevalence, antimicrobial susceptibility, resistance mechanisms, molecular epidemiology and genetic support of RMTs in CPE isolates from Spain. This study included a collection of 468 CPE isolates recovered during 2018 from 32 participating Spanish hospitals. MICs were determined using the broth microdilution method, the agar dilution method (fosfomycin) or MIC gradient strips (plazomicin). All isolates were subjected to hybrid whole-genome sequencing (WGS). Sequence types (STs), core genome phylogenetic relatedness, horizontally acquired resistance mechanisms, plasmid analysis and the genetic environment of RMTs were determined in silico from WGS data in all RMT-positive isolates. Among the 468 CPE isolates evaluated, 24 isolates (5.1%) recovered from nine different hospitals spanning five Spanish regions showed resistance to all aminoglycosides and were positive for an RMT (21 RmtF, 2 ArmA and 1 RmtC). All RMT-producers showed high-level resistance to all aminoglycosides, including plazomicin, and in most cases exhibited an extensively drug-resistant susceptibility profile. The RMT-positive isolates showed low genetic diversity and were global clones of Klebsiella pneumoniae (ST147, ST101, ST395) and Enterobacter cloacae (ST93) bearing bla\n\nEmergence of 16S rRNA methyltransferases among carbapenemase-producing Enterobacterales in Spain studied by whole-genome sequencing.", "token_count": 448, "char_count": 1640, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [ "ST147", "ST395", "ST93", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:34.953845", "source": { "split": "train_shard_00000", "doc_id": 2105 }, "chunk_id": "train_shard_00000_2105_0", "global_id": 2319 }, { "text": "Environmental bacteria contain a wealth of untapped potential in the form of biodegradative genes. Leveraging this potential can often be confounded by a lack of understanding of fundamental survival strategies, like dormancy, for environmental stress. Investigating bacterial dormancy-to-degradation relationships enables improvement of bioremediation. Here, we couple genomic and functional assessment to provide context for key attributes of the organic pollutant-degrading strain Rhodococcus biphenylivorans TG9. Whole genome sequencing, pangenome analysis and functional characterization were performed to elucidate important genes and gene products, including antimicrobial resistance, dormancy, and degradation. Rhodococcus as a genus has strong potential for degradation and dormancy, which we demonstrate using R. biphenylivorans TG9 as a model. We identified four Resuscitation-promoting factor (Rpf) encoding genes in TG9 involved in dormancy and resuscitation. We demonstrate that R. biphenylivorans TG9 grows on fourteen typical organic pollutants, and exhibits a robust ability to degrade biphenyl and several congeners of polychlorinated biphenyls. We further induced TG9 into a dormant state and demonstrated pronounced differences in morphology and activity. Together, these results expand our understanding of the genus Rhodococcus and the relationship between dormancy and biodegradation in the presence of environmental stressors.\n\nPangenomic and functional investigations for dormancy and biodegradation features of an organic pollutant-degrading bacterium Rhodococcus biphenylivorans TG9.", "token_count": 378, "char_count": 1610, "word_count": 205, "semantic_coherence": 1, "information_density": 0.639, "quality_score": 0.8195, "entities": { "genes": [ "TG9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:35.541397", "source": { "split": "train_shard_00000", "doc_id": 2106 }, "chunk_id": "train_shard_00000_2106_0", "global_id": 2320 }, { "text": "Corynebacterium ulcerans is an emerging pathogen able to transmit the acute infection diphtheria to humans. Although there is a well-established vaccine based on the toxin produced by Corynebacterium diphtheriae, another species of this genus known to cause the disease, there is still no vaccine formulations described for C. ulcerans; this fact contributes to the increase in cases of infection that has been observed. In this study, we want to provide information at the genomic level of this bacterium in order to suggest proteins as possible vaccine targets. We carried out an in silico prospection of vaccine candidates through reverse vaccinology for targets that exhibit antigenic potential against diphtheria. We found important virulence factors, such as adhesion-related ones, that are responsible for pathogen-host interaction after infection, but we did not find the diphtheria toxin, which is the main component of the currently available vaccine. This study provides detailed information about the exoproteome and hypothetical proteins from the core genome of C. ulcerans, suggesting vaccine targets to be further tested in vitro for the development of a new vaccine against diphtheria.\n\nProteins from the core genome of Corynebacterium ulcerans respond for pathogenicity and reveal promising vaccine targets for diphtheria.", "token_count": 302, "char_count": 1339, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6294, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:36.099306", "source": { "split": "train_shard_00000", "doc_id": 2107 }, "chunk_id": "train_shard_00000_2107_0", "global_id": 2321 }, { "text": "Bile salts such as cholate are steroid compounds from the digestive tracts of vertebrates, which enter the environment upon excretion, e.g., in manure. Environmental bacteria degrade bile salts aerobically via two pathway variants involving intermediates with Δ\n\nInvestigations on the Degradation of the Bile Salt Cholate via the 9,10-", "token_count": 92, "char_count": 335, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:36.475573", "source": { "split": "train_shard_00000", "doc_id": 2108 }, "chunk_id": "train_shard_00000_2108_0", "global_id": 2322 }, { "text": "Lactic acid bacteria (LAB) are probiotic candidates that may restore the balance of microbiota populations in intestinal microbial ecosystems by controlling pathogens and thereby promoting host health. The goal of this study was to isolate potential probiotic LAB strains and characterize their antimicrobial abilities against pathogens in intestinal microbiota. Among 54 LAB strains isolated from fermented products, five LAB strains (NSMJ15, NSMJ16, NSMJ23, NSMJ42, and NFFJ04) were selected as potential probiotic candidates based on in vitro assays of acid and bile salt tolerance, cell surface hydrophobicity, adhesion to the intestinal epithelium, and antagonistic activity. Phylogenetic analysis based on 16S rRNA genes showed that they have high similarities of 99.58-100% to\n\nIn-Vitro Characterization of Growth Inhibition against the Gut Pathogen of Potentially Probiotic Lactic Acid Bacteria Strains Isolated from Fermented Products.", "token_count": 264, "char_count": 944, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "NSMJ16", "NSMJ15", "NSMJ42", "NFFJ04", "NSMJ23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:37.027992", "source": { "split": "train_shard_00000", "doc_id": 2109 }, "chunk_id": "train_shard_00000_2109_0", "global_id": 2323 }, { "text": "Comparative Genomic Analysis Determines the Functional Genes Related to Bile Salt Resistance in", "token_count": 21, "char_count": 95, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:37.383781", "source": { "split": "train_shard_00000", "doc_id": 2110 }, "chunk_id": "train_shard_00000_2110_0", "global_id": 2324 }, { "text": "A type of monophasic group B Salmonella enterica with the antigenic formula 4,12:a:- (\"Fulica-like\") has been described as associated with harbour porpoises (Phocoena phocoena), most frequently recovered from lung samples. In the present study, lung tissue samples from 47 porpoises found along the Swedish coast or as bycatch in fishing nets were analysed, two of which were positive for S. enterica. Pneumonia due to the infection was considered the likely cause of death for one of the two animals. The recovered isolates were whole genome sequenced and found to belong to sequence type (ST) 416 and to be closely related to ST416/ST417 porpoise isolates from UK waters as determined by core-genome MLST. Serovars Bispebjerg, Fulica and Abortusequi were identified as distantly related to the porpoise isolates, but no close relatives from other host species were found. All ST416/417 isolates had extensive loss of function mutations in key Salmonella pathogenicity islands, but carried accessory genetic elements associated with extraintestinal infection such as iron uptake systems. Gene ontology and pathway analysis revealed reduced secondary metabolic capabilities and loss of function in terms of signalling and response to environmental cues, consistent with adaptation for the extraintestinal niche. A classification system based on machine learning identified ST416/417 as more invasive than classical gastrointestinal serovars. Genome analysis results are thus consistent with ST416/417 as a host-adapted and extraintestinal clonal population of S. enterica, which while found in porpoises without associated pathology can also cause severe opportunistic infections.\n\nGenomic signatures of host adaptation in group B Salmonella enterica ST416/ST417 from harbour porpoises.", "token_count": 437, "char_count": 1786, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [ "ST416", "ST417" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:38.013729", "source": { "split": "train_shard_00000", "doc_id": 2111 }, "chunk_id": "train_shard_00000_2111_0", "global_id": 2325 }, { "text": "Hepatitis B virus (HBV) can hijack the host bile acids (BAs) metabolic pathway during infection in cell and animal models. Additionally, microbiome was known to play critical role in the enterohepatic cycle of BAs. However, the impact of HBV infection and associated gut microbiota on the BA metabolism in chronic hepatitis B (CHB) patients is unknown. This study aimed to unveil the distinct BA profiles in chronic HBV infection (CHB) patients with no or mild hepatic injury, and to explore the relationship between HBV, microbiome and BA metabolism with clinical implications.\n\nDistinct Bile Acid Profiles in Patients With Chronic Hepatitis B Virus Infection Reveal Metabolic Interplay Between Host, Virus and Gut Microbiome.", "token_count": 193, "char_count": 727, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6161, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:38.465540", "source": { "split": "train_shard_00000", "doc_id": 2112 }, "chunk_id": "train_shard_00000_2112_0", "global_id": 2326 }, { "text": "Members of the proposed phylum 'Candidatus Poribacteria' are among the most abundant microorganisms in the highly diverse microbiome of the sponge mesohyl. Genomic and phylogenetic characteristics of this proposed phylum are barely known. In this study, we analyzed metagenome-assembled genomes (MAGs) obtained from the coral reef excavating sponge Thoosa mismalolli from the Mexican Pacific Ocean. Two MAGs were extracted and analyzed together with 32 MAGs and single-amplified genomes (SAGs) obtained from NCBI. The phylogenetic tree based on the sequences of 139 single-copy genes (SCG) showed two clades. Clade A (23 genomes) represented 67.7% of the total of the genomes, while clade B (11 genomes) comprised 32.3% of the genomes. The Average Nucleotide Identity (ANI) showed values between 66 and 99% for the genomes of the proposed phylum, and the pangenome of genomes revealed a total of 37,234 genes that included 1722 core gene. The number of genes used in the phylogenetic analysis increased from 28 (previous studies) to 139 (this study), which allowed a better resolution of the phylogeny of the proposed phylum. The results supported the two previously described classes, 'Candidatus Entoporibacteria' and 'Candidatus Pelagiporibacteria', and the genomes SB0101 and SB0202 obtained in this study belong to two new species of the class 'Candidatus Entoporibacteria'. This is the first comparative study that includes MAGs from a non-sponge host (Porites lutea) to elucidate the taxonomy of the poorly known Candidatus phylum in a polyphasic approach. Finally, our study also contributes to the sponge microbiome project by reporting the first MAGs of the proposed phylum 'Candidatus Poribacteria' isolated from the excavating sponge T. mismalolli.", "token_count": 505, "char_count": 1760, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5665, "quality_score": 0.7833, "entities": { "genes": [ "SB0202", "SB0101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:39.134300", "source": { "split": "train_shard_00000", "doc_id": 2113 }, "chunk_id": "train_shard_00000_2113_0", "global_id": 2327 }, { "text": "Genomics and phylogeny of the proposed phylum 'Candidatus Poribacteria' associated with the excavating sponge Thoosa mismalolli.", "token_count": 40, "char_count": 128, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:39.511880", "source": { "split": "train_shard_00000", "doc_id": 2113 }, "chunk_id": "train_shard_00000_2113_1", "global_id": 2328 }, { "text": "Understanding the evolutionary forces shaping prokaryotic pangenome structure is a major goal of microbial evolution research. Recent work has highlighted that a substantial proportion of accessory genes appear to confer niche-specific adaptations. This work has primarily focused on selection acting at the level of individual cells. Herein, we discuss a lower level of selection that also contributes to pangenome variation: genic selection. This refers to cases where genetic elements, rather than individual cells, are the entities under selection. The clearest examples of this form of selection are selfish mobile genetic elements, which are those that have either a neutral or a deleterious effect on host fitness. We review the major classes of these and other mobile elements and discuss the characteristic features of such elements that could be under genic selection. We also discuss how genetic elements that are beneficial to hosts can also be under genic selection, a scenario that may be more prevalent but not widely appreciated, because disentangling the effects of selection at different levels (i.e., organisms vs. genes) is challenging. Nonetheless, an appreciation for the potential action and implications of genic selection is important to better understand the evolution of prokaryotic pangenomes.\n\nGenic Selection Within Prokaryotic Pangenomes.", "token_count": 271, "char_count": 1369, "word_count": 201, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:40.097682", "source": { "split": "train_shard_00000", "doc_id": 2114 }, "chunk_id": "train_shard_00000_2114_0", "global_id": 2329 }, { "text": "Campylobacteriosis is among the world's most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni. Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using the classifier we named aiSource. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.\n\nMachine learning to predict the source of campylobacteriosis using whole genome data.", "token_count": 376, "char_count": 1818, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:40.706410", "source": { "split": "train_shard_00000", "doc_id": 2115 }, "chunk_id": "train_shard_00000_2115_0", "global_id": 2330 }, { "text": "The increasing levels of estrogens and pollution by other steroids pose considerable challenges to the environment. In this study, the genome of Gordonia polyisoprenivorans strain R9, one of the most effective 17 beta-estradiol- and steroid-degrading bacteria, was sequenced and annotated. The circular chromosome of G. polyisoprenivorans R9 was 6,033,879 bp in size, with an average GC content of 66.91%. More so, 5213 putative protein-coding sequences, 9 rRNA, 49 tRNA, and 3 sRNA genes were predicted. The core-pan gene evolutionary tree for the genus Gordonia showed that G. polyisoprenivorans R9 is clustered with G. polyisoprenivorans VH2 and G. polyisoprenivorans C, with 93.75% and 93.8% similarity to these two strains, respectively. Altogether, the three G. polyisoprenivorans strains contained 3890 core gene clusters. Strain R9 contained 785 specific gene clusters, while 501 and 474 specific gene clusters were identified in strains VH2 and C, respectively. Furthermore, whole genome analysis revealed the existence of the steroids and estrogens degradation pathway in the core genome of all three G. polyisoprenivorans strains, although the G. polyisoprenivorans R9 genome contained more specific estrogen and steroid degradation genes. In strain R9, 207 ABC transporters, 95 short-chain dehydrogenases (SDRs), 26 monooxygenases, 21 dioxygenases, 7 aromatic ring-hydroxylating dioxygenases, and 3 CoA esters were identified, and these are very important for estrogen and steroid transport, and degradation. The results of this study could enhance our understanding of the role of G. polyisoprenivorans R9 in estradiol and steroid degradation as well as evolution within the G. polyisoprenivorans species.", "token_count": 516, "char_count": 1718, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5772, "quality_score": 0.7886, "entities": { "genes": [ "VH2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:19:41.361294", "source": { "split": "train_shard_00000", "doc_id": 2116 }, "chunk_id": "train_shard_00000_2116_0", "global_id": 2331 }, { "text": "Genomic analysis of Gordonia polyisoprenivorans strain R9, a highly effective 17 beta-estradiol- and steroid-degrading bacterium.", "token_count": 41, "char_count": 129, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:41.724224", "source": { "split": "train_shard_00000", "doc_id": 2116 }, "chunk_id": "train_shard_00000_2116_1", "global_id": 2332 }, { "text": "Brucella canis has been isolated for the first time in Italy in a commercial breeding kennel. It was diagnosed after a deep investigation related to the onset of reproductive disorders. Animals were tested with direct and indirect techniques. The agent was first detected in two Chihuahua aborted foetuses by direct culture. Further, it was also isolated from blood samples of dogs hosted in the kennel, which also showed reaction to conventional serological tests (microplate serum agglutination test). The isolates were identified as B. canis by standard microbiological methods and a Bruce‑ladder multiplex PCR. To investigate the genomic diversity, whole genome sequencing was used, applying the core genome Multilocus Sequence Typing (cgMLST ). In a first round of serological testing performed on 598 animals, 269 (46.1%) tested positive. In the second round of laboratory testing carried out 4‑5 weeks apart, the number of serologically positive dogs was 241 out of 683 tested (35.3%), while the number of dogs positive to isolation was 68 out of 683 tested (10.0%). The PCR showed a lack of sensitivity when compared to direct isolation. The epidemiological investigation did not identify the source of the infection, given the time elapsed from the onset of abortions to the definitive diagnosis of B. canis infection in the kennel. The genomic analyses featured the strains as ST21 and, according to the cgMLST, revealed the presence of a tight cluster with a maximum diversity of four allelic differences. The observed limited genomic variation, largely within the known outbreak cut‑offs, suggests that the outbreak herein described was likely caused by a single introduction. Moreover, in a broader scale comparison using the public available genomes, we found that the closest genome, isolated in China, differed by more than 50 alleles making not possible to find out the likely origin of the outbreak. The lack of updated data on B. canis genome sequences in the public databases, together with the limited information retrieved from the epidemiological investigations on the outbreak, hampered identification of the source of B. canis infection.", "token_count": 496, "char_count": 2162, "word_count": 336, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [ "ST21" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:42.377079", "source": { "split": "train_shard_00000", "doc_id": 2117 }, "chunk_id": "train_shard_00000_2117_0", "global_id": 2333 }, { "text": "First Isolation of Brucella canis from a breeding kennel in Italy.", "token_count": 19, "char_count": 66, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:42.727074", "source": { "split": "train_shard_00000", "doc_id": 2117 }, "chunk_id": "train_shard_00000_2117_1", "global_id": 2334 }, { "text": "We aim to advance the discussion on the significance of the conjugation of bile salts (BS) in our organism. We hypothesize that conjugation influences the rate of lipolysis. Since the rate of lipolysis is a compound parameter, we compare the effect of conjugation on four surface parameters, which contribute to the rate. Since deconjugation is due to gut microbiota, we hypothesize that microbiota may affect the rate of lipolysis. A meta-analysis of literature data of critical micelle concentration, β, aggregation number, and molar solubilization ratio has been performed for the first time. In addition, critical micelle concentration (CMC), interfacial tension, and lipolysis rate measurements were performed. It was found that the unconjugated BS in mixed micelles increases the antagonism between the BS, therefore, increasing the CMC. This correlated with the effect of unconjugated BS on the solubilization capacity of mixed micelles. The collected literature information indicates that the role of the BS and its conjugation in our organism is a key factor influencing the functioning of our organism, where too high levels of unconjugated BS may lead to malabsorption of fat-soluble nutrients. The experimental lipolysis results irrevocably showed that conjugation is a significant factor influencing the rate.\n\nImportance of Conjugation of the Bile Salt on the Mechanism of Lipolysis.", "token_count": 330, "char_count": 1397, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5502, "quality_score": 0.7751, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:43.291740", "source": { "split": "train_shard_00000", "doc_id": 2118 }, "chunk_id": "train_shard_00000_2118_0", "global_id": 2335 }, { "text": "Multiple downstream analyses are necessary to interpret the output of bacterial pangenome reconstruction software. This requires integrating diverse kinds of genetic and phenotypic data, which to date are left to each user's criterion. To fill this gap, we created Pagoo, a pangenome post-processing tool that leverages a standardized but flexible and extensible framework for data integration, analysis, and storage. Here, we provide the protocol for running Pagoo and performing from simple to more complex comparative analyses on bacterial pangenome data. For complete details on the use and execution of this protocol, please refer to Ferrés and Iraola (2021).\n\nProtocol for post-processing of bacterial pangenome data using Pagoo pipeline.", "token_count": 169, "char_count": 744, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:43.733354", "source": { "split": "train_shard_00000", "doc_id": 2119 }, "chunk_id": "train_shard_00000_2119_0", "global_id": 2336 }, { "text": "Mycoplasma (M.) hyorhinis is a commensal and pathobiont residing in the upper respiratory tract in swine and with the ability to spread systemically, mainly causing polyserositis and polyarthritis in nursery pigs. Since little is known on the epidemiology of M. hyorhinis infection, whole genome sequences of 73 strains isolated from pigs in Austria (n = 71) and Germany (n = 2), that have been isolated from clinically affected pigs during routine diagnostics, and publicly available genomes of eight M. hyorhinis strains were analyzed in the presented study. For this purpose, a core genome multi locus sequence typing (cgMLST) scheme encompassing 453 target genes was developed using the Ridom© SeqSphere + software. Results were compared to two previously described conventional MLST schemes and to a core genome single nucleotide polymorphism (cgSNP) analysis approach. Core genome MLST showed high diversity among the M. hyorhinis strains studied and while certain isolates from one farm or a single animal formed cgMLST clusters (≤ 8 allele differences), no isolates with identical allele profiles were identified. In addition, cgMLST had superior discriminatory power (Simpson's ID = 0.995) over conventional MLST (Simpson's ID = 0.952 and 0.985), while demonstrating a lack of congruence between conventional MLST and genome-wide relationship. Core genome SNP results were highly congruent with cgMLST results but lacked in resolution when comparing closely related isolates. Thus, cgMLST is the most suitable method for epidemiological investigations such as outbreak analysis, and to gain insights into M. hyorhinis population structure.\n\nA core genome multilocus sequence typing scheme for Mycoplasma hyorhinis.", "token_count": 437, "char_count": 1723, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6575, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:44.364921", "source": { "split": "train_shard_00000", "doc_id": 2120 }, "chunk_id": "train_shard_00000_2120_0", "global_id": 2337 }, { "text": "We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.\n\nPATO: Pangenome Analysis Toolkit.", "token_count": 120, "char_count": 570, "word_count": 79, "semantic_coherence": 1, "information_density": 0.8101, "quality_score": 0.9051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:44.753294", "source": { "split": "train_shard_00000", "doc_id": 2121 }, "chunk_id": "train_shard_00000_2121_0", "global_id": 2338 }, { "text": "Sustainable treatment of petroleum oil sludge still remains as a major challenge to petroleum refineries. Bioremediation is the promising technology involving bacteria for simultaneous production of biosurfactant and followed by degradation of petroleum compounds. Complete genomic knowledge on such potential microbes could accentuate its successful exploitation. The present study discusses the genomic characteristics of novel biosurfactant producing petrophilic/ petroleum hydrocarbon degrading strain, Enterobacter xiangfangensis STP-3, isolated from petroleum refinery oil sludge contaminated soil. The genome has 4,584,462 bp and 4372 protein coding sequences. Functional analysis using the RAST and KEGG databases revealed the presence of biosynthetic gene clusters linked to glycolipid and lipopeptide production and multiple key candidate genes linked with the degradation pathway of petroleum hydrocarbons. Orthology study revealed diversity in gene clusters associated to membrane transport, carbohydrate, amino acid metabolism, virulence and defence mechanisms, and nucleoside and nucleotide synthesis. The comparative analysis with 27 other genomes predicted that the core genome contributes to its inherent bioremediation potential, whereas the accessory genome influences its environmental adaptability in unconventional environmental conditions. Further, experimental results showed that E. xiangfangensis STP-3 was able to degrade PHCs by 82 % in 14 days during the bioremediation of real time petroleum oil sludge with the concomitant production of biosurfactant and metabolic enzymes, To the best of our knowledge, no comprehensive genomic study has been previously reported on the biotechnological prospective of this species.\n\nGenomic characterization of Enterobacter xiangfangensis STP-3: Application to real time petroleum oil sludge bioremediation.", "token_count": 449, "char_count": 1873, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:45.394415", "source": { "split": "train_shard_00000", "doc_id": 2122 }, "chunk_id": "train_shard_00000_2122_0", "global_id": 2339 }, { "text": "Salmonella enterica (\n\nSerotyping, MLST, and Core Genome MLST Analysis of", "token_count": 24, "char_count": 73, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:45.752692", "source": { "split": "train_shard_00000", "doc_id": 2123 }, "chunk_id": "train_shard_00000_2123_0", "global_id": 2340 }, { "text": "Inflammatory bowel disease (IBD) is a refractory disease that endangers both humans and animals. In recent times, Lactobacillus have been used to treat animal diseases. It may be a good choice to try to isolate Lactobacillus with probiotic potential to treat IBD. Equine, as a kind of hindgut fermentation animal has rich intestinal microflora, but data regarding this is scarce. The isolation of Lactobacillus with probiotic potential from equine may become a new method for the treatment of IBD. Four isolates of Lactobacillus were isolated from fresh feces of healthy male adult horses and analyzed their biological characteristics. According to the phylogenetic analysis, A2.5 and A7.1 were identified as Pediococcus pentosaceus, A3 as Lactobacillus plantarum, and B8.2 as Weissella cibaria. All four isolates showed tolerance to the environment of acid, bile salt concentration and simulated artificial gastrointestinal fluid. The hydrophobic rate and self-aggregation rate of A3 were close to 100%, and the adhesion rate was 28.85 ± 0.74%. Four isolates were negative in hemolysis test and sensitive to common antibiotics and different isolates had different sensitivity to antibiotics. The four isolates had antibacterial and antioxidant activities which can reflect their probiotic potential. Furthermore, they could regulate the LPS (Lipopolysaccharides) stimulated Caco-2 cells. We chose A3 as the treatment strain to intervene Dextran sulfate sodium salt (DSS)-induced mice. The results showed that compared with DSS group, DSS + A3 group exhibited reduced Disease activity index (DAI), increased colon length, reduced pathological score and regulated cytokine secretion at the level of gene expression. In this study, four isolates of Lactobacillus with probiotic potential were isolated, and Lactobacillus plantarum A3 with reduced ulcerative colitis in mice was screened. It might provide a potential treatment for IBD.", "token_count": 506, "char_count": 1933, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6184, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:46.389253", "source": { "split": "train_shard_00000", "doc_id": 2124 }, "chunk_id": "train_shard_00000_2124_0", "global_id": 2341 }, { "text": "Probiotic potential of Lactobacillus isolated from horses and its therapeutic effect on DSS-induced colitis in mice.", "token_count": 32, "char_count": 116, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:46.752800", "source": { "split": "train_shard_00000", "doc_id": 2124 }, "chunk_id": "train_shard_00000_2124_1", "global_id": 2342 }, { "text": "Molecular typing methods are used to characterize the relatedness between bacterial isolates involved in infections. These approaches rely mostly on discrete loci or whole-genome sequencing (WGS) analyses of pure cultures. On the other hand, their application to environmental DNA profiling to evaluate epidemiological relatedness among patients and environments has received less attention. We developed a specific, high-throughput short sequence typing (HiSST) method for the opportunistic human pathogen Serratia marcescens. Genes displaying the highest polymorphism were retrieved from the core genome of 60 S. marcescens strains. Bioinformatics analyses showed that use of only three loci (within\n\nA High-Throughput Short Sequence Typing Scheme for Serratia marcescens Pure Culture and Environmental DNA.", "token_count": 189, "char_count": 809, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7798, "quality_score": 0.8899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:47.198036", "source": { "split": "train_shard_00000", "doc_id": 2125 }, "chunk_id": "train_shard_00000_2125_0", "global_id": 2343 }, { "text": "Enteric pathogens, including Salmonella, are capable of long-term survival after desiccation and resist heat treatments that are lethal to hydrated cells. The mechanisms of dry-heat resistance differ from those of wet-heat resistance. To elucidate the mechanisms of dry-heat resistance in Salmonella, screening of the dry-heat resistance of 108 Salmonella strains, representing 39 serotypes, identified the 22 most resistant and the 8 most sensitive strains for comparative genome analysis. A total of 289 genes of the accessory genome were differently distributed between resistant and sensitive strains. Among these genes, 28 proteins with a putative relationship to stress resistance were selected for to quantify relative gene expression before and after desiccation and expression by solid-state cultures on agar plates relative to cultures growing in liquid culture media. Of these 28 genes, 15 genes were upregulated (\n\nGenetic Determinants of Stress Resistance in Desiccated Salmonella enterica.", "token_count": 238, "char_count": 1003, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:47.672356", "source": { "split": "train_shard_00000", "doc_id": 2126 }, "chunk_id": "train_shard_00000_2126_0", "global_id": 2344 }, { "text": "Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individual-specific binding events. GRAFIMO is available as an open-source tool, under the MIT license, at https://github.com/pinellolab/GRAFIMO and https://github.com/InfOmics/GRAFIMO.\n\nGRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs.", "token_count": 362, "char_count": 1509, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6558, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:48.248196", "source": { "split": "train_shard_00000", "doc_id": 2127 }, "chunk_id": "train_shard_00000_2127_0", "global_id": 2345 }, { "text": "Children with nonalcoholic fatty liver disease (NAFLD) display an altered gut microbiota compared with healthy children. However, little is known about the fecal bile acid profiles and their association with gut microbiota dysbiosis in pediatric NAFLD. A total of 68 children were enrolled in this study, including 32 NAFLD patients and 36 healthy children. Fecal samples were collected and analyzed by metagenomic sequencing to determine the changes in the gut microbiota of children with NAFLD, and an ultra-performance liquid chromatography coupled to tandem mass spectrometry (UPLC-MS/MS) system was used to quantify the concentrations of primary and secondary bile acids. The associations between the gut microbiota and concentrations of primary and secondary bile acids in the fecal samples were then analyzed. We found that children with NAFLD exhibited reduced levels of secondary bile acids and alterations in bile acid biotransforming-related bacteria in the feces. Notably, the decrease in Eubacterium and Ruminococcaceae bacteria, which express bile salt hydrolase and 7α-dehydroxylase, was significantly positively correlated with the level of fecal lithocholic acid (LCA). However, the level of fecal LCA was negatively associated with the abundance of the potential pathogen\n\nDisease-Associated Gut Microbiota Reduces the Profile of Secondary Bile Acids in Pediatric Nonalcoholic Fatty Liver Disease.", "token_count": 349, "char_count": 1415, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5545, "quality_score": 0.7772, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:48.816319", "source": { "split": "train_shard_00000", "doc_id": 2128 }, "chunk_id": "train_shard_00000_2128_0", "global_id": 2346 }, { "text": "The StAR-related lipid transfer (START) domain containing proteins or START proteins, encoded by a plant amplified family of evolutionary conserved genes, play important roles in lipid binding, transport, signaling, and modulation of transcriptional activity in the plant kingdom, but there is limited information on their evolution, duplication, and associated sub- or neo-functionalization. Here we perform a comprehensive investigation of this family across the rice pangenome, using 10 wild and cultivated varieties. Conservation of START domains across all 10 rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication and domain structure patterns. Analysis of synteny highlights a preponderance of segmental and dispersed duplication among STARTs, while transcriptomic investigation of the main cultivated variety\n\nStAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication.", "token_count": 230, "char_count": 1055, "word_count": 139, "semantic_coherence": 1, "information_density": 0.705, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:49.290532", "source": { "split": "train_shard_00000", "doc_id": 2129 }, "chunk_id": "train_shard_00000_2129_0", "global_id": 2347 }, { "text": "A phylogenomic study conducted with different bioinformatic tools such as TYGS, REALPHY and AAI comparisons revealed a high rate of misidentified Streptomyces albus genomes in GenBank. Only 9 of the 18 annotated genomes available in the public database were correctly identified as S. albus species. The pangenome of the nine in silico confirmed S. albus genomes was almost closed. Lignocellulosic agroresidues were a common niche among strains of the S. albus clade while carbohydrate active enzymes (CAZymes) were highly conserved. Relevant enzymes for cellulose degradation such as beta glucosidases belonging to the GH1 family, a GH6 cellulase and a monooxygenase AA10-CBM2 were encoded by all S. albus genomes. Among them, one GH1 glycosidase would be regulated by CebR. However, this regulatory mechanism was not confirmed for other genes related to cellulose degradation. Based on AntiSMASH predictions, the core secondary metabolome of S. albus encompassed a total of 23 biosynthetic gene clusters (BGCs), where 4 were related to common metabolites within Streptomyces genus. Species specific BGCs included those related to pseudouridimycin and xantholipin. Additionally, four BGCs encoded putative derivatives of ibomycin, the lasso peptide SSV-2086, the lanthipeptide SapB and the terpene isorenieratene. Known metabolites could not be assigned to ten BGCs and three clusters did not match with any previously described BGC. The core genome of S. albus retrieved from nine closely related genomes revealed a high potential for the discovery of novel bioactive metabolites and underexplored regulatory genomic elements related to lignocellulose deconstruction.\n\nPhylogenomics, CAZyome and core secondary metabolome of Streptomyces albus species.", "token_count": 484, "char_count": 1754, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6206, "quality_score": 0.8103, "entities": { "genes": [ "AA10", "GH6", "GH1", "CBM2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:49.937263", "source": { "split": "train_shard_00000", "doc_id": 2130 }, "chunk_id": "train_shard_00000_2130_0", "global_id": 2348 }, { "text": "The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis, or pangenome exploration. Although homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here, we benchmarked a two-step approach, where repeats were first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, with the k-mer-based Repeat Detector (Red) and two repeat libraries (REdat, last updated in 2013, and nrTEplants, curated for this work). Custom libraries produced by RepeatModeler were also tested. We obtained repeated genome fractions that matched those reported in the literature but with shorter repeated elements than those produced directly by sequence homology. Inspection of the masked regions that overlapped genes revealed no preference for specific protein domains. Most Red-masked sequences could be successfully classified by sequence similarity, with the complete protocol taking less than 2 h on a desktop Linux box. A guide to curating your own repeat libraries and the scripts for masking and annotating plant genomes can be obtained at https://github.com/Ensembl/plant-scripts.\n\nK-mer counting and curated libraries drive efficient annotation of repeats in plant genomes.", "token_count": 320, "char_count": 1476, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:50.503350", "source": { "split": "train_shard_00000", "doc_id": 2131 }, "chunk_id": "train_shard_00000_2131_0", "global_id": 2349 }, { "text": "The dairy yeast Kluyveromyces marxianus is a promising cell factory for producing bioethanol and heterologous proteins, as well as a robust synthetic biology platform host, due to its safe status and beneficial traits, including fast growth and thermotolerance. However, the lack of high-efficiency transformation methods hampers the fundamental research and industrial application of this yeast. Protoplast transformation is one of the most commonly used fungal transformation methods, but it yet remains unexplored in K. marxianus. Here, we established the protoplast transformation method of K. marxianus for the first time. A series of parameters on the transformation efficiency were optimized: cells were collected in the late-log phase and treated with zymolyase for protoplasting; the transformation was performed at 0 °C with carrier DNA, CaCl\n\nProtoplast transformation of Kluyveromyces marxianus.", "token_count": 207, "char_count": 907, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7031, "quality_score": 0.8516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:50.998406", "source": { "split": "train_shard_00000", "doc_id": 2132 }, "chunk_id": "train_shard_00000_2132_0", "global_id": 2350 }, { "text": "Treatment failure of methicillin-resistant\n\nA random forest model based on core genome allelic profiles of MRSA for penicillin plus potassium clavulanate susceptibility prediction.", "token_count": 46, "char_count": 180, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:51.408035", "source": { "split": "train_shard_00000", "doc_id": 2133 }, "chunk_id": "train_shard_00000_2133_0", "global_id": 2351 }, { "text": "Verticilllium wilt of cotton is a devastating soil-borne disease, which is caused by Verticillium dahliae Kleb. Bacillus velezensis strain AL7 was isolated from cotton soil. This strain efficiently inhibited the growth of V. dahliae. But the mechanism of the biocontrol strain AL7 remains poorly understood. To understand the possible genetic determinants for biocontrol traits of this strain, we conducted phenotypic, phylogenetic and comparative genomics analysis. Phenotypic analysis showed that strain AL7 exhibited broad-spectrum antifungal activities. We determined that the whole genome sequence of B. velezensis AL7 is a single circular chromosome that is 3.89 Mb in size. The distribution of putative gene clusters that could benefit to biocontrol activities was found in the genome. Phylogenetic analysis of Bacillus strains by using single core-genome clearly placed strain AL7 into the B. velezensis. Meantime, we performed comparative analyses on four Bacillus strains and observed subtle differences in their genome sequences. In addition, comparative genomics analysis showed that the core genomes of B. velezensis are more abundant in genes relevant to secondary metabolism compared with B. subtilis strains. Single mutant in the biosynthetic genes of fengycin demonstrated the function of fengycin in the antagonistic activity of B. velezensis AL7. Here, we report a new biocontrol bacterium B. velezensis AL7 and fengycin contribute to the biocontrol efficacy of the strain. The results showed in the research further sustain the potential of B. velezensis AL7 for application in agriculture production and may be a worthy biocontrol strain for further studies.\n\nComprehensive genomic analysis of Bacillus velezensis AL7 reveals its biocontrol potential against Verticillium wilt of cotton.", "token_count": 451, "char_count": 1808, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [ "AL7" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:52.073397", "source": { "split": "train_shard_00000", "doc_id": 2134 }, "chunk_id": "train_shard_00000_2134_0", "global_id": 2352 }, { "text": "Bacterial genomes typically consist of one large chromosome, but can also include secondary replicons. These so-called multipartite genomes are scattered on the bacterial tree of life with the majority of cases belonging to Proteobacteria. Within the class gamma-proteobacteria, multipartite genomes are restricted to the two families Vibrionaceae and Pseudoalteromonadaceae. Whereas the genome of vibrios is well studied, information on the Pseudoalteromonadaceae genome is much scarcer. We have studied Pseudoalteromonadaceae with respect to the origin of the chromid, how pangene categories are distributed, how genes are expressed relative to their genomic location, and identified chromid hallmark genes. We calculated the Pseudoalteromonadaceae pangenome based on 25 complete genomes and found that core/softcore are significantly overrepresented in late replicating sectors of the chromid, regardless of how the chromid is replicated. On the chromosome, core/softcore and shell/cloud genes are only weakly overrepresented at the chromosomal replication origin and termination sequences, respectively. Gene expression is trending downwards with increasing distance from the chromosomal oriC, whereas the chromidal expression pattern is more complex. Moreover, we identified 78 chromid hallmark genes, and BLASTp searches suggest that the majority of them were acquired from the ancestral gene pool of Alteromonadales. Finally, our data strongly suggest that the chromid originates from a plasmid that was acquired in a relatively recent event. In summary, this study extends our knowledge on multipartite genomes, and helps us understand how and why secondary replicons are acquired, why they are maintained, and how they are shaped by evolution.\n\nThe Pseudoalteromonas multipartite genome: distribution and expression of pangene categories, and a hypothesis for the origin and evolution of the chromid.", "token_count": 434, "char_count": 1909, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5774, "quality_score": 0.7887, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:52.733055", "source": { "split": "train_shard_00000", "doc_id": 2135 }, "chunk_id": "train_shard_00000_2135_0", "global_id": 2353 }, { "text": "Staphylococcus aureus (S. aureus) is a main pathogen associated with different types of hospital acquired infections. There are various factors associated with the virulence of S. aureus. Among these factors are biofilm formation, antibiotics resistance, alpha-toxin, and phenol-soluble modulins (PSMs) which are encoded by genes within the core genome. The aims of the present study were to identify the prevalence psm-mec gene in MRSA isolated from different types of hospital acquired infections and to study the association of this gene with biofilm formation capacity in S. aureus.\n\nMolecular Study of Mec-Phenol Soluble Modulin Gene in Methicillin Resistant Staphylococcus Aureus.", "token_count": 179, "char_count": 686, "word_count": 99, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:53.180609", "source": { "split": "train_shard_00000", "doc_id": 2136 }, "chunk_id": "train_shard_00000_2136_0", "global_id": 2354 }, { "text": "Clostridium beijerinckii is a well-known anaerobic solventogenic bacterium which inhabits a wide range of different niches. Previously, we isolated five butyrate-producing C. beijerinckii strains from pit mud (PM) of strong-flavor baijiu (SFB) ecosystems. Genome annotation of the five strains showed that they could assimilate various carbon sources as well as ammonium to produce acetate, butyrate, lactate, hydrogen, and esters but did not produce the undesirable flavors isopropanol and acetone, making them useful for further exploration in SFB production. Our analysis of the genomes of an additional 233 C. beijerinckii strains revealed an open pangenome based on current sampling and will likely change with additional genomes. The core genome, accessory genome, and strain-specific genes comprised 1567, 8851, and 2154 genes, respectively. A total of 298 genes were found only in the five C. beijerinckii strains from PM, among which only 77 genes were assigned to Clusters of Orthologous Genes categories. In addition, 15 transposase and 12 phage integrase families were found in all five C. beijerinckii strains from PM. Between 18 and 21 genome islands were predicted for the five C. beijerinckii genomes. The existence of a large number of mobile genetic elements indicated that the genomes of the five C. beijerinckii strains evolved with the loss or insertion of DNA fragments in the PM of SFB ecosystems. This study presents a genomic framework of C. beijerinckii strains from PM that could be used for genetic diversification studies and further exploration of these strains.\n\nComparative genome analysis of Clostridium beijerinckii strains isolated from pit mud of Chinese strong flavor baijiu ecosystem.", "token_count": 464, "char_count": 1722, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5885, "quality_score": 0.7942, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:53.817628", "source": { "split": "train_shard_00000", "doc_id": 2137 }, "chunk_id": "train_shard_00000_2137_0", "global_id": 2355 }, { "text": "A gene in a given taxonomic group is either present in every individual (core) or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensable genes. However, identifying if a gene belongs to the core or dispensable portion of the genome requires the construction of a pangenome, which involves sequencing the genomes of many individuals. Here we aim to leverage the previously characterized core and dispensable gene content for two grass species [Brachypodium distachyon (L.) P. Beauv. and Oryza sativa L.] to construct a machine learning model capable of accurately classifying genes as core or dispensable using only a single annotated reference genome. Such a model may mitigate the need for pangenome construction, an expensive hurdle especially in orphan crops, which often lack the adequate genomic resources.\n\nMachine learning approaches to identify core and dispensable genes in pangenomes.", "token_count": 216, "char_count": 997, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:54.286899", "source": { "split": "train_shard_00000", "doc_id": 2138 }, "chunk_id": "train_shard_00000_2138_0", "global_id": 2356 }, { "text": "Strains of\n\nGastrointestinal transit tolerance, cell surface hydrophobicity, and functional attributes of", "token_count": 24, "char_count": 105, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:54.651004", "source": { "split": "train_shard_00000", "doc_id": 2139 }, "chunk_id": "train_shard_00000_2139_0", "global_id": 2357 }, { "text": "The development of non-antibiotic and environmentally friendly agents is a key consideration for health management in shrimp aquaculture. In this study, the probiotic potential in shrimp aquaculture of Pediococcus pentosaceus MR001, isolated from Macrobrachium rosenbergii, was investigated by means of feeding trial and genetic characterization. In the feeding trial, dietary supplementation with P. pentosaceus MR001 significantly increased weight gain and digestive enzyme activity (p < 0.05) in shrimp, Litopenaeus vannamei. The intestinal histology showed that shrimp given the probiotic diet had healthier guts than the control group. Also, the immune gene expression and the survival rate in the treatment group were significantly increased when compared with the control group. The genetic characteristics of P. pentosaceus strain MR001 were explored by performing whole-genome sequencing (WGS) using the HiSeq 2500 platform and PacBio system, revealing the complete circular genome of 1,804,896 bp. We also identified 1789 coding genes and subsequently characterized genes related to the biosynthesis of bacteriocins, stress resistance, and bile tolerance. Our findings suggest that insights in the functional and genetic characteristics of P. pentosaceus strain MR001 could provide opportunities for applications of such strain in shrimp diet supplementation.\n\nEvaluation of probiotic characteristics and whole genome analysis of Pediococcus pentosaceus MR001 for use as probiotic bacteria in shrimp aquaculture.", "token_count": 376, "char_count": 1522, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "MR001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:55.238620", "source": { "split": "train_shard_00000", "doc_id": 2140 }, "chunk_id": "train_shard_00000_2140_0", "global_id": 2358 }, { "text": "Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking. We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST gene diversity among 602 isolates from sporadic clinical cases, small clusters, or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages. The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii. We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed a short-timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500-cgMLST-mismatch threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible (https://bigsdb.pasteur.fr/diphtheria). Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae. The unified genomic taxonomy of C", "token_count": 512, "char_count": 1961, "word_count": 271, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [ "PW8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:55.890419", "source": { "split": "train_shard_00000", "doc_id": 2141 }, "chunk_id": "train_shard_00000_2141_0", "global_id": 2359 }, { "text": "diphtheriae strains provides a common language for studies of ecology, evolution, and virulence heterogeneity among C. diphtheriae sublineages.\n\nGenomic Epidemiology and Strain Taxonomy of", "token_count": 52, "char_count": 188, "word_count": 24, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:56.252201", "source": { "split": "train_shard_00000", "doc_id": 2141 }, "chunk_id": "train_shard_00000_2141_1", "global_id": 2360 }, { "text": "Pseudomonas stutzeri A1501 is a model strain used to study associative nitrogen fixation, and it possesses the nitrogen regulatory NtrC protein in the core genome. Nitrogen sources represent one of the important factors affecting the efficiency of biological nitrogen fixation in the natural environment. However, the regulation of NtrC during nitrogen metabolism in P. stutzeri A1501 has not been clarified. In this work, a phenotypic analysis of the ntrC mutant characterized the roles of NtrC in nitrogen metabolism and the oxidative stress response of P. stutzeri A1501. To systematically identify NtrC-controlled gene expression, RNA-seq was performed to further analyse the gene expression differences between the wild-type strain and the ∆ntrC mutant under nitrogen fixation conditions. A total of 1431 genes were found to be significantly altered by ntrC deletion, among which 147 associative genes had NtrC-binding sites, and the pathways for nitrogen fixation regulation, nitrogenous compound acquisition and catabolism and nitrate assimilation were discussed. Furthermore, the oxidative stress-related gene (katB), which was upregulated by ntrC deletion, was suggested to be a potential target gene of NtrC, thus highlighting the importance of NtrC in nitrogenase protection against oxygen damage. Based on these findings, we propose that NtrC is a high-ranking element in the regulatory network of P. stutzeri A1501 that controls a variety of nitrogen metabolic and oxidative stress responsive traits required for adaptation to complex rhizosphere environments.\n\nMaster regulator NtrC controls the utilization of alternative nitrogen sources in Pseudomonas stutzeri A1501.", "token_count": 422, "char_count": 1684, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5726, "quality_score": 0.7863, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:56.876701", "source": { "split": "train_shard_00000", "doc_id": 2142 }, "chunk_id": "train_shard_00000_2142_0", "global_id": 2361 }, { "text": "We present pandora, a novel pan-genome graph structure and algorithms for identifying variants across the full bacterial pan-genome. As much bacterial adaptability hinges on the accessory genome, methods which analyze SNPs in just the core genome have unsatisfactory limitations. Pandora approximates a sequenced genome as a recombinant of references, detects novel variation and pan-genotypes multiple samples. Using a reference graph of 578 Escherichia coli genomes, we compare 20 diverse isolates. Pandora recovers more rare SNPs than single-reference-based tools, is significantly better than picking the closest RefSeq reference, and provides a stable framework for analyzing diverse samples without reference bias.\n\nPandora: nucleotide-resolution bacterial pan-genomics with reference graphs.", "token_count": 186, "char_count": 798, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7736, "quality_score": 0.8868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:57.327035", "source": { "split": "train_shard_00000", "doc_id": 2143 }, "chunk_id": "train_shard_00000_2143_0", "global_id": 2362 }, { "text": "Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes. We developed StrainFLAIR with the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph. On simulated data composed of mixtures of strains from the same bacterial species\n\nStrainFLAIR: strain-level profiling of metagenomic samples using variation graphs.", "token_count": 164, "char_count": 792, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7257, "quality_score": 0.8628, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:57.769448", "source": { "split": "train_shard_00000", "doc_id": 2144 }, "chunk_id": "train_shard_00000_2144_0", "global_id": 2363 }, { "text": "Pueraria flavone (PF), the main component of\n\nPueraria flavones-loaded bile salt liposomes with improved intestinal absorption and oral bioavailability:", "token_count": 39, "char_count": 152, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:58.130893", "source": { "split": "train_shard_00000", "doc_id": 2145 }, "chunk_id": "train_shard_00000_2145_0", "global_id": 2364 }, { "text": "The present research is part of an effort to create whey-based functional food. Previously, it was concluded that proteins and peptides in an encapsulation matrix contribute to mechanical properties of beads, fermentative activity, acid and bile tolerance, and the survival of probiotics during the simulated gastrointestinal condition. This research evaluates the effects of using whey protein concentrate and trypsin hydrolysate as components of a matrix for probiotic encapsulation on the antioxidant capacity of a beverage. Carrier with hydrolysate showed better encapsulation efficiency, spherical factor, and antioxidant capacity before and after fermentation compared to the carrier with non-hydrolyzed proteins. Hydrolysis of protein used for carrier formulation positively impacts the beverage's antioxidant properties and probiotic viability during 28 days of storage. Using proteins, especially peptides, as a matrix component achieved three objectives: protection of probiotics, enrichment of products with antioxidants, and neutralization of possible bitter taste (because the bitter tasting peptides are incorporated into the matrix and as such cannot contribute to the taste of the product) that bioactive peptides usually possess.\n\nEnriching alginate matrix used for probiotic encapsulation with whey protein concentrate or its trypsin-derived hydrolysate: Impact on antioxidant capacity and stability of fermented whey-based beverages.", "token_count": 336, "char_count": 1452, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:58.703245", "source": { "split": "train_shard_00000", "doc_id": 2146 }, "chunk_id": "train_shard_00000_2146_0", "global_id": 2365 }, { "text": "Amiodarone is a class 3 antiarrhythmic drug which may be associated with thyroid dysfunction. Amiodarone-induced thyrotoxicosis (AIT) is classified as type 1 (AIT 1; which may develop in the presence of latent autoimmune hyperthyroid condition) or type 2 (AIT 2; which develops in an apparently normal thyroid resulting from destructive thyroiditis). AIT 1 routinely requires treatment with thionamides, whereas AIT 2 is treated with steroids. Resistance to the conventional treatment of hyperthyroidism is not commonly found in clinical practice. This report discusses a case of AIT 2 resistant to conventional treatment. Despite being on high doses of carbimazole and steroids (prednisolone), the patient remained thyrotoxic. Cholestyramine, a bile salt sequestrant, was used as an adjunctive therapy resulting in significant clinical and biochemical improvement. The patient subsequently became euthyroid and is being followed up in endocrine clinic.\n\nResistant type 2 amiodarone-induced thyrotoxicosis responsive to cholestyramine as an adjunctive therapy.", "token_count": 273, "char_count": 1060, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6689, "quality_score": 0.8345, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:59.247784", "source": { "split": "train_shard_00000", "doc_id": 2147 }, "chunk_id": "train_shard_00000_2147_0", "global_id": 2366 }, { "text": "P-glycoprotein (P-gp) plays a critical role in the excretion of xenobiotics into bile. Previous studies have demonstrated that prolactin (PRL) regulates biotransformation and bile salt transport. Here we investigate whether the capability of the liver to transport xenobiotics into bile is altered in hyperprolactinemic states studying the modulation of hepatic P-gp by PRL.\n\nInduction of P-glycoprotein expression and activity by prolactin in female rat liver.", "token_count": 125, "char_count": 461, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:19:59.635350", "source": { "split": "train_shard_00000", "doc_id": 2148 }, "chunk_id": "train_shard_00000_2148_0", "global_id": 2367 }, { "text": "The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an\n\nGene-gene relationships in an", "token_count": 87, "char_count": 384, "word_count": 63, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:00.007820", "source": { "split": "train_shard_00000", "doc_id": 2149 }, "chunk_id": "train_shard_00000_2149_0", "global_id": 2368 }, { "text": "Isolation, characterization and assessment of inhibitor tolerance of thermotolerant yeasts associated with distillery effluent and molasses, and their use in high-temperature ethanol production from alkali-treated rice straw.\n\nBioprospecting thermotolerant yeasts from distillery effluent and molasses for high-temperature ethanol production.", "token_count": 85, "char_count": 342, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7179, "quality_score": 0.859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:00.376991", "source": { "split": "train_shard_00000", "doc_id": 2150 }, "chunk_id": "train_shard_00000_2150_0", "global_id": 2369 }, { "text": "The development of improved methods for genome-wide association studies (GWAS) for genetics of quantitative traits has been an active area of research during the last 25 years. This activity initially started with the use of mixed linear model (MLM), which was variously modified. During the last decade, however, with the availability of high throughput next generation sequencing (NGS) technology, development and use of pangenomes and novel markers including structural variations (SVs) and k-mers for GWAS has taken over as a new thrust area of research. Pangenomes and SVs are now available in humans, livestock, and a number of plant species, so that these resources along with k-mers are being used in GWAS for exploring additional genetic variation that was hitherto not available for analysis. These developments have resulted in significant improvement in GWAS methodology for detection of marker-trait associations (MTAs) that are relevant to human healthcare and crop improvement.\n\nGWAS for genetics of complex quantitative traits: Genome to pangenome and SNPs to SVs and k-mers.", "token_count": 240, "char_count": 1091, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:01.192937", "source": { "split": "train_shard_00000", "doc_id": 2151 }, "chunk_id": "train_shard_00000_2151_0", "global_id": 2370 }, { "text": "Despite many ongoing and innovative approaches, there are still formidable challenges in the clinical translation of oral peptide drugs into marketable products due to their low absorption and poor bioavailability. Herein, a novel nanocarrier platform was developed that employs a hydrophobic ion-pairing (HIP) of model peptide (insulin) and the anionic bile salt (sodium glycodeoxycholate, SGDC), and markedly improves intestinal absorption via the bile acid pathway. The developed HIP-nanocomplexes (C1 and C2) were optimized, characterized, and in vitro and in vivo evaluation were performed to assess oral efficacy of these system. The optimal molar ratios of C1 and C2-nanocomplexes were 30:1 and 6:1 (SGDC:insulin), respectively. Compared to the insulin solution, the C1 and C2 nanocomplexes significantly enhanced the permeation of insulin across the Caco-2 cell monolayers, with 6.36- and 4.05-fold increases in apparent permeability, respectively. Uptake mechanism studies were conducted using different endocytosis inhibitors and apical sodium-dependent bile acid transporter (ASBT)-transfected MDCK cells, which demonstrated the involvement of the energy-dependent ASBT-mediated active transport. Furthermore, the intrajejunal administration of C1 and C2 resulted in their pharmacological availabilities (PA) being 6.44% and 0.10%, respectively, indicating increased potential for C1, when compared to C2. Similarly, the PA and the relative bioavailability with intrajejunal administration of the C1 were 17.89-fold and 16.82-fold greater than those with intracolonic administration, respectively, confirming better jejunal absorption of C1. Overall, these findings indicate that the HIP-nanocomplexes could be a prominent platform for the effective delivery of peptides with improved intestinal absorption.\n\nBile acid transporter-mediated oral absorption of insulin via hydrophobic ion-pairing approach.", "token_count": 490, "char_count": 1915, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:01.841704", "source": { "split": "train_shard_00000", "doc_id": 2152 }, "chunk_id": "train_shard_00000_2152_0", "global_id": 2371 }, { "text": "Dextran-based gels bearing two types of pendant N, N-dimethyl-N-alkyl-N-(2-hydroxypropyl) ammonium chloride groups with different alkyl chain length substituents (C\n\nBile salts adsorption on dextran-based hydrogels.", "token_count": 75, "char_count": 215, "word_count": 25, "semantic_coherence": 1, "information_density": 0.96, "quality_score": 0.98, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:02.220007", "source": { "split": "train_shard_00000", "doc_id": 2153 }, "chunk_id": "train_shard_00000_2153_0", "global_id": 2372 }, { "text": "Microbial astaxanthin with strong antioxidant activity is greatly demanded for diverse applications. Extractive disruption in aqueous biphasic system (ABS) integrates the cells disruption and biomolecules recovery processes in one-step operation, allowing the direct recovery of intracellular biomolecules with biphasic system upon released from cells. In this study, astaxanthin was recovered from recombinant Kluyveromyces marxianus yeast cells via extractive disruption using alcohol/salt ABS. Recombinant K. marxianus yeast is engineered to produce high concentration of free form astaxanthin. Highest partition coefficient (K = 90.02 ± 2.25) and yield (Y = 96.80% ± 0.05) of astaxanthin were obtained with ABS composed of 20% (w/w) 1-propanol and 20% (w/w) sodium citrate of pH 5, 0.5% (w/w) yeast cells loading and additional of 1% (w/w) 1-butyl-3-methylimidazolium tetrafluoroborate (Bmim)BF\n\nEnhanced recovery of astaxanthin from recombinant Kluyveromyces marxianus with ultrasonication-assisted alcohol/salt aqueous biphasic system.", "token_count": 340, "char_count": 1041, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:02.812679", "source": { "split": "train_shard_00000", "doc_id": 2154 }, "chunk_id": "train_shard_00000_2154_0", "global_id": 2373 }, { "text": "The insult necessitating admission to the intensive care unit propels the patient along a course involving increasing oxidative stress, immune dysregulation, and adverse outcomes. As the largest immune organ with the greatest microbial burden, the gastrointestinal (GI) tract may change the speed and direction the patient follows along this pathway. The gut's influence is mediated by a complex process of cross-talk immune signaling between the intestinal epithelium, the liver, and the microbiome. Agents that invoke this response vary from mitochondrial DNA, inflammatory cytokines, and bacterial organisms to short-chain fatty acids and bile salts. The site of action of these agents again varies widely from pattern-recognition receptors, G protein receptors, and farnesoid X receptors in the gut and liver to transcriptional factors in epithelial cells, hepatocytes, macrophages, and neutrophils. Whereas the initial focus of response may be local within the GI tract and liver, the process extends in a systemic manner to affect immune tissue and various organs at distant sites. The gut can modulate this cross-talk signaling through numerous strategies in the design of nutrition therapy. The physiologic response to luminal nutrients and short-chain fatty acids, and more novel approaches like using phosphorylated polyethylene glycol, bovine serum-derived immunoglobulin, and specialized proresolving molecules, may help slow disease progression and even reverse the patient's course toward one of health and recovery. The optimal benefit to be derived from nutrition therapy may have more to do with the degree to which immune cross-talk signaling can be modified by such innovative strategies.\n\nCan feeding strategies alter immune signaling and gut sepsis in critical illness?", "token_count": 413, "char_count": 1790, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:03.458584", "source": { "split": "train_shard_00000", "doc_id": 2155 }, "chunk_id": "train_shard_00000_2155_0", "global_id": 2374 }, { "text": "Bacterial biosensors, or bactosensors, are promising agents for medical and environmental diagnostics. However, the lack of scalable frameworks to systematically program ligand detection limits their applications. Here we show how novel, clinically relevant sensing modalities can be introduced into bactosensors in a modular fashion. To do so, we have leveraged a synthetic receptor platform, termed EMeRALD (Engineered Modularized Receptors Activated via Ligand-induced Dimerization) which supports the modular assembly of sensing modules onto a high-performance, generic signaling scaffold controlling gene expression in E. coli. We apply EMeRALD to detect bile salts, a biomarker of liver dysfunction, by repurposing sensing modules from enteropathogenic Vibrio species. We improve the sensitivity and lower the limit-of-detection of the sensing module by directed evolution. We then engineer a colorimetric bactosensor detecting pathological bile salt levels in serum from patients having undergone liver transplant, providing an output detectable by the naked-eye. The EMeRALD technology enables functional exploration of natural sensing modules and rapid engineering of synthetic receptors for diagnostics, environmental monitoring, and control of therapeutic microbes.\n\nProgrammable receptors enable bacterial biosensors to detect pathological biomarkers in clinical samples.", "token_count": 317, "char_count": 1383, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:04.063403", "source": { "split": "train_shard_00000", "doc_id": 2156 }, "chunk_id": "train_shard_00000_2156_0", "global_id": 2375 }, { "text": "The aim of the present study was to evaluate the effects of chebulagic acid on enzymes involved in carbohydrate metabolism in high-fat diet/streptozotocin-induced diabetic rats. Diabetes was induced in albino male Wistar rats by feeding them with a high-fat diet comprising of 84.3% standard laboratory rat chow, 5% lard, 10% yolk powder, 0.2% cholesterol, and 5% bile salt for 2 weeks. After 2 weeks, the animals were kept in an overnight fast and injected with a low dose of streptozotocin (35 mg/kg, dissolved in 0.1 M sodium citrate buffer, pH 4.5). At the end of the experimental periods, the blood glucose, plasma insulin, hemoglobin, glycated hemoglobin levels, homeostatic model of insulin resistance, glycogen content, glycogen synthase, glycogen phosphorylase were measured in high-fat diet and streptozotocin-induced diabetic rats whereas the glucose metabolic enzymes such as hexokinase, glucose 6 phosphate dehydrogenase, glucose 6 phosphatase, fructose 1,6 bisphosphatase and protein expression of peroxisome proliferator-activated receptor-γ (PPAR-γ) and Glucose transporter 4 (GLUT4) were analyzed. Administration of chebulagic acid to HFD/STZ -induced diabetic rats for 30 days significantly decreased the levels of plasma glucose, homeostatic model assessment of insulin resistance, glycogen phosphorylase and glycosylated hemoglobin and increased the levels of insulin, glycogen content and glycogen synthase. On the other hand, the altered activity of carbohydrate metabolic enzymes, PPAR-γ and GLUT4 were brought back to near-normal levels on treatment with chebulagic acid", "token_count": 516, "char_count": 1594, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8164, "entities": { "genes": [ "GLUT4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:20:04.755213", "source": { "split": "train_shard_00000", "doc_id": 2157 }, "chunk_id": "train_shard_00000_2157_0", "global_id": 2376 }, { "text": "The effect produced by chebulagic acid on various parameters was comparable to that of metformin.\n\nChebulagic acid attenuates HFD/streptozotocin induced impaired glucose metabolism and insulin resistance via up regulations of PPAR γ and GLUT 4 in type 2 diabetic rats.", "token_count": 75, "char_count": 268, "word_count": 40, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:05.128543", "source": { "split": "train_shard_00000", "doc_id": 2157 }, "chunk_id": "train_shard_00000_2157_1", "global_id": 2377 }, { "text": "The reaction sequence for aerobic degradation of bile salts by environmental bacteria resembles degradation of other steroid compounds. Recent findings show that bacteria belonging to the\n\nComparative Analysis of Bile-Salt Degradation in", "token_count": 54, "char_count": 237, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:05.493106", "source": { "split": "train_shard_00000", "doc_id": 2158 }, "chunk_id": "train_shard_00000_2158_0", "global_id": 2378 }, { "text": "To improve understanding of the role of Ralstonia in cystic fibrosis (CF), whole genomes of 18 strains from clinical samples were sequenced using Illumina technology. Sequences were analysed by core genome Multi-Locus Sequence Typing, Average Nucleotide Identity based on BLAST (ANIb), RAST annotation, and by ResFinder. Phylogenetic analysis was performed for the 16S rRNA gene, and the OXA-22 and OXA-60 ß-lactamase families. The minimal inhibitory concentrations (MICs) were determined using broth microdilution. ANIb data for the 18 isolates and 54 strains from GenBank, supported by phylogenetic analysis, showed that 8 groups of clusters (A-H), as well as subgroups that should be considered as species or subspecies. Groups A-C contain strains previously identified as Ralstonia solanacearum and Ralstonia pseudosolanacearum. We propose that group A is a novel species. Group B and C are Ralstonia syzygii, Ralstonia solanacearum, respectively. Group D is composed of Ralstonia mannitolilytica and Group E of Ralstonia pickettii. Group F and G should be considered novel species. Group H strains belong to R. insidiosa. OXA-22 and OXA-60 family ß-lactamases were encoded by all strains. Co-trimoxazole generally showed high activity with low MICs (≤1 mg/l) as did ciprofloxacin (≤0.12 mg/l). MICs against the other antibiotics were more variable, but generally high. RAST annotation revealed limited differences between the strains, and virulence factors were not identified. The taxonomy of the genus Ralstonia is in need of revision, but sequencing additional isolates is needed. Antibiotic resistance levels are high. Annotation did not identify potential virulence factors.\n\nCharacterization of clinical Ralstonia strains and their taxonomic position.", "token_count": 499, "char_count": 1762, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:06.147879", "source": { "split": "train_shard_00000", "doc_id": 2159 }, "chunk_id": "train_shard_00000_2159_0", "global_id": 2379 }, { "text": "Pseudomonas viridiflava is a gram-negative pseudomonad that is phylogenetically placed within the Pseudomonas syringae species complex. P. viridiflava has a wide host range and causes a variety of symptoms in different plant parts, including stems, leaves, and blossoms. Outside of its role as a pathogen, P. viridiflava also exists as an endophyte, epiphyte, and saprophyte. Increased reports of P. viridiflava causing disease on new hosts in recent years coincide with increased research on its genetic variability, virulence, phylogenetics, and phenotypes. There is high variation in its core genome, virulence factors, and phenotypic characteristics. The main virulence factors of this pathogen include the enzyme pectate lyase and virulence genes encoded within one or two pathogenicity islands. The delineation of P. viridiflava in the P. syringae complex has been investigated using several molecular approaches. P. viridiflava comprises its own species, within the complex. While seemingly an outsider to the complex as a whole due to differences in the core genome and virulence genes, low average nucleotide identity to other of P. syringae complex members, and some phenotypic traits, it remains as part of the complex. Defining phylogenetic, phenotypic, and genomic characteristics of P. viridiflava in comparison to other P. syringae members is important to understanding this pathogen and for the development of disease resistance and management practices.\n\nPseudomonas viridiflava: An internal outsider of the Pseudomonas syringae species complex.", "token_count": 406, "char_count": 1562, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5796, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:06.767636", "source": { "split": "train_shard_00000", "doc_id": 2160 }, "chunk_id": "train_shard_00000_2160_0", "global_id": 2380 }, { "text": "Campylobacter enterocolitis may lead to post-infection irritable bowel syndrome (PI-IBS) and while some C. jejuni strains are more likely than others to cause human disease, genomic and virulence characteristics promoting PI-IBS development remain uncharacterized. We combined pangenome-wide association studies and phenotypic assays to compare C. jejuni isolates from patients who developed PI-IBS with those who did not. We show that variation in bacterial stress response (Cj0145_phoX), adhesion protein (Cj0628_CapA), and core biosynthetic pathway genes (biotin: Cj0308_bioD; purine: Cj0514_purQ; isoprenoid: Cj0894c_ispH) were associated with PI-IBS development. In vitro assays demonstrated greater adhesion, invasion, IL-8 and TNFα secretion on colonocytes with PI-IBS compared to PI-no-IBS strains. A risk-score for PI-IBS development was generated using 22 genomic markers, four of which were from Cj1631c, a putative heme oxidase gene linked to virulence. Our finding that specific Campylobacter genotypes confer greater in vitro virulence and increased risk of PI-IBS has potential to improve understanding of the complex host-pathogen interactions underlying this condition.\n\nCampylobacter jejuni genotypes are associated with post-infection irritable bowel syndrome in humans.", "token_count": 360, "char_count": 1289, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7235, "quality_score": 0.8618, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:07.348510", "source": { "split": "train_shard_00000", "doc_id": 2161 }, "chunk_id": "train_shard_00000_2161_0", "global_id": 2381 }, { "text": "Streptococcus dysgalactiae (SD) is an emerging pathogen in human and veterinary medicine, and is associated with several host species, disease phenotypes and virulence mechanisms. SD has traditionally been divided into the subspecies dysgalactiae (SDSD) and subsp. equisimilis (SDSE), but recent molecular studies have indicated that the phylogenetic relationships are more complex. Moreover, the genetic basis for the niche versatility of SD has not been extensively investigated. To expand the knowledge about virulence factors, phylogenetic relationships and host-adaptation strategies of SD, we analyzed 78 SDSD genomes from cows and sheep, and 78 SDSE genomes from other host species. Sixty SDSD and 40 SDSE genomes were newly sequenced in this study. Phylogenetic analysis supported SDSD as a distinct taxonomic entity, presenting a mean value of the average nucleotide identity of 99%. Bovine and ovine associated SDSD isolates clustered separately on pangenome analysis, but no single gene or genetic region was uniquely associated with host species. In contrast, SDSE isolates were more heterogenous and could be delineated in accordance with host. Although phylogenetic clustering suggestive of cross species transmission was observed, we predominantly detected a host restricted distribution of the SD-lineages. Furthermore, lineage specific virulence factors were detected, several of them located in proximity to hotspots for integration of mobile genetic elements. Our study indicates that SD has evolved to adapt to several different host species and infers a potential role of horizontal genetic transfer in niche specialization.\n\nWhole genome sequencing reveals possible host species adaptation of Streptococcus dysgalactiae.", "token_count": 399, "char_count": 1742, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6504, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:07.965163", "source": { "split": "train_shard_00000", "doc_id": 2162 }, "chunk_id": "train_shard_00000_2162_0", "global_id": 2382 }, { "text": "Pangenomes are organized collections of the genomic information from related individuals or groups. Graphical pangenomics is the study of these pangenomes using graphical methods to identify and analyze genes, regions, and mutations of interest to an array of biological questions. This field has seen significant progress in recent years including the development of graph based models that better resolve biological phenomena, and an explosion of new tools for mapping reads, creating graphical genomes, and performing pangenome analysis. In this review, we discuss recent developments in models, algorithms associated with graphical genomes, and comparisons between similar tools. In addition we briefly discuss what these developments may mean for the future of genomics.\n\nMethods and Developments in Graphical Pangenomics.", "token_count": 158, "char_count": 827, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:08.406589", "source": { "split": "train_shard_00000", "doc_id": 2163 }, "chunk_id": "train_shard_00000_2163_0", "global_id": 2383 }, { "text": "Bovine clinical mastitis is an important problem for the dairy industry, and Staphylococcus aureus is a common mastitis-causing pathogen in many countries. Detailed knowledge on genetic variation of Staph. aureus strains within the bovine population, including changes over time, can be useful for mastitis control programs, because severity of disease and effects on milk production are at least partly strain-associated. Therefore, the major aim of this study was to compare sequence types of Staph. aureus isolated from cases of bovine clinical mastitis from 2002 to 2003 with sequence types of a more recent set of isolates collected from 2013 to 2018, using core genome multi-locus sequence typing (cgMLST). We also wanted to compare antibiotic resistance genes of isolates from the 2 sets, to identify changes that may have occurred over time in the Staph. aureus population. A total of 157 isolates of Staph. aureus, almost equally distributed between the 2 time periods, were subjected to high-throughput sequencing and cgMLST. The results showed that the most prevalent sequence types found among the 2002 to 2003 isolates belonged to the clonal complexes CC97, CC133, and CC151, and that those complexes still dominated among the isolates from 2013 to 2018. However, a population shift from CC133 to CC97 and CC151 over time was observed. Likewise, no important differences in prevalence of antibiotic resistance genes were found between the 2 sets of isolates. As expected, genes belonging to the major facilitator superfamily of transporter proteins, and multidrug and toxic compound extrusion transporters, were very common. Moreover, several genes and mutations conferring resistance to fosfomycin were present, but not in CC97 isolates. The β-lactamase gene blaZ was found in only 3 out of 81 isolates from 2002 to 2003 and 1 out of 76 isolates in 2013 to 2018. In conclusion, the results indicate that mastitis-associated Staph", "token_count": 518, "char_count": 1943, "word_count": 302, "semantic_coherence": 1, "information_density": 0.5695, "quality_score": 0.7848, "entities": { "genes": [ "CC151", "CC97", "CC133" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:20:09.038020", "source": { "split": "train_shard_00000", "doc_id": 2164 }, "chunk_id": "train_shard_00000_2164_0", "global_id": 2384 }, { "text": "aureus strains circulating among dairy cows in Sweden exhibit a remarkable genotypic persistence over a time frame of close to 15 yr.\n\nLongitudinal study of Staphylococcus aureus genotypes isolated from bovine clinical mastitis.", "token_count": 64, "char_count": 228, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:09.413087", "source": { "split": "train_shard_00000", "doc_id": 2164 }, "chunk_id": "train_shard_00000_2164_1", "global_id": 2385 }, { "text": "Islatravir (MK-8591) is a nucleoside reverse transcriptase translocation inhibitor in development for the treatment and prevention of HIV-1. The potential for islatravir to interact with commonly co-prescribed medications was studied in vitro. Elimination of islatravir is expected to be balanced between adenosine deaminase-mediated metabolism and renal excretion. Islatravir did not inhibit uridine diphosphate glucuronosyltransferase 1A1 or cytochrome p450 (CYP) enzymes CYP1A2, 2B6, 2C8, 2C9, 2C19, 2D6, or 3A4, nor did it induce CYP1A2, 2B6, or 3A4. Islatravir did not inhibit hepatic transporters organic anion transporting polypeptide (OATP) 1B1, OATP1B3, organic cation transporter (OCT) 1, bile salt export pump (BSEP), multidrug resistance-associated protein (MRP) 2, MRP3, or MRP4. Islatravir was neither a substrate nor a significant inhibitor of renal transporters organic anion transporter (OAT) 1, OAT3, OCT2, multidrug and toxin extrusion protein (MATE) 1, or MATE2K. Islatravir did not significantly inhibit P-glycoprotein and breast cancer resistance protein (BCRP); however, it was a substrate of BCRP, which is not expected to be of clinical significance. These findings suggest islatravir is unlikely to be the victim or perpetrator of drug-drug interactions with commonly co-prescribed medications, including statins, diuretics, anti-diabetic drugs, proton pump inhibitors, anticoagulants, benzodiazepines, and selective serotonin reuptake inhibitors.\n\nIslatravir Is Not Expected to Be a Victim or Perpetrator of Drug-Drug Interactions via Major Drug-Metabolizing Enzymes or Transporters.", "token_count": 514, "char_count": 1610, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [ "OCT2", "MATE2K", "MRP4", "MRP3", "OAT3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:20:10.040195", "source": { "split": "train_shard_00000", "doc_id": 2165 }, "chunk_id": "train_shard_00000_2165_0", "global_id": 2386 }, { "text": "Nocardia is a complex and diverse genus of aerobic actinomycetes that cause complex clinical presentations, which are difficult to diagnose due to being misunderstood. To date, the genetic diversity, evolution, and taxonomic structure of the genus Nocardia are still unclear. In this study, we investigated the pan-genome of 86 Nocardia type strains to clarify their genetic diversity. Our study revealed an open pan-genome for Nocardia containing 265,836 gene families, with about 99.7% of the pan-genome being variable. Horizontal gene transfer appears to have been an important evolutionary driver of genetic diversity shaping the Nocardia genome and may have caused historical taxonomic confusion from other taxa (primarily Rhodococcus, Skermania, Aldersonia, and Mycobacterium). Based on single-copy gene families, we established a high-accuracy phylogenomic approach for Nocardia using 229 genome sequences. Furthermore, we found 28 potentially new species and reclassified 16 strains. Finally, by comparing the topology between a phylogenomic tree and 384 phylogenetic trees (from 384 single-copy genes from the core genome), we identified a novel locus for inferring the phylogeny of this genus. The dapb1 gene, which encodes dipeptidyl aminopeptidase BI, was far superior to commonly used markers for Nocardia and yielded a topology almost identical to that of genome-based phylogeny. In conclusion, the present study provides insights into the genetic diversity, contributes a robust framework for the taxonomic classification, and elucidates the evolutionary relationships of Nocardia. This framework should facilitate the development of rapid tests for the species identification of highly variable species and has given new insight into the behavior of this genus.\n\nWhole genome sequencing reveals the genomic diversity, taxonomic classification, and evolutionary relationships of the genus Nocardia.", "token_count": 470, "char_count": 1913, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6037, "quality_score": 0.8019, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:10.689630", "source": { "split": "train_shard_00000", "doc_id": 2166 }, "chunk_id": "train_shard_00000_2166_0", "global_id": 2387 }, { "text": "Enzyme engineering toward catalytic-tetrad residues usually results in activity loss. Unexpectedly, we found that a directed evolution campaign yielded a beneficial residue A100 in KmCR (a carbonyl reductase from Kluyveromyces marxianus ZJB14056), which is a residue of catalytic tetrad and conserved according to multiple sequence alignment. Inspired by this finding, we performed saturation mutagenesis on all the four residues of catalytic tetrad of KmCR. A number of variants with improved enzymatic activities were obtained. Among them, the variant KmCR_A100S exhibited increased catalytic efficiency (k\n\nTuning enzymatic properties by protein engineering toward catalytic tetrad of carbonyl reductase.", "token_count": 187, "char_count": 707, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7708, "quality_score": 0.8854, "entities": { "genes": [ "ZJB14056" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:11.137013", "source": { "split": "train_shard_00000", "doc_id": 2167 }, "chunk_id": "train_shard_00000_2167_0", "global_id": 2388 }, { "text": "A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools.\n\nRephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies.", "token_count": 205, "char_count": 886, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:11.596775", "source": { "split": "train_shard_00000", "doc_id": 2168 }, "chunk_id": "train_shard_00000_2168_0", "global_id": 2389 }, { "text": "To get a global picture of the population structure of the Escherichia coli phylogroup E, encompassing the O157:H7 EHEC lineage, we analysed the whole genome of 144 strains isolated from various continents, hosts and lifestyles and representative of the phylogroup diversity. The strains possess 4331 to 5440 genes with a core genome of 2771 genes and a pangenome of 33 722 genes. The distribution of these genes among the strains shows an asymmetric U-shaped distribution. E phylogenetic strains have the largest genomes of the species, partly explained by the presence of mobile genetic elements. Sixty-eight lineages were delineated, some of them exhibiting extra-intestinal virulence genes and being virulent in the mouse sepsis model. Except for the EHEC lineages and the reference EPEC, EIEC and ETEC strains, very few strains possess intestinal virulence genes. Most of the strains were devoid of acquired resistance genes, but eight strains possessed extended-spectrum beta-lactamase genes. Human strains belong to specific lineages, some of them being virulent and antibiotic-resistant [sequence type complexes (STcs) 350 and 2064]. The E phylogroup mimics all the features of the species as a whole, a phenomenon already observed at the STc level, arguing for a fractal population structure of E. coli.\n\nThe E phylogroup of Escherichia coli is highly diverse and mimics the whole E. coli species population structure.", "token_count": 387, "char_count": 1427, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5963, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:12.211683", "source": { "split": "train_shard_00000", "doc_id": 2169 }, "chunk_id": "train_shard_00000_2169_0", "global_id": 2390 }, { "text": "The involvement of bile salt-fibroblast growth factor 19 (FGF19) signaling in human liver regeneration (LR) is not well studied. Therefore, we studied aspects of bile salt-FGF19 signaling shortly after liver resection in patients. We compared plasma bile salt and FGF19 levels in arterial, portal and hepatic venous blood, calculated venous-arterial differences (ΔVA), and determined hepatic transcript levels on two intra-operative time points: before (< 1 hour) and immediately after (> 2-3 hours) liver resection (i.e., following surgery). Postoperative bile salt and FGF19 levels were assessed on days 1, 2, and 3. LR was studied by computed tomography (CT)-liver volumetry. Following surgery, the liver, arterial, and portal bile salt levels were elevated (\n\nBile Salt and FGF19 Signaling in the Early Phase of Human Liver Regeneration.", "token_count": 236, "char_count": 841, "word_count": 125, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:12.683218", "source": { "split": "train_shard_00000", "doc_id": 2170 }, "chunk_id": "train_shard_00000_2170_0", "global_id": 2391 }, { "text": "Responding to the recent interest of the yeast research community in non-Saccharomyces cerevisiae species of biotechnological relevance, the N.C.Yeastract (http://yeastract-plus.org/ncyeastract/) was associated to YEASTRACT + (http://yeastract-plus.org/). The YEASTRACT + portal is a curated repository of known regulatory associations between transcription factors (TFs) and target genes in yeasts. N.C.Yeastract gathers all published regulatory associations and TF-binding sites for Komagataellaphaffii (formerly Pichia pastoris), the oleaginous yeast Yarrowia lipolytica, the lactose fermenting species Kluyveromyces lactis and Kluyveromyces marxianus, and the remarkably weak acid-tolerant food spoilage yeast Zygosaccharomyces bailii. The objective of this review paper is to advertise the update of the existing information since the release of N.C.Yeastract in 2019, and to raise awareness in the community about its potential to help the day-to-day work on these species, exploring all the information available in the global YEASTRACT + portal. Using simple and widely used examples, a guided exploitation is offered for several tools: (i) inference of orthologous genes; (ii) search for putative TF binding sites and (iii) inter-species comparison of transcription regulatory networks and prediction of TF-regulated networks based on documented regulatory associations available in YEASTRACT + for well-studied species. The usage potentialities of the new CommunityYeastract platform by the yeast community are also discussed.\n\nThe N.C.Yeastract and CommunityYeastract databases to study gene and genomic transcription regulation in non-conventional yeasts.", "token_count": 428, "char_count": 1667, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:13.313767", "source": { "split": "train_shard_00000", "doc_id": 2171 }, "chunk_id": "train_shard_00000_2171_0", "global_id": 2392 }, { "text": "Since 1817, cholera, caused by Vibrio cholerae, has been characterized by seven distinct pandemics. The ongoing seventh pandemic (7P) began in 1961. In this study, we developed a Multilevel Genome Typing (MGT) tool for classifying the V. cholerae species with a focus on the 7P. MGT is based on multilocus sequence typing (MLST), but the concept has been expanded to include a series of MLST schemes that compare population structure from broad to fine resolutions. The V. cholerae MGT consists of eight levels, with the lowest, MGT1, composed of 7 loci and the highest, MGT8, consisting of the 7P core genome (3,759 loci). We used MGT to analyze 5,771 V. cholerae genomes. The genetic relationships revealed by lower MGT levels recapitulated previous findings of large-scale 7P transmission across the globe. Furthermore, the higher MGT levels provided an increased discriminatory power to differentiate subgroups within a national outbreak. Additionally, we demonstrated the usefulness of MGT for non-7P classification. In a large non-7P MGT1 type, MGT2 and MGT3 described continental and regional distributions, respectively. Finally, MGT described trends of 7P in virulence, and MGT2 to MGT3 sequence types (STs) grouped isolates of the same\n\nMultilevel Genome Typing Describes Short- and Long-Term Vibrio cholerae Molecular Epidemiology.", "token_count": 365, "char_count": 1342, "word_count": 203, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [ "MGT1", "MGT3", "MGT2", "MGT8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:13.888037", "source": { "split": "train_shard_00000", "doc_id": 2172 }, "chunk_id": "train_shard_00000_2172_0", "global_id": 2393 }, { "text": "In total, 50 Escherichia coli bloodstream isolates from the clinical laboratory and 12 E. coli isolates referred for pulsed-field gel electrophoresis (PFGE) were sequenced, assessed for clonality using core genome multilocus sequence typing (cgMLST), and evaluated for genomic susceptibility predictions using ARESdb. Results of sequence typing using whole-genome sequencing (WGS)-based MLST and sequence type (ST)-specific PCR were identical. Overall categorical agreement between genotypic (ARESdb) and phenotypic susceptibility testing for 62 isolates and 11 antimicrobial agents was 91%. Among the referred isolates, high major error rates were found for ceftazidime, cefepime, and piperacillin-tazobactam.\n\nCore Genome Multilocus Sequence Typing and Prediction of Antimicrobial Susceptibility Using Whole-Genome Sequences of Escherichia coli Bloodstream Infection Isolates.", "token_count": 241, "char_count": 878, "word_count": 111, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:14.372823", "source": { "split": "train_shard_00000", "doc_id": 2173 }, "chunk_id": "train_shard_00000_2173_0", "global_id": 2394 }, { "text": "Rheumatoid arthritis (RA) is a long-term autoimmune disorder characterized by chronic inflammation that results in swollen and painful joints and even cartilage and bone damage. The gut microbiota, a novel anti-inflammatory target, is considered an important environmental factor in the development of RA. S-propargyl-cysteine (SPRC), an amino acid analogue, exerts anti-inflammatory, cardioprotective effects, and neuroprotective effects on various diseases. In recent studies, an SPRC treatment exerted anti-inflammatory effects on RA. Meanwhile, gut microbiome dysbiosis in individuals with RA has also been reported by many researchers. However, the relationship between SPRC and gut microbiota in individuals with RA remains unclear.\n\nS-Propargyl-Cysteine Remodels the Gut Microbiota to Alleviate Rheumatoid Arthritis by Regulating Bile Acid Metabolism.", "token_count": 232, "char_count": 858, "word_count": 113, "semantic_coherence": 1, "information_density": 0.708, "quality_score": 0.854, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:14.855451", "source": { "split": "train_shard_00000", "doc_id": 2174 }, "chunk_id": "train_shard_00000_2174_0", "global_id": 2395 }, { "text": "Among pathogens, L. monocytogenes has the capability to persist on Food Processing Environment (FPE), first of all posing safety issues, then economic impact on productivity. The aim of this work was to determine the influence of biofilm forming-ability and molecular features on the persistence of 19 Listeria monocytogenes isolates obtained from FPE, raw and processed products of a cold-smoked salmon processing plant. To verify the phenotypic and genomic correlations among the isolates, different analyses were employed: serotyping, Clonal Complex (CC), core genome Multi-Locus Sequence Typing (cgMLST) and Single Nucleotide Polymorphisms (SNPs) clustering, and evaluation of the presence of virulence- and persistence-associated genes. From our results, the biofilm formation was significantly higher (*P < 0.05) at 37 °C, compared to 30 and 12 °C, suggesting a temperature-dependent behaviour. Moreover, the biofilm-forming ability showed a strain-specific trend, not correlated with CC or with strains persistence. Instead, the presence of internalin (inL), Stress Survival Islet (SSI) and resistance to erythromycin (ermC) genes was correlated with the ability to produce biofilms. Our data demonstrate that the genetic profile influences the adhesion capacity and persistence of L. monocytogenes in food processing plants and could be the result of environmental adaptation in response to the external selective pressure.\n\nGenetic relationships and biofilm formation of Listeria monocytogenes isolated from the smoked salmon industry.", "token_count": 382, "char_count": 1544, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:15.463396", "source": { "split": "train_shard_00000", "doc_id": 2175 }, "chunk_id": "train_shard_00000_2175_0", "global_id": 2396 }, { "text": "Salmonella enterica serovar Gallinarum biovar Pullorum (bvP) and biovar Gallinarum (bvG) are the etiological agents of pullorum disease (PD) and fowl typhoid (FT) respectively, which cause huge economic losses to poultry industry especially in developing countries including India. Vaccination and biosecurity measures are currently being employed to control and reduce the S. Gallinarum infections. High endemicity, poor implementation of hygiene and lack of effective vaccines pose challenges in prevention and control of disease in intensively maintained poultry flocks. Comparative genome analysis unravels similarities and dissimilarities thus facilitating identification of genomic features that aids in pathogenesis, niche adaptation and in tracing of evolutionary history. The present investigation was carried out to assess the genotypic differences amongst S.enterica serovar Gallinarum strains including Indian strain S. Gallinarum Sal40 VTCCBAA614. The comparative genome analysis revealed an open pan-genome consisting of 5091 coding sequence (CDS) with 3270 CDS belonging to core-genome, 1254 CDS to dispensable genome and strain specific genes i.e. singletons ranging from 3 to 102 amongst the analyzed strains. Moreover, the investigated strains exhibited diversity in genomic features such as virulence factors, genomic islands, prophage regions, toxin-antitoxin cassettes, and acquired antimicrobial resistance genes. Core genome identified in the study can give important leads in the direction of design of rapid and reliable diagnostics, and vaccine design for effective infection control as well as eradication. Additionally, the identified genetic differences among the S. enterica serovar Gallinarum strains could be used for bacterial typing, structure based inhibitor development by future experimental investigations on the data generated.\n\nComparative genome analysis of Salmonella enterica serovar Gallinarum biovars Pullorum and Gallinarum decodes strain specific genes.", "token_count": 468, "char_count": 2000, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6479, "quality_score": 0.824, "entities": { "genes": [ "VTCCBAA614" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:16.128856", "source": { "split": "train_shard_00000", "doc_id": 2176 }, "chunk_id": "train_shard_00000_2176_0", "global_id": 2397 }, { "text": "Pseudomonas aeruginosa is an important opportunistic pathogen especially in nosocomial infections due to its easy adaptation to different environments; this characteristic is due to the great genetic diversity that presents its genome. In addition, it is considered a pathogen of critical priority due to the high antimicrobial resistance.\n\nDiversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains.", "token_count": 96, "char_count": 436, "word_count": 61, "semantic_coherence": 1, "information_density": 0.6885, "quality_score": 0.8443, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:16.553493", "source": { "split": "train_shard_00000", "doc_id": 2177 }, "chunk_id": "train_shard_00000_2177_0", "global_id": 2398 }, { "text": "Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution (α) depends on the recombination rate in bacteria. We analyze 3,086 core protein-coding sequences from 196 genomes belonging to five closely related species of the genus Rhizobium. These genes are found in all species and do not display any signs of introgression between species. We estimate α using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of nonadaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by α in the core genome of prokaryote species in agreement with studies in eukaryotes.\n\nRecombination Facilitates Adaptive Evolution in Rhizobial Soil Bacteria.", "token_count": 347, "char_count": 1524, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6081, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:17.141864", "source": { "split": "train_shard_00000", "doc_id": 2178 }, "chunk_id": "train_shard_00000_2178_0", "global_id": 2399 }, { "text": "ABCB11 encodes the bile salt export pump (BSEP), a key regulator in maintaining bile acid (BA) homeostasis. Although inherited ABCB11 mutations have previously been linked to primary liver cancer, whether ABCB11 deficiency leads to liver cancer remains unknown. Here, we analyzed ABCB11 mRNA expression levels in liver tumor specimens [29 with hepatocellular carcinoma (HCC), one with intrahepatic cholangiocarcinoma (ICC), and one with mixed HCC/ICC] with adjacent normal specimens and published human datasets. Liver tissues obtained from Abcb11-deficient (Abcb11\n\nDisordered farnesoid X receptor signaling is associated with liver carcinogenesis in Abcb11-deficient mice.", "token_count": 188, "char_count": 674, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7912, "quality_score": 0.8956, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:18.251822", "source": { "split": "train_shard_00000", "doc_id": 2179 }, "chunk_id": "train_shard_00000_2179_0", "global_id": 2400 }, { "text": "Bacteria have highly flexible pangenomes, which are thought to facilitate evolutionary responses to environmental change, but the impacts of environmental stress on pangenome evolution remain unclear. Using a landscape pangenomics approach, I demonstrate that environmental stress leads to consistent, continuous reduction in genome content along four environmental stress gradients (acidity, aridity, heat, salinity) in naturally occurring populations of Bradyrhizobium diazoefficiens (widespread soil-dwelling plant mutualists). Using gene-level network and duplication functional traits to predict accessory gene distributions across environments, genes predicted to be superfluous are more likely lost in high stress, while genes with multi-functional roles are more likely retained. Genes with higher probabilities of being lost with stress contain significantly higher proportions of codons under strong purifying and positive selection. Gene loss is widespread across the entire genome, with high gene-retention hotspots in close spatial proximity to core genes, suggesting Bradyrhizobium has evolved to cluster essential-function genes (accessory genes with multifunctional roles and core genes) in discrete genomic regions, which may stabilise viability during genomic decay. In conclusion, pangenome evolution through genome streamlining are important evolutionary responses to environmental change. This raises questions about impacts of genome streamlining on the adaptive capacity of bacterial populations facing rapid environmental change.\n\nEnvironmental stress leads to genome streamlining in a widely distributed species of soil bacteria.", "token_count": 324, "char_count": 1654, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:18.821086", "source": { "split": "train_shard_00000", "doc_id": 2180 }, "chunk_id": "train_shard_00000_2180_0", "global_id": 2401 }, { "text": "Adhesion is considered important for Lactiplantibacillus to persist in the human gut and for it to exert probiotic effects. Lactiplantibacillus plantarum contains a considerable number and variety of genes encoding bile salt hydrolases (bsh), but their effects on microbial adhesion remain poorly understood. To clarify the effects of four bsh on adhesion, we tried to knock out bsh (Δbsh) of L. plantarum AR113 using the CRISPR-Cas9 method, and compared the growth, auto-aggregation (R\n\nGenes encoding bile salt hydrolase differentially affect adhesion of Lactiplantibacillus plantarum AR113.", "token_count": 169, "char_count": 593, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [ "AR113" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:19.260293", "source": { "split": "train_shard_00000", "doc_id": 2181 }, "chunk_id": "train_shard_00000_2181_0", "global_id": 2402 }, { "text": "Serratia marcescens is a global spread nosocomial pathogen. This rod-shaped bacterium displays a broad host range and worldwide geographical distribution. Here we analyze an international collection of this multidrug-resistant, opportunistic pathogen from 35 countries to infer its population structure. We show that S. marcescens comprises 12 lineages; Sm1, Sm4, and Sm10 harbor 78.3% of the known environmental strains. Sm5, Sm6, and Sm7 comprise only human-associated strains which harbor smallest pangenomes, genomic fluidity and lowest levels of core recombination, indicating niche specialization. Sm7 and Sm9 lineages exhibit the most concerning resistome; bla\n\nThe global population structure and beta-lactamase repertoire of the opportunistic pathogen Serratia marcescens.", "token_count": 199, "char_count": 781, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7885, "quality_score": 0.8942, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:19.711625", "source": { "split": "train_shard_00000", "doc_id": 2182 }, "chunk_id": "train_shard_00000_2182_0", "global_id": 2403 }, { "text": "Autotaxin is an enzyme that converts lysophospholipid into lysophosphatidic acid (LPA), a highly potent signaling molecule through a range of LPA receptors. It is therefore important to investigate which factors play a role in regulating ATX expression. Since we have reported that ATX levels increase dramatically in patients with various forms of cholestasis, we embarked on a study to reveal factors that influence the enzyme activity ATX as well as its expression level in vitro and in vivo.\n\nInhibition of autotaxin by bile salts and bile salt-like molecules increases its expression by feedback regulation.", "token_count": 152, "char_count": 612, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7447, "quality_score": 0.8723, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:20.152506", "source": { "split": "train_shard_00000", "doc_id": 2183 }, "chunk_id": "train_shard_00000_2183_0", "global_id": 2404 }, { "text": "Due to its safety, convenience, low cost and good compliance, oral administration attracts lots of attention. However, the efficacy of many oral drugs is limited to their unsatisfactory bioavailability in the gastrointestinal tract. One of the critical and most overlooked factors is the symbiotic gut microbiota that can modulate the bioavailability of oral drugs by participating in the biotransformation of oral drugs, influencing the drug transport process and altering some gastrointestinal properties. In this review, we summarized the existing research investigating the possible relationship between the gut microbiota and the bioavailability of oral drugs, which may provide great ideas and useful instructions for the design of novel drug delivery systems or the achievement of personalized medicine.\n\nThe influence of the gut microbiota on the bioavailability of oral drugs.", "token_count": 182, "char_count": 885, "word_count": 128, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:20.596921", "source": { "split": "train_shard_00000", "doc_id": 2184 }, "chunk_id": "train_shard_00000_2184_0", "global_id": 2405 }, { "text": "Among different causes of inflammatory bowel disease (IBD), the imbalance of the gut microbiome (dysbiosis) is one of the main reasons for the development of the disease. Probiotics are live microorganisms that can maintain gut microbiota by different mechanisms. We aimed to isolate and characterize the potential probiotic strains of\n\nIsolation and phenotypic and genotypic characterization of the potential probiotic strains of", "token_count": 105, "char_count": 430, "word_count": 62, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:20.978382", "source": { "split": "train_shard_00000", "doc_id": 2185 }, "chunk_id": "train_shard_00000_2185_0", "global_id": 2406 }, { "text": "Data mining and metagenomic analysis of 277 open reading frame sequences of bipartite RNA viruses of the genus Nepovirus, family Secoviridae, were performed, documenting how challenging it can be to unequivocally assign a virus to a particular species, especially those in subgroups A and C, based on some of the currently adopted taxonomic demarcation criteria. This work suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombination events in members of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were described previously and biologically validated as determinants of nematode transmission was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of members of subgroup A was predicted to be a putative host range determinant based on statistically supported higher π (substitutions per site) values for GFLV and ArMV isolates infecting Vitis spp. compared with non-Vitis-infecting ArMV isolates. This study illustrates how sequence information obtained via high-throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.\n\nMetagenomic analysis of nepoviruses: diversity, evolution and identification of a genome region in members of subgroup A that appears to be important for host range.", "token_count": 389, "char_count": 1716, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:21.594609", "source": { "split": "train_shard_00000", "doc_id": 2186 }, "chunk_id": "train_shard_00000_2186_0", "global_id": 2407 }, { "text": "Chlamydia trachomatis is involved in most sexually transmitted diseases. The species has emerged as a major public health threat due to its multidrug-resistant capabilities, and new therapeutic target inferences have become indispensable to combat its pathogenesis. However, no commercial vaccine is yet available to treat the C. trachomatis infection. In this study, we used the publicly available complete genome sequences of C. trachomatis and performed comparative proteomics and reverse vaccinology analyses to explore novel drug and vaccine targets against this devastating pathogen. We identified 713 core proteins from 71 C. trachomatis complete genome sequences and prioritized them based on their cellular essentiality, virulence, and available antibiotic resistance. The analyses led to the identification of 16 pathogen-specific proteins with no resolved 3D structures, though holding significant druggable potential. The sequences of the three shortlisted candidates' membrane proteins were used for designing vaccine constructs. The antigenicity, toxicity, and solubility profile-based lead epitopes were prioritized for multi-epitope-based vaccine constructs in combination with specific linkers, PADRE sequences, and molecular adjuvants for immunogenicity enhancement. The molecular-level interactions of the prioritized vaccine construct with human immune cells HLA and TLR4/MD were validated by molecular docking and molecular dynamic simulation analyses. Furthermore, the cloning and expression potential of the lead vaccine construct was predicted in the E. coli cloning vector system. Additional testing and experimental validation of these multi-epitope constructs appear promising against C. trachomatis-mediated infection.\n\nChlamydia trachomatis core genome data mining for promising novel drug targets and chimeric vaccine candidates identification.", "token_count": 406, "char_count": 1874, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:22.215451", "source": { "split": "train_shard_00000", "doc_id": 2187 }, "chunk_id": "train_shard_00000_2187_0", "global_id": 2408 }, { "text": "Several classes of polysaccharides have been described to have hypocholesterolemic potential, namely cholesterol bioaccessibility and bioavailability. This review will highlight the main mechanisms by which polysaccharides are known to affect cholesterol homeostasis at the intestine, namely the effect (i) of polysaccharide viscosity and its influence on cholesterol bioaccessibility; (ii) on bile salt sequestration and its dependence on the structural diversity of polysaccharides; (iii) of bio-transformations of polysaccharides and bile salts by the gut microbiota. Different quantitative structure-hypocholesterolemic activity relationships have been explored depending on the mechanism involved, and these were based on polysaccharide physicochemical properties, such as sugar composition and ramification degree, linkage type, size/molecular weight, and charge. The information gathered will support the rationalization of polysaccharides' effect on cholesterol homeostasis and highlight predictive rules towards the development of customized hypocholesterolemic functional food.\n\nPolysaccharide Structures and Their Hypocholesterolemic Potential.", "token_count": 270, "char_count": 1155, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6547, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:22.767640", "source": { "split": "train_shard_00000", "doc_id": 2188 }, "chunk_id": "train_shard_00000_2188_0", "global_id": 2409 }, { "text": "This study aimed to select thermotolerant yeast for bioethanol production from cellulose-rich corncob (CRC) residue. An effective yeast strain was identified as\n\nBioethanol Production from Cellulose-Rich Corncob Residue by the Thermotolerant", "token_count": 68, "char_count": 241, "word_count": 31, "semantic_coherence": 1, "information_density": 0.7742, "quality_score": 0.8871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:23.137304", "source": { "split": "train_shard_00000", "doc_id": 2189 }, "chunk_id": "train_shard_00000_2189_0", "global_id": 2410 }, { "text": "The self-assembly in mixtures of the anionic bile salt surfactant sodium deoxycholate (NaDC) and the zwitterionic phospholipid 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) in physiological saline solution has been investigated using light scattering, small-angle X-ray scattering and cryo-transmission electron microscopy. Rather small tri-axial ellipsoidal NaDC-DMPC mixed micelles form at a high content of bile salt in the mixture, which increase in size as an increasing amount of DMPC is incorporated into the micelles. Eventually, the micelles begin to grow substantially in length to form long wormlike micelles. At higher mole fractions of DMPC, the samples become turbid and cryo-TEM measurements reveal the existence of large perforated vesicles (stomatosomes), coexisting with geometrically open disks. To our knowledge, stomatosomes have not been observed before for any bile salt-phospholipid system. Mixed micelles are found to be the sole aggregate structure in a very wide regime of bile salt-phospholipid compositions, i.e. up to about 77 mol% phospholipid in the micelles. This is much higher than the corresponding value of 25 mol% observed for the conventional surfactant hexadecyltrimethylammonium bromide (CTAB) mixed with DMPC in the same solvent. The enhanced ability of bile salt surfactants to solubilize phospholipid bilayers and form mixed micelles is rationalized using bending elasticity theory. From our theoretical analysis, we are able to conclude that amphiphilic molecules rank in the following order of increasing spontaneous curvature: phospholipids < conventional surfactants < bile salts. The bending rigidity of the different amphiphilic molecules increases according to the following sequence: bile salts < conventional surfactants < phospholipids.\n\nInvestigation of the enhanced ability of bile salt surfactants to solubilize phospholipid bilayers and form mixed micelles.", "token_count": 502, "char_count": 1920, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5925, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:23.787357", "source": { "split": "train_shard_00000", "doc_id": 2190 }, "chunk_id": "train_shard_00000_2190_0", "global_id": 2411 }, { "text": "Bosentan, a well-known cholestatic agent, was not identified as cholestatic at concentrations up to 200 µM based on the drug-induced cholestasis (DIC) index value, determined in a sandwich-cultured human hepatocyte (SCHH)-based DIC assay. To obtain further quantitative insights into the effects of bosentan on cellular bile salt handling by human hepatocytes, the present study determined the effect of 2.5-25 µM bosentan on endogenous bile salt levels and on the disposition of 10 µM chenodeoxycholic acid (CDCA) added to the medium in SCHHs. Bosentan reduced intracellular as well as extracellular concentrations of both endogenous glycochenodeoxycholic acid (GCDCA) and glycocholic acid in a concentration-dependent manner. When exposed to 10 µM CDCA, bosentan caused a shift from canalicular efflux to sinusoidal efflux of GCDCA. CDCA levels were not affected. Our mechanistic model confirmed the inhibitory effect of bosentan on canalicular GCDCA clearance. Moreover, our results in SCHHs also indicated reduced GCDCA formation. We confirmed the direct inhibitory effect of bosentan on CDCA conjugation with glycine in incubations with liver S9 fraction. SIGNIFICANCE STATEMENT: Bosentan was evaluated at therapeutically relevant concentrations (2.5-25 µM) in sandwich-cultured human hepatocytes. It altered bile salt disposition and inhibited canalicular secretion of glycochenodeoxycholic acid (GCDCA). Within 24 hours, bosentan caused a shift from canalicular to sinusoidal efflux of GCDCA. These results also indicated reduced GCDCA formation. This study confirmed a direct effect of bosentan on chenodeoxycholic acid conjugation with glycine in liver S9 fraction.\n\nBosentan Alters Endo- and Exogenous Bile Salt Disposition in Sandwich-Cultured Human Hepatocytes.", "token_count": 508, "char_count": 1773, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5101, "quality_score": 0.7551, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:24.433783", "source": { "split": "train_shard_00000", "doc_id": 2191 }, "chunk_id": "train_shard_00000_2191_0", "global_id": 2412 }, { "text": "White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization of genomic diversity is still missing. Here, we report the genome sequencing of 39 accessions that were used to establish a white lupin pangenome. We defined 32 068 core genes that are present in all individuals and 14 822 that are absent in some and may represent a gene pool for breeding for improved productivity, grain quality, and stress adaptation. We used this new pangenome resource to identify candidate genes for alkaloid synthesis, a key grain quality trait. The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability within this crop. Thus, this pangenome resource is an important step towards the effective and efficient genetic improvement of white lupin to help meet the rapidly growing demand for plant protein sources for human and animal consumption.\n\nPangenome of white lupin provides insights into the diversity of the species.", "token_count": 275, "char_count": 1276, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:24.984647", "source": { "split": "train_shard_00000", "doc_id": 2192 }, "chunk_id": "train_shard_00000_2192_0", "global_id": 2413 }, { "text": "In this study, 22\n\nStudy of growth kinetic and gastrointestinal stability of acid-bile resistant", "token_count": 30, "char_count": 96, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:25.341910", "source": { "split": "train_shard_00000", "doc_id": 2193 }, "chunk_id": "train_shard_00000_2193_0", "global_id": 2414 }, { "text": "Constipation is a gastrointestinal symptom with high incidence rate and large number of patients. It is becoming one of the urgent medical problems. Poor intestinal motility is one of the important causes of constipation. Current drug treatments for constipation are associated with many side effects; thus, it is necessary to study more effective treatment methods and potential mechanism.\n\nThe edible Lactobacillus paracasei X11 with Konjac glucomannan promotes intestinal motility in zebrafish.", "token_count": 119, "char_count": 497, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7746, "quality_score": 0.8873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:25.722212", "source": { "split": "train_shard_00000", "doc_id": 2194 }, "chunk_id": "train_shard_00000_2194_0", "global_id": 2415 }, { "text": "Campylobacter has been one of the most common causative agent of bacterial food-borne gastroenteritis in humans worldwide. However, in Brazil the campylobacteriosis has been a neglected disease and there is insufficient data to estimate the incidence of this pathogen in the country.\n\nCampylobacter coli isolated in Brazil typed by core genome Multilocus Sequence Typing shows high genomic diversity in a global context.", "token_count": 97, "char_count": 420, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7742, "quality_score": 0.8871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:26.105231", "source": { "split": "train_shard_00000", "doc_id": 2195 }, "chunk_id": "train_shard_00000_2195_0", "global_id": 2416 }, { "text": "Antifungal and antibacterial activities of twenty-six combinations of lactic acid bacteria, propionibacteria, acetic acid bacteria and dairy yeasts inoculated in whey and milk were investigated. Associations including acetic acid bacteria were shown to suppress growth of the opportunistic yeast Candida albicans in well-diffusion assays. The protective effect of milk fermented with the two most promising consortia was confirmed in Caco-2 cell culture infected with C. albicans. Indeed, these fermented milks, after heat-treatment or not, suppressed lactate dehydrogenase release after 48 h while significant increase in LDH release was observed in the positive control (C. albicans alone) and with fermented milk obtained using commercial yogurt starter cultures. The analysis of volatile compounds in the cell-free supernatant using solid phase microextraction (SPME) coupled to gas chromatography-mass spectrometry (GC-MS) showed accumulation of significant amount of acetic acid by the consortium composed of Lactobacillus delbrueckii 5, Lactobacillus gallinarum 1, Lentilactobacillus parabuchneri 3, Lacticaseibacillus paracasei 33-4, Acetobacter syzygii 2 and Kluyveromyces marxianus 19, which corresponded to the zone of partial inhibition of C. albicans growth during well-diffusion assays. Interestingly, another part of anti-Candida activity, yielding small and transparent inhibition zones, was linked with the consortium cell fraction. This study showed a correlation between anti-Candida activity and the presence of acetic acid bacteria in dairy associations as well as a significant effect of two dairy associations against C. albicans in a Caco-2 cell model. These two associations may be promising consortia for developing functional dairy products with antagonistic action against candidiasis agents.\n\nDairy associations for the targeted control of opportunistic Candida.", "token_count": 471, "char_count": 1891, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6078, "quality_score": 0.8039, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:26.747299", "source": { "split": "train_shard_00000", "doc_id": 2196 }, "chunk_id": "train_shard_00000_2196_0", "global_id": 2417 }, { "text": "Lactobacillus plantarum (renamed as Lactiplantibacillus plantarum) has been isolated from many sources but very rarely from rhizospheric soil. This is the first report on isolation and assessment of probiotic capabilities of L. plantarum strains isolated from rhizospheric soil. The isolates were confirmed by 16S rRNA gene sequencing and named as NS14, NS16 and NGG. All the isolates were evaluated for bile salt hydrolysis, hypocholestrolemic potential and probiotic attributes. Our results indicated that all the strains harboured bsh and showed in vitro cholesterol assimilation capabilities which increased when bile salts were also present in the culture medium. Also, all the strains remained viable at high temperatures and in the presence of NaCl, lysozyme, simulated gastric juice, bile salts and, exhibited auto- and co-aggregation capabilities. Additionally, L. plantarum strain NS14 survived in the presence of phenols, acidic environment (pH 2-3) and was resistant to many clinically relevant antibiotics. Since, L. plantarum NS14 exhibited most of the desirable and essential characteristics of a probiotic it should be further investigated as a potent probiotic with an additional benefit as a hypocholesterolemic biotherapeutic. Moreover, rhizosphere can be explored as a useful ecological niche for isolating microorganisms with biotechnological and probiotic potential.\n\nRhizospheric Lactobacillus plantarum (Lactiplantibacillus plantarum) strains exhibit bile salt hydrolysis, hypocholestrolemic and probiotic capabilities in vitro.", "token_count": 401, "char_count": 1552, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [ "NS14", "NS16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:27.387844", "source": { "split": "train_shard_00000", "doc_id": 2198 }, "chunk_id": "train_shard_00000_2198_0", "global_id": 2418 }, { "text": "Complex carbohydrates, proteins, and other food components require a longer digestion process to be absorbed by the lining of the alimentary canal. In addition to the enzymes of the gastrointestinal tract, gut microbiota, comprising a large range of bacteria and fungi, has complementary action on the production of digestive enzymes. Within this universe of \"hidden soldiers\", lactobacilli are extensively studied because of their ability to produce lactase, proteases, peptidases, fructanases, amylases, bile salt hydrolases, phytases, and esterases. The administration of living lactobacilli cells has been shown to increase nutrient digestibility. However, it is still little known how these microbial-derived enzymes act in the human body. Enzyme secretion may be affected by variations in temperature, pH, and other extreme conditions faced by the bacterial cells in the human body. Besides, lactobacilli administration cannot itself be considered the only factor interfering with enzyme secretion, human diet (microbial substrate) being determinant in their metabolism. This review highlights the potential of lactobacilli to release functional enzymes associated with the digestive process and how this complex metabolism can be explored to contribute to the human diet. Enzymatic activity of lactobacilli is exerted in a strain-dependent manner, i.e., within the same lactobacilli species, there are different enzyme contents, leading to a large variety of enzymatic activities. Thus, we report current methods to select the most promising lactobacilli strains as sources of bioactive enzymes. Finally, a patent landscape and commercial products are described to provide the state of art of the transfer of knowledge from the scientific sphere to the industrial application.\n\nA review on enzyme-producing lactobacilli associated with the human digestive process: From metabolism to application.", "token_count": 448, "char_count": 1903, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:28.064910", "source": { "split": "train_shard_00000", "doc_id": 2199 }, "chunk_id": "train_shard_00000_2199_0", "global_id": 2419 }, { "text": "Our aim was to isolate, identify and characterize probiotic bacteria as vitamin producers in particular B2 and B9. 150 human fecal samples were collected and used for isolation of vitamin producers-probiotics. 49 isolates were chosen for screening their genome by PCR for the presence of riboflavin and folic acid genes. As a result, three isolates were selected and their production of the B2 and B9 were confirmed by HPLC. The three isolates were identified on species level by sequencing their 16S rRNA gene which showed 100% identical to strains of Pediococcus acidilactici. Thus, they were named as P. acidilactici WNYM01, P. acidilactici WNYM02, P. acidilactici WNYM03 and submitted to the Genbank database with accession numbers. They met the probiotic criteria by expressing 90-95% survival rate at pH (2.0-9.0) and bile salt up to 2% for 3 h in addition to their antimicrobial activity against gram positive and negative microorganisms. They also showed no hemolytic activity and common pattern for antibiotic susceptibility. Our three strains were tested individually or in mixture in vivo on rat colitis model compared to ulcerative group. The strains were administrated orally to rats in daily dose containing CFU 109 for 14 days then followed by induction of colitis using acetic acid then the oral administration was continued for more four days. The histology results, the anti-inflammatory and anti-oxidative stress biomarkers showed the protective role of the strains compared to the ulcerative group. As a conclusion, we introduce novel three probiotic candidates for pharmaceutical preparations and health applications.\n\nInhibition of acetic acid-induced colitis in rats by new Pediococcus acidilactici strains, vitamin producers recovered from human gut microbiota.", "token_count": 459, "char_count": 1785, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [ "WNYM01", "WNYM02", "WNYM03" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:28.738547", "source": { "split": "train_shard_00000", "doc_id": 2200 }, "chunk_id": "train_shard_00000_2200_0", "global_id": 2420 }, { "text": "The purpose of the study was to characterize the resistome, virulome, mobilome and Clustered Regularly Interspaced Short Palindromic Repeats-associated (CRISPR-Cas) system of extended-spectrum β-lactamase producing Klebsiella pneumoniae (ESBL-KP) clinical isolates and to determine their phylogenetic relatedness. The isolates were from Algeria, isolated at the University Hospital Establishment of Oran, between 2011 and 2012. ESBL-KP isolates (n = 193) were screened for several antibiotic resistance genes (ARGs) using qPCR followed by Pulsed-Field Gel Electrophoresis (PFGE). Representative isolates were selected from PFGE clusters and subjected to whole-genome sequencing (WGS). Genomic characterization of the WGS data by studying prophages, CRISPR-Cas systems, Multi-Locus Sequence Typing (MLST), serotype, ARGs, virulence genes, plasmid replicons, and their pMLST. Phylogenetic and comparative genomic were done using core genome MLST and SNP-Based analysis. Generally, the ESBL-KP isolates were polyclonal. The whole genome sequences of nineteen isolates were taken of main PFGE clusters. Sixteen sequence types (ST) were found including high-risk clones ST14, ST23, ST37, and ST147. Serotypes K1 (n = 1), K2 (n = 2), K3 (n = 1), K31 (n = 1), K62 (n = 1), and K151 (n = 1) are associated with hyper-virulence. CRISPR-Cas system was found in 47.4%, typed I-E and I-E*", "token_count": 444, "char_count": 1376, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [ "ST23", "ST37", "ST147", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:29.760551", "source": { "split": "train_shard_00000", "doc_id": 2201 }, "chunk_id": "train_shard_00000_2201_0", "global_id": 2421 }, { "text": "About ARGs, from 193 ESBL-KP, the majority of strains were multidrug-resistant, the CTX-M-1 enzyme was predominant (99%) and the prevalence of plasmid-mediated quinolone resistance (PMQR) genes was high with aac(6')-lb-cr (72.5%) and qnr's (65.8%). From 19 sequenced isolates we identified ESBL, AmpC, and carbapenemase genes: blaCTX-M-15 (n = 19), blaOXA-48 (n = 1), blaCMY-2 (n = 2), and blaCMY-16 (n = 2), as well as non-ESBL genes: qnrB1 (n = 12), qnrS1 (n = 1) and armA (n = 2). We found IncF, IncN, IncL/M, IncA/C2, and Col replicon types, at least once per isolate. This study is the first to report qnrS in ESBL-KP in Algeria. Our analysis shows the concerning co-existence of virulence and resistance genes and would support that genomic surveillance should be a high priority in the hospital environment.\n\nHigh-risk clones of extended-spectrum β-lactamase-producing Klebsiella pneumoniae isolated from the University Hospital Establishment of Oran, Algeria (2011-2012).", "token_count": 361, "char_count": 979, "word_count": 150, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:30.346487", "source": { "split": "train_shard_00000", "doc_id": 2201 }, "chunk_id": "train_shard_00000_2201_1", "global_id": 2422 }, { "text": "Plant genomes demonstrate significant presence/absence variation (PAV) within a species; however, the factors that lead to this variation have not been studied systematically in Brassica across diploids and polyploids. Here, we developed pangenomes of polyploid Brassica napus and its two diploid progenitor genomes B. rapa and B. oleracea to infer how PAV may differ between diploids and polyploids. Modelling of gene loss suggests that loss propensity is primarily associated with transposable elements in the diploids while in B. napus, gene loss propensity is associated with homoeologous recombination. We use these results to gain insights into the different causes of gene loss, both in diploids and following polyploidization, and pave the way for the application of machine learning methods to understanding the underlying biological and physical causes of gene presence/absence.\n\nModelling of gene loss propensity in the pangenomes of three Brassica species suggests different mechanisms between polyploids and diploids.", "token_count": 240, "char_count": 1030, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:30.814202", "source": { "split": "train_shard_00000", "doc_id": 2202 }, "chunk_id": "train_shard_00000_2202_0", "global_id": 2423 }, { "text": "Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae. Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae, these yeasts cannot grow in the absence of oxygen. Responses of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus. Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus. After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.\n\nEngineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth.", "token_count": 332, "char_count": 1286, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:31.381281", "source": { "split": "train_shard_00000", "doc_id": 2203 }, "chunk_id": "train_shard_00000_2203_0", "global_id": 2424 }, { "text": "Bile salt synthesis, secretion into the intestinal lumen, and resorption in the ileum occur in all vertebrate classes. In mammals, bile salt composition is determined by host and microbial enzymes, affecting signaling through the bile salt-binding transcription factor farnesoid X receptor (Fxr). However, these processes in other vertebrate classes remain poorly understood. We show that key components of hepatic bile salt synthesis and ileal transport pathways are conserved and under control of Fxr in zebrafish. Zebrafish bile salts consist primarily of a C\n\nFxr signaling and microbial metabolism of bile salts in the zebrafish intestine.", "token_count": 173, "char_count": 644, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7053, "quality_score": 0.8526, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:31.819337", "source": { "split": "train_shard_00000", "doc_id": 2204 }, "chunk_id": "train_shard_00000_2204_0", "global_id": 2425 }, { "text": "A total of 54 unique clinical Acinetobacter baumannii strains isolated from cerebrospinal fluid (CSF) together with 21 bloodstream isolates collected from five tertiary hospitals in East China between April 2013 and November 2016 were studied for antimicrobial susceptibility patterns and the prevalence of antimicrobial resistance genes. Molecular epidemiological characteristics of CSF isolates and the phylogenetic relationship of isolates from different sources were assessed using multilocus sequence typing (MLST) and core genome MLST (cgMLST). Of the 54 CSF isolates, 51 (94.4%) were bla\n\nAcinetobacter baumannii strains isolated from cerebrospinal fluid (CSF) and bloodstream analysed by cgMLST: the dominance of clonal complex CC92 in CSF infections.", "token_count": 209, "char_count": 759, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "CC92" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:32.292310", "source": { "split": "train_shard_00000", "doc_id": 2205 }, "chunk_id": "train_shard_00000_2205_0", "global_id": 2426 }, { "text": "The transmissible locus of stress tolerance (tLST) is found mainly in beta- and gamma-Proteobacteria and confers tolerance to elevated temperature, pressure, and chlorine. This genomic island, previously referred to as transmissible locus of protein quality control or locus of heat resistance likely originates from an environmental bacterium thriving in extreme habitats, but has been widely transmitted by lateral gene transfer. Although highly conserved, the gene content on the island is subject to evolution and gene products such as small heat shock proteins are present in several functionally distinct sequence variants. A number of these genes are xenologs of core genome genes with the gene products to widen the substrate spectrum and to be highly (complementary) expressed thus their functionality to become dominant over core genome genes. In this review, we will present current knowledge of the function of core tLST genes and discuss current knowledge on selection and counter-selection processes that favor maintenance of the tLST island, with frequent acquisition of gene products involved in cyclic di-GMP signaling, in different habitats from the environment to animals and plants, processed animal and plant products, man-made environments, and subsequently humans.\n\nHorizontal Transmission of Stress Resistance Genes Shape the Ecology of Beta- and Gamma-Proteobacteria.", "token_count": 292, "char_count": 1392, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:32.856818", "source": { "split": "train_shard_00000", "doc_id": 2206 }, "chunk_id": "train_shard_00000_2206_0", "global_id": 2427 }, { "text": "Genomic selection approaches have increased the speed of plant breeding, leading to growing crop yields over the last decade. However, climate change is impacting current and future yields, resulting in the need to further accelerate breeding efforts to cope with these changing conditions. Here we present approaches to accelerate plant breeding and incorporate nonadditive effects in genomic selection by applying state-of-the-art machine learning approaches. These approaches are made more powerful by the inclusion of pangenomes, which represent the entire genome content of a species. Understanding the strengths and limitations of machine learning methods, compared with more traditional genomic selection efforts, is paramount to the successful application of these methods in crop breeding. We describe examples of genomic selection and pangenome-based approaches in crop breeding, discuss machine learning-specific challenges, and highlight the potential for the application of machine learning in genomic selection. We believe that careful implementation of machine learning approaches will support crop improvement to help counter the adverse outcomes of climate change on crop production.\n\nThe application of pangenomics and machine learning in genomic selection in plants.", "token_count": 233, "char_count": 1285, "word_count": 178, "semantic_coherence": 1, "information_density": 0.5674, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:33.330206", "source": { "split": "train_shard_00000", "doc_id": 2207 }, "chunk_id": "train_shard_00000_2207_0", "global_id": 2428 }, { "text": "Cyclosporine A (CyA) causes intrahepatic biliary stasis via inhibition of bile acid excretion through the bile salt export pump. We report a case of a patient in whom ursodeoxycholic acid (UDCA) markedly promoted the absorption of microemulsion-formulated CyA.\n\nUrsodeoxycholic acid markedly promotes the absorption of microemulsion-formulated cyclosporine A: A case report.", "token_count": 105, "char_count": 374, "word_count": 51, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:33.707070", "source": { "split": "train_shard_00000", "doc_id": 2208 }, "chunk_id": "train_shard_00000_2208_0", "global_id": 2429 }, { "text": "Bacillus subtilis is ubiquitous and capable of producing various metabolites, which make the bacterium a good candidate as a biocontrol agent for managing plant diseases. In this study, a phyllosphere bacterium B. subtilis PMB102 isolated from tomato leaf was found to inhibit the growth of Alternaria brassicicola ABA-31 on PDA and suppress Alternaria leaf spot on Chinese cabbage (Brassica rapa). The genome of PMB102 (Accession no. CP047645) was completely sequenced by Nanopore and Illumina technology to generate a circular chromosome of 4,103,088 bp encoding several gene clusters for synthesizing bioactive compounds. PMB102 and the other B. subtilis strains from different sources were compared in pangenome analysis to identify a suite of conserved genes involved in biocontrol and habitat adaptation. Two predicted gene products, surfactin and fengycin, were extracted from PMB102 culture filtrates and verified by LC-MS/MS. The antifungal activity of fengycin was tested on A. brassicicola ABA-31 in bioautography to inhibit hyphae growth, and in co-culturing assays to elicit the formation of swollen hyphae. Our data revealed that B. subtilis PMB102 suppresses Alternaria leaf spot by the production of antifungal metabolites, and fengycin plays an important role to inhibit the vegetative growth of A. brassicicola ABA-31.\n\nGenomic and biochemical characterization of antifungal compounds produced by Bacillus subtilis PMB102 against Alternaria brassicicola.", "token_count": 413, "char_count": 1472, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6161, "quality_score": 0.8081, "entities": { "genes": [ "CP047645", "PMB102" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:34.335812", "source": { "split": "train_shard_00000", "doc_id": 2209 }, "chunk_id": "train_shard_00000_2209_0", "global_id": 2430 }, { "text": "A method for real-time monitoring of lipid digestion based on photonic crystals formed from silica was developed. As an effective \"net\", the highly ordered silica colloidal crystal (SCC) film provides structural support for lipid payload. This method based on optical interferometric film kinetics was used to record the whole kinetics progress of olive oil hydrolysis by lipase in real time and calculate the kinetic Michaelis constant. The kinetic parameters were compared with the results determined by the titration method. The effects of bile salt content on lipase and olive oil layer were studied. This method provides a potential evaluation system for real-time digestion and degradation of edible oil in the food field. It also provides a basis for further real-time evaluation of lipid bioavailability in food systems by real-time recording the release and degradation of lipids in the food nano-matrix.\n\nConstruction of lipid layer and monitoring its digestion by optical interferometry.", "token_count": 219, "char_count": 998, "word_count": 151, "semantic_coherence": 1, "information_density": 0.5828, "quality_score": 0.7914, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:34.805533", "source": { "split": "train_shard_00000", "doc_id": 2210 }, "chunk_id": "train_shard_00000_2210_0", "global_id": 2431 }, { "text": "Acinetobacter baumannii has become one of the most important multidrug-resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages coexisting in hospital settings. Here, using whole-genome sequencing, epidemiological data, and antimicrobial susceptibility tests, we uncover the transmission dynamics of extensive and multidrug-resistant A. baumannii in a tertiary hospital over a decade. Our core genome phylogeny of almost 300 genomes suggests that there were several introductions of lineages from international clone 2 into the hospital. The molecular dating analysis shows that these introductions happened in 2006, 2007, and 2013. Furthermore, using the accessory genome, we show that these lineages were extensively disseminated across many wards in the hospital. Our results demonstrate that accessory genome variation can be a very powerful tool for conducting genomic epidemiology. We anticipate future studies employing the accessory genome along with the core genome as a powerful phylogenomic strategy to track bacterial transmissions over very short microevolutionary scales.\n\nAccessory Genomic Epidemiology of Cocirculating Acinetobacter baumannii Clones.", "token_count": 300, "char_count": 1239, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6726, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:35.375569", "source": { "split": "train_shard_00000", "doc_id": 2211 }, "chunk_id": "train_shard_00000_2211_0", "global_id": 2432 }, { "text": "Bile acids play crucial roles in host physiology by acting both as detergents that aid in digestion and as signaling molecules that bind to host receptors. Gut bacterial bile salt hydrolase (BSH) enzymes perform the gateway reaction leading to the conversion of host-produced primary bile acids into bacterially modified secondary bile acids. Small molecule probes that target BSHs will help elucidate the causal roles of these metabolites in host physiology. We previously reported the development of a covalent BSH inhibitor with low gut permeability. Here, we build on our previous findings and describe the development of a second-generation gut-restricted BSH inhibitor with enhanced potency, reduced off-target effects, and durable\n\nA Gut-Restricted Lithocholic Acid Analog as an Inhibitor of Gut Bacterial Bile Salt Hydrolases.", "token_count": 212, "char_count": 834, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6911, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:35.839773", "source": { "split": "train_shard_00000", "doc_id": 2212 }, "chunk_id": "train_shard_00000_2212_0", "global_id": 2433 }, { "text": "The stiff-stalk heterotic group in Maize (Zea mays L.) is an important source of inbreds used in U.S. commercial hybrid production. Founder inbreds B14, B37, B73, and, to a lesser extent, B84, are found in the pedigrees of a majority of commercial seed parent inbred lines. We created high-quality genome assemblies of B84 and four expired Plant Variety Protection (ex-PVP) lines LH145 representing B14, NKH8431 of mixed descent, PHB47 representing B37, and PHJ40, which is a Pioneer Hi-Bred International (PHI) early stiff-stalk type. Sequence was generated using long-read sequencing achieving highly contiguous assemblies of 2.13-2.18 Gbp with N50 scaffold lengths >200 Mbp. Inbred-specific gene annotations were generated using a core five-tissue gene expression atlas, whereas transposable element (TE) annotation was conducted using de novo and homology-directed methodologies. Compared with the reference inbred B73, synteny analyses revealed extensive collinearity across the five stiff-stalk genomes, although unique components of the maize pangenome were detected. Comparison of this set of stiff-stalk inbreds with the original Iowa Stiff Stalk Synthetic breeding population revealed that these inbreds represent only a proportion of variation in the original stiff-stalk pool and there are highly conserved haplotypes in released public and ex-Plant Variety Protection inbreds. Despite the reduction in variation from the original stiff-stalk population, substantial genetic and genomic variation was identified supporting the potential for continued breeding success in this pool. The assemblies described here represent stiff-stalk inbreds that have historical and commercial relevance and provide further insight into the emerging maize pangenome.\n\nGenomic variation within the maize stiff-stalk heterotic germplasm pool.", "token_count": 473, "char_count": 1836, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8275, "entities": { "genes": [ "NKH8431", "PHB47", "LH145", "PHJ40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:36.484927", "source": { "split": "train_shard_00000", "doc_id": 2213 }, "chunk_id": "train_shard_00000_2213_0", "global_id": 2434 }, { "text": "Future expansion of corn-derived ethanol raises concerns of sustainability and competition with the food industry. Therefore, cellulosic biofuels derived from agricultural waste and dedicated energy crops are necessary. To date, slow and incomplete saccharification as well as high enzyme costs have hindered the economic viability of cellulosic biofuels, and while approaches like simultaneous saccharification and fermentation (SSF) and the use of thermotolerant microorganisms can enhance production, further improvements are needed. Cellulosic emulsions have been shown to enhance saccharification by increasing enzyme contact with cellulose fibers. In this study, we use these emulsions to develop an emulsified SSF (eSSF) process for rapid and efficient cellulosic biofuel production and make a direct three-way comparison of ethanol production between S. cerevisiae, O. polymorpha, and K. marxianus in glucose and cellulosic media at different temperatures.\n\nCellulosic biofuel production using emulsified simultaneous saccharification and fermentation (eSSF) with conventional and thermotolerant yeasts.", "token_count": 258, "char_count": 1111, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6849, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:37.028473", "source": { "split": "train_shard_00000", "doc_id": 2214 }, "chunk_id": "train_shard_00000_2214_0", "global_id": 2435 }, { "text": "Cholesterol overloading and bile acid metabolic disorders play an important role in the onset of cholesterol gallstone (CGS). Short-chain fatty acids (SCFAs) can regulate bile acid metabolism by modulating the gut microbiota. However, the role and mechanism by which sodium butyrate (NaB) targets bile acids to attenuate CGS are still unknown. In this study, continuous administration of 12 mg/day for 8 weeks was decreased the incidence of gallstones induced by lithogenic diet (LD) from 100% to 25%. NaB modulated SCFAs and improved the gut microbiota. The remodeling of the gut microbiota changed the bile acid compositions and decreased cecal tauro-α-muricholic acid (T-α-MCA) and tauro-β-muricholic acid (T-β-MCA) which are effective farnesoid X receptor (FXR) antagonists. The quantitative real-time PCR examination showed that NaB significantly increased levels of ileal Fxr, fibroblast growth factor-15 (Fgf-15) and small heterodimer partner (Shp) mRNA and subsequently inhibited bile acid synthesis. In addition, NaB enhanced bile acid excretion by increasing the levels of hepatic multidrug resistance protein 2 (Mdr2) and bile salt export pump (Bsep) mRNA, and it enhanced bile acid reabsorption in the intestine by increasing the levels of ileal bile acid transporter (Ibat) mRNA. In addition, NaB reduced the absorption of cholesterol in the intestine and inhibited the excretion of cholesterol in the liver, which reduced the cholesterol concentration in serum and bile. Furthermore, the protective effects of NaB administration were abolished by FXR antagonists. Taken together, our results suggest that NaB mitigates CGS by modulating the gut microbiota to regulate the FXR-FGF-15/SHP signaling pathway.", "token_count": 496, "char_count": 1719, "word_count": 250, "semantic_coherence": 1, "information_density": 0.58, "quality_score": 0.79, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:37.673132", "source": { "split": "train_shard_00000", "doc_id": 2215 }, "chunk_id": "train_shard_00000_2215_0", "global_id": 2436 }, { "text": "Sodium butyrate alleviates cholesterol gallstones by regulating bile acid metabolism.", "token_count": 27, "char_count": 85, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:38.027679", "source": { "split": "train_shard_00000", "doc_id": 2215 }, "chunk_id": "train_shard_00000_2215_1", "global_id": 2437 }, { "text": "Sodium deoxycholate is a natural bile salt produced by animals and fulfilling important physiological processes. It is also used as dispersive surfactant and building block for self-assembled architectures in biology and material science. Although long debated, the study of its self-assembly in water is hereto incomplete and the models of the known aggregates are still controversial. This background suggests a complex scenario likely missing of additional mesophases.\n\nRevealing the complex self-assembly behaviour of sodium deoxycholate in aqueous solution.", "token_count": 121, "char_count": 562, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:38.417950", "source": { "split": "train_shard_00000", "doc_id": 2216 }, "chunk_id": "train_shard_00000_2216_0", "global_id": 2438 }, { "text": "Lactic acid bacteria (LAB) are a representative probiotic. As the dominant flora in the human intestinal tract, LAB can regulate the balance of human intestinal flora and improve host health. The purpose of this study was to isolate and screen LAB that are well suited to the intestinal characteristics of the Chinese population, with excellent probiotics and high antibacterial activity. After 16S ribosomal RNA (rRNA) homology and phylogenetic tree analysis, potential probiotics were tested for their antibacterial activity, resistance to artificial gastrointestinal fluid and drugs, surface hydrophobicity, and safety. Three strains of LAB with acid resistance, bile salt resistance, epithelial cell adhesion, and no multidrug resistance were selected:\n\nScreening beneficial bacteriostatic lactic acid bacteria in the intestine and studies of bacteriostatic substances.", "token_count": 209, "char_count": 873, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6885, "quality_score": 0.8443, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:38.880525", "source": { "split": "train_shard_00000", "doc_id": 2217 }, "chunk_id": "train_shard_00000_2217_0", "global_id": 2439 }, { "text": "Natural bacterial populations can display enormous genomic diversity, primarily in the form of gene content variation caused by the frequent exchange of DNA with the local environment. However, the ecological drivers of genomic variability and the role of selection remain controversial. Here, we address this gap by developing a nationwide atlas of 1,854 Listeria isolates, collected systematically from soils across the contiguous United States. We found that Listeria was present across a wide range of environmental parameters, being mainly controlled by soil moisture, molybdenum and salinity concentrations. Whole-genome data from 594 representative strains allowed us to decompose Listeria diversity into 12 phylogroups, each with large differences in habitat breadth and endemism. 'Cosmopolitan' phylogroups, prevalent across many different habitats, had more open pangenomes and displayed weaker linkage disequilibrium, reflecting higher rates of gene gain and loss, and allele exchange than phylogroups with narrow habitat ranges. Cosmopolitan phylogroups also had a large fraction of genes affected by positive selection. The effect of positive selection was more pronounced in the phylogroup-specific core genome, suggesting that lineage-specific core genes are important drivers of adaptation. These results indicate that genome flexibility and recombination are the consequence of selection to survive in variable environments.\n\nNationwide genomic atlas of soil-dwelling Listeria reveals effects of selection and population ecology on pangenome evolution.", "token_count": 337, "char_count": 1569, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:39.476231", "source": { "split": "train_shard_00000", "doc_id": 2218 }, "chunk_id": "train_shard_00000_2218_0", "global_id": 2440 }, { "text": "Kluyveromyces marxianus is a yeast that could be identified from kefir and can use a broad range of substrates, such as glucose and lactate, as carbon sources. The lactate produced in kefir culture can be a substrate for K. marxianus. However, the complexity of the kefir microbiota makes the traits of K. marxianus difficult to study. In this research, we focused on K. marxianus cultured with lactate as the sole carbon source. The optimal growth and released protein in lactate culture were determined under different pH conditions, and the LC-MS/MS-identified proteins were associated with the tricarboxylic acid cycle, glycolysis pathway, and cellular stress responses in cells, indicating that autolysis of K. marxianus had occurred under the culture conditions. The abundant glyceraldehyde-3-phosphate dehydrogenase 1 (GAP1) was cocrystallized with other proteins in the cell-free fraction, and the low transcription level of the GAP1 gene indicated that the protein abundance under autolysis conditions was dependent on protein stability. These results suggest that lactate induces the growth and autolysis of K. marxianus, releasing proteins and peptides. These findings can be fundamental for K. marxianus probiotic and kefir studies in the future.\n\nGrowth and autolysis of the kefir yeast Kluyveromyces marxianus in lactate culture.", "token_count": 357, "char_count": 1343, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5528, "quality_score": 0.7764, "entities": { "genes": [ "GAP1" ], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:40.067023", "source": { "split": "train_shard_00000", "doc_id": 2219 }, "chunk_id": "train_shard_00000_2219_0", "global_id": 2441 }, { "text": "The Study of Association between Laryngopharyngeal Reflux and Vocal Fold Leukoplakia Requires Pepsin and Bile Salt Tissue Analyses.", "token_count": 41, "char_count": 131, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:40.464410", "source": { "split": "train_shard_00000", "doc_id": 2220 }, "chunk_id": "train_shard_00000_2220_0", "global_id": 2442 }, { "text": "In this study, we investigated the probiotic properties and anti-obesity effects of bacterial strains isolated from homemade kimchi. Lactiplantibacillus plantarum KU15117 was isolated using lactobacilli selective medium. L. plantarum KU15117 did not produce β-glucuronidase and showed high tolerance to artificial gastric juice and bile salt, acceptable resistance to antibiotics, and high adhesion ability to HT-29 cells. The anti-adipogenic activity of L. plantarum KU15117 at 10\n\nAnti-adipogenic Effects of the Probiotic Lactiplantibacillus plantarum KU15117 on 3T3-L1 Adipocytes.", "token_count": 193, "char_count": 583, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [ "KU15117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:40.950579", "source": { "split": "train_shard_00000", "doc_id": 2221 }, "chunk_id": "train_shard_00000_2221_0", "global_id": 2443 }, { "text": "Gut microbiota dysbiosis toward adherent-invasive\n\nThe Role of OmpR in Bile Tolerance and Pathogenesis of Adherent-Invasive", "token_count": 41, "char_count": 123, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:41.318259", "source": { "split": "train_shard_00000", "doc_id": 2222 }, "chunk_id": "train_shard_00000_2222_0", "global_id": 2444 }, { "text": "This study aimed to investigate the correlation between the level of exopolysaccharide (EPS) biosynthesis and gastrointestinal tolerance of 12 Lactiplantibacillus plantarum strains.\n\nCorrelation between exopolysaccharide biosynthesis and gastrointestinal tolerance of Lactiplantibacillus plantarum.", "token_count": 87, "char_count": 298, "word_count": 32, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:41.698612", "source": { "split": "train_shard_00000", "doc_id": 2223 }, "chunk_id": "train_shard_00000_2223_0", "global_id": 2445 }, { "text": "Bile salts are amphiphilic steroids with digestive functions in vertebrates. Upon excretion, bile salts are degraded by environmental bacteria. Degradation of the bile salt steroid skeleton resembles the well-studied pathway for other steroids, like testosterone, while specific differences occur during side chain degradation and the initiating transformations of the steroid skeleton. Of the latter, two variants via either Δ\n\nProteome, Bioinformatic, and Functional Analyses Reveal a Distinct and Conserved Metabolic Pathway for Bile Salt Degradation in the", "token_count": 143, "char_count": 560, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:42.125013", "source": { "split": "train_shard_00000", "doc_id": 2224 }, "chunk_id": "train_shard_00000_2224_0", "global_id": 2446 }, { "text": "The aim of this study was to determine the contribution of the contamination of the health care environment in the acquisition of carbapenem-resistant Klebsiella pneumoniae (CRKP) in a CRKP-prevalent setting. We performed a 3-month prospective study in a 20-bed medical intensive care unit (ICU) by collecting rectal/oral swabs from patients within 3 days of ICU admission and weekly thereafter. We also comprehensively sampled the beds and rooms of patients and instruments for patient care every week. CRKP were detected, genome sequenced, and assigned to clones based on core genome analyses. The survival of four CRKP clones was determined under ICU conditions. Seventeen patients were in the ICU at the start of the study, and 99 were admitted afterwards. Six were positive patients, with four detected on initial screening and two during weekly monitoring. CRKP was detected from 76 of 3,699 (2.1%) environment samples, including from the immediate surroundings of 21 patients (five had CRKP from clinical samples and 16 did not). CRKP was not detected outside patient care areas. Among 49 CRKP sequenced isolates (nine from swabs, five from clinical samples, and 35 from environment) from 21 patients, 45 were ST11 and had\n\nSpread of Carbapenem-Resistant Klebsiella pneumoniae in an Intensive Care Unit: A Whole-Genome Sequence-Based Prospective Observational Study.", "token_count": 358, "char_count": 1373, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7967, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:42.702210", "source": { "split": "train_shard_00000", "doc_id": 2225 }, "chunk_id": "train_shard_00000_2225_0", "global_id": 2447 }, { "text": "Peptide drugs face several barriers to oral delivery, including enzymatic degradation in the gastrointestinal tract and low membrane permeability. Importantly, the direct interaction between various biorelevant colloids (i.e., bile salt micelles and bile salt-phospholipid mixed micelles) present in the aqueous gastrointestinal environment and peptide drug molecules has not been studied. In this work, we systematically characterized interactions between a water-soluble model peptide drug, octreotide, and a range of physiologically relevant bile salts in solution. Octreotide membrane flux in pure bile salt solutions and commercially available biorelevant media, i.e., fasted state simulated intestinal fluid (FaSSIF) and fed state simulated intestinal fluid (FeSSIF), was evaluated using a side-by-side diffusion cell equipped with a cellulose dialysis membrane. All seven micellar bile salt solutions as well as FaSSIF and FeSSIF decreased octreotide membrane flux, and dihydroxy bile salts were found to have a much larger effect than trihydroxy bile salts. An inverse relationship between octreotide membrane flux and pancreatic enzymatic stability was also observed; bile salt micelles and bile salt-phospholipid mixed micelles provided a protective effect toward enzymatic degradation and prolonged octreotide half-life in vitro. Diffusion ordered nuclear magnetic resonance (DOSY NMR) spectroscopy and dynamic light scattering (DLS) were used as complementary experimental techniques to confirm peptide-micelle interactions in solution. Experiments were also performed using desmopressin as a second model peptide drug; desmopressin interacted with bile salts in solution, albeit to a lower extent relative to octreotide. The findings described herein demonstrate that amphiphilic, water-soluble peptide drugs do interact with bile salts and phospholipids in solution, with an effect on peptide membrane flux and enzymatic stability. Correspondingly, oral peptide drug absorption and bioavailability may be impacted.", "token_count": 506, "char_count": 2028, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:43.355374", "source": { "split": "train_shard_00000", "doc_id": 2226 }, "chunk_id": "train_shard_00000_2226_0", "global_id": 2448 }, { "text": "Do Macrocyclic Peptide Drugs Interact with Bile Salts under Simulated Gastrointestinal Conditions?", "token_count": 28, "char_count": 98, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:43.711680", "source": { "split": "train_shard_00000", "doc_id": 2226 }, "chunk_id": "train_shard_00000_2226_1", "global_id": 2449 }, { "text": "Variable number tandem repeats (VNTRs) are composed of consecutive repetitive DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. In this work, we solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We develop software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We use this to discover VNTRs with length stratified by continental population, and expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.\n\nProfiling variable-number tandem repeat variation across populations using repeat-pangenome graphs.", "token_count": 233, "char_count": 1088, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:44.185723", "source": { "split": "train_shard_00000", "doc_id": 2227 }, "chunk_id": "train_shard_00000_2227_0", "global_id": 2450 }, { "text": "The identification of bacterial effectors is essential to understand how obligatory intracellular bacteria such as Ehrlichia spp. manipulate the host cell for survival and replication. Infection of mammals-including humans-by the intracellular pathogenic bacteria Ehrlichia spp. depends largely on the injection of virulence proteins that hijack host cell processes. Several hypothetical virulence proteins have been identified in Ehrlichia spp., but one so far has been experimentally shown to translocate into host cells via the type IV secretion system. However, the current challenge is to identify most of the type IV effectors (T4Es) to fully understand their role in Ehrlichia spp. virulence and host adaptation. Here, we predict the T4E repertoires of four sequenced Ehrlichia spp. and four other Anaplasmataceae as comparative models (pathogenic Anaplasma spp. and Wolbachia endosymbiont) using previously developed S4TE 2.0 software. This analysis identified 579 predicted T4Es (228 pT4Es for Ehrlichia spp. only). The effector repertoires of Ehrlichia spp. overlapped, thereby defining a conserved core effectome of 92 predicted effectors shared by all strains. In addition, 69 species-specific T4Es were predicted with non-canonical GC% mostly in gene sparse regions of the genomes and we observed a bias in pT4Es according to host-specificity. We also identified new protein domain combinations, suggesting novel effector functions. This work presenting the predicted effector collection of Ehrlichia spp. can serve as a guide for future functional characterisation of effectors and design of alternative control strategies against these bacteria.\n\nThe super repertoire of type IV effectors in the pangenome of Ehrlichia spp. provides insights into host-specificity and pathogenesis.", "token_count": 443, "char_count": 1796, "word_count": 254, "semantic_coherence": 1, "information_density": 0.622, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:44.821554", "source": { "split": "train_shard_00000", "doc_id": 2228 }, "chunk_id": "train_shard_00000_2228_0", "global_id": 2451 }, { "text": "Koumiss has beneficial therapeutic effects on bacterial diseases. Four antibacterial com- pounds from yeasts (Kluyveromyces marxianus and Saccharomyces cerevisiae) in koumiss were evaluated for their antibacterial effects against three Gram-negative bacteria, three Gram-positive bacteria and five pathogenic Escherichia coli strains. The antibacterial compounds from yeasts in koumiss were extracted, and their main components were determined. The inhibition zones were analyzed, and their minimum inhibition concentrations (MICs) and minimum bactericidal concentrations (MBCs) were determined. Aqueous phases of Kluyveromyces marxianus and Saccharomyces cerevisiae at pH 2.0 and 8.0 produced larger inhibition zones than those in other phases, and then antibacterial compounds from K. marxianus (K2, pH=2.0; K8, pH=8.0) and S. cerevisiae (S2, pH=2.0; S8, pH=8.0) were obtained. Their main components were organic acids and killer toxins. K2 had more propanoic acid and S2 had more oxalic acid than others. The inhibition zones of K2, K8, S2 and S8 against three Gram-negative bacteria and three Gram-positive bacteria were 12.03-23.30 mm, their MICs were 0.01-0.13 g/mL, and MBCs were 0.03-0.50 g/mL. Meantime, the inhibition zones of K2, K8, S2 and S8 against five pathogenic E. coli were 16.10-25.26 mm, their MICs were 0.03-0.13 g/mL, and MBCs were 0.13-1.00 g/mL. These four antibacterial compounds from yeasts in koumiss had broad antibacterial spectrum. In addition, K2 and S2 were better than K8 and S8.\n\nAntibacterial spectrum of four compounds from yeasts in koumiss.", "token_count": 512, "char_count": 1578, "word_count": 227, "semantic_coherence": 1, "information_density": 0.4846, "quality_score": 0.7423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:45.477249", "source": { "split": "train_shard_00000", "doc_id": 2229 }, "chunk_id": "train_shard_00000_2229_0", "global_id": 2452 }, { "text": "The effects of bile salts on the emulsifier adsorption layer play a crucial role in lipid digestion. The current study selected sodium cholate (NaCh) and lecithin as model compounds for bile salts and food emulsifiers, respectively. The interface dilational rheological and emulsification properties of NaCh and lecithin were carried out. The results showed that the NaCh molecules could quickly diffuse from the bulk to interface, which broke the tightly-arranged interfacial layer of lecithin and enhanced the viscoelasticity of interfacial film. As a result, the interfacial adsorption layer, which was originally dominated by the slow relaxation processes within the interface, was transformed into one controlled by the fast molecular diffusion exchange. This accelerated the exchange of materials between the bulk and interface, thereby creating suitable conditions for the interfacial adsorption of lipases, which promoted the digestion process. These results provided a mechanism for the promotion of lipid digestion by bile salts from the perspective of interfacial viscoelasticity and relaxation processes. A deeper understanding of the interfacial behavior of bile salts with emulsifiers would provide a basis for the rational design of interfacial layer for modulating lipid digestion.\n\nEffect of Bile Salts on the Interfacial Dilational Rheology of Lecithin in the Lipid Digestion Process.", "token_count": 312, "char_count": 1402, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5347, "quality_score": 0.7673, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:46.042700", "source": { "split": "train_shard_00000", "doc_id": 2230 }, "chunk_id": "train_shard_00000_2230_0", "global_id": 2453 }, { "text": "Thermotolerant yeast has outstanding potential in industrial applications. Komagataella phaffii (Pichia pastoris) is a common cell factory for industrial production of heterologous proteins.\n\nAugmented peroxisomal ROS buffering capacity renders oxidative and thermal stress cross-tolerance in yeast.", "token_count": 76, "char_count": 299, "word_count": 36, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:46.420886", "source": { "split": "train_shard_00000", "doc_id": 2231 }, "chunk_id": "train_shard_00000_2231_0", "global_id": 2454 }, { "text": "Cholestasis is a complex hepatic disorder underlined with retention of the highly toxic bile components within the hepatocytes. Nifuroxazide (NIF); a nitrofuran derivative, is widely used drug for treatment of acute and chronic diarrhea. The current study was performed to investigate the curative effect of NIF (25 and 50 mg/kg) on lithocholic acid (LCA)-induced cholestasis and compare the observed impact to that of ursodeoxycholic acid (UDCA). Intriguingly, NIF significantly attenuated LCA-induced cholestatic injury. NIF successfully reversed cholestatic injury to a similar extent compared to the mainstay drug, UDCA. NIF administration remarkably attenuated liver/body index and restored liver functions. Moreover, it restored the disrupted balance in oxidative homeostasis. On the other hand, NIF induced a marked improvement in histopathological and immuno-histochemical analysis of liver specimens. Ultimately, NIF mitigated inflammatory response and proliferative ability of hepatocytes with significant reduction in hepatic expression of proliferatingcellnuclearantigen(PCNA), cluster of differentiation 68 (CD68), interlukin-6 (Il-6) and β-catenin. Interestingly, NIF successfully increased bile transformation with increased the hepatic expression of bile salt export pump (BSEP) and multidrug resistance-associated protein 2 (MDRP2). Nevertheless, molecular docking of NIF with β-catenin and BSEP showed a better alignment inside the pocket with strong interaction for both protein binding sites. In conclusion, NIF attenuated experimentally-induced cholestatic dysfunction with an underlined synergistic inhibition of Il-6/Β-catenin pathways and direct enhancement of bile acids transporters gene expression.\n\nNifuroxazide mitigates cholestatic liver injury by synergistic inhibition of Il-6/Β-catenin signaling and enhancement of BSEP and MDRP", "token_count": 490, "char_count": 1861, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [ "MDRP2", "CD68" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:47.072480", "source": { "split": "train_shard_00000", "doc_id": 2232 }, "chunk_id": "train_shard_00000_2232_0", "global_id": 2455 }, { "text": "Serratia sp. cause food losses and waste due to spoilage; it is noteworthy that they represent a dominant population in seafood. The main spoilage associated species comprise S. liquefaciens, S. grimesii, S. proteamaculans and S. quinivorans, also known as S. liquefaciens-like strains. These species are difficult to discriminate since classical 16S rRNA gene-based sequences do not possess sufficient resolution. In this study, a phylogeny based on the short-length luxS gene was able to speciate 47 Serratia isolates from seafood, with S. proteamaculans being the main species from fresh salmon and tuna, cold-smoked salmon, and cooked shrimp while S. liquefaciens was only found in cold-smoked salmon. The genome of the first S. proteamaculans strain isolated from the seafood matrix (CD3406 strain) was sequenced. Pangenome analyses of S. proteamaculans and S. liquefaciens indicated high adaptation potential. Biosynthetic pathways involved in antimicrobial compounds production and in the main seafood spoilage compounds were also identified. The genetic equipment highlighted in this study contributed to gain further insights into the predominance of Serratia in seafood products and their capacity to spoil.\n\nGenomic diversity of Serratia proteamaculans and Serratia liquefaciens predominant in seafood products and spoilage potential analyses.", "token_count": 356, "char_count": 1354, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [ "CD3406" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:47.647551", "source": { "split": "train_shard_00000", "doc_id": 2233 }, "chunk_id": "train_shard_00000_2233_0", "global_id": 2456 }, { "text": "We investigated the ability of lotus seed resistant starch (LRS) to affect the conversion of sodium taurocholate (STCA) by regulating the intestinal flora, using glucose (GLU) and high amylose corn starch (HAMS) as controls. The dominant microbiota in LRS group were mainly Lactobacillus and Escherichia_Shigella, with a small proportion of Bifidobacterium. Meanwhile, Lactobacillus, Bifidobacterium and Enterococcus were dominant microbiota in the HAMS group. Lactobacillus, Burkholderia-Caballeronia-Paraburkholderia and Sphingomonas were found in the GLU group. Furthermore, Bifidobacterium, Enterococcus and Escherichia_Shigella were negatively correlated with STCA and sodium taurodeoxycholate (STDCA), while these bacteria were positively correlated with bile salt hydrolase (BSH) and hydroxysteroid dehydrogenase (HSDH) content. Meanwhile Burkholderia-Caballeronia-Paraburkholderia and Sphingomonas were positively correlated with STCA and STDCA, while these bacteria were negatively correlated with BSH and HSDH content. LRS promoted the proliferation of Bifidobacterium and Escherichia_Shigella to secret more BSH and HSDH, accelerating the hydrolysis of STCA and reducing the conversion of STDCA.\n\nLotus seed resistant starch affects the conversion of sodium taurocholate by regulating the intestinal microbiota.", "token_count": 394, "char_count": 1322, "word_count": 165, "semantic_coherence": 1, "information_density": 0.5394, "quality_score": 0.7697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:48.261213", "source": { "split": "train_shard_00000", "doc_id": 2234 }, "chunk_id": "train_shard_00000_2234_0", "global_id": 2457 }, { "text": "Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis. Since 2005, high throughput genome sequencing methods enabled understanding the genetic landscape and diversity of bacteria as well as their pathogenic role. Here, in order to determine whether specific virulence genes could be related to specific clinical manifestations, we compared the genomes from 27 S. intermedius strains isolated from patients with various types of infections, including 13 that were sequenced in our institute and 14 available in GenBank.\n\nPangenome analysis and virulence profiling of Streptococcus intermedius.", "token_count": 220, "char_count": 887, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7661, "quality_score": 0.8831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:48.726697", "source": { "split": "train_shard_00000", "doc_id": 2235 }, "chunk_id": "train_shard_00000_2235_0", "global_id": 2458 }, { "text": "Banana (Musaceae family) has a complex genetic history and includes a genus Musa with a variety of cultivated clones with edible fruits, Ensete species that are grown for their edible corm, and monospecific Musella whose generic status has been questioned. The most commonly exported banana cultivars belong to Cavendish, a subgroup of Musa triploid cultivars, which is under threat by fungal pathogens, though there are also related species M. balbisiana Colla (B genome), M. textilis Née (T genome), and M. schizocarpa N. W. Simmonds (S genome), along with hybrids of these genomes, which potentially host genes of agronomic interest. Here we present the first cross-genus pangenome of banana, which contains representatives of the Musa and Ensete genera. Clusters based on gene presence-absence variation (PAV) clearly separate Musa and Ensete, while Musa is split further based on species. These results present the first pangenome study across genus boundaries and identifies genes that differentiate between Musaceae species, information that may support breeding programs in these crops.\n\nThe pangenome of banana highlights differences between genera and genomes.", "token_count": 282, "char_count": 1170, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7011, "quality_score": 0.8506, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:49.282730", "source": { "split": "train_shard_00000", "doc_id": 2236 }, "chunk_id": "train_shard_00000_2236_0", "global_id": 2459 }, { "text": "A released exopolysaccharide (rEPS)-producing strain (LM187) with good acid resistance, bile salt resistance, and cholesterol-lowering properties was isolated from Sichuan paocai and identified as\n\nCharacterization and Antioxidant Activity of Released Exopolysaccharide from Potential Probiotic", "token_count": 79, "char_count": 294, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [ "LM187" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:49.651349", "source": { "split": "train_shard_00000", "doc_id": 2237 }, "chunk_id": "train_shard_00000_2237_0", "global_id": 2460 }, { "text": "Microbial fuel cell (MFC) is an optimistic fuel cell technology that applies microorganism's biochemical catalytic activities in consuming organic substrate and produce electricity. In the past, several researchers have reported power generation from Saccharomyces cerevisiae, but nowadays, most of the studies are centred around bacterial biofilms (prokaryotes) as anode biocatalyst. Yeast (a eukaryote) has also been applied as a biocatalyst in MFCs as they are non-pathogenic, easy to handle and tolerant to various environmental conditions. Yeast strains such as Arxula adeninvorans, Candida melibiosica, Hansenula polymorpha, Hansenula anomala, Kluyveromyces marxianus and Saccharomyces cerevisiae have been utilized in MFCs. This review summarizes the application of yeast as an anode biocatalyst together with a discussion on the mechanism of electron transfer from yeast cells to the anode and highlights the techniques applied in improving the efficiency of yeast-based MFCs. The recent challenges and benefits of utilizing yeast in MFCs have been also encapsulated in this review.\n\nRecent trends in upgrading the performance of yeast as electrode biocatalyst in microbial fuel cells.", "token_count": 301, "char_count": 1193, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6369, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:50.213419", "source": { "split": "train_shard_00000", "doc_id": 2238 }, "chunk_id": "train_shard_00000_2238_0", "global_id": 2461 }, { "text": "Lactic acid bacteria (LAB) are used as a probiotic alternative to antibiotics in livestock production. Microencapsulation technology is widely used for probiotic preservation. A variety of microencapsulation protocols have been proposed and compared based on chemicals and mechanical procedures. This study aimed to develop a double-encapsulated coating from alginate (1.5%) and chitosan (0.5%) by extrusion, emulsion, and spray drying methods using the LAB strains Lactobacillus plantarum strains 31F, 25F, 22F, Pediococcus pentosaceus 77F, and P. acidilactici 72N, and to monitor the basic probiotic properties of the encapsulated prototypes. The final products from each microencapsulation protocol were analysed for their appearance, probiotic properties and viable cell count. Using the spray drying method, particles smaller than 15 μm in diameter with a regular spherical shape were obtained, whereas the other methods produced larger (1.4-52 mm) and irregularly shaped microcapsules. After storage for 6 months at room temperature, the LAB viability of the spray-dried particles was the highest among the three methods. In all the LAB strains examined, the encapsulated LAB retained their probiotic properties in relation to acid-bile tolerance and antibacterial activity. This study highlights the efficacy of double-coating microencapsulation for preserving LAB properties and survival rate, and demonstrates its potential for probiotic application in livestock farms.\n\nThe efficacy of three double-microencapsulation methods for preservation of probiotic bacteria.", "token_count": 390, "char_count": 1575, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6435, "quality_score": 0.8218, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:50.832259", "source": { "split": "train_shard_00000", "doc_id": 2239 }, "chunk_id": "train_shard_00000_2239_0", "global_id": 2462 }, { "text": "Diabetes, a chronic metabolic disorder, is characterized by persistent hyperglycemia. This study aimed to evaluate the hypoglycemic and antioxidant activities of lactic acid bacteria strains isolated from humans and food products and investigate the probiotic properties of the selected four strains. The hypoglycemic activity of the isolated strains was examined by evaluating the α-glucosidase and α-amylase inhibitory activities. The antioxidant activity was measured using the DPPH, ABTS, and FRAP assays. Four strains (Lactiplantibacillus plantarum MG4229, MG4296, MG5025, and Lacticaseibacillus paracasei MG5012) exhibited potent α-glucosidase inhibitory (>75%) and α-amylase inhibitory (>85%) activities, which were comparable to those of acarbose (>50%; 1000 μg/mL). Similarly, the radical scavenging and antioxidant activities of the four strains were comparable to those of ascorbic acid (50 μg/mL). Additionally, the probiotic properties of the four selected strains were examined based on acid and bile salt tolerance, auto-aggregation ability, and antibiotic resistance. The four strains were resistant to pH 2 (>50% of survivability) and 0.5% bile salt (>80% of survivability). Therefore, we suggest that the selected strains with hypoglycemic, antioxidant, probiotic properties can potentially prevent diabetes.\n\nIn Vitro Antidiabetic, Antioxidant Activity, and Probiotic Activities of Lactiplantibacillus plantarum and Lacticaseibacillus paracasei Strains.", "token_count": 439, "char_count": 1472, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5699, "quality_score": 0.785, "entities": { "genes": [ "MG4296", "MG4229", "MG5012", "MG5025" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:51.488103", "source": { "split": "train_shard_00000", "doc_id": 2240 }, "chunk_id": "train_shard_00000_2240_0", "global_id": 2463 }, { "text": "Bile acids (BA) play a significant role in the pathophysiology of nonalcoholic steatohepatitis (NASH). The present study evaluates the modulation of bile acid metabolomics by atorvastatin, a cholesterol-lowering agent commonly used to treat cardiovascular complications accompanying NASH. NASH was induced in mice by 24 weeks of consuming a high-saturated fat, high-fructose, and high-cholesterol diet (F), with atorvastatin administered orally (20 mg/kg/day) during the last three weeks. Biochemical and histological analyses confirmed the effectiveness of the F diet in inducing NASH. Untreated NASH animals had significantly reduced biliary secretion of BA and increased fecal excretion of BA via decreased apical sodium-dependent bile salt transporter (Asbt)-mediated reabsorption. Atorvastatin decreased liver steatosis and inflammation in NASH animals consistently with a reduction in crucial lipogenic enzyme stearoyl-coenzyme A (CoA) desaturase-1 and nuclear factor kappa light chain enhancer of activated B-cell pro-inflammatory signaling, respectively. In this group, atorvastatin also uniformly enhanced plasma concentration, biliary secretion and fecal excretion of the secondary BA, deoxycholic acid (DCA). However, in the chow diet-fed animals, atorvastatin decreased plasma concentrations of BA, and reduced BA biliary secretions. These changes stemmed primarily from the increased fecal excretion of BA resulting from the reduced Asbt-mediated BA reabsorption in the ileum and suppression of synthesis in the liver. In conclusion, our results reveal that atorvastatin significantly modulates BA metabolomics by altering their intestinal processing and liver synthesis in control and NASH mice.\n\nAtorvastatin Modulates Bile Acid Homeostasis in Mice with Diet-Induced Nonalcoholic Steatohepatitis.", "token_count": 477, "char_count": 1811, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:52.150723", "source": { "split": "train_shard_00000", "doc_id": 2241 }, "chunk_id": "train_shard_00000_2241_0", "global_id": 2464 }, { "text": "Identifying a Novel Bile Salt Hydrolase from the Keystone Gut Bacterium", "token_count": 22, "char_count": 71, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:52.536460", "source": { "split": "train_shard_00000", "doc_id": 2242 }, "chunk_id": "train_shard_00000_2242_0", "global_id": 2465 }, { "text": "As evidenced in parasitism, host and niche shifts are a source of genomic and phenotypic diversification. Exemplary is a reduction in the core metabolism as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone recent lifestyle or host changes have not been fully investigated. Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a wide and diverse range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyles. Moreover, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaptation in oomycetes. Given the high correlation between lifestyle and genome properties in our oomycete dataset, together with the known convergent evolution of fungal and oomycete genomes, we developed a model that predicts plant pathogenic lifestyles with high accuracy based on functional annotations. These insights into how selective pressures correlate with lifestyle may be crucial to better understand host/lifestyle shifts and their impact on the genome.\n\nPredicting Lifestyle from Positive Selection Data and Genome Properties in Oomycetes.", "token_count": 318, "char_count": 1450, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:53.114579", "source": { "split": "train_shard_00000", "doc_id": 2243 }, "chunk_id": "train_shard_00000_2243_0", "global_id": 2466 }, { "text": "Chlamydiae are highly successful strictly intracellular bacteria associated with diverse eukaryotic hosts. Here we analyzed metagenome-assembled genomes of the \"Genomes from Earth's Microbiomes\" initiative from diverse environmental samples, which almost double the known phylogenetic diversity of the phylum and facilitate a highly resolved view at the chlamydial pangenome. Chlamydiae are defined by a relatively large core genome indicative of an intracellular lifestyle, and a highly dynamic accessory genome of environmental lineages. We observe chlamydial lineages that encode enzymes of the reductive tricarboxylic acid cycle and for light-driven ATP synthesis. We show a widespread potential for anaerobic energy generation through pyruvate fermentation or the arginine deiminase pathway, and we add lineages capable of molecular hydrogen production. Genome-informed analysis of environmental distribution revealed lineage-specific niches and a high abundance of chlamydiae in some habitats. Together, our data provide an extended perspective of the variability of chlamydial biology and the ecology of this phylum of intracellular microbes.\n\nPangenomics reveals alternative environmental lifestyles among chlamydiae.", "token_count": 289, "char_count": 1225, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:53.671504", "source": { "split": "train_shard_00000", "doc_id": 2244 }, "chunk_id": "train_shard_00000_2244_0", "global_id": 2467 }, { "text": "Cyprinus carpio is an important freshwater fish in aquaculture. It was used for the isolation of potential probiotic strain for aquaculture applications. The most dominant strain was isolated on MRS agar from the gastrointestinal (GI) of C. carpio and identified as Lysinibacillus macroides using molecular marker 16S rRNA gene. Various probiotic properties such as acid and bile tolerance and antibiotic susceptibility were analysed under in vitro conditions. Further, formulate pelletized feed using probiotic (L. macroides) in different concentrations (2, 4, 6 and 8%). Rearing of C. carpio was carried out 45 days and fed with formulated feed. The highest length (5.14 ± 0.07 cm) and weight (3.56 ± 0.07 g) of C. carpio fingerlings was recorded in the 8% LM probiotic pelletized feed, while in fingerlings fed with control showed lower in the length (3.02 ± 0.13 cm) and the weight (0.92 ± 0.04 g) on the 45th day of the experiment. Both percentage of weight gain (PWG) and specific growth rate (SGR) were significantly increased (P < 0.05) of C. carpio fingerlings fed with probiotic feed compared to control feed. Hence, the use of probiotic bacteria could be an encouraging alternative feed for future endeavours in the field of aquaculture. In conclusion, L. macroides can serve as probiotic for sustainable, competitive and promising beneficial bacteria to aquaculture industry.\n\nEvaluation of probiotic properties of Lysinibacillus macroides under in vitro conditions and culture of Cyprinus carpio on growth parameters.", "token_count": 444, "char_count": 1530, "word_count": 238, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:54.307634", "source": { "split": "train_shard_00000", "doc_id": 2245 }, "chunk_id": "train_shard_00000_2245_0", "global_id": 2468 }, { "text": "Salmonella spp. is an important foodborne pathogen associated with consumption of contaminated food, especially food of livestock origin. Antimicrobial resistance (AMR) in Salmonella has been reported globally and increasing AMR in food production is a major public health issue worldwide. The objective of this study was to describe the genetic relatedness among Salmonella enterica isolates, which displayed identical DNA fingerprint profiles. Ten S. enterica isolates were selected from meat and human cases with an identical rep-PCR profile of serovars Rissen (n = 4), Weltevreden (n = 4), and Stanley (n = 2). We used long-read whole genome sequencing (WGS) on the MinION sequencing platform to type isolates and investigate in silico the presence of specific AMR genes. Antimicrobial susceptibility testing was tested by disk diffusion and gradient diffusion method to corroborate the AMR phenotype. Multidrug resistance and resistance to more than one antimicrobial agent were observed in eight and nine isolates, respectively. Resistance to colistin with an accompanying mcr-1 gene was observed among the Salmonella isolates. The analysis of core genome and whole genome MLST revealed that the Salmonella from meat and human salmonellosis were genetically related. Hence, it could be concluded that meat is one of the important sources for Salmonella infection in human.\n\nCharacterisation of Salmonella enterica clones carrying mcr-1 plasmids in meat products and patients in Northern Thailand using long read sequencing.", "token_count": 354, "char_count": 1529, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6267, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:54.881247", "source": { "split": "train_shard_00000", "doc_id": 2246 }, "chunk_id": "train_shard_00000_2246_0", "global_id": 2469 }, { "text": "Cheese whey is an abundant and low-cost feedstock with lactose as its main component, but the inability to metabolize lactose prevents Aureobasidium pullulans from using cheese whey directly. In this study, Kluyveromyces marxianus was permeabilized to obtain nonviable but biocatalytic cells for lactose hydrolysis, and the mixed culture of A. pullulans and permeabilized K. marxianus was conducted for polymalic acid (PMA) production from cheese whey. In the mixed culture, PMA titer varied directly to β-galactosidase activity of K. marxianus, but inversely to cell viability of K. marxianus, and ethanol permeabilized K. marxianus was the most compatible with A. pullulans for PMA production. 37.8 g/L PMA was produced in batch fermentation, and PMA titer was increased to 97.3 g/L in fed-batch fermentation, with a productivity of 0.51 g/(L·h) and a yield of 0.56 g/g. This study paved an economical and environmentally friendly way for PMA production from cheese whey.\n\nDirect conversion of cheese whey to polymalic acid by mixed culture of Aureobasidium pullulans and permeabilized Kluyveromyces marxianus.", "token_count": 339, "char_count": 1112, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5361, "quality_score": 0.7681, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:55.452332", "source": { "split": "train_shard_00000", "doc_id": 2247 }, "chunk_id": "train_shard_00000_2247_0", "global_id": 2470 }, { "text": "In recent years, increased rates of yeast infections in humans and animals have been recognized worldwide. Since animals may represent a source of yeast infections for humans, knowing the antifungal susceptibility profile of yeast isolates from milk and evaluating their pathogenic potential would be of great medical importance. Therefore, the aim of this survey was to study yeast diversity in milk samples, analyze the hemolytic and phospholipase activities of isolates and determine minimal inhibition concentration (MIC) for fluconazole, voriconazole and flucytosine. Out of 66 yeast isolates obtained from 910 individual raw milk samples from subclinically infected cows, 26 different yeast species were determined based on sequencing of the D1/D2 and ITS regions. Among them, Pichia kudriavzevii (formerly known as Candida krusei), Kluyveromyces marxianus (formerly known as Candida kefyr) and Debaryomyces hansenii (formerly known as Candida famata) were the most commonly identified. Hemolysin and/or phospholipase activity was observed in 66.7% of isolates. The elevated MIC for fluconazole was determined in 16 isolates from 11 species. The findings of this study demonstrate that yeast isolates from raw milk have the potential to express virulence attributes such as hemolysin and phospholipase, and additionally, some of these strains showed elevated MIC to fluconazole or to flucytosine.\n\nRaw bovine milk as a reservoir of yeast with virulence factors and decreased susceptibility to antifungal agents.", "token_count": 390, "char_count": 1517, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:56.066383", "source": { "split": "train_shard_00000", "doc_id": 2248 }, "chunk_id": "train_shard_00000_2248_0", "global_id": 2471 }, { "text": "The gene content of plants varies between individuals of the same species due to gene presence/absence variation, and selection can alter the frequency of specific genes in a population. Selection during domestication and breeding will modify the genomic landscape, though the nature of these modifications is only understood for specific genes or on a more general level (e.g., by a loss of genetic diversity). Here we have assembled and analyzed a soybean (Glycine spp.) pangenome representing more than 1,000 soybean accessions derived from the USDA Soybean Germplasm Collection, including both wild and cultivated lineages, to assess genomewide changes in gene and allele frequency during domestication and breeding. We identified 3,765 genes that are absent from the Lee reference genome assembly and assessed the presence/absence of all genes across this population. In addition to a loss of genetic diversity, we found a significant reduction in the average number of protein-coding genes per individual during domestication and subsequent breeding, though with some genes and allelic variants increasing in frequency associated with selection for agronomic traits. This analysis provides a genomic perspective of domestication and breeding in this important oilseed crop.\n\nSequencing the USDA core soybean collection reveals gene loss during domestication and breeding.", "token_count": 290, "char_count": 1377, "word_count": 201, "semantic_coherence": 1, "information_density": 0.597, "quality_score": 0.7985, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:56.625259", "source": { "split": "train_shard_00000", "doc_id": 2249 }, "chunk_id": "train_shard_00000_2249_0", "global_id": 2472 }, { "text": "Probiotics play significant roles in enhancing systemic immunity, improving intestinal balance and feed value, enhancing enzymatic digestion, and inhibiting pathogenic microorganisms of freshwater fish. Probiotics from an identical organism's gastrointestinal system promote effective colonization and provide greater benefits than other sources. This study aimed to evaluate the usefulness of probiotic bacteria isolated from the intestines of freshwater fishes for a dietary supplement of freshwater aquaculture. A total of 120 isolates were collected from freshwater fishes of Channa striata, Puntius filamentosus, Oreochromis mossambicus, Cirrhinus mrigala, and Rasbora daniconius. Seven of these isolates exhibited antagonistic activity against fish pathogens: Aeromonas hydrophila, Staphylococcus epidermidis, Staphylococcus aureus, Bacillus cereus, Escherichia coli, and Pseudomonas aeruginosa. Using 16S rRNA gene sequencing analysis, the isolates were identified as Enterococcus sp., Lactococcus lactis, Weissella cibaria, and Limosilactobacillus fermentum. Of these tolerates, L. fermentum URLP18 isolated from C. mrigala exhibited high tolerance to low acidic (pH 2.0) and high bile salt (2%) concentrations, exhibiting a significant hydrophobicity and extracellular enzyme secretions like amylase, protease, and lipase. In vitro evaluations on intestinal mucus indicate that L. fermentum URLP18 have strong adherence capacity, and its survival rate increased after being administered to Artemia nauplii. The results suggest that L. fermentum URLP18 has high probiotic potential and is an effective dietary supplement for freshwater aquaculture.\n\nIsolation of Lactic Acid Bacteria from Intestine of Freshwater Fishes and Elucidation of Probiotic Potential for Aquaculture Application.", "token_count": 489, "char_count": 1795, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6926, "quality_score": 0.8463, "entities": { "genes": [ "URLP18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:57.275063", "source": { "split": "train_shard_00000", "doc_id": 2250 }, "chunk_id": "train_shard_00000_2250_0", "global_id": 2473 }, { "text": "Non-alcoholic steatohepatitis (NASH) has no approved therapy. The farnesoid X nuclear receptor (FXR) agonist obeticholic acid (OCA) has shown promise as a drug for NASH, but can adversely affect plasma lipid profiles. Therefore, the present study aimed to investigate the effects and underlying mechanisms of OCA in combination with simvastatin (SIM) in a high-fat diet (HFD)-induced model of NASH. C57BL/6J mice were fed with a HFD for 16 weeks to establish the NASH model. The mice were randomly divided into the following five groups: HFD, HFD + OCA, HFD + SIM, HFD + OCA + SIM and control. After 16 weeks, the mice were sacrificed under anesthesia. The ratios of liver weight to body weight (Lw/Bw) and of abdominal adipose tissue weight to body weight were calculated. Serum levels of alanine aminotransferase (ALT), aspartate aminotransferase (AST), total cholesterol, triglycerides and low-density lipoprotein were measured. Liver sections were stained with hematoxylin and eosin. The protein levels of FXR, small heterodimeric partner (SHP) and cytochrome P450 family 7 subfamily A member 1 (CYP7A1) in the liver were detected by western blotting, while the mRNA levels of FXR, SHP, CYP7A1, bile salt export pump, interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α), sterol regulatory element binding protein-1 (SREBP1) and fatty acid synthase (FASN) were examined by reverse transcription-quantitative polymerase chain reaction. The administration of OCA with or without SIM reduced the liver inflammation score compared with those of the HFD and HFD + SIM groups, with no significant difference between the HFD + OCA and HFD + OCA + SIM groups. The steatosis score followed similar trends to the inflammation score", "token_count": 504, "char_count": 1726, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8195, "entities": { "genes": [ "SREBP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:58.269226", "source": { "split": "train_shard_00000", "doc_id": 2251 }, "chunk_id": "train_shard_00000_2251_0", "global_id": 2474 }, { "text": "In HFD-fed mice, OCA combined with SIM prevented body weight gain compared with that in HFD and HFD + OCA groups, and reduced the Lw/Bw ratio compared with that in the HFD and HFD + SIM groups. In addition to preventing HFD-induced increases of ALT and AST, the combination of OCA and SIM reduced the mRNA levels of IL-6, TNF-α, SREBP1 and FASN. On the basis of these results, it may be concluded that the strategy of combining OCA with SIM represents an effective pharmacotherapy for NASH.\n\nCo-administration of obeticholic acid and simvastatin protects against high-fat diet-induced non-alcoholic steatohepatitis in mice.", "token_count": 179, "char_count": 623, "word_count": 101, "semantic_coherence": 1, "information_density": 0.6337, "quality_score": 0.8168, "entities": { "genes": [ "SREBP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:58.709848", "source": { "split": "train_shard_00000", "doc_id": 2251 }, "chunk_id": "train_shard_00000_2251_1", "global_id": 2475 }, { "text": "Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity", "token_count": 500, "char_count": 1671, "word_count": 250, "semantic_coherence": 1, "information_density": 0.564, "quality_score": 0.782, "entities": { "genes": [ "ST17", "ST19", "GBS0661", "GBS0609" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:59.367051", "source": { "split": "train_shard_00000", "doc_id": 2252 }, "chunk_id": "train_shard_00000_2252_0", "global_id": 2476 }, { "text": "In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae.\n\nGenomic insights on DNase production in Streptococcus agalactiae ST17 and ST19 strains.", "token_count": 122, "char_count": 448, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8197, "quality_score": 0.9098, "entities": { "genes": [ "ST17", "ST19", "GBS0609" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:20:59.748290", "source": { "split": "train_shard_00000", "doc_id": 2252 }, "chunk_id": "train_shard_00000_2252_1", "global_id": 2477 }, { "text": "Nickel oxide nanoparticles (Nano NiO) evoke hepatotoxicity, while whether it affects the hepatic metabolism remains unclear. The aim of this study was to explore the differential metabolites and their metabolic pathways in rat serum and to further verify the potential mechanism of bile acids' (BAs) metabolism dysregulation after Nano NiO exposure. Sixteen male Wistar rats were intratracheally instilled with Nano NiO (0.24 mg/kg body weight) twice a week for 9 weeks. Liquid chromatography/mass spectrometry was applied to filter the differentially expressed metabolites in rat serum. Western blot was employed to detect the protein contents. Twenty-one differential metabolites that associated with BAs, lipid and phospholipid metabolism pathways were identified in rat serum after Nano NiO exposure. Decreased cholic acid and deoxycholic acid implied that the BAs metabolism was disturbed. The nickel content increased in liver after Nano NiO exposure. The protein expression of cholesterol 7α-hydroxylase (CYP7A1) was down-regulated, and the bile salt export pump was up-regulated after Nano NiO administration in rat liver. Moreover, dehydroepiandrosterone sulphotransferase (SULT2A1) and cytochrome P450 (CYP) 3A4 were elevated in the exposure group. In conclusion, Nano NiO might trigger the disturbances of BAs, lipid and phospholipid metabolism pathways in rats. The diminished serum BAs induced by Nano NiO might be related to the down-regulation of synthetase and to the overexpression of transmembrane protein and detoxification enzymes in BAs metabolism.\n\nA metabolomic-based study on disturbance of bile acids metabolism induced by intratracheal instillation of nickel oxide nanoparticles in rats.", "token_count": 474, "char_count": 1713, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5702, "quality_score": 0.7851, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:00.395893", "source": { "split": "train_shard_00000", "doc_id": 2253 }, "chunk_id": "train_shard_00000_2253_0", "global_id": 2478 }, { "text": "Automated chyme reinfusion (CR) in patients with intestinal failure (IF) and a temporary double enterostomy (TDE) restores intestinal function and protects against liver injury, but the mechanisms are incompletely understood. The aim was to investigate whether the beneficial effects of CR relate to functional recovery of enterohepatic signaling through the bile salt-FGF19 axis.\n\nChyme Reinfusion Restores the Regulatory Bile Salt-FGF19 Axis in Patients With Intestinal Failure.", "token_count": 122, "char_count": 480, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7424, "quality_score": 0.8712, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:00.783308", "source": { "split": "train_shard_00000", "doc_id": 2254 }, "chunk_id": "train_shard_00000_2254_0", "global_id": 2479 }, { "text": "Pangenomes-the cumulative set of genes encoded by a population or species-arise from the interplay of horizontal gene transfer, drift, and selection. The balance of these forces in shaping pangenomes has been debated, and studies to date focused on ancient evolutionary time scales have suggested that pangenomes generally confer niche adaptation to their bacterial hosts. To shed light on pangenome evolution on shorter evolutionary time scales, we inferred the selective pressures acting on mobile genes within individual human microbiomes from 176 Fiji islanders. We mapped metagenomic sequence reads to a set of known mobile genes to identify single nucleotide variants (SNVs) and calculated population genetic metrics to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation without the need to invoke the adaptive value of mobile genes to either bacterial or human hosts. These results stand in contrast with the apparent adaptive value of pangenomes over longer evolutionary time scales. In general, the most highly mobile genes (i.e., those present in more distinct bacterial host genomes) tend to have higher metagenomic read coverage and an excess of low-frequency SNVs, consistent with their rapid spread across multiple bacterial species in the gut. However, a subset of mobile genes-including those involved in defense mechanisms and secondary metabolism-showed a contrasting signature of intermediate-frequency SNVs, indicating species-specific selective pressures or negative frequency-dependent selection on these genes. Together, our evolutionary models and population genetic data show that gene-specific selective pressures predominate over human or bacterial host-specific pressures during the relatively short time scales of a human lifetime.\n\nMobile Gene Sequence Evolution within Individual Human Gut Microbiomes Is Better Explained by Gene-Specific Than Host-Specific Selective Pressures.", "token_count": 441, "char_count": 2163, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5724, "quality_score": 0.7862, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:01.431269", "source": { "split": "train_shard_00000", "doc_id": 2255 }, "chunk_id": "train_shard_00000_2255_0", "global_id": 2480 }, { "text": "In the present study, probiotic potato chips containing a newly isolated probiotic Lactococcus lactis KUMS-T18 strain were produced by using a simple spraying method and then enhancing the stability, survival rate, and sensory characteristics of product during storage at 4 °C and 25 °C was examined for four months. Based on the results, Lactococcus lactis KUMS-T18 isolated from traditional Tarkhineh as a safe strain had high tolerance to low pH and high bile salt, anti-pathogenic activity, hydrophobicity, adhesion to human epithelial cells, auto- and co-aggregation, cholesterol assimilation and antibiotic susceptibility. Meanwhile, by micro-coating the probiotic cells in Tarkhineh formulations, elliptical to spherical shape (460-740 µm) probiotic drops were produced. The results revealed that potato chips produced with turmeric and plain Tarkhineh during storage at 4 °C, had excellent protection abilities for probiotic cells with about 4.52 and 3.46 log decreases in CFU/g respectively. On the other hand, probiotic potato chips, compared to non-probiotic and commercial potato chips, showed the criteria of probiotic products such as excellent quality and superior sensory characteristics. In summary, this study proved that probiotic Lactococcus lactis KUMS-T18 strain covered by Tarkhineh formulations as protective matrix has high potential to be used in the production of probiotic potato chips.\n\nTarkhineh as a new microencapsulation matrix improves the quality and sensory characteristics of probiotic Lactococcus lactis KUMS-T18 enriched potato chips.", "token_count": 425, "char_count": 1573, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5901, "quality_score": 0.795, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:02.061211", "source": { "split": "train_shard_00000", "doc_id": 2256 }, "chunk_id": "train_shard_00000_2256_0", "global_id": 2481 }, { "text": "We investigated possible nosocomial transmission of 3 invasive cases of Group B Streptococcus serotype III disease in newborns delivered in the same facility. All cases were of the same sequence type and clonal complex. Genomic variation was detected within the core genome and capsular region, indicating different sources of acquisition.\n\nInvestigation of Possible Nosocomial-Associated Invasive Group B Streptococcus Disease Using Whole-Genome Sequencing: A Report of 3 Cases.", "token_count": 113, "char_count": 479, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:02.453167", "source": { "split": "train_shard_00000", "doc_id": 2257 }, "chunk_id": "train_shard_00000_2257_0", "global_id": 2482 }, { "text": "Yeast spoilage of fermented dairy products causes challenges for the dairy industry, including economic losses due to wasted product. Food cultures with bioprotective effects are becoming more widely used to help ensure product quality throughout product shelf life. To assist the dairy industry when evaluating product quality throughout shelf life and the effect of bioprotective cultures, we aimed to build stochastic models that provide reliable predictions of yeast spoilage in yogurt with and without bioprotective culture. Growth characterizations of Debaryomyces hansenii, Yarrowia lipolytica, Saccharomyces cerevisiae, and Kluyveromyces marxianus at storage temperatures of 7, 12, and 16°C during a 30-d storage period were conducted in yogurt with and without a bioprotective culture containing Lacticaseibacillus rhamnosus strains. The kinetic growth parameters were calculated using the Buchanan growth model, and these parameters were used as baseline values in Monte Carlo models to translate the yeast growth into spoilage levels. The models were developed using 100,000 simulations and they predicted yeast spoilage levels in yogurt by the 4 yeast types. Each modeled yogurt batch was set to be contaminated with yeast at a concentration drawn from a normal distribution with a mean of 1 log\n\nDevelopment of predictive models evaluating the spoilage-delaying effect of a bioprotective culture on different yeast species in yogurt.", "token_count": 351, "char_count": 1446, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6172, "quality_score": 0.8086, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:03.029084", "source": { "split": "train_shard_00000", "doc_id": 2258 }, "chunk_id": "train_shard_00000_2258_0", "global_id": 2483 }, { "text": "Aldo-keto reductases-catalyzed transformations of ketones to chiral alcohols have become an established biocatalytic process step in the pharmaceutical industry. Previously, we have discovered an aldo-keto reductase (AKR) from Kluyveromyces marxianus that is active to the aliphatic tert-butyl 6-substituted (5R/S)-hydroxy-3-oxohexanoates, but it is inactive to aromatic ketones. In order to acquire an excellent KmAKRmutant for ensuring the simultaneous improvement of activity-thermostability toward tert-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate ((5R)-1) and broadening the universal application prospects toward more substrates covering both aliphatic and aromatic ketones, a fluorescence-based high-throughput (HT) screening technique was established.\n\nFluorescence-based screening for engineered aldo-keto reductase KmAKR with improved catalytic performance and extended substrate scope.", "token_count": 255, "char_count": 893, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:03.543136", "source": { "split": "train_shard_00000", "doc_id": 2259 }, "chunk_id": "train_shard_00000_2259_0", "global_id": 2484 }, { "text": "Streptococcus equi subsp. equi (SEE) is a host-restricted bacterium that causes the common infectious upper respiratory disease known as strangles in horses. Perpetuation of SEE infection appears attributable to inapparent carrier horses because it neither persists long-term in the environment nor infects other host mammals or vectors, and infection results in short-lived immunity. Whether pathogen factors enable SEE to remain in horses without causing clinical signs remains poorly understood. Thus, our objective was to use next-generation sequencing technologies to characterize the genome, methylome, and transcriptome of isolates of SEE from horses with acute clinical strangles and inapparent carrier horses-including isolates recovered from individual horses sampled repeatedly-to assess pathogen-associated changes that might reflect specific adaptions of SEE to the host that contribute to inapparent carriage. The accessory genome elements and methylome of SEE isolates from Sweden and Pennsylvania revealed no significant or consistent differences between acute clinical and inapparent carrier isolates of SEE. RNA sequencing of SEE isolates from Pennsylvania demonstrated no genes that were differentially expressed between acute clinical and inapparent carrier isolates of SEE. The absence of specific, consistent changes in the accessory genomes, methylomes, and transcriptomes of acute clinical and inapparent carrier isolates of SEE indicates that adaptations of SEE to the host are unlikely to explain the carrier state of SEE. Efforts to understand the carrier state of SEE should instead focus on host factors.\n\nDifferences in the genome, methylome, and transcriptome do not differentiate isolates of Streptococcus equi subsp. equi from horses with acute clinical signs from isolates of inapparent carriers.", "token_count": 400, "char_count": 1830, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5137, "quality_score": 0.7569, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:04.175671", "source": { "split": "train_shard_00000", "doc_id": 2260 }, "chunk_id": "train_shard_00000_2260_0", "global_id": 2485 }, { "text": "The objective of this paper is to confine piperine, a poor oral bioavailable herbal drug into bile salt based nano vesicles for improving its aqueous solubility, hence, its therapeutic activity. Piperine-loaded bilosomes were fabricated adopting thin film hydration technique according to 3\n\nStatistical optimization of bile salt deployed nanovesicles as a potential platform for oral delivery of piperine: accentuated antiviral and anti-inflammatory activity in MERS-CoV challenged mice.", "token_count": 122, "char_count": 488, "word_count": 67, "semantic_coherence": 1, "information_density": 0.8657, "quality_score": 0.9328, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:04.599079", "source": { "split": "train_shard_00000", "doc_id": 2261 }, "chunk_id": "train_shard_00000_2261_0", "global_id": 2486 }, { "text": "The gastrointestinal hydrolysis of food proteins has been portrayed in scientific literature to predominantly depend on the activity and specificity of proteolytic enzymes. Human bile has not been considered to facilitate proteolysis in the small intestine, but rather to assist in intestinal lipolysis. However, human bile can potentially influence proteins that are largely resistant to gastric digestion, and which are mainly hydrolysed after they have been transferred to the small intestine. We used purified and food-grade bovine milk β-lactoglobulin (βLg) to assess the impact of bile salts (BS) on the in vitro gastrointestinal digestion of this protein. Quantitative analysis showed that the proteolysis rate increased significantly with increasing BS concentration. The effect was consistent regardless of whether individual BS or real human bile samples, varying in BS concentrations, were used. The total BS content of bile was more important than its BS composition in facilitating the proteolysis of βlg. We also show that the impact of human bile observed during the digestion of purified βLg and βLg-rich whey protein isolate can be closely replicated by the use of individual BS mixed with phosphatidylcholine. This could validate simple BS/phosphatidylcholine mixtures as human-relevant substitutes of difficult-to-obtain human bile for in vitro proteolysis studies.\n\nThe bile salt content of human bile impacts on simulated intestinal proteolysis of β-lactoglobulin.", "token_count": 361, "char_count": 1485, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:05.209382", "source": { "split": "train_shard_00000", "doc_id": 2262 }, "chunk_id": "train_shard_00000_2262_0", "global_id": 2487 }, { "text": "Here we report the 409.5 Mb chromosome-level assembly of the first bred semi-dwarf rice, the Taichung Native 1 (TN1), which served as the template for the development of the Green Revolution (GR) cultivar IR8 \"miracle rice\". We sequenced the TN1 genome utilizing multiple platforms and produced PacBio long reads, Illumina paired-end reads, Illumina mate-pair reads and 10x Genomics linked reads. We used a hybrid approach to assemble the 226× coverage of sequences by a combination of de novo and reference-guided approaches. The assembled TN1 genome has an N50 scaffold size of 33.1 Mb with the longest measuring 45.5 Mb. We annotated 37,526 genes, in which 24,102 (64.23%) were assigned Blast2GO annotations. The genome has 4672 or 95.4% complete BUSCOs and a repeat content of 51.52%. We developed our own method of creating a GR pangenome using the orthologous relationships of the proteins of TN1, IR8, MH63 and IR64, identifying 16,999 core orthologue groups of Green Revolution. From the pangenome, we identified a set of shared and unique gene ontology terms for the accessory clusters, characterizing TN1, IR8, MH63 and IR64. This TN1 genome assembly and GR pangenome will be a resource for new genomic discoveries about Green Revolution, and for improving the disease and insect resistances and the yield of rice.\n\nChromosomal-level genome assembly of the semi-dwarf rice Taichung Native 1, an initiator of Green Revolution.", "token_count": 425, "char_count": 1435, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6504, "quality_score": 0.8252, "entities": { "genes": [ "IR64", "IR8", "TN1", "MH63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:05.836077", "source": { "split": "train_shard_00000", "doc_id": 2263 }, "chunk_id": "train_shard_00000_2263_0", "global_id": 2488 }, { "text": "This study aimed to define the taxonomic position and structure of a novel, taxonomically unique group of 26 Acinetobacter strains, provisionally designated Taxon 24 (T24). The strains were recovered from soil and freshwater ecosystems (n = 21) or animals (n = 5) in Czechia, Scotland, Germany, the Netherlands and Turkey between 1993 and 2015. They were non-glucose-acidifying, nonhemolytic, nonproteolytic, growing at 32 °C and on acetate and ethanol as single carbon sources, but not on 4-hydroxybenzoate and mostly not at 37 °C. Their whole-genome sequences were 3.0-3.7 Mb in size, with GC contents of 39.8-41.3%. Based on core genome phylogenetic analysis, the 26 strains formed a distinct clade within the genus Acinetobacter, with strongly supported subclades termed T24A (n = 11), T24B (n = 8), T24C (n = 2), T24D (n = 3) and T24E (n = 2). The internal genomic ANIb values for these subclades were >94.8%, while the ANIb values between them were <92.5%. The results of MALDI-TOF MS-based analyses agreed with this classification. The five subclades differed from each other in the results of one to six carbon source assimilation tests. Given the genomic and phenotypic distinctness, internal coherence, numbers of available strains and geographically diverse origin of T24A and T24B, we propose the names Acinetobacter terrae sp. nov. and Acinetobacter terrestris sp. nov. for these two taxa, respectively. The type strains are ANC 4282", "token_count": 498, "char_count": 1446, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8311, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:06.497132", "source": { "split": "train_shard_00000", "doc_id": 2264 }, "chunk_id": "train_shard_00000_2264_0", "global_id": 2489 }, { "text": "Delineation of a novel environmental phylogroup of the genus Acinetobacter encompassing Acinetobacter terrae sp. nov., Acinetobacter terrestris sp. nov. and three other tentative species.", "token_count": 50, "char_count": 187, "word_count": 24, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:06.857427", "source": { "split": "train_shard_00000", "doc_id": 2264 }, "chunk_id": "train_shard_00000_2264_1", "global_id": 2490 }, { "text": "Bile salts is one of essential components of bile secreted into the intestine to confer antibacterial protection. Cronobacter species are associated with necrotizing enterocolitis in newborns and show a strong tolerance to bile salts. However, little attempt has been made to focus on the molecular basis of the tolerance to bile salts. In this study, we investigated the roles of tolC on growth, cell morphology, motility, and biofilm formation ability in Cronobacter malonaticus under bile salt stress. The results indicated that the absence of tolC significantly affected the colony morphology and outer membrane structure in a normal situation, compared with those of the wild type strain. The deletion of tolC caused the decline in resistance to bile salt stress, inhibition of growth, and observable reduction in relative growth rate and motility. Moreover, the bacterial stress response promoted the biofilm formation ability of the mutant strain. The expression of the AcrAB-TolC system (acrA, acrB, and tolC) was effectively upregulated compared with the control sample when exposed to different bile salt concentrations. The findings provide valuable information for deeply understanding molecular mechanisms about the roles of tolC under bile salt stress and the prevention and control of C. malonaticus.\n\nEffects of tolC on tolerance to bile salts and biofilm formation in Cronobacter malonaticus.", "token_count": 318, "char_count": 1409, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5735, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:07.419142", "source": { "split": "train_shard_00000", "doc_id": 2265 }, "chunk_id": "train_shard_00000_2265_0", "global_id": 2491 }, { "text": "We investigated the molecular epidemiology of 21 carbapenem-resistant Acinetobacter baumannii isolates from Libya and assessed their relative fitness. Core genome multilocus sequence typing (MLST) revealed five interhospital transmission clusters. Three clusters were associated with the international clones (IC) IC1, IC2, and IC7. Carbapenem-resistance was associated with\n\nDiversity of Sequence Types and Impact of Fitness Cost among Carbapenem-Resistant Acinetobacter baumannii Isolates from Tripoli, Libya.", "token_count": 134, "char_count": 511, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7937, "quality_score": 0.8968, "entities": { "genes": [ "IC2", "IC1", "IC7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:07.845271", "source": { "split": "train_shard_00000", "doc_id": 2266 }, "chunk_id": "train_shard_00000_2266_0", "global_id": 2492 }, { "text": "Managed inoculation of non-Saccharomyces yeast species is regarded as a practical way to introduce new characteristics to wine. However, these yeasts struggle to survive until fermentation is complete. Kluyveromyces marxianus IWBT Y885 is one such yeast. Although it displays interesting oenological properties, a longer persistence during alcoholic fermentation would warranty a stronger impact on wine composition. A key factor for survival, growth and sustained metabolic activity of all yeasts is their nutrient requirements. Thus, identifying nutrients that are essential for maximising fermentation performance, and subsequently ensuring adequate levels of nutrients, is a means to ensure significant contribution of yeasts to wine properties. This study aimed to identify essential nutrients, other than previously studied sugars and nitrogen, for maximum impact of K. marxianus Y885, as well as to characterise the outcomes of their utilisation. A multifactorial experimental design was employed to investigate the impact of nutrient concentrations on fermentation performance with K. marxianus Y885 in synthetic must. B-complex vitamins most significantly impacted fermentation performance of K. marxianus Y885 compared to other nutrient groups investigated. Considering the well-established role of the vitamin, thiamine, for maximum fermentation performance during winemaking and the fact that it may be supplemented to wine fermentations legally, the responses to specifically exogenous thiamine concentration for K. marxianus Y885 and Saccharomyces cerevisiae EC1118 were compared in terms of population viability, fermentation rate, total sugars utilised, thiamine assimilation kinetics, and final wine composition. A saturation effect for initial thiamine concentration of K. marxianus Y885 fermentations was characterised, with a maximum fermentation rate and over 90% of available sugars utilisation obtained at 0.25 mg/L. An appreciably larger comparative increase in exponential cell growth rate, maximum population, fermentation rate and total CO", "token_count": 475, "char_count": 2066, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [ "EC1118" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:08.492930", "source": { "split": "train_shard_00000", "doc_id": 2267 }, "chunk_id": "train_shard_00000_2267_0", "global_id": 2493 }, { "text": "Comparative uptake of exogenous thiamine and subsequent metabolic footprint in Saccharomyces cerevisiae and Kluyveromyces marxianus under simulated oenological conditions.", "token_count": 46, "char_count": 171, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:08.854182", "source": { "split": "train_shard_00000", "doc_id": 2267 }, "chunk_id": "train_shard_00000_2267_1", "global_id": 2494 }, { "text": "In the Medicago truncatula-Sinorhizobium meliloti symbiosis, chemical signaling initiates rhizobial infection of root nodule tissue, where a large portion of the bacteria are endocytosed into root nodule cells to function in nitrogen-fixing organelles. These intracellular bacteria are subjected to an arsenal of plant-derived nodule-specific cysteine-rich (NCR) peptides, which induce the physiological changes that accompany nitrogen fixation. NCR peptides drive these intracellular bacteria toward terminal differentiation. The bacterial peptidase HrrP was previously shown to degrade host-derived NCR peptides and give the bacterial symbionts greater fitness at the expense of host fitness. The hrrP gene is found in roughly 10% of Sinorhizobium isolates, as it is carried on an accessory plasmid. The objective of the present study is to identify peptidase genes in the core genome of S. meliloti that modulate symbiotic outcome in a manner similar to the accessory hrrP gene. In an overexpression screen of annotated peptidase genes, we identified one such symbiosis-associated peptidase (sap) gene, sapA (SMc00451). When overexpressed, sapA leads to a significant decrease in plant fitness. Its promoter is active in root nodules, with only weak expression evident under free-living conditions. The SapA enzyme can degrade a broad range of NCR peptides in vitro.\n\nA conserved rhizobial peptidase that interacts with host-derived symbiotic peptides.", "token_count": 394, "char_count": 1455, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:09.469853", "source": { "split": "train_shard_00000", "doc_id": 2268 }, "chunk_id": "train_shard_00000_2268_0", "global_id": 2495 }, { "text": "Annotated genome sequences provide valuable insight into the functional capabilities of members of microbial communities. Nevertheless, most studies on the microbiome in animal guts use metagenomic data, hampering the assignment of genes to specific microbial taxa. Here, we make use of the readily culturable bacterial communities in the gut of the fruit fly Drosophila melanogaster to obtain draft genome sequences for 96 isolates from wild flies. These include 81 new de novo assembled genomes, assigned to three orders (Enterobacterales, Lactobacillales, and Rhodospirillales) with 80% of strains identified to species level using average nucleotide identity and phylogenomic reconstruction. Based on annotations by the RAST pipeline, among-isolate variation in metabolic function partitioned strongly by bacterial order, particularly by amino acid metabolism (Rhodospirillales), fermentation, and nucleotide metabolism (Lactobacillales) and arginine, urea, and polyamine metabolism (Enterobacterales). Seven bacterial species, comprising 2-3 species in each order, were well-represented among the isolates and included ≥5 strains, permitting analysis of metabolic functions in the accessory genome (i.e., genes not present in every strain). Overall, the metabolic function in the accessory genome partitioned by bacterial order. Two species, Gluconobacter cerinus (Rhodospirillales) and Lactiplantibacillus plantarum (Lactobacillales) had large accessory genomes, and metabolic functions were dominated by amino acid metabolism (G. cerinus) and carbohydrate metabolism (La. plantarum). The patterns of variation in metabolic capabilities at multiple phylogenetic scales provide the basis for future studies of the ecological and evolutionary processes shaping the diversity of microorganisms associated with natural populations of Drosophila.\n\nGenome-Inferred Correspondence between Phylogeny and Metabolic Traits in the Wild Drosophila Gut Microbiome.", "token_count": 492, "char_count": 1957, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6299, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:10.118082", "source": { "split": "train_shard_00000", "doc_id": 2269 }, "chunk_id": "train_shard_00000_2269_0", "global_id": 2496 }, { "text": "Changes in the gut microbiome have been associated with inflammatory bowel disease. A protective role of short chain fatty acids produced by the gut microbiota has been suggested as a causal mechanism. Nevertheless, multi-omic analyses have failed to identify a clear link between changes in specific taxa and disease states. Recently, metagenomic analyses unveiled that gut bacterial species have a previously unappreciated genomic diversity, implying that a geno-centric approach may be better suited to identifying the mechanisms involved. Here, we quantify the abundance of terminal genes in propionate-producing fermentative pathways in the microbiome of a large cohort of healthy subjects and patients with inflammatory bowel disease. The results show that propionate kinases responsible for propionate production in the gut are depleted in patients with Crohn's disease. Our results also indicate that changes in overall species abundances do not necessarily correlate with changes in the abundances of metabolic genes, suggesting that these genes are not part of the core genome. This, in turn, suggests that changes in strain composition may be as important as changes in species abundance in alterations of the gut microbiome associated with pathological conditions.\n\nPropionate Fermentative Genes of the Gut Microbiome Decrease in Inflammatory Bowel Disease.", "token_count": 299, "char_count": 1369, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5628, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:10.678291", "source": { "split": "train_shard_00000", "doc_id": 2270 }, "chunk_id": "train_shard_00000_2270_0", "global_id": 2497 }, { "text": "Excessive use of antibiotics has detrimental consequences, including antibiotic resistance and gut microbiome destruction. Probiotic-rich diets help to restore good microbes, keeping the body healthy and preventing the onset of chronic diseases. Honey contains not only prebiotic oligosaccharides but, like yogurt and fermented foods, is an innovative natural source for probiotic discovery. Here, a collection of three honeybee samples was screened for yeast strains, aiming to characterize their potential in vitro probiotic properties and the ability to produce valuable metabolites. Ninety-four isolates out of one-hundred and four were able to grow at temperatures of 30 °C and 37 °C, while twelve isolates could grow at 42 °C. Fifty-eight and four isolates displayed the ability to grow under stimulated gastrointestinal condition, at pH 2.0-2.5, 0.3% (\n\nSelection of Potential Yeast Probiotics and a Cell Factory for Xylitol or Acid Production from Honeybee Samples.", "token_count": 250, "char_count": 973, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:11.165341", "source": { "split": "train_shard_00000", "doc_id": 2271 }, "chunk_id": "train_shard_00000_2271_0", "global_id": 2498 }, { "text": "The study aimed to evaluate the metabolism and resistance to the gastrointestinal tract conditions of\n\nPhysiological and Genomic Analysis of", "token_count": 31, "char_count": 140, "word_count": 20, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:11.524181", "source": { "split": "train_shard_00000", "doc_id": 2272 }, "chunk_id": "train_shard_00000_2272_0", "global_id": 2499 }, { "text": "The gut microbiota has been increasingly linked to metabolic health and disease over the last few decades. Several factors have been suggested to be involved in lipid metabolism and metabolic responses. One mediator that has gained great interest as a clinically important enzyme is bile salt hydrolase (BSH). BSH enzymes are widely distributed in human gastrointestinal microbial communities and are believed to play key roles in both microbial and host physiology. In this review, we discuss the current evidence related to the role of BSHs in health and provide useful insights that may pave the way for new therapeutic targets in human diseases.\n\nBile Salt Hydrolases: At the Crossroads of Microbiota and Human Health.", "token_count": 168, "char_count": 722, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7281, "quality_score": 0.864, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:12.432662", "source": { "split": "train_shard_00000", "doc_id": 2273 }, "chunk_id": "train_shard_00000_2273_0", "global_id": 2500 }, { "text": "Identification of Bile Salt Hydrolase and Bile Salt Resistance in a Probiotic Bacterium", "token_count": 24, "char_count": 87, "word_count": 13, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:12.799450", "source": { "split": "train_shard_00000", "doc_id": 2274 }, "chunk_id": "train_shard_00000_2274_0", "global_id": 2501 }, { "text": "Lactobacillus plantarum is one of common probiotics in fermented foods. Quorum sensing (QS) is a common communication way within bacteria. It is not clear whether the probiotic properties of L. plantarum mediated by QS. Here, Lb. plantarum YM-4-3 was examined for resistance of pH, bile, antimicrobial and luxS gene expression pattern. The study found that: (1) the supernatant of YM-4-3 had bacteriostatic effect to Escherichia coli O157:H7, Listeria monocytogenes and Staphylococcus aureus; (2) Lb. plantarum YM-4-3 shown tolerance property to the strongest acid culture that pH value of 3; (3) the bile tolerance of Lb. plantarum YM-4-3 was significant difference with the growth stage, the early exponential phase of the growth culture can tolerate bile of 0.4% (w/v), while the stationary growth stage can only tolerate bile of 0.2%; (4) Lb. plantarum YM-4-3 luxS gene was contrary expression along with the growth. (5) Compared with the wild-type strain, the adhesion ability of Lb. plantarum YM-4-3 ΔluxS was decreased obviously. These results showed that AI-2 LuxS quorum sensing system mediating Lb. plantarum acid, bile tolerance, antimicrobial and adhesion of probiotics.\n\nLuxS quorum sensing system mediating Lactobacillus plantarum probiotic characteristics.", "token_count": 393, "char_count": 1271, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6011, "quality_score": 0.8005, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:13.412399", "source": { "split": "train_shard_00000", "doc_id": 2275 }, "chunk_id": "train_shard_00000_2275_0", "global_id": 2502 }, { "text": "The application of Tarkhineh texture to protect probiotics in potato chips has been investigated as the main goal in this paper. In this study, the probiotic assessments, morphological characteristics, sensory evaluation, and survival rates of the covered probiotic cells with Tarkhineh in potato chips during storage time were assessed. Based on results, T34 isolated from traditional Tarkhineh as a safe strain had a high tolerance to low pH and bile salt conditions, displayed acceptable anti-pathogenic activities, and also showed desirable antibiotic susceptibility. Two types of Tarkhineh formulations (plain Tarkhineh and turmeric Tarkhineh) were applied using a simple spraying method for covering T34 cells in potato chips. All formulations showed elliptical to spherical (480-770 μm) shape probiotic drops. Storage stability results revealed that T34 cells mixed with turmeric and plain Tarkhineh during 4 months of storage at 4°C displayed excellent protection abilities with about 3.70 and 2.85 log decreases in CFU/g respectively. Additionally, probiotic potato chips compared to non-probiotic and commercial potato chips, exhibited probiotic product criteria such as excellent quality and superior sensory properties during storage time. In conclusion, Tarkhineh showed high potential as a protective matrix for probiotic cells in potato chips.\n\nApplication of Tarkhineh Fermented Product to Produce Potato Chips With Strong Probiotic Properties, High Shelf-Life, and Desirable Sensory Characteristics.", "token_count": 370, "char_count": 1516, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:14.002439", "source": { "split": "train_shard_00000", "doc_id": 2276 }, "chunk_id": "train_shard_00000_2276_0", "global_id": 2503 }, { "text": "Structural variations (SVs) and gene copy number variations (gCNVs) have contributed to crop evolution, domestication, and improvement. Here, we assembled 31 high-quality genomes of genetically diverse rice accessions. Coupling with two existing assemblies, we developed pan-genome-scale genomic resources including a graph-based genome, providing access to rice genomic variations. Specifically, we discovered 171,072 SVs and 25,549 gCNVs and used an Oryza glaberrima assembly to infer the derived states of SVs in the Oryza sativa population. Our analyses of SV formation mechanisms, impacts on gene expression, and distributions among subpopulations illustrate the utility of these resources for understanding how SVs and gCNVs shaped rice environmental adaptation and domestication. Our graph-based genome enabled genome-wide association study (GWAS)-based identification of phenotype-associated genetic variations undetectable when using only SNPs and a single reference assembly. Our work provides rich population-scale resources paired with easy-to-access tools to facilitate rice breeding as well as plant functional genomics and evolutionary biology research.\n\nPan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations.", "token_count": 291, "char_count": 1266, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:14.563749", "source": { "split": "train_shard_00000", "doc_id": 2277 }, "chunk_id": "train_shard_00000_2277_0", "global_id": 2504 }, { "text": "Advances in next-generation sequencing (NGS) platforms have had a positive impact on biological research, leading to the development of numerous omics approaches, including genomics, transcriptomics, metagenomics, and pangenomics. These analyses provide insights into the gene contents of various organisms. However, to understand the evolutionary processes of these genes, comparative analysis, which is an important tool for annotation, is required. Using comparative analysis, it is possible to infer the functions of gene contents and identify orthologs and paralogous genes via their homology. Although several comparative analysis tools currently exist, most of them are limited to complete genomes. PAN2HGENE, a computational tool that allows identification of gene products missing from the original genome sequence, with automated comparative analysis for both complete and draft genomes, can be used to address this limitation. In this study, PAN2HGENE was used to identify new products, resulting in altering the alpha value behavior in the pangenome without altering the original genomic sequence. Our findings indicate that this tool represents an efficient alternative for comparative analysis, with a simple and intuitive graphical interface. The PAN2HGENE have been uploaded to SourceForge and are available via: https://sourceforge.net/projects/pan2hgene-software.\n\nPAN2HGENE-tool for comparative analysis and identifying new gene products.", "token_count": 314, "char_count": 1457, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6684, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:15.128610", "source": { "split": "train_shard_00000", "doc_id": 2278 }, "chunk_id": "train_shard_00000_2278_0", "global_id": 2505 }, { "text": "Mycobacteroides abscessus (Previously Mycobacterium abscessus) is an emerging microorganism of the newly defined genera Mycobacteroides that causes mainly skin and tissue diseases in humans. The recent availability of total 34 fully sequenced genomes of different strains belonging to this species has provided an opportunity to utilize this genomics data to gain novel insights and guide the development of specific antimicrobial therapies. In the present study, we collected collectively 34 complete genome sequences of M. abscessus from the NCBI GenBank database. Pangenome analysis was conducted on these genomes to understand the genetic diversity and to obtain proteins associated with its core genome. These core proteins were then subjected to various subtractive filters to identify potential antigenic targets that were subjected to multi-epitope vaccine design. Our analysis projected the open pangenome of M. abscessus containing 3443 core genes. After applying various stepwise filtration steps on the core proteins, a total of four potential antigenic targets were identified. Utilizing their constituent CD4 and CD8 T-cell epitopes, a multi-epitope based subunit vaccine was computationally designed. Sequence-based analysis as well as structural characterization revealed the immunological effectiveness of this designed vaccine. Further molecular docking, molecular dynamics simulation and binding free energy estimation with Toll-like receptor 2 indicated strong structural associations of the vaccine with the immune receptor. The promising results are encouraging and need to be validated by additional wet laboratory studies for confirmation.\n\nDesigning a multi-epitope vaccine against Mycobacteroides abscessus by pangenome-reverse vaccinology.", "token_count": 383, "char_count": 1766, "word_count": 239, "semantic_coherence": 1, "information_density": 0.682, "quality_score": 0.841, "entities": { "genes": [ "CD8", "CD4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:15.723535", "source": { "split": "train_shard_00000", "doc_id": 2279 }, "chunk_id": "train_shard_00000_2279_0", "global_id": 2506 }, { "text": "With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge.\n\nA tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.", "token_count": 146, "char_count": 756, "word_count": 99, "semantic_coherence": 1, "information_density": 0.8081, "quality_score": 0.904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:16.174616", "source": { "split": "train_shard_00000", "doc_id": 2280 }, "chunk_id": "train_shard_00000_2280_0", "global_id": 2507 }, { "text": "Neisseria elongata is part of the commensal microbiota of the oropharynx. Although it is not considered pathogenic to humans, N. elongata has been implicated in several cases of infective endocarditis (IE). Here, we report a case of IE caused by N. elongata subsp. nitroreducens (Nel_M001) and compare its genome with 17 N. elongata genomes available in GenBank. We also evaluated resistance and virulence profiles with Comprehensive Antibiotic Resistance and Virulence Finder databases. The results showed a wide diversity among N. elongata isolates. Based on the pangenome cumulative curve, we demonstrate that N. elongata has an open pangenome. We found several different resistance genes, mainly associated with antibiotic efflux pumps. A wide range of virulence genes was observed, predominantly pilus formation genes. Nel_M001 was the only isolate to present two copies of some pilus genes and not present nspA gene. Together, our results provide insights into how this commensal microorganism can cause IE and may assist further biological investigations on nonpathogenic Neisseria spp. Case reporting and pangenome analyses are critical for enhancing our understanding of IE pathogenesis, as well as for alerting physicians and microbiologists to enable rapid identification and treatment to avoid unfavorable outcomes.\n\nGenomic analysis of Neisseria elongata isolate from a patient with infective endocarditis.", "token_count": 360, "char_count": 1419, "word_count": 206, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:16.784697", "source": { "split": "train_shard_00000", "doc_id": 2281 }, "chunk_id": "train_shard_00000_2281_0", "global_id": 2508 }, { "text": "In this experiment, Lactobacillus fermentum CQPC08 (LF-CQPC08) isolated from traditionally fermented pickles was used to study its mitigation effect on lead acetate-induced oxidative stress and lead ion adsorption capacity in rats. In vitro experiments showed that the survival rate in artificial gastric juice and the growth efficiency in artificial bile salt of LF-CQPC08 was 93.6% ± 2.2% and 77.2% ± 0.8%, and the surface hydrophobicity rate was 45.5% ± 0.3%. The scavenging rates of hydroxyl radical, superoxide anion, and 1,1-diphenyl-2-picrylhydrazyl (DPPH) were 47.8% ± 0.9%, 63.9% ± 1.2%, and 83.6% ± 1.5%, respectively, and the reduction power was 107.3 ± 2.8 μmol L-1. LF-CQPC08 could not only adsorb 76.9% ± 1.0% lead ions in aqueous solution but also reduce the lead content in serum, liver, kidneys, and brain tissue of Sprague-Dawley (SD) rats, as well as maintain the cell structure and tissue state of the liver and kidneys. In addition, by examining the indicators of inflammation and oxidation in the serum, liver, and kidneys of SD rats, we found that LF-CQPC08 can reduce the proinflammatory factors interleukin (IL)-1 beta (1β), IL-6, tumor necrosis factor alpha, and interferon gamma in the body, increase the level of anti-inflammatory factor IL-10, enhance the activity of antioxidant enzymes such as superoxide dismutase and catalase and glutathione levels in serum and organ tissues, and reduce the production of reactive oxygen species and accumulation of lipid peroxide malondialdehyde", "token_count": 501, "char_count": 1513, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6638, "quality_score": 0.8319, "entities": { "genes": [ "CQPC08" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:17.444615", "source": { "split": "train_shard_00000", "doc_id": 2282 }, "chunk_id": "train_shard_00000_2282_0", "global_id": 2509 }, { "text": "LF-CQPC08 can also activate the Keap1/Nrf2/ARE signaling pathway to promote high-level expression of the downstream antioxidants heme oxygenase 1 (HO-1), NAD(P)H : quinone oxidoreductase 1 (NQO1), and γ-glutamylcysteine synthetase (γ-GCS). As food-grade lactic acid bacteria, LF-CQPC08 has great potential and research value in removing heavy metals from food and alleviating the toxicity of heavy metals in the future.", "token_count": 146, "char_count": 419, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8103, "quality_score": 0.9052, "entities": { "genes": [ "CQPC08", "NQO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:17.880191", "source": { "split": "train_shard_00000", "doc_id": 2282 }, "chunk_id": "train_shard_00000_2282_1", "global_id": 2510 }, { "text": "Salmonella enterica is a major cause of foodborne diseases, and is also an important pathogenic bacterium in poultry industry. Whole genome sequencing (WGS) has become a crucial molecular typing technology used for the surveillance of the pathogenic bacteria. In the present study, we adopted WGS for tracking transmission of S. enterica in the production chain of broiler chickens. A total of 74 S. enterica strains were isolated from the different steps of breeding and slaughtering in a large production enterprise in Sichuan Province, China. The isolation rate of Salmonella was the highest in procedure of defeathering (50.0%) and evisceration (36.7%). Serotype identification showed that 74 Salmonella isolates included 7 serotypes, among which Mbandaka accounted for the highest proportions (35.1%). WGS revealed that 74 strains belonged to 7 different sequence types (STs), as well as 7 different ribosomal STs and 35 core genome STs. cgMLST-based Minimum Spanning Trees and phylogenetic tree based on the SNPs indicated that three serotypes, Mbandaka, Indiana and Kentucky, could be clonally transmitted between broiler farm and slaughterhouse. Heterogeneous resistant phenotypes and genotypes were found in two serotypes, Indiana and Kentucky. Our study indicated WGS in an accurate tool for molecular typing of S. enterica. Routine surveillance of S. enterica in the production chain of broiler chickens is needed.\n\nTracking Salmonella enterica by whole genome sequencing of isolates recovered from broiler chickens in a poultry production system.", "token_count": 385, "char_count": 1558, "word_count": 230, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:18.497673", "source": { "split": "train_shard_00000", "doc_id": 2283 }, "chunk_id": "train_shard_00000_2283_0", "global_id": 2511 }, { "text": "Campylobacter jejuni (C. jejuni), is considered among the most common bacterial causes of human bacterial gastroenteritis worldwide. The epidemiology and the transmission dynamics of campylobacteriosis in Egypt remain poorly defined due to the limited use of high-resolution typing methods. In this pilot study, we evaluated the discriminatory power of multiple typing 'gene-by-gene based' techniques to characterize C. jejuni obtained from different sources and estimate the relative contribution of different potential sources of C. jejuni infection in Egypt. Whole genome sequencing (WGS) was performed on 90 C. jejuni isolates recovered from clinical samples, retail chicken, and dairy products in Egypt from 2017 to 2018. Comparative genomic analysis was performed using conventional seven-locus multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), allelic variation in 15 host-segregating (HS) markers, and comparative genomic fingerprinting (CGF40). The probabilistic source attribution was performed via STRUCTURE software using MLST, CGF40, cgMLST and allelic variation in HS markers. Comparison of the discriminatory power of the aforementioned genotyping methods revealed cgMLST to be the most discriminative method, followed by HS markers. The source attribution analysis showed the role of retail chicken as a source of infection among clinical cases in Egypt when HS and cgMLST were used (64.2% and 52.3% of clinical isolates were assigned to this source, respectively). Interestingly, the cattle reservoir was also identified as a contributor to C. jejuni infection in Egypt; 35.8% and 47.7% of clinical isolates were assigned to this source by HS and cgMLST, respectively. Here, we provided evidence of the importance of using WGS typing methods to facilitate source tracking of C. jejuni. Our findings suggest the importance of non-poultry sources, together with the previously reported role of retail chicken in human campylobacteriosis in Egypt that can provide insights to inform national control measures.", "token_count": 498, "char_count": 2059, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5661, "quality_score": 0.7831, "entities": { "genes": [ "CGF40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:19.147276", "source": { "split": "train_shard_00000", "doc_id": 2284 }, "chunk_id": "train_shard_00000_2284_0", "global_id": 2512 }, { "text": "A pilot study revealing host-associated genetic signatures for source attribution of sporadic Campylobacter jejuni infection in Egypt.", "token_count": 30, "char_count": 134, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:19.503660", "source": { "split": "train_shard_00000", "doc_id": 2284 }, "chunk_id": "train_shard_00000_2284_1", "global_id": 2513 }, { "text": "Bile salt hydrolase (BSH)-producing bacteria are negatively related to the body weight gain and energy storage of the host. We aimed to obtain a novel BSH-producing strain with excellent anti-obesity effect and explained its mechanism. Here, we selected a strain named Lactiplantibacillus plantarum H-87 (H-87) with excellent ability to hydrolyze glycochenodeoxycholic acid (GCDCA) and tauroursodeoxycholic acid (TUDCA) in vitro from 12 lactobacilli, and evaluated its anti-obesity effect in high-fat diet (HFD)-fed C57BL/6J mice. The results suggested that H-87 could inhibit HFD-induced body weight gain, fat accumulation, liver lipogenesis and injury, insulin resistance and dyslipidemia. In addition, H-87 could colonize in the ileum and hydrolyze GCDCA and TUDCA, reflected as changes in the concentrations of GCDCA, TUDCA, CDCA and UDCA in the ileum or liver. Furthermore, the study identified that H-87 reduced TUDCA and GCDCA levels in the ileum, which decreased the GLP-1 secretion by L cells to alleviate insulin resistance in HFD-fed mice. Furthermore, H-87 increased the CDCA level in the ileum and liver to activate FXR signaling pathways to inhibit liver lipogenesis in HFD-fed mice. In addition, the decrease of intestinal conjugated bile acids (TUDCA and GCDCA) also increased fecal lipid content and decreased intestinal lipid digestibility. In conclusion, H-87 could inhibit liver fat deposition, insulin resistance and lipid digestion by changing bile acid enterohepatic circulation, and eventually alleviate HFD-induced obesity.\n\nLactiplantibacillus plantarum H-87 prevents high-fat diet-induced obesity by regulating bile acid metabolism in C57BL/6J mice.", "token_count": 496, "char_count": 1676, "word_count": 237, "semantic_coherence": 1, "information_density": 0.557, "quality_score": 0.7785, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:20.146638", "source": { "split": "train_shard_00000", "doc_id": 2285 }, "chunk_id": "train_shard_00000_2285_0", "global_id": 2514 }, { "text": "Grain-based carbohydrate sources such as rice comprise 30-50% of commercial pet foods. Some pet foods however have removed the use of grains and have instead incorporated pulses, such as peas and lentils, resulting in grain-free diets. The hypothesis was dog diets with higher levels of dietary fiber will produce a low glycemic response due to decreased rates of digestion and lowered bioavailability of all macronutrients and increased fecal bile salt excretion. This in turn was hypothesized to produce lower plasma concentrations of cysteine, methionine and taurine after 7 days of feeding each test diet in dogs. Six diets were formulated at an inclusion level of 20% available carbohydrate, using white rice flour (grain) or whole pulse flours from smooth pea, fava bean, red lentil or 2 different wrinkled pea varieties (CDC 4,140-4 or Amigold) and fed to beagles in a randomized, cross-over, blinded design. After 7 days feeding each diet, fasting blood glucose was the lowest in the lentil (3.5 ± 0.1 mmol/L) and wrinkled pea (4,140-4; 3.6 ± 0.1 mmol/L) diet periods, while peak glucose levels was lowest after feeding the lentil diet (4.4 ± 0.1 mmol/L) compared to the rice diet. Total tract apparent digestibility of all macronutrients as well as taurine differed among diets yet plasma taurine was not outside normal range. Decreased macronutrient and amino acid digestibility was associated with increasing amylose and dietary fiber content but the specific causative agent could not be determined from this study. Surprisingly, digestibility decreases were not due to increased bile salt loss in the feces since increasing dietary fiber content led to decreased fecal bile salt levels. In conclusion, although pulse-based canine diets have beneficial low glycemic properties, after only 7 days, these pulse-based diets decrease macronutrient and amino acid digestibility", "token_count": 501, "char_count": 1884, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6027, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:20.795062", "source": { "split": "train_shard_00000", "doc_id": 2286 }, "chunk_id": "train_shard_00000_2286_0", "global_id": 2515 }, { "text": "This is likely related at least in part to the lower animal protein content, but on a long-term basis could put domestic dogs at risk for low taurine and dilated cardiomyopathy.\n\nThe Effects of 7 Days of Feeding Pulse-Based Diets on Digestibility, Glycemic Response and Taurine Levels in Domestic Dogs.", "token_count": 82, "char_count": 302, "word_count": 50, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:21.166706", "source": { "split": "train_shard_00000", "doc_id": 2286 }, "chunk_id": "train_shard_00000_2286_1", "global_id": 2516 }, { "text": "Non-diphtherial Corynebacterium species or diphtheroids were previously considered as the mere contaminants of clinical samples. Of late, they have been reckoned as the formidable infection causing agents of various diseases. While the scientific database is filled with articles that document whole genome analysis of individual isolates, a comprehensive comparative genomic analysis of diphtheroids alongside Corynebacterium diphtheriae is expected to enable us in understanding their genomic as well as evolutionary divergence. Here, we have analysed the whole genome sequences of forty strains that were selected from a range of eleven Corynebacterium species (pathogenic and non-pathogenic). A statistical analysis of the pan and core genomes revealed that even though the core genome is saturated, the pan genome is yet open rendering scope for newer gene families to be accumulated in the course of evolution that might further change the pathogenic behavior of these species. Every strain had bacteriophage components integrated in its genome and some of them were intact and consisted of toxins. The presence of diversified genomic islands was observed across the dataset and most of them consisted of genes for virulence and multidrug resistance. Moreover, the phylogenetic analysis showed that a diphtheroid is the last common ancestor of all the Corynebacterium species. The current study is a compilation of genomic features of pathogenic as well as non-pathogenic Corynebacterium species which provides insights into their virulence potential in the times to come.\n\nComparative genome analysis of Corynebacterium species: The underestimated pathogens with high virulence potential.", "token_count": 374, "char_count": 1695, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:21.751565", "source": { "split": "train_shard_00000", "doc_id": 2287 }, "chunk_id": "train_shard_00000_2287_0", "global_id": 2517 }, { "text": "Microplastics (MPs) and tributyltin (TBT) are both potential environmental pollutants that enter organisms through the food chain and affect bodily functions. However, the effects and mechanisms of MPs and TBT exposure (especially the co-exposure of both pollutants) on mammals remain unclear. In this study, Ф5μm MPs (5MP) was administered alone or in combination with TBT to investigate the health risk of oral exposure in mice. All three treatments induced inflammation in the liver, altered gut microbiota composition and disturbed fecal bile acids profiles. In addition to decreasing triglyceride (TG) and increasing aspartate aminotransferase (AST) and macrophage-expressed gene 1 (Mpeg1), 5MP induced hepatic cholestasis by stimulating the expression of the cholesterol hydroxylase enzymes CYP8B1 and CYP27A1, and inhibiting multidrug resistance-associated protein 2 and 3 (MRP2, MRP3), and bile-salt export pump (BSEP) to prevent bile acids for entering the blood and bile. Correspondingly, 5MP treatment decreased 7-ketolithocholic acid (7-ketoLCA) and taurocholic acid (TCA), which were positively correlated with decreased Bacteroides and Marvinbryantia and negatively correlated with increased Bifidobacterium. In addition, TBT increased interferon γ (IFNγ) and Mpeg1 levels to induce inflammation, accompanied by decreased 7-ketoLCA, tauro-alpha-muricholic acid (T-alpha-MCA) and alpha-muricholic acid (alpha-MCA) levels, which were negatively related to Coriobacteriaceae_UCG-002 and Bifidobacterium. Co-exposure to 5MP and TBT also decreased TG and induced bile acids accumulation in the liver due to inhibited BSEP, which might be attributed to the co-regulation of decreased T-alpha-MCA and Harryflintia", "token_count": 510, "char_count": 1720, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8312, "entities": { "genes": [ "MRP2", "MRP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:22.409616", "source": { "split": "train_shard_00000", "doc_id": 2288 }, "chunk_id": "train_shard_00000_2288_0", "global_id": 2518 }, { "text": "In conclusion, the administration of 5MP and TBT alone and in combination could cause gut microbiome dysbiosis and subsequently alter bile acids profiles, while the combined exposure of 5MP and TBT weakened the toxic effects of 5MP and TBT alone.\n\nEffects of microplastics (MPs) and tributyltin (TBT) alone and in combination on bile acids and gut microbiota crosstalk in mice.", "token_count": 104, "char_count": 377, "word_count": 60, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:22.786240", "source": { "split": "train_shard_00000", "doc_id": 2288 }, "chunk_id": "train_shard_00000_2288_1", "global_id": 2519 }, { "text": "The heavy use of prophylactic antibiotics in aquaculture leads to elevated antibiotic residues, posing a huge hidden danger in aquaculture products and other natural aquatic environments. Therefore, this study aims to isolate probiotics that can replace antibiotics from the gut of grass carp for disease control. Bacillus velezensis B8 was isolated from the gut of grass carp and showed broad-spectrum antimicrobial activity against several fish pathogenic bacteria, including Aeromonas hydrophilis, Aeromonas veronii, Vibrio parahaemolyticus, Escherichia coli, Edwardsiella tarda and Vibrio mimicus. The safety evaluation showed that the strain B8 was non-toxic to grass carp, had no hemolytic activity, and was sensitive to most antibiotics. In vitro study indicated that strain B8 was viable at pH 2-7, had weak tolerance to 0.1% (w/v) bile salt, and could grow at 10°C-40 °C. The grass carps were fed with diets containing 0 (control), 10\n\nDietary supplementation of Bacillus velezensis B8 enhances immune response and resistance against Aeromonas veronii in grass carp.", "token_count": 299, "char_count": 1075, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6962, "quality_score": 0.8481, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:23.356117", "source": { "split": "train_shard_00000", "doc_id": 2289 }, "chunk_id": "train_shard_00000_2289_0", "global_id": 2520 }, { "text": "Benign recurrent intrahepatic cholestasis is a rare disorder characterized by recurrent episodes of cholestatic jaundice without liver damage. A mutation in the ABCB11 gene encoding bile salt export pump protein causes the disease. A 16-year-old boy with severe jaundice is presented here. His laboratory tests were consistent with intrahepatic cholestasis despite having normal gamma-glutamyl transpeptidase levels. Acute and chronic liver diseases with viral, metabolic, and autoimmune etiology were excluded. Magnetic resonance imaging revealed normal intra- and extrahepatic bile ducts. A liver biopsy showed cholestasis in the centrilobular and intermediate zones and sinusoidal dilatation. Genetic testing revealed a homozygous c.3083_3084delCAinsTG (Ala1028Val) mutation in the ABCB11 gene. The patient was treated with ursodeoxycholic acid 20 mg/kg/day and cholestyramine 4 g twice daily, and total bilirubin decreased to normal ranges after two months of therapy. This mutation (c.3083_3084delCAinsTG) in the ABCB11 gene is the first reported in a patient with benign recurrent intrahepatic cholestasis type 2.\n\nBenign recurrent intrahepatic cholestasis type 2 in a child: A case report and novel mutation.", "token_count": 358, "char_count": 1215, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:23.936870", "source": { "split": "train_shard_00000", "doc_id": 2290 }, "chunk_id": "train_shard_00000_2290_0", "global_id": 2521 }, { "text": "Candidiasis is an acute or subacute fungal infection caused by fungi that belongs to candida genus, with Candida albicansbeing the most frequent causative agent. Candida kefyr is a rare cause of candidiasis which has been reported in systemic candidiasis and deep infections. However, to date, it has never been reported as a cause in dermatophytosis. We report a case of candidiasis caused by Candida kefyr in a 72-year-old woman with a chief complaint of pruritic erythematous rash on the back from one day prior to admission. Diagnosis was established based on clinical features, direct microscopic examination with 10% potassium hydroxide solution, gram staining. The fungal species was determined by carbohydrate fermentation test which showed a positive result for Candida kefyr. The patient was treated with miconazole cream and fusidic cream and showed significant clinical improvement.\n\nCutaneous candidiasis caused by", "token_count": 230, "char_count": 927, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6691, "quality_score": 0.8345, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:24.409834", "source": { "split": "train_shard_00000", "doc_id": 2291 }, "chunk_id": "train_shard_00000_2291_0", "global_id": 2522 }, { "text": "The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species' guts are not fully understood. In order to identify putative determinants influencing host preferences of distinct lineages, bootstrapping based on stratified random sampling combined with a k-mer-based genome-wide association was conducted on 490 genomes from diverse origins in Germany and Canada. We show a strong association of both the core and the accessory genome characteristics with distinct host animal species, indicating multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems. Here, we demonstrate that adaptation towards a specific host niche ecology is most likely a long evolutionary and multifactorial process, expressed by gene absence or presence and allele variations of core genes. Several host-specific allelic variants from different phylogenetic backgrounds, including dnaE, rpoB, ftsX or pycB play important roles for genome maintenance and metabolic pathways. Thus, variants of genes important for C. jejuni to cope with specific ecological niches or hosts may be useful markers for both surveillance and future pathogen intervention strategies.\n\nGenome-wide insights into population structure and host specificity of Campylobacter jejuni.", "token_count": 306, "char_count": 1457, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7129, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:24.972298", "source": { "split": "train_shard_00000", "doc_id": 2292 }, "chunk_id": "train_shard_00000_2292_0", "global_id": 2523 }, { "text": "The fish pathogen Flavobacterium psychrophilum infects farmed salmonids worldwide, and application of bacteriophages has been suggested for controlling disease outbreaks in aquaculture. Successful application of phages requires detailed knowledge about the variability in phage susceptibility of the host communities. In this study, we analysed the genetic diversity of F. psychrophilum hosts and phages from the Baltic Sea area to identify genetic determinants of phage-host interaction patterns. A host range analysis of 103 phages tested against 177 F. psychrophilum strains (18 231 phage-host interactions) identified nine phage clusters, infecting from 10% to 91% of the strain collection. The core genome-based comparison of 35 F. psychrophilum isolates revealed an extremely low overall genomic diversity (>99.5% similarity). However, a small subset of 16 ORFs, including genes involved in the type IX secretion system (T9SS), gliding motility and hypothetical cell-surface related proteins, exhibited a highly elevated genetic diversity. These specific genetic variations were linked to variability in phage infection patterns obtained from experimental studies, indicating that these genes are key determinants of phage susceptibility. These findings provide novel insights on the molecular mechanisms determining phage susceptibility in F. psychrophilum and emphasizes the importance of phages as drivers of core genomic diversity in this pathogen.\n\nGenome-informed approach to identify genetic determinants of Flavobacterium psychrophilum phage susceptibility.", "token_count": 372, "char_count": 1571, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:25.556578", "source": { "split": "train_shard_00000", "doc_id": 2293 }, "chunk_id": "train_shard_00000_2293_0", "global_id": 2524 }, { "text": "The EDGAR platform, a web server providing databases of precomputed orthology data for thousands of microbial genomes, is one of the most established tools in the field of comparative genomics and phylogenomics. Based on precomputed gene alignments, EDGAR allows quick identification of the differential gene content, i.e. the pan genome, the core genome, or singleton genes. Furthermore, EDGAR features a wide range of analyses and visualizations like Venn diagrams, synteny plots, phylogenetic trees, as well as Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI) matrices. During the last few years, the average number of genomes analyzed in an EDGAR project increased by two orders of magnitude. To handle this massive increase, a completely new technical backend infrastructure for the EDGAR platform was designed and launched as EDGAR3.0. For the calculation of new EDGAR3.0 projects, we are now using a scalable Kubernetes cluster running in a cloud environment. A new storage infrastructure was developed using a file-based high-performance storage backend which ensures timely data handling and efficient access. The new data backend guarantees a memory efficient calculation of orthologs, and parallelization has led to drastically reduced processing times. Based on the advanced technical infrastructure new analysis features could be implemented including POCP and FastANI genomes similarity indices, UpSet intersecting set visualization, and circular genome plots. Also the public database section of EDGAR was largely updated and now offers access to 24,317 genomes in 749 free-to-use projects. In summary, EDGAR 3.0 provides a new, scalable infrastructure for comprehensive microbial comparative gene content analysis. The web server is accessible at http://edgar3.computational.bio.\n\nEDGAR3.0: comparative genomics and phylogenomics on a scalable infrastructure.", "token_count": 440, "char_count": 1890, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8172, "entities": { "genes": [ "EDGAR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:26.186338", "source": { "split": "train_shard_00000", "doc_id": 2294 }, "chunk_id": "train_shard_00000_2294_0", "global_id": 2525 }, { "text": "Hypercholesterolemia is a risk factor for cardiovascular diseases, and hence, reducing serum cholesterol levels could reduce the incidence. In this study, we ascertained the cholesterol-reducing potential of lactic acid bacteria (LAB) isolated from Korean fermented soybean paste. Live, resting, and dead cells of all the bacteria reduced cholesterol in liquid media in a strain-dependent manner. Live cells of Weissella cibaria SCCB2306, Pediococcus acidilactici SDL1402, P. acidilactici SDL1406, and Lactobacillus rhamnosus JDFM6 reduced the most cholesterol in liquid media by 78 ± 3%, 72 ± 3%, 76 ± 3%, 75 ± 5%, and 79 ± 2%, respectively. As the cholesterol levels in the media reduced, cell membrane lipids of P. acidilactici SDL1402, P. acidilactici SDL1406, and L. rhamnosus JDFM6 increased by 23.36 mg/mL, 6.53 mg/mL, and 8.14 mg/mL, respectively, indicating that cholesterol was incorporated into the bacteria cell membranes. All the bacteria displayed bile salt hydrolase activities in a strain-dependent manner. Though all four LAB significantly reduced cholesterol levels in Caenorhabditis elegans irrespective of the order of feeding, L. rhamnosus JDFM6 reduced the most cholesterol in vivo (up to 40% of ingested cholesterol). None of the four LAB hydrolyzed mucin or gelatin and none was toxic to C. elegans. The concentrations of phenylethylamine, putrescine, cadaverine, histamine, and tyramine produced by the LAB were below the toxic limits of biogenic amines set by the European Food Safety Authority. Taken together, our results demonstrate that Weissella cibaria SCCB2306, P", "token_count": 520, "char_count": 1596, "word_count": 236, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [ "SDL1402", "SCCB2306", "SDL1406", "JDFM6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:21:26.841753", "source": { "split": "train_shard_00000", "doc_id": 2295 }, "chunk_id": "train_shard_00000_2295_0", "global_id": 2526 }, { "text": "acidilactici SDL1402, P. acidilactici SDL1405, and L. rhamnosus JDFM6 could be safe cholesterol-reducing probiotic candidates for preventing or managing hypercholesterolemia.\n\nIn Vitro and In Vivo Cholesterol Reducing Ability and Safety of Probiotic Candidates Isolated from Korean Fermented Soya Beans.", "token_count": 101, "char_count": 303, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [ "SDL1402", "SDL1405", "JDFM6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:27.241684", "source": { "split": "train_shard_00000", "doc_id": 2295 }, "chunk_id": "train_shard_00000_2295_1", "global_id": 2527 }, { "text": "Research on secondary metabolites (SMs) has been mostly focused on Gram-positive bacteria, especially Actinobacteria. The association of genomics with robust bioinformatics tools revealed the neglected potential of Gram-negative bacteria as promising sources of new SMs. The family Sphingobacteriaceae belongs to the phylum Bacteroidetes having representatives in practically all environments including humans, rhizosphere, soils, wastewaters, among others. Some genera of this family have demonstrated great potential as plant growth promoters, bioremediators and producers of some value-added compounds such as carotenoids and antimicrobials. However, to date, Sphingobacteriaceae's SMs are still poorly characterized, and likewise, little is known about their chemistry. This study revealed that Sphingobacteriaceae pangenome encodes a total of 446 biosynthetic gene clusters (BGCs), which are distributed across 85 strains, highlighting the great potential of this bacterial family to produce SMs. Pedobacter, Mucilaginibacter and Sphingobacterium were the genera with the highest number of BGCs, especially those encoding the biosynthesis of ribosomally synthesized and post-translationally modified peptides (RiPPs), terpenes, polyketides and nonribosomal peptides (NRPs). In Mucilaginibacter and Sphingobacterium genera, M. lappiensis ATCC BAA-1855, Mucilaginibacter sp. OK098 (both with 11 BGCs) and Sphingobacterium sp. 21 (6 BGCs) are the strains with the highest number of BGCs. Most of the BGCs found in these two genera did not have significant hits with the MIBiG database. These results strongly suggest that the bioactivities and environmental functions of these compounds, especially RiPPs, PKs and NRPs, are still unknown. Among RiPPs, two genera encoded the production of class I and class III lanthipeptides. The last are associated with LanKC proteins bearing uncommon lyase domains, whose dehydration mechanism deserves further investigation", "token_count": 514, "char_count": 1963, "word_count": 263, "semantic_coherence": 1, "information_density": 0.673, "quality_score": 0.8365, "entities": { "genes": [ "OK098" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:21:27.893484", "source": { "split": "train_shard_00000", "doc_id": 2296 }, "chunk_id": "train_shard_00000_2296_0", "global_id": 2528 }, { "text": "This study translated genomics into functional information that unveils the enormous potential of environmental Gram-negative bacteria to produce metabolites with unknown chemistries, bioactivities and, more importantly, unknown ecological roles.\n\nThe Unexplored Wealth of Microbial Secondary Metabolites: the Sphingobacteriaceae Case Study.", "token_count": 75, "char_count": 341, "word_count": 40, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:28.285134", "source": { "split": "train_shard_00000", "doc_id": 2296 }, "chunk_id": "train_shard_00000_2296_1", "global_id": 2529 }, { "text": "Glucose is a preferred carbon source for most living organisms. The metabolism and regulation of glucose utilization are well studied mostly for Saccharomyces cerevisiae. Xylose is the main pentose sugar released from the lignocellulosic biomass, which has a high potential as a renewable feedstock for bioethanol production. The thermotolerant yeast Ogataea (Hansenula) polymorpha, in contrast to S. cerevisiae, is able to metabolize and ferment not only glucose but also xylose. However, in non-conventional yeasts, the regulation of glucose and xylose metabolism remains poorly understood. In this study, we characterize the role of transcriptional factors Mig1, Mig2, Tup1 and Hap4 in the natural xylose-fermenting yeast O. polymorpha. The deletion of MIG1 had no significant influence on ethanol production either from xylose or glucose, however the deletion of both MIG1 and MIG2 reduced the amount of ethanol produced from these sugars. The deletion of HAP4-A and TUP1 genes resulted in increased ethanol production from xylose. Inversely, the overexpression of HAP4-A and TUP1 genes reduced ethanol production during xylose alcoholic fermentation. Thus, HAP4-A and TUP1 are involved in repression of xylose metabolism and fermentation in yeast O. polymorpha and their deletion could be a viable strategy to improve ethanol production from this pentose.\n\nThe role of Mig1, Mig2, Tup1 and Hap4 transcription factors in regulation of xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha.", "token_count": 422, "char_count": 1518, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5381, "quality_score": 0.7691, "entities": { "genes": [ "MIG1", "HAP4", "MIG2", "TUP1" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:28.947473", "source": { "split": "train_shard_00000", "doc_id": 2297 }, "chunk_id": "train_shard_00000_2297_0", "global_id": 2530 }, { "text": "Burkholderia pseudomallei causes the severe disease melioidosis. Whole-genome sequencing (WGS)-based typing methods currently offer the highest resolution for molecular investigations of this genetically diverse pathogen. Still, its routine application in diagnostic laboratories is limited by the need for high computing power, bioinformatic skills, and variable bioinformatic approaches, with the latter affecting the results. We therefore aimed to establish and validate a WGS-based core genome multilocus sequence typing (cgMLST) scheme, applicable in routine diagnostic settings. A soft defined core genome was obtained by challenging the B. pseudomallei reference genome K96243 with 469 environmental and clinical genomes, resulting in 4,221 core and 1,351 accessory targets. The scheme was validated with 320 WGS data sets. We compared our novel typing scheme with single nucleotide polymorphism-based approaches investigating closely and distantly related strains. Finally, we applied our scheme for tracking the environmental source of a recent infection. The validation of the scheme detected >95% good cgMLST target genes in 98.4% of the genomes. Comparison with existing typing methods revealed very good concordance. Our scheme proved to be applicable to investigating not only closely related strains but also the global B. pseudomallei population structure. We successfully utilized our scheme to identify a sugarcane field as the presumable source of a recent melioidosis case. In summary, we developed a robust cgMLST scheme that integrates high resolution, maximized standardization, and fast analysis for the nonbioinformatician. Our typing scheme has the potential to serve as a routinely applicable classification system in B. pseudomallei molecular epidemiology.\n\nDevelopment and Validation of a Burkholderia pseudomallei Core Genome Multilocus Sequence Typing Scheme To Facilitate Molecular Surveillance.", "token_count": 439, "char_count": 1927, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:29.582963", "source": { "split": "train_shard_00000", "doc_id": 2298 }, "chunk_id": "train_shard_00000_2298_0", "global_id": 2531 }, { "text": "Epigallocatechin-3-gallate (EGCG) and caffeine constitute the most effective ingredients of weight loss in tea. However, whether combination of EGCG and caffeine exhibits anti-obesity synergy remains unclear. Here, we showed low-doses of EGCG and caffeine used in combination led to synergistic anti-obesity effects equivalent to those of high-dose EGCG. Furthermore, combination treatment exhibited a synergistic effect on altering gut microbiota, including decreased Firmicutes level and increased Bifidobacterium level. Other notable effects of combination treatment included synergistic effects on: increasing fecal acetic acid, propionic acid, and total SCFAs; decreasing expression of GPR43; and increasing microbial bile salt hydrolase gene copies in the gut, facilitating generation of unconjugated BAs and enhancing fecal BA loss. Additionally, combination treatment demonstrated synergistic effects toward increasing the expression of hepatic TGR5 and decreasing the expression of intestinal FXR-FGF15, resulting in increased expression of hepatic CYP7A1. Thus, the synergistic effect may be attributed to regulation of gut microbiota and BA metabolism.\n\nCombined use of epigallocatechin-3-gallate (EGCG) and caffeine in low doses exhibits marked anti-obesity synergy through regulation of gut microbiota and bile acid metabolism.", "token_count": 345, "char_count": 1340, "word_count": 176, "semantic_coherence": 1, "information_density": 0.5852, "quality_score": 0.7926, "entities": { "genes": [ "FGF15", "TGR5", "GPR43" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:30.155929", "source": { "split": "train_shard_00000", "doc_id": 2299 }, "chunk_id": "train_shard_00000_2299_0", "global_id": 2532 }, { "text": "Many genomic analyses start by aligning sequencing reads to a linear reference genome. However, linear reference genomes are imperfect, lacking millions of bases of unknown relevance and are unable to reflect the genetic diversity of populations. This makes reference-guided methods susceptible to reference-allele bias. To overcome such limitations, we build a pangenome from six reference-quality assemblies from taurine and indicine cattle as well as yak. The pangenome contains an additional 70,329,827 bases compared to the\n\nNovel functional sequences uncovered through a bovine multiassembly graph.", "token_count": 138, "char_count": 604, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:30.584419", "source": { "split": "train_shard_00000", "doc_id": 2300 }, "chunk_id": "train_shard_00000_2300_0", "global_id": 2533 }, { "text": "A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome's accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas species for statistically significant coincident (i.e., co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other-but are not vertically inherited-are more likely to share functional categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into sets of genes that function together within a given strain. Given the similarity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.\n\nEvidence for Selection in the Abundant Accessory Gene Content of a Prokaryote Pangenome.", "token_count": 282, "char_count": 1195, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6149, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:31.484882", "source": { "split": "train_shard_00000", "doc_id": 2301 }, "chunk_id": "train_shard_00000_2301_0", "global_id": 2534 }, { "text": "Aliarcobacter butzleri is an emerging pathogen that may cause enteritis in humans, however, the incidence of disease caused by this member of the Campylobacteriaceae family is still underestimated. Furthermore, little is known about the precise virulence mechanism and behavior during infection. Therefore, in the present study, through complementary use of comparative genomics and physiological tests on human gut models, we sought to elucidate the genetic background of a set of 32 A. butzleri strains of diverse origin and to explore the correlation with the ability to colonize and invade human intestinal cells in vitro. The simulated infection of human intestinal models showed a higher colonization rate in presence of mucus-producing cells. For some strains, human mucus significantly improved the resistance to physical removal from the in vitro mucosa, while short time-frame growth was even observed. Pangenome analysis highlighted a hypervariable accessory genome, not strictly correlated to the isolation source. Likewise, the strain phylogeny was unrelated to their shared origin, despite a certain degree of segregation was observed among strains isolated from different segments of the intestinal tract of pigs. The putative virulence genes detected in all strains were mostly encompassed in the accessory fraction of the pangenome. The LPS biosynthesis and in particular the chain glycosylation of the O-antigen is harbored in a region of high plasticity of the pangenome, which would indicate frequent horizontal gene transfer phenomena, as well as the involvement of this hypervariable structure in the adaptive behavior and sympatric evolution of A. butzleri. Results of the present study deepen the current knowledge on A. butzleri pangenome by extending the pool of genes regarded as virulence markers and provide bases to develop new diagnostic approaches for the detection of those strains with a higher virulence potential.\n\nFunctional pangenome analysis reveals high virulence plasticity of Aliarcobacter butzleri and affinity to human mucus.", "token_count": 464, "char_count": 2069, "word_count": 304, "semantic_coherence": 1, "information_density": 0.6184, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:32.129051", "source": { "split": "train_shard_00000", "doc_id": 2302 }, "chunk_id": "train_shard_00000_2302_0", "global_id": 2535 }, { "text": "In the past decade, metagenomics studies of microbial communities have added billions of sequences to the databases. This extensive amount of data and information has the potential to widen our understanding of the functioning of microbial communities and their roles in the environment. A fundamental step in this process is the functional and taxonomic profiling of the metagenomes, through an accurate gene annotation. This gene-level information can then be placed in the genomic context of metagenome-assembled genomes. Then, on a broader level, we can place this combined data into the context of a pangenome and start characterizing core and accessory gene sets. In this chapter, we provide a workflow to create an annotated gene catalog and to identify core sets of genes in the context of a pangenome. The first section will focus on the methods to provide metagenomic genes with accurate annotations. The second part will describe how to combine the gene catalog information with metagenome-assembled genomes and how to use both to build and investigate a pangenome.\n\nAccurate Annotation of Microbial Metagenomic Genes and Identification of Core Sets.", "token_count": 250, "char_count": 1161, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5389, "quality_score": 0.7694, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:32.619469", "source": { "split": "train_shard_00000", "doc_id": 2303 }, "chunk_id": "train_shard_00000_2303_0", "global_id": 2536 }, { "text": "High availability of fast, cheap, and high-throughput next generation sequencing techniques resulted in acquisition of numerous de novo sequenced and assembled bacterial genomes. It rapidly became clear that digging out useful biological information from such a huge amount of data presents a considerable challenge. In this chapter we share our experience with utilization of several handy open source comparative genomic tools. All of them were applied in the studies focused on revealing inter- and intraspecies variation in pectinolytic plant pathogenic bacteria classified to Dickeya solani and Pectobacterium parmentieri. As the described software performed well on the species within the Pectobacteriaceae family, it presumably may be readily utilized on some closely related taxa from the Enterobacteriaceae family. First of all, implementation of various annotation software is discussed and compared. Then, tools computing whole genome comparisons including generation of circular juxtapositions of multiple sequences, revealing the order of synteny blocks or calculation of ANI or Tetra values are presented. Besides, web servers intended either for functional annotation of the genes of interest or for detection of genomic islands, plasmids, prophages, CRISPR/Cas are described. Last but not least, utilization of the software designed for pangenome studies and the further downstream analyses is explained. The presented work not only summarizes broad possibilities assured by the comparative genomic approach but also provides a user-friendly guide that might be easily followed by nonbioinformaticians interested in undertaking similar studies.\n\nComparative Genomics, from the Annotated Genome to Valuable Biological Information: A Case Study.", "token_count": 363, "char_count": 1759, "word_count": 245, "semantic_coherence": 1, "information_density": 0.7265, "quality_score": 0.8633, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:33.196342", "source": { "split": "train_shard_00000", "doc_id": 2304 }, "chunk_id": "train_shard_00000_2304_0", "global_id": 2537 }, { "text": "Due to the increasing availability of public bacterial genome data and cost efficiency of novel bacterial strain sequencing, phylogenetic analyses based on more than a single or few marker genes have become feasible. In this method protocol, we describe the complete bioinformatic workflow from raw genomic data to final phylogenetic analyses based on 107 conserved single copy genes. This approach can be used to perform phylogenetic reconstructions with high resolution on strain level or across taxa spanning different clades of the bacterial tree of life.\n\nInferring Core Genome Phylogenies for Bacteria.", "token_count": 142, "char_count": 608, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:33.624222", "source": { "split": "train_shard_00000", "doc_id": 2305 }, "chunk_id": "train_shard_00000_2305_0", "global_id": 2538 }, { "text": "Development of the bioeconomy is driven by our ability to access the energy-rich carbon trapped in recalcitrant plant materials. Current strategies to release this carbon rely on expensive enzyme cocktails and physicochemical pretreatment, producing inhibitory compounds that hinder subsequent microbial bioproduction. Anaerobic fungi are an appealing solution as they hydrolyze crude, untreated biomass at ambient conditions into sugars that can be converted into value-added products by partner organisms. However, some carbon is lost to anaerobic fungal fermentation products. To improve efficiency and recapture this lost carbon, we built a two-stage bioprocessing system pairing the anaerobic fungus Piromyces indianae with the yeast Kluyveromyces marxianus, which grows on a wide range of sugars and fermentation products. In doing so we produce fine and commodity chemicals directly from untreated lignocellulose. P. indianae efficiently hydrolyzed substrates such as corn stover and poplar to generate sugars, fermentation acids, and ethanol, which K. marxianus consumed while producing 2.4 g/L ethyl acetate. An engineered strain of K. marxianus was also able to produce 550 mg/L 2-phenylethanol and 150 mg/L isoamyl alcohol from P. indianae hydrolyzed lignocellulosic biomass. Despite the use of crude untreated plant material, production yields were comparable to optimized rich yeast media due to the use of all available carbon including organic acids, which formed up to 97% of free carbon in the fungal hydrolysate. This work demonstrates that anaerobic fungal pretreatment of lignocellulose can sustain the production of fine chemicals at high efficiency by partnering organisms with broad substrate versatility.\n\nHydrolysis of lignocellulose by anaerobic fungi produces free sugars and organic acids for two-stage fine chemical production with Kluyveromyces marxianus.", "token_count": 495, "char_count": 1885, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8195, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:34.276847", "source": { "split": "train_shard_00000", "doc_id": 2306 }, "chunk_id": "train_shard_00000_2306_0", "global_id": 2539 }, { "text": "To improve the bile salt and acid tolerance of probiotics against gastrointestinal stresses, we investigated the effects of soybean lecithin and whey protein concentrate (WPC) 80 on the bile salt tolerance of\n\nApplication of the Combination of Soybean Lecithin and Whey Protein Concentrate 80 to Improve the Bile Salt and Acid Tolerance of Probiotics.", "token_count": 98, "char_count": 351, "word_count": 54, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:34.661773", "source": { "split": "train_shard_00000", "doc_id": 2307 }, "chunk_id": "train_shard_00000_2307_0", "global_id": 2540 }, { "text": "Cyanobacteria thrive in diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus, we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain as well as few genes that are unique to the genus. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle-or reduced genetic complexity of hot spring habitats relative to other environments.\n\nThe Thermosynechococcus Genus: Wide Environmental Distribution, but a Highly Conserved Genomic Core.", "token_count": 405, "char_count": 1844, "word_count": 250, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:35.283320", "source": { "split": "train_shard_00000", "doc_id": 2308 }, "chunk_id": "train_shard_00000_2308_0", "global_id": 2541 }, { "text": "Studies on structural variation in plants have revealed the inadequacy of a single reference genome for an entire species and suggest that it is necessary to build a species-representative genome called a pan-genome to better capture the extent of both structural and nucleotide variation. Here, we present a pan-genome of cultivated soybean (Glycine max), termed PanSoy, constructed using the de novo genome assembly of 204 phylogenetically and geographically representative improved accessions selected from the larger GmHapMap collection. PanSoy uncovers 108 Mb (˜11%) of novel nonreference sequences encompassing 3621 protein-coding genes (including 1659 novel genes) absent from the soybean 'Williams 82' reference genome. Nonetheless, the core genome represents an exceptionally large proportion of the genome, with >90.6% of genes being shared by >99% of the accessions. A majority of PAVs encompassing genes could be confirmed with long-read sequencing on a subset of accessions. The PanSoy is a major step towards capturing the extent of genetic variation in cultivated soybean and provides a resource for soybean genomics research and breeding.\n\nThe pan-genome of the cultivated soybean (PanSoy) reveals an extraordinarily conserved gene content.", "token_count": 321, "char_count": 1256, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6519, "quality_score": 0.826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:35.850492", "source": { "split": "train_shard_00000", "doc_id": 2309 }, "chunk_id": "train_shard_00000_2309_0", "global_id": 2542 }, { "text": "Increasing antibiotic resistance in Gram-negative bacteria has mandated the development of both novel antibiotics and alternative therapeutic strategies. Evidence of interplay between several gastrointestinal peptides and the gut microbiota led us to investigate potential and broad-spectrum roles for the incretin hormone, human glucose-dependent insulinotropic polypeptide (GIP) against the\n\nHuman glucose-dependent insulinotropic polypeptide (GIP) is an antimicrobial adjuvant re-sensitising multidrug-resistant Gram-negative bacteria.", "token_count": 137, "char_count": 538, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8033, "quality_score": 0.9016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:36.281130", "source": { "split": "train_shard_00000", "doc_id": 2310 }, "chunk_id": "train_shard_00000_2310_0", "global_id": 2543 }, { "text": "Development of a system for direct lactose to ethanol fermentation provides a market for the massive amounts of underutilized whey permeate made by the dairy industry. For this system, glucose and galactose metabolism were uncoupled in Saccharomyces cerevisiae by deleting two negative regulatory genes, GAL80 and MIG1, and introducing the essential lactose hydrolase LAC4 and lactose transporter LAC12, from the native but inefficient lactose fermenting yeast Kluyveromyces marxianus.\n\nUncoupling glucose sensing from GAL metabolism for heterologous lactose fermentation in Saccharomyces cerevisiae.", "token_count": 167, "char_count": 600, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7284, "quality_score": 0.8642, "entities": { "genes": [ "MIG1", "LAC12", "GAL80", "LAC4" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:36.732645", "source": { "split": "train_shard_00000", "doc_id": 2311 }, "chunk_id": "train_shard_00000_2311_0", "global_id": 2544 }, { "text": "Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the\n\nRoot Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere", "token_count": 177, "char_count": 792, "word_count": 107, "semantic_coherence": 1, "information_density": 0.7664, "quality_score": 0.8832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:37.173794", "source": { "split": "train_shard_00000", "doc_id": 2312 }, "chunk_id": "train_shard_00000_2312_0", "global_id": 2545 }, { "text": "Cholestasis is a pathological state that leads to serious liver disease; however, therapeutic options remain limited. Yinchen and Gancao are often used in combination at different ratios in traditional Chinese formulae for the treatment of jaundice and cholestasis. In the present study, we investigated the effect of decoctions containing different ratios of Yinchen and Gancao (YGD) on alpha-naphthyl isothiocyanate (ANIT)-treated intrahepatic cholestasis (IC) in mice, and further explored the underlying mechanism. Treatment with 0:4 and 1:4 YGD significantly reduced plasma total bile acid (TBA), total bilirubin (TBIL), aspartate aminotransferase (AST), alanine aminotransferase (ALT), and alkaline phosphatase (ALP) activities; decreased unconjugated and conjugated bile acid levels; and improved hepatocyte necrosis and inflammatory cells recruitment to hepatic sinusoids. Moreover, the expression levels of Toll-like receptor 4 (TLR4), interleukin-1β (IL-1β), IL-6, tumor necrosis factor alpha (TNF-α), C-C ligand 2 (CCL2), and C-X-C ligand 2 (CXCL2) in the liver were significantly reduced. However, treatment with 4:1 and 4:0 YGD increased plasma TBA, TBIL, AST, ALT, and ALP activities and aggravated liver cell injury and inflammation. Moreover, the mRNA expression of the bile salt export pump (BSEP) in the liver was significantly increased in mice treated with 4:0 YGD. The present study demonstrates that YGD containing a high proportion of Gancao, which inhibits the TLR4/NF-κB pathway and reduces the inflammatory response, had protective effects against ANIT-treated IC in mice", "token_count": 469, "char_count": 1597, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [ "TLR4", "CCL2", "CXCL2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:37.803417", "source": { "split": "train_shard_00000", "doc_id": 2313 }, "chunk_id": "train_shard_00000_2313_0", "global_id": 2546 }, { "text": "However, YGD containing a high proportion of Yinchen aggravated the ANIT-treated IC in mice, which may be related to upregulation of BSEP and boosting bile acid regurgitation from damage cholangiocytes to liver in ANIT-treated IC mice.\n\nEffect of Different Ratios of Yinchen and Gancao Decoction on ANIT-Treated Cholestatic Liver Injury in Mice and Its Potential Underlying Mechanism.", "token_count": 111, "char_count": 384, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7719, "quality_score": 0.886, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:38.183036", "source": { "split": "train_shard_00000", "doc_id": 2313 }, "chunk_id": "train_shard_00000_2313_1", "global_id": 2547 }, { "text": "The selection of potential probiotic strains that possess the physiological capacity of performing successfully in the gastrointestinal tract (GIT) is a critical challenge. Probiotic microorganisms must tolerate the deleterious effects of various stresses to survive passage and function in the human GIT. Adhesion to the intestinal mucosa is also an important aspect. Recently, numerous studies have been performed concerning the selection and evaluation of novel probiotic microorganisms, mainly probiotic bacteria isolated from dairy and nondairy products. Therefore, it would be crucial to critically review the assessment methods employed to select the potential probiotics. This article aims to review and discuss the recent approaches, methods used for the selection, and outcomes of the evaluation of novel probiotic strains with the main purpose of supporting future probiotic microbial assessment studies. The findings and approaches used for assessing acid tolerance, bile metabolism and tolerance, and adhesion capability are the focus of this review. In addition, probiotic bile deconjugation and bile salt hydrolysis are explored. The selection of a new probiotic strain has mainly been based on the in vitro tolerance of physiologically related stresses including low pH and bile, to ensure that the potential probiotic microorganism can survive the harsh conditions of the GIT. However, the varied experimental conditions used in these studies (different types of media, bile, pH, and incubation time) hamper the comparison of the results of these investigations. Therefore, standardization of experimental conditions for characterizing and selecting probiotics is warranted.\n\nInvited review: Characterization of new probiotics from dairy and nondairy products-Insights into acid tolerance, bile metabolism and tolerance, and adhesion capability.", "token_count": 397, "char_count": 1862, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5594, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:38.796160", "source": { "split": "train_shard_00000", "doc_id": 2314 }, "chunk_id": "train_shard_00000_2314_0", "global_id": 2548 }, { "text": "Mycoplasma anserisalpingitidis is a bacterial waterfowl pathogen. In these days of growing antibiotic resistance, it is necessary to search for alternative methods of defense against Mycoplasma impacts in flocks. In order to identify prophage-like sequences, three established bioinformatics tools (PHASTER, PhiSpy, Prophage Hunter) were used in this study for the in silico screening of 82 M. anserisalpingitidis whole genomes. The VIBRANT software was used as a novel approach to further investigate the possibility of prophages in the sequences. The commonly used softwares found prophage-like sequences in the strains, but the results were inconclusive. The VIBRANT search resulted in multiple hits, and many of them were over 10,000 base pairs (bp). These putative prophages are comparable in size to the few described mycoplasma phages. The translated coding DNA sequences of the putative prophages were checked with protein BLAST. The functions of the proteins found by the BLASTP search are common among bacteriophages. The BLASTN search of the sequences found that many of these were more similar to the M. anatis NCTC 10156 strain, rather than the available M. anserisalpingitidis strains. The initial screening pointed at the presence of novel bacteriophages in the M. anserisalpingitidis and M. anatis strains. The VIBRANT search results were very similar to each other and none of these sequences were part of the core genome of M. anserisalpingitidis, with a few exceptions. The VIBRANT analysis explored presumably intact, novel prophages.\n\nNovel prophage-like sequences in Mycoplasma anserisalpingitidis.", "token_count": 421, "char_count": 1620, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5481, "quality_score": 0.7741, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:39.452373", "source": { "split": "train_shard_00000", "doc_id": 2315 }, "chunk_id": "train_shard_00000_2315_0", "global_id": 2549 }, { "text": "The reference human genome sequence is inarguably the most important and widely used resource in the fields of human genetics and genomics. It has transformed the conduct of biomedical sciences and brought invaluable benefits to the understanding and improvement of human health. However, the commonly used reference sequence has profound limitations, because across much of its span, it represents the sequence of just one human haplotype. This single, monoploid reference structure presents a critical barrier to representing the broad genomic diversity in the human population. In this review, we discuss the modernization of the reference human genome sequence to a more complete reference of human genomic diversity, known as a human pangenome.\n\nThe Need for a Human Pangenome Reference Sequence.", "token_count": 159, "char_count": 801, "word_count": 120, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:39.912926", "source": { "split": "train_shard_00000", "doc_id": 2316 }, "chunk_id": "train_shard_00000_2316_0", "global_id": 2550 }, { "text": "Beneficial effects of probiotic, prebiotic and polyphenol-rich interventions on fasting lipid profiles have been reported, with changes in the gut microbiota composition believed to play an important role in lipid regulation. Primary bile acids, which are involved in the digestion of fats and cholesterol metabolism, can be converted by the gut microbiota to secondary bile acids, some species of which are less well reabsorbed and consequently may be excreted in the stool. This can lead to increased hepatic bile acid neo-synthesis, resulting in a net loss of circulating low-density lipoprotein. Bile acids may therefore provide a link between the gut microbiota and cardiovascular health. This narrative review presents an overview of bile acid metabolism and the role of probiotics, prebiotics and polyphenol-rich foods in modulating circulating cardiovascular disease (CVD) risk markers and bile acids. Although findings from human studies are inconsistent, there is growing evidence for associations between these dietary components and improved lipid CVD risk markers, attributed to modulation of the gut microbiota and bile acid metabolism. These include increased bile acid neo-synthesis, due to bile sequestering action, bile salt metabolising activity and effects of short-chain fatty acids generated through bacterial fermentation of fibres. Animal studies have demonstrated effects on the FXR/FGF-15 axis and hepatic genes involved in bile acid synthesis (CYP7A1) and cholesterol synthesis (SREBP and HMGR). Further human studies are needed to determine the relationship between diet and bile acid metabolism and whether circulating bile acids can be utilised as a potential CVD risk biomarker.\n\nCirculating bile acids as a link between the gut microbiota and cardiovascular health: impact of prebiotics, probiotics and polyphenol-rich foods.", "token_count": 458, "char_count": 1857, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5448, "quality_score": 0.7724, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:40.584459", "source": { "split": "train_shard_00000", "doc_id": 2317 }, "chunk_id": "train_shard_00000_2317_0", "global_id": 2551 }, { "text": "Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex\n\nPan and Core Genome Analysis of 183", "token_count": 55, "char_count": 213, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:40.987593", "source": { "split": "train_shard_00000", "doc_id": 2318 }, "chunk_id": "train_shard_00000_2318_0", "global_id": 2552 }, { "text": "Improving dissolution properties of active pharmaceutical ingredients (APIs) is a critical step in drug development with the increasing occurrence of sparingly soluble APIs. Cocrystal formation is one of the methods to alter the physicochemical properties of APIs, but its dissolution behavior in biorelevant media has been scrutinized only in recent years. We investigated the combined strategy of cocrystallization and eutectic formation in this regard and utilized the cocrystal model system of naproxen and three pyridinecarboxamide isomers. Binary melting diagrams were constructed to discover the eutectic compositions of the three cocrystals with excess amounts of pyridinecarboxamides. The melt-crystallized eutectics and cocrystals were compared in their dissolution behaviors with respect to neat naproxen. The eutectics enhanced the early dissolution rates of the cocrystals in both the absence and presence of biologically relevant bile salt and phospholipid components, whereas the cocrystal dissolution was expedited and delayed, respectively. The combined strategy in the present study will be advantageous in maximizing the utility of the pharmaceutical cocrystals.\n\nEnhanced Dissolution of Naproxen by Combining Cocrystallization and Eutectic Formation.", "token_count": 304, "char_count": 1270, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:41.557413", "source": { "split": "train_shard_00000", "doc_id": 2319 }, "chunk_id": "train_shard_00000_2319_0", "global_id": 2553 }, { "text": "The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time,\n\nGenome and Pangenome Analysis of", "token_count": 55, "char_count": 251, "word_count": 41, "semantic_coherence": 1, "information_density": 0.8049, "quality_score": 0.9024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:41.921841", "source": { "split": "train_shard_00000", "doc_id": 2320 }, "chunk_id": "train_shard_00000_2320_0", "global_id": 2554 }, { "text": "The metabolism of bile acid by the gut microbiota is associated with host health. Bile salt hydrolases (BSHs) play a crucial role in controlling microbial bile acid metabolism. Herein, we conducted a comparative study to investigate the alterations in the abundance of BSHs using data from three human studies involving dietary interventions, which included a ketogenetic diet (KD) versus baseline diet (BD), overfeeding diet (OFD) versus underfeeding diet, and low-carbohydrate diet (LCD) versus BD. The KD increased BSH abundance compared to the BD, while the OFD and LCD did not change the total abundance of BSHs in the human gut. BSHs can be classified into seven clusters; Clusters 1 to 4 are relatively abundant in the gut. In the KD cohort, the levels of BSHs from Clusters 1, 3, and 4 increased significantly, whereas there was no notable change in the levels of BSHs from the clusters in the OFD and LCD cohorts. Taxonomic studies showed that members of the phyla Bacteroidetes, Firmicutes, and Actinobacteria predominantly produced BSHs. The KD altered the community structure of BSH-active bacteria, causing an increase in the abundance of Bacteroidetes and decrease in Actinobacteria. In contrast, the abundance of BSH-active Bacteroidetes decreased in the OFD cohort, and no significant change was observed in the LCD cohort. These results highlight that dietary patterns are associated with the abundance of BSHs and community structure of BSH-active bacteria and demonstrate the possibility of manipulating the composition of BSHs in the gut through dietary interventions to impact human health.\n\nDiet-Related Alterations of Gut Bile Salt Hydrolases Determined Using a Metagenomic Analysis of the Human Microbiome.", "token_count": 440, "char_count": 1730, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5226, "quality_score": 0.7613, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:42.550246", "source": { "split": "train_shard_00000", "doc_id": 2321 }, "chunk_id": "train_shard_00000_2321_0", "global_id": 2555 }, { "text": "Shigellosis is a diarrheal disease caused mainly by\n\nAccessory Genome Dynamics and Structural Variation of", "token_count": 28, "char_count": 106, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:42.908927", "source": { "split": "train_shard_00000", "doc_id": 2322 }, "chunk_id": "train_shard_00000_2322_0", "global_id": 2556 }, { "text": "Probiotics are beneficial microorganisms, and the evaluation of their safety for human use in the food industry has become critical. This study examines the safety of Bacillus coagulans IDCC 1201 isolated from green malt by analyzing its genomic and phenotypic characteristics and determining its toxicity. The presence of antibiotic resistance and toxigenic genes and gene transferability were investigated using whole-genome analysis. The strain's hemolytic and enzyme activities, minimum inhibitory concentrations of antibiotics, and biogenic amine and D-lactate production were also examined. Furthermore, the principal properties of B. coagulans IDCC 1201 as probiotics, such as resistance to abiotic stress and intestinal adhesion, were studied. The whole-genome analysis demonstrated that B. coagulans IDCC 1201 had no antibiotic resistance or toxigenic genes; the strain was susceptible to the nine antibiotics proposed by the European Food Safety Authority. Moreover, this strain lacked hemolytic and β-glucuronidase activities. Additionally, it was confirmed that B. coagulans IDCC 1201 produced undesirable metabolites, including biogenic amines or D-lactate, at a safe level. Finally, the strain exhibited functional potential as a probiotic in terms of abiotic tolerance, such as bile tolerance and intestinal adhesion in in vitro experiments. In conclusion, B. coagulans IDCC 1201 can be considered as a safe probiotic with regard to human health.\n\nGenomic-, phenotypic-, and toxicity-based safety assessment and probiotic potency of Bacillus coagulans IDCC 1201 isolated from green malt.", "token_count": 417, "char_count": 1602, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:43.528793", "source": { "split": "train_shard_00000", "doc_id": 2323 }, "chunk_id": "train_shard_00000_2323_0", "global_id": 2557 }, { "text": "In this study, a bacterial strain COFCAU_P1, isolated from the digestive tract of a freshwater teleost rohu (Labeo rohita), was identified as Bacillus amyloliquefaciens using 16S rRNA gene sequence analysis combined with amplification of species-specific BamHI and barnase genes. The probiotic potential of the strain was evaluated using an array of in vitro tests along with safety and genetic analyses. The isolate showed potent antimicrobial response against several fish pathogenic bacteria, survived a wide pH range (2-9), and was resistant up to 10% bile salt concentration. With regard to the in vitro adhesion properties, the strain showed significantly high in vitro adhesion to mucus, auto and co-aggregation capacity, and cell surface hydrophobicity. The strain was non-haemolytic, able to produce extracellular enzymes, viz., proteinase, amylase, lipase, and cellulase, and showed significant free radical scavenging activity. A challenge study in rohu revealed the strain COFCAU_P1 as non-pathogenic. The presence of putative probiotic marker genes including 2, 3-bisphosphoglycerate-independent phosphoglycerate mutase, arginine/ornithine antiporter ArcD, choloylglycine hydrolase, LuxS, and E1 β-subunit of the pyruvate dehydrogenase complex was confirmed by PCR, suggesting the molecular basis of the probiotic-specific functional attributes of the isolate. In conclusion, the in vitro and genetic approaches enabled the identification of a potential probiotic from autochthonous source with a potential of its utilization in the aquaculture industry.\n\nDeciphering the Probiotic Potential of Bacillus amyloliquefaciens COFCAU_P1 Isolated from the Intestine of Labeo rohita Through In Vitro and Genetic Assessment.", "token_count": 471, "char_count": 1729, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6271, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:44.170559", "source": { "split": "train_shard_00000", "doc_id": 2324 }, "chunk_id": "train_shard_00000_2324_0", "global_id": 2558 }, { "text": "Biotechnology requires efficient microbial cell factories. The budding yeast Saccharomyces cerevisiae is a vital cell factory, but more diverse cell factories are essential for the sustainable use of natural resources. Here, we benchmarked nonconventional yeasts Kluyveromyces marxianus and Rhodotorula toruloides against S. cerevisiae strains CEN.PK and W303 for their responses to potassium and sodium salt stress. We found an inverse relationship between the maximum growth rate and the median cell volume that was responsive to salt stress. The supplementation of K\n\nPotassium and Sodium Salt Stress Characterization in the Yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and", "token_count": 176, "char_count": 689, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7263, "quality_score": 0.8632, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:44.621784", "source": { "split": "train_shard_00000", "doc_id": 2325 }, "chunk_id": "train_shard_00000_2325_0", "global_id": 2559 }, { "text": "Haemophilus influenzae is a common cause of mucosal infections that warrants accurate surveillance. We aimed to assess the prevalence of the species in clinical specimens, and characterise population structure and resistance to aminopenicillins by whole genome sequencing.We assessed the point prevalence by entering the database records of 1 day in Denmark and examined the genome sequences of nationwide, collected isolates from the same day. The prevalence of H. influenzae in clinical samples on the 10th of January 2018 was 1.78 per 100,000 person-days (all samples), and 2.47 per 1000 hospital bed-days (hospital samples). Of 2009 bacteria deemed clinically relevant and collected in a concerted action by the Danish departments of clinical microbiology, 62 (3.1%) were H. influenzae. All 62 isolates belonged to phylogenetic group I and were unencapsulated. Three strains from separate Danish regions had identical core genome sequences, but a small number of intergenic mutations testified to circulating clones, rather than individual cases of patient-to-patient transmission. The TEM-1 β-lactamase gene was present in 24 strains, while 13 strains were genetically categorised as ampicillin-resistant due to substitutions in penicillin-binding protein 3; shared patterns of amino acid substitutions in unrelated strains indicated putative lateral transfer of chromosomal resistance. Circulating clones of H. influenzae are frequent, and host factors, rather than direct transmission of epidemic strains, may be the primary cause of infection. The bleak presence of ampicillin resistance revealed by sequencing of point prevalence strains underscores the necessity for close examination of testing methods.\n\nHaemophilus influenzae one day in Denmark: prevalence, circulating clones, and dismal resistance to aminopenicillins.", "token_count": 466, "char_count": 1833, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:45.266404", "source": { "split": "train_shard_00000", "doc_id": 2326 }, "chunk_id": "train_shard_00000_2326_0", "global_id": 2560 }, { "text": "The capacity of yeasts to assimilate xylose or arabinose is strongly dependent on plasma membrane transport proteins. Because pentoses comprise a substantial proportion of available sugars in lignocellulosic hydrolysates, their utilisation is centrally important for the development of second generation biorefineries. Relatively few native pentose transporters have been studied and there is intense interest in expanding the repertoire. To aid the identification of novel transporters, we developed a screening platform in the native pentose-utilising yeast Kluyveromyces marxianus. This involved the targeted deletion of twelve transporters of the major facilitator superfamily (MFS) and application of a synthetic biology pipeline for rapid testing of candidate pentose transporters. Using this K. marxianus ΔPT platform, we identified several K. marxianus putative xylose or arabinose transporter proteins that recovered a null strain's ability to growth on these pentoses. Four proteins of the HGT-family were able to support growth in media with high or low concentrations of either xylose or arabinose, while six HXT-like proteins displayed growth only at high xylose concentrations, indicating solely low affinity transport activity. The study offers new insights into the evolution of sugar transporters in yeast and expands the set of native pentose transporters for future functional and biotechnological studies.\n\nIdentification of novel pentose transporters in Kluyveromyces marxianus using a new screening platform.", "token_count": 348, "char_count": 1530, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:45.843657", "source": { "split": "train_shard_00000", "doc_id": 2327 }, "chunk_id": "train_shard_00000_2327_0", "global_id": 2561 }, { "text": "Correction to: Targeting the ileal bile salt transporter in the treatment of non‑alcoholic fatty liver disease.", "token_count": 29, "char_count": 111, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:46.201584", "source": { "split": "train_shard_00000", "doc_id": 2328 }, "chunk_id": "train_shard_00000_2328_0", "global_id": 2562 }, { "text": "Chronic gastroesophageal reflux disease (GERD) is a major risk factor for the development of metaplastic Barrett's esophagus (BE) and its progression to esophageal adenocarcinoma (EAC). Uncontrolled accumulation of reactive oxygen species (ROS) in response to acidic bile salts (ABS) in reflux conditions can be lethal to cells. In this study, we investigated the role of APE1/REF1 in regulating nuclear erythroid factor-like 2 (NRF2), the master antioxidant transcription factor, in response to reflux conditions.\n\nActivation of NRF2 by APE1/REF1 is redox-dependent in Barrett's related esophageal adenocarcinoma cells.", "token_count": 188, "char_count": 620, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [ "REF1", "APE1", "NRF2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:46.644680", "source": { "split": "train_shard_00000", "doc_id": 2329 }, "chunk_id": "train_shard_00000_2329_0", "global_id": 2563 }, { "text": "Kerion-Like Scalp Mycosis Caused by Candida kefyr.", "token_count": 19, "char_count": 50, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:46.999226", "source": { "split": "train_shard_00000", "doc_id": 2330 }, "chunk_id": "train_shard_00000_2330_0", "global_id": 2564 }, { "text": "Low phospholipid-associated cholelithiasis syndrome is characterized by the development of cholelithiasis in early adulthood (<40 years of age) but is rarely diagnosed in childhood. It is associated with gene sequence variants in the ABCB4 gene encoding the multidrug resistance protein 3 which are mostly heterozygous. Transient neonatal cholestasis has been reported with heterozygous mutations in both ABCB4 and ABCB11 (Bile Salt Exporter Protein). We report a 3-month-old male with cholelithiasis and transient neonatal cholestasis in the setting of combined pathogenic heterozygous mutations in the genes ABCB4 and ABCB11. Initiation of ursodeoxycholic acid therapy led to a resolution of the cholestasis and gall stones. Our case highlights the complex nature of the genetics of cholestatic disorders.\n\nCombined Mutations of Canalicular Transporter Proteins Causing Low Phospholipid-Associated Cholelithiasis and Transient Neonatal Cholestasis in an Infant.", "token_count": 262, "char_count": 963, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "ABCB4", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:47.554282", "source": { "split": "train_shard_00000", "doc_id": 2331 }, "chunk_id": "train_shard_00000_2331_0", "global_id": 2565 }, { "text": "The physiological properties of the gastrointestinal tract, such as pH, fluid volume, bile salt concentration, and gastrointestinal transit time, are highly variable in vivo. These properties can affect the dissolution and absorption of a drug, depending on its properties and formulation. The effect of gastrointestinal physiology on the bioperformance of a drug was studied in silico for a delayed-release pantoprazole tablet and an immediate-release dolutegravir tablet. Physiologically based absorption models were developed and virtual clinical trials were performed. Reasons for the variability in drug bioperformance between subjects were investigated, taking into account differences in gastrointestinal tract characteristics, pharmacokinetic parameters, and additional parameters (e.g., permeability). Default software parameters describing gastrointestinal physiology in the fasted and fed states, and variation in these parameters, were altered to match variability in these parameters reported in vivo. The altered model physiologies better described the variability of gastrointestinal conditions, and therefore the results of virtual trials using these physiologies are likely to be more relevant in vivo. With such altered gastrointestinal physiologies used to develop models, it is possible to obtain additional knowledge and improve the understanding of subject-formulation interactions.\n\nEvaluating the Impact of Physiological Properties of the Gastrointestinal Tract On Drug In Vivo Performance Using Physiologically Based Biopharmaceutics Modeling and Virtual Clinical Trials.", "token_count": 334, "char_count": 1596, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:48.114307", "source": { "split": "train_shard_00000", "doc_id": 2332 }, "chunk_id": "train_shard_00000_2332_0", "global_id": 2566 }, { "text": "Lacticin 3147 is a dual-acting two-peptide bacteriocin which is generally active against Gram-positive bacteria, including Listeria monocytogenes and antimicrobial-resistant bacteria such as Closteroides difficile in the colon. L. monocytogenes infections can cause life-long effects in the elderly and vulnerable and can cause severe complications in pregnant women. C. difficile causes one of the most common healthcare-associated infections and can be fatal in vulnerable groups such as the elderly. Although lacticin 3147 is degraded by intestinal proteases and has poor aqueous solubility, encapsulation of the bacteriocin could enable its use as an antimicrobial for treating these bacterial infections locally in the gastrointestinal tract. Lacticin 3147 displayed activity in aqueous solutions at a range of pH values and in gastric and intestinal fluids. Exposure to trypsin and α-chymotrypsin resulted in complete inactivation, implying that lacticin 3147 should be protected from these enzymes to achieve successful local delivery to the gastrointestinal tract. The amount of lacticin 3147 dissolved, i.e. its solution concentration, in water or buffered solutions at pH 1.6 and 7.4 was low and varied with time but increased and was stabilized in gastrointestinal fluids by the phospholipid and bile salt components present. Thus, the feasibility of a solid lipid nanoparticle (SLN) delivery system for local administration of lacticin 3147 was investigated. Bacteriocin activity was observed after encapsulation and release from a lipid matrix. Moreover, activity was seen after exposure to degrading enzymes. Further optimization of SLN delivery systems could enable the successful pharmaceutical development of active lacticin 3147 as an alternative to traditional antibiotics.\n\nPharmaceutical design of a delivery system for the bacteriocin lacticin 3147.", "token_count": 480, "char_count": 1871, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5682, "quality_score": 0.7841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:48.758128", "source": { "split": "train_shard_00000", "doc_id": 2333 }, "chunk_id": "train_shard_00000_2333_0", "global_id": 2567 }, { "text": "The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Viral quasispecies emerge from de novo mutations that occur in individual patients. In combination, these sets of viral mutations provide distinct genetic fingerprints that reveal the patterns of transmission and have utility in contact tracing.\n\nProfiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.", "token_count": 141, "char_count": 569, "word_count": 79, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:49.187857", "source": { "split": "train_shard_00000", "doc_id": 2334 }, "chunk_id": "train_shard_00000_2334_0", "global_id": 2568 }, { "text": "Accurate in vivo predictions of intestinal absorption of low solubility drugs require knowing their solubility in physiologically relevant dissolution media. Aspirated human intestinal fluids (HIF) are the gold standard, followed by simulated intestinal HIF in the fasted and fed state (FaSSIF/FeSSIF). However, current HIF characterization data vary, and there is also some controversy regarding the accuracy of FaSSIF and FeSSIF for predicting drug solubility in HIF. This study aimed at characterizing fasted and fed state duodenal HIF from 16 human volunteers with respect to pH, buffer capacity, osmolarity, surface tension, as well as protein, phospholipid, and bile salt content. The fasted and fed state HIF samples were further used to investigate the equilibrium solubility of 17 representative low-solubility small-molecule drugs, six of which were confidential industry compounds and 11 were known and characterized regarding chemical diversity. These solubility values were then compared to reported solubility values in fasted and fed state HIF, FaSSIF and FeSSIF, as well as with their human bioavailability for both states. The HIF compositions corresponded well to previously reported values and current FaSSIF and FeSSIF compositions. The drug solubility values in HIF (both fasted and fed states) were also well in line with reported solubility data for HIF, as well as simulated FaSSIF and FeSSIF. This indicates that the in vivo conditions in the proximal small intestine are well represented by simulated intestinal fluids in both composition and drug equilibrium solubility. However, increased drug solubility in the fed vs. fasted states in HIF did not correlate with the human bioavailability changes of the same drugs following oral administration in either state.\n\nFasted and fed state human duodenal fluids: Characterization, drug solubility, and comparison to simulated fluids and with human bioavailability.", "token_count": 454, "char_count": 1937, "word_count": 284, "semantic_coherence": 1, "information_density": 0.5035, "quality_score": 0.7518, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:49.820793", "source": { "split": "train_shard_00000", "doc_id": 2335 }, "chunk_id": "train_shard_00000_2335_0", "global_id": 2569 }, { "text": "Progressive familial intrahepatic cholestasis is a heterogeneous group of autosomal recessive disorders defined by defects in bile excretion and transport. We describe a 6-week-old boy from Micronesia presenting with failure to thrive and jaundice. His diagnostic workup was remarkable for direct hyperbilirubinemia, hepatitis, and hepatic ultrasound with possible portosystemic shunting. The presence of toxoplasma IgG initially raised concern for congenital toxoplasmosis. Ultimately, the absence of bile salt export pump staining on liver histology and subsequent genetic studies confirmed a diagnosis of progressive familial intrahepatic cholestasis type 5, an exceedingly rare cause of neonatal cholestasis.\n\nA Diagnostic Quagmire: PFIC5 Presenting as a Rare Cause of Neonatal Cholestasis.", "token_count": 214, "char_count": 794, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7547, "quality_score": 0.8774, "entities": { "genes": [ "PFIC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:50.286638", "source": { "split": "train_shard_00000", "doc_id": 2336 }, "chunk_id": "train_shard_00000_2336_0", "global_id": 2570 }, { "text": "In contrast to many steroid hormones and cholesterol, mammalian bile salts are 5β-steroids, which leads to a bent structure of the steroid core. Bile salts are surface-active steroids excreted into the environment in large amounts, where they are subject to bacterial degradation. Bacterial steroid degradation is initiated by the oxidation of the A-ring leading to canonical Δ\n\nSubstrate Inhibition of 5β-Δ", "token_count": 111, "char_count": 407, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7377, "quality_score": 0.8689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:50.673494", "source": { "split": "train_shard_00000", "doc_id": 2337 }, "chunk_id": "train_shard_00000_2337_0", "global_id": 2571 }, { "text": "Traditional genotyping methods for infection control of antimicrobial-resistant bacteria in healthcare settings have been supplemented by whole-genome sequencing (WGS), often relying on a gene-based approach, e.g., core genome multilocus sequence typing (cgMLST), to cluster-related samples. In this study, we compared clusters of methicillin-resistant\n\nRapid Open-Source SNP-Based Clustering Offers an Alternative to Core Genome MLST for Outbreak Tracing in a Hospital Setting.", "token_count": 122, "char_count": 478, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8689, "quality_score": 0.9344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:51.055186", "source": { "split": "train_shard_00000", "doc_id": 2338 }, "chunk_id": "train_shard_00000_2338_0", "global_id": 2572 }, { "text": "Agroindustrial by-products and residues can be transformed into valuable compounds in biorefineries. Here, we present a new concept: production of fuel ethanol, whey protein, and probiotic yeast from cheese whey. An initial screening under industrially relevant conditions, involving thirty Kluyveromyces marxianus strains, was carried out using spot assays to evaluate their capacity to grow on cheese whey or on whey permeate (100 g lactose/L), under aerobic or anaerobic conditions, in the absence or presence of 5% ethanol, at pH 5.8 or pH 2.5. The four best growing K. marxianus strains were selected and further evaluated in a miniaturized industrial fermentation process using reconstituted whey permeate (100 g lactose/L) with cell recycling (involving sulfuric acid treatment). After five consecutive fermentation cycles, the ethanol yield on sugar reached 90% of the theoretical maximum in the best cases, with 90% cell viability. Cells harvested at this point displayed probiotic properties such as the capacity to survive the passage through the gastrointestinal tract and capacity to modulate the innate immune response of intestinal epithelium, both in vitro. Furthermore, the CIDCA 9121 strain was able to protect against histopathological damage in an animal model of acute colitis. Our findings demonstrate that K. marxianus CIDCA 9121 is capable of efficiently fermenting the lactose present in whey permeate to ethanol and that the remaining yeast biomass has probiotic properties, enabling an integrated process for the obtainment of whey protein (WP), fuel ethanol, and probiotics from cheese whey.Key points• K. marxianus-selected strains ferment whey permeate with 90% ethanol yield.• Industrial fermentation conditions do not affect selected yeast probiotic capacity.• Whey permeate, fuel ethanol, and probiotic biomass can be obtained in a biorefinery.", "token_count": 495, "char_count": 1877, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6204, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:51.757348", "source": { "split": "train_shard_00000", "doc_id": 2339 }, "chunk_id": "train_shard_00000_2339_0", "global_id": 2573 }, { "text": "A biorefinery concept for the production of fuel ethanol, probiotic yeast, and whey protein from a by-product of the cheese industry.", "token_count": 35, "char_count": 133, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:52.131045", "source": { "split": "train_shard_00000", "doc_id": 2339 }, "chunk_id": "train_shard_00000_2339_1", "global_id": 2574 }, { "text": "Bacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum of diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation of the genetic diversity underlying virulence and host specificity can be performed at genome level by using a comprehensive comparative approach called pangenomics. A pangenomic approach, using newly developed functionalities in PanTools, was applied to analyze the complex phylogeny of the Pectobacterium genus. We specifically used the pangenome to investigate genetic differences between virulent and avirulent strains of P. brasiliense, a potato blackleg causing species dominantly present in Western Europe.\n\nThe Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool.", "token_count": 193, "char_count": 863, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7686, "quality_score": 0.8843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:52.620065", "source": { "split": "train_shard_00000", "doc_id": 2340 }, "chunk_id": "train_shard_00000_2340_0", "global_id": 2575 }, { "text": "Edwardsiella ictaluri has been considered an important threat for catfish aquaculture industry for more than 4 decades and an emerging pathogen of farmed tilapia but only 9 sequenced genomes were publicly available. We hereby report two new complete genomes of E. ictaluri originated from diseased hybrid red tilapia (Oreochromis sp.) and striped catfish (Pangasianodon hypophthalmus) in Southeast Asia. E. ictaluri species has an open pan-genome consisting of 2615 core genes and 5592 pan genes. Phylogenetic analysis using core genome MLST (cgMLST) and ANI values consistently placed E. ictaluri isolates into 4 host-specific genotypes. Presence of unique genes and absence of certain genes from each genotype provided potential biomarkers for further development of genotyping scheme. Vaccine candidates with high antigenic, solubility and secretion probabilities were identified in silico from the core genes. Microevolution within the species is brought about by bacteriophages and insertion elements and possibly drive host adaptation.\n\nComparative genomics of Edwardsiellaictaluri revealed four distinct host-specific genotypes and thirteen potential vaccine candidates.", "token_count": 288, "char_count": 1177, "word_count": 162, "semantic_coherence": 1, "information_density": 0.7407, "quality_score": 0.8704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:53.205281", "source": { "split": "train_shard_00000", "doc_id": 2341 }, "chunk_id": "train_shard_00000_2341_0", "global_id": 2576 }, { "text": "Lactobacillaceae presents potential for interspecific Quorum Sensing (QS) in spontaneous cocoa fermentation, correlated with high abundance of luxS. Three Brazilian isolates from cocoa fermentation were characterized by Whole Genome Sequencing and luxS gene was surveyed in their genomes, in comparison with public databases. They were classified as Lactiplantibacillus plantarum, Limosilactobacillus fermentum and Pediococcus acidilactici. LuxS genes were conserved in core genomes of the novel isolates, but in some non-cocoa related Lactic Acid Bacteria (LAB) it was accessory and plasmid-borne. The conservation and horizontal acquisition of luxS reinforces that QS is determinant for bacterial adaptation in several environments, especially taking into account the luxS has been correlated with modulation of bacteriocin production, stress tolerance and biofilm formation. Therefore, in this paper, new clade and species-specific primers were designed for future application for screening of luxS gene in LAB to evaluate the adaptive potential to diverse food fermentations.\n\nPangenome analyses of LuxS-coding genes and enzymatic repertoires in cocoa-related lactic acid bacteria.", "token_count": 288, "char_count": 1185, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7296, "quality_score": 0.8648, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:53.768740", "source": { "split": "train_shard_00000", "doc_id": 2342 }, "chunk_id": "train_shard_00000_2342_0", "global_id": 2577 }, { "text": "Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.", "token_count": 28, "char_count": 105, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:54.127763", "source": { "split": "train_shard_00000", "doc_id": 2343 }, "chunk_id": "train_shard_00000_2343_0", "global_id": 2578 }, { "text": "Although ebastine (EBT) can impede histamine-induced skin allergic reaction and persuade long acting selective H1 receptor antagonistic effects but its poor water solubility circumscribed its clinical application. The main objective of this research work was to improve the aqueous solubility and oral bioavailability of EBT by preparing EBT-loaded bilosomes (EBT-PC-SDC-BS). A thin film hydration method was used to prepare ebastine loaded bilosomes. The prepared-formulations were optimized considering size, morphology and entrapment efficiency. The SEM images revealed regular and spherical shape of bilosomes. Average size of the prepared EBT-PC-SDC-BS was 665.8 nm and zeta potential was around-32.9 mV with 89.05 % average entrapment efficiency (EE).Importantly, the solubility of EBT in water was amplified up to 17.9 μg/ml compared to pure drug (2 μg/mL) reflecting a highest solubility increase of 751 %. In vitro drug release results of prepared EBT-PC-SDC-BS exhibited improved release behavior. Finally, it is established from the results that the EBT-PC-SDC-BS could function as a favorable nano-carrier system to improve the solubility as well as dissolution of EBT.\n\nImprovement of solubility and dissolution of ebastine by fabricating phosphatidylcholine/ bile salt bilosomes.", "token_count": 355, "char_count": 1293, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:54.704582", "source": { "split": "train_shard_00000", "doc_id": 2344 }, "chunk_id": "train_shard_00000_2344_0", "global_id": 2579 }, { "text": "Routine infectious disease surveillance is increasingly based on large-scale whole-genome sequencing databases. Real-time surveillance would benefit from immediate assignments of each genome assembly to hierarchical population structures. Here we present pHierCC, a pipeline that defines a scalable clustering scheme, HierCC, based on core genome multi-locus typing that allows incremental, static, multi-level cluster assignments of genomes. We also present HCCeval, which identifies optimal thresholds for assigning genomes to cohesive HierCC clusters. HierCC was implemented in EnteroBase in 2018 and has since genotyped >530 000 genomes from Salmonella, Escherichia/Shigella, Streptococcus, Clostridioides, Vibrio and Yersinia.\n\nHierCC: a multi-level clustering scheme for population assignments based on core genome MLST.", "token_count": 211, "char_count": 826, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7524, "quality_score": 0.8762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:55.167629", "source": { "split": "train_shard_00000", "doc_id": 2345 }, "chunk_id": "train_shard_00000_2345_0", "global_id": 2580 }, { "text": "2-phenylethanol (2-PE) is a higher aromatic alcohol with a rose-like aroma used in the cosmetic and food industries as a flavoring and displays potential for application as an antifungal. Biotechnological production of 2-PE from yeast is an interesting alternative due to the non-use of toxic compounds and the generation of few by-products. Kluyveromyces marxianus CCT 7735 is a thermotolerant strain capable of producing high 2-PE titers from L-Phenylalanine; however, like other yeast species, its growth has been strongly inhibited by this alcohol. Herein, we aimed to evaluate the effect of 2-PE on cell growth, cell viability, membrane permeability, glucose uptake, metabolism, and morphology in K. marxianus CCT 7735, as well as its adaptive responses. The stress condition was imposed after 4 h of cultivation by adding 3.0 g.L\n\nAdaptive responses of Kluyveromyces marxianus CCT 7735 to 2-phenylethanol stress: Alterations in membrane fatty-acid composition, ergosterol content, exopolysaccharide production and reduction in reactive oxygen species.", "token_count": 304, "char_count": 1057, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:55.740298", "source": { "split": "train_shard_00000", "doc_id": 2346 }, "chunk_id": "train_shard_00000_2346_0", "global_id": 2581 }, { "text": "Trace metals are essential to all domains of life but toxic when found at high concentrations. Although the importance of iron in host-pathogen interactions is firmly established, contemporary studies indicate that other trace metals, including manganese and zinc, are also critical to the infectious process. In this study, we sought to identify and characterize the zinc uptake system(s) of Streptococcus mutans, a keystone pathogen in dental caries and a causative agent of bacterial endocarditis. Different than other pathogenic bacteria, including several streptococci, that encode multiple zinc import systems, bioinformatic analysis indicated that the S. mutans core genome encodes a single, highly conserved, zinc importer commonly known as AdcABC. Inactivation of the genes coding for the metal-binding AdcA (ΔadcA) or both AdcC ATPase and AdcB permease (ΔadcCB) severely impaired the ability of S. mutans to grow under zinc-depleted conditions. Intracellular metal quantifications revealed that both mutants accumulated less zinc when grown in the presence of a subinhibitory concentration of a zinc-specific chelator. Notably, the ΔadcCB strain displayed a severe colonization defect in a rat oral infection model. Both Δadc strains were hypersensitive to high concentrations of manganese, showed reduced peroxide tolerance, and formed less biofilm in sucrose-containing media when cultivated in the presence of the lowest amount of zinc that support their growth, but not when zinc was supplied in excess. Collectively, this study identifies AdcABC as the major high affinity zinc importer of S. mutans and provides preliminary evidence that zinc is a growth-limiting factor within the dental biofilm.\n\nZinc import mediated by AdcABC is critical for colonization of the dental biofilm by Streptococcus mutans in an animal model.", "token_count": 449, "char_count": 1840, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:56.391113", "source": { "split": "train_shard_00000", "doc_id": 2347 }, "chunk_id": "train_shard_00000_2347_0", "global_id": 2582 }, { "text": "The isolation of autochthonous yeast species presents a good strategy to select new microorganisms for developing an adequate inoculum to carry out fermentations and generate representative products of the cider production zone. However, non-Saccharomyces yeasts have been considered to have low capacity to carry out a complete fermentation as Saccharomyces cerevisiae. In this work, five autochthonous yeasts from a cider fermentation process were isolated and identified as Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia membranaefaciens, P. kluyveri and Zygosaccharomyces rouxii. A series of fermentations were developed at laboratory level, using each species individually and it was observed that only S. cerevisiae was able to finish the process. K. marxianus consumed less than 50% of the sugars; P. kluyveri and Z. rouxii consumed less than 70% and P. membranaefaciens consumed more than 90% but the yield (ethanol produced for sugar consumed (Y\n\nUse of non-Saccharomyces yeasts in cider fermentation: Importance of the nutrients addition to obtain an efficient fermentation.", "token_count": 286, "char_count": 1095, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:56.949798", "source": { "split": "train_shard_00000", "doc_id": 2348 }, "chunk_id": "train_shard_00000_2348_0", "global_id": 2583 }, { "text": "Bile secretion by hepatocytes is an osmotic process. The output of bile salts and other organic anions (e.g. glutathione), through the bile salt transporter BSEP/ABCB11 and the organic anion transporter MRP2/ABCC2, respectively, are considered to be the major osmotic driving forces for water secretion into bile canaliculi mainly via aquaporin-8 (AQP8) channels. The down-regulated canalicular expression of these key solute transporters and AQP8 would be a primary event in the establishment of hepatocellular cholestasis. Recent studies in animal models of hepatocellular cholestasis show that the hepatic delivery of AdhAQP1, an adenovector encoding for the archetypical water channel human aquaporin-1 (hAQP1), improves bile secretion and restores to normal the elevated serum bile salt levels. AdhAQP1-transduced hepatocytes show that the canalicularly-expressed hAQP1 not only enhances osmotic membrane water permeability but also induces the transport activities of BSEP/ABCB11 and MRP2/ABCC2 by redistribution in canalicular cholesterol-rich microdomains likely through interactions with the cholesterol-binding protein caveolin-1. Thus, the hepatic gene transfer of hAQP1 improves the bile secretory failure in hepatocellular cholestasis by increasing both biliary output and choleretic efficiency of key osmotic solutes, such as, bile salts and glutathione. The study of hepatocyte aquaporins has provided new insights into the mechanisms of bile formation and cholestasis, and may lead to innovative treatments for cholestatic liver diseases.\n\nAquaporin gene transfer for hepatocellular cholestasis.", "token_count": 446, "char_count": 1611, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.8111, "entities": { "genes": [ "MRP2", "ABCC2", "ABCB11", "AQP8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:57.578093", "source": { "split": "train_shard_00000", "doc_id": 2349 }, "chunk_id": "train_shard_00000_2349_0", "global_id": 2584 }, { "text": "Bile salt hydrolase (BSH) activity in probiotic strains is usually correlated with the ability to lower serum cholesterol levels in hypercholesterolemic patients. The objective of this study was the evaluation of BSH in five probiotic strains of lactic acid bacteria (LAB) and a probiotic yeast. The activity was assessed using a qualitative direct plate test and a quantitative high-performance thin- layer chromatography assay. The six strains differed in their BSH substrate preference and activity.\n\nIn Vitro Bile Salt Hydrolase (BSH) Activity Screening of Different Probiotic Microorganisms.", "token_count": 149, "char_count": 596, "word_count": 86, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:58.018017", "source": { "split": "train_shard_00000", "doc_id": 2350 }, "chunk_id": "train_shard_00000_2350_0", "global_id": 2585 }, { "text": "Bile salt hydrolase (BSH) and penicillin V acylase (PVA) are related enzymes that are classified as choloylglycine hydrolases (CGH). BSH enzymes have attracted significant interest for their ability to modulate the composition of the bile acid pool, alter bile acid signaling events mediated by the host bile acid receptors FXR and TGR5 and influence cholesterol homeostasis in the host, while PVA enzymes have been widely utilised in an industrial capacity in the production of semi-synthetic antibiotics. The similarities between BSH and PVA enzymes suggest common evolution of these enzymes and shared mechanisms for substrate binding and catalysis. Here, we compare BSH and PVA through analysis of the distribution, phylogeny and biochemistry of these microbial enzymes. The development of new annotation approaches based upon functional enzyme analyses and the potential implications of BSH enzymes for host health are discussed.\n\nFunctional and Phylogenetic Diversity of BSH and PVA Enzymes.", "token_count": 253, "char_count": 997, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8197, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:58.844053", "source": { "split": "train_shard_00000", "doc_id": 2351 }, "chunk_id": "train_shard_00000_2351_0", "global_id": 2586 }, { "text": "The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, but the pangenome can be much greater and usually includes genes appearing in one only strain. Once the pangenome of a species is estimated, other studies can be undertaken to generate new knowledge, such as the study of the evolutionary selection for protein-coding genes. Most of the genes of a pangenome are expected to be subject to purifying selection that assures the conservation of function, especially those in the core group. However, some genes can be subject to selection pressure, such as genes involved in virulence that need to escape to the host immune system, which is more common in the accessory group of the pangenome. We analyzed 180 strains of\n\nProtein-Coding Genes of", "token_count": 206, "char_count": 946, "word_count": 157, "semantic_coherence": 1, "information_density": 0.586, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:59.309548", "source": { "split": "train_shard_00000", "doc_id": 2352 }, "chunk_id": "train_shard_00000_2352_0", "global_id": 2587 }, { "text": "Idiosyncratic drug-induced liver injury (IDILI) remains a significant problem for patients and drug development. The idiosyncratic nature of IDILI makes mechanistic studies difficult, and little is known of its pathogenesis for certain. Circumstantial evidence suggests that most, but not all, IDILI is caused by reactive metabolites of drugs that are bioactivated by cytochromes P450 and other enzymes in the liver. Additionally, there is overwhelming evidence that most IDILI is mediated by the adaptive immune system; one example being the association of IDILI caused by specific drugs with specific human leukocyte antigen (HLA) haplotypes, and this may in part explain the idiosyncratic nature of these reactions. The T cell receptor repertoire likely also contributes to the idiosyncratic nature. Although most of the liver injury is likely mediated by the adaptive immune system, specifically cytotoxic CD8+ T cells, adaptive immune activation first requires an innate immune response to activate antigen presenting cells and produce cytokines required for T cell proliferation. This innate response is likely caused by either a reactive metabolite or some form of cell stress that is clinically silent but not idiosyncratic. If this is true it would make it possible to study the early steps in the immune response that in some patients can lead to IDILI. Other hypotheses have been proposed, such as mitochondrial injury, inhibition of the bile salt export pump, unfolded protein response, and oxidative stress although, in most cases, it is likely that they are also involved in the initiation of an immune response rather than representing a completely separate mechanism. Using the clinical manifestations of liver injury from a number of examples of IDILI-associated drugs, this review aims to summarize and illustrate these mechanistic hypotheses.\n\nIdiosyncratic Drug-Induced Liver Injury: Mechanistic and Clinical Challenges.", "token_count": 445, "char_count": 1940, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5744, "quality_score": 0.7872, "entities": { "genes": [ "CD8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:21:59.938584", "source": { "split": "train_shard_00000", "doc_id": 2353 }, "chunk_id": "train_shard_00000_2353_0", "global_id": 2588 }, { "text": "An immunocompromised patient with a known history of cerebrovascular accident (CVA) with right-sided hemiparesis of long duration, type 2 diabetes mellitus, and hypertension presented with signs of rhabdomyolysis and later acute kidney injury (AKI). He subsequently developed Guillain Barre syndrome. Initially, hemodialysis was followed by plasmapheresis. After hemodialysis, the patient presented with multiple episodes of vomiting and weakness of all limbs. A culture showed growth of\n\nAn Unusual Case of Candida kefyr Fungemia in an Immunocompromised Patient.", "token_count": 148, "char_count": 563, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7792, "quality_score": 0.8896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:00.371938", "source": { "split": "train_shard_00000", "doc_id": 2354 }, "chunk_id": "train_shard_00000_2354_0", "global_id": 2589 }, { "text": "Raoultella ornithinolytica is a poorly understood opportunistic pathogen, and the underlying mechanisms of its multidrug resistance and pathogenicity have not yet been comprehensively investigated. The multidrug-resistant (MDR) strain WM1 was isolated from the blood of a male patient in Tianjin, China, in 2018. Here, we describe the complete genome and provide a genomic analysis of R. ornithinolytica WM1. The isolate was resistant to all tested antimicrobials except amikacin, tobramycin, and tigecycline. Two plasmids, pWM1-1 (IncHI5) and pWM1-2 (IncR), carried multidrug-resistance regions. A large antimicrobial resistance island region resided on pWM1-1 and exhibited mosaic structures resulting from the acquisition of complex integrations of variable regions, including genes conferring resistance to multiple classes of antimicrobials. Moreover, WM1 possessed virulence-related elements that encode several virulence factors, including type I fimbriae, Escherichia coli common pilus, type II and VI secretion systems, yersiniabactin, enterobactin, and surface polysaccharide, indicating pathogenic potential. Furthermore, the core genome phylogeny and pan-genome analyses revealed extensive genetic diversity. Our analysis indicates the need for stringent infection control, antimicrobial stewardship, periodic resistance monitoring, and rational medication to address potential threats posed by MDR R. ornithinolytica strains.\n\nGenomic insights into evolution of pathogenicity and resistance of multidrug-resistant Raoultella ornithinolytica WM1.", "token_count": 403, "char_count": 1558, "word_count": 197, "semantic_coherence": 1, "information_density": 0.736, "quality_score": 0.868, "entities": { "genes": [ "WM1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:00.988010", "source": { "split": "train_shard_00000", "doc_id": 2355 }, "chunk_id": "train_shard_00000_2355_0", "global_id": 2590 }, { "text": "Liraglutide is an analog of human glucagon-like peptide-1 which play essential roles in regulation of glycolipid metabolism. To investigate role of lactic acid bacteria (LAB) in lipid-lowering effect of liraglutide, 40 mice were divided into normal food diet (NFD), high-fat food (HFD), 10.0 mg/kg/d simvastatin-treated HFD (SIM + HFD), 200 and 400 µg/kg/d liraglutide-treated HFD (LL + HFD and HL + HFD) groups for 5 weeks. We found that liraglutide could upregulate cholesterol 7α-hydroxylase (CYP7A1) and LDL-receptor (LDLR), whereas downregulate 3-hydroxy-3-methylglutaryl coenzyme A reductase (HMGCR). Besides, liraglutide enhance abundance of lactobacillaceae in gut of hyperlipidemic mice and increase bile tolerance ability of LAB by upregulating bile salt hydrolases, and the lysate of liraglutide-sensitive LAB could also directly downregulate HMGCR, the key enzyme in cholesterol synthesis, and inhibit hepatocyte steatosis. These findings might provide new theoretical guidance for clinical application of liraglutide and research and development of antiobesity, hypolipidemic, and cholesterol-lowering drugs or functional foods.\n\nEnhancing bile tolerance of Lactobacilli is involved in the hypolipidemic effects of liraglutide.", "token_count": 417, "char_count": 1240, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7425, "quality_score": 0.8713, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:01.609774", "source": { "split": "train_shard_00000", "doc_id": 2356 }, "chunk_id": "train_shard_00000_2356_0", "global_id": 2591 }, { "text": "Bile salts, such as cholate, glycocholate, taurocholate, and glycochenodeoxycholate, are taken up from the portal blood into hepatocytes via transporters, such as the Na\n\nCharacterization of Novel Fluorescent Bile Salt Derivatives for Studying Human Bile Salt and Organic Anion Transporters.", "token_count": 87, "char_count": 291, "word_count": 40, "semantic_coherence": 1, "information_density": 0.825, "quality_score": 0.9125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:01.985114", "source": { "split": "train_shard_00000", "doc_id": 2357 }, "chunk_id": "train_shard_00000_2357_0", "global_id": 2592 }, { "text": "Glibenclamide, ATP and metformin increases the expression of human bile salt export pump ABCB11.", "token_count": 27, "char_count": 96, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:02.352278", "source": { "split": "train_shard_00000", "doc_id": 2358 }, "chunk_id": "train_shard_00000_2358_0", "global_id": 2593 }, { "text": "Vancomycin-resistant Enterococcus faecium (VRE) belonging to sequence type 80 (ST80) have been successfully disseminating in hospital settings. This study aimed to explore whole-genome sequencing (WGS)-based approaches in epidemiological typing of VRE by investigating a collection of ST80 strains.\n\nEpidemiological typing of ST80 vancomycin-resistant Enterococcus faecium: core genome multilocus sequence typing versus single nucleotide polymorphism-based typing.", "token_count": 124, "char_count": 464, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:02.740891", "source": { "split": "train_shard_00000", "doc_id": 2359 }, "chunk_id": "train_shard_00000_2359_0", "global_id": 2594 }, { "text": "Probiotic milk-fermented microorganism mixtures (e.g., yogurt, kefir) are perceived as contributing to human health, and possibly capable of protecting against bacterial infections. Co-existence of probiotic microorganisms are likely maintained via complex biomolecular mechanisms, secreted metabolites mediating cell-cell communication, and other yet-unknown biochemical pathways. In particular, deciphering molecular mechanisms by which probiotic microorganisms inhibit proliferation of pathogenic bacteria would be highly important for understanding both the potential benefits of probiotic foods as well as maintenance of healthy gut microbiome.\n\nCross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites.", "token_count": 169, "char_count": 748, "word_count": 89, "semantic_coherence": 1, "information_density": 0.809, "quality_score": 0.9045, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:03.191841", "source": { "split": "train_shard_00000", "doc_id": 2360 }, "chunk_id": "train_shard_00000_2360_0", "global_id": 2595 }, { "text": "In this study, traditional indigenous fermented food isolate Lactobacillus plantarum UBLP40 was screened for in vitro probiotic properties, antibiotic susceptibility, hemolytic activity, production of lactic acid, hydrogen peroxide, bile salt hydrolase and phytase, and antioxidative activity. Results showed that Lact. plantarum UBLP40 can survive simulated gastrointestinal conditions, adhere to mucin, possess a hydrophobic cell surface, ability to auto-aggregation, and possessed antimicrobial activity against Micrococcus luteus MTCC 106, methicillin-resistant Staphylococcus aureus subsp. aureus ATCC® BAA-1720, Pseudomonas aeruginosa MTCC 1688, and Escherichia coli MTCC 1687. Lact. plantarum UBLP40 produced 48.59 U/mg phytase and 1.78 ± 0.01 gm % lactic acid and showed the ability to produce hydrogen peroxide and bile salt hydrolase. Moreover, the usual antibiotic susceptible profile and non-hemolytic activity indicated the safety of the strain. The intracellular extract of UBLP40 showed 13.8 ± 1.4% (equivalent to ~8 µM butylated hydroxytoluene) α,α-diphenyl-β-picrylhydrazyl (DPPH) radical scavenging activity, reducing activity equivalent to 1 µg L-cysteine, Fe\n\nIn Vitro Evaluation of Probiotic Properties of Lactobacillus plantarum UBLP40 Isolated from Traditional Indigenous Fermented Food.", "token_count": 446, "char_count": 1310, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7041, "quality_score": 0.8521, "entities": { "genes": [ "UBLP40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:03.843070", "source": { "split": "train_shard_00000", "doc_id": 2361 }, "chunk_id": "train_shard_00000_2361_0", "global_id": 2596 }, { "text": "Pheromonal bile salts are important for sea lampreys (\n\nBile acid production is life-stage and sex-dependent and affected by primer pheromones in the sea lamprey.", "token_count": 44, "char_count": 162, "word_count": 25, "semantic_coherence": 1, "information_density": 0.88, "quality_score": 0.94, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:04.246116", "source": { "split": "train_shard_00000", "doc_id": 2362 }, "chunk_id": "train_shard_00000_2362_0", "global_id": 2597 }, { "text": "In the current genomic era, knowledge of diversity of Leptospira, the spirochetal agents of leptospirosis, is changing rapidly. Next-generation sequencing has decreased in price and increased in scale, with the potential to democratize large-scale analysis of pathogens in resource-limited, low/middle-income (LMIC) regions. Consequently, the molecular classification of Leptospira, a pathogen disproportionately affecting LMIC countries, has changed dramatically over the last decade. Leptospira classification and molecular understandings of pathogen diversity have rapidly evolved, now most precisely based on core genome analysis supplemented by new insights provided by culture-independent methods directly using body fluids such as blood and urine. In places where leptospirosis disease burden is highest, genomic technologies have not been available, and serology-based methods remain the mainstay of leptospiral classification. Understanding the epidemiology, pathogenesis, and ultimately new approaches to treating and preventing leptospirosis requires detailed knowledge of regionally circulating Leptospira in highly endemic settings. Next-generation sequencing-based, culture-independent typing overcomes the limitation of culture isolation of Leptospira from clinical samples, with promise of providing public health-actionable information applicable to leptospirosis-endemic LMIC settings.\n\nNext-Generation Sequencing Analysis of Pathogenic Leptospira: A Way Forward for Understanding Infectious Disease Dynamics in Low/Middle-Income, Disease-Endemic Settings.", "token_count": 352, "char_count": 1574, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:04.849746", "source": { "split": "train_shard_00000", "doc_id": 2363 }, "chunk_id": "train_shard_00000_2363_0", "global_id": 2598 }, { "text": "Enterococcus faecalis is a commensal and nosocomial pathogen, which is also ubiquitous in animals and insects, representing a classical generalist microorganism. Here, we study E. faecalis isolates ranging from the pre-antibiotic era in 1936 up to 2018, covering a large set of host species including wild birds, mammals, healthy humans, and hospitalised patients. We sequence the bacterial genomes using short- and long-read techniques, and identify multiple extant hospital-associated lineages, with last common ancestors dating back as far as the 19th century. We find a population cohesively connected through homologous recombination, a metabolic flexibility despite a small genome size, and a stable large core genome. Our findings indicate that the apparent hospital adaptations found in hospital-associated E. faecalis lineages likely predate the \"modern hospital\" era, suggesting selection in another niche, and underlining the generalist nature of this nosocomial pathogen.\n\nApparent nosocomial adaptation of Enterococcus faecalis predates the modern hospital era.", "token_count": 257, "char_count": 1074, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7383, "quality_score": 0.8691, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:05.432906", "source": { "split": "train_shard_00000", "doc_id": 2364 }, "chunk_id": "train_shard_00000_2364_0", "global_id": 2599 }, { "text": "The bile salt export pump (BSEP) is a pivotal apical/canalicular bile salt transporter in hepatocytes that drives the bile flow. Defects in BSEP function and canalicular expression could lead to a spectrum of cholestatic liver diseases. One prominent manifestation of BSEP-associated cholestasis is the defective canalicular localization and cytoplasmic retention of BSEP. However, the etiology of impaired BSEP targeting to the canalicular membrane is not fully understood. Our goal was to discover what molecule could interact with BSEP and affect its post-Golgi sorting.\n\nThe ESCRT-III molecules regulate the apical targeting of bile salt export pump.", "token_count": 174, "char_count": 654, "word_count": 95, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:06.718657", "source": { "split": "train_shard_00000", "doc_id": 2365 }, "chunk_id": "train_shard_00000_2365_0", "global_id": 2600 }, { "text": "Clustered regularly interspaced short palindromic repeats (CRISPR) cas genes have been linked to stress response in Salmonella. Our aim was to identify the presence of CRISPR cas in Salmonella and its response to heat in the presence of iron. Whole genomes of Salmonella (n = 50) of seven serovars were compared to identify the presence of CRISPR cas genes, direct-repeats and spacers. All Salmonella genomes had all cas genes present except S. Newport 2393 which lacked these genes. Gene-specific primers were used to confirm the absence of these genes in S. Newport 2393. The presence/absence of CRISPR cas genes was further investigated among 469 S. Newport genomes from PATRIC with 283 genomes selected for pan-genome analysis. The response of eleven Salmonella strains of various serovars to gradual heat in ferrous and ferric forms of iron was investigated. A total of 32/283 S. Newport genomes that lacked all CRISPR cas genes clustered together. S. Newport 2393 was the most heat-sensitive strain at higher iron levels (200 and 220 pm) in ferrous and ferric forms of iron. The absence of CRISPR cas genes in S. Newport 2393 may contribute to its increase in heat sensitivity and iron may play a role in this. The high reduction in numbers of most Salmonella strains exposed to heat makes it unfeasible to extract RNA and conduct transcription studies. Further studies should be conducted to validate the survival of Salmonella when exposed to heat in the presence/absence of CRISPR cas genes and different iron levels.\n\nSurvival of Salmonella Under Heat Stress is Associated with the Presence/Absence of CRISPR Cas Genes and Iron Levels.", "token_count": 438, "char_count": 1645, "word_count": 267, "semantic_coherence": 1, "information_density": 0.4719, "quality_score": 0.736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:07.360285", "source": { "split": "train_shard_00000", "doc_id": 2366 }, "chunk_id": "train_shard_00000_2366_0", "global_id": 2601 }, { "text": "In 2016, Venezuela faced a large diphtheria outbreak that extended until 2019. Nasopharyngeal or oropharyngeal samples were prospectively collected from 51 suspected cases and retrospective data from 348 clinical records was retrieved from 14 hospitals between November 2017 and November 2018. Confirmed pathogenic Corynebactrium isolates were biotyped. Multilocus Sequence Typing (MLST) was performed followed by next-generation-based core genome-MLST and minimum spanning trees were generated. Subjects between 10 and 19 years of age were mostly affected (n = 95; 27.3%). Case fatality rates (CFR) were higher in males (19.4%), as compared to females (15.8%). The highest CFR (31.1%) was observed among those under 5, followed by the 40 to 49 age-group (25.0%). Nine samples corresponded to C. diphtheriae and 1 to C. ulcerans. Two Sequencing Types (ST), ST174 and ST697 (the latter not previously described) were identified among the eight C. diphtheriae isolates from Carabobo state. Cg-MLST revealed only one cluster also from Carabobo. The Whole Genome Sequencing analysis revealed that the outbreak seemed to be caused by different strains with C. diphtheriae and C. ulcerans coexisting. The reemergence and length of this outbreak suggest vaccination coverage problems and an inadequate control strategy.\n\nMolecular and epidemiologic characterization of the diphtheria outbreak in Venezuela.", "token_count": 408, "char_count": 1399, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7277, "quality_score": 0.8639, "entities": { "genes": [ "ST174", "ST697" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:07.977595", "source": { "split": "train_shard_00000", "doc_id": 2367 }, "chunk_id": "train_shard_00000_2367_0", "global_id": 2602 }, { "text": "Mycobacterium avium subsp. paratuberculosis (MAP) is a causative agent of Johne's disease, which is a chronic granulomatous enteropathy in ruminants. Determining the genetic diversity of MAP is necessary to understand the epidemiology and biology of MAP, as well as establishing disease control strategies. In the present study, whole genome-based alignment and comparative analysis were performed using 40 publicly available MAP genomes, including newly sequenced Korean isolates. First, whole genome-based alignment was employed to identify new genomic structures in MAP genomes. Second, the genomic diversity of the MAP population was described by pangenome analysis. A phylogenetic tree based on the core genome and pangenome showed that the MAP was differentiated into two major types (C- and S-type), which was in keeping with the findings of previous studies. However, B-type strains were discriminated from C-type strains. Finally, functional analysis of the pangenome was performed using three virulence factor databases (i.e., PATRIC, VFDB, and Victors) to predict the phenotypic diversity of MAP in terms of pathogenicity. Based on the results of the pangenome analysis, we developed a real-time PCR technique to distinguish among S-, B- and C-type strains. In conclusion, the results of our study suggest that the phenotypic differences between MAP strains can be explained by their genetic polymorphisms. These results may help to elucidate the diversity of MAP, extending from genomic features to phenotypic traits.\n\nGenomic diversity of Mycobacterium avium subsp. paratuberculosis: pangenomic approach for highlighting unique genomic features with newly constructed complete genomes.", "token_count": 409, "char_count": 1698, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:08.596914", "source": { "split": "train_shard_00000", "doc_id": 2368 }, "chunk_id": "train_shard_00000_2368_0", "global_id": 2603 }, { "text": "Leptospirosis is a ubiquitous zoonotic disease and a major clinical challenge owing to the multitude of clinical presentations and manifestations that are possibly attributable to the diversity of Leptospira, the understanding of which is key to study the epidemiology of this emerging global disease threat. Sri Lanka is a hotspot for leptospirosis with high levels of endemicity as well as annual epidemics. We carried out a prospective study of Leptospira diversity in Sri Lanka, covering the full range of climatic zones, geography, and clinical severity. Samples were collected for leptospiral culture from 1,192 patients from 15 of 25 districts in Sri Lanka over two and half years. Twenty-five isolates belonging to four pathogenic Leptospira species were identified: L. interrogans, L. borgpetersenii, L. weilii, and L. kirschneri. At least six serogroups were identified among the isolates: Autumnalis (6), Pyrogenes (4), Icterohaemorrhagiae (2), Celledoni (1), Grippotyphosa (2) and Bataviae (1). Seven isolates did not agglutinate using available antisera panels, suggesting new serogroups. Isolates were sequenced using an Illumina platform. These data add 25 new core genome sequence types and were clustered in 15 clonal groups, including 12 new clonal groups. L. borgpetersenii was found only in the dry zone and L. weilii only in the wet zone. Acute kidney injury and cardiovascular involvement were seen only with L. interrogans infections. Thrombocytopenia and liver impairment were seen in both L. interrogans and L. borgpetersenii infections. The inadequate sensitivity of culture isolation to identify infecting Leptospira species underscores the need for culture-independent typing methods for Leptospira.\n\n12 Novel clonal groups of Leptospira infecting humans in multiple contrasting epidemiological contexts in Sri Lanka.", "token_count": 493, "char_count": 1845, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:09.244128", "source": { "split": "train_shard_00000", "doc_id": 2369 }, "chunk_id": "train_shard_00000_2369_0", "global_id": 2604 }, { "text": "Infectious keratitis is a potentially sight threatening ophthalmological emergency. Contact lens wear is a common risk factor. Diagnostic advances such as MALDI-TOF MS provides new insights into the spectrum of corneal pathogens and on microbes previously considered as commensals. Corynebacterium macginleyi was described in 1995, and in 2018, the genomic features of three isolates were reported after whole-genome sequencing. Here we describe the clinical characteristics of patients with infectious keratitis (n = 29) presumably caused by Corynebacterium macginleyi, and analyze the genomic features of C. macginleyi (n = 22) isolated from the corneal ulcers of these patients. The disease course was uneventful apart from minor interventions such as corneal cross-linking and amniotic membrane transplant. Genome sequencing and comparison revealed a highly conserved core genome of C. macginleyi. Based on the analyses of single nucleotide polymorphisms, the population could be divided into two main clades that also differed in a few clade-specific genomic islands. Patients infected with an isolate belonging to the minor clade (n = 7) presented a more severe disease. Comparisons with other corynebacterial species clearly separated C. macginleyi. C. macginleyi may be considered a corneal pathogen; genomic analysis provided insights into its population structure and disease-causing potential.\n\nClinical and genomic features of Corynebacterium macginleyi-associated infectious keratitis.", "token_count": 389, "char_count": 1498, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:09.860733", "source": { "split": "train_shard_00000", "doc_id": 2370 }, "chunk_id": "train_shard_00000_2370_0", "global_id": 2605 }, { "text": "Transposable elements (TEs) impact genome plasticity, architecture, and evolution in fungal plant pathogens. The wide range of TE content observed in fungal genomes reflects diverse efficacy of host-genome defense mechanisms that can counter-balance TE expansion and spread. Closely related species can harbor drastically different TE repertoires. The evolution of fungal effectors, which are crucial determinants of pathogenicity, has been linked to the activity of TEs in pathogen genomes. Here, we describe how TEs have shaped genome evolution of the fungal wheat pathogen Zymoseptoria tritici and four closely related species. We compared de novo TE annotations and repeat-induced point mutation signatures in 26 genomes from the Zymoseptoria species-complex. Then, we assessed the relative insertion ages of TEs using a comparative genomics approach. Finally, we explored the impact of TE insertions on genome architecture and plasticity. The 26 genomes of Zymoseptoria species reflect different TE dynamics with a majority of recent insertions. TEs associate with accessory genome compartments, with chromosomal rearrangements, with gene presence/absence variation, and with effectors in all Zymoseptoria species. We find that the extent of RIP-like signatures varies among Z. tritici genomes compared to genomes of the sister species. The detection of a reduction of RIP-like signatures and TE recent insertions in Z. tritici reflects ongoing but still moderate TE mobility.\n\nDynamics of transposable elements in recently diverged fungal pathogens: lineage-specific transposable element content and efficiency of genome defenses.", "token_count": 382, "char_count": 1636, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5565, "quality_score": 0.7783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:10.441566", "source": { "split": "train_shard_00000", "doc_id": 2371 }, "chunk_id": "train_shard_00000_2371_0", "global_id": 2606 }, { "text": "Morbidity and mortality caused by infectious diseases rank first among all human illnesses. Many pathogenic mechanisms remain unclear, while misuse of antibiotics has led to the emergence of drug-resistant strains. Infectious diseases spread rapidly and pathogens mutate quickly, posing new threats to human health. However, with the increasing use of high-throughput screening of pathogen genomes, research based on big data mining and visualization analysis has gradually become a hot topic for studies of infectious disease prevention and control. In this paper, the framework was performed on four infectious pathogens (Fusobacterium, Streptococcus, Neisseria, and Streptococcus salivarius) through five functions: 1) genome annotation, 2) phylogeny analysis based on core genome, 3) analysis of structure differences between genomes, 4) prediction of virulence genes/factors with their pathogenic mechanisms, and 5) prediction of resistance genes/factors with their signaling pathways. The experiments were carried out from three angles: phylogeny (macro perspective), structure differences of genomes (micro perspective), and virulence and drug-resistance characteristics (prediction perspective). Therefore, the framework can not only provide evidence to support the rapid identification of new or unknown pathogens and thus plays a role in the prevention and control of infectious diseases, but also help to recommend the most appropriate strains for clinical and scientific research. This paper presented a new genome information visualization analysis process framework based on big data mining technology with the accommodation of the depth and breadth of pathogens in molecular level research.\n\nPrevention and Control of Pathogens Based on Big-Data Mining and Visualization Analysis.", "token_count": 386, "char_count": 1795, "word_count": 246, "semantic_coherence": 1, "information_density": 0.622, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:11.055688", "source": { "split": "train_shard_00000", "doc_id": 2372 }, "chunk_id": "train_shard_00000_2372_0", "global_id": 2607 }, { "text": "In the present study 114 lactic acid bacteria strains, isolated from raw mare milks from pastoral areas for ethnic minorities in northwest China, were screened for probiotic traits, and their characteristics were compared with those of Lactobacillus rhamnosus GG, a commercial strain. Among the 114 strains identified, the most common species was Pediococcus pentosaceus (n = 52), followed by Leuconostoc lactis (n = 35), Lactobacillus helveticus (n = 7), Lactobacillus plantarum (n = 6), Lactobacillus kefiri (n = 5), Lactobacillus curvatus (n = 4), Lactobacillus paracasei (n = 3), and Lactococcus garvieae (n = 3). Based on acid and bile salt tolerance, 15 strains were further selected. All selected strains were subjected to a series of in vitro tests to assess their technological properties, including cell surface hydrophobicity (13.6-56.2%), autoaggregation ability (9.26-38.30%), coaggregation ability, and heat and lysozyme survival rates (84.74-94.01% and 80.52-99.37%, respectively). In vitro antagonism showed that Lb. plantarum (M5-19, M8-60, M8-59) exhibited the most strong inhibitory activity against 7 tested pathogens. Moreover, antibiotic resistance and hemolytic activity were investigated for safety assessment. No strain exhibited hemolytic activity, and most of the strains were sensitive to a series of 14 antibiotics of clinical importance. Ultimately, the principal component analysis of all data obtained above showed that 2 Lb. plantarum strains (M8-59, M8-60) and Lb. paracasei M1-36 exhibited the best potential for their inclusion as adjunct functional cultures in local fermented dairy products.", "token_count": 495, "char_count": 1629, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6624, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:11.704359", "source": { "split": "train_shard_00000", "doc_id": 2373 }, "chunk_id": "train_shard_00000_2373_0", "global_id": 2608 }, { "text": "Evaluation of indigenous lactic acid bacteria of raw mare milk from pastoral areas in Xinjiang, China, for potential use in probiotic fermented dairy products.", "token_count": 39, "char_count": 159, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:12.060843", "source": { "split": "train_shard_00000", "doc_id": 2373 }, "chunk_id": "train_shard_00000_2373_1", "global_id": 2609 }, { "text": "Bile acids are key components of bile required for human health. In humans and mice, conditions of reduced bile flow, cholestasis, induce bile acid detoxification by producing tetrahydroxylated bile acids (THBA), more hydrophilic and less cytotoxic than the usual bile acids, which are typically di- or tri-hydroxylated. Mice deficient in the Bile Salt Export Pump (Bsep, or Abcb11), the primary bile acid transporter in liver cells, produce high levels of THBA, and avoid the severe liver damage typically seen in humans with BSEP deficiencies. THBA can suppress bile acid-induced liver damage in Mdr2-deficient mice, caused by their lack of phospholipids in bile exposing their biliary tracts to unbound bile acids. Here we review THBA-related works in both animals and humans, and discuss their potential relevance and applications as a class of functional bile acids.\n\nThe protective role of hydrophilic tetrahydroxylated bile acids (THBA).", "token_count": 257, "char_count": 944, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:12.606266", "source": { "split": "train_shard_00000", "doc_id": 2374 }, "chunk_id": "train_shard_00000_2374_0", "global_id": 2610 }, { "text": "The present study reports the multi-technique results of the interaction of a series of bile salts, sodium cholate (NaC), sodium taurocholate (NaTC), sodium deoxycholate (NaDC), and sodium taurodeoxycholate (NaTDC) with trypsin under the experimental conditions of 25 °C and pH 7.0. The interactions between trypsin and the bile salts were characterized by the surface tension measurements and various spectroscopic techniques like UV-Visible absorption, steady-state fluorescence, and circular dichroism. The results of surface tension measurements reveal a strong interaction of trypsin (50 μM) with the increasing concentration of bile salts, being higher with the bile salt of greater hydrophobicity. The critical aggregation concentration of bile salts in the presence of trypsin (C\n\nStructural changes in trypsin induced by the bile salts: An effect of amphiphile hydrophobicity.", "token_count": 228, "char_count": 885, "word_count": 125, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:13.071187", "source": { "split": "train_shard_00000", "doc_id": 2375 }, "chunk_id": "train_shard_00000_2375_0", "global_id": 2611 }, { "text": "Phototrophic eukaryotes have evolved mainly by the primary or secondary uptake of photosynthetic organisms. A return to heterotrophy occurred multiple times in various protistan groups such as Chrysophyceae, despite the expected advantage of autotrophy. It is assumed that the evolutionary shift to mixotrophy and further to heterotrophy is triggered by a differential importance of nutrient and carbon limitation. We sequenced the genomes of 16 chrysophyte strains and compared them in terms of size, function, and sequence characteristics in relation to photo-, mixo- and heterotrophic nutrition. All strains were sequenced with Illumina and partly with PacBio. Heterotrophic taxa have reduced genomes and a higher GC content of up to 59% as compared to phototrophic taxa. Heterotrophs have a large pan genome, but a small core genome, indicating a differential specialization of the distinct lineages. The pan genome of mixotrophs and heterotrophs taken together but not the pan genome of the mixotrophs alone covers the complete functionality of the phototrophic strains indicating a random reduction of genes. The observed ploidy ranges from di- to tetraploidy and was found to be independent of taxonomy or trophic mode. Our results substantiate an evolution driven by nutrient and carbon limitation.\n\nNutrient-driven genome evolution revealed by comparative genomics of chrysomonad flagellates.", "token_count": 346, "char_count": 1401, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:13.648154", "source": { "split": "train_shard_00000", "doc_id": 2376 }, "chunk_id": "train_shard_00000_2376_0", "global_id": 2612 }, { "text": "The study aimed to evaluate the probiotic and safety properties of lactic acid bacterial (LAB) strains isolated from the gut microbiota of honey bee Apis mellifera L., since this source remains a promising reservoir of microbial diversity. A total of five bacterial isolates were molecularly identified using 16S rRNA gene sequencing as Enterococcus faecalis-HBE1, Lactobacillus brevis-HBE2, Enterococcus faecalis-HBE3, Enterococcus faecalis-HBE4 and Lactobacillus casei-HBE5. Gut tolerance conditions (low pH and bile salt) were evaluated. Exopolysaccharides (EPS) production, hemolytic, antioxidant activity, resistance toward antibiotics and technological characteristics (starter activity, pH and proteolysis) were examined. The five isolates showed a high survival rate (>95%), under gastrointestinal tract conditions indicating excellent potential for application as probiotics. The isolates showed no hemolytic activities and good acidification rates in the range of pH 4.6-4.98 after incubation at 37°C for 24h. The isolates exhibited promising proteolytic activity as well as DPPH radical scavenging activity in the range of 16.52-59.39%. All the tested isolates had the capability to produce exopolysaccharides except Lactobacillus casei-HBE5. These results put forward that lactic acid bacterial strain isolated from honey bee workers can be considered as promising candidates for future applications as starter cultures and could constitute new potential probiotics for the production of functional dietary products promoting health benefits.\n\nProbiotic capability of novel lactic acid bacteria isolated from worker honey bees gut microbiota.", "token_count": 430, "char_count": 1654, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [ "HBE5", "HBE4", "HBE2", "HBE1", "HBE3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:14.273124", "source": { "split": "train_shard_00000", "doc_id": 2377 }, "chunk_id": "train_shard_00000_2377_0", "global_id": 2613 }, { "text": "Elizabethkingia are found to cause severe neonatal meningitis, nosocomial pneumonia, endocarditis and bacteremia. However, there are few studies on Elizabethkingia genus by comparative genomic analysis. In this study, three species of Elizabethkingia were found: E. meningoseptica, E. anophelis and E. miricola. Resistance genes and associated proteins of seven classes of antibiotics including beta-lactams, aminoglycosides, macrolides, tetracyclines, quinolones, sulfonamides and glycopeptides, as well as multidrug resistance efflux pumps were identified from 20 clinical isolates of Elizabethkingia by whole-genome sequence. Genotype and phenotype displayed a good consistency in beta-lactams, aminoglycosides and glycopeptides, while contradictions exhibited in tetracyclines, quinolones and sulfonamides. Virulence factors and associated genes such as hsp60 (htpB), exopolysaccharide (EPS) (galE/pgi), Mg2+ transport (mgtB/mgtE) and catalase (katA/katG) existed in all clinical and reference strains. The functional analysis of the clusters of orthologous groups indicated that 'metabolism' occupied the largest part in core genome, 'information storage and processing' was the largest group in both accessory genome and unique genome. Abundant mobile elements were identified in E. meningoseptica and E. anophelis. The most significant finding in our study was that a single clone of E. anophelis had been circulating within diversities of departments in a clinical setting for nearly 18 months.\n\nComparison of three species of Elizabethkingia genus by whole-genome sequence analysis.", "token_count": 417, "char_count": 1591, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.8349, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:14.895897", "source": { "split": "train_shard_00000", "doc_id": 2378 }, "chunk_id": "train_shard_00000_2378_0", "global_id": 2614 }, { "text": "Campylobacter spp. is a significant and prevalent public health hazard globally. Campylobacter jejuni is the most frequently recovered species from human cases and poultry are considered the most important reservoir for its transmission to humans. In this study, 30 Campylobacter jejuni isolates were selected from clinical (n = 15) and broiler (n = 15) sources from a larger cohort, based on source, virulence, and antimicrobial resistance profiles. The objective of this study was to further characterise the genomes of these isolates including MLST types, population structure, pan-genome, as well as virulence and antimicrobial resistance determinants. A total of 18 sequence types and 12 clonal complexes were identified. The most common clonal complex was ST-45, which was found in both clinical and broiler samples. We characterised the biological functions that were associated with the core and accessory genomes of the isolates in this study. No significant difference in the prevalence of virulence or antimicrobial resistance determinants was observed between clinical and broiler isolates, although genes associated with severe illness such as neuABC, wlaN and cstIII were only detected in clinical isolates. The ubiquity of virulence factors associated with motility, invasion and cytolethal distending toxin (CDT) synthesis in both clinical and broiler C. jejuni genomes and genetic similarities between groups of broiler and clinical C. jejuni reaffirm that C. jejuni from poultry remains a significant threat to public health.\n\nGenetic characterisation of a subset of Campylobacter jejuni isolates from clinical and poultry sources in Ireland.", "token_count": 389, "char_count": 1660, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5514, "quality_score": 0.7757, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:15.531912", "source": { "split": "train_shard_00000", "doc_id": 2379 }, "chunk_id": "train_shard_00000_2379_0", "global_id": 2615 }, { "text": "Gamma-aminobutyric acid (GABA) is a principal inhibitory neurotransmitter in the central nervous system and is produced by irreversible decarboxylation of glutamate. It possesses several physiological functions such as neurotransmission, diuretic, and tranquilizer effects and also regulates cardiovascular functions such as blood pressure and heart rate in addition to playing a role in the reduction of pain and anxiety. The objective of this study was to evaluate the GABA producing ability and probiotic capability of certain lactic acid bacteria strains isolated from dairy products. Around sixty-four bacterial isolates were collected and screened for their ability to produce GABA from monosodium glutamate, among which nine isolates were able to produce GABA. The most efficient GABA producer was Enterococcus faecium BS5. Further, assessment of several important and desirable probiotic properties showed that Ent. faecium BS5 was resistant to acid stress, bile salt, and antibiotics. Ent. faecium BS5 may potentially be used for large-scale industrial production of GABA and also for functional fermented product development.\n\nEvaluation of GABA Production and Probiotic Activities of Enterococcus faecium BS5.", "token_count": 291, "char_count": 1220, "word_count": 172, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [ "BS5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:16.102711", "source": { "split": "train_shard_00000", "doc_id": 2380 }, "chunk_id": "train_shard_00000_2380_0", "global_id": 2616 }, { "text": "Among seven strains of lactic acid bacteria (LAB) isolated from traditional dairy products, a Lactobacillus strain was identified through 16S rRNA gene sequencing and tentatively designated as Lactobacillus brevis MK05. This strain demonstrated the highest probiotic potential through biochemical analysis, including acid and bile salt resistance, as well as antibacterial activity. The collected cell-free supernatant (CFC) of L. brevis MK05 culture, compared with MRS broth with pH equal to the pH for CFC, revealed antimicrobial activity against Escherichia coli (ATCC 25922) and Staphylococcus aureus subsp. aureus (ATCC 25923), possibly due to the presence of antibacterial metabolites other than organic acids. This strain was, therefore, selected to assess the biological activity of its partially purified secretory proteins against MCF-7 cancer cells and normal fibroblast cells via the MTT assay. The partially purified cell-secreted proteins of this strain (hereafter referred to as Lb-PPSPs) showed a time and dose-dependent anti-cancer and apoptosis induction function. There was a remarkable decline in the survival rate of MCF-7 cells at doses equal to and higher than 0.5 mg/mL after 48 h. The changes in expression of the three genes involved in the apoptosis pathway (BAX, BCL-2, and BCL2L11) in MCF-7 cells treated with the Lb-PPSPs confirm its cytotoxic activity and apoptosis induction.\n\nA Newly Characterized Potentially Probiotic Strain, Lactobacillus brevis MK05, and the Toxicity Effects of its Secretory Proteins Against MCF-7 Breast Cancer Cells.", "token_count": 449, "char_count": 1573, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6404, "quality_score": 0.8202, "entities": { "genes": [ "MK05" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:16.768265", "source": { "split": "train_shard_00000", "doc_id": 2381 }, "chunk_id": "train_shard_00000_2381_0", "global_id": 2617 }, { "text": "Kazakh cheese is a traditional dairy product in Xinjiang, China. To study the function and potential probiotic characteristics of yeast in Kazakh cheese and its contribution to cheese fermentation, we screened the γ-aminobutyric acid (GABA)-producing yeasts Pichia kudriavzevii 1-21, Kluyveromyces marxianus B13-5, Saccharomyces cerevisiae DL6-20, and Kluyveromyces lactis DY1-10. We investigated the potential probiotic properties of these strains and their use in cheese fermentation (cheeses designated CSP, CSM, CSS, and CSI, respectively); a control with no added yeast was designated CS. The results showed that the 4 yeast strains all showed high self-polymerization (2- and 24-h autoaggregation capacity of >80 and 90%, respectively), hydrophobicity (40-92% variation, low hydrophobicity in xylene, but within the range of probiotics), and the ability to survive the gastrointestinal tract (survival rate >75% after simulation), indicating the probiotic ability of the strains in vitro. The GABA production capacity of the CSM cheese increased (to 95.6 mg/100 g), but its protein content did not change significantly, and amino acid degradation was obvious. The GABA production capacity of the CSS cheese decreased (to 450 mg/kg); its protein content declined, and its amino acid content increased. Except for water and protein, we found no obvious differences in most physical and chemical indicators. Kluyveromyces marxianus B13-5 helped to form the desired texture. Multivariate statistical analysis showed that fermentation of the cheese with the 4 yeasts improved the production of esters and alcohols. The CSS cheese had good aroma production performance, because S", "token_count": 450, "char_count": 1679, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [ "DY1", "DL6" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:17.449466", "source": { "split": "train_shard_00000", "doc_id": 2382 }, "chunk_id": "train_shard_00000_2382_0", "global_id": 2618 }, { "text": "cerevisiae DL6-20 produced high concentrations of isoamyl alcohol, hexanoic acid ethyl ester, benzyl alcohol, octanoic acid ethyl ester, 3-hydroxy-2-butanone, and hexanoic acid; the content of 2-methyl-propanoic acid was low. Compared with the CSP cheese, the CSI and CSM cheeses had a fruitier aroma and a milder odor, but the CSI and CSM cheeses had high concentrations of ethyl acetate, butanoic acid, ethyl ester, 3-methyl-1-butanol-acetate, ethyl hexanoate, ethyl octanoate, acetic acid 2-phenylethyl ester, and ethyl lactate; concentrations of 3-methyl-butanoic acid, propanoic acid, acetic acid, and butanoic acid were low. The CSP cheese had stronger acid-producing ability. The order of fragrance production performance was CSS > CSI, CSM > CSP > CS. Research into the fermentation mechanisms of GABA-producing yeast in cheese will provide a theoretical basis for the quality control and industrial production of Kazakh cheese.\n\nProbiotic potential of γ-aminobutyric acid (GABA)-producing yeast and its influence on the quality of cheese.", "token_count": 324, "char_count": 1047, "word_count": 150, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [ "DL6" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:18.010499", "source": { "split": "train_shard_00000", "doc_id": 2382 }, "chunk_id": "train_shard_00000_2382_1", "global_id": 2619 }, { "text": "Pangenome analyses reveal major clues on evolutionary instances and critical genome core conservation. The order Rhizobiales encompasses several families with rather disparate ecological attitudes. Among them, Rhizobiaceae, Bradyrhizobiaceae, Phyllobacteriacreae and Xanthobacteriaceae, include members proficient in mutualistic symbioses with plants based on the bacterial conversion of N\n\nPangenomics of the Symbiotic Rhizobiales. Core and Accessory Functions Across a Group Endowed with High Levels of Genomic Plasticity.", "token_count": 131, "char_count": 524, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:18.432249", "source": { "split": "train_shard_00000", "doc_id": 2383 }, "chunk_id": "train_shard_00000_2383_0", "global_id": 2620 }, { "text": "Ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO) genes play important roles in CO2 fixation and redox balancing in photosynthetic bacteria. In the present study, the kefir yeast Kluyveromyces marxianus 4G5 was used as host for the transformation of form I and form II RubisCO genes derived from the nonsulfur purple bacterium Rhodopseudomonas palustris using the Promoter-based Gene Assembly and Simultaneous Overexpression (PGASO) method. Hungateiclostridium thermocellum ATCC 27405, a well-known bacterium for its efficient solubilization of recalcitrant lignocellulosic biomass, was used to degrade Napier grass and rice straw to generate soluble fermentable sugars. The resultant Napier grass and rice straw broths were used as growth media for the engineered K. marxianus. In the dual microbial system, H. thermocellum degraded the biomass feedstock to produce both C5 and C6 sugars. As the bacterium only used hexose sugars, the remaining pentose sugars could be metabolized by K. marxianus to produce ethanol. The transformant RubisCO K. marxianus strains grew well in hydrolyzed Napier grass and rice straw broths and produced bioethanol more efficiently than the wild type. Therefore, these engineered K. marxianus strains could be used with H. thermocellum in a bacterium-yeast coculture system for ethanol production directly from biomass feedstocks.\n\nConstruction of engineered RuBisCO Kluyveromyces marxianus for a dual microbial bioethanol production system.", "token_count": 416, "char_count": 1481, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6068, "quality_score": 0.8034, "entities": { "genes": [ "CO2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:19.050560", "source": { "split": "train_shard_00000", "doc_id": 2384 }, "chunk_id": "train_shard_00000_2384_0", "global_id": 2621 }, { "text": "Harnessing the microbiota for beneficial outcomes is limited by our poor understanding of the constituent bacteria, as the functions of most of their genes are unknown. Here, we measure the growth of a barcoded transposon mutant library of the gut commensal Bacteroides thetaiotaomicron on 48 carbon sources, in the presence of 56 stress-inducing compounds, and during mono-colonization of gnotobiotic mice. We identify 516 genes with a specific phenotype under only one or a few conditions, enabling informed predictions of gene function. For example, we identify a glycoside hydrolase important for growth on type I rhamnogalacturonan, a DUF4861 protein for glycosaminoglycan utilization, a 3-keto-glucoside hydrolase for disaccharide utilization, and a tripartite multidrug resistance system specifically for bile salt tolerance. Furthermore, we show that B. thetaiotaomicron uses alternative enzymes for synthesizing nitrogen-containing metabolic precursors based on ammonium availability and that these enzymes are used differentially in vivo in a diet-dependent manner.\n\nFunctional genetics of human gut commensal Bacteroides thetaiotaomicron reveals metabolic requirements for growth across environments.", "token_count": 309, "char_count": 1211, "word_count": 164, "semantic_coherence": 1, "information_density": 0.689, "quality_score": 0.8445, "entities": { "genes": [ "DUF4861" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:19.620541", "source": { "split": "train_shard_00000", "doc_id": 2385 }, "chunk_id": "train_shard_00000_2385_0", "global_id": 2622 }, { "text": "The aim of the study was to investigate the impact of Crohn's disease (CD) on the performance of a lipid-based formulation of ciprofloxacin in a complex gastrointestinal simulator (TIM-1, TNO) and to compare the luminal environment in terms of bile salt and lipid composition in CD and healthy conditions. CD conditions were simulated in the TIM-1 system with a reduced concentration of porcine pancreatin and porcine bile. The bioaccessibility of ciprofloxacin was similar in simulated CD and healthy conditions considering its extent as well as its time course in the jejunum and ileum filtrate. Differences were observed in terms of the luminal concentration of triglycerides, monoglycerides, and fatty acids in the different TIM-1 compartments, indicating a reduction and delay in the lipolysis of formulation excipients in CD. The quantitative analysis of bile salts revealed higher concentrations for healthy conditions (standard TIM-1 fasted-state protocol) in the duodenum and jejunum TIM-1 compartments compared to published data in human intestinal fluids of healthy subjects. The reduced concentrations of bile salts in simulated CD conditions correspond to the levels observed in human intestinal fluids of healthy subjects in the fasted state.A lipidomics approach with ultra performance liquid chromatography (UPLC)/mass spectrometry (MS) has proven to be a time-efficient method to semiquantitatively analyze differences in fatty acid and bile salt levels between healthy and CD conditions. The dynamic luminal environment in CD and healthy conditions after administration of a lipid-based formulation can be simulated using the TIM-1 system. For ciprofloxacin, an altered luminal lipid composition had no impact on its performance indicating a low risk of altered performance in CD patients.\n\nInvestigating the Impact of Crohn's Disease on the Bioaccessibility of a Lipid-Based Formulation with an In Vitro Dynamic Gastrointestinal Model.", "token_count": 473, "char_count": 1954, "word_count": 285, "semantic_coherence": 1, "information_density": 0.4561, "quality_score": 0.7281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:20.261873", "source": { "split": "train_shard_00000", "doc_id": 2386 }, "chunk_id": "train_shard_00000_2386_0", "global_id": 2623 }, { "text": "Bile salt hydrolase (BSH) activity is a desirable trait in putative probiotic bacteria, such as those belonging to the Bifidobacterium genus. On the one hand, bile salt hydrolysis is considered to represent a bile detoxification mechanism for gut commensal bacteria and thus the presence of this activity was believed to be a predictor of bile tolerance of putative probiotic strains. On the other hand, it has recently been revealed that chemical modifications of the bile acid pool performed by the gut microbiota strongly impact on host health. This explains the increasing interest to investigate the role played by bile-modifying enzymes of gut commensals on lowering cholesterol levels, on modulating gut inflammation or on influencing the development of cancer or metabolic disorders. This chapter compiles qualitative and quantitative methods to analyse BSH activity in bifidobacteria, though they could be adapted to other bacterial groups of interest.\n\nDetermination of Bile Salt Hydrolase Activity in Bifidobacteria.", "token_count": 238, "char_count": 1027, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:20.737721", "source": { "split": "train_shard_00000", "doc_id": 2387 }, "chunk_id": "train_shard_00000_2387_0", "global_id": 2624 }, { "text": "F-type plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacterales. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of F-type plasmids from environmental (influent, effluent and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable F-type plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The association of F-type plasmids with AMR may reflect their suitability for rapid niche adaptation.\n\nGenomic network analysis of environmental and livestock F-type plasmid populations.", "token_count": 320, "char_count": 1492, "word_count": 200, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:21.300037", "source": { "split": "train_shard_00000", "doc_id": 2388 }, "chunk_id": "train_shard_00000_2388_0", "global_id": 2625 }, { "text": "Staphylococcus aureus (S. aureus) is an opportunistic pathogen capable of causing serious health implications in susceptible individuals once it invades the host's protective barriers. Methicillin-susceptible S. aureus (MSSA) often receives lesser attention although it has been frequently associated with serious infections in human. We aim to investigate the genomic features of a highly virulent yet pan susceptible MSSA strain (coded as HS-MSSA) which caused concurrent bacteraemia in a dengue patient, ultimately resulted in sepsis death of the patient. Whole genome sequence analysis was performed. The draft genome of HS-MSSA is approximately 2.78 Mb (GC content = 32.7%) comprising of 2637 predicted coding sequences. In silico genotyping of the HS-MSSA strain revealed a novel combined genotype (t091/ST2990). The HS-MSSA carries a SaPIn1-like pathogenicity island that harbours the staphylococcal enterotoxin and enterotoxin-like genes (sec3 and selL). The strain-specific β-lactamase (blaZ)-bearing plasmid region was identified in HS-MSSA. Core genome phylogeny showed that the HS-MSSA strain shared a common ancestry with the European MRSA clone. We report herein the genomic features of an MSSA lineage with novel genotype previously not reported elsewhere.\n\nGenomic analysis revealed a novel genotype of methicillin-susceptible Staphylococcus aureus isolated from a fatal sepsis case in dengue patient.", "token_count": 407, "char_count": 1417, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6751, "quality_score": 0.8376, "entities": { "genes": [ "ST2990" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:21.923847", "source": { "split": "train_shard_00000", "doc_id": 2389 }, "chunk_id": "train_shard_00000_2389_0", "global_id": 2626 }, { "text": "Polygonum multiflorum is a traditional Chinese herbal medicine and has many biological activities such as hair-blacking, anti-atherosclerosis, anti-inflammatory and anti-aging. However, the liver injury induced by P. multiflorum has aroused wide attention in recent years. 2,3,5,4'-tetrahydroxystibane-2-O-β-D-glucoside(TSG) is a main component of P. multiflorum, but the role of TSG in inducing liver injury is unclear. The aim of present study was to evaluate TSG's potential liver injury and effects on bile acid homeostasis and phospholipids efflux. C57 BL/6 J mice received intraperitoneal administration of 400 mg·kg~(-1) of TSG daily for 15 days, and then biochemical indexes of liver injury and changes of phospholipid content were detected. The changes of bile acid compositions were detected by LC-MS/MS. The results showed TSG 400 mg·kg~(-1) significantly increased the content of serum total bile acid(TBA) and alkaline phosphatase(ALP). Elevated free bile acid levels were observed in TSG-treated groups, including β-muricholic acid(β-MCA), ursodeoxycholic acid(UDCA), hyodeoxycholic acid(HDCA), chenodeoxycholic acid(CDCA), deoxcholic acid(DCA) in serum and β-MCA, CDCA in liver. TSG inhibited the protein expression of farnesoid X receptor(FXR) and down stream bile salt export pump(BSEP), which may result in the accumulation of bile acid. TSG also inhibited the expression of 25-hydroxycholesterol-7 alpha-hydroxylase(CYP7 B1), which may disturb the alternative pathway for bile acid synthesis. In addition, intraperitoneal injection of TSG 400 mg·kg~(-1) significantly decreased the content of phospholipids in bile", "token_count": 505, "char_count": 1633, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": { "genes": [ "CYP7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:22.575933", "source": { "split": "train_shard_00000", "doc_id": 2390 }, "chunk_id": "train_shard_00000_2390_0", "global_id": 2627 }, { "text": "The research showed that TSG significantly inhibited the expression of multidrug resistance protein 2(MDR2) and destroyed the regular distribution of MDR2 on the bile duct membrane of liver. In vitro results showed that the IC_(50) of TSG on HepG2 cells was about 1 500 μmol·L~(-1) and TSG at 500 μmol·L~(-1)(for 24 h) could destroy the distribution of MDR2 on the bile duct membrane of liver. In conclusion, TSG induced liver injury by disrupting bile acid homeostasis and phospholipids efflux.\n\n[2,3,5,4'-Tetrahydroxystibane-2-O-β-D-glucoside induces liver injury by disrupting bile acid homeostasis and phospholipids efflux].", "token_count": 209, "char_count": 628, "word_count": 91, "semantic_coherence": 1, "information_density": 0.5824, "quality_score": 0.7912, "entities": { "genes": [ "MDR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:23.038774", "source": { "split": "train_shard_00000", "doc_id": 2390 }, "chunk_id": "train_shard_00000_2390_1", "global_id": 2628 }, { "text": "The genus Lactobacillus is an important component of the gastrointestinal tract of human and animals and commonly considered as probiotic. L. taiwanensis has long been proposed to be a probiotic whereas understanding on this species is still in its infancy. Genomic information of L. taiwanensis is fairly limited. Extensive characterization of its beneficial traits is needed.\n\nComplete genome sequencing of Peyer's patches-derived Lactobacillus taiwanensis CLG01, a potential probiotic with antibacterial and immunomodulatory activity.", "token_count": 135, "char_count": 537, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7671, "quality_score": 0.8836, "entities": { "genes": [ "CLG01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:23.467206", "source": { "split": "train_shard_00000", "doc_id": 2391 }, "chunk_id": "train_shard_00000_2391_0", "global_id": 2629 }, { "text": "In the study on fermented acid rice soup (rice-acid) inoculated with L. paracasei H4-11 and K. marxianus L1-1, the concentrations of main flavor components on the third day of fermentation were significantly higher than those on the first day. Transcriptome analysis and proteome analysis based on RNA sequencing and 4D label-free proteomic techniques were combined to provide new insights into the molecular mechanisms of flavor characteristics and antioxidant activity of the two strains during the development of rice-acid. The key up-regulated genes and proteins in L. paracasei and K. marxianus L1-1, which were involved in flavor formation and antioxidant activity in rice-acid development, were different. The KEGG pathways involving the up-regulated genes and proteins in L. paracasei included starch and sucrose metabolism, pyruvate metabolism, amino sugar, and nucleotide sugar metabolism, and glycolysis/guconeogenesis. The KEGG pathways involving the up-regulated genes and proteins in K. marxianus L1-1 mainly included glycolysis/gluconeogenesis, TCA cycle, pyruvate metabolism, and other pathways related to antioxidant capacity. We successfully identified key genes and proteins associated with the metabolism and accumulation of flavor components and antioxidant activity. These findings provide new insights into the molecular mechanisms of flavor formation in co-cultivation with L. paracasei and K. marxianus. SIGNIFICANCE: It is anticipated that this study would provide us an insight into the mechanisms of flavor components accumulation and antioxidant activity of acid rice soup in China's minority areas. Importantly, this research provides the foundation of biological and chemical analysis for the application of the co-culture of L. paracasei H4-11 and K. marxianus in non-dairy products.", "token_count": 463, "char_count": 1815, "word_count": 255, "semantic_coherence": 1, "information_density": 0.4902, "quality_score": 0.7451, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "metabolism", "fermentation" ], "organisms": [ "marxianus" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:24.104939", "source": { "split": "train_shard_00000", "doc_id": 2392 }, "chunk_id": "train_shard_00000_2392_0", "global_id": 2630 }, { "text": "Integrative transcriptomic-proteomic analysis revealed the flavor formation mechanism and antioxidant activity in rice-acid inoculated with Lactobacillus paracasei and Kluyveromyces marxianus.", "token_count": 51, "char_count": 192, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:24.466211", "source": { "split": "train_shard_00000", "doc_id": 2392 }, "chunk_id": "train_shard_00000_2392_1", "global_id": 2631 }, { "text": "Yeast whole cells have been widely used in modern biotechnology as biocatalysts to generate numerous compounds of industrial, chemical, and pharmaceutical importance. Since many of the biocatalysis-utilizing manufactures have become more concerned about environmental issues, seawater is now considered a sustainable alternative to freshwater for biocatalytic processes. This approach plausibly commenced new research initiatives into exploration of salt-tolerant yeast strains. Recently, there has also been a growing interest in possible applications of microbial biofilms in the field of biocatalysis. In these complex communities, cells demonstrate higher resistance to adverse environmental conditions due to their embedment in an extracellular matrix, in which physical, chemical, and physiological gradients exist. Considering these two topics, seawater and biofilms, in this work, we characterized biofilm formation in seawater-based growth media by several salt-tolerant yeast strains with previously demonstrated biocatalytic capacities. The tested strains formed both air-liquid-like biofilms and biofilms on silicone surfaces, with Debaryomyces fabryi, Schwanniomyces etchellsii, Schwanniomyces polymorphus, and Kluyveromyces marxianus showing the highest biofilm formation. The extracted biofilm extracellular matrices mostly consisted of carbohydrates and proteins. The latter group was primarily represented by enzymes involved in metabolic processes, particularly the biosynthetic ones, and in the response to stimuli. Specific features were also found in the carbohydrate composition of the extracellular matrix, which were dependent both on the yeast isolate and the nature of formed biofilms. Overall, our findings presented herein provide a unique data resource for further development and optimization of biocatalytic processes and applications employing seawater and halotolerant yeast biofilms.Key points• Ability for biofilm formation of some yeast-halotolerant strains in seawater medium• ECM composition dependent on strain and biofilm-forming surface• Metabolic enzymes in the ECM with potential applications for biocatalysis.", "token_count": 487, "char_count": 2153, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:25.115798", "source": { "split": "train_shard_00000", "doc_id": 2393 }, "chunk_id": "train_shard_00000_2393_0", "global_id": 2632 }, { "text": "Formation and characterization of biofilms formed by salt-tolerant yeast strains in seawater-based growth medium.", "token_count": 29, "char_count": 113, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:25.471141", "source": { "split": "train_shard_00000", "doc_id": 2393 }, "chunk_id": "train_shard_00000_2393_1", "global_id": 2633 }, { "text": "Staphylococcus saprophyticus is a primary cause of community-acquired urinary tract infections (UTIs) in young women. S. saprophyticus colonizes humans and animals but basic features of its molecular epidemiology are undetermined. We conducted a phylogenomic analysis of 321 S. saprophyticus isolates collected from human UTIs worldwide during 1997-2017 and 232 isolates from human UTIs and the pig-processing chain in a confined region during 2016-2017. We found epidemiologic and genomic evidence that the meat-production chain is a major source of S. saprophyticus causing human UTIs; human microbiota is another possible origin. Pathogenic S. saprophyticus belonged to 2 lineages with distinctive genetic features that are globally and locally disseminated. Pangenome-wide approaches identified a strong association between pathogenicity and antimicrobial resistance, phages, platelet binding proteins, and an increased recombination rate. Our study provides insight into the origin, transmission, and population structure of pathogenic S. saprophyticus and identifies putative new virulence factors.\n\nFoodborne Origin and Local and Global Spread of Staphylococcus saprophyticus Causing Human Urinary Tract Infections.", "token_count": 319, "char_count": 1222, "word_count": 162, "semantic_coherence": 1, "information_density": 0.679, "quality_score": 0.8395, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:26.028484", "source": { "split": "train_shard_00000", "doc_id": 2394 }, "chunk_id": "train_shard_00000_2394_0", "global_id": 2634 }, { "text": "Pertussis is a vaccine-preventable disease, and its recent resurgence might be attributable to the emergence of strains that differ genetically from the vaccine strain. We describe a novel pertussis isolate-based surveillance system and a core genome multilocus sequence typing scheme to assess Bordetella pertussis genetic variability and investigate the increased incidence of pertussis in Austria. During 2018-2020, we obtained 123 B. pertussis isolates and typed them with the new scheme (2,983 targets and preliminary cluster threshold of <6 alleles). B. pertussis isolates in Austria differed genetically from the vaccine strain, both in their core genomes and in their vaccine antigen genes; 31.7% of the isolates were pertactin-deficient. We detected 8 clusters, 1 of them with pertactin-deficient isolates and possibly part of a local outbreak. National expansion of the isolate-based surveillance system is needed to implement pertussis-control strategies.\n\nIsolate-Based Surveillance of Bordetella pertussis, Austria, 2018-2020.", "token_count": 268, "char_count": 1039, "word_count": 144, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:26.577451", "source": { "split": "train_shard_00000", "doc_id": 2395 }, "chunk_id": "train_shard_00000_2395_0", "global_id": 2635 }, { "text": "Until July 2016, vancomycin-resistantEnterococcus faecium (VREfm) was sporadically detected in Odense University Hospital, Denmark. After July 2016, the number of VREfm cases increased. This study aimed to apply a core genome multilocus sequence typing (cgMLST) scheme for E. faecium to type and analyse VREfm isolates collected at a single Danish hospital and to compare the results with cgMLST data from other regions of Denmark to trace transmission.\n\nUsing core genome multilocus sequence typing (cgMLST) for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak.", "token_count": 165, "char_count": 625, "word_count": 88, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:27.019353", "source": { "split": "train_shard_00000", "doc_id": 2396 }, "chunk_id": "train_shard_00000_2396_0", "global_id": 2636 }, { "text": "Correction to: Transcriptome analysis of the thermotolerant yeast Kluyveromyces marxianus CCT 7735 under ethanol stress.", "token_count": 38, "char_count": 120, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:27.380242", "source": { "split": "train_shard_00000", "doc_id": 2397 }, "chunk_id": "train_shard_00000_2397_0", "global_id": 2637 }, { "text": "Paenibacillus larvae is the causative agent of the fatal American foulbrood disease in honeybees (Apis mellifera). Strain identification is vital for preventing the spread of the disease. To date, the most accessible and robust scheme to identify strains is the multilocus sequence typing (MLST) method. However, this approach has limited resolution, especially for epidemiological studies. As the cost of whole-genome sequencing has decreased and as it becomes increasingly available to most laboratories, an extended MLST based on the core genome (cgMLST) presents a valuable tool for high-resolution investigations. In this study, we present a standardized, robust cgMLST scheme for P. larvae typing using whole-genome sequencing. A total of 333 genomes were used to identify, validate and evaluate 2419 core genes. The cgMLST allowed fine-scale differentiation between samples that had the same profile using traditional MLST and allowed for the characterization of strains impossible by MLST. The scheme was successfully used to trace a localized Swedish outbreak, where a cluster of 38 isolates was linked to a country-wide beekeeping operation. cgMLST greatly enhances the power of a traditional typing scheme, while preserving the same stability and standardization for sharing results and methods across different laboratories.\n\nDevelopment and evaluation of a core genome multilocus sequence typing scheme for Paenibacillus larvae, the deadly American foulbrood pathogen of honeybees.", "token_count": 347, "char_count": 1494, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6279, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:27.989131", "source": { "split": "train_shard_00000", "doc_id": 2398 }, "chunk_id": "train_shard_00000_2398_0", "global_id": 2638 }, { "text": "Recently, probiotic yeasts have become an interesting topic of research all over the world. Saccharomyces cerevisiae is well proven probiotic yeast against several gastrointestinal diseases. Current study aimed to explore the probiotic potential and antibacterial properties of Saccharomyces strains isolated from fresh lychee fruits available in local markets of Karachi, Pakistan. Probiotic potential and antibacterial activity of locally isolated probiotic yeast strains (named as S. cerevisiae BEL 1 and S. cerevisiae BEL 9) was studied against gastrointestinal pathogens using standard in vitro screening methods. Comparative analysis was also carried out with commercially available S. boulardii probiotic preparations. Furthermore, for probiotic potential, all the studied yeast strains were exposed to various stress conditions inherent of gastrointestinal tract i.e., thermo tolerance, pH tolerance, bile salts survivability and osmo-tolerance. Isolated strains (BEL 1 and BEL 9) were able to tolerate at the temperatures (40oC and 45oC), moreover survived in the presence of gastric juices, extreme bile salt concentrations (range 0.5%-2%) and different osmotic stress conditions (1M and 1.5 M NaCl). Optimal growth was observed at 37oC. Similar growth pattern and viability of BEL 1 and 9 was found for most of the stress conditions, when compared with the commercially available strains of S. boulardii. Therefore, isolated yeast strains BEL 1 and 9 will be considered as a potential bio-therapeutic agent because of the promising probiotic potential.\n\nProbiotic potential of Saccharomyces strains isolated from Litchi chinensis (Lychee fruit).", "token_count": 426, "char_count": 1656, "word_count": 234, "semantic_coherence": 1, "information_density": 0.594, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "bile", "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:28.639141", "source": { "split": "train_shard_00000", "doc_id": 2399 }, "chunk_id": "train_shard_00000_2399_0", "global_id": 2639 }, { "text": "The effect of 11 buffers as well as the effect of ionic strength were investigated on the binding between the bile salt taurochenodeoxycholate and the ionic sulfobutylether-β-cyclodextrin. The investigations showed that both ionic strength and competitive binding affected the stability constant. The stability constant for the sulfobutylether-β-cyclodextrin complex increased from 34,400 M\n\nSpecific Buffers Affect the Stability of a Charged Cyclodextrin Complex Via Competitive Binding and Ionic Strength.", "token_count": 135, "char_count": 507, "word_count": 68, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:29.092265", "source": { "split": "train_shard_00000", "doc_id": 2400 }, "chunk_id": "train_shard_00000_2400_0", "global_id": 2640 }, { "text": "Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n = 81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for more than one third of the available genome sequences from South American clinical strains. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli. Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.\n\nGenomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile.", "token_count": 371, "char_count": 1614, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5796, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:30.140558", "source": { "split": "train_shard_00000", "doc_id": 2401 }, "chunk_id": "train_shard_00000_2401_0", "global_id": 2641 }, { "text": "Intrahepatic cholestasis of pregnancy (ICP) is a form of liver disease which is unique to pregnancy with a worldwide prevalence ranging from 0.3% and 5.6% of pregnancies. It is presented with skin pruritus and elevated total serum bile salt and liver function test with unknown etiologic agent but suggested hormonal, environmental and genetic risk factors.\n\nThe Recurrent Liver Disorder of a Pregnant Mother: Intrahepatic Cholestasis of Pregnancy - A Case Report and Literature Review.", "token_count": 127, "char_count": 486, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7162, "quality_score": 0.8581, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:30.528978", "source": { "split": "train_shard_00000", "doc_id": 2402 }, "chunk_id": "train_shard_00000_2402_0", "global_id": 2642 }, { "text": "Salmonella enterica is a pathogenic bacterium responsible for intestinal illness and systemic diseases such as typhoid and paratyphoid fevers. Among clinical manifestation classification, non-typhoidal Salmonella is mainly known as foodborne pathogen associated with the consumption of fecal contaminated food and water. Even though Salmonella hosts include humans and warm-blooded animals, it has been found in non-host environments as river water where the bacteria use different strategies to fitness the environment persisting and establishment. Now with the availability of WGS and bioinformatics tools, we can explore bacterial genomes with higher resolution to increase our understanding of specific genetic signatures among environmental and clinical isolates, being the goal of this work. Pangenome construction allowed the detection of specific environmental and clinical gene clusters related to metabolism and secretion systems as the main signature respectively. Specifically, D-galactonate degradation pathway was observed mainly in environmental genomes while T3SS and flagellum genes were detected for all clinical but not for all environmental isolates. Gene duplication and pseudogenes accumulation were detected as the main adaptation strategy for environmental isolates; thus, isolation source may play an important role in genome plasticity, conferring a selective advantage to survive and persist for environmental Salmonella isolates. Intact prophage sequences with cargo genes were observable for both isolation sources playing an important role in virulence contribution.\n\nGenomic signatures of adaptation to natural settings in non-typhoidal Salmonella enterica Serovars Saintpaul, Thompson and Weltevreden.", "token_count": 352, "char_count": 1733, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:31.104562", "source": { "split": "train_shard_00000", "doc_id": 2403 }, "chunk_id": "train_shard_00000_2403_0", "global_id": 2643 }, { "text": "To elucidate the molecular mechanisms involved in the substrate interaction of the bile salt hydrolase of Lactobacillus reuteri CRL 1098 (LrBSH) with bile acids (BAs) and to evaluate potential enzyme inhibitors based on computer and in vitro modeling assays.\n\nCharacterization of substrate specificity and inhibitory mechanism of bile salt hydrolase from Lactobacillus reuteri CRL 1098 using molecular docking analysis.", "token_count": 117, "char_count": 419, "word_count": 59, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:31.492931", "source": { "split": "train_shard_00000", "doc_id": 2404 }, "chunk_id": "train_shard_00000_2404_0", "global_id": 2644 }, { "text": "The frequency and variety of infections caused by fungi are increasing. However, changes and intercenter and regional differences are observed in the distribution of fungal species over the years. It is important to update the epidemiological data in order to enable early and appropriate treatment. In this retrospective study, the number of fungi isolated from clinical samples, their distribution at the genus/ species level and the variations over the years in Hacettepe University hospital which is a regional center for patients at risk of fungal infection were investigated. For this purpose, laboratory records from 2008- 2019 were examined and 21813 fungal strains isolated from 19636 clinical samples were detected. When the first (2008-2013) and second (2014-2019) six-year periods were compared, a 2.5 fold increase was observed in the number of specimens yielding fungal growth (first period; n= 5620, second period; n= 14016). Fungi were most frequently isolated from urine (45.0%), lower respiratory tract (30.7%) and blood (6.8%) samples. Mould isolation rate in all samples increased significantly in the second six-year period (from 8.3% to 10.6%, p≤ 0.001). As expected, the most frequent yeast was Candida albicans (57.0%) and mould was Aspergillus fumigatus complex (50.4%). In the second six-year period, isolation of C.albicans (59.3% to 56.0%, p≤ 0.001) among yeasts and A.fumigatus complex (58.1% to 48.0%, p≤ 0.001) among moulds decreased significantly. In urine specimens, most common fungi were C.albicans (49.8%), Candida glabrata complex (15.6%), Candida tropicalis (8.9%) and Candida kefyr (7.5%)", "token_count": 485, "char_count": 1627, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:32.145741", "source": { "split": "train_shard_00000", "doc_id": 2405 }, "chunk_id": "train_shard_00000_2405_0", "global_id": 2645 }, { "text": "In lower respiratory tract specimens, the most common mould was A.fumigatus complex (51.2%), which has decreased from 63.7% in the first six years to 47.1% in the second period (p≤ 0.001). Over the same period, other Aspergillus species (from 25.5% to 34.1%, p= 0.002) and non-Aspergillus moulds (from 36.3% to 52.9%, p≤ 0.001) were increased. In blood samples, C.albicans (44.4%), Candida parapsilosis complex (21.5%) and C.glabrata complex (13.0%) were the most frequent species. In the second six-year period, the frequency of C.albicans decreased from 47.3% to 42.2% (p= 0.059) and the frequency of C.glabrata complex increased from 9.5% to 15.5% (p≤ 0.001) when compared to the first period. For the sterile specimens other than blood, the most common species were C.albicans (37.8%), C.glabrata complex (9.1%) and C.parapsilosis complex (4.7%). However, the number of fungal isolates and the distribution of the species showed great variation over the years. In our center, a substantial increase in the number of fungal strains isolated from the clinical specimens were observed over a 12-years period. In addition and similar to previously published reports, the increase of strains belonging to species with decreased antifungal susceptibility and/or species with unknown susceptibility were detected. The use of local data is required in order to implement early and appropriate antifungal treatment because of inter-center and regional differences observed in epidemiological trends regarding the distributions of fungal genera and species. Surveillance studies to be conducted with the participation of large and sufficient numbers of centers in our country, as we have done for our center, will also contribute to approaches regarding the management of fungal infections by revealing the epidemiological data in a comprehensive manner.", "token_count": 519, "char_count": 1848, "word_count": 275, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:22:32.793555", "source": { "split": "train_shard_00000", "doc_id": 2405 }, "chunk_id": "train_shard_00000_2405_1", "global_id": 2646 }, { "text": "[Changing Trends in Isolation Frequencies and Species of Clinical Fungal Strains: What Do the 12-years (2008-2019) Mycology Laboratory Data Tell About?].", "token_count": 54, "char_count": 153, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:33.153183", "source": { "split": "train_shard_00000", "doc_id": 2405 }, "chunk_id": "train_shard_00000_2405_2", "global_id": 2647 }, { "text": "Nosocomial infections caused by enterococci are an ongoing global threat. Thus, finding therapeutic agents for the treatment of such infections are crucial. Some Enterococcus faecalis strains are able to produce antimicrobial peptides called bacteriocins. We analyzed 65 E. faecalis isolates from 43 food samples and 22 clinical samples in Egypt for 17 common bacteriocin-encoding genes of Enterococcus spp. These genes were absent in 11 isolates that showed antimicrobial activity putatively due to bacteriocins (three from food, including isolate OS13, and eight from clinical isolates). The food-isolated E. faecalis OS13 produced bacteriocin-like inhibitory substances (BLIS) named enterocin OS13, which comprised two peptides (enterocin OS13α OS13β) that inhibited the growth of antibiotic-resistant nosocomial E. faecalis and E. faecium isolates. The molecular weights of enterocin OS13α and OS13β were determined as 8079 Da and 7859 Da, respectively, and both were heat-labile. Enterocin OS13α was sensitive to proteinase K, while enterocin OS13β was resistant. Characterization of E. faecalis OS13 isolate revealed that it belonged to sequence type 116. It was non-hemolytic, bile salt hydrolase-negative, gelatinase-positive, and sensitive to ampicillin, penicillin, vancomycin, erythromycin, kanamycin, and gentamicin. In conclusion, BLIS as enterocin OS13α and OS13β represent antimicrobial agents with activities against antibiotic-resistant enterococcal isolates.\n\nPurification and characterization of bacteriocins-like inhibitory substances from food isolated Enterococcus faecalis OS13 with activity against nosocomial enterococci.", "token_count": 474, "char_count": 1646, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6204, "quality_score": 0.8102, "entities": { "genes": [ "OS13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:33.795414", "source": { "split": "train_shard_00000", "doc_id": 2406 }, "chunk_id": "train_shard_00000_2406_0", "global_id": 2648 }, { "text": "The fungal community of the gastrointestinal tract has recently become of interest, and knowledge of its relationship with the development of obesity is scarce. The present study aimed to evaluate the cultivable fungal fraction from the microbiota and to analyze its relationship with obesity.\n\nThe intestinal mycobiota and its relationship with overweight, obesity and nutritional aspects.", "token_count": 87, "char_count": 390, "word_count": 56, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:34.174404", "source": { "split": "train_shard_00000", "doc_id": 2407 }, "chunk_id": "train_shard_00000_2407_0", "global_id": 2649 }, { "text": "The current study aimed to load terconazole (TCZ), an antifungal agent with low permeability characteristics, into highly deformable bilosomes (HBs) for augmenting its topical delivery. HBs contain edge activator in addition to the constituents of traditional bilosomes (Span 60, cholesterol, and bile salts). More elasticity is provided to the membrane of vesicles by the existence of edge activator and is expected to increase the topical permeation of TCZ. HBs were formulated using ethanol injection technique based on 2\n\nFabrication of Highly Deformable Bilosomes for Enhancing the Topical Delivery of Terconazole: In Vitro Characterization, Microbiological Evaluation, and In Vivo Skin Deposition Study.", "token_count": 189, "char_count": 709, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7228, "quality_score": 0.8614, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:34.627458", "source": { "split": "train_shard_00000", "doc_id": 2408 }, "chunk_id": "train_shard_00000_2408_0", "global_id": 2650 }, { "text": "The accessory genomes of many pathogenic bacteria include ABC transporters that scavenge metal by siderophore uptake and ABC transporters that contribute to antimicrobial resistance by multidrug efflux. There are mechanistic and recently recognized structural similarities between siderophore importer proteins and efflux pumps. Here we investigated the influence of siderophore importer YbtPQ on antimicrobial resistance of\n\nA Virulence Associated Siderophore Importer Reduces Antimicrobial Susceptibility of", "token_count": 127, "char_count": 509, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:35.012007", "source": { "split": "train_shard_00000", "doc_id": 2409 }, "chunk_id": "train_shard_00000_2409_0", "global_id": 2651 }, { "text": "The bile salt export pump (BSEP/ABCB11) is located on the apical membrane and mediates the secretion of bile salts from hepatocytes into the bile. BSEP-mediated bile salt efflux is the rate-limiting step of bile salt secretion and the main driving force of bile flow. BSEP drives and maintains the enterohepatic circulation of bile salts. In recent years, research efforts have been focused on understanding the physiological and pathological functions and regulatory mechanisms of BSEP. These studies elucidated the roles of farnesoid X receptor (FXR), AMP-activated protein kinase (AMPK), liver receptor homolog-1(LRH-1) and nuclear factor erythroid 2-related factor 2 (Nrf-2) in BSEP expression and discovered some regulatory factors which participate in its post-transcriptional regulation. A series of liver diseases have also been shown to be related to BSEP expression and dysfunction, such as cholestasis, drug-induced liver injury, and gallstones. Here, we systematically review and summarize recent literature on BSEP structure, physiological functions, regulatory mechanisms, and related diseases.\n\nRegulatory mechanisms of the bile salt export pump (BSEP/ABCB11) and its role in related diseases.", "token_count": 313, "char_count": 1208, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:35.575260", "source": { "split": "train_shard_00000", "doc_id": 2410 }, "chunk_id": "train_shard_00000_2410_0", "global_id": 2652 }, { "text": "The study of the gene repertoires of microbial species, their pangenomes, has become a key part of microbial evolution and functional genomics. Yet, the increasing number of genomes available complicates the establishment of the basic building blocks of comparative genomics. Here, we present PanACoTA (https://github.com/gem-pasteur/PanACoTA), a tool that allows to download all genomes of a species, build a database with those passing quality and redundancy controls, uniformly annotate and then build their pangenome, several variants of core genomes, their alignments and a rapid but accurate phylogenetic tree. While many programs building pangenomes have become available in the last few years, we have focused on a modular method, that tackles all the key steps of the process, from download to phylogenetic inference. While all steps are integrated, they can also be run separately and multiple times to allow rapid and extensive exploration of the parameters of interest. PanACoTA is built in Python3, includes a singularity container and features to facilitate its future development. We believe PanACoTa is an interesting addition to the current set of comparative genomics tools, since it will accelerate and standardize the more routine parts of the work, allowing microbial genomicists to more quickly tackle their specific questions.\n\nPanACoTA: a modular tool for massive microbial comparative genomics.", "token_count": 318, "char_count": 1419, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:36.136079", "source": { "split": "train_shard_00000", "doc_id": 2411 }, "chunk_id": "train_shard_00000_2411_0", "global_id": 2653 }, { "text": "This study was performed to evaluate the diversity and prevalence of yeasts associated with esophageal mycosis in domestic ducks and geese. Fungi were isolated from esophageal lesions of dead animals sent for microbiologic laboratory diagnosis. Species identification using a culture-dependent method was carried out by sequencing of the internal transcribed spacer (ITS)1-5.8S rRNA-ITS2 region. The most frequently isolated yeast was Candida albicans (43.1%) followed by Saccharomyces cerevisiae (17.6%), Candida kefyr (11.7%), Kazachstania bovina (11.7%), Candida lambica (3.9%), and single isolates (1.9%) representing Candida inconspicua, Candida rugosa, Candida pelliculosa, Candida krusei, Magnusiomyces capitatus, and Trichosporon asahii. Our results indicate that a number of potentially pathogenic yeast species can be isolated from esophageal mycosis of waterfowls, but additional studies are needed to make conclusions regarding their possible etiologic role in disease.\n\nUnexpected Diversity of Yeast Species in Esophageal Mycosis of Waterfowls.", "token_count": 296, "char_count": 1057, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7266, "quality_score": 0.8633, "entities": { "genes": [ "ITS2" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:36.703303", "source": { "split": "train_shard_00000", "doc_id": 2412 }, "chunk_id": "train_shard_00000_2412_0", "global_id": 2654 }, { "text": "Necrotizing enterocolitis (NEC) is a significant cause of morbidity and mortality in the neonatal population. Formula feeding is among the many risk factors for developing the condition, a practice often required in the cohort most often afflicted with NEC, preterm infants. While the virtues of many bioactive components of breast milk have been extolled, the ability to digest and assimilate the nutritional components of breast milk is often overlooked. The structure of formula differs from that of breast milk, both in lipid composition and chemical configuration. In addition, formula lacks a critical digestive enzyme produced by the mammary gland, bile salt-stimulated lipase (BSSL). The gastrointestinal system of premature infants is often incapable of secreting sufficient pancreatic enzymes for fat digestion, and pasteurization of donor milk (DM) has been shown to inactivate BSSL, among other important compounds. Incompletely digested lipids may oxidize and accumulate in the distal gut. These lipid fragments are thought to induce intestinal inflammation in the neonate, potentially hastening the development of diseases such as NEC. In this review, differences in breast milk, pasteurized DM, and formula lipids are highlighted, with a focus on the ability of those lipids to be digested and subsequently absorbed by neonates, especially those born prematurely and at risk for NEC.\n\nLipid Composition, Digestion, and Absorption Differences among Neonatal Feeding Strategies: Potential Implications for Intestinal Inflammation in Preterm Infants.", "token_count": 374, "char_count": 1562, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:37.288728", "source": { "split": "train_shard_00000", "doc_id": 2413 }, "chunk_id": "train_shard_00000_2413_0", "global_id": 2655 }, { "text": "This study was undertaken to investigate the starter and probiotic potential of lactic acid bacteria isolated from dromedarian camel's milk using both culture-dependent and -independent approaches and metataxonomic analysis. Strains of lactic acid bacteria recovered were examined in vitro for tolerance to gastric acidity, bile, and lysozyme. Bile salt hydrolysis, serum cholesterol-lowering, oxalate degradation, proteolytic activity, exopolysaccharide production, and cell surface characteristics necessary for colonizing intestinal mucosa were also evaluated. A single strain of the species, Lactobacillus fermentum named NPL280, was selected through multivariate analysis as it harbored potential probiotic advantages and fulfilled safety criteria. The strain assimilated cholesterol, degraded oxalate, produced exopolysaccharides, and proved to be a proficient alternate yogurt starter with good viability in stored bio-yogurt. A sensorial analysis of the prepared bio-yogurt was also found to be exemplary. We conclude that the indigenous L. fermentum strain NPL280 has the desired traits of a starter and adjunct probiotic culture for dairy products.\n\nMetataxonomic analysis of microbiota from Pakistani dromedary camelids milk and characterization of a newly isolated Lactobacillus fermentum strain with probiotic and bio-yogurt starter traits.", "token_count": 344, "char_count": 1353, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8343, "entities": { "genes": [ "NPL280" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:37.859307", "source": { "split": "train_shard_00000", "doc_id": 2414 }, "chunk_id": "train_shard_00000_2414_0", "global_id": 2656 }, { "text": "Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only PAV and positional variation (PosV) but that diversity in CNS is nonrandom, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting roles for conserved and variable CNS in gene regulation. Additionally, our data suggests that transposable elements contribute to CNS variation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.\n\nEvolution of Conserved Noncoding Sequences in Arabidopsis thaliana.", "token_count": 260, "char_count": 1305, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7176, "quality_score": 0.8588, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:38.411664", "source": { "split": "train_shard_00000", "doc_id": 2415 }, "chunk_id": "train_shard_00000_2415_0", "global_id": 2657 }, { "text": "Erysipelothrix sp. isolates obtained from a deadly outbreak in farmed turkeys were sequenced and compared to representatives of the genus. Phylogenetic trees-supported by digital DNA:DNA hybridization and Average Nucleotide Identity-revealed a novel monophyletic clade comprising isolates from pigs, turkeys, and fish, including isolates previously described as E. sp. Strain 2. Genes coding for the SpaC protein, typically found in E. sp. Strain 2, were detected in all isolates of the clade. Therefore, we confirm E. sp. Strain 2 represents a unique species that may be isolated from a broad host range, and the name \"Erysipelothrix takahashiae\" is suggested. Core genome analysis showed that the pathogenic species of this genus, E. rhusiopathiae and the clade E. sp. Strain 2, are enriched in core functionalities related to nutrient uptake and transport, but not necessarily homologous pathways. For instance, whereas the aerobic DctA transporter may uptake C\n\nComparative genomics of a novel clade shed light on the evolution of the genus Erysipelothrix and characterise an emerging species.", "token_count": 288, "char_count": 1097, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:38.969391", "source": { "split": "train_shard_00000", "doc_id": 2416 }, "chunk_id": "train_shard_00000_2416_0", "global_id": 2658 }, { "text": "Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. hyointestinalis subsp. lawsonii which is predominantly recovered from pigs, and C. hyointestinalis subsp. hyointestinalis which can be found in a much wider range of mammalian hosts. Despite C. hyointestinalis being reported as an emerging pathogen, its evolutionary and host-associated diversification patterns are still vastly unexplored. For this reason, we generated whole-genome sequences of 13 C. hyointestinalis subsp. hyointestinalis strains and performed a comprehensive comparative analysis including publicly available C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii genomes, to gain insight into the genomic variation of these differentially-adapted subspecies. Both subspecies are distinct phylogenetic lineages which present an apparent barrier to homologous recombination, suggesting genetic isolation. This is further supported by accessory gene patterns that recapitulate the core genome phylogeny. Additionally, C. hyointestinalis subsp. hyointestinalis presents a bigger and more diverse accessory genome, which probably reflects its capacity to colonize different mammalian hosts unlike C. hyointestinalis subsp. lawsonii that is presumably host-restricted. This greater plasticity in the accessory genome of C. hyointestinalis subsp. hyointestinalis correlates to a higher incidence of genome-wide recombination events, that may be the underlying mechanism driving its diversification. Concordantly, both subspecies present distinct patterns of gene families involved in genome plasticity and DNA repair like CRISPR-associated proteins and restriction-modification systems. Together, our results provide an overview of the genetic mechanisms shaping the genomes of C. hyointestinalis subspecies, contributing to understand the biology of Campylobacter species that are increasingly recognized as emerging pathogens.\n\nPangenome analysis reveals genetic isolation in Campylobacter hyointestinalis subspecies adapted to different mammalian hosts.", "token_count": 495, "char_count": 2091, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:39.626044", "source": { "split": "train_shard_00000", "doc_id": 2417 }, "chunk_id": "train_shard_00000_2417_0", "global_id": 2659 }, { "text": "Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as 'core' or 'dispensable' is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to 'conditionally dispensable', this concept still requires the assignment of genes to distinct groups.\n\nReference-based QUantification Of gene Dispensability (QUOD).", "token_count": 164, "char_count": 684, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7245, "quality_score": 0.8622, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:40.097655", "source": { "split": "train_shard_00000", "doc_id": 2418 }, "chunk_id": "train_shard_00000_2418_0", "global_id": 2660 }, { "text": "The genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. However, the evolutionary factors that define the specific shape of this distribution are not thoroughly understood.\n\nAssessment of assumptions underlying models of prokaryotic pangenome evolution.", "token_count": 93, "char_count": 444, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:40.498923", "source": { "split": "train_shard_00000", "doc_id": 2419 }, "chunk_id": "train_shard_00000_2419_0", "global_id": 2661 }, { "text": "Public health and regulatory agencies worldwide sequence all Listeria monocytogenes isolates obtained as part of routine surveillance and outbreak investigations. Many of these entities submit the sequences to the National Center for Biotechnology Information Pathogen Detection (NCBI PD) database, which groups the L. monocytogenes isolates into single nucleotide polymorphism (SNP) clusters based on a pairwise SNP difference threshold of 50 SNPs. Our goal was to assess whether isolates with metadata that suggest different sources or locations could show evidence for close genetic relatedness indicating a recent common ancestor and a possible unknown common source. We compared the whole genome sequencing (WGS) data of 249 L. monocytogenes isolates sequenced here, which have detailed metadata, with WGS data of nonclinical isolates on NCBI PD. The 249 L. monocytogenes isolates originated from natural environments (n = 91) as well as from smoked fish (n = 62), dairy (n = 56), and deli meat (n = 40) operations in the United States. Using a combination of subtyping by core genome multilocus sequence typing and high-quality SNP, we observed five SNP clusters in which study isolates and SNP cluster isolates seemed to be closely related and either (i) shared the same geolocation but showed different source types (one SNP cluster); (ii) shared the same source type but showed different geolocations (two SNP clusters); or (iii) shared neither source type nor geolocation (two SNP clusters). For one of the two clusters under (iii), there was, however, no strong bootstrap support for a common ancestor shared between the study isolates and SNP cluster isolates, indicating the value of in-depth evolutionary analyses when WGS data are used for traceback and epidemiological investigations. Overall, our results demonstrate that some L. monocytogenes subtypes may be associated with specific locations or commodities; these associations can help in investigations involving multi-ingredient foods such as sandwiches. However, at least some L. monocytogenes subtypes can be widespread geographically and can be associated with different sources, which may present a challenge to traceback investigations involving these subtypes.", "token_count": 514, "char_count": 2238, "word_count": 332, "semantic_coherence": 1, "information_density": 0.6084, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:22:41.158576", "source": { "split": "train_shard_00000", "doc_id": 2420 }, "chunk_id": "train_shard_00000_2420_0", "global_id": 2662 }, { "text": "Identification of Closely Related Listeria monocytogenes Isolates with No Apparent Evidence for a Common Source or Location: A Retrospective Whole Genome Sequencing Analysis.", "token_count": 43, "char_count": 174, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:41.565600", "source": { "split": "train_shard_00000", "doc_id": 2420 }, "chunk_id": "train_shard_00000_2420_1", "global_id": 2663 }, { "text": "Holder pasteurization (HoP; 62.5 °C, 30 min) is commonly used to ensure the microbiological safety of donor human milk (DHM) but diminishes its nutritional properties. A high-temperature short-time (HTST) system was designed as an alternative for human milk banks. The objective of this study was to evaluate the effect of this HTST system on different nutrients and the bile salt stimulated lipase (BSSL) activity of DHM. DHM was processed in the HTST system and by standard HoP. Macronutrients were measured with a mid-infrared analyzer. Lactose, glucose,\n\nHigh-Temperature Short-Time and Holder Pasteurization of Donor Milk: Impact on Milk Composition.", "token_count": 184, "char_count": 655, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7245, "quality_score": 0.8622, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:42.009829", "source": { "split": "train_shard_00000", "doc_id": 2421 }, "chunk_id": "train_shard_00000_2421_0", "global_id": 2664 }, { "text": "Streptococcus uberis is one of the most frequent mastitis-causing pathogens isolated from dairy cows. Further understanding of S. uberis genetics may help elucidate the disease pathogenesis. We compared the genomes of S. uberis isolates cultured from dairy cows located in distinctly different geographic regions of Australia. All isolates had novel multi locus sequence types (MLST) indicating a highly diverse population of S. uberis. Global clonal complexes (GCC) were more conserved. GCC ST86 and GCC ST143 represented 30% of the total isolates (n = 27) and were clustered within different geographic regions. Core genome phylogeny revealed low phylogenetic clustering by region, isolation source, and MLST. Identification of putative sortase (srtA) substrates and generation of a custom putative virulence factor database revealed genes which may explain the affinity of S. uberis for mammary tissue, evasion of antimicrobial efforts and disease pathogenesis. Of 27 isolates, four contained antibiotic resistance genes including an antimicrobial resistance cluster containing mel/mef(A), mrsE, vatD, lnuD, and transposon-mediated lnuC was also identified. These are novel genes for S. uberis, which suggests interspecies lateral gene transfer. The presence of resistance genes across the two geographic regions tested within one country supports the need for a careful, tailored, implementation and monitoring of antimicrobial stewardship.\n\nSequence characterisation and novel insights into bovine mastitis-associated Streptococcus uberis in dairy herds.", "token_count": 405, "char_count": 1559, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [ "ST143", "ST86" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:42.625349", "source": { "split": "train_shard_00000", "doc_id": 2422 }, "chunk_id": "train_shard_00000_2422_0", "global_id": 2665 }, { "text": "Prokaryote genomics started in earnest in 1995, with the complete sequences of two small bacterial genomes, those of Haemophilus influenzae and Mycoplasma genitalium. During the next quarter century, the prokaryote genome database has been growing exponentially, with no saturation in sight. For most of these 25 years, genome sequencing remained limited to cultivable microbes. Together with next-generation sequencing methods, advances in metagenomics and single-cell genomics have lifted this limitation, providing for an increasingly unbiased characterization of the global prokaryote diversity. Advances in computational genomics followed the progress of genome sequencing, even if occasionally lagging behind. Several major new branches of bacteria and archaea were discovered, including Asgard archaea, the apparent closest relatives of eukaryotes and expansive groups of bacteria and archaea with small genomes thought to be symbionts of other prokaryotes. Comparative analysis of numerous prokaryote genomes spanning a wide range of evolutionary distances changed the conceptual foundations of microbiology, supplanting the notion of species genomes with fixed gene sets with that of dynamic pangenomes and the notion of a single Tree of Life (ToL) with a statistical tree-like trend among individual gene trees. Strides were also made towards a theory and quantitative laws of prokaryote genome evolution.\n\nEvolution of Microbial Genomics: Conceptual Shifts over a Quarter Century.", "token_count": 338, "char_count": 1491, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:43.194294", "source": { "split": "train_shard_00000", "doc_id": 2423 }, "chunk_id": "train_shard_00000_2423_0", "global_id": 2666 }, { "text": "Develop a rat model of hilar cholangiocarcinoma for detecting bile salt export pump (Bsep) expression in hilar cholangiocarcinoma tissues, in order to provide a new therapeutic target for the gene therapy of hilar cholangiocarcinoma. Sixty male Wistar rats (body weight, 190 ± 8 g) were randomly divided into three groups (the experimental group, the control group and the sham operation group, n = 20 each) as follows: The three groups were fed a standard diet, the experimental group was injected by cholangiocarcinoma QBC939 cell suspension along the hilar bile duct into the bile duct bifurcation with microsyringe, the control group was injected by normal saline, the sham operation group did not inject anything. Every day assess the rats' mental state, diet, and motion by using Basso-Beattie-Bresnahan and combined behavioral score. At 4 weeks, one rat of the experimental group was sacrificed after it was administered anesthesia, and we recorded changes in hilar bile duct size, texture, and form. This procedure was repeated at 6 weeks. After 6 weeks, hilar cholangiocarcinoma developed only in the experimental group, thereby establishing an experimental model for studying QBC939-induced hilar cholangiocarcinoma. Tumor formation was confirmed by pathological examination, and hilar bile duct tissues were harvested from both the groups. A real-time polymerase chain reaction assay and an immunohistochemical assay were used to analyze the expression of Bsep in hilar bile duct tissues of each group. From the second week, the rats in experimental group began to eat less, and their body mass decreased compared with control group and sham operation group. After 6 weeks, we detected hilar cholangiocarcinoma in the hilar bile duct tissues of 18 rats (90%) in the experimental group", "token_count": 476, "char_count": 1795, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5415, "quality_score": 0.7708, "entities": { "genes": [ "QBC939" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:43.840179", "source": { "split": "train_shard_00000", "doc_id": 2424 }, "chunk_id": "train_shard_00000_2424_0", "global_id": 2667 }, { "text": "In the experimental group with hilar cholangiocarcinoma, we found that the levels of total cholesterol, total bilirubin, and direct bilirubin were higher compared with those in the control group and sham operation group. Simultaneously, muddy stones emerged from the bile ducts of rats in the experimental group. The Bsep/Gapdh mRNA ratio in hilar cholangiocarcinoma, control group and sham operation group differed markedly. Light microscopy revealed a granular pattern of Bsep protein expression which reacted with the anti-Bsep antibody. Each section was randomly divided into six regions, with 80 cells were observed in every region. Sections with > 10% positive cells were designated positive, Sections with < 10% positive cells were designated negative. Each group included 4800 cells. In the experimental group, 1200 cells (25%) were positive, in the control group, 3648 cells (76%) were positive and in the sham operation group 3598 cells (75%) were positive, and this difference was statistically significant. Bsep expression significantly decreased in hilar cholangiocarcinoma of rats than those in control group and sham operation group, suggesting that drugs targeting Bsep are a new strategy for hilar cholangiocarcinoma.\n\nBsep expression in hilar cholangiocarcinoma of rat model.", "token_count": 336, "char_count": 1293, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5316, "quality_score": 0.7658, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:44.407744", "source": { "split": "train_shard_00000", "doc_id": 2424 }, "chunk_id": "train_shard_00000_2424_1", "global_id": 2668 }, { "text": "Chickens are the most common birds on Earth and colibacillosis is among the most common diseases affecting them. This major threat to animal welfare and safe sustainable food production is difficult to combat because the etiological agent, avian pathogenic Escherichia coli (APEC), emerges from ubiquitous commensal gut bacteria, with no single virulence gene present in all disease-causing isolates. Here, we address the underlying evolutionary mechanisms of extraintestinal spread and systemic infection in poultry. Combining population scale comparative genomics and pangenome-wide association studies, we compare E. coli from commensal carriage and systemic infections. We identify phylogroup-specific and species-wide genetic elements that are enriched in APEC, including pathogenicity-associated variation in 143 genes that have diverse functions, including genes involved in metabolism, lipopolysaccharide synthesis, heat shock response, antimicrobial resistance and toxicity. We find that horizontal gene transfer spreads pathogenicity elements, allowing divergent clones to cause infection. Finally, a Random Forest model prediction of disease status (carriage vs. disease) identifies pathogenic strains in the emergent ST-117 poultry-associated lineage with 73% accuracy, demonstrating the potential for early identification of emergent APEC in healthy flocks.\n\nGenome evolution and the emergence of pathogenicity in avian Escherichia coli.", "token_count": 339, "char_count": 1450, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7526, "quality_score": 0.8763, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:44.971272", "source": { "split": "train_shard_00000", "doc_id": 2425 }, "chunk_id": "train_shard_00000_2425_0", "global_id": 2669 }, { "text": "The microbiome-produced enzyme bile salt hydrolase (BSH) plays a central role in human health, but its function remains unclear due to the lack of suitable methods for measuring its activity. Here, we have developed a novel optical tool based on ultrasensitive bioluminescent imaging and demonstrated that this assay can be used for quick and cost-effective quantification of BSH activity across a broad range of biological settings including pure enzymes and bacteria, intact fecal slurries, and noninvasive imaging in live animals, as well as for the assessment of BSH activity in the entire gastrointestinal tract of mice and humans. Using this assay, we showed that certain types of prebiotics are capable of increasing BSH activity of the gut microbiota in vivo and successfully demonstrated potential application of this assay as a noninvasive diagnostic test to predict the clinical status of inflammatory bowel disease (IBD) patients.\n\nNoninvasive imaging and quantification of bile salt hydrolase activity: From bacteria to humans.", "token_count": 238, "char_count": 1040, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6624, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:45.442275", "source": { "split": "train_shard_00000", "doc_id": 2426 }, "chunk_id": "train_shard_00000_2426_0", "global_id": 2670 }, { "text": "Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet.\n\nDetecting high-scoring local alignments in pangenome graphs.", "token_count": 114, "char_count": 511, "word_count": 71, "semantic_coherence": 1, "information_density": 0.8592, "quality_score": 0.9296, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:45.825270", "source": { "split": "train_shard_00000", "doc_id": 2427 }, "chunk_id": "train_shard_00000_2427_0", "global_id": 2671 }, { "text": "The recent pandemic Coronavirus disease-19 outbreak had traumatized global countries since its origin in late December 2019. Though the virus originated in China, it has spread rapidly across the world due its firmly established community transmission. To successfully tackle the spread and further infection, there needs a clear multidimensional understanding of the molecular mechanisms. Henceforth, 942 viral genome sequences were analysed to predict the core genomes crucial in virus life cycle. Additionally, 35 small interfering RNA transcripts were predicted that can target specifically the viral core proteins and reduce pathogenesis. The crystal structure of Covid-19 main protease-6LU7 was chosen as an attractive target due to the factors that there were fewer mutations and whose structure had significant identity to the annotated protein sequence of the core genome. Drug repurposing of both recruiting and non recruiting drugs was carried out through molecular docking procedures to recognize bitolterol as a good inhibitor of Covid-19 protease. The study was extended further to screen antiviral phytocompounds through quantitative structure activity relationship and molecular docking to identify davidigenin, from licorice as the best novel lead with good interactions and binding energy. The docking of the best compounds in all three categories was validated with molecular dynamics simulations which implied stable binding of the drug and lead molecule. Though the studies need clinical evaluations, the results are suggestive of curbing the pandemic.\n\nFrom genomes to molecular dynamics - A bottom up approach in extrication of SARS CoV-2 main protease inhibitors.", "token_count": 354, "char_count": 1687, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:46.402001", "source": { "split": "train_shard_00000", "doc_id": 2428 }, "chunk_id": "train_shard_00000_2428_0", "global_id": 2672 }, { "text": "Bread wheat (Triticum aestivum) is one of the world's most important crops; however, a low level of genetic diversity within commercial breeding accessions can significantly limit breeding potential. In contrast, wheat relatives exhibit considerable genetic variation and so potentially provide a valuable source of novel alleles for use in breeding new cultivars. Historically, gene flow between wheat and its relatives may have contributed novel alleles to the bread wheat pangenome. To assess the contribution made by wheat relatives to genetic diversity in bread wheat, we used markers based on single nucleotide polymorphisms to compare bread wheat accessions, created in the past 150 years, with 45 related species. We show that many bread wheat accessions share near-identical haplotype blocks with close relatives of wheat's diploid and tetraploid progenitors, while some show evidence of introgressions from more distant species and structural variation between accessions. Hence, introgressions and chromosomal rearrangements appear to have made a major contribution to genetic diversity in cultivar collections. As gene flow from relatives to bread wheat is an ongoing process, we assess the impact that introgressions might have on future breeding strategies.\n\nThe role of gene flow and chromosomal instability in shaping the bread wheat genome.", "token_count": 288, "char_count": 1357, "word_count": 198, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:46.957204", "source": { "split": "train_shard_00000", "doc_id": 2429 }, "chunk_id": "train_shard_00000_2429_0", "global_id": 2673 }, { "text": "Primary bile acids (BAs) are a collection of host-synthesized metabolites that shape physiology and metabolism. BAs transit the gastrointestinal tract and are subjected to a variety of chemical transformations encoded by indigenous bacteria. The resulting microbiota-derived BA pool is a mediator of host-microbiota interactions. Bacterial bile salt hydrolases (BSHs) cleave the conjugated glycine or taurine from BAs, an essential upstream step for the production of deconjugated and secondary BAs. Probiotic lactobacilli harbor a considerable number and diversity of BSHs; however, their contribution to", "token_count": 159, "char_count": 605, "word_count": 83, "semantic_coherence": 1, "information_density": 0.8072, "quality_score": 0.9036, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:47.395075", "source": { "split": "train_shard_00000", "doc_id": 2430 }, "chunk_id": "train_shard_00000_2430_0", "global_id": 2674 }, { "text": "Targeting the ileal bile salt transporter in the treatment of non-alcoholic fatty liver disease.", "token_count": 25, "char_count": 96, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:47.749912", "source": { "split": "train_shard_00000", "doc_id": 2431 }, "chunk_id": "train_shard_00000_2431_0", "global_id": 2675 }, { "text": "The protozoan Trypanosoma cruzi almost invariably establishes life-long infections in humans and other mammals, despite the development of potent host immune responses that constrain parasite numbers. The consistent, decades-long persistence of T. cruzi in human hosts arises at least in part from the remarkable level of genetic diversity in multiple families of genes encoding the primary target antigens of anti-parasite immune responses. However, the highly repetitive nature of the genome-largely a result of these same extensive families of genes-have prevented a full understanding of the extent of gene diversity and its maintenance in T. cruzi. In this study, we have combined long-read sequencing and proximity ligation mapping to generate very high-quality assemblies of two T. cruzi strains representing the apparent ancestral lineages of the species. These assemblies reveal not only the full repertoire of the members of large gene families in the two strains, demonstrating extreme diversity within and between isolates, but also provide evidence of the processes that generate and maintain that diversity, including extensive gene amplification, dispersion of copies throughout the genome and diversification via recombination and in situ mutations. Gene amplification events also yield significant copy number variations in a substantial number of genes presumably not required for or involved in immune evasion, thus forming a second level of strain-dependent variation in this species. The extreme genome flexibility evident in T. cruzi also appears to create unique challenges with respect to preserving core genome functions and gene expression that sets this species apart from related kinetoplastids.\n\nStrain-specific genome evolution in Trypanosoma cruzi, the agent of Chagas disease.", "token_count": 369, "char_count": 1808, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6231, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:48.331629", "source": { "split": "train_shard_00000", "doc_id": 2432 }, "chunk_id": "train_shard_00000_2432_0", "global_id": 2676 }, { "text": "Cholestatic liver injury is frequently associated with drug inhibition of bile salt transporters, such as the bile salt export pump (BSEP). Reliable\n\nMachine Learning Models to Predict Inhibition of the Bile Salt Export Pump.", "token_count": 58, "char_count": 225, "word_count": 34, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:48.697003", "source": { "split": "train_shard_00000", "doc_id": 2433 }, "chunk_id": "train_shard_00000_2433_0", "global_id": 2677 }, { "text": "The two-component system (TCS) helps bacteria sense and respond to environmental stimuli through histidine kinases and response regulators. TCSs are the largest family of multistep signal transduction processes, and they are involved in many important cellular processes such as antibiotic resistance, pathogenicity, quorum sensing, osmotic stress, and biofilms. Here, we perform the first comprehensive study to highlight the role of TCSs as potential drug targets against ESKAPEE (\n\nPangenome Analytics Reveal Two-Component Systems as Conserved Targets in ESKAPEE Pathogens.", "token_count": 138, "char_count": 576, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:49.127177", "source": { "split": "train_shard_00000", "doc_id": 2434 }, "chunk_id": "train_shard_00000_2434_0", "global_id": 2678 }, { "text": "Porcine Parvovirus (PPV) is a Parvovirinae virus that can cause embryonic and fetal loss and death and mummification in affected fetal pigs. Unlike conventional vaccines, virus-like particles (VLPs) inherit the natural structure of their authentic virions and highly immunostimulatory that can induce strong humoral immune and T cell responses with no risk of pathogenicity. The production of PPV VLPs is still a challenge based on traditional expression platforms due to their low yields and high culture costs. Kluyveromyces marxianus is a safe and fast-growing eukaryote that can get high biomass with low-cost cultures. In this study, we investigated the expression and downstream processes of PPV VLPs in K. marxianus, and the potential for effective stand-alone vaccines.\n\nInvestigation of Kluyveromyces marxianus as a novel host for large-scale production of porcine parvovirus virus-like particles.", "token_count": 229, "char_count": 906, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6894, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:49.597003", "source": { "split": "train_shard_00000", "doc_id": 2435 }, "chunk_id": "train_shard_00000_2435_0", "global_id": 2679 }, { "text": "Cholera, a rapidly dehydrating diarrheal disease caused by toxigenic Vibrio cholerae, is a leading cause of morbidity and mortality in some regions of the world. Core genome multilocus sequence typing (cgMLST) is a promising approach in generating genetic fingerprints from whole-genome sequencing (WGS) data for strain comparison among laboratories.\n\ncgMLST@Taiwan: A web service platform for Vibrio cholerae cgMLST profiling and global strain tracking.", "token_count": 122, "char_count": 454, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8413, "quality_score": 0.9206, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:49.984181", "source": { "split": "train_shard_00000", "doc_id": 2436 }, "chunk_id": "train_shard_00000_2436_0", "global_id": 2680 }, { "text": "Optimizing protein intake for very low birth weight (<1,500 g) infants is fundamental to prevent faltering postnatal growth with the potential association of impaired neurodevelopment. The protein content of human milk is not sufficient to support the growth of very low birth weight infants. To meet their elevated protein requirements, human milk is currently fortified using typically bovine milk-based protein isolates (>85% on a dry basis). However, these products have several limitations for use in this vulnerable population. To overcome the shortcomings of bovine milk-based protein supplement, a human milk protein concentrate (HMPC) was developed. In preliminary attempts using 10 kDa ultrafiltration (UF) membranes, it was not possible to reach the protein content of commercial protein isolates, presumably due to the retention of human milk oligosaccharides (HMO). Consequently, it was hypothesized that the use of a UF membrane with a higher molecular weight cut-off (50 kDa rather than 10 kDa) could improve the transmission of carbohydrates, including HMO, in the permeate, thus increasing the protein purity of the subsequent HMPC. The results showed that permeate fluxes during the concentration step were similar to either UF molecular weight cut-off, but the 50-kDa membrane had a higher permeate flux during the diafiltration sequence. However, it was not sufficient to increase the protein purity of the human milk retentate, as both membranes generated HMPC with similar protein contents of 48.8% (10 kDa) and 50% (50 kDa) on a dry basis. This result was related to the high retention of HMO, mainly during the concentration step, although the diafiltration step was efficient to decrease their content in the HMPC. As the major bioactive proteins (lactoferrin, lysozyme, bile salt stimulated lipase, and α1-antitrypsin) in human milk were detected in both HMPC, the 50-kDa membrane seems the most appropriate to the preparation of HMPC in terms of permeation flux values. However, improving the separation of HMO from proteins is essential to increase the protein purity of HMPC.", "token_count": 519, "char_count": 2104, "word_count": 321, "semantic_coherence": 1, "information_density": 0.5265, "quality_score": 0.7632, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:22:50.618290", "source": { "split": "train_shard_00000", "doc_id": 2437 }, "chunk_id": "train_shard_00000_2437_0", "global_id": 2681 }, { "text": "The ultrafiltration molecular weight cut-off has a limited effect on the concentration and protein profile during preparation of human milk protein concentrates.", "token_count": 29, "char_count": 161, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:50.975643", "source": { "split": "train_shard_00000", "doc_id": 2437 }, "chunk_id": "train_shard_00000_2437_1", "global_id": 2682 }, { "text": "Pan-genomic studies aim at representing the entire sequence diversity within a species to provide useful resources for evolutionary studies, functional genomics and breeding of cultivated plants. Cost reductions in high-throughput sequencing and advances in sequence assembly algorithms have made it possible to create multiple reference genomes along with a catalogue of all forms of genetic variations in plant species with large and complex or polyploid genomes. In this review, we summarize the current approaches to building pan-genomes as an in silico representation of plant sequence diversity and outline relevant methods for their effective utilization in linking structural with phenotypic variation. We propose as future research avenues (i) transcriptomic and epigenomic studies across multiple reference genomes and (ii) the development of user-friendly and feature-rich pan-genome browsers.\n\nBuilding pan-genome infrastructures for crop plants and their use in association genetics.", "token_count": 200, "char_count": 996, "word_count": 137, "semantic_coherence": 1, "information_density": 0.708, "quality_score": 0.854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:51.427159", "source": { "split": "train_shard_00000", "doc_id": 2438 }, "chunk_id": "train_shard_00000_2438_0", "global_id": 2683 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) is an important food-borne pathogen capable of causing severe gastrointestinal diseases in humans. Cattle and sheep are the natural reservoir hosts of STEC strains. Previously, we isolated 56 STEC strains from anal and carcass swab samples of cattle and sheep in farms and slaughterhouses. In this study, we performed whole-genome sequencing of these isolates and determined their serotypes, virulence profiles, sequence types (STs) and genetic relationships. Our results showed that the 56 isolates belong to 20 different STs, 29 O:H serotypes and 8 stx subtype combinations. The highly prevalent serotypes for bovine and ovine isolates were O8:H25 and O87:H16, respectively. Five serotypes of cattle or sheep isolates are novel. The majority (63%) of cattle isolates contain stx1 + stx2, subtyped into stx1a, stx2a and stx2c. In contrast, most of the sheep isolates contain stx1 only, primarily subtyped into stx1a and stx1c. None of the isolates tested eae-positive, but virulence factors such as ehxA and espP were present with variable prevalence rates. The prevalence of saa (19.6%) and espP (12.5%) in cattle isolates is much higher than that in sheep isolates, whereas that of subA (34%), katP (14.3%) and ireA (28.6%) in sheep isolates is considerably higher than that in cattle isolates. Core-genome SNP analysis revealed that the majority of isolates could be clustered based on their serotypes or STs, whereas some clustering is associated with more than one ST or serotype. Five sheep isolates (4 belonging to ST675 and serotype O76:H19 and 1 belonging to ST25 and serotype O128:H2) share STs, serotypes and stx profiles with two hemolytic uremic syndrome-associated enterohemorrhagic E", "token_count": 508, "char_count": 1745, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6142, "quality_score": 0.8071, "entities": { "genes": [ "ST25", "ST675" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:52.121527", "source": { "split": "train_shard_00000", "doc_id": 2439 }, "chunk_id": "train_shard_00000_2439_0", "global_id": 2684 }, { "text": "coli (HUSEC) isolates; a cattle isolate belonging to the same ST as HUSEC isolate HUSEC001 contains all the nine virulence genes tested. These data suggest a potential of the six isolates for causing severe human infections. Collectively, we described the characteristics of cattle and sheep STEC isolates from Xinjiang, China, which may be utilized in comparative studies of other geographic regions and sources of isolation, and for surveillance as well.\n\nCharacterization of Shiga toxin-producing Escherichia coli isolated from Cattle and Sheep in Xinjiang province, China, using whole-genome sequencing.", "token_count": 149, "char_count": 607, "word_count": 88, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "HUSEC001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:52.575198", "source": { "split": "train_shard_00000", "doc_id": 2439 }, "chunk_id": "train_shard_00000_2439_1", "global_id": 2685 }, { "text": "Spontaneous cereal fermentations involve diverse lactic acid bacteria (LAB) and yeasts which may include multifunctional and safe or unsafe strains. This study assessed acidification ability, safety, antifungal activity and free amino acids release ability of LAB and yeasts previously isolated from spontaneously fermented cereal doughs in Benin. Fourteen LAB and thirteen yeast strains were studied in liquid media and/or in a model cereal dough prepared in laboratory conditions. Antifungal activity was assessed against Candida glabrata in liquid medium. Amino acids were determined by pre-column derivatization and separation with reversed-phase HPLC. Antimicrobial susceptibility was analysed by minimum inhibitory concentration determination. The acidification ability was higher for LAB compared to yeast strains. All LAB strains retarded the growth of C. glabrata Cg1 with the highest inhibition recorded for Weissella confusa Wc1 and Wc2. The highest free amino acid content was found in the doughs fermented with Pichia kudriavzevii Pk2 and Pk3. All the LAB strains were susceptible to ampicillin, chloramphenicol, erythromycin, but displayed phenotypic resistance to kanamycin, streptomycin and tetracycline. Positive PCR amplicon of resistance genes were detected in the following cases: 2 LAB strains were positive for kanamycin (aph(3)III), 5 strains were positive for streptomycin (aadA and/or strA and/or strB) and 3 strains were positive for tetracycline (tet (L) and/or tet (M)). For yeasts, most of the P. kudriavzevii strains were resistant to amphotericin B, fluconazole and itraconazole opposite to K. marxianus and Saccharomyces cerevisiae strains which were susceptible. The results obtained are valuable for selecting safe and multifunctional strains for cereal fermentation in West Africa.", "token_count": 488, "char_count": 1816, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:53.257948", "source": { "split": "train_shard_00000", "doc_id": 2441 }, "chunk_id": "train_shard_00000_2441_0", "global_id": 2686 }, { "text": "Multifunctional properties and safety evaluation of lactic acid bacteria and yeasts associated with fermented cereal doughs.", "token_count": 26, "char_count": 124, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:53.652640", "source": { "split": "train_shard_00000", "doc_id": 2441 }, "chunk_id": "train_shard_00000_2441_1", "global_id": 2687 }, { "text": "The binding of ferulic acid (FA) with sodium deoxycholate (NaDC) has been investigated using fluorescence and absorption measurements. The fluorescence probe technique of pyrene reveals that the presence of FA favors the micellization of NaDC, leading to the decreased critical micelle concentrations for the formation of NaDC micelles. As NaDC molecules change gradually from monomers via primary micelles into secondary micelles, the intensities of absorption and fluorescence spectra of FA increase at low NaDC concentrations, but decrease suddenly at intermediate NaDC concentrations, and finally increase again at high NaDC concentrations. These results corroborated well with FA fluorescence lifetime data suggesting that the aryl ring of FA hydrophobically binds to the convex surface of NaDC monomers, whereas the hydrogen bonding between FA and NaDC is significantly involved in NaDC primary micelles, which is gradually overcome by the hydrophobic interaction between FA and NaDC secondary micelles. The absorption and fluorescence spectra as well as the binding constant value of FA indicate the strong binding of FA in the large hydrophobic core of NaDC secondary micelles. At low FA concentrations, the measurement of FA anisotropy suggests that FA can increase the packing order of hydrophobic surfaces in NaDC secondary micelles, whereas the high amount of FA can greatly disrupt the packing structure of NaDC secondary micelles which is ascribed to the formation of FA dimers. The spectroscopic experiments outlined here present the binding events of FA with NaDC monomers and primary and secondary micelles, which are significantly related with the hydrophobic force and hydrogen bonding as well as the unique structural characteristics of bile salt.\n\nSpectroscopic Investigation into the Binding of Ferulic Acid with Sodium Deoxycholate: Hydrophobic Force Versus Hydrogen Bonding.", "token_count": 422, "char_count": 1898, "word_count": 278, "semantic_coherence": 1, "information_density": 0.4604, "quality_score": 0.7302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:54.276794", "source": { "split": "train_shard_00000", "doc_id": 2442 }, "chunk_id": "train_shard_00000_2442_0", "global_id": 2688 }, { "text": "This systematic review aimed at investigating longitudinal changes in human milk bioactive protein concentrations in Chinese population. Both English and Chinese databases were searched. The data were pooled into six defined lactation stages. Weighted means of protein concentrations in each stage and the statistical significance of means of different lactation stages were calculated. The data of 11 bioactive proteins were retrieved. Concentrations of sIgA, IgM, and IgG decreased sharply during the first 14 days of lactation. The levels of α-lactalbumin, lactoferrin, and β-casein also decreased throughout lactation. Conversely, lysozyme levels increased over lactation. The changing patterns of the serum albumin, osteopontin, and bile salt-stimulated lipase (BSSL) were not conclusive. This study represents the most comprehensive summary of bioactive proteins in Chinese human milk. In the future, mass spectrometry-based analysis of human milk proteomics may be used to investigate the longitudinal changes of many more bioactive proteins.\n\nLongitudinal changes in the bioactive proteins in human milk of the Chinese population: A systematic review.", "token_count": 273, "char_count": 1159, "word_count": 162, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:54.827794", "source": { "split": "train_shard_00000", "doc_id": 2443 }, "chunk_id": "train_shard_00000_2443_0", "global_id": 2689 }, { "text": "The mechanistic understanding of bile salt disposition is not well established in suspension human hepatocytes (SHH) because of the limited information on the expression and function of bile salt export protein (BSEP) in this system. We investigated the transport function of BSEP in SHH using a method involving in situ biosynthesis of bile salts from their precursor bile acids, cholic acid (CA) and chenodeoxycholic acid (CDCA). Our data indicated that glycine- and taurine-conjugated CA and CDCA were generated efficiently and transported out of hepatocytes in a concentration- and time-dependent manner. We also observed that the membrane protein abundance of BSEP was similar between SHH and sandwich-cultured human hepatocytes. Furthermore, known cholestatic agents significantly inhibited G-CA and G-CDCA efflux in SHH. Interestingly, cyclosporine A, troglitazone, itraconazole, loratadine, and lovastatin inhibited G-CA efflux more potently than G-CDCA efflux (3- to 5-fold). Because of these significant differential effects on G-CA and G-CDCA efflux inhibition, we determined the IC\n\nFunction and Expression of Bile Salt Export Pump in Suspension Human Hepatocytes.", "token_count": 313, "char_count": 1176, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:55.391478", "source": { "split": "train_shard_00000", "doc_id": 2444 }, "chunk_id": "train_shard_00000_2444_0", "global_id": 2690 }, { "text": "Among bioactive phytochemicals, ellagic acid (EA) is one of the most controversial because its high antioxidant and cancer-preventing effects are strongly inhibited by low gastrointestinal absorption and rapid excretion. Strategies toward an increase of solubility in water and bioavailability, while preserving its structural integrity and warranting its controlled release at the physiological targets, are therefore largely pursued. In this work, EA lysine salt at 1:4 molar ratio (EALYS), exhibiting a more than 400 times increase of water solubility with respect to literature reports, was incorporated at 10% in low methoxylated (LM) and high methoxylated (HM) pectin films. The release of EA in PBS at pH 7.4 from both film preparations was comparable and reached 15% of the loaded compound over 2 h. Under simulated gastric conditions, release of EA from HM and LM pectin films was minimal at gastric pH, whereas higher concentrations-up to 300 μM, corresponding to ca. 50% of the overall content-were obtained in the case of the HM pectin film after 2 h incubation at the slightly alkaline pH of small intestine environment, with the enzyme and bile salt components enhancing the release. EALYS pectin films showed a good prebiotic activity as evaluated by determination of short chain fatty acids (SCFAs) levels following microbial fermentation, with a low but significant increase of the effects produced by the pectins themselves. Overall, these results highlight pectin films loaded with EALYS salt as a promising formulation to improve administration and controlled release of the compound.\n\nPectin-Based Formulations for Controlled Release of an Ellagic Acid Salt with High Solubility Profile in Physiological Media.", "token_count": 439, "char_count": 1731, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6183, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:56.015743", "source": { "split": "train_shard_00000", "doc_id": 2445 }, "chunk_id": "train_shard_00000_2445_0", "global_id": 2691 }, { "text": "The bile salt export pump (BSEP/ABCB11) is responsible for the transport of bile salts from hepatocytes into bile canaliculi. Malfunction of this transporter results in progressive familial intrahepatic cholestasis type 2 (PFIC2), benign recurrent intrahepatic cholestasis type 2 (BRIC2) and intrahepatic cholestasis of pregnancy (ICP). Over the past few years, several small molecular weight compounds have been identified, which hold the potential to treat these genetic diseases (chaperones and potentiators). As the treatment response is mutation-specific, genetic analysis of the patients and their families is required. Furthermore, some of the mutations are refractory to therapy, with the only remaining treatment option being liver transplantation. In this review, we will focus on the molecular structure of ABCB11, reported mutations involved in cholestasis and current treatment options for inherited BSEP deficiencies.\n\nThe Bile Salt Export Pump: Molecular Structure, Study Models and Small-Molecule Drugs for the Treatment of Inherited BSEP Deficiencies.", "token_count": 266, "char_count": 1068, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6622, "quality_score": 0.8311, "entities": { "genes": [ "PFIC2", "ABCB11", "BRIC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:56.572235", "source": { "split": "train_shard_00000", "doc_id": 2446 }, "chunk_id": "train_shard_00000_2446_0", "global_id": 2692 }, { "text": "Microbial bioproduction of chemicals, proteins, and primary metabolites from cheap carbon sources is currently an advancing area in industrial research. The model yeast, Saccharomyces cerevisiae, is a well-established biorefinery host that has been used extensively for commercial manufacturing of bioethanol from myriad carbon sources. However, its Crabtree-positive nature often limits the use of this organism for the biosynthesis of commercial molecules that do not belong in the fermentative pathway. To avoid extensive strain engineering of S. cerevisiae for the production of metabolites other than ethanol, non-conventional yeasts can be selected as hosts based on their natural capacity to produce desired commodity chemicals. Non-conventional yeasts like Kluyveromyces marxianus, K. lactis, Yarrowia lipolytica, Pichia pastoris, Scheffersomyces stipitis, Hansenula polymorpha, and Rhodotorula toruloides have been considered as potential industrial eukaryotic hosts owing to their desirable phenotypes such as thermotolerance, assimilation of a wide range of carbon sources, as well as ability to secrete high titers of protein and lipid. However, the advanced metabolic engineering efforts in these organisms are still lacking due to the limited availability of systems and synthetic biology methods like in silico models, well-characterised genetic parts, and optimized genome engineering tools. This review provides an insight into the recent advances and challenges of systems and synthetic biology as well as metabolic engineering endeavours towards the commercial usage of non-conventional yeasts. Particularly, the approaches in emerging non-conventional yeasts for the production of enzymes, therapeutic proteins, lipids, and metabolites for commercial applications are extensively discussed here. Various attempts to address current limitations in designing novel cell factories have been highlighted that include the advances in the fields of genome-scale metabolic model reconstruction, flux balance analysis, 'omics'-data integration into models, genome-editing toolkit development, and rewiring of cellular metabolisms for desired chemical production. Additionally, the understanding of metabolic networks using", "token_count": 503, "char_count": 2234, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:57.218663", "source": { "split": "train_shard_00000", "doc_id": 2447 }, "chunk_id": "train_shard_00000_2447_0", "global_id": 2693 }, { "text": "Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts.", "token_count": 25, "char_count": 123, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:57.580551", "source": { "split": "train_shard_00000", "doc_id": 2447 }, "chunk_id": "train_shard_00000_2447_1", "global_id": 2694 }, { "text": "Bacteria from the same species can differ widely in their gene content. In Escherichia coli, the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. Although recent advances in bacterial genomics have unravelled genes required for fitness in various experimental conditions, most studies have focused on single model strains. As a result, the impact of the species' genetic diversity on core processes of the bacterial cell remains largely under-investigated. Here, we have developed a CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely related species. We have applied it to assess the importance of ~3,400 nearly ubiquitous genes in three growth conditions in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens revealed extensive variations in gene essentiality between strains and conditions. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we have shown how prophage-encoded defence systems against phage infection can trigger the essentiality of persistent genes that are usually non-essential. This study provides broad insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species under diverse conditions.\n\nThe impact of genetic diversity on gene essentiality within the Escherichia coli species.", "token_count": 327, "char_count": 1594, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:58.141997", "source": { "split": "train_shard_00000", "doc_id": 2448 }, "chunk_id": "train_shard_00000_2448_0", "global_id": 2695 }, { "text": "Banana vascular wilt or Moko is a disease caused by Ralstonia solanacearum. This study aimed to sequence, assemble, annotate, and compare the genomes of R. solanacearum Moko ecotypes of different sequevar strains from Brazil. Average nucleotide identity analyses demonstrated a high correlation (> 96%) between the genome sequences of strains CCRMRs277 (sequevar IIA-24), CCRMRs287 (IIB-4), CCRMRs304 (IIA-24), and CCRMRsB7 (IIB-25), which were grouped into phylotypes IIA and IIB. The number of coding sequences present in chromosomes and megaplasmids varied from 3,070 to 3,521 and 1,669 to 1,750, respectively. Pangenome analysis identified 3,378 clusters in the chromosomes, of which 2,604 were shared by all four analyzed genomes and 2,580 were single copies. In megaplasmids, 1,834 clusters were identified, of which 1,005 were shared by all four genomes and 992 were identified as single copies. Strains CCRMRsB7 and CCRMRs287 differed from the others by having unique clusters in both their chromosomes and megaplasmids, and CCRMRsB7 possessed the largest genome among all Moko ecotype strains sequenced to date. Therefore, the genomic information obtained in this study provides a theoretical basis for the identification, characterization, and phylogenetic analysis of R. solanacearum Moko ecotypes.\n\nGenomic sequencing of different sequevars of Ralstonia solanacearum belonging to the Moko ecotype.", "token_count": 433, "char_count": 1409, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5941, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:58.764761", "source": { "split": "train_shard_00000", "doc_id": 2449 }, "chunk_id": "train_shard_00000_2449_0", "global_id": 2696 }, { "text": "Biopreservation is defined as using microbes, their constituents, or both to control spoilage while satisfying consumer demand for clean-label products. The study objective was to investigate the efficacy of bacterial cultures in biopreserving cottage cheese against postprocessing fungal contamination. Cottage cheese curd and dressing were sourced from a manufacturer in New York State. Dressing was inoculated with 3 different commercial protective cultures-PC1 (mix of Lacticaseibacillus spp. and Lactiplantibacillus spp.), PC2 (Lacticaseibacillus rhamnosus), and PC3 (Lactic. rhamnosus)-following the manufacturer recommended dosage and then mixed with curd. A control with no protective culture was included. Nine species of yeast (Candida zeylanoides, Clavispora lusitaniae, Debaryomyces hansenii, Debaryomyces prosopidis, Kluyveromyces marxianus, Meyerozyma guilliermondii, Pichia fermentans, Rhodotorula mucilaginosa, and Torulaspora delbrueckii) and 11 species of mold (Aspergillus cibarius, Aureobasidium pullulans, Penicillium chrysogenum, Penicillium citrinum, Penicillium commune, Penicillium decumbens, Penicillium roqueforti, Mucor genevensis, Mucor racemosus, Phoma dimorpha, and Trichoderma amazonicum) were included in the study. Fungi strains were previously isolated from dairy processing environments and were inoculated onto the cheese surface at a rate of 20 cfu/g. Cheese was stored at 6 ± 2°C. Yeast levels were enumerated at 0, 7, 14, and 21 d postinoculation. Mold growth was visually observed on a weekly basis through d 42 of storage and imaged. Overall, the protective cultures were limited in their ability to delay the outgrowth in cottage cheese, with only 8 of the 20 fungal strains showing an effect of the cultures compared with the control", "token_count": 515, "char_count": 1777, "word_count": 240, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [ "PC3", "PC1", "PC2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:22:59.422648", "source": { "split": "train_shard_00000", "doc_id": 2450 }, "chunk_id": "train_shard_00000_2450_0", "global_id": 2697 }, { "text": "The protective cultures were not very effective against yeast, with only PC1 able to delay the outgrowth of 3 strains: D. hansenii, Tor. delbrueckii, and Mey. guilliermondii. The efficacy of these protective cultures against molds in cottage cheese was more promising, with all protective cultures showing the ability to delay spoilage of at least 1 mold strain. Both PC1 and PC2 were able to delay Pen. chrysogenum and Pho. dimorpha outgrowth, and PC1 also delayed Pen. commune, Pen. decumbens, and Pen. roqueforti to different extents compared with the controls. This study demonstrates that commercial lactic acid bacteria cultures vary in their performance to delay mold and yeast outgrowth, and thus each protective culture should be evaluated against the specific strains of fungi of concern within each specific dairy facility.\n\nEvaluation of the efficacy of commercial protective cultures to inhibit mold and yeast in cottage cheese.", "token_count": 224, "char_count": 941, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6069, "quality_score": 0.8034, "entities": { "genes": [ "PC1", "PC2" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:22:59.887963", "source": { "split": "train_shard_00000", "doc_id": 2450 }, "chunk_id": "train_shard_00000_2450_1", "global_id": 2698 }, { "text": "Bollo is a traditional Goan fermented food in which coarse wheat/wheat and finger millet is leavened with toddy. We here isolated 42 yeast strains from Bollo batter. Initial screening of the isolates with probiotic properties yielded four yeast isolates (DABRP1, DABRP2, DABRP5 and DABRP12). These isolates exhibited tolerance to high bile salt concentration and acidic pH and resistance to various antibiotics, which indicated their probiotic nature. All these yeast isolates were identified as Saccharomyces cerevisiae through D1D2-LSU-rDNA sequencing. These yeast isolates also showed higher percent hydrophobicity towards chloroform followed by n-hexadecane and o-xylene indicating their mucosal surface-adhesive property. To evaluate the safety of the isolates for them to be called as generally recognized as safe, the pathogenic behavior of the isolates determined through the in vitro hemolysis assay and evaluation of DNase and gelatinase activities. None of the isolates exhibited hemolysis or produced DNase or gelatinase and thus were considered potentially safe. In terms of beneficial effects, the most potent isolate S. cerevisiae DABRP5 showed antibacterial activity against the test pathogens. It also showed excellent antioxidant activity with DPPH free radical scavenging activity of 68.85 ± 0.69%, anti-inflammatory activity with 60.39 ± 0.34% inhibition of protein denaturation, and antidiabetic activity with 71.75 ± 0.45% inhibition of α-amylase activity. The isolate produced α-amylase, lipase, and β-galactosidase. The probiotic potential of the isolate S. cerevisiae DABRP5 was similar to that of the reference strain (Saccharomyces boulardii CNCM I-745) used in this study. The results thus indicate that yeast isolates from Bollo batter have probiotic potential.", "token_count": 512, "char_count": 1790, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8123, "entities": { "genes": [ "DABRP2", "DABRP5", "DABRP12", "DABRP1" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:00.877602", "source": { "split": "train_shard_00000", "doc_id": 2451 }, "chunk_id": "train_shard_00000_2451_0", "global_id": 2699 }, { "text": "In Vitro Assessment of Probiotic Potential of Saccharomyces Cerevisiae DABRP5 Isolated from Bollo Batter, a Traditional Goan Fermented Food.", "token_count": 44, "char_count": 140, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [ "DABRP5" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:01.237697", "source": { "split": "train_shard_00000", "doc_id": 2451 }, "chunk_id": "train_shard_00000_2451_1", "global_id": 2700 }, { "text": "The food processing environments of a newly opened meat processing facility were sampled in ten visits carried out during its first 1.5 years of activity and analyzed for the presence of Listeria monocytogenes. A total of 18 L. monocytogenes isolates were obtained from 229 samples, and their genomes were sequenced to perform comparative genomic analyses. An increase in the frequency of isolation of L. monocytogenes and in the diversity of sequence types (STs) detected was observed along time. Although the strains isolated belonged to six different STs (ST8, ST9, ST14, ST37, ST121 and ST155), ST9 was the most abundant (8 out of 18 strains). Low (0 and 2) single nucleotide polymorphism (SNP) distances were found between two pairs of ST9 strains isolated in both cases 3 months apart from the same processing room (Lm-1267 and Lm-1705, with a 2 SNPs distance in the core genome; Lm-1265 and Lm-1706, with a 0 SNPs distance), which suggests that these strains may be persistent L. monocytogenes strains in the food processing environment. Most strains showed an in silico attenuated virulence potential either through the truncation of InlA (in 67% of the isolates) or the absence of other virulence factors involved in cell adhesion or invasion. Twelve of the eighteen L. monocytogenes isolates contained a plasmid, which ranged in size from 4 to 87 Kb and harbored stress survival, in addition to heavy metals and biocides resistance determinants. Identical or highly similar plasmids were identified for various sets of L. monocytogenes ST9 isolates, which suggests the clonal expansion and persistence of plasmid-containing ST9 strains in the processing environments of the meat facility. Finally, the analysis of the L. monocytogenes genomes available in the NCBI database, and their associated metadata, evidenced that strains from ST9 are more frequently reported in Europe, linked to foods, particularly to meat and pork products, and less represented among clinical isolates than other L", "token_count": 522, "char_count": 2002, "word_count": 314, "semantic_coherence": 1, "information_density": 0.6083, "quality_score": 0.8041, "entities": { "genes": [ "ST155", "ST37", "ST8", "ST14", "ST121", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:23:01.871526", "source": { "split": "train_shard_00000", "doc_id": 2452 }, "chunk_id": "train_shard_00000_2452_0", "global_id": 2701 }, { "text": "monocytogenes STs. It also showed that the ST9 strains here isolated were more closely related to the European isolates, which clustered together and separated from ST9 North American isolates.\n\nUnraveling the emergence and population diversity of Listeria monocytogenes in a newly built meat facility through whole genome sequencing.", "token_count": 78, "char_count": 334, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8958, "quality_score": 0.9479, "entities": { "genes": [ "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:02.248503", "source": { "split": "train_shard_00000", "doc_id": 2452 }, "chunk_id": "train_shard_00000_2452_1", "global_id": 2702 }, { "text": "Plant genomes remain highly fragmented and are often characterized by hundreds to thousands of assembly gaps. Here, we report chromosome-level reference and phased genome assembly of Ophiorrhiza pumila, a camptothecin-producing medicinal plant, through an ordered multi-scaffolding and experimental validation approach. With 21 assembly gaps and a contig N50 of 18.49 Mb, Ophiorrhiza genome is one of the most complete plant genomes assembled to date. We also report 273 nitrogen-containing metabolites, including diverse monoterpene indole alkaloids (MIAs). A comparative genomics approach identifies strictosidine biogenesis as the origin of MIA evolution. The emergence of strictosidine biosynthesis-catalyzing enzymes precede downstream enzymes' evolution post γ whole-genome triplication, which occurred approximately 110 Mya in O. pumila, and before the whole-genome duplication in Camptotheca acuminata identified here. Combining comparative genome analysis, multi-omics analysis, and metabolic gene-cluster analysis, we propose a working model for MIA evolution, and a pangenome for MIA biosynthesis, which will help in establishing a sustainable supply of camptothecin.\n\nChromosome-level genome assembly of Ophiorrhiza pumila reveals the evolution of camptothecin biosynthesis.", "token_count": 342, "char_count": 1286, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6946, "quality_score": 0.8473, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:02.824253", "source": { "split": "train_shard_00000", "doc_id": 2453 }, "chunk_id": "train_shard_00000_2453_0", "global_id": 2703 }, { "text": "The bile salt export pump (BSEP) is responsible for the export of bile acid from hepatocytes. Impaired transcellular transport of bile acids in hepatocytes with mutations in BSEP causes cholestasis. Compensatory mechanisms to regulate the intracellular bile acid concentration in human hepatocytes with BSEP deficiency remain unclear. To define pathways that prevent cytotoxic accumulation of bile acid in hepatocytes, we developed a human induced pluripotent stem cell-based model of isogenic BSEP-deficient hepatocytes in a Transwell culture system. Induced hepatocytes (i-Heps) exhibited defects in the apical export of bile acids but maintained a low intracellular bile acid concentration by inducing basolateral export. Modeling the autoregulation of bile acids on hepatocytes, we found that BSEP-deficient i-Heps suppressed de novo bile acid synthesis using the FXR pathway via basolateral uptake and export without apical export. These observations inform the development of therapeutic targets to reduce the overall bile acid pool in patients with BSEP deficiency.\n\nModeling Human Bile Acid Transport and Synthesis in Stem Cell-Derived Hepatocytes with a Patient-Specific Mutation.", "token_count": 315, "char_count": 1189, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5689, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:03.384085", "source": { "split": "train_shard_00000", "doc_id": 2454 }, "chunk_id": "train_shard_00000_2454_0", "global_id": 2704 }, { "text": "Bariatric surgery is one of the most effective treatment options for severe obesity and its comorbidities. However, it is a major surgery that poses several side effects and risks which impede its clinical use. Therefore, it is urgent to develop alternative safer pharmacological approaches to mimic bariatric surgery. Recent studies suggest that bile acids are key players in mediating the metabolic benefits of bariatric surgery. Bile acids can function as signaling molecules by targeting bile acid nuclear receptors and membrane receptors, like FXR and TGR5 respectively. In addition, the composition of bile acids is regulated by either the hepatic sterol enzymes such as CYP8B1 or the gut microbiome. These bile acid related targets all play important roles in regulating metabolism. Drug development based on these targets could provide new hope for patients without the risks of surgery and at a lower cost. In this review, we summarize the most updated progress on bile acid related targets and development of small molecules as drug candidates based on these targets.\n\nImproving glucose and lipids metabolism: drug development based on bile acid related targets.", "token_count": 266, "char_count": 1172, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6354, "quality_score": 0.8177, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:03.961990", "source": { "split": "train_shard_00000", "doc_id": 2455 }, "chunk_id": "train_shard_00000_2455_0", "global_id": 2705 }, { "text": "The isolation and sequencing of new strains of Pseudomonas aeruginosa created an extensive dataset of closed genomes. Many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. By using different genomic island prediction programs, we could identify a total of 17 genomic islands and 8 genomic islets, marking the majority of the accessory genome that covers ~ 12% of the total genome. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of genomic information with the highly virulent PSE9 and LESB58 strains. For both of these, the increased virulence has been directly linked to their accessory genome before. Hence, the integrated use of previously published data can help to minimize expensive and time consuming wetlab work to determine the pathogenetic potential.\n\nEstimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics.", "token_count": 295, "char_count": 1302, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6392, "quality_score": 0.8196, "entities": { "genes": [ "PSE9", "KRP1", "LESB58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:04.543648", "source": { "split": "train_shard_00000", "doc_id": 2456 }, "chunk_id": "train_shard_00000_2456_0", "global_id": 2706 }, { "text": "Although the rise of antibiotic and multidrug resistant bacteria is one of the biggest current threats to human health, our understanding of the mechanisms involved in antibiotic resistance selection remains scarce. We performed whole genome sequencing of 21 Pseudomonas strains, previously isolated from an active submarine volcano of Greece, the Kolumbo volcano. Our goal was to identify the genetic basis of the enhanced co-tolerance to antibiotics and acidity of these Pseudomonas strains. Pangenome analysis identified 10,908 Gene Clusters (GCs). It revealed that the numbers of phage-related GCs and sigma factors, which both provide the mechanisms of adaptation to environmental stressors, were much higher in the high tolerant Pseudomonas strains compared to the rest ones. All identified GCs of these strains were associated with antimicrobial and multidrug resistance. The present study provides strong evidence that the CO\n\nGenomic adaptation of Pseudomonas strains to acidity and antibiotics in hydrothermal vents at Kolumbo submarine volcano, Greece.", "token_count": 252, "char_count": 1063, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:05.043050", "source": { "split": "train_shard_00000", "doc_id": 2457 }, "chunk_id": "train_shard_00000_2457_0", "global_id": 2707 }, { "text": "The delivery of bio-active molecules through the skin is challenging given the complex structure of its outer layer, the stratum corneum. Here we explore the possibility to encapsulate natural compounds into nanocarriers containing permeation enhancers that can affect the fluidity of the stratum corneum lipids. This approach is expected to facilitate dermal or transdermal release. For this purpose, the application of bile salts, which are natural surfactants involved in vivo in lipid digestion, was exploited. Bile salts were added to lipid liquid crystalline nanoparticles (NPs) made of monoolein for antioxidant topical delivery. Monoolein self-assembly behaviour in water was affected by the presence of bile salts molecules, giving a transition from a bicontinuous cubic to unilamellar vesicles dispersion. By adding oleic acid (OA), the change of curvature in the system led to a reverse hexagonal phase. The morphology, structure and size of the nanocarriers was investigated before the nanoparticles were loaded with catechin, a natural antioxidant occurring in plants and food. The encapsulation did not affect significantly the formulation phase behaviour. The formulation loaded with bile salts and catechin was thereafter tested in vitro on the skin from new-born pig. The results for two different lipid formulations without bile salts were compared under the same experimental conditions and with the same antioxidant. The formulation with bile salts showed the best performance, allowing a superior permeation of catechin in the different skin layers in comparison with formulations without bile salt.\n\nTuning lipid structure by bile salts: Hexosomes for topical administration of catechin.", "token_count": 405, "char_count": 1709, "word_count": 250, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:05.709513", "source": { "split": "train_shard_00000", "doc_id": 2458 }, "chunk_id": "train_shard_00000_2458_0", "global_id": 2708 }, { "text": "Studies on the epidemiology and genomes of isolates harboring OXA-48-like genes in septicemic neonates are rare. Here, isolates producing these carbapenemases which emerged and persisted in an Indian neonatal unit were characterized in terms of their resistome, transmissibility, and genome diversity. Antibiotic susceptibility and whole-genome sequencing were carried out. The sequence types, resistome, virulome, mobile genetic elements, and transmissibility of carbapenem-resistant plasmids were evaluated. Core genome analysis of isolates was shown in a global context with other OXA-48-like carbapenemase-harboring genomes, including those from neonatal studies. Eleven OXA-48-like carbapenemase-producing\n\nOXA-181-Like Carbapenemases in Klebsiella pneumoniae ST14, ST15, ST23, ST48, and ST231 from Septicemic Neonates: Coexistence with NDM-5, Resistome, Transmissibility, and Genome Diversity.", "token_count": 265, "char_count": 899, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [ "ST231", "ST23", "ST48", "ST14", "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:06.260670", "source": { "split": "train_shard_00000", "doc_id": 2459 }, "chunk_id": "train_shard_00000_2459_0", "global_id": 2709 }, { "text": "This study was intended to investigate physico-chemical, rheological, and emulsifying properties of oil-in-water emulsions prepared from the Kluyveromyces marxianus mannoprotein (KMM). Also, the stress-response function of the KMM emulsions was compared with that of the whey protein concentrate (WPC) emulsions in terms of zeta potential, size, and rheology. The stress experiments were conducted at different pH (3 to 9), ionic composition (0 to 500 mM NaCl), and temperatures (30 to 90 °C). The extracted KMM with a molecular weight of 107.2 kDa had 28.8% proteins and 68.22% carbohydrates. With increasing the KMM concentration to 1.5% (w/w), the zeta potential, droplet size, and apparent viscosity of the emulsions reached -35 mV, ∼1 μ, and ∼9 mPa·s, respectively. After applying pH, ionic composition, and temperature, the KMM emulsions were more stable than the WPC emulsions. In conclusion, KMM can be used as a bioemulsifier and be more effective in stabilizing emulsions than WPC. PRACTICAL APPLICATION: Yeasts are a rich source of natural materials. In this study, we extracted mannoproteins from the yeast cell wall and evaluated their functional properties to be used as an emulsifier in oil-in-water emulsions. The results of this study confirm that the yeast-derived mannoproteins are good at stabilizing these emulsions either in the presence or absence of different environmental conditions.\n\nStress response and characterization of oil-in-water emulsions stabilized with Kluyveromyces marxianus mannoprotein.", "token_count": 430, "char_count": 1527, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:06.891297", "source": { "split": "train_shard_00000", "doc_id": 2460 }, "chunk_id": "train_shard_00000_2460_0", "global_id": 2710 }, { "text": "Genomics research has relied principally on the establishment and curation of a reference genome for the species. However, it is increasingly recognized that a single reference genome cannot fully describe the extent of genetic variation within many widely distributed species. Pangenome representations are based on high-quality genome assemblies of multiple individuals and intended to represent the broadest possible diversity within a species. A Bovine Pangenome Consortium (BPC) has recently been established to begin assembling genomes from more than 600 recognized breeds of cattle, together with other related species to provide information on ancestral alleles and haplotypes. Previously reported de novo genome assemblies for Angus, Brahman, Hereford, and Highland breeds of cattle are part of the initial BPC effort. The present report describes a complete single haplotype assembly at chromosome-scale for a fullblood Simmental cow from an F1 bison-cattle hybrid fetus by trio binning. Simmental cattle, also known as Fleckvieh due to their red and white spots, originated in central Europe in the 1830s as a triple-purpose breed selected for draught, meat, and dairy production. There are over 50 million Simmental cattle in the world, known today for their fast growth and beef yields. This assembly (ARS_Simm1.0) is similar in length to the other bovine assemblies at 2.86 Gb, with a scaffold N50 of 102 Mb (max scaffold 156.8 Mb) and meets or exceeds the continuity of the best Bos taurus reference assemblies to date.\n\nA Reference Genome Assembly of Simmental Cattle, Bos taurus taurus.", "token_count": 405, "char_count": 1603, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:07.505268", "source": { "split": "train_shard_00000", "doc_id": 2461 }, "chunk_id": "train_shard_00000_2461_0", "global_id": 2711 }, { "text": "Ehrlichia species are obligatory intracellular bacteria transmitted by arthropods, and some of these species cause febrile diseases in humans and livestock. Genome sequencing has only been performed with cultured Ehrlichia species, and the taxonomic status of such ehrlichiae has been estimated by core genome-based phylogenetic analysis. However, many uncultured ehrlichiae exist in nature throughout the world, including Japan. This study aimed to conduct a molecular-based taxonomic and ecological characterization of uncultured Ehrlichia species or genotypes from ticks in Japan. We first surveyed 616 Haemaphysalis ticks by p28-PCR screening and analyzed five additional housekeeping genes (16S rRNA, groEL, gltA, ftsZ, and rpoB) from 11 p28-PCR-positive ticks. Phylogenetic analyses of the respective genes showed similar trees but with some differences. Furthermore, we found that V1 in the V1-V9 regions of Ehrlichia 16S rRNA exhibited the greatest variability. From an ecological viewpoint, the amounts of ehrlichiae in a single tick were found to equal approx. 6.3E+3 to 2.0E+6. Subsequently, core-partial-RGGFR-based phylogenetic analysis based on the concatenated sequences of the five housekeeping loci revealed six Ehrlichia genotypes, which included potentially new Ehrlichia species. Thus, our approach contributes to the taxonomic profiling and ecological quantitative analysis of uncultured or unidentified Ehrlichia species or genotypes worldwide.\n\nDiversity unearthed by the estimated molecular phylogeny and ecologically quantitative characteristics of uncultured Ehrlichia bacteria in Haemaphysalis ticks, Japan.", "token_count": 438, "char_count": 1634, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:08.134210", "source": { "split": "train_shard_00000", "doc_id": 2462 }, "chunk_id": "train_shard_00000_2462_0", "global_id": 2712 }, { "text": "Gut microbial dysbiosis and altered metabonomics have been implicated in the pathogenesis of Crohn's disease (CD). The aim of our study was to characterize the gut microbiome structure and metabolic activities in pediatric CD patients with different clinical outcomes after infliximab (IFX) therapy. Fecal samples were collected from 20 healthy children and 29 newly diagnosed pediatric CD patients. 16S rRNA/ITS2 gene sequencing and targeted metabolomics analysis were applied to profile the gut bacterial microbiome, mycobiome, and metabolome, respectively. Pediatric CD patients exhibited lower relative abundances of short-chain fatty acids (SCFAs)-producing bacteria including\n\nMicrobial and metabolic features associated with outcome of infliximab therapy in pediatric Crohn's disease.", "token_count": 200, "char_count": 791, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7358, "quality_score": 0.8679, "entities": { "genes": [ "ITS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:08.582602", "source": { "split": "train_shard_00000", "doc_id": 2463 }, "chunk_id": "train_shard_00000_2463_0", "global_id": 2713 }, { "text": "Eleven simulated intestinal fluids (SIF) were designed using a Design of Experiment (DoE) approach. The DoE SIF covered a range of compositions of fasted state human intestinal fluid (FaHIF) with regard to pH, bile salt (BS), and phospholipid (PL). Using the model compound danazol, the apparent crystalline solubility (aCS) and apparent amorphous solubility (aAS), as well as the supersaturation propensity was determined in the DoE SIF media. The aCS of danazol was dependent on the composition of the SIF, with PL as the main factor, and a small effect from BS and an interaction between BS and PL. From the DoE solubility data a model was derived, which could predict aCS in commercially available SIF (FaSSIF-V1 and -V2) and in a range of FaHIF. The aAS of danazol was differently affected by the SIF composition than the aCS; PL was again the main factor influencing the aAS, but interactions between BS and pH, as well as pH and PL were also important. The supersaturation propensities of danazol in the DoE SIF media were affected by the same factors as the aCS. Hence, the supersaturation behaviour and aCS of danazol, were found to be closely related.\n\nExploring the Impact of Intestinal Fluid Components on the Solubility and Supersaturation of Danazol.", "token_count": 342, "char_count": 1264, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5215, "quality_score": 0.7608, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:09.150665", "source": { "split": "train_shard_00000", "doc_id": 2464 }, "chunk_id": "train_shard_00000_2464_0", "global_id": 2714 }, { "text": "One of the major components of the staphylococcal biofilm is surface proteins that assemble as scaffold components of the biofilm matrix. Among the different surface proteins able to contribute to biofilm formation, this review is dedicated to the Biofilm Associated Protein (Bap). Bap is part of the accessory genome of\n\nRevisiting Bap Multidomain Protein: More Than Sticking Bacteria Together.", "token_count": 98, "char_count": 395, "word_count": 59, "semantic_coherence": 1, "information_density": 0.661, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:09.528004", "source": { "split": "train_shard_00000", "doc_id": 2466 }, "chunk_id": "train_shard_00000_2466_0", "global_id": 2715 }, { "text": "P. digitatum, the causative agent of green mold, is one of the most destructive pathogens in the citrus industry. To facilitate basal researches on this important plant pathogen, here we report a finished genome sequence for P. digitatum strain PDW03 using a combination of Illumina, PacBio, and Hi-C sequencing technologies. The assembly comprised 6 chromosomes from telomere to telomere and encodes approximately 9000 proteins. Genomic re-analyses identified 302 Carbohydrate-active enzymes, 420 secreted proteins, and 39 secondary metabolite (SM) gene clusters. Furthermore, we found 10 fragmentary SM clusters in the P. digitatum PDW03 genome. Pangenome analysis based on 5 P. digitatum genomes available showed that conserved orthogroups account for ~68% of the species pangenome. Taken together, this fully completed P. digitatum genome will provide an optimum resource for further researches to investigate the driving forces of fungal host switch and effectors functioning in plant-pathogen interaction.\n\nThe completed genome sequence of the pathogenic ascomycete fungus Penicillium digitatum.", "token_count": 295, "char_count": 1101, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [ "PDW03" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:10.090724", "source": { "split": "train_shard_00000", "doc_id": 2467 }, "chunk_id": "train_shard_00000_2467_0", "global_id": 2716 }, { "text": "The molecular basis of how temperature affects cell metabolism has been a long-standing question in biology, where the main obstacles are the lack of high-quality data and methods to associate temperature effects on the function of individual proteins as well as to combine them at a systems level. Here we develop and apply a Bayesian modeling approach to resolve the temperature effects in genome scale metabolic models (GEM). The approach minimizes uncertainties in enzymatic thermal parameters and greatly improves the predictive strength of the GEMs. The resulting temperature constrained yeast GEM uncovers enzymes that limit growth at superoptimal temperatures, and squalene epoxidase (ERG1) is predicted to be the most rate limiting. By replacing this single key enzyme with an ortholog from a thermotolerant yeast strain, we obtain a thermotolerant strain that outgrows the wild type, demonstrating the critical role of sterol metabolism in yeast thermosensitivity. Therefore, apart from identifying thermal determinants of cell metabolism and enabling the design of thermotolerant strains, our Bayesian GEM approach facilitates modelling of complex biological systems in the absence of high-quality data and therefore shows promise for becoming a standard tool for genome scale modeling.\n\nBayesian genome scale modelling identifies thermal determinants of yeast metabolism.", "token_count": 301, "char_count": 1383, "word_count": 200, "semantic_coherence": 1, "information_density": 0.635, "quality_score": 0.8175, "entities": { "genes": [ "ERG1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:10.661551", "source": { "split": "train_shard_00000", "doc_id": 2468 }, "chunk_id": "train_shard_00000_2468_0", "global_id": 2717 }, { "text": "Recent evidence suggests that probiotics, prebiotics and synbiotics may serve as important dietary components in the prevention (especially) and treatment of cardiovascular diseases (CVD), but the recommendations for their use are often based on brief reports and small clinical studies. This review evaluates the current literature on the correlation between CVD and probiotics, prebiotics and synbiotics. Although research on probiotics, prebiotics and synbiotics has grown exponentially in recent years, particularly regarding the effect of probiotics on CVD, their mechanisms have not been clearly defined. It has been proposed that probiotics lower cholesterol levels, and may protect against CVD, by increasing bile salt synthesis and bile acid deconjugation. Similar effects have also been observed for prebiotics and synbiotics; however, probiotics also appear to have anti-oxidative, anti-platelet and anti-inflammatory properties. Importantly, probiotics not only have demonstrated effects in vitro and in animal models, but also in humans, where supplementation with probiotics decreases the risk factors of CVD. In addition, the properties of commercial probiotics, prebiotics and synbiotics remain undetermined, and further experimental research is needed before these substances can be used in the prevention and treatment of CVD. In particular, well-designed clinical trials are required to determine the influence of probiotics on trimethylamine-N-oxide (TMAO), which is believed to be a marker of CVDs, and to clarify the long-term effects, and action, of probiotic, prebiotic and synbiotic supplementation in combination with drug therapy (for example, aspirin). However, while it cannot be unequivocally stated whether such supplementation yields benefits in the prevention and treatment of CVDs, it is important to note that clinical studies performed to date have not identified any side-effects to use.\n\nProbiotics, Prebiotics and Synbiotics-A Promising Strategy in Prevention and Treatment of Cardiovascular Diseases?", "token_count": 473, "char_count": 2040, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:11.306980", "source": { "split": "train_shard_00000", "doc_id": 2469 }, "chunk_id": "train_shard_00000_2469_0", "global_id": 2718 }, { "text": "There is an increasing concern about the role of animals as reservoirs of Clostridioides difficile. In this study, we investigated prevalence, antimicrobial resistance and zoonotic potential of C. difficile in dogs. Two-hundred and twenty-five dog faecal deposits were collected from trashcans in nine public gardens. C. difficile was isolated using selective plating and enrichment culture, identified by MALDI-TOF, tested for susceptibility to seven antibiotics by E-test, and sequenced on an Illumina NextSeq platform. Genome sequences were analysed to determine multilocus sequence types and resistance and toxin gene profiles. Zoonotic potential was assessed by measuring genetic variations of core genome (cg)MLST types between canine isolates and 216 temporally and spatially related human clinical isolates from a national database. C. difficile was isolated from 11 samples (4.9%). Seven isolates were toxigenic (tcdA+, tcdB+, cdtA/B-) and belonged to the sequence types ST2, ST6, ST10 and ST42. The four non-toxigenic isolates were assigned to ST15, ST26 and one novel ST. ST2, corresponding to PCR ribotype RT014/020, was the dominating lineage (n = 4) and, together with ST26 and ST42 isolates, showed close resemblance to human isolates, i.e. 2-5 allelic differences among the 1999 genes analysed by cgMLST. Three non-toxigenic isolates displayed resistance to clindamycin, erythromycin and tetracycline mediated by erm(B) and tet(M). Resistance to metronidazole, moxifloxacine, rifampicin or vancomycin was not detected. In conclusion, a small proportion of faecal deposits contained toxigenic C. difficile such as ST2 (RT014/020), which is a major cause of community-acquired infections. Our finding suggests that pathogenic strains can be exchanged between dogs and humans.", "token_count": 509, "char_count": 1789, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6784, "quality_score": 0.8392, "entities": { "genes": [ "ST2", "ST6", "ST42", "RT014", "ST10", "ST15", "ST26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:11.967652", "source": { "split": "train_shard_00000", "doc_id": 2470 }, "chunk_id": "train_shard_00000_2470_0", "global_id": 2719 }, { "text": "Dogs are carriers of Clostridioides difficile lineages associated with human community-acquired infections.", "token_count": 27, "char_count": 107, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:12.323920", "source": { "split": "train_shard_00000", "doc_id": 2470 }, "chunk_id": "train_shard_00000_2470_1", "global_id": 2720 }, { "text": "The demand for preservative-free food products is rising, and biopreservation is a potential alternative to replace or reduce the use of chemical preservatives. The objectives of this study were to assess the antifungal activity of lactic acid bacteria (LAB; n = 98) and the efficacy and applicability of the chosen bioprotective cultures against fungal spoilers in dairy products. First, 14 antifungal strains were preliminarily screened by in vitro tests against Pichia pastoris D3, Aspergillus niger D1, Geotrichum candidum N1, Kluyveromyces marxianus W1, and Penicillium chrysogenum B1 and validated by challenge tests in yogurt, indicating that the fungal-inhibiting activity of LAB was species specific and yogurt fermented with antifungal LAB cultures was more effective in extending shelf life. Second, the chosen 14 LAB strains were identified by the 16S rDNA sequence analysis and carbohydrate fermentation test. The results were as follows: nine strains were Lactobacillus plantarum, three were Lactobacillus paracasei, one was Enterococus faecium, and one was Lactobacillus rhamnosus. Among them, active L. plantarum N7 was the chosen and studied factor affecting antifungal activity by using the response surface methodology. Finally, in situ tests were conducted to validate the activity of L. plantarum N7 in actual dairy products (whey beverages). Physicochemical and microbial indices of whey beverages during storage indicated that antifungal L. plantarum N7 could slow yeast growth and be candidates of interest for industrial applications.\n\nScreening of Antifungal Lactic Acid Bacteria as Bioprotective Cultures in Yogurt and a Whey Beverage.", "token_count": 447, "char_count": 1662, "word_count": 241, "semantic_coherence": 1, "information_density": 0.61, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:12.952019", "source": { "split": "train_shard_00000", "doc_id": 2471 }, "chunk_id": "train_shard_00000_2471_0", "global_id": 2721 }, { "text": "2-phenylethanol (2-PE) is a rose-scented flavor and fragrance compound that is used in food, beverages, and personal care products. Compatibility with gasoline also makes it a potential biofuel or fuel additive. A biochemical process converting glucose or other fermentable sugars to 2-PE can potentially provide a more sustainable and economical production route than current methods that use chemical synthesis and/or isolation from plant material.\n\nCRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianus.", "token_count": 156, "char_count": 597, "word_count": 78, "semantic_coherence": 1, "information_density": 0.8718, "quality_score": 0.9359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:13.390433", "source": { "split": "train_shard_00000", "doc_id": 2472 }, "chunk_id": "train_shard_00000_2472_0", "global_id": 2722 }, { "text": "The Himalayan people prepare dry and oval to round-shaped starter cultures to ferment cereals into mild-alcoholic beverages, which contain lactic acid bacteria (LAB) as one of the essential microbiota. There is no report on probiotic characters of LAB isolated from dry starters. Hence, we screened the probiotic and some functional properties of 37 LAB strains isolated from dry starters of the Eastern Himalayas viz. marcha, phab, paa, pee and phut. About 38% of the LAB strains showed high survival rate (> 50%) at pH 3 and 0.3% bile salts. Enterococcus durans BPB21 and SMB7 showed the highest hydrophobicity percentage of 98%. E. durans DMB4 and SMB7 showed maximum cholesterol assimilation activity. About 65% of the LAB strains showed the ability to produce β galactosidase. Majority of the strains showed phytase activity, whereas none of the strain showed amylase activity. About 86% of LAB strains showed an optimum tolerance of 10% ethanol concentration. Genetic screening of some probiotic and functional marker genes have also been analysed. The occurrence of clp L gene, agu A gene (survival of gastrointestinal tract conditions), apf, mub1 and map A gene (adhesion genes) was higher compared to other genes. The occurrence of bsh gene (bile salt tolerance) was detected in Pediococcus pentosaceus SMB13-1 and Enterococcus faecium BPB11. Gene ped B for pediocin with amplicon size of 375 bp was detected in E. durans DMB13 and Pediococcus acidilactici AKB3. Detection of nutritional marker gene rib A and fol P in some strains showed the potential ability to synthesize riboflavin and folic acid. LAB with probiotic and functional properties may be explored for food industry in future.\n\nProbiotic properties of lactic acid bacteria isolated from traditionally prepared dry starters of the Eastern Himalayas.", "token_count": 513, "char_count": 1822, "word_count": 285, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [ "SMB7", "AKB3", "DMB4", "BPB21", "DMB13", "SMB13", "BPB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:23:14.024833", "source": { "split": "train_shard_00000", "doc_id": 2473 }, "chunk_id": "train_shard_00000_2473_0", "global_id": 2723 }, { "text": "Clostridioides difficile is one of the most frequent causes of nosocomial infections in humans leading to (antibiotic-associated) diarrhea and severe pseudomembranous colitis. With an increasing frequency, C. difficile infections (CDI) are also observed independently of hospitalization and the age of the patients in an ambulant setting. One potential source of so-called community-acquired CDI is a zoonotic transmission to humans based on direct contact with animals or the consumption of food. To estimate the exposure of humans with C. difficile via food, we screened 364 different retail fresh poultry meat products purchased in Berlin and Brandenburg, Germany and further characterized the isolates. None of the 42 turkey or chicken meat samples without skin was contaminated. However, 51 (15.8%) of 322 tested fresh chicken meat samples with skin were C. difficile-positive. The vast majority (84.3%) of all isolates exhibited toxin genes tcdA and tcdB, whereas the binary toxin cdtA/B was absent. Most of the isolates (50/51) were susceptible to all six investigated antimicrobials. However, one non-toxigenic strain was multidrug resistant to the antimicrobials clindamycin and erythromycin. The isolates were mainly represented by PCR-ribotypes (RT) 001, RT002, RT005, and RT014, which were already associated with human CDI cases in Germany and were partially detected in poultry. The relatively high contamination rate of fresh retail chicken meat with skin purchased in Germany indicates chicken meat as a potential source of human infections. Moreover, we identified cutting plants with a higher rate of a C. difficile-contamination (21.4-32.8%). To compare the phylogenetic relationship of the isolated strains from certain cutting plants over several months in 2018 and 2019, we analyzed them using NGS followed by core genome MLST", "token_count": 481, "char_count": 1848, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [ "RT005", "RT002", "RT014" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:14.676124", "source": { "split": "train_shard_00000", "doc_id": 2474 }, "chunk_id": "train_shard_00000_2474_0", "global_id": 2724 }, { "text": "Interestingly, highly related strains (0-3 alleles distance) of common clinical RT001 and RT002 isolates, as well as of the non-toxigenic RT205 isolates were detectable in same cutting plants over a period of three and 16 months, respectively.The continuous contamination with the same strain could be explained by the longterm persistence of this strain within the cutting plant (e.g., within the scalder), or with a recurring entry e.g. from the same fattening farm.\n\nPrevalence and phylogenetic relationship of Clostridioides difficile strains in fresh poultry meat samples processed in different cutting plants.", "token_count": 157, "char_count": 615, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7444, "quality_score": 0.8722, "entities": { "genes": [ "RT002", "RT001", "RT205" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:15.123758", "source": { "split": "train_shard_00000", "doc_id": 2474 }, "chunk_id": "train_shard_00000_2474_1", "global_id": 2725 }, { "text": "Xylitol was biotechnologically produced by Kluyveromyces marxianus ATCC36907 using the hemicellulosic hydrolysate of the cashew apple bagasse (CABHH). Sequentially, the present study investigated the recovery and purification of xylitol evaluating different antisolvents [ethanol, isopropanol and the ionic liquid 2-hydroxyl-ethylammonium acetate (2-HEAA)], their proportion in the medium (10-90% v/v), and their cooling rate (V\n\nDevelopment of a purification process via crystallization of xylitol produced for bioprocess using a hemicellulosic hydrolysate from the cashew apple bagasse as feedstock.", "token_count": 180, "char_count": 601, "word_count": 76, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": { "genes": [ "ATCC36907" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:15.566226", "source": { "split": "train_shard_00000", "doc_id": 2475 }, "chunk_id": "train_shard_00000_2475_0", "global_id": 2726 }, { "text": "Pseudomonas cichorii is divided into two subclades based on the 16S ribosomal RNA gene sequence and core genome multilocus sequence typing. It was shown that subclade 2 strains utilize d-tartrate as a sole carbon source, whereas subclade 1 strains do not. Draft genome sequencing was performed with P. cichorii strains to identify d-tartrate utilization genes. By genome comparative and homology search studies, an ∼7.1-kb region was identified to be involved in d-tartrate utilization. The region is subclade 2 specific, and contains tarD and dctA genes, which encode a putative enzyme and transporter of d-tartrate, respectively. When the region was introduced into subclade 1 strains, the transformants were able to utilize d-tartrate. Partial fragments of tarD and dctA were amplified from all subclade 2 strains tested in this study by PCR using gene-specific primers, but not from subclade 1 strains. This is the first report on the genetic analysis of biochemical characteristics corresponding to a specific phylogenetic group in P. cichorii.\n\nd-Tartrate utilization correlates with phylogenetic subclade in Pseudomonas cichorii.", "token_count": 315, "char_count": 1136, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6331, "quality_score": 0.8166, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:16.176566", "source": { "split": "train_shard_00000", "doc_id": 2476 }, "chunk_id": "train_shard_00000_2476_0", "global_id": 2727 }, { "text": "Progressive Familial Intrahepatic Cholestasis (PFIC) are inherited severe liver disorders presenting early in life, with high serum bile salt and bilirubin levels. Six types have been reported, two of these are caused by deficiency of an ABC transporter; ABCB11 (bile salt export pump) in type 2; ABCB4 (phosphatidylcholine floppase) in type 3. In addition, ABCB11 function is affected in 3 other types of PFIC. A lack of effective treatment makes a liver transplantation necessary in most patients. In view of long-term adverse effects, for instance due to life-long immune suppression needed to prevent organ rejection, gene therapy could be a preferable approach, as supported by proof of concept in animal models for PFIC3. This review discusses the feasibility of gene therapy as an alternative for liver transplantation for all forms of PFIC based on their pathological mechanism.\n\nGene Therapy for Progressive Familial Intrahepatic Cholestasis: Current Progress and Future Prospects.", "token_count": 245, "char_count": 990, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7315, "quality_score": 0.8658, "entities": { "genes": [ "ABCB11", "ABCB4", "PFIC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:16.680746", "source": { "split": "train_shard_00000", "doc_id": 2477 }, "chunk_id": "train_shard_00000_2477_0", "global_id": 2728 }, { "text": "Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity.\n\npanRGP: a pangenome-based method to predict genomic islands and explore their diversity.", "token_count": 130, "char_count": 567, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:17.119122", "source": { "split": "train_shard_00000", "doc_id": 2478 }, "chunk_id": "train_shard_00000_2478_0", "global_id": 2729 }, { "text": "We present here the second complete genome of anaerobic ammonium oxidation (anammox) bacterium, Candidatus (Ca.) Brocadia pituitae, along with those of a nitrite oxidizer and two incomplete denitrifiers from the anammox bacterial community (ABC) metagenome. Although NO2- reduction to NO is considered to be the first step in anammox, Ca. B. pituitae lacks nitrite reductase genes (nirK and nirS) responsible for this reaction. Comparative genomics of Ca. B. pituitae with Ca. Kuenenia stuttgartiensis and six other anammox bacteria with nearly complete genomes revealed that their core genome structure contains 1,152 syntenic orthologues. But nitrite reductase genes were absent from the core, whereas two other Brocadia species possess nirK and these genes were horizontally acquired from multiple lineages. In contrast, at least five paralogous hydroxylamine oxidoreductase genes containing candidate ones (hao2 and hao3) encoding another nitrite reductase were observed in the core. Indeed, these two genes were also significantly expressed in Ca. B. pituitae as in other anammox bacteria. Because many nirS and nirK genes have been detected in the ABC metagenome, Ca. B. pituitae presumably utilises not only NO supplied by the ABC members but also NO and/or NH2OH by self-production for anammox metabolism.\n\nThe physiological potential of anammox bacteria as revealed by their core genome structure.", "token_count": 377, "char_count": 1406, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6377, "quality_score": 0.8188, "entities": { "genes": [ "NO2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:17.746725", "source": { "split": "train_shard_00000", "doc_id": 2479 }, "chunk_id": "train_shard_00000_2479_0", "global_id": 2730 }, { "text": "It has been reported that Lactobacillus can remove cholesterol and thus might play an important role in lowering cholesterol in humans, but the underlying mechanism is still controversial. To confirm whether different strains have different cholesterol-lowering mechanisms, we explored the cholesterol-lowering abilities of different Lactobacillus plantarum strains, and the factors influencing their abilities. We found that all nine strains reduced the cholesterol concentration to some extent, but there were significant differences among them. In MRS broth, L. plantarum AR113 and AR171 showed the greatest cholesterol-lowering abilities of 27.89% and 19.90%, respectively, but AR501 and AR300 only showed reductions of 0.34% and 0.91%, respectively. Upon addition of 0.1% ox bile, the cholesterol-removal capability of most strains increased. L. plantarum AR511 showed the highest cholesterol removal rate, which increased from 5.8% to 37.14%, i.e., by a factor of approximately 6.4, but there was no significant change in the cholesterol removal rate of AR171. These results suggested that the effect of ox bile on the cholesterol-lowering ability was strain-specific. Except for the strains AR171, AR237 and AR495, the cholesterol-removal ability of the remaining six strains was positively correlated with the amount of free bile acid released. The addition of a bile salt hydrolase inhibitor had some effect on the cholesterol-removal ability of the six strains of bacteria other than AR171, AR237 and AR495, but little influence on the latter three. The effect of BSH was strain-specific. Similarly, the effect of pH was also strain-specific. Taken together, these results suggest that different strains of L. plantarum have different cholesterol-lowering capacities and different influencing factors. Therefore, further research is needed to explore the exact mechanism by which different strains lower cholesterol.", "token_count": 504, "char_count": 1926, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5543, "quality_score": 0.7772, "entities": { "genes": [ "AR113", "AR495", "AR511", "AR300", "AR501", "AR171", "AR237" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:18.403850", "source": { "split": "train_shard_00000", "doc_id": 2480 }, "chunk_id": "train_shard_00000_2480_0", "global_id": 2731 }, { "text": "Diverse conditions contribute to the cholesterol-lowering ability of different", "token_count": 16, "char_count": 78, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:18.752616", "source": { "split": "train_shard_00000", "doc_id": 2480 }, "chunk_id": "train_shard_00000_2480_1", "global_id": 2732 }, { "text": "The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans sp. nov., P. marinum comb. nov., P. flavum comb. nov. and P. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum. We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26\n\nPhylogenomics reveals the basis of adaptation of Pseudorhizobium species to extreme environments and supports a taxonomic revision of the genus.", "token_count": 267, "char_count": 937, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6739, "quality_score": 0.837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:19.305179", "source": { "split": "train_shard_00000", "doc_id": 2481 }, "chunk_id": "train_shard_00000_2481_0", "global_id": 2733 }, { "text": "Microbial natural products constitute a wide variety of chemical compounds, many which can have antibiotic, antiviral, or anticancer properties that make them interesting for clinical purposes. Natural product classes include polyketides (PKs), nonribosomal peptides (NRPs), and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295 Streptomyces genomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a representative of a novel subfamily of lanthipeptides, which we designate class V. The 2D structure of the new RiPP, which we name pristinin A3 (1), was solved using nuclear magnetic resonance (NMR), tandem mass spectrometry (MS/MS) data, and chemical labeling. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria.", "token_count": 483, "char_count": 2015, "word_count": 289, "semantic_coherence": 1, "information_density": 0.692, "quality_score": 0.846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:19.946851", "source": { "split": "train_shard_00000", "doc_id": 2482 }, "chunk_id": "train_shard_00000_2482_0", "global_id": 2734 }, { "text": "Expansion of RiPP biosynthetic space through integration of pan-genomics and machine learning uncovers a novel class of lanthipeptides.", "token_count": 36, "char_count": 135, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:20.309481", "source": { "split": "train_shard_00000", "doc_id": 2482 }, "chunk_id": "train_shard_00000_2482_1", "global_id": 2735 }, { "text": "Bloodstream infections caused by nontyphoidal Salmonella are a major public health concern in Africa, causing ~49,600 deaths every year. The most common Salmonella enterica pathovariant associated with invasive nontyphoidal Salmonella disease is Salmonella Typhimurium sequence type (ST)313. It has been proposed that antimicrobial resistance and genome degradation has contributed to the success of ST313 lineages in Africa, but the evolutionary trajectory of such changes was unclear. Here, to define the evolutionary dynamics of ST313, we sub-sampled from two comprehensive collections of Salmonella isolates from African patients with bloodstream infections, spanning 1966 to 2018. The resulting 680 genome sequences led to the discovery of a pan-susceptible ST313 lineage (ST313 L3), which emerged in Malawi in 2016 and is closely related to ST313 variants that cause gastrointestinal disease in the United Kingdom and Brazil. Genomic analysis revealed degradation events in important virulence genes in ST313 L3, which had not occurred in other ST313 lineages. Despite arising only recently in the clinic, ST313 L3 is a phylogenetic intermediate between ST313 L1 and L2, with a characteristic accessory genome. Our in-depth genotypic and phenotypic characterization identifies the crucial loss-of-function genetic events that occurred during the stepwise evolution of invasive S. Typhimurium across Africa.\n\nStepwise evolution of Salmonella Typhimurium ST313 causing bloodstream infection in Africa.", "token_count": 397, "char_count": 1505, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [ "ST313" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:20.927822", "source": { "split": "train_shard_00000", "doc_id": 2483 }, "chunk_id": "train_shard_00000_2483_0", "global_id": 2736 }, { "text": "The bacterial strain PO100/5 was isolated from a skin abscess taken from a pig (Sus scrofa domesticus) in the Alentejo region of southern Portugal. It was identified as Corynebacterium pseudotuberculosis using biochemical tests, multiplex PCR and Pulsed Field Gel Electrophoresis. After genome sequencing and rpoB phylogeny, the strain was classified as C. ulcerans. To better understand the taxonomy of this strain and improve identification methods, we compared strain PO100/5 to other publicly available genomes from C. diphtheriae group. Taxonomic analysis reclassified it and three others strains as the recently described C. silvaticum, which have been isolated from wild boar and roe deer in Germany and Austria. The results showed that PO100/5 is the first sequenced genome of a C. silvaticum strain from livestock and a different geographical region, has the unique sequence type ST709, and could be could produce the diphtheriae toxin, along with strain 05-13. Genomic analysis of PO100/5 showed four prophages, and eight conserved genomic islands in comparison to C. ulcerans. Pangenome analysis of 38 C. silvaticum and 76 C. ulcerans genomes suggested that C. silvaticum is a genetically homogeneous species, with 73.6% of its genes conserved and a pangenome near to be closed (α > 0.952). There are 172 genes that are unique to C. silvaticum in comparison to C. ulcerans. Most of these conserved genes are related to nutrient uptake and metabolism, prophages or immunity against them, and could be genetic markers for species identification. Strains PO100/5 (livestock) and KL0182T (wild boar) were predicted to be potential human pathogens. This information may be useful for identification and surveillance of this pathogen.", "token_count": 476, "char_count": 1739, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5925, "quality_score": 0.7962, "entities": { "genes": [ "PO100", "KL0182T", "ST709" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:21.572837", "source": { "split": "train_shard_00000", "doc_id": 2484 }, "chunk_id": "train_shard_00000_2484_0", "global_id": 2737 }, { "text": "Taxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently described Corynebacterium silvaticum.", "token_count": 37, "char_count": 156, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [ "PO100" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:21.929792", "source": { "split": "train_shard_00000", "doc_id": 2484 }, "chunk_id": "train_shard_00000_2484_1", "global_id": 2738 }, { "text": "Bacterial placentitis in horses commonly results in abortion, premature birth or compromised neonatal foal health. Although mycobacterial infections are generally uncommon in horses, 10 equine abortion cases caused by Mycobacterium avium subsp. hominissuis (MAH) infections occurred between 2018 and 2019 in Japan. They occurred on seven Thoroughbred horse farms in the Hidaka district of Hokkaido, but direct contact among the mares on different farms was not recorded. Most cases were characterized by extensive pathological lesions of the placenta, which are not typical in cases of common pathogenic bacteria such as Streptococcus zooepidemicus and Escherichia coli. All abortions featured white-yellow exudates on the surface of the placenta. Mycobacterial granuloma formations were histologically found in the placenta and fetal organs, and acid-fast bacteria were isolated from the placenta, fetal samples (heart, lung, liver, kidney, spleen and stomach contents) or uterine lavage fluid. The greatest number of bacteria was isolated from necrotic lesions on the placenta, which could be an important site for bacterial isolation in mycobacterial equine abortions. The isolates were identified as MAH based on internal genome sequences. In variable number tandem repeat analysis, all patterns of the strains were identical. Single nucleotide polymorphism analysis of the core genome grouped all strains in the II-a/SC3 subcluster. Both results reveal that these strains share the same genetic background, suggesting that the horses had been infected by the same unknown contagious source.\n\nTen cases of Mycobacterium avium subsp. hominissuis infections linked to equine abortions in Japan, 2018-2019.", "token_count": 425, "char_count": 1707, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [ "SC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:22.553140", "source": { "split": "train_shard_00000", "doc_id": 2485 }, "chunk_id": "train_shard_00000_2485_0", "global_id": 2739 }, { "text": "Primary biliary cholangitis (PBC) is characterized by autoimmune damage of intrahepatic bile ducts associated with a loss of tolerance to mitochondrial antigens. PBC etiopathogenesis is intriguing because of different perplexing features, namely: a) although mitochondria are present in all cell types and tissues, the damage is mainly restricted to biliary epithelial cells (BECs); b) despite being an autoimmune disorder, it does not respond to immunosuppressive drugs but rather to ursodeoxycholic acid, a bile salt that induces HCO3- rich choleresis; c) the overwhelming female preponderance of the disease remains unexplained. Here we present an etiopathogenic view of PBC which sheds light on these puzzling facts of the disease.\n\nPrimary biliary cholangitis: pathogenic mechanisms.", "token_count": 209, "char_count": 788, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7946, "quality_score": 0.8973, "entities": { "genes": [ "HCO3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:23.012215", "source": { "split": "train_shard_00000", "doc_id": 2486 }, "chunk_id": "train_shard_00000_2486_0", "global_id": 2740 }, { "text": "The environmental bacterium\n\nEstablishment and Evaluation of a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Pseudomonas aeruginosa.", "token_count": 48, "char_count": 174, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:23.371417", "source": { "split": "train_shard_00000", "doc_id": 2487 }, "chunk_id": "train_shard_00000_2487_0", "global_id": 2741 }, { "text": "The goal of this research was to enhance the transdermal delivery of lornoxicam (LX), using nanovesicular carriers composed of the bile salt sodium deoxycholate (SDC), soybean phosphatidyl choline (SPC) and a permeation enhancer limonene.\n\nBilosomes as Promising Nanovesicular Carriers for Improved Transdermal Delivery: Construction, in vitro Optimization, ex vivo Permeation and in vivo Evaluation.", "token_count": 115, "char_count": 400, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:23.762243", "source": { "split": "train_shard_00000", "doc_id": 2488 }, "chunk_id": "train_shard_00000_2488_0", "global_id": 2742 }, { "text": "Microbial bile salt hydrolases (BSHs) found in the intestine catalyze the deconjugation of taurine- and glycine-linked bile salts produced in the liver. The resulting bile salts are biological detergents and are critical in aiding lipophilic nutrient digestion. Therefore, the activity of BSHs in the gut microbiome is directly linked to human metabolism and overall health. Bile salt metabolism has also been associated with disease phenotypes such as liver and colorectal cancer. In order to reshape the gut microbiome to optimize bile salt metabolism, tools to characterize and quantify these processes must exist to enable a much-improved understanding of how metabolism goes awry in the face of disease, and how it can be improved through an altered lifestyle and environment. Furthermore, it is necessary to attribute metabolic activity to specific members and BSHs within the microbiome. To this end, we have developed activity-based probes with two different reactive groups to target bile salt hydrolases. These probes bind similarly to the authentic bile salt substrates, and we demonstrate enzyme labeling of active bile salt hydrolases by using purified protein, cell lysates, and in human stool.\n\nActivity-Based Protein Profiling of Bile Salt Hydrolysis in the Human Gut Microbiome with Beta-Lactam or Acrylamide-Based Probes.", "token_count": 336, "char_count": 1339, "word_count": 200, "semantic_coherence": 1, "information_density": 0.62, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:24.343833", "source": { "split": "train_shard_00000", "doc_id": 2489 }, "chunk_id": "train_shard_00000_2489_0", "global_id": 2743 }, { "text": "The MucR/Ros family protein is conserved in alpha-proteobacteria and characterized by its zinc-finger motif that has been proposed as the ancestral domain from which the eukaryotic C2H2 zinc-finger structure evolved. In the past decades, accumulated evidences have revealed MucR as a pleiotropic transcriptional regulator that integrating multiple functions such as virulence, symbiosis, cell cycle and various physiological processes. Scattered reports indicate that MucR mainly acts as a repressor, through oligomerization and binding to multiple sites of AT-rich target promoters. The N-terminal region and zinc-finger bearing C-terminal region of MucR mediate oligomerization and DNA-binding, respectively. These features are convergent to those of xenogeneic silencers such as H-NS, MvaT, Lsr2 and Rok, which are mainly found in other lineages. Phylogenetic analysis of MucR homologs suggests an ancestral origin of MucR in alpha- and delta-proteobacteria. Multiple independent duplication and lateral gene transfer events contribute to the diversity and phyletic distribution of MucR. Finally, we posed questions which remain unexplored regarding the putative roles of MucR as a xenogeneic silencer and a general manager in balancing adaptation and regulatory integration in the pangenome context.\n\nAncestral zinc-finger bearing protein MucR in alpha-proteobacteria: A novel xenogeneic silencer?", "token_count": 357, "char_count": 1401, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:24.918458", "source": { "split": "train_shard_00000", "doc_id": 2490 }, "chunk_id": "train_shard_00000_2490_0", "global_id": 2744 }, { "text": "Helicobacter pullorum commonly colonized in the gastrointestinal tract of poultry and caused gastroenteritis. This bacterium could be transmitted to humans through contaminated food and caused colitis and hepatitis. Currently, the genetic characteristics of the H. pullorum were not recognized enough. In this study, the genomes of 23 H. pullorum strains from different counties were comparatively analyzed. Among them, H. pullorum 2013BJHL was the first isolated and reported in China.\n\nComparative genomics of Helicobacter pullorum from different countries.", "token_count": 134, "char_count": 559, "word_count": 77, "semantic_coherence": 1, "information_density": 0.6883, "quality_score": 0.8442, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:25.343142", "source": { "split": "train_shard_00000", "doc_id": 2491 }, "chunk_id": "train_shard_00000_2491_0", "global_id": 2745 }, { "text": "Molecular markers provide researchers with a powerful tool for variation analysis between plant genomes. They are heritable and widely distributed across the genome and for this reason have many applications in plant taxonomy and genotyping. Over the last decade, molecular marker technology has developed rapidly and is now a crucial component for genetic linkage analysis, trait mapping, diversity analysis, and association studies. This chapter focuses on molecular marker discovery, its application, and future perspectives for plant genotyping through pangenome assemblies. Included are descriptions of automated methods for genome and sequence distance estimation, genome contaminant analysis in sequence reads, genome structural variation, and SNP discovery methods.\n\nHigh-Throughput Genotyping Technologies in Plant Taxonomy.", "token_count": 163, "char_count": 833, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7297, "quality_score": 0.8649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:25.784986", "source": { "split": "train_shard_00000", "doc_id": 2492 }, "chunk_id": "train_shard_00000_2492_0", "global_id": 2746 }, { "text": "Kefir grains are a unique symbiotic association of different microbiota, including a variety of bacterial and fungal species. The microbiota in kefir grains is strongly influenced by the geographical origin and sub-culturing environment. After sub-culturing in goat milk for 2 to 4 months, amplicon sequencing (16S rRNA and ITS1 region) was applied for the identification of bacterial and fungal autogenic succession of three kefir grains collected from China (CN, Asia), Germany (DE, Europe) and United States of America (USA, America). Taxonomic analysis displayed three main bacterial and fungal species in kefir grains from different origins during sub-culturing process (Lactobacillus helveticus, Lactobacillus kefiranofaciens and Lactobacillus kefiri for bacteria, Kazachstania unispora, Kluyveromyces marxianus and Saccharomyces cerevisiae for fungi). Based on the results of beta diversity analysis, microbiota in kefir grains from CN and DE would be stable when sub-cultured in goat milk for more than three months. Differently, a highly microbial stability has been found for the sample from USA during the whole sub-culturing process. These results helped to understand the composition and stability of microbiota in kefir grains when sub-cultured in goat milk.\n\nAutogenic successions of bacteria and fungi in kefir grains from different origins when sub-cultured in goat milk.", "token_count": 369, "char_count": 1388, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:26.364570", "source": { "split": "train_shard_00000", "doc_id": 2493 }, "chunk_id": "train_shard_00000_2493_0", "global_id": 2747 }, { "text": "Fungi of the genus Botrytis infect >1,400 plant species and cause losses in many crops. Besides the broad host range pathogen Botrytis cinerea, most other species are restricted to a single host. Long-read technology was used to sequence genomes of eight Botrytis species, mostly pathogenic on Allium species, and the related onion white rot fungus, Sclerotium cepivorum. Most assemblies contained <100 contigs, with the Botrytis aclada genome assembled in 16 gapless chromosomes. The core genome and pan-genome of 16 Botrytis species were defined and the secretome, effector, and secondary metabolite repertoires analyzed. Among those genes, none is shared among all Allium pathogens and absent from non-Allium pathogens. The genome of each of the Allium pathogens contains 8-39 predicted effector genes that are unique for that single species, none stood out as potential determinant for host specificity. Chromosome configurations of common ancestors of the genus Botrytis and family Sclerotiniaceae were reconstructed. The genomes of B. cinerea and B. aclada were highly syntenic with only 19 rearrangements between them. Genomes of Allium pathogens were compared with ten other Botrytis species (nonpathogenic on Allium) and with 25 Leotiomycetes for their repertoire of secondary metabolite gene clusters. The pattern was complex, with several clusters displaying patchy distribution. Two clusters involved in the synthesis of phytotoxic metabolites are at distinct genomic locations in different Botrytis species. We provide evidence that the clusters for botcinic acid production in B. cinerea and Botrytis sinoallii were acquired by horizontal transfer from taxa within the same genus.\n\nDynamics in Secondary Metabolite Gene Clusters in Otherwise Highly Syntenic and Stable Genomes in the Fungal Genus Botrytis.", "token_count": 472, "char_count": 1820, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:27.003937", "source": { "split": "train_shard_00000", "doc_id": 2494 }, "chunk_id": "train_shard_00000_2494_0", "global_id": 2748 }, { "text": "Rhizobium-legume symbioses serve as paradigmatic examples for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and interkingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer. The data suggest that SNF likely emerged several times within the genus Ensifer through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the \"symbiotic\" and \"nonsymbiotic\" clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the nonsymbiotic clade. Initial characterization of a subset of ten Ensifer strains identified several putative phenotypic differences between the clades. Tested strains of the nonsymbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, the tested strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.\n\nSymbiotic and Nonsymbiotic Members of the Genus Ensifer (syn. Sinorhizobium) Are Separated into Two Clades Based on Comparative Genomics and High-Throughput Phenotyping.", "token_count": 486, "char_count": 1923, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5632, "quality_score": 0.7816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:27.653029", "source": { "split": "train_shard_00000", "doc_id": 2495 }, "chunk_id": "train_shard_00000_2495_0", "global_id": 2749 }, { "text": "Breast milk contains bile salt-stimulated lipase (BSSL), which significantly increases the fat digestion capacity of newborns who have limited pancreatic lipase secretion in the first few months after birth. Problematically, Holder pasteurization used in non-profit milk banks to ensure the microbiological safety of donor milk for infants, particularly preterm infants (<37 weeks gestation age), destroys milk BSSL, thus limiting infant fat absorption capacity. Alternative strategies are needed to ensure the safety of donor milk while preserving BSSL activity. Three alternative pasteurization techniques-high-pressure processing (HPP, 550 MPa, 5 min), gamma cell irradiation (IR, 2.5 Mrads) and UV-C (254 nm, 0-33,000 J/L)-were compared with Holder pasteurization (low-temperature long-time, LTLT, 62.5°C, 30 min) for retention of BSSL activity in donor breast milk. As the time required for donor milk pasteurization by UV-C in published methods was not clear, donor breast milk was spiked with seven common bacterial strains and treated by UV-C for variable time periods and the minimum UV-C dosage required to achieve a 5-log\n\nBile Salt-Stimulated Lipase Activity in Donor Breast Milk Influenced by Pasteurization Techniques.", "token_count": 332, "char_count": 1232, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6686, "quality_score": 0.8343, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:28.267478", "source": { "split": "train_shard_00000", "doc_id": 2496 }, "chunk_id": "train_shard_00000_2496_0", "global_id": 2750 }, { "text": "Non-alcoholic fatty liver disease (NAFLD) includes a range of liver diseases that occur in the absence of significant alcohol consumption. The probiotic bacterial strains\n\nBile salt hydrolase-overexpressing", "token_count": 50, "char_count": 206, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:28.650120", "source": { "split": "train_shard_00000", "doc_id": 2497 }, "chunk_id": "train_shard_00000_2497_0", "global_id": 2751 }, { "text": "The positive impact of certain non-Saccharomyces yeasts on the aromatic profile of wines has been well documented in literature and their industrial use in association with S. cerevisiae is now recommended. Competition between non-Saccharomyces species and Saccharomyces cerevisiae for various nutrients, especially nitrogen sources, greatly impacts the production of aroma compounds. In this study, we further explored the impact of different nitrogen nutrition strategies on the production of carbon and sulphur volatile compounds of three non-Saccharomyces strains, namely Pichia burtonii, Kluyveromyces marxianus, Zygoascus meyerae sequentially inoculated with S. cerevisiae in Sauvignon blanc and Shiraz grape musts. Nitrogen additions were implemented according the specific requirement of each species. At the end of fermentation, we observed specific metabolic signatures for each strain in response to the nature of the nitrogen source suggesting strain-specific metabolic fluxes present. Overall, these results confirmed and further explored the interconnection between nitrogen sources and aroma metabolism (including that of higher alcohols, fatty acids, esters and volatile sulphur compounds), and their variations according to species and the nature of the nitrogen source. The knowledge generated provides new insights to modulate the aroma profile of wines produced with non-Saccharomyces species.\n\nNitrogen metabolism in three non-conventional wine yeast species: A tool to modulate wine aroma profiles.", "token_count": 349, "char_count": 1520, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6068, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:29.246937", "source": { "split": "train_shard_00000", "doc_id": 2498 }, "chunk_id": "train_shard_00000_2498_0", "global_id": 2752 }, { "text": "Bile acids are proposed as therapeutic agents for various diseases, including liver diseases and obesity. However, oral or subcutaneous administration of a solubilized version of these drugs has limited efficacy and imposes unwanted side effects. Here, we describe a gold-templating method for fabricating stable, bile salt-cholate or deoxycholate-microparticles. The gold ions' reduction at the oil-water interface in a double emulsion solvent evaporation process enables a gold-bile salt interaction and the formation of bile salt particles. We demonstrate that composite microparticles release cholate/deoxycholate into solution via a surface erosion process. We illustrate these particles' capability to lyse adipocytes, both in vitro and in vivo, with minimal side effects, contrary to the Food and Drug Administration-approved salt solution that leads to severe inflammation and ulceration. Overall, particle-based cholate/deoxycholate opens opportunities for localized delivery of these salts, improving efficacy while minimizing side effects associated with oral and subcutaneous use.\n\nBiodegradable, bile salt microparticles for localized fat dissolution.", "token_count": 268, "char_count": 1164, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7078, "quality_score": 0.8539, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:29.835576", "source": { "split": "train_shard_00000", "doc_id": 2499 }, "chunk_id": "train_shard_00000_2499_0", "global_id": 2753 }, { "text": "Rhein, the active ingredient of rhubarb, a medicinal and edible plant, is widely used in clinical practice. However, the effects of repeated intake of rhein on liver function and bile acid metabolism are rarely reported. In this work, we investigated the alterations of 14 bile acids and hepatic transporters after rats were administered with rhein for 5 weeks. There was no obvious injury to the liver and kidney, and there were no significant changes in biochemical indicators. However, 1,000 mg/kg rhein increased the liver total bile acid (TBA) levels, especially taurine-conjugated bile acids (t-CBAs), inhibited the expression of farnesoid X receptor (FXR), small heterodimer partner (SHP), and bile salt export pump (BSEP) mRNA, and upregulated the expression of (cholesterol 7\n\nEffects of Rhein on Bile Acid Homeostasis in Rats.", "token_count": 239, "char_count": 836, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:30.313917", "source": { "split": "train_shard_00000", "doc_id": 2500 }, "chunk_id": "train_shard_00000_2500_0", "global_id": 2754 }, { "text": "We describe the case of a 71-year-old woman who presented with obstructive jaundice and subhilar bile duct stenosis. MRI showed extensive cholecystolithiasis with an impacted bile stone in the cystic duct suggesting Mirizzi syndrome. Delayed enhancement of the thickened gallbladder wall suggested inflammation instead of carcinoma. After drainage of the obstructed bile duct via ERCP, the patient developed liver abscesses with a nosocomial vancomycin-resistant enterococcus infection treated by linezolid. After 4 weeks, the VRE infection was complicated by a new-onset 23 rRNA gene-mediated linezolid resistance in the same bacterial strain, which was proven via core genome multilocus sequencing. Meropenem and tigecycline were administered according to a resistogram. Furthermore, percutaneous transhepatic biliary drainage of both sides of the liver was necessary. After demission, the patient had to be admitted again due to septic shock. An emergency operation revealed extended, inoperable gallbladder cancer. The patient died a few days later in the intensive care unit. An earlier diagnosis of bile duct infiltrating gallbladder cancer by cholangioscopy or laparoscopy and treatment of vancomycin-resistant enterococcus infection with daptomycin may have changed the clinical course of the disease.\n\nGallbladder Cancer Presenting as Mirizzi Syndrome Complicated by Rapidly Evolving 23 rRNA Gene-Linezolid Resistance with Vancomycin-Resistant Enterococcus Infection Resulting in Fatal Cholangial Sepsis.", "token_count": 399, "char_count": 1513, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:31.271498", "source": { "split": "train_shard_00000", "doc_id": 2501 }, "chunk_id": "train_shard_00000_2501_0", "global_id": 2755 }, { "text": "Salmonella enterica, the causative agent of gastrointestinal diseases and typhoid fever, is a human and animal pathogen that causes significant mortality and morbidity worldwide. In this study, we examine the genomic diversity and phylogenetic relationships of 63 S. enterica isolates from human-derived clinical specimens submitted to the Department of Health and Human Services (DHHS) in the state of New Hampshire, USA in 2017. We found a remarkably large genomic, phylogenetic and serotype variation among the S. enterica isolates, dominated by serotypes Enteritidis (sequence type [ST] 11), Heidelberg (ST 15) and Typhimurium (ST 19). Analysis of the distribution of single nucleotide polymorphisms in the core genome suggests that the ST 15 cluster is likely a previously undetected or cryptic outbreak event that occurred in the south/southeastern part of New Hampshire in August-September. We found that nearly all of the clinical S. enterica isolates carried horizontally acquired genes that confer resistance to multiple classes of antimicrobials, most notably aminoglycosides, fluoroquinolones and macrolides. Majority of the isolates (76.2%) carry at least four resistance determinants per genome. We also detected the genes mdtK and mdsABC that encode multidrug efflux pumps and the gene sdiA that encodes a regulator for a third multidrug resistance pump. Our results indicate rapid microevolution and geographical dissemination of multidrug resistant lineages over a short time span. These findings are critical to aid the DHHS and similar public health laboratories in the development of effective disease control measures, epidemiological studies and treatment options for serious Salmonella infections.\n\nDiverse lineages of multidrug resistant clinical Salmonella enterica and a cryptic outbreak in New Hampshire, USA revealed from a year-long genomic surveillance.", "token_count": 458, "char_count": 1883, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:31.915822", "source": { "split": "train_shard_00000", "doc_id": 2502 }, "chunk_id": "train_shard_00000_2502_0", "global_id": 2756 }, { "text": "Bile salt-dependent lipase (BSDL) within intestinal lumen can be endocytosed by enterocytes and support the intestinal barrier function. However, the epithelial-supporting effect of this protein has not been verified in a human cell line and neither the direct signaling pathway nor the function of endocytosis in this process has been clearly identified. We sought to investigate the signaling pathway and the membrane receptor through which BSDL might exert these effects using intestinal epithelial cells. Caco-2 cells were treated with recombinant BSDL, and the barrier function, cell proliferation, and activation of the Wnt signaling pathway were assessed. The effect of Wnt signaling activation induced by BSDL and BSDL endocytosis was investigated in LRP6-silenced and non-silenced cells. Moreover, caveolae- and clathrin-dependent endocytosis inhibitors were also applied respectively to analyze their effects on Wnt signaling activation induced by BSDL. BSDL treatment increased the barrier function but not proliferation of Caco-2 cells. It also induced β-catenin nuclear translocation and activated Wnt target gene transcription. Moreover, in the Wnt pathway, BSDL increased the levels of non-phosphorylated-β-catenin (Ser33/37/Thr41) and phosphorylated-β-catenin (Ser552). Notably, the silencing of LRP6 expression impaired BSDL endocytosis and decreased BSDL-induced β-catenin nuclear translocation. The inhibition of BSDL endocytosis induced by caveolae-mediated endocytosis inhibitor was stronger than that by clathrin-mediated endocytosis inhibitor, and the Wnt signaling activation associated with its endocytosis was also most likely caveolae-dependent. Our findings suggested that LRP6, a canonical Wnt pathway co-receptor, can mediate BSDL endocytosis and then activate Wnt signaling in Caco-2 cells.\n\nBile salt-dependent lipase promotes the barrier integrity of Caco-2 cells by activating Wnt/β-catenin signaling via LRP6 receptor.", "token_count": 513, "char_count": 1953, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5364, "quality_score": 0.7682, "entities": { "genes": [ "LRP6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:23:32.570498", "source": { "split": "train_shard_00000", "doc_id": 2503 }, "chunk_id": "train_shard_00000_2503_0", "global_id": 2757 }, { "text": "Mycoprotein is the fungal biomass obtained by the fermentation of Fusarium venenatum, whose intake has been shown to lower blood lipid levels. This in vitro study aimed to understand the mechanisms whereby mycoprotein can influence lipid digestion by reducing lipolysis and binding to bile salts. Mycoprotein at 30 mg mL\n\nMycoprotein ingredient structure reduces lipolysis and binds bile salts during simulated gastrointestinal digestion.", "token_count": 116, "char_count": 438, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:32.961903", "source": { "split": "train_shard_00000", "doc_id": 2504 }, "chunk_id": "train_shard_00000_2504_0", "global_id": 2758 }, { "text": "Anastrozole is a selective non-steroidal aromatase inhibitor that blocks the conversion of androgens to estrogens in peripheral tissues. It is used as adjuvant therapy for early-stage hormone-sensitive breast cancer in postmenopausal women. Significant side effects of anastrozole include osteoporosis and increased levels of cholesterol. To date, seven case reports on anastrozole hepatotoxicity have been published. We report the case of an 81-year-old woman with a history of breast cancer, arterial hypertension, type 2 diabetes mellitus, hyperlipidemia, and chronic renal insufficiency. Four days after switching hormone therapy from tamoxifen to anastrozole, icterus developed along with a significant increase in liver enzymes (measured in the blood). The patient was admitted to hospital, where a differential diagnosis of jaundice was made and anastrozole was withdrawn. Subsequently, hepatic functions quickly normalized. The observed liver injury was attributed to anastrozole since other possible causes of jaundice were excluded. However, concomitant pharmacotherapy could have contributed to the development of jaundice and hepatotoxicity, after switching from tamoxifen to anastrozole since several the patient's medications were capable of inhibiting hepatobiliary transport of bilirubin, bile acids, and metabolized drugs through inhibition of ATP-binding cassette proteins. Telmisartan, tamoxifen, and metformin all block bile salt efflux pumps. The efflux function of multidrug resistance protein 2 is known to be reduced by telmisartan and tamoxifen and breast cancer resistance protein is known to be inhibited by telmisartan and amlodipine. Moreover, the activity of P-glycoprotein transporters are known to be decreased by telmisartan, amlodipine, gliquidone, as well as the previously administered tamoxifen. Finally, the role of genetic polymorphisms of cytochrome P450 enzymes and/or drug transporters cannot be ruled out since the patient was not tested for polymorphisms.", "token_count": 519, "char_count": 1999, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:23:33.595323", "source": { "split": "train_shard_00000", "doc_id": 2505 }, "chunk_id": "train_shard_00000_2505_0", "global_id": 2759 }, { "text": "Drug-induced liver injury after switching from tamoxifen to anastrozole in a patient with a history of breast cancer being treated for hypertension and diabetes.", "token_count": 36, "char_count": 161, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9583, "quality_score": 0.9792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:33.963731", "source": { "split": "train_shard_00000", "doc_id": 2505 }, "chunk_id": "train_shard_00000_2505_1", "global_id": 2760 }, { "text": "Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.\n\nImpact of homologous recombination on core genome phylogenies.", "token_count": 176, "char_count": 773, "word_count": 111, "semantic_coherence": 1, "information_density": 0.6937, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:34.407851", "source": { "split": "train_shard_00000", "doc_id": 2506 }, "chunk_id": "train_shard_00000_2506_0", "global_id": 2761 }, { "text": "Theabrownin is one of the most bioactive compounds in Pu-erh tea. Our previous study revealed that the hypocholesterolemic effect of theabrownin was mediated by the modulation of bile salt hydrolase (BSH)-enriched gut microbiota and bile acid metabolism. In this study, we demonstrated that theabrownin ameliorated high-fat-diet (HFD)-induced obesity by modifying gut microbiota, especially those with 7α-dehydroxylation on the species level, and these changed microbes were positively correlated with secondary bile acid (BA) metabolism. Thus, altered intestinal BAs resulted in shifting bile acid biosynthesis from the classic to the alternative pathway. This shift changed the BA pool by increasing non-12α-hydroxylated-BAs (non-12OH-BAs) and decreasing 12α-hydroxylated BAs (12OH-BAs), which improved energy metabolism in white and brown adipose tissue. This study showed that theabrownin was a potential therapeutic modality for obesity and other metabolic disorders via gut microbiota-driven bile acid alternative synthesis.\n\nAnti-Adipogenic Effect of Theabrownin Is Mediated by Bile Acid Alternative Synthesis via Gut Microbiota Remodeling.", "token_count": 327, "char_count": 1147, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6536, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:34.981210", "source": { "split": "train_shard_00000", "doc_id": 2507 }, "chunk_id": "train_shard_00000_2507_0", "global_id": 2762 }, { "text": "The positive effect of common beans on reducing blood cholesterol levels has been linked to their ability to sequester bile salts (BS) and prevent their recycling. We have examined the preferences of major bean components (soluble/insoluble fiber, starch and proteins) to retain BS, and the role played by the bean matrix. Additionally, the kinetics of BS-release were evaluated in bean flours generated by a combination of hydrothermal or high-hydrostatic pressure (HHP), and mechanical treatments. An in vitro digestion model combined with dialysis was used to evaluate separately the retention of primary individual BS. Soluble fiber retained a significant proportion of BS mainly due to an increased digesta viscosity; however, the protein fraction exhibited the greatest BS retention without affecting viscosity. The thermal properties of proteins and starch were more significantly affected in presence of tauro-chenodeoxycholate, which correlated to the affinity of both fractions to retain more hydrophobic BS during digestion. Glyco-chenodeoxycholate and tauro-cholate were the most and least effectively retained BS by bean flours, respectively. Neither of the processing treatments had an impact on the binding preferences of bean flours to the primary BS; however, the largest BS retention was caused by HHP at 600 MPa. Bean materials preferentially delayed the release of chenodeoxycholate BS, which is probably related to BS micelle formation. These findings demonstrate that a combination of viscosity, molecular and compositional factors is triggering the BS-retention capacity of beans, and indicate the importance of evaluating contribution of individual bean components and as whole system.\n\nRetention of primary bile salts by dry beans (Phaseolus vulgaris L.) during in vitro digestion: Role of bean components and effect of food processing.", "token_count": 410, "char_count": 1861, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6052, "quality_score": 0.8026, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:35.601922", "source": { "split": "train_shard_00000", "doc_id": 2508 }, "chunk_id": "train_shard_00000_2508_0", "global_id": 2763 }, { "text": "During passage through the human gastrointestinal tract, enterohemorrhagic\n\nBile Salts Differentially Enhance Resistance of Enterohemorrhagic Escherichia coli O157:H7 to Host Defense Peptides.", "token_count": 62, "char_count": 192, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:35.973469", "source": { "split": "train_shard_00000", "doc_id": 2509 }, "chunk_id": "train_shard_00000_2509_0", "global_id": 2764 }, { "text": "Bile salts play a pivotal role in lipid homeostasis, are sensed by specialized receptors, and have been implicated in various disorders affecting the gut or liver. They may play a role either as culprit or as potential panacea. Four very efficient transporters mediate most of the hepatic and intestinal bile salt uptake and efflux, and are each essential for the efficient enterohepatic circulation of bile salts. Starting from the intestinal lumen, conjugated bile salts cross the otherwise impermeable lipid bilayer of (primarily terminal ileal) enterocytes through the apical sodium-dependent bile acid transporter (gene SLC10A2) and leave the enterocyte through the basolateral heteromeric organic solute transporter, which consists of an alpha and beta subunit (encoded by SLC51A and SLC51B). The Na\n\nTargeting the Four Pillars of Enterohepatic Bile Salt Cycling; Lessons From Genetics and Pharmacology.", "token_count": 243, "char_count": 909, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6866, "quality_score": 0.8433, "entities": { "genes": [ "SLC51B", "SLC51A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:36.459605", "source": { "split": "train_shard_00000", "doc_id": 2510 }, "chunk_id": "train_shard_00000_2510_0", "global_id": 2765 }, { "text": "This study aimed to examine the influence of two prebiotics, fructo-oligosaccharides (FOS) and xylo-oligosaccharides (XOS), on probiotic properties (resistance to low pH and bile salt, hydrophobicity and auto-aggregation), metabolites production, and antimicrobial activity of probiotic Lactiplantibacillus (L. pentosus S42 and L. plantarum S61) and Levilactobacillus (L. brevis S27) strains isolated from fermented olive. The results demonstrated the ability of strains to ferment XOS more than FOS as a sole carbon source, resulting in pH reduction. The prebiotics (FOS and XOS) significantly increased (p < 0.05) their survival in gastro-intestinal conditions (low pH and 0.3% of bile salts), as well as their hydrophobicity, auto-aggregation and production of proteins, compared to glucose (control). The major organic acids produced by Lactiplantibacillus and Levilactobacillus strains, were oxalic, malic and lactic acids from FOS, XOS and glucose, respectively. No antimicrobial activity was observed from cell-free supernatant (CFS) of Lactiplantibacillus and Levilactobacillus strains obtained from FOS. In the presence of XOS the organic acids, produced by Lactiplantibacillus and Levilactobacillus strains, were more diverse with high contents, and exhibited higher antifungal and antibacterial activities, more than that of FOS and glucose. The combination of L. plantarum S61 and XOS demonstrated the highest inhibition zones ranges of 20.7-22.2 mm against pathogenic bacteria and 29.2-30 mm against yeasts. This combination can be used in production of antifungal preservatives and pharmaceuticals, against pathogenic and spoilage yeasts.", "token_count": 490, "char_count": 1652, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6018, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:37.112309", "source": { "split": "train_shard_00000", "doc_id": 2511 }, "chunk_id": "train_shard_00000_2511_0", "global_id": 2766 }, { "text": "The prebiotics (Fructo-oligosaccharides and Xylo-oligosaccharides) modulate the probiotic properties of Lactiplantibacillus and Levilactobacillus strains isolated from traditional fermented olive.", "token_count": 60, "char_count": 196, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:37.494649", "source": { "split": "train_shard_00000", "doc_id": 2511 }, "chunk_id": "train_shard_00000_2511_1", "global_id": 2767 }, { "text": "Colonization of the gastrointestinal tract by enterohaemorrhagic\n\nMolecular basis of bile-salt- and iron-induced enterohaemorrhagic", "token_count": 46, "char_count": 131, "word_count": 14, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:37.858075", "source": { "split": "train_shard_00000", "doc_id": 2513 }, "chunk_id": "train_shard_00000_2513_0", "global_id": 2768 }, { "text": "The current human reference genome (GRCh38), with its superior quality, has contributed significantly to genome analysis. However, GRCh38 may still underrepresent the ethnic genome, specifically for Asians, though exactly what we are missing is still elusive. Here, we juxtaposed GRCh38 with a high-contiguity genome assembly of one Korean (AK1) to show that a part of AK1 genome is missing in GRCh38 and that the missing regions harbored ~1390 putative coding elements. Furthermore, we found that multiple populations shared some certain parts in the missing genome when we analyzed the \"unmapped\" (to GRCh38) reads of fourteen individuals (five East-Asians, four Europeans, and five Africans), amounting to ~5.3 Mb (~0.2% of AK1) of the total genomic regions. The recovered AK1 regions from the \"unmapped reads\", which were the estimated missing regions that did not exist in GRCh38, harbored candidate coding elements. We verified that most of the common (shared by ≥7 individuals) missing regions exist in human and chimpanzee DNA. Moreover, we further identified the occurrence mechanism and ethnic heterogeneity as well as the presence of the common missing regions. This study illuminates a potential advantage of using a pangenome reference and brings up the need for further investigations on the various features of regions globally missed in GRCh38.\n\nA High Quality Asian Genome Assembly Identifies Features of Common Missing Regions.", "token_count": 347, "char_count": 1445, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [ "AK1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:38.435182", "source": { "split": "train_shard_00000", "doc_id": 2514 }, "chunk_id": "train_shard_00000_2514_0", "global_id": 2769 }, { "text": "Next generation sequencing technologies are becoming more accessible and affordable over the years, with entire genome sequences of several pathogens being deciphered in few hours. However, there is the need to analyze multiple genomes within a short time, in order to provide critical information about a pathogen of interest such as drug resistance, mutations and genetic relationship of isolates in an outbreak setting. Many pipelines that currently do this are stand-alone workflows and require huge computational requirements to analyze multiple genomes. We present an automated and scalable pipeline called BAGEP for monomorphic bacteria that performs quality control on FASTQ paired end files, scan reads for contaminants using a taxonomic classifier, maps reads to a reference genome of choice for variant detection, detects antimicrobial resistant (AMR) genes, constructs a phylogenetic tree from core genome alignments and provide interactive short nucleotide polymorphism (SNP) visualization across core genomes in the data set. The objective of our research was to create an easy-to-use pipeline from existing bioinformatics tools that can be deployed on a personal computer. The pipeline was built on the Snakemake framework and utilizes existing tools for each processing step: fastp for quality trimming, snippy for variant calling, Centrifuge for taxonomic classification, Abricate for AMR gene detection, snippy-core for generating whole and core genome alignments, IQ-TREE for phylogenetic tree construction and vcfR for an interactive heatmap visualization which shows SNPs at specific locations across the genomes. BAGEP was successfully tested and validated with\n\nThe Bacteria Genome Pipeline (BAGEP): an automated, scalable workflow for bacteria genomes with Snakemake.", "token_count": 393, "char_count": 1791, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:39.050041", "source": { "split": "train_shard_00000", "doc_id": 2515 }, "chunk_id": "train_shard_00000_2515_0", "global_id": 2770 }, { "text": "A non-invasive, at-home test for neonatal jaundice can facilitate early jaundice detection in infants, improving clinical outcomes for neonates with severe jaundice and helping to prevent the development of kernicterus, a type of brain damage whose symptoms include hearing loss, impairment of cognitive capacity, and death. Here a photonic sensor that utilizes color changes induced by analyte infiltration into a chemically functionalized inverse opal structure is developed. The sensor is calibrated to detect differences in urinary surface tension due to increased bile salt concentration in urine, which is symptomatic of abnormal liver function and linked to jaundice. The correlation between neonatal urinary surface tension and excess serum bilirubin, the physiologic cause of neonatal jaundice, is explored. It is shown that these non-invasive sensors can improve the preliminary diagnosis of neonatal jaundice, reducing the number of invasive blood tests and hospital visits necessary for healthy infants while ensuring that jaundiced infants are treated in a timely manner. The use of inverse opal sensors to measure bulk property changes in bodily fluids can be extended to the detection of several other conditions, making this technology a versatile platform for convenient point-of-care diagnosis.\n\nInverse Opal Films for Medical Sensing: Application in Diagnosis of Neonatal Jaundice.", "token_count": 318, "char_count": 1400, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6634, "quality_score": 0.8317, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:39.607396", "source": { "split": "train_shard_00000", "doc_id": 2516 }, "chunk_id": "train_shard_00000_2516_0", "global_id": 2771 }, { "text": "The past decade has brought a significant rise in antimicrobial resistance, and the ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) have considerably aggravated a threat to public health, causing nosocomial infections worldwide. The objective of the current study was to isolate novel probiotic strain with antimicrobial activity against multidrug-resistant ESKAPE pathogens. For this purpose, eighteen breastfed infant faeces were collected and lactic acid bacteria (LAB) with antagonistic activity were isolated. Out of 102 anaerobic LAB isolated, only nine exhibited inhibitory activity against all ESKAPE pathogens. These selected nine isolates were further characterized for their probiotic attributes such as lysozyme tolerance, simulated gastrointestinal tolerance, cellular auto-aggregation and cell surface hydrophobicity. Bile salt deconjugation and cholesterol-lowering capacity was also determined. Among all nine, isolate LBM220 was found to possess superior probiotic potential. Confirmatory identification of isolate LBM220 was done by both 16S rRNA sequence analysis and mass spectrometric analysis using MALDI-TOF. Based on BLAST result, isolate LBM220 was identified as Lactobacillus gasseri. Phylogenetic analysis of Lactobacillus gasseri LBM220 [accession number MN097539] was performed. Also, detailed safety evaluation study of Lact. gasseri LBM220 showed the presence of intrinsic antibiotic resistance and the absence of hemolytic, DNase, gelatinase and toxic mucinolytic activity. Time kill assay was also performed to confirm the strong kill effect of Lact. gasseri LBM220 on all six multidrug resistant ESKAPE pathogens. Thus, Lact. gasseri LBM220 can be utilized and explored as potential probiotic with therapeutic intervention.", "token_count": 506, "char_count": 1869, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6926, "quality_score": 0.8463, "entities": { "genes": [ "LBM220", "MN097539" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:40.303615", "source": { "split": "train_shard_00000", "doc_id": 2517 }, "chunk_id": "train_shard_00000_2517_0", "global_id": 2772 }, { "text": "Selection of Potential Probiotic Bacteria from Exclusively Breastfed Infant Faeces with Antagonistic Activity Against Multidrug-Resistant ESKAPE Pathogens.", "token_count": 43, "char_count": 155, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:40.678058", "source": { "split": "train_shard_00000", "doc_id": 2517 }, "chunk_id": "train_shard_00000_2517_1", "global_id": 2773 }, { "text": "The yeast Kluyveromyces marxianus offers unique potential for industrial biotechnology because of useful features like rapid growth, thermotolerance and a wide substrate range. As an emerging alternative platform, K. marxianus requires the development and validation of metabolic engineering strategies to best utilise its metabolism as a basis for bio-based production.\n\nRational engineering of Kluyveromyces marxianus to create a chassis for the production of aromatic products.", "token_count": 109, "char_count": 480, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7538, "quality_score": 0.8769, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:41.068097", "source": { "split": "train_shard_00000", "doc_id": 2518 }, "chunk_id": "train_shard_00000_2518_0", "global_id": 2774 }, { "text": "Nature suggests that complex materials result from a hierarchical organization of matter at different length scales. At the nano- and micrometer scale, macromolecules and supramolecular aggregates spontaneously assemble into supracolloidal structures whose complexity is given by the coexistence of various colloidal entities and the specific interactions between them. Here, we demonstrate how such control can be implemented by engineering specially customized bile salt derivative-based supramolecular tubules that exhibit a highly specific interaction with polymeric microgel spheres at their extremities thanks to their scroll-like structure. This design allows for hierarchical supracolloidal self-assembly of microgels and supramolecular scrolls into a regular framework of \"nodes\" and \"linkers\". The supramolecular assembly into scrolls can be triggered by pH and temperature, thereby providing the whole supracolloidal system with interesting stimuli-responsive properties. A colloidal smart assembly is embodied with features of center-linker frameworks as those found in molecular metal-organic frameworks and in structures engineered at human scale, masterfully represented by the Atomium in Bruxelles.\n\nSupracolloidal Atomium.", "token_count": 274, "char_count": 1239, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6937, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:41.662648", "source": { "split": "train_shard_00000", "doc_id": 2519 }, "chunk_id": "train_shard_00000_2519_0", "global_id": 2775 }, { "text": "Data-driven engineering of microbes has been demonstrated for the sustainable production of high-performance chemicals. Metabolic profiling analysis is essential to increase the productivity of target compounds. However, improvement of comprehensive analysis methodologies is required for the high demands of metabolic engineering. Therefore, a liquid chromatography-tandem mass spectrometry (LC-MS/MS) based methodology was designed and applied to cover a wide target range with high precision. Ion-pair free separation of metabolites on a pentafluorophenyl propyl column enabled high-precision quantification of 113 metabolites. The method was further evaluated for high reproducibility and robustness. Target analytes consisted of primary metabolites and intermediate metabolites for microbial production of high-performance chemicals. 95 metabolites could be detected with high reproducibility of peak area (intraday data: CV<15%), and 53 metabolites could be sensitively determined within a wide dynamic linear range (3-4 orders of magnitude). The developed system was further applied to the metabolomic analysis of various prokaryotic and eukaryotic microorganisms. Differences due to culture media and metabolic phenotypes could be observed when comparing the metabolomes of conventional and non-conventional yeast. Furthermore, almost all Kluyveromyces marxianus metabolites could be detected with moderate reproducibility (CV<40%, among independent extractions), where 41 metabolites were detected with very high reproducibility (CV<15%). In addition, the accuracy was validated via a spike-and-recovery test,and 78 metabolites were detected with analyte recovery in the 80-120% range. Together these results establish ion-pair free metabolic profiling as a comprehensive and precise tool for data-driven bioengineering applications.\n\nAn ion-pair free LC-MS/MS method for quantitative metabolite profiling of microbial bioproduction systems.", "token_count": 457, "char_count": 1950, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6064, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:42.317275", "source": { "split": "train_shard_00000", "doc_id": 2520 }, "chunk_id": "train_shard_00000_2520_0", "global_id": 2776 }, { "text": "Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset to quantify error rates in comparisons of identical genomes. We show that all M. chelonae isolates tested were highly dissimilar, as indicated by high pairwise SNV values, consistent with environmental acquisition and not a nosocomial point source. Our control dataset determined a threshold for evaluating identity between strains while controlling for sequencing error. Finally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants were identified that have the potential to modulated drug resistance.\n\nInvestigating hospital Mycobacterium chelonae infection using whole genome sequencing and hybrid assembly.", "token_count": 319, "char_count": 1469, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6373, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:42.880832", "source": { "split": "train_shard_00000", "doc_id": 2521 }, "chunk_id": "train_shard_00000_2521_0", "global_id": 2777 }, { "text": "Yeast communities associated with cacti were studied in three ecosystems of Southeast, Central and North Brazil. A total of 473 yeast strains belonging to 72 species were isolated from 190 samples collected. Cactophilic yeast species were prevalent in necrotic tissues, flowers, fruits and insects of cacti collected in Southeast and North Brazil. Pichia cactophila, Candida sonorensis and species of the Sporopachydermia complex were the most prevalent cactophilic species in Southeast and Central regions. Kodamaea nitidulidarum, Candida restingae and Wickerhamiella cacticola were frequently associated with cactus flowers and fruits. The diversity of yeasts associated with the substrates studied was high. Twenty-one novel species were found. One is described here as Kluyveromyces starmeri sp. nov. based on 21 isolates obtained from necrotic tissues, flowers, fruits and associated insects of the columnar cacti Cereus saddianus, Micranthocereus dolichospermaticus and Pilosocereus arrabidae in two different ecosystems in Brazil. Phylogenetic analyses of sequences encoding the gene of the small subunit (SSU) rRNA gene, the internal transcribed spacer, the 5.8S rRNA gene and the D1/D2 domains of the large subunit (LSU) rRNA showed that the species is related to Kluyveromyces dobzhanskii, Kluyveromyces lactis and Kluyveromyces marxianus. Phylogenomic analyses based on 1264 conserved genes shared among the new species and 19 other members of the Saccharomycetaceae confirmed this phylogenetic relationship. The holotype is K. starmeri sp. nov. CBS 16103\n\nYeast communities associated with cacti in Brazil and the description of Kluyveromyces starmeri sp. nov. based on phylogenomic analyses.", "token_count": 476, "char_count": 1704, "word_count": 240, "semantic_coherence": 1, "information_density": 0.55, "quality_score": 0.775, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:43.526879", "source": { "split": "train_shard_00000", "doc_id": 2522 }, "chunk_id": "train_shard_00000_2522_0", "global_id": 2778 }, { "text": "Akkermansia muciniphila is a prominent member of the gut microbiota and the organism gets exposed to bile acids within this niche. Several gut bacteria have bile response genes to metabolize bile acids or an ability to change their membrane structure to prevent membrane damage from bile acids. To understand the response to bile acids and how A. muciniphila can persist in the gut, we studied the effect of bile acids and individual bile salts on growth. In addition, the change in gene expression under ox-bile condition was studied. The growth of A. muciniphila was inhibited by ox-bile and the bile salts mixture. Individual bile salts have differential effects on the growth. Although most bile salts inhibited the growth of A. muciniphila, an increased growth was observed under culture conditions with sodium deoxycholate. Zaragozic acid A, which is a squalene synthase inhibitor leading to changes in the membrane structure, increased the susceptibility of A. muciniphila to bile acids. Transcriptome analysis showed that gene clusters associated with an ABC transporter and RND transporter were upregulated in the presence of ox-bile. In contrast, a gene cluster containing a potassium transporter was downregulated. Membrane transporter inhibitors also decreased the tolerance to bile acids of A. muciniphila. Our results indicated that membrane transporters and the squalene-associated membrane structure could be major bile response systems required for bile tolerance in A. muciniphila. KEY POINTS: • The growth of Akkermansia muciniphila was inhibited by most bile salts. • Sodium deoxycholate increased the growth of A. muciniphila. • The genes encoding transporters and hopanoid synthesis were upregulated by ox-bile. • The inhibitors of transporters and hopanoid synthesis reduced ox-bile tolerance.\n\nThe effect of bile acids on the growth and global gene expression profiles in Akkermansia muciniphila.", "token_count": 490, "char_count": 1920, "word_count": 288, "semantic_coherence": 1, "information_density": 0.4583, "quality_score": 0.7292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:44.172373", "source": { "split": "train_shard_00000", "doc_id": 2523 }, "chunk_id": "train_shard_00000_2523_0", "global_id": 2779 }, { "text": "Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.\n\nNew insights into homoeologous copy number variations in the hexaploid wheat genome.", "token_count": 411, "char_count": 1751, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:44.793075", "source": { "split": "train_shard_00000", "doc_id": 2524 }, "chunk_id": "train_shard_00000_2524_0", "global_id": 2780 }, { "text": "Clostridioides difficile infections (CDI) are the leading cause of nosocomial antibiotic-associated diarrhea. C. difficile produces dormant spores that serve as infectious agents. Bile salts in the gastrointestinal tract signal spores to germinate into toxin-producing cells. As spore germination is required for CDI onset, anti-germination compounds may serve as prophylactics. CamSA, a synthetic bile salt, was previously shown to inhibit C. difficile spore germination in vitro and in vivo. Unexpectedly, a single dose of CamSA was sufficient to offer multi-day protection from CDI in mice without any observable toxicity. To study this intriguing protection pattern, we examined the pharmacokinetic parameters of CamSA. CamSA was stable to the gut of antibiotic-treated mice but was extensively degraded by the microbiota of non-antibiotic-treated animals. Our data also suggest that CamSA's systemic absorption is minimal since it is retained primarily in the intestinal lumen and liver. CamSA shows weak interactions with CYP3A4, a P450 hepatic isozyme involved in drug metabolism and bile salt modification. Like other bile salts, CamSA seems to undergo enterohepatic circulation. We hypothesize that the cycling of CamSA between the liver and intestines serves as a slow-release mechanism that allows CamSA to be retained in the gastrointestinal tract for days. This model explains how a single CamSA dose can prevent murine CDI even though spores are present in the animal's intestine for up to four days post-challenge.\n\nPharmacokinetics of CamSA, a potential prophylactic compound against Clostridioides difficile infections.", "token_count": 428, "char_count": 1636, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:45.422239", "source": { "split": "train_shard_00000", "doc_id": 2525 }, "chunk_id": "train_shard_00000_2525_0", "global_id": 2781 }, { "text": "Here we present and analyze the complete genome of Alcaligenes faecalis strain Mc250 (Mc250), a bacterium isolated from the roots of Mimosa calodendron, an endemic plant growing in ferruginous rupestrian grasslands in Minas Gerais State, Brazil. The genome has 4,159,911 bp and 3,719 predicted protein-coding genes, in a single chromosome. Comparison of the Mc250 genome with 36 other Alcaligenes faecalis genomes revealed that there is considerable gene content variation among these strains, with the core genome representing only 39% of the protein-coding gene repertoire of Mc250. Mc250 encodes a complete denitrification pathway, a network of pathways associated with phenolic compounds degradation, and genes associated with HCN and siderophores synthesis; we also found a repertoire of genes associated with metal internalization and metabolism, sulfate/sulfonate and cysteine metabolism, oxidative stress and DNA repair. These findings reveal the genomic basis for the adaptation of this bacterium to the harsh environmental conditions from where it was isolated. Gene clusters associated with ectoine, terpene, resorcinol, and emulsan biosynthesis that can confer some competitive advantage were also found. Experimental results showed that Mc250 was able to reduce (~60%) the virulence phenotype of the plant pathogen Xanthomonas citri subsp. citri when co-inoculated in Citrus sinensis, and was able to eradicate 98% of juveniles and stabilize the hatching rate of eggs to 4% in two species of agricultural nematodes. These results reveal biotechnological potential for the Mc250 strain and warrant its further investigation as a biocontrol and plant growth-promoting bacterium.\n\nComplete genome sequence and analysis of Alcaligenes faecalis strain Mc250, a new potential plant bioinoculant.", "token_count": 476, "char_count": 1802, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6187, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:46.060205", "source": { "split": "train_shard_00000", "doc_id": 2526 }, "chunk_id": "train_shard_00000_2526_0", "global_id": 2782 }, { "text": "In this study, we aimed to assess the feasibility of the lactic acid bacterium Lactobacillus kefiranofaciens DN1 (LKF_DN1) and the yeast Kluyveromyces marxianus KU140723-05 (KMA5), recently isolated from kefir, as probiotics. Specifically, we evaluated the effect of early administration of these 2 microbes on the inhibition of Salmonella Enteritidis (SE) colonization in neonatal chicks. We also examined the effects of exposure of chicks to probiotics before SE exposure on the reduction in the number of gut SE. A total of 108 1-day-old specific-pathogen-free male layer chicks were used for 3 independent experiments. The experimental chicks were randomly divided into 6 groups (negative control: basal diet [BD] without probiotics and SE; positive control: BD; probiotic group [PG] 1: BD + LKF_DN1; PG2: BD + KMA5; PG3: BD + LKF_DN1 + KMA5; and PG4: BD+ a commercial product IDF-7), all of which, except negative control, were coadministered with SE strain resistant to rifampicin (SERR). We found that the administration of LKF_DN1 and/or KMA5 reduced the number of viable cells of the SERR strain in chicks by up to 1.90 log\n\nSynergistic effects of the early administration of Lactobacillus kefiranofaciens DN1 and Kluyveromyces marxianus KU140723-05 on the inhibition of Salmonella Enteritidis colonization in young chickens.", "token_count": 419, "char_count": 1334, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8144, "entities": { "genes": [ "DN1", "KMA5", "PG3", "KU140723", "PG2", "PG4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:46.684686", "source": { "split": "train_shard_00000", "doc_id": 2527 }, "chunk_id": "train_shard_00000_2527_0", "global_id": 2783 }, { "text": "Cholesterol homeostasis and trafficking are critical to the maintenance of the asymmetric plasma membrane of eukaryotic cells. Disruption or dysfunction of cholesterol trafficking leads to numerous human diseases. ATP-binding cassette (ABC) transporters play several critical roles in this process, and mutations in these sterol transporters lead to disorders such as Tangier disease and sitosterolemia. Biochemical and structural information on ABC sterol transporters is beginning to emerge, with published structures of ABCA1 and ABCG5/G8; these two proteins function in the reverse cholesterol transport pathway and mediate the efflux of cholesterol and xenosterols to high-density lipoprotein and bile salt micelles, respectively. Although both of these transporters belong to the ABC family and mediate the efflux of a sterol substrate, they have many distinct differences. Here, we summarize the current understanding of sterol transport driven by ABC transporters, with an emphasis on these two extensively characterized transporters.\n\nThe ABCs of Sterol Transport.", "token_count": 252, "char_count": 1073, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8221, "entities": { "genes": [ "ABCA1", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:47.177547", "source": { "split": "train_shard_00000", "doc_id": 2528 }, "chunk_id": "train_shard_00000_2528_0", "global_id": 2784 }, { "text": "Biliary lipids primarily consist of bile salts, phospholipids, and cholesterol. Bile salts have potent detergent properties and deleterious effects on the cell membrane and are cytotoxic to hepatocytes. We have previously reported that phosphatidylcholine (PC), the predominant bile phospholipid, protects hepatocytes from the cytotoxicity of bile salts, whereas cholesterol reverses the cytoprotective effects of PC against bile salts. ABCB4, a member of the ATP-binding cassette transporter family, secretes biliary phospholipids, especially PC, from the hepatocytes into the bile. Using Abcb4 knockout mice and HEK293 cells that stably expressed ABCB4, we examined the effects of taurine- or glycine-conjugated cholate, ursodeoxycholate, and hyodeoxycholate on the ABCB4-mediated efflux of PC. We observed that the biliary secretion of PC in wild-type mice significantly increased following infusion of all the tested bile salts, especially taurohyodeoxycholate. On the other hand, the biliary secretion of PC in Abcb4 knockout mice was not affected by the bile salt infusions. The results also demonstrated that the efflux of PC from ABCB4-expressing HEK293 cells was significantly stimulated by taurohyodeoxycholate, which has a strong potential to form mixed micelles with PC. Furthermore, the results of our study emphasized the possibility that the specific interactions of bile salts with ABCB4 are necessary for the release of PC molecules from the binding pocket of ABCB4 into the aqueous environment. Further understanding of this mechanism will aid in the development of novel therapeutic agents for cholestatic liver diseases.\n\n[Mechanism of Taurohyodeoxycholate-induced Biliary Phospholipid Efflux -Understanding the Function of the ABCB4 Enhancer for Developing Therapeutic Agents against Bile Salt-induced Liver Injury].", "token_count": 493, "char_count": 1837, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": { "genes": [ "ABCB4", "HEK293" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:47.830456", "source": { "split": "train_shard_00000", "doc_id": 2529 }, "chunk_id": "train_shard_00000_2529_0", "global_id": 2785 }, { "text": "Kluyveromyces marxianus is a thermotolerant, ethanol-producing yeast that requires oxygen for efficient ethanol fermentation. Under anaerobic conditions, glucose consumption and ethanol production are retarded, suggesting that oxygen affects the metabolic state of K. marxianus. Mitochondria require oxygen to function, and their forms and number vary according to environmental conditions. In this study, the effect of anoxia on mitochondrial behavior in K. marxianus was examined. Under aerobic growth conditions, mitochondria-targeted GFP exhibited a tubular and dotted localization, representing a typical mitochondrial morphology, but under anaerobic conditions, GFP localized in vacuoles, suggesting that mitophagy occurs under anaerobic conditions. To confirm mitophagy induction, the ATG32, ATG8, ATG11 and ATG19 genes were disrupted. Vacuolar localization of mitochondria-targeted GFP under anaerobic conditions was interrupted in the Δatg32 and Δatg8 strains but not the Δatg11 and Δatg19 strains. Electron microscopy revealed mitochondria-like membrane components in the vacuoles of wild-type cells grown under anaerobic conditions. Quantitative analyses using mitochondria-targeted Pho8 demonstrated that mitophagy was induced in K. marxianus by anoxia but not nitrogen starvation. To the best of our knowledge, this is the first demonstration of anoxia-induced mitophagy in yeasts.\n\nAnoxia-induced mitophagy in the yeast Kluyveromyces marxianus.", "token_count": 406, "char_count": 1458, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "ATG19", "ATG11", "ATG8", "ATG32" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:48.453180", "source": { "split": "train_shard_00000", "doc_id": 2530 }, "chunk_id": "train_shard_00000_2530_0", "global_id": 2786 }, { "text": "In this study the intraspecies diversity of Fructilactobacillus (F.) sanfranciscensis (formerly Lactobacillus sanfranciscensis) was characterized by comparative genomics supported by physiological data. Twenty-four strains of F. sanfranciscensis were analyzed and sorted into six different genomic clusters. The core genome comprised only 43,14 % of the pan genome, i.e. 0.87 Mbp of 2.04 Mbp. The main annotated genomic differences reside in maltose, fructose and sucrose as well as nucleotide metabolism, use of electron acceptors, and exopolysacchride formation. Furthermore, all strains are well equipped to cope with oxidative stress via NADH oxidase and a distinct thiol metabolism. Only ten of 24 genomes contain two maltose phosphorylase genes (mapA and mapB). In F. sanfranciscensis TMW 1.897 only mapA was found. All strains except those from genomic cluster 2 contained the mannitol dehydrogenase and should therefore be able to use fructose as external electron acceptor. Moreover, six strains were able to grow on fructose as sole carbon source, as they contained a functional fructokinase gene. No growth was observed on pentoses, i.e. xylose, arabinose or ribose, as sole carbon source. This can be referred to the absence of ribose pyranase rbsD in all genomes, and absence of or mutations in numerous other genes, which are essential for arabinose and xylose metabolism. Seven strains were able to produce exopolysaccharides (EPS) from sucrose. In addition, the strains containing levS were able to grow on sucrose as sole carbon source. Strains of one cluster exhibit auxotrophies for purine nucleotides. The physiological and genomic analyses suggest that the biodiversity of F. sanfranciscensis is larger than anticipated. Consequently, \"original\" habitats and lifestyles of F", "token_count": 494, "char_count": 1795, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:49.106880", "source": { "split": "train_shard_00000", "doc_id": 2531 }, "chunk_id": "train_shard_00000_2531_0", "global_id": 2787 }, { "text": "sanfranciscensis may vary but can generally be referred to an adaptation to sugary (maltose/sucrose/fructose-rich) and aerobic environments as found in plants and insects. It can dominate sourdoughs as a result of reductive evolution and cooperation with fructose-delivering, acetate-tolerant yeasts.\n\nIntraspecies diversity and genome-phenotype-associations in Fructilactobacillus sanfranciscensis.", "token_count": 115, "char_count": 399, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8478, "quality_score": 0.9239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:49.489906", "source": { "split": "train_shard_00000", "doc_id": 2531 }, "chunk_id": "train_shard_00000_2531_1", "global_id": 2788 }, { "text": "The genus Paenibacillus was originally recognized based on the 16S rRNA gene phylogeny. Recently, a standardized bacterial taxonomy approach based on a genome phylogeny has substantially revised the classification of Paenibacillus, dividing it into 23 genera. However, the metabolic differences among these groups remain undescribed. Here, genomes of 41 Paenibacillus strains comprising 25 species were sequenced, and a comparative genomic analysis was performed considering these and 187 publicly available Paenibacillus genomes to understand their phylogeny and metabolic differences. Phylogenetic analysis indicated that Paenibacillus clustered into 10 subgroups. Core genome and pan-genome analyses revealed similar functional categories among the different Paenibacillus subgroups; however, each group tended to harbor specific gene families. A large proportion of genes in the subgroups A, E, and G are related to carbohydrate metabolism. Among them, genes related to the glycoside hydrolase family were most abundant. Metabolic reconstruction of the newly sequenced genomes showed that the Embden-Meyerhof-Parnas pathway, pentose phosphate pathway, and citric acid cycle are central pathways of carbohydrate metabolism in Paenibacillus. Further, the genomes of the subgroups A and G lack genes involved in glyoxylate cycle and D-galacturonate degradation, respectively. The current study revealed the metabolic diversity of Paenibacillus subgroups assigned based on a genomic phylogeny and could inform the taxonomy of Paenibacillus. KEY POINTS: • Paenibacillus clustered into 10 subgroups. • Genomic content variation and metabolic diversity in the subgroup A, E, and G were described. • Carbohydrate transport and metabolism is important for Paenibacillus survival.\n\nComparative genomic analysis reveals metabolic diversity of different Paenibacillus groups.", "token_count": 491, "char_count": 1867, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5635, "quality_score": 0.7817, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:50.144454", "source": { "split": "train_shard_00000", "doc_id": 2532 }, "chunk_id": "train_shard_00000_2532_0", "global_id": 2789 }, { "text": "The use of thermotolerant yeast strains can improve the efficiency of ethanol fermentation, allowing fermentation to occur at temperatures higher than 40 °C. This characteristic could benefit traditional bio-ethanol production and allow simultaneous saccharification and fermentation (SSF) of starch or lignocellulosic biomass.\n\nPhysiological characterization of a new thermotolerant yeast strain isolated during Brazilian ethanol production, and its application in high-temperature fermentation.", "token_count": 118, "char_count": 496, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8361, "quality_score": 0.918, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:50.528633", "source": { "split": "train_shard_00000", "doc_id": 2533 }, "chunk_id": "train_shard_00000_2533_0", "global_id": 2790 }, { "text": "Candida kefyr causes invasive candidiasis in immunocompromised patients, particularly among those with oncohematological diseases. This study determined the prevalence of C. kefyr among yeast isolates collected during 2011-2018 in Kuwait. Antifungal susceptibility testing (AST) and genotypic heterogeneity among C. kefyr was also studied.\n\nCandida kefyr in Kuwait: Prevalence, antifungal drug susceptibility and genotypic heterogeneity.", "token_count": 122, "char_count": 437, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:50.914757", "source": { "split": "train_shard_00000", "doc_id": 2534 }, "chunk_id": "train_shard_00000_2534_0", "global_id": 2791 }, { "text": "Bloodstream infections due to yeast species especially Candida spp. have been reported to be important healthcare associated infections with high mortality and morbidity rates. Candidemia causes prolonged hospital stays as well as increased cost. In order to prevent or treat these life-threatening bloodstream infections successfully, nationwide epidemiological data should be available about the etiological agents of these infections. Multi-centre national epidemiological data on yeast bloodstream infections in Turkey is lacking. A retrospective study was designed and data from six different centres in Turkey between 2011 and 2016 years were gathered and analysed for the distribution and frequency of yeast species in order to assist clinicians in their choice of early and appropriate antifungal therapy. All laboratories used automated blood culture systems for the isolation of blood strains. All the participating centres performed the identification of their own isolates by conventional methods using germ tube test, morphology on corn meal agar with tween 80 and chromogenic media and the identification was confirmed by API 20C AUX, API ID 32C or matrix-assisted laser desorption/ionization time of flight mass spectrophotometry (MALDI-TOF MS) systems. The analysis of the results was performed on the basis of intensive care units (ICUs), other inpatient clinics (OICs) and totally all clinics (ACs). Totally 2547 yeast isolates were determined from six participating centres during six years. According to the total ACs results, Candida albicans was the most prevalent species (43.1%), followed by Candida parapsilosis complex (29.1%), Candida glabrata (10.1%), Candida tropicalis (7.5%), Candida krusei (2.4%) and Candida kefyr (1.6%) and the remaining (6.2%) of them consisted of other yeast species. The distribution of the Candida species did not show statistically significant difference between the years, however the increase of C.parapsilosis complex in 2016 was statistically significant, (p= 0.02). During the study period, totally 1054 yeast isolates were obtained from the ICUs of the centres", "token_count": 517, "char_count": 2122, "word_count": 305, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:23:51.542220", "source": { "split": "train_shard_00000", "doc_id": 2535 }, "chunk_id": "train_shard_00000_2535_0", "global_id": 2792 }, { "text": "C.albicans predominated with 476 (45.2%) isolates and C.parapsilosis complex (28.7%), C.glabrata (10.7%) and C.tropicalis (7.3%) were the other leading species in ICUs. Among 1493 isolates of the OICs of six centres participated in the study, C.albicans was the most prevalent species with 622 (41.7%) isolates. The other frequent species of OICs were C.parapsilosis complex (29.5%), C.glabrata (9.6%) and C.tropicalis (7.6%) resembling ICU results. It can be concluded that C.albicans is still the leading cause of bloodstream infections in the six different centres located in various geographical areas of Turkey.\n\n[Distribution of Yeast Species Isolated from Blood Cultures for a Six Year Period in Turkey: a Multicentre Study].", "token_count": 236, "char_count": 732, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:52.023439", "source": { "split": "train_shard_00000", "doc_id": 2535 }, "chunk_id": "train_shard_00000_2535_1", "global_id": 2793 }, { "text": "Candidemia is one of the most important health care-associated infections worldwide. Candida species have species-specific antifungal susceptibility profiles and it has been shown that the identification of the Candida species is necessary for the appropriate treatment of the patients with candidemia. Various methods are used to shorten the identification time for the determination of the causative species. Fungal ID multiplex tandem polymerase chain reaction (MT-PCR) (AusDiagnostics, Australia) is a test developed to identify yeasts and molds isolated from clinical specimens. In this study, we aimed to evaluate the Fungal ID MT-PCR test (AusDiagnostics, Australia) for the identification of the yeasts from positive blood cultures in Akdeniz University Hospital Central Laboratory. Between December 2016 and December 2017, blood culture samples from 92 consecutive patients with yeast cells detected in Gram stained smears were tested by Fungal ID MT-PCR and the reference method. After the subculture of the positive signaling blood culture bottles to Sabouraud dextroz agar (SDA), the identification of the yeasts were performed by morphological identification methods (Germ tube test, Corn Meal Tween® 80 agar media, etc.), BD Phoenix Yeast ID Panel (Becton Dickinson, Sparks, MD) and Bruker Biotyper matrix-assisted laser desorption ionization-time of mass spectrometry (MALDI-TOF MS) (Bruker Daltonics, Germany) systems. Identification with MALDI-TOF MS have been accepted as the reference method. Thirty-five of the isolates were identified as Candida albicans, 17 were Candida glabrata, 13 were Candida parapsilosis, 12 were Candida tropicalis, seven were Candida krusei , two were Candida guilliermondii, two were Candida dubliniensis, two were Candida inconspicua, one was Candida kefyr and one was Saprochaete capitata by the reference method. In our study, no blood culture sample yielded more than one yeast species. 94.6% of the strains were presumptively identified by the morphological identification methods", "token_count": 508, "char_count": 2032, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:52.713868", "source": { "split": "train_shard_00000", "doc_id": 2536 }, "chunk_id": "train_shard_00000_2536_0", "global_id": 2794 }, { "text": "Discordant results were not detected between the BD Phoenix Yeast ID Panel and the reference method. Thirty-three of the isolates were identified as C.albicans, 15 were C.glabrata, 13 were C.parapsilosis, 11 were C.tropicalis, five were C.krusei , two were C.guilliermondii, one was C.dubliniensis, one was C.kefyr and 10 were Candida spp. by Fungal ID MT-PCR assay. Since C.inconspicua and S.capitata were not included in the test panel, C.inconspicua was identified as Candida spp. in two samples, while S.capitata could not be identified in one sample. Concordance between Fungal ID MT-PCR and the reference method were found to be 88% at the species level and 98.9% at the genus level. The sensitivity of the Fungal ID MT-PCR test in in the detection of C.krusei and C.glabrata was 71.4% and 88.2%, respectively. Fungal ID MT-PCR test has shown a high performance in the identification at the genus level, but the identification at the species level, which is important for the treatment management, was moderate. Fungal ID MT-PCR can be used as an adjunct test to the traditional identification methods for the early identification of the Candida species.\n\n[Evaluation of a Commercial Multiplex Tandem Polymerase Chain Reaction Method for the Identification of the Yeasts Isolated from Blood Cultures].", "token_count": 381, "char_count": 1307, "word_count": 205, "semantic_coherence": 1, "information_density": 0.522, "quality_score": 0.761, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:53.311166", "source": { "split": "train_shard_00000", "doc_id": 2536 }, "chunk_id": "train_shard_00000_2536_1", "global_id": 2795 }, { "text": "Nosocomial (hospital-acquired) infections remain a serious challenge for health systems. The reason for this lies not only in the local imperfection of medical practices and protocols. The frequency of infection with antibiotic-resistant strains of bacteria is growing every year, both in developed and developing countries. In this work, a pangenome and comparative analysis of 201 genomes of\n\nComparative Analysis of Proteomes of a Number of Nosocomial Pathogens by KEGG Modules and KEGG Pathways.", "token_count": 120, "char_count": 499, "word_count": 73, "semantic_coherence": 1, "information_density": 0.6986, "quality_score": 0.8493, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:53.754310", "source": { "split": "train_shard_00000", "doc_id": 2537 }, "chunk_id": "train_shard_00000_2537_0", "global_id": 2796 }, { "text": "The aim of the paper was to analyse changes in lactic acid bacteria (LAB) populations during spontaneous fermentation of green curly kale juice (Brasicca oleracea L. var. acephala L.) and to determine the probiotic potential of LAB isolates. The analyses revealed that changes in LAB populations were specific for spontaneously fermented vegetable juices. The initial microbiota, composed mostly of Leuconostoc mesenteroides bacteria, was gradually replaced by Lactobacillus species, mainly Lactobacillus plantarum, Lactobacillus sakei, and Lactobacillus coryniformis. Screening tests for the antimicrobial properties and antibiotic susceptibility of isolates allowed for the selection of 12 strains with desirable characteristics. L. plantarum isolates were characterized by the widest spectrum of antimicrobial interactions, both towards Gram-positive and Gram-negative bacteria. Also, L. plantarum strains exhibited the best growth abilities under low pH conditions, and at different NaCl and bile salt concentrations. All strains showed different levels of antibiotic sensitivity, although they were resistant to vancomycin and kanamycin. The present study has shown that bacterial isolates obtained from spontaneously fermented kale juice could constitute valuable probiotic starter cultures, which may be used in fermentation industry.\n\nProbiotic potential of lactic acid bacteria obtained from fermented curly kale juice.", "token_count": 346, "char_count": 1428, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:54.349943", "source": { "split": "train_shard_00000", "doc_id": 2539 }, "chunk_id": "train_shard_00000_2539_0", "global_id": 2797 }, { "text": "The increasing interest in products with functional properties has encouraged the search for new lactic acid bacteria (LAB) present in natural sources, as traditional fermented foods. In this study, a large set of wild LAB isolates (n = 220) from Brazilian artisanal cheeses (BAC) were assessed for their probiotic and biopreservation potential. First, the rational selection was performed. From the tested isolates, 92 (41.8 %) were resistant to low pH (2 and 3). These isolates were submitted to bile salt (0.4 % Oxgall powder) resistance, and 22 were selected and submitted to adhesion assays. The autoaggregation values ranged from 68.5-99% and were considered moderate to high (20-70 %). Hydrophobicity values varied significantly between LAB (5.0-64.3%), and seven isolates presented values higher than 40 %. All selected LAB (n=22) were capable of adhering to Caco-2 (> 70 %) cells, and none isolate displayed any tested gene for biogenic amine production. Most isolates (18/22) showed less than 1 log CFU reduction after passage through the simulated gastrointestinal tract (GIT) conditions. A total of twenty isolates satisfied key in vitro criteria to be considered as probiotics. A hierarchical cluster analysis (HCA) was performed, and two clusters were observed, showing high variability between Lactobacillus plantarum isolates regarding adhesion properties and survival to GIT stress and one influence of the source of isolation on these properties. After screening, the antimicrobial activity of Lb. plantarum (1QB77) was tested in microcheeses in which survival of two relevant pathogenic bacteria (Staphylococcus aureus and Listeria monocytogenes) was monitored along ripening and after a simulated GIT passage, concomitantly. L. plantarum (1QB77) has shown the ability to reach high counts (∼ 9 log CFU/g) at the end of ripening. This isolate was also able to reduce counts of S. aureus and L", "token_count": 519, "char_count": 1911, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:23:55.015573", "source": { "split": "train_shard_00000", "doc_id": 2540 }, "chunk_id": "train_shard_00000_2540_0", "global_id": 2798 }, { "text": "monocytogenes in microcheeses in approx. 2.3 and 2.5 log CFU/g, respectively, until the 21st day of ripening; and about 3.2 and 3.5 log CFU/g after simulated GIT passage. Overall, the assessment of the probiotic properties of a large set of LAB was fundamental for gaining insights on the technological, functional, and potential regional traits of wild LAB isolates that can be used to develop starter cultures for tailored applications.\n\nBiopreservation and probiotic potential of a large set of lactic acid bacteria isolated from Brazilian artisanal cheeses: From screening to in product approach.", "token_count": 155, "char_count": 600, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7283, "quality_score": 0.8641, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:55.453212", "source": { "split": "train_shard_00000", "doc_id": 2540 }, "chunk_id": "train_shard_00000_2540_1", "global_id": 2799 }, { "text": "The aim of this investigation was to isolate and identify Bacillus species isolated from the internal microbiota of Red sea stingrays as potential probiotics. An initial assay on the ability of the isolates to control stingray pathogens of Vibrio species led to the selection of one highly antagonistic isolate. The most potent isolate was identified based on whole genome phylogeny as Bacillus velezensis AMB-y1. Genome mining for secondary metabolites identified five antibacterial biosynthetic clusters that produce, bacilysin, bacillaene, difficidin, macrolactin and mersacidin. Genome mining also identified two antifungal biosynthetic clusters which encode genes to produce bacillomycin D and fengycin. The genome mining also identified an unknown NRPS-transAT-PKS cluster that likely produced another compound with antibiotic activity. The strain was further characterized by the assessment of abiotic stress tolerances that are required in potential probiotic agents. The selected isolate had promising results in abiotic stress tolerance; pH tolerance within the range from 4.0 to 8.0, able to survive concentrations of bile salt up to 0.4% and sodium chloride from 0 to 6.5%. In addition, the strain showed a value of hydrophobicity (31%) along with a higher value of auto-aggregation (49.9%), which demonstrates its potential ability to adhere to the intestinal wall on the basis of its cell surface traits. The strain was evaluated for susceptibility to antimicrobials and the novel B. velezensis AMB-y1 has potential to be used as a probiotic in aquaculture to control marine fish and stingray pathogens.\n\nGenomic and phenotypic characterization of Bacillus velezensis AMB-y1; a potential probiotic to control pathogens in aquaculture.", "token_count": 452, "char_count": 1748, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:57.082044", "source": { "split": "train_shard_00000", "doc_id": 2541 }, "chunk_id": "train_shard_00000_2541_0", "global_id": 2800 }, { "text": "Bacterial \"stand-alone\" response regulators (RRs) are pivotal to the control of gene transcription in response to changing cytosolic and extracellular microenvironments during infection. The genome of group A Streptococcus (GAS) encodes more than 30 stand-alone RRs that orchestrate the expression of virulence factors involved in infecting multiple tissues, so causing an array of potentially lethal human diseases. Here, we analysed the molecular epidemiology and biological associations in the coding sequences (CDSs) and upstream intergenic regions (IGRs) of 35 stand-alone RRs from a collection of global GAS genomes. Of the 944 genomes analysed, 97% encoded 32 or more of the 35 tested RRs. The length of RR CDSs ranged from 297 to 1587 nucleotides with an average nucleotide diversity (π) of 0.012, while the IGRs ranged from 51 to 666 nucleotides with average π of 0.017. We present new evidence of recombination in multiple RRs including mga, leading to mga-2 switching, emm-switching and emm-like gene chimerization, and the first instance of an isolate that encodes both mga-1 and mga-2. Recombination was also evident in rofA/nra and msmR loci with 15 emm-types represented in multiple FCT (fibronectin-binding, collagen-binding, T-antigen)-types, including novel emm-type/FCT-type pairings. Strong associations were observed between concatenated RR allele types, and emm-type, MLST-type, core genome phylogroup, and country of sampling. No strong associations were observed between individual loci and disease outcome. We propose that 11 RRs may form part of future refinement of GAS typing systems that reflect core genome evolutionary associations. This subgenomic analysis revealed allelic traits that were informative to the biological function, GAS strain definition, and regional outbreak detection.", "token_count": 498, "char_count": 1818, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6603, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:57.736838", "source": { "split": "train_shard_00000", "doc_id": 2542 }, "chunk_id": "train_shard_00000_2542_0", "global_id": 2801 }, { "text": "In silico characterisation of stand-alone response regulators of Streptococcus pyogenes.", "token_count": 22, "char_count": 88, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:58.095024", "source": { "split": "train_shard_00000", "doc_id": 2542 }, "chunk_id": "train_shard_00000_2542_1", "global_id": 2802 }, { "text": "The recent advances in sequencing technologies enable the assembly of individual genomes to the quality of the reference genome. How to integrate multiple genomes from the same species and make the integrated representation accessible to biologists remains an open challenge. Here, we propose a graph-based data model and associated formats to represent multiple genomes while preserving the coordinate of the linear reference genome. We implement our ideas in the minigraph toolkit and demonstrate that we can efficiently construct a pangenome graph and compactly encode tens of thousands of structural variants missing from the current reference genome.\n\nThe design and construction of reference pangenome graphs with minigraph.", "token_count": 136, "char_count": 730, "word_count": 106, "semantic_coherence": 1, "information_density": 0.6604, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:58.529671", "source": { "split": "train_shard_00000", "doc_id": 2543 }, "chunk_id": "train_shard_00000_2543_0", "global_id": 2803 }, { "text": "Mixed lipid aggregates, comprising of bile salts and phospholipids, present in the small intestine assist in drug solubilization and subsequent drug dissolution and absorption through the intestinal epithelium. The increased variability in their levels, observed physiologically, may create challenges not only for in vivo bioavailability and bioequivalence studies, but also for in vitro bio-predictive studies as correlations between in vitro and in vivo data are not always successful. The current study investigated the impact of biorelevant dissolution media, with physiologically relevant sodium taurocholate and lecithin levels, on the apparent solubility and affinity of lipophilic compounds with a wide range of physicochemical properties (drug ionization, drug lipophilicity, molecular weight) to mixed lipid aggregates. Apparent solubility data in biorelevant dissolution media for the studied neutral drugs, weak bases and weak acids were compared against a phosphate buffer pH 6.5 in the absence of these lipidic components. Presence of mixed lipid aggregates enhanced the apparent solubility of the majority of compounds and the use of multivariate data analysis identified the significant parameters affecting drug affinity to mixed lipid aggregates based on the chemical class of the drug. For neutral drugs, increasing bile salt concentrations and/or drug lipophilicity resulted in greater enhancement in apparent solubility at 24-hr. For weak bases and weak acids, the effect of increasing bile salt levels on apparent solubility depended mostly on an interplay between drug lipophilicity and drug ionization.\n\nAffinity of Lipophilic Drugs to Mixed Lipid Aggregates in Simulated Gastrointestinal Fluids.", "token_count": 407, "char_count": 1721, "word_count": 242, "semantic_coherence": 1, "information_density": 0.562, "quality_score": 0.781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:59.151742", "source": { "split": "train_shard_00000", "doc_id": 2544 }, "chunk_id": "train_shard_00000_2544_0", "global_id": 2804 }, { "text": "The effects of deoxycholic acid (DCA) on the intestinal microbiota, bile acid (BA) metabolism, and intestinal epithelium can be influenced by various factors. Depending on the specific conditions, DCA can be \"bad\" (proinflammatory) or \"good\" (anti-inflammatory). Mouse models of colitis show an increase in conjugated BAs and gut dysbiosis, including DCA-related dysbiosis, with a significant decrease in bile salt hydrolase (bsh) gene-containing taxa. Human patients with inflammatory bowel disease demonstrate, primarily, a decrease in bile acid-inducible (bai) gene-containing taxa and a deficiency in secondary BAs, suggesting their anti-inflammatory role.\n\nBad \"Good\" Bile Acids and Gut Microbiota Dysbiosis in Inflammatory Bowel Disease: Mice and Humans Are Not the Same.", "token_count": 228, "char_count": 777, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:23:59.621605", "source": { "split": "train_shard_00000", "doc_id": 2545 }, "chunk_id": "train_shard_00000_2545_0", "global_id": 2805 }, { "text": "Bacterial genomes can contain traces of a complex evolutionary history, including extensive homologous recombination, gene loss, gene duplications, and horizontal gene transfer. To reconstruct the phylogenetic and population history of a set of multiple bacteria, it is necessary to examine their pangenome, the composite of all the genes in the set. Here we introduce PEPPAN, a novel pipeline that can reliably construct pangenomes from thousands of genetically diverse bacterial genomes that represent the diversity of an entire genus. PEPPAN outperforms existing pangenome methods by providing consistent gene and pseudogene annotations extended by similarity-based gene predictions, and identifying and excluding paralogs by combining tree- and synteny-based approaches. The PEPPAN package additionally includes PEPPAN_parser, which implements additional downstream analyses, including the calculation of trees based on accessory gene content or allelic differences between core genes. To test the accuracy of PEPPAN, we implemented SimPan, a novel pipeline for simulating the evolution of bacterial pangenomes. We compared the accuracy and speed of PEPPAN with four state-of-the-art pangenome pipelines using both empirical and simulated data sets. PEPPAN was more accurate and more specific than any of the other pipelines and was almost as fast as any of them. As a case study, we used PEPPAN to construct a pangenome of approximately 40,000 genes from 3052 representative genomes spanning at least 80 species of\n\nAccurate reconstruction of bacterial pan- and core genomes with PEPPAN.", "token_count": 354, "char_count": 1592, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:00.195888", "source": { "split": "train_shard_00000", "doc_id": 2546 }, "chunk_id": "train_shard_00000_2546_0", "global_id": 2806 }, { "text": "Anthrax is a natural foci disease in Inner Mongolia, which poses a severe threat to public health. In this study, the incidence number, rate and constituent ratio were used to describe the epidemiological characteristics of anthrax in the region from 1956-2018. The molecular correlation and genetic characteristics of the strains were investigated using canonical single nucleotide polymorphisms (CanSNP), multiple-locus variable-number tandem repeat analysis (MLVA-15) and whole genome sequencing (WGS). The epidemiological characteristics of anthrax in Inner Mongolia have altered significantly. The incidence of anthrax has decreased annually without vaccination, and the regional distribution of anthrax gradually transferred from central and western regions to the eastern. Moreover, the occupation distribution evolved from multiple early occupations to predominated by farmers and herdsmen. This change is closely related to policy factors and to changes in the means of production and the living habits of the local population. This indicates that reformulating the control and prevention strategies is essential. Both A. Br. Ames and A. Br. 001/002 subgroups were the predominant CanSNP genotypes of Bacillus anthracis in Inner Mongolia. A total of 36 strains constituted six shared MLVA-15 genotypes, suggesting an epidemiological link between the strains of each shared genotype. The six shared genotypes ([GT1, 9, 11 and 15] and [GT8 and 12]) consisting of 2-7 strains confirmed the occurrence of multiple point outbreaks and cross-regional transmission caused by multiple common sources of infection. Phylogenetic analysis based on the WGS core genome showed that strains from this study formed an independent clade (C.V.), and they were positioned close to each other, suggesting a common origin. Further comparison analysis should be performed to ascertain the geographic origin of these strains.\n\nChanged epidemiology of anthrax and molecular characteristics of Bacillus anthracis in Inner Mongolia Autonomous Region, China.", "token_count": 475, "char_count": 2041, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6014, "quality_score": 0.8007, "entities": { "genes": [ "GT8", "GT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:00.837196", "source": { "split": "train_shard_00000", "doc_id": 2547 }, "chunk_id": "train_shard_00000_2547_0", "global_id": 2807 }, { "text": "Acute kidney injury (AKI) is a common complication seen in patients with hemophagocytic lymphohistiocytosis (HLH). More than half of patients with HLH require renal replacement therapy (RRT). There are four main causes of kidney dysfunction in HLH, which include acute tubular necrosis (ATN), hypoperfusion, tumor lysis syndrome (TLS), and HLH-related glomerulopathies. Bile cast nephropathy (BCN) is a known cause of kidney injury in patients with liver failure and hyperbilirubinemia. We present the case of a 58-year-old man who presented to the hospital with painless jaundice, choluria, acholia, and generalized malaise and was found to have hyperbilirubinemia and kidney injury in the setting of HLH, who underwent a renal biopsy showing bile salt casts with degenerating tubular lining cells consistent with BCN. This case highlights the importance of considering BCN as a cause of kidney injury when a patient with HLH presents with liver failure and elevated bilirubin levels.\n\nBile Cast Nephropathy Secondary to Hemophagocytic Lymphohistiocytosis With Liver Failure.", "token_count": 305, "char_count": 1076, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:01.411085", "source": { "split": "train_shard_00000", "doc_id": 2548 }, "chunk_id": "train_shard_00000_2548_0", "global_id": 2808 }, { "text": "Exoinulinase catalyzes the successive removal of individual fructose moiety from the non-reducing end of the inulin molecule, which is useful for biotechnological applications like producing fructan-based non-grain biomass energy and high-fructose syrup. In this study, an exoinulinase (KmINU) from Kluyveromyces marxianus DSM 5418 was tailored for increased catalytic activity and acidic adaptation for inulin hydrolysis processes by rational site-directed mutagenesis.\n\nEngineering better catalytic activity and acidic adaptation into Kluyveromyces marxianus exoinulinase using site-directed mutagenesis.", "token_count": 163, "char_count": 606, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:01.851045", "source": { "split": "train_shard_00000", "doc_id": 2549 }, "chunk_id": "train_shard_00000_2549_0", "global_id": 2809 }, { "text": "Several ABC exporters carry a degenerate nucleotide binding site (NBS) that is unable to hydrolyze ATP at a rate sufficient for sustaining transport activity. A hallmark of a degenerate NBS is the lack of the catalytic glutamate in the Walker B motif in the nucleotide binding domain (NBD). The multidrug resistance transporter ABCB1 (P-glycoprotein) has two canonical NBSs, and mutation of the catalytic glutamate E556 in NBS1 renders ABCB1 transport-incompetent. In contrast, the closely related bile salt export pump ABCB11 (BSEP), which shares 49% sequence identity with ABCB1, naturally contains a methionine in place of the catalytic glutamate. The NBD-NBD interfaces of ABCB1 and ABCB11 differ only in four residues, all within NBS1. Mutation of the catalytic glutamate in ABCB1 results in the occlusion of ATP in NBS1, leading to the arrest of the transport cycle. Here we show that despite the catalytic glutamate mutation (E556M), ABCB1 regains its ATP-dependent transport activity, when three additional diverging residues are also replaced. Molecular dynamics simulations revealed that the rescue of ATPase activity is due to the modified geometry of NBS1, resulting in a weaker interaction with ATP, which allows the quadruple mutant to evade the conformationally locked pre-hydrolytic state to proceed to ATP-driven transport. In summary, we show that ABCB1 can be transformed into an active transporter with only one functional catalytic site by preventing the formation of the ATP-locked pre-hydrolytic state in the non-canonical site.\n\nHuman ABCB1 with an ABCB11-like degenerate nucleotide binding site maintains transport activity by avoiding nucleotide occlusion.", "token_count": 448, "char_count": 1682, "word_count": 250, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [ "ABCB1", "ABCB11", "NBS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:02.489255", "source": { "split": "train_shard_00000", "doc_id": 2550 }, "chunk_id": "train_shard_00000_2550_0", "global_id": 2810 }, { "text": "We sought to determine the relative value of conventional molecular methods and whole-genome sequencing (WGS) for subtyping Salmonella enterica serovar Enteritidis recovered from 2000 to 2015 in Tunisia and to investigate the genetic diversity of this serotype. A total of 175 Salmonella Enteritidis isolates were recovered from human, animal, and foodborne outbreak samples. Pulsed-field gel electrophoresis (PFGE), multiple locus variable-number tandem repeat analysis (MLVA), and whole-genome sequencing were performed. Eight pulsotypes were detected for all isolates with PFGE (DI = 0.518). Forty-five Salmonella Enteritidis isolates were selected for the MLVA and WGS techniques. Eighteen MLVA profiles were identified and classified into two major clusters (DI = 0.889). Core genome multilocus typing (cgMLST) analysis revealed 16 profiles (DI = 0.785). Whole-genome analysis indicated 660 single-nucleotide polymorphism (SNP) divergences dividing these isolates into 43 haplotypes (DI = 0.997). The phylogenetic tree supported the classification of Salmonella Enteritidis isolates into two distinct lineages subdivided into five clades and seven subclades. Pairwise SNP differences between the isolates ranged between 302 and 350. We observed about 311 SNP differences between the two foodborne outbreaks, while only less or equal to 4 SNP differences within each outbreak. SNP-based WGS typing showed an excellent discriminatory power comparing with the conventional methods such as PFGE and MLVA. Besides, we demonstrate the added value of WGS as a complementary subtyping method to discriminate outbreak from non-outbreak isolates belonging to common subtypes. It is important to continue the survey of Salmonella Enteritidis lineages in Tunisia using WGS.", "token_count": 486, "char_count": 1766, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:03.475285", "source": { "split": "train_shard_00000", "doc_id": 2551 }, "chunk_id": "train_shard_00000_2551_0", "global_id": 2811 }, { "text": "Comparison of conventional molecular and whole-genome sequencing methods for subtyping Salmonella enterica serovar Enteritidis strains from Tunisia.", "token_count": 36, "char_count": 148, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:03.829529", "source": { "split": "train_shard_00000", "doc_id": 2551 }, "chunk_id": "train_shard_00000_2551_1", "global_id": 2812 }, { "text": "Ethanol was produced by separate hydrolysis and fermentation using Azolla filiculoides as a biomass. Thermal acid hydrolysis and enzymatic saccharification were used as pretreatment methods to produce monosaccharides from Azolla. The optimal content for thermal acid hydrolysis of 14% (w/v) Azolla weed slurry produced 16.7-g/L monosaccharides by using 200 mM H\n\nBioethanol Production from Azolla filiculoides by Saccharomyces cerevisiae, Pichia stipitis, Candida lusitaniae, and Kluyveromyces marxianus.", "token_count": 166, "char_count": 504, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:04.307404", "source": { "split": "train_shard_00000", "doc_id": 2552 }, "chunk_id": "train_shard_00000_2552_0", "global_id": 2813 }, { "text": "A retrospective study of Staphylococcus aureus isolates from orthopaedic patients treated between 2000 and 2017 at Akershus University Hospital, Norway was performed using a genome-wide association approach. The aim was to characterize and investigate molecular characteristics unique to S. aureus isolates from HHA associated prosthetic joint infections and potentially explain the HHA patients' elevated 1-year mortality compared to a non-HHA group. The comparison group consisted of patients with non-HHA lower-extremity implant-related S. aureus infections. S. aureus isolates from diagnostic patient samples were whole-genome sequenced. Univariate and multivariate analyses were performed to detect group-associated genetic signatures. A total of 62 HHA patients and 73 non-HHA patients were included. Median age (81 years vs. 74 years; p < 0.001) and 1-year mortality (44% vs. 15%, p < 0.001) were higher in the HHA group. A total of 20 clonal clusters (CCs) were identified; 75% of the isolates consisted of CC45, CC30, CC5, CC15, and CC1. Analyses of core and accessory genome content, including virulence, resistance genes, and k-mer analysis revealed few group-associated variants, none of which could explain the elevated 1-year mortality in HHA patients. Our findings support the premise that all S. aureus can cause invasive infections given the opportunity.\n\nMolecular characteristics of Staphylococcus aureus associated prosthetic joint infections after hip fractures treated with hemiarthroplasty: a retrospective genome-wide association study.", "token_count": 438, "char_count": 1560, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [ "CC45", "CC15", "CC5", "CC30", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:04.956456", "source": { "split": "train_shard_00000", "doc_id": 2553 }, "chunk_id": "train_shard_00000_2553_0", "global_id": 2814 }, { "text": "Members of the predatory Myxococcales (myxobacteria) possess large genomes, undergo multicellular development, and produce diverse secondary metabolites, which are being actively prospected for novel drug discovery. To direct such efforts, it is important to understand the relationships between myxobacterial ecology, evolution, taxonomy, and genomic variation. This study investigated the genomes and pan-genomes of organisms within the Myxococcaceae, including the genera Myxococcus and Corallococcus, the most abundant myxobacteria isolated from soils. Previously, ten species of Corallococcus were known, whereas six species of Myxococcus phylogenetically surrounded a third genus (Pyxidicoccus) composed of a single species. Here, we describe draft genome sequences of five novel species within the Myxococcaceae (Myxococcus eversor, Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis, Myxococcus vastator, Pyxidicoccus caerfyrddinensis, and Pyxidicoccus trucidator) and for the Pyxidicoccus type species strain, Pyxidicoccus fallax DSM 14698T. Genomic and physiological comparisons demonstrated clear differences between the five novel species and every other Myxococcus or Pyxidicoccus spp. type strain. Subsequent analyses of type strain genomes showed that both the Corallococcus pan-genome and the combined Myxococcus and Pyxidicoccus (Myxococcus/Pyxidicoccus) pan-genome are large and open, but with clear differences. Genomes of Corallococcus spp. are generally smaller than those of Myxococcus/Pyxidicoccus spp. but have core genomes three times larger. Myxococcus/Pyxidicoccus spp. genomes are more variable in size, with larger and more unique sets of accessory genes than those of Corallococcus species", "token_count": 488, "char_count": 1743, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:05.637897", "source": { "split": "train_shard_00000", "doc_id": 2554 }, "chunk_id": "train_shard_00000_2554_0", "global_id": 2815 }, { "text": "In both genera, biosynthetic gene clusters are relatively enriched in the shell pan-genomes, implying they grant a greater evolutionary benefit than other shell genes, presumably by conferring selective advantages during predation.\n\nComparative Genomics and Pan-Genomics of the Myxococcaceae, including a Description of Five Novel Species: Myxococcus eversor sp. nov., Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis sp. nov., Myxococcus vastator sp. nov., Pyxidicoccus caerfyrddinensis sp. nov., and Pyxidicoccus trucidator sp. nov.", "token_count": 175, "char_count": 560, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:06.115190", "source": { "split": "train_shard_00000", "doc_id": 2554 }, "chunk_id": "train_shard_00000_2554_1", "global_id": 2816 }, { "text": "Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to accelerate cultivar development. To help with this, we developed a Sorghum bicolor Practical Haplotype Graph (PHG) pangenome database that stores haplotypes and variant information. We developed two PHGs in sorghum that were used to identify genome-wide variants for 24 founders of the Chibas sorghum breeding program from 0.01x sequence coverage. The PHG called single nucleotide polymorphisms (SNPs) with 5.9% error at 0.01x coverage-only 3% higher than PHG error when calling SNPs from 8x coverage sequence. Additionally, 207 progenies from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes were imputed from PHG parental haplotypes and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from .57-.73 and are similar to prediction accuracies obtained with genotyping-by-sequencing or targeted amplicon sequencing (rhAmpSeq) markers. This study demonstrates the use of a sorghum PHG to impute SNPs from low-coverage sequence data and shows that the PHG can unify genotype calls across multiple sequencing platforms. By reducing input sequence requirements, the PHG can decrease the cost of genotyping, make GS more feasible, and facilitate larger breeding populations. Our results demonstrate that the PHG is a useful research and breeding tool that maintains variant information from a diverse group of taxa, stores sequence data in a condensed but readily accessible format, unifies genotypes across genotyping platforms, and provides a cost-effective option for genomic selection.\n\nA sorghum practical haplotype graph facilitates genome-wide imputation and cost-effective genomic prediction.", "token_count": 443, "char_count": 1809, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:06.744108", "source": { "split": "train_shard_00000", "doc_id": 2555 }, "chunk_id": "train_shard_00000_2555_0", "global_id": 2817 }, { "text": "Variation in partner quality is commonly observed in diverse cooperative relationships, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variation. Here, we investigated how genetic variation in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variation in the core genome and the similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using 9 sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variation represented by plant growth phenotypes, including genotype-by-genotype interactions. Variation in quality was not associated with the presence/absence variation in known symbiosis-related genes in the symbiosis island; rather, it showed significant correlation with the core genome variation. Given the recurrent HGT of the symbiosis islands into diverse Mesorhizobium strains, local Mesorhizobium communities could serve as a major source of variation for core genomes, which might prevent variation in partner quality from fixing, even in the presence of selection favoring high-quality partners. These findings highlight the novel role of HGT of symbiosis islands in maintaining partner quality variation in the legume-rhizobia symbiosis.\n\nMassive rhizobial genomic variation associated with partner quality in Lotus-Mesorhizobium symbiosis.", "token_count": 366, "char_count": 1630, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6161, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:07.324014", "source": { "split": "train_shard_00000", "doc_id": 2556 }, "chunk_id": "train_shard_00000_2556_0", "global_id": 2818 }, { "text": "Shiga toxin-producing\n\nCore and Accessory Genome Comparison of Australian and International Strains of O157 Shiga Toxin-Producing", "token_count": 37, "char_count": 129, "word_count": 16, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:07.694836", "source": { "split": "train_shard_00000", "doc_id": 2557 }, "chunk_id": "train_shard_00000_2557_0", "global_id": 2819 }, { "text": "The aim of this study was to investigate antimicrobial resistance and population structure of bovine mastitis-associated Staphylococcus aureus isolates, and compare them to human isolates obtained from Western Australian hospitals and overseas strains to determine relatedness to human isolates from a zoonotic or reverse zoonotic aspect. Antimicrobial susceptibility testing was performed on 202 S. aureus isolates of which 166 isolates underwent whole genome sequencing. Only resistance to penicillin (12.4%) and erythromycin (0.5%) was identified and of note, no resistance was demonstrated to oxacillin. Genomic characterisation identified 14 multilocus sequence types (STs), with most isolates belonging to clonal complexes 97, 705, and 1. Four distinct clades based on virulence gene composition were identified. The four clades were predominantly ST based, consisting of ST352, ST97, ST81/ST1, and ST705. Core genome comparison of the bovine and human S. aureus isolates demonstrated defined clustering by ST, with the Australian bovine S. aureus isolates clustering together according to their ST separately from human isolates. In addition, a bovine specific cluster comprising Australian ST151 and ST705 isolates, and ST151 isolates from Irish dairy cattle was clearly delineated. Examination of a detailed ST352 phylogeny provided evidence for geographical clustering of Australian strains into a distinct grouping separate from international strains. This study has identified Australian S. aureus isolates have limited genetic diversity and are genetically distinct from human and international bovine S. aureus isolates. Current first line therapies for bovine mastitis in Australian dairy cattle remain appropriate.\n\nAntimicrobial resistance and genomic insights into bovine mastitis-associated Staphylococcus aureus in Australia.", "token_count": 462, "char_count": 1845, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5635, "quality_score": 0.7817, "entities": { "genes": [ "ST81", "ST352", "ST151", "ST97", "ST1", "ST705" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:08.336775", "source": { "split": "train_shard_00000", "doc_id": 2558 }, "chunk_id": "train_shard_00000_2558_0", "global_id": 2820 }, { "text": "An increasing prevalence of hospital acquired infections and foodborne illnesses caused by pathogenic and multidrug-resistant bacteria has stimulated a pressing need for benchtop computational techniques to rapidly and accurately classify bacteria from genomic sequence data, and based on that, to trace the source of infection. BacWGSTdb (http://bacdb.org/BacWGSTdb) is a free publicly accessible database we have developed for bacterial whole-genome sequence typing and source tracking. This database incorporates extensive resources for bacterial genome sequencing data and the corresponding metadata, combined with specialized bioinformatics tools that enable the systematic characterization of the bacterial isolates recovered from infections. Here, we present BacWGSTdb 2.0, which encompasses several major updates, including (i) the integration of the core genome multi-locus sequence typing (cgMLST) approach, which is highly scalable and appropriate for typing isolates belonging to different lineages; (ii) the addition of a multiple genome analysis module that can process dozens of user uploaded sequences in a batch mode; (iii) a new source tracking module for comparing user uploaded plasmid sequences to those deposited in the public databases; (iv) the number of species encompassed in BacWGSTdb 2.0 has increased from 9 to 20, which represents bacterial pathogens of medical importance; (v) a newly designed, user-friendly interface and a set of visualization tools for providing a convenient platform for users are also included. Overall, the updated BacWGSTdb 2.0 bears great utility in continuing to provide users, including epidemiologists, clinicians and bench scientists, with a one-stop solution to bacterial genome sequence analysis.\n\nBacWGSTdb 2.0: a one-stop repository for bacterial whole-genome sequence typing and source tracking.", "token_count": 419, "char_count": 1860, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6289, "quality_score": 0.8145, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:08.960151", "source": { "split": "train_shard_00000", "doc_id": 2559 }, "chunk_id": "train_shard_00000_2559_0", "global_id": 2821 }, { "text": "Vibrio parahaemolyticus is a major foodborne pathogen worldwide. The increasing number of cases of V. parahaemolyticus infections in China indicates an urgent need to evaluate the prevalence and genetic diversity of this pathogenic bacterium. In this paper, we introduce the Foodborne Vibrio parahaemolyticus genome database (FVPGD), the first scientific database of foodborne V. parahaemolyticus distribution and genomic data in China, based on our previous investigations of V. parahaemolyticus contamination in different kinds of food samples across China from 2011 to 2016. The dataset includes records of 2,499 food samples and 643 V. parahaemolyticus strains from supermarkets and marketplaces distributed over 39 cities in China; 268 whole-genome sequences have been deposited in this database. A spatial view on the risk situations of V. parahaemolyticus contamination in different food types is provided. Additionally, the database provides a functional interface of sequence BLAST, core genome multilocus sequence typing, and phylogenetic analysis. The database will become a powerful tool for risk assessment and outbreak investigations of foodborne pathogens in China.\n\nA database for risk assessment and comparative genomic analysis of foodborne Vibrio parahaemolyticus in China.", "token_count": 315, "char_count": 1292, "word_count": 181, "semantic_coherence": 1, "information_density": 0.5746, "quality_score": 0.7873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:09.528179", "source": { "split": "train_shard_00000", "doc_id": 2560 }, "chunk_id": "train_shard_00000_2560_0", "global_id": 2822 }, { "text": "Due to changes in lifestyle, diet structure, and aging worldwide, the incidence of metabolic syndromes such as hyperlipidemia, hypertension, diabetes, and obesity is increasing. Metabolic syndrome is considered to be closely related to cardiovascular disease and severely affects human health. In recent years, researchers have revealed that the gut microbiota, through its own or interacting metabolites, has a positive role in regulating metabolic syndrome. Therefore, the gut microbiota has been a new \"organ\" for the treatment of metabolic syndrome. The role has not been clarified, and more research is necessary to prove the specific role of specific strains. Probiotics are also believed to regulate metabolic syndromes by regulating the gut microbiota and are expected to become a new preparation for treating metabolic syndromes. This review focuses on the regulation of lipid metabolism disorders by the gut microbiota through the effects of bile acids (BA), short-chain fatty acids (SCFAs), bile salt hydrolase (BSH), and genes such as ABCG5 and ABCG8, FXR, NPC1L, and LDL-R.\n\nThe Potential Role of Gut Microbiota in the Prevention and Treatment of Lipid Metabolism Disorders.", "token_count": 295, "char_count": 1187, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6011, "quality_score": 0.8006, "entities": { "genes": [ "NPC1L", "ABCG8", "ABCG5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:10.093303", "source": { "split": "train_shard_00000", "doc_id": 2561 }, "chunk_id": "train_shard_00000_2561_0", "global_id": 2823 }, { "text": "Developing a broad-range promoter set for metabolic engineering in the thermotolerant yeast", "token_count": 22, "char_count": 91, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:10.456846", "source": { "split": "train_shard_00000", "doc_id": 2562 }, "chunk_id": "train_shard_00000_2562_0", "global_id": 2824 }, { "text": "Consumer's vigilance towards health-promoting foods beyond only taste and nutrition has increased the recognition for probiotic products. In the present study, various parameters have been studied to define the probiotic properties of cultures isolated from different fermented products. Around 118 samples were selectively screened for antimicrobial compound (AMC) producing isolates by overlay-plate assay using Micrococcus luteus ATCC9341. Among 134 zone producing isolates, 48 cultures showing Gram-positive, catalase negative, non-spore forming and non-motile rods and cocci were selected. Subsequently, 18 strains were chosen based on non-hemolytic, absence of biogenic amine production, gelatinase and lecithinase negative trait for safer isolates. These were identified by biochemical assays and then subjected to RAPD-PCR. The selected cultures DB-1aa, DB-b2-15b, Cu2-PM7, Cu3-PM8 and IB-pM15 were identified by 16S rDNA sequencing as Enterococcus durans, Enterococcus faecium, Lactobacillus plantarum, and two Lactobacillus fermentum, respectively. Several in vitro experiments were carried out including acid and bile tolerance, survival under simulated gastrointestinal condition, adhesion assay to evaluate the probiotic potential of the isolates. In addition, the isolates were studied for competent properties such as antibacterial, antioxidant activity, and enzyme production for their functional application. The results of the study prove the efficiency of selected isolates as potential probiotic cultures and hence can be recommended for application in any functional food formulations.\n\nIdentification and in vitro evaluation of probiotic attributes of lactic acid bacteria isolated from fermented food sources.", "token_count": 436, "char_count": 1732, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6798, "quality_score": 0.8399, "entities": { "genes": [ "ATCC9341", "PM7", "PM8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:11.086179", "source": { "split": "train_shard_00000", "doc_id": 2563 }, "chunk_id": "train_shard_00000_2563_0", "global_id": 2825 }, { "text": "The environmental species Pseudomonas aeruginosa thrives in a variety of habitats. Within the epidemic population structure of P. aeruginosa, occassionally highly successful clones that are equally capable to succeed in the environment and the human host arise. Framed by a highly conserved core genome, individual members of successful clones are characterized by a high variability in their accessory genome. The abundance of successful clones might be funded in specific features of the core genome or, although not mutually exclusive, in the variability of the accessory genome. In clone C, one of the most predominant clones, the plasmid pKLC102 and the PACGI-1 genomic island are two ubiquitous accessory genetic elements. The conserved transmissible locus of protein quality control (TLPQC) at the border of PACGI-1 is a unique horizontally transferred compository element, which codes predominantly for stress-related cargo gene products such as involved in protein homeostasis. As a hallmark, most TLPQC xenologues possess a core genome equivalent. With elevated temperature tolerance as a characteristic of clone C strains, the unique P. aeruginosa and clone C specific disaggregase ClpG is a major contributor to tolerance. As other successful clones, such as PA14, do not encode the TLPQC locus, ubiquitous denominators of success, if existing, need to be identified.\n\nWhy? - Successful Pseudomonas aeruginosa clones with a focus on clone C.", "token_count": 350, "char_count": 1453, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6037, "quality_score": 0.8018, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:11.659422", "source": { "split": "train_shard_00000", "doc_id": 2564 }, "chunk_id": "train_shard_00000_2564_0", "global_id": 2826 }, { "text": "Alpha-naphthylisothiocyanate (ANIT) is a typical hepatotoxicant that causes cholestasis, which causes toxic bile acid accumulation in the liver and leads to liver injury. Picroside II (PIC), one of the dominant effective components extracted from Picrorhiza scrophulariiflora Pennell, exhibits many pharmacological effects. However, the role of AMP-activated protein kinase (AMPK)-Farnesoid X receptor (FXR) pathway in the hepatoprotective effect of PIC against ANIT-induced cholestasis remains largely unknown. This study aimed to investigate the mechanisms of PIC on ANIT-induced cholestasis in vivo and in vitro. Our results showed that PIC protected against ANIT-induced liver injury in primary mouse hepatocytes, and decreased serum biochemical markers and lessened histological injuries in mice. ANIT inhibited FXR and its target genes of bile acid synthesis enzymes sterol-12α-hydroxylase (CYP8B1), and increase bile acid uptake transporter Na + -dependent taurocholate transporter (NTCP), efflux transporter bile salt export pump (BSEP) and bile acid metabolizing enzymes UDP-glucuronosyltransferase 1a1 (UGT1A1) expressions. PIC prevented its downregulation of FXR, NTCP, BSEP and UGT1A1, and further reduced CYP8B1 by ANIT. Furthermore, ANIT activated AMPK via ERK1/2-LKB1 pathway. PIC inhibited ERK1/2, LKB1 and AMPK phosphorylation in ANIT-induced cholestasis in vivo and in vitro. AICAR, an AMPK agonist, blocked PIC-mediated changes in FXR, CYP8B1 and BSEP expression in vitro. Meanwhile, U0126, an ERK1/2 inhibitor, further repressed ERK1/2-LKB1-AMPK pathway phosphorylation", "token_count": 503, "char_count": 1589, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6698, "quality_score": 0.8349, "entities": { "genes": [ "ERK1", "LKB1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:12.317230", "source": { "split": "train_shard_00000", "doc_id": 2565 }, "chunk_id": "train_shard_00000_2565_0", "global_id": 2827 }, { "text": "In conclusion, PIC regulated bile acid-related transporters and enzymes to protect against ANIT-induced liver injury, which related to ERK1/2-LKB1-AMPK pathway. Thus, this study extends the understanding of the anti-cholestasis effect of PIC and provides new therapeutic targets for cholestasis treatment.\n\nPicroside II alleviates liver injury induced by alpha-naphthylisothiocyanate through AMPK-FXR pathway.", "token_count": 117, "char_count": 409, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8627, "quality_score": 0.9314, "entities": { "genes": [ "ERK1", "LKB1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:12.706394", "source": { "split": "train_shard_00000", "doc_id": 2565 }, "chunk_id": "train_shard_00000_2565_1", "global_id": 2828 }, { "text": "Nucleotide sequence-based methods focusing on the single-nucleotide polymorphisms (SNPs) of Listeria monocytogenes and L. innocua housekeeping genes (multilocus sequence typing) and in the core genome (core genome MLST) facilitate the rapid and interlaboratory comparison in open accessible databases as provided by Institute Pasteur ( https://bigsdb.web.pasteur.fr/listeria/listeria.html ). Strains can be compared on a global level and help to track forward and trace backward pathogen contamination events in food processing facilities and in outbreak scenarios.\n\nMultilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) of Listeria monocytogenes and Listeria innocua.", "token_count": 181, "char_count": 682, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:13.159676", "source": { "split": "train_shard_00000", "doc_id": 2566 }, "chunk_id": "train_shard_00000_2566_0", "global_id": 2829 }, { "text": "Genome graphs can represent genetic variation and sequence uncertainty. Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph. Yet, so far, this step is often prohibitively slow. We present GraphAligner, a tool for aligning long reads to genome graphs. Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory. When employing GraphAligner for error correction, we find it to be more than twice as accurate and over 12x faster than extant tools.Availability: Package manager: https://anaconda.org/bioconda/graphaligner and source code: https://github.com/maickrau/GraphAligner.\n\nGraphAligner: rapid and versatile sequence-to-graph alignment.", "token_count": 199, "char_count": 778, "word_count": 103, "semantic_coherence": 1, "information_density": 0.767, "quality_score": 0.8835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:13.612989", "source": { "split": "train_shard_00000", "doc_id": 2567 }, "chunk_id": "train_shard_00000_2567_0", "global_id": 2830 }, { "text": "Trimethoprim is a synthetic antibacterial agent that targets folate biosynthesis by competitively binding to the di-hydrofolate reductase enzyme (DHFR). Trimethoprim is often administered synergistically with sulfonamide, another chemotherapeutic agent targeting the di-hydropteroate synthase (DHPS) enzyme in the same pathway. Clinical resistance to both drugs is widespread and mediated by enzyme variants capable of performing their biological function without binding to these drugs. These mutant enzymes were assumed to have arisen after the discovery of these synthetic drugs, but recent work has shown that genes conferring resistance to sulfonamide were present in the bacterial pangenome millions of years ago. Here, we apply phylogenetics and comparative genomics methods to study the largest family of mobile trimethoprim-resistance genes (\n\nExploration into the origins and mobilization of di-hydrofolate reductase genes and the emergence of clinical resistance to trimethoprim.", "token_count": 241, "char_count": 990, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6866, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:14.091850", "source": { "split": "train_shard_00000", "doc_id": 2568 }, "chunk_id": "train_shard_00000_2568_0", "global_id": 2831 }, { "text": "Escherichia coli is considered to be the best-known microorganism given the large number of published studies detailing its genes, its genome and the biochemical functions of its molecular components. This vast literature has been systematically assembled into a reconstruction of the biochemical reaction networks that underlie E. coli's functions, a process which is now being applied to an increasing number of microorganisms. Genome-scale reconstructed networks are organized and systematized knowledge bases that have multiple uses, including conversion into computational models that interpret and predict phenotypic states and the consequences of environmental and genetic perturbations. These genome-scale models (GEMs) now enable us to develop pan-genome analyses that provide mechanistic insights, detail the selection pressures on proteome allocation and address stress phenotypes. In this Review, we first discuss the overall development of GEMs and their applications. Next, we review the evolution of the most complete GEM that has been developed to date: the E. coli GEM. Finally, we explore three emerging areas in genome-scale modelling of microbial phenotypes: collections of strain-specific models, metabolic and macromolecular expression models, and simulation of stress responses.\n\nReconstructing organisms in silico: genome-scale models and their emerging applications.", "token_count": 292, "char_count": 1391, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6737, "quality_score": 0.8368, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:14.654582", "source": { "split": "train_shard_00000", "doc_id": 2569 }, "chunk_id": "train_shard_00000_2569_0", "global_id": 2832 }, { "text": "Motivated to find options for prevention or intervention, molecular epidemiology aims to identify the host and microbial factors that determine the transmission, manifestation and progression of infectious disease. The genotyping of cultivatable bacterial strains is performed by either anonymous fingerprinting techniques or sequence-based exploration of variable genomic sites. Multilocus sequence typing of housekeeping genes and allele profiling of the core genome have become standard techniques of bacterial strain typing that may be supplemented by whole genome sequencing to explore all single nucleotide variants and/or the composition of the accessory genome. Next, novel protocols to investigate host and microbiome based upon smart third generation sequencing technologies are being developed for an effective surveillance, rapid diagnosis and real-time tracking of infectious diseases.\n\nMolecular epidemiology in current times.", "token_count": 184, "char_count": 940, "word_count": 125, "semantic_coherence": 1, "information_density": 0.744, "quality_score": 0.872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:15.100246", "source": { "split": "train_shard_00000", "doc_id": 2570 }, "chunk_id": "train_shard_00000_2570_0", "global_id": 2833 }, { "text": "Gypenosides, extracts of Gynostemma yixingense, have been traditionally prescribed to improve metabolic syndrome in Asian folk and local traditional medicine hospitals. However, the mechanism of its action remains unclarified. In this work, our results indicated that chronic administration of 2α-OH-protopanoxadiol (GP2), a metabolite of gypenosides in vivo, protected mice from high-fat diet-induced obesity and improved glucose tolerance by improving intestinal L-cell function. Mechanistically, GP2 treatment inhibited the enzymatic activity of bile salt hydrolase and modulated the proportions of the gut microbiota, which led to an increase in the accumulation of tauro-β-muricholic acid (TβMCA) in the intestine. TβMCA induced GLP-1 production and secretion by reducing the transcriptional activity of nuclear receptor farnesoid X receptor (FXR). Transplantation of GP2-remodelled fecal microbiota into antibiotic-treated mice also increased the intestinal TβMCA content and improved intestinal L-cell function. These findings demonstrate that GP2 ameliorates metabolic syndrome at least partly through the intestinal FXR/GLP-1 axis via gut microbiota remodelling and also suggest that GP2 may serve as a promising oral therapeutic agent for metabolic syndrome.\n\nThe triterpenoid sapogenin (2α-OH-Protopanoxadiol) ameliorates metabolic syndrome via the intestinal FXR/GLP-1 axis through gut microbiota remodelling.", "token_count": 386, "char_count": 1421, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [ "GP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:15.718933", "source": { "split": "train_shard_00000", "doc_id": 2571 }, "chunk_id": "train_shard_00000_2571_0", "global_id": 2834 }, { "text": "Hepatocellular accumulation of bile salts by inhibition of bile salt export pump (BSEP/\n\nA Two-Tiered In Vitro Approach to De-Risk Drug Candidates for Potential Bile Salt Export Pump Inhibition Liabilities in Drug Discovery.", "token_count": 69, "char_count": 224, "word_count": 33, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:16.088022", "source": { "split": "train_shard_00000", "doc_id": 2572 }, "chunk_id": "train_shard_00000_2572_0", "global_id": 2835 }, { "text": "Advances in molecular biology identifying the many carrier-mediated organic anion transporters and advances in microscopy that have provided a more detailed anatomy of the canalicular conduit make updating the concept of osmotically determined canalicular flow possible. For the most part water flow is not transmembrane but via specific pore proteins in both the hepatocyte and the tight junction. These pores independently regulate the rate at which water flows in response to an osmotic gradient and therefore are determinants of canalicular bile acid concentration. Review of the literature indicates that the initial effect on hepatic bile flow of cholestatic agents such as Thorazine and estradiol 17β-glucuronide are on water flow and not bile salt export pump-mediated bile acid transport and thus provides new approaches to the pathogenesis of drug-induced liver injury. Attaining a micellar concentration of bile acids in the canaliculus is essential to the formation of cholesterol-lecithin vesicles, which mostly occur in the periportal region of the canalicular conduit. The other regions, midcentral and pericentral, may transport lesser amounts of bile acid but augment water flow. Broadening the concept of how hepatic bile flow is initiated, provides new insights into the pathogenesis of canalicular cholestasis.\n\nHepatic bile formation: bile acid transport and water flow into the canalicular conduit.", "token_count": 329, "char_count": 1420, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5817, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:16.693339", "source": { "split": "train_shard_00000", "doc_id": 2573 }, "chunk_id": "train_shard_00000_2573_0", "global_id": 2836 }, { "text": "Shewanella algae is not only the most commonly reported species in Shewanella human infections but also capable to inhabit a wide variety of habitats. Although there is evidence that quorum sensing is associated with bacterial adaptation to changing environmental conditions, little is known of the quorum sensing system in S. algae. In this study, we conducted the whole genome sequencing of S. algae strains and applied comparative genomics to reveal the core genome. Genes related to the quorum sensing system were identified by integrated bioinformatics analysis. S. algae harbor genes involved in all three main types of autoinducer systems. This study provides insights into the quorum sensing systems in S. algae, which might be valuable in the future study of cell behavior in S. algae.\n\nComparative genomics reveals insights into characterization and distribution of quorum sensing-related genes in Shewanella algae from marine environment and clinical sources.", "token_count": 215, "char_count": 970, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:17.183786", "source": { "split": "train_shard_00000", "doc_id": 2574 }, "chunk_id": "train_shard_00000_2574_0", "global_id": 2837 }, { "text": "Bacterial therapy, which presents a smart platform for delivering and producing therapeutic agents, as monotherapy or in combination with other therapeutic modes, has provided a breakthrough for the treatment of a range of diseases. The integration of synthetic biology technology with bacteria enables their characteristics like chemotaxis and biomolecule secretion to outperform conventional diagnostics and therapeutics, thereby facilitating their clinical applications in a range of diseases. Compared to injection-administered bacteria, orally-delivered bacteria improve patient compliance while avoiding the risk of systemic infections. However, oral administration of microbes always leads to a substantial loss of viability due to the highly acidic environment in the stomach and bile salt in the intestine. Thus, the formulation of these bacteria into microcapsules using appropriate biomaterials is a promising approach for reducing cell death during gastrointestinal passage and controlling the release of these therapeutic cells across the intestinal tract. In this review, we reveal the basic principles of oral bacterial delivery, from internal genetic engineering approaches to external encapsulation and modification, and summarize the most recent biomedical applications. Finally, we discuss future trends in oral bacterial therapy as well as current challenges that need to be resolved to advance their clinical applications.\n\nOral delivery of bacteria: Basic principles and biomedical applications.", "token_count": 290, "char_count": 1517, "word_count": 206, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:17.777530", "source": { "split": "train_shard_00000", "doc_id": 2575 }, "chunk_id": "train_shard_00000_2575_0", "global_id": 2838 }, { "text": "The pathogenesis of esophageal injury in gastroesophageal reflux disease (GERD) is incompletely understood. We modeled exposure of human esophageal myofibroblasts (HEMFs) to gastroesophageal reflux by repeated treatment with pH 4.5 and pH 4.5 bile salts and determined the effects on the epithelium in a 3D organotypic-like air-liquid interface model. Total, basal and supra-basal thickness of the epithelium were measured and immunostaining for p63, for basal (CK 14) and supra-basal (CK 4) squamous differentiation markers, and for cell proliferation (PCNA) were performed. Epithelial cell proliferation in response to HEMF conditioned media was also assessed in 2D culture. In the 3D organotypic model, total epithelial thickness increased similarly with pH 4.5 and pH 4.5 bile salt treated versus untreated and bile salt treated HEMF conditioned media. Epithelial p63 immunostaining was increased and multilayered. There was expansion of the CK14+ basal and CK4+ supra-basal layers in the epithelium established with conditioned media from pH 4.5 and pH 4.5 bile salt treated HEMFs versus untreated HEMF conditioned media. PCNA + cells per μm of tissue were unchanged in the basal layer across all treatment conditions while PCNA + cells per total DAPI + cells were decreased. In 2D culture, basal epithelial proliferation decreased with conditioned media from pH 4.5 and pH 4.5 bile salt treated HEMFs compared to conditioned media from untreated HEMF conditioned media. Secreted factors from HEMFs treated with acidic stimuli encountered in GERD increase epithelial thickness compared to secreted factors from untreated HEMFs and expand both basal and supra-basal layers", "token_count": 493, "char_count": 1676, "word_count": 249, "semantic_coherence": 1, "information_density": 0.4578, "quality_score": 0.7289, "entities": { "genes": [ "CK14", "CK4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:18.433430", "source": { "split": "train_shard_00000", "doc_id": 2576 }, "chunk_id": "train_shard_00000_2576_0", "global_id": 2839 }, { "text": "Our findings demonstrate for the first time paracrine regulation of the squamous epithelium from acid stimulated HEMFs. The effects of secreted factors from acid treated HEMFs on basal cell proliferation in this model and the mechanism mediating the increase in epithelial thickness merit further investigation.\n\nHuman esophageal myofibroblasts increase squamous epithelial thickness via paracrine mechanisms in an in vitro model of gastroesophageal reflux disease.", "token_count": 117, "char_count": 465, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:18.812475", "source": { "split": "train_shard_00000", "doc_id": 2576 }, "chunk_id": "train_shard_00000_2576_1", "global_id": 2840 }, { "text": "As genome sequencing efforts are unveiling the genetic diversity of the biosphere with an unprecedented speed, there is a need to accurately describe the structural and functional properties of groups of extant species whose genomes have been sequenced, as well as their inferred ancestors, at any given taxonomic level of their phylogeny. Elaborate approaches for the reconstruction of ancestral states at the sequence level have been developed, subsequently augmented by methods based on gene content. While these approaches of sequence or gene-content reconstruction have been successfully deployed, there has been less progress on the explicit inference of functional properties of ancestral genomes, in terms of metabolic pathways and other cellular processes. Herein, we describe PathTrace, an efficient algorithm for parsimony-based reconstructions of the evolutionary history of individual metabolic pathways, pivotal representations of key functional modules of cellular function. The algorithm is implemented as a five-step process through which pathways are represented as fuzzy vectors, where each enzyme is associated with a taxonomic conservation value derived from the phylogenetic profile of its protein sequence. The method is evaluated with a selected benchmark set of pathways against collections of genome sequences from key data resources. By deploying a pangenome-driven approach for pathway sets, we demonstrate that the inferred patterns are largely insensitive to noise, as opposed to gene-content reconstruction methods. In addition, the resulting reconstructions are closely correlated with the evolutionary distance of the taxa under study, suggesting that a diligent selection of target pangenomes is essential for maintaining cohesiveness of the method and consistency of the inference, serving as an internal control for an arbitrary selection of queries. The PathTrace method is a first step towards the large-scale analysis of metabolic pathway evolution and our deeper understanding of functional relationships reflected in emerging pangenome collections.\n\nAncestral state reconstruction of metabolic pathways across pangenome ensembles.", "token_count": 430, "char_count": 2171, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5941, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:19.448799", "source": { "split": "train_shard_00000", "doc_id": 2577 }, "chunk_id": "train_shard_00000_2577_0", "global_id": 2841 }, { "text": "Chimeric mice with humanized livers are considered a useful animal model for predicting human (h-) drug metabolism and toxicity. In this study, the characteristics of fresh h-hepatocytes (cFHHs, PXB-cells®) isolated from chimeric mice (PXB-mice®) were evaluated in vitro to confirm their utility for drug development. cFHHs cultured at high density (2.13 × 105 cells/cm2) displayed stable production of h-albumin and cytochrome P450 (CYP) 3A activities for at least 21 days. The mRNA expression levels of 10 of 13 CYP, UDP-glucuronosyltransferase (UGT), and transporters were maintained at >10% of the levels of freshly isolated cFHHs after 21 days. From 1 week, many bile canaliculi were observed between cFHHs, and the accumulation of the multidrug resistance-associated protein and bile salt export pump substrates in these bile canaliculi was clearly inhibited by cyclosporin A. Microarray analysis of cFHHs cultured at high density and at low density (0.53 × 105 cells/cm2) revealed that high density culture maintained high expressions of some transcription factors (HNF4α, PXR, and FXR) perhaps involved in the high CYP, UGT and transporter gene expressions of cFHHs. These results strongly suggest that cFHHs could be a novel in vitro tool for drug development studies.\n\nCulture density contributes to hepatic functions of fresh human hepatocytes isolated from chimeric mice with humanized livers: Novel, long-term, functional two-dimensional in vitro tool for developing new drugs.", "token_count": 415, "char_count": 1490, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:20.077930", "source": { "split": "train_shard_00000", "doc_id": 2578 }, "chunk_id": "train_shard_00000_2578_0", "global_id": 2842 }, { "text": "Subcellular relocalization of proteins determines an organism's metabolic repertoire and thereby its survival in unique evolutionary niches. In plants, the plastid and its various morphotypes import a large and varied number of nuclear-encoded proteins to orchestrate vital biochemical reactions in a spatiotemporal context. Recent comparative genomics analysis and high-throughput shotgun proteomics data indicate that there are a large number of plastid-targeted proteins that are either semi-conserved or non-conserved across different lineages. This implies that homologs are differentially targeted across different species, which is feasible only if proteins have gained or lost plastid targeting peptides during evolution. In this study, a broad, multi-genome analysis of 15 phylogenetically diverse genera and in-depth analyses of pangenomes from Arabidopsis and Brachypodium were performed to address the question of how proteins acquire or lose plastid targeting peptides. The analysis revealed that random insertions or deletions were the dominant mechanism by which novel transit peptides are gained by proteins. While gene duplication was not a strict requirement for the acquisition of novel subcellular targeting, 40% of novel plastid-targeted genes were found to be most closely related to a sequence within the same genome, and of these, 30.5% resulted from alternative transcription or translation initiation sites. Interestingly, analysis of the distribution of amino acids in the transit peptides of known and predicted chloroplast-targeted proteins revealed monocot and eudicot-specific preferences in residue distribution.\n\nPlastid transit peptides-where do they come from and where do they all belong? Multi-genome and pan-genomic assessment of chloroplast transit peptide evolution.", "token_count": 420, "char_count": 1806, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:20.701382", "source": { "split": "train_shard_00000", "doc_id": 2579 }, "chunk_id": "train_shard_00000_2579_0", "global_id": 2843 }, { "text": "In silico functional prediction of hypothetical proteins from the core genome of", "token_count": 18, "char_count": 80, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:21.068373", "source": { "split": "train_shard_00000", "doc_id": 2580 }, "chunk_id": "train_shard_00000_2580_0", "global_id": 2844 }, { "text": "The accumulation of glycerol is essential for yeast viability upon hyperosmotic stress. In this study, the STL1 homolog KmSTL1, encoding a putative glycerol transporter contributing to cell osmo-tolerance, was identified in Kluyveromyces marxianus NBRC1777. We constructed the KmSTL1, KmGPD1, and KmFPS1 single-deletion mutants and the KmSTL1/KmGPD1 and KmSTL1/KmFPS1 double-deletion mutants of K. marxianus. Deletion of KmSTL1 or KmGPD1 resulted in K. marxianus cell sensitization to hyperosmotic stress, whereas deletion of KmFPS1 improved stress tolerance. The expression of KmSTL1 was osmotically induced, whereas that of KmFPS1 was osmotically inhibited. The expression of KmGPD1 was constitutive and continuous in the ΔKmSTL1 mutant strain but inhibited in the ΔKmFPS1 mutant strain due to feedback suppression by glycerol. In summary, our findings indicated that K. marxianus would increase glycerol synthesis by increasing GPD1 expression, increase glycerol import from the extracellular environment by increasing STL1 expression, and reduce glycerol efflux by reducing FPS1 expression under hyperosmotic stress.\n\nGlycerol uptake and synthesis systems contribute to the osmotic tolerance of Kluyveromyces marxianus.", "token_count": 378, "char_count": 1223, "word_count": 165, "semantic_coherence": 1, "information_density": 0.5818, "quality_score": 0.7909, "entities": { "genes": [ "GPD1", "FPS1", "STL1", "NBRC1777" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:21.643654", "source": { "split": "train_shard_00000", "doc_id": 2581 }, "chunk_id": "train_shard_00000_2581_0", "global_id": 2845 }, { "text": "In this study, we evaluated the efficacy of 3 commercial protective cultures designated PC1 (Lactobacillus spp.), PC2 (Lactobacillus rhamnosus), and PC3 (Lactobacillus rhamnosus) as biopreservatives in queso fresco (QF) against 9 yeast strains (Candida zeylanoides, Clavispora lusitaniae, Debaryomyces hansenii, Debaryomyces prosopidis, Kluyveromyces marxianus, Meyerozyma guilliermondii, Pichia fermentans, Rhodotorula mucilaginosa, and Torulaspora delbrueckii) and 11 mold strains (Aspergillus cibarius, Aureobasidium pullulans, Penicillium chrysogenum, Penicillium citrinum, Penicillium commune, Penicillium decumbens, Penicillium roqueforti, Mucor genevensis, Mucor racemosus, Phoma dimorpha, and Trichoderma amazonicum). All fungal spoilage strains were previously isolated from dairy processing environments. A positive control (C) with no protective culture was included. Fungal spoilage organisms were inoculated on cheese surfaces at an inoculum level of 20 cfu/g, and cheeses were stored at 6 ± 2°C throughout the study. For yeast enumeration, cheeses were sampled on d 0, 7, 14, and 21 postinoculation. Significant inhibition was detected for each yeast strain by comparing yeast counts for each cheese treated with protective culture against the control cheese using one-way ANOVA with Bonferroni correction performed individually at d 7, 14, and 21 postinoculation. Mold growth was visually observed and imaged weekly through 70 d postinoculation. Whereas PC3 inhibited Cl. lusitaniae, Mey. guilliermondii, and Ph. dimorpha, PC2 inhibited the outgrowth of Cl. lusitaniae, D. hansenii, and Ph. dimorpha", "token_count": 524, "char_count": 1614, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [ "PC3", "PC1", "PC2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:24:22.295417", "source": { "split": "train_shard_00000", "doc_id": 2582 }, "chunk_id": "train_shard_00000_2582_0", "global_id": 2846 }, { "text": "Protective culture 1 had the broadest spectrum of efficacy across yeast and molds, delaying spoilage caused by 4 distinct yeast strains (Cl. lusitaniae, D. hansenii, D. prosopidis, and Mey. guilliermondii), and inhibiting visible growth of 2 mold strains (P. chrysogenum and Ph. dimorpha). Results demonstrated that commercial protective cultures vary in performance, as indicated by the breadth of mold and yeast inhibition at both the genus and species level. This study suggests that manufacturers looking into using protective cultures should investigate their efficacy against specific fungal strains of concern.\n\nEvaluation of the efficacy of commercial protective cultures against mold and yeast in queso fresco.", "token_count": 172, "char_count": 719, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:22.735395", "source": { "split": "train_shard_00000", "doc_id": 2582 }, "chunk_id": "train_shard_00000_2582_1", "global_id": 2847 }, { "text": "Given a group of genomes, represented as the sets of genes that belong to them, the discovery of the pangenomic content is based on the search of genetic homology among the genes for clustering them into families. Thus, pangenomic analyses investigate the membership of the families to the given genomes. This approach is referred to as the gene-oriented approach in contrast to other definitions of the problem that takes into account different genomic features. In the past years, several tools have been developed to discover and analyse pangenomic contents. Because of the hardness of the problem, each tool applies a different strategy for discovering the pangenomic content. This results in a differentiation of the performance of each tool that depends on the composition of the input genomes. This review reports the main analysis instruments provided by the current state of the art tools for the discovery of pangenomic contents. Moreover, unlike previous works, the presented study compares pangenomic tools from a methodological perspective, analysing the causes that lead a given methodology to outperform other tools. The analysis is performed by taking into account different bacterial populations, which are synthetically generated by changing evolutionary parameters. The benchmarks used to compare the pangenomic tools, in addition to the computational pipeline developed for this purpose, are available at https://github.com/InfOmics/pangenes-review. Contact: V. Bonnici, R. Giugno Supplementary information: Supplementary data are available at Briefings in Bioinformatics online.\n\nChallenges in gene-oriented approaches for pangenome content discovery.", "token_count": 342, "char_count": 1672, "word_count": 240, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:23.301910", "source": { "split": "train_shard_00000", "doc_id": 2583 }, "chunk_id": "train_shard_00000_2583_0", "global_id": 2848 }, { "text": "Aldo-keto reductase KmAKR-catalyzed asymmetric reduction offers a green approach to produce dichiral diol tert-butyl 6-substituted-(3R,5R/S)-dihydroxyhexanoates, which are important building blocks of statins. In our previous work, we cloned a novel gene of NADPH-specific aldo-keto reductase KmAKR (WT) from a thermotolerant yeast Kluyveromyces marxianus ZJB14056 and a mutant KmAKR-W297H/Y296W/K29H (Variant III) has been constructed and displayed strict diastereoselectivity towards tert-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate ((5R)-1) but moderate activity and stability. Herein, to further co-evolve its activity and thermostability, we performed semi-rational engineering of Variant III by using a combinational screening strategy, consisting of tertiary structure analysis, loop engineering, and alanine scanning. As results, the \"best\" variant KmAKR-W297H/Y296W/K29H/Y28A/T63M (Variant VI) was acquired, whose K\n\nCo-evolution of activity and thermostability of an aldo-keto reductase KmAKR for asymmetric synthesis of statin precursor dichiral diols.", "token_count": 347, "char_count": 1061, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7717, "quality_score": 0.8858, "entities": { "genes": [ "ZJB14056" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:23.876293", "source": { "split": "train_shard_00000", "doc_id": 2584 }, "chunk_id": "train_shard_00000_2584_0", "global_id": 2849 }, { "text": "Whole genome sequencing (WGS) has proven to be the ultimate tool for bacterial isolate characterization and relatedness determination. However, standardized and harmonized workflows, e.g. for DNA extraction, are required to ensure robust and exchangeable WGS data. Data sharing between (inter)national laboratories is essential to support foodborne pathogen control, including outbreak investigation. This study evaluated eight commercial DNA preparation kits for their potential influence on: (i) DNA quality for Nextera XT library preparation; (ii) MiSeq sequencing (data quality, read mapping against plasmid and chromosome references); and (iii) WGS data analysis, i.e. isolate characterization (serotyping, virulence and antimicrobial resistance genotyping) and phylogenetic relatedness (core genome multilocus sequence typing and single nucleotide polymorphism analysis). Shiga toxin-producing Escherichia coli (STEC) was selected as a case study. Overall, data quality and inferred phylogenetic relationships between isolates were not affected by the DNA extraction kit choice, irrespective of the presence of confounding factors such as EDTA in DNA solution buffers. Nevertheless, completeness of STEC characterization was, although not substantially, influenced by the plasmid extraction performance of the kits, especially when using Nextera XT library preparation. This study contributes to addressing the WGS challenges of standardizing protocols to support data portability and to enable full exploitation of its potential.\n\nImpact of DNA extraction on whole genome sequencing analysis for characterization and relatedness of Shiga toxin-producing Escherichia coli isolates.", "token_count": 388, "char_count": 1687, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6787, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:24.492154", "source": { "split": "train_shard_00000", "doc_id": 2585 }, "chunk_id": "train_shard_00000_2585_0", "global_id": 2850 }, { "text": "The core genome represents the set of genes shared by all, or nearly all, strains of a given population or species of prokaryotes. Inferring the core genome is integral to many genomic analyses, however, most methods rely on the comparison of all the pairs of genomes; a step that is becoming increasingly difficult given the massive accumulation of genomic data. Here, we present CoreCruncher; a program that robustly and rapidly constructs core genomes across hundreds or thousands of genomes. CoreCruncher does not compute all pairwise genome comparisons and uses a heuristic based on the distributions of identity scores to classify sequences as orthologs or paralogs/xenologs. Although it is much faster than current methods, our results indicate that our approach is more conservative than other tools and less sensitive to the presence of paralogs and xenologs. CoreCruncher is freely available from: https://github.com/lbobay/CoreCruncher. CoreCruncher is written in Python 3.7 and can also run on Python 2.7 without modification. It requires the python library Numpy and either Usearch or Blast. Certain options require the programs muscle or mafft.\n\nCoreCruncher: Fast and Robust Construction of Core Genomes in Large Prokaryotic Data Sets.", "token_count": 291, "char_count": 1250, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6755, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:25.053276", "source": { "split": "train_shard_00000", "doc_id": 2586 }, "chunk_id": "train_shard_00000_2586_0", "global_id": 2851 }, { "text": "Bile salts are secreted into the gastrointestinal tract to aid in the absorption of lipids. In addition, bile salts show potent antimicrobial activity in part by mediating bacterial protein unfolding and aggregation. Here, using a protein folding sensor, we made the surprising discovery that the Escherichia coli periplasmic glycerol-3-phosphate (G3P)-binding protein UgpB can serve, in the absence of its substrate, as a potent molecular chaperone that exhibits anti-aggregation activity against bile salt-induced protein aggregation. The substrate G3P, which is known to accumulate in the later compartments of the digestive system, triggers a functional switch between UgpB's activity as a molecular chaperone and its activity as a G3P transporter. A UgpB mutant unable to bind G3P is constitutively active as a chaperone, and its crystal structure shows that it contains a deep surface groove absent in the G3P-bound wild-type UgpB. Our work illustrates how evolution may be able to convert threats into signals that first activate and then inactivate a chaperone at the protein level in a manner that bypasses the need for ATP.\n\nA metabolite binding protein moonlights as a bile-responsive chaperone.", "token_count": 308, "char_count": 1206, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:25.619405", "source": { "split": "train_shard_00000", "doc_id": 2587 }, "chunk_id": "train_shard_00000_2587_0", "global_id": 2852 }, { "text": "Bacteriophage genomes rapidly evolve via mutation and horizontal gene transfer to counter evolving bacterial host defenses; such arms race dynamics should lead to divergence between phages from similar, geographically isolated ecosystems. However, near-identical phage genomes can reoccur over large geographical distances and several years apart, conversely suggesting many are stably maintained. Here, we show that phages with near-identical core genomes in distant, discrete aquatic ecosystems maintain diversity by possession of numerous flexible gene modules, where homologous genes present in the pan-genome interchange to create new phage variants. By repeatedly reconstructing the core and flexible regions of phage genomes from different metagenomes, we show a pool of homologous gene variants co-exist for each module in each location, however, the dominant variant shuffles independently in each module. These results suggest that in a natural community, recombination is the largest contributor to phage diversity, allowing a variety of host recognition receptors and genes to counter bacterial defenses to co-exist for each phage.\n\nFlexible genes establish widespread bacteriophage pan-genomes in cryoconite hole ecosystems.", "token_count": 263, "char_count": 1237, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:26.170584", "source": { "split": "train_shard_00000", "doc_id": 2588 }, "chunk_id": "train_shard_00000_2588_0", "global_id": 2853 }, { "text": "Campylobacter jejuni is a major foodborne pathogen that causes gastroenteritis in humans. Chickens act as the reservoir host for C. jejuni, wherein the pathogen asymptomatically colonizes the ceca leading to contamination of carcasses during slaughter. The major colonization factors in C. jejuni include motility, intestinal epithelial attachment, acid/bile tolerance, and quorum sensing. Reducing the expression of the aforementioned factors could potentially reduce C. jejuni colonization in chickens. This study investigated the efficacy of subinhibitory concentration (SIC; compound concentration not inhibiting bacterial growth) of carvacrol in reducing the expression of C. jejuni colonization factors in vitro. Moreover, the effect of carvacrol on the expression of C. jejuni proteome was investigated using liquid chromatography-tandem mass spectrometry. The motility assay was conducted at 42°C, and the motility zone was measured after 24 h of incubation. For the adhesion assay, monolayers of primary chicken enterocytes (∼10\n\nCarvacrol attenuates Campylobacter jejuni colonization factors and proteome critical for persistence in the chicken gut.", "token_count": 289, "char_count": 1159, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:26.728122", "source": { "split": "train_shard_00000", "doc_id": 2589 }, "chunk_id": "train_shard_00000_2589_0", "global_id": 2854 }, { "text": "Lipopolysaccharide (LPS) induces inflammatory cholestasis by impairing expression, localization, and function of carriers involved in bile formation, e.g. bile salt export pump (Bsep) and multidrug resistance-associated protein 2 (Mrp2). A specific therapy against this disease is still lacking. Therefore, we evaluated the anticholestatic effects of spironolactone (SL), a PXR ligand that regulates bile salt homeostasis, up-regulates Mrp2, and bears anti-inflammatory properties.\n\nSpironolactone ameliorates lipopolysaccharide-induced cholestasis in rats by improving Mrp2 function: Role of transcriptional and post-transcriptional mechanisms.", "token_count": 179, "char_count": 645, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8312, "quality_score": 0.9156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:27.178546", "source": { "split": "train_shard_00000", "doc_id": 2590 }, "chunk_id": "train_shard_00000_2590_0", "global_id": 2855 }, { "text": "A bifunctional cholic acid-bis(2-pyridylmethyl)amine (bpa) ligand featuring an amide linker was coordinated to a manganese(i) or rhenium(i) tricarbonyl moiety to give [M(bpacholamide)(CO)3] with M = Mn, Re in good yield and very high purity. Strong antibacterial activity was observed against four strains of methicillin-susceptible (MSSA) and methicillin-resistant (MRSA) Staphylococcus aureus, with minimum inhibitory concentrations (MICs) in the range of 2-3.5 μM. No difference in response was observed for the MSSA vs. MRSA strains. Activity was also independent of the nature of the metal center, as the Mn and Re complexes showed essentially identical MIC values. In contrast to some other metal carbonyl complexes, the activity seems to be unrelated to the release of carbon monoxide, as photoactivation of the Mn complex reduced the potency by a factor of 2-8. Both metal complexes were non-toxic in Galleria mellonella larvae at concentrations of up to 100× the MIC value. In vivo testing in Galleria larvae infected with MRSA/MSSA demonstrated a significant increase in overall survival rates from 46% in the control to 88% in the group treated with the metal complexes. ICP-MS analysis showed that the Mn and Re cholamide complexes are efficiently internalized by E. coli cells and do not interfere with membrane integrity, as evident from a lack of release of intracellular ATP. An increased sensitivity was observed in acrB, acrD, and mdt mutants that are defective in multidrug exporters, indicating that the compounds have an intracellular mechanism of action. Furthermore, E. coli mntP mutants defective in the gene encoding an Mn exporter were more sensitive than the wildtype, while inactivation of the regulator that controls expression of the Mn uptake proteins MntP and MntH slightly increased sensitivity to the compound", "token_count": 509, "char_count": 1843, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:27.808369", "source": { "split": "train_shard_00000", "doc_id": 2591 }, "chunk_id": "train_shard_00000_2591_0", "global_id": 2856 }, { "text": "Single knockout mutants defective in genes linked to bile salt and oxidative stress response (dinF, yiaH, sodA, katE, and soxS) did not show increased sensitivity relative to the wild type. Overall, neither the cholic acid moiety nor the metal-carbonyl fragment alone appear to be responsible for the biological activity observed and thus the search for the primary intracellular target continues.\n\nAntibacterial activity of Mn(I) and Re(I) tricarbonyl complexes conjugated to a bile acid carrier molecule.", "token_count": 130, "char_count": 506, "word_count": 75, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:28.243893", "source": { "split": "train_shard_00000", "doc_id": 2591 }, "chunk_id": "train_shard_00000_2591_1", "global_id": 2857 }, { "text": "The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social, and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells. The S proteins from SARS and SARS-CoV-2 are similar, but structural differences in the receptor binding domain (RBD) preclude the use of SARS-specific neutralizing antibodies to inhibit SARS-CoV-2. Here we used comparative pangenomic analysis of all sequenced reference\n\nFunctional Pangenome Analysis Shows Key Features of E Protein Are Preserved in SARS and SARS-CoV-2.", "token_count": 188, "char_count": 736, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7615, "quality_score": 0.8807, "entities": { "genes": [ "ACE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:28.720941", "source": { "split": "train_shard_00000", "doc_id": 2592 }, "chunk_id": "train_shard_00000_2592_0", "global_id": 2858 }, { "text": "Aquaculture is one of the fastest-growing food-producing sectors in the world. However, its growth is hampered by various disease problems due to infectious microorganisms, including Gram-negative bacteria in finfish aquaculture. Disease control in aquaculture by use of antibiotics is not recommended as it leads to antibiotic residues in the final product, selection, and spread of antibiotic resistance in the environment. Therefore, focus is on disease prevention by vaccination. All Gram-negative bacteria possess surface-associated outer membrane proteins (OMPs), some of which have long been recognized as potential vaccine candidates. OMPs are essential for maintaining the integrity and selective permeability of the bacterial membrane and play a key role in adaptive responses of bacteria such as solute and ion uptake, iron acquisition, antimicrobial resistance, serum resistance, and bile salt resistance and some adhesins have virulence attributes. Antigenic diversity among bacterial strains even within the same bacterial species has constrained vaccine developments, but OMPs that are conserved across serotypes could be used as potential candidates in vaccine development, and several studies have demonstrated their efficacy and potential as vaccine candidates. In this review, we will look into the application of OMPs for the design of vaccines based on recombinant proteins, subunit vaccines, chimeric proteins, and DNA vaccines as new-generation vaccine candidates for major bacterial pathogens of fish for sustainable aquaculture.\n\nApplication of Outer Membrane Protein-Based Vaccines Against Major Bacterial Fish Pathogens in India.", "token_count": 363, "char_count": 1656, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:29.341360", "source": { "split": "train_shard_00000", "doc_id": 2593 }, "chunk_id": "train_shard_00000_2593_0", "global_id": 2859 }, { "text": "Pan-genome is defined as the set of orthologous and unique genes of a specific group of organisms. The pan-genome is composed by the core genome, accessory genome, and species- or strain-specific genes. The pan-genome is considered open or closed based on the alpha value of the Heap law. In an open pan-genome, the number of gene families will continuously increase with the addition of new genomes to the analysis, while in a closed pan-genome, the number of gene families will not increase considerably. The first step of a pan-genome analysis is the homogenization of genome annotation. The same software should be used to annotate genomes, such as GeneMark or RAST. Subsequently, several software are used to calculate the pan-genome such as BPGA, GET_HOMOLOGUES, PGAP, among others. This review presents all these initial steps for those who want to perform a pan-genome analysis, explaining key concepts of the area. Furthermore, we present the pan-genomic analysis of 9 bacterial species. These are the species with the highest number of genomes deposited in GenBank. We also show the influence of the identity and coverage parameters on the prediction of orthologous and paralogous genes. Finally, we cite the perspectives of several research areas where pan-genome analysis can be used to answer important issues.\n\nFirst Steps in the Analysis of Prokaryotic Pan-Genomes.", "token_count": 323, "char_count": 1380, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5668, "quality_score": 0.7834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:29.947106", "source": { "split": "train_shard_00000", "doc_id": 2594 }, "chunk_id": "train_shard_00000_2594_0", "global_id": 2860 }, { "text": "Cholestasis causes the intrahepatic accumulation of bile acids leading to hepatobiliary injury. Recently obeticholic acid, a farnesoid X receptor (FXR) agonist, was FDA-approved to treat cholestatic liver diseases, providing a new therapeutic strategy for cholestasis. The purpose of the current study was to characterize a novel FXR agonist and verify the anti-cholestatic effect of hesperidin (HP) in vivo and in vitro. Based on a molecular docking study that predicted that HP would bind to FXR, the hepatoprotective effect of HP against cholestasis and hepatotoxicity was evaluated in mice and in normal and FXR-suppressed HepaRG cells. HP prevented bile acid toxicity in HepaRG cells, and this effect was blocked by FXR silencing. HP appears to activate FXR to prevent cholestatic liver injury. Dynamic change analysis of bile acids revealed that HP promoted bile acid excretion into feces and reduced hepatic accumulation via the regulation of the FXR-target genes bile salt export pump, multi-drug resistance-associated protein 2, and Na\n\nHesperidin alleviates cholestasis via activation of the farnesoid X receptor in vitro and in vivo.", "token_count": 311, "char_count": 1144, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6105, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:30.561291", "source": { "split": "train_shard_00000", "doc_id": 2595 }, "chunk_id": "train_shard_00000_2595_0", "global_id": 2861 }, { "text": "The prevalence of substrate cross-reactivity between AHL acylases and β-lactam acylases provides a glimpse of probable links between quorum sensing and antibiotic resistance in bacteria. Both these enzyme classes belong to the N-terminal nucleophile (Ntn)-hydrolase superfamily. Penicillin V acylases alongside bile salt hydrolases constitute the cholylglycine hydrolase (CGH) group of the Ntn-hydrolase superfamily. Here we report the ability of two acylases, Slac1 and Slac2, from the marine bacterium Shewanella loihica-PV4 to hydrolyze AHLs. Three-dimensional structure of Slac1reveals the conservation of the Ntn hydrolase fold and CGH active site, making it a unique CGH exclusively active on AHLs. Slac1homologs phylogenetically cluster separate from reported CGHs and AHL acylases, thereby representing a functionally distinct sub-class of CGH that might have evolved as an adaptation to the marine environment. We hypothesize that Slac1 could provide the structural framework for understanding this subclass, and further our understanding of the evolutionary link between AHL acylases and β-lactam acylases.\n\nStructural and enzymatic analysis of a dimeric cholylglycine hydrolase like acylase active on N-acyl homoserine lactones.", "token_count": 337, "char_count": 1239, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6686, "quality_score": 0.8343, "entities": { "genes": [ "PV4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:31.129888", "source": { "split": "train_shard_00000", "doc_id": 2596 }, "chunk_id": "train_shard_00000_2596_0", "global_id": 2862 }, { "text": "[This corrects the article DOI: 10.1371/journal.pntd.0007374.].\n\nCorrection: Genus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance.", "token_count": 62, "char_count": 182, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:31.500909", "source": { "split": "train_shard_00000", "doc_id": 2597 }, "chunk_id": "train_shard_00000_2597_0", "global_id": 2863 }, { "text": "A total of 115 isolates of lactic acid bacteria were screened from traditional fermented foods in Guizhou Province, People's Republic of China. The cholesterol removal rates of 86 isolates ranged from 7.29 to 25.66%, and 18 isolates showed a cholesterol removal rate of more than 15%. According to the results of physiological and biological tests, 13 isolates were selected to determine the fermentation performance; 9 isolates-MT-4, MT-2, PJ-15, SR2-2, SQ-4, SQ-7, ST2-2, ST2-6, and NR1-7-had high tolerance of bile salt and acid and had a survival rate of more than 96% under pH 3.0 and 0.3% bile salt. ST2-2, SR2-2, NR1-7, SQ-4, and MT-4 had high survival rate in different concentrations of NaCl and NaNO2 under different temperatures. According to BLAST comparison results of the 16S rRNA sequence in the GenBank database and the genetic distance of the 16S rRNA sequence with an ortho-connected algorithm, SR2-2, NR1-7, and ST2-2 were identified as Lactobacillus plantarum, MT-4 was identified as Lactobacillus pentosus, and SQ-4 was identified as Lactobacillus paraplantarum. Moreover, strains SQ-4 and MT-4 were added to fermented beef. Results showed that the fermented beef had delicious taste and was popular to consumers because of its proper pH, pleasant colors, high viable cell count, and suitable content of bound and immobilized water. These results provide a basis for the development of new starter formulation for the production of high-quality fermented meat products.\n\nEvaluation and Application of Different Cholesterol-Lowering Lactic Acid Bacteria as Potential Meat Starters.", "token_count": 474, "char_count": 1601, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5679, "quality_score": 0.784, "entities": { "genes": [ "SR2", "ST2", "NR1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:32.141499", "source": { "split": "train_shard_00000", "doc_id": 2598 }, "chunk_id": "train_shard_00000_2598_0", "global_id": 2864 }, { "text": "Rapid development of gene sequencing technologies has led to an exponential increase in microbial sequencing data. Genome research of a single organism does not capture the changes in the characteristics of genetic information within a species. Pan-genome analysis gives us a broader perspective to study the complete genetic information of a species. Paenibacillus polymyxa is a Gram-positive bacterium and an important plant growth-promoting rhizobacterium with the ability to produce multiple antibiotics, such as fusaricidin, lantibiotic, paenilan, and polymyxin. Our study explores the pan-genome of 14 representative P. polymyxa strains isolated from around the world. Heap's law model and curve fitting confirmed an open pan-genome of P. polymyxa. The phylogenetic and collinearity analyses reflected that the evolutionary classification of P. polymyxa strains are not associated with geographical area and ecological niches. Few genes related to phytohormone synthesis and phosphate solubilization were conserved; however, the nif cluster gene associated with nitrogen fixation exists only in some strains. This finding is indicative of nitrogen fixing ability is not stable in P. polymyxa. Analysis of antibiotic gene clusters in P. polymyxa revealed the presence of these genes in both core and accessory genomes. This observation indicates that the difference in living environment led to loss of ability to synthesize antibiotics in some strains. The current pan-genomic analysis of P. polymyxa will help us understand the mechanisms of biological control and plant growth promotion. It will also promote the use of P. polymyxa in agriculture.\n\nPan-genome analysis of Paenibacillus polymyxa strains reveals the mechanism of plant growth promotion and biocontrol.", "token_count": 423, "char_count": 1774, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5843, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:32.761365", "source": { "split": "train_shard_00000", "doc_id": 2599 }, "chunk_id": "train_shard_00000_2599_0", "global_id": 2865 }, { "text": "The nature of the interaction of bile salt micelles with exogenous surfactants used in formulations and the consequent impact on drug solubilisation is not well understood. It is often assumed that addition of any surfactant will lead to an enhanced solubility of drug, which is often true in water alone. In this study we have investigated the interaction of a range of typical non-ionic formulation surfactants (Kolliphor EL, Vitamin E TPGS and a range of Pluronics) with bile salt + phospholipid (BS + PL) mixed micelles using small angle X-ray scattering. The solubility of the model poorly water-soluble drug fenofibrate was determined in the mixed micelles and compared to solubility in the presence of increasing exogenous surfactant alone. It was found that while Pluronic F68 did not appear to interact with bile salt micelles and did not impact on the solubility of the drug in the BS + PL micellar system, addition of hydrophobic surfactants led to a synergistic boost in drug solubility, while addition of more hydrophilic surfactants led to a net reduction in drug solubility. With the exception of Pluronic F68, both hydrophobic and hydrophilic surfactants swelled the bile salt mixed micelles leading to the conclusion that although the micelle size was increased, the solubilising environment was less favourable than in bile salt micelles alone. The results serve as a warning to formulators using these surfactants as solubilising agents to consider their likely interactions with endogenous colloidal structures.\n\nSynergistic and antagonistic effects of non-ionic surfactants with bile salt + phospholipid mixed micelles on the solubility of poorly water-soluble drugs.", "token_count": 424, "char_count": 1688, "word_count": 261, "semantic_coherence": 1, "information_density": 0.4943, "quality_score": 0.7471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:33.386705", "source": { "split": "train_shard_00000", "doc_id": 2600 }, "chunk_id": "train_shard_00000_2600_0", "global_id": 2866 }, { "text": "Bile traditionally was used in wound healing, having erodent, antioxidant and antimicrobial potential. Acinetobacter baumannii is a frequent etiological agent of wound infections, exhibiting high level of resistance to conventional antibiotics.\n\nSynergistic activity of bile salts and their derivatives in combination with conventional antimicrobial agents against Acinetobacter baumannii.", "token_count": 96, "char_count": 389, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:34.125733", "source": { "split": "train_shard_00000", "doc_id": 2601 }, "chunk_id": "train_shard_00000_2601_0", "global_id": 2867 }, { "text": "Several yeasts, which are eukaryotic microorganisms, have long been used in different industries due to their potential applications, both for fermentation and for the production of specific metabolites. Kluyveromyces marxianus is one of the most auspicious nonconventional yeasts, generally isolated from wide-ranging natural habitats such as fermented traditional dairy products, kefir grain, sewage from sugar industries, sisal leaves, and plants. This is a food-grade yeast with various beneficial traits, such as rapid growth rate and thermotolerance that make it appealing for different industrial food and biotechnological applications. K. marxianus is a respiro-fermentative yeast likely to produce energy by either respiration or fermentation pathways. It generates a wide-ranging specific metabolites and could contribute to a variety of different food and biotechnological industries. Although Saccharomyces cerevisiae is the most widely used dominant representative in all aspects, many applications of K. marxianus in biotechnology, food and environment have only started to emerge nowadays; some of the most promising applications are reviewed here. The general physiology of K. marxianus is outlined, and then the different applications are discussed: first, the applications of K. marxianus in biotechnology, and then the recent advances and possible applications in food, feed and environmental industries. Finally, this review provides a discussion of the main challenges and some perspectives for targeted applications of K. marxianus in the modern food technology and applied biotechnology in order to exploit the full potential of this yeast which can be used as a cell factory with great efficiency.\n\nKluyveromyces marxianus: An emerging yeast cell factory for applications in food and biotechnology.", "token_count": 404, "char_count": 1822, "word_count": 257, "semantic_coherence": 1, "information_density": 0.572, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:34.747475", "source": { "split": "train_shard_00000", "doc_id": 2602 }, "chunk_id": "train_shard_00000_2602_0", "global_id": 2868 }, { "text": "High-resolution microbial strain typing is essential for various clinical purposes, including disease outbreak investigation, tracking of microbial transmission events and epidemiological surveillance of bacterial infections. The widely used approach for multilocus sequence typing (MLST) that is based on the core genome, cgMLST, has the advantage of a high level of typeability and maximal discriminatory power. Yet, the transition from a seven loci-based scheme to cgMLST involves several challenges, that include the need by some users to maintain backward compatibility, growing difficulties in the day-to-day communication within the microbiology community with respect to nomenclature and ontology, issues with typeability, especially if a more stringent approach to loci presence is used, and computational requirements concerning laboratory data management and sharing with end-users. Hence, methods for optimizing cgMLST schemes through careful reduction of the number of loci are expected to be beneficial for practical needs in different settings.\n\nminMLST: machine learning for optimization of bacterial strain typing.", "token_count": 226, "char_count": 1131, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7403, "quality_score": 0.8701, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:35.218897", "source": { "split": "train_shard_00000", "doc_id": 2603 }, "chunk_id": "train_shard_00000_2603_0", "global_id": 2869 }, { "text": "The use of probiotic, postbiotic, and anti-aflatoxigenic capabilities of the lactic acid bacteria (LAB) isolated from stressful niches is a major strategy to prepare functional cultures and bio-preservatives for food industries. In the present study, abundant LAB strains isolated from natural honey were screened based on their tolerance to continuous pH and bile salt treatments. Then, the pro-functional properties of the selected LAB were investigated. In accordance with the screening data, a bacilli isolate was selected for further characterization. Sequencing results led to the identification of Lactobacillus kunkeei as the selected LAB isolate. In vitro antibacterial and antifungal activities of the LAB and in situ antifungal activity of the isolate cell-free supernatant (CFS) were verified against food-borne indicators. Accordingly, in vitro antibacterial and antifungal effects of Lact. kunkeei ENH01 on respective Escherichia coli and Aspergillus niger were significantly (P < 0.05) higher than the other indicators. Furthermore, in situ inhibitory effect of Lact. kunkeei CFS on Candida albicans (as the highest in situ effect) was equal to 76.36%. The presence of three antibacterial peptides was also verified in the Lact. kunkeei CFS according to the results of liquid chromatography mass spectrometry (LC/MS) assay. Antibiotic susceptibility profile and auto-aggregation ability of the isolate were noticeable. Anti-mycotoxigenic capabilities of Lact. kunkeei ENH01 as viable and heat-killed cells were also revealed against total aflatoxins according to the HPLC-based analysis. In vivo safety of the isolate was also attested through the evaluation of blood biochemistry and hematological parameters in the Lact. kunkeei ENH01 fed-mice compared with the control. Based on the findings, probiotic properties of Lact. kunkeei ENH01 and postbiotic capabilities of the isolate CFS and its heat-killed cells were approved.", "token_count": 500, "char_count": 1942, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5487, "quality_score": 0.7744, "entities": { "genes": [ "ENH01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:35.868114", "source": { "split": "train_shard_00000", "doc_id": 2604 }, "chunk_id": "train_shard_00000_2604_0", "global_id": 2870 }, { "text": "Postbiotic and Anti-aflatoxigenic Capabilities of Lactobacillus kunkeei as the Potential Probiotic LAB Isolated from the Natural Honey.", "token_count": 41, "char_count": 135, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:36.225438", "source": { "split": "train_shard_00000", "doc_id": 2604 }, "chunk_id": "train_shard_00000_2604_1", "global_id": 2871 }, { "text": "Here, we have analysed and explored the genome sequences of three newly isolated bacteria that were recently characterised for their probiotic activities and ability to produce bacteriocins. These strains, isolated from faeces of animals living in captivity at the zoological garden of Lille (France), are Escherichia coli ICVB443, Enterococcus faecalis ICVB501 and Pediococcus pentosaceus ICVB491. Their genomes have been analysed and compared to those of their pathogenic or probiotic counterparts. The genome analyses of E. coli ICVB443 and Ent. faecalis ICVB501 displayed similarities to those of probiotics E. coli 1917 Nissle, and Ent. faecalis Symbioflor 1, respectively. Furthermore, E. coli ICVB443 shares at least 89 genes with the enteroaggregative E. coli 55989 (EAEC), and Ent. faecalis ICVB501 shares at least 315 genes with the pathogenic Ent. faecalis V583 strain. Unlike Ped. pentosaceus ICVB491, which is devoid of virulence genes, E. coli ICVB443 and Ent. faecalis ICVB501 both carry genes encoding virulence factors on their genomes. Of note, the bioinformatics analysis of these two genomes located the bsh gene, which codes for bile salt hydrolase (BSH). The presence of BSH is of major importance, as it can help to increase the viability of these two strains in the gastrointestinal tract (GIT). The genome analysis of Ped. pentosaceus ICVB491 confirmed its GRAS status (Generally Recognised As Safe), as no genomic virulence factor determinant was found.\n\nIn silico analyses of the genomes of three new bacteriocin-producing bacteria isolated from animal's faeces.", "token_count": 464, "char_count": 1589, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5798, "quality_score": 0.7899, "entities": { "genes": [ "ICVB491", "ICVB501", "ICVB443" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:36.870196", "source": { "split": "train_shard_00000", "doc_id": 2605 }, "chunk_id": "train_shard_00000_2605_0", "global_id": 2872 }, { "text": "Designing nanoparticles that are suitable for fortification of bioactive compounds in foods has always been a challenging task among colloidal scientists and nanotechnologists. To achieve this goal, there are several research objectives in general, including but not limited to: (1) preparation of nanoparticles from edible biomaterials without using organic solvents and toxic chemicals to ensure food-grade status; (2) improving colloidal stability of these nanoparticles under various harsh conditions including food processing (heating, high pressure, drying, etc.) and gastrointestinal environment (low pH, bile salt and digestive enzymes); (3) studying interactions between bioactive compounds and nanoparticles for optimal encapsulation; (4) understanding biological fate of these nanoparticles upon oral administration. Although a variety of nanoparticles may be fabricated from individual biomaterial, such as protein, polysaccharide and lipid, complex or hybrid nanoparticles made with two or more biomaterials have received increasing attention in recent 5-10 years due to many advantageous structural features and physicochemical properties. The major focus of my research group, i.e., the Nanotechnology and Biodelivery Laboratory at the University of Connecticut (CT, USA), is to apply materials science and engineering principles to understand physical and chemical interactions among various natural biomaterials at the nanoscale and design novel nanocarriers for delivery of various bioactive compounds in functional foods. In this Biointerface Perspective, I will first introduce the fundamental principles on the preparation of nanoparticles made from food colloids, and then I will share in detail the critical reflection on my research journey into the development of innovative colloidal binary and ternary nanocomplexes.\n\nFood colloids binary and ternary nanocomplexes: Innovations and discoveries.", "token_count": 417, "char_count": 1921, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:37.496889", "source": { "split": "train_shard_00000", "doc_id": 2606 }, "chunk_id": "train_shard_00000_2606_0", "global_id": 2873 }, { "text": "Bilirubin, the end product of heme catabolism, is produced continuously in the body and may reach toxic levels if accumulates in the serum and tissues; therefore, a highly efficient mechanism evolved for its disposition. Normally, unconjugated bilirubin enters hepatocytes through the uptake transporters organic anion transporting polypeptide (OATP) 1B1 and 1B3, undergoes glucuronidation by the Phase II enzyme UDP glucuronosyltransferase 1A1 (UGT1A1), and conjugated forms are excreted into the bile by the canalicular export pump multidrug resistance protein 2 (MRP2). Any remaining conjugated bilirubin is transported back to the blood by MRP3 and passed on for uptake and excretion by downstream hepatocytes or the kidney. The bile salt export pump BSEP as the main motor of bile flow is indirectly involved in bilirubin disposition. Genetic mutations and xenobiotics that interfere with this machinery may impede bilirubin disposition and cause hyperbilirubinemia. Several pharmaceutical compounds are known to cause hyperbilirubinemia via inhibition of OATP1Bs, UGT1A1, or BSEP. Herein we briefly review the in vitro prediction methods that serve to identify drugs with a potential to induce hyperbilirubinemia. In vitro assays can be deployed early in drug development and may help to minimize late-stage attrition. Based on current evidence, drugs that behave as mono- or multispecific inhibitors of OATP1B1, UGT1A1, and BSEP in vitro are at risk of causing clinically significant hyperbilirubinemia. By integrating inhibition data from in vitro assays, drug serum concentrations, and clinical reports of hyperbilirubinemia, predictor cut-off values have been established and are provisionally suggested in this review. Further validation of in vitro readouts to clinical outcomes is expected to enhance the predictive power of these assays.", "token_count": 495, "char_count": 1851, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6554, "quality_score": 0.8277, "entities": { "genes": [ "MRP2", "MRP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:38.149255", "source": { "split": "train_shard_00000", "doc_id": 2607 }, "chunk_id": "train_shard_00000_2607_0", "global_id": 2874 }, { "text": "Prediction of Drug-Induced Hyperbilirubinemia by In Vitro Testing.", "token_count": 22, "char_count": 66, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:38.503497", "source": { "split": "train_shard_00000", "doc_id": 2607 }, "chunk_id": "train_shard_00000_2607_1", "global_id": 2875 }, { "text": "Whole genome sequencing (WGS) is increasingly used for epidemiological investigations of pathogens. While SNP variant calling is currently considered as the most suitable method, the choice of a representative reference genome and the isolate dependency of results limit standardization and affect resolution in an unknown manner. Whole or core genome Multi Locus Sequence Typing (wg-, cg-MLST) represents an attractive alternative. Here, we assess the accuracy of wg- and cg-MLST by comparing results of four\n\nComparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumerics", "token_count": 140, "char_count": 583, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:38.935726", "source": { "split": "train_shard_00000", "doc_id": 2608 }, "chunk_id": "train_shard_00000_2608_0", "global_id": 2876 }, { "text": "The incidence of nonalcoholic steatohepatitis (NASH) is increasing worldwide, including in Asian countries. We reported that the hepatic expression of bile salt export pump (BSEP) was downregulated in patients with NASH, suggesting that BSEP is involved in the pathogenesis of NASH. To identify the underlying mechanism, we analyzed Bsep heterozygous knock-out (Bsep+/- mice) and wild-type (WT) C57BL/6J mice fed a high-fat diet (HFD) (32.0% animal fat) or normal diet. We examined histological changes, levels of hepatic lipids and hepatic bile acids, and expression of genes related to bile acid and cholesterol metabolism. HFD-fed Bsep+/- mice exhibited milder hepatic steatosis and less weight gain, compared to HFD-fed WT mice. The concentrations of total bile acid, triglycerides, and cholesterols were reduced in the liver of HFD-fed Bsep+/- mice. Regarding hepatic bile acid metabolism, the expression levels of Farnesoid X receptor (Fxr) and Multidrug resistance-associated protein 2 were significantly upregulated in HFD-fed Bsep+/- mice, compared to HFD-fed WT mice. Furthermore, several alterations were observed in upstream cholesterol metabolism in the liver. The expression levels of bile acid metabolism-related genes were also altered in the intestine of HFD-fed Bsep+/- mice. In conclusion, HFD-fed Bsep+/- mice exhibited significant alterations of the expression levels of genes related to bile acid and lipid metabolism in both the liver and ileum, resulting in alleviated steatosis and less weight gain. These results suggest the importance of BSEP for maintenance of bile acid and cholesterol metabolism. Further investigations of the involvement of BSEP in the pathogenesis of NASH will provide greater insight and facilitate the development of novel therapeutic modalities.", "token_count": 492, "char_count": 1797, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5346, "quality_score": 0.7673, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:39.581751", "source": { "split": "train_shard_00000", "doc_id": 2609 }, "chunk_id": "train_shard_00000_2609_0", "global_id": 2877 }, { "text": "Heterozygous knockout of Bile salt export pump ameliorates liver steatosis in mice fed a high-fat diet.", "token_count": 33, "char_count": 103, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:39.942206", "source": { "split": "train_shard_00000", "doc_id": 2609 }, "chunk_id": "train_shard_00000_2609_1", "global_id": 2878 }, { "text": "Lactobacilli commonly used as a probiotic and they can be isolated from various sources such as fermented foods and gastrointestinal tracts of humans and animals. The aims of this study were isolation and identification of lactobacilli from honey and investigation of some probiotic properties and antimicrobial effects against foodborne bacterial pathogens. A total of 88 honey samples were collected from different areas in Iran. About 1.00 g of each honey was cultured in de Man, Rogosa, and Sharpe (MRS) broth and then sub-cultured on MRS agar. The isolates were assessed for probiotic potentials such as tolerance to acid and bile. Then, antimicrobial activity of isolates against seven foodborne pathogens including\n\nSome probiotic properties of", "token_count": 191, "char_count": 751, "word_count": 114, "semantic_coherence": 1, "information_density": 0.6754, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:40.387601", "source": { "split": "train_shard_00000", "doc_id": 2610 }, "chunk_id": "train_shard_00000_2610_0", "global_id": 2879 }, { "text": "The dormant resistant spores of Clostridioides difficile are transformed into metabolically active cells through the process of germination. Spore germination in C. difficile is regulated by the detection of bile salt germinants and amino acid cogerminants by pseudoproteases CspC and CspA, respectively. The germinant signal is transduced to the serine protease CspB, which processes the cortex lytic enzyme SleC, leading to degradation of the spore cortex peptidoglycan and subsequent reactivation of the spore. Divergent C. difficile germination models have been proposed to explain interactions between key regulators and transduction of germinant and cogerminant signals. This review summarises advances in understanding C. difficile germination and outlines current models of germination regulation.\n\nA Revised Understanding of Clostridioides difficile Spore Germination.", "token_count": 221, "char_count": 877, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:40.891238", "source": { "split": "train_shard_00000", "doc_id": 2611 }, "chunk_id": "train_shard_00000_2611_0", "global_id": 2880 }, { "text": "Exo-inulinases are versatile enzymes that have gained attention in recent years due to their ability to hydrolyze linear and branched polyfructose chains found in inulines. Agavin, a branched inulin, is found in Agave plant, the raw matter to produce tequila. Our group has isolated several microbial strains from agave bagasse, an agro-industrial residue from tequila production that increases yearly. Strain ISO3, identified as Kluyveromyces marxianus, showed a remarkable activity towards agavin, and from its fermentation liquor an inulinolytic enzyme (Inu-ISO3) was purified. The isolated enzyme is a glycosylated dimeric protein with a molecular mass of ~256 kDa, as determined by DLS and SEC. The enzyme has an isoelectric pH of 4.6 and has both inulinase and invertase activities with an I/S ratio (ratio of activity with agavin to activity with sucrose) of 1.39. The enzyme has temperature and pH optima of 50 °C and 5.5, respectively, and follows hyperbolic kinetics with agavin (k\n\nPurification and characterization of an inulinase produced by a Kluyveromyces marxianus strain isolated from blue agave bagasse.", "token_count": 324, "char_count": 1121, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "ISO3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:41.484753", "source": { "split": "train_shard_00000", "doc_id": 2612 }, "chunk_id": "train_shard_00000_2612_0", "global_id": 2881 }, { "text": "Glycolysis and the pentose phosphate pathway (PPP) are two basic metabolic pathways that are simultaneously present in yeasts. As the main pathway in most species, the glycolysis provides ATP and NADH for cell metabolism while PPP, as a complementary pathway, supplies NADPH. In this study, the performance of Kluyveromyces marxianus using glycolysis or PPP were studied through the disruption of PGI1 or ZWF1 gene, respectively. K. marxianus using glycolysis as the only pathway showed higher ethanol production ability than that of the Kluyveromyces lactis zwf1Δ mutant; K. marxianus using only PPP showed more robustness than that of Saccharomyces cerevisiae pgi1Δ mutant. Additionally, K. marxianus pgi1Δ strain accumulated much more intracellular NADPH than the wild type strain and co-utilized glucose and xylose more effectively. These findings suggest that phosphoglucose isomerase participates in the regulation of the repression of glucose on xylose utilization in K. marxianus. The NADPH/NADP\n\nFunctional analysis of PGI1 and ZWF1 in thermotolerant yeast Kluyveromyces marxianus.", "token_count": 313, "char_count": 1090, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6115, "quality_score": 0.8057, "entities": { "genes": [ "PGI1", "ZWF1" ], "proteins": [], "pathways": [ "glycolysis", "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:42.087718", "source": { "split": "train_shard_00000", "doc_id": 2613 }, "chunk_id": "train_shard_00000_2613_0", "global_id": 2882 }, { "text": "Colibacillosis, a disease caused by avian pathogenic Escherichia coli (APEC), constitutes a substantial burden to the poultry industry worldwide. APEC has been extensively characterized throughout the world, however, less is known about the genetic background of APEC isolates from Pakistan. In this study, a total of 75 E. coli isolates from colibacillosis affected dead broiler birds in Pakistan were subjected to whole genome sequencing followed by in-silico characterization. These isolates were investigated for virulence and resistance genotypes, serotypes, multi-locus sequence types, plasmid replicon types and single nucleotide polymorphism-based core genome phylogeny. Among the APEC isolates investigated, 14 different sequence types were identified with ST117 (16 %), ST2847 (10.7 %) and ST48 (5.3 %) being the most prevalent. Of the 28 different serotypes identified in this study, O1, O2 and O78 serotypes accounted for 25.3 % of the APEC isolates. The most frequently identified virulence-associated genes (VAGs) were increased serum survival gene; iss (100 %), glutamate decarboxylase; gad (92 %) and the siderophore receptor; iroN (81.3 %). According to the previously established definition, 72 % of isolates fell within the highly pathogenic APEC category by possessing a combination of VAGs; iss, iroN, iutA, hlyF and ompT simultaneously. Of the 75 APEC isolates, 89.3 % contained the genes predicted to encode resistance against aminoglycosides, tetracyclines and sulfonamides. Notably, the acquired colistin resistance gene mcr-1 was found in 38.7 % of the APEC isolates. Our findings reveal a diverse genetic background and high virulence and resistance potentials for APEC isolates in Pakistan.", "token_count": 486, "char_count": 1718, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6466, "quality_score": 0.8233, "entities": { "genes": [ "ST48", "ST2847", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:42.738561", "source": { "split": "train_shard_00000", "doc_id": 2614 }, "chunk_id": "train_shard_00000_2614_0", "global_id": 2883 }, { "text": "Genomic landscape of multi-drug resistant avian pathogenic Escherichia coli recovered from broilers.", "token_count": 27, "char_count": 100, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:43.100855", "source": { "split": "train_shard_00000", "doc_id": 2614 }, "chunk_id": "train_shard_00000_2614_1", "global_id": 2884 }, { "text": "Pseudomonas aeruginosa is one of the most common pathogens related to healthcare-associated infections. The Brazilian isolate, named CCBH4851, is a multidrug-resistant clone belonging to the sequence type 277. The antimicrobial resistance mechanisms of the CCBH4851 strain are associated with the presence of the bla[Formula: see text] gene, encoding a metallo-beta-lactamase, in combination with other exogenously acquired genes. Whole-genome sequencing studies focusing on emerging pathogens are essential to identify key features of their physiology that may lead to the identification of new targets for therapy. Using both Illumina and PacBio sequencing data, we obtained a single contig representing the CCBH4851 genome with annotated features that were consistent with data reported for the species. However, comparative analysis with other Pseudomonas aeruginosa strains revealed genomic differences regarding virulence factors and regulatory proteins. In addition, we performed phenotypic assays that revealed CCBH4851 is impaired in bacterial motilities and biofilm formation. On the other hand, CCBH4851 genome contained acquired genomic islands that carry transcriptional factors, virulence and antimicrobial resistance-related genes. Presence of single nucleotide polymorphisms in the core genome, mainly those located in resistance-associated genes, suggests that these mutations may also influence the multidrug-resistant behavior of CCBH4851. Overall, characterization of Pseudomonas aeruginosa CCBH4851 complete genome revealed the presence of features that strongly relates to the virulence and antibiotic resistance profile of this important infectious agent.\n\nCharacterization of a SPM-1 metallo-beta-lactamase-producing Pseudomonas aeruginosa by comparative genomics and phenotypic analysis.", "token_count": 448, "char_count": 1812, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6137, "quality_score": 0.8069, "entities": { "genes": [ "CCBH4851" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:43.730922", "source": { "split": "train_shard_00000", "doc_id": 2615 }, "chunk_id": "train_shard_00000_2615_0", "global_id": 2885 }, { "text": "Animals produce bile to act as an antibacterial agent and to maximize the absorption of lipophilic nutrients in the gut. The physical properties of bile are largely dictated by amphipathic bile salt molecules, which also participate in signaling pathways by modulating physiological processes upon binding host receptors. Upon excretion of bile salts from the gall bladder into the intestine, the gut microbiota can create metabolites with modified signaling capabilities. The category and magnitude of bile salt metabolism can have positive or negative effects on the host. A key modification is bile salt hydrolysis, which is a prerequisite for all additional microbial transformations. We have synthesized five different fluorogenic bile salts for simple and continuous reporting of hydrolysis in both murine and human fecal samples. Our data demonstrate that most gut microbiomes have the highest capacity for hydrolysis of host-produced primary bile salts, but some microbially modified secondary bile salts also display significant turnover.\n\nSimple Analysis of Primary and Secondary Bile Salt Hydrolysis in Mouse and Human Gut Microbiome Samples by Using Fluorogenic Substrates.", "token_count": 277, "char_count": 1185, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:44.283261", "source": { "split": "train_shard_00000", "doc_id": 2616 }, "chunk_id": "train_shard_00000_2616_0", "global_id": 2886 }, { "text": "Cochlear implants (CIs) are widely used to provide auditory rehabilitation to individuals having severe to profound sensorineural hearing loss (SNHL). However, insertion of electrode leads to inner trauma and activation of inflammatory and apoptotic signaling cascades resulting in loss of residual hearing in implanted individuals. Pharmaceutical interventions that can target these signaling cascades hold great potential for preserving residual hearing by preventing sensory cell damage. Bile salts have shown efficacy in various regions of the body as powerful antioxidants and anti-inflammatory agents. However, their efficacy against inner ear trauma has never been explored. The objective of this study was to determine whether taurodeoxycholic acid (TDCA), a bile salt derivative, can prevent sensory cell damage employing an\n\nEvaluating the Efficacy of Taurodeoxycholic Acid in Providing Otoprotection Using an", "token_count": 214, "char_count": 919, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7323, "quality_score": 0.8661, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:44.746501", "source": { "split": "train_shard_00000", "doc_id": 2617 }, "chunk_id": "train_shard_00000_2617_0", "global_id": 2887 }, { "text": "Lactobacillus fermentum KU200060 was isolated from watery kimchi and its probiotic characteristics were evaluated, including tolerance to artificial gastric acid and bile salt, production of enzymes, ability to adhere to HT-29 cells, and antibiotic susceptibility. The antibacterial and antibiofilm effects of L. fermentum KU200060 against Streptococcus mutans KCTC 5316 were compared to those of Lactobacillus rhamnosus GG and Lactobacillus brevis KU15006. L. fermentum KU200060 demonstrated higher antibacterial activity and inhibition of biofilm formation by S. mutans than L. rhamnosus GG via inhibiting formation of water-insoluble glucan and related gene expression. In addition, L. fermentum KU200060 was applied as a probiotic in yogurt, and its physicochemical property and sensory value demonstrated its potential as a yogurt starter. The physicochemical characteristics and consumer acceptability of the probiotic yogurt containing L. fermentum KU200060 were not significantly different compared to those of the control yogurt. Therefore, L. fermentum KU200060 could be used for oral health in the probiotic industry.\n\nProbiotic Lactobacillus fermentum KU200060 isolated from watery kimchi and its application in probiotic yogurt for oral health.", "token_count": 374, "char_count": 1257, "word_count": 172, "semantic_coherence": 1, "information_density": 0.5465, "quality_score": 0.7733, "entities": { "genes": [ "KU200060", "KU15006" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:45.324286", "source": { "split": "train_shard_00000", "doc_id": 2618 }, "chunk_id": "train_shard_00000_2618_0", "global_id": 2888 }, { "text": "Probiotics have been reported to reduce total cholesterol levels in vitro, but more evidence is needed to determine the clinical relevance of this activity. Chinese traditional fermented pickles are a good source of lactic acid bacteria. Therefore, pickle samples were collected for screening lactic acid bacteria based on their ability to survive stresses encountered during gastrointestinal passage and cholesterol reducing potency.\n\nProbiotic characteristics of Lactobacillus plantarum E680 and its effect on Hypercholesterolemic mice.", "token_count": 124, "char_count": 538, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8767, "quality_score": 0.9384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:45.705861", "source": { "split": "train_shard_00000", "doc_id": 2619 }, "chunk_id": "train_shard_00000_2619_0", "global_id": 2889 }, { "text": "The germination of ingested spores is often a necessary first step required for enabling bacterial outgrowth and host colonization, as in the case of Clostridioides difficile (C. difficile) infection. Spore germination rate in the colon depends on microbiota composition and its level of disruption by antibiotic treatment since secretions by commensal bacteria modulate primary to secondary bile salt levels to control germination. Assessment of C. difficile spore germination typically requires measurement of colony-forming units, which is labor intensive and takes at least 24 h to perform but is regularly required due to the high recurrence rates of nosocomial antibiotic-associated diarrhea. We present a rapid method to assess spore germination by using high throughput single-cell impedance cytometry (>300 events/s) to quantify live bacterial cells, by gating for their characteristic electrophysiology versus spores, so that germination can be assessed after just 4 h of culture at a detection limit of ~100 live cells per 50 μL sample. To detect the phenotype of germinated C. difficile bacteria, we utilize its characteristically higher net conductivity versus that of spore aggregates and non-viable C. difficile forms, which causes a distinctive high-frequency (10 MHz) impedance phase dispersion within moderately conductive media (0.8 S/m). In this manner, we can detect significant differences in spore germination rates within just 4 h, with increasing primary bile salt levels in vitro and using ex vivo microbiota samples from an antibiotic-treated mouse model to assess susceptibility to C. difficile infection. We envision a rapid diagnostic tool for assessing host microbiota susceptibility to bacterial colonization after key antibiotic treatments.\n\nQuantifying bacterial spore germination by single-cell impedance cytometry for assessment of host microbiota susceptibility to Clostridioides difficile infection.", "token_count": 457, "char_count": 1937, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:46.343399", "source": { "split": "train_shard_00000", "doc_id": 2620 }, "chunk_id": "train_shard_00000_2620_0", "global_id": 2890 }, { "text": "Determination of a microbial strain for the joining into sustenance items requires both in vitro and in vivo assessment. A newly isolated bacteriocin-like inhibitory substance (BLIS) producing lactic acid bacterium, Lactococcus lactis Gh1, was isolated from a traditional flavour enhancer and evaluated in vitro for its potential applications in the food industry. Results from this study showed that L. lactis was tolerant to NaCl (≤ 4.0%, w/v), phenol (≤ 0.4%, w/v), 0.3% (w/v) bile salt, and pH 3. BLIS from L. lactis showed antimicrobial activity against Listeria monocytogenes ATCC 15313 and was susceptible to 10 types of antibiotics. The absence of haemolytic activity and the presence of acid phosphatase and naphthol-AS-BI-phosphohydrolase were observed in L. lactis. L. lactis could coagulate milk and showed a negative response to amylolytic and proteolytic activities and did not secrete β-galactosidase. The antimicrobial activity of BLIS was completely abolished at 121 °C. The BLIS was conserved at 4 °C in BHI and MRS medium up to 6-4 months, respectively. BLIS activity was more stable in BHI as compared to MRS after four freeze-thaw cycles and was not affected by a wide range of pH (pH 4-8). BLIS was sensitive to proteinase k and resistant to catalase and trypsin. The antimicrobial activity was slightly reduced by acetone, ethanol, methanol, and acetonitrile at 10% (v/v) and also towards Tween-80, urea, and NaCl 1% (v/v). Results from this study have demonstrated that L. lactis has a vast potential to be applied in the food industry, such as for the preparation of starter culture, functional foods, and probiotic products.", "token_count": 494, "char_count": 1650, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6077, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:46.990527", "source": { "split": "train_shard_00000", "doc_id": 2621 }, "chunk_id": "train_shard_00000_2621_0", "global_id": 2891 }, { "text": "In Vitro Evaluation of Potential Probiotic Strain Lactococcus lactis Gh1 and Its Bacteriocin-Like Inhibitory Substances for Potential Use in the Food Industry.", "token_count": 45, "char_count": 159, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:47.350020", "source": { "split": "train_shard_00000", "doc_id": 2621 }, "chunk_id": "train_shard_00000_2621_1", "global_id": 2892 }, { "text": "The animal model of hyperlipidemia in rats was established to investigate the lipid-lowering effect and mechanism of Danhong Injection on hyperlipidemic rats. SD rats were selected as the research object. The rats in normal group were fed with basic diet, and the rats in other groups were fed with high-fat diet to establish hyperlipidemia model. The successfully modeled rats were randomly divided into model group, Danhong Injection low, medium, high dose(1.0, 2.0, 4.0 mL·kg~(-1)) groups, and simvastatin(2.0 mg·kg~(-1)) group. Danhong Injection groups received intraperitoneal administration, and simvastatin group received intragastrical administration, once a day for 4 weeks. At the first, second, third, and fourth weekends after administration, blood was collected from the orbital vein to detect the levels of total cholesterol(TC), triglyceride(TG), low-density lipoprotein cholesterol(LDL-C), and high-density lipoprotein cholesterol(HDL-C), and then the atherosclerosis index(AI) was calculated. After 4 weeks of administration, the animals were sacrificed, and their heart, liver, spleen, lung, kidney and adipose tissue were extracted and weighed respectively to calculate the organ index of each group. The expressions of acyl-coaoxidase 1(Acox1), adenosine 5'-monophosphate(AMP)-activated protein kinase alpha(AMPK-α), bile salt export pump(BSEP), peroxisome proliferator-activated receptor gamma(PPAR-γ), catalase(CAT) and superoxide dismutase(SOD) mRNA in liver tissues were detected by fluorescence quantitative PCR; the content of cholesteryl ester transfer protein(CETP) and lecithin cholesterol acyltransferase(LCAT) in serum was detected by ELISA", "token_count": 486, "char_count": 1671, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:47.994350", "source": { "split": "train_shard_00000", "doc_id": 2622 }, "chunk_id": "train_shard_00000_2622_0", "global_id": 2893 }, { "text": "The results showed that as compared with the normal group, the levels of serum TC, TG and LDL-C in the model group were significantly increased, and the level of HDL-C was significantly decreased, indicating that the hyperlipidemia rat model was successfully constructed. As compared with the model group, Danhong Injection could decrease the contents of TC, TG, LDL-C and increase the content of HDL-C in hyperlipidemia rats; reduce the body weight of hyperlipidemia rats, and reduce the liver weight, liver index, fat weight and fat index; it had no significant effect on the main organ indexes such as heart, spleen, lung and kidney; but it could increase the expressions of Acox1, AMPK-α, BSEP, PPAR-γ, CAT and SOD mRNA in liver tissues of rats; it could also reduce the level of CETP and increase the level of LCAT in serum; and the regulatory effect of Danhong Injection groups all showed a dose-dependent effect. It can be concluded that Danhong Injection can regulate the blood lipid contents, reduce the blood lipid levels and alleviate the accumulation of body fat in rats with hyperlipidemia. The mechanism may be related to inhibiting lipid metabolism disorder and oxidative stress induced by high-fat diet feeding, and improving the imbalance of lipid transport system.\n\n[Lipid-lowering effect and mechanism of Danhong Injection on hyperlipidemia rats based on lipid metabolism disorder].", "token_count": 365, "char_count": 1401, "word_count": 222, "semantic_coherence": 1, "information_density": 0.518, "quality_score": 0.759, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:48.572586", "source": { "split": "train_shard_00000", "doc_id": 2622 }, "chunk_id": "train_shard_00000_2622_1", "global_id": 2894 }, { "text": "The diversity of maize (Zea mays) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today's highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report de novo genome sequences of four European flint lines assembled to pseudomolecules with scaffold N50 ranging from 6.1 to 10.4 Mb. Comparative analyses with two US Corn Belt lines explains the pronounced differences between both germplasms. While overall syntenic order and consolidated gene annotations reveal only moderate pangenomic differences, whole-genome alignments delineating the core and dispensable genome, and the analysis of heterochromatic knobs and orthologous long terminal repeat retrotransposons unveil the dynamics of the maize genome. The high-quality genome sequences of the flint pool complement the maize pangenome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.\n\nEuropean maize genomes highlight intraspecies variation in repeat and gene content.", "token_count": 265, "char_count": 1112, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6937, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:49.122061", "source": { "split": "train_shard_00000", "doc_id": 2623 }, "chunk_id": "train_shard_00000_2623_0", "global_id": 2895 }, { "text": "Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus-host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB). We have now surveyed the presence of pipolins in a collection of 2,238 human and animal pathogenic Escherichia coli strains and found that, although detected in only 25 positive isolates (1.1%), they are present in E. coli strains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belong to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring genomes from GenBank database spanning strains from diverse origin, further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons. In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulating E. coli and possibly also among other pathogenic bacteria.", "token_count": 495, "char_count": 2076, "word_count": 302, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8113, "entities": { "genes": [ "CC10", "CC32", "CC23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:49.767471", "source": { "split": "train_shard_00000", "doc_id": 2624 }, "chunk_id": "train_shard_00000_2624_0", "global_id": 2896 }, { "text": "High diversity and variability of pipolins among a wide range of pathogenic Escherichia coli strains.", "token_count": 27, "char_count": 101, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:50.121111", "source": { "split": "train_shard_00000", "doc_id": 2624 }, "chunk_id": "train_shard_00000_2624_1", "global_id": 2897 }, { "text": "Non-alcoholic fatty liver disease (NAFLD) has become the main cause of end-stage liver disease. Probiotics have the potential effect of alleviating NAFLD. The aim of this study was to explore functional probiotics and their underlying mechanisms. The bile salt hydrolase (BSH) activity in thirty-four strains was determined in vitro. Then, C57BL/6 mice were used to explore the effects of probiotics on NAFLD. Body weight and food intake were measured, and serum lipid concentrations, oxidative stress and proinflammatory cytokines levels were determined using commercial kits. The expressions of intestinal bile acid pathway genes were evaluated via real-time PCR. The results showed that Lactobacillus casei YRL577 and L. paracasei X11 had higher BSH activity. L. casei YRL577 significantly reduced liver weight and liver index and could regulate the levels of lipid metabolism, oxidative stress and proinflammatory cytokines as compared with L. paracasei X11. Furthermore, the results indicated that L. casei YRL577 up-regulated the mRNA levels of farnesoid X receptor and fibroblast growth factor 15, whereas down-regulated the mRNA level of apical Na-dependent bile acid transporter. These findings suggested that L. casei YRL577 modified genes in the intestinal bile acid pathway which might contribute to the alleviation of NAFLD.", "token_count": 361, "char_count": 1337, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [ "YRL577" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:50.697630", "source": { "split": "train_shard_00000", "doc_id": 2625 }, "chunk_id": "train_shard_00000_2625_0", "global_id": 2898 }, { "text": "Yeasts produce 2-phenylethanol (2-PE) from sugars via de novo synthesis; however, its synthesis is limited due to feedback inhibition on the isofunctional 3-deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthases (Aro3p and Aro4p). This work aimed to select Kluyveromyces marxianus mutant strains with improved capacity to produce 2-PE from sugars.\n\nObtainment, selection and characterization of a mutant strain of Kluyveromyces marxianus that displays improved production of 2-phenylethanol and enhanced DAHP synthase activity.", "token_count": 162, "char_count": 531, "word_count": 67, "semantic_coherence": 1, "information_density": 0.806, "quality_score": 0.903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:51.140307", "source": { "split": "train_shard_00000", "doc_id": 2626 }, "chunk_id": "train_shard_00000_2626_0", "global_id": 2899 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC2) is a severe hepatocellular cholestasis due to biallelic mutations in ABCB11 encoding the canalicular bile salt export pump (BSEP). Nonsense mutations are responsible for the most severe phenotypes. The aim was to assess the ability of drugs to induce readthrough of six nonsense mutations (p.Y354X, p.R415X, p.R470X, p.R1057X, p.R1090X, and p.E1302X) identified in patients with PFIC2.\n\nPharmacological Premature Termination Codon Readthrough of ABCB11 in Bile Salt Export Pump Deficiency: An In Vitro Study.", "token_count": 193, "char_count": 569, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7375, "quality_score": 0.8688, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:52.244526", "source": { "split": "train_shard_00000", "doc_id": 2627 }, "chunk_id": "train_shard_00000_2627_0", "global_id": 2900 }, { "text": "Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content resulting from horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here, we introduce Panaroo, a graph-based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. Panaroo is available at https://github.com/gtonkinhill/panaroo .\n\nProducing polished prokaryotic pangenomes with the Panaroo pipeline.", "token_count": 186, "char_count": 807, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:52.719095", "source": { "split": "train_shard_00000", "doc_id": 2628 }, "chunk_id": "train_shard_00000_2628_0", "global_id": 2901 }, { "text": "Colorectal cancer (CRC) is the third leading cause of cancer and second leading cause of cancer death in the United States. Recent evidence has linked a high fat and animal protein diet and microbial metabolism of host bile acids as environmental risk factors for CRC development. We hypothesize that the primary bile salt taurocholic acid (TCA) is a key, diet-controlled metabolite whose use by bacteria yields a carcinogen and tumor-promoter, respectively. The work is motivated by our published data indicating hydrogen sulfide (H\n\nEffects of taurocholic acid metabolism by gut bacteria: A controlled feeding trial in adult African American subjects at elevated risk for colorectal cancer.", "token_count": 162, "char_count": 692, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7358, "quality_score": 0.8679, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:53.182180", "source": { "split": "train_shard_00000", "doc_id": 2629 }, "chunk_id": "train_shard_00000_2629_0", "global_id": 2902 }, { "text": "A Hopeful Sea-Monster: A Very Large Homologous Recombination Event Impacting the Core Genome of the Marine Pathogen", "token_count": 29, "char_count": 115, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:53.562427", "source": { "split": "train_shard_00000", "doc_id": 2630 }, "chunk_id": "train_shard_00000_2630_0", "global_id": 2903 }, { "text": "The present study was conducted to find the potential of Lactococcus lactis strains naturally present in raw and fermented milk as probiotics and to evaluate their safety and some technological characteristics. There are numerous studies that evaluated probiotic properties of lactococci, nevertheless, limited studies on the probiotic potential of lactococci isolated from raw milk or dairy products were performed. Strains isolation from raw milk or dairy products and their characterization is important when selection of starter strains for the production of functional dairy foods is performed. Depending on aroma production and acidifying activity, 33 L. lactis strains were selected out of 169 and evaluated for safety, technological and probiotic properties. These strains were screened for antibiotic sensitivity, enzymatic activity, hemolytic and gelatinase activities. The strains were also assessed for resistance to bile salts and acid, growth in bile acids and cholesterol, cell surface hydrophobicity. Based on the obtained results, two strains with the best probiotic potential were selected. These two L. lactis strains, with 51% and 67% survival at low pH and more than 80% resistance to various bile salt concentrations, proved their resistance in vitro to gastric conditions. Also these strains proved to be good acidifiers (the pH of milk was reduced by at least 1 unit in 6 h at 30-37 °C) and can be used in the development of functional dairy foods as starter cultures.\n\nSafety Assessment and Preliminary In Vitro Evaluation of Probiotic Potential of Lactococcus lactis Strains Naturally Present in Raw and Fermented Milk.", "token_count": 398, "char_count": 1645, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5341, "quality_score": 0.7671, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:54.205574", "source": { "split": "train_shard_00000", "doc_id": 2631 }, "chunk_id": "train_shard_00000_2631_0", "global_id": 2904 }, { "text": "The yeast species Saccharomyces cerevisiae and Kluyveromyces marxianus are associated with fermentation of West African indigenous foods. The aim of this study was to characterize potential probiotic properties of S. cerevisiae and K. marxianus isolates from the West African milk products lait caillé and nunu and a cereal-based product mawè. The strains (14 in total) were identified by 26S rRNA gene sequencing and characterized for survival at gastrointestinal stress (bile salts and low pH) and adhesion to Caco-2 intestinal epithelial cells. Selected yeast isolates were tested for their effect on the transepithelial electrical resistance (TEER), using the intestinal epithelial cell line Caco-2 and for maintenance of intracellular pH (pH\n\nProbiotic potential of Saccharomyces cerevisiae and Kluyveromyces marxianus isolated from West African spontaneously fermented cereal and milk products.", "token_count": 244, "char_count": 900, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6772, "quality_score": 0.8386, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:54.702728", "source": { "split": "train_shard_00000", "doc_id": 2632 }, "chunk_id": "train_shard_00000_2632_0", "global_id": 2905 }, { "text": "Kluyveromyces marxianus CCT 7735 shows potential for producing ethanol from lactose; however, its low ethanol tolerance is a drawback for its industrial application. The first aim of this study was to obtain four ethanol-tolerant K. marxianus CCT 7735 strains (ETS1, ETS2, ETS3, and ETS4) by adaptive laboratory evolution. The second aim was to select among them the strain that stood out and to evaluate metabolic changes associated with the improved ethanol tolerance in this strain. The ETS4 was selected for displaying a specific growth rate higher than the parental strain under ethanol stress (122%) and specific ethanol production rate (0.26 g/g/h) higher than those presented by the ETS1 (0.22 g/g/h), ETS2 (0.17 g/g/h), and ETS3 (0.17 g/g/h) under non-stress condition. Further analyses were performed with the ETS4 in comparison with its parental strain in order to characterize metabolic changes. Accumulation of valine and metabolites of the citric acid cycle (isocitric acid, citric acid, and cis-aconitic acid) was observed only in the ETS4 subjected to ethanol stress. Their accumulation in this strain may have been important to increase ethanol tolerance. Furthermore, the contents of fatty acid methyl esters and ergosterol were higher in the ETS4 than in the parental strain. These differences likely contributed to enhance ethanol tolerance in the ETS4. KEY POINTS: • K. marxianus ethanol-tolerant strains were selected by adaptive laboratory evolution. • Valine and metabolites of the TCA cycle were accumulated in the ETS4. • High contents of fatty acids and ergosterol contributed to enhance ethanol tolerance.\n\nAssessment of ethanol tolerance of Kluyveromyces marxianus CCT 7735 selected by adaptive laboratory evolution.", "token_count": 487, "char_count": 1745, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5019, "quality_score": 0.751, "entities": { "genes": [ "ETS1", "ETS2", "ETS4", "ETS3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:55.345652", "source": { "split": "train_shard_00000", "doc_id": 2633 }, "chunk_id": "train_shard_00000_2633_0", "global_id": 2906 }, { "text": "Acute liver failure is a clinical emergency associated with high mortality. Accumulating evidence indicates that gut microbiota participates in the progression of liver injury, and preventive therapies based on altering gut microbiota are of great interest. Previous studies demonstrated that Lactobacillus salivarius LI01 attenuates hepatic injury, though efficiency in curtailed in the harsh environment in the gastrointestinal tract. In this study, a system to encapsulate LI01 in alginate-pectin (AP) microgels was investigated. Encapsulation significantly enhances probiotic viability for long-term storage and heat treatment, and in simulated gastrointestinal fluids (SGF or SIF) and bile salt solutions. Acute liver injury was induced in Sprague-Dawley (SD) rats by D-galactosamine (D-GaIN) injection following pretreatment with probiotics. Liver and gut barrier function, cytokines, liver and gut histology, bacterial translocation, and gut microbiota were assessed. Administration of encapsulated LI01 more effectively upregulates hepatic anti-inflammatory cytokine IL-10 and TLR-3, restores expressions of gut barrier biomarkers Claudin-1 and MUC2 and attenuates destruction of mucosal ultrastructure compared with unencapsulated probiotics pretreatment. Pretreatment with AP-LI01 microgels altered the microbial community, decreasing the abundance of pathogenic taxa Ruminiclostridium, Dorea and Ruminococcaceae_UCG-004 and enriching beneficial taxa Ruminococcaceae_UCG-014, Eubacterium, and Prevotella_1 that produce short-chain fatty acids. These results suggest that AP encapsulation of LI01 boosts viability and attenuates liver injury by reducing inflammation and restoring intestinal barrier function. These beneficial effects are probably due to alternation of gut flora. These findings provide new insight into encapsulation technology and prevention of liver failure", "token_count": 480, "char_count": 1886, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6611, "quality_score": 0.8305, "entities": { "genes": [ "MUC2", "LI01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:55.993154", "source": { "split": "train_shard_00000", "doc_id": 2634 }, "chunk_id": "train_shard_00000_2634_0", "global_id": 2907 }, { "text": "KEY POINTS: • Alginate-pectin encapsulation enhances the viability of Lactobacillus salivarius LI01 under simulated commercial conditions and simulated gastrointestinal environment. • AP-LI01 microgel attenuates hepatic and intestinal inflammation and restores gut barrier function. • AP-LI01 microgel alters gut microbial community with increased SCFAs producers and decreased pathogenic microbes. • Beneficial improvements after administration of probiotics are highly associated with alternation of gut microbial community.\n\nLactobacillus salivarius LI01 encapsulated in alginate-pectin microgels ameliorates D-galactosamine-induced acute liver injury in rats.", "token_count": 176, "char_count": 663, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [ "LI01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:56.428029", "source": { "split": "train_shard_00000", "doc_id": 2634 }, "chunk_id": "train_shard_00000_2634_1", "global_id": 2908 }, { "text": "Streptococcus suis (SS) is an emerging zoonotic pathogen that causes severe infections in swine and humans. Among the 33 known serotypes, serotype 2 is most frequently associated with infections in pigs and humans. To better understand the virulence characterization of S. suis serotype 2 (SS2) and discriminate the difference between virulent and avirulent strains in SS2, characterization of the genomic features of strains with different virulence is required. The result showed that Streptococcus suis have an open pan-genome. The pan-genome shared by the 19 S. suis serotype 2 strains was composed of 1,239 core genes and 2,436 accessory genes. COG analysis indicated that core genes are involved in the basic physiological function, but accessory genes related to tachytely evolution. Comparative analysis between core genomes of virulent strains and 9 avirulent strains suggested that srtBCD pilus cluster was a significant discrepancy between virulent and avirulent strains. Analysis between high virulent and group B low virulent strains showed 53 and 58 genes specific to each other. Moreover, genomes of avirulent strains tend to be larger than virulent strains; avirulent strains tend to possess more prophages sequences than virulent strains. Our findings could be contributed to a better understanding of the genomics of S. suis serotype 2.\n\nPan-genome analysis of Streptococcus suis serotype 2 revealed genomic diversity among strains of different virulence.", "token_count": 371, "char_count": 1473, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5297, "quality_score": 0.7648, "entities": { "genes": [ "SS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:57.005607", "source": { "split": "train_shard_00000", "doc_id": 2635 }, "chunk_id": "train_shard_00000_2635_0", "global_id": 2909 }, { "text": "Idiopathic or transient neonatal cholestasis (TNC) represents a group of cholestatic disorders with unidentified origin and remains a diagnosis of exclusion. Dysfunction of hepatobiliary transporters mediating excretion of biliary constituents from hepatocytes may play a central role in the pathogenesis of cholestasis. Despite variants of bile salt (BS) export pump (BSEP/ABCB11) have already been described in TNC, the pathogenic role of BSEP dysfunction in TNC remained so far elusive.\n\nHistological demonstration of BSEP/ABCB11 inhibition in transient neonatal cholestasis: a case report.", "token_count": 164, "char_count": 593, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:57.445572", "source": { "split": "train_shard_00000", "doc_id": 2636 }, "chunk_id": "train_shard_00000_2636_0", "global_id": 2910 }, { "text": "A Core Genome Multilocus Sequence Typing Scheme for Streptococcus mutans.", "token_count": 22, "char_count": 73, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:57.795131", "source": { "split": "train_shard_00000", "doc_id": 2637 }, "chunk_id": "train_shard_00000_2637_0", "global_id": 2911 }, { "text": "Streptococcus (S.) suis is a globally important swine pathogen, which comprises certain zoonotic serotypes. In this study, a detailed characterization of 88 porcine S. suis isolates was performed by analyzing capsular (cps) types, multilocus sequence typing (MLST) and investigation of the minimum core genome (MCG). In order to focus on the virulence potential of presumable invasive disease-associated S. suis isolates, virulence-associated gene profiles were assessed followed by screening a chosen subset of S. suis strains with a molecular pathotyping tool. Results showed a high genetic variability within this strain collection. In total, seventeen cps types were identified with a predominance of cps type 9 (15.9%) and 6 (14.8%). MLST revealed 48 sequence types (STs) including 41 novel ones. The population structure of S. suis was heterogenous and isolates belonged to eight different clonal complexes (CCs) including CC28 (9.1%), CC1109 (8%), CC13/149 (6.8%), CC1237 (5.7%), CC1 (3.4%), CC17 (3.4%), CC87 (2.3%), and CC1112 (1.1%), whereas a significant portion of isolates (60.2%) could not be assigned to any described CCs. Virulence-associated markers, namely extracellular protein factor (epf), muramidase-released protein (mrp), and suilysin (sly), showed a link with STs rather than with cps types. With this study an expanded knowledge about the population structure and the genetic diversity of S. suis could be achieved, which helps to contribute to an optimal public health surveillance system by promoting a focus on strains with an increased virulence and zoonotic potential.\n\nPopulation structure, genetic diversity and pathotypes of Streptococcus suis isolated during the last 13 years from diseased pigs in Switzerland.", "token_count": 488, "char_count": 1746, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [ "CC13", "CC17", "CC28", "CC1112", "CC1109", "CC1237", "CC1", "CC87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:58.435800", "source": { "split": "train_shard_00000", "doc_id": 2638 }, "chunk_id": "train_shard_00000_2638_0", "global_id": 2912 }, { "text": "Infectious and epidemic diseases induced by bacteria have historically caused great distress to people, and have even resulted in a large number of deaths worldwide. At present, many researchers are working on the discovery of viable drug and vaccine targets for bacteria through multiple methods, including the analyses of comparative subtractive genome, core genome, replication-related proteins, transcriptomics and riboswitches, which plays a significant part in the treatment of infectious and pandemic diseases. The 3D structures of the desired target proteins, drugs and epitopes can be predicted and modeled through target analysis. Meanwhile, molecular dynamics (MD) analysis of the constructed drug/epitope-protein complexes is an important standard for testing the suitability of these screened drugs and vaccines. Currently, target discovery, target analysis and MD analysis are integrated into a systematic set of drug and vaccine analysis strategy for bacteria. We hope that this comprehensive strategy will help in the design of high-performance vaccines and drugs.\n\nA systematic strategy for the investigation of vaccines and drugs targeting bacteria.", "token_count": 231, "char_count": 1167, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:58.906244", "source": { "split": "train_shard_00000", "doc_id": 2639 }, "chunk_id": "train_shard_00000_2639_0", "global_id": 2913 }, { "text": "Discovery of genetic variants underlying bacterial phenotypes and the prediction of phenotypes such as antibiotic resistance are fundamental tasks in bacterial genomics. Genome-wide association study (GWAS) methods have been applied to study these relations, but the plastic nature of bacterial genomes and the clonal structure of bacterial populations creates challenges. We introduce an alignment-free method which finds sets of loci associated with bacterial phenotypes, quantifies the total effect of genetics on the phenotype, and allows accurate phenotype prediction, all within a single computationally scalable joint modeling framework. Genetic variants covering the entire pangenome are compactly represented by extended DNA sequence words known as unitigs, and model fitting is achieved using elastic net penalization, an extension of standard multiple regression. Using an extensive set of state-of-the-art bacterial population genomic data sets, we demonstrate that our approach performs accurate phenotype prediction, comparable to popular machine learning methods, while retaining both interpretability and computational efficiency. Compared to those of previous approaches, which test each genotype-phenotype association separately for each variant and apply a significance threshold, the variants selected by our joint modeling approach overlap substantially.\n\nImproved Prediction of Bacterial Genotype-Phenotype Associations Using Interpretable Pangenome-Spanning Regressions.", "token_count": 295, "char_count": 1493, "word_count": 192, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:24:59.469193", "source": { "split": "train_shard_00000", "doc_id": 2640 }, "chunk_id": "train_shard_00000_2640_0", "global_id": 2914 }, { "text": "With the advent of whole-genome sequencing (WGS), comparative analysis has led to the use of core genome MLST (cgMLST) schemes for the high-resolution reproducible typing of bacterial isolates. In cgMLST, hundreds of loci are used for gene-by-gene comparisons of assembled genomes for studying the genetic diversity of clinically important pathogens. Combination of the cgMLST data and metadata of the isolates is useful for epidemiological investigations.Here we present a cgMLST scheme for the high-resolution typing of isolates from the whole Leptospira genus, enabling identification at the level of species, clades, clonal groups, and sequence types. We show several examples how the cgMLST Leptospira database, which is a publicly available web-based database, can be used for the analyses of WGS data of Leptospira isolates. This effort was undertaken in order to facilitate international collaborations and support the global surveillance of leptospirosis.\n\nCore Genome Multi-locus Sequence Typing Analyses of Leptospira spp. Using the Bacterial Isolate Genome Sequence Database.", "token_count": 267, "char_count": 1087, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6323, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:00.019090", "source": { "split": "train_shard_00000", "doc_id": 2641 }, "chunk_id": "train_shard_00000_2641_0", "global_id": 2915 }, { "text": "Telomerase is a ribonucleoprotein enzyme, which maintains genome integrity in eukaryotes and ensures continuous cellular proliferation. Telomerase holoenzyme from the thermotolerant yeast Hansenula polymorpha, in addition to the catalytic subunit (TERT) and telomerase RNA (TER), contains accessory proteins Est1 and Est3, which are essential for in vivo telomerase function. Here we report the high-resolution structure of Est3 from Hansenula polymorpha (HpEst3) in solution, as well as the characterization of its functional relationships with other components of telomerase. The overall structure of HpEst3 is similar to that of Est3 from Saccharomyces cerevisiae and human TPP1. We have shown that telomerase activity in H. polymorpha relies on both Est3 and Est1 proteins in a functionally symmetrical manner. The absence of either Est3 or Est1 prevents formation of a stable ribonucleoprotein complex, weakens binding of a second protein to TER, and decreases the amount of cellular TERT, presumably due to the destabilization of telomerase RNP. NMR probing has shown no direct in vitro interactions of free Est3 either with the N-terminal domain of TERT or with DNA or RNA fragments mimicking the probable telomerase environment. Our findings corroborate the idea that telomerase possesses the evolutionarily variable functionality within the conservative structural context.\n\nInsights into the structure and function of Est3 from the Hansenula polymorpha telomerase.", "token_count": 367, "char_count": 1474, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [ "TPP1" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:00.603330", "source": { "split": "train_shard_00000", "doc_id": 2642 }, "chunk_id": "train_shard_00000_2642_0", "global_id": 2916 }, { "text": "The gut microbiome is the resident microbial community of the gastrointestinal tract. This community is highly diverse, but how microbial diversity confers resistance or susceptibility to intestinal pathogens is poorly understood. Using transplantation of human microbiomes into several animal models of infection, we show that key microbiome species shape the chemical environment of the gut through the activity of the enzyme bile salt hydrolase. The activity of this enzyme reduced colonization by the major human diarrheal pathogen Vibrio cholerae by degrading the bile salt taurocholate that activates the expression of virulence genes. The absence of these functions and species permits increased infection loads on a personal microbiome-specific basis. These findings suggest new targets for individualized preventative strategies of V. cholerae infection through modulating the structure and function of the gut microbiome.\n\nInterpersonal Gut Microbiome Variation Drives Susceptibility and Resistance to Cholera Infection.", "token_count": 230, "char_count": 1030, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:01.079486", "source": { "split": "train_shard_00000", "doc_id": 2643 }, "chunk_id": "train_shard_00000_2643_0", "global_id": 2917 }, { "text": "Core Genome Multilocus Sequence Typing for Food Animal Source Attribution of Human", "token_count": 19, "char_count": 82, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:01.435180", "source": { "split": "train_shard_00000", "doc_id": 2644 }, "chunk_id": "train_shard_00000_2644_0", "global_id": 2918 }, { "text": "Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from\n\nSource Tracking Based on Core Genome SNV and CRISPR Typing of", "token_count": 95, "char_count": 378, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8214, "quality_score": 0.9107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:01.815535", "source": { "split": "train_shard_00000", "doc_id": 2645 }, "chunk_id": "train_shard_00000_2645_0", "global_id": 2919 }, { "text": "S. Pullorum and S. Enteritidis are closely related in genetic terms, but they show very different pathogenicity and host range. S. Enteritidis infects many different hosts, usually causing acute gastroenteritis, while S. Pullorum is restricted to avian, where it causes systemic disease in young animals. The reason why they differ in host range and pathogenicity is unknown. The core-genome denotes those genes that are present in all strains within a clade, and in the present work, an automated bioinformatics workflow was developed and applied to identify core-genome differences between these two serovars with the aim to identify genome features associated with host specificity of S. Pullorum. Results showed that S. Pullorum unique coding sequences (CDS) were mainly concentrated in three regions not present in S. Enteritidis, suggesting that such CDS were taken up probably during the separation of the two types from their common ancestor. One of the unique regions encoded Pathogenicity Islands 19 (SPI-19), which encodes a type VI secretion system (T6SS). Single-nucleotide polymorphism (SNP) analysis identified 1791 conserved SNPs in coding sequences between the two serovars, including several SNPs located in a type IV secretion system (T4SS). Analyzing of 100 bp regions upstream of coding sequences identified 443 conserved SNPs between the two serovars, including SNP variations in type III secretion system effector (T3SE). In conclusion, this analysis has identified genetic features encoding putative factors controlling host-specificity in S. Pullorum. The novel bioinformatic workflow and associated scripts can directly be applied to other bacteria to uncover the genome difference between clades.\n\nA bioinformatic approach to identify core genome difference between Salmonella Pullorum and Salmonella Enteritidis.", "token_count": 426, "char_count": 1840, "word_count": 267, "semantic_coherence": 1, "information_density": 0.603, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:02.451879", "source": { "split": "train_shard_00000", "doc_id": 2646 }, "chunk_id": "train_shard_00000_2646_0", "global_id": 2920 }, { "text": "To recognize diverse threats, plants monitor extracellular molecular patterns and transduce intracellular immune signaling through receptor complexes at the plasma membrane. Pattern recognition occurs through a prototypical network of interacting proteins, comprising A) receptors that recognize inputs associated with a growing number of pest and pathogen classes (bacteria, fungi, oomycetes, caterpillars), B) co-receptor kinases that participate in binding and signaling, and C) cytoplasmic kinases that mediate first stages of immune output. While this framework has been elucidated in reference accessions of model organisms, network components are part of gene families with widespread variation, potentially tuning immunocompetence for specific contexts. Most dramatically, variation in receptor repertoires determines the range of ligands acting as immunogenic inputs for a given plant. Diversification of receptor kinase (RK) and related receptor-like protein (RLP) repertoires may tune responses even within a species. Comparative genomics at pangenome scale will reveal patterns and features of immune network variation.\n\nThe evolving landscape of cell surface pattern recognition across plant immune networks.", "token_count": 267, "char_count": 1221, "word_count": 162, "semantic_coherence": 1, "information_density": 0.7531, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:02.997210", "source": { "split": "train_shard_00000", "doc_id": 2647 }, "chunk_id": "train_shard_00000_2647_0", "global_id": 2921 }, { "text": "In May 2019, the New York City Department of Health and Mental Hygiene (NYCDOHMH) detected an unusual cluster of five salmonellosis patients via automated spatiotemporal analysis of notifiable diseases using free SaTScan software (1). Within 1 day of cluster detection, graduate student interviewers determined that three of the patients had eaten prepared food from the same grocery store (establishment A) located inside the cluster area. NYCDOHMH initiated an investigation to identify additional cases, establish the cause, and provide control recommendations. Overall, 15 New York City (NYC) residents with laboratory-diagnosed salmonellosis who reported eating food from establishment A were identified. The most commonly consumed food item was chicken, reported by 10 patients. All 11 clinical isolates available were serotyped as Salmonella Blockley, sequenced, and analyzed by core genome multilocus sequence typing; isolates had a median difference of zero alleles. Environmental assessments revealed food not held at the proper temperature, food not cooled properly, and potential cross-contamination during chicken preparation. Elevated fecal coliform counts were found in two of four ready-to-eat food samples collected from establishment A, and Bacillus cereus was detected in three. The outbreak strain of Salmonella was isolated from one patient's leftover chicken. Establishing automated spatiotemporal cluster detection analyses for salmonellosis and other reportable diseases could aid in the detection of geographically focused, community-acquired outbreaks even before laboratory subtyping results become available.\n\nSalmonellosis Outbreak Detected by Automated Spatiotemporal Analysis - New York City, May-June 2019.", "token_count": 390, "char_count": 1738, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7119, "quality_score": 0.8559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:03.615245", "source": { "split": "train_shard_00000", "doc_id": 2648 }, "chunk_id": "train_shard_00000_2648_0", "global_id": 2922 }, { "text": "Paenibacillus polymyxa is a well-known Gram-positive biocontrol bacterium. It has been reported that many P. polymyxa strains can inhibit bacteria, fungi and other plant pathogens. Paenibacillus polymyxa employs a variety of mechanisms to promote plant growth, so it is necessary to understand the biocontrol ability of bacteria at the genome level. In the present study, thanks to the widespread availability of Paenibacillus genome data and the development of bioinformatics tools, we were able to analyze and mine the genomes of 43 P. polymyxa strains. The strain NCTC4744 was determined not to be P. polymyxa according to digital DNA-DNA hybridization and average nucleotide identity. By analysis of the pan-genome and the core genome, we found that the pan-genome of P. polymyxa was open and that there were 3,192 core genes. In a gene cluster analysis of secondary metabolites, 797 secondary metabolite gene clusters were found, of which 343 are not similar to known clusters and are expected to reveal a large number of new secondary metabolites. We also analyzed the plant growth-promoting genes that were mined and found, surpisingly, that these genes are highly conserved. The results of the present study not only reveal a large number of unknown potential secondary metabolite gene clusters in P. polymyxa, but also suggest that plant growth promotion characteristics are evolutionary adaptations of P. polymyxa to plant-related habitats.\n\nComparative genome analysis and mining of secondary metabolites of Paenibacillus polymyxa.", "token_count": 392, "char_count": 1542, "word_count": 234, "semantic_coherence": 1, "information_density": 0.547, "quality_score": 0.7735, "entities": { "genes": [ "NCTC4744" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:04.234877", "source": { "split": "train_shard_00000", "doc_id": 2649 }, "chunk_id": "train_shard_00000_2649_0", "global_id": 2923 }, { "text": "The diversity of the human microbiome is positively associated with human health. However, this diversity is endangered by Westernized dietary patterns that are characterized by a decreased nutrient variety. Diversity might potentially be improved by promoting dietary patterns rich in microbial strains. Various collections of bacterial cultures resulting from a century of dairy research are readily available worldwide, and could be exploited to contribute towards this end. We have conducted a functional in silico analysis of the metagenome of 24 strains, each representing one of the species in a bacterial culture collection composed of 626 sequenced strains, and compared the pathways potentially covered by this metagenome to the intestinal metagenome of four healthy, although overweight, humans. Remarkably, the pan-genome of the 24 strains covers 89% of the human gut microbiome's annotated enzymatic reactions. Furthermore, the dairy microbial collection covers biological pathways, such as methylglyoxal degradation, sulfate reduction, g-aminobutyric (GABA) acid degradation and salicylate degradation, which are differently covered among the four subjects and are involved in a range of cardiometabolic, intestinal, and neurological disorders. We conclude that microbial culture collections derived from dairy research have the genomic potential to complement and restore functional redundancy in human microbiomes.\n\nIn Silico Comparison Shows that the Pan-Genome of a Dairy-Related Bacterial Culture Collection Covers Most Reactions Annotated to Human Microbiomes.", "token_count": 361, "char_count": 1580, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:04.874275", "source": { "split": "train_shard_00000", "doc_id": 2650 }, "chunk_id": "train_shard_00000_2650_0", "global_id": 2924 }, { "text": "Galacto-oligosaccharides (GOS) are prebiotic compounds, widely used as ingredients in various food, nutraceutical and pharmaceutical products. Enzymatic synthesis of GOS results in low-purity products that contain high amounts of glucose and lactose beside the valuable GOS. In this study, a systematic approach was used to develop yeast-based fermentation strategies to purify crude GOS. Potentially applicable yeast strains were identified based on an extensive search in literature databases followed by a series of laboratory-scale fermentation tests. Single- and two-step fermentation processes were designed for the removal of glucose alone or together with lactose from crude GOS syrup. Single-step fermentation trials with two strains of previously unreported species, Cyberlindnera jadinii NCAIM Y.00499 and Kluyveromyces nonfermentans NCAIM Y.01443, resulted in purified products free of both glucose and ethanol from a crude GOS syrup diluted to 15 and 10 w/v%, respectively. Simultaneous removal of glucose and lactose was achieved by Kluyveromyces marxianus DMB Km-RK in a single-step fermentation process with a yield of 97.5% and final purity of 100%. A two-step fermentation approach was designed to allow conversion of a glucose-free product into a high-purity GOS by removing glucose with C. jadinii Y.00499 in the first step, and lactose by Kluyveromyces lactis DMB Kl-RK in the second step, resulting in a final product with a yield of 100% and a final purity of 92.1%. These results indicate that the selected nonconventional yeasts are promising candidates for the removal of non-GOS components from commercial crude GOS products by selective fermentation.\n\nProduction of high-purity galacto-oligosaccharides by depleting glucose and lactose from galacto-oligosaccharide syrup with yeasts.", "token_count": 508, "char_count": 1811, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5521, "quality_score": 0.7761, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:05.994331", "source": { "split": "train_shard_00000", "doc_id": 2651 }, "chunk_id": "train_shard_00000_2651_0", "global_id": 2925 }, { "text": "Untreated progressive familial intrahepatic cholestasis (PFIC) type 2, or bile salt exporter protein deficiency, frequently leads to severe pruritus, impaired growth and progressive liver fibrosis with risk of organ failure. We describe a 15-month-old male patient with severe pruritus diagnosed with PFIC type 2 enrolled in an open-label phase 2 study who received 4 weeks of treatment with odevixibat, an ileal bile acid transporter inhibitor under development for cholestatic liver disease treatment. The patient experienced reductions in serum bile acids and improvement in itching and sleep scores, and odevixibat was well tolerated. After the odevixibat study, symptoms returned and the patient underwent partial external biliary diversion (PEBD). Odevixibat treatment and PEBD produced similar normalisation of serum bile acid levels and improvements in pruritus and sleep disruptions. Thus, odevixibat appeared to be as effective as invasive PEBD in treating serum bile acids and cholestatic pruritus in this patient.\n\nOdevixibat and partial external biliary diversion showed equal improvement of cholestasis in a patient with progressive familial intrahepatic cholestasis.", "token_count": 299, "char_count": 1181, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6205, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:06.596595", "source": { "split": "train_shard_00000", "doc_id": 2652 }, "chunk_id": "train_shard_00000_2652_0", "global_id": 2926 }, { "text": "Lactobacillus gasseri JM1, a novel strain isolated from infant feces, exhibited common probiotic properties such as high acid tolerance, bile salt tolerance, and adhesion to epithelial Caco-2 cells, suggesting its ability to survive in the gastrointestinal tract and confer potential probiotic action on the host. In the current study, we aimed to evaluate the immunomodulatory activity of L. gasseri JM1 and explore the underlying signaling pathways in vitro. The results showed that pretreatment with L. gasseri JM1 alleviated lipopolysaccharide-induced inflammatory response, as evidenced by downregulation of genes encoding proinflammatory cytokines [IL1B, IL6, IL8, and tumor necrosis factor-α (TNFA)] and upregulation of genes encoding anti-inflammatory cytokines [IL4, IL10, transforming growth factor-β3 (TGFB3), and IFNG]. A high level of gene expression was noted for toll-like receptor 2 and NOD-like receptor 2. Meanwhile, transcriptomic sequencing obtained 84 differentially expressed genes. Kyoto Encyclopedia of Genes and Genomes analysis revealed the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (Akt) signaling pathway was activated by L. gasseri JM1 in Caco-2 cells. Inhibitor of PI3K/Akt played various roles in the release of cytokines, indicating that the pathway was involved in protecting the host against lipopolysaccharide stress. Moreover, whole-genome sequencing revealed fundamental genetic properties of L. gasseri JM1 and provided clues for probiotic characteristics. In summary, the strain could exert immunomodulatory effects via the toll-like receptor 2 and NOD2-mediated PI3K/Akt signaling pathway and be regarded as a potential probiotic.", "token_count": 468, "char_count": 1682, "word_count": 229, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "IL10", "IL6", "NOD2", "PI3K", "IL4", "IL1B", "TGFB3", "JM1", "IL8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:07.249774", "source": { "split": "train_shard_00000", "doc_id": 2653 }, "chunk_id": "train_shard_00000_2653_0", "global_id": 2927 }, { "text": "Lactobacillus gasseri JM1 with potential probiotic characteristics alleviates inflammatory response by activating the PI3K/Akt signaling pathway in vitro.", "token_count": 45, "char_count": 154, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "PI3K", "JM1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:07.606726", "source": { "split": "train_shard_00000", "doc_id": 2653 }, "chunk_id": "train_shard_00000_2653_1", "global_id": 2928 }, { "text": "Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.\n\nComparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani.", "token_count": 159, "char_count": 715, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7426, "quality_score": 0.8713, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:08.066652", "source": { "split": "train_shard_00000", "doc_id": 2654 }, "chunk_id": "train_shard_00000_2654_0", "global_id": 2929 }, { "text": "The current study used acid hydrolysis of lignocellulosic materials to obtain fermentable sugar for bioethanol production. However, toxic compounds that inhibit fermentation are also produced during the process, which reduces the bioethanol productivity. In this study, atmospheric cold plasma (ACP) was adopted to degrade the toxic compounds within sulfuric acid-hydrolyzed sugarcane bagasse. After ACP treatment, significant decreases in toxic compounds (31% of the formic acid, 45% of the acetic acid, 80% of the hydroxymethylfurfural, and 100% of the furfural) were observed. The toxicity of the hydrolysate was low enough for bioethanol production using Kluyveromyces marxianus. After adopting optimal ACP conditions (200 W power for 25 min), the bioethanol productivity improved from 0.25 to 0.65 g/L/h, which means that ACP could effectively degrade toxic compounds within the hydrolysate, thereby enhancing bioethanol production. Various nitrogen substitute was coordinated with detoxified hydrolysate, and chicken meal group presented the highest bioethanol productivity (0.45 g/L/h).\n\nEnhanced bioethanol production using atmospheric cold plasma-assisted detoxification of sugarcane bagasse hydrolysate.", "token_count": 335, "char_count": 1213, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:08.637755", "source": { "split": "train_shard_00000", "doc_id": 2655 }, "chunk_id": "train_shard_00000_2655_0", "global_id": 2930 }, { "text": "The oral administration of solid dosage forms is the commonest method to achieve systemic therapy and relies on the drug's solubility in human intestinal fluid (HIF), a key factor that influences bioavailability and biopharmaceutical classification. However, HIF is difficult to obtain and is known to be variable, which has led to the development of a range of simulated intestinal fluid (SIF) systems to determine drug solubility in vitro. In this study we have applied a novel multidimensional approach to analyse and characterise HIF composition using a published data set in both fasted and fed states with a view to refining the existing SIF approaches. The data set provided 152 and 172 measurements of five variables (total bile salt, phospholipid, total free fatty acid, cholesterol and pH) in time-dependent HIF samples from 20 volunteers in the fasted and fed state, respectively. The variable data sets for both fasted state and fed state are complex, do not follow normal distributions but the amphiphilic variable concentrations are correlated. When plotted 2-dimensionally a generally ellipsoid shaped data cloud with a positive slope is revealed with boundaries that enclose published fasted or fed HIF compositions. The data cloud also encloses the majority of fasted state and fed state SIF recipes and illustrates that the structured nature of design of experiment (DoE) approaches does not optimally cover the variable space and may examine media compositions that are not biorelevant. A principal component analysis in either fasted or fed state in combination with fitting an ellipsoid shape to enclose the data results in 8 points that capture over 95% of the compositional variability of HIF. The variable's average rate of concentration change in both fasted state and fed state over a short time scale (10 min) is zero and a Euclidean analysis highlights differences between the fasted and fed states and among individual volunteers. The results indicate that a 9-point DoE (8 + 1 central point) could be applied to investigate drug solubility in vitro and provide statistical solubility limits. In addition, a single point could provide a worst-case solubility measurement to define the lowest biopharmaceutical classification boundary or for use during drug development", "token_count": 513, "char_count": 2297, "word_count": 357, "semantic_coherence": 1, "information_density": 0.5798, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:25:09.297942", "source": { "split": "train_shard_00000", "doc_id": 2656 }, "chunk_id": "train_shard_00000_2656_0", "global_id": 2931 }, { "text": "This study has provided a novel description of HIF composition. The approach could be expanded in multiple ways by incorporation of further data sets to improve the statistical coverage or to cover specific patient groups (e.g., paediatric). Further development might also be possible to analyse information on the time dependent behaviour of HIF and to guide HIF sampling and analysis protocols.\n\nMultidimensional analysis of human intestinal fluid composition.", "token_count": 92, "char_count": 462, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7794, "quality_score": 0.8897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:09.673900", "source": { "split": "train_shard_00000", "doc_id": 2656 }, "chunk_id": "train_shard_00000_2656_1", "global_id": 2932 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) are a leading cause of foodborne outbreaks of human disease, but they reside harmlessly as an asymptomatic commensal in the ruminant gut. STEC serogroup O145 are difficult to isolate as routine diagnostic methods are unable to distinguish non-O157 serogroups due to their heterogeneous metabolic characteristics, resulting in under-reporting which is likely to conceal their true prevalence. In light of these deficiencies, the purpose of this study was a twofold approach to investigate enhanced STEC O145 diagnostic culture-based methods: firstly, to use a genomic epidemiology approach to understand the genetic diversity and population structure of serogroup O145 at both a local (New Zealand) (n = 47) and global scale (n = 75) and, secondly, to identify metabolic characteristics that will help the development of a differential media for this serogroup. Analysis of a subset of E. coli serogroup O145 strains demonstrated considerable diversity in carbon utilisation, which varied in association with eae subtype and sequence type. Several carbon substrates, such as D-serine and D-malic acid, were utilised by the majority of serogroup O145 strains, which, when coupled with current molecular and culture-based methods, could aid in the identification of presumptive E. coli serogroup O145 isolates. These carbon substrates warrant subsequent testing with additional serogroup O145 strains and non-O145 strains. Serogroup O145 strains displayed extensive genetic heterogeneity that was correlated with sequence type and eae subtype, suggesting these genetic markers are good indicators for distinct E. coli phylogenetic lineages. Pangenome analysis identified a core of 3,036 genes and an open pangenome of >14,000 genes, which is consistent with the identification of distinct phylogenetic lineages. Overall, this study highlighted the phenotypic and genotypic heterogeneity within E. coli serogroup O145, suggesting that the development of a differential media targeting this serogroup will be challenging.", "token_count": 508, "char_count": 2062, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5864, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:10.311728", "source": { "split": "train_shard_00000", "doc_id": 2657 }, "chunk_id": "train_shard_00000_2657_0", "global_id": 2933 }, { "text": "Genomic epidemiology and carbon metabolism of Escherichia coli serogroup O145 reflect contrasting phylogenies.", "token_count": 34, "char_count": 110, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:10.671355", "source": { "split": "train_shard_00000", "doc_id": 2657 }, "chunk_id": "train_shard_00000_2657_1", "global_id": 2934 }, { "text": "Drug-induced liver injury (DILI) continues to be a major cause of drug attrition and restrictive labeling. Given the importance of farnesoid X receptor (FXR) in bile acid homeostasis, drug-related FXR antagonism may be an important mechanism of DILI. However, a comprehensive assessment of this phenomenon broadly in the context of DILI is lacking. As such, we used an orthogonal approach comprising a FXR target gene assay in primary human hepatocytes and a commercially available FXR reporter assay to investigate the potential FXR antagonistic effects of an extensive test set of 159 compounds with and without association with clinical DILI. Data were omitted from analysis based on the presence of cytotoxicity to minimize false positive assay signals and other complications in data interpretation. Based on the experimental approaches employed and corresponding data, the prevalence of FXR antagonism was relatively low across this broad DILI test set, with 16-24% prevalence based on individual assay results or combined signals in both assays. Moreover, FXR antagonism was not highly predictive for identifying clinically relevant hepatotoxicants retrospectively, where FXR antagonist classification alone had minimal to moderate predictive value as represented by positive and negative likelihood ratios of 2.24-3.84 and 0.72-0.85, respectively. The predictivity did not increase significantly when considering only compounds with high clinical exposure (maximal or efficacious plasma exposures > 1.0 μM). In contrast, modest gains in predictive value of FXR antagonism were observed considering compounds that also inhibit bile salt export pump. In addition, we have identified novel FXR antagonistic effects of well-studied hepatotoxic drugs, including bosentan, tolcapone and ritonavir. In conclusion, this work represents a comprehensive evaluation of FXR antagonism in the context of DILI, including its overall predictivity and challenges associated with detecting this phenomenon in vitro.\n\nIn vitro assessment of farnesoid X receptor antagonism to predict drug-induced liver injury risk.", "token_count": 496, "char_count": 2105, "word_count": 300, "semantic_coherence": 1, "information_density": 0.62, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:11.326704", "source": { "split": "train_shard_00000", "doc_id": 2658 }, "chunk_id": "train_shard_00000_2658_0", "global_id": 2935 }, { "text": "A growing body of evidence has demonstrated that extraintestinal pathogenic E. coli (ExPEC), such as the urinary pathogenic E. coli (UPEC), are common constituents of treated wastewater, and therefore represent a potential public health risk. However, no single virulence gene, or set of virulence genes, can be used to conclusively identify this genetically diverse pathotype. As such we sought to identify and characterize the public health relevance of potential UPEC found in treated sewage/wastewater using a comparative genomics approach. Presumptive wastewater UPEC (W-UPEC) were initially identified by virulence gene screening against 5 virulence genes, and for which isolates containing ≥3 virulence genes were whole genome sequenced (n = 24). Single nucleotide polymorphic (SNP) spanning tree analysis demonstrated that many of these wastewater UPEC (WUPEC) were virtually identical at the core genome (0.4 Mbp) when compared to clinical UPEC (C-UPEC) sequences obtained from NCBI, varying by as little as 1 SNP. Remarkably, at the whole genome level, W-UPEC isolates displayed >96% whole genome similarity to C-UPEC counterparts in NCBI, with one strain demonstrating 99.5% genome similarity to a particular C-UPEC strain. The W-UPEC populations were represented by sequence types (ST) known to be clinically important, including ST131, ST95, ST127 and ST640. Many of the W-UPEC carried the exact same complement of virulence genes as their most closely related C-UPEC strains. For example, O25b-ST131 W-UPEC strains possessed the same 80 virulence genes as their most closely related C-UPEC counterparts. Concerningly, W-UPEC strains also carried a plethora of antibiotic resistance genes, and O25b-ST131strains were designated as extended spectrum beta-lactamase (ESBL) producing E. coli by both genome profiling and phenotypic resistance testing", "token_count": 516, "char_count": 1860, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6306, "quality_score": 0.8153, "entities": { "genes": [ "ST95", "ST131", "ST127", "ST640" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:25:11.982766", "source": { "split": "train_shard_00000", "doc_id": 2659 }, "chunk_id": "train_shard_00000_2659_0", "global_id": 2936 }, { "text": "W-UPEC ST131 strains were found in the effluents of a single treatment plant at different times, as well as different wastewater treatment plants, suggesting a differentially ability to survive wastewater treatment. Indeed, in sewage samples treated with chlorine doses sufficient for inducing a ∼99.99% reduction in total E. coli levels, UPEC represented a significant proportion of the chlorine-resistant population. By contrast, no Shiga toxin-producing E. coli were observed in these chlorinated sewage libraries. Our results suggest that clinically-relevant UPEC exist in treated wastewater effluents and that they appear to be specifically adapted to survive wastewater treatment processes.\n\nCharacterization of water treatment-resistant and multidrug-resistant urinary pathogenic Escherichia coli in treated wastewater.", "token_count": 197, "char_count": 826, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:12.431524", "source": { "split": "train_shard_00000", "doc_id": 2659 }, "chunk_id": "train_shard_00000_2659_1", "global_id": 2937 }, { "text": "Simulated human intestinal media, have proved to be a useful biopharmaceutics tool as a dissolution media for predicting in vivo dissolution and pharmacokinetic profile in humans. During drug product development preclinical animal models are also required to assess drug product performance, and there is a need to develop species specific intestinal media to similarly predict in vivo pharmacokinetic profiles in each preclinical model. Pigs, are increasingly being used in preclinical drug development, however to date there is a lack of quantitative information about the composition of porcine gastrointestinal (GI) fluids. As a result, a porcine biorelevant medium has not yet been developed, which is essential to improve interpretation and forecast of preclinical results using biorelevant in vitro dissolution studies. GI fluid samples, were collected from landrace pigs, and characterized. Fasted State Simulated Intestinal Fluid of pigs (FaSSIFp) was developed based on the physiological composition of the GI fluids in terms of pH, buffer capacity, osmolality, surface tension, as well as the bile salt, phospholipid and free fatty acid content. This study demonstrated that FaSSIFp was superior at predicting the solubility of the six model drugs in porcine intestinal fluids (PIF). A markedly high correlation (r\n\nDevelopment and evaluation of a biorelevant medium simulating porcine gastrointestinal fluids.", "token_count": 340, "char_count": 1421, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:12.998897", "source": { "split": "train_shard_00000", "doc_id": 2660 }, "chunk_id": "train_shard_00000_2660_0", "global_id": 2938 }, { "text": "Genome analysis of the pico-eukaryotic marine green alga Prasinoderma coloniale CCMP 1413 unveils the existence of a novel phylum within green plants (Viridiplantae), the Prasinodermophyta, which diverged before the split of Chlorophyta and Streptophyta. Structural features of the genome and gene family comparisons revealed an intermediate position of the P. coloniale genome (25.3 Mb) between the extremely compact, small genomes of picoplanktonic Mamiellophyceae (Chlorophyta) and the larger, more complex genomes of early-diverging streptophyte algae. Reconstruction of the minimal core genome of Viridiplantae allowed identification of an ancestral toolkit of transcription factors and flagellar proteins. Adaptations of P. coloniale to its deep-water, oligotrophic environment involved expansion of light-harvesting proteins, reduction of early light-induced proteins, evolution of a distinct type of C\n\nThe genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants.", "token_count": 275, "char_count": 1008, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:13.546785", "source": { "split": "train_shard_00000", "doc_id": 2661 }, "chunk_id": "train_shard_00000_2661_0", "global_id": 2939 }, { "text": "Most of the human gene homologs are found in Caenorhabditis elegans. As a wide variety of micro-organisms present in the environment is pathogens, so, C. elegans could be a useful model to track future infectious disease. With this knowledge, in this study, we isolated Acinetobacter courvalinii from the soil and characterized its pathogenicity for the first time. For the isolation, we used Glucose-Yeast extract-Ethanol-Calcium carbonate medium. To this aim, we evaluated the resistivity of bacteria against several stressful microenvironments. As we observed, A. courvalinii JP_A1001 shown highly tolerance against the acidic environment (pH 3-7), resistant against up to 0.2% of phenol content, and survived in the medium supplemented with 0.3% of bile salt. In addition, the bacteria were also resistant against several antibiotics showing the property of multidrug-resistant bacteria. Moreover, the isolated bacteria have shown the biofilm formation ability within 60 h. Further, we found that incubation of C. elegans with A. courvalinii JP_A1001 decreased the body movement and increased the free radical generation which remarkably influenced the life expectancy of C. elegans compared to E. coli OP50. Therefore, we concluded that A. courvalinii JP_A1001 found in the soil could be a future threat as a pathogen to public health.\n\nGenotypic, phenotypic, and pathogenic characterization of the soil isolated Acinetobacter courvalinii.", "token_count": 373, "char_count": 1444, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [ "OP50" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:14.124659", "source": { "split": "train_shard_00000", "doc_id": 2662 }, "chunk_id": "train_shard_00000_2662_0", "global_id": 2940 }, { "text": "Pathogens continuously adapt to changing host environments where variation in their virulence and antigenicity is critical to their long-term evolutionary success. The emergence of novel variants is accelerated in microbial mutator strains (mutators) deficient in DNA repair genes, most often from mismatch repair and oxidized-guanine repair systems (MMR and OG respectively). Bacterial MMR/OG mutants are abundant in clinical samples and show increased adaptive potential in experimental infection models, yet the role of mutators in the epidemiology and evolution of infectious disease is not well understood. Here we investigated the role of mutation rate dynamics in the evolution of a broad host range pathogen, Streptococcus iniae, using a set of 80 strains isolated globally over 40 years. We have resolved phylogenetic relationships using non-recombinant core genome variants, measured in vivo mutation rates by fluctuation analysis, identified variation in major MMR/OG genes and their regulatory regions, and phenotyped the major traits determining virulence in streptococci. We found that both mutation rate and MMR/OG genotype are remarkably conserved within phylogenetic clades but significantly differ between major phylogenetic lineages. Further, variation in MMR/OG loci correlates with occurrence of atypical virulence-associated phenotypes, infection in atypical hosts (mammals), and atypical (osseous) tissue of a vaccinated primary host. These findings suggest that mutators are likely to facilitate adaptations preceding major diversification events and may promote emergence of variation permitting colonization of a novel host tissue, novel host taxa (host jumps), and immune-escape in the vaccinated host.\n\nEvolutionary epidemiology of Streptococcus iniae: Linking mutation rate dynamics with adaptation to novel immunological landscapes.", "token_count": 434, "char_count": 1862, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6299, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:14.750982", "source": { "split": "train_shard_00000", "doc_id": 2663 }, "chunk_id": "train_shard_00000_2663_0", "global_id": 2941 }, { "text": "Lipopolysaccharides (LPS), a main component of the Gram-negative bacterial cell wall, can damage the epithelial wall barrier and induce chronic intestinal inflammation. The purpose of this study is to evaluate whether the novel L. rhamnosus could alleviate intestinal inflammation and damage induced by LPS and explore the possible underlying molecular mechanism. L. rhamnosus JL-1 was selected from five L. rhamnosus strains due to its strong adherence capacity to Caco-2 cells (92.89%) and it could survive in simulated gastrointestinal juices. Whole genome sequencing analysis showed that there were no translocation and inversion regions in the genome of L. rhamnosus JL-1 compared with L. rhamnosus GG. Comparative genomic analysis showed that there were encoding genes related to adhesion, acid resistance and bile salt resistance in the genome of L. rhamnosus JL-1. Both in vitro and in vivo experiments indicated that LPS challenge inhibited the mRNA and protein expression of pro-inflammatory cytokines (TNF-α, IL-1β and IL-6). However, the mRNA and protein expressions of pro-inflammatory cytokines were inhibited by pre-treatment with L. rhamnosus JL-1 in a dose-dependent manner. The result of histopathology analysis of ileum showed that oral administration of L. rhamnosus JL-1 reduced pathological damage induced by LPS. Furthermore, it was revealed that L. rhamnosus JL-1 could inhibit the mRNA and protein expressions of TLR4 and NF-κB. These results strongly suggested that L. rhamnosus JL-1 relieved LPS-induced intestinal inflammation by inhibiting the TLR4/NF-κB signaling pathway. To sum up, L. rhamnosus JL-1 has a potential probiotic function and plays an important role in preventing LPS-induced intestinal inflammation and damage.", "token_count": 480, "char_count": 1756, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5608, "quality_score": 0.7804, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:15.398001", "source": { "split": "train_shard_00000", "doc_id": 2664 }, "chunk_id": "train_shard_00000_2664_0", "global_id": 2942 }, { "text": "Protective effects of a novel Lactobacillus rhamnosus strain with probiotic characteristics against lipopolysaccharide-induced intestinal inflammation in vitro and in vivo.", "token_count": 47, "char_count": 172, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:15.757482", "source": { "split": "train_shard_00000", "doc_id": 2664 }, "chunk_id": "train_shard_00000_2664_1", "global_id": 2943 }, { "text": "Invasive listeriosis is a severe foodborne infection in humans and is difficult to control. Listeriosis incidence is increasing worldwide, but some countries have implemented molecular surveillance programs to improve recognition and management of listeriosis outbreaks. In Germany, routine whole-genome sequencing, core genome multilocus sequence typing, and single nucleotide polymorphism calling are used for subtyping of Listeria monocytogenes isolates from listeriosis cases and suspected foods. During 2018-2019, an unusually large cluster of L. monocytogenes isolates was identified, including 134 highly clonal, benzalkonium-resistant sequence type 6 isolates collected from 112 notified listeriosis cases. The outbreak was one of the largest reported in Europe during the past 25 years. Epidemiologic investigations identified blood sausage contaminated with L. monocytogenes highly related to clinical isolates; withdrawal of the product from the market ended the outbreak. We describe how epidemiologic investigations and complementary molecular typing of food isolates helped identify the outbreak vehicle.\n\nLarge Nationwide Outbreak of Invasive Listeriosis Associated with Blood Sausage, Germany, 2018-2019.", "token_count": 294, "char_count": 1220, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6918, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:16.317143", "source": { "split": "train_shard_00000", "doc_id": 2665 }, "chunk_id": "train_shard_00000_2665_0", "global_id": 2944 }, { "text": "Thanks to the progress and decreasing costs in genome sequencing technologies, more than 250,000 bacterial genomes are currently available in public databases, covering most, if not all, of the major human-associated phylogenetic groups of these microorganisms, pathogenic or not. In addition, for many of them, sequences from several strains of a given species are available, thus enabling to evaluate their genetic diversity and study their evolution. In addition, the significant cost reduction of bacterial whole genome sequencing as well as the rapid increase in the number of available bacterial genomes have prompted the development of pangenomic software tools. The study of bacterial pangenome has many applications in clinical microbiology. It can unveil the pathogenic potential and ability of bacteria to resist antimicrobials as well identify specific sequences and predict antigenic epitopes that allow molecular or serologic assays and vaccines to be designed. Bacterial pangenome constitutes a powerful method for understanding the history of human bacteria and relating these findings to diagnosis in clinical microbiology laboratories in order to optimize patient management.\n\nInterest of bacterial pangenome analyses in clinical microbiology.", "token_count": 268, "char_count": 1261, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6369, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:16.898549", "source": { "split": "train_shard_00000", "doc_id": 2666 }, "chunk_id": "train_shard_00000_2666_0", "global_id": 2945 }, { "text": "Intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacterales (Ent) can be driven by contact with colonized animals and/or contamination of the food chain. We studied the ESC-R-Ent and COL-R-Ent colonizing poultry as well as contaminating chicken meat in Zanzibar (Tanzania). Results were compared with recently published data obtained from rectal swabs of people in the community.\n\nOn the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat.", "token_count": 159, "char_count": 601, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:17.369635", "source": { "split": "train_shard_00000", "doc_id": 2667 }, "chunk_id": "train_shard_00000_2667_0", "global_id": 2946 }, { "text": "Soybean is one of the most important vegetable oil and protein feed crops. To capture the entire genomic diversity, it is needed to construct a complete high-quality pan-genome from diverse soybean accessions. In this study, we performed individual de novo genome assemblies for 26 representative soybeans that were selected from 2,898 deeply sequenced accessions. Using these assembled genomes together with three previously reported genomes, we constructed a graph-based genome and performed pan-genome analysis, which identified numerous genetic variations that cannot be detected by direct mapping of short sequence reads onto a single reference genome. The structural variations from the 2,898 accessions that were genotyped based on the graph-based genome and the RNA sequencing (RNA-seq) data from the representative 26 accessions helped to link genetic variations to candidate genes that are responsible for important traits. This pan-genome resource will promote evolutionary and functional genomics studies in soybean.\n\nPan-Genome of Wild and Cultivated Soybeans.", "token_count": 238, "char_count": 1073, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:17.853909", "source": { "split": "train_shard_00000", "doc_id": 2668 }, "chunk_id": "train_shard_00000_2668_0", "global_id": 2947 }, { "text": "Candida species are among the most important causes of hospital acquired blood borne infections, and with high rates of mortality and morbidity, these infections are still a major problem today. History of gastrointestinal surgery, administration of total parenteral nutrition and/or wide spectrum antibiotics and immune suppression following organ transplantations are considered serious risk factors for these infections. This study aimed to evaluate the patients from our general surgery department with diagnosed candidemia; by means of strain, treatment and prognosis.\n\nRetrospective evaluation of candidemic patients among general surgery department in a tertiary care university hospital.", "token_count": 137, "char_count": 695, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7979, "quality_score": 0.8989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:18.316222", "source": { "split": "train_shard_00000", "doc_id": 2669 }, "chunk_id": "train_shard_00000_2669_0", "global_id": 2948 }, { "text": "Clonal complex 59 (CC59) is the dominant community-associated methicillin-resistant Staphylococcus aureus (MRSA) strain in Taiwan and includes the Asian-Pacific clone with Panton-Valentine leukocidin (PVL)-negative/staphylococcal cassette chromosome mec (SCCmec) IVg and the Taiwan clone characterised as PVL-positive/SCCmec V (5C2&5). Nevertheless, data on the evolutionary history of the two dominant CC59 MRSA clones in Taiwan are scarce. In this study, a total of 258 CC59 S. aureus strains from Taiwan were classified by multiple-locus variable-number tandem repeat analysis (MLVA), which revealed two major clusters (MT1 and MT2) with distinct mobile genetic elements (MGEs). However, sequencing and PCR mapping of the β-lactamase-producing plasmid revealed no difference among all CC59 S. aureus strains. Bayesian evolutionary analysis of 18 of the CC59 S. aureus strains based on core genome alignment revealed two clades: (i) Clade A, which shared the samples with MT1, had the features of mainly harbouring gentamicin-resistant MES\n\nTracking the evolution of the two successful CC59 methicillin-resistant Staphylococcus aureus clones in Taiwan: the divergence time of the two clades is estimated to be the 1980s.", "token_count": 360, "char_count": 1222, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6628, "quality_score": 0.8314, "entities": { "genes": [ "MT1", "CC59", "MT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:18.913189", "source": { "split": "train_shard_00000", "doc_id": 2670 }, "chunk_id": "train_shard_00000_2670_0", "global_id": 2949 }, { "text": "Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for\n\nA Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera.", "token_count": 109, "char_count": 455, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7742, "quality_score": 0.8871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:19.297731", "source": { "split": "train_shard_00000", "doc_id": 2671 }, "chunk_id": "train_shard_00000_2671_0", "global_id": 2950 }, { "text": "Genome shuffling is an efficient way to pool advantageous traits during positive selections of industrial microorganisms. In this study, for the first time, the effectiveness of genome shuffling to improve yielding of heterologous proteins was investigated in Kluyveromyces marxianus (KM), a promising yeast host. After two rounds of mating and screening, a novel KM strain, D\n\nImproving the expression of a heterologous protein by genome shuffling in Kluyveromyces marxianus.", "token_count": 119, "char_count": 476, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7536, "quality_score": 0.8768, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:19.683741", "source": { "split": "train_shard_00000", "doc_id": 2672 }, "chunk_id": "train_shard_00000_2672_0", "global_id": 2951 }, { "text": "Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, can cause significant economic losses and is present worldwide. With the advance of whole genome sequencing technologies, new methods are available for the researchers; one emerging methodology is the core genome Multi-Locus Sequence Typing (cgMLST). The core genome contains a high percentage of the coding DNA sequence (CDS) set of the studied strains. The cgMLST schemas are powerful genotyping tools allowing for the investigation of potential epidemics, and precise and reliable classification of the strains. Although whole genome sequences of M. anserisalpingitidis strains are available, to date, no cgMLST schema has been published for this species.\n\nThe core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis.", "token_count": 199, "char_count": 820, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:20.139807", "source": { "split": "train_shard_00000", "doc_id": 2673 }, "chunk_id": "train_shard_00000_2673_0", "global_id": 2952 }, { "text": "A Core Genome Multilocus Sequence Typing Scheme for", "token_count": 14, "char_count": 51, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:20.486830", "source": { "split": "train_shard_00000", "doc_id": 2674 }, "chunk_id": "train_shard_00000_2674_0", "global_id": 2953 }, { "text": "Our aim was to evaluate the performance of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), routinely used in the microbiology laboratory for bacterial identification, for bacterial typing in the setting of extended spectrum beta-lactamase producing Klebsiella pneumoniae (ESBL-KP) outbreak in the neonatal intensive care unit (NICU). Isolates from a 2011 outbreak in the NICU were retrieved from frozen stocks and analyzed by MALDI-TOF. The MALDI typing was compared with core genome multilocus sequence typing (cg-MLST). MALDI typing divided the 33 outbreak isolates into 2 clones: sequence type (ST)-290 and 405. These results were in complete agreement with cg-MLST results. The differentiation of the outbreak isolates into two clones correlated with the patients' location in the NICU, but also with their place of residence.Conclusion: Here, we show that MALDI-TOF MS, which has been integrated into the microbiology laboratory workflow for microbial species identification, can be secondarily used for epidemiological typing at no added cost. What is Known: • Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) is now routinely used in the microbiology laboratory for bacterial identification What is New: • MALDI typing was used for outbreak investigation in the NICU and divided the outbreak isolates into two clones • MALDI-TOF MS may be secondarily used for epidemiological typing at no added cost.\n\nThe utility of MALDI-TOF MS for outbreak investigation in the neonatal intensive care unit.", "token_count": 410, "char_count": 1588, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5286, "quality_score": 0.7643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:21.109084", "source": { "split": "train_shard_00000", "doc_id": 2675 }, "chunk_id": "train_shard_00000_2675_0", "global_id": 2954 }, { "text": "The study's objective was to determine the influence of vaginal birth compared to cesarean birth on the content of lactic acid bacteria with probiotic characteristics from newborns. Vaginal and cesarean sec tion meconium samples of lactic acid were evaluated, which were duly enriched, seeded and incubated. The resulting colonies were identified to be subjected to bile salt tolerance, acid pH, and fermentation. A greater development of meconium colonies was obtained in those born vaginally compared to those born by caesarean section (p <0.001). A total of 48 strains were isolated, the majority being tolerant to bile salts and acid pH; likewise, the fermentation of lactose in milk was positive. This study supports previous findings that support vaginal birth favors the greatest development of lactic acid bacteria with probiotic characteristics, compared to cesarean birth, and highlights the presence of bacteria of the genus Lactobacillus.\n\nInfluence from the type of birth on the content of lactic acid bacteria in neonate meconium.", "token_count": 251, "char_count": 1044, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5597, "quality_score": 0.7799, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:21.600837", "source": { "split": "train_shard_00000", "doc_id": 2676 }, "chunk_id": "train_shard_00000_2676_0", "global_id": 2955 }, { "text": "Adverse drug reactions (ADRs) are a common cause of attrition in drug discovery and development and drug-induced liver injury (DILI) is a leading cause of preclinical and clinical drug terminations. This perspective outlines many of the known DILI mechanisms and assessment methods used to evaluate and mitigate DILI risk. Literature assessments and retrospective analyses using verified DILI-associated drugs from the Liver Tox Knowledge Base (LTKB) have been used to derive the predictive value of each end point, along with combination approaches of multiple methods. In vitro assays to assess inhibition of the bile salt export pump (BSEP), mitotoxicity, reactive metabolite (RM) formation, and hepatocyte cytolethality, along with physicochemical properties and clinical dose provide useful DILI predictivity. This Perspective also highlights some of the strategies used by medicinal chemists to reduce DILI risk during the optimization of drug candidates.\n\nDrug Induced Liver Injury (DILI). Mechanisms and Medicinal Chemistry Avoidance/Mitigation Strategies.", "token_count": 253, "char_count": 1064, "word_count": 149, "semantic_coherence": 1, "information_density": 0.698, "quality_score": 0.849, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:22.090340", "source": { "split": "train_shard_00000", "doc_id": 2677 }, "chunk_id": "train_shard_00000_2677_0", "global_id": 2956 }, { "text": "Correct identifications of isolates and strains of the Mitis-Group of the genus\n\nA Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of", "token_count": 42, "char_count": 167, "word_count": 23, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:22.459628", "source": { "split": "train_shard_00000", "doc_id": 2678 }, "chunk_id": "train_shard_00000_2678_0", "global_id": 2957 }, { "text": "Kluyveromyces marxianus dairy strains were tested for γ-aminobutyric acid (GABA) production. The genes involved in GABA catabolism (UGA1 and UGA2) and anabolism (GAD1) were found in K. marxianus genome. Their relative expression was evaluated with primer designed ad hoc.\n\nγ-aminobutyric acid production by Kluyveromyces marxianus strains.", "token_count": 106, "char_count": 339, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [ "GAD1", "UGA1", "UGA2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:22.837912", "source": { "split": "train_shard_00000", "doc_id": 2679 }, "chunk_id": "train_shard_00000_2679_0", "global_id": 2958 }, { "text": "The extent and role of horizontal gene transfer (HGT) in phytoplankton and, more broadly, eukaryotic evolution remain controversial topics. Recent studies substantiate the importance of HGT in modifying or expanding functions such as metal or reactive species detoxification and buttressing halotolerance. Yet, the potential of HGT to significantly alter the fate of species in a major eukaryotic assemblage remains to be established. We provide such an example for the ecologically important lineages encompassed by cryptophytes, rhizarians, alveolates, stramenopiles, and haptophytes (\"CRASH\" taxa). We describe robust evidence of prokaryotic HGTs in these taxa affecting functions such as polysaccharide biosynthesis. Numbers of HGTs range from 0.16 to 1.44% of CRASH species gene inventories, comparable to the ca. 1% prokaryote-derived HGTs found in the genomes of extremophilic red algae. Our results substantially expand the impact of HGT in eukaryotes and define a set of general principles for prokaryotic gene fixation in phytoplankton genomes.\n\nPhytoplankton pangenome reveals extensive prokaryotic horizontal gene transfer of diverse functions.", "token_count": 301, "char_count": 1156, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:23.402298", "source": { "split": "train_shard_00000", "doc_id": 2680 }, "chunk_id": "train_shard_00000_2680_0", "global_id": 2959 }, { "text": "Development and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa.", "token_count": 35, "char_count": 142, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:23.777661", "source": { "split": "train_shard_00000", "doc_id": 2681 }, "chunk_id": "train_shard_00000_2681_0", "global_id": 2960 }, { "text": "Listeria monocytogenes is a foodborne pathogen causing systemic infection with high mortality. To allow efficient tracking of outbreaks a clear definition of the genomic signature of a cluster of related isolates is required, but lineage-specific characteristics call for a more detailed understanding of evolution. In our work, we used core genome MLST (cgMLST) to identify new outbreaks combined to core genome SNP analysis to characterize the population structure and gene flow between lineages. Whilst analysing differences between the four lineages of L. monocytogenes we have detected differences in the recombination rate, and interestingly also divergence in the SNP differences between sub-lineages. In addition, the exchange of core genome variation between the lineages exhibited a distinct pattern, with lineage III being the best donor for horizontal gene transfer. Whilst attempting to link bacteriophage-mediated transduction to observed gene transfer, we found an inverse correlation between phage presence in a lineage and the extent of recombination. Irrespective of the profound differences in recombination rates observed between sub-lineages and lineages, we found that the previously proposed cut-off of 10 allelic differences in cgMLST can be still considered valid for the definition of a foodborne outbreak cluster of L. monocytogenes.\n\nLineage-specific evolution and gene flow in Listeria monocytogenes are independent of bacteriophages.", "token_count": 319, "char_count": 1463, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5894, "quality_score": 0.7947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:24.336934", "source": { "split": "train_shard_00000", "doc_id": 2682 }, "chunk_id": "train_shard_00000_2682_0", "global_id": 2961 }, { "text": "Indonesian kefir grains are potential sources of lactic acid bacteria (LAB) that may act as probiotics with specific functional properties. In this study we explored the potential of the probiotic and cholesterol-lowering effect of LAB isolated from Indonesian kefir grains obtained from Bogor, Bandung, Jakarta, and Yogyakarta. The results revealed that 10 isolates showed considerable survivability at low pH and bile salt with total cell reduction of ~3 log colony-forming units per milliliter after exposure to pH 2.5 and 0.5% (w/v) bile salt for 1 and 3 h, respectively. All strains exhibited strong antimicrobial activities against pathogenic bacteria and were sensitive to a wide spectrum of antibiotics but exhibited weak bile salt hydrolase activity. Identification based on 16S RNA suggested that nine isolates were\n\nIn Vitro Characterization of Lactic Acid Bacteria from Indonesian Kefir Grains as Probiotics with Cholesterol-Lowering Effect.", "token_count": 244, "char_count": 953, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:24.822895", "source": { "split": "train_shard_00000", "doc_id": 2683 }, "chunk_id": "train_shard_00000_2683_0", "global_id": 2962 }, { "text": "The intrinsic dissolution rate (IDR) of active pharmaceutical ingredients (API) is a key property that aids in early drug development, especially selecting formulation strategies to improve dissolution and thereby drug absorption in the intestine. Here, we developed a robust method for rapid, medium throughput screening of IDR and established the largest IDR dataset in open literature to date that can be used for pharmaceutical computational modeling. Eighteen compounds with diverse physicochemical properties were studied in both fasted and fed state simulated intestinal fluids. Dissolution profiles were measured in small-scale experimental assays using compound suspensions or discs. IDR measurements were not solely linked to API solubility in either dissolution media. Multivariate data analysis revealed that IDR strongly depends on compound partitioning into bile salt and phospholipid micelles in the simulated intestinal fluids, a process that in turn is governed by API lipophilicity, hydrophobicity, and ionization.\n\nIntrinsic Dissolution Rate Profiling of Poorly Water-Soluble Compounds in Biorelevant Dissolution Media.", "token_count": 252, "char_count": 1138, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7051, "quality_score": 0.8526, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:25.311598", "source": { "split": "train_shard_00000", "doc_id": 2684 }, "chunk_id": "train_shard_00000_2684_0", "global_id": 2963 }, { "text": "Plant pathogens can rapidly overcome resistance of their hosts by mutating key pathogenicity genes encoding for effectors. Pathogen adaptation is fuelled by extensive genetic variability in populations and different strains may not share the same set of genes. Recently, such an intra-specific variation in gene content became formalized as pangenomes distinguishing core genes (i.e. shared) and accessory genes (i.e. lineage or strain-specific). Across pathogens species, key effectors tend to be part of the rapidly evolving accessory genome. Here, we show how the construction and analysis of pathogen pangenomes provide deep insights into the dynamic host adaptation process. We also discuss how pangenomes should ideally be built and how geography, niche and lifestyle likely determine pangenome sizes.\n\nThe rise and fall of genes: origins and functions of plant pathogen pangenomes.", "token_count": 193, "char_count": 888, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7364, "quality_score": 0.8682, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:25.762388", "source": { "split": "train_shard_00000", "doc_id": 2685 }, "chunk_id": "train_shard_00000_2685_0", "global_id": 2964 }, { "text": "The aim of this study was to investigate recurrent infections in individual patients caused by extended-spectrum β-lactamase and plasmid AmpC β-lactamase-producing Escherichia coli (ESBL/pAmpC-Ec) isolates with >12-month interval. The Danish national collection of ESBL/pAmpC-Ec isolates collected from January 2014 through June 2017 was screened for patients with multiple isolates with >12 months between the episodes. Isolates underwent whole-genome sequencing and were analysed for antimicrobial resistance genes, virulence genes and multilocus sequence typing (MLST). Isolates were subtyped by core genome MLST (cgMLST) and CH typing. From a total of 970 patients, 15 unrelated patients experienced recurrent infections with ESBL/pAmpC-Ec. Of the 15 patients, 10 (67%) were found to be infected a second or third time with a genetically identical or similar strain. The resistance and virulence properties of the strains were similar in individual patients, however they were quite diverse when comparing between patients. Recurrent ESBL/pAmpC-Ec bloodstream infections of genetically related strains occurring with >12-month interval might be related to the previous episode and to a lesser extent be caused by re-infection. With >1000 days between the first and second episode of genetically similar strains (four allele differences), the recurrent infection is likely due to long-term host colonisation by ESBL/pAmpC-Ec. From this analysis, strains able to cause such recurrent infection were relatively diverse between patients. Knowledge about host and strain factors influencing such recurrent infections is needed to implement preventive measures.\n\nCharacterisation of extended-spectrum β-lactamase/plasmid AmpC-β-lactamase-producing Escherichia coli isolates from long-term recurrent bloodstream infections.", "token_count": 478, "char_count": 1820, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5679, "quality_score": 0.784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:26.403940", "source": { "split": "train_shard_00000", "doc_id": 2686 }, "chunk_id": "train_shard_00000_2686_0", "global_id": 2965 }, { "text": "Aquatic environments are considered a reservoir for the dissemination of multidrug-resistant (MDR) bacteria, principally Escherichia coli, with the consequent spread of acquired antimicrobial resistance genes (ARGs). Widespread high-risk clones of MDR E. coli are responsible for human infections worldwide. This study aimed to characterise, through whole-genome sequencing (WGS), isolates of MDR E. coli harbouring ARGs obtained from public aquatic environments in Brazil. MDR E. coli isolates were obtained from rivers, streams and lakes that presented different Water Quality Index records and were submitted to WGS. The resistome, mobilome and virulome showed a great diversity of ARGs, plasmids and virulence genes, respectively. In addition, mutations in the quinolone resistance-determining regions of GyrA, ParC and ParE as well as several metal resistance genes (MRGs) and antibacterial biocide resistance genes (ABGs) were detected. Typing and subtyping of MDR E. coli revealed different lineages, with two belonging to widespread high-risk clones (i.e. B2-ST131-fimH30 and F-ST648-fimH27), which are grouped by core genome multilocus sequence typing (cgMLST) in clusters with E. coli lineages obtained from different sources distributed worldwide. MDR bacteria carrying MRGs and ABGs have emerged as a global human and environmental health problem. Detection of widespread high-risk clones calls for attention to the dissemination of fluoroquinolone-resistant QnrS1- and CTX-M-producing E. coli lineages associated with human infections in public aquatic environments.\n\nWidespread high-risk clones of multidrug-resistant extended-spectrum β-lactamase-producing Escherichia coli B2-ST131 and F-ST648 in public aquatic environments.", "token_count": 470, "char_count": 1741, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [ "ST648", "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:27.043882", "source": { "split": "train_shard_00000", "doc_id": 2687 }, "chunk_id": "train_shard_00000_2687_0", "global_id": 2966 }, { "text": "Telomeres are special structures at the ends of chromosomes that play an important role in the protection of the genetic material. Telomere composition is very diverse; noticeable differences can often be observed even among closely related species. Here, we identify the homolog of telomeric protein Cdc13 in the thermotolerant yeast\n\nThe Telomeric Cdc13 Protein from Yeast Hansenula polymorpha.", "token_count": 94, "char_count": 396, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7931, "quality_score": 0.8966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:27.424769", "source": { "split": "train_shard_00000", "doc_id": 2688 }, "chunk_id": "train_shard_00000_2688_0", "global_id": 2967 }, { "text": "Bacillus coagulans is a thermophilic, facultative anaerobic, spore-forming Gram-positive bacterium, which is used as a probiotic in animal feed and human dietary supplements. In the present study, a bile-resistant thermophilic B. coagulans WT-03 strain was isolated and genetically identified. Atmospheric pressure room temperature plasma (ARTP)-induced mutation combined with adaptive laboratory evolution (ALE) was used to improve the probiotic performance of B. coagulans WT-03. After 15 s of ARTP mutation and 40 days of ALE culture, a mutant artp-aleBC15 was obtained and showed the improved tolerance to pH 2.5 and 0.3% bile salt with a survival rate of 22.4%. Further studies showed that the artp-aleBC15 mutant exhibited a relatively stable morphology, lower permeability, and higher hydrophobicity of cell membrane compared with the parent strain of B. coagulans. Additionally, artp-aleBC15 could maintain homeostasis with an intracellular pH of over 4.5 and had the altered contents of saturated fatty acids/unsaturated fatty acids in the cell membrane at pH 2.5. Our study proved that ARTP mutation combined with ALE is an efficient mutagenesis strategy to improve the probiotic performance of B. coagulans for potential industrial use.Key Points• A B. coagulans strain that can grow at 80 °C and 0.3% bile salt was screened.• ARTP combined with ALE effectively mutated B. coagulans WT-03.• B. coagulans artp-aleBC15 mutant showed an improved probiotic performance.• The mutant exhibited the lower permeability and altered fatty acid contents in the cell membrane.\n\nARTP mutation and adaptive laboratory evolution improve probiotic performance of Bacillus coagulans.", "token_count": 480, "char_count": 1677, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5287, "quality_score": 0.7643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:28.072296", "source": { "split": "train_shard_00000", "doc_id": 2689 }, "chunk_id": "train_shard_00000_2689_0", "global_id": 2968 }, { "text": "Oral delivery of poorly water-soluble drugs (PWSDs), which predominate the development pipeline, poses significant challenges. Weakly basic compounds, such as atazanavir, represent a critical class of PWSDs as even the administration of the crystalline solid may invoke supersaturation during gastric-intestinal transfer. The absorption advantage afforded by this supersaturated state can be offset by inherent metastability and a tendency to revert to the lower energy crystalline state. Therefore, it is important to understand the physiological factors that can affect crystallization to improve in vitro-in vivo predictiveness and to regulate inter-individual responses. The first aim of this study was to elucidate the influence of lyso-phosphatidylcholine (lyso-PC) and sodium oleate on crystallization, as the products of phosphatidylcholine (PC) hydrolysis and the major lipid components of human intestinal fluid (HIF) and updated fasted state simulated intestinal fluid version 3 (FaSSIF-V3). Secondly, as an individual's bile acid pool is unique, dynamic and related to gut microbiome community structure, it was of interest to investigate the impact of bile acid pool variations on crystallization from supersaturated solutions. To study the effect of PC hydrolysis, media with 2.8 mM sodium glycocholate (GCA) and sodium taurocholate (TCA) (1:1) but varying concentrations of PC, lyso-PC or sodium oleate were prepared. To investigate the influence of inter-individual variations in intestinal bile acid pool size and composition, media simulating the profiles of six healthy Western volunteers were prepared based on previously published data. The crystalline and amorphous solubility of atazanavir, a weakly basic antiretroviral drug, was firstly determined in these media. Nucleation-induction time experiments were then performed at an equivalent extent of supersaturation in each medium (corresponding to the amorphous solubility)", "token_count": 483, "char_count": 1948, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:28.719840", "source": { "split": "train_shard_00000", "doc_id": 2690 }, "chunk_id": "train_shard_00000_2690_0", "global_id": 2969 }, { "text": "At a constant level of GCA/TCA, increasing concentrations of both PC and lyso-PC accelerated crystallization onset; however, this was at least 2-fold more pronounced with lyso-PC at a given molar concentration. The addition of sodium oleate was also observed to induce crystallization. Interestingly, substituting GCA/TCA with the bile salt fraction of other biorelevant media partially circumvented the crystallization-inducing effect of phospholipids and their digests. The presence of dihydroxy bile salts was found to be particularly significant in decelerating the crystallization process. Nucleation-induction times in simulated volunteer pools were found to be dependent upon bile salt concentration, with higher bile salt levels generally prolonging supersaturation. Differences of up to 6-fold were observed. This study demonstrates that the choice of biorelevant medium used to evaluate supersaturating formulations can influence the observed crystallization kinetics. While the presence of lyso-PC and sodium oleate in FaSSIF-V3 medium is more physiologically relevant, further attention should be paid to the bile salt fraction when designing a biorelevant medium for supersaturating formulations. In vivo, inter-individual differences in the amount and types of bile acids and phospholipids present may influence the behaviour of supersaturating formulations.\n\nImpact of phospholipid digests and bile acid pool variations on the crystallization of atazanavir from supersaturated solutions.", "token_count": 355, "char_count": 1502, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:29.315364", "source": { "split": "train_shard_00000", "doc_id": 2690 }, "chunk_id": "train_shard_00000_2690_1", "global_id": 2970 }, { "text": "Probiotics are live microorganisms that may be able to help prevent and treat some illnesses. Most probiotics on the market are bacterial, primarily Lactobacillus. Yeast are an inevitable part of the microbiota of various fermented foods and beverages and have several beneficial properties that bacteria do not have. In this study, yeast strains were isolated from fermented food and beverages. Various physiological features of the candidate probiotic isolates were preliminarily investigated, including bile salt and acid tolerance, cell surface hydrophobicity, autoaggregation, antioxidant activity, and β-galactosidase activity. Several yeast strains with probiotic potential were selected. Overall, Kluyveromyces marxianus JYC2614 adapted well to the bile salt and acid tolerance test; it also had favorable autoaggregation and good cell-surface hydrophobicity. Klu. marxianus JYC2610 grew well according to the bile salt and acid tolerance test and performed well regarding cell surface hydrophobicity and β-galactosidase activity. Selected yeast species can survive in a gastrointestinal environment and should be further evaluated in vivo as probiotics in the future. Our findings should encourage further studies on the application of the strains in this study as food and feed supplements.\n\nIn Vitro Properties of Potential Probiotic Indigenous Yeasts Originating from Fermented Food and Beverages in Taiwan.", "token_count": 342, "char_count": 1419, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [ "JYC2610", "JYC2614" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:29.903669", "source": { "split": "train_shard_00000", "doc_id": 2691 }, "chunk_id": "train_shard_00000_2691_0", "global_id": 2971 }, { "text": "The thermotolerant yeast\n\nContribution of Complex I NADH Dehydrogenase to Respiratory Energy Coupling in Glucose-Grown Cultures of", "token_count": 42, "char_count": 130, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:30.301765", "source": { "split": "train_shard_00000", "doc_id": 2692 }, "chunk_id": "train_shard_00000_2692_0", "global_id": 2972 }, { "text": "Glycosylation can affect various protein properties such as stability, biological activity, and immunogenicity. To produce human therapeutic proteins, a host that can produce glycoproteins with correct glycan structures is required. Microbial expression systems offer economical, rapid and serum-free production and are more amenable to genetic manipulation. In this study, we developed a protocol for CRISPR/Cas9 multiple gene knockouts and knockins in Kluyveromyces marxianus, a probiotic yeast with a rapid growth rate. As hyper-mannosylation is a common problem in yeast, we first knocked out the α-1,3-mannosyltransferase (ALG3) and α-1,6-mannosyltransferase (OCH1) genes to reduce mannosylation. We also knocked out the subunit of the telomeric Ku domain (KU70) to increase the homologous recombination efficiency of K. marxianus. In addition, we knocked in the MdsI (α-1,2-mannosidase) gene to reduce mannosylation and the GnTI (β-1,2-N-acetylglucosaminyltransferase I) and GnTII genes to produce human N-glycan structures. We finally obtained two strains that can produce low amounts of the core N-glycan Man3GlcNAc2 and the human complex N-glycan Man3GlcNAc4, where Man is mannose and GlcNAc is N-acetylglucosamine. This study lays a cornerstone of glycosylation engineering in K. marxianus toward producing human glycoproteins.\n\nConstructing a human complex type N-linked glycosylation pathway in Kluyveromyces marxianus.", "token_count": 416, "char_count": 1431, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6392, "quality_score": 0.8196, "entities": { "genes": [ "ALG3", "KU70", "OCH1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:30.945847", "source": { "split": "train_shard_00000", "doc_id": 2693 }, "chunk_id": "train_shard_00000_2693_0", "global_id": 2973 }, { "text": "Multidrug-resistant Acinetobacter baumannii is a top-priority Gram-negative pathogen and polymyxins are a last-line therapeutic option. Previous systems pharmacological studies examining polymyxin killing and resistance usually focused on individual strains, and the derived knowledge could be limited by strain-specific genomic context. In this study, we examined the gene expression of five A. baumannii strains (34654, 1207552, 1428368, 1457504 and ATCC 19606) to determine the common differentially expressed genes in response to polymyxin treatments. A pan-genome containing 6061 genes was identified for 89 A. baumannii genomes from RefSeq database which included the five strains examined in this study; 2822 of the 6061 genes constituted the core genome. After 2 mg L\n\nPan-transcriptomic analysis identified common differentially expressed genes of Acinetobacter baumannii in response to polymyxin treatments.", "token_count": 258, "char_count": 917, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:31.489809", "source": { "split": "train_shard_00000", "doc_id": 2694 }, "chunk_id": "train_shard_00000_2694_0", "global_id": 2974 }, { "text": "Encapsulation techniques and materials, explored for addressing compromised probiotic gut survival, report significant production losses resulting in <10% entrapment. Presently, we report three-time enhanced entrapment (30 ± 1.2%) of\n\nPharmabiotic beads with improved encapsulation and gut survival for management of colonic inflammation associated gut derangements.", "token_count": 89, "char_count": 366, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8444, "quality_score": 0.9222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:31.873400", "source": { "split": "train_shard_00000", "doc_id": 2695 }, "chunk_id": "train_shard_00000_2695_0", "global_id": 2975 }, { "text": "BackgroundBoth long- and short-term epidemiology are fundamental to disease control and require accurate bacterial typing. Genomic data resulting from implementation of whole genome sequencing in many public health laboratories can potentially provide highly sensitive and accurate descriptions of strain relatedness. Previous typing efforts using these data have mainly focussed on outbreak detection.AimWe aimed to develop multilevel genome typing (MGT), using consecutive multilocus sequence typing (MLST) schemes of increasing sizes, stepping up from seven-gene MLST to core genome MLST, to allow examination of genetic relatedness at multiple resolution levels.MethodsThe system was applied to\n\nMultilevel genome typing: genomics-guided scalable resolution typing of microbial pathogens.", "token_count": 165, "char_count": 792, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7843, "quality_score": 0.8922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:32.321608", "source": { "split": "train_shard_00000", "doc_id": 2696 }, "chunk_id": "train_shard_00000_2696_0", "global_id": 2976 }, { "text": "Low-cost whole-genome assembly has enabled the collection of haplotype-resolved pangenomes for numerous organisms. In turn, this technological change is encouraging the development of methods that can precisely address the sequence and variation described in large collections of related genomes. These approaches often use graphical models of the pangenome to support algorithms for sequence alignment, visualization, functional genomics, and association studies. The additional information provided to these methods by the pangenome allows them to achieve superior performance on a variety of bioinformatic tasks, including read alignment, variant calling, and genotyping. Pangenome graphs stand to become a ubiquitous tool in genomics. Although it is unclear whether they will replace linearreference genomes, their ability to harmoniously relate multiple sequence and coordinate systems will make them useful irrespective of which pangenomic models become most common in the future.\n\nPangenome Graphs.", "token_count": 197, "char_count": 1005, "word_count": 136, "semantic_coherence": 1, "information_density": 0.7353, "quality_score": 0.8676, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:32.775079", "source": { "split": "train_shard_00000", "doc_id": 2697 }, "chunk_id": "train_shard_00000_2697_0", "global_id": 2977 }, { "text": "The wastewater from the dumping site usually contains high pollutant levels. Biological process and physico-chemical treatments are among several technologies for wastewater treatment. Using microorganisms in the treatment of landfill leachate is an emerging research issue. Furthermore, bioremediation is a feasible approach for pollutants removal from landfill leachate which would provide an efficient way to resolve the issue of landfill leachate. In this study, the performance of yeast and bacteria isolated from kefir grains was assessed for landfill leachate treatment. Kefir grains microbial composition was evaluated by molecular approaches (Rep-PCR and 16S rRNA gene sequencing). The obtained outcomes denoted that high concentrations of lactic acid bacteria and yeast populations (over 10\n\nMixed culture of Lactococcus lactis and Kluyveromyces marxianus isolated from kefir grains for pollutants load removal from Jebel Chakir leachate.", "token_count": 223, "char_count": 948, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:33.250691", "source": { "split": "train_shard_00000", "doc_id": 2698 }, "chunk_id": "train_shard_00000_2698_0", "global_id": 2978 }, { "text": "The canalicular bile salt export pump (BSEP/ABCB11) of hepatocytes is the main adenosine triphosphate (ATP)-binding cassette (ABC) transporter responsible for bile acid secretion. Mutations in ABCB11 cause several cholestatic diseases, including progressive familial intrahepatic cholestasis type 2 (PFIC2) often lethal in absence of liver transplantation. We investigated in vitro the effect and potential rescue of a BSEP mutation by ivacaftor, a clinically approved cystic fibrosis transmembrane conductance regulator (CFTR/ABCC7) potentiator.\n\nFunctional rescue of an ABCB11 mutant by ivacaftor: A new targeted pharmacotherapy approach in bile salt export pump deficiency.", "token_count": 191, "char_count": 676, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7978, "quality_score": 0.8989, "entities": { "genes": [ "PFIC2", "ABCC7", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:33.694868", "source": { "split": "train_shard_00000", "doc_id": 2699 }, "chunk_id": "train_shard_00000_2699_0", "global_id": 2979 }, { "text": "In reverse vaccinology approaches, complete proteomes of bacteria are submitted to multiple computational prediction steps in order to filter proteins that are possible vaccine candidates. Most available tools perform such analysis only in a single strain, or a very limited number of strains. But the vast amount of genomic data had shown that most bacteria contain pangenomes, i.e., their genomic information contains core, conserved genes, and random accessory genes specific to each strain. Therefore, in reverse vaccinology methods it is of the utmost importance to define core proteins and core epitopes. EpitoCore is a decision-tree pipeline developed to fulfill that need. It provides surfaceome prediction of proteins from related strains, defines core proteins within those, calculate their immunogenicity, predicts epitopes for a given set of MHC alleles defined by the user, and then reports if epitopes are located extracellularly and if they are conserved among the core homologs. Pipeline performance is illustrated by mining peptide vaccine candidates in\n\nEpitoCore: Mining Conserved Epitope Vaccine Candidates in the Core Proteome of Multiple Bacteria Strains.", "token_count": 257, "char_count": 1177, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:34.258175", "source": { "split": "train_shard_00000", "doc_id": 2700 }, "chunk_id": "train_shard_00000_2700_0", "global_id": 2980 }, { "text": "Determining the source and genetic characteristics of the imported pathogen is critical in the control of infectious diseases. Here, we reported the investigation of an imported cholera case in China in 2018 with a recent travel history in Nepal and India. Stool culture from the patient was identified as Vibrio cholerae serogroup O1, biotype El Tor, serotype Ogawa. The strain 2018HL24 possessed intact Vibrio seventh pandemic island I (VSP-I), Vibrio pathogenicity Island 1 and 2 (VPI-1, VPI-2). A VSP-II variant with a 13 kb deletion was also detected, which was identical to those observed in V. cholerae in cluster \"Nepal-4\". Phylogenetic analysis based on the core genome SNPs showed that the isolate was most closely related to the V. cholerae isolated in northern India not far from the border of Nepal in 2012 (16 SNPs). Combining the epidemiological data with phylogenetic analysis results, we speculate that the patient may got infected in Nepal-India region.\n\nInvestigation of an imported cholera case in China with whole genome sequencing.", "token_count": 285, "char_count": 1053, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:35.161831", "source": { "split": "train_shard_00000", "doc_id": 2701 }, "chunk_id": "train_shard_00000_2701_0", "global_id": 2981 }, { "text": "In our previous studies, Lactobacillus plantarum Y44 showed antioxidant activity and favorable gastric and intestinal transit tolerance. In the current study, we investigated the physiological function of L. plantarum Y44 based on an analysis of its genotype and phenotype. The complete genome of L. plantarum Y44 contained a single circular chromosome of 3,255,555 bp, with a GC content of 44.6%, and a single circular plasmid of 51,167 bp, with a GC content of 38.8%. The L. plantarum Y44 genome contained 3,293 genes including 3,112 protein coding sequences, 16 rRNAs, 66 tRNAs, 4 small (s)RNAs, and 95 pseudo genes. Lactobacillus plantarum Y44 could metabolize 24 different carbohydrate sources. Nineteen complete phosphoenolpyruvate-dependent sugar phosphotransferase system complex genes and intact Embden-Meyerhof-Parnas pathway and hexose monophosphate pathway enzyme genes, as well as abundant carbohydrate active enzyme genes, were identified in the L. plantarum Y44 genome. We also identified genes related to the biosynthesis of exopolysaccharide and surface proteins. Surface proteins played an important role in the L. plantarum Y44 adhesion to HT-29 cell monolayers, as evidenced by the removal of cell surface proteins leading to decreased adhesion capacity. The L. plantarum Y44 genome contained genes encoding chaperones, intracellular proteases, and 2-component systems, which were associated with the general stress response. Genes encoding bile salt hydrolase, F\n\nPhysiological function analysis of Lactobacillus plantarum Y44 based on genotypic and phenotypic characteristics.", "token_count": 481, "char_count": 1598, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5778, "quality_score": 0.7889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:35.804413", "source": { "split": "train_shard_00000", "doc_id": 2702 }, "chunk_id": "train_shard_00000_2702_0", "global_id": 2982 }, { "text": "Antimicrobial use in livestock production is a driver for the development and proliferation of antimicrobial resistance (AMR). Wildlife interactions with livestock, acquiring associated AMR bacteria and genes, and wildlife's subsequent dispersal across the landscape are hypothesized to play an important role in the ecology of AMR. Here, we examined priority AMR phenotypes and genotypes of Escherichia coli isolated from the gastrointestinal tracts of European starlings (Sturnus vulgaris) found on concentrated animal feeding operations (CAFOs). European starlings may be present in high numbers on CAFOs (>100,000 birds), interact with urban environments, and can migrate distances exceeding 1,500 km in North America. In this study, 1,477 European starlings from 31 feedlots in five U.S. states were sampled for E. coli resistant to third generation cephalosporins (3G-C) and fluoroquinolones. The prevalence of 3G-C and fluoroquinolone-resistant E. coli was 4% and 10%, respectively. Multidrug resistance in the E. coli isolates collected (n = 236) was common, with the majority of isolates displaying resistance to six or more classes of antibiotics. Genetic analyses of a subset of these isolates identified 94 genes putatively contributing to AMR, including seven class A and C β-lactamases as well as mutations in gyrA and parC recognized to confer resistance to quinolones. Phylogenetic and subtyping assessments showed that highly similar isolates (≥99.4% shared core genome, ≥99.6% shared coding sequence) with priority AMR were found in birds on feedlots separated by distances exceeding 150 km, suggesting that European starlings could be involved in the interstate dissemination of priority AMR bacteria.", "token_count": 469, "char_count": 1720, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:36.450972", "source": { "split": "train_shard_00000", "doc_id": 2703 }, "chunk_id": "train_shard_00000_2703_0", "global_id": 2983 }, { "text": "The Role of European Starlings (Sturnus vulgaris) in the Dissemination of Multidrug-Resistant Escherichia coli among Concentrated Animal Feeding Operations.", "token_count": 44, "char_count": 156, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:36.810174", "source": { "split": "train_shard_00000", "doc_id": 2703 }, "chunk_id": "train_shard_00000_2703_1", "global_id": 2984 }, { "text": "It is widely reported how betaine addition regulates lipid metabolism but how betaine affects cholesterol metabolism is still unknown. This study aimed to investigate the role of betaine in hepatic cholesterol metabolism of Sprague-Dawley rats. Rats were randomly allocated to four groups and fed with a basal diet or a high-fat diet with or without 1% betaine. The experiment lasted 28 days. The results showed that dietary betaine supplementation reduced the feed intake of rats with final weight unchanged. Serum low-density-lipoprotein cholesterol was increased with the high-fat diet. The high-fat diet promoted cholesterol synthesis and excretion by enhancing the HMG-CoA reductase and ABCG5/G8, respectively, which lead to a balance of hepatic cholesterol. Rats in betaine groups showed a higher level of hepatic total cholesterol. Dietary betaine addition enhanced cholesterol synthesis as well as conversion of bile acid from cholesterol by increasing the levels of HMGCR and CYP7A1. The high-fat diet decreased the level of bile salt export pump, while dietary betaine addition inhibited this decrease and promoted bile acid efflux and increased total bile acid levels in the intestine. In summary, dietary betaine addition promoted hepatic cholesterol metabolism, including cholesterol synthesis, conversion of bile acids, and bile acid export.\n\nDietary Betaine Addition Promotes Hepatic Cholesterol Synthesis, Bile Acid Conversion, and Export in Rats.", "token_count": 388, "char_count": 1463, "word_count": 213, "semantic_coherence": 1, "information_density": 0.507, "quality_score": 0.7535, "entities": { "genes": [ "ABCG5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:37.428526", "source": { "split": "train_shard_00000", "doc_id": 2704 }, "chunk_id": "train_shard_00000_2704_0", "global_id": 2985 }, { "text": "Bile salts, including sodium deoxycholate (DOC), are secreted into the intestine to aid fat digestion and contribute to antimicrobial protection. Gram-negative pathogens such as Escherichia coli, however, are highly resistant to DOC, using multiple mechanisms of which the multidrug efflux pump AcrAB-TolC is the dominant one. Given that TolC-mediated efflux masks the interaction of DOC with potential targets, we sought to identify those targets by identifying genes whose mutations cause an increase in the MIC to DOC relative to the ∆tolC parental strain, that lacks TolC-associated functional efflux pumps. Using a mutant screen, we isolated twenty independent spontaneous mutants that had a higher MICDOC than the E. coli parental ∆tolC strain. Whole genome sequencing of these mutants mapped most mutations to the ptsI or cyaA gene. Analysis of knock-out mutants and complementation showed that elimination of PtsI, a component of the carbohydrate phosphotransferase system, or one of the two key proteins involved in cAMP synthesis and signaling, adenylate cyclase (CyaA) or cAMP receptor protein (Crp) causes low-level increased resistance of a ∆tolC E. coli strain to DOC.\n\nNovel mechanisms of TolC-independent decreased bile-salt susceptibility in Escherichia coli.", "token_count": 346, "char_count": 1276, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7166, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:37.998843", "source": { "split": "train_shard_00000", "doc_id": 2705 }, "chunk_id": "train_shard_00000_2705_0", "global_id": 2986 }, { "text": "Comparative Genomics, Pangenome, and Phylogenomic Analyses of", "token_count": 20, "char_count": 61, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:38.372201", "source": { "split": "train_shard_00000", "doc_id": 2706 }, "chunk_id": "train_shard_00000_2706_0", "global_id": 2987 }, { "text": "This study aimed to express an inulinase gene from the yeast Kluyveromyces marxianus (KmINU) in Aurantiochytrium sp. and realized one-step utilization of inulin resource for DHA production without any chemical pretreatment. An expression cassette with a length of 6052 bp for expressing the inulinase gene was constructed by a fast two-step PCR method and then was transferred into the Aurantiochytrium sp. cells. The Aurantiochytrium sp. recombinant T39 was selected with an inulinase activity up to 50.1 U/mL in 72 h. In a 5-l fed-batch fermentation, as high as 148.9 g/L of inulin was directly used within 120 h, and only 1.2 g/L of total sugar was left in the medium at the end of fermentation. The biomass of 51.4 g/L with a lipid content of 69.2% DCW and a DHA yield of 14.9 g/L was obtained.\n\nOne-step utilization of inulin for docosahexaenoic acid (DHA) production by recombinant Aurantiochytrium sp. carrying Kluyveromyces marxianus inulinase.", "token_count": 315, "char_count": 952, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6144, "quality_score": 0.8072, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:38.921632", "source": { "split": "train_shard_00000", "doc_id": 2707 }, "chunk_id": "train_shard_00000_2707_0", "global_id": 2988 }, { "text": "In the current batch study, lithium(I) ion sorption behaviors of Aspergillus versicolor fungus and newly isolated Kluyveromyces marxianus yeast were investigated comparatively. Surface and structural characterization studies of the biosorbents carried out with Fourier transform infrared spectrometer (FTIR), scanning electron microscope (SEM), surface area and zeta potential analyses showed that isolated K. marxianus yeast from salty wastes has more preferable properties (i.e. higher porosity, surface area and negativity) for cation sorption. Biosorption studies also supported this estimation; higher lithium(I) sorption capacities were obtained with K. marxianus cells at all experimental conditions studied. Rapid sorption profiles of the sorbents demonstrated that physical interaction is the main mechanism in this system. The effects of pH and initial lithium(I) concentration on the lithium(I) sorption capacities of biosorbents were examined. The maximum adsorption capacities of 347.9 and 409.2 μmol lithium(I)/g biosorbent were obtained at an initial lithium(I) concentration of 20 mg/L at pH 9.0 using A. versicolor and K. marxianus, respectively. The equilibrium data fitted both Langmuir and Freundlich models in the concentration ranges studied. This study revealed that K. marxianus yeast can be used for effective, rapid and low cost capture process of lithium(I) ions from aqueous solutions.\n\nA comparative investigation of lithium(I) biosorption properties of Aspergillus versicolor and Kluyveromyces marxianus.", "token_count": 403, "char_count": 1534, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:39.538030", "source": { "split": "train_shard_00000", "doc_id": 2708 }, "chunk_id": "train_shard_00000_2708_0", "global_id": 2989 }, { "text": "Intrahepatic cholestasis of pregnancy (ICP) is the most common hepatic disorder related to pregnancy in women. It usually develops within the third trimester of pregnancy and presents with pruritus as well as elevated levels of bile acid and/or alanine aminotransferase. Clinical signs quickly resolve after delivery; however, there is a high risk of the disorder recurring in subsequent pregnancies. ICP is associated with an increased risk of perinatal complications (premature birth, respiratory disorders, even stillbirth). Elevated levels of gestational hormones and genetic predispositions are important factors for the development of ICP; among the latter, mutations in hepatobiliary transport proteins (multidrug resistance protein 3-MDR3, bile salt export pump- BSEP) play a major role. Clinical and biochemical symptoms of ICP include pruritus and increased levels of total bile acids (TBA). Serum levels of TBA should be monitored in ICP patients throughout the pregnancy as concentrations above 40 μmol/L, which define that severe ICP isassociated with an increased risk of fetal complications. Therapeutic management is aimed at reducing the clinical symptoms, normalizing maternal biochemistry and preventing complications to the fetus. Pharmacological treatment of intrahepatic cholestasis of pregnancy consists of the administration of ursodeoxycholic acid to lower the levels of TBA and possibly reduce pruritus. If the treatment fails, premature delivery should be considered.\n\nIntrahepatic Cholestasis in Pregnancy: Review of the Literature.", "token_count": 382, "char_count": 1560, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [ "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:40.117426", "source": { "split": "train_shard_00000", "doc_id": 2709 }, "chunk_id": "train_shard_00000_2709_0", "global_id": 2990 }, { "text": "Tenacibaculum maritimum is responsible for tenacibaculosis, a devastating marine fish disease. This filamentous bacterium displays a very broad host range and a worldwide geographical distribution. We analyzed and compared the genomes of 25 T. maritimum strains, including 22 newly draft-sequenced genomes from isolates selected based on available MLST data, geographical origin and host fish. The genome size (~3.356 Mb in average) of all strains is very similar. The core genome is composed of 2116 protein-coding genes accounting for ~75% of the genes in each genome. These conserved regions harbor a moderate level of nucleotide diversity (~0.0071 bp\n\nGenetic diversity and population structure of Tenacibaculum maritimum, a serious bacterial pathogen of marine fish: from genome comparisons to high throughput MALDI-TOF typing.", "token_count": 220, "char_count": 832, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:40.581382", "source": { "split": "train_shard_00000", "doc_id": 2710 }, "chunk_id": "train_shard_00000_2710_0", "global_id": 2991 }, { "text": "Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of Bordetella pertussis has been reported as one of the contributing factors for the resurgence of the disease. Our current knowledge of B. pertussis genetic evolution in circulating strains is mostly based on studies conducted in countries using ACVs targeting only a few antigens used in the production of ACVs. To better understand the adaptation to vaccine-induced selection pressure, it will be essential to study B. pertussis populations in developing countries which are using WCVs. India is a significant user and global supplier of WCVs. We report here comparative genome analyses of vaccine and clinical isolates reported from India. Whole-genome sequences obtained from vaccine strains: WCV (J445, J446, J447 and J448), ACV (BP165) were compared with Tohama-I reference strain and recently reported clinical isolates from India (BPD1, BPD2). Core genome-based phylogenetic analysis was also performed using 166 isolates reported from countries using ACV.\n\nComparative genomics of whole-cell pertussis vaccine strains from India.", "token_count": 304, "char_count": 1228, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [ "BPD2", "BP165", "BPD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:41.197006", "source": { "split": "train_shard_00000", "doc_id": 2711 }, "chunk_id": "train_shard_00000_2711_0", "global_id": 2992 }, { "text": "Extracellular membrane vesicles are produced by all domains of life (bacteria, archaea and eukaryotes). Bacterial extracellular vesicles (outer membrane vesicles or OMVs) are produced by outer membrane blebbing, and contain proteins, nucleic acids, virulence factors, lipids and metabolites. OMV functions depend on their internal composition, therefore understanding the proteome of OMVs, and how it varies between organisms, is imperative. Here, we report a comparative proteomic profiling of OMVs from strains of Myxococcus xanthus, a predatory species of Gram-negative myxobacteria whose secretions include secondary metabolites and hydrolytic enzymes, thought to be involved in prey lysis. Ten strains were chosen for study, of which seven had genome sequences available. The remaining three strains were genome sequenced allowing definition of the core and accessory genes and genome-derived proteins found within the pan-genome and pan-proteome respectively. OMVs were isolated from each strain and proteins identified using mass spectrometry. The M. xanthus OMV pan-proteome was found to contain tens of 'core' and hundreds of 'accessory' proteins. Properties of the OMV pan-proteome were compared with those of the pan-proteome deduced from the M. xanthus pan-genome. On average, 80% of 'core' OMV proteins are encoded by genes of the core genome, yet the OMV proteomes of individual strains contain subsets of core genome-derived proteins which only partially overlap. In addition, the distribution of characteristics of vesicle proteins does not correlate with the genome-derived proteome characteristic distribution. We hypothesize that M. xanthus cells package a personalized subset of proteins whose availability is only partially dictated by the presence/absence of encoding genes within the genome.\n\nWithin-species variation in OMV cargo proteins: the Myxococcus xanthus OMV pan-proteome.", "token_count": 485, "char_count": 1904, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:41.865967", "source": { "split": "train_shard_00000", "doc_id": 2712 }, "chunk_id": "train_shard_00000_2712_0", "global_id": 2993 }, { "text": "The microbiome provides resistance to infection. However, the underlying mechanisms are poorly understood. We demonstrate that colonization with the intestinal bacterium Clostridium scindens protects from Entamoeba histolytica colitis via innate immunity. Introduction of C. scindens into the gut microbiota epigenetically altered and expanded bone marrow granulocyte-monocyte progenitors (GMPs) and resulted in increased intestinal neutrophils with subsequent challenge with E. histolytica. Introduction of C. scindens alone was sufficient to expand GMPs in gnotobiotic mice. Adoptive transfer of bone marrow from C. scindens-colonized mice into naive mice protected against amebic colitis and increased intestinal neutrophils. Children without E. histolytica diarrhea also had a higher abundance of Lachnoclostridia. Lachnoclostridia C. scindens can metabolize the bile salt cholate, so we measured deoxycholate and discovered that it was increased in the sera of C. scindens-colonized specific pathogen-free and gnotobiotic mice, as well as in children protected from amebiasis. Administration of deoxycholate alone increased GMPs and provided protection from amebiasis. We elucidated a mechanism by which C. scindens and the microbially metabolized bile salt deoxycholic acid alter hematopoietic precursors and provide innate protection from later infection with E. histolytica.\n\nGut microbiome communication with bone marrow regulates susceptibility to amebiasis.", "token_count": 378, "char_count": 1468, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:42.505790", "source": { "split": "train_shard_00000", "doc_id": 2713 }, "chunk_id": "train_shard_00000_2713_0", "global_id": 2994 }, { "text": "We report here the draft genome sequence of a\n\nDraft Genome Sequence of a Listeria monocytogenes Isolate of Core Genome Multilocus Sequence Typing Complex Type 2521 from Ready-to-Eat Meat Sausage Related to an Outbreak (Sigma1) in Germany.", "token_count": 73, "char_count": 239, "word_count": 37, "semantic_coherence": 1, "information_density": 0.7838, "quality_score": 0.8919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:42.932782", "source": { "split": "train_shard_00000", "doc_id": 2714 }, "chunk_id": "train_shard_00000_2714_0", "global_id": 2995 }, { "text": "A novel two-stage fermentation strategy was applied to produce xylitol and ethanol from the whole acid-pretreated corn cob slurry. The acid-pretreated corn cob was used without filtration and detoxification by the two-stage fermentation with the robust Kluyveromyces marxianus CICC 1727-5. In the first stage, xylose in the slurry after dilute acid pretreatment of lignocellulosic biomass was used to produce xylitol under micro-aeration conditions. In the second stage, simultaneous saccharification fermentation was carried out, and the ethanol was produced from glucose releasing from the solid. Important parameters, such as aeration rate, cellulase loading during xylose utilization and SSF fermentation were studied for best performance. The two-stage fermentation strategy removed the inhibition of glucose on xylose, and little xylose was left in the fermentation broth. Under the optimized condition, the maximum ethanol and xylitol concentration were 52 g/L and 24.2 g/L corresponding to the yield of 0.41 g/g and 0.82 g/g, respectively.\n\nProduction of bioethanol and xylitol from non-detoxified corn cob via a two-stage fermentation strategy.", "token_count": 319, "char_count": 1153, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5854, "quality_score": 0.7927, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:43.501226", "source": { "split": "train_shard_00000", "doc_id": 2715 }, "chunk_id": "train_shard_00000_2715_0", "global_id": 2996 }, { "text": "Whole genome sequencing (WGS) was performed on 201 Listeria monocytogenes isolates recovered from 102 of 27,389 refrigerated ready-to-eat (RTE) food samples purchased at retail in U.S. FoodNet sites as part of the 2010-2013 interagency L. monocytogenes Market Basket Survey (Lm MBS). Core genome multi-locus sequence typing (cgMLST) and in-silico analyses were conducted, and these data were analyzed with metadata for isolates from five food groups: produce, seafood, dairy, meat, and combination foods. Six of 201 isolates, from 3 samples, were subsequently confirmed as L. welshimeri. Three samples contained one isolate per sample; mmong the 96 samples that contained two isolates per sample, 3 samples each contained two different strains and 93 samples each contained duplicate isolates. After 93 duplicate isolates were removed, the remaining 102 isolates were delineated into 29 clonal complexes (CCs) or singletons based on their sequence type. The five most prevalent CCs were CC155, CC1, CC5, CC87, and CC321. The Shannon's diversity index for clones per food group ranged from 1.49 for dairy to 2.32 for produce isolates, which were not significantly different in pairwise comparisons. The most common molecular serogroup as determined by in-silico analysis was IIa (45.6%), followed by IIb (27.2%), IVb (20.4%), and IIc (4.9%). The proportions of isolates within lineages I, II, and III were 48.0%, 50.0% and 2.0%, respectively. Full-length inlA was present in 89.3% of isolates. Listeria pathogenicity island 3 (LIPI-3) and LIPI-4 were found in 51% and 30.6% of lineage I isolates, respectively", "token_count": 493, "char_count": 1608, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6749, "quality_score": 0.8374, "entities": { "genes": [ "CC5", "CC321", "CC155", "CC1", "CC87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:44.155886", "source": { "split": "train_shard_00000", "doc_id": 2716 }, "chunk_id": "train_shard_00000_2716_0", "global_id": 2997 }, { "text": "Stress survival islet 1 (SSI-1) was present in 34.7% of lineage I isolates, 80.4% of lineage II isolates and the 2 lineage III isolates; SSI-2 was present only in the CC121 isolate. Plasmids were found in 48% of isolates, including 24.5% of lineage I isolates and 72.5% of lineage II isolates. Among the plasmid-carrying isolates, 100% contained at least one cadmium resistance cassette and 89.8% contained bcrABC, involved in quaternary ammonium compound tolerance. Multiple clusters of isolates from different food samples were identified by cgMLST which, along with available metadata, could aid in the investigation of possible cross-contamination and persistence events.\n\nGenetic diversity and profiles of genes associated with virulence and stress resistance among isolates from the 2010-2013 interagency Listeria monocytogenes market basket survey.", "token_count": 247, "char_count": 855, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "CC121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:44.644801", "source": { "split": "train_shard_00000", "doc_id": 2716 }, "chunk_id": "train_shard_00000_2716_1", "global_id": 2998 }, { "text": "We investigated the prognostic significance of Nudix hydrolase 1 (NUDT1) in hepatocellular carcinoma (HCC). NUDT1 mRNA and protein levels were significantly higher in HCC tissues than normal liver tissues. The level of NUDT1 expression correlated with tumor grade, stage, size, differentiation, degree of vascular invasion, overall survival (OS), and disease-free survival (DFS) in HCC patients. Multivariate analysis showed that NUDT1 expression was an independent prognostic factor for OS and DFS in HCC patients. We constructed a prognostic nomogram with NUDT1 expression, AFP levels, vascular invasion, Child-Pugh classification, age, sex, AJCC staging, and tumor differentiation as variables. This nomogram was highly accurate in predicting the 5-year OS of HCC patients (c-index= 0.709; AUC= 0.740). NUDT1 silencing in HCC cells significantly reduced their survival, colony formation, migration, and invasiveness. Gene set enrichment analysis showed that biological pathways related to cell cycle, fatty acid metabolism, bile acid and bile salt metabolism, and PLK1 signaling were associated with NUDT1, as were the gene ontology terms \"DNA binding transcription activator activity,\" \"RNA polymerase II,\" \"nuclear division,\" and \"transmembrane transporter activity.\" Our study thus demonstrates that NUDT1 is a prognostic biomarker with therapeutic potential in HCC patients.\n\nNudix hydrolase 1 is a prognostic biomarker in hepatocellular carcinoma.", "token_count": 398, "char_count": 1455, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8308, "entities": { "genes": [ "NUDT1", "PLK1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:45.274449", "source": { "split": "train_shard_00000", "doc_id": 2717 }, "chunk_id": "train_shard_00000_2717_0", "global_id": 2999 }, { "text": "In this study, 53 Staphylococcus (S.) aureus strains were typed by 16S-23S rDNA intergenic spacer region (ISR) typing and staphylococcal enterotoxin gene (SEg) typing for all the staphylococcal enterotoxin (se) and staphylococcal enterotoxin-like toxin (sel) genes known to date, revealing a higher discriminatory power than that of multi locus sequence typing. Six strains, one of each ISR- and SEg-type, were genome sequenced and the ability to produce some classical and new SEs when growing in milk was investigated. The manual analysis of the six genomes allowed us to confirm, correct and expand the results of common available genomic data pipelines such as VirulenceFinder. Moreover, it enabled us to (i) investigate the actual location of se and sel genes, even for genes such as selY, whose location (in the core genome) was so far unknown, (ii) find novel allelic variants of se and sel genes and pseudogenes, (iii) correctly annotate se and sel genes and pseudogenes, and (iv) discover a novel type of enterotoxin gene cluster (egc), i.e. the egc type 5 in strains 356P and 364P, while S. argenteus MSHR1132 harbored the egc type 6. Four of the six S. aureus strains produced sufficient amounts of SEA, SEC, SED and SEH in milk to cause staphylococcal food poisoning (SFP), with S. aureus 372 P being the highest producer of SED in milk found to date, producing as much as ca. 47,300 ng/mL and 49,200 ng/mL of SED, after 24 and 48 h of incubation in milk at 37 °C, respectively. S. aureus 372 P released a low amount of SER in milk, most likely because the seR gene was present as a pseudogene, putatively encoding only 51 amino acids", "token_count": 507, "char_count": 1646, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6344, "quality_score": 0.8172, "entities": { "genes": [ "MSHR1132" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:46.610635", "source": { "split": "train_shard_00000", "doc_id": 2718 }, "chunk_id": "train_shard_00000_2718_0", "global_id": 3000 }, { "text": "These findings confirm that not only the classical SEs, but also the new ones can represent a potential hazard for the consumers' health if produced in foods in sufficient amounts. Therefore, the detection of SEs in foods, especially if involved in SFP cases, should focus not only on classical, but also on all the new SEs and SEls known to date. Where reference methods are unavailable, the presence of the relevant genes, by using the conventional and real time PCR protocols we exhaustively provided herein, and their nucleotide sequences, should be investigated.\n\nNovel insights into the enterotoxigenic potential and genomic background of Staphylococcus aureus isolated from raw milk.", "token_count": 151, "char_count": 690, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:47.039763", "source": { "split": "train_shard_00000", "doc_id": 2718 }, "chunk_id": "train_shard_00000_2718_1", "global_id": 3001 }, { "text": "A recently reported approach to nanocrystallise encapsulated ciprofloxacin within liposomes has generated increased interest in the solid-state properties of drug nanocrystals within liposomal confinement. To explore the potential application of nanocrystallised drug liposomes in oral delivery, a liposomal ciprofloxacin formulation was used as a model system. An in vitro digestion model coupled to small angle X-ray scattering was used to analyse the solid-state properties of the drug nanocrystals during digestion of the liposomal ciprofloxacin nanocrystal formulations. Results showed a complete polymorphic transformation of the ciprofloxacin hydrate nanocrystals to a new salt form at a threshold sodium taurodeoxycholate to ciprofloxacin molar ratio of 0.6. The in vitro drug release from the nanocrystallised drug containing liposomes showed controlled drug release behaviour under non-digestive conditions, while a 3.5-fold increase in the drug release was seen when they were exposed to the simulated digestive environment. In conclusion, the solid state of the drug inside the liposomes is important in dictating the drug release behaviour from the liposomes. The identification of the solid state transformation during digestion in real time and the bile salt-induced polymorphic transformation of ciprofloxacin from nanocrystallised ciprofloxacin liposome are important to understand how the drug is released in vivo, as well as for future formulation design.\n\nExposure of liposomes containing nanocrystallised ciprofloxacin to digestive media induces solid-state transformation and altered in vitro drug release.", "token_count": 417, "char_count": 1628, "word_count": 223, "semantic_coherence": 1, "information_density": 0.4978, "quality_score": 0.7489, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:47.663864", "source": { "split": "train_shard_00000", "doc_id": 2719 }, "chunk_id": "train_shard_00000_2719_0", "global_id": 3002 }, { "text": "Current problem of antibiotic resistance and the high incidence of bacterial diseases has brought huge losses to the yak breeding industry in Tibet. Therefore, the purpose of this study was to isolate Lactobacillus with safety and beneficial probiotic potential for the prophylaxis of intestinal diseases in yaks. After 16S rDNA sequence, four strains i.e. Lactobacillus sakei (named L4), Enterococcus hirae (named E5), Pediococcus acidilactici (named P7), Weissella confusa (named W8) were isolated from feces of yaks. The results of tolerance to acid, bile salt, enzyme and temperature showed that P7 was highly tolerant to acid, bile salt and digestive enzyme, while E5 was more resistant to temperature. The antibacterial assay showed L4 had a strong inhibitory effect against Staphylococcus aureus (BNCC186335), and E5, P7, W8 had effective antibacterial ability against Escherichia coli (C83902). In addition, L4, E5, P7 and W8 mainly produced organic acids and bacteriocin production to inhibit common intestinal pathogens. The results of antibiotic susceptibility assay indicated that L4, E5, P7 and W8 were highly sensitive to most clinically used antibiotics and didn't contain the VanA and VanB genes on the basis of PCR amplification, and L4, E5, P7 and W8 didn't exhibit hemolytic activity. The animal toxicity experiment results showed that no obvious pathological change was found in intestinal tissue sections, and L4, E5 and W8 strains also promoted the growth performance of mice, consequently, the L4, E5, P7 and W8 had no toxic effect on mice. In conclusion, lactobacillus isolated from feces of yaks not only have potential probiotics and strong antibacterial ability in vitro, but also are safe. Therefore, they have the potential to reduce the occurrence of bacterial diseases as new feed additives.", "token_count": 494, "char_count": 1822, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [ "BNCC186335" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:48.321699", "source": { "split": "train_shard_00000", "doc_id": 2720 }, "chunk_id": "train_shard_00000_2720_0", "global_id": 3003 }, { "text": "Probiotic potential and safety assessment of Lactobacillus isolated from yaks.", "token_count": 19, "char_count": 78, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:48.678118", "source": { "split": "train_shard_00000", "doc_id": 2720 }, "chunk_id": "train_shard_00000_2720_1", "global_id": 3004 }, { "text": "Bile acid metabolism by the gut microbiome exerts both beneficial and harmful effects on host health. Microbial bile salt hydrolases (BSHs), which initiate bile acid metabolism, exhibit both positive and negative effects on host physiology. In this study, 5,790 BSH homologs were collected and classified into seven clusters based on a sequence similarity network. Next, the abundance and distribution of BSH in 380 metagenomes from healthy participants were analyzed. It was observed that different clusters occupied diverse ecological niches in the human microbiome and that the clusters with signal peptides were relatively abundant in the gut. Then, the association between BSH clusters and 12 human diseases was analyzed by comparing the abundances of BSH genes in patients (\n\nMetagenomic analysis of the human microbiome reveals the association between the abundance of gut bile salt hydrolases and host health.", "token_count": 205, "char_count": 917, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:49.136617", "source": { "split": "train_shard_00000", "doc_id": 2721 }, "chunk_id": "train_shard_00000_2721_0", "global_id": 3005 }, { "text": "Recently, biotechnological opportunities have been found in non-Saccharomyces yeasts because they possess metabolic characteristics that lead to the production of compounds of interest. It has been observed that Kluyveromyces marxianus has a great potential in the production of esters, which are aromatic compounds of industrial importance. The genetic bases that govern the synthesis of esters include a large group of enzymes, among which the most important are alcohol acetyl transferases (AATases) and esterases (AEATases), and it is known that some are present in K. marxianus, because it has genetic characteristics like S. cerevisiae. It also has a physiology suitable for biotechnological use since it is the eukaryotic microorganism with the fastest growth rate and has a wide range of thermotolerance with respect to other yeasts. In this work, the enzymatic background of K. marxianus involved in the synthesis of esters is analyzed, based on the sequences reported in the NCBI database.\n\nStudy of the Enzymatic Capacity of Kluyveromyces marxianus for the Synthesis of Esters.", "token_count": 263, "char_count": 1088, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:49.687603", "source": { "split": "train_shard_00000", "doc_id": 2722 }, "chunk_id": "train_shard_00000_2722_0", "global_id": 3006 }, { "text": "Lactobacillus plantarum EM is a probiotic strain with antimicrobial activity, cholesterol-lowering effects, and tolerance to acid and bile. To understand the genetic basis of the probiotic characteristics of this strain, genome sequencing and probiotic-related genetic analysis were performed. The genomic characteristics of L. plantarum EM were confirmed by comparative genomic analysis with 41 probiotic lactic acid bacteria, including 10 L. plantarum strains. L. plantarum EM was shown to contain a circular chromosome of 3,184,808 bp and eight plasmids with various lengths from 5,027 to 76,369 bp. The L. plantarum EM genome had a total of 3560 protein-coding genes, including probiotic-related genes, such as tolerance to acid and bile, temperature stress, and oxidative stress. Comparative genomic analysis showed that L. plantarum EM contained plantaricin and bovicin gene clusters, which are related to antimicrobial activity, and five bile salt hydrolase genes related to serum cholesterol-lowering effects. The genomic analysis confirmed the probiotic properties of L. plantarum EM, and our results indicated that this strain has potential application for use as an industrially important probiotic.\n\nComplete Genome Sequence of Lactobacillus plantarum EM, A Putative Probiotic Strain with the Cholesterol-Lowering Effect and Antimicrobial Activity.", "token_count": 362, "char_count": 1360, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5526, "quality_score": 0.7763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:50.267298", "source": { "split": "train_shard_00000", "doc_id": 2723 }, "chunk_id": "train_shard_00000_2723_0", "global_id": 3007 }, { "text": "The sodium taurocholate cotransporting polypeptide (NTCP) is expressed at the basolateral membrane of hepatocytes, where it mediates the uptake of conjugated bile acids and forms the hepatocyte entry receptor for the hepatitis B and D virus. Here, we aimed to identify novel protein-protein interactions that could play a role in the regulation of NTCP. To this end, NTCP was precipitated from HA-tagged hNTCP-expressing HepG2 cells, and chloride channel CLIC-like 1 (CLCC1) and stomatin were identified as interacting proteins by mass spectrometry. Interaction was confirmed by co-immunoprecipitation. NTCP, CLCC1 and stomatin were found at the plasma membrane in lipid rafts, as demonstrated by a combination of immunofluorescence, cell surface biotinylation and isolation of detergent-resistant membranes. Neither CLCC1 overexpression nor its knockdown had an effect on NTCP function. However, both stomatin overexpression and knockdown increased NTCP-mediated taurocholate uptake while NTCP abundance at the plasma membrane was only increased in stomatin depleted cells. These findings identify stomatin as an interactor of NTCP and show that the interaction modulates bile salt transport.\n\nThe Lipid Raft Component Stomatin Interacts with the Na", "token_count": 323, "char_count": 1250, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8362, "entities": { "genes": [ "CLCC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:50.836270", "source": { "split": "train_shard_00000", "doc_id": 2724 }, "chunk_id": "train_shard_00000_2724_0", "global_id": 3008 }, { "text": "It is of interest to describe the distinctive features gleaned from the comparative genome analysis of clinical and non-clinical isolates of Klebsiella pneumoniae. The core genome of K. pneumoinae consisted of 3568 genes. Comparative genome analysis shows that mdtABCD, toxin-antitoxin systems are unique to clinical isolates and catB, benA, and transporter genes for citrate utilization are exclusive to non-clinical isolates. We further noted aromatic compound degrading genes in non-clinical isolates unlike in the later isolates. We grouped 88 core genes into 3 groups linked to infections, drug-resistance or xenobiotic metabolism using codon usage variation analysis. It is inferred using the neutrality plot analysis of GC12 with GC3 that codon usage variation is dominant over mutation pressure. Thus, we document data to distinguish clinical and non-clinical isolates of K. pneumoniae using comparative genomes analysis for understanding of genome diversity during speciation.\n\nDistinctive features gleaned from the comparative genomes analysis of clinical and non-clinical isolates of Klebsiella pneumoniae.", "token_count": 279, "char_count": 1117, "word_count": 156, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [ "GC3", "GC12" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:51.395252", "source": { "split": "train_shard_00000", "doc_id": 2725 }, "chunk_id": "train_shard_00000_2725_0", "global_id": 3009 }, { "text": "Nonconventional yeast Candida famata and Ogataea polymorpha are interesting organisms for basic and applied studies. O. polymorpha is methylotrophic thermotolerant yeast capable of xylose alcoholic fermentation whereas C. famata is capable of riboflavin overproduction. Still, the new tools for molecular research of these species are needed. The aim of this study was to develop the new dominant selective markers for C. famata and O. polymorpha usable in metabolic engineering experiments. In this work, the BSD gene from Aspergillus terreus coding for blasticidin S deaminase, O. polymorpha AUR1 gene required for sphingolipid synthesis and IMH3 gene, which encodes IMP dehydrogenase, were tested as the new dominant selective marker genes. Our results showed that AUR1 and IMH3 genes could be used as dominant selective markers for O. polymorpha with frequencies of transformation of 40 and 20 transformants per microgram of DNA, respectively. The IMH3 gene was successfully used as the marker for construction of O. polymorpha strains with increased ethanol production from xylose due to overexpression of TAL1, TKL1 and AOX1 genes. The BSD gene from A. terreus, conferring resistance to blasticidin, was found to be efficient for selection of C. famata transformants.\n\nDevelopment of new dominant selectable markers for the nonconventional yeasts Ogataea polymorpha and Candida famata.", "token_count": 365, "char_count": 1391, "word_count": 206, "semantic_coherence": 1, "information_density": 0.568, "quality_score": 0.784, "entities": { "genes": [ "TKL1", "IMH3", "AOX1", "TAL1", "AUR1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:51.976835", "source": { "split": "train_shard_00000", "doc_id": 2726 }, "chunk_id": "train_shard_00000_2726_0", "global_id": 3010 }, { "text": "The increasing number of Chromobacterium haemolyticum human infection reports, especially in tropical regions and connected with environmental sources, resulted in an urge to better describe this species. This study aimed to characterize the C. haemolyticum resistome, virulence determinants and genetic platforms related with genome plasticity. A comparative genomic analysis was conducted between clinical C. haemolyticum genomes publicly available and the genome of an environmental isolate obtained in this study. The pangenome of C. haemolyticum was calculated and a total of 3378 core genes were predicted in its core genome, corresponding to 51.7% of the pangenome. Genetic determinants putatively encoding resistance to beta-lactams, fosfomycin, aminoglycosides and trimethoprim were predicted in all genomes, possibly constituting the intrinsic resistome of this species. In terms of resistance to beta-lactams, 4 genes were predicted encoding beta-lactamases of classes A, C and D. Moreover, the analysis of Chromobacterium genomes and C. haemolyticum environmental isolates reinforced the role of this genus as progenitor of the bla\n\nGenomic analysis of Chromobacterium haemolyticum: insights into the species resistome, virulence determinants and genome plasticity.", "token_count": 313, "char_count": 1277, "word_count": 174, "semantic_coherence": 1, "information_density": 0.5575, "quality_score": 0.7787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:52.538668", "source": { "split": "train_shard_00000", "doc_id": 2727 }, "chunk_id": "train_shard_00000_2727_0", "global_id": 3011 }, { "text": "This study aimed to investigate the bile salt-stimulated lipase (BSSL) concentration in the milk of Chinese women and its correlation with maternal body mass index (BMI), gestational diabetes mellitus (GDM) and gestational hypertensive disorder (GHD). The BSSL levels in the milk samples were measured by enzyme-linked immunosorbent assay (ELISA). BSSL level in colostrum milk of mothers with full-term infants was positively correlated with pregnancy week and negatively correlated with maternal pre-pregnancy BMI and BMI late in pregnancy. Moreover, the BSSL concentration in mature milk was positively correlated with BMI gain during pregnancy. The BSSL concentration in colostrum milk was lower in GDM mothers than in normal mothers. The BSSL helps infants digest fat in early life and its level was associated with lactation. The changes in BSSL characteristics with maternal BMI and GDM in this study may have clinical implications regarding the effects of pregnancy weight and metabolism on the nutrition and health of the offspring.\n\nThe level of bile salt-stimulated lipase in the milk of Chinese women and its association with maternal BMI.", "token_count": 268, "char_count": 1150, "word_count": 174, "semantic_coherence": 1, "information_density": 0.5115, "quality_score": 0.7557, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:53.109619", "source": { "split": "train_shard_00000", "doc_id": 2728 }, "chunk_id": "train_shard_00000_2728_0", "global_id": 3012 }, { "text": "Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe. In this context, we sought to characterize at the population level the Brettanomyces bruxellensis yeast species, which is a major cause of wine spoilage and can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions, whereas aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared with S. cerevisiae. The pangenome is composed of 5,409 ORFs (open reading frames) among which 5,106 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.\n\nHigh Complexity and Degree of Genetic Variation in Brettanomyces bruxellensis Population.", "token_count": 407, "char_count": 1742, "word_count": 250, "semantic_coherence": 1, "information_density": 0.612, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:53.751007", "source": { "split": "train_shard_00000", "doc_id": 2729 }, "chunk_id": "train_shard_00000_2729_0", "global_id": 3013 }, { "text": "Inflammation is a major risk factor of morbidity and mortality in older adults. Although its precise etiology is unknown, low-grade inflammation in older adults is commonly associated with increased intestinal epithelial permeability (leaky gut) and abnormal (dysbiotic) gut microbiota. The increasing older population and lack of treatments to reduce aging-related microbiota dysbiosis, leaky gut, and inflammation culminates in a rise in aging-related comorbidities, constituting a significant public health concern. Here, we demonstrate that a human-origin probiotic cocktail containing 5 Lactobacillus and 5 Enterococcus strains isolated from healthy infant gut prevented high-fat diet-induced (HFD-induced) microbiota dysbiosis, leaky gut, inflammation, metabolic dysfunctions, and physical function decline in older mice. Probiotic-modulated gut microbiota primarily reduced leaky gut by increasing tight junctions, which in turn reduced inflammation. Mechanistically, probiotics modulated microbiota in a way to increase bile salt hydrolase activity, which in turn increased taurine abundance in the gut that stimulated tight junctions and suppressed gut leakiness. Furthermore, in Caenorhabditis elegans, taurine increased life span, reduced adiposity and leaky gut, and enhanced physical function. The results suggest that such probiotic therapies could prevent or treat aging-related leaky gut and inflammation in the elderly.\n\nA human-origin probiotic cocktail ameliorates aging-related leaky gut and inflammation via modulating the microbiota/taurine/tight junction axis.", "token_count": 390, "char_count": 1583, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:54.395538", "source": { "split": "train_shard_00000", "doc_id": 2730 }, "chunk_id": "train_shard_00000_2730_0", "global_id": 3014 }, { "text": "Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus\n\nSelection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus", "token_count": 126, "char_count": 518, "word_count": 76, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:54.825419", "source": { "split": "train_shard_00000", "doc_id": 2731 }, "chunk_id": "train_shard_00000_2731_0", "global_id": 3015 }, { "text": "Next-generation sequencing to elucidate adaptive stress response and plantaricin genes among", "token_count": 22, "char_count": 92, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:55.220823", "source": { "split": "train_shard_00000", "doc_id": 2732 }, "chunk_id": "train_shard_00000_2732_0", "global_id": 3016 }, { "text": "Cholera is an endemic disease in many regions of Asia including, Pakistan. Vibrio cholerae, the causative agent of cholera, is considered as one of the best adapted bacteria due to its ability to withstand severe environmental stresses. The V. cholerae genome is very plastic with many gene additions and deletions. In this study, we sought to understand the diversity of V. cholerae genes in two Pakistani subclades [e.g. Pakistani subclade I (PSC I) and Pakistani subclade II (PSC II)]. We have analyzed 44 PSC I and 56 PSC II strains, respectively. By analyzing our data, it was concluded that subclade group 2 (PSC II) has 2967 core genes repositories, while the PSC 1 group has just 1062 core genes. It was observed that the pangenome in the PSC II group is open while the pan-genome in PSC I are closed. It was also noted that the number of accessory genes (n = 2500) is higher in the PSC I group compared to the PSC II group (n = 550). Furthermore, analysis extended to the study of unique gene profiles suggested that all strains of the PSC II group have unique genes. One strain among the PSC II group had a high number of unique genes (n = 2612). However, in the PSC I group, only a few strains had unique genes with a maximum of 86 unique genes being found in a single strain. Core phylogeny of PSC I indicated that just three groups initially arose from a single common ancestor. At the same time, a complex pattern of evolution was found in the PSC II phylogenetic tree based on core gene information. This comparative genomic analysis has revealed 'waves' of V. cholerae evolution and information on its transmission and ability to modify its genetic content to survive in different environmental conditions. Here, we have investigated how the versatility of V. cholerae, a bacterium that persists across different habitats, is reflected in its genome. The data generated during the study should be extremely beneficial in defining the evolutionary relationship as well as diversity between V. cholerae subclades", "token_count": 520, "char_count": 2026, "word_count": 347, "semantic_coherence": 1, "information_density": 0.5216, "quality_score": 0.7608, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:25:55.852336", "source": { "split": "train_shard_00000", "doc_id": 2733 }, "chunk_id": "train_shard_00000_2733_0", "global_id": 3017 }, { "text": "It will also benefit epidemiological studies and the design of better treatment strategies for controlling epidemics.\n\nComparative core/pan genome analysis of Vibrio cholerae isolates from Pakistan.", "token_count": 44, "char_count": 198, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:56.221694", "source": { "split": "train_shard_00000", "doc_id": 2733 }, "chunk_id": "train_shard_00000_2733_1", "global_id": 3018 }, { "text": "Present study is intended to assess the probiotic properties of Bacillus spp. isolated from idli batter, a traditional fermented food of Southern India and Sri Lanka. A total of 32 isolates were screened for potential pathogenic behaviour through haemolysis assay, DNase activity and antibiotics sensitivity. Two of the isolates were found to be potentially safe and identified as Bacillus spp. These strains were characterized for in vitro probiotic attributes and antioxidant activity. Both the strains showed strong acid and bile tolerance, transit tolerance, lysozyme tolerance, cell surface hydrophobicity, auto-aggregation, co-aggregation, biofilm formation potential and adhesion to human colon adenocarcinoma (HT 29) cell line demonstrating potential probiotic ability. These strains also exhibited considerable cholesterol binding, thermostability, β-galactosidase production, proteolytic, amylolytic and lipolytic activity. Cell-free supernatant inhibited the biofilm formation by Pseudomonas aeruginosa (KT266804) to 90%. Intact cells showed significant DPPH (41%), hydroxyl (31%), radical scavenging activity and lipid peroxidation inhibition (20.38%), while cell-free extracts exhibited significant superoxide anion radical scavenging activity (16.25%). Results revealed that isolates could be potential probiotic candidate after further assessment of in vivo probiotic properties and safety evaluation and could be utilised as starter cultures in functional foods.\n\nProbiotic Potential of Bacillus Strains Isolated from an Acidic Fermented Food Idli.", "token_count": 407, "char_count": 1564, "word_count": 203, "semantic_coherence": 1, "information_density": 0.67, "quality_score": 0.835, "entities": { "genes": [ "KT266804" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:56.839915", "source": { "split": "train_shard_00000", "doc_id": 2734 }, "chunk_id": "train_shard_00000_2734_0", "global_id": 3019 }, { "text": "Crucial Role of the Accessory Genome in the Evolutionary Trajectory of", "token_count": 18, "char_count": 70, "word_count": 11, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:57.205920", "source": { "split": "train_shard_00000", "doc_id": 2735 }, "chunk_id": "train_shard_00000_2735_0", "global_id": 3020 }, { "text": "Beyond the Core Genome: Tracking Plasmids in Outbreaks of Multidrug-resistant Bacteria.", "token_count": 26, "char_count": 87, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:57.565187", "source": { "split": "train_shard_00000", "doc_id": 2736 }, "chunk_id": "train_shard_00000_2736_0", "global_id": 3021 }, { "text": "The self-assembly of pharmaceutical amphiphiles is an important area of research because of the involvement of these amphiphiles in physiological processes. The mixed micellization behavior of antipsychotic drug (chlorpromazine hydrochloride, CPZ) in the presence of bile salt (sodium cholate, SC) was studied by surface tension and fluorescence techniques in aqueous/urea solution. The output of the study has been analyzed by using different models (Clint, Rubingh, and Motomura) for mixed amphiphilic systems. The attractive or synergistic interactions between these two amphiphiles in water/urea were confirmed by the obtained data. Various thermodynamic parameters for the mixed micellization process have been computed and discussed.\n\nAggregation Behavior of Antipsychotic Drug under the Influence of Bile Salt in Aqueous/Urea Solution.", "token_count": 204, "char_count": 842, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:58.028600", "source": { "split": "train_shard_00000", "doc_id": 2737 }, "chunk_id": "train_shard_00000_2737_0", "global_id": 3022 }, { "text": "Phytate-linked nutritional deficiency disorders have plagued poultry for centuries. The application of exogenous phytases in poultry feed has served as a solution to this problem. However, they are linked to certain limitations which include thermal instability during prolonged feed processing. Therefore, in this study, Streptococcus thermophilus 2412 based phytase stability was assessed at higher temperatures up to 90 °C. This was followed by probiotic validation of the same bacterium in an in vitro intestinal model. Bacterial phytase showed thermostability up to 70 °C with a recorded activity of 9.90 U. The bacterium was viable in the intestinal lumen as indicated by the cell count of 6.10 log(CFU/mL) after 16 h. It also showed acid tolerance with a stable cell count of 5.01 log(CFU/mL) after 16 h of incubation at pH 2. The bacterium displayed bile tolerance yielding a cell count of 6.36 log(CFU/mL) in the presence of 0.3% bile. Bacterial susceptibility was observed toward all tested antibiotics with a maximum zone of 20 mm against clindamycin. The maximum antagonistic activity was observed against Staphylococcus aureus, Serratia marcescens, and Escherichia coli with inhibition zone diameters up to 10 mm. The above characteristics prove that S. thermophilus 2412 can be used as an effective phytase-producing poultry probiotic.\n\nProbiotic Validation of a Non-native, Thermostable, Phytase-Producing Bacterium: Streptococcus thermophilus.", "token_count": 425, "char_count": 1459, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8233, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:58.650826", "source": { "split": "train_shard_00000", "doc_id": 2738 }, "chunk_id": "train_shard_00000_2738_0", "global_id": 3023 }, { "text": "Gioddu, also known as \"Miciuratu\", \"Mezzoraddu\" or \"Latte ischidu\" (literally meaning acidulous milk), is the sole variety of traditional Italian fermented milk. The aim of the present study was to elucidate the microbiota and the mycobiota occurring in artisan Gioddu sampled from three Sardinian producers by combining the results of viable counting on selective culture media and high-throughput sequencing. Physico-chemical parameters were also measured. The overall low pH values (3.80-4.22) recorded in the analyzed Gioddu samples attested the strong acidifying activity carried out by lactic acid bacteria during fermentation. Viable counts revealed the presence of presumptive lactococci, presumptive lactobacilli and non-Saccharomyces yeasts. A complex (kefir-like) microbiota of bacteria and yeasts was unveiled through sequencing. In more detail, Lactobacillus delbrueckii was found to dominate in Gioddu together with Streptococcus thermophilus, thus suggesting the establishment of a yogurt-like protocooperation. Unexpectedly, in all the three analyzed batches from two out of the three producers Lactobacillus kefiri was also detected, thus representing an absolute novelty, which suggests the presence of bioactive compounds (e.g. exopolysaccharides) similar to those characterizing milk kefir beverage. Mycobiota population, studied for the very first time in Gioddu, revealed a more complex composition, with Kluyveromyces marxianus, Galactomyces candidum and Geotrichum galactomyces constituting the core species. Further research is needed to disclose the eventual occurence in Gioddu of probiotic cultures and bioactive compounds (e.g. exopolysaccharides, angiotensin-converting enzyme inhibitory peptides and antimicrobial compounds) with potential health-benefits for the consumers.\n\nMicrobiological characterization of Gioddu, an Italian fermented milk.", "token_count": 495, "char_count": 1877, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:59.307902", "source": { "split": "train_shard_00000", "doc_id": 2739 }, "chunk_id": "train_shard_00000_2739_0", "global_id": 3024 }, { "text": "The fried method with suet oil,which can strengthen the effect of Epimedium in warming kidney and enhancing Yang,has been widely used in the processing of Epimedium in traditional Chinese medicine. Based on the formation mechanism of Epimedium flavonoids self-assembled micelles in vivo,the synergistic mechanism of processing excipient suet oil was investigated in this paper from the perspective of pharmaceutics. Baohuoside Ⅰ,as representative component of processed Epimedium,was selected as model drug.Average size and zeta potential were measured and the morphology of micelles was observed under transmission electron microscopy. Caco-2 monolayer cell model,rat intestinal perfusion model and in vivo serum drug concentration method were established to investigate the effect of suet oil on the formation and absorption of the baohuosideⅠ bile salt self-assembled micelles. Baohuoside Ⅰ can form selfassembled micelles under the action of sodium deoxycholate. While,adding suet oil into the baohuoside Ⅰ-bile salt micelles( BSDOC) can make it form a more stable system with a smaller average size,higher Zeta potential,lower polydispersity index( PDI) value,significantly improved encapsulation efficiency and drug loading,indicating that suet oil could significantly improve the micelle formation in vivo. In addition,the permeability coefficient of baohuoside Ⅰ in Caco-2 monolayer cells and the four intestinal organs( duodenum,jejunum,ileum and colon) was increased and the oral bioavailability was also improved after adding the suet oil to BS-DOC.All the results demonstrated that the suet oil can promote the formation and absorption of baohuoside Ⅰ self-assembled micelles,so as to enhance its synergistic effects.\n\n[Effect of processing excipient suet oil on formation and absorption of baohuoside Ⅰ-bile salt self-assembled micelles].", "token_count": 476, "char_count": 1851, "word_count": 255, "semantic_coherence": 1, "information_density": 0.549, "quality_score": 0.7745, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:25:59.946556", "source": { "split": "train_shard_00000", "doc_id": 2740 }, "chunk_id": "train_shard_00000_2740_0", "global_id": 3025 }, { "text": "Lactobacillus plantarum FZU3013, a probiotic previously isolated from the traditional brewing process of Hongqu rice wine, may have the beneficial effect of improving the disorders of lipid metabolism. This study aimed to investigate the role of L. plantarum FZU3013 in improving non-alcoholic fatty liver (NAFL) associated with hyperlipidemia in mice fed a high-fat diet. The results indicated that L. plantarum FZU3013 intervention significantly reduced the HFD-induced body weight gain and the abnormal levels of serum total triglycerides (TG), total cholesterol (TC) and low-density lipoprotein (LDL-C), and inhibited the excessive accumulation of liver lipids. In addition, L. plantarum FZU3013 also promoted the excretion of bile acids through feces. Metagenomic and multivariate statistical analysis revealed that L. plantarum FZU3013 made significant structural changes in the intestinal microbiome of the mice fed with HFD, in particular by modulating the relative abundance of some function related microbial phylotypes. Furthermore, ultra-performance liquid chromatography with quadruple-time of flight mass spectrometry (UPLC-QTOF/MS)-based liver metabolomics demonstrated that L. plantarum FZU3013 had a significant regulatory effect on the composition of liver metabolites in hyperlipidemic mice, especially on the levels of some important biomarkers involved in the pathways of glycerophospholipid metabolism, fatty acid degradation, fatty acid elongation, glycerolipid metabolism, primary bile acid biosynthesis, arachidonic acid metabolism, etc. Moreover, L. plantarum FZU3013 regulated the mRNA expression levels of the genes responsible for liver lipid and cholesterol metabolism. L", "token_count": 467, "char_count": 1701, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6211, "quality_score": 0.8106, "entities": { "genes": [ "FZU3013" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:00.585221", "source": { "split": "train_shard_00000", "doc_id": 2741 }, "chunk_id": "train_shard_00000_2741_0", "global_id": 3026 }, { "text": "plantarum FZU3013 intervention increased the hepatic mRNA levels of cholesterol 7α-hydroxylase (CYP7A1) and the bile salt export pump (BSEP), suggesting enhanced bile acid synthesis and excretion from the liver. These findings present new evidence supporting that L. plantarum FZU3013 has the potential to improve lipid metabolism disorders through modulating specific intestinal microbial phylotypes and regulating hepatic lipid metabolism related genes, therefore it could be used as a potential functional food for the prevention of NAFL and hyperlipidemia.\n\nThe protective mechanism of Lactobacillus plantarum FZU3013 against non-alcoholic fatty liver associated with hyperlipidemia in mice fed a high-fat diet.", "token_count": 200, "char_count": 715, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7938, "quality_score": 0.8969, "entities": { "genes": [ "FZU3013" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:01.030433", "source": { "split": "train_shard_00000", "doc_id": 2741 }, "chunk_id": "train_shard_00000_2741_1", "global_id": 3027 }, { "text": "Calf diarrhea is an important problem that can result in death and which leads to economic losses. Probiotics in the gastrointestinal tract can be effective for the prevention of diarrhea. In this study, some strains were isolated from traditional fermented dairy products (Shubat and Kumiss) and the feces of Holstein calves and heifers. Some probiotic properties were determined using a total of 124 isolates and Lactobacterin-TK\n\nProperties of a New Probiotic Candidate and Lactobacterin-TK", "token_count": 130, "char_count": 493, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:01.463613", "source": { "split": "train_shard_00000", "doc_id": 2742 }, "chunk_id": "train_shard_00000_2742_0", "global_id": 3028 }, { "text": "We present an 8 years old girl who was diagnosed at 6 months of age of Progressive Familial Intrahepatic Cholestasis type 2. Although liver transplantation (LT) was classically considered curative for these patients, cholestasis recurrence with normal gamma-glutamyl transpeptidase (GGT), mediated by anti-bile salt export pump (BSEP) antibodies after LT (auto-antibody Induced BSEP Deficiency, AIBD) has been recently reported. Our patient underwent LT at 14 months. During her evolution, patient presented three episodes of acute rejection. Seven years after the LT, the patient presented pruritus with cholestasis and elevation of liver enzymes with persistent normal GGT. Liver biopsy showed intrahepatic cholestasis and giant-cell transformation with very low BSEP activity. Auto-antibodies against BSEP were detected therefore an AIBD was diagnosed. She was treated with Rituximab and immunoadsorption with resolution of the AIBD. As a complication of the treatment she developed a\n\nSuccessful Treatment with Rituximab and Immunoadsorption for an Auto-Antibody Induced Bile Salt Export Pump Deficiency in a Liver Transplanted Patient.", "token_count": 306, "char_count": 1140, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:02.025385", "source": { "split": "train_shard_00000", "doc_id": 2743 }, "chunk_id": "train_shard_00000_2743_0", "global_id": 3029 }, { "text": "Extensive use of next-generation sequencing has the potential to transform our knowledge on how genomic variation within bacterial species impacts phenotypic versatility. Because different environments have unique selection pressures, they drive divergent evolution. However, there is also parallel or convergent evolution of traits in independent bacterial isolates inhabiting similar environments. The application of tools to describe population-wide genomic diversity provides an opportunity to measure the predictability of genetic changes underlying adaptation. Here, we describe patterns of sequence variations in the core genome among 99 individual Pseudomonas aeruginosa clinical isolates and identified single-nucleotide polymorphisms that are the basis for branching of the phylogenetic tree. We also identified single-nucleotide polymorphisms that were acquired independently, in separate lineages, and not through inheritance from a common ancestor. Although our results demonstrate that the Pseudomonas aeruginosa core genome is highly conserved and in general, not subject to adaptive evolution, instances of parallel evolution will provide an opportunity to uncover genetic changes that underlie phenotypic diversity.\n\nSingle-Nucleotide Polymorphism-Based Genetic Diversity Analysis of Clinical Pseudomonas aeruginosa Isolates.", "token_count": 282, "char_count": 1342, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6824, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:02.574577", "source": { "split": "train_shard_00000", "doc_id": 2744 }, "chunk_id": "train_shard_00000_2744_0", "global_id": 3030 }, { "text": "Aeromonads are ubiquitous aquatic bacteria that cause opportunistic infections in humans, but their pathogenesis remains poorly understood. A pathogenomic approach was undertaken to provide insights into the emergence and evolution of pathogenic traits in aeromonads. The genomes of 64 Aeromonas strains representative of the whole genus were analyzed to study the distribution, phylogeny, and synteny of the flanking sequences of 13 virulence-associated genes. The reconstructed evolutionary histories varied markedly depending on the gene analyzed and ranged from vertical evolution, which followed the core genome evolution (alt and colAh), to complex evolution, involving gene loss by insertion sequence-driven gene disruption, horizontal gene transfer, and paraphyly with some virulence genes associated with a phylogroup (aer, ser, and type 3 secretion system components) or no phylogroup (type 3 secretion system effectors, Ast, ExoA, and RtxA toxins). The general pathogenomic overview of aeromonads showed great complexity with diverse evolution modes and gene organization and uneven distribution of virulence genes in the genus; the results provided insights into aeromonad pathoadaptation or the ability of members of this group to emerge as pathogens. Finally, these findings suggest that aeromonad virulence-associated genes should be examined at the population level and that studies performed on type or model strains at the species level cannot be generalized to the whole species.\n\nComparative and Evolutionary Genomics of Isolates Provide Insight into the Pathoadaptation of Aeromonas.", "token_count": 365, "char_count": 1604, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:03.155559", "source": { "split": "train_shard_00000", "doc_id": 2745 }, "chunk_id": "train_shard_00000_2745_0", "global_id": 3031 }, { "text": "The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don't account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN.\n\nPPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.", "token_count": 365, "char_count": 1680, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:03.737530", "source": { "split": "train_shard_00000", "doc_id": 2746 }, "chunk_id": "train_shard_00000_2746_0", "global_id": 3032 }, { "text": "Gut microbial enzymes, bile salt hydrolases (BSHs) are the gateway enzymes for bile acid (BA) modification in the gut. This activity is a promising target for developing innovative non-antibiotic growth promoters to enhance animal production and health. Compelling evidence has shown that inhibition of BSH activity should enhance weight gain by altering the BA pool, host signalling and lipid metabolism. We recently identified a panel of promising BSH inhibitors. Here, we address the potential of them as alternative, effective, non-antibiotic feed additives, for commercial application, to promote animal growth using a chicken model. In this study, the in vivo efficacy of three BSH inhibitors (caffeic acid phenethylester, riboflavin, carnosic acid) were evaluated. 7-day old chicks (10 birds/group) were either untreated or they received one of the specific BSH inhibitors (25 mg/kg body weight) via oral gavage for 17 days. The chicks in treatment groups consistently displayed higher body weight gain than the untreated chicks. Metabolomic analysis demonstrated that BSH inhibitor treatment led to significant changes in both circulating and intestinal BA signatures in support of blunted intestinal BSH activity. Consistent with this finding, liver and intestinal tissue RNA-Seq analysis showed that carnosic acid treatment significantly altered expression of genes involved in lipid and bile acid metabolism. Taken together, this study validates microbial BSH activity inhibition as an alternative target and strategy to antibiotic treatment for animal growth promotion.\n\nEvaluation of bile salt hydrolase inhibitor efficacy for modulating host bile profile and physiology using a chicken model system.", "token_count": 401, "char_count": 1713, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:04.360009", "source": { "split": "train_shard_00000", "doc_id": 2747 }, "chunk_id": "train_shard_00000_2747_0", "global_id": 3033 }, { "text": "Sequence type (ST) 398 is the most prevalent clone of livestock-associated methicillin-resistant Staphylococcus aureus (MRSA). To evaluate the molecular characteristics and phylogeny of Chinese ST398 isolates, 4 MRSA ST398 strains and 4 methicillin-susceptible S. aureus (MSSA) ST398 strains were collected from patients with bacteremia at 6 teaching hospitals in China between 1999 and 2016. Moreover, 689 ST398 genome sequences were downloaded from the GenBank database for comparison. The 4 MRSA ST398 strains were resistant to β-lactam antibiotics, and 2 strains were also resistant to erythromycin. Among the 4 MSSA ST398 strains, 2 strains displayed multidrug resistance (MDR) and were resistant to penicillin, erythromycin, tetracycline, and gentamicin. The accessory genome of MSSA ST398 was more diverse than that of MRSA ST398. All 4 MRSA ST398 strains carried type V staphylococcal cassette chromosome mec elements; however, MSSA ST398 carried more resistance genes than MRSA ST398. These 4 MRSA ST398 strains carried hemolysin, along with virulence genes associated with immune invasion and protease. Phylogenic analysis showed that the 4 MRSA ST398 strains clustered in 1 clade. The global ST398 phylogeny showed that ST398 was divided into an animal clade and a human clade, and the ST398 strains of this study clustered in the human clade. A small number of human strains were also present in the animal clade and vice versa, suggesting transmission of ST398 between animals and humans. In conclusion, livestock-associated MRSA ST398 has caused severe infections in Chinese hospitals, and it should therefore be paid more attention to and monitored.", "token_count": 504, "char_count": 1664, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5422, "quality_score": 0.7711, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:05.013357", "source": { "split": "train_shard_00000", "doc_id": 2748 }, "chunk_id": "train_shard_00000_2748_0", "global_id": 3034 }, { "text": "Whole-Genome Analysis of Livestock-Associated Methicillin-Resistant Staphylococcus aureus Sequence Type 398 Strains Isolated From Patients With Bacteremia in China.", "token_count": 53, "char_count": 164, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:05.421217", "source": { "split": "train_shard_00000", "doc_id": 2748 }, "chunk_id": "train_shard_00000_2748_1", "global_id": 3035 }, { "text": "Hypervirulent Klebsiella pneumoniae (hvKP) infections can have high morbidity and mortality rates owing to their invasiveness and virulence. However, there are no effective tools or biomarkers to discriminate between hvKP and nonhypervirulent K. pneumoniae (nhvKP) strains. We aimed to use a random forest algorithm to predict hvKP based on core-genome data.\n\nCore Genome Allelic Profiles of Clinical Klebsiella pneumoniae Strains Using a Random Forest Algorithm Based on Multilocus Sequence Typing Scheme for Hypervirulence Analysis.", "token_count": 151, "char_count": 534, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7973, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:05.870265", "source": { "split": "train_shard_00000", "doc_id": 2749 }, "chunk_id": "train_shard_00000_2749_0", "global_id": 3036 }, { "text": "In vivo studies have shown cyclic bile salt (BS) outputs during fasting whereas higher amounts have been observed in fed states. This leads to fluctuations of intestinal BS concentrations ([BS]) that can affect the rate and extent of absorption of lipophilic drugs in particular. However, most PBPK models use fixed values of [BS] in fasted and fed states albeit with different values in different regions of the GI tract. During fasting, there is a relationship between gallbladder volume (GBV) and the phase of the Interdigestive Migrating Motor Complex cycle (IMMCc), showing cyclic GBV changes with periodic filling and emptying. This relationship is also affected by the origin of the IMMCc (antral or duodenal). In fed states, meta-analysis indicated that GB residual volume (% of fasting maximum) was 46.4 ± 27%CV and 30.7 ± 48%CV for low- and high-fat meals, respectively. The corresponding values for the duration of the emptying phase were for low fat meals 0.72h ± 1%CV and for high fat meals 1.17h ± 37%CV. The model, the Advanced Dynamic Bile Salt Model (ADBSM), was built bottom-up and its parameters were not fitted against in vivo measurements of [BS]. It involved update of the dynamic luminal fluid volumes model based on meta-analysis of available imaging data. The ADBSM is incorporated into the Simcyp (v18r2) PBPK simulator. The model predictivity was good (within 1.25-fold error for 11/20 of the clinical studies) and was assessed against clinical studies of luminal [BS] that provide only the type of meal (i.e., low- or high-fat), the timing of the meal and/or water intake events, and the number and age range of the study participants. The model is also an important component of models capturing enterohepatic recirculation of drug and metabolite. Further work is required to validate the current model and compare to simpler models with respect to drug absorption, especially of the lipophilic compounds.", "token_count": 494, "char_count": 1934, "word_count": 310, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:06.555944", "source": { "split": "train_shard_00000", "doc_id": 2750 }, "chunk_id": "train_shard_00000_2750_0", "global_id": 3037 }, { "text": "Population-Based PBPK Model for the Prediction of Time-Variant Bile Salt Disposition within GI Luminal Fluids.", "token_count": 31, "char_count": 110, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:06.950670", "source": { "split": "train_shard_00000", "doc_id": 2750 }, "chunk_id": "train_shard_00000_2750_1", "global_id": 3038 }, { "text": "Foods rich in cereal β-glucan are efficient dietary tools to help reduce serum cholesterol levels and hence the risk of cardiovascular diseases. However, β-glucan undergoes various reactions during food processing, which alter its viscous properties and interactions with components of the gastrointestinal tract. It has been proposed in the literature that oxidation and partial hydrolysis increase β-glucan's bile acid-binding activity, and therefore its effectiveness in lowering cholesterol. Here, the passage kinetics of a bile salt mix across a dialysis membrane was studied with or without oat and barley β-glucan extracts, native or modified (partial hydrolysis and oxidations by sodium periodate or TEMPO (2,2,6,6-tetramethylpiperidine-1-oxyl)). Bile acid-retention turned out to be purely a function of viscosity, with the most viscous native extracts exhibiting the strongest retardation of bile acid permeation. Opposite of what was suggested in the literature, oxidation and molecular weight reduction do not seem to increase the bile acid-binding capability of β-glucan.\n\nBile acid-retention by native and modified oat and barley β-glucan.", "token_count": 305, "char_count": 1153, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:07.956130", "source": { "split": "train_shard_00000", "doc_id": 2751 }, "chunk_id": "train_shard_00000_2751_0", "global_id": 3039 }, { "text": "Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.\n\nA megaplasmid family driving dissemination of multidrug resistance in Pseudomonas.", "token_count": 276, "char_count": 1192, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6894, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:08.522575", "source": { "split": "train_shard_00000", "doc_id": 2752 }, "chunk_id": "train_shard_00000_2752_0", "global_id": 3040 }, { "text": "Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods.\n\nNeisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance.", "token_count": 102, "char_count": 369, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:08.912382", "source": { "split": "train_shard_00000", "doc_id": 2753 }, "chunk_id": "train_shard_00000_2753_0", "global_id": 3041 }, { "text": "Dihydromyricetin (DMY), hyperoside and silybin are phytochemicals that belong to a class called flavonoids, and they have been used in liver protection pharmaceutical preparations, but the specific mechanism of these chemicals is still unclarified. This study aims to investigate the hepatoprotective effects and potential mechanism of these phytochemicals. The immortalized human hepatocyte cell line L02 was treated with 200 μM emodin for 48 h, and this was used as a hepatocyte injury model. The L02 cells were treated with both 200 μM emodin and different concentrations of DMY/hyperoside/silybin for 48 h to investigate the protective effects of these phytochemicals. The CCK-8 assay was used to detect cell viability. RT-qPCR and western blotting were performed to examine the mRNA and protein expression, respectively, of the classic bile acid synthetic pathway gene CYP7A1, the bile acid efflux transporter bile salt export pump (BSEP), the nuclear factor erythroid-2-related factor 2 (Nrf2) and the drug processing gene CYP1A2. DMY, hyperoside and silybin prevented the impairment of cell viability that was caused by emodin-induced hepatotoxicity in a dose-dependent manner, and at a low concentration (10 μM), the protective effect followed the order hyperoside > DMY > silybin, while at a high concentration (160 μM), the protective effect followed the order DMY > hyperoside > silybin. These phytochemicals reduced the expression of CYP7A1 at both the mRNA and protein levels. BSEP was not influenced by the phytochemical intervention. When 200 μM emodin was used for 48 h with the addition of the phytochemicals at 200 μM, the nuclear protein expression of Nrf2 significantly increased and CYP1A2 expression decreased. DMY, hyperoside and silybin prevented the hepatotoxicity induced by emodin in the L02 cells, potentially,", "token_count": 518, "char_count": 1838, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5271, "quality_score": 0.7635, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:26:09.541599", "source": { "split": "train_shard_00000", "doc_id": 2754 }, "chunk_id": "train_shard_00000_2754_0", "global_id": 3042 }, { "text": "Phytochemicals protect L02 cells against hepatotoxicity induced by emodin", "token_count": 21, "char_count": 73, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:09.897245", "source": { "split": "train_shard_00000", "doc_id": 2754 }, "chunk_id": "train_shard_00000_2754_1", "global_id": 3043 }, { "text": "Streptococcus halichoeri is an emerging pathogen with a variety of host species and zoonotic potential. It has been isolated from grey seals and other marine mammals as well as from human infections. Beginning in 2010, two concurrent epidemics were identified in Finland, in fur animals and domestic dogs, respectively. The fur animals suffered from a new disease fur animal epidemic necrotic pyoderma (FENP) and the dogs presented with ear infections with poor treatment response. S. halichoeri was isolated in both studies, albeit among other pathogens, indicating a possible role in the disease etiologies. The aim was to find a possible common origin of the fur animal and dog isolates and study the virulence factors to assess pathogenic potential. Isolates from seal, human, dogs, and fur animals were obtained for comparison. The whole genomes were sequenced from 20 different strains using the Illumina MiSeq platform and annotated using an automatic annotation pipeline RAST. The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. A phylogenetic tree was constructed using the genes of the core genome. Virulence factors were assessed using the Virulence Factor Database (VFDB) concentrating on the previously confirmed streptococcal factors. A core genome was formed which encompassed approximately half of the genes in Streptococcus halichoeri. The resulting core was nearly saturated and would not change significantly by adding more genomes. The remaining genes formed the pangenome which was highly variable and would still evolve after additional genomes. The results highlight the great adaptability of this bacterium possibly explaining the ease at which it switches hosts and environments. Virulence factors were also analyzed and were found primarily in the core genome. They represented many classes and functions, but the largest single category was adhesins which again supports the marine origin of this species.", "token_count": 438, "char_count": 1994, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5967, "quality_score": 0.7983, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:10.524850", "source": { "split": "train_shard_00000", "doc_id": 2755 }, "chunk_id": "train_shard_00000_2755_0", "global_id": 3044 }, { "text": "Bile acids (BAs) regulate hepatic lipid metabolism and inflammation. Bile salt export pump (BSEP) KO mice are metabolically preconditioned with a hydrophilic BA composition protecting them from cholestasis. We hypothesize that changes in hepatic BA profile and subsequent changes in BA signalling may critically determine the susceptibility to steatohepatitis.\n\nAbsence of Bsep/Abcb11 attenuates MCD diet-induced hepatic steatosis but aggravates inflammation in mice.", "token_count": 131, "char_count": 467, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8548, "quality_score": 0.9274, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:10.948281", "source": { "split": "train_shard_00000", "doc_id": 2756 }, "chunk_id": "train_shard_00000_2756_0", "global_id": 3045 }, { "text": "Lactobacillus fermentum is a lactic acid bacterium frequently isolated from mammal tissues, milk, and plant material fermentations, such as sourdough. A comparative genomics analysis of 28 L. fermentum strains enabled the investigation of the core and accessory genes of this species. The core protein phylogenomic tree of the strains examined, consisting of five clades, did not exhibit clear clustering of strains based on isolation source, suggesting a free-living lifestyle. Based on the presence/absence of orthogroups, the largest clade, containing most of the human-related strains, was separated from the rest. The extended core genome included genes necessary for the heterolactic fermentation. Many traits were found to be strain-dependent, for instance utilisation of xylose and arabinose. Compared to other strains, the genome of L. fermentum IMDO 130101, a candidate starter culture strain capable of dominating sourdough fermentations, contained unique genes related to the metabolism of starch degradation products, which could be advantageous for growth in sourdough matrices. This study explained the traits that were previously demonstrated for L. fermentum IMDO 130101 at the genetic level and provided future avenues of research regarding L. fermentum strains isolated from sourdough.\n\nComparative genomics of Lactobacillus fermentum suggests a free-living lifestyle of this lactic acid bacterial species.", "token_count": 346, "char_count": 1425, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8085, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:11.520472", "source": { "split": "train_shard_00000", "doc_id": 2757 }, "chunk_id": "train_shard_00000_2757_0", "global_id": 3046 }, { "text": "The aim of this study was to identify clonally-related carbapenemase-producing Klebsiella pneumoniae complex members that could be involved in outbreaks among hospitalized patients in Denmark, and to identify possible epidemiological links.\n\nInvestigation of possible clonal transmission of carbapenemase-producing Klebsiella pneumoniae complex member isolates in Denmark using core genome MLST and National Patient Registry Data.", "token_count": 101, "char_count": 430, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:11.905729", "source": { "split": "train_shard_00000", "doc_id": 2758 }, "chunk_id": "train_shard_00000_2758_0", "global_id": 3047 }, { "text": "Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this long-term symbiotic relationship to better understand B. pseudomallei persistence in P314's sputum despite intensive initial therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314's airways over a >16-year period, and also sampled the patient's home environment, recovering six closely related B. pseudomallei isolates from the household water system. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a strictly clonal mode of genetic inheritance. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that. Overall, the evolution of this population is nonadaptive and best explained by genetic drift. However, some genetic and phenotypic changes are consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes emerged and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression towards commensalism by a highly virulent pathogen within a single human host.", "token_count": 499, "char_count": 2164, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:12.554718", "source": { "split": "train_shard_00000", "doc_id": 2759 }, "chunk_id": "train_shard_00000_2759_0", "global_id": 3048 }, { "text": "Pathogen to commensal? Longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection.", "token_count": 38, "char_count": 157, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:12.914218", "source": { "split": "train_shard_00000", "doc_id": 2759 }, "chunk_id": "train_shard_00000_2759_1", "global_id": 3049 }, { "text": "Auxotrophies constrain the interactions of bacteria with their environment, but are often difficult to identify. Here, we develop an algorithm (AuxoFind) using genome-scale metabolic reconstruction to predict auxotrophies and apply it to a series of available genome sequences of over 1,300 Gram-negative strains. We identify 54 auxotrophs, along with the corresponding metabolic and genetic basis, using a pangenome approach, and highlight auxotrophies conferring a fitness advantage in vivo. We show that the metabolic basis of auxotrophy is species-dependent and varies with 1) pathway structure, 2) enzyme promiscuity, and 3) network redundancy. Various levels of complexity constitute the genetic basis, including 1) deleterious single-nucleotide polymorphisms (SNPs), in-frame indels, and deletions; 2) single/multigene deletion; and 3) movement of mobile genetic elements (including prophages) combined with genomic rearrangements. Fourteen out of 19 predictions agree with experimental evidence, with the remaining cases highlighting shortcomings of sequencing, assembly, annotation, and reconstruction that prevent predictions of auxotrophies. We thus develop a framework to identify the metabolic and genetic basis for auxotrophies in Gram-negatives.\n\nMetabolic and genetic basis for auxotrophies in Gram-negative species.", "token_count": 336, "char_count": 1332, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:13.486329", "source": { "split": "train_shard_00000", "doc_id": 2760 }, "chunk_id": "train_shard_00000_2760_0", "global_id": 3050 }, { "text": "An amendment to this paper has been published and can be accessed via a link at the top of the paper.\n\nAuthor Correction: MIG1 as a positive regulator for the histidine biosynthesis pathway and as a global regulator in thermotolerant yeast Kluyveromyces marxianus.", "token_count": 72, "char_count": 264, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [ "MIG1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:13.860533", "source": { "split": "train_shard_00000", "doc_id": 2761 }, "chunk_id": "train_shard_00000_2761_0", "global_id": 3051 }, { "text": "Ursodeoxycholic acid (UDCA) treatment can reduce itch and lower endogenous serum bile acids in intrahepatic cholestasis of pregnancy (ICP). We sought to determine how it could influence the gut environment in ICP to alter enterohepatic signalling. The gut microbiota and bile acid content were determined in faeces from 35 pregnant women (14 with uncomplicated pregnancies and 21 with ICP, 17 receiving UDCA). Faecal bile salt hydrolase activity was measured using a precipitation assay. Serum fibroblast growth factor 19 (FGF19) and 7α-hydroxy-4-cholesten-3-one (C4) concentrations were measured following a standardised diet for 21 hours. Women with a high ratio of Bacteroidetes to Firmicutes were more likely to be treated with UDCA (Fisher's exact test p = 0.0178) than those with a lower ratio. Bile salt hydrolase activity was reduced in women with low Bacteroidetes:Firmicutes. Women taking UDCA had higher faecal lithocholic acid (p < 0.0001), with more unconjugated bile acids than women with untreated ICP or uncomplicated pregnancy. UDCA-treatment increased serum FGF19, and reduced C4 (reflecting lower bile acid synthesis). During ICP, UDCA treatment can be associated with enrichment of the gut microbiota with Bacteroidetes. These demonstrate high bile salt hydrolase activity, which deconjugates bile acids enabling secondary modification to FXR agonists, enhancing enterohepatic feedback via FGF19.\n\nUrsodeoxycholic acid enriches intestinal bile salt hydrolase-expressing Bacteroidetes in cholestatic pregnancy.", "token_count": 459, "char_count": 1529, "word_count": 216, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:14.500958", "source": { "split": "train_shard_00000", "doc_id": 2762 }, "chunk_id": "train_shard_00000_2762_0", "global_id": 3052 }, { "text": "Horizontal gene transfer (HGT) promotes the spread of genes within bacterial communities. Among the HGT mechanisms, natural transformation stands out as being encoded by the bacterial core genome. Natural transformation is often viewed as a way to acquire new genes and to generate genetic mixing within bacterial populations. Another recently proposed function is the curing of bacterial genomes of their infectious parasitic mobile genetic elements (MGEs). Here, we propose that these seemingly opposing theoretical points of view can be unified. Although costly for bacterial cells, MGEs can carry functions that are at points in time beneficial to bacteria under stressful conditions (e.g., antibiotic resistance genes). Using computational modeling, we show that, in stochastic environments, an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes, although these MGEs are costly for host cell replication. Based on this dual function (MGE acquisition and removal), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, and this would explain its striking conservation.\n\nBacterial Transformation Buffers Environmental Fluctuations through the Reversible Integration of Mobile Genetic Elements.", "token_count": 264, "char_count": 1320, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6848, "quality_score": 0.8424, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:15.052133", "source": { "split": "train_shard_00000", "doc_id": 2763 }, "chunk_id": "train_shard_00000_2763_0", "global_id": 3053 }, { "text": "A number of veterinary clinical pathology laboratories in New Zealand have been reporting emergence of increased minimum in inhibitory concentrations for β-lactams in the common clinical bovine mastitis pathogen Streptococcus uberis. The objective of this study was to determine the genetic basis of this increase in MIC for β-lactams amongst S. uberis. Illumina sequencing and determination of oxacillin MIC was performed on 265 clinical isolates. Published sequences of the five penicillin binding proteins pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x were used to identify, extract and align these sequences from the study isolates. Amino acid substitutions resulting from single nucleotide polymorphisms (SNP) within these genes were analysed for associations with elevated (≥ 0.5 mg/L) oxacillin MIC together with a genome wide association study. The population structure of the study isolates was approximated using a phylogenetic tree generated from an alignment of the core genome. A total of 53 % of isolates had MIC ≥ 0.5 mg/L for oxacillin. A total of 101 substitutions within the five pbp were identified, of which 11 were statistically associated with an MIC ≥ 0.5 mg/L. All 140 isolates which exhibited an increased β-lactam MIC had SNPs leading to pbp2x E\n\nMechanisms of β-lactam resistance of Streptococcus uberis isolated from bovine mastitis cases.", "token_count": 379, "char_count": 1359, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:15.635658", "source": { "split": "train_shard_00000", "doc_id": 2764 }, "chunk_id": "train_shard_00000_2764_0", "global_id": 3054 }, { "text": "Lactic acid bacteria (LAB) are major microorganisms used for probiotic purposes and prime parts of the human and mammalian gut microbiota, which exert important health-promoting effects on the host. The present study aimed to evaluate and compare the probiotic potential and safety of LAB strains isolated from the gastrointestinal tract of a wild boar from the Greater Khingan Mountains, China. Amongst all of the isolated LAB strains, five isolates identified as\n\nCharacterization of Lactic Acid Bacteria Isolated From the Gastrointestinal Tract of a Wild Boar as Potential Probiotics.", "token_count": 144, "char_count": 587, "word_count": 88, "semantic_coherence": 1, "information_density": 0.6477, "quality_score": 0.8239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:16.062910", "source": { "split": "train_shard_00000", "doc_id": 2765 }, "chunk_id": "train_shard_00000_2765_0", "global_id": 3055 }, { "text": "Xylella fastidiosa subsp. fastidiosa causes Pierce's disease of grapevine (PD) and has been present in California for over a century. A singly introduced genotype spread across the state causing large outbreaks and damaging the grapevine industry. This study presents 122 X. fastidiosa subsp. fastidiosa genomes from symptomatic grapevines, and explores pathogen genetic diversity associated with PD in California. A total of 5218 single-nucleotide polymorphisms (SNPs) were found in the dataset. Strong population genetic structure was found; isolates split into five genetic clusters divided into two lineages. The core/soft-core genome constituted 41.2% of the total genome, emphasizing the high genetic variability of X. fastidiosa genomes. An ecological niche model was performed to estimate the environmental niche of the pathogen within California and to identify key climatic factors involved in dispersal. A landscape genomic approach was undertaken aiming to link local adaptation to climatic factors. A total of 18 non-synonymous polymorphisms found to be under selective pressures were correlated with at least one environmental variable highlighting the role of temperature, precipitation and elevation on X. fastidiosa adaptation to grapevines in California. Finally, the contribution to virulence of three of the genes under positive selective pressure and of one recombinant gene was studied by reverse genetics.\n\nPopulation structure and adaptation of a bacterial pathogen in California grapevines.", "token_count": 353, "char_count": 1515, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:16.641995", "source": { "split": "train_shard_00000", "doc_id": 2766 }, "chunk_id": "train_shard_00000_2766_0", "global_id": 3056 }, { "text": "Breast milk is the main source of nutrition for infants; it contains considerable microflora that can be transmitted to the infant endogenously or by breastfeeding, and it plays an important role in the maturation and development of the immune system. In this study, we isolated and identified lactic acid bacteria (LAB) from human colostrum, and screened 2 strains with probiotic potential. The LAB isolated from 40 human colostrum samples belonged to 5 genera: Lactobacillus, Bifidobacterium, Streptococcus, Enterococcus, and Staphylococcus. We also isolated Propionibacterium and Actinomyces. We identified a total of 197 strains of LAB derived from human colostrum based on their morphology and 16S rRNA sequence, among them 8 strains of Bifidobacterium and 10 strains of Lactobacillus, including 3 Bifidobacterium species and 4 Lactobacillus species. The physiological and biochemical characteristics of strains with good probiotic characteristics were evaluated. The tolerances of some of the Bifidobacterium and Lactobacillus strains to gastrointestinal fluid and bile salts were evaluated in vitro, using the probiotic strains Bifidobacterium lactis BB12 and Lactobacillus rhamnosus GG as controls. Among them, B. lactis Probio-M8 and L. rhamnosus Probio-M9 showed survival rates of 97.25 and 78.33% after digestion for 11 h in artificial gastrointestinal juice, and they exhibited growth delays of 0.95 and 1.87 h, respectively, in 0.3% bile salts. These two strains have the potential for application as probiotics and will facilitate functional studies of probiotics in breast milk and the development of human milk-derived probiotics.\n\nCharacterization of potentially probiotic lactic acid bacteria and bifidobacteria isolated from human colostrum.", "token_count": 493, "char_count": 1760, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6056, "quality_score": 0.8028, "entities": { "genes": [ "BB12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:17.302681", "source": { "split": "train_shard_00000", "doc_id": 2767 }, "chunk_id": "train_shard_00000_2767_0", "global_id": 3057 }, { "text": "Genetic stability of bacterium as a starter culture is vital for product quality in fermentation industry. The commercial strain Lactobacillus plantarum NCU116 widely used in fruit and vegetable fermentation was induced with various stressors to investigate the stability of potential prophages. PHAge Search Tool (PHAST) identified three potential prophages in bacterial genome. By spectrophotometric analysis, mitomycin C (MMC), lactic acid, and bile salt were found to inhibit the growth of L. plantarum NCU116 while ethanol and hydrogen peroxide had no notable impacts. Transcriptions of four phage-synthesizing genes (phaR, phacap, phaada, phatail) and four phage-resistant genes (cas116, helR, hsd1, hsd2) under stressors were investigated by quantitative reverse transcription PCR. MMC was found to most significantly upregulated transcriptions of phage-synthesizing genes, followed by lactic acid and bile salt. By transmission electron microscopy, no virus particles from the lysates of strain NCU116 treated by MMC were observed, corresponding to the result that no phage nucleic acids could be extracted from the supernatants of strain NCU116 treated by MMC. This study suggested that no prophages could be induced from L. plantarum NCU116 by strong inducer MMC, indicating its genetic stability, which supports the comprehensive application of strain NCU116 in industry without causing fermentation failure.\n\nStability of potential prophages in commercial strain Lactobacillus plantarum NCU116 under various stressors.", "token_count": 389, "char_count": 1530, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [ "NCU116" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:17.940645", "source": { "split": "train_shard_00000", "doc_id": 2768 }, "chunk_id": "train_shard_00000_2768_0", "global_id": 3058 }, { "text": "Bacteria survive in the environment with three steps: a sensing environmental conditions, a responding to sensed signals, and an adaptation for proper survival in the environment. An adapting bacterial cell occurs cell division to increase the number of sister cells, termed adaptive growth. Two-component systems (TCSs), representing the main bacterial signal transduction systems, consist of a pair of one sensor kinase (SK) and one response regulator (RR), and RR genes are abundant in most bacterial genomes as part of the core genome. The OmpR gene family, a group of RR genes, is conserved in 95% of known bacterial genomes. The Escherichia coli genome has an estimated 34 RR genes in total, including 14 genes of OmpR family genes. To reveal the contribution of TCSs for fast growth as an adaptive growth strategy of E. coli, we isolated a set of gene knockout strains by using newly developed genome editing technology, the HoSeI (Homologous Sequence Integration) method, based on CRISPR-Cas9. The statistics of single cell observation show a knockout of an arbitrary pair of phoP, phoB, and ompR genes, stably expressed by positive feedback regulation, dramatically inhibit the optimum adaptive growth of E. coli. These insights suggest that the adaptive growth of bacteria is fulfilled by the optimum high intracellular level of regulators acquired during growth under environmental conditions.\n\nEpistatic Effect of Regulators to the Adaptive Growth of Escherichia coli.", "token_count": 361, "char_count": 1480, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6201, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:18.526461", "source": { "split": "train_shard_00000", "doc_id": 2769 }, "chunk_id": "train_shard_00000_2769_0", "global_id": 3059 }, { "text": "Structural elucidation and molecular scrutiny of cerebral vasculature is crucial for understanding the functions and diseases of the brain. Here, we introduce SeeNet, a method for near-complete three-dimensional visualization of cerebral vascular networks with high signal-to-noise ratios compatible with molecular phenotyping. SeeNet employs perfusion of a multifunctional crosslinker, vascular casting by temperature-controlled polymerization of hybrid hydrogels, and a bile salt-based tissue-clearing technique optimized for observation of vascular connectivity. SeeNet is capable of whole-brain visualization of molecularly characterized cerebral vasculatures at the single-microvessel level. Moreover, SeeNet reveals a hitherto unidentified vascular pathway bridging cerebral and hippocampal vessels, thus serving as a potential tool to evaluate the connectivity of cerebral vasculature.\n\nVisualization and molecular characterization of whole-brain vascular networks with capillary resolution.", "token_count": 231, "char_count": 998, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6583, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:19.028318", "source": { "split": "train_shard_00000", "doc_id": 2770 }, "chunk_id": "train_shard_00000_2770_0", "global_id": 3060 }, { "text": "Leptospirosis is a neglected disease causing severe infections in humans and animals. Due in part to misdiagnosis, this infectious disease results in nearly 60,000 deaths per year around the globe. This study represents the first effort to describe the diversity of pathogenic Leptospira in Cuba based on whole-genome sequencing. We have collected nineteen whole-blood samples from patients that were diagnosed as having leptospirosis between 2008 and 2012 in Cuba. In addition, we have enhanced our sample set by three historical strains that were used for the development of a human vaccine in 1990s. The Leptospira strains were grown and serotyped by the microscopic agglutination test, and the draft genomes were generated by NGS (Illumina). Subsequently, the core genomes were analyzed and compared to the genetic data available from other Caribbean islands and countries in Central America. Core genome Multi-locus Sequence Typing (cgMLST) revealed four different core genome clonal groups (cgCGs), with the highest number of samples belonging to L. interrogans, followed by L. borgpetersenii and L. kirschneri. All cgCGs that were found in Cuba have been also identified from multiple origins across the globe, except in neighbor countries and Central America. Serotyping divided the samples into the serogroups Canicola, Ballum and Pomona. The most frequent cgCGs, cgCG28, associated with serogroup Canicola, and cgCG15, associated with serogroup Ballum, have also been identified from samples isolated from dogs, rodents, and pigs; suggesting that these hosts represent the major source of human infection in Cuba. The vaccine strains did not significantly differ from the recent patient isolates. However, the increasing prevalence of samples belonging to the serogroup Ballum combined with the fact that the available vaccine in Cuba represents inactivated Leptospira belonging to serogroups other than Ballum, should be a valuable information for the National and Regional Leptospirosis Control Programs.\n\nA first insight into the genomic diversity of Leptospira strains isolated from patients in Cuba.", "token_count": 499, "char_count": 2114, "word_count": 312, "semantic_coherence": 1, "information_density": 0.5705, "quality_score": 0.7853, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:19.680144", "source": { "split": "train_shard_00000", "doc_id": 2771 }, "chunk_id": "train_shard_00000_2771_0", "global_id": 3061 }, { "text": "The first genomic study of Mediterranei clade using five type strains (V. mediterranei, V. maritimus, V. variabilis, V. thalassae, and V. barjaei) and fourteen reference strains isolated from marine organisms, seawater, water and sediments of the sea was performed. These bacterial strains were characterised by means of a polyphasic approach comprising 16S rRNA gene, multilocus sequence analysis (MLSA) of 139 single-copy genes, the DNA G + C content, ANI, and in silico phenotypic characterisation. We found that the species of the Mediterranei clade formed two separate clusters based in 16S rRNA gene sequence similarity, MLSA, OrthoANI, and Codon and Amino Acid usage. The Mediterranei clade species showed values between 76 and 95% for ANIb, 84 and 95% for ANIm. The core genome consisted of 2057 gene families and the pan-genome of 13,094 gene families. Based on the genomic analyses performed, the Mediterranei clade can be divided in two clusters, one with the strains of V. maritimus, V. variabilis and two potential new species, and the other cluster with the strains of V. mediterranei, V. thalassae, and V. barjaei.\n\nGenomic taxonomy of the Mediterranei clade of the genus Vibrio (Gammaproteobacteria).", "token_count": 368, "char_count": 1216, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:20.272595", "source": { "split": "train_shard_00000", "doc_id": 2772 }, "chunk_id": "train_shard_00000_2772_0", "global_id": 3062 }, { "text": "The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are 'coincident') more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3 and R and is freely available under the GNU license from https://github.com/fwhelan/coinfinder.\n\nCoinfinder: detecting significant associations and dissociations in pangenomes.", "token_count": 240, "char_count": 1004, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7042, "quality_score": 0.8521, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:20.743277", "source": { "split": "train_shard_00000", "doc_id": 2773 }, "chunk_id": "train_shard_00000_2773_0", "global_id": 3063 }, { "text": "Gut microbiota play critical roles in maintaining the human health in several aspects. Bile acids (BAs) are endogenous cholesterol-derived molecules that can be modified by the gut microbiota and act as signaling molecules in the regulation of host metabolic and physiology processes. Gut microbiota release many enzymes that are capable to perform considerable modifications on BAs such as bile salt hydrolases (BSH), 7α-dehydroxylase (CYP7A), and hydroxysteroid dehydrogenase (HSDH). These enzymatic roles can change in the gut microbiota composition, cause alteration in BAs profile and metabolism and even gallstone formation. Patients with 15 years of asymptomatic gallstone have increased risk for colorectal cancer (CRC), which may be related to altered gut microbiota, changes in bile metabolism, as well as cellular and molecular effects in the proximal colon. In gallstone-associated CRC patients, the association between consensus molecular subtypes of CRC should be clarified to identify if specific pathways are related.\n\nThe association between gut microbiota, cholesterol gallstones, and colorectal cancer.", "token_count": 280, "char_count": 1121, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6709, "quality_score": 0.8354, "entities": { "genes": [ "CYP7A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:21.306308", "source": { "split": "train_shard_00000", "doc_id": 2774 }, "chunk_id": "train_shard_00000_2774_0", "global_id": 3064 }, { "text": "Whole genome sequencing (WGS) is replacing traditional microbiological typing methods for investigation of outbreaks in clinical settings. Here, we used a clinical microbiology laboratory core genome multilocus sequence typing (cgMLST) workflow to analyze 40 isolates of K. pneumoniae which are part of the Antimicrobial Resistance Leadership Group (ARLG) isolate collection, alongside 10 Mayo Clinic K. pneumoniae isolates, comparing results to those of pulsed-field gel electrophoresis (PFGE). Additionally, we used the WGS data to predict phenotypic antimicrobial susceptibility (AST). Thirty-one of 40 ARLG K. pneumoniae isolates belonged to the same PFGE type, all of which, alongside 3 isolates of different PFGE types, formed a large cluster by cgMLST. PFGE and cgMLST were completely concordant for the 10 Mayo Clinic K. pneumoniae isolates. For AST prediction, the overall agreement between phenotypic AST and genotypic prediction was 95.6%.\n\nCore genome MLST and resistome analysis of Klebsiella pneumoniae using a clinically amenable workflow.", "token_count": 291, "char_count": 1054, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6913, "quality_score": 0.8456, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:21.863246", "source": { "split": "train_shard_00000", "doc_id": 2775 }, "chunk_id": "train_shard_00000_2775_0", "global_id": 3065 }, { "text": "Mutations in ABCB11 can cause deficiency of the bile salt export pump (BSEP), leading to cholestasis and end-stage liver disease. Owing to the rarity of the disease, the associations between genotype and natural history, or outcomes following surgical biliary diversion (SBD), remain elusive. We aimed to determine these associations by assembling the largest genetically defined cohort of patients with severe BSEP deficiency to date.\n\nGenotype correlates with the natural history of severe bile salt export pump deficiency.", "token_count": 123, "char_count": 525, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:22.256614", "source": { "split": "train_shard_00000", "doc_id": 2776 }, "chunk_id": "train_shard_00000_2776_0", "global_id": 3066 }, { "text": "We investigated the effect of lotus seed resistant starch (LRS) on mice fecal microbiota tolerance to bile salt by culturing organisms compared to inulin (INU) glucose (GLU) and waxy corn starch (WAX). Operational taxonomic units (OTUs) and diversity indices in LRS and INU groups were increased in the presence of 0.03% to 0.3% bile salt, while they were decreased in GLU, and OTUs were decreased in WAX. Specifically, LRS promoted proliferation of Lactobacillus, which potentially used bile acid, and inhibited growth of the potentially harmful bacteria Enterococcus and Staphylococcus. Moreover, Lactobacillus was negatively correlated with Salinicoccus and Granulicatella in GLU, LRS and INU groups at 1.5% bile salt. With LRS, amino acid metabolic pathways were increased while pathogens causing certain diseases were decreased. LRS increased the tolerance of mice fecal microbiota to bile salt by promoting the proliferation of bacteria utilizing bile acid and inhibiting the growth of harmful bacteria.\n\nEffect of lotus seed resistant starch on tolerance of mice fecal microbiota to bile salt.", "token_count": 300, "char_count": 1100, "word_count": 165, "semantic_coherence": 1, "information_density": 0.5515, "quality_score": 0.7758, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:22.823331", "source": { "split": "train_shard_00000", "doc_id": 2777 }, "chunk_id": "train_shard_00000_2777_0", "global_id": 3067 }, { "text": "To understand the epidemiological and genetic background of anthrax cases occurring in Vietnam from 2011 to 2015, we surveilled and genetically analyzed Bacillus anthracis isolated in the north of the country. Epidemiological surveillance showed that most human cutaneous anthrax cases occurred in association with animal dissection. Whole-genome sequences were obtained from six B. anthracis strains from human patients with cutaneous anthrax in the endemic area. Comparative genomic analysis showed that the genetic homogeneity among Vietnamese B. anthracis strains was very high. All Vietnamese B. anthracis strains belonged to the canSNP lineage of A.Br.011/009, which mostly consists of strains of the trans-Eurasian (TEA) group, including the most closely related strain, Carbosap. To clarify the genetic diversity of Vietnamese strains and strains belonging to A.Br.011/009 and A.Br.008/011 canSNP lineages, we applied a reference genome-based single-nucleotide polymorphism (SNP) and gene-by-gene genomic analysis (whole-genome MLST) strategy. The phylogeny from core genome SNPs revealed that the Vietnamese strains were positioned close to each other; moreover, several SNPs specific to Vietnamese B. anthracis were identified. Whole-genome MLST analysis revealed the differences in the number of SNPs between Vietnamese strains, which could enable discrimination at the strain level.\n\nEpidemiological and comparative genomic analysis of Bacillus anthracis isolated from northern Vietnam.", "token_count": 391, "char_count": 1498, "word_count": 203, "semantic_coherence": 1, "information_density": 0.5616, "quality_score": 0.7808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:23.434174", "source": { "split": "train_shard_00000", "doc_id": 2778 }, "chunk_id": "train_shard_00000_2778_0", "global_id": 3068 }, { "text": "Whole-genome sequencing (WGS)-based typing methods have emerged as promising and highly discriminative epidemiological tools. In this study, we combined gene-by-gene allele calling and core genome single nucleotide polymorphism (cgSNP) approaches to investigate the genetic relatedness of a well-characterized collection of OXA-48\n\nCore/Whole Genome Multilocus Sequence Typing and Core Genome SNP-Based Typing of OXA-48-Producing", "token_count": 116, "char_count": 429, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8302, "quality_score": 0.9151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:23.818490", "source": { "split": "train_shard_00000", "doc_id": 2779 }, "chunk_id": "train_shard_00000_2779_0", "global_id": 3069 }, { "text": "Increasing hepatic mitochondrial activity through pyruvate dehydrogenase and elevating enterohepatic bile acid recirculation are promising new approaches for metabolic disease therapy, but neither approach alone can completely ameliorate disease phenotype in high-fat diet-fed mice. This study showed that diet-induced hepatosteatosis, hyperlipidemia, and insulin resistance can be completely prevented in mice with liver-specific HCLS1-associated protein X-1 (HAX-1) inactivation. Mechanistically, we showed that HAX-1 interacts with inositol 1,4,5-trisphosphate receptor-1 (InsP3R1) in the liver, and its absence reduces InsP3R1 levels, thereby improving endoplasmic reticulum-mitochondria calcium homeostasis to prevent excess calcium overload and mitochondrial dysfunction. As a result, HAX-1 ablation activates pyruvate dehydrogenase and increases mitochondria utilization of glucose and fatty acids to prevent hepatosteatosis, hyperlipidemia, and insulin resistance. In contrast to the reduction of InsP3R1 levels, hepatic HAX-1 deficiency increases bile salt exporter protein levels, thereby promoting enterohepatic bile acid recirculation, leading to activation of bile acid-responsive genes in the intestinal ileum to augment insulin sensitivity and of cholesterol transport genes in the liver to suppress hyperlipidemia. The dual mechanisms of increased mitochondrial respiration and enterohepatic bile acid recirculation due to improvement of endoplasmic reticulum-mitochondria calcium homeostasis with hepatic HAX-1 inactivation suggest that this may be a potential therapeutic target for metabolic disease intervention.\n\nHepatic HAX-1 inactivation prevents metabolic diseases by enhancing mitochondrial activity and bile salt export.", "token_count": 470, "char_count": 1746, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "HCLS1" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:24.466316", "source": { "split": "train_shard_00000", "doc_id": 2780 }, "chunk_id": "train_shard_00000_2780_0", "global_id": 3070 }, { "text": "It has been established in recent years that the gut microbiome plays a role in health and disease, potentially via alterations in metabolites that influence host physiology. Although sleep disruption and gut dysbiosis have been associated with many of the same diseases, studies investigating the gut microbiome in the context of sleep disruption have yielded inconsistent results, and have not assessed the fecal metabolome. We exposed mice to five days of sleep disruption followed by four days of ad libitum recovery sleep, and assessed the fecal microbiome and fecal metabolome at multiple timepoints using 16S rRNA gene amplicons and untargeted LC-MS/MS mass spectrometry. We found global shifts in both the microbiome and metabolome in the sleep-disrupted group on the second day of recovery sleep, when most sleep parameters had recovered to baseline levels. We observed an increase in the Firmicutes:Bacteroidetes ratio, along with decreases in the genus Lactobacillus, phylum Actinobacteria, and genus Bifidobacterium in sleep-disrupted mice compared to control mice. The latter two taxa remained low at the fourth day post-sleep disruption. We also identified multiple classes of fecal metabolites that were differentially abundant in sleep-disrupted mice, some of which are physiologically relevant and commonly influenced by the microbiome. This included bile acids, and inference of microbial functional gene content suggested reduced levels of the microbial bile salt hydrolase gene in sleep-disrupted mice. Overall, this study adds to the evidence base linking disrupted sleep to the gut microbiome and expands it to the fecal metabolome, identifying sleep disruption-sensitive bacterial taxa and classes of metabolites that may serve as therapeutic targets to improve health after poor sleep.\n\nRepeated sleep disruption in mice leads to persistent shifts in the fecal microbiome and metabolome.", "token_count": 448, "char_count": 1911, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5765, "quality_score": 0.7883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:25.105249", "source": { "split": "train_shard_00000", "doc_id": 2781 }, "chunk_id": "train_shard_00000_2781_0", "global_id": 3071 }, { "text": "Issues concerning the use of harmful chemical fertilizers and pesticides that have large negative impacts on environmental and human health have generated increasing interest in the use of beneficial microorganisms for the development of sustainable agri-food systems. A successful microbial inoculant has to colonize the root system, establish a positive interaction and persist in the environment in competition with native microorganisms living in the soil through rhizocompetence traits. Currently, several approaches based on culture-dependent, microscopic and molecular methods have been developed to follow bioinoculants in the soil and plant surface over time. Although culture-dependent methods are commonly used to estimate the persistence of bioinoculants, it is difficult to differentiate inoculated organisms from native populations based on morphological characteristics. Therefore, these methods should be used complementary to culture-independent approaches. Microscopy-based techniques (bright-field, electron and fluorescence microscopy) allow to obtain a picture of microbial colonization outside and inside plant tissues also at high resolution, but it is not possible to always distinguish living cells from dead cells by direct observation as well as distinguish bioinoculants from indigenous microbial populations living in soils. In addition, the development of metagenomic techniques, including the use of DNA probes, PCR-based methods, next-generation sequencing, whole-genome sequencing and pangenome methods, provides a complementary approach useful to understand plant-soil-microbe interactions. However, to ensure good results in microbiological analysis, the first fundamental prerequisite is correct soil sampling and sample preparation for the different methodological approaches that will be assayed. Here, we provide an overview of the advantages and limitations of the currently used methods and new methodological approaches that could be developed to assess the presence, plant colonization and soil persistence of bioinoculants in the rhizosphere. We further discuss the possibility of integrating multidisciplinary approaches to examine the variations in microbial communities after inoculation and to track the inoculated microbial strains.\n\nEffectiveness of Plant Beneficial Microbes: Overview of the Methodological Approaches for the Assessment of Root Colonization and Persistence.", "token_count": 489, "char_count": 2425, "word_count": 319, "semantic_coherence": 1, "information_density": 0.5925, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:25.751283", "source": { "split": "train_shard_00000", "doc_id": 2782 }, "chunk_id": "train_shard_00000_2782_0", "global_id": 3072 }, { "text": "Bile salt export pump (BSEP) deficiency manifests a form of progressive intrahepatic cholestasis. This study aimed to establish a scoring system of liver histology for the uncommon genetic condition.\n\nProposal of a liver histology-based scoring system for bile salt export pump deficiency.", "token_count": 69, "char_count": 289, "word_count": 42, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:26.123031", "source": { "split": "train_shard_00000", "doc_id": 2783 }, "chunk_id": "train_shard_00000_2783_0", "global_id": 3073 }, { "text": "Trichosporonaceae incorporates six genera of physiologically and ecologically diverse fungi including both human pathogenic taxa as well as yeasts of biotechnological interest, especially those oleagenic taxa that accumulate large amounts of single cell oils (SCOs). Here, we have undertaken comparative genomic analysis of thirty-three members of the family with a view to gain insight into the molecular determinants underlying their lifestyles and niche specializations. Phylogenomic analysis revealed potential misidentification of three strains which could impact subsequent analyses. Evaluation of the predicted proteins coding sequences showed that the free-living members of the family harbour greater numbers of carbohydrate active enzymes (CAZYmes), metallo- and serine peptidases compared to their host-associated counterparts. Phylogenies of selected lipid biosynthetic enzymes encoded in the genomes of the studied strains revealed disparate evolutionary histories for some proteins inconsistent with the core genome phylogeny. However, the documented oleagenic members distinctly cluster based on the constitution of the upstream regulatory regions of genes encoding acetyl-CoA carboxylase (ACC), ATP-citrate synthase (ACS) and isocitrate dehydrogenase [NADP] (ICDH), which are among the major proteins in the lipid biosynthetic pathway of these yeasts, suggesting a possible pattern in the regulation of these genes.\n\nGenomic insights into the lifestyles, functional capacities and oleagenicity of members of the fungal family Trichosporonaceae.", "token_count": 374, "char_count": 1560, "word_count": 206, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:26.705674", "source": { "split": "train_shard_00000", "doc_id": 2784 }, "chunk_id": "train_shard_00000_2784_0", "global_id": 3074 }, { "text": "Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmark vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.\n\nGenotyping structural variants in pangenome graphs using the vg toolkit.", "token_count": 167, "char_count": 735, "word_count": 103, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:27.149387", "source": { "split": "train_shard_00000", "doc_id": 2785 }, "chunk_id": "train_shard_00000_2785_0", "global_id": 3075 }, { "text": "(1) Background: Cholesterol bioaccessibility is an indicator of cholesterol that is available for absorption and therefore can be a measure of hypocholesterolemic potential. In this work, the effect of commercial espresso coffee and coffee extracts on cholesterol solubility are studied in an in vitro model composed by glycodeoxycholic bile salt, as a measure of its bioaccessibility. (2) Methods: Polysaccharide extracts from coffees obtained with different extraction conditions were purified by selective precipitation with ethanol, and their sugars content were characterized by GC-FID. Hexane extraction allowed us to obtain the coffee lipids. Espresso coffee samples and extracts were tested regarding their concentration dependence on the solubility of labeled\n\nIn Vitro Hypocholesterolemic Effect of Coffee Compounds.", "token_count": 194, "char_count": 826, "word_count": 114, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:27.590557", "source": { "split": "train_shard_00000", "doc_id": 2786 }, "chunk_id": "train_shard_00000_2786_0", "global_id": 3076 }, { "text": "Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pangenome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pangenomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependence of pangenome features (such as the number of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pangenomes for 155 phylogenetically diverse species (from ten phyla) using 7,000 high-quality genomes to each of which the respective habitats were assigned. Species habitat ubiquity was associated with several pangenome features. In particular, core-genome size was more important for ubiquity than accessory genome size. In general, environmental preferences had a stronger impact on pangenome evolution than phylogenetic inertia. Environmental preferences explained up to 49% of the variance for pangenome features, compared with 18% by phylogenetic inertia. This observation was robust when the dataset was extended to 10,100 species (59 phyla). The importance of environmental preferences was further accentuated by convergent evolution of pangenome features in a given habitat type across different phylogenetic clades. For example, the soil environment promotes expansion of pangenome size, while host-associated habitats lead to its reduction. Taken together, we explored the global principles of pangenome evolution, quantified the influence of habitat, and phylogenetic inertia on the evolution of pangenomes and identified criteria governing species ubiquity and habitat specificity.\n\nDisentangling the impact of environmental and phylogenetic constraints on prokaryotic within-species diversity.", "token_count": 413, "char_count": 1841, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5911, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:28.217900", "source": { "split": "train_shard_00000", "doc_id": 2787 }, "chunk_id": "train_shard_00000_2787_0", "global_id": 3077 }, { "text": "The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures.\n\nA 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici.", "token_count": 141, "char_count": 643, "word_count": 86, "semantic_coherence": 1, "information_density": 0.814, "quality_score": 0.907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:28.642365", "source": { "split": "train_shard_00000", "doc_id": 2788 }, "chunk_id": "train_shard_00000_2788_0", "global_id": 3078 }, { "text": "Antifungal susceptibility profiles of rare Saccharomycotina yeasts remain missing, even though an increase in prevalence of such rare Candida species was reported in candidemia. Majority of these rare yeast species carry intrinsic resistances against at least one antifungal compound. Some species are known to be cross-resistant (against multiple drugs of the same drug class) or even multi-drug resistant (against multiple drugs of different drug classes). We performed antifungal susceptibility testing (AFST) according to EUCAST broth microdilution for 14 rare species (Clavispora lusitaniae, Candida intermedia, Candida auris, Diutina rugosa, Wickerhamiella pararugosa, Yarrowia lipolytica, Pichia norvegensis, Candida nivariensis, Kluyveromyces marxianus, Wickerhamomyces anomalus, Candida palmioleophila, Meyerozyma guilliermondii, Meyerozyma caribbica, and Debaryomyces hansenii) known to cause candidemia. In total, 234 isolates were tested for amphotericin B, fluconazole, itraconazole, voriconazole, posaconazole, anidulafungin, micafungin, and caspofungin. Amphothericin B had the broadest efficiency against the 14 tested rare yeast species, while high minimum inhibitory concentrations (MICs) against azole drugs and echinocandins were common. Voriconazole was the most efficient azole drug. Multidrug resistance was observed for the species C. auris and K. marxianus. Multidrug resistant individual isolates were found for Y. lipolytica and M. caribbica. In conclusion, the observed high MIC values of the rare Saccharomycotina species tested limit antifungal treatment options, complicating the management of such infections.\n\nElevated minimum inhibitory concentrations to antifungal drugs prevail in 14 rare species of candidemia-causing Saccharomycotina yeasts.", "token_count": 497, "char_count": 1779, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6372, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:29.288051", "source": { "split": "train_shard_00000", "doc_id": 2789 }, "chunk_id": "train_shard_00000_2789_0", "global_id": 3079 }, { "text": "Bile salt hydrolase (BSH) enzymes are widely expressed by human gut bacteria and catalyze the gateway reaction leading to secondary bile acid formation. Bile acids regulate key metabolic and immune processes by binding to host receptors. There is an unmet need for a potent tool to inhibit BSHs across all gut bacteria to study the effects of bile acids on host physiology. Here, we report the development of a covalent pan-inhibitor of gut bacterial BSHs. From a rationally designed candidate library, we identified a lead compound bearing an alpha-fluoromethyl ketone warhead that modifies BSH at the catalytic cysteine residue. This inhibitor abolished BSH activity in conventional mouse feces. Mice gavaged with a single dose of this compound displayed decreased BSH activity and decreased deconjugated bile acid levels in feces. Our studies demonstrate the potential of a covalent BSH inhibitor to modulate bile acid composition in vivo.\n\nDevelopment of a covalent inhibitor of gut bacterial bile salt hydrolases.", "token_count": 259, "char_count": 1018, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6433, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:29.853465", "source": { "split": "train_shard_00000", "doc_id": 2790 }, "chunk_id": "train_shard_00000_2790_0", "global_id": 3080 }, { "text": "Modern genome analysis and phylogenomic methods have increased the number of fungal species, as well as enhanced appreciation of the degree of diversity within the fungal kingdom. In this context, we describe a new Parengyodontium species, P. americanum, which is phylogenetically related to the opportunistic human fungal pathogen P. album. Five unusual fungal isolates were recovered from five unique and confirmed coccidioidomycosis patients, and these isolates were subsequently submitted to detailed molecular and morphological identification procedures to determine identity. Molecular and morphological diagnostic analyses showed that the isolates belong to the Cordycipitaceae. Subsequently, three representative genomes were sequenced and annotated, and a new species, P. americanum, was identified. Using various genomic analyses, gene family expansions related to novel compounds and potential for ability to grow in diverse habitats are predicted. A general description of the genomic composition of this newly described species and comparison of genome content with Beauveria bassiana, Isaria fumosorosea and Cordyceps militaris shows a shared core genome of 6371 genes, and 148 genes that appear to be specific for P. americanum. This work provides the framework for future investigations of this interesting fungal species.\n\nGenomic characterization of Parengyodontium americanum sp. nov.", "token_count": 310, "char_count": 1403, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6598, "quality_score": 0.8299, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:30.449108", "source": { "split": "train_shard_00000", "doc_id": 2791 }, "chunk_id": "train_shard_00000_2791_0", "global_id": 3081 }, { "text": "The purpose of this study was to isolate Lactobacillus from gastrointestinal tract of healthy postweaning piglets and investigate its synergistic antimicrobial and probiotic effects with ZnO nanoparticles (nZnO).\n\nIsolation of swine-derived Lactobacillus plantarum and its synergistic antimicrobial and health-promoting properties with ZnO nanoparticles.", "token_count": 103, "char_count": 354, "word_count": 43, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:30.866926", "source": { "split": "train_shard_00000", "doc_id": 2792 }, "chunk_id": "train_shard_00000_2792_0", "global_id": 3082 }, { "text": "Vancomycin-resistant enterococci (VRE) are relevant nosocomial pathogens with an increasing incidence in the last decades. Their transmission is optimal in the hospital setting, as it offers two potential, large reservoirs that are closely related: susceptible patients and their environment. Here we investigate the role of the hospital environment in the nosocomial transmission of VRE by establishing concrete links between contaminated surfaces and colonized/infected patients in outbreak and non-outbreak settings. Environmental and patient VRE isolates were collected between 2013 and 2019 and analyzed by whole-genome sequencing (WGS), subsequent multilocus sequence typing (MLST), and core genome (cg) MLST. Pairs of isolates differing in <3 alleles were rated as closely related, making a transmission likely. Fifty-three environmental VRE isolates were analyzed. MLST sequence types (ST) ST203 (50.0%), ST192 (21.3%), ST117 (17.3%), ST721 (8.8%), ST80 (2%), and ST1489 (0.7%) were detected, carrying the resistance determinants\n\nTransmission of Vancomycin-Resistant Enterococci in the Hospital Setting: Uncovering the Patient-Environment Interplay.", "token_count": 304, "char_count": 1158, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6993, "quality_score": 0.8497, "entities": { "genes": [ "ST192", "ST721", "ST1489", "ST117", "ST80", "ST203" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:31.469702", "source": { "split": "train_shard_00000", "doc_id": 2793 }, "chunk_id": "train_shard_00000_2793_0", "global_id": 3083 }, { "text": "Pigeon pea (Cajanus cajan) is an important orphan crop mainly grown by smallholder farmers in India and Africa. Here, we present the first pigeon pea pangenome based on 89 accessions mainly from India and the Philippines, showing that there is significant genetic diversity in Philippine individuals that is not present in Indian individuals. Annotation of variable genes suggests that they are associated with self-fertilization and response to disease. We identified 225 SNPs associated with nine agronomically important traits over three locations and two different time points, with SNPs associated with genes for transcription factors and kinases. These results will lead the way to an improved pigeon pea breeding programme.\n\nTrait associations in the pangenome of pigeon pea (Cajanus cajan).", "token_count": 182, "char_count": 798, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8445, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:31.918762", "source": { "split": "train_shard_00000", "doc_id": 2794 }, "chunk_id": "train_shard_00000_2794_0", "global_id": 3084 }, { "text": "Probiotics are the living and non-pathogenic microbial supplements which, upon administration in adequate quantities, influence the host organism positively by improving gut health and enhancing intestinal mucosal integrity. They suppress potentially pathogenic microorganisms by competing with them for nutrients as well as space for gut adherence. Lactobacillus species are the most commonly used bacteria in the probiotic preparations and studies show that they have cholesterol-lowering effects on the hosts. Lipids are biological molecules that are insoluble in water and bile salts play a major role in their digestion as they are synthesized and conjugated to taurine or glycine in the liver. Bile salt hydrolase deconjugates taurine or glycine from bile salts. Cholesterol metabolism is influenced by the effect of Lactobacillus species on microbial populations as well as overall metabolic activity of human intestinal microflora. Deconjugation of bile salt, concentration of short-chain fatty acids and molar proportion of propionate constitute the major processes by which cholesterol lowering is brought about by Lactobacillus species. This review summarizes the cholesterol-lowering properties of this species. A significant number of Lactobacillus strains have been known to display substantial bile salt hydrolase activities and identifying those strains for use in therapeutic purposes can be a great advancement. Here, this identification is done using phylogenetic relationship for different identified potential probiotic Lactobacillus strains.\n\nCholesterol-Lowering Effects of Lactobacillus Species.", "token_count": 394, "char_count": 1619, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:32.536154", "source": { "split": "train_shard_00000", "doc_id": 2795 }, "chunk_id": "train_shard_00000_2795_0", "global_id": 3085 }, { "text": "Acquisition of mobile elements by horizontal gene transfer can play a major role in bacterial adaptation and genome evolution by providing traits that contribute to bacterial fitness. However, gaining foreign DNA can also impose significant fitness costs to the host bacteria and can even produce detrimental effects. The efficiency of horizontal acquisition of DNA is thought to be improved by the activity of xenogeneic silencers. These molecules are a functionally related group of proteins that possess affinity for the acquired DNA. Binding of xenogeneic silencers suppresses the otherwise uncontrolled expression of genes from the newly acquired nucleic acid, facilitating their integration to the bacterial regulatory networks. Even when the genes encoding for xenogeneic silencers are part of the core genome, homologs encoded by horizontally acquired elements have also been identified and studied. In this article, we discuss the current knowledge about horizontally acquired xenogeneic silencer homologs, focusing on those encoded by genomic islands, highlighting their distribution and the major traits that allow these proteins to become part of the host regulatory networks.\n\nHorizontally Acquired Homologs of Xenogeneic Silencers: Modulators of Gene Expression Encoded by Plasmids, Phages and Genomic Islands.", "token_count": 275, "char_count": 1324, "word_count": 189, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:33.088269", "source": { "split": "train_shard_00000", "doc_id": 2796 }, "chunk_id": "train_shard_00000_2796_0", "global_id": 3086 }, { "text": "Arcobacter butzleri is a foodborne emerging human pathogen, frequently displaying a multidrug resistant character. Still, the lack of comprehensive genome-scale comparative analysis has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small but diverse core-genome with 1165 genes. It presents a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA, a type I secretion system (T1SS) harboring another agglutinin and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) and other antibiotic resistant determinants. We unprecedentedly describe a genetic mechanism of A. butzleri macrolides resistance, (inactivation of a TetR repressor likely regulating an EP). Fluoroquinolones resistance correlated with Thr-85-Ile in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the main antigen PorA, we show that A. butzleri is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats indicates that phase variation likely modulates A. butzleri key adaptive functions. In summary, this study constitutes a turning point on A", "token_count": 524, "char_count": 1959, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:26:33.751915", "source": { "split": "train_shard_00000", "doc_id": 2797 }, "chunk_id": "train_shard_00000_2797_0", "global_id": 3087 }, { "text": "butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast and diverse virulence and antibiotic resistance arsenals that open a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.\n\nVirulence and antibiotic resistance plasticity of Arcobacter butzleri: Insights on the genomic diversity of an emerging human pathogen.", "token_count": 94, "char_count": 399, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:34.131431", "source": { "split": "train_shard_00000", "doc_id": 2797 }, "chunk_id": "train_shard_00000_2797_1", "global_id": 3088 }, { "text": "Acanthamoeba spp. are predominant free-living amoebae of water and soil. They have been used as tools for the isolation and culture of microbes that resist after their phagocytosis, such as Legionella-like bacteria, and, more recently giant viruses for which differences in permissiveness have been reported. However, problems have been reported regarding their identification at the species level. The present work implemented specific PCR systems for the detection and identification of Acanthamoeba species through comparison of sequences and phylogenetic analyses. Thirty-three Acanthamoeba isolates were studied, including 20 reference strains and 13 isolates retrieved from water, soil or clinical samples. Previous delineation of a core genome encompassing 826 genes based on draft genome sequences from 14 Acanthamoeba species allowed designing PCR systems for one of these core genes that encodes an alanine-tRNA ligase. These primers allowed an efficient and specific screening to detect Acanthamoeba presence. In addition, they identified all 20 reference strains, while partial and complete sequences coding for 18S ribosomal RNA identified only 11 (55%). We found that four isolates may be considered as new Acanthamoeba species. Consistent with previous studies, we demonstrated that some Acanthamoeba isolates were incorrectly assigned to species using the 18S rDNA sequences. Our implemented tool may help determining which Acanthamoeba strains are the most efficient for the isolation of associated microorganisms.\n\nCore gene-based molecular detection and identification of Acanthamoeba species.", "token_count": 382, "char_count": 1612, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6311, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:34.722399", "source": { "split": "train_shard_00000", "doc_id": 2798 }, "chunk_id": "train_shard_00000_2798_0", "global_id": 3089 }, { "text": "Diabetes has become the second most severe disease to human health. Probiotics are important for maintaining gastrointestinal homeostasis and energy balance and have been demonstrated to play a positive role in the prevention and treatment of metabolic syndromes, such as obesity, inflammation, dyslipidemia, and hyperglycemia. The objective of this study was to screen potential antidiabetic strains\n\nScreening for Potential Novel Probiotics With Dipeptidyl Peptidase IV-Inhibiting Activity for Type 2 Diabetes Attenuation", "token_count": 134, "char_count": 523, "word_count": 71, "semantic_coherence": 1, "information_density": 0.8169, "quality_score": 0.9085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:35.146242", "source": { "split": "train_shard_00000", "doc_id": 2799 }, "chunk_id": "train_shard_00000_2799_0", "global_id": 3090 }, { "text": "The design of biorelevant conditions for in vitro evaluation of orally administered drug products is contingent on obtaining accurate values for physiologically relevant parameters such as pH, buffer capacity and bile salt concentrations in upper gastrointestinal fluids.\n\nMeasuring pH and Buffer Capacity in Fluids Aspirated from the Fasted Upper Gastrointestinal Tract of Healthy Adults.", "token_count": 91, "char_count": 389, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:35.517178", "source": { "split": "train_shard_00000", "doc_id": 2800 }, "chunk_id": "train_shard_00000_2800_0", "global_id": 3091 }, { "text": "The frequency of esophageal adenocarcinoma is rising despite widespread use of proton pump inhibitors (PPIs), which heal reflux esophagitis but do not prevent reflux of weakly acidic gastric juice and bile in Barrett's esophagus patients. We aimed to determine if weakly acidic (pH 5.5) bile salt medium (WABM) causes DNA damage in Barrett's cells. Because p53 is inactivated frequently in Barrett's esophagus and p38 can assume p53 functions, we explored p38's role in DNA damage response and repair. We exposed Barrett's cells with or without p53 knockdown to WABM, and evaluated DNA damage, its response and repair, and whether these effects are p38 dependent. We also measured phospho-p38 in biopsies of Barrett's metaplasia exposed to deoxycholic acid (DCA). WABM caused phospho-H2AX increases that were blocked by a reactive oxygen species (ROS) scavenger. WABM increased phospho-p38 and reduced bromodeoxyuridine incorporation (an index of S phase entry). Repair of WABM-induced DNA damage proceeded through p38-mediated base excision repair (BER) associated with reduction-oxidation factor 1-apurinic/apyrimidinic endonuclease I (Ref-1/APE1). Cells treated with WABM supplemented with ursodeoxycholic acid (UDCA) exhibited enhanced p38-mediated responses to DNA damage. All of these effects were observed in p53-intact and p53-deficient Barrett's cells. In patients, esophageal DCA perfusion significantly increased phospho-p38 in Barrett's metaplasia. WABM exposure generates ROS, causing oxidative DNA damage in Barrett's cells, a mechanism possibly underlying the rising frequency of esophageal adenocarcinoma despite PPI usage", "token_count": 477, "char_count": 1638, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8268, "entities": { "genes": [ "APE1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:36.516362", "source": { "split": "train_shard_00000", "doc_id": 2801 }, "chunk_id": "train_shard_00000_2801_0", "global_id": 3092 }, { "text": "p38 plays a central role in oxidative DNA damage response and Ref-1/APE1-associated BER, suggesting potential chemopreventive roles for agents like UDCA that increase p38 activity in Barrett's esophagus.\n\nIn Barrett's epithelial cells, weakly acidic bile salt solutions cause oxidative DNA damage with response and repair mediated by p38.", "token_count": 96, "char_count": 338, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [ "APE1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:36.891579", "source": { "split": "train_shard_00000", "doc_id": 2801 }, "chunk_id": "train_shard_00000_2801_1", "global_id": 3093 }, { "text": "With the assembly of increasing numbers of plant genomes, it is becoming accepted that a single reference assembly does not reflect the gene diversity of a species. The production of pangenomes, which reflect the structural variation and polymorphisms in genomes, enables in depth comparisons of variation within species or higher taxonomic groups. In this review, we discuss the current and emerging approaches for pangenome assembly, analysis and visualisation. In addition, we consider the potential of pangenomes for applied crop improvement, evolutionary and biodiversity studies. To fully exploit the value of pangenomes it is important to integrate broad information such as phenotypic, environmental, and expression data to gain insights into the role of variable regions within genomes.\n\nPlant pangenomics: approaches, applications and advancements.", "token_count": 172, "char_count": 858, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7049, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:37.338923", "source": { "split": "train_shard_00000", "doc_id": 2802 }, "chunk_id": "train_shard_00000_2802_0", "global_id": 3094 }, { "text": "This first study performed on traditional fruits consumed in North Africa reveals their richness in microorganisms with beneficial attributes like cholesterol lowering capabilities. Blackberries (Rubus sp.), fresh figs (Ficus carica), and prickly pears (Opuntia ficus-indica) are fruits largely and traditionally consumed in Kabylia, a beautiful northern Algerian region. Here, 85 lactic acid bacteria (LAB)-isolates were isolated and identified by MALDI-TOF mass spectrometry. The identified species belong to Lactobacillus and Leuconostoc genera. These 85 LAB-isolates were then assessed for their capabilities to grow under conditions mimicking the gastrointestinal tract, and the resulting data were statistically treated with principal component analysis (PCA). After which, only 26 LAB-isolates were selected and characterized for their genetic relatedness using random amplified polymorphic DNA (RAPD) method. Following the genetic relatedness assessment, only 10 LAB-strains, among which nine Lactobacillus plantarum and one Lactobacillus paracasei were studied for their pathoproperties and some probiotic features. Interestingly, all of these 10 LAB-strains were devoid of adverse effects, but capable to adhere to human epithelial colorectal adenocarcinoma Caco-2 cells. Of note, these 10 LAB-strains exhibited an important in vitro hypocholesteromia effect, in strain-dependent manner. Moreover, the Lactobacillus strains exhibited a high bile salt hydrolase (BSH) activity which was correlated with expression of bsh2, bsh3 and bsh4 genes.\n\nAbundance of Lactobacillus plantarum Strains with Beneficial Attributes in Blackberries (Rubus sp.), Fresh Figs (Ficus carica), and Prickly Pears (Opuntia ficus-indica) Grown and Harvested in Algeria.", "token_count": 471, "char_count": 1754, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6767, "quality_score": 0.8384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:37.980423", "source": { "split": "train_shard_00000", "doc_id": 2803 }, "chunk_id": "train_shard_00000_2803_0", "global_id": 3095 }, { "text": "Devosia are well known for their dominance in soil habitats contaminated with various toxins and are best characterized for their bioremediation potential. In this study, we compared the genomes of 27 strains of Devosia with aim to understand their metabolic abilities. The analysis revealed their adaptive gene repertoire which was bared from 52% unique pan-gene content. A striking feature of all genomes was the abundance of oligo- and di-peptide permeases (oppABCDF and dppABCDF) with each genome harboring an average of 60.7 ± 19.1 and 36.5 ± 10.6 operon associated genes respectively. Apart from their primary role in nutrition, these permeases may help Devosia to sense environmental signals and in chemotaxis at stressed habitats. Through sequence similarity network analyses, we identified 29 Opp and 19 Dpp sequences that shared very little homology with any other sequence suggesting an expansive short peptidic transport system within Devosia. The substrate determining components of these permeases viz. OppA and DppA further displayed a large diversity that separated into 12 and 9 homologous clusters respectively in addition to large number of isolated nodes. We also dissected the genome scale positive evolution and found genes associated with growth (exopolyphosphatase, HesB_IscA_SufA family protein), detoxification (moeB, nifU-like domain protein, alpha/beta hydrolase), chemotaxis (cheB, luxR) and stress response (phoQ, uspA, luxR, sufE) were positively selected. The study highlights the genomic plasticity of the Devosia spp. for conferring adaptation, bioremediation and the potential to utilize a wide range of substrates. The widespread toxin-antitoxin loci and 'open' state of the pangenome provided evidence of plastic genomes and a much larger genetic repertoire of the genus which is yet uncovered.", "token_count": 477, "char_count": 1831, "word_count": 267, "semantic_coherence": 1, "information_density": 0.7041, "quality_score": 0.8521, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:38.633427", "source": { "split": "train_shard_00000", "doc_id": 2804 }, "chunk_id": "train_shard_00000_2804_0", "global_id": 3096 }, { "text": "Defining the Environmental Adaptations of Genus Devosia: Insights into its Expansive Short Peptide Transport System and Positively Selected Genes.", "token_count": 36, "char_count": 146, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:39.003805", "source": { "split": "train_shard_00000", "doc_id": 2804 }, "chunk_id": "train_shard_00000_2804_1", "global_id": 3097 }, { "text": "Bile acid (BA) signatures are altered in many disease states. BA metabolism is an important microbial function to assist gut colonization and persistence, as well as microbial survival during gastro intestinal (GI) transit and it is an important criteria for potential probiotic bacteria. Microbes that express bile salt hydrolase (BSH), gateway BA modifying enzymes, are considered to have an advantage in the gut. This property is reported as selectively limited to gut-associated microbes. Food-associated microbes have the potential to confer health benefits to the human consumer. Here, we report that food associated Lactobacillus plantarum strains are capable of BA metabolism, they can withstand BA associated stress and propagate, a recognised important characteristic for GIT survival. Furthermore, we report that these food associated Lactobacillus plantarum strains have the selective ability to alter BA signatures in favour of receptor activation that would be beneficial to humans. Indeed, all of the strains examined showed a clear preference to alter human glycol-conjugated BAs, although clear strain-dependent modifications were also evident. This study demonstrates that BA metabolism by food-borne non-pathogenic bacteria is beneficial to both microbe and man and it identifies an evolutionary-conserved characteristic, previously considered unique to gut residents, among food-associated non-pathogenic isolates.\n\nBeneficial bile acid metabolism from Lactobacillus plantarum of food origin.", "token_count": 341, "char_count": 1512, "word_count": 209, "semantic_coherence": 1, "information_density": 0.622, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:39.571397", "source": { "split": "train_shard_00000", "doc_id": 2805 }, "chunk_id": "train_shard_00000_2805_0", "global_id": 3098 }, { "text": "Hydrophobic bile salts are considered to promote liver fibrosis in cholestasis. However, evidence for this widely accepted hypothesis remains scarce. In established animal models of cholestasis, e.g., by\n\nGlycochenodeoxycholate Promotes Liver Fibrosis in Mice with Hepatocellular Cholestasis.", "token_count": 83, "char_count": 292, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:39.951424", "source": { "split": "train_shard_00000", "doc_id": 2806 }, "chunk_id": "train_shard_00000_2806_0", "global_id": 3099 }, { "text": "Hypercholesterolemia is the leading cause of cardiovascular disease worldwide. In this study, the lactic acid bacteria (Lactobacillus plantarum H6) screened from homemade fermented foods in northeastern China were used to study their cholesterol-lowering ability and to analyze their degradation mechanism. Results showed that L. plantarum H6 significantly reduced serum cholesterol levels in C57BL/6 mice fed a hypercholesterolemia diet. It mainly promoted the expression of CYP7A1 gene by inhibiting the farnesoid X receptor pathway to increase the in vivo synthesis of bile acids and improved the intestinal microbial community structure of C57BL/6 mice to increase the abundance of bacterial flora containing bile salt hydrolase activity. Hence, L. plantarum H6 played a role in reducing the cholesterol content in mice.\n\nReduction of serum cholesterol and its mechanism by Lactobacillus plantarum H6 screened from local fermented food products.", "token_count": 252, "char_count": 949, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:41.121595", "source": { "split": "train_shard_00000", "doc_id": 2807 }, "chunk_id": "train_shard_00000_2807_0", "global_id": 3100 }, { "text": "In recent years, numerous outbreaks of multidrug-resistant Pseudomonas aeruginosa have been reported across the world. Once an outbreak occurs, besides routinely testing isolates for susceptibility to antimicrobials, it is required to check their virulence genotypes and clonality profiles. Replacing pulsed-field gel electrophoresis DNA fingerprinting are faster, easier-to-use, and less expensive polymerase chain reaction (PCR)-based methods for characterizing hospital isolates. P. aeruginosa possesses a mosaic genome structure and a highly conserved core genome displaying low sequence diversity and a highly variable accessory genome that communicates with other Pseudomonas species via horizontal gene transfer. Multiple-locus variable-number tandem-repeat analysis and multilocus sequence typing methods allow for phylogenetic analysis of isolates by PCR amplification of target genes with the support of Internet-based services. The target genes located in the core genome regions usually contain low-frequency mutations, allowing the resulting phylogenetic trees to infer evolutionary processes. The multiplex PCR-based open reading frame typing (POT) method, integron PCR, and exoenzyme genotyping can determine a genotype by PCR amplifying a specific insertion gene in the accessory genome region using a single or a multiple primer set. Thus, analyzing P. aeruginosa isolates for their clonality, virulence factors, and resistance characteristics is achievable by combining the clonality evaluation of the core genome based on multiple-locus targeting methods with other methods that can identify specific virulence and antimicrobial genes. Software packages such as eBURST, R, and Dendroscope, which are powerful tools for phylogenetic analyses, enable researchers and clinicians to visualize clonality associations in clinical isolates.\n\nMolecular epidemiology of clinically high-risk Pseudomonas aeruginosa strains: Practical overview.", "token_count": 453, "char_count": 1952, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:41.787463", "source": { "split": "train_shard_00000", "doc_id": 2808 }, "chunk_id": "train_shard_00000_2808_0", "global_id": 3101 }, { "text": "Clinical and in vitro studies showed selected oral microorganisms to be related to delayed wound healing and ulcerative oral mucositis. However, it is not known whether this effect is due to reduced metabolism and/or the reduced reproductive capacity of epithelial cells. Therefore, we studied the influence of the oral microorganisms Porphyromonas gingivalis, Candida glabrata, and Candida kefyr on cell metabolism and reproductive capacity of oral epithelial cells, aimed to further unravel the pathogenesis of oral mucositis.\n\nExploring the role of oral microorganisms in the pathogenesis of mucositis by assessing their impact on metabolic activity and reproductive capacity of epithelial cells in vitro.", "token_count": 179, "char_count": 708, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6078, "quality_score": 0.8039, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:42.252555", "source": { "split": "train_shard_00000", "doc_id": 2809 }, "chunk_id": "train_shard_00000_2809_0", "global_id": 3102 }, { "text": "Transferable DNA markers are essential for breeding and genetics. Grapevine (Vitis) breeders utilize disease resistance alleles from congeneric species ~20 million years divergent, but existing Vitis marker platforms have cross-species transfer rates as low as 2%. Here, we apply a marker strategy targeting the inferred Vitis core genome. Incorporating seven linked-read de novo assemblies and three existing assemblies, the Vitis collinear core genome is estimated to converge at 39.8 Mb (8.67% of the genome). Adding shotgun genome sequences from 40 accessions enables identification of conserved core PCR primer binding sites flanking polymorphic haplotypes with high information content. From these target regions, we develop 2,000 rhAmpSeq markers as a PCR multiplex and validate the panel in four biparental populations spanning the diversity of the Vitis genus, showing transferability increases to 91.9%. This marker development strategy should be widely applicable for genetic studies in many taxa, particularly those ~20 million years divergent.\n\nHaplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.", "token_count": 289, "char_count": 1167, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:42.837527", "source": { "split": "train_shard_00000", "doc_id": 2810 }, "chunk_id": "train_shard_00000_2810_0", "global_id": 3103 }, { "text": "Streptococcus agalactiae are important pathogenic bacteria that cause severe infections in humans, especially neonates. The mechanism by which ST-17 causes invasive infections than other STs is not well understood. In this study, we sequenced the first genome of a S. agalactiae ST-17 strain isolated in Brazil using the Illumina HiSeq 2500 technology. S. agalactiae GBS90356 ST-17 belongs to the capsular type III and was isolated from a neonatal with a fatal case of meningitis. The genome presented a size of 2.03 Mbp and a G + C content of 35.2%. S. agalactiae has 706 genes in its core genome and an open pan-genome with a size of 5.020 genes, suggesting a high genomic plasticity. GIPSy software was used to identify 10 Pathogenicity islands (PAIs) which corresponded to 15% of the genome size. IslandViewer4 corroborated the prediction of six PAIs. The pathogenicity islands showed important virulence factors genes for S. agalactiae e.g. neu, cps, dlt, fbs, cfb, lmb. SignalP detected 20 proteins with signal peptides among the 352 proteins found in PAIs, which 60% were located in the SagPAI_5. SagPAI_2 and 5 were mainly detected in ST-17 strains studied. Moreover, we identified 51 unique genes, 9 recombination regions and a large number of SNPs with an average of 760.3 polymorphisms, which can be related with high genomic plasticity and virulence during host-pathogen interactions. Our results showed implications for pathogenesis, evolution, concept of species and in silico analysis value to understand the epidemiology and genome plasticity of S. agalactiae.\n\nComparative genomic analysis and identification of pathogenicity islands of hypervirulent ST-17 Streptococcus agalactiae Brazilian strain.", "token_count": 501, "char_count": 1716, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6336, "quality_score": 0.8168, "entities": { "genes": [ "GBS90356" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:43.524686", "source": { "split": "train_shard_00000", "doc_id": 2811 }, "chunk_id": "train_shard_00000_2811_0", "global_id": 3104 }, { "text": "The application of green chemistry concepts in catalysis has considerably increased in recent years, and the interest in using sustainable solvents in the chemical industry is growing. One of the recent proposals to fall in line with this is to employ seawater as a solvent in biocatalytic processes. This involves selecting halotolerant strains capable of carrying out chemical conversions in the presence of the salt concentrations found in this solution. Recent studies by our group have revealed the interest in using strains belonging to Debaryomyces and Schwanniomyces for catalytic processes run in this medium. In the present work, we select other yeasts based on their halotolerance to widen the scope of this strategy. We consider them for the monoreduction of 1-phenylpropane-1,2-dione, a well-characterized reaction that produces acyloin intermediates of pharmaceutical interest. The results obtained herein indicate that using seawater as a solvent for this reaction is possible. The best ones were obtained for Saccharomyces cerevisiae FY86 and Kluyveromyces marxianus, for which acyloins with different stereochemistry were obtained with good to excellent enantiomeric excess.\n\nWhole-Cell Biocatalysis in Seawater: New Halotolerant Yeast Strains for the Regio- and Stereoselectivity Reduction of 1-Phenylpropane-1,2-Dione in Saline-Rich Media.", "token_count": 331, "char_count": 1358, "word_count": 192, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "FY86" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:44.091268", "source": { "split": "train_shard_00000", "doc_id": 2812 }, "chunk_id": "train_shard_00000_2812_0", "global_id": 3105 }, { "text": "Genetic diversity and metabolic properties of Lactococcus lactis subsp. lactis were explored using phylogenetic, pan-genomic and metatranscriptomic analysis. The genomes, used in the current study, were available and downloaded from the GenBank which were primarily related with microorganisms isolated from dairy products and secondarily from other foodstuffs. To study the genetic diversity of the microorganism, various bioinformatics tools were employed such as average nucleotide identity, digital DNA-DNA hybridization, phylogenetic analysis, clusters of orthologous groups analysis, KEGG orthology analysis and pan-genomic analysis. The results showed that Lc. lactis subsp. lactis strains cannot be sufficiently separated into phylogenetic lineages based on the 16S rRNA gene sequences and core genome-based phylogenetic analysis was more appropriate. Pan-genomic analysis of the strains indicated that the core, accessory and unique genome comprised of 1036, 3146 and 1296 genes, respectively. Considering the results of pan-genomic and KEGG orthology analyses, the metabolic network of Lc. lactis subsp. lactis was rebuild regarding its carbohydrates' metabolic capabilities. Based on the metatranscriptomic data during the ripening of the Swiss-type Maasdam cheese at 20 °C and 5 °C, it was shown that the microorganism performed mixed acid fermentation producing lactate, formate, acetate, ethanol and 2,3-butanediol. Mixed acid fermentation was more pronounced at higher ripening temperatures. At lower ripening temperatures, the genes involved in mixed acid fermentation were repressed while lactate production remained unaffected resembling to a homolactic fermentation. Comparative genomics and metatranscriptomic analysis are powerful tools to gain knowledge on the genomic diversity of the lactic acid bacteria used as starter cultures as well as on the metabolic activities occurring in fermented dairy products.", "token_count": 486, "char_count": 1931, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6031, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:44.740968", "source": { "split": "train_shard_00000", "doc_id": 2813 }, "chunk_id": "train_shard_00000_2813_0", "global_id": 3106 }, { "text": "Investigation of genomic characteristics and carbohydrates' metabolic activity of Lactococcus lactis subsp. lactis during ripening of a Swiss-type cheese.", "token_count": 43, "char_count": 154, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:45.102460", "source": { "split": "train_shard_00000", "doc_id": 2813 }, "chunk_id": "train_shard_00000_2813_1", "global_id": 3107 }, { "text": "Wheat flour has recently been recognised as an exposure vehicle for the foodborne pathogen Shiga toxin-producing Escherichia coli (STEC). Wheat flour milled on two sequential production days in October 2016, and implicated in a Canada wide outbreak of STEC O121:H19, was analysed for the presence of STEC in November 2018. Stored in sealed containers at ambient temperature, the water activity of individual flour samples was below 0.5 at 6 months post-milling and remained static or decreased slightly in individual samples during 18 months of additional storage. STEC O121 was isolated, with the same genotype (stx2a, eae, hlyA) and core genome multilocus sequence type as previous flour and clinical isolates associated with the outbreak. The result of this analysis demonstrates the potential for STEC to persist in wheat flour at levels associated with outbreak infections for periods of up to two years. This has implications for the potential for STEC to survive in other foods with low water activity.\n\nShiga toxin-producing Escherichia coli survives storage in wheat flour for two years.", "token_count": 270, "char_count": 1096, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6118, "quality_score": 0.8059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:45.652374", "source": { "split": "train_shard_00000", "doc_id": 2814 }, "chunk_id": "train_shard_00000_2814_0", "global_id": 3108 }, { "text": "In the study, Lactobacillus delbrueckii subsp. bulgaricus (L. bulgaricus) and Lactobacillus paracasei subsp. paracasei (L. paracasei) were isolated from food products and identified. The probiotics were co-encapsulated by emulsification technique with transglutaminase-induced gelation of whey protein isolate (WPI). A double layer was formed by xanthan gum (XG). The survival of both free and microencapsulated cells in each step was enumerated. The results showed that high entrapment yield (86.36 ± 1.07%) was achieved, WPI-XG provided significant protection for cells in simulated gastric juice and bile tolerance tests compared with free cells. Besides, the survivability under thermal condition also strengthened. During freeze-drying process, the survival was improved and naked cells cannot be seen on microcapsules surface when trehalose was added into WPI solution as a lyoprotectant. Additionally, the structure changes of WPI/XG in the encapsulation process were investigated by Fourier transform infrared spectrophotometer (FT-IR) and the thermal properties were studied by differential scanning calorimetry (DSC).\n\nLayer (whey protein isolate) -by-layer (xanthan gum) microencapsulation enhances survivability of L. bulgaricus and L. paracasei under simulated gastrointestinal juice and thermal conditions.", "token_count": 345, "char_count": 1320, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:46.224315", "source": { "split": "train_shard_00000", "doc_id": 2815 }, "chunk_id": "train_shard_00000_2815_0", "global_id": 3109 }, { "text": "Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing\n\nDifferential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing", "token_count": 118, "char_count": 481, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7612, "quality_score": 0.8806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:46.608905", "source": { "split": "train_shard_00000", "doc_id": 2816 }, "chunk_id": "train_shard_00000_2816_0", "global_id": 3110 }, { "text": "Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.\n\nGene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance.", "token_count": 472, "char_count": 2321, "word_count": 310, "semantic_coherence": 1, "information_density": 0.5742, "quality_score": 0.7871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:47.258998", "source": { "split": "train_shard_00000", "doc_id": 2817 }, "chunk_id": "train_shard_00000_2817_0", "global_id": 3111 }, { "text": "Functional dyspepsia (FD) is a complex disorder, in which multiple mechanisms underlie symptom generation, including impaired duodenal barrier function. Moreover, an altered duodenal bile salt pool was recently discovered in patients with FD. We aimed to evaluate the relationship between bile salts, bacterial translocation, and duodenal mucosal permeability in FD.\n\nRelationship between bile salts, bacterial translocation, and duodenal mucosal integrity in functional dyspepsia.", "token_count": 116, "char_count": 481, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7302, "quality_score": 0.8651, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:47.643933", "source": { "split": "train_shard_00000", "doc_id": 2818 }, "chunk_id": "train_shard_00000_2818_0", "global_id": 3112 }, { "text": "Hypervirulent Klebsiella pneumoniae (hvKP) causes Klebsiella-induced liver abscess. Capsule is important for the pathogenesis of Klebsiella in systemic infection, but its role in gut colonisation is not well understood. By generating ΔwcaJ, Δwza and Δwzy capsule-null mutants in a prototypical K1 hypervirulent isolate, we show that inactivation of wza (capsule exportase) and wzy (capsule polymerase) confer cell envelope defects in addition to capsule loss, making them susceptible to bile salts and detergent stress. Bile salt resistance is restored when the initial glycosyltransferase wcaJ was inactivated together with wzy, indicating that build-up of capsule intermediates contribute to cell envelope defects. Mouse gut colonisation competition assays show that the capsule and its regulator RmpA were not required for hvKP to persist in the gut, although initial colonisation was decreased in the mutants. Both ΔrmpA and ΔwcaJ mutants gradually outcompeted the wild type in the gut, whereas Δwza and Δwzy mutants were less fit than wild type. Together, our results advise caution in using the right capsule-null mutant for determination of capsule's role in bacterial pathogenesis. With the use of ΔwcaJ mutant, we found that although the capsule is important for bacterial survival outside the gut environment, it imposes a fitness cost in the gut.\n\nCell envelope defects of different capsule-null mutants in K1 hypervirulent Klebsiella pneumoniae can affect bacterial pathogenesis.", "token_count": 393, "char_count": 1491, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7959, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:48.266571", "source": { "split": "train_shard_00000", "doc_id": 2819 }, "chunk_id": "train_shard_00000_2819_0", "global_id": 3113 }, { "text": "The bile salt export pump (BSEP), a key player in hepatic bile acid clearance, has been the center of research on drug-induced cholestasis. However, such studies focus primarily on the direct inhibition of BSEP, often overlooking the potential impact of transcriptional repression. This work aims to explore the disruption of bile acid efflux caused by drug-induced BSEP repression.\n\nMetformin Disrupts Bile Acid Efflux by Repressing Bile Salt Export Pump Expression.", "token_count": 124, "char_count": 467, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:48.651963", "source": { "split": "train_shard_00000", "doc_id": 2820 }, "chunk_id": "train_shard_00000_2820_0", "global_id": 3114 }, { "text": "Antimicrobial combinations have been proven as a promising approach in the confrontation with multi-drug resistant bacterial pathogens. In the present study, we identify and characterize a synergistic interaction of broad-spectrum nitroreductase-activated prodrugs 5-nitrofurans, with a secondary bile salt, Sodium Deoxycholate (DOC) in growth inhibition and killing of enterobacteria.\n\nIn vitro synergy between sodium deoxycholate and furazolidone against enterobacteria.", "token_count": 125, "char_count": 472, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7759, "quality_score": 0.8879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:49.033190", "source": { "split": "train_shard_00000", "doc_id": 2821 }, "chunk_id": "train_shard_00000_2821_0", "global_id": 3115 }, { "text": "The secondary structures of human serum albumin (HSA) and bovine serum albumin (BSA) were disrupted in the solution of sodium dodecyl sulfate (SDS), while being hardly damaged in the solution of the bile salt, sodium cholate (NaCho). In the present work, the removal of dodecyl sulfate (DS) ions bound to these proteins was attempted by adding various amounts of NaCho. The extent of removal was estimated by the restoration of α-helical structure of each protein disrupted by SDS. Increases and decreases in α-helical structure were examined using the mean residue ellipticity at 222 nm, [θ]\n\nRemoval of Dodecyl Sulfate Ions Bound to Human and Bovine Serum Albumins Using Sodium Cholate.", "token_count": 197, "char_count": 688, "word_count": 110, "semantic_coherence": 1, "information_density": 0.5818, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:49.497427", "source": { "split": "train_shard_00000", "doc_id": 2822 }, "chunk_id": "train_shard_00000_2822_0", "global_id": 3116 }, { "text": "Human salmonellosis caused by the consumption of eggs and chicken meat contaminated with Salmonella Enteritidis has become a continuing public health concern worldwide. In this study we adopted whole genome sequencing (WGS) to determine the genetic relationship and antimicrobial resistance of S. enterica strains isolated from a poultry breeding enterprise that consists of one breeding chicken farm, one egg hatchery and one commercial chicken farm. A total of 148 S. enterica including 147 S. Enteritidis strains were isolated from 2100 fecal swab samples, with 16 (5.3 %, 16/300) from breeding chicken farm, 38 (4.2 %, 38/900) from egg hatchery and 94 (10.4 %, 94/900) from commercial chicken farm. WGS revealed that all 147 S. Enteritidis strains belonged to ST11, and further divided into 4 different ribosomal STs and 64 core genome STs. Single nucleotide polymorphism typing suggested the presence of the vertical transmission of S. Enteritidis from breeding chicken to commercial chicken. Three different antimicrobial-resistant plasmids including one bla\n\nVertical transmission of Salmonella Enteritidis with heterogeneous antimicrobial resistance from breeding chickens to commercial chickens in China.", "token_count": 328, "char_count": 1213, "word_count": 176, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:50.057501", "source": { "split": "train_shard_00000", "doc_id": 2823 }, "chunk_id": "train_shard_00000_2823_0", "global_id": 3117 }, { "text": "Earthworms are used as an alternative protein source in aquaculture. These organisms serve as an ideal and favorable site for bacterial growth and activity. Hence, in our present study, we isolated and screened potential probiotic bacteria from African nightcrawler (Eudrilus eugeniae). Among 45 bacterial isolates, four (ANSCI9, BFAR9, RM3, and RM10) were selected based on their hydrophobicity, hydrolytic enzyme production, pH and fish bile tolerance, aggregation, and antimicrobial properties. The selected isolates showed good hydrophobicity (≥ 30%) and enzyme production (≥ 10 mm clearing zones), tolerance to pH and fish bile, and inhibitory properties against pathogenic microorganisms. The isolates were identified as Bacillus sp. RM3 (MH919306), Bacillus sp. RM10 (MH919308), Bacillus sp. ANSCI9 (MH919310) and Bacillus sp. BFAR9 (MH919302). These isolates were individually incorporated in the diets of Nile tilapia (Oreochromis niloticus) fingerlings for 14 days to assess their biosafety. The results showed that the survival rates in all treated groups (98.75 ± 2.5 to 100.00 ± 0.0%) were not significantly different (P < 0.05) from the control group (commercial diet) (96.25 ± 2.5%), suggesting that isolates have no adverse effect on the host. This study revealed the presence of potential probiotic microorganisms in E. eugeniae that are beneficial to the aquaculture industry.\n\nSelection and screening of bacteria from African nightcrawler, Eudrilus eugeniae (Kinberg, 1867) as potential probiotics in aquaculture.", "token_count": 500, "char_count": 1532, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [ "MH919306", "RM10", "MH919302", "BFAR9", "MH919308", "RM3", "MH919310", "ANSCI9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:50.705170", "source": { "split": "train_shard_00000", "doc_id": 2824 }, "chunk_id": "train_shard_00000_2824_0", "global_id": 3118 }, { "text": "We discussed the most recent efforts in wheat functional genomics to discover new genes and their deployment in breeding with special emphasis on advances in Asian countries. Wheat research community is making significant progress to bridge genotype-to-phenotype gap and then applying this knowledge in genetic improvement. The advances in genomics and phenomics have intrigued wheat researchers in Asia to make best use of this knowledge in gene and trait discovery. These advancements include, but not limited to, map-based gene cloning, translational genomics, gene mapping, association genetics, gene editing and genomic selection. We reviewed more than 57 homeologous genes discovered underpinning important traits and multiple strategies used for their discovery. Further, the complementary advancements in wheat phenomics and analytical approaches to understand the genetics of wheat adaptability, resilience to climate extremes and resistance to pest and diseases were discussed. The challenge to build a gold standard reference genome sequence of bread wheat is now achieved and several de novo reference sequences from the cultivars representing different gene pools will be available soon. New pan-genome sequencing resources of wheat will strengthen the foundation required for accelerated gene discovery and provide more opportunities to practice the knowledge-based breeding.\n\nAppraisal of wheat genomics for gene discovery and breeding applications: a special emphasis on advances in Asia.", "token_count": 288, "char_count": 1504, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6462, "quality_score": 0.8231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:51.272010", "source": { "split": "train_shard_00000", "doc_id": 2825 }, "chunk_id": "train_shard_00000_2825_0", "global_id": 3119 }, { "text": "For the first time, an electrophoretic deposition (EPD) method has been developed for the deposition of polymethylmethacrylate (PMMA) and PMMA-alumina films for biomedical implant applications. The proposed biomimetic approach was based on the use of a bile salt, sodium cholate (NaCh), which served as a multifunctional solubilizing, charging, dispersing and film-forming agent. Investigations revealed PMMA-Ch\n\nElectrophoretic deposition of polymethylmethacrylate and composites for biomedical applications.", "token_count": 140, "char_count": 509, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:51.696175", "source": { "split": "train_shard_00000", "doc_id": 2826 }, "chunk_id": "train_shard_00000_2826_0", "global_id": 3120 }, { "text": "A pangenome is a collection of genomic sequences found in the entire species rather than a single individual. It allows for comprehensive, species-wide characterization of genetic variations and mining of variable genes which may play important roles in phenotypes of interest. Recent advances in sequencing technologies have facilitated draft genome sequence construction and have made pangenome constructions feasible. Here, we present a reference genome-based iterative mapping and assembly method to construct a pangenome for a legume species.\n\nLegume Pangenome Construction Using an Iterative Mapping and Assembly Approach.", "token_count": 124, "char_count": 628, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7356, "quality_score": 0.8678, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:52.079341", "source": { "split": "train_shard_00000", "doc_id": 2827 }, "chunk_id": "train_shard_00000_2827_0", "global_id": 3121 }, { "text": "Methylcellulose (MC) has a demonstrated capacity to reduce fat absorption, hypothetically through bile salt (BS) activity inhibition. We investigated MC cholesterol-lowering mechanism, and compared the influence of two BS, sodium taurocholate (NaTC) and sodium taurodeoxycholate (NaTDC), which differ slightly by their architecture and exhibit contrasting functions during lipolysis. BS/MC bulk interactions were investigated by rheology, and BS behaviour at the MC/water interface studied with surface pressure and ellipsometry measurements. In vitro lipolysis studies were performed to evaluate the effect of BS on MC-stabilised emulsion droplets microstructure, with confocal microscopy, and free fatty acids release, with the pH-stat method. Our results demonstrate that BS structure dictates their interactions with MC, which, in turn, impact lipolysis. Compared to NaTC, NaTDC alters MC viscoelasticity more significantly, which may correlate with its weaker ability to promote lipolysis, and desorbs from the interface at lower concentrations, which may explain its higher propensity to destabilise emulsions.\n\nInteractions of bile salts with a dietary fibre, methylcellulose, and impact on lipolysis.", "token_count": 292, "char_count": 1208, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7178, "quality_score": 0.8589, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:52.633960", "source": { "split": "train_shard_00000", "doc_id": 2828 }, "chunk_id": "train_shard_00000_2828_0", "global_id": 3122 }, { "text": "ATP-binding cassette (ABC) transporters are the members of the efflux pumps that are responsible for the removal of cytotoxic substances by active transport. ABCB11, the bile salt efflux pump of hepatocytes, coordinates cellular excretion of numerous conjugated bile salts into the bile canaliculi, whereas ABCB4 acts as an ATP-dependent floppase translocating phosphatidylcholine from the inner to the outer leaflet of the bile canalicular membrane. Loss of functional ABCB11 and ABCB4 proteins causes early-onset refractory cholestasis or cholangiopathy. In this study, we investigated the expression and localization pattern of ABCB11 and ABCB4 using immunohistochemistry and RNA profiling in liver samples from patients with different types and stages of chronic cholestatic liver disease, with emphasis on primary sclerosing cholangitis (PSC), compared to a variety of cholestatic and noncholestatic hepatopathies. Therefore, ABCB11 and ABCB4 expressions were investigated on formalin-fixed and paraffin-embedded (FFPE) material in a patient cohort of total 43 patients with or without cholestatic liver diseases, on protein level using immunohistochemistry and on RNA level using nanoString technology. Intriguingly, our results demonstrated increased expression of ABCB11 and ABCB4 on protein as well as RNA level in PSC, and the expression pattern correlated with disease progression. We concluded from our study that patients with PSC demonstrate altered expression levels and pattern of ABCB11 and ABCB4 which correlated with disease progression; thereby, ABCB11 and ABCB4 analysis may be a useful tool for assessment of disease stages in PSC.\n\nExpression Analysis of ATP-Binding Cassette Transporters ABCB11 and ABCB4 in Primary Sclerosing Cholangitis and Variety of Pediatric and Adult Cholestatic and Noncholestatic Liver Diseases.", "token_count": 475, "char_count": 1844, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5349, "quality_score": 0.7674, "entities": { "genes": [ "ABCB11", "ABCB4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:53.275816", "source": { "split": "train_shard_00000", "doc_id": 2829 }, "chunk_id": "train_shard_00000_2829_0", "global_id": 3123 }, { "text": "The pangenome refers to a collection of genomic sequence found in the entire species or population rather than in a single individual; the sequence can be core, present in all individuals, or accessory (variable or dispensable), found in a subset of individuals only. While pangenomic studies were first undertaken in bacterial species, developments in genome sequencing and assembly approaches have allowed construction of pangenomes for eukaryotic organisms, fungi, plants, and animals, including two large-scale human pangenome projects. Analysis of the these pangenomes revealed key differences, most likely stemming from divergent evolutionary histories, but also surprising similarities.\n\nPangenomics Comes of Age: From Bacteria to Plant and Animal Applications.", "token_count": 163, "char_count": 768, "word_count": 107, "semantic_coherence": 1, "information_density": 0.7757, "quality_score": 0.8879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:53.744339", "source": { "split": "train_shard_00000", "doc_id": 2830 }, "chunk_id": "train_shard_00000_2830_0", "global_id": 3124 }, { "text": "Fabeae legumes such as pea and faba bean form symbiotic nodules with a large diversity of soil Rhizobium leguminosarum symbiovar viciae (Rlv) bacteria. However, bacteria competitive to form root nodules (CFN) are generally not the most efficient to fix dinitrogen, resulting in a decrease in legume crop yields. Here, we investigate differential selection by host plants on the diversity of Rlv. A large collection of Rlv was collected by nodule trapping with pea and faba bean from soils at five European sites. Representative genomes were sequenced. In parallel, diversity and abundance of Rlv were estimated directly in these soils using metabarcoding. The CFN of isolates was measured with both legume hosts. Pea/faba bean CFN were associated to Rlv genomic regions. Variations of bacterial pea and/or faba bean CFN explained the differential abundance of Rlv genotypes in pea and faba bean nodules. No evidence was found for genetic association between CFN and variations in the core genome, but variations in specific regions of the nod locus, as well as in other plasmid loci, were associated with differences in CFN. These findings shed light on the genetic control of CFN in Rlv and emphasise the importance of host plants in controlling Rhizobium diversity.\n\nHost-specific competitiveness to form nodules in Rhizobium leguminosarum symbiovar viciae.", "token_count": 330, "char_count": 1359, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5782, "quality_score": 0.7891, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:54.334218", "source": { "split": "train_shard_00000", "doc_id": 2831 }, "chunk_id": "train_shard_00000_2831_0", "global_id": 3125 }, { "text": "The human pathogens N. gonorrhoeae and N. meningitidis display robust intra- and interstrain glycan diversity associated with their O-linked protein glycosylation (pgl) systems. In an effort to better understand the evolution and function of protein glycosylation operating there, we aimed to determine if other human-restricted, Neisseria species similarly glycosylate proteins and if so, to assess the levels of glycoform diversity. Comparative genomics revealed the conservation of a subset of genes minimally required for O-linked protein glycosylation glycan and established those pgl genes as core genome constituents of the genus. In conjunction with mass spectrometric-based glycan phenotyping, we found that extant glycoform repertoires in N. gonorrhoeae, N. meningitidis and the closely related species N. polysaccharea and N. lactamica reflect the functional replacement of a progenitor glycan biosynthetic pathway. This replacement involved loss of pgl gene components of the primordial pathway coincident with the acquisition of two exogenous glycosyltransferase genes. Critical to this discovery was the identification of a ubiquitous but previously unrecognized glycosyltransferase gene (pglP) that has uniquely undergone parallel but independent pseudogenization in N. gonorrhoeae and N. meningitidis. We suggest that the pseudogenization events are driven by processes of compositional epistasis leading to gene decay. Additionally, we documented instances where inter-species recombination influences pgl gene status and creates discordant genetic interactions due ostensibly to the multi-locus nature of pgl gene networks. In summary, these findings provide a novel perspective on the evolution of protein glycosylation systems and identify phylogenetically informative, genetic differences associated with Neisseria species.\n\nGenetic determinants of genus-level glycan diversity in a bacterial protein glycosylation system.", "token_count": 471, "char_count": 1943, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6124, "quality_score": 0.8062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:55.004402", "source": { "split": "train_shard_00000", "doc_id": 2832 }, "chunk_id": "train_shard_00000_2832_0", "global_id": 3126 }, { "text": "Cocultures bear great potential in the conversion of complex substrates and process intensification, as well as, in the formation of unique components only available due to inter-species interactions. Dynamic data of coculture composition is necessary for understanding and optimizing coculture systems. However, most standard online determined parameters measure the sum of all species in the reactor system. The kinetic behavior of the individual species remains unknown. Up to now, different offline methods are available to determine the culture composition, as well as the online measurement of fluorescence of genetically modified organisms. To avoid any genetic modification, a noninvasive online monitoring tool based on the scattered light spectrum was developed for microtiter plate cultivations. To demonstrate the potential, a coculture consisting of the bacterium Lactococcus lactis and the yeast Kluyveromyces marxianus was cultivated. Via partial least squares regression of scattered light spectra, the online determination of the individual biomass concentrations without further sampling and analyses is possible. The results were successfully validated by a Coulter counter-analysis, taking advantage of the different cell sizes of both organisms. The findings prove the applicability of the new method to follow in detail the dynamics of a coculture.\n\nNoninvasive tool for optical online monitoring of individual biomass concentrations in a defined coculture.", "token_count": 296, "char_count": 1479, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:55.612499", "source": { "split": "train_shard_00000", "doc_id": 2833 }, "chunk_id": "train_shard_00000_2833_0", "global_id": 3127 }, { "text": "The recognition in 2011 of the methicillin resistance determinate mecC among staphylococci has raised many questions over its evolution and epidemiology. While mecC has been best studied in Staphylococcus aureus it has also been described in at least nine other species of staphylococci. In most cases these studies are limited to single isolates. In the widespread animal commensal Staphylococcus sciuri mecC has been described in two isolates and is located within a distinct SCCmec-mecC composite element. In this study, a further 11 mecA/mecC S. sciuri isolated from dairy farms in England and Wales in 2015 and 2016 were genome sequenced and characterised. The results show that two variants of the SCCmec-mecC element are present in S. sciuri, differentiated by different ccr alleles and likely to have arisen by homologous recombination. A phylogeny of sixty genome-sequenced S. sciuri isolates was made using core genome multi-locus sequence typing and reveals a diverse population with the SCCmec-mecC element present in four distinct branches, indicative of four independent acquisitions by S. sciuri. Finally, the study identified the rapid clonal expansion of a mecA/mecC lineage of S. sciuri among dairy farms across a wide geographical area which may contribute to the future dissemination of this methicillin resistance cassette.\n\nGenomic epidemiology of methicillin-resistant Staphylococcus sciuri carrying a SCCmec-mecC hybrid element.", "token_count": 392, "char_count": 1452, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:56.233441", "source": { "split": "train_shard_00000", "doc_id": 2834 }, "chunk_id": "train_shard_00000_2834_0", "global_id": 3128 }, { "text": "Impairment of the oesophageal epithelium in patients with reflux oesophagitis (RE) is a cytokine-mediated injury rather than a chemical burn. The present study was conducted to explore CaSR/NLRP3 inflammasome pathway activation and cytokines IL-1β and IL-18 release in oesophageal epithelia injured by refluxates and the effects of Tojapride on that signal regulation. Using a modified RE rat model with Tojapride administration and Tojapride-pretreated SV40-immortalized human oesophageal epithelial cells (HET-1A) exposed to acidic bile salts pretreated with Tojapride, we evaluated the therapeutic effects of Tojapride on oesophageal epithelial barrier function, the expression of CaSR/NLRP3 inflammasome pathway-related proteins and the release of downstream cytokines in response to acidic bile salt irritation. In vivo, Tojapride treatment ameliorated the general condition and pathological lesions of the oesophageal epithelium in modified RE rats. In addition, Tojapride effectively blocked the CaSR-mediated NLRP3 inflammasome activation in modified RE rats. In vitro, Tojapride treatment can reverse the harmful effect of acidic bile salts, which reduced transepithelial electrical resistance (TEER), up-regulated the CaSR-mediated NLRP3 inflammasome pathway and increased caspase-1 activity, LDH release and cytokines secretion. Taken together, these data show that Tojapride can prevent CaSR-mediated NLRP3 inflammasome activation and alleviate oesophageal epithelial injury induced by acidic bile salt exposure.\n\nTojapride prevents CaSR-mediated NLRP3 inflammasome activation in oesophageal epithelium irritated by acidic bile salts.", "token_count": 471, "char_count": 1646, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5467, "quality_score": 0.7734, "entities": { "genes": [ "NLRP3", "SV40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:56.878992", "source": { "split": "train_shard_00000", "doc_id": 2835 }, "chunk_id": "train_shard_00000_2835_0", "global_id": 3129 }, { "text": "Livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 may be transmitted and cause morbidity and mortality in hospitals. The economic cost of stopping hospital transmission of LA-MRSA CC398 is poorly described. Early detection of transmission may limit the extent of the intervention.\n\nCore genome multi-locus sequence typing as an essential tool in a high-cost livestock-associated meticillin-resistant Staphylococcus aureus CC398 hospital outbreak.", "token_count": 134, "char_count": 494, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7581, "quality_score": 0.879, "entities": { "genes": [ "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:57.309742", "source": { "split": "train_shard_00000", "doc_id": 2836 }, "chunk_id": "train_shard_00000_2836_0", "global_id": 3130 }, { "text": "While there is strong evidence showing that many food-borne probiotics regulate cholesterol metabolism, few studies have examined how probiotics of human origin affect cholesterol metabolism. Because people living in so-called 'longevity villages' are unlikely to have hypercholesterolemia, we hypothesized that probiotics isolated from the residents would have cholesterol-reducing effects on rats with hypercholesterolemia. We isolated 16 strains of Lactobacillus from four longevity populations in China. The strains were tested in vitro for bile salt hydrolase (BSH) activity and two isolates, Lactobacillus reuteri A9 and Lactobacillus mucosae A13, were screened out. These two strains were then administered daily for 28 d to rats fed a cholesterol-rich diet. The serum total cholesterol levels in the L. reuteri A9 and L. mucosae A13 groups decreased by 24.3% and 21.6%, respectively. The serum low density lipoprotein cholesterol levels decreased by 23.8% and 25.2%, respectively. The L. reuteri A9 and L. mucosae A13 groups also exhibited upregulated hepatic mRNA expression of Sterol regulatory element-binding protein 2 (Srebp2) by 2.71-fold and 2.54-fold, respectively. The mRNA expression levels of hepatic low-density lipoprotein receptor (Ldlr) in the two groups were significantly up-regulated by 1.28-fold and 2.17-fold, respectively. The composition of gut microbiota was recovered by oral gavage in both experimental groups, and the destroyed diversity of gut microbiota was relieved.\n\nLactobacillus reuteri A9 and Lactobacillus mucosae A13 isolated from Chinese superlongevity people modulate lipid metabolism in a hypercholesterolemia rat model.", "token_count": 495, "char_count": 1666, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6034, "quality_score": 0.8017, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:57.952658", "source": { "split": "train_shard_00000", "doc_id": 2837 }, "chunk_id": "train_shard_00000_2837_0", "global_id": 3131 }, { "text": "Patients with intestinal ischemia associated with acute aortic dissection often require emergent bowel resection, which results in serious complications. We present a case of successful surgical management of extensive bowel necrosis caused by acute aortic dissection. A 42-year-old man underwent emergent subtotal resection of the small intestine, right colectomy, tube gastrostomy, and transverse colostomy; however, intestinal continuity was not restored. He developed two major postoperative complications: unconsciousness due to metabolic alkalosis caused by massive discharge from the gastrostomy and jaundice due to bile salt depletion caused by disruption of the enterohepatic circulation. His serum bilirubin levels decreased after the infusion of gastric discharge through gastrostomy into the transverse colon through the colostomy; thereafter, a second operation was performed to restore gastrointestinal continuity. Overall, patients undergoing massive bowel resection without intestinal continuity require careful management of electrolytes and bile salt.\n\nSuccessful management of extensive bowel resection without intestinal continuity: a case report.", "token_count": 275, "char_count": 1167, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:58.504234", "source": { "split": "train_shard_00000", "doc_id": 2838 }, "chunk_id": "train_shard_00000_2838_0", "global_id": 3132 }, { "text": "A description of the genetic makeup of a species based on a single genome is often insufficient because it ignores the variability in gene repertoire among multiple strains. The estimation of the pangenome of a species is a solution to this issue as it provides an overview of genes that are shared by all strains and genes that are present in only some of the genomes. These different sets of genes can then be analyzed functionally to explore correlations with unique phenotypes and adaptations. This protocol presents the usage of Roary, a Linux-native pangenome application. Roary is a straightforward software that provides 1) an overview about core and accessory genes for those interested in general trends and, also, 2) detailed information on gene presence/absence in each genome for in-depth analyses. Results are provided both in text and graphic format.\n\nEstimating Pangenomes with Roary.", "token_count": 194, "char_count": 900, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6713, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:58.950169", "source": { "split": "train_shard_00000", "doc_id": 2839 }, "chunk_id": "train_shard_00000_2839_0", "global_id": 3133 }, { "text": "The aim of this study was to evaluate the probiotic characteristics and safety of seven Enterococcus faecalis isolates from fecal samples of healthy Chinese infants. We evaluated the isolates' tolerance to low pH, survival in bile salts and NaCl, adhesion ability, biofilm formation, antimicrobial activity, toxin gene distribution, hemolysis, gelatinase activity, antibiotic resistance, and virulence to Galleria mellonella. All strains survived at pH 5.0, in 7.0% NaCl, and in 3% bile salt. Adhesion to Caco-2 cells was above 10%. Strain A3-1 had higher adhesion ability toward mucin, collagen, and BSA in vitro, better antibacterial activity, and the strongest biofilm production. We detected seven virulence genes with a distribution of asa1 (100%), cylA (71.4%), esp (85.7%), hyl (14.3%), gelE (85.7%), ace (42.9%), and agg (71.4%). Although all strains were γ-hemolytic, none showed gelatinase activity based on physiological activity detection. All isolates were susceptible to benzylpenicillin, ampicillin, ciprofloxacin, levofloxacin, moxifloxacin, tigecycline, nitrofurantoin, linezolid, and vancomycin; they were not susceptible to erythromycin, quinupristin/dalofopine, and clindamycin. The virulence test of G. mellonella showed that, except for strains 106-1 and 113-1, the other strains had toxicity lower than 10%. Strain A3-1 may have the greatest potential to be developed as a probiotic.\n\nProbiotic and Safety Properties Screening of Enterococcus faecalis from Healthy Chinese Infants.", "token_count": 479, "char_count": 1504, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:26:59.589539", "source": { "split": "train_shard_00000", "doc_id": 2840 }, "chunk_id": "train_shard_00000_2840_0", "global_id": 3134 }, { "text": "Obesity is a prevalent health problem in our population. Bariatric surgery is the indicated treatment for severe cases. It is very effective (together with an adequate lifestyle modification) but it is also associated with frequent adverse events. One of the most frequent and disturbing adverse event is diarrhea. Diarrhea after bariatric surgery may be secondary to multiple causes and the physiopathogenic mechanisms may depend on the type of surgery performed. The most frequent diarrhea mechanisms are dumping syndrome, vagotomy, short bowel syndrome, carbohydrate malabsorption, protein malabsorption, alterations of the microbiota, Clostridium difficile infection, bacterial overgrowth, bile salt malabsorption, pancreatic insufficiency, endocrinological disorders, addictive disorders, and other digestive disorders not necessarily related to surgery.\n\nReview of the management of diarrhea syndrome after a bariatric surgery.", "token_count": 219, "char_count": 933, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:00.056329", "source": { "split": "train_shard_00000", "doc_id": 2841 }, "chunk_id": "train_shard_00000_2841_0", "global_id": 3135 }, { "text": "Members of the SAR11 clade, despite their high abundance, are often poorly represented by metagenome-assembled genomes. This fact has hampered our knowledge about their ecology and genetic diversity. Here we examined 175 SAR11 genomes, including 47 new single-amplified genomes. The presence of the first genomes associated with subclade IV suggests that, in the same way as subclade V, they might be outside the proposed Pelagibacterales order. An expanded phylogenomic classification together with patterns of metagenomic recruitment at a global scale have allowed us to define new ecogenomic units of classification (genomospecies), appearing at different, and sometimes restricted, metagenomic data sets. We detected greater microdiversity across the water column at a single location than in samples collected from similar depth across the global ocean, suggesting little influence of biogeography. In addition, pangenome analysis revealed that the flexible genome was essential to shape genomospecies distribution. In one genomospecies preferentially found within the Mediterranean, a set of genes involved in phosphonate utilization was detected. While another, with a more cosmopolitan distribution, was unique in having an aerobic purine degradation pathway. Together, these results provide a glimpse of the enormous genomic diversity within this clade at a finer resolution than the currently defined clades.\n\nEcogenomics of the SAR11 clade.", "token_count": 323, "char_count": 1451, "word_count": 205, "semantic_coherence": 1, "information_density": 0.7415, "quality_score": 0.8707, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:00.617511", "source": { "split": "train_shard_00000", "doc_id": 2842 }, "chunk_id": "train_shard_00000_2842_0", "global_id": 3136 }, { "text": "Au nanoparticles (NPs) were prepared by UV light irradiation of a mixed solution of HAuCl\n\nOxidation of Sodium Deoxycholate Catalyzed by Gold Nanoparticles and Chiral Recognition Performances of Bile Salt Micelles.", "token_count": 65, "char_count": 214, "word_count": 31, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:00.983777", "source": { "split": "train_shard_00000", "doc_id": 2843 }, "chunk_id": "train_shard_00000_2843_0", "global_id": 3137 }, { "text": "Ten probiotic cultures were screened for the ability to hydrolyze soy proteins and bile salt deconjugation (BSD) to select one lactobacilli and one bifidobacteria strain to produce fermented soy beverages (FSBs) containing acerola byproduct (ABP). Next, the effect of the strains and the ABP on the technological and sensory characteristics of these beverages was evaluated during refrigerated storage for up to 28 days. None of the tested strains presented any proteolytic activity against soy proteins. Among the probiotic strains, the best BSD activities were observed for Lactobacillus acidophilus LA-5 and Bifidobacterium longum BB-46, which were further employed, individually or combined, to produce FSB supplemented or not with ABP, using Streptococcus thermophilus TH-4 as a starter, and the effect of these strains and ABP on the technological and sensory acceptability of FSB was evaluated. The probiotic strains did not influence FBS texture parameters, but ABP increased firmness in the ready product. BB-46 increased acidity, therefore decreasing acceptance, whereas the presence of LA-5 and/or ABP increased acceptance, even though the appearance was negatively affected by ABP after 21 days of storage. Thus, the presence of LA-5 and ABP contributed for the sensory acceptance of the FSBs without affecting their technological features. PRACTICAL APPLICATION: Lactobacillus acidophilus LA-5, Bifidobacterium longum BB-46, and/or acerola byproduct (ABP) were applied in the production of fermented soy beverages (FSBs). Principal components analysis was used to evaluate the formulations of the 2\n\nImpact of Acerola (Malpighia emarginata DC) Byproduct and Probiotic Strains on Technological and Sensory Features of Fermented Soy Beverages.", "token_count": 461, "char_count": 1754, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5754, "quality_score": 0.7877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:01.627097", "source": { "split": "train_shard_00000", "doc_id": 2844 }, "chunk_id": "train_shard_00000_2844_0", "global_id": 3138 }, { "text": "The aim of this study was to evaluate probiotic properties of ten Streptococcus thermophilus strains (st1 to st10) isolated from pickles in China. These strains all had β-galactosidase activity, which laid foundation for studying their probiotic properties. In this study, the bile salt hydrolase activity, lysozyme resistance, tolerance to simulated gastric juice, bile salt tolerance, and bacterial adhesion capacity to the Caco-2 cells of these selected strains were detected in vitro conditions. The results indicated that the bile salt hydrolase activities of st2, st6, and st9 were higher than that for other strains. St10 showed the greatest lysozyme resistance (> 80% survival), followed by st9, st8, st7, st5, and st6. As for the tolerance to simulated gastric juice, st5 possessed the highest survival rate (35%), followed by st6 (30%). St6 was the best performer in both bile salt tolerance and bacterial adhesion capacity to the Caco-2 cells. The results of fluorescence microscope and electron microscope further confirmed previous studies and more intuitively demonstrated the st6 strain's tolerance to harsh environments. Overall, these strains were expected to possess beneficial properties and have the potentiality to be probiotics.\n\nFirst Insight into the Probiotic Properties of Ten Streptococcus thermophilus Strains Based on In Vitro Conditions.", "token_count": 342, "char_count": 1367, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5891, "quality_score": 0.7946, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:02.208391", "source": { "split": "train_shard_00000", "doc_id": 2845 }, "chunk_id": "train_shard_00000_2845_0", "global_id": 3139 }, { "text": "Bacteria isolated from different segments of the gastro-intestinal tract (GIT) of healthy free-range broilers were screened for probiotic properties. Six strains were selected and identified as Lactobacillus gallinarum, Lactobacillus johnsonii, Lactobacillus salivarius, Lactobacillus crispatus, Enterococcus faecalis and Bacillus amyloliquefaciens based on 16S rRNA, gyrB and recA gene sequence analyses. All six strains produced exopolysaccharides (EPS) and formed biofilms under conditions simulating the broiler GIT. Lactobacillus johnsonii DPN184 and L. salivarius DPN181 produced hydrogen peroxide, and L. crispatus DPN167 and E. faecalis DPN94 produced bile salt hydrolase (BSH) and phytase. Bacillus amyloliquefaciens DPN123 produced phytase, amylase, surfactin and iturin A1. No abnormalities were observed when broilers were fed the multi-strain combination, suggesting that it could be used as a probiotic.\n\nGenetic and Phenotypic Characteristics of a Multi-strain Probiotic for Broilers.", "token_count": 315, "char_count": 999, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7287, "quality_score": 0.8643, "entities": { "genes": [ "DPN184", "DPN181", "DPN167", "DPN123", "DPN94" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:02.770271", "source": { "split": "train_shard_00000", "doc_id": 2846 }, "chunk_id": "train_shard_00000_2846_0", "global_id": 3140 }, { "text": "U6 snRNA undergoes post-transcriptional 3' end modification prior to incorporation into the active site of spliceosomes. The responsible exoribonuclease is Usb1, which removes nucleotides from the 3' end of U6 and, in humans, leaves a 2',3' cyclic phosphate that is recognized by the Lsm2-8 complex. Saccharomycescerevisiae Usb1 has additional 2',3' cyclic phosphodiesterase (CPDase) activity, which converts the cyclic phosphate into a 3' phosphate group. Here we investigate the molecular basis for the evolution of Usb1 CPDase activity. We examine the structure and function of Usb1 from Kluyveromyces marxianus, which shares 25 and 19% sequence identity to the S. cerevisiae and Homo sapiens orthologs of Usb1, respectively. We show that K. marxianus Usb1 enzyme has CPDase activity and determined its structure, free and bound to the substrate analog uridine 5'-monophosphate. We find that the origin of CPDase activity is related to a loop structure that is conserved in yeast and forms a distinct penultimate (n - 1) nucleotide binding site. These data provide structural and mechanistic insight into the evolutionary divergence of Usb1 catalysis.\n\nStructural basis for the evolution of cyclic phosphodiesterase activity in the U6 snRNA exoribonuclease Usb1.", "token_count": 360, "char_count": 1265, "word_count": 188, "semantic_coherence": 1, "information_density": 0.5904, "quality_score": 0.7952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:03.346393", "source": { "split": "train_shard_00000", "doc_id": 2847 }, "chunk_id": "train_shard_00000_2847_0", "global_id": 3141 }, { "text": "Mobile genetic elements (MGEs) drive extensive horizontal transfer in the gut microbiome. This transfer could benefit human health by conferring new metabolic capabilities to commensal microbes, or it could threaten human health by spreading antibiotic resistance genes to pathogens. Despite their biological importance and medical relevance, MGEs from the gut microbiome have not been systematically characterized. Here, we present a comprehensive analysis of chromosomal MGEs in the gut microbiome using a method that enables the identification of the mobilizable unit of MGEs. We curated a database of 5,219 putative MGEs encompassing seven MGE classes called ImmeDB. We observed that many MGEs carry genes that could confer an adaptive advantage to the gut environment including gene families involved in antibiotic resistance, bile salt detoxification, mucus degradation, capsular polysaccharide biosynthesis, polysaccharide utilization, and sporulation. We find that antibiotic resistance genes are more likely to be spread by conjugation via integrative conjugative elements or integrative mobilizable elements than transduction via prophages. Horizontal transfer of MGEs is extensive within phyla but rare across phyla, supporting phylum level niche-adaptive gene pools in the gut microbiome. ImmeDB will be a valuable resource for future studies on the gut microbiome and MGE communities.\n\nComprehensive analysis of chromosomal mobile genetic elements in the gut microbiome reveals phylum-level niche-adaptive gene pools.", "token_count": 361, "char_count": 1530, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6321, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:03.930248", "source": { "split": "train_shard_00000", "doc_id": 2848 }, "chunk_id": "train_shard_00000_2848_0", "global_id": 3142 }, { "text": "Multicellular animals and bacteria frequently engage in predator-prey and host-pathogen interactions, such as the well-studied relationship between Pseudomonas aeruginosa and the nematode Caenorhabditis elegans. This study investigates the genomic and genetic basis of bacterial-driven variability in P. aeruginosa virulence towards C. elegans to provide evolutionary insights into host-pathogen relationships.\n\nThe Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans.", "token_count": 126, "char_count": 516, "word_count": 60, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:04.319514", "source": { "split": "train_shard_00000", "doc_id": 2849 }, "chunk_id": "train_shard_00000_2849_0", "global_id": 3143 }, { "text": "In the present study, 33 strains of lactic acid bacteria (LAB) previously isolated from natural black Conservolea olives were assessed for their probiotic potential in vitro, as well as for their autoinducer-2 (AI-2) activity under standard growth conditions and the production of γ-aminobutyric acid (GABA). The probiotic tests included the in vitro resistance to low pH and resistance to bile salts, the evaluation of bile salt hydrolase activity, as well as safety tests regarding their possible haemolytic activity and their antimicrobial activity against pathogens. The results indicated that 17 strains were able to survive in low pH and in the presence of bile, with 15 of them also exhibiting partial bile salt hydrolase activity. None of the strains exhibited haemolytic activity or inhibited the growth of any of the examined pathogens. Moreover, the strains displayed generally low AI-2 activity under the growth conditions tested, regardless of the species. Interestingly, in contrast to what has been found in most foods, none of the isolates were found to produce GABA after 48 h of growth. The results from the AI-2 activity and extracellular GABA detection were considered as unexpected for LAB with probiotic attributes.\n\nΙn Vitro Screening of γ-Aminobutyric Acid and Autoinducer-2 Signalling in Lactic Acid Bacteria Exhibiting Probiotic Potential Isolated from Natural Black Conservolea Olives.", "token_count": 352, "char_count": 1412, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5187, "quality_score": 0.7593, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:04.903231", "source": { "split": "train_shard_00000", "doc_id": 2850 }, "chunk_id": "train_shard_00000_2850_0", "global_id": 3144 }, { "text": "In Denmark, outbreaks of salmonella with more than 20 cases have become rare. In November 2018, an outbreak of monophasic Salmonella Typhimurium was detected and an investigation initiated with the aim of identifying the source and controlling the outbreak. Outbreak cases were defined based on core genome multilocus sequence types. We conducted hypothesis-generating interviews, a matched case-control study, food sampling and trace-back investigations. We identified 49 cases distributed across Denmark. In univariable analyses a traditional form of raw Danish pork sausage (medister sausage), pork chops and ground veal/pork showed matched odds ratio of 26 (95% CI 3-207), 4 (95% CI 1-13) and 4 (95% CI 1-10), respectively. In a multivariable analysis, only medister sausage remained significant. Several patients described tasting or eating the sausage raw or undercooked. Samples of medister sausage analysed were negative for salmonella and investigations at the production site did not reveal the mechanism of contamination. In conclusion, in spite of having eliminated salmonella in the egg and broiler industry, Denmark is still at risk of major salmonella outbreaks. We identified a raw pork sausage as a particular risk product that needs to be thoroughly cooked before consumption. Tasting raw meat or eating undercooked pork should be discouraged.\n\nAn outbreak of monophasic", "token_count": 340, "char_count": 1388, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6537, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:05.835056", "source": { "split": "train_shard_00000", "doc_id": 2851 }, "chunk_id": "train_shard_00000_2851_0", "global_id": 3145 }, { "text": "The capacity of high-fiber foods to sequester BS during digestion is considered a mechanism to lower serum-cholesterol. We investigated the effect of hydrothermal (HT) and high-hydrostatic-pressure (HHP) on the bile salt (BS)-binding ability of dry beans, and how this relates to changes in bean microstructure, fiber content (insoluble-IDF/soluble-SDF), and viscosity. HT and HHP-600 MPa led to significant IDF reduction, including resistant starch (RS), whereas 150-450 MPa significantly increased RS, without modifying IDF/SDF content. Microscopy analysis showed that heating disrupted the bean cell wall integrity, protein matrix and starch granules more severely than 600 MPa; however, tightly-packed complexes of globular starch granules-protein-cell wall fiber formed at HHP ≤ 450 MPa. While HT significantly reduced BS-binding efficiency despite no viscosity change, HHP-treatments maintained or enhanced BS-retention. 600 MPa-treatment induced the maximum BS-binding ability and viscosity. These results demonstrate that BS-binding by beans is not solely based on their fiber content or viscosity, but is influenced by additional microstructural factors.\n\nManipulation of the dry bean (Phaseolus vulgaris L.) matrix by hydrothermal and high-pressure treatments: Impact on in vitro bile salt-binding ability.", "token_count": 349, "char_count": 1316, "word_count": 178, "semantic_coherence": 1, "information_density": 0.736, "quality_score": 0.868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:06.448667", "source": { "split": "train_shard_00000", "doc_id": 2852 }, "chunk_id": "train_shard_00000_2852_0", "global_id": 3146 }, { "text": "Aeromonads are mainly opportunistic pathogens; however, many species are emerging as important human pathogens. Therefore, monitoring these bacteria and their accurate characterization of its species is highly important. Aeromonas Aer593 strain was recovered from a diarrhoea outbreak and did not group with any previously described Aeromonas species by housekeeping gene sequencing. To clarify the taxonomic position of Aer593, its genome was sequenced and analysed by multilocus phylogenetic analysis (MLPA), in silico DNA-DNA hybridization (isDDH), average nucleotide identity (ANI) and core genome-based phylogenetic analyzes. The MLPA with the housekeeping genes gyrB, rpoD, recA, dnaJ, gyrA and dnaX ranked the Aer593 isolate into an independent branch suggesting that it could represent a new species. However, the identity percentages of Aer593 to A. caviae strains using robust genomic analysis by isDDH and ANI were at least 81.3% and 97.8%, respectively, defining Aer593 as A. caviae. Multilocus sequence typing (MLST) presented an exact match against only a single allele (groL96) and the novel ST648 was assigned for this strain. The core genome-based phylogenetic analyses with a total of 863 orthologous genes also grouped the Aer593 isolate with A. caviae reference strains. These findings warn about the possibility of misidentification of some Aeromonas strains by MLPA and show that high-resolution genome-wide analysis is essential for the correct identification of ambiguous Aeromonas strains.\n\nHigh-resolution genome-wide analysis is essential for the identification of ambiguous Aeromonas strains.", "token_count": 430, "char_count": 1620, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.821, "entities": { "genes": [ "ST648" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:07.121126", "source": { "split": "train_shard_00000", "doc_id": 2853 }, "chunk_id": "train_shard_00000_2853_0", "global_id": 3147 }, { "text": "Susceptibility of patients to antibiotic-associated\n\nBile salt metabolism is not the only factor contributing to", "token_count": 27, "char_count": 112, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:07.524721", "source": { "split": "train_shard_00000", "doc_id": 2854 }, "chunk_id": "train_shard_00000_2854_0", "global_id": 3148 }, { "text": "The pangenome provides genomic variations in the cultivated gene pool for a given species. However, as the crop's gene pool comprises many species, especially wild relatives with diverse genetic stock, here we suggest using accessions from all available species of a given genus for the development of a more comprehensive and complete pangenome, which we refer to as a super-pangenome. The super-pangenome provides a complete genomic variation repertoire of a genus and offers unprecedented opportunities for crop improvement. This opinion article focuses on recent developments in crop pangenomics, the need for a super-pangenome that should include wild species, and its application for crop improvement.\n\nSuper-Pangenome by Integrating the Wild Side of a Species for Accelerated Crop Improvement.", "token_count": 170, "char_count": 800, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:07.974440", "source": { "split": "train_shard_00000", "doc_id": 2855 }, "chunk_id": "train_shard_00000_2855_0", "global_id": 3149 }, { "text": "Among the so-called non-conventional yeasts, Kluyveromyces marxianus has extremely potent traits that are suitable for industrial applications. Indeed, it has been used for the production of various enzymes, chemicals, and macromolecules in addition to utilization of cell biomass as nutritional materials, feed and probiotics. The yeast is expected to be an efficient ethanol producer with advantages over Saccharomyces cerevisiae in terms of high growth rate, thermotolerance and a wide sugar assimilation spectrum. Results of comprehensive analyses of its genome and transcriptome may accelerate studies for applications of the yeast and may further increase its potential by combination with recent biotechnological tools including the CRISPR/Cas9 system. We thus review published studies by merging with information obtained from comprehensive data including genomic and transcriptomic data, which would be useful for future applications of K. marxianus.\n\nIntegration of comprehensive data and biotechnological tools for industrial applications of Kluyveromyces marxianus.", "token_count": 236, "char_count": 1077, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6986, "quality_score": 0.8493, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:08.452414", "source": { "split": "train_shard_00000", "doc_id": 2856 }, "chunk_id": "train_shard_00000_2856_0", "global_id": 3150 }, { "text": "With the ever-expanding number of available sequences from bacterial genomes, and the expectation that this data type will be the primary one generated from both diagnostic and research laboratories for the foreseeable future, then there is both an opportunity and a need to evaluate how effectively computational approaches can be used within bacterial genomics to predict and understand complex phenotypes, such as pathogenic potential and host source. This article applied various quantitative methods such as diversity indexes, pangenome-wide association studies (GWAS) and dimensionality reduction techniques to better understand the data and then compared how well unsupervised and supervised machine learning (ML) methods could predict the source host of the isolates. The study uses the example of the pangenomes of 1203\n\nA guide to machine learning for bacterial host attribution using genome sequence data.", "token_count": 184, "char_count": 916, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:08.907708", "source": { "split": "train_shard_00000", "doc_id": 2857 }, "chunk_id": "train_shard_00000_2857_0", "global_id": 3151 }, { "text": "Analysis of sequence diversity in the human genome is fundamental for genetic studies. Structural variants (SVs) are frequently omitted in sequence analysis studies, although each has a relatively large impact on the genome. Here, we present GraphTyper2, which uses pangenome graphs to genotype SVs and small variants using short-reads. Comparison to the syndip benchmark dataset shows that our SV genotyping is sensitive and variant segregation in families demonstrates the accuracy of our approach. We demonstrate that incorporating public assembly data into our pipeline greatly improves sensitivity, particularly for large insertions. We validate 6,812 SVs on average per genome using long-read data of 41 Icelanders. We show that GraphTyper2 can simultaneously genotype tens of thousands of whole-genomes by characterizing 60 million small variants and half a million SVs in 49,962 Icelanders, including 80 thousand SVs with high-confidence.\n\nGraphTyper2 enables population-scale genotyping of structural variation using pangenome graphs.", "token_count": 242, "char_count": 1043, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6986, "quality_score": 0.8493, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:09.383267", "source": { "split": "train_shard_00000", "doc_id": 2858 }, "chunk_id": "train_shard_00000_2858_0", "global_id": 3152 }, { "text": "Although conventional antibiotics have evolved as a staple of modern medicine, increasing antibiotic resistance and the lack of antibiotic efficacy against new bacterial threats is becoming a major medical threat. In this work, we employ single-walled carbon nanotubes (SWCNTs) known to deliver and track therapeutics in mammalian cells via intrinsic near-infrared fluorescence as carriers enhancing antibacterial delivery of doxycycline and methicillin. SWCNTs dispersed in water by antibiotics without the use of toxic bile salt surfactants facilitate efficacy enhancement for both antibiotics against\n\nSingle-Walled Carbon Nanotube-Assisted Antibiotic Delivery and Imaging in", "token_count": 168, "char_count": 678, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7667, "quality_score": 0.8833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:09.822573", "source": { "split": "train_shard_00000", "doc_id": 2859 }, "chunk_id": "train_shard_00000_2859_0", "global_id": 3153 }, { "text": "Bacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation.\n\nGene gain and loss push prokaryotes beyond the homologous recombination barrier and accelerate genome sequence divergence.", "token_count": 271, "char_count": 1287, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:10.372203", "source": { "split": "train_shard_00000", "doc_id": 2860 }, "chunk_id": "train_shard_00000_2860_0", "global_id": 3154 }, { "text": "This work investigated the reduction of bovine whey proteins antigenicity by ultrasonic pretreatment and microbial fermentation. Firstly, bovine whey proteins was pretreated by ultrasonic techniques, and its secondary structure was detected by circular dichroism. The pretreated whey proteins was used as the fermentation substrate by Kluyveromyces marxianus for microbial transformation. The single factor design and Box-Behnken Design (BBD) were carried out with the aim to optimize culture temperature, initial pH, inoculum volume and rotation speed. After optimization process, culture temperature, initial pH, inoculum volume and rotation speed were determined. Under culture temperature 35 °C, pH 7.25, inoculum level 10% and shaking speed 150 rpm, the α-LA and β-LG antigenicity in bovine whey proteins were reduced by 29% and 53%, respectively. The findings showed that combined with microbial fermentation for hydrolysis of whey proteins, ultrasonic pretreatment can be used in order to produce hypoallergenic bovine whey proteins.\n\nReducing antigenicity of bovine whey proteins by Kluyveromyces marxianus fermentation combined with ultrasound treatment.", "token_count": 316, "char_count": 1163, "word_count": 160, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:10.925513", "source": { "split": "train_shard_00000", "doc_id": 2861 }, "chunk_id": "train_shard_00000_2861_0", "global_id": 3155 }, { "text": "Bloodstream infection with Candida kefyr/Kluyveromyces marxianus: case report and draft genome.", "token_count": 28, "char_count": 95, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:11.291124", "source": { "split": "train_shard_00000", "doc_id": 2862 }, "chunk_id": "train_shard_00000_2862_0", "global_id": 3156 }, { "text": "This study aimed to investigate the hypoglycemic and hypolipidemic activities of polysaccharides from Grifola frondosa (GFP) in diabetic mice induced by high-fat diet (HFD) and streptozotocin (STZ). Results showed that oral administration of GFP markedly reduced the serum levels of fasting blood glucose (FBG), oral glucose tolerance (OGT), cholesterol (TC), triglyceride (TG) and low-density lipoprotein cholesterol (LDL-C), and significantly decreased the hepatic levels of TC, TG and free fatty acids (FFA). Meanwhile, high-dose of GFP supplementation (900 mg/kg day) also showed powerful effects on moderating the composition of intestinal microflora in diabetic mice, especially altering the functionally relevant intestinal microbial phylotypes. Spearman's correlation network analysis revealed that key microbial phylotypes responding to GFP intervention were strongly correlated with the glucose and lipid metabolic disorders associated parameters. Moreover, GFP treatment regulated mRNA expression levels of the genes responsible for hepatic glucose and lipid metabolism. It is noteworthy that GFP treatment markedly increased mRNA expression of cholesterol 7α-hydroxylase (CYP7A1) and bile salt export pump (BSEP), suggesting an enhancement of bile acids (BAs) synthesis and excretion in liver. These findings demonstrated that GFP could prevent hyperglycemia and hyperlipidemia in diabetic mice by altering gut microbiota and regulating hepatic glycolipid metabolism related genes, and therefore could be used as potential functional food ingredients for the prevention or treatment of hyperglycemia and hyperlipidemia.\n\nHypoglycemic and hypolipidemic activities of Grifola frondosa polysaccharides and their relationships with the modulation of intestinal microflora in diabetic mice induced by high-fat diet and streptozotocin.", "token_count": 501, "char_count": 1841, "word_count": 244, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:11.939154", "source": { "split": "train_shard_00000", "doc_id": 2863 }, "chunk_id": "train_shard_00000_2863_0", "global_id": 3157 }, { "text": "Lipases are hydrolytic enzymes that break the ester bonds of triglycerides, generating free fatty acids and glycerol. Extracellular lipase activity has been reported for the nonconventional yeast Kluyveromyces marxianus, grown in olive oil as a substrate, and the presence of at least eight putative lipases has been detected in its genome. However, to date, there is no experimental evidence on the physiological role of the putative lipases nor their structural and catalytic properties. In this study, a bioinformatic analysis of the genes of the putative lipases from K. marxianus L-2029 was performed, particularly identifying and characterizing the extracellular expected enzymes, due to their biotechnological relevance. The amino acid sequence of 10 putative lipases, obtained by in silico translation, ranged between 389 and 773 amino acids. Two of the analysed putative proteins showed a signal peptide, 25 and 33 amino acids long for KmYJR107Wp and KmLIP3p, and a molecular weight of 44.53 and 58.23 kDa, respectively. The amino acid alignment of KmLIP3p and KmYJR107Wp with the crystallized lipases from a patatin and the YlLip2 lipase from Yarrowia lipolytica, respectively, revealed the presence of the hydrolase characteristic motifs. From the 3D models of putative extracellular K. marxianus L-2029 lipases, the conserved pentapeptide of each was determined, being GTSMG for KmLIP3p and GHSLG for KmYJR107Wp; besides, the genes of these two enzymes (LIP3 and YJR107W) are apparently regulated by oleate response elements. The phylogenetic analysis of all K. marxianus lipases revealed evolutionary affinities with lipases from abH15.03, abH23.01, and abH23.02 families.", "token_count": 512, "char_count": 1685, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [ "LIP3", "YJR107W" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:12.592244", "source": { "split": "train_shard_00000", "doc_id": 2864 }, "chunk_id": "train_shard_00000_2864_0", "global_id": 3158 }, { "text": "Bioinformatic characterization of the extracellular lipases from Kluyveromyces marxianus.", "token_count": 25, "char_count": 89, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:12.947730", "source": { "split": "train_shard_00000", "doc_id": 2864 }, "chunk_id": "train_shard_00000_2864_1", "global_id": 3159 }, { "text": "Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131's origin, adaptation and spread is essential. E. coli ST131's ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131's population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels", "token_count": 495, "char_count": 2106, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6655, "quality_score": 0.8328, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:13.597550", "source": { "split": "train_shard_00000", "doc_id": 2865 }, "chunk_id": "train_shard_00000_2865_0", "global_id": 3160 }, { "text": "Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.\n\nAn Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates.", "token_count": 73, "char_count": 315, "word_count": 42, "semantic_coherence": 1, "information_density": 0.881, "quality_score": 0.9405, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:13.960307", "source": { "split": "train_shard_00000", "doc_id": 2865 }, "chunk_id": "train_shard_00000_2865_1", "global_id": 3161 }, { "text": "The probiotic potential of Lactobacillus rhamnosus RVP1 isolated from Sardinella longiceps was investigated in vitro. The bacterium exhibited highest tolerance at low pH, high bile salt concentration and demonstrated good antioxidant activity, hydrophobicity and inhibited both gram-negative and gram-positive indicator bacteria. To aid in process design and to unravel the fermentation kinetics, response surface methodology was devised to optimize the EPS production from L. rhamnosus and mechanistic models were developed to describe the fermentation kinetics. The optimum pH, dextrose and peptone concentrations for EPS production were 7.07, 19.995 g/L and 23.4 g/L, respectively, with a predicted yield of 724 mg/L. The actual yield under these conditions was 708±29 mg/L which was within the 95% confidence interval. The simulated mechanistic model fit the experimental values with a high degree of correlation with R2 = 0.99, 0.96 and 0.97 for the logistic growth, substrate consumption and EPS production and degradation curves respectively. The kinetic constants μ_max = 0.29 hr\n\nOptimization, kinetics and radioprotective potential of a heteropolysaccharide from L. rhamnosus RVPI.", "token_count": 332, "char_count": 1191, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [ "RVP1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:14.523432", "source": { "split": "train_shard_00000", "doc_id": 2866 }, "chunk_id": "train_shard_00000_2866_0", "global_id": 3162 }, { "text": "Isoniazid (INH) and rifampicin (RIF) continue to be first line anti‑tuberculosis (TB) drugs. However, the use of these drugs is associated with hepatotoxicity. Nuclear factor‑κB (NF‑κB) plays a crucial role in regulating immunity and inflammation. It has been reported that pyrrolidine dithiocarbamate (PDTC), an inhibitor of NF‑κB, exerts a hepatoprotective effect on acute and chronic liver damage. The aim of the present study was to explore the INH/RIF‑induced protective effects and mechanisms of PDTC on liver injury. Rats were intragastrically administered INH (50 mg/kg/day) and RIF (50 mg/kg/day) daily for 28 days. PDTC (50 mg/kg/day) was intraperitoneally injected 2 h after the co‑administration of INH and RIF to compare liver biochemical indicators in the serum, histopathological damage, NF‑κB activity, oxidative stress, hepatic mRNA expression of tumor necrosis factor (TNF)‑α, bile salt export pump (BSEP), and protein expression of BSEP. It was found that the inhibition of NF‑κB activation by PDTC treatment markedly alleviated liver biochemical and histological injury, decreased oxidative stress and mRNA levels of TNF‑α, and prevented decreases in BSEP mRNA and protein expression induced by the co‑administration of INH and RIF. Collectively, the present data suggested that INH/RIF‑induced liver injury is dependent on the activation of NF‑κB. PDTC exerted a therapeutic effect on INH/RIF‑induced liver injury by increasing BSEP expression, and exhibiting antioxidant and anti‑inflammatory activities.\n\nProtective effect of pyrrolidine dithiocarbamate on isoniazid/rifampicin‑induced liver injury in rats.", "token_count": 493, "char_count": 1630, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:15.173075", "source": { "split": "train_shard_00000", "doc_id": 2867 }, "chunk_id": "train_shard_00000_2867_0", "global_id": 3163 }, { "text": "The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.\n\nCurrent strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens.", "token_count": 393, "char_count": 1856, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:15.790966", "source": { "split": "train_shard_00000", "doc_id": 2868 }, "chunk_id": "train_shard_00000_2868_0", "global_id": 3164 }, { "text": "In 2014, antimicrobial drug-resistant Campylobacter jejuni sequence type 6964 emerged contemporaneously in poultry from 3 supply companies in the North Island of New Zealand and as a major cause of campylobacteriosis in humans in New Zealand. This lineage, not previously identified in New Zealand, was resistant to tetracycline and fluoroquinolones. Genomic analysis revealed divergence into 2 major clades; both clades were associated with human infection, 1 with poultry companies A and B and the other with company C. Accessory genome evolution was associated with a plasmid, phage insertions, and natural transformation. We hypothesize that the tetO gene and a phage were inserted into the chromosome after conjugation, leaving a remnant plasmid that was lost from isolates from company C. The emergence and rapid spread of a resistant clone of C. jejuni in New Zealand, coupled with evolutionary change in the accessory genome, demonstrate the need for ongoing Campylobacter surveillance among poultry and humans.\n\nGenomic Analysis of Fluoroquinolone- and Tetracycline-Resistant Campylobacter jejuni Sequence Type 6964 in Humans and Poultry, New Zealand, 2014-2016.", "token_count": 305, "char_count": 1171, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5906, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:16.364992", "source": { "split": "train_shard_00000", "doc_id": 2869 }, "chunk_id": "train_shard_00000_2869_0", "global_id": 3165 }, { "text": "The photophysical behavior of Coumarin 1 (Cou1), a well-known 7-aminocoumarin derivative, is very sensitive to the microenvironment in which it resides. In the present study, the effect of six bile salt variants on the photophysical behavior of Cou1 has been investigated. Dihydroxy (deoxycholates) as well as trihydroxy (cholates) bile salts with conjugated and unconjugated side chains have been chosen to get insight into the role of bile salt structure on the microenvironment of Cou1. Cou1 photophysics was found to be extremely sensitive to the aggregation process of the bile salt variants. The reduced polarity of the micellar environment stabilizes the planar intramolecular charge transferred state of Cou1, resulting in significant modulation in its photophysics in the bile salt media. The changes in the fluorescence parameters such as fluorescence intensity, emission energy, fluorescence quantum yield, anisotropy, and lifetime of Cou1 reveal that there is a distinct difference in the aggregation behavior of deoxycholates from that of cholates. The deoxycholates form micelles more or less critically similar to those of conventional surfactants, whereas the cholates self-assemble rather noncritically over a wide concentration range, thus signifying the vital role of the extra hydroxyl group in the aggregation pattern of trihydroxy bile salts. The conjugated bile salts are found to provide a relatively more compact, rigid, and hydrophobic microenvironment to Cou1 as compared to their unconjugated counterparts. Considering the significant modulation in the photophysical properties of Cou1, it has been employed as a molecular reporter for monitoring the aggregation process of bile salt variants and important information could be obtained about the effect of bile salt structure on the aggregation pattern and also about the micellar properties.\n\nPhotophysical Properties of Coumarin 1 in Bile Salt Aggregates: An Insight into the Role of Bile Salt Structure on the Aggregation Behavior.", "token_count": 482, "char_count": 2013, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5051, "quality_score": 0.7525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:17.010342", "source": { "split": "train_shard_00000", "doc_id": 2870 }, "chunk_id": "train_shard_00000_2870_0", "global_id": 3166 }, { "text": "Diet-microbe interactions play an important role in modulating the early-life microbiota, with Bifidobacterium strains and species dominating the gut of breast-fed infants. Here, we sought to explore how infant diet drives distinct bifidobacterial community composition and dynamics within individual infant ecosystems. Genomic characterisation of 19 strains isolated from breast-fed infants revealed a diverse genomic architecture enriched in carbohydrate metabolism genes, which was distinct to each strain, but collectively formed a pangenome across infants. Presence of gene clusters implicated in digestion of human milk oligosaccharides (HMOs) varied between species, with growth studies indicating that within single infants there were differences in the ability to utilise 2'FL and LNnT HMOs between strains. Cross-feeding experiments were performed with HMO degraders and non-HMO users (using spent or 'conditioned' media and direct co-culture). Further\n\nBreast milk-derived human milk oligosaccharides promote Bifidobacterium interactions within a single ecosystem.", "token_count": 254, "char_count": 1075, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7518, "quality_score": 0.8759, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:17.501295", "source": { "split": "train_shard_00000", "doc_id": 2871 }, "chunk_id": "train_shard_00000_2871_0", "global_id": 3167 }, { "text": "Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salmonella Typhi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758 Salmonella public genomes. Pangenome analysis of pBSSB1-family contigs was performed using roary and we identified three core genes amenable to a minimal pMLST scheme. Population structure analysis based on the newly developed pMLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This in silico pMLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name \"pBSSB1-family\".\n\nDevelopment of a multi-locus typing scheme for an Enterobacteriaceae linear plasmid that mediates inter-species transfer of flagella.", "token_count": 377, "char_count": 1556, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6504, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:18.109570", "source": { "split": "train_shard_00000", "doc_id": 2872 }, "chunk_id": "train_shard_00000_2872_0", "global_id": 3168 }, { "text": "Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar.\n\nWGS based study of the population structure of Salmonella enterica serovar Infantis.", "token_count": 206, "char_count": 965, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:18.611043", "source": { "split": "train_shard_00000", "doc_id": 2873 }, "chunk_id": "train_shard_00000_2873_0", "global_id": 3169 }, { "text": "Salmonella Typhimurium sequence type 313 (S. Typhimurium ST313) has caused invasive disease mainly in sub-Saharan Africa. In Brazil, ST313 strains have been recently described, and there is a lack of studies that assessed by whole genome sequencing (WGS)-the relationship of these strains. The aims of this work were to study the phylogenetic relationship of 70 S. Typhimurium genomes comparing strains of ST313 (n = 9) isolated from humans and food in Brazil among themselves, with other STs isolated in this country (n = 31) and in other parts of the globe (n = 30) by 16S rRNA sequences, the Gegenees software, whole genome multilocus sequence typing (wgMLST), and average nucleotide identity (ANI) for the genomes of ST313. Additionally, pangenome analysis was performed to verify the heterogeneity of these genomes. The phylogenetic analyses showed that the ST313 genomes were very similar among themselves. However, the ST313 genomes were usually clustered more distantly to other STs of strains isolated in Brazil and in other parts of the world. By pangenome calculation, the core genome was 2,880 CDSs and 4,171 CDSs singletons for all the 70 S. Typhimurium genomes studied. Considering the 10 ST313 genomes analyzed the core genome was 4,112 CDSs and 76 CDSs singletons. In conclusion, the ST313 genomes from Brazil showed a high similarity among them which information might eventually help in the development of vaccines and antibiotics. The pangenome analysis showed that the S. Typhimurium genomes studied presented an open pangenome, but specifically tending to become close for the ST313 strains.\n\nPhylogenetic analysis revealed that Salmonella Typhimurium ST313 isolated from humans and food in Brazil presented a high genomic similarity.", "token_count": 492, "char_count": 1755, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5203, "quality_score": 0.7601, "entities": { "genes": [ "ST313" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:19.297288", "source": { "split": "train_shard_00000", "doc_id": 2874 }, "chunk_id": "train_shard_00000_2874_0", "global_id": 3170 }, { "text": "Ammonia-scavenging transmembrane pH-gradient poly(styrene)-b-poly(ethylene oxide) polymersomes are investigated for the oral treatment and diagnosis of hyperammonemia, a condition associated with serious neurologic complications in patients with liver disease as well as in infants with urea cycle disorders. While these polymersomes are highly stable in simulated intestinal fluids at extreme bile salt and osmolality conditions, they unexpectedly do not reduce plasmatic ammonia levels in cirrhotic rats after oral dosing. Incubation in dietary fiber hydrogels mimicking the colonic environment suggests that the vesicles are probably destabilized during the dehydration of the intestinal chyme. The findings question the relevance of commonly used simulated intestinal fluids for studying vesicular stability. With the encapsulation of a pH-sensitive dye in the polymersome core, the local pH increase upon ammonia influx could be exploited to assess the ammonia concentration in the plasma of healthy and cirrhotic rats as well as in other fluids. Due to its high sensitivity and selectivity, this polymersome-based assay could prove useful in the monitoring of hyperammonemic patients and in other applications such as drug screening tests.\n\nAn Investigation of PS-b-PEO Polymersomes for the Oral Treatment and Diagnosis of Hyperammonemia.", "token_count": 333, "char_count": 1344, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:19.888431", "source": { "split": "train_shard_00000", "doc_id": 2875 }, "chunk_id": "train_shard_00000_2875_0", "global_id": 3171 }, { "text": "This study demonstrates that significant perturbation of tween20:cholesterol(1:1) niosome membrane takes place even at premicellar concentration of bile salts. Here, 1-naphthol (1-NpOH), a known and sensitive excited state proton transfer (ESPT) probe, was used to understand the nature of perturbation of the membrane in an unbuffered medium. The significant decrease in 1-NpOH fluorescence intensity in niosome-bile salt mixed system at both lower (10 °C) and higher (50 °C) temperatures indicates the bile salts [sodium cholate (NaC) and sodium deoxycholate (NaDC)] induce perturbation of niosome membranes. Variations in the fluorescence lifetime values of both the prototropic emissions (neutral and anionic species) along with the proton transfer rate of 1-NpOH confirm the bile salts perturb up to the hydrophobic core domain of the niosomal membranes. Bile salts induce size change of the niosomal membrane is confirmed through dynamic light scattering study.\n\nSignificant bile salt induced perturbation of niosome membrane: A molecular level interaction study using 1-Naphthol fluorescence.", "token_count": 309, "char_count": 1099, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:20.459539", "source": { "split": "train_shard_00000", "doc_id": 2876 }, "chunk_id": "train_shard_00000_2876_0", "global_id": 3172 }, { "text": "Plant pathogens colonize their host through the secretion of effector proteins that modulate plant metabolism and immune responses to their benefit. Plants evolve towards effector recognition, leading to host immunity. Typically, pathogen effectors are targets for recognition through plant receptors that are encoded by resistance genes. Resistance gene mediated crop immunity puts a tremendous pressure on pathogens to adapt and alter their effector repertoire to overcome recognition. We argue that the type of effector that is recognized by the host may have considerable implications on the durability of resistance against filamentous plant pathogens. Effector genes that are conserved among pathogens and reside in core genome regions are most likely to hold indispensable virulence functions. Consequently, the cost for the pathogen to overcome recognition by the host is higher than for diversified, host-specific effectors with a quantitative impact on virulence. Consequently, resistance genes that directly target conserved effector proteins without the interception of other effector proteins are potentially excellent resistance resources. © 2019 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.\n\nTarget the core: durable plant resistance against filamentous plant pathogens through effector recognition.", "token_count": 285, "char_count": 1384, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5876, "quality_score": 0.7938, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:21.021303", "source": { "split": "train_shard_00000", "doc_id": 2877 }, "chunk_id": "train_shard_00000_2877_0", "global_id": 3173 }, { "text": "The study, for the first time, reports the efficacy, safety and probiotic properties of two Lactobacillus mucosae strains, Lact. mucosae SRV5 and Lact. mucosae SRV10 isolated from donkey milk. All major in vitro screening assays were employed to evaluate studied strains. Both strains displayed good survivability at gastric pH 2.0, 0.3% bile and simulated oro-gastrointestinal fluid (above 88%). Also, cultures demonstrated good cell surface hydrophobicity and auto-aggregation ability, clearly indicating their effective cell adhesion ability. Furthermore, functional attributes for both strains demonstrated their efficient bile salt hydrolase and cholesterol-reducing ability in spent broth. In addition to this, both strains expressed significant DPPH-radical scavenging ability of both culture supernatant and intact cells. Another auxiliary health benefit exhibited by both these strains is their antimicrobial potential against 18 enteric and 5 multidrug-resistant clinical pathogens with significant inhibition zone size. Extracellular enzyme production such as lipase, amylase, protease and esterase was also studied. Detailed safety evaluation study showed the presence of innate antibiotic resistance and absence of haemolysis, DNAse and gelatinase activity in both the strains. Also, none of the strains possessed toxic mucinolytic activity in mucin degradation assay. To conclude, both donkey milk isolates, Lact. mucosae SRV5[Accession number: MK990014] and Lact. mucosae SRV10 [Accession number: MN064860], exhibited excellent probiotic ability with tolerance to simulated oro-gastrointestinal fluids, cellular hydrophobicity, auto-aggregation, bile salt hydrolase, cholesterol reduction, high antioxidant activity and antimicrobial potential especially against multidrug-resistant pathogens.", "token_count": 484, "char_count": 1808, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6853, "quality_score": 0.8427, "entities": { "genes": [ "SRV10", "SRV5", "MK990014", "MN064860" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:21.673908", "source": { "split": "train_shard_00000", "doc_id": 2878 }, "chunk_id": "train_shard_00000_2878_0", "global_id": 3174 }, { "text": "In Vitro Evaluation of Probiotic Potential and Safety Assessment of Lactobacillus mucosae Strains Isolated from Donkey's Lactation.", "token_count": 40, "char_count": 131, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:22.030573", "source": { "split": "train_shard_00000", "doc_id": 2878 }, "chunk_id": "train_shard_00000_2878_1", "global_id": 3175 }, { "text": "Biomolecule derivatives are transversally used in nanotechnology. Deciphering their aggregation behavior is a crucial issue for the rational design of functional materials. To this end, it is necessary to build libraries of selectively functionalized analogues and infer general rules. In this work we enrich the highly applicative oriented collection of steroid derivatives, by reporting a rare example of C-12 selectively modified bile salt. While nature often exploits such position to encode functions, it is unusual and not trivial to prepare similar analogues in the laboratory. The introduction of a tert-butyl phenyl residue at C-12 provided a molecule with a self-assembly that remarkably switched from rigid pole-like structures to twisted ribbons at a biologically relevant critical temperature (∼25 °C). The system was characterized by microscopy and spectroscopy techniques and compared with the C-3 functionalized analogue. The twisted ribbons generate samples with a gel texture and a viscoelastic response. The parallel analysis of the two systems suggested that the observed thermoresponsive self-assemblies occur at similar critical temperatures and are probably dictated by the nature of the substituent, but involve aggregates with different structures depending on position and orientation of the substituent. This study highlights the self-assembly properties of two appealing thermoresponsive systems. Moreover, it adds fundamental insights hereto missing in the investigations of the relation between self-assembly and structure of synthetic steroids, which are valuable for the rational design of steroidal amphiphiles.\n\nC-12 vs C-3 substituted bile salts: An example of the effects of substituent position and orientation on the self-assembly of steroid surfactant isomers.", "token_count": 385, "char_count": 1799, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6166, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:22.668452", "source": { "split": "train_shard_00000", "doc_id": 2879 }, "chunk_id": "train_shard_00000_2879_0", "global_id": 3176 }, { "text": "Trait stability of Lactobacillus plantarum was studied following daily subculture over a 90-d period. Acid and bile tolerance, self-aggregation ability, cell hydrophobicity, pathogen inhibition activity, and cholesterol removal ability of cultures subcultured 30 (Lp30), 60 (Lp60), or 90 (Lp90) times were not significantly different from the original strain (Lp0). However, carbohydrate metabolism patterns did change; the Lp0 culture was unable to use d-sorbitol, α-methyl-d-mannose, and d-raffinose, whereas Lp30, Lp60, and Lp90 cultures could. Furthermore, gluconate and gentiobiose were fully used by the Lp0 culture but only poorly used by the Lp30, Lp60, and Lp90 cultures. Milk fermentation test confirmed that L. plantarum was unable to use lactose throughout laboratory evolution. Six non-synonymous mutations in genome of the Lp30, Lp60, and Lp90 cultures were identified by whole-genome sequencing, including mutant gene encoding the phosphoglycerate mutase, which is closely related to the transport and metabolism of carbohydrates. These mutations may play an important role in changes of carbohydrate metabolism patterns observed. Understanding the evolutionary characteristics of L. plantarum will help in development for food industry.\n\nGenome-wide analysis of fermentation and probiotic trait stability in Lactobacillus plantarum during continuous culture.", "token_count": 388, "char_count": 1374, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6898, "quality_score": 0.8449, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:23.290592", "source": { "split": "train_shard_00000", "doc_id": 2880 }, "chunk_id": "train_shard_00000_2880_0", "global_id": 3177 }, { "text": "Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli have been reported in natural environments, and may be released through wastewater. In this study, the genetic relationship between ESBL-producing E. coli collected from patient urine samples (n = 45, both hospitalized patients and out-patients) and from environmental water (n = 82, from five locations), during the same time period, was investigated. Three independent water samples were collected from the municipal wastewater treatment plant, both incoming water and treated effluent water; the receiving river and lake; and a bird sanctuary near the lake, on two different occasions. The water was filtered and cultured on selective chromID ESBL agar plates in order to detect and isolate ESBL-producing E. coli. Illumina whole genome sequencing was performed on all bacterial isolates (n = 127). Phylogenetic group B2 was more common among the clinical isolates than the environmental isolates (44.4% vs. 17.1%, p < 0.01) due to a significantly higher prevalence of sequence type (ST) 131 (33.3% vs. 13.4%, p < 0.01). ST131 was, however, one of the most prevalent STs among the environmental isolates. There was no significant difference in diversity between the clinical isolates (DI 0.872 (0.790-0.953)) and the environmental isolates (DI 0.947 (0.920-0.969)). The distribution of ESBL genes was similar: blaCTX-M-15 dominated, followed by blaCTX-M-14 and blaCTX-M-27 in both the clinical (60.0%, 8.9%, and 6.7%) and the environmental isolates (62.2%, 12.2%, and 8.5%). Core genome multi-locus sequence typing showed that five environmental isolates, from incoming wastewater, treated wastewater, Svartån river and Hjälmaren lake, were indistinguishable or closely related (≤10 allele differences) to clinical isolates", "token_count": 509, "char_count": 1793, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8236, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:23.947323", "source": { "split": "train_shard_00000", "doc_id": 2881 }, "chunk_id": "train_shard_00000_2881_0", "global_id": 3178 }, { "text": "Isolates of ST131, serotype O25:H4 and fimtype H30, from the environment were as closely related to the clinical isolates as the isolates from different patients were. This study confirms that ESBL-producing E. coli are common in the aquatic environment even in low-endemic regions and suggests that wastewater discharge is an important route for the release of ESBL-producing E. coli into the aquatic environment.\n\nComparative distribution of extended-spectrum beta-lactamase-producing Escherichia coli from urine infections and environmental waters.", "token_count": 140, "char_count": 551, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:24.366158", "source": { "split": "train_shard_00000", "doc_id": 2881 }, "chunk_id": "train_shard_00000_2881_1", "global_id": 3179 }, { "text": "Human milk provides a range of nutrients and bioactive components, which can support the growth and development of infants. However, human milk composition may change due to geographic and ethnic variation. This study investigated the variation of the Chinese human milk serum proteome based on mothers with different ethnicities living in different parts of China, using TMT labeling combined with Nano-LC Q Exactive HF MS/MS proteomics. In total, 693 proteins were identified and quantified in human milk serum from Yunnan (Han and Bai ethnicity), Gansu (Han and Tibetan ethnicity), Xinjiang (Uygur ethnicity), and Inner Mongolia (Mongolian ethnicity). The biological function distribution of identified proteins and the summed intensity of proteins belonging to each biological function were similar among groups. The five relatively highly abundant milk serum proteins, lactoferrin, serum albumin, polymeric immunoglobulin receptor, macrophage mannose receptor 1, and bile salt-activated lipase were not significantly different among different geographies and ethnicities. On the other hand, we found 34 proteins that did significantly differ with geography and ethnicity. Those significantly different proteins have known strong interaction in inflammation response and regulation of multi-organism processes. Taken together, biological function distribution was similar on both the qualitative and quantitative levels, and proteins with similar abundance are important in providing basic nutrition and protection for infants, whereas the significantly different proteins may be important for the healthy development of infants from different locations and ethnicities.\n\nGeography and ethnicity related variation in the Chinese human milk serum proteome.", "token_count": 378, "char_count": 1759, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:24.950094", "source": { "split": "train_shard_00000", "doc_id": 2882 }, "chunk_id": "train_shard_00000_2882_0", "global_id": 3180 }, { "text": "Kluyveromyces marxianus is a thermotolerant yeast with multiple biotechnological potentials for industrial applications, which can metabolize a broad range of carbon sources, including less conventional sugars like lactose, xylose, arabinose and inulin. These phenotypic traits are sustained even up to 45 °C, what makes it a relevant candidate for industrial biotechnology applications, such as ethanol production. It is therefore of much interest to get more insight into the metabolism of this yeast. Recent studies suggested, that thermotolerance is achieved by reducing the number of growth-determining proteins or suppressing oxidative phosphorylation. Here we aimed to find related factors contributing to the thermotolerance of K. marxianus.\n\nReconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model.", "token_count": 206, "char_count": 837, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7982, "quality_score": 0.8991, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:25.412239", "source": { "split": "train_shard_00000", "doc_id": 2883 }, "chunk_id": "train_shard_00000_2883_0", "global_id": 3181 }, { "text": "Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).\n\nGenetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale.", "token_count": 278, "char_count": 1157, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:25.965338", "source": { "split": "train_shard_00000", "doc_id": 2884 }, "chunk_id": "train_shard_00000_2884_0", "global_id": 3182 }, { "text": "Because of their unusual chemical structure, bile salts (BS) play a fundamental role in intestinal lipid digestion and transport. BS have a planar arrangement of hydrophobic and hydrophilic moieties, which enables the BS molecules to form peculiar self-assembled structures in aqueous solutions. This molecular arrangement also has an influence on specific interactions of BS with lipid molecules and other compounds of ingested food and digestive media. Those comprise the complex scenario in which lipolysis occurs. In this review, we discuss the BS synthesis, composition, bulk interactions and mode of action during lipid digestion and transport. We look specifically into surfactant-related functions of BS that affect lipolysis, such as interactions with dietary fibre and emulsifiers, the interfacial activity in facilitating lipase and colipase anchoring to the lipid substrate interface, and finally the role of BS in the intestinal transport of lipids. Unravelling the roles of BS in the processing of lipids in the gastrointestinal tract requires a detailed analysis of their interactions with different compounds. We provide an update on the most recent findings concerning two areas of BS involvement: lipolysis and intestinal transport. We first explore the interactions of BS with various dietary fibres and food emulsifiers in bulk and at interfaces, as these appear to be key aspects for understanding interactions with digestive media. Next, we explore the interactions of BS with components of the intestinal digestion environment, and the role of BS in displacing material from the oil-water interface and facilitating adsorption of lipase. We look into the process of desorption, solubilisation of lipolysis, products and formation of mixed micelles. Finally, the BS-driven interactions of colloidal particles with the small intestinal mucus layer are considered, providing new findings for the overall assessment of the role of BS in lipid digestion and intestinal transport. This review offers a unique compilation of well-established and most recent studies dealing with the interactions of BS with food emulsifiers, nanoparticles and dietary fibre, as well as with the luminal compounds of the gut, such as lipase-colipase, triglycerides and intestinal mucus. The combined analysis of these complex interactions may provide crucial information on the pattern and extent of lipid digestion", "token_count": 520, "char_count": 2413, "word_count": 356, "semantic_coherence": 1, "information_density": 0.4972, "quality_score": 0.7486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:27:26.624415", "source": { "split": "train_shard_00000", "doc_id": 2885 }, "chunk_id": "train_shard_00000_2885_0", "global_id": 3183 }, { "text": "Such knowledge is important for controlling the uptake of dietary lipids or lipophilic pharmaceuticals in the gastrointestinal tract through the engineering of novel food structures or colloidal drug-delivery systems.\n\nBile salts in digestion and transport of lipids.", "token_count": 63, "char_count": 267, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8378, "quality_score": 0.9189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:26.982699", "source": { "split": "train_shard_00000", "doc_id": 2885 }, "chunk_id": "train_shard_00000_2885_1", "global_id": 3184 }, { "text": "The present study was aimed to explore the antihyperlipidemic and anti-inflammatory effect of acyclic isoprenoid on high fat diet fed rats. Hypercholesterolemia was induced by the diet comprising of the normal rat chow 84.3%, lard 5%, yolk powder 10%, cholesterol 0.2% and 0.5% bile salt were fed to the rats for the period of 8 weeks. The results showed that abnormally elevated levels of plasma lipid profiles. Three different doses of acyclic isoprenoid (20, 40 and 80 mg/kg b.w/day) were administered orally to hypercholesterolemia suffering rats for the period of 30 days. Among these three doses of acyclic isoprenoid, the dose 80 mg/kg b.w. was significantly decreased the plasma lipid profiles when compared to other two doses. The effect produced by acyclic isoprenoid (80 mg/kg b.w) was comparable to that of simvastatin. Therefore, 80 mg/kg b.w was fixed as a effective dose and used for further analyses. Acyclic isoprenoid administration reinstated the elevated levels of cardiac and inflammatory markers in both blood and serum of hypercholesterolemic rats. In addition, acyclic isoprenoid administration decreased activity of 3-hydroxy 3-methyl-glutaryl-CoA reductase and increased the activity of lecithin cholesterol acyl transferase. These findings suggest that the administration of acyclic isoprenoid was potentially ameliorated the cardiac marker enzymes and inflammatory markers in addition to its antihypercholesterolemic effect.\n\nAcyclic Isoprenoid Attenuates Lipid Anomalies and Inflammatory Changes in Hypercholesterolemic Rats.", "token_count": 471, "char_count": 1554, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5605, "quality_score": 0.7803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:27.625185", "source": { "split": "train_shard_00000", "doc_id": 2886 }, "chunk_id": "train_shard_00000_2886_0", "global_id": 3185 }, { "text": "Cell physiology parameters are essential aspects of biological processes; however, they are difficult to determine on-line. Dielectric spectroscopy allows the on-line estimation of viable cells and can provide important information about cell physiology during culture. In this study, we investigated the dielectric property variations in Kluyveromyces marxianus SLP1 and Saccharomyces cerevisiae ERD yeasts stressed by 5-hydroxymethyl-2-furaldehyde and 2-furaldehyde during aerobic growth. The dielectric properties of cell permittivity, specific membrane capacitance (Cm), and intracellular conductivity (σ\n\nDielectric property measurements as a method to determine the physiological state of Kluyveromyces marxianus and Saccharomyces cerevisiae stressed with furan aldehydes.", "token_count": 199, "char_count": 778, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [ "SLP1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:28.079982", "source": { "split": "train_shard_00000", "doc_id": 2887 }, "chunk_id": "train_shard_00000_2887_0", "global_id": 3186 }, { "text": "The Brucella melitensis chronic infection and drug resistance emerged as a severe health problem in humans and domestic cattle. The pathogens fast genome sequences availability fetched the possibility to address novel therapeutics targets in a rationale way. We acquired the core genes set from 56 B. melitensis publically available complete genome sequences. A stringent bioinformatics layout of comparative genomics and reverse vaccinology was followed to identify potential druggable proteins and multi-epitope vaccine constructs from core genes. The 23 proteins were shortlisted as novel druggable targets based on their role in pathogen-specific metabolic pathways, non-homologous to human and human gut microbiome proteins and their druggability potential. Furthermore, potential chimeric vaccine constructs were generated from lead T and B-cell overlapped epitopes in combination with immune enhancer adjuvants and linkers sequences. The molecular docking and MD simulation analyses ensured stable molecular interaction of a finally prioritized vaccine construct with human immune cells receptors.\n\nPotential druggable proteins and chimeric vaccine construct prioritization against Brucella melitensis from species core genome data.", "token_count": 266, "char_count": 1239, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6566, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:28.631184", "source": { "split": "train_shard_00000", "doc_id": 2888 }, "chunk_id": "train_shard_00000_2888_0", "global_id": 3187 }, { "text": "Food animals act as a reservoir for many foodborne pathogens. Salmonella enterica is one of the leading pathogens that cause food borne illness in a broad host range including animals and humans. They can also be associated with a single host species or a subset of hosts, due to genetic factors associated with colonization and infection. Adult swine are often asymptomatic carriers of a broad range of Salmonella servoars and can act as an important reservoir of infections for humans. In order to understand the genetic variations among different Salmonella serovars, Whole Genome Sequences (WGS) of fourteen Salmonella serovars from swine products were analyzed. More than 75% of the genes were part of the core genome in each isolate and the higher fraction of gene assign to different functional categories in dispensable genes indicated that these genes acquired for better adaptability and diversity. High concordance (97%) was detected between phenotypically confirmed antibiotic resistances and identified antibiotic resistance genes from WGS. The resistance determinants were mainly located on mobile genetic elements (MGE) on plasmids or integrated into the chromosome. Most of known and putative virulence genes were part of the core genome, but a small fraction were detected on MGE. Predicted integrated phage were highly diverse and many harbored virulence, metal resistance, or antibiotic resistance genes. CRISPR (Clustered regularly interspaced short palindromic repeats) patterns revealed the common ancestry or infection history among Salmonella serovars. Overall genomic analysis revealed a great deal of diversity among Salmonella serovars due to acquired genes that enable them to thrive and survive during infection.\n\nGenomic comparison of diverse Salmonella serovars isolated from swine.", "token_count": 395, "char_count": 1813, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6067, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:29.248574", "source": { "split": "train_shard_00000", "doc_id": 2889 }, "chunk_id": "train_shard_00000_2889_0", "global_id": 3188 }, { "text": "Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in\n\nHash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile.", "token_count": 170, "char_count": 733, "word_count": 100, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:29.701075", "source": { "split": "train_shard_00000", "doc_id": 2890 }, "chunk_id": "train_shard_00000_2890_0", "global_id": 3189 }, { "text": "Binding constants for thousands of cyclodextrin complexes have been reported in the literature, but much less is known about the kinetics of these host-guest complexes. In the present study, inclusion complexes of bile salts with β-cyclodextrin, γ-cyclodextrin, and a methylated β-cyclodextrin were studied by nuclear magnetic resonance (NMR) lineshape analysis to explore the structural factors that govern the complexation kinetics. For complexes with β-cyclodextrin, the association rate constants ranged from 2 × 10\n\nComplexation Kinetics of Cyclodextrins with Bile Salt Anions: Energy Barriers for the Threading of Ionic Groups.", "token_count": 172, "char_count": 633, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7528, "quality_score": 0.8764, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:30.174635", "source": { "split": "train_shard_00000", "doc_id": 2891 }, "chunk_id": "train_shard_00000_2891_0", "global_id": 3190 }, { "text": "The relationship between bacterial strains and serotonin regulation was studied via the in vitro screening of the strains. Using the transparent visibility of zebrafish, the strains for intestinal peristalsis were quickly screened. The methods and results were as follows: (1) 18 strains with outstanding gastrointestinal viability via their surface hydrophobicity, self-aggregation ability, acid tolerance, bile tolerance, simulated gastric digestion and intestinal fluid tolerance were determined from 54 unpublished strains. (2) 5dpf zebrafish were randomly selected and divided into 22 groups with 12 tails in each group. The intestinal peristalsis frequency of each group within 1 min was calculated after immersing the model zebrafish in a 10\n\nStudy of gastrointestinal tract viability and motility via modulation of serotonin in a zebrafish model by probiotics.", "token_count": 220, "char_count": 868, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6748, "quality_score": 0.8374, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:30.662123", "source": { "split": "train_shard_00000", "doc_id": 2892 }, "chunk_id": "train_shard_00000_2892_0", "global_id": 3191 }, { "text": "Optimal nutrition support has been integral in the management of cystic fibrosis (CF) since the disease was initially described. Nutritional status has a clear relationship with disease outcomes, and malnutrition in CF is typically a result of chronic negative energy balance secondary to malabsorption. As the mechanisms underlying the pathology of CF and its implications on nutrient absorption and energy expenditure have been elucidated, nutrition support has become increasingly sophisticated. Comprehensive nutrition monitoring and treatment guidelines from professional and advocacy organizations have unified the approach to nutrition optimization around the world. Newborn screening allows for early nutrition intervention and improvement in short- and long-term growth and other clinical outcomes. The nutrition support goal in CF care includes achieving optimal nutritional status to support growth and pubertal development in children, maintenance of optimal nutritional status in adult life, and optimizing fat soluble vitamin and essential fatty acid status. The mainstay of this approach is a high calorie, high-fat diet, exceeding age, and sex energy intake recommendations for healthy individuals. For patients with exocrine pancreatic insufficiency, enzyme replacement therapy is required to improve fat and calorie absorption. Enzyme dosing varies by age and dietary fat intake. Multiple potential impediments to absorption, including decreased motility, altered gut luminal bile salt and microbiota composition, and enteric inflammation must be considered. Fat soluble vitamin supplementation is required in patients with pancreatic insufficiency. In this report, nutrition support across the age and disease spectrum is discussed, with a focus on the relationships among nutritional status, growth, and disease outcomes.\n\nGrowth and Nutrition in Cystic Fibrosis.", "token_count": 382, "char_count": 1883, "word_count": 259, "semantic_coherence": 1, "information_density": 0.61, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:31.264814", "source": { "split": "train_shard_00000", "doc_id": 2893 }, "chunk_id": "train_shard_00000_2893_0", "global_id": 3192 }, { "text": "Large-scale genome sequencing and the increasingly massive use of high-throughput approaches produce a vast amount of new information that completely transforms our understanding of thousands of microbial species. However, despite the development of powerful bioinformatics approaches, full interpretation of the content of these genomes remains a difficult task. Launched in 2005, the MicroScope platform (https://www.genoscope.cns.fr/agc/microscope) has been under continuous development and provides analysis for prokaryotic genome projects together with metabolic network reconstruction and post-genomic experiments allowing users to improve the understanding of gene functions. Here we present new improvements of the MicroScope user interface for genome selection, navigation and expert gene annotation. Automatic functional annotation procedures of the platform have also been updated and we added several new tools for the functional annotation of genes and genomic regions. We finally focus on new tools and pipeline developed to perform comparative analyses on hundreds of genomes based on pangenome graphs. To date, MicroScope contains data for >11 800 microbial genomes, part of which are manually curated and maintained by microbiologists (>4500 personal accounts in September 2019). The platform enables collaborative work in a rich comparative genomic context and improves community-based curation efforts.\n\nMicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis.", "token_count": 330, "char_count": 1584, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:31.863636", "source": { "split": "train_shard_00000", "doc_id": 2894 }, "chunk_id": "train_shard_00000_2894_0", "global_id": 3193 }, { "text": "SilkDB is an open-accessibility database and powerful platform that provides comprehensive information on the silkworm (Bombyx mori) genome. Since SilkDB 2.0 was released 10 years ago, vast quantities of data about multiple aspects of the silkworm have been generated, including genome, transcriptome, Hi-C and pangenome. To visualize data at these different biological levels, we present SilkDB 3.0 (https://silkdb.bioinfotoolkits.net), a visual analytic tool for exploring silkworm data through an interactive user interface. The database contains a high-quality chromosome-level assembly of the silkworm genome, and its coding sequences and gene sets are more accurate than those in the previous version. SilkDB 3.0 provides a view of the information for each gene at the levels of sequence, protein structure, gene family, orthology, synteny, genome organization and gives access to gene expression information, genetic variation and genome interaction map. A set of visualization tools are available to display the abundant information in the above datasets. With an improved interactive user interface for the integration of large data sets, the updated SilkDB 3.0 database will be a valuable resource for the silkworm and insect research community.\n\nSilkDB 3.0: visualizing and exploring multiple levels of data for silkworm.", "token_count": 305, "char_count": 1332, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6354, "quality_score": 0.8177, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:32.436560", "source": { "split": "train_shard_00000", "doc_id": 2895 }, "chunk_id": "train_shard_00000_2895_0", "global_id": 3194 }, { "text": "Since the first genome-scale comparisons, it has been evident that the genomes of many species are unbound by strict vertical descent: Large differences in gene content can occur among genomes belonging to the same prokaryotic species, with only a fraction of genes being universal to all genomes. These insights gave rise to the pangenome concept. The pangenome is defined as the set of all the genes present in a given species and can be subdivided into the accessory genome, present in only some of the genomes, and the core genome, present in all the genomes. Pangenomes arise due to gene gain by genomes from other species through horizontal gene transfer and differential gene loss among genomes, and have been described in both prokaryotes and eukaryotes. Our current view of pangenome variation is phenomenological and incomplete. In this review, we outline the mechanistic, ecological and evolutionary drivers of and barriers to horizontal gene transfer that are likely to structure pangenomes. We highlight the key role of conflict between the host chromosome(s) and the mobile genetic elements that mediate gene exchange. We identify shortcomings in our current models of pangenome evolution and suggest directions for future research to allow a more complete understanding of how and why pangenomes evolve.\n\nThe Ecology and Evolution of Pangenomes.", "token_count": 291, "char_count": 1360, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:33.009450", "source": { "split": "train_shard_00000", "doc_id": 2896 }, "chunk_id": "train_shard_00000_2896_0", "global_id": 3195 }, { "text": "This review summarizes progress in the construction of efficient yeast ethanol producers from glucose/sucrose and lignocellulose. Saccharomyces cerevisiae is the major industrial producer of first-generation ethanol. The different approaches to increase ethanol yield and productivity from glucose in S. cerevisiae are described. Construction of the producers of second-generation ethanol is described for S. cerevisiae, one of the best natural xylose fermenters, Scheffersomyces stipitis and the most thermotolerant yeast known Ogataea polymorpha. Each of these organisms has some advantages and drawbacks. S. cerevisiae is the primary industrial ethanol producer and is the most ethanol tolerant natural yeast known and, however, cannot metabolize xylose. S. stipitis can effectively ferment both glucose and xylose and, however, has low ethanol tolerance and requires oxygen for growth. O. polymorpha grows and ferments at high temperatures and, however, produces very low amounts of ethanol from xylose. Review describes how the mentioned drawbacks could be overcome.\n\nConstruction of advanced producers of first- and second-generation ethanol in Saccharomyces cerevisiae and selected species of non-conventional yeasts (Scheffersomyces stipitis, Ogataea polymorpha).", "token_count": 320, "char_count": 1271, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:33.573063", "source": { "split": "train_shard_00000", "doc_id": 2897 }, "chunk_id": "train_shard_00000_2897_0", "global_id": 3196 }, { "text": "The aim of this study was to analyze the β-glucan contents, physicochemical features, and microbial communities in milk kefir prepared using Saccharomyces cerevisiae KU200284 isolated from cucumber jangajji, a fermented vegetable commonly eaten in Korean. Three types of milk kefir were manufactured, with (1) activated kefir grain, (2) activated kefir grain with commercial S. cerevisiae BOF, and (3) activated kefir grain with S. cerevisiae KU200284. β-Glucan contents of milk kefir using kefir grain and kefir grain with S. cerevisiae strains BOF and KU200284 were 8.29, 8.59, and 8.57%, respectively. The pH, titratable acidity, viscosity, Brix level, and alcohol contents of milk kefir using kefir grain with S. cerevisiae strains were acceptable compared with milk kefir using only kefir grain. In milk kefir produced using kefir grains and S. cerevisiae strains, 16S rRNA reads showed representative strains of Lactobacillus kefiranofaciens (>72% relative abundance) and Acetobacter fabarum (>16% relative abundance). In particular, milk kefir using kefir grain with S. cerevisiae KU200284 had the highest relative abundance of L. kefiranofaciens. In addition, the internal transcribed sequence (ITS) rRNA reads in tested milk kefir showed representative strains of Kluyveromyces marxianus (>52% relative abundance) and Saccharomyces cerevisiae (>16% relative abundance). In contrast, milk kefir using S. cerevisiae strains had higher relative abundance of S. cerevisiae (>37%). The β-glucan production, physicochemical properties, and microbial community profiling indicate that S. cerevisiae KU200284 could be used in functional dairy products as a starter culture.", "token_count": 517, "char_count": 1674, "word_count": 236, "semantic_coherence": 1, "information_density": 0.4915, "quality_score": 0.7458, "entities": { "genes": [ "KU200284" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:27:34.238583", "source": { "split": "train_shard_00000", "doc_id": 2898 }, "chunk_id": "train_shard_00000_2898_0", "global_id": 3197 }, { "text": "Short communication: Physicochemical features and microbial community of milk kefir using a potential probiotic Saccharomyces cerevisiae KU200284.", "token_count": 42, "char_count": 146, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "KU200284" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:34.597294", "source": { "split": "train_shard_00000", "doc_id": 2898 }, "chunk_id": "train_shard_00000_2898_1", "global_id": 3198 }, { "text": "Zearalenone (ZEN) is one of the common mycotoxins with quite high occurrence rate and is harmful to animal and human health. Lactobacillus reuteri is known as a probiotic bacterium with active immune stimulating and high inhibitory activity against pathogenic microorganisms. In this study, we expressed the lactonohydrolase from Rhinocladiella mackenziei CBS 650.93 (RmZHD) in L. reuteri via secretion and surface-display patterns, respectively. Endogenous signal peptides from L. reuteri were first screened to achieve high expression for efficient ZEN hydrolysis. For secretion expression, signal peptide from collagen-binding protein showed the best performance, while the one from fructose-2,6-bisphosphatase worked best for surface-display expression. Both of the engineered strains could completely hydrolyze 5.0 mg/L ZEN in 8 h without detrimental effects on bacterial growth. The acid and bile tolerance assay and anchoring experiment on Caco-2 cells indicated both of the abovementioned engineered strains could survive during digestion and colonize on intestinal tract, in which the surface-displayed strain had a better performance on ZEN hydrolysis. Biodetoxification of model ZEN-contaminated maize kernels showed the surface-displayed L. reuteri strain could completely hydrolyze 2.5 mg/kg ZEN within 4 h under low water condition. The strain could also efficiently detoxify natural ZEN-contaminated corn flour in the in vitro digestion model system. The colonized property, survival capacity, and the efficient hydrolysis performance as well as probiotic functionality make L. reuteri strain an ideal host for detoxifying residual ZEN in vivo, which shows a great potential for application in feed industry.\n\nBiodetoxification of fungal mycotoxins zearalenone by engineered probiotic bacterium Lactobacillus reuteri with surface-displayed lactonohydrolase.", "token_count": 481, "char_count": 1872, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:35.247681", "source": { "split": "train_shard_00000", "doc_id": 2899 }, "chunk_id": "train_shard_00000_2899_0", "global_id": 3199 }, { "text": "The growing prevalence of obesity has become an important problem worldwide as obesity has several health risks. Notably, factors such as excessive food consumption, a sedentary way of life, high sugar consumption, a fat-rich diet, and a certain genetic profile may lead to obesity. The present review brings together recent advances regarding the significance of interventions involving intestinal gut bacteria and host metabolic phenotypes. We assess important biological molecular mechanisms underlying the impact of gut microbiota on hosts including bile salt metabolism, short-chain fatty acids, and metabolic endotoxemia. Some previous studies have shown a link between microbiota and obesity, and associated disease reports have been documented. Thus, this review focuses on obesity and gut microbiota interactions and further develops the mechanism of the gut microbiome approach related to human obesity. Specifically, we highlight several alternative diet treatments including dietary changes and supplementation with probiotics. The future direction or comparative significance of fecal transplantation, synbiotics, and metabolomics as an approach to the modulation of intestinal microbes is also discussed.\n\nGut Microbiome Modulation Based on Probiotic Application for Anti-Obesity: A Review on Efficacy and Validation.", "token_count": 286, "char_count": 1331, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6831, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:36.502469", "source": { "split": "train_shard_00000", "doc_id": 2901 }, "chunk_id": "train_shard_00000_2901_0", "global_id": 3200 }, { "text": "This study reports the utility of the hydrophobic probe Nile Red (NR) to understand the concentration induced microenvironmental changes of sodium deoxycholate (NaDC) bile salt from the premicellar to postmicellar range. The spectroscopic properties like absorbance value, fluorescence intensity and fluorescence lifetime of NR are significantly sensitive towards different states of aggregation of NaDC bile salt. The critical aggregation concentrations of different states (dimer to primary micellar aggregates (1.0 mM), secondary micellar aggregates (7.0 mM), and higher micellar aggregates (14 mM)) have been determined from the absorbance value and fluorescence intensity measurements. The E\n\nQuantification of micropolarity and microviscosity of aggregation and salt-induced gelation of sodium deoxycholate (NaDC) using Nile red fluorescence.", "token_count": 209, "char_count": 848, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:36.962800", "source": { "split": "train_shard_00000", "doc_id": 2902 }, "chunk_id": "train_shard_00000_2902_0", "global_id": 3201 }, { "text": "The advent of culture independent approaches has greatly facilitated insights into the vast diversity of bacteria and the ecological importance they hold in nature and human health. Recently, metagenomic surveys and other culture-independent methods have begun to describe the distribution and diversity of microbial metabolism across environmental conditions, often using 16S rRNA gene as a marker to group bacteria into taxonomic units. However, the extent to which similarity at the conserved ribosomal 16S gene correlates with different measures of phylogeny, metabolic diversity, and ecologically relevant gene content remains contentious. Here, we examine the relationship between 16S identity, core genome divergence, and metabolic gene content across the ancient and ecologically important genus\n\nTaxonomic and Metabolic Incongruence in the Ancient Genus", "token_count": 183, "char_count": 862, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8445, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:37.412079", "source": { "split": "train_shard_00000", "doc_id": 2903 }, "chunk_id": "train_shard_00000_2903_0", "global_id": 3202 }, { "text": "In this study, derivatization of epigallocatechin (EGC) by representative phytosterols (stigmasterol and β-sitosterol) was performed employing Steglich esterification. The structural identity and purity of epigallocatechin β-sitosterol (ESi) and epigallocatechin stigmasterol (ESt) were confirmed by NMR, FT-IR, and HPLC-MS. Further evaluation of ESi and ESt revealed their extraordinary antioxidant activities in O/W emulsion. Two different radical sources in oil or aqueous phase were applied to explore the antioxidant behavior in O/W emulsion. The mechanism was further investigated by fluorescent microscopy and transmission electron microscopy (TEM). Furthermore, incorporation of EGC with stigmasterol and β-sitosterol notably enhanced the cholesterol-reducing activity. TEM studies suggested the hydrogen bonding of EGC strengthened the aggregation network of ESi and ESt in the bile salt micelle. The exceptional properties of ESi and ESt signified their intriguing utilization in the food industry.\n\nEnhancement of Antioxidant Activity in O/W Emulsion and Cholesterol-Reducing Capacity of Epigallocatechin by Derivatization with Representative Phytosterols.", "token_count": 315, "char_count": 1167, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:37.966184", "source": { "split": "train_shard_00000", "doc_id": 2904 }, "chunk_id": "train_shard_00000_2904_0", "global_id": 3203 }, { "text": "SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by the strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world's oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.\n\nGlobal ecotypes in the ubiquitous marine clade SAR86.", "token_count": 330, "char_count": 1540, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [ "SAR86" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:38.530976", "source": { "split": "train_shard_00000", "doc_id": 2905 }, "chunk_id": "train_shard_00000_2905_0", "global_id": 3204 }, { "text": "Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss, and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum, F. cortaderiae, and F. meridionale). Our analyses of 8 species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.\n\nComplex Evolutionary Origins of Specialized Metabolite Gene Cluster Diversity among the Plant Pathogenic Fungi of the Fusarium graminearum Species Complex.", "token_count": 415, "char_count": 1863, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6031, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:39.163959", "source": { "split": "train_shard_00000", "doc_id": 2906 }, "chunk_id": "train_shard_00000_2906_0", "global_id": 3205 }, { "text": "The ability of probiotics to exert benefits on host has been associated with different physiological functionalities in these microorganisms, namely cell surface hydrophobicity, autoaggregation, coaggregation with pathogens, antagonistic activity against pathogens and ability to survive the exposure to gastrointestinal conditions. This study assessed the effects of different concentrations of quercetin (QUE) and resveratrol (RES) on the ability of six potentially probiotic\n\nEffects of Quercetin and Resveratrol on", "token_count": 119, "char_count": 518, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7015, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:39.549101", "source": { "split": "train_shard_00000", "doc_id": 2907 }, "chunk_id": "train_shard_00000_2907_0", "global_id": 3206 }, { "text": "In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.\n\nA strategy for building and using a human reference pangenome.", "token_count": 201, "char_count": 1013, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:40.013478", "source": { "split": "train_shard_00000", "doc_id": 2908 }, "chunk_id": "train_shard_00000_2908_0", "global_id": 3207 }, { "text": "The lactic acid bacteria (LAB) and yeast strains with phytate degrading ability were isolated from Iranian traditional sourdough, and based on the acid and bile tolerance, three LAB and three yeast strains were selected and molecularly identified. In this study, baker's yeast (Saccharomyces cerevisiae) was considered as a positive control strain to investigate the nutritional and technological properties of the isolated strains. All of the identified microorganisms were characterized based on additional probiotic properties and were evaluated for nutritional and technological characteristics. The functional features are associated with degradation of phytate, antioxidant capacity, exopolysaccharides, phenolic compound content and in vitro starch digestion. Among all the tested strains the highest amount of phytase production capacity (1.64 Unit/ml) and lowest phytate content (17.49 mg/5 g) belonged to Kluyveromyces marxianus. According to the results, the bread prepared by using Kluyveromyces aestuarii possessed the highest porosity percentage (70.43%), and the lowest hardness (508.71 g).\n\nFunctional effects of phytate-degrading, probiotic lactic acid bacteria and yeast strains isolated from Iranian traditional sourdough on the technological and nutritional properties of whole wheat bread.", "token_count": 327, "char_count": 1310, "word_count": 176, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:40.580430", "source": { "split": "train_shard_00000", "doc_id": 2909 }, "chunk_id": "train_shard_00000_2909_0", "global_id": 3208 }, { "text": "Traditional taxonomy in biology assumes that life is organized in a simple tree. Attempts to classify microorganisms in this way in the genomics era led microbiologists to look for finite sets of 'core' genes that uniquely group taxa as clades in the tree. However, the diversity revealed by large-scale whole genome sequencing is calling into question the long-held model of a hierarchical tree of life, which leads to questioning of the definition of a species. Large-scale studies of microbial genome diversity reveal that the cumulative number of new genes discovered increases with the number of genomes studied as a power law and subsequently leads to the lack of evidence for a unique core genome within closely related organisms. Sampling 'enough' new genomes leads to the discovery of a replacement or alternative to any gene. This power law behaviour points to an underlying self-organizing critical process that may be guided by mutation and niche selection. Microbes in any particular niche exist within a local web of organism interdependence known as the microbiome. The same mechanism that underpins the macro-ecological scaling first observed by MacArthur and Wilson also applies to microbial communities. Recent metagenomic studies of a food microbiome demonstrate the diverse distribution of community members, but also genotypes for a single species within a more complex community. Collectively, these results suggest that traditional taxonomic classification of bacteria could be replaced with a quasispecies model. This model is commonly accepted in virology and better describes the diversity and dynamic exchange of genes that also hold true for bacteria. This model will enable microbiologists to conduct population-scale studies to describe microbial behaviour, as opposed to a single isolate as a representative.\n\nInsular Microbiogeography: Three Pathogens as Exemplars.", "token_count": 393, "char_count": 1897, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6056, "quality_score": 0.8028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:41.196089", "source": { "split": "train_shard_00000", "doc_id": 2910 }, "chunk_id": "train_shard_00000_2910_0", "global_id": 3209 }, { "text": "Multidrug-resistant Staphylococcus aureus is a leading concern worldwide. Coagulase-Negative Staphylococci are claimed to be the reservoir and source of important resistant elements in S. aureus. However, the origin and evolutionary route of resistant genes in S. aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S. aureus strains in comparison with 7,529 non-Staphylococcus aureus reference bacterial genomes. Our results reveal that S. aureus has a large open pan-genome where 97 (55%) of its known resistant-related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome mec (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides, and aminoglycosides. However, the physically linked mec-box genes (MecA-MecR-MecI) that are responsible for the maintenance of SCCmec elements is not unique to S. aureus, instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec-encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec-resistant gene phylogenies reveals that genes such as blaZ, ble, kmA, and tetK that are responsible for beta-lactam, bleomycin, kanamycin, and tetracycline resistance in S. aureus were laterally transferred from non-Staphylococcus sources. In addition, at least 11 non-SCCmec-encoded resistant genes in S. aureus, were laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S. aureus.", "token_count": 505, "char_count": 1835, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:41.848378", "source": { "split": "train_shard_00000", "doc_id": 2911 }, "chunk_id": "train_shard_00000_2911_0", "global_id": 3210 }, { "text": "Phylogenomic Analysis Reveals the Evolutionary Route of Resistant Genes in Staphylococcus aureus.", "token_count": 30, "char_count": 97, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:42.243052", "source": { "split": "train_shard_00000", "doc_id": 2911 }, "chunk_id": "train_shard_00000_2911_1", "global_id": 3211 }, { "text": "The YEASTRACT+ information system (http://YEASTRACT-PLUS.org/) is a wide-scope tool for the analysis and prediction of transcription regulatory associations at the gene and genomic levels in yeasts of biotechnological or human health relevance. YEASTRACT+ is a new portal that integrates the previously existing YEASTRACT (http://www.yeastract.com/) and PathoYeastract (http://pathoyeastract.org/) databases and introduces the NCYeastract (Non-Conventional Yeastract) database (http://ncyeastract.org/), focused on the so-called non-conventional yeasts. The information in the YEASTRACT database, focused on Saccharomyces cerevisiae, was updated. PathoYeastract was extended to include two additional pathogenic yeast species: Candida parapsilosis and Candida tropicalis. Furthermore, the NCYeastract database was created, including five biotechnologically relevant yeast species: Zygosaccharomyces baillii, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica and Komagataella phaffii. The YEASTRACT+ portal gathers 289 706 unique documented regulatory associations between transcription factors (TF) and target genes and 420 DNA binding sites, considering 247 TFs from 10 yeast species. YEASTRACT+ continues to make available tools for the prediction of the TFs involved in the regulation of gene/genomic expression. In this release, these tools were upgraded to enable predictions based on orthologous regulatory associations described for other yeast species, including two new tools for cross-species transcription regulation comparison, based on multi-species promoter and TF regulatory network analyses.\n\nYEASTRACT+: a portal for cross-species comparative genomics of transcription regulation in yeasts.", "token_count": 443, "char_count": 1724, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6238, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:42.904351", "source": { "split": "train_shard_00000", "doc_id": 2912 }, "chunk_id": "train_shard_00000_2912_0", "global_id": 3212 }, { "text": "The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models.\n\nsimurg: simulate bacterial pangenomes in R.", "token_count": 77, "char_count": 350, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:43.285011", "source": { "split": "train_shard_00000", "doc_id": 2913 }, "chunk_id": "train_shard_00000_2913_0", "global_id": 3213 }, { "text": "AcCNET (Accessory genome Constellation Network) is a Perl application to determine the variation of content in any genomic unit (e.g., bacterial genomes, plasmids, and transposons) within large datasets. It provides functional information that can be handled and visualized interactively as a bipartite network. In this chapter, we explain how to perform a statistical analysis of AcCNET data.\n\nStatistical Analysis of Accessory Genome.", "token_count": 102, "char_count": 436, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:43.709267", "source": { "split": "train_shard_00000", "doc_id": 2914 }, "chunk_id": "train_shard_00000_2914_0", "global_id": 3214 }, { "text": "Centers for Disease Control and Prevention (CDC), health departments, and other state and federal partners have linked contact with live poultry to 70 human Salmonella outbreaks in the United States from 2000 to 2017, which resulted in a total of 4,794 illnesses, 894 hospitalizations, and 7 deaths. During human salmonellosis outbreaks environmental sampling is rarely conducted as part of the outbreak investigation. CDC was contacted by state health officials on June 12, 2018, to provide support during an investigation of risk factors for Salmonella infections linked to live poultry originating at a mail-order hatchery. From January 1, 2018, to June 15, 2018, 13 human Salmonella infections in multiple states were attributed to exposure to live poultry from a single hatchery. Two serotypes of Salmonella were associated with these infections, Salmonella Enteritidis and Salmonella Litchfield. Molecular subtyping of the S. Enteritidis clinical isolates revealed they were closely related genetically (within 0 to 9 alleles) by core genome multi-locus sequence typing (cgMLST) to isolates obtained from environmental samples taken from hatchery shipping containers received at retail outlets. Environmental sampling and onsite investigation of practices was conducted at the mail-order hatchery during an investigation on June 19, 2018. A total of 45 environmental samples were collected, and 4 (9%) grew Salmonella. A chick box liner from a box in the pre-shipping area yielded an isolate closely related to the S. Enteritidis outbreak strain (within 1 to 9 alleles by cgMLST). The onsite investigation revealed lapses in biosecurity, sanitation, quality assurance, and education of consumers. Review of Salmonella serotype testing performed by the hatchery revealed that the number of samples and type of samples collected monthly varied. Also, S. Enteritidis was identified at the hatchery every year since testing began in 2016", "token_count": 490, "char_count": 1939, "word_count": 288, "semantic_coherence": 1, "information_density": 0.566, "quality_score": 0.783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:44.375479", "source": { "split": "train_shard_00000", "doc_id": 2915 }, "chunk_id": "train_shard_00000_2915_0", "global_id": 3215 }, { "text": "Recommendations to the hatchery for biosecurity, testing, and sanitation measures were made to help reduce burden of Salmonella in the hatchery and breeding flocks, thereby reducing the occurrence of human illness.\n\nOnsite investigation at a mail-order hatchery following a multistate Salmonella illness outbreak linked to live poultry-United States, 2018.", "token_count": 90, "char_count": 356, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:44.750160", "source": { "split": "train_shard_00000", "doc_id": 2915 }, "chunk_id": "train_shard_00000_2915_1", "global_id": 3216 }, { "text": "BackgroundCarbapenem-resistant Enterobacteriaceae pose a serious threat to public health worldwide, and the role of companion animals as a reservoir is still unclear.AimsThis 4-month prospective observational study evaluated carriage of carbapenem-resistant Enterobacteriaceae at admission and after hospitalisation in a large referral hospital for companion animals in Switzerland.MethodsRectal swabs of dogs and cats expected to be hospitalised for at least 48 h were taken from May to August 2018 and analysed for the presence of carbapenem-resistant Enterobacteriaceae using selective agar plates. Resistant isolates were further characterised analysing whole genome sequences for resistance gene and plasmid identification, and ad hoc core genome multilocus sequence typing.ResultsThis study revealed nosocomial acquisition of\n\nShedding of OXA-181 carbapenemase-producing", "token_count": 207, "char_count": 876, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7477, "quality_score": 0.8739, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:45.216710", "source": { "split": "train_shard_00000", "doc_id": 2916 }, "chunk_id": "train_shard_00000_2916_0", "global_id": 3217 }, { "text": "Intrahepatic cholestasis of pregnancy (ICP) is gestation-specific liver disease associated with liver injury and increased serum and hepatic bile acids. Although the mechanism of ICP is still not fully understood, the reproductive hormones seem to play an important role. Recent studies show that a progesterone metabolite, epiallopregnanolone sulfate (PM5S), is supraphysiologically elevated in the serum of ICP patients, indicating it may play an etiology role in ICP. Bile acid homeostasis is controlled by multiple mechanisms including farnesoid X receptor (FXR)-mediated bile acid export and synthesis. It is known that cholic acid (CA), a primary bile acid, can activate FXR, which is inhibited by PM5S, an FXR antagonist. Here we employed a mouse model of concurrent exposure of CA and PM5S-induced liver injury and determined the effects of probiotic Lactobacillus rhamnosus GG (LGG) in the prevention of the bile acid disorders and liver injury. Mice challenged with CA + PM5S had significantly increased levels of serum and hepatic bile acids and bilirubin and liver enzyme. Pretreatment with LGG significantly reduced bile acid and bilirubin levels associated with reduced liver enzyme level and mRNA expression levels of pro-inflammatory cytokines. We also showed that the beneficial effects of LGG is likely mediated by hepatic FXR activation and bile salt export pump (BSEP) upregulation. In conclusion, our results provide a rationale for the application of probiotics in the management of ICP through gut microbiota-mediated FXR activation.\n\nProbiotic Lactobacillus rhamnosus GG prevents progesterone metabolite epiallaopregnanolone sulfate-induced hepatic bile acid accumulation and liver injury.", "token_count": 454, "char_count": 1713, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7944, "entities": { "genes": [ "PM5S" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:45.854739", "source": { "split": "train_shard_00000", "doc_id": 2917 }, "chunk_id": "train_shard_00000_2917_0", "global_id": 3218 }, { "text": "Acetogenic bacteria are obligate anaerobes with the ability of converting carbon dioxide and other one-carbon substrates into acetate through the Wood-Ljungdahl (WL) pathway. These substrates are becoming increasingly important feedstock in industrial microbiology. The main potential industrial application of acetogenic bacteria is the production of metabolites that constitute renewable energy sources (biofuel); such bacteria are of particular interest for this purpose thanks to their low energy requirements for large-scale cultivation. Here, we report new genome sequences for four species, three of them are reported for the first time, namely Acetobacterium paludosum DSM 8237, Acetobacterium tundrae DSM 917, Acetobacterium bakii DSM 8239, and Alkalibaculum bacchi DSM 221123. We performed a comparative genomic analysis focused on the WL pathway's genes and their encoded proteins, using Acetobacterium woodii as a reference genome. The Average Nucleotide Identity (ANI) values ranged from 70% to 95% over an alignment length of 5.4-6.5 Mbp. The core genome consisted of 363 genes, whereas the number of unique genes in a single genome ranged from 486 in A. tundrae to 2360 in A.bacchi. No significant rearrangements were detected in the gene order for the Wood-Ljungdahl pathway however, two species showed variations in genes involved in formate metabolism: A. paludosum harbor two copies of fhs1, and A. bakii a truncated fdhF1. The analysis of protein networks highlighted the expansion of protein orthologues in A. woodii compared to A. bacchi, whereas protein networks involved in the WL pathway were more conserved. This study has increased our understanding on the evolution of the WL pathway in acetogenic bacteria.\n\nInsights into the genome structure of four acetogenic bacteria with specific reference to the Wood-Ljungdahl pathway.", "token_count": 499, "char_count": 1854, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:46.509515", "source": { "split": "train_shard_00000", "doc_id": 2918 }, "chunk_id": "train_shard_00000_2918_0", "global_id": 3219 }, { "text": "Rifampicin (RFP)-induced cholestatic liver injury is characterized by impaired hepatic bile acid (BA) transport. Bile salt efflux pump (BSEP) and Na+/taurocholate cotransporter (NTCP) are the major BA transporters. However, little is known about the mechanisms underlying these transporters.\n\nTanshinone IIA prevents rifampicin-induced liver injury by regulating BSEP/NTCP expression via epigenetic activation of NRF2.", "token_count": 121, "char_count": 418, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8679, "quality_score": 0.934, "entities": { "genes": [ "NRF2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:46.900506", "source": { "split": "train_shard_00000", "doc_id": 2919 }, "chunk_id": "train_shard_00000_2919_0", "global_id": 3220 }, { "text": "Oral drug administration is the most favorable route of drug administration in the clinic. Intestinal transporters have been shown to play a significant role in the rate and extent of drug absorption of some, but not all, drug molecules. Due to the heterogeneous expression of multiple transporters along the intestine, the preferential absorption sites for drugs may vary significantly. In this chapter, we aim to summarize the current research on the expression, localization, function, and regulation of human intestinal transporters implicated in altering the absorption of low to medium molecular weight drug molecules. The role played by bile acid transport proteins (e.g., ASBT and OST-α/β) is included in the discussion. The synergistic action of intestinal drug metabolism and transport is also discussed. Despite the complicated regulatory factors, the biopharmaceutics drug disposition classification system (BDDCS) put forward by Wu and Benet may help us better predict the effect of transporters on drug absorption. The drug-induced toxicity in the intestine, which may result from drug-drug interaction, gut microbiota, and bile salt toxicity, is also discussed.\n\nIntestinal Transporter-Associated Drug Absorption and Toxicity.", "token_count": 278, "char_count": 1241, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6145, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:47.460382", "source": { "split": "train_shard_00000", "doc_id": 2920 }, "chunk_id": "train_shard_00000_2920_0", "global_id": 3221 }, { "text": "The enzyme carboxyl ester lipase (CEL), known as bile salt-dependent lipase (BSDL) or bile salt-stimulated lipase (BSSL), is mainly expressed in pancreatic acinar cells and lactating mammary glands. To investigate the link between CEL expression of breast cancer (BC) tissues and the survival of BC patients by analyzing The Cancer Genome Atlas Breast Carcinoma (TCGA-BRCA) level 3 data.\n\nA new prognostic factor of breast cancer: High carboxyl ester lipase expression related to poor survival.", "token_count": 139, "char_count": 494, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7703, "quality_score": 0.8851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:47.885716", "source": { "split": "train_shard_00000", "doc_id": 2921 }, "chunk_id": "train_shard_00000_2921_0", "global_id": 3222 }, { "text": "Methods based on single nucleotide polymorphism (SNP), copy number variation (CNV) and presence/absence variation (PAV) discovery provide a valuable resource to study gene structure and evolution. However, as a result of these structural variations, a single reference genome is unable to cover the entire gene content of a species. Therefore, pangenomics analysis is needed to ensure that the genomic diversity within a species is fully represented. Brassica napus is one of the most important oilseed crops in the world and exhibits variability in its resistance genes across different cultivars. Here, we characterized resistance gene distribution across 50 B. napus lines. We identified a total of 1749 resistance gene analogs (RGAs), of which 996 are core and 753 are variable, 368 of which are not present in the reference genome (cv. Darmor-bzh). In addition, a total of 15 318 SNPs were predicted within 1030 of the RGAs. The results showed that core R-genes harbour more SNPs than variable genes. More nucleotide binding site-leucine-rich repeat (NBS-LRR) genes were located in clusters than as singletons, with variable genes more likely to be found in clusters. We identified 106 RGA candidates linked to blackleg resistance quantitative trait locus (QTL). This study provides a better understanding of resistance genes to target for genomics-based improvement and improved disease resistance.\n\nCharacterization of disease resistance genes in the Brassica napus pangenome reveals significant structural variation.", "token_count": 360, "char_count": 1524, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6388, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:48.467191", "source": { "split": "train_shard_00000", "doc_id": 2922 }, "chunk_id": "train_shard_00000_2922_0", "global_id": 3223 }, { "text": "Bile acids (BAs) are important regulators of metabolism and energy balance, but excess BAs cause cholestatic liver injury. The histone methyltransferase mixed-lineage leukemia-4 (MLL4) is a transcriptional coactivator of the BA-sensing nuclear receptor farnesoid X receptor (FXR) and epigenetically up-regulates FXR targets important for the regulation of BA levels, small heterodimer partner (SHP), and bile salt export pump (BSEP). MLL4 expression is aberrantly down-regulated and BA homeostasis is disrupted in cholestatic mice, but the underlying mechanisms are unclear.\n\nMicroRNA-210 Promotes Bile Acid-Induced Cholestatic Liver Injury by Targeting Mixed-Lineage Leukemia-4 Methyltransferase in Mice.", "token_count": 208, "char_count": 705, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [ "MLL4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:48.929416", "source": { "split": "train_shard_00000", "doc_id": 2923 }, "chunk_id": "train_shard_00000_2923_0", "global_id": 3224 }, { "text": "The hepatic risk matrix (HRM) was developed and used to differentiate lead clinical and back-up drug candidates against competitor/marketed drugs within the same pharmaceutical class for their potential to cause human drug-induced liver injury (DILI). The hybrid HRM scoring system blends physicochemical properties (Rule of Two Model: dose and lipophilicity or Partition Model: dose, ionization state, lipophilicity, and fractional carbon bond saturation) with common toxicity mechanisms (cytotoxicity, mitochondrial dysfunction, and bile salt export pump (BSEP) inhibition) that promote DILI. HRM scores are based on bracketed safety margins (<1, 1-10, 10-100, and >100× clinical\n\nMoving beyond Binary Predictions of Human Drug-Induced Liver Injury (DILI) toward Contrasting Relative Risk Potential.", "token_count": 216, "char_count": 801, "word_count": 108, "semantic_coherence": 1, "information_density": 0.8426, "quality_score": 0.9213, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:49.395307", "source": { "split": "train_shard_00000", "doc_id": 2924 }, "chunk_id": "train_shard_00000_2924_0", "global_id": 3225 }, { "text": "Collective integration and processing of information have increased through the history of life, through both the formation of aggregates in which the entities may have very different properties and which jointly coarse-grained environmental variables (ranging from widely varying metabolism in microbial consortia to the ecological diversity of species on reefs) and through collectives of similar entities (such as cells within an organism or social groups). Such increases have been implicated in significant transitions in the history of life, including aspects of the origin of life, the generation of pangenomes among microbes and microbial communities such as stromatolites, multicellularity and social insects. This contribution provides a preliminary overview of the dominant modes of collective information processing in the history of life, their phylogenetic distribution and extent of convergence, and the effects of new modes for integrating and acting upon information on the tempo of evolutionary change.\n\nTempos and modes of collectivity in the history of life.", "token_count": 214, "char_count": 1078, "word_count": 155, "semantic_coherence": 1, "information_density": 0.5935, "quality_score": 0.7968, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:49.864902", "source": { "split": "train_shard_00000", "doc_id": 2925 }, "chunk_id": "train_shard_00000_2925_0", "global_id": 3226 }, { "text": "We have previously demonstrated that the ester conjugation of zidovudine (AZT) with ursodeoxycholic acid (UDCA) allows to obtain a prodrug (U-AZT) which eludes the active efflux transporters (AET). This allows the prodrug to more efficiently permeates and remains in murine macrophages than the parent compound. Here we demonstrate that U-AZT can be formulated, by a nanoprecipitation method, as nanoparticle cores coated by bile acid salt (taurocholate or ursodeoxycholate) corona, without any other excipients. The U-AZT nanoparticles appeared spherical with a mean diameter of ∼200 nm and a zeta potential of ∼-55 mV. During the incubation (5 h) in fetal bovine serum, the ursodeoxycholate-coated nanoparticle size did not change. Differently, taurocholate-coated particle size was firstly reduced and then increased up to 800 µm, thus suggesting the high aptitude of these nanoparticles to interact with serum proteins. The in vitro uptake of taurocholate coated particles by murine macrophages was strongly higher than that of ursodeoxycholate-coated particles or free U-AZT (∼500% and ∼7000%, respectively). AZT was also detected in macrophages following the prodrug uptake, with the greatest amounts observed after the taurocholate-coated nanoparticle incubation. As macrophages in the subarachnoid spaces of cerebrospinal fluid (CSF) constitute one of the most unreachable HIV sanctuaries in the body, we also tested the ability of taurocholate-coated nanoparticles (i.e., nanoparticles highly internalized by macrophages) to reach them after their nasal administration in the presence or absence of chitosan. The results indicate that chitosan allowed to obtain a relatively high uptake (up to 4 µg/ml) of U-AZT in CSF", "token_count": 512, "char_count": 1727, "word_count": 250, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:50.520320", "source": { "split": "train_shard_00000", "doc_id": 2926 }, "chunk_id": "train_shard_00000_2926_0", "global_id": 3227 }, { "text": "Taking into account that chitosan may promote the direct brain nanoparticle uptake, these findings can be considered an initial step toward the in vivo targeting of the subarachnoid macrophages by U-AZT prodrug.\n\nBile salt-coating modulates the macrophage uptake of nanocores constituted by a zidovudine prodrug and enhances its nose-to-brain delivery.", "token_count": 97, "char_count": 352, "word_count": 50, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:50.900437", "source": { "split": "train_shard_00000", "doc_id": 2926 }, "chunk_id": "train_shard_00000_2926_1", "global_id": 3228 }, { "text": "In the present study, Kluyveromyces marxianus was utilized to study the batch fermentation kinetics of biomass production, substrate utilization and bioethanol production from woody stem Prosopis juliflora. The pre-treated substrate was subjected to Simultaneous Saccharification and Fermentation (SSF) under optimised conditions of pH (4.9), temperature (41 °C), substrate concentration 5% (w/v), inoculum concentration 3% (v/v) and the maximum concentration of bioethanol was found to be 21.45 g/l. The experimental data thus obtained from cell growth, substrate utilization and product formation are employed in the determination of kinetic parameters. Biological models such as Logistic model, Hinshelwood model were used for microbial growth and substrate utilization kinetics respectively. In case of product kinetics, Leudking-Piret plot, Gompertz model and Modified Gompertz model were utilised. Based on these models, kinetic parameters like maximum specific growth rate (µm), saturation constant (Ks), growth associated (α), non-growth associated (β) and yield coefficients (Y\n\nBioethanol production from woody stem Prosopis juliflora using thermo tolerant yeast Kluyveromyces marxianus and its kinetics studies.", "token_count": 329, "char_count": 1222, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6748, "quality_score": 0.8374, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:51.471388", "source": { "split": "train_shard_00000", "doc_id": 2927 }, "chunk_id": "train_shard_00000_2927_0", "global_id": 3229 }, { "text": "A microorganism engineered for non-native tasks may suffer stresses it never met before. Therefore, we examined whether a Kluyveromyces marxianus strain engineered with a carotenoid biosynthesis pathway can serve as an anti-stress chassis for building cell factories.\n\nCharacterizing an engineered carotenoid-producing yeast as an anti-stress chassis for building cell factories.", "token_count": 99, "char_count": 379, "word_count": 50, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:51.856309", "source": { "split": "train_shard_00000", "doc_id": 2928 }, "chunk_id": "train_shard_00000_2928_0", "global_id": 3230 }, { "text": "Sphingobium fuliginis ATCC 27551, previously classified as Flavobacterium sp. ATCC 27551, degrades neurotoxic organophosphate insecticides and nerve agents through the activity of a membrane-associated organophosphate hydrolase. This study was designed to determine the complete genome sequence of S. fuliginis ATCC 27551 to unravel its degradative potential and adaptability to harsh environments. The 5,414,624 bp genome with a GC content of 64.4% is distributed between two chromosomes and four plasmids and encodes 5,557 proteins. Of the four plasmids, designated as pSF1, pSF2, pSF3, and pSF4, only two (pSF1 and pSF2) are self-transmissible and contained the complete genetic repertoire for a T4SS. The other two plasmids (pSF3 and pSF4) are mobilizable and both showed the presence of an oriT and relaxase-encoding sequences. The sequence of plasmid pSF3 coincided with the previously determined sequence of pPDL2 and included an opd gene encoding organophosphate hydrolase as a part of the mobile element. About 15,455 orthologous clusters were identified from among the cumulatively annotated genes of 49 Sphingobium species. Phylogenetic analysis done using the core genome consisting of 802 orthologous clusters revealed a close relationship between S. fuliginis ATCC 27551 and bacteria capable of degradation of polyaromatic hydrocarbon compounds. Genes coding for transposases, efflux pumps conferring resistance to heavy metals, and TonR-type outer membrane receptors are selectively enriched in the genome of S. fuliginis ATCC 27551 and appear to contribute to the adaptive potential of the organism to challenging and harsh environments.\n\nGenome Organization and Adaptive Potential of Archetypal Organophosphate Degrading Sphingobium fuliginis ATCC 27551.", "token_count": 505, "char_count": 1771, "word_count": 250, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:52.507512", "source": { "split": "train_shard_00000", "doc_id": 2929 }, "chunk_id": "train_shard_00000_2929_0", "global_id": 3231 }, { "text": "Tailoring transcriptional regulation to coordinate the expression of virulence factors in tandem with the core genome is a hallmark of bacterial pathogen evolution. Bacteria encode hundreds of transcription factors forming the base-level control of gene regulation. Moreover, highly homologous regulators are assumed to control conserved genes between members within a species that harbor the same genetic targets. We have explored this concept in 2\n\nDistinct intraspecies virulence mechanisms regulated by a conserved transcription factor.", "token_count": 112, "char_count": 540, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7973, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:52.901163", "source": { "split": "train_shard_00000", "doc_id": 2930 }, "chunk_id": "train_shard_00000_2930_0", "global_id": 3232 }, { "text": "Staphylococcus aureus is a serious human and animal pathogen. Multilocus sequence type 612 (ST612) is the dominant methicillin-resistant S. aureus (MRSA) clone in certain South African hospitals and is sporadically isolated from horses and horse-associated veterinarians in Australia. Colonisation and infection by ST612-MRSA is increasing in Western Australia. Whole-genome sequencing was performed for 51 isolates of ST612-MRSA from Western Australian patients and healthcare workers, South African hospital patients, Australian veterinarians and New South Wales horses. Core genome phylogenies suggested that Australian equine and veterinarian-associated ST612-MRSA were monophyletic. Individual Western Australian isolates grouped either with this equine-associated lineage or more diverse lineages related to those in South African hospitals. Bioinformatic analyses of the complete ST612-MRSA reference genome SVH7513 confirmed that ST612-MRSA was closely related to ST8 USA500 MRSA. Common use of rifampicin in South Africa and equine veterinarian practice may favour ST612-MRSA in these settings. Humans and horses colonised with ST612-MRSA are potential reservoirs for MRSA in Australia.\n\nMultiple introductions of methicillin-resistant Staphylococcus aureus ST612 into Western Australia associated both with human and equine reservoirs.", "token_count": 347, "char_count": 1345, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [ "USA500", "SVH7513", "ST612", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:53.482424", "source": { "split": "train_shard_00000", "doc_id": 2931 }, "chunk_id": "train_shard_00000_2931_0", "global_id": 3233 }, { "text": "The typical phenotype of arthrogryposis, renal dysfunction, and cholestasis (ARC) syndrome involves three cardinal symptoms as the name describes, harboring biallelic mutations on VPS33B or VIPAS39. Except for ARC syndrome, low gamma-glutamyltransferase (GGT) cholestasis often implies hereditary hepatopathy of different severity; however, some remain undiagnosed. Several monogenic defects typically with multiorgan manifestations may only present liver dysfunction at times, such as DGUOK defect and AGL defect. Previously, four VPS33B mutated cases were reported without arthrogryposis, or with less severe symptoms and longer lifespan, indicating the possibility of incomplete ARC phenotype of isolated hepatopathy. So we retrospectively reviewed all patients with confirmed VPS33B/VIPARS39 defect in our center and identified three presenting isolated low-GGT cholestasis with intractable pruritus. Distinguished from others with typical ARC phenotype, these patients did not suffer the other two typical characteristics, survived much longer, and shared a novel missense VPS33B variation c.1726T>C, p.Cys576Arg, causing declined protein expression and abolished interaction with VIPAS39 in-vitro. Serum bile acid profiles of our VPS33B/VIPAS39 mutated patients revealed similar changes to primary defect of bile salt export pump, among which those with isolated cholestasis phenotype had a higher level of total secondary bile acids than that with typical ARC phenotype, indicating the partial residual function of VPS33B.\n\nNovel missense mutation in VPS33B is associated with isolated low gamma-glutamyltransferase cholestasis: Attenuated, incomplete phenotype of arthrogryposis, renal dysfunction, and cholestasis syndrome.", "token_count": 457, "char_count": 1732, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8451, "entities": { "genes": [ "VIPARS39", "VIPAS39", "VPS33B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:54.122488", "source": { "split": "train_shard_00000", "doc_id": 2932 }, "chunk_id": "train_shard_00000_2932_0", "global_id": 3234 }, { "text": "The gut bacterial bile salt hydrolase (BSH) plays a critical role in host lipid metabolism and energy harvest. Therefore, BSH is a promising microbiome target to develop new therapies to regulate obesity in humans and novel non-antibiotic growth promoters for food animals. We previously reported the 1.90 Å apo crystal structure of BSH from Lactobacillus salivarius (lsBSH). In this study, we soaked the lsBSH crystal with glycocholic acid (GCA), a substrate, and obtained a 2.10 Å structure containing complex of lsBSH bound to GCA and cholic acid (CA), a product. The substrate/product sits in the water-exposed cavity molded by Loops 2 and 3. While the glycine moiety of GCA is exposed into a highly polar pocket, the sterane core of GCA is stabilized by aromatic and hydrophobic interactions. Comparison of product binding with BSH from Clostridium perfringenes reveals a distinct orientation of the sterane core in the binding site. The stability of the substrate-lsBSH complex and the putative catalytic mechanism were explored with molecular dynamics simulations. Site-directed mutagenesis of lsBSH demonstrated that Cys2 and Asn171 are critical for enzymatic activity, while Tyr24, Phe65 and Gln257 contribute to the substrate specificity. Together, this study provides structural insights into BSH-substrate interaction, the mechanism of catalysis and substrate specificity, which facilitate rational design of BSH inhibitors.\n\nThe complex structure of bile salt hydrolase from Lactobacillus salivarius reveals the structural basis of substrate specificity.", "token_count": 408, "char_count": 1567, "word_count": 230, "semantic_coherence": 1, "information_density": 0.613, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:54.763931", "source": { "split": "train_shard_00000", "doc_id": 2933 }, "chunk_id": "train_shard_00000_2933_0", "global_id": 3235 }, { "text": "O-antigens are glycopolymers in lipopolysaccharides expressed on the cell surface of Gram-negative bacteria. Variability in the O-antigen structure constitutes the basis for the establishment of the serotyping schema. We pursued a two-pronged approach to define the basis for O-antigen structural diversity. First, we developed a bottom-up systems biology approach to O-antigen metabolism by building a reconstruction of\n\nSystems Biology and Pangenome of", "token_count": 112, "char_count": 454, "word_count": 62, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:55.191917", "source": { "split": "train_shard_00000", "doc_id": 2934 }, "chunk_id": "train_shard_00000_2934_0", "global_id": 3236 }, { "text": "Whole-genome sequencing (WGS) has revolutionized the genotyping of bacterial pathogens and is expected to become the new gold standard for tracing the transmissions of bacterial infectious diseases for public health purposes. However, it is still unexpectedly demanding to employ WGS for global epidemiological surveillance because of the high degree of similarity between the genomes of intercontinental isolates. The aim of this study was to utilize genomically derived bioinformatics analysis to identify globally distributed A. baumannii ST195 lineage and differentiation outbreaks to address this issue. The genomic sequences and their related epidemiological metadata of 2850 A. baumannii isolates were recruited from NCBI Genbank database. Assignment into sequence type (Oxford scheme) and lineage (global clone 2/CC92) were performed. A total of 91 ST195 A. baumannii isolates were subsequently classified to perform the bacterial source tracking analysis by implementing both core genome MLST (cgMLST) and core genome SNP (cgSNP) strategy that were integrated in our recently updated BacWGSTdb 2.0 server. Antibiotic resistance genes were identified using the ResFinder database. The ST195 A. baumannii isolates distributed widely in eight countries and harboured multiple antimicrobial resistance genes simultaneously. In most cases, the bacterial isolates recovered from geographically distant sources may present less genomic sequence similarity, i.e., the phylogenetic relationship between these ST195 isolates worldwide was roughly congruent with their country of isolation. However, a few isolates collected from distant geographic regions were revealed to possess smaller genetic distances (less than 8 loci or 20 SNPs) than the threshold without an observable epidemiological link. Our study highlights the emerging challenges entailed in the WGS-powered epidemiological surveillance of globally distributed clonal groups. Standardization is urgently required before WGS can be routinely applied to infectious diseases outbreak investigations.\n\nEmerging challenges of whole-genome-sequencing-powered epidemiological surveillance of globally distributed clonal groups of bacterial infections, giving Acinetobacter baumannii ST195 as an example.", "token_count": 510, "char_count": 2260, "word_count": 301, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.8189, "entities": { "genes": [ "ST195", "CC92" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:55.876296", "source": { "split": "train_shard_00000", "doc_id": 2935 }, "chunk_id": "train_shard_00000_2935_0", "global_id": 3237 }, { "text": "Antimicrobial growth promoters (AGPs) are commonly used in the livestock industry at subtherapeutic levels to improve production efficiency, which is achieved mainly through modulation of the intestinal microbiota. However, how different classes of AGPs, particularly ionophores, regulate the gut microbiota remains unclear. In this study, male Cobb broiler chickens were supplemented for 14 days with or without one of five commonly used AGPs including three classical antibiotics (bacitracin methylene disalicylate, tylosin, and virginiamycin) and two ionophores (monensin and salinomycin) that differ in antimicrobial spectrum and mechanisms. Deep sequencing of the V3-V4 region of the bacterial 16S rRNA gene revealed that two ionophores drastically reduced a number of rare bacteria resulting in a significant decrease in richness and a concomitant increase in evenness of the cecal microbiota, whereas three antibiotics had no obvious impact. Although each AGP modulated the gut microbiota differently, the closer the antibacterial spectrum of AGPs, the more similarly the microbiota was regulated. Importantly, all AGPs had a strong tendency to enrich butyrate- and lactic acid-producing bacteria, while reducing bile salt hydrolase-producing bacteria, suggestive of enhanced metabolism and utilization of dietary carbohydrates and lipids and improved energy harvest, which may collectively be responsible for the growth-promoting effect of AGPs.\n\nDifferential Impact of Subtherapeutic Antibiotics and Ionophores on Intestinal Microbiota of Broilers.", "token_count": 387, "char_count": 1557, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8498, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:56.496416", "source": { "split": "train_shard_00000", "doc_id": 2936 }, "chunk_id": "train_shard_00000_2936_0", "global_id": 3238 }, { "text": "Placenta performs the function of several adult organs for the fetus during intrauterine life. Because of the dramatic physiological and metabolic changes during pregnancy and the strong association between maternal metabolism and placental function, the possibility that variation in gene expression patterns during pregnancy might be linked to fetal health warrants investigation. Here, next-generation RNA sequencing was used to investigate the expression profile, including mRNAs and long non-coding RNAs (lncRNAs) of placentas on day 60 of gestation (G60), day 90 of gestation (G90), and on the farrowing day (L0) in pregnant swine. Bioinformatics analysis of differentially expressed mRNAs and lncRNAs consistently showed dysregulation of bile acids transport and detoxification as pregnancy progress. We found the differentially expressed mRNAs, particularly bile salt export pump (\n\nTranscriptome Profiling of Placenta through Pregnancy Reveals Dysregulation of Bile Acids Transport and Detoxification Function.", "token_count": 249, "char_count": 1019, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8417, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:56.988662", "source": { "split": "train_shard_00000", "doc_id": 2937 }, "chunk_id": "train_shard_00000_2937_0", "global_id": 3239 }, { "text": "Human milk fat plays an essential role as the source of energy and cell function regulator; therefore, the preservation of unique human milk donors' lipid composition is of fundamental importance. To compare the effects of high pressure processing (HPP) and holder pasteurization on lipidome, human milk was processed at 62.5 °C for 30 min and at five variants of HPP from 450 MPa to 600 MPa, respectively. Lipase activity was estimated with QuantiChrom™ assay. Fatty acid composition was determined with the gas chromatographic technique, and free fatty acids content by titration with 0.1 M KOH. The positional distribution of fatty acid in triacylglycerols was performed. The oxidative induction time was obtained from the pressure differential scanning calorimetry. Carotenoids in human milk were measured by liquid chromatography. Bile salt stimulated lipase was completely eliminated by holder pasteurization, decreased at 600 MPa, and remained intact at 200 + 400 MPa; 450 MPa. The fatty acid composition and structure of human milk fat triacylglycerols were unchanged. The lipids of human milk after holder pasteurization had the lowest content of free fatty acids and the shortest induction time compared with samples after HPP. HPP slightly changed the β-carotene and lycopene levels, whereas the lutein level was decreased by 40.0% up to 60.2%, compared with 15.8% after the holder pasteurization.\n\nLipid Profile, Lipase Bioactivity, and Lipophilic Antioxidant Content in High Pressure Processed Donor Human Milk.", "token_count": 400, "char_count": 1524, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5783, "quality_score": 0.7891, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:57.605737", "source": { "split": "train_shard_00000", "doc_id": 2938 }, "chunk_id": "train_shard_00000_2938_0", "global_id": 3240 }, { "text": "Lactobacillus fermentum MJM60397 was subjected to in vitro safety tests and in vivo probiotic characterization. The MJM60397 strain was susceptible to antibiotics and was found to be non-mucinolytic and non-hemolytic, and does not produce bioamines. In addition, MJM60397 tolerated simulated oro-gastrointestinal conditions and adhered to Caco-2 cells. MJM60397 also exhibited bile salt hydrolase activity and could deconjugate bile acids. The hypocholesterolemic effects of strain MJM60397 were studied in high-fat diet-induced hypercholesterolemic male ICR mice. The mice were fed a high-cholesterol diet (HCD) and were divided into the following three experimental groups: HCD-control (HCD-Con), mice fed with HCD + L. fermentum MJM60397 (HCD-MJM60397), and mice fed with HCD + L. acidophilus ATCC 43121 (HCD-L.ac) as the positive control. Simultaneously, a normal control diet (NCD) group was maintained. After 7 weeks, the total cholesterol and low-density lipoprotein (LDL) cholesterol levels were significantly reduced in the livers of the HCD-MJM60397 mice when compared to those in the HCD-Con and HCD-L.ac mice. Fecal total bile acid content was significantly (P < 0.05) higher in the HCD-MJM60397 group than in the NCD, HCD-Con, and HCD-L.ac groups. Analysis of gene expression revealed higher expression of LDLR gene in the livers of the HCD-MJM60397 and HCD-L.ac mice than in the livers of the HCD-Con mice", "token_count": 491, "char_count": 1419, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5769, "quality_score": 0.7885, "entities": { "genes": [ "MJM60397" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:58.256953", "source": { "split": "train_shard_00000", "doc_id": 2939 }, "chunk_id": "train_shard_00000_2939_0", "global_id": 3241 }, { "text": "These findings show that the hypocholesterolemic effects of the MJM60397 strain were attributable to its bile salt deconjugating activity, which resulted in decreased bile acid absorption and increased excretion of bile acids in the feces. These results indicate that L. fermentum MJM60397 could be developed into a potential probiotic for reducing the serum cholesterol levels.\n\nProbiotic Characterization of Cholesterol-Lowering Lactobacillus fermentum MJM60397.", "token_count": 132, "char_count": 464, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7903, "quality_score": 0.8952, "entities": { "genes": [ "MJM60397" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:58.677205", "source": { "split": "train_shard_00000", "doc_id": 2939 }, "chunk_id": "train_shard_00000_2939_1", "global_id": 3242 }, { "text": "The prevalence of Clostridioides difficile PCR-ribotype (RT) 018 is low in Europe but variations are observed across countries. We report here the first RT 018-related outbreak in France that took place in 4 geriatric units (GU) in Strasbourg, France. From January to December 2017, 38 patients were diagnosed with C. difficile infection (CDI). Strains were first characterized by PCR ribotyping: 19 out of 38 (50%) strains belonged to RT 018. These strains as well as 12 RT 018 isolated in other French healthcare facilities and 2 strains of RT 018 isolated in the GU in 2015 were characterized by multi locus variable-number tandem repeat (VNTR) analysis (MLVA), whole genome multi locus sequence typing (wgMLST) and core genome single nucleotide polymorphism typing (cgSNP). The MLVA indicated that 15 out of 19 epidemic strains of RT 018 were included in 2 Clonal Complexes (CC). Four RT 018 strains from the outbreak did not belong to the CC. The wgMLST and cgSNP typing analysis revealed a single CC that included 19 strains from the geriatric unit (17 from GU in 2017 and 2 from GU in 2015) and 4 strains (33%) from other healthcare facilities (HCF). Our results suggest that a specific RT 018 clone has spread in the geriatric unit and has evolved slowly over time. MLVA, wgMLST and cgSNP typing results provided fairly consistent information but wgMLST and cgSNP typing better separated epidemic strains from non-epidemic strains. Compared to wgMLST, the cgSNP typing did not provide additional information.\n\nLocal outbreak of Clostridioides difficile PCR-Ribotype 018 investigated by multi locus variable number tandem repeat analysis, whole genome multi locus sequence typing and core genome single nucleotide polymorphism typing.", "token_count": 501, "char_count": 1741, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5217, "quality_score": 0.7609, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:59.328930", "source": { "split": "train_shard_00000", "doc_id": 2940 }, "chunk_id": "train_shard_00000_2940_0", "global_id": 3243 }, { "text": "Kluyveromyces marxianus CCT 7735 has been used to produce ethanol, aromatic compounds, enzymes and heterologous proteins besides assimilates lactose as carbon source. Its genome has 10.7 Mb and encodes 4787 genes distributed in 8 nuclear chromosomes and one mitochondrial. Contrary to Kluyveromyces lactis, which has a unique LAC12 gene (encodes lactose permease), K. marxianus possesses four. The presence of degenerated copies and Solo-LTRs related to retrotransposon TKM close to the LAC12 genes in K. marxianus indicates ectopic recombinations. The Lac12 permeases of K. marxianus and K. lactis are conserved, however the conservation is higher between the copy of the left side of the chromosome three and the unique copy of K. lactis, indicating that this copy is the ancestor. The expression of the four LAC12 genes occurred in aerobiosis and hypoxia. Notably, the high lactose consumption in hypoxia seems to be related to the high expression of the LAC12 genes.\n\nGenomic analysis and lactose transporter expression in Kluyveromyces marxianus CCT 7735.", "token_count": 321, "char_count": 1060, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5901, "quality_score": 0.795, "entities": { "genes": [ "LAC12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:27:59.898251", "source": { "split": "train_shard_00000", "doc_id": 2941 }, "chunk_id": "train_shard_00000_2941_0", "global_id": 3244 }, { "text": "Studying bacterial population diversity is important to understand healthcare associated infections' epidemiology and has a significant impact on dealing with multidrug resistant bacterial outbreaks. We characterised the extended-spectrum beta-lactamase producing K. pneumoniae (ESBLp KPN) population in our hospital using mini-MLST. Then we used whole genome sequencing (WGS) to compare selected isolates belonging to the most prevalent melting types (MelTs) and the colonization/infection pair isolates collected from one patient to study the ESBLp KPN population's genetic diversity. A total of 922 ESBLp KPN isolates collected between 7/2016 and 5/2018 were divided into 38 MelTs using mini-MLST with only 6 MelTs forming 82.8% of all isolates. For WGS, 14 isolates from the most prominent MelTs collected in the monitored period and 10 isolates belonging to the same MelTs collected in our hospital in 2014 were randomly selected. Resistome, virulome and ST were MelT specific and stable over time. A maximum of 23 SNV per core genome and 58 SNV per core and accessory genome were found. To determine the SNV relatedness cut-off values, 22 isolates representing colonization/infection pair samples obtained from 11 different patients were analysed by WGS with a maximum of 22 SNV in the core genome and 40 SNV in the core and accessory genome within pairs. The mini-MLST showed its potential for real-time epidemiology in clinical practice. However, for outbreak evaluation in a low diversity bacterial population, mini-MLST should be combined with more sensitive methods like WGS. Our findings showed there were only minimal differences within the core and accessory genome in the low diversity hospital population and gene based SNV analysis does not have enough discriminatory power to differentiate isolate relatedness. Thus, intergenic regions and mobile elements should be incorporated into the analysis scheme to increase discriminatory power.", "token_count": 477, "char_count": 1955, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:00.541665", "source": { "split": "train_shard_00000", "doc_id": 2942 }, "chunk_id": "train_shard_00000_2942_0", "global_id": 3245 }, { "text": "Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population.", "token_count": 37, "char_count": 155, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:00.899296", "source": { "split": "train_shard_00000", "doc_id": 2942 }, "chunk_id": "train_shard_00000_2942_1", "global_id": 3246 }, { "text": "Enterohemorrhagic Escherichia coli O157:H7 (EHEC) is an important food-borne pathogen that colonizes the colon. Transposon-insertion sequencing (TIS) was used to identify genes required for EHEC and E. coli K-12 growth in vitro and for EHEC growth in vivo in the infant rabbit colon. Surprisingly, many conserved loci contribute to EHEC's but not to K-12's growth in vitro. There was a restrictive bottleneck for EHEC colonization of the rabbit colon, which complicated identification of EHEC genes facilitating growth in vivo. Both a refined version of an existing analytic framework as well as PCA-based analysis were used to compensate for the effects of the infection bottleneck. These analyses confirmed that the EHEC LEE-encoded type III secretion apparatus is required for growth in vivo and revealed that only a few effectors are critical for in vivo fitness. Over 200 mutants not previously associated with EHEC survival/growth in vivo also appeared attenuated in vivo, and a subset of these putative in vivo fitness factors were validated. Some were found to contribute to efficient type-three secretion while others, including tatABC, oxyR, envC, acrAB, and cvpA, promote EHEC resistance to host-derived stresses. cvpA is also required for intestinal growth of several other enteric pathogens, and proved to be required for EHEC, Vibrio cholerae and Vibrio parahaemolyticus resistance to the bile salt deoxycholate, highlighting the important role of this previously uncharacterized protein in pathogen survival. Collectively, our findings provide a comprehensive framework for understanding EHEC growth in the intestine.\n\nTransposon-insertion sequencing screens unveil requirements for EHEC growth and intestinal colonization.", "token_count": 452, "char_count": 1738, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5929, "quality_score": 0.7964, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:01.540710", "source": { "split": "train_shard_00000", "doc_id": 2943 }, "chunk_id": "train_shard_00000_2943_0", "global_id": 3247 }, { "text": "β-Mannanases are crucial enzymes for the breakdown of mannans. As Mannans are being considered as antinutritional factors in poultry production, the search for mannanase-producing probiotic bacteria is now attracting considerable attention as a strategy to enhance nutrients bioavailability. Five soil born Bacilli (US134, US150, US176, US180, and US191) were selected for their ability to produce extracellular β-mannanases that were biochemically characterized. The probiotic properties of these strains were determined to assess their potential as animal feed supplements. Bacillus subtilis US191 was shown to be sensitive to all antibiotics tested, to inhibit growth of the bacterial pathogens tested, and to produce a thermostable β-mannanase. It exhibited a notable acid and bovine bile tolerance and high ability to form biofilm. These features may favor its adherence to the intestinal epithelial cells allowing its survival and persistence in the digestive tract. Furthermore, our study revealed that US191 was among the strains showing the highest ability to digest wheat dry matter in vitro when compared to the commercial feed additive Rovabio\n\nSelection of Bacillus subtilis US191 as a mannanase-producing probiotic candidate.", "token_count": 318, "char_count": 1239, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8362, "entities": { "genes": [ "US191", "US150", "US134", "US180", "US176" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:02.100252", "source": { "split": "train_shard_00000", "doc_id": 2944 }, "chunk_id": "train_shard_00000_2944_0", "global_id": 3248 }, { "text": "Amphotericin B is used for local delivery from polymethylmethacrylate to treat fungal prosthetic joint infections. The optimal amphotericin B formulation and the influence of different poragens in the bone cements are unknown. To investigate the necessary amount of amphotericin B in the bone cement to prevent Candida biofilm several amphotericin B formulations were studied: non-liposomal and liposomal with or without poragen gentamicin. For the non-liposomal formulation, standard bile salt, the sodium deoxycholate, was used and additionally N-methyl-D-glucamine/palmitate was applied. The activity of the released amphotericin B was tested against C. albicans, C. glabrata, C. parapsilosis and C. krusei biofilms with application of the isothermal calorimeter and standard microbiological methods. Compressive strength was measured before and after antifungal elution from the cements. There is less aggregated N-methyl-D-glucamine/palmitate amphotericin B released but its antifungal activity is equivalent with the deoxycholate amphotericin B. The minimum quantity of antifungal preventing the Candida biofilm formation is 12.5 mg in gram of polymer powder for both non-liposomal formulations. The addition of gentamicin reduced the release of sodium deoxycholate amphotericin B. Gentamicin can be added to N-methyl-D-glucamine/palmitate amphotericin B in order to boost the antifungal release. When using liposomal amphotericin B more drug is released. All amphotericin B formulations were active against Candida biofilms. Although compressive strength slightly decreased, the obtained values were above the level of strength recommended for the implant fixation. The finding of this work might be beneficial for the treatment of the prosthetic joint infections caused by Candida spp.\n\nRelease of different amphotericin B formulations from PMMA bone cements and their activity against Candida biofilm.", "token_count": 506, "char_count": 1910, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5305, "quality_score": 0.7653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:02.754488", "source": { "split": "train_shard_00000", "doc_id": 2945 }, "chunk_id": "train_shard_00000_2945_0", "global_id": 3249 }, { "text": "The aim of this study was to improve the ethanol production from pomegranate peels (PPs). Therefore, the effect of enzymatic hydrolysis and different pretreatments on ethanol production by yeasts was examined. There were three different enzyme concentrations (3.6, 7.2, 14.4 FPU/g substrate) tested for enzymatic hydrolysis, and four different PP media, such as WSPP (whole slurry of PP), LFPP (liquid fraction of PP), WSFPP (washed solid fraction of PP) and N-WSFPP (non-washed solid fraction of PP), were prepared. Bioethanol production was monitored for 96 h. Maximum ethanol concentrations were obtained at WSPP medium as 12.69 g/L, 14.35 g/L and 4.23 g/L in Saccharomyces cerevisiae, Kluyveromyces marxianus and Pichia stipitis, respectively. On the other hand, the washing step of biomass increased the kinetic parameters dramatically and the highest theoretical ethanol yields and Y\n\nImprovement of bioethanol production from pomegranate peels via acidic pretreatment and enzymatic hydrolysis.", "token_count": 302, "char_count": 1000, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:03.326961", "source": { "split": "train_shard_00000", "doc_id": 2946 }, "chunk_id": "train_shard_00000_2946_0", "global_id": 3250 }, { "text": "Emergence of a genetically distinct, multidrug-resistant Staphylococcus capitis clone (NRCS-A) present in neonatal intensive care units has recently been extensively reported. The aims of the present study were to investigate which clones of S. capitis isolated from blood in a Swedish neonatal intensive care unit (NICU) have been present since 1987 and to investigate whether the NRCS-A clone has disseminated in Sweden. All S. capitis isolates from blood cultures of neonates (≤ 28 days of age) between 1987 and 2017 (n = 46) were whole-genome sequenced, and core genome multilocus sequence typing (cgMLST) was performed. Single-nucleotide polymorphism (SNP)-based phylogenetic relationships between the S. capitis isolates and in silico predictions of presence of genetic traits specific to the NRCS-A clone were identified. Furthermore, antibiotic susceptibility testing, including screening for heterogeneous glycopeptide-intermediate resistance, was performed. Thirty-five isolates clustered closely to the isolates previously determined as belonging to the NRCS-A clone and had fewer than 81 core genome loci differences out of 1063. Twenty-one of these isolates were multidrug resistant. The NRCS-A clone was found in 2001. Six pairs of isolates had differences of fewer than two SNPs. Genetic traits associated with the NRCS-A clone such as nsr, ebh, tarJ, and CRISPR were found in all 35 isolates. The increasing incidence of S. capitis blood cultures of neonates is predominantly represented by the NRSC-A clone at our NICU in Sweden. Furthermore, there were indications of transmission between cases; adherence to basic hygiene procedures and surveillance measures are thus warranted.\n\nGenomic analysis of Staphylococcus capitis isolated from blood cultures in neonates at a neonatal intensive care unit in Sweden.", "token_count": 487, "char_count": 1827, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5585, "quality_score": 0.7792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:03.973414", "source": { "split": "train_shard_00000", "doc_id": 2947 }, "chunk_id": "train_shard_00000_2947_0", "global_id": 3251 }, { "text": "Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated subpopulations. The reconstruction of core genome-wide strains from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel life span and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi, where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.\n\nHorizontally transmitted symbiont populations in deep-sea mussels are genetically isolated.", "token_count": 289, "char_count": 1338, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:04.546186", "source": { "split": "train_shard_00000", "doc_id": 2948 }, "chunk_id": "train_shard_00000_2948_0", "global_id": 3252 }, { "text": "Toxicological approaches in screening drugs that cause drug-induced liver injury (DILI) are urgently needed to reduce the risk of developing DILI and avoid immense costs resulting from late-stage drug withdrawal from clinical trials. Cholestatic DILI is characterized by bile acid (BA) accumulation in hepatocytes, typically caused by drug-induced inhibition of important bile transporters, such as bile salt export pump (BSEP) and multidrug resistance-associated protein 2/3/4 (MRP2/3/4). Therefore, NTCP expression is essential for construction of an in vitro hepatocellular toxicity evaluation system. Here, we investigated whether sandwich-cultured HepG2-hNTCP-C4 (SCHepG2-hNTCP-C4) cells were applicable for evaluation of cholestatic DILI. In SCHepG2-hNTCP-C4 cells, NTCP and MRP2/4 expression levels were comparable to those in human primary hepatocytes; however, BSEP expression was low. In addition, the substrates tauro-nor-THCA-24 DBD and CDF confirmed the functionality of NTCP and MRP2, respectively. When 22 known hepatotoxins were exposed to BAs to evaluate cholestatic DILI, cytotoxicity in SCHepG2-hNTCP-C4 cells was more frequent than that in SCHepG2 cells. Thus, SCHepG2-hNTCP-C4 cells may be useful preclinical screening tools to predict the risk of cholestatic DILI induced by drug candidates. However, further studies are needed to determine why the cholestatic cytotoxicity of some compounds would be still insufficient in SCHepG2-hNTCP-C4 cells.\n\nDevelopment of an in vitro cholestatic drug-induced liver injury evaluation system using HepG2-hNTCP-C4 cells in sandwich configuration.", "token_count": 459, "char_count": 1606, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8233, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:05.182630", "source": { "split": "train_shard_00000", "doc_id": 2949 }, "chunk_id": "train_shard_00000_2949_0", "global_id": 3253 }, { "text": "The genus Caldicellulosiruptor is comprised of extremely thermophilic, heterotrophic anaerobes that degrade plant biomass using modular, multifunctional enzymes. Prior pangenome analyses determined that this genus is genetically diverse, with the current pangenome remaining open, meaning that new genes are expected with each additional genome sequence added. Given the high biodiversity observed among the genus Caldicellulosiruptor, we have sequenced and added a 14th species, Caldicellulosiruptor changbaiensis, to the pangenome. The pangenome now includes 3791 ortholog clusters, 120 of which are unique to C. changbaiensis and may be involved in plant biomass degradation. Comparisons between C. changbaiensis and Caldicellulosiruptor bescii on the basis of growth kinetics, cellulose solubilization and cell attachment to polysaccharides highlighted physiological differences between the two species which are supported by their respective gene inventories. Most significantly, these comparisons indicated that C. changbaiensis possesses uncommon cellulose attachment mechanisms not observed among the other strongly cellulolytic members of the genus Caldicellulosiruptor.\n\nGenomic and physiological analyses reveal that extremely thermophilic Caldicellulosiruptor changbaiensis deploys uncommon cellulose attachment mechanisms.", "token_count": 335, "char_count": 1335, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6747, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:05.745924", "source": { "split": "train_shard_00000", "doc_id": 2950 }, "chunk_id": "train_shard_00000_2950_0", "global_id": 3254 }, { "text": "This study focuses on fructanase production in a batch reactor by a new strain isolated from agave juice (K. marxianus var. drosophilarum) employing different Agave tequilana fructan (ATF) concentrations as substrate. The experimental data suggest that the fructanase production may be inhibited or repressed by high substrate (50 g/L) and ethanol (20.7 g/L) concentrations present in culture medium. To further analyze these phenomena an unstructured kinetic mathematical model taking into account substrate and products inhibition was proposed and fitted. The mathematical model considers six reaction kinetics and the ethanol evaporation, and predicts satisfactorily the biomass, fructan, glucose, fructose, ethanol, and fructanase behavior for different raw material initial concentrations. The proposed model is the first to satisfactorily describe the production of fructanase from branched ATF with a new strain of K. marxianus.\n\nSubstrates' and products' inhibition in fructanase production by a new Kluyveromyces marxianus CF15 from Agave tequilana fructan in a batch reactor.", "token_count": 283, "char_count": 1085, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8257, "entities": { "genes": [ "CF15" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:06.671468", "source": { "split": "train_shard_00000", "doc_id": 2951 }, "chunk_id": "train_shard_00000_2951_0", "global_id": 3255 }, { "text": "The order Herpesvirales encompasses a wide variety of important and broadly distributed human pathogens. During the last decades, similarities in the viral cycle and the structure of some of their proteins with those of the order Caudovirales, the tailed bacterial viruses, have brought speculation regarding the existence of an evolutionary relationship between these clades. To evaluate such hypothesis, we used over 600 Herpesvirales and 2000 Caudovirales complete genomes to search for the presence or absence of clusters of orthologous protein domains and constructed a dendrogram based on their compositional similarities. The results obtained strongly suggest an evolutionary relationship between the two orders. Furthermore, they allowed to propose a core genome for the Herpesvirales, composed of 4 proteins, including the ATPase subunit of the DNA-packaging terminase, the only protein with previously verified conservation. Accordingly, a phylogenetic tree constructed with sequences derived from the clusters associated to these proteins grouped the Herpesvirales strains accordingly to the established families and subfamilies. Overall, this work provides results supporting the hypothesis that the two orders are evolutionarily related and contributes to the understanding of the history of the Herpesvirales.\n\nDefining a Core Genome for the Herpesvirales and Exploring their Evolutionary Relationship with the Caudovirales.", "token_count": 308, "char_count": 1438, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6281, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:07.252641", "source": { "split": "train_shard_00000", "doc_id": 2952 }, "chunk_id": "train_shard_00000_2952_0", "global_id": 3256 }, { "text": "Clostridium difficile, the causal agent of antibiotic-associated diarrhea, has a complex epidemiology poorly studied in Latin America. We performed a robust genomic and phenotypic profiling of 53 C. difficile clinical isolates established from diarrheal samples from either intrahospital (IH) or community (CO) populations in central Colombia. In vitro tests were conducted to evaluate the cytopathic effect, the minimum inhibitory concentration of ten antimicrobial agents, the sporulation efficiency and the colony forming ability. Eleven different sequence types (STs) were found, the majority present individually in each sample, however in three samples two different STs were isolated. Interestingly, CO patients were infected with STs associated with hypervirulent strains (ST-1 in Clade-2). Three coexistence events (two STs simultaneously detected in the same sample) were observed always involving ST-8 from Clade-1. A total of 2,502 genes were present in 99% of the isolates with 95% of identity or more, it represents a core genome of 28.6% of the 8,735 total genes identified in the set of genomes. A high cytopathic effect was observed for the isolates positive for the two main toxins but negative for binary toxin (TcdA+/TcdB+/CDT- toxin production type), found only in Clade-1. Molecular markers conferring resistance to fluoroquinolones (cdeA and gyrA) and to sulfonamides (folP) were the most frequent in the analyzed genomes. In addition, 15 other markers were found mostly in Clade-2 isolates. These results highlight the regional differences that C. difficile isolates display, being in this case the CO isolates the ones having a greater number of accessory genes and virulence-associated factors.\n\nIntegrated genomic epidemiology and phenotypic profiling of Clostridium difficile across intra-hospital and community populations in Colombia.", "token_count": 477, "char_count": 1864, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6283, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:07.947942", "source": { "split": "train_shard_00000", "doc_id": 2953 }, "chunk_id": "train_shard_00000_2953_0", "global_id": 3257 }, { "text": "Bile salt hydrolase (BSH) activity, hypo-cholesterolemic effect, and probiotic properties have been reported for\n\nEvaluation of Bile Salt Hydrolases, Cholesterol-Lowering Capabilities, and Probiotic Potential of", "token_count": 61, "char_count": 211, "word_count": 25, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:08.350575", "source": { "split": "train_shard_00000", "doc_id": 2954 }, "chunk_id": "train_shard_00000_2954_0", "global_id": 3258 }, { "text": "This study aimed to reveal the mechanisms underlying the interaction between condensed tannins (CTs) and bile salts. The interaction mechanism was analyzed by transmission electron microscopy, exposure to various physicochemical conditions, electrophoresis, fluorescence spectroscopy, isothermal titration calorimetry, and molecular modeling. A new complex was formed from CTs and bile salts. The complex showed a negative enthalpy change and a positive entropy change, demonstrating that the main thermodynamic driving force was both entropy and enthalpy and indicating that binding occurred through hydrogen bonds and hydrophobic interactions. The analysis of the effects of CTs on the stability and digestion properties of bile salt emulsions indicated that CTs were able to inhibit lipid digestion to an extent. Our findings may provide evidence that foods rich in CTs offer health benefits by aggregating with bile salts and reducing the absorption of fat.\n\nCharacterizing the Interactions of Dietary Condensed Tannins with Bile Salts.", "token_count": 228, "char_count": 1040, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6689, "quality_score": 0.8345, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:08.816667", "source": { "split": "train_shard_00000", "doc_id": 2955 }, "chunk_id": "train_shard_00000_2955_0", "global_id": 3259 }, { "text": "Human hepatoma cell lines are useful for evaluation of drug-induced hepatotoxicity, hepatic drug disposition, and drug-drug interactions. However, their applicability is compromised by aberrant expression of hepatobiliary transporters. This study was designed to evaluate whether extracellular matrix (Matrigel) overlay and dexamethasone (DEX) treatment would support cellular maturation of long-term HuH-7 hepatoma cell cultures and improve the expression, localization, and activity of canalicular ATP-binding cassette (ABC) transporters, multidrug resistance protein 1 (MDR1/P-glycoprotein/ABCB1), multidrug resistance-associated protein 2 (MRP2/ABCC2), and bile salt export pump (BSEP/ABCB11). Matrigel overlay promoted the maturation of HuH-7 cells toward cuboidal, hepatocyte-like cells displaying bile canaliculi-like structures visualized by staining for filamentous actin (F-actin), colocalization of MRP2 with F-actin, and by accumulation of the MRP2 substrate 5(6)-carboxy-2',7'-dichlorofluorescein (CDF) within the tubular canaliculi. The cellular phenotype was rather homogenous in the Matrigel-overlaid cultures, whereas the standard HuH-7 cultures contained both hepatocyte-like cells and flat epithelium-like cells. Only Matrigel-overlaid HuH-7 cells expressed MDR1 at the canaliculi and excreted the MDR1 probe substrate digoxin into biliary compartments. DEX treatment resulted in more elongated and branched canaliculi and restored canalicular expression and function of BSEP. These findings suggest that hepatocyte polarity, elongated canalicular structures, and proper localization and function of canalicular ABC transporters can be recovered, at least in part, in human hepatoma HuH-7 cells by applying the modified culture conditions", "token_count": 480, "char_count": 1757, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8394, "entities": { "genes": [ "ABCB1", "MRP2", "MDR1", "ABCC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:09.461474", "source": { "split": "train_shard_00000", "doc_id": 2956 }, "chunk_id": "train_shard_00000_2956_0", "global_id": 3260 }, { "text": "SIGNIFICANCE STATEMENT: We report the first demonstration that proper localization and function of canalicular ABC transporters can be recovered in human hepatoma HuH-7 cells by modification of cell culture conditions. Matrigel overlay and dexamethasone supplementation increased the proportion of hepatocyte-like cells, strongly augmented the canalicular structures between the cells, and restored the localization and function of key canalicular ABC transporters. These results will facilitate the development of reproducible, economical, and easily achievable liver cell models for drug development.\n\nOptimization of Canalicular ABC Transporter Function in HuH-7 Cells by Modification of Culture Conditions.", "token_count": 155, "char_count": 710, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:09.893229", "source": { "split": "train_shard_00000", "doc_id": 2956 }, "chunk_id": "train_shard_00000_2956_1", "global_id": 3261 }, { "text": "Reflux esophagitis is a result of esophageal exposure to acid and bile during episodes of gastroesophageal reflux. Aside from chemical injury to the esophageal epithelium, it has been shown that acid and bile induce cytokine-mediated injury by stimulating the release of pro-inflammatory cytokines. During the repair and healing process following reflux injury, the squamous esophageal cells are replaced with a columnar epithelium causing Barrett's metaplasia, which predisposes patients to esophageal adenocarcinoma. We identified a novel player in gastroesophageal reflux injury, the TGFβ family member Activin A (ActA), which is a known regulator of inflammation and tissue repair. In this study, we show that in response to bile salt and acidified media (pH 4) exposure, emulating the milieu to which the distal esophagus is exposed during gastroesophageal reflux, long-term treated, tolerant esophageal keratinocytes exhibit increased ActA secretion and a pro-inflammatory cytokine signature. Furthermore, we noted increased motility and expression of the stem cell markers SOX9, LGR5 and DCLK1 supporting the notion that repair mechanisms were activated in the bile salt/acid-tolerant keratinocytes. Additionally, these experiments demonstrated that de-differentiation as characterized by the induction of YAP1, FOXO3 and KRT17 was altered by ActA/TGFβ signaling. Collectively, our results suggest a pivotal role for ActA in the inflammatory GERD environment by modulating esophageal tissue repair and de-differentiation.\n\nActivin A-mediated epithelial de-differentiation contributes to injury repair in an in vitro gastrointestinal reflux model.", "token_count": 447, "char_count": 1653, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6388, "quality_score": 0.8194, "entities": { "genes": [ "SOX9", "YAP1", "LGR5", "FOXO3", "KRT17", "DCLK1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:10.520364", "source": { "split": "train_shard_00000", "doc_id": 2957 }, "chunk_id": "train_shard_00000_2957_0", "global_id": 3262 }, { "text": "Drug-induced liver injury (DILI) remains a major challenge in drug development. Although numerous mechanisms for DILI have been identified, few studies have focused on loss of hepatocyte polarization as a DILI mechanism. The current study investigated the effects of valproate (VPA), an antiepileptic drug with DILI risk, on the cellular mechanisms responsible for loss of hepatocyte polarization. Fully polarized collagen sandwich-cultured rat hepatocytes were treated with VPA (1-20 mM) for specified times (3-24 h). Hepatocyte viability was significantly decreased by 10 and 20 mM VPA. Valproate depolarized hepatocytes, even at noncytotoxic concentrations (≤5 mM). Depolarization was associated with significantly decreased canalicular levels of multidrug resistance-associated protein 2 (Mrp2) resulting in reduced canalicular excretion of the Mrp2 substrate carboxydichlorofluorescein. The decreased canalicular Mrp2 was associated with intracellular accumulation of Mrp2 in Rab11-positive recycling endosomes and early endosomes. Mechanistic studies suggested that VPA inhibited canalicular trafficking of Mrp2. This effect of VPA on Mrp2 appeared to be selective in that VPA had less impact on canalicular levels of the bile salt export pump (Bsep) and no detectable effect on P-glycoprotein (P-gp) canalicular levels. Treatment with VPA for 24 h also significantly downregulated levels of tight junction (TJ)-associated protein, zonula occludens 2 (ZO2), but appeared to have no effect on the levels of TJ proteins claudin 1, claudin 2, occludin, ZO1, and ZO3. These findings reveal that two novel mechanisms may contribute to VPA hepatotoxicity: impaired canalicular trafficking of Mrp2 and disruption of ZO2-associated hepatocyte polarization.", "token_count": 493, "char_count": 1754, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.8189, "entities": { "genes": [ "ZO2", "ZO1", "ZO3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:11.174635", "source": { "split": "train_shard_00000", "doc_id": 2958 }, "chunk_id": "train_shard_00000_2958_0", "global_id": 3263 }, { "text": "Novel Mechanisms of Valproate Hepatotoxicity: Impaired Mrp2 Trafficking and Hepatocyte Depolarization.", "token_count": 33, "char_count": 102, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:11.528618", "source": { "split": "train_shard_00000", "doc_id": 2958 }, "chunk_id": "train_shard_00000_2958_1", "global_id": 3264 }, { "text": "Drug-induced liver injury (DILI) is a common side effect of several medications and is considered a major factor responsible for the discontinuation of drugs during their development. Cholestasis is a DILI that results from impairment of bile acid transporters, such as the bile salt export pump (BSEP), leading to accumulation of bile acids. Both in vitro and in vivo studies are required to predict the risk of drug-induced cholestasis. In the present study, we used chimeric mice with humanized liver as a model to study drug-induced cholestasis. Administration of a single dose of ketoconazole or rifampicin, known to potentially cause cholestasis by inhibiting BSEP, did not result in elevated levels of alkaline phosphatase (ALP), which are known hepatic biomarkers. The concentration of taurodeoxycholic acid increased in the liver after ketoconazole administration, whereas rifampicin resulted in increased tauromuricholic acid and taurocholic acid (TCA) levels in the liver and plasma. Furthermore, rifampicin resulted in an increase in the uniform distribution of a compound with m/z 514.3, presumed as TCA through imaging mass spectrometry. The mRNA levels of bile acid-related genes were also altered after treatment with ketoconazole or rifampicin. We believe these observations to be a part of a feedback mechanism to decrease bile acid concentrations. The changes in bile acid concentrations results may reflect the initial responses of the human body to cholestasis. Furthermore, these findings may contribute to the screening of drug candidates, thereby avoiding drug-induced cholestasis during clinical trials and drug development.\n\nChanges in Bile Acid Concentrations after Administration of Ketoconazole or Rifampicin to Chimeric Mice with Humanized Liver.", "token_count": 437, "char_count": 1776, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5654, "quality_score": 0.7827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:12.155357", "source": { "split": "train_shard_00000", "doc_id": 2959 }, "chunk_id": "train_shard_00000_2959_0", "global_id": 3265 }, { "text": "In this study, the antimicrobial, antioxidant and antitumor activity of ethanol extracts obtained from Phlomis russeliana (Sims.) Lag. ex Benth. (Lamiaceae) were evaluated. Disc diffusion and microdilution methods were used to test the extracts for antimicrobial activity against seven bacteria strains (Bacillus cereus ATCC 7064, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 6538P, Escherichia coli ATCC 10538, Proteus vulgaris ATCC 6899, Salmonella typhimurium CCM 5445 and Pseudomonas aeruginosa ATCC 27853) and four yeast strains (Kluyveromyces fragilis ATCC 8608, Rhodotorula rubra ATCC 70403, Debaryomyces hansenii DSM 70238 and Candida albicans ATCC 10239). Notably, they were more effective against the yeast strains than the bacterial strains. Of the yeast cultures, D. hanseii was among the most susceptible, having an inhibition zone of 16.2 mm with minimum inhibitory concentrations (MICs) and minimum fungicidal concentrations (MFCs) of 64(128)µg/ml, respectively. For cytotoxic determination, Caco-2 cells were cultured as per ATCC protocol, and were treated with log concentrations (5-80 mg/ml) of P. russeliana. The potency of cell growth inhibition for each extract was expressed as an IC50 value. Moreover, oxidant capacity was evaluated via TOC assay", "token_count": 438, "char_count": 1280, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:12.790806", "source": { "split": "train_shard_00000", "doc_id": 2960 }, "chunk_id": "train_shard_00000_2960_0", "global_id": 3266 }, { "text": "This product induced antiproliferative activity of 31.33% at 40 mg/ml and 20.96% at 80 mg/ml, without toxic effects on cells, although the oxidant capacity was decreased to 27.06 ± 0.7 nm in the 80 mg/ml-applied group compared to 47.9 ± 1.8 nm in the untreated one. Advanced pharmacological studies are needed to further evaluate P. russeliana for distinctive features.\n\nEvaluating antimicrobial and antioxidant capacity of endemic Phlomis russeliana from Turkey and its antiproliferative effect on Human Caco-2 Cell Lines.", "token_count": 167, "char_count": 523, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:13.226918", "source": { "split": "train_shard_00000", "doc_id": 2960 }, "chunk_id": "train_shard_00000_2960_1", "global_id": 3267 }, { "text": "Incidence of human yersiniosis in New Zealand has increased between 2013 and 2017. For surveillance and outbreak investigations it is essential that an appropriate level of discrimination between pathogenic Yersinia enterocolitica isolates is provided, in order to support epidemiological linking of connected cases. Subtyping of 227 Y. enterocolitica isolates was performed using a range of different typing methods, including biotyping, serotyping and seven loci multiple-locus variable-number tandem-repeat analysis (MLVA). In addition, core genome single-nucleotide polymorphism (core SNP) analysis and multi-locus sequence typing were performed on a subset of 69 isolates. Sixty-seven different MLVA types were identified. One MLVA profile was associated with an outbreak in the Bay of Plenty region, supported by epidemiological data. Core SNP analysis showed that all the outbreak-related isolates clustered together. The subtyping and epidemiological evidence suggests that the outbreak of yersiniosis in the Bay of Plenty region between October and December 2016 could be attributed to a point source. However, subtyping results further suggest that the same clone was isolated from several regions between August 2016 and March 2017. Core SNP analysis and MLVA typing failed to differentiate between Y. enterocolitica biotype 2 and biotype 3. For this reason, we propose that these biotypes should be reported as a single type namely: Y. enterocolitica biotype 2/3 and that the serotype should be prioritised as an indicator of prevalence.\n\nEvaluating sub-typing methods for pathogenic Yersinia enterocolitica to support outbreak investigations in New Zealand.", "token_count": 408, "char_count": 1670, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:13.853551", "source": { "split": "train_shard_00000", "doc_id": 2961 }, "chunk_id": "train_shard_00000_2961_0", "global_id": 3268 }, { "text": "We develop a technique for the sorption of inulinase from Kluyveromyces marxianus on the KU-2 matrix cation-exchanger. The most appropriate conditions for immobilization are: 25 °C, pH 4.5, incubation time 1.5 h, protein content during immobilization 10 mg/g of carrier. At higher (20-100 mg/g) concentrations, inulinase forms local high-concentration domains on the ion-exchanger surface, the enzyme is adsorbed on the protein, not on the carrier. 62% of the initial catalytic activity of inulinase is immobilized on KU-2 by the adsorption method. Upon the enzyme immobilization on KU-2, the number of unordered structures in the protein is reduced by ~10%, that points to the compaction of the molecule. Hydrogen bonds are formed only between the sulfo groups of carrier and the protein molecule, without affecting other structures of the cation exchanger. The highest activity of the inulinase immobilized on KU-2 was observed at 70 °C (cf. 50 °C for the native enzyme). Heating of the solution for 60 min in the temperature range of 50-80 °C failed to inactivate completely the immobilized enzyme; the complete loss of its ability to hydrolyze inulin was achieved only after more than 1 h incubation at 90 °C.\n\nImmobilization of inulinase on KU-2 ion-exchange resin matrix.", "token_count": 403, "char_count": 1277, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6219, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:14.473672", "source": { "split": "train_shard_00000", "doc_id": 2962 }, "chunk_id": "train_shard_00000_2962_0", "global_id": 3269 }, { "text": "Ethanol production at high temperatures has garnered much interest in recent years and a key factor is the availability of thermotolerant yeasts. During an investigation on the diversity of thermotolerant yeasts from different habitats, a novel yeast species from the spent wash of a distillery unit associated with a sugar factory was isolated. Phylogenetic analysis of D1/D2 large subunit and ITS rRNA genes placed this species in the ascomycetous genus", "token_count": 104, "char_count": 455, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:14.861152", "source": { "split": "train_shard_00000", "doc_id": 2963 }, "chunk_id": "train_shard_00000_2963_0", "global_id": 3270 }, { "text": "Cholestatic disorders are divided in the extra and intra-hepatic that created due to the severe liver diseases. ABCB11 encodes the bile salt export pump and this gene is mutated in several forms of intrahepatic cholestasis. So far, some molecular features of this gene was studies.\n\nMolecular Modelling and Evaluation of Hidden Information in ABCB11 Gene Mutations.", "token_count": 93, "char_count": 365, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:15.239135", "source": { "split": "train_shard_00000", "doc_id": 2964 }, "chunk_id": "train_shard_00000_2964_0", "global_id": 3271 }, { "text": "Caliciviruses are single-stranded RNA viruses with 180 copies of capsid protein comprising the T=3 icosahedral capsids. The main capsid feature is a pronounced protruding (P) domain dimer formed by adjacent subunits on the icosahedral surface while the shell domain forms a tight icosahedral sphere around the genome. While the P domain in the crystal structure of human Norwalk virus (genotype I.1) was tightly associated with the shell surface, the cryo-electron microscopy (cryo-EM) structures of several members of the\n\nBile Salts Alter the Mouse Norovirus Capsid Conformation: Possible Implications for Cell Attachment and Immune Evasion.", "token_count": 163, "char_count": 643, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7553, "quality_score": 0.8777, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:15.683096", "source": { "split": "train_shard_00000", "doc_id": 2965 }, "chunk_id": "train_shard_00000_2965_0", "global_id": 3272 }, { "text": "Curcumin is a natural polyphenol compound obtained from the turmeric plant, having numerous promising health benefits. To deliver curcumin into the human body, it is necessary to develop an efficient carrier system for its encapsulation such that the physicochemical properties of curcumin can be preserved during storage. In this study, the encapsulation stability, antioxidant activity, and release properties of curcumin encapsulated in the primary emulsion (PE: 0.0022% (w/w) curcumin, 9.99% (w/w) oil, 0.9% (w/w) whey protein isolate, pH 7) and secondary emulsion (SE: 0.00108% (w/w) curcumin, 4.90% (w/w) oil, 0.443% (w/w) WPI, 0.2% (w/w) sodium alginate, pH 5) prepared using ultrasonication were analyzed. It was observed that the formation of a double-layer coating of secondary biopolymer over the primary coated droplet enhanced the encapsulation efficiency and antioxidant activity of the curcumin during storage for 3 weeks. Moreover, the multilayer emulsions were freeze-dried to see the effect of dehydration of emulsion on the stability of multilayer-coated droplets. Fourier transform infrared analysis indicated the presence of all of the constituents, including curcumin, after the freeze drying of the emulsions. Scanning electron microscopy images showed that the microstructure of emulsion droplets was found to be uniformly distributed in the case of SE. The antioxidant activity of curcumin encapsulated in SE was found to be higher during storage, whereas it was significantly reduced in other encapsulated systems like PE, olive oil, and ethanol. In vitro release of curcumin from the multilayer emulsion was carried out under the simulated intestinal conditions of pancreatin enzyme and bile salt. Maximum releases of 71 and 63% were obtained in SE and PE, respectively, within 2 h of digestion", "token_count": 504, "char_count": 1821, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:16.338653", "source": { "split": "train_shard_00000", "doc_id": 2966 }, "chunk_id": "train_shard_00000_2966_0", "global_id": 3273 }, { "text": "Overall, this study provides useful information on the formation of multilayer emulsion as a carrier system for the better protection and release of curcumin useful for food and pharmaceutical applications.\n\nCurcumin Encapsulation in Multilayer Oil-in-Water Emulsion: Synthesis Using Ultrasonication and Studies on Stability and Antioxidant and Release Activities.", "token_count": 83, "char_count": 364, "word_count": 48, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:16.713141", "source": { "split": "train_shard_00000", "doc_id": 2966 }, "chunk_id": "train_shard_00000_2966_1", "global_id": 3274 }, { "text": "In grape must, nitrogen is available as a complex mixture of various compounds (ammonium and amino acids). Wine yeasts assimilate these multiple sources in order to suitably fulfil their anabolic requirements during alcoholic fermentation. Nevertheless, the order of uptake and the intracellular fate of these sources are likely to differ between strains and species. Using a two-pronged strategy of isotopic filiation and RNA sequencing, the metabolic network of nitrogen utilization and its regulation in Kluyveromyces marxianus were described, in comparison with those of Saccharomyces cerevisiae. The data highlighted differences in the assimilation of ammonium and arginine between the two species. The data also revealed that the metabolic fate of certain nitrogen sources differed, thereby resulting in the production of various amounts of key wine aroma compounds. These observations were corroborated by the gene expression analysis.\n\nA comparison of the nitrogen metabolic networks of Kluyveromyces marxianus and Saccharomyces cerevisiae.", "token_count": 245, "char_count": 1048, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6149, "quality_score": 0.8074, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:17.199781", "source": { "split": "train_shard_00000", "doc_id": 2967 }, "chunk_id": "train_shard_00000_2967_0", "global_id": 3275 }, { "text": "Salmonella enterica serotype Dublin (S. Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated data set comprising of 880 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin in the UK are genomically distinct from US, Brazilian, and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and are mediated by an IncA/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in the serotype. Comparison of S. Dublin to a closely related serotype, S. enterica serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not found in S. Enteritidis. Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.\n\nGeography Shapes the Population Genomics of Salmonella enterica Dublin.", "token_count": 330, "char_count": 1393, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8137, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:17.768737", "source": { "split": "train_shard_00000", "doc_id": 2968 }, "chunk_id": "train_shard_00000_2968_0", "global_id": 3276 }, { "text": "Kefir is a homemade, natural fermented product comprised of a probiotic bacteria and yeast complex. Kefir consumption has been associated with many advantageous properties to general health, including as an antioxidative, anti-obesity, anti-inflammatory, anti-microbial, and anti-tumor moiety. This beverage is commonly found and consumed by people in the United States of America, China, France, Brazil, and Japan. Recently, the consumption of kefir has been popularized in other countries including Malaysia. The microflora in kefir from different countries differs due to variations in culture conditions and the starter media. Thus, this study was aimed at isolating and characterizing the lactic acid bacteria that are predominant in Malaysian kefir grains via macroscopic examination and 16S ribosomal RNA gene sequencing. The results revealed that the Malaysian kefir grains are dominated by three different strains of Lactobacillus strains, which are Lactobacillus harbinensis, Lactobacillusparacasei, and Lactobacillus plantarum. The probiotic properties of these strains, such as acid and bile salt tolerances, adherence ability to the intestinal mucosa, antibiotic resistance, and hemolytic test, were subsequently conducted and extensively studied. The isolated Lactobacillus spp. from kefir H maintained its survival rate within 3 h of incubation at pH 3 and pH 4 at 98.0 ± 3.3% and 96.1 ± 1.7% of bacteria growth and exhibited the highest survival at bile salt condition at 0.3% and 0.5%. The same isolate also showed high adherence ability to intestinal cells at 96.3 ± 0.01%, has antibiotic resistance towards ampicillin, penicillin, and tetracycline, and showed no hemolytic activity. In addition, the results of antioxidant activity tests demonstrated that isolated Lactobacillus spp", "token_count": 487, "char_count": 1801, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:18.447395", "source": { "split": "train_shard_00000", "doc_id": 2969 }, "chunk_id": "train_shard_00000_2969_0", "global_id": 3277 }, { "text": "from kefir G possessed high antioxidant activities for total phenolic content (TPC), total flavonoid content (TFC), ferric reducing ability of plasma (FRAP), and 1,1-diphenyl-2-picryl-hydrazine (DPPH) assay compared to other isolates. From these data, all Lactobacillus spp. isolated from Malaysian kefir serve as promising candidates for probiotics foods and beverage since they exhibit potential probiotic properties and antioxidant activities.\n\nIsolation and Characterization of", "token_count": 132, "char_count": 481, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8226, "quality_score": 0.9113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:18.901571", "source": { "split": "train_shard_00000", "doc_id": 2969 }, "chunk_id": "train_shard_00000_2969_1", "global_id": 3278 }, { "text": "Klebsiella aerogenes is an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens, K. aerogenes population structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidate K. aerogenes clonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure of K. aerogenes based on 97 publicly available genomes by using both multilocus sequence typing and single-nucleotide polymorphisms extracted from the core genome. We also assessed virulence and resistance profiles using Virulence Finder Database and Comprehensive Antibiotic Resistance Database, respectively. We show that K. aerogenes has an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least 10 CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow- and extended-spectrum β-lactamases. Regarding the population structure, we identified two clusters based on virulence profiles because of the presence of the toxin-encoding clb operon and the siderophore production genes, irp and ybt. Notably, CC3 comprises the majority of K. aerogenes isolates associated with hospital outbreaks, emphasizing the importance of constant monitoring of this pathogen. Collectively, our results may provide a foundation for the development of new therapeutic and surveillance strategies worldwide.\n\nGenomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance in Klebsiella aerogenes.", "token_count": 431, "char_count": 1831, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6478, "quality_score": 0.8239, "entities": { "genes": [ "CC9", "CC3", "CC10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:19.551409", "source": { "split": "train_shard_00000", "doc_id": 2970 }, "chunk_id": "train_shard_00000_2970_0", "global_id": 3279 }, { "text": "Probiotic bacteria were isolated from different traditional fermented foods as there are several such foods that are not well explored for their probiotic activities. Hence, the present study was conducted to find the potential of lactic acid bacteria (LAB) as probiotics that were isolated from the sap extract of the coconut palm inflorescence - Neera, which is a naturally fermented drink consumed in various regions of India. A total of 75 isolates were selected from the Neera samples collected aseptically in the early morning (before sunrise). These isolates were initially screened for cultural, microscopic, and biochemical characteristics. The initial screening yielded 40 Gram-positive, catalase-negative isolates that were further subjected to acid - bile tolerance with resistance to phenol. Among 40 isolates, 16 survived screening using analysis of cell surface hydrophobicity, auto aggregation with adhesion to epithelial cells, and gastric-pancreatic digestion for gastrointestinal colonization. The isolates were also assessed for antimicrobial, antibiotic sensitivity, and anti-oxidative potential. The safety of these isolates was evaluated by their hemolytic and deoxyribonuclease (DNase) activities. Based on these results, seven isolates with the best probiotic attributes were selected and presented in this study. These LAB isolates, with 51.91-70.34% survival at low pH, proved their resistance to gastric conditions. The cell surface hydrophobicity of 50.32-77.8% and auto aggregation of 51.02-78.95% represented the adhesion properties of these isolates. All the seven isolates exhibited good antibacterial and antifungal activity, showing hydroxyl-scavenging activity of 32.86-77.87%. The results proved that LAB isolated from Neera exhibited promising probiotic properties and seem favorable for use in functional fermented foods as preservatives.\n\nProbiotic Properties of Lactic Acid Bacteria Isolated From Neera: A Naturally Fermenting Coconut Palm Nectar.", "token_count": 503, "char_count": 1988, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5861, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:20.252878", "source": { "split": "train_shard_00000", "doc_id": 2971 }, "chunk_id": "train_shard_00000_2971_0", "global_id": 3280 }, { "text": "To understand the mechanism of replication used by baculoviruses, it is essential to describe all the factors involved, including virus and host proteins and the sequences where DNA synthesis starts. A lot of work on this topic has been done, but there is still confusion in defining what sequence/s act in such functions, and the mechanism of replication is not very well understood. In this work, we performed an AgMNPV replication kinetics into the susceptible UFL-Ag-286 cells to estimate viral genome synthesis rates. We found that the viral DNA exponentially increases in two different phases that are temporally separated by an interval of 5 h, probably suggesting the occurrence of two different mechanisms of replication. Then, we prepared a plasmid library containing virus fragments (0.5-2 kbp), which were transfected and infected with AgMNPV in UFL-Ag-286 cells. We identified 12 virus fragments which acted as origins of replication (ORI). Those fragments are in close proximity to core genes. This association to the core genome would ensure vertical transmission of ORIs. We also predict the presence of common structures on those fragments that probably recruit the replication machinery, a structure also present in previously reported ORIs in baculoviruses.\n\nIdentification of Multiple Replication Stages and Origins in the Nucleopolyhedrovirus of", "token_count": 309, "char_count": 1366, "word_count": 207, "semantic_coherence": 1, "information_density": 0.628, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:20.818284", "source": { "split": "train_shard_00000", "doc_id": 2972 }, "chunk_id": "train_shard_00000_2972_0", "global_id": 3281 }, { "text": "Idiosyncratic drug-induced liver injury (IDILI) is a significant problem. Little is known with certainty about the mechanisms of IDILI. However, there is growing evidence that most IDILI is immune mediated and caused by reactive metabolites. The two major and complementary hypotheses that link reactive metabolite formation with the induction of an immune response that can lead to IDILI are the hapten and danger hypotheses. Specifically, a reactive metabolite can bind to proteins and make them foreign; however, without activation of antigen presenting cells (APCs), the immune response will be immune tolerance. Not all reactive metabolites are associated with the same risk of causing IDILI. If the reactive metabolite can also cause some cell damage, this can lead to the release of danger-associated molecular pattern molecules (DAMPs) that activate APCs. Other hypotheses for the mechanism of IDILI include mitochondrial injury, inhibition of the bile salt export pump, and endoplasmic reticulum stress. These mechanisms may be complementary to the danger hypothesis in that they may cause the release of DAMPs. None of these hypotheses has been adequately tested. Previous animal models have had characteristics very different from IDILI in humans and are unlikely to involve the same mechanism. However, impairment of immune tolerance has led to a model with characteristics very similar to IDILI in humans. This will make it possible to rigorously test hypotheses. A better mechanistic understanding of IDILI should lead to better methods to screen drug candidates for IDILI risk and treat IDILI when it occurs.\n\nMechanisms of idiosyncratic drug-induced liver injury.", "token_count": 382, "char_count": 1679, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5771, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:21.393573", "source": { "split": "train_shard_00000", "doc_id": 2973 }, "chunk_id": "train_shard_00000_2973_0", "global_id": 3282 }, { "text": "Thermotolerant yeast Kluyveromyces marxianus can assimilate xylose but cannot produce ethanol from xylose under anaerobic conditions. Here, we constructed two recombinant K. marxianus strains, DMB5 and DMB13, that express xylose reductase (XR), NAD\n\nHigh-temperature ethanol production by a series of recombinant xylose-fermenting Kluyveromyces marxianus strains.", "token_count": 118, "char_count": 363, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8444, "quality_score": 0.9222, "entities": { "genes": [ "DMB5", "DMB13" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:21.778910", "source": { "split": "train_shard_00000", "doc_id": 2974 }, "chunk_id": "train_shard_00000_2974_0", "global_id": 3283 }, { "text": "Rhodococcus (Prescottella) equi causes pneumonia-like infections in foals with high mortality rates and can also infect a number of other animals. R. equi is also emerging as an opportunistic human pathogen. In this study, we have sequenced the genome of a novel R. equi isolate, B0269, isolated from the faeces of a bovine host. Comparative genomic analyses with seven other published R. equi genomes, including those from equine or human sources, revealed a pangenome comprising of 6876 genes with 4141 genes in the core genome. Two hundred and 75 genes were specific to the bovine isolate, mostly encoding hypothetical proteins of unknown function. However, these genes include four copies of terA and five copies of terD genes that may be involved in responding to chemical stress. Virulence characteristics in R. equi are associated with the presence of large plasmids carrying a pathogenicity island, including genes from the vap multigene family. A BLAST search of the protein sequences from known virulence-associated plasmids (pVAPA, pVAPB and pVAPN) revealed a similar plasmid backbone on two contigs in bovine isolate B0269; however, no homologues of the main virulence-associated genes, vapA, vapB or vapN, were identified. In summary, this study confirms that R. equi genomes are highly conserved and reports the presence of an apparently novel plasmid in the bovine isolate B0269 that needs further characterisation to understand its potential involvement in virulence properties.\n\nGenomic analysis of a novel Rhodococcus (Prescottella) equi isolate from a bovine host.", "token_count": 417, "char_count": 1583, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:22.400990", "source": { "split": "train_shard_00000", "doc_id": 2975 }, "chunk_id": "train_shard_00000_2975_0", "global_id": 3284 }, { "text": "The present investigation reports a detailed characterization of the interaction of a cationic photosensitizer, phenosafranin (PSF) with sodium deoxycholate (NaDC) bile salt aggregates based on spectroscopic and calorimetric techniques. Our explicit spectroscopic results not only establish the occurrence of PSF-NaDC binding interaction, but also reveal marked lowering of micropolarity at the interaction site (E\n\nRevealing the dynamics and energetics of interaction of a cationic biological photosensitizer within a bile salt aggregate.", "token_count": 127, "char_count": 539, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7324, "quality_score": 0.8662, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:22.788752", "source": { "split": "train_shard_00000", "doc_id": 2976 }, "chunk_id": "train_shard_00000_2976_0", "global_id": 3285 }, { "text": "In the present study, we reported 18 LAB strains isolated from the intestinal contents of Cyprinus carpio, and their probiotic properties both in vitro and in vivo. The results showed that 9 of them had higher in vitro immunomodulatory properties, effectively survived under acidic (pH 2.5) and bile salt (ranging from 0.1% to 0.5%) conditions, and inhibited the growth of 4 pathogens. Among them, Lactococcus lactis Q-8, Lactococcus lactis Q-9, and Lactococcus lactis Z-2 showed the strongest adhesion abilities and inhibition of pathogen adhesion to mucin. When the fish consumed diets containing these 3 strains (5 × 10\n\nEffects of Lactococcus lactis from Cyprinus carpio L. as probiotics on growth performance, innate immune response and disease resistance against Aeromonas hydrophila.", "token_count": 237, "char_count": 790, "word_count": 120, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:23.266938", "source": { "split": "train_shard_00000", "doc_id": 2977 }, "chunk_id": "train_shard_00000_2977_0", "global_id": 3286 }, { "text": "Taurolithocholate (TLC) is a cholestatic bile salt that induces disinsertion of the canalicular transporter Abcc2 (Mrp2, multidrug resistance-associated protein 2). This internalization is mediated by different intracellular signaling proteins such as PI3K, PKCε and MARCK but the initial receptor of TLC remains unknown. A few G protein-coupled receptors interact with bile salts in hepatocytes. Among them, sphingosine-1 phosphate receptor 2 (S1PR2) represents a potential initial receptor for TLC. The aim of this study was to evaluate the role of this receptor and its downstream effectors in the impairment of Abcc2 function induced by TLC. In vitro, S1PR2 inhibition by JTE-013 or its knockdown by small interfering RNA partially prevented the decrease in Abcc2 activity induced by TLC. Moreover, adenylyl cyclase (AC)/PKA and PI3K/Akt inhibition partially prevented TLC effect on canalicular transporter function. TLC produced PKA and Akt activation, which were blocked by JTE-013 and AC inhibitors, connecting S1PR2/AC/PKA and PI3K/Akt in a same pathway. In isolated perfused rat liver, injection of TLC triggered endocytosis of Abcc2 that was accompanied by a sustained decrease in the bile flow and the biliary excretion of the Abcc2 substrate dinitrophenyl-glutathione until the end of the perfusion period. S1PR2 or AC inhibition did not prevent the initial decay, but they accelerated the recovery of these parameters and the reinsertion of Abcc2 into the canalicular membrane. In conclusion, S1PR2 and the subsequent activation of AC, PKA, PI3K and Akt is partially responsible for the cholestatic effects of TLC through sustained internalization of Abcc2.\n\nSphingosine 1-phosphate receptor 2/adenylyl cyclase/protein kinase A pathway is involved in taurolithocholate-induced internalization of Abcc2 in rats.", "token_count": 507, "char_count": 1823, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [ "PI3K" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:23.919365", "source": { "split": "train_shard_00000", "doc_id": 2978 }, "chunk_id": "train_shard_00000_2978_0", "global_id": 3287 }, { "text": "The N-methyl-D-aspartate subfamily of ionotropic glutamate receptors (NMDARs) is well known for its important roles in the central nervous system (CNS), e.g. learning and memory formation. Besides the CNS, NMDARs are also expressed in numerous peripheral tissues including the pancreas, kidney, stomach, and blood cells, where an understanding of their physiological and pathophysiological roles is only evolving. Whereas subunit composition increases functional diversity of NMDARs, a great number of endogenous cues tune receptor signaling. Here, we characterized the effects of the steroid bile salts cholate and chenodeoxycholate (CDC) on recombinantly expressed NMDARs of defined molecular composition. CDC inhibited NMDARs in an isoform-dependent manner, preferring GluN2D and GluN3B over GluN2A and GluN2B receptors. Determined IC\n\nIsoform-specific Inhibition of N-methyl-D-aspartate Receptors by Bile Salts.", "token_count": 262, "char_count": 915, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7787, "quality_score": 0.8893, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:24.468869", "source": { "split": "train_shard_00000", "doc_id": 2979 }, "chunk_id": "train_shard_00000_2979_0", "global_id": 3288 }, { "text": "Kmmig1 as a disrupted mutant of MIG1 encoding a regulator for glucose repression in Kluyveromyces marxianus exhibits a histidine-auxotrophic phenotype. Genome-wide expression analysis revealed that only HIS4 in seven HIS genes for histidine biosynthesis was down-regulated in Kmmig1. Consistently, introduction of HIS4 into Kmmig1 suppressed the requirement of histidine. Considering the fact that His4 catalyzes four of ten steps in histidine biosynthesis, K. marxianus has evolved a novel and effective regulation mechanism via Mig1 for the control of histidine biosynthesis. Moreover, RNA-Seq analysis revealed that there were more than 1,000 differentially expressed genes in Kmmig1, suggesting that Mig1 is directly or indirectly involved in the regulation of their expression as a global regulator.\n\nMIG1 as a positive regulator for the histidine biosynthesis pathway and as a global regulator in thermotolerant yeast Kluyveromyces marxianus.", "token_count": 259, "char_count": 948, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6165, "quality_score": 0.8083, "entities": { "genes": [ "MIG1", "HIS4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:25.017593", "source": { "split": "train_shard_00000", "doc_id": 2980 }, "chunk_id": "train_shard_00000_2980_0", "global_id": 3289 }, { "text": "Drug-induced Liver Injury (DILI) has received increasing attention over the past decades, as it represents the leading cause of drug failure and attrition. One of the most prevalent and severe forms of DILI involves the toxic accumulation of bile acids in the liver, known as Drug-induced Cholestasis (DIC). Traditionally, DIC is studied by exploring the inhibition of hepatic transporters such as Bile Salt Export Pump (BSEP) and multidrug resistance-associated proteins, predominantly through vesicular transport assays. Although this approach has identified numerous drugs that alter bile flow, many DIC drugs do not demonstrate prototypical transporter inhibition, but rather are associated with alternative mechanisms.\n\nA Change in Bile Flow: Looking Beyond Transporter Inhibition in the Development of Drug-induced Cholestasis.", "token_count": 196, "char_count": 833, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:25.463514", "source": { "split": "train_shard_00000", "doc_id": 2981 }, "chunk_id": "train_shard_00000_2981_0", "global_id": 3290 }, { "text": "Porcine pancreatic extracts (PPE), also named pancreatin, are commonly used as a global source of pancreatic enzymes for enzyme replacement therapy in patients with exocrine pancreatic insufficiency. They are considered as a good substitute of human pancreatic enzymes and they have become a material of choice for in vitro models of digestion. Nevertheless, while the global PPE contents in lipase, protease and amylase activities are well characterized, little is known about individual enzymes. Here we characterized the lipase, phospholipase, cholesterol esterase and galactolipase activities of PPE and compared them with those of porcine (PPJ) and human (HPJ) pancreatic juices. The phospholipase to lipase activity ratio was similar in PPJ and HPJ, but was 4-fold lower in PPE. The galactolipase and cholesterol esterase activities were found at lower levels in PPJ compared to HPJ, and they were further reduced in PPE. The enzymes known to display these activities in HPJ, pancreatic lipase-related protein 2 (PLRP2) and carboxylester hydrolase/bile salt-stimulated lipase (CEH/BSSL), were identified in PPJ using gel filtration experiments, SDS-PAGE and LC-MS/MS analysis. The galactolipase and cholesterol esterase activities of PPE indicated that PLRP2 and CEH/BSSL are still present at low levels in this enzyme preparation, but they were not detected by mass spectrometry. Besides differences between porcine and human enzymes, the lower levels of phospholipase, galactolipase and cholesterol esterase activities in PPE are probably due to some proteolysis occurring during the production process. In conclusion, PPE do not provide a full substitution of the lipolytic enzymes present in HPJ.\n\nCharacterization of all the lipolytic activities in pancreatin and comparison with porcine and human pancreatic juices.", "token_count": 489, "char_count": 1827, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5358, "quality_score": 0.7679, "entities": { "genes": [ "PLRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:26.108760", "source": { "split": "train_shard_00000", "doc_id": 2982 }, "chunk_id": "train_shard_00000_2982_0", "global_id": 3291 }, { "text": "Cholestatic drug-induced liver injury (DILI) is a type of hepatotoxicity. Its underlying mechanisms are dysfunction of bile salt export pump (BSEP) and multidrug resistance-associated protein 2/3/4 (MRP2/3/4), which play major roles in bile acid (BA) excretion into the bile canaliculi and blood, resulting in accumulation of BAs in hepatocytes. The sandwich-cultured hepatocyte (SCH) model can simultaneously analyze hepatic uptake and biliary excretion. Therefore, we investigated whether sandwich-cultured human induced pluripotent stem cell (iPS cell)-derived hepatocytes (SCHiHs) are suitable for evaluating cholestatic DILI. Fluorescent N-(24-[7-(4-N,N-dimethylaminosulfonyl-2,1,3-benzoxadiazole)]amino-3α,7α,12α-trihydroxy-27-nor-5β-cholestan-26-oyl)-2'-aminoethanesulfonate (tauro-nor-THCA-24-DBD, a BSEP substrate) was accumulated in bile canaliculi, which supports the presence of a functional bile canaliculi lumen. MRP2 was highly expressed in the Western blot analysis, whereas the mRNA expression of BSEP was hardly detectable. MRP3/4 mRNA levels were maintained. Of the 22 compounds known to cause DILI with BAs, 7 showed significant cytotoxicity. Most high-risk drugs were detected using the developed SCHiH system. However, a shortcoming was the considerably low expression level of BSEP, which prevented the detection of some relevant drugs whose risks should be detected in primary human hepatocytes.\n\nIn vitro bile acid-dependent hepatocyte toxicity assay system using human induced pluripotent stem cell-derived hepatocytes: Current status and disadvantages to overcome.", "token_count": 486, "char_count": 1591, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7186, "quality_score": 0.8593, "entities": { "genes": [ "MRP2", "MRP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:26.754830", "source": { "split": "train_shard_00000", "doc_id": 2983 }, "chunk_id": "train_shard_00000_2983_0", "global_id": 3292 }, { "text": "Thermal damage, high osmolarity, and ethanol toxicity in the yeast Saccharomyces cerevisiae limit titer and productivity in fermentation to produce ethanol. We show that long-term adaptive laboratory evolution at 39.5°C generates thermotolerant yeast strains, which increased ethanol yield and productivity by 10% and 70%, in 2% glucose fermentations. From these strains, which also tolerate elevated-osmolarity, we selected a stable one, namely a strain lacking chromosomal duplications. This strain (TTY23) showed reduced mitochondrial metabolism and high proton efflux, and therefore lower ethanol tolerance. This maladaptation was bolstered by reestablishing proton homeostasis through increasing fermentation pH from 5 to 6 and/or adding potassium to the media. This change allowed the TTY23 strain to produce 1.3-1.6 times more ethanol than the parental strain in fermentations at 40°C with glucose concentrations ~300 g/L. Furthermore, ethanol titers and productivities up to 93.1 and 3.87 g·L\n\nEngineering high-gravity fermentations for ethanol production at elevated temperature with Saccharomyces cerevisiae.", "token_count": 328, "char_count": 1118, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7039, "quality_score": 0.852, "entities": { "genes": [ "TTY23" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:27.329304", "source": { "split": "train_shard_00000", "doc_id": 2984 }, "chunk_id": "train_shard_00000_2984_0", "global_id": 3293 }, { "text": "The aim of the present study was to investigate the diversity of methicillin-resistant Staphylococcus aureus (MRSA) that originated from Austrian companion animals during the last five-year period. A total of 90 non-repetitive MRSA isolates were obtained during diagnostic activities from autumn 2013 to autumn 2018. They originated from horses (n = 62), cats (n = 13), dogs (n = 10), rabbits (n = 2), a domestic canary, a zoo-kept hammer-headed bat (Hypsignathus monstrosus) and a semi-captive northern bald ibis (Geronticus eremita). Antimicrobial susceptibility testing was performed. All isolates were mecA-positive and mecC-negative. The isolates were genotyped by SCCmec, spa and dru typing, Multiple-Locus Variable number of tandem repeat Analyses (MLVA), S. aureus DNA microarray, and whole-genome sequencing (WGS). Eight sequence types (STs - ST398, ST5275 (new ST), ST225, ST8, ST22, ST152, ST1, and ST45), three SCCmec types (II, IV, and V), sixteen spa types (t003, t008, t011, t015, t032, t034, t1381, t1928, t1985, t223, t334, t355, t430, t6447, t6867, and t7105), fourteen dru types (dt10a, dt10az, dt10q, dt10r, dt11a, dt5e, dt6j, dt9a, dt9ak, dt9g, and four new types dt8as, dt7ak, dt4j, dt14n), and thirty-five MLVA types were detected", "token_count": 503, "char_count": 1253, "word_count": 188, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [ "ST22", "ST398", "ST45", "ST5275", "ST225", "ST8", "ST1", "ST152" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:27.978512", "source": { "split": "train_shard_00000", "doc_id": 2985 }, "chunk_id": "train_shard_00000_2985_0", "global_id": 3294 }, { "text": "WGS-based core genome MLST (cgMLST) displayed five main clusters. Compared to the time period 2004-2013, the results of the present study show not only a higher diversity among the MRSA isolates within the population of Austrian companion animals, but also the introduction of new clones. Although ST398 isolates remained predominant, mainly due to high presence of this lineage among horses, increasing isolation rates of human-associated MRSA clones were observed in cats and dogs.\n\nIncreased genetic diversity of methicillin-resistant Staphylococcus aureus (MRSA) isolated from companion animals.", "token_count": 147, "char_count": 599, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8118, "quality_score": 0.9059, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:28.420057", "source": { "split": "train_shard_00000", "doc_id": 2985 }, "chunk_id": "train_shard_00000_2985_1", "global_id": 3295 }, { "text": "Plant pathogens continuously evolve to evade host immune responses. During host colonization, many fungal pathogens secrete effectors to perturb such responses, but these in turn may become recognized by host immune receptors. To facilitate the evolution of effector repertoires, such as the elimination of recognized effectors, effector genes often reside in genomic regions that display increased plasticity, a phenomenon that is captured in the two-speed genome hypothesis. The genome of the vascular wilt fungus Verticillium dahliae displays regions with extensive presence/absence polymorphisms, so-called lineage-specific regions, that are enriched in in planta-induced putative effector genes. As expected, comparative genomics reveals differential degrees of sequence divergence between lineage-specific regions and the core genome. Unanticipated, lineage-specific regions display markedly higher sequence conservation in coding as well as noncoding regions than the core genome. We provide evidence that disqualifies horizontal transfer to explain the observed sequence conservation and conclude that sequence divergence occurs at a slower pace in lineage-specific regions of the V. dahliae genome. We hypothesize that differences in chromatin organisation may explain lower nucleotide substitution rates in the plastic, lineage-specific regions of V. dahliae.\n\nDynamic virulence-related regions of the plant pathogenic fungus Verticillium dahliae display enhanced sequence conservation.", "token_count": 329, "char_count": 1496, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:28.993087", "source": { "split": "train_shard_00000", "doc_id": 2986 }, "chunk_id": "train_shard_00000_2986_0", "global_id": 3296 }, { "text": "In proteomics, peptide information within mass spectrometry (MS) data from a specific organism sample is routinely matched against a protein sequence database that best represent such organism. However, if the species/strain in the sample is unknown or genetically poorly characterized, it becomes challenging to determine a database which can represent such sample. Building customized protein sequence databases merging multiple strains for a given species has become a strategy to overcome such restrictions. However, as more genetic information is publicly available and interesting genetic features such as the existence of pan- and core genes within a species are revealed, we questioned how efficient such merging strategies are to report relevant information. To test this assumption, we constructed databases containing conserved and unique sequences for 10 different species. Features that are relevant for probabilistic-based protein identification by proteomics were then monitored. As expected, increase in database complexity correlates with pangenomic complexity. However,\n\nOn the Impact of the Pangenome and Annotation Discrepancies While Building Protein Sequence Databases for Bacteria Proteogenomics.", "token_count": 236, "char_count": 1219, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6766, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:29.469663", "source": { "split": "train_shard_00000", "doc_id": 2987 }, "chunk_id": "train_shard_00000_2987_0", "global_id": 3297 }, { "text": "Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including bla\n\nPopulation structure and pangenome analysis of Enterobacter bugandensis uncover the presence of bla", "token_count": 159, "char_count": 672, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7159, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:29.909097", "source": { "split": "train_shard_00000", "doc_id": 2988 }, "chunk_id": "train_shard_00000_2988_0", "global_id": 3298 }, { "text": "A dietary fibre prepared from sugarcane stalk was compared with psyllium husk and wheat dextrin. In contrast to the other dietary fibres, sugarcane fibre was found to contain significant amounts of insoluble dietary fibre (73-86%), lignin (18.66-20.23%), and rare minerals such as chromium (0.67-2.54 mg/100 g) and manganese (1.07-2.34 mg/100 g). Analysis of the ethanol extract also detected compounds with antioxidant activity. Characterisation of five sugarcane fibres prepared from selected strains, harvest periods (growth or storage phase), and processing conditions showed these factors influenced the final composition. Furthermore, using in vitro digestion, we found that potassium, magnesium, chromium, and zinc in were bioaccessible in sugarcane samples. Also, sodium was shown to bind to the sugarcane fibre potentially indicating bile salt binding activity. Results from this study support the use of sugarcane as a source of dietary fibre in functional foods.\n\nComparing the chemical composition of dietary fibres prepared from sugarcane, psyllium husk and wheat dextrin.", "token_count": 307, "char_count": 1085, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6581, "quality_score": 0.829, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:30.515489", "source": { "split": "train_shard_00000", "doc_id": 2989 }, "chunk_id": "train_shard_00000_2989_0", "global_id": 3299 }, { "text": "Sodium Taurocholate Co-transporting Polypeptide (NTCP) and Bile Salt Export Pump (BSEP) play significant roles as membrane transporters because of their presence in the enterohepatic circulation of bile salts. They have emerged as promising drug targets in related liver disease.\n\nThe Role of the Sodium-taurocholate Co-transporting Polypeptide (NTCP) and Bile Salt Export Pump (BSEP) in Related Liver Disease.", "token_count": 117, "char_count": 410, "word_count": 57, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:31.730949", "source": { "split": "train_shard_00000", "doc_id": 2990 }, "chunk_id": "train_shard_00000_2990_0", "global_id": 3300 }, { "text": "Advances in whole-genome sequencing (WGS) technologies have documented genetic diversity and epidemiology of the major foodborne pathogen Listeria monocytogenes (Lm) in Europe and North America, but data concerning South America are scarce. Here, we examined the population structure and genetic diversity of this major foodborne pathogen collected in Brazil. Based on core genome multilocus sequence typing (cgMLST), isolates from lineages I (n = 22; 63%) and II (n = 13; 37%) were distributed into 10 different sublineages (SLs) and represented 31 new cgMLST types (CTs). The most prevalent SLs were SL9 (n = 9; 26%), SL3 (n = 6; 17%) and SL2 and SL218 (n = 5; 14%). Isolates belonging to CTs L2-SL9-ST9-CT4420 and L1-SL315-ST520-CT4429 were collected 3 and 9 years apart, respectively, revealing long-term persistence of Lm in Brazil. Genetic elements associated with stress survival were present in 60% of isolates (57% SSI-1 and 3% SSI-2). Pathogenic islands were present in 100% (LIPI-1), 43% (LIPI-3) and 6% (LIPI-4) of the isolates. Mutations leading to premature stop codons were detected in the prfA and inlA virulence genes. This study is an important contribution to understanding the genomic diversity and epidemiology of Lm in South America. In addition, the results highlight the importance of using WGS to reveal Lm long-term persistence.\n\nWhole-genome sequencing reveals Listeria monocytogenes diversity and allows identification of long-term persistent strains in Brazil.", "token_count": 452, "char_count": 1489, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [ "ST520", "CT4429", "SL315", "SL9", "SL218", "SL3", "CT4420", "SL2", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:32.373635", "source": { "split": "train_shard_00000", "doc_id": 2991 }, "chunk_id": "train_shard_00000_2991_0", "global_id": 3301 }, { "text": "Probiotics used in aquaculture are mostly from non-fish sources, as a result ineffective in eliciting the desired effects in aquatic animals. In this study, three Bacillus species were isolated from the digestive tract of freshwater fish Oreochromis niloticus and characterised based on their morphological, biochemical and evolutionary relationships. Their probiotic potentials were evaluated based on their ability to tolerate low pH, bile salt concentration, high temperatures, adhesion ability (auto-aggregation and hydrophobicity), haemolytic activity and antimicrobial activity including biosafety assay. Three Bacillus strains identified as Bacillus velezensis TPS3N (MK130897), Bacillus subtilis TPS4 (MK130899) and Bacillus amyloliquefaciens TPS17 (MK130898) were designated as TPS3N, TPS4 and TPS17, respectively. TPS3N and TPS17 were α-haemolytic, while TPS4 was γ-haemolytic. The three isolates had higher viability ability after exposure to higher temperatures (80 °C, 90 °C and 100 °C) and were resistant to low pH (1) and bile salt concentration (0.5%) as well as high cell surface hydrophobicity and auto-aggregation. The three isolates were compatible with one another and thus can be used in consortia. These strains were susceptible to gentamicin, cephalexin, ampicillin, ceftriaxone, kanamycin, amikacin, penicillin, cefoperazone, chloramphenicol, erythromycin, tetracycline, doxycycline, ciprofloxacin, clindamycin (except TPS4) and furazolidone (except TPS17)", "token_count": 471, "char_count": 1481, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6907, "quality_score": 0.8454, "entities": { "genes": [ "TPS17", "MK130899", "TPS3N", "MK130898", "TPS4", "MK130897" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:33.016368", "source": { "split": "train_shard_00000", "doc_id": 2992 }, "chunk_id": "train_shard_00000_2992_0", "global_id": 3302 }, { "text": "The antimicrobial assessment showed that among the three isolates, TPS3N and TPS17 exhibited good antimicrobial activity against the three fish pathogens (Streptococcus agalactiae, Aeromonas hydrophila, Vibrio harveyi), while TPS4 was effective against Streptococcus agalactiae only. The results of this work suggest that Bacillus strains TPS3N, TPS4 and TPS17 could be considered as potential probiotics in tilapia aquaculture.\n\nIn vitro Assessment of the Probiotic Characteristics of Three Bacillus Species from the Gut of Nile Tilapia, Oreochromis niloticus.", "token_count": 172, "char_count": 561, "word_count": 76, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "TPS4", "TPS17", "TPS3N" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:33.461271", "source": { "split": "train_shard_00000", "doc_id": 2992 }, "chunk_id": "train_shard_00000_2992_1", "global_id": 3303 }, { "text": "The present study aimed to evaluate the probiotic characteristics of certain microbial strains for potential use as feed additives. Three bacterial strains and a yeast previously isolated from different environments were investigated. The strains were subjected to molecular identification and established as Lactobacillus paracasei CP133, Lactobacillus plantarum CP134, Bacillus subtilis CP350 and Saccharomyces cerevisiae CP605. Lactobacillus sp. CP133 and CP134 exhibited antibiosis, antibiotic activity, and relative odor reduction ability. Bacillus subtilis CP350 was thermotolerant, reduced hydrogen sulfide gas and showed significant proteolytic activity, whereas Saccharomyces cerevisiae CP605 exhibited high acid and bile salt tolerance. In general, the isolates in this study demonstrated improved functional characteristics, particularly acid and bile tolerance and relative cell adhesion to HT-29 monolayer cell line. Results in this work provides multifunctional probiotic characteristics of the strains for potential development of probiotics and cleaning of the environment.\n\nInvestigating the probiotic characteristics of four microbial strains with potential application in feed industry.", "token_count": 293, "char_count": 1205, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [ "CP350", "CP605", "CP133", "CP134" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:34.025170", "source": { "split": "train_shard_00000", "doc_id": 2993 }, "chunk_id": "train_shard_00000_2993_0", "global_id": 3304 }, { "text": "The genus\n\nThe poplar pangenome provides insights into the evolutionary history of the genus.", "token_count": 21, "char_count": 93, "word_count": 14, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:34.384039", "source": { "split": "train_shard_00000", "doc_id": 2994 }, "chunk_id": "train_shard_00000_2994_0", "global_id": 3305 }, { "text": "The application of phytases for animal feed in developing countries is limited due to the high cost of these enzymes, determined by the importation fees and the expensive substrates used for their production. In this work, we have used agroindustrial byproducts for the production of extracts containing phytases, which were accessed for their stability focusing on the conditions found in the gastrointestinal tract of pigs. The fungus Acremonim zeae presented higher phytase production in medium containing cornmeal, while the yeast Kluyveromyces marxianus produced 10-fold more phytase when cultivated on rice bran. Process optimization increased the difference in productivity to more than 300 fold. The phytase from A. zeae was thermostable, with higher activity at neutral pH and 50 °C, but was inhibited at pH 2.5 and by various ions. The phytase activity in the K. marxianus extract was stable at a wide range of conditions, which indicates the presence of at least two enzymes. As far as we know, this manuscript describes for the first time the phytase production and the characteristics of the extracts produced by both these microbial species. These enzymes could be produced at low cost and have potential to replace enzymes currently imported for this purpose.\n\nProduction of Fungal Phytases from Agroindustrial Byproducts for Pig Diets.", "token_count": 323, "char_count": 1351, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6048, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:34.948181", "source": { "split": "train_shard_00000", "doc_id": 2995 }, "chunk_id": "train_shard_00000_2995_0", "global_id": 3306 }, { "text": "In the biochemical milieu of human colon, bile acids act as signaling mediators between the host and its gut microbiota. Biotransformation of primary to secondary bile acids have been known to be involved in the immune regulation of human physiology. Several 16S amplicon-based studies with inflammatory bowel disease (IBD) subjects were found to have an association with the level of fecal bile acids. However, a detailed investigation of all the bile salt biotransformation genes in the gut microbiome of healthy and IBD subjects has not been performed.\n\nMetagenomic analysis of bile salt biotransformation in the human gut microbiome.", "token_count": 159, "char_count": 637, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:35.388261", "source": { "split": "train_shard_00000", "doc_id": 2996 }, "chunk_id": "train_shard_00000_2996_0", "global_id": 3307 }, { "text": "Bile salts tend to form micelles in aqueous media and can thereby contribute to drug solubilization; they also exhibit crystallization inhibition properties that can stabilize supersaturated drug solutions. Herein, we explore conjugation of bile salts with polysaccharides to create new, amphiphilic polysaccharide derivatives with intriguing properties, portending broad utility in various applications. We introduce efficient conjugation of cholesterol (as a model steroid), lithocholic acid, and deoxycholic acid by mild, modular olefin cross-metathesis reactions. These small molecules were first modified with an acrylate group from the A-ring hydroxyl, then reacted with cellulose derivatives bearing olefin-terminated metathesis \"handles\". Successful conjugation of bile acids has demonstrated chemoselective cross-metathesis with complex, polyfunctional structures, and large multi-ring systems. It also enabled an efficient, general pathway for polysaccharide-bile salt conjugates, which promise synergy for applications such as amorphous solid dispersion (ASD).\n\nConjugation of bile esters to cellulose by olefin cross-metathesis: A strategy for accessing complex polysaccharide structures.", "token_count": 299, "char_count": 1200, "word_count": 151, "semantic_coherence": 1, "information_density": 0.7748, "quality_score": 0.8874, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:35.954256", "source": { "split": "train_shard_00000", "doc_id": 2997 }, "chunk_id": "train_shard_00000_2997_0", "global_id": 3308 }, { "text": "t-Butyl 6-cyano-(3R,5R)-dihydroxyhexanoate ((3R,5R)-2) is an important chiral diol synthon of atorvastatin calcium. Previously, we constructed a variant KmAKR-W297H (M1) of Kluyveromyces marxianus aldo-keto reductase (KmAKR, designated as M0), possessing excellent diastereoselectivity but moderate activity towards t-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate ((5R)-1). In this work, KmAKR-W297H/Y296W/K29H (M3) was developed via semi-rational design. It exhibited much improved catalytic efficiency towards (5R)-1. The K\n\nImproving the catalytic efficiency of aldo-keto reductase KmAKR towards t-butyl 6-cyano-(3R,5R)-dihydroxyhexanoate via semi-rational design.", "token_count": 253, "char_count": 663, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:36.446566", "source": { "split": "train_shard_00000", "doc_id": 2998 }, "chunk_id": "train_shard_00000_2998_0", "global_id": 3309 }, { "text": "The study was conducted to investigate the expression and activity of key lipolytic enzymes during the ontogenetic development of Clarias magur. After partial characterization, the messenger RNA (mRNA) expression analysis of lipoprotein lipase (LPL), pancreatic triacylglycerol lipase (PL), and bile salt-activated lipase (BAL) genes along with the specific lipase activity were performed in larvae from Day 1 after hatching till 34-day posthatch (dph). Heterogeneous patterns of mRNA expression were shown by the important lipolytic enzymes and were detected before first exogenous feeding during the yolk-sac stage. LPL started increasing from 13 dph and peaked at 16 dph followed by a declining trend till 34 dph. However, the PL observed to be peaking at 9, 22, and 30 dph. Similarly, BAL showed an increasing trend from 11 to 22 dph with a significantly high level of mRNA expression at 16 dph. Later, the specific lipase activity was evaluated which appears at Day 1 after hatching with a progressive increase from 7 to 16 dph and a further declining trend afterwards with a peak at 22 dph. The results indicated the development of exocrine pancreas at 16 dph. Furthermore, the transcript levels and the activity of lipases were regulated with the age. Hence, the present study can be helpful in devising different strategies containing optimum lipid levels at a suitable stage of development for improving the survival during larval rearing. Furthermore, the study could be a baseline for elucidating the optimized dietary lipid levels of this catfish during its larval rearing.\n\nExpression and activity of key lipases during the larval development of walking catfish (Clarias magur).", "token_count": 437, "char_count": 1691, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5379, "quality_score": 0.7689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:37.080478", "source": { "split": "train_shard_00000", "doc_id": 2999 }, "chunk_id": "train_shard_00000_2999_0", "global_id": 3310 }, { "text": "GrainGenes (https://wheat.pw.usda.gov or https://graingenes.org) is an international centralized repository for curated, peer-reviewed datasets useful to researchers working on wheat, barley, rye and oat. GrainGenes manages genomic, genetic, germplasm and phenotypic datasets through a dynamically generated web interface for facilitated data discovery. Since 1992, GrainGenes has served geneticists and breeders in both the public and private sectors on six continents. Recently, several new datasets were curated into the database along with new tools for analysis. The GrainGenes homepage was enhanced by making it more visually intuitive and by adding links to commonly used pages. Several genome assemblies and genomic tracks are displayed through the genome browsers at GrainGenes, including the Triticum aestivum (bread wheat) cv. 'Chinese Spring' IWGSC RefSeq v1.0 genome assembly, the Aegilops tauschii (D genome progenitor) Aet v4.0 genome assembly, the Triticum turgidum ssp. dicoccoides (wild emmer wheat) cv. 'Zavitan' WEWSeq v.1.0 genome assembly, a T. aestivum (bread wheat) pangenome, the Hordeum vulgare (barley) cv. 'Morex' IBSC genome assembly, the Secale cereale (rye) select 'Lo7' assembly, a partial hexaploid Avena sativa (oat) assembly and the Triticum durum cv. 'Svevo' (durum wheat) RefSeq Release 1.0 assembly. New genetic maps and markers were added and can be displayed through CMAP. Quantitative trait loci, genetic maps and genes from the Wheat Gene Catalogue are indexed and linked through the Wheat Information System (WheatIS) portal. Training videos were created to help users query and reach the data they need. GSP (Genome Specific Primers) and PIECE2 (Plant Intron Exon Comparison and Evolution) tools were implemented and are available to use. As more small grains reference sequences become available, GrainGenes will play an increasingly vital role in helping researchers improve crops.", "token_count": 518, "char_count": 1927, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6993, "quality_score": 0.8496, "entities": { "genes": [ "PIECE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:28:37.741271", "source": { "split": "train_shard_00000", "doc_id": 3000 }, "chunk_id": "train_shard_00000_3000_0", "global_id": 3311 }, { "text": "GrainGenes: centralized small grain resources and digital platform for geneticists and breeders.", "token_count": 20, "char_count": 96, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:38.094007", "source": { "split": "train_shard_00000", "doc_id": 3000 }, "chunk_id": "train_shard_00000_3000_1", "global_id": 3312 }, { "text": "Bile salt export pump (BSEP) have been confirmed to play an important role for bile acid canalicular export in the treatment of cholestasis. In this study, we investigated the stimulatory effect of emodin on BSEP signaling pathway in cholestasis.\n\nEmodin Rescues Intrahepatic Cholestasis via Stimulating FXR/BSEP Pathway in Promoting the Canalicular Export of Accumulated Bile.", "token_count": 107, "char_count": 377, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7455, "quality_score": 0.8727, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:38.831326", "source": { "split": "train_shard_00000", "doc_id": 3001 }, "chunk_id": "train_shard_00000_3001_0", "global_id": 3313 }, { "text": "Hydrophilic bile salts, ursodeoxycholate and hyodeoxycholate, have choleretic effects. ABCB4, a member of the ABC transporter family, is essential for the secretion of phospholipids from hepatocytes into bile. In this study, we assessed the effects of taurine- or glycine-conjugated cholate, ursodeoxycholate and hyodeoxycholate on the ABCB4-mediated phosphatidylcholine (PC) efflux using Abcb4 knockout mice and HEK293 cells stably expressing ABCB4. To evaluate the effects of bile salts on bile formation in Abcb4\n\nEnhancing effect of taurohyodeoxycholate on ABCB4-mediated phospholipid efflux.", "token_count": 194, "char_count": 596, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7595, "quality_score": 0.8797, "entities": { "genes": [ "ABCB4", "HEK293" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:39.295742", "source": { "split": "train_shard_00000", "doc_id": 3002 }, "chunk_id": "train_shard_00000_3002_0", "global_id": 3314 }, { "text": "Fermented cereal doughs constitute a predominant part of West African diets. The environment of fermented doughs can be hostile for microbial survival due to high levels of microbial metabolites such as weak carboxylic organic acids and ethanol. In order to get a better understanding of the intrinsic factors affecting the microbial successions of yeasts during dough fermentation, survival and physiological responses of the yeasts associated with West African fermented cereal doughs were investigated at exposure to relevant concentrations of microbial inhibitory compounds. Three strains each of the predominant species, i.e. Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia kudriavzevii as well as the opportunistic pathogen Candida glabrata were studied. The strains were exposed to individual stress factors of cereal doughs, i.e. (i) pH 3.4, (ii) 3% (v/v) ethanol (EtOH\n\nEffects of intrinsic microbial stress factors on viability and physiological condition of yeasts isolated from spontaneously fermented cereal doughs.", "token_count": 272, "char_count": 1038, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6483, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:39.852273", "source": { "split": "train_shard_00000", "doc_id": 3003 }, "chunk_id": "train_shard_00000_3003_0", "global_id": 3315 }, { "text": "Salmonella enterica subsp. enterica serotype Rissen is the predominant serotype found in Thai pork production and can be transmitted to humans through contamination of the food chain. This study was conducted to investigate the genetic relationships between serovar Rissen isolates from all levels of the pork production chain and evaluate the ability of the in silico antimicrobial resistance (AMR) genotypes to predict the phenotype of serovar Rissen. A total of 38 serovar Rissen isolates were tested against eight antibiotic agents by a disk diffusion method and the whole genomes of all isolates were sequenced to detect AMR genetic elements using the ResFinder database.A total of 86.84% of the isolates were resistant to tetracycline, followed by ampicillin (78.96%) and sulfonamide-trimethoprim (71.05%). Resistance to more than one antimicrobial agent was observed in 78.95% of the isolates, with the most common pattern showing resistance to ampicillin, chloramphenicol, streptomycin, sulfonamide-trimethoprim, and tetracycline. The results of genotypic AMR indicated that 89.47% of the isolates carried tet(A), 84.22% carried bla\n\nCore genome sequence analysis to characterize Salmonella enterica serovar Rissen ST469 from a swine production chain.", "token_count": 344, "char_count": 1259, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [ "ST469" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:40.420945", "source": { "split": "train_shard_00000", "doc_id": 3004 }, "chunk_id": "train_shard_00000_3004_0", "global_id": 3316 }, { "text": "Bile salts (BS) form hydrophobic Small's primary micelles at concentrations above the critical micelle concentration (CMC), while at concentrations above 3CMC they form secondary micelles (by the association of primary micelles via H-bonds). In this paper the self-associations of the anions of isohenodeoxycholic acid (3-epimer of henodeoxycholic acid, ICD) and the anions of isoursodeoxycholic acid (3-epimer of ursodeoxycholic acid, IUD) are examined, since the thermodynamic parameters of their self-association have not yet been published. Forming of IUD aggregates with two or three building units is slightly more favorable via α sides of steroid skeletons, regarding hydrophobicity, while regarding steric repulsive interactions it is more favorable to associate via β sides. Due to this, IUD in the vicinity of the CMC can form primary micelles by association of IUD particles both from the convex side and from the concave side of the steroid ring system. Therefore, IUD is significantly more prone to initial micellization than bile salt derivatives whose steroidal skeletons contain equatorially oriented OH groups.\n\nSelf-association of sodium isoursodeoxycholate and sodium isohenodeoxycholate in water.", "token_count": 309, "char_count": 1216, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:40.993191", "source": { "split": "train_shard_00000", "doc_id": 3005 }, "chunk_id": "train_shard_00000_3005_0", "global_id": 3317 }, { "text": "The diversification of microbial populations may be driven by many factors including adaptation to distinct ecological niches and barriers to recombination. We examined the population structure of the bacterial pathogen Pseudomonas aeruginosa by analyzing whole-genome sequences of 739 isolates from diverse sources. We confirmed that the population structure of P. aeruginosa consists of two major groups (referred to as Groups A and B) and at least two minor groups (Groups C1 and C2). Evidence for frequent intragroup but limited intergroup recombination in the core genome was observed, consistent with sexual isolation of the groups. Likewise, accessory genome analysis demonstrated more gene flow within Groups A and B than between these groups, and a few accessory genomic elements were nearly specific to one or the other group. In particular, the exoS gene was highly overrepresented in Group A compared with Group B isolates (99.4% vs. 1.1%) and the exoU gene was highly overrepresented in Group B compared with Group A isolates (95.2% vs. 1.8%). The exoS and exoU genes encode effector proteins secreted by the P. aeruginosa type III secretion system. Together these results suggest that the major P. aeruginosa groups defined in part by the exoS and exoU genes are divergent from each other, and that these groups are genetically isolated and may be ecologically distinct. Although both groups were globally distributed and caused human infections, certain groups predominated in some clinical contexts.\n\nThe Population Structure of Pseudomonas aeruginosa Is Characterized by Genetic Isolation of exoU+ and exoS+ Lineages.", "token_count": 390, "char_count": 1634, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5863, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:41.609091", "source": { "split": "train_shard_00000", "doc_id": 3006 }, "chunk_id": "train_shard_00000_3006_0", "global_id": 3318 }, { "text": "The endo-polygalacturonase enzyme (endoPG: EC 3.2.1.15) plays an important role in the fruit juice and wine industries, so the development of new tools for the quantitative and qualitative analysis of its enzymatic action is necessary. In this work, we report the development of a simple, fast and practical method that did not use any chemical reagent to identify and evaluate the action of the endoPG enzyme, produced by the yeast Kluyveromyces marxianus CCT3172, using attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy combined with principal component analysis-linear discriminant analysis (PCA-LDA). This method evaluated the action of the endoPG enzyme on the polygalacturonic acid (PGA) substrate at 5 different times (0, 10, 15, 20 and 30 minutes), and at each time interval the samples were analyzed by ATR-FTIR. It was demonstrated that there was clear segregation between the samples that were and that were not subjected to the action of the endoPG enzyme, and it was also possible to distinguish the samples that were subjected to different incubation times with the enzyme. Through PCA-LDA it was possible to obtain wavelengths that are biomarkers for this enzymatic reaction and the observed changes as a function of hydrolysis duration were found to be in agreement with the breakdown of the glycosidic chain (1011 cm\n\nEvaluation of Kluyveromyces marxianus endo-polygalacturonase activity through ATR-FTIR.", "token_count": 385, "char_count": 1451, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8005, "entities": { "genes": [ "CCT3172" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:42.257951", "source": { "split": "train_shard_00000", "doc_id": 3007 }, "chunk_id": "train_shard_00000_3007_0", "global_id": 3319 }, { "text": "Enterococcus faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing-based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim of describing the genome dynamics of this species. The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which consisted entirely of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalization. We estimated the evolutionary rate of two clonal groups that each colonized single patients at 12.6 and 25.2 single-nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of 12 different insertion sequence (IS) elements, with ISEfa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread ISEfa5 excision and insertion into the genome during gut colonization. Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the human gut. We observed considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.\n\nEnterococcus faecium genome dynamics during long-term asymptomatic patient gut colonization.", "token_count": 506, "char_count": 2202, "word_count": 318, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:42.950675", "source": { "split": "train_shard_00000", "doc_id": 3008 }, "chunk_id": "train_shard_00000_3008_0", "global_id": 3320 }, { "text": "The aim of this study was to analyze the alarming spread of NDM-1- and OXA-48-co-producing Klebsiella pneumoniae clinical isolates, collected between October 2016 and January 2018 in a neonatal intensive care unit of the University Hospital, Catania, Italy, through whole genome sequencing. All confirmed carbapenem-resistant K. pneumoniae (CRKp) isolates were characterized pheno- and geno-typically, as well as by whole genome sequencing (WGS). A total of 13 CRKp isolates were identified from 13 patients. Pulsed-field gel electrophoresis (PFGE) was performed, and the multilocus sequence typing (MLST) scheme used was based on the gene sequence as published on the MLST Pasteur website. Core genome MLST (cgMLST) was also performed. All isolates co-carried bla\n\nEmergence of two novel sequence types (3366 and 3367) NDM-1- and OXA-48-co-producing K. pneumoniae in Italy.", "token_count": 267, "char_count": 874, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:43.526655", "source": { "split": "train_shard_00000", "doc_id": 3009 }, "chunk_id": "train_shard_00000_3009_0", "global_id": 3321 }, { "text": "Wild birds have been suggested to be reservoirs of antimicrobial resistant and/or pathogenic Enterococcus faecalis (Efs) strains, but the scarcity of studies and available sequences limit our understanding of the population structure of the species in these hosts. Here, we analysed the clonal and plasmid diversity of 97 Efs isolates from wild migratory birds. We found a high diversity, with most sequence types (STs) being firstly described here, while others were found in other hosts including some predominant in poultry. We found that pheromone-responsive plasmids predominate in wild bird Efs while 35% of the isolates entirely lack plasmids. Then, to better understand the ecology of the species, the whole genome of fivestrains with known STs (ST82, ST170, ST16 and ST55) were sequenced and compared with all the Efs genomes available in public databases. Using several methods to analyse core and accessory genomes (AccNET, PLACNET, hierBAPS and PANINI), we detected differences in the accessory genome of some lineages (e.g. ST82) demonstrating specific associations with birds. Conversely, the genomes of other Efs lineages exhibited divergence in core and accessory genomes, reflecting different adaptive trajectories in various hosts. This pangenome divergence, horizontal gene transfer events and occasional epidemic peaks could explain the population structure of the species.\n\nPhylogenomics of Enterococcus faecalis from wild birds: new insights into host-associated differences in core and accessory genomes of the species.", "token_count": 379, "char_count": 1542, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6295, "quality_score": 0.8147, "entities": { "genes": [ "ST82", "ST170", "ST16", "ST55" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:44.143835", "source": { "split": "train_shard_00000", "doc_id": 3010 }, "chunk_id": "train_shard_00000_3010_0", "global_id": 3322 }, { "text": "Weissella cibaria CMU and CMS1 are known to exert beneficial effects on the oral cavity but have not yet been determined to be generally recognized as safe (GRAS), although they are used as commercial strains in Korea. We aimed to verify the safety of W. cibaria CMU and CMS1 strains through phenotypic and genotypic analyses. Their safety was evaluated by a minimum inhibitory concentration assay for 14 antibiotics, DNA analysis for 28 antibiotic resistance genes (ARGs) and one conjugative element, antibiotic resistance gene transferability, virulence gene analysis, hemolysis, mucin degradation, toxic metabolite production, and platelet aggregation reaction. W. cibaria CMU showed higher kanamycin resistance than the European Food Safety Authority (EFSA) cut-off, but this resistance was not transferred to the recipient strain. W. cibaria CMU and CMS1 lacked ARGs in chromosomes and plasmids, and genetic analysis confirmed that antibiotic resistance of kanamycin was an intrinsic characteristic of W. cibaria. Additionally, these strains did not harbor virulence genes associated with pathogenic bacteria and lacked toxic metabolite production, β-hemolysis, mucin degradation, bile salt deconjugation, β-glucuronidase, nitroreductase activity, gelatin liquefaction, phenylalanine degradation, and platelet aggregation. Our findings demonstrate that W. cibaria CMU and CMS1 can achieve the GRAS status in future.\n\nSafety Evaluation of Oral Care Probiotics", "token_count": 380, "char_count": 1463, "word_count": 204, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [ "CMS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:44.728510", "source": { "split": "train_shard_00000", "doc_id": 3011 }, "chunk_id": "train_shard_00000_3011_0", "global_id": 3323 }, { "text": "This study aimed to evaluate the functional and probiotic properties of Lactobacillus acidophilus SJLH001 (La-SJLH001) isolated from fermented food via mechanism analysis based on transcriptomics and culturomics. La-SJLH001 exhibited good tolerance to acid and bile salt conditions with anti-diabetic ability and cholesterol assimilation activity in vitro. Supplementation with La-SJLH001 also resulted in a significant reduction in host oral glucose and serum total cholesterol levels in vivo. Transcriptome profiles and qPCR analysis suggested that La-SJLH001 significantly regulated the transcription of key genes involved in glucose transportation, cholesterol metabolism, ion channels, and immune response, resulting in improved glucose homeostasis and cholesterol metabolism. La-SJLH001 significantly affected the structure of intestinal microbiota when analyzed by using culturomics coupled with MALDI-TOF MS. These results indicated that La-SJLH001 may be a mechanistic target for the control of diabetes with great potential in the application of probiotic products.\n\nMechanism analysis of improved glucose homeostasis and cholesterol metabolism in high-fat-induced obese mice treated with La-SJLH001 via transcriptomics and culturomics.", "token_count": 339, "char_count": 1246, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6646, "quality_score": 0.8323, "entities": { "genes": [ "SJLH001" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:45.301797", "source": { "split": "train_shard_00000", "doc_id": 3012 }, "chunk_id": "train_shard_00000_3012_0", "global_id": 3324 }, { "text": "Microbial bile salt hydrolases (BSHs), a member of cholylglycine hydrolase (CGH) family, catalyze the hydrolysis of glycine and taurine-linked bile salts in the small intestine of human. BSH is evolutionarily related to penicillin V acylase (PVA) which hydrolyses a penicillin V and is also a member of CGH family. Although, five of the six amino acids, C2, R16, D19, N170, N79 and R223, supposed to be responsible for catalytic activity of BSH enzyme, are strictly conserved in all CGH family members, N79 is partially conserved in this family. In this study, in order to analyze the correlation between N79 and catalytic activity or substrate specificity of BSH, the polar and acidic N79 was substituted for the aliphatic and hydrophobic V79 by PCR-based site directed mutagenesis and mutant recombinant BSH was expressed in E. coli BLR(DE3). While the effects of the mutation on catalytic activity and substrate specificity of BSH were detected by ninhydrin assay. The effect of this mutation on the stability of the BSH was observed by SDS-PAGE analysis. Although V79 mutation resulted in stable BSH, it reduced the catalytic activity and altered substrate specificity of BSH. The results suggested that N79 might be important for substrate binding and catalytic turnover of BSH.\n\nAsparagine 79 is an important amino acid for catalytic activity and substrate specificity of bile salt hydrolase (BSH).", "token_count": 402, "char_count": 1404, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5495, "quality_score": 0.7748, "entities": { "genes": [ "DE3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:45.915570", "source": { "split": "train_shard_00000", "doc_id": 3013 }, "chunk_id": "train_shard_00000_3013_0", "global_id": 3325 }, { "text": "To study the formation and characterize the structure of mixed complexes of oppositely charged block copolymers and surfactants are of great significance for practical applications, e.g., in drug carrier formulations that are based on electrostatically assisted assembly. In this context, biocompatible block copolymers and biosurfactants (like bile salts) are particularly interesting. In this work, we report on the co-assembly in dilute aqueous solution between a cationic poly(N-isopropyl acryl amide) (PNIPAM) diblock copolymer and the oppositely charged bile salt surfactant sodium deoxycholate at ambient temperature. The cryogenic transmission electron microscopy (cryo-TEM) experiments revealed the co-existence of two types of co-assembled complexes of radically different morphology and inner structure. They are formed mainly as a result of the electrostatic attraction between the positively charged copolymer blocks and bile salt anions and highlight the potential of using linear amphiphilic block copolymers as bile salt sequestrants in the treatment of bile acid malabsorption and hypercholesterolemia. The first complex of globular morphology has a coacervate core of deoxycholate anions and charged copolymer blocks surrounded by a PNIPAM corona. The second complex has an intriguing tape-like supramolecular morphology of several micrometer in length that is striped in the direction of the long axis. A model is presented in which the stretched cationic blocks of several block copolymers interact electrostatically with the bile salt molecules that are associated to form a zipper-like structure. The tape is covered on both sides by the PNIPAM chains that stabilize the overall complex in solution. In addition to cryo-TEM, the mixed system was investigated in a range of molar charge fractions at a constant copolymer concentration by static light scattering, small angle X-ray scattering, and electrophoretic mobility measurements.\n\nBlock copolymers as bile salt sequestrants: intriguing structures formed in a mixture of an oppositely charged amphiphilic block copolymer and bile salt.", "token_count": 504, "char_count": 2111, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5518, "quality_score": 0.7759, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:46.572892", "source": { "split": "train_shard_00000", "doc_id": 3014 }, "chunk_id": "train_shard_00000_3014_0", "global_id": 3326 }, { "text": "Comparative genomics has proven useful in exploring the biodiversity of phages and understanding phage-host interactions. This knowledge is particularly useful for phages infecting Streptococcus thermophilus, as they constitute a constant threat during dairy fermentations. Here, we explore the genetic diversity of S. thermophilus phages to identify genetic determinants with a signature for host specificity, which could be linked to the bacterial receptor genotype. A comparative genomic analysis was performed on 142 S. thermophilus phage genomes, 55 of which were sequenced in this study. Effectively, 94 phages were assigned to the group cos (DT1), 36 to the group pac (O1205), six to the group 5093, and six to the group 987. The core genome-based phylogeny of phages from the two dominating groups and their receptor binding protein (RBP) phylogeny corresponded to the phage host-range. A role of RBP in host recognition was confirmed by constructing a fluorescent derivative of the RBP of phage CHPC951, followed by studying the binding of the protein to the host strain. Furthermore, the RBP phylogeny of the cos group was found to correlate with the host genotype of the exocellular polysaccharide-encoding operon. These findings provide novel insights towards developing strategies to combat phage infections in dairies.\n\nA comparative genomics approach for identifying host-range determinants in Streptococcus thermophilus bacteriophages.", "token_count": 365, "char_count": 1451, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": { "genes": [ "CHPC951", "DT1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:47.164247", "source": { "split": "train_shard_00000", "doc_id": 3015 }, "chunk_id": "train_shard_00000_3015_0", "global_id": 3327 }, { "text": "The metagenome of the gut microbiome encodes tremendous potential for biosynthesizing and transforming small-molecule metabolites through the activities of enzymes expressed by intestinal bacteria. Accordingly, elucidating this metabolic network is critical for understanding how the gut microbiota contributes to health and disease. Bile acids, which are first biosynthesized in the liver, are modified in the gut by enzymes expressed by commensal bacteria into secondary bile acids, which regulate myriad host processes, including lipid metabolism, glucose metabolism, and immune homeostasis. The gateway reaction of secondary bile acid biosynthesis is mediated by bile salt hydrolases (BSHs), bacterial cysteine hydrolases whose action precedes other bile acid modifications within the gut. To assess how changes in bile acid metabolism mediated by certain intestinal microbiota impact gut physiology and pathobiology, methods are needed to directly examine the activities of BSHs because they are master regulators of intestinal bile acid metabolism. Here, we developed chemoproteomic tools to profile changes in gut microbiome-associated BSH activity. We showed that these probes can label active BSHs in model microorganisms, including relevant gut anaerobes, and in mouse gut microbiomes. Using these tools, we identified altered BSH activities in a murine model of inflammatory bowel disease, in this case, colitis induced by dextran sodium sulfate, leading to changes in bile acid metabolism that could impact host metabolism and immunity. Importantly, our findings reveal that alterations in BSH enzymatic activities within the gut microbiome do not correlate with changes in gene abundance as determined by metagenomic sequencing, highlighting the utility of chemoproteomic approaches for interrogating the metabolic activities of the gut microbiota.\n\nChemoproteomic Profiling of Gut Microbiota-Associated Bile Salt Hydrolase Activity.", "token_count": 470, "char_count": 1946, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5799, "quality_score": 0.79, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:47.810082", "source": { "split": "train_shard_00000", "doc_id": 3016 }, "chunk_id": "train_shard_00000_3016_0", "global_id": 3328 }, { "text": "Probiotic bacteria are usually encapsulated to increase their survival through passage of the simulated gastrointestinal tract (GIT). Four\n\nViability of 4 Probiotic Bacteria Microencapsulated with Arrowroot Starch in the Simulated Gastrointestinal Tract (GIT) and Yoghurt.", "token_count": 74, "char_count": 272, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:48.194838", "source": { "split": "train_shard_00000", "doc_id": 3017 }, "chunk_id": "train_shard_00000_3017_0", "global_id": 3329 }, { "text": "Lyme disease, initially described as Lyme arthritis, was reported before nucleic-acid based detection technologies were available. The most widely used diagnostic tests for Lyme disease are based on the serologic detection of antibodies produced against antigens derived from a single strain of\n\nSingle Core Genome Sequencing for Detection of both", "token_count": 74, "char_count": 347, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:48.566763", "source": { "split": "train_shard_00000", "doc_id": 3018 }, "chunk_id": "train_shard_00000_3018_0", "global_id": 3330 }, { "text": "Active secretion of bile salts into the canalicular lumen drives bile formation and promotes biliary cholesterol and phospholipid output. Disrupting hepatic bile salt uptake, by inhibition of sodium-taurocholate cotransporting polypetide (NTCP; Slc10a1) with Myrcludex B, is expected to limit bile salt flux through the liver and thereby to decrease biliary lipid excretion. Here, we show that Myrcludex B-mediated NTCP inhibition actually causes an increase in biliary cholesterol and phospholipid excretion whereas biliary bile salt output and bile salt composition remains unchanged. Increased lysosomal discharge into bile was excluded as a potential contributor to increased biliary lipid secretion. Induction of cholesterol secretion was not a consequence of increased ATP-binding cassette subfamily G member 5/8 activity given that NTCP inhibition still promoted cholesterol excretion in Abcg8\n\nBlocking Sodium-Taurocholate Cotransporting Polypeptide Stimulates Biliary Cholesterol and Phospholipid Secretion in Mice.", "token_count": 282, "char_count": 1024, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6397, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:49.125008", "source": { "split": "train_shard_00000", "doc_id": 3019 }, "chunk_id": "train_shard_00000_3019_0", "global_id": 3331 }, { "text": "Two-component systems (TCSs) are dominant regulating components in bacteria for responding to environmental stimuli. However, little information is available on how TCSs in\n\nThe LiaFSR and BsrXRS Systems Contribute to Bile Salt Resistance in", "token_count": 57, "char_count": 241, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:49.486802", "source": { "split": "train_shard_00000", "doc_id": 3020 }, "chunk_id": "train_shard_00000_3020_0", "global_id": 3332 }, { "text": "In recent years, the fast and accurate identification of the Candida species is of great importance as the response to antifungal treatment differs among species. Following the treatment of several immunosuppressive diseases, fungal infections can emerge. The aim of this study was to compare the accuracy, costs and time of result periods of the methods used in the identification of the most common human fungal infectious agent, Candida strains. From various clinical samples sent to the Microbiology Laboratory of Karabuk University Training and Research Hospital between July 2016-December 2017, a total of 91 yeast isolates cultivated in blood agar (Becton Dickinson, USA) and/or Sabouraud dextrose agar (SDA-Oxoid, UK), confirmed with colony morphology and microscopic appearance, identified as Candida species with a fully automated identification system (Phoenix™ Yeast ID Panel, Becton Dickinson Diagnostics, USA) were included in the study. All the samples were examined with sequence analysis using ITS1 forward 5'-TCC GTA GGT GAA CCT GCG G-3' and ITS4 reverse 5'-TCC TCC GCT TAT TGA TAT GC-3' primers (Iontek, Turkey) and the matrix-assisted laser desorption-ionisation time of flight mass spectrometry (MALDI TOF-MS) systems. Molecular sequence analysis was accepted as the gold standard method and the results were compared with those of the other methods MALDI TOF-MS and Phoenix™ Yeast ID Panel in respect of the accuracy of the identification of Candida strains. According to the results of the DNA sequence analysis of the 91 Candida isolates included in the study, 24 were identified as Candida albicans, 20 Candida tropicalis, 16 Candida parapsilosis, 13 Candida glabrata, seven Candida kefyr, six Candida krusei, two of each Candida dubliniensis, Candida guilliermondi and one Candida lusitaniae", "token_count": 477, "char_count": 1817, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": { "genes": [ "ITS4", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:50.142601", "source": { "split": "train_shard_00000", "doc_id": 3021 }, "chunk_id": "train_shard_00000_3021_0", "global_id": 3333 }, { "text": "Compared to the results of the DNA sequence analysis, the accurate identification of the fully automated Phoenix™ system and the MALDI TOF-MS system was found as 92.3% and 97.8%, respectively. In addition to accuracy, costs and time of result periods of the three methods were also compared. Disregarding the cost of the device in the 3 methods, when the comparison was made of the cost per test and the time to results after pure production in SDA agar, the MALDI TOF-MS system was determined to have the lowest costs and provided results in the shortest time. As some of the Candida strains have antifungal resistance, identification of the strains must be a priority in respect of starting early treatment. The MALDI TOF-MS system has high performance in accurate identification, low costs and the system provides the results within minutes, thereby allowing immediate decision to be made for the antifungal treatment to be started. Thus, the morbidity, mortality and cost rates will be reduced. In conclusion, as the MALDI TOF-MS is a rapid, reliable and low cost per test system, it can be considered suitable for routine use in laboratories.\n\n[A comparison of the costs, reliability and time of result periods of widely used methods, new molecular methods and MALDI TOF-MS in the routine diagnosis of Candida strains].", "token_count": 302, "char_count": 1324, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5115, "quality_score": 0.7558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:50.699890", "source": { "split": "train_shard_00000", "doc_id": 3021 }, "chunk_id": "train_shard_00000_3021_1", "global_id": 3334 }, { "text": "Tailed bacteriophages are the most abundant and diverse viruses in the world, with genome sizes ranging from 10 kbp to over 500 kbp. Yet, due to historical reasons, all this diversity is confined to a single virus order-Caudovirales, composed of just four families: Myoviridae, Siphoviridae, Podoviridae, and the newly created Ackermannviridae family. In recent years, this morphology-based classification scheme has started to crumble under the constant flood of phage sequences, revealing that tailed phages are even more genetically diverse than once thought. This prompted us, the Bacterial and Archaeal Viruses Subcommittee of the International Committee on Taxonomy of Viruses (ICTV), to consider overall reorganization of phage taxonomy. In this study, we used a wide range of complementary methods-including comparative genomics, core genome analysis, and marker gene phylogenetics-to show that the group of Bacillus phage SPO1-related viruses previously classified into the Spounavirinae subfamily, is clearly distinct from other members of the family Myoviridae and its diversity deserves the rank of an autonomous family. Thus, we removed this group from the Myoviridae family and created the family Herelleviridae-a new taxon of the same rank. In the process of the taxon evaluation, we explored the feasibility of different demarcation criteria and critically evaluated the usefulness of our methods for phage classification. The convergence of results, drawing a consistent and comprehensive picture of a new family with associated subfamilies, regardless of method, demonstrates that the tools applied here are particularly useful in phage taxonomy. We are convinced that creation of this novel family is a crucial milestone toward much-needed reclassification in the Caudovirales order.\n\nAnalysis of Spounaviruses as a Case Study for the Overdue Reclassification of Tailed Phages.", "token_count": 441, "char_count": 1896, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6241, "quality_score": 0.812, "entities": { "genes": [ "SPO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:51.335993", "source": { "split": "train_shard_00000", "doc_id": 3022 }, "chunk_id": "train_shard_00000_3022_0", "global_id": 3335 }, { "text": "Whole-genome sequencing is increasingly adopted in clinical settings to identify pathogen transmissions, though largely as a retrospective tool. Prospective monitoring, in which samples are continuously added and compared to previous samples, can generate more actionable information. To enable prospective pathogen comparison, genomic relatedness metrics based on single-nucleotide differences must be consistent across time, efficient to compute and reliable for a large variety of samples. The choice of genomic regions to compare, i.e., the core genome, is critical to obtain a good metric. We propose a novel core genome method that selects conserved sequences in the reference genome by comparing its k-mer content to that of publicly available genome assemblies. The conserved-sequence genome is sample set-independent, which enables prospective pathogen monitoring. Based on clinical data sets of 3436 S. aureus, 1362 K. pneumoniae and 348 E. faecium samples, ROC curves demonstrate that the conserved-sequence genome disambiguates same-patient samples better than a core genome consisting of conserved genes. The conserved-sequence genome confirms outbreak samples with high sensitivity: in a set of 2335 S. aureus samples, it correctly identifies 44 out of 44 known outbreak samples, whereas the conserved-gene method confirms 38 known outbreak samples.\n\nA core genome approach that enables prospective and dynamic monitoring of infectious outbreaks.", "token_count": 336, "char_count": 1460, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:51.908285", "source": { "split": "train_shard_00000", "doc_id": 3023 }, "chunk_id": "train_shard_00000_3023_0", "global_id": 3336 }, { "text": "Food animals are considered reservoirs of methicillin-resistant Staphylococcus aureus (MRSA) and are implicated in their zoonotic transmission in the farm-to-plate continuum. LA-MRSA has been reported as a zoonotic agent that has the potential to spread to humans and may cause infections in at-risk groups. In this study, whole genome sequencing was used to describe the genetic environment (resistance mechanisms, virulence factors and mobile genetic elements) and investigate the genetic lineages of MRSA isolates from pigs in Cameroonian and South African abattoirs. During March-October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were de novo-assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated, and antibiotic resistance genes, virulence factors, plasmids, SCCmec and phage elements were identified with ResFinder, Virulence Finder, PlasmidFinder, SCCmec Finder and PHAST, respectively. Core genome single nucleotide analysis was undertaken to assess clonal relatedness among isolates. A lower MRSA prevalence was observed in pigs in Cameroon (n = 1/13; 0.07%) compared with South Africa (n = 4/22; 18.18%), and none of the workers were colonized by MRSA. Genome analysis identified various antibiotic resistance genes along with six virulence factors in all isolates. All MRSA isolates belonged to the clonal lineage ST398 (spa-type t011) and harboured the type Vc SCCmec and several plasmids. Our study shows that the livestock-associated MRSA clonal lineage ST398 is already present in both Cameroon and South Africa and is probably underestimated in the absence of molecular epidemiological studies. It reveals the serious food safety and public health threat associated with this animal strain and underscores the need for interventions to contain this resistant clone.", "token_count": 519, "char_count": 1979, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:28:52.564105", "source": { "split": "train_shard_00000", "doc_id": 3024 }, "chunk_id": "train_shard_00000_3024_0", "global_id": 3337 }, { "text": "Genome analysis of methicillin-resistant Staphylococcus aureus isolated from pigs: Detection of the clonal lineage ST398 in Cameroon and South Africa.", "token_count": 45, "char_count": 150, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:52.921478", "source": { "split": "train_shard_00000", "doc_id": 3024 }, "chunk_id": "train_shard_00000_3024_1", "global_id": 3338 }, { "text": "The causative agents of leptospirosis are responsible for an emerging zoonotic disease worldwide. One of the major routes of transmission for leptospirosis is the natural environment contaminated with the urine of a wide range of reservoir animals. Soils and surface waters also host a high diversity of non-pathogenic Leptospira and species for which the virulence status is not clearly established. The genus Leptospira is currently divided into 35 species classified into three phylogenetic clusters, which supposedly correlate with the virulence of the bacteria. In this study, a total of 90 Leptospira strains isolated from different environments worldwide including Japan, Malaysia, New Caledonia, Algeria, mainland France, and the island of Mayotte in the Indian Ocean were sequenced. A comparison of average nucleotide identity (ANI) values of genomes of the 90 isolates and representative genomes of known species revealed 30 new Leptospira species. These data also supported the existence of two clades and 4 subclades. To avoid classification that strongly implies assumption on the virulence status of the lineages, we called them P1, P2, S1, S2. One of these subclades has not yet been described and is composed of Leptospira idonii and 4 novel species that are phylogenetically related to the saprophytes. We then investigated genome diversity and evolutionary relationships among members of the genus Leptospira by studying the pangenome and core gene sets. Our data enable the identification of genome features, genes and domains that are important for each subclade, thereby laying the foundation for refining the classification of this complex bacterial genus. We also shed light on atypical genomic features of a group of species that includes the species often associated with human infection, suggesting a specific and ongoing evolution of this group of species that will require more attention. In conclusion, we have uncovered a massive species diversity and revealed a novel subclade in environmental samples collected worldwide and we have redefined the classification of species in the genus. The implication of several new potentially infectious Leptospira species for human and animal health remains to be determined but our data also provide new insights into the emergence of virulence in the pathogenic species.", "token_count": 507, "char_count": 2342, "word_count": 354, "semantic_coherence": 1, "information_density": 0.5678, "quality_score": 0.7839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:53.552459", "source": { "split": "train_shard_00000", "doc_id": 3025 }, "chunk_id": "train_shard_00000_3025_0", "global_id": 3339 }, { "text": "Revisiting the taxonomy and evolution of pathogenicity of the genus Leptospira through the prism of genomics.", "token_count": 27, "char_count": 109, "word_count": 16, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:53.915351", "source": { "split": "train_shard_00000", "doc_id": 3025 }, "chunk_id": "train_shard_00000_3025_1", "global_id": 3340 }, { "text": "This study was undertaken to investigate the impact of culture pH (4.5-6.5) and temperature (32-37 °C) on the stress resilience of Lactobacillus reuteri DSM 17938 during freeze-drying and post freeze-drying exposure to low pH (pH 2) and bile salts. Response-surface methodology analysis revealed that freeze-drying survival rates [Formula: see text] were linearly related to pH with the highest survival rate of 80% when cells were cultured at pH 6.5 and the lowest was 40% when cells were cultured at pH 4.5. The analysis further revealed that within the chosen temperature range the culture temperature did not significantly affect the freeze-drying survival rate. However, fermentation at pH 4.5 led to better survival rates when rehydrated cells were exposed to low pH shock or bile salts. Thus, the effect of pH on freeze-drying survival was in contrast to effects on low pH and bile salts stress tolerance. The rationale behind this irreconcilability is based on the responses being dissimilar and are not tuned to each other. Culturing strain DSM 17938 at pH values higher than 5.5 could be a useful option to improve the survivability and increase viable cell numbers in the final freeze-dried product. However, the dissimilar responses for the process- and application parameters tested here suggest that an optimal compromise has to be found in order to obtain the most functional probiotic product possible.\n\nImpact of the fermentation parameters pH and temperature on stress resilience of Lactobacillus reuteri DSM 17938.", "token_count": 397, "char_count": 1533, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5583, "quality_score": 0.7792, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:54.560717", "source": { "split": "train_shard_00000", "doc_id": 3026 }, "chunk_id": "train_shard_00000_3026_0", "global_id": 3341 }, { "text": "Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of thermotolerance in yeast impede its full comprehension and the rare physiological data at elevated temperatures has so far not been matched with corresponding metabolic analyses.\n\nElevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts.", "token_count": 146, "char_count": 622, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7865, "quality_score": 0.8933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:55.013996", "source": { "split": "train_shard_00000", "doc_id": 3027 }, "chunk_id": "train_shard_00000_3027_0", "global_id": 3342 }, { "text": "Catechin hydrate is a phytopharmaceutical with promising anticancer effects but poor bioavailability. This study aimed to elaborate catechin loaded chitosan-tethered liposomes (chitosomes) to enhance catechin oral bioavailability. Nanocarriers were optimized via ethanol injection method followed by physicochemical, ex vivo and biological appraisal in male Wistar albino rats. Results demonstrated that chitosomes possessed excellent nanosize of 137 nm, monodispersity (PDI < 0.2) and high Zeta potential of +36.8 mV. Additionally, chitosomes showed significant improvement in digestive stability against bile salt with enhanced ex-vivo intestinal permeation. Pharmacokinetic studies revealed the significant potential of chitosomes to enhance catechin bioavailability (AUC, Cmax) and sustain its effect (Tmax). In conclusion, elaborated chitosomes are promising nanoplatforms to enhance catechin oral efficacy with lower dose, side effects, administration frequency and higher patient compliance.\n\nImproved oral bioavailability of the anticancer drug catechin using chitosomes: Design, in-vitro appraisal and in-vivo studies.", "token_count": 308, "char_count": 1127, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:55.615903", "source": { "split": "train_shard_00000", "doc_id": 3028 }, "chunk_id": "train_shard_00000_3028_0", "global_id": 3343 }, { "text": "A microbiota-generated bile salt induces biofilm formation in", "token_count": 15, "char_count": 61, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:56.027037", "source": { "split": "train_shard_00000", "doc_id": 3029 }, "chunk_id": "train_shard_00000_3029_0", "global_id": 3344 }, { "text": "Hydrophobic bile salts, such as glycochenodeoxycholate (GCDC) can trigger hepatocyte apoptosis, which is prevented by tauroursodesoxycholate (TUDC), but the effects of GCDC and TUDC on sinusoidal bile salt uptake via the Na⁺-taurocholate transporting polypeptide (Ntcp) are unclear.\n\nRegulation of Plasma Membrane Localization of the Na⁺-Taurocholate Co-Transporting Polypeptide by Glycochenodeoxycholate and Tauroursodeoxycholate.", "token_count": 150, "char_count": 431, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8039, "quality_score": 0.902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:56.468503", "source": { "split": "train_shard_00000", "doc_id": 3030 }, "chunk_id": "train_shard_00000_3030_0", "global_id": 3345 }, { "text": "Here we are presenting a novel method to study the sumoylation of proteins and their sub-cellular localization in mammalian cells and nematode oocytes. This method utilizes a recombinant modified SUMO-trapping protein fragment, kmUTAG, derived from the Ulp1 SUMO protease of the stress-tolerant budding yeast Kluyveromyces marxianus. We have adapted the properties of the kmUTAG for the purpose of studying sumoylation in a variety of model systems without the use of antibodies. For the study of SUMO, KmUTAG has several advantages when compared to antibody-based approaches. This stress-tolerant SUMO-trapping reagent is produced recombinantly, it recognizes native SUMO isoforms from many species, and unlike commercially available antibodies it shows reduced affinity for free, unconjugated SUMO. Representative results shown here include the localization of SUMO conjugates in mammalian tissue culture cells and nematode oocytes.\n\nLocalization of SUMO-modified Proteins Using Fluorescent Sumo-trapping Proteins.", "token_count": 257, "char_count": 1016, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:57.012866", "source": { "split": "train_shard_00000", "doc_id": 3031 }, "chunk_id": "train_shard_00000_3031_0", "global_id": 3346 }, { "text": "The number of poorly soluble new drugs is increasing and one of the effective ways to deliver such pharmaceutically active molecules is using hydrophilic polymers to form a solid dispersion. Bile salts play an important role in the solubilisation of poorly soluble compounds in the gastrointestinal tract (gut) prior to absorption. When a poorly water-soluble drug is delivered using a hydrophilic polymer based solid dispersion oral formulation, it is still unclear whether there are any polymer-bile salt interactions, which may influence the drug dissolution and solubilisation. This study, using two widely used hydrophilic model polymers, Hydroxypropyl methylcellulose (HPMC) and polyvynilpirrolidone (PVP), and sodium taurocholate (NaTC) as the model bile salt, aims to investigate the interactions between the polymers and bile salts in simulated fed state (FeSSIF) and fasted state (FaSSIF) gut fluids. The nature of the interactions was characterised using a range of NMR techniques. The results revealed that the aggregation behaviour of NaTC in FaSSIF and FeSSIF is much more complex than in water. The addition of hydrophilic polymers led to the occurrences of NaTC-HPMC and NaTC-PVP aggregation. For both systems, pH and ionic strength strongly influenced the aggregation behavior, while the ion type played a less significant role. The outcome of this study enriched the understanding of the aggregation behaviour of bile salts and typical hydrophilic pharmaceutical polymers in bio-relevant media. Due to the high surface-activity of the bile salts and their ability to interact with polymers, such aggregation behaviour is expected to play a role in drug solubilisation in the gut when the drug is delivered by hydrophilic polymer based dispersions.\n\nProbing the molecular interactions between pharmaceutical polymeric carriers and bile salts in simulated gastrointestinal fluids using NMR spectroscopy.", "token_count": 476, "char_count": 1919, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5603, "quality_score": 0.7801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:57.661405", "source": { "split": "train_shard_00000", "doc_id": 3032 }, "chunk_id": "train_shard_00000_3032_0", "global_id": 3347 }, { "text": "Lactic acid bacteria (LAB) are major probiotics in food supplements. Survival in gastrointestinal (GI) tract is important for the effective use of LAB as probiotics. Bile salt hydrolase (BSH), which catalyzes the conversion of conjugated bile salts into free bile salts, can significantly modulate the gut microbiome. Here, we hypothesize that BSH is important for LAB survival and adhesion in the gut. The aim of this study is to investigate the effect of BSH on the survival of LAB in the GI tract. A panel of bsh genes from murine gut microbiota were amplified, cloned and expressed into Lactobacillus plantarum, which were then administered to mice by gavage. Our data indicated that the survival of BSH-positive L. plantarum was significantly prolonged in the GI tract compared with wild type L. plantarum. Furthermore, BSH-positive strains exhibited increased adhesion to Caco-2 intestinal cells than BSH-deleted L. plantarum. Enhanced adhesion to intestinal cells of BSH positive LAB can therefore be an important criterion for selecting effective probiotic strains in food industry.\n\nBile salt hydrolase can improve Lactobacillus plantarum survival in gastrointestinal tract by enhancing their adhesion ability.", "token_count": 322, "char_count": 1219, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:58.228220", "source": { "split": "train_shard_00000", "doc_id": 3033 }, "chunk_id": "train_shard_00000_3033_0", "global_id": 3348 }, { "text": "During the last two decades, there has been a public health concern of severe invasive infections caused by Group A Streptococcus (GAS) of the emm1 genotype. This study investigated the dynamics of emm1 GAS during 1994-2013 in Belgium. emm1 GAS isolated from blood, tissue, and wounds of patients with invasive infections (n = 23, S1-S23), and from patients with uncomplicated pharyngitis (n = 15, NS1-NS15) were subjected to whole-genome mapping (WGM; kpn) (Opgen). Whole-genome sequencing was performed on 25 strains (WGS; S1-S23 and NS6-NS7) (Illumina Inc.). Belgian GAS belonged to the M1T1 clone typified by the 36-kb chromosomal region encoding extracellular toxins, NAD+-glycohydrolase and streptolysin O. Strains from 1994-1999 clustered together with published strains (MGAS5005 and M1476). From 2001 onward, invasive GAS showed higher genomic divergence in the accessory genome and harbored on average 7% prophage content. Low evolutionary rate (2.49E-008; P > 0.05) was observed in this study, indicating a highly stable genome. The studied invasive and pharyngitis isolates were no genetically distinct populations based on the WGM and core genome phylogeny analyses. Two copies of the speJ superantigen were present in the 1999 and 2010 study strains (n = 3), one being chromosomal and one being truncated and associated with phage remnants. This study showed that emm1 GAS in Belgium, compared with Canada and UK M1 strains, were highly conserved by harboring a remarkable genome stability over a 19-year period with variations observed in the accessory genome.", "token_count": 504, "char_count": 1575, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [ "NS7", "NS15", "MGAS5005", "NS1", "NS6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:58.881061", "source": { "split": "train_shard_00000", "doc_id": 3034 }, "chunk_id": "train_shard_00000_3034_0", "global_id": 3349 }, { "text": "Remarkable Genome Stability among emm1 Group A Streptococcus in Belgium over 19 Years.", "token_count": 26, "char_count": 86, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:59.239553", "source": { "split": "train_shard_00000", "doc_id": 3034 }, "chunk_id": "train_shard_00000_3034_1", "global_id": 3350 }, { "text": "Vancomycin-resistant enterococci (VRE) can rapidly spread through hospitals. Therefore, our hospital employs a screening program whereby rectal swabs are screened for the presence of vanA and vanB, and only PCR-positive broths are cultured on VRE selection agar. Early November 2016, a clinical vanA-/vanB-negative VRE isolate was detected in a vanA/vanB-screening-negative patient, giving the possibility that an undetected VRE might be spreading within our hospital. Whole-genome-sequencing of the isolate showed that resistance was vanD-mediated and core genome multilocus sequence typing showed it was a rare type: ST17/CT154. To determine the prevalence of vanA/B/C/D-carrying enterococci, we designed a real-time PCR for vanC1/2/3 and vanD and screened rectal swabs from 360 patients. vanD was found in 27.8% of the patients, yet culture demonstrated only E. faecium from vanA-positive broths and E. gallinarum from vanC1-positive broths. No vanD-positive VRE were found, limiting the possibility of nosocomial spread of this VRE. Moreover, the high prevalence of non-VRE vanD in rectal swabs makes it unfeasible to include the vanD PCR in our VRE screening. However, having validated the vanC1/2/3 and vanD PCRs allows us to rapidly check future vanA/B-negative VRE for the presence of vanC and vanD genes.\n\nAppearance of vanD-positive Enterococcus faecium in a tertiary hospital in the Netherlands: prevalence of vanC and vanD in hospitalized patients.", "token_count": 422, "char_count": 1460, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": { "genes": [ "ST17", "CT154" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:28:59.863284", "source": { "split": "train_shard_00000", "doc_id": 3035 }, "chunk_id": "train_shard_00000_3035_0", "global_id": 3351 }, { "text": "The overall goal of this study was to determine whether the genome of an important plant pathogen in Africa, Ceratocystis albifundus, is structured into subgenomic compartments, and if so, to establish how these compartments are distributed across the genome. For this purpose, the publicly available genome of C. albifundus was complemented with the genome sequences for four additional isolates using the Illumina HiSeq platform. In addition, a reference genome for one of the individuals was assembled using both PacBio and Illumina HiSeq technologies. Our results showed a high degree of synteny between the five genomes, although several regions lacked detectable long-range synteny. These regions were associated with the presence of accessory genes, lower genetic similarity, variation in read-map depth, as well as transposable elements and genes associated with host-pathogen interactions (e.g. effectors and CAZymes). Such patterns are regarded as hallmarks of accelerated evolution, particularly of accessory subgenomic compartments in fungal pathogens. Our findings thus showed that the genome of C. albifundus is made-up of core and accessory subgenomic compartments, which is an important step towards characterizing its pangenome. This study also highlights the value of comparative genomics for understanding mechanisms that may underly and influence the biology and evolution of pathogens.\n\nGenomic analysis of the aggressive tree pathogen Ceratocystis albifundus.", "token_count": 336, "char_count": 1481, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:00.439389", "source": { "split": "train_shard_00000", "doc_id": 3036 }, "chunk_id": "train_shard_00000_3036_0", "global_id": 3352 }, { "text": "Yeast are usually responsible for spoilage of soft drinks and fruit beverages, because of the particular characteristics of these products (low pH, high C/N ratio). The microbial stability is guaranteed by thermal treatments. However, excessive heat treatments can affect food sensorial quality. In this work the thermal resistance of different yeasts strains (seven belonging to the species Saccharomyces cerevisiae and six belonging to the species Kluyveromyces marxianus, Zygosaccharomyces bisporus, Z. mellis, Z. rouxii, Schizosaccharomyces pombe and Saccharomycodes ludwigii) was assessed in a model system. The results showed non-linear death curves and a high variability also within the same species. The most resistant strain, belonging to the species S. cerevisiae, was chosen for further experiments in orange juice based industrial beverages: first, death curves were performed; then, the probability of beverage spoilage in relation to process parameters (initial inoculum, temperature, treatment time) was evaluated using a logistic regression model. Finally, a cross-validation was performed to investigate the predictive capability of the fitted model. Pasteurization in the soft drink industry is commonly applied according to parameters defined several decades ago, which does not consider the successive findings concerning microbial physiology and stress response, the process improvement and the more recent tools provided by predictive microbiology. In this perspective, this study can fill a gap in the literature on this subject, going to be a basis for optimizing thermal processes. In fact, the data obtained indicated an interesting possibility for food industry to better modulated (and even reduce) thermal treatments, with the aim to guarantee microbial stability while reducing thermal damage and energy costs.\n\nModeling of yeast thermal resistance and optimization of the pasteurization treatment applied to soft drinks.", "token_count": 411, "char_count": 1952, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:01.062812", "source": { "split": "train_shard_00000", "doc_id": 3037 }, "chunk_id": "train_shard_00000_3037_0", "global_id": 3353 }, { "text": "Prey are under selection to minimize predation losses. In aquatic environments, many prey use chemical cues released by predators, which initiate predator avoidance. A prominent example of behavioral predator-avoidance constitutes diel vertical migration (DVM) in the freshwater microcrustacean\n\n5α-cyprinol sulfate, a bile salt from fish, induces diel vertical migration in", "token_count": 93, "char_count": 374, "word_count": 50, "semantic_coherence": 1, "information_density": 0.86, "quality_score": 0.93, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:01.441330", "source": { "split": "train_shard_00000", "doc_id": 3038 }, "chunk_id": "train_shard_00000_3038_0", "global_id": 3354 }, { "text": "Xylitol is a valuable substance utilized by food and biochemical industries. NAD(P)H-dependent xylose reductase (XR)-encoded by the yeast KmXYL1 gene-is the key enzyme which facilitates reduction of xylose to xylitol. Multi-copy integration of a mutant KmXYL1 (mKmXYL1) gene was carried out using thermotolerant yeast Kluyveromyces marxianus KCTC17555ΔURA3, in order to enhance xylitol production. After multi-copy integration, the highest xylitol producing strain was isolated and named K. marxianus 17555-JBP2. This strain exhibited 440% higher xylitol production than the parental strain at 30 °C. Due to a multi-copy integration of the mKmXYL1 gene, various additional differences between K. marxianus 17555-JBP2 and the parental strain were observed, including a 66% increase in NAD(P)H-dependent XR activity at high temperature (45 °C). Quantitative real-time PCR and transcriptome analysis demonstrated that, relative to the parent strain, K. marxianus 17555-JBP2 exhibited two more copies of mKmXY1 genes and a 9.63-fold elevation in transcription of NAD(P)H-dependent XR. After optimization of bioreactor fermentation conditions (agitation speed), high-temperature (40 °C) xylitol productivity of K. marxianus 17555-JBP2 exhibited an 81% improvement relative to the parental strain. In this study, we demonstrated that the overexpression of endogenous XR could enhance xylitol productivity at 40 °C by thermotolerant K. marxianus.\n\nOverexpression of Endogenous Xylose Reductase Enhanced Xylitol Productivity at 40 °C by Thermotolerant Yeast Kluyveromyces marxianus.", "token_count": 489, "char_count": 1574, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": { "genes": [ "JBP2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:02.096124", "source": { "split": "train_shard_00000", "doc_id": 3039 }, "chunk_id": "train_shard_00000_3039_0", "global_id": 3355 }, { "text": "Simultaneous cofermentation of glucose and xylose mixtures would be a cost-effective solution for the conversion of cellulosic biomass to high-value products. However, most yeasts ferment glucose and xylose sequentially due to glucose catabolite repression. A well known thermotolerant yeast,\n\nAlleviation of catabolite repression in", "token_count": 89, "char_count": 333, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7955, "quality_score": 0.8977, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:02.482197", "source": { "split": "train_shard_00000", "doc_id": 3040 }, "chunk_id": "train_shard_00000_3040_0", "global_id": 3356 }, { "text": "Albeit its well known potency as a postmenopausal osteoporosis treatment, Risedronate suffers from poor oral bioavailability and high oral toxicity. This is the first work to assess the potential of bilosomes to address challenges of RS oral delivery. Furthermore, impact of integrating cationic moiety into bilosomes on intestinal digestability and toxicity of RS nanovesicles was first investigated in this article. Prepared formulations were optimized based on physicochemical properties, digestibility, intestinal permeation and local toxicity studies. Optimized preparations were prepared by reversed phase evaporation technique with three extrusion cycles and loaded by 10 mg/ml RS. Molar lipid to bile salt to cholesterol ratio was adjusted to 4:1:1 at pH 5. Addition of cholesterol had significantly improved bilosomes stability to digestive media. Results also revealed that permeation of anionic vesicles increased permeation by 1.5 times more than RS solution and reduced drug toxicity by 2 folds. On the other hand, Cationic bilosomes showed good stability in GIT fluids but their induced oral toxicity could limit their use. In conclusion, bilosomes are superior over liposomes regarding protection of delivery system from the damaging effect of external in digestive bile salts. In addition, it decreases toxicity issues of orally administered drugs.\n\nAnionic versus cationic bilosomes as oral nanocarriers for enhanced delivery of the hydrophilic drug risedronate.", "token_count": 362, "char_count": 1479, "word_count": 212, "semantic_coherence": 1, "information_density": 0.684, "quality_score": 0.842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:03.075466", "source": { "split": "train_shard_00000", "doc_id": 3041 }, "chunk_id": "train_shard_00000_3041_0", "global_id": 3357 }, { "text": "Leptospira is a highly heterogeneous bacterial genus that can be divided into three evolutionary lineages and >300 serovars. The causative agents of leptospirosis are responsible of an emerging zoonotic disease worldwide. To advance our understanding of the biodiversity of Leptospira strains at the global level, we evaluated the performance of whole-genome sequencing (WGS) as a genus-wide strain classification and genotyping tool. Herein we propose a set of 545 highly conserved loci as a core genome MLST (cgMLST) genotyping scheme applicable to the entire Leptospira genus, including non-pathogenic species. Evaluation of cgMLST genotyping was undertaken with 509 genomes, including 327 newly sequenced genomes, from diverse species, sources and geographical locations. Phylogenetic analysis showed that cgMLST defines species, clades, subclades, clonal groups and cgMLST sequence types (cgST), with high precision and robustness to missing data. Novel Leptospira species, including a novel subclade named S2 (saprophytes 2), were identified. We defined clonal groups (CG) optimally using a single-linkage clustering threshold of 40 allelic mismatches. While some CGs such as L. interrogans CG6 (serogroup Icterohaemorrhagiae) are globally distributed, others are geographically restricted. cgMLST was congruent with classical MLST schemes, but had greatly improved resolution and broader applicability. Single nucleotide polymorphisms within single cgST groups was limited to <30 SNPs, underlining a potential role for cgMLST in epidemiological surveillance. Finally, cgMLST allowed identification of serogroups and closely related serovars. In conclusion, the proposed cgMLST strategy allows high-resolution genotyping of Leptospira isolates across the phylogenetic breadth of the genus", "token_count": 465, "char_count": 1794, "word_count": 243, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [ "CG6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:03.717542", "source": { "split": "train_shard_00000", "doc_id": 3042 }, "chunk_id": "train_shard_00000_3042_0", "global_id": 3358 }, { "text": "The unified genomic taxonomy of Leptospira strains, available publicly at http://bigsdb.pasteur.fr/leptospira, will facilitate global harmonization of Leptospira genotyping, strain emergence follow-up and novel collaborative studies of the epidemiology and evolution of this emerging pathogen.\n\nGenus-wide Leptospira core genome multilocus sequence typing for strain taxonomy and global surveillance.", "token_count": 100, "char_count": 400, "word_count": 47, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:04.095346", "source": { "split": "train_shard_00000", "doc_id": 3042 }, "chunk_id": "train_shard_00000_3042_1", "global_id": 3359 }, { "text": "Bile salts (BS) are biosurfactants crucial for emulsification and intestinal absorption of cholesterol and other hydrophobic compounds such as vitamins and fatty acids. Interaction of BS with lipid bilayers is important for understanding their effects on membranes properties. The latter have relevance in passive diffusion processes through intestinal epithelium such as reabsorption of BS, as well as their degree of toxicity to intestinal flora and their potential applications in drug delivery. In this work, we used molecular dynamics simulations to address at the atomic scale the interactions of cholate, deoxycholate, and chenodeoxycholate, as well as their glycine conjugates with POPC bilayers. In this set of BS, variation of three structural aspects was addressed, namely conjugation with glycine, number and position of hydroxyl substituents, and ionization state. From atomistic simulations, the location and orientation of BS inside the bilayer, and their specific interactions with water and host lipid, such as hydrogen bonding and ion-pair formation, were studied in detail. Membrane properties were also investigated to obtain information on the degree of perturbation induced by the different BS. The results are described and related to a recent experimental study (Coreta-Gomes et al., 2015). Differences in macroscopic membrane partition thermodynamics and translocation kinetics are rationalized in terms of the distinct structures and atomic-scale behavior of the bile salt species. In particular, the faster translocation of cholate is explained by its higher degree of local membrane perturbation. On the other hand, the relatively high partition of the polar glycine conjugates is related to the longer and more flexible side chain, which allows simultaneous efficient solvation of the ionized carboxylate and deep insertion of the ring system.\n\nInteraction of Bile Salts With Lipid Bilayers: An Atomistic Molecular Dynamics Study.", "token_count": 447, "char_count": 1959, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:04.733821", "source": { "split": "train_shard_00000", "doc_id": 3043 }, "chunk_id": "train_shard_00000_3043_0", "global_id": 3360 }, { "text": "Drug-induced cholestasis poses a major hurdle for the pharmaceutical industry as it is one the primary mechanisms of drug-induced liver injury. Hence, detection of drug-induced cholestasis during the early stages of drug development is of utmost importance. The most commonly used in vitro models rely on the extent of inhibition of bile salt export pump-mediated taurocholic acid transport, thereby assuming that drug-induced cholestasis mechanisms are merely restricted to the interaction with this sole hepatic transporter. Sandwich-cultured human hepatocytes represent a more holistic in vitro tool to investigate drug-induced cholestasis as they preserve all relevant disposition pathways and cellular functions involved in bile acid homeostasis. We developed and validated a sandwich-cultured human hepatocytes-based in vitro assay which is able to identify compounds causing cholestasis by altering bile acid disposition. The in vitro cholestatic potential is expressed by calculating a drug-induced cholestasis index value, which reflects the relative residual urea formation of sandwich-cultured human hepatocytes co-incubated with bile acids and test compound as compared to sandwich-cultured human hepatocytes treated with test compound alone. In addition, a safety margin can be calculated to determine the in vivo risk for cholestasis based on the determination of the drug-induced cholestasis index at various concentrations and the peak plasma concentration of the drug candidate. This chapter outlines the various steps involved in performing our sandwich-cultured human hepatocytes-based in vitro assay.\n\nDetection of Drug-Induced Cholestasis Potential in Sandwich-Cultured Human Hepatocytes.", "token_count": 402, "char_count": 1709, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5708, "quality_score": 0.7854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:05.346948", "source": { "split": "train_shard_00000", "doc_id": 3044 }, "chunk_id": "train_shard_00000_3044_0", "global_id": 3361 }, { "text": "Drug-induced liver injury is an important reason for drug candidate failure. Alterations in the hepatobiliary disposition of bile acids are a proposed mechanism of cholestatic hepatotoxicity. Bile acids are synthesized in the hepatocyte, and excreted into the bile primarily by the bile salt export pump. Therefore, inhibition of the bile salt export pump by drugs has been postulated as a risk factor in the development of cholestatic hepatotoxicity. However, recent publications have shown a lack of correlation between bile salt export pump inhibition potency and drug-induced liver injury incidence. Following inhibition of the bile salt export pump mediated efflux of bile acids, the liver compensates through various mechanisms (adaptive response) including upregulation of basolateral bile acid efflux mediated by the farnesoid X receptor, the master regulator of bile acid homeostasis. The C-DILI™ assay integrates the effects of bile salt export pump inhibition, farnesoid X receptor antagonism, and basolateral efflux inhibition of bile acids to more accurately predict a drug's potential to cause cholestatic hepatotoxicity and drug-induced liver injury.\n\nThe C-DILI™ Assay: An Integrated In Vitro Approach to Predict Cholestatic Hepatotoxicity.", "token_count": 324, "char_count": 1256, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5333, "quality_score": 0.7667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:05.915287", "source": { "split": "train_shard_00000", "doc_id": 3045 }, "chunk_id": "train_shard_00000_3045_0", "global_id": 3362 }, { "text": "Transporters play a crucial role in the uptake of endo- and exogenous molecules in hepatocytes and efflux into the bile. The bile salt export pump (BSEP; ABCB11) is of major importance for efflux of bile salts to the bile and BSEP inhibition frequently provokes drug-induced cholestasis. This chapter describes two assays to determine inhibition of BSEP-mediated bile salt excretion. The first assay uses inside-out membrane vesicles, prepared from BSEP-transfected cell lines. The cholestasis potential of compounds can be determined by specifically investigating the ability to inhibit BSEP-mediated uptake of tauro-nor-THCA-24-DBD, a fluorescent bile salt derivative. For the second assay, relative accumulation of tauro-nor-THCA-24-DBD in sandwich-cultured hepatocytes, which represents a more biorelevant in vitro system, is investigated. Through incubation with standard or Ca\n\nVesicle- and Hepatocyte-Based Assays for Identification of Drug Candidates Inhibiting BSEP Function.", "token_count": 282, "char_count": 984, "word_count": 134, "semantic_coherence": 1, "information_density": 0.709, "quality_score": 0.8545, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:06.504824", "source": { "split": "train_shard_00000", "doc_id": 3046 }, "chunk_id": "train_shard_00000_3046_0", "global_id": 3363 }, { "text": "Gypenosides (GPS) have been used as traditional medicine for centuries with various pharmacological effects. However, its therapeutic effects were restricted owing to the poor lipid and water solubility and low absorption. This study aimed to develop nanostructured lipid carriers (NLCs) containing a bile salt formulation (sodium glycocholate, SGC) for GPS, and to evaluate the potential of the GPS-SGC-NLCs as an oral delivery system.\n\nFormulation design, characterization, and in vitro and in vivo evaluation of nanostructured lipid carriers containing a bile salt for oral delivery of gypenosides.", "token_count": 153, "char_count": 601, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7093, "quality_score": 0.8547, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:06.971967", "source": { "split": "train_shard_00000", "doc_id": 3047 }, "chunk_id": "train_shard_00000_3047_0", "global_id": 3364 }, { "text": "A 27-month-old girl presented with a short history of jaundice initially attributed to drug-induced liver injury. During the preceding 20 days, she had received a 10-day course of cefprozil and 2 doses of a homeopathic preparation of cantharidin for cystitis. Severe conjugated hyperbilirubinemia was present with normal γ-glutamyl transpeptidase activity. Liver biopsy revealed marked canalicular and hepatocellular cholestasis, with moderate hepatocellular disarray, as well as evidence of chronicity, including moderate portal-tract and perisinusoidal fibrosis. Immunohistochemical studies revealed that bile salt export pump expression was preserved, whereas canalicular γ-glutamyl transpeptidase expression was largely absent. An inherited cholestatic disorder was suspected. The entire coding region of\n\nBeyond an Obvious Cause of Cholestasis in a Toddler: Compound Heterozygosity for", "token_count": 241, "char_count": 890, "word_count": 116, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:07.466178", "source": { "split": "train_shard_00000", "doc_id": 3048 }, "chunk_id": "train_shard_00000_3048_0", "global_id": 3365 }, { "text": "In our study, the potential of bilosomes as novel vesicular carrier for the cutaneous delivery of the sulphone compound, Dapsone, for topical treatment of acne was investigated. The effect of different formulation variables (type and concentration of bile salt, and molar ratio of Span 60:cholesterol) on the properties of DPS-loaded bilosomes was investigated using a full factorial design. Design Expert software was used for data analysis and optimization of DPS-loaded bilosomes. The optimized bilosomes, chosen on the basis of their superior properties giving maximum entrapment,\n\nBilosomes as a novel carrier for the cutaneous delivery for dapsone as a potential treatment of acne: preparation, characterization and", "token_count": 165, "char_count": 721, "word_count": 105, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:07.963952", "source": { "split": "train_shard_00000", "doc_id": 3049 }, "chunk_id": "train_shard_00000_3049_0", "global_id": 3366 }, { "text": "The liver is the primary organ for the metabolic degradation of xenobiotics. Transmembrane transport proteins from the ABC and the SLC families mediate the uptake of endogenous compounds and xenobiotics into the hepatocyte as well as their elimination from the cells. Multiple processes are involved. The uptake of xenobiotics in hepatocytes is mediated by organic anion transporting polypeptides (OATPs) and by organic anion and cation transporters (OATs and OCTs). The elimination of drugs and metabolites from the liver cell back to the bloodstream is accomplished mainly by multidrug resistance-associated protein 3 (MRP3) and MRP4, while the elimination towards the biliary canaliculi is mediated by several different transporters (MRP2, BCRP, MDR1 and MATE1). Since bile acids and their salts are toxic detergents for hepatocytes, they have to be eliminated efficiently. This task is accomplished by the bile salt export pump BSEP. Two further transporters, MDR3 and ATP8B1 are involved in the proper constitution of bile. All these transporters can be influenced, mainly inhibited by a number of drugs, but also by metabolites from endogenous compounds such as estrogens. Additionally, rare monogenetic diseases exist which can be explained by absence of function or dysfunction of specific hepatic transporters, such as progressive familial intrahepatic cholestasis type 2 by genetic modifications in BSEP that lead to a loss of transporter function. Functional impairment of other transporters by genetics or by drugs also leads to liver injury, a potentially life-threatening disease that is still not fully understood. Hence, the interplay between drugs and hepatic transporters is multiple, and the knowledge of this interplay helps in understanding the etiology and molecular mechanisms behind some forms of (drug-induced) liver injury.\n\nDrugs and hepatic transporters: A review.", "token_count": 474, "char_count": 1892, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5986, "quality_score": 0.7993, "entities": { "genes": [ "MATE1", "MRP4", "MRP2", "MRP3", "MDR3", "MDR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:08.613997", "source": { "split": "train_shard_00000", "doc_id": 3050 }, "chunk_id": "train_shard_00000_3050_0", "global_id": 3367 }, { "text": "The purpose of this study was to assess the potential effects of polysaccharides from edible mushroom Grifola frondosa (GFP) on lipid metabolic disorders and gut microbiota dysbiosis, and elucidate their possible regulatory mechanisms on lipid and cholesterol metabolism in high-fat diet (HFD)-exacerbated hyperlipidemic and hypercholesterolemic rats. Results showed that oral administration of GFP markedly alleviated dyslipidaemia through decreasing the serum levels of total triglycerides, total cholesterol, and free fatty acids, and significantly suppressing hepatic lipid accumulation and steatosis. Besides, the excretion of fecal bile acids was also promoted by oral administration of GFP. Metagenomic analysis revealed that GFP supplementation (400 mg kg-1 day-1) resulted in significant structure changes on gut microbiota in HFD-fed rats, in particular modulating the relative abundance of functionally relevant microbial phylotypes compared with the HFD group. Key microbial phylotypes responding to GFP intervention were identified to strongly correlate with the lipid metabolism disorder associated parameters using the correlation network based on Spearman's correlation coefficient. Serum and hepatic lipid profiles were found positively correlated with Clostridium-XVIII, Butyricicoccus and Turicibacter, but negatively correlated with Helicobater, Intestinimonas, Barnesiella, Parasutterella, Ruminococcus and Flavonifracter. Moreover, GFP treatment (400 mg kg-1 day-1) regulated the mRNA expression levels of the genes responsible for hepatic lipid and cholesterol metabolism. Oral supplementation of GFP markedly increased the mRNA expression of cholesterol 7α-hydroxylase (CYP7A1) and bile salt export pump (BSEP), suggesting an enhancement of bile acid (BA) synthesis and excretion from the liver", "token_count": 473, "char_count": 1818, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:09.624596", "source": { "split": "train_shard_00000", "doc_id": 3051 }, "chunk_id": "train_shard_00000_3051_0", "global_id": 3368 }, { "text": "These findings illustrated that GFP could ameliorate lipid metabolic disorders through modulating specific gut microbial phylotypes and regulating hepatic lipid and cholesterol metabolism related genes, and therefore could be used as a potential functional food ingredient for the prevention or treatment of hyperlipidemia.\n\nGrifola frondosa polysaccharides ameliorate lipid metabolic disorders and gut microbiota dysbiosis in high-fat diet fed rats.", "token_count": 114, "char_count": 450, "word_count": 59, "semantic_coherence": 1, "information_density": 0.8305, "quality_score": 0.9153, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:10.010493", "source": { "split": "train_shard_00000", "doc_id": 3051 }, "chunk_id": "train_shard_00000_3051_1", "global_id": 3369 }, { "text": "To investigate the effects of geniposidic acid( GPA) on hepato-enteric circulation in cholestasis rats,and to explore the mechanism based on the sirtuin 1( Sirt1)-farnesol X receptor( FXR) pathway,sixty SD rats were randomly divided into 6 groups:blank control group,ANIT model group,ursodeoxycholic acid group( 100 mg·kg~(-1)·d-1 UDCA),and GPA high,medium and low( 100,50 and 25 mg·kg~(-1)·d-1) dosage groups,10 rats in each group. Corresponding drugs were intragastrically( ig) administered for10 days. After administration on day 8,all rats except blank rats were administered with 65 mg·kg~(-1)α-naphthalene isothiocyanate( ANIT) once. After the last administration,the serum levels of alanine aminotransferase( ALT),glutamine oxalacetate aminotransferase( AST),gamma-glutamyltransferase( γ-GGT),alkaline phosphatase( ALP),total bilirubin( TB) and total bile acid( TBA)were measured,and the mRNA transcription levels of Sirt1,FXR,multidrug resistant associated protein 2( MRP2),bile salt export pump( BSEP),sodium taurocholate contractible polypeptide( NTCP) in liver and apical sodium bile acid transporter( ASBT),ileum bile acid binding protein( IBABP) in ileum were detected by reverse transcription-polymerase chain reaction( RT-PCR). The protein expression levels of Sirt1,FXR and NTCP were detected by Western blot; the expression of MRP2,BSEP in liver and ASBT,IBABP in ileum were determined by immunofluorescence three staining", "token_count": 478, "char_count": 1439, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:10.665075", "source": { "split": "train_shard_00000", "doc_id": 3052 }, "chunk_id": "train_shard_00000_3052_0", "global_id": 3370 }, { "text": "Primary rat hepatocytes were cultured in vitro to investigate the inhibitory effect of GPA on a potent and selective Sirt1 inhibitor( EX 527),and the mRNA and protein expression levels of Sirt1 and FXR were detected by RT-PCR and Western blot. GPA significantly decreased the levels of ALT,AST,γ-GGT,ALP,TB,TBA in serum( P<0.01) and improved the pathological damage of liver tissues in ANIT-induced cholestasis rats; significantly increased the mRNA and protein expression levels of Sirt1,FXR,MRP2,BSEP,NTCP in liver and ASBT,IBABP in ileum( P< 0.01). In vitro primary hepatocytes experiment indicated that the gene and protein expression levels of FXR and Sirt1 were noticeably improved by GPA in primary hepatocytes inhibited by EX-527( P<0.01). It was found that the improvement of GPA was in a dose-dependent manner. GPA could improve bile acid hepatointestinal circulation and play a liver protection and cholagogu role in cholestasis rats induced by ANIT.The mechanism may be that GPA activated FXR by regulating Sirt1,a key regulator of oxidative stress injury,and then the activated FXR could regulate protein of bile acid hepato-enteric circulation.\n\n[Effect of geniposidic acid on hepato-enteric circulation in cholestasis rats through Sirt1-FXR signaling pathway].", "token_count": 372, "char_count": 1275, "word_count": 185, "semantic_coherence": 1, "information_density": 0.5405, "quality_score": 0.7703, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:11.249734", "source": { "split": "train_shard_00000", "doc_id": 3052 }, "chunk_id": "train_shard_00000_3052_1", "global_id": 3371 }, { "text": "The Autotransporter IcsA Promotes Shigella flexneri Biofilm Formation in the Presence of Bile Salts.", "token_count": 31, "char_count": 100, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:11.607598", "source": { "split": "train_shard_00000", "doc_id": 3053 }, "chunk_id": "train_shard_00000_3053_0", "global_id": 3372 }, { "text": "Extended multi-locus sequence typing (eMLST) methods have become popular in the field of genomic epidemiology. Before eMLST methods can be applied in epidemiological investigations, the selection of a suitable scheme is critical. The core genome scheme (cgMLST) has become the most popular eMLST approach for strain typing in the epidemiological domain. In addition to strain typing, many public health researchers and clinical microbiologists wish to investigate which genes cause genetic differences between compared strains. Therefore, a tool that can be used to extract canonical genes with an eMLST scheme would be particularly useful. In this study, we present cano-eMLST, a well-designed program that applies a feature-selection methodology to create a canonical locus combination with discriminatory power by traversing a genetic relatedness tree based on a user-selected scheme. The cano-eMLST program is provided mainly to help infectious disease laboratory researchers identify potential factors related to bacterial pathogenesis. The core program (tree-traversing approach) of cano-eMLST is implemented in Perl and Python. All the necessary dependencies and environmental settings are provided in the encapsulated version (VirtualBox or VMware) and self-installation version (all use source code and libraries).\n\nThe Cano-eMLST Program: An Approach for the Calculation of Canonical Extended Multi-Locus Sequence Typing, Making Comparison of Genetic Differences Among Bunches of Bacterial Strains.", "token_count": 329, "char_count": 1508, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:12.182089", "source": { "split": "train_shard_00000", "doc_id": 3054 }, "chunk_id": "train_shard_00000_3054_0", "global_id": 3373 }, { "text": "Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of Pseudomonas aeruginosa strain PA34. We obtained the complete genome of PA34 utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The susceptibility to heavy metals and cytotoxicity was determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 genomic islands (GIs) were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (AAC(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.\n\nAccessory genome of the multi-drug resistant ocular isolate of Pseudomonas aeruginosa PA34.", "token_count": 445, "char_count": 1754, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [ "PA34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:12.813681", "source": { "split": "train_shard_00000", "doc_id": 3055 }, "chunk_id": "train_shard_00000_3055_0", "global_id": 3374 }, { "text": "Non-typhoidal Salmonella (NTS) bacteremia is a significant cause of morbidity and mortality worldwide. It is considered to be an emerging and neglected tropical disease in Africa. We studied this in two tertiary hospitals-Al Farwaniya and Al Amiri-in Kuwait, a subtropical country, from April 2013-May 2016. NTS bacteremia was present in 30 of 53,860 (0.75%) and 31 of 290,36 (1.33%) blood cultures in the two hospitals respectively. In Al Farwaniya hospital, one-third of the patients were from some tropical developing countries of Asia. About 66% of all patients (40/61) had diarrhea, and of these, 65% had the corresponding blood serovar isolated from stool culture. A few patients had Salmonella cultured from urine. Patients were either young or old. Most of the patients had co-morbidities affecting the immune system. Two patients each died in both hospitals. The number of different serovars cultured in each hospital was 13, and most infections were due to S. Enteritidis (all sequence type [ST]) 11) and S. Typhimurium (all ST19) except in a subgroup of expatriate patients from tropical developing countries in Al Farwaniya hospital. About a quarter of the isolates were multidrug-resistant. Most patients were treated with a cephalosporin with or without other antibiotics. S. Enteritidis and S. Typhimurium isolates were typed by pulsed field-gel electrophoresis (PFGE) and a selected number of isolates were whole-genome sequenced. Up to four different clades were present by PFGE in either species. Whole-genome sequenced isolates showed antibiotic-resistance genes that showed phenotypic correlation, and in some cases, phenotypes showed absence of specific genes. Whole-genome sequenced isolates showed presence of genes that contributed to blood-stream infection. Phylogeny by core genome analysis showed a close relationship with S. Typhimurium and S. Enteritidis from other parts of the world", "token_count": 520, "char_count": 1913, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5544, "quality_score": 0.7772, "entities": { "genes": [ "ST19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:29:13.474410", "source": { "split": "train_shard_00000", "doc_id": 3056 }, "chunk_id": "train_shard_00000_3056_0", "global_id": 3375 }, { "text": "The uniqueness of our study included the finding of a low prevalence of infection, mortality and multidrug-resistance, a relatively high prevalence of gastrointestinal infection in patients, and the characterization of selected isolates of S. Typhimurium and S. Enteritidis serovars by whole-genome sequencing that shed light on phylogeny, virulence and resistance. Similarities with studies from developing countries especially Africa included infection in patients with co-morbidities affecting the immune system, predominance of S. Typhimurium and S. Enteritidis serovars and presence of drug-resistance in isolates.\n\nNon-typhoidal Salmonella blood stream infection in Kuwait: Clinical and microbiological characteristics.", "token_count": 171, "char_count": 725, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:13.914794", "source": { "split": "train_shard_00000", "doc_id": 3056 }, "chunk_id": "train_shard_00000_3056_1", "global_id": 3376 }, { "text": "The bile salt export pump (BSEP, ABCB11) mediates bile acid efflux from hepatocytes into bile. Although the inhibition of BSEP has been implicated as an important mechanism of drug-induced liver injury (DILI), liver injury caused by BSEP-inhibiting drugs is rarely reproduced in experimental animals, probably due to species differences in bile acid composition between humans and rodents. In this study, we tested whether supplementation with chenodeoxycholic acid (CDCA) sodium, a hydrophobic bile salt, could sensitize rats to liver injury caused by a BSEP-inhibiting drug. A potent BSEP inhibitor, ketoconazole (KTZ), which is associated with clinical DILI, was intragastrically administered simultaneously with CDCA at a nontoxic dose once a day for 3 days. Plasma transaminase levels significantly increased in rats receiving CDCA+KTZ, whereas neither treatment with CDCA alone, KTZ alone nor a combination of CDCA and miconazole, a safe analog to KTZ, induced liver injury. In CDCA+KTZ-treated rats, most bile acid species in the liver significantly increased compared with treatment with vehicle or CDCA alone, suggesting that KTZ administration inhibited bile acid excretion. Furthermore, hepatic mRNA expression levels of a bile acid synthesis enzyme, Cyp7a1, and a basolateral bile salt influx transporter, Ntcp, decreased, whereas a canalicular phosphatidylcholine flippase, Mdr2, increased in the CDCA+KTZ group to compensate for hepatic bile acid accumulation. In conclusion, we found that oral CDCA supplementation predisposed rats to KTZ-induced liver injury due to the hepatic accumulation of bile acids. This method may be useful for assessing the potential of BSEP-inhibiting drugs inducing liver injury in vivo.\n\nExperimental Evidence of Liver Injury by BSEP-Inhibiting Drugs With a Bile Salt Supplementation in Rats.", "token_count": 493, "char_count": 1837, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7943, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:14.559891", "source": { "split": "train_shard_00000", "doc_id": 3057 }, "chunk_id": "train_shard_00000_3057_0", "global_id": 3377 }, { "text": "Pregnancy is associated with progressive hypercholanemia, hypercholesterolemia, and hypertriglyceridemia, which can result in metabolic disease in susceptible women. Gut signals modify hepatic homeostatic pathways, linking intestinal content to metabolic activity. We sought to identify whether enteric endocrine signals contribute to raised serum bile acids observed in human and murine pregnancies, by measuring fibroblast growth factor (FGF) 19/15 protein and mRNA levels, and 7α-hydroxy-4-cholesten-3-one. Terminal ileal farnesoid X receptor (FXR)-mediated gene expression and apical sodium bile acid transporter (ASBT) protein concentration were measured by qPCR and western blotting. Shotgun whole-genome sequencing and ultra-performance liquid chromatography tandem mass spectrometry were used to determine the cecal microbiome and metabonome. Targeted and untargeted pathway analyses were performed to predict the systemic effects of the altered metagenome and metabolite profiles. Dietary CA supplementation was used to determine whether the observed alterations could be overcome by intestinal bile acids functioning as FXR agonists. Human and murine pregnancy were associated with reduced intestinal FXR signaling, with lower FGF19/15 and resultant increased hepatic bile acid synthesis. Terminal ileal ASBT protein was reduced in murine pregnancy. Cecal bile acid conjugation was reduced in pregnancy because of elevated bile salt hydrolase-producing Bacteroidetes. CA supplementation induced intestinal FXR signaling, which was not abrogated by pregnancy, with strikingly similar changes to the microbiota and metabonome as identified in pregnancy. Conclusion: The altered intestinal microbiota of pregnancy enhance bile acid deconjugation, reducing ileal bile acid uptake and lowering FXR induction in enterocytes. This exacerbates the effects mediated by reduced bile acid uptake transporters in pregnancy", "token_count": 489, "char_count": 1920, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5952, "quality_score": 0.7976, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:15.215342", "source": { "split": "train_shard_00000", "doc_id": 3058 }, "chunk_id": "train_shard_00000_3058_0", "global_id": 3378 }, { "text": "Thus, in pregnant women and mice, there is reduced FGF19/15-mediated hepatic repression of hepatic bile acid synthesis, resulting in hypercholanemia.\n\nEnhanced Microbial Bile Acid Deconjugation and Impaired Ileal Uptake in Pregnancy Repress Intestinal Regulation of Bile Acid Synthesis.", "token_count": 92, "char_count": 286, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:15.588366", "source": { "split": "train_shard_00000", "doc_id": 3058 }, "chunk_id": "train_shard_00000_3058_1", "global_id": 3379 }, { "text": "Two experiments, 1 in vitro and 1 in vivo study, were conducted to analyze probiotic species characteristics and survival in the intestine of broiler birds. The in vitro study characterized the effect of bile salt supplementation and pH on the proliferation of Lactobacillus reuteri, Pediococcus acidilactici, Bifidobacterium animalis, and Enterococcus faecium. L. reuteri and P. acidilactici growth was maximal when the media was supplemented with 1.0% bile salt, whereas B. animalis and E. faecium growth was maximal when the media was supplemented with 0.5% bile salt. Altering the pH between 2.5 and 5.8 did not significantly (P > 0.05) alter the proliferation of L. reuteri and B. animalis. Decreasing the pH from 5.8 to 2.0 decreased P. acidilactici growth, whereas it increased the E. faecium proliferation. The in vivo study quantified the concentration of L. reuteri, P. acidilactici, B. animalis, E. faecium, and L. salivarius in different intestinal sections from birds supplemented with and without synbiotic containing the above 5 bacteria species. Birds were supplemented with and without synbiotic for 18 d, after which all birds were fed the same basal diet with no synbiotic. At 72 h of feeding, the basal diet with no synbiotics, when the probiotic species in the feed is expected not to confound the recovery of probiotic species from the intestine, intestinal contents were collected. L. reuteri, P. acidilactici, E. faecium, and L. salivarius were below detectable amount in the control group. L. reuteri concentration expressed as copy numbers/g and as percentage of total bacteria was highest in the jejunum and ileum, respectively. E. faecium concentration was highest in the ileum. The copy number of P. acidilactici increased at the duodenum and plateaued after duodenum. L. salivarius concentration was highest in the jejunum", "token_count": 514, "char_count": 1852, "word_count": 288, "semantic_coherence": 1, "information_density": 0.4792, "quality_score": 0.7396, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:29:16.231430", "source": { "split": "train_shard_00000", "doc_id": 3059 }, "chunk_id": "train_shard_00000_3059_0", "global_id": 3380 }, { "text": "It can be concluded that real-time PCR can be applied to quantify the concentrations of probiotic species in the intestine and probiotic species differ in their ability to colonize different sections of the intestine.\n\nIn vitro characterization and analysis of probiotic species in the chicken intestine by real-time polymerase chain reaction.", "token_count": 79, "char_count": 343, "word_count": 51, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:16.605797", "source": { "split": "train_shard_00000", "doc_id": 3059 }, "chunk_id": "train_shard_00000_3059_1", "global_id": 3381 }, { "text": "Gastrointestinal (GI) infection is one of the most common types of infectious diseases. Application of probiotic strains in the control of such infections represents a promising approach. In this study, Lactobacillus fermentum strain 4-17 was isolated from kashkineh, an Iranian cereal fermented food, and identified by sequencing its 16S rRNA gene using universal primers. Its probiotic features, including resistance to acid, bile tolerance, antibacterial activity, resistance to intestinal and gastric juices, and hydrophobicity were evaluated. The ability of this strain to adhere to human intestinal cells as well as the anti-adhesive effect of L. fermentum strain 4-17 against E. coli isolated from patients with urinary tract infection was investigated. L. fermentum strain 4-17 was capable of surviving at various conditions such as low pH values, bile salts exposure, and GI tract environment. It showed 43% cell hydrophobicity. The adhesion level of L. fermentum strain 4-17 to human colon adenocarcinoma Caco-2 cells was 8.5% which was also confirmed by scanning electron microscopy (SEM). Furthermore, this strain showed appropriate anti-adhesive properties (including competition, inhibition and replacement properties) against human pathogenic bacteria. These data suggest that L. fermentum strain 4-17 could be examined further for its useful effects and introduced as a novel candidate probiotic to control GI infection disease.\n\nEvaluation of adherence and anti-infective properties of probiotic Lactobacillus fermentum strain 4-17 against Escherichia coli causing urinary tract infection in humans.", "token_count": 412, "char_count": 1616, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6228, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:17.234704", "source": { "split": "train_shard_00000", "doc_id": 3060 }, "chunk_id": "train_shard_00000_3060_0", "global_id": 3382 }, { "text": "The sequencing of over a thousand Saccharomyces cerevisiae genomes revealed a complex pangenome. Over one third of the discovered genes are not present in the S. cerevisiae core genome but instead are often restricted to a subset of yeast isolates and thus may be important for adaptation to specific environmental niches. We refer to these genes as \"pan-genes,\" being part of the pangenome but not the core genome. Here, we describe the evolutionary journey and characterisation of a novel pan-gene, originally named hypothetical (HYPO) open-reading frame. Phylogenetic analysis reveals that HYPO has been predominantly retained in S. cerevisiae strains associated with brewing but has been repeatedly lost in most other fungal species during evolution. There is also evidence that HYPO was horizontally transferred at least once, from S. cerevisiae to Saccharomyces paradoxus. The phylogenetic analysis of HYPO exemplifies the complexity and intricacy of evolutionary trajectories of genes within the S. cerevisiae pangenome. To examine possible functions for Hypo, we overexpressed a HYPO-GFP fusion protein in both S. cerevisiae and Saccharomyces pastorianus. The protein localised to the plasma membrane where it accumulated initially in distinct foci. Time-lapse fluorescent imaging revealed that when cells are grown in wort, Hypo-gfp fluorescence spreads throughout the membrane during cell growth. The overexpression of Hypo-gfp in S. cerevisiae or S. pastorianus strains did not significantly alter cell growth in medium-containing glucose, maltose, maltotriose, or wort at different concentrations.\n\nEvolutionary journey and characterisation of a novel pan-gene associated with beer strains of Saccharomyces cerevisiae.", "token_count": 448, "char_count": 1730, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:17.869265", "source": { "split": "train_shard_00000", "doc_id": 3061 }, "chunk_id": "train_shard_00000_3061_0", "global_id": 3383 }, { "text": "Pasteurella multocida is a heterogeneous bacterium, which has the capacity to cause disease in a wide range of host species and is also recognized as an important zoonotic pathogen. Two sequential deaths in captive fur seals occurred at Sea World, Australia during December 2017. A fibrinosuppurative bronchopneumonia in a Subantarctic fur seal (Arctocephalus tropicalis) resulted in death within 24 h of nonspecific signs of illness, whereas a septic peritonitis in a New Zealand fur seal (Arctocephalus forsteri) resulted in death within 12 h of clinical presentation. The cases happened within three days in two different pool locations, although both had previously been housed in the same area. A total of six Pasteurella multocida isolates were obtained from several internal organs at necropsy in both cases and were subjected to whole genome sequencing and phylogenomic analysis. In-silico typing of the isolates revealed that all belonged to Multi-Locus Sequence Type 7 and carried lipopolysaccharide outer core biosynthesis loci Type 3. Phylogenomic analysis of the isolates confirmed that the isolates were near identical at the core genome level, suggesting acquisition from a common source. The results also revealed the presence of within host and across animal diversity of P. multocida isolates for the first time even in a clearly connected outbreak.\n\nNovel insights into pasteurellosis in captive pinnipeds.", "token_count": 352, "char_count": 1425, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8233, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:18.495362", "source": { "split": "train_shard_00000", "doc_id": 3062 }, "chunk_id": "train_shard_00000_3062_0", "global_id": 3384 }, { "text": "Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.\n\nCulture-enriched human gut microbiomes reveal core and accessory resistance genes.", "token_count": 200, "char_count": 923, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8228, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:18.963130", "source": { "split": "train_shard_00000", "doc_id": 3063 }, "chunk_id": "train_shard_00000_3063_0", "global_id": 3385 }, { "text": "An inability to standardize the bioinformatic data produced by whole-genome sequencing (WGS) has been a barrier to its widespread use in tuberculosis phylogenetics. The aim of this study was to carry out a phylogenetic analysis of tuberculosis in Wales, United Kingdom, using Ridom SeqSphere software for core genome multilocus sequence typing (cgMLST) analysis of whole-genome sequencing data. The phylogenetics of tuberculosis in Wales have not previously been studied. Sixty-six\n\nPhylogenetic Analysis of Mycobacterium tuberculosis Strains in Wales by Use of Core Genome Multilocus Sequence Typing To Analyze Whole-Genome Sequencing Data.", "token_count": 175, "char_count": 641, "word_count": 90, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:19.431810", "source": { "split": "train_shard_00000", "doc_id": 3064 }, "chunk_id": "train_shard_00000_3064_0", "global_id": 3386 }, { "text": "Listeria monocytogenes is sporadically detected on a range of ready to eat fresh produce lines, such as spinach and rocket, and is a threat to public health. However, little is known about the diversity of L. monocytogenes present on fresh produce and their potential pathogenicity. In this work, fifteen Listeria monocytogenes isolates from the UK fresh produce supply chain were characterised using whole genome sequencing (WGS). Additionally, isolates were characterised based on their ability to form biofilm. Whole genome sequencing data was used to determine the sequence type of isolates based on multi-locus sequence typing (MLST), construct a core single nucleotide polymorphism (SNP) phylogeny and determine the presence of virulence and resistance associated genes. MLST revealed 9 distinct sequence types (STs) spanning 2 lineages (I & II) with one isolate belonging to the ST6 subtype, strains from which have been recently implicated in two large, food-associated L. monocytogenes outbreaks in South Africa and across Europe. Although most of the 15 isolates were different, comparison of core genome SNPs showed 4 pairs of 'indistinguishable' strains (<5 SNPs difference). Virulence profiling revealed that some isolates completely lacked the Listeria pathogenicity island-3 (LIPI-3) amongst other virulence factors. Investigation of the inlA gene showed that no strains in this study contained a premature stop codon (PMSC), an indicator of attenuated virulence. Assessment of biofilm production showed that isolates found in the fresh produce supply chain differ in their ability to form biofilm. This trait is considered important for L. monocytogenes to persist in environments associated with food production and processing. Overall the work indicates that a genetically diverse range of L. monocytogenes strains is present in the UK fresh produce supply chain and the virulence profiles found suggests that at least some of the strains are capable of causing human illness. Interestingly, the presence of some genetically indistinguishable isolates within the 15 isolates examined suggests that cross-contamination in the fresh produce environment does occur", "token_count": 504, "char_count": 2179, "word_count": 320, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": { "genes": [ "ST6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:20.122351", "source": { "split": "train_shard_00000", "doc_id": 3065 }, "chunk_id": "train_shard_00000_3065_0", "global_id": 3387 }, { "text": "These findings have useful implications in terms of food safety and for informing microbial surveillance programmes in the UK fresh produce supply chain.\n\nListeria monocytogenes isolates from ready to eat plant produce are diverse and have virulence potential.", "token_count": 55, "char_count": 260, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:20.498121", "source": { "split": "train_shard_00000", "doc_id": 3065 }, "chunk_id": "train_shard_00000_3065_1", "global_id": 3388 }, { "text": "Illnesses caused by Shiga toxin-producing Escherichia coli (STECs) can be life threatening, such as hemolytic uremic syndrome (HUS). The STECs most frequently identified by USDA's Microbiological Data Program (MDP) carried toxin gene subtypes stx1a and/or stx2a. Here we described the genome sequences of 331 STECs isolated from foods regulated by the FDA 2010-2017, and determined their genomic identity, serotype, sequence type, virulence potential, and prevalence of antimicrobial resistance. Isolates were selected from the MDP archive, routine food testing by FDA field labs (ORA), and food testing by a contract company. Only 276 (83%) strains were confirmed as STECs by in silico analysis. Foods from which STECs were recovered included cilantro (6%), spinach (25%), lettuce (11%), and flour (9%). Phylogenetic analysis using core genome MLST revealed these STEC genomes were highly variable, with some clustering associated with ST types and serotypes. We detected 95 different sequence types (ST); several ST were previously associated with HUS: ST21 and ST29 (O26:H11), ST11 (O157:H7), ST33 (O91:H14), ST17 (O103:H2), and ST16 (O111:H-). in silico virulome analyses showed ~ 51% of these strains were potentially pathogenic [besides stx gene they also carried eae (25%) or 26% saa (26%)]. Virulence gene prevalence was also determined: stx1 only (19%); stx2 only (66%); and stx1/sxt2 (15%). Our data form a new WGS dataset that can be used to support food safety investigations and monitor the recurrence/emergence of E. coli in foods.", "token_count": 488, "char_count": 1545, "word_count": 232, "semantic_coherence": 1, "information_density": 0.7328, "quality_score": 0.8664, "entities": { "genes": [ "ST29", "ST17", "ST21", "ST16", "ST33", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:21.144829", "source": { "split": "train_shard_00000", "doc_id": 3066 }, "chunk_id": "train_shard_00000_3066_0", "global_id": 3389 }, { "text": "Virulence gene profiles and phylogeny of Shiga toxin-positive Escherichia coli strains isolated from FDA regulated foods during 2010-2017.", "token_count": 47, "char_count": 138, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:21.507036", "source": { "split": "train_shard_00000", "doc_id": 3066 }, "chunk_id": "train_shard_00000_3066_1", "global_id": 3390 }, { "text": "Critical illness is associated with a disturbed regulation of gastrointestinal hormones resulting in functional and metabolic anomalies. Fibroblast growth factor 19 (FGF19) is an ileum-derived metabolic hormone induced by bile salts upon gallbladder emptying after enteral nutrient stimulation. Our aim was to study the nutrient-stimulated FGF19 response in 24 patients admitted to the intensive care unit (ICU) compared with 12 healthy controls. All subjects received intraduodenal high-lipid nutrient infusion for 120 minutes. Blood was collected every 30 minutes until 1 hour after infusion, and gallbladder emptying was studied by ultrasound. Serum levels of bile salts and FGF19 were assessed. ICU patients had significantly higher fasting bile salt serum levels compared with controls, whereas FGF19 serum levels were similar. In both groups, nutrient infusion elicited substantial bile salt elevations (P < 0.001), peaking at 90 minutes, albeit with a significantly lower peak in the ICU patients (P = 0.029). In controls, FGF19 was significantly elevated relative to baseline from 120 minutes onward (P < 0.001). In ICU patients, the FGF19 response was blunted, as reflected by significantly lower FGF19 elevations at 120, 150, and 180 minutes (P < 0.05) and significantly lower area under the curve (AUC) values compared with controls (P < 0.001). Gallbladder dysmotility was associated with the impaired FGF19 response in critical illness. The gallbladder ejection fraction correlated positively with FGF19 AUC values (ρ = +0.34, P = 0.045). In 10 of 24 ICU patients, gallbladder emptying was disturbed. These patients had significantly lower FGF19 AUC values (P < 0.001)", "token_count": 499, "char_count": 1681, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5635, "quality_score": 0.7817, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:22.161170", "source": { "split": "train_shard_00000", "doc_id": 3067 }, "chunk_id": "train_shard_00000_3067_0", "global_id": 3391 }, { "text": "Gallbladder emptying and the FGF19 response were respectively disturbed or absent in patients receiving norepinephrine. Conclusion: The nutrient-stimulated FGF19 response is impaired in ICU patients, which is mechanistically linked to gallbladder dysmotility in critical illness. This may contribute to disturbed liver metabolism in these patients and has potential as a nutritional biomarker.\n\nGallbladder Dyskinesia Is Associated With an Impaired Postprandial Fibroblast Growth Factor 19 Response in Critically Ill Patients.", "token_count": 138, "char_count": 526, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7536, "quality_score": 0.8768, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:22.589788", "source": { "split": "train_shard_00000", "doc_id": 3067 }, "chunk_id": "train_shard_00000_3067_1", "global_id": 3392 }, { "text": "Biliary lipids consist mainly of bile salts, phospholipids and cholesterol, which form mixed micelles and vesicles. Bile salts play various physiological roles but have damaging effects on cell membranes due to their detergent properties. The cytotoxicity of bile salts on hepatocytes leads to liver injuries and is largely determined by the bile salt species, the concentrations of bile salts, phospholipids and cholesterol, and the lipid composition of cell membranes. In bile, monomers and simple micelles of bile salts coexist with mixed micelles and vesicles in dynamic equilibrium, and contribute to the cytotoxicity on hepatocytes. The ATP-binding cassette (ABC) transporter family members, ABCB11, ABCB4 and ABCG5/ABCG8, mediate the biliary secretion of bile salts, phospholipids and cholesterol, respectively. Mutations in ABCB4 result in severe cholestatic diseases, and the biliary phospholipids are necessary for the attenuation of bile salt cytotoxicity. On the other hand, cholesterol reverses the cytoprotective effects of phospholipids against bile salts. In addition, phosphatidylethanolamine N-methyltransferase increases the cell resistance to bile salts by changing the phospholipid composition and structures of the apical membranes. In this review, we focus on the molecular mechanisms for the protection of hepatocytes against bile salt cytotoxicity. Further understanding of these mechanisms will help to develop new therapeutic strategies for cholestatic liver diseases.\n\nMolecular Mechanisms for Protection of Hepatocytes against Bile Salt Cytotoxicity.", "token_count": 411, "char_count": 1579, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5253, "quality_score": 0.7627, "entities": { "genes": [ "ABCB11", "ABCB4", "ABCG8", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:23.213571", "source": { "split": "train_shard_00000", "doc_id": 3068 }, "chunk_id": "train_shard_00000_3068_0", "global_id": 3393 }, { "text": "From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.\n\nWGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome.", "token_count": 178, "char_count": 636, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7108, "quality_score": 0.8554, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:23.667220", "source": { "split": "train_shard_00000", "doc_id": 3069 }, "chunk_id": "train_shard_00000_3069_0", "global_id": 3394 }, { "text": "In total, 95 Acinetobacter baumannii isolates recovered from patients from two hospitals in Cochabamba, Bolivia were studied. The presence of class D and B β-lactamases was investigated using polymerase chain reaction, and antimicrobial susceptibility testing was performed by agar dilution and broth microdilution. The resistance rate to carbapenems was 53.7%. All carbapenem-resistant A. baumannii (CRAb, n=51) and four carbapenem-susceptible isolates were further analysed by whole-genome sequencing. The resulting genome assemblies were used to identify the acquired resistome, and core genome multi-locus sequence typing (cgMLST) was used to determine their molecular epidemiology. All but one of the CRAb isolates (n=50) belonged to international clone (IC) 7 and they clustered into five sequence types; on cgMLST, they were found to be separated by ≥40 alleles. All CRAb isolates carried bla\n\nAcinetobacter baumannii analysis by core genome multi-locus sequence typing in two hospitals in Bolivia: endemicity of international clone 7 isolates (CC25).", "token_count": 292, "char_count": 1058, "word_count": 149, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [ "CC25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:24.230754", "source": { "split": "train_shard_00000", "doc_id": 3070 }, "chunk_id": "train_shard_00000_3070_0", "global_id": 3395 }, { "text": "Anthrax, caused by Bacillus anthracis, is a severe zoonosis with a great impact on both human and animal health. In the present study, we identified the phylogenetic relationships among 16 Japanese strains of B. anthracis, including eight bovine strains, two equine strains, five swine strains, and one former vaccine strain, using in silico canonical single nucleotide polymorphism (canSNP) and core genome SNP analyses. The results of our in silico canSNP analysis suggest that these 16 Japanese strains could be divided into four lineages: i) one equine strain in A.Br.Ames, ii) one equine and six bovine strains in A.Br.001/002, iii) five swine and one bovine strain in A.Br.Aust94, and iv) one bovine and one vaccine strain in A.Br.008/011. A comparison with non-Japanese B. anthracis strains revealed a total of 3787 SNPs identified from the whole genome sequences of the Japanese strains; these SNP data were subjected to a phylogenetic analysis using the maximum parsimony (MP) method. Our core genome SNP analysis was also able to detect differences of a few chromosomal SNPs across clonal strains from the same cases that had different storage and passage histories. Additionally, our whole genome SNP analysis clearly indicated that the Japanese swine anthrax cases of 1982 were caused by at least three independent strains; however, their phylogeny revealed no clear relationship with swine strains from other countries. The bovine strain belonging to the A.Br.008/011 lineage differed from a former Japanese vaccine strain by only 12 SNPs. Together with the phylogenic results and epidemiological circumstances, the diversity of strains reveals that the B. anthracis available in Japan probably resulted from multiple relatively recent import events, rather than reflecting the persistence of a more ancient ecologically established group.\n\nComparative genomics and phylogenetic analysis of Bacillus anthracis strains isolated from domestic animals in Japan.", "token_count": 509, "char_count": 1971, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5642, "quality_score": 0.7821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:24.881710", "source": { "split": "train_shard_00000", "doc_id": 3071 }, "chunk_id": "train_shard_00000_3071_0", "global_id": 3396 }, { "text": "Corynebacterium pseudotuberculosis is the etiologic agent of veterinary relevance diseases, such as caseous lymphadenitis, affecting different animal species causing damage to the global agribusiness. So far, there are no completely effective treatment methods to overcome the impacts caused by this pathogen. Several genomes of the species are deposited on public databases, allowing the execution of studies related to the pan-genomic approach. In this study, we used an integrated in silico workflow to prospect novel putative targets using the core genome, a set of shared genes among 65 C. pseudotuberculosis strains. Subsequently, through RNA-Seq data of the same abiotic stresses in two strains, we selected only induced genes to compose the reverse vaccinology workflow based in two different strategies. Our results predicted six probable antigens in both analysis, which indicates that they have a strong potential to be used in further studies as vaccine targets against this bacterium.\n\nPrediction of new vaccine targets in the core genome of Corynebacterium pseudotuberculosis through omics approaches and reverse vaccinology.", "token_count": 253, "char_count": 1139, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:25.372927", "source": { "split": "train_shard_00000", "doc_id": 3072 }, "chunk_id": "train_shard_00000_3072_0", "global_id": 3397 }, { "text": "Yeasts are extremely useful, not only for fermentation but also for a wide spectrum of fuel and chemical productions. We analyzed the overall metabolic turnover and transcript dynamics in glycolysis and the TCA cycle, revealing the difference in adaptive pyruvate metabolic response between a Crabtree-negative species, Kluyveromyces marxianus, and a Crabtree-positive species, Saccharomyces cerevisiae, during aerobic growth. Pyruvate metabolism was inclined toward ethanol production under aerobic conditions in S. cerevisiae, while increased transcript abundances of the genes involved in ethanol metabolism and those encoding pyruvate dehydrogenase were seen in K. marxianus, indicating the augmentation of acetyl-CoA synthesis. Furthermore, different metabolic turnover in the TCA cycle was observed in the two species: malate and fumarate production in S. cerevisiae was higher than in K. marxianus, irrespective of aeration; however, fluxes of both the reductive and oxidative TCA cycles were enhanced in K. marxianus by aeration, implying both the cycles contribute to efficient electron flux without producing ethanol. Additionally, decreased hexokinase activity under aerobic conditions is expected to be important for maintenance of suitable carbon flux. These findings demonstrate differences in the key metabolic trait of yeasts employing respiration or fermentation, and provide important insight into the metabolic engineering of yeasts.\n\nIncreased flux in acetyl-CoA synthetic pathway and TCA cycle of Kluyveromyces marxianus under respiratory conditions.", "token_count": 385, "char_count": 1571, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "metabolism", "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:25.982758", "source": { "split": "train_shard_00000", "doc_id": 3073 }, "chunk_id": "train_shard_00000_3073_0", "global_id": 3398 }, { "text": "High-temperature fermentation is desirable for the industrial production of ethanol, which requires thermotolerant yeast strains. However, yeast thermotolerance is a complicated quantitative trait. The understanding of genetic basis behind high-temperature fermentation performance is still limited. Quantitative trait locus (QTL) mapping by pooled-segregant whole genome sequencing has been proved to be a powerful and reliable approach to identify the loci, genes and single nucleotide polymorphism (SNP) variants linked to quantitative traits of yeast.\n\nQTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast.", "token_count": 152, "char_count": 671, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:26.426919", "source": { "split": "train_shard_00000", "doc_id": 3074 }, "chunk_id": "train_shard_00000_3074_0", "global_id": 3399 }, { "text": "We previously demonstrated the existence of naturalized strains of E. coli in wastewater and herein perform an in-depth comparative whole genome analysis of these strains (n = 17). Fourteen of the Canadian E. coli strains, isolated from geographically separated wastewater treatment plants, were virtually identical at the core genome and were ≥96% similar at the whole genome level, suggesting clonal-relatedness among these isolates. Remarkably, these strains were shown to be extremely similar to the genome of an E. coli isolated from wastewater in Switzerland, suggesting a global distribution of these strains. The genomes of three other Canadian wastewater strains were more diverse but very similar to the genomes of E. coli isolates collected from U.S. wastewater samples. Based on maximum likelihood phylogenetic analysis, wastewater strains from Canada, the U.S. and Switzerland formed a clade separate from other known enteric phylogroups (i.e., A, B1, B2, D, E) and the cryptic clades. All Canadian, Swiss and U.S. wastewater strains possessed a common SNP biomarker pattern across their genomes, and a sub-population (i.e., 14 Canadian and 1 Swiss strain) also possessed a previously identified wastewater-specific marker known as uspC-IS30-flhDC element. Biochemical heat mapping of 518 categories of genes recapitulated phylogeny, with wastewater strains phenotypically clustering separately from enteric and cryptic clades. Wastewater strains were enriched for stress-response genes (i.e., nutrient acquisition/deprivation, DNA repair, oxidative stress, and UV resistance) - elements reflective of their environmental survival challenges. Wastewater strains were shown to carry a plethora of known antibiotic resistance (AR) genes, the patterns of which were remarkably similar among all Canadian, U.S. and Swiss wastewater strains. Virulence gene composition was also similar among all the wastewater strains, with an abundant representation of virulence genes commonly associated with urinary pathogenic E. coli (UPEC) as well as enterohemorrhagic (EHEC) E. coli", "token_count": 522, "char_count": 2081, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5525, "quality_score": 0.7763, "entities": { "genes": [ "IS30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:29:27.758639", "source": { "split": "train_shard_00000", "doc_id": 3075 }, "chunk_id": "train_shard_00000_3075_0", "global_id": 3400 }, { "text": "The remarkable degree of similarity between all wastewater strains from Canada, Switzerland and the U.S. suggests the evolution and global-dissemination of water treatment-resistant clone of E. coli. These finding, along with others, raise some important concerns about the potential for emergence of E. coli pathotypes resistant to water-treatment.\n\nEvidence for the evolution, clonal expansion and global dissemination of water treatment-resistant naturalized strains of Escherichia coli in wastewater.", "token_count": 117, "char_count": 504, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7463, "quality_score": 0.8731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:28.149191", "source": { "split": "train_shard_00000", "doc_id": 3075 }, "chunk_id": "train_shard_00000_3075_1", "global_id": 3401 }, { "text": "Pseudomonads are ubiquitous group of environmental proteobacteria, well known for their roles in biogeochemical cycling, in the breakdown of xenobiotic materials, as plant growth promoters, and as pathogens of a variety of host organisms. We have previously identified a large megaplasmid present within one isolate of the plant pathogen Pseudomonas syringae, and here we report that a second member of this megaplasmid family is found within an environmental Pseudomonad isolate most closely related to Pseudomonas putida. Many of the shared genes are involved in critical cellular processes like replication, transcription, translation, and DNA repair. We argue that presence of these shared pathways sheds new light on discussions about the types of genes that undergo horizontal gene transfer (i.e., the complexity hypothesis) as well as the evolution of pangenomes. Furthermore, although both megaplasmids display a high level of synteny, genes that are shared differ by over 50% on average at the amino acid level. This combination of conservation in gene order despite divergence in gene sequence suggests that this Pseudomonad megaplasmid family is relatively old, that gene order is under strong selection within this family, and that there are likely many more members of this megaplasmid family waiting to be found in nature.\n\nJust the Two of Us? A Family of Pseudomonas Megaplasmids Offers a Rare Glimpse into the Evolution of Large Mobile Elements.", "token_count": 342, "char_count": 1461, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6143, "quality_score": 0.8072, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:28.727936", "source": { "split": "train_shard_00000", "doc_id": 3076 }, "chunk_id": "train_shard_00000_3076_0", "global_id": 3402 }, { "text": "Fish produce and release bile salts as chemical signalling substances that act as sensitive olfactory stimuli. To investigate how bile salts affect olfactory signal transduction in large yellow croaker (\n\nTranscriptome sequencing of olfactory-related genes in olfactory transduction of large yellow croaker (", "token_count": 68, "char_count": 308, "word_count": 43, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:29.099656", "source": { "split": "train_shard_00000", "doc_id": 3077 }, "chunk_id": "train_shard_00000_3077_0", "global_id": 3403 }, { "text": "In order to enrich the library of domestic research about new red fluorescent marker in lactic acid bacteria (LAB), we described a new fusion expression system in Lactobacillus plantarum WCFS1 based on the pSIP vector. This system contained red fluorescent protein mCherry as a marker and bile salt hydrolase gene (bsh) as a reporter gene. Moreover, in this study, four different promoters (PsppA, PldhL, P32 and PslpA) were used to regulate the expression of the fusion protein mCherry-BSH, completing the inducible and constitutive expression in lactic acid bacteria. The recombinant protein mCherry-BSH presented activity of red fluorescence and bile salt hydrolase (BSH). The successful construction of the fusion expression system in LAB using a red fluorescent protein mCherry provides favorable conditions for the distribution, intestinal colonization and survival rate of lactic acid bacteria, so as to reveal the function mechanism of its probiotic characteristics; and the system also could lay the foundation for researches on protein expression, cellular localization and properties identification of active protein in lactic acid bacteria.\n\n[Construction and application of mCherry red fluorescent protein fusion expression system in lactic acid bacteria].", "token_count": 298, "char_count": 1269, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5543, "quality_score": 0.7772, "entities": { "genes": [ "WCFS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:29.659425", "source": { "split": "train_shard_00000", "doc_id": 3078 }, "chunk_id": "train_shard_00000_3078_0", "global_id": 3404 }, { "text": "Mycobacterium chelonae is a member of the Mycobacterium chelonae-abscessus complex and a cause of opportunistic disease in fish, reptiles, birds, and mammals including humans. Isolates in the complex are often difficult to identify and have differing antimicrobial susceptibilities. Thirty-one previously identified rapidly-growing, non-tuberculous Mycobacterium sp. isolates cultured from biofilms, fish, reptiles, mammals, including humans, and three ATCC reference strains were evaluated with nine M. chelonae-abscessus complex whole genome sequences from GenBank by phylogenomic analysis, targeted gene comparisons, and in-vitro antimicrobial susceptibility patterns to assess strain variation among isolates from different sources. Results revealed minimal genetic variation among the M. chelonae strains. However, the core genomic alignment and SNP pattern of the complete 16S rRNA sequence clearly separated the turtle type strain ATCC 35752T from the clinical isolates and human reference strain \"M. chelonae chemovar niacinogenes\" ATCC 19237, providing evidence of two distinct subspecies. Concatenation of the partial rpoB (752 bp) and complete hsp65 (1,626 bp) sequence produced the same species/subspecies delineations as the core phylogeny. Partial rpoB and hsp65 sequences identified all the clinical isolates to the appropriate species level when respective cut-offs of 98% and 98.4% identity to the M. chelonae type strain ATCC 35752T were employed. The human strain, ATCC19237, was the most representative strain for the evaluated human, veterinary, and environmental strains. Additionally, two isolates were identified as Mycobacterium saopaulense, its first identification in a non-fish or non-human host.", "token_count": 460, "char_count": 1724, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.806, "entities": { "genes": [ "ATCC19237" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:30.299309", "source": { "split": "train_shard_00000", "doc_id": 3079 }, "chunk_id": "train_shard_00000_3079_0", "global_id": 3405 }, { "text": "Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns.", "token_count": 53, "char_count": 221, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:30.692789", "source": { "split": "train_shard_00000", "doc_id": 3079 }, "chunk_id": "train_shard_00000_3079_1", "global_id": 3406 }, { "text": "The salmonellae are found in a wide range of animal hosts and many food products for human consumption. Most cases of human disease are caused by S. enterica subspecies I; however as opportunistic pathogens the other subspecies (II-VI) and S. bongori are capable of causing disease. Loci that were not consistently present in all of the species and subspecies were removed from a previously proposed core genome scheme (EBcgMLSTv2.0), the removal of these 252 loci resulted in a core genus scheme (SalmcgMLSTv1.0). SalmcgMLSTv1.0 clustered isolates from the same subspecies more rapidly and more accurately grouped isolates from different subspecies when compared with EBcgMLSTv2.0. All loci within the EBcgMLSTv2.0 scheme were present in over 98% of S. enterica subspecies I isolates and should, therefore, continue to be used for subspecies I analyses, while the SalmcgMLSTv1.0 scheme is more appropriate for cross genus investigations.\n\nA proposed core genome scheme for analyses of the Salmonella genus.", "token_count": 268, "char_count": 1007, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6013, "quality_score": 0.8007, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:31.263760", "source": { "split": "train_shard_00000", "doc_id": 3080 }, "chunk_id": "train_shard_00000_3080_0", "global_id": 3407 }, { "text": "Kluyveromyces marxianus is a promising nonconventional yeast for biobased chemical production due to its rapid growth rate, high TCA cycle flux, and tolerance to low pH and high temperature. Unlike Saccharomyces cerevisiae, K. marxianus grows on low-cost substrates to cell densities that equal or surpass densities in glucose, which can be beneficial for utilization of lignocellulosic biomass (xylose), biofuel production waste (glycerol), and whey (lactose). We have evaluated K. marxianus for the synthesis of polyketides, using triacetic acid lactone (TAL) as the product. The 2-pyrone synthase (2-PS) was expressed on a CEN/ARS plasmid in three different strains, and the effects of temperature, carbon source, and cultivation strategy on TAL levels were determined. The highest titer was obtained in defined 1% xylose medium at 37°C, with substantial titers at 41 and 43°C. The introduction of a high-stability 2-PS mutant and a promoter substitution increased titer four-fold. 2-PS expression from a multi-copy pKD1-based plasmid improved TAL titers a further five-fold. Combining the best plasmid, promoter, and strain resulted in a TAL titer of 1.24 g/L and a yield of 0.0295 mol TAL/mol carbon for this otherwise unengineered strain in 3 ml tube culture. This is an excellent titer and yield (on xylose) before metabolic engineering or fed-batch culture relative to other hosts (on glucose), and demonstrates the promise of this rapidly growing and thermotolerant yeast species for polyketide production.\n\nSynthesis of polyketides from low cost substrates by the thermotolerant yeast Kluyveromyces marxianus.", "token_count": 469, "char_count": 1619, "word_count": 240, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:31.950399", "source": { "split": "train_shard_00000", "doc_id": 3081 }, "chunk_id": "train_shard_00000_3081_0", "global_id": 3408 }, { "text": "We investigated the ultrastructural pattern of colloidal phases in human duodenal fluids. Aspirates were collected from three volunteers in both fasted and fed nutritional states. Analysis methods comprised the combination of asymmetric flow field-flow fractionation (AF4) and multi-angle laser light scattering (MALLS). Furthermore, dynamic light scattering (DLS) and diffusion-ordered NMR spectroscopy (DOSY-NMR) were employed as alternative analytical approaches for comparison. By AF4/MALLS, up to four, and in some cases up to five distinct co-existing fractions could be differentiated in the sub-micron size-range, which, in accordance with a previous study (Elvang et al., 2018), may be assigned to three main types, namely small bile salt micelles, intermediate size mixed bile salt/phospholipid micelles and large phospholipid aggregates / vesicles. Although more or less the same colloidal phases were found to co-exist in all aspirates, their prevalence was found to vary, both over time and between the three individual human volunteers. Any uniform changes of patterns of colloidal phases over time, however, could not be identified. On the other hand, prevalence of specific colloidal phases was identified for aspirates of individual volunteers, which correlated reasonably well with the prevalence of certain lipid species in their molecular composition. It remains to be investigated whether such prevalence of specific colloidal phases influences drug solubilizing capacity as well as drug absorption. If so, this may help to better understand the substantial inter-individual variability seen in many drug absorption profiles.\n\nCo-existing colloidal phases of human duodenal aspirates: Intraindividual fluctuations and interindividual variability in relation to molecular composition.", "token_count": 403, "char_count": 1804, "word_count": 250, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [ "AF4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:32.588486", "source": { "split": "train_shard_00000", "doc_id": 3082 }, "chunk_id": "train_shard_00000_3082_0", "global_id": 3409 }, { "text": "Production of fuel ethanol is one of the possible ways to utilize crude glycerol, substantial amounts of which are produced by biodiesel industry. Earlier, we have described construction of the recombinant strains of methylotrophic thermotolerant yeast Ogataea polymorpha with simultaneous overexpression of the genes PDC1 and ADH1, which produced increased amounts of ethanol from glycerol. In this work, we have further improved these strains by overexpression of genes involved either in oxidative (through dihydroxyacetone) or phosphorylative (through glycerol-3-phosphate) pathway of glycerol catabolism, as well as heterologous gene coding for glycerol transporter FPS1 from Komagataella phaffii (formerly, Pichia pastoris). Obtained recombinant strains produced up to 10.7 g/L of ethanol (with ethanol productivity 30 mg/g of biomass/hr and yield 132 mg/g of consumed glycerol) from pure glycerol and up to 3.55 g/L of ethanol (with ethanol productivity 11.6 mg/g of biomass/hr and yield 72.3 mg/g of consumed glycerol) from crude glycerol as a carbon source, which is approximately 15 times more relative to that of the O. polymorpha wild-type strain and 2.2 more relative to the earlier constructed strain.\n\nOverexpression of the genes of glycerol catabolism and glycerol facilitator improves glycerol conversion to ethanol in the methylotrophic thermotolerant yeast Ogataea polymorpha.", "token_count": 425, "char_count": 1395, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5578, "quality_score": 0.7789, "entities": { "genes": [ "PDC1", "FPS1", "ADH1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:33.223530", "source": { "split": "train_shard_00000", "doc_id": 3083 }, "chunk_id": "train_shard_00000_3083_0", "global_id": 3410 }, { "text": "Inhibition of the bile salt export pump (BSEP) may be associated with clinical drug-induced liver injury, but is poorly predicted by preclinical animal models. Here we present the development of a novel rat model using siRNA knockdown (KD) of Bsep that displayed differentially enhanced hepatotoxicity to 8 Bsep inhibitors and not to 3 Bsep noninhibitors when administered at maximally tolerated doses for 7 days. Bsep KD alone resulted in 3- and 4.5-fold increases in liver and plasma levels, respectively, of the sum of the 3 most prevalent taurine conjugated bile acids (T3-BA), approximately 90% decrease in plasma and liver glycocholic acid, and a distinct bile acid regulating gene expression pattern, without resulting in hepatotoxicity. Among the Bsep inhibitors, only asunaprevir and TAK-875 resulted in serum transaminase and total bilirubin increases associated with increases in plasma T3-BA that were enhanced by Bsep KD. Benzbromarone, lopinavir, and simeprevir caused smaller increases in plasma T3-BA, but did not result in hepatotoxicity in Bsep KD rats. Bosentan, cyclosporine A, and ritonavir, however, showed no enhancement of T3-BA in plasma in Bsep KD rats, as well as Bsep noninhibitors acetaminophen, MK-0974, or clarithromycin. T3-BA findings were further strengthened through monitoring TCA-d4 converted from cholic acid-d4 overcoming interanimal variability in endogenous bile acids. Bsep KD also altered liver and/or plasma levels of asunaprevir, TAK-875, TAK-875 acyl-glucuronide, benzbromarone, and bosentan. The Bsep KD rat model has revealed differences in the effects on bile acid homeostasis among Bsep inhibitors that can best be monitored using measures of T3-BA and TCA-d4 in plasma", "token_count": 500, "char_count": 1719, "word_count": 254, "semantic_coherence": 1, "information_density": 0.622, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:33.876773", "source": { "split": "train_shard_00000", "doc_id": 3084 }, "chunk_id": "train_shard_00000_3084_0", "global_id": 3411 }, { "text": "However, the phenotype caused by Bsep inhibition is complex due to the involvement of several compensatory mechanisms.\n\nUse of a Bile Salt Export Pump Knockdown Rat Susceptibility Model to Interrogate Mechanism of Drug-Induced Liver Toxicity.", "token_count": 59, "char_count": 242, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8857, "quality_score": 0.9429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:34.241839", "source": { "split": "train_shard_00000", "doc_id": 3084 }, "chunk_id": "train_shard_00000_3084_1", "global_id": 3412 }, { "text": "Fourteen Lactobacillus plantarum strains isolated from various food sources and two different climatic regions, Ireland and Pakistan were analyzed for their probiotic functions. RecA gene based multiplex PCR amplifications and pulsed-field gel electrophoresis (PFGE) were performed to genetically characterize these strains at subspecies level. All the strains were tested for bacteriocin activity against major food borne pathogens (L. innocua and L. monocytogenes). Bacteriocin was further purified using HPLC and identified with MALDI TOF MS analysis. Identification of gene encoding plantaracin 423 along with its enzyme sensitivity assays to protinease K and pepsin were also performed. Probiotic properties of bacteriocin producing strains were also analyzed by acid tolerance, bile salt tolerance, survival in simulated gastric juice and antibiotic resistance tests. Ten distinctly different strains of PFGE patterns were identified following ApaI digestion. Antimicrobial screening showed five L. plantarum strains as the potential producers of bacteriocin, expressing GIZ (Growth inhibition zone) up to 12, 12, 14, 11 and 13 mm, respectively against L. innocua. Molecular characterization of these strains further exhibited that plantaracin gene was present in the genome of L. plantarum strains AS-4, AS-6, AS-7, AS-13 and AS-14. All strains presented significant in vitro functional probiotic potential. Current study therefore, not only highlights bacteriocin regulated probiotic potential of L. plantarum strains isolated from different sources and climatic regions but also designates high heterogeneity in functional properties of the L. plantarum strains.\n\nFunctional probiotic attributes and gene encoding plantaracin among variant Lactobacillus Plantarum strains.", "token_count": 446, "char_count": 1781, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:34.877287", "source": { "split": "train_shard_00000", "doc_id": 3085 }, "chunk_id": "train_shard_00000_3085_0", "global_id": 3413 }, { "text": "Chiral separation is an important process in the chemical and pharmaceutical industries. From the analytical chemistry perspective, chiral separation is required for assessing the fit-for-purpose and the safety of chemical products. Capillary electrophoresis, in the electrokinetic chromatography mode is an established analytical technique for chiral separations. A water-soluble chiral selector is typically used. This review therefore examines the use of various chiral selectors in electrokinetic chromatography during 2017⁻2018. The chiral selectors were both low and high (macromolecules) molecular mass molecules as well as molecular aggregates (supramolecules). There were 58 papers found by search in Scopus, indicating continuous and active activity in this research area. The macromolecules were sugar-, amino acid-, and nucleic acid-based polymers. The supramolecules were bile salt micelles. The low molecular mass selectors were mainly ionic liquids and complexes with a central ion. A majority of the papers were on the use or preparation of sugar-based macromolecules, e.g., native or derivatised cyclodextrins. Studies to explain chiral recognition of macromolecular and supramolecular chiral selectors were mainly done by molecular modelling and nuclear magnetic resonance spectroscopy. Demonstrations were predominantly on drug analysis for the separation of racemates.\n\nChiral Selectors in Capillary Electrophoresis: Trends During 2017⁻2018.", "token_count": 356, "char_count": 1461, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:35.463676", "source": { "split": "train_shard_00000", "doc_id": 3086 }, "chunk_id": "train_shard_00000_3086_0", "global_id": 3414 }, { "text": "Spectral-fluorescent properties of polymethine dye probes anionic 3,3'-di(sulfopropyl)-4,5,4',5'-dibenzo-9-ethylthiacarbocyanine-betaine (DEC) and cationic 3,3',9-trimethylthiacarbocyanine iodide (Cyan 2) in the presence of biological surfactants, bile salts sodium cholate (NaC), sodium deoxycholate (NaDC) and sodium taurocholate (NaTC), as well as sodium dodecyl sulfate (SDS), have been studied in a wide range of surfactant concentrations. When a surfactant is introduced into a solution of DEC, changes of the spectral-fluorescent properties are observed due to decomposition of dye dimers into cis-monomers and cis-trans conversion of the resulting monomers. In the presence of SDS, both processes occur in parallel, caused by noncovalent interaction of dye monomers with micelles, and mainly occur near the critical micelle concentration (CMC). In contrast, upon the introduction of increasing concentrations of bile salts, decomposition of dye dimers into the monomers begins at lower concentrations than cis-trans conversion. The former process is almost completed at concentrations close to CMC of secondary micelles (CMC2), while the latter process occurs even at concentrations of bile salts much higher than CMC2. Hence, DEC can serve as a probe that permits estimating the value of CMC2 and is indicative of reorganization of secondary micelles upon an increase in bile salt concentration. Aggregation of DEC and Cyan 2 on bile salts is also observed. Since it is observed at relatively low concentrations of bile salts (25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population.\n\nGenomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.", "token_count": 445, "char_count": 1796, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5547, "quality_score": 0.7773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:41.061952", "source": { "split": "train_shard_00000", "doc_id": 3096 }, "chunk_id": "train_shard_00000_3096_0", "global_id": 3425 }, { "text": "Streptococcus pneumoniae, a normal commensal of the upper respiratory tract, is a major public health concern, responsible for substantial global morbidity and mortality due to pneumonia, meningitis and sepsis. Why some pneumococci invade the bloodstream or CSF (so-called invasive pneumococcal disease; IPD) is uncertain. In this study we identify genes associated with IPD. We transform whole genome sequence (WGS) data into a sequence typing scheme, while avoiding the caveat of using an arbitrary genome as a reference by substituting it with a constructed pangenome. We then employ a random forest machine-learning algorithm on the transformed data, and find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of the genes we identified as associated with IPD, we find 23 genes previously shown to be directly relevant to IPD, as well as 18 uncharacterized genes. We suggest that these uncharacterized genes identified by us are also likely to be relevant for IPD.\n\nIdentifying genes associated with invasive disease in S. pneumoniae by applying a machine learning approach to whole genome sequence typing data.", "token_count": 278, "char_count": 1193, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:41.612043", "source": { "split": "train_shard_00000", "doc_id": 3097 }, "chunk_id": "train_shard_00000_3097_0", "global_id": 3426 }, { "text": "Toxoplasma gondii is an important protozoan pathogen that infects many wild and domestic animals and causes infections in immunocompromised humans. However, there has been little investigation of the molecular evolutionary trajectories of this pathogenic protozoa using comparative genomics data. Here, we employed a comparative evolutionary genomics approach to identify genes that are under site- and lineage-specific positive selection in nine strains of T. gondii, including two closely related species, Neospora caninum and Hammondia hammondi. Based on the analyses of five coccidian core genomes, 4.5% of the 5788 core genome genes showed strong signals for positive selection in the site model. In addition, the branch-site model analyses in the nine T. gondii core genomes indicated that 2 to 20 genes underwent significant positive selection along each lineage leading to T. gondii strains. Many of the protein products encoded by the positively selected genes are secretory or surface proteins that have previously been implicated in host pathogenesis. The adaptive changes in these positively selected genes might be related to dynamic interactions between the host immune systems and might play a crucial role in the infection and pathogenic processes of T. gondii.\n\nGenome-wide analyses reveal genes subject to positive selection in Toxoplasma gondii.", "token_count": 313, "char_count": 1364, "word_count": 200, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:42.169508", "source": { "split": "train_shard_00000", "doc_id": 3098 }, "chunk_id": "train_shard_00000_3098_0", "global_id": 3427 }, { "text": "Air flow rate and agitation speed for inulinase production by Kluyveromyces marxianus were optimized based on metabolic heat release profiles. Shear stress and oxygen transfer (k\n\nEffect of aeration and agitation on yeast inulinase production: a biocalorimetric investigation.", "token_count": 67, "char_count": 276, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8684, "quality_score": 0.9342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:42.567941", "source": { "split": "train_shard_00000", "doc_id": 3099 }, "chunk_id": "train_shard_00000_3099_0", "global_id": 3428 }, { "text": "Five Lactobacillus strains isolated from vegetable and dairy products showed 99% similarity with Lactobacillus plantarum 1(Lp-1) using API -CHL 50 kit. Most of them proved to be sensitive to bacterial cell-wall inhibitors i.e. penicillin, ampicillin, amoxicillin and methicillin as studied by disc-diffusion method. These strains manifested profound tolerance to acidic-stress where Lp86 and Lp36 exhibited a good survival pattern at pH-2 for 4 hr retaining a survival count of 85% and 50%, respectively. A high survival of 85.7% was witnessed in Lp86 in presence of protease while Lp36 maintained 94.55% and 92.65% of population under the influence of enzyme pancreatin and pepsin. All the strains displayed marked tolerance against trypsin as the count did not drop below 77%. Absorbance and growth in terms of cfu/ml for bile-tolerance was examined for concentrations reflecting those in the GIT of humans, all the Lp-1 strains when grown with 1% bile showed a drop in the viable count by 1 log cycle i.e. from 1010 to 109cfu/ml. Fulfilling the above mentioned criteria these probiotic candidates displayed their capacity to reach the colon as viable metabolically active cells after successfully surviving under conditions similar to the gastrointestinal tract of humans. Upon examining the viability and stability of these probiotic candidates in most common foods serving as vehicle for probiotic delivery to the intestine, it was noticed that all the isolates tested sustained a probiotic approved number of 107 cfu/ml for effective function as recommended by WHO, after a maximum storage for one month. Hence, it could be justified that the selected probiotic candidates possess prominent probiotic potential. Therefore, L. plantarum 1 strains could prove to be an efficient probiotic after further in vivo studies to explore its safety in human subjects.", "token_count": 492, "char_count": 1863, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:43.266424", "source": { "split": "train_shard_00000", "doc_id": 3100 }, "chunk_id": "train_shard_00000_3100_0", "global_id": 3429 }, { "text": "Probiotic potential of novel strains of Lactobacillus plantarum Lp -1: In vitro studies.", "token_count": 28, "char_count": 88, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:43.632817", "source": { "split": "train_shard_00000", "doc_id": 3100 }, "chunk_id": "train_shard_00000_3100_1", "global_id": 3430 }, { "text": "The bile salts and phospholipids are secreted by the gallbladder to form dietary mixed micelles in which the solvation of poorly absorbed lipophilic drugs and nutraceuticals take place. A comprehensive understanding of the micellization and structure of the mixed micelles are crucial to design effective delivery systems for such substances. In this study, the evolution of the dietary mixed micelle formation under physiologically relevant concentrations and the dependence of structural properties on micelle size were investigated through coarse-grained molecular dynamics simulations. The MARTINI force field was used to model cholate and POPC as the representative bile salt and phospholipid, respectively. The micellization behavior was similar under both fasted and fed state concentrations. Total lipids concentration and the micelle size did not affect the internal structure of the micelles. All the micelles were slightly ellipsoidal in shape independent of their size. The extent of deviation from spherical geometry was found to depend on the micellar POPC/cholate ratio. We also found that the surface and core packing density of the micelles increased with micelle size. The former resulted in more perpendicular alignments of cholates with respect to the surface, while the latter resulted in an improved alignment of POPC tails with the radial direction and more uniform core density.\n\nCharacterization of the self-assembly and size dependent structural properties of dietary mixed micelles by molecular dynamics simulations.", "token_count": 320, "char_count": 1543, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:44.662440", "source": { "split": "train_shard_00000", "doc_id": 3101 }, "chunk_id": "train_shard_00000_3101_0", "global_id": 3431 }, { "text": "Oral administration of a solid dosage form requires drug dissolution in the gastrointestinal tract before absorption. Solubility is a key factor controlling dissolution, and it is recognized that, within the intestinal tract, this is influenced by the luminal fluid pH, amphiphile content, and composition. Various simulated intestinal fluid recipes have been introduced to mimic this behavior and studied using a range of different experimental techniques. In this article, we have measured equilibrium solubility utilizing a novel four component mixture design (4CMD) with biorelevant amphiphiles (bile salt, phospholipid, oleate, and monoglyceride) within a matrix of three pH values (5, 6, and 7) and total amphiphile concentrations (11.7, 30.6, and 77.5 mM) to provide a topographical and statistical overview. Three poorly soluble drugs representing acidic (indomethacin), basic (carvedilol), and neutral (fenofibrate) categories have been studied. The macroscopic solubility behavior agrees with literature and exhibits an overall increasing solubility from low pH and total amphiphile concentration to high pH and total amphiphile concentration. Within the matrix, all three drugs display different topographies, which can be related to the statistical effect levels of the individual amphiphiles or amphiphile interactions on solubility. The study also identifies previously unreported three and four way factor interactions notably between bile salt, phospholipid, pH, and total amphiphile concentration. In addition, the results also reveal that solubility variability is linked to the number of amphiphiles and the respective ratios in the measurement fluid, with the minimum variation present in systems containing all four amphiphiles. The individual 4CMD experiments within the matrix can be linked to provide a possible intestinal solubility window for each drug that could be applied in PBPK modeling systems. Overall the approach provides a novel overview of intestinal solubility topography along with greater detail on the impact of the various factors studied; however, each matrix requires 351 individual solubility measurements. Further studies will be required to refine the experimental protocol in order the maximize information garnered while minimizing the number of measurements required.", "token_count": 518, "char_count": 2317, "word_count": 326, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:29:45.325719", "source": { "split": "train_shard_00000", "doc_id": 3102 }, "chunk_id": "train_shard_00000_3102_0", "global_id": 3432 }, { "text": "Topography of Simulated Intestinal Equilibrium Solubility.", "token_count": 14, "char_count": 58, "word_count": 6, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:45.668215", "source": { "split": "train_shard_00000", "doc_id": 3102 }, "chunk_id": "train_shard_00000_3102_1", "global_id": 3433 }, { "text": "Bile salt hydrolases: Gatekeepers of bile acid metabolism and host-microbiome crosstalk in the gastrointestinal tract.", "token_count": 37, "char_count": 118, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:46.022567", "source": { "split": "train_shard_00000", "doc_id": 3103 }, "chunk_id": "train_shard_00000_3103_0", "global_id": 3434 }, { "text": "Hypercholesterolemia is closely associated with cardiovascular disease. Supplementation with probiotics has been shown to contribute to improving lipid metabolism. The probiotic mechanisms of cholesterol reduction are complicated and remain unclear. One of the potential probiotic mechanisms for cholesterol reduction is the deconjugation of bile salts. We previously found a high bile salt hydrolase (BSH) activity of Lactobacillus casei pWQH01 (overexpression of bsh1) and Lactobacillus plantarum AR113, but found no BSH activity for Lactobacillus casei LC2W in vitro. Therefore, we decided to investigate whether the high BSH activity of L. plantarum AR113 and L. casei pWQH01 could exert a cholesterol-reducing effect in vivo. Compared to the high-cholesterol diet (HCD) group, AR113 and pWQH01 groups had a significantly lower body weight (BW), serum total cholesterol (TC), low density lipoprotein cholesterol (LDL-C) levels and atherogenic index (AI), whereas the LC2W group had a poor capability to mitigate the blood lipid levels in the hypercholesterolemic mice. In addition, the AR113 and pWQH01 groups decreased the hepatic levels of TC and LDL-C and improved hepatic steatosis compared with the HCD group. To explore their cholesterol-lowering mechanisms of action, we determined the expression levels of these genes on the cholesterol metabolic pathways. AR113 and pWQH01 groups downregulated the expression of farnesoid X receptor (FXR) and small heterodimer partner (SHP) genes, but upregulated the expression of the cholesterol 7α-hydroxylase (CYP7A1) gene in the liver. Simultaneously, the expression of cholesterol liver X receptor (LXR) and low density lipoprotein receptor (LDLR) genes was upregulated in the liver. These results indicated that L. plantarum AR113 and L", "token_count": 524, "char_count": 1790, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5525, "quality_score": 0.7763, "entities": { "genes": [ "AR113", "LC2W" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:29:46.655013", "source": { "split": "train_shard_00000", "doc_id": 3104 }, "chunk_id": "train_shard_00000_3104_0", "global_id": 3435 }, { "text": "casei pWQH01 could inhibit the cholesterol absorption and accelerate the cholesterol transportation. Taken together, these findings suggest that Lactobacillus strain overexpression of bile salt hydrolase has beneficial effects against hypercholesterolemia by reducing cholesterol absorption and increasing cholesterol catabolism.\n\nCholesterol-lowering potentials of Lactobacillus strain overexpression of bile salt hydrolase on high cholesterol diet-induced hypercholesterolemic mice.", "token_count": 126, "char_count": 484, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:47.038957", "source": { "split": "train_shard_00000", "doc_id": 3104 }, "chunk_id": "train_shard_00000_3104_1", "global_id": 3436 }, { "text": "Bile salt hydrolases involved in the effectiveness of FMT for Clostridium difficile infection.", "token_count": 23, "char_count": 94, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:47.401325", "source": { "split": "train_shard_00000", "doc_id": 3105 }, "chunk_id": "train_shard_00000_3105_0", "global_id": 3437 }, { "text": "The vaginal microbiota of healthy women is dominated by lactobacilli, which exerts important health-promoting effects to the host. In the present study, 261 lactobacilli isolated from vagina of healthy women were screened for their potential probiotic characteristics. Safety features (haemolytic activity, antibiotic susceptibility, bile salt hydrolase activity) and functional properties (resistance to low pH and bile salts, lysozyme tolerance, gastrointestinal survival, antagonistic activity against pathogens, hydrophobicity, auto-aggregation, and co-aggregation abilities, hydrogen peroxide production, biofilm formation, exopolysaccharide production, adhesion capacity to both normal human vagina epithelial cells and Caco-2 epithelial cells, and lactic acid production) were in depth evaluated. Seven strains, identified as Lactobacillus rhamnosus, Lactobacillus helveticus and Lactobacillus salivarius fulfilled the criteria described above. Therefore, the vaginal ecosystem represents a suitable source of probiotic candidates that could be used in new functional formulates for both gastrointestinal and vaginal eubiosis.\n\nDetection of vaginal lactobacilli as probiotic candidates.", "token_count": 301, "char_count": 1193, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7466, "quality_score": 0.8733, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:47.956940", "source": { "split": "train_shard_00000", "doc_id": 3106 }, "chunk_id": "train_shard_00000_3106_0", "global_id": 3438 }, { "text": "The Asparagaceae family is endemic from America, being the Agave genus the most important. The Agave species possess economic relevance and are use as raw material to produce several distilled alcoholic beverages, as bacanora, tequila, and mezcal. The fermentation process has been carry out either spontaneously or by adding a selected yeast strain. The latter is generally responsible for the production of ethanol and volatile compounds. This study comprised five Agave species (A. angustifolia, A. cupreata, A. durangensis, A. salmiana, and A. tequilana) and eight endogenous yeast strains: five of them were non-Saccharomyces (Torulaspora delbrueckii, Zygosaccharomyces bisporus, Candida ethanolica, and two Kluyveromyces marxianus) and three Saccharomyces cerevisiae strains. The results showed that the S. cerevisiae strains were not able to grow on A. durangensis and A. salmiana juices. The Kluyveromyces marxianus strains grew and fermented all the agave juices and displayed high ethanol production (48-52 g L\n\nFermentative capabilities of native yeast strains grown on juices from different Agave species used for tequila and mezcal production.", "token_count": 324, "char_count": 1156, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6988, "quality_score": 0.8494, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:48.521319", "source": { "split": "train_shard_00000", "doc_id": 3107 }, "chunk_id": "train_shard_00000_3107_0", "global_id": 3439 }, { "text": "Vibrio cholerae, the causative agent of severe watery diarrheal disease cholera, requires production of a number of virulence factors during infection which results from the activity of a cascading system of regulatory factors by sensing to different environmental signals. TcpP, a membrane-localized transcription activator in V. cholerae, activates virulence factors production by responding to human host signals. To better characterize the transmembrane helix in regard to its roles on TcpP positive effectors sensitivity, site-directed mutagenesis was performed to identify specific mutations in this region which could enhance TcpP transcription activity in the absence of stimuli, like bile salts. We found that TcpP L152A constitutively forms homodimer and activates toxT expression in the absence of bile salts. However, being active, TcpP L152A needs to form disulfide bonds between the cysteine residues in the periplasmic domain of TcpP. We also found that TcpP L152A showed a competitive advantage in the infant mouse colonization model by coadministrating the bile salt-sequestering resin cholestyramine. All these results demonstrate that the transmembrane helix of TcpP plays an important role in regulating TcpP transcription activity in response to its positive effectors.\n\nTcpP L152A Constitutively Activating Virulence Gene Expression in Vibrio cholerae.", "token_count": 343, "char_count": 1374, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:49.087706", "source": { "split": "train_shard_00000", "doc_id": 3108 }, "chunk_id": "train_shard_00000_3108_0", "global_id": 3440 }, { "text": "Strains of Lactobacillus sakei can be isolated from a variety of sources including meat, fermented sausages, sake, sourdough, sauerkraut or kimchi. Selected strains are widely used as starter cultures for sausage fermentation. Recently we have demonstrated that control about the lactic microbiota in fermenting sausages is achieved rather by pairs or strain sets than by single strains. In this work we characterized the pan genome of L. sakei to enable exploitation of the genomic diversity of L. sakei for the establishment of assertive starter strain sets. We have established the full genome sequences of nine L. sakei strains from different sources of isolation and included in the analysis the genome of L. sakei 23K. Comparative genomics revealed an accessory genome comprising about 50% of the pan genome and different lineages of strains with no relation to their source of isolation. Group and strain specific differences could be found, which namely referred to agmatine and citrate metabolism. The presence of genes encoding metabolic pathways for fructose, sucrose and trehalose as well as gluconate in all strains suggests a general adaptation to plant/sugary environments and a life in communities with other genera. Analysis of the plasmidome did not reveal any specific mechanisms of adaptation to a habitat. The predicted differences of metabolic settings enable prediction of partner strains, which can occupy the meat environment to a large extent and establish competitive exclusion of autochthonous microbiota. This may assist the development of a new generation of meat starter cultures containing L. sakei strains.\n\nComparative genomics of Lactobacillus sakei supports the development of starter strain combinations.", "token_count": 393, "char_count": 1741, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:49.701829", "source": { "split": "train_shard_00000", "doc_id": 3109 }, "chunk_id": "train_shard_00000_3109_0", "global_id": 3441 }, { "text": "Faecal microbiota transplant (FMT) effectively treats recurrent\n\nMicrobial bile salt hydrolases mediate the efficacy of faecal microbiota transplant in the treatment of recurrent", "token_count": 48, "char_count": 178, "word_count": 23, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:50.059875", "source": { "split": "train_shard_00000", "doc_id": 3110 }, "chunk_id": "train_shard_00000_3110_0", "global_id": 3442 }, { "text": "This study describes the use of alternative operational strategies in the solid-state fermentation of the agro-industrial leftover sugar cane bagasse (SCB) supplemented with l-phenylalanine, for bioproducing natural 2-phenylethanol (2-PE) and 2-phenethyl acetate (2-PEA) using K. marxianus. Here, fed-batch and sequential-batch have been assessed at two scales (1.6 and 22 L) as tools to increase the production, as well as to enhance the sustainability of this residue-based process. While in the reference batch strategy a maximum of 17 mg of 2-PE+2-PEA per gram of added SCB was reached at both scales, the implementation of fed-batch mode induced a production increase of 11.6% and 12.5%, respectively. Also, the production was increased by 16.9% and 2.4% as compared to the batch when a sequential-batch mode was used. Furthermore, the use of these strategies was accompanied by lower consumption of key resources like the inoculum, air, and time, promoting savings between 22% and 76% at both scales.\n\nFed-Batch and Sequential-Batch Approaches To Enhance the Bioproduction of 2-Phenylethanol and 2-Phenethyl Acetate in Solid-State Fermentation Residue-Based Systems.", "token_count": 337, "char_count": 1172, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6257, "quality_score": 0.8129, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:50.624030", "source": { "split": "train_shard_00000", "doc_id": 3111 }, "chunk_id": "train_shard_00000_3111_0", "global_id": 3443 }, { "text": "Sesquizygotic multiple pregnancy is an exceptional intermediate between monozygotic and dizygotic twinning. We report a monochorionic twin pregnancy with fetal sex discordance. Genotyping of amniotic fluid from each sac showed that the twins were maternally identical but chimerically shared 78% of their paternal genome, which makes them genetically in between monozygotic and dizygotic; they are sesquizygotic. We observed no evidence of sesquizygosis in 968 dizygotic twin pairs whom we screened by means of pangenome single-nucleotide polymorphism genotyping. Data from published repositories also show that sesquizygosis is a rare event. Detailed genotyping implicates chimerism arising at the juncture of zygotic division, termed heterogonesis, as the likely initial step in the causation of sesquizygosis.\n\nMolecular Support for Heterogonesis Resulting in Sesquizygotic Twinning.", "token_count": 252, "char_count": 886, "word_count": 120, "semantic_coherence": 1, "information_density": 0.775, "quality_score": 0.8875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:51.112309", "source": { "split": "train_shard_00000", "doc_id": 3112 }, "chunk_id": "train_shard_00000_3112_0", "global_id": 3444 }, { "text": "The extent of human intestinal absorption (HIA) for a drug is considered to be an important pharmacokinetic parameter which must be determined for orally administered drugs. Traditional experimental methods relied upon animal testing and are renowned for being time consuming and expensive as well as being ethically unfavourable. As a result, the development of alternative methods to evaluate a drug's pharmacokinetics is crucial. Micellar liquid chromatography is considered to be one of these methods that can replace the use of animals in the prediction of HIA. In this study, the combination of an aminopropyl column with the biosurfactant sodium deoxycholate bile salt was used in the experimental determination of micelle-water partition coefficients (log P\n\nPrediction of human intestinal absorption using micellar liquid chromatography with an aminopropyl stationary phase.", "token_count": 196, "char_count": 883, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:51.561401", "source": { "split": "train_shard_00000", "doc_id": 3113 }, "chunk_id": "train_shard_00000_3113_0", "global_id": 3445 }, { "text": "The objective of the studies reported in this research communication was to investigate the use of whey contaminated with antibiotics such as cephalosporins, quinolones and tetracyclines as a nutrient medium for the growth of Kluyveromyces marxianus with particular attention to the effect of thermal treatment used to overcome the inhibitory effects of antibiotic concentrations close to the Maximum Residue Limits. The heat treatments at 120 °C for 40 min, 120 °C for 83 min, and 120 °C for 91 min caused total inactivation of cephalosporins, tetracyclines and quinolone residues in whey respectively.\n\nEffect of thermal treatment of whey contaminated with antibiotics on the growth of Kluyveromyces marxianus.", "token_count": 195, "char_count": 712, "word_count": 107, "semantic_coherence": 1, "information_density": 0.5888, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:52.007109", "source": { "split": "train_shard_00000", "doc_id": 3114 }, "chunk_id": "train_shard_00000_3114_0", "global_id": 3446 }, { "text": "Orphan genes (also known as ORFans [i.e., orphan open reading frames]) are new genes that enable an organism to adapt to its specific living environment. Our focus in this study is to compare ORFans between pathogens (P) and nonpathogens (NP) of the same genus. Using the pangenome idea, we have identified 130,169 ORFans in nine bacterial genera (505 genomes) and classified these ORFans into four groups: (i) SS-ORFans (P), which are only found in a single pathogenic genome; (ii) SS-ORFans (NP), which are only found in a single nonpathogenic genome; (iii) PS-ORFans (P), which are found in multiple pathogenic genomes; and (iv) NS-ORFans (NP), which are found in multiple nonpathogenic genomes. Within the same genus, pathogens do not always have more genes, more ORFans, or more pathogenicity-related genes (PRGs)-including prophages, pathogenicity islands (PAIs), virulence factors (VFs), and horizontal gene transfers (HGTs)-than nonpathogens. Interestingly, in pathogens of the nine genera, the percentages of PS-ORFans are consistently higher than those of SS-ORFans, which is not true in nonpathogens. Similarly, in pathogens of the nine genera, the percentages of PS-ORFans matching the four types of PRGs are also always higher than those of SS-ORFans, but this is not true in nonpathogens. All of these findings suggest the greater importance of PS-ORFans for bacterial pathogenicity.\n\nOrphan Genes Shared by Pathogenic Genomes Are More Associated with Bacterial Pathogenicity.", "token_count": 421, "char_count": 1490, "word_count": 223, "semantic_coherence": 1, "information_density": 0.565, "quality_score": 0.7825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:52.629342", "source": { "split": "train_shard_00000", "doc_id": 3115 }, "chunk_id": "train_shard_00000_3115_0", "global_id": 3447 }, { "text": "Although the pan and the core genome of Acinetobacter baumannii and its essential genes are relatively well characterized, functional characterization of these genes has not paralleled the genome-level studies. However, recently developed genetic tools and optimized protocols are poised to accelerate genetic manipulation of A. baumannii. Transferring exogenous DNA into the cytosol of bacteria cells is a critical step in genetic characterizations. Conjugation is restricted to the transfer of DNA from one bacterial cell to another, and only a portion of A. baumannii clinical isolates are naturally competent. Electroporation, which is thought to transiently create aqueous pores in the membrane, is a preferred method in transferring exogenous DNA as it does not have such limitations. Several factors contribute to efficiency of electroporation and often need to be empirically optimized to maximize efficiency of this procedure. Here we provide an optimized electroporation protocol and guidance for electroporation of clinical MDR isolates of A. baumannii.\n\nTransformation of Acinetobacter baumannii: Electroporation.", "token_count": 250, "char_count": 1125, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6519, "quality_score": 0.8259, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:53.114424", "source": { "split": "train_shard_00000", "doc_id": 3116 }, "chunk_id": "train_shard_00000_3116_0", "global_id": 3448 }, { "text": "To identify the mechanism in which way maltodextrin enhance bile tolerance in Lactobacillus plantarum Lp-115.\n\nEnhancement of bile resistance by maltodextrin supplementation in Lactobacillus plantarum Lp-115.", "token_count": 70, "char_count": 208, "word_count": 26, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:53.483428", "source": { "split": "train_shard_00000", "doc_id": 3117 }, "chunk_id": "train_shard_00000_3117_0", "global_id": 3449 }, { "text": "In obstructive cholestasis, there is an integral adaptive response aimed to diminish the bile flow and minimize the injury of bile ducts caused by increased intraluminal pressure and harmful levels of bile salts and bilirrubin. Canalicular bicarbonate secretion, driven by the anion exchanger 2 (AE2), is an influential determinant of the canalicular bile salt-independent bile flow. In this work, we ascertained whether AE2 expression and/or activity is reduced in hepatocytes from rats with common bile duct ligation (BDL), as part of the adaptive response to cholestasis. After 4 days of BDL, we found that neither AE2 mRNA expression (measured by quantitative real-time PCR) nor total levels of AE2 protein (assessed by western blot) were modified in freshly isolated hepatocytes. However, BDL led to a decrease in the expression of AE2 protein in plasma membrane fraction as compared with SHAM control. Additionally, AE2 activity (JOH-, mmol/L/min), measured in primary cultured hepatocytes from BDL and SHAM rats, was decreased in the BDL group versus the control group (1.9 ± 0.3 vs. 3.1 ± 0.2, p<0.005). cAMP-stimulated AE2 activity, however, was not different between SHAM and BDL groups (3.7 ± 0.3 vs. 3.5 ± 0.3), suggesting that cAMP stimulated insertion into the canalicular membrane of AE2-containing intracellular vesicles, that had remained abnormally internalized after BDL. In conclusion, our results point to the existence of a novel adaptive mechanism in cholestasis aimed to reduce biliary pressure, in which AE2 internalization in hepatocytes might result in decreased canalicular HCO3- output and decreased bile flow.\n\nAdaptive downregulation of Cl-/HCO3- exchange activity in rat hepatocytes under experimental obstructive cholestasis.", "token_count": 491, "char_count": 1758, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [ "HCO3", "AE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:54.131691", "source": { "split": "train_shard_00000", "doc_id": 3118 }, "chunk_id": "train_shard_00000_3118_0", "global_id": 3450 }, { "text": "Attention to environmental sources of Mycobacterium avium complex (MAC) infection is a vital component of disease prevention and control. We investigated MAC colonization of household plumbing in suburban Philadelphia, Pennsylvania, USA. We used variable-number tandem-repeat genotyping and whole-genome sequencing with core genome single-nucleotide variant analysis to compare M. avium from household plumbing biofilms with M. avium isolates from patient respiratory specimens. M. avium was recovered from 30 (81.1%) of 37 households, including 19 (90.5%) of 21 M. avium patient households. For 11 (52.4%) of 21 patients with M. avium disease, isolates recovered from their respiratory and household samples were of the same genotype. Within the same community, 18 (85.7%) of 21 M. avium respiratory isolates genotypically matched household plumbing isolates. Six predominant genotypes were recovered across multiple households and respiratory specimens. M. avium colonizing municipal water and household plumbing may be a substantial source of MAC pulmonary infection.\n\nMycobacterium avium in Community and Household Water, Suburban Philadelphia, Pennsylvania, USA, 2010-2012.", "token_count": 308, "char_count": 1178, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:54.735481", "source": { "split": "train_shard_00000", "doc_id": 3119 }, "chunk_id": "train_shard_00000_3119_0", "global_id": 3451 }, { "text": "During a randomized Phase 1 clinical trial the drug candidate, PF-04895162 (ICA-105665), caused transaminase elevations (≥grade 1) in six of eight healthy subjects treated at 300 mg twice daily for 2-weeks (NCT01691274). This was unexpected since studies in rats (<6 months) and cynomolgus monkeys (<9 months) treated up to 100 mg/kg/day did not identify the liver as a target organ. Mechanistic studies showed PF-04895162 had low cytotoxic potential in human hepatocytes, but inhibited liver mitochondrial function and bile salt export protein (BSEP) transport. Clinical relevance of these postulated mechanisms of liver injury was explored in three treated subjects that consented to analysis of residual pharmacokinetic plasma samples. Compared to a nonresponder, two subjects with transaminase elevations displayed higher levels of miRNA122 and total/conjugated bile acid species, whereas one demonstrated impaired postprandial clearance of systemic bile acids. Elevated taurine and glycine conjugated to unconjugated bile acid ratios were observed in two subjects, one before the onset of elevated transaminases. Based on the affinity of conjugated bile acid species for transport by BSEP, the profile of plasma conjugated/unconjugated bile acid species was consistent with inhibition of BSEP. These data collectively suggest that the human liver injury by PF-04895162 was due to alterations in bile acid handling driven by dual BSEP/mitochondrial inhibition, two important risk factors associated with drug-induced liver injury in humans. Alterations in systemic bile acid composition were more important than total bile acids in the manifestation of clinical liver injury and may be a very early biomarker of BSEP inhibition.", "token_count": 471, "char_count": 1732, "word_count": 250, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [ "NCT01691274" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:55.404869", "source": { "split": "train_shard_00000", "doc_id": 3120 }, "chunk_id": "train_shard_00000_3120_0", "global_id": 3452 }, { "text": "Phase I study of PF‐04895162, a Kv7 channel opener, reveals unexpected hepatotoxicity in healthy subjects, but not rats or monkeys: clinical evidence of disrupted bile acid homeostasis.", "token_count": 55, "char_count": 185, "word_count": 27, "semantic_coherence": 1, "information_density": 0.963, "quality_score": 0.9815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:55.786727", "source": { "split": "train_shard_00000", "doc_id": 3120 }, "chunk_id": "train_shard_00000_3120_1", "global_id": 3453 }, { "text": "Probiotics are well known for their wide range of beneficial activities. However, recent use of probiotic Bifidobacterium, Enterococcus, and Lactobacillus spp. has been plagued by certain disadvantages such as complex growth requirements, high maintenance cost, susceptibility to the gastrointestinal environment, pathogenic gene transfer, non-standardized dosage, cell lysis at extreme acidic pH, widespread antibiotic resistance, and lower bacterial viability due to the lack of spore formation. Therefore, spore-forming bacteria belonging to Sporosarcina genus such as pasteurii, globispora, and psychrophila were assessed for probiotic characteristics such as biofilm formation, intestinal adhesion, acid and bile tolerance, antibiotic sensitivity, and anti-pathogenic activity. This ensures bacterial viability under gastrointestinal conditions and enabled the same to colonize effectively in the intestinal lumen (in vitro). The bacterial cell counts ranging from 6.59 to 6.91 log(CFU/mL) was observed for Sporosarcina spp. after 16 h. This indicated that there is no significant difference in the cell counts (P-value = 0.90). The cell counts of Sporosarcina spp. ranging from 5.57 to 5.93 log(CFU/mL) displayed strong acid tolerance at pH 2. They were also viable at higher bile (0.5%) concentration. Among the Sporosarcina spp., pasteurii showed better tolerance (6.90 log(CFU/mL)) even after 16 h. Among the selected bacteria, Sporosarcina psychrophila was more susceptible to teicoplanin and meropenem with an inhibition zone of 30 mm. Maximum antagonistic activity was observed against Serratia marcescens (with inhibition zone up to 15 mm). Our results suggest that bacteria belonging to Sporosarcina genus possess all the required characteristics to be used as potential poultry probiotics.", "token_count": 493, "char_count": 1804, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6787, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:56.475013", "source": { "split": "train_shard_00000", "doc_id": 3121 }, "chunk_id": "train_shard_00000_3121_0", "global_id": 3454 }, { "text": "A Preliminary Study on Probiotic Characteristics of Sporosarcina spp. for Poultry Applications.", "token_count": 26, "char_count": 95, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:56.830075", "source": { "split": "train_shard_00000", "doc_id": 3121 }, "chunk_id": "train_shard_00000_3121_1", "global_id": 3455 }, { "text": "The 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced in the United States in 2010. Using a large paediatric carriage sample collected from shortly after the introduction of PCV-7 to several years after the introduction of PCV-13, we investigate alterations in the composition of the pneumococcal population following the introduction of PCV-13, evaluating the extent to which the post-vaccination non-vaccine type (NVT) population mirrors that from prior to vaccine introduction and the effect of PCV-13 on vaccine type lineages. Draft genome assemblies from 736 newly sequenced and 616 previously published pneumococcal carriage isolates from children in Massachusetts between 2001 and 2014 were analysed. Isolates were classified into one of 22 sequence clusters (SCs) on the basis of their core genome sequence. We calculated the SC diversity for each sampling period as the probability that any two randomly drawn isolates from that period belong to different SCs. The sampling period immediately after the introduction of PCV-13 (2011) was found to have higher diversity than preceding (2007) or subsequent (2014) sampling periods {Simpson's D 2007: 0.915 [95 % confidence interval (CI) 0.901, 0.929]; 2011:  0.935 [0.927, 0.942]; 2014 :  0.912 [0.901, 0.923]}. Amongst NVT isolates, we found the distribution of SCs in 2011 to be significantly different from that in 2007 or 2014 (Fisher's exact test P=0.018, 0.0078), but did not find a difference comparing 2007 to 2014 (Fisher's exact test P=0.24), indicating greater similarity between samples separated by a longer time period than between samples from closer time periods", "token_count": 499, "char_count": 1649, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:57.479042", "source": { "split": "train_shard_00000", "doc_id": 3122 }, "chunk_id": "train_shard_00000_3122_0", "global_id": 3456 }, { "text": "We also found changes in the accessory gene content of the NVT population between 2007 and 2011 to have been reduced by 2014. Amongst the new serotypes targeted by PCV-13, four were present in our sample. The proportion of our sample composed of PCV-13-only vaccine serotypes 19A, 6C and 7F decreased between 2007 and 2014, but no such reduction was seen for serotype 3. We did, however, observe differences in the genetic composition of the pre- and post-PCV-13 serotype 3 population. Our isolates were collected during discrete sampling periods from a small geographical area, which may limit the generalizability of our findings. Pneumococcal diversity increased immediately following the introduction of PCV-13, but subsequently returned to pre-vaccination levels. This is reflected in the distribution of NVT lineages, and, to a lesser extent, their accessory gene frequencies. As such, there may be a period during which the population is particularly disrupted by vaccination before returning to a more stable distribution. The persistence and shifting genetic composition of serotype 3 is a concern and warrants further investigation.\n\nPopulation genomics of pneumococcal carriage in Massachusetts children following introduction of PCV-13.", "token_count": 301, "char_count": 1248, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:58.042442", "source": { "split": "train_shard_00000", "doc_id": 3122 }, "chunk_id": "train_shard_00000_3122_1", "global_id": 3457 }, { "text": "Probiotics are known for their health-promoting abilities through the production of various metabolites, and also benefits are membrane associated. Probiotic Enterococcus faecalis AG5 has been previously assessed for its probiotic properties and this study further strengthens that claim. Strain AG5 was inoculated with 0.3% sodium glychocholate (glycine conjugated) and bile salt mixture for different time periods. The percentage assimilation of cholesterol ranged from 14% to 33.1% in the bile salt mixture, but was slightly higher, ranging from 16.55% to 53.1%, in sodium thioglycocholate alone. Similarly, the bile salt hydrolysis activity was measured in terms of cholic acid release at different intervals. The overall range of cholic acid released ranged from 70.4 to 479 µg/mL. Fatty acid production is also an important criterion for a probiotic selection and it was found that the strain produced several long-chain fatty acids (LCFA) such as tetradecanoic acid, hexadecanoic acid, octadecanoic acid and bis(6-methylheptyl) phthalate. Besides LCFA, AG5 produced short-chain fatty acids (SCFA) such as propionic acid, which was estimated comparing liquid chromatography and mass spectrometry with standard SCFA. Thus the ability of deconjugation of bile salt and SCFA production is a value-added property of probiotic AG5, with the promise of being beneficial for human health.\n\nProbiotic Enterococcus faecalis AG5 effectively assimilates cholesterol and produces fatty acids including propionate.", "token_count": 409, "char_count": 1507, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8178, "entities": { "genes": [ "AG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:58.657636", "source": { "split": "train_shard_00000", "doc_id": 3123 }, "chunk_id": "train_shard_00000_3123_0", "global_id": 3458 }, { "text": "Bacillus cytotoxicus is a member of the Bacillus cereus group linked to fatal cases of diarrheal disease. Information on B. cytotoxicus is very limited; in particular comprehensive genomic data is lacking. Thus, we applied a genomic approach to characterize B. cytotoxicus and decipher its population structure. To this end, complete genomes of ten B. cytotoxicus were sequenced and compared to the four publicly available full B. cytotoxicus genomes and genomes of other B. cereus group members. Average nucleotide identity, core genome, and pan genome clustering resulted in clear distinction of B. cytotoxicus strains from other strains of the B. cereus group. Genomic content analyses showed that a hydroxyphenylalanine operon is present in B. cytotoxicus, but absent in all other members of the B. cereus group. It enables degradation of aromatic compounds to succinate and pyruvate and was likely acquired from another Bacillus species. It allows for utilization of tyrosine and might have given a B. cytotoxicus ancestor an evolutionary advantage resulting in species differentiation. Plasmid content showed that B. cytotoxicus is flexible in exchanging genes, allowing for quick adaptation to the environment. Genome-based phylogenetic analyses divided the B. cytotoxicus strains into four clades that also differed in virulence gene content.\n\nWhole-genome-based phylogeny of Bacillus cytotoxicus reveals different clades within the species and provides clues on ecology and evolution.", "token_count": 370, "char_count": 1493, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7959, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:59.246707", "source": { "split": "train_shard_00000", "doc_id": 3124 }, "chunk_id": "train_shard_00000_3124_0", "global_id": 3459 }, { "text": "Nowadays, phage therapy emerges as one of the alternative solutions to the problems arising from antibiotic resistance in pathogenic bacteria. Although phage therapy has been successfully applied both in vitro and in vivo, one of the biggest concerns in this regard is the stability of phages in body environment. Within the scope of this study, microencapsulation technology was used to increase the resistance of phages to physiological conditions, and the resulting microcapsules were tested in environments simulating body conditions. For this purpose, Bacillus subtilis, Salmonella enterica subsp. enterica serovar Enteritidis (Salmonella Enteritidis), and Salmonella enterica subsp. enterica serovar Typhimurium (Salmonella Typhimurium) phages were isolated from different sources and then microencapsulated with 1.33% (w/v) sodium alginate using a spray dryer to minimize the damage of physiological environment. Stability of microcapsules in simulated gastric fluid and bile salt presence was tested. As a consequence, the maximum titer decrease of microencapsulated phages after 2-h incubation was found to be 2.29 log unit for B. subtilis phages, 1.71 log unit for S. Enteritidis phages, and 0.60 log unit for S. Typhimurium phages, while free phages lost their viability even after a 15-min incubation. Similarly, microencapsulation was found to increase the stability of phages in the bile salt medium and it was seen that after 3 h of incubation, the difference between the titers of microencapsulated phages and free phages could reach up to 3 log unit.\n\nMicroencapsulation of phages to analyze their demeanor in physiological conditions.", "token_count": 423, "char_count": 1652, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5496, "quality_score": 0.7748, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:29:59.872717", "source": { "split": "train_shard_00000", "doc_id": 3125 }, "chunk_id": "train_shard_00000_3125_0", "global_id": 3460 }, { "text": "Citric acid is considered as the most economically feasible product of microbiological production, therefore studies on cheap and renewable raw materials for its production are highly desirable. In this study citric acid was synthesized by genetically engineered strains of Yarrowia lipolytica from widely available, renewable polysaccharide - inulin. Hydrolysis of inulin by the Y. lipolytica strains was established by expressing the inulinase gene (INU1 gene; GenBank: X57202.1) with its native secretion signal sequence was amplified from genomic DNA from Kluyveromyces marxianus CBS6432. To ensure the maximum citric acid titer, the optimal cultivation strategy-repeated-batch culture was applied.\n\nProduction of high titer of citric acid from inulin.", "token_count": 192, "char_count": 756, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [ "CBS6432", "INU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:00.325205", "source": { "split": "train_shard_00000", "doc_id": 3126 }, "chunk_id": "train_shard_00000_3126_0", "global_id": 3461 }, { "text": "As potential probiotic traits of human milk-isolated bacteria have increasingly been recognized, this study aimed to evaluate the probiotic properties of bacteriocin-producing Enterococcus faecium strains isolated from human milk and colostrum. Among 118 human milk- and colostrum-isolated lactic cocci, only 29 were identified as Enterococcus. Of these, only four Enterococcus faecium isolates exhibited bacteriocigenic activity against several pathogenic Gram-positive bacteria, including Listeria monocytogenes. These isolates exhibited high acid (up to pH 3.0) and bile tolerance (0.5% oxgall) in simulated gastrointestinal conditions, demonstrating their ability to survive through the upper gastrointestinal tract. All of the E. faecium strains were shown to be sensitive to most of the antibiotics including vancomycin, tetracycline, rifampicin, and erythromycin, while they were resistant to kanamycin and chloramphenicol. None of the strains showed any virulence (gelE, agg2, clyA, clyB, clyM) and antibiotic resistance genes (vanA, vanB, ermB, tetM, and aac(6')-le-aph(2″)-la). In addition, all the strains were able to assimilate cholesterol, ranging between 25.2-64.1% and they exhibited variable adherence (19-36%) to Caco-2 cells. Based on the overall results of this in vitro study, four of the E. faecium strains isolated from human milk and colostrum can be considered as promising probiotic candidates; however, further in vivo evaluations are required.\n\nProbiotic characteristics of bacteriocin-producing Enterococcus faecium strains isolated from human milk and colostrum.", "token_count": 450, "char_count": 1592, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:00.962097", "source": { "split": "train_shard_00000", "doc_id": 3127 }, "chunk_id": "train_shard_00000_3127_0", "global_id": 3462 }, { "text": "Yeast was the first microorganism used by mankind for biotransformation of feedstock that laid the foundations of industrial biotechnology. Long historical use, vast amount of data, and experience paved the way for Saccharomyces cerevisiae as a first yeast cell factory, and still it is an important expression platform as being the production host for several large volume products. Continuing special needs of each targeted product and different requirements of bioprocess operations have led to identification of different yeast expression systems. Modern bioprocess engineering and advances in omics technology, i.e., genomics, transcriptomics, proteomics, secretomics, and interactomics, allow the design of novel genetic tools with fine-tuned characteristics to be used for research and industrial applications. This chapter focuses on established and upcoming yeast expression platforms that have exceptional characteristics, such as the ability to utilize a broad range of carbon sources or remarkable resistance to various stress conditions. Besides the conventional yeast S. cerevisiae, established yeast expression systems including the methylotrophic yeasts Pichia pastoris and Hansenula polymorpha, the dimorphic yeasts Arxula adeninivorans and Yarrowia lipolytica, the lactose-utilizing yeast Kluyveromyces lactis, the fission yeast Schizosaccharomyces pombe, and upcoming yeast platforms, namely, Kluyveromyces marxianus, Candida utilis, and Zygosaccharomyces bailii, are compiled with special emphasis on their genetic toolbox for recombinant protein production.\n\nEstablished and Upcoming Yeast Expression Systems.", "token_count": 372, "char_count": 1630, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:01.543463", "source": { "split": "train_shard_00000", "doc_id": 3128 }, "chunk_id": "train_shard_00000_3128_0", "global_id": 3463 }, { "text": "Lactobacillus mucosae DPC 6426 has previously demonstrated potentially cardio-protective properties, in the form of dyslipidaemia and hypercholesterolemia correction in an apolipoprotein-E deficient mouse model. This study aims to characterise the manner in which this microbe may modulate host bile pool composition and immune response, in the context of cardiovascular disease. Lactobacillus mucosae DPC 6426 was assessed for bile salt hydrolase activity and specificity. The microbe was compared against several other enteric strains of the same species, as well as a confirmed bile salt hydrolase-active strain, Lactobacillus reuteri APC 2587.\n\nLactobacillus mucosae DPC 6426 as a bile-modifying and immunomodulatory microbe.", "token_count": 214, "char_count": 729, "word_count": 99, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:02.008102", "source": { "split": "train_shard_00000", "doc_id": 3129 }, "chunk_id": "train_shard_00000_3129_0", "global_id": 3464 }, { "text": "Probiotics are the healthy living bacteria when administered in adequate amounts confers health benefits in the host. The main objective of present study was to screen the bacteria for potential probiotic characters and enzyme production. The probiotic characters like tolerance to low pH, bile salts, antibiotic sensitivity, hydrophobicity and auto-aggregation properties were evaluated. Among all isolates\n\nScreening of potential probiotic lactic acid bacteria and production of amylase and its partial purification.", "token_count": 111, "char_count": 518, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:02.396434", "source": { "split": "train_shard_00000", "doc_id": 3130 }, "chunk_id": "train_shard_00000_3130_0", "global_id": 3465 }, { "text": "The habenula (Hb) plays important roles in emotion-related behaviors. Besides receiving inputs from the limbic system and basal ganglia, Hb also gets inputs from multiple sensory modalities. Sensory responses of Hb neurons in zebrafish are asymmetrical: the left dorsal Hb and right dorsal Hb (dHb) preferentially respond to visual and olfactory stimuli, respectively, implying different functions of the left and right dHb. While visual responses of the left dHb (L-dHb) have been implicated in light-preference behavior, the significance of olfactory responses of the right dHb (R-dHb) remains under-examined. It was reported that the R-dHb can gate innate attraction to a bile salt. However, considering a broad range of odors that R-dHb respond to, it is of interest to examine the role of R-dHb in other olfactory behaviors, especially food seeking, which is essential for animals' survival. Here, using in vivo whole-cell recording and calcium imaging, we first characterized food extract-evoked responses of Hb neurons. Responsive neurons preferentially locate in the R- but not L-dHb and exhibit either ON- (~87%) or OFF-type responses (~13%). Interestingly, this right-to-left asymmetry of olfactory responses converts into a ventral-to-dorsal pattern in the interpeduncular nucleus (IPN), a main downstream target of Hb. Combining behavior assay, we further found that genetic dysfunction or lesion of the R-dHb and its corresponding downstream ventral IPN (V-IPN) impair the food seeking-associated increase of swimming activity. Thus, our study indicates that the asymmetrical olfactory response in the R-dHb to V-IPN pathway plays an important role in food-seeking behavior of zebrafish larvae.\n\nRole of Olfactorily Responsive Neurons in the Right Dorsal Habenula-Ventral Interpeduncular Nucleus Pathway in Food-Seeking Behaviors of Larval Zebrafish.", "token_count": 501, "char_count": 1863, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:03.048940", "source": { "split": "train_shard_00000", "doc_id": 3131 }, "chunk_id": "train_shard_00000_3131_0", "global_id": 3466 }, { "text": "Several ABC transporters of the human liver are responsible for the secretion of bile salts, lipids and cholesterol. Their interplay protects the biliary tree from the harsh detergent activity of bile salts. Among these transporters, ABCB4 is essential for the translocation of phosphatidylcholine (PC) lipids from the inner to the outer leaflet of the canalicular membrane of hepatocytes. ABCB4 deficiency can result in altered PC to bile salt ratios, which led to intrahepatic cholestasis of pregnancy, low phospholipid associated cholelithiasis, drug induced liver injury or even progressive familial intrahepatic cholestasis type 3. Although PC lipids only account for 30-40% of the lipids in the canalicular membrane, 95% of all phospholipids in bile are PC lipids. We discuss this discrepancy in the light of PC synthesis and bile salts favoring certain lipids. Nevertheless, the in vivo extraction of PC lipids from the outer leaflet of the canalicular membrane by bile salts should be considered as a separate step in bile formation. Therefore, methods to characterize disease causing ABCB4 mutations should be considered carefully, but such an analysis represents a crucial point in understanding the currently unknown transport mechanism of this ABC transporter.\n\nABCB4/MDR3 in health and disease - at the crossroads of biochemistry and medicine.", "token_count": 340, "char_count": 1356, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6127, "quality_score": 0.8064, "entities": { "genes": [ "ABCB4", "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:03.618093", "source": { "split": "train_shard_00000", "doc_id": 3132 }, "chunk_id": "train_shard_00000_3132_0", "global_id": 3467 }, { "text": "Reference genomes are essential for metagenomic analyses and functional characterization of the human gut microbiota. We present the Culturable Genome Reference (CGR), a collection of 1,520 nonredundant, high-quality draft genomes generated from >6,000 bacteria cultivated from fecal samples of healthy humans. Of the 1,520 genomes, which were chosen to cover all major bacterial phyla and genera in the human gut, 264 are not represented in existing reference genome catalogs. We show that this increase in the number of reference bacterial genomes improves the rate of mapping metagenomic sequencing reads from 50% to >70%, enabling higher-resolution descriptions of the human gut microbiome. We use the CGR genomes to annotate functions of 338 bacterial species, showing the utility of this resource for functional studies. We also carry out a pan-genome analysis of 38 important human gut species, which reveals the diversity and specificity of functional enrichment between their core and dispensable genomes.\n\n1,520 reference genomes from cultivated human gut bacteria enable functional microbiome analyses.", "token_count": 267, "char_count": 1113, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:04.171988", "source": { "split": "train_shard_00000", "doc_id": 3133 }, "chunk_id": "train_shard_00000_3133_0", "global_id": 3468 }, { "text": "The microbiota of the mammalian gut plays a dynamic role in controlling host physiology. The effect of gut microbiota activity on host health is particularly evident in the case of bile homeostasis. Bile is produced by the host and is modified by the gut microbiota, which impacts the net hydrophobicity of the total bile acid pool, and also modulates host signaling pathways. A key mechanism by which the microbiota modify bile is through deconjugation of bile salts through bile salt hydrolase (BSH) enzymatic activity, which is postulated to be a prerequisite for all further microbial metabolism. BSH activity in the gut is largely considered to be beneficial for the host, and genes encoding BSHs are found in the genomes of many taxa found in over-the-counter probiotics. Despite the therapeutic relevance of this enzyme, there is no sensitive and simple assay for continuous monitoring of BSH activity, and there are no non-destructive means of characterizing its activity in whole cell or microbial community samples. Herein, we describe a continuous fluorescence assay that can be used for characterization of BSH activity with purified protein, cell lysates, whole cells, and in human gut microbiome samples. The method is a \"turn-on\" reporter strategy, which employs synthetic substrates that yield a fluorescent product upon BSH-dependent turnover. This assay is used to show the first in vivo characterization of BSH activity. We also demonstrate continuous, non-destructive quantification of BSH activity in a human fecal microbiome sample containing recombinant BSH.\n\nA continuous fluorescence assay for simple quantification of bile salt hydrolase activity in the gut microbiome.", "token_count": 407, "char_count": 1695, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5251, "quality_score": 0.7625, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:04.791069", "source": { "split": "train_shard_00000", "doc_id": 3134 }, "chunk_id": "train_shard_00000_3134_0", "global_id": 3469 }, { "text": "Kluyveromyces marxianus is an aerobic yeast and is interested to be applied in many industries. This research was aimed to study the effect of the sterol alternative to ergosterol on the freezing stress of K. marxianus UBU1-11, a thermotolerant yeast. The 0-9 mgL\n\nSurvival of Kluyveromyces marxianus with stigmasterol as subjected to freezing stress.", "token_count": 107, "char_count": 351, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [ "UBU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:05.173636", "source": { "split": "train_shard_00000", "doc_id": 3135 }, "chunk_id": "train_shard_00000_3135_0", "global_id": 3470 }, { "text": "The concept of the species 'pan-genome', the union of 'core' conserved genes and all 'accessory' non-conserved genes across all strains of a species, was first proposed in prokaryotes to account for intraspecific variability. Species pan-genomes have been extensively studied in prokaryotes, but evidence of species pan-genomes has also been demonstrated in eukaryotes such as plants and fungi. Using a previously published methodology based on sequence homology and conserved microsynteny, in addition to bespoke pipelines, we have investigated the pan-genomes of four model fungal species: Saccharomyces cerevisiae, Candida albicans, Cryptococcus neoformans var. grubii and Aspergillus fumigatus. Between 80 and 90 % of gene models per strain in each of these species are core genes that are highly conserved across all strains of that species, many of which are involved in housekeeping and conserved survival processes. In many of these species, the remaining 'accessory' gene models are clustered within subterminal regions and may be involved in pathogenesis and antimicrobial resistance. Analysis of the ancestry of species core and accessory genomes suggests that fungal pan-genomes evolve by strain-level innovations such as gene duplication as opposed to wide-scale horizontal gene transfer. Our findings lend further supporting evidence to the existence of species pan-genomes in eukaryote taxa.\n\nPan-genome analyses of model fungal species.", "token_count": 354, "char_count": 1452, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:05.765890", "source": { "split": "train_shard_00000", "doc_id": 3136 }, "chunk_id": "train_shard_00000_3136_0", "global_id": 3471 }, { "text": "Bifidobacteria are members of the gut microbiota of animals, including mammals, birds, and social insects. In this study, we analyzed and determined the pangenome of\n\nDissecting the Evolutionary Development of the Species", "token_count": 55, "char_count": 221, "word_count": 32, "semantic_coherence": 1, "information_density": 0.7812, "quality_score": 0.8906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:06.127493", "source": { "split": "train_shard_00000", "doc_id": 3137 }, "chunk_id": "train_shard_00000_3137_0", "global_id": 3472 }, { "text": "Lignocellulosic biomass is one of the most abundant materials for biochemicals production. However, efficient co-utilization of glucose and xylose from the lignocellulosic biomass is a challenge due to the glucose repression in microorganisms. Kluyveromyces marxianus is a thermotolerant and efficient xylose-utilizing yeast. To realize the glucose-xylose co-utilization, analyzing the glucose repression of xylose utilization in K. marxianus is necessary. In addition, a glucose-xylose co-utilization platform strain will facilitate the construction of lignocellulosic biomass-utilizing strains.\n\nRelease of glucose repression on xylose utilization in Kluyveromyces marxianus to enhance glucose-xylose co-utilization and xylitol production from corncob hydrolysate.", "token_count": 220, "char_count": 766, "word_count": 94, "semantic_coherence": 1, "information_density": 0.5638, "quality_score": 0.7819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:06.605838", "source": { "split": "train_shard_00000", "doc_id": 3138 }, "chunk_id": "train_shard_00000_3138_0", "global_id": 3473 }, { "text": "Efficient bioconversion of lignocellulosic biomass is one of the key challenges for the production of bioethanol and chemicals. Therefore, the present work focuses on finding a robust microorganism able to convert all sugars in lignocellulosic hydrolysates efficiently. The fermentation performance showed that Kluyveromyces marxianus CICC 1727-5 could produce ethanol from glucose with productivity 4.2 g/L/h and higher ethanol yields (0.44 g/g) under 40 °C, outdistance the productivity 0.258 g/L/h of S. passalidarum ATCC MYA-4345. The xylose utilization of S. passalidarum ATCC MYA-4345 was faster than K. marxianus CICC 1727-5 with the ethanol yield 0.31 g/g at 30 °C. However, K. marxianus CICC 1727-5 could produce xylitol from xylose with the yield 0.58 g/g at 40 °C. Meanwhile, the two yeasts both had the ability to use arabinose naturally, but K. marxianus CICC 1727-5 could consume arabinose completely and quickly. Furthermore, the two yeasts both could ferment glucose and xylose simultaneously, but K. marxianus CICC 1727-5 showed much better performance in the cofermentation. The peak ethanol concentration of K. marxianus CICC 1727-5 and S. passalidarum ATCC MYA-4345 was 42.6 and 31.9 g/L, respectively. In the saccharification and cofermentation (SSCF) process using non-detoxificated corncob, K. marxianus CICC 1727-5 showed better performance. K", "token_count": 479, "char_count": 1367, "word_count": 200, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:07.284293", "source": { "split": "train_shard_00000", "doc_id": 3139 }, "chunk_id": "train_shard_00000_3139_0", "global_id": 3474 }, { "text": "marxianus CICC 1727-5 was more tolerant in the presence of formic acid, acetic acid, and mix inhibitors and even was capable to grow in the medium with the acetic acid concentration up to 15 g/L. K. marxianus CICC 1727-5 is a promising candidate strain for further metabolic engineering to develop robust industrial strains for the lignocellulosic ethanol.\n\nThe production of ethanol from lignocellulosic biomass by Kluyveromyces marxianus CICC 1727-5 and Spathaspora passalidarum ATCC MYA-4345.", "token_count": 163, "char_count": 495, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7162, "quality_score": 0.8581, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:07.726439", "source": { "split": "train_shard_00000", "doc_id": 3139 }, "chunk_id": "train_shard_00000_3139_1", "global_id": 3475 }, { "text": "Shotgun sequencing of samples taken from the human microbiome often reveals only partial mapping of the sequenced metagenomic reads to existing reference genomes. Such partial mappability indicates that many genomes are missing in our reference genome set. This is particularly true for non-Western populations and for samples that do not originate from the gut. Pasolli et al. (E. Pasolli, F. Asnicar, S. Manara, M. Zolfo, et al., Cell, 2019, https://doi.org/10.1016/j.cell.2019.01.001) perform a grand effort to expand the reference set, and to better classify its members, revealing a wider pangenome of existing species as well as identifying new species of previously unknown taxonomic branches.\n\nA Significant Expansion of Our Understanding of the Composition of the Human Microbiome.", "token_count": 210, "char_count": 790, "word_count": 116, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:08.240569", "source": { "split": "train_shard_00000", "doc_id": 3140 }, "chunk_id": "train_shard_00000_3140_0", "global_id": 3476 }, { "text": "In 2016, the Austrian Agency for Health and Food Safety started a pilot project to investigate antimicrobial resistance in surface water. Here we report on the characterisation of carbapenem resistant and ESBL-producing K. pneumoniae isolates from Austrian river water samples compared to 95 clinical isolates recently obtained in Austrian hospitals. Ten water samples were taken from four main rivers, collected upstream and downstream of major cities in 2016. For subtyping and comparison, public core genome multi locus sequence typing (cgMLST) schemes were used. The presence of AMR genes, virulence genes and plasmids was extracted from whole genome sequence (WGS) data. In total three ESBL-producing strains and two carbapenem resistant strains were isolated. WGS based comparison of these five water isolates to 95 clinical isolates identified three clusters. Cluster 1 (ST11) and cluster 2 (ST985) consisted of doublets of carbapenem resistant strains (one water and one clinical isolate each). Cluster 3 (ST405) consisted of three ESBL-producing strains isolated from one water sample and two clinical specimens. The cities, in which patient isolates of cluster 2 and 3 were collected, were in concordance with the water sampling locations downstream from these cities. The genetic concordance between isolates from river water samples and patient isolates raises concerns regarding the release of wastewater treatment plant effluents into surface water. From a public health perspective these findings demand attention and strategies are required to minimize the spread of multiresistant strains to the environment.\n\nWhole genome sequencing reveals resemblance between ESBL-producing and carbapenem resistant Klebsiella pneumoniae isolates from Austrian rivers and clinical isolates from hospitals.", "token_count": 418, "char_count": 1808, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5444, "quality_score": 0.7722, "entities": { "genes": [ "ST985", "ST11", "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:08.868218", "source": { "split": "train_shard_00000", "doc_id": 3141 }, "chunk_id": "train_shard_00000_3141_0", "global_id": 3477 }, { "text": "While many bacteria have been used as probiotics by industries, only two yeasts, Saccharomyces cerevisiae var. boulardii and Kluyveromyces fragilis (B0399), have been used for this purpose. In the present work, a total of 116 yeasts isolated from Brazilian indigenous fermented food, cocoa fermentation, and kefir were in vitro characterized for probiotic attributes. From 116 isolates, 36 were tolerant to gastrointestinal conditions evaluated by tolerance to pH 2.0, bile salts (0.3% w/v), and 37 °C temperature. From those, 15 isolates showed a similar or higher percentage (P < 0.05) of hydrophobicity, autoaggregation, and coaggregation with E. coli than the reference strain S. boulardii. All these strains showed a high percentage of adhesion to Caco-2 cells (> 63%) and antioxidant activity (ranging from 18 to 62%). Phytate hydrolysis was evaluated for these yeasts and 13 strains showed positive results, which is important for nutrient availability in plant-based foods. These results are important insights for characterization of novel probiotic yeast strains as well as to aggregate functional value to these food products.\n\nProbiotic Potential, Antioxidant Activity, and Phytase Production of Indigenous Yeasts Isolated from Indigenous Fermented Foods.", "token_count": 358, "char_count": 1267, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6973, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:09.453700", "source": { "split": "train_shard_00000", "doc_id": 3142 }, "chunk_id": "train_shard_00000_3142_0", "global_id": 3478 }, { "text": "Bile salts are steroid compounds from the digestive tract of vertebrates and enter the environment via defecation. Many aerobic bile-salt degrading bacteria are known but no bacteria that completely degrade bile salts under anoxic conditions have been isolated so far. In this study, the facultatively anaerobic Betaproteobacterium Azoarcus sp. strain Aa7 was isolated that grew with bile salts as sole carbon source under anoxic conditions with nitrate as electron acceptor. Phenotypic and genomic characterization revealed that strain Aa7 used the 2,3-seco pathway for the degradation of bile salts as found in other denitrifying steroid-degrading bacteria such as Sterolibacterium denitrificans. Under oxic conditions strain Aa7 used the 9,10-seco pathway as found in, for example, Pseudomonas stutzeri Chol1. Metabolite analysis during anaerobic growth indicated a reductive dehydroxylation of 7α-hydroxyl bile salts. Deletion of the gene hsh2\n\nThe 7α-hydroxysteroid dehydratase Hsh2 is essential for anaerobic degradation of the steroid skeleton of 7α-hydroxyl bile salts in the novel denitrifying bacterium Azoarcus sp. strain Aa7.", "token_count": 336, "char_count": 1137, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:10.029637", "source": { "split": "train_shard_00000", "doc_id": 3143 }, "chunk_id": "train_shard_00000_3143_0", "global_id": 3479 }, { "text": "Doxorubicin hydrochloride (DX) is one of the most powerful anticancer agents though its clinical use is impaired by severe undesired side effects. DX encapsulation in nanocarrier systems has been introduced as a mean to reduce its toxicity. Micelles of the nonionic triblock copolymers of poly(ethylene oxide) (PEO) and poly(propylene oxide) (PPO) (PEO-PPO-PEO), are very promising carrier systems. The positive charge of DX confines the drug to the hydrophilic corona region of the micelles. The use of mixed micelles of PEO-PPO-PEO copolymers and a negatively charged bile salt should favour the solubilization of DX in the apolar core region of the micelles.\n\nA fluorescence study of the loading and time stability of doxorubicin in sodium cholate/PEO-PPO-PEO triblock copolymer mixed micelles.", "token_count": 233, "char_count": 797, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6555, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:10.498302", "source": { "split": "train_shard_00000", "doc_id": 3144 }, "chunk_id": "train_shard_00000_3144_0", "global_id": 3480 }, { "text": "Bile salt hydrolase plays an important role in bile acid-mediated signaling pathways, which regulate lipid absorption, glucose metabolism, and energy homeostasis. Several reports suggest that changes in the composition of bile acids are found in many diseases caused by dysbacteriosis.\n\nTaxonomic profiling and populational patterns of bacterial bile salt hydrolase (BSH) genes based on worldwide human gut microbiome.", "token_count": 102, "char_count": 418, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8448, "quality_score": 0.9224, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:10.878476", "source": { "split": "train_shard_00000", "doc_id": 3145 }, "chunk_id": "train_shard_00000_3145_0", "global_id": 3481 }, { "text": "The thermotolerant Kluyveromyces marxianus is a potential candidate for high-temperature ethanol fermentation. Although K. marxianus exhibited high ethanol productivity at 45 °C during the early fermentation stage, we observed a fermentation arrest due to the accumulated inhibitors. The stress responses of K. marxianus during high-temperature fermentation were revealed based on integration of RNA sequencing (RNA-Seq) and metabolite data. High temperature stimulated mitochondrial respiration but repressed the tricarboxylic acid (TCA) cycle, leading to increased generation of reactive oxygen species (ROS) and a lowered ratio of reduced nicotinamide adenine dinucleotide (NADH)/oxidized nicotinamide adenine dinucleotide (NAD\n\nUnderstanding the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation based on integration of RNA-Seq and metabolite data.", "token_count": 242, "char_count": 907, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6435, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:11.364437", "source": { "split": "train_shard_00000", "doc_id": 3146 }, "chunk_id": "train_shard_00000_3146_0", "global_id": 3482 }, { "text": "Homologous recombination (HR) enables the exchange of genetic material between and within species. Recent studies suggest that this process plays a major role in the microevolution of microbial genomes, contributing to core genome homogenization and to the maintenance of cohesive population structures. However, we still have a very poor understanding of the possible adaptive roles of intraspecific HR and of the factors that determine its differential impact across clades and lifestyles. Here we used a unified methodological framework to assess HR in 338 complete genomes from 54 phylogenetically diverse and representative prokaryotic species, encompassing different lifestyles and a broad phylogenetic distribution. Our results indicate that lifestyle and presence of restriction-modification (RM) machineries are among the main factors shaping HR patterns, with symbionts and intracellular pathogens having the lowest HR levels. Similarly, the size of exchanged genomic fragments correlated with the presence of RM and competence machineries. Finally, genes exchanged by HR showed functional enrichments which could be related to adaptations to different environments and ecological strategies. Taken together, our results clarify the factors underlying HR impact and suggest important adaptive roles of genes exchanged through this mechanism. Our results also revealed that the extent of genetic exchange correlated with lifestyle and some genomic features. Moreover, the genes in exchanged regions were enriched for functions that reflected specific adaptations, supporting identification of HR as one of the main evolutionary mechanisms shaping prokaryotic core genomes.\n\nImpact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes.", "token_count": 367, "char_count": 1763, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6189, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:11.933060", "source": { "split": "train_shard_00000", "doc_id": 3147 }, "chunk_id": "train_shard_00000_3147_0", "global_id": 3483 }, { "text": "Ochrobactrum spp. are ubiquitous bacteria attracting growing attention as important members of microbiomes of plants and nematodes and as a source of enzymes for biotechnology. Strain Ochrobactrum sp. A44T was isolated from the rhizosphere of a field-grown potato in Gelderland, the Netherlands. The strain can interfere with quorum sensing (QS) of Gram-negative bacteria through inactivation of N-acyl homoserine lactones (AHLs) and protect plant tissue against soft rot pathogens, the virulence of which is governed by QS. Phylogenetic analysis based on 16S rRNA gene alone and concatenation of 16S rRNA gene and MLSA genes (groEL and gyrB) revealed that the closest relatives of A44T are O. grignonense OgA9aT, O. thiophenivorans DSM 7216T, O. pseudogrignonense CCUG 30717T, O. pituitosum CCUG 50899T, and O. rhizosphaerae PR17T. Genomes of all six type strains were sequenced, significantly expanding the possibility of genome-based analyses in Ochrobactrum spp. Average nucleotide identity (ANIb) and genome-to-genome distance (GGDC) values for A44T and the related strains were below the single species thresholds (95% and 70%, respectively), with the highest scores obtained for O. pituitosum CCUG 50899T (87.31%; 35.6%), O. rhizosphaerae PR17T (86.80%; 34.3%), and O. grignonense OgA9aT (86.30%; 33.6%). Distinction of A44T from the related type strains was supported by chemotaxonomic and biochemical analyses. Comparative genomics revealed that the core genome for the newly sequenced strains comprises 2731 genes, constituting 50-66% of each individual genome", "token_count": 517, "char_count": 1570, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [ "PR17T" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:30:12.587848", "source": { "split": "train_shard_00000", "doc_id": 3148 }, "chunk_id": "train_shard_00000_3148_0", "global_id": 3484 }, { "text": "Through phenotype-to-genotype study, we found that the non-motile strain O. thiophenivorans DSM 7216T lacks a cluster of genes related to flagella formation. Moreover, we explored the genetic background of distinct urease activity among the strains. Here, we propose to establish a novel species Ochrobactrum quorumnocens, with A44T as the type strain (= LMG 30544T = PCM 2957T).\n\nOchrobactrum quorumnocens sp. nov., a quorum quenching bacterium from the potato rhizosphere, and comparative genome analysis with related type strains.", "token_count": 160, "char_count": 533, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7922, "quality_score": 0.8961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:13.025062", "source": { "split": "train_shard_00000", "doc_id": 3148 }, "chunk_id": "train_shard_00000_3148_1", "global_id": 3485 }, { "text": "A thermotolerant ethanol fermenting yeast strain is a key requirement for effective ethanol production at high temperature. This work aimed to select a thermotolerant yeast producing a high ethanol concentration from molasses and increasing its ethanol production by mutagenesis. Saccharomyces cerevisiae DMKU 3-S087 was selected from 168 ethanol producing strains because it produced the highest ethanol concentration from molasses at 40 °C. Optimization of molasses broth composition was performed by the response surface method using Box-Behnken design. In molasses broth containing optimal total fermentable sugars (TFS) of 200 g/L and optimal (NH\n\nSelection of thermotolerant Saccharomyces cerevisiae for high temperature ethanol production from molasses and increasing ethanol production by strain improvement.", "token_count": 208, "char_count": 816, "word_count": 111, "semantic_coherence": 1, "information_density": 0.6126, "quality_score": 0.8063, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:13.488653", "source": { "split": "train_shard_00000", "doc_id": 3149 }, "chunk_id": "train_shard_00000_3149_0", "global_id": 3486 }, { "text": "Bile salt export pump (BSEP) deficiency is an important reason for chronic cholestasis leading to liver transplantation (LT) in early childhood. The underlying pathology is a dysfunction of BSEP due to various mutations in the ABCB11 gene. Cases of clinical recurrence after LT due to alloantibodies directed against BSEP (antibody-induced BSEP deficiency [AIBD]) have been reported. Most of these patients could be controlled by intensified immunosuppression.\n\nAlloimmunity and Cholestasis After Liver Transplantation in Children With Progressive Familial Intrahepatic Cholestasis.", "token_count": 152, "char_count": 582, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8987, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:13.920091", "source": { "split": "train_shard_00000", "doc_id": 3150 }, "chunk_id": "train_shard_00000_3150_0", "global_id": 3487 }, { "text": "Reports of raw meat pet food containing zoonotic foodborne bacteria, including Salmonella, Escherichia coli, and Listeria monocytogenes, are increasing. Contaminated raw pet food and biological waste from pets consuming those diets may pose a public health risk. The U.S. Food and Drug Administration Veterinary Laboratory Investigation and Response Network conducted 2 case investigations, involving 3 households with animal illnesses, which included medical record review, dietary and environmental exposure interviews, animal sample testing, and whole genome sequencing (WGS) of bacteria isolated from the pets and the raw pet food. For each case investigation, WGS with core genome multi-locus sequence typing analysis showed that the animal clinical isolates were closely related to one or more raw pet food bacterial isolates. WGS and genomic analysis of paired animal clinical and animal food isolates can confirm suspected outbreaks of animal foodborne illness.\n\nWhole genome sequencing confirms source of pathogens associated with bacterial foodborne illness in pets fed raw pet food.", "token_count": 234, "char_count": 1093, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:14.741096", "source": { "split": "train_shard_00000", "doc_id": 3151 }, "chunk_id": "train_shard_00000_3151_0", "global_id": 3488 }, { "text": "Primary enterolithiasis is a relatively uncommon but important cause of small bowel obstruction. We present a case of a 69-year-old male with a history of laparoscopic Roux-en-Y gastric bypass and asymptomatic duodenal diverticulum diagnosed with small bowel obstruction. CT imaging showed an obstruction distal to the jejunojejunostomy, and surgical intervention was warranted. A 4.5 cm enterolith removed from the distal jejunum was found to contain 100% bile salts, consistent with a primary enterolith. Clinicians should retain a high index of suspicion for enteroliths as a cause of small bowel obstruction, especially if multiple risk factors for enterolith formation are present.\n\nBile Salt Enterolith: An Unusual Etiology Mimicking Gallstone Ileus.", "token_count": 205, "char_count": 756, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7339, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:15.202684", "source": { "split": "train_shard_00000", "doc_id": 3152 }, "chunk_id": "train_shard_00000_3152_0", "global_id": 3489 }, { "text": "Holder pasteurization (62.5 °C, 30 min) of human milk denatures beneficial proteins. The present paper aimed to assess whether this can affect the kinetics of peptide release during digestion at the preterm stage. Raw (RHM) or pasteurized (PHM) human milk were digested in triplicates using an in vitro dynamic system. Mass spectrometry and multivariate statistics were conducted. Pre-proteolysis occurred mostly on β-casein, for which cumulative peptide abundance was significantly greater in PHM over 28% of the hydrolysed sequence. Eight clusters resumed the kinetics of peptide release during digestion, which differed on seven clusters (69% of the 1134 peptides). Clusters associated to the heat-denaturated proteins, lactoferrin and bile salt-stimulated lipase, presented different kinetics of release during digestion, unlike that for β-casein. Some bioactive peptides from β-casein presented significant different abundances between PHM and RHM before digestion (1-18, 185-211) or in during intestinal digestion (154-160, 161-166). Further physiological consequences should be investigated.\n\nImpact of human milk pasteurization on the kinetics of peptide release during in vitro dynamic digestion at the preterm newborn stage.", "token_count": 344, "char_count": 1234, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:15.776709", "source": { "split": "train_shard_00000", "doc_id": 3153 }, "chunk_id": "train_shard_00000_3153_0", "global_id": 3490 }, { "text": "Bacteriophages with genomes larger than 200 kbp are considered giant phages, and the giant Phicbkviruses are the most frequently isolated Caulobacter crescentus phages. In this study, we compare six bacteriophage genomes that differ from the genomes of the majority of Phicbkviruses. Four of these genomes are much larger than those of the rest of the Phicbkviruses, with genome sizes that are more than 250 kbp. A comparison of 16 Phicbkvirus genomes identified a 'core genome' of 69 genes that is present in all of these Phicbkvirus genomes, as well as shared accessory genes and genes that are unique for each phage. Most of the core genes are clustered into the regions coding for structural proteins or those involved in DNA replication. A phylogenetic analysis indicated that these 16 CaulobacterPhicbkvirus genomes are related, but they represent four distinct branches of the Phicbkvirus genomic tree with distantly related branches sharing little nucleotide homology. In contrast, pairwise comparisons within each branch of the phylogenetic tree showed that more than 80 % of the entire genome is shared among phages within a group. This conservation of the genomes within each branch indicates that horizontal gene transfer events between the groups are rare. Therefore, the Phicbkvirus genus consists of at least four different phylogenetic branches that are evolving independently from one another. One of these branches contains a 27-gene inversion relative to the other three branches. Also, an analysis of the tRNA genes showed that they are relatively mobile within the Phicbkvirus genus.\n\nAnalyses of four new Caulobacter Phicbkviruses indicate independent lineages.", "token_count": 413, "char_count": 1683, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5603, "quality_score": 0.7802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:16.393829", "source": { "split": "train_shard_00000", "doc_id": 3154 }, "chunk_id": "train_shard_00000_3154_0", "global_id": 3491 }, { "text": "The\n\nGlobal genomic similarity and core genome sequence diversity of the", "token_count": 16, "char_count": 72, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:16.758657", "source": { "split": "train_shard_00000", "doc_id": 3155 }, "chunk_id": "train_shard_00000_3155_0", "global_id": 3492 }, { "text": "Among enterococci,\n\nA Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis.", "token_count": 30, "char_count": 94, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:17.122711", "source": { "split": "train_shard_00000", "doc_id": 3156 }, "chunk_id": "train_shard_00000_3156_0", "global_id": 3493 }, { "text": "In 2017, an outbreak of gastroenteritis in England attributed to Salmonella Adjame was detected and investigated. With the introduction of whole genome sequencing (WGS) for microbial typing, methods for comparing international outbreak data require evaluation. A case was defined as a person resident in England with a clinical sample from 1 June 2017 to 27 July 2017 from whom S. Adjame was isolated. Cases were interviewed and exposures analysed. Backward tracing of food provenance was undertaken. WGS was performed on isolates from cases and historical isolates and compared using Public Health England's SnapperDB high-quality SNP pipeline and Enterobase's Salmonella core genome multi-locus sequence typing (cgMLST) scheme. In total, 14 cases were identified. The majority were vegetarian, probably of South Asian descent, with a median age of 66.5 years with no recent international travel reported. Cases consumed a range of fresh food products including herbs and spices bought from South Asian grocers. Backward tracing did not identify a common source. WGS typing showed sub-clustering and considerable genetic variation across human samples. cgMLST allele-based analysis was comparable to SNP-derived phylogenetic analysis and clusters were defined using each method. Imported herbs or spices were suspected vehicles. The cases were linked in time and place but WGS showed marked heterogeneity, atypical of a point source Salmonella outbreak. The application of incorporating SNP or allelic differences into the case definition may not always be appropriate. With further validation, cgMLST could be used for international outbreak alerts when WGS analysis is being undertaken to facilitate comparison.\n\nGenomic approaches used to investigate an atypical outbreak of Salmonella Adjame.", "token_count": 411, "char_count": 1797, "word_count": 261, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:17.743434", "source": { "split": "train_shard_00000", "doc_id": 3157 }, "chunk_id": "train_shard_00000_3157_0", "global_id": 3494 }, { "text": "Pathogenic bacteria use specific host factors to modulate virulence and stress responses during infection. We found previously that the host factor bile and the bile component glyco-conjugated cholate (NaGCH, sodium glycocholate) upregulate the colonization factor CS5 in enterotoxigenic Escherichia coli (ETEC). To further understand the global regulatory effects of bile and NaGCH, we performed Illumina RNA-Seq and found that crude bile and NaGCH altered the expression of 61 genes in CS5 + CS6 ETEC isolates. The most striking finding was high induction of the CS5 operon (csfA-F), its putative transcription factor csvR, and the putative ETEC virulence factor cexE. iTRAQ-coupled LC-MS/MS proteomic analyses verified induction of the plasmid-borne virulence proteins CS5 and CexE and also showed that NaGCH affected the expression of bacterial membrane proteins. Furthermore, NaGCH induced bacteria to aggregate, increased their adherence to epithelial cells, and reduced their motility. Our results indicate that CS5 + CS6 ETEC use NaGCH present in the small intestine as a signal to initiate colonization of the epithelium.\n\nThe bile salt glycocholate induces global changes in gene and protein expression and activates virulence in enterotoxigenic Escherichia coli.", "token_count": 358, "char_count": 1273, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6033, "quality_score": 0.8016, "entities": { "genes": [ "CS5", "CS6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:18.320046", "source": { "split": "train_shard_00000", "doc_id": 3158 }, "chunk_id": "train_shard_00000_3158_0", "global_id": 3495 }, { "text": "Chronic kidney disease (CKD) is accompanied by accumulating levels of uremic solutes in the circulation. Changes in the size and composition of the bile acid pool have also been observed. We investigated via which mechanisms uremic solutes may interfere with hepatocyte function and thus contribute to altered bile acid handling. We studied interference on the level of bile acid synthesis by cytochrome P450 7A1 (CYP7A1), explored effects on hepatic bile acid transporters, and investigated effects on mitochondrial function. In HEK293 cells overexpressing bile salt transporters, we observed that p-cresyl sulfate inhibited Na\n\nUremic solutes modulate hepatic bile acid handling and induce mitochondrial toxicity.", "token_count": 186, "char_count": 715, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6796, "quality_score": 0.8398, "entities": { "genes": [ "HEK293" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:18.800575", "source": { "split": "train_shard_00000", "doc_id": 3159 }, "chunk_id": "train_shard_00000_3159_0", "global_id": 3496 }, { "text": "Understanding underlying mechanisms involved in microbial persistence in the built environment (BE) is essential for strategically mitigating potential health risks. To test the hypothesis that BEs impose selective pressures resulting in characteristic adaptive responses, we performed a pangenomics meta-analysis leveraging 189 genomes (accessed from GenBank) of two epidemiologically important taxa, Bacillus cereus and Staphylococcus aureus, isolated from various origins: the International Space Station (ISS; a model BE), Earth-based BEs, soil, and humans. Our objectives were to (i) identify differences in the pangenomic composition of generalist and host-associated organisms, (ii) characterize genes and functions involved in BE-associated selection, and (iii) identify genomic signatures of ISS-derived strains of potential relevance for astronaut health. The pangenome of B. cereus was more expansive than that of S. aureus, which had a dominant core component. Genomic contents of both taxa significantly correlated with isolate origin, demonstrating an importance for biogeography and potential niche adaptations. ISS/BE-enriched functions were often involved in biosynthesis, catabolism, materials transport, metabolism, and stress response. Multiple origin-enriched functions also overlapped across taxa, suggesting conserved adaptive processes. We further characterized two mobile genetic elements with local neighborhood genes encoding biosynthesis and stress response functions that distinctively associated with B. cereus from the ISS. Although antibiotic resistance genes were present in ISS/BE isolates, they were also common in counterparts elsewhere. Overall, despite differences in microbial lifestyle, some functions appear common to remaining viable in the BE, and those functions are not typically associated with direct impacts on human health.\n\nPangenomic Approach To Understanding Microbial Adaptations within a Model Built Environment, the International Space Station, Relative to Human Hosts and Soil.", "token_count": 445, "char_count": 2033, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6767, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:19.454046", "source": { "split": "train_shard_00000", "doc_id": 3160 }, "chunk_id": "train_shard_00000_3160_0", "global_id": 3497 }, { "text": "Serratia marcescens is a Gram-negative bacterial species that can be found in a wide range of environments like soil, water and plant surfaces, while it is also known as an opportunistic human pathogen in hospitals and as a plant growth promoting bacteria (PGPR) in crops. We have used a pangenome-based approach, based on publicly available genomes, to apply whole genome multilocus sequence type schemes to assess whether there is an association between source and genotype, aiming at differentiating between isolates from nosocomial sources and the environment, and between strains reported as PGPR from other environmental strains. Most genomes from a nosocomial setting and environmental origin could be assigned to the proposed nosocomial or environmental MLSTs, which is indicative of an association between source and genotype. The fact that a few genomes from a nosocomial source showed an environmental MLST suggests that a minority of nosocomial strains have recently derived from the environment. PGPR strains were assigned to different environmental types and clades but only one clade comprised strains accumulating a low number of known virulence and antibiotic resistance determinants and was exclusively from environmental sources. This clade is envisaged as a group of promissory MLSTs for selecting prospective PGPR strains.\n\nPangenome of Serratia marcescens strains from nosocomial and environmental origins reveals different populations and the links between them.", "token_count": 315, "char_count": 1485, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8005, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:20.044626", "source": { "split": "train_shard_00000", "doc_id": 3161 }, "chunk_id": "train_shard_00000_3161_0", "global_id": 3498 }, { "text": "Helicobacter pylori encodes a large number of restriction-modification (R-M) systems despite its small genome. R-M systems have been described as 'primitive immune systems' in bacteria, but the role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H. pylori strain harbours a unique set of R-M systems resulting in a highly diverse methylome. We identified a highly conserved GCGC-specific m5C MTase (JHP1050) that was predicted to be active in all of 459 H. pylori genome sequences analyzed. Transcriptome analysis of two H. pylori strains and their respective MTase mutants showed that inactivation of the MTase led to changes in the expression of 225 genes in strain J99, and 29 genes in strain BCM-300. Ten genes were differentially expressed in both mutated strains. Combining bioinformatic analysis and site-directed mutagenesis, we demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects. Thus, m5C methylation modifies the transcription of multiple genes, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.\n\nThe core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori.", "token_count": 358, "char_count": 1416, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6601, "quality_score": 0.83, "entities": { "genes": [ "JHP1050" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:20.651107", "source": { "split": "train_shard_00000", "doc_id": 3162 }, "chunk_id": "train_shard_00000_3162_0", "global_id": 3499 }, { "text": "Kluyveromyces marxianus IIPE453 can utilize biomass-derived fermentable sugars for xylitol and ethanol fermentation. In this study, the xylitol production in the native strain was improved by overexpression of endogenous d-xylose reductase gene. A suitable expression cassette harboring the gene of interest was constructed and incorporated in the native yeast. qPCR analysis demonstrated the 2.1-fold enhancement in d-xylose reductase transcript levels in the modified strain with 1.62-fold enhancement in overall xylitol yield without affecting its ethanol fermenting capacity. Material balance analysis on 2 kg of sugar cane bagasse-derived fermentable sugars illustrated an excess of 58.62 ± 0.15 g of xylitol production by transformed strain in comparison to the wild variety with similar ethanol yield. The modified strain can be suitably used as a single biocatalyst for multiproduct biorefinery application.\n\nXylitol Production from Lignocellulosic Pentosans: A Rational Strain Engineering Approach toward a Multiproduct Biorefinery.", "token_count": 269, "char_count": 1041, "word_count": 142, "semantic_coherence": 1, "information_density": 0.669, "quality_score": 0.8345, "entities": { "genes": [ "IIPE453" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:21.825877", "source": { "split": "train_shard_00000", "doc_id": 3163 }, "chunk_id": "train_shard_00000_3163_0", "global_id": 3500 }, { "text": "The purpose of this meta-analysis was to investigate the relationship between bile salt export pump (BSEP) polymorphisms and intrahepatic cholestasis of pregnancy (ICP) susceptibility. Retrieved studies from Pubmed, EMBASE, Web of Science, Cochrane Library and CBM databases about BSEP polymorphisms and ICP susceptibility were included. Odds ratio (OR) and 95% confidence interval (CI) and publication bias were calculated. Ten related case-control studies on BSEP polymorphisms and ICP susceptibility were included. The pooled results showed a significant association between BSEP rs2287622 polymorphism and ICP risk in Asian population (OR >1, p < .01 for A vs. a and AA vs. Aa/aa) and general population (OR >1, p < .05 for A vs. a, Aa vs. aa, AA/Aa vs. aa), and a borderline statistical significance was found between BSEP rs473351 polymorphism and ICP susceptibility (OR = 1.66, p < .05), and no statistical significance was found in D482G or rs853782 polymorphisms and ICP risk (all p > .05). Additionally, no publication bias was found in these studies (all p > .05). Our current meta-analysis indicated that BSEP rs2287622 polymorphism could increase the susceptibility of ICP in Asians and in general populations, while rs473351, D482G, and rs853782 polymorphisms were not obviously associated with ICP risk, but it needs further larger study with ethnicity and various etiologies.\n\nAssociation between bile salt export pump polymorphisms and intrahepatic cholestasis of pregnancy susceptibility: a meta-analysis of case-control studies.", "token_count": 481, "char_count": 1547, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5368, "quality_score": 0.7684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:22.472134", "source": { "split": "train_shard_00000", "doc_id": 3164 }, "chunk_id": "train_shard_00000_3164_0", "global_id": 3501 }, { "text": "The bile salt export pump (BSEP) is the primary canalicular transporter responsible for the secretion of bile acids from hepatocytes into bile canaliculi, and inhibition of this transporter has been associated with drug-induced liver injury (DILI). A common variant (rs2287622; p.V444A) in the gene encoding BSEP has been associated with an increased risk of cholestatic DILI. Although p.444V BSEP (reference) and p.444A BSEP (variant) do not differ in their transport kinetics of taurocholic acid (TCA), transport of the more abundant glycocholic acid (GCA) has not been investigated. Importantly, differences in the susceptibility of p.444V and p.444A BSEP to inhibition by drugs causing cholestatic DILI have not been investigated. To address these issues, the transport kinetics of GCA were evaluated by incubating membrane vesicles expressing either p.444V or p.444A BSEP with GCA over a range of concentrations (1, 10, 25, 50, and 100 μM). The abilities of commonly used cholestatic medications to inhibit the transport of TCA and GCA by the reference and variant proteins were compared. Resulting data indicated that GCA transport kinetics for reference and variant BSEP followed Michaelis-Menten kinetics and were not statistically different [ V\n\nEffect of a Common Genetic Variant (p.V444A) in the Bile Salt Export Pump on the Inhibition of Bile Acid Transport by Cholestatic Medications.", "token_count": 406, "char_count": 1397, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5545, "quality_score": 0.7773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:23.089997", "source": { "split": "train_shard_00000", "doc_id": 3165 }, "chunk_id": "train_shard_00000_3165_0", "global_id": 3502 }, { "text": "Multipartite genomes, containing at least two large replicons, are found in diverse bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to gain insights into the role and emergence of multipartite genomes. Almost all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae. These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that interreplicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon's pangenome indicated a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also overrepresented on the chromosomes of the environmental genera (Paraburkholderia and Cupriavidus) compared with the pathogenic genera (Burkholderia and Ralstonia). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in replicons enriched in genes associated with adaptation to novel environments.\n\nChromids Aid Genome Expansion and Functional Diversification in the Family Burkholderiaceae.", "token_count": 436, "char_count": 1952, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6145, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:23.722999", "source": { "split": "train_shard_00000", "doc_id": 3166 }, "chunk_id": "train_shard_00000_3166_0", "global_id": 3503 }, { "text": "In this study, in order to directly and efficiently convert inulin into a single-cell oil (SCO), an INU1 gene encoding inulinase from Kluyveromyces marxianus was integrated into the genomic DNA and actively expressed in an SCO producer Aureobasidium melanogenum P10. The transformant API41 obtained produced 28.5 U/mL of inulinase and its wild-type strain P10 yielded only 8.62 U/mL. Most (97.5%) of the inulinase produced by the transformant API41 was secreted into the culture. During a 10-L fermentation, 66.2% (w/w) lipid in the yeast cells of the transformant API41 and 14.38 g/L of cell dry weight were attained from inulin of 80.0 g/L within 120 h, high inulinase activity (23.7 U/mL) was also produced within 72 h, and the added inulin was actively hydrolyzed. This confirmed that the genetically engineered yeast of A. melanogenum P10 is suitable for direct production of lipids from inulin. The lipids produced could be used as feedstocks for biodiesel production.\n\nOverexpression of an Inulinase Gene in an Oleaginous Yeast, Aureobasidium melanogenum P10, for Efficient Lipid Production from Inulin.", "token_count": 343, "char_count": 1110, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8081, "entities": { "genes": [ "API41", "INU1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:24.300833", "source": { "split": "train_shard_00000", "doc_id": 3167 }, "chunk_id": "train_shard_00000_3167_0", "global_id": 3504 }, { "text": "The corresponding author (Motonari Shibakami) inadvertently failed to include his ORCID ID: http://orcid.org/0000-0003-4484-2982 In the published article.\n\nCorrection to: Creation of Straight-Chain Cationic Polysaccharide-Based Bile Salt Sequestrants Made from Euglenoid β-1,3-Glucan as Potential Antidiabetic Agents.", "token_count": 110, "char_count": 317, "word_count": 35, "semantic_coherence": 1, "information_density": 0.9714, "quality_score": 0.9857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:24.681289", "source": { "split": "train_shard_00000", "doc_id": 3168 }, "chunk_id": "train_shard_00000_3168_0", "global_id": 3505 }, { "text": "Kluyveromyces marxianus CCT 7735 offers advantages to ethanol production over Saccharomyces cerevisiae, including thermotolerance and the ability to convert lactose to ethanol. However, its growth is impaired at high ethanol concentrations. Herein we report on the protein and intracellular metabolite profiles of K. marxianus at 1 and 4 h under ethanol exposure. The concentration of some amino acids, trehalose and ergosterol were also measured. We observed that proteins and metabolites from carbon pathways and translation were less abundant, mainly at 4 h of ethanol stress. Nevertheless, the concentration of some amino acids and trehalose increased at 8 and 12 h under ethanol stress, indicating an adaptive response. Moreover, our results show that the abundance of proteins and metabolites related to the oxidative stresses responses increased. The results obtained in this study provide insights into understanding the physiological changes in K. marxianus under ethanol stress, indicating possible targets for ethanol tolerant strains construction.\n\nEthanol stress responses of Kluyveromyces marxianus CCT 7735 revealed by proteomic and metabolomic analyses.", "token_count": 294, "char_count": 1169, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:25.247245", "source": { "split": "train_shard_00000", "doc_id": 3169 }, "chunk_id": "train_shard_00000_3169_0", "global_id": 3506 }, { "text": "Ethanol production by simultaneous saccharification and fermentation (SSF) using sugarcane bagasse as substrate was developed using batch and fed-batch mode. Acid, alkali, hydrothermal and hydrogen peroxide pretreatments to the sugarcane bagasse were tested. Experiments were carried out to optimize the enzyme load of cellulases and β-glucosidase. Four strains, two of Saccharomyces cerevisiae and two of Kluyveromyces marxianus yeast species were evaluate using SSF to produce ethanol. A kinetic study in bioreactor was carried out to optimize the SSF. The batch process was optimized using 1.0 g/L of inoculum, 15.0 FPU/g cellulose of cellulases and 6.0% of initial cellulose reaching 92.0% of theoretical ethanol yield after 18 h using the bagasse pretreate by acid-alkali and S. cerevisiae PE-2. The fed-batch process with enzyme load three times lower than that was used in batch process, obtained 88% of theoretical ethanol yield in 40 h. Therefore, the use of the lignocellulosic biomass (sugarcane bagasse) for producing a biofuel (ethanol) reduces the need for oil and is an environmental-friendly process.\n\nEthanol production from sugarcane bagasse: Use of different fermentation strategies to enhance an environmental-friendly process.", "token_count": 360, "char_count": 1247, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:25.824244", "source": { "split": "train_shard_00000", "doc_id": 3170 }, "chunk_id": "train_shard_00000_3170_0", "global_id": 3507 }, { "text": "Eight yeast strains of the genera Saccharomyces and Kluyveromyces were screened to ferment high lactose-load cheese whey permeate (CWP) (>130 g/L lactose) without nutrient supplementation. The fermentation conditions (temperature, pH and time) were optimized to maximize the fermentation performance (ethanol titer, ethanol yield and lactose consumption) for the two preselected strains, K. marxianus DSM 5422 and S. cerevisiae Ethanol Red, using a response surface methodology (RSM). Under optimized conditions, K. marxianus DSM 5422 attained ethanol titers of 6% (v/v) in only 44 h. Moreover, the feasibility of immobilizing this strain on four different inorganic supports (plastic, glass and Tygon silicone Raschig rings and alumina beads) was assessed. Glass Raschig rings and alumina beads showed a more stable performance over time, yielding ethanol titers of 60 g/L during 1,000 hours, which remarkably reduces yeast cultivation costs. Results demonstrate the feasibility of using CWP for successful ethanol production in a simple and economical process, which represents an attractive alternative for waste treatment in dairy industries.\n\nYeast screening and cell immobilization on inert supports for ethanol production from cheese whey permeate with high lactose loads.", "token_count": 352, "char_count": 1279, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6868, "quality_score": 0.8434, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:26.399352", "source": { "split": "train_shard_00000", "doc_id": 3171 }, "chunk_id": "train_shard_00000_3171_0", "global_id": 3508 }, { "text": "Enterotoxigenic Escherichia coli (ETEC) are an important cause of diarrhea globally, particularly among children under the age of five in developing countries. ETEC O6 is the most common ETEC serogroup, yet the genome wide population structure of isolates of this serogroup is yet to be determined. In this study, we have characterized 40 ETEC O6 isolates collected between 1975-2016 by whole genome sequencing (WGS) and by phenotypic antimicrobial susceptibility testing. To determine the relatedness of isolates, we evaluated two methods-whole genome high-quality single nucleotide polymorphism (whole genome-hqSNP) and core genome SNP analyses using Lyve-SET and Parsnp respectively. All isolates were tested for antimicrobial susceptibility using a panel of 14 antibiotics. ResFinder 2.1 and a custom quinolone resistance determinants workflow were used for resistance determinant detection. VirulenceFinder 1.5 was used for prediction of the virulence genes. Thirty-seven isolates clustered into three major clades (I, II, III) by whole genome-hqSNP and core genome SNP analyses, while three isolates included in the whole genome-hqSNP analysis only did not cluster with clades I-III by both analyses and formed a distantly related outgroup, designated clade IV. Median number of pairwise whole genome-hqSNPs in clonal ETEC O6 outbreaks ranged from 0 to 5. Of the 40 isolates tested for antimicrobial susceptibility, 18 isolates were pansusceptible. Twenty-two isolates were resistant to at least one antibiotic, nine of which were multidrug resistant. Phenotypic antimicrobial resistance (AR) correlated with AR determinants in 22 isolates. Thirty-two isolates harbored both enterotoxin virulence genes while the remaining 8 isolates had only one of the two virulence genes", "token_count": 491, "char_count": 1779, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:27.045106", "source": { "split": "train_shard_00000", "doc_id": 3172 }, "chunk_id": "train_shard_00000_3172_0", "global_id": 3509 }, { "text": "In summary, whole genome-hqSNP and core genome SNP analyses from this study revealed similar evolutionary relationships and an overall diversity of ETEC O6 isolates independent of time of isolation. Less than 5 pairwise hqSNPs between ETEC O6 isolates is circumstantially indicative of an outbreak cluster. Findings from this study will be a basis for quicker outbreak detection and control by efficient subtyping by WGS.\n\nGenome wide characterization of enterotoxigenic Escherichia coli serogroup O6 isolates from multiple outbreaks and sporadic infections from 1975-2016.", "token_count": 149, "char_count": 573, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7439, "quality_score": 0.872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:27.477096", "source": { "split": "train_shard_00000", "doc_id": 3172 }, "chunk_id": "train_shard_00000_3172_1", "global_id": 3510 }, { "text": "Bile acids, amphipathic molecules known for their facilitating role in fat absorption, are also recognized as signalling molecules acting via nuclear and membrane receptors. Of the bile acid-activated receptors, the Farnesoid X Receptor (FXR) and the G protein-coupled bile acid receptor-1 (Gpbar1 or TGR5) have been studied most extensively. Bile acid signaling is critical in the regulation of bile acid metabolism itself, but it also plays a significant role in glucose, lipid and energy metabolism. Activation of FXR and TGR5 leads to reduced hepatic bile salt load, improved insulin sensitivity and glucose regulation, increased energy expenditure, and anti-inflammatory effects. These beneficial effects render bile acid signaling an interesting therapeutic target for the treatment of diseases such as cholestasis, non-alcoholic fatty liver disease, and diabetes. Here, we summarize recent findings on bile acid signaling and discuss potential and current limitations of bile acid receptor agonist and modulators of bile acid transport as future therapeutics for a wide-spectrum of diseases.\n\nDevelopments in bile salt based therapies: A critical overview.", "token_count": 287, "char_count": 1163, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6826, "quality_score": 0.8413, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:28.035113", "source": { "split": "train_shard_00000", "doc_id": 3173 }, "chunk_id": "train_shard_00000_3173_0", "global_id": 3511 }, { "text": "What is the central question of this study? Is the responsiveness of isolated segments of the rat oesophagus to contractile or relaxant stimuli susceptible to acute luminal exposure of the oesophagus to an acid solution that contains pepsin and bile salt? What is the main finding and its importance? The study reveals that luminal acidity is an important factor that disrupts barrier function in the oesophagus to allow the diffusion of noxious agents, such as bile acid, that alter the contractile status of the oesophageal body, even in the absence of inflammation.\n\nImpairment of rat oesophageal muscle contractility associated with experimental non-erosive oesophageal mucosal damage.", "token_count": 167, "char_count": 689, "word_count": 105, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:28.474462", "source": { "split": "train_shard_00000", "doc_id": 3174 }, "chunk_id": "train_shard_00000_3174_0", "global_id": 3512 }, { "text": "Moraxella bovoculi is frequently cultured from the ocular secretions and conjunctiva of cattle with Infectious Bovine Keratoconjunctivitis (IBK). Previous work has shown that single nucleotide polymorphism (SNP) diversity in this species is quite high with 81,284 SNPs identified in eight genomes representing two distinct genotypes isolated from IBK affected eyes (genotype 1) and the nasopharynx of cattle without clinical IBK signs (genotype 2), respectively. The goals of this study were to identify SNPs from a collection of geographically diverse and epidemiologically unlinked M. bovoculi strains from the eyes of IBK positive cattle (n = 183) and another from the eyes of cattle (most from a single population at a single time-point) without signs of IBK (n = 63) and to characterize the genetic diversity. Strains of both genotypes were identified from the eyes of cattle without IBK signs. Only genotype 1 strains were identified from IBK affected eyes, however, these strains were isolated before the discovery of genotype 2, and the protocol for their isolation would have preferentially selected genotype 1 M. bovoculi. The core genome comprised ~74% of the whole and contained >127,000 filtered SNPs. More than 80% of these characterize diversity within genotype 1 while 23,611 SNPs (~18%) delimit the two major genotypes. Genotype 2 strains lacked a repeats-in-toxin (RTX) putative pathogenesis factor and any of ten putative antibiotic resistance genes carried within a genomic island. Within genotype 1, prevalence of these elements was 0.85 and 0.12 respectively in strains from eyes that were IBK positive. Recombination appears to be an important source of genetic diversity for genotype 1 and undermines the utility of ribosomal-locus-based species identification. The extremely high genetic diversity in genotype 1 presents a challenge to the development of an efficacious vaccine directed against them, however, several low-diversity pilin-like genes were identified", "token_count": 511, "char_count": 1989, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5522, "quality_score": 0.7761, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:29.105539", "source": { "split": "train_shard_00000", "doc_id": 3175 }, "chunk_id": "train_shard_00000_3175_0", "global_id": 3513 }, { "text": "Finally, the genotype-defining SNPs described in this study are a resource that can facilitate the development of more accurate M. bovoculi diagnostic tests.\n\nWhole genome sequencing of Moraxella bovoculi reveals high genetic diversity and evidence for interspecies recombination at multiple loci.", "token_count": 68, "char_count": 297, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9268, "quality_score": 0.9634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:29.477988", "source": { "split": "train_shard_00000", "doc_id": 3175 }, "chunk_id": "train_shard_00000_3175_1", "global_id": 3514 }, { "text": "Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious nosocomial pathogen that causes a variety of serious, often life-threatening, infections and outbreaks. This study aimed to investigate the molecular epidemiology of clinical CRAB isolates from an outbreak that occurred in the intensive care unit (ICU) of an Italian hospital.\n\nEpidemiological investigation of an Acinetobacter baumannii outbreak using core genome multilocus sequence typing.", "token_count": 112, "char_count": 457, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8167, "quality_score": 0.9083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:29.857603", "source": { "split": "train_shard_00000", "doc_id": 3176 }, "chunk_id": "train_shard_00000_3176_0", "global_id": 3515 }, { "text": "Toxin-antitoxin (TA) systems are ubiquitous among bacteria, frequently expressed in multiple copies, and important for functions such as antibiotic resistance and persistence. Type I TA systems are composed of a stable toxic peptide whose expression is repressed by an unstable RNA antitoxin. Here, we investigated the functionalities, regulation, and possible cross-talk between three core genome copies of the pathogenicity island-encoded 'sprG1/sprF1' type I TA system in the human pathogen Staphylococcus aureus. Except for SprG4, all RNA from these pairs, sprG2/sprF2, sprG3/sprF3, sprG4/sprF4, are expressed in the HG003 strain. SprG2 and SprG3 RNAs encode toxic peptides whose overexpression triggers bacteriostasis, which is counteracted at the RNA level by the overexpression of SprF2 and SprF3 antitoxins. Complex formation between each toxin and its cognate antitoxin involves their overlapping 3' ends, and each SprF antitoxin specifically neutralizes the toxicity of its cognate SprG toxin without cross-talk. However, overexpression studies suggest cross-regulations occur at the RNA level between the SprG/SprF TA systems during growth. When subjected to H2O2-induced oxidative stress, almost all antitoxin levels dropped, while only SprG1 and SprF1 were reduced during phagocytosis-induced oxidative stress. SprG1, SprF1, SprF2, SprG3 and SprF3 levels also decrease during hyperosmotic stress. This suggests that novel SprG/SprF TA systems are involved in S. aureus persistence.\n\nFunctionality and cross-regulation of the four SprG/SprF type I toxin-antitoxin systems in Staphylococcus aureus.", "token_count": 454, "char_count": 1609, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [ "HG003" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:30.504707", "source": { "split": "train_shard_00000", "doc_id": 3177 }, "chunk_id": "train_shard_00000_3177_0", "global_id": 3516 }, { "text": "Glycochenodeoxycholate acid (GCDA) is a toxic component in bile salts. It plays an important role in the development and progression of liver cancer. In this study, we investigated the underlying mechanism of GCDA in hepatocarcinogenesis and chemotherapy resistance.\n\nBile salt (glycochenodeoxycholate acid) induces cell survival and chemoresistance in hepatocellular carcinoma.", "token_count": 100, "char_count": 378, "word_count": 50, "semantic_coherence": 1, "information_density": 0.82, "quality_score": 0.91, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:30.919450", "source": { "split": "train_shard_00000", "doc_id": 3178 }, "chunk_id": "train_shard_00000_3178_0", "global_id": 3517 }, { "text": "Bile acids (BA) are increasingly recognized as pleiotropic and hormone-like signaling molecules with metabolic and endocrine functions. However, the role of BA in white adipocyte physiology remains somewhat obscure. It was the aim to investigate the BA receptors (FXR, TGR5) and FGFR1 (Fibroblast growth factor receptor 1) as well as Bsep (bile salt export pump) in white adipocytes and in murine and human adipose tissue (AT) and to investigate effects of different BA species in adipocyte physiology.\n\nEvidence of functional bile acid signaling pathways in adipocytes.", "token_count": 157, "char_count": 570, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7326, "quality_score": 0.8663, "entities": { "genes": [ "FGFR1", "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:31.403097", "source": { "split": "train_shard_00000", "doc_id": 3179 }, "chunk_id": "train_shard_00000_3179_0", "global_id": 3518 }, { "text": "Straight-chain polysaccharides have a greater potential of selectively adsorbing hydrophobic bile salts than resin-based bile salt sequesters because of ionic and hydrophobic interactions; hence, they may possess antidiabetic activity. The feasibility of using cationic polysaccharides made from euglenoid β-1,3-glucan (referred to as paramylon) as potential antidiabetic agents was examined by using in vitro and animal experiments.\n\nCreation of Straight-Chain Cationic Polysaccharide-Based Bile Salt Sequestrants Made from Euglenoid β-1,3-Glucan as Potential Antidiabetic Agents.", "token_count": 164, "char_count": 581, "word_count": 72, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:31.860030", "source": { "split": "train_shard_00000", "doc_id": 3180 }, "chunk_id": "train_shard_00000_3180_0", "global_id": 3519 }, { "text": "Genome-wide association studies (GWAS) in microbes have different challenges to GWAS in eukaryotes. These have been addressed by a number of different methods. pyseer brings these techniques together in one package tailored to microbial GWAS, allows greater flexibility of the input data used, and adds new methods to interpret the association results.\n\npyseer: a comprehensive tool for microbial pangenome-wide association studies.", "token_count": 98, "char_count": 432, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7869, "quality_score": 0.8934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:32.286797", "source": { "split": "train_shard_00000", "doc_id": 3181 }, "chunk_id": "train_shard_00000_3181_0", "global_id": 3520 }, { "text": "With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method to assign species designations is needed that is consistent with classically obtained taxonomic analyses. This is particularly acute for unculturable, obligate intracellular bacteria with which classically defined methods, like DNA-DNA hybridization, cannot be used, such as those in the\n\nUsing Core Genome Alignments To Assign Bacterial Species.", "token_count": 103, "char_count": 461, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:32.713516", "source": { "split": "train_shard_00000", "doc_id": 3182 }, "chunk_id": "train_shard_00000_3182_0", "global_id": 3521 }, { "text": "Intraspecific variability of the behavior of most foodborne pathogens is well described and taken into account in Quantitative Microbial Risk Assessment (QMRA), but factors (strain origin, serotype, …) explaining these differences are scarce or contradictory between studies. Nowadays, Whole Genome Sequencing (WGS) offers new opportunities to explain intraspecific variability of food pathogens, based on various recently published bioinformatics tools. The objective of this study is to get a better insight into different existing bioinformatics approaches to associate bacterial phenotype(s) and genotype(s). Therefore, a dataset of 51 L. monocytogenes strains, isolated from multiple sources (i.e. different food matrices and environments) and belonging to 17 clonal complexes (CC), were selected to represent large population diversity. Furthermore, the phenotypic variability of growth at low temperature was determined (i.e. qualitative phenotype), and the whole genomes of selected strains were sequenced. The almost exhaustive gene content, as well as the core genome SNPs based phylogenetic reconstruction, were derived from the whole sequenced genomes. A Bayesian inference method was applied to identify the branches on which the phenotype distribution evolves within sub-lineages. Two different Genome Wide Association Studies (i.e. gene- and SNP-based GWAS) were independently performed in order to link genetic mutations to the phenotype of interest. The genomic analyses presented in this study were successfully applied on the selected dataset. The Bayesian phylogenetic approach emphasized an association with \"slow\" growth ability at 2 °C of the lineage I, as well as CC9 of the lineage II. Moreover, both gene- and SNP-GWAS approaches displayed significant statistical associations with the tested phenotype. A list of 114 significantly associated genes, including genes already known to be involved in the cold adaption mechanism of L. monocytogenes and genes associated to mobile genetic elements (MGE), resulted from the gene-GWAS", "token_count": 468, "char_count": 2054, "word_count": 289, "semantic_coherence": 1, "information_density": 0.654, "quality_score": 0.827, "entities": { "genes": [ "CC9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:33.368704", "source": { "split": "train_shard_00000", "doc_id": 3183 }, "chunk_id": "train_shard_00000_3183_0", "global_id": 3522 }, { "text": "On the other hand, a group of 184 highly associated SNPs were highlighted by SNP-GWAS, including SNPs detected in genes which were already likely involved in cold adaption; hypothetical proteins; and intergenic regions where for example promotors and regulators can be located. The successful application of combined bioinformatics approaches associating WGS-genotypes and specific phenotypes, could contribute to improve prediction of microbial behaviors in food. The implementation of this information in hazard identification and exposure assessment processes will open new possibilities to feed QMRA-models.\n\nInsights from genome-wide approaches to identify variants associated to phenotypes at pan-genome scale: Application to L. monocytogenes' ability to grow in cold conditions.", "token_count": 171, "char_count": 785, "word_count": 106, "semantic_coherence": 1, "information_density": 0.783, "quality_score": 0.8915, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:33.812316", "source": { "split": "train_shard_00000", "doc_id": 3183 }, "chunk_id": "train_shard_00000_3183_1", "global_id": 3523 }, { "text": "Biamphiphilic ionic liquids (BAILs) having amphiphilic cation and anion are thought to exhibit improved surface activity and colloidal stability to be utilized in different applications. For their effective use, a control over synergetic hydrophobic and electrostatic interactions between oppositely charged ions along with the possibility of tuning of hydrophobicity of the core of aggregates is required. Focusing on this, new BAILs comprising a bile salt anion, deoxycholate, [DC]\n\nHydrophobically Driven Morphologically Diverse Self-Assembled Architectures of Deoxycholate and Imidazolium-Based Biamphiphilic Ionic Liquids in Aqueous Medium.", "token_count": 170, "char_count": 645, "word_count": 84, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:34.260563", "source": { "split": "train_shard_00000", "doc_id": 3184 }, "chunk_id": "train_shard_00000_3184_0", "global_id": 3524 }, { "text": "Autophagy is important for hepatic homeostasis, nutrient regeneration, and organelle quality control. We investigated the mechanisms by which liver injury occurred in the absence of autophagy function. We found that mice deficient in autophagy because of the lack of autophagy-related gene 7 or autophagy-related gene 5, key autophagy-related genes, manifested intracellular cholestasis with increased levels of serum bile acids, a higher ratio of tauromuricholic acid/taurocholic acid in the bile, increased hepatic bile acid load, abnormal bile canaliculi, and altered expression of hepatic transporters. In determining the underlying mechanism, we found that autophagy sustained and promoted the basal and up-regulated expression of farnesoid X receptor (Fxr) in the fed and starved conditions, respectively. Consequently, expression of Fxr and its downstream genes, particularly bile salt export pump, and the binding of FXR to the promoter regions of these genes, were suppressed in autophagy-deficient livers. In addition, codeletion of nuclear factor erythroid 2-related factor 2 (Nrf2) in autophagy deficiency status reversed the FXR suppression. Furthermore, the cholestatic injury of autophagy-deficient livers was reversed by enhancement of FXR activity or expression, or by Nrf2 deletion. Conclusion: Together with earlier reports that FXR can suppress autophagy, our findings indicate that autophagy and FXR form a regulatory loop and deficiency of autophagy causes abnormal FXR functionality, leading to the development of intracellular cholestasis and liver injury.\n\nHepatic Autophagy Deficiency Compromises Farnesoid X Receptor Functionality and Causes Cholestatic Injury.", "token_count": 422, "char_count": 1688, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5733, "quality_score": 0.7866, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:34.878173", "source": { "split": "train_shard_00000", "doc_id": 3185 }, "chunk_id": "train_shard_00000_3185_0", "global_id": 3525 }, { "text": "The link between antibiotic treatment and IF-associated liver disease (IFALD) is unclear. Here, we study the effect of antibiotic treatment on bile acid (BA) metabolism and investigate the involved mechanisms. The results showed that pediatric IF patients with cholestasis had a significantly lower abundance of BA-biotransforming bacteria than patients without cholestasis. In addition, the BA composition was altered in the serum, feces, and liver of pediatric IF patients with cholestasis, as reflected by the increased proportion of primary BAs. In the ileum, farnesoid X receptor (FXR) expression was reduced in patients with cholestasis. Correspondingly, the serum FGF19 levels decreased significantly in patients with cholestasis. In the liver, the expression of the rate-limiting enzyme in bile salt synthesis, cytochrome P450 7a1 (CYP7A1), increased noticeably in IF patients with cholestasis. In mice, we showed that oral antibiotics (gentamicin, GM or vancomycin, VCM) reduced colonic microbial diversity, with a decrease in both Gram-negative bacteria (GM affected Eubacterium and Bacteroides) and Gram-positive bacteria (VCM affected Clostridium, Bifidobacterium and Lactobacillus). Concomitantly, treatment with GM or VCM decreased secondary BAs in the colonic contents, with a simultaneous increase in primary BAs in plasma. Moreover, the changes in the colonic BA profile especially that of tauro-beta-muricholic acid (TβMCA), were predominantly associated with the inhibition of the FXR and further altered BA synthesis and transport. In conclusion, the administration of antibiotics significantly decreased the intestinal microbiota diversity and subsequently altered the BA composition. The alterations in BA composition contributed to cholestasis in IF patients by regulating FXR signaling.\n\nAdministration of antibiotics contributes to cholestasis in pediatric patients with intestinal failure via the alteration of FXR signaling.", "token_count": 487, "char_count": 1951, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5299, "quality_score": 0.7649, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:35.526946", "source": { "split": "train_shard_00000", "doc_id": 3186 }, "chunk_id": "train_shard_00000_3186_0", "global_id": 3526 }, { "text": "Emodin is an active ingredient in many herbal medicines and has a broad spectrum of pharmacological activities. The current data indicate that emodin exerts its beneficial effect on alpha-naphthylisothiocyanate (ANIT)-induced intrahepatic cholestasis through its anti-oxidant and anti-inflammatory activities. Emodin has little effect on the concentrations of bile acids (BAs) in livers of ANIT-treated mice. Instead, emodin shows a potential pro-cholestatic effect by interfering with the crosstalk between AMP-activated protein kinase (AMPK) and farnesoid X receptor (Fxr) in the liver, which leads to a suppression of bile salt export pump (Bsep). Two emodin-containing herbs, namely Polygonum multiflorum (PM) and Semen cassiae (SC), markedly aggravate the intrahepatic cholestasis in ANIT-treated mice. SC interferes with the AMPK-Fxr crosstalk and suppresses Bsep in livers of mice. ANIT markedly increases the hepatic retention of emodin in SC-treated mice. The major SC constituents, in particular three anthraquinones, are able to activate AMPK in HepG2 cells and inhibit Bsep in primary mouse hepatocytes, with emodin showing the strongest activities. Together, the present study identifies a potential pro-cholestatic role of emodin in the hepatotoxicity of herbs.\n\nParadoxical Effects of Emodin on ANIT-Induced Intrahepatic Cholestasis and Herb-Induced Hepatotoxicity in Mice.", "token_count": 413, "char_count": 1388, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:36.148450", "source": { "split": "train_shard_00000", "doc_id": 3187 }, "chunk_id": "train_shard_00000_3187_0", "global_id": 3527 }, { "text": "The pathogenesis of Salmonella enterica serovar Typhi (S. Typhi), the cause of typhoid fever in humans, is mainly attributed to the acquisition of horizontally acquired DNA elements. Salmonella pathogenicity islands (SPIs) are indubitably the most important form of horizontally acquired DNA with respect to pathogenesis of this bacterium. The insertion or deletion of any of these transferrable SPIs may have impact on the virulence potential of S. Typhi. In this study, the virulence potential and genetic relatedness of 35 S. Typhi isolates, collected from 2004 to 2013 was determined by identification of SPI and non-SPI virulence factors through a combination of techniques including virulotyping, Whole Genome Sequencing (WGS), and Variable Number of Tandem Repeats (VNTR) profiling. In order to determine the virulence potential of local S. Typhi isolates, 56 virulence related genes were studied by PCR. These genes are located in the core as well as accessory genome (SPIs and plasmid). Major variations among studied virulence determinants were found in case of SPI-7 and SPI-10 associated genes. On the basis of presence of virulence related genes, the studied S. Typhi isolates from Pakistan were clustered into two virulotypes Vi-positive and Vi-negative. Interestingly, SPI-7 and SPI-10 were collectively absent or present in Vi-negative and Vi-positive strains, respectively. Two Vi-negative and 11 Vi-positive S. Typhi strains were also analyzed by whole genome sequencing (WGS) and their results supported the PCR results. Genetic diversity was tested by VNTR-based molecular typing. All 35 isolates were clustered into five groups. Overall, all Vi-negative isolates were placed in a single group (T5) whereas Vi-positive isolates were grouped into four types. Vi-negative and Vi-positive isolates were mutually exclusive. This is the first report on the comparative distribution of SPI and non-SPI related virulence genes in Vi-negative and Vi-positive S. Typhi isolates with an important finding that SPI-10 is absent in all Vi-negative isolates.", "token_count": 524, "char_count": 2065, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5359, "quality_score": 0.768, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:30:36.810298", "source": { "split": "train_shard_00000", "doc_id": 3188 }, "chunk_id": "train_shard_00000_3188_0", "global_id": 3528 }, { "text": "Virulotyping of Salmonella enterica serovar Typhi isolates from Pakistan: Absence of complete SPI-10 in Vi negative isolates.", "token_count": 35, "char_count": 125, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:37.167687", "source": { "split": "train_shard_00000", "doc_id": 3188 }, "chunk_id": "train_shard_00000_3188_1", "global_id": 3529 }, { "text": "During the last decade a special interest has been focused on studying the relationship between the composition and structure of emulsions and the extent of lipolysis, driven by the necessity of modulate lipid digestion to decrease or delay fats absorption or increase healthy fat nutrients bioavailability. Because bile salts (BS) play a crucial role in lipids metabolism, understanding how typical food emulsifiers affect the structures of BS under duodenal conditions, can aid to further understand how to control lipids digestion. In the present work the BS-binding capacity of three emulsifiers (Lecithin, Tween 80 and β-lactoglobulin) was studied under duodenal conditions. The combination of several techniques (DLS, TEM, ζ-potential and conductivity) allowed the characterization of molecular assemblies resulting from the interactions, as modulated by the relative amounts of BS and emulsifiers in solution.\n\nStudies on the interactions between bile salts and food emulsifiers under in vitro duodenal digestion conditions to evaluate their bile salt binding potential.", "token_count": 241, "char_count": 1077, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:37.653686", "source": { "split": "train_shard_00000", "doc_id": 3189 }, "chunk_id": "train_shard_00000_3189_0", "global_id": 3530 }, { "text": "The huge increase in the availability of bacterial genomes led us to a point in which we can investigate and query pan-genomes, for example, the full set of genes of a given bacterial species or clade. Here, we used a data set of 1,311 high-quality genomes from the human pathogen Pseudomonas aeruginosa, 619 of which were newly sequenced, to show that a pan-genomic approach can greatly refine the population structure of bacterial species, provide new insights to define species boundaries, and generate hypotheses on the evolution of pathogenicity. The 665-gene P. aeruginosa core genome presented here, which constitutes only 1% of the entire pan-genome, is the first to be in the same order of magnitude as the minimal bacterial genome and represents a conservative estimate of the actual core genome. Moreover, the phylogeny based on this core genome provides strong evidence for a five-group population structure that includes two previously undescribed groups of isolates. Comparative genomics focusing on antimicrobial resistance and virulence genes showed that variation among isolates was partly linked to this population structure. Finally, we hypothesized that horizontal gene transfer had an important role in this respect, and found a total of 3,010 putative complete and fragmented plasmids, 5% and 12% of which contained resistance or virulence genes, respectively. This work provides data and strategies to study the evolutionary trajectories of resistance and virulence in P. aeruginosa.\n\nThe Pseudomonas aeruginosa Pan-Genome Provides New Insights on Its Population Structure, Horizontal Gene Transfer, and Pathogenicity.", "token_count": 382, "char_count": 1641, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:38.242204", "source": { "split": "train_shard_00000", "doc_id": 3190 }, "chunk_id": "train_shard_00000_3190_0", "global_id": 3531 }, { "text": "The use of thermotolerant yeast strains is an important attribute for a cost-effective high temperature biofermentation processes. However, the availability of thermotolerant yeast strains remains a major challenge. Isolation of temperature resistant strains from extreme environments or the improvements of current strains are two major strategies known to date. We hypothesised that bacteria are potential \"hurdles\" in the life cycle of yeasts, which could influence the evolution of extreme phenotypes, such as thermotolerance. We subjected a wild-type yeast, Lachancea thermotolerans to six species of bacteria sequentially for several generations. After coevolution, we observed that three replicate lines of yeasts grown in the presence of bacteria grew up to 37 °C whereas the controls run in parallel without bacteria could only grow poorly at 35 °C retaining the ancestral mesophilic trait. In addition to improvement of thermotolerance, our results show that the fermentative ability was also elevated, making the strains more ideal for the alcoholic fermentation process because the overall productivity and ethanol titers per unit volume of substrate consumed during the fermentation process was increased. Our unique method is attractive for the development of thermotolerant strains or to augment the available strain development approaches for high temperature industrial biofermentation.\n\nImprovement of thermotolerance in Lachancea thermotolerans using a bacterial selection pressure.", "token_count": 321, "char_count": 1501, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6476, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:38.811486", "source": { "split": "train_shard_00000", "doc_id": 3191 }, "chunk_id": "train_shard_00000_3191_0", "global_id": 3532 }, { "text": "Some of the most common infectious diseases are caused by bacteria that naturally colonise humans asymptomatically. Combating these opportunistic pathogens requires an understanding of the traits that differentiate infecting strains from harmless relatives. Staphylococcus epidermidis is carried asymptomatically on the skin and mucous membranes of virtually all humans but is a major cause of nosocomial infection associated with invasive procedures. Here we address the underlying evolutionary mechanisms of opportunistic pathogenicity by combining pangenome-wide association studies and laboratory microbiology to compare S. epidermidis from bloodstream and wound infections and asymptomatic carriage. We identify 61 genes containing infection-associated genetic elements (k-mers) that correlate with in vitro variation in known pathogenicity traits (biofilm formation, cell toxicity, interleukin-8 production, methicillin resistance). Horizontal gene transfer spreads these elements, allowing divergent clones to cause infection. Finally, Random Forest model prediction of disease status (carriage vs. infection) identifies pathogenicity elements in 415 S. epidermidis isolates with 80% accuracy, demonstrating the potential for identifying risk genotypes pre-operatively.\n\nDisease-associated genotypes of the commensal skin bacterium Staphylococcus epidermidis.", "token_count": 303, "char_count": 1366, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:39.372122", "source": { "split": "train_shard_00000", "doc_id": 3192 }, "chunk_id": "train_shard_00000_3192_0", "global_id": 3533 }, { "text": "In order to colonize the human gastrointestinal tract and exert their beneficial effects, bifidobacteria must effectively cope with toxic bile salts in the intestine; however, the molecular mechanism underlying bile tolerance is poorly understood. In this study, heterologous expression of a MarR family transcriptional regulator, BmrR, significantly reduced the ox bile resistance of\n\nThe MarR Family Regulator BmrR Is Involved in Bile Tolerance of", "token_count": 107, "char_count": 449, "word_count": 64, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:39.756906", "source": { "split": "train_shard_00000", "doc_id": 3193 }, "chunk_id": "train_shard_00000_3193_0", "global_id": 3534 }, { "text": "Candida species are harmless commensals of hosts, including humans, but they can cause infection when the immune system is compromised. Infections with non-albicans species can occur, ranging from urinary tract infections to sepsis, especially among patients in intensive care units.\n\nCase Report of a Tubo-ovarian Abscess Caused by Candida kefyr.", "token_count": 86, "char_count": 347, "word_count": 50, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:40.143993", "source": { "split": "train_shard_00000", "doc_id": 3194 }, "chunk_id": "train_shard_00000_3194_0", "global_id": 3535 }, { "text": "Bile acids have received considerable interest in the drug delivery research due to their peculiar physicochemical properties and biocompatibility. The main advantage of bile acids as drug absorption enhancers is their ability to act as both drug solubilizing and permeation-modifying agents. Therefore, bile acids may improve bioavailability of drugs whose absorption-limiting factors include either poor aqueous solubility or low membrane permeability. Besides, bile acids may withstand the gastrointestinal impediments and aid in the transporter-mediated absorption of physically complexed or chemically conjugated drug molecules. These biomolecules may increase the drug bioavailability also at submicellar levels by increasing the solubility and dissolution rate of non-polar drugs or through the partition into the membrane and increase of membrane fluidity and permeability. Most bile acid-induced effects are mediated by the nuclear receptors that activate transcriptional networks, which then affect the expression of a number of target genes, including those for membrane transport proteins, affecting the bioavailability of a number of drugs. Besides micellar solubilization, there are many other types of interactions between bile acids and drug molecules, which can influence the drug transport across the biological membranes. Most common drug-bile salt interaction is ion-pairing and the formed complexes may have either higher or lower polarity compared to the drug molecule itself. Furthermore, the hydroxyl and carboxyl groups of bile acids can be utilized for the covalent conjugation of drugs, which changes their physicochemical and pharmacokinetic properties. Bile acids can be utilized in the formulation of conventional dosage forms, but also of novel micellar, vesicular and polymer-based therapeutic systems. The availability of bile acids, along with their simple derivatization procedures, turn them into attractive building blocks for the design of novel pharmaceutical formulations and systems for the delivery of drugs, biomolecules and vaccines. Although toxic properties of hydrophobic bile acids have been described, their side effects are mostly produced when present in supraphysiological concentrations", "token_count": 489, "char_count": 2239, "word_count": 309, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:40.794307", "source": { "split": "train_shard_00000", "doc_id": 3195 }, "chunk_id": "train_shard_00000_3195_0", "global_id": 3536 }, { "text": "Besides, minor structural modifications of natural bile acids may lead to the creation of bile acid derivatives with the reduced toxicity and preserved absorption-enhancing activity.\n\nBile Acids and Their Derivatives as Potential Modifiers of Drug Release and Pharmacokinetic Profiles.", "token_count": 64, "char_count": 285, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:41.159441", "source": { "split": "train_shard_00000", "doc_id": 3195 }, "chunk_id": "train_shard_00000_3195_1", "global_id": 3537 }, { "text": "The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here, we introduce panini (Pangenome Neighbour Identification for Bacterial Populations), a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding based on the t-SNE (t-distributed stochastic neighbour embedding) algorithm. panini is browser-based and integrates with the Microreact platform for rapid online visualization and exploration of both core and accessory genome evolutionary signals, together with relevant epidemiological, geographical, temporal and other metadata. Several case studies with single- and multi-clone pneumococcal populations are presented to demonstrate the ability to identify biologically important signals from gene content data. panini is available at http://panini.pathogen.watch and code at http://gitlab.com/cgps/panini.\n\nPANINI: Pangenome Neighbour Identification for Bacterial Populations.", "token_count": 270, "char_count": 1266, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:41.710758", "source": { "split": "train_shard_00000", "doc_id": 3196 }, "chunk_id": "train_shard_00000_3196_0", "global_id": 3538 }, { "text": "The genomes of Streptococcus agalactiae (group B streptococcus; GBS) collected from diseased fish in Thailand and Vietnam over a nine-year period (2008-2016) were sequenced and compared (n = 21). Based on capsular serotype and multilocus sequence typing (MLST), GBS isolates are divided into 2 groups comprised of i) serotype Ia; sequence type (ST)7 and ii) serotype III; ST283. Population structure inferred by core genome (cg)MLST and Bayesian clustering analysis also strongly indicated distribution of two GBS populations in both Thailand and Vietnam. Deep phylogenetic analysis implied by CRISPR array's spacer diversity was able to cluster GBS isolates according to their temporal and geographic origins, though ST7 has varying CRISPR1-spacer profiles when compared to ST283 strains. Based on overall genotypic features, Thai ST283 strains were closely related to the Singaporean ST283 strain causing foodborne illness in humans in 2015, thus, signifying zoonotic potential of this GBS population in the country.\n\nComparative genomics inferred two distinct populations of piscine pathogenic Streptococcus agalactiae, serotype Ia ST7 and serotype III ST283, in Thailand and Vietnam.", "token_count": 325, "char_count": 1187, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": { "genes": [ "ST283", "ST7", "CRISPR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:42.275172", "source": { "split": "train_shard_00000", "doc_id": 3197 }, "chunk_id": "train_shard_00000_3197_0", "global_id": 3539 }, { "text": "Lactic acid is an important industrial product and the production from inexpensive and renewable lignocellulose can reduce the cost and environmental pollution. In this study, a Kluyveromyces marxianus strain which produced lactic acid efficiently from corncob was constructed. Firstly, two of six different lactate dehydrogenases, which from Plasmodium falciparum and Bacillus subtilis, respectively, were proved to be effective for l-lactic acid production. Then, five single genetic modifications were conducted. The overexpression of Saccharomyces cerevisiae proton-coupled monocarboxylate transporter, K. marxianus 6-phosphofructokinase, or disruption of K. marxianus putative d-lactate dehydrogenase enhanced the l-lactic acid accumulation. Finally, the strain YKX071, obtained via combination of above effective genetic engineering, produced 103.00 g/L l-lactic acid at 42 °C with optical purity of 99.5% from corncob residue via simultaneous saccharification and co-fermentation. This study first developed an effective platform for high optical purity l-lactic acid production from lignocellulose using yeast with inexpensive nitrogen sources.\n\nEfficient l-lactic acid production from corncob residue using metabolically engineered thermo-tolerant yeast.", "token_count": 340, "char_count": 1263, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [ "YKX071" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:42.857381", "source": { "split": "train_shard_00000", "doc_id": 3198 }, "chunk_id": "train_shard_00000_3198_0", "global_id": 3540 }, { "text": "The decline in invasive pneumococcal disease (IPD), following the introduction of the 7-valent pneumococcal conjugate vaccination (PCV-7), was tempered by emergence of non-vaccine serotypes, particularly 19A. In Australia, three years after PCV-7 was replaced by PCV-13, containing 19A and 19F antigens, serogroup 19 was still a prominent cause of IPD in children under five. In this study we examined the evolution of serogroup 19 before and after introduction of paediatric vaccines in New South Wales (NSW), Australia. Genomes of 124 serogroup 19 IPD isolates collected before (2004) and after introduction of PCV-7 (2008) and PCV-13 (2014), from children under five in NSW, were analysed. Eleven core genome sequence clusters (cgSC) and 35 multilocus sequence types (ST) were identified. The majority (78/124) of the isolates belonged to four cgSCs: cgSC7 (ST199), cgSC11 (ST320), cgSC8 (ST63) and cgSC9 (ST2345). ST63 and ST2345 were exclusively serotype 19A and accounted for its predominantly intermediate penicillin resistance; these two clusters first appeared in 2008 and largely disappeared after introduction of PCV-13. Serogroup 19 was responsible for the highest proportion of vaccine failures in NSW. Relatively low immunogenicity of serogroup 19 antigens and Australia's three-dose vaccine schedule could affect the population dynamics of this serogroup.\n\nGenome-wide analysis of Streptococcus pneumoniae serogroup 19 in the decade after the introduction of pneumococcal conjugate vaccines in Australia.", "token_count": 457, "char_count": 1519, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [ "ST2345", "ST63", "ST320", "ST199" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:43.512179", "source": { "split": "train_shard_00000", "doc_id": 3199 }, "chunk_id": "train_shard_00000_3199_0", "global_id": 3541 }, { "text": "Enterococci are colonizers of the mammalian gastrointestinal tract (GIT) and normally live in healthy association with their human host. However, enterococci are also major causes of healthcare-acquired infections, prompting the US Centers for Disease Control and Prevention to declare vancomycin-resistant enterococci (VRE) a serious threat to public health. Because of both intrinsic and acquired antibiotic resistance, enterococci proliferate in the GIT during antibiotic therapy, leading to dissemination and disease. The recognition that colonization of the GIT is a pre-requisite for enterococcal infections has prompted research to study mechanisms used by enterococci to colonize this niche. This review discusses major findings of recent research to understand GIT colonization by enterococci using diverse experimental models, each of which exhibits unique strengths. This work has revealed enterococcal transcriptional reprogramming in the GIT, contributions of specific enterococcal genes encoded by the core genome to GIT colonization, the impact of genome plasticity, and roles for intra-species and inter-species interactions in modulation of GIT colonization.\n\nColonization of the mammalian intestinal tract by enterococci.", "token_count": 292, "char_count": 1239, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6407, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:44.110609", "source": { "split": "train_shard_00000", "doc_id": 3200 }, "chunk_id": "train_shard_00000_3200_0", "global_id": 3542 }, { "text": "The adenosine 5'‑triphosphate binding cassette subfamily B member (ABCB)11 gene is involved in bile transport, and mutations in this gene are associated with cholestasis and cholelithiasis. Therefore, the aim of the present study was to investigate the association between ABCB11 gene mutation and primary intrahepatic stone (PIS)s and to investigate the mechanism through which ABCB11 gene mutations affect the expression of the corresponding protein. Mutations of the ABCB11 gene in 443 PIS patients and 560 healthy participants were detected by exon sequencing. The expression levels of ABCB11 mRNA and bile salt export pump (BSEP) protein in the liver tissues of patients with PISs were measured by quantitative polymerase chain reaction and western blot analysis. The mutant plasmids constructed by site‑directed mutagenesis of the human BSEP gene were transfected into human embryonic kidney 293 (293) cells and Madin‑Darby canine kidney (MDCK) cells, and the expression and distribution of rs118109635 of BSEP was measured. There were two significant mutations in the ABCB11 gene of the PIS patients compared with the healthy population; a missense mutation, rs118109635 (P=0.025), and a synonymous mutation, rs497692 (P=0.006). The two mutations were associated with the occurrence of preoperative jaundice (P=0.026, and P=0.011, respectively). The expression levels of BSEP in PIS patients with the missense mutation rs118109635 was decreased, whereas its mRNA expression levels remained unchanged. In PIS patients with the synonymous mutation rs497692, the expression levels of ABCB11 were decreased at both the mRNA and protein level", "token_count": 467, "char_count": 1644, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5167, "quality_score": 0.7583, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:45.204038", "source": { "split": "train_shard_00000", "doc_id": 3201 }, "chunk_id": "train_shard_00000_3201_0", "global_id": 3543 }, { "text": "It was also found that mutation A865V reduced the expression levels of BSEP in 293 cells at the cellular level; its distribution in MDCK cell membranes was decreased, whereas its mRNA levels remained unchanged. The mutated loci at rs118109635 and rs497692 of the ABCB11 gene were correlated with PISs, causing a decreased expression of BSEP and reduced distribution of the protein in the cell membrane. Therefore, mutations at rs118109635 and rs497692 of the ABCB11 gene may be risk factors for PISs.\n\nFunctional analysis of the correlation between ABCB11 gene mutation and primary intrahepatic stone.", "token_count": 178, "char_count": 601, "word_count": 94, "semantic_coherence": 1, "information_density": 0.6383, "quality_score": 0.8191, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:45.638743", "source": { "split": "train_shard_00000", "doc_id": 3201 }, "chunk_id": "train_shard_00000_3201_1", "global_id": 3544 }, { "text": "The Gram positive bacterium\n\nPuzzling Over the Pneumococcal Pangenome.", "token_count": 21, "char_count": 70, "word_count": 9, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:45.993828", "source": { "split": "train_shard_00000", "doc_id": 3202 }, "chunk_id": "train_shard_00000_3202_0", "global_id": 3545 }, { "text": "We aimed to investigate the effects of red ginseng extract (RGE) on the expression of efflux transporters and to study the pharmacokinetics of representative substrate. For this, rats received single or repeated administration of RGE (1.5 g/kg/day) for 1 and 2 weeks via oral gavage. mRNA and protein levels of multidrug resistance-associated protein2 (Mrp2), bile salt export pump (Bsep), and P-glycoprotein (P-gp) in the rat liver were measured via real-time polymerase chain reaction and Western blot analysis. Ginsenosides concentrations from the rat plasma were also monitored using a liquid chromatography⁻tandem mass spectrometry (LC⁻MS/MS) system. Plasma concentrations of ginsenoside Rb1, Rb2, Rc, and Rd following repeated administration of RGE for 1 and 2 weeks were comparable but significantly higher than those after single administration of RGE. These dosing regimens did not induce significant biochemical abnormalities in the liver, kidneys, and lipid homeostasis. In the RGE repeated oral administration groups, the mRNA and protein levels of Mrp2 significantly decreased. Accordingly, we investigated the changes in the pharmacokinetics of methotrexate, a probe substrate for Mrp2, following intravenous administration of 3 mg/kg methotrexate to rats in the RGE 1-week repeated oral administration group, compared to that in the control group. Biliary excretion, but not urinary excretion, of methotrexate decreased in the RGE repeated administration group, compared to that in the control group. Consequently, the plasma concentrations of methotrexate slightly increased in the RGE repeated administration group. In conclusion, repeated administration of RGE for 1 week resulted in a decrease in Mrp2 expression without inducing significant liver or kidney damage. Pharmacokinetic herb⁻drug interaction between RGE and methotrexate might occur owing to the decrease in the mRNA and protein levels of Mrp2.", "token_count": 494, "char_count": 1925, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5326, "quality_score": 0.7663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:46.639597", "source": { "split": "train_shard_00000", "doc_id": 3203 }, "chunk_id": "train_shard_00000_3203_0", "global_id": 3546 }, { "text": "Effects of Red Ginseng Extract on the Pharmacokinetics and Elimination of Methotrexate via Mrp2 Regulation.", "token_count": 35, "char_count": 107, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:46.991999", "source": { "split": "train_shard_00000", "doc_id": 3203 }, "chunk_id": "train_shard_00000_3203_1", "global_id": 3547 }, { "text": "Borrelia burgdorferi sensu lato comprises a species complex of tick-transmitted bacteria that includes the agents of human Lyme borreliosis. Borrelia turdi is a genospecies of this complex that exists in cryptic transmission cycles mainly between ornithophilic tick vectors and their avian hosts. The species has been originally discovered in avian transmission cycles in Asia but has increasingly been found in Europe. Next generation sequencing was used to sequence the genome of B. turdi isolates obtained from ticks feeding on birds in Portugal to better understand the evolution and phylogenetic relationship of this avian and ornithophilic tick-associated genospecies. Here we use draft genomes of these B. turdi isolates for comparative analysis and to determine the taxonomic position within the B. burgdorferi s.l. species complex. The main chromosomes showed a maximum similarity of 93% to other Borrelia species whilst most plasmids had lower similarities. All three isolates had nine or 10 plasmids and, interestingly, one plasmid with a novel partitioning protein; this plasmid was termed lp30. Phylogenetic analysis of multilocus sequence typing housekeeping genes and 113 single copy orthologous genes revealed that the isolates clustered according to their classification as B. turdi. In phylogenies generated from these 113 genes the isolates cluster together with other Eurasian genospecies and form a sister clade to the avian associated B. garinii and the rodent associated B. bavariensis. These findings show that Borrelia species maintained in cryptic ecological cycles need to be included to fully understand the complex ecology and evolutionary history of this bacterial species complex.\n\nCore genome phylogenetic analysis of the avian associated Borrelia turdi indicates a close relationship to Borrelia garinii.", "token_count": 438, "char_count": 1837, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5746, "quality_score": 0.7873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:47.613581", "source": { "split": "train_shard_00000", "doc_id": 3204 }, "chunk_id": "train_shard_00000_3204_0", "global_id": 3548 }, { "text": "Plant-beneficial Pseudomonas spp. competitively colonize the rhizosphere and display plant-growth promotion and/or disease-suppression activities. Some strains within the P. fluorescens species complex produce phenazine derivatives, such as phenazine-1-carboxylic acid. These antimicrobial compounds are broadly inhibitory to numerous soil-dwelling plant pathogens and play a role in the ecological competence of phenazine-producing Pseudomonas spp. We assembled a collection encompassing 63 strains representative of the worldwide diversity of plant-beneficial phenazine-producing Pseudomonas spp. In this study, we report the sequencing of 58 complete genomes using PacBio RS II sequencing technology. Distributed among four subgroups within the P. fluorescens species complex, the diversity of our collection is reflected by the large pangenome which accounts for 25 413 protein-coding genes. We identified genes and clusters encoding for numerous phytobeneficial traits, including antibiotics, siderophores and cyclic lipopeptides biosynthesis, some of which were previously unknown in these microorganisms. Finally, we gained insight into the evolutionary history of the phenazine biosynthetic operon. Given its diverse genomic context, it is likely that this operon was relocated several times during Pseudomonas evolution. Our findings acknowledge the tremendous diversity of plant-beneficial phenazine-producing Pseudomonas spp., paving the way for comparative analyses to identify new genetic determinants involved in biocontrol, plant-growth promotion and rhizosphere competence.\n\nDiversity of phytobeneficial traits revealed by whole-genome analysis of worldwide-isolated phenazine-producing Pseudomonas spp.", "token_count": 427, "char_count": 1719, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6729, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:48.248179", "source": { "split": "train_shard_00000", "doc_id": 3205 }, "chunk_id": "train_shard_00000_3205_0", "global_id": 3549 }, { "text": "Porcine circovirus type 2 (PCV2) is a ubiquitous virus with high pathogenicity closely associated with the postweaning multisystemic wasting syndrome (PMWS) and porcine circovirus diseases (PCVDs), which caused significant economic losses in the swine industry worldwide every year. The PCV2 virus-like particles (VLPs) are a powerful subunit vaccine that can elicit high immune response due to its native PCV2 virus morphology. The baculovirus expression system is the widely used platform for producing commercial PCV2 VLP vaccines, but its yield and cost limited the development of low-cost vaccines for veterinary applications. Here, we applied a nonconventional yeast Kluyveromyces marxianus to enhance the production of PCV2 VLPs. After codon optimization, the PCV2 Cap protein was expressed in K. marxianus and assemble spontaneously into VLPs. Using a chemically defined medium, we achieved approximately 1.91 g/L of PCV2 VLP antigen in a 5-L bioreactor after high cell density fermentation for 72 h. That yield greatly exceeded to recently reported PCV2 VLPs obtained by baculovirus-insect cell, Escherichia coli and Pichia pastoris. By the means of two-step chromatography, 652.8 mg of PCV2 VLP antigen was obtained from 1 L of the recombinant K. marxianus cell culture. The PCV2 VLPs induced high level of anti-PCV2 IgG antibody in mice serums and decreased the virus titers in both livers and spleens of the challenged mice. These results illustrated that K. marxianus is a powerful yeast for cost-effective production of PCV2 VLP vaccines.\n\nEfficient production of porcine circovirus virus-like particles using the nonconventional yeast Kluyveromyces marxianus.", "token_count": 465, "char_count": 1674, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8117, "entities": { "genes": [ "PCV2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:48.890060", "source": { "split": "train_shard_00000", "doc_id": 3206 }, "chunk_id": "train_shard_00000_3206_0", "global_id": 3550 }, { "text": "It is generally considered that bile salt hydrolase (BSH) activity is hardly detected in nonintestinal lactic acid bacteria (LAB). The aim of this study was to investigate the distribution and intensity of BSH activity in LAB isolated from naturally fermented vegetables and milk. A total of 624 lactic acid bacterial strains classified into 6 genera and 50 species were isolated from 144 naturally fermented vegetable samples and 103 naturally fermented milk samples, and their BSH activity was screened by gas chromatography with electron capture detection. The BSH-positive strains were further analyzed quantitatively for their deconjugation ability against six human-conjugated bile salts by HPLC based on the disappearance of the conjugated bile salts from the reaction mixture. The results showed that 39% of the strains possessed BSH activity distributed in 24 lactic acid bacterial species. The strains of the fermented vegetable origin showed a 0.5-fold higher incidence of BSH-positive strains than those of the fermented milk origin, and the lactic acid bacilli exhibited 2.5-fold higher incidence of BSH-positive strains than the lactic acid cocci in general. The strains of the fermented vegetable origin generally had greater bile salt deconjugation ability than those of the fermented milk origin. More than 97% and 93% of the BSH-positive strains exhibited a greater substrate preference for glycoconjugated bile salts than tauroconjugated bile salts and for dihydroxy bile salts than trihydroxy bile salts, respectively. This study demonstrated that BSH activity was also present in nonintestinal LAB.\n\nBile salt hydrolase activity is present in nonintestinal lactic acid bacteria at an intermediate level.", "token_count": 441, "char_count": 1724, "word_count": 255, "semantic_coherence": 1, "information_density": 0.4824, "quality_score": 0.7412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:49.529775", "source": { "split": "train_shard_00000", "doc_id": 3207 }, "chunk_id": "train_shard_00000_3207_0", "global_id": 3551 }, { "text": "Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or detailed assessment of marker effect. Recently, alignment-free methods based on k-mer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are sometimes hard to interpret. Here we introduce DBGWAS, an extended k-mer-based GWAS method producing interpretable genetic variants associated with distinct phenotypes. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes, identified by the association model, into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is alignment-free and only requires a set of contigs and phenotypes. In particular, it does not require prior annotation or reference genomes. It produces subgraphs representing phenotype-associated genetic variants such as local polymorphisms and mobile genetic elements (MGE). It offers a graphical framework which helps interpret GWAS results. Importantly it is also computationally efficient-experiments took one hour and a half on average. We validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis, and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa-along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature. An open-source tool implementing DBGWAS is available at https://gitlab.com/leoisl/dbgwas.\n\nA fast and agnostic method for bacterial genome-wide association studies: Bridging the gap between k-mers and genetic events.", "token_count": 413, "char_count": 1838, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6895, "quality_score": 0.8448, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:50.151284", "source": { "split": "train_shard_00000", "doc_id": 3208 }, "chunk_id": "train_shard_00000_3208_0", "global_id": 3552 }, { "text": "Bile acid imbalance causes progressive familial intrahepatic cholestasis type 2 (PFIC2) or type 3 (PFIC3), severe liver diseases associated with genetic defects in the biliary bile acid transporter bile salt export pump (BSEP; ABCB11) or phosphatidylcholine transporter multidrug resistance protein 3 (MDR3; ABCB4), respectively.\n\nHydrophilic bile acids prevent liver damage caused by lack of biliary phospholipid in", "token_count": 121, "char_count": 416, "word_count": 57, "semantic_coherence": 1, "information_density": 0.807, "quality_score": 0.9035, "entities": { "genes": [ "ABCB4", "MDR3", "PFIC2", "ABCB11", "PFIC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:50.542169", "source": { "split": "train_shard_00000", "doc_id": 3209 }, "chunk_id": "train_shard_00000_3209_0", "global_id": 3553 }, { "text": "Weaning glass eels with compound diets (36% proteins, 16% lipids) differing in their fishmeal (FM) level (50, 75 and 100% FM replaced by a blend of plant proteins, PP) was compared to a group fed cod roe. Weaning lasted for 20 days and then, eels were fed compound diets for 70 days, whereas the other group was only fed cod roe (90 days). Diets were tested with four replicates and evaluated in terms of growth, survival, glass eels metamorphosis into elvers, oxidative stress status and activity of digestive enzymes. Although glass eels are traditionally fed with fish roe and progressively weaned onto compound diets, results revealed that this strategy should not be prolonged for a long time, since feeding glass eels with cod roe for 90 days negatively affected their growth (2 times lower than fish fed compound diets), delayed their metamorphosis, as well as the maturation of their digestive function as the ratio of alkaline phosphatase and leucine-alanine peptidase indicated. Weaning glass eels onto compound diets differing in their FM levels did not affect their growth, metamorphic stage nor the activity of pancreatic enzymes (total alkaline proteases, trypsin, bile salt-activated lipase and α-amylase), although 75% FM replacement by PP sources delayed the level of intestinal maturation in eels. In comparison to glass eels fed the 100% FM diet, survival was negatively affected in groups fed diets with 50 and 75% FM replacement by PP ingredients, which indicated that further improvement is needed in diet formulation for this stage of development.\n\nWeaning European glass eels (Anguilla anguilla) with plant protein-based diets and its effects on intestinal maturation.", "token_count": 452, "char_count": 1692, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5693, "quality_score": 0.7846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:51.178495", "source": { "split": "train_shard_00000", "doc_id": 3210 }, "chunk_id": "train_shard_00000_3210_0", "global_id": 3554 }, { "text": "Yeasts, lactic and acetic acid bacteria are responsible of microbial spoilage of alcoholic beverages. However species involved in deterioration of sorghum beer produced in Côte d'Ivoire has not been investigated. This study was carried out to identify species of yeast, LAB and AAB during spoilage of tchapalo in order to define the best strategy for beer preservative. Thus, a total of 210 yeasts, LAB and AAB were isolated from samples of tchapalo stored at ambient temperature and at 4 °C for 3 days. Based on PCR-RFLP of the ITS region and the sequencing of D1/D2 domain, yeast isolates were assigned to seven species (Saccharomyces cerevisiae, Candida tropicalis, Rhodotorula mucilaginosa, Trichosporon asahii, Kluyveromyces marxianus, Meyerozyma guilliermondii and Trichosporon coremiiforme). During the storage at ambient temperature and at 4 °C, S. cerevisiae was the predominant species (> 76%). Excepted R. mucilaginosa, occurrence of non-Saccharomyces species was sporadic. LAB species detected in fresh samples using molecular methods were Pediococcus acidilactici, Lactobacillus paracasei, Lb. curvatus, Lb. fermentum and Weisssella paramesenteroides. P. acidilactici was the dominant species (47.8%) followed by Lb. paracasei (17.5%). W. paramesenteroides and Lb. fermentum were not detected during the spoilage at ambient temperature while at 4 °C W. paramesenteroides and Lb. paracasei have not been detected. For AAB, the species found were Acetobacter pasteurianus sub paradoxus and Acetobacter cerevisiae. These species were common to all samples during spoilage and A. pasteurianus sub paradoxus was the most frequently detected.", "token_count": 493, "char_count": 1649, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5865, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:51.826844", "source": { "split": "train_shard_00000", "doc_id": 3211 }, "chunk_id": "train_shard_00000_3211_0", "global_id": 3555 }, { "text": "Molecular identification of yeast, lactic and acetic acid bacteria species during spoilage of tchapalo, a traditional sorghum beer from Côte d'Ivoire.", "token_count": 41, "char_count": 150, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:52.184172", "source": { "split": "train_shard_00000", "doc_id": 3211 }, "chunk_id": "train_shard_00000_3211_1", "global_id": 3556 }, { "text": "Comparative genomic/metabolomic analysis is a powerful tool to disclose the potential of microbes for the biosynthesis of novel specialized metabolites. In the group of marine myxobacteria only a limited number of isolated species and sequenced genomes is so far available. However, the few compounds isolated thereof so far show interesting bioactivities and even novel chemical scaffolds; thereby indicating a huge potential for natural product discovery. In this study, all marine myxobacteria with accessible genome data (n = 5), including Haliangium ochraceum DSM 14365, Plesiocystis pacifica DSM 14875, Enhygromyxa salina DSM 15201 and the two newly sequenced species Enhygromyxa salina SWB005 and SWB007, were analyzed. All of these accessible genomes are large (~10 Mb), with a relatively small core genome and many unique coding sequences in each strain. Genome analysis revealed a high variety of biosynthetic gene clusters (BGCs) between the strains and several resistance models and essential core genes indicated the potential to biosynthesize antimicrobial molecules. Polyketides (PKs) and terpenes represented the majority of predicted specialized metabolite BGCs and contributed to the highest share between the strains. BGCs coding for non-ribosomal peptides (NRPs), PK/NRP hybrids and ribosomally synthesized and post-translationally modified peptides (RiPPs) were mostly strain specific. These results were in line with the metabolomic analysis, which revealed a high diversity of the chemical features between the strains. Only 6-11% of the metabolome was shared between all the investigated strains, which correlates to the small core genome of these bacteria (13-16% of each genome). In addition, the compound enhygrolide A, known from E. salina SWB005, was detected for the first time and structurally elucidated from Enhygromyxa salina SWB006", "token_count": 497, "char_count": 1866, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.806, "entities": { "genes": [ "SWB005", "SWB006", "SWB007" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:52.834944", "source": { "split": "train_shard_00000", "doc_id": 3212 }, "chunk_id": "train_shard_00000_3212_0", "global_id": 3557 }, { "text": "The here acquired data corroborate that these microorganisms represent a most promising source for the detection of novel specialized metabolites.\n\nAnalysis of the Genome and Metabolome of Marine Myxobacteria Reveals High Potential for Biosynthesis of Novel Specialized Metabolites.", "token_count": 67, "char_count": 282, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:53.200063", "source": { "split": "train_shard_00000", "doc_id": 3212 }, "chunk_id": "train_shard_00000_3212_1", "global_id": 3558 }, { "text": "Cholestasis impairs liver regeneration following partial liver resection (PHx). Bile acid receptor farnesoid X-receptor (FXR) is a key mediator of liver regeneration. The effects of FXR agonist obeticholic acid (OCA) on liver (re)growth were therefore studied in cholestatic rats. Animals underwent sham surgery or reversible bile duct ligation (rBDL). PHx with concurrent internal biliary drainage was performed 7 days after rBDL. Animals were untreated or received OCA (10 mg/kg/day) per oral gavage from rBDL until sacrifice. After 7 days of OCA treatment, dry liver weight increased in the rBDL + OCA group, indicating OCA-mediated liver growth. Enhanced proliferation in the rBDL + OCA group prior to PHx concurred with a rise in Ki67-positive hepatocytes, elevated hepatic Ccnd1 and Cdc25b expression, and an induction of intestinal fibroblast growth factor 15 expression. Liver regrowth after PHx was initially stagnant in the rBDL + OCA group, possibly due to hepatomegaly prior to PHx. OCA increased hepatobiliary injury markers during BDL, which was accompanied by upregulation of the bile salt export pump. There were no differences in histological liver injury. In conclusion, OCA induces liver growth in cholestatic rats prior to PHx but exacerbates biliary injury during cholestasis, likely by forced pumping of bile acids into an obstructed biliary tree.\n\nFXR agonist obeticholic acid induces liver growth but exacerbates biliary injury in rats with obstructive cholestasis.", "token_count": 441, "char_count": 1489, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:53.831270", "source": { "split": "train_shard_00000", "doc_id": 3213 }, "chunk_id": "train_shard_00000_3213_0", "global_id": 3559 }, { "text": "The current study documents enhanced apparent solubility of the BCS class II drug celecoxib (CXB) when formulated as solid phospholipid dispersion (SPD) with either mono- or diacyl-phospholipids by freeze drying from hydro-alcoholic solvent. The enhanced solubility upon dispersion in buffer or fasted state simulated intestinal fluid (FaSSIF) is interpreted to be due to two effects: (1) amorphization of CXB, inducing supersaturation, which is also observed when CXB is freeze dried in the absence of phospholipids and (2) association of CXB with spontaneously forming colloidal structures, such as vesicles and/or micelles, promoting solubilization. The latter effect depended on the CXB-to-phospholipid ratio, where monoacyl-phospholipid was a more efficient solubilizer than diacyl-phospholipid. In the case of diacyl-phospholipid, solubilization also depended strongly on the dispersion medium, where FaSSIF induced a more pronounced solubilization effect than buffer. In contrast, a significantly enhanced in-vitro permeability of CXB across a biomimetic barrier (Permeapad®) was found only with low lipid contents up to a CXB to phospholipid mass-ratio of 1:10 or in the absence of phospholipid; above this critical ratio, permeability was not enhanced, i.e. comparable to that observed with a suspension of non-processed (crystalline) drug. This non-linear dissolution-/permeation-behavior was observed independently of (1) the type of phospholipid (monoacyl- or diacyl-) employed and (2) the dispersion medium (buffer or FaSSIF), despite the fact that different patterns of co-existing colloidal states were observed from mono-/diacyl-phospholipid formulations in buffer/FaSSIF (small bile salt micelles, intermediate size mixed micelles and large vesicular structures), assessed by asymmetric flow field-flow fractionation/multi angle laser light scattering", "token_count": 512, "char_count": 1868, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6574, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:54.489712", "source": { "split": "train_shard_00000", "doc_id": 3214 }, "chunk_id": "train_shard_00000_3214_0", "global_id": 3560 }, { "text": "A uniform mechanistic hypothesis is presented to describe the impact of phospholipids on CXB permeation behavior: Obviously, the critical drug-to-phospholipid ratio represents a compromise between optimal stabilization of the amorphous state-induced supersaturation and reduced thermodynamic activity of CXB due to association with colloidal states, where the type of colloidal state (vesicle or micelle) appears to be of minor importance.\n\nA dynamic in vitro permeation study on solid mono- and diacyl-phospholipid dispersions of celecoxib.", "token_count": 134, "char_count": 541, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7671, "quality_score": 0.8836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:54.932556", "source": { "split": "train_shard_00000", "doc_id": 3214 }, "chunk_id": "train_shard_00000_3214_1", "global_id": 3561 }, { "text": "The gut microbiome regulates important host metabolic pathways including xenobiotic metabolism and intermediary metabolism, such as the conversion of primary bile acids (BAs) into secondary BAs. The nuclear receptors pregnane X receptor (PXR) and constitutive androstane receptor (CAR) are well-known regulators for xenobiotic biotransformation in liver. However, little is known regarding the potential effects of PXR and CAR on the composition and function of the gut microbiome. To test our hypothesis that activation of PXR and CAR regulates gut microbiota and secondary BA synthesis, 9-week-old male conventional and germ-free mice were orally gavaged with corn oil, PXR agonist PCN (75 mg/kg), or CAR agonist TCPOBOP (3 mg/kg) once daily for 4 days. PCN and TCPOBOP decreased two taxa in the Bifidobacterium genus, which corresponded with decreased gene abundance of the BA-deconjugating enzyme bile salt hydrolase. In liver and small intestinal content of germ-free mice, there was a TCPOBOP-mediated increase in total, primary, and conjugated BAs corresponding with increased Cyp7a1 mRNA. Bifidobacterium, Dorea, Peptociccaceae, Anaeroplasma, and Ruminococcus positively correlated with T-UDCA in LIC, but negatively correlated with T-CDCA in serum. In conclusion, PXR and CAR activation downregulates BA-metabolizing bacteria in the intestine and modulates BA homeostasis in a gut microbiota-dependent manner.\n\nPharmacological Activation of PXR and CAR Downregulates Distinct Bile Acid-Metabolizing Intestinal Bacteria and Alters Bile Acid Homeostasis.", "token_count": 448, "char_count": 1561, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:55.600635", "source": { "split": "train_shard_00000", "doc_id": 3215 }, "chunk_id": "train_shard_00000_3215_0", "global_id": 3562 }, { "text": "The purpose of this study was to evaluate Bacillus sp. SJ-10, isolated from traditional Korean seafood, as a probiotic. Strain SJ-10 was demonstrated to be safe, on the basis of in vitro tests confirming the absence of cytotoxicity, hemolysis, and genes with toxigenic potential, and was susceptible to antibiotics. It met the probiotic prerequisites of a spore count that remained almost constant, acid and bile tolerance under simulated gastrointestinal conditions, and significant adhesion to Caco-2 cells. Moreover, SJ-10 demonstrated beneficial properties as a probiotic: broad-spectrum antimicrobial activity, hydroxyl radical, antioxidant activity, production of functional enzymes such as β-galactosidase and phytase, and selective growth via β-glucan fermentation. The fish-feeding trial demonstrated that olive flounder fed diets containing SJ-10 alone or in combination with β-glucan exhibited significantly higher growth performance and pathogenic disease resistance compared with those fed diets containing β-glucan alone, indicating that SJ-10 diets exerted a beneficial effect as an antibiotic replacer in terms of growth performance and disease resistance in olive flounder.\n\nCharacterization of a Bacillus sp. isolated from fermented food and its synbiotic effect with barley β-glucan as a biocontrol agent in the aquaculture industry.", "token_count": 350, "char_count": 1352, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:56.208060", "source": { "split": "train_shard_00000", "doc_id": 3216 }, "chunk_id": "train_shard_00000_3216_0", "global_id": 3563 }, { "text": "To analyze the glucose repression mechanism in the thermotolerant yeast Kluyveromyces marxianus, disrupted mutants of genes for Mig1 and Rag5 as orthologs of Mig1 and Hxk2, respectively, in Saccharomyces cerevisiae were constructed, and their characteristics were compared with those of the corresponding mutants of S. cerevisiae. MIG1 mutants of both yeasts exhibited more resistance than the corresponding parental strains to 2-deoxyglucose (2-DOG). Histidine was found to be essential for the growth of Kmmig1, but not that of Kmrag5, suggesting that MIG1 is required for histidine biosynthesis in K. marxianus. Moreover, Kmrag5 and Schxk2 were more resistant than the corresponding MIG1 mutant to 2-DOG, and only the latter increased the utilization speed of sucrose in the presence of glucose. Kmrag5 exhibited very low activities for gluco-hexokinase and hexokinase and, unlike Schxk2, showed very slow growth and a low level of ethanol production in a glucose medium. Furthermore, Kmrag5, but not Kmmig1, exhibited high inulinase activity in a glucose medium and exhibited greatly delayed utilization of accumulated fructose in the medium containing both glucose and sucrose. Transcription analysis revealed that the expression levels of INU1 for inulinase and GLK1 for glucokinase in Kmrag5 were higher than those in the parental strain; the expression level of INU1 in Kmmig1 was higher, but the expression levels of RAG1 for a low-affinity glucose transporter in Kmmig1 and Kmrag5 were lower. These findings suggest that except for regulation of histidine biosynthesis, Mig1 and Rag5 of K. marxianus play similar roles in the regulation of gene expression and share some functions with Mig1 and Hxk2, respectively, in S. cerevisiae.\n\nFunctional analysis of Mig1 and Rag5 as expressional regulators in thermotolerant yeast Kluyveromyces marxianus.", "token_count": 509, "char_count": 1856, "word_count": 276, "semantic_coherence": 1, "information_density": 0.4891, "quality_score": 0.7446, "entities": { "genes": [ "GLK1", "MIG1", "INU1", "RAG1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:56.893063", "source": { "split": "train_shard_00000", "doc_id": 3217 }, "chunk_id": "train_shard_00000_3217_0", "global_id": 3564 }, { "text": "CRISPR/Cas-based (clustered regularly interspaced short palindromic repeats/CRISPR-associated) screening has been proved to be an efficient method to study functional genomics from yeast to human. In this study, we report the development of a focused CRISPR/Cas-based gene activation library in Saccharomyces cerevisiae and its application in gene identification based on functional screening towards improved thermotolerance. The gene activation library was subjected to screening at 42°C, and the same library cultured at 30°C was set as a control group. After five successive subcultures, five clones were randomly picked from the libraries cultured at 30 and 42°C, respectively. The five clones selected at 30°C contain the specificity sequences of five different single guide RNAs, whereas all the five clones selected at 42°C contain the specificity sequence of one sgRNA that targets the promoter region of OLE1. A crucial role of OLE1 in thermotolerance was identified: the overexpression of OLE1 increased fatty acid unsaturation, and thereby helped counter lipid peroxidation caused by heat stress, rendering the yeast thermotolerant. This study described the application of CRISPR/Cas-based gene activation screening with an example of thermotolerant yeast screening, demonstrating that this method can be used to identify functional genes in yeast.\n\nCRISPR/Cas-based screening of a gene activation library in Saccharomyces cerevisiae identifies a crucial role of OLE1 in thermotolerance.", "token_count": 366, "char_count": 1499, "word_count": 212, "semantic_coherence": 1, "information_density": 0.566, "quality_score": 0.783, "entities": { "genes": [ "OLE1" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:57.475037", "source": { "split": "train_shard_00000", "doc_id": 3218 }, "chunk_id": "train_shard_00000_3218_0", "global_id": 3565 }, { "text": "The human-restricted bacterium Haemophilus influenzae is responsible for respiratory infections in both children and adults. While colonization begins in the upper airways, it can spread throughout the respiratory tract potentially leading to invasive infections. Although the spread of H. influenzae serotype b (Hib) has been prevented by vaccination, the emergence of infections by other serotypes as well as by non-typeable isolates (NTHi) have been observed, prompting the need for novel prevention strategies. Here, we aimed to study the population structure of H. influenzae and to get some insights into its pan-genome. We studied 305H. influenzae strains, enrolling 217 publicly available genomes, as well as 88 newly sequenced H. influenzae invasive strains isolated in Portugal, spanning a 24-year period. NTHi isolates presented a core-SNP-based genetic diversity about 10-fold higher than the one observed for Hib. The analysis of key factors involved in pathogenesis, such as lipooligosaccharides, hemagglutinating pili and High Molecular Weight-adhesins, suggests that NTHi shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion and persistence. Discreet NTHi subpopulations structures are proposed based on core-genome supported with 17 candidate genetic markers identified in the accessory genome. Additionally, this study provides two bioinformatics tools for in silico rapid identification of H. influenzae serotypes and NTHi clades previously proposed, obviating laboratory-based demanding procedures. The present study constitutes an important genomic framework that could lay way for future studies on the genetic determinants underlying invasiveness and disease and population structure of H. influenzae.\n\nInsights into the population structure and pan-genome of Haemophilus influenzae.", "token_count": 450, "char_count": 1893, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6808, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:58.105398", "source": { "split": "train_shard_00000", "doc_id": 3219 }, "chunk_id": "train_shard_00000_3219_0", "global_id": 3566 }, { "text": "In this experiment, 426 strains were isolated from the intestinal tract of Litopenaeus vannamei, and 11 strains showed strong digestive enzyme production activity and antagonistic effect against common bacterial pathogens of shrimp. After hemolysis activity test and drug sensitivity test, 2 candidate probiotics with good bacteriostatic activity, strong enzyme production ability and relatively sensitive to antibiotics were screened out, and were identified by 16s rDNA molecular identification and Biolog-System as Enterobacter hominis (E3) and lactobacillus (L3). First, the biological characteristics of 2 candidate probiotics were studied. The optimum growth conditions of E3: temperature, 30 °C; pH, 8.0; NaCl, 2.5%; bovine bile salt, 0.15%; and the optimum growth conditions of L3: temperature, 40 °C; pH, 6.0; NaCl, 0.5%; bovine bile salt, 0.0015%. Secondly, a 28-day feeding experiment was conducted using probiotic concentration of 10\n\nScreening of intestinal probiotics and the effects of feeding probiotics on the growth, immune, digestive enzyme activity and intestinal flora of Litopenaeus vannamei.", "token_count": 330, "char_count": 1114, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:58.675007", "source": { "split": "train_shard_00000", "doc_id": 3220 }, "chunk_id": "train_shard_00000_3220_0", "global_id": 3567 }, { "text": "Lactococcus lactis ssp. lactis is one of the most important starter bacteria used in dairy technology and it is of great economic importance because of its use in the production of dairy products, including cheese, butter, cream, and fermented milks. Numerous studies have evaluated the biochemical and probiotic properties of lactococci; however, limited studies on the probiotic characteristics of lactococci were conducted using strains originating from raw milk and dairy products. Characterizing the probiotic properties of strains isolated from raw milk and fermented milk products is important in terms of selecting starter culture strains for the production of functional dairy products. In this study, biochemical properties (including antibiotic sensitivity, lipolytic activity, amino acid decarboxylation, antioxidant activity) and probiotic properties (including antimicrobial activity, growth in the presence of bile salts, bile salts deconjugation, and hydrophobicity) of 14 Lactococcus lactis strains isolated from raw milk and kefir grains were investigated. Strains originating from kefir grains had better characteristics in terms of antimicrobial activity and bile salt deconjugation, whereas strains from raw milk had better hydrophobicity and antioxidant activity characteristics. None of the strains were able to grow in the presence of bile salt and did not show amino acid decarboxylation or lipolytic activities. Biochemical and probiotic properties of L. lactis strains varied depending on the strain and some of these strains could be used as functional cultures depending on their properties. However, these strains did not possess all of the properties required to meet the definition of a probiotic.\n\nProbiotic potential and biochemical and technological properties of Lactococcus lactis ssp. lactis strains isolated from raw milk and kefir grains.", "token_count": 452, "char_count": 1878, "word_count": 267, "semantic_coherence": 1, "information_density": 0.4644, "quality_score": 0.7322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:59.310569", "source": { "split": "train_shard_00000", "doc_id": 3221 }, "chunk_id": "train_shard_00000_3221_0", "global_id": 3568 }, { "text": "Lactose within whey can be fermented and distilled to produce a potable distilled spirit. The aim of this study was to determine if acid and sweet whey types can be fermented and distilled using similar processes and to investigate differences in volatile aroma compounds for the 2 distillates. Fermentation and distillation of the 2 whey types progressed in a similar manner, using Kluyveromyces marxianus for the initial fermentation and a glass still fitted with a Vigreux column for the subsequent distillation. Ethanol content of the wash (fermented whey) varied considerably following each fermentation and ranged from 1.2 and 2.0% (wt/wt) with no clear trend between acid and sweet whey samples. Volatile aroma compounds were extracted using headspace solid-phase microextraction and identified via gas chromatography-mass spectrometry. Acid and sweet whey distillates contained unique volatile aromatic compounds, and significant differences in compound peak areas were observed. These differences may have an effect upon the organoleptic qualities of spirits produced from whey; therefore, whey source may be an important factor when fermenting and distilling whey.\n\nVolatile aroma composition of distillates produced from fermented sweet and acid whey.", "token_count": 293, "char_count": 1262, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:30:59.871611", "source": { "split": "train_shard_00000", "doc_id": 3222 }, "chunk_id": "train_shard_00000_3222_0", "global_id": 3569 }, { "text": "Streptococcus suis is a major zoonotic pathogen that causes severe disease in both humans and pigs. Australia's pig herd has been quarantined for over 30 years, however S. suis remains a significant cause of disease. In this study, we investigated S. suis from 148 cases of clinical disease in pigs from 46 pig herds over a period of seven years, to determine the level of genetic difference from international isolates that may have arisen over the 30 years of separation. Isolates underwent whole genome sequencing, genome analysis and antimicrobial susceptibility testing. Data was compared at the core genome level to clinical isolates from overseas. Results demonstrated five predominant multi-locus sequence types and two major cps gene types (cps2 and 3). At the core genome level Australian isolates clustered predominantly within one large clade consisting of isolates from the UK, Canada and North America. A small proportion of Australian swine isolates (5%) were phylogenetically associated with south-east Asian and UK isolates, many of which were classified as causing systemic disease, and derived from cases of human and swine disease. Based on this dataset we provide a comprehensive outline of the current S. suis clones associated with disease in Australian pigs and their global context, with the main finding being that, despite three decades of separation, Australian S. suis are genomically similar to overseas strains. In addition, we show that ST1 clones carry a constellation of putative virulence genes not present in other Australian STs.\n\nExamination of Australian Streptococcus suis isolates from clinically affected pigs in a global context and the genomic characterisation of ST1 as a predictor of virulence.", "token_count": 406, "char_count": 1740, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6045, "quality_score": 0.8022, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:00.490890", "source": { "split": "train_shard_00000", "doc_id": 3223 }, "chunk_id": "train_shard_00000_3223_0", "global_id": 3570 }, { "text": "Pharmacokinetic research at the host-microbe interface has been primarily directed toward effects on drug metabolism, with fewer investigations considering the absorption process. We previously demonstrated that the transcriptional expression of genes encoding intestinal transporters involved in lipid translocation are altered in germ-free and conventionalized mice possessing distinct bile acid signatures. It was consequently hypothesized that microbial bile acid metabolism, which is the deconjugation and dehydroxylation of the bile acid steroid nucleus by gut bacteria, may impact upon drug transporter expression and/or activity and potentially alter drug disposition. Using a panel of three human intestinal cell lines (Caco-2, T84, and HT-29) that differ in basal transporter expression level, bile acid conjugation-, and hydroxylation-status was shown to influence the transcription of genes encoding several major influx and efflux transporter proteins. We further investigated if these effects on transporter mRNA would translate to altered drug disposition and activity. The results demonstrated that the conjugation and hydroxylation status of the bile acid steroid nucleus can influence the cellular response to multidrug resistance (MDR) substrates, a finding that did not directly correlate with directionality of gene or protein expression. In particular, we noted that the cytotoxicity of cyclosporine A was significantly augmented in the presence of the unconjugated bile acids deoxycholic acid (DCA) and chenodeoxycholic acid (CDCA) in P-gp positive cell lines, as compared to their taurine/glycine-conjugated counterparts, implicating P-gp in the molecular response. Overall this work identifies a novel mechanism by which gut microbial metabolites may influence drug accumulation and suggests a potential role for the microbial bile acid-deconjugating enzyme bile salt hydrolase (BSH) in ameliorating multidrug resistance through the generation of bile acid species with the capacity to access and inhibit P-gp ATPase", "token_count": 473, "char_count": 2041, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:01.134506", "source": { "split": "train_shard_00000", "doc_id": 3224 }, "chunk_id": "train_shard_00000_3224_0", "global_id": 3571 }, { "text": "The physicochemical property of nonionization is suggested to underpin the preferential ability of unconjugated bile acids to attenuate the efflux of P-gp substrates and to sensitize tumorigenic cells to cytotoxic therapeutics in vitro. This work provides new impetus to investigate whether perturbation of the gut microbiota, and thereby the bile acid component of the intestinal metabolome, could alter drug pharmacokinetics in vivo. These findings may additionally contribute to the development of less toxic P-gp modulators, which could overcome MDR.\n\nGut Microbiota-Mediated Bile Acid Transformations Alter the Cellular Response to Multidrug Resistant Transporter Substrates in Vitro: Focus on P-glycoprotein.", "token_count": 184, "char_count": 714, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7041, "quality_score": 0.852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:01.579481", "source": { "split": "train_shard_00000", "doc_id": 3224 }, "chunk_id": "train_shard_00000_3224_1", "global_id": 3572 }, { "text": "Functional dyspepsia is a common functional gastrointestinal disorder in which a variety of pathophysiological mechanisms such as increased intestinal permeability and low-grade inflammation are involved. The factor causing these alterations, however, has not been identified.\n\nAltered duodenal bile salt concentration and receptor expression in functional dyspepsia.", "token_count": 82, "char_count": 367, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8913, "quality_score": 0.9457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:01.953536", "source": { "split": "train_shard_00000", "doc_id": 3225 }, "chunk_id": "train_shard_00000_3225_0", "global_id": 3573 }, { "text": "Brucellosis is a zoonotic disease caused by Brucella spp. Brucella spp. can be sub-typed by multilocus sequence typing (MLST) method, which targets a set of housekeeping genes. We have developed a core genome MLST (cgMLST) typing scheme to distinguish and differentiate species of Brucella up to biovar level. A total of 407 whole (complete and draft) genome sequences of different Brucella strains were used in this study. Genome sequences were filtered using the BLAST score ratio (BSR)-based allele calling algorithm, and we found that 164 cgMLST target loci are shared in all the 407 genome sequences. These 164 loci were used to develop the cgMLST scheme and further evaluated to sub-type different species of Brucella. Based on our cgMLST scheme, Brucella spp. were classified into 287 sequence types (STs). A phylogenetic tree was constructed based on the STs derived from the cgMLST analysis. The phylogenetic tree differentiated all the 11 Brucella spp. and five biovars of B. suis. B. vulpis formed the outmost clade followed by B. inopinata and B. microti. Among the four subgroups of B. abortus, group A and B were differentiated based on their geographic origins. Similarly, three subgroups of B. melitensis were separated based on their geographical origins with few exceptions. B. neotomae that infect rodents were distinguished from other Brucella spp. B. canis showed the closest relationship with B. suis bv. 4, followed by B. suis bv. 3 and bv. 1. Brucella spp. associated with the marine mammals, such as B. ceti and B. pinnipedialis were closely related. Of these, B. ceti strains isolated from dolphins and porpoise were differentiated into two groups. We incorporated our cgMLST tool in BrucellaBase (http://www.dbtbrucellosis.in/brucella_cgmlst.html), which will be helpful to predict the cgMLST allelic profile and the ST of a newly sequenced genome.\n\nDevelopment and evaluation of a core genome multilocus sequence typing (cgMLST) scheme for Brucella spp.", "token_count": 551, "char_count": 1981, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5534, "quality_score": 0.7767, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:31:02.594238", "source": { "split": "train_shard_00000", "doc_id": 3226 }, "chunk_id": "train_shard_00000_3226_0", "global_id": 3574 }, { "text": "This article describes the discovery and characterization of nanocolloidal structures formed between VX-985 (an orally administered inhibitor of hepatitis C virus protease) and the bile salt, sodium taurocholate at concentrations of the latter >4 mM. These complexes (1) distribute narrowly in size around a mean diameter of 260 nm, (2) separate from solution only with ultracentrifugation, and (3) appear to influence the absorption of VX-985 from the intestinal tract in vivo, in rodents and humans. Although the oral bioavailability of suspensions of its solid forms is poor, addition of vitamin E D-alpha-tocopherol polyethylene glycol 1000 succinate to dosing vehicles improves the fraction absorbed of the compound in vivo. In vitro characterization is compatible with the hypothesis that surfactants like D-alpha-tocopherol polyethylene glycol 1000 succinate preclude nanocolloidal structures and increase the bioavailability by increasing the rate of absorption of VX-985. This study, while specific to VX-985, provides a route to circumvent the poor oral bioavailability caused by formation of kinetically stable complexes between bile salts and drug molecules. This study also underscores the importance of characterizing aggregation phenomenon that may be observed in solubility measurements during preclinical formulation development.\n\nOvercoming the Bile Salt-Mediated Formation of Nanocolloids That Inhibit Oral Absorption of VX-985.", "token_count": 374, "char_count": 1447, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6517, "quality_score": 0.8259, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:03.186347", "source": { "split": "train_shard_00000", "doc_id": 3227 }, "chunk_id": "train_shard_00000_3227_0", "global_id": 3575 }, { "text": "Geniposide (GE) is a major component isolated from\n\nMechanistic insights into geniposide regulation of bile salt export pump (BSEP) expression.", "token_count": 38, "char_count": 143, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:03.543570", "source": { "split": "train_shard_00000", "doc_id": 3228 }, "chunk_id": "train_shard_00000_3228_0", "global_id": 3576 }, { "text": "To characterise the progression of lipid digestion capacity in gilthead seabream across life cycle, the activities of bile salt-activated lipase (BAL) and phospholipase A\n\nLipid digestion capacity in gilthead seabream (Sparus aurata) from first feeding to commercial size.", "token_count": 76, "char_count": 272, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:03.918532", "source": { "split": "train_shard_00000", "doc_id": 3229 }, "chunk_id": "train_shard_00000_3229_0", "global_id": 3577 }, { "text": "Comparative analysis of the expanding genomic resources for scleractinian corals may provide insights into the evolution of these organisms, with implications for their continued persistence under global climate change. Here, we sequenced and annotated the genome of Pocillopora damicornis, one of the most abundant and widespread corals in the world. We compared this genome, based on protein-coding gene orthology, with other publicly available coral genomes (Cnidaria, Anthozoa, Scleractinia), as well as genomes from other anthozoan groups (Actiniaria, Corallimorpharia), and two basal metazoan outgroup phlya (Porifera, Ctenophora). We found that 46.6% of P. damicornis genes had orthologs in all other scleractinians, defining a coral 'core' genome enriched in basic housekeeping functions. Of these core genes, 3.7% were unique to scleractinians and were enriched in immune functionality, suggesting an important role of the immune system in coral evolution. Genes occurring only in P. damicornis were enriched in cellular signaling and stress response pathways, and we found similar immune-related gene family expansions in each coral species, indicating that immune system diversification may be a prominent feature of scleractinian coral evolution at multiple taxonomic levels. Diversification of the immune gene repertoire may underlie scleractinian adaptations to symbiosis, pathogen interactions, and environmental stress.\n\nComparative analysis of the Pocillopora damicornis genome highlights role of immune system in coral evolution.", "token_count": 387, "char_count": 1547, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:04.538552", "source": { "split": "train_shard_00000", "doc_id": 3230 }, "chunk_id": "train_shard_00000_3230_0", "global_id": 3578 }, { "text": "While colloids have been widely employed as models for atoms and molecules, the current study proposes to extend their use as building blocks for supracolloidal frameworks. Hereby, the self-assembly between highly anisotropic supramolecular microtubules and soft spherical fluorescent microgels is explored using confocal laser scanning microscopy. The influence of the particle size and charge with respect to the catanionic tubule composition, which consists of two oppositely charged bile salt derivatives, is investigated. Under certain conditions, microgel particles are found to specifically interact with the extremities of the tubular aggregates and hierarchically self-assemble into various superstructures varying from virus-like assemblies to supracolloidal networks. The reported approach is envisioned to open new self-assembly routes toward ordered hybrid superstructures where the spherical colloids act as responsive linkers of tubular structures.\n\nSphere-Tubule Superstructures through Supramolecular and Supracolloidal Assembly Pathways.", "token_count": 235, "char_count": 1055, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7481, "quality_score": 0.8741, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:05.016705", "source": { "split": "train_shard_00000", "doc_id": 3231 }, "chunk_id": "train_shard_00000_3231_0", "global_id": 3579 }, { "text": "Jaundice is a common symptom of inherited or acquired liver diseases or a manifestation of diseases involving red blood cell metabolism. Recent progress has elucidated the molecular mechanisms of bile metabolism, hepatocellular transport, bile ductular development, intestinal bile salt reabsorption, and the regulation of bile acids homeostasis.\n\nJaundice revisited: recent advances in the diagnosis and treatment of inherited cholestatic liver diseases.", "token_count": 109, "char_count": 455, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7213, "quality_score": 0.8607, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:05.401728", "source": { "split": "train_shard_00000", "doc_id": 3232 }, "chunk_id": "train_shard_00000_3232_0", "global_id": 3580 }, { "text": "Microbial spoilage of raw meat causes huge economic losses every year. An understanding of the microbial ecology associated with the spoilage and its dynamics during the refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. The raw meat microbiota is usually complex, but only a few members will develop during storage and cause spoilage upon the pressure from several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under vacuum during refrigerated storage to explore how different packaging conditions may influence the microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored aerobically or in vacuum packaging. Moreover, the pangenomes of\n\nStrain-Level Diversity Analysis of Pseudomonas fragi after", "token_count": 191, "char_count": 932, "word_count": 127, "semantic_coherence": 1, "information_density": 0.685, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:05.857288", "source": { "split": "train_shard_00000", "doc_id": 3233 }, "chunk_id": "train_shard_00000_3233_0", "global_id": 3581 }, { "text": "Komagataeibacter species are well-recognized bionanocellulose (BNC) producers. This bacterial genus, formerly assigned to Gluconacetobacter, is known for its phenotypic diversity manifested by strain-dependent carbon source preference, BNC production rate, pellicle structure, and strain stability. Here, we performed a comparative study of nineteen Komagataeibacter genomes, three of which were newly contributed in this work. We defined the core genome of the genus, clarified phylogenetic relationships among strains, and provided genetic evidence for the distinction between the two major clades, the K. xylinus and the K. hansenii. We found genomic traits, which likely contribute to the phenotypic diversity between the Komagataeibacter strains. These features include genome flexibility, carbohydrate uptake and regulation of its metabolism, exopolysaccharides synthesis, and the c-di-GMP signaling network. In addition, this work provides a comprehensive functional annotation of carbohydrate metabolism pathways, such as those related to glucose, glycerol, acetan, levan, and cellulose. Findings of this multi-genomic study expand understanding of the genetic variation within the Komagataeibacter genus and facilitate exploiting of its full potential for bionanocellulose production at the industrial scale.\n\nComparative genomics of the Komagataeibacter strains-Efficient bionanocellulose producers.", "token_count": 352, "char_count": 1409, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6778, "quality_score": 0.8389, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:06.429008", "source": { "split": "train_shard_00000", "doc_id": 3234 }, "chunk_id": "train_shard_00000_3234_0", "global_id": 3582 }, { "text": "The efficiency of human butyrylcholinesterase (BChE) as a stoichiometric bioscavenger of nerve agents is well established. However, wide use is currently limited by production and purification costs. Aiming at identifying an alternative human protein bioscavenger, we looked for an original scaffold candidate by virtual screening of the Protein Data Bank for functional similarity using the \"Surfing the Molecules\" software (sumo-pbil.ibcp.fr) and a search model based on the BChE active site topology. Besides the expected acetylcholinesterase and butyrylcholinesterase, we identified a set of bile salt activated lipases structures, among which the human pancreatic lipase (hBAL) that shares 34% identity with BChE. We produced the recombinant enzyme in mammalian cells, purified it, and measured the inhibition constants for paraoxon and surrogates of VX, sarin and tabun. We solved the X-ray structure of apo hBAL and conjugates with paraoxon and the surrogates at resolutions in the 2-Å range. These structures allow the assessment of hBAL for scavenging nerve agents. They revealed that hBAL has inverted stereoselectivity for the surrogates of nerve agent compared to human cholinesterases. We observed a remarkable flip of the catalytic histidine driven by the chelation of Zn\n\nX-ray structures of human bile-salt activated lipase conjugated to nerve agents surrogates.", "token_count": 362, "char_count": 1378, "word_count": 200, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:07.037599", "source": { "split": "train_shard_00000", "doc_id": 3235 }, "chunk_id": "train_shard_00000_3235_0", "global_id": 3583 }, { "text": "The emergence of CRISPR-Cas9 for targeted genome editing and regulation has enabled the manipulation of desired traits and enhanced strain development of nonmodel microorganisms. The natural capacity of the yeast Kluyveromyces marxianus to produce volatile esters at high rate and at elevated temperatures make it a potentially valuable production platform for industrial biotechnology. Here, we identify the native localization of ethyl acetate biosynthesis in K. marxianus and use this information to develop a multiplexed CRISPRi system for redirecting carbon flux along central metabolic pathways, increasing ethyl acetate productivity. First, we identified the primary pathways of precursor and acetate ester biosynthesis. A genetic knockout screen revealed that the alcohol acetyltransferase Eat1 is the critical enzyme for ethyl, isoamyl, and phenylethyl acetate production. Truncation studies revealed that high ester biosynthesis is contingent on Eat1 mitochondrial localization. As ethyl acetate is formed from the condensation of ethanol and acetyl-CoA, we modulated expression of the TCA cycle and electron transport chain genes using a highly multiplexed CRISPRi approach. The simultaneous knockdown of ACO2b, SDH2, RIP1, and MSS51 resulted in a 3.8-fold increase in ethyl acetate productivity over the already high natural capacity. This work demonstrates that multiplexed CRISPRi regulation of central carbon flux, supported by a fundamental understanding of pathway biochemistry, is a potent strategy for metabolic engineering in nonconventional microorganisms.\n\nHighly Multiplexed CRISPRi Repression of Respiratory Functions Enhances Mitochondrial Localized Ethyl Acetate Biosynthesis in Kluyveromyces marxianus.", "token_count": 436, "char_count": 1729, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [ "RIP1", "MSS51", "SDH2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:07.688763", "source": { "split": "train_shard_00000", "doc_id": 3236 }, "chunk_id": "train_shard_00000_3236_0", "global_id": 3584 }, { "text": "The large and complex genome of Pseudomonas aeruginosa, which consists of significant portions (up to 20%) of transferable genetic elements contributes to the rapid development of antibiotic resistance. The whole genome sequences of 22 strains isolated from eye and cystic fibrosis patients in Australia and India between 1992 and 2007 were used to compare genomic divergence and phylogenetic relationships as well as genes for antibiotic resistance and virulence factors. Analysis of the pangenome indicated a large variation in the size of accessory genome amongst 22 stains and the size of the accessory genome correlated with number of genomic islands, insertion sequences and prophages. The strains were diverse in terms of sequence type and dissimilar to that of global epidemic P. aeruginosa clones. Of the eye isolates, 62% clustered together within a single lineage. Indian eye isolates possessed genes associated with resistance to aminoglycoside, beta-lactams, sulphonamide, quaternary ammonium compounds, tetracycline, trimethoprims and chloramphenicols. These genes were, however, absent in Australian isolates regardless of source. Overall, our results provide valuable information for understanding the genomic diversity of P. aeruginosa isolated from two different infection types and countries.\n\nComparative genomics of clinical strains of Pseudomonas aeruginosa strains isolated from different geographic sites.", "token_count": 339, "char_count": 1429, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6231, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:08.297037", "source": { "split": "train_shard_00000", "doc_id": 3237 }, "chunk_id": "train_shard_00000_3237_0", "global_id": 3585 }, { "text": "Since Saccharomyces cerevisiae strains display no to weak pectinase activity, the utilization of external pectinase is a common practice in winemaking to enhance the extraction of compounds located in the grape berry skins during maceration. In this study, the activity of the native endopolygalacturonase of a Kluyveromyces marxianus strain, isolated from grape juice, was characterized in Shiraz grape must during alcoholic fermentation with or without prefermentative cold maceration. The wines made with K. marxianus had a higher methanol concentration, more free-run wine, an altered volatile compound profile, and displayed pectinase activity in cell-free wine samples. Moreover, the results strongly suggest that K. marxianus' pectinase released polygalacturonic acid soluble fragments, unlike fungal pectinases, which mostly release monomers. Overall, this study shows that K. marxianus is an effective pectinase producer in wine with potential benefits for wine properties.\n\nKluyveromyces marxianus Secretes a Pectinase in Shiraz Grape Must That Impacts Technological Properties and Aroma Profile of Wine.", "token_count": 281, "char_count": 1114, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:08.879617", "source": { "split": "train_shard_00000", "doc_id": 3238 }, "chunk_id": "train_shard_00000_3238_0", "global_id": 3586 }, { "text": "Dietary supplementation with lactic acid bacteria to maintain or improve intestinal health is advocated.\n\nEnhancement of viability, acid, and bile tolerance and accelerated stability in lyophilized", "token_count": 46, "char_count": 197, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:09.246051", "source": { "split": "train_shard_00000", "doc_id": 3239 }, "chunk_id": "train_shard_00000_3239_0", "global_id": 3587 }, { "text": "Neonatal sepsis is a major cause of infant mortality in developing countries because of delayed injectable treatment, making it urgent to develop noninjectable formulations that can reduce treatment delays in resource-limited settings. Ceftriaxone, available only for injection, needs absorption enhancers to achieve adequate bioavailability via nonparenteral administration. This article presents all available data on the nonparenteral absorption of ceftriaxone in humans and animals, including unpublished work carried out by F. Hoffmann-La Roche (Roche) in the 1980s and new data from preclinical studies with rabbits, and discusses the importance of these data for the development of noninjectable formulations for noninvasive treatment. The combined results indicate that the rectal absorption of ceftriaxone is feasible and likely to lead to a bioavailable formulation that can reduce treatment delays in neonatal sepsis. A bile salt, chenodeoxycholate sodium salt (Na-CDC), used as an absorption enhancer at a 125-mg dose, together with a 500-mg dose of ceftriaxone provided 24% rectal absorption of ceftriaxone and a maximal plasma concentration of 21 µg/ml with good tolerance in human subjects. The rabbit model developed can also be used to screen for the bioavailability of other formulations before assessment in humans.\n\nCeftriaxone Absorption Enhancement for Noninvasive Administration as an Alternative to Injectable Solutions.", "token_count": 347, "char_count": 1444, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8177, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:09.829462", "source": { "split": "train_shard_00000", "doc_id": 3240 }, "chunk_id": "train_shard_00000_3240_0", "global_id": 3588 }, { "text": "Lactobacillus casei F0822-fermented milk has exhibited significant hypocholesterolemic activity in hamsters in the previous study. Under this premise, the objective of this study is to further explore whether bile salt hydrolase (BSH) and S-layer protein (SLP) of the strain have a significant influence on hypocholesterolemic activity of the fermented milk.\n\nBile Salt Hydrolase and S-Layer Protein are the Key Factors Affecting the Hypocholesterolemic Activity of Lactobacillus casei-Fermented Milk in Hamsters.", "token_count": 146, "char_count": 513, "word_count": 70, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:10.272062", "source": { "split": "train_shard_00000", "doc_id": 3241 }, "chunk_id": "train_shard_00000_3241_0", "global_id": 3589 }, { "text": "Drug-induced liver injury (DILI), herbal-induced liver injury, and herbal and dietary supplement (HDS)-induced liver injury are an important aspect of drug safety. Knowledge regarding responsible drugs, mechanisms, risk factors, and the diagnostic tools to detect liver injury have continued to grow in the past year. This review highlights what we considered the most significant publications from among more than 1800 articles relating to liver injury from medications, herbal products, and dietary supplements in 2017 and 2018. The US Drug-Induced Liver Injury Network (DILIN) prospective study highlighted several areas of ongoing study, including the potential utility of human leukocyte antigens and microRNAs as DILI risk factors and new data on racial differences, the role of alcohol consumption, factors associated with prognosis, and updates on the clinical signatures of autoimmune DILI, thiopurines, and HDS agents. Novel data were also generated from the Spanish and Latin American DILI registries as well as from Chinese and Korean case series. A few new agents causing DILI were added to the growing list in the past 2 years, including sodium-glucose co-transporter-2 inhibitors, as were new aspects of chemotherapy-associated liver injury. A number of cases reported previously described hepatotoxins confirmed via the Roussel Uclaf Causality Assessment Method (RUCAM; e.g., norethisterone, methylprednisolone, glatiramer acetate) and/or the DILIN method (e.g., celecoxib, dimethyl fumarate). Additionally, much work centered on elucidating the pathophysiology of DILI, including the importance of bile salt export pumps and immune-mediated mechanisms. Finally, it must be noted that, while hundreds of new studies described DILI in 2017-2018, the quality of such reports must always be addressed. Björnsson reminds us to remain very critical of the data when addressing the future utility of a study, which is why it is so important to adhere to a standardized method such as RUCAM when determining DILI causality", "token_count": 504, "char_count": 2031, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:10.927433", "source": { "split": "train_shard_00000", "doc_id": 3242 }, "chunk_id": "train_shard_00000_3242_0", "global_id": 3590 }, { "text": "While drug-induced hepatotoxicity remains a diagnosis of exclusion, the diverse array of publications that appeared in 2017 and 2018 provided important advances in our understanding of DILI, paving the way for our improved ability to make a more definitive diagnosis and risk assessment.\n\nDrug-Induced Liver Injury: Highlights of the Recent Literature.", "token_count": 86, "char_count": 352, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7843, "quality_score": 0.8922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:11.310294", "source": { "split": "train_shard_00000", "doc_id": 3242 }, "chunk_id": "train_shard_00000_3242_1", "global_id": 3591 }, { "text": "Cytochrome P450 monooxygenases (P450) are enzymes with high potential as biocatalysts for industrial applications. Their large-scale applications are, however, limited by instability and requirement for coproteins and/or expensive cofactors. These problems are largely overcome when whole cells are used as biocatalysts. We previously screened various yeast species heterologously expressing self-sufficient P450s for their potential as whole-cell biocatalysts. Most P450s are, however, not self-sufficient and consist of two or three protein component systems. Therefore, in the present study, we screened different yeast species for coexpression of P450 and P450-reductase (CPR) partners, using CYP53B1 from Rhodotorula minuta as an exemplary P450. The abilities of three different coexpressed CPR partners to support P450 activity were investigated, two from basidiomycetous origin and one from an ascomycete. The various P450-CPR combinations were cloned into strains of Saccharomyces cerevisiae, Kluyveromyces marxianus, Hansenula polymorpha, Yarrowia lipolytica and Arxula adeninivorans, using a broad-range yeast expression vector. The results obtained supported the previous finding that recombinant A. adeninivorans strains perform excellently as whole-cell biocatalysts. This study also demonstrated for the first time the P450 reductase activity of the CPRs from R. minuta and U. maydis. A very interesting observation was the variation in the supportive activity provided by the different reductase partners tested and demonstrated better P450 activity enhancement by a heterologous CPR compared to its natural partner CPR. This study highlights reductase selection as a critical variable for consideration in the pursuit of optimal P450-based catalytic systems. The usefulness of A. adeninivorans as both a host for recombinant P450s and whole-cell biocatalyst was emphasized, supporting earlier findings.", "token_count": 495, "char_count": 1918, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:11.964007", "source": { "split": "train_shard_00000", "doc_id": 3243 }, "chunk_id": "train_shard_00000_3243_0", "global_id": 3592 }, { "text": "Heterologous coexpression of the benzoate-para-hydroxylase CYP53B1 with different cytochrome P450 reductases in various yeasts.", "token_count": 42, "char_count": 127, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:12.327204", "source": { "split": "train_shard_00000", "doc_id": 3243 }, "chunk_id": "train_shard_00000_3243_1", "global_id": 3593 }, { "text": "Legionella spp. are the cause of a severe bacterial pneumonia known as Legionnaires' disease (LD). In some cases, current genetic subtyping methods cannot resolve LD outbreaks caused by common, potentially endemic L. pneumophila (Lp) sequence types (ST), which complicates laboratory investigations and environmental source attribution. In the United States (US), ST1 is the most prevalent clinical and environmental Lp sequence type. In order to characterize the ST1 population, we sequenced 289 outbreak and non-outbreak associated clinical and environmental ST1 and ST1-variant Lp strains from the US and, together with international isolate sequences, explored their genetic and geographic diversity. The ST1 population was highly conserved at the nucleotide level; 98% of core nucleotide positions were invariant and environmental isolates unassociated with human disease (n = 99) contained ~65% more nucleotide diversity compared to clinical-sporadic (n = 139) or outbreak-associated (n = 28) ST1 subgroups. The accessory pangenome of environmental isolates was also ~30-60% larger than other subgroups and was enriched for transposition and conjugative transfer-associated elements. Up to ~10% of US ST1 genetic variation could be explained by geographic origin, but considerable genetic conservation existed among strains isolated from geographically distant states and from different decades. These findings provide new insight into the ST1 population structure and establish a foundation for interpreting genetic relationships among ST1 strains; these data may also inform future analyses for improved outbreak investigations.\n\nGenomic heterogeneity differentiates clinical and environmental subgroups of Legionella pneumophila sequence type 1.", "token_count": 396, "char_count": 1754, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6792, "quality_score": 0.8396, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:12.944473", "source": { "split": "train_shard_00000", "doc_id": 3244 }, "chunk_id": "train_shard_00000_3244_0", "global_id": 3594 }, { "text": "The objective of this study was to isolate the lactic acid bacteria from fermented silage sample and analyze their antibacterial activities, probiotic properties, and fermentation potential in silage. Eleven lactic acid bacteria (LAB) were selected based on distinct morphologies and preliminary studies. Cell-free supernatant (CFS) was then prepared from the selected strains for antibacterial analysis. L-30 strain and its CFS showed highest inhibition (> 10 mm) against tested foodborne pathogens as compared to other strains. Hereafter, the strain L-30 was named as KCC-30 and used for further studies. KCC-30 can survive in the harsh conditions of GIT such as low pH ( 2) and bile salt environment (oxgal) than standard\n\nEvaluation of probiotic", "token_count": 190, "char_count": 749, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7434, "quality_score": 0.8717, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:13.392926", "source": { "split": "train_shard_00000", "doc_id": 3245 }, "chunk_id": "train_shard_00000_3245_0", "global_id": 3595 }, { "text": "The unique character of bile salts to self-assemble into hydrogels in the presence of halide salts was exploited in this work to facilitate the prediction of human intestinal absorption (%HIA) for a set of 25 compounds. This was achieved by firstly incorporating each compound separately within the process of gel formation to create a series of gel-drug membranes. Scanning electron microscopy analysis of the freeze-dried samples of the blank bile salt hydrogels and drug-loaded bile salt hydrogels indicated a unique microstructure made of a network of intertwined fibrils. Drug-loaded sodium deoxycholate hydrogels were then utilized as the donor phase to study permeability using flow-through and static diffusion cells. The resulting values of the release-permeability coefficient (K\n\nFormation of a Bile Salt-Drug Hydrogel to Predict Human Intestinal Absorption.", "token_count": 207, "char_count": 869, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:13.855628", "source": { "split": "train_shard_00000", "doc_id": 3246 }, "chunk_id": "train_shard_00000_3246_0", "global_id": 3596 }, { "text": "Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana, as well as among subspecies in M. acuminata. Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata. These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana. Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.\n\nThree New Genome Assemblies Support a Rapid Radiation in Musa acuminata (Wild Banana).", "token_count": 413, "char_count": 1835, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:14.476075", "source": { "split": "train_shard_00000", "doc_id": 3247 }, "chunk_id": "train_shard_00000_3247_0", "global_id": 3597 }, { "text": "Cosmc is ubiquitously expressed and acts as a specific molecular chaperone assisting the folding and stability of core 1 synthase. Thus, it plays a crucial role in the biosynthesis of O-linked glycosylation of proteins. Here, we show that ablation of Cosmc in the exocrine pancreas of mice causes expression of truncated O-glycans (Tn antigen), resulting in exocrine pancreatic insufficiency with decreased activities of digestive enzymes and diabetes. To understand the molecular causes of the pleiotropic phenotype, we used Vicia villosa agglutinin to enrich Tn antigen-modified proteins from Cosmc-KO pancreatic lysates and performed a proteomic analysis. Interestingly, a variety of proteins were identified, of which bile salt-activated lipase (also denoted carboxyl-ester lipase, Cel) was the most abundant. In humans, frameshift mutations in CEL cause maturity-onset diabetes of the young type 8 (MODY8), a monogenic syndrome of diabetes and pancreatic exocrine dysfunction. Here, we provide data suggesting that differentially O-glycosylated Cel could negatively affect beta cell function. Taken together, our findings demonstrate the importance of correct O-glycan formation for normal exocrine and endocrine pancreatic function, implying that aberrant O-glycans might be relevant for pathogenic mechanisms of the pancreas.\n\nLoss of complex O-glycosylation impairs exocrine pancreatic function and induces MODY8-like diabetes in mice.", "token_count": 380, "char_count": 1443, "word_count": 200, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [ "MODY8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:15.062795", "source": { "split": "train_shard_00000", "doc_id": 3248 }, "chunk_id": "train_shard_00000_3248_0", "global_id": 3598 }, { "text": "Birds of prey and from Psittacidae family are host to fungal microbiota and play an important role in the epidemiology of zoonoses. Few studies in the literature have characterized mycelial and yeast fungi in the droppings of these birds and correlated the isolates with the zoonotic potential of the microorganisms. Droppings from 149 birds were evaluated and divided into two groups: captive: Rhea americana araneipes, Primolius maracana, Ara ararauna, Ara chloropterus, Anodorhynchus hyacinthinus, Amazona aestiva, Ara macao macao, Ramphastos toco, Sarcoramphus papa, Busarellus nigricollis, Bubo virginianus nacurutu, Buteogallus coronatus, Buteogallus urubitinga urubitinga, Spizaetus melanoleucus, Spizaetus ornatus ornatus, Buteo albonotatus, Geranoaetus albicaudatus albicaudatus, Rupornis magnirostris magnirostris and Harpia harpyja, and quarantined birds: Amazona aestiva and Eupsitulla aurea. The fungal isolates were identified according to macroscopic (gross colony appearance), micromorphological and biochemical characteristics. Among birds displayed in enclosures, Aspergillus niger (41.1%) and Candida kefyr (63.8%) were the fungi most frequently isolated in Harpia harpyja and Ramphastos toco, respectively. For quarantined birds, the following percentages were observed in Eupsittula aurea , (76.6%) C. krusei, (84.4%) C. kefyr and (15.2%) C. famata, while in Amazona aestiva, (76.2%) C. krusei was observed. These findings indicate potentially pathogenic species in the bird droppings assessed, which constitute a risk of exposure for keepers and individuals who visit the zoo", "token_count": 496, "char_count": 1597, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6981, "quality_score": 0.8491, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:15.715147", "source": { "split": "train_shard_00000", "doc_id": 3249 }, "chunk_id": "train_shard_00000_3249_0", "global_id": 3599 }, { "text": "Birds of the Cerrado and Pantanal of Mato Grosso (Central Western region of Brazil) could act in the epidemiological chain of important zoonoses.\n\nYeasts and filamentous fungi in psittacidae and birds of prey droppings in midwest region of Brazil: a potential hazard to human health.", "token_count": 77, "char_count": 283, "word_count": 45, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:16.083891", "source": { "split": "train_shard_00000", "doc_id": 3249 }, "chunk_id": "train_shard_00000_3249_1", "global_id": 3600 }, { "text": "We recently identified clonal complex 10 (CC10) Escherichia coli as the predominant clonal group in two populations of healthy Australian food-production pigs. CC10 are highly successful, colonizing humans, food-production animals, fresh produce and environmental niches. Furthermore, E. coli within CC10 are frequently drug resistant and increasingly reported as human and animal extra-intestinal pathogens. In order to develop a high-resolution global phylogeny and determine the repertoire of antimicrobial-resistance genes, virulence-associated genes and plasmid types within this clonal group, we downloaded 228 publicly available CC10 short-read genome sequences for comparison with 20 porcine CC10 we have previously described. Core genome single nucleotide polymorphism phylogeny revealed a highly diverse global phylogeny consisting of multiple lineages that did not cluster by geography or source of the isolates. Australian porcine strains belonged to several of these divergent lineages, indicative that CC10 is present in these animals due to multiple colonization events. Differences in resistance gene and plasmid carriage between porcine strains and the global collection highlighted the role of lateral gene transfer in the evolution of CC10 strains. Virulence profiles typical of extra-intestinal pathogenic E. coli were present in both Australian porcine strains and the broader collection. As both the core phylogeny and accessory gene characteristics appeared unrelated to the geography or source of the isolates, it is likely that the global expansion of CC10 is not a recent event and may be associated with faecal carriage in humans.\n\nAustralian porcine clonal complex 10 (CC10) Escherichia coli belong to multiple sublineages of a highly diverse global CC10 phylogeny.", "token_count": 426, "char_count": 1793, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5771, "quality_score": 0.7885, "entities": { "genes": [ "CC10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:16.714275", "source": { "split": "train_shard_00000", "doc_id": 3250 }, "chunk_id": "train_shard_00000_3250_0", "global_id": 3601 }, { "text": "Microencapsulation enhances the oral delivery of probiotic bacteria. In this study, the probiotic Escherichia coli Nissle 1917 (EcN) was microencapsulated using alginate and chitosan nanoparticles. The result showed 90% encapsulation yield of EcN, and the encapsulated EcN displayed significantly (P < 0.05) increased survival in low pH (1.5), high bile salt concentration (4%), and high temperature (70 °C). The most effective cryopreservatives of EcN during freezing and thawing was skim milk and sucrose. Exposure to microencapsulated EcN significantly (P < 0.05) reduced the Campylobacter jejuni growth by 2 log CFU. The rate of EcN release from microcapsule was 9.2 × 10\n\nE. coli Nissle microencapsulation in alginate-chitosan nanoparticles and its effect on Campylobacter jejuni in vitro.", "token_count": 257, "char_count": 794, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7069, "quality_score": 0.8534, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:17.596540", "source": { "split": "train_shard_00000", "doc_id": 3251 }, "chunk_id": "train_shard_00000_3251_0", "global_id": 3602 }, { "text": "Recent human gut microbiome studies have supported that the genus\n\nIsolation and Characterization of", "token_count": 20, "char_count": 100, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:17.946985", "source": { "split": "train_shard_00000", "doc_id": 3252 }, "chunk_id": "train_shard_00000_3252_0", "global_id": 3603 }, { "text": "The chief objective of this research was to appraise liposomes embodying a bile salt, sodium glycocholate (SGC), as oral nanoscale drug delivery system to strengthen the bioavailability of a water-soluble and weakly penetrable pharmaceutical, notoginsenoside R1 (NGR1). NGR1-loaded liposomes were prepared with the improved supercritical reverse evaporation (ISCRPE) method and the preparation conditions were optimized with response surface methodology (RSM). The mean encapsulation efficiency (EE), particle size, and polydispersity index (PDI) of the optimized liposomal formulation (NGR1@Liposomes) were 49.49%, 308.3 nm, and 0.229, respectively. SGC-mediated liposomes (NGR1@SGC-Liposomes) were formulated based on the optimal preparation conditions and the mean EE, particle size, and PDI were 41.51%, 200.1 nm, and 0.130, respectively. The in vitro Caco-2 cellular uptake of fluorescent marker was increased by loading into NGR1@SGC-Liposomes as compared with the conventional liposomes. Furthermore, the intestinal permeability as well as the intestinal absorption of NGR1 were both significantly improved with NGR1@SGC-Liposomes as the nanovesicles. The in vivo pharmacokinetic study results showed that AUC\n\nImproved oral bioavailability of notoginsenoside R1 with sodium glycocholate-mediated liposomes: Preparation by supercritical fluid technology and evaluation in vitro and in vivo.", "token_count": 412, "char_count": 1397, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [ "NGR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:18.564069", "source": { "split": "train_shard_00000", "doc_id": 3253 }, "chunk_id": "train_shard_00000_3253_0", "global_id": 3604 }, { "text": "We investigated in vitro and in vivo antioxidant activity of Lactobacillus paracasei ssp. paracasei YBJ01 (LPSP-YBJ01) isolated and identified from fermented yogurt. Strain LPSP-YBJ01 had stress tolerance against acidity, bile salt, and osmotic pressure. Five in vitro antioxidant assays were used to evaluate antioxidant activity of LPSP-YBJ01, which could scavenge free radicals (2,2-diphenyl-1-picrylhydrazyl and hydroxyl) and superoxide anion in vitro. In addition, strain LPSP-YBJ01 had stronger antilipid peroxidation activity and weak reducing power in vitro. We measured in vivo antioxidant activity of LPSP-YBJ01 in an oxidation mouse model induced by d-galactose injection. Strain LPSP-YBJ01 significantly increased serum superoxide dismutase (SOD), glutathione peroxidase, and total-antioxidant capability, and inhibited generation of malondialdehyde in a dose-dependent manner. In addition, strain LPSP-YBJ01 also increased the hepatic and splenic protein expressions of some antioxidant enzymes such as catalase, Cu/Zn-SOD, and Mn-SOD in mice treated with d-galactose. Thus, LPSP-YBJ01 had antioxidant activity in vitro and in vivo and may be a useful probiotic.\n\nLactobacillus paracasei ssp. paracasei YBJ01 reduced d-galactose-induced oxidation in male Kuming mice.", "token_count": 427, "char_count": 1280, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6213, "quality_score": 0.8107, "entities": { "genes": [ "YBJ01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:19.222391", "source": { "split": "train_shard_00000", "doc_id": 3254 }, "chunk_id": "train_shard_00000_3254_0", "global_id": 3605 }, { "text": "TAK-875 (fasiglifam), a GPR40 agonist in development for the treatment of type 2 diabetes (T2D), was voluntarily terminated in Phase III trials due to adverse liver effects. The potential mechanisms of TAK-875 toxicity were explored by combining in vitro experiments with quantitative systems toxicology (QST) using DILIsym, a mathematical representation of drug-induced liver injury. In vitro assays revealed that bile acid transporters were inhibited by both TAK-875 and its metabolite, TAK-875-Glu. Experimental data indicated that human bile salt export pump (BSEP) inhibition by TAK-875 was mixed whereas sodium taurocholate co-transporting polypeptide (NTCP) inhibition by TAK-875 was competitive. Furthermore, experimental data demonstrated that both TAK-875 and TAK-875-Glu inhibit mitochondrial electron transport chain (ETC) enzymes. These mechanistic data were combined with a physiologically based pharmacokinetic (PBPK) model constructed within DILIsym to estimate liver exposure of TAK-875 and TAK-875-Glu. In a simulated population (SimPops) constructed to reflect T2D patients, 16/245 (6.5%) simulated individuals developed alanine aminotransferase (ALT) elevations, an incidence similar to that observed with 200 mg daily dosing in clinical trials. Determining the mode of bile acid transporter inhibition (Ki) was critical to accurate predictions. In addition, simulations conducted on a sensitive subset of individuals (SimCohorts) revealed that when either BSEP or ETC inhibition was inactive, ALT elevations were not predicted to occur, suggesting that the two mechanisms operate synergistically to produce the observed clinical response. These results demonstrate how utilizing QST methods to interpret in vitro experimental results can lead to an improved understanding of the clinically relevant mechanisms underlying drug-induced toxicity.", "token_count": 476, "char_count": 1864, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6693, "quality_score": 0.8347, "entities": { "genes": [ "GPR40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:19.896520", "source": { "split": "train_shard_00000", "doc_id": 3255 }, "chunk_id": "train_shard_00000_3255_0", "global_id": 3606 }, { "text": "Quantitative Systems Toxicology Analysis of In Vitro Mechanistic Assays Reveals Importance of Bile Acid Accumulation and Mitochondrial Dysfunction in TAK-875-Induced Liver Injury.", "token_count": 53, "char_count": 179, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:20.283040", "source": { "split": "train_shard_00000", "doc_id": 3255 }, "chunk_id": "train_shard_00000_3255_1", "global_id": 3607 }, { "text": "Medically refractory, severe, cholestasis-induced pruritus in Alagille syndrome may be improved by surgical interruption of the enterohepatic circulation. This multicenter trial (NCT02057692) tested the hypothesis that the intestinal bile acid transport inhibitor maralixibat would similarly reduce pruritus in Alagille syndrome. Thirty-seven children with Alagille syndrome were randomly assigned to double-blinded administration of placebo, 70, 140, or 280 µg/kg/day of maralixibat for 13 weeks. Pruritus was assessed by caregiver (itch-reported outcome instrument [ItchRO]) and clinician report (range, 0-4 [severe]). Liver chemistries and serum bile acids were measured. The primary outcome was the change from baseline to week 13 in ItchRO relative to placebo. In the\n\nPlacebo-Controlled Randomized Trial of an Intestinal Bile Salt Transport Inhibitor for Pruritus in Alagille Syndrome.", "token_count": 259, "char_count": 891, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6975, "quality_score": 0.8487, "entities": { "genes": [ "NCT02057692" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:20.869092", "source": { "split": "train_shard_00000", "doc_id": 3256 }, "chunk_id": "train_shard_00000_3256_0", "global_id": 3608 }, { "text": "Taking into account its thermotolerance, high growth rate, and broad substrate spectrum,\n\nImproved secretory expression of lignocellulolytic enzymes in", "token_count": 40, "char_count": 151, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:21.246114", "source": { "split": "train_shard_00000", "doc_id": 3257 }, "chunk_id": "train_shard_00000_3257_0", "global_id": 3609 }, { "text": "Lipid metabolism can influence host's health. There is increasing evidence for interplay between two key regulating factors in lipid metabolism: bile acids (BAs) and gut microbiota. However, very little is known about how types of different diet-supplemented bile salts (BS) influence this interaction\n\nDietary Bile Salt Types Influence the Composition of Biliary Bile Acids and Gut Microbiota in Grass Carp.", "token_count": 106, "char_count": 408, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7833, "quality_score": 0.8917, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:21.631814", "source": { "split": "train_shard_00000", "doc_id": 3258 }, "chunk_id": "train_shard_00000_3258_0", "global_id": 3610 }, { "text": "Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here, we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome networks from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes,revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa.\n\nMetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks.", "token_count": 345, "char_count": 1542, "word_count": 210, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:22.218150", "source": { "split": "train_shard_00000", "doc_id": 3259 }, "chunk_id": "train_shard_00000_3259_0", "global_id": 3611 }, { "text": "Ulcerative colitis (UC), a chronic inflammatory bowel disease, substantially impacts patients' health-related quality of life. In this study, an effective strategy for discovering high-efficiency probiotics has been developed. First, in order to survive in the conditions of the stomach and intestine, high bile salt-resistant and strong acid-resistant strains were screened out from the fecal flora of healthy adults. Next, the probiotic candidates were rescreened by examining the induction ability of IL-10 (anti-inflammatory factor) production in dextran sodium sulfate (DSS)-induced colitis mice, and\n\nSemi-Rational Screening of Probiotics from the Fecal Flora of Healthy Adults against DSS-Induced Colitis Mice by Enhancing Anti-Inflammatory Activity and Modulating the Gut Microbiota.", "token_count": 210, "char_count": 791, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7547, "quality_score": 0.8774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:22.687054", "source": { "split": "train_shard_00000", "doc_id": 3260 }, "chunk_id": "train_shard_00000_3260_0", "global_id": 3612 }, { "text": "A strain of bacteria in the Bacillus subtilis species complex was isolated from a building's air vent in the Washington DC area, USA, and produced strong antifungal activity with in vitro assays. This strain, designated (HU Biol-II), showed pronounced inhibitory effects on mycelial growth of a wide spectrum of fungi. The objectives of this study were to use genome sequencing to confirm the taxonomy of HU Biol-II, evaluate its antifungal activity and implement genome mining and HPLC-MS/MS to characterize the bioactive secondary metabolites. The strain, as determined by multilocus sequence alignment analysis, was identified as a member of Bacillus subtilis subsp. inaquosorum clade. Core genome phylogeny showed that the isolate is most closely related to B. subtilis subsp. inaquosorum strain DE111, a commercially produced human probiotic. The investigation identified eight bioactive metabolite clusters in the genome. HPLC MS/MS was able to confirm the production of seven of the metabolites. This study is the first to report the production of two antifungal cyclic lipopeptides (bacillomycin F and fengycin) from a member of B. subtilis subsp. inaquosorum. The strain also produced the antibacterial aurantinin B, which confirms the biosynthetic cluster responsible for its production. Comparative genomics and metabolomics demonstrated the commercial probiotic strain DE111 produced the same metabolites, with the exception of aurantinin B. These findings are the first description of the secondary metabolites produced by a strain of B. subtilis subsp. inaquosorum.\n\nThe first report of antifungal lipopeptide production by a Bacillus subtilis subsp. inaquosorum strain.", "token_count": 430, "char_count": 1684, "word_count": 245, "semantic_coherence": 1, "information_density": 0.551, "quality_score": 0.7755, "entities": { "genes": [ "DE111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:23.313208", "source": { "split": "train_shard_00000", "doc_id": 3261 }, "chunk_id": "train_shard_00000_3261_0", "global_id": 3613 }, { "text": "Metaplastic glands buried under squamous epithelium are frequently detected in patients with Barrett esophagus (BE). This subsquamous intestinal metaplasia might be responsible for cancers that develop despite endoscopic surveillance and for metaplasia recurrences after endoscopic ablation. To determine whether reflux induces BE cells to undergo an epithelial-to-mesenchymal transition (EMT) that produces subsquamous intestinal metaplasia, we assessed EMT in BE cells exposed to acidic bile salts and in rat and human esophageal tissues.\n\nAcidic Bile Salts Induce Epithelial to Mesenchymal Transition via VEGF Signaling in Non-Neoplastic Barrett's Cells.", "token_count": 186, "char_count": 657, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:23.757402", "source": { "split": "train_shard_00000", "doc_id": 3262 }, "chunk_id": "train_shard_00000_3262_0", "global_id": 3614 }, { "text": "Thermotolerant yeast strains were isolated from\n\nIsolation of thermotolerant yeast", "token_count": 23, "char_count": 82, "word_count": 10, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:24.112553", "source": { "split": "train_shard_00000", "doc_id": 3263 }, "chunk_id": "train_shard_00000_3263_0", "global_id": 3615 }, { "text": "The gut microbiome (GMB) of folivores metabolizes dietary fiber into nutrients, including short-chain fatty acids (SCFAs); however, experiments probing the consequences of foliage quality on host GMBs are lacking. We therefore examined GMB structure and function via amplicon sequencing and Nuclear Magnetic Resonance spectroscopy in 31 captive sifakas (Propithecus coquereli) during dietary manipulations associated with husbandry. Supplementing standard diets with diverse foliage blends, versus with a single plant species, promoted more diverse GMBs, enriched for taxa implicated in plant-fiber metabolism, but depleted in taxa implicated in starch metabolism and bile tolerance. The consumption of diverse blends was associated with greater concentrations of colonic SCFAs. Abundant foliage, via forest access, promoted compositionally distinct and more stable GMBs, but reduced concentrations of SCFAs, possibly reflecting selection of high-quality leaves. In 11 subjects denied forest access, we examined the temporal pace of microbial shifts when supplemental foliage was abruptly switched between diverse blends and single species. The sifaka GMB responded within days, with community diversity and composition closely tracking foliage diversity. By providing experimental evidence that the folivore GMB is sensitive to minor changes in dietary foliage, we reveal the fragility of specialist GMBs, with implications for managing the wellbeing of endangered wildlife.\n\nThe critical role of dietary foliage in maintaining the gut microbiome and metabolome of folivorous sifakas.", "token_count": 374, "char_count": 1585, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6759, "quality_score": 0.838, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:24.697744", "source": { "split": "train_shard_00000", "doc_id": 3264 }, "chunk_id": "train_shard_00000_3264_0", "global_id": 3616 }, { "text": "Throughout history, the yeast\n\nEngineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host.", "token_count": 31, "char_count": 111, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:25.055341", "source": { "split": "train_shard_00000", "doc_id": 3265 }, "chunk_id": "train_shard_00000_3265_0", "global_id": 3617 }, { "text": "The thermotolerant yeast Kluyveromyces marxianus, growing at high temperature (45℃) , showed stronger survival under heat shock at 50℃ than the brewing yeast Saccharomyces cerevisiae, which was unable to grow at 45℃. The survival rate of K. marxianus decreased to 10% during heat shock at 50℃ for 20 min, and to less than 0.01% at 60℃ for 20 min. Cells with damaged cellular membranes were infrequently observed at 50℃ and had decreased significantly from heat shock at 60℃. The metabolic activity of K. marxianus was retained at 50℃, whereas that of S. cerevisiae was not. The trehalose content of K. marxianus was approximately two times that of S. cerevisiae. These results suggest that K. marxianus protects itself from heat shock-induced damage through the use of trehalose (a protective molecule in S. cerevisiae) as well as other different factors.\n\nThermotolerant Yeast Kluyveromyces marxianus Reveals More Tolerance to Heat Shock than the Brewery Yeast Saccharomyces cerevisiae.", "token_count": 296, "char_count": 987, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.8019, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:25.619056", "source": { "split": "train_shard_00000", "doc_id": 3266 }, "chunk_id": "train_shard_00000_3266_0", "global_id": 3618 }, { "text": "Directed evolutionary approach and random mutagenesis were performed on thermotolerant yeast Kluyveromyces marxianus KCTC17694 for isolating a yeast strain producing ethanol from xylose efficiently. The isolated mutant strain, K. marxianus 17694-DH1, showed 290% and 131% improvement in ethanol concentration and ethanol production yield from xylose, respectively, as compared with the parental strain. Sequencing of the KmXYL1 gene of K. marxianus 17694-DH1 revealed substitutions of arginine and tryptophan with lysine and leucine at positions 25 and 202, respectively, as compared to the parental strain. In addition, sequencing of the KmXYL2 gene uncovered a substitution of glutamate with leucine at position 232. When enzymatic assays of xylose reductase (XR) and xylitol dehydrogenase (XDH) from the parental strain and K. marxianus 17694-DH1 were performed, XR activities were not significantly different whereas XDH activities were significantly improved in the mutant strain up to 50 °C of reaction temperatures. RNA-Seq based transcriptome analysis showed that alcohol dehydrogenases and glucose transporters were up-regulated while TCA cycle involved enzymes were down-regulated in K. marxianus 17694-DH1.\n\nEthanol production from xylose is highly increased by the Kluyveromyces marxianus mutant 17694-DH1.", "token_count": 402, "char_count": 1318, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6077, "quality_score": 0.8039, "entities": { "genes": [ "DH1", "KCTC17694" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:26.236064", "source": { "split": "train_shard_00000", "doc_id": 3267 }, "chunk_id": "train_shard_00000_3267_0", "global_id": 3619 }, { "text": "Interactions between hydrophobic drugs and endogenous gastrointestinal substances have the potential to manipulate drug concentration in the human gastrointestinal system, and thus likely play an important role in determining the rate of absorption for hydrophobic drugs. The effects of phospholipids, bile salts and digestive proteins on the solution behaviour of clofazimine in biorelevant media was demonstrated here using dissolution experiments and solid state analytical techniques. Clofazimine is a hydrophobic, anti-mycobacterial agent with virtually no detectable water solubility in its free base form. Salt forms of the drug offer improved aqueous solubility but are unstable in solutions at low pH (pH 1.6) or high pH (pH 6.5). At low pH and high chloride ion concentrations, CFZ in solution experiences a high driving force to crystallize from solution as a hydrochloride salt, which is insoluble, while at high pH CFZ does not dissolve to any extent. In this study, it is demonstrated that amphipathic compounds present in the gastric and intestinal systems can overcome the instability experienced by CFZ at these pH values. This is done by encapsulation of the hydrophobic drug in mixed bile salt phospholipid micelles in both the gastric and intestinal fluid, and by the drug actively binding with the digestive enzyme pepsin in the gastric system. Pepsin binds and solubilises the drug at even relatively low concentration (0.1 mg/mL). When pepsin concentration is increased in the gastric media, a corresponding increase in the solution stability of CFZ is observed.\n\nInvestigating the effects of amphipathic gastrointestinal compounds on the solution behaviour of salt and free base forms of clofazimine: An in vitro evaluation.", "token_count": 443, "char_count": 1748, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5682, "quality_score": 0.7841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:26.868902", "source": { "split": "train_shard_00000", "doc_id": 3268 }, "chunk_id": "train_shard_00000_3268_0", "global_id": 3620 }, { "text": "Bile salts (BSs) are naturally occurring rigid surfactants with a steroidal skeleton and specific self-assembly and interface behaviors. Using bile salts as precursors, derivatives can be synthesized to obtain molecules with specific functionalities and amphiphilic structure. Modifications on single molecules are normally performed by substituting the least-hindered hydroxyl group on carbon C-3 of the steroidal A ring or at the end of the lateral chain. This leads to monosteroidal rigid building blocks that are often able to self-organize into 1D structures such as tubules, twisted ribbons, and fibrils with helical supramolecular packing. Tubular aggregates are of particular interest, and they are characterized by cross-section inner diameters spanning a wide range of values (3-500 nm). They can form through appealing pH- or temperature-responsive aggregation and in mixtures of bile salt derivatives to provide mixed tubules with tunable charge and size. Other derivatives can be prepared by covalently linking two or more bile salt molecules to provide complex systems such as oligomers, dendrimers, and polymeric materials. The unconventional amphiphilic molecular structure imparts specific features to BSs and derivatives that can be exploited in the formulation of capsules, drug carriers, dispersants, and templates for the synthesis of nanomaterials.\n\nBile Salts: Natural Surfactants and Precursors of a Broad Family of Complex Amphiphiles.", "token_count": 352, "char_count": 1460, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:27.441096", "source": { "split": "train_shard_00000", "doc_id": 3269 }, "chunk_id": "train_shard_00000_3269_0", "global_id": 3621 }, { "text": "Buccal delivery of insulin is still a challenging issue for the researchers due to the presence of permeability barrier (buccal mucosa) in the buccal cavity. The main objective of this study was to investigate the safety, effectiveness, and potential of various liposomes containing different bile salts to improve the permeation of insulin across in vitro TR146 buccal cell layers.\n\nFacilitated permeation of insulin across TR146 cells by cholic acid derivatives-modified elastic bilosomes.", "token_count": 121, "char_count": 491, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [ "TR146" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:27.827914", "source": { "split": "train_shard_00000", "doc_id": 3270 }, "chunk_id": "train_shard_00000_3270_0", "global_id": 3622 }, { "text": "The liver is the primary organ involved in handling of bile salts, a class of amphipathic molecules with signaling activities as well as desired and detrimental detergent actions. To allow in-depth investigation of functions of bile salts in healthy and diseased liver, the spatial distribution of bile salt species within the liver needs to be studied. Therefore, the aim of our study was to determine hepatic bile salt distribution and identify specific lipid markers that define the structural elements of the liver. Matrix-assisted laser desorption/ionization-mass spectrometry imaging (MALDI-MSI) was used to monitor the spatial distribution of bile salts and lipids in liver sections of rat, dog, and patients with unaffected and cholestatic parenchyma. MALDI-MSI in negative ion mode showed the local presence of a variety of bile salts, predominantly taurine-conjugates, as localized patches of varying sizes (representing the bile ducts) throughout the liver tissue. Specific molecular markers were identified for the connective tissue (phosphatidic acids, e.g., [PA (18:0_18:1)-H]\n\nCross-Species Molecular Imaging of Bile Salts and Lipids in Liver: Identification of Molecular Structural Markers in Health and Disease.", "token_count": 310, "char_count": 1228, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:28.404836", "source": { "split": "train_shard_00000", "doc_id": 3271 }, "chunk_id": "train_shard_00000_3271_0", "global_id": 3623 }, { "text": "Brassica oleracea is an important agricultural species encompassing many vegetable crops including cabbage, cauliflower, broccoli and kale; however, it can be susceptible to a variety of fungal diseases such as clubroot, blackleg, leaf spot and downy mildew. Resistance to these diseases is meditated by specific disease resistance genes analogs (RGAs) which are differently distributed across B. oleracea lines. The sequenced reference cultivar does not contain all B. oleracea genes due to gene presence/absence variation between individuals, which makes it necessary to search for RGA candidates in the B. oleracea pangenome. Here we present a comparative analysis of RGA candidates in the pangenome of B. oleracea. We show that the presence of RGA candidates differs between lines and suggests that in B. oleracea, SNPs and presence/absence variation drive RGA diversity using separate mechanisms. We identified 59 RGA candidates linked to Sclerotinia, clubroot, and Fusarium wilt resistance QTL, and these findings have implications for crop breeding in B. oleracea, which may also be applicable in other crops species.\n\nVariation in abundance of predicted resistance genes in the Brassica oleracea pangenome.", "token_count": 292, "char_count": 1214, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6348, "quality_score": 0.8174, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:28.972728", "source": { "split": "train_shard_00000", "doc_id": 3272 }, "chunk_id": "train_shard_00000_3272_0", "global_id": 3624 }, { "text": "In the present study, we sequenced the complete genomes of three novel bacteriophages v_B-Bak1, v_B-Bak6, v_B-Bak10 previously isolated from historical anthrax burial sites in the South Caucasus country of Georgia. We report here major trends in the molecular evolution of these phages, which we designate as \"Basilisk-Like-Phages\" (BLPs), and illustrate patterns in their evolution, genomic plasticity and core genome architecture.\n\nGenomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis.", "token_count": 141, "char_count": 524, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:29.402111", "source": { "split": "train_shard_00000", "doc_id": 3273 }, "chunk_id": "train_shard_00000_3273_0", "global_id": 3625 }, { "text": "Lactococcus garvieae is now recognized as a species with clinical significance for human and veterinary medicine. The aim of this study was to evaluate the presence of this pathogen in sand bedding and milk samples. Two farms in Minnesota with problems of clinical and subclinical mastitis due to streptococci-like organisms were selected. Twenty-four Lactococcus garvieae isolates from sand bedding and 18 isolates from quarter milk were comparatively studied using a genotypic approach. RAPD (random amplification of polymorphic DNA) PCR and REP (repetitive element palindromic) PCR experiments highlighted a similar electrophoretic profile. When genes belonging to the core genome of L. garvieae were tested through a MLRT (multilocus restriction typing), we again observed that all L. garvieae isolates coming from sand bedding and milk shared a common profile, distinguishable from previously studied representative L. garvieae strains. These data indicate that the L. garvieae isolated from sand bedding and milk originated from a few strains adapted to persist in the same habitat. This supports the hypothesis that sand bedding can represent a reservoir of L. garvieae strains and be a potential vehicle for their dissemination in dairy farms.\n\nSand bedding as a reservoir for Lactococcus garvieae dissemination in dairy farms.", "token_count": 323, "char_count": 1335, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5808, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:29.964681", "source": { "split": "train_shard_00000", "doc_id": 3274 }, "chunk_id": "train_shard_00000_3274_0", "global_id": 3626 }, { "text": "Enterococcus faecalis is a common commensal bacterium in animal gastrointestinal (GI) tracts and a leading cause of opportunistic infections of humans in the modern health care setting. E. faecalis OG1RF is a plasmid-free strain that contains few mobile elements yet retains the robust survival characteristics, intrinsic antibiotic resistance, and virulence traits characteristic of most E. faecalis genotypes. To facilitate interrogation of the core enterococcal genetic determinants for competitive fitness in the GI tract, biofilm formation, intrinsic antimicrobial resistance, and survival in the environment, we generated an arrayed, sequence-defined set of chromosomal transposon insertions in OG1RF. We used an orthogonal pooling strategy in conjunction with Illumina sequencing to identify a set of mutants with unique, single\n\nComprehensive Functional Analysis of the Enterococcus faecalis Core Genome Using an Ordered, Sequence-Defined Collection of Insertional Mutations in Strain OG1RF.", "token_count": 241, "char_count": 999, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:30.449839", "source": { "split": "train_shard_00000", "doc_id": 3275 }, "chunk_id": "train_shard_00000_3275_0", "global_id": 3627 }, { "text": "Many bacteria, often associated with eukaryotic hosts and of relevance for biotechnological applications, harbor a multipartite genome composed of more than one replicon. Biotechnologically relevant phenotypes are often encoded by genes residing on the secondary replicons. A synthetic biology approach to developing enhanced strains for biotechnological purposes could therefore involve merging pieces or entire replicons from multiple strains into a single genome. Here we report the creation of a genomic hybrid strain in a model multipartite genome species, the plant-symbiotic bacterium Sinorhizobium meliloti. We term this strain as cis-hybrid, since it is produced by genomic material coming from the same species' pangenome. In particular, we moved the secondary replicon pSymA (accounting for nearly 20% of total genome content) from a donor S. meliloti strain to an acceptor strain. The cis-hybrid strain was screened for a panel of complex phenotypes (carbon/nitrogen utilization phenotypes, intra- and extracellular metabolomes, symbiosis, and various microbiological tests). Additionally, metabolic network reconstruction and constraint-based modeling were employed for in silico prediction of metabolic flux reorganization. Phenotypes of the cis-hybrid strain were in good agreement with those of both parental strains. Interestingly, the symbiotic phenotype showed a marked cultivar-specific improvement with the cis-hybrid strains compared to both parental strains. These results provide a proof-of-principle for the feasibility of genome-wide replicon-based remodelling of bacterial strains for improved biotechnological applications in precision agriculture.\n\nCreation and Characterization of a Genomically Hybrid Strain in the Nitrogen-Fixing Symbiotic Bacterium Sinorhizobium meliloti.", "token_count": 435, "char_count": 1805, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:31.093679", "source": { "split": "train_shard_00000", "doc_id": 3276 }, "chunk_id": "train_shard_00000_3276_0", "global_id": 3628 }, { "text": "Bilosomes were developed in order to investigate their efficacy as nanocarriers for transdermal delivery of Tizanidine HCl (TZN), a skeletal muscle relaxant with low oral bioavailability. Full factorial experimental design consisting of 27 combinations was generated to study the effects of surfactant type, surfactant-to-cholesterol ratio and the amount of bile salt on the entrapment efficiency (EE), the vesicle size (VS) and in vitro dissolution of the TZN-loaded bilosomes. The permeation through the stratum cornea was optimized with the vertical diffusion assembly using excised rat skin. The permeation parameters of the selected bilosomes were compared to the unformulated drug and it was shown that TZN-B24 exhibited the highest enhancement ratio (ER = 8.8).The optimal formula (TZN-B24) consisting of span 60 in a ratio with cholesterol of 1:1 and 20 mg of bile salt was obtained by employing the desirability function of Design-Expert\n\nEvaluation of bilosomes as nanocarriers for transdermal delivery of tizanidine hydrochloride: in vitro and ex vivo optimization.", "token_count": 295, "char_count": 1076, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:31.672693", "source": { "split": "train_shard_00000", "doc_id": 3277 }, "chunk_id": "train_shard_00000_3277_0", "global_id": 3629 }, { "text": "Gracilaria verrucosa, red seaweed, is a promising biomass for bioethanol production due to its high carbohydrate content. The optimal hyper thermal (HT) acid hydrolysis conditions are 12% (w/v) G. verrucosa with 0.2 M H\n\nApplication of the Severity Factor and HMF Removal of Red Macroalgae Gracilaria verrucosa to Production of Bioethanol by Pichia stipitis and Kluyveromyces marxianus with Adaptive Evolution.", "token_count": 133, "char_count": 410, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8167, "quality_score": 0.9083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:32.111453", "source": { "split": "train_shard_00000", "doc_id": 3278 }, "chunk_id": "train_shard_00000_3278_0", "global_id": 3630 }, { "text": "Uricase as an important healthcare-related protein is extensively used in the treatment of tumor lysis syndrome and in the manufacture of serum uric-acid diagnostic kits. In this study, a gene of a new thermostable uricase (KmUOX) was cloned from thermotolerant yeast\n\nEfficient purification of a recombinant tag-free thermostable", "token_count": 91, "char_count": 330, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:32.516262", "source": { "split": "train_shard_00000", "doc_id": 3279 }, "chunk_id": "train_shard_00000_3279_0", "global_id": 3631 }, { "text": "This study presents a new method for detection of between-herd livestock movements to facilitate disease tracing and more accurately describe network behaviour of relevance for spread of infectious diseases, including within-livestock business risk-carrying contacts that are not necessarily recorded anywhere. The study introduces and substantiates the concept of grouping livestock herds into business-units based on ownership and location in the tracing analysis of animal movement-based contact networks. To test the utility of this approach, whole core genome sequencing of 196 Salmonella Dublin isolates stored from previous surveillance and project activities was combined with information on cattle movements recorded in the Danish Cattle Database between 1997 and 2017. The aim was to investigate alternative explanations for S. Dublin circulation in groups of herds connected by ownership, but without complete records of livestock movements. The EpiContactTrace R-package was used to trace the contact networks between businesses and compare the network characteristics of businesses sharing strains of S. Dublin with different levels of genetic relatedness. The ownership-only definition proved to be an unreliable grouping approach for large businesses, which could have internal distances larger than 250 km and therefore do not represent useful epidemiological units. Therefore, the grouping was refined using spatial analysis. More than 90% of final business units formed were composed of one single cattle property, whereas multi-property businesses could reach up to eight properties in a given year, with up to 15 cattle herds having been part of the same business through the study period. Results showed markedly higher probabilities of introduction of infectious animals between proposed businesses from which the same clone of S. Dublin had been isolated, when compared to businesses with non-related strains, thus substantiating the business-unit as an important epidemiological feature to consider in contact network analysis and tracing of infection routes. However, this approach may overestimate real-life contacts between cattle properties and putatively overestimate the degree of risk-contacts within each business, since it is based solely on information about property ownership and location. This does not consider administrative and individual farmers behaviours that essentially keep two properties separated. Despite this, we conclude that defining epidemiological units based on businesses is a promising approach for future disease tracing tasks.", "token_count": 492, "char_count": 2585, "word_count": 363, "semantic_coherence": 1, "information_density": 0.6116, "quality_score": 0.8058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:33.188370", "source": { "split": "train_shard_00000", "doc_id": 3280 }, "chunk_id": "train_shard_00000_3280_0", "global_id": 3632 }, { "text": "Combining Salmonella Dublin genome information and contact-tracing to substantiate a new approach for improved detection of infectious transmission routes in cattle populations.", "token_count": 32, "char_count": 177, "word_count": 22, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:33.549359", "source": { "split": "train_shard_00000", "doc_id": 3280 }, "chunk_id": "train_shard_00000_3280_1", "global_id": 3633 }, { "text": "The present study aimed to isolate and identify the potential probiotic lactic acid bacteria (LAB) from traditionally fermented wheat flour dough known as \"babroo.\" A total of 26 lactic isolates were obtained from 50 different samples collected from different locations of the Himalayan province (Himachal Pradesh). To ascertain non-pathogenic nature, the isolates were screened by hemolytic activity leading to 20 non-hemolytic strains which were subjected to tolerance to simulated gastrointestinal conditions. Seven different strains were selected based on their tolerance to gastrointestinal conditions. All the selected seven isolates were found to be susceptible to ampicillin and resistant to gentamicin. The phylogenetic analysis revealed three different strains of Lactobacillus fermentum, two strains of Lactobacillus plantarum, and two of Pediococcus acidilactici. The isolates exhibit different degrees of cell surface hydrophobicity (20.0-42.0%), cellular autoaggregation (5.0-41.0%), and adhesion to mucin (35.0-78.0%). The different lactic strains also possessed higher antioxidant properties (87.6-92.9%) determined in terms of free radical scavenging activity, bile salt hydrolase activity, cholesterol lowering activity (49.0-75.0%), and exopolysaccharide production. The principal component analysis (PCA) on probiotic attributes indicated that L. plantarum K90, L. fermentum K75, and L. fermentum K78 can be used as potential probiotic candidates.\n\nSelection and Evaluation of Probiotic and Functional Characteristics of Autochthonous Lactic Acid Bacteria Isolated from Fermented Wheat Flour Dough Babroo.", "token_count": 449, "char_count": 1625, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:34.190462", "source": { "split": "train_shard_00000", "doc_id": 3281 }, "chunk_id": "train_shard_00000_3281_0", "global_id": 3634 }, { "text": "The yeast Kluyveromyces marxianus is an emerging cell factory for heterologous protein biosynthesis and its use holds tremendous advantages for multiple applications. However, which genes influence the productivity of desired proteins in K. marxianus has so far been investigated by very few studies.\n\nMutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus.", "token_count": 102, "char_count": 426, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:34.572507", "source": { "split": "train_shard_00000", "doc_id": 3282 }, "chunk_id": "train_shard_00000_3282_0", "global_id": 3635 }, { "text": "Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how metagenome sequencing can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes, was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicated a core genome for the species, and a number of variant genes and subsystems suggested strain level differentiation, especially for nutrient utilization and stress response. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes to both reconstruct the model organisms in silico and identify their ecosystem functions as well as to identify novel clades and propose their role in the biogeochemical cycling of mats. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and revealed significant diversity in the Bacteroidetes, presumably in heterotrophic cycling. This analysis also revealed evidence of putative phototrophs within the Gemmatimonadetes and Gammaproteobacteria residing in microbial mats. This study shows that metagenomic analysis can produce insights into the systems biology of microbial ecosystems from a genetic perspective and to suggest further studies of novel microbes.\n\nMetagenomics reveals niche partitioning within the phototrophic zone of a microbial mat.", "token_count": 433, "char_count": 1853, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5927, "quality_score": 0.7964, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:35.206853", "source": { "split": "train_shard_00000", "doc_id": 3283 }, "chunk_id": "train_shard_00000_3283_0", "global_id": 3636 }, { "text": "Three novel bile acid derivatives, petromylidenes A⁻C (\n\nPetromylidenes A⁻C: 2-Alkylidene Bile Salt Derivatives Isolated from Sea Lamprey (", "token_count": 55, "char_count": 139, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:35.572080", "source": { "split": "train_shard_00000", "doc_id": 3284 }, "chunk_id": "train_shard_00000_3284_0", "global_id": 3637 }, { "text": "Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as\n\nUnveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping", "token_count": 62, "char_count": 239, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:35.935177", "source": { "split": "train_shard_00000", "doc_id": 3285 }, "chunk_id": "train_shard_00000_3285_0", "global_id": 3638 }, { "text": "Elucidating the relationships between antimicrobial resistance and virulence is key to understanding the evolution and population dynamics of resistant pathogens. Here, we show that the susceptibility of the gram-positive bacterium Listeria monocytogenes to the antibiotic fosfomycin is a complex trait involving interactions between resistance and virulence genes and the environment. We found that a FosX enzyme encoded in the listerial core genome confers intrinsic fosfomycin resistance to both pathogenic and non-pathogenic Listeria spp. However, in the genomic context of the pathogenic L. monocytogenes, FosX-mediated resistance is epistatically suppressed by two members of the PrfA virulence regulon, hpt and prfA, which upon activation by host signals induce increased fosfomycin influx into the bacterial cell. Consequently, in infection conditions, most L. monocytogenes isolates become susceptible to fosfomycin despite possessing a gene that confers high-level resistance to the drug. Our study establishes the molecular basis of an epistatic interaction between virulence and resistance genes controlling bacterial susceptibility to an antibiotic. The reported findings provide the rationale for the introduction of fosfomycin in the treatment of Listeria infections even though these bacteria are intrinsically resistant to the antibiotic in vitro.\n\nEpistatic control of intrinsic resistance by virulence genes in Listeria.", "token_count": 340, "char_count": 1439, "word_count": 196, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:36.506512", "source": { "split": "train_shard_00000", "doc_id": 3286 }, "chunk_id": "train_shard_00000_3286_0", "global_id": 3639 }, { "text": "There is evidence that a diet low in Fermentable Oligo-, Di-, Monosaccharides And Polyols (FODMAPs) alleviates symptoms in approx. 70% of the patients suffering from irritable bowel syndrome. Through fructans, wheat containing products are a major source of FODMAPs in the western diet. Although fructans are partially degraded during dough fermentation by Saccharomyces cerevisiae invertase, wheat bread contains notable fructan levels. In this study, it was shown that Kluyveromyces marxianus strain CBS6014 can degrade more than 90% of the fructans initially present in wheat whole meal during bread making, which can be attributed to its high inulinase activity. As K. marxianus CBS6014 was not able to consume maltose during fermentation, alternative sugars (sucrose) or glucose releasing enzymes (amyloglucosidase) had to be included in the bread making recipe to ensure sufficient production of CO\n\nKluyveromyces marxianus yeast enables the production of low FODMAP whole wheat breads.", "token_count": 263, "char_count": 992, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7448, "quality_score": 0.8724, "entities": { "genes": [ "CBS6014" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:37.051712", "source": { "split": "train_shard_00000", "doc_id": 3287 }, "chunk_id": "train_shard_00000_3287_0", "global_id": 3640 }, { "text": "As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another. In order to facilitate this, a novel mapping method, KMA (k-mer alignment), was designed. KMA is able to map raw reads directly against redundant databases, it also scales well for large redundant databases. KMA uses k-mer seeding to speed up mapping and the Needleman-Wunsch algorithm to accurately align extensions from k-mer seeds. Multi-mapping reads are resolved using a novel sorting scheme (ConClave scheme), ensuring an accurate selection of templates.\n\nRapid and precise alignment of raw reads against redundant databases with KMA.", "token_count": 212, "char_count": 939, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7299, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:37.521622", "source": { "split": "train_shard_00000", "doc_id": 3288 }, "chunk_id": "train_shard_00000_3288_0", "global_id": 3641 }, { "text": "The pentose phosphate pathway (PPP) plays an important role in the synthesis of ribonucleotides and aromatic amino acids. During bioethanol production from cellulosic biomass composed mainly of D-glucose and D-xylose, the PPP is also involved in xylose metabolism by engineered Saccharomyces cerevisiae. Although the activities and thermostabilities of the four PPP enzymes (transaldolase: TAL1, transketolase: TKL1, ribose-5-phosphate ketol-isomerase: RKI1 and D-ribulose-5-phosphate 3-epimerase: RPE1) can affect the efficiency of cellulosic ethanol production at high temperatures, little is known about the suitable expression levels of these PPP genes. Here, we overexpressed PPP genes from S. cerevisiae and the thermotolerant yeast Kluyveromyces marxianus either singly or in combination in recombinant yeast strains harboring a mutant of xylose isomerase (XI) and evaluated xylose consumption and ethanol production of these yeast transformants in glucose/xylose mixed media at 36 °C. Among the PPP genes examined, we found that: (1) strains that overexpressed S. cerevisiae TKL1 exhibited the highest rate of xylose consumption relative to strains that overexpressed other PPP genes alone; (2) overexpression of RKI1 and TAL1 derived from K. marxianus with S. cerevisiae TKL1 increased the xylose consumption rate by 1.87-fold at 24 h relative to the control strain (from 0.55 to 1.03 g/L/h); (3) the strains with XI showed higher ethanol yield than strains with xylose reductase and xylitol dehydrogenase and (4) PHO13 disruption did not improve xylose assimilation under the experimental conditions", "token_count": 485, "char_count": 1609, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6332, "quality_score": 0.8166, "entities": { "genes": [ "TKL1", "RPE1", "PHO13", "RKI1", "TAL1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:38.173300", "source": { "split": "train_shard_00000", "doc_id": 3289 }, "chunk_id": "train_shard_00000_3289_0", "global_id": 3642 }, { "text": "Together these results indicated that optimization of PPP activity improves xylose metabolism in genetically engineered yeast strains, which could be useful for commercial production of ethanol from cellulosic material.\n\nSystematic optimization of gene expression of pentose phosphate pathway enhances ethanol production from a glucose/xylose mixed medium in a recombinant Saccharomyces cerevisiae.", "token_count": 94, "char_count": 398, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:38.546140", "source": { "split": "train_shard_00000", "doc_id": 3289 }, "chunk_id": "train_shard_00000_3289_1", "global_id": 3643 }, { "text": "Considerable variation in feed efficiency (FE) has been observed in indigenous and selected meat-type chicken populations. Although this variation could be partially linked to extrinsic factors like diet, housing environment and microbiota, it further illustrates the existence of strong molecular mechanisms enabling the differential allocation of resources for various physiological processes. To further deepen the molecular basis of individual allocation capacity in male and female broilers, an RNA-seq experiment was conducted which based on a phenotyped chicken population divergent in FE. Transcriptional differences linked to FE were pronounced in intestinal and muscular tissue sites of male animals. Specifically, signalling pathways of farnesoid X receptor (FXR) and retinoid X receptor (RXR) might contribute to mediate individual FE. The transcriptional profiles suggested ACSBG2 (muscular lipid utilisation), ASBT (intestinal bile salt transport), CLEC2B (natural killer cell activation), HMGCS2 (jejunal, duodenal and muscular ketogenesis), and SCARB1 (jejunal lipid uptake) as potential mediators driving FE. Results indicate that improvements in FE exploit shifts in resource allocation which might occur at the expense of general immune responsiveness in high efficient male chickens. Consequently, to further improve FE traits and to explore causative molecular patterns, effects originating from sex-dimorphism in chickens need to be taken into consideration.\n\nTranscriptional shifts account for divergent resource allocation in feed efficient broiler chickens.", "token_count": 334, "char_count": 1582, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6981, "quality_score": 0.8491, "entities": { "genes": [ "CLEC2B", "SCARB1", "ACSBG2", "HMGCS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:39.116049", "source": { "split": "train_shard_00000", "doc_id": 3290 }, "chunk_id": "train_shard_00000_3290_0", "global_id": 3644 }, { "text": "Life-long bacterial infections in cystic fibrosis (CF) airways constitute an excellent model both for persistent infections and for microbial adaptive evolution in complex dynamic environments. Using high-resolution transcriptomics applied on CF sputum, we profile transcriptional phenotypes of Pseudomonas aeruginosa populations in patho-physiological conditions. Here we show that the soft-core genome of genetically distinct populations, while maintaining transcriptional flexibility, shares a common expression program tied to the lungs environment. We identify genetically independent traits defining P. aeruginosa physiology in vivo, documenting the connection between several previously identified mutations in CF isolates and some of the convergent phenotypes known to develop in later stages of the infection. In addition, our data highlight to what extent this organism can exploit its extensive repertoire of physiological pathways to acclimate to a new niche and suggest how alternative nutrients produced in the lungs may be utilized in unexpected metabolic contexts.\n\nHigh-resolution in situ transcriptomics of Pseudomonas aeruginosa unveils genotype independent patho-phenotypes in cystic fibrosis lungs.", "token_count": 273, "char_count": 1219, "word_count": 160, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:39.661043", "source": { "split": "train_shard_00000", "doc_id": 3291 }, "chunk_id": "train_shard_00000_3291_0", "global_id": 3645 }, { "text": "The aims of the present study were to characterize the mechanisms of resistance to fluoroquinolones, macrolides, and imipenem in Haemophilus influenzae, to assess the extent of the AcrAB-TolC-mediated resistance, and to define a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae by using whole-genome sequencing. Four amino acid substitutions in GyrA (at Ser84 and Asp88), ParC (at Ser84), and ParE (at Asp420) were found to be closely associated to the MICs. We did not find any amino acid substitution surrounding the three highly conserved amino acid motifs in PBP3 related to imipenem resistance. All the isolates possessed the ermB gene. Carbonyl cyanide m-chlorophenylhydrazone (CCCP) decreased the MIC of imipenem by twofold for FQR-6 and fourfold for GE47 and GE88 strains. For erythromycin, the MICs were decreased by twofold. We found that the six FQR isolates were clustered in two groups. The number of different loci within FQR-1_FQR-3_FQR-5 cluster was 6, while FQR-2 and FQR-4 differed for 21 loci. FQR-1_FQR-3_FQR-5 and FQR-2_FQR-4 clusters were distant among each other and compared to 19 genomes downloaded from NCBI, to 8 strains heteroresistant to imipenem, and to 4 strains monoresistant to ciprofloxacin isolated in Denmark. We confirmed that specific amino acid substitutions in GyrA, ParC, and ParE are implicated in quinolone resistance. Additionally, the degree of resistance is related to the number of these amino acid substitutions. We provide robust evidence that drug efflux is one of the substantial mechanisms of imipenem and erythromycin resistance in H. influenzae.", "token_count": 503, "char_count": 1623, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6098, "quality_score": 0.8049, "entities": { "genes": [ "PBP3", "GE47", "GE88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:40.319287", "source": { "split": "train_shard_00000", "doc_id": 3292 }, "chunk_id": "train_shard_00000_3292_0", "global_id": 3646 }, { "text": "Molecular characterization of fluoroquinolones, macrolides, and imipenem resistance in Haemophilus influenzae: analysis of the mutations in QRDRs and assessment of the extent of the AcrAB-TolC-mediated resistance.", "token_count": 61, "char_count": 213, "word_count": 26, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:40.698402", "source": { "split": "train_shard_00000", "doc_id": 3292 }, "chunk_id": "train_shard_00000_3292_1", "global_id": 3647 }, { "text": "Bile salt export pump (BSEP) inhibition has emerged as an important mechanism that may contribute to the initiation of human drug-induced liver injury (DILI). Proactive evaluation and understanding of BSEP inhibition is recommended in drug discovery and development to aid internal decision making on DILI risk. BSEP inhibition can be quantified using in vitro assays. When interpreting assay data, it is important to consider in vivo drug exposure. Currently, this can be undertaken most effectively by consideration of total plasma steady state drug concentrations (C\n\nCan Bile Salt Export Pump Inhibition Testing in Drug Discovery and Development Reduce Liver Injury Risk? An International Transporter Consortium Perspective.", "token_count": 163, "char_count": 728, "word_count": 106, "semantic_coherence": 1, "information_density": 0.717, "quality_score": 0.8585, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:41.137486", "source": { "split": "train_shard_00000", "doc_id": 3293 }, "chunk_id": "train_shard_00000_3293_0", "global_id": 3648 }, { "text": "Through current investigation, we presented a lucrative way to formulate amphotericin B loaded bile salt stabilized carbohydrate polymer i.e. chitosan nanoparticles (NPs) for enhancing gastrointestinal stability of NPs thereby increasing the oral bioavailability of the drug. NPs were prepared using ionic gelation method, and stabilized using bile salt to provide gastric pH stability to chitosan NPs. NPs were optimized on different parameters such as particle size, encapsulation efficiency and estimated for their in vitro and in vivo performance. Developed NPs presented a higher stability in gastrointestinal milieu, reduced haemolytic toxicity and significantly higher uptake in Caco-2 cell lines followed by increased bioavailability as compared to naive drug, marketed formulation i.e. Fungizone® and uncoated chitosan NPs. Biochemical parameters and histology further substantiated the lower toxicity. In nutshell, the present research explored the bioadhesive and higher uptake potential of cationic carbohydrate polymer at the same time along with bile salts for stabilization of NPs in gastric milieu.\n\nAmphotericin B Loaded Chitosan Nanoparticles: Implication of Bile Salt Stabilization on Gastrointestinal Stability, Permeability and Oral Bioavailability.", "token_count": 324, "char_count": 1270, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6279, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:41.701885", "source": { "split": "train_shard_00000", "doc_id": 3294 }, "chunk_id": "train_shard_00000_3294_0", "global_id": 3649 }, { "text": "Probiotics are commensals with special characteristics that are essential for the development of the immune system, and may protect mucosal surfaces against pathogens. In this study, a total of 40 lactic acid bacteria (LAB) were isolated from different raw and fermented camel's milk samples collected from Saudi Arabia (Makkah area) and Egypt (Fayoum), and tested for the probiotic properties. Among them, Pro 4 and Pro 7 isolates exhibited excellent probiotic potential including bile salt (0.2-0.6%), phenol tolerance (0.2-0.4%) and salt tolerance (0.0-10%). Furthermore, both strains exhibited antimicrobial activity against wide range of food-borne pathogens and Dermatophytes with average zone inhibition of 37.5, 35.5, 34.5, 27.5, 25 and 23.5 mm for Staphylococcus aureus, Trichophyton mentagrophytes, Escherichia coli, Listeria monocytogens, Candida albicans and Salmonella typhi, respectively. Furthermore, the in vivo study indicated that these strains significantly improved the mucosal immune responses through an increase in expression of TLR2 and IFNγ mRNA in mice intestine as well as increased the synthesis of polyclonal IgG, IgM and IgA in mice blood sera. Accordingly, due to these unique probiotic properties, both selected strains could be potentially used as probiotic starter cultures for fermented dairy foods as well as functional food and health products.\n\nIn vitro and in vivo evidences for innate immune stimulators lactic acid bacterial starters isolated from fermented camel dairy products.", "token_count": 429, "char_count": 1520, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8463, "entities": { "genes": [ "TLR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:42.332638", "source": { "split": "train_shard_00000", "doc_id": 3295 }, "chunk_id": "train_shard_00000_3295_0", "global_id": 3650 }, { "text": "The pattern of glucose repression in most Kluyveromyces marxianus strains does not correlate with fermentative behaviour; however, glucose repression and fermentative metabolism appear to be linked to the kinetics of sugar uptake. In this work, we show that lactose transport in K. marxianus CCT 7735 by lactose-grown cells is mediated by a low-affinity H\n\nSugar transport systems in Kluyveromyces marxianus CCT 7735.", "token_count": 127, "char_count": 417, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:42.723401", "source": { "split": "train_shard_00000", "doc_id": 3296 }, "chunk_id": "train_shard_00000_3296_0", "global_id": 3651 }, { "text": "Bile acids (BA), the major components of bile, are biological detergents that facilitate the emulsification and solubilization of dietary lipids and also display potent antimicrobial activity, the bacterial membranes being their main targets. Considering the complicated nature of the stress produced by bile and BA, the microorganism tolerance requires different defence mechanisms including the presence of efflux pumps, bile salt hydrolase (BSH) enzyme, the intrinsic capacity of cells to maintain intracellular homeostasis and modifications in the architecture and composition of the cell membrane. Besides, the expression of proteins involved in carbohydrate and fatty acid metabolism, amino acid and nitrogenous base biosynthesis, and general stress response are commonly affected by the presence of bile. Among the microbial transformations, deconjugation of BA by BSH is the most important. Several studies indicate that BSH activity affects both the host physiology and the microbiota. In fact, it was strongly suggested that BSH could play an important role in the colonization and survival of bacteria in the gut. Also, recent work has shown that BSH and free BA participate in a variety of metabolic processes that include regulation of dietary lipid absorption, cholesterol metabolism, and energy and inflammation homeostasis. In this review we summarize recent advances in the understanding of the mechanisms involved in the tolerance of bacteria to bile, with special emphasis on the contributions of studies applying an omic approach. Besides, the physiological and ecological role of BSH enzyme and its relevance to human health as well as the function of bile acid as metabolic regulator are also discussed.\n\nNew insights into bacterial bile resistance mechanisms: the role of bile salt hydrolase and its impact on human health.", "token_count": 410, "char_count": 1846, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5964, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:43.398724", "source": { "split": "train_shard_00000", "doc_id": 3297 }, "chunk_id": "train_shard_00000_3297_0", "global_id": 3652 }, { "text": "The lungs have potential as a means of systemic drug delivery of macromolecules. Systemic delivery requires crossing of the air-blood barrier, however with molecular size-dependent limitations in lung absorption of large molecules. Systemic availability after inhalation can be improved by absorption enhancers, such as bile salts. Enhancers may potentially interfere with the different constituents of the lungs, e.g. the lung surfactant lining the alveoli or the lung epithelium. We used two in vitro models to investigate the potential effects of bile salts on lung surfactant function (with the constrained drop surfactometer) and on the epithelium in the proximal airways (with the MucilAir™ cell system), respectively. In addition, we measured direct effects on respiration in mice inhaling bile salt aerosols. The bile salts inhibited lung surfactant function at different dose levels, however they did not affect the integrity of ciliated cells at the tested doses. Furthermore, the bile salt aerosols induced changes in the breathing pattern of mice indicative of pulmonary irritation. The bile salts were ranked according to potency in vitro for surfactant function disruption and in vivo for induction of pulmonary irritation. The ranking was the same, suggesting a correlation between the interference with lung surfactant and the respiratory response.\n\nBile salt enhancers for inhalation: Correlation between in vitro and in vivo lung effects.", "token_count": 339, "char_count": 1456, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5674, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:44.000085", "source": { "split": "train_shard_00000", "doc_id": 3298 }, "chunk_id": "train_shard_00000_3298_0", "global_id": 3653 }, { "text": "The worldwide trend of limiting the use of antibiotic growth promoters (AGPs) in animal production creates challenges for the animal feed industry, thus necessitating the development of effective non-antibiotic alternatives to improve animal performance. Increasing evidence has shown that the growth-promoting effect of AGPs is highly correlated with the reduced activity of bile salt hydrolase (BSH, EC 3.5.1.24), an intestinal bacteria-producing enzyme that has a negative impact on host fat digestion and energy harvest. Therefore, BSH inhibitors may become novel, attractive alternatives to AGPs. Detailed knowledge of BSH substrate preferences and the wealth of structural data on BSHs provide a solid foundation for rationally tailored BSH inhibitor design. This review focuses on the relationship between structure and function of BSHs based on the crystal structure, kinetic data, molecular docking and comparative structural analyses. The molecular basis for BSH substrate recognition is also discussed. Finally, recent advances and future prospectives in the development of potent, safe, and cost-effective BSH inhibitors are described.\n\nBile salt hydrolases: Structure and function, substrate preference, and inhibitor development.", "token_count": 268, "char_count": 1243, "word_count": 172, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:44.588018", "source": { "split": "train_shard_00000", "doc_id": 3299 }, "chunk_id": "train_shard_00000_3299_0", "global_id": 3654 }, { "text": "This work reports the comparison of the genome sequence and the ability to inhibit fungal growth of two Pseudomonas protegens related strains that were isolated from the same hydroponic culture of lamb's lettuce. The two strains were very similar in their core genome but one strain, Pf4, contained three gene clusters for the production of secondary metabolites, i.e., pyoluteorin (plt), pyrrolnitrin (prn), and rhizoxin (rzx), that were missing in the other strain, Pf11. The difference between the two strains was not due to simple insertion events, but to a relatively complex differentiation focused on the accessory genomes. In dual culture assays, both strains inhibited nearly all tested fungal strains, yet Pf4 exerted a significantly stronger fungal growth inhibition than Pf11. In addition to the differences in the secondary metabolite production associated genes abundance, the genome of Pf4 was more stable, smaller in size and with a lower number of transposons. The preservation of a dynamic equilibrium within natural populations of different strains comprised in the same species but differing in their secondary metabolite repertoire and in their genome stability may be functional to the adaptation to environmental changes.\n\nGenome Sequence and Antifungal Activity of Two Niche-Sharing Pseudomonas protegens Related Strains Isolated from Hydroponics.", "token_count": 317, "char_count": 1371, "word_count": 203, "semantic_coherence": 1, "information_density": 0.601, "quality_score": 0.8005, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:45.182537", "source": { "split": "train_shard_00000", "doc_id": 3300 }, "chunk_id": "train_shard_00000_3300_0", "global_id": 3655 }, { "text": "In this issue of EBioMedicine, Kohl and colleagues describe the development of a new core genome MLST scheme (cgMLST) for Mycobacterium tuberculosis complex strains based on a set of 2891 genes. Here, the application of the scheme to a number of tuberculosis surveillance studies is examined.\n\nDevelopment of a New Genome-Wide MLST Scheme for High-Resolution Typing of Diverse Mycobacterium tuberculosis Complex Strains.", "token_count": 118, "char_count": 420, "word_count": 62, "semantic_coherence": 1, "information_density": 0.6613, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:45.914476", "source": { "split": "train_shard_00000", "doc_id": 3301 }, "chunk_id": "train_shard_00000_3301_0", "global_id": 3656 }, { "text": "Lactobacillus rhamnosus is a lactic acid bacterium with a diverse ecological habitat. We recently isolated a L. rhamnosus strain (LRB) from a healthy baby-tooth that had naturally fallen out. We determined the whole genome sequence of LRB and found that the isolate is closely genetically related to an intestinal isolate, L. rhamnosus GG (ATCC 53103). However, the LRB genome had lost about a 75-kb segment and undergone a genomic rearrangement. We assessed LRB's capacity to survive in the gut environment, at least temporarily. We found that LRB, like the intestinal isolate ATCC 53103, showed resistance to low pH but sensitive to bile salt. Surprisingly, we found that this oral isolate LRB showed strong antimicrobial activity against a variety of oral streptococci including Streptococcus mutans. The production of antimicrobial activity is dependent on media composition since some media supported the production while others did not. The production of antimicrobial activity is also dependent on growth temperature, with optimal production at 37°C. The antimicrobial activity was not restricted to streptococci, but effective against a variety of organisms, including ESKAPE pathogens.\n\nLactobacillus rhamnosus LRB mediated inhibition of oral streptococci.", "token_count": 338, "char_count": 1265, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6183, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:46.491173", "source": { "split": "train_shard_00000", "doc_id": 3302 }, "chunk_id": "train_shard_00000_3302_0", "global_id": 3657 }, { "text": "Stenotrophomonas maltophilia has evolved as one of the leading multidrug-resistant pathogens responsible for a variety of nosocomial infections especially in highly debilitated patients. As information on the genomic and intraspecies diversity of this clinically important pathogen is limited, we sequenced the whole genome of 27 clinical isolates from hospitalized patients. Phylogenomic analysis along with the genomes of type strains suggested that the clinical isolates are distributed over the Stenotrophomonas maltophilia complex (Smc) within the genus Stenotrophomonas. Further genome-based taxonomy coupled with the genomes of type strains of the genus Stenotrophomonas allowed us to identify five cryptic genomospecies, which are associated with the clinical isolates of S. maltophilia and are potentially novel species. These isolates share a very small core genome that implies a high level of genetic diversity within the isolates. Recombination analysis of core genomes revealed that the impact of recombination is more than mutation in the diversification of clinical S. maltophilia isolates. Distribution analysis of well-characterized antibiotic-resistance and efflux pump genes of S. maltophilia across multiple novel genomospecies provided insights into its antibiotic-resistant ability. This study supports the existence of multiple cryptic species within the Smc besides S. maltophilia, which are associated with human infections, and highlights the importance of genome-based approaches to delineate bacterial species. This data will aid in improving clinical diagnosis and for understanding species-specific clinical manifestations of infection due to Stenotrophomonas species.\n\nTaxonogenomics reveal multiple novel genomospecies associated with clinical isolates of Stenotrophomonas maltophilia.", "token_count": 411, "char_count": 1818, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5667, "quality_score": 0.7833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:47.109997", "source": { "split": "train_shard_00000", "doc_id": 3303 }, "chunk_id": "train_shard_00000_3303_0", "global_id": 3658 }, { "text": "The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strains. We also wanted to explore whether sbGC for each strain was associated with the corresponding species' core genome GC content (cgGC). We present a simple mathematical model that estimates sbGC from cgGC. The model assumes only that the estimated sbGC is a function of cgGC proportional to fixed AT→GC (α) and GC → AT (β) mutation rates. Non-linear regression was used to estimate parameters α and β from the empirical data described above.\n\nModeling of the GC content of the substituted bases in bacterial core genomes.", "token_count": 182, "char_count": 730, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:47.554578", "source": { "split": "train_shard_00000", "doc_id": 3304 }, "chunk_id": "train_shard_00000_3304_0", "global_id": 3659 }, { "text": "Carnobacterium spp. are frequently isolated from vacuum-packaged (VP) meat. Specific strains of Carnobacterium and their growth characteristics may be associated with the storage life of such products. This study investigated the growth of 44 Carnobacterium isolates obtained from VP meat cuts produced at three Canadian abattoirs (A, B and C) under the following conditions: pH 5.4, 6.2 and 7.4; lactic acid at 60 and 90 mM; acetic acid at 33.6 mM. Whole genome sequencing was performed for all 44 isolates and a core genome phylogenetic tree was created to identify strain variability among isolates from different abattoirs. The isolates were clustered into 11 groups. All isolates from abattoirs B and C were identified as C. divergens, while the isolates from abattoir A included both C. maltaromaticum and C. divergens at equal proportions. C. divergens isolates from abattoir A belonged to two phylogenetic groups and none of them was found in the phylogenetic groups containing isolates from abattoirs B or C. Whole genome sequencing revealed that identical strains were isolated from different samples obtained at the same abattoir. The mean growth rate and maximum population density of the C. maltaromaticum isolates were lower than those of the C. divergens isolates. C. divergens isolates from abattoir A had higher growth rates and maximum population density than those from abattoirs B and C. In conclusion, growth characteristic and whole genome analysis both demonstrated strain variability of Carnobacterium among abattoirs, which could be a result of the difference in the antimicrobial interventions used for carcasses at different abattoirs, and may be associated with different storage lives of VP meats produced from different abattoirs.\n\nGrowth of Carnobacterium spp. isolated from chilled vacuum-packaged meat under relevant acidic conditions.", "token_count": 469, "char_count": 1868, "word_count": 282, "semantic_coherence": 1, "information_density": 0.4965, "quality_score": 0.7482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:48.199498", "source": { "split": "train_shard_00000", "doc_id": 3305 }, "chunk_id": "train_shard_00000_3305_0", "global_id": 3660 }, { "text": "Bacterial plasmids constitute a wealth of shared DNA amounting to about 20% of the total prokaryotic pangenome. Plasmids replicate autonomously and control their replication by maintaining a fairly constant number of copies within a given host. Plasmids should acquire a good fitness to their hosts so that they do not constitute a genetic load. Here we review some basic concepts in plasmid biology, pertaining to the control of replication and distribution of plasmid copies among daughter cells. A particular class of plasmids is constituted by those that replicate by the rolling circle mode (rolling circle-replicating [RCR]-plasmids). They are small double-stranded DNA molecules, with a rather high number of copies in the original host. RCR-plasmids control their replication by means of a small short-lived antisense RNA, alone or in combination with a plasmid-encoded transcriptional repressor protein. Two plasmid prototypes have been studied in depth, namely the staphylococcal plasmid pT181 and the streptococcal plasmid pMV158, each corresponding to the two types of replication control circuits, respectively. We further discuss possible applications of the plasmid-encoded antisense RNAs and address some future directions that, in our opinion, should be pursued in the study of these small molecules. This article is categorized under: Regulatory RNAs/RNAi/Riboswitches > Regulatory RNAs RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems.\n\nAntisense and yet sensitive: Copy number control of rolling circle-replicating plasmids by small RNAs.", "token_count": 396, "char_count": 1587, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5983, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:48.821801", "source": { "split": "train_shard_00000", "doc_id": 3306 }, "chunk_id": "train_shard_00000_3306_0", "global_id": 3661 }, { "text": "To explore the role of the abnormal expression of the bile salt export pump (BSEP) and multidrug resistance protein 2 (MRP2) in isoniazid (INH)-induced liver injury, we assessed the liver injury induced by INH in rats and HepG2 cells in vitro. The regulatory pathways via Sirtuin 1 (SIRT1) and farnesoid X receptor (FXR) were also determined. Rat liver injury was assessed by histopathological and biochemical analysis and HepG2 cytotoxicity was assessed by a 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) test. The levels of protein were determined by Western blot. The results indicated that INH could induce hepatotoxicity in vivo and in vitro in a dose dependent manner. The liver index and serum biochemical analysis, especially the levels of total bile acids (TBA), total bilirubin (TBIL), and direct bilirubin (DBIL), were significantly increased in rats. The INH hepatotoxicity was severe in the high dose group, and occurred alongside the down-regulation of BSEP and MRP2 in vivo and in vitro, leading to the accumulation of toxic substrates in the hepatocytes. The SIRT1/FXR pathway was identified as being important for the down-regulation of transporters. In summary, our study indicated that the down-regulation of BSEP and MRP2 represents one mechanism of INH-induced liver injury and the down-regulation of SIRT1/FXR may be a key regulator. This will inform the development of novel therapies and enable the prevention of INH-induced liver injury.\n\nDysregulation of BSEP and MRP2 May Play an Important Role in Isoniazid-Induced Liver Injury via the SIRT1/FXR Pathway in Rats and HepG2 Cells.", "token_count": 473, "char_count": 1627, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5407, "quality_score": 0.7703, "entities": { "genes": [ "MRP2", "SIRT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:49.463966", "source": { "split": "train_shard_00000", "doc_id": 3307 }, "chunk_id": "train_shard_00000_3307_0", "global_id": 3662 }, { "text": "The maize W22 inbred has served as a platform for maize genetics since the mid twentieth century. To streamline maize genome analyses, we have sequenced and de novo assembled a W22 reference genome using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to the B73 reference genome at multiple scales, from transposon composition and copy number variation to single-nucleotide polymorphisms. The generation of this reference genome enables accurate placement of thousands of Mutator (Mu) and Dissociation (Ds) transposable element insertions for reverse and forward genetics studies. Annotation of the genome has been achieved using RNA-seq analysis, differential nuclease sensitivity profiling and bisulfite sequencing to map open reading frames, open chromatin sites and DNA methylation profiles, respectively. Collectively, the resources developed here integrate W22 as a community reference genome for functional genomics and provide a foundation for the maize pan-genome.\n\nThe maize W22 genome provides a foundation for functional genomics and transposon biology.", "token_count": 250, "char_count": 1125, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6474, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:49.952813", "source": { "split": "train_shard_00000", "doc_id": 3308 }, "chunk_id": "train_shard_00000_3308_0", "global_id": 3663 }, { "text": "The technological advancement of molecular epidemiological analysis using next-generation sequencing (NGS) for foodborne pathogens has a groundbreaking impact over the past three years. In particular, the emergence of cg (core genome) multilocus sequence typing(MLST) has a significant impact. This is because this technology made it possible for many researchers to carry out molecular epidemiological analysis on foodborne pathogens in a common language, using common definitions. The resolution of core genome MLST (cgMLST) far surpasses that of MLST, which only uses seven (usually, in some cases five) housekeeping genes. Therefore, cgMLST would in no doubt terminate the role of conventional MLST as the molecular epidemiological tool. However, the role of MLST would probably not end all together. Rather, the sequence type (ST) of the conventional MLST is expected to be used as in silico MLST by a wider range of researchers than ever in the next 10 years. This is because, with the arrival of the NGS era, we have come to be able to obtain ST of conventional MLST by simply entering the NGS text file into one's own PC. In other words, acquisition of ST data is no longer limited to researchers aiming to conduct MLST for the first place. The impact of such a change is large. In silico MLST will continue to be used as a tool for understanding the broad characteristics of bacterial strains. This review aimed to summarize the main information on STs that have been accumulated for representative foodborne pathogens, in particular for potential NGS users in this new era who have been not familiar with MLST until now.\n\nWill the emergence of core genome MLST end the role of in silico MLST?", "token_count": 387, "char_count": 1702, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5663, "quality_score": 0.7832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:50.567931", "source": { "split": "train_shard_00000", "doc_id": 3309 }, "chunk_id": "train_shard_00000_3309_0", "global_id": 3664 }, { "text": "Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae.\n\nFunctional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.", "token_count": 174, "char_count": 599, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7024, "quality_score": 0.8512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:51.009301", "source": { "split": "train_shard_00000", "doc_id": 3310 }, "chunk_id": "train_shard_00000_3310_0", "global_id": 3665 }, { "text": "Kefir is a natural fermentation agent composed of various microorganisms. To address the mechanism of kefir grain formation, we investigated the microbial role in forming kefir biofilms. The results showed that a biofilm could be formed in kefir-fermented milk and the biofilm forming ability reached the maximum at 13 days. The strains Kluyveromyces marxianus, Lactococcus lactis, Leuconostoc mesenteroides, Lactobacillus kefiri, Lactobacillus sunkii and Acetobacter orientalis were isolated from kefir biofilms by the streak-plate method. These microorganisms were analysed with respect to biofilm forming properties, including their surface characterisation (hydrophobicity and zeta potentials) and the microbial aggregation. The results indicated that Klu. marxianus possessed the strongest biofilm forming properties with the strongest hydrophobicity, lowest zeta potential and greatest auto-aggregation ability. When Klu. marxianus and Ac. orientalis were co-cultured with kefir LAB strains respectively, it was found that mixing Klu. marxianus with Lb. sunkii produced the highest co-aggregation ability. These results elucidated the mechanism of kefir biofilm formation and the microorganisms involved.\n\nInvestigation of microorganisms involved in kefir biofilm formation.", "token_count": 329, "char_count": 1280, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:51.572421", "source": { "split": "train_shard_00000", "doc_id": 3311 }, "chunk_id": "train_shard_00000_3311_0", "global_id": 3666 }, { "text": "Giant viruses of amoebae are distinct from classical viruses by the giant size of their virions and genomes. Pandoraviruses are the record holders in size of genomes and number of predicted genes. Three strains,\n\nA Large Open Pangenome and a Small Core Genome for Giant Pandoraviruses.", "token_count": 75, "char_count": 285, "word_count": 46, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:51.947812", "source": { "split": "train_shard_00000", "doc_id": 3312 }, "chunk_id": "train_shard_00000_3312_0", "global_id": 3667 }, { "text": "The capacity for some pathogens to jump into different host-species populations is a major threat to public health and food security. Staphylococcus aureus is a multi-host bacterial pathogen responsible for important human and livestock diseases. Here, using a population-genomic approach, we identify humans as a major hub for ancient and recent S. aureus host-switching events linked to the emergence of endemic livestock strains, and cows as the main animal reservoir for the emergence of human epidemic clones. Such host-species transitions are associated with horizontal acquisition of genetic elements from host-specific gene pools conferring traits required for survival in the new host-niche. Importantly, genes associated with antimicrobial resistance are unevenly distributed among human and animal hosts, reflecting distinct antibiotic usage practices in medicine and agriculture. In addition to gene acquisition, genetic diversification has occurred in pathways associated with nutrient acquisition, implying metabolic remodelling after a host switch in response to distinct nutrient availability. For example, S. aureus from dairy cattle exhibit enhanced utilization of lactose-a major source of carbohydrate in bovine milk. Overall, our findings highlight the influence of human activities on the multi-host ecology of a major bacterial pathogen, underpinned by horizontal gene transfer and core genome diversification.\n\nGene exchange drives the ecological success of a multi-host bacterial pathogen.", "token_count": 326, "char_count": 1514, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:52.511287", "source": { "split": "train_shard_00000", "doc_id": 3313 }, "chunk_id": "train_shard_00000_3313_0", "global_id": 3668 }, { "text": "Genomic islands (GIs) are discrete gene clusters encoding for a variety of functions including antibiotic and heavy metal resistance, some of which are tightly associated to lineages of the core genome phylogenetic tree. We have investigated the functions of two distinct integrase genes in the mobilization of two metal resistant GIs, G08 and G62, of\n\nIntegrase-Controlled Excision of Metal-Resistance Genomic Islands in", "token_count": 98, "char_count": 421, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:52.892598", "source": { "split": "train_shard_00000", "doc_id": 3314 }, "chunk_id": "train_shard_00000_3314_0", "global_id": 3669 }, { "text": "Peroxisomes and peroxisomal transketolase and transaldolase enzymes are essential for xylose alcoholic fermentation by the methylotrophic thermotolerant yeast,", "token_count": 48, "char_count": 159, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:53.255663", "source": { "split": "train_shard_00000", "doc_id": 3315 }, "chunk_id": "train_shard_00000_3315_0", "global_id": 3670 }, { "text": "Bulk soil and rhizosphere are soil compartments selecting different microbial communities. However, it is unknown whether this selection also can change the genome content of specific bacterial taxa, splitting a population in distinct ecotypes. To answer this question we compared the genome sequences of 53 isolates obtained from sugarcane rhizosphere (28) and bulk soil (25). These isolates were previously classified in the Pseudomonas koreensis subgroup of the P. fluorescens complex. Phylogenomics showed a trend of separation between bulk soil and rhizosphere isolates. Discriminant analysis of principal components (DAPC) identified differences in the accessory genome of rhizosphere and bulk soil sub-populations. We found significant changes in gene frequencies distinguishing rhizosphere from bulk soil ecotypes, for example, enrichment of phosphatases and xylose utilization (xut) genes, respectively. Phenotypic assays and deletion of xutA gene indicated that accumulation of xut genes in the bulk soil sub-population provided a higher growth capacity in a d-xylose medium, supporting the corresponding genomic differences. Despite the clear differences distinguishing the two ecotypes, all 53 isolates were classified in a single 16S rRNA gene OTU. Collectively, our results revealed that the gene pool and ecological behavior of a bacterial population can be different for ecotypes living in neighbouring soil habitats.\n\nGenome variations between rhizosphere and bulk soil ecotypes of a Pseudomonas koreensis population.", "token_count": 364, "char_count": 1534, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:53.841470", "source": { "split": "train_shard_00000", "doc_id": 3316 }, "chunk_id": "train_shard_00000_3316_0", "global_id": 3671 }, { "text": "Salmonella enterica serovar Paratyphi C causes enteric (paratyphoid) fever in humans. Its presentation can range from asymptomatic infections of the blood stream to gastrointestinal or urinary tract infection or even a fatal septicemia [1]. Paratyphi C is very rare in Europe and North America except for occasional travelers from South and East Asia or Africa, where the disease is more common [2, 3]. However, early 20\n\nPan-genome Analysis of Ancient and Modern Salmonella enterica Demonstrates Genomic Stability of the Invasive Para C Lineage for Millennia.", "token_count": 143, "char_count": 560, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:54.271278", "source": { "split": "train_shard_00000", "doc_id": 3317 }, "chunk_id": "train_shard_00000_3317_0", "global_id": 3672 }, { "text": "Lactobacillus (L.) curvatus reaches high numbers in a variety of habitats, which suggests a high (genomic) diversity within this species. Empirically selected strains are used as starter cultures in sausage fermentation. Determinants for the assertiveness of a strain in this environment are assumed to be multifactorial. We used comparative genomics and in silico proteomics of 10 L. curvatus strains, which were representative of its genetic and physiological biodiversity, to possibly derive genetic determinants for strain or group specific assertiveness in sausage fermentation. Their genome sizes ranged from 1.7 Mb up to 2.0 Mb. The estimated pan- and core genomes were 3.0 Mb and 1.4 Mb, respectively. The accessory genome, GC-content and coding density revealed a significant genomic diversity within this species. Plasmids were found, which were either closely related or unique in several strains. Putative assertiveness determinants including CRISPR/Cas systems, prophages, bacteriocin production, or specific metabolic settings were detected. Such traits of the accessory genome could not be correlated with the source of isolation. Pathways, which previously have been predicted for a relation with adaptation to meat of L. sakei, are part of the core genome of L curvatus. Intraspecies differences in the accessory genome of L. curvatus comprise ribose metabolism, enzymes involved in nucleotide metabolism (nucleoside phosphorylases, phosphopentomutase, adenosine deaminase, ribose transporters), and tyrosine decarboxylases, ornithine decarboxylases. One group of the strains encoded a phosphotransferase system (PTS) as ribose transporter, whereas the second group encoded an ATP binding cassette (ABC) transporter. Analysis of the ribose uptake by HPLC analysis revealed different efficiencies of both transporter systems. Except for bacteriocin formation, no strain specific traits were identified predicting assertiveness of single strains. This fits our previous observation that single strains of L. curvatus could not override others in a competitive setting", "token_count": 521, "char_count": 2082, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6151, "quality_score": 0.8076, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:31:54.911154", "source": { "split": "train_shard_00000", "doc_id": 3318 }, "chunk_id": "train_shard_00000_3318_0", "global_id": 3673 }, { "text": "Rather, pairs or sets of strains, comprising metabolically synergistic or non-assertive partner strains were able to dominate the fermentation. Indeed, this work suggests that assertive partnerships can be predicted along their complementary accessory genomes.\n\nComparative genomics of Lactobacillus curvatus enables prediction of traits relating to adaptation and strategies of assertiveness in sausage fermentation.", "token_count": 91, "char_count": 417, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8868, "quality_score": 0.9434, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:55.313451", "source": { "split": "train_shard_00000", "doc_id": 3318 }, "chunk_id": "train_shard_00000_3318_1", "global_id": 3674 }, { "text": "Herein, we explore the probiotic potentials and soybean meal (SBM) compound feed fermentative applications of Lactobacillus plantarum SK1305 strain isolated previously from Korean green chili pickled pepper (gochu-jangajji). The isolate exhibited higher acid (pH 2.5) and bile tolerance (0.3%, w/v) up to 2 h and 4 h, respectively. The cell-free culture supernatant (CFCS) displayed a broad spectrum antibacterial activities against various pathogens, which may be ascribed to high lactic acid production (L-form, 86.8 ± 0.8 mM and D-form, 44.8 ± 0.2 mM). Further, the strain displayed high cell-surface hydrophobicity (92.7 ± 1.0%), coupled with low auto-aggregation (23.6 ± 4.4%) but relatively higher co-aggregation properties with C. perfringens (49.6 ± 0.6%) as well as H\n\nExploring the Probiotic and Compound Feed Fermentative Applications of Lactobacillus plantarum SK1305 Isolated from Korean Green Chili Pickled Pepper.", "token_count": 323, "char_count": 928, "word_count": 133, "semantic_coherence": 1, "information_density": 0.7293, "quality_score": 0.8647, "entities": { "genes": [ "SK1305" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:55.893384", "source": { "split": "train_shard_00000", "doc_id": 3319 }, "chunk_id": "train_shard_00000_3319_0", "global_id": 3675 }, { "text": "In vitro assays are commonly used during drug discovery to try to decrease the risk of idiosyncratic drug-induced liver injury (iDILI). But how effective are they at predicting risk? One of the most widely used methods evaluates cell cytotoxicity. Cytotoxicity assays that used cell lines that are very different from normal hepatocytes, and high concentrations of drug, were not very accurate at predicting idiosyncratic drug reaction risk. Even cytotoxicity assays that use more biologically normal cells resulted in many false-positive and false-negative results. Assays that quantify reactive metabolite formation, mitochondrial injury, and bile salt export pump (BSEP) inhibition have also been described. Although evidence suggests that reactive metabolite formation and BSEP inhibition can play a role in the mechanism of iDILI, these assays are not very accurate at predicting risk. In contrast, inhibition of the mitochondrial electron transport chain appears not to play an important role in the mechanism of iDILI, although other types of mitochondrial injury may do so. It is likely that there are many additional mechanisms by which drugs can cause iDILI. However, simply measuring more parameters is unlikely to provide better predictive assays unless those parameters are actually involved in the mechanism of iDILI. Hence, a better mechanistic understanding of iDILI is required; however, mechanistic studies of iDILI are very difficult. There is substantive evidence that most iDILI is immune mediated; therefore, the most accurate assays may involve those that determine immune responses to drugs. New methods to manipulate immune tolerance may greatly facilitate development of more suitable methods.\n\nDo In Vitro Assays Predict Drug Candidate Idiosyncratic Drug-Induced Liver Injury Risk?", "token_count": 406, "char_count": 1808, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5623, "quality_score": 0.7811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:56.536078", "source": { "split": "train_shard_00000", "doc_id": 3320 }, "chunk_id": "train_shard_00000_3320_0", "global_id": 3676 }, { "text": "The human gut microbiota impacts host metabolism and has been implicated in the pathophysiology of obesity and metabolic syndromes. However, defining the roles of specific microbial activities and metabolites on host phenotypes has proven challenging due to the complexity of the microbiome-host ecosystem. Here, we identify strains from the abundant gut bacterial phylum Bacteroidetes that display selective bile salt hydrolase (BSH) activity. Using isogenic strains of wild-type and BSH-deleted\n\nA selective gut bacterial bile salt hydrolase alters host metabolism.", "token_count": 143, "char_count": 567, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7215, "quality_score": 0.8608, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:57.029460", "source": { "split": "train_shard_00000", "doc_id": 3321 }, "chunk_id": "train_shard_00000_3321_0", "global_id": 3677 }, { "text": "Effect of the Synthetic Bile Salt Analog CamSA on the Hamster Model of Clostridium difficile Infection.", "token_count": 29, "char_count": 103, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:57.430146", "source": { "split": "train_shard_00000", "doc_id": 3322 }, "chunk_id": "train_shard_00000_3322_0", "global_id": 3678 }, { "text": "The advent of high throughput sequencing (HTS) technologies raises a major concern about storage and transmission of data produced by these technologies. In particular, large-scale sequencing projects generate an unprecedented volume of genomic sequences ranging from tens to several thousands of genomes per species. These collections contain highly similar and redundant sequences, also known as pangenomes. The ideal way to represent and transfer pangenomes is through compression. A number of HTS-specific compression tools have been developed to reduce the storage and communication costs of HTS data, yet none of them is designed to process a pangenome. In this article, we present dynamic alignment-free and reference-free read compression (DARRC), a new alignment-free and reference-free compression method. It addresses the problem of pangenome compression by encoding the sequences of a pangenome as a guided de Bruijn graph. The novelty of this method is its ability to incrementally update DARRC archives with new genome sequences without full decompression of the archive. DARRC can compress both single-end and paired-end read sequences of any length using all symbols of the IUPAC nucleotide code. On a large Pseudomonas aeruginosa data set, our method outperforms all other tested tools. It provides a 30% compression ratio improvement in single-end mode compared with the best performing state-of-the-art HTS-specific compression method in our experiments.\n\nDynamic Alignment-Free and Reference-Free Read Compression.", "token_count": 326, "char_count": 1534, "word_count": 220, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:57.989019", "source": { "split": "train_shard_00000", "doc_id": 3323 }, "chunk_id": "train_shard_00000_3323_0", "global_id": 3679 }, { "text": "In this comparative genomics study our aim was to unravel genes under positive selection in the core genome of the Bacillus cereus group. Indeed, the members of this group share close genetic relationships but display a rather large phenotypic and ecological diversity, providing a unique opportunity for studying how genomic changes reflect ecological adaptation during the divergence of a bacterial group. For this purpose, we screened ten completely sequenced genomes of four pathogenic Bacillus species, finding that 254 out of 3093 genes have codon sites with d\n\nGenes under positive selection in the core genome of pathogenic Bacillus cereus group members.", "token_count": 151, "char_count": 662, "word_count": 101, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:58.425190", "source": { "split": "train_shard_00000", "doc_id": 3324 }, "chunk_id": "train_shard_00000_3324_0", "global_id": 3680 }, { "text": "In order to better understand the relationships among current Nostocales cyanobacterial blooms, eight genomes were sequenced from cultured isolates or from environmental metagenomes of recent planktonic Nostocales blooms. Phylogenomic analysis of publicly available sequences placed the new genomes among a group of 15 genomes from four continents in a distinct ADA clade (Anabaena/Dolichospermum/Aphanizomenon) within the Nostocales. This clade contains four species-level groups, two of which include members with both Anabaena-like and Aphanizomenon flos-aquae-like morphology. The genomes contain many repetitive genetic elements and a sizable pangenome, in which ABC-type transporters are highly represented. Alongside common core genes for photosynthesis, the differentiation of N\n\nA closely-related clade of globally distributed bloom-forming cyanobacteria within the Nostocales.", "token_count": 222, "char_count": 886, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7434, "quality_score": 0.8717, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:58.888303", "source": { "split": "train_shard_00000", "doc_id": 3325 }, "chunk_id": "train_shard_00000_3325_0", "global_id": 3681 }, { "text": "Efficient bioconversion of lignocellulosic biomass to bioethanol is one of key challenges in the situation of increasing bioethanol demand. The ethanologenic microbes for such conversion are required to possess abilities of utilization of various sugars including xylose and arabinose in lignocellulosic biomass. As required additional characteristics, there are a weak or no glucose repression that allows cells to simultaneously utilize various sugars together with glucose and thermotolerance for fermentation at high temperatures, which has several advantages including reduction of cooling cost. Spathaspora passalidarum ATCC MYA-4345, a type strains, isolated previously have mainly of these abilities or characteristics but its thermotolerance is not so strong and its glucose repression on xylose utilization is revealed.\n\nHighly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1-2.", "token_count": 236, "char_count": 974, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6769, "quality_score": 0.8385, "entities": { "genes": [ "CMUWF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:59.365841", "source": { "split": "train_shard_00000", "doc_id": 3326 }, "chunk_id": "train_shard_00000_3326_0", "global_id": 3682 }, { "text": "Lyme disease is emerging in southern Canada due to range expansion of the tick vector, followed by invasion of the agent of Lyme disease Borrelia burgdorferi sensu stricto. Strain diversity, as determined by Multi Locus Sequence Typing, occurs in this zone of emergence, and this may have its origins in adaptation to ecological niches, and have phenotypic consequences for pathogenicity and serological test performance. Sixty-four unique strains were cultured from ticks collected in southern Canada and the genomes sequenced using the Illumina MiSeq platform. A maximum likelihood phylogenetic tree of the chromosome revealed two large clades with multiple subclades. Consistent with previous studies on this species, the clades were not geographically defined, and some Canadian strains were highly divergent from previously sequenced US strains. There was evidence for recombination in the chromosome but this did not affect the phylogeny. Analysis of chromosomal genes indicated that these are under intense purifying selection. Phylogenies of the accessory genome and chromosome were congruent. Therefore strain differences identified in the phylogeny of chromosomal genes likely act as a proxy for genetic determinants of phenotypic differences amongst strains that are harboured in the accessory genome. Further studies on health implications of strain diversity are needed.\n\nWhole genome sequencing and phylogenetic analysis of strains of the agent of Lyme disease Borrelia burgdorferi from Canadian emergence zones.", "token_count": 347, "char_count": 1526, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:31:59.944755", "source": { "split": "train_shard_00000", "doc_id": 3327 }, "chunk_id": "train_shard_00000_3327_0", "global_id": 3683 }, { "text": "Pseudomonas aeruginosa is an important opportunistic pathogen in hospitals, responsible for various infections that are difficult to treat due to intrinsic and acquired antibiotic resistance. Here, 20 epidemiologically unrelated strains isolated from patients in a general hospital over a time period of two decades were analyzed using whole genome sequencing. The genomes were compared in order to assess the presence of a predominant clone or sequence type (ST). No clonal structure was identified, but core genome-based single nucleotide polymorphism (SNP) analysis distinguished two major, previously identified phylogenetic groups. Interestingly, most of the older strains isolated between 1994 and 1998 harbored exoU, encoding a cytotoxic phospholipase. In contrast, most strains isolated between 2011 and 2016 were exoU-negative and phylogenetically very distinct from the older strains, suggesting a population shift of nosocomial P. aeruginosa over time. Three out of 20 strains were ST235 strains, a global high-risk clonal lineage; these carried several additional resistance determinants including aac(6')Ib-cr encoding an aminoglycoside N-acetyltransferase that confers resistance to fluoroquinolones. Core genome comparison with ST235 strains from other parts of the world showed that the three strains clustered together with other Brazilian/Argentinean isolates. Despite this regional relatedness, the individuality of each of the three ST235 strains was revealed by core genome-based SNPs and the presence of genomic islands in the accessory genome. Similarly, strain-specific characteristics were detected for the remaining strains, indicative of individual evolutionary histories and elevated genome plasticity.\n\nComparative Genomics of Nonoutbreak Pseudomonas aeruginosa Strains Underlines Genome Plasticity and Geographic Relatedness of the Global Clone ST235.", "token_count": 458, "char_count": 1881, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:00.583169", "source": { "split": "train_shard_00000", "doc_id": 3328 }, "chunk_id": "train_shard_00000_3328_0", "global_id": 3684 }, { "text": "To investigate the therapeutic effect of glycyrrhizin arginine salt on rat cholestatic cirrhosis, we subjected male Sprague Dawley rats to common bile duct ligation for 14 days and treated them with distilled water (model group), arginine, or a low or high dose of glycyrrhizin arginine salt by gavage. A sham-operated group was used as a control group. Treatment with glycyrrhizin arginine salt substantially improved animal growth rates, reduced the ratio of liver weight to body weight and decreased total bilirubin, aspartate aminotransferase, 8-isoprostane and malondialdehyde compared with the values measured in the model group. The progress of liver fibrosis, as detected by hematoxylin and eosin and Masson's trichrome staining, was slower in the glycyrrhizin arginine salt groups than in the model group or the arginine group. Reductions of bile salt pool size, hepatic hydroxyproline content and fibrosis score were also seen in the glycyrrhizin arginine salt groups compared with the model group. Furthermore, glycyrrhizin arginine salt significantly reduced the expression of transforming growth factor [Formula: see text]1 (TGF-[Formula: see text]1), [Formula: see text]-smooth muscle actin, tumor necrosis factor-[Formula: see text] and matrix metalloproteinases 2 and 9. Glycyrrhizin arginine salt also inhibited the expression of [Formula: see text]-SMA and matrix metalloproteinases 2 and 9 in response to TGF-[Formula: see text]1 in LX-2 cells and primary rat hepatic stellate cells and mitigated the cytotoxicity induced by rat bile in HepG2 cells and primary rat hepatocytes.\n\nTherapeutic Effect of Glycyrrhizin Arginine Salt on Rat Cholestatic Cirrhosis and its Mechanism.", "token_count": 496, "char_count": 1694, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5366, "quality_score": 0.7683, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:01.238098", "source": { "split": "train_shard_00000", "doc_id": 3329 }, "chunk_id": "train_shard_00000_3329_0", "global_id": 3685 }, { "text": "Self-assembled structures formed by mixtures of cationic and anionic surfactants are interesting tools for applications requiring interactions with charged particles and molecules. Nevertheless, they present instability close to the equimolar composition and poor morphological versatility, which is generally restricted to vesicles and micelles. Against this general trend, we report on bile salt derivative based catanionic mixtures assembling in tubules and lamellae depending on the mixture composition. Electrophoretic mobility measurements prove that the composition also dictates their superficial charge, which can be tuned from negative to positive by increasing the positively charged surfactant fraction in the mixtures. The study of the catanionic aggregates was conducted by means of microscopy and spectroscopy techniques and compared to the self-assembly behaviors of the individual building blocks. This study broadens the so far small array of bile salt derivative catanionic systems, confirming their distinctive behavior in the spectrum of catanionic mixtures.\n\nBile acid derivative-based catanionic mixtures: versatile tools for superficial charge modulation of supramolecular lamellae and nanotubes.", "token_count": 262, "char_count": 1220, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:01.789320", "source": { "split": "train_shard_00000", "doc_id": 3330 }, "chunk_id": "train_shard_00000_3330_0", "global_id": 3686 }, { "text": "Rhizobial symbiosis genes are often carried on symbiotic islands or plasmids that can be transferred (horizontal transfer) between different bacterial species. Symbiosis genes involved in horizontal transfer have different phylogenies with respect to the core genome of their ‘host’. Here, the literature on legume⁻rhizobium symbioses in field soils was reviewed, and cases of phylogenetic incongruence between rhizobium core and symbiosis genes were collated. The occurrence and importance of horizontal transfer of rhizobial symbiosis genes within and between bacterial genera were assessed. Horizontal transfer of symbiosis genes between rhizobial strains is of common occurrence, is widespread geographically, is not restricted to specific rhizobial genera, and occurs within and between rhizobial genera. The transfer of symbiosis genes to bacteria adapted to local soil conditions can allow these bacteria to become rhizobial symbionts of previously incompatible legumes growing in these soils. This, in turn, will have consequences for the growth, life history, and biogeography of the legume species involved, which provides a critical ecological link connecting the horizontal transfer of symbiosis genes between rhizobial bacteria in the soil to the above-ground floral biodiversity and vegetation community structure.\n\nHorizontal Transfer of Symbiosis Genes within and Between Rhizobial Genera: Occurrence and Importance.", "token_count": 343, "char_count": 1444, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5533, "quality_score": 0.7766, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:02.366584", "source": { "split": "train_shard_00000", "doc_id": 3331 }, "chunk_id": "train_shard_00000_3331_0", "global_id": 3687 }, { "text": "In recent years, an increasing number of Campylobacter species have been associated with human gastrointestinal (GI) diseases including gastroenteritis, inflammatory bowel disease, and colorectal cancer. Campylobacter concisus, an oral commensal historically linked to gingivitis and periodontitis, has been increasingly detected in the lower GI tract. In the present study, we generated robust genome sequence data from C. concisus strains and undertook a comprehensive pangenome assessment to identify C. concisus virulence properties and to explain potential adaptations acquired while residing in specific ecological niche(s) of the GI tract. Genomes of 53 new C. concisus strains were sequenced, assembled, and annotated including 36 strains from gastroenteritis patients, 13 strains from Crohn's disease patients and four strains from colitis patients (three collagenous colitis and one lymphocytic colitis). When compared with previous published sequences, strains clustered into two main groups/genomospecies (GS) with phylogenetic clustering explained neither by disease phenotype nor sample location. Paired oral/faecal isolates, from the same patient, indicated that there are few genetic differences between oral and gut isolates which suggests that gut isolates most likely reflect oral strain relocation. Type IV and VI secretion systems genes, genes known to be important for pathogenicity in the Campylobacter genus, were present in the genomes assemblies, with 82% containing Type VI secretion system genes. Our findings indicate that C. concisus strains are genetically diverse, and the variability in bacterial secretion system content may play an important role in their virulence potential.\n\nComparative genomics of Campylobacter concisus: Analysis of clinical strains reveals genome diversity and pathogenic potential.", "token_count": 430, "char_count": 1840, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:02.991645", "source": { "split": "train_shard_00000", "doc_id": 3332 }, "chunk_id": "train_shard_00000_3332_0", "global_id": 3688 }, { "text": "The coinage \"pan-genome\" was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species' basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile", "token_count": 103, "char_count": 459, "word_count": 67, "semantic_coherence": 1, "information_density": 0.806, "quality_score": 0.903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:03.381509", "source": { "split": "train_shard_00000", "doc_id": 3333 }, "chunk_id": "train_shard_00000_3333_0", "global_id": 3689 }, { "text": "Catechin exhibits antimicrobial activity against various microorganisms, such as EHEC O157:H7. This study reports the bactericidal effect of catechin on EHEC O157:H7 in simulated human gastrointestinal environment and the underlying antibacterial mechanism. Bacteriostasis test results showed that the minimum bactericidal concentration of catechin for EHEC O157:H7 was 5 g/L. The bactericidal effect of catechin in the gastrointestinal juice became more significant with increased culture time, and catechin exhibited a synergistic effect with bile salt in inhibiting EHEC O157:H7. Changes in the profile of protein expression in EHEC O157:H7 in response to catechin intervention were investigated. Two-dimensional electrophoresis identified 34 proteins with significantly altered expression. A total of 2 and 12 proteins were upregulated and downregulated, respectively. However, 20 proteins disappeared. No new protein was expressed compared with the control. Hence, catechin intervention resulted in diverse changes in the expression of proteins associated with cell structure and genetic information processing. Catechin could cause the disappearance of certain proteins or the destruction of certain peptides. These processes lead to the inhibition of EHEC O157: H7 cells.\n\nProteomic changes in EHEC O157:H7 under catechin intervention.", "token_count": 349, "char_count": 1342, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.8049, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:03.953583", "source": { "split": "train_shard_00000", "doc_id": 3334 }, "chunk_id": "train_shard_00000_3334_0", "global_id": 3690 }, { "text": "Progressive familial intrahepatic cholestasis 2 is an autosomal-recessive disorder caused by mutations in the ABCB11 gene, which encodes the bile salt export pump (BSEP). Recurrence of BSEP deficiency after liver transplantation is caused by the development of anti-BSEP antibodies. Antibody-induced BSEP deficiency is typically treated by increasing immunosuppressive therapy. We report, in a child, the first case of allogeneic haematopoietic stem cell transplantation for antibody-induced BSEP deficiency that was refractory to intensive pharmacological immunosuppression and immunoadsorption. After haematopoietic stem cell transplantation, anti-BSEP antibodies were cleared from the patient's serum and later from the canalicular space of the liver graft.\n\nAllogeneic haematopoietic stem cell transplantation eliminates alloreactive inhibitory antibodies after liver transplantation for bile salt export pump deficiency.", "token_count": 247, "char_count": 925, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6325, "quality_score": 0.8162, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:04.443073", "source": { "split": "train_shard_00000", "doc_id": 3335 }, "chunk_id": "train_shard_00000_3335_0", "global_id": 3691 }, { "text": "Human OATP1B1 is highly expressed at the basolateral membrane of the hepatocyte. It plays an important role in the sodium-independent transport of bile acids and bile salts and contributes to the systemic clearance of many drugs. In this study, the interaction of at least one representative of all major chemical classes of bile acids and bile salts, which include the bile acid chenodeoxycholate (CDC), monovalent (amidated) bile salts glycochenodeoxycholate (GCDC), taurochenodeoxycholate (TCDC) and taurocholate (TC), a sulfated bile acid 3-sulfo-chenodeoxycholate (3S-CDC) and a divalent (amidated and sulfated) bile salt 3-sulfo-glycolithocholate (3S-GLC) were tested with OATP1B1 overexpressed in HEK293 cells. All bile acid derivatives except for CDC showed an efficient transport by OATP1B1. 3S-GLC gave the lowest K\n\nHuman OATP1B1 (SLCO1B1) transports sulfated bile acids and bile salts with particular efficiency.", "token_count": 300, "char_count": 924, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [ "HEK293" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:04.999079", "source": { "split": "train_shard_00000", "doc_id": 3336 }, "chunk_id": "train_shard_00000_3336_0", "global_id": 3692 }, { "text": "Genetic diversity in plants is remarkably high. Recent whole genome sequencing (WGS) of 67 rice accessions recovered 10,872 novel genes. Comparison of the genetic architecture among divergent populations or between crops and wild relatives is essential for obtaining functional components determining crucial traits. However, many major crops have gigabase-scale genomes, which are not well-suited to WGS. Existing cost-effective sequencing approaches including re-sequencing, exome-sequencing and restriction enzyme-based methods all have difficulty in obtaining long novel genomic sequences from highly divergent population with large genome size. The present study presented a reference-independent core genome targeted sequencing approach, CGT-seq, which employed epigenomic information from both active and repressive epigenetic marks to guide the assembly of the core genome mainly composed of promoter and intragenic regions. This method was relatively easily implemented, and displayed high sensitivity and specificity for capturing the core genome of bread wheat. 95% intragenic and 89% promoter region from wheat were covered by CGT-seq read. We further demonstrated in rice that CGT-seq captured hundreds of novel genes and regulatory sequences from a previously unsequenced ecotype. Together, with specific enrichment and sequencing of regions within and nearby genes, CGT-seq is a time- and resource-effective approach to profiling functionally relevant regions in sequenced and non-sequenced populations with large genomes.\n\nCGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome.", "token_count": 355, "char_count": 1645, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:05.576172", "source": { "split": "train_shard_00000", "doc_id": 3337 }, "chunk_id": "train_shard_00000_3337_0", "global_id": 3693 }, { "text": "The concept of operational taxonomic units (OTUs), which constructs \"mathematically\" defined taxa, is widely accepted and applied to describe bacterial communities using amplicon sequencing of 16S rRNA gene. OTUs are often used to infer functional traits since they are considered to fairly represent of community members. However, the link between molecular taxa, real taxa, and OTUs seems to be much more complicated. Strains of the same bacterial species (ideally belonging to the same OTU) typically only share some genes (the core genome), while other genes are strain-specific and unique. It is thus unclear to what extent are important functional traits homogeneous within an OTU and how correctly can functional traits be inferred for individual OTU members. Here, we have tested in silico the similarity of all genes and, more specifically, the set of genes encoding for glycoside hydrolases (GH) in bacterial genomes that belong to the same OTU. Genome similarity varied among OTUs, but as many as 5-78% of genes were not shared between the two bacterial genomes in the pair. The complement of GH families (the presence of gene families and the number of genes per family) differed in 95% of OTUs. In average, 43% of GH families either differed in gene counts or were present in one genome and absent in the other. These results show a serious limitation of the OTU-based approaches when used to infer the functional traits of bacterial communities and open the questions how to link environmental sequencing data and microbial functions.\n\nThe concept of operational taxonomic units revisited: genomes of bacteria that are regarded as closely related are often highly dissimilar.", "token_count": 391, "char_count": 1689, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:06.194524", "source": { "split": "train_shard_00000", "doc_id": 3338 }, "chunk_id": "train_shard_00000_3338_0", "global_id": 3694 }, { "text": "With the rapid development of high-throughput sequencing technology, the analysis of metagenomic sequencing data and the accurate and efficient estimation of relative microbial abundance have become important ways to explore the microbial composition and function of microbes. In addition, the accuracy and efficiency of the relative microbial abundance estimation are closely related to the algorithm and the selection of the reference sequence for sequence alignment. We introduced the microbial core genome as the reference sequence for potential microbes in a metagenomic sample, and we constructed a finite mixture and latent Dirichlet models and used the Gibbs sampling algorithm to estimate the relative abundance of microorganisms. The simulation results showed that our approach can improve the efficiency while maintaining high accuracy and is more suitable for high-throughput metagenomic data. The new approach was implemented in our CoreProbe package which provides a pipeline for an accurate and efficient estimation of the relative abundance of microbes in a community. This tool is available free of charge from the CoreProbe's website: Access the Docker image with the following instruction: sudo docker pull panhongfei/coreprobe:1.0.\n\nCoreProbe: A Novel Algorithm for Estimating Relative Abundance Based on Metagenomic Reads.", "token_count": 270, "char_count": 1343, "word_count": 191, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:06.744926", "source": { "split": "train_shard_00000", "doc_id": 3339 }, "chunk_id": "train_shard_00000_3339_0", "global_id": 3695 }, { "text": "The use of whole-genome sequencing (WGS) using next-generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through single-nucleotide polymorphism (SNP) calling from a reference sequence analysis for\n\nCore Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections.", "token_count": 128, "char_count": 538, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7536, "quality_score": 0.8768, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:07.167639", "source": { "split": "train_shard_00000", "doc_id": 3340 }, "chunk_id": "train_shard_00000_3340_0", "global_id": 3696 }, { "text": "The hepatic Na+/taurocholate co-transporting polypeptide (NTCP in man, Ntcp in animals) is the high-affinity receptor for the hepatitis B (HBV) and hepatitis D (HDV) viruses. Species barriers for human HBV/HDV within the order Primates were previously attributed to Ntcp sequence variations that disable virus-receptor interaction. However, only a limited number of primate Ntcps have been analysed so far. In the present study, a total of 11 Ntcps from apes, Old and New World monkeys were cloned and expressed in vitro to characterise their interaction with HBV and HDV. All Ntcps showed intact bile salt transport. Human NTCP as well as the Ntcps from the great apes chimpanzee and orangutan showed transport-competing binding of HBV derived myr-preS1-peptides. In contrast, all six Ntcps from the group of Old World monkeys were insensitive to HBV myr-preS1-peptide binding and HBV/HDV infection. This is basically predetermined by the amino acid arginine at position 158 of all studied Old World monkey Ntcps. An exchange from arginine to glycine (as present in humans and great apes) at this position (R158G) alone was sufficient to achieve full transport-competing HBV myr-preS1-peptide binding and susceptibility for HBV/HDV infection. New World monkey Ntcps showed higher sequence heterogeneity, but in two cases with 158G showed transport-competing HBV myr-preS1-peptide binding, and in one case (Saimiri sciureus) even susceptibility for HBV/HDV infection. In conclusion, amino acid position 158 of NTCP/Ntcp is sufficient to discriminate between the HBV/HDV susceptible group of humans and great apes (158G) and the non-susceptible group of Old World monkeys (158R)", "token_count": 490, "char_count": 1677, "word_count": 250, "semantic_coherence": 1, "information_density": 0.552, "quality_score": 0.776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:07.838860", "source": { "split": "train_shard_00000", "doc_id": 3341 }, "chunk_id": "train_shard_00000_3341_0", "global_id": 3697 }, { "text": "In the case of the phylogenetically more distant New World monkey Ntcps amino acid 158 plays a significant, but not exclusive role.\n\nCharacterisation of the hepatitis B virus cross-species transmission pattern via Na+/taurocholate co-transporting polypeptides from 11 New World and Old World primate species.", "token_count": 82, "char_count": 308, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:08.226227", "source": { "split": "train_shard_00000", "doc_id": 3341 }, "chunk_id": "train_shard_00000_3341_1", "global_id": 3698 }, { "text": "From 2016 through the middle of 2017, the German Consiliary Laboratory on Diphtheria noted an increase in nontoxigenic Corynebacterium diphtheriae isolates submitted from cities in northern Germany. Many patients for whom epidemiologic data were available were homeless, alcohol or drug abusers, or both. After performing routine diagnostics and multilocus sequence typing (MLST), we analyzed isolates of sequence type (ST) 8 and previously submitted isolates by whole-genome sequencing. Results were analyzed for phylogenetic relationship by core genome MLST (cg-MLST) and whole-genome single-nucleotide polymorphism profiles. Next-generation sequencing-based cg-MLST revealed several outbreak clusters caused by ST8; the geographic focus was in the metropolitan areas of Hamburg and Berlin. To achieve enhanced analytical depth, we used additional cg-MLST target genes and genome-wide single-nucleotide polymorphisms. We identified patient characteristics and detected transmission events, providing evidence that nontoxigenic C. diphtheriae infection is a potential public health threat in industrialized countries.\n\nGeographically Diverse Clusters of Nontoxigenic Corynebacterium diphtheriae Infection, Germany, 2016-2017.", "token_count": 308, "char_count": 1226, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7597, "quality_score": 0.8799, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:08.825202", "source": { "split": "train_shard_00000", "doc_id": 3342 }, "chunk_id": "train_shard_00000_3342_0", "global_id": 3699 }, { "text": "Metabolomics is used to evaluate the bioavailability of food components, as well as to validate the metabolic changes associated with food consumption. This study was conducted to investigate the effects of the dietary supplement Kluyveromyces marxianus on the serum metabolite profile in broiler chickens. A total of 240 1-d-old broilers were divided into 2 groups with 8 replicates. Birds were fed basal diets without or with K. marxianus supplementation (5 × 1010 CFU kg-1 of diet). Serum samples were collected on d 21 and were analyzed by high-performance liquid chromatography with quadrupole time-of flight/mass spectrometry. The results showed that supplemental K. marxianus altered the concentrations of a variety of metabolites in the serum. Thereinto, a total of 39 metabolites were identified at higher (P < 0.05) concentrations while 21 metabolites were identified at lower (P < 0.05) concentrations in the treatment group as compared with the control. These metabolites were primarily involved with the regulation of amino acids and carbohydrate metabolism. Further metabolic pathway analysis revealed that glutamine and glutamate metabolism was the most relevant and critical pathway identified from these two groups. The activated pathway may partially interpret the beneficial effects of K. marxianus. Overall, the present research could promote our understanding of the probiotic action of K. marxianus and provide new insight into the design and application of K. marxianus-containing functional foods.\n\nDietary supplemental Kluyveromyces marxianus alters the serum metabolite profile in broiler chickens.", "token_count": 405, "char_count": 1624, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:10.088841", "source": { "split": "train_shard_00000", "doc_id": 3343 }, "chunk_id": "train_shard_00000_3343_0", "global_id": 3700 }, { "text": "The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as \"non-orthologous gene displacement\" that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of\n\nVariability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of", "token_count": 301, "char_count": 1466, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5575, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:10.653423", "source": { "split": "train_shard_00000", "doc_id": 3344 }, "chunk_id": "train_shard_00000_3344_0", "global_id": 3701 }, { "text": "The small subunit ribosomal RNA gene (16S rRNA) has been successfully used to catalogue and study the diversity of prokaryotic species and communities but it offers limited resolution at the species and finer levels, and cannot represent the whole-genome diversity and fluidity. To overcome these limitations, we introduced the Microbial Genomes Atlas (MiGA), a webserver that allows the classification of an unknown query genomic sequence, complete or partial, against all taxonomically classified taxa with available genome sequences, as well as comparisons to other related genomes including uncultivated ones, based on the genome-aggregate Average Nucleotide and Amino Acid Identity (ANI/AAI) concepts. MiGA integrates best practices in sequence quality trimming and assembly and allows input to be raw reads or assemblies from isolate genomes, single-cell sequences, and metagenome-assembled genomes (MAGs). Further, MiGA can take as input hundreds of closely related genomes of the same or closely related species (a so-called 'Clade Project') to assess their gene content diversity and evolutionary relationships, and calculate important clade properties such as the pangenome and core gene sets. Therefore, MiGA is expected to facilitate a range of genome-based taxonomic and diversity studies, and quality assessment across environmental and clinical settings. MiGA is available at http://microbial-genomes.org/.\n\nThe Microbial Genomes Atlas (MiGA) webserver: taxonomic and gene diversity analysis of Archaea and Bacteria at the whole genome level.", "token_count": 360, "char_count": 1557, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:11.234330", "source": { "split": "train_shard_00000", "doc_id": 3345 }, "chunk_id": "train_shard_00000_3345_0", "global_id": 3702 }, { "text": "In the present study, we conducted an RNA-Seq analysis to characterize the genes and pathways involved in acute thermal and cold stress responses in the liver of black rockfish, a viviparous teleost that has the ability to cope with a wide range of temperature changes. A total of 584 annotated differentially expressed genes (DEGs) were identified in all three comparisons (HT vs NT, HT vs LT and LT vs NT). Based on an enrichment analysis, DEGs with a potential role in stress accommodation were classified into several categories, including protein folding, metabolism, immune response, signal transduction, molecule transport, membrane, and cell proliferation/apoptosis. Considering that thermal stress has a greater effect than cold stress in black rockfish, 24 shared DEGs in the intersection of the HT vs LT and HT vs NT groups were enriched in 2 oxidation-related gene ontology (GO) terms. Nine important heat-stress-reducing pathways were significantly identified and classified into 3 classes: immune and infectious diseases, organismal immune system and endocrine system. Eight DEGs (early growth response protein 1, bile salt export pump, abcb11, hsp70a, rtp3, 1,25-dihydroxyvitamin d(3) 24-hydroxylase, apoa4, transcription factor jun-b-like and an uncharacterized gene) were observed among all three comparisons, strongly implying their potentially important roles in temperature stress responses.\n\nDeep Transcriptomic Analysis of Black Rockfish (Sebastes schlegelii) Provides New Insights on Responses to Acute Temperature Stress.", "token_count": 394, "char_count": 1545, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:11.857713", "source": { "split": "train_shard_00000", "doc_id": 3346 }, "chunk_id": "train_shard_00000_3346_0", "global_id": 3703 }, { "text": "Intestinal permeability assessment is an important aspect of drug development, which strongly depends on the solvent system used in the intestinal donor compartment. For this purpose, human intestinal fluids (HIF) can be considered as the golden standard. A recent study demonstrated a reduced apparent permeation across rat intestinal tissue from fed versus fasted state HIF for 9 out of 16 compounds tested. Commercially available fed and fasted state simulated fluids (FeSSIF and FaSSIF) reproduced this food effect for only 3 out of 16 compounds. To elucidate this observed difference, the current study assessed the impact of relevant intestinal fluid factors (bile salt, phospholipids, cholesterol, free fatty acids (FFA), monoacylglycerides (MAG)) and 2-factor interactions at a fixed pH of 6.5 on drug permeation across both rat tissue (Ussing chambers setup) and an artificial membrane (dialysis setup). Four representative compounds were selected for the permeation experiments: for propranolol and indomethacin, a food-induced permeation reduction was previously seen in both HIF and SIF; for metoprolol and darunavir, a reduction was only seen in HIF. Using a fractional 2\n\nHuman intestinal fluid factors affecting intestinal drug permeation in vitro.", "token_count": 327, "char_count": 1263, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:12.424689", "source": { "split": "train_shard_00000", "doc_id": 3347 }, "chunk_id": "train_shard_00000_3347_0", "global_id": 3704 }, { "text": "Pseudomonas aeruginosa is an important opportunistic pathogen, especially in the context of infections of cystic fibrosis (CF). In order to facilitate coordinated study of this pathogen, an international reference panel of P. aeruginosa isolates was assembled. Here we report the genome sequencing and analysis of 33 of these isolates and 7 reference genomes to further characterise this panel. Core genome single nucleotide variant phylogeny demonstrated that the panel strains are widely distributed amongst the P. aeruginosa population. Common loss-of-function mutations reported as adaptive during CF (such as in mucA and mexA) were identified amongst isolates from chronic respiratory infections. From the 40 strains analysed, 37 unique resistomes were predicted, based on the Resistance Gene Identifier method using the Comprehensive Antibiotic Resistance Database. Notably, hierarchical clustering and phylogenetic reconstructions based on the presence/absence of genomic islands (GIs), prophages and other regions of genome plasticity (RGPs) supported the subdivision of P. aeruginosa into two main groups. This is the largest, most diverse analysis of GIs and associated RGPs to date, and the results suggest that, at least at the largest clade grouping level (group 1 vs group 2), each group may be drawing upon distinct mobile gene pools.\n\nGenomic characterisation of an international Pseudomonas aeruginosa reference panel indicates that the two major groups draw upon distinct mobile gene pools.", "token_count": 355, "char_count": 1508, "word_count": 217, "semantic_coherence": 1, "information_density": 0.659, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:13.000633", "source": { "split": "train_shard_00000", "doc_id": 3348 }, "chunk_id": "train_shard_00000_3348_0", "global_id": 3705 }, { "text": "A quantitative assay using high-performance thin-layer chromatography (HPTLC) was developed to investigate bile salt hydrolase (BSH) activity in Pediococcus pentosaceus LAB6 and Lactobacillus plantarum LAB12 probiotic bacteria isolated from Malaysian fermented food. Lactic acid bacteria (LAB) were cultured in de Man Rogosa and Sharpe (MRS) broth containing 1 mmol/L of sodium-based glyco- and tauro-conjugated bile salts for 24 h. The cultures were centrifuged and the resultant cell free supernatant was subjected to chromatographic separation on a HPTLC plate. Conjugated bile salts were quantified by densitometric scans at 550 nm and results were compared to digital image analysis of chromatographic plates after derivatisation with anisaldehyde/sulfuric acid. Standard curves for bile salts determination with both methods show good linearity with high coefficient of determination (R\n\nA new high-performance thin-layer chromatographic method for determining bile salt hydrolase activity.", "token_count": 275, "char_count": 996, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7481, "quality_score": 0.8741, "entities": { "genes": [ "LAB6", "LAB12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:13.547736", "source": { "split": "train_shard_00000", "doc_id": 3349 }, "chunk_id": "train_shard_00000_3349_0", "global_id": 3706 }, { "text": "Shiga toxin-producing E. coli (STEC) O80:H2 is an uncommon hybrid pathotype that has recently emerged in France. We analysed 18 STEC O80:H2 isolated from humans in Switzerland during 2010-2017. All isolates carried stx2a or stx2d, the rare eae variant eae-ξ and at least seven virulence genes associated with pS88, a plasmid that is found in extraintestinal pathogenic E. coli (ExPEC). Whole genome sequencing (WGS) identified additional chromosomal extraintestinal virulence genes encoding for type 1 fimbria (fimA, fimC and fimH), aerobactin (iuc/iutA) and afimbrial adhesins (afaA/C/D/E-VIII). Core genome multi-locus sequence typing (cgMLST) detected two closely related but distinct subclusters with different stx2 and iuc/iutA genotypes. All isolates were multidrug resistant (MDR), but susceptible to third generation cephalosporins and azithromycin. STEC/ExPEC hybrid pathotypes such as STEC O80:H2 represent a therapeutical challenge in the event of extraintestinal infection.\n\nGenetic characterization of Shiga toxin producing Escherichia coli belonging to the emerging hybrid pathotype O80:H2 isolated from humans 2010-2017 in Switzerland.", "token_count": 363, "char_count": 1150, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7564, "quality_score": 0.8782, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:14.120889", "source": { "split": "train_shard_00000", "doc_id": 3350 }, "chunk_id": "train_shard_00000_3350_0", "global_id": 3707 }, { "text": "Members of the Omp85 protein superfamily have important roles in Gram-negative bacteria, with the archetypal protein BamA being ubiquitous given its essential function in the assembly of outer membrane proteins. In some bacterial lineages, additional members of the family exist and, in most of these cases, the function of the protein is unknown. We detected one of these Omp85 proteins in the pathogen Klebsiella pneumoniae B5055, and refer to the protein as BamK. Here, we show that bamK is a conserved element in the core genome of Klebsiella, and its expression rescues a loss-of-function ∆bamA mutant. We developed an E. coli model system to measure and compare the specific activity of BamA and BamK in the assembly reaction for the critical substrate LptD, and find that BamK is as efficient as BamA in assembling the native LptDE complex. Comparative structural analysis revealed that the major distinction between BamK and BamA is in the external facing surface of the protein, and we discuss how such changes may contribute to a mechanism for resistance against infection by bacteriophage.\n\nAn investigation into the Omp85 protein BamK in hypervirulent Klebsiella pneumoniae, and its role in outer membrane biogenesis.", "token_count": 306, "char_count": 1229, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5928, "quality_score": 0.7964, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:15.036373", "source": { "split": "train_shard_00000", "doc_id": 3351 }, "chunk_id": "train_shard_00000_3351_0", "global_id": 3708 }, { "text": "Calcium plays an important dual role in lipid digestion: promoting removal of long-chain fatty acids from the oil-water interface by forming insoluble calcium soaps while also limiting their bioaccessibility. This becomes more significant in food containing high calcium concentration, such as dairy products. Nevertheless, scarce attention has been paid to the effect of calcium on the interfacial properties during lipid digestion, despite this being largely an interfacial reaction. This study focused on the dynamics of the formation of calcium soaps at the oil-water interface during lipolysis by pancreatic lipase in the absence and presence of the two primary human bile salts (sodium glycocholate or sodium glycochenodeoxycholate). The competitive adsorption of lipase, bile salts, and lipolysis products, as well as the formation of calcium soaps in the presence of increasing concentrations of calcium were mainly characterized by recording the interfacial tension and dilatational modulus in situ. In the absence of bile salts, calcium complexes with fatty acids at the oil-water interface forming a relatively strong viscoelastic network of calcium soaps over time. The dilatational modulus of the calcium soap network is directly related to the interfacial concentration of lipolysis products and the calcium bulk concentration. Calcium soaps are also visualized forming a continuous rough layer on the surface of oil droplets immersed in simulated intestinal aqueous phase. Despite bile salts having different surface activity, they play a similar role on the interfacial competition with lipase and lipolysis products although altering their kinetics. The presence of bile salts disrupts the network of calcium soaps, as suggested by the decrease in the dilatational modulus and the formation of calcium soap islands on the surface of the oil droplets. The accelerant effect of calcium on lipolysis is probably because of fatty acid complexation and subsequent removal from the interface rather than reduced electrostatic repulsion between lipase and bile salt molecules and promoted lipase adsorption. The work shown here has implications for the delivery of oil-soluble bioactives in the presence of calcium.", "token_count": 497, "char_count": 2225, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5046, "quality_score": 0.7523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:15.685989", "source": { "split": "train_shard_00000", "doc_id": 3352 }, "chunk_id": "train_shard_00000_3352_0", "global_id": 3709 }, { "text": "Calcium Alters the Interfacial Organization of Hydrolyzed Lipids during Intestinal Digestion.", "token_count": 25, "char_count": 93, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:16.041294", "source": { "split": "train_shard_00000", "doc_id": 3352 }, "chunk_id": "train_shard_00000_3352_1", "global_id": 3710 }, { "text": "The effects of probiotics on host gastrointestinal health have become an area of particular interest in the field of probiotic research. However, the impact of the host intestinal environment on genomic changes in probiotic organisms remains largely unknown. To investigate,\n\nGenomic Variations in Probiotic", "token_count": 68, "char_count": 307, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:16.409163", "source": { "split": "train_shard_00000", "doc_id": 3353 }, "chunk_id": "train_shard_00000_3353_0", "global_id": 3711 }, { "text": "Talaromyces thermophilus lipase (TTL) was found to hydrolyze monogalactosyl diacylglycerol (MGDG) and digalactosyl diacylglycerol (DGDG) substrates presented in various forms to the enzyme. Different assay techniques were used for each substrate: pHstat with dioctanoyl galactolipid-bile salt mixed micelles, barostat with dilauroyl galactolipid monomolecular films spread at the air-water interface, and UV absorption using a novel MGDG substrate containing α-eleostearic acid as chromophore and coated on microtiter plates. The kinetic properties of TTL were compared to those of the homologous lipase from Thermomyces lanuginosus (TLL), guinea pig pancreatic lipase-related protein 2 and Fusarium solani cutinase. TTL was found to be the most active galactolipase, with a higher activity on micelles than on monomolecular films or surface-coated MGDG. Nevertheless, the UV absorption assay with coated MGDG was highly sensitive and allowed measuring significant activities with about 10 ng of enzymes, against 100 ng to 10 μg with the pHstat. TTL showed longer lag times than TLL for reaching steady state kinetics of hydrolysis with monomolecular films or surface-coated MGDG. These findings and 3D-modelling of TTL based on the known structure of TLL pointed out to two phenylalanine to leucine substitutions in TTL, that could be responsible for its slower adsorption at lipid-water interface. TTL was found to be more active on MGDG than on DGDG using both galactolipid-bile salt mixed micelles and galactolipid monomolecular films. These later experiments suggest that the second galactose on galactolipid polar head impairs the enzyme adsorption on its aggregated substrate.", "token_count": 480, "char_count": 1683, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:17.054170", "source": { "split": "train_shard_00000", "doc_id": 3354 }, "chunk_id": "train_shard_00000_3354_0", "global_id": 3712 }, { "text": "Galactolipase activity of Talaromyces thermophilus lipase on galactolipid micelles, monomolecular films and UV-absorbing surface-coated substrate.", "token_count": 44, "char_count": 146, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:17.413429", "source": { "split": "train_shard_00000", "doc_id": 3354 }, "chunk_id": "train_shard_00000_3354_1", "global_id": 3713 }, { "text": "Lactobacillus curvatus is a lactic acid bacterium encountered in many different types of fermented food (meat, seafood, vegetables, and cereals). Although this species plays an important role in the preservation of these foods, few attempts have been made to assess its genomic diversity. This study uses comparative analyses of 13 published genomes (complete or draft) to better understand the evolutionary processes acting on the genome of this species. Phylogenomic analysis, based on a coalescent model of evolution, revealed that the 6,742 sites of single nucleotide polymorphism within the L. curvatus core genome delineate two major groups, with lineage 1 represented by the newly sequenced strain FLEC03, and lineage 2 represented by the type-strain DSM20019. The two lineages could also be distinguished by the content of their accessory genome, which sheds light on a long-term evolutionary process of lineage-dependent genetic acquisition and the possibility of population structure. Interestingly, one clade from lineage 2 shared more accessory genes with strains of lineage 1 than with other strains of lineage 2, indicating recent convergence in carbohydrate catabolism. Both lineages had a wide repertoire of accessory genes involved in the fermentation of plant-derived carbohydrates that are released from polymers of α/β-glucans, α/β-fructans, and N-acetylglucosan. Other gene clusters were distributed among strains according to the type of food from which the strains were isolated. These results give new insight into the ecological niches in which L. curvatus may naturally thrive (such as silage or compost heaps) in addition to fermented food.\n\nPhylogenomic Analysis of Lactobacillus curvatus Reveals Two Lineages Distinguished by Genes for Fermenting Plant-Derived Carbohydrates.", "token_count": 454, "char_count": 1804, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [ "DSM20019", "FLEC03" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:18.049859", "source": { "split": "train_shard_00000", "doc_id": 3355 }, "chunk_id": "train_shard_00000_3355_0", "global_id": 3714 }, { "text": "Clinically severe infection-related inflammation after major liver resection may cause hyperbilirubinemia. This study aims to clarify the impact of bacterial infection and endotoxins on the hepatobiliary transporter system and to explore possible mechanisms of endotoxin-related postoperative hyperbilirubinemia.\n\nDe Novo Endotoxin-Induced Production of Antibodies against the Bile Salt Export Pump Associated with Bacterial Infection following Major Hepatectomy.", "token_count": 116, "char_count": 463, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8214, "quality_score": 0.9107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:18.433571", "source": { "split": "train_shard_00000", "doc_id": 3356 }, "chunk_id": "train_shard_00000_3356_0", "global_id": 3715 }, { "text": "Lactic acid bacteria isolated from indigenous milk of different animals were investigated for their efficacy, safety, and probiotic potential. The most potential isolate MMP4 was screened from mare's milk, which was further identified as Lactobacillus pentosus by using 16S rRNA gene sequencing and phylogeny. The probiotic potential of strain MMP4 was assessed by its ability to survive under acidic environment and in presence of bile salts along with the ability to inhibit food-borne as well as clinical pathogenic microorganisms such as Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, and Salmonella typhi. The phenol tolerance with cogent hydrophobicity to different hydrocarbons was demonstrated. Bile salt hydrolase activity of L. pentosus MMP4 was confirmed by detecting the Bsh gene by using colony PCR. The presence of Mub, Map, and EF-Tu genes involved in adhesion conferred the behavior of passage and adherence to gastrointestinal tract. Scanning electron microscopy of intestinal autopsy from albino mice revealed the attachment of bacterial cells on the mucus-lined intestinal walls against pathogens and further proved in vivo adhesion ability. The presence of intrinsic antibiotic resistance and lack of DNase, gelatinase, and hemolytic activity in MMP4 support its safety as probiotic traits. Thus, MMP4 bears an excellent and pragmatic properties for being used as probiotic and may be exploited in dairy industry.\n\nEvaluation of Probiotic Potential and Safety Assessment of Lactobacillus pentosus MMP4 Isolated From Mare's Lactation.", "token_count": 413, "char_count": 1570, "word_count": 227, "semantic_coherence": 1, "information_density": 0.63, "quality_score": 0.815, "entities": { "genes": [ "MMP4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:19.059504", "source": { "split": "train_shard_00000", "doc_id": 3357 }, "chunk_id": "train_shard_00000_3357_0", "global_id": 3716 }, { "text": "The potential for genome-wide modelling of epistasis has recently surfaced given the possibility of sequencing densely sampled populations and the emerging families of statistical interaction models. Direct coupling analysis (DCA) has previously been shown to yield valuable predictions for single protein structures, and has recently been extended to genome-wide analysis of bacteria, identifying novel interactions in the co-evolution between resistance, virulence and core genome elements. However, earlier computational DCA methods have not been scalable to enable model fitting simultaneously to 10\n\nSuperDCA for genome-wide epistasis analysis.", "token_count": 129, "char_count": 649, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:19.520089", "source": { "split": "train_shard_00000", "doc_id": 3358 }, "chunk_id": "train_shard_00000_3358_0", "global_id": 3717 }, { "text": "Pasteurella multocida is a gram-negative, non-motile bacterial pathogen, which is associated with chronic and acute infections as snuffles, pneumonia, atrophic rhinitis, fowl cholera and hemorrhagic septicemia. These diseases affect a wide range of domestic animals, leading to significant morbidity and mortality and causing significant economic losses worldwide. Due to the interest in deciphering the genetic diversity and process adaptive between P. multocida strains, this work aimed was to perform a pan-genome analysis to evidence horizontal gene transfer and positive selection among 23 P. multocida strains isolated from distinct diseases and hosts. The results revealed an open pan-genome containing 3585 genes and an accessory genome presenting 1200 genes. The phylogenomic analysis based on the presence/absence of genes and islands exhibit high levels of plasticity, which reflects a high intraspecific diversity and a possible adaptive mechanism responsible for the specific disease manifestation between the established groups (pneumonia, fowl cholera, hemorrhagic septicemia and snuffles). Additionally, we identified differences in accessory genes among groups, which are involved in sugar metabolism and transport systems, virulence-related genes and a high concentration of hypothetical proteins. However, there was no specific indispensable functional mechanism to decisively correlate the presence of genes and their adaptation to a specific host/disease. Also, positive selection was found only for two genes from sub-group hemorrhagic septicemia, serotype B. This comprehensive comparative genome analysis will provide new insights of horizontal gene transfers that play an essential role in the diversification and adaptation mechanism into P. multocida species to a specific disease.\n\nPan-genomic approach shows insight of genetic divergence and pathogenic-adaptation of Pasteurella multocida.", "token_count": 434, "char_count": 1918, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:20.175485", "source": { "split": "train_shard_00000", "doc_id": 3359 }, "chunk_id": "train_shard_00000_3359_0", "global_id": 3718 }, { "text": "In Brazil, bioethanol is produced by sucrose fermentation from sugarcane by Saccharomyces cerevisiae in a fed-batch process that uses high density of yeast cells (15-25 % of wet weight/v) and high sugar concentration (18-22 % of total sugars). Several research efforts have been employed to improve the efficiency of this process through the isolation of yeasts better adapted to the Brazilian fermentation conditions. Two important wild strains named CAT-1 and PE-2 were isolated during the fermentation process and were responsible for almost 60 % of the total ethanol production in Brazil. However, in the last decade the fermentative substrate composition was much modified, since new sugar cane crops were developed, the use of molasses instead of sugar cane juice increase and with the prohibition of burning of sugarcane prior harvest. As consequence, these previously isolated strains are being replaced by new wild yeasts in most of ethanol plants. In this new scenario the isolation of novel better adapted yeasts with improved fermentative characteristics is still a big challenge. Here, we discuss the main aspects of Brazilian ethanol production and the efforts for the selection, characterization and genetic modifications of new strains with important phenotypic traits such as thermotolerance.\n\nImprovement of Brazilian bioethanol production - Challenges and perspectives on the identification and genetic modification of new strains of Saccharomyces cerevisiae yeasts isolated during ethanol process.", "token_count": 335, "char_count": 1517, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:20.766428", "source": { "split": "train_shard_00000", "doc_id": 3360 }, "chunk_id": "train_shard_00000_3360_0", "global_id": 3719 }, { "text": "The mammary gland and maternal milk are the product of millions of years of evolution that resul ted in an optimal composition that sustains the growth and development of newborns and infants. Maternal milk supports the growth, adaptation and survival of this immature organism. Recent studies have detected 1606 different proteins in human milk, most of them synthesized in the acini of the glandular tissue while others originate from distant organs such as the lymphoid tissue and the digestive tract. Maternal milk enzymes modify its proteins and liberate peptides with antimicrobial, antihypertensive or stimulatory activities. This proteolytic activity occurs at specific sites in peptide chains. To prevent the extemporaneous activation of these proteolytic enzymes, that would result in inflammatory processes, maternal milk also contains inhibitory peptides that together with the stimulatory peptides conform a complex regulatory system. Some enzymes in maternal milk main tain their activity in the gastrointestinal tract of infants and compensate for the decreased activity of digestive tract enzymes in newborns. Thus, the milk enterokynase stimulates the release of pancreatic proteases as it induces the liberation of cholecystokynin/pancreozymin. The bile salt-activated lipase of human milk is activated in the duodenum by the infants' bile salts and partially compensates for the low levels of pancreatic lipase in newborns. These milk enzymes probably contribute to the nutrition of premature infants as they increase the availability of amino acids and peptides in their upper gastrointestinal tract; furthermore, as their intestinal epithelium is more permeable to peptides and partially digested protein this may help induce immune tolerance. The most relevant issues in the physiology and composition of the maternal milk are presented in this review.\n\n[Advances in the knowledge about human milk proteins].", "token_count": 463, "char_count": 1930, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5709, "quality_score": 0.7855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:21.434281", "source": { "split": "train_shard_00000", "doc_id": 3361 }, "chunk_id": "train_shard_00000_3361_0", "global_id": 3720 }, { "text": "Prokaryotes benefit from having accessory genes, but it is unclear how accessory genes can be linked with the core regulatory network when developing adaptations to new niches. Here we determined hierarchical core/accessory subsets in the multipartite pangenome (composed of genes from the chromosome, chromid and plasmids) of the soybean microsymbiont Sinorhizobium fredii by comparing twelve Sinorhizobium genomes. Transcriptomes of two S. fredii strains at mid-log and stationary growth phases and in symbiotic conditions were obtained. The average level of gene expression, variation of expression between different conditions, and gene connectivity within the co-expression network were positively correlated with the gene conservation level from strain-specific accessory genes to genus core. Condition-dependent transcriptomes exhibited adaptive transcriptional changes in pangenome subsets shared by the two strains, while strain-dependent transcriptomes were enriched with accessory genes on the chromid. Proportionally more chromid genes than plasmid genes were co-expressed with chromosomal genes, while plasmid genes had a higher within-replicon connectivity in expression than chromid ones. However, key nitrogen fixation genes on the symbiosis plasmid were characterized by high connectivity in both within- and between-replicon analyses. Among those genes with host-specific upregulation patterns, chromosomal znu and mdt operons, encoding a conserved high-affinity zinc transporter and an accessory multi-drug efflux system, respectively, were experimentally demonstrated to be involved in host-specific symbiotic adaptation. These findings highlight the importance of integrative regulation of hierarchical core/accessory components in the multipartite genome of bacteria during niche adaptation and in shaping the prokaryotic pangenome in the long run.\n\nCoordinated regulation of core and accessory genes in the multipartite genome of Sinorhizobium fredii.", "token_count": 456, "char_count": 1974, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5946, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:22.072698", "source": { "split": "train_shard_00000", "doc_id": 3362 }, "chunk_id": "train_shard_00000_3362_0", "global_id": 3721 }, { "text": "The commensal genus Bifidobacterium has probiotic properties. We prepared a public library of the gene functions of the genus Bifidobacterium for its online annotation. Orthologous gene cluster analysis showed that the pan genomes of Bifidobacterium and Lactobacillus exhibit striking similarities when mapped to the Clusters of Orthologous Group (COG) database of proteins. When the core genes in each genus were selected based on our statistical definition of \"core genome\", core genes were present in at least 92% of 52 Bifidobacterium and in 97% of 178 Lactobacillus genomes. Functional comparison of the core genes of the two genera revealed a significant difference in the categories \"amino acid transport and metabolism\" representing their difference in niche specificity. Over-represented Bifidobacterium protein families were primarily involved in host interactions, the complex compound metabolism, and in stress responses. These findings coincide with the published information and validate our bias-resilient definition of the core genome.\n\nComparative analysis of probiotic bacteria based on a new definition of core genome.", "token_count": 265, "char_count": 1137, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8086, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:22.620530", "source": { "split": "train_shard_00000", "doc_id": 3363 }, "chunk_id": "train_shard_00000_3363_0", "global_id": 3722 }, { "text": "Sciaenops ocellatus has a long history in aquaculture and many difficulties associated with its commercial culture have been addressed and successfully resolved; nevertheless, further research in lipid nutrition could address more comprehensive questions on the way these nutrients are utilized. The purpose of this study was to evaluate S. ocellatus growth and lipase gene expression in response to increasing dietary lipid supplementation. Four experimental diets were formulated to provide 3, 10, 16, or 23% lipid using menhaden fish oil. Twenty juveniles (mean initial weight 2.3 ± 0.1 g) were stocked per aquaria in a recirculating system; each diet was assigned to three aquaria and fed to fish for 6 weeks. At the end of the study, fish fed 3% of dietary lipid were significantly (P < 0.0001) smaller and showed significantly lower feed efficiency, condition factor, hepatosomatic index, and intraperitoneal fat than fish fed the other diets, but no differences were observed among fish fed 10, 16, or 23% lipid. A straight broken-line regression model for thermal growth coefficient provided an estimated value of 9.4% of dietary lipid as the optimal inclusion level. The bile salt-dependent lipase (BSDL) of red drum was 80.3 kDa. Relative gene expression of BSDL was significantly higher (P = 0.0007) in fish fed 10% lipid, with no differences among the other dietary treatments. Results provided could help monitor the metabolic status of farmed fish and contribute to optimize diet formulations based on maximum gene expression of BSDL for supplementation of dietary lipid.\n\nRed drum Sciaenops ocellatus growth and expression of bile salt-dependent lipase in response to increasing dietary lipid supplementation.", "token_count": 444, "char_count": 1724, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:23.262041", "source": { "split": "train_shard_00000", "doc_id": 3364 }, "chunk_id": "train_shard_00000_3364_0", "global_id": 3723 }, { "text": "Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome.\n\nWhole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.", "token_count": 290, "char_count": 1363, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:23.824690", "source": { "split": "train_shard_00000", "doc_id": 3365 }, "chunk_id": "train_shard_00000_3365_0", "global_id": 3724 }, { "text": "Biofilm formation is a dynamic, multistage process that occurs in bacteria under harsh environmental conditions or times of stress. For enteric pathogens, a significant stress response is induced during gastrointestinal transit and upon bile exposure, a normal component of human digestion. To overcome the bactericidal effects of bile, many enteric pathogens form a biofilm hypothesized to permit survival when transiting through the small intestine. Here we present methodologies to define biofilm formation through solid-phase adherence assays as well as extracellular polymeric substance (EPS) matrix detection and visualization. Furthermore, biofilm dispersion assessment is presented to mimic the analysis of events triggering release of bacteria during the infection process. Crystal violet staining is used to detect adherent bacteria in a high-throughput 96-well plate adherence assay. EPS production assessment is determined by two assays, namely microscopy staining of the EPS matrix and semi-quantitative analysis with a fluorescently-conjugated polysaccharide binding lectin. Finally, biofilm dispersion is measured through colony counts and plating. Positive data from multiple assays support the characterization of biofilms and can be utilized to identify bile salt-induced biofilm formation in other bacterial strains.\n\nBile Salt-induced Biofilm Formation in Enteric Pathogens: Techniques for Identification and Quantification.", "token_count": 319, "char_count": 1444, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6736, "quality_score": 0.8368, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:24.390959", "source": { "split": "train_shard_00000", "doc_id": 3366 }, "chunk_id": "train_shard_00000_3366_0", "global_id": 3725 }, { "text": "Extended-spectrum beta-lactamases (ESBLs), especially those of the CTX-M type, represent a major public health problem throughout the world. Although the carriage of ESBL-producing Enterobacteriaceae (EPE) in feces of horses is now well recognized, little is known about the diversity of EPE after treatment of horses with antibiotics. We undertook this study to assess and follow the diversity of EP Escherichia coli isolated from horses after antibiotic treatment for an infection. Fecal samples from two horses treated and two that were untreated were tested for the presence of EPE on different days. All isolated E. coli strains were evaluated for antimicrobial resistance (AMR) and by whole-genome sequencing. Multi locus sequence typing, phylogrouping, resistance genes and plasmid content were extracted from genomic data. A phylogenetic analysis based on single nucleotide polymorphism (SNP) divergence was also performed on the core genome. We isolated 35 strains belonging to the A, B1 and C phylo-groups. All but one expressed SHV-12 enzymes and one expressed CTX-M-1. Intra- and inter-horse genetic diversity of E. coli strains was identified in the genome analysis and 10 AMR profiles. Two distinct EP E. coli-resistant populations (phylo-group B1: ST4164-AMR3 and ST155-AMR2) were found in one horse, and five other resistant populations were found in the second horse (phylo-group A: ST1250-AMR1; phylo-group B1: ST1250-AMR1, ST6981-AMR1 and phylo-group C: ST10-AMR4). Some persistent EP E. coli strains were detected at least 1 month after treatment. These results indicate that EP E. coli strains isolated from horse feces show intra- and inter-host genetic diversity, even in a region with low ESBL prevalence and in horses that are rarely treated with third-generation cephalosporins. These results also suggest that horizontal gene transfer and/or selection of resistance genes probably occurs in vivo within the horse gut microbiome. Follow-up of EP E", "token_count": 530, "char_count": 1973, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8055, "entities": { "genes": [ "AMR4", "AMR1", "AMR3", "ST155", "ST6981", "AMR2", "ST4164", "ST10", "ST1250" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:32:25.040088", "source": { "split": "train_shard_00000", "doc_id": 3367 }, "chunk_id": "train_shard_00000_3367_0", "global_id": 3726 }, { "text": "coli resistance profiles for at least 1 month after treatment is warranted to prevent persistence of EP E. coli.\n\nHigh genetic diversity of extended-spectrum β-lactamases producing Escherichia coli in feces of horses.", "token_count": 57, "char_count": 217, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9062, "quality_score": 0.9531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:25.408916", "source": { "split": "train_shard_00000", "doc_id": 3367 }, "chunk_id": "train_shard_00000_3367_1", "global_id": 3727 }, { "text": "Bordetella pertussis causes whooping cough, a highly contagious respiratory disease that is reemerging in many world regions. The spread of antigen-deficient strains may threaten acellular vaccine efficacy. Dynamics of strain transmission are poorly defined because of shortcomings in current strain genotyping methods. Our objective was to develop a whole-genome genotyping strategy with sufficient resolution for local epidemiologic questions and sufficient reproducibility to enable international comparisons of clinical isolates. We defined a core genome multilocus sequence typing scheme comprising 2,038 loci and demonstrated its congruence with whole-genome single-nucleotide polymorphism variation. Most cases of intrafamilial groups of isolates or of multiple isolates recovered from the same patient were distinguished from temporally and geographically cocirculating isolates. However, epidemiologically unrelated isolates were sometimes nearly undistinguishable. We set up a publicly accessible core genome multilocus sequence typing database to enable global comparisons of B. pertussis isolates, opening the way for internationally coordinated surveillance.\n\nGenomic Sequencing of Bordetella pertussis for Epidemiology and Global Surveillance of Whooping Cough.", "token_count": 287, "char_count": 1275, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:25.963760", "source": { "split": "train_shard_00000", "doc_id": 3368 }, "chunk_id": "train_shard_00000_3368_0", "global_id": 3728 }, { "text": "The yeast strain SJP-SNU was investigated as a probiotic and was characterized with respect to growth temperature, bile salt resistance, hydrogen sulfide reducing activity, intestinal survival ability and chicken embryo pathogenicity. In addition, we determined the complete genomic and mitochondrial sequences of SJP-SNU and conducted comparative genomics analyses. SJP-SNU grew rapidly at 37 °C and formed colonies on MacConkey agar containing bile salt. SJP-SNU reduced hydrogen sulfide produced by Salmonella serotype Enteritidis and, after being fed to 4-week-old chickens, could be isolated from cecal feces. SJP-SNU did not cause mortality in 10-day-old chicken embryos. From 13 initial contigs, 11 were finally assembled and represented 10 chromosomal sequences and 1 mitochondrial DNA sequence. Comparative genomic analyses revealed that SJP-SNU was a strain of Pichia kudriavzevii. Although SJP-SNU possesses pathogenicity-related genes, they showed very low amino acid sequence identities to those of Candida albicans. Furthermore, SJP-SNU possessed useful genes, such as phytases and cellulase. Thus, SJP-SNU is a useful yeast possessing the basic traits of a probiotic, and further studies to demonstrate its efficacy as a probiotic in the future may be warranted.\n\nGenomic and probiotic characterization of SJP-SNU strain of Pichia kudriavzevii.", "token_count": 382, "char_count": 1359, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6911, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:26.535541", "source": { "split": "train_shard_00000", "doc_id": 3369 }, "chunk_id": "train_shard_00000_3369_0", "global_id": 3729 }, { "text": "Bosentan is well known to induce cholestatic liver toxicity in humans. The present study was set up to characterize the hepatotoxic effects of this drug at the transcriptomic, proteomic, and metabolomic levels. For this purpose, human hepatoma-derived HepaRG cells were exposed to a number of concentrations of bosentan during different periods of time. Bosentan was found to functionally and transcriptionally suppress the bile salt export pump as well as to alter bile acid levels. Pathway analysis of both transcriptomics and proteomics data identified cholestasis as a major toxicological event. Transcriptomics results further showed several gene changes related to the activation of the nuclear farnesoid X receptor. Induction of oxidative stress and inflammation were also observed. Metabolomics analysis indicated changes in the abundance of specific endogenous metabolites related to mitochondrial impairment. The outcome of this study may assist in the further optimization of adverse outcome pathway constructs that mechanistically describe the processes involved in cholestatic liver injury.\n\nOmics-based responses induced by bosentan in human hepatoma HepaRG cell cultures.", "token_count": 268, "char_count": 1186, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:27.101239", "source": { "split": "train_shard_00000", "doc_id": 3370 }, "chunk_id": "train_shard_00000_3370_0", "global_id": 3730 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) with normal circulating gamma-glutamyl transpeptidase levels can result from mutations in the\n\nOutcomes of surgical management of familial intrahepatic cholestasis 1 and bile salt export protein deficiencies.", "token_count": 73, "char_count": 261, "word_count": 32, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:27.477080", "source": { "split": "train_shard_00000", "doc_id": 3371 }, "chunk_id": "train_shard_00000_3371_0", "global_id": 3731 }, { "text": "The aim of this study was to determine the effects of Lactobacillus plantarum YS-3 (LP-YS3) on activated carbon-induced constipation in Kunming mice. The results of the experiment show that the antigastric acid activity and bile salt tolerance of LP-YS3 were stronger than those of Lactobacillus bulgaricus (LB). LP-YS3 inhibited loss of body weight caused by constipation and further reductions in fecal weight, particle number, and water content in mice. Moreover, LP-YS3 elevated the gastrointestinal transit rate and reduced the time required for initial black stool defecation. LP-YS3 also elevated motilin (MTL), endothelin (ET), acetylcholinesterase (AChE), substance P (SP), and VIP serum levels and reduced somatostatin (SS) levels in constipated mice. Hematoxylin-eosin (H&E) staining revealed that high concentration of LP-YS3 reduced the incidence of injuries to small intestine villi and the intestinal wall compared to carbon-induced constipation groups. Reverse transcription-polymerase chain reaction and western blot experiments demonstrated that LP-YS3 upregulated c-Kit, stem cell factor, and glial cell line-derived neurotrophic factor mRNA and protein expression and downregulated transient receptor potential vanilloid 1 and nitric oxide synthase expression in small intestine tissue from constipated mice. In conclusion, high concentrations of LP-YS3 had stronger and more beneficial effects than LB. Based on these results, we conclude that LP-YS3 can effectively inhibit constipation.\n\nLactobacillus plantarum YS-3 Prevents Activated Carbon-Induced Constipation in Mice.", "token_count": 437, "char_count": 1595, "word_count": 217, "semantic_coherence": 1, "information_density": 0.659, "quality_score": 0.8295, "entities": { "genes": [ "YS3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:28.113364", "source": { "split": "train_shard_00000", "doc_id": 3372 }, "chunk_id": "train_shard_00000_3372_0", "global_id": 3732 }, { "text": "Brucella canis is one of zoonotic pathogens causing infection in human. In this study, we isolated and sequenced 38 B. canis strains from 11 cases. Core genome multilocus sequence typing analysis classified all B. canis isolates into two genogroups, GI and GII. All 38 isolates cluster together forming a 2016 Ohio cluster, in which they form five subclusters reflecting their geographical differences. Unlike GI, the isolates of the GII are from diverse geographical locations including Asia, America, Africa, and Europe and form Asia and South America clusters. Overall, our findings could be useful to investigate and track B. canis of future outbreaks.\n\nSequencing and phylogenetic characterization of Brucella canis isolates, Ohio, 2016.", "token_count": 191, "char_count": 742, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:28.561633", "source": { "split": "train_shard_00000", "doc_id": 3373 }, "chunk_id": "train_shard_00000_3373_0", "global_id": 3733 }, { "text": "Tissue diagnosis is the gold standard for mass lesions of the liver, but needle core biopsies may sometimes prove challenging. Presented here is a review of a panel of immunohistochemical stains, including hepatocyte in paraffin 1, arginase-1, polyclonal carcinoembryonic antigen, CD10, bile salt export pump, glypican-3, as well as in situ hybridization for albumin RNA, to establish hepatocellular origin in cases in which hepatocellular carcinoma is suspected but the sample is limited or the morphology is challenging, as it may be with cases of scirrhous, fibrolamellar carcinoma, intrahepatic cholangiocarcinoma, and combined hepatocellular-cholangiocarcinoma.\n\nUpdate on Ancillary Testing in the Evaluation of High-Grade Liver Tumors.", "token_count": 213, "char_count": 741, "word_count": 103, "semantic_coherence": 1, "information_density": 0.767, "quality_score": 0.8835, "entities": { "genes": [ "CD10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:29.025765", "source": { "split": "train_shard_00000", "doc_id": 3374 }, "chunk_id": "train_shard_00000_3374_0", "global_id": 3734 }, { "text": "Bile salt hydrolase (BSH) is a well-known enzyme that has been commonly characterized in probiotic bacteria, as it has cholesterol-lowering effects. However, its molecular investigations are scarce. Here, we build a local database of BSH sequences from\n\nA Comprehensive Genome Survey Provides Novel Insights into Bile Salt Hydrolase (BSH) in Lactobacillaceae.", "token_count": 99, "char_count": 359, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8431, "quality_score": 0.9216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:29.412027", "source": { "split": "train_shard_00000", "doc_id": 3375 }, "chunk_id": "train_shard_00000_3375_0", "global_id": 3735 }, { "text": "Kluyveromyces marxianus, a probiotic yeast, is important in industrial applications because it has a broad substrate spectrum, a rapid growth rate and high thermotolerance. To date, however, there has been little effort in its genetic engineering by the CRISPR/Cas9 system. Therefore, we aimed at establishing the CRISPR/Cas9 system in K. marxianus and creating stable haploid strains, which will make genome engineering simpler. First, we predicted the genome-wide target sites of CRISPR/Cas9 that have been conserved among the eight sequenced genomes of K. marxianus strains. Second, we established the CRISPR/Cas9 system in the K. marxianus 4G5 strain, which was selected for its high thermotolerance, rapid growth, a pH range of pH3-9, utilization of xylose, cellobiose and glycerol, and toxin tolerance, and we knocked out its MATα3 to prevent mating-type switching. Finally, we used K. marxianus MATα3 knockout diploid strains to obtain stable haploid strains with a growth rate comparable to that of the diploid 4G5 strain. In summary, we present the workflow from identifying conserved CRISPR/Cas9 targets in the genome to knock out the MATα3 genes in K. marxianus to obtain a stable haploid strain, which can facilitate genome engineering applications.\n\nGenome-wide prediction of CRISPR/Cas9 targets in Kluyveromyces marxianus and its application to obtain a stable haploid strain.", "token_count": 384, "char_count": 1390, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5459, "quality_score": 0.7729, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:30.025666", "source": { "split": "train_shard_00000", "doc_id": 3376 }, "chunk_id": "train_shard_00000_3376_0", "global_id": 3736 }, { "text": "Chronic inflammation promotes oncogenic transformation and tumor progression. Many inflammatory agents also generate a toxic microenvironment, implying that adaptive mechanisms must be deployed for cells to survive and undergo transformation in such unfavorable contexts. A paradigmatic case is represented by cancers occurring in pediatric patients with genetic defects of hepatocyte phosphatidylcholine transporters and in the corresponding mouse model (Mdr2-/- mice), in which impaired bile salt emulsification leads to chronic hepatocyte damage and inflammation, eventually resulting in oncogenic transformation. By combining genomics and metabolomics, we found that the transition from inflammation to cancer in Mdr2-/- mice was linked to the sustained transcriptional activation of metabolic detoxification systems and transporters by the Constitutive Androstane Receptor (CAR), a hepatocyte-specific nuclear receptor. Activation of CAR-dependent gene expression programs coincided with reduced content of toxic bile acids in cancer nodules relative to inflamed livers. Treatment of Mdr2-/- mice with a CAR inhibitor blocked cancer progression and caused a partial regression of existing tumors. These results indicate that the acquisition of resistance to endo- or xeno-biotic toxicity is critical for cancers that develop in toxic microenvironments.\n\nSustained activation of detoxification pathways promotes liver carcinogenesis in response to chronic bile acid-mediated damage.", "token_count": 343, "char_count": 1486, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:30.600034", "source": { "split": "train_shard_00000", "doc_id": 3377 }, "chunk_id": "train_shard_00000_3377_0", "global_id": 3737 }, { "text": "The genetic and environmental homogeneity in agricultural ecosystems is thought to impose strong and uniform selection pressures. However, the impact of this selection on plant pathogen genomes remains largely unknown. We aimed to identify the proportion of the genome and the specific gene functions under positive selection in populations of the fungal wheat pathogen Zymoseptoria tritici. First, we performed genome scans in four field populations that were sampled from different continents and on distinct wheat cultivars to test which genomic regions are under recent selection. Based on extended haplotype homozygosity and composite likelihood ratio tests, we identified 384 and 81 selective sweeps affecting 4% and 0.5% of the 35 Mb core genome, respectively. We found differences both in the number and the position of selective sweeps across the genome between populations. Using a XtX-based outlier detection approach, we identified 51 extremely divergent genomic regions between the allopatric populations, suggesting that divergent selection led to locally adapted pathogen populations. We performed an outlier detection analysis between two sympatric populations infecting two different wheat cultivars to identify evidence for host-driven selection. Selective sweep regions harboured genes that are likely to play a role in successfully establishing host infections. We also identified secondary metabolite gene clusters and an enrichment in genes encoding transporter and protein localization functions. The latter gene functions mediate responses to environmental stress, including interactions with the host. The distinct gene functions under selection indicate that both local host genotypes and abiotic factors contributed to local adaptation.\n\nGenome-wide evidence for divergent selection between populations of a major agricultural pathogen.", "token_count": 374, "char_count": 1863, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:31.184268", "source": { "split": "train_shard_00000", "doc_id": 3378 }, "chunk_id": "train_shard_00000_3378_0", "global_id": 3738 }, { "text": "Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of the bean pulp by microorganisms is essential for developing the precursors of chocolate flavour. Currently, the cocoa fermentation is still conducted by an uncontrolled traditional process via a consortium of indigenous species of yeasts, lactic acid bacteria and acetic acid bacteria. Although the essential contribution of yeasts to the production of good quality beans and, typical chocolate character is generally agreed, the roles of lactic acid bacteria and acetic acid bacteria are less certain. The objective of this study was to investigate the contribution of LAB and AAB in cocoa bean fermentation by conducting small scale laboratory fermentations under aseptic conditions, inoculated with different groups of microorganisms previously isolated from spontaneous cocoa fermentations. The inoculation protocols were: (1) four yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii, Kluyveromyces marxianus and Saccharomyces cerevisiae; (2) four yeasts plus the lactic acid bacteria Lactobacillus plantarum and Lactobacillus fermentum; (3) four yeasts plus the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateuri and (4) four yeasts plus two lactic acid bacteria and two acetic acid bacteria. Only the inoculated species were detected in the microbiota of their respective fermentations. Beans from the inoculated fermentations showed no significant differences in colour, shell weights and concentrations of residual sugars, alcohols and esters (p>0.05), but they were slightly different in contents of lactic acid and acetic acid (p<0.05). All beans were fully brown and free of mould. Residual sugar levels were less than 2.6 mg/g while the shell contents and ethanol were in the range of 11-13.4% and 4.8-7 mg/g, respectively", "token_count": 471, "char_count": 1857, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5585, "quality_score": 0.7792, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:31.850283", "source": { "split": "train_shard_00000", "doc_id": 3379 }, "chunk_id": "train_shard_00000_3379_0", "global_id": 3739 }, { "text": "Beans fermented in the presence of LAB contained higher levels of lactic acid (0.6-1.2 mg/g) whereas higher concentrations of acetic acid (1.8-2.2 mg/g) were detected in beans inoculated with AAB. Triangle and hedonic sensory evaluations of chocolates prepared from beans taken from the three fermentations showed no significant differences (p > 0.05). It was concluded that the growth of lactic acid bacteria and acetic acid bacteria may not be essential for the fermentation of cocoa beans.\n\nUnravelling the contribution of lactic acid bacteria and acetic acid bacteria to cocoa fermentation using inoculated organisms.", "token_count": 167, "char_count": 621, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:32.309656", "source": { "split": "train_shard_00000", "doc_id": 3379 }, "chunk_id": "train_shard_00000_3379_1", "global_id": 3740 }, { "text": "The bile acid activated transcription factor farnesoid X receptor (FXR) regulates numerous metabolic processes and is a rising target for the treatment of hepatic and metabolic disorders. FXR agonists have revealed efficacy in treating non-alcoholic steatohepatitis (NASH), diabetes and dyslipidemia. Here we characterize imatinib as first-in-class allosteric FXR modulator and report the development of an optimized descendant that markedly promotes agonist induced FXR activation in a reporter gene assay and FXR target gene expression in HepG2 cells. Differential effects of imatinib on agonist-induced bile salt export protein and small heterodimer partner expression suggest that allosteric FXR modulation could open a new avenue to gene-selective FXR modulators.\n\nAllosteric modulation of the farnesoid X receptor by a small molecule.", "token_count": 215, "char_count": 840, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:32.805140", "source": { "split": "train_shard_00000", "doc_id": 3380 }, "chunk_id": "train_shard_00000_3380_0", "global_id": 3741 }, { "text": "Colloidal phases (self-assemblies) in aqueous dispersions of selected binary bile salt/phospholipid blends were studied utilizing the combined analytical approach of asymmetrical flow field-flow fractionation (AF4) and multi-angle laser light scattering (MALLS) in order to resolve the co-existence of different colloidal assemblies. The binary blends were prepared by freeze-drying from tert-butanol/water co-solvent solutions. The blends contained one of two bile salts (sodium taurocholate (TC) or sodium glycodeoxycholate (GDX)) and a mono- or di-acyl phospholipid (lyso-phosphatidylcholine (L-PC) and phosphatidylcholine (PC), respectively). Bile salt and phospholipid (PL) concentrations and their respective ratios were varied systematically within the physiological range found in human intestinal fluids. Furthermore, the BCS class II drug Celecoxib was incorporated in selected blends to assess its potential impact on colloidal phases. To further investigate the smallest self-assemblies observed in AF4/MALLS analysis, dispersions of TC and GDX, respectively, were prepared and analyzed by dynamic light scattering (DLS). AF4/MALLS analysis revealed that binary bile-salt/phospholipid blends form three distinct particle fractions, when the concentration of bile-salt was sufficiently high (≥3.5 mM). Those fractions were assumed to be very small pure bile-salt dimeric/oligomeric self-assemblies (Ø ≈ 2-3 nm), mid-sized mixed micelles (Ø ≈ 10-50 nm) and large liposomes/aggregates (Ø ≈ 150-280 nm). If present, Celecoxib was found solubilized within the structures, but at the lowest TC concentration triggered the formation of an additional (vesicular) phase.", "token_count": 488, "char_count": 1673, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [ "AF4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:33.467461", "source": { "split": "train_shard_00000", "doc_id": 3381 }, "chunk_id": "train_shard_00000_3381_0", "global_id": 3742 }, { "text": "Co-existing colloidal phases in artificial intestinal fluids assessed by AF4/MALLS and DLS: A systematic study into cholate & (lyso-) phospholipid blends, incorporating celecoxib as a model drug.", "token_count": 57, "char_count": 195, "word_count": 27, "semantic_coherence": 1, "information_density": 0.963, "quality_score": 0.9815, "entities": { "genes": [ "AF4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:33.826509", "source": { "split": "train_shard_00000", "doc_id": 3381 }, "chunk_id": "train_shard_00000_3381_1", "global_id": 3743 }, { "text": "The enzymatic hydrolysis of poly- and oligosaccharides from plants seems like an advantageous approach for sugars production. Two inulinases producing fructose from plant oligosaccharides were isolated from yeast Kluyveromyces marxianus and plant Helianthus tuberosus. Both enzymes were immobilized on polymeric carriers by using the static adsorption approach. We could save 80.4% of the initial catalytic activity of plant inulinase immobilized on KU-2 cation-exchange resin and 75.5% of yeast enzyme activity adsorbed on AV-17-2P anion-exchange resin. After immobilization, the Km values increased 1.5 and 6 times for enzymes from K. marxianus and H. tuberosus, respectively. The optimal temperatures for catalysis of both enzymes were increased from 48-50 °C up to 70 °C. The activities of both immobilized enzymes remained unchanged after the 10 cycles of 20-min hydrolysis reaction at 70 °C model batch reactor. Sorbents, native and immobilized enzymes did not exhibit any mutagenic or cytotoxic activity.\n\nEfficient fructose production from plant extracts by immobilized inulinases from Kluyveromyces marxianus and Helianthus tuberosus.", "token_count": 348, "char_count": 1143, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8168, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:34.405001", "source": { "split": "train_shard_00000", "doc_id": 3382 }, "chunk_id": "train_shard_00000_3382_0", "global_id": 3744 }, { "text": "The evolution of asexual organisms is driven not only by the inheritance of genetic modification but also by the acquisition of foreign DNA. The contribution of vertical and horizontal processes to genome evolution depends on their rates per year and is quantified by the ratio of recombination to mutation. These rates have been estimated for bacteria; however, no estimates have been reported for phages. Here, we delineate the contribution of mutation and recombination to dsDNA phage genome evolution. We analyzed 34 isolates of the 936 group of Siphoviridae phages using a Lactococcus lactis strain from a single dairy over 29 years. We estimate a constant substitution rate of 1.9 × 10-4 substitutions per site per year due to mutation that is within the range of estimates for eukaryotic RNA and DNA viruses. The reconstruction of recombination events reveals a constant rate of five recombination events per year and 4.5 × 10-3 nucleotide alterations due to recombination per site per year. Thus, the recombination rate exceeds the substitution rate, resulting in a relative effect of recombination to mutation (r/m) of ∼24 that is homogenous over time. Especially in the early transcriptional region, we detect frequent gene loss and regain due to recombination with phages of the 936 group, demonstrating the role of the 936 group pangenome as a reservoir of genetic variation. The observed substitution rate homogeneity conforms to the neutral theory of evolution; hence, the neutral theory can be applied to phage genome evolution and also to genetic variation brought about by recombination.\n\nRates of Mutation and Recombination in Siphoviridae Phage Genome Evolution over Three Decades.", "token_count": 425, "char_count": 1700, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5301, "quality_score": 0.765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:35.028753", "source": { "split": "train_shard_00000", "doc_id": 3383 }, "chunk_id": "train_shard_00000_3383_0", "global_id": 3745 }, { "text": "D-Allulose as a low-energy and special bioactive monosaccharide sugar is essential for human health. In this study, the D-psicose-3-epimerase gene (DPEase) of Agrobacterium tumefaciens was transferred into thermotolerant Kluyveromyces marxianus to decrease the production cost of D-allulose and reduce the number of manufacturing procedures. The cell regeneration of K. marxianus and cyclic catalysis via whole-cell reaction were investigated to achieve the sustainable application of K. marxianus and the consumption of residual D-fructose. Results showed that DPEase, encoding a 33 kDa protein, could be effectively expressed in thermotolerant K. marxianus. The engineered K. marxianus produced 190 g L\n\nCell regeneration and cyclic catalysis of engineered Kluyveromyces marxianus of a D-psicose-3-epimerase gene from Agrobacterium tumefaciens for D-allulose production.", "token_count": 243, "char_count": 872, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:35.513752", "source": { "split": "train_shard_00000", "doc_id": 3384 }, "chunk_id": "train_shard_00000_3384_0", "global_id": 3746 }, { "text": "Mycoplasma synoviae (MS) is a poultry pathogen with reported increased prevalence and virulence in recent years. MS strain identification is essential for prevention, control efforts and epidemiological outbreak investigations. Multiple multilocus based sequence typing schemes have been developed for MS, yet the resolution of these schemes could be limited for outbreak investigation. The cost of whole genome sequencing became close to that of sequencing the seven MLST targets; however, there is no standardized method for typing MS strains based on whole genome sequences. In this paper, we propose a core genome multilocus sequence typing (cgMLST) scheme as a standardized and reproducible method for typing MS based whole genome sequences. A diverse set of 25 MS whole genome sequences were used to identify 302 core genome genes as cgMLST targets (35.5% of MS genome) and 44 whole genome sequences of MS isolates from six countries in four continents were used for typing applying this scheme. cgMLST based phylogenetic trees displayed a high degree of agreement with core genome SNP based analysis and available epidemiological information. cgMLST allowed evaluation of two conventional MLST schemes of MS. The high discriminatory power of cgMLST allowed differentiation between samples of the same conventional MLST type. cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation between MS isolates. Like conventional MLST, it provides stable and expandable nomenclature, allowing for comparing and sharing the typing results between different laboratories worldwide.\n\nDevelopment of Mycoplasma synoviae (MS) core genome multilocus sequence typing (cgMLST) scheme.", "token_count": 391, "char_count": 1728, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5605, "quality_score": 0.7802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:36.130481", "source": { "split": "train_shard_00000", "doc_id": 3385 }, "chunk_id": "train_shard_00000_3385_0", "global_id": 3747 }, { "text": "Salmonella enterica serovar Typhimurium (S. Typhimurium) and the monophasic variant Salmonella I 4,[5],12:i:- are two clinically-important non-typhoidal Salmonella serovars worldwide. However, the genomic information of these two organisms, especially the monophasic variant, is still lacking in Malaysia. The objective of the study was to compare the genomic features of a monophasic variant and two endemic S. Typhimurium strains isolated from humans. All three strains were subjected to whole genome sequencing followed by comparative genomic and phylogenetic analyses. Extensive genomic deletion in the fljAB operon (from STM2757 to iroB) is responsible for the monophasic phenotype of STM032/04. The two S. Typhimurium genomes (STM001/70 and STM057/05) were essentially identical, despite being isolated 35 years apart. All three strains were of sequence type ST19. Both S. Typhimurium genomes shared unique prophage regions not identified in the monophasic STM032/04 genome. Core genome phylogenetic analyses showed that the monophasic STM032/04 was closely-related to the S. Typhimurium LT2, forming a distinctive clade separated from the two endemic S. Typhimurium strains in Malaysia. The presence of serovar Typhimurium-specific mdh gene, conserved Gifsy and Fels-1 prophages, and the close genomic resemblance with S. Typhimurium LT2 suggested that the monophasic STM032/04 was originated from an LT2-like S. Typhimurium ancestor in Malaysia, following an evolutionary path different from the S. Typhimurium strains. In conclusion, the monophasic Salmonella I 4,[5],12:i:- and the S. Typhimurium strains isolated in Malaysia descended from different phylogenetic lineages. The high genomic resemblance between the two S", "token_count": 523, "char_count": 1730, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5375, "quality_score": 0.7688, "entities": { "genes": [ "STM057", "ST19", "STM032", "STM001", "LT2", "STM2757" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:32:36.790781", "source": { "split": "train_shard_00000", "doc_id": 3386 }, "chunk_id": "train_shard_00000_3386_0", "global_id": 3748 }, { "text": "Typhimurium strains isolated for at least 35 years apart indicated their successful evolutionary lineage. The identification of multiple virulence and antimicrobial resistance determinants in the Salmonella I 4,[5],12:i:- and S. Typhimurium genomes explained the pathogenic nature of the organisms.\n\nGenomic characterization of endemic Salmonella enterica serovar Typhimurium and Salmonella enterica serovar I 4,[5],12:i:- isolated in Malaysia.", "token_count": 129, "char_count": 444, "word_count": 56, "semantic_coherence": 1, "information_density": 0.6964, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:37.209614", "source": { "split": "train_shard_00000", "doc_id": 3386 }, "chunk_id": "train_shard_00000_3386_1", "global_id": 3749 }, { "text": "Lactic acid bacteria (LAB) play an important role in pig health and performance that arises from their beneficial impacts on the balance of gastrointestinal microbes, ability to fight enteric pathogens, and capacity to support the immune system. The aim of this study was to evaluate the functional and safety aspects of five previously isolated autochthonous LAB strains, (Lactobacillus plantarum 22F, 25F and 31F, Pediococcus acidilactici 72N and Pediococcus pentosaceus 77F) from pig faeces as potential probiotics for a pig feed supplement. The functional and safety properties of the strains were assessed by in vitro tests. The functional properties tested were their abilities in tolerating low pH values under simulated gastric conditions, their cell surface properties (hydrophobicity, auto- and co-aggregation), antibacterial activity against the common enteric pathogenic bacteria in pigs (such as pathogenic Escherichia coli, Salmonella Choleraesuis and Streptococcus suis), and diacetyl production. The safety of the strains was analyzed based on the absent of haemolysis on blood and bile salt hydrolase activity. Although all strains demonstrated diacetyl production, good survivability and antibacterial activities, L. plantarum 22F and 25F showed the best performance with the strongest antibacterial actions against the indicator pathogens. Of the strains, only P. pentosaceus 77F exhibited haemolysis or bile salt hydrolase activity. Furthermore, a principal component analysis revealed that L. plantarum 22F possessed superior functional and safety aspects compared to the other four autochthonous strains and to reference strains L. plantarum JCM 1149 and P. acidilactici DSM 20284. Further in vivo studies using oral administration of the strains are justified to assess their effectiveness as feed supplements for pigs.\n\nAutochthonous lactic acid bacteria isolated from pig faeces in Thailand show probiotic properties and antibacterial activity against enteric pathogenic bacteria.", "token_count": 498, "char_count": 2005, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5816, "quality_score": 0.7908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:37.861816", "source": { "split": "train_shard_00000", "doc_id": 3387 }, "chunk_id": "train_shard_00000_3387_0", "global_id": 3750 }, { "text": "The non-conserved accessory genome of bacteria can be associated with important adaptive characteristics that can contribute to niche specificity or pathogenicity of strains. High degrees of structural and compositional diversity in genomic islands and other elements of the accessory genome can complicate characterization of accessory genome contents among populations of strains. Methods for easily and effectively defining the distributions of discrete elements of the accessory genome among bacterial strains in a population are needed to explore the relationships between the flexible genome and bacterial adaptive traits.\n\nClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements.", "token_count": 142, "char_count": 728, "word_count": 99, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:38.292350", "source": { "split": "train_shard_00000", "doc_id": 3388 }, "chunk_id": "train_shard_00000_3388_0", "global_id": 3751 }, { "text": "Intestinal adaptation is important for the short bowel syndrome (SBS) patients. Growing evidence has suggested that bile salt dependent lipase (BSDL) not only has the lipolytic activity, but also the immune-modulating and pro-proliferative activities. The purpose of the present study was to investigate the effects of BSDL on intestinal adaptive growth and gut barrier function in a rat model of SBS. Twenty-four male Sprague-Dawley rats were randomly divided into three experimental groups: sham group (rats underwent bowel transection and re-anastomosis), SBS group (rats underwent 80% bowel resection), SBS-BSDL group (SBS rats orally administered BSDL). The animals were weighed daily. The intestinal morpho-histochemical changes and intestinal barrier function were determined 14 days after the operations. Meanwhile, the expressions of Wnt signaling molecules in enterocytes were also analyzed by immunohistochemistry and Western blot. The postoperative weight gain was faster in the SBS rats treated with BSDL than in the SBS/untreated group. The SBS rats treated with BSDL had significantly greater villus height, crypt depth, and enterocyte proliferation in their residual intestines, as compared with the SBS/untreated group. The recovery of intestinal barrier function was promoted and the expressions of tight-junction proteins were increased in the SBS rats treated with BSDL. Additionally, the data indicated that the proadaptive activities of BSDL might be mediated by Wnt signaling activation in the enterocytes. These observations suggested that enteral BSDL administration promoted intestinal adaptive growth and barrier repairing by activating Wnt signaling pathway in SBS rats.\n\nBile salt dependent lipase promotes intestinal adaptation in rats with massive small bowel resection.", "token_count": 435, "char_count": 1801, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5827, "quality_score": 0.7913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:38.923628", "source": { "split": "train_shard_00000", "doc_id": 3389 }, "chunk_id": "train_shard_00000_3389_0", "global_id": 3752 }, { "text": "The members of the Enterococcus genus are widely distributed in nature. Its strains have been extensively reported to be present in plant surfaces, soil, water and food. In an attempt to assess their potential application in food industry, four Enterococcus faecium group-strains recently isolated from Argentinean regional cheese products were evaluated using a combination of whole genome analyses and in vivo assays. In order to identify these microorganisms at species level, in silico analyses using their newly reported sequences were conducted. The average nucleotide identity (ANI), in silico DNA-DNA hybridization, and phylogenomic trees constructed using core genome data allowed IQ110, GM70 and GM75 strains to be classified as E. faecium while IQ23 strain was identified as E. durans. Besides their common origin, the strains showed differences in their genetic structure and mobile genetic element content. Furthermore, it was possible to determine the absence or presence of specific features related to growth in milk, cheese ripening, probiotic capability and gut adaptation including sugar, amino acid, and peptides utilization, flavor compound production, bile salt tolerance as well as biogenic amine production. Remarkably, all strains encoded for peptide permeases, maltose utilization, bile salt tolerance, diacetyl and tyramine production genes. On the other hand, some variability was observed regarding citrate and lactose utilization, esterase, and cell wall-associated proteinase. In addition, while strains were predicted to be non-human pathogens by the in silico inspection of pathogenicity and virulence factors, only the GM70 strain proved to be non-virulent in Galleria mellonella model. In conclusion, we propose that, in order to improve the rational selection of strains for industrial applications, a holistic approach involving a comparative genomic analysis of positive and negative features as well as in vivo evaluation of virulence behavior should be performed.\n\nSafety assessment and functional properties of four enterococci strains isolated from regional Argentinean cheese.", "token_count": 472, "char_count": 2119, "word_count": 302, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [ "GM70", "IQ110", "GM75", "IQ23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:39.570616", "source": { "split": "train_shard_00000", "doc_id": 3390 }, "chunk_id": "train_shard_00000_3390_0", "global_id": 3753 }, { "text": "Important aspects of the selection of probiotics to be used for mixing in animal feed include host species specificity and probiotic cell survival during production and storage of their products. The research was to screen and investigate some probiotic properties of lactic acid bacteria (LAB) isolated from pig fecal samples. One hundred and thirty-eight representative LAB isolates, which were isolated from 51 pig fecal samples, were tested for acid and bile tolerance, antimicrobial susceptibility, antibacterial activity, potential adhesion to the cell surface, and survival rates when stored in varied microencapsulation forms: freeze-dried, spray-dried, and micro-beads. The antibacterial activity results of the ten LAB isolates, which were acid- (pH 2, 3 h) and bile- (50% (v/v) fresh pig bile, 8 h) tolerant and suitable for resisting the five antibiotics commonly used for treating pig infections with pathogenic indicator strains, showed that three isolates (L21, L80, L103) had strong inhibition to Escherichia coli, Salmonella group B, and Salmonella group D using co-culturing and agar spot assays. The three isolates had high hydrophobicity (65-73%) and did not show antagonistic growth against each other. All three selected isolates had greater than 80% survival in freeze-dried and micro-bead forms at 25-30 °C after 2 days of storage (80.4-86.75%, 7.31-7.89 log CFU/ml). Sequence analysis of the 16S rRNA genes demonstrated that the three isolates belong to Lactobacillus plantarum (strain L21 and strain L80) and L. paraplantarum (strain L103). The single and multiple strains of these bacteria may have potential use as probiotics in pig diets.\n\nEncapsulating Viability of Multi-strain Lactobacilli as Potential Probiotic in Pigs.", "token_count": 491, "char_count": 1753, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6834, "quality_score": 0.8417, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:40.221580", "source": { "split": "train_shard_00000", "doc_id": 3391 }, "chunk_id": "train_shard_00000_3391_0", "global_id": 3754 }, { "text": "The increase of infections due to non-Candida albicans species made it very necessary to conduct adequate characterization to be able to identify the species of Candida isolated from traditional fermented foods. In this study, based on their hue on Candida Chromogenic Agar medium, a total of 136 yeast strains were isolated from tchapalo and bangui. Molecular identification based on PCR-RFLP of internal transcribed spacers of rDNA (ITS) and sequencing of the ITS and the D1/D2 regions allowed us to assign these isolates to seven species: Candida tropicalis, Candida inconspicua, Candida rugosa, Saccharomyces cerevisiae, Kluyveromyces marxianus, Hanseniaspora guilliermondii, Trichosporon asahii. With the respect to each beverage, six species were found among with four species are regarded as opportunistic pathogens. From these, C. tropicalis, C. inconspicua and K. marxianus were the most commonly encountered. The enzyme activities of the potential pathogens assessed using API ZYM system showed that almost strains had esterase, esterase lipase, valine and cystine arylamidase, alpha chymotrypsin, alkaline phosphatase and naphthol phosphohydrolase activities. The activity of α-glucosidase was found only in C. tropicalis and C. inconspicua strains isolated from tchapalo while β-glucosidase activity was found in all strains from tchapalo and only in C. inconspicua isolated from bangui.\n\nCandida species in tchapalo and bangui, two traditional alcoholic beverages from Côte d'Ivoire.", "token_count": 433, "char_count": 1496, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:40.857894", "source": { "split": "train_shard_00000", "doc_id": 3392 }, "chunk_id": "train_shard_00000_3392_0", "global_id": 3755 }, { "text": "The goal of this study was to compare the molecular features of bovine- and human community-acquired extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in Israel. Bovine ESBL-producing E. coli were isolated during a point-prevalence study from the main farming locations throughout Israel. Human ESBL-producing E. coli isolates were collected from community-acquired urinary tract infection cases. Molecular typing was done initially by repetitive extragenic palindromic-PCR. Representative isolates were subjected to next-generation sequencing (NGS) and analyzed for multilocus sequence typing (MLST), core genome MLST (cgMLST), bla\n\nDistinctiveness and Similarities Between Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Cattle and the Community in Israel.", "token_count": 213, "char_count": 795, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6939, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:41.323839", "source": { "split": "train_shard_00000", "doc_id": 3393 }, "chunk_id": "train_shard_00000_3393_0", "global_id": 3756 }, { "text": "Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.\n\nAccessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi.", "token_count": 321, "char_count": 1462, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7438, "quality_score": 0.8719, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:41.888465", "source": { "split": "train_shard_00000", "doc_id": 3394 }, "chunk_id": "train_shard_00000_3394_0", "global_id": 3757 }, { "text": "During pretreatment of lignocellulosic biomass, toxic compounds were released and inhibited the growth and fermentation of microorganisms. Here the global transcriptional response of\n\nTranscriptomic analysis of thermotolerant yeast", "token_count": 55, "char_count": 231, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8214, "quality_score": 0.9107, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:42.254176", "source": { "split": "train_shard_00000", "doc_id": 3395 }, "chunk_id": "train_shard_00000_3395_0", "global_id": 3758 }, { "text": "The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria.\n\nInferring the Minimal Genome of", "token_count": 361, "char_count": 1341, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:42.831795", "source": { "split": "train_shard_00000", "doc_id": 3396 }, "chunk_id": "train_shard_00000_3396_0", "global_id": 3759 }, { "text": "Weissella confusa has recently received attention for its probiotic potential. Some W. confusa and Weissella cibaria strains isolated from fermented foods show favorable probiotic effects. However, the probiotic properties of W. confusa isolated from giant panda remain unreported to date. Thus, this study isolated a W. confusa strain from giant panda feces and then investigated its characteristics and probiotic properties. A lactic acid bacteria strain was isolated from giant panda fecal samples. The isolated strain was screened by in vitro probiotic property tests, including in vitro antimicrobial test, antioxidant test, surface hydrophobicity, and stress resistance. On the basis of biochemical identification and 16S rDNA sequencing, the W. confusa strain was identified as BSP201703. This Weissella confusa strain can survive at pH 2 and 0.3% (w/v) concentration of bile salt environment and inhibit common intestinal pathogens. It also possesses an in vitro antioxidant capacity, a high auto-aggregation ability, and a high surface hydrophobicity. BSP201703 might serve as a probiotic to giant pandas.\n\nIsolation and Preliminary Screening of a Weissella confusa Strain from Giant Panda (Ailuropoda melanoleuca).", "token_count": 322, "char_count": 1224, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "BSP201703" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:43.407436", "source": { "split": "train_shard_00000", "doc_id": 3397 }, "chunk_id": "train_shard_00000_3397_0", "global_id": 3760 }, { "text": "Kluyveromyces marxianus is a thermotolerant, crabtree-negative yeast, which preferentially directs metabolism (e.g., from the tricarboxylic acid cycle) to aerobic alcoholic fermentation. Thus K. marxianus has great potential for engineering to produce various materials under aerobic cultivation conditions. In this study, we engineered K. marxianus to produce and secrete a single-chain antibody (scFv), a product that is highly valuable but has historically proven difficult to generate at large scale. scFv production was obtained with strains carrying either plasmid-borne or genomically integrated constructs using various combinations of promoters (P\n\nGenetic and physiological basis for antibody production by Kluyveromyces marxianus.", "token_count": 183, "char_count": 741, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8144, "quality_score": 0.9072, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:43.890400", "source": { "split": "train_shard_00000", "doc_id": 3398 }, "chunk_id": "train_shard_00000_3398_0", "global_id": 3761 }, { "text": "Mezcal, a traditional beverage that originated in Mexico, is produced from species of the Agavaceae family. The esters associated with the yeasts utilized during fermentation are important for improving the organoleptic properties of the beverage. We improved the ester contents in a mezcal beverage by using the yeast Kluyveromyces marxianus, which was engineered with the ATF1 gene. ATF1 expression in the recombinant yeast significantly increased compared with that in the parental yeast, but its fermentative parameters were unchanged. Volatile-organic-compound-content analysis showed that esters had significantly increased in the mezcal produced with the engineered yeast. In a sensory-panel test, 48% of the panelists preferred the mezcal produced from the engineered yeast, 30% preferred the mezcal produced from the wild type, and 15 and 7% preferred the two mezcal types produced following the routine procedure. Correlation analysis showed that the fruitiness/sweetness description of the mezcal produced using the ATF1-engineered K. marxianus yeast correlated with the content of the esters, whose presence improved the organoleptic properties of the craft mezcal beverage.\n\nImproving the Organoleptic Properties of a Craft Mezcal Beverage by Increasing Fatty Acid Ethyl Ester Contents through ATF1 Expression in an Engineered Kluyveromyces marxianus UMPe-1 Yeast.", "token_count": 340, "char_count": 1377, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5052, "quality_score": 0.7526, "entities": { "genes": [ "ATF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:44.486135", "source": { "split": "train_shard_00000", "doc_id": 3399 }, "chunk_id": "train_shard_00000_3399_0", "global_id": 3762 }, { "text": "Zearalenone (ZEN) is a mycotoxin produced by Fusarium species, which is one of the main animal feed contaminants causing reproductive disorders in livestock. The aim of this study was to evaluate the probiotic characteristics and ZEN removal ability of a Bacillus licheniformis strain CK1. The probiotic properties, including acidic tolerance, bile salt tolerance, adherence capability, and anti-pathogenic activities of CK1 were evaluated. CK1 survived after incubation at pH 2.0 or 3.0 for 3 h, grew well in LB broth containing 0.3% oxgall, possessed adherence capability to Caco-2 cells, and inhibited the growth of Escherichia coli O157:H7 and Listeria monocytogenes. The ZEN removal ability of CK1 was compared with a mineral mycotoxin-adsorbing agent, hydrated sodium calcium aluminosilicate (HSCAS), and a well-characterized biological mycotoxin-adsorbing agent, Lactobacillus rhamnosus GG (LGG). At 37°C in phosphate-buffered saline (PBS, pH 7.0) containing 5 μg mL-1 of ZEN, the ZEN removal percentage of CK1 was 73.0%, which was significantly higher than that of HSCAS and LGG (45.9% and 48.4%, respectively). In the pH range of 2.5-8.0, CK1 removed up to 65% of ZEN. At temperatures between 4 and 42°C, CK1 removed more than 75% of ZEN. In the adsorption stability analysis, the amounts of ZEN removed by CK1 was over 30% even after five consecutive rounds of washing procedures. These findings demonstrated that CK1 displayed probiotic characteristics and removed ZEN effectively. Therefore, CK1 has a great potential for the development of feed additive to remove ZEN.\n\nProbiotic characteristics and zearalenone-removal ability of a Bacillus licheniformis strain.", "token_count": 509, "char_count": 1676, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8092, "entities": { "genes": [ "CK1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:45.188919", "source": { "split": "train_shard_00000", "doc_id": 3400 }, "chunk_id": "train_shard_00000_3400_0", "global_id": 3763 }, { "text": "Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty three species each. Pairwise average nucleotide identities and alignment fractions were calculated for the data set of the 166 type strains and 1224 genomes of Pseudomonas available in public databases. Results revealed that 394 of the 1224 genomes were distinct from any type strain, suggesting that the type strains represent only a fraction of the genomic diversity of the genus. The core genome of Pseudomonas was determined to contain 794 genes conferring primarily housekeeping functions. The results of this study provide a phylogenetic framework for future studies aiming to resolve the classification and phylogenetic relationships, identify new gene functions and phenotypes, and explore the ecological and metabolic potential of the Pseudomonas spp.\n\nGenome-based evolutionary history of Pseudomonas spp.", "token_count": 322, "char_count": 1304, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6053, "quality_score": 0.8026, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:46.171387", "source": { "split": "train_shard_00000", "doc_id": 3401 }, "chunk_id": "train_shard_00000_3401_0", "global_id": 3764 }, { "text": "Candida auris is an emerging yeast pathogen of global significance. Its multidrug-resistant nature and inadequacies of conventional identification systems pose diagnostic and therapeutic challenges. This study investigated occurrence of C. auris in clinical specimens in Kuwait and its susceptibility to antifungal agents. Clinical yeast strains isolated during 3.5-year period and forming pink-colored colonies on CHROMagar Candida were studied by wet mount examination for microscopic morphology and Vitek 2 yeast identification system. A simple species-specific PCR assay was developed for molecular identification and results were confirmed by PCR-sequencing of rDNA. Antifungal susceptibility testing of one isolate from each patient was determined by Etest. The 280 isolates forming pink-colored colonies on CHROMagar Candida, were identified by Vitek 2 as Candida haemulonii (n = 166), Candida utilis (n = 49), Candida kefyr (n = 45), Candida guilliermondii (n = 9), Candida famata (n = 6) and Candida conglobata (n = 5). Species-specific PCR and PCR-sequencing of rDNA identified 166 C. haemulonii isolates as C. auris (n = 158), C. haemulonii (n = 6) and Candida duobushaemulonii (n = 2). C. auris isolates originated from diverse clinical specimens from 56 patients. Of 56 C. auris isolates tested, all were resistant to fluconazole, 41/56 (73%) and 13/56 (23%) were additionally resistant to voriconazole and amphotericin B, respectively. Eleven (20%) isolates were resistant to fluconazole, voriconazole and amphotericin B. One isolate was resistant to caspofungin and micafungin. Increasing isolation of C. auris in recent years from diverse clinical specimens including bloodstream shows that C. auris is an emerging non-albicans Candida species in Kuwait causing a variety of infections", "token_count": 521, "char_count": 1801, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5229, "quality_score": 0.7615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:32:46.827768", "source": { "split": "train_shard_00000", "doc_id": 3402 }, "chunk_id": "train_shard_00000_3402_0", "global_id": 3765 }, { "text": "Inability of conventional identification methods to accurately identify this pathogen and multidrug-resistant nature of many strains calls for a greater understanding of its epidemiology, risk factors for acquiring C. auris infection and management strategies in high-risk patients. This is the first comprehensive study on the emergence of this multidrug-resistant yeast from Kuwait and the Middle East.\n\nIncreasing prevalence, molecular characterization and antifungal drug susceptibility of serial Candida auris isolates in Kuwait.", "token_count": 114, "char_count": 534, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7887, "quality_score": 0.8944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:47.214569", "source": { "split": "train_shard_00000", "doc_id": 3402 }, "chunk_id": "train_shard_00000_3402_1", "global_id": 3766 }, { "text": "2-Phenylethanol (2-PE) and 2-phenethyl acetate (2-PEA) are important aroma compounds widely used in food and cosmetic industries due to their rose-like odor. Nowadays, due to the growing demand for natural products, the development of bioprocesses for obtaining value-added compounds has become of great significance. 2-PE and 2-PEA can be produced through the biotransformation of L-phenylalanine using the generally recognized as safe strain Kluyveromyces marxianus. L-phenylalanine bioconversion systems have been typically focused on submerged fermentation processes (SmF), but there is no information about other alternative productive approaches. Here, the solid-state fermentation (SSF) of sugarcane bagasse supplemented with L-phenylalanine was investigated as a sustainable alternative for producing 2-PE and 2-PEA in a residue-based system using Kluyveromyces marxianus as inoculum. An initial screening of the operational variables indicated that air supply, temperature, and initial moisture content significantly affect the product yield. Besides, it was found that the feeding strategy also affects the production and the efficiency of the process. While a basic batch system produced 16 mg\n\nBioproduction of 2-phenylethanol and 2-phenethyl acetate by Kluyveromyces marxianus through the solid-state fermentation of sugarcane bagasse.", "token_count": 346, "char_count": 1348, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:47.791654", "source": { "split": "train_shard_00000", "doc_id": 3403 }, "chunk_id": "train_shard_00000_3403_0", "global_id": 3767 }, { "text": "The interfacial activity of pancreatic lipases (PL) depends on the presence of colipase and bile salt. The activity of PL is inhibited by micellar concentrations of bile salt which can be restored by the addition of colipase. Though the formation of 1:1:1 tertiary complex by lipase-colipase-bile salt micelle is well accepted, the residue-level interactions between lipase-colipase and bile salt are yet to be clearly understood. Molecular dynamic simulations of lipase-colipase complex, lipase and colipase were performed in the presence of a model bile salt, sodium taurocholate (NaTC), at its near-CMC and supra-micellar concentrations. From the interactions obtained from the molecular dynamic simulations, the ternary complex was modelled and compared with earlier reports. The analysis suggested that a micelle of NaTC consisting of nine monomers was formed at the concave groove between lipase and colipase chain and it mainly interacted with the fourth finger of colipase. This complex was mainly stabilized by van der Waals interactions. Interestingly, the C-terminal domain of lipase which holds the colipase did not show any significant role in formation or stabilization of NaTC micelle.\n\nBinding orientation and interaction of bile salt in its ternary complex with pancreatic lipase-colipase system.", "token_count": 319, "char_count": 1313, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5855, "quality_score": 0.7927, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:48.358195", "source": { "split": "train_shard_00000", "doc_id": 3404 }, "chunk_id": "train_shard_00000_3404_0", "global_id": 3768 }, { "text": "During a study to assess the faecal microbiome of common seals (Phoca vitulina) in a Dutch seal rehabilitation centre, 16S rRNA gene sequences of an unknown Campylobacter taxon were identified. Campylobacter isolates, which differed from the established Campylobacter taxa, were cultured and their taxonomic position was determined by a polyphasic study based on ten isolates. The isolates were characterized by 16S rRNA and atpA gene sequence analyses and by conventional phenotypic testing. Based on the whole genome sequences, the average nucleotide identity and core genome phylogeny were determined. The isolates formed a separate phylogenetic clade, divergent from all other Campylobacter taxa and most closely related to Campylobacter corcagiensis, Campylobacter geochelonis and Campylobacter ureolyticus. The isolates can be distinguished phenotypically from all other Campylobacter taxa based on their lack of motility, growth at 25 °C and growth on MacConkey agar. This study shows that these isolates represent a novel species within the genus Campylobacter, for which the name Campylobacter blaseri sp. nov. is proposed. The type strain for this novel species is 17S00004-5\n\nCampylobacter blaseri sp. nov., isolated from common seals (Phoca vitulina).", "token_count": 338, "char_count": 1263, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8104, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:48.922905", "source": { "split": "train_shard_00000", "doc_id": 3405 }, "chunk_id": "train_shard_00000_3405_0", "global_id": 3769 }, { "text": "For many decades, Salmonella enterica has been subdivided by serological properties into serovars or further subdivided for epidemiological tracing by a variety of diagnostic tests with higher resolution. Recently, it has been proposed that so-called eBurst groups (eBGs) based on the alleles of seven housekeeping genes (legacy multilocus sequence typing [MLST]) corresponded to natural populations and could replace serotyping. However, this approach lacks the resolution needed for epidemiological tracing and the existence of natural populations had not been independently validated by independent criteria. Here, we describe EnteroBase, a web-based platform that assembles draft genomes from Illumina short reads in the public domain or that are uploaded by users. EnteroBase implements legacy MLST as well as ribosomal gene MLST (rMLST), core genome MLST (cgMLST), and whole genome MLST (wgMLST) and currently contains over 100,000 assembled genomes from Salmonella. It also provides graphical tools for visual interrogation of these genotypes and those based on core single nucleotide polymorphisms (SNPs). eBGs based on legacy MLST are largely consistent with eBGs based on rMLST, thus demonstrating that these correspond to natural populations. rMLST also facilitated the selection of representative genotypes for SNP analyses of the entire breadth of diversity within Salmonella. In contrast, cgMLST provides the resolution needed for epidemiological investigations. These observations show that genomic genotyping, with the assistance of EnteroBase, can be applied at all levels of diversity within the Salmonella genus.\n\nA genomic overview of the population structure of Salmonella.", "token_count": 388, "char_count": 1694, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:49.535645", "source": { "split": "train_shard_00000", "doc_id": 3406 }, "chunk_id": "train_shard_00000_3406_0", "global_id": 3770 }, { "text": "Bacterial whole-genome sequencing in the clinical setting has the potential to bring major improvements to infection control and clinical practice. Sequencing instruments are not currently available in the majority of routine microbiology laboratories worldwide, but an alternative is to use external sequencing providers. To foster discussion around this we investigated whether send-out services were a viable option. Four providers offering MiSeq sequencing were selected based on cost and evaluated based on the service provided and sequence data quality. DNA was prepared from five methicillin-resistant Staphylococcus aureus (MRSA) isolates, four of which were investigated during a previously published outbreak in the UK together with a reference MRSA isolate (ST22 HO 5096 0412). Cost of sequencing per isolate ranged from £155 to £342 and turnaround times from DNA postage to arrival of sequence data ranged from 12 to 63 days. Comparison of commercially generated genomes against the original sequence data demonstrated very high concordance, with no more than one single nucleotide polymorphism (SNP) difference on core genome mapping between the original sequences and the new sequence for all four providers. Multilocus sequence type could not be assigned based on assembly for the two cheapest sequence providers due to fragmented assemblies probably caused by a lower output of sequence data per isolate. Our results indicate that external providers returned highly accurate genome data, but that improvements are required in turnaround time to make this a viable option for use in clinical practice.\n\nAre commercial providers a viable option for clinical bacterial sequencing?", "token_count": 356, "char_count": 1693, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6265, "quality_score": 0.8133, "entities": { "genes": [ "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:50.111945", "source": { "split": "train_shard_00000", "doc_id": 3407 }, "chunk_id": "train_shard_00000_3407_0", "global_id": 3771 }, { "text": "Pinelliae Rhizoma Praeparatum (PRP) as traditional Chinese medicine had been used for hepatic diseases in combinative forms. However, the effect of PRP was not clear when used alone. So to explore the hepatoprotective/hepatotoxin of PRP is necessary. The activities of PRP were investigated in acetaminophen-induced hepatic injury mice. Liver function markers, hepatic oxidative stress markers were evaluated. Bile acids metabolic transports and nuclear factor erythroid 2-related factor 2 (Nrf2) were detected. As a drug for the treatment of liver diseases, PRP slightly restored the parameters towards normal in model mice only in low dosage, and also had no antioxidant activity and regulate Nrf2. Cholestasis was significantly elevated in model mice when pretreatment with routine or high dosage of PRP, but had no effect on normal mice. Bile salt export pump (Bsep) and multidrug resistance-associated protein 2 (Mrp2) in model mice were markedly increased when pretreatment with low dose PRP, but significantly decreased when pretreatment in routine or high dosage. Mrp3 was significantly induced in model mice after pretreatment of PRP. But the adjustment effect to bile acids transporters by PRP was not significant in normal mice. These results reveal that PRP has the different effects on bile acids transporter in hepatic injury mice, and therefore, the dosage of PRP need to be paid attention to when it is used in clinical hepatic injury.\n\nPinelliae Rhizoma Praeparatum Involved in the Regulation of Bile Acids Metabolism in Hepatic Injury.", "token_count": 409, "char_count": 1553, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5527, "quality_score": 0.7764, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:50.731102", "source": { "split": "train_shard_00000", "doc_id": 3408 }, "chunk_id": "train_shard_00000_3408_0", "global_id": 3772 }, { "text": "Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.", "token_count": 36, "char_count": 120, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:51.091860", "source": { "split": "train_shard_00000", "doc_id": 3409 }, "chunk_id": "train_shard_00000_3409_0", "global_id": 3773 }, { "text": "Clostridiodes difficile strains from the NAPCR1/ST54 and NAP1/ST01 types have caused outbreaks despite of their notable differences in genome diversity. By comparing whole genome sequences of 32 NAPCR1/ST54 isolates and 17 NAP1/ST01 recovered from patients infected with C. difficile we assessed whether mutation, homologous recombination (r) or nonhomologous recombination (NHR) through lateral gene transfer (LGT) have differentially shaped the microdiversification of these strains. The average number of single nucleotide polymorphisms (SNPs) in coding sequences (NAPCR1/ST54 = 24; NAP1/ST01 = 19) and SNP densities (NAPCR1/ST54 = 0.54/kb; NAP1/ST01 = 0.46/kb) in the NAPCR1/ST54 and NAP1/ST01 isolates was comparable. However, the NAP1/ST01 isolates showed 3× higher average dN/dS rates (8.35) that the NAPCR1/ST54 isolates (2.62). Regarding r, whereas 31 of the NAPCR1/ST54 isolates showed 1 recombination block (3,301-8,226 bp), the NAP1/ST01 isolates showed no bases in recombination. As to NHR, the pangenome of the NAPCR1/ST54 isolates was larger (4,802 gene clusters, 26% noncore genes) and more heterogeneous (644 ± 33 gene content changes) than that of the NAP1/ST01 isolates (3,829 gene clusters, ca. 6% noncore genes, 129 ± 37 gene content changes)", "token_count": 481, "char_count": 1263, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [ "ST54", "NAPCR1", "NAP1", "ST01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:51.736950", "source": { "split": "train_shard_00000", "doc_id": 3410 }, "chunk_id": "train_shard_00000_3410_0", "global_id": 3774 }, { "text": "Nearly 55% of the gene content changes seen among the NAPCR1/ST54 isolates (355 ± 31) were traced back to MGEs with putative genes for antimicrobial resistance and virulence factors that were only detected in single isolates or isolate clusters. Congruently, the LGT/SNP rate calculated for the NAPCR1/ST54 isolates (26.8 ± 2.8) was 4× higher than the one obtained for the NAP1/ST1 isolates (6.8 ± 2.0). We conclude that NHR-LGT has had a greater role in the microdiversification of the NAPCR1/ST54 strains, opposite to the NAP1/ST01 strains, where mutation is known to play a more prominent role.\n\nTwo Groups of Cocirculating, Epidemic Clostridiodes difficile Strains Microdiversify through Different Mechanisms.", "token_count": 240, "char_count": 713, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [ "ST54", "ST01", "NAPCR1", "ST1", "NAP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:52.209926", "source": { "split": "train_shard_00000", "doc_id": 3410 }, "chunk_id": "train_shard_00000_3410_1", "global_id": 3775 }, { "text": "In the United States, the introduction of the heptavalent pneumococcal conjugate vaccine (PCV) largely eliminated vaccine serotypes (VT); non-vaccine serotypes (NVT) subsequently increased in carriage and disease. Vaccination also disrupts the composition of the pneumococcal pangenome, which includes mobile genetic elements and polymorphic non-capsular antigens important for virulence, transmission, and pneumococcal ecology. Antigenic proteins are of interest for future vaccines; yet, little is known about how the they are affected by PCV use. To investigate the evolutionary impact of vaccination, we assessed recombination, evolution, and pathogen demographic history of 937 pneumococci collected from 1998-2012 among Navajo and White Mountain Apache Native American communities. We analyzed changes in the pneumococcal pangenome, focusing on metabolic loci and 19 polymorphic protein antigens. We found the impact of PCV on the pneumococcal population could be observed in reduced diversity, a smaller pangenome, and changing frequencies of accessory clusters of orthologous groups (COGs). Post-PCV7, diversity rebounded through clonal expansion of NVT lineages and inferred in-migration of two previously unobserved lineages. Accessory COGs frequencies trended toward pre-PCV7 values with increasing time since vaccine introduction. Contemporary frequencies of protein antigen variants are better predicted by pre-PCV7 values (1998-2000) than the preceding period (2006-2008), suggesting balancing selection may have acted in maintaining variant frequencies in this population. Overall, we present the largest genomic analysis of pneumococcal carriage in the United States to date, which includes a snapshot of a true vaccine-naïve community prior to the introduction of PCV7. These data improve our understanding of pneumococcal evolution and emphasize the need to consider pangenome composition when inferring the impact of vaccination and developing future protein-based pneumococcal vaccines.", "token_count": 481, "char_count": 2006, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6679, "quality_score": 0.834, "entities": { "genes": [ "PCV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:52.861507", "source": { "split": "train_shard_00000", "doc_id": 3411 }, "chunk_id": "train_shard_00000_3411_0", "global_id": 3776 }, { "text": "The impact of serotype-specific vaccination on phylodynamic parameters of Streptococcus pneumoniae and the pneumococcal pan-genome.", "token_count": 37, "char_count": 131, "word_count": 15, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:53.219317", "source": { "split": "train_shard_00000", "doc_id": 3411 }, "chunk_id": "train_shard_00000_3411_1", "global_id": 3777 }, { "text": "Homologous recombination is a major driver of bacterial speciation. Genetic divergence and host association are important factors influencing homologous recombination. Here, we study these factors for Campylobacter fetus, which shows a distinct intraspecific host dichotomy. Campylobacter fetus subspecies fetus (Cff) and venerealis are associated with mammals, whereas C. fetus subsp. testudinum (Cft) is associated with reptiles. Recombination between these genetically divergent C. fetus lineages is extremely rare. Previously it was impossible to show whether this barrier to recombination was determined by the differential host preferences, by the genetic divergence between both lineages or by other factors influencing recombination, such as restriction-modification, CRISPR/Cas, and transformation systems. Fortuitously, a distinct C. fetus lineage (ST69) was found, which was highly related to mammal-associated C. fetus, yet isolated from a chelonian. The whole genome sequences of two C. fetus ST69 isolates were compared with those of mammal- and reptile-associated C. fetus strains for phylogenetic and recombination analysis. In total, 5.1-5.5% of the core genome of both ST69 isolates showed signs of recombination. Of the predicted recombination regions, 80.4% were most closely related to Cft, 14.3% to Cff, and 5.6% to C. iguaniorum. Recombination from C. fetus ST69 to Cft was also detected, but to a lesser extent and only in chelonian-associated Cft strains. This study shows that despite substantial genetic divergence no absolute barrier to homologous recombination exists between two distinct C. fetus lineages when occurring in the same host type, which provides valuable insights in bacterial speciation and evolution.\n\nHomologous Recombination between Genetically Divergent Campylobacter fetus Lineages Supports Host-Associated Speciation.", "token_count": 476, "char_count": 1867, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5486, "quality_score": 0.7743, "entities": { "genes": [ "ST69" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:53.860137", "source": { "split": "train_shard_00000", "doc_id": 3412 }, "chunk_id": "train_shard_00000_3412_0", "global_id": 3778 }, { "text": "The orange-spotted grouper (OG), Epinephelus coioides, is an ecologically and economically important species with strong market demand. However, larval rearing for this species is especially difficult, with mass mortality occurring at multiple stages including the period coinciding with metamorphic development. The aim of the present study was to characterise the molecular ontogenesis of genes that influence appetite, feeding, and digestion in OG larvae head and body tissue at 12, 18, and 50 days post hatch (dph), which coincides with the beginning and end of metamorphic development. The sequences of many transcripts involved in the regulation of appetite, feeding and digestive processes were detected from 12 dph in OG larvae, including those that were differentially expressed in body tissue in fish at different stages of development such as cholecystokinin, peptide Y, and meprin A. Of the transcripts encoding digestive enzymes, only the expression level of bile salt-activated lipase decreased as development progressed. In contrast, a dramatic increase in expression for other body-expressed transcripts encoding digestive enzymes and a proton pump subunit was observed at 50 dph, which is indicative of an increase in digestive capacity. In addition, we have provided evidence suggesting that various trypsinogen isoforms are present, and have differing expression patterns throughout larval development in whole body tissue. We also report on the presence of a prey-specific transcript encoding α-amylase that was present in the body-transcriptome. Taken together, these results give insight into the processes underpinning attainment of digestive capacity, and form the basis of a new transcriptomic database that will aid further study into the digestive development and dietary requirements of orange-spotted grouper larvae.\n\nA transcriptomic investigation of digestive processes in orange-spotted grouper, Epinephelus coioides, before, during, and after metamorphic development.", "token_count": 474, "char_count": 2000, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5936, "quality_score": 0.7968, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:54.507299", "source": { "split": "train_shard_00000", "doc_id": 3413 }, "chunk_id": "train_shard_00000_3413_0", "global_id": 3779 }, { "text": "Hepatology played an important role in ESPGAN from the beginning. In 1989, the Hepatology Committee was started. In the early 1990s H for hepatology was included in ESPGHAN. Hepatology Summer schools were held from 1995 and later monothematic conferences met the needs of many young ESPGHAN members. The role of ESPGHAN members in the progress of diagnostic and therapeutic measures in hepatitis B and C will be elucidated (Chapter 6.1) as well as the role of other ESPGHAN members in the understanding of immunological hepatic disorders of childhood (Chapter 6.2). During childhood, many metabolic hepatic disorders threaten the life and health of children making orchestrated measures in diagnostic and therapeutic efforts necessary (Chapter 6.3). The pathophysiology of cholestasis was cleared by the detection of bile salt transporters, which were identified by ESPGHAN members in the Netherlands, France, United Kingdom and Germany (Chapter 6.4). Finally liver transplantation for acute fulminant and chronic end stage liver disease was established as a meanwhile standard treatment option (Chapter 6.5). Immunosupression in liver transplantation was improved and standardized through the cooperation of many ESPGHAN member driven studies (Chapter 6.6).\n\nChapter 6.0. History of Paediatric Hepatology in ESPGHAN.", "token_count": 345, "char_count": 1317, "word_count": 192, "semantic_coherence": 1, "information_density": 0.599, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:55.082269", "source": { "split": "train_shard_00000", "doc_id": 3414 }, "chunk_id": "train_shard_00000_3414_0", "global_id": 3780 }, { "text": "The effect of the addition of galactooligosaccharides (GOS) on sterol bioaccessibility in three plant sterol (PS)-enriched milk-based fruit beverages (without GOS addition (MfB) and with 2.5 g (MfB-G2) and 5.0 g (MfB-G5) GOS per 250 mL) was evaluated after micellar gastrointestinal digestion. Cholesterol bioaccessibility was very similar among beverages, though a slight significant increase (from 80% to 85%) was observed by the addition of 5.0 g GOS. The addition of GOS did not affect total PS bioaccessibility (≈37%). Based on the results obtained after micellar digestion, it has been demonstrated that these beverages could be a suitable food matrix for simultaneous enrichment with PS and GOS. The harmonized in vitro digestion model INFOGEST was applied to the MfB beverage, but the cholesterol content could not be quantified due to its contribution of bile salts. Hence, it was proposed: (i) a change in porcine bile salt concentration from 10 mM to 1.4 mM (in order to compare with micellar digestion); or (ii) a change of bile salt origin (bovine instead of porcine), maintaining physiological concentration (10 mM, INFOGEST condition). Both options allowed cholesterol quantification, with bioaccessibilities of 62% (reduction of bile salts) and 38% (replacement of the bile salt source), whereas plant sterol bioaccessibilities were 22% and 14%, respectively. Therefore, the change of bile salt origin maintaining INFOGEST concentration is proposed as a method to evaluate sterol (cholesterol and PS) bioaccessibility in these beverages, demonstrating the need for the selection of appropriate conditions of the INFOGEST harmonized method according to the food matrix and compounds to be determined.\n\nThe impact of galactooligosaccharides on the bioaccessibility of sterols in a plant sterol-enriched beverage: adaptation of the harmonized INFOGEST digestion method.", "token_count": 508, "char_count": 1882, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5612, "quality_score": 0.7806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:55.773103", "source": { "split": "train_shard_00000", "doc_id": 3415 }, "chunk_id": "train_shard_00000_3415_0", "global_id": 3781 }, { "text": "The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria\n\nPangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of", "token_count": 173, "char_count": 797, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:56.250644", "source": { "split": "train_shard_00000", "doc_id": 3416 }, "chunk_id": "train_shard_00000_3416_0", "global_id": 3782 }, { "text": "In December 2013, Public Health England (PHE) observed an increase in the number of cases of Shigella sonnei linked to the Orthodox Jewish Community (OJC). Ultimately, 52 cases of S. sonnei phage type (PT) P and PT7 were notified between November 2013 and July 2014. Whole-genome sequencing (WGS) was performed on a HiSeq 2500 platform (Illumina) on isolates of S. sonnei submitted to PHE during the investigation. Quality trimmed sequence reads were mapped to a reference genome using BWA-MEM, and single-nucleotide polymorphisms (SNPs) were identified using GATK2. Analysis of the core genome SNP positions (>90 % consensus, minimum depth 10×, MQ≥30) revealed that isolates linked to the outbreak could be categorized as members of distinct monophyletic clusters (MPCs) representing concurrent regional outbreaks occurring in the OJCs across the United Kingdom. A dated phylogeny predicted the date of the most recent common ancestor of the MPCs to be approximately 3.1 years previously [95 % highest posterior density (HPD), 2.4-3.4]. Isolates of S. sonnei from cases from the OJCs in Israel included in the phylogeny, branched from nodes basal to the UK OJC outbreak clusters, indicating they were ancestral to the UK OJC isolates, and that the UK isolates represented multiple importations of S. sonnei into the UK population from Israel. The level of discrimination exhibited by WGS facilitated the identification of clusters of isolates within the closely related bacterial populations circulating in the OJC that may be linked to a unique point sources or transmission routes, thus enabling a more appropriate public health response and targeted interventions.\n\nWhole-genome sequencing revealed concurrent outbreaks of shigellosis in the English Orthodox Jewish Community caused by multiple importations of Shigella sonnei from Israel.", "token_count": 483, "char_count": 1843, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6079, "quality_score": 0.804, "entities": { "genes": [ "GATK2", "PT7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:56.928460", "source": { "split": "train_shard_00000", "doc_id": 3417 }, "chunk_id": "train_shard_00000_3417_0", "global_id": 3783 }, { "text": "Treponema pallidum is an uncultivable bacterium and the causative agent of syphilis (subsp. pallidum [TPA]), human yaws (subsp. pertenue [TPE]), and bejel (subsp. endemicum). Several species of nonhuman primates in Africa are infected by treponemes genetically undistinguishable from known human TPE strains. Besides Treponema pallidum, the equally uncultivable Treponema carateum causes pinta in humans. In lagomorphs, Treponema paraluisleporidarum ecovar Cuniculus and ecovar Lepus are the causative agents of rabbit and hare syphilis, respectively. All uncultivable pathogenic treponemes harbor a relatively small chromosome (1.1334-1.1405 Mbp) and show gene synteny with minimal genetic differences (>98% identity at the DNA level) between subspecies and species. While uncultivable pathogenic treponemes contain a highly conserved core genome, there are a number of highly variable and/or recombinant chromosomal loci. This is also reflected in the occurrence of intrastrain heterogeneity (genetic diversity within an infecting bacterial population). Molecular differences at several different chromosomal loci identified among TPA strains or isolates have been used for molecular typing and the epidemiological characterization of syphilis isolates. This review summarizes genome structure of uncultivable pathogenic treponemes including genetically variable regions.\n\nGenetics of human and animal uncultivable treponemal pathogens.", "token_count": 386, "char_count": 1438, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6898, "quality_score": 0.8449, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:57.572290", "source": { "split": "train_shard_00000", "doc_id": 3418 }, "chunk_id": "train_shard_00000_3418_0", "global_id": 3784 }, { "text": "Multi-country outbreaks of foodborne bacterial disease present challenges in their detection, tracking, and notification. As food is increasingly distributed across borders, such outbreaks are becoming more common. This increases the need for high-resolution, accessible, and replicable isolate typing schemes. Here we evaluate a core genome multilocus typing (cgMLST) scheme for the high-resolution reproducible typing of Salmonella enterica (S. enterica) isolates, by its application to a large European outbreak of S. enterica serovar Enteritidis. This outbreak had been extensively characterised using single nucleotide polymorphism (SNP)-based approaches. The cgMLST analysis was congruent with the original SNP-based analysis, the epidemiological data, and whole genome MLST (wgMLST) analysis. Combination of the cgMLST and epidemiological data confirmed that the genetic diversity among the isolates predated the outbreak, and was likely present at the infection source. There was consequently no link between country of isolation and genetic diversity, but the cgMLST clusters were congruent with date of isolation. Furthermore, comparison with publicly available Enteritidis isolate data demonstrated that the cgMLST scheme presented is highly scalable, enabling outbreaks to be contextualised within the Salmonella genus. The cgMLST scheme is therefore shown to be a standardised and scalable typing method, which allows Salmonella outbreaks to be analysed and compared across laboratories and jurisdictions.\n\nComparative analysis of core genome MLST and SNP typing within a European Salmonella serovar Enteritidis outbreak.", "token_count": 366, "char_count": 1634, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8213, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:58.152233", "source": { "split": "train_shard_00000", "doc_id": 3419 }, "chunk_id": "train_shard_00000_3419_0", "global_id": 3785 }, { "text": "Bifidobacterium longum BL-05 encapsulated beads were developed by using whey protein concentrate (WPC) and pectin (PE) as encapsulating material through extrusion/ionic gelation technique with the objective to improve survival of probiotics in harsh gastrointestinal conditions. B. longum BL-05 was grown in MRS (de man rogosa and sharpe) broth, centrifuged and mixed with polymeric gel solution. Bead formulations E\n\nDevelopment of Whey Protein Concentrate-Pectin-Alginate Based Delivery System to Improve Survival of B. longum BL-05 in Simulated Gastrointestinal Conditions.", "token_count": 165, "char_count": 576, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7532, "quality_score": 0.8766, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:58.594068", "source": { "split": "train_shard_00000", "doc_id": 3420 }, "chunk_id": "train_shard_00000_3420_0", "global_id": 3786 }, { "text": "Enterococci, in particular vancomycin-resistant enterococci (VRE), are a leading cause of hospital-acquired infections. Promoting intestinal resistance against enterococci could reduce the risk of VRE infections. We investigated the effects of two Lactobacillus strains to prevent intestinal VRE. We used an intestinal colonisation mouse model based on an antibiotic-induced microbiota dysbiosis to mimic enterococci overgrowth and VRE persistence. Each Lactobacillus spp. was administered daily to mice starting one week before antibiotic treatment until two weeks after antibiotic and VRE inoculation. Of the two strains, Lactobacillus paracasei CNCM I-3689 decreased significantly VRE numbers in the feces demonstrating an improvement of the reduction of VRE. Longitudinal microbiota analysis showed that supplementation with L. paracasei CNCM I-3689 was associated with a better recovery of members of the phylum Bacteroidetes. Bile salt analysis and expression analysis of selected host genes revealed increased level of lithocholate and of ileal expression of camp (human LL-37) upon L. paracasei CNCM I-3689 supplementation. Although a direct effect of L. paracasei CNCM I-3689 on the VRE reduction was not ruled out, our data provide clues to possible anti-VRE mechanisms supporting an indirect anti-VRE effect through the gut microbiota. This work sustains non-antibiotic strategies against opportunistic enterococci after antibiotic-induced dysbiosis.\n\nLactobacillus paracasei CNCM I-3689 reduces vancomycin-resistant Enterococcus persistence and promotes Bacteroidetes resilience in the gut following antibiotic challenge.", "token_count": 444, "char_count": 1633, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6175, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:59.221785", "source": { "split": "train_shard_00000", "doc_id": 3421 }, "chunk_id": "train_shard_00000_3421_0", "global_id": 3787 }, { "text": "Protein denaturation is under intensive research, since it leads to neurological disorders of severe consequences. Avoiding denaturation and stabilizing the proteins in their native state is of great importance, especially when proteins are used as drug molecules or vaccines. It is preferred to add pharmaceutical excipients in protein formulations to avoid denaturation and thereby stabilize them. The present study aimed at using bile salts (BSs), a group of well-known drug delivery systems, for stabilization of proteins. Bovine serum albumin (BSA) was taken as the model protein, whose association with two BSs, namely sodium cholate (NaC) and sodium deoxycholate (NaDC), was studied. Denaturation studies on the pre-formed BSA-BS systems were carried out under chemical and physical denaturation conditions. Urea was used as the chemical denaturant and BSA-BS systems were subjected to various temperature conditions to understand the thermal (physical) denaturation. With the denaturation conditions prescribed here, the data obtained is informative on the association of BSA-BS systems to be hydrophobic and this effect of hydrophobicity plays an important role in stabilizing the serum albumin in its native state under both chemical and thermal denaturation.\n\nDenaturation studies on bovine serum albumin-bile salt system: Bile salt stabilizes bovine serum albumin through hydrophobicity.", "token_count": 325, "char_count": 1399, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6181, "quality_score": 0.809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:32:59.789674", "source": { "split": "train_shard_00000", "doc_id": 3422 }, "chunk_id": "train_shard_00000_3422_0", "global_id": 3788 }, { "text": "Kluyveromyces marxianus protein hydrolysates were prepared by two different sonicated-enzymatic (trypsin and chymotrypsin) hydrolysis treatments to obtain antioxidant and ACE-inhibitory peptides. Trypsin and chymotrypsin hydrolysates obtained by 5 h, exhibited the highest antioxidant and ACE-inhibitory activities. After fractionation using ultrafiltration and reverse phase high performance liquid chromatography (RP-HPLC) techniques, two new peptides were identified. One fragment (LL-9, MW = 1180 Da) with the amino acid sequence of Leu-Pro-Glu-Ser-Val-His-Leu-Asp-Lys showed significant ACE inhibitory activity (IC\n\nProduction of antioxidant and ACE-inhibitory peptides from Kluyveromyces marxianus protein hydrolysates: Purification and molecular docking.", "token_count": 231, "char_count": 761, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7753, "quality_score": 0.8876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:00.257404", "source": { "split": "train_shard_00000", "doc_id": 3423 }, "chunk_id": "train_shard_00000_3423_0", "global_id": 3789 }, { "text": "Lactobacillus plantarum (L. plantarum) K25 is a probiotic strain isolated from Tibetan kefir. Previous studies showed that this exopolysaccharide (EPS)-producing strain was antimicrobial active and cold tolerant. These functional traits were evidenced by complete genome sequencing of strain K25 with a circular 3,175,846-bp chromosome and six circular plasmids, encoding 3365 CDSs, 16 rRNA genes and 70 tRNA genes. Genomic analysis of L. plantarum K25 illustrates that this strain contains the previous reported mechanisms of probiotic functionality and cold tolerance, involving plantaricins, lysozyme, bile salt hydrolase, chaperone proteins, osmoprotectant, oxidoreductase, EPSs and terpenes. Interestingly, strain K25 harbors more genes that function in defense mechanisms, and lipid transport and metabolism, in comparison with other L. plantarum strains reported. The present study demonstrates the comprehensive analysis of genes related to probiotic functionalities of an EPS-producing L. plantarum strain based on whole genome sequencing.\n\nComplete genome sequencing of exopolysaccharide-producing Lactobacillus plantarum K25 provides genetic evidence for the probiotic functionality and cold endurance capacity of the strain.", "token_count": 334, "char_count": 1236, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:00.830404", "source": { "split": "train_shard_00000", "doc_id": 3424 }, "chunk_id": "train_shard_00000_3424_0", "global_id": 3790 }, { "text": "Recent guidelines indicate that oral probiotics, living microorganisms able to confer a health benefit on the host, should be safe for human consumption, when administered in a sufficient amount, and resist acid and bile to exert their beneficial effects (e.g., metabolic, immunomodulatory, anti-inflammatory, competitive). This study evaluated quantitative and qualitative aspects and the viability in simulated gastric and intestinal juices of commercial probiotic formulations available in Italy. Plate counting and MALDI-TOF mass spectrometry were used to enumerate and identify the contained organisms.\n\nCompositional Quality and Potential Gastrointestinal Behavior of Probiotic Products Commercialized in Italy.", "token_count": 163, "char_count": 717, "word_count": 94, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:01.267043", "source": { "split": "train_shard_00000", "doc_id": 3425 }, "chunk_id": "train_shard_00000_3425_0", "global_id": 3791 }, { "text": "The herbal medicine Yin Huang Mixture (YHHJ; patent no. 200910031240.7) is an aqueous extract composed from various herbs, including\n\nEffect of YHHJ on the expression of the hepatocellular bile acid transporters multidrug resistance-associated protein 2 and bile salt export pump in ethinylestradiol-induced cholestasis.", "token_count": 102, "char_count": 320, "word_count": 43, "semantic_coherence": 1, "information_density": 0.907, "quality_score": 0.9535, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:01.650377", "source": { "split": "train_shard_00000", "doc_id": 3426 }, "chunk_id": "train_shard_00000_3426_0", "global_id": 3792 }, { "text": "The human gut microbiome plays a crucial role in human health and efforts need to be done for cultivation and characterisation of bacteria with potential health benefits. Here, we isolated a bacterium from a healthy Indian adult faeces and investigated its potential as probiotic. The cultured bacterial strain 17OM39 was identified as Enterococcus faecium by 16S rRNA gene sequencing. The strain 17OM39 exhibited tolerance to acidic pH, showed antimicrobial activity and displayed strong cell surface traits such as hydrophobicity and autoaggregation capacity. The strain was able to tolerate bile salts and showed bile salt hydrolytic (BSH) activity, exopolysaccharide production and adherence to human HT-29 cell line. Importantly, partial haemolytic activity was detected and the strain was susceptible to the human serum. Genomics investigation of strain 17OM39 revealed the presence of diverse genes encoding for proteolytic enzymes, stress response systems and the ability to produce essential amino acids, vitamins and antimicrobial compound Bacteriocin-A. No virulence factors and plasmids were found in this genome of the strain 17OM39. Collectively, these physiological and genomic features of 17OM39 confirm the potential of this strain as a candidate probiotic.\n\nGenomic and physiological analyses of an indigenous strain, Enterococcus faecium 17OM39.", "token_count": 347, "char_count": 1364, "word_count": 195, "semantic_coherence": 1, "information_density": 0.641, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:02.235601", "source": { "split": "train_shard_00000", "doc_id": 3427 }, "chunk_id": "train_shard_00000_3427_0", "global_id": 3793 }, { "text": "Correction: The importance of membrane microdomains for bile salt-dependent biliary lipid secretion (doi:10.1242/jcs.211524).", "token_count": 45, "char_count": 125, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:02.600154", "source": { "split": "train_shard_00000", "doc_id": 3428 }, "chunk_id": "train_shard_00000_3428_0", "global_id": 3794 }, { "text": "The present study was aimed to examine the interaction of two bile salts viz. sodium cholate (NaC) and sodium deoxycholate (NaDC) with three ethylene polyoxide-polypropylene polyoxide (PEO-PPO-PEO) triblock copolymers with similar PPO but varying PEO micelles with a focus on the effect of pH on mixed micelles. Mixed micelles of moderately hydrophobic Pluronic\n\nPluronic", "token_count": 112, "char_count": 371, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:02.979241", "source": { "split": "train_shard_00000", "doc_id": 3429 }, "chunk_id": "train_shard_00000_3429_0", "global_id": 3795 }, { "text": "Pancreatic adenocarcinomas and diabetes mellitus are responsible for the deaths of around two million people each year worldwide. Patients with chronic pancreatitis do not die directly of this disease, except where the pathology is hereditary. Much current literature supports the involvement of bile salt-dependent lipase (BSDL), also known as carboxyl ester lipase (CEL), in the pathophysiology of these pancreatic diseases. The purpose of this review is to shed light on connections between chronic pancreatitis, diabetes, and pancreatic adenocarcinomas by gaining an insight into BSDL and its variants. This enzyme is normally secreted by the exocrine pancreas, and is diverted within the intestinal lumen to participate in the hydrolysis of dietary lipids. However, BSDL is also expressed by other cells and tissues, where it participates in lipid homeostasis. Variants of BSDL resulting from germline and/or somatic mutations (nucleotide insertion/deletion or nonallelic homologous recombination) are expressed in the pancreas of patients with pancreatic pathologies such as chronic pancreatitis, MODY-8, and pancreatic adenocarcinomas. We discuss the possible link between the expression of BSDL variants and these dramatic pancreatic pathologies, putting forward the suggestion that BSDL and its variants are implicated in the cell lipid metabolism/reprogramming that leads to the dyslipidemia observed in chronic pancreatitis, MODY-8, and pancreatic adenocarcinomas. We also propose potential strategies for translation to therapeutic applications.\n\nPancreatic adenocarcinoma, chronic pancreatitis, and MODY-8 diabetes: is bile salt-dependent lipase (or carboxyl ester lipase) at the crossroads of pancreatic pathologies?", "token_count": 449, "char_count": 1730, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:03.612561", "source": { "split": "train_shard_00000", "doc_id": 3430 }, "chunk_id": "train_shard_00000_3430_0", "global_id": 3796 }, { "text": "The pangenome of Escherichia coli is composed of a conserved core and variable genomic regions. The constant genetic component allows to determine the phylogeny of the microorganism, while genetic variability promoted the emergence of intestinal pathogenic strains and extraintestinal strains. In this study we characterized 85 extraintestinal pathogenic isolates genetically isolated from canines and felines. We used the Clermont scheme that includes intestinal (A and B1) and extraintestinal (B2 and D) phylogroups, virulence markers (pap1-2, pap3-4, sfa, afa, hlyA, aer and cnf) and hybrid pathogens. A percentage of 69.4% of the isolates belonged to phylogroup A; 1.2% to phylogroup B1; 16.5% to phylogroup B2 and 12.9% to phylogroup D. The most commonly found gene was sfa (21/85), followed by pap1-2 and cnf (20/85) and pap3-4 (19/85). No hybrids were detected. Animal isolates should be studied due to the zoonotic potential of the microorganism.\n\n[Characterization of extraintestinal pathogenic Escherichia coli strains isolated from household dogs and cats in Buenos Aires, Argentina].", "token_count": 332, "char_count": 1095, "word_count": 160, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:04.186307", "source": { "split": "train_shard_00000", "doc_id": 3431 }, "chunk_id": "train_shard_00000_3431_0", "global_id": 3797 }, { "text": "The purpose of the present study was to isolate Lactobacillus bacteria from mother's milk and to assess their probiotic potential. Sixty breast milk samples were collected from the volunteered mothers aged from 19 to 35 and from rural areas of Lorestan and Markazi Provinces, Iran. At first, 970 bacill-shaped bacterial colonies were isolated from these samples and stored in proper condition. Two hundred isolates were randomly selected and investigated for their ability to tolerate acidic condition and to tolerate bile salt as well. Only 33 isolates could withstand the exposure to low pH and bile salt. The isolates were identified using PCR primer specific to Lactobacillus and it was demonstrated that eighteen of thirty-three isolates were belonged to the Lactobacillus. Among the isolates, 16 and 2 of them were Lactobacillus reuteri and L. gasseri, respectively. In addition, the antibiotic resistance of the isolates was determined using disc diffusion method and all of the isolates were shown to be sensitive to eight out of the twelve investigated antibiotics. Moreover, the antagonistic effect of the isolates was inspected on ten indicator pathogens. Interestingly, all of the pathogenic bacteria were inhibited by Lactobacillus isolates. In addition, to partially understand the nature of inhibition mechanism, well diffusion deployed for two randomly-selected indicator bacteria and the resulting halos of three isolates were statistically significant compared to other lactobacillus (p < 0.05). Subsequently, bacteriocin genes (plnS, Laf, gasA) were identified by PCR among the isolates. The results showed that only 2 isolates possessed the gasA gene which were in accordance with well diffusion test. Consequently, eighteen Lactobacillus isolated from breast milk samples which all of them were able to tolerate low pH and bile salt. Similarly, all of the Lactobacillus isolates were proved to inhibit the growth of pathogen strains and two of them possess a bacteriocin-related gene.\n\nCharacterization of bacteriocin production in Lactobacillus spp. isolated from mother's milk.", "token_count": 507, "char_count": 2100, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5335, "quality_score": 0.7668, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:04.839537", "source": { "split": "train_shard_00000", "doc_id": 3432 }, "chunk_id": "train_shard_00000_3432_0", "global_id": 3798 }, { "text": "The desideratum aim of the present context was to isolate a promising antagonist probiotic bacterium from fermented food item as biocontrol agent against uropathogens. Among diversified isolates evaluated for antagonistic trait, Staphylococcus succinus strain AAS2 was found to be an auspicious candidate against urinary tract infection (UTI) causing bacterial pathogens, being the most active against Staphylococcus aureus with substantial activity of 352.5 ± 5.4 AU/mL. Further, the in vitro probiotic attributes of strain AAS2 were assessed using systematic methodology. The isolate exhibited tolerance to acidic condition (up to pH 3.0) and simulated gastric juice (at pH 3.0) with fairly high survival logarithmic cell counts of 5.3 ± 0.15 and 5.23 ± 0.02 log cfu/mL, respectively. Additionally, strain AAS2 showed capability to resist 0.5% w/v bile salt too. It also revealed significant values of auto-aggregation (32.5 ± 1.3-56.5 ± 1.4%) and cell surface hydrophobicity (38.35 ± 1.4%) properties. The isolate showed resistivity towards phenol (6.8 ± 0.08 log cfu/mL) and lysozyme (58.6 ± 1.6%). Further, the susceptibility trait of strain AAS2 to conventional antibiotics made this isolate a promising probiotic bacterium. Most importantly, the isolate depicted DPPH (2,2-Diphenyl-1-picrylhydrazyl) and hydroxyl radical scavenging activities in a concentration dependent manner, thereby exhibiting its propitious antioxidative properties. In a nutshell, the outcomes of this investigation divulge the plausible use of S", "token_count": 492, "char_count": 1527, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7005, "quality_score": 0.8502, "entities": { "genes": [ "AAS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:05.488727", "source": { "split": "train_shard_00000", "doc_id": 3433 }, "chunk_id": "train_shard_00000_3433_0", "global_id": 3799 }, { "text": "succinus strain AAS2 as biocontrol agent against uropathogens, and recommended further applications in pharmaceutics due to its pronounced probiotic traits.\n\nAntagonistic trait of Staphylococcus succinus strain AAS2 against uropathogens and assessment of its in vitro probiotic characteristics.", "token_count": 73, "char_count": 294, "word_count": 37, "semantic_coherence": 1, "information_density": 0.7568, "quality_score": 0.8784, "entities": { "genes": [ "AAS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:05.858649", "source": { "split": "train_shard_00000", "doc_id": 3433 }, "chunk_id": "train_shard_00000_3433_1", "global_id": 3800 }, { "text": "Imidazolium ionic liquids (ILs) are promising solvents for lignocellulosic biomass (LCB) pretreatment and allow the achievement of higher ethanolic yields after enzymatic hydrolysis and ethanolic fermentation. However, residual ILs entrapped in pretreated biomass are often toxic for fermentative microorganisms, but interaction mechanisms between ILs and cells are still unknown. Here we studied the effects of 1-ethyl-3-methylimidazolium acetate [Emim][OAc] and 1-ethyl-3-methylimidazolium methylphosphonate [Emim][MeO(H)PO₂] on\n\nKluyveromyces marxianus, an Attractive Yeast for Ethanolic Fermentation in the Presence of Imidazolium Ionic Liquids.", "token_count": 208, "char_count": 649, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7564, "quality_score": 0.8782, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:06.325327", "source": { "split": "train_shard_00000", "doc_id": 3434 }, "chunk_id": "train_shard_00000_3434_0", "global_id": 3801 }, { "text": "Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. This serovar ranks second and third among serovars that cause human infections in Québec and Canada, respectively, and has been associated with severe infections. Traditional typing methods such as PFGE do not display adequate discrimination required to resolve outbreak investigations due to the low level of genetic diversity of isolates belonging to this serovar. This study evaluates the ability of four whole genome sequence (WGS)-based typing methods to differentiate among 145 S. Heidelberg strains involved in four distinct outbreak events and sporadic cases of salmonellosis that occurred in Québec between 2007 and 2016. Isolates from all outbreaks were indistinguishable by PFGE. The core genome single nucleotide variant (SNV), core genome multilocus sequence typing (MLST) and whole genome MLST approaches were highly discriminatory and separated outbreak strains into four distinct phylogenetic clusters that were concordant with the epidemiological data. The clustered regularly interspaced short palindromic repeats (CRISPR) typing method was less discriminatory. However, CRISPR typing may be used as a secondary method to differentiate isolates of S. Heidelberg that are genetically similar but epidemiologically unrelated to outbreak events. WGS-based typing methods provide a highly discriminatory alternative to PFGE for the laboratory investigation of foodborne outbreaks.\n\nComparison of advanced whole genome sequence-based methods to distinguish strains of Salmonella enterica serovar Heidelberg involved in foodborne outbreaks in Québec.", "token_count": 394, "char_count": 1673, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6217, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:06.941901", "source": { "split": "train_shard_00000", "doc_id": 3435 }, "chunk_id": "train_shard_00000_3435_0", "global_id": 3802 }, { "text": "The accuracy of amorphous solubility advantage calculation was evaluated by experimental solubility measurement. Ten structurally diverse compounds were studied to test the generlity of the theoretical calculation. Three reported methods of calculating Gibbs free energy difference between amorphous and crystalline solids were evaluated. Experimental solubility advantage was measured by direct dissolution of amorphous solid in buffer. When necessary, hydroxypropyl methylcellulose acetate succinate (HPMCAS) was predissolved in buffer to inhibit desupersaturation. By direct dissolution, the effect of different preparation methods on amorphous solubility was also studied. Finally, solubility measurement was performed in fasted state simulated intestinal fluid (FaSSIF) to assess the effect of bile salt on the concentration-based amorphous solubility advantage. The results showed that the assumption of constant heat capacity differences between crystal and supercooled liquid or amorphous solid is sufficient for accurate theoretical calculation, which is attributed to the fact that the heat capacity of crystal is nearly parallel to that of supercooled liquid or amorphous solid. Different preparation methods do not have significant impact on amorphous solubility advantage. Experimental measurement agrees with the theoretical calculation within a factor of 0.7 to 1.8. The concentration-based amorphous solubility advantage in FaSSIF agrees well with theoretical calculation. This work demonstrates that theoretical calculation of amorphous solubility advantage is robust and can be applied in early drug development for assessing the utility of the amorphous phase.\n\nEvaluation of Accuracy of Amorphous Solubility Advantage Calculation by Comparison with Experimental Solubility Measurement in Buffer and Biorelevant Media.", "token_count": 386, "char_count": 1837, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5267, "quality_score": 0.7634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:07.576365", "source": { "split": "train_shard_00000", "doc_id": 3436 }, "chunk_id": "train_shard_00000_3436_0", "global_id": 3803 }, { "text": "Excess copper is highly toxic and forms part of the host innate immune system's antibacterial arsenal, accumulating at sites of infection and acting within macrophages to kill engulfed pathogens. We show for the first time that a novel, horizontally gene transferred copper resistance locus (copXL), uniquely associated with the SCCmec elements of the highly virulent, epidemic, community acquired methicillin resistant Staphylococcus aureus (CA-MRSA) USA300, confers copper hyper-resistance. These genes are additional to existing core genome copper resistance mechanisms, and are not found in typical S. aureus lineages, but are increasingly identified in emerging pathogenic isolates. Our data show that CopX, a putative P\n\nA horizontally gene transferred copper resistance locus confers hyper-resistance to antibacterial copper toxicity and enables survival of community acquired methicillin resistant Staphylococcus aureus USA300 in macrophages.", "token_count": 229, "char_count": 950, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6899, "quality_score": 0.845, "entities": { "genes": [ "USA300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:08.078703", "source": { "split": "train_shard_00000", "doc_id": 3437 }, "chunk_id": "train_shard_00000_3437_0", "global_id": 3804 }, { "text": "Large-scale microbiome studies have established that most of the diversity contained in the gastrointestinal tract is represented at the strain level; however, exhaustive genomic and physiological characterization of human isolates is still lacking. With increased use of probiotics as interventions for gastrointestinal disorders, genomic and functional characterization of novel microorganisms becomes essential. In this study, we explored the impact of strain-level genomic variability on bacterial physiology of two novel human\n\nIntra-species Genomic and Physiological Variability Impact Stress Resistance in Strains of Probiotic Potential.", "token_count": 138, "char_count": 644, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7108, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:08.519478", "source": { "split": "train_shard_00000", "doc_id": 3438 }, "chunk_id": "train_shard_00000_3438_0", "global_id": 3805 }, { "text": "Bacterial plasmids can vary from small selfish genetic elements to large autonomous replicons that constitute a significant proportion of total cellular DNA. By conferring novel function to the cell, plasmids may facilitate evolution but their mobility may be opposed by co-evolutionary relationships with chromosomes or encouraged via the infectious sharing of genes encoding public goods. Here, we explore these hypotheses through large-scale examination of the association between plasmids and chromosomal DNA in the phenotypically diverse Bacillus cereus group. This complex group is rich in plasmids, many of which encode essential virulence factors (Cry toxins) that are known public goods. We characterized population genomic structure, gene content and plasmid distribution to investigate the role of mobile elements in diversification. We analysed coding sequence within the core and accessory genome of 190 B. cereus group isolates, including 23 novel sequences and genes from 410 reference plasmid genomes. While cry genes were widely distributed, those with invertebrate toxicity were predominantly associated with one sequence cluster (clade 2) and phenotypically defined Bacillus thuringiensis. Cry toxin plasmids in clade 2 showed evidence of recent horizontal transfer and variable gene content, a pattern of plasmid segregation consistent with transfer during infectious cooperation. Nevertheless, comparison between clades suggests that co-evolutionary interactions may drive association between plasmids and chromosomes and limit wider transfer of key virulence traits. Proliferation of successful plasmid and chromosome combinations is a feature of specialized pathogens with characteristic niches (Bacillus anthracis, B. thuringiensis) and has occurred multiple times in the B. cereus group.\n\nLineage-specific plasmid acquisition and the evolution of specialized pathogens in Bacillus thuringiensis and the Bacillus cereus group.", "token_count": 436, "char_count": 1950, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6466, "quality_score": 0.8233, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:09.194445", "source": { "split": "train_shard_00000", "doc_id": 3439 }, "chunk_id": "train_shard_00000_3439_0", "global_id": 3806 }, { "text": "Increase of undigested complexes of phytic acid in food is gaining serious attention to overcome nutritional challenges due to chelation effects. We investigated soil-borne yeast phytase from Saccharomyces cerevisiae (NCIM 3662) for dephytinization of foods, probiotic properties, and process development. The strain produced 45 IU/DCG by cell-bound phytase in an unoptimized medium was increased fourfold (164 IU/DCG) in 12 h using statistical media optimization. The process was scaled-up up to 10-L fermenter scale with increased phytase productivity of 6.4 IU/DCG/h as compared to the lab scale. The strain displayed probiotic characteristics like tolerance to artificial gastric acid conditions, hydrophobicity, autoaggregation, coaggregation, and bile salt hydrolase (BSH) activity. Further, it could dephytinize (removal of phytic acid; an anti-nutritional factor) functional foods like ragi (finger millet) flour, soya flour, chickpea flour, and poultry animal feed. A combination of cell-bound dephytinizing phytase and nutrition-ameliorating probiotic traits of S. cerevisiae (NCIM 3662) presents profound applications in food technology sector.\n\nDephytinizing and Probiotic Potentials of Saccharomyces cerevisiae (NCIM 3662) Strain for Amelioration of Nutritional Quality of Functional Foods.", "token_count": 368, "char_count": 1303, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6936, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:09.790461", "source": { "split": "train_shard_00000", "doc_id": 3440 }, "chunk_id": "train_shard_00000_3440_0", "global_id": 3807 }, { "text": "The bile salt export pump (BSEP) plays an important role in biliary secretion. Mutations in ABCB11, the gene encoding BSEP, induce progressive familial intrahepatic cholestasis type 2 (PFIC2), which presents with severe jaundice and liver dysfunction. A less severe phenotype, called benign recurrent intrahepatic cholestasis type 2, is also known. About 200 missense mutations in ABCB11 have been reported. However, the phenotype-genotype correlation has not been clarified. Furthermore, the frequencies of ABCB11 mutations differ between Asian and European populations. We report a patient with PFIC2 carrying a homozygous ABCB11 mutation c.386G>A (p.C129Y) that is most frequently reported in Japan. The pathogenicity of BSEP\n\nClinical phenotype and molecular analysis of a homozygous ABCB11 mutation responsible for progressive infantile cholestasis.", "token_count": 238, "char_count": 854, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7542, "quality_score": 0.8771, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:10.270351", "source": { "split": "train_shard_00000", "doc_id": 3441 }, "chunk_id": "train_shard_00000_3441_0", "global_id": 3808 }, { "text": "Few studies have used molecular epidemiological methods to study transmission links to clinical isolates in intensive care units. Ninety-four multidrug-resistant organisms (MDROs) cultured from routine specimens from intensive care unit (ICU) patients over 13 weeks were stored (11 meticillin-resistant Staphylococcus aureus (MRSA), two vancomycin-resistant enterococci and 81 Gram-negative bacteria). Medical staff personal mobile phones, departmental phones, and ICU keyboards were swabbed and cultured for MDROs; MRSA was isolated from two phones. Environmental and patient isolates of the same genus were selected for whole genome sequencing. On whole genome sequencing, the mobile phone isolates had a pairwise single nucleotide polymorphism (SNP) distance of 183. However, >15,000 core genome SNPs separated the mobile phone and clinical isolates. In a low-endemic setting, mobile phones and keyboards appear unlikely to contribute to hospital-acquired MDROs.\n\nMobile phones and computer keyboards: unlikely reservoirs of multidrug-resistant organisms in the tertiary intensive care unit.", "token_count": 279, "char_count": 1094, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6918, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:10.825818", "source": { "split": "train_shard_00000", "doc_id": 3442 }, "chunk_id": "train_shard_00000_3442_0", "global_id": 3809 }, { "text": "There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.\n\nGenomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages.", "token_count": 351, "char_count": 1625, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:11.425094", "source": { "split": "train_shard_00000", "doc_id": 3443 }, "chunk_id": "train_shard_00000_3443_0", "global_id": 3810 }, { "text": "Pyruvate decarboxylase (Pdc) is a cytosolic enzyme located at the branch point between fermentative and respiratory sugar catabolism. Here, we identified and functionally characterized KmPDC1 and KmPDC5 encoding two homologs of Pdc in the thermotolerant yeast Kluyveromyces marxianus KCTC 17555. Despite the conservation of important Pdc domains, a few amino acid sequences essential for enzymatic activity are not conserved in KmPdc5p. Deletion of KmPDC1 alone eliminated most of Pdc activity, but the growth of the Kmpdc1Δ strain on glucose was comparable to that of the wild type (WT) strain under aerobic conditions. In contrast to the WT, Kmpdc1Δ could not grow on glucose under oxygen-limited conditions. The KmPDC5 deletion did not generate any apparent change in Pdc activity or growth patterns under several tested conditions. Whereas the expression of KmPDC1 was enhanced by glucose, the basic expression levels of KmPDC5 were very low, without a detectable difference between glucose and nonfermentable carbon sources. Moreover, KmPDC5 overexpression was unable to complement the growth defect of Kmpdc1Δ in the presence of antimycin A, and the purified recombinant KmPdc5p was inactive in Pdc activity assay, supporting the notion that KmPdc5p may lack Pdc enzymatic activity. Notably, compared to the WT, Kmpdc1Δ single and Kmpdc1Δpdc5Δ double mutants produced significantly less glycerol, acetate, and ethanol while accumulating pyruvate. Altogether, our data indicate that a single deletion of KmPDC1 is sufficient in Crabtree-negative K. marxianus strains to generate a starting host strain for engineering of production of high-value biomaterials derived from pyruvate without byproduct formation.\n\nMolecular and functional characterization of two pyruvate decarboxylase genes, PDC1 and PDC5, in the thermotolerant yeast Kluyveromyces marxianus.", "token_count": 513, "char_count": 1862, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6067, "quality_score": 0.8034, "entities": { "genes": [ "PDC1", "PDC5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:33:12.078544", "source": { "split": "train_shard_00000", "doc_id": 3444 }, "chunk_id": "train_shard_00000_3444_0", "global_id": 3811 }, { "text": "This study aimed to analyze the bile acid patterns in commercially available oxgall powders used for evaluation of the bile tolerance ability of probiotic bacteria. Qxgall powders purchased from Sigma-Aldrich, Oxoid and BD Difco were dissolved in distilled water, and analyzed. Conjugated bile acids were profiled by ion-pair high-performance liquid chromatography (HPLC), free bile acids were detected as their p-bromophenacyl ester derivatives using reversed-phase HPLC after extraction with acetic ether, and total bile acids were analyzed by enzymatic-colorimetric assay. The results showed that 9 individual bile acids (i.e., taurocholic acid, glycocholic acid, taurodeoxycholic acid, glycodeoxycholic acid, taurochenodeoxycholic acid, glycochenodeoxycholic acid, cholic acid, chenodeoxycholic acid, deoxycholic acid) were present in each of the oxgall powders tested. The content of total bile acid among the three oxgall powders was similar; however, the relative contents of the individual bile acids among these oxgall powders were significantly different (P < 0.001). The oxgall powder from Sigma-Aldrich was closer to human bile in the ratios of glycine-conjugated bile acids to taurine-conjugated bile acids, dihydroxy bile acids to trihydroxy bile acids, and free bile acids to conjugated bile acids than the other powders were. It was concluded that the oxgall powder from Sigma-Aldrich should be used instead of those from Oxoid and BD Difco to evaluate the bile tolerance ability of probiotic bacteria as human bile model.\n\nBile acid patterns in commercially available oxgall powders used for the evaluation of the bile tolerance ability of potential probiotics.", "token_count": 473, "char_count": 1678, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5021, "quality_score": 0.751, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:12.721043", "source": { "split": "train_shard_00000", "doc_id": 3445 }, "chunk_id": "train_shard_00000_3445_0", "global_id": 3812 }, { "text": "Fifteen cases of Shiga toxin-producing Escherichia coli (STEC) O157 infection were associated with the consumption of contaminated food from two related butchers' premises in the north-east of England. Ten cases were admitted to hospital and seven cases developed haemolytic uraemic syndrome. A case control study found a statistically significant association with the purchase of raw and/or ready-to-eat (RTE) food supplied by the implicated butchers' shops. Isolates of STEC O157 were detected in two raw lamb burgers taken from one of the butchers' premises. Subsequent environmental sampling identified STEC O157 in bovine faecal samples on the farm supplying cattle to the implicated butchers for slaughter. Whole genome sequencing (WGS) was performed on the Illumina HiSeq 2500 platform on all cultures isolated from humans, food and cattle during the investigation. Quality trimmed Illumina reads were mapped to the STEC O157 reference genome Sakai using bwa-mem, and single nucleotide polymorphisms (SNPs) were identified using gatk2. Analysis of the core genome SNP positions (>90 % consensus, minimum depth 10×, mapping quality (MQ)≥30) revealed that all isolates from humans, food and cattle differed by two SNPs. WGS analysis provided forensic-level microbiological evidence to support the epidemiological links between the farm, the butchers' premises and the clinical cases. Cross-contamination from raw meat to RTE foods at the butchers' premises was the most plausible transmission route. The evidence presented here highlights the importance of taking measures to mitigate the risks of cross-contamination in this setting.\n\nFarm-to-fork investigation of an outbreak of Shiga toxin-producing Escherichia coli O157.", "token_count": 449, "char_count": 1730, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:13.364770", "source": { "split": "train_shard_00000", "doc_id": 3446 }, "chunk_id": "train_shard_00000_3446_0", "global_id": 3813 }, { "text": "Black tea is a highly popular beverage, and its pigments, polymerized catechins such as theaflavins (TFs), are attracting attention due to their beneficial health effects. In this study, to test the inhibitory activities of TFs on the intestinal absorption of cholesterol, we investigated their effects on phosphatidylcholine (PC) vesicles in the absence or presence of a bile salt. (-)-Epicatechin gallate, (-)-epigallocatechin gallate, and TFs formed insoluble complexes with PC vesicles. Galloylated TFs such as TF2A, TF2B, and TF3 precipitated far more than other polyphenols. The subsequent addition of taurocholate redispersed the polyphenol-PC complexes, except that a large amount of TF2A remained insoluble. After incubation with taurocholate-PC micelles, TF2A elevated the turbidity of the micelle solution, providing red sediments. The TF2A-specific effect was dependent on the PC concentration. These results suggest that TF2A interacts with PC and aggregates in a specific manner different from catechins and other TFs.\n\nTheaflavin-3-gallate specifically interacts with phosphatidylcholine, forming a precipitate resistant against the detergent action of bile salt.", "token_count": 320, "char_count": 1178, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7117, "quality_score": 0.8558, "entities": { "genes": [ "TF2A", "TF2B", "TF3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:13.936120", "source": { "split": "train_shard_00000", "doc_id": 3447 }, "chunk_id": "train_shard_00000_3447_0", "global_id": 3814 }, { "text": "Bacteria within the genus Alcaligenes, exhibit diverse properties but remain largely unexplored at genome scale. To shed light on the genome structure, heterogeneity and traits of Alcaligenes species, the genome of a tannery effluent isolated Alcaligenes faecalis subsp. phenolicus MB207 was sequenced and assembled. The genome was compared to the whole genome sequences of genus Alcaligenes present in the National Centre for Biotechnology Information database. Core, pan and species specific gene sequences i.e. singletons were identified. Members of this genus did not portray exceptional genetic heterogeneity or conservation and out of 5,166 protein coding genes from pooled genome dataset, 2429 (47.01%) contributed to the core, 1193 (23.09%) to singletons and 1544 (29.88%) to accessory genome. Secondary metabolite forming apparatus, antibiotic production and resistance was also profiled. Alcaligenes faecalis subsp. phenolicus MB207 genome consisted of a copious amount of bioremediation genes i.e. metal tolerance and xenobiotic degrading genes. This study marks this strain as a prospective eco-friendly bacterium with numerous benefits for the environment related research. Availability of the whole genome sequence heralds an opportunity for researchers to explore enzymes and apparatus for sustainable environmental clean-up as well as important compounds/substance production.\n\nGenome sequencing and analysis of Alcaligenes faecalis subsp. phenolicus MB207.", "token_count": 374, "char_count": 1473, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8308, "entities": { "genes": [ "MB207" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:14.527546", "source": { "split": "train_shard_00000", "doc_id": 3448 }, "chunk_id": "train_shard_00000_3448_0", "global_id": 3815 }, { "text": "Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Western Australia (WA). Unlike isolates from the major Australian population centres, the remote community isolates have low rates of antimicrobial resistance (AMR). Population structure and whole-genome comparison of 59 isolates from the Western Australian N. gonorrhoeae collection were used to investigate relatedness of isolates cultured in the metropolitan and remote areas. Core genome phylogeny, multilocus sequencing typing (MLST), N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) in addition to hierarchical clustering of sequences were used to characterize the isolates.\n\nGenomic epidemiology and population structure of Neisseria gonorrhoeae from remote highly endemic Western Australian populations.", "token_count": 244, "char_count": 997, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:15.009832", "source": { "split": "train_shard_00000", "doc_id": 3449 }, "chunk_id": "train_shard_00000_3449_0", "global_id": 3816 }, { "text": "Membrane fatty acid composition has an important role in yeast stress resistance, particularly in temperature tolerance. Most studies investigating temperature and membrane fatty acids use the yeast Saccharomyces cerevisiae without considering other yeasts, such as Kluyveromyces marxianus, which has physiological differences and industrial advantages with respect to S. cerevisiae. One of the primary traits of K. marxianus is its thermotolerance. The effect of fatty acid addition (oleic acid, linoleic acid, linolenic acid and araquidic acid) on the thermotolerance of the K. marxianus strain SLP1 was evaluated. SLP1 yeast exhibited temperature tolerance of up to 50°C; at 55°C, viability was reduced significantly, probably due to an increase in the generation of reactive oxygen chemical species. Externally added fatty acids were incorporated in the yeast membrane, increasing their proportion to approximately 70%, thereby changing membrane fluidity. SLP1 cells supplemented with polyunsaturated fatty acids decreased cell thermotolerance and increased the degree of lipoperoxidation, while arachidic acid addition exhibited a tendency to increase yeast thermotolerance.\n\nFatty acid addition and thermotolerance of Kluyveromyces marxianus.", "token_count": 306, "char_count": 1248, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8195, "entities": { "genes": [ "SLP1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:15.576853", "source": { "split": "train_shard_00000", "doc_id": 3450 }, "chunk_id": "train_shard_00000_3450_0", "global_id": 3817 }, { "text": "Several divalent minerals, including the macroelements calcium and magnesium, are essential nutrients for humans. However, their intake, especially via high-dose supplements, has been suspected to reduce the availability of lipophilic dietary constituents, including lipids, liposoluble vitamins, and several phytochemicals such as carotenoids. These constituents require emulsification in order to be bioavailable, and high divalent mineral concentrations may perturb this process, due to precipitations of free fatty acids or bile salt complexation, both pivotal for mixed micelle formation. Though in part based on in vitro or indirect evidence, it appears likely that high-dose supplements of divalent minerals around or even below their recommended dietary allowance perturb the availability of certain liposoluble miroconstituents, in addition to reducing absorption of dietary lipids/cholesterol. In this review, we investigate possible negative influences of divalent minerals, including trace elements (iron, zinc), on the digestion and intestinal uptake of lipophilic dietary constituents, with a focus on carotenoids.\n\nInteraction of divalent minerals with liposoluble nutrients and phytochemicals during digestion and influences on their bioavailability - a review.", "token_count": 303, "char_count": 1277, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:16.487388", "source": { "split": "train_shard_00000", "doc_id": 3451 }, "chunk_id": "train_shard_00000_3451_0", "global_id": 3818 }, { "text": "In this article, we have unveiled the aggregation behavior of a potent chemotherapeutic drug, doxorubicin hydrochloride (Dox) in a well-known imidazolium based surface active ionic liquid (SAIL), 1-octyl-3-methylimidazolium chloride (C\n\nUnveiling the Aggregation Behavior of Doxorubicin Hydrochloride in Aqueous Solution of 1-Octyl-3-methylimidazolium Chloride and the Effect of Bile Salt on These Aggregates: A Microscopic Study.", "token_count": 145, "char_count": 430, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:16.920579", "source": { "split": "train_shard_00000", "doc_id": 3452 }, "chunk_id": "train_shard_00000_3452_0", "global_id": 3819 }, { "text": "Bile Salt Hydrolase Activities: A Novel Target to Screen Anti-", "token_count": 18, "char_count": 62, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:17.277389", "source": { "split": "train_shard_00000", "doc_id": 3453 }, "chunk_id": "train_shard_00000_3453_0", "global_id": 3820 }, { "text": "Chronic airway infections with Pseudomonas aeruginosa determine morbidity in most individuals with cystic fibrosis (CF). P. aeruginosa may persist for decades in CF lungs, which provides a rare opportunity to study the long-term within-host evolution of a bacterial airway pathogen. In this work, we sought to resolve the genetic adaptation of P. aeruginosa in CF lungs from the onset of colonization until the patient's death or permanent replacement by another P. aeruginosa clone. We followed the microevolution of the first persisting P. aeruginosa clone by whole-genome sequencing of serial isolates from highly divergent clinical courses of airway infection, i.e., a fatal outcome because of respiratory insufficiency within less than 15 years, or a rather normal daily life 25-35 years after acquisition of P. aeruginosa. Nonneutral mutations predominantly emerged in P. aeruginosa genes relevant for protection against and communication with signals from the lung environment, i.e., antibiotic resistance, cell wall components, and two-component systems. Drastic and loss-of-function mutations preferentially happened during the severe courses of infection, and the bacterial lineages of the mild courses more proficiently incorporated extra metabolic genes into their accessory genome. P. aeruginosa followed different evolutionary paths depending on whether the bacterium had taken up residence in a patient with CF and normal or already compromised lung function.\n\nLong-Term Microevolution of Pseudomonas aeruginosa Differs between Mildly and Severely Affected Cystic Fibrosis Lungs.", "token_count": 366, "char_count": 1594, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:17.851567", "source": { "split": "train_shard_00000", "doc_id": 3454 }, "chunk_id": "train_shard_00000_3454_0", "global_id": 3821 }, { "text": "The bile salt export pump (BSEP) is expressed at the canalicular domain of hepatocytes, where it mediates the elimination of monovalent bile salts into the bile. Inhibition of BSEP is considered a susceptibility factor for drug-induced liver injury that often goes undetected during nonclinical testing. Although in vitro assays exist for screening BSEP inhibition, a reliable and specific method for confirming Bsep inhibition in vivo would be a valuable follow up to a BSEP screening strategy, helping to put a translatable context around in vitro inhibition data, incorporating processes such as metabolism, protein binding, and other exposure properties that are lacking in most in vitro BSEP models. Here, we describe studies in which methods of quantitative intravital microscopy were used to identify dose-dependent effects of two known BSEP/Bsep inhibitors, 2-[4-[4-(butylcarbamoyl)-2-[(2,4-dichlorophenyl)sulfonylamino]phenoxy]-3-methoxyphenyl]acetic acid (AMG-009) and bosentan, on hepatocellular transport of the fluorescent bile salts cholylglycyl amidofluorescein and cholyl-lysyl-fluorescein in rats. Results of these studies demonstrate that the intravital microscopy approach is capable of detecting Bsep inhibition at drug doses well below those found to increase serum bile acid levels, and also indicate that basolateral efflux transporters play a significant role in preventing cytosolic accumulation of bile acids under conditions of Bsep inhibition in rats. Studies of this kind can both improve our understanding of exposures needed to inhibit Bsep in vivo and provide unique insights into drug effects in ways that can improve our ability interpret animal studies for the prediction of human drug hepatotoxicity.\n\nIntravital Multiphoton Microscopy with Fluorescent Bile Salts in Rats as an In Vivo Biomarker for Hepatobiliary Transport Inhibition.", "token_count": 491, "char_count": 1871, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:18.506115", "source": { "split": "train_shard_00000", "doc_id": 3455 }, "chunk_id": "train_shard_00000_3455_0", "global_id": 3822 }, { "text": "The territory of Siberia and the Far East of Russia is classified as epidemically safe for cholera; however, in the 1970s and 1990s a number of infection importation cases and acute outbreaks associated with the cholera importation were reported. Here, we analyze genomes of four Vibrio cholerae El Tor strains isolated from humans during epidemic complications (imported cases, an outbreak) in the 1990s. The analyzed strains harbor the classical allele of the cholera toxin subunit B gene (ctxB1); thus, belong to genetically altered variants of the El Tor biotype. Analysis of the genomes revealed their high homology with the V. cholerae N16961 reference strain: 85-93 SNPs were identified in the core genome as compared to the reference. The determined features of SNPs in the CTX prophage made it possible to propose the presence of a new subtype - CTX-2a in two strains; the other two strains carried the prophage of CTX-3 type. Results of phylogenetic analysis based on SNP-typing demonstrated that two strains belonged to the second wave, and two - to the early third wave of cholera dissemination in the world. Phylogenetic reconstruction in combination with epidemiological data permitted to trace the origin of the strains and the way of their importation to the Russian Federation directly or through temporary cholera foci.\n\nComparative genomics of Vibrio cholerae El Tor strains isolated at epidemic complications in Siberia and at the Far East.", "token_count": 375, "char_count": 1460, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5905, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:19.084449", "source": { "split": "train_shard_00000", "doc_id": 3456 }, "chunk_id": "train_shard_00000_3456_0", "global_id": 3823 }, { "text": "Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and\n\nComparative Genomics of Completely Sequenced", "token_count": 96, "char_count": 459, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8254, "quality_score": 0.9127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:19.469452", "source": { "split": "train_shard_00000", "doc_id": 3457 }, "chunk_id": "train_shard_00000_3457_0", "global_id": 3824 }, { "text": "The aims of this study are to isolate new bacteriocinogenic lactic acid bacterial strains from white (Penaeus vannamei) and pink (Palaemon serratus) raw shrimps and evaluate their technological and probiotic potentialities. Seven strains were selected, among fifty active isolates, as producing interesting antimicrobial activity. Identified as Enterococcus lactis, these isolates were able to produce enterocins A, B and/or P. The safety aspect, assessed by microbiological and molecular tests, demonstrated that the strains were susceptible to relevant antibiotics such as vancomycin, negative for haemolysin and gelatinase activities, and did not harbour virulence and antibiotic resistance genes. The assessment of potential probiotic and technological properties showed a low or no lipolytic activity, moderate milk-acidifying ability, high reducing power, proteolytic activity and tolerance to bile (P < 0.05) and good autoaggregation and coaggregation capacities. Two strains designated as CQ and C43 exhibiting high enzymatic activities and bile salt hydrolase activity were found to display high survival under simulated in vitro oral cavity and gastrointestinal tract conditions caused by presence of lysozyme, pepsin, pancreatin, bile salts and acidic pH. This study highlights safe Enterococcus lactis strains with great technological and probiotic potentials for future application as new starter, adjunct, protective or probiotic cultures in food industry.\n\nSafety, potential biotechnological and probiotic properties of bacteriocinogenic Enterococcus lactis strains isolated from raw shrimps.", "token_count": 399, "char_count": 1607, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7051, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:20.106913", "source": { "split": "train_shard_00000", "doc_id": 3458 }, "chunk_id": "train_shard_00000_3458_0", "global_id": 3825 }, { "text": "Lignocellulosic biomass belongs to main sustainable renewable sources for global energy supply. One of the main challenges in the conversion of saccharified lignocellulosic biomass into bioethanol is the utilization of xylose, since lignocellulosic feedstocks contain a significant amount of this pentose. The non-conventional thermotolerant yeast Ogataea polymorpha naturally ferments xylose to ethanol at elevated temperatures (45°C). Studying the molecular mechanisms of regulation of xylose metabolism is a promising way toward increased xylose conversion to ethanol. Insertional mutagenesis was applied to yeast O. polymorpha to identify genes involved in regulation of xylose fermentation. An insertional mutant selected as 3-bromopyruvate resistant strain possessed 50% increase in ethanol production as compared to the parental strain. Increase in ethanol production was caused by disruption of an autophagy-related gene ATG13. Involvement of Atg13 in regulation of xylose fermentation was confirmed by deletion of that gene. The atg13Δ strain also produced an elevated amount of ethanol from xylose. Insertion in ATG13 gene did not disrupt HORMA domain and did not lead to defects in autophagy whereas knock out of this gene impaired autophagy process. We suggest that Atg13 plays two different functions and its role in regulation of xylose fermentation differs from that in autophagy.\n\nAutophagy-related gene ATG13 is involved in control of xylose alcoholic fermentation in the thermotolerant methylotrophic yeast Ogataea polymorpha.", "token_count": 402, "char_count": 1544, "word_count": 217, "semantic_coherence": 1, "information_density": 0.576, "quality_score": 0.788, "entities": { "genes": [ "ATG13" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:20.749538", "source": { "split": "train_shard_00000", "doc_id": 3459 }, "chunk_id": "train_shard_00000_3459_0", "global_id": 3826 }, { "text": "During middle age, women are less susceptible to nonalcoholic steatohepatitis (NASH) than men. Thus, we investigated the underlying molecular mechanisms behind these sexual differences using an established rat model of NASH. Mature female and male stroke-prone spontaneously hypertensive 5/Dmcr rats were fed control or high-fat-cholesterol (HFC) diets for 2, 8, and 14 weeks. Although HFC-induced hepatic fibrosis was markedly less severe in females than in males, only minor gender differences were observed in expression levels of cytochrome P450 enzymes (CYP)7A1, CYP8B1 CYP27A1, and CYP7B1, and multidrug resistance-associated protein 3, and bile salt export pump, which are involved in fibrosis-related bile acid (BA) kinetics. However, the BA detoxification-related enzymes UDP-glucuronosyltransferase (UGT) and sulfotransferase (SULT) 2A1, and the nuclear receptors constitutive androstane receptor (CAR) and pregnane X receptor (PXR), were strongly suppressed in HFC-fed males, and were only slightly changed in HFC-diet fed females. Expression levels of the farnesoid X receptor and its small heterodimer partner were similarly regulated in a gender-dependent fashion following HFC feeding. Hence, the pronounced female resistance to HFC-induced liver damage likely reflects sustained expression of the nuclear receptors CAR and PXR and the BA detoxification enzymes UGT and SULT.\n\nBile acid detoxifying enzymes limit susceptibility to liver fibrosis in female SHRSP5/Dmcr rats fed with a high-fat-cholesterol diet.", "token_count": 429, "char_count": 1525, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [ "SHRSP5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:21.412710", "source": { "split": "train_shard_00000", "doc_id": 3460 }, "chunk_id": "train_shard_00000_3460_0", "global_id": 3827 }, { "text": "Membrane separation systems represent a hot - spot for biofilm formation in juice industries. Sodium hypochlorite (NaOCl) has been traditionally the disinfectant of choice; however, its effectiveness over well-established biofilms is limited. In this work the study of biofilm formation on ultrafiltration membranes was proposed. The effectiveness of cleaning and disinfection procedures commonly used in juice industry was tested on the removal and killing of cells. The species used (Rhodotorula mucilaginosa, Candida krusei, Candida kefyr and Candida tropicalis) were isolated from ultrafiltration modules of a clarified apple juice industry. Industrial concentrations of NaOCl (200mgCL∙L\n\nDisinfection efficacy over yeast biofilms of juice processing industries.", "token_count": 185, "char_count": 766, "word_count": 103, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:21.870518", "source": { "split": "train_shard_00000", "doc_id": 3461 }, "chunk_id": "train_shard_00000_3461_0", "global_id": 3828 }, { "text": "Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated.\n\nGenomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease.", "token_count": 101, "char_count": 400, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:22.246905", "source": { "split": "train_shard_00000", "doc_id": 3462 }, "chunk_id": "train_shard_00000_3462_0", "global_id": 3829 }, { "text": "Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a\n\nLinking pangenomes and metagenomes: the", "token_count": 165, "char_count": 860, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7652, "quality_score": 0.8826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:22.694367", "source": { "split": "train_shard_00000", "doc_id": 3463 }, "chunk_id": "train_shard_00000_3463_0", "global_id": 3830 }, { "text": "Background and Summary: Traditionally, functional gastrointestinal disorders (FGID), including functional dyspepsia or irritable bowel syndrome (IBS), are defined by more or less specific symptoms and the absence of structural or biochemical abnormalities that cause these symptoms. This concept is now considered to be outdated; if appropriate tests are applied, structural or biochemical abnormalities that explain or cause the symptoms may be found in many patients. Another feature of FGID are the highly prevalent psychiatric comorbidities, such as depression and anxiety. It is implied that mood disorders \"cause\" gastrointestinal symptoms. In fact, epidemiological data now provide strong evidence that in subsets of cases, gastrointestinal (GI) symptoms arise first and mood disorders occur later, while in other patients the reverse appears to happen. Possible mechanisms for gut-brain dysfunction have been identified, with systemic minimal inflammation as a causal factor in at least some subjects. Other mechanisms that play a role in FGID include chronic infections, intestinal microbiota, low-grade mucosal inflammation including the increase of eosinophils, systemic immune activation, altered intestinal permeability, in diarrhea predominant IBS altered bile salt metabolism, abnormalities in the serotonin metabolism and genetic factors. All these factors might be modulated by environmental factors such as diet. Key Messages: While a number of factors can be linked to specific symptoms (e.g., pain or diarrhea), it is evident that the symptom-based categorization of patients will not allow targeted treatments that specifically address the underlying pathophysiology.\n\nPathophysiology of Functional Gastrointestinal Disorders: A Holistic Overview.", "token_count": 398, "char_count": 1768, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6529, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:23.309063", "source": { "split": "train_shard_00000", "doc_id": 3464 }, "chunk_id": "train_shard_00000_3464_0", "global_id": 3831 }, { "text": "Alternative models explaining the biliary lipid secretion at the canalicular membrane of hepatocytes exist: successive lipid extraction by preformed bile salt micelles, or budding of membrane fragments with formation of mixed micelles. To test the feasibility of the latter mechanism, we developed a mathematical model that describes the formation of lipid microdomains in the canalicular membrane. Bile salt monomers intercalate into the external hemileaflet of the canalicular membrane, to form a rim to liquid disordered domain patches that then pinch off to form nanometer-scale mixed micelles. Model simulations perfectly recapitulate the measured dependence of bile salt-dependent biliary lipid extraction rates upon modulation of the membrane cholesterol (lack or overexpression of the cholesterol transporter Abcg5-Abcg8) and phosphatidylcholine (lack of Mdr2, also known as Abcb4) content. The model reveals a strong dependence of the biliary secretion rate on the protein density of the membrane. Taken together, the proposed model is consistent with crucial experimental findings in the field and provides a consistent explanation of the central molecular processes involved in bile formation.\n\nThe importance of membrane microdomains for bile salt-dependent biliary lipid secretion.", "token_count": 291, "char_count": 1294, "word_count": 181, "semantic_coherence": 1, "information_density": 0.5801, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:23.876090", "source": { "split": "train_shard_00000", "doc_id": 3465 }, "chunk_id": "train_shard_00000_3465_0", "global_id": 3832 }, { "text": "Genetic defects causing dysfunction in bile salt export pump (BSEP/ABCB11) lead to liver diseases. ABCB11 mutations alter the bile acid metabolome. We asked whether profiling plasma bile acids could reveal compensatory mechanisms and track genetic and clinical status.\n\nComprehensive bile acid profiling in hereditary intrahepatic cholestasis: Genetic and clinical correlations.", "token_count": 97, "char_count": 378, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:24.254017", "source": { "split": "train_shard_00000", "doc_id": 3466 }, "chunk_id": "train_shard_00000_3466_0", "global_id": 3833 }, { "text": "Bacteria use two-component systems (TCSs) to sense and respond to environmental changes. The core genome of the major human pathogen Staphylococcus aureus encodes 16 TCSs, one of which (WalRK) is essential. Here we show that S. aureus can be deprived of its complete sensorial TCS network and still survive under growth arrest conditions similarly to wild-type bacteria. Under replicating conditions, however, the WalRK system is necessary and sufficient to maintain bacterial growth, indicating that sensing through TCSs is mostly dispensable for living under constant environmental conditions. Characterization of S. aureus derivatives containing individual TCSs reveals that each TCS appears to be autonomous and self-sufficient to sense and respond to specific environmental cues, although some level of cross-regulation between non-cognate sensor-response regulator pairs occurs in vivo. This organization, if confirmed in other bacterial species, may provide a general evolutionarily mechanism for flexible bacterial adaptation to life in new niches.\n\nSensory deprivation in Staphylococcus aureus.", "token_count": 253, "char_count": 1103, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7386, "quality_score": 0.8693, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:24.747786", "source": { "split": "train_shard_00000", "doc_id": 3467 }, "chunk_id": "train_shard_00000_3467_0", "global_id": 3834 }, { "text": "Benign recurrent intrahepatic cholestasis (BRIC) is a peculiar familial disease caused by mutations of the genes encoding hepatocanalicular flippase for phosphatidylserine (ATP8B1; BRIC type 1) or the bile salt export pump (ABCB11; BRIC type 2). Here, we report on a patient with nasobiliary drainage-refractory BRIC type 2 who improved under plasma separation and anion absorption therapy. We also suggest that nasobiliary drainage might be an ineffective approach in carriers of severe loss-of-function mutations of the bile salt export pump ABCB11. (\n\nCan genetic testing guide the therapy of cholestatic pruritus? A case of benign recurrent intrahepatic cholestasis type 2 with severe nasobiliary drainage-refractory itch.", "token_count": 203, "char_count": 726, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7115, "quality_score": 0.8558, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:25.204234", "source": { "split": "train_shard_00000", "doc_id": 3468 }, "chunk_id": "train_shard_00000_3468_0", "global_id": 3835 }, { "text": "Colonization, Infection, and the Accessory Genome of", "token_count": 14, "char_count": 52, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:25.540528", "source": { "split": "train_shard_00000", "doc_id": 3469 }, "chunk_id": "train_shard_00000_3469_0", "global_id": 3836 }, { "text": "Methylene blue (MB) is a hydrophobic drug molecule, having importance both as a staining reagent and pharmaceutical agent. MB is strongly fluorescent, with an emission peak at 686 nm (\n\nBile salt induced solubilization of methylene blue: Study on methylene blue fluorescence properties and molecular mechanics calculation.", "token_count": 84, "char_count": 322, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8723, "quality_score": 0.9362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:25.914819", "source": { "split": "train_shard_00000", "doc_id": 3470 }, "chunk_id": "train_shard_00000_3470_0", "global_id": 3837 }, { "text": "Campylobacter hyointestinalis is a member of an emerging group of zoonotic Campylobacter spp. that are increasingly identified in both gastric and non-gastric disease in humans. Here, we discovered C. hyointestinalis in three separate classes of New Zealand ruminant livestock; cattle, sheep and deer. To investigate the relevance of these findings we performed a systematic literature review on global C. hyointestinalis epidemiology and used comparative genomics to better understand and classify members of the species. We found that C. hyointestinalis subspecies hyointestinalis has an open pangenome, with accessory gene contents involved in many essential processes such as metabolism, virulence and defence. We observed that horizontal gene transfer is likely to have played an overwhelming role in species diversification, favouring a public-goods-like mechanism of gene 'acquisition and resampling' over a tree-of-life-like vertical inheritance model of evolution. As a result, simplistic gene-based inferences of taxonomy by similarity are likely to be misleading. Such genomic plasticity will also mean that local evolutionary histories likely influence key species characteristics, such as host-association and virulence. This may help explain geographical differences in reported C. hyointestinalis epidemiology and limits what characteristics may be generalised, requiring further genomic studies of C. hyointestinalis in areas where it causes disease.\n\nUpdating the genomic taxonomy and epidemiology of Campylobacter hyointestinalis.", "token_count": 350, "char_count": 1548, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:26.490112", "source": { "split": "train_shard_00000", "doc_id": 3471 }, "chunk_id": "train_shard_00000_3471_0", "global_id": 3838 }, { "text": "Salmonella enterica serovar Heidelberg (S. Heidelberg) is one of the top serovars causing human salmonellosis. The core genome single nucleotide variant pipeline (cgSNV) is one of several whole genome based sequence typing methods used for the laboratory investigation of foodborne pathogens. SNV detection using this method requires a reference genome. The purpose of this study was to investigate the impact of the choice of the reference genome on the cgSNV-informed phylogenetic clustering and inferred isolate relationships. We found that using a draft or closed genome of S. Heidelberg as reference did not impact the ability of the cgSNV methodology to differentiate among 145 S. Heidelberg isolates involved in foodborne outbreaks. We also found that using a distantly related genome such as S. Dublin as choice of reference led to a loss in resolution since some sporadic isolates were found to cluster together with outbreak isolates. In addition, the genetic distances between outbreak isolates as well as between outbreak and sporadic isolates were overall reduced when S. Dublin was used as the reference genome as opposed to S. Heidelberg.\n\nImpact of the choice of reference genome on the ability of the core genome SNV methodology to distinguish strains of Salmonella enterica serovar Heidelberg.", "token_count": 307, "char_count": 1311, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5297, "quality_score": 0.7649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:27.060201", "source": { "split": "train_shard_00000", "doc_id": 3472 }, "chunk_id": "train_shard_00000_3472_0", "global_id": 3839 }, { "text": "In this study, 29 strains of Kluyveromyces marxianus with peculiar genetic and phenotypic traits previously isolated from a fermented goat milk of Yaghnob valley were investigated for chromosome length polymorphism (CLP) by PFGE, adhesion properties and carbon usage by Biolog analysis. Obtained data showed that strains differed in terms of number and size of chromosome bands. The number of bands ranged from 5 to 7, suggesting a probable genome size from 1.4 to 2.6 Mb. Strains showed a certain level of cell surface hydrophobicity ranging from 32% to 77.7%. Strains were also tested for their ability to form a biofilm on polystyrene plates: planktonic cells ranged from 6.3 cfu/mL to 7.95 cfu/mL, while sessile from 7.11 cfu/mL to 8.6 cfu/mL. The strains able to adhere to polystyrene plates were also able to form a mature MAT. Biolog analysis revealed that almost all strains were able to use putrescine, malic acid, α-D lactose, phenylethylamine, β-methyl D-gucoside and xylose; 5 strains were able to grow on cellobiose and 3 were able to catabolise α-ketobutyric. The obtained data highlighted a number of interesting features underlying the peculiar capacities of these strains for industrial applications.\n\nIntraspecies polymorphisms of Kluyveromyces marxianus strains from Yaghnob valley.", "token_count": 388, "char_count": 1301, "word_count": 200, "semantic_coherence": 1, "information_density": 0.61, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:27.671236", "source": { "split": "train_shard_00000", "doc_id": 3473 }, "chunk_id": "train_shard_00000_3473_0", "global_id": 3840 }, { "text": "Six Bifidobacterium strains, i.e., Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B, were isolated from domestic goose (Anser domesticus), European hamster (Cricetus cricetus), European rabbit (Oryctolagus cuniculus), emperor tamarin (Saguinus imperator) and pygmy marmoset (Callithrix pygmaea). Cells are Gram-positive, non-motile, non-sporulating, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA, ITS-, multilocus- sequences and the core genome revealed that bifidobacterial strains Goo31D, Ham19E, Rab10A, Tam1G, Uis4E and Uis1B exhibit close phylogenetic relatedness with Bifidobacterium choerinum LMG 10510, Bifidobacterium hapali DSM 100202, Bifidobacterium saguini DSM 23967 and Bifidobacterium stellenboschense DSM 23968. Genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium anseris sp. nov. (Goo31D=LMG 30189\n\nPhylogenetic classification of six novel species belonging to the genus Bifidobacterium comprising Bifidobacterium anseris sp. nov., Bifidobacterium criceti sp. nov., Bifidobacterium imperatoris sp. nov., Bifidobacterium italicum sp. nov., Bifidobacterium margollesii sp. nov. and Bifidobacterium parmae sp. nov.", "token_count": 499, "char_count": 1387, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6412, "quality_score": 0.8206, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:28.325410", "source": { "split": "train_shard_00000", "doc_id": 3474 }, "chunk_id": "train_shard_00000_3474_0", "global_id": 3841 }, { "text": "Clostridium difficile PCR ribotype 106 (also identified as restriction endonuclease analysis [REA] group DH) recently emerged as the most common strain causing C. difficile infection (CDI) among US adults. We previously identified this strain predominating our pediatric cohort. Pediatric clinical CDI isolates previously characterized by REA underwent antibiotic resistance testing and whole genome sequencing. Of 134 isolates collected from children, 31 (23%) were REA group DH. We performed a comparative genomics analysis to identify DH-associated accessory genes. We identified five DH-associated genes that are associated with virulence in other bacterial species but not previously known to contribute to CDI. These genes are associated with intestinal mucosal adhesion (collagen-binding surface protein), sporulation (sporulation integral membrane protein YtvI), and protection from oxidative stress and foreign DNA (DNA phosphorothioation-dependent restriction proteins, sulfurtransferase, and DNA sulfur modification proteins). The association of these genes was validated in a cohort of 623 publicly available C. difficile sequences, 10 (1.6%) of which were monophyletic to REA group DH through in silico multilocus sequence typing and core genome phylogenetic analysis. Further investigation is required to determine the contribution of these genes to the emergence and virulence of this epidemic strain.\n\nComparative genomics analysis of Clostridium difficile epidemic strain DH/NAP11/106.", "token_count": 374, "char_count": 1502, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6866, "quality_score": 0.8433, "entities": { "genes": [ "NAP11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:28.911284", "source": { "split": "train_shard_00000", "doc_id": 3475 }, "chunk_id": "train_shard_00000_3475_0", "global_id": 3842 }, { "text": "Two feeding trials were conducted to investigate the effects of hydrolyzed (HY) or non-hydrolyzed (NHY) yeast (Kluyveromyces fragilis) in isoenergetic and isonitrogeneous diets in the postweaning period. In experiment 1, a total of 550 unsexed pigs (6.5 ± 0.5 kg BW), weaned at 24 ± 2 d of age, were allocated to five treatment groups, receiving either a control diet (CON) or diets with 1%, 3%, and 5% HY (groups HY1, HY3, and HY5, respectively), or a diet with 3% NHY (group NHY3). In experiment 2, a total of 48 male and female pigs (6.2 ± 0.3 kg BW, weaned at d 25) were allocated to three dietary groups (n = 8 replicates with two pigs) receiving a control diet (CON) or diets with 1% NHY or 1% HY. Eight animals were sacrificed 2 wk after weaning for histological investigations in the jejunum and colon, determination of apparent ileal digestibility (AID) of CP and ether extract (EE), and electrophysiological measurements in the jejunal tissue after addition of carbachol or l-glutamine using Ussing chambers. In experiment 1, different treatments had no significant effect on pig performance, but diet HY1 tended to increase ADG and G:F in wk 2 after weaning (P < 0.1). In experiment 2, diet HY1 increased feed intake in wk 2 (P < 0.05), whereas NHY yeast had no effect on feed intake. Villus height, villus/crypt ratio in jejunum (P < 0.05), and crypt depth in colon (P < 0.01) were increased in group HY1. Crypt depth in jejunum and small intestinal length were not affected by different treatments. The AID of CP and EE tended to increase in group HY1 (P < 0.1) compared with groups CON and NHY", "token_count": 506, "char_count": 1607, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5674, "quality_score": 0.7837, "entities": { "genes": [ "HY1", "HY3", "HY5", "NHY3" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:29.563275", "source": { "split": "train_shard_00000", "doc_id": 3476 }, "chunk_id": "train_shard_00000_3476_0", "global_id": 3843 }, { "text": "In the Ussing chamber experiments, no changes in basal electrophysiological parameters were observed, and the reactions of the treatment groups to carbachol and l-glutamine were comparable. ADFI was positively correlated with different parameters of intestinal morphology (villus height, villus/crypt ratio, crypt depth in colon, length of small intestine), AID of CP, EE, and performance. The results suggest that a supplementation of 1% HY based on K. fragilis to pig diets may positively influence ADFI and intestinal morphology in pig in the early postweaning period (d 1 to 14).\n\nInfluence of differently processed yeast (Kluyveromyces fragilis) on feed intake and gut physiology in weaned pigs.", "token_count": 181, "char_count": 700, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7212, "quality_score": 0.8606, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:30.004267", "source": { "split": "train_shard_00000", "doc_id": 3476 }, "chunk_id": "train_shard_00000_3476_1", "global_id": 3844 }, { "text": "Bile acids (BAs), the most important endogenous and signaling molecules regulate the target transporters and enzymes at transcriptional level, participate in a wide variety of processes throughout the entire gastrointestinal tract to orchestrate homeostasis in vivo. BAs and their metabolism and transportation appear to follow the clear circadian rhythms, and they are recently proposed also as the potential chronobiological signals that can affect the molecular clock mechanism. Cholecystectomy are believed to affect the circadian rhythms of BAs and the relevant enterohepatic transporters and enzymes systems and their regulatory signaling pathways, for the reason that the circadian cycle of gallbladder filling and emptying play a pivotal role in controlling the flow of bile into the intestine and the enterohepatic circulation of BAs. Here, in the present study, the circadian rhythms about BAs concentration and composition and the mRNA expression of genes involved in BAs transportation, metabolism and regulation in liver and ileum of mice with or without gallbladder were evaluated. As a result, it has been found that, mice with gallbladder exhibited significant and distinct circadian oscillations in BAs concentration, mRNA expression of enterohepatic transporters and enzymes systems and farnesoid X receptor-mediated regulatory pathways both in liver and ileum during gallbladder emptying period (1:00 AM and 1:00 PM), despite food was restricted during these periods; the circadian rhythmicity of BAs pool and hepatic and ileal BAs diminished but the BAs composition had no significant alteration in liver and ileum after cholecystectomy as compared with sham-operated mice; in parallel to the alteration of BAs levels in liver and ileum after cholecystectomy, the day/night circadian oscillations in the mRNA expression of the relevant transporting and metabolic genes and the farnesoid X receptor signaling pathway-mediated “intestine-liver†regulatory axis also shifted", "token_count": 494, "char_count": 1994, "word_count": 286, "semantic_coherence": 1, "information_density": 0.528, "quality_score": 0.764, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:30.653856", "source": { "split": "train_shard_00000", "doc_id": 3477 }, "chunk_id": "train_shard_00000_3477_0", "global_id": 3845 }, { "text": "In conclusion, the BAs concentration and the corresponding genes exhibit significant circadian rhythms in mice with gallbladder, and the circadian oscillations of most of the investigation factors are flattened and altered following by cholecystectomy, which could mainly ascribe to the disappearance of the filling and emptying cycle of gallbladder and might result in pathological states or drug chronopharmacology alternation. We expect that this study would provide a cue for patients with cholecystectomy.\n\nThe influences of cholecystectomy on the circadian rhythms of bile acids as well as the enterohepatic transporters and enzymes systems in mice.", "token_count": 161, "char_count": 655, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7234, "quality_score": 0.8617, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:31.092353", "source": { "split": "train_shard_00000", "doc_id": 3477 }, "chunk_id": "train_shard_00000_3477_1", "global_id": 3846 }, { "text": "The aim of present study was to develop and evaluate vesicles containing bile salt formulation of telmisartan for the treatment of diabetic nephropathy. Different vesicles containing bile salt formulations were developed by varying ratios of soybean phosphatidylcholine and sodium deoxycholate. Prepared formulations were characterized for their size, polydispersity index, zeta potential, morphology and entrapment efficiency. Further, the renoprotective outcome of optimized formulation was studied in streptozotocin-induced diabetic nephropathy rat model. Results of the present study demonstrated that the average vesicles size, polydispersity index, zeta potential and entrapment efficiency were found to be in the range of 64.98 ± 1.40 to 167.60 ± 6.46 nm, 0.02 ± 0.04 to 0.31 ± 0.01, -24.30 ± 1.39 to -42.60 ± 6.67 mV and 29.68 ± 1.08% to 77.21 ± 0.52%, respectively. Further, the best chosen formulation F4 presented vesicles size, polydispersity index, zeta potential and entrapment efficiency of 64.98 ± 1.40 nm, 0.24 ± 0.02, -35.40 ± 1.48 mV and 77.21 ± 0.52%, respectively. In addition, formulation F4 improved the biological indices in streptozotocin-induced diabetic nephropathy in rats. It was concluded that prepared formulation exerts a valuable results on diabetic nephropathy and it may be a potential pharmaceutical dosage form for the treatment of diabetic nephropathy.", "token_count": 515, "char_count": 1390, "word_count": 203, "semantic_coherence": 1, "information_density": 0.5123, "quality_score": 0.7562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:33:31.744583", "source": { "split": "train_shard_00000", "doc_id": 3478 }, "chunk_id": "train_shard_00000_3478_0", "global_id": 3847 }, { "text": "Development and biological evaluation of vesicles containing bile salt of telmisartan for the treatment of diabetic nephropathy.", "token_count": 30, "char_count": 128, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:32.134501", "source": { "split": "train_shard_00000", "doc_id": 3478 }, "chunk_id": "train_shard_00000_3478_1", "global_id": 3848 }, { "text": "The arms race between bacteria and phages led to the development of sophisticated antiphage defense systems, including CRISPR-Cas and restriction-modification systems. Evidence suggests that known and unknown defense systems are located in \"defense islands\" in microbial genomes. Here, we comprehensively characterized the bacterial defensive arsenal by examining gene families that are clustered next to known defense genes in prokaryotic genomes. Candidate defense systems were systematically engineered and validated in model bacteria for their antiphage activities. We report nine previously unknown antiphage systems and one antiplasmid system that are widespread in microbes and strongly protect against foreign invaders. These include systems that adopted components of the bacterial flagella and condensin complexes. Our data also suggest a common, ancient ancestry of innate immunity components shared between animals, plants, and bacteria.\n\nSystematic discovery of antiphage defense systems in the microbial pangenome.", "token_count": 208, "char_count": 1028, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6739, "quality_score": 0.837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:32.609704", "source": { "split": "train_shard_00000", "doc_id": 3479 }, "chunk_id": "train_shard_00000_3479_0", "global_id": 3849 }, { "text": "The production of extracellular proteins by the thermotolerant yeast Kluyveromyces marxianus, which utilizes various sugars, was investigated using media containing sugars such as glucose, galactose, and xylose. SDS-PAGE analysis of culture supernatants revealed abundant production of an extracellular protein when cells were grown in xylose medium. The N-terminal sequence of the extracellular protein was identical to a part of the inulinase encoded by INU1 in the genome. Inulinase is an enzyme hydrolyzing β-2,1-fructosyl bond in inulin and sucrose and is not required for xylose assimilation. Disruption of INU1 in the strain DMKU 3-1042 lost the production of the extracellular protein and resulted in growth defect in sucrose and inulin media, indicating that the extracellular protein was inulinase (sucrase). In addition, six K. marxianus strains among the 16 strains that were analyzed produced more inulinase in xylose medium than in glucose medium. However, expression analysis indicated that the INU1 promoter activity was lower in the xylose medium than in the glucose medium, suggesting that enhanced production of inulinase is controlled in a post-transcriptional manner. The production of inulinase was also higher in cultures with more agitation, suggesting that oxygen supply affects the production of inulinase. Taken together, these results suggest that both xylose and oxygen supply shift cellular metabolism to enhance the production of extracellular inulinase.\n\nEnhanced production of extracellular inulinase by the yeast Kluyveromyces marxianus in xylose catabolic state.", "token_count": 406, "char_count": 1597, "word_count": 229, "semantic_coherence": 1, "information_density": 0.524, "quality_score": 0.762, "entities": { "genes": [ "INU1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:33.273084", "source": { "split": "train_shard_00000", "doc_id": 3480 }, "chunk_id": "train_shard_00000_3480_0", "global_id": 3850 }, { "text": "In Germany salmonellosis still represents the 2nd most common bacterial foodborne disease. The majority of infections are caused by Salmonella (S.) Typhimurium and S. Enteritidis followed by a variety of other broad host-range serovars. Salmonella Derby is one of the five top-ranked serovars isolated from humans and it represents one of the most prevalent serovars in pigs, thus bearing the potential risk for transmission to humans upon consumption of pig meat and products thereof. From November 2013 to January 2014 S. Derby caused a large outbreak that affected 145 primarily elderly people. Epidemiological investigations identified raw pork sausage as the probable source of infection, which was confirmed by microbiological evidence. During the outbreak isolates from patients, food specimen and asymptomatic carriers were investigated by conventional typing methods. However, the quantity and quality of available microbiological and epidemiological data made this outbreak highly suitable for retrospective investigation by Whole Genome Sequencing (WGS) and subsequent evaluation of different bioinformatics approaches for cluster definition. Overall the WGS-based methods confirmed the results of the conventional typing but were of significant higher discriminatory power. That was particularly beneficial for strains with incomplete epidemiological data. For our data set both, single nucleotide polymorphism (SNP)- and core genome multilocus sequence typing (cgMLST)-based methods proved to be appropriate tools for cluster definition.\n\nEvaluation of WGS based approaches for investigating a food-borne outbreak caused by Salmonella enterica serovar Derby in Germany.", "token_count": 364, "char_count": 1682, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6638, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:33.864990", "source": { "split": "train_shard_00000", "doc_id": 3481 }, "chunk_id": "train_shard_00000_3481_0", "global_id": 3851 }, { "text": "The genus Tenacibaculum encompasses several species pathogenic for marine fish. Tenacibaculum dicentrarchi and \"Tenacibaculum finnmarkense\" (Quotation marks denote species that have not been validly named.) were retrieved from skin lesions of farmed fish such as European sea bass or Atlantic salmon. They cause a condition referred to as tenacibaculosis and severe outbreaks and important fish losses have been reported in Spanish, Norwegian, and Chilean marine farms. We report here the draft genomes of the T. dicentrarchi and \"T. finnmarkense\" type strains. These genomes were compared with draft genomes from field isolates retrieved from Chile and Norway and with previously published Tenacibaculum genomes. We used Average Nucleotide Identity and core genome-based phylogeny as a proxy index for species boundary delineation. This work highlights evolution of closely related fish-pathogenic species and suggests that homologous recombination likely contributes to genome evolution. It also corrects the species affiliation of strain AYD7486TD claimed by Grothusen et al. (2016).\n\nComparative Genomics of Tenacibaculum dicentrarchi and \"Tenacibaculum finnmarkense\" Highlights Intricate Evolution of Fish-Pathogenic Species.", "token_count": 310, "char_count": 1230, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6946, "quality_score": 0.8473, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:34.434738", "source": { "split": "train_shard_00000", "doc_id": 3482 }, "chunk_id": "train_shard_00000_3482_0", "global_id": 3852 }, { "text": "The present study aimed to isolate an optimal lactic acid bacterial strain from the feces of healthy giant pandas. The strain exhibited good stability at low pH and high bile salt concentrations, activity against pathogens relevant to pandas, and antibiotic susceptibility. In the current study, 25 isolates were obtained from de Man, Rogosa, and Sharpe agar. Two (E21 and G83) and eight (E1, E2, E16, E18, E21, E69, E70, and G83) isolates demonstrated good performance at pH 2.0 and bile 2% (w/v), respectively. Three isolates (G83, G88, and G90) possessed better antimicrobial effect on enterotoxigenic Escherichia coli CVCC196 (ETEC) than the rest. One isolate (G83) strongly affected Salmonella, whereas three (G83, G87, and G88) exhibited inhibitory activity against Staphylococcus aureus. All isolates were multi-drug resistant. These isolates were identified as Lactobacillus (5 isolates) and Enterococcus (20 isolates) by 16S rRNA sequencing. Virulence genes were detected in Enterococcus isolates. Isolate G83 was identified as Lactobacillus plantarum and was considered as the best probiotic candidate among all of the experimental isolates. This study provided necessary and important theoretical guidance for further experiments on G83 in vivo.\n\nInvestigation of Lactic Acid Bacteria Isolated from Giant Panda Feces for Potential Probiotics In Vitro.", "token_count": 404, "char_count": 1362, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6884, "quality_score": 0.8442, "entities": { "genes": [ "CVCC196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:35.050795", "source": { "split": "train_shard_00000", "doc_id": 3483 }, "chunk_id": "train_shard_00000_3483_0", "global_id": 3853 }, { "text": "SUMO proteases of the SENP/Ulp family are master regulators of both sumoylation and desumoylation and regulate SUMO homeostasis in eukaryotic cells. SUMO conjugates rapidly increase in response to cellular stress, including nutrient starvation, hypoxia, osmotic stress, DNA damage, heat shock, and other proteotoxic stressors. Nevertheless, little is known about the regulation and targeting of SUMO proteases during stress. To this end we have undertaken a detailed comparison of the SUMO-binding activity of the budding yeast protein Ulp1 (ScUlp1) and its ortholog in the thermotolerant yeast Kluyveromyces marxianus, KmUlp1. We find that the catalytic UD domains of both ScUlp1 and KmUlp1 show a high degree of sequence conservation, complement a ulp1Δ mutant in vivo, and process a SUMO precursor in vitro. Next, to compare the SUMO-trapping features of both SUMO proteases we produced catalytically inactive recombinant fragments of the UD domains of ScUlp1 and KmUlp1, termed ScUTAG and KmUTAG respectively. Both ScUTAG and KmUTAG were able to efficiently bind a variety of purified SUMO isoforms and bound immobilized SUMO1 with nanomolar affinity. However, KmUTAG showed a greatly enhanced ability to bind SUMO and SUMO-modified proteins in the presence of oxidative, temperature and other stressors that induce protein misfolding. We also investigated whether a SUMO-interacting motif (SIM) in the UD domain of KmULP1 that is not conserved in ScUlp1 may contribute to the SUMO-binding properties of KmUTAG. In summary, our data reveal important details about how SUMO proteases target and bind their sumoylated substrates, especially under stress conditions. We also show that the robust pan-SUMO binding features of KmUTAG can be exploited to detect and study SUMO-modified proteins in cell culture systems.\n\nSUMO targeting of a stress-tolerant Ulp1 SUMO protease.", "token_count": 500, "char_count": 1874, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [ "SUMO1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:35.703428", "source": { "split": "train_shard_00000", "doc_id": 3484 }, "chunk_id": "train_shard_00000_3484_0", "global_id": 3854 }, { "text": "Eukaryotes, including the unicellular eukaryotes such as yeasts, employ multiple levels of gene regulation. Regulation of chromatin structure through chromatin compaction cascades, and influenced by transcriptional insulators, might play a role in the coordinated regulation of genes situated at adjacent loci and expressed as a co-regulated cluster. Subtelomeric gene silencing, which has previously been described in the yeast Saccharomyces cerevisiae, is an example of this phenomenon. Transcription from a common regulatory element located around a shared intergenic region is another factor that could coordinate the transcription of genes at adjacent loci. Additionally, the presence of DNA binding sites for the same transcription factor may coordinate expression of multiple genes. Yeasts such as the industrially important Kluyveromyces marxianus may also display these modes of regulation, but this has not been explored to date. An exploration was done using a complete genome and RNA-seq data from a previous study of the transcriptional response to glucose or xylose as the carbon source in a defined culture medium, and investigating whether the species displays clusters of co-localised differentially expressed genes. Regions of possible subtelomeric silencing were evident, but were non-responsive to the carbon sources tested here. Additionally, glucose or xylose responsive clusters were discovered far from telomeres which contained some of the most significantly differentially expressed genes, encoding enzymes involved in the utilisation of alternative carbon sources such as the industrially important inulinase gene INU1. These clusters contained putative binding sites for the carbon source responsive transcription factors Mig1 and Adr1. Additionally, we investigated the potential contribution of common intergenic regions in co-regulation. Some observations were also made in terms of the evolutionary conservation of these clusters among yeast species and the presence of potential transcriptional insulators at the periphery of these clusters.\n\nGene regulation in Kluyveromyces marxianus in the context of chromosomes.", "token_count": 449, "char_count": 2149, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5552, "quality_score": 0.7776, "entities": { "genes": [ "INU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:36.346548", "source": { "split": "train_shard_00000", "doc_id": 3485 }, "chunk_id": "train_shard_00000_3485_0", "global_id": 3855 }, { "text": "The yeast Kluyveromyces marxianus possesses advantageous traits like rapid growth, GRAS (generally regarded as safe) status and thermotolerance that make it very suitable for diverse biotechnological applications. Although physiological studies demonstrate wide phenotypic variation within the species, there is only limited information available on the genetic diversity of K. marxianus. The aim of this work was to develop a multilocus sequence typing (MLST) method for K. marxianus to improve strain classification and selection. Analysis of housekeeping genes in a number of sequenced strains led to the selection of five genes, IPP1, TFC1, GPH1, GSY2 and SGA1, with sufficient polymorphic sites to allow MLST analysis. These loci were sequenced in an additional 76 strains and used to develop the MLST. This revealed wide diversity in the species and separation of the culture collection and wild strains into multiple distinct clades. Two subsets of strains that shared sources of origin were subjected to MLST and split decomposition analysis. The latter revealed evidence of recombination, indicating that this yeast undergoes mating in the wild. A public access web-based portal was established to allow expansion of the database and application of MLST to additional K. marxianus strains. This will aid understanding of the genetic diversity of the yeast and facilitate biotechnological exploitation.\n\nDevelopment and implementation of multilocus sequence typing to study the diversity of the yeast Kluyveromyces marxianus in Italian cheeses.", "token_count": 349, "char_count": 1552, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6123, "quality_score": 0.8062, "entities": { "genes": [ "SGA1", "GPH1", "IPP1", "TFC1", "GSY2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:36.923930", "source": { "split": "train_shard_00000", "doc_id": 3486 }, "chunk_id": "train_shard_00000_3486_0", "global_id": 3856 }, { "text": "A new in vitro method was developed to determine the bile tolerance of potentially probiotic lactobacilli. The overnight culture of various lactobacilli strains was inoculated into sterile, half-strength MRS broth supplemented with and without 0.3% (wt/vol) oxgall, buffered with 0.1 M sodium phosphate buffer at a final pH of 7.3, and incubated at 37 °C for 12 h under anaerobic conditions. The bile tolerance ability of the lactobacilli strains was expressed as the percentage of the propagation generations of the bacterial cells in the presence of oxgall to those in the absence of oxgall. The bile tolerance ability of 11 strains of 8 Lactobacillus species, including 3 bile salt hydrolase (BSH)-negative strains and 8 BSH-positive strains, was analyzed using the newly developed method and two traditional methods. The results showed that bile tolerance ability of the strains was considerably different depending on the analysis method used. The newly developed method mimics the physiological environment of the human small intestine, and avoids changes in pH and bile salt composition during the incubation period, which are drawbacks of the traditional bile tolerance test methods. Therefore, the analysis method developed in this study is more suitable to screen or compare the bile tolerance ability of lactobacilli strains.\n\nA new method for the in vitro determination of the bile tolerance of potentially probiotic lactobacilli.", "token_count": 365, "char_count": 1442, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5409, "quality_score": 0.7705, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:37.498835", "source": { "split": "train_shard_00000", "doc_id": 3487 }, "chunk_id": "train_shard_00000_3487_0", "global_id": 3857 }, { "text": "Understanding liver exposure of hepatic transporter substrates in clinical studies is often critical, as it typically governs pharmacodynamics, drug-drug interactions, and toxicity for certain drugs. However, this is a challenging task since there is currently no easy method to directly measure drug concentration in the human liver. Using bosentan as an example, we demonstrate a new approach to estimate liver exposure based on observed systemic pharmacokinetics from clinical studies using physiologically based pharmacokinetic modeling. The prediction was verified to be both accurate and precise using sensitivity analysis. For bosentan, the predicted pseudo steady-state unbound liver-to-unbound systemic plasma concentration ratio was 34.9 (95% confidence interval: 4.2, 50). Drug-drug interaction (i.e., CYP3A and CYP2B6 induction) and inhibition of hepatic transporters (i.e., bile salt export pump, multidrug resistance-associated proteins, and sodium-taurocholate cotransporting polypeptide) were predicted based on the estimated unbound liver tissue or plasma concentrations. With further validation and refinement, we conclude that this approach may serve to predict human liver exposure and complement other methods involving tissue biopsy and imaging.\n\nA Study on Pharmacokinetics of Bosentan with Systems Modeling, Part 1: Translating Systemic Plasma Concentration to Liver Exposure in Healthy Subjects.", "token_count": 333, "char_count": 1420, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6878, "quality_score": 0.8439, "entities": { "genes": [ "CYP3A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:38.068103", "source": { "split": "train_shard_00000", "doc_id": 3488 }, "chunk_id": "train_shard_00000_3488_0", "global_id": 3858 }, { "text": "Whole-genome sequencing (WGS) has become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance. It provides precise geographical delineation of spread and enables incidence monitoring of pathogens at genotype level. Coupled with epidemiological and environmental investigations, it delivers ultimate resolution for tracing sources of epidemic infections. To ascertain the level of implementation of WGS-based typing for national public health surveillance and investigation of prioritized diseases in the European Union (EU)/European Economic Area (EEA), two surveys were conducted in 2015 and 2016. The surveys were designed to determine the national public health reference laboratories' access to WGS and operational WGS-based typing capacity for national surveillance of selected foodborne pathogens, antimicrobial-resistant pathogens, and vaccine-preventable diseases identified as priorities for European genomic surveillance. Twenty-eight and twenty-nine out of the 30 EU/EEA countries participated in the survey in 2015 and 2016, respectively. National public health reference laboratories in 22 and 25 countries had access to WGS-based typing for public health applications in 2015 and 2016, respectively. Reported reasons for limited or no access were lack of funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data analysis was limited. By mid-2016, half of the EU/EEA countries were using WGS analysis either as first- or second-line typing method for surveillance of the pathogens and antibiotic resistance issues identified as EU priorities. The sampling frame as well as bioinformatics analysis varied by pathogen/resistance issue and country. Core genome multilocus allelic profiling, also called cgMLST, was the most frequently used annotation approach for typing bacterial genomes suggesting potential bioinformatics pipeline compatibility. Further capacity development for WGS-based typing is ongoing in many countries and upon consolidation and harmonization of methods should enable pan-EU data exchange for genomic surveillance in the medium-term subject to the development of suitable data management systems and appropriate agreements for data sharing.", "token_count": 514, "char_count": 2390, "word_count": 323, "semantic_coherence": 1, "information_density": 0.5728, "quality_score": 0.7864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:33:38.725379", "source": { "split": "train_shard_00000", "doc_id": 3489 }, "chunk_id": "train_shard_00000_3489_0", "global_id": 3859 }, { "text": "Survey on the Use of Whole-Genome Sequencing for Infectious Diseases Surveillance: Rapid Expansion of European National Capacities, 2015-2016.", "token_count": 44, "char_count": 142, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:39.086575", "source": { "split": "train_shard_00000", "doc_id": 3489 }, "chunk_id": "train_shard_00000_3489_1", "global_id": 3860 }, { "text": "To analyse Klebsiella pneumoniae (KP) isolates from an outbreak of extended-spectrum β-lactamase (ESBL)-producing KP and Escherichia coli (EC) among infants admitted to neonatal intensive care units and to determine the duration of the intestinal colonization.\n\nNeonatal intestinal colonization with extended-spectrum β-lactamase-producing Enterobacteriaceae-a 5-year follow-up study.", "token_count": 117, "char_count": 384, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8222, "quality_score": 0.9111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:39.475790", "source": { "split": "train_shard_00000", "doc_id": 3490 }, "chunk_id": "train_shard_00000_3490_0", "global_id": 3861 }, { "text": "Bile Salt Hydrolase (BSH), a member of Cholylglycine hydrolase family, catalyzes the de-conjugation of bile acids and is evolutionarily related to penicillin V acylase (PVA) that hydrolyses a different substrate such as penicillin V. We report the three-dimensional structure of a BSH enzyme from the Gram-positive bacteria Enterococcus faecalis (EfBSH) which has manifold higher hydrolase activity compared to other known BSHs and displays unique allosteric catalytic property. The structural analysis revealed reduced secondary structure content compared to other known BSH structures, particularly devoid of an anti-parallel β-sheet in the assembly loop and part of a β-strand is converted to increase the length of a substrate binding loop 2. The analysis of the substrate binding pocket showed reduced volume owing to altered loop conformations and increased hydrophobicity contributed by a higher ratio of hydrophobic to hydrophilic groups present. The aromatic residues F18, Y20 and F65 participate in substrate binding. Thus, their mutation affects enzyme activity. Docking and Molecular Dynamics simulation studies showed effective polar complementarity present for the three hydroxyl (-OH) groups of GCA substrate in the binding site contributing to higher substrate specificity and efficient catalysis. These are unique features characteristics of this BSH enzyme and thought to contribute to its higher activity and specificity towards bile salts as well as allosteric effects. Further, mechanism of autocatalytic processing of Cholylglycine Hydrolases by the excision of an N-terminal Pre-peptide was examined by inserting different N-terminal pre-peptides in EfBSH sequence. The results suggest that two serine residues next to nucleophile cysteine are essential for autocalytic processing to remove precursor peptide. Since pre-peptide is absent in EfBSH the mutation of these serines is tolerated. This suggests that an evolution-mediated subordination of the pre-peptide excision site resulted in loss of pre-peptide in EfBSH and other related Cholylglycine hydrolases.", "token_count": 514, "char_count": 2086, "word_count": 294, "semantic_coherence": 1, "information_density": 0.5816, "quality_score": 0.7908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:33:40.109373", "source": { "split": "train_shard_00000", "doc_id": 3491 }, "chunk_id": "train_shard_00000_3491_0", "global_id": 3862 }, { "text": "Structure and function of a highly active Bile Salt Hydrolase (BSH) from Enterococcus faecalis and post-translational processing of BSH enzymes.", "token_count": 40, "char_count": 144, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:40.477607", "source": { "split": "train_shard_00000", "doc_id": 3491 }, "chunk_id": "train_shard_00000_3491_1", "global_id": 3863 }, { "text": "Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence.\n\nPangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome.", "token_count": 138, "char_count": 637, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7711, "quality_score": 0.8855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:40.904081", "source": { "split": "train_shard_00000", "doc_id": 3492 }, "chunk_id": "train_shard_00000_3492_0", "global_id": 3864 }, { "text": "A fundamental question in human susceptibility to bacterial infections is to what extent variability is a function of differences in the pathogen species or in individual humans. To focus on the pathogen species, we compared in the same individual the human adaptive T and B cell immune response to multiple strains of two major human pathogens, Staphylococcus aureus and Streptococcus pyogenes. We found wide variability in the acute adaptive immune response induced by various strains of a species, with a unique combination of activation within the two arms of the adaptive response. Further, this was also accompanied by a dramatic difference in the intensity of the specific protective T helper (Th) response. Importantly, the same immune response differences induced by the individual strains were maintained across multiple healthy human donors. A comparison of isogenic phage KO strains, demonstrated that of the pangenome, prophages were the major contributor to inter-strain immune heterogeneity, as the T cell response to the remaining \"core genome\" was noticeably blunted. Therefore, these findings extend and modify the notion of an adaptive response to a pathogenic bacterium, by implying that the adaptive immune response signature of a bacterial species should be defined either per strain or alternatively to the species' 'core genome', common to all of its strains. Further, our results demonstrate that the acquired immune response variation is as wide among different strains within a single pathogenic species as it is among different humans, and therefore may explain in part the clinical heterogeneity observed in patients infected with the same species.\n\nStrains of bacterial species induce a greatly varied acute adaptive immune response: The contribution of the accessory genome.", "token_count": 374, "char_count": 1805, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5311, "quality_score": 0.7656, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:41.510372", "source": { "split": "train_shard_00000", "doc_id": 3493 }, "chunk_id": "train_shard_00000_3493_0", "global_id": 3865 }, { "text": "Swine dysentery (SD) is an economically important diarrheal disease in pigs caused by different strongly hemolytic Brachyspira (B.) species, such as B. hyodysenteriae, B. suanatina and B. hampsonii. Possible associations of epidemiologic data, such as multilocus sequence types (STs) to virulence gene profiles and antimicrobial susceptibility are rather scarce, particularly for B. hyodysenteriae isolates from Germany. In this study, B. hyodysenteriae (n = 116) isolated from diarrheic pigs between 1990 and 2016 in Germany were investigated for their STs, susceptibility to the major drugs used for treatment of SD (tiamulin and valnemulin) and genes that were previously linked with virulence and encode for hemolysins (tlyA, tlyB, tlyC, hlyA, BHWA1_RS02885, BHWA1_RS09085, BHWA1_RS04705, and BHWA1_RS02195), outer membrane proteins (OMPs) (bhlp16, bhlp17.6, bhlp29.7, bhmp39f, and bhmp39h) as well as iron acquisition factors (ftnA and bitC). Multilocus sequence typing (MLST) revealed that 79.4% of the isolates belonged to only three STs, namely ST52 (41.4%), ST8 (12.1%), and ST112 (25.9%) which have been observed in other European countries before. Another 24 isolates belonged to twelve new STs (ST113-118, ST120-123, ST131, and ST193). The temporal distribution of STs revealed the presence of new STs as well as the regular presence of ST52 over three decades (1990s-2000s)", "token_count": 483, "char_count": 1386, "word_count": 200, "semantic_coherence": 1, "information_density": 0.705, "quality_score": 0.8525, "entities": { "genes": [ "ST131", "ST193", "ST113", "ST112", "ST52", "ST8", "ST120" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:42.154838", "source": { "split": "train_shard_00000", "doc_id": 3494 }, "chunk_id": "train_shard_00000_3494_0", "global_id": 3866 }, { "text": "The proportion of strains that showed resistance to both tiamulin und valnemulin (39.1%) varied considerably among the most frequent STs ranging from 0% (0/14 isolates resistant) in ST8 isolates to 46.7% (14/30), 52.1% (25/48), and 85.7% (6/7) in isolates belonging to ST112, ST52, and ST114, respectively. All hemolysin genes as well as the iron-related gene ftnA and the OMP gene bhlp29.7 were regularly present in the isolates, while the OMP genes bhlp17.6 and bhmp39h could not be detected. Sequence analysis of hemolysin genes of selected isolates revealed co-evolution of tlyB, BHWA1_RS02885, BHWA1_RS09085, and BHWA1_RS02195 with the core genome and suggested independent evolution of tlyA, tlyC, and hlyA. Our data indicate that in Germany, swine dysentery might be caused by a limited number of B. hyodysenteriae clonal groups. Major STs (ST8, ST52, and ST112) are shared with other countries in Europe suggesting a possible role of the European intra-Community trade of pigs in the dissemination of certain clones. The identification of several novel STs, some of which are single or double locus variants of ST52, may on the other hand hint towards an ongoing diversification of the pathogen in the studied area. The linkage of pleuromutilin susceptibility and sequence type of an isolate might reflect a clonal expansion of the underlying resistance mechanism, namely mutations in the ribosomal RNA genes. A linkage between single virulence-associated genes (VAGs) or even VAG patterns and the phylogenetic background of the isolates could not be established, since almost all VAGs were regularly present in the isolates.\n\nPhylogenetic diversity, antimicrobial susceptibility and virulence gene profiles of Brachyspira hyodysenteriae isolates from pigs in Germany.", "token_count": 519, "char_count": 1776, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [ "ST52", "ST112", "ST114", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:33:42.802701", "source": { "split": "train_shard_00000", "doc_id": 3494 }, "chunk_id": "train_shard_00000_3494_1", "global_id": 3867 }, { "text": "MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing data, MLST methods have evolved towards larger typing schemes, based on a few hundred genes [core genome MLST (cgMLST)] to a few thousand genes [whole genome MLST (wgMLST)]. Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k-mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST schemes with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST.\n\nMentaLiST - A fast MLST caller for large MLST schemes.", "token_count": 329, "char_count": 1508, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:43.370489", "source": { "split": "train_shard_00000", "doc_id": 3495 }, "chunk_id": "train_shard_00000_3495_0", "global_id": 3868 }, { "text": "In most cholestatic liver diseases the primary cholestasis-causing lesions are located in the biliary tree and may be of (auto)immune origin. Bile salts are responsible for the secondary toxic consequences. Bile salt and nuclear hormone directed therapies primarily aim at improving this secondary toxic injury. In primary biliary cholangitis, trials show statistically significant responses on biochemical endpoints. Preclinical studies suggest that FXR- and PPAR-agonists, inhibitors of the apical sodium-dependent bile salt transporter (ASBT-inhibitors) and the C\n\nNew therapies target the toxic consequences of cholestatic liver disease.", "token_count": 152, "char_count": 641, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:43.841476", "source": { "split": "train_shard_00000", "doc_id": 3496 }, "chunk_id": "train_shard_00000_3496_0", "global_id": 3869 }, { "text": "Drug-induced liver injury (DILI) is a common reason for drug withdrawal from the market. An important cause of DILI is drug-induced cholestasis. One of the major players involved in drug-induced cholestasis is the bile salt efflux pump (BSEP; ABCB11). Inhibition of BSEP by drugs potentially leads to cholestasis due to increased (toxic) intrahepatic concentrations of bile acids with subsequent cell injury. In order to investigate the possibilities for in silico prediction of cholestatic effects of drugs, we developed a mechanistic biokinetic model for human liver bile acid handling populated with human in vitro data. For this purpose we considered nine groups of bile acids in the human bile acid pool, i.e. chenodeoxycholic acid, deoxycholic acid, the remaining unconjugated bile acids and the glycine and taurine conjugates of each of the three groups. Michaelis-Menten kinetics of the human uptake transporter Na\n\nDevelopment of a mechanistic biokinetic model for hepatic bile acid handling to predict possible cholestatic effects of drugs.", "token_count": 280, "char_count": 1050, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.807, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:44.413486", "source": { "split": "train_shard_00000", "doc_id": 3497 }, "chunk_id": "train_shard_00000_3497_0", "global_id": 3870 }, { "text": "There is increasing interest in paediatric drug absorption and the development of biopharmaceutics tools to facilitate the development of oral formulations for neonates, infants and children. We describe the development and application of a physiologically-based model of paediatric drug absorption applicable from full term birth onwards. Paediatric age-specific parameters were included for salivary flow, gastric pH, gastric emptying (and associated food effects) and duodenal bile salt concentrations and the associated algorithms were integrated into a dissolution, absorption and metabolism model as part of a PBPK platform. For other parameters, there was either evidence for no age-related changes or a lack of data, so that adult values were applied. An initial assessment of the model was carried out by simulating the oral absorption of theophylline, paracetamol and ketoconazole over a range of paediatric ages. The absorption of the first two drugs, both BCS class 1 compounds, was predicted to be slower in early neonates compared to older age groups (median t\n\nDevelopment and applications of a physiologically-based model of paediatric oral drug absorption.", "token_count": 266, "char_count": 1173, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8198, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:44.993207", "source": { "split": "train_shard_00000", "doc_id": 3498 }, "chunk_id": "train_shard_00000_3498_0", "global_id": 3871 }, { "text": "Many bacteria from different phylogenetic groups are able to degrade eukaryotic steroid compounds, but the underlying metabolic pathways are still not well understood.\n\nGenome Sequence of the Bile Salt-Degrading Bacterium", "token_count": 57, "char_count": 221, "word_count": 30, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:45.398261", "source": { "split": "train_shard_00000", "doc_id": 3499 }, "chunk_id": "train_shard_00000_3499_0", "global_id": 3872 }, { "text": "The elongation of single-stranded DNA repeats at the 3'-ends of chromosomes by telomerase is a key process in maintaining genome integrity in eukaryotes. Abnormal activation of telomerase leads to uncontrolled cell division, whereas its down-regulation is attributed to ageing and several pathologies related to early cell death. Telomerase function is based on the dynamic interactions of its catalytic subunit (TERT) with nucleic acids-telomerase RNA, telomeric DNA and the DNA/RNA heteroduplex. Here, we present the crystallographic and NMR structures of the N-terminal (TEN) domain of TERT from the thermotolerant yeast Hansenula polymorpha and demonstrate the structural conservation of the core motif in evolutionarily divergent organisms. We identify the TEN residues that are involved in interactions with the telomerase RNA and in the recognition of the 'fork' at the distal end of the DNA product/RNA template heteroduplex. We propose that the TEN domain assists telomerase biological function and is involved in restricting the size of the heteroduplex during telomere repeat synthesis.\n\nStructure and function of the N-terminal domain of the yeast telomerase reverse transcriptase.", "token_count": 293, "char_count": 1193, "word_count": 172, "semantic_coherence": 1, "information_density": 0.593, "quality_score": 0.7965, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:45.958417", "source": { "split": "train_shard_00000", "doc_id": 3500 }, "chunk_id": "train_shard_00000_3500_0", "global_id": 3873 }, { "text": "Opportunistic infections due to Candida species occur frequently in intensive care settings. We investigated the prevalence of Candida species among 65 clinical specimens obtained from 200 cancer patients by phenotypic and molecular (ITS sequencing and AFLP) methods. Among the 65 yeast isolates, Candida albicans was the most commonly isolated species (n = 34, 52.3%), whereas other Candida species comprised 47.7% (n = 31) and consisted of Candida glabrata (n = 14, 21.5%), Candida tropicalis (n = 5, 7.7%) and uncommon Candida species (n = 12, 18.5%) such as Candida pelliculosa (n = 3, 4.6%), Pichia kudriavzevii (= Candida krusei, n = 2, 3.1%), Candida orthopsilosis (n = 2, 3.1%), Candida parapsilosis (n = 1, 1.5%), Candida infanticola (n = 2, 3.1%), Candida spencermartinsiae (n = 1, 1.5%), and Kluyveromyces marxianus (=Candida kefyr, n = 1, 1.5%). Candida infanticola and Candida spencermartinsiae were recovered from oral lesions of cancer patients. Matrix assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) easily confirmed these isolates as less common Candida isolates (4.6%). The in vitro antifungal susceptibilities of C. spencermartinsiae and the two strains of C. infanticola were determined according to CLSI guidelines (M27-A3)", "token_count": 503, "char_count": 1281, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:46.952610", "source": { "split": "train_shard_00000", "doc_id": 3501 }, "chunk_id": "train_shard_00000_3501_0", "global_id": 3874 }, { "text": "MIC results among these isolates showed they were susceptible to isavuconazole, posaconazole and voriconazole, however, fluconazole and caspofungin had high MIC values. These Candida species that may occur more commonly in infections remain unnoticed using commonly used phenotypical methods in routine microbiology laboratories. MALDI-TOF MS proved to be a more fast and robust diagnostic technique for identification of the yeasts isolated from different clinical specimens of cancer patients.\n\nCandida infanticola and Candida spencermartinsiae yeasts: Possible emerging species in cancer patients.", "token_count": 144, "char_count": 600, "word_count": 80, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:47.378358", "source": { "split": "train_shard_00000", "doc_id": 3501 }, "chunk_id": "train_shard_00000_3501_1", "global_id": 3875 }, { "text": "Oil-in-water emulsions were prepared with carrot- or tomato-enriched olive oil (5%w/v) and stabilized with Tween80 or sucrose esters (0.5%w/v) with different hydrophilic-lipophilic balance (8; 11 or 16). All emulsions had similar initial oil droplet sizes and were submitted to simulated gastrointestinal conditions using a kinetic digestion procedure. Sucrose esters induced an unstable system after gastric conditions leading to coalesced oil droplets, while Tween80 emulsions remained stable. Emulsion particle sizes at the end of the gastric phase were directly associated with the lipolysis kinetics during the intestinal phase. Moreover, a direct relationship was observed between lipolysis and carotenoid micellarisation for all emulsions, and depended mainly on the surfactant structure used. Tween80 emulsions led to a higher lipolysis extent (53-57%) and carotenoid bioaccessibility (17-42%) compared to sucrose ester emulsions (33-52% and 9-27%, respectively). These findings show the importance of the emulsifier structure and emulsion stability during gastrointestinal conditions in modulating lipolysis kinetics.\n\nEmulsion stability during gastrointestinal conditions effects lipid digestion kinetics.", "token_count": 328, "char_count": 1215, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6478, "quality_score": 0.8239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:47.946546", "source": { "split": "train_shard_00000", "doc_id": 3502 }, "chunk_id": "train_shard_00000_3502_0", "global_id": 3876 }, { "text": "The present study aimed to observe the effects of perioperative oral supplementation with fish oil (FO) on liver regeneration in mice and examine the potential mechanism. A total of 120 male ICR mice were randomly divided into 5 groups: Sham, Control, fish oil (FO), Compound C [the AMP‑activated protein kinase (AMPK) inhibitor dorsomorphin], and Compound C + FO. Changes in liver function, alterations in hepatocyte proliferation and in the expression of polarization markers, and activation of AMPK signaling were examined following partial hepatectomy (PH). The results demonstrated that restoration of serum alanine aminotransferase (ALT) and total bilirubin (TBIL) levels were significantly faster in FO‑treated mice compared with Control mice, and this effect was suppressed by treatment with Compound C. FO‑treated mice exhibited increased numbers of Ki‑67 positive hepatocytes and their postoperative liver‑to‑body weight ratio was significantly increased compared with the Control mice, which was also suppressed by co‑treatment with the AMPK inhibitor. Furthermore, protein expression of Occludin, Claudin‑3, tight junction protein 1 and bile salt export pump was gradually increased in FO‑treated mice compared with Control, whereas Compound C treatment reversed this effect. Therefore, the present study revealed that perioperative oral supplementation with FO may promote liver regeneration and improved liver function in mice following PH through AMPK activation.\n\nPerioperative oral supplementation with fish oil promotes liver regeneration following partial hepatectomy in mice via AMPK activation.", "token_count": 386, "char_count": 1615, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5752, "quality_score": 0.7876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:48.556701", "source": { "split": "train_shard_00000", "doc_id": 3503 }, "chunk_id": "train_shard_00000_3503_0", "global_id": 3877 }, { "text": "Progressive familial cholestasis type 2 is caused by a genetically determined absence or reduction in the activity of the bile salt export pump (BSEP). Reduction or absence of BSEP activity causes a failure of bile salt excretion, leading to accumulation of bile salts in hepatocytes and subsequent hepatic damage. Clinically, patients are jaundiced, suffer from severe intractable pruritus, and evidence progressive liver dysfunction. A low level of serum γ-glutamyl transpeptidase, when associated with the described signs and symptoms, is often an early identifier of this condition. Treatment options to date include liver transplantation and the use of biliary diversion. We report a multidrug regimen of 4-phenylbutyrate, oxcarbazepine, and maralixibat (an experimental drug owned by Shire Pharmaceuticals, Dublin, Republic of Ireland) that completely controlled symptoms in 2 siblings with partial loss of BSEP activity.\n\nA Drug Regimen for Progressive Familial Cholestasis Type 2.", "token_count": 249, "char_count": 988, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:49.043503", "source": { "split": "train_shard_00000", "doc_id": 3504 }, "chunk_id": "train_shard_00000_3504_0", "global_id": 3878 }, { "text": "Cheese is a typical handcrafted fermented food in Kazak minority from the Uighur Autonomy Region in China and Central Asia. Among the microbial community that is responsible for Kazak cheese fermentation, yeasts play important role in flavor formation during ripening. To develop ripening cultures, we isolated 123 yeasts from 25 cheese products in Kazak, and identified 87 isolates by the D1/D2 domain of the large subunit rRNA gene sequence. Pichia kudriavzevii was the dominant yeast in Kazak cheese, followed by Kluyveromyces marxianus and Kluyveromyces lactis. Of these, the ability to exhibit enzyme of dominant isolates and contribution to the typical flavor of cheeses was assessed. Enzyme producing yeast strains were inoculated in Hazak cheese-like medium and volatile compounds were identified by head space solid phase micro extraction coupled to gas chromatography and mass spectroscopy. Pichia kudriavzevii N-X displayed the strongest extracellular proteolytic and activity on skim milk agar and produced a range of aroma compounds (ethanol, ethyl acetate, 3-methylbutanol, and acetic acid) for Kazak cheese flavor, could be explored as ripening cultures in commercial production of Kazak cheeses.\n\nPotential characterization of yeasts isolated from Kazak artisanal cheese to produce flavoring compounds.", "token_count": 343, "char_count": 1318, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6649, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:49.621477", "source": { "split": "train_shard_00000", "doc_id": 3505 }, "chunk_id": "train_shard_00000_3505_0", "global_id": 3879 }, { "text": "Lactobacillus mucosae is currently of interest as putative probiotics due to their metabolic capabilities and ability to colonize host mucosal niches. L. mucosae LM1 has been studied in its functions in cell adhesion and pathogen inhibition, etc. It demonstrated unique abilities to use energy from carbohydrate and non-carbohydrate sources. Due to these functions, we report the first complete genome sequence of an L. mucosae strain, L. mucosae LM1. Analysis of the pan-genome in comparison with closely-related Lactobacillus species identified a complete glycogen metabolism pathway, as well as folate biosynthesis, complementing previous proteomic data on the LM1 strain. It also revealed common and unique niche-adaptation genes among the various L. mucosae strains. The aim of this study was to derive genomic information that would reveal the probable mechanisms underlying the probiotic effect of L. mucosae LM1, and provide a better understanding of the nature of L. mucosae sp.\n\nComparative genomic analysis of Lactobacillus mucosae LM1 identifies potential niche-specific genes and pathways for gastrointestinal adaptation.", "token_count": 298, "char_count": 1134, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6871, "quality_score": 0.8436, "entities": { "genes": [ "LM1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:50.173685", "source": { "split": "train_shard_00000", "doc_id": 3506 }, "chunk_id": "train_shard_00000_3506_0", "global_id": 3880 }, { "text": "Lactose is an energy source for culture bacteria. Bile tolerance is an important probiotic property. Our aim was to elucidate the effect of lactose on bile tolerance of yogurt starter culture Lactobacillus bulgaricus LB-12 and Streptococcus thermophilus ST-M5. Bile tolerance of pure cultures was determined using 0.3% oxgall in MRS THIO broth (Difco, Becton Dickinson, Sparks, MD) for L. bulgaricus and 0.3% oxgall in M17 broth (Oxoid, Basingstoke, UK) for Strep. thermophilus. Lactose was added to both broths at 0 (control), 1, 3, and 5% (wt/vol) broth. Dilutions were plated hourly for 12 h. Experiments were replicated 3 times. At 2, 4, and 12 h of incubation, lactose incorporated at all amounts, 1, 3, and 5% (wt/vol), showed higher counts of Strep. thermophilus ST-M5 compared with the control. Lactose use at 5% (wt/vol) significantly enhanced bile tolerance of both L. bulgaricus and Strep. thermophilus compared with control.\n\nShort communication: Lactose enhances bile tolerance of yogurt culture bacteria.", "token_count": 333, "char_count": 1018, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6051, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:50.738532", "source": { "split": "train_shard_00000", "doc_id": 3507 }, "chunk_id": "train_shard_00000_3507_0", "global_id": 3881 }, { "text": "Inhibition of the bile salt export pump (BSEP) by a drug has been implicated as a risk factor for a drug's potential to cause drug-induced liver injury (DILI) and is thought to be an important mechanism leading to DILI. For a wide variety of drugs a correlation has been observed between the potency of in vitro BSEP inhibition and its propensity to cause DILI in humans. These findings were interpreted to suggest that BSEP inhibition could be an important mechanism to help explain how some drugs initiate DILI. Because the Biopharmaceutics Drug Disposition Classification System (BDDCS) can be useful in characterizing and predicting some important transporter effects in terms of drug-drug interactions, we evaluated the information provided by BDDCS in order to understand the inhibition propensity of BSEP. Here we analyze the relationship between a compound's ability to inhibit BSEP function and cause liver injury in humans using a compilation of published DILI datasets that have screened for BSEP inhibitors, other hepatic transporters and other mechanism-based toxicity key events. Our results demonstrate that there is little support for in vitro BSEP inhibition being universally DILI predictive. Rather we show that most potent BSEP inhibitors are BDDCS class 2 drugs, which we have demonstrated previously is the BDDCS class most likely to be DILI related. Since BDDCS class is not related to any proposed DILI mechanistic hypotheses, we maintain that if measures of BSEP inhibition alone or together with inhibition of other transporters cannot be differentiated from class 2 assignment, there is no support for in vitro BSEP inhibition being DILI predictive.\n\nMeasures of BSEP Inhibition In Vitro Are Not Useful Predictors of DILI.", "token_count": 413, "char_count": 1749, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5458, "quality_score": 0.7729, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:51.359291", "source": { "split": "train_shard_00000", "doc_id": 3508 }, "chunk_id": "train_shard_00000_3508_0", "global_id": 3882 }, { "text": "Prokaryote genomes are the result of a dynamic flux of genes, with increases achieved via horizontal gene transfer and reductions occurring through gene loss. The ecological and selective forces that drive this genomic flexibility vary across species. Bacillus subtilis is a naturally competent bacterium that occupies various environments, including plant-associated, soil, and marine niches, and the gut of both invertebrates and vertebrates. Here, we quantify the genomic diversity of B. subtilis and infer the genome dynamics that explain the high genetic and phenotypic diversity observed. Phylogenomic and comparative genomic analyses of 42 B. subtilis genomes uncover a remarkable genome diversity that translates into a core genome of 1,659 genes and an asymptotic pangenome growth rate of 57 new genes per new genome added. This diversity is due to a large proportion of low-frequency genes that are acquired from closely related species. We find no gene-loss bias among wild isolates, which explains why the cloud genome, 43% of the species pangenome, represents only a small proportion of each genome. We show that B. subtilis can acquire xenologous copies of core genes that propagate laterally among strains within a niche. While not excluding the contributions of other mechanisms, our results strongly suggest a process of gene acquisition that is largely driven by competence, where the long-term maintenance of acquired genes depends on local and global fitness effects. This competence-driven genomic diversity provides B. subtilis with its generalist character, enabling it to occupy a wide range of ecological niches and cycle through them.\n\nGenetic Competence Drives Genome Diversity in Bacillus subtilis.", "token_count": 396, "char_count": 1726, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8198, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:51.977549", "source": { "split": "train_shard_00000", "doc_id": 3509 }, "chunk_id": "train_shard_00000_3509_0", "global_id": 3883 }, { "text": "Bacteria belonging to the genus Cronobacter are opportunistic pathogens known for causing rare but serious infections in neonates, including meningitis, necrotising enterocolitis and sepsis. Cronobacter infections occur also in adult populations, however, they generally have milder manifestations and their prevalence is uncertain. In this study, the presence of Cronobacter strains from adult patients in the University Hospital in Bratislava was investigated and overall 18 confirmed isolates from 321 patients (5.3%) were recovered. No Cronobacter positive sample was detected in 215 sputum samples from outpatients. The highest occurrence of Cronobacter strains was observed from stroke patients and this may be associated with an abnormal swallowing ability. The isolated strains belonged to the species Cronobacter sakazakii and Cronobacter malonaticus. In silico genotyping (MLST, CRISPR-cas array profiling) of whole genome sequences assigned the strains to three different MLST clones. The majority (12/18) of the isolated strains were sequence type ST513 or single locus variants ST514 and ST515, thereby being members of C. sakazakii pathovar clonal complex CC4. However, according to core genome MLST analysis the ST513-ST515 strains created a unique cluster substantially different from other CC4 strains. The isolated strains were susceptible to 18 tested antibiotics. All strains possess a genomic island encoding for increased thermal tolerance. As Cronobacter strains are frequently present in dried foods of plant origin, spread of a specific clone within a hospital may be caused by food transmission and may be facilitated by its tolerance to environmental stresses such as desiccation and temperature.\n\nCharacterisation of Cronobacter strains isolated from hospitalised adult patients.", "token_count": 432, "char_count": 1807, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [ "ST514", "ST513", "ST515", "CC4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:52.601294", "source": { "split": "train_shard_00000", "doc_id": 3510 }, "chunk_id": "train_shard_00000_3510_0", "global_id": 3884 }, { "text": "An important feature of the intestinal microbiota, particularly in the case of administered probiotic microorganisms, is their resistance to conditions in the gastrointestinal tract, particularly tolerance to and growth in the presence of bile salts. Bacteria can use several defence mechanisms against bile, including special transport mechanisms, the synthesis of various types of surface proteins and fatty acids or the production of exopolysaccharides. The ability to enzymatically hydrolyse bile salts occurs in a variety of bacteria. Choloylglycine hydrolase (EC 3.5.1.24), a bile salt hydrolase, is a constitutive intracellular enzyme responsible for the hydrolysis of an amide bond between glycine or taurine and the steroid nucleus of bile acids. Its presence was demonstrated in specific microorganisms from several bacterial genera (Lactobacillus spp., Bifidobacterium spp., Clostridium spp., Bacteroides spp.). Occurrence and gene arrangement encoding this enzyme are highly variable in probiotic microorganisms. Bile salt hydrolase activity may provide the possibility to use the released amino acids by bacteria as sources of carbon and nitrogen, to facilitate detoxification of bile or to support the incorporation of cholesterol into the cell wall. Deconjugation of bile salts may be directly related to a lowering of serum cholesterol levels, from which conjugated bile salts are synthesized de novo. Furthermore, the ability of microorganisms to assimilate or to bind ingested cholesterol to the cell wall or to eliminate it by co-precipitation with released cholic acid was also documented. Some intestinal microflora produce cholesterol reductase that catalyses the conversion of cholesterol to insoluble coprostanol, which is subsequently excreted in faeces, thereby also reducing the amount of exogenous cholesterol.\n\nImportance of microbial defence systems to bile salts and mechanisms of serum cholesterol reduction.", "token_count": 489, "char_count": 1940, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:53.252012", "source": { "split": "train_shard_00000", "doc_id": 3511 }, "chunk_id": "train_shard_00000_3511_0", "global_id": 3885 }, { "text": "Paramphistomosis, caused by Calicophoron daubneyi, is an emerging infection of ruminants throughout Western Europe. Despite its prevalence, many questions remain regarding the basic biology of this parasite and how it interacts with its host. Consequently, there is a need to develop methods to study C. daubneyi in vitro to improve our understanding of rumen fluke biology. Towards this, we aimed to identify a suitable protocol for in vitro excystment of C. daubneyi metacercariae. Six methods that have been used to excyst metacercariae from a number of trematode species were tested with C. daubneyi metacercariae. Three of these achieved an average of >50% excystment whilst one method, which included an acid-pepsin treatment, incubation in reducing conditions and an alkaline/bile salt solution to activate the larvae, consistently gave >80% excystment. The latter protocol also showed no detrimental effect on the motility of newly excysted juvenile (NEJ) parasites when observed for up to 24 h in RPMI 1640 medium post-excystment. The successful production of C. daubneyi NEJs in vitro is a significant step forward, and will enable the discovery of infective stage-specific parasite antigens and facilitate drug screening trials, to aid the development of much needed diagnostic and therapeutic options for paramphistomosis.\n\nOptimized conditions for the in vitro excystment of Calicophoron daubneyi metacercariae.", "token_count": 365, "char_count": 1424, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:53.832342", "source": { "split": "train_shard_00000", "doc_id": 3512 }, "chunk_id": "train_shard_00000_3512_0", "global_id": 3886 }, { "text": "Extreme antibiotic resistance in bacteria is associated with the expression of powerful inactivating enzymes and other functions encoded in accessory genomic elements. The contribution of core genome processes to high-level resistance in such bacteria has been unclear. In the work reported here, we evaluated the relative importance of core and accessory functions for high-level resistance to the aminoglycoside tobramycin in the nosocomial pathogen\n\nImportance of Core Genome Functions for an Extreme Antibiotic Resistance Trait.", "token_count": 116, "char_count": 532, "word_count": 74, "semantic_coherence": 1, "information_density": 0.6081, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:54.216570", "source": { "split": "train_shard_00000", "doc_id": 3513 }, "chunk_id": "train_shard_00000_3513_0", "global_id": 3887 }, { "text": "The enzyme carboxyl ester lipase (CEL), also known as bile salt-dependent or -stimulated lipase (BSDL, BSSL), hydrolyzes dietary fat, cholesteryl esters and fat-soluble vitamins in the duodenum. CEL is mainly expressed in pancreatic acinar cells and lactating mammary glands. The human CEL gene resides on chromosome 9q34.3 and contains a variable number of tandem repeats (VNTR) region that encodes a mucin-like protein tail. Although the number of normal repeats does not appear to significantly influence the risk for pancreatic disease, single-base pair deletions in the first VNTR repeat cause a syndrome of endocrine and exocrine dysfunction denoted MODY8. Hallmarks are low fecal elastase levels and pancreatic lipomatosis manifesting before the age of twenty, followed by development of diabetes and pancreatic cysts later in life. The mutant protein forms intracellular and extracellular aggregates, suggesting that MODY8 is a protein misfolding disease. Recently, a recombined allele between CEL and its pseudogene CELP was discovered. This allele (CEL-HYB) encodes a chimeric protein with impaired secretion increasing five-fold the risk for chronic pancreatitis. The CEL gene has proven to be exceptionally polymorphic due to copy number variants of the CEL-CELP locus and alterations involving the VNTR. Genome-wide association studies or deep sequencing cannot easily pick up this wealth of genetic variation. CEL is therefore an attractive candidate gene for further exploration of links to pancreatic disease.\n\nThe role of the carboxyl ester lipase (CEL) gene in pancreatic disease.", "token_count": 421, "char_count": 1598, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [ "MODY8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:54.844256", "source": { "split": "train_shard_00000", "doc_id": 3514 }, "chunk_id": "train_shard_00000_3514_0", "global_id": 3888 }, { "text": "Coronary heart disease (CHD) is one of the major causes of death and disability in industrialised countries, with elevated blood cholesterol an established risk factor. Total plasma cholesterol reduction in populations suffering from primary hypercholesterolemia may lower CHD incidence. This study investigated the cholesterol reducing capacity of Lactobacillus plantarum ECGC 13110402, a strain selected for its high bile salt hydrolase activity, in 49 normal to mildly hypercholesterolaemic adults. Primary efficacy outcomes included effect on blood lipids (total cholesterol (TC), low density lipoproteins (LDL-C), high density lipoproteins (HDL-C) and triacylgycerides (TAG), inflammatory biomarkers and occurrence/severity of gastrointestinal side effects to establish safety and tolerance of the intervention. Secondary outcomes included blood pressure, immune biomarkers, gut microbiota characterisation and metabonome changes. The study was run in a parallel, double blind, placebo controlled, randomised design in which the active group ingested 2x109 CFU encapsulated Lactobacillus plantarum ECGC 13110402 twice daily. Daily ingestion of the active treatment resulted in a statistically significant reduction in LDL-C in volunteers with baseline TC<5mM during the 0-12 week period (13.9%, P = 0.030), a significant reduction in TC in volunteers with baseline TC≥6mM in the 0-6 week period (37.6%, P = 0.045), a significant decrease in TAG (53.9% P = 0.030) and an increase in HDL-C (14.7%, P = 0.007) in the over 60 years population in the 6-12 week period. A statistically significant reduction in systolic blood pressure was also observed across the active study group in the 6-12-week period (6.6%, P = 0.003). No impact on gastrointestinal function and side effects was observed during the study", "token_count": 510, "char_count": 1810, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6231, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:55.502949", "source": { "split": "train_shard_00000", "doc_id": 3515 }, "chunk_id": "train_shard_00000_3515_0", "global_id": 3889 }, { "text": "Similar to blood and urine metabonomic analyses, faecal metagenomics did not reveal significant changes upon active or placebo intake. The results of this study suggest that Lactobacillus plantarum ECGC 13110402 is a well-tolerated, natural probiotic, that may be used as an alternative or supplement to existing treatments to reduce cardiovascular risk.\n\nAn in vivo assessment of the cholesterol-lowering efficacy of Lactobacillus plantarum ECGC 13110402 in normal to mildly hypercholesterolaemic adults.", "token_count": 145, "char_count": 505, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:55.969009", "source": { "split": "train_shard_00000", "doc_id": 3515 }, "chunk_id": "train_shard_00000_3515_1", "global_id": 3890 }, { "text": "Bacterial transformation can insert or delete genomic islands (GIs), depending on the donor and recipient genotypes, if an homologous recombination spans the GI's integration site and includes sufficiently long flanking homologous arms. Combining mathematical models of recombination with experiments using pneumococci found GI insertion rates declined geometrically with the GI's size. The decrease in acquisition frequency with length (1.08×10-3 bp-1) was higher than a previous estimate of the analogous rate at which core genome recombinations terminated. Although most efficient for shorter GIs, transformation-mediated deletion frequencies did not vary consistently with GI length, with removal of 10-kb GIs ∼50% as efficient as acquisition of base substitutions. Fragments of 2 kb, typical of transformation event sizes, could drive all these deletions independent of island length. The strong asymmetry of transformation, and its capacity to efficiently remove GIs, suggests nonmobile accessory loci will decline in frequency without preservation by selection.\n\nTransformation Asymmetry and the Evolution of the Bacterial Accessory Genome.", "token_count": 264, "char_count": 1147, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7643, "quality_score": 0.8822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:56.544378", "source": { "split": "train_shard_00000", "doc_id": 3516 }, "chunk_id": "train_shard_00000_3516_0", "global_id": 3891 }, { "text": "An efficient production system for optically pure l- and d-lactic acid (LA) from Jerusalem artichoke tuber powder (JAP) was developed by metabolic engineering of Kluyveromyces marxianus. To construct LA-producing strains, the ethanol fermentation pathway of K. marxianus was redirected to LA production by disruption of KmPDC1 and expression of l- and d-lactate dehydrogenase (LDH) genes derived from Lactobacillus plantarum under the control of the K. marxianus translation elongation factor 1α promoter. To further increase the LA titer, the l-LA and d-LA consumption pathway of host strains was blocked by deletion of the oxidative LDH genes KmCYB2 and KmDLD1. The recombinant strains produced 130g/L l-LA and 122g/L d-LA by direct fermentation from 230g/L JAP containing 140g/L inulin, without pretreatment or nutrient supplementation. The conversion efficiency and optical purity were ≫>95% and ≫>99%, respectively. This system using JAP and the inulin-assimilating yeast K. marxianus could lead to a cost-effective process for the production of LA.\n\nDirect fermentation of Jerusalem artichoke tuber powder for production of l-lactic acid and d-lactic acid by metabolically engineered Kluyveromyces marxianus.", "token_count": 363, "char_count": 1214, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6069, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:57.168037", "source": { "split": "train_shard_00000", "doc_id": 3517 }, "chunk_id": "train_shard_00000_3517_0", "global_id": 3892 }, { "text": "Bacteroides fragilis, an important component of the human gastrointestinal microbiota, can cause lethal extra-intestinal infection upon escape from the gastrointestinal tract. We demonstrated transfer and recombination of large chromosomal segments from B. fragilis HMW615, a multidrug resistant clinical isolate, to B. fragilis 638R. In one example, the transfer of a segment of ~435 Kb/356 genes replaced ~413 Kb/326 genes of the B. fragilis 638R chromosome. In addition to transfer of antibiotic resistance genes, these transfers (1) replaced complete divergent polysaccharide biosynthesis loci; (2) replaced DNA inversion-controlled intergenic shufflons (that control expression of genes encoding starch utilization system outer membrane proteins) with more complex, divergent shufflons; and (3) introduced additional intergenic shufflons encoding divergent Type 1 restriction/modification systems. Conjugative transposon-like genes within a transferred segment and within a putative integrative conjugative element (ICE5) ~45 kb downstream from the transferred segment both encode proteins that may be involved in the observed transfer. These data indicate that chromosomal transfer is a driver of antigenic diversity and nutrient adaptation in Bacteroides that (1) contributes to the dissemination of the extensive B. fragilis pan-genome, (2) allows rapid adaptation to a changing environment and (3) can confer pathogenic characteristics to host symbionts.\n\nNovel large-scale chromosomal transfer in Bacteroides fragilis contributes to its pan-genome and rapid environmental adaptation.", "token_count": 413, "char_count": 1593, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [ "ICE5", "HMW615" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:57.823048", "source": { "split": "train_shard_00000", "doc_id": 3518 }, "chunk_id": "train_shard_00000_3518_0", "global_id": 3893 }, { "text": "Most Staphylococcus aureus isolates can cause invasive disease given the right circumstances, but it is unknown if some isolates are more likely to cause severe infections than others. S. aureus bloodstream isolates from 120 patients with definite infective endocarditis and 121 with S. aureus bacteraemia without infective endocarditis underwent whole-genome sequencing. Genome-wide association analysis was performed using a variety of bioinformatics approaches including SNP analysis, accessory genome analysis and k-mer based analysis. Core and accessory genome analyses found no association with either of the two clinical groups. In this study, the genome sequences of S. aureus bloodstream isolates did not discriminate between bacteraemia and infective endocarditis. Based on our study and the current literature, it is not convincing that a specific S. aureus genotype is clearly associated to infective endocarditis in patients with S. aureus bacteraemia.\n\nWhole-genome sequencing of bloodstream Staphylococcus aureus isolates does not distinguish bacteraemia from endocarditis.", "token_count": 272, "char_count": 1088, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6242, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:58.379797", "source": { "split": "train_shard_00000", "doc_id": 3519 }, "chunk_id": "train_shard_00000_3519_0", "global_id": 3894 }, { "text": "Homoeologous exchanges (HEs) have been shown to generate novel gene combinations and phenotypes in a range of polyploid species. Gene presence/absence variation (PAV) is also a major contributor to genetic diversity. In this study, we show that there is an association between these two events, particularly in recent Brassica napus synthetic accessions, and that these represent a novel source of genetic diversity, which can be captured for the improvement of this important crop species. By assembling the pangenome of B. napus, we show that 38% of the genes display PAV behaviour, with some of these variable genes predicted to be involved in important agronomic traits including flowering time, disease resistance, acyl lipid metabolism and glucosinolate metabolism. This study is a first and provides a detailed characterization of the association between HEs and PAVs in B. napus at the pangenome level.\n\nHomoeologous exchange is a major cause of gene presence/absence variation in the amphidiploid Brassica napus.", "token_count": 240, "char_count": 1021, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6323, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:58.857198", "source": { "split": "train_shard_00000", "doc_id": 3520 }, "chunk_id": "train_shard_00000_3520_0", "global_id": 3895 }, { "text": "Campylobacter jejuni, the leading cause of bacterial acute gastroenteritis worldwide, secretes an arsenal of virulence-associated proteins within outer membrane vesicles (OMVs). C. jejuni OMVs contain three serine proteases (HtrA, Cj0511, and Cj1365c) that cleave the intestinal epithelial cell (IEC) tight and adherens junction proteins occludin and E-cadherin, promoting enhanced C. jejuni adhesion to and invasion of IECs. C. jejuni OMVs also induce IECs innate immune responses. The bile salt sodium taurocholate (ST) is sensed as a host signal to coordinate the activation of virulence-associated genes in the enteric pathogen Vibrio cholerae. In this study, the effect of ST on C. jejuni OMVs was investigated. Physiological concentrations of ST do not have an inhibitory effect on C. jejuni growth until the early stationary phase. Coculture of C. jejuni with 0.1% or 0.2% (w/v) ST stimulates OMV production, increasing both lipid and protein concentrations. C. jejuni ST-OMVs possess increased proteolytic activity and exhibit a different protein profile compared to OMVs isolated in the absence of ST. ST-OMVs exhibit enhanced cytotoxicity and immunogenicity to T84 IECs and enhanced killing of Galleria mellonella larvae. ST increases the level of mRNA transcripts of the OMVs-associated serine protease genes and the cdtABC operon that encodes the cytolethal distending toxin. Coculture with ST significantly enhances the OMVs-induced cleavage of E-cadherin and occludin. C. jejuni OMVs also cleave the major endoplasmic reticulum chaperone protein BiP/GRP78 and this activity is associated with the Cj1365c protease. These data suggest that C", "token_count": 497, "char_count": 1654, "word_count": 241, "semantic_coherence": 1, "information_density": 0.639, "quality_score": 0.8195, "entities": { "genes": [ "GRP78" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:59.508265", "source": { "split": "train_shard_00000", "doc_id": 3521 }, "chunk_id": "train_shard_00000_3521_0", "global_id": 3896 }, { "text": "jejuni responds to the presence of physiological concentrations of the bile salt ST that increases OMV production and the synthesis of virulence-associated factors that are secreted within the OMVs. We propose that these events contribute to pathogenesis.\n\nThe bile salt sodium taurocholate induces Campylobacter jejuni outer membrane vesicle production and increases OMV-associated proteolytic activity.", "token_count": 101, "char_count": 404, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:33:59.885341", "source": { "split": "train_shard_00000", "doc_id": 3521 }, "chunk_id": "train_shard_00000_3521_1", "global_id": 3897 }, { "text": "Self-emulsifying drug delivery systems, commonly used for oral delivery of poorly soluble compounds, were used to formulate water soluble but moisture labile compounds for rectal application. The objective was to use the oily phase of the system to formulate a liquid, non-aqueous product while obtaining the advantages of self-emulsification, rapid contact with the rectal mucosa and rapid absorption post-administration. Ceftriaxone was used as a model drug and the human bile salt sodium chenodeoxycholate was used as an absorption enhancer. After preliminary screening of 23 excipients, based on their emulsification ability and emulsion fineness in binary and ternary mixtures, a full factorial design was used to screen different formulations of three preselected excipients. The optimal formulation contained 60% of excipients, namely Capryol 90, Kolliphor EL and Kolliphor PS20 in 4 : 6 : 6 ratio and 40% of a powder blend that included 500 mg of ceftriaxone. Characterization of the system showed that it complied with the requirements for rectal administration, in particular rapid emulsification in a small quantity of liquid. Rabbit bioavailability showed rapid absorption of ceftriaxone, achieving 128% bioavailability compared to powder control formulation. These results demonstrated the potential of self-emulsifying formulations for rectal administration of Class 3 BCS drugs.\n\nDevelopment of rectal self-emulsifying suspension of a moisture-labile water-soluble drug.", "token_count": 365, "char_count": 1485, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8152, "entities": { "genes": [ "PS20" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:00.473027", "source": { "split": "train_shard_00000", "doc_id": 3522 }, "chunk_id": "train_shard_00000_3522_0", "global_id": 3898 }, { "text": "Cellulose is a renewable feedstock for green industry. It is therefore important to develop a technique to construct a host with a high cellulolytic efficiency to digest cellulose. In this study, we developed a convenient host-engineering technique to adjust the expression levels of heterologous genes in the host by promoter rearrangement and gene copy number adjustment. Using genes from different glycoside hydrolase (GH) families including GH2, GH3, GH5, GH6, GH7, and GH12 from Aspergillus niger, Trichoderma reesei, and Neocallimastix patriciarum, we constructed a cellulolytic Kluyveromyces marxianus with eight cellulase gene-cassettes that produced a cellulase cocktail with a high cellulolytic efficiency, leading to a significant reduction in enzyme cost in a rice straw saccharification process. Our technique can be used to design a host that can efficiently convert biomass feedstock to biofuel.\n\nConstructing a cellulosic yeast host with an efficient cellulase cocktail.", "token_count": 258, "char_count": 986, "word_count": 141, "semantic_coherence": 1, "information_density": 0.695, "quality_score": 0.8475, "entities": { "genes": [ "GH2", "GH6", "GH5", "GH3", "GH7", "GH12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:01.021113", "source": { "split": "train_shard_00000", "doc_id": 3523 }, "chunk_id": "train_shard_00000_3523_0", "global_id": 3899 }, { "text": "In the last few years, the demand for the tremendous therapeutic applications of indigenous probiotic bacteria from diversified fermented food products has surged. In view of this, the present study was documented to evaluate the anti-tubercular and probiotic properties of coagulase-negative staphylococci (CNS) indigenous to Koozh, a traditional fermented food product of South India. A total of 18 isolates were purified from Koozh, and tested for anti-tubercular activity against Mycobacterium tuberculosis H37Rv using luciferase reporter phage (LRP) assay. Among them, six isolates revealed higher percentage (>90%) of relative light unit (RLU) reduction. These six isolates were further evaluated for their in vitro probiotic attributes using standard protocols. All six staphylococci strains disclosed good probiotic properties. Moreover, Staphylococcus hominis strain MANF2 showed high cell survival percentage (92.2%) at pH 2.0 as well as towards simulated gastric juice (88.51%). Furthermore, strain MANF2 was found to be resistant to bile salt after 24 h of incubation with maximal viability of 5.71 ± 0.02 log cfu/mL, and depicted the deconjugation of bile salt as well. All the isolates exhibited strong auto-aggregation capacity (44.4 ± 1.2-68.1 ± 1.5%), and hydrophobicity against toluene (55.0 ± 1.2-72.0 ± 1.1%). Additionally, strain MANF2 was observed to be highly resistant to phenol (6.27 ± 0.01 log cfu/mL) and lysozyme (81.1 ± 1.6% viability). Most importantly, all six isolates depicted good hypocholesterolemic effect, slight β-galactosidase activity, and moderate proteolytic property. The strains were sensitive to all the tested conventional antibiotics, except Nalidixic acid", "token_count": 510, "char_count": 1703, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [ "MANF2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:02.414442", "source": { "split": "train_shard_00000", "doc_id": 3524 }, "chunk_id": "train_shard_00000_3524_0", "global_id": 3900 }, { "text": "In addition to this, all staphylococci strains demonstrated significant DPPH (2,2-Diphenyl-1-picrylhydrazyl) scavenging, hydrogen peroxide tolerance, and hydroxyl radical scavenging activity in a dose dependent manner, thereby exhibiting the potent antioxidative properties of isolates. The negative results obtained from haemolytic, DNase, and gelatinase tests revealed the non-pathogenicity and safety aspect of these strains. In a nutshell, the present investigation divulges the persuasive anti-tubercular and probiotic properties of staphylococci, particularly strain MANF2, and recommended the further exploitation of Koozh associated CNS in pharmaceutics.\n\nAnti-tubercular and probiotic properties of coagulase-negative staphylococci isolated from Koozh, a traditional fermented food of South India.", "token_count": 220, "char_count": 806, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7347, "quality_score": 0.8673, "entities": { "genes": [ "MANF2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:02.876328", "source": { "split": "train_shard_00000", "doc_id": 3524 }, "chunk_id": "train_shard_00000_3524_1", "global_id": 3901 }, { "text": "The extent of genome divergence and the evolutionary events leading to speciation of marine bacteria have mostly been studied for (locally) abundant, free-living groups. The genus Phaeobacter is found on different marine surfaces, seems to occupy geographically disjunct habitats, and is involved in different biotic interactions, and was therefore targeted in the present study. The analysis of the chromosomes of 32 closely related but geographically spread Phaeobacter strains revealed an exceptionally large, highly syntenic core genome. The flexible gene pool is constantly but slightly expanding across all Phaeobacter lineages. The horizontally transferred genes mostly originated from bacteria of the Roseobacter group and horizontal transfer most likely was mediated by gene transfer agents. No evidence for geographic isolation and habitat specificity of the different phylogenomic Phaeobacter clades was detected based on the sources of isolation. In contrast, the functional gene repertoire and physiological traits of different phylogenomic Phaeobacter clades were sufficiently distinct to suggest an adaptation to an associated lifestyle with algae, to additional nutrient sources, or toxic heavy metals. Our study reveals that the evolutionary trajectories of surface-associated marine bacteria can differ significantly from free-living marine bacteria or marine generalists.\n\nTrajectories and Drivers of Genome Evolution in Surface-Associated Marine Phaeobacter.", "token_count": 312, "char_count": 1478, "word_count": 200, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:03.441622", "source": { "split": "train_shard_00000", "doc_id": 3525 }, "chunk_id": "train_shard_00000_3525_0", "global_id": 3902 }, { "text": "Fermented foods are known for their potential as main source of probiotics. The present study aimed at investigating the probiotic properties of bacteria isolated from fermented mango pickle. Non-hemolytic fermenting microbiota isolated from mango pickle was screened in vitro for their basic probiotic properties such as acid tolerance, bile salt, lysozyme and salt tolerance. They were also tested for their beneficial characters like cholesterol removal, bacterial adhesion to hydrocarbons, auto-aggregation, antimicrobial activity, β-galactosidase activity, exopolysaccharide production and adhesion to HT-29 cell line. Outputs of these parameters were subjected to principal component analysis (PCA) and these results were interpreted to select prospective bacterial isolates that can be used as potential probiotics. Out of eight isolates, PUFSTP35 (\n\nCharacterization of probiotic potential of", "token_count": 219, "char_count": 900, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [ "PUFSTP35" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:03.911299", "source": { "split": "train_shard_00000", "doc_id": 3526 }, "chunk_id": "train_shard_00000_3526_0", "global_id": 3903 }, { "text": "Liposomes are considered a major route for encapsulation of hydrophilic and hydrophobic molecules. Chitosan coated liposomes could represent an alternative way as a carrier for delivery of drugs in human body. In this study the preparation and applicability of chitosan-coated liposomes containing curcumin as well as curcumin loaded anionic liposomes were evaluated. The applicability of the carriers was tested by means of an in-vitro digestion procedure allowing for measurement of the bioaccessibility of ingested curcumin. Values of diameter, polydispersity index and surface charge for curcumin loaded anionic liposomes obtained through dynamic light scattering and ζ-potential measurements were 129nm, 0.095 and -49mV, respectively. After chitosan-coating, diameter and polydispersity index remain unvaried while the surface charge gets positive. Slightly higher curcumin concentrations were found after the mouth and the stomach digestion phases when curcumin was loaded in anionic liposomes. On the contrary, after the intestinal phase, a higher percentage of curcumin was found when chitosan-coated liposomes were used as carrier, both in the raw digesta and in the bile salt micellar phase. It was shown that the presence of a positively charged surface allows a better absorption of curcumin in the small intestine phase, which increases the overall curcumin bioavailability. The mechanism behind these results can be understood from the composition of the different environments generated by the digestive fluids that differently interact with anionic or cationic surfaces.\n\nIn-vitro digestion of curcumin loaded chitosan-coated liposomes.", "token_count": 391, "char_count": 1652, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:04.533066", "source": { "split": "train_shard_00000", "doc_id": 3527 }, "chunk_id": "train_shard_00000_3527_0", "global_id": 3904 }, { "text": "Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.\n\nA novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.", "token_count": 83, "char_count": 327, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8409, "quality_score": 0.9205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:04.908165", "source": { "split": "train_shard_00000", "doc_id": 3528 }, "chunk_id": "train_shard_00000_3528_0", "global_id": 3905 }, { "text": "Many of the bacterial genomic studies exploring evolution processes of the host adaptation focus on the accessory genome describing how the gains and losses of genes can explain the colonization of new habitats. Consequently, we developed a new approach focusing on the coregenome in order to describe the host adaptation of Salmonella serovars.\n\nFirst gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts.", "token_count": 113, "char_count": 506, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:05.288815", "source": { "split": "train_shard_00000", "doc_id": 3529 }, "chunk_id": "train_shard_00000_3529_0", "global_id": 3906 }, { "text": "The bioprospecting proficient of novel pigmented probiotic strains with respect to aquaculture industry was unexplored hitherto. In this study, we investigated the probiotic potential of novel pigmented bacterial strains isolated from the indigenous soil sediments in their vicinal habitats, which were screened for their antimicrobial activity against aquatic pathogens using agar well diffusion assay. The strains namely Exiguobacterium acetylicum (S01), Aeromonas veronii (V03), and Chryseobacterium joostei (V04) were phenotypically identified and confirmed by 16S rRNA gene sequence analysis. Further characterization revealed that strains S01 and V03 survive relatively in lower pH and higher bile salt concentrations and possess good adherence ability and broad-spectrum antibiotic susceptibility. The isolate S01 exhibited the higher adhesion ability to hydrocarbons (82%) and mannose-specific adhesion (msa) gene expression. Additionally, the probiotic effects were evaluated in Artemia nauplii fed with algae supplemented with S01, V03, and V04 strains (2.7 × 10\n\nFunctional Characterization of Probiotic Potential of Novel Pigmented Bacterial Strains for Aquaculture Applications.", "token_count": 326, "char_count": 1191, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7006, "quality_score": 0.8503, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:05.855695", "source": { "split": "train_shard_00000", "doc_id": 3530 }, "chunk_id": "train_shard_00000_3530_0", "global_id": 3907 }, { "text": "Apolipoprotein E (ApoE) plays a central role in lipid transport and cholesterol metabolism, with surplus cholesterol being removed from the liver through bile acid (BA) synthesis. Furthermore, BAs are of critical importance in fat absorption by forming intestinal lipid-bile salt mixed micelles. To define ApoE's role in BA homeostasis, the metabolism of cholesterol and BA was investigated in liver tissue and gallbladder bile of ApoE-deficient mice given a chow or high-cholesterol/high-fat diet (HCHF) diet for 6 months. When compared to wild-type mice, muricholic acid (MCA) and chenodeoxycholic acid (CDCA) increased approximately 15-, 82-, 22- and 38-fold, respectively, in hepatic tissue of ApoE-deficient mice given a chow or HCHF diet. Moreover, ApoE-deficient mice on an HCHF diet increased the amounts of hepatic free cholesterol, MCA and CDCA by 61%, 61% and 50% (P<.05). Conversely, total cholesterol and cholesterol esters were unchanged, and the bile acids taurohyodeoxycholic acid, taurodeoxycholic acid and hyodeoxycholic acid decreased to one third as compared to the chow diet (P<.05). Additionally, quantitative reverse-transcription polymerase chain reaction assays revealed induced expression of the bile acid receptor (Fxr) and associated transcription factors, i.e.Fxr, Lrh, Lxra and Srebp1c. Transcript expression of Cyp2a12, Cyp1b1, Cyp2e1, Cyp3a16 and Cyp4a10 was also induced. Note that Cyp4a10 catalyzes ω-hydroxylation of arachidonic acid to epoxy- and hydroxyeicosatrienoic acids to control vascular tone. Altogether, MCA and CDCA synthesis is selectively induced in ApoE-deficient mice", "token_count": 516, "char_count": 1617, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:34:06.515769", "source": { "split": "train_shard_00000", "doc_id": 3531 }, "chunk_id": "train_shard_00000_3531_0", "global_id": 3908 }, { "text": "These hydrophilic BAs alter micellar size and structure to lower intestinal cholesterol solubilization. Furthermore, CDCA and MCA are potent FXR agonist and antagonist, respectively, and function in a regulatory loop to mitigate impaired ApoE function.\n\nApoE is a major determinant of hepatic bile acid homeostasis in mice.", "token_count": 90, "char_count": 323, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:06.886915", "source": { "split": "train_shard_00000", "doc_id": 3531 }, "chunk_id": "train_shard_00000_3531_1", "global_id": 3909 }, { "text": "The present work reveals the binding interactions of a credible cancer cell photosensitizer, harmane (HM), with some selected bile salt aggregates of dissimilar hydrophobicity viz. sodium deoxycholate (NaDC), sodium cholate (NaC) and sodium taurocholate (NaTC). The explicit variation of the prototropic equilibrium of the photosensitizer both in the ground and excited state has been utilized to scrutinize the interaction phenomena. Differential modulation in the prototropic equilibrium of HM in the aforesaid aggregates has been explained on the basis of the structural dissimilarities of the bile salt monomers. The contrived hydrophobic surroundings provided by the aggregates have been reflected on the spectroscopic results, especially in the time-resolved fluorescence and the rotational dynamical behavior of the molecule of interest. Slow solvent reorientation time with regard to the lifetime of HM proliferated by the red-edge effect in two specific bile salts namely NaC and NaTC, whereas its absence in NaDC aggregates has also been elucidated on the basis of accessibility of the solvent molecules within the aggregates.\n\nDifferential Perturbation of the Protrotropic Equilibrium of a Biological Photosensitizer within Bile Salt Aggregates of Varying Hydrophobicity: A Fluorimetric Investigation.", "token_count": 322, "char_count": 1312, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5815, "quality_score": 0.7908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:07.461212", "source": { "split": "train_shard_00000", "doc_id": 3532 }, "chunk_id": "train_shard_00000_3532_0", "global_id": 3910 }, { "text": "Mango fruits (Mangifera indica L.) are highly perishable, causing postharvest losses and producing agroindustrial waste. In the present work, native yeasts were used to evaluate ethanol production in overripe mango pulp. The two isolated strains showed similar sequences in the 18S rDNA region corresponding to Kluyveromyces marxianus, being different to the data reported in the NCBI database. Values of up to 5% ethanol (w/v) were obtained at the end of fermentation, showing a productivity of 4g/l/day, a yield of up to 49% of ethanol and a process efficiency of 80%. These results represent a viable option for using the surplus production and all the fruits that have suffered mechanical injury that are not marketable and are considered as agroindustrial waste, thus achieving greater income and less postharvest losses.\n\nNative yeasts for alternative utilization of overripe mango pulp for ethanol production.", "token_count": 228, "char_count": 916, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6714, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:07.951959", "source": { "split": "train_shard_00000", "doc_id": 3533 }, "chunk_id": "train_shard_00000_3533_0", "global_id": 3911 }, { "text": "Lactobacillus plantarum MA2 was isolated from traditional Chinese Tibetan kefir grains. Its antioxidant properties had been demonstrated in vitro and in vivo previously. In the present study, the probiotic characteristics of this strain were further evaluated by investigating its acid and bile salt tolerances, cell surface hydrophobicity, and autoaggregation, respectively. In addition, the cellular antioxidant activity (CAA) assay was applied to test the antioxidant capacity of the isolate in different growth phases. Same method was also used to evaluate the antioxidant capacity of its fermentation supernatant, cell-free extract, and intact cell quantitatively. The results of probiotic characteristic tests showed that MA2 could survive at pH 2.5 and 0.3% bile salt. Meanwhile, the measurements of cell surface hydrophobicity and autoaggregation were 45.29 ± 2.15 and 6.30 ± 0.34%, respectively. The results of cellular antioxidant activity tests indicated that MA2 had high antioxidant potential. The CAA value of logarithmic phase cell-free extract of MA2 (39,450.00 ± 424.05 μmol quercetin equivalents/100 g sample) was significantly higher than that in stationary phase cell-free extract (3395.98 ± 126.06 μmol quercetin equivalents/100 g sample) and that of fermentation supernatant in logarithmic phase (2174.41 ± 224.47 μmol quercetin equivalents/100 g sample) (p < 0.05). The CAA method was successively applied to evaluate the antioxidant capacity of MA2 in this study, which suggests that it could be used as a useful method for lactic acid bacteria antioxidant potential evaluation.", "token_count": 491, "char_count": 1602, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5584, "quality_score": 0.7792, "entities": { "genes": [ "MA2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:08.625073", "source": { "split": "train_shard_00000", "doc_id": 3534 }, "chunk_id": "train_shard_00000_3534_0", "global_id": 3912 }, { "text": "Probiotic Properties and Cellular Antioxidant Activity of Lactobacillus plantarum MA2 Isolated from Tibetan Kefir Grains.", "token_count": 37, "char_count": 121, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "MA2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:08.995925", "source": { "split": "train_shard_00000", "doc_id": 3534 }, "chunk_id": "train_shard_00000_3534_1", "global_id": 3913 }, { "text": "The interaction of pancreatic lipase-related protein 2 (PLRP2) with various micelles containing phospholipids was investigated using pHstat enzyme activity measurements, differential light scattering, size exclusion chromatography (SEC) and transmission IR spectroscopy. Various micelles of 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) and lysophosphatidylcholine were prepared with either bile salts (sodium taurodeoxycholate or glycodeoxycholate) or Triton X-100, which are substrate-dispersing agents commonly used for measuring phospholipase activities. PLRP2 displayed a high activity on all phospholipid-bile salt micelles, but was totally inactive on phospholipid-Triton X-100 micelles. These findings clearly differentiate PLRP2 from secreted pancreatic phospholipase A2 which is highly active on both types of micelles. Using an inactive variant of PLRP2, SEC experiments allowed identifying two populations of PLRP2-DPPC-bile salt complexes corresponding to a high molecular weight 1:1 PLRP2-micelle association and to a low molecular weight association of PLRP2 with few monomers of DPPC/bile salts. IR spectroscopy analysis showed how DPPC-bile salt micelles differ from DPPC-Triton X-100 micelles by a higher fluidity of acyl chains and higher hydration/H-bonding of the interfacial carbonyl region. The presence of bile salts allowed observing changes in the IR spectrum of DPPC upon addition of PLRP2 (higher rigidity of acyl chains, dehydration of the interfacial carbonyl region), while no change was observed with Triton X-100. The differences between these surfactants and their impact on substrate recognition by PLRP2 are discussed, as well as the mechanism by which high and low molecular weight PLRP2-DPPC-bile salt complexes may be involved in the overall process of DPPC hydrolysis.", "token_count": 499, "char_count": 1813, "word_count": 243, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [ "PLRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:09.692221", "source": { "split": "train_shard_00000", "doc_id": 3535 }, "chunk_id": "train_shard_00000_3535_0", "global_id": 3914 }, { "text": "IR spectroscopy analysis of pancreatic lipase-related protein 2 interaction with phospholipids: 2. Discriminative recognition of various micellar systems and characterization of PLRP2-DPPC-bile salt complexes.", "token_count": 57, "char_count": 209, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [ "PLRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:10.071572", "source": { "split": "train_shard_00000", "doc_id": 3535 }, "chunk_id": "train_shard_00000_3535_1", "global_id": 3915 }, { "text": "Brucellosis is an important zoonotic disease caused by Brucella spp. We present a phylogeny of 552 strains based on genome-wide single nucleotide polymorphisms (SNPs) determined by an alignment-free k-mer approach. A total of 138,029 SNPs were identified from 552 Brucella genomes. Of these, 31,152 and 106,877 were core and non-core SNPs, respectively. Based on pan-genome analysis 11,937 and 972 genes were identified as pan and core genome, respectively. The pan-genome-wide analysis studies (Pan-GWAS) could not identify the group-specific variants in Brucella spp. Therefore, we focused on SNP based genome-wide association studies (SNP-GWAS) to identify the species-specific genetic determinants in Brucella spp. Phylogenetic tree representing eleven recognized Brucella spp. showed 16 major lineages. We identified 143 species-specific SNPs in Brucella abortus that are conserved in 311 B. abortus genomes. Of these, 141 species-specific SNPs were confined in the positively significant SNPs of B. abortus using SNP-GWAS. Since conserved in all the B. abortus genomes studied, these SNPs might have originated very early during the evolution of B. abortus and might be responsible for the evolution of B. abortus with cattle as the preferred host. Similarly, we identified 383 species-specific SNPs conserved in 132 Brucella melitensis genomes. Of these 379 species-specific SNPs were identified as positively associated using GWAS. Interestingly, >98% of the SNPs that are significantly, positively associated with the traits showed 100% sensitivity and 100% specificity. These identified species-specific core-SNPs identified in Brucella genomes could be responsible for the speciation and their respective host adaptation.\n\nIdentification of genetic variants of Brucella spp. through genome-wide association studies.", "token_count": 499, "char_count": 1826, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5234, "quality_score": 0.7617, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:10.723043", "source": { "split": "train_shard_00000", "doc_id": 3536 }, "chunk_id": "train_shard_00000_3536_0", "global_id": 3916 }, { "text": "High potential, thermotolerant, ethanol-producing yeasts were successfully isolated in this study. Based on molecular identification and phylogenetic analysis, the isolated thermotolerant yeasts were clustered in the genera of Pichia kudriavzevii, Candida tropicalis, Candida orthopsilosis, Candida glabrata and Kodamea ohmeri. A comparative study of ethanol production using 160g/L glucose as a substrate revealed several yeast strains that could produce high ethanol concentrations at high temperatures. When sugarcane bagasse (SCB) hydrolysate containing 85g/L glucose was used as a substrate, the yeast strain designated P. kudriavzevii RZ8-1 exhibited the highest ethanol concentrations of 35.51g/L and 33.84g/L at 37°C and 40°C, respectively. It also exhibited multi-stress tolerance, such as heat, ethanol and acetic acid tolerance. During ethanol fermentation at high temperature (42°C), genes encoding heat shock proteins (ssq1 and hsp90), alcohol dehydrogenases (adh1, adh2, adh3 and adh4) and glyceraldehyde-3-phosphate dehydrogenase (tdh2) were up-regulated, suggesting that these genes might play a crucial role in the thermotolerance ability of P. kudriavzevii RZ8-1 under heat stress. These findings suggest that the growth and ethanol fermentation activities of this organism under heat stress were restricted to the expression of genes involved not only in heat shock response but also in the ethanol production pathway.\n\nThe potential of the newly isolated thermotolerant yeast Pichia kudriavzevii RZ8-1 for high-temperature ethanol production.", "token_count": 455, "char_count": 1562, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8152, "entities": { "genes": [ "RZ8" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:11.371198", "source": { "split": "train_shard_00000", "doc_id": 3537 }, "chunk_id": "train_shard_00000_3537_0", "global_id": 3917 }, { "text": "Comprehension of underlying mechanisms of probiotic action will support rationale selection of probiotic strains and targeted clinical study design with a higher likelihood of success. This will consequently contribute to better substantiation of health claims. Here, we aim to provide a perspective from a microbiology point of view that such comprehensive understanding is not straightforward. We show examples of well-documented probiotic effector molecules in Lactobacillus and Bifidobacterium strains, including surface-located molecules such as specific pili, S-layer proteins, exopolysaccharides, muropeptides, as well as more widely produced metabolites such as tryptophan-related and histamine-related metabolites, CpG-rich DNA, and various enzymes such as lactase and bile salt hydrolases. We also present recent advances in genetic tool development, microbiome analyses and model systems, as well as perspectives on how the field could further progress. This opinion is based on a discussion group organized at the annual meeting of the International Scientific Association on Probiotics and Prebiotics (ISAPP) in June 2017.\n\nIdentification of probiotic effector molecules: present state and future perspectives.", "token_count": 279, "char_count": 1223, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7212, "quality_score": 0.8606, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:11.929317", "source": { "split": "train_shard_00000", "doc_id": 3538 }, "chunk_id": "train_shard_00000_3538_0", "global_id": 3918 }, { "text": "Fusarium oxysporum is a large species complex of both plant and human pathogens that attack a diverse array of species in a host-specific manner. Comparative genomic studies have revealed that the host-specific pathogenicity of the F. oxysporum species complex (FOSC) was determined by distinct sets of supernumerary (SP) chromosomes. In contrast to common vertical transfer, where genetic materials are transmitted via cell division, SP chromosomes can be transmitted horizontally between phylogenetic lineages, explaining the polyphyletic nature of the host-specific pathogenicity of the FOSC. The existence of a diverse array of SP chromosomes determines the broad host range of this species complex, while the conserved core genome maintains essential house-keeping functions. Recognition of these SP chromosomes enables the functional and structural compartmentalization of F. oxysporum genomes. In this review, we examine the impact of this group of cross-kingdom pathogens on agricultural productivity and human health. Focusing on the pathogenicity of F. oxysporum in the phylogenomic framework of the genus Fusarium, we elucidate the evolution of pathogenicity within the FOSC. We conclude that a population genomics approach within a clearly defined phylogenomic framework is essential not only for understanding the evolution of the pathogenicity mechanism but also for identifying informative candidates associated with pathogenicity that can be developed as targets in disease management programs.\n\nDeciphering Pathogenicity of Fusarium oxysporum From a Phylogenomics Perspective.", "token_count": 353, "char_count": 1593, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:12.501521", "source": { "split": "train_shard_00000", "doc_id": 3539 }, "chunk_id": "train_shard_00000_3539_0", "global_id": 3919 }, { "text": "In the central microbiology laboratory of Gazi University Hospital Candida kefyr was isolated from different clinical samples as 5.3% in 2016 and in 2017 this rate increased to 9.3% which was nearly two-fold and this has drawn our attention. The aim of this study was to evaluate the special characteristics, antifungal susceptibility and virulence properties of C.keyfr species. Germ tube, corn meal-tween 80 agar morphology and carbohydrate assimilation profiles on ID32C yeast identification system were used for the diagnosis of Candida species. In this study, DNA sequencing was performed using ITS1 and ITS4 primers amplifying fungal gene between 5.8S and 18S regions of rRNA. Antifungal susceptibility was performed using M27A microdilution method recommended by Clinical and Laboratory Standards Institute (CLSI). Minimum inhibitory concentration (MIC) values for amphotericin B, fluconazole, voriconazole and itraconazole were determined. MIC distribution, MIC50 and MIC90 values and geometric mean (GM) were detected. The existence of virulence factors caseinase, secreted aspartyl proteinase, esterase and phospholipase were investigated in vitro. A total of 865 Candida species were isolated from different clinical samples in the central microbiology laboratory of Gazi University Hospital in 2016. Among them, 46 (5.3%) were C.kefyr. In the first four months of 2017, 30 (9.3%) C.kefyr were identified among 320 Candida isolates. Ten isolates which have shown atypical morphology on corn meal agar were selected. Among these 10 isolates, nine of them were identified as C.kefyr by using ID32C system and DNA sequencing method. Amphotericin B MIC value was 2 µg/ml for one isolate, and fluconazole MIC value was 8 µg/ml for another isolate among 46 isolates", "token_count": 493, "char_count": 1770, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [ "ID32C", "ITS1", "MIC90", "ITS4", "MIC50" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:13.157172", "source": { "split": "train_shard_00000", "doc_id": 3540 }, "chunk_id": "train_shard_00000_3540_0", "global_id": 3920 }, { "text": "Among the 30 isolates of the year 2017, one of them presented MIC value for fluconazole as 8 µg/ml. No marked antifungal resistance was detected in our isolate group. Caseinase was positive in one C.kefyr isolate, and phospholipase were positive in eight of nine isolates. As a result, the reason of increase in the incidence of this Candida species, which does not show significant resistance and presents mostly phospholipase activity as a virulence factor, should be investigated in more detail.\n\n[Emerging pathogen: Candida kefyr (Kluvyeromyces marxianus)].", "token_count": 156, "char_count": 561, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7558, "quality_score": 0.8779, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:13.594058", "source": { "split": "train_shard_00000", "doc_id": 3540 }, "chunk_id": "train_shard_00000_3540_1", "global_id": 3921 }, { "text": "Drug-induced liver injury (DILI) has been the most frequent cause of post-marketing drug withdrawals in the last 50years. The multifactorial nature of events that precede severe liver injury in human patients is difficult to model in rodents due to a variety of confounding or contributing factors that include disease state, concurrent medications, and translational species differences. In retrospective analyses, a consistent risk factor for DILI has been the inhibition of the Bile Salt Export Pump (BSEP). One compound known for potent BSEP inhibition and severe DILI is troglitazone. The purpose of the current study is to determine if serum profiling of 19 individual bile acids by liquid chromatography-mass spectrometry (LC/MS) can detect perturbations in bile acid homeostasis in rats after acute intravenous (IV) administration of vehicle or 5, 25, or 50mg/kg troglitazone. Minimal serum transaminase elevations (approximately two-fold) were observed with no evidence of microscopic liver injury. However, marked changes in individual serum bile acids occurred, with dose-dependent increases in the majority of the bile acids profiled. When compared to predose baseline values, tauromuricholic acid and taurocholic acid had the most robust increase in serum levels and dynamic range, with a maximum fold increase from baseline of 34-fold and 29-fold, respectively. Peak bile acid increases occurred within 2hours (h) after dosing and returned to baseline values before 24h. In conclusion, serum bile acid profiling can potentially identify a mechanistic risk of clinical DILI that could be poorly detected by traditional toxicity endpoints.\n\nIndividual serum bile acid profiling in rats aids in human risk assessment of drug-induced liver injury due to BSEP inhibition.", "token_count": 441, "char_count": 1780, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6069, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:14.228299", "source": { "split": "train_shard_00000", "doc_id": 3541 }, "chunk_id": "train_shard_00000_3541_0", "global_id": 3922 }, { "text": "The present work is the first report on spontaneous fermentation of curly kale and characteristics of autochthonous lactic acid bacteria (LAB). Our results indicate that curly kale fermentation is the new possibility of the technological use of this vegetable. Bacteria representing ten different species were isolated from three phases of curly kale fermentation and identified by MALDI-TOF mass spectrometry and 16S rRNA gene sequencing. Among them, four species were identified as Lactobacillus spp. (Lb. plantarum 332, Lb. paraplantarum G2114, Lb. brevis R413, Lb. curvatus 154), two as Weissella spp. (W. hellenica 152, W. cibaria G44), two as Pediococcus spp. (P. pentosaceus 45AN, P. acidilactici 2211), one as Leuconostoc mesenteroides 153, and one as Lactococcus lactis 37BN. The functional properties of isolates, i.e. acid, NaCl and bile salt tolerance, enzyme activities, adhesion to hydrocarbons, and antibiotic resistance, were examined. Among the tested strains, Lb. plantarum 332, Lb. paraplantarum G2114, P. pentosaceus 2211, and Lb. brevis R413 exhibited the best hydrophobicity value and high tolerance to bile salts, NaCl, and low pH.\n\nComposition of lactic acid bacteria during spontaneous curly kale (Brassica oleracea var. sabellica) fermentation.", "token_count": 416, "char_count": 1270, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:14.854327", "source": { "split": "train_shard_00000", "doc_id": 3542 }, "chunk_id": "train_shard_00000_3542_0", "global_id": 3923 }, { "text": "This study investigated the cancer chemopreventive, the antiradical, and the antiproliferative properties of polysaccharides extracts from cell wall of Saccharomyces boulardii and Kluyveromyces marxianus. β-glucan, mannan, and chitin were also quantified to identify the most important extract responsible for these biological properties. Soluble and insoluble glucans as well as mannoprotein were extracted from cell wall using single hot-alkaline method. Superoxide anion scavenging (antiradical capacity), NAD(P)H: quinone reductase (QR) (EC 1.6.99.2) induction, and antiproliferative assays were done for the evaluation of biological properties of those extracts. The insoluble glucan from S. boulardii revealed the most relevant biological properties by increasing QR activity and exhibiting the highest growth inhibition against colorectal cancer cells. Moreover, high amount of glucan, high glucan/total sugars ratios, and low chitin/glucan ratios were shown to have an impact on enhancing cancer chemopreventive and antiproliferative properties. To our knowledge, this is the first study that demonstrates QR activity by yeast cell wall components in a dose-dependent manner.\n\nCancer Chemopreventive, Antiproliferative, and Superoxide Anion Scavenging Properties of Kluyveromyces marxianus and Saccharomyces cerevisiae var. boulardii Cell Wall Components.", "token_count": 369, "char_count": 1363, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6384, "quality_score": 0.8192, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:15.441139", "source": { "split": "train_shard_00000", "doc_id": 3543 }, "chunk_id": "train_shard_00000_3543_0", "global_id": 3924 }, { "text": "American foulbrood (AFB), caused by Paenibacillus larvae, is a devastating disease in honeybees. In most countries, the disease is controlled through compulsory burning of symptomatic colonies causing major economic losses in apiculture. The pathogen is endemic to honeybees world-wide and is readily transmitted via the movement of hive equipment or bees. Molecular epidemiology of AFB currently largely relies on placing isolates in one of four ERIC-genotypes. However, a more powerful alternative is multi-locus sequence typing (MLST) using whole-genome sequencing (WGS), which allows for high-resolution studies of disease outbreaks. To evaluate WGS as a tool for AFB-epidemiology, we applied core genome MLST (cgMLST) on isolates from a recent outbreak of AFB in Sweden. The high resolution of the cgMLST allowed different bacterial clones involved in the disease outbreak to be identified and to trace the source of infection. The source was found to be a beekeeper who had sold bees to two other beekeepers, proving the epidemiological link between them. No such conclusion could have been made using conventional MLST or ERIC-typing. This is the first time that WGS has been used to study the epidemiology of AFB. The results show that the technique is very powerful for high-resolution tracing of AFB-outbreaks.\n\nUsing whole genome sequencing to study American foulbrood epidemiology in honeybees.", "token_count": 346, "char_count": 1406, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:16.016995", "source": { "split": "train_shard_00000", "doc_id": 3544 }, "chunk_id": "train_shard_00000_3544_0", "global_id": 3925 }, { "text": "Ursodeoxycholic acid (UDCA) is considered the first-choice therapy for cholestatic disorders. To enhance solubility and exploit specific transporters in liver, we synthesized a new galactosyl pro-drug of UDCA (UDCAgal). Ethinylestradiol (EE)-induced cholestasis was used to study and compare the effects of UDCAgal with UDCA on bile flow, hepatic canalicular efflux transporter expression, and inflammation. UDCAgal resulted quite stable both at pH 7.4 and 1.2 and regenerated the parent drug after incubation in human plasma. Its solubility, higher than UDCA, was pH- and temperature-independent. UDCAgal displayed a higher cell permeation compared to UDCA in liver HepG2 cells. Moreover, in cholestatic rats, UDCAgal showed a higher potency compared to UDCA in reducing serum biomarkers (AST, ALT, and ALP) and cytokines (TNF-α and IL-1β). The higher effect of UDCAgal on the increase in bile salt export pump and multidrug resistance-associated protein 2 transcription indicated an improved spillover of bile acids from the liver. UDCAgal showed a reduction in CCL2, as well as TNF-α, IL-1β, and cyclooxygeanse-2 mRNAs, indicating a reduction in hepatic neutrophil accumulation and inflammation. Moreover, UDCAgal, similarly to UDCA, heightens bile flow and modulates biliary acids secretion. These results indicate that UDCAgal has a potential in the treatment of cholestatic disease.\n\nGalactosylated Pro-Drug of Ursodeoxycholic Acid: Design, Synthesis, Characterization, and Pharmacological Effects in a Rat Model of Estrogen-Induced Cholestasis.", "token_count": 456, "char_count": 1551, "word_count": 218, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [ "CCL2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:16.652971", "source": { "split": "train_shard_00000", "doc_id": 3545 }, "chunk_id": "train_shard_00000_3545_0", "global_id": 3926 }, { "text": "Type three secretion systems (T3SS) are specialized nanomachines that support infection by injecting bacterial proteins directly into host cells. The Shigella T3SS has uniquely evolved to sense environmental levels of the bile salt deoxycholate (DOC) and upregulate virulence in response to DOC. In this study, we describe a rare i + 5 hydrogen bonding secondary structure element (π-helix) within the type three secretion system tip protein IpaD that plays a critical role in DOC-enhanced virulence. Specifically, engineered mutations within the π-helix altered the pathogen's response to DOC, with one mutant construct in particular exhibiting an unprecedented reduction in virulence following DOC exposure. Fluorescence polarization binding assays showed that these altered DOC responses are not the result of differences in affinity between IpaD and DOC, but rather differences in the DOC-dependent T3SS tip maturation resulting from binding of IpaD to translocator/effector protein IpaB. Together, these findings begin to uncover the complex mechanism of DOC-enhanced Shigella virulence while identifying an uncommon structural element that may provide a much needed target for non-antibiotic treatment of Shigella infection.\n\nDeoxycholate-Enhanced Shigella Virulence Is Regulated by a Rare π-Helix in the Type Three Secretion System Tip Protein IpaD.", "token_count": 333, "char_count": 1356, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6615, "quality_score": 0.8307, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:17.219511", "source": { "split": "train_shard_00000", "doc_id": 3546 }, "chunk_id": "train_shard_00000_3546_0", "global_id": 3927 }, { "text": "Lactococcus garvieae has emerged as an important zoonotic pathogen. However, information regarding mechanisms and factors related to its pathogenicity is lacking. In the present study, we investigated the distribution and functionality of genes related to virulence factors in L. garvieae strains isolated from different niches (diseased fish, humans, meat and dairy products, vegetables), using both post-genomic and genotypic analysis. Putative genes encoding hemolysin, fibronectin-binding protein, and penicillin acylase were detected in all analyzed genomes/strains. Their expression was significantly induced by bile salt stress. Putative genes encoding bile salt hydrolase were found in a few strains from dairy and human sources, as well as the mobilizable tet genes. Finally, all genomes possessed a folate gene cluster, in which mutations in the dihydropteroate synthase gene (folP) could be related to sulfonamide resistance. To the best of our knowledge, this is the first study aimed to explore the pathogenic potential of L. garvieae through the analysis of numerous L. garvieae genomes/strains, coming from different sources. This approach allowed the detection of virulence-related genes not yet investigated in the species and the study of their expression after exposure to different environmental stresses. The results obtained suggest a virulence potential in some L. garvieae strains that can be exploited for survival in the human gastrointestinal tract.\n\nDetection of virulence-related genes in Lactococcus garvieae and their expression in response to different conditions.", "token_count": 369, "char_count": 1596, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6018, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:17.800757", "source": { "split": "train_shard_00000", "doc_id": 3547 }, "chunk_id": "train_shard_00000_3547_0", "global_id": 3928 }, { "text": "Bile plays an important role in digestion, absorption of fats, and the excretion of waste products, while concurrently providing a critical barrier against colonization by harmful bacteria. Previous studies have demonstrated that gut pathogens react to bile by adapting their protein synthesis. The ability of pathogens to respond to bile is remarkably complex and still incompletely understood. Here we show that Campylobacter jejuni, a leading bacterial cause of human diarrheal illness worldwide, responds to deoxycholate, a component of bile, by altering global gene transcription in a manner consistent with a strategy to mitigate exposure to reactive oxygen stress. More specifically, continuous growth of C. jejuni in deoxycholate was found to: 1) induce the production of reactive oxygen species (ROS); 2) decrease succinate dehydrogenase activity (complex II of the electron transport chain); 3) increase catalase activity that is involved in H\n\nThe food-borne pathogen Campylobacter jejuni responds to the bile salt deoxycholate with countermeasures to reactive oxygen species.", "token_count": 251, "char_count": 1087, "word_count": 157, "semantic_coherence": 1, "information_density": 0.707, "quality_score": 0.8535, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:18.285769", "source": { "split": "train_shard_00000", "doc_id": 3548 }, "chunk_id": "train_shard_00000_3548_0", "global_id": 3929 }, { "text": "This study evaluated the antioxidant, antiproliferative, and immunostimulatory properties of cell wall α-d-mannan fractions from yeast Kluyveromyces marxianus CCT7735. Filter centrifugation was used to obtain four fractions (KMM-1, KMM-2, KMM-3, and KMM-4) with molecular weight ranging from 7.6 to 75.1kDa. KMM-1 and KMM-2 comprised D-mannose with traces of D-glucose, whereas other fractions contained only D-mannose. Total sugar found in samples ranged from 85.9% to 96.1%, while protein and phenolic contents were 1.21% and 0.41%, respectively. Although only KMM-1 was able to scavenge superoxide radicals, all fractions presented total antioxidant capacity as well as reducing power, hydroxyl-radical scavenging, and copper- and iron-chelating activities. No fraction was cytotoxic to HeLa cells. However, all samples inhibited the proliferation of the tumor cell Hep-G2 and presented minor cytotoxicity against normal 3T3 cells. All fractions showed mitogenic activity in macrophages and all, except KMM-4, induced nitric oxide production in macrophages, suggestive of their immunostimulatory effects.\n\nAntioxidant, antiproliferative, and immunostimulatory effects of cell wall α-d-mannan fractions from Kluyveromyces marxianus.", "token_count": 377, "char_count": 1234, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6933, "quality_score": 0.8466, "entities": { "genes": [ "CCT7735" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:18.867076", "source": { "split": "train_shard_00000", "doc_id": 3549 }, "chunk_id": "train_shard_00000_3549_0", "global_id": 3930 }, { "text": "Perfluorochemicals produce hepatotoxic effects via activation of peroxisome proliferator-activated receptor alpha (PPARα) and constitutive androstane receptor (CAR) nuclear receptors in animals. Bile formation is one major liver function. But it remains unknown whether perfluorochemicals alter metabolism of bile acids (BAs) in liver. The present study was designed to determine the impact of perfluorononanoic acid (PFNA) on BA and cholesterol homeostasis in mice. A single dose of PFNA (0.1 mmol/kg) was intraperitoneally administered to adult male wild-type (WT), PPARα-null, and CAR-null mice. PFNA caused cholestasis in the WT mice, indicated by increased serum alanine aminotransferase, hyperbilirubinemia, elevated BA concentrations in mouse serum, and appearance of bile plugs in mouse liver. In addition, PFNA decreased total and some individual BAs in mouse liver. PFNA increased the concentrations of total and taurine-conjugated, as well as some individual BAs in the serum of WT and CAR-null mice but not in PPARα-null mice, indicating a PPARα-dependent mechanism. PFNA decreased mRNA expression of most BA-related transporters (sodium-taurocholate cotransporting polypeptide, organic anion transporting polypeptide [Oatp]1a1, Oatp1b2, and bile salt export pump) and BA biosynthetic enzymes (Cyp7a1, 7b1, 8b1, and 27a1) in mouse liver, but increased mRNA expression of some efflux transporters (breast cancer resistance protein, multidrug resistance transporter 2, multidrug resistance-associated protein [Mrp] 2, Mrp3, and Mrp4), primarily via a PPARα-dependent mechanism. Moreover, PFNA increased free and total cholesterol in mouse liver but not in mouse serum", "token_count": 506, "char_count": 1677, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6043, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:19.518949", "source": { "split": "train_shard_00000", "doc_id": 3550 }, "chunk_id": "train_shard_00000_3550_0", "global_id": 3931 }, { "text": "Furthermore, PFNA increased mRNA expression of sterol transporters, namely Abca1, g1, g5/g8, and steroidogenic acute regulatory protein via PPARα. In conclusion, PFNA produced cholestasis in mouse liver, and the activation of PPARα plays a central role in regulating BA and cholesterol metabolism and transport in mouse serum and liver.\n\nAlteration of Bile Acid and Cholesterol Biosynthesis and Transport by Perfluorononanoic Acid (PFNA) in Mice.", "token_count": 132, "char_count": 446, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:19.942463", "source": { "split": "train_shard_00000", "doc_id": 3550 }, "chunk_id": "train_shard_00000_3550_1", "global_id": 3932 }, { "text": "Acinetobacter lactucae and Acinetobacter dijkshoorniae were recently described as novel species, and both were reported to be closely related to Acinetobacter pittii. Because they were reviewed and published almost concurrently, their descriptions did not include a specific comparison between these two novel species. Genomic data were provided in both initial descriptions, which simplifies the comparisons. Genome comparisons based on in silico DNA-DNA hybridizations, average nucleotide identity and core genome phylogeny of the type strain genomes establish that these strains are conspecific. Based on the rules of priority, A. dijkshoorniae should be reclassified as a later heterotypic synonym of A. lactucae.\n\nAcinetobacter dijkshoorniae is a later heterotypic synonym of Acinetobacter lactucae.", "token_count": 201, "char_count": 804, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6909, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:20.870764", "source": { "split": "train_shard_00000", "doc_id": 3551 }, "chunk_id": "train_shard_00000_3551_0", "global_id": 3933 }, { "text": "The draft genome assembly of the Wolbachia endosymbiont of Wuchereria bancrofti (wWb) consists of 1060 850 bp in 100 contigs and contains 961 ORFs, with a single copy of the 5S rRNA, 16S rRNA and 23S rRNA and each of the 34 tRNA genes. Phylogenetic core genome analyses show wWb to cluster with other strains in supergroup D of the Wolbachia phylogeny, while being most closely related to the Wolbachia endosymbiont of Brugia malayi strain TRS (wBm). The wWb and wBm genomes share 779 orthologous clusters with wWb having 101 unclustered genes and wBm having 23 unclustered genes. The higher number of unclustered genes in the wWb genome likely reflects the fragmentation of the draft genome.\n\nDraft genome sequence of the Wolbachia endosymbiont of Wuchereria bancrofti wWb.", "token_count": 272, "char_count": 774, "word_count": 127, "semantic_coherence": 1, "information_density": 0.5906, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:21.455381", "source": { "split": "train_shard_00000", "doc_id": 3552 }, "chunk_id": "train_shard_00000_3552_0", "global_id": 3934 }, { "text": "mcr-1 has been reported as the first plasmid-encoded gene conferring colistin resistance. In KPC-producing Klebsiella pneumoniae (KPC-KP), however, colistin resistance is rapidly emerging through other mechanisms. Resistance is frequently due to disruption of the mgrB gene by insertion sequences, e.g. ISL3. The aim of this study was to investigate the expansion of mgrB-mutated KPC-KP isolates. In addition, the localisation and targets of ISL3 sequences within the core and accessory genome of common KPC-KP lineages were identified. A total of 29 clinical K. pneumoniae isolates collected from Italian patients were randomly selected. Whole genome sequences were analysed for resistance genes, plasmids and insertion sequences. In addition, 27 colistin-resistant KPC-KP isolates from a previous study from Crete (Greece) were assessed. Clonal expansion of KPC-KP isolates with various mutations in mgrB among all lineages was observed. In two Italian MLST ST512 isolates and eight Greek ST258 isolates, an identical copy of ISL3 was inserted in mgrB nucleotide position 133. ISL3, a transposable restriction-modification system of 8154 nucleotides, was located on pKpQIL-like plasmids and may transpose into the chromosome. In four isolates, chromosomal integration of ISL3 in diverse inner membrane proteins other than mgrB was identified. Colistin resistance is most often explained by clonal expansion of isolates with mutated mgrB. pKpQIL-like plasmids, which are omnipresent in KPC-KP, carry insertion sequences such as ISL3 that have mgrB as a target hotspot for transposition. Transposition of insertion sequences from plasmids and subsequent clonal expansion may contribute to the emerging colistin resistance in KPC-KP.\n\nExpansion of KPC-producing Klebsiella pneumoniae with various mgrB mutations giving rise to colistin resistance: the role of ISL3 on plasmids.", "token_count": 508, "char_count": 1876, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5655, "quality_score": 0.7828, "entities": { "genes": [ "ST258", "ISL3", "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:22.129256", "source": { "split": "train_shard_00000", "doc_id": 3553 }, "chunk_id": "train_shard_00000_3553_0", "global_id": 3935 }, { "text": "Bile salt export pump (BSEP) adenosine triphosphate-binding cassette B11 (ABCB11) is a liver-specific ABC transporter that mediates canalicular bile salt excretion from hepatocytes. Human mutations in ABCB11 cause progressive familial intrahepatic cholestasis type 2. Although over 150 ABCB11 variants have been reported, our understanding of their biological consequences is limited by the lack of an experimental model that recapitulates the patient phenotypes. We applied CRISPR/Cas9-based genome editing technology to knock out abcb11b, the ortholog of human ABCB11, in zebrafish and found that these mutants died prematurely. Histological and ultrastructural analyses showed that abcb11b mutant zebrafish exhibited hepatocyte injury similar to that seen in patients with progressive familial intrahepatic cholestasis type 2. Hepatocytes of mutant zebrafish failed to excrete the fluorescently tagged bile acid that is a substrate of human BSEP. Multidrug resistance protein 1, which is thought to play a compensatory role in Abcb11 knockout mice, was mislocalized to the hepatocyte cytoplasm in abcb11b mutant zebrafish and in a patient lacking BSEP protein due to nonsense mutations in ABCB11. We discovered that BSEP deficiency induced autophagy in both human and zebrafish hepatocytes. Treatment with rapamycin restored bile acid excretion, attenuated hepatocyte damage, and extended the life span of abcb11b mutant zebrafish, correlating with the recovery of canalicular multidrug resistance protein 1 localization.\n\nZebrafish abcb11b mutant reveals strategies to restore bile excretion impaired by bile salt export pump deficiency.", "token_count": 454, "char_count": 1641, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6053, "quality_score": 0.8026, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:22.775249", "source": { "split": "train_shard_00000", "doc_id": 3554 }, "chunk_id": "train_shard_00000_3554_0", "global_id": 3936 }, { "text": "Estradiol-17β-D-glucuronide (E17G), through the activation of different signaling proteins, induces acute endocytic internalization of canalicular transporters in rat, including multidrug resistance-associated protein 2 (Abcc2) and bile salt export pump (Abcb11), generating cholestasis. Insulin-like growth factor 1 receptor (IGF-1R) is a membrane-bound tyrosine kinase receptor that can potentially interact with proteins activated by E17G. The aim of this study was to analyze the potential role of IGF-1R in the effects of E17G in isolated perfused rat liver (IPRL) and isolated rat hepatocyte couplets. In vitro, IGF-1R inhibition by tyrphostin AG1024 (TYR, 100 nM), or its knock-down with siRNA, strongly prevented E17G-induced impairment of Abcc2 and Abcb11 function and localization. The protection by TYR was not additive to that produced by wortmannin (PI3K inhibitor, 100 nM), and both protections share the same dependency on microtubule integrity, suggesting that IGF-1R shared the signaling pathway of PI3K/Akt. Further analysis of the activation of Akt and IGF-1R induced by E17G indicated a sequence of activation GPR30-IGF-1R-PI3K/Akt. In IPRL, an intraportal injection of E17G triggered endocytosis of Abcc2 and Abcb11, and this was accompanied by a sustained decrease in the bile flow and the biliary excretion of Abcc2 and Abcb11 substrates. TYR did not prevent the initial decay, but it greatly accelerated the recovery to normality of these parameters and the reinsertion of transporters into the canalicular membrane. In conclusion, the activation of IGF-1R is a key factor in the alteration of canalicular transporter function and localization induced by E17G, and its activation follows that of GPR30 and precedes that of PI3K/Akt.", "token_count": 515, "char_count": 1756, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7988, "entities": { "genes": [ "PI3K", "AG1024", "GPR30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:34:23.437306", "source": { "split": "train_shard_00000", "doc_id": 3555 }, "chunk_id": "train_shard_00000_3555_0", "global_id": 3937 }, { "text": "Activation of insulin-like growth factor 1 receptor participates downstream of GPR30 in estradiol-17β-D-glucuronide-induced cholestasis in rats.", "token_count": 50, "char_count": 144, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [ "GPR30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:23.795522", "source": { "split": "train_shard_00000", "doc_id": 3555 }, "chunk_id": "train_shard_00000_3555_1", "global_id": 3938 }, { "text": "Metabolic syndrome (MS) comprises central obesity, increased plasma glucose levels, hyperlipidemia and hypertension, and its incidence is increasing due to changes in lifestyle and dietary structure in recent years. MS has been proven to be associated with an increased incidence of cardiovascular diseases and type 2 diabetes mellitus, leading to morbidity and mortality. In this manuscript, we review recent studies concerning the role of the gut microbiota in MS modulation. Manipulation of the gut microbiota through the administration of prebiotics or probiotics may assist in weight loss and reduce plasma glucose and serum lipid levels, decreasing the incidence of cardiovascular diseases and type 2 diabetes mellitus. To the best of our knowledge, short-chain fatty acids (SCFAs), bile salt hydrolase (BSH), metabolic endotoxemia and the endocannabinoid (eCB) system are essential in regulating the initiation and progression of MS through the normalization of adipogenesis and the regulation of insulin secretion, fat accumulation, energy homeostasis, and plasma cholesterol levels. Therefore, the gut microbiota may serve as a potential therapeutic target for MS. However, further studies are needed to enhance our understanding of manipulating the gut microbiota and the role of the gut microbiota in MS prevention and treatment.\n\nGut microbiota as a potential target of metabolic syndrome: the role of probiotics and prebiotics.", "token_count": 347, "char_count": 1440, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:24.380286", "source": { "split": "train_shard_00000", "doc_id": 3556 }, "chunk_id": "train_shard_00000_3556_0", "global_id": 3939 }, { "text": "Lipopolysaccharides (LPS) are known to cause cholestasis in sepsis. There is evidence that a defective expression of canalicular aquaporin water channels contributes to bile secretory failure in LPS-induced cholestasis. Thus, we studied whether the hepatic adenovirus-mediated transfer of human aquaporin-1 gene (haqp1) can improve the cholestasis induced by LPS. Adenoviral vector encoding hAQP1 (AdhAQP1) or control vector was administered to rats by retrograde intrabiliary infusion. Hepatocyte canalicular hAQP1 expression was assessed by liver immunostaining and immunoblotting in purified plasma membranes. LPS reduced bile flow and biliary bile acid excretion by 30% and 45%, respectively. AdhAQP1-treatment normalized both bile flow and biliary bile acid excretion in LPS-induced cholestasis. Moreover, markedly elevated serum bile acid levels in cholestatic rats, were also normalized with the AdhAQP1 hepatic transduction. Bile flow and serum or biliary bile acids in normal rats were not significantly altered by AdhAQP1. AdhAQP1 delivery unaffected the downregulated protein expression of canalicular bile salt export pump (BSEP/ABCB11) in cholestasis, but improved its transport activity restoring reduced canalicular cholesterol content. Our data suggest that the adenovirus-mediated hepatocyte hAQP1 expression improves LPS-induced cholestasis in rats by stimulating the BSEP/ABCB11-mediated biliary bile acid excretion; a finding that might contribute to the understanding and treatment of sepsis-associated cholestatic diseases. © 2017 IUBMB Life, 69(12):978-984, 2017.\n\nAdenovirus-mediated human aquaporin-1 expression in hepatocytes improves lipopolysaccharide-induced cholestasis.", "token_count": 509, "char_count": 1700, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:25.033366", "source": { "split": "train_shard_00000", "doc_id": 3557 }, "chunk_id": "train_shard_00000_3557_0", "global_id": 3940 }, { "text": "Multiple lignocellulose-derived inhibitors represent great challenges for bioethanol production from lignocellulosic materials. These inhibitors that are related to the levels of intracellular reactive oxidative species (ROS) make oxidoreductases a potential target for an enhanced tolerance in yeasts.\n\nSynergistic effect of thioredoxin and its reductase from Kluyveromyces marxianus on enhanced tolerance to multiple lignocellulose-derived inhibitors.", "token_count": 117, "char_count": 453, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:25.424051", "source": { "split": "train_shard_00000", "doc_id": 3558 }, "chunk_id": "train_shard_00000_3558_0", "global_id": 3941 }, { "text": "Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates-the pan-genome-is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de. Custom pan-genomes can be visualized either using a web server or by serving panX locally as a browser-based application.\n\npanX: pan-genome analysis and exploration.", "token_count": 255, "char_count": 1152, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:25.915167", "source": { "split": "train_shard_00000", "doc_id": 3559 }, "chunk_id": "train_shard_00000_3559_0", "global_id": 3942 }, { "text": "Clostridium difficile infection (CDI) is one of the most common nosocomial infections. Dysbiosis of the gut microbiota due to consumption of antibiotics is a major contributor to CDI. Recently, fecal microbiota transplantation (FMT) has been applied to treat CDI. However, FMT has important limitations including uncontrolled exposure to pathogens and standardization issues. Therefore, it is necessary to evaluate alternative treatment methods, such as bacteriotherapy, as well as the mechanism through which beneficial bacteria inhibit the growth of C. difficile. Here, we report bile acid-mediated inhibition of C. difficile by Bacteroides strains which can produce bile salt hydrolase (BSH). Bacteroides strains are not commonly used to treat CDI; however, as they comprise a large proportion of the intestinal microbiota, they can contribute to bile acid-mediated inhibition of C. difficile. The inhibitory effect on C. difficile growth increased with increasing bile acid concentration in the presence of Bacteroides ovatus SNUG 40239. Furthermore, this inhibitory effect on C. difficile growth was significantly attenuated when bile acid availability was reduced by cholestyramine, a bile acid sequestrant. The findings of this study are important due to the discovery of a new bacterial strain that in the presence of available bile acids inhibits growth of C. difficile. These results will facilitate development of novel bacteriotherapy strategies to control CDI.\n\nBile salt hydrolase-mediated inhibitory effect of Bacteroides ovatus on growth of Clostridium difficile.", "token_count": 382, "char_count": 1579, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5796, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:26.506165", "source": { "split": "train_shard_00000", "doc_id": 3560 }, "chunk_id": "train_shard_00000_3560_0", "global_id": 3943 }, { "text": "The oral route is the preferred option for drug administration but contains the inherent issue of drug absorption from the gastro-intestinal tract (GIT) in order to elicit systemic activity. A prerequisite for absorption is drug dissolution, which is dependent upon drug solubility in the variable milieu of GIT fluid, with poorly soluble drugs presenting a formulation and biopharmaceutical challenge. Multiple factors within GIT fluid influence solubility ranging from pH to the concentration and ratio of amphiphilic substances, such as phospholipid, bile salt, monoglyceride, and cholesterol. To aid in vitro investigation simulated intestinal fluids (SIF) covering the fasted and fed state have been developed. SIF media is complex and statistical design of experiment (DoE) investigations have revealed the range of solubility values possible within each state due to physiological variability along with the media factors and factor interactions which influence solubility. However, these studies require large numbers of experiments (>60) and are not feasible or sensible within a drug development setting. In the current study a smaller dual level, reduced experimental number (20) DoE providing three arms covering the fasted and fed states along with a combined analysis has been investigated. The results indicate that this small scale investigation is feasible and provides solubility ranges that encompass published data in human and simulated fasted and fed fluids. The measured fasted and fed solubility ranges are in agreement with published large scale DoE results in around half of the cases, with the differences due to changes in media composition between studies. Indicating that drug specific behaviors are being determined and that careful media factor and concentration level selection is required in order to determine a physiologically relevant solubility range. The study also correctly identifies the major single factor or factors which influence solubility but it is evident that lower significance factors (for example bile salt) are not picked up due to the lower sample number employed. A similar issue is present with factor interactions with only a limited number available for study and generally not determined to have a significant solubility impact due to the lower statistical power of the study. The study indicates that a reduced experimental number DoE is feasible, will provide solubility range results with identification of major solubility factors however statistical limitations restrict the analysis", "token_count": 508, "char_count": 2549, "word_count": 377, "semantic_coherence": 1, "information_density": 0.5305, "quality_score": 0.7653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:27.165598", "source": { "split": "train_shard_00000", "doc_id": 3561 }, "chunk_id": "train_shard_00000_3561_0", "global_id": 3944 }, { "text": "The approach therefore represents a useful initial screening tool that can guide further in depth analysis of a drug's behavior in gastrointestinal fluids.\n\nDual Level Statistical Investigation of Equilibrium Solubility in Simulated Fasted and Fed Intestinal Fluid.", "token_count": 60, "char_count": 265, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8919, "quality_score": 0.9459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:27.533096", "source": { "split": "train_shard_00000", "doc_id": 3561 }, "chunk_id": "train_shard_00000_3561_1", "global_id": 3945 }, { "text": "Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum.", "token_count": 32, "char_count": 113, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:27.895455", "source": { "split": "train_shard_00000", "doc_id": 3562 }, "chunk_id": "train_shard_00000_3562_0", "global_id": 3946 }, { "text": "Lactobacillus mucosae strain AN1 isolated from sheep milk and characterized for its probiotic suitability. In vitro evaluation of critical gut endurance properties of this strain were assessed by different screening methods such as bile salt, gastric acid, lysozyme tolerance assays, hemolytic, cholesterol reduction properties, and HT-29 cell line adhesion assay. Antibacterial peptide from this strain was purified using ammonium sulphate precipitation, gel filtration chromatography and reverse-phase HPLC. The molecular mass of peptides was determined by Tricine-SDS-PAGE and confirmed by matrix-assisted laser desorption ionization-time of flight mass spectroscopy (MALDI-TOF-MS). Purified peptide was named as AN1 having a molecular mass of 10.66 kDa. Helical structures of peptide were determined using circular dichroism spectroscopy. Stability of peptide AN1 towards different parameters such as pH, temperature, organic solvents, proteolytic, and glycolytic enzymes was also analyzed.\n\nIsolation, Identification of Lactobacillus mucosae AN1 and its Antilisterial Peptide Purification and Characterization.", "token_count": 299, "char_count": 1115, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [ "AN1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:28.468061", "source": { "split": "train_shard_00000", "doc_id": 3563 }, "chunk_id": "train_shard_00000_3563_0", "global_id": 3947 }, { "text": "Tannase is considered one of the most important industrial enzymes that find great applications in various sectors. Production of tannases through solid state fermentation (SSF) using agro-industrial wastes is an eco-friendly and cheap technology. Tannase was produced by the yeast Kluyveromyces marxianus using olive pomace as a solid support under SSF. It was purified using ammonium sulfate fractional precipitation followed by Sephadex G-200 gel filtration resulting in 64.6% enzyme yield with 1026.12U/mg specific activity and 24.21 purification fold. Pure tannase had molecular weight of 65 KDa and 66.62 KDa by SDS-PAGE and gel filtration, respectively. It showed a maximal activity at 35°C having two different pH optima, one of which is acidic (4.5) and the other one is alkaline (8.5). The enzyme was stable in the acidic range of pH (4.0-5.5) for 30min, and thermostable within the temperature range 30-70°C. Using tannic acid, the enzyme had a Km value of 0.77mM and Vmax of 263.20μmolemin\n\nPurification and characterization of a novel tannase produced by Kluyveromyces marxianus using olive pomace as solid support, and its promising role in gallic acid production.", "token_count": 357, "char_count": 1178, "word_count": 180, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:29.050695", "source": { "split": "train_shard_00000", "doc_id": 3564 }, "chunk_id": "train_shard_00000_3564_0", "global_id": 3948 }, { "text": "Bile salts and bacteria have intricate relationships. The composition of the intestinal pool of bile salts is shaped by bacterial metabolism. In turn, bile salts play a role in intestinal homeostasis by controlling the size and the composition of the intestinal microbiota. As a consequence, alteration of the microbiome-bile salt homeostasis can play a role in hepatic and gastrointestinal pathological conditions. Intestinal bacteria use bile salts as environmental signals and in certain cases as nutrients and electron acceptors. However, bile salts are antibacterial compounds that disrupt bacterial membranes, denature proteins, chelate iron and calcium, cause oxidative damage to DNA, and control the expression of eukaryotic genes involved in host defense and immunity. Bacterial species adapted to the mammalian gut are able to endure the antibacterial activities of bile salts by multiple physiological adjustments that include remodeling of the cell envelope and activation of efflux systems and stress responses. Resistance to bile salts permits that certain bile-resistant pathogens can colonize the hepatobiliary tract, and an outstanding example is the chronic infection of the gall bladder by\n\nInteractions between Bacteria and Bile Salts in the Gastrointestinal and Hepatobiliary Tracts.", "token_count": 311, "char_count": 1304, "word_count": 187, "semantic_coherence": 1, "information_density": 0.5615, "quality_score": 0.7807, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:29.614185", "source": { "split": "train_shard_00000", "doc_id": 3565 }, "chunk_id": "train_shard_00000_3565_0", "global_id": 3949 }, { "text": "The Gram-positive bacterium\n\nModulators of Enterococcus faecalis Cell Envelope Integrity and Antimicrobial Resistance Influence Stable Colonization of the Mammalian Gastrointestinal Tract.", "token_count": 55, "char_count": 188, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:29.977388", "source": { "split": "train_shard_00000", "doc_id": 3566 }, "chunk_id": "train_shard_00000_3566_0", "global_id": 3950 }, { "text": "The faecal flora is a common reservoir for urinary tract infection (UTI), and Escherichia coli (E. coli) is frequently found in this reservoir without causing extraintestinal infection. We investigated these E. coli reservoirs by whole-genome sequencing a large collection of E. coli from healthy controls (faecal), who had never previously had UTI, and from UTI patients (faecal and urinary) sampled from the same geographical area. We compared MLST types, phylogenetic relationship, accessory genome content and FimH type between patient and control faecal isolates as well as between UTI and faecal-only isolates, respectively. Comparison of the accessory genome of UTI isolates to faecal isolates revealed 35 gene families which were significantly more prevalent in the UTI isolates compared to the faecal isolates, although none of these were unique to one of the two groups. Of these 35, 22 belonged to a genomic island and three putatively belonged to a type VI secretion system (T6SS). MLST types and SNP phylogeny indicated no clustering of the UTI or faecal E. coli from patients distinct from the control faecal isolates, although there was an overrepresentation of UTI isolates belonging to clonal lineages CC73 and CC12. One combination of mutations in FimH, N70S/S78N, was significantly associated to UTI, while phylogenetic analysis of FimH and fimH identified no signs of distinct adaptation of UTI isolates compared to faecal-only isolates not causing UTI. In summary, the results showed that (i) healthy women who had never previously had UTI carried faecal E", "token_count": 407, "char_count": 1577, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5615, "quality_score": 0.7807, "entities": { "genes": [ "CC12", "CC73" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:30.599514", "source": { "split": "train_shard_00000", "doc_id": 3567 }, "chunk_id": "train_shard_00000_3567_0", "global_id": 3951 }, { "text": "coli which were overall closely related to UTI and faecal isolates from UTI patients; (ii) UTI isolates do not cluster separately from faecal-only isolates based on SNP analysis; and (iii) 22 gene families of a genomic island, putative T6SS proteins as well as specific metabolism and virulence associated proteins were significantly more common in UTI isolates compared to faecal-only isolates and (iv) evolution of fimH for these isolates was not linked to the clinical source of the isolates, apart from the mutation combination N70S/S78N, which was correlated to UTI isolates of phylogroup B2. Combined, these findings illustrate that faecal and UTI isolates, as well as faecal-only and faecal-UTI isolates, are closely related and can only be distinguished, if at all, by their accessory genome.\n\nWhole-genome comparison of urinary pathogenic Escherichia coli and faecal isolates of UTI patients and healthy controls.", "token_count": 248, "char_count": 922, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:31.083580", "source": { "split": "train_shard_00000", "doc_id": 3567 }, "chunk_id": "train_shard_00000_3567_1", "global_id": 3952 }, { "text": "Intestinal failure-associated liver disease (IFALD) is a clinical challenge. The pathophysiol-ogy is multifactorial and remains poorly understood. Disturbed recirculation of bile salts,\n\nFXR agonism protects against liver injury in a rat model of intestinal failure-associated liver disease.", "token_count": 76, "char_count": 291, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8108, "quality_score": 0.9054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:31.456787", "source": { "split": "train_shard_00000", "doc_id": 3568 }, "chunk_id": "train_shard_00000_3568_0", "global_id": 3953 }, { "text": "In this report, the solubilization behaviour of a hydrophobic drug Clozapine (CLZ) in micellar suspensions of pluronics having different hydrophilic lipophilic balance (HLB) ratios viz. P84, F127 and F108 in the absence and presence of bile salt sodium deoxycholate (SDC) has been studied. UV-Vis spectroscopy has been exploited to determine the solubilization capacity of the investigated micellar systems in terms of drug loading efficiency, average number of drug molecules solubilized per micelle (n\n\nSodium deoxycholate mediated enhanced solubilization and stability of hydrophobic drug Clozapine in pluronic micelles.", "token_count": 177, "char_count": 623, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:31.904288", "source": { "split": "train_shard_00000", "doc_id": 3569 }, "chunk_id": "train_shard_00000_3569_0", "global_id": 3954 }, { "text": "The transport of bile acids facilitated by NTCP is an important factor in establishing bile flow. In this study, we examine the kinetics associated with human NTCP-dependent transport of two quantitatively important bile acids comprising the human bile acid pool, chenodeoxycholic acid and glycine-chenodeoxycholate, and secondary bile salt, 3-sulfo-glycolithocholate of potential toxicological significance. The study employed human NTCP overexpressing Chinese Hamster Ovary cells and results compared with taurocholate, a prototypical bile salt commonly used in transporter studies. GCDC and 3S-GLC but not CDCA were transported by NTCP. The efficient uptake of GCDC, TCA and 3S-GLC by NTCP enabled the determination of kinetics. GCDC displayed a lower K\n\nKinetic characterization of bile salt transport by human NTCP (SLC10A1).", "token_count": 225, "char_count": 830, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:32.401654", "source": { "split": "train_shard_00000", "doc_id": 3570 }, "chunk_id": "train_shard_00000_3570_0", "global_id": 3955 }, { "text": "Twelve previously isolated Lactobacillus strains were investigated for their in vitro bioactivities, including bile salt hydrolase (BSH), cholesterol-reducing and antioxidant activities, cytotoxic effects against cancer cells, enzyme activity, and biogenic amine production. Among them, only 4 strains showed relatively high BSH activity, whereas the rest exhibited low BSH activity. All 12 strains showed cholesterol-reducing and antioxidant activities, especially in their intact cells, which in most of the cases, the isolated strains were stronger in these activities than the tested commercial reference strains. None of the tested strains produced harmful enzymes (β-glucosidase and β-glucuronidase) or biogenic amines. Among the 12 strains, 3 strains were tested for their cytotoxic effects against 3 cancer cell lines, which exhibited strong cytotoxic effects, and they also showed selectivity in killing cancer cells when compared to normal cells. Hence, all 12 Lactobacillus strains could be considered good potential probiotic candidates because of their beneficial functional bioactivities.\n\nIn Vitro Assessment of Bioactivities of Lactobacillus Strains as Potential Probiotics for Humans and Chickens.", "token_count": 306, "char_count": 1214, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6242, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:32.984295", "source": { "split": "train_shard_00000", "doc_id": 3571 }, "chunk_id": "train_shard_00000_3571_0", "global_id": 3956 }, { "text": "Blooms of the potentially toxic cyanobacterium Microcystis are increasing worldwide. In the Laurentian Great Lakes they pose major socioeconomic, ecological, and human health threats, particularly in western Lake Erie. However, the interpretation of \"omics\" data is constrained by the highly variable genome of Microcystis and the small number of reference genome sequences from strains isolated from the Great Lakes. To address this, we sequenced two Microcystis isolates from Lake Erie (Microcystis aeruginosa LE3 and M. wesenbergii LE013-01) and one from upstream Lake St. Clair (M. cf aeruginosa LSC13-02), and compared these data to the genomes of seventeen Microcystis spp. from across the globe as well as one metagenome and seven metatranscriptomes from a 2014 Lake Erie Microcystis bloom. For the publically available strains analyzed, the core genome is ~1900 genes, representing ~11% of total genes in the pan-genome and ~45% of each strain's genome. The flexible genome content was related to Microcystis subclades defined by phylogenetic analysis of both housekeeping genes and total core genes. To our knowledge this is the first evidence that the flexible genome is linked to the core genome of the Microcystis species complex. The majority of strain-specific genes were present and expressed in bloom communities in Lake Erie. Roughly 8% of these genes from the lower Great Lakes are involved in genome plasticity (rapid gain, loss, or rearrangement of genes) and resistance to foreign genetic elements (such as CRISPR-Cas systems). Intriguingly, strain-specific genes from Microcystis cultured from around the world were also present and expressed in the Lake Erie blooms, suggesting that the Microcystis pangenome is truly global. The presence and expression of flexible genes, including strain-specific genes, suggests that strain-level genomic diversity may be important in maintaining Microcystis abundance during bloom events.", "token_count": 483, "char_count": 1948, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5764, "quality_score": 0.7882, "entities": { "genes": [ "LE3", "LSC13", "LE013" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:33.699386", "source": { "split": "train_shard_00000", "doc_id": 3572 }, "chunk_id": "train_shard_00000_3572_0", "global_id": 3957 }, { "text": "Genome sequences of lower Great Lakes Microcystis sp. reveal strain-specific genes that are present and expressed in western Lake Erie blooms.", "token_count": 32, "char_count": 142, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:34.085813", "source": { "split": "train_shard_00000", "doc_id": 3572 }, "chunk_id": "train_shard_00000_3572_1", "global_id": 3958 }, { "text": "The in vivo effects of administering free and microencapsulated Lactobacillus plantarum LIP-1 cells (2·0×109 colony-forming units/d) were evaluated in high-fat-diet-induced hyperlipidaemic rats. Results from real-time quantitative PCR targeting to LIP-1 cells showed a higher colon colonisation count of LIP-1 in the rats receiving microencapsulated cells compared with free cells (P<0·05). Moreover, the microencapsulated LIP-1 treatment resulted in a more obvious lipid-lowering effect (P<0·05). Meanwhile, their faecal samples had significantly less lipopolysaccharide-producing bacteria (especially Bilophila, Sutterella and Oscillibacter) and mucosa-damaging bacteria (Bilophila and Akkermansia muciniphila), whereas significantly more SCFA-producing bacteria (P<0·05) (namely Lactobacillus, Alloprevotella, Coprococcus, Eubacterium and Ruminococcus) and bacteria that potentially possessed bile salt hydrolase activity (Bacteroides, Clostridium, Eubacterium and Lactobacillus), and other beneficial bacteria (Alistipes and Turicibacter). Further, Spearman's correlation analysis showed significant correlations between some of the modulated gut bacteria and the serum lipid levels. These results together confirm that microcapsulation enhanced the colon colonisation of LIP-1 cells, which subsequently exhibited more pronounced effects in improving the gut microbiota composition of hyperlipidaemic rats and lipid reduction.\n\nEffects of microencapsulated Lactobacillus plantarum LIP-1 on the gut microbiota of hyperlipidaemic rats.", "token_count": 418, "char_count": 1537, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:34.717512", "source": { "split": "train_shard_00000", "doc_id": 3573 }, "chunk_id": "train_shard_00000_3573_0", "global_id": 3959 }, { "text": "It is important for probiotics that are currently utilized in the dairy industry to have clear genetic backgrounds. In this study, the genetic characteristics of Lactobacillus kefiranofaciens ZW3 were studied by undertaking a comparative genomics study, and key genes for adaptation to different environments were investigated and validated in vitro. Evidence for horizontal gene transfer resulting in strong self-defense mechanisms was detected in the ZW3 genome. We identified a series of genes relevant for dairy environments and the intestinal tract, particularly for extracellular polysaccharide (EPS) production. Reverse transcription-qPCR (RT-qPCR) revealed significant increases in the relative expression of pgm, ugp, and uge during the mid-logarithmic phase, whereas the expression of pgi was higher at the beginning of the stationary phase. The enzymes encoded by these four genes concertedly regulated carbon flux, which in turn modulated the production of EPS precursors. Moreover, ZW3 tolerated pH 3.5 and 3% bile salt and retained cell surface hydrophobicity and auto-aggregation. In conclusion, we explored the potential of ZW3 for utilization in both the dairy industry and in probiotic applications. Additionally, we elucidated the regulation of the relevant genes involved in EPS production.\n\nComparative genomics of Lactobacillus kefiranofaciens ZW3 and related members of Lactobacillus. spp reveal adaptations to dairy and gut environments.", "token_count": 349, "char_count": 1461, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6262, "quality_score": 0.8131, "entities": { "genes": [ "ZW3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:35.292008", "source": { "split": "train_shard_00000", "doc_id": 3574 }, "chunk_id": "train_shard_00000_3574_0", "global_id": 3960 }, { "text": "Schaftoside (SS) is a bioactive compound present in the Herba Desmodii Styracifolii (DS), a herb that has been used to treat cholelithiasis and urolithiasis in Chinese medicine. Whether SS inhibits cholesterol (Ch) gallstone formation has not been investigated. This study examined the effects of oral intake of SS on Ch gallstone formation in C57BL/6 mice fed a lithogenic diet. The rate of gallstone formation was recorded. Levels of Ch, triglycerides (TG) and bile salts (BS) were measured in the bile and serum. Liver histopathology was examined microscopically, and mRNA expression levels of key genes involved in cholesterol and bile metabolism were determined by qPCR. Mice fed SS were protected against gallstone formation, had increased biliary levels of BS, and reduced biliary Ch levels, resulting in a lower Ch saturation index (CSI). In addition, mice fed SS had lower serum TG and Ch levels, increased mRNA expression of liver X receptor α, ATP binding cassette transporter 5/8 (ABCG5/8), and ileal bile acid binding protein (IBABP) in the ileum, and of farnesoid X receptor and bile salt export protein (BSEP) in the liver and ileum. SS also protected against histologically determined liver damage. Overall, these data indicate that SS protects against Ch gallstone formation in mice, and that the effect is mediated by activation of ileal liver X receptor α and hepatic farnesoid X receptor.\n\nPrevention of cholesterol gallstone disease by schaftoside in lithogenic diet-induced C57BL/6 mouse model.", "token_count": 415, "char_count": 1516, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5466, "quality_score": 0.7733, "entities": { "genes": [ "ABCG5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:35.915642", "source": { "split": "train_shard_00000", "doc_id": 3575 }, "chunk_id": "train_shard_00000_3575_0", "global_id": 3961 }, { "text": "The activity of fluconazole, amphotericin B, caspofungin and micafungin was determined using XTT-based fungal damage assays against planktonic cells, early and mature biofilms of Candida kefyr. Median MICs of planktonic cells were 0.25 mg/l, 0.25 mg/l, 0.5 mg/l, and 0.06 mg/l for fluconazole, amphotericin B, caspofungin, and micafungin, respectively. Fluconazole showed at least 50% fungal damage at ≥4 mg/l (51.5% ± 6.63% to 78.38% ± 1.44%) and at ≥128 mg/l (57.88% ± 9.2% to 67.25% ± 9.59%), while amphotericin B produced an even higher anti-biofilm effect at ≥0.5 mg/l (64.63% ± 6.79% to 79.5% ± 5.9%) and at ≥0.12 mg/l (77.63% ± 8.43% to 92.75% ± 1.89%) against early and mature biofilms, respectively. In case of micafungin, 50% fungal damage was observed at ≥0.06 mg/l (66.88% ± 10.16% to 98.63% ± 1.24%) and ≥0.25 mg/l (74.13% ± 10.77% to 99.38% ± 0.38%) for early and mature biofilms, respectively", "token_count": 453, "char_count": 907, "word_count": 148, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:36.555061", "source": { "split": "train_shard_00000", "doc_id": 3576 }, "chunk_id": "train_shard_00000_3576_0", "global_id": 3962 }, { "text": "Caspofungin-exposed cells showed an unexpected susceptibility pattern, that is, planktonic cells showed significantly decreased susceptibility at concentrations ranging from 0.015 mg/l to 1 mg/l compared to biofilms (P < .05-.01). The damage in planktonic cells and biofilms was comparable at higher concentrations. For planktonic cells and biofilms, 50% fungal damage was observed first at 0.5 mg/l (59.75% ± 3.16%) and at 0.06 mg/l (70.25% ± 10.95%), respectively. This unexpected pattern was confirmed using scanning electron microscopy. The unusual susceptibility pattern observed at lower caspofungin concentrations may explain the poorer outcome of caspofungin-treated C. kefyr infections documented in certain patient populations. As this phenomenon was markedly less apparent in case of micafungin, these data suggest that micafungin may be a more reliable option than caspofungin for the treatment of C. kefyr infections.\n\nIn vitro antifungal susceptibility patterns of planktonic and sessile Candida kefyr clinical isolates.", "token_count": 297, "char_count": 1034, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:37.117533", "source": { "split": "train_shard_00000", "doc_id": 3576 }, "chunk_id": "train_shard_00000_3576_1", "global_id": 3963 }, { "text": "Upon oral administration the solubility of a drug in intestinal fluid is a key property influencing bioavailability. It is also recognised that simple aqueous solubility does not reflect intestinal solubility and to optimise in vitro investigations simulated intestinal media systems have been developed. Simulated intestinal media which can mimic either the fasted or fed state consists of multiple components each of which either singly or in combination may influence drug solubility, a property that can be investigated by a statistical design of experiment technique. In this study a design of experiment covering the full range from the lower limit of fasted to the upper limit of fed parameters and using a small number of experiments has been performed. The measured equilibrium solubility values are comparable with literature values for simulated fasted and fed intestinal fluids as well as human fasted and fed intestinal fluids. The equilibrium solubility data range is statistically equivalent to a combination of published fasted and fed design of experiment data in six (indomethacin, phenytoin, zafirlukast, carvedilol, fenofibrate and probucol) drugs with three (aprepitant, tadalafil and felodipine) drugs not equivalent. In addition the measured equilibrium solubility data sets were not normally distributed. Further studies will be required to determine the reasons for these results however it implies that a single solubility measurement without knowledge of the solubility distribution will be of limited value. The statistically significant media factors which promote equilibrium solubility (pH, sodium oleate and bile salt) were in agreement with published results but the number of determined significant factors and factor interactions was fewer in this study, lecithin for example did not influence solubility. This may be due to the reduction in statistical sensitivity from the lower number of experimental data points or the fact that using the full range will examine media parameters ratios that are not biorelevant. Overall the approach will provide an estimate of the solubility range and the most important media factors but will not be equivalent to larger scale focussed studies. Further investigations will be required to determine why some drugs do not produce equivalent DoE solubility distributions, for example combined fasted and fed DoE, but this simply may be due to the complexity and individuality of the interactions between a drug and the media components.", "token_count": 511, "char_count": 2508, "word_count": 376, "semantic_coherence": 1, "information_density": 0.4814, "quality_score": 0.7407, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:37.769629", "source": { "split": "train_shard_00000", "doc_id": 3577 }, "chunk_id": "train_shard_00000_3577_0", "global_id": 3964 }, { "text": "Statistical investigation of the full concentration range of fasted and fed simulated intestinal fluid on the equilibrium solubility of oral drugs.", "token_count": 30, "char_count": 147, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:38.127137", "source": { "split": "train_shard_00000", "doc_id": 3577 }, "chunk_id": "train_shard_00000_3577_1", "global_id": 3965 }, { "text": "The composition of the human intestinal fluids varies both intra- and inter-individually. This will influence the solubility of orally administered drug compounds, and hence, the absorption and efficacy of compounds displaying solubility limited absorption. The purpose of this study was to assess the influence of simulated intestinal fluid (SIF) composition on the solubility of poorly soluble compounds. Using a Design of Experiments (DoE) approach, a set of 24 SIF was defined within the known compositions of human fasted state intestinal fluid. The SIF were composed of phospholipid, bile salt, and different pH, buffer capacities and osmolarities. On a small scale semi-robotic system, the solubility of 6 compounds (aprepitant, carvedilol, felodipine, fenofibrate, probucol, and zafirlukast) was determined in the 24 SIF. Compound specific models, describing key factors influencing the solubility of each compound, were identified. Although all models were different, the level of phospholipid and bile salt, the pH, and the interactions between these, had the biggest influences on solubility overall. Thus, a reduction of the DoE from five to three factors was possible (11-13 media), making DoE solubility studies feasible compared to single SIF solubility studies. Applying this DoE approach will lead to a better understanding of the impact of intestinal fluid composition on the solubility of a given drug compound.\n\nEffect of composition of simulated intestinal media on the solubility of poorly soluble compounds investigated by design of experiments.", "token_count": 384, "char_count": 1568, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5609, "quality_score": 0.7804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:38.737047", "source": { "split": "train_shard_00000", "doc_id": 3578 }, "chunk_id": "train_shard_00000_3578_0", "global_id": 3966 }, { "text": "Beer-spoilage-related lactic acid bacteria (BSR LAB) belong to multiple genera and species; however, beer-spoilage capacity is isolate-specific and partially acquired via horizontal gene transfer within the brewing environment. Thus, the extent to which genus-, species-, or environment- (i.e., brewery-) level genetic variability influences beer-spoilage phenotype is unknown. Publicly available Lactobacillus brevis genomes were analyzed via BlAst Diagnostic Gene findEr (BADGE) for BSR genes and assessed for pangenomic relationships. Also analyzed were functional coding capacities of plasmids of LAB inhabiting extreme niche environments. Considerable genetic variation was observed in L. brevis isolated from clinical samples, whereas 16 candidate genes distinguish BSR and non-BSR L. brevis genomes. These genes are related to nutrient scavenging of gluconate or pentoses, mannose, and metabolism of pectin. BSR L. brevis isolates also have higher average nucleotide identity and stronger pangenome association with one another, though isolation source (i.e., specific brewery) also appears to influence the plasmid coding capacity of BSR LAB. Finally, it is shown that niche-specific adaptation and phenotype are plasmid-encoded for both BSR and non-BSR LAB. The ultimate combination of plasmid-encoded genes dictates the ability of L. brevis to survive in the most extreme beer environment, namely, gassed (i.e., pressurized) beer.\n\nComparative genomic and plasmid analysis of beer-spoiling and non-beer-spoiling Lactobacillus brevis isolates.", "token_count": 390, "char_count": 1552, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:39.357334", "source": { "split": "train_shard_00000", "doc_id": 3579 }, "chunk_id": "train_shard_00000_3579_0", "global_id": 3967 }, { "text": "Fibrates and their receptor, namely peroxisome proliferator-activated receptor α (PPARα), have been reported to regulate bile acid (BA) synthesis and transport. However, the effect of fibrate treatment and PPARα activation on BA homeostasis remains controversial. In this study, both wild-type (WT) and PPARα-null male mice were treated with clofibrate (CLOF) for 4 days to evaluate the effects of short-term PPARα activation on BA homeostasis. Although a decrease in total BAs (ΣBAs) was observed in livers of CLOF-treated WT mice, it was not observed in PPARα-null mice. CLOF-mediated decrease in ΣBAs in the liver was not likely due to the reduction in BA synthesis or BA uptake, as evidenced by an increase in the BA synthetic enzyme (Cyp7a1) and 2 BA uptake transporters (Na (+)-taurocholate cotransporting polypeptide [Ntcp] and organic anion transporting polypeptide [Oatp]1b2). Instead, the decrease in liver BAs by CLOF is largely a result of increased biliary excretion of BAs, which was associated with a significant induction of the canalicular efflux transporter (bile salt export pump [Bsep]) in the liver. The PPARα-mediated increase in Cyp7a1 in CLOF-treated WT mice was not due to farnesoid X receptor (Fxr)-small heterodimer partner (Shp) signaling in the liver, but due to suppression of Fxr- fibroblast growth factor15 signaling in the ileum. Additionally, CLOF also suppressed intestinal BA transporters (apical sodium-dependent bile acid transporter and organic solute transporterβ) and cholesterol efflux transporters (Abcg5 and Abcg8) in a PPARα-dependent manner. In summary, this study provides the first comprehensive analysis on the effect of a short-term CLOF treatment on BA homeostasis, and revealed an essential role of PPARα in regulating BA synthesis, transport and signaling.", "token_count": 518, "char_count": 1809, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:34:40.010139", "source": { "split": "train_shard_00000", "doc_id": 3580 }, "chunk_id": "train_shard_00000_3580_0", "global_id": 3968 }, { "text": "Editor's Highlight: Clofibrate Decreases Bile Acids in Livers of Male Mice by Increasing Biliary Bile Acid Excretion in a PPARα-Dependent Manner.", "token_count": 48, "char_count": 145, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:40.367351", "source": { "split": "train_shard_00000", "doc_id": 3580 }, "chunk_id": "train_shard_00000_3580_1", "global_id": 3969 }, { "text": "Study on Micelle Formation of Bile Salt Using Nuclear Magnetic Resonance Spectroscopy.", "token_count": 24, "char_count": 86, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:40.720275", "source": { "split": "train_shard_00000", "doc_id": 3581 }, "chunk_id": "train_shard_00000_3581_0", "global_id": 3970 }, { "text": "This study investigated the yeast community present in the traditional Portuguese cheese, Serpa, by culture-dependent and -independent methods. Sixteen batches of Serpa cheeses from various regional industries registered with the Protected Designation of Origin (PDO) versus non-PDO registered, during spring and winter, were used. Irrespective of the producer, the yeast counts were around 5log CFU/g in winter and, overall, were lower in spring. The yeast species identified at the end of ripening (30days), using PCR-RFLP analysis and sequencing of the 26S rRNA, mainly corresponded to Debaryomyces hansenii and Kluyveromyces marxianus, with Candida spp. and Pichia spp. present to a lesser extent. The culture-independent results, obtained using high-throughput sequencing analysis, confirmed the prevalence of Debaryomyces spp. and Kluyveromyces spp. but, also, that Galactomyces spp. was relevant for three of the five producers, which indicates its importance during the early stages of the cheese ripening process, considering it was not found among the dominant viable yeast species. In addition, differences between the identified yeast isolated from cheeses obtained from PDO and non-PDO registered industries, showed that the lack of regulation of the cheese-making practice, may unfavourably influence the final yeast microbiota. The new knowledge provided by this study of the yeast diversity in Serpa cheese, could be used to modify the cheese ripening conditions, to favour desirable yeast species. Additionally, the prevalent yeast isolates identified, Debaryomyces hansenii and Kluyveromyces spp., may have an important role during cheese ripening and in the final sensorial characteristics. Thus, the study of their technological and functional properties could be relevant, in the development of an autochthonous starter culture, to ensure final quality and safety of the cheese.\n\nYeast community in traditional Portuguese Serpa cheese by culture-dependent and -independent DNA approaches.", "token_count": 461, "char_count": 2009, "word_count": 284, "semantic_coherence": 1, "information_density": 0.5739, "quality_score": 0.787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:41.359597", "source": { "split": "train_shard_00000", "doc_id": 3582 }, "chunk_id": "train_shard_00000_3582_0", "global_id": 3971 }, { "text": "Primary biliary cholangitis (PBC) is a chronic fibrosing cholangiopathy characterized by an autoimmune stereotype and defective biliary bicarbonate secretion due to down-regulation of anion exchanger 2 (AE2). Despite the autoimmune features, immunosuppressants are ineffective while two bile acid-based therapies (ursodeoxycholic acid and obeticholic acid) have been shown to improve biochemical and histological features of cholestasis and long-term prognosis. However, the etiology and pathogenesis of PBC is largely unknown. Recently, it has been shown that microRNA-506 (miR-506) on chromosome X is up-regulated in PBC cholangiocytes and suppresses AE2 expression, which sensitizes cholangiocytes to bile salt-induced apoptosis by activating soluble adenylyl cyclase (sAC), an evolutionarily conserved bicarbonate sensor. In this review, we discuss the experimental evidence for the emerging role of the miR-506-AE2-sAC axis in PBC pathogenesis. We further hypothesize that the initial disease trigger induces an X-linked epigenetic change, leading to a female-biased activation of the miR-506-AE2-sAC axis. This article is part of a Special Issue entitled: Cholangiocytes in Health and Diseaseedited by Jesus Banales, Marco Marzioni and Peter Jansen.\n\nRole of the bicarbonate-responsive soluble adenylyl cyclase in cholangiocyte apoptosis in primary biliary cholangitis; a new hypothesis.", "token_count": 403, "char_count": 1393, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [ "AE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:41.996185", "source": { "split": "train_shard_00000", "doc_id": 3583 }, "chunk_id": "train_shard_00000_3583_0", "global_id": 3972 }, { "text": "Enhanced precision of epidemiological typing in clinically suspected nosocomial outbreaks is crucial. Our aim was to investigate whether single nucleotide polymorphism (SNP) analysis and core genome (cg) multilocus sequence typing (MLST) of whole genome sequencing (WGS) data would more reliably identify a nosocomial outbreak, compared to earlier molecular typing methods. Sixteen isolates from a nosocomial outbreak of ESBL E. coli ST-131 in southeastern Sweden and three control strains were subjected to WGS. Sequences were explored by SNP analysis and cgMLST. cgMLST clearly differentiated between the outbreak isolates and the control isolates (>1400 differences). All clinically identified outbreak isolates showed close clustering (≥2 allele differences), except for two isolates (>50 allele differences). These data confirmed that the isolates with >50 differing genes did not belong to the nosocomial outbreak. The number of SNPs within the outbreak was ≤7, whereas the two discrepant isolates had >700 SNPs. Two of the ESBL E. coli ST-131 isolates did not belong to the clinically identified outbreak. Our results illustrate the power of WGS in terms of resolution, which may avoid overestimation of patients belonging to outbreaks as judged from epidemiological data and previously employed molecular methods with lower discriminatory ability.\n\nEpidemiological characterization of a nosocomial outbreak of extended spectrum β-lactamase Escherichia coli ST-131 confirms the clinical value of core genome multilocus sequence typing.", "token_count": 374, "char_count": 1542, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:42.577252", "source": { "split": "train_shard_00000", "doc_id": 3584 }, "chunk_id": "train_shard_00000_3584_0", "global_id": 3973 }, { "text": "Bacterial genomics studies are getting more extensive and complex, requiring new ways to envision analyses. Using the Ray Surveyor software, we demonstrate that comparison of genomes based on their k-mer content allows reconstruction of phenetic trees without the need of prior data curation, such as core genome alignment of a species. We validated the methodology using simulated genomes and previously published phylogenomic studies of Streptococcus pneumoniae and Pseudomonas aeruginosa. We also investigated the relationship of specific genetic determinants with bacterial population structures. By comparing clusters from the complete genomic content of a genome population with clusters from specific functional categories of genes, we can determine how the population structures are correlated. Indeed, the strain clustering based on a subset of k-mers allows determination of its similarity with the whole genome clusters. We also applied this methodology on 42 species of bacteria to determine the correlational significance of five important bacterial genomic characteristics. For example, intrinsic resistance is more important in P. aeruginosa than in S. pneumoniae, and the former has increased correlation of its population structure with antibiotic resistance genes. The global view of the pangenome of bacteria also demonstrated the taxa-dependent interaction of population structure with antibiotic resistance, bacteriophage, plasmid, and mobile element k-mer data sets.\n\nPhenetic Comparison of Prokaryotic Genomes Using k-mers.", "token_count": 319, "char_count": 1546, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6168, "quality_score": 0.8084, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:43.144606", "source": { "split": "train_shard_00000", "doc_id": 3585 }, "chunk_id": "train_shard_00000_3585_0", "global_id": 3974 }, { "text": "A fundamental requirement for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to use this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in the whole genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in both small and population-scale sequencing studies.\n\nGraphtyper enables population-scale genotyping using pangenome graphs.", "token_count": 256, "char_count": 1097, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:43.691234", "source": { "split": "train_shard_00000", "doc_id": 3586 }, "chunk_id": "train_shard_00000_3586_0", "global_id": 3975 }, { "text": "Recurrent bile salt export pump (rBSEP) disease has been reported in progressive familial intrahepatic cholestasis type 2 (PFIC2) patients following liver transplantation (LT) and is often refractory to standard anti-cellular rejection immunosuppressants. The mechanism of rBSEP disease is proposed to be a form of type II hypersensitivity reaction with de novo anti-BSEP antibodies blocking the function of allograft BSEP. Utilization of C4d has not been evaluated in rBSEP. We describe a girl with 3 episodes of rBSEP with severe pruritus at 8.9, 10.3, and 11.0 years post-LT, respectively. Patient's serum reacted with normal liver canaliculi by indirect immunofluorescence (IF), whereas patient's liver showed canalicular immunoglobulin G deposition. The histologic features of all 3 liver biopsies recapitulate PFIC2 with cholestatic giant cell hepatitis. Canalicular BSEP expression was not detected in areas of feathery degeneration by immunohistochemistry, but was retained in morphologically normal liver. By direct IF, C4d showed diffuse sinusoidal staining in the third biopsy. Patient responded well to rituximab with or without intravenous immunoglobulin with subsiding symptoms and normalization of serum bile acid levels. In conclusion, rBSEP disease should be considered in the differential diagnosis when evaluating for rejection in a PFIC2 patient post-LT presenting with pruritus. A portion of liver core may be snap frozen in OCT medium for possible direct IF for C4d, that can serve as a surrogate marker for complement activation and antibody-mediated graft dysfunction.\n\nPost-transplant Recurrent Bile Salt Export Pump Disease: A Form of Antibody-mediated Graft Dysfunction and Utilization of C4d.", "token_count": 468, "char_count": 1720, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6626, "quality_score": 0.8313, "entities": { "genes": [ "PFIC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:44.371758", "source": { "split": "train_shard_00000", "doc_id": 3587 }, "chunk_id": "train_shard_00000_3587_0", "global_id": 3976 }, { "text": "Probiotics have become highly recognized as supplements for humans and animals because of their beneficial effects on health and well-being. The present review aims to provide an overview of different steps through which microbial strains become applicable probiotics in food and/or feed industries. Isolation of potential probiotic strains is the first step. Lactic acid bacteria are the most frequently used microorganisms as probiotics, which can be isolated from human, animal, plant, and environment. The next steps are identification of the isolates and characterization of them based on the main selection criteria for any potential probiotic microorganism, including resistance to gastric acidity and bile salt, adherence to mucus and/or intestinal epithelial cells and cell lines, and antimicrobial and antagonism activity against potentially pathogenic microbes. There are additional probiotic properties that may be considered for selection of probiotic strains with specific effects, such as cholesterol reduction ability, antioxidant activity, or cytotoxic effect against cancer cells. However, a potential probiotic does not need to fulfill all such selection criteria. As the last step, safety status of probiotics for humans is verified by taxonomy clarification, in vitro and in vivo tests, human trials, and genome sequencing.\n\nProbiotics: From Isolation to Application.", "token_count": 305, "char_count": 1388, "word_count": 197, "semantic_coherence": 1, "information_density": 0.7005, "quality_score": 0.8503, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:44.963619", "source": { "split": "train_shard_00000", "doc_id": 3588 }, "chunk_id": "train_shard_00000_3588_0", "global_id": 3977 }, { "text": "We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes but are unable to resolve strain-level variation. DESMAN identifies variants in core genes and uses co-occurrence across samples to link variants into haplotypes and abundance profiles. These are then searched for against non-core genes to determine the accessory genome of each strain. We validated DESMAN on a complex 50-species 210-genome 96-sample synthetic mock data set and then applied it to the Tara Oceans microbiome.\n\nDESMAN: a new tool for de novo extraction of strains from metagenomes.", "token_count": 187, "char_count": 749, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7407, "quality_score": 0.8704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:45.436444", "source": { "split": "train_shard_00000", "doc_id": 3589 }, "chunk_id": "train_shard_00000_3589_0", "global_id": 3978 }, { "text": "In this study, an astaxanthin-biosynthesis Kluyveromyces marxianus strain Sm23 was first constructed, which could produce 31µg/g DCW astaxanthin. Then, repeated genome integration of the key astaxanthin biosynthesis genes Hpchyb and bkt was done to increase gene copy number and astaxanthin yield. Four improved strains were obtained and the yield of astaxanthin and the total yield of carotenoids in a strain increased with the copy numbers of Hpchyb and bkt. To improve the yield further, the gene Hpchyb from Haematococcus pluvialis was modified by site-directed mutagenesis to increase the enzyme efficiency or/and to prevent the heterologous protein degradation by ubiquitination. Using repeated-integration approach of bkt and the mutated Hpchyb into Sm23, the S3-2 strain was obtained and shown to produce the 3S, 3'S-astaxanthin at 9972µg/g DCW in a 5L fermentor.\n\nMetabolic engineering a yeast to produce astaxanthin.", "token_count": 275, "char_count": 926, "word_count": 136, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:46.024073", "source": { "split": "train_shard_00000", "doc_id": 3590 }, "chunk_id": "train_shard_00000_3590_0", "global_id": 3979 }, { "text": "Vibrio fluvialis is recognized as an emerging pathogen. However, not much is known about the mechanism of its pathogenesis, and its adaptation to a special niche such as the gall bladder. Here we describe two V. fluvialis strains that cause acute cholecystitis. It is noteworthy that both strains were susceptible to all antibiotics tested, which is in contrast to previous studies, suggesting substantial genetic diversity among V. fluvialis isolates. In agreement with their survival and growth in the gall bladder, the genomes of strains 12605 and 3663 contain a considerable number of genes that confer resistance to bile, including toxR, omp U, tolC, cmeABC, rlpB, yrbK, rpoS, damX and gltK. Furthermore, integrative and conjugative elements (ICEs), virulence factors and prophage regions were also detected in strains 12605 and 3663, reflecting their flexibility in recombination during the evolution of pathogenicity. Comparative analysis of nine available genomes of V. fluvialis revealed a core genome consisting of 3,147 genes. Our results highlight the association of V. fluvialis with a rare disease profile and shed light on the evolution of pathogenesis and niche adaptation of V. fluvialis.\n\nGenome characterization of two bile-isolated Vibrio fluvialis strains: an insight into pathogenicity and bile salt adaption.", "token_count": 348, "char_count": 1331, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6633, "quality_score": 0.8317, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:46.592900", "source": { "split": "train_shard_00000", "doc_id": 3591 }, "chunk_id": "train_shard_00000_3591_0", "global_id": 3980 }, { "text": "The variation in Mycoplasma lipoproteins attributed to genome rearrangements and genetic insertions leads to phenotypic plasticity that allows for the evasion of the host's defence system and pathogenesis. This paper compared for the first time the genomes of four human urogenital Mycoplasma species (M. penetrans HF-2, M. fermentans JER, M. genitalium G37 and M. hominis PG21) to categorise the metabolic functions of the core genes and to assess the effects of tandem repeats, phage-like genetic elements and prophages on the virulence genes. The results of this comparative in silico genomic analysis revealed that the genes constituting their core genomes can be separated into three distinct categories: nuclear metabolism, protein metabolism and energy generation each making up 52%, 31% and 23%, respectively. The genomes have repeat sequences ranging from 3.7% in M. hominis PG21 to 9.5% in M. fermentans JER. Tandem repeats (mostly minisatellites) and phage-like proteins (including DNA gyrases/topoisomerases) were randomly distributed in the Mycoplasma genomes. Here, we identified a coiled-coil structure containing protein in M. penetrans HF-2 which is significantly similar to the Mem protein of M. fermentans ɸMFV1. Therefore, a Mycoplasma prophage seems to be embedded within M. penetrans HF-2 unannotated genome. To the best of our knowledge, no Mycoplasma phages or prophages have been detected in M. penetrans. This study is important not only in understanding the complex genetic factors involved in phenotypic plasticity and virulence in the relatively understudied Mycoplasma species but also in elucidating the effective arrangement of their redundant minimal genomes.\n\nComparative genomics of four Mycoplasma species of the human urogenital tract: Analysis of their core genomes and virulence genes.", "token_count": 473, "char_count": 1824, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5865, "quality_score": 0.7932, "entities": { "genes": [ "PG21" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:47.243317", "source": { "split": "train_shard_00000", "doc_id": 3592 }, "chunk_id": "train_shard_00000_3592_0", "global_id": 3981 }, { "text": "Silver nanoparticles (AgNPs) have been synthesized in situ in micelles formed by the bile salt sodium deoxycholate (NaDC). The AgNPs exhibit \"green\" fluorescence. It has been shown in the present study that they can disrupt the components of gall stones/pigment stones. This unique ability of the AgNPs has been observed upon detailed study of the interaction between the endobiotic pigment bilirubin (BR) and bile salt (NaDC). In addition, these AgNPs show significant cytotoxicity towards the breast cancer cells (MCF-7). Thus the AgNPs synthesized in this work show important physiological activity and can serve as prospective \"Theranostic Materials\" in future. Their green fluorescence bears relevance to future diagnostic applications while their anticancer activity and disruptive action upon BR aggregates in bile salt micelles is extremely important for therapeutic purpose. This is the first report of the use of metal nanoparticles in disruption of components of gall stones/pigment stones and thus the present work has very important physiological significance. The detailed spectral studies indicate that bile salts increase the dimerization of BR which could be linked to increased solubilisation of BR in bile salt media and consequent bile stone/pigment stone formation. Importantly, an increase in red fluorescence was observed (upon dimerization of BR), which is important for cancer detection and studying the metabolism of biological tissues.\n\n\"Theranostic\" role of bile salt-capped silver nanoparticles - gall stone/pigment stone disruption and anticancer activity.", "token_count": 376, "char_count": 1586, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5677, "quality_score": 0.7838, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:47.827331", "source": { "split": "train_shard_00000", "doc_id": 3593 }, "chunk_id": "train_shard_00000_3593_0", "global_id": 3982 }, { "text": "Inulinase from Kluyveromyces marxianus (KmINU1) has wide application in industrial biotechnology, and it is supposed that its expression is regulated at the transcriptional level via the promoter. Therefore, in this study, the KmINU1 promoter, fused to the reporter EGFP gene, was analyzed to determine its fundamental regulatory mechanisms in Saccharomyces cerevisiae S288C (ATCC 204508). Induction by inulin and repression by high glucose concentrations of KmINU1 promoters are reported, and the promoter with a length of 353 bp was shown to have the highest strength with the weakest responses to high glucose concentration. Responses of the KmINU1 promoter to carbon source were shown to be related to the Mig1 binding site extending from -496 to -485 bp. Hence, we propose clear regulation mechanisms of the inulinase promoter, which may provide a powerful theoretical reference for its application in protein production.\n\nCharacterization of inulinase promoter from Kluyveromyces marxianus for intensive protein expression in industrial biotechnology.", "token_count": 269, "char_count": 1057, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:48.381562", "source": { "split": "train_shard_00000", "doc_id": 3594 }, "chunk_id": "train_shard_00000_3594_0", "global_id": 3983 }, { "text": "Mutations in ATP8B1 or ATP11C (members of P4-type ATPases) cause progressive familial intrahepatic cholestasis type 1 in human or intrahepatic cholestasis in mice. Transmembrane protein 30A (TMEM30A), a β-subunit, is essential for the function of ATP8B1 and ATP11C. However, its role in the etiology of cholestasis remains poorly understood. To investigate the function of TMEM30A in bile salt (BS) homeostasis, we developed Tmem30a liver-specific knockout (LKO) mice. Tmem30a LKO mice experienced hyperbilirubinemia, hypercholanemia, inflammatory infiltration, ductular proliferation, and liver fibrosis. The expression and membrane localization of ATP8B1 and ATP11C were significantly reduced in Tmem30a LKO mice, which correlated with the impaired expression and localization of BS transporters, such as OATP1A4, OATP1B2, NTCP, BSEP, and MRP2. The proteasome inhibitor bortezomib partially restored total protein levels of BS transporters but not the localization of BS transporters in the membrane. Furthermore, the expression of nuclear receptors, including FXRα, RXRα, HNF4α, LRH-1, and SHP, was also down-regulated. A cholic acid-supplemented diet exacerbated the liver damage in Tmem30a LKO mice. TMEM30A deficiency led to intrahepatic cholestasis in mice by impairing the expression and localization of BS transporters and the expression of related nuclear receptors. Therefore, TMEM30A may be a novel genetic determinant of intrahepatic cholestasis.\n\nHepatic Tmem30a Deficiency Causes Intrahepatic Cholestasis by Impairing Expression and Localization of Bile Salt Transporters.", "token_count": 497, "char_count": 1587, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [ "ATP11C", "MRP2", "TMEM30A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:49.027373", "source": { "split": "train_shard_00000", "doc_id": 3595 }, "chunk_id": "train_shard_00000_3595_0", "global_id": 3984 }, { "text": "While fungal infections of the bovine uterus are well-known diseases in pregnant cattle, very limited knowledge exists on the presence and significance of fungi in the uterus of non-pregnant cows. Presence of fungi in the uterine lumen of postpartum (pp) cows has been reported, but little attention has been paid to this as most studies of the bovine pp uterus have focused on bacteria.\n\nColonization of the bovine uterus by Candida kefyr.", "token_count": 118, "char_count": 440, "word_count": 72, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:49.418179", "source": { "split": "train_shard_00000", "doc_id": 3596 }, "chunk_id": "train_shard_00000_3596_0", "global_id": 3985 }, { "text": "Bile salt hydrolase (BSH) activity against the bile acid tauro-beta-muricholic acid (T-β-MCA) was recently reported to mediate host bile acid, glucose, and lipid homeostasis via the farnesoid X receptor (FXR) signaling pathway. An earlier study correlated decreased Lactobacillus abundance in the cecum with increased concentrations of intestinal T-β-MCA, an FXR antagonist. While several studies have characterized BSHs in lactobacilli, deconjugation of T-β-MCA remains poorly characterized among members of this genus, and therefore it was unclear what strain(s) were responsible for this activity. Here, a strain of L. johnsonii with robust BSH activity against T-β-MCA in vitro was isolated from the cecum of a C57BL/6J mouse. A screening assay performed on a collection of 14 Lactobacillus strains from nine different species identified BSH substrate specificity for T-β-MCA only in two of three L. johnsonii strains. Genomic analysis of the two strains with this BSH activity revealed the presence of three bsh genes that are homologous to bsh genes in the previously sequenced human-associated strain L. johnsonii NCC533. Heterologous expression of several bsh genes in E. coli followed by enzymatic assays revealed broad differences in substrate specificity even among closely related bsh homologs, and suggests that the phylogeny of these enzymes does not closely correlate with substrate specificity. Predictive modeling allowed us to propose a potential mechanism driving differences in BSH activity for T-β-MCA in these homologs. Our data suggests that L. johnsonii regulates T-β-MCA levels in the mouse intestinal environment, and that this species may play a central role in FXR signaling in the mouse.\n\nIdentification of a mouse Lactobacillus johnsonii strain with deconjugase activity against the FXR antagonist T-β-MCA.", "token_count": 495, "char_count": 1836, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5762, "quality_score": 0.7881, "entities": { "genes": [ "NCC533" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:50.068487", "source": { "split": "train_shard_00000", "doc_id": 3597 }, "chunk_id": "train_shard_00000_3597_0", "global_id": 3986 }, { "text": "Microorganisms develop biofilms on indwelling medical devices and are associated with biofilm-related infections, resulting in substantial morbidity and mortality. Therefore, to prevent and control biofilm-associated infections, the present study was designed to assess the anti-biofilm potential of postbiotics derived from probiotic organisms against most prevalent biofilm-forming Pseudomonas aeruginosa PAO1. Eighty lactic acid bacteria isolated from eight neonatal fecal samples possessed antibacterial activity against P. aeruginosa PAO1. Among these, only four lactic acid bacteria produced both bacteriocin and exopolysaccharides but only one isolate was found to maximally attenuate the P. aeruginosa PAO1 biofilm. More specifically, the phenotypic and probiotic characterization showed that the isolated lactic acid bacteria were gram positive, non-motile, and catalase and oxidase negative; tolerated acidic and alkaline pH; has bile salt concentration; showed 53% hydrophobicity; and was found to be non-hemolytic. Phylogenetically, the organism was found to be probiotic Lactobacillus fermentum with accession no. KT998657. Interestingly, pre-coating of a microtiter plate either with bacteriocin or with exopolysaccharides as well as their combination significantly (p < 0.05) reduced the number of viable cells forming biofilms to 41.7% compared with simultaneous coating of postbiotics that had 72.4% biofilm-forming viable cells as observed by flow cytometry and confocal laser scanning microscopy. Therefore, it can be anticipated that postbiotics as the natural biointerventions can be employed as the prophylactic agents for medical devices used to treat gastrointestinal and urinary tract infections.\n\nEffect of bacteriocin and exopolysaccharides isolated from probiotic on P. aeruginosa PAO1 biofilm.", "token_count": 465, "char_count": 1822, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6405, "quality_score": 0.8202, "entities": { "genes": [ "KT998657", "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:50.707897", "source": { "split": "train_shard_00000", "doc_id": 3598 }, "chunk_id": "train_shard_00000_3598_0", "global_id": 3987 }, { "text": "t-Butyl 6-cyano-(3R,5R)-dihydroxyhexanoate ((3R,5R)-1b) is a valuable chiral synthon of atorvastatin calcium. A novel NADPH-specific aldo-keto reductase (AKR) was identified from a thermotolerant yeast Kluyveromyces marxianus ZJB14056 by genome database mining, displaying t-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate ((5R)-1a) reducing activity and moderate diastereoselectivity (de\n\nRational design of Kluyveromyces marxianus ZJB14056 aldo-keto reductase KmAKR to enhance diastereoselectivity and activity.", "token_count": 192, "char_count": 507, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [ "ZJB14056" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:51.149777", "source": { "split": "train_shard_00000", "doc_id": 3599 }, "chunk_id": "train_shard_00000_3599_0", "global_id": 3988 }, { "text": "Kluyveromyces marxianus, as unconventional yeast, attracts more and more attention in the biofuel fermentation. Although this sort of yeasts can ferment pentose sugars, the fermentation capacity differs largely. Xylose and arabinose fermentation by three K. marxianus strains (K. m 9009, K. m 1911 and K. m 1727) were compared at different temperatures. The results showed that the fermentation performance of the three strains had significant difference under different fermentation temperatures. Especially, the sugar consumption rate and alcohol yield of K. m 9009 and K. m 1727 at 40 ℃ were better than 30 ℃. This results fully reflect the fermentation advantages of K. marxianus yeast under high-temperature. On this basis, five genes (XR, XDH, XK, AR and LAD) coding key metabolic enzymes in three different yeasts were amplified by PCR, and the sequence were compared by Clustalx 2.1. The results showed that the amino acid sequences coding key enzymes have similarity of over 98% with the reference sequences reported in the literature. Furthermore, the difference of amino acid was not at the key site of its enzyme, so the differences between three stains were not caused by the gene level, but by transcribed or translation regulation level. By real-time PCR experiment, we determined the gene expression levels of four key enzymes (XR, XDH, XK and ADH) in the xylose metabolism pathway of K. m 1727 and K. m 1911 at different fermentation time points. The results showed that, for thermotolerant yeast K. m 1727, the low expression level of XDH and XK genes was the main factors leading to accumulation of xylitol. In addition, according to the pathway of Zygosaccharomyces bailii, which have been reported in NCBI and KEGG, the xylose and arabinose metabolic pathways of K. marxianus were identified, which laid foundation for further improving the pentose fermentation ability by metabolic engineering.", "token_count": 522, "char_count": 1916, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5314, "quality_score": 0.7657, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:34:51.780933", "source": { "split": "train_shard_00000", "doc_id": 3600 }, "chunk_id": "train_shard_00000_3600_0", "global_id": 3989 }, { "text": "[Fermentations of xylose and arabinose by Kluyveromyces marxianus].", "token_count": 25, "char_count": 67, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:52.143375", "source": { "split": "train_shard_00000", "doc_id": 3600 }, "chunk_id": "train_shard_00000_3600_1", "global_id": 3990 }, { "text": "A one step, in situ, room temperature synthesis of yellow luminescent CdSe QDs was achieved in a metallohydrogel derived from a facially amphiphilic bile salt, resulting in a QD-gel hybrid. An ordered self-assembly and homogeneous distribution of the CdSe QDs in the hydrogel network was observed from optical and electron micrographs. The different excited state behavior of the CdSe QDs in the hybrid was revealed for the first time using time resolved spectroscopy. We also describe the successful isolation of the photoluminescent CdSe QDs from the gel followed by their re-dispersion in an organic solvent using suitable capping ligands.\n\nIn situ formation of luminescent CdSe QDs in a metallohydrogel: a strategy towards synthesis, isolation, storage and re-dispersion of the QDs.", "token_count": 198, "char_count": 786, "word_count": 120, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:52.941765", "source": { "split": "train_shard_00000", "doc_id": 3601 }, "chunk_id": "train_shard_00000_3601_0", "global_id": 3991 }, { "text": "Horizontal gene transfer (HGT) serves as an important source of innovation for bacterial species. We used a pangenome-based approach to identify genes that were horizontally acquired by four closely related bacterial species, belonging to the\n\nHorizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species.", "token_count": 74, "char_count": 331, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8043, "quality_score": 0.9022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:53.313193", "source": { "split": "train_shard_00000", "doc_id": 3602 }, "chunk_id": "train_shard_00000_3602_0", "global_id": 3992 }, { "text": "Liposomes have been studied as a colloidal carrier in drug delivery systems, especially for oral administration. However, their low structural integrity in the gut is still a major shortcoming. Membrane disruptive effects of physiological bile salts in the small intestine result in premature drug release prior to intestinal absorption. Thus, we analyzed the stabilizing effect of sodium deoxycholate when incorporated into nano-sized liposomes.\n\nNanosized Liposomes Containing Bile Salt: A Vesicular Nanocarrier for Enhancing Oral Bioavailability of BCS Class III Drug.", "token_count": 136, "char_count": 571, "word_count": 80, "semantic_coherence": 1, "information_density": 0.825, "quality_score": 0.9125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:53.742741", "source": { "split": "train_shard_00000", "doc_id": 3603 }, "chunk_id": "train_shard_00000_3603_0", "global_id": 3993 }, { "text": "Invasive candidiasis is a major cause of morbidity and mortality in children. However, limited data are available on the epidemiology of this infection in paediatric settings in Iran. The aim of this study was to determine the prevalence, microbial epidemiology, risk factors and clinical outcomes associated with candidaemia in intensive care units at the Children's Medical Center, Tehran, Iran. All blood and other normally sterile specimen cultures positive for Candida species were included. Isolates were identified by morphological and molecular methods. Unidentified/doubtful yeast isolates were subjected to ITS sequencing. A total of 156 episodes of invasive candidiasis, with an overall incidence of 15.2 per 1000 ICU admissions, was recorded. Risk factors included presence of central venous lines (89.1%), mechanical ventilation (55.8%) and parenteral nutrition (51.3%). Candida albicans (57.1%) and Candida parapsilosis (24.4%) were the most commonly isolated species. Candida orthopsilosis, Candida glabrata, Candida dubliniensis, Candida lusitaniae, Candida kefyr and Candida intermedia accounted for about 11% of the cases. The overall mortality rate was 42.5%. Non-albicans Candida species accounted for nearly half of the cases of paediatric candidaemia. This is the first prospective study of candidaemia in paediatric settings in Iran and serves to inform necessary interventions for the prevention of candidaemia.\n\nMicrobial epidemiology of candidaemia in neonatal and paediatric intensive care units at the Children's Medical Center, Tehran.", "token_count": 416, "char_count": 1564, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6055, "quality_score": 0.8028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:54.368124", "source": { "split": "train_shard_00000", "doc_id": 3604 }, "chunk_id": "train_shard_00000_3604_0", "global_id": 3994 }, { "text": "Intestinal resection is a common therapeutic approach for human diseases such as obesity, inflammatory bowel disease, Crohn's disease, and colon cancer that often results in severe short bowel syndrome-like adverse effects including bile acid diarrhea, dehydration, electrolyte disturbances, and nutrient malabsorption. Here we introduce a murine ileal resection model, termed ileectomy, to evaluate tissue communication and the maintenance of systemic homeostasis. After ileal resection, circulating blood is permanently devoid of the ileum-specific endocrine hormone fibroblast growth factor 15 (FGF15), which releases its endocrinal inhibition of bile acid synthesis in the liver. In combination with the increased production and abolished reabsorption of bile acids after removing the ileum, mice that underwent surgery suffer from bile salt overaccumulation in the intestine and associated diarrhea, morbidity, and mortality. Novel usage of the surgery model introduced in this study may provide mechanistic and functional insights into ileal control of systemic metabolic regulation in physiology and disease.\n\nIleectomy-induced Bile Overaccumulation in Mouse Intestine.", "token_count": 292, "char_count": 1176, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7342, "quality_score": 0.8671, "entities": { "genes": [ "FGF15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:54.933963", "source": { "split": "train_shard_00000", "doc_id": 3605 }, "chunk_id": "train_shard_00000_3605_0", "global_id": 3995 }, { "text": "Fermentable oligo-, di-, and monosaccharides and polyols (FODMAPs) are small molecules that are poorly absorbed in the small intestine and rapidly fermented in the large intestine. There is evidence that a diet low in FODMAPs reduces abdominal symptoms in approximately 70% of the patients suffering from irritable bowel syndrome. Wheat contains relatively high fructan levels and is therefore a major source of FODMAPs in our diet. In this study, a yeast-based strategy was developed to reduce FODMAP levels in (whole wheat) bread. Fermentation of dough with an inulinase-secreting Kluyveromyces marxianus strain allowed to reduce fructan levels in the final product by more than 90%, while only 56%  reduction was achieved when a control Saccharomyces cerevisiae strain was used. To ensure sufficient CO\n\nSaccharomyces cerevisiae and Kluyveromyces marxianus Cocultures Allow Reduction of Fermentable Oligo-, Di-, and Monosaccharides and Polyols Levels in Whole Wheat Bread.", "token_count": 263, "char_count": 975, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6503, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:55.484669", "source": { "split": "train_shard_00000", "doc_id": 3606 }, "chunk_id": "train_shard_00000_3606_0", "global_id": 3996 }, { "text": "DNA-wrapped carbon nanotubes are a class of bionano hybrid molecules that have enabled carbon nanotube sorting, controlled assembly, and biosensing and bioimaging applications. The current method of synthesizing these hybrids via direct sonication of DNA/nanotube mixtures is time-consuming and not suitable for high-throughput synthesis and combinatorial sequence screening. Additionally, the direct sonication method does not make use of nanotubes presorted by extensively developed surfactant-based methods, is not effective for large diameter (>1 nm) tubes, and cannot maintain secondary and tertiary structural and functional domains present in certain DNA sequences. Here, we report a simple, quick, and robust process to produce DNA-wrapped carbon nanotube hybrids with nanotubes of broad diameter range and DNA of arbitrary sequence. This is accomplished by exchanging strong binding bile salt surfactant coating with DNA in methanol/water mixed solvent and subsequent precipitation with isopropyl alcohol. The exchange process can be completed within 10 min and converts over 90% nanotubes into the DNA wrapped form. Applying the exchange process to nanotubes presorted by surfactant-based methods, we show that the resulting DNA-wrapped carbon nanotubes can be further sorted to produce nanotubes with defined handedness, helicity, and endohedral filling. The exchange method greatly expands the structural and functional variety of DNA-wrapped carbon nanotubes and opens possibilities for DNA-directed assembly of structurally sorted nanotubes and high-throughput screening of properties that are controlled by the wrapping DNA sequences.\n\nA Low Energy Route to DNA-Wrapped Carbon Nanotubes via Replacement of Bile Salt Surfactants.", "token_count": 401, "char_count": 1743, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5792, "quality_score": 0.7896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:56.101643", "source": { "split": "train_shard_00000", "doc_id": 3607 }, "chunk_id": "train_shard_00000_3607_0", "global_id": 3997 }, { "text": "Bile salts are the water-soluble end products of hepatic cholesterol catabolism that are released into the duodenum and solubilize lipids due to their amphipathic structure. Bile salts also act as endogenous ligands for dedicated nuclear receptors that exert a plethora of biological processes, mostly related to metabolism. Bile salts are actively reclaimed in the distal part of the small intestine, released into the portal system, and subsequently extracted by the liver. This enterohepatic cycle is critically dependent on dedicated bile salt transporters. In the intestinal lumen, bile salts exert direct antimicrobial activity based on their detergent property and shape the gut microbiota. Bile salt metabolism by gut microbiota serves as a mechanism to counteract this toxicity and generates bile salt species that are distinct from those of the host. Innate immune cells of the liver play an important role in the early recognition and effector response to invading microbes. Bile salts signal primarily via the membrane receptor TGR5 and the intracellular farnesoid-x receptor, both present in innate immune cells. In this review, the interactions between bile salts, gut microbiota, and hepatic innate immunity are discussed.\n\nInteractions between bile salts, gut microbiota, and hepatic innate immunity.", "token_count": 324, "char_count": 1316, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8051, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:56.700041", "source": { "split": "train_shard_00000", "doc_id": 3608 }, "chunk_id": "train_shard_00000_3608_0", "global_id": 3998 }, { "text": "Intrahepatic cholestasis induced by drug toxicity, bile salt export pump (BSEP) deficiency, or pregnancy frequently causes cholestatic liver damage, which ultimately may lead to liver fibrosis and cirrhosis. Here, the preventive and therapeutic effects of peroxisome proliferator-activated receptor α (PPARα) signaling activated by fenofibrate was evaluated on cholestatic liver damage. Metabolomic analysis revealed that alpha-naphthyl isothiocyanate (ANIT)-induced intrahepatic cholestasis resulted in the accumulation of serum long-chain acylcarnitines and triglyceride, and the reduced expression of four fatty acid β-oxidation (β-FAO) relevant genes (Cpt1b, Cpt2, Mcad and Hadha), indicating the disruption of β-FAO. The increase of acylcarnitines in hepatic cell resulted in the enhanced expression of anti-oxidative genes glutathione S-transferases (Gsta2 and Gstm3) directly. As direct PPARα-regulated genes, Cpt1b, Cpt2, and Mcad were up-regulated after pretreatment with PPARα agonist, fenofibrate, indicating the improvement of β-FAO. In the end, the disrupted bile acid metabolism in the enterohepatic circulation and the enhanced oxidative stress and inflammation cytokines induced by ANIT exposure were significantly recovered with the improvement of β-FAO using fenofibrate treatment. These findings provide the rationale for the use of PPARα agonists as therapeutic alternatives for cholestatic liver damage.\n\nPPARα activation protects against cholestatic liver injury.", "token_count": 412, "char_count": 1485, "word_count": 193, "semantic_coherence": 1, "information_density": 0.658, "quality_score": 0.829, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:57.350444", "source": { "split": "train_shard_00000", "doc_id": 3609 }, "chunk_id": "train_shard_00000_3609_0", "global_id": 3999 }, { "text": "Protective effect of the extracellular peptide fraction (reactivating factors, RF) produced by yeasts of various taxonomic groups (Saccharomyces cerevisiae, Kluyveromyces lactis, Candida utilis, and Yarrowia li- polytica) on probiotic lactic acid bacteria (LAB) Lactobacillus casei, L. acidophilus,'and L. reuteri under bile salt (BS)-induced stress was shown. RF of all yeasts were shown to be of peptide nature; the active component of the S. cerevisiae RF was identified as a combination of low-molecular polypeptides with molecular masses of 0.6 to 1.5 kDa. The protective and reactivating effects of the yeast factors were not species-specific and were similar to those of the Luteococcusjaponicus subsp. casei R. In BS-treated cells of the tester bacteria, a pro- tective effect was observed after 10-min preincubation of the LAB cell suspension with yeast RE: the number of surviving cells (CFU) was 2 to 4.5 times higher than in the control. The reactivating effect was observed when RF was added to LAB cell suspensions not later than 15 min after stress treatment. It was less pro- nounced than the protector effect, with the CFU number I to 3 times that of the control. Both the protector and the reactivating effects were most pronounced in the S. cerevisiae and decreased in the row: C. utilis > K. lactis > Y lipolytica. The efficiency of protective action of yeast RF was found to depend on the properties of recepient LAB cells, with the L. casei strain being most sensitive to BS treatment. In both variants, the highest protective effect of RF (increase in the CFU number) was observed for L. acidophilus, while the least pronounced one, for L. casei. The reasons for application of the LAB strains combining high stress resistance and high response to stress-protecting metabolites, including RF factors, as probiotics, is discussed.", "token_count": 496, "char_count": 1852, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5593, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:58.823400", "source": { "split": "train_shard_00000", "doc_id": 3610 }, "chunk_id": "train_shard_00000_3610_0", "global_id": 4000 }, { "text": "Characterization of Extracellular Yeast Peptide Factors and Their Stress-Protective Effect on Probiotic Lactic Acid Bacteria.", "token_count": 37, "char_count": 125, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:59.179252", "source": { "split": "train_shard_00000", "doc_id": 3610 }, "chunk_id": "train_shard_00000_3610_1", "global_id": 4001 }, { "text": "Salmonella enterica subsp enterica serovar Typhimurium (S. Typhimurium) is a serovar with broad host range. To determine the genomic diversity of S. Typhimurium, we sequenced 39 isolates (37 Australian and 2 UK isolates) representing 14 Repeats Groups (RGs) determined primarily by clustered regularly interspaced short palindromic repeats (CRISPR). Analysis of single nucleotide polymorphisms (SNPs) among the 39 isolates yielded an average of 1,232 SNPs per isolate, ranging from 128 SNPs to 11,339 SNPs relative to the reference strain LT2. Phylogenetic analysis of the 39 isolates together with 66 publicly available genomes divided the 105 isolates into five clades and 19 lineages, with the majority of the isolates belonging to clades I and II. The composition of CRISPR profiles correlated well with the lineages, showing progressive deletion and occasional duplication of spacers. Prophage genes contributed nearly a quarter of the S. Typhimurium accessory genome. Prophage profiles were found to be correlated with lineages and CRISPR profiles. Three new variants of HP2-like P2 prophage, several new variants of P22 prophage and a plasmid-like genomic island StmGI_0323 were found. This study presents evidence of horizontal transfer from other serovars or species and provides a broader understanding of the global genomic diversity of S. Typhimurium.\n\nComparative genomics of Australian and international isolates of Salmonella Typhimurium: correlation of core genome evolution with CRISPR and prophage profiles.", "token_count": 414, "char_count": 1525, "word_count": 221, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [ "HP2", "LT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:34:59.800356", "source": { "split": "train_shard_00000", "doc_id": 3611 }, "chunk_id": "train_shard_00000_3611_0", "global_id": 4002 }, { "text": "Bile salts represent signalling molecules with a variety of endocrine functions. Bile salt effects are mediated by different receptor molecules, comprising ligand-activated nuclear transcription factors as well as G protein-coupled membrane-bound receptors. The farnesoid X receptor (FXR) and the plasma membrane-bound G protein-coupled receptor TGR5 (Gpbar-1) are prototypic bile salt receptors of both classes and are highly expressed in the liver including the biliary tree as well as in the intestine. In liver, TGR5 is localized in different non-parenchymal cells such as sinusoidal endothelial cells, Kupffer cells, hepatic stellate cells and small and large cholangiocytes. Through TGR5 bile salts can mediate choleretic, cell-protective as well as proliferative effects in cholangiocytes. A disturbance of these signalling mechanisms can contribute to the development of biliary diseases. In line with the important role of TGR5 for bile salt signalling, TGR5 knockout mice are more susceptible to cholestatic liver damage. Furthermore, in absence of TGR5 cholangiocyte proliferation in response to cholestasis is attenuated and intrahepatic and extrahepatic bile ducts show increased cell damage, underscoring the role of the receptor for biliary physiology. Decreased TGR5 expression may also contribute to the development or progression of cholangiopathies like primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC) since reduced TGR5-dependent cell-protective mechanisms such as bicarbonate secretion renders cholangiocytes more vulnerable towards bile salt toxicity. Nevertheless, TGR5 overexpression or constant stimulation of the receptor can promote cholangiocyte proliferation leading to cyst growth in polycystic liver disease or even progression of cholangiocarcinoma", "token_count": 475, "char_count": 1807, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5738, "quality_score": 0.7869, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:00.444738", "source": { "split": "train_shard_00000", "doc_id": 3612 }, "chunk_id": "train_shard_00000_3612_0", "global_id": 4003 }, { "text": "Not only the stimulation of TGR5-mediated pathways by suitable TGR5 agonists but also the inhibition of TGR5 signalling by the use of antagonists represent potential therapeutic approaches for different types of biliary diseases. This article is part of a Special Issue entitled: Cholangiocytes in Health and Disease edited by Jesus Banales, Marco Marzioni, Nicholas LaRusso and Peter Jansen.\n\nBile acid receptors in the biliary tree: TGR5 in physiology and disease.", "token_count": 121, "char_count": 466, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7714, "quality_score": 0.8857, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:00.835567", "source": { "split": "train_shard_00000", "doc_id": 3612 }, "chunk_id": "train_shard_00000_3612_1", "global_id": 4004 }, { "text": "To investigate the relation of two different mutations to the outcome of partial external biliary diversion (PEBD) in severe bile salt export pump (BSEP) deficiency.\n\nPartial external biliary diversion in bile salt export pump deficiency: Association between outcome and mutation.", "token_count": 62, "char_count": 280, "word_count": 40, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:01.202085", "source": { "split": "train_shard_00000", "doc_id": 3613 }, "chunk_id": "train_shard_00000_3613_0", "global_id": 4005 }, { "text": "Nonobstructive cholestasis after pediatric liver transplantation is a common diagnostic and therapeutic dilemma. We describe a girl with neonatal cholestasis because of progressive familial intrahepatic cholestasis 2 (PFIC-2) and presence of a homozygous splice site mutation in the ABCB11 gene. Liver transplantation was performed because of end-stage liver disease at the age of 6. Cholestasis with normal gamma-glutamyl transferase (GGT) developed 8 years after liver transplantation. A liver biopsy showed canalicular cholestasis and giant cell hepatitis without evidence of rejection, mimicking PFIC-2. Immunofluorescence staining of normal human liver sections with patient's serum revealed reactivity toward a canalicular epitope, which could be identified as bile salt export pump (BSEP) using BSEP-yellow fluorescent protein (YFP) transfected cells. Our patient developed a recurrence of a PFIC-2 phenotype due to production of antibodies against BSEP (alloimmune BSEP disease [AIBD]). Intensification of immunosuppressive therapy as well as antibody treatment with plasmapheresis and Rituximab were initiated, leading to stabilization of the clinical condition and depletion of anti-BSEP antibodies in serum. However, after 1 year liver transplantation was necessary again because of end-stage liver insufficiency. Afterward, immunomodulatory treatment consisted of tacrolimus, mycophenolate mofetil, prednisone, immunoadsorption, and high-dose immunoglobulin therapy (1 g/kg/d).\n\nCholestasis After Pediatric Liver Transplantation-Recurrence of a Progressive Familial Intrahepatic Cholestasis Phenotype as a Rare Differential Diagnosis: A Case Report.", "token_count": 457, "char_count": 1661, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6589, "quality_score": 0.8294, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:01.838175", "source": { "split": "train_shard_00000", "doc_id": 3614 }, "chunk_id": "train_shard_00000_3614_0", "global_id": 4006 }, { "text": "Fructus Gardenia (FG), containing the major active constituent Geniposide, is widely used in China for medicinal purposes. Currently, clinical reports of FG toxicity have not been published, however, animal studies have shown FG or Geniposide can cause hepatotoxicity in rats. We investigated Geniposide-induced hepatic injury in male Sprague-Dawley rats after 3-day intragastric administration of 100 mg/kg or 300 mg/kg Geniposide. Changes in hepatic histomorphology, serum liver enzyme, serum and hepatic bile acid profiles, and hepatic bile acid synthesis and transportation gene expression were measured. The 300 mg/kg Geniposide caused liver injury evidenced by pathological changes and increases in serum alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP) and γ-glutamytransferase (γ-GT). While liver, but not sera, total bile acids (TBAs) were increased 75% by this dose, dominated by increases in taurine-conjugated bile acids (t-CBAs). The 300 mg/kg Geniposide also down-regulated expression of Farnesoid X receptor (FXR), small heterodimer partner (SHP) and bile salt export pump (BSEP). In conclusion, 300 mg/kg Geniposide can induce liver injury with associated changes in bile acid regulating genes, leading to an accumulation of taurine conjugates in the rat liver. Taurocholic acid (TCA), taurochenodeoxycholic acid (TCDCA) as well as tauro-α-muricholic acid (T-α-MCA) are potential markers for Geniposide-induced hepatic damage.\n\nDose-related liver injury of Geniposide associated with the alteration in bile acid synthesis and transportation.", "token_count": 495, "char_count": 1601, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6422, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:02.494158", "source": { "split": "train_shard_00000", "doc_id": 3615 }, "chunk_id": "train_shard_00000_3615_0", "global_id": 4007 }, { "text": "Kluyveromyces marxianus, a non-conventional thermotolerant yeast, is potentially useful for production of ethanol and other products. This species has a strong tendency to randomly integrate transforming DNA fragments, making necessary the development of more precise methods for gene targeting. In this study, we first demonstrated that K. marxianus NBRC1777 is cold-tolerant, and then established a highly efficient and precise technique for gene editing by introducing genes encoding deaminase-mediated targeted point mutagenesis (Target-AID) and clustered regularly interspaced short palindromic repeats (CRISPR) associated proteins (CRISPR-Cas9). We used Target-AID to introduce targeted point mutations that disrupted Nej1 or Dnl4, genes that are involved in non-homologous end-joining (NHEJ). Both of the resulting mutant strains showed enhanced proportions of homology-mediated integration compared to the wild-type parent. In combination with target cleavage by CRISPR-Cas9, markerless integration was performed using short (~50 bp) flanking homologous sequences. Together, these tools render this species fully tractable for gene manipulation, permitting targeted genetic changes in the cold- and thermo-tolerant yeast K. marxianus.\n\nDevelopment of a comprehensive set of tools for genome engineering in a cold- and thermo-tolerant Kluyveromyces marxianus yeast strain.", "token_count": 345, "char_count": 1379, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7127, "quality_score": 0.8564, "entities": { "genes": [ "NBRC1777" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:03.071611", "source": { "split": "train_shard_00000", "doc_id": 3616 }, "chunk_id": "train_shard_00000_3616_0", "global_id": 4008 }, { "text": "Two novel sulfated bile salt-like dienones, featuring either a unique, rearranged side chain or a rare cis-11,12-diol on the steroidal C-ring, herein named petromyzene A (1) and B (2), respectively, were isolated from water conditioned with spawning male sea lamprey (Petromyzon marinus; a jawless vertebrate animal). The structures of these natural products were elucidated by mass spectrometry and NMR spectroscopy. Petromyzenes A and B exhibited high olfactory potency for adult sea lamprey and strong behavioral attraction for spawning females.\n\nBile Salt-like Dienones Having a Novel Skeleton or a Rare Substitution Pattern Function as Chemical Cues in Adult Sea Lamprey.", "token_count": 188, "char_count": 676, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7677, "quality_score": 0.8838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:03.512300", "source": { "split": "train_shard_00000", "doc_id": 3617 }, "chunk_id": "train_shard_00000_3617_0", "global_id": 4009 }, { "text": "Premature atherosclerosis in diabetes accounts for much of the decreased life span. New treatments have reduced this risk considerably. This review explores the relationship among the disturbances in glucose, lipid, and bile salt metabolic pathways that occur in diabetes. In particular, excess nutrient intake and starvation have major metabolic effects, which have allowed us new insights into the disturbance that occurs in diabetes. Metabolic regulators such as the forkhead transcription factors, the farnesyl X transcription factors, and the fibroblast growth factors have become important players in our understanding of the dysregulation of metabolism in diabetes and overnutrition. The disturbed regulation of lipoprotein metabolism in both the intestine and the liver has been more clearly defined over the past few years, and the atherogenicity of the triglyceride-rich lipoproteins, and - in tandem - low levels of high-density lipoproteins, is seen now as very important. New information on the apolipoproteins that control lipoprotein lipase activity has been obtained. This is an exciting time in the battle to defeat diabetic atherosclerosis.\n\nDiabetes and dyslipidemia: characterizing lipoprotein metabolism.", "token_count": 290, "char_count": 1225, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:04.076814", "source": { "split": "train_shard_00000", "doc_id": 3618 }, "chunk_id": "train_shard_00000_3618_0", "global_id": 4010 }, { "text": "Coronary atherosclerotic disease is a serious disease in humans, but no suitable animal model is available currently for further studies. We used apolipoprotein E gene knockout (ApoE KO) rats to induce hypercholesterolemia through a special high cholesterol/bile salt diet (Paigen diet), then analyzed aortic and coronary atherosclerosis lesions and the myocardial injury in order to establish a novel small animal model of coronary atherosclerosis. Plasma cholesterol of ApoE KO rats increased 7.6-fold compared with wild-type rats after 8 weeks on the Paigen diet. After 10 to 12 weeks of subsisting on the Paigen diet, ApoE KO rats developed mild aortic atherosclerosis with severe coronary atherosclerosis. Hematoxilyn and eosin staining showed that 11 out of 12 ApoE KO male rats had right coronary artery atherosclerosis, 7 of them were>70% occluded. Oil Red O (Lipid Stain), Mac2 immuno-staining and Masson's trichrome staining demonstrated substantial amounts of lipid, macrophages and collagen fibers in coronary atherosclerosis plaques. In addition, ApoE KO male rats had severe myocardial focal lesions with cholesterol ester as the main component in the lesions. In conclusion, ApoE KO rats developed severe hypercholesterolemia, coronary atherosclerosis and myocardial cholesterol ester deposition after subsisting on the Paigen diet and can be used as a novel animal model for studies on cholesterol metabolism and coronary atherosclerotic disease.\n\nEstablishment of a rat model with diet-induced coronary atherosclerosis.", "token_count": 454, "char_count": 1536, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5676, "quality_score": 0.7838, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:04.711463", "source": { "split": "train_shard_00000", "doc_id": 3619 }, "chunk_id": "train_shard_00000_3619_0", "global_id": 4011 }, { "text": "5α-Cyprinol 27-sulfate is the major biliary bile salt present in cypriniform fish including the zebrafish (Danio rerio). The current study was designed to identify the zebrafish cytosolic sulfotransferase (Sult) enzyme(s) capable of sulfating 5α-cyprinol and to characterize the zebrafish 5α-cyprinol-sulfating Sults in comparison with human SULT2A1. Enzymatic assays using zebrafish homogenates showed 5α-cyprinol-sulfating activity. A systematic analysis, using a panel of recombinant zebrafish Sults, revealed two Sult2 subfamily members, Sult2st2 and Sult2st3, as major 5α-cyprinol-sulfating Sults. Both enzymes showed higher activities using 5α-cyprinol as the substrate, compared to their activity with DHEA, a representative substrate for mammalian SULT2 family members, particularly SULT2A1. pH-Dependence and kinetics experiments indicated that the catalytic properties of zebrafish Sult2 family members in mediating the sulfation of 5α-cyprinol were different from those of either zebrafish Sult3st4 or human SULT2A1. Collectively, these results imply that both Sult2st2 and Sult2st3 have evolved to sulfate specifically C\n\nIdentification and characterization of 5α-cyprinol-sulfating cytosolic sulfotransferases (Sults) in the zebrafish (Danio rerio).", "token_count": 404, "char_count": 1262, "word_count": 161, "semantic_coherence": 1, "information_density": 0.646, "quality_score": 0.823, "entities": { "genes": [ "SULT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:05.333418", "source": { "split": "train_shard_00000", "doc_id": 3620 }, "chunk_id": "train_shard_00000_3620_0", "global_id": 4012 }, { "text": "Farnesoid X receptor (FXR) is a master regulator of bile acid homeostasis through transcriptional regulation of genes involved in bile acid synthesis and cellular membrane transport. Impairment of bile acid efflux due to cholangiopathies results in chronic cholestasis leading to abnormal elevation of intrahepatic and systemic bile acid levels. Obeticholic acid (OCA) is a potent and selective FXR agonist that is 100-fold more potent than the endogenous ligand chenodeoxycholic acid (CDCA). The effects of OCA on genes involved in bile acid homeostasis were investigated using sandwich-cultured human hepatocytes. Gene expression was determined by measuring mRNA levels. OCA dose-dependently increased fibroblast growth factor-19 (FGF-19) and small heterodimer partner (SHP) which, in turn, suppress mRNA levels of cholesterol 7-alpha-hydroxylase (CYP7A1), the rate-limiting enzyme for de novo synthesis of bile acids. Consistent with CYP7A1 suppression, total bile acid content was decreased by OCA (1 μmol/L) to 42.7 ± 20.5% relative to control. In addition to suppressing de novo bile acids synthesis, OCA significantly increased the mRNA levels of transporters involved in bile acid homeostasis. The bile salt excretory pump (BSEP), a canalicular efflux transporter, increased by 6.4 ± 0.8-fold, and the basolateral efflux heterodimer transporters, organic solute transporter α (OST\n\nObeticholic acid, a selective farnesoid X receptor agonist, regulates bile acid homeostasis in sandwich-cultured human hepatocytes.", "token_count": 453, "char_count": 1521, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:05.980761", "source": { "split": "train_shard_00000", "doc_id": 3621 }, "chunk_id": "train_shard_00000_3621_0", "global_id": 4013 }, { "text": "Lactobacillus fermentum NCDC 400 is a commonly used and a comprehensively studied probiotic organism. The distinctive capability to endure the harsh environment of the gastrointestinal tract owing to the presence of bile salts in gastric juice facilitates gut microbiota, especially the probiotic organisms to transiently inhabit the host gut. In the present study, Label-Free Quantification (LFQ) approach has been employed to analyze the expression pattern of Lactobacillus fermentum NCDC 400 strain proteins, under bile acid stress, using high-resolution mass spectrometer connected to nano-liquid chromatography (LC) system. We report the identification of a total of 538 differentially expressed (DE) proteins in response to 1.2% bile salt which is required for the growth of this bacterium. Among the DE proteins, 80 were found to be up-regulated, with greater than 1.3 fold change vis-à-vis 107 proteins which were down-regulated with <0.76 fold change (p<0.05). The functions of down-regulated proteins were largely unknown nevertheless; the putative functions of the up-regulated proteins were categorized into categories viz. stress response, DNA repair, peptidoglycan biosynthesis, amino acids metabolism, signal transduction, transcription, translation, and carbohydrate metabolism. These results suggest that the differentially expressed proteins provide the tolerance towards the various gastrointestinal challenges and involved in bile acid stress response mechanism.\n\nLabel-free quantitative proteomic analysis of Lactobacillus fermentum NCDC 400 during bile salt exposure.", "token_count": 410, "char_count": 1589, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:06.599326", "source": { "split": "train_shard_00000", "doc_id": 3622 }, "chunk_id": "train_shard_00000_3622_0", "global_id": 4014 }, { "text": "This study presents the bioreduction of six β-ketoesters by whole cells of Kluyveromyces marxianus and molecular investigation of a series of 13 β-ketoesters by hologram quantitative structure-activity relationship (HQSAR) in order to relate with conversion and enantiomeric excess of β-stereogenic-hydroxyesters obtained by the same methodology. Four of these were obtained as (R)-configuration and two (S)-configuration, among them four compounds exhibited >99% enantiomeric excess. The β-ketoesters series LUMO maps showed that the β-carbon of the ketoester scaffold are exposed to undergo nucleophilic attack, suggesting a more favorable β-carbon side to enzymatic reduction based on adopted molecular conformation at the reaction moment. The HQSAR method was performed on the β-ketoesters derivatives separating them into those provided predominantly (R)- or (S)-β-hydroxyesters. The HQSAR models for both (R)- and (S)-configuration showed high predictive capacity. The HQSAR contribution maps suggest the importance of β-ketoesters scaffold as well as the substituents attached therein to asymmetric reduction, showing a possible influence of the ester group carbonyl position on the molecular conformation in the enzyme catalytic site, exposing a β-carbon side to the bioconversion to (S)- and (R)-enantiomers.\n\nAsymmetric bioreduction of β-ketoesters derivatives by Kluyveromyces marxianus: influence of molecular structure on the conversion and enantiomeric excess.", "token_count": 396, "char_count": 1474, "word_count": 198, "semantic_coherence": 1, "information_density": 0.601, "quality_score": 0.8005, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:07.220445", "source": { "split": "train_shard_00000", "doc_id": 3623 }, "chunk_id": "train_shard_00000_3623_0", "global_id": 4015 }, { "text": "Pathogenicity Locus, Core Genome, and Accessory Gene Contributions to", "token_count": 17, "char_count": 69, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:07.574862", "source": { "split": "train_shard_00000", "doc_id": 3624 }, "chunk_id": "train_shard_00000_3624_0", "global_id": 4016 }, { "text": "In light of the biomedical interest for self-assembling amphiphiles bearing the tripeptide Arg-Gly-Gly (RGD), a cholic acid derivative was synthesized by introducing an aromatic moiety on the steroidal skeleton and the RGD sequence on the carboxylic function of its chain 17-24, thus forming a peptide amphiphile with the unconventional rigid amphiphilic structure of bile salts. In aqueous solution, the compound self-assembled into long twisted ribbons characterized by a very low degree of polydispersity in terms of width (≈25nm), thickness (≈4.5nm) and pitch (≈145nm). It was proposed that in the ribbon the molecules are arranged in a bilayer structure with the aromatic moieties in the interior, strongly involved in the intermolecular interaction, whereas the RGD residues are located at the bilayer-water interface. The nanostructure is significantly different from those generally provided by RGD-containing amphiphiles with the conventional peptide-tail structure, for which fibers with a circular cross-section were observed, and successfully tested as scaffolds for tissue regeneration. From previous work on the use of this kind of nanostructures, it is known that features like morphology, rigidity, epitope spacing and periodicity are important factors that dramatically affect cell adhesion and signaling. Within this context, the reported results demonstrate that bile salt-based peptide surfactants are promising building blocks in the preparation of non-trivial RGD-decorated nanoaggregates with well-defined morphologies and epitope distributions.\n\nTwisted nanoribbons from a RGD-bearing cholic acid derivative.", "token_count": 399, "char_count": 1632, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8356, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:08.238160", "source": { "split": "train_shard_00000", "doc_id": 3625 }, "chunk_id": "train_shard_00000_3625_0", "global_id": 4017 }, { "text": "The bile salt export pump (BSEP/ABCB11) transports bile salts from hepatocytes into bile canaliculi. Its malfunction is associated with severe liver disease. One reason for functional impairment of BSEP is systemic administration of drugs, which as a side effect inhibit the transporter. Therefore, drug candidates are routinely screened for potential interaction with this transporter. Hence, understanding the functional biology of BSEP is of key importance. In this study, we engineered the transporter to dissect interdomain communication paths. We introduced mutations in noncanonical and in conserved residues of either of the two nucleotide binding domains and determined the effect on BSEP basal and substrate-stimulated ATPase activity as well as on taurocholate transport. Replacement of the noncanonical methionine residue M584 (Walker B sequence of nucleotide binding site 1) by glutamate imparted hydrolysis competency to this site. Importantly, this mutation was able to sustain 15% of wild-type transport activity, when the catalytic glutamate of the canonical nucleotide binding site 2 was mutated to glutamine. Kinetic modeling of experimental results for the ensuing M584E/E1244Q mutant suggests that a transfer of hydrolytic capacity from the canonical to the noncanonical nucleotide binding site results in loss of active and adoption of facilitative characteristics. This facilitative transport is ATP-gated. To the best of our knowledge, this result is unprecedented in ATP-binding cassette proteins with one noncanonical nucleotide binding site. Our study promotes an understanding of the domain interplay in BSEP as a basis for exploration of drug interactions with this transporter.\n\nMolecular Mechanism of Taurocholate Transport by the Bile Salt Export Pump, an ABC Transporter Associated with Intrahepatic Cholestasis.", "token_count": 450, "char_count": 1845, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5763, "quality_score": 0.7882, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:08.898238", "source": { "split": "train_shard_00000", "doc_id": 3626 }, "chunk_id": "train_shard_00000_3626_0", "global_id": 4018 }, { "text": "Host diet is a major determinant of the composition and function of the intestinal microbiome. Less understood is the importance of diet on ingested strains with probiotic significance. We investigated the population dynamics of exogenous Lactobacillus plantarum and its interactions with intestinal bacteria in mice undergoing switches between high-fat, high-sugar (HFHSD) and low-fat, plant-polysaccharide rich (LFPPD) diets. The survival and persistence of ingested L. plantarum WCFS1 was significantly improved during mouse consumption of HFHSD and was negatively associated with the numbers of indigenous Lactobacillus species. Diet also rapidly changed the composition of the indigenous microbiota, but with some taxa differentially affected between HFHSD periods. L. plantarum was not integrated into indigenous bacterial community networks according to co-occurrence patterns but still conferred distinct effects on bacterial species diversity and microbiota stability largely in a diet-dependent manner. Metagenome predictions supported the premise that L. plantarum dampens the effects of diet on the microbiome. This strain also consistently altered the predicted genetic content in the distal gut by enriching for genes encoding glyosyltransferases and bile salt hydrolases. Our findings demonstrate the interactions between ingested, transient probiotic bacteria and intestinal bacterial communities and how they can differ depending on host diet.\n\nDietary perturbations alter the ecological significance of ingested Lactobacillus plantarum in the digestive tract.", "token_count": 355, "char_count": 1577, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [ "WCFS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:09.512967", "source": { "split": "train_shard_00000", "doc_id": 3627 }, "chunk_id": "train_shard_00000_3627_0", "global_id": 4019 }, { "text": "Drug-induced liver injury remains the most common cause of acute liver failure and a frequently indicated reason for withdrawal of drugs. For the purpose of evaluating the relevance of liver cell models for assessing hepatotoxic risks in intact humans, we here aimed to benchmark 'omics-derived mechanistic data from three in vitro models for parenchymal liver function, intended for the investigation of drug-induced cholestasis, against 'omics data from cholestatic patients. Transcriptomic changes in HepG2 cells, primary mouse hepatocytes and primary human hepatocytes exposed to known cholestatic compounds were analyzed using microarrays. Some of the differentially expressed genes in HepG2 cells were also differentially expressed into the same direction in human cholestasis. The overlap between drug-induced transcriptomic responses in primary mouse hepatocytes and primary human hepatocytes appeared limited and no genes overlapping with in vivo cholestasis were found. Thereupon, a pathway for drug-induced cholestasis was used to map the drug-induced transcriptomic modifications involved in bile salt homeostasis. Indications of an adaptive response to prevent and reduce intracellular bile salt accumulation were observed in vivo as well as in the in vitro liver models. Furthermore, drug-specific changes were found, which may be indicative for their cholestatic properties. Furthermore, connectivity mapping was applied in order to investigate the predictive value of the in vitro models for in vivo cholestasis. This analysis resulted in a positive connection score for most compounds, which may indicate that for identifying cholestatic compounds the focus should be on gene expression signatures rather than on differentially expressed genes.\n\nValidation of gene expression profiles from cholestatic hepatotoxicants in vitro against human in vivo cholestasis.", "token_count": 419, "char_count": 1878, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5551, "quality_score": 0.7776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:10.150810", "source": { "split": "train_shard_00000", "doc_id": 3628 }, "chunk_id": "train_shard_00000_3628_0", "global_id": 4020 }, { "text": "The thermotolerant yeast Kluyveromyces marxianus displays a potential to be used for ethanol production from both whey and lignocellulosic biomass at elevated temperatures, which is highly alluring to reduce the cost of the bioprocess. Nevertheless, contrary to Saccharomyces cerevisiae, K. marxianus cannot tolerate high ethanol concentrations. We report the transcriptional profile alterations in K. marxianus under ethanol stress in order to gain insights about mechanisms involved with ethanol response. Time-dependent changes have been characterized under the exposure of 6% ethanol and compared with the unstressed cells prior to the ethanol addition. Our results reveal that the metabolic flow through the central metabolic pathways is impaired under the applied ethanol stress. Consistent with these results, we also observe that genes involved with ribosome biogenesis are downregulated and gene-encoding heat shock proteins are upregulated. Remarkably, the expression of some gene-encoding enzymes related to unsaturated fatty acid and ergosterol biosynthesis decreases upon ethanol exposure, and free fatty acid and ergosterol measurements demonstrate that their content in K. marxianus does not change under this stress. These results are in contrast to the increase previously reported with S. cerevisiae subjected to ethanol stress and suggest that the restructuration of K. marxianus membrane composition differs in the two yeasts which gives important clues to understand the low ethanol tolerance of K. marxianus compared to S. cerevisiae.\n\nTranscriptome analysis of the thermotolerant yeast Kluyveromyces marxianus CCT 7735 under ethanol stress.", "token_count": 405, "char_count": 1663, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6094, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:10.770795", "source": { "split": "train_shard_00000", "doc_id": 3629 }, "chunk_id": "train_shard_00000_3629_0", "global_id": 4021 }, { "text": "Bile acids are regulators of lipid and glucose metabolism, and modulate inflammation in the liver and other tissues. Primary bile acids such as cholic acid and chenodeoxycholic acid (CDCA) are produced in the liver, and converted into secondary bile acids such as deoxycholic acid (DCA) and lithocholic acid by gut microbiota. Here we investigated the possible roles of bile acids in non-alcoholic fatty liver disease (NAFLD) pathogenesis and the impact of the gut microbiome on bile acid signalling in NAFLD.\n\nSuppressed hepatic bile acid signalling despite elevated production of primary and secondary bile acids in NAFLD.", "token_count": 169, "char_count": 624, "word_count": 96, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:11.226006", "source": { "split": "train_shard_00000", "doc_id": 3630 }, "chunk_id": "train_shard_00000_3630_0", "global_id": 4022 }, { "text": "Zearalenone (ZEN) is a non-steroidal estrogenic mycotoxin produced by Fusarium species, which has been shown to be associated with reproductive disorders in livestock, and to a lesser extent with hyperoestrogenic syndromes in humans. The aim of this study was to characterize a Bacillus amyloliquefaciens strain with ZEN removal ability. A pure culture of a strain designated LN isolated from moldy corn samples showed a high ZEN removal capability. Based on microscopic observations, biochemical characteristics, and phylogenetic analysis of the 16S rRNA gene sequence, LN was identified as B. amyloliquefaciens. After incubation of B. amyloliquefaciens LN in Luria-Bertani (LB) medium containing 3.5 ppm of ZEN, the ZEN concentration fell below the detection limit within 24 h. In ZEN-contaminated corn meal medium, B. amyloliquefaciens LN decreased ZEN concentration by 92% after 36 h of incubation. In phosphate-buffered saline (PBS) containing 5 ppm of ZEN, B. amyloliquefaciens LN reduced the ZEN concentration from 5 ppm to 3.28 ppm immediately after coming into contact with ZEN, and further reduced the ZEN concentration to 0.36 ppm after 4 h of incubation. The amounts of ZEN adsorbed by the cells of B. amyloliquefaciens LN did not increase with the extension of incubation time, indicating that B. amyloliquefaciens LN not only possessed ZEN adsorption ability, but also exhibited the ability to degrade ZEN. In addition, B. amyloliquefaciens LN was non-hemolytic, non-enterotoxin producing, and displayed probiotic characteristics including acidic tolerance, bile salt tolerance, and anti-pathogenic activities. These findings suggest that B. amyloliquefaciens LN has a potential to be used as a feed additive to reduce the concentrations of ZEN in feedstuffs.", "token_count": 506, "char_count": 1773, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5779, "quality_score": 0.789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:11.864364", "source": { "split": "train_shard_00000", "doc_id": 3631 }, "chunk_id": "train_shard_00000_3631_0", "global_id": 4023 }, { "text": "Isolation and characterization of a Bacillus amyloliquefaciens strain with zearalenone removal ability and its probiotic potential.", "token_count": 33, "char_count": 131, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:12.238564", "source": { "split": "train_shard_00000", "doc_id": 3631 }, "chunk_id": "train_shard_00000_3631_1", "global_id": 4024 }, { "text": "The increased consumers' interest on the positive role of food in wellbeing and health underscores the need to determine new probiotic microorganisms. Triggered by the fact that artisanal food products can be a valuable source of novel probiotic strains, 106 lactic acid bacteria, all isolated from traditional Greek dairy products, namely Feta, Kasseri, Xynotyri, Graviera, Formaela, Galotyri, and Kefalotyri cheeses as well as yogurt and milk, were studied for probiotic properties. Based on their survival at pH 2.5 and their stability in the presence of bile salts, 20 strains were selected for further analysis. These strains exhibited diverse susceptibility to commonly used antibiotics, while none was hemolytic. Seven out of the 20 strains produced functional bile salt hydrolases in vitro. The only antimicrobial activity detected of Streptococcus thermophilus ACA-DC 26 against the oral pathogen Streptococcus mutans LMG 14558\n\nProbiotic Features of Lactic Acid Bacteria Isolated from a Diverse Pool of Traditional Greek Dairy Products Regarding Specific Strain-Host Interactions.", "token_count": 291, "char_count": 1090, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7278, "quality_score": 0.8639, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:12.801778", "source": { "split": "train_shard_00000", "doc_id": 3632 }, "chunk_id": "train_shard_00000_3632_0", "global_id": 4025 }, { "text": "In this study, seven bacteriocinogenic and non-bacteriocinogenic LAB strains previously isolated from the intestines of Nile tilapia and common carp and that showed potent antibacterial activity against host-derived and non-host-derived fish pathogens were assayed for their probiotic and safety properties so as to select promising candidates for in vivo application as probiotic in aquaculture. All the strains were investigated for acid and bile tolerances, transit tolerance in simulated gastrointestinal conditions, for cell surface characteristics including hydrophobicity, co-aggregation and auto-aggregation, and for bile salt hydrolase activity. Moreover, haemolytic, gelatinase and biogenic amine-producing abilities were investigated for safety assessment. The strains were found to be tolerant at low pH (two strains at pH 2.0 and all the strains at pH 3.0). All of them could also survive in the presence of bile salts (0.3% oxgall) and in simulated gastric and intestinal juices conditions. Besides, three of them were found to harbour the gtf gene involved in pH and bile salt survival. The strains also showed remarkable cell surface characteristics, and 57.14% exhibited the ability to deconjugate bile salts. When assayed for their safety properties, the strains prove to be free from haemolytic activity, gelatinase activity and they could neither produce biogenic amines nor harbour the hdc gene. They did not also show antibiotic resistance, thus confirming to be safe for application as probiotics. Among them, Lactobacillus brevis 1BT and Lactobacillus plantarum 1KMT exhibited the best probiotic potentials, making them the most promising candidates.\n\nIn Vitro Evaluation of the Probiotic and Safety Properties of Bacteriocinogenic and Non-Bacteriocinogenic Lactic Acid Bacteria from the Intestines of Nile Tilapia and Common Carp for Their Use as Probiotics in Aquaculture.", "token_count": 493, "char_count": 1898, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5385, "quality_score": 0.7692, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:13.458824", "source": { "split": "train_shard_00000", "doc_id": 3633 }, "chunk_id": "train_shard_00000_3633_0", "global_id": 4026 }, { "text": "Many pathogens such as Shigella and other bacteria assemble the type III secretion system (T3SS) nanoinjector to inject virulence proteins into their target cells to cause infectious diseases in humans. The rise of drug resistance among pathogens that rely on the T3SS for infectivity, plus the dearth of new antibiotics require alternative strategies in developing new antibiotics. The Shigella T3SS tip protein IpaD is an attractive target for developing anti-infectives because of its essential role in virulence and its exposure on the bacterial surface. Currently, the only known small molecules that bind to IpaD are bile salt sterols. In this study we identified four new small-molecule scaffolds that bind to IpaD, based on the methylquinoline, pyrrolidine-aniline, hydroxyindole, and morpholinoaniline scaffolds. NMR mapping revealed potential hotspots in IpaD for binding small molecules. These scaffolds can be used as building blocks in developing small-molecule inhibitors of IpaD that could lead to new anti-infectives.\n\nCharacterization of Small-Molecule Scaffolds That Bind to the Shigella Type III Secretion System Protein IpaD.", "token_count": 295, "char_count": 1145, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:14.011381", "source": { "split": "train_shard_00000", "doc_id": 3634 }, "chunk_id": "train_shard_00000_3634_0", "global_id": 4027 }, { "text": "The absorption of poorly water-soluble drugs is influenced by the luminal gastrointestinal fluid content and composition, which control solubility. Simulated intestinal fluids have been introduced into dissolution testing including endogenous amphiphiles and digested lipids at physiological levels; however, in vivo individual variation exists in the concentrations of these components, which will alter drug absorption through an effect on solubility. The use of a factorial design of experiment and varying media by introducing different levels of bile, lecithin, and digested lipids has been previously reported, but here we investigate the solubility variation of poorly soluble drugs through more complex biorelevant amphiphile interactions. A four-component mixture design was conducted to understand the solubilization capacity and interactions of bile salt, lecithin, oleate, and monoglyceride with a constant total concentration (11.7 mM) but varying molar ratios. The equilibrium solubility of seven low solubility acidic (zafirlukast), basic (aprepitant, carvedilol), and neutral (fenofibrate, felodipine, griseofulvin, and spironolactone) drugs was investigated. Solubility results are comparable with literature values and also our own previously published design of experiment studies. Results indicate that solubilization is not a sum accumulation of individual amphiphile concentrations, but a drug specific effect through interactions of mixed amphiphile compositions with the drug. This is probably due to a combined interaction of drug characteristics; for example, lipophilicity, molecular shape, and ionization with amphiphile components, which can generate specific drug-micelle affinities. The proportion of each component can have a remarkable influence on solubility with, in some cases, the highest and lowest points close to each other. A single-point solubility measurement in a fixed composition simulated media or human intestinal fluid sample will therefore provide a value without knowledge of the surrounding solubility topography meaning that variability may be overlooked. This study has demonstrated how the amphiphile ratios influence drug solubility and highlights the importance of the envelope of physiological variation when simulating in vivo drug behavior.", "token_count": 495, "char_count": 2300, "word_count": 310, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:14.655579", "source": { "split": "train_shard_00000", "doc_id": 3635 }, "chunk_id": "train_shard_00000_3635_0", "global_id": 4028 }, { "text": "Influence of Physiological Gastrointestinal Surfactant Ratio on the Equilibrium Solubility of BCS Class II Drugs Investigated Using a Four Component Mixture Design.", "token_count": 42, "char_count": 164, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:15.012112", "source": { "split": "train_shard_00000", "doc_id": 3635 }, "chunk_id": "train_shard_00000_3635_1", "global_id": 4029 }, { "text": "Multiple emitting components in a fluorophoric system often produce complicated emission spectra. Extracting the individual spectral information from the composite spectra is important in order to comprehend the photophysical processes occurring in the multifluorophoric systems. Although the combination of Principal Component Analysis and Multivariate Curve Resolution-Alternate Least Square (PCA/MCR-ALS) technique is a well-known approach for curve deconvolution, its applicability in the spectral deconvolution of vibronically and electronically mixed up emitting systems as well as systems merged up with multiple electronic bands without a priori knowledge of the individual emitting species, is not properly studied. The present work highlights the strength of PCA/MCR-ALS in retrieving pure spectral information from the set of complex spectra arising out of the regular variation of causative factors that result in the variation of spectral composition. The retrieval of the emission bands utilizing the PCA/MCR-ALS technique has been made without having a priori information of the emitting species present in the multifluorophoric systems and the resolved spectra correspond well with the fluorescence spectra of the individual chemical species. The common curve fitting methods such as Gaussian and Lorentzian techniques have been found to be unsuccessful in providing meaningful photophysical information through the retrieved spectra. A comparative study of the curve fitting techniques MCR-ALS, Gaussian and Lorentzian in a set of complicated emission spectra of (i) pyrene and its excimer, (ii) pyrene and its excimer in presence of benzo[a]pyrene, and (iii) fisetin in bile salt medium is presented herein in details.\n\nApplication of Multivariate Curve Resolution-Alternate Least Square Technique on Extracting Pure Spectral Components from Multiple Emitting Systems: a Case Study.", "token_count": 418, "char_count": 1900, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5189, "quality_score": 0.7595, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:15.635199", "source": { "split": "train_shard_00000", "doc_id": 3636 }, "chunk_id": "train_shard_00000_3636_0", "global_id": 4030 }, { "text": "Bile salt stimulated lipase (BSSL; Enzyme Commission (EC) number 3.1.1.13) has been a candidate triglyceridase for improving enzyme therapy for pancreatic insufficiency; however, its efficacy is near absent. We hypothesise that similarly to pancreatic lipase, BSSL is inhibited by phospholipids and this inhibition is relieved by Phospholipase A\n\nBile salt stimulated lipase: Inhibition by phospholipids and relief by phospholipase A", "token_count": 129, "char_count": 433, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:16.056736", "source": { "split": "train_shard_00000", "doc_id": 3637 }, "chunk_id": "train_shard_00000_3637_0", "global_id": 4031 }, { "text": "The influence of inorganic salt on the structure of lecithin/bile salt mixtures in aqueous solution is studied by means of dissipative particle dynamics simulations. We propose a coarse-grained model of phosphatidylcholine and two types of bile salts (sodium cholate and sodium deoxycholate) and also take into account the presence of low molecular weight salt. This model allows us to study the system on rather large time and length scales (up to about ∼20 μs and 50 nm) and to reveal mechanisms of experimentally observed increasing viscosity upon increasing the low molecular weight salt concentration in this system. We show that increasing the low molecular weight salt concentration induces the growth of cylinder-like micelles formed in lecithin/bile salt mixtures in water. These wormlike micelles can entangle into transient networks displaying perceptible viscoelastic properties. Computer simulation results are in good qualitative agreement with experimental observations.\n\nSelf-Assembly of Lecithin and Bile Salt in the Presence of Inorganic Salt in Water: Mesoscale Computer Simulation.", "token_count": 252, "char_count": 1101, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:16.546587", "source": { "split": "train_shard_00000", "doc_id": 3638 }, "chunk_id": "train_shard_00000_3638_0", "global_id": 4032 }, { "text": "The bile salt export pump (BSEP, ABCB11), multidrug resistance protein 3 (MDR3, ABCB4) and the ATPase familial intrahepatic cholestasis 1 (FIC1, ATP8B1) mediate bile formation. This study aimed to determine the contribution of mutations and common variants in the FIC1, BSEP and MDR3 genes to cholestatic disorders of differing disease onset and severity.\n\nSequencing of FIC1, BSEP and MDR3 in a large cohort of patients with cholestasis revealed a high number of different genetic variants.", "token_count": 150, "char_count": 491, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7467, "quality_score": 0.8733, "entities": { "genes": [ "ABCB4", "ABCB11", "MDR3", "FIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:16.996199", "source": { "split": "train_shard_00000", "doc_id": 3639 }, "chunk_id": "train_shard_00000_3639_0", "global_id": 4033 }, { "text": "A novel triterpenoidal compound named 'amnomopin' (3β-diglucoside-5,12-28-oic acid), which is named IUPAC as 3-O-(2' ➔ 1″diglucoside)1,2,3,4,4a,5,6,6a,6b,7,9,10,11,12,12a,12b,13,14b-octadecahydro-10-hydroxy-2,2,6a,6b,9,9,12a-heptamethylpicene-4a-carboxylic acid, was isolated from the extract Petriella setifera. The total alcoholic extract of P. setifera showed a great activity against clinically isolated Candida species, including Candida albicans, Candida dubliniensis, Candida famata, Candida glabrata, Candida inconspicua, Candida kefyr, Candida krusei, Candida norvegensis, Candida parapsilosis and Candida tropicalis. Also, the new compound amnomopin was active against all the investigated Candida species. The highest anticandidal activity of P. setifera extract was obtained against C. kefyr (22.6 ± 1.5 mm), C. albicans and C. norvegensis (21.3 ± 0.63 mm) and C. krusei (20.6 ± 1.5 mm). Moreover, the minimum inhibitory concentrations of both the total extract and the isolated compound were low. The minimum inhibitory concentration of the compound isolated from P. setifera was 0.49 μg/mL against C. kefyr, 0.98 μg/mL against C. albicans and C. norvegensis and 1.95 μg/mL against C. krusei. The oral dosing of the extract and the isolated compound did not show any significant effect on the activity of alanine aminotransferase, aspirate aminotransferase and the levels of blood urea and serum creatinine", "token_count": 516, "char_count": 1419, "word_count": 188, "semantic_coherence": 1, "information_density": 0.5426, "quality_score": 0.7713, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:35:17.630538", "source": { "split": "train_shard_00000", "doc_id": 3640 }, "chunk_id": "train_shard_00000_3640_0", "global_id": 4034 }, { "text": "Copyright © 2017 John Wiley & Sons, Ltd.\n\nAnticandidal Activity of Extracts and a Novel Compound, Amnomopin, Isolated From Petriella setifera.", "token_count": 50, "char_count": 142, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:17.992795", "source": { "split": "train_shard_00000", "doc_id": 3640 }, "chunk_id": "train_shard_00000_3640_1", "global_id": 4035 }, { "text": "To investigate gene expression profiles of the thermotolerant yeast Saccharomyces cerevisiae strain KKU-VN8, a potential high-ethanol producer, in response to various stresses during high-temperature ethanol fermentation using sweet sorghum juice (SSJ) under optimal conditions.\n\nGene expression profiles of the thermotolerant yeast Saccharomyces cerevisiae strain KKU-VN8 during high-temperature ethanol fermentation using sweet sorghum juice.", "token_count": 118, "char_count": 444, "word_count": 53, "semantic_coherence": 1, "information_density": 0.6604, "quality_score": 0.8302, "entities": { "genes": [ "VN8" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:18.376564", "source": { "split": "train_shard_00000", "doc_id": 3641 }, "chunk_id": "train_shard_00000_3641_0", "global_id": 4036 }, { "text": "The extensive environmental adaptability of the genus Paenibacillus is related to the enormous diversity of its gene repertoires. Paenibacillus sp. SSG-1 has previously been reported, and its agar-degradation trait has attracted our attention. Here, the genome sequence of Paenibacillus sp. SSG-1, together with 76 previously sequenced strains, was comparatively studied. The results show that the pan-genome of Paenibacillus is open and indicate that the current taxonomy of this genus is incorrect. The incessant flux of gene repertoires resulting from the processes of gain and loss largely contributed to the difference in genomic content and genome size in Paenibacillus. Furthermore, a large number of genes gained are associated with carbohydrate transport and metabolism. It indicates that the evolution of glycometabolism is a key factor for the environmental adaptability of Paenibacillus species. Interestingly, through horizontal gene transfer, Paenibacillus sp. SSG-1 acquired an approximately 150 kb DNA fragment and shows an agar-degrading characteristic distinct from most other non-marine bacteria. This region may be transported in bacteria as a complete unit responsible for agar degradation. Taken together, these results provide insights into the evolutionary pattern of Paenibacillus and have implications for studies on the taxonomy and functional genomics of this genus.\n\nComparative genomic analysis of Paenibacillus sp. SSG-1 and its closely related strains reveals the effect of glycometabolism on environmental adaptation.", "token_count": 368, "char_count": 1550, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6267, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:18.952302", "source": { "split": "train_shard_00000", "doc_id": 3642 }, "chunk_id": "train_shard_00000_3642_0", "global_id": 4037 }, { "text": "This study was designed to isolate and identify the potential probionts present in 32 healthy mothers' breast milk. Microbial culture media and 16SrRNA sequencing were used to isolate and identify the bacteria and all isolates were analyzed for their antagonistic potential, resistance to acidic pH, bile salts and survival under simulated gastric and intestinal conditions. The colonization potential was further assessed based on adherence to human enterocyte-like Caco-2 cell lines. The breast milk samples harbored significant numbers of Gram positive and catalase negative (85%) bacteria. Based on 16SrRNA sequencing, these isolates were identified as Lactobacillus casei, L.gasseri, L.fermentum, L.plantarum, Pediococcus acidilactici, and Enterococcus facieum. Among the isolates, P. acidilactici was the most frequent species (71%) present in these samples. Few Gram and catalase positive isolates, Staphylococcus aureus and S.hominiis were also observed. The isolates were viable and unviable in pH 3 and 1.5, respectively, while all isolates survived in 1.0% bile salt. As putative probionts, P.acidilactici 1C showed a significantly higher percentage of adhesion to Caco-2 cells (p< 0.05)than the other two isolates L.plantarum 7A and E.facieum 2C. Bacterial strains isolated from human breast milk were shown to have probiotic properties including anti-infective protection and may be considered as future therapeutics for infants.\n\nCharacterization of Candidate probionts isolated from human breast milk.", "token_count": 410, "char_count": 1519, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:19.572898", "source": { "split": "train_shard_00000", "doc_id": 3643 }, "chunk_id": "train_shard_00000_3643_0", "global_id": 4038 }, { "text": "Three hundred and sixty presumptive lactic acid bacteria (LAB) isolated from pregnant sows, newborn, suckling, and weaned piglets were preliminarily screened for anti-Salmonella activity. Fifty-eight isolates consisting of Lactobacillus reuteri (n = 32), Lactobacillus salivarius (n = 10), Lactobacillus mucosae (n = 8), Lactobacillus johnsonii (n = 5), and Lactobacillus crispatus (n = 3) were selected and further characterized for probiotic properties including production of antimicrobial substances, acid and bile tolerance, and cell adherence to Caco-2 cells. Eight isolates including Lact. johnsonii LJ202 and Lact. reuteri LR108 were identified as potential probiotics. LJ202 was selected for further use in co-culture studies of two-bacterial and multiple-bacterial species to examine its inhibitory activity against Salmonella enterica serovar Enteritidis DMST7106 (SE7106). Co-culture of LJ202 and SE7106 showed that LJ202 could completely inhibit the growth of SE7106 in 10 h of co-culture. In co-culture of multiple-bacterial species, culturable fecal bacteria from pig feces were used as representative of multiple-bacterial species. The study was performed to examine whether interactions among multiple-bacterial species would influence antagonistic activity of LJ202 against SE7106 and fecal coliform bacteria. Co-culture of SE7106 with different combinations of fecal bacteria and probiotic (LJ202 and LR108) or non-probiotic (Lact. mucosae LM303) strains revealed that the growth of SE7106 was completely inhibited either in the presence or in the absence of probiotic strains. Intriguingly, LJ202 exhibited notable inhibitory activity against fecal coliform bacteria while LR108 did not", "token_count": 511, "char_count": 1706, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5751, "quality_score": 0.7876, "entities": { "genes": [ "LJ202", "LM303", "DMST7106", "SE7106", "LR108" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:20.257270", "source": { "split": "train_shard_00000", "doc_id": 3644 }, "chunk_id": "train_shard_00000_3644_0", "global_id": 4039 }, { "text": "Taken together, the results of co-culture studies suggested that LJ202 is a good probiotic candidate for further study its inhibitory effects against pathogen infections in pigs.\n\nSelection of Potential Probiotic Lactobacillus with Inhibitory Activity Against Salmonella and Fecal Coliform Bacteria.", "token_count": 76, "char_count": 299, "word_count": 40, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [ "LJ202" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:20.653818", "source": { "split": "train_shard_00000", "doc_id": 3644 }, "chunk_id": "train_shard_00000_3644_1", "global_id": 4040 }, { "text": "In this study, we report the comparative genomics and phylogenetic analysis of Corynebacterium diphtheriae strain B-D-16-78 that was isolated from a clinical specimen in 2016. The complete genome of C. diphtheriae strain B-D-16-78 was sequenced using PacBio Single Molecule, Real-Time sequencing technology and consists of a 2,474,151-bp circular chromosome with an average GC content of 53.56%. The core genome of C. diphtheriae was also deduced from a total of 74 strains with complete or draft genome sequences and the core genome-based phylogenetic analysis revealed close genetic relationship among strains that shared the same MLST allelic profile. In the context of CRISPR-Cas system, which confers adaptive immunity against re-invading DNA, 73 out of 86 spacer sequences were found to be unique to Malaysian strains which harboured only type-II-C and/or type-I-E-a systems. A total of 48 tox genes which code for the diphtheria toxin were retrieved from the 74 genomes and with the exception of one truncated gene, only nucleotide substitutions were detected when compared to the tox gene sequence of PW8. More than half were synonymous substitution and only two were nonsynonymous substitutions whereby H24Y was predicted to have a damaging effect on the protein function whilst T262V was predicted to be tolerated. Both toxigenic and non-toxigenic toxin-gene bearing strains have been isolated in Malaysia but the repeated isolation of toxigenic strains with the same MLST profile suggests the possibility of some of these strains may be circulating in the population. Hence, efforts to increase herd immunity should be continued and supported by an effective monitoring and surveillance system to track, manage and control outbreak of cases.\n\nComparative genomic and phylogenetic analysis of a toxigenic clinical isolate of Corynebacterium diphtheriae strain B-D-16-78 from Malaysia.", "token_count": 508, "char_count": 1894, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5972, "quality_score": 0.7986, "entities": { "genes": [ "PW8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:21.296563", "source": { "split": "train_shard_00000", "doc_id": 3645 }, "chunk_id": "train_shard_00000_3645_0", "global_id": 4041 }, { "text": "To shed light on the genetic background behind the virulence and salt tolerance of Staphylococcus equorum, we performed comparative genome analysis of six S. equorum strains. Data on four previously published genome sequences were obtained from the NCBI database, while those on strain KM1031 displaying resistance to multiple antibiotics and strain C2014 causing haemolysis were determined in this study. Examination of the pan-genome of five of the six S. equorum strains showed that the conserved core genome retained the genes for general physiological processes and survival of the species. In this comparative genomic analysis, the factors that distinguish the strains from each other, including acquired genomic factors in mobile elements, were identified. Additionally, the high salt tolerance of strains enabling growth at a NaCl concentration of 25% (w/v) was attributed to the genes encoding potassium voltage-gated channels. Among the six strains, KS1039 does not possess any of the functional virulence determinants expressed in the other strains.\n\nGenomic insights into the virulence and salt tolerance of Staphylococcus equorum.", "token_count": 261, "char_count": 1143, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6347, "quality_score": 0.8174, "entities": { "genes": [ "KS1039", "KM1031" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:21.907502", "source": { "split": "train_shard_00000", "doc_id": 3646 }, "chunk_id": "train_shard_00000_3646_0", "global_id": 4042 }, { "text": "To investigate the effects of Kluyveromyces marxianus on immune responses, intestinal structure and microbiota in broilers, 840 1-d-old broiler chicks were randomly divided into seven groups (eight replicates) and were fed basal diets without or with 0.25, 0.50, 1.0, 1.5, 2.0, and 2.5 g/kg of K. marxianus (2.0×1010 CFU/g). Serum and intestine samples were collected at 21 d of age. The results showed that increasing K. marxianus addition linearly reduced feed conversion ratio but linearly elevated relative thymus weight, as well as quadratically increased serum lysozyme and IgG levels, with the medium dose (1.0 g/kg) being the most effective. The ratio of villus height to crypt depth of jejunum and ileum, ileal villus height and sucrase activity, as well as the mRNA expression of ileal mucin-2, claudin-1 and sodium glucose cotransporter 1 linearly responded to the increasing K. marxianus addition. Supplemental K. marxianus at low (0.5 g/kg), medium (1.5 g/kg) and high (2.5 g/kg) dose all decreased the abundance of phylum Cyanobacteria, increased the abundance of phylum Firmicutes and genus Lactobacillus in ileum. The high dose of K. marxianus addition also reduced the abundance of order Rickettsiales and Pseudomonadales along with species Acinetobacter junii. Ileal bacterial communities between K. marxianus-treated and untreated groups formed distinctly different clusters. In summary, K. marxianus supplementation benefits feed efficiency and immune function, as well as intestinal structure in broilers, which might be attributed to the improved ileal microbial structure. Supplemental K. marxianus at high dose (2.5 g/kg) was more effective for feed efficiency and intestinal health of broilers, while the innate immunity was optimized at a medium dose (1.0 g/kg).", "token_count": 525, "char_count": 1788, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5865, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:35:22.565620", "source": { "split": "train_shard_00000", "doc_id": 3647 }, "chunk_id": "train_shard_00000_3647_0", "global_id": 4043 }, { "text": "Effects of Kluyveromyces marxianus supplementation on immune responses, intestinal structure and microbiota in broiler chickens.", "token_count": 32, "char_count": 128, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:22.926483", "source": { "split": "train_shard_00000", "doc_id": 3647 }, "chunk_id": "train_shard_00000_3647_1", "global_id": 4044 }, { "text": "Type II toxin-antitoxin (TA) systems are most commonly composed of two genes encoding a stable toxin, which harms the cell, and an unstable antitoxin that can inactivate it. TA systems were initially characterized as selfish elements, but have recently gained attention for regulating general stress responses responsible for pathogen virulence, formation of drug-tolerant persister cells and biofilms-all implicated in causing recalcitrant chronic infections. We use a bioinformatics approach to explore the distribution and evolution of type II TA loci of the opportunistic pathogen,\n\nDiversity, Prevalence, and Longitudinal Occurrence of Type II Toxin-Antitoxin Systems of", "token_count": 163, "char_count": 675, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7872, "quality_score": 0.8936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:23.370659", "source": { "split": "train_shard_00000", "doc_id": 3648 }, "chunk_id": "train_shard_00000_3648_0", "global_id": 4045 }, { "text": "Ileal bile acid-binding protein, IBABP, participates in the intracellular trafficking of bile salts and influences their signaling activities. The recently discovered variant, IBABP-L, bearing an N-terminal 49-amino acid extension, was found to be associated with colorectal cancer and to protect cancer cells from the cytotoxic effects of deoxycholate. However, the precise function and the molecular properties of this variant are currently unknown.\n\nThe long variant of human ileal bile acid-binding protein associated with colorectal cancer exhibits sub-cellular localization and lipid binding behaviour distinct from those of the common isoform.", "token_count": 155, "char_count": 650, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7191, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:23.810371", "source": { "split": "train_shard_00000", "doc_id": 3649 }, "chunk_id": "train_shard_00000_3649_0", "global_id": 4046 }, { "text": "Bile acid transporters and the nuclear factor erythroid 2-related factor (Nrf-2)-mediated adaptive response play important roles in the development of drug-induced liver injury (DILI). However, little is known about the contribution of the adaptive response to rifampicin (RFP)-induced cell injury. In this study, we found RFP decreased the survival rate of HepG2 cells and increased the levels of lactate dehydrogenase (LDH), alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (AKP), γ-glutamyl-transferase (γ-GT), total bilirubin (TBIL), direct bilirubin (DBIL), indirect bilirubin (IBIL), total bile acid (TBA) and adenosine triphosphate (ATP) in the cell culture supernatants in both a concentration- and a time-dependent manner. RFP increased the expression levels of bile acid transporter proteins and mRNAs, such as bile salt export pump (BSEP), multidrug resistance protein 1 (MDR1), multidrug resistance-associated protein 2 (MRP2), Na\n\nRifampicin-induced injury in HepG2 cells is alleviated by TUDCA via increasing bile acid transporters expression and enhancing the Nrf2-mediated adaptive response.", "token_count": 340, "char_count": 1145, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6797, "quality_score": 0.8399, "entities": { "genes": [ "MDR1", "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:24.373394", "source": { "split": "train_shard_00000", "doc_id": 3650 }, "chunk_id": "train_shard_00000_3650_0", "global_id": 4047 }, { "text": "In this study, we examined a novel method of microencapsulation with calcium alginate-chitosan and Eudragit S100 nanoparticles for the improving viability of probiotic bacteria, Lactobacillus acidophilus and Lactobacillus rhamnosus. Extrusion technique was carried out in microencapsulation process. The viability of two probiotics in single coated beads (with only chitosan), double coated beads (with chitosan and Eudragit nanoparticles), and as free cells (unencapsulated) were conducted in simulated gastric juice (pH 1.55, without pepsin) followed by incubation in simulated intestinal juice (pH 7.5, with 1% bile salt). In case of single coated beads, presumably, lack of sufficient strength of chitosan under simulated gastric condition was the main reason of 4-log and 5-log reduction of the counts of the L. acidophilus and L. rhamnosus respectively. The results showed that with the second coat forming (Eudragit nanoparticles) over the first coat (chitosan), the strength of the beads and then viability rate of the bacteria were increased in comparison with the single coated beads.\n\nEffect of Eudragit S100 nanoparticles and alginate chitosan encapsulation on the viability of Lactobacillus acidophilus and Lactobacillus rhamnosus.", "token_count": 352, "char_count": 1244, "word_count": 177, "semantic_coherence": 1, "information_density": 0.5763, "quality_score": 0.7881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:25.293829", "source": { "split": "train_shard_00000", "doc_id": 3651 }, "chunk_id": "train_shard_00000_3651_0", "global_id": 4048 }, { "text": "Colon cancer is one of the most prevalent cancers, and intestinal microbial community plays a pivotal role in colorectal tumor genesis. Probiotics as live microorganisms may be able to exert an anticancer effect in colon cancer. The aim of this study was to isolate and identify Lactobacillus spp. from traditional dairy products with probiotic properties and to investigate their anticancer effects through ErbB-2 and ErbB-3 gene expression in colon cancer cells. The isolated lactobacilli from yogurt and cheese samples were molecularly identified by blasting of 16-23s rDNA region PCR sequenced products. The probiotic properties, including acid and bile tolerance, antimicrobial activity, and antibiotic susceptibility, were assayed. The proliferation inhibition effects of lactobacilli secretion metabolites with probiotic potential on colon cancer cell lines (HT-29 and caco-2) were analyzed using MTT assay. The real-time PCR was used for assessment of ErbB-2 and ErbB-3 gene expression after being treated with probiotics. Four species of bacteria with the most probiotic properties, including Lactobacillus casei, Lactobacillus paracasei, Lactobacillus rhamnosus, and Lactobacillus plantarum, were characterized and their effects on different human cell lines were taken into consideration. Total bacterial secretions significantly reduced the viability of HT-29 and caco-2 cancer cells compared with untreated controls. The metabolites secreted by bacteria downregulated the expression of ErbB-2 and ErbB-3 genes in colon cancer cells. The present study indicated that probiotic bacteria isolated from traditional dairy products exert anticancer effect on colon cancer cells through the downregulation of ErbB-2 and ErbB-3 gene expression.\n\nProphylactic effects of secretion metabolites of dairy lactobacilli through downregulation of ErbB-2 and ErbB-3 genes on colon cancer cells.", "token_count": 488, "char_count": 1891, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5344, "quality_score": 0.7672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:25.941095", "source": { "split": "train_shard_00000", "doc_id": 3652 }, "chunk_id": "train_shard_00000_3652_0", "global_id": 4049 }, { "text": "Escherichia coli is both a harmless commensal in the intestines of many mammals, as well as a dangerous pathogen. The evolutionary paths taken by strains of this species in the commensal-to-pathogen transition are complex and can involve changes both in the core genome, as well in the pan-genome. One way to understand the likely paths that a commensal strain of E. coli takes when evolving pathogenicity is through experimentally evolving the strain under the selective pressures that it will have to withstand as a pathogen. Here, we report that a commensal strain, under continuous pressure from macrophages, recurrently acquired a transposable element insertion, which resulted in two key phenotypic changes: increased intracellular survival, through the delay of phagosome maturation and increased ability to escape macrophages. We further show that the acquisition of the pathoadaptive traits was accompanied by small but significant changes in the transcriptome of macrophages upon infection. These results show that under constant pressures from a key component of the host immune system, namely macrophage phagocytosis, commensal E. coli rapidly acquires pathoadaptive mutations that cause transcriptome changes associated to the host-microbe duet.\n\nCommensal-to-pathogen transition: One-single transposon insertion results in two pathoadaptive traits in Escherichia coli -macrophage interaction.", "token_count": 332, "char_count": 1406, "word_count": 199, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:26.510789", "source": { "split": "train_shard_00000", "doc_id": 3653 }, "chunk_id": "train_shard_00000_3653_0", "global_id": 4050 }, { "text": "In this review, we describe the epidemiology and clinical significance of resistance in Candida spp. and other non-Cryptococcus yeasts. The rise in echinocandin resistance, azole resistance and cross-resistance to two or more antifungal classes [multidrug resistance (MDR)] has been a worrisome trend, mainly in US large tertiary and oncology centres, particularly as it relates to Candida glabrata. Candida kefyr is also a concern as it can be resistant to echinocandins and polyenes, especially in patients with haematological malignancies. Lately, Candida auris has drawn a lot of attention: this uncommon Candida spp. is the first globally emerging fungal pathogen that exhibits MDR and strong potential for nosocomial transmission. Its almost simultaneous spread in four continents could be indicative of increasing selection pressures from the use of antifungal agents. Echinocandin non-susceptibility is also common among non-Candida, non-Cryptococcus yeasts. As Candida resistance patterns reflect, in part, institutional practices of antifungal administration, the benefits of antifungal stewardship protocols are increasingly recognised and endorsed in recent guidelines. Development of rapid diagnostic methods for detecting or ruling out the presence of candidaemia and antifungal resistance, as well as discovery of novel antifungals, are key priorities in medical mycology research.\n\nEpidemiology of antifungal resistance in human pathogenic yeasts: current viewpoint and practical recommendations for management.", "token_count": 366, "char_count": 1527, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6635, "quality_score": 0.8317, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:27.092450", "source": { "split": "train_shard_00000", "doc_id": 3654 }, "chunk_id": "train_shard_00000_3654_0", "global_id": 4051 }, { "text": "The interaction of Ribonuclease A (RNase A) with the bile salt, sodium deoxycholate (NaDC) is meticulously investigated using various spectroscopic techniques. The binding isotherm constructed from the modulation of intrinsic tyrosine fluorescence of the protein following interaction with NaDC conspicuously reveals an intrinsically complex stepwise interaction process which proceeds through the formation of distinct conformational states of the protein. The conformational transitions are found to occur at c\n\nStepwise unfolding of Ribonuclease A by a biosurfactant.", "token_count": 133, "char_count": 570, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:27.521501", "source": { "split": "train_shard_00000", "doc_id": 3655 }, "chunk_id": "train_shard_00000_3655_0", "global_id": 4052 }, { "text": "In the course of replication of eukaryotic chromosomes, the telomere length is maintained due to activity of telomerase, the ribonucleoprotein reverse transcriptase. Abolishing telomerase function causes progressive shortening of telomeres and, ultimately, cell cycle arrest and replicative senescence. To better understand the cellular response to telomerase deficiency, we performed a transcriptomic study for the thermotolerant methylotrophic yeast Hansenula polymorpha DL-1 lacking telomerase activity.\n\nThe genome-wide transcription response to telomerase deficiency in the thermotolerant yeast Hansenula polymorpha DL-1.", "token_count": 159, "char_count": 626, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:27.962696", "source": { "split": "train_shard_00000", "doc_id": 3656 }, "chunk_id": "train_shard_00000_3656_0", "global_id": 4053 }, { "text": "The family Enterobacteriaceae harbors many important pathogens, however it has proven difficult to reliably distinguish different members of this family or discern their interrelationships. To understand the interrelationships among the Enterobacteriaceae species, we have constructed two comprehensive phylogenetic trees for 78 genome-sequenced Enterobacteriaceae species based on 2487 core genome proteins, and another set of 118 conserved proteins. The genome sequences of Enterobacteriaceae species were also analyzed for genetic relatedness based on average amino acid identity and 16S rRNA sequence similarity. In parallel, comparative genomic studies on protein sequences from the Enterobacteriaceae have identified 88 molecular markers in the form of conserved signature indels (CSIs) that are uniquely shared by specific members of the family. All of these multiple lines of investigations provide consistent evidence that most of the species/genera within the family can be assigned to 6 different subfamily level clades which are designated as the \"Escherichia clade\", \"Klebsiella clade\", \"Enterobacter clade\", \"Kosakonia clade\", \"Cronobacter clade\" and \"Cedecea clade\". The members of the six described clades, in addition to their distinct branching in phylogenetic trees, can now be reliably demarcated in molecular terms on the basis of multiple identified CSIs that are exclusively shared by the group members. Several additional CSIs identified in this work that are either specific for individual genera (viz. Kosakonia, Kluyvera and Escherichia-Shigella), or are present at various taxonomic depths, offer information regarding the interrelationships among the different clades. The described molecular markers provide novel means for diagnostic as well as genetic and biochemical studies on the Enterobacteriaceae species and for resolving the polyphyly of its several genera viz. Escherichia, Enterobacter and Kluyvera. On the bases of our results, we are proposing the reclassification of Escherichia vulneris and Enterobacter massiliensis into two novel genera viz. Pseudescherichia gen. nov. and Metakosakonia gen. nov., respectively", "token_count": 519, "char_count": 2157, "word_count": 297, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:35:28.592860", "source": { "split": "train_shard_00000", "doc_id": 3657 }, "chunk_id": "train_shard_00000_3657_0", "global_id": 4054 }, { "text": "Additionally, our results also support the transfer of \"Enterobacter lignolyticus\" and \"Kluyvera intestini\" to the genera Pluralibacter and Metakosakonia, respectively.\n\nPhylogenomics and comparative genomic studies delineate six main clades within the family Enterobacteriaceae and support the reclassification of several polyphyletic members of the family.", "token_count": 93, "char_count": 358, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:28.975986", "source": { "split": "train_shard_00000", "doc_id": 3657 }, "chunk_id": "train_shard_00000_3657_1", "global_id": 4055 }, { "text": "The focus of the present work was to investigate the interaction of the anticancer drug mitoxantrone with two bile salts, sodium taurodeoxycholate (NaTDC) and sodium taurocholate (NaTC). Ultraviolet-visible (UV-Vis) absorption and electron paramagnetic resonance (EPR) spectroscopy were used to quantify the interaction and to obtain information on the location of mitoxantrone in bile salt micelles. The presence of submicellar concentrations of both bile salts induces mitoxantrone aggregation and the extent of drug aggregation in NaTDC is higher than in NaTC. For micellar bile salts concentrations, mitoxantrone monomers are entrapped in the micellar core. Binding constants, micelle/water partition coefficients and the corresponding thermodynamic parameters for binding and partitioning processes were estimated using the changes in monomer absorbance in the presence of bile salts. Binding interaction of mitoxantrone is stronger for NaTDC than NaTC micelles, whereas partitioning efficiency is higher for NaTC micelles for all investigated temperatures. Thermodynamic parameters indicate that both binding and partitioning processes are spontaneous and entropy controlled. The spectral behavior and thermodynamic parameters indicate distinct types of mitoxantrone interaction with NaTDC and NaTC micelles supported by the differences in nature and structure of bile salts micelles.\n\nSpectroscopic Investigation of the Interaction of the Anticancer Drug Mitoxantrone with Sodium Taurodeoxycholate (NaTDC) and Sodium Taurocholate (NaTC) Bile Salts.", "token_count": 380, "char_count": 1555, "word_count": 208, "semantic_coherence": 1, "information_density": 0.4904, "quality_score": 0.7452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:29.551138", "source": { "split": "train_shard_00000", "doc_id": 3658 }, "chunk_id": "train_shard_00000_3658_0", "global_id": 4056 }, { "text": "The thermotolerant yeast\n\nCRISPR-Cas9-enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in", "token_count": 39, "char_count": 125, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:29.911954", "source": { "split": "train_shard_00000", "doc_id": 3659 }, "chunk_id": "train_shard_00000_3659_0", "global_id": 4057 }, { "text": "A capillary micellar electrokinetic chromatography (MEKC) method was developed enabling the stereoselective separation of the insecticide bioallethrin. The use of sodium deoxycholate bile salt and acetyl-β-cyclodextrin (acetyl-β-CD) made possible the separation of bioallethrin stereoisomers with a high enantioresolution (7.4) in a short analysis time (6.5min). The analytical characteristics of the developed method were evaluated in terms of linearity, accuracy, precision, and limits of detection (LOD) and quantitation (LOQ) showing a good performance for the quantitation of bioallethrin stereoisomers with LODs of 0.2 and 0.3mg/L. The developed method was applied to the stereoselective analysis of a commercial bioallethrin pediculicide formulation and to evaluate the toxicity of bioallethrin stereoisomers on the growth of the unicellular freshwater green alga Pseudokirchneriella subcapitata and on the germination of the higher plant Sorghum bicolor (non-target organisms). The analysis of the commercial pediculicide showed a good agreement between the contents determined for the two stereoisomers and those labelled in the commercial samples. Different toxic responses and biodegradation profiles were found for each stereoisomer in ecotoxicity assays. The mixture of S/R stereoisomers of bioallethrin resulted more toxic than S-bioallethrin for green algae, with EC50 values of 1.10±0.06 for the mixture and of 1.73±0.05mg/L for the pure S-biallethrin (esbiol). Germination of plants seeds was also affected.\n\nA capillary micellar electrokinetic chromatography method for the stereoselective quantitation of bioallethrin in biotic and abiotic samples.", "token_count": 449, "char_count": 1667, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5268, "quality_score": 0.7634, "entities": { "genes": [ "EC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:30.545263", "source": { "split": "train_shard_00000", "doc_id": 3660 }, "chunk_id": "train_shard_00000_3660_0", "global_id": 4058 }, { "text": "The interference of bile acid secretion through bile salt export pump (BSEP) inhibition is one of the mechanisms for troglitazone (TGZ)-induced hepatotoxicity. Here, we investigated the impact of single or repeated oral doses of TGZ (200 mg/kg/day, 7 days) on bile acid homoeostasis in wild-type (WT) and Bsep knockout (KO) rats. Following oral doses, plasma exposures of TGZ were not different between WT and KO rats, and were similar on day 1 and day 7. However, plasma exposures of the major metabolite, troglitazone sulfate (TS), in KO rats were 7.6- and 9.3-fold lower than in WT on day 1 and day 7, respectively, due to increased TS biliary excretion. With Bsep KO, the mRNA levels of multidrug resistance-associated protein 2 (Mrp2), Mrp3, Mrp4, Mdr1, breast cancer resistance protein (Bcrp), sodium taurocholate cotransporting polypeptide, small heterodimer partner, and Sult2A1 were significantly altered in KO rats. Following seven daily TGZ treatments, Cyp7A1 was significantly increased in both WT and KO rats. In the vehicle groups, plasma exposures of individual bile acids demonstrated variable changes in KO rats as compared with WT. WT rats dosed with TGZ showed an increase of many bile acid species in plasma on day 1, suggesting the inhibition of Bsep. Conversely, these changes returned to base levels on day 7. In KO rats, alterations of most bile acids were observed after seven doses of TGZ. Collectively, bile acid homeostasis in rats was regulated through bile acid synthesis and transport in response to Bsep deficiency and TGZ inhibition. Additionally, our study is the first to demonstrate that repeated TGZ doses can upregulate Cyp7A1 in rats.", "token_count": 487, "char_count": 1673, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:31.191631", "source": { "split": "train_shard_00000", "doc_id": 3661 }, "chunk_id": "train_shard_00000_3661_0", "global_id": 4059 }, { "text": "Bile Salt Homeostasis in Normal and Bsep Gene Knockout Rats with Single and Repeated Doses of Troglitazone.", "token_count": 31, "char_count": 107, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:31.546322", "source": { "split": "train_shard_00000", "doc_id": 3661 }, "chunk_id": "train_shard_00000_3661_1", "global_id": 4060 }, { "text": "Biliary complications are the most frequent cause of morbidity, re-transplantation, and even mortality after liver transplantation. In general, biliary leakage and anastomotic and non-anastomotic biliary strictures (NAS) can be recognized. There is no consensus on the exact definition of NAS and different names and criteria have been used in literature. We propose to use the term post-transplant cholangiopathy for the spectrum of abnormalities of large donor bile ducts, that includes NAS, but also intraductal casts and intrahepatic biloma formation, in the presence of a patent hepatic artery. Combinations of these manifestations of cholangiopathy are not infrequently found in the same liver and ischemia-reperfusion injury is generally considered the common underlying mechanism. Other factors that contribute to post-transplant cholangiopathy are biliary injury due to bile salt toxicity and immune-mediated injury. This review provides an overview of the various types of post-transplant cholangiopathy, the presumed pathogenesis, clinical implications, and preventive strategies.\n\nPost-transplant cholangiopathy: Classification, pathogenesis, and preventive strategies.", "token_count": 284, "char_count": 1181, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:32.110776", "source": { "split": "train_shard_00000", "doc_id": 3662 }, "chunk_id": "train_shard_00000_3662_0", "global_id": 4061 }, { "text": "During 2015-2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,743 Listeria monocytogenes isolates collected as part of routine surveillance were characterized in parallel by PFGE and core genome multilocus sequence typing (cgMLST) extracted from WGS. We investigated PFGE and cgMLST clusters containing human isolates. Discrimination of isolates was significantly higher by cgMLST than by PFGE (p<0.001). cgMLST discriminated unrelated isolates that shared identical PFGE profiles and phylogenetically closely related isolates with distinct PFGE profiles. This procedure also refined epidemiologic investigations to include only phylogenetically closely related isolates, improved source identification, and facilitated epidemiologic investigations, enabling identification of more outbreaks at earlier stages. WGS-based typing should replace PFGE as the primary typing method for L. monocytogenes.\n\nReal-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France.", "token_count": 306, "char_count": 1221, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:32.697312", "source": { "split": "train_shard_00000", "doc_id": 3663 }, "chunk_id": "train_shard_00000_3663_0", "global_id": 4062 }, { "text": "Despite their relevance to human health, not all staphylococcal species have been characterized. As such, the potential zoonotic threats posed by uninvestigated species and their contribution to the staphylococcal pangenome are unclear. Here, we report the complete genome sequence of\n\nComplete Genome Sequence of", "token_count": 75, "char_count": 313, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:33.093593", "source": { "split": "train_shard_00000", "doc_id": 3664 }, "chunk_id": "train_shard_00000_3664_0", "global_id": 4063 }, { "text": "Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses.\n\nEDEN: evolutionary dynamics within environments.", "token_count": 158, "char_count": 809, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7156, "quality_score": 0.8578, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:33.571646", "source": { "split": "train_shard_00000", "doc_id": 3665 }, "chunk_id": "train_shard_00000_3665_0", "global_id": 4064 }, { "text": "The impact of a structured environment on genome evolution can be determined through comparative population genomics of species that live in the same habitat. Recent work comparing three genome sequences of Sulfolobus acidocaldarius suggested that highly structured, extreme, hot spring environments do not limit dispersal of this thermoacidophile, in contrast to other co-occurring Sulfolobus species. Instead, a high level of conservation among these three S. acidocaldarius genomes was hypothesized to result from rapid, global-scale dispersal promoted by low susceptibility to viruses that sets S. acidocaldarius apart from its sister Sulfolobus species. To test this hypothesis, we conducted a comparative analysis of 47 genomes of S. acidocaldarius from spatial and temporal sampling of two hot springs in Yellowstone National Park. While we confirm the low diversity in the core genome, we observe differentiation among S. acidocaldarius populations, likely resulting from low migration among hot spring \"islands\" in Yellowstone National Park. Patterns of genomic variation indicate that differing geological contexts result in the elimination or preservation of diversity among differentiated populations. We observe multiple deletions associated with a large genomic island rich in glycosyltransferases, differential integrations of the Sulfolobus turreted icosahedral virus, as well as two different plasmid elements. These data demonstrate that neither rapid dispersal nor lack of mobile genetic elements result in low diversity in the S. acidocaldarius genomes. We suggest instead that significant differences in the recent evolutionary history, or the intrinsic evolutionary rates, of sister Sulfolobus species result in the relatively low diversity of the S. acidocaldarius genome.\n\nStructured Populations of Sulfolobus acidocaldarius with Susceptibility to Mobile Genetic Elements.", "token_count": 400, "char_count": 1896, "word_count": 261, "semantic_coherence": 1, "information_density": 0.567, "quality_score": 0.7835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:34.223189", "source": { "split": "train_shard_00000", "doc_id": 3666 }, "chunk_id": "train_shard_00000_3666_0", "global_id": 4065 }, { "text": "Vancomycin-resistant enterococci (VRE) are a challenge to the health-care system regarding transmission rate and treatment of infections. VRE outbreaks have to be controlled from the first cases which means that appropriate and sensitive genotyping methods are needed. The aim of this study was to investigate the applicability of whole genome sequencing based analysis compared to Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) in epidemiological investigations as well as the development of a user friendly method for daily laboratory use. Out of 14,000 VRE - screening samples, a total of 60 isolates positive for either vanA or vanB gene were isolated of which 38 were from patients with epidemiological links from three suspected outbreaks at Uppsala University Hospital. The isolates were genotypically characterised with PFGE, MLST, and WGS based core genome Average Nucleotide Identity analysis (cgANI). PFGE was compared to WGS and MLST regarding reliability, resolution, and applicability capacity. The PFGE analysis of the 38 isolates confirmed the epidemiological investigation that three outbreaks had occurred but gave an unclear picture for the largest cluster. The WGS analysis could clearly distinguish six ANI clusters for those 38 isolates. As result of the comparison of the investigated methods, we recommend WGS-ANI analysis for epidemiological issues with VRE. The recommended threshold for Enterococcus faecium VRE outbreak strain delineation with core genome based ANI is 98.5%. All referred sequences of this study are available from the NCBI BioProject number PRJNA301929.\n\nTime to review the gold standard for genotyping vancomycin-resistant enterococci in epidemiology: Comparing whole-genome sequencing with PFGE and MLST in three suspected outbreaks in Sweden during 2013-2015.", "token_count": 450, "char_count": 1840, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [ "PRJNA301929" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:34.863291", "source": { "split": "train_shard_00000", "doc_id": 3667 }, "chunk_id": "train_shard_00000_3667_0", "global_id": 4066 }, { "text": "Poorly water soluble drug candidates have been common in developmental pipelines over the last several decades. This has fueled considerable research around understanding how bile salt and model micelles can improve drug particle dissolution rates and human drug exposure levels. However, in the pharmaceutical context only a single mechanism of how micelles load solute has been assumed, that being the direct loading mechanism put forth by Cussler and coworkers (Am Inst Chem Eng J. 1976;22(6):1006-1012) 40 years ago. In this model, micelles load at the particle surface and will be loaded to their equilibrium loading values. More recently, Kumar and Gandhi and coworkers (Langmuir. 2003;19:4014-4026) developed a comprehensive theory of micelle solubilization which also features an indirect loading mechanism which they argue should operate in ionic surfactant systems. In this mechanism, micelles cannot directly load at the solute particle surface and thus may not reach equilibrium loading values within the particle diffusion layer. In this work, we endeavor to understand if the indirect micelle loading mechanism represents a plausible description in the pharmaceutical context. The overall data in SLS and FaSSIF systems obtained here, as well as several other previously published datasets, can be described by the indirect micelle loading mechanism. Implications for pharmaceutical development of poorly soluble compounds are discussed.\n\nIncomplete Loading of Sodium Lauryl Sulfate and Fasted State Simulated Intestinal Fluid Micelles Within the Diffusion Layers of Dispersed Drug Particles During Dissolution.", "token_count": 368, "char_count": 1625, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6581, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:35.457334", "source": { "split": "train_shard_00000", "doc_id": 3668 }, "chunk_id": "train_shard_00000_3668_0", "global_id": 4067 }, { "text": "Flavobacterium columnare is one of the deadliest fish pathogens causing devastating mortality in various freshwater fish species globally. To gain an insight into bacterial genomic contents and structures, comparative genome analyses were performed using the reference and newly sequenced genomes of F. columnare including genomovar I, II and I/II strains isolated from Thailand, Europe and the USA. Bacterial genomes varied in size from 3.09 to 3.39Mb (2714 to 3101 CDSs). The pan-genome analysis revealed open pan-genome nature of F. columnare strains, which possessed at least 4953 genes and tended to increase progressively with the addition of a new genome. Genomic islands (GIs) present in bacterial genomes were diverse, in which 65% (39 out of 60) of possible GIs were strain-specific. A CRISPR/cas investigation indicated at least two different CRISPR systems with varied spacer profiles. On the other hand, putative virulence genes, including those related to gliding motility, type IX secretion system (T9SS), outer membrane proteins (Omp), were equally distributed among F. columnare strains. The MLSA scheme categorized bacterial strains into nine different sequence types (ST 9-17). Phylogenetic analyses based on either 16S rRNA, MLSA and concatenated SNPs of core genome revealed the diversity of F. columnare strains. DNA homology analysis indicated that the estimated digital DNA-DNA hybridization (dDDH) between strains of genomovar I and II can be as low as 42.6%, while the three uniquely tilapia-originated strains from Thailand (1214, NK01 and 1215) were clearly dissimilar to other F. columnare strains as the dDDH values were only 27.7-30.4%. Collectively, this extensive diversity among bacterial strains suggested that species designation of F. columnare would potentially require re-emendation.\n\nComparative genome analysis of fish pathogen Flavobacterium columnare reveals extensive sequence diversity within the species.", "token_count": 510, "char_count": 1950, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [ "NK01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:36.110192", "source": { "split": "train_shard_00000", "doc_id": 3669 }, "chunk_id": "train_shard_00000_3669_0", "global_id": 4068 }, { "text": "Probiotic bacteria are beneficial to the health of poultry animals, thus are used as alternative candidates for antibiotics used as growth promoters (AGPs). However, they also reduce the body weight gain due to innate bile salt hydrolase (BSH) activity. Hence, the addition of a suitable BSH inhibitor along with the probiotic feed can decrease the BSH activity. In this study, a BSH gene (981 bp) encoding 326-amino acids was identified from the genome of\n\nCharacterization of Bile Salt Hydrolase from", "token_count": 129, "char_count": 502, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7375, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:36.544032", "source": { "split": "train_shard_00000", "doc_id": 3670 }, "chunk_id": "train_shard_00000_3670_0", "global_id": 4069 }, { "text": "Bacteria represent the most genetically diverse kingdom of life. While great progress has been made in describing this diversity, it remains difficult to identify the phylogenetic and ecological characteristics that delineate groups of bacteria that possess species-like properties. One major challenge associated with species delineations is that not all shared genes have the same evolutionary history, and thus the choice of loci can have a major impact on phylogenetic reconstruction. Sequencing the genomes of large numbers of closely related strains provides new opportunities to distinguish ancestral from acquired alleles and assess the effects of recombination on phylogenetic inference. Here we analyzed the genomes of 119 strains of the marine actinomycete genus Salinispora, which is currently comprised of three named species that share 99% 16S rRNA gene sequence identity. While 63% of the core genome showed evidence of recombination, this had no effect on species-level phylogenomic resolution. Recombination did however blur intra-species relationships and biogeographic resolution. The genome-wide average nucleotide identity provided a new perspective on Salinispora diversity, revealing as many as seven new species. Patterns of orthologous group distributions reveal a genetic basis to delineation the candidate taxa and insight into the levels of genetic cohesion associated with bacterial species.\n\nPhylogenomic Insight into Salinispora (Bacteria, Actinobacteria) Species Designations.", "token_count": 335, "char_count": 1508, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6971, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:37.110679", "source": { "split": "train_shard_00000", "doc_id": 3671 }, "chunk_id": "train_shard_00000_3671_0", "global_id": 4070 }, { "text": "In 2015, in addition to a United States multistate outbreak linked to contaminated ice cream, another outbreak linked to ice cream was reported in the Pacific Northwest of the United States. It was a hospital-acquired outbreak linked to milkshakes, made from contaminated ice cream mixes and milkshake maker, served to patients. Here we performed multiple analyses on isolates associated with this outbreak: pulsed-field gel electrophoresis (PFGE), whole genome single nucleotide polymorphism (SNP) analysis, species-specific core genome multilocus sequence typing (cgMLST), lineage-specific cgMLST and whole genome-specific MLST (wgsMLST)/outbreak-specific cgMLST. We also analyzed the prophages and virulence genes.\n\nWhole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State.", "token_count": 218, "char_count": 868, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7119, "quality_score": 0.8559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:37.583508", "source": { "split": "train_shard_00000", "doc_id": 3672 }, "chunk_id": "train_shard_00000_3672_0", "global_id": 4071 }, { "text": "Bile acids are synthesized from cholesterol in the liver and released into the intestine to aid the digestion of dietary lipids. The host enzymes that contribute to bile acid synthesis in the liver and the regulatory pathways that influence the composition of the total bile acid pool in the host have been well established. In addition, the gut microbiota provides unique contributions to the diversity of bile acids in the bile acid pool. Gut microbial enzymes contribute significantly to bile acid metabolism through deconjugation and dehydroxylation reactions to generate unconjugated bile acids and secondary bile acids. These microbial enzymes (which include bile salt hydrolase (BSH) and bile acid-inducible (BAI) enzymes) are essential for bile acid homeostasis in the host and represent a vital contribution of the gut microbiome to host health. Perturbation of the gut microbiota in disease states may therefore significantly influence bile acid signatures in the host, especially in the context of gastrointestinal or systemic disease. Given that bile acids are ligands for host cell receptors (including the FXR, TGR5 and Vitamin D Receptor) alterations to microbial enzymes and associated changes to bile acid signatures have significant consequences for the host. In this review we examine the contribution of microbial enzymes to the process of bile acid metabolism in the host and discuss the implications for microbe-host signalling in the context of C. difficile infection, inflammatory bowel disease and other disease states.\n\nInteractions between gut bacteria and bile in health and disease.", "token_count": 385, "char_count": 1611, "word_count": 244, "semantic_coherence": 1, "information_density": 0.4959, "quality_score": 0.748, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:38.198191", "source": { "split": "train_shard_00000", "doc_id": 3673 }, "chunk_id": "train_shard_00000_3673_0", "global_id": 4072 }, { "text": "A novel, simple and accurate on-line green methodology for Se(IV) monitoring by molecular fluorescence has been developed. Because the analyte does not exhibit fluorescence, the organic dye Chrome azurol S (CAS) has been chosen to allow detection. The effect of metal-quenching on CAS excitation and emission conditions (λex=300nm; λem=407nm) was used as criterion for analyte quantification in presence of sodium cholate bile salt (NaC). The quenching mechanism was explored, and it can be classified as a collisional type with a Stern-Volmer constant value of 3.0×10\n\nDevelopment of on-line spectrofluorimetric methodology for selenium monitoring in foods and biological fluids using Chrome azurol S quenching.", "token_count": 194, "char_count": 712, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7573, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:38.655711", "source": { "split": "train_shard_00000", "doc_id": 3674 }, "chunk_id": "train_shard_00000_3674_0", "global_id": 4073 }, { "text": "We have employed whole genome sequencing to define and evaluate a core genome multilocus sequence typing (cgMLST) scheme for Acinetobacter baumannii. To define a core genome we downloaded a total of 1,573 putative A. baumannii genomes from NCBI as well as representative isolates belonging to the eight previously described international A. baumannii clonal lineages. The core genome was then employed against a total of fifty-three carbapenem-resistant A. baumannii isolates that were previously typed by PFGE and linked to hospital outbreaks in eight German cities. We defined a core genome of 2,390 genes of which an average 98.4% were called successfully from 1,339 A. baumannii genomes, while Acinetobacter nosocomialis, Acinetobacter pittii, and Acinetobacter calcoaceticus resulted in 71.2%, 33.3%, and 23.2% good targets, respectively. When tested against the previously identified outbreak strains, we found good correlation between PFGE and cgMLST clustering, with 0-8 allelic differences within a pulsotype, and 40-2,166 differences between pulsotypes. The highest number of allelic differences was between the isolates representing the international clones. This typing scheme was highly discriminatory and identified separate A. baumannii outbreaks. Moreover, because a standardised cgMLST nomenclature is used, the system will allow inter-laboratory exchange of data.\n\nDevelopment and evaluation of a core genome multilocus typing scheme for whole-genome sequence-based typing of Acinetobacter baumannii.", "token_count": 397, "char_count": 1518, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:39.266550", "source": { "split": "train_shard_00000", "doc_id": 3675 }, "chunk_id": "train_shard_00000_3675_0", "global_id": 4074 }, { "text": "Cyanobacteria, a group of photosynthetic prokaryotes, dominate the earth with ~ 1015 g wet biomass. Despite diversity in habitats and an ancient origin, cyanobacterial phylum has retained a significant core genome. Cyanobacteria are being explored for direct conversion of solar energy and carbon dioxide into biofuels. For this, efficient cyanobacterial strains will need to be designed via metabolic engineering. This will require identification of target knockouts to channelize the flow of carbon toward the product of interest while minimizing deletions of essential genes. We propose \"Gene Conservation Index\" (GCI) as a quick measure to predict gene essentiality in cyanobacteria. GCI is based on phylogenetic profile of a gene constructed with a reduced dataset of cyanobacterial genomes. GCI is the percentage of organism clusters in which the query gene is present in the reduced dataset. Of the 750 genes deemed to be essential in the experimental study on S. elongatus PCC 7942, we found 494 to be conserved across the phylum which largely comprise of the essential metabolic pathways. On the contrary, the conserved but non-essential genes broadly comprise of genes required under stress conditions. Exceptions to this rule include genes such as the glycogen synthesis and degradation enzymes, deoxyribose-phosphate aldolase (DERA), glucose-6-phosphate 1-dehydrogenase (zwf) and fructose-1,6-bisphosphatase class1, which are conserved but non-essential. While the essential genes are to be avoided during gene knockout studies as potentially lethal deletions, the non-essential but conserved set of genes could be interesting targets for metabolic engineering. Further, we identify clusters of co-evolving genes (CCG), which provide insights that may be useful in annotation. Principal component analysis (PCA) plots of the CCGs are demonstrated as data visualization tools that are complementary to the conventional heatmaps. Our dataset consists of phylogenetic profiles for 23,643 non-redundant cyanobacterial genes", "token_count": 511, "char_count": 2031, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6151, "quality_score": 0.8076, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:39.918154", "source": { "split": "train_shard_00000", "doc_id": 3676 }, "chunk_id": "train_shard_00000_3676_0", "global_id": 4075 }, { "text": "We believe that the data and the analysis presented here will be a great resource to the scientific community interested in cyanobacteria.\n\nGene essentiality, conservation index and co-evolution of genes in cyanobacteria.", "token_count": 50, "char_count": 221, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8438, "quality_score": 0.9219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:40.275633", "source": { "split": "train_shard_00000", "doc_id": 3676 }, "chunk_id": "train_shard_00000_3676_1", "global_id": 4076 }, { "text": "Improving the oral absorption of compounds with low aqueous solubility is a common challenge that often requires an enabling technology. Frequently, oral absorption can be improved by formulating the compound as an amorphous solid dispersion (ASD). Upon dissolution, an ASD can reach a higher concentration of unbound drug than the crystalline form, and often generates a large number of sub-micrometer, rapidly dissolving drug-rich colloids. These drug-rich colloids have the potential to decrease the diffusional resistance across the unstirred water layer of the intestinal tract (UWL) by acting as rapidly diffusing shuttles for unbound drug. In a prior study utilizing a membrane flux assay, we demonstrated that, for itraconazole, increasing the concentration of drug-rich colloids increased membrane flux in vitro. In this study, we evaluate spray-dried amorphous solid dispersions (SDDs) of itraconazole with hydroxypropyl methylcellulose acetate succinate (HPMCAS) to study the impact of varying concentrations of drug-rich colloids on the oral absorption of itraconazole in rats, and to quantify their impact on in vitro flux as a function of bile salt concentration. When Sporanox and itraconazole/AFFINISOL High Productivity HPMCAS SDDs were dosed in rats, the maximum absorption rate for each formulation rank-ordered with membrane flux in vitro. The relative maximum absorption rate in vivo correlated well with the in vitro flux measured in 2% SIF (26.8 mM bile acid concentration), a representative bile acid concentration for rats. In vitro it was found that as the bile salt concentration increases, the importance of colloids for improving UWL permeability is diminished. We demonstrate that drug-containing micelles and colloids both contribute to aqueous boundary layer diffusion in proportion to their diffusion coefficient and drug loading. These data suggest that, for compounds with very low aqueous solubility and high epithelial permeability, designing amorphous formulations that produce colloids on dissolution may be a viable approach to improve oral bioavailability.", "token_count": 501, "char_count": 2097, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5578, "quality_score": 0.7789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:40.924906", "source": { "split": "train_shard_00000", "doc_id": 3677 }, "chunk_id": "train_shard_00000_3677_0", "global_id": 4077 }, { "text": "Impact of Drug-Rich Colloids of Itraconazole and HPMCAS on Membrane Flux in Vitro and Oral Bioavailability in Rats.", "token_count": 37, "char_count": 115, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:41.284248", "source": { "split": "train_shard_00000", "doc_id": 3677 }, "chunk_id": "train_shard_00000_3677_1", "global_id": 4078 }, { "text": "Hypercholesterolaemia is a major risk factor for cardiovascular disease and it has been found that some probiotic bacteria possess cholesterol-lowering capabilities. In this study, the ability of the Lab4 probiotic consortium to hydrolyse bile salts, assimilate cholesterol and regulate cholesterol transport by polarised Caco-2 enterocytes was demonstrated. Furthermore, in wild-type C57BL/6J mice fed a high fat diet, 2-weeks supplementation with Lab4 probiotic consortium plus Lactobacillus plantarum CUL66 resulted in significant reductions in plasma total cholesterol levels and suppression of diet-induced weight gain. No changes in plasma levels of very low-density lipoprotein/low-density lipoprotein, high-density lipoprotein, triglycerides, cytokines or bile acids were observed. Increased amounts of total and unconjugated bile acids in the faeces of the probiotic-fed mice, together with modulation of hepatic small heterodimer partner and cholesterol-7α-hydroxylase mRNA expression, implicates bile salt hydrolase activity as a potential mechanism of action. In summary, this study demonstrates the cholesterol-lowering efficacy of short-term feeding of the Lab4 probiotic consortium plus L. plantarum CUL66 in wild-type mice and supports further assessment in human trials.\n\nThe anti-cholesterolaemic effect of a consortium of probiotics: An acute study in C57BL/6J mice.", "token_count": 388, "char_count": 1385, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "CUL66" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:41.900061", "source": { "split": "train_shard_00000", "doc_id": 3678 }, "chunk_id": "train_shard_00000_3678_0", "global_id": 4079 }, { "text": "The present study reports a meticulous characterization of the interaction of a potent anti-cancer drug, berberine chloride (BR) with a series of bile salt aggregates having varying hydrophobicity (sodium deoxycholate (NaDC), sodium cholate (NaC), and sodium taurocholate (NaTC)). The absorption spectrum of BR reveals a complex profile comprised of four distinct peaks. Analysis of the modulations of the absorption spectral properties of BR following interaction with the bile salts raising deeper questions unveils a critical insight into the mode of interaction of the cationic drug (BR) with the bile salts; a greater degree of perturbation of the microenvironment of the isoquinolinic part of BR compared to the benzenoid part. The remarkable modulation of the fluorescence profile of BR with added bile salts provides a sensitive indicator for monitoring the interaction scenario. However, an intriguing observation in this context reveals differential fluorescence behavior of BR in various bile salt aggregates, that is, similar observations in NaDC and NaC (which are legitimately interpreted according to the 'two-step association model') in comparison to NaTC. Such contrasting behavior of BR in NaTC aggregates has been rationalized on the basis of the possibility of formation of dye aggregate facilitated because of the proximity of the cationic drug molecules to the anionic headgroup of NaTC bile salt. Surprisingly, our spectroscopic results evidence for binding location of the drug at the interfacial region in all the bile salt aggregates. To this end, the time-resolved fluorescence decay behavior of the drug within various bile salt aggregates has been meticulously studied. The fluorescence decay results are found to be highly sensitive to the structure and size of the bile salt aggregates eventually leading to characterization of the interaction of the drug with the bile salts in excellent corroboration with the steady-state data. Furthermore, the time-resolved fluorescence anisotropy decay measurements yielded insight into the modulation of rotational dynamical behavior of the drug within the bile salt aggregates.\n\nDifferential interaction behaviors of an alkaloid drug berberine with various bile salts.", "token_count": 500, "char_count": 2240, "word_count": 329, "semantic_coherence": 1, "information_density": 0.4954, "quality_score": 0.7477, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:42.556715", "source": { "split": "train_shard_00000", "doc_id": 3679 }, "chunk_id": "train_shard_00000_3679_0", "global_id": 4080 }, { "text": "Lactobacillus kefiranofaciens M1 is a probiotic strain isolated from Taiwanese kefir grains. The present study evaluated the effects of heat, cold, acid and bile salt adaptations on the stress tolerance of L. kefiranofaciens M1. The regulation of protein expression of L. kefiranofaciens M1 under these adaptation conditions was also investigated. The results showed that adaptation of L. kefiranofaciens M1 to heat, cold, acid and bile salts induced homologous tolerance and cross-protection against heterologous challenge. The extent of induced tolerance varied depending on the type and condition of stress. Proteomic analysis revealed that 27 proteins exhibited differences in expression between non-adapted and stress-adapted L. kefiranofaciens M1 cells. Among these proteins, three proteins involved in carbohydrate metabolism (triosephosphate isomerase, enolase and NAD-dependent glycerol-3-phosphate dehydrogenase), two proteins involved in pH homeostasis (ATP synthase subunits AtpA and AtpB), two stress response proteins (chaperones DnaK and GroEL) and one translation-related protein (30S ribosomal protein S2) were up-regulated by three of the four adaptation treatments examined. The increased synthesis of these stress proteins might play a critical protective role in the cellular defense against heat, cold, acid and bile salt stresses.\n\nEffects of heat, cold, acid and bile salt adaptations on the stress tolerance and protein expression of kefir-isolated probiotic Lactobacillus kefiranofaciens M1.", "token_count": 402, "char_count": 1517, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:43.173342", "source": { "split": "train_shard_00000", "doc_id": 3680 }, "chunk_id": "train_shard_00000_3680_0", "global_id": 4081 }, { "text": "Staphylococcus aureus is a leading cause of bacteremia in hospitalized patients. Whether or not S. aureus bacteremia (SAB) is associated with clonality, implicating potential nosocomial transmission, has not, however, been investigated. Herein, we examined the epidemiology of SAB using whole genome sequencing (WGS). 152 SAB isolates collected over the course of 2015 at a single large Minnesota medical center were studied. Staphylococcus protein A (spa) typing was performed by PCR/Sanger sequencing; multilocus sequence typing (MLST) and core genome MLST (cgMLST) were determined by WGS. Forty-eight isolates (32%) were methicillin-resistant S. aureus (MRSA). The isolates encompassed 66 spa types, clustered into 11 spa clonal complexes (CCs) and 10 singleton types. 88% of 48 MRSA isolates belonged to spa CC-002 or -008. Methicillin-susceptible S. aureus (MSSA) isolates were more genotypically diverse, with 61% distributed across four spa CCs (CC-002, CC-012, CC-008 and CC-084). By MLST, there was 31 sequence types (STs), including 18 divided into 6 CCs and 13 singleton STs. Amongst MSSA isolates, the common MLST clones were CC5 (23%), CC30 (19%), CC8 (15%) and CC15 (11%). Common MRSA clones were CC5 (67%) and CC8 (25%); there were no MRSA isolates in CC45 or CC30. By cgMLST analysis, there were 9 allelic differences between two isolates, with the remaining 150 isolates differing from each other by over 40 alleles. The two isolates were retroactively epidemiologically linked by medical record review. Overall, cgMLST analysis resulted in higher resolution epidemiological typing than did multilocus sequence or spa typing.", "token_count": 519, "char_count": 1642, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [ "CC45", "CC8", "CC15", "CC5", "CC30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:35:43.828683", "source": { "split": "train_shard_00000", "doc_id": 3681 }, "chunk_id": "train_shard_00000_3681_0", "global_id": 4082 }, { "text": "Molecular epidemiology of Staphylococcus aureus bacteremia in a single large Minnesota medical center in 2015 as assessed using MLST, core genome MLST and spa typing.", "token_count": 49, "char_count": 166, "word_count": 25, "semantic_coherence": 1, "information_density": 0.96, "quality_score": 0.98, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:44.192727", "source": { "split": "train_shard_00000", "doc_id": 3681 }, "chunk_id": "train_shard_00000_3681_1", "global_id": 4083 }, { "text": "Inhibition of bile salt export pump (BSEP) causes hepatic accumulation of toxic bile acid (BA), leading to hepatocyte death. We reported a sandwich-cultured hepatocyte (SCH)-based model that can estimate potential cholestatic compounds by assessing their ability to induce hepatotoxicity in combination with a titrated amount of human 12 BA species. However, there is little information about the specific BAs responsible for hepatotoxicity, when BSEP is inhibited. This study measured the accumulation of each BA in rat SCHs in the presence of 10 μM cyclosporine A (CsA), which only inhibits BSEP, and 50 μM CsA, which further inhibits basolateral BA efflux transporters. The accumulation of all BAs (not significant for deoxycholic acid [DCA]) was observed in the presence of 10 μM CsA. In particular, 3 BAs (chenodeoxycholic acid [CDCA], DCA, and glyco-DCA [GDCA]) showed increased toxicity in the presence of 10 μM CsA, whereas the other BAs did not. In addition to these BAs, taurolithocholic acid, glyco-CDCA, and glycocholic acid showed increased toxicity in the presence of 50 μM CsA, but additional accumulation of these BAs could not be observed. These results indicate the inhibiting BSEP results in the accumulation of CDCA, GDCA, and partially DCA, thereby resulting in hepatotoxicity.\n\nIdentification of Bile Acids Responsible for Inhibiting the Bile Salt Export Pump, Leading to Bile Acid Accumulation and Cell Toxicity in Rat Hepatocytes.", "token_count": 424, "char_count": 1454, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5856, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:44.844799", "source": { "split": "train_shard_00000", "doc_id": 3682 }, "chunk_id": "train_shard_00000_3682_0", "global_id": 4084 }, { "text": "This study investigated the influence of aeration and minimal medium conditions on antioxidant and antibacterial activities of 21 probiotic Lactobacillus strains isolated from dairy products. The probiotic potential of the isolates was evaluated by pH and bile tolerance. Random amplified polymorphic DNA polymerase chain reaction (RAPD-PCR) was used to confirm the phenotypic identification of isolates. Antioxidant producer isolates were screened by resistance to reactive oxygen species (ROS). The antioxidant and antibacterial activities of extracellular materials after 48 h fermentation with antioxidative strains were determined using 2,2-diphenyl-1-picrylhydrazyl (DPPH) and broth microdilution assays, respectively. The results indicate that the antioxidant capacity of supernatants was increased by using of both minimal medium and agitation. The antibacterial activity was increased in minimal medium, but there has nearly no change in the antibacterial properties by using both agitation and minimal medium. The maximum antibacterial activity was observed during mid-exponential phase until the beginning of the early-stationary phase, but the maximum antioxidant activity was detected at the stationary growth phase. There is a significant relationship between antioxidant and antibacterial activities of the cell-free probiotic extracts, and their production rates are closely related to the fermentation type. The bioactive materials from probiotics could be extracted in a large amount at an appropriate time under a suitable condition.\n\nIn vitro study of antioxidant and antibacterial activities of Lactobacillus probiotic spp.", "token_count": 389, "char_count": 1644, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5946, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:45.490610", "source": { "split": "train_shard_00000", "doc_id": 3683 }, "chunk_id": "train_shard_00000_3683_0", "global_id": 4085 }, { "text": "Epidemiological findings of a listeriosis outbreak in 2013 implicated Hispanic-style cheese produced by company A, and pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS) were performed on clinical isolates and representative isolates collected from company A cheese and environmental samples during the investigation. The results strengthened the evidence for cheese as the vehicle. Surveillance sampling and WGS 3 months later revealed that the equipment purchased by company B from company A yielded an environmental isolate highly similar to all outbreak isolates. The whole genome and core genome multilocus sequence typing and single nucleotide polymorphism (SNP) analyses results were compared to demonstrate the maximum discriminatory power obtained by using multiple analyses, which were needed to differentiate outbreak-associated isolates from a PFGE-indistinguishable isolate collected in a nonimplicated food source in 2012. This unrelated isolate differed from the outbreak isolates by only 7 to 14 SNPs, and as a result, the minimum spanning tree from the whole genome analyses and certain variant calling approach and phylogenetic algorithm for core genome-based analyses could not provide differentiation between unrelated isolates. Our data also suggest that SNP/allele counts should always be combined with WGS clustering analysis generated by phylogenetically meaningful algorithms on a sufficient number of isolates, and the SNP/allele threshold alone does not provide sufficient evidence to delineate an outbreak. The putative prophages were conserved across all the outbreak isolates. All outbreak isolates belonged to clonal complex 5 and serotype 1/2b and had an identical\n\nWhole Genome and Core Genome Multilocus Sequence Typing and Single Nucleotide Polymorphism Analyses of Listeria monocytogenes Isolates Associated with an Outbreak Linked to Cheese, United States, 2013.", "token_count": 444, "char_count": 1922, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5858, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:46.158143", "source": { "split": "train_shard_00000", "doc_id": 3684 }, "chunk_id": "train_shard_00000_3684_0", "global_id": 4086 }, { "text": "Haw pectin penta-oligogalacturonide (HPPS) has important role in improving cholesterol metabolism and promoting the conversion of cholesterol to bile acids (BA) in mice fed high-cholesterol diet (HCD). However, the mechanism is not clear. This study aims to investigate the effects of HPPS on cholesterol accumulation and the regulation of hepatic BA synthesis and transport in HCD-fed mice. Results showed that HPPS significantly decreased plasma and hepatic TC levels but increased plasma high-density lipoprotein cholesterol (HDL-C) and apolipoprotein A-I (apoA-I) levels, compared to HCD. BA analysis showed that HPPS markedly decreased hepatic and small intestine BA levels but increased the gallbladder BA levels, and finally decreased the total BA pool size, compared to HCD. Studies of molecular mechanism revealed that HPPS promoted hepatic ATP-binding cassette transporter A1 (ABCA1), ATP-binding cassette transporter G1 (ABCG1), and scavenger receptor BI (SR-BI) expression but did not affect ATB binding cassette transporter G5/G8 (ABCG5/8) expression. HPPS inactivated hepatic farnesoid X receptor (FXR) and target genes expression, which resulted in significant increase of cholesterol 7α-hydroxylase 1 (CYP7A1) and sterol 12α-hydroxylase (CYP8B1) expression, with up-regulations of 204.2% and 33.5% for mRNA levels, respectively, compared with HCD. In addition, HPPS markedly enhanced bile salt export pump (BSEP) expression but didn't affect the sodium/taurocholate co-transporting polypeptide (NTCP) expression. In conclusion, the study revealed that HPPS reduced cholesterol accumulation by promoting BA synthesis in the liver and excretion in the feces, and might promote macrophage-to-liver reverse cholesterol transport (RCT) but did not liver-to-fecal RCT.", "token_count": 516, "char_count": 1778, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [ "ABCA1", "ABCG1", "ABCG5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:35:46.825100", "source": { "split": "train_shard_00000", "doc_id": 3685 }, "chunk_id": "train_shard_00000_3685_0", "global_id": 4087 }, { "text": "Pectin penta-oligogalacturonide reduces cholesterol accumulation by promoting bile acid biosynthesis and excretion in high-cholesterol-fed mice.", "token_count": 47, "char_count": 144, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:47.183935", "source": { "split": "train_shard_00000", "doc_id": 3685 }, "chunk_id": "train_shard_00000_3685_1", "global_id": 4088 }, { "text": "The cofactor balances in metabolism is of paramount importance in the design of a metabolic engineering strategy and understanding the regulation of metabolism in general. ATP, NAD+ and NADP+ balances are central players linking the various fluxes in central metabolism as well as biomass formation. NADP+ is especially important in the metabolic engineering of yeasts for xylose fermentation, since NADPH is required by most yeasts in the initial step of xylose utilisation, including the fast-growing Kluyveromyces marxianus. In this simulation study of yeast metabolism, the complex interplay between these cofactors was investigated; in particular, how they may affect the possible roles of fructose-1,6-bisphosphatase, the pentose phosphate pathway, glycerol production and the pyruvate dehydrogenase bypass. Using flux balance analysis, it was found that the potential role of fructose-1,6-bisphosphatase was highly dependent on the cofactor specificity of the oxidative pentose phosphate pathway and on the carbon source. Additionally, the excessive production of ATP under certain conditions might be involved in some of the phenomena observed, which may have been overlooked to date. Based on these findings, a strategy is proposed for the metabolic engineering of a future xylose-fermenting yeast for biofuel production.\n\nElucidation of new condition-dependent roles for fructose-1,6-bisphosphatase linked to cofactor balances.", "token_count": 357, "char_count": 1437, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6219, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:47.761944", "source": { "split": "train_shard_00000", "doc_id": 3686 }, "chunk_id": "train_shard_00000_3686_0", "global_id": 4089 }, { "text": "Oral drug absorption is a process influenced by the physicochemical and biopharmaceutical properties of the drug and its inter-relationship with the gastrointestinal tract. Drug solubility, dissolution and permeability across intestinal barrier are the key parameters controlling absorption. This review provides an overview of the factors that affect drug absorption and the classification of a drug on the basis of solubility and permeability. The biopharmaceutical classification system (BCS) was introduced in early 90׳s and is a regulatory tool used to predict bioavailability problems associated with a new entity, thereby helping in the development of a drug product. Strategies to combat solubility and permeability issues are also discussed.\n\nUnderstanding", "token_count": 163, "char_count": 765, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6542, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:48.204029", "source": { "split": "train_shard_00000", "doc_id": 3687 }, "chunk_id": "train_shard_00000_3687_0", "global_id": 4090 }, { "text": "Enterotoxigenic Escherichia coli (ETEC), defined by their elaboration of heat-labile (LT) and/or heat-stable (ST) enterotoxins, are a common cause of diarrheal illness in developing countries. Efficient delivery of these toxins requires ETEC to engage target host enterocytes. This engagement is accomplished using a variety of pathovar-specific and conserved E. coli adhesin molecules as well as plasmid encoded colonization factors. Some of these adhesins undergo significant transcriptional modulation as ETEC encounter intestinal epithelia, perhaps suggesting that they cooperatively facilitate interaction with the host. Among genes significantly upregulated on cell contact are those encoding type 1 pili. We therefore investigated the role played by these pili in facilitating ETEC adhesion, and toxin delivery to model intestinal epithelia. We demonstrate that type 1 pili, encoded in the E. coli core genome, play an essential role in ETEC virulence, acting in concert with plasmid-encoded pathovar specific colonization factor (CF) fimbriae to promote optimal bacterial adhesion to cultured intestinal epithelium (CIE) and to epithelial monolayers differentiated from human small intestinal stem cells. Type 1 pili are tipped with the FimH adhesin which recognizes mannose with stereochemical specificity. Thus, enhanced production of highly mannosylated proteins on intestinal epithelia promoted FimH-mediated ETEC adhesion, while conversely, interruption of FimH lectin-epithelial interactions with soluble mannose, anti-FimH antibodies or mutagenesis of fimH effectively blocked ETEC adhesion. Moreover, fimH mutants were significantly impaired in delivery of both heat-stable and heat-labile toxins to the target epithelial cells in vitro, and these mutants were substantially less virulent in rabbit ileal loop assays, a classical model of ETEC pathogenesis. Collectively, our data suggest that these highly conserved pili play an essential role in virulence of these diverse pathogens.", "token_count": 516, "char_count": 2001, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8266, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:35:48.840125", "source": { "split": "train_shard_00000", "doc_id": 3688 }, "chunk_id": "train_shard_00000_3688_0", "global_id": 4091 }, { "text": "Highly conserved type 1 pili promote enterotoxigenic E. coli pathogen-host interactions.", "token_count": 25, "char_count": 88, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:49.203226", "source": { "split": "train_shard_00000", "doc_id": 3688 }, "chunk_id": "train_shard_00000_3688_1", "global_id": 4092 }, { "text": "The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins.\n\nGenomic relatedness of Staphylococcus pettenkoferi isolates of different origins.", "token_count": 122, "char_count": 509, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:49.584783", "source": { "split": "train_shard_00000", "doc_id": 3689 }, "chunk_id": "train_shard_00000_3689_0", "global_id": 4093 }, { "text": "Optimum utilization of fermentable sugars from lignocellulosic biomass to deliver multiple products under biorefinery concept has been reported in this work. Alcohol fermentation has been carried out with multiple cell recycling of Kluyveromyces marxianus IIPE453. The yeast utilized xylose-rich fraction from acid and steam treated biomass for cell generation and xylitol production with an average yield of 0.315±0.01g/g while the entire glucose rich saccharified fraction had been fermented to ethanol with high productivity of 0.9±0.08g/L/h. A detailed insight into its genome illustrated the strain's complete set of genes associated with sugar transport and metabolism for high-temperature fermentation. A set flocculation proteins were identified that aided in high cell recovery in successive fermentation cycles to achieve alcohols with high productivity. We have brought biomass derived sugars, yeast cell biomass generation, and ethanol and xylitol fermentation in one platform and validated the overall material balance. 2kg sugarcane bagasse yielded 193.4g yeast cell, and with multiple times cell recycling generated 125.56g xylitol and 289.2g ethanol (366mL).\n\nLignocellulosic sugar management for xylitol and ethanol fermentation with multiple cell recycling by Kluyveromyces marxianus IIPE453.", "token_count": 356, "char_count": 1310, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8156, "entities": { "genes": [ "IIPE453" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:50.161117", "source": { "split": "train_shard_00000", "doc_id": 3690 }, "chunk_id": "train_shard_00000_3690_0", "global_id": 4094 }, { "text": "The bile salt export pump (BSEP) actively transports conjugated monovalent bile acids from the hepatocytes into the bile. This facilitates the formation of micelles and promotes digestion and absorption of dietary fat. Inhibition of BSEP leads to decreased bile flow and accumulation of cytotoxic bile salts in the liver. A number of compounds have been identified to interact with BSEP, which results in drug-induced cholestasis or liver injury. Therefore, in silico approaches for flagging compounds as potential BSEP inhibitors would be of high value in the early stage of the drug discovery pipeline. Up to now, due to the lack of a high-resolution X-ray structure of BSEP, in silico based identification of BSEP inhibitors focused on ligand-based approaches. In this study, we provide a homology model for BSEP, developed using the corrected mouse P-glycoprotein structure (PDB ID: 4M1M). Subsequently, the model was used for docking-based classification of a set of 1212 compounds (405 BSEP inhibitors, 807 non-inhibitors). Using the scoring function ChemScore, a prediction accuracy of 81% on the training set and 73% on two external test sets could be obtained. In addition, the applicability domain of the models was assessed based on Euclidean distance. Further, analysis of the protein-ligand interaction fingerprints revealed certain functional group-amino acid residue interactions that could play a key role for ligand binding. Though ligand-based models, due to their high speed and accuracy, remain the method of choice for classification of BSEP inhibitors, structure-assisted docking models demonstrate reasonably good prediction accuracies while additionally providing information about putative protein-ligand interactions.\n\nStructure based classification for bile salt export pump (BSEP) inhibitors using comparative structural modeling of human BSEP.", "token_count": 445, "char_count": 1872, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6347, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:50.791235", "source": { "split": "train_shard_00000", "doc_id": 3691 }, "chunk_id": "train_shard_00000_3691_0", "global_id": 4095 }, { "text": "The aim of this study was to evaluate the probiotic potential of lactic acid bacteria (LAB) strains isolated from Horreh. Some probiotic properties, e.g., resistance to acid, bile tolerance, antibacterial activity, and antibiotic susceptibility, were investigated. A total of 140 Gram-positive and catalase-negative isolates from Horreh were subjected to identification and grouping by cultural methods and the 16S rRNA sequencing. The new isolates were identified to be Lactobacillus (fermentum, plantarum, and brevis) Weissella cibaria, Enterococcus (faecium and faecalis), Leuconostoc (citreum and mesenteroides subsp. mesenteroides) and Pediococcus pentosaceus. Probiotic potential study of LAB isolates showed that Lb. plantarum and Leu. mesenteroides subsp. mesenteroides isolates were able to grow at pH 2.5 and 3.5. Lactobacillus plantarum (isolate A44) showed the highest cell hydrophobicity (84.5%). According to antibacterial activity tests, Listeria innocua and Staphylococcus aureus were the most sensitive indicators against the selected LAB strains, while Escherichia coli and Bacillus cereus were the most resistant. In addition, all the isolated LAB species were resistant to vancomycin. The results of the present study suggested that the Lactobacillus fermentum and plantarum isolated from Horreh, characterized in this study, have potential use for industrial purposes as probiotics.\n\nDiversity and Probiotic Potential of Lactic Acid Bacteria Isolated from Horreh, a Traditional Iranian Fermented Food.", "token_count": 426, "char_count": 1522, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6232, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:51.416360", "source": { "split": "train_shard_00000", "doc_id": 3692 }, "chunk_id": "train_shard_00000_3692_0", "global_id": 4096 }, { "text": "The objective of this study is to develop an oral formulation of famotidine niosomes coated with a mucoadhesive polymer, chitosan. Famotidine (FMT) has low oral bioavailability of 40-45% and short half-life between 2.5 to 4 h. Famotidine is classified as class IV in BCS because of its low aqueous solubility (0.1% w/v) and low permeability. Thus, FMT was loaded to the bioadhesive coated niosomes to improve its solubility, enhance its oral bioavailability, and sustain FMT release pattern. Different formulations were prepared by thin-film hydration method and characterized in terms of entrapment efficiency, morphological features, vesicle size, and zeta potential. In vitro release and ex vivo permeability of famotidine from the formulations were evaluated. The optimized formula was coated with chitosan and its mucoadhesion and stability in bile salt was tested. The optimized formula showed a high entrapment efficiency of 74%, as well sustained the in vitro release of FMT in the simulated gastric medium and enhanced its permeation through an excised goat's intestinal membrane by 1.4 fold in comparison to FMT control suspension. The mucoadhesive coated formula exhibited a significantly higher (p < 0.05) mucoadhesive efficiency and more stability in the bile salt as compared to the uncoated formula. Therefore, it could be considered as an efficient delivery system to maintain the prolonged release of FMT and improve its oral bioavailability.\n\nOptimized Mucoadhesive Coated Niosomes as a Sustained Oral Delivery System of Famotidine.", "token_count": 412, "char_count": 1550, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5622, "quality_score": 0.7811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:52.037853", "source": { "split": "train_shard_00000", "doc_id": 3693 }, "chunk_id": "train_shard_00000_3693_0", "global_id": 4097 }, { "text": "Hepatotoxicity is of major concern for humans exposed to industrial chemicals and drugs. Disruption of farnesoid X receptor (FXR), a master regulator of bile acid (BA) metabolism, enhanced the sensitivity to liver injury in mice after toxicant exposure, but the precise mechanism remains unclear. In this study, the interconnection between BA metabolism, FXR, and chemically induced hepatotoxicity was investigated using metabolomics, Fxr-null mice (Fxr-/-) and hepatocytes, and recombinant adenoviruses. A single low-dose intraperitoneal injection of carbon tetrachloride (CCl4), an inducer of acute hepatitis in mice, resulted in more severe hepatocyte damage and higher induction of pro-inflammatory mediators, such as chemokine (C-C motif) ligand 2 (Ccl2), in Fxr-/-. Serum metabolomics analysis revealed marked increases in circulating taurocholate (TCA) and tauro-β-muricholate (T-β-MCA) in these mice, and forced expression of bile salt export protein (BSEP) by recombinant adenovirus in Fxr-/- ameliorated CCl4-induced liver damage. Treatment of Fxr-null hepatocytes with TCA, but not T-β-MCA, significantly increased c-Jun-N-terminal kinase (JNK) activation and Ccl2 mRNA levels, and up-regulation of Ccl2 mRNA was attenuated by co-treatment with a JNK inhibitor SP600125, indicating that TCA directly amplifies hepatocyte inflammatory signaling mainly mediated by JNK under FXR-deficiency. Additionally, pretreatment with SP600125 or restoration of FXR expression in liver by use of recombinant adenovirus, attenuated CCl4-induced liver injury", "token_count": 476, "char_count": 1553, "word_count": 208, "semantic_coherence": 1, "information_density": 0.726, "quality_score": 0.863, "entities": { "genes": [ "SP600125" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:52.681338", "source": { "split": "train_shard_00000", "doc_id": 3694 }, "chunk_id": "train_shard_00000_3694_0", "global_id": 4098 }, { "text": "Collectively, these results suggest that the TCA-JNK axis is likely associated with increased susceptibility to CCl4-induced acute liver injury in Fxr-/-, and provide clues to the mechanism by which FXR and its downstream gene targets, such as BSEP, protects against chemically induced hepatotoxicity.\n\nEditor's Highlight: Farnesoid X Receptor Protects Against Low-Dose Carbon Tetrachloride-Induced Liver Injury Through the Taurocholate-JNK Pathway.", "token_count": 127, "char_count": 449, "word_count": 59, "semantic_coherence": 1, "information_density": 0.8644, "quality_score": 0.9322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:53.071079", "source": { "split": "train_shard_00000", "doc_id": 3694 }, "chunk_id": "train_shard_00000_3694_1", "global_id": 4099 }, { "text": "The absorption of eicosapentaenoic acid (EPA; 20:5n-3) and docosahexaenoic acid (DHA; 22:6n-3) omega-3-acid ethyl esters (EEs) is influenced by food. There is a need for a formulation of EE that is less impacted by food effect. SC401 is a novel Advanced Lipid Technologies-based formulation of EPA-EE and DHA-EE. In the presence of an aqueous medium, Advanced Lipid Technologies forms stable micelles in situ independent of bile salt secretion. This effect is hypothesized to improve EPA-EE and DHA-EE bioavailability while it helps mitigate the food effect associated with their consumption.\n\nMinimal food effect for eicosapentaenoic acid and docosahexaenoic acid bioavailability from omega-3-acid ethyl esters with an Advanced Lipid Technologies", "token_count": 216, "char_count": 747, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [ "SC401" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:54.387242", "source": { "split": "train_shard_00000", "doc_id": 3695 }, "chunk_id": "train_shard_00000_3695_0", "global_id": 4100 }, { "text": "Bifidobacteria are commensals that colonize the orogastrointestinal tract and rarely cause invasive human infections. However, an increasing number of bifidobacterial blood culture isolates has lately been observed in Norway. In order to investigate the pathogenicity of the\n\nBifidobacterium Bacteremia: Clinical Characteristics and a Genomic Approach To Assess Pathogenicity.", "token_count": 93, "char_count": 376, "word_count": 48, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:54.763761", "source": { "split": "train_shard_00000", "doc_id": 3696 }, "chunk_id": "train_shard_00000_3696_0", "global_id": 4101 }, { "text": "Neisseria meningitidis infections are a major issue for global health. The invasive MenC ST-103 clonal complex (CC103) has been the most prevalent in meningococcal outbreaks in Brazil, occurring also in several countries worldwide. Here we have analysed the population structure and accessory genome of MenC CC103 strains from a global perspective. An in-depth phylogenomic analysis revealed a lineage of N. meningitidis causing meningitis in Brazil and the United Kingdom. This lineage was also characterized as harbouring a particular accessory genome composed of CRISPR/Cas and restriction modification systems. This lineage was also characterized by a genomic island resembling an integrative and conjugative element. This island carried genes potentially associated with virulence and fitness. We propose this accessory gene repertoire could be contributing to the spatial-temporal persistence of the invasive MenC CC103 lineage.\n\nThe invasive Neisseria meningitidis MenC CC103 from Brazil is characterized by an accessory gene repertoire.", "token_count": 254, "char_count": 1044, "word_count": 146, "semantic_coherence": 1, "information_density": 0.637, "quality_score": 0.8185, "entities": { "genes": [ "CC103" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:55.257088", "source": { "split": "train_shard_00000", "doc_id": 3697 }, "chunk_id": "train_shard_00000_3697_0", "global_id": 4102 }, { "text": "Troglitazone and pioglitazone were developed as thiazolidinedione-type antidiabetes drugs, but only troglitazone was withdrawn from the markets due to severe liver injury. As both troglitazone and its sulfate metabolite are strong inhibitors of the bile salt export pump (BSEP), troglitazone-induced bile acid (BA) retention is thought to be one of the underlying mechanisms of liver injury. However, pioglitazone is also a strong BSEP inhibitor, indicating other mechanisms may also be involved in troglitazone-induced BA retention. Although retention of hydrophobic BAs (eg, chenodeoxycholic acid [CDCA]: a nonamidated BA) is known to cause hepatocyte injury, little is known about the hepatic conversion of nonamidated, hydrophobic BA species into less toxic hydrophilic BAs (eg, glycochenodeoxycholic acid: amidated BA) as a mechanism of drug-induced liver injury. In this study, we, therefore, investigated the effects of troglitazone and pioglitazone on BA amidation and the role of amidated BAs in troglitazone-associated BA-mediated hepatotoxicity. We also evaluated the intracellular BA composition of human hepatocytes treated with nonamidated BA species (CDCA or deoxycholic acid [DCA]) in the presence of troglitazone or pioglitazone. Amidation of CDCA and DCA was significantly inhibited by troglitazone (IC50: 5 and 3 µmol/l, respectively), but not pioglitazone. Moreover, treatment with troglitazone led to the retention of CDCA and DCA and decrease of glycine-amidation in hepatocytes. From these results, we suggest that troglitazone-induced liver injury might be caused by the accumulation of nonamidated BAs in hepatocytes due to inhibition of BA amidation.\n\nTroglitazone Inhibits Bile Acid Amidation: A Possible Risk Factor for Liver Injury.", "token_count": 510, "char_count": 1761, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5703, "quality_score": 0.7851, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:55.908120", "source": { "split": "train_shard_00000", "doc_id": 3698 }, "chunk_id": "train_shard_00000_3698_0", "global_id": 4103 }, { "text": "Escherichia coli can commonly be found, either as a commensal, probiotic or a pathogen, in the human gastrointestinal (GI) tract. Biofilm formation and its regulation is surprisingly variable, although distinct regulatory pattern of red, dry and rough (rdar) biofilm formation arise in certain pathovars and even clones. In the GI tract, environmental conditions, signals from the host and from commensal bacteria contribute to shape E. coli biofilm formation within the multi-faceted multicellular communities in a complex and integrated fashion. Although some major regulatory networks, adhesion factors and extracellular matrix components constituting E. coli biofilms have been recognized, these processes have mainly been characterized in vitro and in the context of interaction of E. coli strains with intestinal epithelial cells. However, direct observation of E. coli cells in situ, and the vast number of genes encoding surface appendages on the core or accessory genome of E. coli suggests the complexity of the biofilm process to be far from being fully understood. In this review, we summarize biofilm formation mechanisms of commensal, probiotic and pathogenic E. coli in the context of the gastrointestinal tract.\n\n\"It's a gut feeling\" - Escherichia coli biofilm formation in the gastrointestinal tract environment.", "token_count": 310, "char_count": 1329, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:56.513274", "source": { "split": "train_shard_00000", "doc_id": 3699 }, "chunk_id": "train_shard_00000_3699_0", "global_id": 4104 }, { "text": "Salmonella Typhimurium is the leading cause of human non-typhoidal gastroenteritis in the US. S. Kentucky is one the most commonly recovered serovars from commercially processed poultry carcasses. This study compared the genotypic and phenotypic properties of two Salmonella enterica strains Typhimurium (ST221_31B) and Kentucky (SK222_32B) recovered from commercially processed chicken carcasses using whole genome sequencing, phenotype characterizations and an intracellular killing assay. Illumina MiSeq platform was used for sequencing of two Salmonella genomes. Phylogenetic analysis employing homologous alignment of a 1,185 non-duplicated protein-coding gene in the Salmonella core genome demonstrated fully resolved bifurcating patterns with varying levels of diversity that separated ST221_31B and SK222_32B genomes into distinct monophyletic serovar clades. Single nucleotide polymorphism (SNP) analysis identified 2,432 (ST19) SNPs within 13 Typhimurium genomes including ST221_31B representing Sequence Type ST19 and 650 (ST152) SNPs were detected within 13 Kentucky genomes including SK222_32B representing Sequence Type ST152. In addition to serovar-specific conserved coding sequences, the genomes of ST221_31B and SK222_32B harbor several genomic regions with significant genetic differences. These included phage and phage-like elements, carbon utilization or transport operons, fimbriae operons, putative membrane associated protein-encoding genes, antibiotic resistance genes, siderophore operons, and numerous hypothetical protein-encoding genes", "token_count": 437, "char_count": 1565, "word_count": 194, "semantic_coherence": 1, "information_density": 0.7268, "quality_score": 0.8634, "entities": { "genes": [ "ST152", "ST19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:57.173980", "source": { "split": "train_shard_00000", "doc_id": 3700 }, "chunk_id": "train_shard_00000_3700_0", "global_id": 4105 }, { "text": "Phenotype microarray results demonstrated that ST221_31B is capable of utilizing certain carbon compounds more efficiently as compared to SK222_3B; namely, 1,2-propanediol, M-inositol, L-threonine, α-D-lactose, D-tagatose, adonitol, formic acid, acetoacetic acid, and L-tartaric acid. ST221_31B survived for 48 h in macrophages, while SK222_32B was mostly eliminated. Further, a 3-fold growth of ST221_31B was observed at 24 hours post-infection in chicken granulosa cells while SK222_32B was unable to replicate in these cells. These results suggest that Salmonella Typhimurium can survive host defenses better and could be more invasive than Salmonella Kentucky and provide some insights into the genomic determinants responsible for these differences.\n\nGenotypic and phenotypic characterization of multidrug resistant Salmonella Typhimurium and Salmonella Kentucky strains recovered from chicken carcasses.", "token_count": 269, "char_count": 909, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7627, "quality_score": 0.8814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:57.753445", "source": { "split": "train_shard_00000", "doc_id": 3700 }, "chunk_id": "train_shard_00000_3700_1", "global_id": 4106 }, { "text": "Elevated levels of polycyclic aromatic hydrocarbons (PAHs) are detected in aquafeeds where fish oils are (partially) replaced by vegetable oils. The highly lipophilic PAHs solubilize readily in oil droplets and micelles in the intestinal lumen that can affect enzymatic lipid digestion by altering lipase activity. We therefore investigated the effect of two PAHs, benzo[a]pyrene (BaP) and phenanthrene (PHE), on bile salt-activated lipase (BAL) activity in desalted luminal extracts of the proximal intestine of rainbow trout (Oncorhynchus mykiss) using the triacylglycerides rapeseed oil and fish oil as substrates. The hydrolysis of rapeseed oil and fish oil measured at a calculated substrate concentration of 2.2mM, increased linearly up to 30min at 15°C. Substrate dependency under initial velocity conditions was described by simple Michaelis-Menten kinetics with a K\n\nThe polycyclic aromatic hydrocarbons benzo[a]pyrene and phenanthrene inhibit intestinal lipase activity in rainbow trout (Oncorhynchus mykiss).", "token_count": 302, "char_count": 1019, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:58.784853", "source": { "split": "train_shard_00000", "doc_id": 3701 }, "chunk_id": "train_shard_00000_3701_0", "global_id": 4107 }, { "text": "In order to identify fish enzymes displaying novel biochemical properties, we choose the common smooth-hound (Mustelus mustelus) as a starting biological material to characterize the digestive lipid hydrolyzing enzyme. A smooth-hound digestive lipase (SmDL) was purified from a delipidated pancreatic powder. The SmDL molecular weight was around 50kDa. Specific activities of 2200 and 500U/mg were measured at pH 9 and 40°C using tributyrin and olive oil emulsion as substrates, respectively. Unlike known mammal pancreatic lipases, the SmDL was stable at 50°C and it retained 90% of its initial activity after 15min of incubation at 60°C. Interestingly, bile salts act as an activator of the SmDL. It's worth to notice that the SmDL was also salt-tolerant since it was active in the presence of high salt concentrations reaching 0.8M. Fatty acid (FA) analysis of oil from the smooth-hound viscera showed a dominance of unsaturated ones (UFAs). Interestingly, the major n-3 fatty acids were DHA and EPA with contents of 18.07% and 6.14%, respectively. In vitro digestibility model showed that the smooth hound oil was efficiently hydrolyzed by pancreatic lipases, which suggests the higher assimilation of fish oils by consumers.\n\nThe smooth-hound lipolytic system: Biochemical characterization of a purified digestive lipase, lipid profile and in vitro oil digestibility.", "token_count": 389, "char_count": 1372, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:59.400918", "source": { "split": "train_shard_00000", "doc_id": 3702 }, "chunk_id": "train_shard_00000_3702_0", "global_id": 4108 }, { "text": "Bile salt-stimulated lipase (BSSL) is a lipolytic digestive enzyme with broad substrate specificity secreted from exocrine pancreas into the intestinal lumen in all species and from the lactating mammary gland into the milk of some species, notably humans but not cows. BSSL in breast milk facilitates digestion and absorption of milk fat and promotes growth of small for gestational age preterm infants. Thus, purified recombinant human BSSL (rhBSSL) can be used for treatment of patients with fat malabsorption and expressing rhBSSL in the milk of transgenic cloned cows would therefore be a mean to meet a medical need. In the present study, a vector pBAC-hLF-hBSSL was constructed, which efficiently expressed active rhBSSL in milk of transgenic cloned cows to a concentration of 9.8 mg/ml. The rhBSSL purified from cow milk had the same enzymatic activity, N-terminal amino acid sequence, amino acid composition and isoelectric point and similar physicochemical characteristics as human native BSSL. Our study supports the use of transgenic cattle for the cost-competitive, large-scale production of therapeutic rhBSSL.\n\nPurification and characterization of recombinant human bile salt-stimulated lipase expressed in milk of transgenic cloned cows.", "token_count": 326, "char_count": 1253, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6324, "quality_score": 0.8162, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:35:59.972155", "source": { "split": "train_shard_00000", "doc_id": 3703 }, "chunk_id": "train_shard_00000_3703_0", "global_id": 4109 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is the common name for a heterogeneous group of highly drug-resistant staphylococci. Two major MRSA classes are distinguished based on epidemiology, namely community-associated (CA) and hospital-associated (HA) MRSA. Notably, the distinction of CA- and HA-MRSA based on molecular traits remains difficult due to the high genomic plasticity of S. aureus. Here we sought to pinpoint global distinguishing features of CA- and HA-MRSA through a comparative genome and proteome analysis of the notorious MRSA lineage USA300. We show for the first time that CA- and HA-MRSA isolates can be distinguished by 2 distinct extracellular protein abundance clusters that are predictive not only for epidemiologic behavior, but also for their growth and survival within epithelial cells. This 'exoproteome profiling' also groups more distantly related HA-MRSA isolates into the HA exoproteome cluster. Comparative genome analysis suggests that these distinctive features of CA- and HA-MRSA isolates relate predominantly to the accessory genome. Intriguingly, the identified exoproteome clusters differ in the relative abundance of typical cytoplasmic proteins, suggesting that signatures of cytoplasmic proteins in the exoproteome represent a new distinguishing feature of CA- and HA-MRSA. Our comparative genome and proteome analysis focuses attention on potentially distinctive roles of 'liberated' cytoplasmic proteins in the epidemiology and intracellular survival of CA- and HA-MRSA isolates. Such extracellular cytoplasmic proteins were recently invoked in staphylococcal virulence, but their implication in the epidemiology of MRSA is unprecedented.\n\nSignatures of cytoplasmic proteins in the exoproteome distinguish community- and hospital-associated methicillin-resistant Staphylococcus aureus USA300 lineages.", "token_count": 469, "char_count": 1856, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [ "USA300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:00.616693", "source": { "split": "train_shard_00000", "doc_id": 3704 }, "chunk_id": "train_shard_00000_3704_0", "global_id": 4110 }, { "text": "ToxR is a transmembrane transcription factor that is essential for virulence gene expression and human colonization by Vibrio cholerae. ToxR requires its operon partner ToxS, a periplasmic integral membrane protein, for full activity. These two proteins are thought to interact through their respective periplasmic domains, ToxRp and ToxSp. In addition, ToxR is thought to be responsive to various environmental cues, such as bile salts and alkaline pH, but how these factors influence ToxR is not yet understood. Using NMR and reciprocal pull down assays, we present the first direct evidence that ToxR and ToxS physically interact. Furthermore, using NMR and DSF, it was shown that the bile salts cholate and chenodeoxycholate interact with purified ToxRp and destabilize it. Surprisingly, bile salt destabilization of ToxRp enhanced the interaction between ToxRp and ToxSp. In contrast, alkaline pH, which is one of the factors that leads to ToxR proteolysis, decreased the interaction between ToxRp and ToxSp. Taken together, these data suggest a model whereby bile salts or other detergents destabilize ToxR, increasing its interaction with ToxS to promote full ToxR activity. Subsequently, as V. cholerae alkalinizes its environment in late stationary phase, the interaction between the two proteins decreases, allowing ToxR proteolysis to proceed.\n\nBile salts and alkaline pH reciprocally modulate the interaction between the periplasmic domains of Vibrio cholerae ToxR and ToxS.", "token_count": 397, "char_count": 1486, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:01.232349", "source": { "split": "train_shard_00000", "doc_id": 3705 }, "chunk_id": "train_shard_00000_3705_0", "global_id": 4111 }, { "text": "Neisseria meningitidis serogroups B and C have been responsible for the majority of invasive meningococcal disease in Australia, with serogroup B strains causing an increasing proportion of cases in recent years. Serogroup Y has typically caused sporadic disease in Australia. In 2002, a cluster of 4 cases was reported from a rural region in Queensland. Three of these cases were serogroup C, with 1 case diagnosed by molecular detection only, and the fourth case was identified as a serogroup Y infection. Genomic analysis, including antigen finetyping, multilocus sequence typing (MLST), and core genome MLST, demonstrated that the serogroup Y case, though spatially and temporally linked to a serogroup C disease cluster, was not the product of a capsule switch and that one of the serogroup C isolates had a deletion of the entire porA sequence.\n\nGenetic characterization of a Neisseria meningitidis cluster in Queensland, Australia.", "token_count": 228, "char_count": 938, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6483, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:01.705064", "source": { "split": "train_shard_00000", "doc_id": 3706 }, "chunk_id": "train_shard_00000_3706_0", "global_id": 4112 }, { "text": "Mefloquine (Mef), a poorly soluble and highly bitter drug, has been used for malaria prophylaxis and treatment. The dosage form for Mef is mostly available as adult tablets, and thus children under the age of 5 suffer from poor medication adherence. We have developed a stable, rapidly dissolvable, and palatable pediatric formulation for Mef using liposomes composed of 1,2-distearoyl-sn-glycero-3-phosphocholine (DSPC) and cholesterol with a mean diameter of ∼110 nm. Mef was actively loaded into the liposomes via an ammonium sulfate gradient using the solvent-assisted loading technology (SALT) developed in our lab. Complete loading of Mef inside the liposomal core was achieved at a high drug-to-lipid ratio (D/L) of 0.1-0.2 (w/w), and the final drug content in the formulation was ∼8 mg/mL, well above the solubility of Mef (<0.6 mg/mL in simulated fluids). The strong bitterness of Mef was masked by the liposomal encapsulation as measured by an electronic tongue. Incubating the Mef-liposomes (Mef-Lipo) in the simulated gastric fluid (pH 1.2) and the simulated intestinal fluid containing 3 mM sodium taurocholate (pH 6.8) induced changes in liposome size and the polydispersity, resulting in drug release (∼40% in 2 h). However, no drug release from the Mef-Lipo was measured in the bile salt-free intestinal fluid or simulated saliva (0% in 3 h). These data suggest that drug release from the Mef-Lipo was mediated by a low pH and the presence of a surfactant. Pancreatic lipase did not degrade DSPC in the Mef-Lipo after 8 h of incubation nor induce Mef release from the liposomes, indicating that lipid digestion played a minor role for drug release from the Mef-Lipo", "token_count": 511, "char_count": 1681, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:02.358775", "source": { "split": "train_shard_00000", "doc_id": 3707 }, "chunk_id": "train_shard_00000_3707_0", "global_id": 4113 }, { "text": "In order to improve long-term room temperature storage, the Mef-Lipo was lyophilized to obtain a solid formulation, which was completely dissolvable in water in 10 s and displayed similar in vitro profiles of release as the liquid form. The lyophilized Mef-Lipo was stable at room temperature for >3 months. In mice, orally delivered liquid and lyophilized Mef-Lipo displayed comparable absorption with bioavailability (BA) of 81-86%, while the absorption of the standard Mef suspension was significantly lower with BA of 70% and 20% decreased maximal plasma concentration and area under the curve. Our data suggest that the Mef-Lipo was a stable, palatable, and bioavailable formulation that might be suitable for pediatric use.\n\nDevelopment of a Rapidly Dissolvable Oral Pediatric Formulation for Mefloquine Using Liposomes.", "token_count": 216, "char_count": 826, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:02.820275", "source": { "split": "train_shard_00000", "doc_id": 3707 }, "chunk_id": "train_shard_00000_3707_1", "global_id": 4114 }, { "text": "This study has been actually performed with the aim to develop vitamin E derived vesicles individually from a surface active ionic liquid (1-Hexadecyl-3-Methylimidazolium chloride ([C\n\nInfluence of bile salt on vitamin E derived vesicles involving a surface active ionic liquid and conventional cationic micelle.", "token_count": 82, "char_count": 312, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7955, "quality_score": 0.8977, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:03.195835", "source": { "split": "train_shard_00000", "doc_id": 3708 }, "chunk_id": "train_shard_00000_3708_0", "global_id": 4115 }, { "text": "Clostridium botulinum, a formidable pathogen is responsible for the emerging cause of food poisoning cases on the global canvas. The endemicity of bacterium Clostridium botulinum is reflected by the sudden hospital outbreaks and increased resistance towards multiple drugs. Therefore, a combined approach of in-silico comparative genomic analysis with statistical analysis was applied to overcome the limitation of bench-top technologies. Owing to the paucity of genomic data available by the advent of third generation sequencing technologies, several 'omics' technologies were applied to understand the underlying evolutionary pattern and lifestyle of the bacterial pathogen using phylogenomics. The calculation of pan-genome, core genome and singletons provides view of genetic repertoire of the bacterial pathogen lineage at the successive level, orthology shared and specific gene subsets. In addition, assessment of pathogenomic potential, resistome, toxin/antitoxin family in successive pathogenic strains of Clostridium botulinum aids in revealing more specific targets for drug design and development.\n\nPan-genome analysis of Clostridium botulinum reveals unique targets for drug development.", "token_count": 260, "char_count": 1201, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:03.747247", "source": { "split": "train_shard_00000", "doc_id": 3709 }, "chunk_id": "train_shard_00000_3709_0", "global_id": 4116 }, { "text": "Human campylobacteriosis, caused by\n\nCore Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.", "token_count": 52, "char_count": 175, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:04.113054", "source": { "split": "train_shard_00000", "doc_id": 3710 }, "chunk_id": "train_shard_00000_3710_0", "global_id": 4117 }, { "text": "The non-conventional yeast Kluyveromyces marxianus is an emerging industrial producer for many biotechnological processes. Here, we show the application of a biomass-linked stoichiometric model of central metabolism that is experimentally validated, and mass and charge balanced for assessing the carbon conversion efficiency of wild type and modified K. marxianus. Pairs of substrates (lactose, glucose, inulin, xylose) and products (ethanol, acetate, lactate, glycerol, ethyl acetate, succinate, glutamate, phenylethanol and phenylalanine) are examined by various modelling and optimisation methods. Our model reveals the organism's potential for industrial application and metabolic engineering. Modelling results imply that the aeration regime can be used as a tool to optimise product yield and flux distribution in K. marxianus. Also rebalancing NADH and NADPH utilisation can be used to improve the efficiency of substrate conversion. Xylose is identified as a biotechnologically promising substrate for K. marxianus.\n\nModel-based biotechnological potential analysis of Kluyveromyces marxianus central metabolism.", "token_count": 282, "char_count": 1120, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6824, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:04.675627", "source": { "split": "train_shard_00000", "doc_id": 3711 }, "chunk_id": "train_shard_00000_3711_0", "global_id": 4118 }, { "text": "Kluyveromyces marxianus is a safe yeast used in the food and biotechnology sectors. One of the important traits that sets it apart from the familiar yeasts, Saccharomyces cerevisiae, is its capacity to grow using lactose as a carbon source. Like in its close relative, Kluyveromyces lactis, this requires lactose transport via a permease and intracellular hydrolysis of the disaccharide. Given the importance of the trait, it was intriguing that most, but not all, strains of K. marxianus are reported to consume lactose efficiently. In this study, primarily through heterologous expression in S. cerevisiae and K. marxianus, it was established that a single gene, LAC12, is responsible for lactose uptake in K. marxianus. Strains that failed to transport lactose showed variation in 13 amino acids in the Lac12p protein, rendering the protein non-functional for lactose transport. Genome analysis showed that the LAC12 gene is present in four copies in the subtelomeric regions of three different chromosomes but only the ancestral LAC12 gene encodes a functional lactose transporter. Other copies of LAC12 may be non-functional or have alternative substrates. The analysis raises some interesting questions regarding the evolution of sugar transporters in K. marxianus.\n\nPolymorphisms in the LAC12 gene explain lactose utilisation variability in Kluyveromyces marxianus strains.", "token_count": 361, "char_count": 1380, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8098, "entities": { "genes": [ "LAC12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:05.256638", "source": { "split": "train_shard_00000", "doc_id": 3712 }, "chunk_id": "train_shard_00000_3712_0", "global_id": 4119 }, { "text": "Buruli ulcer (BU) is a necrotizing infection of the skin and subcutaneous tissue caused by Mycobacterium ulcerans. BU wounds may also be colonized with other microorganisms including Staphylococcus aureus. This study aimed to characterize the virulence factors of S. aureus isolated from BU patients. Previously sequenced genomes of 21 S. aureus isolates from BU patients were screened for the presence of virulence genes. The results show that all S. aureus isolates harbored on their core genomes genes for known virulence factors like α-hemolysin, and the α- and β-phenol soluble modulins. Besides the core genome virulence genes, mobile genetic elements (MGEs), i.e. prophages, genomic islands, pathogenicity islands and a Staphylococcal cassette chromosome (SCC) were found to carry different combinations of virulence factors, among them genes that are known to encode factors that promote immune evasion, superantigens and Panton-Valentine Leucocidin. The present observations imply that the S. aureus isolates from BU patients harbor a diverse repertoire of virulence genes that may enhance bacterial survival and persistence in the wound environment and potentially contribute to delayed wound healing.\n\nVirulence potential of Staphylococcus aureus isolates from Buruli ulcer patients.", "token_count": 336, "char_count": 1294, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:05.820296", "source": { "split": "train_shard_00000", "doc_id": 3713 }, "chunk_id": "train_shard_00000_3713_0", "global_id": 4120 }, { "text": "After the introduction of a ban on the use of antibiotic growth promoters (AGPs) for livestock, reuterin-producing Lactobacillus reuteri is getting attention as an alternative to AGPs. In this study, we investigated genetic features of L. reuteri associated with host specificity and antipathogenic effect. We isolated 104 L. reuteri strains from porcine feces, and 16 strains, composed of eight strains exhibiting the higher antipathogenic effect (group HS) and eight strains exhibiting the lower effect (group LS), were selected for genomic comparison. We generated draft genomes of the 16 isolates and investigated their pan-genome together with the 26 National Center for Biotechnology Information-registered genomes. L. reuteri genomes organized six clades with multi-locus sequence analysis, and the clade IV includes the 16 isolates. First, we identified six L. reuteri clade IV-specific genes including three hypothetical protein-coding genes. The three annotated genes encode transposases and cell surface proteins, indicating that these genes are the result of adaptation to the host gastrointestinal epithelia and that these host-specific traits were acquired by horizontal gene transfer. We also identified differences between groups HS and LS in the pdu-cbi-cob-hem gene cluster, which is essential for reuterin and cobalamin synthesis, and six genes specific to group HS are revealed. While the strains of group HS possessed all genes of this cluster, LS strains have lost many genes of the cluster. This study provides a deeper understanding of the relationship between probiotic properties and genomic features of L. reuteri.\n\nPan-Genomic Approaches in Lactobacillus reuteri as a Porcine Probiotic: Investigation of Host Adaptation and Antipathogenic Activity.", "token_count": 440, "char_count": 1776, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:06.446022", "source": { "split": "train_shard_00000", "doc_id": 3714 }, "chunk_id": "train_shard_00000_3714_0", "global_id": 4121 }, { "text": "Glyburide is widely used for the treatment of type 2 diabetes. We studied the mechanisms involved in the disposition of glyburide and its pharmacologically active hydroxy metabolites M1 and M2b and evaluated their clinical pharmacokinetics and the potential role in glyburide-induced cholestasis employing physiologically based pharmacokinetic (PBPK) modeling. Transport studies of parent and metabolites in human hepatocytes and transfected cell systems imply hepatic uptake mediated by organic anion-transporting polypeptides. Metabolites are also subjected to basolateral and biliary efflux by P-glycoprotein, breast cancer resistance protein, and multidrug resistance-associated proteins, and are substrates to renal organic anion transporter 3. A PBPK model in combination with a Bayesian approach was developed considering the identified disposition mechanisms. The model reasonably described plasma concentration time profiles and urinary recoveries of glyburide and the metabolites, implying the role of multiple transport processes in their pharmacokinetics. Predicted free liver concentrations of the parent (∼30-fold) and metabolites (∼4-fold) were higher than their free plasma concentrations. Finally, all three compounds showed bile salt export pump inhibition in vitro; however, significant in vivo inhibition was not apparent for any compound on the basis of a predicted unbound liver exposure-response effect model using measured in vitro IC\n\nTransporter-Mediated Disposition, Clinical Pharmacokinetics and Cholestatic Potential of Glyburide and Its Primary Active Metabolites.", "token_count": 374, "char_count": 1594, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6762, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:07.022937", "source": { "split": "train_shard_00000", "doc_id": 3715 }, "chunk_id": "train_shard_00000_3715_0", "global_id": 4122 }, { "text": "The role of bile salt export protein (BSEP) inhibition in drug-induced liver injury (DILI) has been investigated widely, while inhibition of the canalicular multidrug resistant protein 3 (MDR3) has received less attention. This transporter plays a pivotal role in secretion of phospholipids into bile and functions coordinately with BSEP to mediate the formation of bile acid-containing biliary micelles. Therefore, inhibition of MDR3 in human hepatocytes was examined across 125 drugs (70 of Most-DILI-concern and 55 of No-DILI-concern). Of these tested, 41% of Most-DILI-concern and 47% of No-DILI-concern drugs had MDR3 IC\n\nEvaluating the Role of Multidrug Resistance Protein 3 (MDR3) Inhibition in Predicting Drug-Induced Liver Injury Using 125 Pharmaceuticals.", "token_count": 236, "char_count": 765, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6514, "quality_score": 0.8257, "entities": { "genes": [ "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:07.490200", "source": { "split": "train_shard_00000", "doc_id": 3716 }, "chunk_id": "train_shard_00000_3716_0", "global_id": 4123 }, { "text": "Palbociclib free base capsule is a weak base drug with highly pH-dependent solubility. In vitro and in vivo studies evaluated the impact of acid-reducing agents on exposure of palbociclib and determined whether the impact, if any, can be mitigated by food. A drug-drug interaction study (study 1) was conducted first under fasted conditions and showed that coadministration of multiple doses of the proton-pump inhibitor rabeprazole substantially reduced palbociclib mean area under the concentration-time curve from time 0 to infinity and maximum observed plasma concentration by 62% and 80%, respectively. In vitro assessment suggested that the presence of bile salt mixed micelles to mimic the fed state can significantly enhance the solubility of palbociclib. Subsequently, study 2 was conducted under fed conditions and demonstrated that coadministration of rabeprazole decreased palbociclib maximum observed plasma concentration by 41% but had limited impact on area under the concentration-time curve from 0 to infinity (13% decrease). This study also showed that the histamine-2 receptor antagonist famotidine and local antacid with staggered dosing had no impact on palbociclib exposure under fed conditions. Food intake effectively mitigated the impact of acid-reducing agents on palbociclib exposure. Palbociclib free base capsule should be taken with food, and acid-reducing agent use does not need to be avoided.\n\nImpact of Acid-Reducing Agents on the Pharmacokinetics of Palbociclib, a Weak Base With pH-Dependent Solubility, With Different Food Intake Conditions.", "token_count": 391, "char_count": 1578, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5507, "quality_score": 0.7753, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:08.101139", "source": { "split": "train_shard_00000", "doc_id": 3717 }, "chunk_id": "train_shard_00000_3717_0", "global_id": 4124 }, { "text": "Progressive Familial Intrahepatic Cholestasis type 2 (PFIC2) is a rare cholestatic disorder diagnosed in infancy or childhood that can lead to severe hepatic fibrosis and liver failure. Mutations in the ABCB11 gene result in a deficiency of the bile salt export protein (BSEP) and accumulation of bile inside the hepatocytes. Hepatocellular carcinoma is another condition associated with severe forms of deletion mutations in the ABCB11 gene. Treatment options including ursodeoxycholic acid biliary diversion have mixed outcomes and some patients require liver transplantation. Here, we describe two siblings with an extremely mild form of PFIC2 inherited from heterozygous parents. The elder sibling had acute liver failure at the age of six months and both siblings had pruritus, cholestasis, coagulopathy and fat-soluble-vitamin deficiencies in infancy but have been asymptomatic past infancy. Genetic testing of the siblings revealed that each were compound heterozygotes for two missense mutations of the ABCB11 gene: p.C68Y and p.R832H. Medical treatment typical for PFIC2 has not been necessary for either patient. This is the first report of these variants following a mild course in two affected patients.\n\nA Rare BSEP Mutation Associated with a Mild Form of Progressive Familial Intrahepatic Cholestasis Type 2.", "token_count": 344, "char_count": 1322, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:08.707805", "source": { "split": "train_shard_00000", "doc_id": 3718 }, "chunk_id": "train_shard_00000_3718_0", "global_id": 4125 }, { "text": "Traditionally, irritable bowel syndrome has been considered to be a disorder with no known underlying structural or biochemical explanation, but this concept is likely to be outdated. In this Review we challenge the widely accepted view that irritable bowel syndrome is an unexplained brain-gut disorder. There is epidemiological evidence that, in a major subset of patients, gastrointestinal symptoms arise first and only later do incident mood disorders occur. Additionally, possible mechanisms for gut-brain dysfunction have been identified, suggesting primary gut disturbances might be the underlying cause in a subgroup. Underlying mechanisms that could lead to irritable bowel syndrome include genetic factors (most notably an identified mutation of SCN5A); post-infectious changes, chronic infections and disturbances in the intestinal microbiota; low-grade mucosal inflammation, immune activation, and altered intestinal permeability; disordered bile salt metabolism (in 10-20% of cases with diarrhoea); abnormalities in serotonin metabolism; and alterations in brain function, which could be primary or secondary factors. Identical irritable bowel syndrome symptoms are probably due to different disease processes; grouping patients with this disorder into either diarrhoea-predominant or constipation-predominant subtypes promotes heterogeneity. An approach based on the underlying pathophysiology could help to develop therapies that target causes and ultimately provide a cure for patients with irritable bowel syndrome.\n\nPathophysiology of irritable bowel syndrome.", "token_count": 346, "char_count": 1578, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [ "SCN5A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:09.297518", "source": { "split": "train_shard_00000", "doc_id": 3719 }, "chunk_id": "train_shard_00000_3719_0", "global_id": 4126 }, { "text": "As an increasing number of plant genome sequences become available, it is clear that gene content varies between individuals, and the challenge arises to predict the gene content of a species. However, genome comparison is often confounded by variation in assembly and annotation. Differentiating between true gene absence and variation in assembly or annotation is essential for the accurate identification of conserved and variable genes in a species. Here, we present the de novo assembly of the B. napus cultivar Tapidor and comparison with an improved assembly of the Brassica napus cultivar Darmor-bzh. Both cultivars were annotated using the same method to allow comparison of gene content. We identified genes unique to each cultivar and differentiate these from artefacts due to variation in the assembly and annotation. We demonstrate that using a common annotation pipeline can result in different gene predictions, even for closely related cultivars, and repeat regions which collapse during assembly impact whole genome comparison. After accounting for differences in assembly and annotation, we demonstrate that the genome of Darmor-bzh contains a greater number of genes than the genome of Tapidor. Our results are the first step towards comparison of the true differences between B. napus genomes and highlight the potential sources of error in future production of a B. napus pangenome.\n\nAssembly and comparison of two closely related Brassica napus genomes.", "token_count": 311, "char_count": 1475, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5446, "quality_score": 0.7723, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:09.914402", "source": { "split": "train_shard_00000", "doc_id": 3720 }, "chunk_id": "train_shard_00000_3720_0", "global_id": 4127 }, { "text": "The epidemiologically most important mechanism of antibiotic resistance in Staphylococcus aureus is associated with mecA-an acquired gene encoding an extra penicillin-binding protein (PBP2a) with low affinity to virtually all β-lactams. The introduction of mecA into the S. aureus chromosome has led to the emergence of methicillin-resistant S. aureus (MRSA) pandemics, responsible for high rates of mortality worldwide. Nonetheless, little is known regarding the origin and evolution of mecA. Different mecA homologues have been identified in species belonging to the Staphylococcus sciuri group representing the most primitive staphylococci. In this study we aimed to identify evolutionary steps linking these mecA precursors to the β-lactam resistance gene mecA and the resistance phenotype. We sequenced genomes of 106 S. sciuri, S. vitulinus and S. fleurettii strains and determined their oxacillin susceptibility profiles. Single-nucleotide polymorphism (SNP) analysis of the core genome was performed to assess the genetic relatedness of the isolates. Phylogenetic analysis of the mecA gene homologues and promoters was achieved through nucleotide/amino acid sequence alignments and mutation rates were estimated using a Bayesian analysis. Furthermore, the predicted structure of mecA homologue-encoded PBPs of oxacillin-susceptible and -resistant strains were compared. We showed for the first time that oxacillin resistance in the S. sciuri group has emerged multiple times and by a variety of different mechanisms. Development of resistance occurred through several steps including structural diversification of the non-binding domain of native PBPs; changes in the promoters of mecA homologues; acquisition of SCCmec and adaptation of the bacterial genetic background. Moreover, our results suggest that it was exposure to β-lactams in human-created environments that has driven evolution of native PBPs towards a resistance determinant. The evolution of β-lactam resistance in staphylococci highlights the numerous resources available to bacteria to adapt to the selective pressure of antibiotics.", "token_count": 513, "char_count": 2109, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:36:10.578373", "source": { "split": "train_shard_00000", "doc_id": 3721 }, "chunk_id": "train_shard_00000_3721_0", "global_id": 4128 }, { "text": "Evidence for the evolutionary steps leading to mecA-mediated β-lactam resistance in staphylococci.", "token_count": 30, "char_count": 98, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:10.939786", "source": { "split": "train_shard_00000", "doc_id": 3721 }, "chunk_id": "train_shard_00000_3721_1", "global_id": 4129 }, { "text": "The genomes of the type B3 bacteriophages that infect Caulobacter crescentus are among the largest phage genomes thus far deposited into GenBank with sizes over 200 kb. In this study, we introduce six new bacteriophage genomes which were obtained from phage collected from various water systems in the southeastern United States and from tropical locations across the globe. A comparative analysis of the 12 available genomes revealed a \"core genome\" which accounts for roughly 1/3 of these bacteriophage genomes and is predominately localized to the head, tail, and lysis gene regions. Despite being isolated from geographically distinct locations, the genomes of these bacteriophages are highly conserved in both genome sequence and gene order. We also identified the insertions, deletions, translocations, and horizontal gene transfer events which are responsible for the genomic diversity of this group of bacteriophages and demonstrated that these changes are not consistent with the idea that modular reassortment of genomes occurs in this group of bacteriophages.\n\nGenomic Diversity of Type B3 Bacteriophages of Caulobacter crescentus.", "token_count": 263, "char_count": 1142, "word_count": 168, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:11.487259", "source": { "split": "train_shard_00000", "doc_id": 3722 }, "chunk_id": "train_shard_00000_3722_0", "global_id": 4130 }, { "text": "Organochlorine pesticides (OCPs) can persistently accumulate in body and threaten human health. Bile acids and intestinal microbial metabolism have emerged as important signaling molecules in the host. However, knowledge on which intestinal microbiota and bile acids are modified by OCPs remains unclear. In this study, adult male C57BL/6 mice were exposed to p, p'-dichlorodiphenyldichloroethylene (p, p'-DDE) and β-hexachlorocyclohexane (β-HCH) for 8 weeks. The relative abundance and composition of various bacterial species were analyzed by 16S rRNA gene sequencing. Bile acid composition was analyzed by metabolomic analysis using UPLC-MS. The expression of genes involved in hepatic and enteric bile acids metabolism was measured by real-time PCR. Expression of genes in bile acids synthesis and transportation were measured in HepG2 cells incubated with p, p'-DDE and β-HCH. Our findings showed OCPs changed relative abundance and composition of intestinal microbiota, especially in enhanced Lactobacillus with bile salt hydrolase (BSH) activity. OCPs affected bile acid composition, enhanced hydrophobicity, decreased expression of genes on bile acid reabsorption in the terminal ileum and compensatory increased expression of genes on synthesis of bile acids in the liver. We demonstrated that chronic exposure of OCPs could impair intestinal microbiota; as a result, hepatic and enteric bile acid profiles and metabolism were influenced. The findings in this study draw our attention to the hazards of chronic OCPs exposure in modulating bile acid metabolism that might cause metabolic disorders and their potential to cause related diseases in human.\n\nOrganochloride pesticides modulated gut microbiota and influenced bile acid metabolism in mice.", "token_count": 459, "char_count": 1758, "word_count": 250, "semantic_coherence": 1, "information_density": 0.564, "quality_score": 0.782, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:12.130218", "source": { "split": "train_shard_00000", "doc_id": 3723 }, "chunk_id": "train_shard_00000_3723_0", "global_id": 4131 }, { "text": "Bile formation is a key function of the liver. Disturbance of bile flow may lead to liver disease and is called cholestasis. Cholestasis may be inherited, for example, in progressive familial intrahepatic cholestasis or acquired, for example, by drug-mediated inhibition of bile salt export from hepatocytes into the canaliculi. The key transport system for exporting bile salts into the canaliculi is the bile salt export pump. Inhibition of the bile salt export pump by drugs is a well-established cause of drug-induced cholestasis. Investigation of the role of the multidrug resistance protein 3, essential for biliary phospholipid secretion, is emerging now. This overview summarizes current concepts and methods with an emphasis on in vitro model systems for the investigation of drug-induced cholestasis in the general context of drug-induced liver injury.\n\nModel Systems for Studying the Role of Canalicular Efflux Transporters in Drug-Induced Cholestatic Liver Disease.", "token_count": 243, "char_count": 977, "word_count": 144, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:12.621557", "source": { "split": "train_shard_00000", "doc_id": 3724 }, "chunk_id": "train_shard_00000_3724_0", "global_id": 4132 }, { "text": "Post-transcriptional control provides bacterial pathogens a method by which they can rapidly adapt to environmental change. Dual exo- and endonucleolytic activities of RNase J enzymes contribute to Gram-positive RNA processing and decay. First discovered in Bacillus subtilis, RNase J1 plays a key role in mRNA maturation and degradation, while the function of the paralogue RNase J2 is largely unknown. Previously, we discovered that deletion of the Enterococcus faecalis rnjB gene significantly attenuates expression of a major virulence factor involved in enterococcal pathogenesis, the Ebp pili. In this work, we demonstrate that E. faecalis rnjB encodes an active RNase J2, and that the ribonuclease activity of RNase J2 is required for regulation of Ebp pili. To further investigate how rnjB affects E. faecalis gene expression on a global scale, we compared transcriptomes of the E. faecalis strain OG1RF with its isogenic rnjB deletion mutant (ΔrnjB). In addition to Ebp pili regulation, previously demonstrated to have a profound effect on the ability of E. faecalis to form biofilm or establish infection, we identified that rnjB regulates the expression of several other genes involved in bacterial virulence and fitness, including gls24 (a virulence factor important in stress response). We further demonstrated that the E. faecalis RNase J2 deletion mutant is more sensitive to bile salt and greatly attenuated in in vivo organ infection as determined by an IV-sublethal challenge infection mouse model, indicating that E. faecalis RNase J2 plays an important role in E. faecalis virulence.\n\nFunctional studies of E. faecalis RNase J2 and its role in virulence and fitness.", "token_count": 440, "char_count": 1686, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5603, "quality_score": 0.7802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:13.247455", "source": { "split": "train_shard_00000", "doc_id": 3725 }, "chunk_id": "train_shard_00000_3725_0", "global_id": 4133 }, { "text": "Lactococcus lactis subsp. lactis NCDO 2118 was recently reported to alleviate colitis symptoms via its anti-inflammatory and immunomodulatory activities, which are exerted by exported proteins that are not produced by L. lactis subsp. lactis IL1403. Here, we used in vitro and in silico approaches to characterize the genomic structure, the safety aspects, and the immunomodulatory activity of this strain. Through comparative genomics, we identified genomic islands, phage regions, bile salt and acid stress resistance genes, bacteriocins, adhesion-related and antibiotic resistance genes, and genes encoding proteins that are putatively secreted, expressed in vitro and absent from IL1403. The high degree of similarity between all Lactococcus suggests that the Symbiotic Islands commonly shared by both NCDO 2118 and KF147 may be responsible for their close relationship and their adaptation to plants. The predicted bacteriocins may play an important role against the invasion of competing strains. The genes related to the acid and bile salt stresses may play important roles in gastrointestinal tract survival, whereas the adhesion proteins are important for persistence in the gut, culminating in the competitive exclusion of other bacteria. Finally, the five secreted and expressed proteins may be important targets for studies of new anti-inflammatory and immunomodulatory proteins. Altogether, the analyses performed here highlight the potential use of this strain as a target for the future development of probiotic foods.\n\nAnalyses of the probiotic property and stress resistance-related genes of Lactococcus lactis subsp. lactis NCDO 2118 through comparative genomics and in vitro assays.", "token_count": 420, "char_count": 1701, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5779, "quality_score": 0.7889, "entities": { "genes": [ "IL1403", "KF147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:13.878149", "source": { "split": "train_shard_00000", "doc_id": 3726 }, "chunk_id": "train_shard_00000_3726_0", "global_id": 4134 }, { "text": "Over the past decade, there has been a rising interest in Achromobacter sp., an emerging opportunistic pathogen responsible for nosocomial and cystic fibrosis lung infections. Species of this genus are ubiquitous in the environment, can outcompete resident microbiota, and are resistant to commonly used disinfectants as well as antibiotics. Nevertheless, the Achromobacter genus suffers from difficulties in diagnosis, unresolved taxonomy and limited understanding of how it adapts to the cystic fibrosis lung, not to mention other host environments. The goals of this first genus-wide comparative genomics study were to clarify the taxonomy of this genus and identify genomic features associated with pathogenicity and host adaptation. This was done with a widely applicable approach based on pan-genome analysis. First, using all publicly available genomes, a combination of phylogenetic analysis based on 1,780 conserved genes with average nucleotide identity and accessory genome composition allowed the identification of a largely clinical lineage composed of Achromobacter xylosoxidans, Achromobacter insuavis, Achromobacter dolens, and Achromobacter ruhlandii. Within this lineage, we identified 35 positively selected genes involved in metabolism, regulation and efflux-mediated antibiotic resistance. Second, resistome analysis showed that this clinical lineage carried additional antibiotic resistance genes compared with other isolates. Finally, we identified putative mobile elements that contribute 53% of the genus's resistome and support horizontal gene transfer between Achromobacter and other ecologically similar genera. This study provides strong phylogenetic and pan-genomic bases to motivate further research on Achromobacter, and contributes to the understanding of opportunistic pathogen evolution.\n\nA Pan-Genomic Approach to Understand the Basis of Host Adaptation in Achromobacter.", "token_count": 428, "char_count": 1907, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:14.501999", "source": { "split": "train_shard_00000", "doc_id": 3727 }, "chunk_id": "train_shard_00000_3727_0", "global_id": 4135 }, { "text": "Drug-induced liver injury (DILI) is a severe drug adverse response, which cannot always be reliably predicted in preclinical or clinical studies. Lack of observation of DILI during preclinical and clinical drug development has led to DILI being a leading cause of drug withdrawal from the market. As DILI is potentially fatal, pharmaceutical companies have been developing in vitro tools to screen for potential liver injury. Screens for physicochemical properties, mitochondrial function, and transport protein inhibition have all been employed to varying degrees of success. In vitro inhibition of the bile salt export pump (BSEP) has become a major risk factor for in vivo DILI predictions, yet discrepancies exist in which methods to use and the extent to which BSEP inhibition predicts clinical DILI. The presented work focuses on optimizing DILI predictions by comparing BSEP inhibition via the membrane vesicle assay and the hepatocyte-based BSEPcyte assay, as well as dual and triple liabilities. BSEP transport inhibition of taurcholic acids and glycocholic acids were similar for up to 29 drugs tested, in both the vesicle and hepatocyte-based assays. Positive and negative DILI predictions were optimized at a 50-µM cutoff value for 50 drugs using both NIH Livertox and PharmaPendium databases. Additionally, dual inhibition of BSEP and other efflux transporters (multidrug resistance-associated protein [MRP]2, MRP3, or MRP4) provided no observable predictive benefit compared with BSEP inhibition alone. Eighty-five percent of drugs with high molecular weight (>600 Da), high cLogP (>3), or a daily dose >100 mg and BSEP inhibition were associated with DILI. Triple liability of BSEP inhibition, high molecular weight, and high cLogP attained a 100% positive prediction rate.\n\nIn Vitro Drug-Induced Liver Injury Prediction: Criteria Optimization of Efflux Transporter IC50 and Physicochemical Properties.", "token_count": 507, "char_count": 1917, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.805, "entities": { "genes": [ "MRP4", "MRP3", "IC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:15.155416", "source": { "split": "train_shard_00000", "doc_id": 3728 }, "chunk_id": "train_shard_00000_3728_0", "global_id": 4136 }, { "text": "Recurring epidemics of kiwifruit (Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae (Psa). In order to strengthen understanding of population structure, phylogeography, and evolutionary dynamics, we isolated Pseudomonas from cultivated and wild kiwifruit across six provinces in China. Based on the analysis of 80 sequenced Psa genomes, we show that China is the origin of the pandemic lineage but that strain diversity in China is confined to just a single clade. In contrast, Korea and Japan harbor strains from multiple clades. Distinct independent transmission events marked introduction of the pandemic lineage into New Zealand, Chile, Europe, Korea, and Japan. Despite high similarity within the core genome and minimal impact of within-clade recombination, we observed extensive variation even within the single clade from which the global pandemic arose.\n\nOrigin and Evolution of the Kiwifruit Canker Pandemic.", "token_count": 229, "char_count": 958, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7194, "quality_score": 0.8597, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:15.625458", "source": { "split": "train_shard_00000", "doc_id": 3729 }, "chunk_id": "train_shard_00000_3729_0", "global_id": 4137 }, { "text": "The conjugative virulence plasmid is a key component of the Rhodococcus equi accessory genome essential for pathogenesis. Three host-associated virulence plasmid types have been identified the equine pVAPA and porcine pVAPB circular variants, and the linear pVAPN found in bovine (ruminant) isolates. We recently characterized the R. equi pangenome (Anastasi E, et al. 2016. Pangenome and phylogenomic analysis of the pathogenic actinobacterium Rhodococcus equi. Genome Biol Evol. 8:3140-3148.) and we report here the comparative analysis of the virulence plasmid genomes. Plasmids within each host-associated type were highly similar despite their diverse origins. Variation was accounted for by scattered single nucleotide polymorphisms and short nucleotide indels, while larger indels-mostly in the plasticity region near the vap pathogencity island (PAI)-defined plasmid genomic subtypes. Only one of the plasmids analyzed, of pVAPN type, was exceptionally divergent due to accumulation of indels in the housekeeping backbone. Each host-associated plasmid type carried a unique PAI differing in vap gene complement, suggesting animal host-specific evolution of the vap multigene family. Complete conservation of the vap PAI was observed within each host-associated plasmid type. Both diversity of host-associated plasmid types and clonality of specific chromosomal-plasmid genomic type combinations were observed within the same R. equi phylogenomic subclade. Our data indicate that the overall strong conservation of the R. equi host-associated virulence plasmids is the combined result of host-driven selection, lateral transfer between strains, and geographical spread due to international livestock exchanges.\n\nComparative Genomics of Rhodococcus equi Virulence Plasmids Indicates Host-Driven Evolution of the vap Pathogenicity Island.", "token_count": 489, "char_count": 1843, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6024, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:16.273289", "source": { "split": "train_shard_00000", "doc_id": 3730 }, "chunk_id": "train_shard_00000_3730_0", "global_id": 4138 }, { "text": "Snake gallbladder, a traditional Chinese medicine, has been believed in various Asian countries to improve visual acuity and alleviate rheumatism. Bile acids, a major component of the gallbladder, are toxic to the liver and kidney in humans and animals due to its detergent effects, while also exhibiting therapeutic effects due to an increase in the gallbladder contractions of muscle strips in patients with cholesterol gallstones. Secretion of bile acids in human and mammals depends on the bile salt export pump (BSEP), a liver-specific adenosine triphosphate (ATP)-binding cassette transporter encoded by ABCB11. However, the presence of BSEP in snakes has not been thoroughly explored. Here we confirm the existence of BSEP and its coding DNA sequence in snakes on both the proteomic and genetic level. This work provides information on the snake ABCB11 sequence and helps further potential genetic manipulation to affect bile salt metabolism. Our study provides the foundation for research on bile acid production from snakes by using modern genetic and proteomic methodologies.\n\nGenetic and Proteomic characterization of Bile Salt Export Pump (BSEP) in Snake Liver.", "token_count": 280, "char_count": 1173, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6384, "quality_score": 0.8192, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:16.818897", "source": { "split": "train_shard_00000", "doc_id": 3731 }, "chunk_id": "train_shard_00000_3731_0", "global_id": 4139 }, { "text": "Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 were recently isolated from a traditional French cheese, Tomme d'Orchies, and characterized here for their advantages using a different application perspective. First, we established their anti-Salmonella activity and downregulation of the virulence sopD gene of Salmonella enterica subsp. enterica serovar Typhimurium, mainly in the presence of K. marxianus S-2-05. In addition to their antagonism, these non-Saccharomyces yeasts were able to survive under conditions mimicking the gastrointestinal environment and to form biofilms on an abiotic device such as polystyrene. These strains also displayed highly hydrophilic cell wall surfaces properties and capacity for adhesion to intestinal Caco-2 cells, thus enhancing their potential as probiotic strains.\n\nAnti-Salmonella activity and probiotic trends of Kluyveromyces marxianus S-2-05 and Kluyveromyces lactis S-3-05 isolated from a French cheese, Tomme d'Orchies.", "token_count": 274, "char_count": 983, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:17.366710", "source": { "split": "train_shard_00000", "doc_id": 3732 }, "chunk_id": "train_shard_00000_3732_0", "global_id": 4140 }, { "text": "The application of high-potential thermotolerant yeasts is a key factor for successful ethanol production at high temperatures. Two hundred and thirty-four yeast isolates from Greater Mekong Subregion (GMS) countries, i.e., Thailand, The Lao People's Democratic Republic (Lao PDR) and Vietnam were obtained. Five thermotolerant yeasts, designated Saccharomyces cerevisiae KKU-VN8, KKU-VN20, and KKU-VN27, Pichia kudriavzevii KKU-TH33 and P. kudriavzevii KKU-TH43, demonstrated high temperature and ethanol tolerance levels up to 45°C and 13% (v/v), respectively. All five strains produced higher ethanol concentrations and exhibited greater productivities and yields than the industrial strain S. cerevisiae TISTR5606 during high-temperature fermentation at 40°C and 43°C. S. cerevisiae KKU-VN8 demonstrated the best performance for ethanol production from glucose at 37°C with an ethanol concentration of 72.69g/L, a productivity of 1.59g/L/h and a theoretical ethanol yield of 86.27%. The optimal conditions for ethanol production of S. cerevisiae KKU-VN8 from sweet sorghum juice (SSJ) at 40°C were achieved using the Box-Behnken experimental design (BBD). The maximal ethanol concentration obtained during fermentation was 89.32g/L, with a productivity of 2.48g/L/h and a theoretical ethanol yield of 96.32%. Thus, the newly isolated thermotolerant S. cerevisiae KKU-VN8 exhibits a great potential for commercial-scale ethanol production in the future.\n\nHigh-temperature ethanol production using thermotolerant yeast newly isolated from Greater Mekong Subregion.", "token_count": 490, "char_count": 1566, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5913, "quality_score": 0.7957, "entities": { "genes": [ "TH43", "VN8", "TISTR5606", "VN27", "VN20", "TH33" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:18.013145", "source": { "split": "train_shard_00000", "doc_id": 3733 }, "chunk_id": "train_shard_00000_3733_0", "global_id": 4141 }, { "text": "Many prokaryote species are known to have fluid genomes, with different strains varying markedly in accessory gene content through the combined action of gene loss, gene gain via lateral transfer, as well as gene duplication. However, the evolutionary forces determining genome fluidity are not yet well understood. We here for the first time systematically analyse the degree to which this distinctive genomic feature differs between bacterial species. We find that genome fluidity is positively correlated with synonymous nucleotide diversity of the core genome, a measure of effective population size N\n\nProkaryote genome fluidity is dependent on effective population size.", "token_count": 140, "char_count": 676, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7677, "quality_score": 0.8838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:18.445357", "source": { "split": "train_shard_00000", "doc_id": 3734 }, "chunk_id": "train_shard_00000_3734_0", "global_id": 4142 }, { "text": "Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production.\n\nComparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.", "token_count": 80, "char_count": 345, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8302, "quality_score": 0.9151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:18.812229", "source": { "split": "train_shard_00000", "doc_id": 3735 }, "chunk_id": "train_shard_00000_3735_0", "global_id": 4143 }, { "text": "The\n\nAnalysis of Shigella flexneri Resistance, Biofilm Formation, and Transcriptional Profile in Response to Bile Salts.", "token_count": 32, "char_count": 120, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:19.179934", "source": { "split": "train_shard_00000", "doc_id": 3736 }, "chunk_id": "train_shard_00000_3736_0", "global_id": 4144 }, { "text": "Inulins are polysaccharides that belong to an important class of carbohydrates known as fructans and are used by many plants as a means of storing energy. Inulins contain 20 to several thousand fructose units joined by β-2,1 glycosidic bonds, typically with a terminal glucose unit. Plants with high concentrations of inulin include: agave, asparagus, coffee, chicory, dahlia, dandelion, garlic, globe artichoke, Jerusalem artichoke, jicama, onion, wild yam, and yacón. To utilize inulin as its carbon and energy source directly, a microorganism requires an extracellular inulinase to hydrolyze the glycosidic bonds to release fermentable monosaccharides. Inulinase is produced by many microorganisms, including species of Aspergillus, Kluyveromyces, Penicillium, and Pseudomonas. We review various inulinase-producing microorganisms and inulin feedstocks with potential for industrial application as well as biotechnological efforts underway to develop sustainable practices for the disposal of residues from processing inulin-containing crops. A multi-stage biorefinery concept is proposed to convert cellulosic and inulin-containing waste produced at crop processing operations to valuable biofuels and bioproducts using Kluyveromyces marxianus, Yarrowia lipolytica, Rhodotorula glutinis, and Saccharomyces cerevisiae as well as thermochemical treatments.\n\nUtilization of inulin-containing waste in industrial fermentations to produce biofuels and bio-based chemicals.", "token_count": 389, "char_count": 1471, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:19.795986", "source": { "split": "train_shard_00000", "doc_id": 3737 }, "chunk_id": "train_shard_00000_3737_0", "global_id": 4145 }, { "text": "Idiosyncratic drug-induced liver injury (IDILI) is a rare but potentially severe adverse drug reaction that should be considered in patients who develop laboratory criteria for liver injury secondary to the administration of a potentially hepatotoxic drug. Although currently used liver parameters are sensitive in detecting DILI, they are neither specific nor able to predict the patient's subsequent clinical course. Genetic risk assessment is useful mainly due to its high negative predictive value, with several human leucocyte antigen alleles being associated with DILI. New emerging biomarkers which could be useful in assessing DILI include total keratin18 (K18) and caspase-cleaved keratin18 (ccK18), macrophage colony-stimulating factor receptor 1, high mobility group box 1 and microRNA-122. From the numerous in vitro test systems that are available, monocyte-derived hepatocytes generated from patients with DILI show promise in identifying the DILI-causing agent from among a panel of coprescribed drugs. Several computer-based algorithms are available that rely on cumulative scores of known risk factors such as the administered dose or potential liabilities such as mitochondrial toxicity, inhibition of the bile salt export pump or the formation of reactive metabolites. A novel DILI cluster score is being developed which predicts DILI from multiple complimentary cluster and classification models using absorption-distribution-metabolism-elimination-related as well as physicochemical properties, diverse substructural descriptors and known structural liabilities. The provision of more advanced scientific and regulatory guidance for liver safety assessment will depend on validating the new diagnostic markers in the ongoing DILI registries, biobanks and public-private partnerships.\n\nDrug-induced liver injury: recent advances in diagnosis and risk assessment.", "token_count": 419, "char_count": 1882, "word_count": 254, "semantic_coherence": 1, "information_density": 0.7047, "quality_score": 0.8524, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:20.416725", "source": { "split": "train_shard_00000", "doc_id": 3738 }, "chunk_id": "train_shard_00000_3738_0", "global_id": 4146 }, { "text": "In yeast, the hexose assimilation is started at hexose phosphorylation. However, in Kluyveromyces marxianus, the hexokinase (HXK) and glucokinase (GLK) genes were not identified by experiments. Meanwhile, the glucose-free fructose product requires more cost-efficient method. In this study, the KmHXK1 and KmGLK1 genes were functionally identified through gene disruption, over-expression and recombinant enzymes characterization. Both glucose and fructose assimilation ability decreased significantly in KmHXK1 disrupted strain YLM001, however, this ability was not changed obviously in KmGLK1 disrupted strain YLM002. When over-expressing KmGLK1 in YLM001, only the glucose assimilation ability was recovered in obtained strain (YLM005). The kinetic constant analysis of recombinant enzymes also proved that KmHXK1 could phosphorylate glucose (Vmax 553.01 U/mg, Km 0.83 mM) and fructose (Vmax 609.82 U/mg, Km 0.52 mM), and KmGLK1 only phosphorylate glucose with a Vmax of 0.73 U/mg and a Km 4.09 mM. A thermo-tolerant strain YGR003 which produced glucose-free fructose from Jerusalem artichoke tuber in one step was constructed based on the obtained information. The highest production and fastest productivity were 234.44 g/L and 10.26 g/L/h, respectively, which were several folds of the results in previous reports.\n\nIdentification of hexose kinase genes in Kluyveromyces marxianus and thermo-tolerant one step producing glucose-free fructose strain construction.", "token_count": 484, "char_count": 1468, "word_count": 201, "semantic_coherence": 1, "information_density": 0.592, "quality_score": 0.796, "entities": { "genes": [ "YLM001", "YLM005", "YGR003", "YLM002" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:21.077922", "source": { "split": "train_shard_00000", "doc_id": 3739 }, "chunk_id": "train_shard_00000_3739_0", "global_id": 4147 }, { "text": "At present, the most used methods for\n\nDefining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of", "token_count": 42, "char_count": 152, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:21.458623", "source": { "split": "train_shard_00000", "doc_id": 3740 }, "chunk_id": "train_shard_00000_3740_0", "global_id": 4148 }, { "text": "Bile salts have potent detergent properties and damaging effects on cell membranes, leading to liver injury. However, the molecular mechanisms for the protection of hepatocytes against bile salts are not fully understood. In this study, we demonstrated that the cytotoxicity of nine human major bile salts to HepG2 cells and primary human hepatocytes was prevented by phosphatidylcholine (PC). In contrast, cholesterol had no direct cytotoxic effects but suppressed the cytoprotective effects of PC. PC reduced the cell-association of bile salt, which was reversed by cholesterol. Light scattering measurements and gel filtration chromatography revealed that cholesterol within bile salt/PC dispersions decreased mixed micelles but increased vesicles, bile salt simple micelles and monomers. These results suggest that cholesterol attenuates the cytoprotective effects of PC against bile salts by facilitating the formation of bile salt simple micelles and monomers. Therefore, biliary PC and cholesterol may play different roles in the pathogenesis of bile salt-induced liver injury.\n\nCholesterol attenuates cytoprotective effects of phosphatidylcholine against bile salts.", "token_count": 290, "char_count": 1174, "word_count": 162, "semantic_coherence": 1, "information_density": 0.5988, "quality_score": 0.7994, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:22.063132", "source": { "split": "train_shard_00000", "doc_id": 3741 }, "chunk_id": "train_shard_00000_3741_0", "global_id": 4149 }, { "text": "The aim of this study was to select aerobic spore-formers for animal feed based on their in vitro probiotic potential, including their enzyme-producing ability and safety assessment. Seven isolates out of 187 spore-forming bacteria were selected for their ability to produce cellulase (89.21-1668.32 U/ml), xylanase (1399.68-4351.10 U/ml), and phytase (2.72-28.70 U/ml). Among seven isolates, five had activities towards a broad range of p-nitrophenyl esters with acyl chain lengths from C2 to C12. The probiotic properties of all selected isolates varied with respect to their acid and bile salt tolerance under simulated gastrointestinal tract (GIT) conditions, and their adherence ability to human intestinal cell lines (Caco-2 and HT-29). The safety assessment revealed that the isolate CM40 was not cytotoxic to Caco-2 and HT-29, did not exhibit hemolytic activity, carried no enterotoxin or emetic toxin genes, and was susceptible to ten antibiotics, including six key antibiotics (chloramphenicol, erythromycin, gentamicin, tetracycline, streptomycin, and kanamycin) as recommended by the European Food Safety Authority (EFSA). Co-incubation of isolate CM40 with enteric bacteria (Salmonella Typhi, Salmonella Enteritidis 1781, and Escherichia coli) demonstrated that CM40 significantly decreased the number of pathogens (about 30-48%) adhering to Caco-2 and HT-29 (P < 0.05). Analysis of gene encoding 16S rRNA, gyrase A (gyrA) and the cheA histidine kinase revealed that CM40 belongs to Bacillus subtilis. On the basis of probiotic properties and basic safety aspects, the B", "token_count": 483, "char_count": 1583, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7004, "quality_score": 0.8502, "entities": { "genes": [ "CM40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:22.706943", "source": { "split": "train_shard_00000", "doc_id": 3742 }, "chunk_id": "train_shard_00000_3742_0", "global_id": 4150 }, { "text": "subtilis strain CM40 was found to possess desirable in vitro probiotic properties, and may be a potential candidate for supplementation of animal feed.\n\nIn vitro evaluation of candidate Bacillus spp. for animal feed.", "token_count": 53, "char_count": 216, "word_count": 33, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [ "CM40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:23.063698", "source": { "split": "train_shard_00000", "doc_id": 3742 }, "chunk_id": "train_shard_00000_3742_1", "global_id": 4151 }, { "text": "Defining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.", "token_count": 33, "char_count": 112, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:23.440520", "source": { "split": "train_shard_00000", "doc_id": 3743 }, "chunk_id": "train_shard_00000_3743_0", "global_id": 4152 }, { "text": "The pangenome for the genus Clostridium sensu stricto, which was obtained using highly curated and annotated genomes from 16 species is presented; some of these cause disease, while others are used for the production of added-value chemicals. Multilocus sequencing analysis revealed that species of this genus group into at least two clades that include non-pathogenic and pathogenic strains, suggesting that pathogenicity is dispersed across the phylogenetic tree. The core genome of the genus includes 546 protein families, which mainly comprise those involved in protein translation and DNA repair. The GS-GOGAT may represent the central pathway for generating organic nitrogen from inorganic nitrogen sources. Glycerol and glucose metabolism genes are well represented in the core genome together with a set of energy conservation systems. A metabolic network comprising proteins/enzymes, RNAs and metabolites, whose topological structure is a non-random and scale-free network with hierarchically structured modules was built. These modules shed light on the interactions between RNAs, proteins and metabolites, revealing biological features of transcription and translation, cell wall biosynthesis, C1 metabolism and N metabolism. Network analysis identified four nodes that function as hubs and bottlenecks, namely, coenzyme A, HPr kinases, S-adenosylmethionine and the ribonuclease P-protein, suggesting pivotal roles for them in Clostridium.\n\nThe pangenome of the genus Clostridium.", "token_count": 356, "char_count": 1491, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:24.013185", "source": { "split": "train_shard_00000", "doc_id": 3744 }, "chunk_id": "train_shard_00000_3744_0", "global_id": 4153 }, { "text": "Gene delivery to skeletal muscle is a promising strategy for the treatment of muscle disorders and for the systemic secretion of therapeutic proteins. In addition, muscle is an attractive target tissue because it is easily accessible. However, very few synthetic vectors proved capable of surpassing naked DNA mediated muscle gene transfer. In fact, only neutral copolymers, in particular poloxamers, demonstrated capacities to increase transgene expression in skeletal muscles. Here, we studied in vitro and in vivo behaviour of different bile salts. We report that sodium deoxycholate (DOC) and derivatives thereof increase after intramuscular injection by more than 100-fold the levels of the reporter gene luciferase compared to naked DNA. Using a LacZ expression cassette, we found that more than 20% of the muscle fibers expressed the reporter gene. Prolonged expression of a secreted reporter gene derived from a natural murine alkaline phosphatase enzyme could be documented. Altogether, our results demonstrate that bile salts belong to the most efficient chemicals identified so far for skeletal muscle gene transfer. Importantly, since these compounds are naturally found in the body, there is no risk of immune response against them and in addition several bile salts are already used in human medicine. Bile salt mediated muscle gene transfer may thus have broad applications in gene therapy.\n\nThe absorption enhancer sodium deoxycholate promotes high gene transfer in skeletal muscles.", "token_count": 329, "char_count": 1499, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:24.580558", "source": { "split": "train_shard_00000", "doc_id": 3745 }, "chunk_id": "train_shard_00000_3745_0", "global_id": 4154 }, { "text": "Streptococcus agalactiae or Group B streptococci (GBS) are a common cause of serious diseases of newborns and adults. GBS pathogenicity largely depends on genes located on the accessory genome including several pathogenicity islands (PAI). The present paper is focused on the structure and molecular epidemiological analysis of one of the GBS pathogenicity islands-the pathogenicity island PAI XII (Glaser et al. Mol Microbiol 45(6):1499-1513, 2002). This PAI was found to be composed of three different mobile genetic elements: a composite transposon (PAI-C), a genomic islet (PAI-B), and a pathogenicity island associated with gene sspB1 (PAI-A). PAI-A in GBS has a homolog--PAI-A1 with similar, but a different genetic constellation. PCR-based analysis of GBS collections from different countries revealed that a strains lineage with PAI-A is less common than PAI-A1 and was determined to be present only among the strains obtained from Russia. Our results suggest that PAI-A and PAI-A1 have the same progenitor, which evolved independently and appeared in the GBS genome as separate genetic events. Results of this study reflect specific geographical distribution of the GBS strains with the mobile genetic element under study.\n\nClinical strains of Streptococcus agalactiae carry two different variants of pathogenicity island XII.", "token_count": 349, "char_count": 1335, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6224, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:25.155720", "source": { "split": "train_shard_00000", "doc_id": 3746 }, "chunk_id": "train_shard_00000_3746_0", "global_id": 4155 }, { "text": "In an era of ever-increasing energy demands, a promising technology is being developed: the use of oleaginous microorganisms such as Yarrowia lipolytica to convert waste materials into biofuels. Here, we constructed two Y. lipolytica strains that displayed both increased lipid accumulation and more efficient use of biomass-derived sugars, including glucose, fructose, galactose and inulin. The first strain, Y. lipolytica YLZ150, was derived from the French wild-type strain W29. It had inhibited triacylglycerol mobilization (∆tgl4) and β-oxidation (∆pox1-6), and it overexpressed GPD1, DGA2, HXK1, the native Leloir pathway, SUC2 from Saccharomyces cerevisiae and INU1 from Kluyveromyces marxianus. The second strain, Y. lipolytica Y4779, was derived from the Polish A-101 strain. It had inhibited β-oxidation (∆mfe2) and overexpressed GPD1, DGA1, HXK1, YHT3, SUC2 and INU1. In the first experiment, strain YLZ150 was batch-cultured in media containing different hexoses; the highest values for lipid concentration and yield of lipids from the substrate were obtained using fructose (20.3 g dm\n\nTransforming sugars into fat - lipid biosynthesis using different sugars in Yarrowia lipolytica.", "token_count": 373, "char_count": 1195, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [ "YHT3", "YLZ150", "HXK1", "SUC2", "DGA1", "GPD1", "INU1", "DGA2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:25.732647", "source": { "split": "train_shard_00000", "doc_id": 3747 }, "chunk_id": "train_shard_00000_3747_0", "global_id": 4156 }, { "text": "The apical sodium--dependent bile acid transporter (ASBT) is the main transporter to promote re-absorption of bile acids from the intestinal tract into the enterohepatic circulation. Inhibition of ASBT could increase the excretion of bile acids, thus increasing bile acid synthesis and consequently cholesterol consumption. Therefore, ASBT is an attractive target for developing new cholesterol-lowering drugs. In this report, a series of 1-(2,4-bifluorophenyl)-7-dialkylamino-1,8-naphthyridine-3-carboxamides were designed as inhibitors of ASBT. Most of them demonstrated potency against ASBT transport of bile acids. In particular, compound\n\nA novel class of apical sodium--dependent bile salt transporter inhibitors: 1-(2,4-bifluorophenyl)-7-dialkylamino-1,8-naphthyridine-3-carboxamides.", "token_count": 239, "char_count": 791, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7204, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:26.203859", "source": { "split": "train_shard_00000", "doc_id": 3748 }, "chunk_id": "train_shard_00000_3748_0", "global_id": 4157 }, { "text": "European researchers have underscored associations between single nucleotide polymorphism (SNP) rs2287622 of the hepatobiliary bile salt export pump (BSEP) gene and the risk of hepatitis C virus (HCV) infection. The distributions of SNP rs2287622 are racially specific. This study was aimed to preliminarily investigate the distribution of BSEP gene SNP rs2287622 in the Han patients with chronic HCV-infection (CHC) in Hunan, China.\n\nA preliminary investigation on single nucleotide polymorphism rs2287622 of bile salt export pump gene in patients with chronic hepatitis C virus infection in Hunan, China.", "token_count": 172, "char_count": 606, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:26.647636", "source": { "split": "train_shard_00000", "doc_id": 3749 }, "chunk_id": "train_shard_00000_3749_0", "global_id": 4158 }, { "text": "Some scholars caution that long-term ad libitum feeding with probiotic fermented food poses potential health risks to baby animals. We conducted a feeding experiment to investigate the influence of ad libitum feeding of pre-and post-weaned piglets with a Bacillus subtilis fermented diet on the gut microbiome, gut metabolomic profiles, bile acid metabolism, proinflammatory cytokines and faecal consistency. Compared with piglets fed a Bacillus subtilis-supplemented pellet diet, piglets fed the Bacillus subtilis fermented liquid diet had lower intestinal bacterial diversity (P > 0.05), higher intestinal fungal diversity (P > 0.05), more Firmicutes (P > 0.05), fewer Bacteroidetes, Actinobacteria and Proteobacteria (P > 0.05), higher concentrations of 3-hydroxypropionic acid (P < 0.05), orotic acid (P < 0.05), interleukin-6 (P < 0.01), lactic acid (P < 0.01), deoxycholic acid (P > 0.05) and lithocholic acid (P < 0.01) and a higher incidence of diarrhoea (P > 0.05). The data show that ad libitum feeding of piglets with a Bacillus subtilis fermented liquid diet during the suckling and early post-weaning periods promotes the growth of lactic acid bacteria, bile salt hydrolase-active bacteria and 7a-dehydroxylase-active bacteria in the intestinal lumen; disturbs the normal production of lactic acid, orotic acid and unconjugated bile acids; and increases circulating interleukin-6 levels and diarrhoea incidence.", "token_count": 499, "char_count": 1424, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5243, "quality_score": 0.7621, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:27.298038", "source": { "split": "train_shard_00000", "doc_id": 3750 }, "chunk_id": "train_shard_00000_3750_0", "global_id": 4159 }, { "text": "Influence of ad Libitum Feeding of Piglets With Bacillus Subtilis Fermented Liquid Feed on Gut Flora, Luminal Contents and Health.", "token_count": 44, "char_count": 130, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:27.655285", "source": { "split": "train_shard_00000", "doc_id": 3750 }, "chunk_id": "train_shard_00000_3750_1", "global_id": 4160 }, { "text": "Increasing evidence suggests that a single individual is insufficient to capture the genetic diversity within a species due to gene presence absence variation. In order to understand the extent to which genomic variation occurs in a species, the construction of its pangenome is necessary. The pangenome represents the complete set of genes of a species; it is composed of core genes, which are present in all individuals, and variable genes, which are present only in some individuals. Aside from variations at the gene level, single nucleotide polymorphisms (SNPs) are also an important form of genetic variation. The advent of next-generation sequencing (NGS) coupled with the heritability of SNPs make them ideal markers for genetic analysis of human, animal, and microbial data. SNPs have also been extensively used in crop genetics for association mapping, quantitative trait loci (QTL) analysis, analysis of genetic diversity, and phylogenetic analysis. This review focuses on the use of pangenomes for SNP discovery. It highlights the advantages of using a pangenome rather than a single reference for this purpose. This review also demonstrates how extra information not captured in a single reference alone can be used to provide additional support for linking genotypic data to phenotypic data.\n\nSNP Discovery Using a Pangenome: Has the Single Reference Approach Become Obsolete?", "token_count": 298, "char_count": 1390, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:28.564990", "source": { "split": "train_shard_00000", "doc_id": 3751 }, "chunk_id": "train_shard_00000_3751_0", "global_id": 4161 }, { "text": "High cholesterol level in serum is a major factor of influence for coronary heart disease. The cholesterol-lowering ability of lactic acid bacteria (LAB) without side effects makes them more and more attractive. Seventy-nine strains of LAB isolated from fermented food were screened in vitro for their ability to assimilate cholesterol. Then, ten strains which exhibited higher ability of cholesterol assimilation were investigated with the characteristics of acidic resistance, bile salt tolerance, and cell adhesion. According to the results, the best strain LP96 was picked out, and used to evaluate its effects on the high-cholesterol diet-fed rats. The results demonstrated that the levels of serum triglyceride (TG), total cholesterol (TC), low-density lipoprotein cholesterol, and liver TC and TG were reduced significantly in the groups that received the strain LP96 solution compared with the model group, and that the serum high-density lipoprotein cholesterol levels were increased without any significant difference. Furthermore, LP96 also showed good antioxidative activity and improvement of intestinal microbial balance in the rats. Thus, LP96 may be a promising probiotics with potential cholesterol-lowering ability.\n\nSelection of Cholesterol-Lowering Lactic Acid Bacteria and its Effects on Rats Fed with High-Cholesterol Diet.", "token_count": 333, "char_count": 1345, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6474, "quality_score": 0.8237, "entities": { "genes": [ "LP96" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:29.125695", "source": { "split": "train_shard_00000", "doc_id": 3752 }, "chunk_id": "train_shard_00000_3752_0", "global_id": 4162 }, { "text": "There is strong evidence indicating that gut microbiota have the potential to modify, or be modified by the drugs and nutritional interventions that we rely upon. This study aims to characterize the compositional and functional effects of several nutritional, neutraceutical, and pharmaceutical cardiovascular disease interventions on the gut microbiome, through metagenomic and metabolomic approaches. Apolipoprotein-E-deficient mice were fed for 24 weeks either high-fat/cholesterol diet alone (control, HFC) or high-fat/cholesterol in conjunction with one of three dietary interventions, as follows: plant sterol ester (PSE), oat β-glucan (OBG) and bile salt hydrolase-active Lactobacillus reuteri APC 2587 (BSH), or the drug atorvastatin (STAT). The gut microbiome composition was then investigated, in addition to the host fecal and serum metabolome.\n\nMicrobiome and metabolome modifying effects of several cardiovascular disease interventions in apo-E", "token_count": 258, "char_count": 957, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7578, "quality_score": 0.8789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:29.671212", "source": { "split": "train_shard_00000", "doc_id": 3753 }, "chunk_id": "train_shard_00000_3753_0", "global_id": 4163 }, { "text": "During the aging of yeast culture, Kluyveromyces marxianus undergoes a number of changes in physiology and these changes play a significant role during fermentation. Aged stationary phase cells were found to contain more reactive oxygen species. Additionally, the level of oxidant is counteracted by the antioxidant defense system of the cells. Comparison of 3-day-old culture of K. marxianus with 45-day stationary phase culture represents an increased level of ROS inside the cells. Moreover, a decrease in glutathione content was observed over the set of the incubation period. The increased level of superoxide dismutase (SOD) and catalase also revealed that there is oxidative stress during the long period incubation of the stationary phase cells of K. marxianus. The actual phenomenon of aging in dairy yeast K. marxianus is a complex process, but the present study signifies that role of antioxidant defense system during aging in stationary phase cells of K. marxianus.\n\nComparative Analysis of Oxidative Stress During Aging of Kluyveromyces marxianus in Synthetic and Whey Media.", "token_count": 273, "char_count": 1089, "word_count": 165, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:30.225135", "source": { "split": "train_shard_00000", "doc_id": 3754 }, "chunk_id": "train_shard_00000_3754_0", "global_id": 4164 }, { "text": "Few tissue markers are currently available to pathologists in the study of hepatocellular tumors. These markers should be used carefully taking into consideration not only morphology but also, and sometimes even more important, the clinical setting where the lesion to be diagnosed had developed. Glypican-3, heat shock protein 70, and glutamine synthetase (GS) are markers currently used, as a single panel, to discriminate the nature of a <2 cm hepatocellular lesion lacking radiological features of hepatocellular carcinoma (HCC) detected in a cirrhotic patient under surveillance. Their use, which can be improved by clathrin heavy chain, is mostly requested on liver biopsy. Hepatocyte paraffin 1, arginase-1, polyclonal carcinoembryonic antigen, CD10, and bile salt export pump are tissue markers used to confirm, at histology, the diagnosis of HCC made by imaging before enrollment for phase III studies on novel anti-HCC drugs. In this setting, pathologists are usually requested a conclusive diagnosis on a liver biopsy of a poorly differentiated, necrotic, enriched in stem-phenotype, carcinoma. Liver fatty acid-binding protein, serum amyloid A, C-reactive protein, prostaglandin D2 synthetase, GS, and β-catenin can be used either on biopsy or surgical specimen to classify hepatocellular adenoma into hepatocyte nuclear factor (HNF-1α) inactivated (steatotic), inflammatory, with dysregulation of sonic hedgehog and prostaglandin pathways, β-catenin mutated, and unclassified.\n\nTissue Biomarkers in Hepatocellular Tumors: Which, When, and How.", "token_count": 435, "char_count": 1556, "word_count": 219, "semantic_coherence": 1, "information_density": 0.7123, "quality_score": 0.8562, "entities": { "genes": [ "CD10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:30.854082", "source": { "split": "train_shard_00000", "doc_id": 3755 }, "chunk_id": "train_shard_00000_3755_0", "global_id": 4165 }, { "text": "Whey is the main byproduct of the cheese industry. While the composition is variable, it retains up to 55% of milk nutrients. The beneficial features of whey indicates a promising source of new potentially probiotic strains for the development of food additives destined for animal production. The aim of this study was to identify Kluyveromyces spp. isolated from whey, to study some probiotic properties and to select the best strain to be encapsulated using derivatised chitosan. Kluyveromyces marxianus strains (VM003, VM004 and VM005) were isolated from whey and identified by phenotypic and molecular techniques. These three yeast strains were able to survive under gastrointestinal conditions. Moreover, they exhibited weak auto-aggregation and co-aggregation with pathogenic bacteria (Salmonella sp., Serratia sp., Escherichia coli and Salmonella typhimurium). In general the K. marxianus strains had a strong antimicrobial activity against pathogenic bacteria. The potential probiotic K. marxianus VM004 strain was selected for derivatised-chitosan encapsulation. Material treated with native chitosan exhibited a strong antimicrobial activity of K. marxianus, showing a total growth inhibition at 10 min exposure. However, derivatised-chitosan encapsulation showed a reduced antimicrobial activity. This is the first study to show some probiotic properties of whey-native K. marxianus, in vitro. An encapsulation strategy was applied using derivatised chitosan.\n\nEncapsulated whey-native yeast Kluyveromyces marxianus as a feed additive for animal production.", "token_count": 411, "char_count": 1569, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6065, "quality_score": 0.8032, "entities": { "genes": [ "VM005", "VM004", "VM003" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:31.477204", "source": { "split": "train_shard_00000", "doc_id": 3756 }, "chunk_id": "train_shard_00000_3756_0", "global_id": 4166 }, { "text": "A Pseudomonas aeruginosa AUST-02 strain sub-type (M3L7) has been identified in Australia, infects the lungs of some people with cystic fibrosis and is associated with antibiotic resistance. Multiple clonal lineages may emerge during treatment with mutations in chromosomally encoded antibiotic resistance genes commonly observed. Here we describe the within-host diversity and antibiotic resistance of M3L7 during and after antibiotic treatment of an acute pulmonary exacerbation using whole genome sequencing and show both variation and shared mutations in important genes. Eleven isolates from an M3L7 population (n = 134) isolated over 3 months from an individual with cystic fibrosis underwent whole genome sequencing. A phylogeny based on core genome SNPs identified three distinct phylogenetic groups comprising two groups with higher rates of mutation (hypermutators) and one non-hypermutator group. Genomes were screened for acquired antibiotic resistance genes with the result suggesting that M3L7 resistance is principally driven by chromosomal mutations as no acquired mechanisms were detected. Small genetic variations, shared by all 11 isolates, were found in 49 genes associated with antibiotic resistance including frame-shift mutations (mexA, mexT), premature stop codons (oprD, mexB) and mutations in quinolone-resistance determining regions (gyrA, parE). However, whole genome sequencing also revealed mutations in 21 genes that were acquired following divergence of groups, which may also impact the activity of antibiotics and multi-drug efflux pumps. Comparison of mutations with minimum inhibitory concentrations of anti-pseudomonal antibiotics could not easily explain all resistance profiles observed. These data further demonstrate the complexity of chronic and antibiotic resistant P. aeruginosa infection where a multitude of co-existing genotypically diverse sub-lineages might co-exist during and after intravenous antibiotic treatment.\n\nWithin-host whole genome analysis of an antibiotic resistant Pseudomonas aeruginosa strain sub-type in cystic fibrosis.", "token_count": 502, "char_count": 2086, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6263, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:32.127873", "source": { "split": "train_shard_00000", "doc_id": 3757 }, "chunk_id": "train_shard_00000_3757_0", "global_id": 4167 }, { "text": "Inhibition of the bile salt export pump (BSEP) has been recognized as a key factor in the development of drug-induced cholestasis (DIC). The risk of DIC in humans has been previously assessed using in vitro BSEP inhibition data (IC\n\nAssessing the Risk of Drug-Induced Cholestasis Using Unbound Intrahepatic Concentrations.", "token_count": 92, "char_count": 322, "word_count": 49, "semantic_coherence": 1, "information_density": 0.6939, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:32.525377", "source": { "split": "train_shard_00000", "doc_id": 3758 }, "chunk_id": "train_shard_00000_3758_0", "global_id": 4168 }, { "text": "Ursodeoxycholate and its taurine conjugate tauroursodeoxycholate (TUDC) promote choleresis by triggering the insertion of transport proteins for bile acids into the canalicular and basolateral membranes of hepatocytes. In addition, TUDC exerts hepatoprotective and anti-apoptotic effects, can counteract the action of toxic bile acids and reduce endoplasmic reticulum stress. TUDC can also initiate the differentiation of multipotent mesenchymal stem cells (MSC) including hepatic stellate cells and promote their development into hepatocyte-like cells. Although the hepatoprotective and choleretic action of TUDC is empirically used in clinical medicine since decades, the underlying molecular mechanisms remained largely unclear. Since TUDC has little or no potency to activate known bile acid receptors, such as farnesoid X receptor and transmembrane G protein-coupled bile acid receptor, other receptors must be involved in TUDC-mediated signaling. Recent research demonstrates that integrins serve as sensors for TUDC. After binding of TUDC to α5β1-integrin, the β1-integrin subunit becomes activated through a conformational change, thereby triggering integrin signaling with the downstream activation of focal adhesion kinase, c-Src, the epidermal growth factor receptor and activation of the mitogen-activated protein kinases, Erks and p38. These events trigger choleresis through a coordinated insertion of the sodium-taurocholate cotransporting polypeptide into the basolateral membrane and of the bile salt export pump into the canalicular membrane. In addition to its choleretic action, TUDC-induced integrin activation triggers a cyclic adenosine monophosphate-dependent protein kinase A activation in hepatocytes, which provides the basis for the anti-apoptotic effect of TUDC. On the other hand, the TUDC-induced stimulation of MSC differentiation appears not to be mediated by integrins. This article gives a brief overview about our work on the signaling network-mediating hepatoprotection by TUDC.", "token_count": 520, "char_count": 2015, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:36:33.191298", "source": { "split": "train_shard_00000", "doc_id": 3759 }, "chunk_id": "train_shard_00000_3759_0", "global_id": 4169 }, { "text": "Mechanisms of Tauroursodeoxycholate-Mediated Hepatoprotection.", "token_count": 21, "char_count": 62, "word_count": 4, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:33.564956", "source": { "split": "train_shard_00000", "doc_id": 3759 }, "chunk_id": "train_shard_00000_3759_1", "global_id": 4170 }, { "text": "Primary biliary cholangitis (PBC; previously referred to as primary biliary cirrhosis) is a chronic fibrosing cholangiopathy with the signature of an autoimmune disease and features of intrahepatic cholestasis. Immunosuppressing treatments are largely unsuccessful. Responsiveness to ursodeoxycholic acid and reduced expression of anion exchanger 2 (AE2) on canalicular membranes and small bile ducts underline the importance of bicarbonate transportation in its disease mechanism. Soluble adenylyl cyclase (sAC; ADCY10) is an evolutionarily conserved bicarbonate sensor that regulates apoptosis, barrier function and TNF signaling. Key Messages: The biliary epithelium defends against the toxic bile by bicarbonate secretion and by maintaining a tight barrier. Passive diffusion of weak acid conjugates (e.g. bile salts and other toxins) across plasma membrane is pH-dependent. Reduced AE2 expression results in both reduced bicarbonate secretion and accumulation of bicarbonate in the cells. Increased intracellular bicarbonate leads to increased sAC activity, which regulates bile salt-induced apoptosis. Reduced bicarbonate secretion causes more bile salts to enter cells, which further increase sAC activity by releasing intracellular Ca2+ store. In vitro studies demonstrate that inhibition of sAC not only corrects sensitization to bile salt-induced apoptosis as a result of AE2 down-regulation but also prevents bile salt-induced apoptosis altogether. Targeting sAC is also likely to slow down disease progression by strengthening the barrier function of biliary epithelia and by reducing oxidative stress as a result of chronic inflammation.\n\nThe Emerging Role of Soluble Adenylyl Cyclase in Primary Biliary Cholangitis.", "token_count": 454, "char_count": 1729, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6043, "quality_score": 0.8021, "entities": { "genes": [ "ADCY10", "AE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:34.236298", "source": { "split": "train_shard_00000", "doc_id": 3760 }, "chunk_id": "train_shard_00000_3760_0", "global_id": 4171 }, { "text": "We present the first patient with a defect in the Na+-taurocholate cotransporting polypeptide SLC10A1 (NTCP), which plays a key role in the enterohepatic circulation of bile salts. The clinical presentation of the child was mild and the child showed no signs of liver dysfunction or pruritus despite extremely elevated plasma bile salt levels (>100-fold upper-limit of normal). A homozygous point mutation was found in the SLC10A1 gene (resulting in amino acid change R252H) and functional studies confirmed the pathogenicity of the mutation. This confirms the role of NTCP as the major transporter of conjugated bile salts into the liver as part of the enterohepatic circulation and shows that other transporters partly can take over its function, resulting in a relatively mild phenotype. This work was published previously in [Vaz et al.: Hepatology 2015;61:260-267] and supplemented with some follow-up information of the patient.\n\nExtended Abstract: Deficiency of Sodium Taurocholate Cotransporting Polypeptide (SLC10A1): A New Inborn Error of Metabolism with an Attenuated Phenotype.", "token_count": 301, "char_count": 1089, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:34.815992", "source": { "split": "train_shard_00000", "doc_id": 3761 }, "chunk_id": "train_shard_00000_3761_0", "global_id": 4172 }, { "text": "Efficient xylose alcoholic fermentation is one of the key to a successful lignocellulosic ethanol production. However, regulation of this process in the native xylose-fermenting yeasts is poorly understood. In this work, we paid attention to the transcriptional factor Cat8 and its possible role in xylose alcoholic fermentation in Ogataea (Hansenula) polymorpha. In Saccharomyces cerevisiae, organism, which does not metabolize xylose, gene CAT8 encodes a Zn-cluster transcriptional activator necessary for expression of genes involved in gluconeogenesis, respiration, glyoxylic cycle and ethanol utilization. Xylose is a carbon source that could be fermented to ethanol and simultaneously could be used in gluconeogenesis for hexose synthesis. This potentially suggests involvement of CAT8 in xylose metabolism.\n\nTranscriptional activator Cat8 is involved in regulation of xylose alcoholic fermentation in the thermotolerant yeast Ogataea (Hansenula) polymorpha.", "token_count": 257, "char_count": 964, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8023, "entities": { "genes": [ "CAT8" ], "proteins": [], "pathways": [ "metabolism", "fermentation", "respiration" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:35.360839", "source": { "split": "train_shard_00000", "doc_id": 3762 }, "chunk_id": "train_shard_00000_3762_0", "global_id": 4173 }, { "text": "Polygoni Multiflori Radix (PMR) has been widely used as a tonic for centuries. However, hepatotoxicity cases linked to PMR have been frequently reported and appropriate biomarkers for clinical diagnosis are currently lacking. Here, an approach using UPLC-QqQ/MS-based targeted metabolomics of bile acids (BAs) complemented with biochemistry and histopathology was applied to characterize the development and recovery processes of PMR-induced hepatotoxicity in rats and to identify biomarkers. The expression of bile salt export pump (Bsep) and sodium taurocholate cotransporting polypeptide (Ntcp) were evaluated to investigate the underlying mechanism. Steatosis and inflammatory cell infiltration were observed in PMR-treated rats, which were accompanied by the elevation of serum biochemistry. The metabolic profiles of BAs were analyzed by Principal Component Analysis, hyodeoxycholic acid (HDCA) in serum and tauro-β-muricholic acid (TβMCA) in urine were identified as potential biomarkers for PMR-induced hepatotoxicity. The elevated expression of Bsep and decreased expression of Ntcp in the liver of PMRtreated rats indicated that hepatotoxicity was related to the disorders of BAs metabolism. Our study demonstrated that BAs may be used for clinical diagnosis of PMR-induced hepatotoxicity. Urine TβMCA was identified as a promising biomarker to facilitate the clinical monitoring of PMR-induced hepatotoxicity and may serve as potential therapeutic target.\n\nIdentification of urine tauro-β-muricholic acid as a promising biomarker in Polygoni Multiflori Radix-induced hepatotoxicity by targeted metabolomics of bile acids.", "token_count": 439, "char_count": 1632, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5818, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:35.992118", "source": { "split": "train_shard_00000", "doc_id": 3763 }, "chunk_id": "train_shard_00000_3763_0", "global_id": 4174 }, { "text": "There is an increasing understanding that variation in gene presence-absence plays an important role in the heritability of agronomic traits; however, there have been relatively few studies on variation in gene presence-absence in crop species. Hexaploid wheat is one of the most important food crops in the world and intensive breeding has reduced the genetic diversity of elite cultivars. Major efforts have produced draft genome assemblies for the cultivar Chinese Spring, but it is unknown how well this represents the genome diversity found in current modern elite cultivars. In this study we build an improved reference for Chinese Spring and explore gene diversity across 18 wheat cultivars. We predict a pangenome size of 140 500 ± 102 genes, a core genome of 81 070 ± 1631 genes and an average of 128 656 genes in each cultivar. Functional annotation of the variable gene set suggests that it is enriched for genes that may be associated with important agronomic traits. In addition to variation in gene presence, more than 36 million intervarietal single nucleotide polymorphisms were identified across the pangenome. This study of the wheat pangenome provides insight into genome diversity in elite wheat as a basis for genomics-based improvement of this important crop. A wheat pangenome, GBrowse, is available at http://appliedbioinformatics.com.au/cgi-bin/gb2/gbrowse/WheatPan/, and data are available to download from http://wheatgenome.info/wheat_genome_databases.php.\n\nThe pangenome of hexaploid bread wheat.", "token_count": 379, "char_count": 1525, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6044, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:36.577783", "source": { "split": "train_shard_00000", "doc_id": 3764 }, "chunk_id": "train_shard_00000_3764_0", "global_id": 4175 }, { "text": "Bile acid reflux in the esophagus plays an important role in the carcinogenesis of esophageal adenocarcinoma (EAC). The G-protein coupled bile acid receptor (TGR5) has been associated with the development of gastrointestinal cancer. However, little is known regarding the role of TGR5 in esophageal carcinoma and precancerous lesions. We analyzed genomic DNA from 116 EACs for copy number aberrations via Affymetrix SNP6.0 microarrays. The\n\nBile salt receptor TGR5 is highly expressed in esophageal adenocarcinoma and precancerous lesions with significantly worse overall survival and gender differences.", "token_count": 167, "char_count": 604, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7176, "quality_score": 0.8588, "entities": { "genes": [ "TGR5", "SNP6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:37.025921", "source": { "split": "train_shard_00000", "doc_id": 3765 }, "chunk_id": "train_shard_00000_3765_0", "global_id": 4176 }, { "text": "Increasing evidence supports the view that intestinal farnesoid X receptor (FXR) is involved in glucose tolerance and that FXR signaling can be profoundly impacted by the gut microbiota. Selective manipulation of the gut microbiota-FXR signaling axis was reported to significantly impact glucose intolerance, but the precise molecular mechanism remains largely unknown. Here, caffeic acid phenethyl ester (CAPE), an over-the-counter dietary supplement and an inhibitor of bacterial bile salt hydrolase, increased levels of intestinal tauro-β-muricholic acid, which selectively suppresses intestinal FXR signaling. Intestinal FXR inhibition decreased ceramide levels by suppressing expression of genes involved in ceramide synthesis specifically in the intestinal ileum epithelial cells. The lower serum ceramides mediated decreased hepatic mitochondrial acetyl-CoA levels and pyruvate carboxylase (PC) activities and attenuated hepatic gluconeogenesis, independent of body weight change and hepatic insulin signaling in vivo; this was reversed by treatment of mice with ceramides or the FXR agonist GW4064. Ceramides substantially attenuated mitochondrial citrate synthase activities primarily through the induction of endoplasmic reticulum stress, which triggers increased hepatic mitochondrial acetyl-CoA levels and PC activities. These results reveal a mechanism by which the dietary supplement CAPE and intestinal FXR regulates hepatic gluconeogenesis and suggest that inhibiting intestinal FXR is a strategy for treating hyperglycemia.\n\nAn Intestinal Farnesoid X Receptor-Ceramide Signaling Axis Modulates Hepatic Gluconeogenesis in Mice.", "token_count": 433, "char_count": 1643, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [ "GW4064" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:37.654270", "source": { "split": "train_shard_00000", "doc_id": 3766 }, "chunk_id": "train_shard_00000_3766_0", "global_id": 4177 }, { "text": "In this study, we analyzed Chinese traditional fermented food to isolate and identify new lactic acid bacteria (LAB) strains with novel functional properties and to evaluate their cellular antioxidant and bile salt hydrolase (BSH) activities in vitro. A sequential screening strategy was developed to efficiently isolate and obtain 261 LAB strains tolerant of bile salt, acid, and H\n\nIsolation, Identification, and Evaluation of New Lactic Acid Bacteria Strains with Both Cellular Antioxidant and Bile Salt Hydrolase Activities In Vitro.", "token_count": 135, "char_count": 537, "word_count": 79, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:38.086942", "source": { "split": "train_shard_00000", "doc_id": 3767 }, "chunk_id": "train_shard_00000_3767_0", "global_id": 4178 }, { "text": "Bile salts are natural detergents required to solubilise dietary fat and lipid soluble vitamins. They are synthesised in hepatocytes and secreted into the luminal space of the biliary tree by the bile salt export pump (BSEP), an ATP-binding cassette (ABC) transporter in the canalicular membrane. BSEP deficiency causes cytotoxic accumulation of bile salts in the hepatocyte that results in mild-to-severe forms of cholestasis. The resulting inflammation can also progress to hepatocellular cancer via a novel mechanism involving upregulation of proliferative signalling pathways. A second ABC transporter of the canalicular membrane is also critical for bile formation. ABCB4 flops phosphatidylcholine into the outer leaflet of the membrane to be extracted by bile salts in the canalicular space. These mixed micelles reduce the detergent action of the bile salts and protect the biliary tree from their cytotoxic activity. ABCB4 deficiency also causes cholestasis, and might be expected to cause cholangitis and predispose to liver cancer. Non-synonymous SNPs in ABCB4 have now been described in patients with liver cancer or with inflammatory liver diseases that are known to predispose to cancer, but data showing that the SNPs are sufficiently deleterious to be an etiological factor are lacking. Here, we report the first characterisation at the protein level of six ABCB4 variants (D243A, K435T, G535D, I490T, R545C, and S978P) previously found in patients with inflammatory liver diseases or liver cancer. All significantly impair the transporter with a range of phenotypes exhibited, including low abundance, intracellular retention, and reduced floppase activity, suggesting that ABCB4 deficiency is the root cause of the pathology in these cases.", "token_count": 454, "char_count": 1757, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [ "ABCB4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:38.728461", "source": { "split": "train_shard_00000", "doc_id": 3768 }, "chunk_id": "train_shard_00000_3768_0", "global_id": 4179 }, { "text": "ABCB4 missense mutations D243A, K435T, G535D, I490T, R545C, and S978P significantly impair the lipid floppase and likely predispose to secondary pathologies in the human population.", "token_count": 66, "char_count": 181, "word_count": 25, "semantic_coherence": 1, "information_density": 0.92, "quality_score": 0.96, "entities": { "genes": [ "ABCB4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:39.096668", "source": { "split": "train_shard_00000", "doc_id": 3768 }, "chunk_id": "train_shard_00000_3768_1", "global_id": 4180 }, { "text": "To propose media for simulating the intragastric environment under reduced gastric acid secretion in the fasted state at three levels of simulation of the gastric environment and evaluate their usefulness in evaluating the intragastric dissolution of salts of weak bases. To evaluate the importance of bicarbonate buffer in biorelevant in vitro dissolution testing when using Level II biorelevant media simulating the environment in the fasted upper small intestine, regardless of gastric acid secretions.\n\nThe impact of reduced gastric acid secretion on dissolution of salts of weak bases in the fasted upper gastrointestinal lumen: Data in biorelevant media and in human aspirates.", "token_count": 156, "char_count": 683, "word_count": 101, "semantic_coherence": 1, "information_density": 0.5248, "quality_score": 0.7624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:39.535031", "source": { "split": "train_shard_00000", "doc_id": 3769 }, "chunk_id": "train_shard_00000_3769_0", "global_id": 4181 }, { "text": "Claudins are a family of integral membrane proteins and are components of tight junctions (TJs). Many TJ proteins are known to tighten the cell structure and maintain a barrier. Claudin-2 forms gated paracellular channels and allows sodium ions and other small positively charged ions to cross between adjacent cells. Recently, we found that vitamin D receptor (VDR) enhanced Claudin-2 expression in colon and that bile salt receptors VDR and Takeda G-protein coupled receptor5 (TGR5) were highly expressed in esophageal adenocarcinoma (EAC) and precancerous lesions. Here, we examined the expression of Claudin-2 in EAC and precancerous lesions and its association with VDR and TGR5 expression.\n\nHigh expression of Claudin-2 in esophageal carcinoma and precancerous lesions is significantly associated with the bile salt receptors VDR and TGR5.", "token_count": 219, "char_count": 845, "word_count": 125, "semantic_coherence": 1, "information_density": 0.664, "quality_score": 0.832, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:40.003009", "source": { "split": "train_shard_00000", "doc_id": 3770 }, "chunk_id": "train_shard_00000_3770_0", "global_id": 4182 }, { "text": "TAK-875, a GPR40 agonist, was withdrawn from Phase III clinical trials due to drug-induced liver injury (DILI). Mechanistic studies were conducted to identify potential DILI hazards (covalent binding burden (CVB), hepatic transporter inhibition, mitochondrial toxicity, and liver toxicity in rats) associated with TAK-875. Treatment of hepatocytes with radiolabeled TAK-875 resulted in a CVB of 2.0 mg/day, which is above the threshold of 1 mg/day considered to be a risk for DILI. Covalent binding to hepatocytes was due to formation of a reactive acyl glucuronide (AG) and, possibly, an acyl-CoA thioester intermediate. Formation of TAK-875AG in hepatocytes and/or in vivo was in the order of non-rodents > human (in vitro only) > rat. These data suggest that non-rodents, and presumably humans, form TAK-875AG more efficiently than rats, and that AG-mediated toxicities in rats may only occur at high doses. TAK-875 (1000 mg/kg/day) formed significant amounts of AG metabolite (≤32.7 μM) in rat liver that was associated with increases in ALT (×4), bilirubin (×9), and bile acids (×3.4), and microscopic findings of hepatocellular hypertrophy and single cell necrosis. TAK-875 and TAK-875AG had similar potencies (within 3-fold) for human multi-drug resistant associated protein 2/4 (MRP2/4) and bile salt export pump, but TAK-875AG was exceptionally potent against MRP3 (0.21 μM). Inhibition of MRPs may contribute to liver accumulation of TAK-875AG", "token_count": 491, "char_count": 1453, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7176, "quality_score": 0.8588, "entities": { "genes": [ "MRP2", "MRP3", "GPR40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:40.647145", "source": { "split": "train_shard_00000", "doc_id": 3771 }, "chunk_id": "train_shard_00000_3771_0", "global_id": 4183 }, { "text": "TAK-875 also inhibited mitochondrial respiration in HepG2 cells, and mitochondrial Complex 1 and 2 activities in isolated rat mitochondria. In summary, formation of TAK-875AG, and possibly TAK-875CoA in hepatocytes, coupled with inhibition of hepatic transporters and mitochondrial respiration may be key contributors to TAK-875-mediated DILI.\n\nFasiglifam (TAK-875): Mechanistic Investigation and Retrospective Identification of Hazards for Drug Induced Liver Injury.", "token_count": 144, "char_count": 467, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7966, "quality_score": 0.8983, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:41.079271", "source": { "split": "train_shard_00000", "doc_id": 3771 }, "chunk_id": "train_shard_00000_3771_1", "global_id": 4184 }, { "text": "This study aimed to identify yeasts from the gastrointestinal tract of scarlet ibises (Eudocimus ruber) and from plant material collected from the environment where they live. Then, the isolates phenotypically identified as Candida famata were submitted to molecular identification of their closely related species and evaluated for their antifungal susceptibility and possible resistance mechanisms to antifungal drugs. Cloacal swabs from 20 scarlet ibises kept in captivity at Mangal das Garças Park (Brazil), pooled stool samples (n = 20) and samples of trunks and hollow of trees (n = 20) obtained from their enclosures were collected. The samples were seeded on Sabouraud agar supplemented with chloramphenicol. The 48 recovered isolates were phenotypically identified as 15 Candida famata, 13 Candida catenulata, 2 Candida intermedia, 1 Candida lusitaniae, 2 Candida guilliermondii, 1 Candida kefyr, 1 Candida amapae, 1 Candida krusei, 8 Trichosporon spp., and 4 Rhodotorula spp. The C. famata isolates were further identified as 3 C. famata, 8 Debaryomyces nepalensis, and 4 C. palmioleophila. All C. famata and C. palmioleophila were susceptible to caspofungin and itraconazole, while one D. nepalensis was resistant to fluconazole and voriconazole. This same isolate and another D. nepalensis had lower amphotericin B susceptibility. The azole resistant strain had an increased efflux of rhodamine 6G and an alteration in the membrane sterol content, demonstrating multifactorial resistance mechanism. Finally, this research shows that scarlet ibises and their environment harbor C. famata and closely related species, including antifungal resistant isolates, emphasizing the need of monitoring the antifungal susceptibility of these yeast species.", "token_count": 484, "char_count": 1757, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:41.724744", "source": { "split": "train_shard_00000", "doc_id": 3772 }, "chunk_id": "train_shard_00000_3772_0", "global_id": 4185 }, { "text": "Yeasts from Scarlet ibises (Eudocimus ruber): A focus on monitoring the antifungal susceptibility of Candida famata and closely related species.", "token_count": 37, "char_count": 144, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:42.084735", "source": { "split": "train_shard_00000", "doc_id": 3772 }, "chunk_id": "train_shard_00000_3772_1", "global_id": 4186 }, { "text": "Nine Shiga toxin-producing Escherichia coli O157:H7/H- (O157) strains were serially cultured three times on LB agar plates. After each sub-culture, five colonies were picked for DNA isolation and whole genome sequence (WGS) analysis. After exclusion of possible recombination-related SNPs, 11, 9, and 34 single-nucleotide polymorphisms (SNPs) were detected in genes in the backbone, O-island, and mobile elements gene categories. This suggested that those SNPs due to cultivation could influence the threshold value set for molecular epidemiological studies of O157. Significant differences were observed by the Kruskal-Wallis test (P < 0.01) when the number of the SNPs in a strain was compared to that in other strains. This indicated that a specific number of strains could be used for setting the threshold value in molecular epidemiological studies. Due to cultivation, the SNPs were also detected in genes in a few core genome or core gene sets, suggesting that those SNPs could affect studies of phylogeny as well as molecular epidemiology. To improve the accuracy of phylogenetic and molecular epidemiological studies, genes in which the SNPs have arisen due to cultivation should be excluded from WGS data.\n\nSingle-Nucleotide Polymorphisms in the Whole-Genome Sequence Data of Shiga Toxin-Producing Escherichia coli O157:H7/H- Strains by Cultivation.", "token_count": 374, "char_count": 1359, "word_count": 201, "semantic_coherence": 1, "information_density": 0.597, "quality_score": 0.7985, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:42.660378", "source": { "split": "train_shard_00000", "doc_id": 3773 }, "chunk_id": "train_shard_00000_3773_0", "global_id": 4187 }, { "text": "The bile salt-activated transcription factor farnesoid X receptor (FXR) is a key mediator of proliferative bile salt signalling, which is assumed to play a role in the early phase of compensatory liver growth. The aim of this study was to evaluate the effect of a potent FXR agonist (obeticholic acid, OCA) on liver growth following portal vein embolization (PVE).\n\nEffect of obeticholic acid on liver regeneration following portal vein embolization in an experimental model.", "token_count": 121, "char_count": 475, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7162, "quality_score": 0.8581, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:43.065821", "source": { "split": "train_shard_00000", "doc_id": 3774 }, "chunk_id": "train_shard_00000_3774_0", "global_id": 4188 }, { "text": "The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding accessory genomes in 36 species, represented by the genomes of 731 bacterial strains, to assess the impact of selective forces on base composition in microbes. We also explore, in turn, how these results compare with findings for whole genome intragenic regions.\n\nThe nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes.", "token_count": 153, "char_count": 727, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:43.504907", "source": { "split": "train_shard_00000", "doc_id": 3775 }, "chunk_id": "train_shard_00000_3775_0", "global_id": 4189 }, { "text": "In recent years, the gut microbiome has gained increasing appreciation as a determinant of the health status of the human host. Bile salts that are secreted into the intestine may be biotransformed by enzymes produced by the gut bacteria. To date, bile acid research at the host-microbe interface has primarily been directed toward effects on host metabolism. The aim of this work was to investigate the effect of changes in gut microbial bile acid metabolism on the solubilization capacity of bile salt micelles and consequently intraluminal drug solubility. First, the impact of bile acid metabolism, mediated in vivo by the microbial enzymes bile salt hydrolase (BSH) and 7α-dehydroxylase, on drug solubility was assessed by comparing the solubilization capacity of (a) conjugated vs deconjugated and (b) primary vs secondary bile salts. A series of poorly water-soluble drugs (PWSDs) were selected as model solutes on the basis of an increased tendency to associate with bile micelles. Subsequently, PWSD solubility and dissolution was evaluated in conventional biorelevant simulated intestinal fluid containing host-derived bile acids, as well as in media modified to contain microbial bile acid metabolites. The findings suggest that deconjugation of the bile acid steroidal core, as dictated by BSH activity, influences micellar solubilization capacity for some PWSDs; however, these differences appear to be relatively minor. In contrast, the extent of bile acid hydroxylation, regulated by microbial 7α-dehydroxylase, was found to significantly affect the solubilization capacity of bile salt micelles for all nine drugs studied (p < 0.05). Subsequent investigations in biorelevant media containing either the trihydroxy bile salt sodium taurocholate (TCA) or the dihydroxy bile salt sodium taurodeoxycholate (TDCA) revealed altered drug solubility and dissolution. Observed differences in biorelevant media appeared to be both drug- and amphiphile (bile salt/lecithin) concentration-dependent", "token_count": 519, "char_count": 2002, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:36:44.135764", "source": { "split": "train_shard_00000", "doc_id": 3776 }, "chunk_id": "train_shard_00000_3776_0", "global_id": 4190 }, { "text": "Our studies herein indicate that bile acid modifications occurring at the host-microbe interface could lead to alterations in the capacity of intestinal bile salt micelles to solubilize drugs, providing impetus to consider the gut microbiota in the drug absorption process. In the clinical setting, disruption of the gut microbial ecosystem, through disease or antibiotic treatment, could transform the bile acid pool with potential implications for drug absorption and bioavailability.\n\nImpact of Gut Microbiota-Mediated Bile Acid Metabolism on the Solubilization Capacity of Bile Salt Micelles and Drug Solubility.", "token_count": 142, "char_count": 616, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:44.584691", "source": { "split": "train_shard_00000", "doc_id": 3776 }, "chunk_id": "train_shard_00000_3776_1", "global_id": 4191 }, { "text": "Yeasts capable of growing and surviving at high temperatures are regarded as thermotolerant. For appropriate functioning of cellular processes and cell survival, the maintenance of an optimal redox state is critical of reducing and oxidizing species. We studied mitochondrial functions of the thermotolerant Kluyveromyces marxianus SLP1 and the mesophilic OFF1 yeasts, through the evaluation of its mitochondrial membrane potential (ΔΨ\n\nElectron transport chain in a thermotolerant yeast.", "token_count": 114, "char_count": 488, "word_count": 67, "semantic_coherence": 1, "information_density": 0.806, "quality_score": 0.903, "entities": { "genes": [ "OFF1", "SLP1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:44.998905", "source": { "split": "train_shard_00000", "doc_id": 3777 }, "chunk_id": "train_shard_00000_3777_0", "global_id": 4192 }, { "text": "The pentose phosphate pathway (PPP) plays an important role in the efficiency of xylose fermentation during cellulosic ethanol production. In simultaneous saccharification and co-fermentation (SSCF), the optimal temperature for cellulase hydrolysis of lignocellulose is much higher than that of fermentation. Successful use of SSCF requires optimization of the expression of PPP genes at elevated temperatures. This study examined the combinatorial expression of PPP genes at high temperature. The results revealed that over-expression of TAL1 and TKL1 in Saccharomyces cerevisiae (S. cerevisiae) at 30 °C and over-expression of all PPP genes at 36 °C resulted in the highest ethanol productivities. Furthermore, combinatorial over-expression of PPP genes derived from S. cerevisiae and a thermostable yeast Kluyveromyces marxianus allowed the strain to ferment xylose with ethanol productivity of 0.51 g/L/h, even at 38 °C. These results clearly demonstrate that xylose metabolism can be improved by the utilization of appropriate combinations of thermostable PPP genes in high-temperature production of ethanol.\n\nGenetic improvement of xylose metabolism by enhancing the expression of pentose phosphate pathway genes in Saccharomyces cerevisiae IR-2 for high-temperature ethanol production.", "token_count": 341, "char_count": 1292, "word_count": 178, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7978, "entities": { "genes": [ "TKL1", "TAL1" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:45.593584", "source": { "split": "train_shard_00000", "doc_id": 3778 }, "chunk_id": "train_shard_00000_3778_0", "global_id": 4193 }, { "text": "The complete genome sequence of Brevundimonas diminuta represented a chromosome (∼4.15 Mb) and two plasmids (pCMS1 and pCMS2) with sizes of 65,908 and 30,654 bp, respectively. The sequence of the genome showed no significant similarity with the known bacterial genome sequences, instead showed weak similarity with the members of different genera of family, Sphingomonadaceae. Contradicting existing taxonomic position, the core genome-guided phylogenetic tree placed B. diminuta in the genus Sphingopyxis and showed sufficient genome-to-genome distance warranting a new species name. Reflecting the strains ability to grow in harsh environments, the genome-contained genetic repertoire required for mineralization of several recalcitrant man-made aromatic compounds.\n\nGenome-Guided Insights Reveal Organophosphate-Degrading Brevundimonas diminuta as Sphingopyxis wildii and Define Its Versatile Metabolic Capabilities and Environmental Adaptations.", "token_count": 263, "char_count": 949, "word_count": 120, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:46.193932", "source": { "split": "train_shard_00000", "doc_id": 3779 }, "chunk_id": "train_shard_00000_3779_0", "global_id": 4194 }, { "text": "Whole-genome sequencing (WGS) of microbial pathogens from clinical samples is a highly sensitive tool used to gain a deeper understanding of the biology, epidemiology, and drug resistance mechanisms of many infections. However, WGS of organisms which exhibit low densities in their hosts is challenging due to high levels of host genomic DNA (gDNA), which leads to very low coverage of the microbial genome. WGS of Plasmodium vivax, the most widely distributed form of malaria, is especially difficult because of low parasite densities and the lack of an ex vivo culture system. Current techniques used to enrich P. vivax DNA from clinical samples require significant resources or are not consistently effective. Here, we demonstrate that selective whole-genome amplification (SWGA) can enrich P. vivax gDNA from unprocessed human blood samples and dried blood spots for high-quality WGS, allowing genetic characterization of isolates that would otherwise have been prohibitively expensive or impossible to sequence. We achieved an average genome coverage of 24×, with up to 95% of the P. vivax core genome covered by ≥5 reads. The single-nucleotide polymorphism (SNP) characteristics and drug resistance mutations seen were consistent with those of other P. vivax sequences from a similar region in Peru, demonstrating that SWGA produces high-quality sequences for downstream analysis. SWGA is a robust tool that will enable efficient, cost-effective WGS of P. vivax isolates from clinical samples that can be applied to other neglected microbial pathogens.\n\nSelective Whole-Genome Amplification Is a Robust Method That Enables Scalable Whole-Genome Sequencing of Plasmodium vivax from Unprocessed Clinical Samples.", "token_count": 407, "char_count": 1716, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:46.822430", "source": { "split": "train_shard_00000", "doc_id": 3780 }, "chunk_id": "train_shard_00000_3780_0", "global_id": 4195 }, { "text": "We have studied the uptake of quercetin aglycone into CaCo-2/TC7 cells in the presence and absence of mixed micelles that are present in the human small intestine. The micelles inhibited the transport of quercetin into the cells. To gain an understanding of why this is the case we examined the solubilisation of quercetin in micelles of differing composition and into pure lipid phases. We did this by using the environmental sensitivity of quercetin's UV-visible absorption spectra and measurement of free quercetin by filtration of the micellar solutions. The nature of the micelles was also studied by pyrene fluorescence. We found that the partitioning of quercetin into simple bile salt micelles was low and for mixed micelles was inhibited by increasing the bile salt concentration. The affinity of quercetin decreased in the order egg phosphatidylcholine (PC) = lysoPC > mixed micelles > bile salts. These results, together with the innate properties of quercetin, contribute to an understanding of the low bioavailability of quercetin.\n\nTowards an Understanding of the Low Bioavailability of Quercetin: A Study of Its Interaction with Intestinal Lipids.", "token_count": 292, "char_count": 1162, "word_count": 179, "semantic_coherence": 1, "information_density": 0.5419, "quality_score": 0.7709, "entities": { "genes": [ "TC7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:47.388580", "source": { "split": "train_shard_00000", "doc_id": 3781 }, "chunk_id": "train_shard_00000_3781_0", "global_id": 4196 }, { "text": "As important lactic acid bacteria, Enterococcus species are widely used in the production of fermented food. However, as some strains of Enterococcus are opportunistic pathogens, their safety has not been generally accepted. In recent years, a large number of new species have been described and classified within the genus Enterococcus, so a better understanding of the genetic relationships and evolution of Enterococcus species is needed. In this study, the genomes of 29 type strains of Enterococcus species were sequenced. In combination with eight complete genome sequences from the Genbank database, the whole genomes of 37 strains of Enterococcus were comparatively analyzed. The average length of Enterococcus genomes was 3.20Mb and the average GC content was 37.99%. The core- and pan- genomes were defined based on the genomes of the 37 strains of Enterococcus. The core-genome contained 605 genes, a large proportion of which were associated with carbohydrate metabolism, protein metabolism, DNA and RNA metabolism. The phylogenetic tree showed that habitat is very important in the evolution of Enterococcus. The genetic relationships were closer in strains that come from similar habitats. According to the topology of the time tree, we found that humans and mammals may be the original hosts of Enterococcus, and then species from humans and mammals made a host-shift to plants, birds, food and other environments. However, it was just an evolutionary scenario, and more data and efforts were needed to prove this postulation. The comparative genomic analysis provided a snapshot of the evolution and genetic diversity of the genus Enterococcus, which paves the way for follow-up studies on its taxonomy and functional genomics.\n\nComparative genomic analysis of the genus Enterococcus.", "token_count": 419, "char_count": 1800, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5568, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:48.006160", "source": { "split": "train_shard_00000", "doc_id": 3782 }, "chunk_id": "train_shard_00000_3782_0", "global_id": 4197 }, { "text": "Bacillus velezensis CC09, which was isolated from healthy leaves of Cinnamomum camphora and previously identified as Bacillus amyloliquefaciens CC09, shows great potential as a new biocontrol agent, in control of many phytopathogenic diseases. To extend our understanding of the potential antifungal capacities, we did a whole genome analysis of strain CC09. Result shows that strain CC09 has a relatively large genome size (4.17Mb) with an average GC content of 46.1%, and 4021 predicted genes. Thirteen secondary metabolites encoding clusters have been identified within the genome of B. velezensis CC09 using genome mining technique. Data of comparative genomic analysis indicated that 3 of the clusters are conserved by all strains of B. velezensis, B. amyloliquefaciens and B. subtilis 168, 9 by B. velezensis and B. amyloliquefaciens, and 2 by all strains of B. velezensis. Another 2 clusters encoding NRPS (Non-Ribosomal Peptide Synthetases) and NRPS-TransATPKS (NRPS and trans-Acyl Transferase Polyketide Synthetases) respectively are observed only in 15 B. velezensis strains, which might lead to the synthesis of novel bioactive compounds and could be explored as antimicrobial agents in the future. These clusters endow B. velezensis CC09 with strong and broad antimicrobial activities, for example, in control of wheat powdery mildew disease. Moreover, our data further confirmed the taxonomy of strain CC09 is a member of B. velezensis rather than a strain of B. amyloliquefaciens based on core genome sequence analysis using phylogenomic approach.\n\nGenomic and metabolic traits endow Bacillus velezensis CC09 with a potential biocontrol agent in control of wheat powdery mildew disease.", "token_count": 475, "char_count": 1700, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5737, "quality_score": 0.7869, "entities": { "genes": [ "CC09" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:48.643552", "source": { "split": "train_shard_00000", "doc_id": 3783 }, "chunk_id": "train_shard_00000_3783_0", "global_id": 4198 }, { "text": "Haplotypes A and B of 'Candidatus Liberibacter solanacearum' (CLso) are associated with diseases of solanaceous plants, especially Zebra chip disease of potato, and haplotypes C, D and E are associated with symptoms on apiaceous plants. To date, one complete genome of haplotype B and two high quality draft genomes of haplotype A have been obtained for these unculturable bacteria using metagenomics from the psyllid vector Bactericera cockerelli. Here, we present the first genomic sequences obtained for the carrot-associated CLso. These two genomic sequences of haplotype C, FIN114 (1.24 Mbp) and FIN111 (1.20 Mbp), were obtained from carrot psyllids (Trioza apicalis) harboring CLso. Genomic comparisons between the haplotypes A, B and C revealed that the genome organization differs between these haplotypes, due to large inversions and other recombinations. Comparison of protein-coding genes indicated that the core genome of CLso consists of 885 ortholog groups, with the pan-genome consisting of 1327 ortholog groups. Twenty-seven ortholog groups are unique to CLso haplotype C, whilst 11 ortholog groups shared by the haplotypes A and B, are not found in the haplotype C. Some of these ortholog groups that are not part of the core genome may encode functions related to interactions with the different host plant and psyllid species.\n\nGenomic sequence of 'Candidatus Liberibacter solanacearum' haplotype C and its comparison with haplotype A and B genomes.", "token_count": 403, "char_count": 1468, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [ "FIN111", "FIN114" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:49.260575", "source": { "split": "train_shard_00000", "doc_id": 3784 }, "chunk_id": "train_shard_00000_3784_0", "global_id": 4199 }, { "text": "To effectively mitigate antimicrobial resistance in the agricultural ecosystem, there is an increasing pressure to reduce and eliminate the use of in-feed antibiotics for growth promotion and disease prevention in food animals. However, limiting antibiotic use could compromise animal production efficiency and health. Thus, there is an urgent need to develop effective alternatives to antibiotic growth promoters (AGPs). Increasing evidence has shown that the growth-promoting effect of AGPs was highly correlated with the reduced activity of bile salt hydrolase (BSH), an intestinal bacterial enzyme that has a negative impact on host fat digestion and energy harvest; consistent with this finding, the population of Lactobacillus species, the major intestinal BSH-producer, was significantly reduced in response to AGP use. Thus, BSH is a key mechanistic microbiome target for developing novel alternatives to AGPs. Despite recent significant progress in the characterization of diverse BSH enzymes, research on BSH is still in its infancy. This review is focused on the function of BSH and its significant impacts on host physiology in human beings, laboratory animals and food animals. The gaps in BSH-based translational microbiome research for enhanced animal health are also identified and discussed.\n\nBacterial bile salt hydrolase: an intestinal microbiome target for enhanced animal health.", "token_count": 299, "char_count": 1400, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:50.610860", "source": { "split": "train_shard_00000", "doc_id": 3785 }, "chunk_id": "train_shard_00000_3785_0", "global_id": 4200 }, { "text": "Erratum for Inokuma et al., Complete Genome Sequence of Kluyveromyces marxianus NBRC1777, a Nonconventional Thermotolerant Yeast.", "token_count": 46, "char_count": 129, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "NBRC1777" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:50.974602", "source": { "split": "train_shard_00000", "doc_id": 3786 }, "chunk_id": "train_shard_00000_3786_0", "global_id": 4201 }, { "text": "Bile salt export pump (BSEP) plays an important role in hepatic secretion of bile acids and its deficiency results in severe cholestasis and liver failure. Mutation of the ABCB11 gene encoding BSEP induces BSEP deficiency and progressive familial intrahepatic cholestasis type 2 (PFIC2). Because liver transplantation remains standard treatment for PFIC2, the development of a novel therapeutic option is desired. However, a well reproducible model, which is essential for the new drug development for PFIC2, has not been established. Therefore, we attempted to establish a PFIC2 model by using iPSC technology. Human iPSCs were generated from patients with BSEP-deficiency (BD-iPSC), and were differentiated into hepatocyte-like cells (HLCs). In the BD-iPSC derived HLCs (BD-HLCs), BSEP was not expressed on the cell surface and the biliary excretion capacity was significantly impaired. We also identified a novel mutation in the 5'-untranslated region of the ABCB11 gene that led to aberrant RNA splicing in BD-HLCs. Furthermore, to evaluate the drug efficacy, BD-HLCs were treated with 4-phenylbutyrate (4PBA). The membrane BSEP expression level and the biliary excretion capacity in BD-HLCs were rescued by 4PBA treatment. In summary, we succeeded in establishing a PFIC2 model, which may be useful for its pathophysiological analysis and drug development.\n\nGeneration of a bile salt export pump deficiency model using patient-specific induced pluripotent stem cell-derived hepatocyte-like cells.", "token_count": 412, "char_count": 1501, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:51.599298", "source": { "split": "train_shard_00000", "doc_id": 3787 }, "chunk_id": "train_shard_00000_3787_0", "global_id": 4202 }, { "text": "The bile salt export pump (BSEP, ABCB11) belongs to the ATP-binding-cassette superfamily of transporters and is predominately found in the liver. BSEP is an efflux transporter that plays a critical role in the secretion of bile salts into the bile. Inhibition of BSEP function by drugs can result in the buildup of bile salts in the liver and eventually leads to cholestasis and drug-induced liver injury (DILI). DILI is a major cause of withdrawal of drugs from the pharmaceutical market and accounts for >50% of acute liver failures. Therefore, early detection of BSEP inhibition by drugs can help to mitigate the possibility of BSEP-associated liver injury. This unit describes two assays that investigate the relationship between drug interference with BSEP function and liver injury using membrane vesicles prepared from Hi5 insect cells transfected with human BSEP. Comprehensive protocols for assessing BSEP inhibition in a 384-well format using radiolabeled and liquid chromatography/mass spectrometry (LC/MS)-based detection methods are described. © 2017 by John Wiley & Sons, Inc.\n\nAssessment of Bile Salt Export Pump (BSEP) Inhibition in Membrane Vesicles Using Radioactive and LC/MS-Based Detection Methods.", "token_count": 323, "char_count": 1219, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:52.156287", "source": { "split": "train_shard_00000", "doc_id": 3788 }, "chunk_id": "train_shard_00000_3788_0", "global_id": 4203 }, { "text": "The increase in available microbial genome sequences has resulted in an increase in the size of the pangenomes being analyzed. Current pangenome visualizations are not intended for the pangenome sizes possible today and new approaches are necessary in order to convert the increase in available information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis.\n\nHierarchical sets: analyzing pangenome structure through scalable set visualizations.", "token_count": 115, "char_count": 577, "word_count": 84, "semantic_coherence": 1, "information_density": 0.6548, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:52.540983", "source": { "split": "train_shard_00000", "doc_id": 3789 }, "chunk_id": "train_shard_00000_3789_0", "global_id": 4204 }, { "text": "Seven genomes of Corynebacterium pseudotuberculosis biovar equi were sequenced on the Ion Torrent PGM platform, generating high-quality scaffolds over 2.35 Mbp. This bacterium is the causative agent of disease known as \"pigeon fever\" which commonly affects horses worldwide. The pangenome of biovar equi was calculated and two phylogenomic approaches were used to identify clustering patterns within Corynebacterium genus. Furthermore, other comparative analyses were performed including the prediction of genomic islands and prophages, and SNP-based phylogeny. In the phylogenomic tree, C. pseudotuberculosis was divided into two distinct clades, one formed by nitrate non-reducing species (biovar ovis) and another formed by nitrate-reducing species (biovar equi). In the latter group, the strains isolated from California were more related to each other, while the strains CIP 52.97 and 1/06-A formed the outermost clade of the biovar equi. A total of 1,355 core genes were identified, corresponding to 42.5% of the pangenome. This pangenome has one of the smallest core genomes described in the literature, suggesting a high genetic variability of biovar equi of C. pseudotuberculosis. The analysis of the similarity between the resistance islands identified a higher proximity between the strains that caused more severe infectious conditions (infection in the internal organs). Pathogenicity islands were largely conserved between strains. Several genes that modulate the pathogenicity of C. pseudotuberculosis were described including peptidases, recombination enzymes, micoside synthesis enzymes, bacteriocins with antimicrobial activity and several others. Finally, no genotypic differences were observed between the strains that caused the three different types of infection (external abscess formation, infection with abscess formation in the internal organs, and ulcerative lymphangitis). Instead, it was noted that there is a higher phenetic correlation between strains isolated at California compared to the other strains. Additionally, high variability of resistance islands suggests gene acquisition through several events of horizontal gene transfer.", "token_count": 515, "char_count": 2167, "word_count": 298, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:36:53.174951", "source": { "split": "train_shard_00000", "doc_id": 3790 }, "chunk_id": "train_shard_00000_3790_0", "global_id": 4205 }, { "text": "Assessing the Genotypic Differences between Strains of Corynebacterium pseudotuberculosis biovar equi through Comparative Genomics.", "token_count": 38, "char_count": 131, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:53.543221", "source": { "split": "train_shard_00000", "doc_id": 3790 }, "chunk_id": "train_shard_00000_3790_1", "global_id": 4206 }, { "text": "With the advent of novel vesicular drug delivery systems especially bilosomes, for large molecular weight proteins and peptides, their oral administration seems a viable approach. These nano-vesicles have shown promising results for the effective delivery of insulin and other therapeutics, perhaps due to their structural composition. The present review has elaborated the biopharmaceutical challenges for the oral delivery of therapeutic proteins and peptides as well as presented a novel approach to deliver the essential macromolecules through oral route as bilosomes. The extensive search has been presented related to the formulation, evaluation and in vivo performance of bilosomes. Some of the crucial findings related to bilosomes have corroborated them superior to other colloidal carriers. The successful drug delivery through bilosomes requires significant justifications related to their interaction with the biological membranes. The other aspects such as absolute absorption, safety and toxicity of bilosome drug delivery should also be equally considered.\n\nBile Salt Stabilized Vesicles (Bilosomes): A Novel Nano-Pharmaceutical Design for Oral Delivery of Proteins and Peptides.", "token_count": 250, "char_count": 1194, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6242, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:54.024712", "source": { "split": "train_shard_00000", "doc_id": 3791 }, "chunk_id": "train_shard_00000_3791_0", "global_id": 4207 }, { "text": "Elucidation of the evolutionary history and interrelatedness of Plasmodium species that infect humans has been hampered by a lack of genetic information for three human-infective species: P. malariae and two P. ovale species (P. o. curtisi and P. o. wallikeri). These species are prevalent across most regions in which malaria is endemic and are often undetectable by light microscopy, rendering their study in human populations difficult. The exact evolutionary relationship of these species to the other human-infective species has been contested. Using a new reference genome for P. malariae and a manually curated draft P. o. curtisi genome, we are now able to accurately place these species within the Plasmodium phylogeny. Sequencing of a P. malariae relative that infects chimpanzees reveals similar signatures of selection in the P. malariae lineage to another Plasmodium lineage shown to be capable of colonization of both human and chimpanzee hosts. Molecular dating suggests that these host adaptations occurred over similar evolutionary timescales. In addition to the core genome that is conserved between species, differences in gene content can be linked to their specific biology. The genome suggests that P. malariae expresses a family of heterodimeric proteins on its surface that have structural similarities to a protein crucial for invasion of red blood cells. The data presented here provide insight into the evolution of the Plasmodium genus as a whole.\n\nPlasmodium malariae and P. ovale genomes provide insights into malaria parasite evolution.", "token_count": 363, "char_count": 1567, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:54.603225", "source": { "split": "train_shard_00000", "doc_id": 3792 }, "chunk_id": "train_shard_00000_3792_0", "global_id": 4208 }, { "text": "Planktothrix is a dominant cyanobacterial genus forming toxic blooms in temperate freshwater ecosystems. We sequenced the genome of planktic and non planktic Planktothrix strains to better represent this genus diversity and life style at the genomic level. Benthic and biphasic strains are rooting the Planktothrix phylogenetic tree and widely expand the pangenome of this genus. We further investigated in silico the genetic potential dedicated to gas vesicles production, nitrogen fixation as well as natural product synthesis and conducted complementary experimental tests by cell culture, microscopy and mass spectrometry. Significant differences for the investigated features could be evidenced between strains of different life styles. The benthic Planktothrix strains showed unexpected characteristics such as buoyancy, nitrogen fixation capacity and unique natural product features. In comparison with Microcystis, another dominant toxic bloom-forming genus in freshwater ecosystem, different evolutionary strategies were highlighted notably as Planktothrix exhibits an overall greater genetic diversity but a smaller genomic plasticity than Microcystis. Our results are shedding light on Planktothrix evolution, phylogeny and physiology in the frame of their diverse life styles.\n\nInsights into the Planktothrix genus: Genomic and metabolic comparison of benthic and planktic strains.", "token_count": 318, "char_count": 1393, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:55.163609", "source": { "split": "train_shard_00000", "doc_id": 3793 }, "chunk_id": "train_shard_00000_3793_0", "global_id": 4209 }, { "text": "Prebiotics are the non-digestible carbohydrate, which passes through the small intestine into unmetabolized form, reaches the large intestine and undergoes fermentation by the colonic bacteria thus; prebiotics stimulate the growth of probiotic bacteria. Further, bile salt hydrolase (BSH) is an enzyme that catalyses the deconjugation of bile salt, so it has enormous potential toward utilizing such capability of\n\nCatalytic Interactions and Molecular Docking of Bile Salt Hydrolase (BSH) from", "token_count": 136, "char_count": 493, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7681, "quality_score": 0.8841, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:55.593322", "source": { "split": "train_shard_00000", "doc_id": 3794 }, "chunk_id": "train_shard_00000_3794_0", "global_id": 4210 }, { "text": "Probiotic yeast has become a field of interest to scientists in recent years.\n\nAntimicrobial and antioxidant activities of Saccharomyces cerevisiae IFST062013, a potential probiotic.", "token_count": 55, "char_count": 182, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [ "IFST062013" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:55.951237", "source": { "split": "train_shard_00000", "doc_id": 3795 }, "chunk_id": "train_shard_00000_3795_0", "global_id": 4211 }, { "text": "Drug-induced liver injury (DILI) is a common toxicity observed in drug development and can lead to withdrawal of approved drugs from the market. To better understand the numerous mechanisms of DILI, recent efforts have focused on transporter inhibition, specifically liver canalicular bile salt export pump (Bsep) as one mechanism of DILI, and on the potential use of plasma bile acids as monitorable mechanism-based biomarkers of Bsep inhibition. To explore alternative mechanisms of bile acid increases in plasma, 6 antibiotic and 2 nonantibiotic drugs unlikely to be Bsep inhibitors were evaluated in rat studies. Surprisingly, all 6 antibiotics demonstrated 2- to 14-fold increases of plasma taurocholic acid (TCA). Also, unconjugated primary bile acids and secondary bile acids (both taurine-conjugated and unconjugated) were decreased in rat plasma after antibiotic treatments, but not with the nonantibiotic drugs. These results suggest alternative mechanisms of bile acids regulation such as attenuation of bacterial deconjugation of bile acids following reduction of gut microflora by antibiotics. Measurements of TCA transport in rat hepatocytes and Bsep-containing membrane vesicles suggest that inhibition of uptake into hepatocytes could also contribute to increases in plasma bile acid concentrations, while excluding inhibition of Bsep as a mechanism. These studies further demonstrate that there are several mechanisms that can lead to conjugated bile acid increases in plasma. By carefully considering the time course and magnitude of changes of individual bile acids relative to any changes seen in transaminases and bilirubin, interpretations and conclusions of the involvement of Bsep inhibition are enabled.\n\nAntibiotic-Induced Elevations of Plasma Bile Acids in Rats Independent of Bsep Inhibition.", "token_count": 434, "char_count": 1820, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5846, "quality_score": 0.7923, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:56.583493", "source": { "split": "train_shard_00000", "doc_id": 3796 }, "chunk_id": "train_shard_00000_3796_0", "global_id": 4212 }, { "text": "The present study highlights the fabrication of novel food-grade hydrogel particles based on pectin and starch for probiotic colon delivery. Lactobacillus plantarum ATCC:13643 (L. plantarum) cells were encapsulated in pectin/starch hydrogels by extrusion method. Four batches were formulated with different ratios of starch/pectin solutions. Optical and scanning electron microscopy obviously showed the random distribution of L. plantarum throughout the hydrogel network. The viability of encapsulated cells in simulated gastric fluid (SGF) and bile salt solution was significantly higher when compared to nonencapsulated cells. Results demonstrated that encapsulated cells in pectin/starch hydrogels were resistant against adverse conditions of the gastro-intestinal tract and bile salt solution compared to non-encapsulated cells. After sequential exposure to simulated gastric fluid (SGF) and simulated intestinal fluid (SIF) for 2h almost complete death of free cells was observed however the numbers of surviving cells were 5.15 and 6.67 Log CFU/g for pectin and pectin/starch hydrogel, respectively.\n\nInvestigation of pectin/starch hydrogel as a carrier for oral delivery of probiotic bacteria.", "token_count": 304, "char_count": 1201, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:57.173557", "source": { "split": "train_shard_00000", "doc_id": 3797 }, "chunk_id": "train_shard_00000_3797_0", "global_id": 4213 }, { "text": "We report the investigation of an outbreak situation of methicillin-resistant Staphylococcus aureus (MRSA) that occurred at the Academic Hospital Paramaribo (AZP) in the Republic of Suriname from April to May 2013. We performed whole genome sequencing with complete gap closure for chromosomes and plasmids on all isolates. The outbreak involved 12 patients and 1 healthcare worker/nurse at the AZP. In total 24 isolates were investigated. spa typing, genome-wide single nucleotide polymorphism (SNP) analysis, ad hoc whole genome multilocus sequence typing (wgMLST), stable core genome MLST (cgMLST) and in silico PFGE were used to determine phylogenetic relatedness and to identify transmission. Whole-genome sequencing (WGS) showed that all isolates were members of genomic variants of the North American USA300 clone. However, WGS revealed a heterogeneous population structure of USA300 circulating at the AZP. We observed up to 8 SNPs or up to 5 alleles of difference by wgMLST when the isolates were recovered from different body sites of the same patient or if direct transmission between patients was most likely. This work describes the usefulness of complete genome sequencing of bacterial chromosomes and plasmids providing an unprecedented level of detail during outbreak investigations not being visible by using conventional typing methods.\n\nComplete-genome sequencing elucidates outbreak dynamics of CA-MRSA USA300 (ST8-spa t008) in an academic hospital of Paramaribo, Republic of Suriname.", "token_count": 386, "char_count": 1505, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6743, "quality_score": 0.8372, "entities": { "genes": [ "USA300", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:57.809924", "source": { "split": "train_shard_00000", "doc_id": 3798 }, "chunk_id": "train_shard_00000_3798_0", "global_id": 4214 }, { "text": "In a hospital-acquired infection with multidrug-resistant Elizabethkingia, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene analysis identified the pathogen as Elizabethkingia miricola. Whole-genome sequencing, genus-level core genome analysis, and in silico DNA-DNA hybridization of 35 Elizabethkingia strains indicated that the species taxonomy should be further explored.\n\nDetermination of Elizabethkingia Diversity by MALDI-TOF Mass Spectrometry and Whole-Genome Sequencing.", "token_count": 140, "char_count": 524, "word_count": 59, "semantic_coherence": 1, "information_density": 0.8305, "quality_score": 0.9153, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:58.268311", "source": { "split": "train_shard_00000", "doc_id": 3799 }, "chunk_id": "train_shard_00000_3799_0", "global_id": 4215 }, { "text": "Clostridium difficile is a Gram-positive spore-forming obligate anaerobe that is a leading cause of antibiotic-associated diarrhea worldwide. In order for C. difficile to initiate infection, its aerotolerant spore form must germinate in the gut of mammalian hosts. While almost all spore-forming organisms use transmembrane germinant receptors to trigger germination, C. difficile uses the pseudoprotease CspC to sense bile salt germinants. CspC activates the related subtilisin-like protease CspB, which then proteolytically activates the cortex hydrolase SleC. Activated SleC degrades the protective spore cortex layer, a step that is essential for germination to proceed. Since CspC incorporation into spores also depends on CspA, a related pseudoprotease domain, Csp family proteins play a critical role in germination. However, how Csps are incorporated into spores remains unknown. In this study, we demonstrate that incorporation of the CspC, CspB, and CspA germination regulators into spores depends on CD0311 (renamed GerG), a previously uncharacterized hypothetical protein. The reduced levels of Csps in gerG spores correlate with reduced responsiveness to bile salt germinants and increased germination heterogeneity in single-spore germination assays. Interestingly, asparagine-rich repeat sequences in GerG's central region facilitate spontaneous gel formation in vitro even though they are dispensable for GerG-mediated control of germination. Since GerG is found exclusively in C. difficile, our results suggest that exploiting GerG function could represent a promising avenue for developing C. difficile-specific anti-infective therapies.\n\nA Clostridium difficile-Specific, Gel-Forming Protein Required for Optimal Spore Germination.", "token_count": 453, "char_count": 1750, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6709, "quality_score": 0.8355, "entities": { "genes": [ "CD0311" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:58.913611", "source": { "split": "train_shard_00000", "doc_id": 3800 }, "chunk_id": "train_shard_00000_3800_0", "global_id": 4216 }, { "text": "Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.\n\nThe pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.", "token_count": 146, "char_count": 721, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7717, "quality_score": 0.8859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:36:59.688046", "source": { "split": "train_shard_00000", "doc_id": 3801 }, "chunk_id": "train_shard_00000_3801_0", "global_id": 4217 }, { "text": "Stress tolerance is a key attribute that must be considered when using yeast cells for industrial applications. High temperature is one factor that can cause stress in yeast. High environmental temperature in particular may exert a natural selection pressure to evolve yeasts into thermotolerant strains. In the present study, three yeasts (Saccharomyces cerevisiae, MC4, and Kluyveromyces marxianus, OFF1 and SLP1) isolated from hot environments were exposed to increased temperatures and were then compared with a laboratory yeast strain. Their resistance to high temperature, oxidative stress, and antioxidant response were evaluated, along with the fatty acid composition of their cell membranes. The SLP1 strain showed a higher specific growth rate, biomass yield, and biomass volumetric productivity while also showing lower duplication time, reactive oxygen species (ROS) production, and lipid peroxidation. In addition, the SLP1 strain demonstrated more catalase activity after temperature was increased, and this strain also showed membranes enriched in saturated fatty acids. It is concluded that the SLP1 yeast strain is a thermotolerant yeast with less oxidative stress and a greater antioxidant response. Therefore, this strain could be used for fermentation at high temperatures.\n\nOxidative stress and antioxidant response in a thermotolerant yeast.", "token_count": 313, "char_count": 1363, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6495, "quality_score": 0.8247, "entities": { "genes": [ "OFF1", "MC4", "SLP1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:00.240063", "source": { "split": "train_shard_00000", "doc_id": 3802 }, "chunk_id": "train_shard_00000_3802_0", "global_id": 4218 }, { "text": "Drug-induced liver injury (DILI) is one of the major causes of drug attrition and failure. Currently, there is increasing evidence that direct inhibition of the human bile salt export pump (BSEP/ABCB11) by drugs and/or metabolites is one of the most important mechanisms of cholestatic DILI. In the present study, we employ two in silico methods, random forest (RF) and the pharmacophore method, to recognize potential BSEP inhibitors that could cause cholestatic DILI, with the aim of mitigating the risk of cholestatic DILI to some extent. The RF model achieved the best prediction performance, producing AUC (area under receiver operating characteristic curve) values of 0.901, 0.929 and 0.996 for leave-one-out cross-validation, the test set and the external test set, respectively, indicating that the built RF model has a satisfactory identification ability. As a complement to the RF model, the pharmacophore model was also built and was proved to be reliable with good predictive performance based on the internal and external validation results. Further analysis indicates that hydrophobicity, molecular size and polarity are important factors that influence the inhibitory activity of BSEP. Furthermore, the two models are applied to screen FDA-approved small molecule drugs, among which the drugs with the potential risk of cholestatic DILI are reported. In conclusion, the RF and pharmacophore models that we present can be considered as integrated screening tools to indicate the potential risk of cholestatic DILI by inhibition of BSEP.\n\nThe in silico identification of human bile salt export pump (ABCB11) inhibitors associated with cholestatic drug-induced liver injury.", "token_count": 398, "char_count": 1686, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:00.858485", "source": { "split": "train_shard_00000", "doc_id": 3803 }, "chunk_id": "train_shard_00000_3803_0", "global_id": 4219 }, { "text": "Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus\n\nBioinformatic Analyses of Unique (Orphan) Core Genes of the Genus", "token_count": 62, "char_count": 231, "word_count": 33, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:01.233756", "source": { "split": "train_shard_00000", "doc_id": 3804 }, "chunk_id": "train_shard_00000_3804_0", "global_id": 4220 }, { "text": "Tetrahydroxy bile acids (THBAs) are hydrophilic and are present at minimal or undetectable levels in healthy human adults, but are present at high levels in bile salt export pump (\n\nPrognostic roles of tetrahydroxy bile acids in infantile intrahepatic cholestasis.", "token_count": 78, "char_count": 264, "word_count": 40, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:01.613190", "source": { "split": "train_shard_00000", "doc_id": 3805 }, "chunk_id": "train_shard_00000_3805_0", "global_id": 4221 }, { "text": "Currently, echinocandins are first-line drugs for treatment of invasive candidiasis. However, data on how serum influences killing activity of echinocandins against uncommon Candida species are limited. Therefore, the killing activity of micafungin in RPMI-1640 and in 50% serum was compared against Candida guilliermondii, Candida lusitaniae, and Candida kefyr. Minimum inhibitory concentration (MIC) ranges in RPMI-1640 were 0.5-1, 0.12-0.25, and 0.06-0.12 mg/L, respectively. In 50% serum, MICs increased 32- to 256-fold. In RPMI-1640 ≥ 0.25, ≥4, and 32 mg/L micafungin was fungicidal against all four C. kefyr (≤4.04 hours), two of three C. lusitaniae (≤16.10 hours), and two of three C. guilliermondii (≤12.30 hours), respectively. In 50% serum, all three species grew at ≤4 mg/L. Micafungin at 16-32 mg/L was fungicidal against all C. kefyr isolates (≤3.03 hours) and at 32 mg/L was fungistatic against one of three C. lusitaniae isolates. Two C. lusitaniae isolates and all three C. guilliermondii grew at all tested concentrations. Adding human serum to susceptibility test media drew attention to loss of fungicidal or fungistatic activity of micafungin in the presence of serum proteins, which is not predicted by MICs in case of C. kefyr and C. lusitaniae in RPMI-1640. Our results strongly suggest that micafungin and probably other echinocandins should be used with caution against rare Candida species.", "token_count": 510, "char_count": 1416, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5399, "quality_score": 0.77, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:02.248132", "source": { "split": "train_shard_00000", "doc_id": 3806 }, "chunk_id": "train_shard_00000_3806_0", "global_id": 4222 }, { "text": "Decreased Killing Activity of Micafungin Against Candida guilliermondii, Candida lusitaniae, and Candida kefyr in the Presence of Human Serum.", "token_count": 44, "char_count": 142, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:02.615279", "source": { "split": "train_shard_00000", "doc_id": 3806 }, "chunk_id": "train_shard_00000_3806_1", "global_id": 4223 }, { "text": "Lysobacter enzymogenes M497-1 is a producer of commercialized achromopeptidase and is expected to harbour genes encoding various other antimicrobial enzymes. Here, we present the complete sequence of the genome of M497-1 and the expression profiles of the genes for various antimicrobial enzymes. Of the 117 peptidase-encoding genes found in the 6.1-Mb genome of M497-1, 15 genes (aside from the gene encoding the achromopeptidase) were expressed at a level higher than that of the average ribosomal protein genes in the 24-h culture. Thus, the strain was found more valuable than hitherto considered. In addition, M497-1 harbours 98 genes involved in the biosynthesis of various natural products, 16 of which are M497-1-specific across 4 Lysobacter species. A gene cluster starting at LEN_2603 through LEN_2673 among the 98 genes closely resembled the lysobactin biosynthesis gene cluster of Lysobacter sp. ATCC 53042. It is likely that M497-1 may produce lysobactin or related antibacterial compounds. Furthermore, comparative genomic analysis of M497-1 and four other Lysobacter species revealed that their core genome structure comprises 3,737 orthologous groups. Our findings are expected to advance further biotechnological application of Lysobacter spp. as a promising source of natural bioactive compounds.\n\nComplete genome sequence and expression profile of the commercial lytic enzyme producer Lysobacter enzymogenes M497-1.", "token_count": 417, "char_count": 1434, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5971, "quality_score": 0.7985, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:03.234831", "source": { "split": "train_shard_00000", "doc_id": 3807 }, "chunk_id": "train_shard_00000_3807_0", "global_id": 4224 }, { "text": "Clostridium perfringens is an important cause of foal necrotizing enteritis and canine acute hemorrhagic diarrhea. A major virulence determinant of the strains associated with these diseases appears to be a beta-sheet pore-forming toxin, NetF, encoded within a pathogenicity locus (NetF locus) on a large tcp-conjugative plasmid. Strains producing NetF also produce the putative toxin NetE, encoded within the same pathogenicity locus, as well as CPE enterotoxin and CPB2 on a second plasmid, and sometimes the putative toxin NetG within a pathogenicity locus (NetG locus) on another separate large conjugative plasmid. Previous genome sequences of two netF-positive C. perfringens showed that they both shared three similar plasmids, including the NetF/NetE and CPE/CPB2 toxins-encoding plasmids mentioned above and a putative bacteriocin-encoding plasmid. The main purpose of this study was to determine whether all NetF-producing strains share this common plasmid profile and whether their distinct NetF and CPE pathogenicity loci are conserved. To answer this question, 15 equine and 15 canine netF-positive isolates of C. perfringens were sequenced using Illumina Hiseq2000 technology. In addition, the clonal relationships among the NetF-producing strains were evaluated by core genome multilocus sequence typing (cgMLST). The data obtained showed that all NetF-producing strains have a common plasmid profile and that the defined pathogenicity loci on the plasmids are conserved in all these strains. cgMLST analysis showed that the NetF-producing C. perfringens strains belong to two distinct clonal complexes. The pNetG plasmid was absent from isolates of one of the clonal complexes, and there were minor but consistent differences in the NetF/NetE and CPE/CPB2 plasmids between the two clonal complexes.\n\nNetF-producing Clostridium perfringens: Clonality and plasmid pathogenicity loci analysis.", "token_count": 514, "char_count": 1906, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5593, "quality_score": 0.7796, "entities": { "genes": [ "CPB2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:37:03.884353", "source": { "split": "train_shard_00000", "doc_id": 3808 }, "chunk_id": "train_shard_00000_3808_0", "global_id": 4225 }, { "text": "PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses.\n\nPanViz: interactive visualization of the structure of functionally annotated pangenomes.", "token_count": 138, "char_count": 640, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7191, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:04.319964", "source": { "split": "train_shard_00000", "doc_id": 3809 }, "chunk_id": "train_shard_00000_3809_0", "global_id": 4226 }, { "text": "The plague agent Yersinia pestis persists for years in the soil. Two millennia after swiping over Europe and North Africa, plague established permanent foci in North Africa but not in neighboring Europe. Mapping human plague foci reported in North Africa for 70 years indicated a significant location at <3 kilometers from the Mediterranean seashore or the edge of salted lakes named chotts. In Algeria, culturing 352 environmental specimens naturally containing 0.5 to 70 g/L NaCl yielded one Y. pestis Orientalis biotype isolate in a 40 g/L NaCl chott soil specimen. Core genome SNP analysis placed this isolate within the Y. pestis branch 1, Orientalis biovar. Culturing Y. pestis in broth steadily enriched in NaCl indicated survival up to 150 g/L NaCl as L-form variants exhibiting a distinctive matrix assisted laser desorption-ionization time-of-flight mass spectrometry peptide profile. Further transcriptomic analyses found the upregulation of several outer-membrane proteins including TolC efflux pump and OmpF porin implied in osmotic pressure regulation. Salt tolerance of Y. pestis L-form may play a role in the maintenance of natural plague foci in North Africa and beyond, as these geographical correlations could be extended to 31 plague foci in the northern hemisphere (from 15°N to 50°N).\n\nYersinia pestis halotolerance illuminates plague reservoirs.", "token_count": 387, "char_count": 1368, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:04.935046", "source": { "split": "train_shard_00000", "doc_id": 3810 }, "chunk_id": "train_shard_00000_3810_0", "global_id": 4227 }, { "text": "The data in this paper are additional information to the research article entiltled \"Inhibition of cholesterol transport in an intestine cell model by pine-derived phytosterols\" (Yi et al.,2016) [1]. The data derived from the measurement on six liquid formulations of commercial pine-derived phytosterol (CPP) by dynamic light scattering. The data cover micelle size and the zeta-potential for formulations with cholesterol including monoglyceride, oleic acid, and bile salt. The data demonstrate the critical effect of the bile salt concentration on the size of cholesterol-digested fat micelles.\n\nData for the size of cholesterol-fat micelles as a function of bile salt concentration and the physico-chemical properties of six liquid experimental pine-derived phytosterol formulations in a cholesterol-containing artificial intestine fluid.", "token_count": 211, "char_count": 842, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:05.401470", "source": { "split": "train_shard_00000", "doc_id": 3811 }, "chunk_id": "train_shard_00000_3811_0", "global_id": 4228 }, { "text": "Characterizing the immune response to pneumococcal proteins is critical in understanding this bacterium's epidemiology and vaccinology. Probing a custom-designed proteome microarray with sera from 35 healthy US adults revealed a continuous distribution of IgG affinities for 2,190 potential antigens from the species-wide pangenome. Reproducibly elevated IgG binding was elicited by 208 \"antibody binding targets\" (ABTs), which included 109 variants of the diverse pneumococcal surface proteins A and C (PspA and PspC) and zinc metalloprotease A and B (ZmpA and ZmpB) proteins. Functional analysis found ABTs were enriched in motifs for secretion and cell surface association, with extensive representation of cell wall synthesis machinery, adhesins, transporter solute-binding proteins, and degradative enzymes. ABTs were associated with stronger evidence for evolving under positive selection, although this varied between functional categories, as did rates of diversification through recombination. Particularly rapid variation was observed at some immunogenic accessory loci, including a phage protein and a phase-variable glycosyltransferase ubiquitous among the diverse set of genomic islands encoding the serine-rich PsrP glycoprotein. Nevertheless, many antigens were conserved in the core genome, and strains' antigenic profiles were generally stable. No strong evidence was found for any epistasis between antigens driving population dynamics, or redundancy between functionally similar accessory ABTs, or age stratification of antigen profiles. These results highlight the paradox of why substantial variation is observed in only a subset of epitopes. This result may indicate only some interactions between immunoglobulins and ABTs clear pneumococcal colonization or that acquired immunity to pneumococci is an accumulation of individually weak responses to ABTs evolving under different levels of functional constraint.\n\nDiverse evolutionary patterns of pneumococcal antigens identified by pangenome-wide immunological screening.", "token_count": 488, "char_count": 2043, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:06.064536", "source": { "split": "train_shard_00000", "doc_id": 3812 }, "chunk_id": "train_shard_00000_3812_0", "global_id": 4229 }, { "text": "Drug induced liver injury (DILI) has contributed more to marketed pharmaceutical withdrawals and clinical development failures than any other human organ toxicity. DILI seen in animal studies also frequently leads to the discontinuation of promising drug candidates very early in the pipeline. This manuscript reviews and critically assesses the current regulatory expectations; the current drug development approaches, strategies, and gaps; and the numerous exciting opportunities becoming available to address these gaps through technological advances. Emerging integrated pharmaceutical development strategies, while far from uniform, have generally evolved to currently inform early DILI risk potential using supplemental assays for reactive metabolite formation, mitochondrial toxicity, inhibition of bile salt transport, and cellular imaging endpoints including cytotoxicity. Despite these approaches and robust animal testing, significant gaps in addressing human DILI remain. Increasingly sophisticated in vitro humanized test systems, new animal models, emerging computational models, and novel translational biomarkers are being introduced to improve our ability to more accurately predict DILI. Expectations are high for a future state with more predictive tools and problem solving strategies that will improve pharmaceutical discovery and development in relation to understanding human DILI risk potential and make it less dependent on animal studies for successfully developing safer drug candidates.\n\nThe Promise of New Technologies to Reduce, Refine, or Replace Animal Use while Reducing Risks of Drug Induced Liver Injury in Pharmaceutical Development.", "token_count": 317, "char_count": 1669, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6906, "quality_score": 0.8453, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:06.624089", "source": { "split": "train_shard_00000", "doc_id": 3813 }, "chunk_id": "train_shard_00000_3813_0", "global_id": 4230 }, { "text": "Holder pasteurization has been reported to modify human milk composition and structure by inactivating bile salt-stimulated lipase (BSSL) and partially denaturing some of its proteins, potentially affecting its subsequent digestion.\n\nImpact of human milk pasteurization on gastric digestion in preterm infants: a randomized controlled trial.", "token_count": 78, "char_count": 341, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:06.994007", "source": { "split": "train_shard_00000", "doc_id": 3814 }, "chunk_id": "train_shard_00000_3814_0", "global_id": 4231 }, { "text": "To investigate the protective effect of glutamine (Gln) against obstructive cholestasis in association with farnesoid X receptor (FXR) activation, an obstructive cholestasis model was established in male Sprague-Dawley rats by bile duct ligation (BDL). Serum biomarkers and hematoxylin plus eosin staining were used to identify the degree of hepatic injury in the rats with obstructive cholestasis after Gln treatment. Immunohistochemistry, real-time PCR, Western blot, cultured primary rat hepatocytes with FXR knockdown, and dual-luciferase reporter assay were performed to elucidate the mechanisms underlying Gln hepatoprotection. We found that Gln treatment protected against obstructive cholestasis induced by BDL through reducing hepatocyte injury. Upregulation of the hepatic efflux transporters small heterodimer partner (Shp), bile salt export pump (Bsep), and multidrug resistance-associated protein 2 (Mrp2), and inhibition of the hepatic uptake transporter Na\n\nGlutamine attenuates obstructive cholestasis in rats via farnesoid X receptor-mediated regulation of Bsep and Mrp2.", "token_count": 301, "char_count": 1088, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7153, "quality_score": 0.8576, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:07.555812", "source": { "split": "train_shard_00000", "doc_id": 3815 }, "chunk_id": "train_shard_00000_3815_0", "global_id": 4232 }, { "text": "Attenuation can be regarded as a tool to modulate the metabolism of probiotic bacteria and, consequently, a strategy to reduce the acidification of the active drinks. Attenuation can be done through chemical and physical approaches and ultrasound (US) is a possibility, previously tested to modulate the metabolism of lactic acid bacteria inoculated in a rice drink, but no data are available on the effect of this treatment of the overall profile of probiotic bacteria. Therefore, the main topic of this paper was to study the effect of US-attenuation on some properties of Lactobacillus reuteri, Lactobacillus plantarum, Bifidobacterium longum, and Bifidobacterium infantis (survival at pH2, and 2.5, and with 0.3% of bile salt added, hydrophobicity, acidification, and growth at different temperatures, pH or in presence of 7% NaCl). A preliminary screening was done by using 3 power levels (40, 60, and 80%) and 3 different treatment times (2, 4, and 6min); immediately after sonication, acidification and viable count were tested. The best combination to avoid post-acidification was the following one: power, 60%; time, 6min; pulse, 2s. The effect of this combination on the overall profile of the test strains (functional and technological properties) was studied. This combination exerted a positive effect on the hydrophobicity and adhesion to Caco-2 cells of L. reuteri, although the growth at pH4 was negatively affected. In the other strains, there a was negative effect on acid and bile resistance.\n\nUltrasound attenuation of lactobacilli and bifidobacteria: Effect on some technological and probiotic properties.", "token_count": 425, "char_count": 1626, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5813, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:08.175891", "source": { "split": "train_shard_00000", "doc_id": 3816 }, "chunk_id": "train_shard_00000_3816_0", "global_id": 4233 }, { "text": "Human hepatoma cells may represent a valuable alternative to the use of human hepatocytes for studying hepatic drug transporters, which is now a regulatory issue during drug development. In the present work, we have characterized hepatic drug transporter expression, activity and regulation in human hepatoma HuH-7 cells, in order to determine the potential relevance of these cells for drug transport assays. HuH-7 cells displayed notable multidrug resistance-associated protein (MRP) activity, presumed to reflect expression of various hepatic MRPs, including MRP2. By contrast, they failed to display functional activities of the uptake transporters sodium taurocholate co-transporting polypeptide (NTCP), organic anion-transporting polypeptides (OATPs) and organic cation transporter 1 (OCT1), and of the canalicular transporters P-glycoprotein and breast cancer resistance protein (BCRP). Concomitantly, mRNA expressions of various sinusoidal and canalicular hepatic drug transporters were not detected (NTCP, OATP1B1, organic anion transporter 2 (OAT2), OCT1 and bile salt export pump) or were found to be lower (OATP1B3, OATP2B1, multidrug and toxin extrusion protein 1, BCRP and MRP3) in hepatoma HuH-7 cells than those found in human hepatocytes, whereas other transporters such as OAT7, MRP4 and MRP5 were up-regulated. HuH-7 cells additionally exhibited farnesoid X receptor (FXR)- and nuclear factor erythroid 2-related factor 2 (Nrf2)-related up-regulation of some transporters. Such data indicate that HuH-7 cells, although expressing rather poorly some main hepatic drug transporters, may be useful for investigating interactions of drugs with MRPs, notably MRP2, and for studying FXR- or Nrf2-mediated gene regulation.\n\nDrug Transporter Expression and Activity in Human Hepatoma HuH-7 Cells.", "token_count": 488, "char_count": 1807, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [ "OCT1", "OAT2", "MRP2", "MRP4", "MRP3", "OAT7", "MRP5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:08.853417", "source": { "split": "train_shard_00000", "doc_id": 3817 }, "chunk_id": "train_shard_00000_3817_0", "global_id": 4234 }, { "text": "In the present study, the interactions between chitosan-coated magnetic nanoparticles (C-MNP) and Trichoderma sp. spores as well as Kluyveromyces marxianus cells were studied. By Plackett-Burman design, it was demonstrated that factors which directly influenced on yeast cell immobilization and magnetic separation were inoculum and C-MNP quantity, stirring speed, interaction time, and volume of medium, while in the case of fungal spores, the temperature also was disclosed as an influencing factor. Langmuir and Freundlich models were applied for the mathematical analysis of adsorption isotherms at 30°C. For Trichoderma sp. spore adsorption isotherm, the highest correlation coefficient was observed for lineal function of Langmuir model with a maximum adsorption capacity at 5.00E + 09 spores (C-MNP g\n\nTrichoderma sp. spores and Kluyveromyces marxianus cells magnetic separation: Immobilization on chitosan-coated magnetic nanoparticles.", "token_count": 253, "char_count": 944, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:09.367002", "source": { "split": "train_shard_00000", "doc_id": 3818 }, "chunk_id": "train_shard_00000_3818_0", "global_id": 4235 }, { "text": "Parenteral nutrition (PN), a lifesaving therapy in patients with intestinal failure, has been associated with hepatobiliary complications including steatosis, cholestasis and fibrosis, collectively known as parenteral nutrition-associated liver disease (PNALD). To date, the pathogenesis of PNALD is poorly understood and therapeutic options are limited. Impaired bile salt homeostasis has been proposed to contribute PNALD. The objective of this study was to establish a PNALD model in rats and to evaluate the effects of continuous parenteral nutrition (PN) on bile salt homeostasis.\n\nParenteral nutrition dysregulates bile salt homeostasis in a rat model of parenteral nutrition-associated liver disease.", "token_count": 177, "char_count": 707, "word_count": 96, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:09.823397", "source": { "split": "train_shard_00000", "doc_id": 3819 }, "chunk_id": "train_shard_00000_3819_0", "global_id": 4236 }, { "text": "To evaluate the efficacy of nontransplant surgery for pediatric cholestasis, 58 clinically diagnosed children, including 20 with Alagille syndrome (ALGS), 16 with familial intrahepatic cholestasis-1 (FIC1), 18 with bile salt export pump (BSEP) disease, and 4 others with low γ-glutamyl transpeptidase disease (levels <100 U/L), were identified across 14 Childhood Liver Disease Research Network (ChiLDReN) centers. Data were collected retrospectively from individuals who collectively had 39 partial external biliary diversions (PEBDs), 11 ileal exclusions (IEs), and seven gallbladder-to-colon (GBC) diversions. Serum total bilirubin decreased after PEBD in FIC1 (8.1 ± 4.0 vs. 2.9 ± 4.1 mg/dL, preoperatively vs. 12-24 months postoperatively, respectively; P = 0.02), but not in ALGS or BSEP. Total serum cholesterol decreased after PEBD in ALGS patients (695 ± 465 vs. 457 ± 319 mg/dL, preoperatively vs. 12-24 months postoperatively, respectively; P = 0.0001). Alanine aminotransferase levels increased in ALGS after PEBD (182 ± 70 vs. 260 ± 73 IU/L, preoperatively vs. 24 months; P = 0.03), but not in FIC1 or BSEP. ALGS, FIC1, and BSEP patients experienced less severely scored pruritus after PEBD (ALGS, 100% vs. 9% severe; FIC1, 64% vs. 10%; BSEP, 50% vs. 20%, preoperatively vs. >24 months postoperatively, respectively; P < 0.001). ALGS patients experienced a trend toward greater freedom from xanthomata after PEBD", "token_count": 510, "char_count": 1425, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6934, "quality_score": 0.8467, "entities": { "genes": [ "FIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:10.511271", "source": { "split": "train_shard_00000", "doc_id": 3820 }, "chunk_id": "train_shard_00000_3820_0", "global_id": 4237 }, { "text": "There was a trend toward decreased pruritus in FIC1 after IE and GBC. Vitamin K supplementation increased in ALGS after PEBD (33% vs. 77%; P = 0.03). Overall, there were 15 major complications after surgery. Twelve patients (3 ALGS, 3 FIC1, and 6 BSEP) subsequently underwent liver transplantation.\n\nAnalysis of surgical interruption of the enterohepatic circulation as a treatment for pediatric cholestasis.", "token_count": 122, "char_count": 408, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8871, "quality_score": 0.9435, "entities": { "genes": [ "FIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:10.907154", "source": { "split": "train_shard_00000", "doc_id": 3820 }, "chunk_id": "train_shard_00000_3820_1", "global_id": 4238 }, { "text": "Hereditary cholestasis in childhood and infancy with normal serum gamma-glutamyltransferase (GGT) activity is linked to several genes. Many patients, however, remain genetically undiagnosed. Defects in myosin VB (MYO5B; encoded by MYO5B) cause microvillus inclusion disease (MVID; MIM251850) with recurrent watery diarrhea. Cholestasis, reported as an atypical presentation in MVID, has been considered a side effect of parenteral alimentation. Here, however, we report on 10 patients who experienced cholestasis associated with biallelic, or suspected biallelic, mutations in MYO5B and who had neither recurrent diarrhea nor received parenteral alimentation. Seven of them are from two study cohorts, together comprising 31 undiagnosed low-GGT cholestasis patients; 3 are sporadic. Cholestasis in 2 patients was progressive, in 3 recurrent, in 2 transient, and in 3 uncategorized because of insufficient follow-up. Liver biopsy specimens revealed giant-cell change of hepatocytes and intralobular cholestasis with abnormal distribution of bile salt export pump (BSEP) at canaliculi, as well as coarse granular dislocation of MYO5B. Mass spectrometry of plasma demonstrated increased total bile acids, primary bile acids, and conjugated bile acids, with decreased free bile acids, similar to changes in BSEP-deficient patients. Literature review revealed that patients with biallelic mutations predicted to eliminate MYO5B expression were more frequent in typical MVID than in isolated-cholestasis patients (11 of 38 vs. 0 of 13).\n\nDefects in myosin VB are associated with a spectrum of previously undiagnosed low γ-glutamyltransferase cholestasis.", "token_count": 467, "char_count": 1648, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7004, "quality_score": 0.8502, "entities": { "genes": [ "MIM251850", "MYO5B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:11.550882", "source": { "split": "train_shard_00000", "doc_id": 3821 }, "chunk_id": "train_shard_00000_3821_0", "global_id": 4239 }, { "text": "Perfluoroalkyl sulfonates (PFSAs) such as perfluorohexane sulfonate (PFHxS) and perfluorooctane sulfonate (PFOS) have very long serum elimination half-lives in humans, and preferentially distribute to serum and liver. The enterohepatic circulation of PFHxS and PFOS likely contributes to their extended elimination half-lives. We previously demonstrated that perfluorobutane sulfonate (PFBS), PFHxS, and PFOS are transported into hepatocytes both in a sodium-dependent and a sodium-independent manner. We identified Na+/taurocholate cotransporting polypeptide (NTCP) as the responsible sodium-dependent transporter. Furthermore, we demonstrated that the human apical sodium-dependent bile salt transporter (ASBT) contributes to the intestinal reabsorption of PFOS. However, so far no sodium-independent uptake transporters for PFSAs have been identified in human hepatocytes or enterocytes. In addition, perfluoroalkyl carboxylates (PFCAs) with 8 and 9 carbons were shown to preferentially distribute to the liver of rodents; however, no rat or human liver uptake transporters are known to transport these PFCAs. Therefore, we tested whether PFBS, PFHxS, PFOS, and PFCAs with 7-10 carbons are substrates of organic anion transporting polypeptides (OATPs). We used CHO and HEK293 cells to demonstrate that human OATP1B1, OATP1B3, and OATP2B1 can transport PFBS, PFHxS, PFOS, and the 2 PFCAs (C8 and C9). In addition, we show that rat OATP1A1, OATP1A5, OATP1B2, and OATP2B1 transport all 3 PFSAs", "token_count": 469, "char_count": 1493, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6098, "quality_score": 0.8049, "entities": { "genes": [ "HEK293" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:12.193760", "source": { "split": "train_shard_00000", "doc_id": 3822 }, "chunk_id": "train_shard_00000_3822_0", "global_id": 4240 }, { "text": "In conclusion, our results suggest that besides NTCP and ASBT, OATPs also are capable of contributing to the enterohepatic circulation and extended human serum elimination half-lives of the tested perfluoroalkyl acids.\n\nOrganic Anion Transporting Polypeptides Contribute to the Disposition of Perfluoroalkyl Acids in Humans and Rats.", "token_count": 85, "char_count": 333, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8043, "quality_score": 0.9022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:12.569190", "source": { "split": "train_shard_00000", "doc_id": 3822 }, "chunk_id": "train_shard_00000_3822_1", "global_id": 4241 }, { "text": "Bile salt hydrolase (BSH) plays an essential role in the cholesterol-removing effect of lactic acid bacteria, which hydrolyze conjugated bile salts to amino acid and deconjugated bile salts. However, Lactobacillus casei lacks the bsh gene, which may make it highly sensitive to bile salt stress. We wanted to improve the BSH activity of L. casei for various food-industry applications (e.g., milk fermentation). Plate assay testing indicated that Lactobacillus plantarum AR113 has the highest BSH activity. We cloned and sequenced 4 bsh genes from the genome of L. plantarum AR113. Structure modeling and molecular docking of BSH indicated that BSH1 and BSH3 could react efficiently with bile salts, so we selected BSH1 and BSH3 for heterologous expression in L. casei. Compared with single expression of BSH1 or BSH3, co-expression of both protein sequences showed the highest hydrolysis activity by HPLC analysis. Our results suggested that heterologous expression of BSH in L. casei can significantly improve host activity against bile salts, and in silico molecular docking could be an efficient method of rapid screening for BSH with high activity.\n\nShort communication: Improving the activity of bile salt hydrolases in Lactobacillus casei based on in silico molecular docking and heterologous expression.", "token_count": 339, "char_count": 1311, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.7929, "entities": { "genes": [ "AR113", "BSH1", "BSH3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:13.140309", "source": { "split": "train_shard_00000", "doc_id": 3823 }, "chunk_id": "train_shard_00000_3823_0", "global_id": 4242 }, { "text": "The aim of this study was to optimize the in vitro transfer model and to increase its biorelevance to more accurately mimic the in vivo supersaturation and precipitation behaviour of weak basic drugs. Therefore, disintegration of the formulation, volumes of the stomach and intestinal compartments, transfer rate, bile salt concentration, pH range and paddle speed were varied over a physiological relevant range. The supersaturation and precipitation data from these experiments for Ketoconazole (KTZ) were coupled to physiologically based pharmacokinetic (PBPK) model using Stella® software, which also incorporated the disposition kinetics of KTZ taken from the literature, in order to simulate the oral absorption and plasma profile in humans. As expected for a poorly soluble weak base, KTZ demonstrated supersaturation followed by precipitation under various in vitro conditions simulating the proximal small intestine with the results influenced by transfer rate, hydrodynamics, volume, bile salt concentration and pH values. When the in vitro data representing the \"average\" GI conditions was coupled to the PBPK model, the simulated profiles came closest to the observed mean plasma profiles for KTZ. In line with the high permeability of KTZ, the simulated profiles were highly influenced by supersaturation whilst precipitation was not predicted to occur in vivo. A physiological relevant in vitro \"standard\" transfer model setup to investigate supersaturation and precipitation was established. For translating the in vitro data to the in vivo setting, it is important that permeability is considered which can be achieved by coupling the in vitro data to PBPK modelling.\n\nPrediction of Ketoconazole absorption using an updated in vitro transfer model coupled to physiologically based pharmacokinetic modelling.", "token_count": 407, "char_count": 1823, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5358, "quality_score": 0.7679, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:13.763028", "source": { "split": "train_shard_00000", "doc_id": 3824 }, "chunk_id": "train_shard_00000_3824_0", "global_id": 4243 }, { "text": "Fibroblast growth factor 19 (FGF19) is an ileum-derived endrocrine factor that is produced in response to transepithelial bile salt flux. FGF19 represses bile salt synthesis in the liver. Despite the general assumption that FGF19 signals to the liver via portal blood, no human data are available to support this notion. The aim was to study portal FGF19 levels, and determined bile salt and FGF19 fluxes across visceral organs in humans. Bile salt and FGF19 levels were assessed in arterial, portal, and hepatic venous blood collected from fasted patients who underwent partial liver resection for colorectal liver metastases (n = 30). Fluxes across the portal-drained viscera (PDV), liver, and splanchnic area were calculated. Portal bile salt levels (7.8 [5.0-12.4] μmol/L) were higher than levels in arterial (2.7 [1.7-5.5] μmol/L, P < 0.0001) and hepatic venous blood (3.4 [2.5-6.5] μmol/L, P < 0.0001). Bile salts released by the PDV (+1.2 [+0.7-+2.0] mmol kg\n\nThe portal-drained viscera release fibroblast growth factor 19 in humans.", "token_count": 358, "char_count": 1040, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:14.338473", "source": { "split": "train_shard_00000", "doc_id": 3825 }, "chunk_id": "train_shard_00000_3825_0", "global_id": 4244 }, { "text": "CVD affect a large proportion of the world's population, with dyslipidaemia as the major risk factor. The regular consumption of both probiotic bacteria and yeast has been associated with improvement in the serum lipid profile. Thus, the present review aims to describe and discuss the potential mechanisms responsible for the hypocholesterolaemic effect of regular consumption of probiotic bacteria and yeast. Regarding the hypocholesterolaemic effect of probiotic bacteria, the potential mechanisms responsible include: deconjugation of bile salts; modulation of lipid metabolism; and decreased absorption of intestinal cholesterol through co-precipitation of intestinal cholesterol with the deconjugated bile salts, incorporation and assimilation of cholesterol in the cell membrane of the probiotics, intestinal conversion of cholesterol in coprostanol, and inhibition of the expression of the intestinal cholesterol transporter Niemann-Pick C1 like 1 (NPC1L1) in the enterocytes. The potential mechanisms responsible for the hypocholesterolaemic effect of probiotic yeasts include: deconjugation of bile salts; co-precipitation of intestinal cholesterol with the deconjugated bile salts; incorporation and assimilation of cholesterol in the cell membrane; and inhibition of hepatic cholesterol synthesis. The regular consumption of probiotic bacteria and yeast, as a non-pharmaceutical approach to help manage cardiovascular risk, holds promise, according to the beneficial hypocholesterolaemic effects described herein. However, the hypocholesterolaemic effects vary according to the strains used, the physiological state of the host, and the type of diet to which the probiotics are added. Further studies are necessary to fill the gaps with regard to the knowledge related to this topic.\n\nMechanisms responsible for the hypocholesterolaemic effect of regular consumption of probiotics.", "token_count": 461, "char_count": 1893, "word_count": 254, "semantic_coherence": 1, "information_density": 0.4646, "quality_score": 0.7323, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:14.973891", "source": { "split": "train_shard_00000", "doc_id": 3826 }, "chunk_id": "train_shard_00000_3826_0", "global_id": 4245 }, { "text": "In this study, a combination of catalytic and biotechnological processes was proposed for the first time for application in a cellulose biorefinery for the production of 5-hydroxymethylfurfural (5-HMF) and bioethanol. Hydrolytic dehydration of the mechanically activated microcrystalline cellulose over a carbon-based mesoporous Sibunt-4 catalyst resulted in moderate yields of glucose and 5-HMF (21.1-25.1 and 6.6-9.4 %). 5-HMF was extracted from the resulting mixture with isobutanol and subjected to ethanol fermentation. A number of yeast strains were isolated that also revealed high thermotolerance (up to 50 °C) and resistance to inhibitors found in the hydrolysates. The strains Kluyveromyces marxianus C1 and Ogataea polymorpha CBS4732 were capable of producing ethanol from processed catalytic hydrolysates of cellulose at 42 °C, with yields of 72.0±5.7 and 75.2±4.3 % from the maximum theoretical yield of ethanol, respectively.\n\nCellulose Biorefinery Based on a Combined Catalytic and Biotechnological Approach for Production of 5-HMF and Ethanol.", "token_count": 339, "char_count": 1059, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8176, "entities": { "genes": [ "CBS4732" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:15.544907", "source": { "split": "train_shard_00000", "doc_id": 3827 }, "chunk_id": "train_shard_00000_3827_0", "global_id": 4246 }, { "text": "In this study, we evaluated the survival of Enterococcus faecium and Enterococcus durans, isolated from cheese, in the presence of medications and under simulated in vitro gastrointestinal conditions. The presence of genes encoding virulence factors, the susceptibility to antimicrobial agents, and adhesion properties were also assessed. Enterococcus faecium and E. durans both exhibited resistance to most of the tested medications but showed a large sensitivity to analgesics and antihypertensives; they also showed wide susceptibility to antimicrobial agents. Enterococcus durans SJRP29 had greater resistance to the presence of medications in comparison with the probiotic Lactobacillus acidophilus La-5. The strains, except for E. durans SJRP05, did not harbor virulence genes. Enterococcus durans SJRP14, SJRP17, and SJRP26 were sensitive to all tested antimicrobial agents. Enterococcus faecium was more stable during the simulation of gastrointestinal tract and showed greater viability. At the end of the assay, except for E. durans SJRP17, all strains showed high viability (>7 log cfu/mL). Enterococcus durans SJRP29 stood out from the other strains and was selected for further evaluation; it tolerated up to 3.0% NaCl at 30 and 37°C, besides having good adhesion properties (high values of auto-aggregation, co-aggregation, and hydrophobicity). Additionally, the microorganism did not show bile salt hydrolase activity or mucin degradation. These results encourage carrying out additional tests to evaluate the probiotic features by using in vitro dynamic models and in vivo tests before applying these strains to a food system.\n\nEnterococcus faecium and Enterococcus durans isolated from cheese: Survival in the presence of medications under simulated gastrointestinal conditions and adhesion properties.", "token_count": 473, "char_count": 1819, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5508, "quality_score": 0.7754, "entities": { "genes": [ "SJRP14", "SJRP05", "SJRP17", "SJRP29", "SJRP26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:16.179540", "source": { "split": "train_shard_00000", "doc_id": 3828 }, "chunk_id": "train_shard_00000_3828_0", "global_id": 4247 }, { "text": "Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease with high morbidity and mortality that predominantly affects preterm neonates during outbreaks. In a previous study, the present authors identified 15 Clostridium butyricum isolates from stool samples during a series of NEC cases involving four neonatal intensive care units. A clonal lineage of these strains was observed by in-silico multi-locus sequence typing.\n\nMulti-spacer typing as an effective method to distinguish the clonal lineage of Clostridium butyricum strains isolated from stool samples during a series of necrotizing enterocolitis cases.", "token_count": 155, "char_count": 629, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7558, "quality_score": 0.8779, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:16.624665", "source": { "split": "train_shard_00000", "doc_id": 3829 }, "chunk_id": "train_shard_00000_3829_0", "global_id": 4248 }, { "text": "Cell wall polysaccharides from filamentous fungi and yeasts have been reported as antioxidant and antiproliferative polymers. Thus, we evaluated these activities from cell wall polysaccharides from Kluyveromyces marxianus CCT7735. By using a centrifugal filter, a 203kDa α-d-mannan (KMM-5) was obtained. KMM-5 exhibited no effect on HeLa cells and a weak antiproliferative activity against Hep-G2 cells. In addition, at higher concentrations, it presented a cytotoxicity to the normal cell line, 3T3. However, KMM-5 showed copper- and iron-chelating abilities, the latter of which presented improved activity. By using 2D-NMR COSY, HSQC edited and HMBC experiments, a structure arrangement was proposed. The main chain was formed by 6)-α-d-Manp-(1→6) units substituted at the 2-O-position by non-reducing terminals α-d-Manp-(1→2) and by a branched tetrasaccharide. The latter was formed by an internal 2)-α-d-Manp-(1→2) unit with linked to it a 2,3)-α-d-Manp-(1→2) unit substituted at the 2-O-position by a non-reducing terminal α-d-Manp-(1→2), and at the 3-O-position by a non-reducing terminal α-d-Manp-(1→3). In conclusion, we considered K. marxianus CCT7735 a source of natural and renewable polysaccharides with pharmacological properties.\n\nChemical structure, antiproliferative and antioxidant activities of a cell wall α-d-mannan from yeast Kluyveromyces marxianus.", "token_count": 448, "char_count": 1372, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [ "CCT7735" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:17.259115", "source": { "split": "train_shard_00000", "doc_id": 3830 }, "chunk_id": "train_shard_00000_3830_0", "global_id": 4249 }, { "text": "Metformin is established as the first-line therapy for type 2 diabetes (T2DM), but its mode of action remains elusive. Elucidation of the mechanisms underlying the anti-diabetic action of metformin may have the potential to optimise its glucose-lowering efficacy and lead to the development of agents acting on novel targets for the management of type 2 diabetes. Areas covered: This review highlights key pharmacokinetic features of metformin, summarises recent insights into its hepatic and gastrointestinal actions relevant to blood glucose homeostasis, and discusses the common gastrointestinal side effects of metformin. Literature concerning these areas was reviewed on PubMed. Expert commentary: The mechanisms by which metformin improves glycaemic control in type 2 diabetes are complex. Although novel hepatic pathways continue to be reported in preclinical studies, there is a lack of human evidence for most of these. Considering the fundamental role of the gastrointestinal tract in the regulation of blood glucose homeostasis and pleiotropic actions of metformin on several gastrointestinal targets relevant to glycaemic control, the gut is likely to represent at least as important a site of metformin action as the liver in the management of type 2 diabetes.\n\nNew insights into the anti-diabetic actions of metformin: from the liver to the gut.", "token_count": 318, "char_count": 1359, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5743, "quality_score": 0.7871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:17.819841", "source": { "split": "train_shard_00000", "doc_id": 3831 }, "chunk_id": "train_shard_00000_3831_0", "global_id": 4250 }, { "text": "In this review we develop the argument that cholestatic liver diseases, particularly primary biliary cholangitis and primary sclerosing cholangitis (PSC), evolve over time with anatomically an ascending course of the disease process. The first and early lesions are in \"downstream\" bile ducts. This eventually leads to cholestasis, and this causes bile salt (BS)-mediated toxic injury of the \"upstream\" liver parenchyma. BS are toxic in high concentration. These concentrations are present in the canalicular network, bile ducts, and gallbladder. Leakage of bile from this network and ducts could be an important driver of toxicity. The liver has a great capacity to adapt to cholestasis, and this may contribute to a variable symptom-poor interval that is often observed. Current trials with drugs that target BS toxicity are effective in only about 50%-60% of primary biliary cholangitis patients, with no effective therapy in PSC. This motivated us to develop and propose a new view on the pathophysiology of primary biliary cholangitis and PSC in the hope that these new drugs can be used more effectively. These views may lead to better stratification of these diseases and to recommendations on a more \"tailored\" use of the new therapeutic agents that are currently tested in clinical trials. Apical sodium-dependent BS transporter inhibitors that reduce intestinal BS absorption lower the BS load and are best used in cholestatic patients. The effectiveness of BS synthesis-suppressing drugs, such as farnesoid X receptor agonists, is greatest when optimal adaptation is not yet established. By the time cytochrome P450 7A1 expression is reduced these drugs may be less effective. Anti-inflammatory agents are probably most effective in early disease, while drugs that antagonize BS toxicity, such as ursodeoxycholic acid and nor-ursodeoxycholic acid, may be effective at all disease stages. Endoscopic stenting in PSC should be reserved for situations of intercurrent cholestasis and cholangitis, not for cholestasis in end-stage disease. These are arguments to consider a step-wise pathophysiology for these diseases, with therapy adjusted to disease stage", "token_count": 517, "char_count": 2165, "word_count": 325, "semantic_coherence": 1, "information_density": 0.5662, "quality_score": 0.7831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:37:18.477208", "source": { "split": "train_shard_00000", "doc_id": 3832 }, "chunk_id": "train_shard_00000_3832_0", "global_id": 4251 }, { "text": "An obstacle in such an approach is that disease stage-defining biomarkers are still lacking. This review is meant to serve as a call to prioritize the development of biomarkers that help to obtain a better stratification of these diseases. (Hepatology 2017;65:722-738).\n\nThe ascending pathophysiology of cholestatic liver disease.", "token_count": 93, "char_count": 330, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:18.857819", "source": { "split": "train_shard_00000", "doc_id": 3832 }, "chunk_id": "train_shard_00000_3832_1", "global_id": 4252 }, { "text": "Intestinal failure (IF)-associated liver disease (IFALD), as a major complication, contributes to significant morbidity in pediatric IF patients. However, the pathogenesis of IFALD is still uncertain. We here investigate the roles of bile acid (BA) dysmetabolism in the unclear pathogenesis of IFALD. It found that the histological evidence of pediatric IF patients exhibited liver injury, which was characterized by liver bile duct proliferation, inflammatory infiltration, hepatocyte apoptosis and different stages of fibrosis. The BA compositions were altered in serum and liver of pediatric IF patients, as reflected by a primary BA dominant composition. In IF patients, the serum FGF19 levels decreased significantly, and were conversely correlated with ileal inflammation grades (r = -0.50, p < 0.05). In ileum, the inflammation grades were inversely associated with farnesoid X receptor (FXR) expression (r = -0.55, p < 0.05). In liver, the expression of induction of the rate-limiting enzyme in bile salt synthesis, cytochrome P450 7a1 (CYP7A1) increased evidently. In conclusion, ileum inflammation decreases FXR expression corresponding to reduce serum FGF19 concentration, along with increased hepatic bile acid synthesis, leading to liver damages in IF patients.\n\nAltered systemic bile acid homeostasis contributes to liver disease in pediatric patients with intestinal failure.", "token_count": 393, "char_count": 1390, "word_count": 198, "semantic_coherence": 1, "information_density": 0.601, "quality_score": 0.8005, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:19.477768", "source": { "split": "train_shard_00000", "doc_id": 3833 }, "chunk_id": "train_shard_00000_3833_0", "global_id": 4253 }, { "text": "Xylose and glucose from lignocellulose are sustainable sources for production of pyruvate, which is the starting material for the synthesis of many drugs and agrochemicals. In this study, the pyruvate decarboxylase gene (KmPDC1) and glycerol-3-phosphate dehydrogenase gene (KmGPD1) of Kluyveromyces marxianus YZJ051 were disrupted to prevent ethanol and glycerol accumulation. The deficient growth of PDC disruption was rescued by overexpressing mutant KmMTH1-ΔT. Then pentose phosphate pathway and xylitol dehydrogenase SsXYL2-ARS genes were overexpressed to obtain strain YZB053 which produced pyruvate with xylose other than glucose. It produced 24.62g/L pyruvate from 80g/L xylose with productivity of 0.51g/L/h at 42°C. Then, xylose-specific transporter ScGAL2-N376F was overexpressed to obtain strain YZB058, which simultaneously consumed 40g/L glucose and 20g/L xylose and produced 29.21g/L pyruvate with productivity of 0.81g/L/h at 42°C. Therefore, a platform for pyruvate production from glucose and xylose at elevated temperature was developed.\n\nEngineered Kluyveromyces marxianus for pyruvate production at elevated temperature with simultaneous consumption of xylose and glucose.", "token_count": 399, "char_count": 1192, "word_count": 157, "semantic_coherence": 1, "information_density": 0.5987, "quality_score": 0.7994, "entities": { "genes": [ "YZJ051", "YZB053", "YZB058" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:20.093696", "source": { "split": "train_shard_00000", "doc_id": 3834 }, "chunk_id": "train_shard_00000_3834_0", "global_id": 4254 }, { "text": "Lactobacillus plantarum ST8Sh, isolated from Bulgarian salami \"shpek\" and previously characterized as bacteriocin producer, was evaluated for its beneficial properties. Based on the PCR analysis, Lb. plantarum ST8Sh was shown to host a gene related to the production of adhesion proteins such as Mab, Mub, EF, and PrgB. Genetic and physiological tests suggest Lb. plantarum ST8Sh to represent a potential probiotic candidate, including survival in the presence of low levels of pH and high levels of ox bile, production of β-galactosidase, bile salt deconjugation, high level of hydrophobicity, functional auto- and co-aggregation properties, and adhesion to cell lines. Application of semi-purified bacteriocin produced by Lb. plantarum ST8Sh in combination with ciprofloxacin presented synergistic effect on inhibition of Listeria monocytogenes Scott A. Based on observed properties, Lb. plantarum ST8Sh can be considered as a potential probiotic candidate with additional bacteriocinogenic properties.\n\nIn Vitro Evaluation of Beneficial Properties of Bacteriocinogenic Lactobacillus plantarum ST8Sh.", "token_count": 294, "char_count": 1102, "word_count": 151, "semantic_coherence": 1, "information_density": 0.649, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:20.657152", "source": { "split": "train_shard_00000", "doc_id": 3835 }, "chunk_id": "train_shard_00000_3835_0", "global_id": 4255 }, { "text": "The search for probiotic candidates among lactic acid bacteria (LAB) isolated from food may uncover new strains with promising health and technological properties. Lactobacillus mucosae strains attracted recent research attention due to their ability to adhere to intestinal mucus and to inhibit pathogens in the gastrointestinal tract, both related to a probiotic potential. Properties of interest and safety aspects of three Lb. mucosae strains (CNPC006, CNPC007, and CNPC009) isolated from goat milk were investigated employing in vitro tests. The presence of genetic factors related to bile salt hydrolase production (bsh), intestinal adhesion properties (msa, map, mub, and ef-tu), virulence, and biogenic amine production were also verified. All strains exhibited the target map, mub, and ef-tu sequences; the msa gene was detected in CNPC006 and CNPC007 strains. Some of the searched sequences for virulence factors were detected, especially in the CNPC009 strain; all strains carried the hyl gene, related to the production of hyaluronidase. Lb. mucosae CNPC007 exhibited a high survival rate in simulated gastric and enteric conditions. Besides, all strains exhibited the bsh sequence, and CNPC006 and CNPC007 were able to deconjugate salts of glycodeoxycholic acid (GDC). Regarding technological properties for dairy product applications, a relatively higher milk acidification and clotting capacity, diacetyl production, and proteolytic activity were registered for CNPC007 in comparison to the other strains. Collectively, the results aim at Lb. mucosae CNPC007 as a promising probiotic candidate for application in dairy products, deserving further studies to confirm and explore its potential.\n\nFunctional Properties of Lactobacillus mucosae Strains Isolated from Brazilian Goat Milk.", "token_count": 485, "char_count": 1798, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5961, "quality_score": 0.798, "entities": { "genes": [ "CNPC009", "CNPC006", "CNPC007" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:21.327948", "source": { "split": "train_shard_00000", "doc_id": 3836 }, "chunk_id": "train_shard_00000_3836_0", "global_id": 4256 }, { "text": "The evolution, molecular behavior, and physiological function of nuclear receptors are of particular interest given their diverse roles in regulating essential biological processes. The vitamin D receptor (VDR) is well known for its canonical roles in calcium homeostasis and skeletal maintenance. Additionally, VDR has received an increased amount of attention due to the discovery of numerous non-calcemic functions, including the detoxification of lithocholic acid. Lithocholic acid is a toxic metabolite of chenodeoxycholic acid, a primary bile acid. The partnership between the VDR and lithocholic acid has been hypothesized to be a recent adaptation that evolved to mediate the detoxification and elimination of lithocholic acid from the gut. This partnership is speculated to be limited to higher vertebrates (birds and mammals), as lower vertebrates do not synthesize the parent compound of lithocholic acid. However, the molecular functions associated with the observed insensitivity of basal VDRs to lithocholic acid have not been explored. Here we characterize canonical nuclear receptor functions of VDRs from select species representing key nodes in vertebrate evolution and span a range of bile salt phenotypes. Competitive ligand binding assays revealed that the receptor's affinity for lithocholic acid is highly conserved across species, suggesting that lithocholic acid affinity is an ancient and non-adaptive trait. However, transient transactivation assays revealed that lithocholic acid-mediated VDR activation might have evolved more recently, as the non-mammalian receptors did not respond to lithocholic acid unless exogenous coactivator proteins were co-expressed. Subsequent functional assays indicated that differential lithocholic acid-mediated receptor activation is potentially driven by differential protein-protein interactions between VDR and nuclear receptor coregulator proteins. We hypothesize that the vitamin D receptor-lithocholic acid partnership evolved as a by-product of natural selection on the ligand-receptor partnership between the vitamin D receptor and the native VDR ligand: 1α,25-dihydroxyvitamin D3, the biologically active metabolite of vitamin D3.", "token_count": 508, "char_count": 2201, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5652, "quality_score": 0.7826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:21.999963", "source": { "split": "train_shard_00000", "doc_id": 3837 }, "chunk_id": "train_shard_00000_3837_0", "global_id": 4257 }, { "text": "Evolutionary and Functional Diversification of the Vitamin D Receptor-Lithocholic Acid Partnership.", "token_count": 26, "char_count": 99, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:22.391467", "source": { "split": "train_shard_00000", "doc_id": 3837 }, "chunk_id": "train_shard_00000_3837_1", "global_id": 4258 }, { "text": "Gastrointestinal fluid is a complex milieu and it is recognised that gut drug solubility is different to that observed in simple aqueous buffers. Simulated gastrointestinal media have been developed covering fasted and fed states to facilitate in vitro prediction of gut solubility and product dissolution. However, the combination of bile salts, phospholipids, fatty acids and proteins in an aqueous buffered system creates multiple phases and drug solubility is therefore a complex interaction between these components, which may create unique environments for each API. The impact on solubility can be assessed through a statistical design of experiment (DoE) approach, to determine the influence and relationships between factors. In this paper DoE has been applied to fed simulated gastrointestinal media consisting of eight components (pH, bile salt, lecithin, sodium oleate, monoglyceride, buffer, salt and pancreatin) using a two level D-optimal design with forty-four duplicate measurements and four centre points. The equilibrium solubility of a range of poorly soluble acidic (indomethacin, ibuprofen, phenytoin, valsartan, zafirlukast), basic (aprepitant, carvedilol, tadalafil, bromocriptine) and neutral (fenofibrate, felodipine, probucol, itraconazole) drugs was investigated. Results indicate that the DoE provides equilibrium solubility values that are comparable to literature results for other simulated fed gastrointestinal media systems or human intestinal fluid samples. For acidic drugs the influence of pH predominates but other significant factors related to oleate and bile salt or interactions between them are present. For basic drugs pH, oleate and bile salt have equal significance along with interactions between pH and oleate and lecithin and oleate. Neutral drugs show diverse effects of the media components particularly with regard to oleate, bile salt, pH and lecithin but the presence of monoglyceride, pancreatin and buffer have significant but smaller effects on solubility. There are fourteen significant interactions between factors mainly related to the surfactant components and pH, indicating that the solubility of neutral drugs in fed simulated media is complex", "token_count": 520, "char_count": 2207, "word_count": 311, "semantic_coherence": 1, "information_density": 0.5563, "quality_score": 0.7781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:37:23.035297", "source": { "split": "train_shard_00000", "doc_id": 3838 }, "chunk_id": "train_shard_00000_3838_0", "global_id": 4259 }, { "text": "The results also indicate that the equilibrium solubility of each drug can exhibit individualistic behaviour associated with the drug's chemical structure, physicochemical properties and interaction with media components. The utility of DoE for fed simulated media has been demonstrated providing equilibrium solubility values comparable with similar in vitro systems whilst also providing greater information on the influence of media factors and their interactions. The determination of a drug's gastrointestinal solubility envelope provides useful limits that can potentially be applied to in silico modelling and in vivo experiments.\n\nStatistical investigation of simulated fed intestinal media composition on the equilibrium solubility of oral drugs.", "token_count": 141, "char_count": 755, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:23.467002", "source": { "split": "train_shard_00000", "doc_id": 3838 }, "chunk_id": "train_shard_00000_3838_1", "global_id": 4260 }, { "text": "The intracellular pathogen Piscirickettsia salmonis is the etiological agent of piscirickettsiosis, the most important bacterial disease that affects the Chilean salmon industry. Despite its importance, little is known regarding the biology of the pathogen. In this study, recently published sequencing data was used in order to characterize the genome of P. salmonis, defining groups of genes associated with bacterial processes such as, invasion and intracellular survival. Moreover, one Chilean P. salmonis isolate, which is known to be virulent at in vitro and in vivo assays, was sequenced, assembled, annotated and functionally characterized. Whole-genome comparisons between public P. salmonis isolates confirmed the existence of two different genogroups associated with the LF-89 and EM-90 strains, and the bacterial pan and core genome were defined. Additionally, differences were observed at the genomic level between the P. salmonis reference strain and a Norwegian isolate, which is known to produce milder piscirickettsiosis outbreaks. Finally, candidate genes for invasion and intracellular survival were chosen from phylogenetically related bacteria, and annotated in P. salmonis using comparative genomics. These results showed the presence of several genes that might be related to bacterial pathogenesis, for example those of the type III, IV and VI secretion systems, in which some amino acidic differences within both genogroups and the Norwegian isolate were established. Altogether, these results will be relevant for understanding the host-pathogen interaction and further studies, aimed at generating new disease control strategies, should be devised using this information.\n\nWhole-genome comparative analysis of the pathogen Piscirickettsia salmonis.", "token_count": 405, "char_count": 1775, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6073, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:24.089545", "source": { "split": "train_shard_00000", "doc_id": 3839 }, "chunk_id": "train_shard_00000_3839_0", "global_id": 4261 }, { "text": "Intrahepatic cholestasis of pregnancy (ICP) represents the most common pregnancy-related liver disease in women. Women frequently present in the third trimester with pruritus and elevated serum bile acid and/or alanine transaminase levels. Clinical symptoms quickly resolve after delivery; however, recurrence in subsequent pregnancies has to be expected. Intrahepatic cholestasis of pregnancy is associated with increased perinatal complications, such as premature delivery, meconium staining of the amniotic fluid, respiratory distress, low Apgar scores, and even stillbirth. The risk for the fetus is significantly increased with maternal serum bile acid levels above 40 µmol/L, which characterize severe ICP. An important factor for ICP development is a rise of gestational hormones leading to cholestasis in genetically predisposed women. Variants in the bile salt export pump (BSEP) and the multidrug resistance protein 3 (MDR3) are most often identified in ICP. Here, we give an overview of the current literature on ICP and present the case of a woman with recurrent severe ICP. A common BSEP polymorphism as well as a rare MDR3 mutation may underlie the development of ICP in our patient. She had a premature delivery with meconium staining of the amniotic fluid. The neonate showed signs of respiratory distress with a low Apgar score. This case emphasizes that women with severe ICP have an increased risk for perinatal complications. Furthermore, severe ICP was associated with a MDR3 mutation, which has already been described in adult patients with liver cirrhosis. Thus, ICP may unmask an underlying MDR3 defect, which may predispose to development of hepatobiliary diseases such as gallstone disease, liver fibrosis/cirrhosis, as well as hepatobiliary malignancies. Therefore, genetic testing should be considered in women with severe as well as early onset ICP. Furthermore, regular follow-up should be discussed for women with genetic variants.\n\nIntrahepatic cholestasis of pregnancy (ICP): case report and review of the literature.", "token_count": 500, "char_count": 2050, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5644, "quality_score": 0.7822, "entities": { "genes": [ "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:24.743413", "source": { "split": "train_shard_00000", "doc_id": 3840 }, "chunk_id": "train_shard_00000_3840_0", "global_id": 4262 }, { "text": "Drug-induced cholestasis is a leading cause of drug withdrawal. However, the use of primary human hepatocytes (PHHs), the gold standard for predicting cholestasis in vitro, is limited by their high cost and batch-to-batch variability. Mature hepatocyte characteristics have been observed in human induced hepatocytes (hiHeps) derived from human fibroblast transdifferentiation. Here, we evaluated whether hiHeps could biosynthesize and excrete bile acids (BAs) and their potential as PHH alternatives for cholestasis investigations. Quantitative real-time PCR (qRT-PCR) and western blotting indicated that hiHeps highly expressed BA synthases and functional transporters. Liquid chromatography tandem mass spectrometry (LC-MS/MS) showed that hiHeps produced normal intercellular unconjugated BAs but fewer conjugated BAs than human hepatocytes. When incubated with representative cholestatic agents, hiHeps exhibited sensitive drug-induced bile salt export pump (BSEP) dysfunction, and their response to cholestatic agent-mediated cytotoxicity correlated well with that of PHHs (r\n\nFunctional human induced hepatocytes (hiHeps) with bile acid synthesis and transport capacities: A novel in vitro cholestatic model.", "token_count": 321, "char_count": 1214, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7452, "quality_score": 0.8726, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:25.311616", "source": { "split": "train_shard_00000", "doc_id": 3841 }, "chunk_id": "train_shard_00000_3841_0", "global_id": 4263 }, { "text": "We performed molecular dynamics (MD) simulations to obtain insights into the structure and molecular interactions of colloidal structures present in fasted state intestinal fluid. Drug partitioning and interaction were studied with a mixed system of the bile salt taurocholate (TCH) and 1,2-dilinoleoyl-sn-glycero-3-phosphocholine (DLiPC). Spontaneous aggregation of TCH and DLiPC from unconstrained MD simulations at the united-atom level using the Berger/Gromos54A7 force fields demonstrated that intermolecular hydrogen bonding between TCH molecules was an important factor in determining the overall TCH and DLiPC configuration. In bilayered systems, these intermolecular hydrogen bonds resulted in embedded transmembrane TCH clusters. Free energy simulations using the umbrella sampling technique revealed that the stability of these transmembrane TCH clusters was superior when they consisted of 3 or 4 TCH per bilayer leaflet. All-atom simulations using the Slipids/GAFF force fields showed that the TCH embedded in the bilayer decreased the energy barrier to penetrate the bilayer (ΔG\n\nPartitioning into Colloidal Structures of Fasted State Intestinal Fluid Studied by Molecular Dynamics Simulations.", "token_count": 293, "char_count": 1208, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6258, "quality_score": 0.8129, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:25.870965", "source": { "split": "train_shard_00000", "doc_id": 3842 }, "chunk_id": "train_shard_00000_3842_0", "global_id": 4264 }, { "text": "Progressive familial intrahepatic cholestasis 2 (PFIC2) is the result of mutations in the ABCB11, which encodes for bile salt export pump (BSEP). An absence of BSEP in the canalicular membrane causes cholestasis and leads to the development of end-stage liver disease in the first decade of life. Liver transplantation (LT) has been considered curative for BSEP disease. However, patients with PFIC2 having undergone LT have recently been reported to develop recurrence of cholestasis together with the clinical and histological features of primary BSEP disease.\n\nRecurrence of Progressive Familial Intrahepatic Cholestasis Type 2 Phenotype After Living-donor Liver Transplantation: A Case Report.", "token_count": 181, "char_count": 697, "word_count": 100, "semantic_coherence": 1, "information_density": 0.69, "quality_score": 0.845, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:26.315891", "source": { "split": "train_shard_00000", "doc_id": 3843 }, "chunk_id": "train_shard_00000_3843_0", "global_id": 4265 }, { "text": "Several studies have suggested that resistant maltodextrin (RMD) suppresses intestinal lipid absorption in experimental animals and humans. However, possible mechanisms underlying this effect are not known. In this study, effects of RMD on processes of the absorption of various lipids were investigated in vitro. RMD dose-dependently suppressed the solubility of various lipid components, including 1-mono-oleoylglycerol, oleic acid, and phosphatidylcholine in bile salt micelles in vitro. When the diffusion rate of bile salt micelles through a filter membrane was investigated in vitro, bile salt micelles containing RMD diffused more slowly than those without RMD. Incorporation of [1-\n\nResistant Maltodextrin Decreases Micellar Solubility of Lipids and Diffusion of Bile Salt Micelles and Suppresses Incorporation of Micellar Fatty Acids into Caco-2 Cells.", "token_count": 222, "char_count": 861, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:26.786263", "source": { "split": "train_shard_00000", "doc_id": 3844 }, "chunk_id": "train_shard_00000_3844_0", "global_id": 4266 }, { "text": "Enterococcus faecalis, a leading nosocomial pathogen and yet a prominent member of gut microbiome, lacks clear demarcation between pathogenic and non-pathogenic strains at genome level. Here we present the comparative genome analysis of 36 E. faecalis strains with different pathogenic features and from different body-habitats. This study begins by addressing the genome dynamics, which shows that the pan-genome of E. faecalis is still open, though the core genome is nearly saturated. We identified eight uncharacterized strains as potential pathogens on the basis of their co-segregation with reported pathogens in gene presence-absence matrix and Pathogenicity Island (PAI) distribution. A ~7.4 kb genomic-cassette, which is itself a part of PAI, is found to exist in all reported and potential pathogens, but not in commensals and other uncharacterized strains. This region encodes four genes and among them, products of two hypothetical genes are predicted to be intrinsically disordered that may serve as novel targets for therapeutic measures. Exclusive existence of 215, 129, 4 and 1 genes in the blood, gastrointestinal tract, urogenital tract, oral cavity and lymph node derived E. faecalis genomes respectively suggests possible employment of distinct habitat-specific genetic strategies in the adaptation of E. faecalis in human host.\n\nAssessment of virulence potential of uncharacterized Enterococcus faecalis strains using pan genomic approach - Identification of pathogen-specific and habitat-specific genes.", "token_count": 376, "char_count": 1525, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:27.377738", "source": { "split": "train_shard_00000", "doc_id": 3845 }, "chunk_id": "train_shard_00000_3845_0", "global_id": 4267 }, { "text": "Pseudomonas is a highly versatile genus containing species that can be harmful to humans and plants while others are widely used for bioengineering and bioremediation. We analysed 432 sequenced Pseudomonas strains by integrating results from a large scale functional comparison using protein domains with data from six metabolic models, nearly a thousand transcriptome measurements and four large scale transposon mutagenesis experiments. Through heterogeneous data integration we linked gene essentiality, persistence and expression variability. The pan-genome of Pseudomonas is closed indicating a limited role of horizontal gene transfer in the evolutionary history of this genus. A large fraction of essential genes are highly persistent, still non essential genes represent a considerable fraction of the core-genome. Our results emphasize the power of integrating large scale comparative functional genomics with heterogeneous data for exploring bacterial diversity and versatility.\n\nComparison of 432 Pseudomonas strains through integration of genomic, functional, metabolic and expression data.", "token_count": 226, "char_count": 1102, "word_count": 149, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:27.844748", "source": { "split": "train_shard_00000", "doc_id": 3846 }, "chunk_id": "train_shard_00000_3846_0", "global_id": 4268 }, { "text": "The type VI secretion system (T6SS) is an anti-bacterial weapon comprising a contractile tail anchored to the cell envelope by a membrane complex. The TssJ, TssL, and TssM proteins assemble a 1.7-MDa channel complex that spans the cell envelope, including the peptidoglycan layer. The electron microscopy structure of the TssJLM complex revealed that it has a diameter of ~18 nm in the periplasm, which is larger than the size of peptidoglycan pores (~2 nm), hence questioning how the T6SS membrane complex crosses the peptidoglycan layer. Here, we report that the MltE housekeeping lytic transglycosylase (LTG) is required for T6SS assembly in enteroaggregative Escherichia coli Protein-protein interaction studies further demonstrated that MltE is recruited to the periplasmic domain of TssM. In addition, we show that TssM significantly stimulates MltE activity in vitro and that MltE is required for the late stages of T6SS membrane complex assembly. Collectively, our data provide the first example of domestication and activation of a LTG encoded within the core genome for the assembly of a secretion system.\n\nDomestication of a housekeeping transglycosylase for assembly of a Type VI secretion system.", "token_count": 325, "char_count": 1209, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5815, "quality_score": 0.7908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:28.413796", "source": { "split": "train_shard_00000", "doc_id": 3847 }, "chunk_id": "train_shard_00000_3847_0", "global_id": 4269 }, { "text": "Shiga toxin-producing Escherichia coli O157:H7 primarily resides in cattle asymptomatically, and can be transmitted to humans through food. A study by Lupolova et al. applied a machine-learning approach to complex pan-genome information and predicted that only a small subset of bovine isolates have the potential to cause diseases in humans.\n\nDecoding the Ecological Function of Accessory Genome.", "token_count": 100, "char_count": 397, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8596, "quality_score": 0.9298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:28.794361", "source": { "split": "train_shard_00000", "doc_id": 3848 }, "chunk_id": "train_shard_00000_3848_0", "global_id": 4270 }, { "text": "Lactobacillus kefiranofaciens XL10, with a high yield of extracellular polysaccharide (EPS), is isolated from Tibetan kefir grain and benefits the health of human beings and has been considered to exhibit probiotic potential in vitro and in vivo. The probiotic function of the strain was studied extensively, viz., acid and bile salt tolerances, cell surface hydrophobicity and autoaggregation, the modulation of gut microbiota, and the distribution and colonization of XL10 in the mouse intestinal tract after oral administration. XL10 could survive 3-h incubation at pH 3.5 and exhibited cell surface hydrophobicity of ∼79.9% and autoaggregation of ∼27.8%. After continuous oral administration of XL10 for 2 weeks, the Bifidobacteriaceae family increased, accompanied by an observable decline in Proteobacteria phyla in the tested mice. Butyrivibrio and Pseudobutyrivibrio, recognized as butyric acid-producing bacteria, could also be detected at day 7 and day 14, respectively. The most abundant community in the mouse gut had formed by day 14. Additionally, we found that XL10 successfully adhered to the mucous tissue and colonized the ileum of the mice based on fluorescence imaging, flow cytometry, and qPCR. Our results suggested that XL10 has excellent probiotic properties and represents an alternative for exploitation in the development of novel functional foods.\n\nIn vitro and in vivo evaluation of the probiotic attributes of Lactobacillus kefiranofaciens XL10 isolated from Tibetan kefir grain.", "token_count": 412, "char_count": 1509, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6409, "quality_score": 0.8205, "entities": { "genes": [ "XL10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:29.417605", "source": { "split": "train_shard_00000", "doc_id": 3849 }, "chunk_id": "train_shard_00000_3849_0", "global_id": 4271 }, { "text": "Disruptions to circadian rhythm in mice and humans have been associated with an increased risk of obesity and metabolic syndrome. The gut microbiota is known to be essential for the maintenance of circadian rhythm in the host suggesting a role for microbe-host interactions in the regulation of the peripheral circadian clock. Previous work suggested a role for gut bacterial bile salt hydrolase (BSH) activity in the regulation of host circadian gene expression. Here we demonstrate that unconjugated bile acids, known to be generated through the BSH activity of the gut microbiota, are potentially chronobiological regulators of host circadian gene expression. We utilised a synchronised Caco-2 epithelial colorectal cell model and demonstrated that unconjugated bile acids, but not the equivalent tauro-conjugated bile salts, enhance the expression levels of genes involved in circadian rhythm. In addition oral administration of mice with unconjugated bile acids significantly altered expression levels of circadian clock genes in the ileum and colon as well as the liver with significant changes to expression of hepatic regulators of circadian rhythm (including Dbp) and associated genes (Per2, Per3 and Cry2). The data demonstrate a potential mechanism for microbe-host crosstalk that significantly impacts upon host circadian gene expression.\n\nUnconjugated Bile Acids Influence Expression of Circadian Genes: A Potential Mechanism for Microbe-Host Crosstalk.", "token_count": 348, "char_count": 1466, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5213, "quality_score": 0.7607, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:29.992484", "source": { "split": "train_shard_00000", "doc_id": 3850 }, "chunk_id": "train_shard_00000_3850_0", "global_id": 4272 }, { "text": "The primary purpose of the present study was to design and optimize a liposomal formulation of the poorly water-soluble drug oleanolic acid (OA) to improve its oral bioavailability, and prolong the duration of therapeutic drug level. Liposomes containing a soybean lecithin and cholesterol lipid bilayer, a protective hydrophilic polyvinylpyrrolidone-K30 (PVP-K30) coating, and a protective bile salt, sodium deoxycholate, were prepared by a thin-film dispersion method coupled with sonication. Several properties of the PVP-modified OA liposomes (PVPOALs), including surface morphology, particle size, zeta potential and entrapment efficiency were extensively characterized. The pharmacokinetic parameters of PVPOALs in rats were determined by UPLC-MS/MS following oral administration. The results of the characterization studies demonstrated that PVPOALs were spherical particles with an average particle size of 179.4nm and a zeta potential of -28.8mV. The drug encapsulation efficiency was more than 90%. After freeze-drying, the prepared liposomes possessed high entrapment efficiency of more than 90%. The mean particle size was 194.8nm, and the zeta potential was about -30.9mV. Furthermore, as compared to the commercial tablets, the liposomal formulation enhanced the maximum plasma concentration (C\n\nPreparation, characterization and in vivo pharmacokinetic study of PVP-modified oleanolic acid liposomes.", "token_count": 372, "char_count": 1415, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6053, "quality_score": 0.8026, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:30.917405", "source": { "split": "train_shard_00000", "doc_id": 3851 }, "chunk_id": "train_shard_00000_3851_0", "global_id": 4273 }, { "text": "Interactions between members of the intestinal microbiota and the mucosal immune system can significantly impact human health, and in this context, fungi and food-related yeasts are known to influence intestinal inflammation through direct interactions with specialized immune cells in vivo. The aim of the present study was to characterize the immune modulating properties of the food-related yeast Kluyveromyces marxianus in terms of adaptive immune responses indicating inflammation versus tolerance and to explore the mechanisms behind the observed responses. Benchmarking against a Saccharomyces boulardii strain with probiotic effects documented in clinical trials, we evaluated the ability of K. marxianus to modulate human dendritic cell (DC) function in vitro. Further, we assessed yeast induced DC modulation of naive T cells toward effector responses dominated by secretion of IFNγ and IL-17 versus induction of a Treg response characterized by robust IL-10 secretion. In addition, we blocked relevant DC surface receptors and investigated the stimulating properties of β-glucan containing yeast cell wall extracts. K. marxianus and S. boulardii induced distinct levels of DC cytokine secretion, primarily driven by Dectin-1 recognition of β-glucan components in their cell walls. Upon co-incubation of yeast exposed DCs and naive T cells, S. boulardii induced a potent IFNγ response indicating TH1 mobilization. In contrast, K. marxianus induced a response dominated by Foxp3+ Treg cells, a characteristic that may benefit human health in conditions characterized by excessive inflammation and positions K. marxianus as a strong candidate for further development as a novel yeast probiotic.\n\nKluyveromyces marxianus and Saccharomyces boulardii Induce Distinct Levels of Dendritic Cell Cytokine Secretion and Significantly Different T Cell Responses In Vitro.", "token_count": 449, "char_count": 1870, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5547, "quality_score": 0.7774, "entities": { "genes": [ "TH1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:31.555629", "source": { "split": "train_shard_00000", "doc_id": 3852 }, "chunk_id": "train_shard_00000_3852_0", "global_id": 4274 }, { "text": "Androst-3β,5α,6β-triol (Triol) is a promising neuroprotective agent, but its poor solubility restricts its development into parenteral preparations. In this study, Triol is significantly solubilized by bile salt/phosphatidylcholine mixed micelles (BS/PC-MM). All BS/PC-MM systems are tested to remarkably improve the drug solubility with various stabilities after drug loading. Among them, the sodium glycocholate (SGC)/egg phosphatidylcholine (EPC) system with 2:1 ratio in weight and the total concentration of SGC and EPC of 100 mg/mL is proved to produce stable mixed micelles with high drug loading. It is found that the stability of drug-loaded mixed micelles is quite different, which might be related to the change in critical micelle concentration (CMC) after incorporating drugs. SGC/EPC and SGC/soya phosphatidylcholine (SPC) remain transparent under accelerated conditions and manifest a decreased CMC (dropping from 0.105 to 0.056 mg/mL and from 0.067 to 0.024 mg/mL, respectively). In contrast, swine bile acid-sodium salt (SBA-Na)/PC and sodium deoxycholate (SDC)/PC are accompanied by drug precipitation and reached the maximum CMC on the first and the third days, respectively. Interestingly, the variation of CMC under accelerated testing conditions highly matches the drug-precipitating event in the primary stability experiment. In brief, the bile salt/phosphatidylcholine system exists as a potential strategy of improving sterol drug solubility. CMC variation under accelerated testing conditions might be a simple and easy method to predict the stability of drug-loaded mixed micelles.\n\nComparison of bile salt/phosphatidylcholine mixed micelles in solubilization to sterols and stability.", "token_count": 458, "char_count": 1712, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:32.198188", "source": { "split": "train_shard_00000", "doc_id": 3853 }, "chunk_id": "train_shard_00000_3853_0", "global_id": 4275 }, { "text": "The opalescent appearance of the newly produced olive oil is due to the presence of solid particles and microdrops of vegetation water in which the microorganisms from the olives' carposphere are trapped. Present research has demonstrated that the microbiota of the fresh extracted olive oil, produced in the mills, is mainly composed of yeasts and to a lesser extent of molds. The close link between the composition of the microbiota of the olives' carposphere undergoing to processing, and that of the microbiota of the newly produced olive oil, concerns only the yeasts and molds, given that the bacterial component is by and large destroyed mainly in the kneaded paste during the malaxation process. Six physiologically homogenous yeast groups were highlighted in the wash water, kneaded paste and newly produced olive oil from the Taggiasca variety which had been collected in mills located in the Liguria region. The more predominant yeasts of each group belonged to a single species called respectively: Kluyveromyces marxianus, Candida oleophila, Candida diddensiae, Candida norvegica, Wickerhamomyces anomalus and Debaryomyces hansenii. Apart from K. marxianus, which was found only in the wash water, all the other species were found in the wash water and in the kneaded paste as well as in the newly produced olive oil, while in the six-month stored olive oil, was found only one physiologically homogeneous group of yeast represented by the W. anomalus specie. These findings in according to our previous studies carried out on other types of mono varietal olive oils, confirms that the habitat of the Taggiascas' extra virgin olive oil, had a strong selective pressure on the yeast biota, allowing only to a few member of yeast species, contaminating the fresh product, to survive and reproduce in it during storage.\n\nTaggiasca extra virgin olive oil colonization by yeasts during the extraction process.", "token_count": 451, "char_count": 1917, "word_count": 302, "semantic_coherence": 1, "information_density": 0.4967, "quality_score": 0.7483, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:32.863041", "source": { "split": "train_shard_00000", "doc_id": 3854 }, "chunk_id": "train_shard_00000_3854_0", "global_id": 4276 }, { "text": "This study explored whether bacterial endotoxins, in the form of lipopolysaccharides (LPS), could have an injurious effect on the biliary tract in conjunction with ischemia. A total of 64 rats were randomly assigned to 4 groups: sham operation (sham group), 1 mg/kg LPS intraperitoneal (LPS group), hepatic ischemia/reperfusion (IR; IR group), and IR combined with LPS (IR+LPS group). Following 1 or 6 hours of reperfusion, serum liver tests, bile duct histology, immunofluorescence microscopy (zonula occludens-1 [ZO-1]), bile composition (bile salts, phospholipids, lactate dehydrogenase), hepatic gene expression (bile salt transporters and inflammatory mediators), as well as serum and biliary cytokine concentrations were quantified and compared between the study groups. In addition, the integrity of the blood biliary barrier (BBB) was assayed in vivo using horseradish peroxidase (HRP). LPS administration induced severe small bile duct injury following 6 hours of reperfusion. Furthermore, total bile salts and bilirubin concentrations in serum were increased in the LPS groups compared with sham controls (LPS, + 3.3-fold and +1.9-fold; IR+LPS, + 3.8-fold and +1.7-fold, respectively). The BBB was impaired in the LPS groups as evidenced by elevated levels of HRP in bile (+4.9-fold), and decreased expression of claudin 1 (-6.7-fold) and claudin 3 (-3.6-fold). LPS was found to be a potent inducer of small bile duct injury following hepatic ischemia and 6 hours of reperfusion. This injury was associated with increased permeability of the BBB and impaired hepatic bile salt clearance. Liver Transplantation 23 194-206 2017 AASLD.", "token_count": 514, "char_count": 1642, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:37:33.534204", "source": { "split": "train_shard_00000", "doc_id": 3855 }, "chunk_id": "train_shard_00000_3855_0", "global_id": 4277 }, { "text": "Low-Dose Lipopolysaccharide Causes Biliary Injury by Blood Biliary Barrier Impairment in a Rat Hepatic Ischemia/Reperfusion Model.", "token_count": 41, "char_count": 130, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:33.902100", "source": { "split": "train_shard_00000", "doc_id": 3855 }, "chunk_id": "train_shard_00000_3855_1", "global_id": 4278 }, { "text": "Streptococcus agalactiae is an emerging pathogen of nonpregnant human adults worldwide and a reemerging pathogen of dairy cattle in parts of Europe. To learn more about interspecies transmission of this bacterium, we compared contemporaneously collected isolates from humans and cattle in Finland and Sweden. Multilocus sequence typing identified 5 sequence types (STs) (ST1, 8, 12, 23, and 196) shared across the 2 host species, suggesting possible interspecies transmission. More than 54% of the isolates belonged to those STs. Molecular serotyping and pilus island typing of those isolates did not differentiate between populations isolated from different host species. Isolates from humans and cattle differed in lactose fermentation, which is encoded on the accessory genome and represents an adaptation to the bovine mammary gland. Serotype IV-ST196 isolates were obtained from multiple dairy herds in both countries. Cattle may constitute a previously unknown reservoir of this strain.\n\nStreptococcus agalactiae Serotype IV in Humans and Cattle, Northern Europe", "token_count": 266, "char_count": 1068, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [ "ST196", "ST1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:34.520412", "source": { "split": "train_shard_00000", "doc_id": 3856 }, "chunk_id": "train_shard_00000_3856_0", "global_id": 4279 }, { "text": "Lactic acid (LA) is a versatile compound used in the food, pharmaceutical, textile, leather, and chemical industries. Biological production of LA is possible by yeast strains expressing a bacterial gene encoding l-lactate dehydrogenase (LDH). Kluyveromyces marxianus is an emerging non-conventional yeast with various phenotypes of industrial interest. However, it has not been extensively studied for LA production. In this study, K. marxianus was engineered to express and co-express various heterologous LDH enzymes that were reported to have different pH optimums. Specifically, three LDH enzymes originating from Staphylococcus epidermidis (SeLDH; optimal at pH 5.6), Lactobacillus acidophilus (LaLDH; optimal at pH 5.3), and Bos taurus (BtLDH; optimal at pH 9.8) were functionally expressed individually and in combination in K. marxianus, and the resulting strains were compared in terms of LA production. A strain co-expressing SeLDH and LaLDH (KM5 La+SeLDH) produced 16.0g/L LA, whereas the strains expressing those enzymes individually produced only 8.4 and 6.8g/L, respectively. This co-expressing strain produced 24.0g/L LA with a yield of 0.48g/g glucose in the presence of CaCO\n\nCo-expression of two heterologous lactate dehydrogenases genes in Kluyveromyces marxianus for l-lactic acid production.", "token_count": 389, "char_count": 1312, "word_count": 184, "semantic_coherence": 1, "information_density": 0.663, "quality_score": 0.8315, "entities": { "genes": [ "KM5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:35.138247", "source": { "split": "train_shard_00000", "doc_id": 3857 }, "chunk_id": "train_shard_00000_3857_0", "global_id": 4280 }, { "text": "Ammonia-oxidizing archaea (AOA) are among the most abundant microorganisms and key players in the global nitrogen and carbon cycles. They share a common energy metabolism but represent a heterogeneous group with respect to their environmental distribution and adaptions, growth requirements, and genome contents. We report here the genome and proteome of Nitrososphaera viennensis EN76, the type species of the archaeal class Nitrososphaeria of the phylum Thaumarchaeota encompassing all known AOA. N. viennensis is a soil organism with a 2.52-Mb genome and 3,123 predicted protein-coding genes. Proteomic analysis revealed that nearly 50% of the predicted genes were translated under standard laboratory growth conditions. Comparison with genomes of closely related species of the predominantly terrestrial Nitrososphaerales as well as the more streamlined marine Nitrosopumilales [Candidatus (Ca.) order] and the acidophile \"Ca. Nitrosotalea devanaterra\" revealed a core genome of AOA comprising 860 genes, which allowed for the reconstruction of central metabolic pathways common to all known AOA and expressed in the N. viennensis and \"Ca Nitrosopelagicus brevis\" proteomes. Concomitantly, we were able to identify candidate proteins for as yet unidentified crucial steps in central metabolisms. In addition to unraveling aspects of core AOA metabolism, we identified specific metabolic innovations associated with the Nitrososphaerales mediating growth and survival in the soil milieu, including the capacity for biofilm formation, cell surface modifications and cell adhesion, and carbohydrate conversions as well as detoxification of aromatic compounds and drugs.\n\nProteomics and comparative genomics of Nitrososphaera viennensis reveal the core genome and adaptations of archaeal ammonia oxidizers.", "token_count": 466, "char_count": 1806, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6345, "quality_score": 0.8173, "entities": { "genes": [ "EN76" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:35.785765", "source": { "split": "train_shard_00000", "doc_id": 3858 }, "chunk_id": "train_shard_00000_3858_0", "global_id": 4281 }, { "text": "The pangenome of a bacterial species population is formed by genetic reduction and genetic expansion over the long course of evolution. Gene loss is a pervasive source of genetic reduction, and (exogenous and endogenous) gene gain is the main driver of genetic expansion. To understand the genetic innovation and speciation of the family Corynebacteriaceae, which cause a wide range of serious infections in humans and animals, we analyzed the pangenome of this family, and reconstructed its phylogeny using a phylogenomics approach. Genetic variations have occurred throughout the whole evolutionary history of the Corynebacteriaceae. Gene loss has been the primary force causing genetic changes, not only in terms of the number of protein families affected, but also because of its continuity on the time series. The variation in metabolism caused by these genetic changes mainly occurred for membrane transporters, two-component systems, and metabolism related to amino acids and carbohydrates. Interestingly, horizontal gene transfer (HGT) not only caused changes related to pathogenicity, but also triggered the acquisition of antimicrobial resistance. The Darwinian theory of evolution did not adequately explain the effects of dispersive HGT and/or gene loss in the evolution of the Corynebacteriaceae. These findings provide new insight into the evolution and speciation of Corynebacteriaceae and advance our understanding of the genetic innovation in microbial populations.\n\nThe underlying mechanisms of genetic innovation and speciation in the family Corynebacteriaceae: A phylogenomics approach.", "token_count": 351, "char_count": 1606, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5677, "quality_score": 0.7838, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:36.370089", "source": { "split": "train_shard_00000", "doc_id": 3859 }, "chunk_id": "train_shard_00000_3859_0", "global_id": 4282 }, { "text": "Gastrointestinal drug administration is the preferred route for the majority of drugs however, the natural physiology and physicochemistry of the gastrointestinal tract is critical to absorption but complex and influenced by factors such as diet or disease. The pharmaceutical sciences drive for product consistency has led to the development of in vitro product performance tests whose utility and interpretation is hindered by the complexity, variability and a lack of understanding. This article explores some of these issues with respect to the drug, formulation and the presence of surfactant excipients and how these interact with the natural bile salt surfactants. Interactions start in the mouth and during swallowing but the stomach and small intestine present the major challenges related to drug dissolution, solubility, the impact of surfactants and supersaturation along with precipitation. The behaviour of lipid based formulations and the influence of surfactant excipients is explored along with the difficulties of translating in vitro results to in vivo performance. Possible future research areas are highlighted with the conclusion that, \"a great deal of work using modern methods is still required to clarify the situation\".\n\nThe gut in the beaker: Missing the surfactants?", "token_count": 263, "char_count": 1294, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:36.920130", "source": { "split": "train_shard_00000", "doc_id": 3860 }, "chunk_id": "train_shard_00000_3860_0", "global_id": 4283 }, { "text": "Certain modified diets containing saturated fatty acids, cholesterol or fructose lead to the development of nonalcoholic steatohepatitis (NASH)-related fibrosis in rodents; however, progression to cirrhosis is rare. Experimental liver cirrhosis models have relied on genetic manipulation or administration of hepatotoxins. This study aimed to establish a reliable dietary model of NASH-related cirrhosis in a relatively short period. Male Sprague-Dawley rats (9 weeks of age) were randomly assigned to normal, high-fat (HF), or two types (1.25% or 2.5% cholesterol) of high-fat and high-cholesterol (HFC) diets for 18 weeks. All HFC diets contained 2% cholic acid by weight. Histopathological analysis revealed that the HFC diets induced obvious hepatic steatosis, inflammation with hepatocyte ballooning and advanced fibrosis (stage 3-4) in all 12 rats at 27 weeks of age. In contrast, all five rats given the HF diet developed mild steatosis and inflammation without fibrosis. The amount of cholesterol in the liver and hepatocellular mitochondrial and microsomal fractions was significantly higher in rats fed the HFC diets than the normal or HF diets. The HFC diets significantly suppressed mRNA levels of microsomal triglyceride transfer protein, adenosine triphosphate binding cassette transporter G5, bile acid CoA: amino acid N-acyltransferase and bile salt export pump, as well as the enzymatic activity of carnitine palmitoyltransferase in the liver. In conclusion, the HFC diets induced liver cirrhosis in conjunction with hepatic features of NASH in Sprague-Dawley rats within 18 weeks, and altered gene expression and enzyme activity to accumulate lipid and bile acid in the liver.\n\nA diet-induced Sprague-Dawley rat model of nonalcoholic steatohepatitis-related cirrhosis.", "token_count": 503, "char_count": 1786, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6328, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:37.570919", "source": { "split": "train_shard_00000", "doc_id": 3861 }, "chunk_id": "train_shard_00000_3861_0", "global_id": 4284 }, { "text": "Bacterial surveys of the vaginal and bladder human microbiota have revealed an abundance of many similar bacterial taxa. As the bladder was once thought to be sterile, the complex interactions between microbes within the bladder have yet to be characterized. To initiate this process, we have begun sequencing isolates, including the clinically relevant genus Gardnerella. Herein, we present the genomic sequences of four Gardnerella strains isolated from the bladders of women with symptoms of urgency urinary incontinence; these are the first Gardnerella genomes produced from this niche. Congruent to genomic characterization of Gardnerella isolates from the reproductive tract, isolates from the bladder reveal a large pangenome, as well as evidence of high frequency horizontal gene transfer. Prophage gene sequences were found to be abundant amongst the strains isolated from the bladder, as well as amongst publicly available Gardnerella genomes from the vagina and endometrium, motivating an in depth examination of these sequences. Amongst the 39 Gardnerella strains examined here, there were more than 400 annotated prophage gene sequences that we could cluster into 95 homologous groups; 49 of these groups were unique to a single strain. While many of these prophages exhibited no sequence similarity to any lytic phage genome, estimation of the rate of phage acquisition suggests both vertical and horizontal acquisition. Furthermore, bioinformatic evidence indicates that prophage acquisition is ongoing within both vaginal and bladder Gardnerella populations. The abundance of prophage sequences within the strains examined here suggests that phages could play an important role in the species' evolutionary history and in its interactions within the complex communities found in the female urinary and reproductive tracts.\n\nGenomes of Gardnerella Strains Reveal an Abundance of Prophages within the Bladder Microbiome.", "token_count": 432, "char_count": 1934, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5374, "quality_score": 0.7687, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:38.202476", "source": { "split": "train_shard_00000", "doc_id": 3862 }, "chunk_id": "train_shard_00000_3862_0", "global_id": 4285 }, { "text": "Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer. The three other accessory chromosomes in the Fol reference strain may also be important for virulence towards tomato. Expression of effector genes in Fol is highly up-regulated upon infection and requires Sge1, a transcription factor encoded on the core genome. Interestingly, the pathogenicity chromosome itself contains 13 predicted transcription factor genes and for all except one, there is a homolog on the core genome. We determined DNA binding specificity for nine transcription factors using oligonucleotide arrays. The binding sites for homologous transcription factors were highly similar, suggesting that extensive neofunctionalization of DNA binding specificity has not occurred. Several DNA binding sites are enriched on accessory chromosomes, and expression of FTF1, its core homolog FTF2 and SGE1 from a constitutive promoter can induce expression of effector genes. The DNA binding sites of only these three transcription factors are enriched among genes up-regulated during infection. We further show that Ftf1, Ftf2 and Sge1 can activate transcription from their binding sites in yeast. RNAseq analysis revealed that in strains with constitutive expression of FTF1, FTF2 or SGE1, expression of a similar set of plant-responsive genes on the pathogenicity chromosome is induced, including most effector genes. We conclude that the Fol pathogenicity chromosome may be partially transcriptionally autonomous, but there are also extensive transcriptional connections between core and accessory chromosomes.", "token_count": 485, "char_count": 2147, "word_count": 302, "semantic_coherence": 1, "information_density": 0.553, "quality_score": 0.7765, "entities": { "genes": [ "FTF2", "FTF1", "SGE1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:38.852673", "source": { "split": "train_shard_00000", "doc_id": 3863 }, "chunk_id": "train_shard_00000_3863_0", "global_id": 4286 }, { "text": "Transcription Factors Encoded on Core and Accessory Chromosomes of Fusarium oxysporum Induce Expression of Effector Genes.", "token_count": 33, "char_count": 122, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:39.212082", "source": { "split": "train_shard_00000", "doc_id": 3863 }, "chunk_id": "train_shard_00000_3863_1", "global_id": 4287 }, { "text": "Probiotics are \"live microorganisms which, when consumed in adequate amounts, confer a health benefit to the host\". A number of attributes are highly sought after among these microorganisms, including immunomodulation, epithelial barrier maintenance, competitive exclusion, production of short-chain fatty acids, and bile salt metabolism. Bacteriocin production is also generally regarded as a probiotic trait, but it can be argued that, in contrast to other traits, it is often considered a feature that is desirable, rather than a key probiotic trait. As such, the true potential of these antimicrobials has yet to be realised.\n\nBacteriocin production: a relatively unharnessed probiotic trait?", "token_count": 162, "char_count": 696, "word_count": 100, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:39.657638", "source": { "split": "train_shard_00000", "doc_id": 3864 }, "chunk_id": "train_shard_00000_3864_0", "global_id": 4288 }, { "text": "Vibrio cholerae is the causative bacteria of the diarrheal disease cholera, but it also persists in aquatic environments, where it displays an expression profile that is distinct from that during infection. Upon entry into the host, a tightly regulated circuit coordinates the induction of two major virulence factors: cholera toxin and a toxin-coregulated pilus (TCP). It has been shown that a set of bile salts, including taurocholate, serve as host signals to activate V. cholerae virulence through inducing the activity of the transmembrane virulence regulator TcpP. In this study, we investigated the role of calcium, an abundant mental ion in the gut, in the regulation of virulence. We show that whereas Ca\n\nCalcium Enhances Bile Salt-Dependent Virulence Activation in Vibrio cholerae.", "token_count": 207, "char_count": 792, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:40.114720", "source": { "split": "train_shard_00000", "doc_id": 3865 }, "chunk_id": "train_shard_00000_3865_0", "global_id": 4289 }, { "text": "An extracellular inulinase was partially purified by ethanol precipitation and gel exclusion chromatography from a cell free extract of Kluyveromyces marxianus. Partially purified inulinase exhibited 420 IU/mg specific activity and it was immobilized on chitosan beads. Activity yield of immobilized inulinase was optimized with glutaraldehyde concentration (1-5%), glutaraldehyde treatment time (30-240min), enzyme coupling-time (2-16h) and enzyme loading (5-30 IU) as functions. Under the optimized conditions maximum yield 65.5% of immobilized inulinase was obtained. Maximum hydrolysis of inulin 84.5% and 78.2% was observed at 125rpm after 4h by immobilized and free enzyme, respectively. A retention-time of 4h and 5h was found optimal for the hydrolysis of inulin under agitation (125rpm) by free and immobilized enzyme, respectively. The recycling of the developed immobilized biocatalyst was carried out after 5h of inulin hydrolysis in a batch system. The developed immobilized biocatalyst was successfully used for the hydrolysis of inulin for 14 batches. This is the first report on the immobilization of yeast inulinase on chitosan beads for the hydrolysis of inulin in a batch system.\n\nImmobilization of yeast inulinase on chitosan beads for the hydrolysis of inulin in a batch system.", "token_count": 386, "char_count": 1299, "word_count": 188, "semantic_coherence": 1, "information_density": 0.484, "quality_score": 0.742, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:40.729857", "source": { "split": "train_shard_00000", "doc_id": 3866 }, "chunk_id": "train_shard_00000_3866_0", "global_id": 4290 }, { "text": "A metabolic heat-based model was used for estimating the growth of Kluyveromyces marxianus, and the modified Luedeking-Piret kinetic model was used for describing the inulinase production kinetics. For the first time, a relationship was developed to relate inulinase production kinetics directly to metabolic heat generated, which corroborated well with the experimental data (with R\n\nModeling of exo-inulinase biosynthesis by Kluyveromyces marxianus in fed-batch mode: correlating production kinetics and metabolic heat fluxes.", "token_count": 138, "char_count": 528, "word_count": 71, "semantic_coherence": 1, "information_density": 0.6901, "quality_score": 0.8451, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:41.154589", "source": { "split": "train_shard_00000", "doc_id": 3867 }, "chunk_id": "train_shard_00000_3867_0", "global_id": 4291 }, { "text": "Microdiversification of a planktonic freshwater bacterium was studied by comparing 37 Polynucleobacter asymbioticus strains obtained from three geographically separated sites in the Austrian Alps. Genome comparison of nine strains revealed a core genome of 1.8 Mb, representing 81% of the average genome size. Seventy-five percent of the remaining flexible genome is clustered in genomic islands (GIs). Twenty-four genomic positions could be identified where GIs are potentially located. These positions are occupied strain specifically from a set of 28 GI variants, classified according to similarities in their gene content. One variant, present in 62% of the isolates, encodes a pathway for the degradation of aromatic compounds, and another, found in 78% of the strains, contains an operon for nitrate assimilation. Both variants were shown in ecophysiological tests to be functional, thus providing the potential for microniche partitioning. In addition, detected interspecific horizontal exchange of GIs indicates a large gene pool accessible to Polynucleobacter species. In contrast to core genes, GIs are spread more successfully across spatially separated freshwater habitats. The mobility and functional diversity of GIs allow for rapid evolution, which may be a key aspect for the ubiquitous occurrence of Polynucleobacter bacteria.\n\nMicrodiversification of a Pelagic Polynucleobacter Species Is Mainly Driven by Acquisition of Genomic Islands from a Partially Interspecific Gene Pool.", "token_count": 357, "char_count": 1496, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6604, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:41.736348", "source": { "split": "train_shard_00000", "doc_id": 3868 }, "chunk_id": "train_shard_00000_3868_0", "global_id": 4292 }, { "text": "There is an increasing awareness that as a result of structural variation, a reference sequence representing a genome of a single individual is unable to capture all of the gene repertoire found in the species. A large number of genes affected by presence/absence and copy number variation suggest that it may contribute to phenotypic and agronomic trait diversity. Here we show by analysis of the Brassica oleracea pangenome that nearly 20% of genes are affected by presence/absence variation. Several genes displaying presence/absence variation are annotated with functions related to major agronomic traits, including disease resistance, flowering time, glucosinolate metabolism and vitamin biosynthesis.\n\nThe pangenome of an agronomically important crop plant Brassica oleracea.", "token_count": 177, "char_count": 782, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6964, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:42.175419", "source": { "split": "train_shard_00000", "doc_id": 3869 }, "chunk_id": "train_shard_00000_3869_0", "global_id": 4293 }, { "text": "The interpretation of high-throughput gene expression data for non-model microorganisms remains obscured because of the high fraction of hypothetical genes and the limited number of methods for the robust inference of gene networks. Therefore, to elucidate gene-gene and gene-condition linkages in the bioremediation-important genus Dehalococcoides, we applied a Bayesian inference strategy called Reverse Engineering/Forward Simulation (REFS™) on transcriptomic data collected from two organohalide-respiring communities containing different Dehalococcoides mccartyi strains: the Cornell University mixed community D2 and the commercially available KB-1® bioaugmentation culture. In total, 49 and 24 microarray datasets were included in the REFS™ analysis to generate an ensemble of 1,000 networks for the Dehalococcoides population in the Cornell D2 and KB-1® culture, respectively. Considering only linkages that appeared in the consensus network for each culture (exceeding the determined frequency cutoff of ≥ 60%), the resulting Cornell D2 and KB-1® consensus networks maintained 1,105 nodes (genes or conditions) with 974 edges and 1,714 nodes with 1,455 edges, respectively. These consensus networks captured multiple strong and biologically informative relationships. One of the main highlighted relationships shared between these two cultures was a direct edge between the transcript encoding for the major reductive dehalogenase (tceA (D2) or vcrA (KB-1®)) and the transcript for the putative S-layer cell wall protein (DET1407 (D2) or KB1_1396 (KB-1®)). Additionally, transcripts for two key oxidoreductases (a [Ni Fe] hydrogenase, Hup, and a protein with similarity to a formate dehydrogenase, \"Fdh\") were strongly linked, generalizing a strong relationship noted previously for Dehalococcoides mccartyi strain 195 to multiple strains of Dehalococcoides", "token_count": 488, "char_count": 1866, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8294, "entities": { "genes": [ "DET1407" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:42.825347", "source": { "split": "train_shard_00000", "doc_id": 3870 }, "chunk_id": "train_shard_00000_3870_0", "global_id": 4294 }, { "text": "Notably, the pangenome array utilized when monitoring the KB-1® culture was capable of resolving signals from multiple strains, and the network inference engine was able to reconstruct gene networks in the distinct strain populations.\n\nInferring Gene Networks for Strains of Dehalococcoides Highlights Conserved Relationships between Genes Encoding Core Catabolic and Cell-Wall Structural Proteins.", "token_count": 91, "char_count": 398, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8491, "quality_score": 0.9245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:43.197306", "source": { "split": "train_shard_00000", "doc_id": 3870 }, "chunk_id": "train_shard_00000_3870_1", "global_id": 4295 }, { "text": "Enterohemorrhagic Escherichia coli (EHEC) O157:H7/NM strains are significant foodborne pathogens intensively studied, while other sero- and pathotypes of the O157 serogroup only began to receive more attention. Here we report the first genome sequence of a cytolethal distending toxin (CDT-V) producing E. coli O157:H43 strain (T22) isolated from cattle. The genome consists of a 4.9Mb chromosome assembled into three contigs and one plasmid of 82.4kb. Comparative genomic investigations conducted with the core genomes of representative E. coli strains in GenBank (n=62) confirmed the separation of T22 from the EHEC and enteropathogenic (EPEC) O157 lineages. Gene content based pangenome analysis revealed as many as 261 T22-specific coding sequences without orthologs in EDL933 EHEC O157 prototypic and two phylogenetically related commensal E. coli strains. The genome sequence revealed 10 prophage-like regions which harbor several virulence-associated genes including cdt and heat-labile enterotoxin (LT-II) encoding operons. Our results indicate that the evolutionary path of T22 is largely independent from that of EHEC and EPEC O157:H7/NM strains. Thus, the CDT-producing T22 E. coli O157:H43 strain represents a unique lineage of E. coli O157.\n\nCytolethal distending toxin producing Escherichia coli O157:H43 strain T22 represents a novel evolutionary lineage within the O157 serogroup.", "token_count": 438, "char_count": 1396, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [ "EDL933" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:43.836309", "source": { "split": "train_shard_00000", "doc_id": 3871 }, "chunk_id": "train_shard_00000_3871_0", "global_id": 4296 }, { "text": "Bile acids are important signaling molecules that regulate cholesterol, glucose, and energy homoeostasis and have thus been implicated in the development of metabolic disorders. Their bioavailability is strongly modulated by the gut microbiota, which contributes to generation of complex individual-specific bile acid profiles. Hence, it is important to have accurate methods at hand for precise measurement of these important metabolites. Here, a rapid and sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for simultaneous identification and quantitation of primary and secondary bile acids as well as their taurine and glycine conjugates was developed and validated. Applicability of the method was demonstrated for mammalian tissues, biofluids, and cell culture media. The analytical approach mainly consists of a simple and rapid liquid-liquid extraction procedure in presence of deuterium-labeled internal standards. Baseline separation of all isobaric bile acid species was achieved and a linear correlation over a broad concentration range was observed. The method showed acceptable accuracy and precision on intra-day (1.42-11.07 %) and inter-day (2.11-12.71 %) analyses and achieved good recovery rates for representative analytes (83.7-107.1 %). As a proof of concept, the analytical method was applied to mouse tissues and biofluids, but especially to samples from in vitro fermentations with gut bacteria of the family Coriobacteriaceae. The developed method revealed that the species Eggerthella lenta and Collinsella aerofaciens possess bile salt hydrolase activity, and for the first time that the species Enterorhabdus mucosicola is able to deconjugate and dehydrogenate primary bile acids in vitro.\n\nRapid analysis of bile acids in different biological matrices using LC-ESI-MS/MS for the investigation of bile acid transformation by mammalian gut bacteria.", "token_count": 461, "char_count": 1900, "word_count": 264, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:44.477297", "source": { "split": "train_shard_00000", "doc_id": 3872 }, "chunk_id": "train_shard_00000_3872_0", "global_id": 4297 }, { "text": "Hundreds of small RNAs (sRNAs) have been identified in diverse bacterial species, and while the functions of most remain unknown, some regulate key processes, particularly stress responses. The sRNA DicF was identified over 25 years ago as an inhibitor of cell division but since then has remained uncharacterized. DicF consists of 53 nucleotides and is encoded by a gene carried on a prophage (Qin) in the genomes of many\n\nA Prophage-Encoded Small RNA Controls Metabolism and Cell Division in", "token_count": 129, "char_count": 493, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7848, "quality_score": 0.8924, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:44.939491", "source": { "split": "train_shard_00000", "doc_id": 3873 }, "chunk_id": "train_shard_00000_3873_0", "global_id": 4298 }, { "text": "Except for conversion to bile salts, there is no major cholesterol degradation pathway in mammals. Efficient excretion from the body is therefore a crucial element in cholesterol homeostasis. Yet, the existence and importance of cholesterol degradation pathways in humans is a matter of debate. We quantified cholesterol fluxes in 15 male volunteers using a cholesterol balance approach. Ten participants repeated the protocol after 4 weeks of treatment with ezetimibe, an inhibitor of intestinal and biliary cholesterol absorption. Under basal conditions, about 65% of daily fecal neutral sterol excretion was bile derived, with the remainder being contributed by direct transintestinal cholesterol excretion (TICE). Surprisingly, ezetimibe induced a 4-fold increase in cholesterol elimination via TICE. Mouse studies revealed that most of ezetimibe-induced TICE flux is mediated by the cholesterol transporter Abcg5/Abcg8. In conclusion, TICE is active in humans and may serve as a novel target to stimulate cholesterol elimination in patients at risk for cardiovascular disease.\n\nTransintestinal Cholesterol Transport Is Active in Mice and Humans and Controls Ezetimibe-Induced Fecal Neutral Sterol Excretion.", "token_count": 317, "char_count": 1212, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:45.515115", "source": { "split": "train_shard_00000", "doc_id": 3874 }, "chunk_id": "train_shard_00000_3874_0", "global_id": 4299 }, { "text": "Streptococcus agalactiae (GBS) causes serious infections in humans and other species. A total of 25 complete GBS genomes, including the first sequenced serotype VI genome (GBS-M002), were compared in this study. The power law model suggested that the pan-genome of GBS is open, with approximately 1300 genes in the core genome of GBS, accounting for approximately 60% of the average genome content. GBS-M002 has 73 specific genes and is one of the five strains containing >60 specific genes. Based on COG (Cluster of Orthologous Groups of proteins) functional classification, 24% of the genes related to defense mechanisms are specific among the strains. A phylogenetic tree shows that GBS-M002 is closely related to certain strains of serotypes III and V from humans and to isolates of unknown serotype from dog and bovine hosts, suggesting the universal infection potential of GBS from humans to other mammal and fish hosts.\n\nThe genome of serotype VI Streptococcus agalactiae serotype VI and comparative analysis.", "token_count": 267, "char_count": 1016, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:46.766165", "source": { "split": "train_shard_00000", "doc_id": 3875 }, "chunk_id": "train_shard_00000_3875_0", "global_id": 4300 }, { "text": "Bile salt-mediated conformational modification of hemoglobin (Hb) was examined at three different pHs i.e., 3.2, 7.4 and 9.0. The added bile salt, sodium deoxycholate (NaDC), decreases the α-helicity in Hb (α-helix: 71.3% → 61.7% in the presence of 9.6 mM NaDC, and 83.2% → 66.2% in the presence of 14 mM NaDC, at pH 7.4 and 9.0, respectively), while a reverse pattern of modification in the Circular Dichroism (CD) spectra of Hb is found at pH 3.2. The acid-induced denatured Hb (pH 3.2) regains its structural integrity by changing conformation from a random coil to an α-helix rich secondary structure upon addition of NaDC (α-helix: 10.4% → 53.4%, β-sheet: 31.0% → 18.5% and random coil: 58.6% → 28.1%, in the presence of 0.65 mM NaDC). Also, a step-wise binding interaction pattern of Hb with NaDC was revealed at pH 7.4 and 9.0 upon variation of steady-state fluorescence intensity and average lifetime of Hb. From the fluorescence lifetime decay pattern, the decrement of energy transfer from Trp to a heme group was found upon the addition of NaDC at pH 7.4 and 9.0. However, at pH 3.2, the modification of the time-resolved fluorescence decay behavior of Hb within NaDC is typically reversed, where the energy transfer from Trp to heme is restored to some extent. Thermodynamic analysis suggests that the Hb-NaDC binding interaction is characterized by a dominant entropic contribution interpreted on the basis of release of ordered water molecules to the bulk aqueous phase.\n\nContrasting effects of pH on the modulation of the structural integrity of hemoglobin induced by sodium deoxycholate.", "token_count": 510, "char_count": 1603, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5441, "quality_score": 0.772, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:47.418020", "source": { "split": "train_shard_00000", "doc_id": 3876 }, "chunk_id": "train_shard_00000_3876_0", "global_id": 4301 }, { "text": "Vancomycin-resistant Enterococcus faecium high-resolution typing by core genome multilocus sequence typing.", "token_count": 29, "char_count": 107, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:47.802942", "source": { "split": "train_shard_00000", "doc_id": 3877 }, "chunk_id": "train_shard_00000_3877_0", "global_id": 4302 }, { "text": "We report a comparative study of 29 representative genomes of the animal pathogen Rhodococcus equi The analyses showed that R. equi is genetically homogeneous and clonal, with a large core genome accounting for ≈80% of an isolates' gene content. An open pangenome, even distribution of accessory genes among the isolates, and absence of significant core-genome recombination, indicated that gene gain/loss is a main driver of R. equi genome evolution. Traits previously predicted to be important in R. equi physiology, virulence and niche adaptation were part of the core genome. This included the lack of a phosphoenolpyruvate:carbohydrate transport system (PTS), unique among the rhodococci except for the closely related Rhodococcus defluvii, reflecting selective PTS gene loss in the R. equi-R. defluvii sublineage. Thought to be asaccharolytic, rbsCB and glcP non-PTS sugar permease homologues were identified in the core genome and, albeit inefficiently, R. equi utilized their putative substrates, ribose and (irregularly) glucose. There was no correlation between R. equi whole-genome phylogeny and host or geographical source, with evidence of global spread of genomovars. The distribution of host-associated virulence plasmid types was consistent with the exchange of the plasmids (and corresponding host shifts) across the R. equi population, and human infection being zoonotically acquired. Phylogenomic analyses demonstrated that R. equi occupies a central position in the Rhodococcus phylogeny, not supporting the recently proposed transfer of the species to a new genus.\n\nPangenome and Phylogenomic Analysis of the Pathogenic Actinobacterium Rhodococcus equi.", "token_count": 441, "char_count": 1674, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:48.429929", "source": { "split": "train_shard_00000", "doc_id": 3878 }, "chunk_id": "train_shard_00000_3878_0", "global_id": 4303 }, { "text": "A thermostable metalloprotease, produced from an environmental strain of Candida kefyr 41 PSB, was purified 16 fold with a 60% yield by cold ethanol precipitation and affinity chromatography (bentonite-acrylamide-cysteine microcomposite). The purified enzyme appeared as a single protein band at 43kDa. Its optimum pH and temperature points were found to be 7.0 and 105°C, respectively. K\n\nProduction, purification, and characterization of metalloprotease from Candida kefyr 41 PSB.", "token_count": 146, "char_count": 482, "word_count": 67, "semantic_coherence": 1, "information_density": 0.8358, "quality_score": 0.9179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:48.886911", "source": { "split": "train_shard_00000", "doc_id": 3879 }, "chunk_id": "train_shard_00000_3879_0", "global_id": 4304 }, { "text": "Mycobacterium avium subsp. hominissuis (MAH) is an opportunistic human pathogen widespread in the environment. Genomic islands (GI)s represent a part of the accessory genome of bacteria and influence virulence, drug-resistance or fitness and trigger bacterial evolution. We previously identified a novel GI in four MAH genomes. Here, we further explored this GI in a larger collection of MAH isolates from Germany (n=41), including 20 clinical and 21 environmental isolates. Based on comparative whole genome analysis, we detected this GI in 39/41 (95.1%) isolates. Although all these GIs integrated in the same insertion hotspot, there is high variability in the genetic structure of this GI: eight different types of GI have been identified, designated A-H (sized 6.2-73.3kb). These GIs were arranged as single GI (23/41, 56.1%), combination of two different GIs (14/41, 34.1%) or combination of three different GIs (2/41, 4.9%) in the insertion hotspot. Moreover, two GI types shared more than 80% sequence identity with sequences of M. canettii, responsible for Tuberculosis. A total of 253 different genes were identified in all GIs, among which the previously documented virulence-related genes mmpL10 and mce. The diversity of the GI and the sequence similarity with other mycobacteria suggests cross-species transfer, involving also highly pathogenic species. Shuffling of potential virulence genes such as mmpL10 via this GI may create new pathogens that can cause future outbreaks.\n\nA hypervariable genomic island identified in clinical and environmental Mycobacterium avium subsp. hominissuis isolates from Germany.", "token_count": 435, "char_count": 1626, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6527, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:49.516077", "source": { "split": "train_shard_00000", "doc_id": 3880 }, "chunk_id": "train_shard_00000_3880_0", "global_id": 4305 }, { "text": "Human intestinal absorption (HIA) will dictate biopharmaceutical performance through its influence on absorption, distribution, metabolism, and elimination and can vary significantly depending upon the nature of the compound under consideration. In this study, an in vitro assay method is proposed for the prediction of HIA through the measurement of drug solubility in an aqueous phase containing micellar bile salt, namely sodium deoxycholate. A series of twenty compounds, displaying a range of physicochemical properties and known HIA values, were analyzed using UV spectroscopy to determine a solubilization ratio for each compound. A micelle/water partition coefficient (K\n\nThe Use of Bile Salt Micelles for the Prediction of Human Intestinal Absorption.", "token_count": 174, "char_count": 760, "word_count": 108, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:49.965152", "source": { "split": "train_shard_00000", "doc_id": 3881 }, "chunk_id": "train_shard_00000_3881_0", "global_id": 4306 }, { "text": "We have quantified the inhibition of intestinal cholesterol transport by pine-derived phytosterols using an HT29-MTX intestine cell model that forms a mucus layer similar to that in the intestine. An artificial intestinal fluid consisting of digested fat, bile salt, cholesterol, and phytosterols was formulated in order to mimic the conditions in the intestine. The apparent permeability coefficient (P\n\nInhibition of cholesterol transport in an intestine cell model by pine-derived phytosterols.", "token_count": 132, "char_count": 497, "word_count": 70, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [ "HT29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:50.384541", "source": { "split": "train_shard_00000", "doc_id": 3882 }, "chunk_id": "train_shard_00000_3882_0", "global_id": 4307 }, { "text": "Little is known with certainty about the mechanisms of idiosyncratic drug reactions (IDRs); however, there is substantive evidence that reactive metabolites are involved in most, but not all, IDRs. In addition, evidence also suggests that most IDRs are immune mediated. That raises the question of how reactive metabolites induce an immune response that can lead to an IDR. The dominant hypotheses are the hapten and danger hypotheses. These are complementary hypotheses: a reactive metabolite can act as a hapten to produce neoantigens, and it can also cause cell damage leading to the release of danger-associated molecular pattern molecules that activate antigen presenting cells. Both are required for an immune response. In addition, drugs may induce an immune response through inflammasome activation. We have found examples in which the ability to activate inflammasomes differentiated drugs that cause IDRs from similar drugs that do not. There are other hypotheses that do not involve an immune mechanism such as mitochondrial injury and bile salt export pump (BSEP) inhibition. With some possible exceptions, these hypotheses are unlikely to be able to completely explain IDRs. However, some types of mitochondrial injury or BSEP inhibition could produce danger signals. The major mechanism that protects us from IDRs appears to be immune tolerance. Consistent with this hypothesis, we used checkpoint inhibition to develop the first animal model of idiosyncratic drug-induced liver injury that has the same characteristics as the idiosyncratic injury in humans. This was accomplished by treating Pd-1\n\nHow Reactive Metabolites Induce an Immune Response That Sometimes Leads to an Idiosyncratic Drug Reaction.", "token_count": 386, "char_count": 1719, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5798, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:51.005659", "source": { "split": "train_shard_00000", "doc_id": 3883 }, "chunk_id": "train_shard_00000_3883_0", "global_id": 4308 }, { "text": "The objective of this work was to encapsulate terconazole (TCZ), a water insoluble antifungal drug, into novel ultradeformable bilosomes (UBs) for achieving enhanced ocular delivery. In addition to the constituents of the conventional bilosomes; namely, Span 60, cholesterol, and the bile salts, UBs contain an edge activator which imparts extra elasticity to the vesicles and consequently hypothesized to result in improved corneal permeation. In this study, TCZ loaded UBs were prepared utilizing ethanol injection method according to 2\n\nFabrication of novel ultradeformable bilosomes for enhanced ocular delivery of terconazole: In vitro characterization, ex vivo permeation and in vivo safety assessment.", "token_count": 188, "char_count": 708, "word_count": 100, "semantic_coherence": 1, "information_density": 0.74, "quality_score": 0.87, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:51.456417", "source": { "split": "train_shard_00000", "doc_id": 3884 }, "chunk_id": "train_shard_00000_3884_0", "global_id": 4309 }, { "text": "The three-base periodicity property is characteristic of protein-coding sequences. Here, we report on three-base periodicity of sequence variation in the core genome of bacteria. Single nucleotide polymorphism (SNP) syntenies were extracted from pairwise genome alignments of 41 Staphylococcus aureus or 20 Pseudomonas aeruginosa strains. The length of fragment pairs with identical nucleotides at all SNP positions showed a length-dependent overrepresentation of multiples of three nucleotides at corresponding codon positions of the AT-rich S. aureus and the GC-rich P. aeruginosa. Three-base SNP periodicity seems to be a characteristic feature of the tightly arranged bacterial core genome.\n\nThree-base periodicity of sites of sequence variation in Pseudomonas aeruginosa and Staphylococcus aureus core genomes.", "token_count": 204, "char_count": 815, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:51.918429", "source": { "split": "train_shard_00000", "doc_id": 3885 }, "chunk_id": "train_shard_00000_3885_0", "global_id": 4310 }, { "text": "Lactobacillus salivarius LI01, isolated from healthy humans, has demonstrated probiotic properties in the prevention and treatment of liver failure. Tolerance to bile stress is crucial to allow lactobacilli to survive in the gastrointestinal tract and exert their benefits. In this work, we used a Digital Gene Expression transcriptomic and iTRAQ LC-MS/MS proteomic approach to examine the characteristics of LI01 in response to bile stress. Using culture medium with or without 0.15% ox bile, 591 differentially transcribed genes and 347 differentially expressed proteins were detected in LI01. Overall, we found the bile resistance of LI01 to be based on a highly remodeled cell envelope and a reinforced bile efflux system rather than on the activity of bile salt hydrolases. Additionally, some differentially expressed genes related to regulatory systems, the general stress response and central metabolism processes, also play roles in stress sensing, bile-induced damage prevention and energy efficiency. Moreover, bile salts appear to enhance proteolysis and amino acid uptake (especially aromatic amino acids) by LI01, which may support the liver protection properties of this strain. Altogether, this study establishes a model of global response mechanism to bile stress in L. salivarius LI01.\n\nIntegrated transcriptomic and proteomic analysis of the bile stress response in probiotic Lactobacillus salivarius LI01.", "token_count": 343, "char_count": 1424, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [ "LI01" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:52.486676", "source": { "split": "train_shard_00000", "doc_id": 3886 }, "chunk_id": "train_shard_00000_3886_0", "global_id": 4311 }, { "text": "Bile cast nephropathy is a tubulo-interstitial nephropathy. Its diagnosis may be under-estimated. It develops in patients who have cholestatic jaundice, with high bilirubinemia. Bile salts are freely filtered through glomerulus. Under certain circumstances, it forms casts into the tubule and cause an acute tubular necrosis. The diagnosis evidence is histologic, but fulfilment of renal biopsy is often made difficult, because of the hemostatic abnormalities that patients with hepatocellular injury develop. The treatment is supportive and etiological. We report here the case of a patient who presented a drug-induced hepatic jaundice, complicated with acute kidney failure secondary to bile cast nephropathy. We present the histological diagnosis evidence.\n\n[Bile salt nephropathy/cholemic nephrosis].", "token_count": 214, "char_count": 805, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7545, "quality_score": 0.8773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:52.948235", "source": { "split": "train_shard_00000", "doc_id": 3887 }, "chunk_id": "train_shard_00000_3887_0", "global_id": 4312 }, { "text": "Bile salt hydrolase (BSH) enzyme is responsible for the de-conjugation of bile salts by commensal bacteria, thus playing a vital role in their colonization and survival in the mammalian intestine and determination of their probiotic potential. Further, bile deconjugation also leads to lowering of cholesterol and alterations in energy homeostasis, thus making BSH a clinically important enzyme.\n\nMolecular features of bile salt hydrolases and relevance in human health.", "token_count": 122, "char_count": 470, "word_count": 68, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:53.330822", "source": { "split": "train_shard_00000", "doc_id": 3888 }, "chunk_id": "train_shard_00000_3888_0", "global_id": 4313 }, { "text": "As a third-generation sequencing (TGS) method, single-molecule real-time (SMRT) technology provides long read length, and it is well suited for resequencing projects and de novo assembly. In the present study, Pseudomonas aeruginosa PA1 was characterized and resequenced using SMRT technology. PA1 was also subjected to genomic, comparative and pan-genomic analyses. The multidrug resistant strain PA1 possesses a 6,498,072 bp genome and a sequence type of ST-782. The genome of PA1 was also visualized, and the results revealed the details of general genome annotations, virulence factors, regulatory proteins (RPs), secretion system proteins, type II toxin-antitoxin (T-A) pairs and genomic islands. Whole genome comparison analysis suggested that PA1 exhibits similarity to other P. aeruginosa strains but differs in terms of horizontal gene transfer (HGT) regions, such as prophages and genomic islands. Phylogenetic analyses based on 16S rRNA sequences demonstrated that PA1 is closely related to PAO1, and P. aeruginosa strains can be divided into two main groups. The pan-genome of P. aeruginosa consists of a core genome of approximately 4,000 genes and an accessory genome of at least 6,600 genes. The present study presented a detailed, visualized and comparative analysis of the PA1 genome, to enhance our understanding of this notorious pathogen.\n\nGenomic analyses of multidrug resistant Pseudomonas aeruginosa PA1 resequenced by single-molecule real-time sequencing.", "token_count": 400, "char_count": 1479, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6526, "quality_score": 0.8263, "entities": { "genes": [ "PA1", "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:53.945149", "source": { "split": "train_shard_00000", "doc_id": 3889 }, "chunk_id": "train_shard_00000_3889_0", "global_id": 4314 }, { "text": "Drug-induced cholestasis (DIC) is poorly understood and its preclinical prediction is mainly limited to assessing the compound's potential to inhibit the bile salt export pump (BSEP). Here, we evaluated two 3D spheroid models, one from primary human hepatocytes (PHH) and one from HepaRG cells, for the detection of compounds with cholestatic liability. By repeatedly co-exposing both models to a set of compounds with different mechanisms of hepatotoxicity and a non-toxic concentrated bile acid (BA) mixture for 8 days we observed a selective synergistic toxicity of compounds known to cause cholestatic or mixed cholestatic/hepatocellular toxicity and the BA mixture compared to exposure to the compounds alone, a phenomenon that was more pronounced after extending the exposure time to 14 days. In contrast, no such synergism was observed after both 8 and 14 days of exposure to the BA mixture for compounds that cause non-cholestatic hepatotoxicity. Mechanisms behind the toxicity of the cholestatic compound chlorpromazine were accurately detected in both spheroid models, including intracellular BA accumulation, inhibition of ABCB11 expression and disruption of the F-actin cytoskeleton. Furthermore, the observed synergistic toxicity of chlorpromazine and BA was associated with increased oxidative stress and modulation of death receptor signalling. Combined, our results demonstrate that the hepatic spheroid models presented here can be used to detect and study compounds with cholestatic liability.\n\nHepatic 3D spheroid models for the detection and study of compounds with cholestatic liability.", "token_count": 390, "char_count": 1608, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5541, "quality_score": 0.7771, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:54.561235", "source": { "split": "train_shard_00000", "doc_id": 3890 }, "chunk_id": "train_shard_00000_3890_0", "global_id": 4315 }, { "text": "Bile Salt Export Pump (BSEP) Deficiency disease, including Progressive Familial Intrahepatic Cholestasis type 2 (PFIC2), is a rare disease, usually leading within the first ten years to portal hypertension, liver failure, hepatocellular carcinoma. Often liver transplantation is needed. Sodium 4-phenylbutyrate (4-PB) seems to be a potential therapeutic compound for PFIC2. Psychiatric side effects in the adolescent population are little known and little studied since the drug used to treat children and infants. So we described a case of Caucasian boy, suffering from a late onset PFIC2, listed for a liver transplant when he was sixteen and treated with 4-FB (200 mg per kilogram of body weight per day). The drug was discontinued for the onset of bipolar and related disorders. This case illustrates possible psychiatric side effects of the drug.\n\nBipolar and Related Disorders Induced by Sodium 4-Phenylbutyrate in a Male Adolescent with Bile Salt Export Pump Deficiency Disease.", "token_count": 263, "char_count": 985, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6913, "quality_score": 0.8456, "entities": { "genes": [ "PFIC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:55.112277", "source": { "split": "train_shard_00000", "doc_id": 3891 }, "chunk_id": "train_shard_00000_3891_0", "global_id": 4316 }, { "text": "The purpose of this study was to evaluate the probiotic properties of Enterococcus strains isolated from traditional naturally fermented cream in China. Four Enterococcus isolates showed high cholesterol removal ability in media were identified as Enterococcus durans (KLDS 6.0930 and 6.0933) and Enterococcus faecalis (KLDS 6.0934 and 6.0935) by 16S rRNA and pheS gene sequences, respectively, and selected for further evaluation. In order to assess the probiotic potential and safety of these strains, the property of four Enterococcus strains were examined, including acid and bile tolerance, adherence to Caco-2 cells and antibiotics susceptibility. All four strains showed potential cholesterol assimilation, de-conjugation of bile salts and/or cholesterol degradation to remove cholesterol in vitro. In addition, the potential effect of E. durans KLDS 6.0930 on serum cholesterol levels was evaluated in Sprague-Dawley rats. After 4 weeks administration, compared with rats fed a high-cholesterol diet without lactic acid bacteria supplementation, there was a significant (P < 0.05) decrease in the total cholesterol and low-density lipoprotein cholesterol levels in the serum of rats treated with KLDS 6.0930. Furthermore, total bile acid level in the feces was significantly (P < 0.05) increased after KLDS 6.0930 administration. These observations suggested that the strain E. durans KLDS 6.0930 may be used in the future as a good candidate for lowering human serum cholesterol levels.\n\nProbiotic properties of Enterococcus strains isolated from traditional naturally fermented cream in China.", "token_count": 465, "char_count": 1603, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5652, "quality_score": 0.7826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:55.747571", "source": { "split": "train_shard_00000", "doc_id": 3892 }, "chunk_id": "train_shard_00000_3892_0", "global_id": 4317 }, { "text": "Gene loss is a major contributor to the evolution of bacterial gene content. Gene loss may occur as a result of shifts in environment leading to changes in the intensity and/or directionality of selection applied for the maintenance of specific genes. Gene loss may also occur in a more neutral manner, when gene functions are lost that were not subject to strong selection to be maintained, irrespective of changes to environment. Here, we used a pangenome-based approach to investigate patterns of gene loss across 15 bacterial species. We demonstrate that gene loss tends to occur mostly within a pool of genes that are less constrained within species, even in those strains from which they are not lost, and less conserved across bacterial species. Our results indicate that shifts in selection, resulting from shifts in environment are not required to explain the majority of gene loss events occurring within a diverse collection of bacterial species. Caution should therefore be taken when attributing differences in gene content to differences in environment.\n\nBacterial intra-species gene loss occurs in a largely clocklike manner mostly within a pool of less conserved and constrained genes.", "token_count": 235, "char_count": 1201, "word_count": 189, "semantic_coherence": 1, "information_density": 0.5238, "quality_score": 0.7619, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:56.220941", "source": { "split": "train_shard_00000", "doc_id": 3893 }, "chunk_id": "train_shard_00000_3893_0", "global_id": 4318 }, { "text": "A common belief is that the phylogeny of bacteria may reflect molecular functions and phenotypic characteristics, pointing towards phylogenetic conservatism of traits. Here, we tested this hypothesis for a large set of Acinetobacter strains. Members of the genus Acinetobacter are widespread in nature, demonstrate a high metabolic diversity and are resistant to several environmental stressors. Notably, some species are known to cause opportunistic human infections. A total of 133 strains belonging to 33 species with validly published names, two genomic species and species of an as-yet unknown taxonomic status were analyzed using the GENIII technology of Biolog, which allows high-throughput phenotyping. We estimated the strength and significance of the phylogenetic signal of each trait across phylogenetic reconstructions based on partial RNA polymerase subunit B (rpoB) and core genome sequences. Secondly, we tested whether phylogenetic distance was a good predictor of trait differentiation by Mantel test analysis. And finally, evolutionary model fitting was used to determine if the data for each phenotypic character was consistent with a phylogenetic or an essentially random model of trait distribution. Our data revealed that some key phenotypic traits related to substrate assimilation and chemical sensitivity are linked to the phylogenetic placement of Acinetobacter species. The strongest phylogenetic signals found were for utilization of different carbon sources such as some organic acids, amino acids and sugars, thus suggesting that in the diversification of Acinetobacter carbon source assimilation has had a relevant role. Future work should be aimed to clarify how such traits have shaped the remarkable ability of this bacterial group to dominate in a wide variety of habitats.\n\nPhylogenetic signal in phenotypic traits related to carbon source assimilation and chemical sensitivity in Acinetobacter species.", "token_count": 430, "char_count": 1939, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6272, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:56.860889", "source": { "split": "train_shard_00000", "doc_id": 3894 }, "chunk_id": "train_shard_00000_3894_0", "global_id": 4319 }, { "text": "Acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (CO\n\nAnalysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria.", "token_count": 49, "char_count": 160, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:57.251147", "source": { "split": "train_shard_00000", "doc_id": 3895 }, "chunk_id": "train_shard_00000_3895_0", "global_id": 4320 }, { "text": "Giardiasis, currently considered a neglected disease, is caused by the intestinal protozoan parasite\n\nDeconjugated Bile Salts Produced by Extracellular Bile-Salt Hydrolase-Like Activities from the Probiotic", "token_count": 61, "char_count": 206, "word_count": 25, "semantic_coherence": 1, "information_density": 0.92, "quality_score": 0.96, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:57.630943", "source": { "split": "train_shard_00000", "doc_id": 3896 }, "chunk_id": "train_shard_00000_3896_0", "global_id": 4321 }, { "text": "Members of the Acidithiobacillus genus are widely found in extreme environments characterized by low pH and high concentrations of toxic substances, thus it is necessary to identify the cellular mechanisms needed to cope with these harsh conditions. Pan-genome analysis of ten bacteria belonging to the genus Acidithiobacillus suggested the existence of core genome, most of which were assigned to the metabolism-associated genes. Additionally, the unique genes of Acidithiobacillus ferrooxidans were much less than those of other species. A large proportion of Acidithiobacillus ferrivorans-specific genes were mapped especially to metabolism-related genes, indicating that diverse metabolic pathways might confer an advantage for adaptation to local environmental conditions. Analyses of functional metabolisms revealed the differences of carbon metabolism, nitrogen metabolism, and sulfur metabolism at the species and/or strain level. The findings also showed that Acidithiobacillus spp. harbored specific adaptive mechanisms for thriving under extreme environments. The genus Acidithiobacillus had the genetic potential to resist and metabolize toxic substances such as heavy metals and organic solvents. Comparison across species and/or strains of Acidithiobacillus populations provided a deeper appreciation of metabolic differences and environmental adaptation, as well as highlighting the importance of cellular mechanisms that maintain the basal physiological functions under complex acidic environmental conditions.\n\nComparative genomics unravels metabolic differences at the species and/or strain level and extremely acidic environmental adaptation of ten bacteria belonging to the genus Acidithiobacillus.", "token_count": 374, "char_count": 1718, "word_count": 224, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:58.262417", "source": { "split": "train_shard_00000", "doc_id": 3897 }, "chunk_id": "train_shard_00000_3897_0", "global_id": 4322 }, { "text": "The aim of this study is to investigate Emodin on alleviating intrahepatic cholestasis by regulation of liver farnesoid X receptor (FXR) pathway. Cell and animal models of intrahepatic cholestatis were established. Biochemical tests and histomorphology were performed. The messenger RNA (mRNA) and protein expression of FXR, small heterodimer partner (SHP), uridine diphosphate glucuronosyltransferase 2 family polypeptide B4 (UGT2B4), and bile salt export pump (BSEP) was detected. As a result, compared with the model group, the serum levels of biochemical test were significantly lower in the Emodin group (P <0.01). The histopathological changes were remitted significantly by Emodin treatment. In the model group, the mRNA and protein expression of FXR, SHP, UGT2B4, and BSEP was significantly lower than in the normal group in cell models (P <0.05). With Emodin intervention, the expression of FXR, SHP, UGT2B4, and BSEP was notably increased (P <0.05). In conclusion, Emodin plays a protective role in intrahepatic cholestasis by promoting FXR signal pathways.\n\nPreliminary study on Emodin alleviating alpha-naphthylisothiocyanate-induced intrahepatic cholestasis by regulation of liver farnesoid X receptor pathway.", "token_count": 357, "char_count": 1223, "word_count": 173, "semantic_coherence": 1, "information_density": 0.5607, "quality_score": 0.7803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:58.843553", "source": { "split": "train_shard_00000", "doc_id": 3898 }, "chunk_id": "train_shard_00000_3898_0", "global_id": 4323 }, { "text": "The Lactobacillus genus represents the largest and most diverse genera of all the lactic acid bacteria (LAB), encompassing species with applications in industrial, biotechnological and medical fields. The increasing number of available Lactobacillus genome sequences has allowed understanding of genetic and metabolic potential of this LAB group. Pangenome and core genome studies are available for numerous species, demonstrating the plasticity of the Lactobacillus genomes and providing the evidence of niche adaptability. Advancements in the application of lactobacilli in the dairy industry lie in exploring the genetic background of their commercially important characteristics, such as flavour development potential or resistance to the phage attack. The integration of available genomic and metabolomic data through the generation of genome scale metabolic models has enabled the development of computational models that predict the behaviour of organisms under specific conditions and present a route to metabolic engineering. Lactobacilli are recognised as potential cell factories, confirmed by the successful production of many compounds. In this review, we discuss the current knowledge of genomics, metabolomics and metabolic engineering of the prevalent Lactobacillus species associated with the production of fermented dairy foods. In-depth understanding of their characteristics opens the possibilities for their future knowledge-based applications.\n\nAdvances in the genomics and metabolomics of dairy lactobacilli: A review.", "token_count": 321, "char_count": 1541, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:59.415791", "source": { "split": "train_shard_00000", "doc_id": 3899 }, "chunk_id": "train_shard_00000_3899_0", "global_id": 4324 }, { "text": "Bile salts likely contribute to liver injury in patients with primary sclerosing cholangitis (PSC) and primary biliary cholangitis (PBC). Fibroblast growth factor 19 (FGF19) is a bile salt-induced enterokine with hepatoprotective potential as it suppresses de novo bile salt synthesis. Here, we evaluated the bile salt receptor FXR/FGF19 gut-liver axis in PSC and PBC patients.\n\nProlonged fibroblast growth factor 19 response in patients with primary sclerosing cholangitis after an oral chenodeoxycholic acid challenge.", "token_count": 153, "char_count": 520, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7397, "quality_score": 0.8699, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:37:59.854659", "source": { "split": "train_shard_00000", "doc_id": 3900 }, "chunk_id": "train_shard_00000_3900_0", "global_id": 4325 }, { "text": "Salmonella enterica subsp. enterica serovar Kentucky is frequently isolated from healthy poultry and dairy cows and is occasionally isolated from people with clinical disease. A genomic analysis of 119 isolates collected in the United States from dairy cows, ground beef, poultry and poultry products, and human clinical cases was conducted. Results of the analysis demonstrated that the majority of poultry and bovine-associated S. Kentucky were sequence type (ST) 152. Several bovine-associated (n = 3) and food product isolates (n = 3) collected from the United States and the majority of human clinical isolates were ST198, a sequence type that is frequently isolated from poultry and occasionally from human clinical cases in Northern Africa, Europe and Southeast Asia. A phylogenetic analysis indicated that both STs are more closely related to other Salmonella serovars than they are to each other. Additionally, there was strong evidence of an evolutionary divergence between the poultry-associated and bovine-associated ST152 isolates that was due to polymorphisms in four core genome genes. The ST198 isolates recovered from dairy farms in the United States were phylogenetically distinct from those collected from human clinical cases with 66 core genome SNPs differentiating the two groups, but more isolates are needed to determine the significance of this distinction. Identification of S. Kentucky ST198 from dairy animals in the United States suggests that the presence of this pathogen should be monitored in food-producing animals.\n\nGenomic and Evolutionary Analysis of Two Salmonella enterica Serovar Kentucky Sequence Types Isolated from Bovine and Poultry Sources in North America.", "token_count": 399, "char_count": 1702, "word_count": 252, "semantic_coherence": 1, "information_density": 0.4921, "quality_score": 0.746, "entities": { "genes": [ "ST152", "ST198" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:00.825687", "source": { "split": "train_shard_00000", "doc_id": 3901 }, "chunk_id": "train_shard_00000_3901_0", "global_id": 4326 }, { "text": "Cefotaxime is a class III drug according to the Biopharmaceutical Classification System due to low intestinal permeability based on poor oral bioavailability. Bile salt compounds have been shown to be effective additive for drug permeation through several biological membranes. The main purpose of this study was to investigate the ability of a mixed micelles made of phosphatidylcholine, sodium deoxycholate, and loaded with a cefotaxime-3α,7α-dihydroxy-12-keto-5β-cholanate complex to enhance the oral bioavailability of cefotaxime in rats.\n\nMixed Micelles Loaded with Bile Salt: An Approach to Enhance Intestinal Transport of the BCS Class III Drug Cefotaxime in Rats.", "token_count": 186, "char_count": 671, "word_count": 95, "semantic_coherence": 1, "information_density": 0.6737, "quality_score": 0.8368, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:01.278907", "source": { "split": "train_shard_00000", "doc_id": 3902 }, "chunk_id": "train_shard_00000_3902_0", "global_id": 4327 }, { "text": "Bacterial core and accessory genome components are analogous to the operating system and applications of smartphones. The core genome provides stable taxonomy and species lists, but phenotypes reflect the mobile pool of accessory genes. This suggests changes to the ways we define bacterial species and describe bacterial communities.\n\nBacteria Are Smartphones and Mobile Genes Are Apps.", "token_count": 81, "char_count": 387, "word_count": 56, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:01.656155", "source": { "split": "train_shard_00000", "doc_id": 3903 }, "chunk_id": "train_shard_00000_3903_0", "global_id": 4328 }, { "text": "Conventional gene synthesis is usually accompanied by sequence errors, which are often deletions derived from chemically synthesized oligonucleotides. Such deletions lead to frame shifts and mostly result in premature translational terminations. Therefore, in-frame fusion of a marker gene to the downstream of a synthetic gene is an effective strategy to select for frame-shift-free synthetic genes. Functional expression of fused marker genes indicates that synthetic genes are translated without premature termination, i.e., error-less synthetic genes. A recently developed nonhomologous end joining (NHEJ)-mediated DNA cloning method in the yeast Kluyveromyces marxianus is suitable for the selection of frame-shift-free synthetic genes. Transformation and NHEJ-mediated in-frame joining of a synthetic gene with a selection marker gene enables colony formation of only the yeast cells containing synthetic genes without premature termination. This method increased selection frequency of error-less synthetic genes by 3- to 12-fold.\n\nSelection of Error-Less Synthetic Genes in Yeast.", "token_count": 239, "char_count": 1088, "word_count": 146, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:02.139262", "source": { "split": "train_shard_00000", "doc_id": 3904 }, "chunk_id": "train_shard_00000_3904_0", "global_id": 4329 }, { "text": "AcCNET (Accessory genome Constellation Network) is a Perl application that aims to compare accessory genomes of a large number of genomic units, both at qualitative and quantitative levels. Using the proteomes extracted from the analysed genomes, AcCNET creates a bipartite network compatible with standard network analysis platforms. AcCNET allows merging phylogenetic and functional information about the concerned genomes, thus improving the capability of current methods of network analysis. The AcCNET bipartite network opens a new perspective to explore the pangenome of bacterial species, focusing on the accessory genome behind the idiosyncrasy of a particular strain and/or population.\n\nAcCNET (Accessory Genome Constellation Network): comparative genomics software for accessory genome analysis using bipartite networks.", "token_count": 181, "char_count": 830, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:02.587321", "source": { "split": "train_shard_00000", "doc_id": 3905 }, "chunk_id": "train_shard_00000_3905_0", "global_id": 4330 }, { "text": "Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.\n\nThe Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers.", "token_count": 133, "char_count": 617, "word_count": 90, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:03.007465", "source": { "split": "train_shard_00000", "doc_id": 3906 }, "chunk_id": "train_shard_00000_3906_0", "global_id": 4331 }, { "text": "Bile salts such as cholate are surface-active steroid compounds with functions for digestion and signaling in vertebrates. Upon excretion into soil and water bile salts are an electron- and carbon-rich growth substrate for environmental bacteria. Degradation of bile salts proceeds via intermediates with a 3-keto-Δ\n\nAn unexplored pathway for degradation of cholate requires a 7α-hydroxysteroid dehydratase and contributes to a broad metabolic repertoire for the utilization of bile salts in Novosphingobium sp. strain Chol11.", "token_count": 147, "char_count": 526, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7027, "quality_score": 0.8514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:03.442104", "source": { "split": "train_shard_00000", "doc_id": 3907 }, "chunk_id": "train_shard_00000_3907_0", "global_id": 4332 }, { "text": "The gut microbiota is associated with metabolic diseases including obesity, insulin resistance, and nonalcoholic fatty liver disease, as shown by correlative studies and by transplant of microbiota from obese humans and mice into germ-free mice. Modification of the microbiota by treatment of high-fat diet (HFD)-fed mice with tempol or antibiotics resulted in decreased adverse metabolic phenotypes. This was owing to lower levels of the genera Lactobacillus and decreased bile salt hydrolase (BSH) activity. The decreased BSH resulted in increased levels of tauro-β-muricholic acid (MCA), a substrate of BSH and a potent farnesoid X receptor (FXR) antagonist. Mice lacking expression of FXR in the intestine were resistant to HFD-induced obesity, insulin resistance, and nonalcoholic fatty liver disease, thus confirming that intestinal FXR is involved in the potentiation of metabolic disease. A potent intestinal FXR antagonist, glycine-β-MCA (Gly-MCA), which is resistant to BSH, was developed, which, when administered to HFD-treated mice, mimics the effect of the altered microbiota on HFD-induced metabolic disease. Gly-MCA had similar effects on genetically obese leptin-deficient mice. The decrease in adverse metabolic phenotype by tempol, antibiotics, and Gly-MCA was caused by decreased serum ceramides. Mice lacking FXR in the intestine also have lower serum ceramide levels, and are resistant to HFD-induced metabolic disease, and this was reversed by injection of C16:0 ceramide. In mouse ileum, because of the presence of endogenous FXR agonists produced in the liver, FXR target genes involved in ceramide synthesis are activated and when Gly-MCA is administered they are repressed, which likely accounts for the decrease in serum ceramides. These studies show that ceramides produced in the ileum under control of FXR influence metabolic diseases.", "token_count": 519, "char_count": 1866, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5387, "quality_score": 0.7694, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:38:04.068731", "source": { "split": "train_shard_00000", "doc_id": 3908 }, "chunk_id": "train_shard_00000_3908_0", "global_id": 4333 }, { "text": "An Intestinal Microbiota-Farnesoid X Receptor Axis Modulates Metabolic Disease.", "token_count": 25, "char_count": 79, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:04.431483", "source": { "split": "train_shard_00000", "doc_id": 3908 }, "chunk_id": "train_shard_00000_3908_1", "global_id": 4334 }, { "text": "Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets.\n\nPangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets.", "token_count": 134, "char_count": 600, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7901, "quality_score": 0.8951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:04.849623", "source": { "split": "train_shard_00000", "doc_id": 3909 }, "chunk_id": "train_shard_00000_3909_0", "global_id": 4335 }, { "text": "Multidrug-resistant bacteria are responsible for substantial morbidity and mortality worldwide. Tracking the nosocomial spread of resistant bacteria is critical to infection control. Mellmann et al. (J. Clin. Microbiol. 54:2874-2881, 2016, http://dx.doi.org/10.1128/JCM.00790-16) have described prospective whole-genome sequencing with core genome multilocus sequencing typing (cgMLST) analysis for real-time surveillance and have addressed the practical aspects of implementing this type of operation in the hospital setting.\n\nNext-Generation Epidemiology: Using Real-Time Core Genome Multilocus Sequence Typing To Support Infection Control Policy.", "token_count": 179, "char_count": 649, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7922, "quality_score": 0.8961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:05.288176", "source": { "split": "train_shard_00000", "doc_id": 3910 }, "chunk_id": "train_shard_00000_3910_0", "global_id": 4336 }, { "text": "The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could provide unparalleled detail of the evolution of a bacterial population. Here we demonstrate this principle by applying it to a worldwide multi-host sample of the important pathogenic E. coli lineage ST131. Our approach reveals the existence of multiple circulating subtypes of the major drug-resistant clade of ST131 and provides the first ever population level evidence of core genome substitutions in gene regulatory regions associated with the acquisition and maintenance of different accessory genome elements.\n\nCombined Analysis of Variation in Core, Accessory and Regulatory Genome Regions Provides a Super-Resolution View into the Evolution of Bacterial Populations.", "token_count": 243, "char_count": 1213, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6412, "quality_score": 0.8206, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:05.772983", "source": { "split": "train_shard_00000", "doc_id": 3911 }, "chunk_id": "train_shard_00000_3911_0", "global_id": 4337 }, { "text": "Intermittent cholestatic liver disease may indicate an inherited deficiency of bile salt transport proteins. Episodes of cholestasis may start during pregnancy or during use of oral contraceptives or other medication. We describe the case of a 22-year-old mother with increasing jaundice and severe pruritus two weeks after starting hormonal contraception. A few months before she was suffering from intrahepatic cholestasis of pregnancy (ICP). Liver biopsy showed bland cholestasis with canalicular bile plugs. Treatment with ursodeoxycholic acid was not effective. Finally, rifampicin induced a complete remission of the cholestasis. Genetic testing showed a heterozygous mutation in the ABCB11 gene encoding the bile salt export pump (BSEP). Rifampicin activates nuclear receptors and may induce alternative pathways for the excretion of bile salts in patients with ABCB11 deficiency.\n\n[A 22-year-old mother with severe pruritus and increasing jaundice two weeks after starting hormonal contraception].", "token_count": 261, "char_count": 1005, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6643, "quality_score": 0.8321, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:06.319202", "source": { "split": "train_shard_00000", "doc_id": 3912 }, "chunk_id": "train_shard_00000_3912_0", "global_id": 4338 }, { "text": "Thermotolerant ethanologenic yeast Kluyveromyces marxianus is capable of fermenting various sugars including xylose but glucose represses to hamper the utilization of other sugars. To acquire glucose repression-defective strains, 33 isolates as 2-deoxyglucose (2-DOG)-resistant mutants were acquired from about 100 colonies grown on plates containing 2-DOG, which were derived from an efficient strain DMKU 3-1042. According to the characteristics of sugar consumption abilities and cell growth and ethanol accumulation along with cultivation time, they were classified into three groups. The first group (3 isolates) utilized glucose and xylose in similar patterns along with cultivation to those of the parental strain, presumably due to reduction of the uptake of 2-DOG or enhancement of its export. The second group (29 isolates) showed greatly delayed utilization of glucose, presumably by reduction of the uptake or initial catabolism of glucose. The last group, only one isolate, showed enhanced utilization ability of xylose in the presence of glucose. Further analysis revealed that the isolate had a single nucleotide mutation to cause amino acid substitution (G270S) in RAG5 encoding hexokinase and exhibited very low activity of the enzyme. The possible mechanism of defectiveness of glucose repression in the mutant is discussed in this paper. [Int Microbiol 18(4):235-244 (2015)].\n\nA Kluyveromyces marxianus 2-deoxyglucose-resistant mutant with enhanced activity of xylose utilization.", "token_count": 405, "char_count": 1499, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [ "RAG5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:06.930395", "source": { "split": "train_shard_00000", "doc_id": 3913 }, "chunk_id": "train_shard_00000_3913_0", "global_id": 4339 }, { "text": "High Throughput Sequencing provides a cost effective means of generating high resolution data for hundreds or even thousands of strains, and is rapidly superseding methodologies based on a few genomic loci. The wealth of genomic data deposited on public databases such as Sequence Read Archive/European Nucleotide Archive provides a powerful resource for evolutionary analysis and epidemiological surveillance. However, many of the analysis tools currently available do not scale well to these large datasets, nor provide the means to fully integrate ancillary data. Here we present PHYLOViZ 2.0, an extension of PHYLOViZ tool, a platform independent Java tool that allows phylogenetic inference and data visualization for large datasets of sequence based typing methods, including Single Nucleotide Polymorphism (SNP) and whole genome/core genome Multilocus Sequence Typing (wg/cgMLST) analysis. PHYLOViZ 2.0 incorporates new data analysis algorithms and new visualization modules, as well as the capability of saving projects for subsequent work or for dissemination of results.\n\nPHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods.", "token_count": 273, "char_count": 1194, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6807, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:07.479061", "source": { "split": "train_shard_00000", "doc_id": 3914 }, "chunk_id": "train_shard_00000_3914_0", "global_id": 4340 }, { "text": "The present study was undertaken to gain knowledge on the role of bile components and lecithin on development of aberrations in digestive functions which seemingly have increased in Atlantic salmon in parallel with the increased use of plant ingredients in fish feed. Post smolt Atlantic salmon were fed for 77 days one of three basal diets: a high fish meal diet (HFM), a low fishmeal diet (LFM), or a diet with high protein soybean meal (HPS). Five additional diets were made from the LFM diet by supplementing with: purified taurocholate (1.8 %), bovine bile salt (1.8 %), taurine (0.4 %), lecithin (1.5 %), or a mix of supplements (suppl mix) containing taurocholate (1.8 %), cholesterol (1.5 %) and lecithin (0.4 %). Two additional diets were made from the HPS diet by supplementing with: bovine bile salt (1.8 %) or the suppl mix. Body and intestinal weights were recorded, and blood, bile, intestinal tissues and digesta were sampled for evaluation of growth, nutrient metabolism and intestinal structure and function.\n\nBile components and lecithin supplemented to plant based diets do not diminish diet related intestinal inflammation in Atlantic salmon.", "token_count": 329, "char_count": 1162, "word_count": 187, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7914, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:08.045386", "source": { "split": "train_shard_00000", "doc_id": 3915 }, "chunk_id": "train_shard_00000_3915_0", "global_id": 4341 }, { "text": "Pancreatic adenocarcinoma (PDAC) is a dismal disease. The lack of specific symptoms still leads to a delay in diagnosis followed by death within months for most patients. Exon 11 of the bile salt-dependent lipase (BSDL) gene encoding variable number of tandem repeated (VNTR) sequences has been involved in pancreatic pathologies. We hypothesized that BSDL VNTR sequences may be mutated in PDAC. The amplification of BSDL VNTR from RNA extracted from pancreatic SOJ-6 cells allowed us to identify a BSDL amplicon in which a cytosine residue is inserted in a VNTR sequence. This insertion gives rise to a premature stop codon, resulting in a truncated protein and to a modification of the C-terminal amino-acid sequence; that is PRAAHG instead of PAVIRF. We produced antibodies directed against these sequences and examined pancreatic tissues from patients with PDAC and PanIN. Albeit all tissues were positive to anti-PAVIRF antibodies, 72.2% of patient tissues gave positive reaction with anti-PRAAHG antibodies, particularly in dysplastic areas of the tumor. Neoplastic cells with ductal differentiation were not reactive to anti-PRAAHG antibodies. Some 70% of PanIN tissues were also reactive to anti-PRAAHG antibodies, suggesting that the C insertion occurs early during pancreatic carcinogenesis. Data suggest that anti-PRAAHG antibodies were uniquely reactive with a short isoform of BSDL specifically expressed in pre-neoplastic lesions of the pancreas. The detection of truncated BSDL reactive to antibodies against the PRAAHG C-terminal sequence in pancreatic juice or in pancreatic biopsies may be a new tool in the early diagnosis of PDAC.\n\nExpression of truncated bile salt-dependent lipase variant in pancreatic pre-neoplastic lesions.", "token_count": 472, "char_count": 1748, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5736, "quality_score": 0.7868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:08.729058", "source": { "split": "train_shard_00000", "doc_id": 3916 }, "chunk_id": "train_shard_00000_3916_0", "global_id": 4342 }, { "text": "During the last years the interest in donkey milk has increased significantly mainly because of its compelling functional elements. Even if the composition and nutritional properties of donkey milk are known, its microbiota is less studied. This Research Communication aimed to provide a comprehensive characterisation of the lactic acid bacteria in raw donkey milk. RAPD-PCR assay combined with 16S rDNA sequencing analysis were used to describe the microbial diversity of several donkey farms in the North West part of Italy. The more frequently detected species were: Lactobacillus paracasei, Lactococcus lactis and Carnobacterium maltaromaticum. Less abundant genera were Leuconostoc, Enterococcus and Streptococcus. The yeast Kluyveromyces marxianus was also isolated. The bacterial and biotype distribution notably diverged among the farms. Several of the found species, not previously detected in donkey milk, could have an important probiotic activity and biotechnological potential. This study represents an important insight to the ample diversity of the microorganisms present in the highly selective ecosystem of raw donkey milk.\n\nIsolation and characterisation of lactic acid bacteria from donkey milk.", "token_count": 276, "char_count": 1215, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6784, "quality_score": 0.8392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:09.296912", "source": { "split": "train_shard_00000", "doc_id": 3917 }, "chunk_id": "train_shard_00000_3917_0", "global_id": 4343 }, { "text": "Despite many documented differences in gut physiology compared to humans, the beagle dog has been successfully used as a preclinical model for assessing the relative bioavailability of dosage forms during formulation development. However, differences in pH and bile salt concentration and micellar structure between dog and human intestinal fluids may influence the solubility and dissolution behavior of especially BCS II/IV compounds. Recently, a canine fasted simulated intestinal fluid (FaSSIFc) mimicking the composition in the lumen of the beagle dog under the fasted state has been proposed. In this manuscript, we present the utilization of FaSSIFc to compare solubility of several preclinical candidates against human FaSSIF. While solubility of free bases and neutral compounds was easily predicted by the relative amounts of sodium taurocholate in the fluids, free acids were shown to be much more soluble in FaSSIFc owing to both the solubility at higher pH as well as the increased bile salt concentration. For one of the model compounds, we demonstrate that the high solubility necessitates the need for a formulation comparison at a relatively higher dose in the dog to mimic the outcome of a human relative bioavailability study. Finally, we show how using the solubility value in FaSSIFc for the same compound results in better predictability of the plasma concentration profiles in dogs from a physiologically based absorption model. The collective data indicate that caution and more detailed measurements are required if the dog is used as the preclinical model for the development of formulations of weak acids.\n\nComparing Dog and Human Intestinal Fluids: Implications on Solubility and Biopharmaceutical Risk Assessment.", "token_count": 389, "char_count": 1742, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5856, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:09.954049", "source": { "split": "train_shard_00000", "doc_id": 3918 }, "chunk_id": "train_shard_00000_3918_0", "global_id": 4344 }, { "text": "PSM-mec is a secreted virulence factor that belongs to the phenol-soluble modulin (PSM) family of amphipathic, alpha-helical peptide toxins produced by Staphylococcus species. All known PSMs are core genome-encoded with the exception of PSM-mec, whose gene is found in specific sub-types of SCCmec methicillin resistance mobile genetic elements present in methicillin-resistant Staphylococcus aureus and coagulase-negative staphylococci. In addition to the cytolytic translational product, PSM-mec, the psm-mec locus encodes a regulatory RNA. In S. aureus, the psm-mec locus influences cytolytic capacity, methicillin resistance, biofilm formation, cell spreading, and the expression of other virulence factors, such as other PSMs, which results in a significant impact on immune evasion and disease. However, these effects are highly strain-dependent, which is possibly due to differences in PSM-mec peptide vs. psm-mec RNA-controlled effects. Here, we summarize the functional properties of PSM-mec and the psm-mec RNA molecule and their roles in staphylococcal pathogenesis and physiology.\n\nPSM-Mec-A Virulence Determinant that Connects Transcriptional Regulation, Virulence, and Antibiotic Resistance in Staphylococci.", "token_count": 359, "char_count": 1222, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6894, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:10.548032", "source": { "split": "train_shard_00000", "doc_id": 3919 }, "chunk_id": "train_shard_00000_3919_0", "global_id": 4345 }, { "text": "Cholestasis is characterized by intrahepatic accumulation of potentially cytotoxic bile acids (BAs) subsequently leading to liver injury with disruption of hepatocellular integrity, inflammation, fibrosis and ultimately liver cirrhosis. Bile salt export pump (BSEP/ABCB11) is the main canalicular BA transporter and therefore the rate limiting step for hepatobiliary BA excretion. In this study we aimed to investigate the role of BSEP/ABCB11 in the development of acquired cholestatic liver and bile duct injury.\n\nMetabolic preconditioning protects BSEP/ABCB11", "token_count": 150, "char_count": 561, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7733, "quality_score": 0.8867, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:11.001371", "source": { "split": "train_shard_00000", "doc_id": 3920 }, "chunk_id": "train_shard_00000_3920_0", "global_id": 4346 }, { "text": "In the present investigation, probiotic potential (antagonistic activity, enzyme production, hemolytic activity, biosafety, antibiotic sensitivity and bile tolerance level) of Bacillus subtilis LR1 was evaluated. Bacteriocin produced by the bacterial strain B. subtilis LR1 isolated from the gastrointestinal tract of Labeo rohita was purified and characterized. The molecular weight of the purified bacteriocin was ~50 kDa in 12 % Native PAGE and showed inhibitory activity against four fish pathogens such as Bacillus mycoides, Aeromonas salmonicida, Pseudomonas fluorescens and Aeromonas hydrophila. The purified bacteriocin was maximally active at temperature 40 °C and pH 7.0, while none of the tested surfactants affect the bacteriocin activity. Extracellular enzyme activity of the selected bacterial strain was also evaluated. Amylase activity was estimated to be highest (38.23 ± 1.15 µg of maltose liberated mg\n\nAssessment of hemolytic activity, enzyme production and bacteriocin characterization of Bacillus subtilis LR1 isolated from the gastrointestinal tract of fish.", "token_count": 305, "char_count": 1081, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6309, "quality_score": 0.8154, "entities": { "genes": [ "LR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:11.565668", "source": { "split": "train_shard_00000", "doc_id": 3921 }, "chunk_id": "train_shard_00000_3921_0", "global_id": 4347 }, { "text": "Here, we report the draft genome sequence of Kluyveromyces marxianus fragilis B0399, the first yeast approved as a probiotic for human consumption not belonging to the genus Saccharomyces The genome is composed of 8 chromosomes, with a total size of 11.44 Mb, including mitochondrial DNA.\n\nDraft Genome Sequence of the Probiotic Yeast Kluyveromyces marxianus fragilis B0399.", "token_count": 115, "char_count": 374, "word_count": 56, "semantic_coherence": 1, "information_density": 0.6964, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:11.948673", "source": { "split": "train_shard_00000", "doc_id": 3922 }, "chunk_id": "train_shard_00000_3922_0", "global_id": 4348 }, { "text": "Microbial epidemiology and population genomics have previously been carried out near-exclusively for organisms grown in vitro. Metagenomics helps to overcome this limitation, but it is still challenging to achieve strain-level characterization of microorganisms from culture-independent data with sufficient resolution for epidemiological modelling. Here, we have developed multiple complementary approaches that can be combined to profile and track individual microbial strains. To specifically profile highly recombinant neisseriae from oral metagenomes, we integrated four metagenomic analysis techniques: single nucleotide polymorphisms in the clade's core genome, DNA uptake sequence signatures, metagenomic multilocus sequence typing and strain-specific marker genes. We applied these tools to 520 oral metagenomes from the Human Microbiome Project, finding evidence of site tropism and temporal intra-subject strain retention. Although the opportunistic pathogen Neisseria meningitidis is enriched for colonization in the throat, N. flavescens and N. subflava populate the tongue dorsum, and N. sicca, N. mucosa and N. elongata the gingival plaque. The buccal mucosa appeared as an intermediate ecological niche between the plaque and the tongue. The resulting approaches to metagenomic strain profiling are generalizable and can be extended to other organisms and microbiomes across environments.\n\nUncovering oral Neisseria tropism and persistence using metagenomic sequencing.", "token_count": 344, "char_count": 1485, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7128, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:12.513263", "source": { "split": "train_shard_00000", "doc_id": 3923 }, "chunk_id": "train_shard_00000_3923_0", "global_id": 4349 }, { "text": "The global expansion in aquaculture production implies an emerging need of suitable and sustainable protein sources. Currently, the fish feed industry is dependent on high-quality protein sources of marine and plant origin. Yeast derived from processing of low-value and non-food lignocellulosic biomass is a potential sustainable source of protein in fish diets. Following enzymatic hydrolysis, the hexose and pentose sugars of lignocellulosic substrates and supplementary nutrients can be converted into protein-rich yeast biomass by fermentation. Studies have shown that yeasts such as Saccharomyces cerevisiae, Candida utilis and Kluyveromyces marxianus have favourable amino acid composition and excellent properties as protein sources in diets for fish, including carnivorous species such as Atlantic salmon and rainbow trout. Suitable downstream processing of the biomass to disrupt cell walls is required to secure high nutrient digestibility. A number of studies have shown various immunological and health benefits from feeding fish low levels of yeast and yeast-derived cell wall fractions. This review summarises current literature on the potential of yeast from lignocellulosic biomass as an alternative protein source for the aquaculture industry. It is concluded that further research and development within yeast production can be important to secure the future sustainability and economic viability of intensive aquaculture. © 2016 Society of Chemical Industry.\n\nYeast derived from lignocellulosic biomass as a sustainable feed resource for use in aquaculture.", "token_count": 348, "char_count": 1577, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7986, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:13.093319", "source": { "split": "train_shard_00000", "doc_id": 3924 }, "chunk_id": "train_shard_00000_3924_0", "global_id": 4350 }, { "text": "In this study, a total of 121 bacterial strains were isolated from the gastrointestinal tract of four teleostean species, namely striped snakehead (Channa striatus), striped dwarf catfish (Mystus vittatus), orangefin labeo (Labeo calbasu) and mrigal carp (Cirrhinus mrigala), among which 8 isolates showed promising antibacterial activity against four potential fish pathogens, Aeromonas hydrophila, Aeromonas salmonicida, Aeromonas sobria and Pseudomonas fluorescens and were non-hemolytic. The isolates were further screened in response to fish bile tolerance and extracellular digestive enzyme activity. Two bacterial strains MVF1 and MVH7 showed highest tolerance and extracellular enzymes activities, and selected for further studies. Antagonistic activity of these two isolates was further confirmed by in vitro growth inhibition assay against four selected fish pathogens in liquid medium. Finally, these two bacterial strains MVF1 and MVH7 were selected as potential probiotic candidates and thus identification by partial 16S rRNA gene sequence analysis. The bacterial isolates MVF1 and MVH7 were identified as two strains of Bacillus sp.\n\nProbiotic Potential of Autochthonous Bacteria Isolated from the Gastrointestinal Tract of Four Freshwater Teleosts.", "token_count": 339, "char_count": 1264, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6105, "quality_score": 0.8052, "entities": { "genes": [ "MVF1", "MVH7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:13.656199", "source": { "split": "train_shard_00000", "doc_id": 3925 }, "chunk_id": "train_shard_00000_3925_0", "global_id": 4351 }, { "text": "In this work we have studied the photophysics of biologically active flavin molecule lumichrome (LCM) in different bile-salt aggregates. With alteration of the functional groups of the bile salts, the photophysics of confined fluorophore is largely affected and shows difference in their spectral behavior. This study also reveals the selective prototropic species of LCM present in bile salt aggregates. In the presence of the bile salt aggregates, LCM molecule shows excitation and emission wavelength-dependent emission properties, indicating switch over of the structural change of different prototropic form of the LCM molecule. The observation of higher rotational relaxation time in NaDC aggregates compared to NaTC aggregates clearly reflects that NaDC aggregates are more rigid due to its greater hydrophobicity and large in size, which is capable to bind the guest molecule more into their nanoconfined medium. Moreover, due to less acidic nature, NaDC aggregates have more ability to accept hydrogen bond from the LCM molecule and show the selective formation of isoalloxazine N10 anion (A1 monoanionic form) of LCM.\n\nInteraction of Biologically Active Flavins inside Bile Salt Aggregates: Molecular Level Investigation.", "token_count": 286, "char_count": 1231, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:14.215151", "source": { "split": "train_shard_00000", "doc_id": 3926 }, "chunk_id": "train_shard_00000_3926_0", "global_id": 4352 }, { "text": "This study aimed to select autochthonous lactic acid bacteria (LAB) with probiotic and functional properties from goat dairies and test their addition to artisanal cheese for the inhibition of Salmonella typhi. In vitro tests, including survival in the gastrointestinal tract (GIT), auto- and co-aggregation, the hemolytic test, DNase activity, antimicrobial susceptibility, antibacterial activity, tolerance to NaCl and exopolysaccharide (EPS), gas and diacetyl production were conducted for sixty isolates. Based on these tests, four LAB isolates (UNIVASF CAP 16, 45, 84 and 279) were selected and identified. Additional tests, such as production of lactic and citric acids by UNIVASF CAP isolates were performed in addition to assays of bile salt hydrolase (BSH), β-galactosidase and decarboxylase activity. The four selected LAB produced high lactic acid (>17 g/L) and low citric acid (0.2 g/L) concentrations. All selected strains showed BSH and β-galactosidase activity and none showed decarboxylase activity. Three goat cheeses (1, 2 and control) were produced and evaluated for the inhibitory action of selected LAB against Salmonella typhi. The cheese inoculated with LAB (cheese 2) decreased 0.38 log10 CFU/g of S. Typhy population while in the cheese without LAB inoculation (cheese 1) the pathogen population increased by 0.29 log units. Further, the pH value increased linearly over time, by 0.004 units per day in cheese 1. In the cheese 2, the pH value decreased linearly over time, by 0.066 units per day. The cocktail containing selected Lactobacillus strains with potential probiotic and technological properties showed antibacterial activity against S. typhi in vitro and in artisanal goat cheese", "token_count": 489, "char_count": 1715, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5804, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:14.863244", "source": { "split": "train_shard_00000", "doc_id": 3927 }, "chunk_id": "train_shard_00000_3927_0", "global_id": 4353 }, { "text": "Thus, goat milk is important source of potential probiotic LAB which may be used to inhibit the growth of Salmonella population in cheese goat, contributing to safety and functional value of the product.\n\nSelection of autochthonous lactic acid bacteria from goat dairies and their addition to evaluate the inhibition of Salmonella typhi in artisanal cheese.", "token_count": 82, "char_count": 357, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7818, "quality_score": 0.8909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:15.238964", "source": { "split": "train_shard_00000", "doc_id": 3927 }, "chunk_id": "train_shard_00000_3927_1", "global_id": 4354 }, { "text": "Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this.\n\nLiving apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen.", "token_count": 116, "char_count": 539, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:15.622263", "source": { "split": "train_shard_00000", "doc_id": 3928 }, "chunk_id": "train_shard_00000_3928_0", "global_id": 4355 }, { "text": "Acidithiobacillus thiooxidans known for its ubiquity in diverse acidic and sulfur-bearing environments worldwide was used as the research subject in this study. To explore the genomic fluidity and intraspecific diversity of Acidithiobacillus thiooxidans (A. thiooxidans) species, comparative genomics based on nine draft genomes was performed. Phylogenomic scrutiny provided first insights into the multiple groupings of these strains, suggesting that genetic diversity might be potentially correlated with their geographic distribution as well as geochemical conditions. While these strains shared a large number of common genes, they displayed differences in gene content. Functional assignment indicated that the core genome was essential for microbial basic activities such as energy acquisition and uptake of nutrients, whereas the accessory genome was thought to be involved in niche adaptation. Comprehensive analysis of their predicted central metabolism revealed that few differences were observed among these strains. Further analyses showed evidences of relevance between environmental conditions and genomic diversification. Furthermore, a diverse pool of mobile genetic elements including insertion sequences and genomic islands in all A. thiooxidans strains probably demonstrated the frequent genetic flow (such as lateral gene transfer) in the extremely acidic environments. From another perspective, these elements might endow A. thiooxidans species with capacities to withstand the chemical constraints of their natural habitats. Taken together, our findings bring some valuable data to better understand the genomic diversity and econiche adaptation within A. thiooxidans strains.\n\nComparative Genomics of the Extreme Acidophile Acidithiobacillus thiooxidans Reveals Intraspecific Divergence and Niche Adaptation.", "token_count": 401, "char_count": 1831, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6736, "quality_score": 0.8368, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:16.249936", "source": { "split": "train_shard_00000", "doc_id": 3929 }, "chunk_id": "train_shard_00000_3929_0", "global_id": 4356 }, { "text": "Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, is important for disease management. Developments in molecular methods have contributed to increase the resolution for accurate pathogen identification, but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium, Pseudomonas savastanoi, Pantoea agglomerans, and Rhodococcus. Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.\n\nGall-ID: tools for genotyping gall-causing phytopathogenic bacteria.", "token_count": 369, "char_count": 1626, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6986, "quality_score": 0.8493, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:16.826423", "source": { "split": "train_shard_00000", "doc_id": 3930 }, "chunk_id": "train_shard_00000_3930_0", "global_id": 4357 }, { "text": "Although data are available on the change of expression/activity of drug-metabolizing enzymes in liver cirrhosis patients, corresponding data on transporter protein expression are not available. Therefore, using quantitative targeted proteomics, we compared our previous data on noncirrhotic control livers (n = 36) with the protein expression of major hepatobiliary transporters, breast cancer resistance protein (BCRP), bile salt export pump (BSEP), multidrug and toxin extrusion protein 1 (MATE1), multidrug resistance-associated protein (MRP)2, MRP3, MRP4, sodium taurocholate-cotransporting polypeptide (NTCP), organic anion-transporting polypeptides (OATP)1B1, 1B3, 2B1, organic cation transporter 1 (OCT1), and P-glycoprotein (P-gp) in alcoholic (n = 27) and hepatitis C cirrhosis (n = 30) livers. Compared with control livers, the yield of membrane protein from alcoholic and hepatitis C cirrhosis livers was significantly reduced by 56 and 67%, respectively. The impact of liver cirrhosis on transporter protein expression was transporter-dependent. Generally, reduced protein expression (per gram of liver) was found in alcoholic cirrhosis livers versus control livers, with the exception that the expression of MRP3 was increased, whereas no change was observed for MATE1, MRP2, OATP2B1, and P-gp. In contrast, the impact of hepatitis C cirrhosis on protein expression of transporters (per gram of liver) was diverse, showing an increase (MATE1), decrease (BSEP, MRP2, NTCP, OATP1B3, OCT1, and P-gp), or no change (BCRP, MRP3, OATP1B1, and 2B1). The expression of hepatobiliary transporter protein differed in different diseases (alcoholic versus hepatitis C cirrhosis)", "token_count": 484, "char_count": 1680, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5671, "quality_score": 0.7835, "entities": { "genes": [ "OCT1", "MATE1", "MRP4", "MRP2", "MRP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:17.477999", "source": { "split": "train_shard_00000", "doc_id": 3931 }, "chunk_id": "train_shard_00000_3931_0", "global_id": 4358 }, { "text": "Finally, incorporation of protein expression of OATP1B1 in alcoholic cirrhosis into the Simcyp physiologically based pharmacokinetics cirrhosis module improved prediction of the disposition of repaglinide in liver cirrhosis patients. These transporter expression data will be useful in the future to predict transporter-mediated drug disposition in liver cirrhosis patients.\n\nTransporter Expression in Liver Tissue from Subjects with Alcoholic or Hepatitis C Cirrhosis Quantified by Targeted Quantitative Proteomics.", "token_count": 120, "char_count": 516, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:17.858258", "source": { "split": "train_shard_00000", "doc_id": 3931 }, "chunk_id": "train_shard_00000_3931_1", "global_id": 4359 }, { "text": "Our whole genome sequence (WGS) pipeline was assessed for accurate prediction of antimicrobial phenotypes. For 2316 invasive pneumococcal isolates recovered during 2015 we compared WGS pipeline data to broth dilution testing (BDT) for 18 antimicrobials. For 11 antimicrobials categorical discrepancies were assigned when WGS-predicted MICs and BDT MICs predicted different categorizations for susceptibility, intermediate resistance or resistance, ranging from 0.9% (tetracycline) to 2.9% (amoxicillin). For β-lactam antibiotics, the occurrence of at least four-fold differences in MIC ranged from 0.2% (meropenem) to 1.0% (penicillin), although phenotypic retesting resolved 25%-78% of these discrepancies. Non-susceptibility to penicillin, predicted by penicillin-binding protein types, was 2.7% (non-meningitis criteria) and 23.8% (meningitis criteria). Other common resistance determinants included mef (475 isolates), ermB (191 isolates), ermB + mef (48 isolates), tetM (261 isolates) and cat (51 isolates). Additional accessory resistance genes (tetS, tet32, aphA-3, sat4) were rarely detected (one to three isolates). Rare core genome mutations conferring erythromycin-resistance included a two-codon rplD insertion (rplD69-KG-70) and the 23S rRNA A2061G substitution (six isolates). Intermediate cotrimoxazole-resistance was associated with one or two codon insertions within folP (238 isolates) or the folA I100L substitution (38 isolates), whereas full cotrimoxazole-resistance was attributed to alterations in both genes (172 isolates)", "token_count": 493, "char_count": 1546, "word_count": 198, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:18.510027", "source": { "split": "train_shard_00000", "doc_id": 3932 }, "chunk_id": "train_shard_00000_3932_0", "global_id": 4360 }, { "text": "The two levofloxacin-resistant isolates contained parC and/or gyrA mutations. Of 11 remaining isolates with moderately elevated MICs to both ciprofloxacin and levofloxacin, seven contained parC or gyrA mutations. The two rifampin-resistant isolates contained rpoB mutations. WGS-based antimicrobial phenotype prediction was an informative alternative to BDT for invasive pneumococci.\n\nUsing whole genome sequencing to identify resistance determinants and predict antimicrobial resistance phenotypes for year 2015 invasive pneumococcal disease isolates recovered in the United States.", "token_count": 162, "char_count": 583, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7397, "quality_score": 0.8699, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:18.947551", "source": { "split": "train_shard_00000", "doc_id": 3932 }, "chunk_id": "train_shard_00000_3932_1", "global_id": 4361 }, { "text": "Intrahepatic cholestasis represents 20%-40% of drug-induced injuries from which a large proportion remains unpredictable. We aimed to investigate mechanisms underlying drug-induced cholestasis and improve its early detection using human HepaRG cells and a set of 12 cholestatic drugs and six noncholestatic drugs. In this study, we analyzed bile canaliculi dynamics, Rho kinase (ROCK)/myosin light chain kinase (MLCK) pathway implication, efflux inhibition of taurocholate [a predominant bile salt export pump (BSEP) substrate], and expression of the major canalicular and basolateral bile acid transporters. We demonstrated that 12 cholestatic drugs classified on the basis of reported clinical findings caused disturbances of both bile canaliculi dynamics, characterized by either dilatation or constriction, and alteration of the ROCK/MLCK signaling pathway, whereas noncholestatic compounds, by contrast, had no effect. Cotreatment with ROCK inhibitor Y-27632 [4-(1-aminoethyl)-N-(4-pyridyl) cyclohexanecarboxamide dihydrochloride] and MLCK activator calmodulin reduced bile canaliculi constriction and dilatation, respectively, confirming the role of these pathways in drug-induced intrahepatic cholestasis. By contrast, inhibition of taurocholate efflux and/or human BSEP overexpressed in membrane vesicles was not observed with all cholestatic drugs; moreover, examples of noncholestatic compounds were reportedly found to inhibit BSEP. Transcripts levels of major bile acid transporters were determined after 24-hour treatment. BSEP, Na\n\nEarly Alterations of Bile Canaliculi Dynamics and the Rho Kinase/Myosin Light Chain Kinase Pathway Are Characteristics of Drug-Induced Intrahepatic Cholestasis.", "token_count": 471, "char_count": 1706, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6743, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:19.589286", "source": { "split": "train_shard_00000", "doc_id": 3933 }, "chunk_id": "train_shard_00000_3933_0", "global_id": 4362 }, { "text": "Codon usage bias, as a combined interplay from mutation and selection, has been intensively studied in Escherichia coli. However, codon usage analysis in an E. coli pangenome remains unexplored and the relative importance of mutation and selection acting on core genes and strain-specific genes is unknown. Here we perform comprehensive codon usage analyses based on a collection of multiple complete genome sequences of E. coli. Our results show that core genes that are present in all strains have higher codon usage bias than strain-specific genes that are unique to single strains. We further explore the forces in influencing codon usage and investigate the difference of the major force between core and strain-specific genes. Our results demonstrate that although mutation may exert genome-wide influences on codon usage acting similarly in different gene sets, selection dominates as an important force to shape biased codon usage as genes are present in an increased number of strains. Together, our results provide important insights for better understanding genome plasticity and complexity as well as evolutionary mechanisms behind codon usage bias.\n\nPangenome Evidence for Higher Codon Usage Bias and Stronger Translational Selection in Core Genes of Escherichia coli.", "token_count": 273, "char_count": 1281, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5573, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:20.144687", "source": { "split": "train_shard_00000", "doc_id": 3934 }, "chunk_id": "train_shard_00000_3934_0", "global_id": 4363 }, { "text": "Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder. It is uncertain if simple steatosis, the initial and prevailing form of NAFLD, sensitizes the liver to cholestasis. Here, we compared the effects of obstructive cholestasis in rats with a normal liver versus rats with simple steatosis induced by a methionine/choline-deficient diet. We found that plasma liver enzymes were higher and hepatic neutrophil influx, inflammation, and fibrosis were more pronounced in animals with combined steatosis and cholestasis compared to cholestasis alone. Circulating bile salt levels were markedly increased and hepatic bile salt composition shifted from hydrophilic tauro-β-muricholate to hydrophobic taurocholate. This shift was cytotoxic for HepG2 hepatoma cells. Gene expression analysis revealed induction of the rate-limiting enzyme in bile salt synthesis, cytochrome P450 7a1 (CYP7A1), and modulation of the hepatic bile salt transport system. In conclusion, simple steatosis sensitizes the liver to cholestatic injury, inflammation, and fibrosis in part due to a cytotoxic shift in bile salt composition. Plasma bile salt levels were elevated, linked to dysregulation of bile salt synthesis and enhanced trafficking of bile salts from the liver to the systemic circulation.\n\nSimple steatosis sensitizes cholestatic rats to liver injury and dysregulates bile salt synthesis and transport.", "token_count": 376, "char_count": 1415, "word_count": 201, "semantic_coherence": 1, "information_density": 0.5572, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:20.766332", "source": { "split": "train_shard_00000", "doc_id": 3935 }, "chunk_id": "train_shard_00000_3935_0", "global_id": 4364 }, { "text": "The Mitis group of the genus Streptococcus currently comprises 20 species with validly published names, including the pathogen S. pneumoniae. They have been the subject of much taxonomic confusion, due to phenotypic overlap and genetic heterogeneity, which has hampered a full appreciation of their clinical significance. The purpose of this study was to critically re-examine the taxonomy of the Mitis group using 195 publicly available genomes, including designated type strains for phylogenetic analyses based on core genomes, multilocus sequences and 16S rRNA gene sequences, combined with estimates of average nucleotide identity (ANI) and in silico and in vitro analyses of specific phenotypic characteristics. Our core genomic phylogenetic analyses revealed distinct clades that, to some extent, and from the clustering of type strains represent known species. However, many of the genomes have been incorrectly identified adding to the current confusion. Furthermore, our data show that 16S rRNA gene sequences and ANI are unsuitable for identifying and circumscribing new species of the Mitis group of the genus Streptococci. Based on the clustering patterns resulting from core genome phylogenetic analysis, we conclude that S. oligofermentans is a later synonym of S. cristatus. The recently described strains of the species Streptococcus dentisani includes one previously referred to as 'S. mitis biovar 2'. Together with S. oralis, S. dentisani and S. tigurinus form subclusters within a coherent phylogenetic clade. We propose that the species S. oralis consists of three subspecies: S. oralis subsp. oralis subsp. nov., S. oralis subsp. tigurinus comb. nov., and S. oralis subsp. dentisani comb. nov.", "token_count": 436, "char_count": 1715, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5906, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:21.426275", "source": { "split": "train_shard_00000", "doc_id": 3936 }, "chunk_id": "train_shard_00000_3936_0", "global_id": 4365 }, { "text": "Re-evaluation of the taxonomy of the Mitis group of the genus Streptococcus based on whole genome phylogenetic analyses, and proposed reclassification of Streptococcus dentisani as Streptococcus oralis subsp. dentisani comb. nov., Streptococcus tigurinus as Streptococcus oralis subsp. tigurinus comb. nov., and Streptococcus oligofermentans as a later synonym of Streptococcus cristatus.", "token_count": 120, "char_count": 388, "word_count": 50, "semantic_coherence": 1, "information_density": 0.58, "quality_score": 0.79, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:21.816539", "source": { "split": "train_shard_00000", "doc_id": 3936 }, "chunk_id": "train_shard_00000_3936_1", "global_id": 4366 }, { "text": "The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable and thus difficult to analyze using short-read sequencing technologies. Here, we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, indel and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that indels are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and indel markers to analyze patterns of meiotic recombination, confirming a high rate of crossover events and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of meiotic recombination within copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired.\n\nIndels, structural variation, and recombination drive genomic diversity in Plasmodium falciparum.", "token_count": 308, "char_count": 1418, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:22.430401", "source": { "split": "train_shard_00000", "doc_id": 3937 }, "chunk_id": "train_shard_00000_3937_0", "global_id": 4367 }, { "text": "Advances in genome and metabolic pathway engineering have enabled large combinatorial libraries of mutant microbial hosts for chemical biosynthesis. Despite these advances, strain development is often limited by the lack of high throughput functional assays for effective library screening. Recent synthetic biology efforts have engineered microbes that synthesize acetyl and acyl esters and many yeasts naturally produce esters to significant titers. Short and medium chain volatile esters have value as fragrance and flavor compounds, while long chain acyl esters are potential replacements for diesel fuel. Here, we developed a biotechnology method for the rapid screening of microbial ester biosynthesis. Using a colorimetric reaction scheme, esters extracted from fermentation broth were quantitatively converted to a ferric hydroxamate complex with strong absorbance at 520 nm. The assay was validated for ethyl acetate, ethyl butyrate, isoamyl acetate, ethyl hexanoate, and ethyl octanoate, and achieved a z-factor of 0.77. Screening of ethyl acetate production from a combinatorial library of four Kluyveromyces marxianus strains on seven carbon sources revealed ethyl acetate biosynthesis from C5, C6, and C12 sugars. This newly adapted method rapidly identified novel properties of K. marxianus metabolism and promises to advance high throughput microbial strain engineering for ester biosynthesis.\n\nHigh throughput, colorimetric screening of microbial ester biosynthesis reveals high ethyl acetate production from Kluyveromyces marxianus on C5, C6, and C12 carbon sources.", "token_count": 400, "char_count": 1583, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:23.053281", "source": { "split": "train_shard_00000", "doc_id": 3938 }, "chunk_id": "train_shard_00000_3938_0", "global_id": 4368 }, { "text": "A facultatively anaerobic, spore-forming Bacillus strain, FSL W8-0169T, collected from raw milk stored in a silo at a dairy powder processing plant in the north-eastern USA was initially identified as a Bacillus cereus group species based on a partial sequence of the rpoB gene and 16S rRNA gene sequence. Analysis of core genome single nucleotide polymorphisms clustered this strain separately from known B. cereus group species. Pairwise average nucleotide identity blast values obtained for FSL W8-0169T compared to the type strains of existing B. cereus group species were <95 % and predicted DNA-DNA hybridization values were <70 %, suggesting that this strain represents a novel B. cereus group species. We characterized 10 additional strains with the same or closely related rpoB allelic type, by whole genome sequencing and phenotypic analyses. Phenotypic characterization identified a higher content of iso-C16 : 0 fatty acid and the combined inability to ferment sucrose or to hydrolyse arginine as the key characteristics differentiating FSL W8-0169T from other B. cereus group species. FSL W8-0169T is psychrotolerant, produces haemolysin BL and non-haemolytic enterotoxin, and is cytotoxic in a HeLa cell model. The name Bacillus wiedmannii sp. nov. is proposed for the novel species represented by the type strain FSL W8-0169T (=DSM 102050T=LMG 29269T).\n\nBacillus wiedmannii sp. nov., a psychrotolerant and cytotoxic Bacillus cereus group species isolated from dairy foods and dairy environments.", "token_count": 449, "char_count": 1510, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:23.694182", "source": { "split": "train_shard_00000", "doc_id": 3939 }, "chunk_id": "train_shard_00000_3939_0", "global_id": 4369 }, { "text": "Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak.\n\nCore Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes.", "token_count": 419, "char_count": 1853, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:24.318045", "source": { "split": "train_shard_00000", "doc_id": 3940 }, "chunk_id": "train_shard_00000_3940_0", "global_id": 4370 }, { "text": "Salmonella enterica subsp. enterica serotype Enteritidis is a major cause of human salmonellosis worldwide; however, little is known about the genetic relationships between S Enteritidis clinical strains and S Enteritidis strains from other sources in Chile. We compared the whole genomes of 30 S Enteritidis strains isolated from gulls, domestic chicken eggs, and humans in Chile, to investigate their phylogenetic relationships and to establish their relatedness to international strains. Core genome multilocus sequence typing (cgMLST) analysis showed that only 246/4,065 shared loci differed among these Chilean strains, separating them into two clusters (I and II), with cluster II being further divided into five subclusters. One subcluster (subcluster 2) contained strains from all surveyed sources that differed at 1 to 18 loci (of 4,065 loci) with 1 to 18 single-nucleotide polymorphisms (SNPs), suggesting interspecies transmission of S Enteritidis in Chile. Moreover, clusters were formed by strains that were distant geographically, which could imply that gulls might be spreading the pathogen throughout the country. Our cgMLST analysis, using other S Enteritidis genomes available in the National Center for Biotechnology Information (NCBI) database, showed that S Enteritidis strains from Chile and the United States belonged to different lineages, which suggests that S Enteritidis regional markers might exist and could be used for trace-back investigations.\n\nWhole-Genome Sequencing Analysis of Salmonella enterica Serovar Enteritidis Isolates in Chile Provides Insights into Possible Transmission between Gulls, Poultry, and Humans.", "token_count": 410, "char_count": 1651, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:24.943181", "source": { "split": "train_shard_00000", "doc_id": 3941 }, "chunk_id": "train_shard_00000_3941_0", "global_id": 4371 }, { "text": "The aim of this study was to evaluate the effects of alginate entrapment on fermentation metabolites of Kluyveromyces marxianus grown in agrowastes that served as the liquid culture media. K. marxianus cells entrapped in Na-alginate were prepared using the traditional liquid-droplet-forming method. Whey and pomaces from processed tomatoes, peppers, and grapes were used as the culture media. The changes in the concentrations of sugar, alcohol, organic acids, and flavor compounds were analyzed using gas chromatography-mass spectrometry (GC-MS) and high pressure liquid chromatography (HPLC). Both free and entrapped, K. marxianus were used individually to metabolize sugars, organic acids, alcohols, and flavor compounds in the tomato, pepper, grape, and acid whey based media. Marked changes in the fermentation behaviors of entrapped and free K. marxianus were observed in each culture. A 1.45-log increase was observed in the cell numbers of free K. marxianus during fermentation. On the contrary, the cell numbers of entrapped K. marxianus remained the same. Both free and entrapped K. marxianus brought about the fermentation of sugars such as glucose, fructose, and lactose in the agrowaste cultures. The highest volume of ethanol was produced by K. marxianus in the whey based media. The concentrations of flavor compounds such as ethyl acetate, isoamyl alcohol, isoamyl acetate, 2-phenylethyl isobutyrate, phenylethyl acetate, and phenylethyl alcohol were higher in fermented agrowaste based media compared to the control.\n\nVolatile metabolites produced from agro-industrial wastes by Na-alginate entrapped Kluyveromyces marxianus.", "token_count": 440, "char_count": 1643, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5021, "quality_score": 0.7511, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:25.583691", "source": { "split": "train_shard_00000", "doc_id": 3942 }, "chunk_id": "train_shard_00000_3942_0", "global_id": 4372 }, { "text": "Various nutrients modulate the expression of transporters; however, the effect of a high-cholesterol (HC) diet on the expression and function of hepatic transporters remains unclear. Here, we examined the effects of an HC diet on drug disposition via hepatic transporters, including organic anion-transporting polypeptide (Oatp), multidrug resistance-associated protein (Mrp), and bile salt export pump (Bsep).\n\nEffects of High-cholesterol Diet on Pravastatin Disposition in the Perfused Rat Liver.", "token_count": 133, "char_count": 498, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:26.004665", "source": { "split": "train_shard_00000", "doc_id": 3943 }, "chunk_id": "train_shard_00000_3943_0", "global_id": 4373 }, { "text": "Parenteral nutrition (PN) is a lifesaving therapy but is associated with gut atrophy and cholestasis. While bile acids (BAs) can modulate intestinal growth via gut receptors, the gut microbiome likely influences gut proliferation and inflammation. BAs also regulate the bile salt export pump (BSEP) involved in cholestasis. We hypothesized that the BA receptor agonist oleanolic acid (OA) regulates gut TGR5 receptor and modulates gut microbiota to prevent PN-associated injury.\n\nPreserved Gut Microbial Diversity Accompanies Upregulation of TGR5 and Hepatobiliary Transporters in Bile Acid-Treated Animals Receiving Parenteral Nutrition.", "token_count": 184, "char_count": 638, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7816, "quality_score": 0.8908, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:26.450331", "source": { "split": "train_shard_00000", "doc_id": 3944 }, "chunk_id": "train_shard_00000_3944_0", "global_id": 4374 }, { "text": "Bacterial inactivation by 405 nm light is accredited to the photoexcitation of intracellular porphyrin molecules resulting in energy transfer and the generation of reactive oxygen species that impart cellular oxidative damage. The specific mechanism of cellular damage, however, is not fully understood. Previous work has suggested that destruction of nucleic acids may be responsible for inactivation; however, microscopic imaging has suggested membrane damage as a major constituent of cellular inactivation. This study investigates the membrane integrity of Escherichia coli and Staphylococcus aureus exposed to 405 nm light. Results indicated membrane damage to both species, with loss of salt and bile tolerance by S. aureus and E. coli, respectively, consistent with reduced membrane integrity. Increased nucleic acid release was also demonstrated in 405 nm light-exposed cells, with up to 50 % increase in DNA concentration into the extracellular media in the case of both organisms. SYTOX green fluorometric analysis, however, demonstrated contradictory results between the two test species. With E. coli, increasing permeation of SYTOX green was observed following increased exposure, with >500 % increase in fluorescence, whereas no increase was observed with S. aureus. Overall, this study has provided good evidence that 405 nm light exposure causes loss of bacterial membrane integrity in E. coli, but the results with S. aureus are more difficult to explain. Further work is required to gain greater understanding of the inactivation mechanism in different bacterial species, as there are likely to be other targets within the cell that are also impaired by the oxidative damage from photo-generated reactive oxygen species.\n\nThe effects of 405 nm light on bacterial membrane integrity determined by salt and bile tolerance assays, leakage of UV-absorbing material and SYTOX green labelling.", "token_count": 459, "char_count": 1905, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5516, "quality_score": 0.7758, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:27.087601", "source": { "split": "train_shard_00000", "doc_id": 3945 }, "chunk_id": "train_shard_00000_3945_0", "global_id": 4375 }, { "text": "Mycobacterium abscessus subsp. abscessus (MAB) is a highly drug resistant mycobacterium and the most common respiratory pathogen among the rapidly growing non-tuberculous mycobacteria. MAB is also one of the most deadly of the emerging cystic fibrosis (CF) pathogens requiring prolonged treatment with multiple antibiotics. In addition to its \"mycobacterial\" virulence genes, the genome of MAB harbours a large accessory genome, presumably acquired via lateral gene transfer including homologs shared with the CF pathogens Pseudomonas aeruginosa and Burkholderia cepacia. While multiple genome sequences are available there is little functional genomics data available for this important pathogen.\n\nFunctional characterization of the Mycobacterium abscessus genome coupled with condition specific transcriptomics reveals conserved molecular strategies for host adaptation and persistence.", "token_count": 217, "char_count": 888, "word_count": 116, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:27.552095", "source": { "split": "train_shard_00000", "doc_id": 3946 }, "chunk_id": "train_shard_00000_3946_0", "global_id": 4376 }, { "text": "The aim of this work was to study the production of bioactive protein hydrolysates using yeasts isolated from chhurpi. For this, a total of 125 proteolytic yeasts were isolated and molecular identification was carried out by analysis of the restriction digestion pattern generated by digesting the PCR amplified internal transcribed spacer region and 5.8S rRNA gene (ITS1-5.8S-ITS2) using three endonucleases (HaeIII, CfoI and HinfI). The results obtained showed that different proteolytic yeasts were dominant in marketed products (Kluyveromyces marxianus and Issatchenkia orientalis) and samples from production centers (Trichosporon asahii, Saccharomyces cerevisiae and Exophiala dermatitidis). Proteolytic strains in individual groups showed their ability to hydrolyze milk protein and enhance antioxidant property. Among the isolates, fermentation using K. marxianus YMP45 and S. cerevisiae YAM14 resulted in higher antioxidant activity. This is the first report on application of yeast isolated from fermented food of North-East India for the production of bioactive protein hydrolysate.\n\nProduction of bioactive protein hydrolysate using the yeasts isolated from soft chhurpi.", "token_count": 315, "char_count": 1183, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [ "ITS2", "YMP45", "YAM14", "ITS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:28.110394", "source": { "split": "train_shard_00000", "doc_id": 3947 }, "chunk_id": "train_shard_00000_3947_0", "global_id": 4377 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) is a heterogeneous group of autosomal recessive cholestatic diseases of childhood and represents the main indication for liver transplantation at this age; PFIC2 involves ABCB11 gene, that encodes the ATPdependent canalicular bile salt export pump (BSEP). Benign intrahepatic cholestasis (BRIC) identifies a group of diseases involving the same genes and characterized by intermittent attacks of cholestasis with no progression to liver cirrhosis. Diagnosis with standard sequencing techniques is expensive and available only at a few tertiary centers. We report the application of next generation sequencing (NGS) in the diagnosis of the familial intrahepatic cholestasis with a parallel sequencing of three causative genes. We identified the molecular defects in ABCB11 gene in two different probands who developed a severe cholestatic disease of unknown origin. In the first patient a compound heterozygosity for the novel frameshift mutation p.Ser1100GlnfsX38 and the missense variant p.Glu135Lys was detected. In the second patient, triggered by contraceptive therapy, we identified homozygosity for a novel missense variant p.Ala523Gly. In conclusion, these mutations seem to have a late onset and a less aggressive clinical impact, acting as an intermediate form between BRIC and PFIC.\n\nBile salt export pump deficiency disease: two novel, late onset, ABCB11 mutations identified by next generation sequencing.", "token_count": 369, "char_count": 1470, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6377, "quality_score": 0.8188, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:28.690038", "source": { "split": "train_shard_00000", "doc_id": 3948 }, "chunk_id": "train_shard_00000_3948_0", "global_id": 4378 }, { "text": "Six lactic acid bacterial (LAB) strains were isolated from traditionally fermented Xinjiang cheese and evaluated for functional and probiotic properties and potentials as starter cultures. The isolated six LAB strains comprised Lactobacillus rhamnosus (one strain), Lactobacillus helveticus (one strain), and Enterococcus hirae (four strains). All of the six strains were tolerant to acidic and bile salt conditions. Among which, the L. rhamnosus R4 strain showed more desirable antimicrobial, auto-aggregation, and hydrophobic activity. In addition, the strain L. rhamnosus R4 exhibited the highest level of free radical scavenging activity (53.78% of 1,1-diphenyl-2-picrylhydrazyl (DPPH) free radicals and 45.79% of hydroxyl radicals). L. rhamnosus R4 also demonstrated cholesterol and triglyceride degradation by 50.97% and 28.92%, respectively. To further examine the health-promoting effects of these LAB strains on host lifespan, Caenorhabditis elegans was used as an in vivo model. Worms fed LAB as a food source had significant differences in lifespan compared to those fed Escherichia coli OP50 (as a negative control). Feeding of L. rhamnosus R4 extended the mean lifespan of C. elegans by up to 36.1% compared to that of the control. The results suggest that the strains isolated from Xinjiang fermented dairy products have high potential as starter cultures in the cheese industry.\n\nProbiotic properties of lactic acid bacteria isolated from traditionally fermented Xinjiang cheese.", "token_count": 427, "char_count": 1494, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.8061, "entities": { "genes": [ "OP50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:29.316309", "source": { "split": "train_shard_00000", "doc_id": 3949 }, "chunk_id": "train_shard_00000_3949_0", "global_id": 4379 }, { "text": "Intestinal fluids contain several constituents with affinity for cyclodextrins that have the potential of displacing drugs from the cyclodextrin cavity by competition. In this study, the solubilizing capacity of 2-hydroxypropyl-β-cyclodextrin (HP-β-CD) for itraconazole was studied in presence of selected bile salts and phosphatidylcholine. Despite the fact that these competing agents significantly lowered the solubility of itraconazole in presence of cyclodextrins, the addition of concentrated solutions of these bile constituents to a solution containing itraconazole solubilized by HP-β-CD did not result in precipitation, even at bile salt and phospholipid concentrations where itraconazole precipitation would be anticipated based on solubility studies. This phenomenon was further investigated in more dynamic conditions via in vitro transfer studies, mimicking the gastrointestinal transfer of HP-β-CD solutions saturated with itraconazole. Intestinal supersaturation upon transfer was observed for all conditions tested and a concentration dependent impact of bile salts and phospholipids on the precipitation behavior of itraconazole was demonstrated: high concentrations of bile salts and phospholipids generated the highest degrees of supersaturation shortly after the transfer step but also resulted in stronger itraconazole precipitation at later time points. These findings demonstrate the possible impact of the variable intestinal fluid composition on the behavior of cyclodextrin containing formulations.\n\nDisplacement of itraconazole from cyclodextrin complexes in biorelevant media: In vitro evaluation of supersaturation and precipitation behavior.", "token_count": 388, "char_count": 1672, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5741, "quality_score": 0.787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:29.933074", "source": { "split": "train_shard_00000", "doc_id": 3950 }, "chunk_id": "train_shard_00000_3950_0", "global_id": 4380 }, { "text": "The bile salt export pump (BSEP, ABCB11) plays an essential role in the formation of bile. In hepatocytes, BSEP is localized within the apical (canalicular) membrane and a deficiency of canalicular BSEP function is associated with severe forms of cholestasis. Regulation of correct trafficking to the canalicular membrane and of activity is essential to ensure BSEP functionality and thus normal bile flow. However, little is known about the identity of interaction partners regulating function and localization of BSEP. In our study, interaction partners of BSEP were identified in a complementary approach: Firstly, BSEP interaction partners were co-immunoprecipitated from human liver samples and identified by mass spectrometry (MS). Secondly, a membrane yeast two-hybrid (MYTH) assay was used to determine protein interaction partners using a human liver cDNA library. A selection of interaction partners identified both by MYTH and MS were verified by in vitro interaction studies using purified proteins. By these complementary approaches, a set of ten novel BSEP interaction partners was identified. With the exception of radixin, all other interaction partners were integral or membrane-associated proteins including proteins of the early secretory pathway and the bile acyl-CoA synthetase, the second to last, ER-associated enzyme of bile salt synthesis.\n\nAnalysis of the Bile Salt Export Pump (ABCB11) Interactome Employing Complementary Approaches.", "token_count": 346, "char_count": 1460, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:30.857676", "source": { "split": "train_shard_00000", "doc_id": 3951 }, "chunk_id": "train_shard_00000_3951_0", "global_id": 4381 }, { "text": "Four Vibrio spp. isolates from the historical culture collection at the Centers for Disease Control and Prevention, obtained from human blood specimens (n=3) and river water (n=1), show characteristics distinct from those of isolates of the most closely related species, Vibrio navarrensis and Vibrio vulnificus, based on phenotypic and genotypic tests. They are specifically adapted to survival in both freshwater and seawater, being able to grow in rich media without added salts as well as salinities above that of seawater. Phenotypically, these isolates resemble V. navarrensis, their closest known relative with a validly published name, but the group of isolates is distinguished from V. navarrensis by the ability to utilize l-rhamnose. Average nucleotide identity and percent DNA-DNA hybridization values obtained from the pairwise comparisons of whole-genome sequences of these isolates to V. navarrensis range from 95.4-95.8 % and 61.9-64.3 %, respectively, suggesting that the group represents a different species. Phylogenetic analysis of the core genome, including four protein-coding housekeeping genes (pyrH, recA, rpoA and rpoB), places these four isolates into their own monophyletic clade, distinct from V. navarrensis and V. vulnificus. Based on these differences, we propose these isolates represent a novel species of the genus Vibrio, for which the name Vibrio cidicii sp. nov. is proposed; strain LMG 29267T (=CIP 111013T=2756-81T), isolated from river water, is the type strain.\n\nCharacterization of clinical and environmental isolates of Vibrio cidicii sp. nov., a close relative of Vibrio navarrensis.", "token_count": 449, "char_count": 1628, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:31.487950", "source": { "split": "train_shard_00000", "doc_id": 3952 }, "chunk_id": "train_shard_00000_3952_0", "global_id": 4382 }, { "text": "To investigate the role of farnesoid X receptor (FXR) and its downstream molecules small heterodimer partner (SHP), UDP-glucuronosyltransferase 2B4 (UGT2B4), and bile salt export pump (BSEP) in rats with acute cholestatic hepatitis.\n\n[Role of farnesoid X receptor in rats with acute cholestatic hepatitis].", "token_count": 104, "char_count": 306, "word_count": 43, "semantic_coherence": 1, "information_density": 0.7674, "quality_score": 0.8837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:31.873124", "source": { "split": "train_shard_00000", "doc_id": 3953 }, "chunk_id": "train_shard_00000_3953_0", "global_id": 4383 }, { "text": "S-Adenosyl-L-methionine (SAM), which exists in all living organisms, serves as an activated group donor in a range of metabolic reactions, including trans-methylation, trans-sulfuration and trans-propylamine. Compared with its chemical synthesis and enzyme catalysis production, the microbial production of SAM is feasible for industrial applications. The current clinical demand for SAM is constantly increasing. Therefore, vast interest exists in engineering the SAM metabolism in cells for increasing product titers. Here, we provided an overview of updates on SAM microbial productivity improvements with an emphasis on various strategies that have been used to enhance SAM production based on increasing the precursor and co-factor availabilities in microbes. These strategies included the sections of SAM-producing microbes and their mutant screening, optimization of the fermentation process, and the metabolic engineering. The SAM-producing strains that were used extensively were Saccharomyces cerevisiae, Pichia pastoris, Candida utilis, Scheffersomyces stipitis, Kluyveromyces lactis, Kluyveromyces marxianus, Corynebacterium glutamicum, and Escherichia coli, in addition to others. The optimization of the fermentation process mainly focused on the enhancement of the methionine, ATP, and other co-factor levels through pulsed feeding as well as the optimization of nitrogen and carbon sources. Various metabolic engineering strategies using precise control of gene expression in engineered strains were also highlighted in the present review. In addition, some prospects on SAM microbial production were discussed.\n\nProgress in the microbial production of S-adenosyl-L-methionine.", "token_count": 401, "char_count": 1693, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:32.495293", "source": { "split": "train_shard_00000", "doc_id": 3954 }, "chunk_id": "train_shard_00000_3954_0", "global_id": 4384 }, { "text": "Elizabethkingia anophelis is an emerging pathogen involved in human infections and outbreaks in distinct world regions. We investigated the phylogenetic relationships and pathogenesis-associated genomic features of two neonatal meningitis isolates isolated 5 years apart from one hospital in Central African Republic and compared them with Elizabethkingia from other regions and sources. Average nucleotide identity firmly confirmed that E. anophelis, E. meningoseptica and E. miricola represent demarcated genomic species. A core genome multilocus sequence typing scheme, broadly applicable to Elizabethkingia species, was developed and made publicly available (http://bigsdb.pasteur.fr/elizabethkingia). Phylogenetic analysis revealed distinct E. anophelis sublineages and demonstrated high genetic relatedness between the African isolates, compatible with persistence of the strain in the hospital environment. CRISPR spacer variation between the African isolates was mirrored by the presence of a large mobile genetic element. The pan-genome of E. anophelis comprised 6,880 gene families, underlining genomic heterogeneity of this species. African isolates carried unique resistance genes acquired by horizontal transfer. We demonstrated the presence of extensive variation of the capsular polysaccharide synthesis gene cluster in E. anophelis. Our results demonstrate the dynamic evolution of this emerging pathogen and the power of genomic approaches for Elizabethkingia identification, population biology and epidemiology.\n\nGenomic epidemiology and global diversity of the emerging bacterial pathogen Elizabethkingia anophelis.", "token_count": 358, "char_count": 1634, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:33.132867", "source": { "split": "train_shard_00000", "doc_id": 3955 }, "chunk_id": "train_shard_00000_3955_0", "global_id": 4385 }, { "text": "Paclitaxel (PTX), a BCS class IV drug that is characterized by its poor solubility and is a substrate for P-glycoprotein, is one of the most widely used antineoplastic agents. However, oral administration of PTX for chemotherapy is highly challenging. The aim of this study was to develop bile-salt liposomes (BS-Lips) to enhance the absorption of PTX and thus improve its therapeutic outcome. The BS-Lips were prepared by the thin-film hydration method and characterized in terms of particle size and morphology. Drug release and in vitro stability in simulated gastrointestinal fluids and in media of different pH values were evaluated, as well as in vivo performance, including antitumor activity and pharmacokinetics in rats, with the plasma concentrations determined by a HPLC method. The PTX-loaded BS-Lips were successfully prepared with a diameter of approximately 150 nm and an entrapment efficiency of greater than 90 percent. Moreover, the BS-Lips were not affected by gastrointestinal enzymes or pH alternation, as evident from the unchanged particle size and the drug retained in BS-Lips after 6 h incubation. The insertion of bile salt into the lipid layer of liposomes increased the lymphatic transport of PTX by twofold. Importantly, BS-Lips increased the oral bioavailability of PTX by 2.5 and 4-fold, respectively, compared with conventional liposomes (Lips) and Taxol (free drug), thereby displaying a better inhibition of tumor growth that was similar to the group injected intravenously with Taxol. In conclusion, the BS-Lips represent promising vehicles for the oral delivery of PTX, thereby enabling an intravenous-to-oral switch for cancer chemotherapy.\n\nBile salt liposomes for enhanced lymphatic transport and oral bioavailability of paclitaxel.", "token_count": 443, "char_count": 1771, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5947, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:33.781241", "source": { "split": "train_shard_00000", "doc_id": 3956 }, "chunk_id": "train_shard_00000_3956_0", "global_id": 4386 }, { "text": "Candida spp. are the most common opportunistic mycosis worldwide. Although Candida albicans is the most common cause of urinary tract infections, the frequency of non-albicans Candida species is increasing with common use of antifungal in the prophylaxis and treatment. This may lead to difficulties in treatment. Antifungal tests should be applied with identification of species for effective treatment. In this study, identification of Candida species isolated from urine culture and investigation of susceptibility of these strains to amphotericin B, flucytosine, fluconazole, voriconazole was aimed. In this study, 58 Candida strains isolated from urine cultures at Osmaniye State Hospital between January 2012 and April 2013 were included. Urine culture and antifungal susceptibility tests were applied. Incidence rate of Candida spp. was determined as C. albicans (56.9%), Candida glabrata (20.6%), Candida tropicalis (10.3%), Candida parapsilosis (7%), Candida krusei (3.4%), Candida kefyr (1.8%). Most of the isolates were susceptible to amphotericin B, flucytosine, fluconazole, voriconazole. Twenty three (39.7%) Candida strains were isolated from internal medical branches and Intensive Care Unit and 12 (20.6%) from the Surgical Medical Branches. C. albicans and C. glabrata species were isolated most frequently as a candiduria factor in this hospital between January 2012 and April 2013. The analysis of antifungal susceptibility profile shows no significant resistance to antifungals.\n\nAntifungal susceptibilities of Candida species isolated from urine culture.", "token_count": 427, "char_count": 1576, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5297, "quality_score": 0.7648, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:34.439751", "source": { "split": "train_shard_00000", "doc_id": 3957 }, "chunk_id": "train_shard_00000_3957_0", "global_id": 4387 }, { "text": "Multi isolate whole genome sequencing (WGS) and typing for outbreak investigations has become a reality in the post-genomics era. We applied this technology to strains from Escherichia coli O157:H7 outbreaks. These include isolates from seven North America outbreaks, as well as multiple isolates from the same patient and from different infected individuals in the same household. Customized high-resolution bioinformatics sequence typing strategies were developed to assess the core genome and mobilome plasticity. Sequence typing was performed using an in-house single nucleotide polymorphism (SNP) discovery and validation pipeline. Discriminatory power becomes of particular importance for the investigation of isolates from outbreaks in which macrogenomic techniques such as pulse-field gel electrophoresis or multiple locus variable number tandem repeat analysis do not differentiate closely related organisms. We also characterized differences in the phage inventory, allowing us to identify plasticity among outbreak strains that is not detectable at the core genome level. Our comprehensive analysis of the mobilome identified multiple plasmids that have not previously been associated with this lineage. Applied phylogenomics approaches provide strong molecular evidence for exceptionally little heterogeneity of strains within outbreaks and demonstrate the value of intra-cluster comparisons, rather than basing the analysis on archetypal reference strains. Next generation sequencing and whole genome typing strategies provide the technological foundation for genomic epidemiology outbreak investigation utilizing its significantly higher sample throughput, cost efficiency, and phylogenetic relatedness accuracy. These phylogenomics approaches have major public health relevance in translating information from the sequence-based survey to support timely and informed countermeasures. Polymorphisms identified in this work offer robust phylogenetic signals that index both short- and long-term evolution and can complement currently employed typing schemes for outbreak ex- and inclusion, diagnostics, surveillance, and forensic studies.\n\nWhole Genome Sequencing for Genomics-Guided Investigations of Escherichia coli O157:H7 Outbreaks.", "token_count": 467, "char_count": 2250, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:35.092308", "source": { "split": "train_shard_00000", "doc_id": 3958 }, "chunk_id": "train_shard_00000_3958_0", "global_id": 4388 }, { "text": "Streptococcus agalactiae (Group B Streptococcus, GBS) causes life-threatening infections in newborns and adults with chronic medical conditions. Serotype IV strains are emerging both among carriers and as cause of invasive disease and recent studies revealed two main Sequence Types (STs), ST-452 and ST-459 assigned to Clonal Complexes CC23 and CC1, respectively. Whole genome sequencing of 70 type IV GBS and subsequent phylogenetic analysis elucidated the localization of type IV isolates in a SNP-based phylogenetic tree and suggested that ST-452 could have originated through genetic recombination. SNPs density analysis of the core genome confirmed that the founder strain of this lineage originated from a single large horizontal gene transfer event between CC23 and the hypervirulent CC17. Indeed, ST-452 genomes are composed by two parts that are nearly identical to corresponding regions in ST-24 (CC23) and ST-291 (CC17). Chromosome mapping of the major GBS virulence factors showed that ST-452 strains have an intermediate yet unique profile among CC23 and CC17 strains. We described unreported large recombination events, involving the cps IV operon and resulting in the expansion of serotype IV to CC23. This work sheds further light on the evolution of GBS providing new insights on the recent emergence of serotype IV.\n\nSerotype IV Streptococcus agalactiae ST-452 has arisen from large genomic recombination events between CC23 and the hypervirulent CC17 lineages.", "token_count": 388, "char_count": 1480, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [ "CC17", "CC1", "CC23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:35.709763", "source": { "split": "train_shard_00000", "doc_id": 3959 }, "chunk_id": "train_shard_00000_3959_0", "global_id": 4389 }, { "text": "Unlike most Pseudomonas, the root-associated bacterium Pseudomonas stutzeri A1501 fixes nitrogen after the horizontal acquisition of a nitrogen-fixing (nif) island. A genome-wide search for small noncoding RNAs (ncRNAs) in P. stutzeri A1501 identified the novel P. stutzeri-specific ncRNA NfiS in the core genome, whose synthesis was significantly induced under nitrogen fixation or sorbitol stress conditions. The expression of NfiS was RNA chaperone Hfq-dependent and activated by the sigma factor RpoN/global nitrogen activator NtrC/nif-specific activator NifA regulatory cascade. The nfiS-deficient mutant displayed reduced nitrogenase activity, as well as increased sensitivity to multiple stresses, such as osmotic and oxidative stresses. Secondary structure prediction and complementation studies confirmed that a stem-loop structure was essential for NfiS to regulate the nitrogenase gene nifK mRNA synthesis and thus nitrogenase activity. Microscale thermophoresis and physiological analysis showed that NfiS directly pairs with nifK mRNA and ultimately enhances nitrogenase activity by increasing the translation efficiency and the half-life of nifK mRNA. Our data also suggest structural and functional divergence of NfiS evolution in diazotrophic and nondiazotrophic backgrounds. It is proposed that NfiS was recruited by nifK mRNA as a novel regulator to integrate the horizontally acquired nif island into host global networks.\n\nThe novel regulatory ncRNA, NfiS, optimizes nitrogen fixation via base pairing with the nitrogenase gene nifK mRNA in Pseudomonas stutzeri A1501.", "token_count": 430, "char_count": 1588, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:36.343090", "source": { "split": "train_shard_00000", "doc_id": 3960 }, "chunk_id": "train_shard_00000_3960_0", "global_id": 4390 }, { "text": "Gene sequences are the target of evolution operating at different levels, including the nucleotide, codon, and amino acid levels. Disentangling the impact of those different levels on gene sequences requires developing a probabilistic model with three layers. Here we present SENCA (site evolution of nucleotides, codons, and amino acids), a codon substitution model that separately describes 1) nucleotide processes which apply on all sites of a sequence such as the mutational bias, 2) preferences between synonymous codons, and 3) preferences among amino acids. We argue that most synonymous substitutions are not neutral and that SENCA provides more accurate estimates of selection compared with more classical codon sequence models. We study the forces that drive the genomic content evolution, intraspecifically in the core genome of 21 prokaryotes and interspecifically for five Enterobacteria. We retrieve the existence of a universal mutational bias toward AT, and that taking into account selection on synonymous codon usage has consequences on the measurement of selection on nonsynonymous substitutions. We also confirm that codon usage bias is mostly driven by selection on preferred codons. We propose new summary statistics to measure the relative importance of the different evolutionary processes acting on sequences.\n\nSENCA: A Multilayered Codon Model to Study the Origins and Dynamics of Codon Usage.", "token_count": 308, "char_count": 1419, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:36.915276", "source": { "split": "train_shard_00000", "doc_id": 3961 }, "chunk_id": "train_shard_00000_3961_0", "global_id": 4391 }, { "text": "Cellular mechanisms that mediate steatohepatitis, an increasingly prevalent condition in the Western world for which no therapies are available, are poorly understood. Despite the fact that its synthetic agonists induce fatty liver, the liver X receptor (LXR) transcription factor remains a target of interest because of its anti-atherogenic, cholesterol removal, and anti-inflammatory activities. Here we show that tetratricopeptide repeat domain protein 39B (Ttc39b, C9orf52) (T39), a high-density lipoprotein gene discovered in human genome-wide association studies, promotes the ubiquitination and degradation of LXR. Chow-fed mice lacking T39 (T39(-/-)) display increased high-density lipoprotein cholesterol levels associated with increased enterocyte ATP-binding cassette transporter A1 (Abca1) expression and increased LXR protein without change in LXR messenger RNA. When challenged with a high fat/high cholesterol/bile salt diet, T39(-/-) mice or mice with hepatocyte-specific T39 deficiency show increased hepatic LXR protein and target gene expression, and unexpectedly protection from steatohepatitis and death. Mice fed a Western-type diet and lacking low-density lipoprotein receptor (Ldlr(-/-)T39(-/-)) show decreased fatty liver, increased high-density lipoprotein, decreased low-density lipoprotein, and reduced atherosclerosis. In addition to increasing hepatic Abcg5/8 expression and limiting dietary cholesterol absorption, T39 deficiency inhibits hepatic sterol regulatory element-binding protein 1 (SREBP-1, ADD1) processing. This is explained by an increase in microsomal phospholipids containing polyunsaturated fatty acids, linked to an LXRα-dependent increase in expression of enzymes mediating phosphatidylcholine biosynthesis and incorporation of polyunsaturated fatty acids into phospholipids", "token_count": 491, "char_count": 1823, "word_count": 227, "semantic_coherence": 1, "information_density": 0.674, "quality_score": 0.837, "entities": { "genes": [ "ADD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:37.563950", "source": { "split": "train_shard_00000", "doc_id": 3962 }, "chunk_id": "train_shard_00000_3962_0", "global_id": 4392 }, { "text": "The preservation of endogenous LXR protein activates a beneficial profile of gene expression that promotes cholesterol removal and inhibits lipogenesis. T39 inhibition could be an effective strategy for reducing both steatohepatitis and atherosclerosis.\n\nTTC39B deficiency stabilizes LXR reducing both atherosclerosis and steatohepatitis.", "token_count": 87, "char_count": 338, "word_count": 42, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [ "TTC39B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:37.937347", "source": { "split": "train_shard_00000", "doc_id": 3962 }, "chunk_id": "train_shard_00000_3962_1", "global_id": 4393 }, { "text": "Bile is an important component of the human gastrointestinal tract with an essential role in food absorption and antimicrobial activities. Enteric bacterial pathogens have developed strategies to sense bile as an environmental cue to regulate virulence genes during infection. We discovered that Vibrio parahaemolyticus VtrC, along with VtrA and VtrB, are required for activating the virulence type III secretion system 2 in response to bile salts. The VtrA/VtrC complex activates VtrB in the presence of bile salts. The crystal structure of the periplasmic domains of the VtrA/VtrC heterodimer reveals a β-barrel with a hydrophobic inner chamber. A co-crystal structure of VtrA/VtrC with bile salt, along with biophysical and mutational analysis, demonstrates that the hydrophobic chamber binds bile salts and activates the virulence network. As part of a family of conserved signaling receptors, VtrA/VtrC provides structural and functional insights into the evolutionarily conserved mechanism used by bacteria to sense their environment.\n\nBile salt receptor complex activates a pathogenic type III secretion system.", "token_count": 287, "char_count": 1118, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8168, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:38.499190", "source": { "split": "train_shard_00000", "doc_id": 3963 }, "chunk_id": "train_shard_00000_3963_0", "global_id": 4394 }, { "text": "Use of probiotic biofilms can be an alternative approach for reducing the formation of pathogenic biofilms in food industries. The aims of this study were (i) to evaluate the probiotic properties of bacteriocinogenic (Lactococcus lactis VB69, L. lactis VB94, Lactobacillus sakei MBSa1, and Lactobacillus curvatus MBSa3) and non-bacteriocinogenic (L. lactis 368, Lactobacillus helveticus 354, Lactobacillus casei 40, and Weissela viridescens 113) lactic acid bacteria (LAB) isolated from Brazilian's foods and (ii) to develop protective biofilms with these strains and test them for exclusion of Listeria monocytogenes, Escherichia coli O157:H7, and Salmonella Typhimurium. LAB were tested for survival in acid and bile salt conditions, surface properties, biosurfactant production, β-galactosidase and gelatinase activity, antibiotic resistance and presence of virulence genes. Most strains survived exposure to pH 2 and 4% bile salts. The highest percentages of auto-aggregation were obtained after 24 h of incubation. Sixty-seven percentage auto-aggregation value was observed in W. viridescens 113 and Lactobacillus curvatus MBSa3 exhibited the highest co-aggregation (69% with Listeria monocytogenes and 74.6% with E. coli O157:H7), while the lowest co-aggregation was exhibited by W. viridescens 113 (53.4% with Listeria monocytogenes and 38% with E. coli O157:H7). Tests for hemolytic activity, bacterial cell adherence with xylene, and drop collapse confirmed the biosurfactant-producing ability of most strains. Only one strain (L. lactis 368) produced β-galactosidase", "token_count": 512, "char_count": 1576, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6574, "quality_score": 0.8287, "entities": { "genes": [ "VB69", "VB94" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:39.156670", "source": { "split": "train_shard_00000", "doc_id": 3964 }, "chunk_id": "train_shard_00000_3964_0", "global_id": 4395 }, { "text": "All strains were negative for virulence genes cob, ccf, cylLL, cylLs, cyllM, cylB, cylA and efaAfs and gelatinase production. The antibiotic susceptibility tests indicated that the MIC for ciprofloxacin, clindamycin, gentamicin, kanamycin, and streptomycin did not exceed the epidemiological cut-off suggested by the European Food Safety Authority. Some strains were resistant to one or more antibiotics and resistance to antibiotics was species and strain dependent. In the protective biofilm assays, strains L. lactis 368 (bac-), Lactobacillus curvatus MBSa3 (bac+), and Lactobacillus sakei MBSa1 (bac+) resulted in more than six log reductions in the pathogens counts when compared to the controls. This effect could not be attributed to bacteriocin production. These results suggest that these potential probiotic strains can be used as alternatives for control of biofilm formation by pathogenic bacteria in the food industry, without conferring a risk to the consumers.\n\nUse of Potential Probiotic Lactic Acid Bacteria (LAB) Biofilms for the Control of Listeria monocytogenes, Salmonella Typhimurium, and Escherichia coli O157:H7 Biofilms Formation.", "token_count": 322, "char_count": 1155, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7134, "quality_score": 0.8567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:39.724285", "source": { "split": "train_shard_00000", "doc_id": 3964 }, "chunk_id": "train_shard_00000_3964_1", "global_id": 4396 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STEC(per)) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STEC(spo)) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STEC(per) isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STEC(spo) isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STEC(per) isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STEC(spo) isolates", "token_count": 461, "char_count": 1479, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6749, "quality_score": 0.8374, "entities": { "genes": [ "ST300", "ST119", "ST1079", "ST21", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:40.370977", "source": { "split": "train_shard_00000", "doc_id": 3965 }, "chunk_id": "train_shard_00000_3965_0", "global_id": 4397 }, { "text": "Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STEC(per) from STEC(spo) isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.\n\nThe Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle.", "token_count": 96, "char_count": 378, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8627, "quality_score": 0.9314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:40.745039", "source": { "split": "train_shard_00000", "doc_id": 3965 }, "chunk_id": "train_shard_00000_3965_1", "global_id": 4398 }, { "text": "Kefir is a fermented milk beverage consumed for nutritional and health tonic benefits in many parts of the world. It is produced by the fermentation of milk with a consortium of bacteria and yeast embedded within a polysaccharide matrix. This consortium is not well defined and can vary substantially between kefir grains. There are little data on the microbial stability of kefir grains, nor on interactions between microbes in the grain and in the milk. To study this, a grain was split, with one half of each stored at -20°C and the other half passaged repeatedly in whole unpasteurised milk. Grains passaged in the unpasteurised milk recovered vigour and acquired the yeast Kluyveromyces marxainus from the milk which was confirmed to be the same strain by molecular typing. Furthermore, these passaged grains produced kefir that was distinguished chemically and organoleptically from the stored grains. Some changes in ultrastructure were also observed by scanning electron microscopy. The study showed that kefir grains can acquire yeast from their environment and the final product can be influenced by these newly acquired yeasts. Kluyveromyces marxianus is considered to be responsible for some of the most important characteristics of kefir so the finding that this yeast is part of the less stable microbiota is significant.\n\nAcquisition of the yeast Kluyveromyces marxianus from unpasteurised milk by a kefir grain enhances kefir quality.", "token_count": 347, "char_count": 1450, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5442, "quality_score": 0.7721, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:41.330286", "source": { "split": "train_shard_00000", "doc_id": 3966 }, "chunk_id": "train_shard_00000_3966_0", "global_id": 4399 }, { "text": "Roux-en-Y gastric bypass (RYGB) alters the anatomical structure of the gastrointestinal tract, which can result in alterations in drug disposition. The aim of the present study was to evaluate the oral disposition of two compounds belonging to the Biopharmaceutical Classification System Class II - fenofibrate (bile salt-dependent solubility) and posaconazole (gastric pH-dependent dissolution) - before and after RYGB in the same individuals.\n\nDrug disposition before and after gastric bypass: fenofibrate and posaconazole.", "token_count": 141, "char_count": 525, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:42.485232", "source": { "split": "train_shard_00000", "doc_id": 3967 }, "chunk_id": "train_shard_00000_3967_0", "global_id": 4400 }, { "text": "We characterized two epidemiologically similar Acinetobacter baumannii clusters from two separate intensive care units (ICU) using core genome multilocus sequence typing. Clonal spread was confirmed in ICU-1 (12 of 14 isolates shared genotypes); in ICU-2, all genotypes (13 isolates) were diverse, thus excluding transmissions and enabling adequate infection control measures.\n\nWhole-Genome Sequencing Elucidates Epidemiology of Nosocomial Clusters of Acinetobacter baumannii.", "token_count": 126, "char_count": 476, "word_count": 60, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:42.872639", "source": { "split": "train_shard_00000", "doc_id": 3968 }, "chunk_id": "train_shard_00000_3968_0", "global_id": 4401 }, { "text": "Lactobacillus rhamnosus is a diverse Gram-positive species with strains isolated from different ecological niches. Here, we report the genome sequence analysis of 40 diverse strains of L. rhamnosus and their genomic comparison, with a focus on the variable genome. Genomic comparison of 40 L. rhamnosus strains discriminated the conserved genes (core genome) and regions of plasticity involving frequent rearrangements and horizontal transfer (variome). The L. rhamnosus core genome encompasses 2,164 genes, out of 4,711 genes in total (the pan-genome). The accessory genome is dominated by genes encoding carbohydrate transport and metabolism, extracellular polysaccharides (EPS) biosynthesis, bacteriocin production, pili production, the cas system, and the associated clustered regularly interspaced short palindromic repeat (CRISPR) loci, and more than 100 transporter functions and mobile genetic elements like phages, plasmid genes, and transposons. A clade distribution based on amino acid differences between core (shared) proteins matched with the clade distribution obtained from the presence-absence of variable genes. The phylogenetic and variome tree overlap indicated that frequent events of gene acquisition and loss dominated the evolutionary segregation of the strains within this species, which is paralleled by evolutionary diversification of core gene functions. The CRISPR-Cas system could have contributed to this evolutionary segregation. Lactobacillus rhamnosus strains contain the genetic and metabolic machinery with strain-specific gene functions required to adapt to a large range of environments. A remarkable congruency of the evolutionary relatedness of the strains' core and variome functions, possibly favoring interspecies genetic exchanges, underlines the importance of gene-acquisition and loss within the L. rhamnosus strain diversification.\n\nThe Variable Regions of Lactobacillus rhamnosus Genomes Reveal the Dynamic Evolution of Metabolic and Host-Adaptation Repertoires.", "token_count": 491, "char_count": 2010, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:43.524319", "source": { "split": "train_shard_00000", "doc_id": 3969 }, "chunk_id": "train_shard_00000_3969_0", "global_id": 4402 }, { "text": "Transport processes in the canalicular membrane are key elements in bile formation and are the driving force of the enterohepatic circulation of bile salts. The canalicular membrane is constantly exposed to the detergent action of bile salts. One potential element protecting the canalicular membrane from the high canalicular bile salt concentrations may be bile salt resistant microdomains, however additional factors are likely to play a role. To obtain more insights into the molecular composition of the canalicular membrane, the proteome of highly purified rat canalicular membrane vesicles was determined. Isolated rat canalicular membrane vesicles were stripped from adhering proteins, deglycosylated and protease digested before subjecting the samples to shot gun proteomic analysis. The expression of individual candidates was studied by PCR, Western blotting and immunohistochemistry. A total of 2449 proteins were identified, of which 1282 were predicted to be membrane proteins. About 50% of the proteins identified here were absent from previously published liver proteomes. In addition to ATP8B1, four more P4-ATPases were identified. ATP8A1 and ATP9A showed expression specific to the canalicular membrane, ATP11C at the bLPM and ATP11A in an intracellular vesicular compartment partially colocalizing with RAB7A and EEA1 as markers of the endosomal compartment. This study helped to identify additional P4-ATPases from rat liver particularly in the canalicular membrane, previously not known to be expressed in liver. These P4-ATPases might be contributing for maintaining transmembrane lipid homeostasis in hepatocytes.\n\nProteomic Analysis of the Rat Canalicular Membrane Reveals Expression of a Complex System of P4-ATPases in Liver.", "token_count": 423, "char_count": 1752, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5863, "quality_score": 0.7932, "entities": { "genes": [ "EEA1", "ATP9A", "ATP11C", "RAB7A", "ATP11A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:44.180185", "source": { "split": "train_shard_00000", "doc_id": 3970 }, "chunk_id": "train_shard_00000_3970_0", "global_id": 4403 }, { "text": "The viability and functionality of probiotics may be influenced by industrial production processes resulting in a decrease in probiotic efficiency that benefit the health of humans. This study aimed to investigate the probiotic characteristics of Bifidobacterium strains isolated from fecal samples of healthy Thai infants. In the present work, three local strains (BF014, BF052, and BH053) belonging to Bifidobacterium animalis showed a great resistance against conditions simulating the gastrointestinal tract. Among these, B. animalis BF052 possessed considerable probiotic properties, including high acid and bile tolerance, strong adhesion capability to Caco-2 cells, and inhibitory activity against pathogens including Salmonella typhimurium and Vibrio cholerae. This strain also exhibited a high survival rate compared to commercial strains during storage in a wide variety of products, including pasteurized milk, soy milk, drinking yogurt, and orange juice. The impact of food processing processes as well as the freeze-drying process, storage of freeze-dried powders, and incorporation of freeze-dried cells in food matrix on probiotic properties was also determined. The stability of the probiotic properties of the BF052 strain was not affected by food processing chain, especially its resistance in the simulated gastrointestinal conditions and its adherence ability to Caco-2 cells. It indicates that it satisfies the criteria as a potential probiotic and may be used as an effective probiotic starter in food applications.\n\nEffects of the Food Manufacturing Chain on the Viability and Functionality of Bifidobacterium animalis through Simulated Gastrointestinal Conditions.", "token_count": 385, "char_count": 1688, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7957, "entities": { "genes": [ "BF014", "BF052", "BH053" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:44.802846", "source": { "split": "train_shard_00000", "doc_id": 3971 }, "chunk_id": "train_shard_00000_3971_0", "global_id": 4404 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) and extended-spectrum β-lactamase (ESBL) producing enterobacteria (ESBL-E) have emerged in livestock. This study prospectively investigates the prevalence of MRSA and ESBL-E on pig farms and in nasal and stool samples from farmers and compares molecular characteristics of these ESBL-E isolates. In 2014, samples were derived at 51 pig farms in Germany. Per farm, five dust and five fecal samples were collected; one nasal and one stool sample were retrieved from farmers. ESBL-E isolates from humans and environmental isolates from the respective farms were characterized using whole genome sequencing for classical multilocus sequence typing (MLST), determination of ESBL-encoding genes and an ad hoc core genome MLST (cgMLST) analysis. MRSA and ESBL-E were detected on 49 (96%) and 31 (61%) of the farms, respectively; in most cases (59%) simultaneously. Nasal MRSA carriage was detected in 72 of 85 (84.7%) farmers and five of 84 (6.0%) farmers carried ESBL-E. ESBL-Escherichia coli isolates from farmers belonged to MLST STs/ESBL-genes ST10/CTX-M-1, ST196/TEM-52, ST278/TEM-52, ST410/CTX-M-15 and ST453/CTX-M-1. In one case, the human ESBL-E isolate was clonally identical to isolates from the farm environment; in the other four cases typing results indicated potential exchange of resistance determinants between human and environmental isolates, but, comparing the isolates within a minimum spanning tree indicated differences in cgMLST-patterns between the farms (p=0.076). This study demonstrated rectal ESBL-E carriage rates among farmers, which were similar to those in the general population. Molecular typing suggested that cross-transmission between the farmers and the farm environment is possible.", "token_count": 489, "char_count": 1765, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8044, "entities": { "genes": [ "ST410", "ST278", "ST196", "ST10", "ST453" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:45.482694", "source": { "split": "train_shard_00000", "doc_id": 3972 }, "chunk_id": "train_shard_00000_3972_0", "global_id": 4405 }, { "text": "Simultaneous occurrence of MRSA and ESBL-producing Enterobacteriaceae on pig farms and in nasal and stool samples from farmers.", "token_count": 33, "char_count": 127, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:45.850562", "source": { "split": "train_shard_00000", "doc_id": 3972 }, "chunk_id": "train_shard_00000_3972_1", "global_id": 4406 }, { "text": "In this study, three lactic acid bacteria (LAB), isolated from barley, traditional dried meat and fermented olive were characterized and tested for their anti-bacterial and anti-biofilm activities against oral bacteria. Our results revealed that the tested LAB were γ-hemolytic and were susceptible to four antibiotics. All the strains were resistant to low pH, bile salt, pepsin and pancreatin. Furthermore, FB2 displayed a high aut-oaggregative phenotype (99.54%) while FF2 exhibited the best co-aggregation rate. Concerning the microbial adhesion to solvent, FB2 was the most hydrophobic strain (data obtained with chloroform and n-hexadecane). In addition Pediococcus pentosaceus FB2 and Lactobacillus brevis FF2 displayed a significant inhibitory effect against Streptococcus salivarius B468 (MIC = 10%). Moreover the selected strains were able to inhibit biofilm formation of Bacillus cereus ATCC14579 (MBIC50 = 28.16%) and S. salivarius B468 (MBIC50 = 42.28%). The selected LAB could be considered as candidate probiotics for further application in functional food and mainly in the prevention of oral diseases.\n\nAnti-bacterial and anti-biofilm activity of probiotic bacteria against oral pathogens.", "token_count": 347, "char_count": 1206, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7041, "quality_score": 0.8521, "entities": { "genes": [ "FF2", "MBIC50", "ATCC14579", "FB2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:46.465154", "source": { "split": "train_shard_00000", "doc_id": 3973 }, "chunk_id": "train_shard_00000_3973_0", "global_id": 4407 }, { "text": "Alpha-naphthylisothiocyanate (ANIT) is a toxicant that is widely used in rodents to model human intrahepatic cholestasis. The aim of the study is to investigate whether effects of dioscin on ANIT-induced cholestasis are related to changes in expression of hepatic transporters in rats. Effects of dioscin on cholestasis were examined by histology and biochemical marker levels. The functional changes of hepatic transporters were determined by in vitro, in situ and in vivo. qRT-PCR and western blot were used to assess the expression of hepatic transporters in cholestatic rats. Dioscin administration could ameliorate cholestasis, as evidenced by reduced biochemical markers as well as improved liver pathology. The uptakes of organic anion transporting polypeptide (Oatp) substrates were altered in liver uptake index in vivo, perfused rat liver in situ and isolated rat hepatocytes in vitro in cholestasis rats. qRT-PCR and western blot analysis indicated co-treatment of ANIT with dioscin prevented the adaptive down-regulation of Oatp1a1, 1b2, and prompted the up-regulation of Oatp1a4, multidrug resistance-associated protein (Mrp) 2 and bile salt export pump (Bsep). In addition, concerted effects on Mrp2 and Bsep occurred through up-regulation of small heterodimer partner by activating farnesoid X receptor. Dioscin might prevent impairment of hepatic function by restoring hepatic transporter expression.\n\nDioscin protects against ANIT-induced cholestasis via regulating Oatps, Mrp2 and Bsep expression in rats.", "token_count": 427, "char_count": 1523, "word_count": 216, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:47.097904", "source": { "split": "train_shard_00000", "doc_id": 3974 }, "chunk_id": "train_shard_00000_3974_0", "global_id": 4408 }, { "text": "The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms Oasisia alvinae, Riftia pachyptila, Tevnia jerichonana, and Ridgeia piscesae belong to the same phylotype of gammaproteobacteria, \"Candidatus Endoriftia persephone.\" Comparisons of symbiont genomes between the East Pacific Rise tubeworms R. pachyptila and T. jerichonana confirmed that these two hosts share the same symbionts. Two Ridgeia symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced Riftia and Tevnia symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that \"Ca Endoriftia persephone\" symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity.\n\nInsights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers.", "token_count": 374, "char_count": 1403, "word_count": 186, "semantic_coherence": 1, "information_density": 0.672, "quality_score": 0.836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:47.688171", "source": { "split": "train_shard_00000", "doc_id": 3975 }, "chunk_id": "train_shard_00000_3975_0", "global_id": 4409 }, { "text": "We investigated the transcriptomic response of a new strain of the yeast Kluyveromyces marxianus, in glucose and xylose media using RNA-seq. The data were explored in a number of innovative ways using a variety of networks types, pathway maps, enrichment statistics, reporter metabolites and a flux simulation model, revealing different aspects of the genome-scale response in an integrative systems biology manner. The importance of the subcellular localisation in the transcriptomic response is emphasised here, revealing new insights. As was previously reported by others using a rich medium, we show that peroxisomal fatty acid catabolism was dramatically up-regulated in a defined xylose mineral medium without fatty acids, along with mechanisms to activate fatty acids and transfer products of β-oxidation to the mitochondria. Notably, we observed a strong up-regulation of the 2-methylcitrate pathway, supporting capacity for odd-chain fatty acid catabolism. Next we asked which pathways would respond to the additional requirement for NADPH for xylose utilisation, and rationalised the unexpected results using simulations with Flux Balance Analysis. On a fundamental level, we investigated the contribution of the hierarchical and metabolic regulation levels to the regulation of metabolic fluxes. Metabolic regulation analysis suggested that genetic level regulation plays a major role in regulating metabolic fluxes in adaptation to xylose, even for the high capacity reactions, which is unexpected. In addition, isozyme switching may play an important role in re-routing of metabolic fluxes in subcellular compartments in K. marxianus.\n\nDifferential RNA-seq, Multi-Network Analysis and Metabolic Regulation Analysis of Kluyveromyces marxianus Reveals a Compartmentalised Response to Xylose.", "token_count": 418, "char_count": 1802, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:48.315060", "source": { "split": "train_shard_00000", "doc_id": 3976 }, "chunk_id": "train_shard_00000_3976_0", "global_id": 4410 }, { "text": "Enterococcus faecalis is an opportunistic pathogen and a leading cause of nosocomial infections. Conjugative pheromone-responsive plasmids are narrow-host-range mobile genetic elements (MGEs) that are rapid disseminators of antibiotic resistance in the faecalis species. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification confer acquired and innate immunity, respectively, against MGE acquisition in bacteria. Most multidrug-resistant E. faecalis isolates lack CRISPR-Cas and possess an orphan locus lacking cas genes, CRISPR2, that is of unknown function. Little is known about restriction-modification defense in E. faecalis. Here, we explore the hypothesis that multidrug-resistant E. faecalis strains are immunocompromised. We assessed MGE acquisition by E. faecalis T11, a strain closely related to the multidrug-resistant hospital isolate V583 but which lacks the ~620 kb of horizontally acquired genome content that characterizes V583. T11 possesses the E. faecalis CRISPR3-cas locus and a predicted restriction-modification system, neither of which occurs in V583. We demonstrate that CRISPR-Cas and restriction-modification together confer a 4-log reduction in acquisition of the pheromone-responsive plasmid pAM714 in biofilm matings. Additionally, we show that the orphan CRISPR2 locus is functional for genome defense against another pheromone-responsive plasmid, pCF10, only in the presence of cas9 derived from the E. faecalis CRISPR1-cas locus, which most multidrug-resistant E. faecalis isolates lack. Overall, our work demonstrated that the loss of only two loci led to a dramatic reduction in genome defense against a clinically relevant MGE, highlighting the critical importance of the E. faecalis accessory genome in modulating horizontal gene transfer. Our results rationalize the development of antimicrobial strategies that capitalize upon the immunocompromised status of multidrug-resistant E. faecalis", "token_count": 513, "char_count": 1974, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [ "CRISPR2", "CRISPR3", "CRISPR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:38:48.969719", "source": { "split": "train_shard_00000", "doc_id": 3977 }, "chunk_id": "train_shard_00000_3977_0", "global_id": 4411 }, { "text": "IMPORTANCE Enterococcus faecalis is a bacterium that normally inhabits the gastrointestinal tracts of humans and other animals. Although these bacteria are members of our native gut flora, they can cause life-threatening infections in hospitalized patients. Antibiotic resistance genes appear to be readily shared among high-risk E. faecalis strains, and multidrug resistance in these bacteria limits treatment options for infections. Here, we find that CRISPR-Cas and restriction-modification systems, which function as adaptive and innate immune systems in bacteria, significantly impact the spread of antibiotic resistance genes in E. faecalis populations. The loss of these systems in high-risk E. faecalis suggests that they are immunocompromised, a tradeoff that allows them to readily acquire new genes and adapt to new antibiotics.\n\nCRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis.", "token_count": 234, "char_count": 980, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:49.435560", "source": { "split": "train_shard_00000", "doc_id": 3977 }, "chunk_id": "train_shard_00000_3977_1", "global_id": 4412 }, { "text": "Combining micellar electrokinetic capillary chromatography (MEKC) and nuclear magnetic resonance (NMR) experimentation, we shed light on the structural basis for the chirally selective solubilization of atropisomeric binaphthyl compounds by bile salt micelles comprised of cholate (NaC) or deoxycholate (NaDC). The model binaphthyl analyte R,S-BNDHP exhibits chirally selective interactions with primary micellar aggregates of cholate and deoxycholate, as does the closely related analyte binaphthol (R,S-BN). Chiral selectivity was localized, by NMR chemical shift analysis, to the proton at the C12 position of these bile acids. Correspondingly, MEKC results show that the 12α-OH group of either NaC or NaDC is necessary for chirally selective resolution of these model binaphthyl analytes by bile micelles, and the S isomer is more highly retained by the micelles. With NMR, the chemical shift of 12β-H was perturbed more strongly in the presence of S-BNDHP than R-BNDHP. Intermolecular NOEs demonstrate that R,S-BNDHP and R,S-BN interact with a similar hydrophobic planar pocket lined with the methyl groups of the bile salts, and are best explained by the existence of an antiparallel dimeric unit of bile salts. Finally, chemical shift data and intermolecular NOEs support different interactions of the enantiomers with the edges of dimeric bile units, indicating that R,S-BNDHP enantiomers sample the same binding site preferentially from opposite edges of the dimeric bile unit. Chirality 28:525-533, 2016. © 2016 Wiley Periodicals, Inc.\n\nAn Edge Selection Mechanism for Chirally Selective Solubilization of Binaphthyl Atropisomeric Guests by Cholate and Deoxycholate Micelles.", "token_count": 480, "char_count": 1685, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:50.083170", "source": { "split": "train_shard_00000", "doc_id": 3978 }, "chunk_id": "train_shard_00000_3978_0", "global_id": 4413 }, { "text": "Programmed cell death in bacteria is generally associated with two-component toxin-antitoxin systems. The SpoIISABC system, originally identified in Bacillus subtilis, consists of three components: a SpoIISA toxin and the SpoIISB and SpoIISC antitoxins. SpoIISA is a membrane-bound protein, while SpoIISB and SpoIISC are small cytosolic antitoxins, which are able to bind SpoIISA and neutralize its toxicity. In the presented bioinformatics analysis, a taxonomic distribution of the genes of the SpoIISABC system is investigated; their conserved regions and residues are identified; and their phylogenetic relationships are inferred. The SpoIISABC system is part of the core genome in members of the Bacillus genus of the Firmicutes phylum. Its presence in some non-bacillus species is likely the result of horizontal gene transfer. The SpoIISB and SpoIISC antitoxins originated by gene duplications, which occurred independently in the B. subtilis and B. cereus lineages. In the B. cereus lineage, the SpoIIS module is present in two different architectures.\n\nEvolution of the SpoIISABC Toxin-Antitoxin-Antitoxin System in Bacilli.", "token_count": 329, "char_count": 1132, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5963, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:50.646058", "source": { "split": "train_shard_00000", "doc_id": 3979 }, "chunk_id": "train_shard_00000_3979_0", "global_id": 4414 }, { "text": "In the present study, we have analysed the genetic diversity in Kluyveromyces marxianus isolated from Parmigiano Reggiano and Pecorino di Farindola cheesemaking environment. Molecular typing methods inter-RTL fingerprint and mtDNA RFLPs, as well as, sequence diversity and heterozygosity in the intergenic region between KmSSB1 and KmRIO2 genes and analysis of the mating locus were applied to 54 K. marxianus strains. Inter-RTL fingerprint revealed a large degree of genetic heterogeneity and clustering allowed differentiation of K. marxianus strains from different geographical origins. In general, inter-LTR profiles were more discriminating than RFLPs of mtDNA; however our results also indicate that both techniques could be complementary unveiling different degrees of genetic diversity. Sequence analysis of the intergenic region between KmSSB1 and KmRIO2 genes revealed 26 variable positions in which a double peak could be observed in the sequence chromatogram. Further analysis revealed the presence of heterozygous strains in the K. marxianus population isolated from Parmigiano Reggiano. On the other hand, all strains isolated from Pecorino di Farindola were homozygous. Two very different groups of haplotypes could be observed as well as mixtures between them. Phylogenetic reconstruction divided K. marxianus dairy strains into two separate populations. A few heterozygous strains in an intermediate position between them could also be observed. Mating type locus analysis revealed a large population of diploid strains containing both MATa and MATα alleles and few haploid strains, most of them presenting the MATα allele. Different scenarios explaining the presence and maintaining of homozygous and heterozygous diploids as well as hybrids between them in the Parmigiano Reggiano K. marxianus population are proposed. A principal component analysis supported the large differences between K. marxianus isolated from Parmigiano Reggiano and Pecorino di Farindola.", "token_count": 490, "char_count": 1982, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5143, "quality_score": 0.7571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:51.297557", "source": { "split": "train_shard_00000", "doc_id": 3980 }, "chunk_id": "train_shard_00000_3980_0", "global_id": 4415 }, { "text": "Multilocus analysis reveals large genetic diversity in Kluyveromyces marxianus strains isolated from Parmigiano Reggiano and Pecorino di Farindola cheeses.", "token_count": 42, "char_count": 155, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:51.656163", "source": { "split": "train_shard_00000", "doc_id": 3980 }, "chunk_id": "train_shard_00000_3980_1", "global_id": 4416 }, { "text": "Evidence indicates that the polymorphisms in bile salt export pump (BSEP, encoded by ABCB11) may play an important role in the development of anti-tuberculosis drug-induced liver injury (ATDILI) and we aim to investigate the association between genetic variants of ABCB11 and the risk of ATDILI in a Chinese cohort. A total of 89 tuberculosis patients with ATDILI and 356 matched ATDILI -free patients constituted cases and controls. Genetic polymorphisms of ABCB11 were determined by TaqMan single-nucleotide polymorphism (SNP) genotyping assay. Odds ratio (OR) with 95% confidence intervals (CIs) was estimated by conditional logistic regression model. There were no significant differences in genotype frequencies of ABCB11 between cases and controls. In the subgroup analysis, polymorphisms of rs2287616 were found to be associated with cholestatic/mixed pattern of liver injury under dominant and addictive model (OR = 3.84, 95% CI:1.16-12.75, P = 0.028 and OR = 2.51, 95% CI:1.12-5.62, P = 0.025, respectively), however the significance disappeared after Bonferroni correction. This study suggested that genetic variants of ABCB11 gene might contribute to anti-tuberculosis drug-induced cholestatic liver injury in Chinese patients. Studies in larger, varied populations are required to confirm these findings.\n\nRole of polymorphic bile salt export pump (BSEP, ABCB11) transporters in anti-tuberculosis drug-induced liver injury in a Chinese cohort.", "token_count": 448, "char_count": 1455, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8068, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:52.289730", "source": { "split": "train_shard_00000", "doc_id": 3981 }, "chunk_id": "train_shard_00000_3981_0", "global_id": 4417 }, { "text": "Whole genome sequencing (WGS) is currently becoming the method of choice for characterization of Listeria monocytogenes isolates in national reference laboratories (NRLs). WGS is superior with regards to accuracy, resolution and analysis speed in comparison to several other methods including serotyping, PCR, pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), multilocus variable number tandem repeat analysis (MLVA), and multivirulence-locus sequence typing (MVLST), which have been used thus far for the characterization of bacterial isolates (and are still important tools in reference laboratories today) to control and prevent listeriosis, one of the major sources of foodborne diseases for humans. Backward compatibility of WGS to former methods can be maintained by extraction of the respective information from WGS data. Serotyping was the first subtyping method for L. monocytogenes capable of differentiating 12 serovars and national reference laboratories still perform serotyping and PCR-based serogrouping as a first level classification method for Listeria monocytogenes surveillance. Whole genome sequence based core genome MLST analysis of a L. monocytogenes collection comprising 172 isolates spanning all 12 serotypes was performed for serogroup determination. These isolates clustered according to their serotypes and it was possible to group them either into the IIa, IIc, IVb or IIb clusters, respectively, which were generated by minimum spanning tree (MST) and neighbor joining (NJ) tree data analysis, demonstrating the power of the new approach.\n\nWhole genome sequence-based serogrouping of Listeria monocytogenes isolates.", "token_count": 402, "char_count": 1674, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:52.908195", "source": { "split": "train_shard_00000", "doc_id": 3982 }, "chunk_id": "train_shard_00000_3982_0", "global_id": 4418 }, { "text": "Staphylococcus aureus is a preeminent bacterial pathogen capable of colonizing diverse ecological niches within its human host. We describe here the pangenome of S. aureus based on analysis of genome sequences from 64 strains of S. aureus spanning a range of ecological niches, host types, and antibiotic resistance profiles. Based on this set, S. aureus is expected to have an open pangenome composed of 7,411 genes and a core genome composed of 1,441 genes. Metabolism was highly conserved in this core genome; however, differences were identified in amino acid and nucleotide biosynthesis pathways between the strains. Genome-scale models (GEMs) of metabolism were constructed for the 64 strains of S. aureus These GEMs enabled a systems approach to characterizing the core metabolic and panmetabolic capabilities of the S. aureus species. All models were predicted to be auxotrophic for the vitamins niacin (vitamin B3) and thiamin (vitamin B1), whereas strain-specific auxotrophies were predicted for riboflavin (vitamin B2), guanosine, leucine, methionine, and cysteine, among others. GEMs were used to systematically analyze growth capabilities in more than 300 different growth-supporting environments. The results identified metabolic capabilities linked to pathogenic traits and virulence acquisitions. Such traits can be used to differentiate strains responsible for mild vs. severe infections and preference for hosts (e.g., animals vs. humans). Genome-scale analysis of multiple strains of a species can thus be used to identify metabolic determinants of virulence and increase our understanding of why certain strains of this deadly pathogen have spread rapidly throughout the world.\n\nComparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.", "token_count": 467, "char_count": 1841, "word_count": 261, "semantic_coherence": 1, "information_density": 0.59, "quality_score": 0.795, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:53.546526", "source": { "split": "train_shard_00000", "doc_id": 3983 }, "chunk_id": "train_shard_00000_3983_0", "global_id": 4419 }, { "text": "To understand the bioaccessibility of the flavonoid quercetin we studied its interaction with bile salt micelles. The environmental sensitivity of quercetin's UV-visible absorption spectrum gave information about quercetin partitioning. Two quercetin absorption peaks gave complementary information: Peak A (240-280nm) on the intermicellar phase and Peak B (340-440nm) on the micellar phase. Thus, by altering pH, we showed that only non-ionised quercetin partitions into micelles. We validated our interpretation by studying quercetin's interaction with SDS micelles. Pyrene fluorescence and the quercetin UV-visible spectra show that the adsorption site for pyrene and quercetin in bile salt micelles is more hydrophobic than that for SDS micelles. Also, both quercetin and pyrene reported a higher critical micelle concentration for bile salts than for SDS. Our method of using a flavonoid as an intrinsic probe, is generally applicable to other lipophilic bioactives, whenever they have observable environmental dependent properties.\n\nQuercetin solubilisation in bile salts: A comparison with sodium dodecyl sulphate.", "token_count": 294, "char_count": 1121, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:54.110920", "source": { "split": "train_shard_00000", "doc_id": 3984 }, "chunk_id": "train_shard_00000_3984_0", "global_id": 4420 }, { "text": "This is the first Romanian investigation of oral candidosis in patients suffering of HIV-infection or type 1 diabetes mellitus (T1DM). Candida albicans was the dominant species in both types of isolates: n = 14 (46.7%) in T1DM, n = 60 (69.8%) in HIV. The most frequent non-albicans Candida spp. were Candida kefyr (n = 6; 20%) in T1DM and Candida dubliniensis (n = 8; 9.3%) in HIV. Resistance to fluconazole was detected only in the HIV non-albicans Candida group (n = 8; 9.3%). All isolates were susceptible to VOR. The experimental drug MXP had MIC values equal or close to the ones of VOR. Echinocandin resistance was more frequent than azole resistance.\n\nEtiologic Agents and Antifungal Susceptibility of Oral Candidosis from Romanian patients with HIV-infection or type 1 diabetes mellitus.", "token_count": 252, "char_count": 795, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:54.590003", "source": { "split": "train_shard_00000", "doc_id": 3985 }, "chunk_id": "train_shard_00000_3985_0", "global_id": 4421 }, { "text": "Lipids play an important role in the diet of preterm and term infants providing a key energy source and essential lipid components for development. While a lot is known about adult lipid digestion, our understanding of infant digestion physiology is still incomplete, the greatest gap being on the biochemistry of the small intestine, particularly the activity and relative importance of the various lipases active in the intestine. The literature has been reviewed to identify the characteristics of lipid digestion of preterm and term infants, but also to better understand the physiology of the infant gastrointestinal tract compared to adults that impacts the absorption of lipids. The main differences are a higher gastric pH, submicellar bile salt concentration, a far more important role of gastric lipases as well as differences at the level of the intestinal barrier. Importantly, the consequences of improper in vitro replication of gastric digestions conditions (pH and lipase specificity) are demonstrated using examples from the most recent of studies. It is true that some animal models could be adapted to study infant lipid digestion physiology, however the ethical relevance of such models is questionable, hence the development of accurate in vitro models is a must. In vitro models that combine up to date knowledge of digestion biochemistry with intestinal cells in culture are the best choice to replicate digestion and absorption in infant population, this would allow the adaptation of infant formula for a better digestion and absorption of dietary lipids by preterm and term infants.\n\nInfant digestion physiology and the relevance of in vitro biochemical models to test infant formula lipid digestion.", "token_count": 371, "char_count": 1726, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5564, "quality_score": 0.7782, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:55.187048", "source": { "split": "train_shard_00000", "doc_id": 3986 }, "chunk_id": "train_shard_00000_3986_0", "global_id": 4422 }, { "text": "The genomes of many filamentous fungi consist of a 'core' part containing conserved genes essential for normal development as well as conditionally dispensable (CD) or lineage-specific (LS) chromosomes. In the plant-pathogenic fungus Fusarium oxysporum f. sp. lycopersici, one LS chromosome harbours effector genes that contribute to pathogenicity. We employed flow cytometry to select for events of spontaneous (partial) loss of either the two smallest LS chromosomes or two different core chromosomes. We determined the rate of spontaneous loss of the 'effector' LS chromosome in vitro at around 1 in 35 000 spores. In addition, a viable strain was obtained lacking chromosome 12, which is considered to be a part of the core genome. We also isolated strains carrying approximately 1-Mb deletions in the LS chromosomes and in the dispensable core chromosome. The large core chromosome 1 was never observed to sustain deletions over 200 kb. Whole-genome sequencing revealed that some of the sites at which the deletions occurred were the same in several independent strains obtained for the two chromosomes tested, indicating the existence of deletion hotspots. For the core chromosome, this deletion hotspot was the site of insertion of the marker used to select for loss events. Loss of the core chromosome did not affect pathogenicity, whereas loss of the effector chromosome led to a complete loss of pathogenicity.\n\nDispensable chromosomes in Fusarium oxysporum f. sp. lycopersici.", "token_count": 382, "char_count": 1487, "word_count": 228, "semantic_coherence": 1, "information_density": 0.557, "quality_score": 0.7785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:55.761141", "source": { "split": "train_shard_00000", "doc_id": 3987 }, "chunk_id": "train_shard_00000_3987_0", "global_id": 4423 }, { "text": "Three bacteriophages (RD-1410W1-01, RD-1410Ws-07, and DS-1410Ws-06) were isolated from the surface water of Sanya Bay, northern South China Sea, on two marine bacteria type strains of the Roseobacter lineage. These phages have an isometric head and a short tail, morphologically belonging to the Podoviridae family. Two of these phages can infect four of seven marine roseobacter strains tested and the other one can infect three of them, showing relatively broader host ranges compared to known N4-like roseophages. One-step growth curves showed that these phages have similar short latent periods (1-2 h) but highly variable burst sizes (27-341 pfu cell(-1)). Their complete genomes show high level of similarities to known N4-like roseophages in terms of genome size, G + C content, gene content, and arrangement. The morphological and genomic features of these phages indicate that they belong to the N4likevirus genus. Moreover, comparative genomic analysis based on 43 N4-like phages (10 roseobacter phages and 33 phages infecting other lineages of bacteria) revealed a core genome of 18 genes shared by all the 43 phages and 38 genes shared by all the ten roseophages. The 38 core genes of N4-like roseophages nearly make up 70 % of each genome in length. Phylogenetic analysis based on the concatenated core gene products showed that our phage isolates represent two new phyletic branches, suggesting the broad genetic diversity of marine N4-like roseophages remains.\n\nCharacterization and Complete Genome Sequences of Three N4-Like Roseobacter Phages Isolated from the South China Sea.", "token_count": 427, "char_count": 1594, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:56.388404", "source": { "split": "train_shard_00000", "doc_id": 3988 }, "chunk_id": "train_shard_00000_3988_0", "global_id": 4424 }, { "text": "We isolated, identified and characterized yeast strains from grapes, and their fermented musts, sampled in the small island of Linosa, where there are no wineries and therefore the possibility of territory contamination by industrial strains is minimal. By traditional culture-dependent methods, we isolated 3805 colonies, distinguished by molecular methods in 17 different species. Five hundred and forty-four isolates were analysed for the main oenological characteristics such as fermentative vigour with and without sulphites, sugar consumption and production of alcohol, volatile acidity, hydrogen sulphide, glycerol and β-glucosidase. This analysis identified Kluyveromyces marxianus (seldomly used in winemaking) as the most interesting candidate yeast for the production of innovative wines.\n\nIsolation, identification and oenological characterization of non-Saccharomyces yeasts in a Mediterranean island.", "token_count": 208, "char_count": 914, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:56.857261", "source": { "split": "train_shard_00000", "doc_id": 3989 }, "chunk_id": "train_shard_00000_3989_0", "global_id": 4425 }, { "text": "We aimed to investigate the frequency of oral yeast colonization (OYC) and the risk factors for patients who received continuous ambulatory peritoneal dialysis (CAPD) or hemodialysis (HD) or were renal transplant recipients (RTRs). The patients admitted to the Nephrology Clinic at Ataturk University Medical School from January through April 2013 were included in the study. A questionnaire about risk factors was filled out, and swab cultures were taken from the tongue surface of each participant. OYC was detected in 32.1% of the RTRs, 40% of the HD patients, 20.9% of the CAPD patients, and 18% of the healthy control (HC) group. Of the 42 yeast strains isolated from the renal replacement therapy groups, 26 strains (61.9%) were Candida albicans, nine (21.4%) were Candida glabrata, two (4.7%) were Candida krusei, two (4.7%) were Candida kefyr, one (2.38%) was Candida parapsilosis, and two (4.7%) were Geotrichum candidum. Risk factors for OYC in the RTRs group included antibiotic use and the presence of dental prostheses; however, in patients with chronic renal failure undergoing CAPD, only the presence of dental prostheses was found to be a statistically significant risk factor. Although OYC was mostly detected in patients with chronic kidney disease (undergoing HD, a variety of isolated yeast strains in the RTRs was noted. The rates of OYC and isolated Candida species in CAPD were similar to those of the HC group.\n\nOral yeast colonization in peritoneal dialysis and hemodialysis patients and renal transplant recipients.", "token_count": 429, "char_count": 1541, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5394, "quality_score": 0.7697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:57.502453", "source": { "split": "train_shard_00000", "doc_id": 3990 }, "chunk_id": "train_shard_00000_3990_0", "global_id": 4426 }, { "text": "The preferentially respiring and thermotolerant yeast Kluyveromyces marxianus is an emerging host for heterologous protein synthesis, surpassing the traditional preferentially fermenting yeast Saccharomyces cerevisiae in some important aspects: K . marxianus can grow at temperatures 10 °C higher than S. cerevisiae, which may result in decreased costs for cooling bioreactors and reduced contamination risk; has ability to metabolize a wider variety of sugars, such as lactose and xylose; is the fastest growing eukaryote described so far; and does not require special cultivation techniques (such as fed-batch) to avoid fermentative metabolism. All these advantages exist together with a high secretory capacity, performance of eukaryotic post-translational modifications, and with a generally regarded as safe (GRAS) status. In the last years, replication origins from several Kluyveromyces spp. have been used for the construction of episomal vectors, and also integrative strategies have been developed based on the tendency for non-homologous recombination displayed by K. marxianus. The recessive URA3 auxotrophic marker and the dominant Kan(R) are mostly used for selection of transformed cells, but other markers have been made available. Homologous and heterologous promoters and secretion signals have been characterized, with the K. marxianus INU1 expression and secretion system being of remarkable functionality. The efficient synthesis of roughly 50 heterologous proteins has been demonstrated, including one thermophilic enzyme. In this mini-review, we summarize the physiological characteristics of K. marxianus relevant for its use in the efficient synthesis of heterologous proteins, the efforts performed hitherto in the development of a molecular toolbox for this purpose, and some successful examples.\n\nKluyveromyces marxianus as a host for heterologous protein synthesis.", "token_count": 445, "char_count": 1894, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [ "URA3", "INU1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:58.151214", "source": { "split": "train_shard_00000", "doc_id": 3991 }, "chunk_id": "train_shard_00000_3991_0", "global_id": 4427 }, { "text": "Conversion of byproduct from biodiesel production glycerol to high-value compounds is of great importance. Ethanol is considered a promising product of glycerol bioconversion. The methylotrophic thermotolerant yeast Ogataea (Hansenula) polymorpha is of great interest for this purpose as the glycerol byproduct contains methanol and heavy metals as contaminants, and this yeast utilizes methanol and is relatively resistant to heavy metals. Besides, O. polymorpha shows robust growth on glycerol and produces ethanol from various carbon sources. The thermotolerance of this yeast is an additional advantage, allowing increased fermentation temperature to 45-48 °C, leading to increased rate of the fermentation process and a fall in the cost of distillation. The wild-type strain of O. polymorpha produces insignificant amounts of ethanol from glycerol (0.8 g/l). Overexpression of PDC1 coding for pyruvate decarboxylase enhanced ethanol production up to 3.1 g/l, whereas simultaneous overexpression of PDC1 and ADH1 (coding for alcohol dehydrogenase) led to further increase in ethanol production from glycerol. Moreover, the increased temperature of fermentation up to 45 °C stimulated the production of ethanol from glycerol used as the only carbon source up to 5.0 g/l, which exceeds the data obtained by methylotrophic yeast strains reported so far. Copyright © 2016 John Wiley & Sons, Ltd.\n\nOverexpression of the genes PDC1 and ADH1 activates glycerol conversion to ethanol in the thermotolerant yeast Ogataea (Hansenula) polymorpha.", "token_count": 443, "char_count": 1539, "word_count": 222, "semantic_coherence": 1, "information_density": 0.545, "quality_score": 0.7725, "entities": { "genes": [ "PDC1", "ADH1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:58.826435", "source": { "split": "train_shard_00000", "doc_id": 3992 }, "chunk_id": "train_shard_00000_3992_0", "global_id": 4428 }, { "text": "Hepatitis B virus (HBV) and bile salt metabolism seem tightly connected. HBV enters hepatocytes by binding to sodium taurocholate cotransporting polypeptide (NTCP), the genome of which contains 2 active farnesoid X receptor (FXR) α response elements that participate in HBV transcriptional activity. We investigated in differentiated HepaRG cells and in primary human hepatocytes (PHHs) effects of FXR activation on HBV replication and of infection on the FXR pathway. In HepaRG cells, FXR agonists (6-ethyl chenodeoxycholic acid and GW4064), but no antagonist, and an FXR-unrelated bile salt inhibited viral mRNA, DNA, and protein production (IC50, 0.1-0.5 μM) and reduced covalently closed circular DNA pool size. These effects were independent of the NTCP inhibitor cyclosporine-A, which suggests inhibition occurred at a postentry step. Similar results were obtained in PHHs with GW4064. Infection of these cells increased expression of FXR and modified expression of FXR-regulated genes SHP, APOA1, NTCP, CYP7A1, and CYP8B1 with a more pronounced effect in PHHs than in HepaRG cells. FXR agonists reversed all but one of the HBV-induced FXR gene profile modifications. HBV replication and FXR regulation seem to be interdependent, and altered bile salt metabolism homeostasis might contribute to the persistence of HBV infection.-Radreau, P., Porcherot, M., Ramière, C., Mouzannar, K., Lotteau, V., André, P. Reciprocal regulation of farnesoid X receptor α activity and hepatitis B virus replication in differentiated HepaRG cells and primary human hepatocytes.\n\nReciprocal regulation of farnesoid X receptor α activity and hepatitis B virus replication in differentiated HepaRG cells and primary human hepatocytes.", "token_count": 505, "char_count": 1720, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5904, "quality_score": 0.7952, "entities": { "genes": [ "GW4064", "APOA1", "IC50" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:38:59.491364", "source": { "split": "train_shard_00000", "doc_id": 3993 }, "chunk_id": "train_shard_00000_3993_0", "global_id": 4429 }, { "text": "Major depressive disorder (MDD) is a highly prevalent and debilitating mental illness with substantial impairments in quality of life and functioning. However, the pathophysiology of major depression remains poorly understood. Combining the brain and body should provide a comprehensive understanding of the etiology of MDD. As the largest internal organ of the human body, the liver has an important function, yet no proteomic study has assessed liver protein expression in a preclinical model of depression. Using the chronic unpredictable mild stress (CUMS) mouse model of depression, differential protein expression between CUMS and control (CON) mice was examined in the liver proteome using isobaric tag for relative and absolute quantitation (iTRAQ) coupled with tandem mass spectrometry. More than 4000 proteins were identified and 66 most significantly differentiated proteins were used for further bioinformatic analysis. According to the ingenuity pathway analysis (IPA), we found that proteins related to the inflammation response, immune regulation, lipid metabolism and NFκB signaling network were altered by CUMS. Moreover, four proteins closely associated with these processes, hemopexin, haptoglobin, cytochrome P450 2A4 (CYP2A4) and bile salt sulfotransferase 1 (SULT2A1), were validated by western blotting. In conclusion, we report, for the first time, the liver protein expression profile in the CUMS mouse model of depression. Our findings provide novel insight (liver-brain axis) into the multifaceted mechanisms of major depressive disorder.\n\nQuantitative proteomics analysis of the liver reveals immune regulation and lipid metabolism dysregulation in a mouse model of depression.", "token_count": 399, "char_count": 1705, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:00.116621", "source": { "split": "train_shard_00000", "doc_id": 3994 }, "chunk_id": "train_shard_00000_3994_0", "global_id": 4430 }, { "text": "Feeding strategies are critical for healthy growth in preterm infants. Bile salt-stimulated lipase (BSSL), present in human milk, is important for fat digestion and absorption but is inactivated during pasteurization and absent in formula. This study evaluated if recombinant human BSSL (rhBSSL) improves growth in preterm infants when added to formula or pasteurized breast milk.\n\nRecombinant Bile Salt-Stimulated Lipase in Preterm Infant Feeding: A Randomized Phase 3 Study.", "token_count": 120, "char_count": 476, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7794, "quality_score": 0.8897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:00.501002", "source": { "split": "train_shard_00000", "doc_id": 3995 }, "chunk_id": "train_shard_00000_3995_0", "global_id": 4431 }, { "text": "Bifidobacteria are important members of the human gastrointestinal tract that promote the establishment of a healthy microbial consortium in the gut of infants. Recent studies have established that the Bifidobacterium genus is a polymorphic phylogenetic clade, which encompasses a diversity of species and subspecies that encode a broad range of proteins implicated in complex and non-digestible carbohydrate uptake and catabolism, ranging from human breast milk oligosaccharides, to plant fibers. Recent genomic studies have created a need to properly place Bifidobacterium species in a phylogenetic tree. Current approaches, based on core-genome analyses come at the cost of intensive sequencing and demanding analytical processes. Here, we propose a typing method based on sequences of glycolysis genes and the proteins they encode, to provide insights into diversity, typing, and phylogeny in this complex and broad genus. We show that glycolysis genes occur broadly in these genomes, to encode the machinery necessary for the biochemical spine of the cell, and provide a robust phylogenetic marker. Furthermore, glycolytic sequences-based trees are congruent with both the classical 16S rRNA phylogeny, and core genome-based strain clustering. Furthermore, these glycolysis markers can also be used to provide insights into the adaptive evolution of this genus, especially with regards to trends toward a high GC content. This streamlined method may open new avenues for phylogenetic studies on a broad scale, given the widespread occurrence of the glycolysis pathway in bacteria, and the diversity of the sequences they encode.\n\nPhylogenetic Analysis of the Bifidobacterium Genus Using Glycolysis Enzyme Sequences.", "token_count": 418, "char_count": 1720, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6024, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:01.127780", "source": { "split": "train_shard_00000", "doc_id": 3996 }, "chunk_id": "train_shard_00000_3996_0", "global_id": 4432 }, { "text": "The aim of the present study is to evaluate the probiotic attributes of Bacillus subtilis AMS6 isolated from fermented soybean (Churpi). This isolate exhibited tolerance to low pH (pH 2.0) and bile salt (0.3%), capability to autoaggregate and coaggregate. AMS6 also showed highest antibacterial activity against the pathogenic indicator strain Salmonella enterica typhimurium (MTCC 1252) and susceptibility towards different antibiotics tested. The isolate was effective in inhibiting the adherence of food borne pathogens to Caco-2 epithelial cell lines, and was also found to be non-hemolytic which further strengthen the candidature of the isolate as a potential probiotic. Further studies revealed B. subtilis AMS6 showed cellulolytic activity (0.54±0.05 filter paper units mL(-1)) at 37°C. The isolate was found to hydrolyze carboxymethyl cellulose, filter paper and maize (Zea mays) straw. The maize straw digestion was confirmed by scanning electron microscopy studies. The isolate was able to degrade filter paper within 96h of incubation. A full length cellulase gene of AMS6 was amplified using degenerate primers consisting of 1499 nucleotides. The ORF encoded for a protein of 499 amino acids residues with a predicted molecular mass of 55.04kDa. The amino acids sequence consisted of a glycosyl hydrolase family 5 domain at N-terminal; Glycosyl hydrolase catalytic core and a CBM-3 cellulose binding domain at its C terminal. The study suggests potential probiotic B. subtilis AMS6 as a promising candidate envisaging its application as an animal feed additive for enhanced fiber digestion and gut health of animal.\n\nCellulolytic potential of probiotic Bacillus Subtilis AMS6 isolated from traditional fermented soybean (Churpi): An in-vitro study with regards to application as an animal feed additive.", "token_count": 506, "char_count": 1816, "word_count": 267, "semantic_coherence": 1, "information_density": 0.618, "quality_score": 0.809, "entities": { "genes": [ "AMS6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:01.798059", "source": { "split": "train_shard_00000", "doc_id": 3997 }, "chunk_id": "train_shard_00000_3997_0", "global_id": 4433 }, { "text": "Engineered Kluyveromyces marxianus strains were constructed through over-expression of various transporters for simultaneous co-fermentation of glucose and xylose. The glucose was converted into ethanol, whereas xylose was converted into xylitol which has higher value than ethanol. Over-expressing xylose-specific transporter ScGAL2-N376F mutant enabled yeast to co-ferment glucose and xylose and the co-fermentation ability was obviously improved through increasing ScGAL2-N376F expression. The production of glycerol was blocked and acetate production was reduced by disrupting gene KmGPD1. The obtained K. marxianus YZJ119 utilized 120g/L glucose and 60g/L xylose simultaneously and produced 50.10g/L ethanol and 55.88g/L xylitol at 42°C. The yield of xylitol from consumed xylose was over 98% (0.99g/g). Through simultaneous saccharification and co-fermentation at 42°C, YZJ119 produced a maximal concentration of 44.58g/L ethanol and 32.03g/L xylitol or 29.82g/L ethanol and 31.72g/L xylitol, respectively, from detoxified or non-detoxified diluted acid pretreated corncob.\n\nSimultaneous fermentation of glucose and xylose at elevated temperatures co-produces ethanol and xylitol through overexpression of a xylose-specific transporter in engineered Kluyveromyces marxianus.", "token_count": 417, "char_count": 1280, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8025, "entities": { "genes": [ "YZJ119" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:02.426164", "source": { "split": "train_shard_00000", "doc_id": 3998 }, "chunk_id": "train_shard_00000_3998_0", "global_id": 4434 }, { "text": "The shark bile alcohol, 5β-scymnol, protects mice from the hepatotoxic effects of paracetamol (APAP) overdose. To elucidate the hepatoprotective structural moiety of scymnol, we compared its effect with that of its analogue and natural bile salt, sodium scymnol sulfate, in a clinically relevant model of APAP-induced toxicity. Exposure of healthy male Swiss mice to a toxic overdose of APAP (350 mg/kg, ip) significantly increased serum hepatocellular enzyme activities, decreased hepatocellular glutathione (GSH) levels, and induced severe centrilobular hepatocellular necrosis. Repeated low-dose scymnol (5 mg/kg/day for 7 days, ip) significantly reduced the extent of APAP-induced hepatotoxicity without preventing GSH depletion. Sodium scymnol sulfate, which lacks the tri-hydroxyl-substituted aliphatic side chain of scymnol, failed to reduce the APAP hepatotoxicity or prevent GSH depletion when tested under the same experimental conditions. We conclude that the tri-hydroxyl-substituted aliphatic side chain is the hepatoprotective structural moiety of 5β-scymnol that suppresses APAP-induced cytotoxicity in mice.\n\nElucidation of the hepatoprotective moiety of 5β-scymnol that suppresses paracetamol toxicity in mice.", "token_count": 384, "char_count": 1227, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6358, "quality_score": 0.8179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:03.044476", "source": { "split": "train_shard_00000", "doc_id": 3999 }, "chunk_id": "train_shard_00000_3999_0", "global_id": 4435 }, { "text": "Exposure to long-term environmental changes across >100s of generations results in adapted phenotypes, but little is known about how metabolic and transcriptional responses are optimized in these processes. Here, we show that thermotolerant yeast strains selected by adaptive laboratory evolution to grow at increased temperature, activated a constitutive heat stress response when grown at the optimal ancestral temperature, and that this is associated with a reduced growth rate. This preventive response was perfected by additional transcriptional changes activated when the cultivation temperature is increased. Remarkably, the sum of global transcriptional changes activated in the thermotolerant strains when transferred from the optimal to the high temperature, corresponded, in magnitude and direction, to the global changes observed in the ancestral strain exposed to the same transition. This demonstrates robustness of the yeast transcriptional program when exposed to heat, and that the thermotolerant strains streamlined their path to rapidly and optimally reach post-stress transcriptional and metabolic levels. Thus, long-term adaptation to heat improved yeasts ability to rapidly adapt to increased temperatures, but this also causes a trade-off in the growth rate at the optimal ancestral temperature.\n\nThermotolerant yeasts selected by adaptive evolution express heat stress response at 30 °C.", "token_count": 291, "char_count": 1411, "word_count": 196, "semantic_coherence": 1, "information_density": 0.551, "quality_score": 0.7755, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:03.599576", "source": { "split": "train_shard_00000", "doc_id": 4000 }, "chunk_id": "train_shard_00000_4000_0", "global_id": 4436 }, { "text": "Microencapsulation is an effective way to improve the survival of probiotics in simulated gastrointestinal (GI) conditions and yoghurt. In this study, microencapsulation of Lactobacillus rhamnosus GG (LGG) was prepared by first cross-linking of soy protein isolate (SPI) using transglutaminase (TGase), followed by embedding the bacteria in cross-linked SPI, and then freeze-drying. The survival of microencapsulated LGG was evaluated in simulated GI conditions and yoghurt. The results showed that a high microencapsulation yield of 67.4% was obtained. The diameter of the microencapsulated LGG was in the range of 52.83 to 275.16 μm. Water activity did not differ between free and microencapsulated LGG after freeze-drying. The survival of microencapsulated LGG under simulated gastric juice (pH 2.5 and 3.6), intestinal juice (0.3% and 2% bile salt) and storage at 4 °C were significantly higher than that of free cells. The survival of LGG in TGase cross-linked SPI microcapsules was also improved to 14.5 ± 0.5% during storage in yoghurt. The microencapsulation of probiotics by TGase-treated SPI can be a suitable alternative to polysaccharide gelation technologies.\n\nMicroencapsulation of Lactobacillus rhamnosus GG by Transglutaminase Cross-Linked Soy Protein Isolate to Improve Survival in Simulated Gastrointestinal Conditions and Yoghurt.", "token_count": 392, "char_count": 1349, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5469, "quality_score": 0.7734, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:04.560883", "source": { "split": "train_shard_00000", "doc_id": 4001 }, "chunk_id": "train_shard_00000_4001_0", "global_id": 4437 }, { "text": "We examine the mechanism of formation of micelles of dihydroxy bile salts using a coarse-grained, implicit solvent model and Langevin dynamics simulations. We find that bile salt micelles primarily form via addition and removal of monomers, similarly to surfactants with typical head-tail molecular structures, and not via a two-stage mechanism - involving formation of oligomers and their subsequent aggregation to form larger micelles - originally proposed for bile salts. The free energy barrier to removal of single bile monomers from micelles is ≈2kBT, much less than what has been observed for head-tail surfactants. Such a low barrier may be biologically relevant: it allows for rapid release of bile monomers into the intestine, possibly enabling the coverage of fat droplets by bile salt monomers and subsequent release of micelles containing fats and bile salts - a mechanism that is not possible for ionic head-tail surfactants of similar critical micellar concentrations.\n\nKinetics of formation of bile salt micelles from coarse-grained Langevin dynamics simulations.", "token_count": 249, "char_count": 1079, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5839, "quality_score": 0.7919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:05.045131", "source": { "split": "train_shard_00000", "doc_id": 4002 }, "chunk_id": "train_shard_00000_4002_0", "global_id": 4438 }, { "text": "The changes in structure and catalytic properties of fungal lipases (Candida rugosa, Rhizomucor miehei, Mucor javanicus) were investigated in micellar solutions of bile salts that differ in hydrophilic-lypophilic balance and reaction medium properties. The methods of circular dichroism and tryptophan fluorescence were applied to estimate the changes in peptide structure within complexes with bile salt micelles. Bile salts do not exert a significant influence on the structure of the enzymes under study: in Rh. miehei and M. javanicus lipases the alpha helix content slightly decreased, the influence of bile salts on the C. rugosa structure was not revealed. Despite negligible structural modifications in the enzymes, in bile salt solutions a considerable change in their catalytic properties was observed: an abrupt decrease in catalytic effectiveness. Substrate-bile salts micelles complex formation was demonstrated by the NMR self-diffusion method. The model of a regulation of fungal lipase activity was proposed.\n\n[Structure and Activity of Fungal Lipases in Bile Salt Solutions].", "token_count": 261, "char_count": 1092, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6051, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:05.594184", "source": { "split": "train_shard_00000", "doc_id": 4003 }, "chunk_id": "train_shard_00000_4003_0", "global_id": 4439 }, { "text": "Vibrio cholerae causes cholera, a severe diarrheal disease. Understanding the local genetic diversity and transmission of V. cholerae will improve our ability to control cholera. Vibrio cholerae isolates clustered in genetically related groups (clonal complexes, CC) by multilocus variable tandem-repeat analysis (MLVA) were compared by whole genome sequencing (WGS). Isolates in CC1 had been isolated from two geographical locations. Isolates in a second genetically distinct group, CC2, were isolated only at one location. Using WGS, CC1 isolates from both locations revealed, on average, 43.8 nucleotide differences, while those strains comprising CC2 averaged 19.7 differences. Strains from both MLVA-CCs had an average difference of 106.6. Thus, isolates comprising CC1 were more closely related (P < 10(-6)) to each other than to isolates in CC2. Within a MLVA-CC, after removing all paralogs, alternative alleles were found in all possible combinations on separate chromosomes indicative of recombination within the core genome. Including recombination did not affect the distinctiveness of the MLVA-CCs when measured by WGS. We found that WGS generally reflected the same genetic relatedness of isolates as MLVA, indicating that isolates from the same MLVA-CC shared a more recent common ancestor than isolates from the same location that clustered in a distinct MLVA-CC.\n\nComparison of inferred relatedness based on multilocus variable-number tandem-repeat analysis and whole genome sequencing of Vibrio cholerae O1.", "token_count": 388, "char_count": 1525, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [ "CC2", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:06.213930", "source": { "split": "train_shard_00000", "doc_id": 4004 }, "chunk_id": "train_shard_00000_4004_0", "global_id": 4440 }, { "text": "Conjugative plasmids from the IncHI1 incompatibility group play an important role in transferring antibiotic resistance in Salmonella Typhimurium. However, knowledge of their genome structure or gene expression is limited. In this study, we determined the complete nucleotide sequences of four IncHI1 plasmids transferring resistance to antibiotics by two different next generation sequencing protocols and protein expression by mass spectrometry. Sequence data including additional 11 IncHI1 plasmids from GenBank were used for the definition of the IncHI1 plasmid core-genome and pan-genome. The core-genome consisted of approximately 123 kbp and 122 genes while the total pan-genome represented approximately 600 kbp. When the core-genome sequences were used for multiple alignments, the 15 tested IncHI1 plasmids were separated into two main lineages. GC content in core-genome genes was around 46% and 50% in accessory genome genes. A multidrug resistance region present in all 4 sequenced plasmids extended over 20 kbp and, except for tet(B), the genes responsible for antibiotic resistance were those with the highest GC content. IncHI1 plasmids therefore represent replicons that evolved in low GC content bacteria. From their original host, they spread to Salmonella and during this spread these plasmids acquired multiple accessory genes including those coding for antibiotic resistance. Antibiotic-resistance genes belonged to genes with the highest level of expression and were constitutively expressed even in the absence of antibiotics. This is the likely mechanism that facilitates host cell survival when antibiotics suddenly emerge in the environment.\n\nAntibiotic Resistance, Core-Genome and Protein Expression in IncHI1 Plasmids in Salmonella Typhimurium.", "token_count": 419, "char_count": 1773, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5743, "quality_score": 0.7871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:06.837083", "source": { "split": "train_shard_00000", "doc_id": 4005 }, "chunk_id": "train_shard_00000_4005_0", "global_id": 4441 }, { "text": "We have examined a collection of the free-living marine bacterium Alteromonas genomes with cores diverging in average nucleotide identities ranging from 99.98% to 73.35%, i.e., from microbes that can be considered members of a natural clone (like in a clinical epidemiological outbreak) to borderline genus level. The genomes were largely syntenic allowing a precise delimitation of the core and flexible regions in each. The core was 1.4 Mb (ca. 30% of the typical strain genome size). Recombination rates along the core were high among strains belonging to the same species (37.7-83.7% of all nucleotide polymorphisms) but they decreased sharply between species (18.9-5.1%). Regarding the flexible genome, its main expansion occurred within the boundaries of the species, i.e., strains of the same species already have a large and diverse flexible genome. Flexible regions occupy mostly fixed genomic locations. Four large genomic islands are involved in the synthesis of strain-specific glycosydic receptors that we have called glycotypes. These genomic regions are exchanged by homologous recombination within and between species and there is evidence for their import from distant taxonomic units (other genera within the family). In addition, several hotspots for integration of gene cassettes by illegitimate recombination are distributed throughout the genome. They code for features that give each clone specific properties to interact with their ecological niche and must flow fast throughout the whole genus as they are found, with nearly identical sequences, in different species. Models for the generation of this genomic diversity involving phage predation are discussed.\n\nPangenome Evolution in the Marine Bacterium Alteromonas.", "token_count": 411, "char_count": 1743, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6353, "quality_score": 0.8176, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:07.466459", "source": { "split": "train_shard_00000", "doc_id": 4006 }, "chunk_id": "train_shard_00000_4006_0", "global_id": 4442 }, { "text": "In this study, an inulin-binding module from Bacillus macerans was successfully fused to an exo-inulinase from Kluyveromyces marxianus, creating a hybrid functional enzyme. The recombinant exo-inulinase (rINU), the hybrid enzyme (rINUIBM), and the recombinant inulin-binding module (rIBM) were, respectively, heterologously expressed and biochemically characterized. It was found that both the inulinase activity and the catalytic efficiency (k cat/K m(app)) of the rINUIBM were considerably higher than those of rINU. Though the rINU and the rINUIBM shared the same optimum pH of 4.5, the optimum temperature of the rINUIBM (60 °C) was 5 °C higher than that of the rINU. Notably, the fused IBM significantly enhanced both the pH stability and the thermostability of the rINUIBM, suggesting that the rINUIBM obtained would have more extensive potential applications. Furthermore, the fusion of the IBM could substantially improve the inulin-binding capability of the rINUIBM, which was consistent with the determination of the K m(app). This meant that the fused IBM could play a critical role in the recognition of polysaccharides and enhanced the hydrolase activity of the associated inulinase by increasing enzyme-substrate proximity. Besides, the extra supplement of the independent non-catalytic rIBM could also improve the inulinase activity of the rINU. However, this improvement was much better in case of the fusion. Consequently, the IBM could be designated as a multifunctional domain that was responsible for the activity enhancement, the stabilization, and the substrate binding of the rINUIBM. All these features obtained in this study make the rINUIBM become an attractive candidate for an efficient inulin hydrolysis.\n\nEnhanced exo-inulinase activity and stability by fusion of an inulin-binding module.", "token_count": 460, "char_count": 1819, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5358, "quality_score": 0.7679, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:08.107361", "source": { "split": "train_shard_00000", "doc_id": 4007 }, "chunk_id": "train_shard_00000_4007_0", "global_id": 4443 }, { "text": "Two isolates of a Gram-stain-positive, strictly aerobic, motile, rod-shaped, endospore-forming bacterium were identified during a survey of the Bacillus diversity of the Agriculture Research Service Culture Collection. These strains were originally isolated from soil and have a phenotype of producing a dark pigment on tryptic soy agar. Phylogenetic analysis of the 16S rRNA gene indicated that these strains were related most closely to Bacillus subtilis subsp. inaquosorum (99.7 % similarity) and Bacillus axarquiensis (99.7 %). In phenotypic characterization, the novel strains were found to grow between 17 and 50 °C and can tolerate up to 9 % (w/v) NaCl. Furthermore, the strains grew in media of pH 5.5-10 (optimal growth at pH 7.0-8.0). The predominant cellular fatty acids were anteiso-C15 : 0 (34.8 %) and iso-C15 : 0 (21.9 %). The cell-wall peptidoglycan contained meso-diaminopimelic acid. A draft genome of both strains was completed. The DNA G+C content was 43.8 mol%. A phylogenomic analysis on the core genome of these two new strains and all members of the Bacillus subtilis group revealed these two strains formed a distinct monophyletic clade with the nearest neighbour Bacillus amyloliquefaciens. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations showed the two strains were conspecific (93.8 %), while values with all other species (<31.5 %) were well below the species threshold of 70 %. Based on the consensus of phylogenetic and phenotypic analyses, these strains are considered to represent a novel species within the genus Bacillus, for which the name Bacillus nakamurai sp. nov", "token_count": 518, "char_count": 1621, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:39:08.764831", "source": { "split": "train_shard_00000", "doc_id": 4008 }, "chunk_id": "train_shard_00000_4008_0", "global_id": 4444 }, { "text": "is proposed, with type strain NRRL B-41091T (=CCUG 68786T).\n\nBacillus nakamurai sp. nov., a black-pigment-producing strain.", "token_count": 55, "char_count": 123, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:09.157899", "source": { "split": "train_shard_00000", "doc_id": 4008 }, "chunk_id": "train_shard_00000_4008_1", "global_id": 4445 }, { "text": "Production of probiotic food supplements that are shelf-stable at room temperature has been developed for consumer's convenience, but information on the stability in acid and bile environment is still scarce. Viability and acid and bile tolerance of microencapsulated Bifidobacterium spp. and Lactobacillus acidophilus and 4 commercial probiotic supplements were evaluated. Bifidobacterium and L. acidophilus were encapsulated with casein-based emulsion using spray drying. Water activity (aw ) of the microspheres containing Bifidobacterium or L. acidophilus (SD GM product) was adjusted to 0.07 followed by storage at 25 °C for 10 wk. Encapsulated Bifidobacterium spp. and Lactobacillus acidophilus and 4 commercial probiotic supplement products (AL, GH, RE, and BM) were tested. Since commercial probiotic products contained mixed bacteria, selective media MRS-LP (containing L-cysteine and Na-propionate) and MRS-clindamycin agar were used to grow Bifidobacterium spp. or L. acidophilus, respectively, and to inhibit the growth of other strains. The results showed that aw had a strong negative correlation with the viability of dehydrated probiotics of the 6 products. Viable counts of Bifidobacterium spp. and L. acidophilus of SD GM, AL, and GH were between 8.3 and 9.2 log CFU/g, whereas that of BM and RE were between 6.7 and 7.3 log CFU/g. Bifidobacterium in SD GM, in AL, and in GH products and L. acidophilus in SD GM, in AL, and in BM products demonstrated high tolerance to acid. Most of dehydrated probiotic bacteria were able to survive in bile environment except L. acidophilus in RE product. Exposure to gastric juice influenced bacterial survivability in subsequent bile environment.", "token_count": 479, "char_count": 1702, "word_count": 254, "semantic_coherence": 1, "information_density": 0.563, "quality_score": 0.7815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:09.822282", "source": { "split": "train_shard_00000", "doc_id": 4009 }, "chunk_id": "train_shard_00000_4009_0", "global_id": 4446 }, { "text": "Viability, Acid and Bile Tolerance of Spray Dried Probiotic Bacteria and Some Commercial Probiotic Supplement Products Kept at Room Temperature.", "token_count": 39, "char_count": 144, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:10.187498", "source": { "split": "train_shard_00000", "doc_id": 4009 }, "chunk_id": "train_shard_00000_4009_1", "global_id": 4447 }, { "text": "Ischemic-type biliary lesions (ITBL) are the most troublesome biliary complication after liver transplantation (LT) from non-heart-beating donors (NHBD) and frequently result in death or re-transplantation. In transplantation process, warm ischemia (WI) in the donor, cold ischemia and reperfusion injury in the recipient altogether inducing ischemia-reperfusion injury (IRI) is strongly associated with ITBL. This is a cascading injury process, involving in a complex series of inter-connecting events causing variety of cells activation and damage associated with the massive release of inflammatory cytokines and generation of reactive oxygen species (ROS). These damaged cells such as sinusoidal endothelial cells (SECs), Kupffer cells (KCs), hepatocytes and biliary epithelial cells (BECs), coupled with immunological injury and bile salt toxicity altogether contribute to ITBL in NHBD LT. Developed therapeutic strategies to attenuate IRI are essential to improve outcome after LT. Among them, single pharmaceutical interventions blocking a specific pathway of IRI in rodent models play an absolutely dominant role, and show a beneficial effect in some given controlled experiments. But this will likely prove ineffective in complex clinical setting in which more risk parameters are involved. Therefore, we intend to design a multidrug cocktail approach to block different pathways on more than one stage (WI, cold ischemia and reperfusion) of the process of IRI-induced ITBL simultaneously. This multidrug cocktail will include six drugs containing streptokinase, epoprostenol, thiazolidinediones (TZDs), N-Acetylcysteine (NAC), hemin and tauroursodeoxycholic acid (TUDC). These drugs show protective effects by targeting the different key events of IRI, such as anti-inflammatory, anti-fibrosis, anti-oxidation, anti-apoptosis and reduced bile salt toxicity. Ideally, the compounds, dosage, and method of application of drugs included in cocktail should not be definitive. We can consider removing or adding some drugs to the proposed cocktail based on further research", "token_count": 512, "char_count": 2078, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6713, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:10.856459", "source": { "split": "train_shard_00000", "doc_id": 4010 }, "chunk_id": "train_shard_00000_4010_0", "global_id": 4448 }, { "text": "But given the multitude of different combinations, it is extremely difficult to determent which combination is the optimization design. Nevertheless, regardless of the difficulty, our multidrug cocktail approach designed to block different mechanisms on more than one stage of IRI simultaneously may represent a future preventive and therapeutic avenue for ITBL.\n\nA multidrug cocktail approach attenuates ischemic-type biliary lesions in liver transplantation from non-heart-beating donors.", "token_count": 103, "char_count": 490, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8308, "quality_score": 0.9154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:11.243624", "source": { "split": "train_shard_00000", "doc_id": 4010 }, "chunk_id": "train_shard_00000_4010_1", "global_id": 4449 }, { "text": "Bile salt hydrolase (BSH) is a gut-bacterial enzyme that negatively influences host fat digestion and energy harvesting. The BSH enzyme activity functions as a gateway reaction in the small intestine by the deconjugation of glycine-conjugated or taurine-conjugated bile acids. Extensive gut-microbiota studies have suggested that BSH is a key mechanistic microbiome target for the development of novel non-antibiotic food additives to improve animal feed production and for the design of new measures to control obesity in humans. However, research on BSH is still in its infancy, particularly in terms of the structural basis of BSH function, which has hampered the development of BSH-based strategies for improving human and animal health. As an initial step towards the structure-function analysis of BSH, C-terminally His-tagged BSH from Lactobacillus salivarius NRRL B-30514 was crystallized in this study. The 1.90 Å resolution crystal structure of L. salivarius BSH was determined by molecular replacement using the structure of Clostridium perfringens BSH as a starting model. It revealed this BSH to be a member of the N-terminal nucleophile hydrolase superfamily. Crystals of apo BSH belonged to space group P21212, with unit-cell parameters a = 90.79, b = 87.35, c = 86.76 Å (PDB entry 5hke). Two BSH molecules packed perfectly as a dimer in one asymmetric unit. Comparative structural analysis of L. salivarius BSH also identified potential residues that contribute to catalysis and substrate specificity.\n\nCrystal structure of bile salt hydrolase from Lactobacillus salivarius.", "token_count": 438, "char_count": 1590, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:11.875319", "source": { "split": "train_shard_00000", "doc_id": 4011 }, "chunk_id": "train_shard_00000_4011_0", "global_id": 4450 }, { "text": "Economically important plants contain large amounts of inulin. Disposal of waste resulting from their processing presents environmental issues. Finding microorganisms capable of converting inulin waste to biofuel and valuable co-products at the processing site would have significant economic and environmental impact. We evaluated the ability of two mutant strains of Kluyveromyces marxianus (Km7 and Km8) to utilize inulin for ethanol production. In glucose medium, both strains consumed all glucose and produced 0.40 g ethanol/g glucose at 24 h. In inulin medium, Km7 exhibited maximum colony forming units (CFU)/mL and produced 0.35 g ethanol/g inulin at 24 h, while Km8 showed maximum CFU/mL and produced 0.02 g ethanol/g inulin at 96 h. At 24 h in inulin + glucose medium, Km7 produced 0.40 g ethanol/g (inulin + glucose) and Km8 produced 0.20 g ethanol/g (inulin + glucose) with maximum CFU/mL for Km8 at 72 h, 40 % of that for Km7 at 36 h. Extracellular inulinase activity at 6 h for both Km7 and Km8 was 3.7 International Units (IU)/mL.\n\nGrowth, ethanol production, and inulinase activity on various inulin substrates by mutant Kluyveromyces marxianus strains NRRL Y-50798 and NRRL Y-50799.", "token_count": 412, "char_count": 1199, "word_count": 189, "semantic_coherence": 1, "information_density": 0.5503, "quality_score": 0.7751, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:12.491615", "source": { "split": "train_shard_00000", "doc_id": 4012 }, "chunk_id": "train_shard_00000_4012_0", "global_id": 4451 }, { "text": "Cheese whey fermentation to ethanol using immobilized Kluyveromyces marxianus cells was investigated in batch and continuous operation. In batch fermentation, the yeast cells were immobilized in carboxymethyl cellulose (CMC) polymer and also synthesized graft copolymer of CMC with N-vinyl-2-pyrrolidone, denoted as CMC-g-PVP, and the efficiency of the two developed cell entrapped beads for lactose fermentation to ethanol was examined. The yeast cells immobilized in CMC-g-PVP performed slightly better than CMC with ethanol production yields of 0.52 and 0.49 g ethanol/g lactose, respectively. The effect of supplementation of cheese whey with lactose (42, 70, 100 and 150 g/l) on fermentative performance of K. marxianus immobilized in CMC beads was considered and the results were used for kinetic studies. The first order reaction model was suitable to describe the kinetics of substrate utilization and modified Gompertz model was quite successful to predict the ethanol production. For continuous ethanol fermentation, a packed-bed immobilized cell reactor (ICR) was operated at several hydraulic retention times; HRTs of 11, 15 and 30 h. At the HRT of 30 h, the ethanol production yield using CMC beads was 0.49 g/g which implies that 91.07 % of the theoretical yield was achieved.\n\nImmobilized Kluyveromyces marxianus cells in carboxymethyl cellulose for production of ethanol from cheese whey: experimental and kinetic studies.", "token_count": 427, "char_count": 1438, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5566, "quality_score": 0.7783, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:13.117018", "source": { "split": "train_shard_00000", "doc_id": 4013 }, "chunk_id": "train_shard_00000_4013_0", "global_id": 4452 }, { "text": "Burkholderia is an incredibly diverse and versatile Gram-negative genus, within which over 80 species have been formally named and multiple other genotypic groups likely represent new species. Phylogenetic analysis based on the 16S rRNA gene sequence and core genome ribosomal multilocus sequence typing analysis indicates the presence of at least three major clades within the genus. Biotechnologically, Burkholderia are well-known for their bioremediation and biopesticidal properties. Within this review, we explore the ability of Burkholderia to synthesise a wide range of antimicrobial compounds ranging from historically characterised antifungals to recently described antibacterial antibiotics with activity against multiresistant clinical pathogens. The production of multiple Burkholderia antibiotics is controlled by quorum sensing and examples of quorum sensing pathways found across the genus are discussed. The capacity for antibiotic biosynthesis and secondary metabolism encoded within Burkholderia genomes is also evaluated. Overall, Burkholderia demonstrate significant biotechnological potential as a source of novel antibiotics and bioactive secondary metabolites.\n\nBurkholderia: an update on taxonomy and biotechnological potential as antibiotic producers.", "token_count": 286, "char_count": 1276, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7195, "quality_score": 0.8598, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:13.678088", "source": { "split": "train_shard_00000", "doc_id": 4014 }, "chunk_id": "train_shard_00000_4014_0", "global_id": 4453 }, { "text": "Background. The honey bee (Apis mellifera) is the most important pollinator in agriculture worldwide. However, the number of honey bees has fallen significantly since 2006, becoming a huge ecological problem nowadays. The principal cause is CCD, or Colony Collapse Disorder, characterized by the seemingly spontaneous abandonment of hives by their workers. One of the characteristics of CCD in honey bees is the alteration of the bacterial communities in their gastrointestinal tract, mainly due to the decrease of Firmicutes populations, such as the Lactobacilli. At this time, the causes of these alterations remain unknown. We recently isolated a strain of Lactobacillus kunkeei (L. kunkeei strain MP2) from the gut of Chilean honey bees. L. kunkeei, is one of the most commonly isolated bacterium from the honey bee gut and is highly versatile in different ecological niches. In this study, we aimed to elucidate in detail, the L. kunkeei genetic background and perform a comparative genome analysis with other Lactobacillus species. Methods. L. kunkeei MP2 was originally isolated from the guts of Chilean A. mellifera individuals. Genome sequencing was done using Pacific Biosciences single-molecule real-time sequencing technology. De novo assembly was performed using Celera assembler. The genome was annotated using Prokka, and functional information was added using the EggNOG 3.1 database. In addition, genomic islands were predicted using IslandViewer, and pro-phage sequences using PHAST. Comparisons between L. kunkeei MP2 with other L. kunkeei, and Lactobacillus strains were done using Roary. Results. The complete genome of L. kunkeei MP2 comprises one circular chromosome of 1,614,522 nt. with a GC content of 36,9%. Pangenome analysis with 16 L. kunkeei strains, identified 113 unique genes, most of them related to phage insertions. A large and unique region of L. kunkeei MP2 genome contains several genes that encode for phage structural protein and replication components. Comparative analysis of MP2 with other Lactobacillus species, identified several unique genes of L", "token_count": 535, "char_count": 2094, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5751, "quality_score": 0.7875, "entities": { "genes": [ "MP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:39:14.348659", "source": { "split": "train_shard_00000", "doc_id": 4015 }, "chunk_id": "train_shard_00000_4015_0", "global_id": 4454 }, { "text": "kunkeei MP2 related with metabolism, biofilm generation, survival under stress conditions, and mobile genetic elements (MGEs). Discussion. The presence of multiple mobile genetic elements, including phage sequences, suggest a high degree of genetic variability in L. kunkeei. Its versatility and ability to survive in different ecological niches (bee guts, flowers, fruits among others) could be given by its genetic capacity to change and adapt to different environments. L. kunkeei could be a new source of Lactobacillus with beneficial properties. Indeed, L. kunkeei MP2 could play an important role in honey bee nutrition through the synthesis of components as isoprenoids.\n\nGenome sequencing and analysis of the first complete genome of Lactobacillus kunkeei strain MP2, an Apis mellifera gut isolate.", "token_count": 191, "char_count": 806, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7119, "quality_score": 0.8559, "entities": { "genes": [ "MP2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:14.805282", "source": { "split": "train_shard_00000", "doc_id": 4015 }, "chunk_id": "train_shard_00000_4015_1", "global_id": 4455 }, { "text": "The bile salt export pump BSEP mediates bile formation. Over 150 BSEP mutations are associated with progressive familial intrahepatic cholestasis type 2 (PFIC-2), with few characterised specifically. We examined liver tissues from two PFIC-2 patients compound heterozygous for the splice-site mutation c.150 + 3A > C and either c.2783_2787dup5 resulting in a frameshift with a premature termination codon (child 1) or p.R832C (child 2). Splicing was analysed with a minigene system and mRNA sequencing from patients' livers. Protein expression was shown by immunofluorescence. Using the minigene, c.150 + 3A > C causes complete skipping of exon 3. In liver tissue of child 1, c.2783_2787dup5 was found on DNA but not on mRNA level, implying nonsense-mediated mRNA decay (NMD) when c.2783_2787dup5 is present. Still, BSEP protein as well as mRNA with and without exon 3 were detectable and can be assigned to the c.150 + 3A > C allele. Correctly spliced transcripts despite c.150 + 3A > C were also confirmed in liver of child 2. In conclusion, we provide evidence (1) for effective NMD due to a BSEP frameshift mutation and (2) partial exon-skipping due to c.150 + 3A > C. The results illustrate that the extent of exon-skipping depends on the genomic and cellular context and that regulation of splicing may have therapeutic potential.\n\nExon-skipping and mRNA decay in human liver tissue: molecular consequences of pathogenic bile salt export pump mutations.", "token_count": 512, "char_count": 1459, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:15.440140", "source": { "split": "train_shard_00000", "doc_id": 4016 }, "chunk_id": "train_shard_00000_4016_0", "global_id": 4456 }, { "text": "Drug-induced liver injury is an important clinical entity resulting in a considerable number of hospitalizations. While drug-induced cholestasis due to the inhibition of the bile salt export pump (BSEP) is well investigated, only limited information on the interaction of drugs with multidrug resistance protein 3 (MDR3) exists and its role in the pathogenesis of drug-induced cholestasis is poorly understood. Therefore, we aimed to study the interaction of drugs with MDR3 and the effect of drugs on canalicular lipid secretion in a newly established polarized cell line system that serves as a model of canalicular lipid secretion. LLC-PK1 cells were stably transfected with human Na(+)-taurocholate cotransporting polypeptide, BSEP, MDR3, and ABCG5/G8 and grown in the Transwell system. Apical phospholipid secretion and taurocholate transport were assayed to investigate the effect of selected drugs on MDR3-mediated phospholipid secretion as well as inhibition of BSEP. The established cell line displayed vectorial bile salt transport and specific phosphatidylcholine secretion into the apical compartment. The antifungal azoles, posaconazole, itraconazole, and ketoconazole, significantly inhibited MDR3-mediated phosphatidylcholine secretion. In contrast, amoxicillin clavulanate and troglitazone did not interfere with MDR3 activity. Drugs interfering with MDR3 activity did not display a parallel inhibition of BSEP. Our in vitro model for MDR3-mediated phospholipid secretion facilitates parallel screening for MDR3 and BSEP inhibitors. Our data demonstrate that the cholestatic potential of certain drugs may be aggravated by simultaneous inhibition of BSEP and MDR3.\n\nRole of Multidrug Resistance Protein 3 in Antifungal-Induced Cholestasis.", "token_count": 465, "char_count": 1755, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5667, "quality_score": 0.7833, "entities": { "genes": [ "MDR3", "PK1", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:16.085493", "source": { "split": "train_shard_00000", "doc_id": 4017 }, "chunk_id": "train_shard_00000_4017_0", "global_id": 4457 }, { "text": "Human hepatic membrane-embedded transporter proteins are involved in trafficking endogenous and exogenous substrates. Even though impact of transporters on pharmacokinetics is recognized, little is known on maturation of transporter protein expression levels, especially during early life. We aimed to study the protein expression of 10 transporters in liver tissue from fetuses, infants, and adults. Transporter protein expression levels [ATP-binding cassette transporter (ABC)B1, ABCG2, ABCC2, ABCC3, bile salt efflux pump, glucose transporter 1, monocarboxylate transporter 1, organic anion transporter polypeptide (OATP)1B1, OATP2B1, and organic cation/carnitine transporter 2) were quantified using ultraperformance liquid chromatography tandem mass spectrometry in snap-frozen postmortem fetal, infant, and adult liver samples. Protein expression was quantified in isolated crude membrane fractions. The possible association between postnatal and postmenstrual age versus protein expression was studied. We studied 25 liver samples, as follows: 10 fetal [median gestational age 23.2 wk (range 16.4-37.9)], 12 infantile [gestational age at birth 35.1 wk (27.1-41.0), postnatal age 1 wk (0-11.4)], and 3 adult. The relationship of protein expression with age was explored by comparing age groups. Correlating age within the fetal/infant age group suggested four specific protein expression patterns, as follows: stable, low to high, high to low, and low-high-low. The impact of growth and development on human membrane transporter protein expression is transporter-dependent. The suggested age-related differences in transporter protein expression may aid our understanding of normal growth and development, and also may impact the disposition of substrate drugs in neonates and young infants.\n\nProteomic Analysis of the Developmental Trajectory of Human Hepatic Membrane Transporter Proteins in the First Three Months of Life.", "token_count": 503, "char_count": 1931, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": { "genes": [ "ABCC2", "ABCC3", "ABCG2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:16.755706", "source": { "split": "train_shard_00000", "doc_id": 4018 }, "chunk_id": "train_shard_00000_4018_0", "global_id": 4458 }, { "text": "Knowledge about colloidal assemblies present in human intestinal fluids (HIFs), such as bile salt micelles and phospholipid vesicles, is regarded of importance for a better understanding of the in vivo dissolution and absorption behavior of poorly soluble drugs (Biopharmaceutics Classification System class II/IV drugs) because of their drug-solubilizing ability. The characterization of these potential drug-solubilizing compartments is a prerequisite for further studies of the mechanistic interplays between drug molecules and colloidal structures within HIFs. The aim of the present study was to apply asymmetrical flow field-flow fractionation (AF4) in combination with multiangle laser light scattering in an attempt to reveal coexistence of colloidal particles in both artificial and aspirated HIFs and to determine their sizes. Asymmetrical flow field-flow fractionation/multiangle laser light scattering analysis of the colloidal phase of intestinal fluids allowed for a detailed insight into the whole spectrum of submicron- to micrometer-sized particles. With respect to the simulated intestinal fluids mimicking fasted and fed state (FaSSIF-V1 and FeSSIF-V1, respectively), FaSSIF contained one distinct size fraction of colloidal assemblies, whereas FeSSIF contained 2 fractions of colloidal species with significantly different sizes. These size fractions likely represent (1) mixed taurocholate-phospholipid-micelles, as indicated by a size range up to 70 nm (in diameter) and a strong UV absorption and (2) small phospholipid vesicles of 90-210 nm diameter. In contrast, within the colloidal phase of the fasted state aspirate of a human volunteer, 4 different size fractions were separated from each other in a consistent and reproducible manner. The 2 fractions containing large particles showed mean sizes of approximately 50 and 200 nm, respectively (intensity-weighted mean diameter, Dz), likely representing mixed cholate/phospholipid micelles and phospholipid vesicles, respectively", "token_count": 490, "char_count": 2006, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8066, "entities": { "genes": [ "AF4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:17.406381", "source": { "split": "train_shard_00000", "doc_id": 4019 }, "chunk_id": "train_shard_00000_4019_0", "global_id": 4459 }, { "text": "The sizes of the smaller 2 fractions being below the size range of multiangle laser light scattering analysis (<20 nm) and their strong UV absorption indicates that they represent either pure cholate micelles or small mixed micelles. Within the colloidal fraction of the fed-state human aspirate, similar colloidal assemblies were detected as in the fasted state human aspirates. The observed differences between SIF and HIF indicate that the simulated intestinal fluids (FaSSIF-V1 and FeSSIF-V1) represent rather simplified models of the real human intestinal environment in terms of coexisting colloidal particles. It is hypothesized that the different supramolecular assemblies detected differ in their lipid composition, which may affect their affinity toward drug compounds and thus the drug-solubilizing capabilities.\n\nBile Salt Micelles and Phospholipid Vesicles Present in Simulated and Human Intestinal Fluids: Structural Analysis by Flow Field-Flow Fractionation/Multiangle Laser Light Scattering.", "token_count": 234, "char_count": 1007, "word_count": 139, "semantic_coherence": 1, "information_density": 0.705, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:17.877351", "source": { "split": "train_shard_00000", "doc_id": 4019 }, "chunk_id": "train_shard_00000_4019_1", "global_id": 4460 }, { "text": "This study was performed in order to isolate lactobacilli from chicken droppings and to select strains with the most promising probiotic properties. Lactobacillus strains were isolated from a flock of healthy laying hens. The first selection criterion was the ability to inhibit the growth of Salmonella Enteritidis. Then the tolerance to low pH and bile salt, the ability to coaggregate with pathogenic bacteria and hydrogen peroxide production were evaluated. Four isolates showing the best antagonistic activity against Salmonella Enetritidis were selected for further research. All isolates tested tolerated low pH and bile salt, likewise all produced hydrogen peroxide. They efficiently coaggregated with C. perfringens and relatively less with E. coli. Isolate 03'04 displayed above-average results in all criteria, thus it is considered as a potential probiotic for chickens, and will be further evaluated for health promoting effect in animals. The results presented in this study confirm the strain specific probiotic properties and prove the probiotic potential of isolate 03'04. Strong antagonistic properties against C. perfringens exhibited by certain Lactobacillus strains indicate the possibility to use them as a component of probiotic supplement in necrotic enteritis of poultry.\n\nAssessment of potentially probiotic properties of Lactobacillus strains isolated from chickens.", "token_count": 328, "char_count": 1393, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:18.441318", "source": { "split": "train_shard_00000", "doc_id": 4020 }, "chunk_id": "train_shard_00000_4020_0", "global_id": 4461 }, { "text": "The consumption of lactic acid bacteria capable of binding or degrading food-borne carcinogens may reduce human exposure to these deleterious compounds. In this study, 25 Lactobacillus strains isolated from human, plant, or dairy environments were investigated for their potential probiotic capacity against perfluorooctanoate (PFOA) toxicity. The PFOA binding, tolerance ability, and acid and bile salt tolerance were investigated and assessed by principal component analysis. Additionally, the effect of different pH levels and binding times was assessed. These strains exhibited different degrees of PFOA binding; the strain with the highest PFOA binding capability was Lactobacillus plantarum CCFM738, which bound to 49.40 ± 1.5 % of available PFOA. This strain also exhibited relatively good cellular antioxidative properties, acid and bile salt tolerance, and adhesion to Caco-2 cells. This study suggests that L. plantarum CCFM738 could be used as a potential probiotic in food applications against PFOA toxicity.\n\nScreening of potential probiotic lactic acid bacteria based on gastrointestinal properties and perfluorooctanoate toxicity.", "token_count": 290, "char_count": 1145, "word_count": 159, "semantic_coherence": 1, "information_density": 0.673, "quality_score": 0.8365, "entities": { "genes": [ "CCFM738" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:19.001802", "source": { "split": "train_shard_00000", "doc_id": 4021 }, "chunk_id": "train_shard_00000_4021_0", "global_id": 4462 }, { "text": "Experiments have been undertaken to determine the extent to which cholic acid conjugates of insulin were absorbed from the small intestine of anaesthetised rats by means of the bile salt transporters of the ileum. The measure used to assess the absorption of the cholyl-insulins was the amount of hypoglycaemia following infusion into the small intestine. Control experiments involving infusion of natural insulin into the ileum showed either nil absorption or absorption of a small amount of insulin as indicated by transient dip in the blood glucose concentration. However, when insulin was co-infused with the bile salt taurocholate, this was followed by a marked hypoglycaemic response which was specific to the ileum and did not occur on infusion into the jejunum. When the two cholyl conjugates of insulin were tested viz. B(29)-Lys-cholyl-insulin and B(1)-Phe-cholyl-insulin, both were biologically active as indicated by hypoglycaemic responses on systemic injection, though their potency was about 40% of that of natural insulin. While there was no evidence for the absorption of B(29)-Lys-cholyl-insulin when infused into the ileum, B(1)-Phe-cholyl-insulin did cause a long lasting hypoglycaemic response, indicating that absorption had occurred. Since the hypoglycaemic response was blocked on co-infusion with taurocholate and was absent for infusion of the conjugate into the jejunum, these results were taken as evidence that B(1)-Phe-cholyl-insulin had been taken up by the ileal bile salt transporters. This would indicate that B(1)-Phe-cholyl-insulin is worthy of further investigation for use in an oral insulin formulation.\n\nInvestigations into the absorption of insulin and insulin derivatives from the small intestine of the anaesthetised rat.", "token_count": 467, "char_count": 1764, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5175, "quality_score": 0.7588, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:19.643204", "source": { "split": "train_shard_00000", "doc_id": 4022 }, "chunk_id": "train_shard_00000_4022_0", "global_id": 4463 }, { "text": "The solubility of cholesterol in bile salt (BS) micelles is important to understand the availability of cholesterol for absorption in the intestinal epithelium and to develop strategies to decrease cholesterol intake from the intestinal lumen. This has been the subject of intense investigation, due to the established relation between the development of diseases such as atherosclerosis and high levels of cholesterol in the blood. In this work we quantify the effect of BS variability on the amount of cholesterol solubilized. The effect of some known hypocholesterolemic agents usually found in the diet is also evaluated, as well as some insight regarding the mechanisms involved. The results show that, depending on the bile salt composition, the average value of sterol per micelle is equal to or lower than 1. The amount of cholesterol solubilized in the BS micelles is essentially equal to its total concentration until the solubility limit is reached. Altogether, this indicates that the maximum cholesterol solubility in the BS micellar solution is the result of saturation of the aqueous phase and depends on the partition coefficient of cholesterol between the aqueous phase and the micellar pseudophase. The effect on cholesterol maximum solubility for several food ingredients usually encountered in the diet was characterized using methodology developed recently by us. This method allows the simultaneous quantification of both cholesterol and food ingredient solubilized in the BS micelles even in the presence of larger aggregates, therefore avoiding their physical separation with possible impacts on the overall equilibrium. The phytosterols stigmasterol and stigmastanol significantly decreased cholesterol solubility with a concomitant reduction in the total amount of sterol solubilized, most pronounced for stigmasterol. Those results point toward coprecipitation being the major cause for the decrease in cholesterol solubilization by the BS micelles. The presence of tocopherol and oleic acid leads to a small decrease in the amount of cholesterol solubilized while palmitic acid slightly increases the solubility of cholesterol", "token_count": 486, "char_count": 2154, "word_count": 317, "semantic_coherence": 1, "information_density": 0.5205, "quality_score": 0.7603, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:20.289731", "source": { "split": "train_shard_00000", "doc_id": 4023 }, "chunk_id": "train_shard_00000_4023_0", "global_id": 4464 }, { "text": "Those dietary food ingredients are completely solubilized by the BS micelles, indicating that the effects on cholesterol solubility are due to changes in the properties of the mixed micelles.\n\nQuantification of Cholesterol Solubilized in Dietary Micelles: Dependence on Human Bile Salt Variability and the Presence of Dietary Food Ingredients.", "token_count": 83, "char_count": 343, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:20.654258", "source": { "split": "train_shard_00000", "doc_id": 4023 }, "chunk_id": "train_shard_00000_4023_1", "global_id": 4465 }, { "text": "Autotaxin (ATX) generates the lipid mediator lysophosphatidic acid (LPA). ATX-LPA signalling is involved in multiple biological and pathophysiological processes, including vasculogenesis, fibrosis, cholestatic pruritus and tumour progression. ATX has a tripartite active site, combining a hydrophilic groove, a hydrophobic lipid-binding pocket and a tunnel of unclear function. We present crystal structures of rat ATX bound to 7α-hydroxycholesterol and the bile salt tauroursodeoxycholate (TUDCA), showing how the tunnel selectively binds steroids. A structure of ATX simultaneously harbouring TUDCA in the tunnel and LPA in the pocket, together with kinetic analysis, reveals that bile salts act as partial non-competitive inhibitors of ATX, thereby attenuating LPA receptor activation. This unexpected interplay between ATX-LPA signalling and select steroids, notably natural bile salts, provides a molecular basis for the emerging association of ATX with disorders associated with increased circulating levels of bile salts. Furthermore, our findings suggest potential clinical implications in the use of steroid drugs.\n\nSteroid binding to Autotaxin links bile salts and lysophosphatidic acid signalling.", "token_count": 307, "char_count": 1208, "word_count": 162, "semantic_coherence": 1, "information_density": 0.716, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:21.260557", "source": { "split": "train_shard_00000", "doc_id": 4024 }, "chunk_id": "train_shard_00000_4024_0", "global_id": 4466 }, { "text": "Flavobacterium psychrophilum is a fish pathogen in salmonid aquaculture worldwide that causes cold water disease (CWD) and rainbow trout fry syndrome (RTFS). Comparative genome analyses of 11 F. psychrophilum isolates representing temporally and geographically distant populations were used to describe the F. psychrophilum pan-genome and to examine virulence factors, prophages, CRISPR arrays, and genomic islands present in the genomes. Analysis of the genomic DNA sequences were complemented with selected phenotypic characteristics of the strains. The pan genome analysis showed that F. psychrophilum could hold at least 3373 genes, while the core genome contained 1743 genes. On average, 67 new genes were detected for every new genome added to the analysis, indicating that F. psychrophilum possesses an open pan genome. The putative virulence factors were equally distributed among isolates, independent of geographic location, year of isolation and source of isolates. Only one prophage-related sequence was found which corresponded to the previously described prophage 6H, and appeared in 5 out of 11 isolates. CRISPR array analysis revealed two different loci with dissimilar spacer content, which only matched one sequence in the database, the temperate bacteriophage 6H. Genomic Islands (GIs) were identified in F. psychrophilum isolates 950106-1/1 and CSF 259-93, associated with toxins and antibiotic resistance. Finally, phenotypic characterization revealed a high degree of similarity among the strains with respect to biofilm formation and secretion of extracellular enzymes. Global scale dispersion of virulence factors in the genomes and the abilities for biofilm formation, hemolytic activity and secretion of extracellular enzymes among the strains suggested that F. psychrophilum isolates have a similar mode of action on adhesion, colonization and destruction of fish tissues across large spatial and temporal scales of occurrence. Overall, the genomic characterization and phenotypic properties may provide new insights to the mechanisms of pathogenicity in F. psychrophilum.", "token_count": 519, "char_count": 2099, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6115, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:39:21.942513", "source": { "split": "train_shard_00000", "doc_id": 4025 }, "chunk_id": "train_shard_00000_4025_0", "global_id": 4467 }, { "text": "Comparative Genome Analysis Provides Insights into the Pathogenicity of Flavobacterium psychrophilum.", "token_count": 26, "char_count": 101, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:22.322532", "source": { "split": "train_shard_00000", "doc_id": 4025 }, "chunk_id": "train_shard_00000_4025_1", "global_id": 4468 }, { "text": "Staphylococcus aureus is an important cause of both hospital- and community-associated methicillin-resistant S. aureus (MRSA) infections worldwide. β-Lactam antibiotics are the drugs of choice to treat S. aureus infections, but resistance to these and other antibiotics make treatment problematic. High-level β-lactam resistance of S. aureus has always been attributed to the horizontally acquired penicillin binding protein 2a (PBP 2a) encoded by the mecA gene. Here, we show that S. aureus can also express high-level resistance to β-lactams, including new-generation broad-spectrum cephalosporins that are active against methicillin-resistant strains, through an uncanonical core genome-encoded penicillin binding protein, PBP 4, a nonessential enzyme previously considered not to be important for staphylococcal β-lactam resistance. Our results show that PBP 4 can mediate high-level resistance to β-lactams.\n\nPBP 4 Mediates High-Level Resistance to New-Generation Cephalosporins in Staphylococcus aureus.", "token_count": 292, "char_count": 1009, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6692, "quality_score": 0.8346, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:22.921600", "source": { "split": "train_shard_00000", "doc_id": 4026 }, "chunk_id": "train_shard_00000_4026_0", "global_id": 4469 }, { "text": "A new method for determination of the optimum temperature and activation energies based on an idea of the average rate of enzymatic reaction has been developed. A mathematical model describing the effect of temperature on a dimensionless activity for enzyme deactivation following the first-order kinetics has been derived. The necessary condition for existence of the function extreme of the optimal temperature has been applied in the model. The developed method has been verified using the experimental data for inulinase from Kluyveromyces marxianus.\n\nA new method to determine optimum temperature and activation energies for enzymatic reactions.", "token_count": 126, "char_count": 650, "word_count": 95, "semantic_coherence": 1, "information_density": 0.5895, "quality_score": 0.7947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:23.322411", "source": { "split": "train_shard_00000", "doc_id": 4027 }, "chunk_id": "train_shard_00000_4027_0", "global_id": 4470 }, { "text": "Researchers contest the importance of gene flow in bacterial core genomes, as traditionalists view microbes as predominantly clonal, asexually reproducing organisms. Contrary to the traditional perspective,\n\nGene flow in microbial communities could explain unexpected patterns of synonymous variation in the", "token_count": 63, "char_count": 307, "word_count": 40, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:23.689259", "source": { "split": "train_shard_00000", "doc_id": 4028 }, "chunk_id": "train_shard_00000_4028_0", "global_id": 4471 }, { "text": "A total of 30 Legionella pneumophila serogroup 1 isolates representing 10 separate legionellosis laboratory investigations (\"outbreaks\") that occurred in New York State between 2004 and 2012 were selected for evaluation of whole-genome sequencing (WGS) approaches for molecular subtyping of this organism. Clinical and environmental isolates were available for each outbreak and were initially examined by pulsed-field gel electrophoresis (PFGE). Sequence-based typing alleles were extracted from WGS data yielding complete sequence types (ST) for isolates representing 8 out of the 10 outbreaks evaluated in this study. Isolates from separate outbreaks sharing the same ST also contained the fewest differences in core genome single nucleotide polymorphisms (SNPs) and the greatest proportion of identical allele sequences in a whole-genome multilocus sequence typing (wgMLST) scheme. Both core SNP and wgMLST analyses distinguished isolates from separate outbreaks, including those from two outbreaks sharing indistinguishable PFGE profiles. Isolates from a hospital-associated outbreak spanning multiple years shared indistinguishable PFGE profiles but displayed differences in their genome sequences, suggesting the presence of multiple environmental sources. Finally, the rtx gene demonstrated differences in the repeat region sequence among ST1 isolates from different outbreaks, suggesting that variation in this gene may be useful for targeted molecular subtyping approaches for L. pneumophila This study demonstrates the utility of various genome sequence analysis approaches for L. pneumophila for environmental source attribution studies while furthering the understanding of Legionella ecology.\n\nGenomic Resolution of Outbreak-Associated Legionella pneumophila Serogroup 1 Isolates from New York State.", "token_count": 404, "char_count": 1814, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:24.317801", "source": { "split": "train_shard_00000", "doc_id": 4029 }, "chunk_id": "train_shard_00000_4029_0", "global_id": 4472 }, { "text": "Whey is a byproduct of the dairy industry, which has prospects of using as a source for production of various valuable compounds. The lactose present in whey is considered as an environmental pollutant and its utilization for enzyme and fuel production, may be effective for whey bioremediation. The dairy yeast Kluyveromyces marxianus have the ability to utilize lactose sharply as the major carbon source for the production of the enzyme. Five strains were tested for the production of the β-galactosidase using whey. The maximum β-galactosidase activity of 1.74 IU/mg dry weight was achieved in whey using K. marxianus MTCC 1389. The biocatalyst was further immobilized on chitosan macroparticles and exhibited excellent functional activity at 35 °C. Almost 89 % lactose hydrolysis was attained for concentrated whey (100 g/L) and retained 89 % catalytic activity after 15 cycles of reuse. Finally, β-galactosidase was immobilized on chitosan and Saccharomyces cerevisiae on calcium alginate, and both were used together for the production of ethanol from concentrated whey. Maximal ethanol titer of 28.9 g/L was achieved during fermentation at 35 °C. The conclusions generated by employing two different matrices will be beneficial for the future modeling using engineered S. cerevisiae in scale-up studies.\n\nUtilization of Cheese Whey Using Synergistic Immobilization of β-Galactosidase and Saccharomyces cerevisiae Cells in Dual Matrices.", "token_count": 407, "char_count": 1444, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:24.935700", "source": { "split": "train_shard_00000", "doc_id": 4030 }, "chunk_id": "train_shard_00000_4030_0", "global_id": 4473 }, { "text": "The bile salt export pump (BSEP) is expressed on the canalicular membrane of hepatocytes regulating liver bile salt excretion, and impairment of BSEP function may lead to cholestasis in humans. This study explored drug biliary excretion, as well as serum chemistry, individual bile acid concentrations and liver transporter expressions, in the SAGE Bsep knockout (KO) rat model. It was observed that the Bsep protein in KO rats was decreased to 15% of that in the wild type (WT), as quantified using LC-MS/MS. While the levels of Ntcp and Mrp2 were not significantly altered, Mrp3 expression increased and Oatp1a1 decreased in KO animals. Compared with the WT rats, the KO rats had similar serum chemistry and showed normal liver transaminases. Although the total plasma bile salts and bile flow were not significantly changed in Bsep KO rats, individual bile acids in plasma and liver demonstrated variable changes, indicating the impact of Bsep KO. Following an intravenous dose of deuterium labeled taurocholic acid (D4-TCA, 2 mg/kg), the D4-TCA plasma exposure was higher and bile excretion was delayed by approximately 0.5 h in the KO rats. No differences were observed for the pravastatin plasma concentration-time profile or the biliary excretion after intravenous administration (1 mg/kg). Collectively, the results revealed that these rats have significantly lower Bsep expression, therefore affecting the biliary excretion of endogenous bile acids and Bsep substrates. However, these rats are able to maintain a relatively normal liver function through the remaining Bsep protein and via the regulation of other transporters. Copyright © 2016 John Wiley & Sons, Ltd.\n\nBiliary excretion of pravastatin and taurocholate in rats with bile salt export pump (Bsep) impairment.", "token_count": 463, "char_count": 1781, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5861, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:25.572293", "source": { "split": "train_shard_00000", "doc_id": 4031 }, "chunk_id": "train_shard_00000_4031_0", "global_id": 4474 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) is one of the major causes of human gastrointestinal disease and has been implicated in sporadic cases and outbreaks of diarrhoea, haemorrhagic colitis and haemolytic uremic syndrome worldwide. In this study, we determined the molecular characteristics and phylogenetic relationship of STEC isolates, and their genetic diversity was compared to that of other E. coli populations. Whole genome sequencing was performed on 132 clinical STEC isolates obtained from the faeces of 129 Dutch patients with gastrointestinal complaints. STEC isolates of this study belonged to 44 different sequence types (STs), 42 serogenotypes and 14 stx subtype combinations. Antibiotic resistance genes were more frequently present in stx1-positive isolates compared to stx2 and stx1 + stx2-positive isolates. The iha, mchB, mchC, mchF, subA, ireA, senB, saa and sigA genes were significantly more frequently present in eae-negative than in eae-positive STEC isolates. Presence of virulence genes encoding type III secretion proteins and adhesins was associated with isolates obtained from patients with bloody diarrhoea. Core genome phylogenetic analysis showed that isolates clustered according to their ST or serogenotypes irrespective of stx subtypes. Isolates obtained from patients with bloody diarrhoea were from diverse phylogenetic backgrounds. Some STEC isolates shared common ancestors with non-STEC isolates. Whole genome sequencing is a powerful tool for clinical microbiology, allowing high-resolution molecular typing, population structure analysis and detailed molecular characterization of strains. STEC isolates of a substantial genetic diversity and of distinct phylogenetic groups were observed in this study.\n\nMolecular characterization and phylogeny of Shiga toxin-producing Escherichia coli isolates obtained from two Dutch regions using whole genome sequencing.", "token_count": 489, "char_count": 1910, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:26.218708", "source": { "split": "train_shard_00000", "doc_id": 4032 }, "chunk_id": "train_shard_00000_4032_0", "global_id": 4475 }, { "text": "Pediococcus spp. were isolated from poultry rectum, faeces and food as good probiotic candidates in order to select strains to be used as probiotic in poultry feed. A total of 168 lactic acid bacteria were isolated and 51 isolates including 31 Lactobacillus spp. and 20 Pediococcus spp. were able to survive in low pH and bile salt concentration. The Pediococcus spp. were identified and their ability to form biofilm, adhesion to Caco-2 cells and antimicrobial activities against enteric pathogenic bacteria were determined. The results showed the presence of two strains, Pediococcus acidilactici P17 and P19 in rectal swab samples from 21-d old chickens with significant antibacterial activities against Salmonella enteritidis and Escherichia coli. The results suggest that only a few isolates of Pediococcus with potential probiotic activities are present in the poultry industry.\n\nEvaluation of potential probiotic characteristics and antibacterial effects of strains of Pediococcus species isolated from broiler chickens.", "token_count": 270, "char_count": 1027, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:26.767737", "source": { "split": "train_shard_00000", "doc_id": 4033 }, "chunk_id": "train_shard_00000_4033_0", "global_id": 4476 }, { "text": "Bioethanol was produced from Kappaphycus alvarezii seaweed biomass using separate hydrolysis and fermentation (SHF). Pretreatment was evaluated for 60 min at 121°C using 12% (w/v) biomass slurry with 364 mM H2SO4. Enzymatic saccharification was then carried out at 45°C for 48 h using Celluclast 1.5 L. Ethanol fermentation with 12% (w/v) K. alvarezii hydrolyzate was performed using the yeasts Saccharomyces cerevisiae KCTC1126, Kluyveromyces marxianus KCTC7150, and Candida lusitaniae ATCC42720 with or without prior adaptation to high concentrations of galactose. When non-adapted S. cerevisiae, K. marxianus, and C. lusitaniae were used, 11.5 g/l, 6.7 g/l, and 6.0 g/l of ethanol were produced, respectively. When adapted S. cerevisiae, K. marxianus, and C. lusitaniae were used, 15.8 g/l, 11.6 g/l, and 13.4 g/l of ethanol were obtained, respectively. The highest ethanol concentration was 15.8 g/l, with YEtOH = 0.43 and YT% = 84.3%, which was obtained using adapted S. cerevisiae.\n\nEvaluation of Galactose Adapted Yeasts for Bioethanol Fermentation from Kappaphycus alvarezii Hydrolyzates.", "token_count": 423, "char_count": 1096, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [ "KCTC1126", "KCTC7150", "ATCC42720" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:27.393865", "source": { "split": "train_shard_00000", "doc_id": 4034 }, "chunk_id": "train_shard_00000_4034_0", "global_id": 4477 }, { "text": "Herein, we present an endeavor toward exploring the lacuna underlying the host:guest chemistry of inclusion complex formation between bile salt(s) and β-cyclodextrin(s) (βCDs). An extensive thermodynamic investigation based on isothermal titration calorimetry (ITC) demonstrates a dominant contribution from exothermic enthalpy change (ΔH < 0) accompanying the phenomenon of inclusion complex formation, along with a relatively smaller contribution to total free energy change from the entropic component. However, the negative heat capacity change (ΔCp < 0) displays the hallmark for a pivotal role of hydrophobic effect underlying the interaction. Contrary to the classical hydrophobic effect, such apparently paradoxical thermodynamic signature has been adequately described under the notion of \"nonclassical hydrophobic effect\". On the basis of our results, the displacement of disordered water from hydrophobic binding sites has been argued to mark the enthalpic signature and the key role of such interaction forces is further corroborated from enthalpy-entropy compensation behavior showing indication for almost complete compensation. To this end, we have quantified the interaction of two bile salt molecules (namely, sodium deoxycholate and sodium glycocholate) with a series of varying chemical substituents on the host counterpart, namely, βCD, (2-hydroxypropyl)-βCD, and methyl βCD.\n\nInteraction of Bile Salts with β-Cyclodextrins Reveals Nonclassical Hydrophobic Effect and Enthalpy-Entropy Compensation.", "token_count": 371, "char_count": 1518, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6601, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:27.977715", "source": { "split": "train_shard_00000", "doc_id": 4035 }, "chunk_id": "train_shard_00000_4035_0", "global_id": 4478 }, { "text": "Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.\n\nLateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.", "token_count": 457, "char_count": 1980, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:28.618302", "source": { "split": "train_shard_00000", "doc_id": 4036 }, "chunk_id": "train_shard_00000_4036_0", "global_id": 4479 }, { "text": "The gut microbiota is found to be strongly associated with atherosclerosis (AS). Resveratrol (RSV) is a natural phytoalexin with anti-AS effects; however, its mechanisms of action remain unclear. Therefore, we sought to determine whether the anti-AS effects of RSV were related to changes in the gut microbiota. We found that RSV attenuated trimethylamine-N-oxide (TMAO)-induced AS in ApoE(-/-) mice. Meanwhile, RSV decreased TMAO levels by inhibiting commensal microbial trimethylamine (TMA) production via gut microbiota remodeling in mice. Moreover, RSV increased levels of the genera Lactobacillus and Bifidobacterium, which increased the bile salt hydrolase activity, thereby enhancing bile acid (BA) deconjugation and fecal excretion in C57BL/6J and ApoE(-/-) mice. This was associated with a decrease in ileal BA content, repression of the enterohepatic farnesoid X receptor (FXR)-fibroblast growth factor 15 (FGF15) axis, and increased cholesterol 7a-hydroxylase (CYP7A1) expression and hepatic BA neosynthesis. An FXR antagonist had the same effect on FGF15 and CYP7A1 expression as RSV, while an FXR agonist abolished RSV-induced alterations in FGF15 and CYP7A1 expression. In mice treated with antibiotics, RSV neither decreased TMAO levels nor increased hepatic BA synthesis. Additionally, RSV-induced inhibition of TMAO-caused AS was also markedly abolished by antibiotics. In conclusion, RSV attenuated TMAO-induced AS by decreasing TMAO levels and increasing hepatic BA neosynthesis via gut microbiota remodeling, and the BA neosynthesis was partially mediated through the enterohepatic FXR-FGF15 axis.", "token_count": 494, "char_count": 1617, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6205, "quality_score": 0.8103, "entities": { "genes": [ "FGF15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:29.276076", "source": { "split": "train_shard_00000", "doc_id": 4037 }, "chunk_id": "train_shard_00000_4037_0", "global_id": 4480 }, { "text": "Resveratrol Attenuates Trimethylamine-N-Oxide (TMAO)-Induced Atherosclerosis by Regulating TMAO Synthesis and Bile Acid Metabolism via Remodeling of the Gut Microbiota.", "token_count": 60, "char_count": 168, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:29.638316", "source": { "split": "train_shard_00000", "doc_id": 4037 }, "chunk_id": "train_shard_00000_4037_1", "global_id": 4481 }, { "text": "A growing body of evidence has demonstrated that bile salts are important for liver regeneration following partial hepatectomy. The relative bile salt overload after partial liver resection causes activation of bile salt receptors in non-parenchymal (viz. the plasma membrane receptor TGR5) and parenchymal (viz. the intracellular receptor FXR) cells in the liver, thus, providing signals to the regenerative process. Impaired bile salt signaling in mice with genetic deficiency of Tgr5 or Fxr results in delayed liver regeneration after partial hepatectomy, and is accompanied by mortality in case of Fxr knock-out mice. Conversely, compensatory liver re-growth in hepatectomized mice can be stimulated by feeding of bile salts or alisol B 23-acetate, a natural triterpenoid agonist of Fxr. A large number of animal studies underscore the importance of strict maintenance of bile salt homeostasis for proper progression of liver regeneration. Both ileal and hepatic Fxr play a key role in regulation of bile salt homeostasis and, thus, preventing hepatotoxicity caused by excessive levels of bile salts. They further contribute to liver regeneration by induction of mitogenic factors. Agents that target bile salt receptors hold promise as drugs to stimulate liver regeneration in selected patients.\n\nThe role of bile salts in liver regeneration.", "token_count": 342, "char_count": 1347, "word_count": 200, "semantic_coherence": 1, "information_density": 0.605, "quality_score": 0.8025, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:30.209300", "source": { "split": "train_shard_00000", "doc_id": 4038 }, "chunk_id": "train_shard_00000_4038_0", "global_id": 4482 }, { "text": "In Georgia, one of the most ancient vine-growing environment, the homemade production of wine is still very popular in every rural family and spontaneous fermentation of must, without addition of chemical preservatives, is the norm. The present work investigated the yeast biodiversity in five Georgian areas (Guria, Imereti, Kakheti, Kartli, Ratcha-Lechkhumi) sampling grapes and wines from 22 different native cultivars, in 26 vineyards and 19 family cellars. One hundred and eighty-two isolates were ascribed to 15 different species by PCR-ITS and RFLP, and partial sequencing of D1/D2 domain 26S rDNA gene. Metschnikowia pulcherrima (F' = 0.56, I' = 0.32), Hanseniaspora guilliermondii (F' = 0.49, I' = 0.27), and Cryptococcus flavescens (F' = 0.31, I' = 0.11) were the dominant yeasts found on grapes, whereas Saccharomyces cerevisiae showed the highest prevalence into wine samples. Seventy four isolates with fermentative potential were screened for oenological traits such as ethanol production, resistance to SO2, and acetic acid, glycerol and H2S production. Three yeast strains (Kluyveromyces marxianus UMY207, S. cerevisiae UMY255, Torulaspora delbrueckii UMY196) were selected and separately inoculated in vinifications experiments at a Georgian cellar. Musts were prepared from healthy grapes of local varieties, Goruli Mtsvane (white berry cultivar) and Saperavi (black berry cultivar). Physical (°Brix) and microbial analyses (plate counts) were performed to monitor the fermentative process. The isolation of indigenous S. cerevisiae yeasts beyond the inoculated strains indicated that a co-presence occurred during the vinification tests", "token_count": 493, "char_count": 1655, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7191, "quality_score": 0.8596, "entities": { "genes": [ "SO2", "UMY207", "UMY255", "UMY196" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:30.864130", "source": { "split": "train_shard_00000", "doc_id": 4039 }, "chunk_id": "train_shard_00000_4039_0", "global_id": 4483 }, { "text": "Results from quantitative GC-FID analysis of volatile compounds revealed that the highest amount of fermentation flavors, such as 4-ethoxy-4-oxobutanoic acid (monoethyl succinate), 2-methylpropan-1-ol, ethyl 2-hydroxypropanoate, and 2-phenylethanol, were significantly more produced in fermentation conducted in Saperavi variety inoculated with K. marxianus, whereas other aromatic compounds like 3-methylbutyl acetate, ethyl hexanoate and dihydrofuran-2(3H)-one (γ- butyrolactone) showed a higher content in Goruli Mtsvane variety samples fermented by S. cerevisiae. The selected yeast strains have proved to be promising for enhancing the flavor potential in low aromatic Georgian cultivars. This work intends to be a knowledge contribution for a precision oenology toward the strategic concept of \"one grape variety-one yeast\".\n\nIndigenous Georgian Wine-Associated Yeasts and Grape Cultivars to Edit the Wine Quality in a Precision Oenology Perspective.", "token_count": 272, "char_count": 956, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7742, "quality_score": 0.8871, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:31.414683", "source": { "split": "train_shard_00000", "doc_id": 4039 }, "chunk_id": "train_shard_00000_4039_1", "global_id": 4484 }, { "text": "The bacterium Myxococcus xanthus glides through soil in search of prey microbes, but when food sources run out, cells cooperatively construct and sporulate within multicellular fruiting bodies. M. xanthus strains isolated from a 16 × 16-cm-scale patch of soil were previously shown to have diversified into many distinct compatibility types that are distinguished by the failure of swarming colonies to merge upon encounter. We sequenced the genomes of 22 isolates from this population belonging to the two most frequently occurring multilocus sequence type (MLST) clades to trace patterns of incipient genomic divergence, specifically related to social divergence. Although homologous recombination occurs frequently within the two MLST clades, we find an almost complete absence of recombination events between them. As the two clades are very closely related and live in sympatry, either ecological or genetic barriers must reduce genetic exchange between them. We find that the rate of change in the accessory genome is greater than the rate of amino-acid substitution in the core genome. We identify a large genomic tract that consistently differs between isolates that do not freely merge and therefore is a candidate region for harbouring gene(s) responsible for self/non-self discrimination.\n\nA barrier to homologous recombination between sympatric strains of the cooperative soil bacterium Myxococcus xanthus.", "token_count": 318, "char_count": 1418, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6827, "quality_score": 0.8413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:31.977913", "source": { "split": "train_shard_00000", "doc_id": 4040 }, "chunk_id": "train_shard_00000_4040_0", "global_id": 4485 }, { "text": "The order 'Megavirales' represents a group of eukaryotic viruses with a large genome encoding a few hundred up to two thousand five hundred genes. Several members of Megavirales possess genes involved in major DNA repair pathways. Some of these genes were likely inherited from an ancient virus world and some others were derived from the genomes of their hosts. Here we examine molecular phylogenies of key DNA repair enzymes in light of recent hypotheses on the origin of Megavirales, and propose that the last common ancestors of the individual families of the order Megavirales already possessed DNA repair functions to achieve and maintain a moderately large genome and that this repair capacity gradually increased, in a family-dependent manner, during their recent evolution.\n\nDNA repair genes in the Megavirales pangenome.", "token_count": 178, "char_count": 830, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:32.424265", "source": { "split": "train_shard_00000", "doc_id": 4041 }, "chunk_id": "train_shard_00000_4041_0", "global_id": 4486 }, { "text": "Understanding intestinal absorption for pharmaceutical compounds is vital to estimate the bioavailability and therefore the in vivo potential of a drug. This study considers the application of micellar liquid chromatography (MLC) to predict passive intestinal absorption with a selection of model compounds. MLC is already known to aid prediction of absorption using simple surfactant systems; however, with this study the focus was on the presence of a more complex, bile salt surfactant, as would be encountered in the in vivo environment. As a result, MLC using a specific bile salt has been confirmed as an ideal in vitro system to predict the intestinal permeability for a wide range of drugs, through the development of a quantitative partition-absorption relationship. MLC offers many benefits including environmental, economic, time-saving and ethical advantages compared with the traditional techniques employed to obtain passive intestinal absorption values. Copyright © 2016 John Wiley & Sons, Ltd.\n\nPredicting human intestinal absorption in the presence of bile salt with micellar liquid chromatography.", "token_count": 240, "char_count": 1115, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6258, "quality_score": 0.8129, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:32.893598", "source": { "split": "train_shard_00000", "doc_id": 4042 }, "chunk_id": "train_shard_00000_4042_0", "global_id": 4487 }, { "text": "Most Escherichia coli strains are nonpathogenic. However, for clinical diagnosis and food safety analysis, current identification methods for pathogenic E. coli either are time-consuming and/or provide limited information. Here, we utilized a custom DNA microarray with informative genetic features extracted from 368 sequence sets for rapid and high-throughput pathogen identification. The FDA Escherichia coli Identification (FDA-ECID) platform contains three sets of molecularly informative features that together stratify strain identification and relatedness. First, 53 known flagellin alleles, 103 alleles of wzx and wzy, and 5 alleles of wzm provide molecular serotyping utility. Second, 41,932 probe sets representing the pan-genome of E. coli provide strain-level gene content information. Third, approximately 125,000 single nucleotide polymorphisms (SNPs) of available whole-genome sequences (WGS) were distilled to 9,984 SNPs capable of recapitulating the E. coli phylogeny. We analyzed 103 diverse E. coli strains with available WGS data, including those associated with past foodborne illnesses, to determine robustness and accuracy. The array was able to accurately identify the molecular O and H serotypes, potentially correcting serological failures and providing better resolution for H-nontypeable/nonmotile phenotypes. In addition, molecular risk assessment was possible with key virulence marker identifications. Epidemiologically, each strain had a unique comparative genomic fingerprint that was extended to an additional 507 food and clinical isolates. Finally, a 99.7% phylogenetic concordance was established between microarray analysis and WGS using SNP-level data for advanced genome typing. Our study demonstrates FDA-ECID as a powerful tool for epidemiology and molecular risk assessment with the capacity to profile the global landscape and diversity of E. coli", "token_count": 456, "char_count": 1892, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6902, "quality_score": 0.8451, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:33.559326", "source": { "split": "train_shard_00000", "doc_id": 4043 }, "chunk_id": "train_shard_00000_4043_0", "global_id": 4488 }, { "text": "FDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny.", "token_count": 57, "char_count": 164, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:33.941269", "source": { "split": "train_shard_00000", "doc_id": 4043 }, "chunk_id": "train_shard_00000_4043_1", "global_id": 4489 }, { "text": "The view on bile salts has evolved over the years from being regarded as simple detergents that aid intestinal absorption of fat-soluble nutrients to being important hormone-like integrators of metabolism. This review provides an update on the rapidly developing field of interactions between bile salts and lipid metabolism, with a particular emphasis on the underlying mechanisms.\n\nBile salts in control of lipid metabolism.", "token_count": 97, "char_count": 426, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:34.332394", "source": { "split": "train_shard_00000", "doc_id": 4044 }, "chunk_id": "train_shard_00000_4044_0", "global_id": 4490 }, { "text": "Accurate characterization of dispersed-phase nanoparticle properties such as density, size, solvation, and charge is necessary for their utilization in applications such as medicine, energy, and materials. Herein, analytical ultracentrifugation (AUC) is used to quantify bile salt surfactant adsorption on length sorted (7,6) single-wall carbon nanotubes (SWCNTs) as a function of bulk surfactant concentration and in the presence of varying quantities of a monovalent salt-sodium chloride. These measurements provide high precision adsorbed surfactant density values in the literature for only the second SWCNT structure to date and report the quantity of adsorbed surfactant across a broad range of bulk surfactant concentrations utilized in SWCNT dispersion processing. Second, the measurements presented herein unambiguously demonstrate, via AUC, a direct relation between the size of the counterion cloud around a surfactant-stabilized SWCNT and solution ionic strength. The results show that changes in the size of the counterion cloud around surfactant-stabilized SWCNT are attributable to electrostatic phenomenon and not to changes in the quantity of adsorbed surfactant with salt addition. These results provide important reference values for projecting SWCNT dispersion behavior as a function of solution conditions and extend the range of nanoparticle properties measurable via AUC.\n\nCharacterizing the Effect of Salt and Surfactant Concentration on the Counterion Atmosphere around Surfactant Stabilized SWCNTs Using Analytical Ultracentrifugation.", "token_count": 357, "char_count": 1561, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5687, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:34.960078", "source": { "split": "train_shard_00000", "doc_id": 4045 }, "chunk_id": "train_shard_00000_4045_0", "global_id": 4491 }, { "text": "The fermentation ability of thermotolerant Kluyveromyces marxianus BUNL-21 isolated in Laos was investigated. Comparison with thermotolerant K. marxianus DMKU3-1042 as one of the most thermotolerant yeasts isolated previously revealed that the strain possesses stronger ability for conversion of xylose to ethanol, resistance to 2-deoxyglucose in the case of pentose, and tolerance to various stresses including high temperature and hydrogen peroxide. K. marxianus BUNL-21 was found to have ethanol fermentation activity from xylose that is slightly lower and much higher than that of Scheffersomyces stipitis (Pichia stipitis) at 30 °C and at higher temperatures, respectively. The lower ethanol production seems to be due to large accumulation of acetic acid. The possible mechanism of acetic acid accumulation is discussed. In addition, it was found that both K. marxianus strains produced ethanol in the presence of 10 mM hydroxymethylfurfural or furfural, at a level almost equivalent to that in their absence. Therefore, K. marxianus BUNL-21 is a highly competent yeast for high-temperature ethanol fermentation with lignocellulosic biomass.\n\nEfficient conversion of xylose to ethanol by stress-tolerant Kluyveromyces marxianus BUNL-21.", "token_count": 350, "char_count": 1242, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "DMKU3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:35.545864", "source": { "split": "train_shard_00000", "doc_id": 4046 }, "chunk_id": "train_shard_00000_4046_0", "global_id": 4492 }, { "text": "Delamanid (Deltyba, OPC-67683) is the first approved drug in a novel class of nitro-dihydro-imidazooxazoles developed for the treatment of multidrug-resistant tuberculosis. Patients with tuberculosis require treatment with multiple drugs, several of which have known drug-drug interactions. Transporters regulate drug absorption, distribution, and excretion; therefore, the inhibition of transport by one agent may alter the pharmacokinetics of another, leading to unexpected adverse events. Therefore, it is important to understand how delamanid affects transport activity. In the present study, the potencies of delamanid and its main metabolites as the substrates and inhibitors of various transporters were evaluated in vitro Delamanid was not transported by the efflux ATP-binding cassette (ABC) transporters P-glycoprotein (P-gp; MDR1/ABCB1) and breast cancer resistance protein (BCRP/ABCG2), solute carrier (SLC) transporters, organic anion-transporting polypeptides, or organic cation transporter 1. Similarly, metabolite 1 (M1) was not a substrate for any of these transporters except P-gp. Delamanid showed no inhibitory effect on ABC transporters MDR1, BCRP, and bile salt export pump (BSEP; ABCB11), SLC transporters, or organic anion transporters. M1 and M2 inhibited P-gp- and BCRP-mediated transport but did so only at the 50% inhibitory concentrations (M1, 4.65 and 5.71 μmol/liter, respectively; M2, 7.80 and 6.02 μmol/liter, respectively), well above the corresponding maximum concentration in plasma values observed following the administration of multiple doses in clinical trials. M3 and M4 did not affect the activities of any of the transporters tested. These in vitro data suggest that delamanid is unlikely to have clinically relevant interactions with drugs for which absorption and disposition are mediated by this group of transporters.", "token_count": 499, "char_count": 1864, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6848, "quality_score": 0.8424, "entities": { "genes": [ "MDR1", "ABCB1", "ABCB11", "ABCG2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:36.200365", "source": { "split": "train_shard_00000", "doc_id": 4047 }, "chunk_id": "train_shard_00000_4047_0", "global_id": 4493 }, { "text": "Antitubercular Agent Delamanid and Metabolites as Substrates and Inhibitors of ABC and Solute Carrier Transporters.", "token_count": 32, "char_count": 115, "word_count": 15, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:36.560712", "source": { "split": "train_shard_00000", "doc_id": 4047 }, "chunk_id": "train_shard_00000_4047_1", "global_id": 4494 }, { "text": "Tolvaptan is a selective V2-receptor antagonist primarily metabolized by CYP3A. The present study investigated the hepatocellular disposition of tolvaptan and the generated tolvaptan metabolites, DM-4103 and DM-4107, as well as the potential for drug-drug interaction (DDIs) with metabolic and transport proteins in sandwich-cultured human hepatocytes (SCHH). Tolvaptan was incubated with SCHH and quantified by LC-MS/MS. Pioglitazone, verapamil, MK-571 and elacridar were used as inhibitors to investigate mechanisms of transport and metabolism of tolvaptan and metabolites. Taurocholate (TCA), pravastatin, digoxin, and metformin were used as transporter probes to investigate which transport proteins were inhibited by tolvaptan and metabolites. Cellular accumulation of tolvaptan (0.15-50 μM), DM-4103 and DM-4107 in SCHH was concentration dependent. Tolvaptan accumulation (15 μM) in SCHH was not altered markedly by 50 μM pioglitazone, verapamil or MK-571, or 10 μM elacridar. Co-incubation of tolvaptan with pioglitazone, verapamil, MK-571 and elacridar reduced DM-4107 accumulation by 45.6, 79.8, 94.5 and 23.0%, respectively, relative to control. Co-incubation with increasing tolvaptan concentrations (0.15-50 μM) decreased TCA (2.5 μM) cell+bile accumulation and the TCA biliary excretion index (BEI; from 76% to 51%), consistent with inhibition of the bile salt export pump (BSEP). Tolvaptan (15 μM) had no effect on the cellular accumulation of 2.5 μM pravastatin or metformin", "token_count": 515, "char_count": 1489, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5784, "quality_score": 0.7892, "entities": { "genes": [ "CYP3A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:39:37.188702", "source": { "split": "train_shard_00000", "doc_id": 4048 }, "chunk_id": "train_shard_00000_4048_0", "global_id": 4495 }, { "text": "Digoxin cellular accumulation increased and the BEI of digoxin decreased from 23.9% to 8.1% in the presence of 15 μM tolvaptan, consistent with inhibition of P-glycoprotein (P-gp). In summary, SCHH studies revealed potential metabolic- and transporter-mediated DDIs involving tolvaptan and metabolites.\n\nHepatocellular Disposition and Transporter Interactions with Tolvaptan and Metabolites in Sandwich-Cultured Human Hepatocytes.", "token_count": 132, "char_count": 430, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:37.611223", "source": { "split": "train_shard_00000", "doc_id": 4048 }, "chunk_id": "train_shard_00000_4048_1", "global_id": 4496 }, { "text": "Few-layer transition-metal dichalcogenide WSe2/MoSe2 nanosheets are fabricated by a liquid exfoliation technique using sodium deoxycholate bile salt as surfactant, and their nonlinear optical properties are investigated based on a balanced twin-detector measurement scheme. It is demonstrated that both types of nanosheets exhibit nonlinear saturable absorption properties at the wavelength of 1.55 μm. By depositing the nanosheets on side polished fiber (SPF) or mixing the nanosheets with polyvinyl alcohol (PVA) solution, SPF-WSe2 saturable absorber (SA), SPF-MoSe2 SA, PVA-WSe2 SA, and PVA-MoSe2 SA are successfully fabricated and further tested in erbium-doped fiber lasers. The SPF-based SA is capable of operating at the high pump regime without damage, and a train of 3252.65 MHz harmonically mode-locked pulses are obtained based on the SPF-WSe2 SA. Soliton mode locking operations are also achieved in the fiber laser separately with other three types of SAs, confirming that the WSe2 and MoSe2 nanosheets could act as cost-effective high-power SAs for ultrafast optics.\n\nErbium-doped fiber laser passively mode locked with few-layer WSe2/MoSe2 nanosheets.", "token_count": 332, "char_count": 1166, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6848, "quality_score": 0.8424, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:38.180161", "source": { "split": "train_shard_00000", "doc_id": 4049 }, "chunk_id": "train_shard_00000_4049_0", "global_id": 4497 }, { "text": "Efficient use of xylose along with glucose is necessary for the economic production of lignocellulosic based biofuels. Xylose transporters play an important role in the microorganisms for efficient utilization of xylose. In the present study, a novel method has been developed for a rapid assay of xylose transport activity in the xylose-utilizing isolates and other known yeasts. An assay was conducted to compare the activity of β-xylosidase using p-nitrophenyl-β-D-xylopyranoside (pNPX) in the intact, intracellular, and extracellular yeasts cells showing xylose transporter. Saccharomyces cerevisiae (MTCC 170) showed no xylosidase activity, while little growth was observed in the xylose-containing medium. Although other yeasts, i.e., Kluyveromyces marxianus NIRE-K1 (MTCC 5933), K. marxianus NIRE-K3 (MTCC 5934), and Candida tropicalis (MTCC 230), showed xylosidase activity in intact, intracellular, and extracellular culture. The xylosidase activity in intact cell was higher than that of extracellular and intracellular activity in all the yeast cells. The enzyme activity was higher in case of K. marxianus NIRE-K1 and K. marxianus NIRE-K3 rather than the C. tropicalis. Further, better xylosidase activity was observed in adapted K. marxianus cells which were 2.79-28.46 % higher than that of native (non-adapted) strains, which indicates the significant improvement in xylose transportation.\n\nEffect of Evolutionary Adaption on Xylosidase Activity in Thermotolerant Yeast Isolates Kluyveromyces marxianus NIRE-K1 and NIRE-K3.", "token_count": 472, "char_count": 1538, "word_count": 212, "semantic_coherence": 1, "information_density": 0.566, "quality_score": 0.783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:38.831059", "source": { "split": "train_shard_00000", "doc_id": 4050 }, "chunk_id": "train_shard_00000_4050_0", "global_id": 4498 }, { "text": "The number of genomes that have been deposited in databases has increased exponentially after the advent of Next-Generation Sequencing (NGS), which produces high-throughput sequence data; this circumstance has demanded the development of new bioinformatics software and the creation of new areas, such as comparative genomics. In comparative genomics, the genetic content of an organism is compared against other organisms, which helps in the prediction of gene function and coding region sequences, identification of evolutionary events and determination of phylogenetic relationships. However, expanding comparative genomics to a large number of related bacteria, we can infer their lifestyles, gene repertoires and minimal genome size. In this context, a powerful approach called Pan-genome has been initiated and developed. This approach involves the genomic comparison of different strains of the same species, or even genus. Its main goal is to establish the total number of non-redundant genes that are present in a determined dataset. Pan-genome consists of three parts: core genome; accessory or dispensable genome; and species-specific or strain-specific genes. Furthermore, pan-genome is considered to be \"open\" as long as new genes are added significantly to the total repertoire for each new additional genome and \"closed\" when the newly added genomes cannot be inferred to significantly increase the total repertoire of the genes. To perform all of the required calculations, a substantial amount of software has been developed, based on orthologous and paralogous gene identification.\n\nInside the Pan-genome - Methods and Software Overview.", "token_count": 349, "char_count": 1655, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:39.758747", "source": { "split": "train_shard_00000", "doc_id": 4051 }, "chunk_id": "train_shard_00000_4051_0", "global_id": 4499 }, { "text": "The genus Vibrio includes several food-borne pathogens that cause a spectrum of clinical conditions including septicemia, cholera and milder forms of gastroenteritis. Several Vibrio spp. are commonly associated with food-borne transmission including Vibrio cholerae, Vibrio parahemolyticus, and Vibrio vulnificus. Microbiological analysis for enumeration and isolation of Vibrio spp. were carried out for a total of 93 samples of seafood, meat and meat products from different geographic localities in Libya (Tripoli, Regdalin, Janzour and Tobruk). Vibrio spp. were detected by conventional cultural and molecular method using PCR and sequencing of 16S rDNA. Out of the 93 cultured samples only 48 (51.6%) yielded colonies on Thiosulfate Citrate Bile Salt agar (TCBS) with culture characteristics of Vibrio spp. More than half (n=27) of processed seafood samples (n=46) yielded colonies on TCBS, while only 44.6 % of samples of meat and meat products showed colonies on TCBS. Among cultured seafood samples, the highest bacterial count was recorded in clam with a count of 3.8 ×10(4) CFU\\g. Chicken burger samples showed the highest bacterial count with 6.5 ×10(4) CFU\\g. Molecular analysis of the isolates obtained in this study, showed that 11 samples out of 48 (22.9%) were Vibrio spp. Vibrio parahemolyticus was isolated from camel meat for the first time. This study is an initial step to provide a baseline for future molecular research targeting Vibrio spp. foodborne illnesses. This data will be used to provide information on the magnitude of such pathogens in Libyan seafood, meat and meat products.\n\nIsolation and molecular identification of Vibrio spp. by sequencing of 16S rDNA from seafood, meat and meat products in Libya.", "token_count": 482, "char_count": 1737, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5396, "quality_score": 0.7698, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:41.513916", "source": { "split": "train_shard_00000", "doc_id": 4052 }, "chunk_id": "train_shard_00000_4052_0", "global_id": 4500 }, { "text": "Interference of bile salt transport is one of the underlying mechanisms for drug-induced liver injury (DILI). We developed a novel bile salt transport activity assay involving in situ biosynthesis of bile salts from their precursors in primary human, monkey, dog, rat, and mouse hepatocytes in suspension as well as LC-MS/MS determination of extracellular bile salts transported out of hepatocytes. Glycine- and taurine-conjugated bile acids were rapidly formed in hepatocytes and effectively transported into the extracellular medium. The bile salt formation and transport activities were time‒ and bile-acid-concentration‒dependent in primary human hepatocytes. The transport activity was inhibited by the bile salt export pump (BSEP) inhibitors ketoconazole, saquinavir, cyclosporine, and troglitazone. The assay was used to test 86 drugs for their potential to inhibit bile salt transport activity in human hepatocytes, which included 35 drugs associated with severe DILI (sDILI) and 51 with non-severe DILI (non-sDILI). Approximately 60% of the sDILI drugs showed potent inhibition (with IC50 values <50 μM), but only about 20% of the non-sDILI drugs showed this strength of inhibition in primary human hepatocytes and these drugs are associated only with cholestatic and mixed hepatocellular cholestatic (mixed) injuries. The sDILI drugs, which did not show substantial inhibition of bile salt transport activity, are likely to be associated with immune-mediated liver injury. Twenty-four drugs were also tested in monkey, dog, rat and mouse hepatocytes. Species differences in potency were observed with mouse being less sensitive than other species to inhibition of bile salt transport. In summary, a novel assay has been developed using hepatocytes in suspension from human and animal species that can be used to assess the potential for drugs and/or drug-derived metabolites to inhibit bile salt transport and/or formation activity", "token_count": 504, "char_count": 1941, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5319, "quality_score": 0.766, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:42.170166", "source": { "split": "train_shard_00000", "doc_id": 4053 }, "chunk_id": "train_shard_00000_4053_0", "global_id": 4501 }, { "text": "Drugs causing sDILI, except those by immune-mediated mechanism, are highly associated with potent inhibition of bile salt transport.\n\nInhibition of bile salt transport by drugs associated with liver injury in primary hepatocytes from human, monkey, dog, rat, and mouse.", "token_count": 66, "char_count": 269, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7949, "quality_score": 0.8974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:42.533433", "source": { "split": "train_shard_00000", "doc_id": 4053 }, "chunk_id": "train_shard_00000_4053_1", "global_id": 4502 }, { "text": "The emergence of genomics over the last 10 years has provided new insights into the evolution and virulence of extraintestinal Escherichia coli. By combining population genetics and phylogenetic approaches to analyze whole-genome sequences, it became possible to link genomic features to specific phenotypes, such as the ability to cause urinary tract infections. An E. coli chromosome can vary extensively in length, ranging from 4.3 to 6.2 Mb, encoding 4,084 to 6,453 proteins. This huge diversity is structured as a set of less than 2,000 genes (core genome) that are conserved between all the strains and a set of variable genes. Based on the core genome, the history of the species can be reliably reconstructed, revealing the recent emergence of phylogenetic groups A and B1 and the more ancient groups B2, F, and D. Urovirulence is most often observed in B2/F/D group strains and is a multigenic process involving numerous combinations of genes and specific alleles with epistatic interactions, all leading down multiple evolutionary paths. The genes involved mainly code for adhesins, toxins, iron capture systems, and protectins, as well as metabolic pathways and mutation-rate-control systems. However, the barrier between commensal and uropathogenic E. coli strains is difficult to draw as the factors that are responsible for virulence have probably also been selected to allow survival of E. coli as a commensal in the intestinal tract. Genomic studies have also demonstrated that infections are not the result of a unique and stable isolate, but rather often involve several isolates with variable levels of diversity that dynamically changes over time.\n\nPopulation Phylogenomics of Extraintestinal Pathogenic Escherichia coli.", "token_count": 430, "char_count": 1741, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:43.157374", "source": { "split": "train_shard_00000", "doc_id": 4054 }, "chunk_id": "train_shard_00000_4054_0", "global_id": 4503 }, { "text": "The adenoviral gene transfer of human aquaporin-1 (hAQP1) water channels to the liver of 17α-ethinylestradiol-induced cholestatic rats improves bile flow, in part by enhancing canalicular hAQP1-mediated osmotic water secretion. To gain insight into the mechanisms of 17α-ethinylestradiol cholestasis improvement, we studied the biliary output of bile salts (BS) and the functional expression of the canalicular BS export pump (BSEP; ABCB11). Adenovector encoding hAQP1 (AdhAQP1) or control vector was administered by retrograde intrabiliary infusion. AdhAQP1-transduced cholestatic rats increased the biliary output of major endogenous BS (50%-80%, P < 0.05) as well as that of taurocholate administered in choleretic or trace radiolabel amounts (around 60%, P < 0.05). Moreover, liver transduction with AdhAQP1 normalized serum BS levels, otherwise markedly elevated in cholestatic animals. AdhAQP1 treatment was unable to improve BSEP protein expression in cholestasis; however, its transport activity, assessed by adenosine triphosphate-dependent taurocholate transport in canalicular membrane vesicles, was induced by 90% (P < 0.05). AdhAQP1 administration in noncholestatic rats induced no significant changes in either biliary BS output or BSEP activity. Canalicular BSEP, mostly present in raft (high cholesterol) microdomains in control rats, was largely found in nonraft (low cholesterol) microdomains in cholestasis. Considering that BSEP activity directly depends on canalicular membrane cholesterol content, decreased BSEP presence in rafts may contribute to BSEP activity decline in 17α-ethinylestradiol cholestasis", "token_count": 485, "char_count": 1628, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:43.804504", "source": { "split": "train_shard_00000", "doc_id": 4055 }, "chunk_id": "train_shard_00000_4055_0", "global_id": 4504 }, { "text": "In AdhAQP1-transduced cholestatic rats, BSEP showed a canalicular microdomain distribution similar to that of control rats, which provides an explanation for the improved BSEP activity.\n\nHepatic gene transfer of human aquaporin-1 improves bile salt secretory failure in rats with estrogen-induced cholestasis.", "token_count": 84, "char_count": 309, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9024, "quality_score": 0.9512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:44.177149", "source": { "split": "train_shard_00000", "doc_id": 4055 }, "chunk_id": "train_shard_00000_4055_1", "global_id": 4505 }, { "text": "Identifying microbial strains and characterizing their functional potential is essential for pathogen discovery, epidemiology and population genomics. We present pangenome-based phylogenomic analysis (PanPhlAn; http://segatalab.cibio.unitn.it/tools/panphlan), a tool that uses metagenomic data to achieve strain-level microbial profiling resolution. PanPhlAn recognized outbreak strains, produced the largest strain-level population genomic study of human-associated bacteria and, in combination with metatranscriptomics, profiled the transcriptional activity of strains in complex communities.\n\nStrain-level microbial epidemiology and population genomics from shotgun metagenomics.", "token_count": 163, "char_count": 682, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8219, "quality_score": 0.911, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:44.634844", "source": { "split": "train_shard_00000", "doc_id": 4056 }, "chunk_id": "train_shard_00000_4056_0", "global_id": 4506 }, { "text": "The aim of this study was to evaluate the safety of enterococci isolated from Chinese infants and screen out potential probiotic candidates. One hundred eight strains were isolated from feces of 34 healthy infants, and 38 strains of Enterococcus spp. were categorized as follows: E. faecalis (22), E. faecium (10), E. hirae (3), E. durans (2), and E. casseliflavus (1). Of these, 72.7% of E. faecalis came from infants delivered by cesarean and 62.5% of E. faecium from infants delivered vaginally. For safety evaluation of strains, we determined presence of virulence genes; production of hemolysin, gelatinase, and biofilm; and antimicrobial susceptibility of enterococci. Six out of 14 virulence genes were detected with a distribution of gelE (26.3%), cylA (39.4%), esp (15.8%), efaA (63.2%), asa1 (50.0%), and ace (50.0%). In phenotype analysis, 36.8% of the strains exhibited positive hemolytic activity and 17.5% were positive for production of gelatinase. Results of antimicrobial susceptibility showed that different percentages of the strains were resistant to ciprofloxacin (5.2%), vancomycin (7.8%), rifampicin (10.5%), erythromycin (52.6%), and gentamycin (52.6%); remarkably, none of the strains were resistant to ampicillin or chloramphenicol. In total, 10 strains, including 6 E. faecium, which are free of virulence determinants and sensitive to common antimicrobial agents (e.g., ampicillin and vancomycin), were further assessed for their probiotic properties. All strains survived well in simulated gastric fluid and intestinal tract, with maximum reductions of 0.600 and 0.887 log cfu/mL, respectively. Six strains of E", "token_count": 528, "char_count": 1640, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:39:45.285046", "source": { "split": "train_shard_00000", "doc_id": 4057 }, "chunk_id": "train_shard_00000_4057_0", "global_id": 4507 }, { "text": "faecium could resist 0.3 to 1.0% bile salt, of which E. faecium WEFA23 presented the highest growth (75.06%) at 1.0% bile salt. All strains showed bile salt hydrolase activity on glycodeoxycholic acid, but only 3 of E. faecium showed activity on taurodeoxycholic acid. These results deliver useful information on the safety of enterococci in infants in China, and provide a protocol to screen probiotics for absence of virulence and antimicrobial susceptibility of enterococci.\n\nScreening probiotic strains for safety: Evaluation of virulence and antimicrobial susceptibility of enterococci from healthy Chinese infants.", "token_count": 179, "char_count": 620, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [ "WEFA23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:45.752167", "source": { "split": "train_shard_00000", "doc_id": 4057 }, "chunk_id": "train_shard_00000_4057_1", "global_id": 4508 }, { "text": "The large legume genus Mimosa is known to be associated with both alphaproteobacterial and betaproteobacterial symbionts, depending on environment and plant taxonomy, e.g., Brazilian species are preferentially nodulated by Burkholderia, whereas those in Mexico are associated with alphaproteobacterial symbionts. Little is known, however, about the symbiotic preferences of Mimosa spp. at the southern subtropical limits of the genus. In the present study, rhizobia were isolated from field-collected nodules from Mimosa species that are native to a region in southern Uruguay. Phylogenetic analyses of sequences of the 16S rRNA, recA, and gyrB core genome and the nifH and nodA symbiosis-essential loci confirmed that all the isolates belonged to the genus Cupriavidus However, none were in the well-described symbiotic species C. taiwanensis, but instead they were closely related to other species, such as C. necator, and to species not previously known to be symbiotic (or diazotrophic), such as C. basilensis and C. pinatubonensis Selection of these novel Cupriavidus symbionts by Uruguayan Mimosa spp. is most likely due to their geographical separation from their Brazilian cousins and to the characteristics of the soils in which they were found.\n\nNovel Cupriavidus Strains Isolated from Root Nodules of Native Uruguayan Mimosa Species.", "token_count": 362, "char_count": 1344, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:46.360050", "source": { "split": "train_shard_00000", "doc_id": 4058 }, "chunk_id": "train_shard_00000_4058_0", "global_id": 4509 }, { "text": "Genomic islands are genomic fragments of alien origin in bacterial and archaeal genomes, usually involved in symbiosis or pathogenesis. In this work, we described Zisland Explorer, a novel tool to predict genomic islands based on the segmental cumulative GC profile. Zisland Explorer was designed with a novel strategy, as well as a combination of the homogeneity and heterogeneity of genomic sequences. While the sequence homogeneity reflects the composition consistence within each island, the heterogeneity measures the composition bias between an island and the core genome. The performance of Zisland Explorer was evaluated on the data sets of 11 different organisms. Our results suggested that the true-positive rate (TPR) of Zisland Explorer was at least 10.3% higher than that of four other widely used tools. On the other hand, the new tool did not lose overall accuracy with the improvement in the TPR and showed better equilibrium among various evaluation indexes. Also, Zisland Explorer showed better accuracy in the prediction of experimental island data. Overall, the tool provides an alternative solution over other tools, which expands the field of island prediction and offers a supplement to increase the performance of the distinct predicting strategy. We have provided a web service as well as a graphical user interface and open-source code across multiple platforms for Zisland Explorer, which is available at http://cefg.uestc.edu.cn/Zisland_Explorer/ or http://tubic.tju.edu.cn/Zisland_Explorer/.\n\nZisland Explorer: detect genomic islands by combining homogeneity and heterogeneity properties.", "token_count": 366, "char_count": 1617, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6094, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:46.978551", "source": { "split": "train_shard_00000", "doc_id": 4059 }, "chunk_id": "train_shard_00000_4059_0", "global_id": 4510 }, { "text": "Anion exchanger 2 (AE2), the principal bicarbonate secretor in the human biliary tree, is down-regulated in primary biliary cholangitis. AE2 creates a \"bicarbonate umbrella\" that protects cholangiocytes from the proapoptotic effects of bile salts by maintaining them deprotonated. We observed that knockdown of AE2 sensitized immortalized H69 human cholangiocytes to not only bile salt-induced apoptosis (BSIA) but also etoposide-induced apoptosis. Because the toxicity of etoposide is pH-independent, there could be a more general mechanism for sensitization of AE2-depleted cholangiocytes to apoptotic stimuli. We found that AE2 deficiency led to intracellular bicarbonate accumulation and increased expression and activity of soluble adenylyl cyclase (sAC), an evolutionarily conserved bicarbonate sensor. Thus, we hypothesized that sAC regulates BSIA. H69 cholangiocytes and primary mouse cholangiocytes were used as models. The sAC-specific inhibitor KH7 not only reversed sensitization to BSIA in AE2-depleted H69 cholangiocytes but even completely prevented BSIA. sAC knockdown by tetracycline-inducible short hairpin RNA also prevented BSIA. In addition, sAC inhibition reversed BSIA membrane blebbing, nuclear condensation, and DNA fragmentation. Furthermore, sAC inhibition also prevented BSIA in primary mouse cholangiocytes. Mechanistically, sAC inhibition prevented Bax phosphorylation at Thr167 and mitochondrial translocation of Bax and cytochrome c release but not c-Jun N-terminal kinase activation during BSIA. Finally, BSIA in H69 cholangiocytes was inhibited by intracellular Ca(2+) chelation, aggravated by thapsigargin, and unaffected by removal of extracellular calcium.", "token_count": 503, "char_count": 1693, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6306, "quality_score": 0.8153, "entities": { "genes": [ "KH7", "AE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:47.633962", "source": { "split": "train_shard_00000", "doc_id": 4060 }, "chunk_id": "train_shard_00000_4060_0", "global_id": 4511 }, { "text": "Soluble Adenylyl Cyclase Regulates Bile Salt-Induced Apoptosis in Human Cholangiocytes.", "token_count": 30, "char_count": 87, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:47.986108", "source": { "split": "train_shard_00000", "doc_id": 4060 }, "chunk_id": "train_shard_00000_4060_1", "global_id": 4512 }, { "text": "Background. Not all yeast alcohol dehydrogenase 2 (ADH2) are repressed by glucose, as reported in Saccharomyces cerevisiae. Pichia stipitis ADH2 is regulated by oxygen instead of glucose, whereas Kluyveromyces marxianus ADH2 is regulated by neither glucose nor ethanol. For this reason, ADH2 regulation of yeasts may be species dependent, leading to a different type of expression and fermentation efficiency. Lachancea fermentati is a highly efficient ethanol producer, fast-growing cells and adapted to fermentation-related stresses such as ethanol and organic acid, but the metabolic information regarding the regulation of glucose and ethanol production is still lacking. Methods. Our investigation started with the stimulation of ADH2 activity from S. cerevisiae and L. fermentati by glucose and ethanol induction in a glucose-repressed medium. The study also embarked on the retrospective analysis of ADH2 genomic and protein level through direct sequencing and sites identification. Based on the sequence generated, we demonstrated ADH2 gene expression highlighting the conserved NAD(P)-binding domain in the context of glucose fermentation and ethanol production. Results. An increase of ADH2 activity was observed in starved L. fermentati (LfeADH2) and S. cerevisiae (SceADH2) in response to 2% (w/v) glucose induction. These suggest that in the presence of glucose, ADH2 activity was activated instead of being repressed. An induction of 0.5% (v/v) ethanol also increased LfeADH2 activity, promoting ethanol resistance, whereas accumulating acetic acid at a later stage of fermentation stimulated ADH2 activity and enhanced glucose consumption rates. The lack in upper stream activating sequence (UAS) and TATA elements hindered the possibility of Adr1 binding to LfeADH2. Transcription factors such as SP1 and RAP1 observed in LfeADH2 sequence have been implicated in the regulation of many genes including ADH2. In glucose fermentation, L", "token_count": 509, "char_count": 1950, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.8089, "entities": { "genes": [ "ADH2", "RAP1", "SP1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:48.612982", "source": { "split": "train_shard_00000", "doc_id": 4061 }, "chunk_id": "train_shard_00000_4061_0", "global_id": 4513 }, { "text": "fermentati exhibited a bell-shaped ADH2 expression, showing the highest expression when glucose was depleted and ethanol-acetic acid was increased. Meanwhile, S. cerevisiae showed a constitutive ADH2 expression throughout the fermentation process. Discussion. ADH2 expression in L. fermentati may be subjected to changes in the presence of non-fermentative carbon source. The nucleotide sequence showed that ADH2 transcription could be influenced by other transcription genes of glycolysis oriented due to the lack of specific activation sites for Adr1. Our study suggests that if Adr1 is not capable of promoting LfeADH2 activation, the transcription can be controlled by Rap1 and Sp1 due to their inherent roles. Therefore in future, it is interesting to observe ADH2 gene being highly regulated by these potential transcription factors and functioned as a promoter for yeast under high volume of ethanol and organic acids.\n\nEffects of glucose, ethanol and acetic acid on regulation of ADH2 gene from Lachancea fermentati.", "token_count": 246, "char_count": 1024, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6954, "quality_score": 0.8477, "entities": { "genes": [ "ADH2" ], "proteins": [], "pathways": [ "glycolysis", "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:49.095284", "source": { "split": "train_shard_00000", "doc_id": 4061 }, "chunk_id": "train_shard_00000_4061_1", "global_id": 4514 }, { "text": "In order to identify daily changes in digestive physiology in developing gilthead seabream larvae, the enzyme activity (trypsin, lipases and α-amylase) and gene expression (trypsinogen-try, chymotrypsinogen-ctrb, bile salt-activated lipase-cel1b, phospholipase A2-pla2 and α-amylase-amy2a) were measured during a 24h cycle in larvae reared under a 12h light/12h dark photoperiod. Larvae were sampled at 10, 18, 30 and 60days post-hatch. In each sampling day, larvae were sampled every 3h during a complete 24h cycle. The enzyme activity and gene expression exhibited a marked dependent behavior to the light/darkness cycle in all tested ages. The patterns of activity and expression of all tested enzymes were compared to the feeding pattern found in the same larvae, which showed a rhythmic feeding pattern with a strong light synchronization. In the four tested ages, the activities of trypsin, and to a lesser extent lipases and amylase, were related to feeding activity. Molecular expression of the pancreatic enzymes tended to increase during the night, probably as an anticipation of the forthcoming ingestion of food that will take place during the next light period. It follows that the enzymatic activities are being regulated at translational and/or post-translational level. The potential variability of enzyme secretion along the whole day is an important factor to take into account in future studies. A particularly striking consequence of the present results is the reliability of studies based in only one daily sample taken at the same hour of the day, as those focused to assess ontogeny of digestive enzymes.\n\nDaily rhythms of digestive enzyme activity and gene expression in gilthead seabream (Sparus aurata) during ontogeny.", "token_count": 464, "char_count": 1745, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5741, "quality_score": 0.7871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:49.731617", "source": { "split": "train_shard_00000", "doc_id": 4062 }, "chunk_id": "train_shard_00000_4062_0", "global_id": 4515 }, { "text": "Saccharomyces cerevisiae is used as a host strain in bioproduction, because of its rapid growth, ease of genetic manipulation, and high reducing capacity. However, the heat produced during the fermentation processes inhibits the biological activities and growth of the yeast cells. We performed whole-genome sequencing of 19 intermediate strains previously obtained during adaptation experiments under heat stress; 49 mutations were found in the adaptation steps. Phylogenetic tree revealed at least five events in which these strains had acquired mutations in the CDC25 gene. Reconstructed CDC25 point mutants based on a parental strain had acquired thermotolerance without any growth defects. These mutations led to the downregulation of the cAMP-dependent protein kinase (PKA) signaling pathway, which controls a variety of processes such as cell-cycle progression and stress tolerance. The one-point mutations in CDC25 were involved in the global transcriptional regulation through the cAMP/PKA pathway. Additionally, the mutations enabled efficient ethanol fermentation at 39 °C, suggesting that the one-point mutations in CDC25 may contribute to bioproduction.\n\nReconstruction of thermotolerant yeast by one-point mutation identified through whole-genome analyses of adaptively-evolved strains.", "token_count": 303, "char_count": 1300, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8362, "entities": { "genes": [ "CDC25" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:50.299831", "source": { "split": "train_shard_00000", "doc_id": 4063 }, "chunk_id": "train_shard_00000_4063_0", "global_id": 4516 }, { "text": "Sulfurospirillum spp. play an important role in sulfur and nitrogen cycling, and contain metabolic versatility that enables reduction of a wide range of electron acceptors, including thiosulfate, tetrathionate, polysulfide, nitrate, and nitrite. Here we describe the assembly of a Sulfurospirillum genome obtained from the metagenome of an electrosynthetic microbiome. The ubiquity and persistence of this organism in microbial electrosynthesis systems suggest it plays an important role in reactor stability and performance. Understanding why this organism is present and elucidating its genetic repertoire provide a genomic and ecological foundation for future studies where Sulfurospirillum are found, especially in electrode-associated communities. Metabolic comparisons and in-depth analysis of unique genes revealed potential ecological niche-specific capabilities within the Sulfurospirillum genus. The functional similarities common to all genomes, i.e., core genome, and unique gene clusters found only in a single genome were identified. Based upon 16S rRNA gene phylogenetic analysis and average nucleotide identity, the Sulfurospirillum draft genome was found to be most closely related to Sulfurospirillum cavolei. Characterization of the draft genome described herein provides pathway-specific details of the metabolic significance of the newly described Sulfurospirillum cavolei MES and, importantly, yields insight to the ecology of the genus as a whole. Comparison of eleven sequenced Sulfurospirillum genomes revealed a total of 6246 gene clusters in the pan-genome. Of the total gene clusters, 18.5% were shared among all eleven genomes and 50% were unique to a single genome. While most Sulfurospirillum spp. reduce nitrate to ammonium, five of the eleven Sulfurospirillum strains encode for a nitrous oxide reductase (nos) cluster with an atypical nitrous-oxide reductase, suggesting a utility for this genus in reduction of the nitrous oxide, and as a potential sink for this potent greenhouse gas.", "token_count": 500, "char_count": 2020, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:50.946807", "source": { "split": "train_shard_00000", "doc_id": 4064 }, "chunk_id": "train_shard_00000_4064_0", "global_id": 4517 }, { "text": "Comparative Genomic Analysis of Sulfurospirillum cavolei MES Reconstructed from the Metagenome of an Electrosynthetic Microbiome.", "token_count": 36, "char_count": 129, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:51.312972", "source": { "split": "train_shard_00000", "doc_id": 4064 }, "chunk_id": "train_shard_00000_4064_1", "global_id": 4518 }, { "text": "In 2003, Acanthamoeba polyphaga mimivirus (APMV) was discovered as parasitizing Acanthamoeba. It was revealed to exhibit remarkable features, especially odd genomic characteristics, and founded viral family Mimiviridae. Subsequently, a second family of giant amoebal viruses was described, Marseilleviridae, whose prototype member is Marseillevirus, discovered in 2009. Currently, the genomes of seven different members of this family have been fully sequenced. Previous phylogenetic analysis suggested the existence of three Marseilleviridae lineages: A, B and C. Here, we describe a new member of this family, Brazilian Marseillevirus (BrMV), which was isolated from a Brazilian sample and whose genome was fully sequenced and analyzed. Surprisingly, data from phylogenetic analyses and comparative genomics, including mean amino acid identity between BrMV and other Marseilleviridae members and the analyses of the core genome and pan-genome of marseilleviruses, indicated that this virus can be assigned to a new Marseilleviridae lineage. Even if the BrMV genome is one of the smallest among Marseilleviridae members, it harbors the second largest gene content into this family. In addition, the BrMV genome encodes 29 ORFans. Here, we describe the isolation and genome analyses of the BrMV strain, and propose its classification as the prototype virus of a new lineage D within the family Marseilleviridae.\n\nA Brazilian Marseillevirus Is the Founding Member of a Lineage in Family Marseilleviridae.", "token_count": 395, "char_count": 1503, "word_count": 216, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:51.926979", "source": { "split": "train_shard_00000", "doc_id": 4065 }, "chunk_id": "train_shard_00000_4065_0", "global_id": 4519 }, { "text": "Clostridium perfringens type A is a common source of foodborne illness (FBI) in humans. Vegetative cells sporulate in the small intestinal tract and produce the major pathogenic factor C. perfringens enterotoxin. Although sporulation plays a critical role in the pathogenesis of FBI, the mechanisms inducing sporulation remain unclear. Bile salts were shown previously to induce sporulation, and we confirmed deoxycholate (DCA)-induced sporulation in C. perfringens strain NCTC8239 cocultured with human intestinal epithelial Caco-2 cells. In the present study, we performed transcriptome analyses of strain NCTC8239 in order to elucidate the mechanism underlying DCA-induced sporulation. Of the 2,761 genes analyzed, 333 were up- or downregulated during DCA-induced sporulation and included genes for cell division, nutrient metabolism, signal transduction, and defense mechanisms. In contrast, the virulence-associated transcriptional regulators (the VirR/VirS system, the agr system, codY, and abrB) were not activated by DCA. DCA markedly increased the expression of signaling molecules controlled by Spo0A, the master regulator of the sporulation process, whereas the expression of spo0A itself was not altered in the presence or absence of DCA. The phosphorylation of Spo0A was enhanced in the presence of DCA. Collectively, these results demonstrated that DCA induced sporulation, at least partially, by facilitating the phosphorylation of Spo0A and activating Spo0A-regulated genes in strain NCTC8239 while altering the expression of various genes.\n\nTranscriptional Profile during Deoxycholate-Induced Sporulation in a Clostridium perfringens Isolate Causing Foodborne Illness.", "token_count": 448, "char_count": 1685, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6201, "quality_score": 0.81, "entities": { "genes": [ "NCTC8239" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:52.562309", "source": { "split": "train_shard_00000", "doc_id": 4066 }, "chunk_id": "train_shard_00000_4066_0", "global_id": 4520 }, { "text": "The objective of the present study was to prepare quercitin (QT) loaded o/w nanoemulsion using food grade surfactants (saponin and tween 80). The prepared nanoemulsion) was stable up to 30 days. The average particle size of the nanoemulsion was 52 ± 10 nm. The formation of saponin stabilized nanoemulsion was confirmed by transmission electron microscopy. Quercitin (QT) trapped nanoemulsion showed higher stability on exposure to UV light (254 nm) as compared to water/ethanol system. The degradation rate was found to decrease from 9 ± 1%, 11 ± 1% at pH 7.4, 8.0 respectively as compared to 42 ± 2% in water/ethanol system. Attempt was also made to study the interaction of QT with two different bile salts (sodium cholate and sodium taurocholate). The free radical scavenging activity of DPPH quercitin and curcumin was compared in NEm media. The obtained IC50 value of quercitin, curcumin and ascorbic acid are 28.88 ± 1, 45.53 ± 2 and 51.51 ± 2 μM respectively. The values of binding constant for sodium cholate (NaC) and sodium taurocholate (NaTC) are 2.66 × 10(5) and 2.72 × 10(4) M(-1) respectively. Sodium cholate (NaC) was found to show strong interaction towards quercitin (QT) due to more electron density on oxygen atom of carboxylate ion.\n\nFormulation of saponin stabilized nanoemulsion by ultrasonic method and its role to protect the degradation of quercitin from UV light.", "token_count": 444, "char_count": 1390, "word_count": 226, "semantic_coherence": 1, "information_density": 0.615, "quality_score": 0.8075, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:53.189923", "source": { "split": "train_shard_00000", "doc_id": 4067 }, "chunk_id": "train_shard_00000_4067_0", "global_id": 4521 }, { "text": "ISIS 141923 is a model compound of 2'-O-(2-methoxyethyl) (2'-MOE) modified antisense oligonucleotides (ASOs). The purpose of this study is to determine whether ISIS 141923 is a substrate or an inhibitor against a panel of nine major uptake or efflux drug transporters, namely breast cancer resistance protein (BCRP), P-glycoprotein (P-gp), organic anion transporter (OAT)1, OAT3, organic cation transporter (OCT)1, OCT2, organic anion transporting polypeptide 1B (OATP1B)1, OATP1B3, and bile salt export pump (BSEP), in vitro. The uptake test system for transporters in the solute carrier (SLC) family (OAT1, OAT3, OCT1, OCT2, OATP1B1, and OATP1B3) was studied in Madin-Darby canine kidney (MDCK)-II cells transfected to express the transporters of interest. BCRP was studied using carcinoma colon-2 (Caco-2) cells with endogenously expressed BCRP. P-gp transporter was studied in MDCK-multi-drug resistance 1 (MDR1) cells, while BSEP was studied using Spodoptera frugiperda 9 (Sf9) membrane vesicles containing human BSEP. The ISIS 141293 concentrations evaluated were 10 and 100 μM for the substrate and inhibition study, respectively. Cellular uptake of ISIS 141923 was analyzed using a high performance liquid chromatography-mass spectrometry method, while concentrations of known substrates (used as positive controls) of each transporters evaluated were determined by radiometric detection", "token_count": 449, "char_count": 1395, "word_count": 194, "semantic_coherence": 1, "information_density": 0.7062, "quality_score": 0.8531, "entities": { "genes": [ "OCT1", "OCT2", "OAT1", "MDR1", "OATP1B", "OAT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:53.823489", "source": { "split": "train_shard_00000", "doc_id": 4068 }, "chunk_id": "train_shard_00000_4068_0", "global_id": 4522 }, { "text": "At 10 μM ISIS 141923, there was no significant transporter-mediated uptake of ISIS 141923 (P > 0.05) in the SLC family, and the efflux ratios were not above 2.0 for either BCRP or P-gp. Therefore, no transporter-mediated uptake of ISIS 141923 was observed by any of the nine transporters studied. At 100 μM ISIS 141923, the % inhibition was in the range of -16.0% to 19.0% for the nine transporters evaluated. Therefore, ISIS 141923 is not considered as an inhibitor of the nine transporters studied. Overall, the results from this study suggest that it is unlikely that ISIS 141923 or similar 2'-MOE ASOs would interact with small molecule drugs either as a victim (substrate) or perpetrator (inhibitor) of major transporters in humans. The results from available clinical drug-drug interaction studies conducted with this class of compounds to date are also supportive of this conclusion.\n\nLack of Interactions Between an Antisense Oligonucleotide with 2'-O-(2-Methoxyethyl) Modifications and Major Drug Transporters.", "token_count": 320, "char_count": 1019, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:54.396851", "source": { "split": "train_shard_00000", "doc_id": 4068 }, "chunk_id": "train_shard_00000_4068_1", "global_id": 4523 }, { "text": "In this study, 69 lactobacilli isolated from Tibetan Qula, a raw yak milk cheese, were screened for their potential use as probiotics. The isolates were tested in terms of: Their ability to survive at pH 2.0, pH 3.0, and in the presence of 0.3% bile salts; tolerance of simulated gastric and intestinal juices; antimicrobial activity; sensitivity against 11 specific antibiotics; and their cell surface hydrophobicity. The results show that out of the 69 strains, 29 strains (42%) had survival rates above 90% after 2 h of incubation at pH values of 2.0 or 3.0. Of these 29 strains, 21 strains showed a tolerance for 0.3% bile salt. Incubation of these 21 isolates in simulated gastrointestinal fluid for 3 h revealed survival rates above 90%; the survival rate for 20 of these isolates remained above 90% after 4 h of incubation in simulated intestinal fluid. The viable counts of bacteria after incubation in simulated gastric fluid for 3 h and simulated intestinal fluid for 4 h were both significantly different compared with the counts at 0 h (p<0.001). Further screening performed on the above 20 isolates indicated that all 20 lactobacilli strains exhibited inhibitory activity against Micrococcus luteus ATCC 4698, Bacillus subtilis ATCC 6633, Listeria monocytogenes ATCC 19115, and Salmonella enterica ATCC 43971. Moreover, all of the strains were resistant to vancomycin and streptomycin", "token_count": 430, "char_count": 1397, "word_count": 223, "semantic_coherence": 1, "information_density": 0.565, "quality_score": 0.7825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:55.023124", "source": { "split": "train_shard_00000", "doc_id": 4069 }, "chunk_id": "train_shard_00000_4069_0", "global_id": 4524 }, { "text": "Of the 20 strains, three were resistant to all 11 elected antibiotics (ciprofloxacin, erythromycin, tetracycline, penicillin G, ampicillin, streptomycin, polymyxin B, vancomycin, chloramphenicol, rifampicin, and gentamicin) in this study, and five were sensitive to more than half of the antibiotics. Additionally, the cell surface hydrophobicity of seven of the 20 lactobacilli strains was above 70%, including strains Lactobacillus casei 1,133 (92%), Lactobacillus plantarum 1086-1 (82%), Lactobacillus casei 1089 (81%), Lactobacillus casei 1138 (79%), Lactobacillus buchneri 1059 (78%), Lactobacillus plantarum1141 (75%), and Lactobacillus plantarum 1197 (71%). Together, these results suggest that these seven strains are good probiotic candidates, and that tolerance against bile acid, simulated gastric and intestinal juices, antimicrobial activity, antibiotic resistance, and cell surface hydrophobicity could be adopted for preliminary screening of potentially probiotic lactobacilli.\n\nScreening of Probiotic Activities of Lactobacilli Strains Isolated from Traditional Tibetan Qula, A Raw Yak Milk Cheese.", "token_count": 387, "char_count": 1114, "word_count": 143, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:55.638309", "source": { "split": "train_shard_00000", "doc_id": 4069 }, "chunk_id": "train_shard_00000_4069_1", "global_id": 4525 }, { "text": "Listeria monocytogenes is an important foodborne pathogen responsible for the disease listeriosis, and can be found throughout the environment, in many foods and in food processing facilities. The main cause of listeriosis is consumption of food contaminated from sources in food processing environments. Persistence in food processing facilities has previously been shown for the L. monocytogenes sequence type (ST) 8 subtype. In the current study, five ST8 strains were subjected to whole-genome sequencing and compared with five additionally available ST8 genomes, allowing comparison of strains from salmon, poultry and cheese industry, in addition to a human clinical isolate. Genome-wide analysis of single-nucleotide polymorphisms (SNPs) confirmed that almost identical strains were detected in a Danish salmon processing plant in 1996 and in a Norwegian salmon processing plant in 2001 and 2011. Furthermore, we show that L. monocytogenes ST8 was likely to have been transferred between two poultry processing plants as a result of relocation of processing equipment. The SNP data were used to infer the phylogeny of the ST8 strains, separating them into two main genetic groups. Within each group, the plasmid and prophage content was almost entirely conserved, but between groups, these sequences showed strong divergence. The accessory genome of the ST8 strains harbored genetic elements which could be involved in rendering the ST8 strains resilient to incoming mobile genetic elements. These included two restriction-modification loci, one of which was predicted to show phase variable recognition sequence specificity through site-specific domain shuffling. Analysis indicated that the ST8 strains harbor all important known L. monocytogenes virulence factors, and ST8 strains are commonly identified as the causative agents of invasive listeriosis. Therefore, the persistence of this L. monocytogenes subtype in food processing facilities poses a significant concern for food safety.\n\nGenome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains.", "token_count": 495, "char_count": 2159, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5728, "quality_score": 0.7864, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:56.287121", "source": { "split": "train_shard_00000", "doc_id": 4070 }, "chunk_id": "train_shard_00000_4070_0", "global_id": 4526 }, { "text": "Hyper thermal (HT) acid hydrolysis of Kappaphycus alvarezii, a red seaweed, was optimized to 12% (w/v) seaweed slurry content, 180mM H2SO4 at 140°C for 5min. The maximum monosaccharide concentration of 38.3g/L and 66.7% conversion from total fermentable monosaccharides of 57.6g/L with 120gdw/L K. alvarezii slurry were obtained from HT acid hydrolysis and enzymatic saccharification. HT acid hydrolysis at a severity factor of 0.78 efficiently converted the carbohydrates of seaweed to monosaccharides and produced a low concentration of inhibitory compounds. The levels of ethanol production by separate hydrolysis and fermentation with non-adapted and adapted Kluyveromyces marxianus to high concentration of galactose were 6.1g/L with ethanol yield (YEtOH) of 0.19 at 84h and 16.0g/L with YEtOH of 0.42 at 72h, respectively. Development of the HT acid hydrolysis process and adapted yeast could enhance the overall ethanol fermentation yields of K. alvarezii seaweed.\n\nEvaluation of hyper thermal acid hydrolysis of Kappaphycus alvarezii for enhanced bioethanol production.", "token_count": 357, "char_count": 1077, "word_count": 153, "semantic_coherence": 1, "information_density": 0.5948, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:56.866346", "source": { "split": "train_shard_00000", "doc_id": 4071 }, "chunk_id": "train_shard_00000_4071_0", "global_id": 4527 }, { "text": "Staphylococcus aureus is a globally disseminated drug-resistant bacterial species. It remains a leading cause of hospital-acquired infection, primarily among immunocompromised patients. In 2012, the Affiliated People's Hospital of Jiangsu University experienced a putative outbreak of methicillin-resistant S. aureus (MRSA) that affected 12 patients in the Neurosurgery Department. In this study, whole-genome sequencing (WGS) was used to gain insight into the epidemiology of the outbreak caused by MRSA, and traditional bacterial genotyping approaches were also applied to provide supportive evidence for WGS. We sequenced the DNA from 6 isolates associated with the outbreak. Phylogenetic analysis was constructed by comparing single-nucleotide polymorphisms (SNPs) in the core genome of 6 isolates in the present study and another 3 referenced isolates from GenBank. Of the 6 MRSA sequences in the current study, 5 belonged to the same group, clustering with T0131, while the other one clustered closely with TW20. All of the isolates were identified as ST239-SCCmecIII clones. Whole-genome analysis revealed that four of the outbreak isolates were more tightly clustered into a group and SA13002 together with SA13009 were distinct from the outbreak strains, which were considered non-outbreak strains. Based on the sequencing results, the antibiotic-resistance gene status (present or absent) was almost perfectly concordant with the results of phenotypic susceptibility testing. Various toxin genes were also analyzed successfully. Our analysis demonstrates that using traditional molecular methods and WGS can facilitate the identification of outbreaks and help to control nosocomial transmission.\n\nWhole-Genome Sequencing for the Investigation of a Hospital Outbreak of MRSA in China.", "token_count": 443, "char_count": 1793, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6454, "quality_score": 0.8227, "entities": { "genes": [ "SA13002", "SA13009", "TW20", "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:57.564706", "source": { "split": "train_shard_00000", "doc_id": 4072 }, "chunk_id": "train_shard_00000_4072_0", "global_id": 4528 }, { "text": "Shiga-toxin producing Escherichia coli (STEC) strains possess a large accessory genome composed of virulence genes existing in multiple allelic variants, which sometimes segregate with specific STEC subpopulations. We analyzed the allelic variability of 91 virulence genes of STEC by Real Time PCR followed by melting curves analysis in 713 E. coli strains including 358 STEC. The 91 genes investigated were located on the locus of enterocyte effacement (LEE), OI-57, and OI-122 pathogenicity islands and displayed a total of 476 alleles in the study population. The combinations of the 91 alleles of each strain were termed allelic signatures and used to perform cluster analyses. We termed such an approach High Resolution Virulence Allelic Profiling (HReVAP) and used it to investigate the phylogeny of STEC of multiple serogroups. The dendrograms obtained identified groups of STEC segregating approximately with the serogroups and allowed the identification of subpopulations within the single groups. The study of the allelic signatures provided further evidence of the coevolution of the LEE and OI-122, reflecting the occurrence of their acquisition through a single event. The HReVAP analysis represents a sensitive tool for studying the evolution of LEE-positive STEC.\n\nDevelopment of a High Resolution Virulence Allelic Profiling (HReVAP) Approach Based on the Accessory Genome of Escherichia coli to Characterize Shiga-Toxin Producing E. coli (STEC).", "token_count": 387, "char_count": 1462, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5701, "quality_score": 0.785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:58.207649", "source": { "split": "train_shard_00000", "doc_id": 4073 }, "chunk_id": "train_shard_00000_4073_0", "global_id": 4529 }, { "text": "We report new methods for multilabel immunofluorescence (MIF) and reprobing of antigen epitopes on the same formalin-fixed paraffin-embedded (FFPE) sections. The MIF method includes an antigen-retrieval step followed by multilabel immunostaining and examination by confocal microscopy. As examples, we illustrate epitopes localized to the apical and basolateral membranes, and the cytoplasm of enterocytes of normal small intestine and in cases of congenital enteropathies (microvillous inclusion disease and congenital tufting enteropathy). We also demonstrate localization of the bile salt excretion pump protein (BSEP) in bile canalicular membrane of normal hepatocytes and in cases of primary sclerosing cholangitis. To demonstrate colocalization of cytoplasmic and nuclear epitopes we analyzed normal control and hyperplastic pulmonary neuroendocrine cells (PNEC) and neuroepithelial bodies (NEBs), presumed airway sensors in the lungs of infants with bronchopulmonary dysplasia (BPD). As cytoplasmic markers we used anti-bombesin or anti-synaptic vesicle protein 2 (SV2) antibody, respectively, and for nuclear localization, antibodies against neurogenic genes mammalian achaete-scute homolog (Mash1) and prospero homeobox 1 (Prox1), essential for NEB cells differentiation and maturation, hypoxia-inducible factor 1α (HIF1α) a downstream modulator of hypoxia response and a proliferation marker Ki67. The reprobing method consisted of removal of the previously immunolabeled target and immunostaining with different antibodies, facilitating colocalization of enterocyte brush border epitopes as well as HIF1α, Mash1 and Prox1 in PNEC/NEB PNEC and NEBs", "token_count": 466, "char_count": 1658, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8394, "entities": { "genes": [ "SV2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:58.890532", "source": { "split": "train_shard_00000", "doc_id": 4074 }, "chunk_id": "train_shard_00000_4074_0", "global_id": 4530 }, { "text": "As these methods are suitable for routine FFPE pathology samples from various tissues, allowing visualization of multiple epitopes in the same cells/sections with superior contrast and resolution, they are suitable for a wide range of applications in diagnostic pathology and may be particularly well suited for precision medicine diagnostics.\n\nMultilabel immunofluorescence and antigen reprobing on formalin-fixed paraffin-embedded sections: novel applications for precision pathology diagnosis.", "token_count": 102, "char_count": 496, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7969, "quality_score": 0.8984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:59.308410", "source": { "split": "train_shard_00000", "doc_id": 4074 }, "chunk_id": "train_shard_00000_4074_1", "global_id": 4531 }, { "text": "Emerging evidence strongly suggest that the human \"microbiome\" plays an important role in both health and disease. Bile acids function both as detergents molecules promoting nutrient absorption in the intestines and as hormones regulating nutrient metabolism. Bile acids regulate metabolism via activation of specific nuclear receptors (NR) and G-protein coupled receptors (GPCRs). The circulating bile acid pool composition consists of primary bile acids produced from cholesterol in the liver, and secondary bile acids formed by specific gut bacteria. The various biotransformation of bile acids carried out by gut bacteria appear to regulate the structure of the gut microbiome and host physiology. Increased levels of secondary bile acids are associated with specific diseases of the GI system. Elucidating methods to control the gut microbiome and bile acid pool composition in humans may lead to a reduction in some of the major diseases of the liver, gall bladder and colon.\n\nConsequences of bile salt biotransformations by intestinal bacteria.", "token_count": 247, "char_count": 1051, "word_count": 156, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:39:59.801203", "source": { "split": "train_shard_00000", "doc_id": 4075 }, "chunk_id": "train_shard_00000_4075_0", "global_id": 4532 }, { "text": "Due to the mounting awareness of the risks associated with the use of antibiotics in aquaculture, treatment with probiotics has recently emerged as the preferred environmental-friendly prophylactic approach in marine larviculture. However, the presence of unknown and variable microbiota in fish larvae makes it impossible to disentangle the efficacy of treatment with probiotics. In this respect, the recent development of a germ-free culture model for European sea bass (Dicentrarchus labrax L.) larvae opened the door for more controlled studies on the use of probiotics. In the present study, 206 bacterial isolates, retrieved from sea bass larvae and adults, were screened in vitro for haemolytic activity, bile tolerance and antagonistic activity against six sea bass pathogens. Subsequently, the harmlessness and the protective effect of the putative probiotic candidates against the sea bass pathogen Vibrio harveyi were evaluated in vivo adopting the previously developed germ-free sea bass larval model. An equivalence trial clearly showed that no harmful effect on larval survival was elicited by all three selected probiotic candidates: Bacillus sp. LT3, Vibrio lentus and Vibrio proteolyticus. Survival of Vibrio harveyi challenged larvae treated with V. lentus was superior in comparison with the untreated challenged group, whereas this was not the case for the larvae supplemented with Bacillus sp. LT3 and V. proteolyticus. In this respect, our results unmistakably revealed the protective effect of V. lentus against vibriosis caused by V. harveyi in gnotobiotic sea bass larvae, rendering this study the first in its kind.\n\nVibrio lentus protects gnotobiotic sea bass (Dicentrarchus labrax L.) larvae against challenge with Vibrio harveyi.", "token_count": 451, "char_count": 1758, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5659, "quality_score": 0.7829, "entities": { "genes": [ "LT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:00.441404", "source": { "split": "train_shard_00000", "doc_id": 4076 }, "chunk_id": "train_shard_00000_4076_0", "global_id": 4533 }, { "text": "Collagenous colitis (CC) is an increasingly recognized cause of chronic inflammatory bowel disease characterized by watery non-bloody diarrhea. As a lesser studied inflammatory bowel disease, many aspects of the CC's natural history are poorly understood. This review discusses strategies to optimally manage CC. The goal of therapy is to induce clinical remission, <3 stools a day or <1 watery stool a day with subsequent improved quality of life (QOL). Antidiarrheal can be used as monotherapy or with other medications to control diarrhea. Budesonide therapy has revolutionized treatment and is superior to prednisone, however, the treatment is associated with high-relapse rates and the management of refractory disease is challenging. Ongoing trials will address the safety and efficacy of low-dose maintenance therapy. For those with refractory disease, case reports and case series support the role of biologic agents. Diversion of the fecal stream normalizes colonic mucosal changes and ileostomy may be considered where anti-tumor necrosis factor (TNF)-α agents are contraindicated. Underlying celiac disease, bile salt diarrhea, and associated thyroid dysfunction should be ruled out. The author recommends smoking cessation as well as avoidance of nonsteroidal anti-inflammatories as well as other associated medications.\n\nOptimal management of collagenous colitis: a review.", "token_count": 332, "char_count": 1386, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6904, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:01.015363", "source": { "split": "train_shard_00000", "doc_id": 4077 }, "chunk_id": "train_shard_00000_4077_0", "global_id": 4534 }, { "text": "This study was conducted to select Lactobacillus strains from various sources on the basis of their probiotic attributes, such as acid and bile tolerance, binding to intestinal cells, and antimicrobial activity. Twelve isolates were obtained from human and food sources and were evaluated against standard probiotic Lactobacillus rhamnosus GG (LGG). Isolates were also studied for their antibiotic susceptibility. Isolate Lactobacillus fermentum GPI-6 showed the best survival profile at 0.3% and 1% bile salt, as compared with LGG. Isolates Lactobacillus plantarum GRI-2 and Lactobacillus salivarius GPI-4 showed no reduction in survival rate at pH 2.5. As expected, isolates showed strain-specific differences when comparing various attributes. Isolates GPI-4, GPI-7, and FA-5 showed better adhesion to HT-29, while isolate GPI-4 adhered better to Caco-2 cells than did LGG. However, when studying their ability to compete with Escherichia coli O26:H11, isolates GPI-6 and GPI-7 significantly inhibited E. coli adhesion to both HT-29 and Caco-2 cells compared with LGG. In conclusion, isolates GPI-4, GPI-7, and FA-5 showed excellent binding ability and antagonistic activity and better tolerance to acidic pH (pH 2.5) and to different bile salt concentrations in comparison with LGG, and hence, they could be considered as potential probiotic candidates.\n\nIsolation and characterization of lactobacilli from human faeces and indigenous fermented foods for their potential application as probiotics.", "token_count": 417, "char_count": 1501, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:01.639197", "source": { "split": "train_shard_00000", "doc_id": 4078 }, "chunk_id": "train_shard_00000_4078_0", "global_id": 4535 }, { "text": "ATP11C is a homolog of ATP8B1, both of which catalyze the transport of phospholipids in biological membranes. Mutations in ATP8B1 cause progressive familial intrahepatic cholestasis type1 in humans, which is characterized by a canalicular cholestasis. Mice deficient in ATP11C are characterized by a conjugated hyperbilirubinemia and an unconjugated hypercholanemia. Here, we have studied the hypothesis that ATP11C deficiency interferes with basolateral uptake of unconjugated bile salts, a process mediated by organic anion-transporting polypeptide (OATP) 1B2. ATP11C localized to the basolateral membrane of central hepatocytes in the liver lobule of control mice. In ATP11C-deficient mice, plasma total bilirubin levels were 6-fold increased, compared to control, of which ∼65% was conjugated and ∼35% unconjugated. Plasma total bile salts were 10-fold increased and were mostly present as unconjugated species. Functional studies in ATP11C-deficient mice indicated that hepatic uptake of unconjugated bile salts was strongly impaired whereas uptake of conjugated bile salts was unaffected. Western blotting and immunofluorescence analysis demonstrated near absence of basolateral bile salt uptake transporters OATP1B2, OATP1A1, OATP1A4, and Na(+) -taurocholate-cotransporting polypeptide only in central hepatocytes of ATP11C-deficient liver. In vivo application of the proteasome inhibitor, bortezomib, partially restored expression of these proteins, but not their localization. Furthermore, we observed post-translational down-regulation of ATP11C protein in livers from cholestatic mice, which coincided with reduced OATP1B2 levels.", "token_count": 497, "char_count": 1641, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [ "ATP11C" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:02.298513", "source": { "split": "train_shard_00000", "doc_id": 4079 }, "chunk_id": "train_shard_00000_4079_0", "global_id": 4536 }, { "text": "ATP11C targets basolateral bile salt transporter proteins in mouse central hepatocytes.", "token_count": 24, "char_count": 87, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ATP11C" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:02.656026", "source": { "split": "train_shard_00000", "doc_id": 4079 }, "chunk_id": "train_shard_00000_4079_1", "global_id": 4537 }, { "text": "Commercial probiotics preparation containing Bacillus coagulans have been sold in the market for several decades. Due to its high intra-species genomic diversity, it is very likely that B. coagulans strain may alter in different ways over multiple years of production. Therefore, the present study focuses to evaluate the genetic consistency and probiotic potential of B. coagulans MTCC 5856. Phenotypic and genotypic techniques including biochemical profiling, 16S rRNA sequencing, GTG 5″, BOX PCR fingerprinting, and Multi-Locus-Sequence typing (MLST) were carried out to evaluate the identity and consistency of the B. coagulans MTCC 5856. Further, in vitro probiotic potential, safety and stability at ambient temperature conditions of B. coagulans MTCC 5856 were evaluated. All the samples were identified as B. coagulans by biochemical profiling and 16S rRNA sequencing. GTG 5″, BOX PCR fingerprints and MLST studies revealed that the same strain was present over 3 years of commercial production. B. coagulans MTCC 5856 showed resistance to gastric acid, bile salt and exhibited antimicrobial activity in in-vitro studies. Additionally, B. coagulans MTCC 5856 was found to be non-mutagenic, non-cytotoxic, negative for enterotoxin genes and stable at ambient temperature (25 ± 2 °C) for 36 months. The data of the study verified that the same strain of B. coagulans MTCC 5856 was present in commercial preparation over multiple years of production.\n\nEvaluation of genetic and phenotypic consistency of Bacillus coagulans MTCC 5856: a commercial probiotic strain.", "token_count": 445, "char_count": 1569, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5517, "quality_score": 0.7759, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:03.294360", "source": { "split": "train_shard_00000", "doc_id": 4080 }, "chunk_id": "train_shard_00000_4080_0", "global_id": 4538 }, { "text": "The main purpose of this study was to develop a pure culture starter for producing kefir. In order to accomplish starter recycling, yeasts (Kluyveromyces marxianus strain, Pichia kudriavzevii clone), lactic acid bacteria (Lactobacillus kefiri strain F4Aa, Lactobacillus kefiri strain NM131-7, Lactobacillus kefiri strain NM132-3, Lactobacillus kefiri strain NM180-3, respectively), and acetic acid bacteria (Acetobacter lovaniensis strain) were entrapped in liquid core capsules based on the distribution ratio in kefir grains. The microbiological, antimicrobial, and chemical properties of kefir made with capsules (M) and kefir grains (K) were measured and compared. According to the results of plate counts in different selective medium, the number of yeasts and bacteria in the liquid core capsules gradually increased and stabilized after eight fermentation cycles. The results of gas chromatography-mass spectrometry showed that almost all the aroma components existed in the two type of kefir, except the ethyl lactate. There was no significant difference in alcohol content, protein content, and fat content, except the acidity and sugar content. Water holding capacity of kefir K was higher than kefir M. There were 14 same free amino acids in kefir M and kefir K, and the content of most free amino acids was similar. In antimicrobial test, there was no significant difference in both kefirs.\n\nThe evaluation of kefir pure culture starter: Liquid-core capsule entrapping microorganisms isolated from kefir grains.", "token_count": 409, "char_count": 1523, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6143, "quality_score": 0.8072, "entities": { "genes": [ "NM180", "NM132", "NM131" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:03.920216", "source": { "split": "train_shard_00000", "doc_id": 4081 }, "chunk_id": "train_shard_00000_4081_0", "global_id": 4539 }, { "text": "Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of industrial biotechnology.\n\nFunctional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.", "token_count": 118, "char_count": 440, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:04.309218", "source": { "split": "train_shard_00000", "doc_id": 4082 }, "chunk_id": "train_shard_00000_4082_0", "global_id": 4540 }, { "text": "Variation in gene regulation may be involved in the differences observed for life history traits within species. American eel (Anguilla rostrata) is well known to harbor distinct ecotypes within a single panmictic population. We examined the expression of genes involved in the regulation of appetite as well as lipid and glycogen among glass eels migrating to different locations on the Canadian east coast and captured at two different periods of upstream migration. Gene expression levels of three reference and five candidate genes were analyzed by real-time PCR with Taqman probes in recently captured wild glass eels. All gene transcripts were detected in glass eels. Of the five candidate genes, bile salt activated and triacylglycerol lipases were respectively 7.65 and 3.25 times more expressed in glass eels from the St. Lawrence estuary than in those from Nova Scotia, and there was no effect related to the two-week difference in capture date. These two genes explained 82.41% of the dissimilarity between the two rivers. In contrast, glycogen phosphorylase, ghrelin, and leptin receptor genes showed no significant differences in gene transcription. These results confirmed at the molecular level an observation that was recently made at the phenotypic level that glass eels from the St. Lawrence estuary have a greater capacity to use lipid reserves to sustain their metabolic needs. These observations add to the body of evidence supporting the hypothesis that regional phenotypic variation observed in American eel is determined early in life and that part of this variation is likely under genetic control.\n\nRegional variation of gene regulation associated with storage lipid metabolism in American glass eels (Anguilla rostrata).", "token_count": 382, "char_count": 1747, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5843, "quality_score": 0.7921, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:04.901647", "source": { "split": "train_shard_00000", "doc_id": 4083 }, "chunk_id": "train_shard_00000_4083_0", "global_id": 4541 }, { "text": "Staphylococcus aureus is a successful human and animal pathogen. Its pathogenicity is linked to its ability to secrete a large amount of virulence factors. These secreted proteins interfere with many critical components of the immune system, both innate and adaptive, and hamper proper immune functioning. In recent years, numerous studies have been conducted in order to understand the molecular mechanism underlying the interaction of evasion molecules with the host immune system. Structural studies have fundamentally contributed to our understanding of the mechanisms of action of the individual factors. Furthermore, such studies revealed one of the most striking characteristics of the secreted immune evasion molecules: their conserved structure. Despite high-sequence variability, most immune evasion molecules belong to a small number of structural categories. Another remarkable characteristic is that S. aureus carries most of these virulence factors on mobile genetic elements (MGE) or ex-MGE in its accessory genome. Coevolution of pathogen and host has resulted in immune evasion molecules with a highly host-specific function and prevalence. In this review, we explore how these shared structures and genomic locations relate to function and host specificity. This is discussed in the context of therapeutic options for these immune evasion molecules in infectious as well as in inflammatory diseases.\n\nStaphylococcal Immune Evasion Proteins: Structure, Function, and Host Adaptation.", "token_count": 312, "char_count": 1500, "word_count": 213, "semantic_coherence": 1, "information_density": 0.615, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:05.459172", "source": { "split": "train_shard_00000", "doc_id": 4084 }, "chunk_id": "train_shard_00000_4084_0", "global_id": 4542 }, { "text": "The Pseudomonas fluorescens complex includes Pseudomonas strains that have been taxonomically assigned to more than fifty different species, many of which have been described as plant growth-promoting rhizobacteria (PGPR) with potential applications in biocontrol and biofertilization. So far the phylogeny of this complex has been analyzed according to phenotypic traits, 16S rDNA, MLSA and inferred by whole-genome analysis. However, since most of the type strains have not been fully sequenced and new species are frequently described, correlation between taxonomy and phylogenomic analysis is missing. In recent years, the genomes of a large number of strains have been sequenced, showing important genomic heterogeneity and providing information suitable for genomic studies that are important to understand the genomic and genetic diversity shown by strains of this complex. Based on MLSA and several whole-genome sequence-based analyses of 93 sequenced strains, we have divided the P. fluorescens complex into eight phylogenomic groups that agree with previous works based on type strains. Digital DDH (dDDH) identified 69 species and 75 subspecies within the 93 genomes. The eight groups corresponded to clustering with a threshold of 31.8% dDDH, in full agreement with our MLSA. The Average Nucleotide Identity (ANI) approach showed inconsistencies regarding the assignment to species and to the eight groups. The small core genome of 1,334 CDSs and the large pan-genome of 30,848 CDSs, show the large diversity and genetic heterogeneity of the P. fluorescens complex. However, a low number of strains were enough to explain most of the CDSs diversity at core and strain-specific genomic fractions. Finally, the identification and analysis of group-specific genome and the screening for distinctive characters revealed a phylogenomic distribution of traits among the groups that provided insights into biocontrol and bioremediation applications as well as their role as PGPR.\n\nGenomic and Genetic Diversity within the Pseudomonas fluorescens Complex.", "token_count": 500, "char_count": 2059, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5567, "quality_score": 0.7783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:06.116555", "source": { "split": "train_shard_00000", "doc_id": 4085 }, "chunk_id": "train_shard_00000_4085_0", "global_id": 4543 }, { "text": "The bacterial speciesMoraxella catarrhalishas been hypothesized as being composed of two distinct lineages (referred to as the seroresistant [SR] and serosensitive [SS]) with separate evolutionary histories based on several molecular typing methods, whereas 16S ribotyping has suggested an additional split within the SS lineage. Previously, we characterized whole-genome sequences of 12 SR-lineage isolates, which revealed a relatively small supragenome when compared with other opportunistic nasopharyngeal pathogens, suggestive of a relatively short evolutionary history. Here, we performed whole-genome sequencing on 18 strains from both ribotypes of the SS lineage, an additional SR strain, as well as four previously identified highly divergent strains based on multilocus sequence typing analyses. All 35 strains were subjected to a battery of comparative genomic analyses which clearly show that there are three lineages-the SR, SS, and the divergent. The SR and SS lineages are closely related, but distinct from each other based on three different methods of comparison: Allelic differences observed among core genes; possession of lineage-specific sets of core and distributed genes; and by an alignment of concatenated core sequences irrespective of gene annotation. All these methods show that the SS lineage has much longer interstrain branches than the SR lineage indicating that this lineage has likely been evolving either longer or faster than the SR lineage. There is evidence of extensive horizontal gene transfer (HGT) within both of these lineages, and to a lesser degree between them. In particular, we identified very high rates of HGT between these two lineages for ß-lactamase genes. The four divergent strains aresui generis, being much more distantly related to both the SR and SS groups than these other two groups are to each other. Based on average nucleotide identities, gene content, GC content, and genome size, this group could be considered as a separate taxonomic group. The SR and SS lineages, although distinct, clearly form a single species based on multiple criteria including a large common core genome, average nucleotide identity values, GC content, and genome size", "token_count": 490, "char_count": 2209, "word_count": 329, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:06.770084", "source": { "split": "train_shard_00000", "doc_id": 4086 }, "chunk_id": "train_shard_00000_4086_0", "global_id": 4544 }, { "text": "Although neither of these lineages arose from within the other based on phylogenetic analyses, the question of how and when these lineages split and then subsequently reunited in the human nasopharynx is explored.\n\nComparative Genomic Analyses of the Moraxella catarrhalis Serosensitive and Seroresistant Lineages Demonstrate Their Independent Evolution.", "token_count": 84, "char_count": 354, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:07.148537", "source": { "split": "train_shard_00000", "doc_id": 4086 }, "chunk_id": "train_shard_00000_4086_1", "global_id": 4545 }, { "text": "Metabolically active cells produce a wide array of metabolites that can inhibit their growth. Acetate is a widely known preservative, and it is also produced by yeast cells during their growth. Kluyveromyces marxianus DSM 5422 is a promising yeast strain that could be employed in biotechnological processes, but the knowledge of its stress physiology is scarce. Here, we investigate the effects of acetate on growth and changes in cell population structure during adaptation to elevated concentrations of acetate in K. marxianus DSM 5422. Our results indicate that acetate inhibits growth in a pH-dependent manner and has pronounced effects if yeast is grown on lactose or galactose. When challenged with acetate, culture extends lag phase, during which cells adapt to elevated acetate concentrations, and growth reoccurs, albeit at a slower rate, when majority of the population is acetate resistant. Acetate resistance is maintained only if acetate is present in the media or if the culture has reached end of active growth phase. This study shows possible caveats in lactose fermentation with K. marxianus and gives a further perspective in non-conventional yeast applications in biotechnology.\n\nEffects of acetate on Kluyveromyces marxianus DSM 5422 growth and metabolism.", "token_count": 316, "char_count": 1277, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5825, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:07.707808", "source": { "split": "train_shard_00000", "doc_id": 4087 }, "chunk_id": "train_shard_00000_4087_0", "global_id": 4546 }, { "text": "The increased presence of extended-spectrum beta-lactamase (ESBL)-producing bacteria in humans, animals, and their surrounding environments is of global concern. Currently there is limited information on ESBL presence in rural farming communities worldwide. We performed a cross-sectional study in Mwanza, Tanzania, involving 600 companion and domestic farm animals between August/September 2014. Rectal swab/cloaca specimens were processed to identify ESBL-producing Enterobacteriaceae. We detected 130 (21.7%) animals carrying ESBL-producing bacteria, the highest carriage being among dogs and pigs [39.2% (51/130) and 33.1% (43/130), respectively]. The majority of isolates were Escherichia coli [93.3% (125/134)] and exotic breed type [OR (95%CI) = 2.372 (1.460-3.854), p-value < 0.001] was found to be a predictor of ESBL carriage among animals. Whole-genome sequences of 25 ESBL-producing E. coli were analyzed for phylogenetic relationships using multi-locus sequence typing (MLST) and core genome comparisons. Fourteen different sequence types were detected of which ST617 (7/25), ST2852 (3/25), ST1303 (3/25) were the most abundant. All isolates harbored the bla CTX-M-15 allele, 22/25 carried strA and strB, 12/25 aac(6')-lb-cr, and 11/25 qnrS1. Antibiotic resistance was associated with IncF, IncY, as well as non-typable plasmids. Eleven isolates carried pPGRT46-related plasmids, previously reported from isolates in Nigeria. Five isolates had plasmids exhibiting 85-99% homology to pCA28, previously detected in isolates from the US. Our findings indicate a pan-species distribution of ESBL-producing E", "token_count": 511, "char_count": 1616, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7512, "quality_score": 0.8756, "entities": { "genes": [ "ST2852", "ST1303", "ST617" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:08.363178", "source": { "split": "train_shard_00000", "doc_id": 4088 }, "chunk_id": "train_shard_00000_4088_0", "global_id": 4547 }, { "text": "coli clonal groups in farming communities and provide evidence for plasmids harboring antibiotic resistances of regional and international impact.\n\nMultiple ESBL-Producing Escherichia coli Sequence Types Carrying Quinolone and Aminoglycoside Resistance Genes Circulating in Companion and Domestic Farm Animals in Mwanza, Tanzania, Harbor Commonly Occurring Plasmids.", "token_count": 95, "char_count": 366, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:08.736189", "source": { "split": "train_shard_00000", "doc_id": 4088 }, "chunk_id": "train_shard_00000_4088_1", "global_id": 4548 }, { "text": "Bacterial genomes undergo numerous events of gene losses and gains that generate genome variability among strains of the same species (microevolution). Our aim was to compare the genomes and relevant phenotypes of three Bacillus coahuilensis strains from two oligotrophic hydrological systems in the Cuatro Ciénegas Basin (México), to unveil the environmental challenges that this species cope with, and the microevolutionary differences in these genotypes. Since the strains were isolated from a low P environment, we placed emphasis on the search of different phosphorus acquisition strategies. The three B. coahuilensis strains exhibited similar numbers of coding DNA sequences, of which 82% (2,893) constituted the core genome, and 18% corresponded to accessory genes. Most of the genes in this last group were associated with mobile genetic elements (MGEs) or were annotated as hypothetical proteins. Ten percent of the pangenome consisted of strain-specific genes. Alignment of the three B. coahuilensis genomes indicated a high level of synteny and revealed the presence of several genomic islands. Unexpectedly, one of these islands contained genes that encode the 2-keto-3-deoxymannooctulosonic acid (Kdo) biosynthesis enzymes, a feature associated to cell walls of Gram-negative bacteria. Some microevolutionary changes were clearly associated with MGEs. Our analysis revealed inconsistencies between phenotype and genotype, which we suggest result from the impossibility to map regulatory features to genome analysis. Experimental results revealed variability in the types and numbers of auxotrophies between the strains that could not consistently be explained by in silico metabolic models. Several intraspecific differences in preferences for carbohydrate and phosphorus utilization were observed. Regarding phosphorus recycling, scavenging, and storage, variations were found between the three genomes. The three strains exhibited differences regarding alkaline phosphatase that revealed that in addition to gene gain and loss, regulation adjustment of gene expression also has contributed to the intraspecific diversity of B. coahuilensis.", "token_count": 498, "char_count": 2155, "word_count": 299, "semantic_coherence": 1, "information_density": 0.612, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:09.388099", "source": { "split": "train_shard_00000", "doc_id": 4089 }, "chunk_id": "train_shard_00000_4089_0", "global_id": 4549 }, { "text": "Microevolution Analysis of Bacillus coahuilensis Unveils Differences in Phosphorus Acquisition Strategies and Their Regulation.", "token_count": 33, "char_count": 127, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:09.776839", "source": { "split": "train_shard_00000", "doc_id": 4089 }, "chunk_id": "train_shard_00000_4089_1", "global_id": 4550 }, { "text": "Isothermal titration calorimetry (ITC) is shown to be a sensitive reporter of bile salt micellization and chiral recognition. Detailed ITC characterization of bile micelle formation as well as the chiral recognition capabilities of sodium cholate (NaC), deoxycholate (NaDC), and taurodeoxycholate (NaTDC) micelle systems are reported. The ΔH(demic) of these bile salt micelle systems is directly observable and is strongly temperature-dependent, allowing also for the determination of ΔCp(demic). Using the pseudo-phase separation model, ΔG(demic) and TΔS(demic) were also calculated. Chirally selective guest-host binding of model racemic compounds 1,1'-bi-2-napthol (BN) and 1,1'-binaphthyl-2,2'-diylhydrogenphosphate (BNDHP) to bile salt micelles was then investigated. The S-isomer was shown to bind more tightly to the bile salt micelles in all cases. A model was developed that allows for the quantitative determination of the enthalpic difference in binding affinity that corresponds to chiral selectivity, which is on the order of 1 kJ mol(-1).\n\nDirect Measurement of the Thermodynamics of Chiral Recognition in Bile Salt Micelles.", "token_count": 319, "char_count": 1139, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6242, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:10.366216", "source": { "split": "train_shard_00000", "doc_id": 4090 }, "chunk_id": "train_shard_00000_4090_0", "global_id": 4551 }, { "text": "Multidrug resistance protein 3 (MDR3, ABCB4) is a hepatocellular membrane protein that mediates biliary secretion of phosphatidylcholine. Null mutations in ABCB4 gene give rise to severe early-onset cholestatic liver disease. We have previously shown that the disease-associated mutations p.G68R, p.G228R, p.D459H, and p.A934T resulted in retention of ABCB4 in the endoplasmic reticulum, thus failing to target the plasma membrane. In the present study, we tested the ability of two compounds with chaperone-like activity, 4-phenylbutyrate and curcumin, to rescue these ABCB4 mutants by assessing their effects on subcellular localization, protein maturation, and phospholipid efflux capability. Incubation of transfected cells at a reduced temperature (30°C) or exposure to pharmacological doses of either 4-PBA or curcumin restored cell surface expression of mutants G228R and A934T. The delivery of these mutants to the plasma membrane was accompanied by a switch in the ratio of mature to inmature protein forms, leading to a predominant expression of the mature protein. This effect was due to an improvement in the maturation rate and not to the stabilization of the mature forms. Both mutants were also functionally rescued, displaying bile salt-dependent phospholipid efflux activity after addition of 4-PBA or curcumin. Drug-induced rescue was mutant specific, given neither 4-PBA nor curcumin had an effect on the ABCB4 mutants G68R and A934T. Collectively, these data indicate that the functionality of selected trafficking-defective ABCB4 mutants can be recovered by chemical chaperones through restoration of membrane localization, suggesting a potential treatment for patients carrying such mutations.\n\nFunctional Rescue of Trafficking-Impaired ABCB4 Mutants by Chemical Chaperones.", "token_count": 479, "char_count": 1796, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6285, "quality_score": 0.8142, "entities": { "genes": [ "ABCB4", "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:11.031617", "source": { "split": "train_shard_00000", "doc_id": 4091 }, "chunk_id": "train_shard_00000_4091_0", "global_id": 4552 }, { "text": "The ocular barriers (cornea, blood-retinal barrier, and blood-aqueous humor barrier) make treating eye diseases with therapeutic drugs challenging. The tight capillary endothelium of the iris and the ciliary body epithelium form the blood-aqueous humor barrier. The iris and ciliary body (iris-ciliary body) express a variety of drug transporters in the ATP-binding cassette and solute carrier (SLC) families. ATP-binding cassette family drug transporters that are present in the iris-ciliary body include P-glycoprotein, breast cancer resistance protein, and several multidrug resistance-associated proteins. SLC family drug transporters that are present in the iris-ciliary body include organic anion transporters, organic anion transporting polypeptides, bile acid transporters (apical sodium-dependent bile salt transporter and sodium taurocholate cotransporter), organic cation transporters (novel organic cation transporter and multidrug and toxin extrusion transporter) and peptide transporters. Freshly dissected iris-ciliary body preparations actively accumulate a variety of substrates of SLC drug transporters that are expressed in the tissue. The ciliary body in vitro supports active transport in the aqueous humor-to-blood direction of several substrates of organic anion transporters and multidrug resistance-associated proteins, consistent with the subcellular localization of these transporters in the ciliary body epithelium. In vivo data suggest that drug transporters in the iris-ciliary body reduce the permeation of drugs in the direction of blood-to-aqueous humor, thereby reducing ocular drug bioavailability, and are also involved in active drug elimination from the aqueous humor. An understanding of the influence on pharmacokinetics of drug transporters in the blood-aqueous humor barrier should help improve drug delivery and efficacy in the eye.\n\nDrug Transport by the Blood-Aqueous Humor Barrier of the Eye.", "token_count": 478, "char_count": 1938, "word_count": 259, "semantic_coherence": 1, "information_density": 0.4942, "quality_score": 0.7471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:11.688641", "source": { "split": "train_shard_00000", "doc_id": 4092 }, "chunk_id": "train_shard_00000_4092_0", "global_id": 4553 }, { "text": "Legionella pneumophila is an important human pathogen causing Legionnaires' disease. In this study, whole genome sequencing (WGS) was used to study the characteristics and population structure of L. pneumophila strains. We sequenced and compared 53 isolates of L. pneumophila covering different serogroups and sequence-based typing (SBT) types (STs). We found that 1,896 single-copy orthologous genes were shared by all isolates and were defined as the minimum core genome (MCG) of L. pneumophila. A total of 323,224 single-nucleotide polymorphisms (SNPs) were identified among the 53 strains. After excluding 314,059 SNPs which were likely to be results of recombination, the remaining 9,165 SNPs were referred to as MCG SNPs. Population Structure analysis based on MCG divided the 53 L. pneumophila into nine MCG groups. The within-group distances were much smaller than the between-group distances, indicating considerable divergence between MCG groups. MCG groups were also supplied by phylogenetic analysis and may be considered as robust taxonomic units within L. pneumophila. Among the nine MCG groups, eight showed high intracellular growth ability while one showed low intracellular growth ability. Furthermore, MCG typing also showed high resolution in subtyping ST1 strains. The results obtained in this study provided significant insights into the evolution, population structure and pathogenicity of L. pneumophila.\n\nPopulation structure and minimum core genome typing of Legionella pneumophila.", "token_count": 384, "char_count": 1508, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:12.312269", "source": { "split": "train_shard_00000", "doc_id": 4093 }, "chunk_id": "train_shard_00000_4093_0", "global_id": 4554 }, { "text": "Neonatal cholestasis is a potentially life-threatening condition requiring prompt diagnosis. Mutations in several different genes can cause progressive familial intrahepatic cholestasis, but known genes cannot account for all familial cases. Here we report four individuals from two unrelated families with neonatal cholestasis and mutations in NR1H4, which encodes the farnesoid X receptor (FXR), a bile acid-activated nuclear hormone receptor that regulates bile acid metabolism. Clinical features of severe, persistent NR1H4-related cholestasis include neonatal onset with rapid progression to end-stage liver disease, vitamin K-independent coagulopathy, low-to-normal serum gamma-glutamyl transferase activity, elevated serum alpha-fetoprotein and undetectable liver bile salt export pump (ABCB11) expression. Our findings demonstrate a pivotal function for FXR in bile acid homeostasis and liver protection.\n\nMutations in the nuclear bile acid receptor FXR cause progressive familial intrahepatic cholestasis.", "token_count": 262, "char_count": 1014, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7287, "quality_score": 0.8643, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:12.863039", "source": { "split": "train_shard_00000", "doc_id": 4094 }, "chunk_id": "train_shard_00000_4094_0", "global_id": 4555 }, { "text": "The evolutionary adaptation was carried out on the thermotolerant yeast Kluyveromyces marxianus NIRE-K1 at 45 °C up to 60 batches to enhance its xylose utilization capability. The adapted strain showed higher specific growth rate and 3-fold xylose uptake rate and short lag phase as compared to the native strain. During aerobic growth adapted yeast showed 2.81-fold higher xylose utilization than that of native. In anaerobic batch fermentation, adapted yeast utilized about 91% of xylose in 72 h and produced 2.88 and 18.75 g l⁻¹ of ethanol and xylitol, respectively, which were 5.11 and 5.71-fold higher than that of native. Ethanol yield, xylitol yield and specific sugar consumption rate obtained by the adapted cells were found to be 1.57, 1.65 and 4.84-fold higher than that of native yeast, respectively. Aforesaid results suggested that the evolutionary adaptation will be a very effective strategy in the near future for economic lignocellulosic ethanol production.\n\nEnhancement in xylose utilization using Kluyveromyces marxianus NIRE-K1 through evolutionary adaptation approach.", "token_count": 312, "char_count": 1090, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:13.423591", "source": { "split": "train_shard_00000", "doc_id": 4095 }, "chunk_id": "train_shard_00000_4095_0", "global_id": 4556 }, { "text": "Microorganisms have evolved to occupy certain environmental niches, and the metabolic genes essential for growth in these locations are retained in the genomes. Many microorganisms inhabit niches located in the human body, sometimes causing disease, and may retain genes essential for growth in locations such as the bloodstream and urinary tract, or growth during intracellular invasion of the hosts' macrophage cells. Strains of Escherichia coli (E. coli) and Salmonella spp. are thought to have evolved over 100 million years from a common ancestor, and now cause disease in specific niches within humans. Here we have used a genome scale metabolic model representing the pangenome of E. coli which contains all metabolic reactions encoded by genes from 16 E. coli genomes, and have simulated environmental conditions found in the human bloodstream, urinary tract, and macrophage to determine essential metabolic genes needed for growth in each location. We compared the predicted essential genes for three E. coli strains and one Salmonella strain that cause disease in each host environment, and determined that essential gene retention could be accurately predicted using this approach. This project demonstrated that simulating human body environments such as the bloodstream can successfully lead to accurate computational predictions of essential/important genes.\n\nPredicting Essential Metabolic Genome Content of Niche-Specific Enterobacterial Human Pathogens during Simulation of Host Environments.", "token_count": 322, "char_count": 1509, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5945, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:13.983244", "source": { "split": "train_shard_00000", "doc_id": 4096 }, "chunk_id": "train_shard_00000_4096_0", "global_id": 4557 }, { "text": "Nesterenkonia sp. AN1 is a polyextremophile isolated from Antarctic desert soil. Genomic analyses and genome comparisons with three mesophilic Nesterenkonia strains indicated that the unique genome fraction of Nesterenkonia sp. AN1 contains adaptive features implicated in the response to cold stress including modulation of membrane fluidity as well as response to cold-associated osmotic and oxidative stress. The core genome also encodes a number of putative cold stress response proteins. RNA-Seq-based transcriptome analyses of Nesterenkonia sp. AN1 grown at 5ºC and 21°C showed that there was significant induction of transcripts that code for antioxidants at 5ºC, demonstrated by the upregulation of sodA, bcp and bpoA2. There was also overexpression of universal stress protein genes related to uspA, along with genes encoding other characterized cold stress features. Genes encoding the two key enzymes of the glyoxylate cycle, isocitrate lyase (ICL) and malate synthase (AceB) were induced at 5ºC, suggesting possible adaptation strategies for energy metabolism in cold habitats. These genomic features may contribute to the survival of Nesterenkonia sp. AN1 in arid Antarctic soils.\n\nThe genome of the Antarctic polyextremophile Nesterenkonia sp. AN1 reveals adaptive strategies for survival under multiple stress conditions.", "token_count": 345, "char_count": 1336, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "AN1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:14.556056", "source": { "split": "train_shard_00000", "doc_id": 4097 }, "chunk_id": "train_shard_00000_4097_0", "global_id": 4558 }, { "text": "A mature female squirrel monkey was noted during routine semiannual examinations to have moderate progressive weight loss. Serum chemistry panels revealed marked increases in hepatic enzyme, bilirubin, and bile salt concentrations and hypoalbuminemia. Abdominal ultrasonography revealed echogenic, shadowing debris in the gallbladder, consistent with cholelithiasis. At necropsy, marked thickening and distension of the gallbladder, cystic duct, and common bile duct was noted, and more than 50 irregularly shaped, black gallstones were removed from the biliary tract. Gallbladder tissue, bile, and gallstones cultured positive for Escherichia coli and Proteus spp., suggesting a brown-pigment gallstone type secondary to a bacterial nidus. Histopathology revealed severe chronic-active diffuse cholecystitis and severe chronic-active hepatic degeneration and necrosis with severe cholestasis. To our knowledge, this report is the first description of spontaneous choleilthiasis in a squirrel monkey.\n\nSpontaneous Cholelithiasis in a Squirrel Monkey (Saimiri sciureus).", "token_count": 287, "char_count": 1069, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7338, "quality_score": 0.8669, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:15.111830", "source": { "split": "train_shard_00000", "doc_id": 4098 }, "chunk_id": "train_shard_00000_4098_0", "global_id": 4559 }, { "text": "To serve as inoculants of legumes, nitrogen-fixing rhizobium strains should be competitive and tolerant of diverse environments. We hybridized the genomes of symbiotically efficient and salt tolerant Sinorhizobium inoculant strains onto the Sinorhizobium meliloti Rm1021 microarray. The number of variable genes, that is, divergent or putatively multiplied genes, ranged from 503 to 1556 for S. meliloti AK23, S. meliloti STM 1064 and S. arboris HAMBI 1552. The numbers of divergent genes affiliated with the symbiosis plasmid pSymA and related to DNA replication, recombination and repair were significantly higher than expected. The variation was mainly in the accessory genome, implying that it was important in shaping the adaptability of the strains.\n\nDivergent genes in potential inoculant Sinorhizobium strains are related to DNA replication, recombination, and repair.", "token_count": 249, "char_count": 876, "word_count": 125, "semantic_coherence": 1, "information_density": 0.664, "quality_score": 0.832, "entities": { "genes": [ "AK23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:15.593286", "source": { "split": "train_shard_00000", "doc_id": 4099 }, "chunk_id": "train_shard_00000_4099_0", "global_id": 4560 }, { "text": "To objective of this study was to better understand the biological functions of breast milk proteins in relation to the growth and development of infants over the first six months of life. Breast milk samples from four individual women collected at seven time points in the first six months after delivery were analyzed by filter aided sample preparation and dimethyl labeling combined with liquid chromatography tandem mass spectrometry. A total of 247 and 200 milk serum proteins were identified and quantified, respectively. The milk serum proteome showed a high similarity (80% overlap) on the qualitative level between women and over lactation. The quantitative changes in milk serum proteins were mainly caused by three groups of proteins, enzymes, and transport and immunity proteins. Of these 21 significantly changed proteins, 30% were transport proteins, such as serum albumin and fatty acid binding protein, which are both involved in transporting nutrients to the infant. The decrease of the enzyme bile salt-activated lipase as well as the immunity proteins immunoglobulins and lactoferrin coincide with the gradual maturation of the digestive and immune system of infants. The human milk serum proteome didn't differ qualitatively but it did quantitatively, both between mothers and as lactation advanced. The changes of the breast milk serum proteome over lactation corresponded with the development of the digestive and immune system of infants.\n\nChanges over lactation in breast milk serum proteins involved in the maturation of immune and digestive system of the infant.", "token_count": 360, "char_count": 1588, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5331, "quality_score": 0.7665, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:16.168482", "source": { "split": "train_shard_00000", "doc_id": 4100 }, "chunk_id": "train_shard_00000_4100_0", "global_id": 4561 }, { "text": "Cholesterol gallstone disease (CGD) is a hepatobiliary disorder which results from a biochemical imbalance in the gallbladder bile. Here we show that loss of CAV1 sensitized mice to lithogenic diet-induced gallbladder cholesterol crystallization, which was associated with dysregulation of several hepatic transporters that efflux cholesterol, phospholipids, and bile salts. The combined effect of increased biliary cholesterol concentration and decreased biliary bile salt secretion in CAV1(-/-) mice led to an increased cholesterol saturation index and the formation of cholesterol crystals. At the signaling level, the ERK/AP-1 pathway seems to mediate the effects of CAV1 on biliary BA homeostasis and might be developed as a therapeutic target for CGD. We propose that CAV1 is an anti-lithogenic factor and that the CAV1(-/-) mice may offer a convenient CGD model to develop therapeutic interventions for this disease. J. Cell. Biochem. 117: 2118-2127, 2016. © 2016 Wiley Periodicals, Inc.\n\nCAV1 Prevents Gallbladder Cholesterol Crystallization by Regulating Biosynthesis and Transport of Bile Salts.", "token_count": 330, "char_count": 1105, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [ "CAV1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:17.094330", "source": { "split": "train_shard_00000", "doc_id": 4101 }, "chunk_id": "train_shard_00000_4101_0", "global_id": 4562 }, { "text": "Taurine (2-aminoethanesulfonic acid), a conditionally essential sulfur-containing amino acid, is mainly obtained from diet in humans. Experimental studies have shown that taurine's main biological actions include bile salt conjugation, blood pressure regulation, anti-oxidation, and anti-inflammation.\n\nSerum Taurine and Stroke Risk in Women: A Prospective, Nested Case-Control Study.", "token_count": 101, "char_count": 384, "word_count": 47, "semantic_coherence": 1, "information_density": 0.9149, "quality_score": 0.9574, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:17.484561", "source": { "split": "train_shard_00000", "doc_id": 4102 }, "chunk_id": "train_shard_00000_4102_0", "global_id": 4563 }, { "text": "Subtotal gastrectomy (i.e., partial removal of the stomach), a surgical treatment for early-stage distal gastric cancer, is usually accompanied by highly selective vagotomy and Billroth II reconstruction, leading to dramatic changes in the gastric environment. Based on accumulating evidence of a strong link between human gut microbiota and host health, a 2-year follow-up study was conducted to characterize the effects of subtotal gastrectomy. Gastric microbiota and predicted gene functions inferred from 16S rRNA gene sequencing were analyzed before and after surgery. The results demonstrated that gastric microbiota is significantly more diverse after surgery. Ralstonia and Helicobacter were the top two genera of discriminant abundance in the cancerous stomach before surgery, while Streptococcus and Prevotella were the two most abundant genera after tumor excision. Furthermore, N-nitrosation genes were prevalent before surgery, whereas bile salt hydrolase, NO and N2O reductase were prevalent afterward. To our knowledge, this is the first report to document changes in gastric microbiota before and after surgical treatment of stomach cancer.\n\nGastric microbiota and predicted gene functions are altered after subtotal gastrectomy in patients with gastric cancer.", "token_count": 296, "char_count": 1277, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6257, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:18.048633", "source": { "split": "train_shard_00000", "doc_id": 4103 }, "chunk_id": "train_shard_00000_4103_0", "global_id": 4564 }, { "text": "Ginseng fruit saponins (GFS) extracted from the ginseng fruit are the bioactive triterpenoid saponin components. The aim of the present study was to develop a drug delivery system called proliposome using sodium deoxycholate (NaDC) as a bile salt to improve the oral bioavailability of GFS in rats. The liposomes of GFS were prepared by a conventional ethanol injection and formed the solid proliposomes (P-GFS) using spray drying method on mannitol carriers. The formulation of P-GFS was optimized using the response surface methodology. The physicochemical properties of liposome suspensions including encapsulation efficiency, in vitro drug release studies, particle size of the reconstituted liposome were tested. The solid state characterization studies using the method of Field emission-scanning electron microscope (FE-SEM), Fourier transform infrared (FT-IR) and Differential scanning colorimetric (DSC) were tested to study the molecular state of P-GFS and to indicate the interactions among the formulation ingredients. In vitro studies showed a delayed release of ginsenoside Re (GRe). In vivo studies were carried out in rats. The concentrations of GRe in plasma of rats and its pharmacokinetic behaviors after oral administration of GFS, Zhenyuan tablets (commercial dosage form of GFS) and P-GFS were studied using ultra performance liquid chromatography tandem mass spectrometry. It was founded that the GRe concentration time curves of GFS, Zhenyuan tablets and P-GFS were much more different in rats. Pharmacokinetic behaviors of P-GFS showed a second absorption peak on the concentration time curve", "token_count": 399, "char_count": 1617, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:18.673143", "source": { "split": "train_shard_00000", "doc_id": 4104 }, "chunk_id": "train_shard_00000_4104_0", "global_id": 4565 }, { "text": "The pharmacokinetic parameters of GFS, Zhenyuan tablets, P-GFS in rats were separately listed as follows: T max 0.25 h, C max 474.96 ± 66.06 ng/ml and AUC0-∞ 733.32 ± 113.82 ng/ml h for GFS; T max 0.31 ± 0.043 h, C max 533.94 ± 106.54 ng/ml and AUC0-∞ 1151.38 ± 198.29 ng/ml h for Zhenyuan tablets; T max 0.5 h, C max 680.62 ± 138.051 ng/ml and AUC0-∞ 2082.49 ± 408.33 ng/ml h for the P-GFS. The bioavailability of P-GFS was nearly 284% and 181% of the GFS and Zhengyuan tablets respectively. In conclusion, the proliposomes significantly enhanced the drug bioavailability, absorption in the gastrointestinal tract and decreased its elimination time of GRe in rats and could be selectively applied for oral delivery of GFS.\n\nImprovement of oral availability of ginseng fruit saponins by a proliposome delivery system containing sodium deoxycholate.", "token_count": 359, "char_count": 848, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.805, "entities": { "genes": [ "AUC0" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:19.245681", "source": { "split": "train_shard_00000", "doc_id": 4104 }, "chunk_id": "train_shard_00000_4104_1", "global_id": 4566 }, { "text": "Candida kefyr is an emerging pathogen able to cause disseminated infection, especially in immunocompromised patients. Although guidelines for the treatment of invasive candidiasis have been published, no specific recommendations against C. kefyr are available. We determine the in vitro killing activity of amphotericin B (AMB), fluconazole (FLC) and caspofungin (CFG) as well as their efficacy in a murine model of systemic infection by two C. kefyr strains. Time-kill curves of AMB, FLC and CFG were determined in final volumes of 10 ml containing the assayed drugs ranged from 0.03 to 32 μg ml\n\nAntifungal therapies in murine infections by Candida kefyr.", "token_count": 181, "char_count": 657, "word_count": 101, "semantic_coherence": 1, "information_density": 0.802, "quality_score": 0.901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:19.690188", "source": { "split": "train_shard_00000", "doc_id": 4105 }, "chunk_id": "train_shard_00000_4105_0", "global_id": 4567 }, { "text": "New and emerging environmental pathogens pose some of the greatest threats to modern aquaculture, a critical source of food protein globally. As with other intensive farming practices, increasing our understanding of the biology of infections is important to improve animal welfare and husbandry. The gill infection epitheliocystis is increasingly problematic in gilthead seabream (Sparus aurata), a major Mediterranean aquaculture species. Epitheliocystis is generally associated with chlamydial bacteria, yet we were not able to localise chlamydial targets within the major gilthead seabream lesions. Two previously unidentified species within a novel β-proteobacterial genus were instead identified. These co-infecting intracellular bacteria have been characterised using high-resolution imaging and genomics, presenting the most comprehensive study on epitheliocystis agents to date. Draft genomes of the two uncultured species, Ca. Ichthyocystis hellenicum and Ca. Ichthyocystis sparus, have been de novo sequenced and annotated from preserved material. Analysis of the genomes shows a compact core indicating a metabolic dependency on the host, and an accessory genome with an unprecedented number of tandemly arrayed gene families. This study represents a critical insight into novel, emerging fish pathogens and will be used to underpin future investigations into the bacterial origins, and to develop diagnostic and treatment strategies.\n\nEmerging pathogens of gilthead seabream: characterisation and genomic analysis of novel intracellular β-proteobacteria.", "token_count": 366, "char_count": 1567, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:20.267817", "source": { "split": "train_shard_00000", "doc_id": 4106 }, "chunk_id": "train_shard_00000_4106_0", "global_id": 4568 }, { "text": "Background. Diagnosis of progressive familial intrahepatic cholestasis (PFIC) is a challenging matter that involves the summation of clinical, laboratory, radiological, and liver histological parameters; in addition to specific investigations to exclude other causes of neonatal cholestasis. The aim of this study was to evaluate liver tissue immunohistochemistry of bile salt export pump (BSEP) and multidrug resistance 3 (MDR3) proteins in differentiating PFIC from other causes of neonatal cholestasis, particularly, when genotyping is unavailable.\n\nHepatic immunohistochemistry of bile transporters in progressive familial intrahepatic cholestasis.", "token_count": 169, "char_count": 652, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7229, "quality_score": 0.8614, "entities": { "genes": [ "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:20.714045", "source": { "split": "train_shard_00000", "doc_id": 4107 }, "chunk_id": "train_shard_00000_4107_0", "global_id": 4569 }, { "text": "Tolcapone and entacapone are catechol-O-methyltransferase (COMT) inhibitors developed as adjunct therapies for treating Parkinson's disease. While both drugs have been shown to cause mitochondrial dysfunction and inhibition of the bile salt export protein (BSEP), liver injury has only been associated with the use of tolcapone. Here we used a multiscale, mechanistic model (DILIsym(®)) to simulate the response to tolcapone and entacapone. In a simulated population (SimPops™) receiving recommended doses of tolcapone (200 mg t.i.d.), increases in serum alanine transaminase (ALT) >3× the upper limit of normal (ULN) were observed in 2.2% of the population. In contrast, no simulated patients receiving recommended doses of entacapone (200 mg 8× day) experienced serum ALT >3× ULN. Further, DILIsym(®) analyses revealed patient-specific risk factors that may contribute to tolcapone-mediated hepatotoxicity. In summary, the simulations demonstrated that differences in mitochondrial uncoupling potency and hepatic exposure primarily account for the difference in hepatotoxic potential for tolcapone and entacapone.\n\nElucidating Differences in the Hepatotoxic Potential of Tolcapone and Entacapone With DILIsym(®), a Mechanistic Model of Drug-Induced Liver Injury.", "token_count": 357, "char_count": 1264, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6608, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:21.286542", "source": { "split": "train_shard_00000", "doc_id": 4108 }, "chunk_id": "train_shard_00000_4108_0", "global_id": 4570 }, { "text": "Gastroesophageal reflux disease (GERD) is a very common disorder with increasing prevalence. It is estimated that up to 20%-25% of Americans experience symptoms of GERD weekly. Excessive reflux of acidic often with alkaline bile salt gastric and duodenal contents results in a multitude of symptoms for the patient including heartburn, regurgitation, cough, and dysphagia. There are also associated complications of GERD including erosive esophagitis, Barrett's esophagus, stricture and adenocarcinoma of the esophagus. While first line treatments for GERD involve mainly lifestyle and non-surgical therapies, surgical interventions have proven to be effective in appropriate circumstances. Anti-reflux operations are aimed at creating an effective barrier to reflux at the gastroesophageal junction and thus attempt to improve physiologic and mechanical issues that may be involved in the pathogenesis of GERD. The decision for surgical intervention in the treatment of GERD, moreover, requires an objective confirmation of the diagnosis. Confirmation is achieved using various preoperative evaluations including: ambulatory pH monitoring, esophageal manometry, upper endoscopy (esophagogastroduodenoscopy) and barium swallow. Upon confirmation of the diagnosis and with appropriate patient criteria met, an anti-reflux operation is a good alternative to prolonged medical therapy. Currently, minimally invasive gastro-esophageal fundoplication is the gold standard for surgical intervention of GERD. Our review outlines the many factors that are involved in surgical decision-making. We will review the prominent features that reflect appropriate anti-reflux surgery and present suggestions that are pertinent to surgical practices, based on evidence-based studies.\n\nGastroesophageal reflux disease: A review of surgical decision making.", "token_count": 432, "char_count": 1839, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:21.946876", "source": { "split": "train_shard_00000", "doc_id": 4109 }, "chunk_id": "train_shard_00000_4109_0", "global_id": 4571 }, { "text": "The bile salt export pump is expressed at the canalicular membrane of hepatocytes and mediates biliary excretion of bile salts. 4-Phenylbutyrate (4 PB), a drug used to treat ornithine transcarbamylase deficiency, has been found to increase the hepatocanalicular expression of bile salt export pump. The beneficial effects of 4-phenylbutyrate therapy have been reported for patients with progressive familial intrahepatic cholestasis, an inherited autosomal recessive liver disease. This is the first study to show the therapeutic effect of 4 PB in a preterm infant with cholestasis and liver fibrosis. The preterm infant had severe cholestasis with jaundice and failure to thrive refractory to ursodeoxycholic acid. Histology indicated giant cell hepatitis, cholestasis, and severe fibrosis. Bile salt export pump immunostaining showed lower expression than in a control. Oral 4 PB was started at a daily dose of 200 mg/kg/day. After the start of 4 PB therapy, cholestasis improved.\n\nEffects of 4-phenylbutyrate therapy in a preterm infant with cholestasis and liver fibrosis.", "token_count": 311, "char_count": 1076, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:22.544613", "source": { "split": "train_shard_00000", "doc_id": 4110 }, "chunk_id": "train_shard_00000_4110_0", "global_id": 4572 }, { "text": "Synechococcus is among the most important contributors to global primary productivity. The genomes of several strains of this taxon have been previously sequenced in an effort to understand the physiology and ecology of these highly diverse microorganisms. Here we present a comparative study of Synechococcus genomes. For that end, we developed GenTaxo, a program written in Perl to perform genomic taxonomy based on average nucleotide identity, average amino acid identity and dinucleotide signatures, which revealed that the analyzed strains are drastically distinct regarding their genomic content. Phylogenomic reconstruction indicated a division of Synechococcus in two clades (i.e. Synechococcus and the new genus Parasynechococcus), corroborating evidences that this is in fact a polyphyletic group. By clustering protein encoding genes into homologue groups we were able to trace the Pangenome and core genome of both marine and freshwater Synechococcus and determine the genotypic traits that differentiate these lineages.\n\nComparative genomics of Synechococcus and proposal of the new genus Parasynechococcus.", "token_count": 272, "char_count": 1120, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6943, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:23.126573", "source": { "split": "train_shard_00000", "doc_id": 4111 }, "chunk_id": "train_shard_00000_4111_0", "global_id": 4573 }, { "text": "The study aimed to evaluate the probiotic properties, antioxidant activity and fermentative capacity of Acremonium charticola and Rhizopus oryzae isolated from the Indonesian fermented dried cassava, with particular application on poultry. A. charticola inhibited the growth of Escherichia coli and Aspergillus flavus. A. charticola and R. oryzae grew in potato dextrose agar (PDA) adjusted to pH 3 and 8 or in PDA supplemented with bile salt up to 0.8%. After soaking for 8 hr, the survival rate of A. charticola in the simulated gastric juice (pH 2) and bile solutions (2% bile salt) was lower than that of R. oryzae. A. charticola and R. oryzae exhibited strong antioxidant activities. Compared to unfermented cassava pulp (control), the fibre content of cassava pulp tended to be lower after fermentation with A. charticola for 14 days. The populations of A. charticola and R. oryzae were significantly higher in fermented cassava pulp than in unfermented one. Coliform was higher in cassava pulp fermented with R. oryzae or A. charticola + R. oryzae compared to control after 7 days of fermentation, however, the bacteria were not different between A. charticola-fermented cassava pulp and control. Lactic acid bacteria (LAB) were higher in A. charticola- and R. oryzae-fermented cassava pulp than those in control, however, no difference of LAB was observed between A. charticola + R. oryzae-fermented cassava pulp and control. In conclusion, A. charticola exhibited antibacterial, antifungal and antioxidant activity, gastrointestinal persistence and fermentative capacity that may be beneficial for poultry industry.", "token_count": 483, "char_count": 1624, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5122, "quality_score": 0.7561, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:23.789308", "source": { "split": "train_shard_00000", "doc_id": 4112 }, "chunk_id": "train_shard_00000_4112_0", "global_id": 4574 }, { "text": "Functional Properties of Filamentous Fungi Isolated from the Indonesian Fermented Dried Cassava, with Particular Application on Poultry.", "token_count": 34, "char_count": 136, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:24.147653", "source": { "split": "train_shard_00000", "doc_id": 4112 }, "chunk_id": "train_shard_00000_4112_1", "global_id": 4575 }, { "text": "Hypercholesterolemia drives the development of cardiovascular disease, the leading cause of mortality in western society. Supplementation with probiotics that interfere with cholesterol metabolism may provide a contribution to disease prevention. Lactobacillus plantarum CUL66 (NCIMB 30280) has been assessed in vitro for its ability to impact cholesterol absorption. L. plantarum CUL66 tested positive for bile salt hydrolase activity and the ability to assimilate cholesterol from culture media. RT-qPCR analysis showed that the bacterium significantly decreased the expression of Niemann-Pick C1-like 1 and ATP-binding cassette transporter-1 in polarised Caco-2 cells after 6 h exposure. Conversely, the expression of ATP-binding cassette sub-family G member (ABCG)-5 and ABCG-8, and 3-hydroxy-3-methylglutaryl-CoA reductase were significantly increased. Using a radiolabelled assay, we also observed significant reductions in the uptake and basolateral efflux of cholesterol by Caco-2 cells exposed to L. plantarum CUL66. This in vitro study identified L. plantarum CUL66 as a cholesterol lowering bacteria by highlighting its ability to beneficially regulate multiple in vitro events associated with intestinal cholesterol metabolism and provides evidence of efficacy for its inclusion in future in vivo studies.\n\nLactobacillus plantarum CUL66 can impact cholesterol homeostasis in Caco-2 enterocytes.", "token_count": 394, "char_count": 1406, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8209, "entities": { "genes": [ "CUL66" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:24.766826", "source": { "split": "train_shard_00000", "doc_id": 4113 }, "chunk_id": "train_shard_00000_4113_0", "global_id": 4576 }, { "text": "Probiotics, as live microbial food ingredients or functional foods, are often related to health promotion and diseases prevention. The growth of these beneficial probiotics was improved by non-digestible food ingredients that are defined as prebiotics. Inulin is one of the known prebiotics that improves the gastrointestinal health.\n\nThe Effects of Inulin on Characteristics of Lactobacillus paracasei TD3 (IBRC-M 10784) as Probiotic Bacteria in vitro.", "token_count": 122, "char_count": 453, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7969, "quality_score": 0.8984, "entities": { "genes": [ "TD3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:25.154089", "source": { "split": "train_shard_00000", "doc_id": 4114 }, "chunk_id": "train_shard_00000_4114_0", "global_id": 4577 }, { "text": "Streptococcus thermophilus (ST) is a lactic acid bacterium widely used in dairy industry and displays several properties which could be beneficial for host. The objective of this study was to investigate, in vitro, the implication of sortase A (SrtA) and sortase-dependent proteins (SDPs) in the adhesion of ST LMD-9 strain to intestinal epithelial cells (IECs) and resistance to bile salt mixture (BSM; taurocholoate, deoxycholate, and cholate). The effect of mutations in prtS (protease), mucBP (MUCin-Binding Protein), and srtA genes in ST LMD-9 in these mechanisms were examined. The HT29-MTX, HT29-CL.16E, and Caco-2 TC7 cell lines were used. HT29-MTX and HT29-CL.16E cells express different mucins found in the gastro intestinal tract; whereas, Caco-2 TC7 express cell surface proteins found in the small intestine. All mutants showed different adhesion profiles depending on cell lines. The mutation in genes srtA and mucBP leads to a significant decrease in LMD-9 adhesion capacity to Caco-2 TC7 cells. A mutation in mucBP gene has also shown a significant decrease in LMD-9 adhesion capacity to HT29-CL.16E cells. However, no difference was observed using HT29-MTX cells. Furthermore, ST LMD-9 and srtA mutant were resistant to BSM up to 3 mM. Contrariwise, no viable bacteria were detected for prtS and mucBP mutants at this concentration. Two conclusions could be drawn. First, SDPs could be involved in the LMD-9 adhesion depending on the cell lines indicating the importance of eukaryotic-cell surface components in adherence. Second, SDPs could contribute to resistance to bile salts probably by maintaining the cell membrane integrity.\n\nImplication of sortase-dependent proteins of Streptococcus thermophilus in adhesion to human intestinal epithelial cell lines and bile salt tolerance.", "token_count": 511, "char_count": 1802, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5279, "quality_score": 0.7639, "entities": { "genes": [ "TC7", "HT29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:25.787500", "source": { "split": "train_shard_00000", "doc_id": 4115 }, "chunk_id": "train_shard_00000_4115_0", "global_id": 4578 }, { "text": "Detection of proteins containing single amino acid polymorphisms (SAPs) encoded by nonsynonymous SNPs (nsSNPs) can aid researchers in studying the functional significance of protein variants. Most proteogenomic approaches for large-scale SAPs mapping require construction of a sample-specific database containing protein variants predicted from the next-generation sequencing (NGS) data. Searching shotgun proteomic data sets against these NGS-derived databases allowed for identification of SAP peptides, thus validating the proteome-level sequence variation. Contrary to the conventional approaches, our study presents a novel strategy for proteome-wide SAP detection without relying on sample-specific NGS data. By searching a deep-coverage proteomic data set from an industrial thermotolerant yeast strain using our strategy, we identified 337 putative SAPs compared to the reference genome. Among the SAP peptides identified with stringent criteria, 85.2% of SAP sites were validated using whole-genome sequencing data obtained for this organism, which indicates high accuracy of SAP identification with our strategy. More interestingly, for certain SAP peptides that cannot be predicted by genomic sequencing, we used synthetic peptide standards to verify expression of peptide variants in the proteome. Our study has provided a unique tool for proteogenomics to enable proteome-wide direct SAP identification and capture nongenetic protein variants not linked to nsSNPs.\n\nAn NGS-Independent Strategy for Proteome-Wide Identification of Single Amino Acid Polymorphisms by Mass Spectrometry.", "token_count": 366, "char_count": 1596, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:26.374737", "source": { "split": "train_shard_00000", "doc_id": 4116 }, "chunk_id": "train_shard_00000_4116_0", "global_id": 4579 }, { "text": "Escherichia coli, one of the main causative agents of bovine mastitis, is responsible for significant losses on dairy farms. In order to better understand the pathogenicity of E. coli mastitis, an accurate characterization of E. coli strains isolated from mastitis cases is required. By using phylogenetic analyses and whole genome comparison of 5 currently available mastitis E. coli genome sequences, we searched for genotypic traits specific for mastitis isolates. Our data confirm that there is a bias in the distribution of mastitis isolates in the different phylogenetic groups of the E. coli species, with the majority of strains belonging to phylogenetic groups A and B1. An interesting feature is that clustering of strains based on their accessory genome is very similar to that obtained using the core genome. This finding illustrates the fact that phenotypic properties of strains from different phylogroups are likely to be different. As a consequence, it is possible that different strategies could be used by mastitis isolates of different phylogroups to trigger mastitis. Our results indicate that mastitis E. coli isolates analyzed in this study carry very few of the virulence genes described in other pathogenic E. coli strains. A more detailed analysis of the presence/absence of genes involved in LPS synthesis, iron acquisition and type 6 secretion systems did not uncover specific properties of mastitis isolates. Altogether, these results indicate that mastitis E. coli isolates are rather characterized by a lack of bona fide currently described virulence genes.\n\nGenomic Comparative Study of Bovine Mastitis Escherichia coli.", "token_count": 383, "char_count": 1651, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5538, "quality_score": 0.7769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:26.955047", "source": { "split": "train_shard_00000", "doc_id": 4117 }, "chunk_id": "train_shard_00000_4117_0", "global_id": 4580 }, { "text": "Lactobacillus plantarum WLPL04, a specific strain isolated from human breast milk, was investigated for its survival capacity (acid and bile salt tolerance, survival in simulated gastrointestinal tract, inhibition of pathogens, antibiotic susceptibility, yield of exopolysaccharides) and probiotic properties (antiadhesion of pathogens, protection from harmful effect of sodium dodecyl sulfate, and antiinflammatory stress on Caco-2 cells). The results showed that Lb. plantarum WLPL04 had broad-spectrum activity against gram-positive strains (Listeria monocytogenes CMCC54007, Bacillus cereus ATCC14579, and Staphylococcus aureus CMCC26003) and gram-negative strains (Pseudomonas aeruginosa MCC10104, Shigella sonnei ATCC25931, Enterobacter sakazakii ATCC29544, Salmonella typhimurium ATCC13311, and Escherichia coli O157:H7). Antibiotic susceptibility tests showed that Lb. plantarum WLPL04 was susceptible to 8 of 14 antibiotics (e.g., erythromycin and nitrofurantoin) and resistant to 6 of 14 antibiotics (e.g., kanamycin and bacitracin). Lactobacillus plantarum WLPL04 was able to survive at pH 2.5 for 3h and at 0.45% bile salt for 12h, suggesting that it can survive well in the gastrointestinal tract. In addition, the exopolysaccharide yield of Lb. plantarum WLPL04 reached 426.73 ± 65.56 mg/L at 24h. With strategies of competition, inhibition, and displacement, Lb. plantarum WLPL04 reduced the adhesion of E. coli O157:H7 (35.51%), Sal", "token_count": 513, "char_count": 1448, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [ "CMCC54007", "ATCC29544", "MCC10104", "ATCC13311", "ATCC25931", "WLPL04", "CMCC26003", "ATCC14579" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:40:27.608483", "source": { "split": "train_shard_00000", "doc_id": 4118 }, "chunk_id": "train_shard_00000_4118_0", "global_id": 4581 }, { "text": "typhimurium ATCC 13311 (8.10%), and Staph. aureus CMCC 26003 (40.30%) on Caco-2 cells by competition, and subsequently by 59.80, 62.50, and 42.60%, respectively, for the 3 pathogens through inhibition, and by 75.23, 39.97, and 52.88%, respectively, through displacement. Lactobacillus plantarum WLPL04 attenuated the acute stress induced by sodium dodecyl sulfate on Caco-2 cells and significantly inhibited the expression of inflammatory cytokines (IL-6, IL-8 and tumor necrosis factor-α) on Caco-2 cells but increased IL-10 expression in vitro compared with the Salmonella-treated group. In summary, Lb. plantarum WLPL04 from breast milk could be considered as a probiotic candidate for dairy products to promote human health.\n\nEvaluation of probiotic properties of Lactobacillus plantarum WLPL04 isolated from human breast milk.", "token_count": 283, "char_count": 831, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7069, "quality_score": 0.8534, "entities": { "genes": [ "WLPL04" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:28.162242", "source": { "split": "train_shard_00000", "doc_id": 4118 }, "chunk_id": "train_shard_00000_4118_1", "global_id": 4582 }, { "text": "This work aims to develop an encapsulated oral-synbiotic supplement by studying the effect of adding inulin in alginate beads and observing its ability to protect three probiotic strains: Pediocucus acidilactici, Lactobacillus reuteri and Lactobacillus salivarius. Beads of different inulin concentrations 0%, 5%, 10%, 15% and 20% (w/v) in 2% (w/v) alginate solution were prepared by the extrusion/ionotropic gelation method. Polymer distribution within beads was characterised using confocal laser scanning microscopy. Interactions between alginate and inulin were monitored by Fourier transform infra-red spectroscopy (FTIR). Effect of encapsulation on viability, antimicrobial ability, acid tolerance and bile tolerance of probiotic strains were investigated. Antimicrobial and probiotic properties of bacterial strains were not affected by encapsulation. Bacterial protection against acidity was increased by adding inulin. Beads with 5% w/v inulin were the most effective in bacterial protection against bile-salts. To our knowledge, this work is the first to use such high concentrations of inulin.\n\nA prebiotic matrix for encapsulation of probiotics: physicochemical and microbiological study.", "token_count": 319, "char_count": 1200, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:28.720086", "source": { "split": "train_shard_00000", "doc_id": 4119 }, "chunk_id": "train_shard_00000_4119_0", "global_id": 4583 }, { "text": "For nearly 100 years serotyping has been the gold standard for the identification of Salmonella serovars. Despite the increasing adoption of DNA-based subtyping approaches, serotype information remains a cornerstone in food safety and public health activities aimed at reducing the burden of salmonellosis. At the same time, recent advances in whole-genome sequencing (WGS) promise to revolutionize our ability to perform advanced pathogen characterization in support of improved source attribution and outbreak analysis. We present the Salmonella In Silico Typing Resource (SISTR), a bioinformatics platform for rapidly performing simultaneous in silico analyses for several leading subtyping methods on draft Salmonella genome assemblies. In addition to performing serovar prediction by genoserotyping, this resource integrates sequence-based typing analyses for: Multi-Locus Sequence Typing (MLST), ribosomal MLST (rMLST), and core genome MLST (cgMLST). We show how phylogenetic context from cgMLST analysis can supplement the genoserotyping analysis and increase the accuracy of in silico serovar prediction to over 94.6% on a dataset comprised of 4,188 finished genomes and WGS draft assemblies. In addition to allowing analysis of user-uploaded whole-genome assemblies, the SISTR platform incorporates a database comprising over 4,000 publicly available genomes, allowing users to place their isolates in a broader phylogenetic and epidemiological context. The resource incorporates several metadata driven visualizations to examine the phylogenetic, geospatial and temporal distribution of genome-sequenced isolates. As sequencing of Salmonella isolates at public health laboratories around the world becomes increasingly common, rapid in silico analysis of minimally processed draft genome assemblies provides a powerful approach for molecular epidemiology in support of public health investigations. Moreover, this type of integrated analysis using multiple sequence-based methods of sub-typing allows for continuity with historical serotyping data as we transition towards the increasing adoption of genomic analyses in epidemiology. The SISTR platform is freely available on the web at https://lfz.corefacility.ca/sistr-app/.", "token_count": 508, "char_count": 2236, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6027, "quality_score": 0.8013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:29.376925", "source": { "split": "train_shard_00000", "doc_id": 4120 }, "chunk_id": "train_shard_00000_4120_0", "global_id": 4584 }, { "text": "The Salmonella In Silico Typing Resource (SISTR): An Open Web-Accessible Tool for Rapidly Typing and Subtyping Draft Salmonella Genome Assemblies.", "token_count": 42, "char_count": 146, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:29.742348", "source": { "split": "train_shard_00000", "doc_id": 4120 }, "chunk_id": "train_shard_00000_4120_1", "global_id": 4585 }, { "text": "Molybdenum disulfide (MoS2 ) and tungsten disulfide (WS2 ), two representative transition metal dichalcogenide materials, have captured tremendous interest for their unique electronic, optical, and chemical properties. Compared with MoS2 and WS2 , molybdenum ditelluride (MoTe2 ) and tungsten ditelluride (WTe2 ) possess similar lattice structures while having smaller bandgaps (less than 1 eV), which is particularly interesting for applications in the near-infrared wavelength regime. Here, few-layer MoTe2 /WTe2 nanosheets are fabricated by a liquid exfoliation method using sodium deoxycholate bile salt as surfactant, and the nonlinear optical properties of the nanosheets are investigated. The results demonstrate that MoTe2 /WTe2 nanosheets exhibit nonlinear saturable absorption property at 1.55 μm. Soliton mode-locking operations are realized separately in erbium-doped fiber lasers utilizing two types of MoTe2 /WTe2 -based saturable absorbers, one of which is prepared by depositing the nanosheets on side polished fibers, while the other is fabricated by mixing the nanosheets with polyvinyl alcohol and then evaporating them on substrates. Numerous applications may benefit from the nonlinear saturable absorption features of MoTe2 /WTe2 nanosheets, such as visible/near-infrared pulsed laser, materials processing, optical sensors, and modulators.\n\nNonlinear Saturable Absorption of Liquid-Exfoliated Molybdenum/Tungsten Ditelluride Nanosheets.", "token_count": 386, "char_count": 1459, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8464, "entities": { "genes": [ "WS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:30.360939", "source": { "split": "train_shard_00000", "doc_id": 4121 }, "chunk_id": "train_shard_00000_4121_0", "global_id": 4586 }, { "text": "Poultry is known to be a major reservoir of Salmonella. The use of lactic acid bacteria has become one of successful strategies to control Salmonella in poultry. The purpose of this study was to select lactic acid bacteria strains by their in vitro immunomodulatory properties for potential use as probiotics against Salmonella infection in broiler chicks. Among 101 isolated lactic acid bacteria strains, 13 strains effectively survived under acidic (pH 2.5) and bile salt (ranging from 0.1% to 1.0%) conditions, effectively inhibited growth of 6 pathogens, and adhered to Caco-2 cells. However, their in vitro immunomodulatory activities differed significantly. Finally, three strains with higher in vitro immunomodulatory properties (Lactobacillus plantarum PZ01, Lactobacillus salivarius JM32 and Pediococcus acidilactici JH231) and three strains with lower in vitro immunomodulatory activities (Enterococcus faecium JS11, Lactobacillus salivarius JK22 and Lactobacillus salivarius JM2A1) were compared for their inhibitory effects on Salmonella adhesion and invasion to Caco-2 cells in vitro and their antimicrobial effects in vivo. The former three strains inhibited Salmonella adhesion and invasion to Caco-2 cells in vitro, reduced the number of Salmonella in intestinal content, spleen and liver, reduced the levels of lipopolysaccharide-induced TNF-α factor (LITAF), IL-1β, IL-6 and IL-12 in serum and increased the level of IL-10 in serum during a challenge study in vivo more efficiently than the latter three strains. These results suggest that in vitro immunomodulatory activities could be used as additional parameters to select more effective probiotics as feed supplements for poultry.\n\nUsing In Vitro Immunomodulatory Properties of Lactic Acid Bacteria for Selection of Probiotics against Salmonella Infection in Broiler Chicks.", "token_count": 514, "char_count": 1846, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5458, "quality_score": 0.7729, "entities": { "genes": [ "PZ01", "JH231", "JS11", "JK22", "JM32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:40:31.022378", "source": { "split": "train_shard_00000", "doc_id": 4122 }, "chunk_id": "train_shard_00000_4122_0", "global_id": 4587 }, { "text": "Extraintestinal pathogenic Escherichia coli (ExPEC) that causes extraintestinal infections often harbor plasmids encoding fitness traits such as resistance and virulence determinants that are of clinical importance. We determined the complete nucleotide sequence of plasmid pEC302/04 from a multidrug-resistant E. coli EC302/04 which was isolated from the tracheal aspirate of a patient in Malaysia. In addition, we also performed comparative sequence analyses of 18 related IncFIIA plasmids to determine the phylogenetic relationship and diversity of these plasmids. The 140,232 bp pEC302/04 is a multireplicon plasmid that bears three replication systems (FII, FIA, and FIB) with subtype of F2:A1:B1. The plasmid is self-transmissible with a complete transfer region. pEC302/04 also carries antibiotic resistance genes such as bla TEM-1 and a class I integron containing sul1, cml and aadA resistance genes, conferring multidrug resistance (MDR) to its host, E. coli EC302/04. Besides, two iron acquisition systems (SitABCD and IutA-IucABCD) which are the conserved virulence determinants of ExPEC-colicin V or B and M (ColV/ColBM)-producing plasmids were identified in pEC302/04. Multiple toxin-antitoxin (TA)-based addiction systems (i.e., PemI/PemK, VagC/VagD, CcdA/CcdB, and Hok/Sok) and a plasmid partitioning system, ParAB, and PsiAB, which are important for plasmid maintenance were also found. Comparative plasmid analysis revealed only one conserved gene, the repA1 as the core genome, showing that there is an extensive diversity among the IncFIIA plasmids", "token_count": 476, "char_count": 1568, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6514, "quality_score": 0.8257, "entities": { "genes": [ "EC302" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:31.669136", "source": { "split": "train_shard_00000", "doc_id": 4123 }, "chunk_id": "train_shard_00000_4123_0", "global_id": 4588 }, { "text": "The phylogenetic relationship of 18 IncF plasmids based on the core regions revealed that ColV/ColBM-plasmids and non-ColV/ColBM plasmids were separated into two distinct groups. These plasmids, which carry highly diverse genetic contents, are also mosaic in nature. The atypical combination of genetic materials, i.e., the MDR- and ColV/ColBM-plasmid-virulence encoding regions in a single ExPEC plasmid is rare but of clinical importance. Such phenomenon is bothersome when the plasmids are transmissible, facilitating the spread of virulence and resistance plasmids among pathogenic bacteria. Notably, certain TA systems are more commonly found in particular ExPEC plasmid types, indicating the possible relationships between certain TA systems and ExPEC pathogenesis.\n\nThe Complete Sequence and Comparative Analysis of a Multidrug-Resistance and Virulence Multireplicon IncFII Plasmid pEC302/04 from an Extraintestinal Pathogenic Escherichia coli EC302/04 Indicate Extensive Diversity of IncFII Plasmids.", "token_count": 270, "char_count": 1008, "word_count": 133, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "EC302" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:32.216926", "source": { "split": "train_shard_00000", "doc_id": 4123 }, "chunk_id": "train_shard_00000_4123_1", "global_id": 4589 }, { "text": "The objective of the present study was to formulate a multi-pathogen enrichment broth which could support the simultaneous growth of five common foodborne pathogens (Salmonella enterica, Staphylococcus aureus, Shigella flexneri, Listeria monocytogenes and Escherichia coli O157:H7). The formulated broth SSSLE was composed of potassium tellurite, bile salt, lithium chloride, and sodium chloride as growth-inhibitors; glucose, esculin, mannitol and sodium pyruvate as growth-promoters. Compared with the respective specific selective enrichment broths, the individual growth pattern of each target pathogen in SSSLE was equal, or even better, except in the case of S. flexneri. In mixed-culture experiments, the gram-negative bacteria showed higher growth capabilities than the gram-positive bacteria after 8-h enrichment; however, the cell numbers after 24-h enrichment indicated that SSSLE could support the concurrent growth of five target pathogens irrespective of whether pathogens were inoculated initially at equal or unequal levels. For natural food samples under the high background flora, the final cell numbers enriched in SSSLE for five targets were enough to be detected by multiplex PCR. In conclusion, SSSLE was capable of supporting the growth of five target pathogens concurrently. The new broth formulated in this study has the potential of saving time, efforts and costs in multi-pathogen enrichment procedures.\n\nDevelopment of a multi-pathogen enrichment broth for simultaneous growth of five common foodborne pathogens.", "token_count": 396, "char_count": 1540, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:32.834746", "source": { "split": "train_shard_00000", "doc_id": 4124 }, "chunk_id": "train_shard_00000_4124_0", "global_id": 4590 }, { "text": "In this review, bile salt, bile salt-surfactant, and bile salt-drug interactions and their solubilization studies are mainly focused. Usefulness of bile salts in digestion, absorption, and excretion of various compounds and their rare properties in ordering the shape and size of the micelles owing to the presence of hydrophobic and hydrophilic faces are taken into consideration while compiling this review. Bile salts as potential bio-surfactants to solubilize drugs of interest are also highlighted. This review will give an insight into the selection of drugs in different applications as their properties get modified by interaction with bile salts, thus influencing their solution behavior which, in turn, modifies the phase-forming behavior, microemulsion, and clouding phenomenon, besides solubilization. Finally, their future perspectives are taken into consideration to assess their possible uses as bio-surfactants without side effects to human beings.\n\nSolubilization and Interaction Studies of Bile Salts with Surfactants and Drugs: a Review.", "token_count": 235, "char_count": 1056, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:33.310808", "source": { "split": "train_shard_00000", "doc_id": 4125 }, "chunk_id": "train_shard_00000_4125_0", "global_id": 4591 }, { "text": "Probiotics are living micro-organisms that do not naturally have shelf life, and normally are weakly protected against the digestive action of the GI tract. A new dual coating technology has been developed in an effort to maximize survival, that is, to be able to reach the intestine alive and in sufficient numbers to confer the beneficial health effects on the host. Dual-coating of lactic acid bacteria (LAB) is the result of fourth-generation coating technology for the protection of these bacteria at least 100-fold or greater than the uncoated LAB. This innovative technique involves a first pH-dependent protein layer that protects bacteria from gastric acid and bile salt, and a second polysaccharide matrix that protects bacteria from external factors, such as humidity, temperature and pressure, as well as the digestive action during the passage through the GI tract. Dual-coated probiotic formulation is applicable to different therapeutic areas, including irritable bowel syndrome, atopic dermatitis, acute diarrhea, chronic constipation, Helicobacter pylori eradication, and prevention of antibiotic-associated diarrhea. An updated review of the efficacy of doubly coated probiotic strains for improving bacterial survival in the intestinal tract and its consequent clinical benefits in humans is here presented.\n\nDual-coated lactic acid bacteria: an emerging innovative technology in the field of probiotics.", "token_count": 330, "char_count": 1423, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6845, "quality_score": 0.8422, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:33.915606", "source": { "split": "train_shard_00000", "doc_id": 4126 }, "chunk_id": "train_shard_00000_4126_0", "global_id": 4592 }, { "text": "Transformation of the solid-state form of a drug compound in the lumen of the gastrointestinal tract may alter the drug bioavailability and in extreme cases result in patient fatalities. The solution-mediated anhydrate-to-hydrate phase transformation was examined using an in vitro model with different biorelevant media, simulated fasted and fed state intestinal fluids containing bile salt and dioleoylphosphatidylcholine (DOPC) micelles, DOPC/sodium dodecyl sulfate (SDS) mixture, bile salt solution and water. Two anhydrate compounds (carbamazepine, CBZ and nitrofurantoin, NF) with different overall transformation time into hydrate form were used as model compounds. The transformations were monitored using direct structural information from time-resolved synchrotron X-ray diffraction. The kinetics of these transformations were estimated using multivariate data analysis (principal component analysis, PCA) and compared to those for nitrofurantoin (NF). The study showed that the solution-mediated phase transformation of CBZ anhydrate was remarkably faster in the DOPC/SDS medium compared to transformation in all the other aqueous dispersion media. The conversion time for CBZ anhydrate in water was shorter than for DOPC/SDS but still faster than the conversion seen in fed and fasted state micellar media. The conversion of CBZ anhydrate to hydrate was the slowest in the solution containing bile salt alone. In contrast, the solution-mediated phase transformations of NF did only show limited kinetic dependence on the dispersion media used, indicating the complexity of the nucleation process. Furthermore, when the CBZ and NF material was compacted into tablets the transformation times were remarkably slower. Results suggest that variations in the composition of the contents of the stomach/gut may affect the recrystallization kinetics, especially when investigating compounds with relatively fast overall transformation time, such as CBZ.\n\nAnhydrate to hydrate solid-state transformations of carbamazepine and nitrofurantoin in biorelevant media studied in situ using time-resolved synchrotron X-ray diffraction.", "token_count": 512, "char_count": 2132, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5395, "quality_score": 0.7698, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:34.590740", "source": { "split": "train_shard_00000", "doc_id": 4127 }, "chunk_id": "train_shard_00000_4127_0", "global_id": 4593 }, { "text": "Bile alcohols and bile acids from gallbladder bile of the Arapaima gigas, a large South American freshwater fish, were isolated by reversed-phase high-performance liquid chromatography. The structures of the major isolated compounds were determined by electrospray-tandem mass spectrometry and nuclear magnetic resonance using (1)H- and (13)C-NMR spectra. The novel bile salts identified were six variants of 2-hydroxy bile acids and bile alcohols in the 5α- and 5β-series, with 29% of all compounds having hydroxylation at C-2. Three C27 bile alcohols were present (as ester sulfates): (24ξ,25ξ)-5α-cholestan-2α,3α,7α,12α,24,26-hexol; (25ξ)-5β-cholestan-2β,3α,7α,12α,26,27-hexol, and (25ξ)-5α-cholestan-2α,3α,7α,12α,26,27-hexol. A single C27 bile acid was identified: (25ξ)-2α,3α,7α,12α-tetrahydroxy-5α-cholestan-26-oic acid, present as its taurine conjugate. Two novel C24 bile acids were identified: the 2α-hydroxy derivative of allochenodeoxycholic acid and the 2β-hydroxy derivative of cholic acid, both occurring as taurine conjugates. These studies extend previous work in establishing the natural occurrence of novel 2α- and 2β-hydroxy-C24 and C27 bile acids as well as C27 bile alcohols in both the normal (5β) as well as the (5α) \"allo\" A/B-ring juncture. The bile salt profile of A. gigas appears to be unique among vertebrates.", "token_count": 489, "char_count": 1339, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8045, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:35.292513", "source": { "split": "train_shard_00000", "doc_id": 4128 }, "chunk_id": "train_shard_00000_4128_0", "global_id": 4594 }, { "text": "Novel, major 2α- and 2β-hydroxy bile alcohols and bile acids in the bile of Arapaima gigas, a large South American river fish.", "token_count": 44, "char_count": 126, "word_count": 22, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:35.675536", "source": { "split": "train_shard_00000", "doc_id": 4128 }, "chunk_id": "train_shard_00000_4128_1", "global_id": 4595 }, { "text": "The aim of this study was to evaluate the functional properties of lactic acid bacteria from various sources and to identify strains for use as probiotics. Ten Lactobacillus strains were selected and their properties such as bile tolerance, acid resistance, cholesterol assimilation activity, and adherence to HT-29 cells were assessed to determine their potential as probiotics. Lactobacillus sp. JNU 8829, L. casei MB3, L. sakei MA9, L. sakei CH8, and L. acidophilus M23 were found to show full tolerance to the 0.3% bile acid. All strains without L. acidophilus M23 were the most acid-tolerant strains. After incubating the strains at pH 2.5 for 2 h, their viability decreased by 3 Log cells. Some strains survived at pH 2.5 in the presence of pepsin and 0.3% bile acid. Lactobacillus sp. JNU 8829, L. acidophilus KU41, L. acidophilus M23, L. fermentum NS2, L. plantarum M13, and L. plantarum NS3 were found to reduce cholesterol levels by >50% in vitro. In the adhesion assay, Lactobacillus sp. JNU 8829, L. casei MB3, L. sakei MA9, and L. sakei CH8 showed higher adhesion activities after 2 h of co-incubation with the intestinal cells. The results of this comprehensive analysis shows that this new probiotic strain named, Lactobacillus sp. JNU 8829 could be a promising candidate for dairy products.\n\nCharacterization of Selected Lactobacillus Strains for Use as Probiotics.", "token_count": 443, "char_count": 1381, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5405, "quality_score": 0.7703, "entities": { "genes": [ "MA9", "NS2", "NS3", "CH8", "KU41", "MB3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:36.316619", "source": { "split": "train_shard_00000", "doc_id": 4129 }, "chunk_id": "train_shard_00000_4129_0", "global_id": 4596 }, { "text": "The objective of this study was to identify lactic acid bacteria (LAB) isolated from kimchi and to evaluate its characteristics and functional properties for application in fermented dairy products as a probiotic or commercial starter culture. Eight stains isolated from kimchi were selected through an investigation of phenotypic characteristics. Two strains (DK211 and DK303) were identified as Lactobacillus plantarum, another two (DK207 and DK215) as Lactobacillus paracasei, and one (DK301) as Lactobacillus sakei. The remaining three strains were identified as species of Weissella. All selected Lactobacillus strains had acid and bile tolerance, even though there was wide variation in the ability of each strain. DK303 showed a remarkably higher proteolytic activity. There were no significant differences in β-galactosidase activity among the tested strains, except that DK301 showed no activity. Auto-aggregation varied between 82.1 and 90.0%, and hydrophobicity values ranged from 0.5 to 51.6%.The strongest auto-aggregation and hydrophobicity were observed in DK211. All selected strains showed better 1,1-diphenyl-2-picrylhydrzyl (DPPH) scavenging activity than commercial strains. DK211, DK215, DK301, and DK303 had effective inhibitory activity against all pathogens tested except E. coli. When selected strains were used for yogurt preparation as a single starter culture, the time required to reach target titratable acidity (0.9) was 11-12 h. The yogurt fermented with DK211 had favorable panelists ratings for most sensory attributes, which were comparable with yogurt fermented with a commercial strain. The results suggest that strains isolated from kimchi could be potential probiotic and starter cultures for use in yogurt manufacturing.", "token_count": 485, "char_count": 1760, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6113, "quality_score": 0.8057, "entities": { "genes": [ "DK303", "DK211", "DK301", "DK215", "DK207" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:36.968834", "source": { "split": "train_shard_00000", "doc_id": 4130 }, "chunk_id": "train_shard_00000_4130_0", "global_id": 4597 }, { "text": "Assessment of Characteristics and Functional Properties of Lactobacillus Species Isolated from Kimchi for Dairy Use.", "token_count": 29, "char_count": 116, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:37.334837", "source": { "split": "train_shard_00000", "doc_id": 4130 }, "chunk_id": "train_shard_00000_4130_1", "global_id": 4598 }, { "text": "The present study was conducted to screen candidate probiotic strains for anti-inflammatory activity. Initially, a nitric oxide (NO) assay was used to test selected candidate probiotic strains for anti-inflammatory activity in cultures of the murine macrophage cell line, RAW 264.7. Then, the in vitro probiotic properties of the strains, including bile tolerance, acid resistance, and growth in skim milk media, were investigated. We also performed an in vitro hydrophobicity test and an intestinal adhesion assay using Caenorhabditis elegans as a surrogate in vivo model. From our screening, we obtained 4 probiotic candidate lactic acid bacteria (LAB) strains based on their anti-inflammatory activity in lipopolysaccharide (LPS)-stimulated RAW 264.7 cell cultures and the results of the in vitro and in vivo probiotic property assessments. Molecular characterization using 16S rDNA sequencing analysis identified the 4 LAB strains as Lactobacillus plantarum. The selected L. plantarum strains (CAU1054, CAU1055, CAU1064, and CAU1106) were found to possess desirable in vitro and in vivo probiotic properties, and these strains are good candidates for further investigations in animal models and human clinical studies to elucidate the mechanisms underlying their anti-inflammatory activities.\n\nScreening and Characterization of Lactic Acid Bacteria Strains with Anti-inflammatory Activities through in vitro and Caenorhabditis elegans Model Testing.", "token_count": 395, "char_count": 1453, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5941, "quality_score": 0.797, "entities": { "genes": [ "CAU1054", "CAU1106", "CAU1055", "CAU1064" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:37.944572", "source": { "split": "train_shard_00000", "doc_id": 4131 }, "chunk_id": "train_shard_00000_4131_0", "global_id": 4599 }, { "text": "Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains.\n\nPangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.", "token_count": 169, "char_count": 802, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7207, "quality_score": 0.8604, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:39.184302", "source": { "split": "train_shard_00000", "doc_id": 4132 }, "chunk_id": "train_shard_00000_4132_0", "global_id": 4600 }, { "text": "Bile salts are steroid biosurfactants that have a significant role in fat digestion, cholesterol micellar solubilization, and regulation of metabolism. They are important in pharmaceutical studies as modulators of the transport-permeability of drugs or as ligands for certain receptors. For the rational application of bile salts in medicine, it is necessary to have detailed knowledge of their aggregation capabilities (which determine their membranotoxicity and solubilization capacity). From the examination of bile salt derivatives, the in plane of lnk (RPHPLC) and micelle aggregation number n, as well as the anion of 7-oxodeoxycholic acid (7-OxD) and anion of cholic acid (C), are considered to be outliers, related to linear hydrophobic congeneric groups, which means that their micelles, in addition to being determined by hydrophobic interactions, are determined by hydrogen bonds, i.e., they form micelles with higher aggregation numbers than would be expected from the hydrophobicity of their steroid skeleton. For bile salts of the normal series in the formation of hydrogen bonds in secondary micelles, the crucial structural elements of the steroid skeleton are: α-equatorial-C3-OH group and α-axial-C12-OH group. Bile salts of the allo series, including allocholic (aC), allodeoxycholic (aDC) and allochenodeoxycholic acid (aCD), belong to the linear hydrophobic congeneric group. Their micelles are determined by hydrophobic interactions. It is assumed that for the analyzed allo derivatives, the A ring of the steroid skeleton is in the twisted boat conformation, which explains the spatial sheltering of their C3-OH group in micelles.\n\nChemometric and conformational approach to the analysis of the aggregation capabilities in a set of bile salts of the allo and normal series.", "token_count": 454, "char_count": 1796, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5305, "quality_score": 0.7653, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:39.823147", "source": { "split": "train_shard_00000", "doc_id": 4133 }, "chunk_id": "train_shard_00000_4133_0", "global_id": 4601 }, { "text": "We herein examined the immunohistochemical expression of 2 hepatocyte-specific transporters (bile salt export pump [BSEP] and multidrug-resistance protein 3 [MDR3]) in hepatocellular carcinomas (HCCs, n=54), intrahepatic cholangiocarcinomas (n=34), combined hepatocellular and cholangiocarcinomas (n=23), and hepatoid carcinomas originated from extrahepatic organs (n=27) to compare their diagnostic values with those of arginase-1 (ARG1) and hepatocyte paraffin-1 (HepPar-1). BSEP was expressed in 91% of HCCs and MDR3 in 83%. Although their sensitivities were slightly lower than those of ARG1 (96%) and HepPar-1 (93%), the 2 transporters appeared to be more specific for HCCs. ARG1 and HepPar-1 were expressed in intrahepatic cholangiocarcinomas (9% and 6%) and hepatoid carcinomas (22% and 44%, respectively), whereas BSEP and MDR3 were entirely negative in these neoplasms, except for 1 case of BSEP-positive hepatoid carcinoma of the esophagus. The highly specific expression of BSEP and MDR3 in hepatocytes was recapitulated in additional examinations of combined hepatocellular and cholangiocarcinomas, in which the expression of the transporters was restricted to morphologically hepatocellular areas. In contrast, ARG1 and HepPar-1 were also variably positive in areas of biliary or indeterminate differentiation. We also applied BSEP and MDR3 immunohistochemistry to 8 biopsy cases of poorly differentiated primary liver cancer, in which the original diagnosis was not conclusive. The diagnosis of HCC was retrospectively suggested in 2 cases expressing both BSEP and MDR3", "token_count": 485, "char_count": 1583, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5734, "quality_score": 0.7867, "entities": { "genes": [ "ARG1", "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:40.488467", "source": { "split": "train_shard_00000", "doc_id": 4134 }, "chunk_id": "train_shard_00000_4134_0", "global_id": 4602 }, { "text": "In conclusion, given the highly specific expression of BSEP and MDR3 in HCCs, immunohistochemistry for these transporters will be useful not only for determining hepatocellular differentiation in primary liver cancers but also for discriminating HCCs from hepatoid carcinomas.\n\nBSEP and MDR3: Useful Immunohistochemical Markers to Discriminate Hepatocellular Carcinomas From Intrahepatic Cholangiocarcinomas and Hepatoid Carcinomas.", "token_count": 124, "char_count": 432, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [ "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:40.872229", "source": { "split": "train_shard_00000", "doc_id": 4134 }, "chunk_id": "train_shard_00000_4134_1", "global_id": 4603 }, { "text": "The ability of any organism to sense and respond to challenges presented in the environment is critically important for promoting or restricting colonization of specific sites. Recent work has demonstrated that the host metabolite D-serine has the ability to markedly influence the outcome of infection by repressing the type III secretion system of enterohaemorrhagic Escherichia coli (EHEC) in a concentration-dependent manner. However, exactly how EHEC monitors environmental D-serine is not understood. In this work, we have identified two highly conserved members of the E. coli core genome, encoding an inner membrane transporter and a transcriptional regulator, which collectively help to \"sense\" levels of D-serine by regulating its uptake from the environment and in turn influencing global gene expression. Both proteins are required for full expression of the type III secretion system and diversely regulated prophage-encoded effector proteins demonstrating an important infection-relevant adaptation of the core genome. We propose that this system acts as a key safety net, sampling the environment for this metabolite, thereby promoting colonization of EHEC to favorable sites within the host.\n\nA Highly Conserved Bacterial D-Serine Uptake System Links Host Metabolism and Virulence.", "token_count": 293, "char_count": 1297, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:41.444913", "source": { "split": "train_shard_00000", "doc_id": 4135 }, "chunk_id": "train_shard_00000_4135_0", "global_id": 4604 }, { "text": "Whether and to what extent solid lipid nanoparticles (SLNs) can be absorbed integrally via oral delivery should be clarified because it is the basis for elucidation of absorption mechanisms. To address this topic, the in vivo fate of SLNs as well as their interaction with biomembranes is investigated using water-quenching fluorescent probes that can signal structural variations of lipid-based nanocarriers. Live imaging indicates prolonged retention of SLNs in the stomach, whereas in the intestine, SLNs can be digested quickly. No translocation of intact SLNs to other organs or tissues can be observed. The in situ perfusion study shows bioadhesion of both SLNs and simulated mixed micelles (SMMs) to intestinal mucus, but no evidence of penetration of integral nanocarriers. Both SLNs and SMMs exhibit significant cellular uptake, but fail to penetrate cell monolayers. Confocal laser scanning microscopy reveals that nanocarriers mainly concentrate on the surface of the monolayers, and no evidence of penetration of intact vehicles can be obtained. The mucous layer acts as a barrier to the penetration of both SLNs and SMMs. Both bile salt-decoration and SMM formulation help to strengthen the interaction with biomembranes. It is concluded that evidence does not support absorption of intact SLNs via oral delivery.\n\nEvidence does not support absorption of intact solid lipid nanoparticles via oral delivery.", "token_count": 339, "char_count": 1419, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5888, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:42.015197", "source": { "split": "train_shard_00000", "doc_id": 4136 }, "chunk_id": "train_shard_00000_4136_0", "global_id": 4605 }, { "text": "Brucella spp. are facultative intracellular pathogens, that cause a contagious zoonotic disease, that can result in such outcomes as abortion or sterility in susceptible animal hosts and grave, debilitating illness in humans. For deciphering the survival mechanism of Brucella spp. in vivo, 42 Brucella complete genomes from NCBI were analyzed for the pan-genome and core genome by identification of their composition and function of Brucella genomes. The results showed that the total 132,143 protein-coding genes in these genomes were divided into 5369 clusters. Among these, 1710 clusters were associated with the core genome, 1182 clusters with strain-specific genes and 2477 clusters with dispensable genomes. COG analysis indicated that 44 % of the core genes were devoted to metabolism, which were mainly responsible for energy production and conversion (COG category C), and amino acid transport and metabolism (COG category E). Meanwhile, approximately 35 % of the core genes were in positive selection. In addition, 1252 potential essential genes were predicted in the core genome by comparison with a prokaryote database of essential genes. The results suggested that the core genes in Brucella genomes are relatively conservation, and the energy and amino acid metabolism play a more important role in the process of growth and reproduction in Brucella spp. This study might help us to better understand the mechanisms of Brucella persistent infection and provide some clues for further exploring the gene modules of the intracellular survival in Brucella spp.\n\nAnalysis of pan-genome to identify the core genes and essential genes of Brucella spp.", "token_count": 394, "char_count": 1660, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5476, "quality_score": 0.7738, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:42.633535", "source": { "split": "train_shard_00000", "doc_id": 4137 }, "chunk_id": "train_shard_00000_4137_0", "global_id": 4606 }, { "text": "The presence of dilated intercellular spaces in the stratified squamous lining of the esophagus is the pathognomonic feature of reflux esophagitis secondary to gastroesophageal reflux disease (GERD). In addition to stomach acid, bile salts are major constituents of gastroesophageal refluxate. The aim of our study was to determine the effect of bile salts cocktail at different pHs on epithelial junctions in an in vitro transwell model of stratified esophageal squamous epithelium.\n\nBile Salts at Low pH Cause Dilation of Intercellular Spaces in In Vitro Stratified Primary Esophageal Cells, Possibly by Modulating Wnt Signaling.", "token_count": 177, "char_count": 631, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:43.074149", "source": { "split": "train_shard_00000", "doc_id": 4138 }, "chunk_id": "train_shard_00000_4138_0", "global_id": 4607 }, { "text": "Changes of bile salt tolerance, morphology and amount of bile acid within cells were studied to evaluate the exact effects of bile salt hydrolase (BSH) on bile salt tolerance of microorganism.\n\nBile salt tolerance of Lactococcus lactis is enhanced by expression of bile salt hydrolase thereby producing less bile acid in the cells.", "token_count": 81, "char_count": 331, "word_count": 53, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:43.453506", "source": { "split": "train_shard_00000", "doc_id": 4139 }, "chunk_id": "train_shard_00000_4139_0", "global_id": 4608 }, { "text": "Bacterial populations differentiate at the subspecies level into clonal complexes. Intraclonal genome diversity was studied in 100 isolates of the two dominant Pseudomonas aeruginosa clones C and PA14 collected from the inanimate environment, acute and chronic infections. The core genome was highly conserved among clone members with a median pairwise within-clone single nucleotide sequence diversity of 8 × 10(-6) for clone C and 2 × 10(-5) for clone PA14. The composition of the accessory genome was, on the other hand, as variable within the clone as between unrelated clones. Each strain carried a large cargo of unique genes. The two dominant worldwide distributed P. aeruginosa clones combine an almost invariant core with the flexible gain and loss of genetic elements that spread by horizontal transfer.\n\nIntraclonal genome diversity of the major Pseudomonas aeruginosa clones C and PA14.", "token_count": 229, "char_count": 898, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8358, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:43.920492", "source": { "split": "train_shard_00000", "doc_id": 4140 }, "chunk_id": "train_shard_00000_4140_0", "global_id": 4609 }, { "text": "Microbial communities can show astonishing ecological and phylogenetic diversity. What is the role of pervasive horizontal gene transfer (HGT) in shaping this diversity in the presence of clonally expanding \"killer strains\"? Does HGT of antibiotic production and resistance genes erase phylogenetic structure? To answer these questions, we study a spatial eco-evolutionary model of prokaryotes, inspired by recent findings on antagonistic interactions in Vibrionaceae populations. We find toxin genes evolve to be highly mobile, whereas resistance genes minimize mobility. This differential gene mobility is a requirement to maintain a diverse and dynamic ecosystem. The resistance gene repertoire acts as a core genome that corresponds to the phylogeny of cells, whereas toxin genes do not follow this phylogeny and have a patchy distribution. We also show that interstrain HGT makes the emergent phylogenetic structure robust to selective sweeps. Finally, in this evolved ecosystem we observe antagonistic interactions between, rather than within, spatially structure subpopulations, as has been previously observed for prokaryotes in soils and oceans. In contrast to ascribing the diversification and evolution of microbial communities to clonal dynamics, we show that multilevel evolution can elegantly explain the observed phylogenetic structure and ecosystem diversity.\n\nIn Silico Gene-Level Evolution Explains Microbial Population Diversity through Differential Gene Mobility.", "token_count": 329, "char_count": 1483, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:44.492073", "source": { "split": "train_shard_00000", "doc_id": 4141 }, "chunk_id": "train_shard_00000_4141_0", "global_id": 4610 }, { "text": "Penicillin V acylases (PVA) catalyze the deacylation of the beta-lactam antibiotic phenoxymethylpenicillin (Pen V). They are members of the Ntn hydrolase family and possess an N-terminal cysteine as the main catalytic nucleophile residue. They form the evolutionarily related cholylglycine hydrolase (CGH) group which includes bile salt hydrolases (BSH) responsible for bile deconjugation. Even though a few PVA and BSH structures have been reported, no structure of a functional PVA from Gram-negative bacteria is available. Here, we report the crystal structure of a highly active PVA from Gram-negative Pectobacterium atrosepticum (PaPVA) at 2.5Å resolution. Structural comparison with PVAs from Gram-positive bacteria revealed that PaPVA had a distinctive tetrameric structure and active site organization. In addition, mutagenesis of key active site residues and biochemical characterization of the resultant variants elucidated the role of these residues in substrate binding and catalysis. The importance of residue Trp23 and Trp87 side chains in binding and correct positioning of Pen V by PVAs was confirmed using mutagenesis and substrate docking with a 15ns molecular dynamics simulation. These results establish the unique nature of Gram-negative CGHs and necessitate further research about their substrate spectrum.\n\nStructural analysis of a penicillin V acylase from Pectobacterium atrosepticum confirms the importance of two Trp residues for activity and specificity.", "token_count": 379, "char_count": 1482, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6635, "quality_score": 0.8317, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:45.087360", "source": { "split": "train_shard_00000", "doc_id": 4142 }, "chunk_id": "train_shard_00000_4142_0", "global_id": 4611 }, { "text": "Isolation of wildlife into fragmented populations as a consequence of anthropogenic-mediated environmental change may alter host-pathogen relationships. Our understanding of some of the epidemiological features of infectious disease in vulnerable populations can be enhanced by the use of commensal bacteria as a proxy for invasive pathogens in natural ecosystems. The distinctive population structure of a well-described meta-population of a New Zealand endangered flightless bird, the takahe (Porphyrio hochstetteri), provided a unique opportunity to investigate the influence of host isolation on enteric microbial diversity. The genomic epidemiology of a prevalent rail-associated endemic commensal bacterium was explored using core genome and ribosomal multilocus sequence typing (rMLST) of 70 Campylobacter sp. nova 1 isolated from one third of the takahe population resident in multiple locations. While there was evidence of recombination between lineages, bacterial divergence appears to have occurred and multivariate analysis of 52 rMLST genes revealed location-associated differentiation of C. sp. nova 1 sequence types. Our results indicate that fragmentation and anthropogenic manipulation of populations can influence host-microbial relationships, with potential implications for niche adaptation and the evolution of micro-organisms in remote environments. This study provides a novel framework in which to explore the complex genomic epidemiology of micro-organisms in wildlife populations.\n\nMicrobial Genomics of a Host-Associated Commensal Bacterium in Fragmented Populations of Endangered Takahe.", "token_count": 360, "char_count": 1616, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:45.662371", "source": { "split": "train_shard_00000", "doc_id": 4143 }, "chunk_id": "train_shard_00000_4143_0", "global_id": 4612 }, { "text": "In 2011, a Shiga toxin-producing Enteroaggregative Escherichia coli (EAEC Stx2a+) O104:H4 strain caused a serious outbreak of acute gastroenteritis and hemolytic-uremic syndrome (HUS) in Germany. In 2013, E. coli O104:H4 isolates were obtained from a patient with HUS and her friend showing only gastrointestinal complaints. The antimicrobial resistance and virulence profiles of these isolates together with three EAEC Stx2a+ O104:H4 isolates from 2011 were determined and compared. Whole-genome sequencing (WGS) was performed for detailed characterization and to determine genetic relationship of the isolates. Four additional genomes of EAEC Stx2a+ O104:H4 isolates of 2009 and 2011 available on NCBI were included in the virulence and phylogenetic analysis. All E. coli O104:H4 isolates tested were positive for stx2a, aatA, and terD but were negative for escV. All, except one 2011 isolate, were positive for aggR and were therefore considered EAEC. The EAEC Stx2a+ O104:H4 isolates of 2013 belonged to sequence type (ST) ST678 as the 2011 isolates and showed slightly different resistance and virulence patterns compared to the 2011 isolates. Core-genome phylogenetic analysis showed that the isolates of 2013 formed a separate cluster from the isolates of 2011 and 2009 by 27 and 20 different alleles, respectively. In addition, only a one-allele difference was found between the isolate of the HUS-patient and that of her friend. Our study shows that EAEC Stx2a+ O104:H4 strains highly similar to the 2011 outbreak clone in their core genome are still circulating necessitating proper surveillance to prevent further outbreaks with these potentially pathogenic strains", "token_count": 508, "char_count": 1676, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [ "ST678" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:46.339173", "source": { "split": "train_shard_00000", "doc_id": 4144 }, "chunk_id": "train_shard_00000_4144_0", "global_id": 4613 }, { "text": "In addition, WGS not only provided a detailed characterization of the isolates but its high discriminatory power also enabled us to discriminate the 2013 isolates from the isolates of 2009 and 2011 expediting the use of WGS in public health services to rapidly apply proper infection control strategies.\n\nComprehensive Characterization of Escherichia coli O104:H4 Isolated from Patients in the Netherlands.", "token_count": 105, "char_count": 406, "word_count": 60, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:46.732107", "source": { "split": "train_shard_00000", "doc_id": 4144 }, "chunk_id": "train_shard_00000_4144_1", "global_id": 4614 }, { "text": "The bile salt export pump protein (BSEP), expressed on the canalicular membranes of hepatocytes, is primarily responsible for the biliary excretion of bile salts. The inhibition of BSEP transport activity can lead to an increase in intracellular bile salt levels and liver injury. This review discusses the various in vitro assays currently available for assessing the effect of drugs or other chemical entities to modulate BSEP transport activity. BSEP transporter assays use one of the following platforms: Xenopus laevis oocytes; canalicular membrane vesicles (CMV); BSEP-expressed membrane vesicles; cell lines expressing BSEP; sandwich cultured hepatocytes (SCH); and hepatocytes in suspension. Two of these, BSEP-expressed insect membrane vesicles and sandwich cultured hepatocytes, are the most commonly used assays. BSEP membrane vesicles prepared from transfected insect cells are useful for assessing BSEP inhibition or substrate specificity and exploring mechanisms of BSEP-associated genetic diseases. This model can be applied in a high-throughput format for discovery-drug screening. However, experimental results from use of membrane vesicles may lack physiological relevance and the model does not allow for investigation of in situ metabolism in modulation of BSEP activity. Hepatocyte-based assays that use the SCH format provide results that are generally more physiologically relevant than membrane assays. The SCH model is useful in detailed studies of the biliary excretion of drugs and BSEP inhibition, but due to the complexity of SCH preparation, this model is used primarily for determining biliary clearance and BSEP inhibition in a limited number of compounds. The newly developed hepatocyte in suspension assay avoids many of the complexities of the SCH method. The use of pooled cryopreserved hepatocytes in suspension minimizes genetic variance and individual differences in BSEP activity and also provides the opportunity for higher throughput screening and cross-species comparisons.\n\nIn vitro model systems to investigate bile salt export pump (BSEP) activity and drug interactions: A review.", "token_count": 504, "char_count": 2126, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5461, "quality_score": 0.773, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:47.434637", "source": { "split": "train_shard_00000", "doc_id": 4145 }, "chunk_id": "train_shard_00000_4145_0", "global_id": 4615 }, { "text": "Comamonas plasmids play important roles in shaping the phenotypes of their hosts and the adaptation of these hosts to changing environments, and understanding the evolutionary strategy of these plasmids is thus of great concern. In this study, the sequence of the 119-kb 3,5-dibromo-4-hydroxybenzonitrile-catabolizing plasmid pBHB from Comamonas sp. strain 7D-2 was studied and compared with those of three other Comamonas haloaromatic catabolic plasmids. Incompatibility group determination based on a phylogenetic analysis of 24 backbone gene proteins, as well as TrfA, revealed that these four plasmids all belong to the IncP-1β subgroup. Comparison of the four plasmids revealed a conserved backbone region and diverse genetic-load regions. The four plasmids share a core genome consisting of 40 genes (>50% similarities) and contain 12 to 50 unique genes each, most of which are xenobiotic-catabolic genes. Two functional reductive dehalogenase gene clusters are specifically located on pBHB, showing distinctive evolution of pBHB for haloaromatics. The higher catabolic ability of the bhbA2B2 cluster than the bhbAB cluster may be due to the transcription levels and the character of the dehalogenase gene itself rather than that of its extracytoplasmic binding receptor gene. The plasmid pBHB is riddled with transposons and insertion sequence (IS) elements, and ISs play important roles in the evolution of pBHB. The analysis of the origin of the bhb genes on pBHB suggested that these accessory genes evolved independently. Our work provides insights into the evolutionary strategies of Comamonas plasmids, especially into the adaptation mechanism employed by pBHB for haloaromatics.\n\nComparison of Four Comamonas Catabolic Plasmids Reveals the Evolution of pBHB To Catabolize Haloaromatics.", "token_count": 480, "char_count": 1800, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5747, "quality_score": 0.7874, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:48.088455", "source": { "split": "train_shard_00000", "doc_id": 4146 }, "chunk_id": "train_shard_00000_4146_0", "global_id": 4616 }, { "text": "In contrast to humans and dogs, diazepam has been reported to induce severe hepatic side effects in cats, particularly after repeated dosing. With the aim to elucidate the mechanisms underlying this apparent sensitivity of cats to drug-induced liver injury, in a series of in vitro experiments, the feline-specific biotransformation of diazepam was studied with liver microsomes obtained from cats and dogs and the possible inhibition of the bile salt export pump (Bsep) was measured in isolated membrane vesicles overexpressing feline and canine Bsep. In line with previous in vivo studies, the phase I metabolites nordiazepam, temazepam and oxazepam were measurable in microsomal incubations, although enzyme velocity of demethylases and hydroxylases differed significantly between cats and dogs. In cats, the main metabolite was temazepam, which also could be glucuronidated. In contrast to dogs, no other glucuronidated metabolites could be observed. In addition, in the membrane vesicles an inhibition of the transport of the Bsep substrate taurocholic acid could be observed in the presence of diazepam and its metabolites. It was concluded that both mechanisms, the slow biotransformation of diazepam as well the inhibition of the bile acid efflux that results in an accumulation of bile acids in the hepatocytes, seem to contribute to the liver injury observed in cats following repetitive treatment with diazepam.\n\nFeline hepatic biotransformation of diazepam: Differences between cats and dogs.", "token_count": 378, "char_count": 1504, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5785, "quality_score": 0.7892, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:48.674028", "source": { "split": "train_shard_00000", "doc_id": 4147 }, "chunk_id": "train_shard_00000_4147_0", "global_id": 4617 }, { "text": "Familial intrahepatic cholestases (FICs) are a heterogeneous group of autosomal recessive disorders of childhood that disrupt bile formation and present with cholestasis of hepatocellular origin. Three distinct forms are described: FIC1 and FIC2, associated with low/normal GGT level in serum, which are caused by impaired bile salt secretion due to defects in ATP8B1 encoding the FIC1 protein and defects in ABCB11 encoding bile salt export pump protein, respectively; FIC3, linked to high GGT level, involves impaired biliary phospholipid secretion due to defects in ABCB4, encoding multidrug resistance 3 protein. Different mutations in these genes may cause either a progressive familial intrahepatic cholestasis (PFIC) or a benign recurrent intrahepatic cholestasis (BRIC). For the purposes of the present study we genotyped 27 children with intrahepatic cholestasis, diagnosed on either a clinical or histological basis. Two BRIC, 23 PFIC and 2 BRIC/PFIC were identified. Thirty-four different mutations were found of which 11 were novel. One was a 2Mb deletion (5'UTR- exon 18) in ATP8B1. In another case microsatellite analysis of chromosome 2, including ABCB11, showed uniparental disomy. Two cases were compound heterozygous for BRIC/PFIC2 mutations. Our results highlight the importance of the pathogenic role of novel mutations in the three genes and unusual modes of their transmission.\n\nGenetics and Molecular Modeling of New Mutations of Familial Intrahepatic Cholestasis in a Single Italian Center.", "token_count": 419, "char_count": 1514, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [ "ABCB4", "FIC3", "PFIC2", "FIC2", "ABCB11", "FIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:49.300859", "source": { "split": "train_shard_00000", "doc_id": 4148 }, "chunk_id": "train_shard_00000_4148_0", "global_id": 4618 }, { "text": "In the last decades, understanding of genetic variants contributing to liver disease development has considerably improved through novel genotyping techniques. Genetic variants of single genes are known to be decisive for the development of monogenetic liver diseases of varying severity. Identification of genetic variants is an important part of the diagnostic process, e. g. the majority of patients with high iron [Fe] (HFE)-associated hemochromatosis carry the homozygous mutation p.C282Y. Detection of mutations in genes encoding hepatobiliary transport proteins like familial intrahepatic cholestasis 1 (FIC1), bile salt export pump (BSEP), or multidrug resistance protein 3 (MDR3) is the basis to differentiate various forms of intrahepatic cholestasis. Moreover, genetic variants in a variety of genes are known to act as disease modifiers and represent risk factors for disease progression and the development of cirrhosis or even hepatocellular carcinoma. Success of drug treatment or appearance of severe side effects can also be influenced by specific genetic variants. All these aspects underscore the increasing importance of genetic variants, which in the future may help to identify patients at risk for disease progression or help to guide treatment decisions. In the present overview, specific frequent genetic variants are summarized that play roles in monogenetic liver diseases, forms of intrahepatic cholestasis, gallstone development, fatty liver disease, drug-induced liver injury, and liver disease progression as well as hepatocellular carcinoma development.\n\nGenetic variants in adult liver diseases.", "token_count": 366, "char_count": 1628, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [ "MDR3", "FIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:49.881629", "source": { "split": "train_shard_00000", "doc_id": 4149 }, "chunk_id": "train_shard_00000_4149_0", "global_id": 4619 }, { "text": "We report the draft genome sequence of Xanthomonas sp. strain Mitacek01, isolated from an indoor environment vending machine surface with frequent human use in Stillwater, Oklahoma, USA, as part of the Student-Initiated Microbial Discovery project. The genome has a total size of 3,617,426 bp and a contig N50 of 1,906,967 bp.\n\nThe Draft Genome Sequence of Xanthomonas sp. Strain Mitacek01 Expands the Pangenome of a Genus of Plant Pathogens.", "token_count": 137, "char_count": 442, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:50.307343", "source": { "split": "train_shard_00000", "doc_id": 4150 }, "chunk_id": "train_shard_00000_4150_0", "global_id": 4620 }, { "text": "Lactobacillus reuteri is a dominant member of intestinal microbiota of vertebrates, and occurs in food fermentations. The stable presence of L. reuteri in sourdough provides the opportunity to study the adaptation of vertebrate symbionts to an extra-intestinal habitat. This study evaluated this adaptation by comparative genomics of 16 strains of L. reuteri. A core genome phylogenetic tree grouped L. reuteri into 5 clusters corresponding to the host-adapted lineages. The topology of a gene content tree, which includes accessory genes, differed from the core genome phylogenetic tree, suggesting that the differentiation of L. reuteri is shaped by gene loss or acquisition. About 10% of the core genome (124 core genes) were under positive selection. In lineage III sourdough isolates, 177 genes were under positive selection, mainly related to energy conversion and carbohydrate metabolism. The analysis of the competitiveness of L. reuteri in sourdough revealed that the competitivess of sourdough isolates was equal or higher when compared to rodent isolates. This study provides new insights into the adaptation of L. reuteri to food and intestinal habitats, suggesting that these two habitats exert different selective pressure related to growth rate and energy (carbohydrate) metabolism.\n\nComparative genomics Lactobacillus reuteri from sourdough reveals adaptation of an intestinal symbiont to food fermentations.", "token_count": 363, "char_count": 1424, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5485, "quality_score": 0.7743, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:51.233433", "source": { "split": "train_shard_00000", "doc_id": 4151 }, "chunk_id": "train_shard_00000_4151_0", "global_id": 4621 }, { "text": "Nitrite-oxidizing bacteria (NOB) of the genus Nitrospina have exclusively been found in marine environments. In the brine-seawater interface layer of Atlantis II Deep (Red Sea), Nitrospina-like bacteria constitute up to one-third of the bacterial 16S ribosomal RNA (rRNA) gene sequences. This is much higher compared with that reported in other marine habitats (~10% of all bacteria), and was unexpected because no NOB culture has been observed to grow above 4.0% salinity, presumably due to the low net energy gained from their metabolism that is insufficient for both growth and osmoregulation. Using phylogenetics, single-cell genomics and metagenomic fragment recruitment approaches, we document here that these Nitrospina-like bacteria, designated as Candidatus Nitromaritima RS, are not only highly diverged from the type species Nitrospina gracilis (pairwise genome identity of 69%) but are also ubiquitous in the deeper, highly saline interface layers (up to 11.2% salinity) with temperatures of up to 52 °C. Comparative pan-genome analyses revealed that less than half of the predicted proteome of Ca. Nitromaritima RS is shared with N. gracilis. Interestingly, the capacity for nitrite oxidation is also conserved in both genomes. Although both lack acidic proteomes synonymous with extreme halophiles, the pangenome of Ca. Nitromaritima RS specifically encodes enzymes with osmoregulatory and thermoprotective roles (i.e., ectoine/hydroxyectoine biosynthesis) and of thermodynamic importance (i.e., nitrate and nitrite reductases). Ca. Nitromaritima RS also possesses many hallmark traits of microaerophiles and high-affinity NOB. The abundance of the uncultured Ca. Nitromaritima lineage in marine oxyclines suggests their unrecognized ecological significance in deoxygenated areas of the global ocean.", "token_count": 497, "char_count": 1814, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:51.884601", "source": { "split": "train_shard_00000", "doc_id": 4152 }, "chunk_id": "train_shard_00000_4152_0", "global_id": 4622 }, { "text": "Diversification and niche adaptations of Nitrospina-like bacteria in the polyextreme interfaces of Red Sea brines.", "token_count": 30, "char_count": 114, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:52.245475", "source": { "split": "train_shard_00000", "doc_id": 4152 }, "chunk_id": "train_shard_00000_4152_1", "global_id": 4623 }, { "text": "Cholera is often caused when drinking water is contaminated through environmental sources. In recent years, the drastic cholera epidemics in Odisha (2007) and Haiti (2010) were associated with natural disasters (flood and Earthquake). Almost every year the state of Assam India witnesses flood in Brahamputra River valley during reversal of wind system (monsoon). This is often followed by outbreak of diarrheal diseases including cholera. Beside the incidence of cholera outbreaks, there is lack of experimental evidence for prevalence of the bacterium in aquatic environment and its association with cholera during/after flood in the state. A molecular surveillance during 2012-14 was carried out to study prevalence, strain differentiation, and clonality of Vibrio cholerae in inland aquatic reservoirs flooded by Brahamputra River in Assam. Water samples were collected, filtered, enriched in alkaline peptone water followed by selective culturing on thiosulfate bile salt sucrose agar. Environmental isolates were identified as V. cholerae, based on biochemical assays followed by sero-grouping and detailed molecular characterization. The incidence of the presence of the bacterium in potable water sources was higher after flood. Except one O1 isolate, all of the strains were broadly grouped under non-O1/non-O139 whereas some of them did have cholera toxin (CT). Surprisingly, we have noticed Haitian ctxB in two non-O1/non-O139 strains. MLST analyses based on pyrH, recA and rpoA genes revealed clonality in the environmental strains. The isolates showed varying degree of antimicrobial resistance including tetracycline and ciprofloxacin. The strains harbored the genetic elements SXT constins and integrons responsible for multidrug resistance. Genetic characterization is useful as phenotypic characters alone have proven to be unsatisfactory for strain discrimination. An assurance to safe drinking water, sanitation and monitoring of the aquatic reservoirs is of utmost importance for combating the impending epidemic threat in the flood affected areas", "token_count": 513, "char_count": 2067, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:40:52.886012", "source": { "split": "train_shard_00000", "doc_id": 4153 }, "chunk_id": "train_shard_00000_4153_0", "global_id": 4624 }, { "text": "Further, the management of flood through multi-prong approaches and sustainable utilization of environmental resources would be effective in disease management.\n\nMolecular epidemiology of Vibrio cholerae associated with flood in Brahamputra River valley, Assam, India.", "token_count": 58, "char_count": 268, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:53.260566", "source": { "split": "train_shard_00000", "doc_id": 4153 }, "chunk_id": "train_shard_00000_4153_1", "global_id": 4625 }, { "text": "Basidiomycetous and ascomycetous yeast species were tested for manganese tolerance. Basidiomycetous Cryptococcus humicola, Cryptococcus terricola, Cryptococcus curvatus and ascomycetous Candida maltosa, Kluyveromyces marxianus, Kuraishia capsulata, Lindnera fabianii and Sacharomyces cerevisiae were able to grow at manganese excess (2.5 mmol/L), while the growth of basidiomycetous Rhodotorula bogoriensis was completely suppressed. The lag phase duration increased and the exponential growth rate decreased at manganese excess. The increase of cell size and enlargement of vacuoles were characteristics for the cells grown at manganese excess. The alterations in inorganic polyphosphate content and cellular localization were studied. L. fabianii, K. capsulata, C. maltosa, and Cr. humicola accumulated the higher amounts of inorganic polyphosphates, while Cr. terricola and Cr. curvatus demonstrated no such accumulation. The polyphosphate content in the cell wall tested by DAPI staining increased in all species under the study; however, this effect was more pronounced in Cr. terricola and Cr. curvatus. The accumulation of Mg(2+) in the cell wall under Mn(2+) excess was observed in Cr. humicola, Cr. curvatus and Cr. terricola. The accumulation of polyphosphate and magnesium in the cell wall was supposed to be a factor of manganese tolerance in yeasts.\n\nManganese tolerance in yeasts involves polyphosphate, magnesium, and vacuolar alterations.", "token_count": 407, "char_count": 1454, "word_count": 200, "semantic_coherence": 1, "information_density": 0.55, "quality_score": 0.775, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:53.885836", "source": { "split": "train_shard_00000", "doc_id": 4154 }, "chunk_id": "train_shard_00000_4154_0", "global_id": 4626 }, { "text": "The bile salt export pump (BSEP) is an ABC-transporter expressed at the canalicular membrane of hepatocytes. Its physiological role is to expel bile salts into the canaliculi from where they drain into the bile duct. Inhibition of this transporter may lead to intrahepatic cholestasis. Predictive computational models of BSEP inhibition may allow for fast identification of potentially harmful compounds in large databases. This article presents a predictive in silico model based on physicochemical descriptors that is able to flag compounds as potential BSEP inhibitors. This model was built using a training set of 670 compounds with available BSEP inhibition potencies. It successfully predicted BSEP inhibition for two independent test sets and was in a further step used for a virtual screening experiment. After in vitro testing of selected candidates, a marketed drug, bromocriptin, was identified for the first time as BSEP inhibitor. This demonstrates the usefulness of the model to identify new BSEP inhibitors and therefore potential cholestasis perpetrators.\n\nFlagging Drugs That Inhibit the Bile Salt Export Pump.", "token_count": 271, "char_count": 1127, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:54.440183", "source": { "split": "train_shard_00000", "doc_id": 4155 }, "chunk_id": "train_shard_00000_4155_0", "global_id": 4627 }, { "text": "We present a rare case of progressive familial intrahepatic cholestasis within a family. A 34-yearold female became a living-related liver transplant donor for her son, who had the disease. Nine years after the transplant, the mother developed severe intrahepatic cholestasis, for which she was evaluated after using an oral contraceptive drug. She presented with jaundice, pruritus, and increased bilirubin levels, together with elevated gamma glutamyl transferase and alkaline phosphatase levels. A liver biopsy revealed findings consistent with intrahepatic cholestasis. However, despite follow-up management and cessation of the insulting drug, her total bilirubin count continuously increased to 20 mg/dL and was accompanied by intractable pruritus. A total of 9 plasmapheresis sessions were performed, and she was started on a regimen of ursodeoxycholic acid (13 mg/kg/d) and cholestyramine (4 g, 3 times daily). The clinical and laboratory picture dramatically improved following cessation of the oral contraceptive, plasmapheresis sessions, and drug treatment. The patient's cholestasis normalized within 3 months, and she recovered uneventfully. A genetic analysis of the whole family revealed that both parents were heterozygous for the mutation c.124G>A in ABCB11, and the son was homozygous for this mutation. These findings supported varying degrees of bile salt export pump deficiency in the family members. Defective bile salt excretory system function can result in a wide spectrum of clinical presentations, ranging from progressive familial intrahepatic cholestasis requiring liver transplant to late-onset drug-induced cholestasis. Our findings suggest that, in a heterozygous carrier of a progressive familial intrahepatic cholestasis mutation, drug-induced cholestasis is responsive to treatment, after which the clinical picture can normalize within 3 months.", "token_count": 477, "char_count": 1881, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:55.088927", "source": { "split": "train_shard_00000", "doc_id": 4156 }, "chunk_id": "train_shard_00000_4156_0", "global_id": 4628 }, { "text": "Late-Onset Drug-Induced Cholestasis in a Living-Related Liver Transplant Donor With Progressive Familial Intrahepatic Cholestasis.", "token_count": 38, "char_count": 130, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:55.450580", "source": { "split": "train_shard_00000", "doc_id": 4156 }, "chunk_id": "train_shard_00000_4156_1", "global_id": 4629 }, { "text": "Enterococcus lactis IW5 was obtained from human gut and the potential probiotic characteristics of this organism were then evaluated. Results showed that this strain was highly resistant to low pH and high bile salt and adhered strongly to Caco-2 human epithelial colorectal cell lines. The supernatant of E. lactis IW5 strongly inhibited the growth of several pathogenic bacteria and decreased the viability of different cancer cells, such as HeLa, MCF-7, AGS, HT-29, and Caco-2. Conversely, E. lactis IW5 did not inhibit the viability of normal FHs-74 cells. This strain did not generate toxic enzymes, including β-glucosidase, β-glucuronidase, and N-acetyl-β-glucosaminidase and was highly susceptible to ampicillin, gentamycin, penicillin, vancomycin, clindamycin, sulfamethoxazol, and chloramphenicol but resistant to erythromycin and tetracyclin. This study provided evidence for the effect of E. lactis IW5 on cancer cells. Therefore, E. lactis IW5, as a bioactive therapeutics, should be subjected to other relevant tests to verify the therapeutic suitability of this strain for clinical applications.\n\nThe Prophylactic Effect of Probiotic Enterococcus lactis IW5 against Different Human Cancer Cells.", "token_count": 355, "char_count": 1209, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.8099, "entities": { "genes": [ "IW5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:56.028290", "source": { "split": "train_shard_00000", "doc_id": 4157 }, "chunk_id": "train_shard_00000_4157_0", "global_id": 4630 }, { "text": "Ethanol production from acidic-alkaline pretreated cashew apple bagasse (CAB-OH) was investigated using separated hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) processes. First, a screening of Kluyveromyces strains was conducted by SHF and a maximum ethanol concentration of 24.1 g L(-1) was obtained using Kluyveromyces marxianus ATCC36907, which presented similar profiles when compared to results obtained by a Saccharomyces strain. The effect of temperature on ethanol production conducted by SHF using K. marxianus ATCC36907 was investigated, and the maximum ethanol yield (YE/G) was obtained at 40 °C (0.46 g g(-1)) using a synthetic medium. In the SHF using CAB-OH hydrolysate, the maximum ethanol concentration obtained was 24.9 g L(-1), 5.92 g L(-1) h(-1) of productivity, and ethanol yield of 0.43 g g(-1) at 40 °C. Afterwards, K. marxianus ATCC36907 was used in the bioconversion of CAB-OH by SSF, and an ethanol concentration of 41.41 ± 0.2 g L(-1) was obtained using 10 % CAB-OH at 40 °C, 150 rpm and 24 h, resulting in a Y'E/G of 0.50 gE gG (-1) and an efficiency of 98.4 %, in the process conducted with cellobiase supplementation. SHF and SSF processes using CAB-OH and K. marxianus ATCC36907 can be used to ethanol production, but the SSF process required only one step to achieve the same production.\n\nThe Bioconversion of Pretreated Cashew Apple Bagasse into Ethanol by SHF and SSF Processes.", "token_count": 483, "char_count": 1456, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5109, "quality_score": 0.7555, "entities": { "genes": [ "ATCC36907" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:56.674401", "source": { "split": "train_shard_00000", "doc_id": 4158 }, "chunk_id": "train_shard_00000_4158_0", "global_id": 4631 }, { "text": "Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.\n\nThe pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract.", "token_count": 135, "char_count": 518, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:57.106727", "source": { "split": "train_shard_00000", "doc_id": 4159 }, "chunk_id": "train_shard_00000_4159_0", "global_id": 4632 }, { "text": "A standardised method for determining Escherichia coli O157:H7 strain relatedness using whole genome sequencing or virulence gene profiling is not yet established. We sought to assess the capacity of either high-throughput polymerase chain reaction (PCR) of 49 virulence genes, core-genome single nt variants (SNVs) or k-mer clustering to discriminate between outbreak-associated and sporadic E. coli O157:H7 isolates. Three outbreaks and multiple sporadic isolates from the province of Alberta, Canada were included in the study. Two of the outbreaks occurred concurrently in 2014 and one occurred in 2012. Pulsed-field gel electrophoresis (PFGE) and multilocus variable-number tandem repeat analysis (MLVA) were employed as comparator typing methods. The virulence gene profiles of isolates from the 2012 and 2014 Alberta outbreak events and contemporary sporadic isolates were mostly identical; therefore the set of virulence genes chosen in this study were not discriminatory enough to distinguish between outbreak clusters. Concordant with PFGE and MLVA results, core genome SNV and k-mer phylogenies clustered isolates from the 2012 and 2014 outbreaks as distinct events. k-mer phylogenies demonstrated increased discriminatory power compared with core SNV phylogenies. Prior to the widespread implementation of whole genome sequencing for routine public health use, issues surrounding cost, technical expertise, software standardisation, and data sharing/comparisons must be addressed.\n\nThe utility of multiple molecular methods including whole genome sequencing as tools to differentiate Escherichia coli O157:H7 outbreaks.", "token_count": 417, "char_count": 1631, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:57.743730", "source": { "split": "train_shard_00000", "doc_id": 4160 }, "chunk_id": "train_shard_00000_4160_0", "global_id": 4633 }, { "text": "Increase in the production of 1st generation ethanol from glucose is possible by the reduction in the production of ethanol co-products, especially biomass. We have developed a method to reduce biomass accumulation of Saccharomyces cerevisiae by the manipulation of the intracellular ATP level due to overexpression of genes of alkaline phosphatase, apyrase or enzymes involved in futile cycles. The strains constructed accumulated up to 10% more ethanol on a cornmeal hydrolysate medium. Similar increase in ethanol accumulation was observed in the mutants resistant to the toxic inhibitors of glycolysis like 3-bromopyruvate and others. Substantial increase in fuel ethanol production will be obtained by the development of new strains of yeasts that ferment sugars of the abundant lignocellulosic feedstocks, especially xylose, a pentose sugar. We have found that xylose can be fermented under elevated temperatures by the thermotolerant yeast, Hansenula polymorpha. We combined protein engineering of the gene coding for xylose reductase (XYL1) along with overexpression of the other two genes responsible for xylose metabolism in yeast (XYL2, XYL3) and the deletion of the global transcriptional activator CAT8, with the selection of mutants defective in utilizing ethanol as a carbon source using the anticancer drug, 3-bromopyruvate. Resulted strains accumulated 20-25 times more ethanol from xylose at the elevated temperature of 45°C with up to 12.5 g L(-1) produced. Increase in ethanol yield and productivity from xylose was also achieved by overexpression of genes coding for the peroxisomal enzymes: transketolase (DAS1) and transaldolase (TAL2), and deletion of the ATG13 gene.\n\nNew approaches for improving the production of the 1st and 2nd generation ethanol by yeast.", "token_count": 486, "char_count": 1784, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5741, "quality_score": 0.7871, "entities": { "genes": [ "CAT8", "XYL2", "XYL3", "XYL1", "ATG13", "TAL2", "DAS1" ], "proteins": [], "pathways": [ "glycolysis", "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:58.415950", "source": { "split": "train_shard_00000", "doc_id": 4161 }, "chunk_id": "train_shard_00000_4161_0", "global_id": 4634 }, { "text": "Two main classes of interaction between soluble dietary fibres (SDFs), such as (1,3:1,4)-β-D-glucan (βG) and arabinoxylan (AX) and bile salt (BS) or diluted porcine bile, were identified by (13)C NMR and small angle X-ray scattering (SAXS). Small chemical shift differences of BS NMR resonances were consistent with effective local concentration or dilution of BS micelles mostly by βG, suggesting dynamic interactions; whilst the reduced line widths/intensities observed were mostly caused by wheat AX and the highest molecular size and concentrations of βG. SAXS showed evidence of changes in βG but not AX in the presence of BS micelles, at >13 nm length scale consistent with molecular level interactions. Thus intermolecular interactions between SDF and BS depend on both SDF source and its molecular weight and may occur alone or in combination.\n\nMolecular interactions of a model bile salt and porcine bile with (1,3:1,4)-β-glucans and arabinoxylans probed by (13)C NMR and SAXS.", "token_count": 273, "char_count": 986, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6755, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:58.989404", "source": { "split": "train_shard_00000", "doc_id": 4162 }, "chunk_id": "train_shard_00000_4162_0", "global_id": 4635 }, { "text": "A comprehensive experimental study on the interaction between the PEO-PPO-PEO block copolymer P123 (EO20PO68EO20) and the anionic bile salt sodium glycodeoxycholate (NaGDC) in water has been performed. The work was aimed at investigating the suitability of using P123 as bile salt sequestrant beside the fundamental aspects of PEO-PPO-PEO block copolymer-bile salt interactions. Various experimental techniques including dynamic and static light scattering, small-angle X-ray scattering, and differential scanning calorimetry (DSC) were employed in combination with electrophoretic mobility measurements. The system was investigated at a constant P123 concentration of 1.74 mM and with varying bile salt concentrations up to approximately 250 mM NaGDC (or a molar ratio n(NaGDC)/n(P123) = 144). In the mixed P123-NaGDC solutions, the endothermic process related to the self-assembly of P123 was observed to gradually decrease in enthalpy and shift to higher temperatures upon progressive addition of NaGDC. To explain this effect, the formation of NaGDC micelles carrying partly dehydrated P123 unimers was proposed and translated into a stoichiometric model, which was able to fit the experimental DSC data. In the mixtures at low molar ratios, NaGDC monomers associated with the P123 micelle forming a charged \"P123 micelle-NaGDC\" complex with a dehydrated PPO core. These complexes disintegrated upon increasing NaGDC concentration to form small \"NaGDC-P123\" complexes visualized as bile salt micelles including one or a few P123 copolymer chains.\n\nEffects of Bile Salt Sodium Glycodeoxycholate on the Self-Assembly of PEO-PPO-PEO Triblock Copolymer P123 in Aqueous Solution.", "token_count": 462, "char_count": 1678, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6118, "quality_score": 0.8059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:40:59.661432", "source": { "split": "train_shard_00000", "doc_id": 4163 }, "chunk_id": "train_shard_00000_4163_0", "global_id": 4636 }, { "text": "In the present study, evaluation and optimization of taro waste (TW), which was mainly composed of taro peels that contain many starch residues, as the main carbon source in medium were studied. The flask studies showed the optimal medium was using 170g/L of TW which is about 100g/L of glucose and 9g/L of CGM as alternative nitrogen source. Simultaneous saccharification and fermentation (SSF) exhibited higher bioethanol productivity toward separation hydrolysis and fermentation (SHF). The optimal condition of SSF was 5% of Kluyveromyces marxianus K21 inoculum at 40°C resulting in the maximum ethanol concentration (48.98g/L) and productivity (2.23g/L/h) after 22h of cultivation. The scaling up experiment in a 5L bioreactor demonstrated that K21 can still maintain its capability. After 20h of cultivation, 43.78g/L of ethanol (2.19g/L/h of productivity) was achieved corresponding to a 94.2% theoretical ethanol yield.\n\nBioethanol production from taro waste using thermo-tolerant yeast Kluyveromyces marxianus K21.", "token_count": 308, "char_count": 1023, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6939, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:00.240908", "source": { "split": "train_shard_00000", "doc_id": 4164 }, "chunk_id": "train_shard_00000_4164_0", "global_id": 4637 }, { "text": "Stability of composition and sequence of genes was shown earlier in 13 mitochondrial genomes of mosses (Rensing, S. A., et al. (2008) Science, 319, 64-69). It is of interest to study the evolution of mitochondrial genomes not only at the gene level, but also on the level of nucleotide sequences. To do this, we have constructed a \"nucleotide pangenome\" for mitochondrial genomes of 24 moss species. The nucleotide pangenome is a set of aligned nucleotide sequences of orthologous genome fragments covering the totality of all genomes. The nucleotide pangenome was constructed using specially developed new software, NPG-explorer (NPGe). The stable part of the mitochondrial genome (232 stable blocks) is shown to be, on average, 45% of its length. In the joint alignment of stable blocks, 82% of positions are conserved. The phylogenetic tree constructed with the NPGe program is in good correlation with other phylogenetic reconstructions. With the NPGe program, 30 blocks have been identified with repeats no shorter than 50 bp. The maximal length of a block with repeats is 140 bp. Duplications in the mitochondrial genomes of mosses are rare. On average, the genome contains about 500 bp in large duplications. The total length of insertions and deletions was determined in each genome. The losses and gains of DNA regions are rather active in mitochondrial genomes of mosses, and such rearrangements presumably can be used as additional markers in the reconstruction of phylogeny.\n\nMoss Phylogeny Reconstruction Using Nucleotide Pangenome of Complete Mitogenome Sequences.", "token_count": 427, "char_count": 1578, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:00.866567", "source": { "split": "train_shard_00000", "doc_id": 4165 }, "chunk_id": "train_shard_00000_4165_0", "global_id": 4638 }, { "text": "The alphabaculovirus Anticarsia gemmatalis multiple nucleopolyhedrovirus (AgMNPV) is the world's most successful viral bioinsecticide. Through the 1980s and 1990s, this virus was extensively used for biological control of populations of Anticarsia gemmatalis (Velvetbean caterpillar) in soybean crops. During this period, genetic studies identified several variable loci in the AgMNPV; however, most of them were not characterized at the sequence level. In this study we report a full genome comparison among 17 wild-type isolates of AgMNPV. We found the pangenome of this virus to contain at least 167 hypothetical genes, 151 of which are shared by all genomes. The gene bro-a that might be involved in host specificity and carrying transporter is absent in some genomes, and new hypothetical genes were observed. Among these genes there is a unique rnf12-like gene, probably implicated in ubiquitination. Events of gene fission and fusion are common, as four genes have been observed as single or split open reading frames. Gains and losses of genomic fragments (from 20 to 900 bp) are observed within tandem repeats, such as in eight direct repeats and four homologous regions. Most AgMNPV genes present low nucleotide diversity, and variable genes are mainly located in a locus known to evolve through homologous recombination. The evolution of AgMNPV is mainly driven by small indels, substitutions, gain and loss of nucleotide stretches or entire coding sequences. These variations may cause relevant phenotypic alterations, which probably affect the infectivity of AgMNPV. This work provides novel information on genomic evolution of the AgMNPV in particular and of baculoviruses in general.\n\nThe Pangenome of the Anticarsia gemmatalis Multiple Nucleopolyhedrovirus (AgMNPV).", "token_count": 460, "char_count": 1782, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:01.514341", "source": { "split": "train_shard_00000", "doc_id": 4166 }, "chunk_id": "train_shard_00000_4166_0", "global_id": 4639 }, { "text": "Besides aiding digestion, bile salts are important signal molecules exhibiting a regulatory role in metabolic processes. Human ileal bile acid binding protein (I-BABP) is an intracellular carrier of bile salts in the epithelial cells of the distal small intestine and has a key role in the enterohepatic circulation of bile salts. Positive binding cooperativity combined with site selectivity of glycocholate and glycochenodeoxycholate, the two most abundant bile salts in the human body, make human I-BABP a unique member of the family of intracellular lipid binding proteins. Solution NMR structure of the ternary complex of human I-BABP with glycocholate and glycochenodeoxycholate reveals an extensive network of hydrogen bonds and hydrophobic interactions stabilizing the bound bile salts. Conformational changes accompanying bile salt binding affects four major regions in the protein including the C/D, E/F and G/H loops as well as the helical segment. Most of these protein regions coincide with a previously described network of millisecond time scale fluctuations in the apo protein, a motion absent in the bound state. Comparison of the heterotypic doubly ligated complex with the unligated form provides further evidence of a conformation selection mechanism of ligand entry. Structural and dynamic aspects of human I-BABP-bile salt interaction are discussed and compared with characteristics of ligand binding in other members of the intracellular lipid binding protein family.\n\nStructural determinants of ligand binding in the ternary complex of human ileal bile acid binding protein with glycocholate and glycochenodeoxycholate obtained from solution NMR.", "token_count": 402, "char_count": 1670, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:02.131514", "source": { "split": "train_shard_00000", "doc_id": 4167 }, "chunk_id": "train_shard_00000_4167_0", "global_id": 4640 }, { "text": "In the present work, the potential for the enhancement of the adaptive capacity of microbe-plant systems (MPSs) through the integration of the symbiosis partners' genomes is considered on the example of different types of symbiotic relationships. The accumulated data on the genetic control of interactions for both the plant and microbe, which are discussed in the paper with respect to signaling genes, suggest that it is the complementarity of genetic determinants that underlies the successful formation of MPSs. A eukaryotic genome with limited information content, which is stable throughout a generation, is complemented by a virtually unlimited prokaryotic metagenome. The microsymbiont's ability to adapt to different living conditions is based on the restructuring of the accessory genome by different mechanisms, which are likely to be activated under the influence of plants, although the details of such a regulation remain unknown. Features of the genetic control of the interaction, particularly its universal character for different symbionts, allow us to formulate a principle of genome-complementarity with respect to interacting organisms and consider it an important factor, an adaptation that enhances the abilities of M PSs for their sustainable development in natural ecosystems and for high plant productivity in agrocenoses.\n\n[The Principle of Genome Complementarity in the Enhancement of Plant Adaptive Capacities].", "token_count": 303, "char_count": 1441, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:02.701201", "source": { "split": "train_shard_00000", "doc_id": 4168 }, "chunk_id": "train_shard_00000_4168_0", "global_id": 4641 }, { "text": "Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates.\n\nPhylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa.", "token_count": 411, "char_count": 1590, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:03.327101", "source": { "split": "train_shard_00000", "doc_id": 4169 }, "chunk_id": "train_shard_00000_4169_0", "global_id": 4642 }, { "text": "Enterococcus durans KLDS6.0930 strain was originally isolated from traditional naturally fermented cream in Inner Mongolia of China. The complete genome sequence of E. durans KLDS6.0930 was carried out using the PacBio RSII platform. The genome contains a circular chromosome and two circular plasmids. Genome sequencing information provides the genetic basis for bioinformatics analysis of bile salt and acid tolerance, cell adhesion, and molecular mechanisms responsible for lipid metabolism.\n\nComplete genome sequence of Enterococcus durans KLDS6.0930, a strain with probiotic properties.", "token_count": 155, "char_count": 591, "word_count": 80, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [ "KLDS6" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:03.764328", "source": { "split": "train_shard_00000", "doc_id": 4170 }, "chunk_id": "train_shard_00000_4170_0", "global_id": 4643 }, { "text": "UV-induced changes in the catalytic activity and radiuses of inulinases molecules from various producers (plants, fungy, yeast) are studied. It is established that specific enzymes activity and the sizes of inulinases molecules from Helianthus tuberosus and Kluyveromyces marxianus under the influence of UV-light in the ranges of doses 4530-6040 and 755-6040 J/m2, respectively, are subjected to changes more than structural and functional characteristics of inulinase fromAspergillus niger. It is probably connected with lower contents in it of aromatic amino acids such as tyrosine and phenylalanine. The most expressed loss of functional properties of inulinase from Helianthus tuberosus can be caused by the'existence of significantly more numbers of cysteine in plant fructan-exohydrolases in relation to microbic enzymes. A scheme for the stages of response of inulinases of various origins on the influence of UV-light in a certain range of radiation doses is offered.\n\n[Research of UV-Induced Changes in the Structural and Functional Properties of Inulinases].", "token_count": 277, "char_count": 1069, "word_count": 154, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:04.321730", "source": { "split": "train_shard_00000", "doc_id": 4171 }, "chunk_id": "train_shard_00000_4171_0", "global_id": 4644 }, { "text": "Bacterial evolution is accelerated by mobile genetic elements. To spread horizontally and to benefit the recipient bacteria, genes encoded on these elements must be properly regulated. Among the legionellae are multiple integrative conjugative elements (ICEs) that each encode a paralog of the broadly conserved regulator csrA. Using bioinformatic analyses, we deduced that specific csrA paralogs are coinherited with particular lineages of the type IV secretion system that mediates horizontal spread of its ICE, suggesting a conserved regulatory interaction. As a first step to investigate the contribution of csrA regulators to this class of mobile genetic elements, we analyzed here the activity of the csrA paralog encoded on Legionella pneumophila ICE-βox. Deletion of this gene, which we name csrT, had no observed effect under laboratory conditions. However, ectopic expression of csrT abrogated the protection to hydrogen peroxide and macrophage degradation that ICE-βox confers to L. pneumophila. When ectopically expressed, csrT also repressed L. pneumophila flagellin production and motility, a function similar to the core genome's canonical csrA. Moreover, csrT restored the repression of motility to csrA mutants of Bacillus subtilis, a finding consistent with the predicted function of CsrT as an mRNA binding protein. Since all known ICEs of legionellae encode coinherited csrA-type IV secretion system pairs, we postulate that CsrA superfamily proteins regulate ICE activity to increase their horizontal spread, thereby expanding L. pneumophila versatility.\n\ncsrT Represents a New Class of csrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila.", "token_count": 428, "char_count": 1710, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:04.947879", "source": { "split": "train_shard_00000", "doc_id": 4172 }, "chunk_id": "train_shard_00000_4172_0", "global_id": 4645 }, { "text": "We report the genome of a Staphylococcus aureus strain (ILRI_Eymole1/1) isolated from a nasal swab of a dromedary camel (Camelus dromedarius) in North Kenya. The complete genome sequence of this strain consists of a circular chromosome of 2,874,302 bp with a GC-content of 32.88 %. In silico annotation predicted 2755 protein-encoding genes and 76 non-coding genes. This isolate belongs to MLST sequence type 30 (ST30). Phylogenetic analysis based on a subset of 283 core genes revealed that it falls within the human clonal complex 30 (CC30) S. aureus isolate cluster but is genetically distinct. About 79 % of the protein encoding genes are part of the CC30 core genome (genes common to all CC30 S. aureus isolates), ~18 % were within the variable genome (shared among multiple but not all isolates) and ~ 3 % were found only in the genome of the camel isolate. Among the 85 isolate-specific genes, 79 were located within putative phages and pathogenicity islands. Protein encoding genes associated with bacterial adhesion, and secretory proteins that are essential components of the type VII secretion system were also identified. The complete genome sequence of S. aureus strain ILRI_Eymole1/1 has been deposited in the European Nucleotide Archive under the accession no LN626917.1.\n\nComplete genome sequence of Staphylococcus aureus, strain ILRI_Eymole1/1, isolated from a Kenyan dromedary camel.", "token_count": 424, "char_count": 1401, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6055, "quality_score": 0.8028, "entities": { "genes": [ "LN626917", "CC30", "ST30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:05.580849", "source": { "split": "train_shard_00000", "doc_id": 4173 }, "chunk_id": "train_shard_00000_4173_0", "global_id": 4646 }, { "text": "As an increasing number of genome sequences become available for a wide range of species, there is a growing understanding that the genome of a single individual is insufficient to represent the gene diversity within a whole species. Many studies examine the sequence diversity within genes, and this allelic variation is an important source of phenotypic variation which can be selected for by man or nature. However, the significant gene presence/absence variation that has been observed within species and the impact of this variation on traits is only now being studied in detail. The sum of the genes for a species is termed the pangenome, and the determination and characterization of the pangenome is a requirement to understand variation within a species. In this review, we explore the current progress in pangenomics as well as methods and approaches for the characterization of pangenomes for a wide range of plant species.\n\nTowards plant pangenomics.", "token_count": 193, "char_count": 962, "word_count": 153, "semantic_coherence": 1, "information_density": 0.5752, "quality_score": 0.7876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:06.030369", "source": { "split": "train_shard_00000", "doc_id": 4174 }, "chunk_id": "train_shard_00000_4174_0", "global_id": 4647 }, { "text": "We used whole-genome sequencing to determine evolutionary relationships among 20 outbreak-associated clinical isolates of Listeria monocytogenes serotypes 1/2a and 1/2b. Isolates from 6 of 11 outbreaks fell outside the clonal groups or \"epidemic clones\" that have been previously associated with outbreaks, suggesting that epidemic potential may be widespread in L. monocytogenes and is not limited to the recognized epidemic clones. Pairwise comparisons between epidemiologically related isolates within clonal complexes showed that genome-level variation differed by 2 orders of magnitude between different comparisons, and the distribution of point mutations (core versus accessory genome) also varied. In addition, genetic divergence between one closely related pair of isolates from a single outbreak was driven primarily by changes in phage regions. The evolutionary analysis showed that the changes could be attributed to horizontal gene transfer; members of the diverse bacterial community found in the production facility could have served as the source of novel genetic material at some point in the production chain. The results raise the question of how to best utilize information contained within the accessory genome in outbreak investigations. The full magnitude and complexity of genetic changes revealed by genome sequencing could not be discerned from traditional subtyping methods, and the results demonstrate the challenges of interpreting genetic variation among isolates recovered from a single outbreak. Epidemiological information remains critical for proper interpretation of nucleotide and structural diversity among isolates recovered during outbreaks and will remain so until we understand more about how various population histories influence genetic variation.\n\nDetermination of Evolutionary Relationships of Outbreak-Associated Listeria monocytogenes Strains of Serotypes 1/2a and 1/2b by Whole-Genome Sequencing.", "token_count": 405, "char_count": 1945, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6113, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:06.657012", "source": { "split": "train_shard_00000", "doc_id": 4175 }, "chunk_id": "train_shard_00000_4175_0", "global_id": 4648 }, { "text": "We report a 3.07-Mb complete genome sequence of a lactic acid bacterium, Lactobacillus sp. HFC8. The gene-coding clusters are predicated for probiotic characteristics, like bacteriocin production, cell adhesion, bile salt hydrolysis, lactose metabolism, autoaggregation, and tolerance to oxidative stress.\n\nComplete Genome Sequence of Potential Probiotic Lactobacillus sp. HFC8, Isolated from Human Gut Using PacBio SMRT Sequencing.", "token_count": 128, "char_count": 432, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [ "HFC8" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:07.074553", "source": { "split": "train_shard_00000", "doc_id": 4176 }, "chunk_id": "train_shard_00000_4176_0", "global_id": 4649 }, { "text": "BlastKOALA and GhostKOALA are automatic annotation servers for genome and metagenome sequences, which perform KO (KEGG Orthology) assignments to characterize individual gene functions and reconstruct KEGG pathways, BRITE hierarchies and KEGG modules to infer high-level functions of the organism or the ecosystem. Both servers are made freely available at the KEGG Web site (http://www.kegg.jp/blastkoala/). In BlastKOALA, the KO assignment is performed by a modified version of the internally used KOALA algorithm after the BLAST search against a non-redundant dataset of pangenome sequences at the species, genus or family level, which is generated from the KEGG GENES database by retaining the KO content of each taxonomic category. In GhostKOALA, which utilizes more rapid GHOSTX for database search and is suitable for metagenome annotation, the pangenome dataset is supplemented with Cd-hit clusters including those for viral genes. The result files may be downloaded and manipulated for further KEGG Mapper analysis, such as comparative pathway analysis using multiple BlastKOALA results.\n\nBlastKOALA and GhostKOALA: KEGG Tools for Functional Characterization of Genome and Metagenome Sequences.", "token_count": 305, "char_count": 1202, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:07.648454", "source": { "split": "train_shard_00000", "doc_id": 4177 }, "chunk_id": "train_shard_00000_4177_0", "global_id": 4650 }, { "text": "Streptococcus suis is a major porcine and zoonotic pathogen responsible for significant economic losses in the pig industry and an increasing number of human cases. Multiple isolates of S. suis show marked genomic diversity. Here, we report the analysis of whole genome sequences of nine pig isolates that caused disease typical of S. suis and had phenotypic characteristics of S. suis, but their genomes were divergent from those of many other S. suis isolates. Comparison of protein sequences predicted from divergent genomes with those from normal S. suis reduced the size of core genome from 793 to only 397 genes. Divergence was clear if phylogenetic analysis was performed on reduced core genes and MLST alleles. Phylogenies based on certain other genes (16S rRNA, sodA, recN, and cpn60) did not show divergence for all isolates, suggesting recombination between some divergent isolates with normal S. suis for these genes. Indeed, there is evidence of recent recombination between the divergent and normal S. suis genomes for 249 of 397 core genes. In addition, phylogenetic analysis based on the 16S rRNA gene and 132 genes that were conserved between the divergent isolates and representatives of the broader Streptococcus genus showed that divergent isolates were more closely related to S. suis. Six out of nine divergent isolates possessed a S. suis-like capsule region with variation in capsular gene sequences but the remaining three did not have a discrete capsule locus. The majority (40/70), of virulence-associated genes in normal S. suis were present in the divergent genomes. Overall, the divergent isolates extend the current diversity of S. suis species but the phenotypic similarities and the large amount of gene exchange with normal S. suis gives insufficient evidence to assign these isolates to a new species or subspecies. Further, sampling and whole genome analysis of more isolates is warranted to understand the diversity of the species.\n\nWhole genome investigation of a divergent clade of the pathogen Streptococcus suis.", "token_count": 505, "char_count": 2053, "word_count": 321, "semantic_coherence": 1, "information_density": 0.486, "quality_score": 0.743, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:08.305404", "source": { "split": "train_shard_00000", "doc_id": 4178 }, "chunk_id": "train_shard_00000_4178_0", "global_id": 4651 }, { "text": "Salmonella enterica serovar Heidelberg is the second most frequently occurring serovar in Quebec and the third-most prevalent in Canada. Given that conventional pulsed-field gel electrophoresis (PFGE) subtyping for common Salmonella serovars, such as S. Heidelberg, yields identical subtypes for the majority of isolates recovered, public health laboratories are desperate for new subtyping tools to resolve highly clonal S. Heidelberg strains involved in outbreak events. As PFGE was unable to discriminate isolates from three epidemiologically distinct outbreaks in Quebec, this study was conducted to evaluate whole-genome sequencing (WGS) and phylogenetic analysis as an alternative to conventional subtyping tools. Genomes of 46 isolates from 3 Quebec outbreaks (2012, 2013, and 2014) supported by strong epidemiological evidence were sequenced and analyzed using a high-quality core genome single-nucleotide variant (hqSNV) bioinformatics approach (SNV phylogenomics [SNVphyl] pipeline). Outbreaks were indistinguishable by conventional PFGE subtyping, exhibiting the same PFGE pattern (SHEXAI.0001/SHEBNI.0001). Phylogenetic analysis based on hqSNVs extracted from WGS separated the outbreak isolates into three distinct groups, 100% concordant with the epidemiological data. The minimum and maximum number of hqSNVs between isolates from the same outbreak was 0 and 4, respectively, while >59 hqSNVs were measured between 2 previously indistinguishable outbreaks having the same PFGE and phage type, thus corroborating their distinction as separate unrelated outbreaks. This study demonstrates that despite the previously reported high clonality of this serovar, the WGS-based hqSNV approach is a superior typing method, capable of resolving events that were previously indistinguishable using classic subtyping tools.", "token_count": 472, "char_count": 1826, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:08.944992", "source": { "split": "train_shard_00000", "doc_id": 4179 }, "chunk_id": "train_shard_00000_4179_0", "global_id": 4652 }, { "text": "Usefulness of High-Quality Core Genome Single-Nucleotide Variant Analysis for Subtyping the Highly Clonal and the Most Prevalent Salmonella enterica Serovar Heidelberg Clone in the Context of Outbreak Investigations.", "token_count": 58, "char_count": 216, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:09.307942", "source": { "split": "train_shard_00000", "doc_id": 4179 }, "chunk_id": "train_shard_00000_4179_1", "global_id": 4653 }, { "text": "Alcoholic liver disease (ALD) is one of the major causes of liver morbidity and mortality worldwide. Chronic alcohol consumption leads to development of liver pathogenesis encompassing steatosis, inflammation, fibrosis, cirrhosis, and in extreme cases, hepatocellular carcinoma. Moreover, ALD may also associate with cholestasis. Emerging evidence now suggests that farnesoid X receptor (FXR) and bile acids also play important roles in ALD. In this review, we discuss the effects of alcohol consumption on FXR, bile acids and gut microbiome as well as their impacts on ALD. Moreover, we summarize the findings on FXR, FoxO3a (forkhead box-containing protein class O3a) and PPARα (peroxisome proliferator-activated receptor alpha) in regulation of autophagy-related gene transcription program and liver injury in response to alcohol exposure.\n\nRole of farnesoid X receptor and bile acids in alcoholic liver disease.", "token_count": 237, "char_count": 915, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:09.795165", "source": { "split": "train_shard_00000", "doc_id": 4180 }, "chunk_id": "train_shard_00000_4180_0", "global_id": 4654 }, { "text": "Bile acids (BAs) are not only digestive surfactants but also important cell signaling molecules, which stimulate several signaling pathways to regulate some important biological processes. The bile-acid-activated nuclear receptor, farnesoid X receptor (FXR), plays a pivotal role in regulating bile acid, lipid and glucose homeostasis as well as in regulating the inflammatory responses, barrier function and prevention of bacterial translocation in the intestinal tract. As expected, FXR is involved in the pathophysiology of a wide range of diseases of gastrointestinal tract, including inflammatory bowel disease, colorectal cancer and type 2 diabetes. In this review, we discuss current knowledge of the roles of FXR in physiology of the digestive system and the related diseases. Better understanding of the roles of FXR in digestive system will accelerate the development of FXR ligands/modulators for the treatment of digestive system diseases.\n\nBile acid nuclear receptor FXR and digestive system diseases.", "token_count": 243, "char_count": 1014, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:10.295778", "source": { "split": "train_shard_00000", "doc_id": 4181 }, "chunk_id": "train_shard_00000_4181_0", "global_id": 4655 }, { "text": "The human body is now viewed as a complex ecosystem that on a cellular and gene level is mainly prokaryotic. The mammalian liver synthesizes and secretes hydrophilic primary bile acids, some of which enter the colon during the enterohepatic circulation, and are converted into numerous hydrophobic metabolites which are capable of entering the portal circulation, returned to the liver, and in humans, accumulating in the biliary pool. Bile acids are hormones that regulate their own synthesis, transport, in addition to glucose and lipid homeostasis, and energy balance. The gut microbial community through their capacity to produce bile acid metabolites distinct from the liver can be thought of as an \"endocrine organ\" with potential to alter host physiology, perhaps to their own favor. We propose the term \"sterolbiome\" to describe the genetic potential of the gut microbiome to produce endocrine molecules from endogenous and exogenous steroids in the mammalian gut. The affinity of secondary bile acid metabolites to host nuclear receptors is described, the potential of secondary bile acids to promote tumors, and the potential of bile acids to serve as therapeutic agents are discussed.\n\nThe human gut sterolbiome: bile acid-microbiome endocrine aspects and therapeutics.", "token_count": 304, "char_count": 1280, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5876, "quality_score": 0.7938, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:10.873802", "source": { "split": "train_shard_00000", "doc_id": 4182 }, "chunk_id": "train_shard_00000_4182_0", "global_id": 4656 }, { "text": "Drug resistance is a costly consequence of pathogen evolution and a major concern in public health. In this review, we show how population genetics can be used to study the evolution of drug resistance and also how drug resistance evolution is informative as an evolutionary model system. We highlight five examples from diverse organisms with particular focus on: (i) identifying drug resistance loci in the malaria parasite Plasmodium falciparum using the genomic signatures of selective sweeps, (ii) determining the role of epistasis in drug resistance evolution in influenza, (iii) quantifying the role of standing genetic variation in the evolution of drug resistance in HIV, (iv) using drug resistance mutations to study clonal interference dynamics in tuberculosis and (v) analysing the population structure of the core and accessory genome of Staphylococcus aureus to understand the spread of methicillin resistance. Throughout this review, we discuss the uses of sequence data and population genetic theory in studying the evolution of drug resistance.\n\nThe population genetics of drug resistance evolution in natural populations of viral, bacterial and eukaryotic pathogens.", "token_count": 248, "char_count": 1184, "word_count": 175, "semantic_coherence": 1, "information_density": 0.5657, "quality_score": 0.7829, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:11.398415", "source": { "split": "train_shard_00000", "doc_id": 4183 }, "chunk_id": "train_shard_00000_4183_0", "global_id": 4657 }, { "text": "The self-assembly of lecithin-bile salt mixtures in solutions has long been an important research topic, not only because they are both biosurfactants closely relevant to physiological functions but also for the potential biomedical applications. In this paper, we report an unusual biological hydrogel formed by mixing bile salts and lecithin at low bile salt/lecithin molar ratios (B0) in water. The gel can be prepared at a total lipid concentration as low as ∼15 wt %, and the solidlike property of the solutions was confirmed by dynamic rheological measurements. We used cryo-TEM and SAXS/SANS techniques to probe the self-assembled structure and clearly evidence that the gel is made up of jammed swollen multilamellar vesicles (liposomes), instead of typical fibrous networks found in conventional gels. A mechanism-based on the strong repulsion between bilayers due to the incorporation of negatively charged bile salts is proposed to explain the swelling of the liposomes. In addition to gel, a series of phases, including viscoelastic, gel-like, and low-viscosity fluids, can be created by increasing B0. Such a variety of phase behaviors are caused by the transformation of bilayers into cylindrical and spheroidal micelles upon the change of the effective molecular geometry with B0.\n\nBiological Hydrogels Formed by Swollen Multilamellar Liposomes.", "token_count": 334, "char_count": 1360, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6912, "quality_score": 0.8456, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:11.973269", "source": { "split": "train_shard_00000", "doc_id": 4184 }, "chunk_id": "train_shard_00000_4184_0", "global_id": 4658 }, { "text": "The bile salt export pump (BSEP/ABCB11), residing in the apical membrane of hepatocyte, mediates the secretion of bile salts into the bile. A range of human diseases is associated with the malfunction of BSEP, including fatal hereditary liver disorders and mild cholestatic conditions. Manifestation of these diseases primarily depends on the mutation type; however, other factors such as hormonal changes and drug interactions can also trigger or influence the related diseases.\n\nRecent advances in the exploration of the bile salt export pump (BSEP/ABCB11) function.", "token_count": 138, "char_count": 568, "word_count": 84, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:12.406388", "source": { "split": "train_shard_00000", "doc_id": 4185 }, "chunk_id": "train_shard_00000_4185_0", "global_id": 4659 }, { "text": "To improve the inulinase application in biotechnology, the characteristic of inulinase from Kluyveromyces marxianus YX01 was investigated. The inu gene of K. marxianus YX01 was transformed into Pichiapastoris GS115 host cells with molecular biology techniques. Then we achieved the heterologous expression of exo-inulinase whose molecular mass was about 86.0 kDa by sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE). Furthermore, six His-tag was added to the inulinase and a two-step method was applied in the purification of inulinase, including concentration via dialysis by polyethylene glycol 20 000 and metal Ni-NTA Agarose affinity adsorption. The purification factor of purified protein was 3.6 and the recovery rate of enzyme activity was 33.1%. We characterized the purified inulinase. The optimum temperature was 60 degrees C and pH was 4.62. When inulin and sucrose were used as substrates, the K(m) and V(max) values were 80.53 g/L vs 4.49 g/(L x min) and 183.10 g/L vs 20.20 g/(L x min), respectively. In addition, metal ions including Mn2+, Ca2+, Cu2+, Zn2+ and Fe2+ exhibited different degrees of inhibition on the enzyme activity, and Cu2+, Zn2+ and Fe2+ exhibited the most significant inhibition. Our findings might lay a good foundation for industrial application of inulinase.\n\n[Heterologous expression, purification and characterization of exo-inulinase from Kluyveromyces marxianus YX01].", "token_count": 434, "char_count": 1428, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [ "YX01", "GS115" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:13.037294", "source": { "split": "train_shard_00000", "doc_id": 4186 }, "chunk_id": "train_shard_00000_4186_0", "global_id": 4660 }, { "text": "Podoviruses are among the major viral groups that infect marine picocyanobacteria Prochlorococcus and Synechococcus. Here, we reported the genome sequences of five Synechococcus podoviruses isolated from the estuarine environment, and performed comparative genomic and phylogenomic analyses based on a total of 20 cyanopodovirus genomes. The genomes of all the known marine cyanopodoviruses are highly syntenic. A pan-genome of 349 clustered orthologous groups was determined, among which 15 were core genes. These core genes make up nearly half of each genome in length, reflecting the high level of genome conservation among this cyanophage type. The whole genome phylogenies based on concatenated core genes and gene content were highly consistent and confirmed the separation of two discrete marine cyanopodovirus clusters MPP-A and MPP-B. The genomes within cluster MPP-B grouped into subclusters mainly corresponding to Prochlorococcus or Synechococcus host types. Auxiliary metabolic genes tend to occur in a specific phylogenetic group of these cyanopodoviruses. All the MPP-B phages analyzed here encode the photosynthesis gene psbA, which are absent in all the MPP-A genomes thus far. Interestingly, all the MPP-B and two MPP-A Synechococcus podoviruses encode the thymidylate synthase gene thyX, while at the same genome locus all the MPP-B Prochlorococcus podoviruses encode the transaldolase gene talC. Both genes are hypothesized to have the potential to facilitate the biosynthesis of deoxynucleotide for phage replication. Inheritance of specific functional genes could be important to the evolution and ecological fitness of certain cyanophage genotypes. Our analyses demonstrate that cyanopodoviruses of estuarine and oceanic origins share a conserved core genome and suggest that accessory genes may be related to environmental adaptation.", "token_count": 492, "char_count": 1858, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5871, "quality_score": 0.7936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:13.689075", "source": { "split": "train_shard_00000", "doc_id": 4187 }, "chunk_id": "train_shard_00000_4187_0", "global_id": 4661 }, { "text": "Comparative Genomic and Phylogenomic Analyses Reveal a Conserved Core Genome Shared by Estuarine and Oceanic Cyanopodoviruses.", "token_count": 39, "char_count": 126, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:14.044218", "source": { "split": "train_shard_00000", "doc_id": 4187 }, "chunk_id": "train_shard_00000_4187_1", "global_id": 4662 }, { "text": "The aim of this study was to isolate, from pulque, Lactobacillus spp. capable of survival in simulated gastrointestinal stress conditions. Nine Gram-positive rods were isolated; however, only one strain (J57) shared identity with Lactobacillus and was registered as Lactobacillus casei J57 (GenBank accession: JN182264). The other strains were identified as Bacillus spp. The most significant observation during the test of tolerance to simulated gastrointestinal conditions (acidity, gastric juice and bile salts) was that L. casei J57 showed a rapid decrease (p ≤ 0.05) in the viable population at 0 h. Bile salts were the stress condition that most affected its survival, from which deoxycholic acid and the mix of bile salts (oxgall) were the most toxic. L. casei J57 showed bile salt hydrolase activity over primary and secondary bile salts as follows: 44.91, 671.72, 45.27 and 61.57 U/mg to glycocholate, taurocholate, glycodeoxycholate and taurodeoxycholate. In contrast, the control strain (L. casei Shirota) only showed activity over tauroconjugates. These results suggest that L. casei J57 shows potential for probiotic applications.\n\nIsolation, Identification and Partial Characterization of a Lactobacillus casei Strain with Bile Salt Hydrolase Activity from Pulque.", "token_count": 381, "char_count": 1278, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6183, "quality_score": 0.8091, "entities": { "genes": [ "JN182264" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:14.625675", "source": { "split": "train_shard_00000", "doc_id": 4188 }, "chunk_id": "train_shard_00000_4188_0", "global_id": 4663 }, { "text": "Environmental adaptation is considered as one of the most challenging subjects in biology to understand evolutionary or ecological diversification processes and in biotechnology to obtain useful microbial strains. Temperature is one of the important environmental stresses; however, microbial adaptation to higher temperatures has not been studied extensively. For industrial purposes, the use of thermally adapted strains is important, not only to reduce the cooling expenses of the fermentation system, but also to protect fermentation production from accidental failure of thermal management. Recent progress in next-generation sequencing provides a powerful tool to track the genomic changes of the adapted strains and allows us to compare genomic DNA sequences of conventional strains with those of their closely related thermotolerant strains. In this article, we have attempted to summarize our recent approaches to produce thermotolerant strains by thermal adaptation and comparative genomic analyses of Acetobacter pasteurianus for high-temperature acetic acid fermentations, and Zymomonas mobilis and Kluyveromyces marxianus for high-temperature ethanol fermentations. Genomic analysis of the adapted strains has found a large number of mutations and/or disruptions in highly diversified genes, which could be categorized into groups related to cell surface functions, ion or amino acid transporters, and some transcriptional factors. Furthermore, several phenotypic and genetic analyses revealed that the thermal adaptation could lead to decreased ROS generation in cells that produce higher ROS levels at higher temperatures. Thus, it is suggested that the thermally adapted cells could become robust and resistant to many stressors, and thus could be useful for high-temperature fermentations.\n\nGenomic analyses of thermotolerant microorganisms used for high-temperature fermentations.", "token_count": 396, "char_count": 1898, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:15.255794", "source": { "split": "train_shard_00000", "doc_id": 4189 }, "chunk_id": "train_shard_00000_4189_0", "global_id": 4664 }, { "text": "Whole-genome sequencing (WGS) with next-generation DNA sequencing (NGS) is an increasingly accessible and affordable method for genotyping hundreds of Mycobacterium tuberculosis (Mtb) isolates, leading to more effective epidemiological studies involving single nucleotide variations (SNVs) in core genomic sequences based on molecular evolution. We developed an all-in-one web-based tool for genotyping Mtb, referred to as the Total Genotyping Solution for TB (TGS-TB), to facilitate multiple genotyping platforms using NGS for spoligotyping and the detection of phylogenies with core genomic SNVs, IS6110 insertion sites, and 43 customized loci for variable number tandem repeat (VNTR) through a user-friendly, simple click interface. This methodology is implemented with a KvarQ script to predict MTBC lineages/sublineages and potential antimicrobial resistance. Seven Mtb isolates (JP01 to JP07) in this study showing the same VNTR profile were accurately discriminated through median-joining network analysis using SNVs unique to those isolates. An additional IS6110 insertion was detected in one of those isolates as supportive genetic information in addition to core genomic SNVs. The results of in silico analyses using TGS-TB are consistent with those obtained using conventional molecular genotyping methods, suggesting that NGS short reads could provide multiple genotypes to discriminate multiple strains of Mtb, although longer NGS reads (≥ 300-mer) will be required for full genotyping on the TGS-TB web site. Most available short reads (~100-mer) can be utilized to discriminate the isolates based on the core genome phylogeny. TGS-TB provides a more accurate and discriminative strain typing for clinical and epidemiological investigations; NGS strain typing offers a total genotyping solution for Mtb outbreak and surveillance. TGS-TB web site: https://gph.niid.go.jp/tgs-tb/.", "token_count": 487, "char_count": 1892, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [ "IS6110", "JP07", "JP01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:15.907403", "source": { "split": "train_shard_00000", "doc_id": 4190 }, "chunk_id": "train_shard_00000_4190_0", "global_id": 4665 }, { "text": "TGS-TB: Total Genotyping Solution for Mycobacterium tuberculosis Using Short-Read Whole-Genome Sequencing.", "token_count": 34, "char_count": 106, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:16.266086", "source": { "split": "train_shard_00000", "doc_id": 4190 }, "chunk_id": "train_shard_00000_4190_1", "global_id": 4666 }, { "text": "Aim of the present study was to characterise and evaluate probiotic potential of lactobacilli isolated from indigenous poultry. Lactobacilli were isolated from poultry droppings and identified by genus specific polymerase chain reaction and 16S rRNA gene sequencing. Isolates were characterised in vitro by their ability to tolerate low pH and bile salts, phytase activity, antimicrobial activity, antibiotic susceptibility profile, and autoaggregation and coaggregation with poultry gut pathogens. In vivo evaluation of selected isolates was done by their effect on the body weight gain and immune response of broiler chicks. Total of 90, one-day old chicks, were randomly divided in 9 groups and given selected lactobacilli alone and in combinations (10\n\nSelection, characterisation and evaluation of potential probiotic Lactobacillus spp. isolated from poultry droppings.", "token_count": 222, "char_count": 874, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:16.731246", "source": { "split": "train_shard_00000", "doc_id": 4191 }, "chunk_id": "train_shard_00000_4191_0", "global_id": 4667 }, { "text": "Inflammatory bowel diseases (IBDs) are complex affections with increasing incidence worldwide. Multiple factors are involved in the development and maintenance of the symptoms including enhanced oxidative stress in intestinal mucosa. The conventional therapeutic approaches for IBDs are based on the use anti-inflammatory drugs with important collateral effects and partial efficacy. In the present work we tested the anti-inflammatory capacity of Kluyveromyces marxianus CIDCA 8154 in different models. In vitro, we showed that the pretreatment of epithelial cells with the yeast reduce the levels of intracellular reactive oxygen species. Furthermore, in a murine model of trinitro benzene sulfonic acid-induced colitis, yeast-treated animals showed a reduced histopathological score (P<0.05) and lower levels of circulating interleukin 6 (P<0.05). The capacity to modulate oxidative stress in vivo was assessed using a Caenorhabditis elegans model. The yeast was able to protect the nematodes from oxidative stress by modulating the SKN-1 transcription factor trough the DAF-2 pathway. These results indicate that K. marxianus CIDCA 8154 could control the intestinal inflammation and cellular oxidative stress. Deciphering the mechanisms of action of different probiotics might be useful for the rational formulation of polymicrobial products containing microorganisms targeting different anti-inflammatory pathways.\n\nProbiotic yeast Kluyveromyces marxianus CIDCA 8154 shows anti-inflammatory and anti-oxidative stress properties in in vivo models.", "token_count": 406, "char_count": 1551, "word_count": 208, "semantic_coherence": 1, "information_density": 0.649, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:17.352228", "source": { "split": "train_shard_00000", "doc_id": 4192 }, "chunk_id": "train_shard_00000_4192_0", "global_id": 4668 }, { "text": "Guggulsterone [4, 17(20)-pregnadiene-3, 16-dione] is a plant sterol derived from the gum resin of the tree Commiphora wightii. The gum resin of the guggul tree has been used in traditional medicine for centuries to treat obesity, liver disorders, internal tumors, malignant sores, ulcers, urinary complaints, intestinal worms, leucoderma, sinus, edema and sudden paralytic seizures. Guggulsterone has been shown to modulate the nuclear receptors, farnesoid X receptor, pregnane X receptor, CYP 2b10 gene expression, and the bile salt export pump for cholesterol elimination. Recent research indicates that the active components of gum guggul, E- and Zguggulsterone have the potential to both prevent and treat cancers. Guggulsterone inhibits the growth of a wide variety of tumor cells and induces apoptosis through down regulation of antiapoptotic gene products (IAP1, xIAP, Bfl-1/A1, Bcl-2, cFLIP, and survivin), modulation of cell cycle proteins (cyclin D1 and c-Myc), activation of caspases, inhibition of Akt, and activation of JNK. Guggulsterone modulates the expression of gene products involved in metastasis (MMP-9, COX-2, and VEGF) of tumor cells. Guggulsterone mediates gene expression through the modulation of several transcription factors, including NF-κB, STAT3, C/EBPα, androgen receptor, and glucocorticoid receptors. This review describes the anti-cancer properties, molecular targets, and the apoptotic effects of guggulsterone.\n\nGuggulsterone for Chemoprevention of Cancer.", "token_count": 442, "char_count": 1493, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6812, "quality_score": 0.8406, "entities": { "genes": [ "IAP1", "STAT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:17.989349", "source": { "split": "train_shard_00000", "doc_id": 4193 }, "chunk_id": "train_shard_00000_4193_0", "global_id": 4669 }, { "text": "Rickettsia is a genus of intracellular bacteria whose hosts and transmission strategies are both impressively diverse, and this is reflected in a highly dynamic genome. Some previous studies have described the evolutionary history of Rickettsia as non-tree-like, due to incongruity between phylogenetic reconstructions using different portions of the genome. Here, we reconstruct the Rickettsia phylogeny using whole-genome data, including two new genomes from previously unsampled host groups. We find that a single topology, which is supported by multiple sources of phylogenetic signal, well describes the evolutionary history of the core genome. We do observe extensive incongruence between individual gene trees, but analyses of simulations over a single topology and interspersed partitions of sites show that this is more plausibly attributed to systematic error than to horizontal gene transfer. Some conflicting placements also result from phylogenetic analyses of accessory genome content (i.e., gene presence/absence), but we argue that these are also due to systematic error, stemming from convergent genome reduction, which cannot be accommodated by existing phylogenetic methods. Our results show that, even within a single genus, tests for gene exchange based on phylogenetic incongruence may be susceptible to false positives.\n\nThe Phylogeny of Rickettsia Using Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?", "token_count": 327, "char_count": 1450, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:18.557293", "source": { "split": "train_shard_00000", "doc_id": 4194 }, "chunk_id": "train_shard_00000_4194_0", "global_id": 4670 }, { "text": "Erratum for Kulohoma et al., Comparative genomic analysis of meningitis- and bacteremia-causing pneumococci identifies a common core genome.", "token_count": 42, "char_count": 140, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:18.921734", "source": { "split": "train_shard_00000", "doc_id": 4195 }, "chunk_id": "train_shard_00000_4195_0", "global_id": 4671 }, { "text": "Vibrio parahaemolyticus is widely distributed in the marine environments and considered the leading cause of human gastroenteritis in Asian countries. A total of 150 marketed fish and 50 water and sediment samples from the Gulf of Aqaba were examined for the prevalence of pathogenic strains of V. parahaemolyticus. A total of 132 typical isolates obtained from the primary selective medium (thiosulfate-citrate bile salt sucrose agar) and showed positive biochemical properties were subjected to confirmation by polymerase chain reaction targeting the gyrB and toxR genes. These genes were confirmed at rates of 82% (108 isolates) and 72% (95 isolates), respectively. The toxR positive isolates were tested for the presence of thermolabile hemolysin (tlh), thermostable direct hemolysin (tdh), and tdh-related hemolysin (trh) virulence genes. Accordingly, the prevalence rates of pathogenic V. parahaemolyticus were 4%, 8%, and 12% in sediment, water, and fish samples, respectively. The 16S rRNA amplification and sequences were conducted for confirmation of the isolates and showing the relatedness among these isolates. The results showed that both 16S rRNA and toxR assays had same sensitivity and tested isolates had high nucleotide similarity irrespective of their sources.\n\nDetection, Identification, and Prevalence of Pathogenic Vibrio parahaemolyticus in Fish and Coastal Environment in Jordan.", "token_count": 374, "char_count": 1404, "word_count": 201, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:19.508012", "source": { "split": "train_shard_00000", "doc_id": 4196 }, "chunk_id": "train_shard_00000_4196_0", "global_id": 4672 }, { "text": "In this study, the survival of the functional yeast Kluyveromyces marxianus B0399 in an industrially produced fermented milk was evaluated. In particular, the yeast viability was assessed throughout the entire shelf-life of the product (30 d) to ensure the presence of the effective yeast dose (20 million viable cells for each serving of 125 g) while avoiding, by sorbic acid addition, yeast growth, which could affect product quality and stability. To find the best combination of yeast and sorbic acid concentration, 13 different combinations were tested, and then 2 of them were chosen for industrial production. In production at lower concentrations (30 million viable cells, 150 mg/kg of sorbic acid) the effective dose was maintained only at 4 and 6°C, whereas at higher dosages (70 million viable cells, 250 mg/kg of sorbic acid) the effect of temperature was less evident. In all the trials, the concentration of sorbic acid was not affected by microbial metabolism and remained stable throughout the entire shelf-life.\n\nSurvival of the functional yeast Kluyveromyces marxianus B0399 in fermented milk with added sorbic acid.", "token_count": 288, "char_count": 1134, "word_count": 177, "semantic_coherence": 1, "information_density": 0.5819, "quality_score": 0.791, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:20.065200", "source": { "split": "train_shard_00000", "doc_id": 4197 }, "chunk_id": "train_shard_00000_4197_0", "global_id": 4673 }, { "text": "Starch is the dominant feedstock consumed for the bioethanol production, accounting for 60 % of its global production. Considering the significant contribution of bioethanol to the global fuel market, any improvement in its major operating technologies is economically very attractive. It was estimated that up to 40 % of the final ethanol unit price is derived from the energy input required for the substrate pre-treatment. Application of raw starch hydrolyzing enzymes (RSHE), combined with operation of the process according to a simultaneous saccharification and fermentation (SSF) strategy, constitutes the most promising solutions to the current technologies limitations. In this study, we expressed the novel RSHE derived from an insect in Saccharomyces cerevisiae strain dedicated for the protein overexpression. Afterwards, the enzyme performance was assessed in SSF process conducted by industrial ethanologenic or thermotolerant yeast species. Comparison of the insect-derived RSHE preparation with commercially available amylolytic RSH preparation was conducted. Our results demonstrate that the recombinant alpha-amylase from rice weevil can be efficiently expressed and secreted with its native signal peptide in S. cerevisiae INVSc-pYES2-Amy1 expression system (accounting for nearly 72 % of the strain's secretome). Application of the recombinant enzyme-based preparation in SSF process secured sufficient amylolytic activity for the yeast cell propagation and ethanol formation from raw starch. (Oligo)saccharide profiles generated by the compared preparations differed with respect to homogeneity of the sugar mixtures. Concomitantly, as demonstrated by a kinetic model developed in this study, the kinetic parameters describing activity of the compared preparations were different.\n\nEvaluation of a recombinant insect-derived amylase performance in simultaneous saccharification and fermentation process with industrial yeasts.", "token_count": 444, "char_count": 1947, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6084, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:20.697433", "source": { "split": "train_shard_00000", "doc_id": 4198 }, "chunk_id": "train_shard_00000_4198_0", "global_id": 4674 }, { "text": "A thermo-tolerant NADP(H)-preferring xylose pathway was constructed in Kluyveromyces marxianus for ethanol production with xylose at elevated temperatures (Zhang et al., 2015 [25]). Ethanol production yield and efficiency was enhanced by pathway engineering in the engineered strains. The constructed strain, YZJ088, has the ability to co-ferment glucose and xylose for ethanol and xylitol production, which is a critical step toward enabling economic biofuel production from lignocellulosic biomass. This study contains the fermentation results of strains using the metabolic pathway engineering procedure. The ethanol-producing abilities of various yeast strains under various conditions were compared, and strain YZJ088 showed the highest production and fastest productivity at elevated temperatures. The YZJ088 xylose fermentation results indicate that it fermented well with xylose at either low or high inoculum size. When fermented with an initial cell concentration of OD600=15 at 37 °C, YZJ088 consumed 200 g/L xylose and produced 60.07 g/L ethanol; when the initial cell concentration was OD600=1 at 37 °C, YZJ088 consumed 98.96 g/L xylose and produced 33.55 g/L ethanol with a productivity of 0.47 g/L/h. When fermented with 100 g/L xylose at 42 °C, YZJ088 produced 30.99 g/L ethanol with a productivity of 0.65 g/L/h, which was higher than that produced at 37 °C.\n\nData for rapid ethanol production at elevated temperatures by engineered thermotolerant Kluyveromyces marxianus via the NADP(H)-preferring xylose reductase-xylitol dehydrogenase pathway.", "token_count": 500, "char_count": 1563, "word_count": 222, "semantic_coherence": 1, "information_density": 0.545, "quality_score": 0.7725, "entities": { "genes": [ "YZJ088", "OD600" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:21.352581", "source": { "split": "train_shard_00000", "doc_id": 4199 }, "chunk_id": "train_shard_00000_4199_0", "global_id": 4675 }, { "text": "The aim of this investigation was to develop a procedure to improve the dissolution and bioavailability of silymarin (SM) by using bile salt-containing liposomes that were prepared by supercritical fluid technology (ie, solution-enhanced dispersion by supercritical fluids [SEDS]). The process for the preparation of SM-loaded liposomes containing a bile salt (SM-Lip-SEDS) was optimized using a central composite design of response surface methodology with the ratio of SM to phospholipids (w/w), flow rate of solution (mL/min), and pressure (MPa) as independent variables. Particle size, entrapment efficiency (EE), and drug loading (DL) were dependent variables for optimization of the process and formulation variables. The particle size, zeta potential, EE, and DL of the optimized SM-Lip-SEDS were 160.5 nm, -62.3 mV, 91.4%, and 4.73%, respectively. Two other methods to produce SM liposomes were compared to the SEDS method. The liposomes obtained by the SEDS method exhibited the highest EE and DL, smallest particle size, and best stability compared to liposomes produced by the thin-film dispersion and reversed-phase evaporation methods. Compared to the SM powder, SM-Lip-SEDS showed increased in vitro drug release. The in vivo AUC(0-t) of SM-Lip-SEDS was 4.8-fold higher than that of the SM powder. These results illustrate that liposomes containing a bile salt can be used to enhance the oral bioavailability of SM and that supercritical fluid technology is suitable for the preparation of liposomes.\n\nEnhanced oral bioavailability of silymarin using liposomes containing a bile salt: preparation by supercritical fluid technology and evaluation in vitro and in vivo.", "token_count": 433, "char_count": 1681, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5344, "quality_score": 0.7672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:22.030649", "source": { "split": "train_shard_00000", "doc_id": 4200 }, "chunk_id": "train_shard_00000_4200_0", "global_id": 4676 }, { "text": "Brucella is a facultative intracellular bacterium belongs to the class alpha proteobacteria. It causes zoonotic disease brucellosis to wide range of animals. Brucella species are highly conserved in nucleotide level. Here, we employed a comparative genomics approach to examine the role of homologous recombination and positive selection in the evolution of Brucella. For the analysis, we have selected 19 complete genomes from 8 species of Brucella. Among the 1599 core genome predicted, 24 genes were showing signals of recombination but no significant breakpoint was found. The analysis revealed that recombination events are less frequent and the impact of recombination occurred is negligible on the evolution of Brucella. This leads to the view that Brucella is clonally evolved. On other hand, 56 genes (3.5 % of core genome) were showing signals of positive selection. Results suggest that natural selection plays an important role in the evolution of Brucella. Some of the genes that are responsible for the pathogenesis of Brucella were found positively selected, presumably due to their role in avoidance of the host immune system.\n\nIdentification of Recombination and Positively Selected Genes in Brucella.", "token_count": 283, "char_count": 1218, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:23.036519", "source": { "split": "train_shard_00000", "doc_id": 4201 }, "chunk_id": "train_shard_00000_4201_0", "global_id": 4677 }, { "text": "A New Delhi Metallo-beta-lactamase-5 (NDM-5)-producing ST16 Klebsiella pneumoniae strain was isolated from a Dutch patient in a long-term care facility without recent travel history abroad. Core genome multilocus sequence typing (cgMLST) revealed that the Dutch isolate was clonally related to isolates detected in four patients in Denmark in 2014. Public health experts and clinicians need to be informed; repetitive screening may be needed in patients without known risk factors for carbapenemases-producing Enterobacteriaceae who have undergone antibiotic treatment.\n\nIsolation of an NDM-5-producing ST16 Klebsiella pneumoniae from a Dutch patient without travel history abroad, August 2015.", "token_count": 180, "char_count": 694, "word_count": 94, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [ "ST16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:23.524895", "source": { "split": "train_shard_00000", "doc_id": 4202 }, "chunk_id": "train_shard_00000_4202_0", "global_id": 4678 }, { "text": "Escherichia albertii is a recently recognized close relative of Escherichia coli. This emerging enteropathogen possesses a type III secretion system (T3SS) encoded by the locus of enterocyte effacement, similar to enteropathogenic and enterohemorrhagic E. coli (EPEC and EHEC). Shiga toxin-producing strains have also been identified. The genomic features of E. albertii, particularly differences from other Escherichia species, have not yet been well clarified. Here, we sequenced the genome of 29 E. albertii strains (3 complete and 26 draft sequences) isolated from multiple sources and performed intraspecies and intragenus genomic comparisons. The sizes of the E. albertii genomes range from 4.5 to 5.1 Mb, smaller than those of E. coli strains. Intraspecies genomic comparisons identified five phylogroups of E. albertii. Intragenus genomic comparison revealed that the possible core genome of E. albertii comprises 3,250 genes, whereas that of the genus Escherichia comprises 1,345 genes. Our analysis further revealed several unique or notable genetic features of E. albertii, including those responsible for known biochemical features and virulence factors and a possibly active second T3SS known as ETT2 (E. coli T3SS 2) that is inactivated in E. coli. Although this organism has been observed to be nonmotile in vitro, genes for flagellar biosynthesis are fully conserved; chemotaxis-related genes have been selectively deleted. Based on these results, we have developed a nested polymerase chain reaction system to directly detect E. albertii. Our data define the genomic features of E. albertii and provide a valuable basis for future studies of this important emerging enteropathogen.\n\nDefining the Genome Features of Escherichia albertii, an Emerging Enteropathogen Closely Related to Escherichia coli.", "token_count": 481, "char_count": 1817, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [ "ETT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:24.180368", "source": { "split": "train_shard_00000", "doc_id": 4203 }, "chunk_id": "train_shard_00000_4203_0", "global_id": 4679 }, { "text": "Population samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be 'genomically coherent', even though there is no consensus on how this should be determined.\n\nRecombination produces coherent bacterial species clusters in both core and accessory genomes.", "token_count": 102, "char_count": 485, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7465, "quality_score": 0.8732, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:24.566483", "source": { "split": "train_shard_00000", "doc_id": 4204 }, "chunk_id": "train_shard_00000_4204_0", "global_id": 4680 }, { "text": "Lactic acid bacteria have been identified to be effective in reducing cholesterol levels. Most of the mechanistic studies were focused on the bile salt deconjugation ability of bile salt hydrolase in lactic acid bacteria. However, the mechanism by which Lactobacillus decreases cholesterol levels has not been thoroughly studied in intact primate cells. 3-Hydroxy-3- methyl-glutaryl-coenzyme A reductase (HMGCR) is the vital enzyme in cholesterol synthesis. To confirm the effect of probiotic Lactobacillus strains on HMGCR level, in the present study, human hepatoma HepG2 cells were treated with Lactobacillus strains, and then the HMGCR level was illustrated by luciferase reporter assay and RT-PCR. The results showed that the level of HMGCR was suppressed after being treated with the live Lactobacillus strains. These works might set a foundation for the following study of the antihyperlipidemic effects of L. acidophilus, and contribute to the development of functional foods or drugs that benefit patients suffering from hyperlipidemia diseases.\n\nRegulation of the Lactobacillus Strains on HMGCoA Reductase Gene Transcription in Human HepG2 Cells via Nuclear Factor-κB.", "token_count": 316, "char_count": 1178, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:25.133048", "source": { "split": "train_shard_00000", "doc_id": 4205 }, "chunk_id": "train_shard_00000_4205_0", "global_id": 4681 }, { "text": "Streptococcus pneumoniae is common nasopharyngeal commensal bacterium and important human pathogen. Vaccines against a subset of pneumococcal antigenic diversity have reduced rates of disease, without changing the frequency of asymptomatic carriage, through altering the bacterial population structure. These changes can be studied in detail through using genome sequencing to characterise systematically-sampled collections of carried S. pneumoniae. This dataset consists of 616 annotated draft genomes of isolates collected from children during routine visits to primary care physicians in Massachusetts between 2001, shortly after the seven valent polysaccharide conjugate vaccine was introduced, and 2007. Also made available are a core genome alignment and phylogeny describing the overall population structure, clusters of orthologous protein sequences, software for inferring serotype from Illumina reads, and whole genome alignments for the analysis of closely-related sets of pneumococci. These data can be used to study both bacterial evolution and the epidemiology of a pathogen population under selection from vaccine-induced immunity.\n\nPopulation genomic datasets describing the post-vaccine evolutionary epidemiology of Streptococcus pneumoniae.", "token_count": 284, "char_count": 1259, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7439, "quality_score": 0.872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:25.690428", "source": { "split": "train_shard_00000", "doc_id": 4206 }, "chunk_id": "train_shard_00000_4206_0", "global_id": 4682 }, { "text": "Phylogenetic classification divides the major facilitator superfamily (MFS) into 82 families, including 25 families that are comprised of transporters with no characterized functions. This study describes functional data for BC3310 from Bacillus cereus ATCC 14579, a member of the \"unknown major facilitator family-2\" (UMF-2). BC3310 was shown to be a multidrug efflux pump conferring resistance to ethidium bromide, SDS and silver nitrate when heterologously expressed in Escherichia coli DH5α ΔacrAB. A conserved aspartate residue (D105) in putative transmembrane helix 4 was identified, which was essential for the energy dependent ethidium bromide efflux by BC3310. Transport proteins of the MFS comprise specific sequence motifs. Sequence analysis of UMF-2 proteins revealed that they carry a variant of the MFS motif A, which may be used as a marker to distinguish easily between this family and other MFS proteins. Genes orthologous to bc3310 are highly conserved within the B. cereus group of organisms and thus belong to the core genome, suggesting an important conserved functional role in the normal physiology of these bacteria.\n\nBacillus cereus efflux protein BC3310 - a multidrug transporter of the unknown major facilitator family, UMF-2.", "token_count": 351, "char_count": 1247, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [ "BC3310" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:26.267228", "source": { "split": "train_shard_00000", "doc_id": 4207 }, "chunk_id": "train_shard_00000_4207_0", "global_id": 4683 }, { "text": "We studied the dynamics of ethanol production on lactose-hydrolyzed whey (LHW) and lactose-hydrolyzed whey permeate (LHWP) in batch fluidized-bed bioreactors using single and co-cultures of immobilized cells of industrial strains of Saccharomyces cerevisiae and non-industrial strains of Kluyveromyces marxianus. Although the co-culture of S. cerevisiae CAT-1 and K. marxianus CCT 4086 produced two- to fourfold the ethanol productivity of single cultures of S. cerevisiae, the single cultures of the K. marxianus CCT 4086 produced the best results in both media (Y EtOH/S = 0.47-0.49 g g(-1) and Q P = 1.39-1.68 g L(-1) h(-1), in LHW and LHWP, respectively). Ethanol production on concentrated LHWP (180 g L(-1)) reached 79.1 g L(-1), with yields of 0.46 g g(-1) for K. marxianus CCT 4086 cultures. Repeated batches of fluidized-bed bioreactor on concentrated LHWP led to increased ethanol productivity, reaching 2.8 g L(-1) h(-1).\n\nDynamics of yeast immobilized-cell fluidized-bed bioreactors systems in ethanol fermentation from lactose-hydrolyzed whey and whey permeate.", "token_count": 374, "char_count": 1074, "word_count": 157, "semantic_coherence": 1, "information_density": 0.5732, "quality_score": 0.7866, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:26.851838", "source": { "split": "train_shard_00000", "doc_id": 4208 }, "chunk_id": "train_shard_00000_4208_0", "global_id": 4684 }, { "text": "Patients presenting with abdominal pain and diarrhea are often labelled as suffering from irritable bowel syndrome, and medications may be used often without success. Advances in the understanding of the causes of the symptoms (including pelvic floor weakness and incontinence, bile salt malabsorption and food intolerance) mean that effective, safe and well tolerated treatments are now available.\n\nFood, fibre, bile acids and the pelvic floor: An integrated low risk low cost approach to managing irritable bowel syndrome.", "token_count": 119, "char_count": 524, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7922, "quality_score": 0.8961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:27.235204", "source": { "split": "train_shard_00000", "doc_id": 4209 }, "chunk_id": "train_shard_00000_4209_0", "global_id": 4685 }, { "text": "The Pseudomonas genus contains a metabolically versatile group of organisms that are known to occupy numerous ecological niches, including the rhizosphere and endosphere of many plants. Their diversity influences the phylogenetic diversity and heterogeneity of these communities. On the basis of average amino acid identity, comparative genome analysis of >1,000 Pseudomonas genomes, including 21 Pseudomonas strains isolated from the roots of native Populus deltoides (eastern cottonwood) trees resulted in consistent and robust genomic clusters with phylogenetic homogeneity. All Pseudomonas aeruginosa genomes clustered together, and these were clearly distinct from other Pseudomonas species groups on the basis of pangenome and core genome analyses. In contrast, the genomes of Pseudomonas fluorescens were organized into 20 distinct genomic clusters, representing enormous diversity and heterogeneity. Most of our 21 Populus-associated isolates formed three distinct subgroups within the major P. fluorescens group, supported by pathway profile analysis, while two isolates were more closely related to Pseudomonas chlororaphis and Pseudomonas putida. Genes specific to Populus-associated subgroups were identified. Genes specific to subgroup 1 include several sensory systems that act in two-component signal transduction, a TonB-dependent receptor, and a phosphorelay sensor. Genes specific to subgroup 2 contain hypothetical genes, and genes specific to subgroup 3 were annotated with hydrolase activity. This study justifies the need to sequence multiple isolates, especially from P. fluorescens, which displays the most genetic variation, in order to study functional capabilities from a pangenomic perspective. This information will prove useful when choosing Pseudomonas strains for use to promote growth and increase disease resistance in plants.\n\nDiversity of Pseudomonas Genomes, Including Populus-Associated Isolates, as Revealed by Comparative Genome Analysis.", "token_count": 472, "char_count": 1978, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:27.885768", "source": { "split": "train_shard_00000", "doc_id": 4210 }, "chunk_id": "train_shard_00000_4210_0", "global_id": 4686 }, { "text": "Bile is synthesized in the liver and is essential for the emulsification of dietary lipids and lipid-soluble vitamins. It is a complex mixture of amphiphilic bile acids (BAs; which act as detergent molecules), the membrane phospholipid phosphatidylcholine (PC), cholesterol and a variety of endogenous metabolites and waste products. Over the last 20 years, the combined effort of clinicians, geneticists, physiologists and biochemists has shown that each of these bile components is transported across the canalicular membrane of the hepatocyte by its own specific ATP-binding cassette (ABC) transporter. The bile salt export pump (BSEP) ABCB11 transports the BAs and drives bile flow from the liver, but it is now clear that two lipid transporters, ABCB4 (which flops PC into the bile) and the P-type ATPase ATP8B1/CDC50 (which flips a different phospholipid in the opposite direction) play equally critical roles that protect the biliary tree from the detergent activity of the bile acids. Understanding the interdependency of these lipid floppases and flippases has allowed the development of an assay to measure ABCB4 function. ABCB4 harbours numerous mis-sense mutations which probably reflects the spectrum of liver disease rooted in ABCB4 aetiology. Characterization of the effect of these mutations at the protein level opens the possibility for the development of personalized prognosis and treatment.\n\nLipid flopping in the liver.", "token_count": 380, "char_count": 1441, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6372, "quality_score": 0.8186, "entities": { "genes": [ "ABCB11", "ABCB4", "CDC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:28.478304", "source": { "split": "train_shard_00000", "doc_id": 4211 }, "chunk_id": "train_shard_00000_4211_0", "global_id": 4687 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC-2) is caused by mutations in ABCB11, encoding the bile salt export pump (BSEP). In 2009, we described a child with PFIC-2 who developed PFIC-like symptoms after orthotopic liver transplantation (OLT). BSEP-reactive antibodies were demonstrated to account for disease recurrence. Here, we characterize the nature of this antibody response in 7 more patients with antibody-induced BSEP deficiency (AIBD). Gene sequencing and immunostaining of native liver biopsies indicated absent or strongly reduced BSEP expression in all 7 PFIC-2 patients who suffered from phenotypic disease recurrence post-OLT. Immunofluorescence, western blotting analysis, and transepithelial transport assays demonstrated immunoglobulin (Ig) G-class BSEP-reactive antibodies in these patients. In all cases, the N-terminal half of BSEP was recognized, with reaction against its first extracellular loop (ECL1) in six sera. In five, antibodies reactive against the C-terminal half also were found. Only the sera recognizing ECL1 showed inhibition of transepithelial taurocholate transport. In a vesicle-based functional assay, transport inhibition by anti-BSEP antibodies binding from the cytosolic side was functionally proven as well. Within 2 hours of perfusion with antibodies purified from 1 patient, rat liver showed canalicular IgG staining that was absent after perfusion with control IgG.\n\nBile salt export pump-reactive antibodies form a polyclonal, multi-inhibitory response in antibody-induced bile salt export pump deficiency.", "token_count": 427, "char_count": 1571, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6808, "quality_score": 0.8404, "entities": { "genes": [ "ABCB11", "ECL1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:29.102610", "source": { "split": "train_shard_00000", "doc_id": 4212 }, "chunk_id": "train_shard_00000_4212_0", "global_id": 4688 }, { "text": "Recently [Neubrand, M. W., et al. (2015) Biochemistry 54, 1542-1557], we determined a concentration-dependent monomer-dimer-tetramer equilibrium in aqueous bilirubin ditaurate (BDT) solutions and explored the nature of high-affinity binding of BDT monomers with monomers and micelles of the common taurine-conjugated bile salts (BS). We now investigate, employing complementary physicochemical methods, including fluorescence emission spectrophotometry and quasi-elastic light scattering spectroscopy, the influence of phosphatidylcholine (PC), the predominant phospholipid of bile and calcium, the major divalent biliary cation, on these self-interactions and heterointeractions. We have used short-chain, lyso and long-chain PC species as models and contrasted our results with those of parallel studies employing unconjugated bilirubin (UCB) as the fully charged dianion. Both bile pigments interacted with the zwitterionic headgroup of short-chain lecithins, forming water-soluble (BDT) and insoluble ion-pair complexes (UCB), respectively. Upon micelle formation, BDT monomers apparently remained at the headgroup mantle of short-chain PCs, but the ion pairs with UCB became internalized within the micelle's hydrophobic core. BDT interacted with the headgroups of unilamellar egg yolk (EY) PC vesicles; however, with the simultaneous addition of CaCl2, a reversible aggregation took place, but not vesicle fusion. With mixed EYPC/BS micelles, BDT became bound to the hydrophilic surface (as with simple BS micelles), and in turn, both BDT and BS bound calcium, but not other divalent cations. The calcium complexation of BDT and BS was enhanced strongly with increases in micellar EYPC, suggesting calcium-mediated cross-bridging of hydrophilic headgroups at the micelle's surface", "token_count": 498, "char_count": 1786, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:29.760898", "source": { "split": "train_shard_00000", "doc_id": 4213 }, "chunk_id": "train_shard_00000_4213_0", "global_id": 4689 }, { "text": "Therefore, the physicochemical binding of BDT to BS in an artificial bile medium is influenced not only by BS species and concentration but also by long-chain PCs and calcium ions that exert a specific rather than a counterion effect. This work should serve as a physicochemical template for studies with other conjugated bilirubins, including bilirubin diglucuronoside (BDG), the principal bilirubin conjugate (cBR) in human bile.\n\nInfluence of Phosphatidylcholine and Calcium on Self-Association and Bile Salt Mixed Micellar Binding of the Natural Bile Pigment, Bilirubin Ditaurate.", "token_count": 162, "char_count": 584, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7765, "quality_score": 0.8882, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:30.199781", "source": { "split": "train_shard_00000", "doc_id": 4213 }, "chunk_id": "train_shard_00000_4213_1", "global_id": 4690 }, { "text": "The aim of this work was to evaluate the ability of a kefir-isolated microbial mixture containing three bacterial and two yeast strains (MM) to protect intestinal epithelial cells against Shigella flexneri invasion, as well as to analyse the effect on pro-inflammatory response elicited by this pathogen. A significant decrease in S. flexneri strain 72 invasion was observed on both HT-29 and Caco-2 cells pre-incubated with MM. Pre-incubation with the individual strains Saccharomyces cerevisiae CIDCA 8112 or Lactococcus lactis subsp. lactis CIDCA 8221 also reduced the internalisation of S. flexneri into HT-29 cells although in a lesser extent than MM. Interestingly, Lactobacillus plantarum CIDCA 83114 exerted a protective effect on the invasion of Caco-2 and HT-29 cells by S. flexneri. Regarding the pro-inflammatory response on HT-29 cells, S. flexneri infection induced a significant activation of the expression of interleukin 8 (IL-8), chemokine (C-C motif) ligand 20 (CCL20) and tumour necrosis factor alpha (TNF-α) encoding genes (P<0.05), whereas incubation of cells with MM did not induce the expression of any of the mediators assessed. Interestingly, pre-incubation of HT-29 monolayer with MM produced an inhibition of S. flexneri-induced IL-8, CCL20 and TNF-α mRNA expression. In order to gain insight on the effect of MM (or the individual strains) on this pro-inflammatory response, a series of experiments using a HT-29-NF-κB-hrGFP reporter system were performed. Pre-incubation of HT-29-NF-κB-hrGFP cells with MM significantly dampened Shigella-induced activation. Our results showed that the contribution of yeast strain Kluyveromyces marxianus CIDCA 8154 seems to be crucial in the observed effect", "token_count": 522, "char_count": 1722, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5976, "quality_score": 0.7988, "entities": { "genes": [ "CCL20" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:41:30.835109", "source": { "split": "train_shard_00000", "doc_id": 4214 }, "chunk_id": "train_shard_00000_4214_0", "global_id": 4691 }, { "text": "In conclusion, results presented in this study demonstrate that pre-treatment with a microbial mixture containing bacteria and yeasts isolated from kefir, resulted in inhibition of S. flexneri internalisation into human intestinal epithelial cells, along with the inhibition of the signalling via NF-κB that in turn led to the attenuation of the inflammatory response.\n\nKefir-isolated bacteria and yeasts inhibit Shigella flexneri invasion and modulate pro-inflammatory response on intestinal epithelial cells.", "token_count": 129, "char_count": 510, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:31.263402", "source": { "split": "train_shard_00000", "doc_id": 4214 }, "chunk_id": "train_shard_00000_4214_1", "global_id": 4692 }, { "text": "Taurine (TAU) is a sulfur-containing amino acid that is involved in a diverse array of biological and physiological functions, including bile salt conjugation, osmoregulation, membrane stabilization, calcium modulation, anti-oxidation, and immunomodulation. Several studies have established that treatment with TAU significantly protects cerebral, cardiac and testicular injury from ischemia-reperfusion (IR). The purpose of the present study was to examine the effect of TAU on intestinal recovery and enterocyte turnover after intestinal IR injury in rats.\n\nEffect of taurine on intestinal recovery following intestinal ischemia-reperfusion injury in a rat.", "token_count": 165, "char_count": 659, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7126, "quality_score": 0.8563, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:31.707533", "source": { "split": "train_shard_00000", "doc_id": 4215 }, "chunk_id": "train_shard_00000_4215_0", "global_id": 4693 }, { "text": "The dosing of drugs in an aqueous cyclodextrin formulation requires sufficient amount of cyclodextrins to fully solubilize the drug, as described by Stella's cyclodextrin utility number (UCD). However, this framework does not take biopharmaceutical elements into account, such as the displacement of drug from the cyclodextrin cavity by bile salts present in the small intestine. As bile salts in the intestine are present at concentrations above the critical micelle concentration, an understanding of the interaction between cyclodextrins and bile salts at such supramicellar concentrations (SMC) is required for a better biopharmaceutical understanding of the release mechanism from orally dosed cyclodextrin complexes. To address this, experiments were conducted by isothermal titration calorimetry to determine how various β-cyclodextrins and bile salt interacts at SMC. Combined analysis of the current results and earlier data demonstrated that direct interactions between bile salt micelles and cyclodextrin were negligible. From this knowledge, an extended form of the UCD was suggested to describe the concentration of cyclodextrins to achieve full drug solubilization in the intestine where bile salts are present. Dosing cyclodextrins above this limit will diminish the free drug concentration, potentially decreasing the amount of drug absorbed.\n\nDisplacement of Drugs From Cyclodextrin Complexes by Bile Salts: A Suggestion of an Intestinal Drug-Solubilizing Capacity From an In Vitro Model.", "token_count": 368, "char_count": 1505, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:32.291694", "source": { "split": "train_shard_00000", "doc_id": 4216 }, "chunk_id": "train_shard_00000_4216_0", "global_id": 4694 }, { "text": "Pancreatic cancer (PC) is a devastating disease progressing asymptomatically until death within months after diagnosis. Defining at-risk populations should promote its earlier diagnosis and hence also avoid its development. Considering the known involvement in pancreatic disease of exon 11 of the bile salt-dependent lipase (BSDL) gene that encodes variable number of tandem repeat (VNTR) sequences, we hypothesized upon the existence of a genetic link between predisposition to PC and mutations in VNTR loci. To test this, BSDL VNTR were amplified by touchdown-PCR performed on genomic DNA extracted from cancer tissue or blood samples from a French patient cohort and amplicons were Sanger sequenced. A robust method using probes for droplet digital (dd)-PCR was designed to discriminate the C/C major from C/T or T/T minor genotypes. We report that the c.1719C > T transition (SNP rs488087) present in BSDL VNTR may be a useful marker for defining a population at risk of developing PC (occurrence: 63.90% in the PC versus 27.30% in the control group). The odds ratio of 4.7 for the T allele was larger than those already determined for other SNPs suspected to be predictive of PC. Further studies on tumor pancreatic tissue suggested that a germline T allele may favor Kras G12R/G12D somatic mutations which represent negative prognostic factors associated with reduced survival. We propose that the detection of the T allele in rs488087 SNP should lead to an in-depth follow-up of patients in whom an association with other potential risk factors of pancreatic cancer may be present.\n\nRs488087 single nucleotide polymorphism as predictive risk factor for pancreatic cancers.", "token_count": 437, "char_count": 1680, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8352, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:32.923339", "source": { "split": "train_shard_00000", "doc_id": 4217 }, "chunk_id": "train_shard_00000_4217_0", "global_id": 4695 }, { "text": "The present work describes the synthesis and photophysical studies of two fluorescent dansylamide derivatives, in which the amine group is acylated by a long hydrophobic chain (a part of a biologically relevant palmitic acid) and by a short hydrophobic tail (a part of acetic acid). The long chain tethered dansyl analogue is successfully utilized in estimating critical micellar concentration (CMC) of bile salts (NaDC, NaC) as well as anionic and cationic surfactants (SDS, CTAB) with the help of enhanced fluorescence intensity facilitated by better solubilization of the molecule in microheterogeneous media. The long chain tethered dansylamide derivative shows significant fluorescence solvatochromism with a red shift (ca. 4000 cm(-1)) from hexane to water. In contrast, the solvatochromism exhibited by the parent/short acyl chain analogue is much less (ca. 2230 cm(-1) from hexane to water) and the fluorescence is not sensitive to micellization. Interestingly, the long chain tethered fluorescent probe shows high sensitivity towards premicellar aggregation of sodium deoxycholate (NaDC) bile salt, through a clear blue shift of emission maxima and concomitant enhancement of fluorescent intensity. Such an observation of fluorescence sensing of premicellar aggregation is unusual.\n\nFluorescence of N-acylated dansylamide with a long hydrophobic tail: sensitive response to premicellar aggregation of sodium deoxycholate.", "token_count": 383, "char_count": 1430, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5891, "quality_score": 0.7946, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:33.507107", "source": { "split": "train_shard_00000", "doc_id": 4218 }, "chunk_id": "train_shard_00000_4218_0", "global_id": 4696 }, { "text": "Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits.\n\nPangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.", "token_count": 124, "char_count": 523, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:33.907864", "source": { "split": "train_shard_00000", "doc_id": 4219 }, "chunk_id": "train_shard_00000_4219_0", "global_id": 4697 }, { "text": "The pangenomic diversity in Burkholderia pseudomallei is high, with approximately 5.8% of the genome consisting of genomic islands. Genomic islands are known hotspots for recombination driven primarily by site-specific recombination associated with tRNAs. However, recombination rates in other portions of the genome are also high, a feature we expected to disrupt gene order. We analyzed the pangenome of 37 isolates of B. pseudomallei and demonstrate that the pangenome is 'open', with approximately 136 new genes identified with each new genome sequenced, and that the global core genome consists of 4568±16 homologs. Genes associated with metabolism were statistically overrepresented in the core genome, and genes associated with mobile elements, disease, and motility were primarily associated with accessory portions of the pangenome. The frequency distribution of genes present in between 1 and 37 of the genomes analyzed matches well with a model of genome evolution in which 96% of the genome has very low recombination rates but 4% of the genome recombines readily. Using homologous genes among pairs of genomes, we found that gene order was highly conserved among strains, despite the high recombination rates previously observed. High rates of gene transfer and recombination are incompatible with retaining gene order unless these processes are either highly localized to specific sites within the genome, or are characterized by symmetrical gene gain and loss. Our results demonstrate that both processes occur: localized recombination introduces many new genes at relatively few sites, and recombination throughout the genome generates the novel multi-locus sequence types previously observed while preserving gene order.\n\nPangenome Analysis of Burkholderia pseudomallei: Genome Evolution Preserves Gene Order despite High Recombination Rates.", "token_count": 417, "char_count": 1859, "word_count": 268, "semantic_coherence": 1, "information_density": 0.541, "quality_score": 0.7705, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:34.566507", "source": { "split": "train_shard_00000", "doc_id": 4220 }, "chunk_id": "train_shard_00000_4220_0", "global_id": 4698 }, { "text": "The objectives of this study were to (i) investigate the impact of feeding oat on the population of bifidobacteria and (ii) evaluate their probiotic potential. In this study, we investigated the effects of supplementing sows' gestation and lactation feed with 15% oat (prebiotic source) on the levels of probiotic population in milk. We found that dietary inclusion of oat during lactation and gestation resulted in increased levels of bifidobacteria compared to lactobacilli in sow milk. Furthermore bifidobacteria within the sow milk samples were further evaluated for probiotic potential based on aggregating properties, and acid- and bile-tolerance after exposure to hydrochloric acid (pH 2.5) and bile salts (0%, 0.25%, 0.50%, 1.0% and 2.0%). All isolates survived under the condition of low pH and bile 2.0%. Autoaggregation ability ranged from 17.5% to 73%. These isolates also showed antimicrobial activity against E. coli O157:H7.Together our results suggest that inclusion of oat in feeding systems could have the potential to improve the intestinal health of piglets by increasing the population of bifidobacteria.\n\nInclusion of Oat in Feeding Can Increase the Potential Probiotic Bifidobacteria in Sow Milk.", "token_count": 337, "char_count": 1219, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.8049, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:35.159353", "source": { "split": "train_shard_00000", "doc_id": 4221 }, "chunk_id": "train_shard_00000_4221_0", "global_id": 4699 }, { "text": "KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an integrated database resource for biological interpretation of genome sequences and other high-throughput data. Molecular functions of genes and proteins are associated with ortholog groups and stored in the KEGG Orthology (KO) database. The KEGG pathway maps, BRITE hierarchies and KEGG modules are developed as networks of KO nodes, representing high-level functions of the cell and the organism. Currently, more than 4000 complete genomes are annotated with KOs in the KEGG GENES database, which can be used as a reference data set for KO assignment and subsequent reconstruction of KEGG pathways and other molecular networks. As an annotation resource, the following improvements have been made. First, each KO record is re-examined and associated with protein sequence data used in experiments of functional characterization. Second, the GENES database now includes viruses, plasmids, and the addendum category for functionally characterized proteins that are not represented in complete genomes. Third, new automatic annotation servers, BlastKOALA and GhostKOALA, are made available utilizing the non-redundant pangenome data set generated from the GENES database. As a resource for translational bioinformatics, various data sets are created for antimicrobial resistance and drug interaction networks.\n\nKEGG as a reference resource for gene and protein annotation.", "token_count": 334, "char_count": 1433, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:36.478039", "source": { "split": "train_shard_00000", "doc_id": 4222 }, "chunk_id": "train_shard_00000_4222_0", "global_id": 4700 }, { "text": "Hepatitis B virus (HBV) is one of the world's major unconquered infections, resulting in progressive liver disease, and current treatments rarely cure infection. A limitation to discovering new therapies is our limited knowledge of HBV entry and dissemination pathways that hinders the development of in vitro culture systems. To address this gap in our understanding we optimized the genesis of infectious lentiviral pseudoparticles (HBVpps). The recent discovery that the bile salt transporter sodium taurocholate co-transporting polypeptide (NTCP) acts as a receptor for HBV enabled us to assess the receptor dependency of HBVpp infection. HBVpps preferentially infect hepatoma cells expressing NTCP, whereas other non-liver cells engineered to express NTCP do not support infection, suggesting that additional hepatocyte-specific factors are required for HBVpp internalization. These results highlight the value of the HBVpp system to dissect the pathways of HBV entry and dissemination.\n\nLentiviral hepatitis B pseudotype entry requires sodium taurocholate co-transporting polypeptide and additional hepatocyte-specific factors.", "token_count": 279, "char_count": 1133, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6883, "quality_score": 0.8442, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:37.027020", "source": { "split": "train_shard_00000", "doc_id": 4223 }, "chunk_id": "train_shard_00000_4223_0", "global_id": 4701 }, { "text": "The aim of this study was to gain knowledge about the role of triacylglycerol (TAG) composition in fatty acids (FA) of o/w emulsions on both the pancreatic lipolysis kinetics and the bioaccessibility of released products (i.e. contained within the bile salt micellar phase). A mathematical model was developed and its predictions were compared to a set of experimental data obtained during an in vitro digestion of a whey protein stabilized emulsion. Modeling results show that FA residues of TAG were hydrolyzed at specific rates, inducing different bioaccessibility kinetics. The estimated lipolysis rate constants of the studied FA (C8:0, C10:0≫C18:1 n-9≫C12:0>C14:0>C16:0≈C16:1 n-7>C22:6 n-3) were in close agreement with the available literature on the substrate specificity of pancreatic lipase. Results also suggest that lipolysis products are very rapidly solubilized in the bile salt mixed micelles with no fractionation according to the FA carbon chain.\n\nDynamic modeling of in vitro lipid digestion: individual fatty acid release and bioaccessibility kinetics.", "token_count": 292, "char_count": 1071, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:37.586788", "source": { "split": "train_shard_00000", "doc_id": 4224 }, "chunk_id": "train_shard_00000_4224_0", "global_id": 4702 }, { "text": "Streptococcus agalactiae, or Group B streptococcus (GBS), is a highly virulent pathogen in aquatic animals, causing huge mortalities worldwide. In Thailand, the serotype Ia, β-hemolytic GBS, belonging to sequence type (ST) 7 of clonal complex (CC) 7, was found to be the major cause of streptococcosis outbreaks in fish farms. In this study, we performed an in silico genomic comparison, aiming to investigate the phylogenetic relationship between the pathogenic fish strains of Thai ST7 and other ST7 from different hosts and geographical origins. In general, the genomes of Thai ST7 strains are closely related to other fish ST7s, as the core genome is shared by 92-95% of any individual fish ST7 genome. Among the fish ST7 genomes, we observed only small dissimilarities, based on the analysis of clustered regularly interspaced short palindromic repeats (CRISPRs), surface protein markers, insertions sequence (IS) elements and putative virulence genes. The phylogenetic tree based on single nucleotide polymorphisms (SNPs) of the core genome sequences clearly categorized the ST7 strains according to their geographical and host origins, with the human ST7 being genetically distant from other fish ST7 strains. A pan-genome analysis of ST7 strains detected a 48-kb gene island specifically in the Thai ST7 isolates. The orientations and predicted amino acid sequences of the genes in the island closely matched those of Tn5252, a streptococcal conjugative transposon, in GBS 2603V/R serotype V, Streptococcus pneumoniae and Streptococcus suis. Thus, it was presumed that Thai ST7 acquired this Tn5252 homologue from related streptococci. The close phylogenetic relationship between the fish ST7 strains suggests that these strains were derived from a common ancestor and have diverged in different geographical regions and in different hosts.", "token_count": 494, "char_count": 1848, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [ "ST7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:38.240374", "source": { "split": "train_shard_00000", "doc_id": 4225 }, "chunk_id": "train_shard_00000_4225_0", "global_id": 4703 }, { "text": "Genomic comparison between pathogenic Streptococcus agalactiae isolated from Nile tilapia in Thailand and fish-derived ST7 strains.", "token_count": 36, "char_count": 131, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:38.597158", "source": { "split": "train_shard_00000", "doc_id": 4225 }, "chunk_id": "train_shard_00000_4225_1", "global_id": 4704 }, { "text": "Vibrio metoecus is the closest relative of Vibrio cholerae, the causative agent of the potent diarrheal disease cholera. Although the pathogenic potential of this new species is yet to be studied in depth, it has been co-isolated with V. cholerae in coastal waters and found in clinical specimens in the United States. We used these two organisms to investigate the genetic interaction between closely related species in their natural environment. The genomes of 20 V. cholerae and 4 V. metoecus strains isolated from a brackish coastal pond on the US east coast, as well as 4 clinical V. metoecus strains were sequenced and compared with reference strains. Whole genome comparison shows 86-87% average nucleotide identity (ANI) in their core genes between the two species. On the other hand, the chromosomal integron, which occupies approximately 3% of their genomes, shows higher conservation in ANI between species than any other region of their genomes. The ANI of 93-94% observed in this region is not significantly greater within than between species, meaning that it does not follow species boundaries. Vibrio metoecus does not encode toxigenic V. cholerae major virulence factors, the cholera toxin and toxin-coregulated pilus. However, some of the pathogenicity islands found in pandemic V. cholerae were either present in the common ancestor it shares with V. metoecus, or acquired by clinical and environmental V. metoecus in partial fragments. The virulence factors of V. cholerae are therefore both more ancient and more widespread than previously believed. There is high interspecies recombination in the core genome, which has been detected in 24% of the single-copy core genes, including genes involved in pathogenicity. Vibrio metoecus was six times more often the recipient of DNA from V. cholerae as it was the donor, indicating a strong bias in the direction of gene transfer in the environment.", "token_count": 478, "char_count": 1915, "word_count": 301, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:39.241185", "source": { "split": "train_shard_00000", "doc_id": 4226 }, "chunk_id": "train_shard_00000_4226_0", "global_id": 4705 }, { "text": "The Dynamics of Genetic Interactions between Vibrio metoecus and Vibrio cholerae, Two Close Relatives Co-Occurring in the Environment.", "token_count": 38, "char_count": 134, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:39.598675", "source": { "split": "train_shard_00000", "doc_id": 4226 }, "chunk_id": "train_shard_00000_4226_1", "global_id": 4706 }, { "text": "Accumulating evidence suggests that probiotic bacteria play a vital role in modulating various aspects integral to the health and well-being of humans. In the present study, probiotic attributes and the antioxidant, anti-inflammatory and neuromodulatory potential of Enterococcus faecium CFR 3003 were investigated by employing suitable model systems. E. faecium exhibited robust resistance to gastrointestinal stress conditions as it could withstand acid stress at pH 1.5, 2 and 3. The bacterium also survived at a bile salt concentration of 0.45 %, and better tolerance was observed towards pepsin and trypsin. E. faecium produced lactic acid as a major metabolic product, followed by butyric acid. Lyophilized cell-free supernatant (LCS) of E. faecium exhibited significant antioxidant capacity evaluated against 1,1-diphenyl-2-picryl-hydrazyl, ascorbate auto-oxidation, oxygen radical absorbance and reducing power. Interestingly, E. faecium, Lactobacillus rhamnosus GG MTCC 1408 and LCS showed a significant anti-inflammatory effect by negatively modulating TNF-α production and upregulating IL-10 levels in LPS-stimulated macrophage cell lines. In an in vivo mice model, the propensity of probiotic supplements to modulate endogenous oxidative markers and redox status in brain regions was assessed. Young mice provided with oral supplements (daily for 28 days) of E. faecium and L. rhamnosus exhibited diminished oxidative markers in the brain and enhanced activities of antioxidant enzymes with a concomitant increase in γ-aminobutyric acid and dopamine levels. Collectively, our findings clearly suggest the propensity of these bacteria to protect against tissue damage mediated through free radicals and inflammatory cytokines. Although the underlying molecular mechanisms need further studies, it is tempting to speculate that probiotics confer a neuroprotective advantage in vivo against oxidative damage-mediated neurodegenerative conditions.", "token_count": 520, "char_count": 1955, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6868, "quality_score": 0.8434, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:41:40.234897", "source": { "split": "train_shard_00000", "doc_id": 4227 }, "chunk_id": "train_shard_00000_4227_0", "global_id": 4707 }, { "text": "Probiotic attributes, antioxidant, anti-inflammatory and neuromodulatory effects of Enterococcus faecium CFR 3003: in vitro and in vivo evidence.", "token_count": 49, "char_count": 145, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:40.597653", "source": { "split": "train_shard_00000", "doc_id": 4227 }, "chunk_id": "train_shard_00000_4227_1", "global_id": 4708 }, { "text": "Biliary atresia (BA) is a severe chronic cholestasis disorder of infants that leads to death if not treated on time. Neonatal hepatitis syndrome (NHS) is another leading cause of neonatal cholestasis confounding the diagnosis of BA. Recent studies indicate that altered bile acid metabolism is closely associated with liver injury and cholestasis. In this study, we systematically measured the bile acid metabolome in plasma of BA, NHS, and healthy controls. Liver bile acids were also measured using biopsy samples from 48 BA and 16 NHS infants undergoing operative cholangiography as well as 5 normal adjacent nontumor liver tissues taken from hepatoblastoma patients as controls. Both BA and NHS samples had significantly elevated bile acid levels in plasma compared to normal controls. BA patients showed a distinct bile acid profile characterized by the higher taurochenodeoxycholic acid (TCDCA) level and lower chenodeoxycholic acid (CDCA) level than those in NHS patients. The ratio of TCDCA to CDCA in plasma was significantly higher in BA compared to healthy infants (p < 0.001) or NHS (p < 0.001). The area under receiver operating characteristic curve for TCDCA/CDCA to differentiate BA from NHS was 0.923 (95% CI: 0.862-0.984). These findings were supported by significantly altered expression levels of bile acid transporters and nuclear receptors in liver including farnesoid X receptor (FXR), small heterodimer partner (SHP), bile salt export pump (BSEP), and multidrug resistant protein 3 (MDR3) in BA compared to NHS. Taken together, the plasma bile acid profiles are distinct in BA, NHS, and normal infants, as characterized by the ratio of TCDCA/CDCA differentially distributed among the three groups of infants.\n\nDistinct Plasma Bile Acid Profiles of Biliary Atresia and Neonatal Hepatitis Syndrome.", "token_count": 484, "char_count": 1819, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5812, "quality_score": 0.7906, "entities": { "genes": [ "MDR3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:41.249747", "source": { "split": "train_shard_00000", "doc_id": 4228 }, "chunk_id": "train_shard_00000_4228_0", "global_id": 4709 }, { "text": "Genetic variation in an infectious disease pathogen can be driven by ecological niche dissimilarities arising from different host species and different geographical locations. Whole genome sequencing was used to compare E. coli O157 isolates from host reservoirs (cattle and sheep) from Scotland and to compare genetic variation of isolates (human, animal, environmental/food) obtained from Scotland, New Zealand, Netherlands, Canada and the USA. Nei's genetic distance calculated from core genome single nucleotide polymorphisms (SNPs) demonstrated that the animal isolates were from the same population. Investigation of the Shiga toxin bacteriophage and their insertion sites (SBI typing) revealed that cattle and sheep isolates had statistically indistinguishable rarefaction profiles, diversity and genotypes. In contrast, isolates from different countries exhibited significant differences in Nei's genetic distance and SBI typing. Hence, after successful international transmission, which has occurred on multiple occasions, local genetic variation occurs, resulting in a global patchwork of continental and trans-continental phylogeographic clades. These findings are important for three reasons: first, understanding transmission and evolution of infectious diseases associated with multiple host reservoirs and multi-geographic locations; second, highlighting the relevance of the sheep reservoir when considering farm based interventions; and third, improving our understanding of why human disease incidence varies across the world.\n\nWhole Genome Sequencing demonstrates that Geographic Variation of Escherichia coli O157 Genotypes Dominates Host Association.", "token_count": 348, "char_count": 1671, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:41.823943", "source": { "split": "train_shard_00000", "doc_id": 4229 }, "chunk_id": "train_shard_00000_4229_0", "global_id": 4710 }, { "text": "Autophagy is a conserved degradation process in which autophagosomes are generated by cooperative actions of multiple autophagy-related (Atg) proteins. Previous studies using the model yeast Saccharomyces cerevisiae have provided various insights into the molecular basis of autophagy; however, because of the modest stability of several Atg proteins, structural and biochemical studies have been limited to a subset of Atg proteins, preventing us from understanding how multiple Atg proteins function cooperatively in autophagosome formation. With the goal of expanding the scope of autophagy research, we sought to identify a novel organism with stable Atg proteins that would be advantageous for in vitro analyses. Thus, we focused on a newly isolated thermotolerant yeast strain, Kluyveromyces marxianus DMKU3-1042, to utilize as a novel system elucidating autophagy. We developed experimental methods to monitor autophagy in K. marxianus cells, identified the complete set of K. marxianus Atg homologs, and confirmed that each Atg homolog is engaged in autophagosome formation. Biochemical and bioinformatic analyses revealed that recombinant K. marxianus Atg proteins have superior thermostability and solubility as compared with S. cerevisiae Atg proteins, probably due to the shorter primary sequences of KmAtg proteins. Furthermore, bioinformatic analyses showed that more than half of K. marxianus open reading frames are relatively short in length. These features make K. marxianus proteins broadly applicable as tools for structural and biochemical studies, not only in the autophagy field but also in other fields.\n\nThe Thermotolerant Yeast Kluyveromyces marxianus Is a Useful Organism for Structural and Biochemical Studies of Autophagy.", "token_count": 434, "char_count": 1751, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5927, "quality_score": 0.7964, "entities": { "genes": [ "DMKU3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:42.453803", "source": { "split": "train_shard_00000", "doc_id": 4230 }, "chunk_id": "train_shard_00000_4230_0", "global_id": 4711 }, { "text": "The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position.\n\nThe bacterial pangenome as a new tool for analysing pathogenic bacteria.", "token_count": 182, "char_count": 766, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:42.906952", "source": { "split": "train_shard_00000", "doc_id": 4231 }, "chunk_id": "train_shard_00000_4231_0", "global_id": 4712 }, { "text": "Bacterial vaginosis is one of the most common urogenital diseases affecting women in reproductive age. The administration of probiotics as vaginal suppository has been proposed as a strategy to cure this condition and reduce its recurrence. Nonetheless, also oral consumption of probiotics, which is a more practical route of administration, proved to be an efficient strategy. In this perspective, we studied Lactobacillus paracasei LPC-S01 (DSM 26760), a human vaginal isolate included in commercial probiotic preparations for topical use, in order to assess if this bacterium can also perform as gastrointestinal probiotic. Comparative genomics revealed the presence of several accessory genes suggesting that LPC-S01 is a niche-generalist member of its species. According to a procedure conventionally used to predict the probiotic potential, we demonstrated that the probiotic properties of strain LPC-S01, with respect to those of the well-known probiotic references L. paracasei Shirota and DG, are equal for the bile tolerance and the reduction of NF-κB activation in Caco-2 cells, or superior for the tolerance to gastric juice and the adhesion to Caco-2 epithelial cells. We then demonstrated that LPC-S01 is susceptible to antibiotics indicated by EFSA and does not produce biogenic amines. Finally, a double-blind cross-over pilot intervention trial on healthy human volunteers showed that, after a 7-days oral consumption of capsules containing about 24 billion live cells, the fecal cell concentrations of strains LPC-S01 and DG (evaluated by qPCR) were not dissimilar. Specifically, both probiotics' cell concentrations were above the detection limit for an average of 5 days from the end of the treatment, corresponding to a mean number of evacuations of 7 ± 2. Taken together, these data demonstrate that the vaginal isolate L. paracasei LPC-S01 possesses safety and functional properties that may support its use as probiotic to be administered per os for potential intestinal as well as vaginal applications.", "token_count": 497, "char_count": 2027, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6436, "quality_score": 0.8218, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:43.556318", "source": { "split": "train_shard_00000", "doc_id": 4232 }, "chunk_id": "train_shard_00000_4232_0", "global_id": 4713 }, { "text": "The vaginal isolate Lactobacillus paracasei LPC-S01 (DSM 26760) is suitable for oral administration.", "token_count": 37, "char_count": 100, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:43.918889", "source": { "split": "train_shard_00000", "doc_id": 4232 }, "chunk_id": "train_shard_00000_4232_1", "global_id": 4714 }, { "text": "Comparative genomics, metagenomics, and single-cell technologies have shown that populations of microbial species encompass assemblages of closely related strains. This raises the question of whether individual bacterial lineages respond to the presence of their close relatives by modifying their gene expression or, instead, whether assemblages simply act as the arithmetic addition of their individual components. Here, we took advantage of transcriptome sequencing to address this question. For this, we analyzed the transcriptomes of two closely related strains of the extremely halophilic bacterium Salinibacter ruber grown axenically and in coculture. These organisms dominate bacterial assemblages in hypersaline environments worldwide. The strains used here cooccurred in the natural environment and are 100% identical in their 16S rRNA genes, and each strain harbors an accessory genome representing 10% of its complete genome. Overall, transcriptomic patterns from pure cultures were very similar for both strains. Expression was detected along practically the whole genome albeit with some genes at low levels. A subset of genes was very highly expressed in both strains, including genes coding for the light-driven proton pump xanthorhodopsin, genes involved in the stress response, and genes coding for transcriptional regulators. Expression differences between pure cultures affected mainly genes involved in environmental sensing. When the strains were grown in coculture, there was a modest but significant change in their individual transcription patterns compared to those in pure culture. Each strain sensed the presence of the other and responded in a specific manner, which points to fine intraspecific transcriptomic modulation.\n\nInteractions between closely related bacterial strains are revealed by deep transcriptome sequencing.", "token_count": 387, "char_count": 1854, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:44.536623", "source": { "split": "train_shard_00000", "doc_id": 4233 }, "chunk_id": "train_shard_00000_4233_0", "global_id": 4715 }, { "text": "This study investigated dioxin-induced changes in metabolomes in pubertal rat excrement. The administration of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) or restricting dietary intake (pair-fed group) markedly altered the metabolomic profile including lipids, hormones, and vitamins in the urine and feces. TCDD caused an increase in the fecal chenodeoxycholic acid and taurocholic acid content and in urinary adrenaline and 17β-estradiol, while the urinary melatonin level was reduced by TCDD. These changes were not observed in the pair-fed group. In accordance with the elevated level of fecal bile acids, TCDD reduced the intestinal expression of the apical sodium-dependent bile salt transporter, which plays a role in resorbing bile acids from the bile duct. In addition, CYP7A1, a rate-limiting enzyme for bile acid biosynthesis, was attenuated by TCDD treatment, although TCDD induced hepatic CYP8B1, an enzyme essential for cholic acid synthesis. Supplying cholic acid or chenodeoxycholic acid to TCDD-exposed rats tended to restore the TCDD-produced reduction in serum triglycerides, whereas no similar trend was observed in wasting syndrome and lipid accumulation in the liver. These results suggest that: 1) TCDD alters the circulating levels of bile acids and hormones via a mechanism distinct from an attenuation in dietary intake, although the majority of TCDD-induced changes in nutrient contents in the excrement is due to a reduction in food intake; and 2) TCDD facilitates the excretion of bile acids and disrupts their biosynthesis, resulting in the disturbance of lipid homeostasis.\n\nDioxin-Produced Alteration in the Profiles of Fecal and Urinary Metabolomes: A Change in Bile Acids and Its Relevance to Toxicity.", "token_count": 501, "char_count": 1735, "word_count": 253, "semantic_coherence": 1, "information_density": 0.585, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:45.192045", "source": { "split": "train_shard_00000", "doc_id": 4234 }, "chunk_id": "train_shard_00000_4234_0", "global_id": 4716 }, { "text": "We have determined the expression pattern of key pancreatic enzymes precursors (trypsinogen, try; chymotrypsinogen, ctrb; phospholipase A2, pla2; bile salt-activated lipase, cel; and α-amylase, amy2a) during the larval stage of gilthead seabream (Sparus aurata) up to 60days after hatching (dph). Previously, complete sequences of try, cel, and amy2a were cloned and phylogenetically analyzed. One new isoform was found for cel transcript (cel1b). Expression of all enzyme precursors was detected before the mouth opening. Expression of try and ctrb increased during the first days of development and then maintained high values with some fluctuations during the whole larval stage. The prolipases pla2 and cel1b increased from first-feeding with irregular fluctuation until the end of the experiment. Contrarily, cel1a maintained low expression values during most of the larval stage increasing at the end of the period. Nevertheless, cel1a expression was negligible as compared with cel1b. The expression of amy2a sharply increased during the first week followed by a gradual decrease. In addition, a food-deprivation experiment was performed to find the differences in relation to presence/absence of gut content after the opening of the mouth. The food-deprived larvae died at 10dph. The expression levels of all digestive enzymes increased up to 7dph, declining sharply afterwards. This expression pattern up to 7dph was the same observed in fed larvae, confirming the genetic programming during the early development. Main digestive enzymes in gilthead seabream larvae exhibited the same expression profiles than other marine fish with carnivorous preferences in their juvenile stages.\n\nCloning and molecular ontogeny of digestive enzymes in fed and food-deprived developing gilthead seabream (Sparus aurata) larvae.", "token_count": 479, "char_count": 1822, "word_count": 263, "semantic_coherence": 1, "information_density": 0.597, "quality_score": 0.7985, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:45.882555", "source": { "split": "train_shard_00000", "doc_id": 4235 }, "chunk_id": "train_shard_00000_4235_0", "global_id": 4717 }, { "text": "The protective effects of encapsulation on the survival of Lactobacillus reuteri and the retention of the bacterium's probiotic properties under simulated gastrointestinal conditions were investigated. Viable counts and the remaining probiotic properties of calcium (Ca)-alginate encapsulated (A group), chitosan-Ca-alginate encapsulated (CA group), and unencapsulated, free L. reuteri (F group) were determined. Encapsulation improved the survival of L. reuteri subjected to simulated gastrointestinal conditions, with the greatest protective effect achieved in the CA group. The degree of cell membrane injury increased with increasing bile salt concentrations at constant pH, but the extent of injury was less in the encapsulated than in the free cells. Adherence rates were, in descending order: CA (0.524%)>A (0.360%)>F (0.275%). Lactobacillus reuteri cells retained their antagonistic activity toward Listeria monocytogenes even after incubation of the lactobacilli under simulated gastrointestinal conditions. Displacement of the pathogen by cells released from either of the encapsulation matrices was higher than that by free cells. The safety of L. reuteri was demonstrated in an in vitro invasion assay.\n\nProperties of Lactobacillus reuteri chitosan-calcium-alginate encapsulation under simulated gastrointestinal conditions.", "token_count": 346, "char_count": 1336, "word_count": 176, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:46.476452", "source": { "split": "train_shard_00000", "doc_id": 4236 }, "chunk_id": "train_shard_00000_4236_0", "global_id": 4718 }, { "text": "Nineteen fungi and seven yeast strains were isolated from sugarcane bagasse piles from an alcohol plant located at Brazilian Cerrado and identified up to species level on the basis of the gene sequencing of 5.8S-ITS and 26S ribosomal DNA regions. Four species were identified: Kluyveromyces marxianus, Aspergillus niger, Aspergillus sydowii and Aspergillus fumigatus, and the isolates were screened for the production of key enzymes in the saccharification of lignocellulosic material. Among them, three strains were selected as good producers of hemicellulolitic enzymes: A. niger (SBCM3), A. sydowii (SBCM7) and A. fumigatus (SBC4). The best β-xylosidase producer was A. niger SBCM3 strain. This crude enzyme presented optimal activity at pH 3.5 and 55 °C (141 U/g). For β-glucosidase and xylanase the best producer was A. fumigatus SBC4 strain, whose enzymes presented maximum activity at 60 °C and pH 3.5 (54 U/g) and 4.0 (573 U/g), respectively. All these crude enzymes presented stability around pH 3.0-8.0 and up to 60 °C, which can be very useful in industrial processes that work at high temperatures and low pHs. These enzymes also exhibited moderate tolerance to ethanol and the sugars glucose and xylose. These similar characteristics among these fungal crude enzymes suggest that they can be used synergistically in cocktails in future studies of biomass conversion with potential application in several biotechnological sectors.\n\nThermotolerant and mesophylic fungi from sugarcane bagasse and their prospection for biomass-degrading enzyme production.", "token_count": 471, "char_count": 1565, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [ "SBC4", "SBCM7", "SBCM3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:47.160847", "source": { "split": "train_shard_00000", "doc_id": 4237 }, "chunk_id": "train_shard_00000_4237_0", "global_id": 4719 }, { "text": "For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost-effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data.\n\nPanFP: pangenome-based functional profiles for microbial communities.", "token_count": 207, "char_count": 1038, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:47.662369", "source": { "split": "train_shard_00000", "doc_id": 4238 }, "chunk_id": "train_shard_00000_4238_0", "global_id": 4720 }, { "text": "Drug-induced liver injury (DILI) is a leading cause of acute hepatic failure and a major reason for market withdrawal of drugs. Idiosyncratic DILI is multifactorial, with unclear dose-dependency and poor predictability since the underlying patient-related susceptibilities are not sufficiently understood. Because of these limitations, a pharmaceutical research option would be to reduce the compound-related risk factors in the drug-discovery process. Here we describe the development and validation of a methodology for the assessment of DILI risk of drug candidates. As a training set, 81 marketed or withdrawn compounds with differing DILI rates - according to the FDA categorization - were tested in a combination of assays covering different mechanisms and endpoints contributing to human DILI. These include the generation of reactive metabolites (CYP3A4 time-dependent inhibition and glutathione adduct formation), inhibition of the human bile salt export pump (BSEP), mitochondrial toxicity and cytotoxicity (fibroblasts and human hepatocytes). Different approaches for dose- and exposure-based calibrations were assessed and the same parameters applied to a test set of 39 different compounds. We achieved a similar performance to the training set with an overall accuracy of 79% correctly predicted, a sensitivity of 76% and a specificity of 82%. This test system may be applied in a prospective manner to reduce the risk of idiosyncratic DILI of drug candidates.\n\nMinimizing DILI risk in drug discovery - A screening tool for drug candidates.", "token_count": 360, "char_count": 1554, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8084, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:48.255662", "source": { "split": "train_shard_00000", "doc_id": 4239 }, "chunk_id": "train_shard_00000_4239_0", "global_id": 4721 }, { "text": "To understand how different diets, the consumers' gut microbiota, and the enteric nervous system (ENS) interact to regulate gut motility, we developed a gnotobiotic mouse model that mimics short-term dietary changes that happen when humans are traveling to places with different culinary traditions. Studying animals transplanted with the microbiota from humans representing diverse culinary traditions and fed a sequence of diets representing those of all donors, we found that correlations between bacterial species abundances and transit times are diet dependent. However, the levels of unconjugated bile acids-generated by bacterial bile salt hydrolases (BSH)-correlated with faster transit, including during consumption of a Bangladeshi diet. Mice harboring a consortium of sequenced cultured bacterial strains from the Bangladeshi donor's microbiota and fed a Bangladeshi diet revealed that the commonly used cholekinetic spice, turmeric, affects gut motility through a mechanism that reflects bacterial BSH activity and Ret signaling in the ENS. These results demonstrate how a single food ingredient interacts with a functional microbiota trait to regulate host physiology.\n\nRegulators of gut motility revealed by a gnotobiotic model of diet-microbiome interactions related to travel.", "token_count": 290, "char_count": 1292, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:48.814042", "source": { "split": "train_shard_00000", "doc_id": 4240 }, "chunk_id": "train_shard_00000_4240_0", "global_id": 4722 }, { "text": "Oncofetal fucose-rich glycovariants of the pathological bile salt-dependent lipase (pBSDL) appear during human pancreatic oncogenesis and are detected by themonoclonal antibody J28 (mAbJ28). We aimed to identify murine counterparts onpancreatic ductal adenocarcinoma (PDAC) cells and tissue and investigate the potential of dendritic cells (DC) loaded with this unique pancreatic tumor antigen to promote immunotherapy in preclinical trials. Pathological BSDLs purified from pancreatic juices of patients with PDAC were cleaved to generate glycosylated C-terminal moieties (C-ter) containing mAbJ28-reactive glycoepitopes. Immunoreactivity of the murine PDAC line Panc02 and tumor tissue to mAbJ28 was detected by immunohistochemistry and flow cytometry. C-ter-J28+ immunization promoted Th1-dominated immune responses. In vitro C-ter-J28+-loaded DCskewed CD3+ T-cells toward Th1 polarization. C-ter-J28+-DC-vaccinations selectively enhanced cell immunoreactivity to Panc02, as demonstrated by CD4+- and CD8+-T-cell activation, increased percentages of CD4+- and CD8+-T-cells and NK1.1+ cells expressing granzyme B, and T-cell cytotoxicity. Prophylactic and therapeutic C-ter-J28+-DC-vaccinations reduced ectopic Panc02-tumor growth, provided long-lasting protection from Panc02-tumor development in 100% of micebut not from melanoma, and attenuated progression of orthotopic tumors as revealed by MRI. Thusmurine DC loaded with pancreatic tumor-specific glycoepitope C-ter-J28+ induce efficient anticancer adaptive immunity and represent a potential adjuvant therapy for patients afflicted with PDAC.", "token_count": 497, "char_count": 1601, "word_count": 196, "semantic_coherence": 1, "information_density": 0.7296, "quality_score": 0.8648, "entities": { "genes": [ "CD8", "CD3", "NK1", "CD4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:49.465511", "source": { "split": "train_shard_00000", "doc_id": 4241 }, "chunk_id": "train_shard_00000_4241_0", "global_id": 4723 }, { "text": "A pancreatic tumor-specific biomarker characterized in humans and mice as an immunogenic onco-glycoprotein is efficient in dendritic cell vaccination.", "token_count": 43, "char_count": 150, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:49.821478", "source": { "split": "train_shard_00000", "doc_id": 4241 }, "chunk_id": "train_shard_00000_4241_1", "global_id": 4724 }, { "text": "Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism(SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.\n\nCore Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.", "token_count": 460, "char_count": 1862, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:50.461066", "source": { "split": "train_shard_00000", "doc_id": 4242 }, "chunk_id": "train_shard_00000_4242_0", "global_id": 4725 }, { "text": "The O-specific antigen (OSA) in Pseudomonas aeruginosa lipopolysaccharide is highly varied by sugar identity, side chains, and bond between O-repeats. These differences classified P. aeruginosa into 20 distinct serotypes. In the past few decades, O12 has emerged as the predominant serotype in clinical settings and outbreaks. These serotype O12 isolates exhibit high levels of resistance to various classes of antibiotics. Here, we explore how the P. aeruginosa OSA biosynthesis gene clusters evolve in the population by investigating the association between the phylogenetic relationships among 83 P. aeruginosa strains and their serotypes. While most serotypes were closely linked to the core genome phylogeny, we observed horizontal exchange of OSA biosynthesis genes among phylogenetically distinct P. aeruginosa strains. Specifically, we identified a \"serotype island\" ranging from 62 kb to 185 kb containing the P. aeruginosa O12 OSA gene cluster, an antibiotic resistance determinant (gyrA(C248T)), and other genes that have been transferred between P. aeruginosa strains with distinct core genome architectures. We showed that these genes were likely acquired from an O12 serotype strain that is closely related to P. aeruginosa PA7. Acquisition and recombination of the \"serotype island\" resulted in displacement of the native OSA gene cluster and expression of the O12 serotype in the recipients. Serotype switching by recombination has apparently occurred multiple times involving bacteria of various genomic backgrounds. In conclusion, serotype switching in combination with acquisition of an antibiotic resistance determinant most likely contributed to the dissemination of the O12 serotype in clinical settings.\n\nThe Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters.", "token_count": 482, "char_count": 1913, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5301, "quality_score": 0.765, "entities": { "genes": [ "PA7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:51.104553", "source": { "split": "train_shard_00000", "doc_id": 4243 }, "chunk_id": "train_shard_00000_4243_0", "global_id": 4726 }, { "text": "The progressive rise in energy crisis followed by green house gas (GHG) emissions is serving as the driving force for bioethanol production from renewable resources. Current bioethanol research focuses on lignocellulosic feedstocks as these are abundantly available, renewable, sustainable and exhibit no competition between the crops for food and fuel. However, the technologies in use have some drawbacks including incapability of pentose fermentation, reduced tolerance to products formed, costly processes, etc. Therefore, the present study was carried out with the objective of isolating hexose and pentose fermenting thermophilic/thermotolerant ethanologens with acceptable product yield. Two thermotolerant isolates, NIRE-K1 and NIRE-K3 were screened for fermenting both glucose and xylose and identified as Kluyveromyces marxianus NIRE-K1 and K. marxianus NIRE-K3. After optimization using Face-centered Central Composite Design (FCCD), the growth parameters like temperature and pH were found to be 45.17°C and 5.49, respectively for K. marxianus NIRE-K1 and 45.41°C and 5.24, respectively for K. marxianus NIRE-K3. Further, batch fermentations were carried out under optimized conditions, where K. marxianus NIRE-K3 was found to be superior over K. marxianus NIRE-K1. Ethanol yield (Y x∕s ), sugar to ethanol conversion rate (%), microbial biomass concentration (X) and volumetric product productivity (Q p ) obtained by K. marxianus NIRE-K3 were found to be 9.3, 9.55, 14.63, and 31.94% higher than that of K. marxianus NIRE-K1, respectively. This study revealed the promising potential of both the screened thermotolerant isolates for bioethanol production.\n\nA new search for thermotolerant yeasts, its characterization and optimization using response surface methodology for ethanol production.", "token_count": 505, "char_count": 1807, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6653, "quality_score": 0.8327, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:51.759024", "source": { "split": "train_shard_00000", "doc_id": 4244 }, "chunk_id": "train_shard_00000_4244_0", "global_id": 4727 }, { "text": "Bacillus subtilis is the focus of both academic and industrial research. Previous studies have reported a number of sequence variations in different B. subtilis strains. To uncover the genetic variation and evolutionary pressure in B. subtilis strains, we performed whole genome sequencing of two B. subtilis isolates, KM and CGMCC63528. Comparative genomic analyses of these two strains with other B. subtilis strains identified high sequence variations including large insertions, deletions and SNPs. Most SNPs in genes were synonymous and the average frequency of synonymous mutations was significantly higher than that of the non-synonymous mutations. Pan-genome analysis of B. subtilis strains showed that the core genome had lower dN/dS values than the accessory genome. Whole genome comparisons of these two isolates with other B. subtilis strains showed that strains in different subspecies have similar dN/dS values. Nucleotide diversity analysis showed that spizizenii subspecies have higher nucleotide diversity than subtilis subspecies. Our results indicate that genes in B. subtilis strains are under high purifying selection pressure. The evolutionary pressure in different subspecies of B. subtilis is complex.\n\nGenomic Diversity and Evolution of Bacillus subtilis.", "token_count": 311, "char_count": 1280, "word_count": 182, "semantic_coherence": 1, "information_density": 0.5385, "quality_score": 0.7692, "entities": { "genes": [ "CGMCC63528" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:52.335887", "source": { "split": "train_shard_00000", "doc_id": 4245 }, "chunk_id": "train_shard_00000_4245_0", "global_id": 4728 }, { "text": "In this study, we evaluated the probiotic properties of Lactobacillus plantarum, Lactobacillus pentosus, and Lactobacillus fermentum strains isolated from fermented radish. All the strains survived the simulated oro-gastrointestinal transit condition and showed significantly higher adherence to Caco-2 cells compared with the probiotic strain Lactobacillus rhamnosus GG. The strains showed broad-spectrum antimicrobial activity, autoaggregation, and coaggregation capacity with pathogens. Furthermore, the Lactobacillus strains inhibited the adherence of Yersinia enterocolitica subsp. enterocolitica, Shigella boydii, and Salmonella choleraesuis to the Caco-2 cell line. The strains possessed bile salt hydrolase activity and their cholesterol-lowering activity in vitro was above 50% in the presence of bile. Strains of L. plantarum and L. pentosus possessed the plantaricin-encoding plnEF gene. In addition, the Lactobacillus strains maintained about 80% cell viability after freeze-drying in the presence of a combination of 5% skim milk and 5% maltodextrin as cryoprotectant, and 70% recovery of cell viability was observed in the absence of any cryoprotectant.\n\nIn vitro probiotic characterization of Lactobacillus strains from fermented radish and their anti-adherence activity against enteric pathogens.", "token_count": 374, "char_count": 1312, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5906, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:52.916146", "source": { "split": "train_shard_00000", "doc_id": 4246 }, "chunk_id": "train_shard_00000_4246_0", "global_id": 4729 }, { "text": "Streptococcus suis is a major swine pathogen and a zoonotic agent. Serotype 2 strains are the most frequently associated with disease. However, not all serotype 2 lineages are considered virulent. Indeed, sequence type (ST) 28 serotype 2 S. suis strains have been described as a homogeneous group of low virulence. However, ST28 strains are often isolated from diseased swine in some countries, and at least four human ST28 cases have been reported. Here, we used whole-genome sequencing and animal infection models to test the hypothesis that the ST28 lineage comprises strains of different genetic backgrounds and different virulence. We used 50 S. suis ST28 strains isolated in Canada, the United States and Japan from diseased pigs, and one ST28 strain from a human case isolated in Thailand. We report a complex population structure among the 51 ST28 strains. Diversity resulted from variable gene content, recombination events and numerous genome-wide polymorphisms not attributable to recombination. Phylogenetic analysis using core genome single-nucleotide polymorphisms revealed four discrete clades with strong geographic structure, and a fifth clade formed by US, Thai and Japanese strains. When tested in experimental animal models, strains from this latter clade were significantly more virulent than a Canadian ST28 reference strain, and a closely related Canadian strain. Our results highlight the limitations of MLST for both phylogenetic analysis and virulence prediction and raise concerns about the possible emergence of ST28 strains in human clinical cases.\n\nComplex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28.", "token_count": 409, "char_count": 1708, "word_count": 252, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [ "ST28" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:53.537721", "source": { "split": "train_shard_00000", "doc_id": 4247 }, "chunk_id": "train_shard_00000_4247_0", "global_id": 4730 }, { "text": "The Farnesoid X receptor (FXR) regulates bile salt, glucose and cholesterol homeostasis by binding to DNA response elements, thereby activating gene expression (direct transactivation). FXR also inhibits the immune response via tethering to NF-κB (tethering transrepression). FXR activation therefore has therapeutic potential for liver and intestinal inflammatory diseases. We aim to identify and develop gene-selective FXR modulators, which repress inflammation, but do not interfere with its metabolic capacity. In a high-throughput reporter-based screen, mometasone furoate (MF) was identified as a compound that reduced NF-κB reporter activity in an FXR-dependent manner. MF reduced mRNA expression of pro-inflammatory cytokines, and induction of direct FXR target genes in HepG2-GFP-FXR cells and intestinal organoids was minor. Computational studies disclosed three putative binding modes of the compound within the ligand binding domain of the receptor. Interestingly, mutation of W469A residue within the FXR ligand binding domain abrogated the decrease in NF-κB activity. Finally, we show that MF-bound FXR inhibits NF-κB subunit p65 recruitment to the DNA of pro-inflammatory genes CXCL2 and IL8. Although MF is not suitable as selective anti-inflammatory FXR ligand due to nanomolar affinity for the glucocorticoid receptor, we show that separation between metabolic and anti-inflammatory functions of FXR can be achieved.\n\nThe glucocorticoid mometasone furoate is a novel FXR ligand that decreases inflammatory but not metabolic gene expression.", "token_count": 422, "char_count": 1558, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [ "CXCL2", "IL8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:54.161811", "source": { "split": "train_shard_00000", "doc_id": 4248 }, "chunk_id": "train_shard_00000_4248_0", "global_id": 4731 }, { "text": "Detailed laboratory characterization of Escherichia coli O157 is essential to inform epidemiological investigations. This study assessed the utility of whole-genome sequencing (WGS) for outbreak detection and epidemiological surveillance of E. coli O157, and the data were used to identify discernible associations between genotypes and clinical outcomes. One hundred five E. coli O157 strains isolated over a 5-year period from human fecal samples in Lothian, Scotland, were sequenced with the Ion Torrent Personal Genome Machine. A total of 8,721 variable sites in the core genome were identified among the 105 isolates; 47% of the single nucleotide polymorphisms (SNPs) were attributable to six \"atypical\" E. coli O157 strains and included recombinant regions. Phylogenetic analyses showed that WGS correlated well with the epidemiological data. Epidemiological links existed between cases whose isolates differed by three or fewer SNPs. WGS also correlated well with multilocus variable-number tandem repeat analysis (MLVA) typing data, with only three discordant results observed, all among isolates from cases not known to be epidemiologically related. WGS produced a better-supported, higher-resolution phylogeny than MLVA, confirming that the method is more suitable for epidemiological surveillance of E. coli O157. A combination of in silico analyses (VirulenceFinder, ResFinder, and local BLAST searches) were used to determine stx subtypes, multilocus sequence types (15 loci), and the presence of virulence and acquired antimicrobial resistance genes. There was a high level of correlation between the WGS data and our routine typing methods, although some discordant results were observed, mostly related to the limitation of short sequence read assembly. The data were used to identify sublineages and clades of E. coli O157, and when they were correlated with the clinical outcome data, they showed that one clade, Ic3, was significantly associated with severe disease. Together, the results show that WGS data can provide higher resolution of the relationships between E. coli O157 isolates than that provided by MLVA", "token_count": 518, "char_count": 2134, "word_count": 310, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:41:54.819413", "source": { "split": "train_shard_00000", "doc_id": 4249 }, "chunk_id": "train_shard_00000_4249_0", "global_id": 4732 }, { "text": "The method has the potential to streamline the laboratory workflow and provide detailed information for the clinical management of patients and public health interventions.\n\nUtility of Whole-Genome Sequencing of Escherichia coli O157 for Outbreak Detection and Epidemiological Surveillance.", "token_count": 65, "char_count": 290, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:55.185392", "source": { "split": "train_shard_00000", "doc_id": 4249 }, "chunk_id": "train_shard_00000_4249_1", "global_id": 4733 }, { "text": "In this article, we have investigated the effect of a hydrophilic ionic liquid, 1-butyl-3-methylimidazolium tetrafluoroborate ([bmim]-BF4), on the aggregation properties of a biological surfactant, sodium deoxycholate (NaDC), in water. In solution, unlike conventional surfactants it shows stepwise aggregation and the effect of the conventional ionic liquid on the aggregation properties is rather interesting. We have observed concentration dependent dual role of the ionic liquid; at their low concentration, the aggregated structure of NaDC reorganizes itself into an elongated rod like structure. However, the aggregated network is disintegrated into small aggregates upon further addition of ionic liquid. TEM (Transmission Electron Microscopy), SEM (Scanning Electron Microscopy) and FLIM (Fluorescence Lifetime Imaging Microscopy) images also confirmed the structural alteration of NaDC upon varying the concentration of the ionic liquid. The proton NMR data indicate that hydrophobic as well as electrostatic interaction is solely responsible for such structural adaptation of NaDC in the presence of an ionic liquid. The host-guest interaction inside the aggregates is monitored using Coumarin-153 (C-153) and the location of C-153 is probed by varying the excitation wavelength from 375 nm to 440 nm and the two binding sites of the aggregates are affected in a different fashion in the presence of ionic liquid. Excitation in the blue region selects the fluorophores which preferably bind to the buried region of the aggregates, whereas 440 nm excitation corresponds to the guest molecules which are exposed to the solvent molecules. The average solvation time of C-153 is increased in the presence of 1.68 wt% [bmim]-BF4 at λexc = 440 nm i.e. the probe molecules relocate themselves to a more restricted region. However, the average solvation time became 2.6 times faster in the presence of 11.2 wt% [bmim]-BF4, which corresponds to a more polar and exposed region", "token_count": 509, "char_count": 1977, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5563, "quality_score": 0.7782, "entities": { "genes": [ "BF4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:55.821923", "source": { "split": "train_shard_00000", "doc_id": 4250 }, "chunk_id": "train_shard_00000_4250_0", "global_id": 4734 }, { "text": "The time resolved anisotropy measurements and polarity determined by pyrene also supported our results in addition to solvation dynamics measurements. In summary, ionic liquids can modulate the host-guest interaction of bile salt aggregates, which can be used as nanocarriers for drug delivery.\n\nModulation of the aggregation properties of sodium deoxycholate in presence of hydrophilic imidazolium based ionic liquid: water dynamics study to probe the structural alteration of the aggregates.", "token_count": 112, "char_count": 493, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7971, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:56.204512", "source": { "split": "train_shard_00000", "doc_id": 4250 }, "chunk_id": "train_shard_00000_4250_1", "global_id": 4735 }, { "text": "To understand the growth-promoting and disease-inhibiting activities of plant growth-promoting rhizobacteria (PGPR) strains, the genomes of 12 Bacillus subtilis group strains with PGPR activity were sequenced and analyzed. These B. subtilis strains exhibited high genomic diversity, whereas the genomes of B. amyloliquefaciens strains (a member of the B. subtilis group) are highly conserved. A pairwise BLASTp matrix revealed that gene family similarity among Bacillus genomes ranges from 32 to 90%, with 2839 genes within the core genome of B. amyloliquefaciens subsp. plantarum. Comparative genomic analyses of B. amyloliquefaciens strains identified genes that are linked with biological control and colonization of roots and/or leaves, including 73 genes uniquely associated with subsp. plantarum strains that have predicted functions related to signaling, transportation, secondary metabolite production, and carbon source utilization. Although B. amyloliquefaciens subsp. plantarum strains contain gene clusters that encode many different secondary metabolites, only polyketide biosynthetic clusters that encode difficidin and macrolactin are conserved within this subspecies. To evaluate their role in plant pathogen biocontrol, genes involved in secondary metabolite biosynthesis were deleted in a B. amyloliquefaciens subsp. plantarum strain, revealing that difficidin expression is critical in reducing the severity of disease, caused by Xanthomonas axonopodis pv. vesicatoria in tomato plants. This study defines genomic features of PGPR strains and links them with biocontrol activity and with host colonization.\n\nDeciphering the conserved genetic loci implicated in plant disease control through comparative genomics of Bacillus amyloliquefaciens subsp. plantarum.", "token_count": 455, "char_count": 1778, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:57.204699", "source": { "split": "train_shard_00000", "doc_id": 4251 }, "chunk_id": "train_shard_00000_4251_0", "global_id": 4736 }, { "text": "The consensus view of olfactory processing is that the axons of receptor-specific primary olfactory sensory neurons (OSNs) converge to a small subset of glomeruli, thus preserving the odour identity before the olfactory information is processed in higher brain centres. In the present study, we show that two different subsets of ciliated OSNs with different odorant specificities converge to the same glomeruli. In order to stain different ciliated OSNs in the crucian carp Carassius carassius we used two different chemical odorants, a bile salt and a purported alarm substance, together with fluorescent dextrans. The dye is transported within the axons and stains glomeruli in the olfactory bulb. Interestingly, the axons from the ciliated OSNs co-converge to the same glomeruli. Despite intermingled innervation of glomeruli, axons and terminal fields from the two different subsets of ciliated OSNs remained mono-coloured. By 4-6 days after staining, the dye was transported trans-synaptically to separately stained axons of relay neurons. These findings demonstrate that specificity of the primary neurons is retained in the olfactory pathways despite mixed innervation of the olfactory glomeruli. The results are discussed in relation to the emerging concepts about non-mammalian glomeruli.\n\nMixed input to olfactory glomeruli from two subsets of ciliated sensory neurons does not impede relay neuron specificity in the crucian carp.", "token_count": 353, "char_count": 1441, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5213, "quality_score": 0.7607, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:57.785618", "source": { "split": "train_shard_00000", "doc_id": 4252 }, "chunk_id": "train_shard_00000_4252_0", "global_id": 4737 }, { "text": "Microbial contamination in food processing plants can play a fundamental role in food quality and safety. In this study, the microbiota in a dairy plant was studied by both 16S rRNA- and 26S rRNA-based culture-independent high-throughput amplicon sequencing. Environmental samples from surfaces and tools were studied along with the different types of cheese produced in the same plant. The microbiota of environmental swabs was very complex, including more than 200 operational taxonomic units with extremely variable relative abundances (0.01 to 99%) depending on the species and sample. A core microbiota shared by 70% of the samples indicated a coexistence of lactic acid bacteria with a remarkable level of Streptococcus thermophilus and possible spoilage-associated bacteria, including Pseudomonas, Acinetobacter, and Psychrobacter, with a relative abundance above 50%. The most abundant yeasts were Kluyveromyces marxianus, Yamadazyma triangularis, Trichosporon faecale, and Debaryomyces hansenii. Beta-diversity analyses showed a clear separation of environmental and cheese samples based on both yeast and bacterial community structure. In addition, predicted metagenomes also indicated differential distribution of metabolic pathways between the two categories of samples. Cooccurrence and coexclusion pattern analyses indicated that the occurrence of potential spoilers was excluded by lactic acid bacteria. In addition, their persistence in the environment can be helpful to counter the development of potential spoilers that may contaminate the cheeses, with possible negative effects on their microbiological quality.\n\nCoexistence of Lactic Acid Bacteria and Potential Spoilage Microbiota in a Dairy Processing Environment.", "token_count": 406, "char_count": 1737, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:58.416596", "source": { "split": "train_shard_00000", "doc_id": 4253 }, "chunk_id": "train_shard_00000_4253_0", "global_id": 4738 }, { "text": "Reconstruction of the regulatory network is an important step in understanding how organisms control the expression of gene products and therefore phenotypes. Recent studies have pointed out the importance of regulatory network plasticity in bacterial adaptation and evolution. The evolution of such networks within and outside the species boundary is however still obscure. Sinorhizobium meliloti is an ideal species for such study, having three large replicons, many genomes available and a significant knowledge of its transcription factors (TF). Each replicon has a specific functional and evolutionary mark; which might also emerge from the analysis of their regulatory signatures. Here we have studied the plasticity of the regulatory network within and outside the S. meliloti species, looking for the presence of 41 TFs binding motifs in 51 strains and 5 related rhizobial species. We have detected a preference of several TFs for one of the three replicons, and the function of regulated genes was found to be in accordance with the overall replicon functional signature: house-keeping functions for the chromosome, metabolism for the chromid, symbiosis for the megaplasmid. This therefore suggests a replicon-specific wiring of the regulatory network in the S. meliloti species. At the same time a significant part of the predicted regulatory network is shared between the chromosome and the chromid, thus adding an additional layer by which the chromid integrates itself in the core genome. Furthermore, the regulatory network distance was found to be correlated with both promoter regions and accessory genome evolution inside the species, indicating that both pangenome compartments are involved in the regulatory network evolution. We also observed that genes which are not included in the species regulatory network are more likely to belong to the accessory genome, indicating that regulatory interactions should also be considered to predict gene conservation in bacterial pangenomes.\n\nEvolution of Intra-specific Regulatory Networks in a Multipartite Bacterial Genome.", "token_count": 431, "char_count": 2086, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5357, "quality_score": 0.7679, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:59.065273", "source": { "split": "train_shard_00000", "doc_id": 4254 }, "chunk_id": "train_shard_00000_4254_0", "global_id": 4739 }, { "text": "This study is aimed at unrevealing the yeast diversity of handmade cheese, Tomme d'orchies, produced and marketed in the north of France. A total of 185 yeast colonies were isolated from the surface and core of this cheese. From these, 80 morphologically different colonies were selected and subjected to rep-PCR analysis. The isolates were clustered into six distinct groups based on their DNA fingerprints. From each group, at least 30% of isolates were selected and identified to species level by biochemical characteristics (ID32C Api system) and sequencing of the ITS1-5.8S-ITS2 and 26S rDNA regions. The isolates belonged to Yarrowia lipolytica, Debaryomyces hansenii, Kluyveromyces lactis and Kluyveromyces marxianus, frequently isolated, and less frequently isolated Saturnispora mendoncae and Clavispora lusitaniae. Two isolates designated as Kluyveromyces lactis (isolate S-3-05) and Kluyveromyces marxianus (isolate S-2-05) were non-hemolytic, sensitive to antifungal compounds and able to inhibit the growth of pathogens including Candida albicans, Listeria monocytogenes and some bacilli.\n\nYeast diversity in a traditional French cheese \"Tomme d'orchies\" reveals infrequent and frequent species with associated benefits.", "token_count": 349, "char_count": 1233, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6824, "quality_score": 0.8412, "entities": { "genes": [ "ITS2", "ID32C", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:41:59.692620", "source": { "split": "train_shard_00000", "doc_id": 4255 }, "chunk_id": "train_shard_00000_4255_0", "global_id": 4740 }, { "text": "Few researchers have investigated the use of multiple physiological enhancers combined with synthetic carriers to augment delivery of nutraceuticals. The current work describes the development of an oral delivery system termed a bioactive association platform (BAP) capable of delivering nutraceutical actives from a formulation framework specifically for enhancing the in vitro and in vivo performance of model vitamin, cholecalciferol (Vitamin D\n\nA novel bile salts-lipase polymeric film-infused minitablet system for enhanced oral delivery of cholecalciferol.", "token_count": 126, "char_count": 562, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7867, "quality_score": 0.8933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:00.074947", "source": { "split": "train_shard_00000", "doc_id": 4256 }, "chunk_id": "train_shard_00000_4256_0", "global_id": 4741 }, { "text": "Oral drug delivery is the most preferred route for patients; however, the low solubility of drugs and the resultant poor absorption compromise the benefits of oral administration. On the other hand, for years, the overwhelmingly accepted mechanism for enhanced oral absorption using lipid nanocarriers was based on the process of lipid digestion and drug solubilization in the small intestine. Few reports indicated that other bypass pathways are involved in drug absorption in the gastrointestinal tract (GIT) for oral delivery of nanocarriers. Herein, we report a new nanoemulsion system with a denatured globular protein with a diameter of 30 nm, soybean protein isolates (SPI), and bile salt as emulsifiers, aiming to enhance the absorption of insoluble drugs and explore other pathways for absorption. A BCS class II drug, fenofibrate (FB), was used as the model drug. The SPI and bile salt-coated Ns with a diameter of approximately 150 nm were prepared via a high-pressure homogenizing procedure. Interestingly, the present Ns could be converted to solid dosage form using fluid-bed coating technology, maintaining a nanoscale size. Most importantly, in a model of in situ rat intestinal perfusion, Ns could penetrate across the intestinal epithelial barrier into the systemic circulation and then obtain biodistribution into other tissues. In addition, Ns significantly improved FB oral absorption, exhibited as a greater than 2- and 2.5-fold increase in Cmax and AUC0-t, respectively, compared to the suspension formulation. Overall, the present Ns are promising nanocarriers for the oral delivery of insoluble drugs, and the penetration of intact Ns across the GIT barrier into systemic circulation may be a new strategy for improved drug absorption with the use of nanocarriers.\n\nDenatured globular protein and bile salt-coated nanoparticles for poorly water-soluble drugs: Penetration across the intestinal epithelial barrier into the circulation system and enhanced oral bioavailability.", "token_count": 477, "char_count": 2000, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [ "AUC0" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:00.731320", "source": { "split": "train_shard_00000", "doc_id": 4257 }, "chunk_id": "train_shard_00000_4257_0", "global_id": 4742 }, { "text": "Kefir is a type of fermented milk containing lactic and acetic acid bacteria and yeast. In this study, we evaluated the antimicrobial activity of kefir supernatant against Cronobacter sakazakii in powdered infant formula (PIF). In a spot-on-lawn test, the growth of 20 C. sakazakii strains, including 10 clinical and 10 food isolates, was completely inhibited in the presence of kefir supernatant. Significant differences in the diameters of inhibition zones were observed upon treatment with kefir compared with the results for Lactobacillus kefiri and Candida kefyr culture supernatants or solutions of lactic and acetic acid and ethyl alcohol in the agar well diffusion test (P < 0.05). The addition of 100 μl of kefir supernatant to 1 ml of nutrient broth completely inhibited the growth of C. sakazakii, as evaluated by spectrophotometry. The antimicrobial activity of kefir supernatant in experimentally contaminated PIF was also tested; we found no viable C. sakazakii cells remaining in PIF rehydrated with 30% kefir supernatant solution for 1 h, demonstrating that the antimicrobial activity of kefir supernatant against C. sakazakii could be applied in real food samples.\n\nGrowth Inhibition of Cronobacter sakazakii in Experimentally Contaminated Powdered Infant Formula by Kefir Supernatant.", "token_count": 373, "char_count": 1302, "word_count": 195, "semantic_coherence": 1, "information_density": 0.559, "quality_score": 0.7795, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:01.322035", "source": { "split": "train_shard_00000", "doc_id": 4258 }, "chunk_id": "train_shard_00000_4258_0", "global_id": 4743 }, { "text": "The central idea observes a recursive mapping of [Formula: see text]-body intramolecular interactions to [Formula: see text]-body terms that is consistent with the molecular topology. Iterative application of the line graph transformation is identified as a natural and elegant tool to accomplish the recursion. The procedure readily generalizes to arbitrary [Formula: see text]-body potentials. In particular, the method yields a complete characterization of [Formula: see text]-body interactions. The hierarchical structure of atomic index lists for each interaction order [Formula: see text] is compactly expressed as a directed acyclic graph. A pseudo-code description of the generating algorithm is given. With suitable data structures (e.g., edge lists or adjacency matrices), automatic enumeration and indexing of [Formula: see text]-body interactions can be implemented straightforwardly to handle large bio-molecular systems. Explicit examples are discussed, including a chemically relevant effective potential model of taurocholate bile salt.\n\nEnumerating and indexing many-body intramolecular interactions: a graph theoretic approach.", "token_count": 246, "char_count": 1145, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:01.814130", "source": { "split": "train_shard_00000", "doc_id": 4259 }, "chunk_id": "train_shard_00000_4259_0", "global_id": 4744 }, { "text": "The ability of Escherichia coli O157:H7 to induce cellular damage leading to disease in humans is related to numerous virulence factors, most notably the stx gene, encoding Shiga toxin (Stx) and carried by a bacteriophage. Loss of the Stx-encoding bacteriophage may occur during infection or culturing of the strain. Here, we collected stx-positive and stx-negative variants of E. coli O157:H7/NM (nonmotile) isolates from patients with gastrointestinal complaints. Isolates were characterized by whole-genome sequencing (WGS), and their virulence properties and phylogenetic relationship were determined. Because of the presence of the eae gene but lack of the bfpA gene, the stx-negative isolates were considered atypical enteropathogenic E. coli (aEPEC). However, they had phenotypic characteristics similar to those of the Shiga toxin-producing E. coli (STEC) isolates and belonged to the same sequence type, ST11. Furthermore, EPEC and STEC isolates shared similar virulence genes, the locus of enterocyte effacement region, and plasmids. Core genome phylogenetic analysis using a gene-by-gene typing approach showed that the sorbitol-fermenting (SF) stx-negative isolates clustered together with an SF STEC isolate and that one non-sorbitol-fermenting (NSF) stx-negative isolate clustered together with NSF STEC isolates. Therefore, these stx-negative isolates were thought either to have lost the Stx phage or to be a progenitor of STEC O157:H7/NM. As detection of STEC infections is often based solely on the identification of the presence of stx genes, these may be misdiagnosed in routine laboratories. Therefore, an improved diagnostic approach is required to manage identification, strategies for treatment, and prevention of transmission of these potentially pathogenic strains.", "token_count": 472, "char_count": 1791, "word_count": 252, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:02.457384", "source": { "split": "train_shard_00000", "doc_id": 4260 }, "chunk_id": "train_shard_00000_4260_0", "global_id": 4745 }, { "text": "Is Shiga Toxin-Negative Escherichia coli O157:H7 Enteropathogenic or Enterohemorrhagic Escherichia coli? Comprehensive Molecular Analysis Using Whole-Genome Sequencing.", "token_count": 60, "char_count": 168, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:02.826507", "source": { "split": "train_shard_00000", "doc_id": 4260 }, "chunk_id": "train_shard_00000_4260_1", "global_id": 4746 }, { "text": "Thirty-nine strains of Kluyveromyces marxianus from Pecorino di Farindola cheese in comparison with 3 strains from Parmigiano Reggiano cheese, 1 from fermented milk, 3 from cow whey and two type strains K. marxianus CBS 834(T) and Kluyveromyces lactis CBS 683(T) were tested for genetic and metabolic characteristics. Intraspecific diversity of chromosome arrangements was evaluated by pulsed field gel electrophoresis (PFGE) analysis. Among K. marxianus strains chromosome polymorphisms were evident with 11 patterns that differed in size and number of the chromosomal bands. The number of the bands varied from 4 to 7 with sizes ranging from about 1.0 to 2.7 Mb. Twelve strains were selected for determining their growth capacity and volatile compound production in two wheys (raw cheese whey and ricotta cheese whey) under limited oxygen availability. The growth kinetics highlighted four different biotypes and the influence of whey composition on K. marxianus development. The main volatile compounds detected after the growth were alcohols, acids, esters, ketones and aldehydes. Ethanol was the most abundant in both wheys. Aldehydes and other minor compounds were produced only when the strains were inoculated in ricotta cheese whey, while esters, butanoic, decanoic and octanoic acids were qualitatively and quantitatively more present in raw cheese whey. This study highlights a great genetic and metabolic biodiversity within Pecorino di Farindola K. marxianus strains and it could be exploited to improve the knowledge of this yeast for biotechnological uses.\n\nChromosome arrangement, differentiation of growth kinetics and volatile molecule profiles in Kluyveromyces marxianus strains from Italian cheeses.", "token_count": 452, "char_count": 1719, "word_count": 250, "semantic_coherence": 1, "information_density": 0.612, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:03.466483", "source": { "split": "train_shard_00000", "doc_id": 4261 }, "chunk_id": "train_shard_00000_4261_0", "global_id": 4747 }, { "text": "This study investigated the functional diversity of Lactobacillus helveticus KLDS1.8701 by carrying out a whole-genome sequence analyses of L. helveticus KLDS1.8701. L. helveticus KLDS1.8701 strain was isolated from traditional sour milk in Sinkiang of China with desirable probiotic properties. Here we report the complete genome sequence of this organism and its genetic basis for adhesion, exopolysaccharides (EPS) production, acid and bile tolerance, bacteriocin production and immune system against bacteriophage.\n\nComplete genome sequence of Lactobacillus helveticus KLDS1.8701, a probiotic strain producing bacteriocin.", "token_count": 176, "char_count": 626, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7407, "quality_score": 0.8704, "entities": { "genes": [ "KLDS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:03.919080", "source": { "split": "train_shard_00000", "doc_id": 4262 }, "chunk_id": "train_shard_00000_4262_0", "global_id": 4748 }, { "text": "In perfused rat liver, hepatocyte shrinkage induces a Fyn-dependent retrieval of the bile salt export pump (Bsep) and multidrug resistance-associated protein 2 (Mrp2) from the canalicular membrane (Cantore, M., Reinehr, R., Sommerfeld, A., Becker, M., and Häussinger, D. (2011) J. Biol. Chem. 286, 45014-45029) leading to cholestasis. However little is known about the effects of hyperosmolarity on short term regulation of the Na(+)-taurocholate cotransporting polypeptide (Ntcp), the major bile salt uptake system at the sinusoidal membrane of hepatocytes. The aim of this study was to analyze hyperosmotic Ntcp regulation and the underlying signaling events. Hyperosmolarity induced a significant retrieval of Ntcp from the basolateral membrane, which was accompanied by an activating phosphorylation of the Src kinases Fyn and Yes but not of c-Src. Hyperosmotic internalization of Ntcp was sensitive to SU6656 and PP-2, suggesting that Fyn mediates Ntcp retrieval from the basolateral membrane. Hyperosmotic internalization of Ntcp was also found in livers from wild-type mice but not in p47(phox) knock-out mice. Tauroursodeoxycholate (TUDC) and cAMP reversed hyperosmolarity-induced Fyn activation and triggered re-insertion of the hyperosmotically retrieved Ntcp into the membrane. This was associated with dephosphorylation of the Ntcp on serine residues. Insertion of Ntcp by TUDC was sensitive to the integrin inhibitory hexapeptide GRGDSP and inhibition of protein kinase A. TUDC also reversed the hyperosmolarity-induced retrieval of bile salt export pump from the canalicular membrane. These findings suggest a coordinated and oxidative stress- and Fyn-dependent retrieval of sinusoidal and canalicular bile salt transport systems from the corresponding membranes", "token_count": 508, "char_count": 1776, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [ "SU6656" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:04.547800", "source": { "split": "train_shard_00000", "doc_id": 4263 }, "chunk_id": "train_shard_00000_4263_0", "global_id": 4749 }, { "text": "Ntcp insertion was also identified as a novel target of β1-integrin-dependent TUDC action, which is frequently used in the treatment of cholestatic liver disease.\n\nRegulation of plasma membrane localization of the Na+-taurocholate cotransporting polypeptide (Ntcp) by hyperosmolarity and tauroursodeoxycholate.", "token_count": 86, "char_count": 310, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8974, "quality_score": 0.9487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:04.931288", "source": { "split": "train_shard_00000", "doc_id": 4263 }, "chunk_id": "train_shard_00000_4263_1", "global_id": 4750 }, { "text": "The ubiquitous bacterial second messenger cyclic di-GMP (c-di-GMP) has recently become prominent as a trigger for biofilm formation in many bacteria. It is generated by diguanylate cyclases (DGCs; with GGDEF domains) and degraded by specific phosphodiesterases (PDEs; containing either EAL or HD-GYP domains). Most bacterial species contain multiples of these proteins with some having specific functions that are based on direct molecular interactions in addition to their enzymatic activities. Escherichia coli K-12 laboratory strains feature 29 genes encoding GGDEF and/or EAL domains, resulting in a set of 12 DGCs, 13 PDEs, and four enzymatically inactive \"degenerate\" proteins that act by direct macromolecular interactions. We present here a comparative analysis of GGDEF/EAL domain-encoding genes in 61 genomes of pathogenic, commensal, and probiotic E. coli strains (including enteric pathogens such as enteroaggregative, enterohemorrhagic, enteropathogenic, enterotoxigenic, and adherent and invasive Escherichia coli and the 2011 German outbreak O104:H4 strain, as well as extraintestinal pathogenic E. coli, such as uropathogenic and meningitis-associated E. coli). We describe additional genes for two membrane-associated DGCs (DgcX and DgcY) and four PDEs (the membrane-associated PdeT, as well as the EAL domain-only proteins PdeW, PdeX, and PdeY), thus showing the pangenome of E. coli to contain at least 35 GGDEF/EAL domain proteins. A core set of only eight proteins is absolutely conserved in all 61 strains: DgcC (YaiC), DgcI (YliF), PdeB (YlaB), PdeH (YhjH), PdeK (YhjK), PdeN (Rtn), and the degenerate proteins CsrD and CdgI (YeaI)", "token_count": 512, "char_count": 1654, "word_count": 237, "semantic_coherence": 1, "information_density": 0.7089, "quality_score": 0.8544, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:05.564377", "source": { "split": "train_shard_00000", "doc_id": 4264 }, "chunk_id": "train_shard_00000_4264_0", "global_id": 4751 }, { "text": "In all other GGDEF/EAL domain genes, diverse point and frameshift mutations, as well as small or large deletions, were discovered in various strains.\n\nGenome-Based Comparison of Cyclic Di-GMP Signaling in Pathogenic and Commensal Escherichia coli Strains.", "token_count": 72, "char_count": 255, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8611, "quality_score": 0.9306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:05.940360", "source": { "split": "train_shard_00000", "doc_id": 4264 }, "chunk_id": "train_shard_00000_4264_1", "global_id": 4752 }, { "text": "Food-borne pathogens are among the most significant problems in maintaining the health of people. Many probiotics have been widely reported to alleviate and protect against gastrointestinal infections through antibacterial secretion. However, the majority of them cannot always play antagonistic roles under gut conditions. Probiotic bacteria of human origin must possess other protective mechanisms to survive, out-compete intestinal flora and to successfully establish in their new host at a significant level.\n\nAntagonistic Characteristics Against Food-borne Pathogenic Bacteria of Lactic Acid Bacteria and Bifidobacteria Isolated from Feces of Healthy Thai Infants.", "token_count": 149, "char_count": 669, "word_count": 89, "semantic_coherence": 1, "information_density": 0.809, "quality_score": 0.9045, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:06.378292", "source": { "split": "train_shard_00000", "doc_id": 4265 }, "chunk_id": "train_shard_00000_4265_0", "global_id": 4753 }, { "text": "The study was aimed to characterize the probiotic properties of a Pediococcus pentosaceus strain, KID7, by in vitro and in vivo studies. The strain possessed tolerance to oro-gastrointestinal transit, adherence to the Caco-2 cell line, and antimicrobial activity. KID7 exhibited bile salt hydrolase activity and cholesterol-lowering activity, in vitro. In vivo cholesterol-lowering activity of KID7 was studied using atherogenic diet-fed hypercholesterolemic mice. The experimental animals (C57BL/6J mice) were divided into 4 groups viz., normal diet-fed group (NCD), atherogenic diet-fed group (HCD), atherogenic diet- and KID7-fed group (HCD-KID7), and atherogenic diet- and Lactobacillus acidophilus ATCC 43121-fed group (HCD-L.ac) as positive control. Serum total cholesterol (T-CHO) level was significantly decreased by 19.8% in the HCD-KID7 group (P < 0.05), but not in the HCD-L.ac group compared with the HCD group. LDL cholesterol levels in both HCD-KID7 and HCD-L.ac groups were decreased by 35.5 and 38.7%, respectively, compared with HCD group (both, P < 0.05). Glutamyl pyruvic transaminase (GPT) level was significantly lower in the HCD-KID7 and HCD-L.ac groups compared to HCD group and was equivalent to that of the NCD group. Liver T-CHO levels in the HCD-KID7 group were reduced significantly compared with the HCD group (P < 0.05) but not in the HCD-L.ac group", "token_count": 452, "char_count": 1379, "word_count": 203, "semantic_coherence": 1, "information_density": 0.5468, "quality_score": 0.7734, "entities": { "genes": [ "KID7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:07.016688", "source": { "split": "train_shard_00000", "doc_id": 4266 }, "chunk_id": "train_shard_00000_4266_0", "global_id": 4754 }, { "text": "Analysis of expression of genes associated with lipid metabolism in liver showed that low-density lipoprotein receptor (LDLR), cholesterol-7α-hydroxylase (CYP7A1) and apolipoprotein E (APOE) mRNA expression was significantly increase in the HCD-KID7 group compared to the HCD group. Furthermore, KID7 exhibited desired viability under freeze-drying and subsequent storage conditions with a combination of skim milk and galactomannan. P. pentosaceus KID7 could be a potential probiotic strain, which can be used to develop cholesterol-lowering functional food after appropriate human clinical trials.\n\nPreliminary probiotic and technological characterization of Pediococcus pentosaceus strain KID7 and in vivo assessment of its cholesterol-lowering activity.", "token_count": 198, "char_count": 757, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7835, "quality_score": 0.8918, "entities": { "genes": [ "KID7" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:07.463982", "source": { "split": "train_shard_00000", "doc_id": 4266 }, "chunk_id": "train_shard_00000_4266_1", "global_id": 4755 }, { "text": "Hospital-associated methicillin-resistant Staphylococcus aureus (MRSA) infections are frequently caused by predominant clusters of closely related isolates that cannot be discriminated by conventional diagnostic typing methods. Whole genome sequencing (WGS) and DNA microarray (MA) now allow for better discrimination within a prevalent clonal complex (CC). This single center exploratory study aims to distinguish invasive (blood stream infection) and non-invasive (nasal colonization) MRSA isolates of the same CC5 into phylogenetic- and virulence-associated genotypic subgroups by WGS and MA. A cohort of twelve blood stream and fifteen nasal MRSA isolates of CC5 (spa-types t003 and t504) was selected. Isolates were propagated at the same period of time from unrelated patients treated at the University of Saarland Medical Center, Germany. Rooted phylotyping based on WGS with core-genome single nucleotide polymorphism (SNP) analysis revealed two local clusters of closely related CC5 subgroups (t504 and Clade1 t003) which were separated from other local t003 isolates and from unrelated CC5 MRSA reference isolates of German origin. Phylogenetic subtyping was not associated with invasiveness when comparing blood stream and nasal isolates. Clustering based on MA profiles was not concordant with WGS phylotyping, but MA profiles may identify subgroups of isolates with nasal and blood stream origin. Among the new putative virulence associated genes identified by WGS, the strongest association with blood stream infections was shown for ebhB mutants. Analysis of the core-genome together with the accessory genome enables subtyping of closely related MRSA isolates according to phylogeny and presumably also to the potential virulence capacity of isolates.\n\nWhole genome sequence typing and microarray profiling of nasal and blood stream methicillin-resistant Staphylococcus aureus isolates: Clues to phylogeny and invasiveness.", "token_count": 482, "char_count": 1939, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5815, "quality_score": 0.7907, "entities": { "genes": [ "CC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:08.115080", "source": { "split": "train_shard_00000", "doc_id": 4267 }, "chunk_id": "train_shard_00000_4267_0", "global_id": 4756 }, { "text": "Two independent isolates of a Gram-stain-positive, facultatively anaerobic, motile, rod-shaped bacterium were recovered from cheonggukjang, a Korean fermented soybean paste food product. Preliminary sequencing analysis of the 16S rRNA gene indicated that these strains were related most closely to Bacillus sonorensis KCTC-13918T and Bacillus licheniformis DSM 13T. In phenotypic characterization, the novel strains were found to grow between 15 and 55 °C and to tolerate up to 8 % (w/v) NaCl. Furthermore, the strains grew in media of pH 5-10 (optimal growth at pH 7.0). The predominant cellular fatty acids were anteiso-C15 : 0 and iso-C15 : 0.The isoprenoid quinone was menaquinone 7 (MK-7). The cell-wall peptidoglycan contained meso-diaminopimelic acid. The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine and an unknown glycolipid. Draft genomes of the two strains were determined and in silico DNA-DNA hybridizations with their nearest neighbour (B. sonorensis KCTC-13918T) revealed 29.9 % relatedness for both strains. Phylogenomic analysis of the genomes was conducted with the core genome (799 genes) of all strains in the Bacillus subtilis group and the two strains formed a distinct monophyletic cluster. In addition, the strains differed from the two most closely related species in that they did not metabolize maltose, d-galactose, d-sorbitol or d-gluconic acid. The DNA G+C content was 45.9 mol%", "token_count": 482, "char_count": 1458, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:08.767761", "source": { "split": "train_shard_00000", "doc_id": 4268 }, "chunk_id": "train_shard_00000_4268_0", "global_id": 4757 }, { "text": "Based upon the consensus of phylogenetic and phenotypic analyses, these strains represent a novel species of the genus Bacillus, for which the name Bacillus glycinifermentans sp. nov. is proposed. The type strain is GO-13T ( = KACC 18425T = NRRL B-65291T).\n\nBacillus glycinifermentans sp. nov., isolated from fermented soybean paste.", "token_count": 124, "char_count": 333, "word_count": 50, "semantic_coherence": 1, "information_density": 0.82, "quality_score": 0.91, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:09.153413", "source": { "split": "train_shard_00000", "doc_id": 4268 }, "chunk_id": "train_shard_00000_4268_1", "global_id": 4758 }, { "text": "‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.", "token_count": 498, "char_count": 1345, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5753, "quality_score": 0.7877, "entities": { "genes": [ "XY18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:09.810658", "source": { "split": "train_shard_00000", "doc_id": 4269 }, "chunk_id": "train_shard_00000_4269_0", "global_id": 4759 }, { "text": "Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis.", "token_count": 35, "char_count": 106, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:10.206437", "source": { "split": "train_shard_00000", "doc_id": 4269 }, "chunk_id": "train_shard_00000_4269_1", "global_id": 4760 }, { "text": "Probiotic bacteria must have not only tolerance against bile salt but also no genes for antibiotic resistance. Leuconostoc citreum is a dominant lactic acid bacterium in various fermented foods, but it is not regarded as a probiotic because it lacks bile salt resistance. Therefore, we aimed to construct a bile salt-resistant L. citreum strain by transforming it with a bile salt hydrolase gene (bsh). We obtained the 1,001 bp bsh gene from the chromosomal DNA of Lactobacillus plantarum and subcloned it into the pCB4170 vector under a constitutive P710 promoter. The resulting vector, pCB4170BSH was transformed into L. citreum CB2567 by electroporation, and bile saltresistant transformants were selected. Upon incubation with glycodeoxycholic acid sodium salt (GDCA), the L. citreum transformants grew and formed colonies, successfully transcribed the bsh gene, and expressed the BSH enzyme. The recombinant strain grew in up to 0.3% (w/v) GDCA, conditions unsuitable for the host strain. In in vitro digestion conditions of 10 mM bile salt, the transformant was over 67.6% viable, whereas only 0.8% of the host strain survived.\n\nDevelopment of Bile Salt-Resistant Leuconostoc citreum by Expression of Bile Salt Hydrolase Gene.", "token_count": 357, "char_count": 1232, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8102, "entities": { "genes": [ "CB2567" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:10.808201", "source": { "split": "train_shard_00000", "doc_id": 4270 }, "chunk_id": "train_shard_00000_4270_0", "global_id": 4761 }, { "text": "The human gastrointestinal epithelium makes up the largest barrier separating the body from the external environment. Whereas invasive pathogens cause epithelial barrier disruption, probiotic micro-organisms modulate tight junction regulation and improve epithelial barrier function. In addition, probiotic strains may be able to reduce epithelial barrier disruption caused by pathogenic species. The aim of this study was to explore non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Benchmarking against established probiotic strains, we evaluated the ability of four nonpathogenic yeast species to modulate transepithelial electrical resistance (TER) across a monolayer of differentiated human colonocytes (Caco-2 cells). Further, we assessed yeast modulation of a Salmonella Typhimurium-induced epithelial cell barrier function insult. Our findings demonstrate distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function. While the established probiotic yeast Saccharomyces boulardii increased TER across a Caco-2 monolayer by 30%, Kluyveromyces marxianus exhibited significantly stronger properties of TER enhancement (50% TER increase). In addition, our data demonstrate significant yeast-mediated modulation of Salmonella-induced epithelial cell barrier disruption and identify K. marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion.\n\nNon-Saccharomyces yeasts protect against epithelial cell barrier disruption induced by Salmonella enterica subsp. enterica serovar Typhimurium.", "token_count": 409, "char_count": 1632, "word_count": 202, "semantic_coherence": 1, "information_density": 0.604, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:11.467688", "source": { "split": "train_shard_00000", "doc_id": 4271 }, "chunk_id": "train_shard_00000_4271_0", "global_id": 4762 }, { "text": "Fasiglifam (TAK-875), a selective G-protein-coupled receptor 40 agonist, was developed for the treatment of type 2 diabetes mellitus; however, its development was terminated in phase III clinical trials because of liver safety concerns. Our preliminary study indicated that intravenous administration of 100 mg/kg of TAK-875 increased the serum total bile acid concentration by 3 to 4 times and total bilirubin levels by 1.5 to 2.6 times in rats. In the present study, we examined the inhibitory effects of TAK-875 on hepatobiliary transporters to explore the mechanisms underlying its hepatotoxicity. TAK-875 decreased the biliary excretion index and the in vitro biliary clearance of d₈-taurocholic acid in sandwich-cultured rat hepatocytes, suggesting that TAK-875 impaired biliary excretion of bile acids, possibly by inhibiting bile salt export pump (Bsep). TAK-875 inhibited the efflux transporter multidrug resistance-associated protein 2 (Mrp2) in rat hepatocytes using 5 (and 6)-carboxy-2',7'-dichlorofluorescein as a substrate. Inhibition of MRP2 was further confirmed by reduced transport of vinblastine in Madin-Darby canine kidney cells overexpressing MRP2 with IC₅₀ values of 2.41 μM. TAK-875 also inhibited the major bile acid uptake transporter Na(+)/taurocholate cotransporting polypeptide (Ntcp), which transports d₈-taurocholic acid into rat hepatocytes, with an IC₅₀ value of 10.9 μM. TAK-875 significantly inhibited atorvastatin uptake in organic anion transporter protein (OATP) 1B1 and OATP1B3 cells with IC₅₀ values of 2.28 and 3.98 μM, respectively", "token_count": 514, "char_count": 1573, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:42:12.139317", "source": { "split": "train_shard_00000", "doc_id": 4272 }, "chunk_id": "train_shard_00000_4272_0", "global_id": 4763 }, { "text": "These results indicate that TAK-875 inhibited the efflux transporter MRP2/Mrp2 and uptake transporters Ntcp and OATP/Oatp, which may affect bile acid and bilirubin homeostasis, resulting in hyperbilirubinemia and cholestatic hepatotoxicity.\n\nFasiglifam (TAK-875) Inhibits Hepatobiliary Transporters: A Possible Factor Contributing to Fasiglifam-Induced Liver Injury.", "token_count": 126, "char_count": 366, "word_count": 43, "semantic_coherence": 1, "information_density": 0.9302, "quality_score": 0.9651, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:12.525127", "source": { "split": "train_shard_00000", "doc_id": 4272 }, "chunk_id": "train_shard_00000_4272_1", "global_id": 4764 }, { "text": "In 2013 Zhou et al. concluded that Salmonella enterica serovar Agona represents a genetically monomorphic lineage of recent ancestry, whose most recent common ancestor existed in 1932, or earlier. The Abstract stated 'Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s.' These conclusions have now been criticized by Pettengill, who claims that the evolutionary models used to date Agona may not have been appropriate, the dating estimates were inaccurate, and the age of emergence of Agona should have been qualified by an upper limit reflecting the date of its divergence from an outgroup, serovar Soerenga. We dispute these claims. Firstly, Pettengill's analysis of Agona is not justifiable on technical grounds. Secondly, an upper limit for divergence from an outgroup would only be meaningful if the outgroup were closely related to Agona, but close relatives of Agona are yet to be identified. Thirdly, it is not possible to reliably date the time of divergence between Agona and Soerenga. We conclude that Pettengill's criticism is comparable to a tempest in a teapot.\n\nFormal Comment to Pettengill: The Time to Most Recent Common Ancestor Does Not (Usually) Approximate the Date of Divergence.", "token_count": 356, "char_count": 1415, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:13.105636", "source": { "split": "train_shard_00000", "doc_id": 4273 }, "chunk_id": "train_shard_00000_4273_0", "global_id": 4765 }, { "text": "Ethanol production from non-crop materials, such as Jerusalem artichokes, would make a great contribution to the energy industry. The non-conventional yeast, Kluyveromyces marxianus, is able to carry out ethanol fermentation of sugar molecules obtained from inulin-containing materials by consolidated bioprocessing. Lower inulin concentrations and micro-aeration can lead to a relatively fast and ideal fermentation process; however, it is unclear what causes the inhibition of higher concentrations of inulin and the promotion effect of aeration.\n\nTranscriptional analysis of Kluyveromyces marxianus for ethanol production from inulin using consolidated bioprocessing technology.", "token_count": 163, "char_count": 681, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:13.543104", "source": { "split": "train_shard_00000", "doc_id": 4274 }, "chunk_id": "train_shard_00000_4274_0", "global_id": 4766 }, { "text": "Swertianlarin is an herbal agent abundantly distributed in Swertia mussotii Franch, a Chinese traditional herb used for treatment of jaundice. To study the therapeutic effect of swertianlarin on cholestasis, liver injury, serum proinflammatory cytokines, and bile salt concentrations were measured by comparing rats treated with swertianlarin 100 mg/kg/d or saline for 3, 7, or 14 days after bile duct ligation (BDL). Serum alanine aminotransferase (ATL) and aspartate aminotransferase (AST) levels were significantly decreased in BDL rats treated with swertianlarin for 14 days (P < 0.05). The reduced liver injury in BDL rats by swertianlarin treatment for 14 days was further confirmed by liver histopathology. Levels of serum tumor necrosis factor alpha (TNFα) were decreased by swertianlarin in BDL rats for 3 and 7 days (P < 0.05). Moreover, reductions in serum interleukins IL-1β and IL-6 levels were also observed in BDL rats treated with swertianlarin (P < 0.05). In addition, most of serum toxic bile salt concentrations (e.g., chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA)) in cholestatic rats were decreased by swertianlarin (P < 0.05). In conclusion, the data suggest that swertianlarin derived from Swertia mussotii Franch attenuates liver injury, inflammation, and cholestasis in bile duct-ligated rats.\n\nSwertianlarin, an Herbal Agent Derived from Swertia mussotii Franch, Attenuates Liver Injury, Inflammation, and Cholestasis in Common Bile Duct-Ligated Rats.", "token_count": 481, "char_count": 1487, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5115, "quality_score": 0.7558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:14.190062", "source": { "split": "train_shard_00000", "doc_id": 4275 }, "chunk_id": "train_shard_00000_4275_0", "global_id": 4767 }, { "text": "To investigate the effects of Kluyveromyces marxianus M3 isolated from Tibetan mushrooms on diet-induced hypercholesterolemia in rats, female Wistar rats were fed a high-cholesterol diet (HCD) for 28 d to generate hyperlipidemic models. Hyperlipidemic rats were assigned to four groups, which were individually treated with three different dosages of K. marxianus M3+HCD or physiological saline+HCD via oral gavage for 28 d. The total cholesterol (TC), triglycerides (TG), high-density lipoprotein cholesterol (HDL-C), and low-density lipoprotein cholesterol (LDL-C) levels in the serum and liver of the rats were measured using commercially available enzyme kits. In addition, the liver morphology was also examined using hematoxylin and eosin staining and optical microscopy. According to our results, the serum and liver TC, TG, LDL-C levels and atherogenic index (AI) were significantly decreased in rats orally administered K. marxianus M3 (p <0.01), and the HDL-C levels and anti atherogenic index (AAI) were significantly increased (p <0.01) compared to the control group. Moreover, K. marxianus M3 treatment also reduced the build-up of lipid droplets in the liver and exhibited normal hepatocytes, suggesting a protective effect of K. marxianus M3 in hyperlipidemic rats.\n\nHypocholesterolemic effects of Kluyveromyces marxianus M3 isolated from Tibetan mushrooms on diet-induced hypercholesterolemia in rat.", "token_count": 423, "char_count": 1416, "word_count": 200, "semantic_coherence": 1, "information_density": 0.595, "quality_score": 0.7975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:14.820133", "source": { "split": "train_shard_00000", "doc_id": 4276 }, "chunk_id": "train_shard_00000_4276_0", "global_id": 4768 }, { "text": "Bile salts are ionic amphiphilic compounds with a steroid skeleton. Among the most important physiological properties of bile salts are lipid transport by solubilization and transport of some drugs through hydrophobic barriers. Bile salts have been extensively studied to enhance transepithelial permeability for different marker molecules and drugs. They readily agglomerate at concentrations above their critical micelle concentration (CMC). The mechanism of absorption enhancement by bile salts appears to be complex. The aim of the present article was to review bile salt structure and their application as absorption enhancers and the probable mechanism for increasing permeation based on previous studies.\n\nAbsorption-Enhancing Effects of Bile Salts.", "token_count": 167, "char_count": 756, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:15.267343", "source": { "split": "train_shard_00000", "doc_id": 4277 }, "chunk_id": "train_shard_00000_4277_0", "global_id": 4769 }, { "text": "Pseudomonas putida are strict aerobes that proliferate in a range of temperate niches and are of interest for environmental applications due to their capacity to degrade pollutants and ability to promote plant growth. Furthermore solvent-tolerant strains are useful for biosynthesis of added-value chemicals. We present a comprehensive comparative analysis of nine strains and the first characterization of the Pseudomonas putida pangenome. The core genome of P. putida comprises approximately 3386 genes. The most abundant genes within the core genome are those that encode nutrient transporters. Other conserved genes include those for central carbon metabolism through the Entner-Doudoroff pathway, the pentose phosphate cycle, arginine and proline metabolism, and pathways for degradation of aromatic chemicals. Genes that encode transporters, enzymes and regulators for amino acid metabolism (synthesis and degradation) are all part of the core genome, as well as various electron transporters, which enable aerobic metabolism under different oxygen regimes. Within the core genome are 30 genes for flagella biosynthesis and 12 key genes for biofilm formation. Pseudomonas putida strains share 85% of the coding regions with Pseudomonas aeruginosa; however, in P. putida, virulence factors such as exotoxins and type III secretion systems are absent.\n\nAnalysis of the core genome and pangenome of Pseudomonas putida.", "token_count": 366, "char_count": 1421, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:15.853147", "source": { "split": "train_shard_00000", "doc_id": 4278 }, "chunk_id": "train_shard_00000_4278_0", "global_id": 4770 }, { "text": "Streptococcus pneumoniae is a nasopharyngeal commensal that occasionally invades normally sterile sites to cause bloodstream infection and meningitis. Although the pneumococcal population structure and evolutionary genetics are well defined, it is not clear whether pneumococci that cause meningitis are genetically distinct from those that do not. Here, we used whole-genome sequencing of 140 isolates of S. pneumoniae recovered from bloodstream infection (n = 70) and meningitis (n = 70) to compare their genetic contents. By fitting a double-exponential decaying-function model, we show that these isolates share a core of 1,427 genes (95% confidence interval [CI], 1,425 to 1,435 genes) and that there is no difference in the core genome or accessory gene content from these disease manifestations. Gene presence/absence alone therefore does not explain the virulence behavior of pneumococci that reach the meninges. Our analysis, however, supports the requirement of a range of previously described virulence factors and vaccine candidates for both meningitis- and bacteremia-causing pneumococci. This high-resolution view suggests that, despite considerable competency for genetic exchange, all pneumococci are under considerable pressure to retain key components advantageous for colonization and transmission and that these components are essential for access to and survival in sterile sites.\n\nComparative Genomic Analysis of Meningitis- and Bacteremia-Causing Pneumococci Identifies a Common Core Genome.", "token_count": 368, "char_count": 1514, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:16.432727", "source": { "split": "train_shard_00000", "doc_id": 4279 }, "chunk_id": "train_shard_00000_4279_0", "global_id": 4771 }, { "text": "Listeria monocytogenes is an opportunistic food-borne pathogen responsible for listeriosis, a disease associated with high mortality rates. L. monocytogenes causes invasive syndromes and case-fatality can be as high as 30%, in specific high-risk population groups such as the elderly, immuno-compromised individuals, fetuses and newborns. Acquisition of the disease is mainly due to consumption of contaminated (predominantly ready-to-eat) food. We aimed to provide a state-of-the-art collection of different likely evolutionary models, based on recombination and positive selection, and the phylogenetic relationship between lineages of L. monocytogenes and between them and other Listeria species. We described the most recent findings in comparative pan-genomics, considering the core and accessory genome in relation to virulence and adaptation to different environments. Finally, this review illustrates L. monocytogenes epidemiology and transmission in humans, foods and animals, the surveillance systems of the European Union and United States and the application of molecular techniques as a core tool in epidemiological investigation.\n\nThe evolution and epidemiology of Listeria monocytogenes in Europe and the United States.", "token_count": 285, "char_count": 1234, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6506, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:16.989841", "source": { "split": "train_shard_00000", "doc_id": 4280 }, "chunk_id": "train_shard_00000_4280_0", "global_id": 4772 }, { "text": "Very limited information exists on the exclusion of pathogens by probiotics in the gut of the host challenged with pathogens. In this study, we tested probiotic characteristics in vitro and anticolonization ability of Lactobacillus paracasei FJ861111.1 in mice infected with selected pathogenic microorganisms. The in vitro results indicated that L. paracasei FJ861111.1 had a high survival in acidic conditions at pH 2.5 and bile salt concentration at 0.3%, and strong inhibition ability against common pathogens including Shigella dysenteriae, Staphylococcus aureus, Cronobacter sakazakii, Escherichia coli, and Candida albicans. The cell adhesion assays showed that L. paracasei FJ861111.1 exhibited strong adherence to HT-29 cells and excluded the adhesion of selected food-borne pathogens to HT-29 cells. The in vivo results showed that fermented milk with L. paracasei and viili (a Nordic yogurt product) significantly improved the population of total bacteria and of Lactobacillus in the feces of mice, and significantly inhibited the colonization of C. albicans to the intestines of mice post-C. albicans infection. Thus, it appears that this strain could be used as a probiotic organism for manufacturing functional fermented milk.\n\nIn vitro and in vivo examination of anticolonization of pathogens by Lactobacillus paracasei FJ861111.1.", "token_count": 391, "char_count": 1346, "word_count": 193, "semantic_coherence": 1, "information_density": 0.601, "quality_score": 0.8005, "entities": { "genes": [ "FJ861111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:17.604440", "source": { "split": "train_shard_00000", "doc_id": 4281 }, "chunk_id": "train_shard_00000_4281_0", "global_id": 4773 }, { "text": "Many microbial lipases have been successfully expressed in yeasts, but not in industrially attractive Kluyveromyces lactis, which among other benefits can be cultivated on a medium supplemented with whey--cheap and easily available industrial waste. A new bacterial lipase from Serratia sp. was isolated and for the first time expressed into the yeast Kluyveromyces lactis by heterologous protein expression system based on a strong promoter of Kluyveromyces marxianus triosephosphate isomerase gene and signal peptide of Kluyveromyces marxianus endopolygalacturonase gene. In addition, the bacterial lipase gene was synthesized de novo by taking into account a codon usage bias optimal for K. lactis and was expressed into the yeast K. lactis also. Both resulting strains were characterized by high output level of the target protein secreted extracellularly. Secreted lipases were characterized for activity and stability.\n\nYeast Kluyveromyces lactis as host for expression of the bacterial lipase: cloning and adaptation of the new lipase gene from Serratia sp.", "token_count": 264, "char_count": 1064, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8084, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:18.150693", "source": { "split": "train_shard_00000", "doc_id": 4282 }, "chunk_id": "train_shard_00000_4282_0", "global_id": 4774 }, { "text": "Lactobacilli are used widely in food, feed, and health applications. The taxonomy of the genus Lactobacillus, however, is confounded by the apparent lack of physiological markers for phylogenetic groups of lactobacilli and the unclear relationships between the diverse phylogenetic groups. This study used the core and pan-genomes of 174 type strains of Lactobacillus and Pediococcus to establish phylogenetic relationships and to identify metabolic properties differentiating phylogenetic groups. The core genome phylogenetic tree separated homofermentative lactobacilli and pediococci from heterofermentative lactobacilli. Aldolase and phosphofructokinase were generally present in homofermentative but not in heterofermentative lactobacilli; a two-domain alcohol dehydrogenase and mannitol dehydrogenase were present in most heterofermentative lactobacilli but absent in most homofermentative organisms. Other genes were predominantly present in homofermentative lactobacilli (pyruvate formate lyase) or heterofermentative lactobacilli (lactaldehyde dehydrogenase and glycerol dehydratase). Cluster analysis of the phylogenomic tree and the average nucleotide identity grouped the genus Lactobacillus sensu lato into 24 phylogenetic groups, including pediococci, with stable intra- and intergroup relationships. Individual groups may be differentiated by characteristic metabolic properties. The link between phylogeny and physiology that is proposed in this study facilitates future studies on the ecology, physiology, and industrial applications of lactobacilli.\n\nA Genomic View of Lactobacilli and Pediococci Demonstrates that Phylogeny Matches Ecology and Physiology.", "token_count": 465, "char_count": 1674, "word_count": 207, "semantic_coherence": 1, "information_density": 0.599, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:18.785450", "source": { "split": "train_shard_00000", "doc_id": 4283 }, "chunk_id": "train_shard_00000_4283_0", "global_id": 4775 }, { "text": "Conversion of xylose to ethanol by yeasts is a challenge because of the redox imbalances under oxygen-limited conditions. The thermotolerant yeast Kluyveromyces marxianus grows well with xylose as a carbon source at elevated temperatures, but its xylose fermentation ability is weak. In this study, a combination of the NADPH-preferring xylose reductase (XR) from Neurospora crassa and the NADP(+)-preferring xylitol dehydrogenase (XDH) mutant from Scheffersomyces stipitis (Pichia stipitis) was constructed. The xylose fermentation ability and redox balance of the recombinant strains were improved significantly by over-expression of several downstream genes. The intracellular concentrations of coenzymes and the reduced coenzyme/oxidized coenzyme ratio increased significantly in these metabolic strains. The byproducts, such as glycerol and acetic acid, were significantly reduced by the disruption of glycerol-3-phosphate dehydrogenase (GPD1). The resulting engineered K. marxianus YZJ088 strain produced 44.95 g/L ethanol from 118.39 g/L xylose with a productivity of 2.49 g/L/h at 42 °C. Additionally, YZJ088 realized glucose and xylose co-fermentation and produced 51.43 g/L ethanol from a mixture of 103.97 g/L xylose and 40.96 g/L glucose with a productivity of 2.14 g/L/h at 42 °C. These promising results validate the YZJ088 strain as an excellent producer of ethanol from xylose through the synthetic xylose assimilation pathway.\n\nRapid ethanol production at elevated temperatures by engineered thermotolerant Kluyveromyces marxianus via the NADP(H)-preferring xylose reductase-xylitol dehydrogenase pathway.", "token_count": 508, "char_count": 1622, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5708, "quality_score": 0.7854, "entities": { "genes": [ "GPD1", "YZJ088" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:19.443483", "source": { "split": "train_shard_00000", "doc_id": 4284 }, "chunk_id": "train_shard_00000_4284_0", "global_id": 4776 }, { "text": "The increasing prevalence of overweight and obesity requires new, effective prevention and treatment strategies. One approach to reduce energy intake is by developing novel foods with increased satiating properties, which may be accomplished by slowing down lipolysis to deliver substrates to the ileum, thereby enhancing natural gut-brain signaling pathways of satiety that are normally induced by meal intake. To develop slow release food additives, their processing in the gastrointestinal tract has to be understood; therefore, we start from a general description of the digestive system and relate that to in vitro modeling, satiety, and lipolytic mechanisms. The effects of physicochemical lipid composition, encapsulation matrix, and interfacial structure on lipolysis are emphasized. We give an overview of techniques and materials used, and discuss partitioning, which may be a key factor for encapsulation performance. Targeted release capsules that delay lipolysis form a real challenge because of the high efficiency of the digestive system; hardly any proof was found that intact orally ingested lipids can be released in the ileum and thereby induce satiety. We expect that this challenge could be tackled with structured o/w-emulsion-based systems that have some protection against lipase, e.g., by hindering bile salt adsorption and/or delaying lipase diffusion.\n\nFood-grade micro-encapsulation systems that may induce satiety via delayed lipolysis: A review.", "token_count": 327, "char_count": 1475, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7156, "quality_score": 0.8578, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:20.008686", "source": { "split": "train_shard_00000", "doc_id": 4285 }, "chunk_id": "train_shard_00000_4285_0", "global_id": 4777 }, { "text": "Carvedilol (CRV) is an antihypertensive drug with both alpha and beta receptor blocking activity used to preclude angina and cardiac arrhythmias. To overcome the low, variable oral bioavailability of CRV, niosomal formulations were prepared and characterized: plain niosomes (without bile salts), bile salt-enriched niosomes (bilosomes containing various percentages of sodium cholate or sodium taurocholate), and charged niosomes (negative, containing dicetyl phosphate and positive, containing hexadecyl trimethyl ammonium bromide). All formulations were characterized in terms of encapsulation efficiency, size, zeta potential, release profile, stability, and morphology. Various formulations were administered orally to ten groups of Wistar rats (n=6 per group). The plasma levels of CRV were measured by a validated high-performance liquid chromatography (HPLC) method and pharmacokinetic properties of different formulations were characterized. Contribution of lymphatic transport to the oral bioavailability of niosomes was also investigated using a chylomicron flow-blocking approach. Of the bile salt-enriched vesicles examined, bilosomes containing 20% sodium cholate (F2) and 30% sodium taurocholate (F5) appeared to give the greatest enhancement of intestinal absorption. The relative bioavailability of F2 and F5 formulations to the suspension was estimated to be 1.84 and 1.64, respectively. With regard to charged niosomes, the peak plasma concentrations (Cmax) of CRV for positively (F7) and negatively charged formulations (F10) were approximately 2.3- and 1.7-fold higher than after a suspension. Bioavailability studies also revealed a significant increase in extent of drug absorption from charged vesicles. Tissue histology revealed no signs of inflammation or damage. The study proved that the type and concentration of bile salts as well as carrier surface charge had great influences on oral bioavailability of niosomes. Blocking the lymphatic absorption pathway significantly reduced oral bioavailability of CRV niosomes", "token_count": 503, "char_count": 2045, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6413, "quality_score": 0.8207, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:20.664392", "source": { "split": "train_shard_00000", "doc_id": 4286 }, "chunk_id": "train_shard_00000_4286_0", "global_id": 4778 }, { "text": "Overall twofold enhancement in bioavailability in comparison with drug suspension confers the potential of niosomes as suitable carriers for improved oral delivery of CRV.\n\nNiosomal carriers enhance oral bioavailability of carvedilol: effects of bile salt-enriched vesicles and carrier surface charge.", "token_count": 68, "char_count": 301, "word_count": 40, "semantic_coherence": 1, "information_density": 0.825, "quality_score": 0.9125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:21.029586", "source": { "split": "train_shard_00000", "doc_id": 4286 }, "chunk_id": "train_shard_00000_4286_1", "global_id": 4779 }, { "text": "CHAPSO and CHAPS are zwitterionic surfactants derived from bile salts which are usually employed in protein purification and for the preparation of liposomes and bicelles. Despite their spread use, there are significant discrepancies on the critical concentrations that determine their aggregation behavior. In this work, we study the interaction between these surfactants with the negative fluorescent dye pyranine (HPTS) by absorbance, fluorescence, and infrared spectrometry to establish their concentration-dependent aggregation. For the studied surfactants, we detect three critical concentrations showing their concentration-dependent presence as a monomeric form, premicellar aggregates, micelles, and a second type of micelle in aqueous medium. The nature of the interaction of HPTS with the surfactants was studied using analogues of their tails and the negative bile salt taurocholate (TC) as reference for the sterol ring. The results indicate that the chemical groups involved are the hydroxyl groups of the polar face of the sterol ring and the sulfonate groups of the dye. This interaction causes not only the incorporation of the negative dye in CHAPSO and CHAPS micelles but also its association with their premicellar aggregates. Surprisingly, this hosting behavior for a negative charged molecule was also detected for the negative bile salt TC, bypassing, in this way, the electrostatic repulsion between the guest and the host.\n\nSteroidal Surfactants: Detection of Premicellar Aggregation, Secondary Aggregation Changes in Micelles, and Hosting of a Highly Charged Negative Substance.", "token_count": 376, "char_count": 1604, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5652, "quality_score": 0.7826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:21.617285", "source": { "split": "train_shard_00000", "doc_id": 4287 }, "chunk_id": "train_shard_00000_4287_0", "global_id": 4780 }, { "text": "Attaching and effacing Escherichia coli (AEEC) strains are a genomically diverse group of diarrheagenic E. coli strains that are characterized by the presence of the locus of enterocyte effacement (LEE) genomic island, which encodes a type III secretion system that is essential to virulence. AEEC strains can be further classified as either enterohemorrhagic E. coli (EHEC), typical enteropathogenic E. coli (EPEC), or atypical EPEC, depending on the presence or absence of the Shiga toxin genes or bundle-forming pilus (BFP) genes. Recent AEEC genomic studies have focused on the diversity of the core genome, and less is known regarding the genetic diversity and relatedness of AEEC plasmids. Comparative genomic analyses in this study demonstrated genetic similarity among AEEC plasmid genes involved in plasmid replication conjugative transfer and maintenance, while the remainder of the plasmids had sequence variability. Investigation of the EPEC adherence factor (EAF) plasmids, which carry the BFP genes, demonstrated significant plasmid diversity even among isolates within the same phylogenomic lineage, suggesting that these EAF-like plasmids have undergone genetic modifications or have been lost and acquired multiple times. Global transcriptional analyses of the EPEC prototype isolate E2348/69 and two EAF plasmid mutants of this isolate demonstrated that the plasmid genes influence the expression of a number of chromosomal genes in addition to the LEE. This suggests that the genetic diversity of the EAF plasmids could contribute to differences in the global virulence regulons of EPEC isolates.\n\nComparative Genomics Provides Insight into the Diversity of the Attaching and Effacing Escherichia coli Virulence Plasmids.", "token_count": 440, "char_count": 1740, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5754, "quality_score": 0.7877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:22.276141", "source": { "split": "train_shard_00000", "doc_id": 4288 }, "chunk_id": "train_shard_00000_4288_0", "global_id": 4781 }, { "text": "Antibiotic resistance determinants are frequently associated with plasmids and other mobile genetic elements, which simplifies their horizontal transmission. Several groups of plasmids (including replicons of the IncL/M incompatibility group) were found to play an important role in the dissemination of resistance genes encoding β-lactamases. The IncL/M plasmids are large, broad host range, and self-transmissible replicons. We have identified and characterized two novel members of this group: pARM26 (isolated from bacteria inhabiting activated sludge from a wastewater treatment plant) and pIGT15 (originating from a clinical strain of Escherichia coli). This instigated a detailed comparative analysis of all available sequences of IncL/M plasmids encoding β-lactamases. The core genome of these plasmids is comprised of 20 genes with conserved synteny. Phylogenetic analyses of these core genes allowed clustering of the plasmids into four separate groups, which reflect their antibiotic resistance profiles. Examination of the biogeography of the IncL/M plasmids revealed that they are most frequently found in bacteria of the family Enterobacteriaceae originating from the Mediterranean region and Western Europe and that they are able to persist in various ecological niches even in the absence of direct antibiotic selection pressure.\n\nDiversity and Global Distribution of IncL/M Plasmids Enabling Horizontal Dissemination of β-Lactam Resistance Genes among the Enterobacteriaceae.", "token_count": 352, "char_count": 1492, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:22.869308", "source": { "split": "train_shard_00000", "doc_id": 4289 }, "chunk_id": "train_shard_00000_4289_0", "global_id": 4782 }, { "text": "We investigated the kinetics of whey bioconversion into ethanol by Kluyveromyces marxianus in continuous bioreactors using the \"accelerostat technique\" (A-stat). Cultivations using free and Ca-alginate immobilized cells were evaluated using two different acceleration rates (a). The kinetic profiles of these systems were modeled using four different unstructured models, differing in the expressions for the specific growth (μ) and substrate consumption rates (r s), taking into account substrate limitation and product inhibition. Experimental data showed that the dilution rate (D) directly affected cell physiology and metabolism. The specific growth rate followed the dilution rate (μ≈D) for the lowest acceleration rate (a = 0.0015 h(-2)), condition in which the highest ethanol yield (0.52 g g(-1)) was obtained. The highest acceleration rate (a = 0.00667 h(-2)) led to a lower ethanol yield (0.40 g g(-1)) in the system where free cells were used, whereas with immobilized cells ethanol yields increased by 23 % (0.49 g g(-1)). Among the evaluated models, Monod and Levenspiel combined with Ghose and Tyagi models were found to be more appropriate for describing the kinetics of whey bioconversion into ethanol. These results may be useful in scaling up the process for ethanol production from whey.\n\nThe modeling of ethanol production by Kluyveromyces marxianus using whey as substrate in continuous A-Stat bioreactors.", "token_count": 373, "char_count": 1428, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5991, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:23.484370", "source": { "split": "train_shard_00000", "doc_id": 4290 }, "chunk_id": "train_shard_00000_4290_0", "global_id": 4783 }, { "text": "Aggregation of misfolded protein in the endoplasmic reticulum (ER) induces a cellular protective response to ER stress, the unfolded protein response (UPR), which is mediated by a basic leucine zipper (bZIP) transcription factor, Hac1p/Xbp1. In this study, we identified and studied the molecular functions of a HAC1 homolog from the thermotolerant yeast Hansenula polymorpha (HpHAC1). We found that the HpHAC1 mRNA contains a nonconventional intron of 177 bp whose interaction with the 5' untranslated region is responsible for the translational inhibition of the HpHAC1 mRNA. The H. polymorpha hac1-null (Hphac1Δ) mutant strain grew slowly, even under normal growth conditions, and was less thermotolerant than the wild-type (WT) strain. The mutant strain was also more sensitive to cell wall-perturbing agents and to the UPR-inducing agents dithiothreitol (DTT) and tunicamycin (TM). Using comparative transcriptome analysis of the WT and Hphac1Δ strains treated with DTT and TM, we identified HpHAC1-dependent core UPR targets, which included genes involved in protein secretion and processing, particularly those required for N-linked protein glycosylation. Notably, different glycosylation and processing patterns of the vacuolar glycoprotein carboxypeptidase Y were observed in the WT and Hphac1Δ strains. Moreover, overexpression of active HpHac1p significantly increased the N-linked glycosylation efficiency and TM resistance. Collectively, our results suggest that the function of HpHac1p is important not only for UPR induction but also for efficient glycosylation in H. polymorpha.\n\nHansenula polymorpha Hac1p Is Critical to Protein N-Glycosylation Activity Modulation, as Revealed by Functional and Transcriptomic Analyses.", "token_count": 487, "char_count": 1737, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6722, "quality_score": 0.8361, "entities": { "genes": [ "HAC1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:24.135780", "source": { "split": "train_shard_00000", "doc_id": 4291 }, "chunk_id": "train_shard_00000_4291_0", "global_id": 4784 }, { "text": "Clostridium difficile is a spore-forming obligate anaerobe that is a leading cause of healthcare-associated infections. C. difficile infections begin when its metabolically dormant spores germinate in the gut of susceptible individuals. Binding of bile salt germinants to the Csp family pseudoprotease CspC triggers a proteolytic signaling cascade consisting of the Csp family protease CspB and the cortex hydrolase SleC. Conserved across many of the Clostridia, Csp proteases are subtilisin-like serine proteases that activate pro-SleC by cleaving off its inhibitory pro-peptide. Active SleC degrades the protective cortex layer, allowing spores to resume metabolism and growth. This signaling pathway, however, is differentially regulated in C. difficile, since CspC functions both as a germinant receptor and regulator of CspB activity. CspB is also produced as a fusion to a catalytically inactive CspA domain that subsequently undergoes interdomain processing during spore formation. In this study, we investigated the role of the CspA pseudoprotease domain in regulating C. difficile spore germination. Mutational analyses revealed that the CspA domain controls CspC germinant receptor levels in mature spores and is required for optimal spore germination, particularly when CspA is fused to the CspB protease. During spore formation, the YabG protease separates these domains, although YabG itself is dispensable for germination. Bioinformatic analyses of Csp family members suggest that the CspC-regulated signaling pathway characterized in C. difficile is conserved in related Peptostreptococcaceae family members but not in the Clostridiaceae or Lachnospiraceae. Our results indicate that pseudoproteases play critical roles in regulating C. difficile spore germination and highlight that diverse mechanisms control spore germination in the Clostridia.\n\nRegulation of Clostridium difficile spore germination by the CspA pseudoprotease domain.", "token_count": 504, "char_count": 1952, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5725, "quality_score": 0.7862, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:24.796447", "source": { "split": "train_shard_00000", "doc_id": 4292 }, "chunk_id": "train_shard_00000_4292_0", "global_id": 4785 }, { "text": "Benign recurrent intrahepatic cholestasis type 2 (BRIC2) is caused by mutations in ABCB11, a gene encoding the bile salt export pump (BSEP) that mediates biliary bile salt secretion, and presents with repeated intermittent cholestasis with refractory itching. Currently, no effective medical therapy has been established. We previously provided experimental and clinical evidence suggesting the therapeutic potential of 4-phenylbutyrate (4PB) for the cholestatic attacks of BRIC2.\n\nSuccessful treatment with 4-phenylbutyrate in a patient with benign recurrent intrahepatic cholestasis type 2 refractory to biliary drainage and bilirubin absorption.", "token_count": 174, "char_count": 648, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [ "ABCB11", "BRIC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:25.245321", "source": { "split": "train_shard_00000", "doc_id": 4293 }, "chunk_id": "train_shard_00000_4293_0", "global_id": 4786 }, { "text": "Two genes from Kluyveromyces marxianus strain DMB1, YGL039w1 and YGL039w2, encode putative uncharacterized oxidoreductases that respectively share 42 and 44% identity with the Saccharomyces cerevisiae S288c NADPH-dependent methylglyoxal reductase (EC 1.1.1.283). To determine the enzymatic characteristics of their products, the two genes were expressed in recombinant Escherichia coli cells, after which the YGL039w1 and YGL039w2 proteins were purified to homogeneity. In the presence of NADPH, both enzymes showed reductive activities toward at least nine aldehyde substrates, but no NADP(+)-dependent oxidative activities. These two YGL039w proteins thus appear to be aldehyde reductases. In addition, although both enzymes retained more than 70% of their activities after incubation for 30 min at temperatures below 40°C or at pHs between 5.5 and 11.3, YGL039w2 was slightly more thermostable than YGL039w1.\n\nMolecular cloning and characterization of two YGL039w genes encoding broad specificity NADPH-dependent aldehyde reductases from Kluyveromyces marxianus strain DMB1.", "token_count": 343, "char_count": 1077, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7172, "quality_score": 0.8586, "entities": { "genes": [ "DMB1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:25.819753", "source": { "split": "train_shard_00000", "doc_id": 4294 }, "chunk_id": "train_shard_00000_4294_0", "global_id": 4787 }, { "text": "The oxidant scavenging ability (OSA) of catalase-rich Candida albicans is markedly enhanced by chlorhexidine digluconate (CHX), polymyxin B, the bile salt ursodeoxycholate and by lysophosphatidylcholine, which all act as detergents facilitating the penetration of oxidants and their intracellular decomposition. Quantifications of the OSA of Candida albicans were measured by a highly sensitive luminol-dependent chemiluminescence assay and by the Thurman's assay, to quantify hydrogen peroxide (H2O2). The OSA enhancing activity by CHX depends to some extent on the media on which candida grew. The OSA of candida treated by CHX was modulated by whole human saliva, red blood cells, lysozyme, cationic peptides and by polyphenols. Concentrations of CHX, which killed over 95 % of Candida albicans cells, did not affect the cells' abilities to scavenge reactive oxygen species (ROS). The OSA of Candida cells treated by CHX is highly refractory to H2O2 (50 mM) but is strongly inhibited by hypochlorous acid, lecithin, trypan blue and by heparin. We speculate that similarly to catalase-rich red blood cells, Candida albicans and additional catalase-rich microbiota may also have the ability to scavenge oxidants and thus can protect catalase-negative anaerobes and facultative anaerobes cariogenic streptococci against peroxide and thus secure their survival in the oral cavity.\n\nChlorhexidine markedly potentiates the oxidants scavenging abilities of Candida albicans.", "token_count": 423, "char_count": 1470, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:26.440073", "source": { "split": "train_shard_00000", "doc_id": 4295 }, "chunk_id": "train_shard_00000_4295_0", "global_id": 4788 }, { "text": "We describe the use of a commercially available high content cell imaging algorithm (Cellomics Arrayscan Spot Detector) to quantify biliary excretion of the fluorescent probe substrate cholyl-l-lysyl-fluorescein (CLF) from rat hepatocytes cultured in collagen/matrigel sandwich configuration and to explore inhibition of this process by a variety of test compounds. The method provided robust, reproducible data. Twenty-nine pharmaceuticals inhibited biliary CLF efflux from hepatocytes and a broad range of potencies of inhibition were observed (IC50 values ranged between <1 and 794 µM). Thirteen drugs that inhibited CLF efflux also inhibited hepatocellular uptake of the probe substrate [(3)H]-taurocholate. Although no clear correlation between the potencies of inhibition of the 2 processes was evident, these data highlight the need to consider possible uptake transporter inhibition when interpreting hepatocyte CLF inhibition data. It has been reported that CLF is transported by MRP2. The CLF efflux inhibition data correlated closely with published data on inhibition by the drugs of the bile salt export pump (Bsep), which suggests that the tested drugs inhibit both Bsep and Mrp2. Calculation of the ratios between the maximum human plasma concentrations of the drugs and their CLF efflux inhibition IC50 values raised the possibility that for many, but not all, of them the in vitro effects may be functionally significant in vivo and that Mrp2 inhibition might be a drug-induced liver injury (DILI) risk factor. These data indicate that imaging hepatocyte CLF inhibition is a promising new method for quantification of biliary efflux inhibition by drugs, which could aid assessment of compound-related DILI risk.\n\nQuantification of Drug-Induced Inhibition of Canalicular Cholyl-l-Lysyl-Fluorescein Excretion From Hepatocytes by High Content Cell Imaging.", "token_count": 479, "char_count": 1869, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5836, "quality_score": 0.7918, "entities": { "genes": [ "MRP2", "IC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:27.087151", "source": { "split": "train_shard_00000", "doc_id": 4296 }, "chunk_id": "train_shard_00000_4296_0", "global_id": 4789 }, { "text": "Lipid-based formulations are gaining interest for use as drug delivery systems for poorly water-soluble drug compounds. During digestion, the lipolysis products self-assemble with endogenous surfactants in the gastrointestinal tract to form colloidal structures, enabling enhanced drug solubilisation. Although earlier studies in the literature focus on assembled equilibrium systems, little is known about structure formation under dynamic lipolysis conditions. The purpose of this study was to investigate the likely colloidal structure formation in the small intestine after the ingestion of lipids, under equilibrium and dynamic conditions. The structural aspects were studied using small angle X-ray scattering and dynamic light scattering, and were found to depend on lipid composition, lipid chain length, prandial state and emulsification. Incorporation of phospholipids and lipolysis products into bile salt micelles resulted in swelling of the structure. At insufficient bile salt concentrations, a co-existing lamellar phase was observed, due to a reduction in the solubilisation capacity for lipolysis products. Emulsification accelerated the rate of lipolysis and structure formation.\n\nHow relevant are assembled equilibrium samples in understanding structure formation during lipid digestion?", "token_count": 271, "char_count": 1306, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:27.639468", "source": { "split": "train_shard_00000", "doc_id": 4297 }, "chunk_id": "train_shard_00000_4297_0", "global_id": 4790 }, { "text": "Sequence-based typing (SBT) for Legionella pneumophila (Lp) has dramatically improved Legionnaires’ disease (LD) cluster investigation. Microbial whole genome sequencing (WGS) is a promising modality for investigation but sequence analysis methods are neither standardised, nor agreed. We sought to develop a WGS-based typing scheme for Lp using de novo assembly and a genome-wide gene-by-gene approach (core genome multilocus sequence typing, cgMLST). We analysed 17 publicly available Lp genomes covering the whole species variation to define a core genome (1,521 gene targets) which was validated using 21 additional published genomes. The genomes of 12 Lp strains implicated in three independent cases of paediatric humidifier-associated LD were subject to cgMLST together with three 'outgroup' strains. cgMLST was able to resolve clustered strains and clearly identify related and unrelated strains. Thus, a cgMLST scheme was readily achievable and provided high-resolution analysis of Lp strains. cgMLST appears to have satisfactory discriminatory power for LD cluster analysis and is advantageous over mapping followed by single nucleotide polymorphism (SNP) calling as it is portable and easier to standardise. cgMLST thus has the potential for becoming a gold standard tool for LD investigation. Humidifiers pose an ongoing risk as vehicles for LD and should be considered in cluster investigation and control efforts.\n\nDesign and application of a core genome multilocus sequence typing scheme for investigation of Legionnaires' disease incidents.", "token_count": 373, "char_count": 1556, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:28.217658", "source": { "split": "train_shard_00000", "doc_id": 4298 }, "chunk_id": "train_shard_00000_4298_0", "global_id": 4791 }, { "text": "Severe drug-induced liver injury (DILI) remains a major safety issue due to its frequency of occurrence, idiosyncratic nature, poor prognosis, and diverse underlying mechanisms. Numerous experimental approaches have been published to improve human DILI prediction with modest success. A retrospective analysis of 125 drugs (70 = most-DILI, 55 = no-DILI) from the Food and Drug Administration Liver Toxicity Knowledge Base was used to investigate DILI prediction based on consideration of human exposure alone or in combination with mechanistic assays of hepatotoxic liabilities (cytotoxicity, bile salt export pump inhibition, or mitochondrial inhibition/uncoupling). Using this dataset, human plasma Cmax,total ≥ 1.1 µM alone distinguished most-DILI from no-DILI compounds with high sensitivity/specificity (80/73%). Accounting for human exposure improved the sensitivity/specificity for each assay and helped to derive predictive safety margins. Compounds with plasma Cmax,total ≥ 1.1 µM and triple liabilities had significantly higher odds ratio for DILI than those with single/dual liabilities. Using this approach, a subset of recent pharmaceuticals with evidence of liver injury during clinical development was recognized as potential hepatotoxicants. In summary, plasma Cmax,total ≥ 1.1 µM along with multiple mechanistic liabilities is a major driver for predictions of human DILI potential. In applying this approach during drug development the challenge will be generating accurate estimates of plasma Cmax,total at efficacious doses in advance of generating true exposure data from clinical studies. In the meantime, drug candidates with multiple hepatotoxic liabilities should be deprioritized, since they have the highest likelihood of causing DILI in case their efficacious plasma Cmax,total in humans is higher than anticipated.\n\nSetting Clinical Exposure Levels of Concern for Drug-Induced Liver Injury (DILI) Using Mechanistic in vitro Assays.", "token_count": 468, "char_count": 1960, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8007, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:28.865074", "source": { "split": "train_shard_00000", "doc_id": 4299 }, "chunk_id": "train_shard_00000_4299_0", "global_id": 4792 }, { "text": "A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥ 40 °C). Using adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40 °C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3 °C, whereas they showed a growth trade-off at temperatures below 34 °C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49 °C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes.\n\nThermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses.", "token_count": 443, "char_count": 2046, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5368, "quality_score": 0.7684, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:29.502184", "source": { "split": "train_shard_00000", "doc_id": 4300 }, "chunk_id": "train_shard_00000_4300_0", "global_id": 4793 }, { "text": "Bile salt hydrolase (BSH, EC 3.5.1.24) is considered as an ideal way with lower cost and less side effects to release the risk of coronary heart disease caused by hypercholesterolemia. As bile salt hydrolase from Lactobacillus plantarum BBE7 could not be efficiently exported by PelB signal peptide of the general secretory (Sec) pathway, three twin-arginine signal peptides from twin-arginine translocation (Tat) pathway were synthesized, fused with bsh gene, inserted into expression vectors pET-20b(+) and pET-22b(+), and transformed into four different Escherichia coli hosts, respectively. Among the 24 recombinant bacteria obtained, E. coli BL21 (DE3) pLysS (pET-20b(+)-dmsA-bsh) showed the highest BSH activity in periplasmic fraction, which was further increased to 1.21 ± 0.03 U/mL by orthogonal experimental design. And, signal peptide dimethyl sulfoxide reductase subunit DmsA (DMSA) had the best activity of exported BSH. More importantly, the presence of BSH in the periplasm had proven to be caused by the export rather than cell leakage. For the first time, we report the periplasmic expression of BSH by signal peptides from the Tat pathway. This will lay a solid foundation for the purification and biochemical characterization of BSH from the supernatant, and strategies adopted here could be used for the periplasmic expression of other proteins in E. coli.\n\nPeriplasmic Export of Bile Salt Hydrolase in Escherichia coli by the Twin-Arginine Signal Peptides.", "token_count": 441, "char_count": 1477, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [ "BL21", "DE3", "BBE7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:30.478831", "source": { "split": "train_shard_00000", "doc_id": 4301 }, "chunk_id": "train_shard_00000_4301_0", "global_id": 4794 }, { "text": "The pneumococcal genome is variable and there are minimal data on the influence of the accessory genome on phenotype. Pneumococcal serotype 14 sequence type (ST) 46 had been the most prevalent clone causing pneumonia in children in Taiwan. A microarray was constructed using the genomic DNA of a clinical strain (NTUH-P15) of serotype 14 ST46. Using DNA hybridization, genomic variations in NTUH-P15 were compared to those of 3 control strains. Microarray analysis identified 7 genomic regions that had significant increases in hybridization signals in the NTUH-P15 strain compared to control strains. One of these regions encoded PblB, a phage-encoded virulence factor implicated (in Streptococcus mitis) in infective endocarditis. The isogenic pblB mutant decreased adherence to A549 human lung epithelial cell compared to wild-type NTUH-P15 strain (P = 0.01). Complementation with pblB restored the adherence. PblB is predicted to contain a galactose-binding domain-like region. Preincubation of NTUH-P15 with D-galactose resulted in decreases of adherence to A549 cell in a dose-dependent manner. Challenge of mice with NTUH-P15, isogenic pblB mutant and pblB complementation strains determined that PblB was required for bacterial persistence in the nasopharynx and lung. PblB, as an adhesin mediating the galactose-specific adhesion activity of pneumococci, promote pneumococcal clonal success.\n\nIdentification of PblB mediating galactose-specific adhesion in a successful Streptococcus pneumoniae clone.", "token_count": 431, "char_count": 1510, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8042, "entities": { "genes": [ "ST46" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:31.113608", "source": { "split": "train_shard_00000", "doc_id": 4302 }, "chunk_id": "train_shard_00000_4302_0", "global_id": 4795 }, { "text": "In an attempt to design an oral drug delivery system, suited to protect labile drug compounds like peptides and proteins against the harsh environment in the stomach and upper intestine, we have prepared liposomes from phospholipids, cholesterol and archaeal lipids. As source for the archaeal lipids we used Sulfolobus islandicus, a hyperthermophilic archaeon, whose lipids have not been used in liposomes before. Culturing conditions and extraction protocols for its membrane lipids were established and the lipid composition of the crude lipid extract was characterized. The extracted membrane lipid fraction of S. islandicus consisted primarily of diether lipids with only a small fraction of tetraether lipids. Small unilamellar liposomes with 18% (mol/mol) of crude archaeal lipid extract were from S. islandicus were produced, for the first time and proven to be stabilized against aggressive bile salts as determined by loss of entrapped marker (calcein). At 4.4mM taurocholate (physiological taurocholate level) liposomes containing archaeal lipids retained entrapped marker better than liposomes made of egg phosphatidylcholine (PC) alone and to an extent similar to liposomes made of egg PC and cholesterol. Our findings showed that crude archaeal lipid extracts have, to a certain extent, stabilizing effects on liposomes similar to purified tetraether lipid fractions tested previously.\n\nLiposomes containing lipids from Sulfolobus islandicus withstand intestinal bile salts: An approach for oral drug delivery?", "token_count": 380, "char_count": 1524, "word_count": 219, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:31.692669", "source": { "split": "train_shard_00000", "doc_id": 4303 }, "chunk_id": "train_shard_00000_4303_0", "global_id": 4796 }, { "text": "Obligate bacterial symbionts are widespread in many invertebrates, where they are often confined to specialized host cells and are transmitted directly from mother to progeny. Increasing numbers of these bacteria are being characterized but questions remain about their population structure and evolution. Here we take a comparative genomics approach to investigate two prominent bacterial symbionts (BFo1 and BFo2) isolated from geographically separated populations of western flower thrips, Frankliniella occidentalis. Our multifaceted approach to classifying these symbionts includes concatenated multilocus sequence analysis (MLSA) phylogenies, ribosomal multilocus sequence typing (rMLST), construction of whole-genome phylogenies, and in-depth genomic comparisons. We showed that the BFo1 genome clusters more closely to species in the genus Erwinia, and is a putative close relative to Erwinia aphidicola. BFo1 is also likely to have shared a common ancestor with Erwinia pyrifoliae/Erwinia amylovora and the nonpathogenic Erwinia tasmaniensis and genetic traits similar to Erwinia billingiae. The BFo1 genome contained virulence factors found in the genus Erwinia but represented a divergent lineage. In contrast, we showed that BFo2 belongs within the Enterobacteriales but does not group closely with any currently known bacterial species. Concatenated MLSA phylogenies indicate that it may have shared a common ancestor to the Erwinia and Pantoea genera, and based on the clustering of rMLST genes, it was most closely related to Pantoea ananatis but represented a divergent lineage. We reconstructed a core genome of a putative common ancestor of Erwinia and Pantoea and compared this with the genomes of BFo bacteria. BFo2 possessed none of the virulence determinants that were omnipresent in the Erwinia and Pantoea genera. Taken together, these data are consistent with BFo2 representing a highly novel species that maybe related to known Pantoea.", "token_count": 498, "char_count": 1962, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5893, "quality_score": 0.7946, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:32.348069", "source": { "split": "train_shard_00000", "doc_id": 4304 }, "chunk_id": "train_shard_00000_4304_0", "global_id": 4797 }, { "text": "Draft Genomes, Phylogenetic Reconstruction, and Comparative Genomics of Two Novel Cohabiting Bacterial Symbionts Isolated from Frankliniella occidentalis.", "token_count": 45, "char_count": 154, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:32.705385", "source": { "split": "train_shard_00000", "doc_id": 4304 }, "chunk_id": "train_shard_00000_4304_1", "global_id": 4798 }, { "text": "E. coli is a ubiquitous member of the intestinal microbiome. This organism resides in a biofilm comprised of a complex microbial community within the mucus layer where it must compete for the limiting nutrients that it needs to grow fast enough to stably colonize. In this article we discuss the nutritional basis of intestinal colonization. Beginning with basic ecological principles we describe what is known about the metabolism that makes E. coli such a remarkably successful member of the intestinal microbiota. To obtain the simple sugars and amino acids that it requires, E. coli depends on degradation of complex glycoproteins by strict anaerobes. Despite having essentially the same core genome and hence the same metabolism when grown in the laboratory, different E. coli strains display considerable catabolic diversity when colonized in mice. To explain why some E. coli mutants do not grow as well on mucus in vitro as their wild type parents yet are better colonizers, we postulate that each one resides in a distinct \"Restaurant\" where it is served different nutrients because it interacts physically and metabolically with different species of anaerobes. Since enteric pathogens that fail to compete successfully for nutrients cannot colonize, a basic understanding of the nutritional basis of intestinal colonization will inform efforts to develop prebiotics and probiotics to combat infection.\n\nCommensal and Pathogenic Escherichia coli Metabolism in the Gut.", "token_count": 353, "char_count": 1477, "word_count": 226, "semantic_coherence": 1, "information_density": 0.615, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:33.283757", "source": { "split": "train_shard_00000", "doc_id": 4305 }, "chunk_id": "train_shard_00000_4305_0", "global_id": 4799 }, { "text": "The triblock copolymer of the type (PEO)20-(PPO)70-(PEO)20 (P123) forms a mixed supramolecular aggregate with different bile salts, sodium deoxycholate (NaDC) and sodium taurocholate (NaTC), having different hydrophobicity. These mixed micellar systems have been investigated through dynamic light scattering (DLS) and other various spectroscopic techniques. DLS measurements reveal that the bile salts penetrate into the core-corona region of the P123 micelle and further addition of bile salts causes formation of a new supramolecular aggregate. Further CONTIN analysis confirms existence of two types of complexes at higher molar ratios of bile salt-P123 (>1 : 3). Due to the bile salt penetration, the polarity of the core-corona region of bile salt-P123 mixed micelle increases which results in red shift in the absorption and emission spectra of coumarin 153 (C153) and coumarin 480 (C480). The rotational diffusion of the hydrophobic probe C153 and a hydrophilic probe C480 has been investigated in these bile salt-P123 mixed systems and for both the probes a decrease in the average reorientation time has been observed. The reason behind this decrease in the average reorientation time is the increase in both polarity and hydration of the core-corona region in these mixed micelles. Moreover, these bile salt-P123 mixed micelles are characterized by fluorescence correlation spectroscopy (FCS) techniques. As hydrophobic solute 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl)-4H-pyran (DCM) resides in the core region of the bile salt-P123 mixed micelles, the translational diffusion of DCM becomes faster in these mixed micelles compared to that in pure P123 micelle", "token_count": 485, "char_count": 1686, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:34.633861", "source": { "split": "train_shard_00000", "doc_id": 4306 }, "chunk_id": "train_shard_00000_4306_0", "global_id": 4800 }, { "text": "However, for cationic probe rhodamine 6G perchlorate (R6G), a totally opposite trend in the translational diffusion coefficients has been observed. Both anisotropy and FCS measurements confirm that bile salts affect the core region of the P123 micelle more than the corona region. Besides, all these characterizations confirm that more hydrophobic NaDC interacts in a better way than NaTC with the P123 micelle.\n\nHow does bile salt penetration affect the self-assembled architecture of pluronic P123 micelles?--light scattering and spectroscopic investigations.", "token_count": 141, "char_count": 561, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7848, "quality_score": 0.8924, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:35.086492", "source": { "split": "train_shard_00000", "doc_id": 4306 }, "chunk_id": "train_shard_00000_4306_1", "global_id": 4801 }, { "text": "The aim of the study was to isolate and characterize the lactic acid bacteria (LAB) from animal manure. Among the thirty LAB strains, four strains, namely, KCC-25, KCC-26, KCC-27, and KCC-28, showed good cell growth and antifungal activity and were selected for further characterization. Biochemical and physiology properties of strains confirmed that the strains are related to the Lactobacillus sp.; further, the 16S rRNA sequencing confirmed 99.99% sequence similarity towards Lactobacillus plantarum. The strains exhibited susceptibility against commonly used antibiotics with negative hemolytic property. Strains KCC-25, KCC-26, KCC-27, and KCC-28 showed strong antifungal activity against Aspergillus fumigatus, Penicillium chrysogenum, Penicillium roqueforti, Botrytis elliptica, and Fusarium oxysporum, respectively. Fermentation studies noted that the strains were able to produce significant amount of lactic, acetic, and succinic acids. Further, the production of extracellular proteolytic and glycolytic enzymes, survival under low pH, bile salts, and gastric juice together with positive bile salt hydrolase (Bsh) activity, cholesterol lowering, cell surface hydrophobicity, and aggregation properties were the strains advantages. Thus, KCC-25, KCC-26, KCC-27, and KCC-28 could have the survival ability in the harsh condition of the digestive system in the gastrointestinal tract. In conclusion, novel L. plantarum KCC-25, KCC-26, KCC-27, and KCC-28 could be considered as potential antimicrobial probiotic strains.\n\nProbiotic Potential of Lactobacillus Strains with Antifungal Activity Isolated from Animal Manure.", "token_count": 484, "char_count": 1629, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:35.767790", "source": { "split": "train_shard_00000", "doc_id": 4307 }, "chunk_id": "train_shard_00000_4307_0", "global_id": 4802 }, { "text": "The genomes of the 21 completely sequenced Thermococcales display a characteristic high level of rearrangements. As a result, the prediction of their origin and termination of replication on the sole basis of chromosomal DNA composition or skew is inoperative. Using a different approach based on biologically relevant sequences, we were able to determine oriC position in all 21 genomes. The position of dif, the site where chromosome dimers are resolved before DNA segregation could be predicted in 19 genomes. Computation of the core genome uncovered a number of essential gene clusters with a remarkably stable chromosomal position across species, in sharp contrast with the scrambled nature of their genomes. The active chromosomal reorganization of numerous genes acquired by horizontal transfer, mainly from mobile elements, could explain this phenomenon.\n\nComparative genomics reveals conserved positioning of essential genomic clusters in highly rearranged Thermococcales chromosomes.", "token_count": 219, "char_count": 993, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7183, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:36.242599", "source": { "split": "train_shard_00000", "doc_id": 4308 }, "chunk_id": "train_shard_00000_4308_0", "global_id": 4803 }, { "text": "Fermentation at higher temperatures can potentially reduce the cooling cost in large-scale fermentation and reduce the contamination risk. Thus, the thermotolerant yeast, Kluyveromyces marxianus, which can grow and ferment at elevated temperatures, is a promising biotechnological tool for future applications. However, the promoters used in K. marxianus are not well characterized, especially at elevated temperatures, which is important in efficient metabolic pathway construction. In this study, six constitutive promoters (P(TDH3), P(PGK), and P(ADH1) from both Saccharomyces cerevisiae and K. marxianus) were evaluated in K. marxianus through the heterologous expression of the KlLAC4, GUSA, and SH BLE genes at various temperatures, with various carbon sources and oxygen conditions. The expression was evaluated at the transcription and protein level using real-time PCR and protein activity determination to eliminate the effect of heterologous protein stability. While the transcription of all the promoters decreased at higher temperatures, the order of their promoting strength at various temperatures with glucose as the carbon source was P(KmPGK) > P(KmTDH3) > P(ScPGK) > P(ScTDH3) > P(KmADH1) > P(ScADH1). When glycerol or xylose was supplied as the carbon source at 42 °C, the order of promoter strength was P(KmPGK) > P(ScPGK) > P(KmADH1) > P(ScADH1) > P(ScTDH3) > P(KmTDH3). The promoter activity of P TDH3 decreased significantly, while the promoter activity of both of the P(ADH1) promoters increased. Oxygen conditions had non-significant effect. The results of this study provide important information for fine-tuned pathway construction for the metabolic engineering of K. marxianus.\n\nCharacterizing yeast promoters used in Kluyveromyces marxianus.", "token_count": 478, "char_count": 1770, "word_count": 250, "semantic_coherence": 1, "information_density": 0.54, "quality_score": 0.77, "entities": { "genes": [ "TDH3", "ADH1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:36.889531", "source": { "split": "train_shard_00000", "doc_id": 4309 }, "chunk_id": "train_shard_00000_4309_0", "global_id": 4804 }, { "text": "To distinguish the lithogenic effect of the classical estrogen receptor α (ERα) from that of the G protein-coupled receptor 30 (GPR30), a new estrogen receptor, on estrogen-induced gallstones, we investigated the entire spectrum of cholesterol crystallization pathways and sequences during the early stage of gallstone formation in gallbladder bile of ovariectomized female wild-type, GPR30((-/-)), ERα((-/-)), and GPR30((-/-))/ERα((-/-)) mice treated with 17β-estradiol (E2) at 6 µg/day and fed a lithogenic diet for 12 days. E2 disrupted biliary cholesterol and bile salt metabolism through ERα and GPR30, leading to supersaturated bile and predisposing to the precipitation of cholesterol monohydrate crystals. In GPR30((-/-)) mice, arc-like and tubular crystals formed first, followed by classical parallelogram-shaped cholesterol monohydrate crystals. In ERα((-/-)) mice, precipitation of lamellar liquid crystals, typified by birefringent multilamellar vesicles, appeared earlier than cholesterol monohydrate crystals. Both crystallization pathways were accelerated in wild-type mice with the activation of GPR30 and ERα by E2. However, cholesterol crystallization was drastically retarded in GPR30((-/-))/ERα((-/-)) mice. We concluded that E2 activates GPR30 and ERα to produce liquid crystalline versus anhydrous crystalline metastable intermediates evolving to cholesterol monohydrate crystals from supersaturated bile. GPR30 produces a synergistic lithogenic action with ERα to enhance E2-induced gallstone formation.\n\nEstrogen induces two distinct cholesterol crystallization pathways by activating ERα and GPR30 in female mice.", "token_count": 508, "char_count": 1639, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": { "genes": [ "GPR30" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:37.539155", "source": { "split": "train_shard_00000", "doc_id": 4310 }, "chunk_id": "train_shard_00000_4310_0", "global_id": 4805 }, { "text": "Lactobacillus plantarum ZDY 2013, a novel strain isolated from Chinese traditional fermented acid beans, was systematically evaluated for its survival capacity under stress conditions (pH, bile salt, simulated gastrointestinal tract, and antibiotics), production of exopolysaccharide and antagonism against 8 pathogens. Its effect on mice gut microbiota was also investigated by quantitative PCR and PCR-denaturing gradient gel electrophoresis. The results showed that ZDY 2013 can grow at pH 3.5 and survive at pH 2.0 for 6 h and at 0.45% bile salt for 3 h. The exopolysaccharide yield was up to 204±7.68 mg/L. The survival rate of ZDY 2013 in a simulated gastrointestinal tract was as high as 65.84%. Antagonism test with a supernatant of ZDY 2013 showed maximum halo of 28 mm against Listeria monocytogenes. The inhibition order was as follows: Listeria monocytogenes, Salmonella typhimurium, Escherichia coli, Pseudomonas aeruginosa, Shigella sonnei, Enterobacter sakazakii, and Staphylococcus aureus. Lactobacillus plantarum ZDY 2013 was sensitive to some antibiotics (e.g., macrolide, sulfonamides, aminoglycoside, tetracyclines and β-lactams), whereas it was resistant to glycopeptides, quinolones, and cephalosporins antibiotics. Denaturing gradient gel electrophoresis profile demonstrated that ZDY 2013 administration altered the composition of the microbiota at various intestinal loci of the mice", "token_count": 454, "char_count": 1408, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:38.182112", "source": { "split": "train_shard_00000", "doc_id": 4311 }, "chunk_id": "train_shard_00000_4311_0", "global_id": 4806 }, { "text": "Moreover, the quantitative PCR test showed that the administration of ZDY 2013 enhanced the populations of Bifidobacterium and Lactobacillus in either the colon or cecum, and reduced the potential enteropathogenic bacteria (e.g., Enterococcus, Enterobacterium, and Clostridium perfringens). Lactobacillus plantarum ZDY 2013 exhibited high resistance against low pH, bile salt, and gastrointestinal fluid, and possessed antibacterial and gut microbiota modulation properties with a potential application in the development of dairy food and nutraceuticals.\n\nIn vitro probiotic characteristics of Lactobacillus plantarum ZDY 2013 and its modulatory effect on gut microbiota of mice.", "token_count": 190, "char_count": 680, "word_count": 90, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:38.626387", "source": { "split": "train_shard_00000", "doc_id": 4311 }, "chunk_id": "train_shard_00000_4311_1", "global_id": 4807 }, { "text": "The aim of the study was a detail evaluation of genetic diversity among the lactic acid bacteria (LAB) strains having an advantage of a starter culture in order to select genotypically diverse strains with enhanced antimicrobial effect on some harmfull and pathogenic microorganisms. Antimicrobial activity of LAB was performed by the agar well diffusion method and was examined against the reference strains and foodborne isolates of Bacillus cereus, Listeria monocytogenes, Escherichia coli, Staphylococcus aureus and Salmonella Typhimurium. Antifungal activity was tested against the foodborne isolates of Candida parapsilosis, Debaromyces hansenii, Kluyveromyces marxianus, Pichia guilliermondii, Yarowia lipolytica, Aspergillus brasiliensis, Aspergillus versicolor, Cladosporium herbarum, Penicillium chrysogenum and Scopulariopsis brevicaulis. A total 40 LAB strains representing Lactobacillus (23 strains), Lactococcus (13 strains) and Streptococcus spp. (4 strains) were characterised by repetitive sequence based polymerase chain reaction fingerprinting which generated highly discriminatory profiles, confirmed the identity and revealed high genotypic heterogeneity among the strains. Many of tested LAB demonstrated strong antimicrobial activity specialised against one or few indicator strains. Twelve LAB strains were superior in suppressing growth of the whole complex of pathogenic bacteria and fungi. These results demonstrated that separate taxonomic units offered different possibilities of selection for novel LAB strains could be used as starter cultures enhancing food preservation.\n\nSelection of enhanced antimicrobial activity posing lactic acid bacteria characterised by (GTG)5-PCR fingerprinting.", "token_count": 442, "char_count": 1721, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6909, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:39.262881", "source": { "split": "train_shard_00000", "doc_id": 4312 }, "chunk_id": "train_shard_00000_4312_0", "global_id": 4808 }, { "text": "Gene expression analysis provides valuable information to evaluate cellular state. Unlike quantitative mRNA analysis techniques like reverse-transcription PCR and microarray, expression analysis using a reporter gene has not been commonly used for multiple-gene analysis, probably due to the difficulty in preparing multiple reporter-gene constructs. To circumvent this problem, we developed a novel one-step reporter-gene construction system mediated by non-homologous end joining (NHEJ) in the yeast Kluyveromyces marxianus. As a selectable reporter gene, the ScURA3 selection marker was fused in frame with a red fluorescent gene yEmRFP (ScURA3:yEmRFP). The N-terminally truncated ScURA3:yEmRFP fragment was prepared by PCR. Promoter sequences were also prepared by PCR using primers containing the sequence of the deleted ScURA3 N-terminus to attach at their 3(') ends. The two DNA fragments were used for the transformation of a ura3(-) strain of K. marxianus, in which two DNA fragments are randomly joined and integrated into the chromosome through NHEJ. Only the correctly aligned fragments produced transformants on uracil-deficient medium and expressed red fluorescence under the control of the introduced promoters. A total of 36 gene promoters involved in glycolysis and other pathways were analyzed. Fluorescence measurements of these strains allowed real-time gene expression analysis in different culture conditions.\n\nGene expression analysis using strains constructed by NHEJ-mediated one-step promoter cloning in the yeast Kluyveromyces marxianus.", "token_count": 371, "char_count": 1564, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:39.836545", "source": { "split": "train_shard_00000", "doc_id": 4313 }, "chunk_id": "train_shard_00000_4313_0", "global_id": 4809 }, { "text": "Corrigendum: Massive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency.", "token_count": 33, "char_count": 126, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:40.194334", "source": { "split": "train_shard_00000", "doc_id": 4314 }, "chunk_id": "train_shard_00000_4314_0", "global_id": 4810 }, { "text": "Whole-genome sequencing is becoming a leading technology in the typing and epidemiology of microbial pathogens, but the increase in genomic information necessitates significant investment in bioinformatic resources and expertise, and currently used methodologies struggle with genetically heterogeneous bacteria such as the human gastric pathogen Helicobacter pylori. Here we demonstrate that the alignment-free analysis method feature frequency profiling (FFP) can be used to rapidly construct phylogenetic trees of draft bacterial genome sequences on a standard desktop computer and that coupling with in silico genotyping methods gives useful information for comparative and clinical genomic and molecular epidemiology applications. FFP-based phylogenetic trees of seven gastric Helicobacter species matched those obtained by analysis of 16S rRNA genes and ribosomal proteins, and FFP- and core genome single nucleotide polymorphism-based analysis of 63 H. pylori genomes again showed comparable phylogenetic clustering, consistent with genomotypes assigned by using multilocus sequence typing (MLST). Analysis of 377 H. pylori genomes highlighted the conservation of genomotypes and linkage with phylogeographic characteristics and predicted the presence of an incomplete or nonfunctional cag pathogenicity island in 18/276 genomes. In silico analysis of antibiotic susceptibility markers suggests that most H. pylori hspAmerind and hspEAsia isolates are predicted to carry the T2812C mutation potentially conferring low-level clarithromycin resistance, while levels of metronidazole resistance were similar in all multilocus sequence types. In conclusion, the use of FFP phylogenetic clustering and in silico genotyping allows determination of genome evolution and phylogeographic clustering and can contribute to clinical microbiology by genomotyping for outbreak management and the prediction of pathogenic potential and antibiotic susceptibility.\n\nUse of Alignment-Free Phylogenetics for Rapid Genome Sequence-Based Typing of Helicobacter pylori Virulence Markers and Antibiotic Susceptibility.", "token_count": 502, "char_count": 2102, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:40.845560", "source": { "split": "train_shard_00000", "doc_id": 4315 }, "chunk_id": "train_shard_00000_4315_0", "global_id": 4811 }, { "text": "Whole-genome sequencing (WGS) has emerged today as an ultimate typing tool to characterize Listeria monocytogenes outbreaks. However, data analysis and interlaboratory comparability of WGS data are still challenging for most public health laboratories. Therefore, we have developed and evaluated a new L. monocytogenes typing scheme based on genome-wide gene-by-gene comparisons (core genome multilocus the sequence typing [cgMLST]) to allow for a unique typing nomenclature. Initially, we determined the breadth of the L. monocytogenes population based on MLST data with a Bayesian approach. Based on the genome sequence data of representative isolates for the whole population, cgMLST target genes were defined and reappraised with 67 L. monocytogenes isolates from two outbreaks and serotype reference strains. The Bayesian population analysis generated five L. monocytogenes groups. Using all available NCBI RefSeq genomes (n = 36) and six additionally sequenced strains, all genetic groups were covered. Pairwise comparisons of these 42 genome sequences resulted in 1,701 cgMLST targets present in all 42 genomes with 100% overlap and ≥90% sequence similarity. Overall, ≥99.1% of the cgMLST targets were present in 67 outbreak and serotype reference strains, underlining the representativeness of the cgMLST scheme. Moreover, cgMLST enabled clustering of outbreak isolates with ≤10 alleles difference and unambiguous separation from unrelated outgroup isolates. In conclusion, the novel cgMLST scheme not only improves outbreak investigations but also enables, due to the availability of the automatically curated cgMLST nomenclature, interlaboratory exchange of data that are crucial, especially for rapid responses during transsectorial outbreaks.\n\nDefining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Listeria monocytogenes.", "token_count": 481, "char_count": 1893, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:41.501794", "source": { "split": "train_shard_00000", "doc_id": 4316 }, "chunk_id": "train_shard_00000_4316_0", "global_id": 4812 }, { "text": "Yeasts and yeast-like fungal isolates were recovered from apple orchards and apple juice processing plants located in the Shaanxi province of China. The strains were evaluated for osmotolerance by growing them in 50% (w/v) glucose. Of the strains tested, 66 were positive for osmotolerance and were subsequently identified by 26S or 5.8S-ITS ribosomal RNA (rRNA) gene sequencing. Physiological tests and RAPD-PCR analysis were performed to reveal the polymorphism of isolates belonging to the same species. Further, the spoilage potential of the 66 isolates was determining by evaluating their growth in 50% to 70% (w/v) glucose and measuring gas generation in 50% (w/v) glucose. Thirteen osmotolerant isolates representing 9 species were obtained from 10 apple orchards and 53 target isolates representing 19 species were recovered from 2 apple juice processing plants. In total, members of 14 genera and 23 species of osmotolerant isolates including yeast-like molds were recovered from all sources. The commonly recovered osmotolerant isolates belonged to Kluyveromyces marxianus, Hanseniaspora uvarum, Saccharomyces cerevisiae, Zygosaccharomyces rouxii, Candida tropicalis, and Pichia kudriavzevii. The polymorphism of isolates belonging to the same species was limited to 1 to 3 biotypes. The majority of species were capable of growing within a range of glucose concentration, similar to sugar concentrations found in apple juice products with a lag phase from 96 to 192 h. Overall, Z. rouxii was particularly the most tolerant to high glucose concentration with the shortest lag phase of 48 h in 70% (w/v) glucose and the fastest gas generation rate in 50% (w/v) glucose.", "token_count": 476, "char_count": 1678, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5397, "quality_score": 0.7698, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:42.146997", "source": { "split": "train_shard_00000", "doc_id": 4317 }, "chunk_id": "train_shard_00000_4317_0", "global_id": 4813 }, { "text": "Characterization of Osmotolerant Yeasts and Yeast-Like Molds from Apple Orchards and Apple Juice Processing Plants in China and Investigation of Their Spoilage Potential.", "token_count": 44, "char_count": 170, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:42.515170", "source": { "split": "train_shard_00000", "doc_id": 4317 }, "chunk_id": "train_shard_00000_4317_1", "global_id": 4814 }, { "text": "Genes encoding L-arabinose transporters in Kluyveromyces marxianus and Pichia guilliermondii were identified by functional complementation of Saccharomyces cerevisiae whose growth on L-arabinose was dependent on a functioning L-arabinose transporter, or by screening a differential display library, respectively. These transporters also transport D-xylose and were designated KmAXT1 (arabinose-xylose transporter) and PgAXT1, respectively. Transport assays using L-arabinose showed that KmAxt1p has K(m) 263 mM and V(max) 57 nM/mg/min, and PgAxt1p has K(m) 0.13 mM and V(max) 18 nM/mg/min. Glucose, galactose and xylose significantly inhibit L-arabinose transport by both transporters. Transport assays using D-xylose showed that KmAxt1p has K(m) 27 mM and V(max) 3.8 nM/mg/min, and PgAxt1p has K(m) 65 mM and V(max) 8.7 nM/mg/min. Neither transporter is capable of recovering growth on glucose or galactose in a S. cerevisiae strain deleted for hexose and galactose transporters. Transport kinetics of S. cerevisiae Gal2p showed K(m) 371 mM and V(max) 341 nM/mg/min for L-arabinose, and K(m) 25 mM and V(max) 76 nM/mg/min for galactose", "token_count": 450, "char_count": 1136, "word_count": 160, "semantic_coherence": 1, "information_density": 0.5437, "quality_score": 0.7719, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:43.154208", "source": { "split": "train_shard_00000", "doc_id": 4318 }, "chunk_id": "train_shard_00000_4318_0", "global_id": 4815 }, { "text": "Due to the ability of Gal2p and these two newly characterized transporters to transport both L-arabinose and D-xylose, one scenario for the complete usage of biomass-derived pentose sugars would require only the low-affinity, high-throughput transporter Gal2p and one additional high-affinity general pentose transporter, rather than dedicated D-xylose or L-arabinose transporters. Additionally, alignment of these transporters with other characterized pentose transporters provides potential targets for substrate recognition engineering.\n\nNovel transporters from Kluyveromyces marxianus and Pichia guilliermondii expressed in Saccharomyces cerevisiae enable growth on L-arabinose and D-xylose.", "token_count": 177, "char_count": 695, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:43.594778", "source": { "split": "train_shard_00000", "doc_id": 4318 }, "chunk_id": "train_shard_00000_4318_1", "global_id": 4816 }, { "text": "Saccharomyces cerevisiae has been used for millennia in the production of food and beverages and is by far the most studied yeast species. Currently, it is also the most used microorganism in the production of first-generation bioethanol from sugar or starch crops. Second-generation bioethanol, on the other hand, is produced from lignocellulosic feedstocks that are pretreated and hydrolyzed to obtain monomeric sugars, mainly D-glucose, D-xylose and L-arabinose. Recently, S. cerevisiae recombinant strains capable of fermenting pentose sugars have been generated. However, the pretreatment of the biomass results in hydrolysates with high osmolarity and high concentrations of inhibitors. These compounds negatively influence the fermentation process. Therefore, robust strains with high stress tolerance are required. Up to now, more than 2000 yeast species have been described and some of these could provide a solution to these limitations because of their high tolerance to the most predominant stress conditions present in a second-generation bioethanol reactor. In this review, we will summarize what is known about the non-conventional yeast species showing unusual tolerance to these stresses, namely Zygosaccharomyces rouxii (osmotolerance), Kluyveromyces marxianus and Ogataea (Hansenula) polymorpha (thermotolerance), Dekkera bruxellensis (ethanol tolerance), Pichia kudriavzevii (furan derivatives tolerance) and Z. bailii (acetic acid tolerance).\n\nLooking beyond Saccharomyces: the potential of non-conventional yeast species for desirable traits in bioethanol fermentation.", "token_count": 415, "char_count": 1591, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6808, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:44.216581", "source": { "split": "train_shard_00000", "doc_id": 4319 }, "chunk_id": "train_shard_00000_4319_0", "global_id": 4817 }, { "text": "Polypyrrole (PPy)-bile salt composite was used for sensing ethanol vapor. PPy was synthesized by interface polymerization for subsequent fabrication of thin film of its composite with bile salt, by in-situ co-dispersion method and then exposed to ethanol vapour. Sensing was visualized through changes in morphological, structural and optical characterizations. The ethanol exposed film showed larger agglomeration as revealed in its surface morphology on scanning electron microscope (SEM) and greater crystallinity as seen through X-Ray diffraction (XRD). Fourier transform infra red (FTIR) and nuclear magnetic resonance spectroscopy (NMR) of the ethanol incorporated film also gave signature of the presence of bile salt and alcohol. Alcohol incorporation pattern resulted in increase in electrical conductance from 7.08539 x 10(-5) mA/V to 8.0356 x 10(-5) mA/V, as determined from current voltage characterizations. Average molecular weight (M(n)) obtained from gel permeation chromatography changed from 6160 to 10300 on ethanol intake. Photoluminescence (PL) intensity was quenched and the PL peak shifted from 430 to 409 on ethanol exposure. Changes in morphological, structural, optical and electrical properties of the composite on ethanol exposure showed its prospective application for sensing ethanol.\n\nBile salt incorporated polypyrrole thin film for ethanol sensing.", "token_count": 360, "char_count": 1381, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6302, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:44.789792", "source": { "split": "train_shard_00000", "doc_id": 4320 }, "chunk_id": "train_shard_00000_4320_0", "global_id": 4818 }, { "text": "Proliposomes containing a bile salt were developed to improve the oral bioavailability of Ginkgo biloba extract (GbE). GbE loaded proliposomes (P-GbE) were successfully prepared by spray drying method. The formulation was optimized using the response surface methodology. FE-SEM, DSC, and FT-IR were used to study the surface morphology and molecular state of proliposomes, and demonstrated key interactions between the formulation ingredients. In vitro studies showed delayed release and enhanced dissolution of Ginkgo flavonoids and terpene lactones from GbE proliposomes. Proliposomes significantly enhanced GbE absorption in the gastrointestinal tract and decreased its elimination. The bioavailabilities of quercetin, kaempferol, isorhmnetin, ginkgolide A, ginkgolide B and ginkgolide C from proliposomes relative to the control were 245%, 211%, 264%, 203%, 333%, and 294%, respectively. Proliposomes were shown to selectively deliver GbE to critical target tissues. In conclusion, development of proliposomes formulation for GbE solved the problem of its poor oral bioavailability, prolonged its duration of action, and increased drug distribution in critical tissues, especially in the brain, therefore, warrant further investigation.\n\nProliposomes containing a bile salt for oral delivery of Ginkgo biloba extract: Formulation optimization, characterization, oral bioavailability and tissue distribution in rats.", "token_count": 371, "char_count": 1420, "word_count": 189, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:45.372287", "source": { "split": "train_shard_00000", "doc_id": 4321 }, "chunk_id": "train_shard_00000_4321_0", "global_id": 4819 }, { "text": "While a high-cholesterol diet induces hepatic steatosis, the role of intracellular sterol carrier protein-2/sterol carrier protein-x (SCP-2/SCP-x) proteins is unknown. We hypothesized that ablating SCP-2/SCP-x [double knockout (DKO)] would impact hepatic lipids (cholesterol and cholesteryl ester), especially in high-cholesterol-fed mice. DKO did not alter food consumption, and body weight (BW) gain decreased especially in females, concomitant with hepatic steatosis in females and less so in males. DKO-induced steatosis in control-fed wild-type (WT) mice was associated with 1) loss of SCP-2; 2) upregulation of liver fatty acid binding protein (L-FABP); 3) increased mRNA and/or protein levels of sterol regulatory element binding proteins (SREBP1 and SREBP2) as well as increased expression of target genes of cholesterol synthesis (Hmgcs1 and Hmgcr) and fatty acid synthesis (Acc1 and Fas); and 4) cholesteryl ester accumulation was also associated with increased acyl-CoA cholesterol acyltransferase-2 (ACAT2) in males. DKO exacerbated the high-cholesterol diet-induced hepatic cholesterol and glyceride accumulation, without further increasing SREBP1, SREBP2, or target genes. This exacerbation was associated both with loss of SCP-2 and concomitant downregulation of Ceh/Hsl, apolipoprotein B (ApoB), MTP, and/or L-FABP protein expression. DKO diminished the ability to secrete excess cholesterol into bile and oxidize cholesterol to bile acid for biliary excretion, especially in females", "token_count": 463, "char_count": 1499, "word_count": 203, "semantic_coherence": 1, "information_density": 0.67, "quality_score": 0.835, "entities": { "genes": [ "SREBP1", "SREBP2", "ACAT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:46.063672", "source": { "split": "train_shard_00000", "doc_id": 4322 }, "chunk_id": "train_shard_00000_4322_0", "global_id": 4820 }, { "text": "This suggested that SCP-2/SCP-x affects cholesterol transport to particular intracellular compartments, with ablation resulting in less to the endoplasmic reticulum for SREBP regulation, making more available for cholesteryl ester synthesis, for cholesteryl-ester storage in lipid droplets, and for bile salt synthesis and/or secretion. These alterations are significant findings, since they affect key processes in regulation of sterol metabolism.\n\nImpact of SCP-2/SCP-x gene ablation and dietary cholesterol on hepatic lipid accumulation.", "token_count": 144, "char_count": 540, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8286, "quality_score": 0.9143, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:46.513499", "source": { "split": "train_shard_00000", "doc_id": 4322 }, "chunk_id": "train_shard_00000_4322_1", "global_id": 4821 }, { "text": "The human body has long provided pharmaceutical science with biomaterials of interesting applications. Bile salts (BSs) are biomaterials reminiscent of traditional surfactants with peculiar structure and self-assembled topologies. In the pharmaceutical field, BSs were employed on the basis of two different concepts. The first concept exploited BSs' metabolic and homeostatic functions in disease modulation, whereas the second one utilized BSs' potential to modify drug-delivery characteristics, which recently involved nanotechnology. This review is the first to gather major pharmaceutical applications of BSs from endogenous organotropism up to integration into nanomedicine, with a greater focus on the latter domain. Endogenous applications highlighted the role of BS in modulating hypercholesterolemia and cancer therapy in view of enterohepatic circulation. In addition, recent BS-integrated nanomedicines have been surveyed, chiefly size-tunable cholate nanoparticles, BS-lecithin mixed micelles, bilosomes, probilosomes, and surface-engineered bilosomes. A greater emphasis has been laid on nanosystems for vaccine and cancer therapy. The comparative advantages of BS-integrated nanomedicines over conventional nanocarriers have been noted. Paradoxical effects, current pitfalls, future perspectives, and opinions have also been outlined.\n\nMultifaceted applications of bile salts in pharmacy: an emphasis on nanomedicine.", "token_count": 332, "char_count": 1432, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:47.092445", "source": { "split": "train_shard_00000", "doc_id": 4323 }, "chunk_id": "train_shard_00000_4323_0", "global_id": 4822 }, { "text": "During the digestive procedure, pancreatic lipase is known as the main enzyme in vivo for digestion and absorption of dietary fat, consisting of pancreatic triglyceride lipase, pancreatic lipase related proteins 1 and 2, bile salt - stimulated Lipase and phospholipase A2. The changes of the development pattern of pancreatic lipase have confirmed associations with metabolic diseases such as obesity, not only because age is connected with the development of pancreatic lipase, but also pancreatic lipase itself is regulated by the dietary structure and endocrine hormone.\n\n[The Progress of Research About Pancreatic Lipase].", "token_count": 162, "char_count": 626, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6739, "quality_score": 0.837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:47.569591", "source": { "split": "train_shard_00000", "doc_id": 4324 }, "chunk_id": "train_shard_00000_4324_0", "global_id": 4823 }, { "text": "The suitable properties of potential probiotic lactic acid bacteria (LAB) strains (preselected among 153 strains on the basis of their potential technological properties) isolated from traditional Çubuk pickles were examined in vitro. For this purpose, these strains (21 Lactobacillus plantarum, 11 Pediococcus ethanolidurans, and 7 Lactobacillus brevis) were tested for the ability to survive at pH 2.5, resistance to bile salts, viability in the presence of pepsin-pancreatin, ability to deconjugate bile salts, cholesterol assimilation, and surface hydrophobicity properties. Most of the properties tested could be assumed to be strain-dependent. However, L. plantarum and L. brevis species were found to possess desirable probiotic properties to a greater extent compared to P. ethanolidurans. In contrast to P. ethanolidurans strains, the tested L. plantarum and L. brevis strains exhibited bile salt tolerance, albeit to different extent. All tested strains showed less resistance to intestinal conditions than gastric juice environment. Based on the survival under gastrointestinal conditions, 22 of the 39 strains were selected for further characterization. The eight strains having the highest cholesterol assimilation and surface hydrophobicity ratios could be taken as promising probiotic candidates for further in vivo studies, because of the strongest variations found among the tested strains with regard to these properties.\n\nIn Vitro Properties of Potential Probiotic Indigenous Lactic Acid Bacteria Originating from Traditional Pickles.", "token_count": 384, "char_count": 1553, "word_count": 216, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:48.191436", "source": { "split": "train_shard_00000", "doc_id": 4325 }, "chunk_id": "train_shard_00000_4325_0", "global_id": 4824 }, { "text": "Klebsiella pneumoniae is now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections. K. pneumoniae is ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure of K. pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework for K. pneumoniae based on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting of K. pneumoniae into three distinct species, KpI (K. pneumoniae), KpII (K. quasipneumoniae), and KpIII (K. variicola). Further, for K. pneumoniae (KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We show K. pneumoniae has a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasive K. pneumoniae infections; our data provide the whole-genome framework against which to track the emergence of such threats.\n\nGenomic analysis of diversity, population structure, virulence, and antimicrobial resistance in Klebsiella pneumoniae, an urgent threat to public health.", "token_count": 455, "char_count": 1916, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6031, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:48.831289", "source": { "split": "train_shard_00000", "doc_id": 4326 }, "chunk_id": "train_shard_00000_4326_0", "global_id": 4825 }, { "text": "In this research, whey protein/pullulan (WP/pullulan) microcapsules were developed in order to assess its protective effect on the viability of Lactobacillus acidophilus NRRL-B 4495 under in vitro gastrointestinal conditions. Results demonstrated that WP/pullulan microencapsulated cells exhibited significantly (p ≤ 0.05) higher resistance to simulated gastric acid and bile salt. Pullulan incorporation into protein wall matrix resulted in improved survival as compared to free cells after 3 h incubation in simulated gastric solution. Moreover WP/pullulan microcapsules were found to release over 70% of encapsulated L. acidophilus NRRL-B 4495 cells within 1 h. The effect of encapsulation during refrigerated storage was also studied. Free bacteria exhibited 3.96 log reduction while, WP/pullulan encapsulated bacteria showed 1.64 log reduction after 4 weeks of storage.\n\nProtection of Lactobacillus acidophilus NRRL-B 4495 under in vitro gastrointestinal conditions with whey protein/pullulan microcapsules.", "token_count": 281, "char_count": 1012, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6963, "quality_score": 0.8481, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:49.390518", "source": { "split": "train_shard_00000", "doc_id": 4327 }, "chunk_id": "train_shard_00000_4327_0", "global_id": 4826 }, { "text": "Bacterial spot disease of pepper and tomato is caused by four distinct Xanthomonas species and is a severely limiting factor on fruit yield in these crops. The genetic diversity and the type III effector repertoires of a large sampling of field strains for this disease have yet to be explored on a genomic scale, limiting our understanding of pathogen evolution in an agricultural setting. Genomes of 67 Xanthomonas euvesicatoria (Xe), Xanthomonas perforans (Xp), and Xanthomonas gardneri (Xg) strains isolated from diseased pepper and tomato fields in the southeastern and midwestern United States were sequenced in order to determine the genetic diversity in field strains. Type III effector repertoires were computationally predicted for each strain, and multiple methods of constructing phylogenies were employed to understand better the genetic relationship of strains in the collection. A division in the Xp population was detected based on core genome phylogeny, supporting a model whereby the host-range expansion of Xp field strains on pepper is due, in part, to a loss of the effector AvrBsT. Xp-host compatibility was further studied with the observation that a double deletion of AvrBsT and XopQ allows a host range expansion for Nicotiana benthamiana. Extensive sampling of field strains and an improved understanding of effector content will aid in efforts to design disease resistance strategies targeted against highly conserved core effectors.\n\nPhylogenomics of Xanthomonas field strains infecting pepper and tomato reveals diversity in effector repertoires and identifies determinants of host specificity.", "token_count": 368, "char_count": 1624, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5768, "quality_score": 0.7884, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:49.976352", "source": { "split": "train_shard_00000", "doc_id": 4328 }, "chunk_id": "train_shard_00000_4328_0", "global_id": 4827 }, { "text": "Clostridium difficile infection (CDI) is the leading cause of antimicrobial and health care-associated diarrhea in humans, presenting a significant burden to global health care systems. In the last 2 decades, PCR- and sequence-based techniques, particularly whole-genome sequencing (WGS), have significantly furthered our knowledge of the genetic diversity, evolution, epidemiology, and pathogenicity of this once enigmatic pathogen. C. difficile is taxonomically distinct from many other well-known clostridia, with a diverse population structure comprising hundreds of strain types spread across at least 6 phylogenetic clades. The C. difficile species is defined by a large diverse pangenome with extreme levels of evolutionary plasticity that has been shaped over long time periods by gene flux and recombination, often between divergent lineages. These evolutionary events are in response to environmental and anthropogenic activities and have led to the rapid emergence and worldwide dissemination of virulent clonal lineages. Moreover, genome analysis of large clinically relevant data sets has improved our understanding of CDI outbreaks, transmission, and recurrence. The epidemiology of CDI has changed dramatically over the last 15 years, and CDI may have a foodborne or zoonotic etiology. The WGS era promises to continue to redefine our view of this significant pathogen.\n\nDiversity and Evolution in the Genome of Clostridium difficile.", "token_count": 332, "char_count": 1449, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6878, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:50.543226", "source": { "split": "train_shard_00000", "doc_id": 4329 }, "chunk_id": "train_shard_00000_4329_0", "global_id": 4828 }, { "text": "Vibrios are natural inhabitants of estuarine ecosystems and some species may pose public health problem as agents of sporadic or collective food-borne infections associated with the consumption of fish or shellfish. Samples of raw shrimp (n = 299), fished in coastal areas of the city of Agadir, Morocco, and collected from its fish marketplace, were examined for the presence of pathogenic vibrios. Microbiological analysis was carried out according to a protocol using thiosulphate citrate bile sucrose (TCBS) agar and CHROMagar Vibrio (CV) as selective media. Presumptive-positive colonies were identified by biochemical and species-specific PCR systems, and further tested by PCR for the presence of pathogenicity factors. The overall prevalence of Vibrio spp. in shrimps was 55·8%. Vibrio parahaemolyticus was recovered from 25 of 299 samples (8·4%), Vibrio cholerae from six samples (2%) and Vibrio alginolyticus from 161 samples (53·8%). No virulence genes were found among V. parahaemolyticus and V. cholerae isolates. The CHROMagar Vibrio plating medium was found to be more efficient than the Thiosulphate Citrate Bile salt Sucrose (TCBS) Agar in the isolation of Vibrio organisms.\n\nPrevalence of Vibrio spp. in raw shrimps (Parapenaeus longirostris) and performance of a chromogenic medium for the isolation of Vibrio strains.", "token_count": 388, "char_count": 1337, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:51.152727", "source": { "split": "train_shard_00000", "doc_id": 4330 }, "chunk_id": "train_shard_00000_4330_0", "global_id": 4829 }, { "text": "Plant pathogens and endophytes co-exist and often interact with the host plant and within its microbial community. The outcome of these interactions may lead to healthy plants through beneficial interactions, or to disease through the inducible production of molecules known as virulence factors. Unravelling the role of virulence in endophytes may crucially improve our understanding of host-associated microbial communities and their correlation with host health. Virulence is the outcome of a complex network of interactions, and drawing the line between pathogens and endophytes has proven to be conflictive, as strain-level differences in niche overlapping, ecological interactions, state of the host's immune system and environmental factors are seldom taken into account. Defining genomic differences between endophytes and plant pathogens is decisive for understanding the boundaries between these two groups. Here we describe the major differences at the genomic level between seven grapevine endophytic test bacteria, and 12 reference strains. We describe the virulence factors detected in the genomes of the test group, as compared to endophytic and non-endophytic references, to better understand the distribution of these traits in endophytic genomes. To do this, we adopted a comparative whole-genome approach, encompassing BLAST-based searches through the GUI-based tools Mauve and BRIG as well as calculating the core and accessory genomes of three genera of enterobacteria. We outline divergences in metabolic pathways of these endophytes and reference strains, with the aid of the online platform RAST. We present a summary of the major differences that help in the drawing of the boundaries between harmless and harmful bacteria, in the spirit of contributing to a microbiological definition of endophyte.\n\nWhole-genome comparative analysis of virulence genes unveils similarities and differences between endophytes and other symbiotic bacteria.", "token_count": 434, "char_count": 1964, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5464, "quality_score": 0.7732, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:51.786961", "source": { "split": "train_shard_00000", "doc_id": 4331 }, "chunk_id": "train_shard_00000_4331_0", "global_id": 4830 }, { "text": "Oral immunization with vaccines has proven its worth by eradicating several diseases worldwide, yet only few oral vaccines exist in practice. This is because the oral route is plagued with various challenges for successful delivery of vaccines, such as limited absorption and high degradation in the gastrointestinal tract. Tremendous research in the last decade has made bilosomes a potential carrier system for oral immunization. Bilosomes with its name derived from bile salts (which is one of its major constituent), is a 'niosome-like' colloidal carrier. The collective information addressed through this review, convincingly points out that factors such as size, composition (type of bile salt, and lipid), charge, ligand attached, etc., which show significant influence on the type, and amount of immunity developed following the oral administration of bilosomes. These bile salts containing vesicular carriers have been employed to treat various serious conditions. Some of these methods have been successfully established into patents. Bilosomes loaded with antigens, peptides and other biological materials for the treatment of influenza, heart failure, diuresis, Irritable Bowel Syndrome (IBS) and other gastrointestinal disorders have been discussed in the present article.\n\nBilosomes: A Novel Approach to Meet the Challenges in Oral Immunization.", "token_count": 305, "char_count": 1359, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:52.359188", "source": { "split": "train_shard_00000", "doc_id": 4332 }, "chunk_id": "train_shard_00000_4332_0", "global_id": 4831 }, { "text": "Extraintestinal pathogenic Escherichia coli (ExPEC) are among the most frequently isolated bacterial pathogens in hospitals. They are considered opportunistic pathogens and are found mostly in urinary and bloodstream infections. They are genetically diverse, and many studies have sought associations between genotypes or virulence genes and infection site, severity, or outcome, with varied, often contradictory, results. To understand these difficulties, we have analyzed the diversity patterns in the core genomes and virulomes of more than 500 ExPEC isolates from 5 different collections. The core genome was analyzed using a multilocus sequence type-based single-nucleotide polymorphism (SNP) pyrosequencing approach, while the virulence gene content (the virulome) was studied by polymerase chain reaction detection of 25 representative genes. SNP typing showed a similar population structure in the different collections: half of the isolates belong to a few sequence types (5 to 8), while the other half is composed of a large diversity of sequence types that are found once or twice. Sampling analysis by rarefaction plots of SNP profiles showed saturation curves indicative of a limited diversity. Contrary to this, the virulome shows an extremely high diversity, with almost as many gene profiles as isolates, and linear, nonsaturating, rarefaction plots, even within sequence types. These data show that genetic exchange rates are very heterogeneous along the chromosome, being much higher in the virulome fraction of the genome than in the core genome.\n\nUncoupling between core genome and virulome in extraintestinal pathogenic Escherichia coli.", "token_count": 383, "char_count": 1658, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:52.946546", "source": { "split": "train_shard_00000", "doc_id": 4333 }, "chunk_id": "train_shard_00000_4333_0", "global_id": 4832 }, { "text": "To achieve the food-grade expression of bile salt hydrolase (BSH, EC 3.5.1.24) from Lactobacillus plantarum BBE7, the nisin controlled gene expression system (NICE), food-grade selection maker and signal peptide of Lactococcus lactis were used in this study. The open reading frame of BSH was optimized based on the codon bias of L. lactis, resulting in 12-fold and 9.5% increases in the intracellular and extracellular BSH activities, respectively. Three synthetic propeptides, LEISSTCDA (acidic), LGISSTCNA (neutral) and LKISSTCHA (basic) were also fused with signal peptide SPusp45 of vector pNZ8112 and introduced into the food-grade expression vector pNZ8149, respectively. Among these propeptides, acidic propeptide was effective in increasing the secretion efficiency and yield of BSH in recombinant bacteria, while neutral propeptide had no significant effect on the secretion of BSH. In contrast, basic propeptide strongly reduced the extracellular expression of BSH. By using codon optimization and the acidic propeptide together, the extracellular BSH activity was increased by 11.3%, reaching its maximum of 3.56 U/mg. To the best of our knowledge, this is the first report on the intracellular and extracellular expression of BSH using food-grade expression system, which would lay a solid foundation for large-scale production of BSH and other heterologous proteins in L. lactis.\n\nCodon and Propeptide Optimizations to Improve the Food-grade Expression of Bile Salt Hydrolase in Lactococcus lactis.", "token_count": 429, "char_count": 1512, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5826, "quality_score": 0.7913, "entities": { "genes": [ "BBE7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:53.570712", "source": { "split": "train_shard_00000", "doc_id": 4334 }, "chunk_id": "train_shard_00000_4334_0", "global_id": 4833 }, { "text": "Small non-coding RNAs constitute a large family of regulatory molecules with diverse function. Knowledge about small RNAs in fungi remains limited. Here, a RNA-seq-based analysis of small RNA transcriptome from the wheat pathogenic fungus Zymoseptoria tritici under nutrient-stress and nutrient-rich growth conditions is presented. Small RNAs mapped to Z. tritici genomic features including sense and antisense strands of genes, repetitive elements, rRNAs, snRNA, snoRNA and tRNA loci throughout the chromosomes. The majority of small RNAs from rich condition mapped to all the chromosomes, primarily the sense strand of chromosome seven, but under stress condition, small RNAs were enriched in accessory genome. Inspection of the predominant small RNAs matching to protein-coding genes, repeats and rRNAs revealed that intron and LTP retrotransposon-derived small RNAs accumulated upon stress, whereas rRNA-derived small RNAs were enriched for nutrient-rich condition. U enrichment at position 1 of small RNAs mapping to repeats and antisense-strand genes was only observed from stress library. Additionally, target analysis of one predicted milRNA suggests its potential role in fungal pathogenesis and manipulation of host immunity. Taken together, the findings provide a new insight into the function of small RNAs in regulating growth and development, stress adaptation, and possibly pathogenesis in Z. tritici.\n\nGenome-wide analysis of small RNAs in the wheat pathogenic fungus Zymoseptoria tritici.", "token_count": 386, "char_count": 1505, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:54.185542", "source": { "split": "train_shard_00000", "doc_id": 4335 }, "chunk_id": "train_shard_00000_4335_0", "global_id": 4834 }, { "text": "The bile salt export pump (BSEP or Bsep) functions as an apical transporter to eliminate bile acids (BAs) from hepatocytes into the bile. BSEP or Bsep inhibitors engender BA retention, suggested as an underlying mechanism of cholestatic drug-induced liver injury. We previously reported a method to evaluate BSEP-mediated BA-dependent hepatocyte toxicity by using sandwich-cultured hepatocytes (SCHs). However, basal efflux transporters, including multidrug resistance-associated proteins (MRP or Mrp) 3 and 4, also participate in BA efflux. This study examined the contribution of basal efflux transporters to BA-dependent hepatocyte toxicity in rat SCHs. The apical efflux of [(3)H]taurocholic acid (TC) was potently inhibited by 10 μM cyclosporine A (CsA), with later inhibition of basal [(3)H]TC efflux, while MK571 simultaneously inhibited both apical and basal [(3)H]TC efflux. CsA-induced BA-dependent hepatocyte toxicity was 30% at most at 10 μM CsA and ∼60% at 50 μM, while MK571 exacerbated hepatocyte toxicity at concentrations of ≥50 μM. Quinidine inhibited only basal [(3)H]TC efflux and showed BA-dependent hepatocyte toxicity in rat SCHs. Hence, inhibition of basal efflux transporters as well as Bsep may precipitate BA-dependent hepatocyte toxicity in rat SCHs.\n\nBasal efflux of bile acids contributes to drug-induced bile acid-dependent hepatocyte toxicity in rat sandwich-cultured hepatocytes.", "token_count": 457, "char_count": 1412, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5678, "quality_score": 0.7839, "entities": { "genes": [ "MK571" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:54.822945", "source": { "split": "train_shard_00000", "doc_id": 4336 }, "chunk_id": "train_shard_00000_4336_0", "global_id": 4835 }, { "text": "Bacteriocin producing strain BDU3 was isolated from a traditional fermented fish of Manipur Ngari. The strain BDU3 was identified as Bacillus coagulans by phenotypic and genotypic characterization. The BDU3 produced novel bacteriocin, which showed an antimicrobial spectrum toward a wide spectrum of food borne, and closely related pathogens with a MIC that ranged between 0.5 and 2.5 μg/mL. The isolate was able to tolerate pH as low as 2.0 and up to 0.2% bile salt concentration. Three step purification was employed to increase the specific activity of the antimicrobial compound. The fractions were further chromatographed by Rp-HPLC C-18 column and the purified bacteriocin had a specific activity of ∼8500 AU/mg. However, the potency of bacteriocin was susceptible to digestion with Proteinase K, Pepsin, SDS, EDTA and Urea. Molecular mass of purified bacteriocin was found to be 1.4 kDa using matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). The functional group was revealed by FTIR analysis. The cytotoxicity assay (MTT) using purified bacteriocin showed 2 times lower EC50 values compared to SDS. This is the smaller bacteriocin ever reported before from B. coagulans with greater antimicrobial potency with lower cytotoxicity. This bacteriocin raises the possibilities to be used as a biopreservative in food industries.\n\nBacteriocinogenic potential of a probiotic strain Bacillus coagulans [BDU3] from Ngari.", "token_count": 413, "char_count": 1443, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [ "EC50", "BDU3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:55.445678", "source": { "split": "train_shard_00000", "doc_id": 4337 }, "chunk_id": "train_shard_00000_4337_0", "global_id": 4836 }, { "text": "Immunohistochemistry often plays an important role in the evaluation of liver tumors. Recent advances have established a classification system for hepatocellular adenomas (HCAs) based on morphology, molecular alterations, and immunohistochemistry. Specifically, loss of liver fatty acid binding protein is seen in HNF1α-inactivated HCA, staining with serum amyloid A is seen in inflammatory HCA, and diffuse staining with glutamine synthetase (GS) is seen in β-catenin activated HCA. A panel of immunohistochemical stains including glypican-3 (GPC-3), heat shock protein 70, and GS are useful in distinguishing HCC from non-malignant dysplastic nodules. Immunohistochemistry is also useful to determine whether a liver tumor is of primary hepatocellular or metastatic origin. Recently described markers useful for this purpose include arginase-1, GPC-3, and bile salt export pump. These newer markers may offer superior utility when compared to traditional markers of hepatocellular differentiation such as alpha-fetoprotein, hepatocyte paraffin-1, polyclonal carcinoembryonic antigen, and CD10. This paper will review recent advances in the immunohistochemical evaluation of liver tumors.\n\nCurrent concepts in the immunohistochemical evaluation of liver tumors.", "token_count": 342, "char_count": 1262, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6845, "quality_score": 0.8423, "entities": { "genes": [ "CD10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:56.026978", "source": { "split": "train_shard_00000", "doc_id": 4338 }, "chunk_id": "train_shard_00000_4338_0", "global_id": 4837 }, { "text": "Pseudomonas fluorescens is a well-known food spoiler, able to cause serious economic losses in the food industry due to its ability to produce many extracellular, and often thermostable, compounds. The most outstanding spoilage events involving P. fluorescens were blue discoloration of several food stuffs, mainly dairy products. The bacteria involved in such high-profile cases have been identified as belonging to a clearly distinct phylogenetic cluster of the P. fluorescens group. Although the blue pigment has recently been investigated in several studies, the biosynthetic pathway leading to the pigment formation, as well as its chemical nature, remain challenging and unsolved points. In the present paper, genomic and transcriptomic data of 4 P. fluorescens strains (2 blue-pigmenting strains and 2 non-pigmenting strains) were analyzed to evaluate the presence and the expression of blue strain-specific genes. In particular, the pangenome analysis showed the presence in the blue-pigmenting strains of two copies of genes involved in the tryptophan biosynthesis pathway (including trpABCDF). The global expression profiling of blue-pigmenting strains versus non-pigmenting strains showed a general up-regulation of genes involved in iron uptake and a down-regulation of genes involved in primary metabolism. Chromogenic reaction of the blue-pigmenting bacterial cells with Kovac's reagent indicated an indole-derivative as the precursor of the blue pigment. Finally, solubility tests and MALDI-TOF mass spectrometry analysis of the isolated pigment suggested that its molecular structure is very probably a hydrophobic indigo analog.\n\nA genomic and transcriptomic approach to investigate the blue pigment phenotype in Pseudomonas fluorescens.", "token_count": 428, "char_count": 1754, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:56.650172", "source": { "split": "train_shard_00000", "doc_id": 4339 }, "chunk_id": "train_shard_00000_4339_0", "global_id": 4838 }, { "text": "The present work aimed to identify probiotic bacteria from healthy human infant faecal and dairy samples. Subsequently, an assay was developed to evaluate the probiotic properties using comparative genetic approach for marker genes involved in adhesion to the intestinal epithelial layer. Several in vitro properties including tolerance to biological barriers (such as acid and bile), antimicrobial spectrum, resistance to simulated digestive fluids and cellular hydrophobicity were assessed. The potential probiotic cultures were rapidly characterized by morphological, physiological and molecular-based methods [such as RFLP, ITS, RAPD and (GTG)5]. Further analysis by 16S rDNA sequencing revealed that the selected isolates belong to Lactobacillus, Pediococcus and Enterococcus species. Two cultures of non-lactic, non-pathogenic Staphylococcus spp. were also isolated. The native isolates were able to survive under acidic, bile and simulated intestinal conditions. In addition, these cultures inhibited the growth of tested bacterial pathogens. Further, no correlation was observed between hydrophobicity and adhesion ability. Sequencing of probiotic marker genes such as bile salt hydrolase (bsh), fibronectin-binding protein (fbp) and mucin-binding protein (mub) for selected isolates revealed nucleotide variation. The probiotic binding domains were detected by several bioinformatic tools. The approach used in the study enabled the identification of potential probiotic domains responsible for adhesion of bacteria to intestinal epithelial layer, which may further assist in screening of novel probiotic bacteria. The rapid detection of binding domains will help in revealing the beneficial properties of the probiotic cultures. Further, studies will be performed to develop a novel probiotic product which will contribute in food and feed industry.\n\nScreening, Characterization and In Vitro Evaluation of Probiotic Properties Among Lactic Acid Bacteria Through Comparative Analysis.", "token_count": 454, "char_count": 1993, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:57.292925", "source": { "split": "train_shard_00000", "doc_id": 4340 }, "chunk_id": "train_shard_00000_4340_0", "global_id": 4839 }, { "text": "Taxonomic classification of Clostridium botulinum is based on the production of botulinum neurotoxin (BoNT), while closely related, nontoxic organisms are classified as Clostridium sporogenes. However, this taxonomic organization does not accurately mirror phylogenetic relationships between these species. A phylogenetic reconstruction using 2,016 orthologous genes shared among strains of C. botulinum group I and C. sporogenes clearly separated these two species into discrete clades which showed ∼93% average nucleotide identity (ANI) between them. Clustering of strains based on the presence of variable orthologs revealed 143 C. sporogenes clade-specific genetic signatures, a subset of which were further evaluated for their ability to correctly classify a panel of presumptive C. sporogenes strains by PCR. Genome sequencing of several C. sporogenes strains lacking these signatures confirmed that they clustered with C. botulinum strains in a core genome phylogenetic tree. Our analysis also identified C. botulinum strains that contained C. sporogenes clade-specific signatures and phylogenetically clustered with C. sporogenes strains. The genome sequences of two bont/B2-containing strains belonging to the C. sporogenes clade contained regions with similarity to a bont-bearing plasmid (pCLD), while two different strains belonging to the C. botulinum clade carried bont/B2 on the chromosome. These results indicate that bont/B2 was likely acquired by C. sporogenes strains through horizontal gene transfer. The genome-based classification of these species used to identify candidate genes for the development of rapid assays for molecular identification may be applicable to additional bacterial species that are challenging with respect to their classification.\n\nImplications of Genome-Based Discrimination between Clostridium botulinum Group I and Clostridium sporogenes Strains for Bacterial Taxonomy.", "token_count": 472, "char_count": 1918, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5676, "quality_score": 0.7838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:57.943000", "source": { "split": "train_shard_00000", "doc_id": 4341 }, "chunk_id": "train_shard_00000_4341_0", "global_id": 4840 }, { "text": "This paper presents the results of a study to determine the effect of Quillaja saponaria saponins on the lysis of industrial yeast strains. Cell lysis induced by saponin from Q. saponaria combined with the plasmolysing effect of 5% NaCl for Saccharomyces cerevisiae, Kluyveromyces marxianus yeasts biomass was conducted at 50 °C for 24-48 h. Membrane permeability and integrity of the yeast cells were monitored using fluorescent techniques and concentrations of proteins, free amino nitrogen (FAN) and free amino acids in resulting lysates were analyzed. Protein release was significantly higher in the case of yeast cell lysis promoted with 0.008% Q. saponaria and 5% NaCl in comparison to plasmolysis triggered by NaCl only.\n\nCell lysis induced by membrane-damaging detergent saponins from Quillaja saponaria.", "token_count": 228, "char_count": 812, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:58.437868", "source": { "split": "train_shard_00000", "doc_id": 4342 }, "chunk_id": "train_shard_00000_4342_0", "global_id": 4841 }, { "text": "Destruction of cholangiocytes is the hallmark of chronic cholangiopathies such as primary biliary cirrhosis. Under physiologic conditions, cholangiocytes display a striking resistance to the high, millimolar concentrations of toxic bile salts present in bile. We recently showed that a 'biliary HCO3(-) umbrella', i.e. apical cholangiocellular HCO3(-) secretion, prevents cholangiotoxicity of bile acids, and speculated on a role for extracellular membrane-bound glycans in the stabilization of this protective layer. This paper summarizes published and thus far unpublished evidence supporting the role of the glycocalyx in stabilizing the 'biliary HCO3(-) umbrella' and thus preventing cholangiotoxicity of bile acids.\n\nThe Cholangiocyte Glycocalyx Stabilizes the 'Biliary HCO3 Umbrella': An Integrated Line of Defense against Toxic Bile Acids.", "token_count": 242, "char_count": 846, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8451, "entities": { "genes": [ "HCO3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:58.935264", "source": { "split": "train_shard_00000", "doc_id": 4343 }, "chunk_id": "train_shard_00000_4343_0", "global_id": 4842 }, { "text": "Infection of hepatitis B virus (HBV) remains a major public health problem worldwide. Understanding the viral infection and developing antivirals against HBV have been hampered by the lack of convenient culture systems and animal models for the infection. Sodium taurocholate cotransporting polypeptide (NTCP), a key bile acid transporter expressed in liver, was recently identified as a critical receptor for viral entry of HBV and its satellite virus hepatitis D virus (HDV). This finding enabled a reliable cell culture system for the viruses. Detailed studies have shown that NTCP is the major determinant for the species specificity of HBV and HDV at entry level. NTCP is responsible for most sodium-dependent bile salt uptake in liver. The molecular determinant critical for HBV/HDV infection overlaps with that for bile acids transporting on NTCP. We evaluated bile acids as potential antivirals for HBV and HDV infection, and developed bile acid derivatives that effectively block taurocholate transporting as well as viral infections. The discovery that NTCP acts as a receptor for HBV has opens a new door for future studies towards the ultimate goal of curative treatment of HBV infection.\n\nSodium taurocholate cotransporting polypeptide acts as a receptor for hepatitis B and D virus.", "token_count": 321, "char_count": 1296, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5628, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:42:59.543404", "source": { "split": "train_shard_00000", "doc_id": 4344 }, "chunk_id": "train_shard_00000_4344_0", "global_id": 4843 }, { "text": "A directed evolution and random mutagenesis were carried out with thermotolerant yeast Kluyveromyces marxianus ATCC 36907 for efficient xylitol production. The final selected strain, K. marxianus 36907-FMEL1, exhibited 120 and 39 % improvements of xylitol concentration and xylitol yield, respectively, as compared to the parental strain, K. marxianus ATCC 36907. According to enzymatic assays for xylose reductase (XR) activities, XR activity from K. marxianus 36907-FMEL1 was around twofold higher than that from the parental strain. Interestingly, the ratios of NADH-linked and NADPH-linked XR activities were highly changed from 1.92 to 1.30 when K. marxianus ATCC 36907 and K. marxianus 36907-FMEL1 were compared. As results of KmXYL1 genes sequencing, it was found that cysteine was substituted to tyrosine at position 36 after strain development which might cause enhanced XR activity from K. marxianus 36907-FMEL1.\n\nEnhanced Xylitol Production by Mutant Kluyveromyces marxianus 36907-FMEL1 Due to Improved Xylose Reductase Activity.", "token_count": 343, "char_count": 1040, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6463, "quality_score": 0.8231, "entities": { "genes": [ "FMEL1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:00.131916", "source": { "split": "train_shard_00000", "doc_id": 4345 }, "chunk_id": "train_shard_00000_4345_0", "global_id": 4844 }, { "text": "The development of rapid and efficient genome sequencing methods has enabled us to study the evolutionary background of bacterial genetic information. Here, we present comparative genomic analysis of 17 Streptomyces species, for which the genome has been completely sequenced, using the pan-genome approach. The analysis revealed that 34,592 ortholog clusters constituted the pan-genome of these Streptomyces species, including 2,018 in the core genome, 11,743 in the dispensable genome, and 20,831 in the unique genome. The core genome was converged to a smaller number of genes than reported previously, with 3,096 gene families. Functional enrichment analysis showed that genes involved in transcription were most abundant in the Streptomyces pan-genome. Finally, we investigated core genes for the sigma factors, mycothiol biosynthesis pathway, and secondary metabolism pathways; our data showed that many genes involved in stress response and morphological differentiation were commonly expressed in Streptomyces species. Elucidation of the core genome offers a basis for understanding the functional evolution of Streptomyces species and provides insights into target selection for the construction of industrial strains.\n\nComparative Genomics Reveals the Core and Accessory Genomes of Streptomyces Species.", "token_count": 310, "char_count": 1313, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8104, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:00.706074", "source": { "split": "train_shard_00000", "doc_id": 4346 }, "chunk_id": "train_shard_00000_4346_0", "global_id": 4845 }, { "text": "Biorelevant media are commonly used to simulate the physiological composition of human intestinal fluids (HIF) in in vitro solubility and dissolution investigations. In comparison with the surfactant solutions or blank buffers, these media are able to better reflect the physiological solubility and dissolution behavior of poorly soluble active pharmaceutical ingredients (APIs). The aim of this investigation was to review the composition of FaSSIF and FaSSIF-V2 according to recently summarized data about the physiological composition of fasted state human intestinal fluid and propose an updated version, FaSSIF-V3. Furthermore the surface tension was considered as a possible surrogate parameter to gauge the physiological correctness of new versions of biorelevant media. Various prototypes of FaSSIF-V3 were prepared with each of the following five bile salts: taurocholate (TC), glycocholate (GC), tauroursodeoxycholate (TUDC), taurochenodeoxycholate (TCDC) and glycochenodeoxycholate (GCDC) as well as replacing lecithin with its hydrolysis products, lysolecithin and sodium oleate. Two additional media consisting of a mixture of glycocholate (GC) and taurocholate (TG), with or without 0.2mM cholesterol, were also investigated. Solubilities of ten model compounds in various prototypes of FaSSIF-V3 were measured using HPLC-UV and compared to the solubilities in the existing biorelevant media (FaSSIF and FaSSIF-V2), fasted HIF, blank buffer and a 0.5% sodium dodecyl sulfate (SDS) solution. Additionally, the influence on the surface tension properties of various combinations of bile salts, phospholipids and their hydrolysis products and cholesterol in these media was investigated and an attempt was made to calculate the CMC of the various generations of FaSSIF. The results demonstrated that the amount and the type of phospholipids as well as the type of bile salt had a significant influence on the solubility and surface tension in the various FaSSIF-V3 prototypes and existing biorelevant media", "token_count": 516, "char_count": 2018, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5474, "quality_score": 0.7737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:43:01.368189", "source": { "split": "train_shard_00000", "doc_id": 4347 }, "chunk_id": "train_shard_00000_4347_0", "global_id": 4846 }, { "text": "In contrast to results with biorelevant media, it was demonstrated that blank buffers generally underestimate and SDS solutions highly overestimate the physiological relevant solubilities of all investigated APIs. The prototype containing FaSSIF-V3-GC/TC_Chol was able to better reflect the solubilities of the most investigated APIs in fasted HIF than the existing media, and it also matched the physiological surface tension reported for the fasted human gut, and was designated FaSSIF-V3.\n\nAdvances in the design of fasted state simulating intestinal fluids: FaSSIF-V3.", "token_count": 137, "char_count": 572, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:01.794470", "source": { "split": "train_shard_00000", "doc_id": 4347 }, "chunk_id": "train_shard_00000_4347_1", "global_id": 4847 }, { "text": "Colloidal dispersions of crystalline nonpolar lipids are under intensive investigation as carrier systems in pharmaceutics and nutrition. In this context, the controlled preparation of particles in a metastable polymorphic state is of some interest for the delivery of active substances. In the present study, tristearin particles stabilized with three α-polymorph-preserving emulsifier regimes ((I) sodium glycocholate/saturated long-chain phospholipids, (II) sodium glycocholate, and (III) poly(vinyl alcohol) (PVA)) were investigated concerning the stability of the metastable α-polymorph after controlled crystallization of the particles from the melt. Upon long-term storage, the α-polymorph was preserved best in PVA-stabilized dispersions, followed by those stabilized with the glycocholate/phospholipid mixture and finally those stabilized solely with the bile salt. In particular for rapidly crystallized nanoparticles, the formation of an α-polymorph with highly reduced lamellarity was observed. According to time-/temperature-resolved synchrotron X-ray diffraction analysis with simultaneous DSC (differential scanning calorimetry) studies, this less-ordered α-polymorph transformed into the common, lamellar α-form upon heating. Although the presence of the less-ordered form is probably related to the extraordinarily high stability of the metastable α-polymorph observed in some of the dispersions, it could not completely prevent the transition into the stable β-polymorph. The higher the transition temperature of the less-ordered α-form to the ordered one, the slower was the polymorphic transition to the stable β-polymorph. To estimate the polymorphic stability of the differently stabilized particles upon isothermal long-term storage, standard DSC measurements on samples stored at 23 °C for 4 weeks seem to be of predictive value.\n\nStability of the Metastable α-Polymorph in Solid Triglyceride Drug-Carrier Nanoparticles.", "token_count": 492, "char_count": 1944, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:02.445168", "source": { "split": "train_shard_00000", "doc_id": 4348 }, "chunk_id": "train_shard_00000_4348_0", "global_id": 4848 }, { "text": "Palm empty fruit bunches (EFBs) are abundant lignocellulosic wastes from palm oil mills. They are potential sources of sugars which can be converted to microbial lipids by oleaginous yeasts. To produce sugars from EFB, two-step and one-step hydrolysis reactions were performed. In the first step, the use of diluted sulfuric acid (0.5 % w/v) hydrolyzed hemicelluloses and released mainly pentoses, and in the second step of hydrolysis of residual pulp using 2.5 % (w/v), sulfuric acid released more hexoses. The use of 2.5 % (w/v) sulfuric acid in one-step hydrolysis of holocelluloses released the highest amount of sugars (38.3 g/L), but it also produced high concentration of potential inhibitors (>1 g/L). Three oleaginous yeasts, Rhodotorula mucilaginosa, Kluyveromyces marxianus, and Candida tropicalis, were isolated and screened for their ability to convert EFB hydrolysates into lipids. These yeasts grew well and produced lipids from EFB hemicellulose and holocellulose hydrolysate after potential inhibitors were removed. This study shows that EFB can be used for lipid production.\n\nLipid Production from Hemicellulose and Holocellulose Hydrolysate of Palm Empty Fruit Bunches by Newly Isolated Oleaginous Yeasts.", "token_count": 359, "char_count": 1224, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:03.020773", "source": { "split": "train_shard_00000", "doc_id": 4349 }, "chunk_id": "train_shard_00000_4349_0", "global_id": 4849 }, { "text": "Salmonella enterica serovar Typhimurium is the most common Salmonella serovar causing foodborne infections in Australia and many other countries. Twenty-one S. Typhimurium strains from Salmonella reference collection A (SARA) were analyzed using Illumina high-throughput genome sequencing. Single nucleotide polymorphisms (SNPs) in 21 SARA strains ranged from 46 to 11,916 SNPs, with an average of 1,577 SNPs per strain. Together with 47 strains selected from publicly available S. Typhimurium genomes, the S. Typhimurium core genes (STCG) were determined. The STCG consist of 3,846 genes, a set that is much larger than that of the 2,882 Salmonella core genes (SCG) found previously. The STCG together with 1,576 core intergenic regions (IGRs) were defined as the S. Typhimurium core genome. Using 93 S. Typhimurium genomes from 13 epidemiologically confirmed community outbreaks, we demonstrated that typing based on the S. Typhimurium core genome (STCG plus core IGRs) provides superior resolution and higher discriminatory power than that based on SCG for outbreak investigation and molecular epidemiology of S. Typhimurium. STCG and STCG plus core IGR typing achieved 100% separation of all outbreaks compared to that of SCG typing, which failed to separate isolates from two outbreaks from background isolates. Defining the S. Typhimurium core genome allows standardization of genes/regions to be used for high-resolution epidemiological typing and genomic surveillance of S. Typhimurium.\n\nDefining the Core Genome of Salmonella enterica Serovar Typhimurium for Genomic Surveillance and Epidemiological Typing.", "token_count": 451, "char_count": 1616, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5819, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:03.654289", "source": { "split": "train_shard_00000", "doc_id": 4350 }, "chunk_id": "train_shard_00000_4350_0", "global_id": 4850 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC 2) results from mutations in ABCB11 gene coding bile salt export pump (BSEP). Medical treatment is usually unsuccessful and surgery intervention is necessary. Partial external biliary diversion (PEBD) is regarded as the first choice of surgical treatment. Ileal exclusion (IE) is an alternative operation if external stoma is not tolerated; however, a favorable outcome is uncertain. In chronic liver diseases pregnancy brings additional risk of deterioration of liver function and generally is not recommended. We present the first case report of successful pregnancy in a genetically confirmed PFIC 2 patient after surgical conversion from PEBD to IE.\n\nSuccessful pregnancy after ileal exclusion in progressive familial intrahepatic cholestasis type 2.", "token_count": 186, "char_count": 813, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7155, "quality_score": 0.8578, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:04.452427", "source": { "split": "train_shard_00000", "doc_id": 4351 }, "chunk_id": "train_shard_00000_4351_0", "global_id": 4851 }, { "text": "Non-alcoholic fatty liver disease (NAFLD) is the most common cause of chronic liver disease. Patients with non-alcoholic steatohepatitis (NASH) have increased plasmatic and hepatic concentrations of bile acids (BA), suggesting that they can be associated with the progression of the disease. Hepatic nuclear receptors are known to modulate genes controlling BA metabolism; thus, in this work we aimed to compare the expression of liver nuclear receptors -farnesoid X (FXR), small heterodimer partner (SHP) and liver X alpha (LXRα) receptors- and BA transporters -sodium+/taurocholate cotransporting polypeptide (NTCP) and bile salt export pump (BSEP)- in liver biopsy samples of patients with simple steatosis (SS) and NASH.\n\nThe nuclear receptor FXR, but not LXR, up-regulates bile acid transporter expression in non-alcoholic fatty liver disease.", "token_count": 236, "char_count": 848, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:04.918627", "source": { "split": "train_shard_00000", "doc_id": 4352 }, "chunk_id": "train_shard_00000_4352_0", "global_id": 4852 }, { "text": "Eggs of the pig whipworm, Trichuris suis ova (TSO), are currently tested in human clinical trials for their potential immunomodulatory capacity. The biological potency of TSO (egg viability and infectivity) is traditionally assessed in Göttingen minipigs as the establishment of intestinal larvae after inoculation with a known number of eggs. To minimize testing in animal models, development of an in vitro egg hatching assay is proposed as a reliable, cost-effective, and a faster alternative to test the egg viability. The present study aimed to investigate the influence of different chemical, physical, and biological factors on egg hatching. Thus, in a series of experiments and in different combinations, the eggs were stimulated with glass beads, artificial gastric juice, bile salt and trypsin solution, fermentation gut medium, or stimulated with mucosal scrapings from the ileum and the large intestine of the infected and uninfected Göttingen minipig. Mechanical stimulation with glass beads presented a simple and reproducible method for egg hatching. However, incubation of eggs with mucosal scrapings from the ileum, caecum, and colon for 24 h at 38 °C significantly increased hatching.\n\nIn vitro hatching of Trichuris suis eggs.", "token_count": 318, "char_count": 1245, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:05.482843", "source": { "split": "train_shard_00000", "doc_id": 4353 }, "chunk_id": "train_shard_00000_4353_0", "global_id": 4853 }, { "text": "The objective of this study was to characterize native Lactobacillus fermentum isolates for their probiotic attributes. Accordingly, 12 L. fermentum isolates selected from indigenous fermented dairy products and infant fecal samples were evaluated for their probiotic properties by in vitro and PCR methods. The cultures exhibited high tolerance to acid and bile as well as survival in simulated transit fluids (above 70 %). Cell surface hydrophobicity was in the range of 0.55-57.69 % for xylene and 0.45-77.12 % for hexadecane, whereas auto-aggregation ranged between 9 and 62 %. Isolates exhibited efficient binding to mucin and fibronectin, bile salt hydrolase activity, cholesterol assimilation (49-76 %), and radical scavenging activity (37-77 %). The isolates demonstrated antibacterial activity against Listeria monocytogenes Scott A and Micrococcus luteus ATCC 9341. Molecular fingerprinting and identification of the isolates were achieved by PCR with GTG5 as well as 16S rRNA, phenylalanyl-tRNA synthetase alpha subunit (pheS), and RNA polymerase alpha subunit (rpoA) genes. This revealed the genomic diversity of the isolates from the two sources. Gene-specific amplification of probiotic marker genes was attained by PCR-based methods, and resultant products were sequenced. Multiple sequence alignment of the probiotic marker genes using bioinformatics revealed similarity to completely sequenced genomes of L. fermentum CECT 5716 and IFO 3956 with a few variations in mucin-binding protein gene sequences. Isolates designated as L. fermentum MCC 2759 and L. fermentum MCC 2760 showed the best probiotic attributes with high survival in simulated gastrointestinal fluids, in vitro adhesion, cholesterol reduction, and high antioxidative potential. Thus, these cultures could be potential probiotic candidates for application as functional foods.", "token_count": 515, "char_count": 1859, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6336, "quality_score": 0.8168, "entities": { "genes": [ "GTG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:43:06.135159", "source": { "split": "train_shard_00000", "doc_id": 4354 }, "chunk_id": "train_shard_00000_4354_0", "global_id": 4854 }, { "text": "Probiotic attributes of Lactobacillus fermentum isolated from human feces and dairy products.", "token_count": 24, "char_count": 93, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:06.498431", "source": { "split": "train_shard_00000", "doc_id": 4354 }, "chunk_id": "train_shard_00000_4354_1", "global_id": 4855 }, { "text": "β-Galactosidases from Kluyveromyces lactis and Kluyveromyces marxianus isolated from artisanal ewes' milk cheeses, were used to transgalactosylate lactose from cheese whey permeate (WP). The content of galactooligosaccharides (GOS) obtained by transgalactosylation was comparable with that formed using pure lactose as substrate. In order to obtain a mixture with higher prebiotic oligosaccharide content, isomerisation of the transgalactosylated WP was carried out using sodium aluminate as catalyst. The transgalactosylated mixtures at 6 h of reaction contained amounts of prebiotic carbohydrates (tagatose, lactulose, GOS and oligosaccharides derived from lactulose, OsLu) close to 50 g/100 g of total carbohydrates for all the strains tested, corresponding to 322 g prebiotics/kg whey permeate. Thus, the suitability of this methodology to produce mixtures of dietary non-digestible carbohydrates with prebiotic properties from WP has been demonstrated, which is interesting for the food industry since it increases the value and the applicability of this by-product from cheese manufacture.\n\nProduction of lactulose oligosaccharides by isomerisation of transgalactosylated cheese whey permeate obtained by β-galactosidases from dairy Kluyveromyces.", "token_count": 356, "char_count": 1253, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6506, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:07.072788", "source": { "split": "train_shard_00000", "doc_id": 4355 }, "chunk_id": "train_shard_00000_4355_0", "global_id": 4856 }, { "text": "The aim of this study was to develop a new selective and differential medium for isolating Shigella sonnei (designated 3SD medium). The new medium was based on three carbohydrates (lactose, sorbitol, and xylose) and a chromogenic substrate (5-bromo-4-chloro-3-indolyl-β-D-galactopyranoside, X-Gal). S. sonnei cannot ferment lactose, sorbitol, or xylose, but can ferment X-Gal, which generates turquoise-blue colonies with rough edges. Other bacteria (54 strains of foodborne pathogens and spoilage bacteria) produced visually distinct colonies on 3SD medium (colorless or pink-violet colonies), or their growth was inhibited on 3SD medium. The optimum concentration of 50 mg/L X-Gal was selected because it yielded the highest level of morphological discrimination between S. sonnei and other bacteria, and this concentration was cost-effective. Bile salt concentration optimization was performed using healthy, heat-injured, and acid-injured S. sonnei. The recovery rate differed significantly depending on the bile salt concentration; media containing >1.0 g/L bile salt showed significantly lower recovery of stress-injured cells than medium containing 0.5 g/L bile salt (P<0.05). Growth of all Gram-positive bacteria was inhibited on medium containing 0.5 g/L bile salt; therefore, this concentration was used as the optimal concentration. Previous media used to isolate Shigella spp. (MacConkey, xylose lysine desoxycholate, and Salmonella-Shigella agar) showed poor performance when used to support the growth of injured S. sonnei cells, whereas 3SD medium supported a high growth rate of injured and healthy cells (equivalent to that obtained with nutrient-rich tryptic soy agar). To validate the performance of 3SD medium with real specimens, S. sonnei and other bacteria were spiked into samples such as untreated water, carrot, salad, and oyster. 3SD medium showed superior specificity (100%) and sensitivity (100%) for S", "token_count": 522, "char_count": 1931, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:43:07.727703", "source": { "split": "train_shard_00000", "doc_id": 4356 }, "chunk_id": "train_shard_00000_4356_0", "global_id": 4857 }, { "text": "sonnei, and yielded no false-positive or false-negative results. Thus, the novel 3SD medium described herein is a powerful tool for the rapid and efficient selective isolation of S. sonnei in research and clinical laboratories, and the food industry.\n\nDevelopment of selective and differential medium for Shigella sonnei using three carbohydrates (lactose, sorbitol, and xylose) and X-Gal.", "token_count": 106, "char_count": 389, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:08.104548", "source": { "split": "train_shard_00000", "doc_id": 4356 }, "chunk_id": "train_shard_00000_4356_1", "global_id": 4858 }, { "text": "Among the perfluoroalkyl sulfonates (PFASs), perfluorohexane sulfonate (PFHxS), and perfluorooctane sulfonate (PFOS) have half-lives of several years in humans, mainly due to slow renal clearance and potential hepatic accumulation. Both compounds undergo enterohepatic circulation. To determine whether transporters involved in the enterohepatic circulation of bile acids are also involved in the disposition of PFASs, uptake of perfluorobutane sulfonate (PFBS), PFHxS, and PFOS was measured using freshly isolated human and rat hepatocytes in the absence or presence of sodium. The results demonstrated sodium-dependent uptake for all 3 PFASs. Given that the Na(+)/taurocholate cotransporting polypeptide (NTCP) and the apical sodium-dependent bile salt transporter (ASBT) are essential for the enterohepatic circulation of bile acids, transport of PFASs was investigated in stable CHO Flp-In cells for human NTCP or HEK293 cells transiently expressing rat NTCP, human ASBT, and rat ASBT. The results demonstrated that both human and rat NTCP can transport PFBS, PFHxS, and PFOS. Kinetics with human NTCP revealed Km values of 39.6, 112, and 130 µM for PFBS, PFHxS, and PFOS, respectively. For rat NTCP Km values were 76.2 and 294 µM for PFBS and PFHxS, respectively. Only PFOS was transported by human ASBT whereas rat ASBT did not transport any of the tested PFASs. Human OSTα/β was also able to transport all 3 PFASs. In conclusion, these results suggest that the long half-live and the hepatic accumulation of PFOS in humans are at least, in part, due to transport by NTCP and ASBT.", "token_count": 488, "char_count": 1587, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [ "HEK293" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:08.755076", "source": { "split": "train_shard_00000", "doc_id": 4357 }, "chunk_id": "train_shard_00000_4357_0", "global_id": 4859 }, { "text": "Na+/Taurocholate Cotransporting Polypeptide and Apical Sodium-Dependent Bile Acid Transporter Are Involved in the Disposition of Perfluoroalkyl Sulfonates in Humans and Rats.", "token_count": 57, "char_count": 174, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:09.113519", "source": { "split": "train_shard_00000", "doc_id": 4357 }, "chunk_id": "train_shard_00000_4357_1", "global_id": 4860 }, { "text": "In the present study 177 Lactobacillus spp. strains, isolated from Ragusano and Pecorino Siciliano cheeses, were in vitro screened for probiotic traits, and their characteristics were compared to those of Lactobacillus rhamnosus GG, commercial strain. Based on acidic and bile salt resistance, thirteen Lactobacillus strains were selected. The multiplex-PCR application revealed that nine strains belonged to L. rhamnosus species and four to Lactobacillus paracasei species. All selected strains were further investigated for transit tolerance in simulated upper gastrointestinal tract (GI), for adhesion capacity to human intestinal cell lines, for hydrophobicity, for co-aggregation and auto-aggregation and for antimicrobial activities. Moreover, antibiotic resistance, hemolytic and bile salt hydrolase activities were investigated for safety assessment. Viable counts after simulated gastric and duodenal transit revealed that overall the selected lactobacilli tolerated better pancreatic juice and bile salts than acidic juice. In particular, three L. rhamnosus strains (FS10, FS2, and PS11) and one L. paracasei strain (PM8) increased their cell density after the simulated GI transit. The same strains showed also high percentage of auto-aggregation and co-aggregation with Escherichia coli. All strains were effective against both Staphylococcus aureus and E. coli and variability was achieved versus Listeria monocytogenes and Enterococcus faecalis used as pathogenic indicator strains. Different behavior was revealed by strains for adhesion ability and hydrophobicity, which are not always linked each other and are strongly strain-dependent. From the safety point of view, no isolate showed hemolytic and bile salt hydrolase activities, except one, and most of the strains were sensitive to a broad range of clinical antibiotics. This work showed that the L. rhamnosus FS10 and the L. paracasei PM8 are good promising probiotic candidates for further in vivo investigations.", "token_count": 511, "char_count": 1987, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6137, "quality_score": 0.8069, "entities": { "genes": [ "FS2", "PS11", "FS10", "PM8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:09.745174", "source": { "split": "train_shard_00000", "doc_id": 4358 }, "chunk_id": "train_shard_00000_4358_0", "global_id": 4861 }, { "text": "Probiotic features of Lactobacillus strains isolated from Ragusano and Pecorino Siciliano cheeses.", "token_count": 31, "char_count": 98, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:10.140718", "source": { "split": "train_shard_00000", "doc_id": 4358 }, "chunk_id": "train_shard_00000_4358_1", "global_id": 4862 }, { "text": "The fermented milk matsoni is a traditional, national food product of both Georgia and Armenia. Little is known about the effects of biogeography and milk type on the microbial biodiversity of matsoni or the fungal composition of matsoni fermentations. High-throughput marker-gene sequencing was used to survey the bacterial and fungal communities of matsoni from different milk types and regions throughout Armenia and Georgia. Results demonstrate that both production region and milk type influence matsoni microbiota, suggesting that the traditional production methods preserve the transfer of unique regional microbiota from batch to batch. Bacterial profiles were dominated by Lactobacillus and Streptococcus species. Yeast profiles varied dramatically, with Kluyveromyces marxianus, Candida famata, Saccharomyces cerevisiae, Lodderomyces elongisporus, and Kluyveromyces lactis being the most important species distinguishing production regions and milk types. This survey will enable more detailed capture and characterization of specific microbiota detected within these fermentations.\n\nMicrobial biogeography of the transnational fermented milk matsoni.", "token_count": 264, "char_count": 1161, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:10.717518", "source": { "split": "train_shard_00000", "doc_id": 4359 }, "chunk_id": "train_shard_00000_4359_0", "global_id": 4863 }, { "text": "Lactobacillus salivarius is a member of the indigenous microbiota of the human gastrointestinal tract (GIT), and some L. salivarius strains are considered as probiotics. Bile tolerance is a crucial property for probiotic bacteria to survive the transit through the GIT and exert their beneficial effects. In this work, the functional role of oppA encoding an oligopeptide transporter substrate-binding protein from L. salivarius Ren in bile salt tolerance was investigated. In silico analysis revealed that the oppA gene encodes a 61.7-kDa cell surface-anchored hydrophilic protein with a canonical lipoprotein signal peptide. Homologous overexpression of OppA was shown to confer 20-fold higher tolerance to 0.5 % oxgall in L. salivarius Ren. Furthermore, the recombinant strain exhibited 1.8-fold and 3.6-fold higher survival when exposed to the sublethal concentration of sodium taurocholate and sodium taurodeoxycholate, respectively, while no significant change was observed when exposed to sodium glycocholate and sodium glycodeoxycholate (GDCA). Our results indicate that OppA confers specific resistance to taurine-conjugated bile salts in L. salivarius Ren. In addition, the OppA overexpression strain also showed significant increased resistance to heat and salt stresses, suggesting the protective role of OppA against multiple stresses in L. salivarius Ren.\n\nFunctional role of oppA encoding an oligopeptide-binding protein from Lactobacillus salivarius Ren in bile tolerance.", "token_count": 382, "char_count": 1488, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5942, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:11.334219", "source": { "split": "train_shard_00000", "doc_id": 4360 }, "chunk_id": "train_shard_00000_4360_0", "global_id": 4864 }, { "text": "NRL972 (Fluorescein Lisicol), a fluorescent-labelled bile salt, is an investigational marker of hepatic biliary transporter function.\n\nEffects of renal insufficiency on the elimination of fluorescein lisicol (NRL972), an investigational marker of hepatic transporter function.", "token_count": 80, "char_count": 276, "word_count": 34, "semantic_coherence": 1, "information_density": 0.7353, "quality_score": 0.8676, "entities": { "genes": [ "NRL972" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:11.755998", "source": { "split": "train_shard_00000", "doc_id": 4361 }, "chunk_id": "train_shard_00000_4361_0", "global_id": 4865 }, { "text": "Streptococcus pyogenes (Group A Streptococcus, GAS) remains a major public health burden worldwide, infecting over 750 million people leading to over 500,000 deaths annually. GAS pathogenesis is complex, involving genetically distinct GAS strains and multiple infection sites. To overcome fastidious genetic manipulations and accelerate pathogenesis investigations in GAS, we developed a mariner-based system (Krmit) for en masse monitoring of complex mutant pools by transposon sequencing (Tn-seq). Highly saturated transposant libraries (Krmit insertions in ca. every 25 nucleotides) were generated in two distinct GAS clinical isolates, a serotype M1T1 invasive strain 5448 and a nephritogenic serotype M49 strain NZ131, and analyzed using a Bayesian statistical model to predict GAS essential genes, identifying sets of 227 and 241 of those genes in 5448 and NZ131, respectively. A large proportion of GAS essential genes corresponded to key cellular processes and metabolic pathways, and 177 were found conserved within the GAS core genome established from 20 available GAS genomes. Selected essential genes were validated using conditional-expression mutants. Finally, comparison to previous essentiality analyses in S. sanguinis and S. pneumoniae revealed significant overlaps, providing valuable insights for the development of new antimicrobials to treat infections by GAS and other pathogenic streptococci.\n\nEssential Genes in the Core Genome of the Human Pathogen Streptococcus pyogenes.", "token_count": 393, "char_count": 1498, "word_count": 208, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.851, "entities": { "genes": [ "NZ131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:12.377211", "source": { "split": "train_shard_00000", "doc_id": 4362 }, "chunk_id": "train_shard_00000_4362_0", "global_id": 4866 }, { "text": "Thermotolerant inulin-utilizing yeast strains were successfully isolated in this study. Among the isolated strains, Kluyveromyces marxianus DBKKU Y-102 was found to be the most effective strain for direct ethanol fermentation at high temperature from fresh Jerusalem artichoke (JA) tubers without inulin hydrolysis under consolidated bioprocessing (CBP). The maximum ethanol concentrations produced by this strain under the optimum culture conditions were 104.83 and 97.46 g L(-1) at 37 and 40 °C, respectively. Data from this study clearly demonstrated that the use of thermotolerant inulin-utilizing yeast K. marxianus for ethanol production from fresh JA tubers in the CBP process not only provided high levels of ethanol, but also could eliminate the addition of external enzyme for inulin hydrolysis, which might lead to the reduction of operating costs. The expression of genes involved in carbohydrate metabolism in K. marxianus DBKKU Y-102 during ethanol fermentation was investigated by real-time RT-PCR, and the results revealed that expression levels were distinctive depending on the growth phase and growth conditions. However, among the genes tested, adh4 and tdh2 were highly expressed under high temperature conditions in both exponential- and stationary-growth phases, suggesting that these genes might play a crucial role in acquiring thermotolerance ability in this organism under stress conditions.\n\nEthanol production from Jerusalem artichoke tubers at high temperature by newly isolated thermotolerant inulin-utilizing yeast Kluyveromyces marxianus using consolidated bioprocessing.", "token_count": 396, "char_count": 1604, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5919, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:12.992327", "source": { "split": "train_shard_00000", "doc_id": 4363 }, "chunk_id": "train_shard_00000_4363_0", "global_id": 4867 }, { "text": "Mitochondrial dysfunction has been associated with liver cholestatis. Toxic bile salt accumulation leads to chronic injury with mitochondrial damage, ROS increase and apoptosis, resulting in liver dysfunction. This study aimed to analyze mitochondrial bioenergetics in rats with hepatic fibrosis induced by bile duct ligation (BDL) after BMMNC transplantation. Livers were collected from normal rats, fibrotic rats after 14 and 21 days of BDL (F14d and F21d) and rats that received BMMNC at 14 days of BDL, analyzed after 7 days. F21d demonstrated increased collagen I content and consequently decrease after BMMNC transplantation. Both F14d and F21d had significantly reduced mitochondrial oxidation capacity and increased mitochondrial uncoupling, which were restored to levels similar to those of normal group after BMMNC transplantation. In addition, F21d had a significantly increase of UCP2, and reduced PGC-1α content. However, after BMMNC transplantation both proteins returned to levels similar to normal group. Moreover, F14d had a significantly increase in 4-HNE content compared to normal group, but after BMMNC transplantation 4-HNE content significantly reduced, suggesting oxidative stress reduction. Therefore, BMMNC transplantation has a positive effect on hepatic mitochondrial bioenergetics of cholestatic rats, increasing oxidative capacity and reducing oxidative stress, which, in turn, contribute to liver function recover.\n\nBone marrow mononuclear cell transplantation improves mitochondrial bioenergetics in the liver of cholestatic rats.", "token_count": 406, "char_count": 1562, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5748, "quality_score": 0.7874, "entities": { "genes": [ "UCP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:13.607183", "source": { "split": "train_shard_00000", "doc_id": 4364 }, "chunk_id": "train_shard_00000_4364_0", "global_id": 4868 }, { "text": "Among a number of yeast strains screened for whole cell transgalactosylating activity, Kluyveromyces marxianus NCIM 3551 was found to be most suitable biocatalyst for production of galacto-oligosaccharides (GOS). Cell permeabilization lead to an efficient bioconversion by β-galactosidase resulting in synthesis of GOS. A maximum GOS yield of 36% (w/w) of total sugars was achieved and the products consisted of tri- and tetra-galacto-oligosaccharides. A lactose conversion rate of 80% and productivity of 24g/L/h was obtained under the optimum conditions at lactose concentration of 20% (w/v), temperature 40°C, pH 6.5 and enzyme units after 3h of reaction time. Tetrasaccharides were the main component of the reaction mixture. The products were quantitated by HPLC and structurally characterized by mass spectrometry.\n\nTransgalactosylation of lactose for synthesis of galacto-oligosaccharides using Kluyveromyces marxianus NCIM 3551.", "token_count": 283, "char_count": 936, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6899, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:14.161037", "source": { "split": "train_shard_00000", "doc_id": 4365 }, "chunk_id": "train_shard_00000_4365_0", "global_id": 4869 }, { "text": "Psychological stress is a risk factor for atherosclerosis, yet the pathophysiological mechanisms involved remain elusive. The transfer of cholesterol from macrophage foam cells to liver and feces (the macrophage-specific reverse cholesterol transport, m-RCT) is an important antiatherogenic pathway. Because exposure of mice to physical restraint, a model of psychological stress, increases serum levels of corticosterone, and as bile acid homeostasis is disrupted in glucocorticoid-treated animals, we investigated if chronic intermittent restraint stress would modify m-RCT by altering the enterohepatic circulation of bile acids. C57Bl/6J mice exposed to intermittent stress for 5 days exhibited increased transit through the large intestine and enhanced fecal bile acid excretion. Of the transcription factors and transporters that regulate bile acid homeostasis, the mRNA expression levels of the hepatic farnesoid X receptor (FXR), the bile salt export pump (BSEP), and the intestinal fibroblast growth factor 15 (FGF15) were reduced, whereas those of the ileal apical sodium-dependent bile acid transporter (ASBT), responsible for active bile acid absorption, remained unchanged. Neither did the hepatic expression of cholesterol 7α-hydroxylase (CYP7A1), the key enzyme regulating bile acid synthesis, change in the stressed mice. Evaluation of the functionality of the m-RCT pathway revealed increased fecal excretion of bile acids that had been synthesized from macrophage-derived cholesterol. Overall, our study reveals that chronic intermittent stress in mice accelerates m-RCT specifically by increasing fecal excretion of bile acids. This novel mechanism of m-RCT induction could have antiatherogenic potential under conditions of chronic stress.\n\nChronic intermittent psychological stress promotes macrophage reverse cholesterol transport by impairing bile acid absorption in mice.", "token_count": 486, "char_count": 1895, "word_count": 256, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "FGF15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:14.807468", "source": { "split": "train_shard_00000", "doc_id": 4366 }, "chunk_id": "train_shard_00000_4366_0", "global_id": 4870 }, { "text": "Propionibacterium acnes is one of the most commonly implicated etiologic agents of sarcoidosis. We previously reported a complete genome sequence of the C1 strain of P. acnes as a clinical isolate from subcutaneous granulomatous inflammatory lesions in a patient with sarcoidosis. In the present study, we initially searched for genetic profiles specific to the C1 strain by core genome analysis and multiple genome alignment with database sequences from 76 and 9 P. acnes strains, respectively. The analysis revealed that the C1 strain was phylogenetically independent and carried an 18.8-kbp transposon sequence unique to the sarcoid isolate. The unique composite transposon comprised a novel insertion sequence and extrinsic genes from bacteria other than P. acnes. Multilocus sequence typing using 24 sarcoid and 36 non-sarcoid isolates revealed a total of 28 sequence types (STs), including ST26, which was most frequently found without specificity for sarcoid isolates. All 13 ST26 isolates exhibited cell-invasiveness and were confirmed to carry the novel insertion sequence and 4 of the 27 extrinsic CDSs in the transposon, with one exception. ST26 of P. acnes with the composite transposon is the most unique strain detected to date and should be further examined as a causative strain of sarcoidosis.\n\nGenetic profiles of Propionibacterium acnes and identification of a unique transposon with novel insertion sequences in sarcoid and non-sarcoid isolates.", "token_count": 367, "char_count": 1465, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5297, "quality_score": 0.7648, "entities": { "genes": [ "ST26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:15.385058", "source": { "split": "train_shard_00000", "doc_id": 4367 }, "chunk_id": "train_shard_00000_4367_0", "global_id": 4871 }, { "text": "Pseudomonas aeruginosa is an opportunistic bacterial pathogen able to thrive in highly diverse ecological niches and to infect compromised patients. Its genome exhibits a mosaic structure composed of a core genome into which accessory genes are inserted en bloc at specific sites. The size and the content of the core genome are open for debate as their estimation depends on the set of genomes considered and the pipeline of gene detection and clustering. Here, we redefined the size and the content of the core genome of P. aeruginosa from fully re-analyzed genomes of 17 reference strains. After the optimization of gene detection and clustering parameters, the core genome was defined at 5,233 orthologs, which represented ~ 88% of the average genome. Extrapolation indicated that our panel was suitable to estimate the core genome that will remain constant even if new genomes are added. The core genome contained resistance determinants to the major antibiotic families as well as most metabolic, respiratory, and virulence genes. Although some virulence genes were accessory, they often related to conserved biological functions. Long-standing prophage elements were subjected to a genetic drift to eventually display a G+C content as higher as that of the core genome. This contrasts with the low G+C content of highly conserved ribosomal genes. The conservation of metabolic and respiratory genes could guarantee the ability of the species to thrive on a variety of carbon sources for energy in aerobiosis and anaerobiosis. Virtually all the strains, of environmental or clinical origin, have the complete toolkit to become resistant to the major antipseudomonal compounds and possess basic pathogenic mechanisms to infect humans. The knowledge of the genes shared by the majority of the P. aeruginosa isolates is a prerequisite for designing effective therapeutics to combat the wide variety of human infections.\n\nWhat It Takes to Be a Pseudomonas aeruginosa? The Core Genome of the Opportunistic Pathogen Updated.", "token_count": 469, "char_count": 2024, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5815, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:16.032027", "source": { "split": "train_shard_00000", "doc_id": 4368 }, "chunk_id": "train_shard_00000_4368_0", "global_id": 4872 }, { "text": "In fear of animal-associated diseases, there is a trend in searching for non-animal derived substitutes for existing excipients in the pharmaceutical industries. This paper aimed to screen cholesterol analogues as membrane stabilizers of liposomes from botanical sterols, including β-sitosterol, stigmasterol, ergosterol and lanosterol. Liposomes containing four kinds of sterols were prepared and evaluated in vitro and in vivo as oral delivery system of insulin. Liposomes containing β-sitosterol (Si-Lip), stigmasterol (St-Lip) and lanosterol (La-Lip) was found not to protect insulin against degradation. Only 10% of the initial insulin in liposomes was preserved after a 30 min exposure to simulated gastric fluids. However, the protective ability of liposomes containing ergosterol (Er-Lip) was similar to that of liposomes containing sodium glycocholate (Sgc-Lip) and superior to that of liposomes containing cholesterol (Ch-Lip). In addition, the blood glucose level can decrease to about 50% of initial level after oral Er-Lip which was significantly superior to the in vivo performance of Si-Lip and Ch-Lip and similar to Sgc-Lip. Er-Lips of ergosterol/phospholipids ratios of 1:4 or 1:6 exerts more pronounced protective ability of insulin in simulated gastrointestinal fluids and hypoglycemic effects in rats than other formulations. Furthermore, Er-Lips exerted low toxicity to Caco-2 cells through a cell viability study. Meahwhile, insulin permeability was significantly increased across Caco-2 monolayers by encapsulating in Er-Lip. It was concluded that ergosterol could be used as a substitute for cholesterol and bile salt derivatives in liposomes to enhance oral bioavailability of insulin.\n\nLiposomes containing cholesterol analogues of botanical origin as drug delivery systems to enhance the oral absorption of insulin.", "token_count": 498, "char_count": 1842, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5891, "quality_score": 0.7946, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:16.682713", "source": { "split": "train_shard_00000", "doc_id": 4369 }, "chunk_id": "train_shard_00000_4369_0", "global_id": 4873 }, { "text": "Both solid lipid nanoparticles (SLNs) and nanostructured lipid carriers (NLCs) were artificially broken down into lipolysates. Their oral bioavailability, with silymarin as a model drug, was compared in dogs to highlight the contribution of their integral structure. The lipid nanoparticles were prepared using a conventional hot homogenization method, whereas the lipolysates were obtained through lipolysis in phospholipid- and bile salt-enriched simulated intestinal fluid. More than 80% of vehicle-associated drugs could be transformed into the water-soluble form of mixed micelles. Pharmacokinetics analysis in dogs showed a decrease in bioavailability of 74.86% and 59.09% for lipolysates compared to integral NLCs and SLNs, respectively. It was indicated that lipolysates contributed to a majority of drug absorption. Integral nanoparticles were superior to their lipolysate counterparts, but only marginally; if the approximately 20% of the drug that precipitated during in vitro lipolysis was deducted from the overall absorption amount, the superiority of integral nanoparticles would be significantly compromised. In conclusion, lipolysis was the predominant in vivo absorption mechanism, and the contribution of intact lipid nanoparticles was limited.\n\nComparison of the oral bioavailability of silymarin-loaded lipid nanoparticles with their artificial lipolysate counterparts: implications on the contribution of integral structure.", "token_count": 347, "char_count": 1446, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:17.259365", "source": { "split": "train_shard_00000", "doc_id": 4370 }, "chunk_id": "train_shard_00000_4370_0", "global_id": 4874 }, { "text": "20(R)-Ginsenoside Rg3 (G-Rg3) has good inhibition of tumor angiogenesis and anti-tumor effect. However, its poor aqueous solubility and liposolubility are not ideal for clinical applications. In this study, a G-Rg3 bile salt-phosphatidylcholine-based mixed micelle system (BS-PC-MMS) was prepared. The optimization of G-Rg3 BS-PC-MMS was carried out using response surface methodology based on a central composite design. The encapsulation efficiency (EE) and light transmission (LT) of the optimized formulation were 90.69±2.54% and 99.10±3.12%, respectively. The average particle size of micelles was 20 nm. To increase the stability of G-Rg3 BS-PC-MMS, the lyophilized formulation of micelles was prepared. The G-Rg3 BS-PC-MMS did not produce hemolysis of erythrocytes within a certain concentration range and exhibited a good inhibition of tumor cells. The chick embryo chorioallantoic membrane assay results showed that the G-Rg3 BS-PC-MMS significantly inhibited angiogenesis. The G-Rg3 BS-PC-MMS is thus shown to be a safe, stable, and promising drug delivery system.\n\nGinsenoside Rg3 bile salt-phosphatidylcholine-based mixed micelles: design, characterization, and evaluation.", "token_count": 366, "char_count": 1185, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6918, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:17.838251", "source": { "split": "train_shard_00000", "doc_id": 4371 }, "chunk_id": "train_shard_00000_4371_0", "global_id": 4875 }, { "text": "The development of clean or novel alternative energy has become a global trend that will shape the future of energy. In the present study, 3 microbial strains with different oxygen requirements, including Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, were used to construct a hydrogen production system that was composed of a mixed aerobic-facultative anaerobic-anaerobic consortium. The effects of metal ions, organic acids and carbohydrate substrates on this system were analyzed and compared using electrochemical and kinetic assays. It was then tested using small-scale experiments to evaluate its ability to convert starch in 5 L of organic wastewater into hydrogen. For the one-step biohydrogen production experiment, H1 medium (nutrient broth and potato dextrose broth) was mixed directly with GAM broth to generate H2 medium (H1 medium and GAM broth). Finally, Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D of three species microbial co-culture to produce hydrogen under anaerobic conditions. For the two-step biohydrogen production experiment, the H1 medium, after cultured the microbial strains Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, was centrifuged to remove the microbial cells and then mixed with GAM broth (H2 medium). Afterward, the bacterial strain Clostridium acetobutylicum ATCC 824 was inoculated into the H2 medium to produce hydrogen by anaerobic fermentation.\n\nFeasibility of biohydrogen production from industrial wastes using defined microbial co-culture.", "token_count": 459, "char_count": 1616, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5796, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:18.480949", "source": { "split": "train_shard_00000", "doc_id": 4372 }, "chunk_id": "train_shard_00000_4372_0", "global_id": 4876 }, { "text": "Penicillin V acylases (PVAs, E.C.3.5.11) belong to the Ntn hydrolase super family of enzymes that catalyze the deacylation of the side chain from phenoxymethyl penicillin (penicillin V). Penicillin acylases find use in the pharmaceutical industry for the production of semi-synthetic antibiotics. PVAs employ the N-terminal cysteine residue as catalytic nucleophile and are structurally and evolutionarily related to bile salt hydrolases (BSHs). Here, we report the cloning and characterization of a PVA enzyme from the Gram-negative plant pathogen, Pectobacterium atrosepticum (PaPVA). The enzyme was cloned and expressed in Escherichia coli attaining a very high yield (250 mg/l) and a comparatively high specific activity (430 IU/mg). The enzyme showed marginally better pH and thermo-stability over PVAs characterized from Gram-positive bacteria. The enzyme also showed enhanced activity in presence of organic solvents and detergents. The enzyme kinetics turned out to be significantly different from that of previously reported PVAs, displaying positive cooperativity and substrate inhibition. The presence of bile salts had a modulating effect on PaPVA activity. Sequence analysis and characterization reveal the distinctive nature of these enzymes and underscore the need to study PVAs from Gram-negative bacteria.\n\nPenicillin V acylase from Pectobacterium atrosepticum exhibits high specific activity and unique kinetics.", "token_count": 387, "char_count": 1430, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8232, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:19.098855", "source": { "split": "train_shard_00000", "doc_id": 4373 }, "chunk_id": "train_shard_00000_4373_0", "global_id": 4877 }, { "text": "An approach for tailoring self-assembled tubular structures is described. By controlling the relative composition of a two-component surfactant mixture comprising the natural bile salt lithocholate and its bolamphiphilic derivative, it was possible to finely tune the nanotube cross-section of the mixed tubular aggregates that self-associated spontaneously in aqueous solution at pH 12. The diameter was found to vary up to 50% when the stoichiometric ratio of the two bile salts was changed. The tuning of supramolecular nanochannels with such remarkable precision is of significant interest for technological applications of these materials.\n\nTailoring supramolecular nanotubes by bile salt based surfactant mixtures.", "token_count": 173, "char_count": 720, "word_count": 100, "semantic_coherence": 1, "information_density": 0.74, "quality_score": 0.87, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:19.538429", "source": { "split": "train_shard_00000", "doc_id": 4374 }, "chunk_id": "train_shard_00000_4374_0", "global_id": 4878 }, { "text": "Whole-genome characterisation in clinical microbiology enables to detect trends in infection dynamics and disease transmission. Here, we report a case of bacteraemia due to Campylobacter fetus subsp. fetus in a rural worker under cancer treatment that was diagnosed with cellulitis; the patient was treated with antibiotics and recovered. The routine typing methods were not able to identify the microorganism causing the infection, so it was further analysed by molecular methods and whole-genome sequencing. The multi-locus sequence typing (MLST) revealed the presence of the bovine-associated ST-4 genotype. Whole-genome comparisons with other C. fetus strains revealed an inconsistent phylogenetic position based on the core genome, discordant with previous ST-4 strains. To the best of our knowledge, this is the first C. fetus subsp. fetus carrying the ST-4 isolated from humans and represents a probable case of zoonotic transmission from cattle.\n\nA rural worker infected with a bovine-prevalent genotype of Campylobacter fetus subsp. fetus supports zoonotic transmission and inconsistency of MLST and whole-genome typing.", "token_count": 268, "char_count": 1129, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8168, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:20.092323", "source": { "split": "train_shard_00000", "doc_id": 4375 }, "chunk_id": "train_shard_00000_4375_0", "global_id": 4879 }, { "text": "Expression of the genes encoding the enzymes involved in inulin, sucrose, and glucose metabolism in the yeasts Saccharomyces cerevisiae and Kluyveromyces marxianus was studied. The exon-intron structure of the relevant genes was identified and the primers for quantitative PCR were optimized. Expression of the genes was found to depend on the carbon source. Glucose was shown to exhibit a repressive effect on inulinase synthesis by K. marxianus, while in S. cerevisiae glucose and sucrose were inulinase inducer and repressor, respectively.\n\n[Expression of inulinase genes in the yeasts Saccharomyces cerevisiae and Kluyveromyces marxianus].", "token_count": 173, "char_count": 643, "word_count": 92, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:20.534089", "source": { "split": "train_shard_00000", "doc_id": 4376 }, "chunk_id": "train_shard_00000_4376_0", "global_id": 4880 }, { "text": "To screen for potential probiotics with high adhesion capability, a chemostat model-based cultured human feces and denaturing gradient gel electrophoresis methods were applied, and the adhesion capability of the isolates was evaluated in vitro and in vivo. Lactobacillus plantarum (HM218749), Lactobacillus reuteri (EU547310), and Enterococcus faecalis (HM218543) were isolated from the slime on the chemostat wall, as these organisms could grow better at 37°C in an anaerobic environment and could resist harsh conditions (pH 1.5 and 0.30% bile salt). Lactobacillus plantarum, L. reuteri, and E. faecalis could adhere to HT-29 cells and reduce the adhesion of Shigella dysenteriae 2457, Staphylococcus aureus Cowan1, Enterobacter sakazakii 45401, and Escherichia coli 44102 to HT-29 cells. Moreover, the animal experiment showed that L. plantarum could adhere to mice intestine, increasing the number of lactobacilli and decreasing the number of enterococci.\n\nA novel method for screening of potential probiotics for high adhesion capability.", "token_count": 335, "char_count": 1043, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6824, "quality_score": 0.8412, "entities": { "genes": [ "HM218749", "EU547310", "HM218543" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:21.107837", "source": { "split": "train_shard_00000", "doc_id": 4377 }, "chunk_id": "train_shard_00000_4377_0", "global_id": 4881 }, { "text": "Phytate is known as a strong chelate of minerals causing their reduced uptake by the human intestine. Ninety-three yeast isolates from traditional African fermented food products, belonging to nine species (Pichia kudriavzevii, Saccharomyces cerevisiae, Clavispora lusitaniae, Kluyveromyces marxianus, Millerozyma farinosa, Candida glabrata, Wickerhamomyces anomalus, Hanseniaspora guilliermondii and Debaryomyces nepalensis) were screened for phytase production on solid and liquid media. 95% were able to grow in the presence of phytate as sole phosphate source, P. kudriavzevii being the best growing species. A phytase coding gene of P. kudriavzevii (PHYPk) was identified and its expression was studied during growth by RT-qPCR. The expression level of PHYPk was significantly higher in phytate-medium, compared to phosphate-medium. In phytate-medium expression was seen in the lag phase. Significant differences in gene expression were detected among the strains as well as between the media. A correlation was found between the PHYPk expression and phytase extracellular activity.\n\nPhytase-producing capacity of yeasts isolated from traditional African fermented food products and PHYPk gene expression of Pichia kudriavzevii strains.", "token_count": 339, "char_count": 1241, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:21.672291", "source": { "split": "train_shard_00000", "doc_id": 4378 }, "chunk_id": "train_shard_00000_4378_0", "global_id": 4882 }, { "text": "We determined the genome sequence of the thermotolerant yeast Kluyveromyces marxianus strain NBRC1777. The genome of strain NBRC1777 is composed of 4,912 open reading frames (ORFs) on 8 chromosomes, with a total size of 10,895,581 bp, including mitochondrial DNA.\n\nComplete Genome Sequence of Kluyveromyces marxianus NBRC1777, a Nonconventional Thermotolerant Yeast.", "token_count": 132, "char_count": 366, "word_count": 50, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [ "NBRC1777" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:22.127351", "source": { "split": "train_shard_00000", "doc_id": 4379 }, "chunk_id": "train_shard_00000_4379_0", "global_id": 4883 }, { "text": "Studies of the transmission epidemiology of antimicrobial-resistant Escherichia coli, such as strains harboring extended-spectrum beta-lactamase (ESBL) genes, frequently use selective culture of rectal surveillance swabs to identify isolates for molecular epidemiological investigation. Typically, only single colonies are evaluated, which risks underestimating species diversity and transmission events. We sequenced the genomes of 16 E. coli colonies from each of eight fecal samples (n = 127 genomes; one failure), taken from different individuals in Cambodia, a region of high ESBL-producing E. coli prevalence. Sequence data were used to characterize both the core chromosomal diversity of E. coli isolates and their resistance/virulence gene content as a proxy measure of accessory genome diversity. The 127 E. coli genomes represented 31 distinct sequence types (STs). Seven (88%) of eight subjects carried ESBL-positive isolates, all containing blaCTX-M variants. Diversity was substantial, with a median of four STs/individual (range, 1 to 10) and wide genetic divergence at the nucleotide level within some STs. In 2/8 (25%) individuals, the same blaCTX-M variant occurred in different clones, and/or different blaCTX-M variants occurred in the same clone. Patterns of other resistance genes and common virulence factors, representing differences in the accessory genome, were also diverse within and between clones. The substantial diversity among intestinally carried ESBL-positive E. coli bacteria suggests that fecal surveillance, particularly if based on single-colony subcultures, will likely underestimate transmission events, especially in high-prevalence settings.\n\nExtensive Within-Host Diversity in Fecally Carried Extended-Spectrum-Beta-Lactamase-Producing Escherichia coli Isolates: Implications for Transmission Analyses.", "token_count": 468, "char_count": 1845, "word_count": 242, "semantic_coherence": 1, "information_density": 0.7066, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:22.794088", "source": { "split": "train_shard_00000", "doc_id": 4380 }, "chunk_id": "train_shard_00000_4380_0", "global_id": 4884 }, { "text": "ᅟ: Listeria monocytogenes is a food-borne pathogen and the causative agent of listeriosis, a severe infection to those with a pre-disposition. Infections often arise through consumption of contaminated foods, where high intrinsic resistance to food processing practises permit survival and growth. Several practises, including refrigeration, acidification and oxygen limitation are ineffective in controlling L. monocytogenes, therefore foods which do not undergo thermal processing, e.g. ready-to-eat products, are considered high risk. While the responses to several food processing practises have been investigated, there are few reports on the responses of L. monocytogenes to oxygen limitation. Therefore the aim of this study was to investigate the effects of oxygen limitation on stress response andsurvival capacity during simulated gastro-intestinal transit.\n\nOxygen limitation induces acid tolerance and impacts simulated gastro-intestinal transit in Listeria monocytogenes J0161.", "token_count": 223, "char_count": 990, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7023, "quality_score": 0.8511, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:23.297905", "source": { "split": "train_shard_00000", "doc_id": 4381 }, "chunk_id": "train_shard_00000_4381_0", "global_id": 4885 }, { "text": "Targeting of cellular proteins to the extracellular environment is directed by a secretory signal sequence located at the N-terminus of a secretory protein. These signal sequences usually contain an N-terminal basic amino acid followed by a stretch containing hydrophobic residues, although no consensus signal sequence has been identified. In this study, simple modeling of signal sequences was attempted using Gaussia princeps secretory luciferase (GLuc) in the yeast Kluyveromyces marxianus, which allowed comprehensive recombinant gene construction to substitute synthetic signal sequences.\n\nSynthetic signal sequences that enable efficient secretory protein production in the yeast Kluyveromyces marxianus.", "token_count": 152, "char_count": 711, "word_count": 94, "semantic_coherence": 1, "information_density": 0.734, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:23.778558", "source": { "split": "train_shard_00000", "doc_id": 4382 }, "chunk_id": "train_shard_00000_4382_0", "global_id": 4886 }, { "text": "Cocoa beans (Theobroma cacao L.) are the raw material for chocolate production. Fermentation of cocoa pulp by microorganisms is crucial for developing chocolate flavor precursors. Yeasts conduct an alcoholic fermentation within the bean pulp that is essential for the production of good quality beans, giving typical chocolate characters. However, the roles of bacteria such as lactic acid bacteria and acetic acid bacteria in contributing to the quality of cocoa bean and chocolate are not fully understood. Using controlled laboratory fermentations, this study investigated the contribution of lactic acid bacteria to cocoa bean fermentation. Cocoa beans were fermented under conditions where the growth of lactic acid bacteria was restricted by the use of nisin and lysozyme. The resultant microbial ecology, chemistry and chocolate quality of beans from these fermentations were compared with those of indigenous (control) fermentations. The yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii, Kluyveromyces marxianus and Saccharomyces cerevisiae, the lactic acid bacteria Lactobacillus plantarum, Lactobacillus pentosus and Lactobacillus fermentum and the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateurii were the major species found in control fermentations. In fermentations with the presence of nisin and lysozyme, the same species of yeasts and acetic acid bacteria grew but the growth of lactic acid bacteria was prevented or restricted. These beans underwent characteristic alcoholic fermentation where the utilization of sugars and the production of ethanol, organic acids and volatile compounds in the bean pulp and nibs were similar for beans fermented in the presence of lactic acid bacteria. Lactic acid was produced during both fermentations but more so when lactic acid bacteria grew. Beans fermented in the presence or absence of lactic acid bacteria were fully fermented, had similar shell weights and gave acceptable chocolates with no differences in sensory rankings. It was concluded that lactic acid bacteria may not be necessary for successful cocoa fermentation.\n\nThe effect of lactic acid bacteria on cocoa bean fermentation.", "token_count": 513, "char_count": 2183, "word_count": 313, "semantic_coherence": 1, "information_density": 0.4856, "quality_score": 0.7428, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:43:24.420327", "source": { "split": "train_shard_00000", "doc_id": 4383 }, "chunk_id": "train_shard_00000_4383_0", "global_id": 4887 }, { "text": "Co-treatment of isoniazid (INH) and rifampicin (RFP) is well known for clinically apparent liver injury. However, the mechanism of INH/RFP-induced liver injury is controversial. Emerging evidence shows links between inhibition of bile acids transporters and drug-induced liver injury (DILI). The present study investigates whether sodium taurocholate cotransporting polypeptide (NTCP/Ntcp; SLC10A1) and bile salt export pump (BSEP/Bsep; ABCB11) are involved in the anti-tuberculosis medicines induced liver injury. ICR female mice were intragastrically treated with INH (50 or 100 mg/kg), RFP (100 or 200 mg/kg), or the combination of INH/RFP (50 + 100 mg/kg or 100 + 200 mg/kg) for 14 consecutive days. Liver histopathological examination, serum biochemical and liver malondialdehyde tests were evaluated. Apparent histopathological alterations and hepatic oxidative stress showed in INH (100 mg/kg), RFP (200 mg/kg) and their combination group. The hepatoxic effect was also indicated by increased serum biomarkers, such as aspartate transaminase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), direct bilirubin (DBil), total bilirubin (TBil) and total bile acids (TBA). Both doses of INH/RFP administration significantly down-regulated the expression of Ntcp and Bsep in liver. Furthermore, the combination of INH and RFP displayed stronger effect on the expression of Ntcp compared with the corresponding dose of INH or RFP alone. In conclusion, down-regulated expression of hepatic Ntcp and Bsep might play an important role in the development of INH and RFP induced liver injury.", "token_count": 502, "char_count": 1604, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8084, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:25.075489", "source": { "split": "train_shard_00000", "doc_id": 4384 }, "chunk_id": "train_shard_00000_4384_0", "global_id": 4888 }, { "text": "The inhibition of hepatic bile acids transporters Ntcp and Bsep is involved in the pathogenesis of isoniazid/rifampicin-induced hepatotoxicity.", "token_count": 45, "char_count": 143, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:25.442155", "source": { "split": "train_shard_00000", "doc_id": 4384 }, "chunk_id": "train_shard_00000_4384_1", "global_id": 4889 }, { "text": "The bacterial genus Mycobacterium is of great interest in the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, significant gaps in knowledge between genome and phenome seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium.\n\nComparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium.", "token_count": 171, "char_count": 772, "word_count": 99, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:25.883830", "source": { "split": "train_shard_00000", "doc_id": 4385 }, "chunk_id": "train_shard_00000_4385_0", "global_id": 4890 }, { "text": "In the aim of testing tools for tracing cell trafficking of exogenous cholesterol, two fluorescent derivatives of cholesterol, 22-nitrobenzoxadiazole-cholesterol (NBD-Chol) and 21-methylpyrenyl-cholesterol (Pyr-met-Chol), with distinctive chemico-physical characteristics, have been compared for their cell incorporation properties, using two cell models differently handling cholesterol, with two incorporation routes. In the Caco-2 cell model, the cholesterol probes were delivered in bile salt micelles, as a model of intestinal absorption. The two probes displayed contrasting behaviors for cell uptake characteristics, cell staining, and efflux kinetics. In particular, Pyr-met-Chol cell incorporation involved SR-BI, while that of NBD-Chol appeared purely passive. In the PC-3 cell model, which overexpresses lipoprotein receptors, the cholesterol probes were delivered via the serum components, as a model of systemic delivery. We showed that Pyr-met-Chol-labelled purified LDL or HDL were able to specifically deliver Pyr-met-Chol to the PC-3 cells, while NBD-Chol incorporation was independent of lipoproteins. Observations by fluorescence microscopy evidenced that, while NBD-Chol readily stained the cytosolic lipid droplets, Pyr-met-Chol labelling led to the intense staining of intracellular structures of membranous nature, in agreement with the absence of detectable esterification of Pyr-met-Chol. A 48 h incubation of PC-3 cells with either Pyr-met-Chol-labelled LDL or HDL gave same staining patterns, mainly colocalizing with Lamp1, caveolin-1 and CD63. These data indicated convergent trafficking downwards their respective receptors, LDL-R and SR-BI, toward the cholesterol-rich internal membrane compartments, late endosomes and multivesicular bodies", "token_count": 490, "char_count": 1772, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "CD63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:26.530336", "source": { "split": "train_shard_00000", "doc_id": 4386 }, "chunk_id": "train_shard_00000_4386_0", "global_id": 4891 }, { "text": "Interestingly, Pyr-met-Chol staining of these structures exhibited a high excimer fluorescence emission, revealing their ordered membrane environment, and indicating that Pyr-met-Chol behaves as a fair cholesterol tracer regarding its preferential incorporation into cholesterol-rich domains. We conclude that, while NBD-Chol is a valuable marker of cholesterol esterification, Pyr-met-Chol is a reliable new lipoprotein fluorescent marker which allows to probe specific intracellular trafficking of cholesterol-rich membranes.\n\nSpecific cellular incorporation of a pyrene-labelled cholesterol: lipoprotein-mediated delivery toward ordered intracellular membranes.", "token_count": 171, "char_count": 664, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7662, "quality_score": 0.8831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:26.972481", "source": { "split": "train_shard_00000", "doc_id": 4386 }, "chunk_id": "train_shard_00000_4386_1", "global_id": 4892 }, { "text": "Organisms from diverse phylogenetic origins can thrive within the same ecological niches. They might be induced to evolve convergent adaptations in response to a similar landscape of selective pressures. Their genomes should bear the signature of this process. The study of unrelated virus lineages infecting the same host panels guarantees a clear identification of phyletically independent convergent adaptation. Here, we investigate the evolutionary history of genes in the accessory genome shared by unrelated insect large dsDNA viruses: the entomopoxviruses (EPVs, Poxviridae) and the baculoviruses (BVs). EPVs and BVs have overlapping ecological niches and have independently evolved similar infection processes. They are, in theory, subjected to the same selective pressures from their host's immune responses. Their accessory genomes might, therefore, bear analogous genomic signatures of convergent adaption and could point out key genomic mechanisms of adaptation hitherto undetected in viruses. We uncovered 32 homologous, yet independent acquisitions of genes originating from insect hosts, different eukaryotes, bacteria and viruses. We showed different evolutionary levels of gene acquisition convergence in these viruses, underlining a continuous evolutionary process. We found both recent and ancient gene acquisitions possibly involved to the adaptation to both specific and distantly related hosts. Multidirectional and multipartite gene exchange networks appear to constantly drive exogenous gene assimilations, bringing key adaptive innovations and shaping the life histories of large DNA viruses. This evolutionary process might lead to genome level adaptive convergence.\n\nGene acquisition convergence between entomopoxviruses and baculoviruses.", "token_count": 386, "char_count": 1766, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:27.584412", "source": { "split": "train_shard_00000", "doc_id": 4387 }, "chunk_id": "train_shard_00000_4387_0", "global_id": 4893 }, { "text": "Extra-slow-growing bradyrhizobia from root nodules of field-grown soybeans harbor abundant insertion sequences (ISs) and are termed highly reiterated sequence-possessing (HRS) strains. We analyzed the genome organization of HRS strains with the focus on IS distribution and symbiosis island structure. Using pulsed-field gel electrophoresis, we consistently detected several plasmids (0.07 to 0.4 Mb) in the HRS strains (NK5, NK6, USDA135, 2281, USDA123, and T2), whereas no plasmids were detected in the non-HRS strain USDA110. The chromosomes of the six HRS strains (9.7 to 10.7 Mb) were larger than that of USDA110 (9.1 Mb). Using MiSeq sequences of 6 HRS and 17 non-HRS strains mapped to the USDA110 genome, we found that the copy numbers of ISRj1, ISRj2, ISFK1, IS1632, ISB27, ISBj8, and IS1631 were markedly higher in HRS strains. Whole-genome sequencing showed that the HRS strain NK6 had four small plasmids (136 to 212 kb) and a large chromosome (9,780 kb). Strong colinearity was found between 7.4-Mb core regions of the NK6 and USDA110 chromosomes. USDA110 symbiosis islands corresponded mainly to five small regions (S1 to S5) within two variable regions, V1 (0.8 Mb) and V2 (1.6 Mb), of the NK6 chromosome. The USDA110 nif gene cluster (nifDKENXSBZHQW-fixBCX) was split into two regions, S2 and S3, where ISRj1-mediated rearrangement occurred between nifS and nifB", "token_count": 491, "char_count": 1377, "word_count": 213, "semantic_coherence": 1, "information_density": 0.662, "quality_score": 0.831, "entities": { "genes": [ "USDA123", "NK6", "ISB27", "IS1632", "USDA110", "ISFK1", "IS1631", "USDA135", "NK5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:28.237249", "source": { "split": "train_shard_00000", "doc_id": 4388 }, "chunk_id": "train_shard_00000_4388_0", "global_id": 4894 }, { "text": "ISs were also scattered in NK6 core regions, and ISRj1 insertion often disrupted some genes important for survival and environmental responses. These results suggest that HRS strains of soybean bradyrhizobia were subjected to IS-mediated symbiosis island shuffling and core genome degradation.\n\nSymbiosis island shuffling with abundant insertion sequences in the genomes of extra-slow-growing strains of soybean bradyrhizobia.", "token_count": 116, "char_count": 426, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7719, "quality_score": 0.886, "entities": { "genes": [ "NK6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:28.618413", "source": { "split": "train_shard_00000", "doc_id": 4388 }, "chunk_id": "train_shard_00000_4388_1", "global_id": 4895 }, { "text": "Human hepatocytes cultured in a monolayer configuration represent a well-established in vitro model in liver toxicology, notably used in drug transporter studies. Polarized status of drug transporters, i.e., their coordinated location at sinusoidal or canalicular membranes, remains however incompletely documented in these cultured hepatocytes. The present study was therefore designed to analyze transporter expression and location in such cells. Most of drug transporters were first shown to be present at notable mRNA levels in monolayer-cultured human hepatocytes. Cultured human hepatocytes, which morphologically exhibited bile canaliculi-like structures, were next demonstrated, through immunofluorescence staining, to express the influx transporters organic anion transporting polypeptide (OATP) 1B1, OATP2B1 and organic cation transporter (OCT) 1 and the efflux transporter multidrug resistance-associated protein (MRP) 3 at their sinusoidal pole. In addition, the efflux transporters P-glycoprotein and MRP2 were detected at the canalicular pole of monolayer-cultured human hepatocytes. Moreover, canalicular secretion of reference substrates for the efflux transporters bile salt export pump, MRP2 and P-glycoprotein as well as sinusoidal drug transporter activities were observed. This polarized and functional expression of drug transporters in monolayer-cultured human hepatocytes highlights the interest of using this human in vitro cell model in xenobiotic transport studies.\n\nPolarized location of SLC and ABC drug transporters in monolayer-cultured human hepatocytes.", "token_count": 405, "char_count": 1586, "word_count": 206, "semantic_coherence": 1, "information_density": 0.568, "quality_score": 0.784, "entities": { "genes": [ "MRP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:29.238756", "source": { "split": "train_shard_00000", "doc_id": 4389 }, "chunk_id": "train_shard_00000_4389_0", "global_id": 4896 }, { "text": "The tubercle complex consists of closely related mycobacterium species which appear to be variants of a single species. Comparative genome analysis of different strains could provide useful clues and insights into the genetic diversity of the species. We integrated genome assemblies of 96 strains from Mycobacterium tuberculosis complex (MTBC), which included 8 Indian clinical isolates sequenced and assembled in this study, to understand its pangenome architecture. We predicted genes for all the 96 strains and clustered their respective CDSs into homologous gene clusters (HGCs) to reveal a hard-core, soft-core and accessory genome component of MTBC. The hard-core (HGCs shared amongst 100% of the strains) was comprised of 2,066 gene clusters whereas the soft-core (HGCs shared amongst at least 95% of the strains) comprised of 3,374 gene clusters. The change in the core and accessory genome components when observed as a function of their size revealed that MTBC has an open pangenome. We identified 74 HGCs that were absent from reference strains H37Rv and H37Ra but were present in most of clinical isolates. We report PCR validation on 9 candidate genes depicting 7 genes completely absent from H37Rv and H37Ra whereas 2 genes shared partial homology with them accounting to probable insertion and deletion events. The pangenome approach is a promising tool for studying strain specific genetic differences occurring within species. We also suggest that since selecting appropriate target genes for typing purposes requires the expected target gene be present in all isolates being typed, therefore estimating the core-component of the species becomes a subject of prime importance.\n\nComparative whole-genome analysis of clinical isolates reveals characteristic architecture of Mycobacterium tuberculosis pangenome.", "token_count": 427, "char_count": 1827, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:29.865435", "source": { "split": "train_shard_00000", "doc_id": 4390 }, "chunk_id": "train_shard_00000_4390_0", "global_id": 4897 }, { "text": "The use of live probiotic bacteria as food supplement has become popular. Capability of probiotic bacteria to be kept at room temperature becomes necessary for customer's convenience and manufacturer's cost reduction. Hence, production of dried form of probiotic bacteria is important. Two common drying methods commonly used for microencapsulation are freeze drying and spray drying. In spite of their benefits, both methods have adverse effects on cell membrane integrity and protein structures resulting in decrease in bacterial viability. Microencapsulation of probiotic bacteria has been a promising technology to ensure bacterial stability during the drying process and to preserve their viability during storage without significantly losing their functional properties such acid tolerance, bile tolerance, surface hydrophobicity, and enzyme activities. Storage at room temperatures instead of freezing or low temperature storage is preferable for minimizing costs of handling, transportation, and storage. Concepts of water activity and glass transition become important in terms of determination of bacterial survival during the storage. The effectiveness of microencapsulation is also affected by microcapsule materials. Carbohydrate- and protein-based microencapsulants and their combination are discussed in terms of their protecting effect on probiotic bacteria during dehydration, during exposure to harsh gastrointestinal transit and small intestine transit and during storage.\n\nSurvival of Microencapsulated Probiotic Bacteria after Processing and during Storage: A Review.", "token_count": 314, "char_count": 1588, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:30.433345", "source": { "split": "train_shard_00000", "doc_id": 4391 }, "chunk_id": "train_shard_00000_4391_0", "global_id": 4898 }, { "text": "The open reading frame YGL157w in the genome of the yeast Kluyveromyces marxianus strain DMB1 encodes a putative uncharacterized oxidoreductase. However, this protein shows 46% identity with the Saccharomyces cerevisiae S288c NADPH-dependent methylglyoxal reductase, which exhibits broad substrate specificity for aldehydes. In the present study, the YGL157w gene product (KmGRE2) was purified to homogeneity from overexpressing Escherichia coli cells and found to be a monomer. The enzyme was strictly specific for NADPH and was active with a wide variety of substrates, including aliphatic (branched-chain and linear) and aromatic aldehydes. The optimal pH for methylglyoxal reduction was 5.5. With methylglyoxal as a substrate, the optimal temperature for enzyme activity at pH 5.5 was 45°C. The enzyme retained more than 70% of its activity after incubation for 30 min at temperatures below 35°C or at pHs between 5.5 and 9.0. In addition, the KmGRE2-overexpressing E. coli showed improved growth when cultivated in cedar hydrolysate, as compared to cells not expressing the enzyme. Taken together, these results indicate that KmGRE2 is potentially useful as an inhibit decomposer in E. coli cells.\n\nCharacterization of the Kluyveromyces marxianus strain DMB1 YGL157w gene product as a broad specificity NADPH-dependent aldehyde reductase.", "token_count": 405, "char_count": 1343, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8256, "entities": { "genes": [ "DMB1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:31.052364", "source": { "split": "train_shard_00000", "doc_id": 4392 }, "chunk_id": "train_shard_00000_4392_0", "global_id": 4899 }, { "text": "Troglitazone causes severe hepatic injury in certain individuals and multiple mechanisms related to hepato-toxicity has been reported creating confusion. In the present study, the mechanism for the hepatic injury of glitazones was investigated by PASS. The results suggest that chromane containing glitazones are apoptic agonist (activating p53 by intrinsic pathway leading to the apoptosis) and those which do not contain the chromane are devoid of this. In case of hepato-toxicity by non-chromane glitazone and their metabolite such as M-3, RM-3, rosiglitazone and pioglitazone; PASS suggest that these chemicals are not apoptic agonist but they are the substrate for CYP enzyme (Phase-I Oxidative Enzyme) and Phase-II conjugating enzymes; interfering with bile acid metabolism rendering bile acid more toxic (cholestasis). This unmetabolised bile salt further initiates the process apoptosis via intrinsic and extrinsic pathway leading to the apoptosis. Immunoblot analysis further confirm our hypothesis that troglitazone (chromane containing glitazone), but not rosiglitazone and pioglitazone (non-chromane containing glitazone) increased the levels of p53 in a time-dependent manner. Hence our prediction related to the mechanism of hepato-toxicity by apoptosis and structural insight of glitazone can be helpful in improving the drug profile of this category.\n\nStructural insight of glitazone for hepato-toxicity: Resolving mystery by PASS.", "token_count": 385, "char_count": 1447, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8085, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:32.407617", "source": { "split": "train_shard_00000", "doc_id": 4393 }, "chunk_id": "train_shard_00000_4393_0", "global_id": 4900 }, { "text": "Mutations in the gene encoding the canalicular bile salt export pump (BSEP) can result in progressive familial intrahepatic cholestasis type 2 (PFIC-2). Treatment options are limited, and PFIC-2 often necessitates liver transplantation. We report on a young woman and a boy who clinically presented with PFIC-2 phenotypes and dramatically improved with steroid treatment. Gene sequencing of ABCB11 encoding for BSEP revealed 2 relevant mutations in both patients. The young woman was compound heterozygous for p.T919del and p.R1235X. At the age of 5 years, partial biliary diversion was performed and rescued liver function but left serum bile salt levels elevated. At age 23 she developed systemic lupus erythematosus. Unexpectedly, steroid therapy normalized serum bile salt levels, with a strong correlation with the steroid dose. She is currently in clinical remission. The boy was compound heterozygous for the ABCB11 mutations c.150+3A>C and p.R832C and presented with intractable pruritus. When he developed colitis, he was treated with steroids. The pruritus completely disappeared and relapsed when steroids were withdrawn. To date, with low-dose budesonide, the boy has been symptom-free for >3 years. In conclusion, the clinical courses suggest that patients with BSEP deficiency and residual BSEP activity may benefit from steroid-based therapy, which represents a new treatment option.\n\nTwo Case Reports of Successful Treatment of Cholestasis With Steroids in Patients With PFIC-2.", "token_count": 397, "char_count": 1494, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:33.024031", "source": { "split": "train_shard_00000", "doc_id": 4394 }, "chunk_id": "train_shard_00000_4394_0", "global_id": 4901 }, { "text": "We investigated predictors of clinical evolution in progressive familial intrahepatic cholestasis type 2 patients and how they relate to bile salt export pump (BSEP) expression and its (re)targeting. Our retrospective study included 22 children with progressive familial intrahepatic cholestasis type 2. Clinical, biochemical, and histological characteristics were reviewed on admittance and following treatment with either ursodeoxycholic acid alone (10 mg/kg thrice daily, n = 19) or partial biliary diversion (n = 3). Immunostaining of BSEP was performed in 20 patients. Response to treatment was defined as normalization of pruritus, disappearance of jaundice, and alanine aminotransferase (ALT) levels <1.5 times the upper limit of normal. Ten of 22 patients were responders, and paired biopsies were available in six. De novo or retargeted canalicular expression of BSEP occurred in four of these six, two of whom exhibited baseline intracellular expression. Twelve of 22 were nonresponders and exhibited earlier onset of jaundice (<9 months), neonatal cholestasis, and higher ALT levels. An ALT >165 IU/L produced 72% sensitivity and 55% specificity in predicting nonresponse. Seven patients were still responding at last follow-up (median = 20 months, range 5-67 months). Three responders relapsed after 56, 72, and 82 months, respectively. Of nine surviving responders, median relapse-free survival time was 72 months (95% confidence interval 48-96 months) and 5-year relapse-free survival was 75% (95% confidence interval 33-100%). Intracellular BSEP at baseline was seen in six, of whom five were responders. Genetic analysis was performed in 17 of 22, confirming diagnosis in 13 (76%) and in four (24%) in whom only heterozygous mutation was identified.", "token_count": 516, "char_count": 1765, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6899, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:43:33.686396", "source": { "split": "train_shard_00000", "doc_id": 4395 }, "chunk_id": "train_shard_00000_4395_0", "global_id": 4902 }, { "text": "Retargeting of bile salt export pump and favorable outcome in children with progressive familial intrahepatic cholestasis type 2.", "token_count": 32, "char_count": 129, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:34.047069", "source": { "split": "train_shard_00000", "doc_id": 4395 }, "chunk_id": "train_shard_00000_4395_1", "global_id": 4903 }, { "text": "Bile salts are steroidal biosurfactants. Micellar systems of bile salts are not only important for solubilization of cholesterol, but they also interact with certain drugs thus changing their bioavailability.\n\nMicellization parameters (number average, aggregation number and critical micellar concentration) of bile salt 3 and 7 ethylidene derivatives: Role of the steroidal skeleton II.", "token_count": 98, "char_count": 387, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8113, "quality_score": 0.9057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:34.463090", "source": { "split": "train_shard_00000", "doc_id": 4396 }, "chunk_id": "train_shard_00000_4396_0", "global_id": 4904 }, { "text": "This study sought to evaluate the probiotic potential of lactic acid bacteria (LAB) isolated from traditionally fermented south Indian koozh and gherkin (cucumber). A total of 51 LAB strains were isolated, among which four were identified as Lactobacillus spp. and three as Weissella spp. The strains were screened for their probiotic potential. All isolated Lactobacillus and Weissella strains were capable of surviving under low pH and bile salt conditions. GI9 and FKI21 were able to survive at pH 2.0 and 0.50% bile salt for 3 h without losing their viability. All LAB strains exhibited inhibitory activity against tested pathogens and were able to deconjugate bile salt. Higher deconjugation was observed in the presence of sodium glycocholate (P < 0.05). Strain FKI21 showed maximum auto-aggregation (79%) and co-aggregation with Escherichia coli MTCC 1089 (68%). Exopolysaccharide production of LAB strains ranged from 68.39 to 127.12 mg/L (P < 0.05). Moreover, GI9 (58.08 μg/ml) and FKI21 (56.25 μg/ml) exhibited maximum cholesterol reduction with bile salts. 16S rRNA sequencing confirmed GI9 and FKI21 as Lactobacillus crispatus and Weissella koreensis, respectively. This is the first study to report isolation of W. koreensis FKI21 from fermented koozh and demonstrates its cholesterol-reducing potential.\n\nDetermining the probiotic potential of cholesterol-reducing Lactobacillus and Weissella strains isolated from gherkins (fermented cucumber) and south Indian fermented koozh.", "token_count": 481, "char_count": 1492, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5972, "quality_score": 0.7986, "entities": { "genes": [ "FKI21", "GI9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:35.122771", "source": { "split": "train_shard_00000", "doc_id": 4397 }, "chunk_id": "train_shard_00000_4397_0", "global_id": 4905 }, { "text": "A large outbreak of gastrointestinal disease occurred in 2011 in Germany which resulted in almost 4000 patients with acute gastroenteritis or hemorrhagic colitis, 855 cases of a hemolytic uremic syndrome and 53 deaths. The pathogen was an uncommon, multiresistant Escherichia coli strain of serotype O104:H4 which expressed a Shiga toxin characteristic of enterohemorrhagic E. coli and in addition virulence factors common to enteroaggregative E. coli. During post-epidemic surveillance of Shiga toxin-producing E. coli (STEC) all but two of O104:H4 isolates were indistinguishable from the epidemic strain. Here we describe two novel STEC O104:H4 strains isolated in close spatiotemporal proximity to the outbreak which show a virulence gene panel, a Shiga toxin-mediated cytotoxicity towards Vero cells and aggregative adherence to Hep-2 cells comparable to the outbreak strain. They differ however both from the epidemic strain and from each other, by their antibiotic resistance phenotypes and some other features as determined by routine epidemiological subtyping methods. Whole genome sequencing of these two strains, of ten outbreak strain isolates originating from different time points of the outbreak and of one historical sporadic EHEC O104:H4 isolate was performed. Sequence analysis revealed a clear phylogenetic distance between the two variant strains and the outbreak strain finally identifying them as epidemiologically unrelated isolates from sporadic cases. These findings add to the knowledge about this emerging pathogen, illustrating a certain diversity within the bacterial core genome as well as loss and gain of accessory elements. Our results do also support the view that distinct new variants of STEC O104:H4 repeatedly might originate from yet unknown reservoirs, rather than that there would be a continuous diversification of a single epidemic strain established and circulating in Germany after the large outbreak in 2011.", "token_count": 486, "char_count": 1954, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6514, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:35.812405", "source": { "split": "train_shard_00000", "doc_id": 4398 }, "chunk_id": "train_shard_00000_4398_0", "global_id": 4906 }, { "text": "Comparative genomic analysis of two novel sporadic Shiga toxin-producing Escherichia coli O104:H4 strains isolated 2011 in Germany.", "token_count": 45, "char_count": 131, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:36.193994", "source": { "split": "train_shard_00000", "doc_id": 4398 }, "chunk_id": "train_shard_00000_4398_1", "global_id": 4907 }, { "text": "High-temperature fermentation technology with thermotolerant microbes has been expected to reduce the cost of bioconversion of cellulosic biomass to fuels or chemicals. Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. These capabilities have been found to exceed those of the traditional ethanol producer Saccharomyces cerevisiae or lignocellulose-bioconvertible ethanologenic Scheffersomyces stipitis.\n\nGenetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses.", "token_count": 163, "char_count": 654, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8987, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:36.632869", "source": { "split": "train_shard_00000", "doc_id": 4399 }, "chunk_id": "train_shard_00000_4399_0", "global_id": 4908 }, { "text": "Milk kefir is produced by fermenting milk in the presence of kefir grains. This beverage has several benefits for human health. The aim of this experiment was to analyze 5 kefir grains (and their products) using a targeted metagenetic approach. Of the 5 kefir grains analyzed, 1 was purchased in a supermarket, 2 were provided by the Ministry of Agriculture (Namur, Belgium), and 2 were provided by individuals. The metagenetic approach targeted the V1-V3 fragment of the 16S ribosomal (r)DNA for the grains and the resulting beverages at 2 levels of grain incorporation (5 and 10%) to identify the bacterial species population. In contrast, the 26S rDNA pyrosequencing was performed only on kefir grains with the aim of assessing the yeast populations. In parallel, pH measurements were performed on the kefir obtained from the kefir grains using 2 incorporation rates. Regarding the bacterial population, 16S pyrosequencing revealed the presence of 20 main bacterial species, with a dominance of the following: Lactobacillus kefiranofaciens, Lactococcus lactis ssp. cremoris, Gluconobacter frateurii, Lactobacillus kefiri, Acetobacter orientalis, and Acetobacter lovaniensis. An important difference was noticed between the kefir samples: kefir grain purchased from a supermarket (sample E) harbored a much higher proportion of several operational taxonomic units of Lactococcus lactis and Leuconostoc mesenteroides. This sample of grain was macroscopically different from the others in terms of size, apparent cohesion of the grains, structure, and texture, probably associated with a lower level of Lactobacillus kefiranofaciens. The kefir (at an incorporation rate of 5%) produced from this sample of grain was characterized by a lower pH value (4.5) than the others. The other 4 samples of kefir (5%) had pH values above 5", "token_count": 496, "char_count": 1828, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5471, "quality_score": 0.7736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:37.294354", "source": { "split": "train_shard_00000", "doc_id": 4400 }, "chunk_id": "train_shard_00000_4400_0", "global_id": 4909 }, { "text": "Comparing the kefir grain and the kefir, an increase in the population of Gluconobacter in grain sample B was observed. This was also the case for Acetobacter orientalis in sample D. In relation to 26S pyrosequencing, our study revealed the presence of 3 main yeast species: Naumovozyma spp., Kluyveromyces marxianus, and Kazachastania khefir. For Naumovozyma, further studies are needed to assess the isolation of new species. In conclusion, this study has proved that it is possible to establish the patterns of bacterial and yeast composition of kefir and kefir grain. This was only achieved with the use of high-throughput sequencing techniques.\n\nShort communication: Evaluation of the microbiota of kefir samples using metagenetic analysis targeting the 16S and 26S ribosomal DNA fragments.", "token_count": 208, "char_count": 795, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6777, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:37.756746", "source": { "split": "train_shard_00000", "doc_id": 4400 }, "chunk_id": "train_shard_00000_4400_1", "global_id": 4910 }, { "text": "Efforts to control the spread of Buruli ulcer--an emerging ulcerative skin infection caused by Mycobacterium ulcerans--have been hampered by our poor understanding of reservoirs and transmission. To help address this issue, we compared whole genomes from 18 clinical M. ulcerans isolates from a 30 km2 region within the Asante Akim North District, Ashanti region, Ghana, with 15 other M. ulcerans isolates from elsewhere in Ghana and the surrounding countries of Ivory Coast, Togo, Benin and Nigeria. Contrary to our expectations of finding minor DNA sequence variations among isolates representing a single M. ulcerans circulating genotype, we found instead two distinct genotypes. One genotype was closely related to isolates from neighbouring regions of Amansie West and Densu, consistent with the predicted local endemic clone, but the second genotype (separated by 138 single nucleotide polymorphisms [SNPs] from other Ghanaian strains) most closely matched M. ulcerans from Nigeria, suggesting another introduction of M. ulcerans to Ghana, perhaps from that country. Both the exotic genotype and the local Ghanaian genotype displayed highly restricted intra-strain genetic variation, with less than 50 SNP differences across a 5.2 Mbp core genome within each genotype. Interestingly, there was no discernible spatial clustering of genotypes at the local village scale. Interviews revealed no obvious epidemiological links among BU patients who had been infected with identical M. ulcerans genotypes but lived in geographically separate villages. We conclude that M. ulcerans is spread widely across the region, with multiple genotypes present in any one area. These data give us new perspectives on the behaviour of possible reservoirs and subsequent transmission mechanisms of M. ulcerans. These observations also show for the first time that M. ulcerans can be mobilized, introduced to a new area and then spread within a population. Potential reservoirs of M. ulcerans thus might include humans, or perhaps M. ulcerans-infected animals such as livestock that move regularly between countries.", "token_count": 484, "char_count": 2101, "word_count": 310, "semantic_coherence": 1, "information_density": 0.6645, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:38.750910", "source": { "split": "train_shard_00000", "doc_id": 4401 }, "chunk_id": "train_shard_00000_4401_0", "global_id": 4911 }, { "text": "Whole genome comparisons suggest random distribution of Mycobacterium ulcerans genotypes in a Buruli ulcer endemic region of Ghana.", "token_count": 34, "char_count": 131, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:39.105526", "source": { "split": "train_shard_00000", "doc_id": 4401 }, "chunk_id": "train_shard_00000_4401_1", "global_id": 4912 }, { "text": "As an issue of biosecurity, it is important to identify the origin of a suspected sample to distinguish whether it originated from the release of a bioterrorism agent or from environmental contamination with a virulent agent. Here we have developed an analytical pipeline that can infer the phylogenetic position of Bacillus cereus group species, including B. anthracis, from next-generation sequencing reads without extensive genomics skills. GcoGSA-BA can also detect the existence of anthrax plasmid pXO1 carrying 3 anthrax toxins (lethal factor, edema factor, and protective antigen). This pipeline can also be used to correctly infer the phylogenetic position and to detect the suspected isolate carrying anthrax toxins among B. cereus group.\n\nGcoGSA-BA: a global core genome SNP analysis for Bacillus anthracis.", "token_count": 203, "char_count": 817, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:39.564764", "source": { "split": "train_shard_00000", "doc_id": 4402 }, "chunk_id": "train_shard_00000_4402_0", "global_id": 4913 }, { "text": "Burkholderia pseudomallei is the causative agent of melioidosis and a potential bioterrorism agent. In the development of medical countermeasures against B. pseudomallei infection, the US Food and Drug Administration (FDA) animal Rule recommends using well-characterized strains in animal challenge studies. In this study, whole genome sequence data were generated for 6 B. pseudomallei isolates previously identified as candidates for animal challenge studies; an additional 5 isolates were sequenced that were associated with human inhalational melioidosis. A core genome single nucleotide polymorphism (SNP) phylogeny inferred from a concatenated SNP alignment from the 11 isolates sequenced in this study and a diverse global collection of isolates demonstrated the diversity of the proposed Animal Rule isolates. To understand the genomic composition of each isolate, a large-scale blast score ratio (LS-BSR) analysis was performed on the entire pan-genome; this demonstrated the variable composition of genes across the panel and also helped to identify genes unique to individual isolates. In addition, a set of ~550 genes associated with pathogenesis in B. pseudomallei were screened against the 11 sequenced genomes with LS-BSR. Differential gene distribution for 54 virulence-associated genes was observed between genomes and three of these genes were correlated with differential virulence observed in animal challenge studies using BALB/c mice. Differentially conserved genes and SNPs associated with disease severity were identified and could be the basis for future studies investigating the pathogenesis of B. pseudomallei. Overall, the genetic characterization of the 11 proposed Animal Rule isolates provides context for future studies involving B. pseudomallei pathogenesis, differential virulence, and efficacy to therapeutics.\n\nGenomic characterization of Burkholderia pseudomallei isolates selected for medical countermeasures testing: comparative genomics associated with differential virulence.", "token_count": 451, "char_count": 2017, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5568, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:40.198742", "source": { "split": "train_shard_00000", "doc_id": 4403 }, "chunk_id": "train_shard_00000_4403_0", "global_id": 4914 }, { "text": "Diesel exhaust particles (DEPs) are common environmental air pollutants primarily affecting the lung. DEPs or chemicals adsorbed on DEPs also exert extra-pulmonary effects, including alteration of hepatic drug detoxifying enzyme expression. The present study was designed to determine whether organic DEP extract (DEPe) may target hepatic drug transporters that contribute in a major way to drug detoxification. Using primary human hepatocytes and transporter-overexpressing cells, DEPe was first shown to strongly inhibit activities of the sinusoidal solute carrier (SLC) uptake transporters organic anion-transporting polypeptides (OATP) 1B1, 1B3 and 2B1 and of the canalicular ATP-binding cassette (ABC) efflux pump multidrug resistance-associated protein 2, with IC50 values ranging from approximately 1 to 20 μg/mL and relevant to environmental exposure situations. By contrast, 25 μg/mL DEPe failed to alter activities of the SLC transporter organic cation transporter (OCT) 1 and of the ABC efflux pumps P-glycoprotein and bile salt export pump (BSEP), whereas it only moderately inhibited those of sodium taurocholate co-transporting polypeptide and of breast cancer resistance protein (BCRP). Treatment by 25 μg/mL DEPe was next demonstrated to induce expression of BCRP at both mRNA and protein level in cultured human hepatic cells, whereas it concomitantly repressed mRNA expression of various transporters, including OATP1B3, OATP2B1, OCT1 and BSEP. Such changes in transporter expression were found to be highly correlated to those caused by 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), a reference activator of the aryl hydrocarbon receptor (AhR) pathway. This suggests that DEPe, which is enriched in known ligands of AhR like polycyclic aromatic hydrocarbons, alters drug transporter expression via activation of the AhR cascade", "token_count": 513, "char_count": 1844, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6977, "quality_score": 0.8488, "entities": { "genes": [ "OCT1", "IC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:43:40.857671", "source": { "split": "train_shard_00000", "doc_id": 4404 }, "chunk_id": "train_shard_00000_4404_0", "global_id": 4915 }, { "text": "Taken together, these data established human hepatic transporters as targets of organic chemicals containing in DEPs, which may contribute to their systemic effects through impairing hepatic transport of endogenous compound or drug substrates of these transporters.\n\nRegulation of human hepatic drug transporter activity and expression by diesel exhaust particle extract.", "token_count": 77, "char_count": 371, "word_count": 50, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:41.229116", "source": { "split": "train_shard_00000", "doc_id": 4404 }, "chunk_id": "train_shard_00000_4404_1", "global_id": 4916 }, { "text": "Recent studies have demonstrated beneficial effects of specific probiotics on alleviating obesity-related disorders. Here we aimed to identify probiotics with potential antiobesity activity among 88 lactic acid bacterial strains via in vitro screening assays, and a Lactobacillus plantarum strain K21 was found to harbor abilities required for hydrolyzing bile salt, reducing cholesterol, and inhibiting the accumulation of lipid in 3T3-L1 preadipocytes. Furthermore, effects of K21 on diet-induced obese (DIO) mice were examined. Male C57Bl/6J mice received a normal diet, high-fat diet (HFD), or HFD with K21 administration (10(9) CFU in 0.2 mL PBS/day) for eight weeks. Supplementation of K21, but not placebo, appeared to alleviate body weight gain and epididymal fat mass accumulation, reduce plasma leptin levels, decrease cholesterol and triglyceride levels, and mitigate liver damage in DIO mice. Moreover, the hepatic expression of peroxisome proliferator-activated receptor-γ (PPAR-γ) related to adipogenesis was significantly downregulated in DIO mice by K21 intervention. We also found that K21 supplementation strengthens intestinal permeability and modulates the amount of Lactobacillus spp., Bifidobacterium spp., and Clostridium perfringens in the cecal contents of DIO mice. In conclusion, our results suggest that dietary intake of K21 protects against the onset of HFD-induced obesity through multiple mechanisms of action.\n\nEffect of Lactobacillus plantarum Strain K21 on High-Fat Diet-Fed Obese Mice.", "token_count": 443, "char_count": 1521, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7109, "quality_score": 0.8555, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:41.866499", "source": { "split": "train_shard_00000", "doc_id": 4405 }, "chunk_id": "train_shard_00000_4405_0", "global_id": 4917 }, { "text": "This study evaluated the effect of soy lecithin on the bile resistance of Lactobacillus plantarum. Six strains were cultured in MRS broth supplemented with soy lecithin at different concentrations. The strains incubated in MRS broth with 1·0% soy lecithin showed no inhibitory effect on cell growth. After culturing in MRS broth with 0·2-1·0% soy lecithin, the survival rate of harvested cells increased significantly (P < 0·05) in the 0·3% bile challenge compared with the no added soy lecithin group. The cells incubated with 0·6% soy lecithin were able to grow in an MRS broth with a higher bile salt content. The surface hydrophobicity and cell leakage in the bile challenge were assessed to reveal the physical changes caused by the addition of soy lecithin. The cell surface hydrophobicity was enhanced and the membrane integrity in the bile challenge increased after culturing with soy lecithin. A shift in the fatty acid composition was also observed, illustrating the cell membrane change in the soy lecithin culture.\n\nEnhancement of bile resistance in Lactobacillus plantarum strains by soy lecithin.", "token_count": 311, "char_count": 1110, "word_count": 175, "semantic_coherence": 1, "information_density": 0.4914, "quality_score": 0.7457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:42.432716", "source": { "split": "train_shard_00000", "doc_id": 4406 }, "chunk_id": "train_shard_00000_4406_0", "global_id": 4918 }, { "text": "The aim of the present work was to isolate a bile salt hydrolase (BSH) producer from fermented soy curd and explore the ability of the BSH produced to cleave bacterial quorum sensing signals. Bacterial isolates with possible ability to deconjugate bile salts were enriched and isolated on De Man, Rogosa and Sharpe (MRS) medium containing 0.2% bile salts. BSH-producing positive isolate with orange-pink-pigmented colonies was isolated and was identified as a strain of Staphylococcus epidermidis using biochemical and phylogenetic tools. S. epidermidis RM1 was shown to possess both potent BSH and N-acyl homoserine lactone (AHL) cleavage activity. Genetic basis of this dual-enzyme activity was explored by means of specific primers designed using S. epidermidis ATCC 12228 genome as template. It was observed that a single enzyme was not responsible for both the activity. Two different genetic elements corresponding to each of the enzymatic activity were successfully amplified from the genomic DNA of the isolate.\n\nPossible Correlation Between Bile Salt Hydrolysis and AHL Deamidation: Staphylococcus epidermidis RM1, a Potent Quorum Quencher and Bile Salt Hydrolase Producer.", "token_count": 328, "char_count": 1182, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [ "RM1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:43.002290", "source": { "split": "train_shard_00000", "doc_id": 4407 }, "chunk_id": "train_shard_00000_4407_0", "global_id": 4919 }, { "text": "Lipid metabolism is accompanied by the solubilization of lipid bilayer membranes by bile salts. We use Brownian dynamics simulations to study the solubilization of model membranes and vesicles by sodium cholate. The solubilization pathways of small and large vesicles are found to be different. Both results for small and large vesicles can be compared with predictions of a macroscopic theoretical description. The line tension of bilayer edges is an important parameter in the solubilization process. We propose a simple method to determine the line tension by analyzing the shape fluctuations of planar membrane patches. Macroscopic mechanical models provide a reasonable explanation for processes observed when a spherical vesicle consisting of lipids and adsorbed bile salt molecules is transformed into mixed lipid-bile salt micelles.\n\nVesicle solubilization by bile salts: comparison of macroscopic theory and simulation.", "token_count": 207, "char_count": 928, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6269, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:43.464038", "source": { "split": "train_shard_00000", "doc_id": 4408 }, "chunk_id": "train_shard_00000_4408_0", "global_id": 4920 }, { "text": "Taurine is a sulfur-containing amino acid that is present in mammalian tissues in millimolar concentrations. Taurine is involved in a diverse array of biological and physiological functions, including bile salt conjugation, osmoregulation, membrane stabilization, calcium modulation, anti-oxidation, and immunomodulation. The prevalence of obesity and being overweight continues to rise worldwide at an alarming rate. Obesity is associated with a higher risk of metabolic and cardiovascular diseases, cancer, and other clinical conditions. Ingestion of taurine has been shown to alleviate metabolic diseases such as hyperlipidemia, diabetes, hypertension, and obesity in animal models. A global epidemiological survey showed that 24-h urinary taurine excretion, as a marker of dietary taurine intake, was inversely associated with BMI, blood pressure, and plasma cholesterol in humans. In addition, taurine chloramine, an endogenous product derived from activated neutrophils, has been reported to suppress obesity-induced oxidative stress and inflammation in adipocytes. Synthetic activity and concentration of taurine in adipose tissues and plasma have been shown to decrease in humans and animals during the development of obesity, suggesting a relationship between taurine deficiency and obesity. In this review, I summarize the effects of taurine on the progression of obesity in animal models and humans. Furthermore, I discuss possible mechanisms underlying the antiobesity effects of taurine.\n\nRole of taurine in the pathogenesis of obesity.", "token_count": 385, "char_count": 1549, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:44.080101", "source": { "split": "train_shard_00000", "doc_id": 4409 }, "chunk_id": "train_shard_00000_4409_0", "global_id": 4921 }, { "text": "The fundamentals of this research were to exploit non-ionic surfactant technology for delivery and administration of vaccine antigens across the oral route and to gain a better understanding of vaccine trafficking. Using a newly developed method for manufacture of non-ionic surfactant vesicles (niosomes and bilosomes) lower process temperatures were adopted thus reducing antigen exposure to potentially damaging conditions. Vesicles prepared by this method offered high protection to enzymatic degradation, with only ∼10 % antigen loss measured when vesicles incorporating antigen were exposed to enzyme digestion. Interestingly, when formulated using this new production method, the addition of bile salt to the vesicles offered no advantage in terms of stability within simulated gastro-intestinal conditions. Considering their ability to deliver antigen to their target site, results demonstrated that incorporation of antigen within vesicles enhanced delivery and targeting of the antigen to the Peyer's Patch, again with niosomes and bilosomes offering similar efficiency. Delivery to both the Peyer's patches and mesentery lymphatics was shown to be dose dependent at lower concentrations, with saturation kinetics applying at higher concentrations. This demonstrates that in the formulation of vaccine delivery systems, the lipid/antigen dose ratio is not only a key factor in production cost, but is equally a key factor in the kinetics of delivery and targeting of a vaccine system.\n\nConsideration of the efficacy of non-ionic vesicles in the targeted delivery of oral vaccines.", "token_count": 353, "char_count": 1590, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5746, "quality_score": 0.7873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:44.654514", "source": { "split": "train_shard_00000", "doc_id": 4410 }, "chunk_id": "train_shard_00000_4410_0", "global_id": 4922 }, { "text": "Defining the essential genome of bacterial pathogens is central to developing an understanding of the biological processes controlling disease. This has proven elusive for Pseudomonas aeruginosa during chronic infection of the cystic fibrosis (CF) lung. In this paper, using a Monte Carlo simulation-based method to analyze high-throughput transposon sequencing data, we establish the P. aeruginosa essential genome with statistical precision in laboratory media and CF sputum. Reconstruction of the global requirements for growth in CF sputum compared with defined growth conditions shows that the latter requires several cofactors including biotin, riboflavin, and pantothenate. Comparison of P. aeruginosa strains PAO1 and PA14 demonstrates that essential genes are primarily restricted to the core genome; however, some orthologous genes in these strains exhibit differential essentiality. These results indicate that genes with similar molecular functions may have distinct genetic roles in different P. aeruginosa strains during growth in CF sputum. We also show that growth in a defined growth medium developed to mimic CF sputum yielded virtually identical fitness requirements to CF sputum, providing support for this medium as a relevant in vitro model for CF microbiology studies.\n\nEssential genome of Pseudomonas aeruginosa in cystic fibrosis sputum.", "token_count": 300, "char_count": 1362, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6218, "quality_score": 0.8109, "entities": { "genes": [ "PA14", "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:45.222031", "source": { "split": "train_shard_00000", "doc_id": 4411 }, "chunk_id": "train_shard_00000_4411_0", "global_id": 4923 }, { "text": "Taurine (2-aminoethane sulfonic acid) plays important roles in multiple physiological processes including osmoregulation, bile salt conjugation and membrane protection. It is known that taurine biosynthesis varies in different fish species. However, its ontogenetic regulation has not been clear. In the present study, we found that the hepatic concentrations of taurine increased marginally with rainbow trout growth. The mRNA expression, protein levels and enzyme activities of key enzymes involved in taurine biosynthesis, cysteine dioxygenase (CDO) and cysteine sulfinate decarboxylase (CSD), were analyzed. Our results showed that the mRNA levels and protein abundances of CSD increased dramatically with the development of rainbow trout stages while the enzyme activities showed a slight improvement. However, the expression and activities of CDO decreased with rainbow trout growth. These results provide valuable information on defining the exact supplementation of taurine in diets for different stages of rainbow trout and give new insights into elucidating the regulation of taurine metabolism in rainbow trout.\n\nOntogenetic taurine biosynthesis ability in rainbow trout (Oncorhynchus mykiss).", "token_count": 297, "char_count": 1204, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6242, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:45.783347", "source": { "split": "train_shard_00000", "doc_id": 4412 }, "chunk_id": "train_shard_00000_4412_0", "global_id": 4924 }, { "text": "In the present study twelve Lactobacillus isolates (LBS 1-LBS 12) were characterized for probiotic properties. Out of the twelve, eight isolates (LBS 1-6, 8 and 11) were bile resistant (survival > 50% at 0.3% bile salt w/v) and five isolates (LBS 1, 2, 5, 6 and 11) were found acid pH value resistant (survival > 50% at pH 3). All twelve isolates inhibited the growth of Staphylococcus aureus whereas isolate LBS 2 also inhibited the growth of Escherichia coli and Salmonella typhimurium. Antibiotic susceptibility testing of isolates was also performed and isolate LBS 2 was selected for further study based on its broad spectrum effect in clinical pathogen inhibition. LBS 2 was characterized phenotypically at Institute of Microbial Technology (IMTECH), Chandigarh, India and was confirmed as Lactobacillus rhamnosus by 16S rDNA sequencing and subsequent analysis using BLAST. The gene sequence was deposited in GenBank with accession number KJ562858. Scanning electron microscopy (SEM) study was used to study in vitro epithelial cell adherence and bile salt effect on isolate LBS 2. Epithelial cells adherence assay showed positive results and surface roughness of LBS 2 increased with increase in bile salt (0.15-0.45% w/v).\n\nCharacterization of Lactobacillus isolated from dairy samples for probiotic properties.", "token_count": 405, "char_count": 1319, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6219, "quality_score": 0.8109, "entities": { "genes": [ "KJ562858" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:46.435816", "source": { "split": "train_shard_00000", "doc_id": 4413 }, "chunk_id": "train_shard_00000_4413_0", "global_id": 4925 }, { "text": "During recent years, the significant and increasing interest in novel bifidobacterial strains with health-promoting characteristics has catalyzed the development of methods for efficient and reliable identification of Bifidobacterium strains at (sub) species level. We developed an assay based on recently acquired bifidobacterial genomic data and involving 98 primer pairs, called the Bifidobacterium-ampliseq panel. This panel includes multiplex PCR primers that target both core and variable genes of the pangenome of this genus. Our results demonstrate that the employment of the Bifidobacterium-ampliseq panel allows rapid and specific identification of the so far recognized 48 (sub)species harboring the Bifidobacterium genus, and thus represents a cost- and time-effective bifidobacterial screening methodology.\n\nA genome-based identification approach for members of the genus Bifidobacterium.", "token_count": 211, "char_count": 901, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7288, "quality_score": 0.8644, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:46.920174", "source": { "split": "train_shard_00000", "doc_id": 4414 }, "chunk_id": "train_shard_00000_4414_0", "global_id": 4926 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) is a group of rare disorders which are caused by defect in bile secretion and present with intrahepatic cholestasis, usually in infancy and childhood. These are autosomal recessive in inheritance. The estimated incidence is about 1 per 50,000 to 1 per 100,000 births, although exact prevalence is not known. These diseases affect both the genders equally and have been reported from all geographical areas. Based on clinical presentation, laboratory findings, liver histology and genetic defect, these are broadly divided into three types-PFIC type 1, PFIC type 2 and PFIC type 3. The defect is in ATP8B1 gene encoding the FIC1 protein, ABCB 11 gene encoding BSEP protein and ABCB4 gene encoding MDR3 protein in PFIC1, 2 and 3 respectively. The basic defect is impaired bile salt secretion in PFIC1/2 whereas in PFIC3, it is reduced biliary phospholipid secretion. The main clinical presentation is in the form of cholestatic jaundice and pruritus. Serum gamma glutamyl transpeptidase (GGT) is normal in patients with PFIC1/2 while it is raised in patients with PFIC3. Treatment includes nutritional support (adequate calories, supplementation of fat soluble vitamins and medium chain triglycerides) and use of medications to relieve pruritus as initial therapy followed by biliary diversion procedures in selected patients. Ultimately liver transplantation is needed in most patients as they develop progressive liver fibrosis, cirrhosis and end stage liver disease. Due to the high risk of developing liver tumors in PFIC2 patients, monitoring is recommended from infancy. Mutation targeted pharmacotherapy, gene therapy and hepatocyte transplantation are being explored as future therapeutic options.\n\nProgressive familial intrahepatic cholestasis.", "token_count": 471, "char_count": 1804, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [ "ABCB4", "MDR3", "PFIC1", "PFIC2", "FIC1", "PFIC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:47.583708", "source": { "split": "train_shard_00000", "doc_id": 4415 }, "chunk_id": "train_shard_00000_4415_0", "global_id": 4927 }, { "text": "A new strain of Bacillus coagulans CGMCC 9551, which has a broad range of antibacterial activities against six main pathogenic bacteria including Escherichia coli O8, Staphylococcus aureus, Salmonella enterica subsp. enterica serovar enteritidis, Streptococcus suis, Listeria monocytogenes and Pasteurella multocida, was isolated from healthy piglet feces. In adhesion assay, the isolate exhibited a stronger adhesion to pig intestinal mucus than that of B. subtilis JT143 and L. acidophilus LY24 respectively isolated from BioPlus(®)2B and FloraFIT(®) Probiotics (P < 0.05). The adhesion activity reached 44.5 ± 3.2, 48.9 ± 2.6, 42.6 ± 3.3 and 37.6 ± 2.4% to jejunum, ileum, transverse colon and sigmoid colon, separately. The survival rate of B. coagulans CGMCC 9551 was reduced by only 20% at 4 h exposure under 0.9% w/v bile salt. The strain was fully resistant to pH 2 for 2 h with 90.1 ± 3.5% survival and susceptible to 15 antibiotics commonly used in veterinary medicine. Additionally, the bacteria showed amylase, protease and cellulase activities. The safety assessment demonstrated the lack of toxicity potential in B. coagulans CGMCC 9551 by ligated rabbit ileal loop assay, acute and subchronic toxicity test. These results implied that that the new strain of B. coagulans CGMCC 9951 isolated from healthy piglet feces has promising probiotic characteristics and offers desirable opportunities for its successful commercialization as one excellent candidate probiotic.\n\nPotential probiotic attributes of a new strain of Bacillus coagulans CGMCC 9951 isolated from healthy piglet feces.", "token_count": 506, "char_count": 1598, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [ "JT143", "LY24" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:48.286772", "source": { "split": "train_shard_00000", "doc_id": 4416 }, "chunk_id": "train_shard_00000_4416_0", "global_id": 4928 }, { "text": "The aim of the present study is to construct a cysteine modified polyion complex micelles made of Pluronic F127-chitosan (PF127-CS), Pluronic F127-cysteine (PF127-cysteine) and sodium cholate (NaC) and to evaluate the potential of the micelles as an oral drug delivery system for paclitaxel. Systematic studies on physicochemical properties including size distribution, zeta-potential and morphology were conducted to validate the formation of micelle structure. Compared with Pluronic micelles, drug-loading capacity of PF127-CS/PF127-cysteine/NaC micelles was increased from 3.35% to 12.77%. Both the critical micelle concentration and the stability test confirmed that the PF127-CS/PF127-cysteine/NaC micelles were more stable in aqueous solution than sodium cholate micelles. Pharmacokinetic study demonstrated that when oral administration the area under the plasma concentration-time curve (AUC0-∞) and the absolute bioavailability of paclitaxel-loaded micelles were five times greater than that of the paclitaxel solution. In general, PF127-CS/PF127-cysteine/NaC micelles were proven to be a potential oral drug delivery system for paclitaxel.\n\nCysteine modified and bile salt based micelles: preparation and application as an oral delivery system for paclitaxel.", "token_count": 358, "char_count": 1270, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [ "AUC0", "PF127" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:48.864498", "source": { "split": "train_shard_00000", "doc_id": 4417 }, "chunk_id": "train_shard_00000_4417_0", "global_id": 4929 }, { "text": "Novel delivery technology using cell-penetrating peptides (CPPs) have recently shown their potential and are emerging as promising candidates for an oral protein and peptide delivery systems. As with for the development of any absorption enhancer that is meant to function across an epithelial layer covering a surface highly exposed to pathogens such as the intestines, concern arises about the safety of such enhancers. The purpose of this study was to investigate the effect of 7 d of consecutive oral administrations of CPPs and a typical enterotoxin, lipopolysaccharide (LPS) to mice to determine the degree, if any, of damage caused to the hepatic tissue. Following the 7-d dosing regimen, we could not detect significantly increased levels of the liver enzymes alanine aminotransferase and aspartate aminotransferase in plasma of mice treated with CPP and LPS compared to the controls, whereas heightened levels were observed in animals receiving the bile salt. In conclusion, the repeated use of CPPs as an oral absorption enhancer for macromolecules was found to be a safe strategy.\n\nSafety of the cell-penetrating peptide penetratin as an oral absorption enhancer.", "token_count": 284, "char_count": 1174, "word_count": 180, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:49.428550", "source": { "split": "train_shard_00000", "doc_id": 4418 }, "chunk_id": "train_shard_00000_4418_0", "global_id": 4930 }, { "text": "Various factors affect intestinal absorption of cholesterol and plant sterols and stanols. Plant sterols and stanols are generally less absorptive than cholesterol. Differential absorption rates among various plant sterols and stanols have been also reported. Although it was suggested that differential absorption among cholesterol and various plant sterols was determined by difference in excretion rates of sterols and stanols through ATP-binding cassette transporter (ABC) G5/ABCG8 of intestinal cells, our study suggests that affinity for and solubility in bile salt micelles can be important determinants for differential absorption of plant sterols and stanols. It was also suggested that plant sterols were transiently incorporated into intestinal cells and then excreted to intestinal lumen through ABCG5/ABCG8. However, in a rat study, transient incorporation of sitosterol into intestinal cells was not observed, suggesting that sitosterol is differentiated from cholesterol at the incorporation site of intestinal cells. It is well established that plant sterols inhibit intestinal absorption of cholesterol and exert a hypocholesterolemic activity. Plant sterols are solubilized in bile salt micelles as cholesterol. Our study clearly showed that because the sterol-solubilizing capacity of bile salt micelles was limited, plant sterols solubilized in micelles reduced the solubility of cholesterol. This can be the major cause of inhibition of cholesterol absorption by plant sterols. Pancreatic cholesterol esterase accelerates intestinal absorption of unesterified cholesterol. Although it was suggested that cholesterol esterase accelerated esterification of cholesterol incorporated into intestinal cells and acted as a transporter at the surface of intestinal cells, our research revealed that the accelerated cholesterol absorption was caused by hydrolysis of phosphatidylcholine in bile salt micelles. It is thought that hydrolysis of phosphatidylcholine reduces the affinity of cholesterol for the micelles and accelerates the incorporation of cholesterol released from the micelles into intestinal cells.", "token_count": 502, "char_count": 2127, "word_count": 289, "semantic_coherence": 1, "information_density": 0.4118, "quality_score": 0.7059, "entities": { "genes": [ "ABCG8", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:50.080253", "source": { "split": "train_shard_00000", "doc_id": 4419 }, "chunk_id": "train_shard_00000_4419_0", "global_id": 4931 }, { "text": "Factors affecting intestinal absorption of cholesterol and plant sterols and stanols.", "token_count": 21, "char_count": 85, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:50.439117", "source": { "split": "train_shard_00000", "doc_id": 4419 }, "chunk_id": "train_shard_00000_4419_1", "global_id": 4932 }, { "text": "Drug-induced liver injury (DILI) is an important cause of drug toxicity. Inhibition of multidrug resistance protein 4 (MRP4), in addition to bile salt export pump (BSEP), might be a risk factor for the development of cholestatic DILI. Recently, we demonstrated that inhibition of MRP4, in addition to BSEP, may be a risk factor for the development of cholestatic DILI. Here, we aimed to develop computational models to delineate molecular features underlying MRP4 and BSEP inhibition. Models were developed using 257 BSEP and 86 MRP4 inhibitors and noninhibitors in the training set. Models were externally validated and used to predict the affinity of compounds toward BSEP and MRP4 in the DrugBank database. Compounds with a score above the median fingerprint threshold were considered to have significant inhibitory effects on MRP4 and BSEP. Common feature pharmacophore models were developed for MRP4 and BSEP with LigandScout software using a training set of nine well characterized MRP4 inhibitors and nine potent BSEP inhibitors. Bayesian models for BSEP and MRP4 inhibition/noninhibition were developed with cross-validated receiver operator curve values greater than 0.8 for the test sets, indicating robust models with acceptable false positive and false negative prediction rates. Both MRP4 and BSEP inhibitor pharmacophore models were characterized by hydrophobic and hydrogen-bond acceptor features, albeit in distinct spatial arrangements. Similar molecular features between MRP4 and BSEP inhibitors may partially explain why various drugs have affinity for both transporters. The Bayesian (BSEP, MRP4) and pharmacophore (MRP4, BSEP) models demonstrated significant classification accuracy and predictability.\n\nToward predicting drug-induced liver injury: parallel computational approaches to identify multidrug resistance protein 4 and bile salt export pump inhibitors.", "token_count": 456, "char_count": 1884, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5543, "quality_score": 0.7772, "entities": { "genes": [ "MRP4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:51.070147", "source": { "split": "train_shard_00000", "doc_id": 4420 }, "chunk_id": "train_shard_00000_4420_0", "global_id": 4933 }, { "text": "Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go. Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing. There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology", "token_count": 495, "char_count": 2158, "word_count": 326, "semantic_coherence": 1, "information_density": 0.5798, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:51.722345", "source": { "split": "train_shard_00000", "doc_id": 4421 }, "chunk_id": "train_shard_00000_4421_0", "global_id": 4934 }, { "text": "In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.\n\nInsights from 20 years of bacterial genome sequencing.", "token_count": 56, "char_count": 245, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8611, "quality_score": 0.9306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:52.084224", "source": { "split": "train_shard_00000", "doc_id": 4421 }, "chunk_id": "train_shard_00000_4421_1", "global_id": 4935 }, { "text": "This study analyses the effect of the crude enzymatic extract produced by Kluyveromyces marxianus (EEB) in the maceration and clarification of juice produced from Ives (Vitis labrusca) grapes compared to the commercial enzyme preparation Pectinex(®)Ultra Color (PEC). Treatments were conducted with a total pectinolytic activity of 1 U/mL of fruit juice, at 40 °C, for 60 min. After the enzymatic treatment, the juices were evaluated with respect to yield, viscosity, and degree of clarification, as well as the effect of the enzymes on polyphenol concentration, anthocyanins, and juice color. The results showed that both EEB and PEC increase yield, reduce viscosity and contribute to the clarification of grape juice. After enzyme treatment with the EEB preparation, the extraction yield increased 28.02 % and decreased 50.70 % in viscosity during the maceration of the pulp. During the juice production process clarification increased 11.91 %. With PEC, higher values for these parameters: 42.36, 63.20, and 26.81 % respectively, were achieved. The addition of EEB resulted in grape juice with better color intensity and extraction of phenolic compounds and anthocyanins. Considering all comparison criteria, the enzymatic extract of K. marxianus NRRL-Y-7571 can potentially be used in the production of juice.\n\nComparison of a pectinolytic extract of Kluyveromyces marxianus and a commercial enzyme preparation in the production of Ives (Vitis labrusca) grape juice.", "token_count": 412, "char_count": 1470, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5525, "quality_score": 0.7763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:52.709567", "source": { "split": "train_shard_00000", "doc_id": 4422 }, "chunk_id": "train_shard_00000_4422_0", "global_id": 4936 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC2) is a result of mutations in ABCB11 encoding bile salt export pump (BSEP), the canalicular bile salt export pump of hepatocyte. In some PFIC2 patients with missense mutations, BSEP is not detected at the canaliculus owing to mistrafficking of BSEP mutants. In vitro, chaperone drugs, such as 4-phenylbutyrate (4-PB), have been shown to partially correct mistrafficking. Four PFIC2 patients harboring at least one missense mutation (p.G982R, p.R1128C, and p.T1210P) were treated orally with 4-PB and followed prospectively. Patient mutations were reproduced in a Bsep/green fluorescent protein plasmid. Cellular localization of the resulting Bsep mutants was studied in a hepatocellular line (Can 10), and effects of treatment with 4-PB and/or ursodeoxycholic acid (UDCA) were assessed. In Can 10 cells, Bsep mutants were detected in the endoplasmic reticulum instead of at the canalicular membrane. Treatment with 4-PB and UDCA partially corrected Bsep mutant targeting. With 4-PB, we observed, in all patients, a decrease of pruritus and serum bile acid concentration (BAC) as well as an improvement of serum liver tests. Pathological liver injuries improved, and BSEP, which was not detected at the canalicular membrane before treatment, appeared at the canalicular membrane. Bile analyses showed an increase in BAC with 4-PB. Patient conditions remained stable with a median follow-up of 40 months (range, 3-53), and treatment tolerance was good.\n\nTargeted pharmacotherapy in progressive familial intrahepatic cholestasis type 2: Evidence for improvement of cholestasis with 4-phenylbutyrate.", "token_count": 480, "char_count": 1655, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:53.366415", "source": { "split": "train_shard_00000", "doc_id": 4423 }, "chunk_id": "train_shard_00000_4423_0", "global_id": 4937 }, { "text": "The bile salt export pump (BSEP) plays an important role in bile acid excretion. Impaired BSEP function may result in liver injury. Bile acids also undergo basolateral efflux, but the relative contributions of biliary (CLBile) versus basolateral efflux (CLBL) clearance to hepatocellular bile acid excretion have not been determined. In the present study, taurocholic acid (TCA; a model bile acid) disposition was characterized in human and rat sandwich-cultured hepatocytes (SCH) combined with pharmacokinetic modeling. In human SCH, biliary excretion of TCA predominated (CLBile = 0.14 ± 0.04 ml/min per g liver; CLBL = 0.042 ± 0.019 ml/min per g liver), whereas CLBile and CLBL contributed approximately equally to TCA hepatocellular excretion in rat SCH (CLBile = 0.34 ± 0.07 ml/min per g liver; CLBL = 0.26 ± 0.07 ml/min per g liver). Troglitazone decreased TCA uptake, CLBile, and CLBL; membrane vesicle assays revealed for the first time that the major metabolite, troglitazone sulfate, was a noncompetitive inhibitor of multidrug resistance-associated protein 4, a basolateral bile acid efflux transporter. Simulations revealed that decreased CLBile led to a greater increase in hepatic TCA exposure in human than in rat SCH. A decrease in both excretory pathways (CLBile and CLBL) exponentially increased hepatic TCA in both species, suggesting that 1) drugs that inhibit both pathways may have a greater risk for hepatotoxicity, and 2) impaired function of an alternate excretory pathway may predispose patients to hepatotoxicity when drugs that inhibit one pathway are administered. Simulations confirmed the protective role of uptake inhibition, suggesting that a drug's inhibitory effects on bile acid uptake also should be considered when evaluating hepatotoxic potential", "token_count": 516, "char_count": 1785, "word_count": 267, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:43:54.025401", "source": { "split": "train_shard_00000", "doc_id": 4424 }, "chunk_id": "train_shard_00000_4424_0", "global_id": 4938 }, { "text": "Overall, the current study precisely characterized basolateral efflux of TCA, revealed species differences in hepatocellular TCA efflux pathways, and provided insights about altered hepatic bile acid exposure when multiple transport pathways are impaired.\n\nSpecies differences in hepatobiliary disposition of taurocholic acid in human and rat sandwich-cultured hepatocytes: implications for drug-induced liver injury.", "token_count": 97, "char_count": 417, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:54.414182", "source": { "split": "train_shard_00000", "doc_id": 4424 }, "chunk_id": "train_shard_00000_4424_1", "global_id": 4939 }, { "text": "The Périgord black truffle (Tuber melanosporum Vittad.), considered a gastronomic delicacy worldwide, is an ectomycorrhizal filamentous fungus that is ecologically important in Mediterranean French, Italian and Spanish woodlands. In this study, we developed a novel resource of single nucleotide polymorphisms (SNPs) for T. melanosporum using Illumina high-throughput resequencing. The genome from six T. melanosporum geographical accessions was sequenced to a depth of approximately 20×. These geographical accessions were selected from different populations within the northern and southern regions of the geographical species distribution. Approximately 80% of the reads for each of the six resequenced geographical accessions mapped against the reference T. melanosporum genome assembly, estimating the core genome size of this organism to be approximately 110 Mbp. A total of 442 326 SNPs corresponding to 3540 SNPs/Mbps were identified as being included in all seven genomes. The SNPs occurred more frequently in repeated sequences (85%), although 4501 SNPs were also identified in the coding regions of 2587 genes. Using the ratio of nonsynonymous mutations per nonsynonymous site (pN) to synonymous mutations per synonymous site (pS) and Tajima's D index scanning the whole genome, we were able to identify genomic regions and genes potentially subjected to positive or purifying selection. The SNPs identified represent a valuable resource for future population genetics and genomics studies.\n\nA survey of genome-wide single nucleotide polymorphisms through genome resequencing in the Périgord black truffle (Tuber melanosporum Vittad.).", "token_count": 413, "char_count": 1646, "word_count": 231, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:55.033951", "source": { "split": "train_shard_00000", "doc_id": 4425 }, "chunk_id": "train_shard_00000_4425_0", "global_id": 4940 }, { "text": "It is established that ion exchange resins AV-17-2P, KU-2, AV-16-GS, AM 21A, IMAC-HP, PUROLITE and fiber VION KN-1 can be applied as carriers for inulinase immobilization. The analysis of IR spectra for an enzyme, carriers and heterogeneous enzyme preparations showed that inulinase binding to matrices of various carriers occurs in general through electrostatic interactions. It is assumed that the mechanisms of interaction between inulinase from Kluyveromyces marxianus and the matrices of cation- and anion exchange polymers differ essentially from each other: different sites of protein molecule take part in adsorption that causes various conformational reorganizations in an enzyme molecule.\n\n[Investigation of mechanisms of interaction between inulinase from Kluyveromyces marxianus and the matrices of ion-exchange resins and fiber].", "token_count": 213, "char_count": 842, "word_count": 117, "semantic_coherence": 1, "information_density": 0.641, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:55.497110", "source": { "split": "train_shard_00000", "doc_id": 4426 }, "chunk_id": "train_shard_00000_4426_0", "global_id": 4941 }, { "text": "Salmonid habitats can be impacted by several environmental factors, such as salinization, which can also affect salmonid tolerance to anthropogenic stressors, such as pesticides. Previous studies have shown that hypersaline acclimation enhances the acute toxicity of certain organophosphate and carbamate pesticides to euryhaline fish; however, sublethal impacts have been far less studied. The current study aims to determine how hypersaline acclimation and exposure to the organophosphate chlorpyrifos (CPF) impact salmonid olfaction. Combined acclimation and exposure to CPF was shown to impact rainbow trout olfaction at the molecular, physiological, and behavioral levels. Concurrent exposure to hypersalinity and 0.5μg/L CPF upregulated four genes (chloride intracellular channel 4, G protein zgc:101761, calcium calmodulin dependent protein kinase II delta, and adrenergic alpha 2C receptor) that inhibit olfactory signal transduction. At the physiological level, hypersalinity and chlorpyrifos caused a decrease in sensory response to the amino acid l-serine and the bile salt taurocholic acid. Combined acclimation and exposure also negatively impacted behavior and reduced the avoidance of a predator cue (l-serine). Thus, acclimation to hypersaline conditions and exposure to environmentally relevant concentrations of chlorpyrifos caused an inhibition of olfactory signal transduction leading to a decreased response to odorants and impairment of olfactory mediated behaviors.\n\nSublethal toxicity of chlorpyrifos to salmonid olfaction after hypersaline acclimation.", "token_count": 410, "char_count": 1577, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:56.117001", "source": { "split": "train_shard_00000", "doc_id": 4427 }, "chunk_id": "train_shard_00000_4427_0", "global_id": 4942 }, { "text": "The bile fluid contains various lipids that are secreted at the canalicular membrane of hepatocytes. As the secretion mechanism is still a matter of debate and a direct experimental observation of the secretion process is not possible so far, we used a mathematical model to simulate the extraction of the major bile lipids cholesterol, phosphatidylcholine and sphingomyelin from the outer leaflet of the canalicular membrane. Lipid diffusion was modeled as random movement on a triangular lattice governed by next-neighbor interaction energies. Phase separation in liquid-ordered and liquid-disordered domains was modeled by assigning two alternative ordering states to each lipid species and minimization of next-neighbor ordering energies. Parameterization of the model was performed such that experimentally determined diffusion rates and phases in ternary lipid mixtures of model membranes were correctly recapitulated. The model describes the spontaneous formation of nanodomains in the external leaflet of the canalicular membrane in a time window between 0.1 ms to 10 ms at varying lipid proportions. The extraction of lipid patches from the bile salt soluble nanodomain into the bile reproduced observed biliary phospholipid compositions for a physiological membrane composition. Comparing the outcome of model simulations with available experimental observations clearly favors the extraction of tiny membrane patches composed of about 100-400 lipids as the likely mechanism of biliary lipid secretion.\n\nComputer simulations suggest a key role of membranous nanodomains in biliary lipid secretion.", "token_count": 355, "char_count": 1607, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:56.697633", "source": { "split": "train_shard_00000", "doc_id": 4428 }, "chunk_id": "train_shard_00000_4428_0", "global_id": 4943 }, { "text": "The role of hepatobiliary transporters in drug-induced liver injury remains poorly understood. Various in vivo and in vitro biological approaches are currently used for studying hepatic transporters; however, appropriate localization and functional activity of these transporters are essential for normal biliary flow and drug transport. Human hepatocytes (HHs) are considered as the most suitable in vitro cell model but erratic availability and inter-donor functional variations limit their use. In this work, we aimed to compare localization of influx and efflux transporters and their functional activity in differentiated human HepaRG hepatocytes with fresh HHs in conventional (CCHH) and sandwich (SCHH) cultures. All tested influx and efflux transporters were correctly localized to canalicular [bile salt export pump (BSEP), multidrug resistance-associated protein 2 (MRP2), multidrug resistance protein 1 (MDR1), and MDR3] or basolateral [Na(+)-taurocholate co-transporting polypeptide (NTCP) and MRP3] membrane domains and were functional in all models. Contrary to other transporters, NTCP and BSEP were less abundant and active in HepaRG cells, cellular uptake of taurocholate was 2.2- and 1.4-fold and bile excretion index 2.8- and 2.6-fold lower, than in SCHHs and CCHHs, respectively. However, when taurocholate canalicular efflux was evaluated in standard and divalent cation-free conditions in buffers or cell lysates, the difference between the three models did not exceed 9.3%. Interestingly, cell imaging showed higher bile canaliculi contraction/relaxation activity in HepaRG hepatocytes and larger bile canaliculi networks in SCHHs. Altogether, our results bring new insights in mechanisms involved in bile acids accumulation and excretion in HHs and suggest that HepaRG cells represent a suitable model for studying hepatobiliary transporters and drug-induced cholestasis.", "token_count": 496, "char_count": 1895, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6437, "quality_score": 0.8218, "entities": { "genes": [ "MRP2", "MRP3", "MDR1", "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:57.348828", "source": { "split": "train_shard_00000", "doc_id": 4429 }, "chunk_id": "train_shard_00000_4429_0", "global_id": 4944 }, { "text": "Comparative Localization and Functional Activity of the Main Hepatobiliary Transporters in HepaRG Cells and Primary Human Hepatocytes.", "token_count": 35, "char_count": 134, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:57.712262", "source": { "split": "train_shard_00000", "doc_id": 4429 }, "chunk_id": "train_shard_00000_4429_1", "global_id": 4945 }, { "text": "Bile salt aggregates are promising candidates for drug delivery vehicles due to their unique fat-solubilizing ability. However, the toxicity of bile salts increases with improving fat-solubilizing capability and so an optimal combination of efficient solubilization and low toxicity is necessary. To improve hydrophilicity (and decrease toxicity), we substituted hydroxyl groups of several natural bile acid (BA) molecules for oxogroups and studied their intrinsic molecular association behavior. Here we present the comparative Langmuir trough study of the two-dimensional (2D) association behavior of eight natural BAs and four oxoderivatives (traditionally called keto-derivatives) floated on an aqueous subphase. The series of BAs and derivatives showed systematic changes in the shape of the compression isotherms. Two types of association could be distinguished: the first transition was assigned to the formation of dimers through H-bonding and the second to the hydrophobic aggregation of BA dimers. Hydrophobic association of BA molecules in the films is linked to the ability of forming H-bonded dimers. Both H-bond formation and hydrophobic association weakened with increasing number of hydroxyl groups, decreasing distance between hydroxyl groups, and increasing oxosubstitution. The results also show that the Langmuir trough method is extremely useful in selecting appropriate BA molecules to design drug delivery systems.\n\nThe effect of hydroxyl moieties and their oxosubstitution on bile acid association studied in floating monolayers.", "token_count": 348, "char_count": 1553, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:58.310146", "source": { "split": "train_shard_00000", "doc_id": 4430 }, "chunk_id": "train_shard_00000_4430_0", "global_id": 4946 }, { "text": "The cause of Cystic fibrosis liver disease (CFLD), is unknown. It is well recognized that hepatic exposure to hydrophobic bile salts is associated with the development of liver disease. For this reason, we hypothesize that, CFTR dependent variations, in the hepatic handling of hydrophobic bile salts, are related to the development CFLD. To test our hypothesis we studied, in Cftr-/- and control mice, bile production, bile composition and liver pathology, in normal feeding condition and during cholate exposure, either acute (intravenous) or chronic (three weeks via the diet). In Cftr-/- and control mice the basal bile production was comparable. Intravenous taurocholate increased bile production to the same extent in Cftr-/- and control mice. However, chronic cholate exposure increased the bile flow significantly less in Cftr-/- mice than in controls, together with significantly higher biliary bile salt concentration in Cftr-/- mice. Prolonged cholate exposure, however, did not induce CFLD like pathology in Cftr-/- mice. Chronic cholate exposure did induce a significant increase in liver mass in controls that was absent in Cftr-/- mice. Chronic cholate administration induces a cystic fibrosis-specific hepatobiliary phenotype, including changes in bile composition. These changes could not be associated with CFLD like pathological changes in CF mouse livers. However, chronic cholate administration induces liver growth in controls that is absent in Cftr-/- mice. Our findings point to an impaired adaptive homeotrophic liver response to prolonged hydrophobic bile salt exposure in CF conditions.\n\nCholic acid induces a Cftr dependent biliary secretion and liver growth response in mice.", "token_count": 427, "char_count": 1704, "word_count": 249, "semantic_coherence": 1, "information_density": 0.51, "quality_score": 0.755, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:58.944787", "source": { "split": "train_shard_00000", "doc_id": 4431 }, "chunk_id": "train_shard_00000_4431_0", "global_id": 4947 }, { "text": "Some known mechanisms proposed for the reduction of blood cholesterol by dietary fibre are: binding with bile salts in the duodenum and prevention of lipid absorption, which can be partially related with the bile salt binding. In order to gain new insights into the mechanisms of the binding of dietary fibre to bile salts, the goal of this work is to study the main interactions between cellulose derivatives and two types of bile salts. Commercial cellulose ethers: methyl (MC), hydroxypropyl (HPC) and hydroxypropylmethyl cellulose (HPMC), have been chosen as dietary fibre due to their highly functional properties important in manufactured food products. Two types of bile salts: sodium taurocholate (NaTC) and sodium taurodeoxycholate (NaTDC), have been chosen to understand the effect of the bile salt type. Interactions in the bulk have been investigated by means of differential scanning calorimetry (DSC) and linear mechanical spectroscopy. Results show that both bile salts have inhibitory effects on the thermal structuring of cellulose ethers and this depends on the number and type of substitution in the derivatised celluloses, and is not dependent upon molecular weight. Concerning the bile salt type, the more hydrophobic bile salt (NaTDC) has greater effect on these interactions, suggesting more efficient adsorption onto cellulose ethers. These findings may have implications in the digestion of cellulose-stabilised food matrices, providing a springboard to develop new healthy cellulose-based food products with improved functional properties.\n\nEffect of substituent pattern and molecular weight of cellulose ethers on interactions with different bile salts.", "token_count": 393, "char_count": 1680, "word_count": 247, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:43:59.586789", "source": { "split": "train_shard_00000", "doc_id": 4432 }, "chunk_id": "train_shard_00000_4432_0", "global_id": 4948 }, { "text": "Cholestasis, including primary biliary cirrhosis (PBC) and primary sclerosing cholangitis (PSC), results from an impairment or disruption of bile production and causes intracellular retention of toxic bile constituents, including bile salts. If left untreated, cholestasis leads to liver fibrosis and cirrhosis, which eventually results in liver failure and the need for liver transplantation. Currently, the only therapeutic option available for these patients is ursodeoxycholic acid (UDCA), which slows the progression of PBC, particularly in stage I and II of the disease. However, some patients have an incomplete response to UDCA therapy, whereas other, more advanced cases often remain unresponsive. For PSC, UDCA therapy does not improve survival, and recommendations for its use remain controversial. These considerations emphasize the need for alternative therapies. Hepatic transporters, located along basolateral (sinusoidal) and apical (canalicular) membranes of hepatocytes, are integral determinants of bile formation and secretion. Nuclear receptors (NRs) are critically involved in the regulation of these hepatic transporters and are natural targets for therapy of cholestatic liver diseases. One of these NRs is peroxisome proliferator-activated receptor alpha (PPARα), which plays a central role in maintaining cholesterol, lipid, and bile acid homeostasis by regulating genes responsible for bile acid synthesis and transport in humans, including cytochrome P450 (CYP) isoform 7A1 (CYP7A1), CYP27A1, CYP8B1, uridine 5'-diphospho-glucuronosyltransferase 1A1, 1A3, 1A4, 1A6, hydroxysteroid sulfotransferase enzyme 2A1, multidrug resistance protein 3, and apical sodium-dependent bile salt transporter. Expression of many of these genes is altered in cholestatic liver diseases, but few have been extensively studied or had the mechanism of PPARα effect identified", "token_count": 503, "char_count": 1882, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6941, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:00.273815", "source": { "split": "train_shard_00000", "doc_id": 4434 }, "chunk_id": "train_shard_00000_4434_0", "global_id": 4949 }, { "text": "In this review, we examine what is known about these mechanisms and consider the rationale for the use of PPARα ligand therapy, such as fenofibrate, in various cholestatic liver disorders.\n\nFibrates and cholestasis.", "token_count": 55, "char_count": 215, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:00.632634", "source": { "split": "train_shard_00000", "doc_id": 4434 }, "chunk_id": "train_shard_00000_4434_1", "global_id": 4950 }, { "text": "With the development of new drugs that directly affect CFTR protein function, clinical trials are being designed or initiated for a growing number of patients with cystic fibrosis. The currently available and accepted clinical endpoints, FEV1 and BMI, have limitations. The aim of this report is to draw attention to the need and the ample possibilities for the development and validation of relevant gastrointestinal clinical endpoints for scientific evaluation of CFTR modulation treatment, particularly in young children and infants. The gastrointestinal tract offers very good opportunities to measure CFTR protein function and systematically evaluate CF related clinical outcomes based on the principal clinical gastrointestinal manifestations of CF: intestinal pH, intestinal transit time, intestinal bile salt malabsorption, intestinal inflammation, exocrine pancreatic function and intestinal fat malabsorption. We present a descriptive analysis of a variety of gastrointestinal outcome measures for clinical relevance, reliability, validity, responsiveness to interventions, feasibility in particular in young children and the availability of reference values.\n\nCystic fibrosis and the role of gastrointestinal outcome measures in the new era of therapeutic CFTR modulation.", "token_count": 273, "char_count": 1283, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [ "FEV1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:01.188658", "source": { "split": "train_shard_00000", "doc_id": 4435 }, "chunk_id": "train_shard_00000_4435_0", "global_id": 4951 }, { "text": "Rhodococcus erythropolis is a worldwide-distributed actinobacterium that exhibits a remarkable metabolic versatility illustrated by its ability to degrade complex compounds, such as quorum-sensing signals N-acylhomoserine lactones (NAHLs), phenols, sterols and fuel derivatives. Because of its catabolic properties, R. erythropolis strains are proposed as anti-biofouling agents against NAHL-dependent biofilms, biocontrol agents against NAHL-emitting plant pathogens, and bioremediation agents in contaminated waters and soils. Here, we used the PacBio technology to resolve the complete genome sequence of the biocontrol strain R. erythropolis R138. Its genome consisted in a circular chromosome (6,236,862 bp), a linear plasmid pLRE138 (477,915 bp) and a circular plasmid pCRE138 (91,729 bp). In addition, draft genomes of five R. erythropolis strains were determined by Illumina technology and compared with the other five R. erythropolis genomes that are available in public databases: 5,825 common CDSs were present in all of the eleven analyzed genomes and represented up to 87 % of those identified in R. erythropolis R138. This study highlighted the high proportion of core-genome genes in R. erythropolis, but a high variability of the plasmid content. Key-metabolic pathways which are involved in the degradation of complex molecules, such as NAHLs and phenol, catechol and sterol derivatives are coded by the R. erythropolis core-genome.\n\nCore genome and plasmidome of the quorum-quenching bacterium Rhodococcus erythropolis.", "token_count": 455, "char_count": 1537, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:01.829402", "source": { "split": "train_shard_00000", "doc_id": 4436 }, "chunk_id": "train_shard_00000_4436_0", "global_id": 4952 }, { "text": "Sinorhizobium fredii HH103 is a fast-growing rhizobial strain infecting a broad range of legumes including both American and Asiatic soybeans. In this work, we present the sequencing and annotation of the HH103 genome (7.25 Mb), consisting of one chromosome and six plasmids and representing the structurally most complex sinorhizobial genome sequenced so far. Comparative genomic analyses of S. fredii HH103 with strains USDA257 and NGR234 showed that the core genome of these three strains contains 4,212 genes (61.7% of the HH103 genes). Synteny plot analysis revealed that the much larger chromosome of USDA257 (6.48 Mb) is colinear to the HH103 (4.3 Mb) and NGR324 chromosomes (3.9 Mb). An additional region of the USDA257 chromosome of about 2 Mb displays similarity to plasmid pSfHH103e. Remarkable differences exist between HH103 and NGR234 concerning nod genes, flavonoid effect on surface polysaccharide production, and quorum-sensing systems. Furthermore a number of protein secretion systems have been found. Two genes coding for putative type III-secreted effectors not previously described in S. fredii, nopI and gunA, have been located on the HH103 genome. These differences could be important to understand the different symbiotic behavior of S. fredii strains HH103, USDA257, and NGR234 with soybean.\n\nThe Sinorhizobium fredii HH103 Genome: A Comparative Analysis With S. fredii Strains Differing in Their Symbiotic Behavior With Soybean.", "token_count": 454, "char_count": 1455, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8171, "entities": { "genes": [ "NGR234", "NGR324", "HH103", "USDA257" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:02.473731", "source": { "split": "train_shard_00000", "doc_id": 4437 }, "chunk_id": "train_shard_00000_4437_0", "global_id": 4953 }, { "text": "Among diseases unique to pregnancy, intrahepatic cholestasis of pregnancy is the most prevalent disorder with elevated serum bile acid levels. We have previously shown that estrogen 17β-estradiol (E2) transrepresses bile salt export pump (BSEP) through an interaction between estrogen receptor (ER)-α and farnesoid X receptor (FXR) and transrepression of BSEP by E2/ERα is an etiological contributing factor to intrahepatic cholestasis of pregnancy. Currently the mechanistic insights into such transrepression are not fully understood. In this study, the dynamics of coregulator recruitment to BSEP promoter after FXR activation and E2 treatment were established with quantitative chromatin immunoprecipitation assays. Coactivator peroxisome proliferator-activated receptor-γ coactivator-1 was predominantly recruited to the BSEP promoter upon FXR activation, and its recruitment was decreased by E2 treatment. Meanwhile, recruitment of nuclear receptor corepressor was markedly increased upon E2 treatment. Functional evaluation of ERα and ERβ chimeras revealed that domains AC of ERα are the determinants for ERα-specific transrepression on BSEP. Further studies with various truncated ERα proteins identified the domains in ERα responsible for ligand-dependent and ligand-independent transrepression. Truncated ERα-AD exhibited potent ligand-independent transrepressive activity, whereas ERα-CF was fully capable of transrepressing BSEP ligand dependently in vitro in Huh 7 cells and in vivo in mice. Both ERα-AD and ERα-CF proteins were associated with FXR in the coimmunoprecipitation assays. In conclusion, E2 repressed BSEP expression through diminishing peroxisome proliferator-activated receptor-γ coactivator-1 recruitment with a concurrent increase in nuclear receptor corepressor recruitment to the BSEP promoter. Domains AD and CF in ERα mediated ligand-independent and ligand-dependent transrepression on BSEP, respectively, through interacting with FXR.", "token_count": 503, "char_count": 1969, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6016, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:03.123404", "source": { "split": "train_shard_00000", "doc_id": 4438 }, "chunk_id": "train_shard_00000_4438_0", "global_id": 4954 }, { "text": "Estrogen and Estrogen Receptor-α-Mediated Transrepression of Bile Salt Export Pump.", "token_count": 25, "char_count": 83, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:03.486009", "source": { "split": "train_shard_00000", "doc_id": 4438 }, "chunk_id": "train_shard_00000_4438_1", "global_id": 4955 }, { "text": "Sorghum-based traditional fermented food was screened for potential probiotic lactic acid bacteria. The isolates were identified by biochemical, physiological and genetic methods. Species identification was done by 16s rRNA sequence analysis. The functional probiotic potential of the two Lactobacillus species viz., Lactobacillus plantarum (Lact. plantarum) and Lactobacillus pentosus (Lact. pentosus) was assessed by different standard parameters. The strains were tolerant to pH 2 for 1 h and resistant to methicillin, kanamycin, vancomycin and norfloxacin. Two (Lact. plantarum COORG-3 and Lact. pentosus COORG-8) out of eight isolates recorded the cell surface hydrophobicity to be 59.12 and 64.06%, respectively. All the strains showed tolerance to artificial duodenum juice (pH 2) for 3 h, positive for bile salt hydrolase test and negative for haemolytic test. The neutralized cell-free supernatant of the strains Lact. pentosus COORG-4, Lact. plantarum COORG-1, Lact. plantarum COORG-7, Lact. pentosus COORG-8 and Lact. plantarum COORG-3 showed good antibiofilm activity. Lact. pentosus COORG-8 exhibited 74% activity against Pseudomonas aeruginosa-MTCC 7903 and Lact. plantarum COORG-7 showed 68% inhibition of biofilm against Klebsiella pneumonia MTCC 7407. Three (Lact. plantarum COORG-7, Lact. pentosus COORG-5 and Lact. pentosus COORG 8) out of eight isolates exhibited a good antimicrobial activity against Listeria monocytogenes and five isolates (Lact. pentosus COORG 2, Lact. plantarum COORG 1, Lact. plantarum COORG 4, Lact. pentosus COORG 3 and Lact", "token_count": 527, "char_count": 1569, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5688, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:44:04.118935", "source": { "split": "train_shard_00000", "doc_id": 4439 }, "chunk_id": "train_shard_00000_4439_0", "global_id": 4956 }, { "text": "plantarum COORG 6) are active against Escherichia coli, Bacillus subtilis, Pseudomonas aeruginosa, Enterobacter aerogenes, Klebsiella pneumonia, Enterococcus faecalis. The study also evaluated the cholesterol lowering property of the Lactobacillus strains using hen egg yolk as the cholesterol source. The cholesterol in hen egg yolk was assimilated by 74.12 and 68.26% by Lact. plantarum COORG 4 and Lact. pentosus COORG 7, respectively. The results of the present study suggest that the Lactobacillus strains isolated and characterized from sorghum-based fermented product may be used as probiotic strains for therapeutic applications.\n\nProbiotic potential of lactobacillus strains isolated from sorghum-based traditional fermented food.", "token_count": 224, "char_count": 739, "word_count": 99, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:04.599979", "source": { "split": "train_shard_00000", "doc_id": 4439 }, "chunk_id": "train_shard_00000_4439_1", "global_id": 4957 }, { "text": "The chromosome of Pseudomonas putida KT2440 carries two clusters of genes, denoted ars1 and ars2, that are annotated as putative arsenic resistance operons. In this work, we present evidence that both operons encode functional arsenic-response regulatory genes as well as arsenic extrusion systems that confer resistance to both arsenite [As(III)] and arsenate [As(V)]. Transcriptional fusions of P(ars1) and P(ars2) to lacZ revealed that expression of both operons was induced by arsenite and arsenate. We generated single mutants in ars1 and ars2, which showed lower resistance to arsenic than the wild-type strain. A double ars1/ars2 was found to be highly sensitive to arsenic. Minimum inhibitory concentrations (MICs) for single mutants decreased two- to fourfold with respect to the parental strain, while in the double mutant the MIC decreased 128-fold for arsenite and 32-fold for arsenate. Bioinformatic analysis revealed that the ars2 resistance operon is part of the core genome of P. putida, while the ars1 operon appears to only occur in the KT2440 strain, suggesting that ars1 was acquired by horizontal gene transfer. The presence of ars1 in KT2440 may explain why it exhibits higher resistance to arsenic than other P. putida strains, which bear only the ars2 operon.\n\nSynergic role of the two ars operons in arsenic tolerance in Pseudomonas putida KT2440.", "token_count": 395, "char_count": 1372, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [ "KT2440" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:05.211952", "source": { "split": "train_shard_00000", "doc_id": 4440 }, "chunk_id": "train_shard_00000_4440_0", "global_id": 4958 }, { "text": "In 1996 a common-source outbreak of severe soft tissue and bloodstream infections erupted among Israeli fish farmers and fish consumers due to changes in fish marketing policies. The causative pathogen was a new strain of Vibrio vulnificus, named biotype 3, which displayed a unique biochemical and genotypic profile. Initial observations suggested that the pathogen erupted as a result of genetic recombination between two distinct populations. We applied a whole genome shotgun sequencing approach using several V. vulnificus strains from Israel in order to study the pan genome of V. vulnificus and determine the phylogenetic relationship of biotype 3 with existing populations. The core genome of V. vulnificus based on 16 draft and complete genomes consisted of 3068 genes, representing between 59 and 78% of the whole genome of 16 strains. The accessory genome varied in size from 781 to 2044 kbp. Phylogenetic analysis based on whole, core, and accessory genomes displayed similar clustering patterns with two main clusters, clinical (C) and environmental (E), all biotype 3 strains formed a distinct group within the E cluster. Annotation of accessory genomic regions found in biotype 3 strains and absent from the core genome yielded 1732 genes, of which the vast majority encoded hypothetical proteins, phage-related proteins, and mobile element proteins. A total of 1916 proteins (including 713 hypothetical proteins) were present in all human pathogenic strains (both biotype 3 and non-biotype 3) and absent from the environmental strains. Clustering analysis of the non-hypothetical proteins revealed 148 protein clusters shared by all human pathogenic strains; these included transcriptional regulators, arylsulfatases, methyl-accepting chemotaxis proteins, acetyltransferases, GGDEF family proteins, transposases, type IV secretory system (T4SS) proteins, and integrases. Our study showed that V. vulnificus biotype 3 evolved from environmental populations and formed a genetically distinct group within the E-cluster", "token_count": 519, "char_count": 2032, "word_count": 294, "semantic_coherence": 1, "information_density": 0.5884, "quality_score": 0.7942, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:44:05.878111", "source": { "split": "train_shard_00000", "doc_id": 4441 }, "chunk_id": "train_shard_00000_4441_0", "global_id": 4959 }, { "text": "The unique epidemiological circumstances facilitated disease outbreak and brought this genotype to the attention of the scientific community.\n\nComparative genomic analysis of clinical and environmental Vibrio vulnificus isolates revealed biotype 3 evolutionary relationships.", "token_count": 52, "char_count": 275, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8788, "quality_score": 0.9394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:06.242051", "source": { "split": "train_shard_00000", "doc_id": 4441 }, "chunk_id": "train_shard_00000_4441_1", "global_id": 4960 }, { "text": "This work characterizes a set of lactobacilli strains isolated from the stomach of healthy humans that might serve as probiotic cultures. Ten different strains were recognized by rep-PCR and PFGE fingerprinting among 19 isolates from gastric biopsies and stomach juice samples. These strains belonged to five species, Lactobacillus gasseri (3), Lactobacillus reuteri (2), Lactobacillus vaginalis (2), Lactobacillus fermentum (2) and Lactobacillus casei (1). All ten strains were subjected to a series of in vitro tests to assess their functional and technological properties, including acid resistance, bile tolerance, adhesion to epithelial gastric cells, production of antimicrobial compounds, inhibition of Helicobacter pylori, antioxidative activity, antibiotic resistance, carbohydrate fermentation, glycosidic activities, and ability to grow in milk. As expected, given their origin, all strains showed good resistance to low pH (3.0), with small reductions in counts after 90 min exposition to this pH. Species- and strain-specific differences were detected in terms of the production of antimicrobials, antagonistic effects toward H. pylori, antioxidative activity and adhesion to gastric epithelial cells. None of the strains showed atypical resistance to a series of 16 antibiotics of clinical and veterinary importance. Two L. reuteri strains were deemed as the most appropriate candidates to be used as potential probiotics against microbial gastric disorders; these showed good survival under gastrointestinal conditions reproduced in vitro, along with strong anti-Helicobacter and antioxidative activities. The two L. reuteri strains further displayed appropriated technological traits for their inclusion as adjunct functional cultures in fermented dairy products.\n\nProbiotic and technological properties of Lactobacillus spp. strains from the human stomach in the search for potential candidates against gastric microbial dysbiosis.", "token_count": 494, "char_count": 1948, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6113, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:06.897004", "source": { "split": "train_shard_00000", "doc_id": 4442 }, "chunk_id": "train_shard_00000_4442_0", "global_id": 4961 }, { "text": "There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome.\n\nStreptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression.", "token_count": 275, "char_count": 1182, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6084, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:07.452598", "source": { "split": "train_shard_00000", "doc_id": 4443 }, "chunk_id": "train_shard_00000_4443_0", "global_id": 4962 }, { "text": "Gallstone disease, including cholesterol precipitation in bile, increased bile salt hydrophobicity and gallbladder inflammation. Here, we investigated miRNA and mRNA involved in the formation of gallstones, and explored the molecular mechanisms in the development of gallstones. Differentially expressed 17 miRNAs and 525 mRNA were identified based on Illumina sequencing from gallbladder mucosa of patients with or without gallstones, and were validated by randomly selected 6 miRNAs and 8 genes using quantitative RT-PCR. 114 miRNA target genes were identified, whose functions and regulating pathways were related to gallstones. The differentially expressed genes were enriched upon lipoprotein binding and some metabolic pathways, and differentially expressed miRNAs enriched upon ABC transportation and cancer related pathways. A molecular regulatory network consisting of 17 differentially expressed miRNAs, inclusive of their target genes, was constructed. miR-210 and its potential target gene ATP11A were found to be differentially expressed in both miRNA and mRNA profiles. ATP11A was a direct target of miR-210, which was predicted to regulate the ABC-transporters pathway. The expression levels of ATP11A in the gallstone showed inverse correlation with miR-210 expression, and up-regulation of miR-210 could reduce ATP11A expression in HGBEC. This is the first report that indicates the existence of differences in miRNA and mRNA expression in patients with or without gallstones. Our data shed light on further investigating the mechanisms of gallstone formation.\n\nAn integrated analysis of differential miRNA and mRNA expressions in human gallstones.", "token_count": 411, "char_count": 1665, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5708, "quality_score": 0.7854, "entities": { "genes": [ "ATP11A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:08.075583", "source": { "split": "train_shard_00000", "doc_id": 4444 }, "chunk_id": "train_shard_00000_4444_0", "global_id": 4963 }, { "text": "Fatty acid binding proteins (FABPs) act as intracellular carriers of lipid molecules, and play a role in global metabolism regulation. Liver FABP (L-FABP) is prominent among FABPs for its wide ligand repertoire, which includes long-chain fatty acids as well as bile acids (BAs). In this work, we performed a detailed molecular- and atomic-level analysis of the interactions established by human L-FABP with nine BAs to understand the binding specificity for this important class of cholesterol-derived metabolites. Protein-ligand complex formation was monitored using heteronuclear NMR, steady-state fluorescence spectroscopy, and mass spectrometry. BAs were found to interact with L-FABP with dissociation constants in the narrow range of 0.6-7 μm; however, the diverse substitution patterns of the sterol nucleus and the presence of side-chain conjugation resulted in complexes endowed with various degrees of conformational heterogeneity. Trihydroxylated BAs formed monomeric complexes in which single ligand molecules occupied similar internal binding sites, based on chemical-shift perturbation data. Analysis of NMR line shapes upon progressive addition of taurocholate indicated that the binding mechanism departed from a simple binary association equilibrium, and instead involved intermediates along the binding path. The co-linear chemical shift behavior observed for L-FABP complexes with cholate derivatives added insight into conformational dynamics in the presence of ligands. The observed spectroscopic features of L-FABP/BA complexes, discussed in relation to ligand chemistry, suggest possible molecular determinants of recognition, with implications regarding intracellular BA transport. Our findings suggest that human L-FABP is a poorly selective, universal BA binder.\n\nBile salt recognition by human liver fatty acid binding protein.", "token_count": 432, "char_count": 1854, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6865, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:08.704200", "source": { "split": "train_shard_00000", "doc_id": 4445 }, "chunk_id": "train_shard_00000_4445_0", "global_id": 4964 }, { "text": "Genomic information about Clostridium tetani, the causative agent of the tetanus disease, is scarce. The genome of strain E88, a strain used in vaccine production, was sequenced about 10 years ago. One additional genome (strain 12124569) has recently been released. Here we report three new genomes of C. tetani and describe major differences among all five C. tetani genomes. They all harbor tetanus-toxin-encoding plasmids that contain highly conserved genes for TeNT (tetanus toxin), TetR (transcriptional regulator of TeNT) and ColT (collagenase), but substantially differ in other plasmid regions. The chromosomes share a large core genome that contains about 85% of all genes of a given chromosome. The non-core chromosome comprises mainly prophage-like genomic regions and genes encoding environmental interaction and defense functions (e.g. surface proteins, restriction-modification systems, toxin-antitoxin systems, CRISPR/Cas systems) and other fitness functions (e.g. transport systems, metabolic activities). This new genome information will help to assess the level of genome plasticity of the species C. tetani and provide the basis for detailed comparative studies.\n\nGenomics of Clostridium tetani.", "token_count": 322, "char_count": 1214, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7118, "quality_score": 0.8559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:09.269965", "source": { "split": "train_shard_00000", "doc_id": 4446 }, "chunk_id": "train_shard_00000_4446_0", "global_id": 4965 }, { "text": "Bile acids, which are synthesized from cholesterol in the hepatocytes of the liver, are amphipathic molecules with a steroid backbone. Studies have shown that bile acid exhibits important effects on liver regeneration. However, the mechanism underlying these effects remains unclear. The aim of the present study was to investigate the effect of bile acid and the farnesoid X receptor (FXR) on hepatic regeneration and lipid metabolism. Rats were fed with 0.2% bile acid or glucose for 7 days and then subjected to a 50 or 70% hepatectomy. Hepatic regeneration rate, serum and liver levels of bile acid, and expression of FXR and Caveolin‑1, were detected at 24, 48 or 72 h following hepatectomy. The expression of proliferating cell nuclear antigen (PCNA) in the liver was measured using immunohistochemistry at the end of the study. Hepatocytes isolated from rats were treated with bile acid, glucose, FXR agonist and FXR antagonist, separately or in combination. Lipid metabolism, the expression of members of the FXR signaling pathway and energy metabolism‑related factors were measured using ELISA kits or western blotting. Bile acid significantly increased the hepatic regeneration rate and the expression of FXR, Caveolin‑1 and PCNA. Levels of total cholesterol and high density lipoprotein were increased in bile acid‑ or FXR agonist‑treated hepatocytes in vitro. Levels of triglyceride, low density lipoprotein and free fatty acid were decreased. In addition, bile acid and FXR agonists increased the expression of bile salt export pump and small heterodimer partner, and downregulated the expression of apical sodium‑dependent bile acid transporter, Na+/taurocholate cotransporting polypeptide and cholesterol 7α‑hydroxylase. These results suggested that physiological concentrations of bile acid may promote liver regeneration via FXR signaling pathways, and may be associated with energy metabolism.", "token_count": 521, "char_count": 1911, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5355, "quality_score": 0.7677, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:44:09.924936", "source": { "split": "train_shard_00000", "doc_id": 4447 }, "chunk_id": "train_shard_00000_4447_0", "global_id": 4966 }, { "text": "Bile acid promotes liver regeneration via farnesoid X receptor signaling pathways in rats.", "token_count": 25, "char_count": 90, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:10.299176", "source": { "split": "train_shard_00000", "doc_id": 4447 }, "chunk_id": "train_shard_00000_4447_1", "global_id": 4967 }, { "text": "We report the evaluation of probiotic properties of potent lactic acid bacteria (LAB) from the gut of freshwater fishes, Labeo rohita and Catla catla, for eventually developing probiotic strains for the prevention of bacterial infections in aquaculture and food preservation. Five different LAB strains were isolated and characterized for their probiotic properties. Based on physiological, morphological and biochemical characteristics, three isolates from Labeo rohita and two from Catla catla were identified as putative probiotics and were denoted as LR11, LR14 and LR16 and CC3 and CC4, respectively. Isolates CC3 and CC4 were acid (pH 2.5) and bile salt (0.3% oxygall) tolerant and exhibited strong antibacterial activities against all pathogens including Aeromonas hydrophila. In addition, all LAB isolates were susceptible to tested antibiotics, except CC3 and CC4 which were vancomycin resistant. Furthermore, the isolates CC3 and CC4 showed significantly higher in vitro cell surface properties, i.e., hydrophobicity, auto- and co-aggregation. Biochemical tests, PCR detection and 16S rRNA sequence analysis established that LR11, LR14, LR16, CC3 and CC4 are Enterococcus avium TSU11, Enterococcus pseudoavium TSU14, Enterococcus raffinosus TSU16, Lactobacillus gasseri TSU3 and Lactobacillus animalis TSU4, respectively. Studies revealed that, Lactobacillus gasseri TSU3 and Lactobacillus animalis TSU4 are ideal probiotic candidates for its use in aquaculture and require further exploratory in vivo evaluation and safety studies.\n\nIn Vitro Evaluation of Probiotic Properties of Lactic Acid Bacteria from the Gut of Labeo rohita and Catla catla.", "token_count": 471, "char_count": 1657, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5948, "quality_score": 0.7974, "entities": { "genes": [ "LR11", "TSU16", "TSU4", "LR16", "LR14", "TSU14", "TSU3", "CC3", "CC4", "TSU11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:10.954157", "source": { "split": "train_shard_00000", "doc_id": 4448 }, "chunk_id": "train_shard_00000_4448_0", "global_id": 4968 }, { "text": "Cftr(-/-tm1Unc) mice develop progressive hepato-biliary pathology. We hypothesize that this liver pathology is related to alterations in biliary bile hydrophobicity and bile salt metabolism in Cftr(-/-tm1Unc) mice.\n\nAltered intestinal bile salt biotransformation in a cystic fibrosis (Cftr-/-) mouse model with hepato-biliary pathology.", "token_count": 111, "char_count": 336, "word_count": 42, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:11.355798", "source": { "split": "train_shard_00000", "doc_id": 4449 }, "chunk_id": "train_shard_00000_4449_0", "global_id": 4969 }, { "text": "Bifidobacteria are generally acknowledged as major gut microflora used as probiotics, which promote human health. In this study, the effects of the administration of Bifidobacterim bifidum on modulating gastrointestinal (GI) tract microflora, acid and bile resistance, and physiological indices in BALB/c mice were investigated. Results showed that B. bifidum can significantly improve the ecosystem of the GI tract by increasing the amount of probiotics and reducing the populations of pathogenic bacteria, as measured by plate count and real-time PCR. After exposure to simulated GI tract conditions, the growth of gut microflora in the B. bifidum group was higher than that in the control group when incubated for 12 h in MRS or nutrient broth adjusted to pH 2.0 or 3.0 or in the presence of a concentration of bile salt (0.45% m/v). The blood biochemical index was examined, and the physiological effect of the cell-free extract of gut microflora was evaluated by measuring the activity of various enzymes, including α-glucosidases, esterase, and lactate dehydrogenase. This study suggested that a B. bifidum strain can stabilize blood sugar, lower cholesterol levels in serum, and improve metabolic activity. Moreover, B. bifidum was a promising enhancer of microbial diversity in mouse intestine and played a vital role in human physiological processes, which can benefit the health of a host.\n\nOral administration of Bifidobacterim bifidum for modulating microflora, acid and bile resistance, and physiological indices in mice.", "token_count": 398, "char_count": 1534, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5819, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:12.019419", "source": { "split": "train_shard_00000", "doc_id": 4450 }, "chunk_id": "train_shard_00000_4450_0", "global_id": 4970 }, { "text": "Acid tolerance and bile tolerance are important probiotic characteristics. Whey proteins contain branched-chain amino acids, which play a role in muscle building and are popular among athletes. Increasing emphasis is being placed on diets containing less carbohydrate, less fat, and more protein. The effect of incremental additions of whey protein isolate (WPI) on probiotic characteristics of pure cultures is not known. The objective of this study was to determine the influence of added WPI on acid tolerance and bile tolerance of pure cultures of Streptococcus thermophilus ST-M5 and Lactobacillus bulgaricus LB-12. The WPI was used at 0 (control), 1, 2 and 3% (wt/vol). Assessment of acid tolerance was conducted on pure cultures at 30-min intervals for 2h of acid exposure and bile tolerance at 1-h intervals for 5h of bile exposure. Use of 1, 2, and 3% WPI improved acid tolerance of Strep. thermophilus ST-M5 and Lb. bulgaricus LB-12. The highest counts for acid tolerance of Strep. thermophilus ST-M5 and Lb. bulgaricus LB-12 were obtained when 3% WPI was used. Use of 2 and 3% WPI improved bile tolerance of Strep. thermophilus ST-M5 and Lb. bulgaricus LB-12 over 5h of bile exposure. The use of WPI is recommended to improve acid and bile tolerance of the yogurt culture bacteria Strep. thermophilus ST-M5 and Lb. bulgaricus LB-12.\n\nWhey protein isolate improves acid and bile tolerances of Streptococcus thermophilus ST-M5 and Lactobacillus delbrueckii ssp. bulgaricus LB-12.", "token_count": 445, "char_count": 1488, "word_count": 234, "semantic_coherence": 1, "information_density": 0.4487, "quality_score": 0.7244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:13.056299", "source": { "split": "train_shard_00000", "doc_id": 4451 }, "chunk_id": "train_shard_00000_4451_0", "global_id": 4971 }, { "text": "Investigation on the use of herbal-based biopolymers for probiotic-Lactobacillus plantarum 15HN-encapsulation is presented. The objectives are to enhance its oral delivery, colonic release and survival rate of these probiotic cultures in gastrointestinal environment.\n\nMicroencapsulation of probiotic bacteria Lactobacillus plantarum 15HN using alginate-psyllium-fenugreek polymeric blends.", "token_count": 112, "char_count": 390, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8864, "quality_score": 0.9432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:13.449444", "source": { "split": "train_shard_00000", "doc_id": 4452 }, "chunk_id": "train_shard_00000_4452_0", "global_id": 4972 }, { "text": "Bioflavours are called natural flavour and/or fragrance compounds which are produced using metabolic pathway of the microorganism and/or plant cells or their enzyme systems with bioengineering approaches. The aim of this study was to investigate bioflavour production from tomato and red pepper pomaces by Kluyveromyces marxianus and Debaryomyces hansenii. Obtained specific growth rates of K. marxianus and D. hansenii in tomato pomace were 0.081/h and 0.177/h, respectively. The bioflavour profile differed between the yeasts. Both yeasts can produce esters and alcohols such as phenyl ethyl alcohol, isoamyl alcohol, isoamyl acetate, phenyl ethyl acetate and isovaleric acid. \"Tarhana\" and \"rose\" were descriptive flavour terms for tomato and pepper pomaces fermented by K. marxianus, respectively. Tomato pomace fermented by D. hansenii had the most intense \"green bean\" flavour while \"fermented vegetable\" and \"storage/yeast\" were defined as characteristic flavour terms for pepper pomaces fermented by D. hansenii.\n\nBioflavour production from tomato and pepper pomaces by Kluyveromyces marxianus and Debaryomyces hansenii.", "token_count": 322, "char_count": 1128, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6051, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:14.016211", "source": { "split": "train_shard_00000", "doc_id": 4453 }, "chunk_id": "train_shard_00000_4453_0", "global_id": 4973 }, { "text": "The size and composition of the circulating bile acid (BA) pool are important factors in regulating the human gut microbiota. Disrupted regulation of BA metabolism is implicated in several chronic diseases. Bile salt hydrolase (BSH)-active Lactobacillus reuteri NCIMB 30242, previously shown to decrease LDL-cholesterol and increase circulating BA, was investigated for its dose response effect on BA profile in a pilot clinical study. Ten otherwise healthy hypercholesterolemic adults, recruited from a clinical trial site in London, ON, were randomized to consume delayed release or standard release capsules containing L. reuteri NCIMB 30242 in escalating dose over 4 weeks. In another aspect, 4 healthy normocholesterolemic subjects with LDL-C below 3.4 mmol/l received delayed release L. reuteri NCIMB 30242 at a constant dose over 4 weeks. The primary outcome measure was the change in plasma BA profile over the intervention period. Additional outcomes included circulating fibroblast growth factor (FGF)-19, plant sterols and LDL-cholesterol as well as fecal microbiota and bsh gene presence. After one week of intervention subjects receiving delayed release L. reuteri NCIMB 30242 increased total BA by 1.13 ± 0.67 μmol/l (P = 0.02), conjugated BA by 0.67 ± 0.39 μmol/l (P = 0.02) and unconjugated BA by 0.46 ± 0.43 μmol/l (P = 0.07), which represented a greater than 2-fold change relative to baseline. Increases in BA were largely maintained post-week 1 and were generally correlated with FGF-19 and inversely correlated with plant sterols. This is the first clinical support showing that a BSH-active probiotic can significantly and rapidly influence BA metabolism and may prove useful in chronic diseases beyond hypercholesterolemia.", "token_count": 487, "char_count": 1746, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6489, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:14.662921", "source": { "split": "train_shard_00000", "doc_id": 4454 }, "chunk_id": "train_shard_00000_4454_0", "global_id": 4974 }, { "text": "Changes in bile acids, FGF-19 and sterol absorption in response to bile salt hydrolase active L. reuteri NCIMB 30242.", "token_count": 41, "char_count": 117, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:15.016871", "source": { "split": "train_shard_00000", "doc_id": 4454 }, "chunk_id": "train_shard_00000_4454_1", "global_id": 4975 }, { "text": "Pluronic/bile salt/phospholipid mixed micelles (Pluronic/BS/PS-MM) drug carrier system for solubilization hydrophobic drugs was developed. A typical hydrophobic compound, pyrene, was selected as a representative hydrophobic compound to model the hydrophobic drugs. Five Pluronics, F68, F88, F98, F108, and F127 with different PPO chain length were studied. CMC data and solubilization capacities were obtained from a pyrene solubilization method. A closed association model was used to obtain the thermodynamic parameters: Gibbs free energy (ΔG°), enthalpy, (ΔH°) and entropy (ΔS°) of micellization. The results obtained from these experiments suggest that the mixed micelles was more stable and solubilize more pyrene than single one; and the solubilization of pyrene was strong effected by the PPO block size, thus accentuating synergistic interaction mechanism in Pluronic/BS/PS-MM. The study generated an important dataset so as to compare the effect of different Pluronics on solubility capacity of Pluronic/BS/PS-MM.\n\nPreparation of Pluronic/Bile salt/Phospholipid Mixed Micelles as Drug Solubility Enhancer and Study the Effect of the PPO Block Size on the Solubility of Pyrene.", "token_count": 332, "char_count": 1185, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6242, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:15.591513", "source": { "split": "train_shard_00000", "doc_id": 4455 }, "chunk_id": "train_shard_00000_4455_0", "global_id": 4976 }, { "text": "Palmatine (PAL) is one of the main alkaloids in Coptis chinensis. The present aim was to investigate the hypolipidemic effect and mechanism of palmatine in hamsters fed with high-fat diet (HFD). PAL treatment decreased serum total cholesterol (TC), triglyceride (TG), and low-density lipoprotein cholesterol (LDL-C) levels, as well as increased fecal excretion of TC and total bile acids (TBA) in hyperlipidemic hamsters. Furthermore, PAL treatment up-regulated low-density lipoprotein receptor (LDLR) and cholesterol 7α-hydroxylase (CYP7A1) mRNA and protein expression and down-regulated apical sodium-dependent bile salt transporter (ASBT) mRNA and protein expression. These results demonstrated that PAL as a potential natural cholesterol lowering agent works by up-regulating LDLR and CYP7A1 mRNA and protein expression, down-regulating ASBT mRNA and protein expression, as well as enhancing fecal excretion of TC and TBA. The findings in our study suggest that palmatine could be a potential natural agent for treating hyperlipidemia.\n\nHypolipidemic Effect and Mechanism of Palmatine from Coptis chinensis in Hamsters Fed High-Fat diet.", "token_count": 332, "char_count": 1141, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:16.158996", "source": { "split": "train_shard_00000", "doc_id": 4456 }, "chunk_id": "train_shard_00000_4456_0", "global_id": 4977 }, { "text": "Tauroursodeoxycholic acid (TUDCA) a bile salt and chemical chaperone reduces stress-induced aggregation of proteins; activates PERK [PKR (RNA-dependent protein kinase)-like ER (endoplasmic reticulum) kinase] or EIF2AK3, one of the hall marks of ER stress induced unfolded protein response (UPR) in human hepatoblastoma HepG2 cells; prevents heat and dithiothreitol (DTT) induced aggregation of BSA (bovine serum albumin), and reduces ANS (1-anilino-naphthalene-8-sulfonate) bound BSA fluorescence in vitro. TUDCA inactivates heat treated, but not the native EcoR1 enzyme, and reduces heat-induced aggregation and activity of COX-1 (cyclooxygenase enzyme-1) in vitro. These findings suggest that TUDCA binds to the hydrophobic regions of proteins and prevents their subsequent aggregation. This may stabilize unfolded proteins that can mount UPR or facilitate their degradation through cellular degradation pathways.\n\nTauroursodeoxycholic acid prevents stress induced aggregation of proteins in vitro and promotes PERK activation in HepG2 cells.", "token_count": 304, "char_count": 1044, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6739, "quality_score": 0.837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:16.727534", "source": { "split": "train_shard_00000", "doc_id": 4457 }, "chunk_id": "train_shard_00000_4457_0", "global_id": 4978 }, { "text": "Orientia tsutsugamushi is the causative agent of scrub typhus, a major cause of febrile illness in rural area of Asia-Pacific region. A multi-locus sequence typing (MLST) analysis was performed on strains isolated from human patients from 3 countries in Southeast Asia: Cambodia, Vietnam and Thailand. The phylogeny of the 56-kDa protein encoding gene was analyzed on the same strains and showed a structured topology with genetically distinct clusters. MLST analysis did not lead to the same conclusion. DNA polymorphism and phylogeny of individual gene loci indicated a significant level of recombination and genetic diversity whereas the ST distribution indicated the presence of isolated patches. No correlation was found with the geographic origin. This work suggests that weak divergence in core genome and ancestral haplotypes are maintained by permanent recombination in mites while the 56-kDa protein gene is diverging in higher speed due to selection by the mammalian immune system.\n\nOrientia tsutsugamushi, agent of scrub typhus, displays a single metapopulation with maintenance of ancestral haplotypes throughout continental South East Asia.", "token_count": 267, "char_count": 1154, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:17.274298", "source": { "split": "train_shard_00000", "doc_id": 4458 }, "chunk_id": "train_shard_00000_4458_0", "global_id": 4979 }, { "text": "Biological samples collected from the crime scenes often contain some compounds that can inhibit the polymerase chain reaction (PCR). The removal of PCR inhibitors from the extracts prior to the PCR amplification is vital for successful forensic DNA typing. This paper aimed to evaluate the ability of four different methods (PowerClean® DNA Clean-Up kit, DNA IQ™ System, Phenol-Chloroform extraction and Chelex®-100 methods) to remove eight commonly encountered PCR inhibitors including: melanin, humic acid, collagen, bile salt, hematin, calcium ions, indigo and urea. Each of these PCR inhibitors was effectively removed by the PowerClean® DNA Clean-Up kit and DNA IQ™ System as demonstrated by generating more complete short tandem repeat (STR) profiles from the cleaned up inhibitor samples than from the raw inhibitor samples. The Phenol-Chloroform extraction and Chelex®-100 methods, however, could only remove some of eight PCR inhibitors. Our results demonstrated that the PowerClean® DNA Clean-Up kit and DNA IQ™ System were very effective for the removal of known PCR inhibitors that are routinely found in DNA extracts from forensic samples.\n\nA comparison of four methods for PCR inhibitor removal.", "token_count": 292, "char_count": 1210, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:17.831800", "source": { "split": "train_shard_00000", "doc_id": 4459 }, "chunk_id": "train_shard_00000_4459_0", "global_id": 4980 }, { "text": "Human bile salt export pump (BSEP) mutations underlie progressive familial intrahepatic cholestasis type 2 (PFIC2). In the PFIC2 animal model, Bsep(-/-) mice, biliary secretion of bile salts (BS) is decreased, but that of phospholipids (PL) and cholesterol (CH) is increased. Under physiological conditions, the biliary secretion of PL and CH is positively related (\"coupled\") to that of BS. We aimed to elucidate the mechanism of increased biliary lipid secretion in Bsep(-/-) mice. The secretion of the BS tauro-β-muricholic acid (TβMCA) is relatively preserved in Bsep(-/-) mice. We infused Bsep(-/-) and Bsep(+/+) (control) mice with TβMCA in stepwise increasing dosages (150-600 nmol/min) and determined biliary bile flow, BS, PL, and CH secretion. mRNA and protein expression of relevant canalicular transporters was analyzed in livers from noninfused Bsep(-/-) and control mice. TβMCA infusion increased BS secretion in both Bsep(-/-) and control mice. The secreted PL or CH amount per BS, i.e., the \"coupling,\" was continuously two- to threefold higher in Bsep(-/-) mice (P < 0.05). Hepatic mRNA expression of canalicular lipid transporters Mdr2, Abcg5, and Abcg8 was 45-55% higher in Bsep(-/-) mice (Abcg5; P < 0.05), as was canalicular Mdr2 and Abcg5 protein expression. Potential other explanations for the increased coupling of the biliary secretion of PL and CH to that of BS in Bsep(-/-) mice could be excluded. We conclude that the mechanism of increased biliary lipid secretion in Bsep(-/-) mice is based on increased expression of the responsible canalicular transporter proteins.\n\nThe mechanism of increased biliary lipid secretion in mice with genetic inactivation of bile salt export pump.", "token_count": 509, "char_count": 1709, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5116, "quality_score": 0.7558, "entities": { "genes": [ "PFIC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:18.486030", "source": { "split": "train_shard_00000", "doc_id": 4460 }, "chunk_id": "train_shard_00000_4460_0", "global_id": 4981 }, { "text": "The gut microbiota plays a crucial role in regulating many physiological systems of the host, including the metabolic and immune system. Disturbances in microbiota composition are increasingly correlated with disease; however, the underlying mechanisms are not well understood. Recent evidence suggests that changes in microbiota composition directly affect the metabolism of bile salts. Next to their role in digestion of dietary fats, bile salts function as signaling molecules for bile salt receptors such as Farnesoid X receptor (FXR) and G protein-coupled bile acid receptor (TGR5). Complementary to their role in metabolism, FXR and TGR5 are shown to play a role in intestinal homeostasis and immune regulation. This review presents an overview of evidence showing that changes in bile salt pool and composition due to changes in gut microbial composition contribute to the pathogenesis of inflammatory bowel disease and metabolic disease, possibly through altered activation of TGR5 and FXR. We further discuss how dietary interventions, such as pro- and synbiotics, may be used to treat metabolic disease and inflammatory bowel disease (IBD) through normalization of bile acid dysregulation directly or indirectly through normalization of the intestinal microbiota.\n\nThe Gut Microbiota as a Therapeutic Target in IBD and Metabolic Disease: A Role for the Bile Acid Receptors FXR and TGR5.", "token_count": 336, "char_count": 1396, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [ "TGR5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:19.055706", "source": { "split": "train_shard_00000", "doc_id": 4461 }, "chunk_id": "train_shard_00000_4461_0", "global_id": 4982 }, { "text": "Micelle formation of cholesterol with lecithin and bile salts is a key process for intestinal absorption of lipids. Some dietary fibers commonly used to reduce the lipid content in the body are thought to inhibit lipid absorption by binding to bile salts and decreasing the lipid solubility. Amongst these, α-cyclodextrin (α-CD) is reportedly one of the most powerful dietary fibers for decreasing blood cholesterol. However, it is difficult to believe that α-CD directly removes cholesterol because it has a very low affinity for cholesterol and its mechanism of action is less well understood than those of other dietary fibers. To identify this mechanism, we investigated the interaction of α-CD with lecithin and bile salts, which are essential components for the dissolution of cholesterol in the small intestine, and the effect of α-CD on micellar solubility of cholesterol.\n\nA study on the inhibitory mechanism for cholesterol absorption by α-cyclodextrin administration.", "token_count": 252, "char_count": 978, "word_count": 149, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:19.545106", "source": { "split": "train_shard_00000", "doc_id": 4462 }, "chunk_id": "train_shard_00000_4462_0", "global_id": 4983 }, { "text": "The present study demonstrates a detailed characterization of the interaction of a series of bile salts, sodium deoxycholate (NaDC), sodium cholate (NaC), and sodium taurocholate (NaTC), with a model transport protein, human serum albumin (HSA). Here, steady-state and time-resolved fluorescence spectroscopic techniques have been used to characterize the interaction of the bile salts with HSA. The binding isotherms constructed from steady-state fluorescence intensity measurements demonstrate that the interaction of the bile salts with HSA can be characterized by three distinct regions, which were also successfully reproduced from the significant variation of the emission wavelength (λ(em)) of the intrinsic tryptophan (Trp) moiety of HSA. The time-resolved fluorescence decay behavior of the Trp residue of HSA was also found to corroborate the steady-state results. The effect of interaction with the bile salts on the native conformation of the protein has been explored in a circular dichroism (CD) study, which reveals a decrease in α-helicity of HSA induced by the bile salts. In accordance with this, the esterase activity of the protein-bile salt aggregates is found to be reduced in comparison to that of the native protein. Our results exclusively highlight the fact that it is the hydrophobic character of the bile salt that governs the extent of interaction with the protein. Isothermal titration calorimetry (ITC) and molecular docking studies further substantiate our other experimental findings.\n\nHydrophobicity is the governing factor in the interaction of human serum albumin with bile salts.", "token_count": 381, "char_count": 1616, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5546, "quality_score": 0.7773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:20.123407", "source": { "split": "train_shard_00000", "doc_id": 4463 }, "chunk_id": "train_shard_00000_4463_0", "global_id": 4984 }, { "text": "Current work was conducted to evaluate the cholesterol-lowering effect of coptisine extracted from Rhizoma coptidis in Syrian golden hamsters. The safety results indicated that coptisine was a safe and low-toxic compound. Coptisine showed a beneficial effect in the abnormal serum lipid levels induced by a high-fat and high-cholesterol diet (HFHC): at a concentration of 70.05 mg/kg, coptisine significantly led to a decrease in total cholesterol, triglycerides, and low-density lipoprotein cholesterol (LDL-c) levels by 26.70, 15.38, and 22.22 %, respectively, and high-density lipoprotein cholesterol (HDL-c) was increased by 41.74 % in serum of hamsters (p < 0.01). In addition, total bile acid (TBA) levels in feces of hamsters were elevated after coptisine administration. Further investigation has suggested that the mRNA and protein expression of 3-hydroxy-3-methyl-glutaryl-CoA reductase (HMGCR) in the liver of hamsters was down-regulated by high-dosage coptisine treatment (p < 0.05); mRNA and protein expression of low-density lipoprotein receptor (LDLR) and cholesterol 7α-hydroxylase (CYP7A1) were dramatically up-regulated by coptisine administration. The apical sodium-dependent bile salt transporter expression was down-regulated in the coptisine-treated animals, but showed no significant differences from the HFHC groups. Taken together, our results demonstrate that a high dosage of coptisine could inhibit cholesterol synthesis via suppressing the HMGCR expression and promoting the use and excretion of cholesterol via up-regulating LDLR and CYP7A1 expression. These findings suggest a critical role for coptisine in anti- hypercholesterolemia, and thus it needs to be considered as a potential natural cholesterol lowering agent.", "token_count": 505, "char_count": 1752, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6125, "quality_score": 0.8063, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:20.774311", "source": { "split": "train_shard_00000", "doc_id": 4464 }, "chunk_id": "train_shard_00000_4464_0", "global_id": 4985 }, { "text": "The safety and anti-hypercholesterolemic effect of coptisine in Syrian golden hamsters.", "token_count": 23, "char_count": 87, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:21.128948", "source": { "split": "train_shard_00000", "doc_id": 4464 }, "chunk_id": "train_shard_00000_4464_1", "global_id": 4986 }, { "text": "The effect of combinations and ratios between different enzymes has been investigated in order to assess the optimal conditions for hydrolysis of cashew apple bagasse pretreated with alkaline hydrogen peroxide (the solids named CAB-AHP). The separate hydrolysis and fermentation (SHF) and simultaneous saccharification and fermentation (SSF) processes were evaluated in the ethanol production. The enzymatic hydrolysis conducted with cellulase complex and β-glucosidase in a ratio of 0.61:0.39, enzyme loading of 30FPU/g(CAB-AHP) and 66CBU/g(CAB-AHP), respectively, using 4% cellulose from CAB-AHP, turned out to be the most effective conditions, with glucose and xylose yields of 511.68 mg/g(CAB-AHP) and 237.8 mg/g(CAB-AHP), respectively. Fermentation of the pure hydrolysate by Kluyveromyces marxianus ATCC 36907 led to an ethanol yield of 61.8kg/ton(CAB), corresponding to 15 g/L ethanol and productivity of 3.75 g/( Lh). The ethanol production obtained for SSF process using K. marxianus ATCC 36907 was 18 g/L corresponding to 80% yield and 74.2kg/ton(CAB).\n\nEnhanced enzymatic hydrolysis and ethanol production from cashew apple bagasse pretreated with alkaline hydrogen peroxide.", "token_count": 393, "char_count": 1186, "word_count": 163, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:21.740742", "source": { "split": "train_shard_00000", "doc_id": 4465 }, "chunk_id": "train_shard_00000_4465_0", "global_id": 4987 }, { "text": "Brazilian kefir is a homemade fermented beverage that is obtained by incubating milk or a brown sugar solution with kefir grains that contribute their different microbiological compositions. It is highly important to isolate and characterize microorganisms from Brazilian kefir grains to obtain starter cultures for the industrial production of a standardized commercial kefir. Thus, the present study aimed to isolate lactic acid bacteria from eight kefir grains that were propagated in milk or sugar solutions from five different locations in Brazil and to select Lactobacillus isolates based on desirable in vitro probiotic properties. One hundred eight isolates from both substrates were identified by amplified ribosomal DNA restriction analysis and/or 16S rRNA gene sequencing and were determined to belong to the following 11 species from the genera: Lactococcus, Leuconostoc, Lactobacillus (L.), and Oenococcus. Leuconostoc mesenteroides, Lactobacillus kefiri, and Lactobacillus kefiranofaciens were isolated only from milk grains, whereas Lactobacillus perolens, Lactobacillus parafarraginis, Lactobacillus diolivorans, and Oenococcus oeni were isolated exclusively from sugar water grains. When the microbial compositions of four kefir grains were evaluated with culture-independent analyses, L. kefiranofaciens was observed to predominant in milk grains, whereas Lactobacillus hilgardii was most abundant in sugar water kefir. Unfortunately, L. hilgardii was not isolated from any grain, although this bacteria was detected with a culture-independent methodology. Fifty-two isolated Lactobacilli were tested for gastric juice and bile salt tolerance, antagonism against pathogens, antimicrobial resistance, and surface hydrophobicity. Three Lactobacillus strains (L. kefiranofaciens 8U, L. diolivorans 1Z, and Lactobacillus casei 17U) could be classified as potential probiotics", "token_count": 511, "char_count": 1889, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:22.420633", "source": { "split": "train_shard_00000", "doc_id": 4466 }, "chunk_id": "train_shard_00000_4466_0", "global_id": 4988 }, { "text": "In conclusion, several lactic acid bacteria that could be used in combination with yeasts as starter cultures for both milk kefir and sugar water kefir were characterized, and the functional properties of several of the lactobacilli isolated from the kefir grains were suggestive of their possible use as probiotics in both kefir and other dairy products.\n\nSelection of lactic acid bacteria from Brazilian kefir grains for potential use as starter or probiotic cultures.", "token_count": 108, "char_count": 470, "word_count": 73, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:22.844039", "source": { "split": "train_shard_00000", "doc_id": 4466 }, "chunk_id": "train_shard_00000_4466_1", "global_id": 4989 }, { "text": "This study aimed to evaluate the identification of clinical fungal isolates (yeast and molds) by protein profiling using Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF/MS). A total of 125 clinical fungal culture isolates (yeast and filamentous fungi) were collected. The test set included 88 yeast isolates (Candida albicans, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida parapsilosis, Candida rugosa, Candida tropicalis and Cryptococcus neoformans) and 37 isolates of molds (Alternaria spp., Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Cunninghamella spp., Histoplasma capsulatum, Microsporum gypseum, Microsporum nanum, Rhizomucor spp. and Trichophyton spp.). The correlation between MALDI TOF MS and conventional identification for all these 125 fungal isolates included in the study was 87.2% at the species level and 90.4% at the genus level. MALDI TOF MS results revealed that the correlation in yeast (n=88) identification was 100% both at the genus and species levels whereas, the correlation in mold (n=37) identification was more heterogeneous i.e. 10.81% isolates had correct identification up to the genus level, 56.7% isolates had correct identification both at the genus and species levels, whereas 32.42% isolates were deemed Not Reliable Identification (NRI). But, with the modification in sample preparation protocol for molds, there was a significant improvement in identification. 86.4% isolates had correct identification till the genus and species levels whereas, only 2.7% isolates had Not Reliable Identification. In conclusion, this study demonstrates that MALDI-TOF MS could be a possible alternative to conventional techniques both for the identification and differentiation of clinical fungal isolates", "token_count": 496, "char_count": 1822, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5502, "quality_score": 0.7751, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:23.524545", "source": { "split": "train_shard_00000", "doc_id": 4467 }, "chunk_id": "train_shard_00000_4467_0", "global_id": 4990 }, { "text": "However, the main limitation of this technique is that MS identification could be more precise only if the reference spectrum of the fungal species is available in the database.\n\nMALDI-TOF mass spectrometry for rapid identification of clinical fungal isolates based on ribosomal protein biomarkers.", "token_count": 65, "char_count": 298, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:23.928233", "source": { "split": "train_shard_00000", "doc_id": 4467 }, "chunk_id": "train_shard_00000_4467_1", "global_id": 4991 }, { "text": "Toxin/antitoxin (TA) systems are ubiquitous within bacterial genomes, and the mechanisms of many TA systems are well characterized. As such, several roles for TA systems have been proposed, such as phage inhibition, gene regulation and persister cell formation. However, the significance of these roles is nebulous due to the subtle influence from individual TA systems. For example, a single TA system has only a minor contribution to persister cell formation. Hence, there is a lack of defining physiological roles for individual TA systems. In this study, phenotype assays were used to determine that the MqsR/MqsA type II TA system of Escherichia coli is important for cell growth and tolerance during stress from the bile salt deoxycholate. Using transcriptomics and purified MqsR, we determined that endoribonuclease toxin MqsR degrades YgiS mRNA, which encodes a periplasmic protein that promotes deoxycholate uptake and reduces tolerance to deoxycholate exposure. The importance of reducing YgiS mRNA by MqsR is evidenced by improved growth, reduced cell death and reduced membrane damage when cells without ygiS are stressed with deoxycholate. Therefore, we propose that MqsR/MqsA is physiologically important for E. coli to thrive in the gallbladder and upper intestinal tract, where high bile concentrations are prominent.\n\nThe MqsR/MqsA toxin/antitoxin system protects Escherichia coli during bile acid stress.", "token_count": 369, "char_count": 1422, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:24.512144", "source": { "split": "train_shard_00000", "doc_id": 4468 }, "chunk_id": "train_shard_00000_4468_0", "global_id": 4992 }, { "text": "Bacteriophages that infect the opportunistic pathogen Pseudomonas aeruginosa have been classified into several groups. One of them, which includes temperate phage particles with icosahedral heads and long flexible tails, bears genomes whose architecture and replication mechanism, but not their nucleotide sequences, are like those of coliphage Mu. By comparing the genomic sequences of this group of P. aeruginosa phages one could draw conclusions about their ontogeny and evolution.\n\nCore and accessory genome architecture in a group of Pseudomonas aeruginosa Mu-like phages.", "token_count": 132, "char_count": 577, "word_count": 81, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:24.936226", "source": { "split": "train_shard_00000", "doc_id": 4469 }, "chunk_id": "train_shard_00000_4469_0", "global_id": 4993 }, { "text": "Bile salt hydrolase (BSH), a widely distributed function of the gut microbiota, has a profound impact on host lipid metabolism and energy harvest. Recent studies suggest that BSH inhibitors are promising alternatives to antibiotic growth promoters (AGP) for enhanced animal growth performance and food safety. Using a high-purity BSH from Lactobacillus salivarius strain, we have identified a panel of BSH inhibitors. However, it is still unknown if these inhibitors also effectively inhibit the function of the BSH enzymes from other bacterial species with different sequence and substrate spectrum. In this study, we performed bioinformatics analysis and determined the inhibitory effect of identified BSH inhibitors on a BSH from L. acidophilus. Although the L. acidophilus BSH is phylogenetically distant from the L. salivarius BSH, sequence analysis and structure modeling indicated the two BSH enzymes contain conserved, catalytically important amino residues and domain. His-tagged recombinant BSH from L. acidophilus was further purified and used to determine inhibitory effect of specific compounds. Previously identified BSH inhibitors also exhibited potent inhibitory effects on the L. acidophilus BSH. In conclusion, this study demonstrated that the BSH from L. salivarius is an ideal candidate for screening BSH inhibitors, the promising alternatives to AGP for enhanced feed efficiency, growth performance and profitability of food animals.\n\nEffect of Bile Salt Hydrolase Inhibitors on a Bile Salt Hydrolase from Lactobacillus acidophilus.", "token_count": 366, "char_count": 1553, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5676, "quality_score": 0.7838, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:25.514899", "source": { "split": "train_shard_00000", "doc_id": 4470 }, "chunk_id": "train_shard_00000_4470_0", "global_id": 4994 }, { "text": "Vibrio vulnificus is an aquatic bacterium and an important human pathogen. Strains of V. vulnificus are classified into three different biotypes. The newly emerged biotype 3 has been found to be clonal and restricted to Israel. In the family Vibrionaceae, horizontal gene transfer is the main mechanism responsible for the emergence of new pathogen groups. To better understand the evolution of the bacterium, and in particular to trace the evolution of biotype 3, we performed genome-wide SNP genotyping of 254 clinical and environmental V. vulnificus isolates with worldwide distribution recovered over a 30-year period, representing all phylogeny groups. A custom single-nucleotide polymorphism (SNP) array implemented on the Illumina GoldenGate platform was developed based on 570 SNPs randomly distributed throughout the genome. In general, the genotyping results divided the V. vulnificus species into three main phylogenetic lineages and an additional subgroup, clade B, consisting of environmental and clinical isolates from Israel. Data analysis suggested that 69% of biotype 3 SNPs are similar to SNPs from clade B, indicating that biotype 3 and clade B have a common ancestor. The rest of the biotype 3 SNPs were scattered along the biotype 3 genome, probably representing multiple chromosomal segments that may have been horizontally inserted into the clade B recipient core genome from other phylogroups or bacterial species sharing the same ecological niche. Results emphasize the continuous evolution of V. vulnificus and support the emergence of new pathogenic groups within this species as a recurrent phenomenon. Our findings contribute to a broader understanding of the evolution of this human pathogen.\n\nGenome-wide SNP-genotyping array to study the evolution of the human pathogen Vibrio vulnificus biotype 3.", "token_count": 436, "char_count": 1830, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5735, "quality_score": 0.7868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:26.138475", "source": { "split": "train_shard_00000", "doc_id": 4471 }, "chunk_id": "train_shard_00000_4471_0", "global_id": 4995 }, { "text": "Third-generation cephalosporins are a class of β-lactam antibiotics that are often used for the treatment of human infections caused by Gram-negative bacteria, especially Escherichia coli. Worryingly, the incidence of human infections caused by third-generation cephalosporin-resistant E. coli is increasing worldwide. Recent studies have suggested that these E. coli strains, and their antibiotic resistance genes, can spread from food-producing animals, via the food-chain, to humans. However, these studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these strains. We therefore used whole-genome sequencing (WGS) to study the relatedness of cephalosporin-resistant E. coli from humans, chicken meat, poultry and pigs. One strain collection included pairs of human and poultry-associated strains that had previously been considered to be identical based on Multi-Locus Sequence Typing, plasmid typing and antibiotic resistance gene sequencing. The second collection included isolates from farmers and their pigs. WGS analysis revealed considerable heterogeneity between human and poultry-associated isolates. The most closely related pairs of strains from both sources carried 1263 Single-Nucleotide Polymorphisms (SNPs) per Mbp core genome. In contrast, epidemiologically linked strains from humans and pigs differed by only 1.8 SNPs per Mbp core genome. WGS-based plasmid reconstructions revealed three distinct plasmid lineages (IncI1- and IncK-type) that carried cephalosporin resistance genes of the Extended-Spectrum Beta-Lactamase (ESBL)- and AmpC-types. The plasmid backbones within each lineage were virtually identical and were shared by genetically unrelated human and animal isolates. Plasmid reconstructions from short-read sequencing data were validated by long-read DNA sequencing for two strains. Our findings failed to demonstrate evidence for recent clonal transmission of cephalosporin-resistant E. coli strains from poultry to humans, as has been suggested based on traditional, low-resolution typing methods", "token_count": 518, "char_count": 2108, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6143, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:44:26.802409", "source": { "split": "train_shard_00000", "doc_id": 4472 }, "chunk_id": "train_shard_00000_4472_0", "global_id": 4996 }, { "text": "Instead, our data suggest that cephalosporin resistance genes are mainly disseminated in animals and humans via distinct plasmids.\n\nDissemination of cephalosporin resistance genes between Escherichia coli strains from farm animals and humans by specific plasmid lineages.", "token_count": 67, "char_count": 271, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:27.168573", "source": { "split": "train_shard_00000", "doc_id": 4472 }, "chunk_id": "train_shard_00000_4472_1", "global_id": 4997 }, { "text": "Bacterial whole genome sequence (WGS) methods are rapidly overtaking classical sequence analysis. Many bacterial sequencing projects focus on mobilome changes, since macroevolutionary events, such as the acquisition or loss of mobile genetic elements, mainly plasmids, play essential roles in adaptive evolution. Existing WGS analysis protocols do not assort contigs between plasmids and the main chromosome, thus hampering full analysis of plasmid sequences. We developed a method (called plasmid constellation networks or PLACNET) that identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets. The workflow of the method is based on three types of data: assembly information (including scaffold links and coverage), comparison to reference sequences and plasmid-diagnostic sequence features. The resulting network is pruned by expert analysis, to eliminate confounding data, and implemented in a Cytoscape-based graphic representation. To demonstrate PLACNET sensitivity and efficacy, the plasmidome of the Escherichia coli lineage ST131 was analyzed. ST131 is a globally spread clonal group of extraintestinal pathogenic E. coli (ExPEC), comprising different sublineages with ability to acquire and spread antibiotic resistance and virulence genes via plasmids. Results show that plasmids flux in the evolution of this lineage, which is wide open for plasmid exchange. MOBF12/IncF plasmids were pervasive, adding just by themselves more than 350 protein families to the ST131 pangenome. Nearly 50% of the most frequent γ-proteobacterial plasmid groups were found to be present in our limited sample of ten analyzed ST131 genomes, which represent the main ST131 sublineages.\n\nPlasmid flux in Escherichia coli ST131 sublineages, analyzed by plasmid constellation network (PLACNET), a new method for plasmid reconstruction from whole genome sequences.", "token_count": 480, "char_count": 1966, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6679, "quality_score": 0.8339, "entities": { "genes": [ "ST131", "MOBF12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:27.822457", "source": { "split": "train_shard_00000", "doc_id": 4473 }, "chunk_id": "train_shard_00000_4473_0", "global_id": 4998 }, { "text": "Lactic acid bacteria (LAB) with proteolitic activity are used as aromatic and antibacterial substances, cholesterol reduces, bile salt hydrolyses, and probiotic. The aims of this project were to isolate and identify natural LAB flora involved in traditional fermentation in cheeses of Khoramabad city and also to survey their probiotic potential. In order to achieve this goal, LAB were isolated and characterized using phenotypic and genotypic methods (PCR-sequencing); in the next stage, they were analyzed lowering cholesterol medium, hydrolysis of the bile, resistance to bile-resistant PH acidic stomach. At the end of the study, 88 cocci and 3 bacill were found: 58 Enterococcus faecium, 16 Enterococcus hirae, 5 Lactococcus lactis, 3 Lactobacillus plantarum, and 9 undetermined. The probiotic results of the bacteria had effects on the reduction of cholesterol, resistance to stomach acid, had relative antibacterial effects, and some strains had effects on hydrolyzing the bile. For further identification, the PCR method and the application of 16s-DNA-ITS genes and its sequencing were found useful. This study showed that lactic acid bacteria in the traditional cheese of the Khorramabad city have relative probiotic effect and that these lactic acid bacteria in fermented milk are suitable.\n\nPhenotypic and genotypic characterization of lactic acid bacteria from traditional cheese in Khorramabad city of Iran with probiotic potential.", "token_count": 377, "char_count": 1446, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5991, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:28.409191", "source": { "split": "train_shard_00000", "doc_id": 4474 }, "chunk_id": "train_shard_00000_4474_0", "global_id": 4999 }, { "text": "We performed an analysis to determine the importance of bile acid modification genes in the gut microbiome of inflammatory bowel disease and type 2 diabetic patients. We used publicly available metagenomic datasets from the Human Microbiome Project and the MetaHIT consortium, and determined the abundance of bile salt hydrolase gene (bsh), 7 alpha-dehydroxylase gene (adh) and 7-alpha hydroxysteroid dehydrogenase gene (hsdh) in fecal bacteria in diseased populations of Crohn's disease (CD), Ulcerative Colitis (UC) and Type 2 diabetes mellitus (T2DM). Phylum level abundance analysis showed a significant reduction in Firmicute-derived bsh in UC and T2DM patients but not in CD patients, relative to healthy controls. Reduction of adh and hsdh genes was also seen in UC and T2DM patients, while an increase was observed in the CD population as compared to healthy controls. A further analysis of the bsh genes showed significant differences in the correlations of certain Firmicutes families with disease or healthy populations. From this observation we proceeded to analyse BSH protein sequences and identified BSH proteins clusters representing the most abundant strains in our analysis of Firmicute bsh genes. The abundance of the bsh genes corresponding to one of these protein clusters was significantly reduced in all disease states relative to healthy controls. This cluster includes bsh genes derived from Lachospiraceae, Clostridiaceae, Erysipelotrichaceae and Ruminococcaceae families. This metagenomic analysis provides evidence of the importance of bile acid modifying enzymes in health and disease. It further highlights the importance of identifying gene and protein clusters, as the same gene may be associated with health or disease, depending on the strains expressing the enzyme, and differences in the enzymes themselves.\n\nBacterial bile metabolising gene abundance in Crohn's, ulcerative colitis and type 2 diabetes metagenomes.", "token_count": 455, "char_count": 1951, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5333, "quality_score": 0.7667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:29.859289", "source": { "split": "train_shard_00000", "doc_id": 4475 }, "chunk_id": "train_shard_00000_4475_0", "global_id": 5000 }, { "text": "The WxL domain recently has been identified as a novel cell wall binding domain found in numerous predicted proteins within multiple Gram-positive bacterial species. However, little is known about the function of proteins containing this novel domain. Here, we identify and characterize 6 Enterococcus faecium proteins containing the WxL domain which, by reverse transcription-PCR (RT-PCR) and genomic analyses, are located in three similarly organized operons, deemed WxL loci A, B, and C. Western blotting, electron microscopy, and enzyme-linked immunosorbent assays (ELISAs) determined that genes of WxL loci A and C encode antigenic, cell surface proteins exposed at higher levels in clinical isolates than in commensal isolates. Secondary structural analyses of locus A recombinant WxL domain-containing proteins found they are rich in β-sheet structure and disordered segments. Using Biacore analyses, we discovered that recombinant WxL proteins from locus A bind human extracellular matrix proteins, specifically type I collagen and fibronectin. Proteins encoded by locus A also were found to bind to each other, suggesting a novel cell surface complex. Furthermore, bile salt survival assays and animal models using a mutant from which all three WxL loci were deleted revealed the involvement of WxL operons in bile salt stress and endocarditis pathogenesis. In summary, these studies extend our understanding of proteins containing the WxL domain and their potential impact on colonization and virulence in E. faecium and possibly other Gram-positive bacterial species.\n\nThe identification and functional characterization of WxL proteins from Enterococcus faecium reveal surface proteins involved in extracellular matrix interactions.", "token_count": 413, "char_count": 1743, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:30.486125", "source": { "split": "train_shard_00000", "doc_id": 4476 }, "chunk_id": "train_shard_00000_4476_0", "global_id": 5001 }, { "text": "The nuclear receptor FXR acts as an intracellular bile salt sensor that regulates synthesis and transport of bile salts within their enterohepatic circulation. In addition, FXR is involved in control of a variety of crucial metabolic pathways. Four FXR splice variants are known, i.e. FXRα1-4. Although these isoforms show differences in spatial and temporal expression patterns as well as in transcriptional activity, the physiological relevance hereof has remained elusive. We have evaluated specific roles of hepatic FXRα2 and FXRα4 by stably expressing these isoforms using liver-specific self-complementary adeno-associated viral vectors in total body FXR knock-out mice. The hepatic gene expression profile of the FXR knock-out mice was largely normalized by both isoforms. Yet, differential effects were also apparent; FXRα2 was more effective in reducing elevated HDL levels and transrepressed hepatic expression of Cyp8b1, the regulator of cholate synthesis. The latter coincided with a switch in hydrophobicity of the bile salt pool. Furthermore, FXRα2-transduction caused an increased neutral sterol excretion compared to FXRα4 without affecting intestinal cholesterol absorption. Our data show, for the first time, that hepatic FXRα2 and FXRα4 differentially modulate bile salt and lipoprotein metabolism in mice.\n\nHepatic farnesoid X-receptor isoforms α2 and α4 differentially modulate bile salt and lipoprotein metabolism in mice.", "token_count": 378, "char_count": 1444, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6716, "quality_score": 0.8358, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:31.077671", "source": { "split": "train_shard_00000", "doc_id": 4477 }, "chunk_id": "train_shard_00000_4477_0", "global_id": 5002 }, { "text": "Aqueous solution behaviour of a nonionic surfactant Triton X-100 is investigated in the presence of two bile salts namely sodium deoxycholate (NaDC) and sodium cholate (NaC) at different pH, temperatures and in the presence of sodium chloride and the resultant structural changes to accordingly formed mixed micelles were analyzed by using cloud point (CP), viscosity and scattering techniques. Both the bile salts increased the CP and showed a corresponding decrease in viscosity and apparent hydrodynamic diameter (Dh), which can further be subsided with the progressive addition of sodium chloride and an increase in temperature. Interestingly, in the presence of bile salt below pH ∼5, CP decreased with corresponding increase in viscosity, while a reversed trend was observed above pH∼8. Small angle neutron scattering data reveal that nearly spherical mixed micelles were formed in the presence of bile salt which grow and transform to prolate ellipsoidal ones at pH∼3. These morphological changes are facilitated by the protonation of carboxylic acid group of bile salt and deeper penetration of bile acid molecules into TX-100 micelles at lower pH. Proposed molecular interactions are extremely informative to understand more about these biologically important compounds playing a crucial role in digestion processes.\n\nInvestigations on microstructural changes in pH responsive mixed micelles of Triton X-100 and bile salt.", "token_count": 334, "char_count": 1431, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:31.647557", "source": { "split": "train_shard_00000", "doc_id": 4478 }, "chunk_id": "train_shard_00000_4478_0", "global_id": 5003 }, { "text": "This study aimed to investigate the potential of Bacillus methylotrophicus as a probiotic.\n\nIn vitro assessment of the gastrointestinal tolerance and immunomodulatory function of Bacillus methylotrophicus isolated from a traditional Korean fermented soybean food.", "token_count": 70, "char_count": 263, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:32.024790", "source": { "split": "train_shard_00000", "doc_id": 4479 }, "chunk_id": "train_shard_00000_4479_0", "global_id": 5004 }, { "text": "Koumiss is a low-alcohol product made from fermented mare's milk, which is popular in Kazakhstan, Russia, and other countries of Central Asia, China, and Mongolia. Natural mare's milk is fermented in symbiosis of two types of microorganisms (lactobacteria and yeast). Koumiss's microbial composition varies depending on the geographical, climatic, and cultural conditions. Based on a phenotypic characteristic from samples, Wu, R. and colleagues identified the following bacteria isolated in inner Mongolia, an autonomous region of China: L.casei, L.helveticus, L.plantarum, L.coryniformis subsp. coryniformis, L.paracasei, L.kefiranofaciens, L.curvatus, L.fermentum, and W.kandleri. Studies of the yeast composition in koumiss also showed significant variations. Thus, there were Saccharomyces unisporus related 48.3% of isolates, to Kluyveromyces marxianus (27.6%), Pichia membranaefaciens (15.0%), and Saccharomyces cerevisiae (9.2%) from 87 isolated yeast cultures. The purpose of this study was to examine the bacterial composition in koumiss.\n\nMetagenomic Analysis of Koumiss in Kazakhstan.", "token_count": 326, "char_count": 1096, "word_count": 143, "semantic_coherence": 1, "information_density": 0.7343, "quality_score": 0.8671, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:32.592929", "source": { "split": "train_shard_00000", "doc_id": 4480 }, "chunk_id": "train_shard_00000_4480_0", "global_id": 5005 }, { "text": "Kluyveromyces marxianus converts whey-borne sugar into ethyl acetate, an environmentally friendly solvent with many applications. K. marxianus DSM 5422 presumably synthesizes ethyl acetate from acetyl-SCoA. Iron limitation as a trigger for this synthesis is explained by a diminished aconitase and succinate dehydrogenase activity (both enzymes depend on iron) causing diversion of acetyl-SCoA from the tricarboxic acid cycle to ester synthesis. Copper limitation as another trigger for ester synthesis in this yeast refers to involvement of the electron transport chain (all ETC complexes depend on iron and complex IV requires copper). This hypothesis was checked by using several ETC inhibitors. Malonate was ineffective but carboxin partially inhibited complex II and initiated ester synthesis. Antimycin A and cyanide as complexes III and IV inhibitors initiated ester synthesis only at moderate levels while higher concentrations disrupted all respiration and caused ethanol formation. A restricted supply of oxygen (the terminal electron acceptor) also initiated some ester synthesis but primarily forced ethanol production. A switch from aerobic to anaerobic conditions nearly stopped ester synthesis and induced ethanol formation. Iron-limited ester formation was compared with anaerobic ethanol production; the ester yield was lower than the ethanol yield but a higher market price, a reduced number of process stages, a faster process, and decreased expenses for product recovery by stripping favor biotechnological ester production.\n\nStudies on the mechanism of synthesis of ethyl acetate in Kluyveromyces marxianus DSM 5422.", "token_count": 395, "char_count": 1637, "word_count": 231, "semantic_coherence": 1, "information_density": 0.632, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:33.204751", "source": { "split": "train_shard_00000", "doc_id": 4481 }, "chunk_id": "train_shard_00000_4481_0", "global_id": 5006 }, { "text": "Controlled, reductionist approaches are required in order to obtain a more complete understanding of the functional capabilities of the gut microbiota. We recently identified microbial bile salt hydrolase (BSH) activity as a gut microbial activity that has the capacity to profoundly alter both local (gastrointestinal) and systemic (hepatic) host functions. Using both germ free and conventionally-raised mouse models we demonstrated that gastrointestinal expression of BSH results in local bile acid deconjugation with concomitant alterations in lipid and cholesterol metabolism, signaling functions and weight gain. Key mediators of cholesterol homeostasis (Abcg5/8), gut homeostasis (RegIIIγ) and circadian rhythm (Dbp) were influenced by elevated BSH in our study. In this addendum we discuss the implications of this work for the rational development of probiotics with the potential to modulate host weight gain.\n\nBacterial bile salt hydrolase in host metabolism: Potential for influencing gastrointestinal microbe-host crosstalk.", "token_count": 253, "char_count": 1037, "word_count": 142, "semantic_coherence": 1, "information_density": 0.669, "quality_score": 0.8345, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:33.692906", "source": { "split": "train_shard_00000", "doc_id": 4482 }, "chunk_id": "train_shard_00000_4482_0", "global_id": 5007 }, { "text": "During lipolysis of triglyceride by lipase, monoglyceride and fatty acids are produced which combine with gastrointestinal fluids to form self-assembled structures. These solubilize hydrophobic food components to promote their absorption. The aim of this study was a detailed understanding of structure formation from triglyceride digestion products with saturated short-, medium- and long chain fatty acids. Complementary characterization methods have been applied comprising small angle X-ray and neutron scattering – the latter involving the contrast matching technique using fully deuterated fatty acids – polarized and depolarized dynamic light scattering and cryogenic-transmission electron microscopy. Shape, size and solubilization capacity of the self-assembled structures was dependent on composition and lipid chain length. Crystallization of fatty acid was observed when the solubility limit in the mixed bile salt micelles was exceeded; however, increasing pH and temperature increased the fatty acid solubility. The results provide insight into structure formation and crystallization of incorporated lipolysis products; this is important for a detailed understanding of food structure and nutrition, as well as the rational design of lipid based drug delivery systems.\n\nDisposition and crystallization of saturated fatty acid in mixed micelles of relevance to lipid digestion.", "token_count": 301, "char_count": 1391, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6614, "quality_score": 0.8307, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:34.270903", "source": { "split": "train_shard_00000", "doc_id": 4483 }, "chunk_id": "train_shard_00000_4483_0", "global_id": 5008 }, { "text": "An infant's complete diet, human breast milk, is the basis for its survival and development. It contains water-soluble and poorly water-soluble bioactive components, metabolic messages, and energy, all of which are made bioavailable during the digestion process in the infant's gastrointestinal tract. Reported is the first discovery of highly geometrically organized structures formed during the digestion of human breast milk under simulated in vivo conditions using small-angle X-ray scattering and cryogenic transmission electron microscopy. Time of digestion, pH, and bile salt concentration were found to have symbiotic effects gradually tuning the oil-based environment inside the breast milk globules to more water-like structures with high internal surface area. The structure formation is necessarily linked to its function as carriers for poorly water-soluble molecules in the digestive tract of the infant.\n\nSelf-assembly structure formation during the digestion of human breast milk.", "token_count": 212, "char_count": 996, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8417, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:34.763127", "source": { "split": "train_shard_00000", "doc_id": 4484 }, "chunk_id": "train_shard_00000_4484_0", "global_id": 5009 }, { "text": "The aim of this study was to evaluate the prevalence of mycotic mastitis in different mammary gland statuses. The study was conducted on 304 dairy cows from ten farms in two north-eastern regions in Algeria; Guelma and Souk Ahras with 922 and 199 samples, respectively, forming thus a total number of 1,121 milk samples. A total of 321 milk samples were collected from clinical mastitis, 544 milk samples from subclinical mastitis and 256 milk samples from healthy mammary glands. Mycological analyses revealed that 10.17% of the treated samples were positive recording 114 species of fungi including 88 yeasts and 26 moulds. The most frequent species was Candida kefyr followed by C. albicans, C. guilliermondii, C. famata, C. tropicalis, C. colliculosa, C. krusei, C. rugosa, C. glabrata, C. parapsilosis, C. inconspicua, Trichosporon sp., Rhodotorula glutinis and Saccharomyces fragilis. Mould species have also been isolated from samples of both healthy milk and clinical mastitis milk. Aspergillus amstelodami (from glaucus group), A. fumigatus and Geotrichum candidum were identified, while the other species including Penicillium sp. and Cladosporium sp. were not identified.\n\nSurvey of bovine mycotic mastitis in different mammary gland statuses in two north-eastern regions of Algeria.", "token_count": 386, "char_count": 1294, "word_count": 194, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:35.390384", "source": { "split": "train_shard_00000", "doc_id": 4485 }, "chunk_id": "train_shard_00000_4485_0", "global_id": 5010 }, { "text": "The surrounding capsule of Streptococcus pneumoniae has been identified as a major virulence factor and is targeted by pneumococcal conjugate vaccines (PCV). However, nonencapsulated S. pneumoniae (non-Ec-Sp) have also been isolated globally, mainly in carriage studies. It is unknown if non-Ec-Sp evolve sporadically, if they have high antibiotic nonsusceptiblity rates and a unique, specific gene content. Here, whole-genome sequencing of 131 non-Ec-Sp isolates sourced from 17 different locations around the world was performed. Results revealed a deep-branching classic lineage that is distinct from multiple sporadic lineages. The sporadic lineages clustered with a previously sequenced, global collection of encapsulated S. pneumoniae (Ec-Sp) isolates while the classic lineage is comprised mainly of the frequently identified multilocus sequences types (STs) ST344 (n = 39) and ST448 (n = 40). All ST344 and nine ST448 isolates had high nonsusceptiblity rates to β-lactams and other antimicrobials. Analysis of the accessory genome reveals that the classic non-Ec-Sp contained an increased number of mobile elements, than Ec-Sp and sporadic non-Ec-Sp. Performing adherence assays to human epithelial cells for selected classic and sporadic non-Ec-Sp revealed that the presence of a integrative conjugative element (ICE) results in increased adherence to human epithelial cells (P = 0.005). In contrast, sporadic non-Ec-Sp lacking the ICE had greater growth in vitro possibly resulting in improved fitness. In conclusion, non-Ec-Sp isolates from the classic lineage have evolved separately. They have spread globally, are well adapted to nasopharyngeal carriage and are able to coexist with Ec-Sp. Due to continued use of PCV, non-Ec-Sp may become more prevalent.", "token_count": 492, "char_count": 1769, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6285, "quality_score": 0.8142, "entities": { "genes": [ "ST344", "ST448" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:36.070450", "source": { "split": "train_shard_00000", "doc_id": 4486 }, "chunk_id": "train_shard_00000_4486_0", "global_id": 5011 }, { "text": "Global phylogenomic analysis of nonencapsulated Streptococcus pneumoniae reveals a deep-branching classic lineage that is distinct from multiple sporadic lineages.", "token_count": 42, "char_count": 163, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:36.468158", "source": { "split": "train_shard_00000", "doc_id": 4486 }, "chunk_id": "train_shard_00000_4486_1", "global_id": 5012 }, { "text": "Lactobacillus crispatus is a ubiquitous micro-organism encountered in a wide range of host-associated habitats. It can be recovered from the gastrointestinal tract of animals and it is a common constituent of the vaginal microbiota of humans. Moreover, L. crispatus can contribute to the urogenital health of the host through competitive exclusion and the production of antimicrobial agents. In order to investigate the genetic diversity of this important urogenital species, we performed a comparative genomic analysis of L. crispatus.\n\nComparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis.", "token_count": 158, "char_count": 667, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6559, "quality_score": 0.828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:36.907773", "source": { "split": "train_shard_00000", "doc_id": 4487 }, "chunk_id": "train_shard_00000_4487_0", "global_id": 5013 }, { "text": "Using an in vitro digestion model, we studied the effect of six saponin extracts on the bioaccessibility of cholesterol and saturated fatty acids (SFAs). In the absence of saponins, around 78% of the available cholesterol was solubilized in the simulated intestinal fluids. The addition of two extracts, Quillaja Dry (QD) and Sapindin (SAP), was found to decrease cholesterol bioaccessibility to 19% and 44%, respectively. For both extracts, the main mechanism of this effect is the displacement of cholesterol molecules from the bile salt micelles, leading to formation of cholesterol precipitates that cannot pass through the mucus layer of the intestine. QD decreased strongly the SFA bioaccessibility as well, from 69 to 9%, due to formation of calcium-SFA precipitates, while SAP had no effect on SFA. We studied the in vivo activity of QD and SAP extracts by measuring serum cholesterol in mice fed with experimental diets within a 7-day period. Both extracts were found to prevent dietary hypercholesterolemia in mice fed on a cholesterol-rich diet. The other saponin extracts did not show any significant effect in vitro and, therefore, were not studied in vivo. The cholesterol lowering ability of Sapindin extract is reported for the first time in the current study.\n\nLowering of cholesterol bioaccessibility and serum concentrations by saponins: in vitro and in vivo studies.", "token_count": 377, "char_count": 1386, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5741, "quality_score": 0.787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:37.493368", "source": { "split": "train_shard_00000", "doc_id": 4488 }, "chunk_id": "train_shard_00000_4488_0", "global_id": 5014 }, { "text": "Imatinib mesylate has been evaluated for possible potential in treatment of colon cancer in recent times. However, due to significant reporting of P-gp expression in colon cancer, it can come across set back due to MDR. Therefore, in present work the liposomal formulation containing imatinib-bile salt conjugate was developed and investigated for its comparative performance in MDR colon cancer cells and surface modified with hyaluronic acid for achieving low hemotoxicity with stealth characteristics. Imatinib was successfully conjugated with sodium-deoxycholate by charged conjugation and evaluated through FTIR, DSC and PXRD. The developed conjugate (IM-SD) was encapsulated in liposomes and the conditions were optimized by Box-Behnken statistical design to achieve a size of 56.56±1.23 nm along with 99.11±0.89% entrapment efficiency (LIPO). The liposomes were surface modified with hyaluronic acid and the size was enhanced to 159.14±3.2 nm (HA-LIPO). Flow cytometric studies demonstrated the enhanced uptake of P-gp substrate rhodamine dye in P-gp positive colo 320 colon cancer cells. In addition, an enhanced cellular internalization of HA-LIPO in CD-44 positive HT-29 and colo 320 cells indicates the targeting attributes of the hyaluronan coated liposomes. Finally, the hyaluronan coated liposomes were also found to have low opsonization activity.\n\nHyaluronan coated liposomes as the intravenous platform for delivery of imatinib mesylate in MDR colon cancer.", "token_count": 398, "char_count": 1474, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6048, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:38.105025", "source": { "split": "train_shard_00000", "doc_id": 4489 }, "chunk_id": "train_shard_00000_4489_0", "global_id": 5015 }, { "text": "Enzymatic- gravimetric method was used to obtain three fractions of dietary from defatted rice bran. The functional and physiological properties such as viscosity, cation exchange capacity (CEC), and glucose dialysis retardation index (GDRI), cholesterol and bile salt adsorption capacity of the resultant fractions were evaluated. Insoluble dietary fibre (IDF) and soluble dietary fibre (SDF) when compared showed that SDF exhibited significantly (p < 0.05) higher viscosity (2.35 mPa.s), greater GDRI value (17.65 %) at 60 min and significantly lowered concentration of cholesterol at pH 7 (29.90 %, p < 0.05). However IDF showed the highest CEC and its adsorption capacity of bile salt was higher than SDF (18.20 % vs. 13.76 %; p < 0.05), while CEC and cholesterol absorption capacity of TDF were similar to SDF. These properties indicate that rice bran soluble, insoluble and total fibres are functional ingredients which can be added to various food products and dietetic, low-calorie high-fiber foods to enhance their nutraceutical properties and health benefits.\n\nFunctional and physiological properties of total, soluble, and insoluble dietary fibres derived from defatted rice bran.", "token_count": 362, "char_count": 1191, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:38.684605", "source": { "split": "train_shard_00000", "doc_id": 4490 }, "chunk_id": "train_shard_00000_4490_0", "global_id": 5016 }, { "text": "Infectious complications often occur in acute pancreatitis, related to impaired intestinal barrier function, with prolonged disease course and even mortality as a result. The bile salt nuclear receptor farnesoid X receptor (FXR), which is expressed in the ileum, liver and other organs including the pancreas, exhibits anti-inflammatory effects by inhibiting NF-κB activation and is implicated in maintaining intestinal barrier integrity and preventing bacterial overgrowth and translocation. Here we explore, with the aid of complementary animal and human experiments, the potential role of FXR in acute pancreatitis.\n\nImpact of global Fxr deficiency on experimental acute pancreatitis and genetic variation in the FXR locus in human acute pancreatitis.", "token_count": 183, "char_count": 754, "word_count": 106, "semantic_coherence": 1, "information_density": 0.717, "quality_score": 0.8585, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:39.128944", "source": { "split": "train_shard_00000", "doc_id": 4491 }, "chunk_id": "train_shard_00000_4491_0", "global_id": 5017 }, { "text": "This study analyzes the occurrence of bile salt hydrolase in fourteen strains belonging to the genus Bifidobacterium. Deconjugation activity was detected using a plate test, two-step enzymatic reaction and activity staining on a native polyacrylamide gel. Subsequently, bile salt hydrolases from B. pseudocatenulatum and B. longum subsp. suis were purified using a two-step chromatographic procedure. Biochemical characterization of the bile salt hydrolases showed that the purified enzymes hydrolyzed all of the six major human bile salts under the pH and temperature conditions commonly found in the human gastrointestinal tract. Next, the dynamic rheometry was applied to monitor the gelation process of deoxycholic acid under different conditions. The results showed that bile acids displayed aqueous media gelating properties. Finally, gel-forming abilities of bifidobacteria exhibiting bile salt hydrolase activity were analyzed. Our investigations have demonstrated that the release of deconjugated bile acids led to the gelation phenomenon of the enzymatic reaction solution containing purified BSH. The presented results suggest that bile salt hydrolase activity commonly found among intestinal microbiota increases hydrogel-forming abilities of certain bile salts. To our knowledge, this is the first report showing that bile salt hydrolase activity among Bifidobacterium is directly connected with the gelation process of bile salts. In our opinion, if such a phenomenon occurs in physiological conditions of human gut, it may improve bacterial ability to colonize the gastrointestinal tract and their survival in this specific ecological niche.\n\nA new insight into the physiological role of bile salt hydrolase among intestinal bacteria from the genus Bifidobacterium.", "token_count": 413, "char_count": 1780, "word_count": 250, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:39.749352", "source": { "split": "train_shard_00000", "doc_id": 4492 }, "chunk_id": "train_shard_00000_4492_0", "global_id": 5018 }, { "text": "We investigated the probiotic properties of Lactobacillus acidophilus NS1, such as acid resistance, bile tolerance, adherence to HT-29 cells, and cholesterol assimilation activity. In an animal study, 7-wk-old male C57BL/6 mice were fed a normal diet, a high-fat diet (HFD), or an HFD with L. acidophilus NS1 (ca. 1.0×10(8) cfu/mL) for 10 wk. Total cholesterol and low-density lipoprotein (LDL) cholesterol levels were significantly lower in mice fed an HFD with L. acidophilus NS1 than in those fed an HFD only, whereas high-density lipoprotein cholesterol levels were similar between these 2 groups. To understand the mechanism of the cholesterol-lowering effect of L. acidophilus NS1 on the HFD-mediated increase in plasma cholesterol levels, we determined mRNA levels of genes involved in cholesterol homeostasis in the liver. Expression of sterol regulatory element-binding protein 2 (Srebp2) and LDL receptor (Ldlr) in the liver was dramatically reduced in mice fed a HFD compared with those fed a normal diet. When L. acidophilus NS1 was administered orally to HFD-fed mice, an HFD-induced suppression of Srebp2 and Ldlr expression in the liver was abolished. These results suggest that the oral administration of L. acidophilus NS1 to mice fed an HFD increased the expression of Srebp2 and Ldlr in the liver, which was inhibited by high fat intake, thus leading to a decrease in plasma cholesterol levels. Lactobacillus acidophilus NS1 could be a useful probiotic microorganism for cholesterol-lowering dairy products and the improvement of hyperlipidemia and hepatic lipid metabolism.\n\nEffect of Lactobacillus acidophilus NS1 on plasma cholesterol levels in diet-induced obese mice.", "token_count": 500, "char_count": 1691, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5433, "quality_score": 0.7717, "entities": { "genes": [ "NS1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:40.402286", "source": { "split": "train_shard_00000", "doc_id": 4493 }, "chunk_id": "train_shard_00000_4493_0", "global_id": 5019 }, { "text": "Intracellular lipid binding proteins (iLBPs) are a family of evolutionarily related small cytoplasmic proteins implicated in the transcellular transport of lipophilic ligands. Subfamily-II iLBPs include the liver fatty acid binding protein (L-FABP), and the ileal and the liver and ileal bile acid binding proteins (L-BABP and I-BABP). Atomic-level investigations during the past 15-20 years have delivered relevant information on bile acid binding by this protein group, revealing unique features including binding cooperativity, promiscuity, and site selectivity. Using NMR spectroscopy and other biophysical techniques, our laboratories have contributed to an understanding of the molecular determinants of some of these properties and their generality among proteins from different animal species. We focused especially on formation of heterotypic complexes, considering the mixed compositions of physiological bile acid pools. Experiments performed with synthetic bile acid derivatives showed that iLBPs could act as targets for cell-specific contrast agents and, more generally, as effective carriers of amphiphilic drugs. This review collects the major findings related to bile salt interactions with iLBPs aiming to provide keys for a deeper understanding of protein-mediated intracellular bile salt trafficking.\n\nThe unique ligand binding features of subfamily-II iLBPs with respect to bile salts and related drugs.", "token_count": 336, "char_count": 1424, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:40.976417", "source": { "split": "train_shard_00000", "doc_id": 4494 }, "chunk_id": "train_shard_00000_4494_0", "global_id": 5020 }, { "text": "Drug-induced liver injury has been observed in patients treated with the endothelin receptor antagonists sitaxentan and bosentan, but not following treatment with ambrisentan. The aim of our studies was to assess the possible role of multiple contributory mechanisms in this clinically relevant toxicity. Inhibition of the bile salt export pump (BSEP) and multidrug resistance-associated protein 2 was quantified using membrane vesicle assays. Inhibition of mitochondrial respiration in human liver-derived HuH-7 cells was determined using a Seahorse XF(e96) analyzer. Cytochrome P450 (P450)-independent and P450-mediated cell toxicity was assessed using transfected SV40-T-antigen-immortalized human liver epithelial (THLE) cell lines. Exposure-adjusted assay ratios were calculated by dividing the maximum human drug plasma concentrations by the IC50 or EC50 values obtained in vitro. Covalent binding (CVB) of radiolabeled drugs to human hepatocytes was quantified, and CVB body burdens were calculated by adjusting CVB values for fractional drug turnover in vitro and daily therapeutic dose. Sitaxentan exhibited positive exposure-adjusted signals in all five in vitro assays and a high CVB body burden. Bosentan exhibited a positive exposure-adjusted signal in one assay (BSEP inhibition) and a moderate CVB body burden. Ambrisentan exhibited no positive exposure-adjusted assay signals and a low CVB body burden. These data indicate that multiple mechanisms contribute to the rare, but potentially severe liver injury caused by sitaxentan in humans; provide a plausible rationale for the markedly lower propensity of bosentan to cause liver injury; and highlight the relative safety of ambrisentan.\n\nMultiple compound-related adverse properties contribute to liver injury caused by endothelin receptor antagonists.", "token_count": 458, "char_count": 1820, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [ "EC50", "IC50", "SV40" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:41.615673", "source": { "split": "train_shard_00000", "doc_id": 4495 }, "chunk_id": "train_shard_00000_4495_0", "global_id": 5021 }, { "text": "Three transporter genes including Kluyveromyces marxianus aquaglyceroporin gene (KmFPS1), Candida intermedia glucose/xylose facilitator gene (CiGXF1) or glucose/xylose symporter gene (CiGXS1) were over-expressed in K. marxianus YZJ017 to improve xylitol production at elevated temperatures. The xylitol production of YZJ074 that harbored CiGXF1 was improved to 147.62g/L in Erlenmeyer flask at 42°C. In fermenter, 99.29 and 149.60g/L xylitol were produced from 99.55 and 151.91g/L xylose with productivity of 4.14 and 3.40g/L/h respectively at 42°C. Even at 45°C, YZJ074 could produce 101.30g/L xylitol from 101.41g/L xylose with productivity of 2.81g/L/h. Using fed-batch fermentation through repeatedly adding non-sterilized substrate directly, YZJ074 could produce 312.05g/L xylitol which is the highest yield reported to date. The engineered strains YZJ074 which can produce xylitol at elevated temperatures is an excellent foundation for xylitol bioconversion.\n\nImproving xylitol production at elevated temperature with engineered Kluyveromyces marxianus through over-expressing transporters.", "token_count": 396, "char_count": 1097, "word_count": 140, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [ "YZJ074", "YZJ017" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:42.234647", "source": { "split": "train_shard_00000", "doc_id": 4496 }, "chunk_id": "train_shard_00000_4496_0", "global_id": 5022 }, { "text": "Determination of fluxes by (13)C tracer experiments depends on monitoring the (13)C labeling pattern of metabolites during isotope experiments. In metabolome-based (13)C metabolic flux analysis, liquid chromatography combined with mass spectrometry or tandem mass spectrometry (LC/MS or LC/MS/MS, respectively) has been mainly used as an analytical platform for isotope pattern studies of central carbon metabolites. However, gas chromatography with mass spectrometry (GC/MS) has several advantages over LC/MS, such as high sensitivity, low cost, ease of operation, and availability of mass spectra databases for comparison. In this study, analysis of isotope pattern for central carbon metabolites using GC/MS was demonstrated. First, a proper set of mass ions for central carbon metabolites was selected based on carbon backbone information and structural isomers of mass fragment ions. A total of 34 mass fragment ions was selected and used for the quantification of 25 central carbon metabolites. Then, to quantify isotope fractions, a natural mass isotopomer library for selected mass fragment ions was constructed and subtracted from isotopomer mass spectra data. The results revealed a surprisingly high abundance of partially labeled (13)C intermediates, such as 56.4% of fructose 6-phosphate and 47.6% of dihydroxyacetone phosphate at isotopic steady state, which were generated in the pentose phosphate pathway. Finally, dynamic changes of isotope fragments of central metabolites were monitored with a U-(13)C glucose stimulus response experiment in Kluyveromyces marxianus. With a comprehensive study of isotope patterns of central carbon metabolites using GC/MS, 25 central carbon metabolites and their isotopic fractions were successfully quantified. Dynamic and precise acquisition of isotope pattern can then be used in combination with proper kinetic models to calculate metabolic fluxes.\n\nIsotope labeling pattern study of central carbon metabolites using GC/MS.", "token_count": 488, "char_count": 1980, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5504, "quality_score": 0.7752, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:42.884568", "source": { "split": "train_shard_00000", "doc_id": 4497 }, "chunk_id": "train_shard_00000_4497_0", "global_id": 5023 }, { "text": "The taxonomic diversity of forty-two Rhizobium strains, isolated from nodules of faba bean grown in Egypt, was studied using 16S rRNA sequencing, multilocus sequence analyses (MLSA) of three chromosomal housekeeping loci and one nodulation gene (nodA). Based on the 16S rRNA gene sequences, most of the strains were related to Rhizobium leguminosarum, Rhizobium etli, and Rhizobium radiobacter (syn. Agrobacterium tumefaciens). A maximum likelihood (ML) tree built from the concatenated sequences of housekeeping proteins encoded by glnA, gyrB and recA, revealed the existence of three distinct genospecies (I, II and III) affiliated to the defined species within the genus Rhizobium/Agrobacterium. Seventeen strains in genospecies I could be classified as R. leguminosarum sv. viciae. Whereas, a single strain of genospecies II was linked to R. etli. Interestingly, twenty-four strains of genospecies III were identified as A. tumefaciens. Strains of R. etli and A. tumefaciens have been shown to harbor the nodA gene and formed effective symbioses with faba bean plants in Leonard jar assemblies. In the nodA tree, strains belonging to the putative genospecies were closely related to each other and were clustered tightly to R. leguminosarum sv. viciae, supporting the hypothesis that symbiotic and core genome of the species have different evolutionary histories and indicative of horizontal gene transfer among these rhizobia.\n\nPhylogenetic multilocus sequence analysis of native rhizobia nodulating faba bean (Vicia faba L.) in Egypt.", "token_count": 421, "char_count": 1540, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:43.510016", "source": { "split": "train_shard_00000", "doc_id": 4498 }, "chunk_id": "train_shard_00000_4498_0", "global_id": 5024 }, { "text": "The discordant prevalence of Helicobacter pylori and its related diseases, for a long time, fostered certain enigmatic situations observed in the countries of the southern world. Variation in H. pylori infection rates and disease outcomes among different populations in multi-ethnic Malaysia provides a unique opportunity to understand dynamics of host-pathogen interaction and genome evolution. In this study, we extensively analyzed and compared genomes of 27 Malaysian H. pylori isolates and identified three major phylogeographic lineages: hspEastAsia, hpEurope and hpSouthIndia. The analysis of the virulence genes within the core genome, however, revealed a comparable pathogenic potential of the strains. In addition, we identified four genes limited to strains of East-Asian lineage. Our analyses identified a few strain-specific genes encoding restriction modification systems and outlined 311 core genes possibly under differential evolutionary constraints, among the strains representing different ethnic groups. The cagA and vacA genes also showed variations in accordance with the host genetic background of the strains. Moreover, restriction modification genes were found to be significantly enriched in East-Asian strains. An understanding of these variations in the genome content would provide significant insights into various adaptive and host modulation strategies harnessed by H. pylori to effectively persist in a host-specific manner.\n\nComparative genomic analysis of Helicobacter pylori from Malaysia identifies three distinct lineages suggestive of differential evolution.", "token_count": 335, "char_count": 1597, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:44.080825", "source": { "split": "train_shard_00000", "doc_id": 4499 }, "chunk_id": "train_shard_00000_4499_0", "global_id": 5025 }, { "text": "Cholesterol metabolism is closely interrelated with cardiovascular disease in humans. Dietary supplementation with omega-6 polyunsaturated fatty acids including arachidonic acid (AA) was shown to favorably affect plasma LDL-C and HDL-C. However, the underlying mechanisms are poorly understood. By combining data from a GWAS screening in >100,000 individuals of European ancestry, mediator lipidomics, and functional validation studies in mice, we identify the AA metabolome as an important regulator of cholesterol homeostasis. Pharmacological modulation of AA metabolism by aspirin induced hepatic generation of leukotrienes (LTs) and lipoxins (LXs), thereby increasing hepatic expression of the bile salt export pump Abcb11. Induction of Abcb11 translated in enhanced reverse cholesterol transport, one key function of HDL. Further characterization of the bioactive AA-derivatives identified LX mimetics to lower plasma LDL-C. Our results define the AA metabolomeasconserved regulator of cholesterol metabolism, and identify AA derivatives as promising therapeutics to treat cardiovascular disease in humans.\n\nThe arachidonic acid metabolome serves as a conserved regulator of cholesterol metabolism.", "token_count": 306, "char_count": 1203, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7044, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:44.648478", "source": { "split": "train_shard_00000", "doc_id": 4500 }, "chunk_id": "train_shard_00000_4500_0", "global_id": 5026 }, { "text": "A rare case of bloodstream infection caused by Candida kefyr is described. The diagnosis was established by repeatedly isolating the yeast in blood cultures and by detecting C. kefyr-specific DNA in serum samples. Demonstration of elevated serum levels of β-D-glucan and Candida mannan also provided additional diagnostic evidence. The identity of the isolates was confirmed by PCR sequencing of the ITS region of rDNA. This is the first report of C. kefyr candidemia from Kuwait and the Middle East. The report highlights emerging clinical significance of rare Candida spp. in etiology of candidemia and reinforces the adjunctive role of biomarkers in diagnosis.\n\nCandida kefyr as a cause of bloodstream infection and adjunctive role of biomarkers in its diagnosis.", "token_count": 192, "char_count": 766, "word_count": 118, "semantic_coherence": 1, "information_density": 0.5763, "quality_score": 0.7881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:45.445155", "source": { "split": "train_shard_00000", "doc_id": 4501 }, "chunk_id": "train_shard_00000_4501_0", "global_id": 5027 }, { "text": "The human body normally lives in symbiosis with a considerable microscopic environment present on all interfaces with the external environment; it hosts ten times more microbes (microbiota) that it has somatic or germ cells, representing a gene diversity (microbiome) 100-150 times higher than the human genome. These germs are located mainly in the gut, where they represent a mass of about one kilogram. The primary colonization of the gastrointestinal tract depends on the delivery route, the bacterial flora rewarding then depending on the environment, food hygiene, medical treatments. The intestinal microbiota plays an important role in the maturation of the immune system and in different physiological functions: digestion of polysaccharides, glycosaminoglycans and glycoproteins, vitamins biosynthesis, bile salt metabolism of some amino acids and xenobiotics. Quantitative and qualitative changes in the microbiota are observed in a wide range of diseases: obesity, colorectal cancer, liver cancer, inflammatory bowel disease, autoimmune diseases, allergies... pharmacobiotics aim to modify the intestinal microbiota in a therapeutic goal and this by various means: prebiotics, probiotics, antibiotics or fecal transplants. Intestinal flora also plays a direct role in the metabolism of certain drugs and the microbiota should be considered as a predictive parameter of response to some chemotherapies.\n\n[Intestinal microbiota].", "token_count": 359, "char_count": 1439, "word_count": 202, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:46.023619", "source": { "split": "train_shard_00000", "doc_id": 4502 }, "chunk_id": "train_shard_00000_4502_0", "global_id": 5028 }, { "text": "The INU1 gene encoding an exo-inulinase from the marine-derived yeast Candida membranifaciens subsp. flavinogenie W14-3 was cloned and characterized. It had an open reading frame of 1,536 bp long encoding an inulinase. The coding region of it was not interrupted by any intron. The cloned gene encoded 512 amino acid residues of a protein with a putative signal peptide of 23 amino acids and a calculated molecular mass of 57.8 kDa. The protein sequence deduced from the inulinase gene contained the inulinase consensus sequences (WMNDPNGL), (RDP), ECP FS and Q. The protein also had six conserved putative N-glycosylation sites. The deduced inulinase from the yeast strain W14-3 was found to be closely related to that from Candida kutaonensis sp. nov. KRF1, Kluyveromyces marxianus, and Cryptococcus aureus G7a. The inulinase gene with its signal peptide encoding sequence was subcloned into the pMIRSC11 expression vector and expressed in Saccharomyces sp. W0. The recombinant yeast strain W14-3-INU-112 obtained could produce 16.8 U/ml of inulinase activity and 12.5 % (v/v) ethanol from 250 g/l of inulin within 168 h. The monosaccharides were detected after the hydrolysis of inulin with the crude inulinase (the yeast culture). All the results indicated that the cloned gene and the recombinant yeast strain W14-3-INU-112 had potential applications in biotechnology.\n\nCloning and characterization of an inulinase gene from the marine yeast Candida membranifaciens subsp. flavinogenie W14-3 and its expression in Saccharomyces sp. W0 for ethanol production.", "token_count": 473, "char_count": 1563, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5636, "quality_score": 0.7818, "entities": { "genes": [ "KRF1", "INU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:46.711383", "source": { "split": "train_shard_00000", "doc_id": 4503 }, "chunk_id": "train_shard_00000_4503_0", "global_id": 5029 }, { "text": "The aim of the present work was to investigate the in situ rheological behavior of yeast biofilms growing on stainless steel under static and turbulent flow. The species used (Rhodototula mucilaginosa, Candida krusei, Candida kefyr and Candida tropicalis) were isolated from a clarified apple juice industry. The flow conditions impacted biofilm composition over time, with a predominance of C. krusei under static and turbulent flow. Likewise, structural variations occurred, with a tighter appearance under dynamic flow. Under turbulent flow there was an increase of 112 μm in biofilm thickness at 11 weeks (p < 0.001) and cell morphology was governed by hyphal structures and rounded cells. Using the in situ growth method introduced here, yeast biofilms were determined to be viscoelastic materials with a predominantly solid-like behavior, and neither this nor the G'0 values were significantly affected by the flow conditions or the growth time, and at large deformations their weak structure collapsed beyond a critical strain of about 1.5-5%. The present work could represent a starting point for developing in situ measurements of yeast rheology and contribute to a thin body of knowledge about fungal biofilm formation.\n\nIn situ rheology of yeast biofilms.", "token_count": 299, "char_count": 1266, "word_count": 194, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:47.301129", "source": { "split": "train_shard_00000", "doc_id": 4504 }, "chunk_id": "train_shard_00000_4504_0", "global_id": 5030 }, { "text": "The properties of bicelles composed of mixtures of long-chain lipids dimyristoylphosphatidylcholine (DMPC) and dimyristoylphosphatidylglycerol (DMPG), stabilized by zwitterionic bile salt analogue 3-[(3-cholamidopropyl)dimethyl-d6-ammonio]-2-hydroxy-1-propanesulfonate (CHAPSO-d6), deuterated at both amino methyls, were investigated by a combination of (31)P and (2)H NMR, focusing on the behavior of CHAPSO as a function of temperature. For compositions of molar ratio q = [DMPC + DMPG]/[CHAPSO] = 3, R = [DMPG]/[DMPC + DMPG] = 0, 0.01 and 0.10 and lipid concentration CL = 25 wt % lipid at temperatures of between 30 and 60 °C, magnetic alignment was readily achieved as assessed via both (31)P NMR of the phospholipids and (2)H NMR of CHAPSO-d6. Increasing temperature yielded higher values for the chemical shift anisotropy of the former and the quadrupole splitting of the latter, consistent with the progressive migration of CHAPSO from edge regions into planar regions of the bicellar assemblies. However, relative to dihexadecyl phosphatidylcholine (DHPC), CHAPSO exhibited lower miscibility with DMPC, although the presence of DMPG enhanced this miscibility. At 65 °C, thermal instability became evident in the appearance of a separate isotropic component in both (31)P and (2)H NMR spectra. This isotropic phase was CHAPSO-enriched but less so as a function of increasing DMPG. These findings indicate that the enhanced thermal stability of CHAPSO- versus DHPC-containing bicelles arises from a combination of the larger surface area that edge CHAPSO is able to mask, mole for mole, and its relative preference for edge regions, plus, possibly, specific interactions with DMPG.", "token_count": 512, "char_count": 1688, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:47.984405", "source": { "split": "train_shard_00000", "doc_id": 4505 }, "chunk_id": "train_shard_00000_4505_0", "global_id": 5031 }, { "text": "Thermal stabilization of bicelles by a bile-salt-derived detergent: a combined ³¹P and ²H nuclear magnetic resonance study.", "token_count": 38, "char_count": 123, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:48.383037", "source": { "split": "train_shard_00000", "doc_id": 4505 }, "chunk_id": "train_shard_00000_4505_1", "global_id": 5032 }, { "text": "Inhibition of the bile salt export pump (BSEP) has been linked to incidence of drug-induced liver injury (DILI), presumably by the accumulation of toxic bile acids in the liver. We have previously constructed and validated a model of bile acid disposition within DILIsym®, a mechanistic model of DILI. In this paper, we use DILIsym® to simulate the DILI response of the hepatotoxic BSEP inhibitors bosentan and CP-724,714 and the non-hepatotoxic BSEP inhibitor telmisartan in humans in order to explore whether we can predict that hepatotoxic BSEP inhibitors can cause bile acid accumulation to reach toxic levels. We also simulate bosentan in rats in order to illuminate potential reasons behind the lack of toxicity in rats compared to the toxicity observed in humans. DILIsym® predicts that bosentan, but not telmisartan, will cause mild hepatocellular ATP decline and serum ALT elevation in a simulated population of humans. The difference in hepatotoxic potential between bosentan and telmisartan is consistent with clinical observations. However, DILIsym® underpredicts the incidence of bosentan toxicity. DILIsym® also predicts that bosentan will not cause toxicity in a simulated population of rats, and that the difference between the response to bosentan in rats and in humans is primarily due to the less toxic bile acid pool in rats. Our simulations also suggest a potential synergistic role for bile acid accumulation and mitochondrial electron transport chain (ETC) inhibition in producing the observed toxicity in CP-724,714, and suggest that CP-724,714 metabolites may also play a role in the observed toxicity. Our work also compares the impact of competitive and noncompetitive BSEP inhibition for CP-724,714 and demonstrates that noncompetitive inhibition leads to much greater bile acid accumulation and potential toxicity. Our research demonstrates the potential for mechanistic modeling to contribute to the understanding of how bile acid transport inhibitors cause DILI.", "token_count": 511, "char_count": 1993, "word_count": 298, "semantic_coherence": 1, "information_density": 0.453, "quality_score": 0.7265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:49.017784", "source": { "split": "train_shard_00000", "doc_id": 4506 }, "chunk_id": "train_shard_00000_4506_0", "global_id": 5033 }, { "text": "Exploring BSEP inhibition-mediated toxicity with a mechanistic model of drug-induced liver injury.", "token_count": 25, "char_count": 98, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:49.380492", "source": { "split": "train_shard_00000", "doc_id": 4506 }, "chunk_id": "train_shard_00000_4506_1", "global_id": 5034 }, { "text": "The prokaryotic pangenome partitions genes into core and dispensable genes. The order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. Based on data from 30 species, including 425 genomes from six phyla, we grouped core genes into syntenic blocks in the context of a pangenome according to their stability across multiple isolates. A subset of the core genes, often species specific and lineage associated, formed a core-gene-defined genome organizational framework (cGOF). Such cGOFs are either single segmental (one-third of the species analyzed) or multisegmental (the rest). Multisegment cGOFs were further classified into symmetric or asymmetric according to segment orientations toward the origin-terminus axis. The cGOFs in Gram-positive species are exclusively symmetric and often reversible in orientation, as opposed to those of the Gram-negative bacteria, which are all asymmetric and irreversible. Meanwhile, all species showing strong strand-biased gene distribution contain symmetric cGOFs and often specific DnaE (α subunit of DNA polymerase III) isoforms. Furthermore, functional evaluations revealed that cGOF genes are hub associated with regard to cellular activities, and the stability of cGOF provides efficient indexes for scaffold orientation as demonstrated by assembling virtual and empirical genome drafts. cGOFs show species specificity, and the symmetry of multisegmental cGOFs is conserved among taxa and constrained by DNA polymerase-centric strand-biased gene distribution. The definition of species-specific cGOFs provides powerful guidance for genome assembly and other structure-based analysis.\n\nFlexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks.", "token_count": 453, "char_count": 1965, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6212, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:50.021062", "source": { "split": "train_shard_00000", "doc_id": 4507 }, "chunk_id": "train_shard_00000_4507_0", "global_id": 5035 }, { "text": "Before use in practice, it is necessary to precisely identify and characterize a new probiotic candidate. Eight animal lactobacilli and collection strain Lactobacillus reuteri CCM 3625 were studied from the point of saccharide fermentation profiles, bile salt resistance, antibiogram profiles, and influence of bile on sensitivity to antibiotics. Studied lactobacilli differed in their sugar fermentation ability determined by API 50CHL and their identification based on these profiles did not correspond with molecular-biological one in most cases. Survival of strains Lactobacillus murinus C and L. reuteri KO4b was not affected by presence of bile. The resistance of genus Lactobacillus to vancomycin and quinolones (ofloxacin, ciprofloxacin) was confirmed in all strains tested. This study provides the new information about oxgall (0.5 and 1 %) effect on the lactobacilli antibiotic susceptibility. Antibiotic profiles were not noticeably affected, and both bile concentrations tested had comparable impact on the lactobacilli antibiotic sensitivity. Interesting change was noticed in L. murinus C, where the resistance to cephalosporins was reverted to susceptibility. Similarly, susceptibility of L. reuteri E to ceftazidime arose after incubation in both concentration of bile. After influence of 1 % bile, Lactobacillus mucosae D lost its resistance to gentamicin. On the base of gained outcomes, the best probiotic properties manifested L. reuteri KO4b, Lactobacillus plantarum KG4, and L. reuteri E due to their survival in the presence of bile.\n\nBile tolerance and its effect on antibiotic susceptibility of probiotic Lactobacillus candidates.", "token_count": 444, "char_count": 1655, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5763, "quality_score": 0.7881, "entities": { "genes": [ "KG4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:50.651761", "source": { "split": "train_shard_00000", "doc_id": 4508 }, "chunk_id": "train_shard_00000_4508_0", "global_id": 5036 }, { "text": "In prokaryotic species equipped with glycogen metabolism machinery, the co-regulation of glycogen biosynthesis and degradation has been associated with the synthesis of energy storage compounds and various crucial physiological functions, including global cellular processes such as carbon and nitrogen metabolism, energy sensing and production, stress response and cell-cell communication. In addition, the glycogen metabolic pathway was proposed to serve as a carbon capacitor that regulates downstream carbon fluxes, and in some microorganisms the ability to synthesize intracellular glycogen has been implicated in host persistence. Among lactobacilli, complete glycogen metabolic pathway genes are present only in select species predominantly associated with mammalian hosts or natural environments. This observation highlights the potential involvement of glycogen biosynthesis in probiotic activities and persistence of intestinal lactobacilli in the human gastrointestinal tract. In this review, we summarize recent findings on (i) the presence and potential ecological distribution of glycogen metabolic pathways among lactobacilli, (ii) influence of carbon substrates and growth phases on glycogen metabolic gene expression and glycogen accumulation in L. acidophilus, and (iii) the involvement of glycogen metabolism on growth, sugar utilization and bile tolerance. Our present in vivo studies established the significance of glycogen biosynthesis on the competitive retention of L. acidophilus in the mouse intestinal tract, demonstrating for the first time that the ability to synthesize intracellular glycogen contributes to gut fitness and retention among probiotic microorganisms.\n\nInsights into glycogen metabolism in Lactobacillus acidophilus: impact on carbohydrate metabolism, stress tolerance and gut retention.", "token_count": 443, "char_count": 1832, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5851, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:51.291525", "source": { "split": "train_shard_00000", "doc_id": 4509 }, "chunk_id": "train_shard_00000_4509_0", "global_id": 5037 }, { "text": "The use of probiotics as food components combats not only cardiovascular diseases but also many gastrointestinal tract disorders. Their health benefits along with their increased global market have interested scientists for better formulation and appropriate administration to the consumers. However, the lack of clear elucidation of their cholesterol-lowering mechanisms has complicated their proper dosage and administration to the beneficiaries. In this review, proposed mechanisms of cholesterol reduction such as deconjugation of bile via bile salt hydrolase activity, binding of cholesterol to probiotic cellular surface and incorporation into their cell membrane, production of SCFAs from oligosaccharides, coprecipitation of cholesterol with deconjugated bile, and cholesterol conversion to coprostanol have been discussed. Also, hypocholesterolemic effects on human- and animal-trial results, commonly used probiotics and synbiotics with effect on serum cholesterol regulation, types of bile salt hydrolase genes, and substrate specificities have been discussed.\n\nThe perspective on cholesterol-lowering mechanisms of probiotics.", "token_count": 261, "char_count": 1138, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6735, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:51.841965", "source": { "split": "train_shard_00000", "doc_id": 4510 }, "chunk_id": "train_shard_00000_4510_0", "global_id": 5038 }, { "text": "Kluyveromyces marxianus is emerging as a new platform organism for the production of flavour and fragrance (F&F) compounds. This food-grade yeast has advantageous traits, such as thermotolerance and rapid growth, that make it attractive for cell factory applications. The major impediment to its development has been limited fundamental knowledge of its genetics and physiology, but this is rapidly changing. K. marxianus produces a wide array of volatile molecules and contributes to the flavour of a range of different fermented beverages. Advantage is now being taken of this to develop strains for the production of metabolites such as 2-phenylethanol and ethyl acetate. Strains that were selected from initial screens were used to optimize processes for production of these F&F molecules. Most developments have focused on optimizing growth conditions and the fermentation process, including product removal, with future advancement likely to involve development of new strains through the application of evolutionary or rational engineering strategies. This is being facilitated by new genomic and molecular tools. Furthermore, synthetic biology offers a route to introduce new biosynthetic pathways into this yeast for F&F production. Consumer demand for biologically-synthesized molecules for use in foods and other products creates an opportunity to exploit the unique potential of K. marxianus for this cell factory application.\n\nCell factory applications of the yeast Kluyveromyces marxianus for the biotechnological production of natural flavour and fragrance molecules.", "token_count": 347, "char_count": 1582, "word_count": 226, "semantic_coherence": 1, "information_density": 0.615, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:52.418661", "source": { "split": "train_shard_00000", "doc_id": 4511 }, "chunk_id": "train_shard_00000_4511_0", "global_id": 5039 }, { "text": "Primary biliary cirrhosis (PBC) is a chronic and progressive cholestasis liver disease. Bile salt export pump (BSEP) is the predominant bile salt efflux system of hepatocytes. BSEP gene has been attached great importance in the susceptibility of PBC and the response rate of ursodeoxycholic acid (UDCA) treatment of PBC patients.\n\nThe association between bile salt export pump single-nucleotide polymorphisms and primary biliary cirrhosis susceptibility and ursodeoxycholic acid response.", "token_count": 127, "char_count": 488, "word_count": 68, "semantic_coherence": 1, "information_density": 0.6618, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:52.810714", "source": { "split": "train_shard_00000", "doc_id": 4512 }, "chunk_id": "train_shard_00000_4512_0", "global_id": 5040 }, { "text": "The lactating human mammary gland and the pancreas both produce bile salt-stimulated lipase (BSSL), a lipolytic enzyme acting on a wide range of substrates, including triglyceride, cholesterol esters, and fat-soluble vitamins esters. Breast milk BSSL has a particularly important role in the digestion of milk fat by newborn infants. We report the generation of transgenic mice that harbored a human BSSL gene controlled by a mammary gland-specific promoter. BSSL levels in transgenic mouse milk were raised to 376.8 μg/ml, corresponding to an activity of 9.15 U/ml. Premature wild-type neonates nursed by transgenic dams exhibited significantly higher survival rate than did the control neonates nursed by wild dams (95 vs. 83.3 % and, P < 0.05). They also showed 43.8 % greater body weight gain and 33.3 % lesser fecal crude fat levels than did the controls. This study provides significant evidence that increased levels of BSSL in milk may reduce mortality and improve the growth and fat absorption in premature mice during neonatal development.\n\nTransgenic mouse milk expressing human bile salt-stimulated lipase improves the survival and growth status of premature mice.", "token_count": 322, "char_count": 1176, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6575, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:53.379605", "source": { "split": "train_shard_00000", "doc_id": 4513 }, "chunk_id": "train_shard_00000_4513_0", "global_id": 5041 }, { "text": "The symptoms of Clostridium difficile infection are caused by two closely related toxins, TcdA and TcdB, which are encoded by the 19.6 kb Pathogenicity Locus (PaLoc). The PaLoc is variably present among strains, and in this respect it resembles a mobile genetic element. The C. difficile population structure consists mainly of five phylogenetic clades designated 1-5. Certain genotypes of clade 5 are associated with recently emergent highly pathogenic strains causing human disease and animal infections. The aim of this study was to explore the evolutionary history of the PaLoc in C. difficile clade 5. Phylogenetic analyses and annotation of clade 5 PaLoc variants and adjoining genomic regions were undertaken using a representative collection of toxigenic and nontoxigenic strains. Comparison of the core genome and PaLoc phylogenies obtained for clade 5 and representatives of the other clades identified two distinct PaLoc acquisition events, one involving a toxin A(+)B(+) PaLoc variant and the other an A(-)B(+) variant. Although the exact mechanism of each PaLoc acquisition is unclear, evidence of possible homologous recombination with other clades and between clade 5 lineages was found within the PaLoc and adjacent regions. The generation of nontoxigenic variants by PaLoc loss via homologous recombination with PaLoc-negative members of other clades was suggested by analysis of cdu2, although none is likely to have occurred recently. A variant of the putative holin gene present in the clade 5 A(-)B(+) PaLoc was likely acquired via allelic exchange with an unknown element. Fine-scale phylogenetic analysis of C. difficile clade 5 revealed the extent of its genetic diversity, consistent with ancient evolutionary origins and a complex evolutionary history for the PaLoc.\n\nThe complexity and diversity of the Pathogenicity Locus in Clostridium difficile clade 5.", "token_count": 469, "char_count": 1883, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5426, "quality_score": 0.7713, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:54.026286", "source": { "split": "train_shard_00000", "doc_id": 4514 }, "chunk_id": "train_shard_00000_4514_0", "global_id": 5042 }, { "text": "Understanding behavior of rare-earth ions (REI) in crowded environments is crucial for several nano- and bio-technological applications. Evolution of REI photoluminescence (PL) in small compartments inside a silica hydrogel, mimic to a soft matter bio-environment, has been studied and explained within a solvation model. The model uncovered the origin of high PL efficiency to be the formation of REI complexes, surrounded by bile salt (DOC) molecules. Comparative study of these REI-DOC complexes in bulk water solution and those enclosed inside the hydrogel revealed a strong correlation between an up to 5×-longer lifetime of REIs and appearance of the DOC ordered phase, further confirmed by dynamics of REI solvation shells, REI diffusion experiments and morphological characterization of microstructure of the hydrogel.\n\nFormation and dynamics of \"waterproof\" photoluminescent complexes of rare earth ions in crowded environment.", "token_count": 219, "char_count": 936, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7015, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:54.497966", "source": { "split": "train_shard_00000", "doc_id": 4515 }, "chunk_id": "train_shard_00000_4515_0", "global_id": 5043 }, { "text": "Bile salt export pump (BSEP) is a transporter expressed exclusively at hepatic canaliculi and drives bile-salt efflux. Minimal data exist about BSEP expression in tumours. We hypothesized that BSEP immunohistochemistry would be specific for hepatocellular carcinoma (HCC).\n\nBile salt export pump: a sensitive and specific immunohistochemical marker of hepatocellular carcinoma.", "token_count": 107, "char_count": 377, "word_count": 50, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:54.882416", "source": { "split": "train_shard_00000", "doc_id": 4516 }, "chunk_id": "train_shard_00000_4516_0", "global_id": 5044 }, { "text": "Here, we present the draft genome sequence of Kluyveromyces marxianus CCT 7735 (UFV-3), including the eight chromosomes and the mitochondrial genomic sequences.\n\nGenomic Sequence of the Yeast Kluyveromyces marxianus CCT 7735 (UFV-3), a Highly Lactose-Fermenting Yeast Isolated from the Brazilian Dairy Industry.", "token_count": 106, "char_count": 311, "word_count": 42, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:55.265008", "source": { "split": "train_shard_00000", "doc_id": 4517 }, "chunk_id": "train_shard_00000_4517_0", "global_id": 5045 }, { "text": "Polysaccharides are prospective hosts for the delivery and sequestration of bioactive guest molecules. Polysaccharides of dietary fiber, specifically cereal (1 → 3)(1 → 4)-β-glucans, play a role in lowering the blood plasma cholesterol level in humans. Direct host-guest interactions between β-glucans and conjugated bile salts are among the possible molecular mechanisms explaining the hypocholesterolemic effects of β-glucans. The present study shows that (1)H-(13)C NMR assays on a time scale of minutes detect minute signal changes in both bile salts and β-glucans, thus indicating dynamic interactions between bile salts and β-glucans. Experiments are consistent with stronger interactions at pH 5.3 than at pH 6.5 in this in vitro assay. The changes in bile salt and β-glucan signals suggest a stabilization of bile salt micelles and concomitant conformational changes in β-glucans.\n\nProbing interactions between β-glucan and bile salts at atomic detail by ¹H-¹³C NMR assays.", "token_count": 276, "char_count": 981, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6503, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:55.813575", "source": { "split": "train_shard_00000", "doc_id": 4518 }, "chunk_id": "train_shard_00000_4518_0", "global_id": 5046 }, { "text": "There are major gaps in the understanding of how genetic variation is generated in the asexual pathogen Verticillium dahliae. On the one hand, V. dahliae is a haploid organism that reproduces clonally. On the other hand, single-nucleotide polymorphisms and chromosomal rearrangements were found between V. dahliae strains. Lineage-specific (LS) regions comprising about 5% of the genome are highly variable between V. dahliae strains. Nonetheless, it is unknown whether horizontal gene transfer plays a major role in generating genetic variation in V. dahliae. Here, we analyzed a previously sequenced V. dahliae population of nine strains from various geographical locations and hosts. We found highly homologous elements in LS regions of each strain; LS regions of V. dahliae strain JR2 are much richer in highly homologous elements than the core genome. In addition, we discovered, in LS regions of JR2, several structural forms of nonhomologous recombination, and two or three homologous sequence types of each form, with almost each sequence type present in an LS region of another strain. A large section of one of the forms is known to be horizontally transferred between V. dahliae strains. We unexpectedly found that 350 kilobases of dynamic LS regions were much more conserved than the core genome between V. dahliae and a closely related species (V. albo-atrum), suggesting that these LS regions were horizontally transferred recently. Our results support the view that genetic variation in LS regions is generated by horizontal transfer between strains, and by chromosomal reshuffling reported previously.\n\nHorizontal transfer generates genetic variation in an asexual pathogen.", "token_count": 412, "char_count": 1690, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5333, "quality_score": 0.7667, "entities": { "genes": [ "JR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:56.429214", "source": { "split": "train_shard_00000", "doc_id": 4519 }, "chunk_id": "train_shard_00000_4519_0", "global_id": 5047 }, { "text": "The cladodes of Opuntia ficus-indica (prickly pear cactus) have a low protein content; for use as a balanced feed, supplementation with other protein sources is therefore desirable. We investigated protein enrichment by cultivation of the yeasts Candida utilis and Kluyveromyces marxianus in an enzymatic hydrolysate of the cladode biomass.\n\nProtein enrichment of an Opuntia ficus-indica cladode hydrolysate by cultivation of Candida utilis and Kluyveromyces marxianus.", "token_count": 132, "char_count": 469, "word_count": 65, "semantic_coherence": 1, "information_density": 0.6615, "quality_score": 0.8308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:56.855570", "source": { "split": "train_shard_00000", "doc_id": 4520 }, "chunk_id": "train_shard_00000_4520_0", "global_id": 5048 }, { "text": "Vibrio cholerae causes human infection through ingestion of contaminated food and water, leading to the devastating diarrheal disease cholera. V. cholerae forms matrix-encased aggregates, known as biofilms, in the native aquatic environment. While the formation of V. cholerae biofilms has been well studied, little is known about the dispersal from biofilms, particularly upon entry into the host. In this study, we found that the exposure of mature biofilms to physiologic levels of the bile salt taurocholate, a host signal for the virulence gene induction of V. cholerae, induces an increase in the number of detached cells with a concomitant decrease in biofilm mass. Scanning electron microscopy micrographs of biofilms exposed to taurocholate revealed an altered, perhaps degraded, appearance of the biofilm matrix. The inhibition of protein synthesis did not alter rates of detachment, suggesting that V. cholerae undergoes a passive dispersal. Cell-free media from taurocholate-exposed biofilms contains a larger amount of free polysaccharide, suggesting an abiotic degradation of biofilm matrix by taurocholate. Furthermore, we found that V. cholerae is only able to induce virulence in response to taurocholate after exit from the biofilm. Thus, we propose a model in which V. cholerae ingested as a biofilm has coopted the host-derived bile salt signal to detach from the biofilm and go on to activate virulence.\n\nHost intestinal signal-promoted biofilm dispersal induces Vibrio cholerae colonization.", "token_count": 396, "char_count": 1513, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:57.472872", "source": { "split": "train_shard_00000", "doc_id": 4521 }, "chunk_id": "train_shard_00000_4521_0", "global_id": 5049 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) cause infections in humans ranging from asymptomatic carriage to bloody diarrhoea and haemolytic uremic syndrome (HUS). Here we present whole genome comparison of Norwegian non-O157 STEC strains with the aim to distinguish between strains with the potential to cause HUS and less virulent strains. Whole genome sequencing and comparisons were performed across 95 non-O157 STEC strains. Twenty-three of these were classified as HUS-associated, including strains from patients with HUS (n = 19) and persons with an epidemiological link to a HUS-case (n = 4). Genomic comparison revealed considerable heterogeneity in gene content across the 95 STEC strains. A clear difference in gene profile was observed between strains with and without the Locus of Enterocyte Effacement (LEE) pathogenicity island. Phylogenetic analysis of the core genome showed high degree of diversity among the STEC strains, but all HUS-associated STEC strains were distributed in two distinct clusters within phylogroup B1. However, non-HUS strains were also found in these clusters. A number of accessory genes were found to be significantly overrepresented among HUS-associated STEC, but none of them were unique to this group of strains, suggesting that different sets of genes may contribute to the pathogenic potential in different phylogenetic STEC lineages. In this study we were not able to clearly distinguish between HUS-associated and non-HUS non-O157 STEC by extensive genome comparisons. Our results indicate that STECs from different phylogenetic backgrounds have independently acquired virulence genes that determine pathogenic potential, and that the content of such genes is overlapping between HUS-associated and non-HUS strains.\n\nComparative genomics to delineate pathogenic potential in non-O157 Shiga toxin-producing Escherichia coli (STEC) from patients with and without haemolytic uremic syndrome (HUS) in Norway.", "token_count": 499, "char_count": 1955, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5484, "quality_score": 0.7742, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:58.126463", "source": { "split": "train_shard_00000", "doc_id": 4522 }, "chunk_id": "train_shard_00000_4522_0", "global_id": 5050 }, { "text": "Metastable and equilibrium phase diagrams for unconjugated bilirubin IXα (UCB) in bile are yet to be determined for understanding the physical chemistry of pigment gallstone formation. Also, UCB is a molecule of considerable biomedical importance because it is a potent antioxidant and an inhibitor of atherogenesis. We employed principally a titrimetric approach to obtain metastable and equilibrium UCB solubilities in model bile systems composed of taurine-conjugated bile salts, egg yolk lecithin (mixed long-chain phosphatidylcholines), and cholesterol as functions of total lipid concentration, biliary pH values, and CaCl2 plus NaCl concentrations. Metastable and equilibrium precipitation pH values were obtained, and average pKa values of the two carboxyl groups of UCB were calculated. Added lecithin and increased temperature decreased UCB solubility markedly, whereas increases in bile salt concentrations and molar levels of urea augmented solubility. A wide range of NaCl and cholesterol concentrations resulted in no specific effects, whereas added CaCl2 produced large decreases in UCB solubilities at alkaline pH values only. UV-visible absorption spectra were consistent with both hydrophobic and hydrophilic interactions between UCB and bile salts that were strongly influenced by pH. Reliable literature values for UCB compositions of native gallbladder biles revealed that biles from hemolytic mice and humans with black pigment gallstones are markedly supersaturated with UCB and exhibit more acidic pH values, whereas biles from nonstone control animals and patients with cholesterol gallstone are unsaturated with UCB.\n\nMetastable and equilibrium phase diagrams of unconjugated bilirubin IXα as functions of pH in model bile systems: Implications for pigment gallstone formation.", "token_count": 443, "char_count": 1803, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5952, "quality_score": 0.7976, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:58.793938", "source": { "split": "train_shard_00000", "doc_id": 4523 }, "chunk_id": "train_shard_00000_4523_0", "global_id": 5051 }, { "text": "Sulfated bile salts function as chemical cues that coordinate reproduction in sea lamprey, Petromyzon marinus. 7α, 12α, 24-trihydroxy-5α-cholan-3-one 24-sulfate (3kPZS) is the most abundant known bile salt released by sexually mature male sea lampreys and attracts ovulated females. However, previous studies showed that the male-produced pheromone consists of unidentified components in addition to 3kPZS. Here, analysis of water conditioned with mature male sea lampreys indicated the presence of 4 oxidized, unsaturated compounds with molecular weights of 466 Da, 468 Da, and 2 of 470 Da. These compounds were not detectable in water conditioned with immature male sea lampreys. By using mass spectrometry, 4 A-ring unsaturated sulfated bile salts were tentatively identified from male washings as 2 4-ene, a 1-ene, and a 1,4-diene analogs. These were synthesized to determine if they attracted ovulated female sea lampreys to spawning nests in natural streams. One of the novel synthetic bile salts, 3 keto-1-ene PZS, attracted ovulated females to the point of application at a concentration of 10(-12) M. This study reveals the structural diversity of bile salts in sea lamprey, some of which have been demonstrated to be pheromonal cues.\n\nInvestigations of novel unsaturated bile salts of male sea lamprey as potential chemical cues.", "token_count": 388, "char_count": 1339, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:44:59.431529", "source": { "split": "train_shard_00000", "doc_id": 4524 }, "chunk_id": "train_shard_00000_4524_0", "global_id": 5052 }, { "text": "Two bacteriophages, RPP1 and RLP1, infecting members of the marine Roseobacter clade were isolated from seawater. Their linear genomes are 74.7 and 74.6 kb and encode 91 and 92 coding DNA sequences, respectively. Around 30% of these are homologous to genes found in Enterobacter phage N4. Comparative genomics of these two new Roseobacter phages and 23 other sequenced N4-like phages (three infecting members of the Roseobacter lineage and 20 infecting other Gammaproteobacteria) revealed that N4-like phages share a core genome of 14 genes responsible for control of gene expression, replication and virion proteins. Phylogenetic analysis of these genes placed the five N4-like roseophages (RN4) into a distinct subclade. Analysis of the RN4 phage genomes revealed they share a further 19 genes of which nine are found exclusively in RN4 phages and four appear to have been acquired from their bacterial hosts. Proteomic analysis of the RPP1 and RLP1 virions identified a second structural module present in the RN4 phages similar to that found in the Pseudomonas N4-like phage LIT1. Searches of various metagenomic databases, including the GOS database, using CDS sequences from RPP1 suggests these phages are widely distributed in marine environments in particular in the open ocean environment.\n\nComparative genomics defines the core genome of the growing N4-like phage genus and identifies N4-like Roseophage specific genes.", "token_count": 373, "char_count": 1429, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5853, "quality_score": 0.7926, "entities": { "genes": [ "RLP1", "RN4", "RPP1", "LIT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:00.058549", "source": { "split": "train_shard_00000", "doc_id": 4525 }, "chunk_id": "train_shard_00000_4525_0", "global_id": 5053 }, { "text": "Integrated Microbial Genomes and Metagenomes (IMG) is a biocomputational system that allows to provide information and support for annotation and comparative analysis of microbial genomes and metagenomes. IMG has been developed by the US Department of Energy (DOE)-Joint Genome Institute (JGI). IMG platform contains both draft and complete genomes, sequenced by Joint Genome Institute and other public and available genomes. Genomes of strains belonging to Archaea, Bacteria, and Eukarya domains are present as well as those of viruses and plasmids. Here, we provide some essential features of IMG system and case study for pangenome analysis.\n\nThe integrated microbial genome resource of analysis.", "token_count": 166, "char_count": 699, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:00.539629", "source": { "split": "train_shard_00000", "doc_id": 4526 }, "chunk_id": "train_shard_00000_4526_0", "global_id": 5054 }, { "text": "The ability to relate genomic differences in bacterial species to their variability in expressed phenotypes is one of the most challenging tasks in today's biology. Such task is of paramount importance towards the understanding of biotechnologically relevant pathways and possibly for their manipulation. Fundamental prerequisites are the genome-wide reconstruction of metabolic pathways and a comprehensive measurement of cellular phenotypes. Cellular pathways can be reliably reconstructed using the KEGG database, while the OmniLog™ Phenotype Microarray (PM) technology may be used to measure nearly 2,000 growth conditions over time. However, few computational tools that can directly link PM data with the gene(s) of interest followed by the extraction of information on gene-phenotype correlation are available. In this chapter the use of the DuctApe software suite is presented, which allows the joint analysis of bacterial genomic and phenomic data, highlighting those pathways and reactions most probably associated with phenotypic variability. A case study on four Sinorhizobium meliloti strains is presented; more example datasets are available online.\n\nFrom pangenome to panphenome and back.", "token_count": 266, "char_count": 1203, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7278, "quality_score": 0.8639, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:01.089087", "source": { "split": "train_shard_00000", "doc_id": 4527 }, "chunk_id": "train_shard_00000_4527_0", "global_id": 5055 }, { "text": "Since the advent of ultra-massive sequencing techniques, the consequent drop-off in both price and time required made feasible the sequencing of increasingly more genomes from microbes belonging to the same taxonomic unit. Eventually, this led to the concept of pangenome, that is, the entire set of genes present in a group of representatives of the same genus/species, which, in turn, can be divided into core genome, defined as the set of those genes present in all the genomes under study, and a dispensable genome, the set of genes possessed only by one or a subset of organism. When analyzing a pangenome, an interesting point is to measure its size, thus estimating the gene repertoire of a given taxonomic group. This is usually performed counting the novel genes added to the overall pangenome when new genomes are sequenced and annotated. A pangenome can be also classified as open or close: in an open pangenome its size increases indefinitely when adding new genomes; thus sequencing additional strains will likely yield novel genes. Conversely, in a close pangenome, adding new genomes will not lead to the discovery of new coding capabilities. A central point in pangenomics is the definition of homology relationships between genes belonging to different genomes. This may turn into the search of those genes with similar sequences between different organisms (and including both paralogous and orthologous genes). In this chapter, methods for finding groups of orthologs between genomes and for estimating the pangenome size are discussed. Also, working codes to address these tasks are provided.\n\nDefining orthologs and pangenome size metrics.", "token_count": 367, "char_count": 1660, "word_count": 261, "semantic_coherence": 1, "information_density": 0.567, "quality_score": 0.7835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:01.674590", "source": { "split": "train_shard_00000", "doc_id": 4528 }, "chunk_id": "train_shard_00000_4528_0", "global_id": 5056 }, { "text": "Different strains of the same organism can share a large amount of their genetic material, the so called core pangenome. Nevertheless, these species can display different lifestyles and it is still not well known to what extent the core pangenome plays a role in the divergence of lifestyles between the two organisms. Here, we present a procedure for uncovering the conservation and divergence of gene expression by using large expression compendia. We will use data from two Salmonella enterica serovar Typhimurium strains as an example here, strain LT2 and strain 14028S, to assess if there are orthologous gene pairs with different expression domains related in both strains.\n\nComparative analysis of gene expression: uncovering expression conservation and divergence between Salmonella enterica serovar Typhimurium strains LT2 and 14028S.", "token_count": 199, "char_count": 843, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6508, "quality_score": 0.8254, "entities": { "genes": [ "LT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:02.123290", "source": { "split": "train_shard_00000", "doc_id": 4529 }, "chunk_id": "train_shard_00000_4529_0", "global_id": 5057 }, { "text": "Mitochondria frequently change their shape through fission and fusion in response to physiological stimuli as well as pathological insults. Disrupted mitochondrial morphology has been observed in cholestatic liver disease. However, the role of mitochondrial shape change in cholestasis is not defined. In this study, using in vitro and in vivo models of bile acid-induced liver injury, we investigated the contribution of mitochondrial morphology to the pathogenesis of cholestatic liver disease. We found that the toxic bile salt glycochenodeoxycholate (GCDC) rapidly fragmented mitochondria, both in primary mouse hepatocytes and in the bile transporter-expressing hepatic cell line McNtcp.24, leading to a significant increase in cell death. GCDC-induced mitochondrial fragmentation was associated with an increase in reactive oxygen species (ROS) levels. We found that preventing mitochondrial fragmentation in GCDC by inhibiting mitochondrial fission significantly decreased not only ROS levels but also cell death. We also induced cholestasis in mouse livers via common bile duct ligation. Using a transgenic mouse model inducibly expressing a dominant-negative fission mutant specifically in the liver, we demonstrated that decreasing mitochondrial fission substantially diminished ROS levels, liver injury, and fibrosis under cholestatic conditions. Taken together, our results provide new evidence that controlling mitochondrial fission is an effective strategy for ameliorating cholestatic liver injury.\n\nDecreasing mitochondrial fission prevents cholestatic liver injury.", "token_count": 379, "char_count": 1582, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:02.706431", "source": { "split": "train_shard_00000", "doc_id": 4530 }, "chunk_id": "train_shard_00000_4530_0", "global_id": 5058 }, { "text": "Severe cholestasis may result in end-stage liver disease with the need of liver transplantation (LTX). In children, about 10 % of LTX are necessary because of cholestatic liver diseases. Apart from bile duct atresia, three types of progressive familial intrahepatic cholestasis (PFIC) are common causes of severe cholestasis in children. The three subtypes of PFIC are defined by the involved genes: PFIC-1, PFIC-2, and PFIC-3 are due to mutations of P-type ATPase ATP8B1 (familial intrahepatic cholestasis 1, FIC1), the ATP binding cassette transporter ABCB11 (bile salt export pump, BSEP), or ABCB4 (multidrug resistance protein 3, MDR3), respectively. All transporters are localized in the canalicular membrane of hepatocytes and together mediate bile salt and phospholipid transport. In some patients with PFIC-2 disease, recurrence has been observed after LTX, which mimics a PFIC phenotype. It could be shown by several groups that inhibitory anti-BSEP antibodies emerge, which most likely cause disease recurrence. The prevalence of severe BSEP mutations (e.g., splice site and premature stop codon mutations) is very high in this group of patients. These mutations often result in the complete absence of BSEP, which likely accounts for an insufficient auto-tolerance against BSEP. Although many aspects of this \"new\" disease are not fully elucidated, the possibility of anti-BSEP antibody formation has implications for the pre- and posttransplant management of PFIC-2 patients. This review will summarize the current knowledge including diagnosis, pathomechanisms, and management of \"autoimmune BSEP disease.\"\n\nAutoimmune BSEP disease: disease recurrence after liver transplantation for progressive familial intrahepatic cholestasis.", "token_count": 467, "char_count": 1743, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "ABCB11", "ABCB4", "FIC1", "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:03.351006", "source": { "split": "train_shard_00000", "doc_id": 4531 }, "chunk_id": "train_shard_00000_4531_0", "global_id": 5059 }, { "text": "Despite the considerable number of in vivo and in vitro studies on the digestive fate of lipophilic nutrients, micronutrients, and bioactives, the effects of the structure and composition of foods on the physicochemical mechanisms of luminal digestion are still poorly understood. Studying them is indeed complex because the number of parameters is high and many of them are interdependent. To solve this problem, an in silico simulation based on a multi-agent system was recently proposed to study the intestinal bioaccessibility of lipophilic nutrients and micronutrients from a single oil droplet. The roles of lipolysis and solubilization in bile salt were included. The effects of several food and digestion parameters were in line with those reported in the experimental literature. The goal of the research reported in this new article was to include more digestion parameters in the simulation in order to make it more realistic against complex cases. This was done in one specific digestion condition reflecting in vitro experiments, using droplets of tricaprylin or triolein containing vitamin A. The structure and principles of the original model were kept, with independent local modifications in order to study each factor separately. First, a gastric step was added where lipolysis took place, and only a marginal effect on the following intestinal step was found. Then, the chemical form of vitamin A, either non-hydrolyzed retinyl ester or retinyl ester instantly hydrolyzed into retinol, was investigated by considering different localizations in the droplet, resulting in a higher bioaccessibility for the retinol. The case of a mixture of tricaprylin and triolein indicated an influence of the oil phase viscosity. The consideration of mixed micelles compared to simple bile salt micelles was also investigated, and resulted in a higher vitamin A bioaccessibility, especially with triolein. Finally, a full model including the most influential parameters was tested to simulate the digestion of triglyceride-limonene mixtures, giving bioaccessibility trends in very good agreement with the literature.\n\nRefining in silico simulation to study digestion parameters affecting the bioaccessibility of lipophilic nutrients and micronutrients.", "token_count": 495, "char_count": 2256, "word_count": 333, "semantic_coherence": 1, "information_density": 0.5435, "quality_score": 0.7718, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:04.003233", "source": { "split": "train_shard_00000", "doc_id": 4532 }, "chunk_id": "train_shard_00000_4532_0", "global_id": 5060 }, { "text": "Hepatotoxicity is a major side effect of treatment with bosentan in patients with pulmonary hypertension (PH). Bosentan is metabolized by the cytochrome CYP2C9 and inhibits the bile salt export pump, which is encoded by ABCB11. This suggests that genetic variants of CYP2C9 and/or ABCB11 may predispose patients to bosentan-induced liver injury.\n\nGenetic susceptibility to hepatoxicity due to bosentan treatment in pulmonary hypertension.", "token_count": 124, "char_count": 438, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:04.396921", "source": { "split": "train_shard_00000", "doc_id": 4533 }, "chunk_id": "train_shard_00000_4533_0", "global_id": 5061 }, { "text": "Isoniazide (INH) is a classic antituberculosis drug associated with clinical idiosyncratic drug-induced liver injury. It has been hypothesized that the interaction between a drug and modest inflammation results in a decreased threshold for drug toxicity. In this study, we tested the hypothesis that INH causes liver injury in rats when coadministered with lipopolysaccharide (LPS). Neither INH nor LPS alone caused liver injury. The coadministration of INH and LPS was associated with increases in serum and histopathological markers of liver injury. Tumour necrosis factor-α expression was significantly increased in the coadministered group. The downregulation of the bile acid transporter, bile salt export pump, and multidrug resistance protein 2 at both mRNA and protein levels was observed. Furthermore, the level of Farnesoid X receptor, which regulates the bile salt export pump and multidrug resistance protein 2, were clearly decreased. These results indicate that the coadministration of nontoxic doses of LPS and INH causes liver injury; the disruption of biliary excretion is considered the primary inflammation-related characteristic of INH-induced hepatotoxicity.\n\nLipopolysaccharide exposure augments isoniazide-induced liver injury.", "token_count": 302, "char_count": 1250, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:04.961703", "source": { "split": "train_shard_00000", "doc_id": 4534 }, "chunk_id": "train_shard_00000_4534_0", "global_id": 5062 }, { "text": "Variations of the ABCB4 and ABCB11 genes affect the composition of bile and are associated with cholestasis and cholelithiasis. However, their roles in the formation of primary intrahepatic stones (PIS) remains to be elucidated. The aim of the present study was to determine whether there is an association between PIS and variations in these genes. Exon sequencing was performed in order to analyze the ABCB4 and ABCB11 genes of 176 patients with PIS and 178 healthy subjects. One mutation in ABCB4 (no. 69233, G>A) and two other mutations in ABCB11, reference single nucleotide polymorphism (rs)118109635 and rs497692, were identified in association with PIS (P<0.001, P=0.04 and P=0.02, respectively). A synonymous mutation at no. 69233 G>A was detected in exon 26 of ABCB4 in 23 heterozygous patients with PIS. This mutation was not detected in healthy individuals or in the Single Nucleotide Polymorphism Database. No. 69233 G>A in ABCB4 was not associated with altered protein expression but with a reduced rate of PIS recurrence (P=0.01). The missense mutation rs118109635 was located on exon 21 of ABCB11 and was associated with the increased expression of ABCB11 protein (P=0.032) as well as altered bile salt export pump function. Another synonymous mutation, rs497692 in exon 24 was reported to decrease ABCB11 protein expression (P=0.001). In addition, the mutations of ABCB11 were associated with preoperative jaundice (P<0.001 and P=0.03, respectively). Consistently decreased levels of ABCB11 protein were associated with recurrent episodes of cholangitis (P=0.006) and preoperative jaundice (P=0.015)", "token_count": 510, "char_count": 1616, "word_count": 243, "semantic_coherence": 1, "information_density": 0.535, "quality_score": 0.7675, "entities": { "genes": [ "ABCB4", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:05.616261", "source": { "split": "train_shard_00000", "doc_id": 4535 }, "chunk_id": "train_shard_00000_4535_0", "global_id": 5063 }, { "text": "By contrast, ABCB4 expression was not found to be associated with clinical manifestations of PIS.\n\nVariations of ABCB4 and ABCB11 genes are associated with primary intrahepatic stones.", "token_count": 46, "char_count": 184, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8519, "quality_score": 0.9259, "entities": { "genes": [ "ABCB4", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:05.970517", "source": { "split": "train_shard_00000", "doc_id": 4535 }, "chunk_id": "train_shard_00000_4535_1", "global_id": 5064 }, { "text": "The present study was aimed to investigate the nutritive profiles, microbial counts and fermentation metabolites in rye, Italian rye-grass (IRG) and barley supplemented with Lactobacillus plantarum under the field condition, and its probiotic properties. After preparation of silage, the content of crude protein (CP), crude ash, acid detergent fiber (ADF), and neutral detergent fiber (NDF), microbes such as lactic acid bacteria (LAB), yeast and fungi counts, and fermentation metabolites lactic acid, acetic acid and butyric acid was assessed. Results indicated that the content of ADF and NDF were significantly varied between rye, IRG and barley mediated silages. The content of CP was increased in L. plantarum supplemented with IRG, but slightly decreased in rye and barley mediated silages. The maximum LAB count was recorded at 53.10 × 10(7) cfu/g in rye, 16.18 × 10(7) cfu/g in IRG and 2.63 × 10(7) cfu/g in barley silages respectively. A considerable number of the yeasts were observed in the IRG silages than the rye silages (P < 0.05). The amount of lactic acid production is higher in L. plantarum supplemented silages as compared with control samples (P < 0.05). It was confirmed that higher amount of lactic acid produced only due to more number of LAB found in the silages. L. plantarum was able to survive at low pH and bile salt and the duodenum passage with the highest percentage of hydrophobicity. Furthermore, the strain was sensitive towards the antibiotics commonly used to maintain the microbes in food industrial setups. In conclusion, supplementation of L. plantarum is most beneficial in rye, IRG and barley silage preparations and probiotic characteristics of L. plantarum was an intrinsic feature for the application in the preparation of animal feeds and functional foods.\n\nEnhancing Nutritional Quality of Silage by Fermentation with Lactobacillus plantarum.", "token_count": 507, "char_count": 1891, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5322, "quality_score": 0.7661, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:06.592417", "source": { "split": "train_shard_00000", "doc_id": 4536 }, "chunk_id": "train_shard_00000_4536_0", "global_id": 5065 }, { "text": "The aim of the present investigation was to isolate a probiotic strain from 23 samples of yurts cheese and 21 samples of kumiss (collected from scattered households in Xinjiang and Inner Mongolia), and from eN-Lac Capsules, a health-promoting product. The isolates were subjected to biochemical characterization analysis and were tested for tolerance to low pH, sodium salt, bile salt, pepsin, and trypsin. 16S DNA sequence analysis was conducted to identify the strain. The possible dose-dependent role of strain LP2 in immunomodulation was investigated using the ICR mouse model (from the Institute of Cancer Research). Daily, we conducted clinical observations, a carbon clearance test, a spleen lymphocyte proliferation test, and measurements of body mass and lymphoid organ index. Natural killer cell activity and delayed-type hypersensitivity reaction were determined. The results showed that 3 selected strains (LP2, LP4, and LP9) had high tolerance to low pH, sodium chloride, and bile salt and were not significantly different from Lactobacillus paracasei in terms of morphology, colony, and biochemistry characterizations. A further tolerance test showed that LP2 had the highest survival rate (90%) under the conditions of pH 3.0, 0.3% bile salt, 10 mg/mL pepsin, and 10 mg/mL trypsin for 24 h. The sequence heterogeneities within the 16S rDNA genes molecularly elucidated that the LP2 belongs to the L. paracasei family, on the basis of a homology of 99.6%. A significant enhanced footpad swelling reaction and natural killer cell activity in the middle-dose (10(8) cfu/mL) and the high-dose (10(9) cfu/mL) groups were observed but without obvious dose dependence (P < 0.05). Lymphocyte proliferation was also increased significantly in a dose-dependent manner (P < 0.01) compared with that of the control group, indicating a positive immunoregulatory effect.", "token_count": 508, "char_count": 1871, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [ "LP2", "LP4", "LP9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:07.230800", "source": { "split": "train_shard_00000", "doc_id": 4537 }, "chunk_id": "train_shard_00000_4537_0", "global_id": 5066 }, { "text": "A tolerant lactic acid bacteria, Lactobacillus paracasei, and its immunoregulatory function.", "token_count": 29, "char_count": 92, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:07.593025", "source": { "split": "train_shard_00000", "doc_id": 4537 }, "chunk_id": "train_shard_00000_4537_1", "global_id": 5067 }, { "text": "Nile Blue A (NB) is one of the most studied benzophenoxazine dyes, as a potent photosensitizer for photodynamic therapy. The dye when administered intravenously disperses throughout the body by circulating through blood and is taken up by most cells that emphasize its interaction with various biomolecules. Therefore a rational understanding of the interaction of NB with relevant biological and biomimicking systems appears important. The focus of the present work is to investigate the interaction of NB with two bile salts sodium deoxycholate (NaDC) and sodium cholate (NaC) by spectroscopic techniques. The bile salts, in their premicellar concentration range, induce NB dimerization. Both H- and J-dimers are formed, however a major contribution is from the H-dimers. The extent of NB dimerization in NaDC, the dihydroxy bile salt, is higher than that in NaC, the trihydroxy bile salt. The bile salts when present above their micellar concentrations solubilize NB in its monomeric form. NB exhibits stronger binding and partitioning efficiency toward NaDC than NaC micelles at a given temperature. Binding and partitioning of NB to these micelles are spontaneous and exothermic in nature and these are enthalpy-driven processes. The spectral profiles and thermodynamic parameters of NB point toward the dissimilar nature of its environment in the micelles formed by the above two bile salts.\n\nSpectroscopic investigation of interaction of Nile Blue A, a potent photosensitizer, with bile salts in aqueous medium.", "token_count": 378, "char_count": 1518, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:08.174554", "source": { "split": "train_shard_00000", "doc_id": 4538 }, "chunk_id": "train_shard_00000_4538_0", "global_id": 5068 }, { "text": "The salivarius group of streptococci is of particular importance for humans. This group consists of three genetically similar species, Streptococcus salivarius, Streptococcus vestibularis and Streptococcus thermophilus. S. salivarius and S. vestibularis are commensal organisms that may occasionally cause opportunistic infections in humans, whereas S. thermophilus is a food bacterium widely used in dairy production. We developed Multilocus sequence typing (MLST) and comparative genomic analysis to confirm the clear separation of these three species. These analyses also identified a subgroup of four strains, with a core genome diverging by about 10%, in terms of its nucleotide sequence, from that of S. salivarius sensu stricto. S. thermophilus species displays a low level of nucleotide variability, due to its recent emergence with the development of agriculture. By contrast, nucleotide variability is high in the other two species of the salivarius group, reflecting their long-standing association with humans. The species of the salivarius group have genome sizes ranging from the smallest (∼ 1.7 Mb for S. thermophilus) to the largest (∼ 2.3 Mb for S. salivarius) among streptococci, reflecting genome reduction linked to a narrow, nutritionally rich environment for S. thermophilus, and natural, more competitive niches for the other two species. Analyses of genomic content have indicated that the core genes of S. salivarius account for about two thirds of the genome, indicating considerable variability of gene content and differences in potential adaptive features. Furthermore, we showed that the genome of this species is exceptionally rich in genes encoding surface factors, glycosyltransferases and response regulators. Evidence of widespread genetic exchanges was obtained, probably involving a natural competence system and the presence of diverse mobile elements. However, although the S. salivarius strains studied were isolated from several human body-related sites (all levels of the digestive tract, skin, breast milk, and body fluids) and included clinical strains, no genetic or genomic niche-specific features could be identified to discriminate specific group.", "token_count": 504, "char_count": 2195, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5987, "quality_score": 0.7994, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:08.829124", "source": { "split": "train_shard_00000", "doc_id": 4539 }, "chunk_id": "train_shard_00000_4539_0", "global_id": 5069 }, { "text": "Genomics of Streptococcus salivarius, a major human commensal.", "token_count": 20, "char_count": 62, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:09.180674", "source": { "split": "train_shard_00000", "doc_id": 4539 }, "chunk_id": "train_shard_00000_4539_1", "global_id": 5070 }, { "text": "The yeast Kluyveromyces marxianus produces a range of volatile molecules with applications as fragrances or flavours. The purpose of this study was to establish how nutritional conditions influence the production of these metabolites. Four strains were grown on synthetic media, using a variety of carbon and nitrogen sources and volatile metabolites analysed using gas chromatography-mass spectrometry (GC-MS). The nitrogen source had pronounced effects on metabolite production: levels of the fusel alcohols 2-phenylethanol and isoamyl alcohol were highest when yeast extract was the nitrogen source, and ammonium had a strong repressing effect on production of 2-phenylethyl acetate. In contrast, the nitrogen source did not affect production of isoamyl acetate or ethyl acetate, indicating that more than one alcohol acetyl transferase activity is present in K. marxianus. Production of all acetate esters was low when cells were growing on lactose (as opposed to glucose or fructose), with a lower intracellular pool of acetyl CoA being one explanation for this observation. Bioinformatic and phylogenetic analysis of the known yeast alcohol acetyl transferases ATF1 and ATF2 suggests that the ancestral protein Atf2p may not be involved in synthesis of volatile acetate esters in K. marxianus, and raises interesting questions as to what other genes encode this activity in non-Saccharomyces yeasts. Identification of all the genes involved in ester synthesis will be important for development of the K. marxianus platform for flavour and fragrance production.\n\nInfluence of carbon and nitrogen source on production of volatile fragrance and flavour metabolites by the yeast Kluyveromyces marxianus.", "token_count": 419, "char_count": 1705, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5743, "quality_score": 0.7871, "entities": { "genes": [ "ATF2", "ATF1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:09.803273", "source": { "split": "train_shard_00000", "doc_id": 4540 }, "chunk_id": "train_shard_00000_4540_0", "global_id": 5071 }, { "text": "There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation.\n\nAn evolutionary analysis of genome expansion and pathogenicity in Escherichia coli.", "token_count": 237, "char_count": 1068, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:10.274145", "source": { "split": "train_shard_00000", "doc_id": 4541 }, "chunk_id": "train_shard_00000_4541_0", "global_id": 5072 }, { "text": "Excess cholesterol is associated with cardiovascular diseases (CVD), an important cause of mortality worldwide. Current CVD therapeutic measures, lifestyle and dietary interventions, and pharmaceutical agents for regulating cholesterol levels are inadequate. Probiotic bacteria have demonstrated potential to lower cholesterol levels by different mechanisms, including bile salt hydrolase activity, production of compounds that inhibit enzymes such as 3-hydroxy-3-methylglutaryl coenzyme A, and cholesterol assimilation. This work investigates 11 Lactobacillus strains for cholesterol assimilation. Probiotic strains for investigation were selected from the literature: Lactobacillus reuteri NCIMB 11951, L. reuteri NCIMB 701359, L. reuteri NCIMB 702655, L. reuteri NCIMB 701089, L. reuteri NCIMB 702656, Lactobacillus fermentum NCIMB 5221, L. fermentum NCIMB 8829, L. fermentum NCIMB 2797, Lactobacillus rhamnosus ATCC 53103 GG, Lactobacillus acidophilus ATCC 314, and Lactobacillus plantarum ATCC 14917. Cholesterol assimilation was investigated in culture media and under simulated intestinal conditions. The best cholesterol assimilator was L. plantarum ATCC 14917 (15.18±0.55 mg/10(10) cfu) in MRS broth. L. reuteri NCIMB 701089 assimilated over 67% (2254.70±63.33 mg/10(10) cfu) of cholesterol, the most of all the strains, under intestinal conditions. This work demonstrates that probiotic bacteria can assimilate cholesterol under intestinal conditions, with L", "token_count": 527, "char_count": 1468, "word_count": 188, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:45:10.964488", "source": { "split": "train_shard_00000", "doc_id": 4542 }, "chunk_id": "train_shard_00000_4542_0", "global_id": 5073 }, { "text": "reuteri NCIMB 701089 showing great potential as a CVD therapeutic.\n\nCholesterol assimilation by Lactobacillus probiotic bacteria: an in vitro investigation.", "token_count": 51, "char_count": 156, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:11.349306", "source": { "split": "train_shard_00000", "doc_id": 4542 }, "chunk_id": "train_shard_00000_4542_1", "global_id": 5074 }, { "text": "Legionella pneumophila is a strictly environmental pathogen and the etiological agent of legionellosis. It is known that non-vertical processes have a major role in the short-term evolution of pathogens, but little is known about the relevance of these and other processes in environmental bacteria. We report the whole-genome sequencing of 69 L. pneumophila strains linked to recurrent outbreaks in a single location (Alcoy, Spain) over 11 years. We found some examples where the genome sequences of isolates of the same sequence type and outbreak did not cluster together and were more closely related to sequences from different outbreaks. Our analyses identify 16 recombination events responsible for almost 98% of the SNPs detected in the core genome and an apparent acceleration in the evolutionary rate. These results have profound implications for the understanding of microbial populations and for public health interventions in Legionella outbreak investigations.\n\nRecombination drives genome evolution in outbreak-related Legionella pneumophila isolates.", "token_count": 233, "char_count": 1065, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6732, "quality_score": 0.8366, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:11.841215", "source": { "split": "train_shard_00000", "doc_id": 4543 }, "chunk_id": "train_shard_00000_4543_0", "global_id": 5075 }, { "text": "The potential probiotic properties of lactic acid bacteria (LAB) after treatment with gastrointestinal (GI) conditions were investigated. Some LAB strains that survived simulated GI treatment retained their adhesiveness and antagonism against the pathogen. Therefore pre-challenging LAB with simulated GI conditions is a suitable way for potential probiotic studies.\n\nTo pre-challenge lactic acid bacteria with simulated gastrointestinal conditions is a suitable approach to studying potential probiotic properties.", "token_count": 114, "char_count": 515, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:12.268445", "source": { "split": "train_shard_00000", "doc_id": 4544 }, "chunk_id": "train_shard_00000_4544_0", "global_id": 5076 }, { "text": "The aim of this research was to study how the yeast cell immobilization technique influences the growth and fermentation profiles of Kluyveromyces marxianus cultivated on apple/chokeberry and apple/cranberry pomaces. Encapsulation of the cells was performed by droplet formation from a foamed alginate solution. The growth and metabolic profiles were evaluated for both free and immobilized cells. Culture media with fruit waste produced good growth of free as well as immobilized yeast cells. The fermentation profiles of K. marxianus were different with each waste material. The most varied aroma profiles were noted for immobilized yeast cultivated on apple/chokeberry pomace.\n\nGrowth and by-product profiles of Kluyveromyces marxianus cells immobilized in foamed alginate.", "token_count": 184, "char_count": 776, "word_count": 110, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:12.753966", "source": { "split": "train_shard_00000", "doc_id": 4545 }, "chunk_id": "train_shard_00000_4545_0", "global_id": 5077 }, { "text": "Clostridium difficile infections (CDI) are a growing concern in North America, because of their increasing incidence and severity. Using integrated approaches, we correlated pathogen genotypes and host clinical characteristics for 46 C. difficile infections in a tertiary care medical center during a 6-month interval from January to June 2010. Multilocus sequence typing (MLST) demonstrated 21 known and 2 novel sequence types (STs), suggesting that the institution's C. difficile strains are genetically diverse. ST-1 (which corresponds to pulsed-field gel electrophoresis strain type NAP1/ribotype 027) was the most prevalent (32.6%); 43.5% of the isolates were binary toxin gene positive, of which 75% were ST-1. All strains were ciprofloxacin resistant and metronidazole susceptible, and 8.3% and 13.0% of the isolates were resistant to clindamycin and tetracycline, respectively. The corresponding resistance loci, including potential novel mutations, were identified from the whole-genome sequencing (WGS) of the resistant strains. Core genome single nucleotide polymorphisms (SNPs) determining the phylogenetic relatedness of the 46 strains recapitulated MLST types and provided greater interstrain differentiation. The disease severity was greatest in patients infected with ST-1 and/or binary gene-positive strains, but genome-wide SNP analysis failed to provide additional associations with CDI severity within the same STs. We conclude that MLST and core genome SNP typing result in the same phylogenetic grouping of the 46 C. difficile strains collected in a single hospital. WGS also has the capacity to differentiate those strains within STs and allows the comparison of strains at the individual gene level and at the whole-genome level.\n\nPhenotypic and genotypic analysis of Clostridium difficile isolates: a single-center study.", "token_count": 489, "char_count": 1846, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8185, "entities": { "genes": [ "NAP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:13.401771", "source": { "split": "train_shard_00000", "doc_id": 4546 }, "chunk_id": "train_shard_00000_4546_0", "global_id": 5078 }, { "text": "Significant technological advances in gene sequence analysis and construction of genetically-modified animals during the last two decades made it possible to reveal that many transporters are associated with diseases. The bile salt export pump (BSEP/ABCB11), a member of the family of ATP-binding cassette transporters, is localized on the canalicular membrane of hepatocytes and predominantly mediates the biliary excretion of bile salts. A hereditary defect of BSEP results in severe cholestasis called progressive familial intrahepatic cholestasis type 2 (PFIC2). Without liver transplantation, this disease progresses to liver failure and death before adulthood; therefore the development of new, less invasive medical therapy for PFIC2 is of the highest priority. We have previously shown that in many cases of PFIC2 patients, the dysfunction of BSEP is attributable to decreased BSEP expression on the hepatocanalicular membrane and that 4-phenylbutyrate (4PB), an approved drug for urea cycle disorder, may be a compound with potential to restore BSEP expression. This drug inhibits ubiquitination of cell surface-resident BSEP and thereby its clathrin-mediated endocytosis through the AP2 adaptor complex, leading to increase in BSEP expression on the canalicular membrane. Clinical studies to investigate the efficacy of 4PB in the treatment of PFIC2 revealed that 4PB therapy biochemically and histologically improved liver function without any side effect. Therefore, 4PB therapy may become the preferred choice, instead of liver transplantation, for PFIC2 patients. The strategy employed and findings in this study would be valuable for the drug development of transporter-related disorders.\n\n[Development of new therapeutic strategy for transporter-related diseases].", "token_count": 423, "char_count": 1780, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6305, "quality_score": 0.8153, "entities": { "genes": [ "PFIC2", "ABCB11", "AP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:14.029788", "source": { "split": "train_shard_00000", "doc_id": 4547 }, "chunk_id": "train_shard_00000_4547_0", "global_id": 5079 }, { "text": "The aim of the present study is to screen and characterize endogenous microbiota Bacillus spp. from the gastrointestinal (GI) tract of Labeo rohita in order to evaluate their probiotic attributes. A total of 74 isolates from the GI of L. rohita were evaluated for their antimicrobial properties by agar well-diffusion method against fish pathogens. Based on the better antibacterial features, three isolates (KADR1, KADR3, and KADR4) were selected for further delineation. The three selected isolates exhibited higher tolerance to bile salt, moderate tolerance to low pH, high surface hydrophobicity to solvents, and capable to autoaggregate. All three isolates demonstrated notable proteolytic, catalase activity and susceptibility to various antibiotics. Partial 16S rRNA sequencing revealed that the isolates exhibited 99 % sequence homology with Bacillus subtilis, Bacillus aerophilus, and Bacillus firmus of the database substantiating morphological and physiological characterization. Survivability in low pH and bile salt ensures their adaptability in the fish intestinal microenvironment. The ability to autoaggregate reveals colonization potential in the GI of the fish. Absence of hemolytic activity, antibiotic susceptibility to certain antibiotics, presence of protease and catalase activity, and non-pathogenic caliber of the above-mentioned isolates could be feasible characteristics when considering them as probiotics in the aquaculture industry.\n\nCharacterization of Bacillus spp. from the gastrointestinal tract of Labeo rohita--towards to identify novel probiotics against fish pathogens.", "token_count": 409, "char_count": 1607, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [ "KADR1", "KADR4", "KADR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:14.652088", "source": { "split": "train_shard_00000", "doc_id": 4548 }, "chunk_id": "train_shard_00000_4548_0", "global_id": 5080 }, { "text": "In this study, yeasts from Turkish fermented sucuks were identified and their functional and technological properties were evaluated. Two hundred fifty-five yeast isolates were obtained from 35 different sucuk samples from different regions of Turkey. The yeast isolates were determined as genotypic using 2 different polymerase chain reaction (PCR) methods (rep-PCR and RAPD-PCR). Functional and technological properties of including proteolytic, lipolytic, and catalase activities, tolerance to NaCl and bile, as well as growing rates at different temperature and pH conditions selected yeast strains were also evaluated. Candida zeylanoides and Debaryomyces hansenii were dominant strains in sucuk samples. All C. zeylanoides and D. hansenii tested could grow at the condition of 15% NaCl and 0.3% bile salt. However, none of the strains were able to grow at 37 °C, even though catalase activity, weak proteolytic and lipolytic activities was still observed. D. hansenii were able to grow only at pH 3, while some of C. zeylanoides could grow at lower pH levels (pH 2). Three and 4 strains of C. zeylanoides showed β-hemolysis activity and nitrate reduction ability to nitrite, respectively. D. hansenii did not have properties, which are β-hemolysis, nitrate reduction, or hydrogen sulfide production. Overall, diverse yeast mycobiota present in Turkish fermented sucuk and their functional and technological properties were revealed with this study.\n\nBiodiversity of yeast mycobiota in \"sucuk,\" a traditional Turkish fermented dry sausage: phenotypic and genotypic identification, functional and technological properties.", "token_count": 417, "char_count": 1626, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:15.281039", "source": { "split": "train_shard_00000", "doc_id": 4549 }, "chunk_id": "train_shard_00000_4549_0", "global_id": 5081 }, { "text": "Vibrio diabolicus, a marine bacterium originating from deep-sea hydrothermal vents, produces the HE800 exopolysaccharide with high value for biotechnological purposes, especially for human health. Its genome was sequenced and analyzed; phylogenetic analysis using the core genome revealed V. diabolicus is close to another deep-sea Vibrio sp. (Ex25) within the Harveyi clade and Alginolyticus group. A genetic locus homologous to the syp cluster from Vibrio fischeri was demonstrated to be involved in the HE800 production. However, few genetic particularities suggest that the regulation of syp expression may be different in V. diabolicus. The presence of several types of glycosyltransferases within the locus indicates a capacity to generate diversity in the glycosidic structure, which may confer an adaptability to environmental conditions. These results contribute to better understanding exopolysaccharide biosynthesis and for developing new efficient processes to produce this molecule for biotechnological applications.\n\nGenome sequence of Vibrio diabolicus and identification of the exopolysaccharide HE800 biosynthesis locus.", "token_count": 273, "char_count": 1137, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "HE800" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:15.837940", "source": { "split": "train_shard_00000", "doc_id": 4550 }, "chunk_id": "train_shard_00000_4550_0", "global_id": 5082 }, { "text": "The structural organization of inulinases from yeasts, fungi, and plants are researched. For studying their sizes, molecular weight, and permolecular organization, an approach consisting of a combination of atomic force microscopy with methods of dynamic light scattering, gel chromatography, and electrophoresis was used. It is shown that inulinases from Kluyveromyces marxianus and Aspergillus niger form geterodimers and inulinases from tubers of Helianthus tuberosus are present as both dimers and monomers. The role of various forms in the functional activity of inulinase molecules is discussed.\n\n[Inulinases from various producers: the features of their permolecular organization].", "token_count": 162, "char_count": 688, "word_count": 94, "semantic_coherence": 1, "information_density": 0.734, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:16.623538", "source": { "split": "train_shard_00000", "doc_id": 4551 }, "chunk_id": "train_shard_00000_4551_0", "global_id": 5083 }, { "text": "The aim of this study was to characterize the probiotic characteristics of Lactobacillus fermentum strains isolated from Tulum cheese. Seven L. fermentum strains were selected among the isolated and identified lactobacillus strains due to their abundance. When the gastric condition was considered, L. fermentum LP3 and LP4 were able to tolerate pH 2.5 and 1% bile salt. All L. fermentum strains had similar enzymatic activity and antibiotic resistance pattern but the highest antagonistic effect was detected within LP3, LP4 and LP6. Cholesterol assimilation amount of L. fermentum strains ranged between 12.1 and 45.3% in MRS and 20.7-71.1% in MRS with bile. The highest cholesterol assimilation in MRS and MRS with bile was occurred by LP3 and LP4, respectively. L. fermentum LP2 adhered to caco-2 cells more than Lactobacillus rhamnosus LGG where LP3, LP4 and LP5 adhered at similar level. In conclusion, L. fermentum LP3 and LP4 fulfilled sufficient criteria to be probiotics for use as a starter culture in the production of tulum cheese or other dairy products. Also this study indicated that some food-associated Lactobacillus strains non-predominant for gut biota have significant probiotic potential.\n\nProbiotic characteristics of Lactobacillus fermentum strains isolated from tulum cheese.", "token_count": 371, "char_count": 1300, "word_count": 195, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7897, "entities": { "genes": [ "LP2", "LP5", "LP4", "LP6", "LP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:17.213864", "source": { "split": "train_shard_00000", "doc_id": 4552 }, "chunk_id": "train_shard_00000_4552_0", "global_id": 5084 }, { "text": "Most important during probiotic selection are gastric acid and bile tolerance, the adhesion to the luminal epithelium to colonize the lower gastrointestinal tract of a human and safety for human consumption. The aim of this study was to evaluate the selected probiotic in vitro properties of Lactobacillus spp. Strains isolated from traditional fermented food. A total 38 strains were isolated from the pickled samples and 14 were identified as Lactobacillus spp. The survival of almost all strains after incubation at pH 2.5 did not change markedly, and remained at above 90 % (10(9) CFU/mL). The strains also exhibited a high survival rate at pH 3.5 (>90 %), whereas pH 1.5 all were died. Just four strains could survive 90 min. at pH 1.5 (<39 %). The incubation with 0.2 % bile salt solution resulted in a survival rates of 81-94 % after 24 h, whereas after incubation in 2 and 4 % bile salt solution it was 59-94 %. All tested strains showed very good and good resistance to 0.4 % phenol addition, however only Lb. johnsonii K4 was able to multiply. The hydrophobic nature of the cell surface of the tested strains was moderated recording hydrophobicity of Lb. johnsonii K4 and Lb. rhamnosus K3 above 60 %. Safety evaluation excluded four of tested strains as candidate probiotics, according to antibiotic resistance patterns and certain metabolic activities. On the basis on the results 10 of the selected Lactobacillus strains are safe and can survive under gastrointestinal conditions, which requires them to future in vitro and in vivo probiotic studies.\n\nIn vitro screening of selected probiotic properties of Lactobacillus strains isolated from traditional fermented cabbage and cucumber.", "token_count": 474, "char_count": 1698, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5507, "quality_score": 0.7754, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:17.864800", "source": { "split": "train_shard_00000", "doc_id": 4553 }, "chunk_id": "train_shard_00000_4553_0", "global_id": 5085 }, { "text": "The perceived health benefit of probiotics has led to a rapid expansion of their use in various health-based products. The beneficial effect of these probiotic cells is largely dependent on their ability to reach their appropriate site of action, usually the distal gut, in a viable condition and in sufficient numbers. In an attempt to establish a microbiota in formula-fed infants resembling that of breast-fed ones, infant formula manufacturers are increasingly incorporating probiotics into their products. The administration of probiotic cells via oral administration is associated with a large decrease in the number of viable cells due to the high acid and bile salt concentrations present in the stomach. Powdered infant formulae are also expected to have long term stability particularly in comparison to products normally associated with probiotics, which can adversely affect the viability of probiotic cells. Finally, the processing techniques used to generate infant formula can cause a dramatic loss in the number of viable cells present in the product by the time it is consumed. Microencapsulation technology is emerging as an effective way to protect cells during food processing and also allows targeted delivery of the cells to appropriate sites in the gastro-intestinal tract improving the efficacy of the final product and lowering the economic cost incurred by producers due to logistic and stability issues. In this review, the current situation of probiotics in infant formula, and the encapsulation techniques being developed using milk and pea proteins as encapsulating materials to improve their viability are discussed.\n\nProbiotic bacteria in infant formula and follow-up formula: Microencapsulation using milk and pea proteins to improve microbiological quality.", "token_count": 352, "char_count": 1791, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5655, "quality_score": 0.7828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:18.437703", "source": { "split": "train_shard_00000", "doc_id": 4554 }, "chunk_id": "train_shard_00000_4554_0", "global_id": 5086 }, { "text": "The aim of the present study was to characterize lactic acid bacteria (LAB) strains isolated from traditional fermented gilaburu fruit juice and their probiotic potential. The LAB counts of the fermented gilaburu fruit juice were in the range of 3.92-8.30logcfu/g. Total of 332 isolates belonging to Lactobacillus and Leuconostoc species were characterized from traditional fermented gilaburu juice by genotypic methods. It was also determined that the major LAB strains belong to Lactobacillus plantarum (173 isolates), Lactobacillus casei (52 isolates) and Lactobacillus brevis (24 isolates), while Lactobacillus buchneri, Lactobacillus parabuchneri, Lactobacillus pantheris, Leuconostoc pseudomesenteroides and Lactobacillus harbinensis were the least in isolated LAB strains. In terms of the probiotic potentials, Lb. plantarum strains were able to grow at pH2.5, but 3 of Lb. casei strains, one of each Lb. brevis and Lb. buchneri strains could not grow at the same pH. All selected LAB stains were resistant to bile salt at ≤0.3% concentration. While all the LAB species grew at 15°C, two Lactobacillus hordei strains could also grow at 45°C. The highest cell hydrophobicity degrees were for Lb. casei (G20a) and Lb. plantarum (G19e) as 87.5 and 86.0%, respectively. Listeria monocytogenes and Bacillus cereus were the most sensitive bacteria against the selected LAB strains, while Escherichia coli and Staphylococcus aureus were the most resistant. Again all the isolated LAB species were resistant to three antibiotics; kanamycin, streptomycin and vancomycin", "token_count": 494, "char_count": 1567, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5351, "quality_score": 0.7675, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:19.089666", "source": { "split": "train_shard_00000", "doc_id": 4555 }, "chunk_id": "train_shard_00000_4555_0", "global_id": 5087 }, { "text": "Characterization and probiotic potentials of the LAB isolated from fermented gilaburu (Viburnum opulus) juice were studied first time, and further research needs to be done on their behaviors in similar food formulations as a probiotic.\n\nDiversity and probiotic potentials of lactic acid bacteria isolated from gilaburu, a traditional Turkish fermented European cranberrybush (Viburnum opulus L.) fruit drink.", "token_count": 103, "char_count": 409, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8246, "quality_score": 0.9123, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:19.469362", "source": { "split": "train_shard_00000", "doc_id": 4555 }, "chunk_id": "train_shard_00000_4555_1", "global_id": 5088 }, { "text": "The Escherichia coli species is divided in phylogenetic groups that differ in their virulence and commensal distribution. Strains belonging to the B2 group are involved in extra-intestinal pathologies but also appear to be more prevalent as commensals among human occidental populations. To investigate the genetic specificities of B2 sub-group, we used 128 sequenced genomes and identified genes of the core genome that showed marked difference between B2 and non-B2 genomes. We focused on the gene and its surrounding region with the strongest divergence between B2 and non-B2, the antiporter gene nhaA. This gene is part of the nhaAR operon, which is in the core genome but flanked by mobile regions, and is involved in growth at high pH and high sodium concentrations. Consistently, we found that a panel of non-B2 strains grew faster than B2 at high pH and high sodium concentrations. However, we could not identify differences in expression of the nhaAR operon using fluorescence reporter plasmids. Furthermore, the operon deletion had no differential impact between B2 and non-B2 strains, and did not result in a fitness modification in a murine model of gut colonization. Nevertheless, sequence analysis and experiments in a murine model of septicemia revealed that recombination in nhaA among B2 strains was observed in strains with low virulence. Finally, nhaA and nhaAR operon deletions drastically decreased virulence in one B2 strain. This effect of nhaAR deletion appeared to be stronger than deletion of all pathogenicity islands. Thus, a population genetic approach allowed us to identify an operon in the core genome without strong effect in commensalism but with an important role in extra-intestinal virulence, a landmark of the B2 strains.\n\nThe conserved nhaAR operon is drastically divergent between B2 and non-B2 Escherichia coli and is involved in extra-intestinal virulence.", "token_count": 468, "char_count": 1898, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5358, "quality_score": 0.7679, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:20.113635", "source": { "split": "train_shard_00000", "doc_id": 4556 }, "chunk_id": "train_shard_00000_4556_0", "global_id": 5089 }, { "text": "The bacterium Lactobacillus reuteri LR6, an isolate from breast-fed human infant feces, was tested positive for bile tolerance and bile salt hydrolase activity. It was also evaluated as a potential probiotic with cholesterol-lowering effect in vivo. In this study, 32 male Albino rats were divided into four groups consisting of eight mice per group. For 60 d, group I was fed with normal synthetic diet, group II was fed with cholesterol-enriched diet only, group III was fed with cholesterol-enriched diet supplemented with skimmed milk, and group IV was fed with cholesterol-enriched diet supplemented with L. reuteri LR6-fermented skimmed milk (10(8) cfu/mL). Blood samples were taken to study lipid profile on 0th, 15th, 30th and 60th day. Compared with the control group, the values for total cholesterol (TC), triglyceride (TG), and LDL were reduced significantly in group fed with L. reuteri LR6 but for HDL this difference was not significant. The results indicated that L. reuteri LR6 might be effective as a probiotic with cholesterol-lowering activities.\n\nHypocholesterolemic effects of Lactobacillus reuteri LR6 in rats fed on high-cholesterol diet.", "token_count": 345, "char_count": 1162, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6497, "quality_score": 0.8249, "entities": { "genes": [ "LR6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:20.686877", "source": { "split": "train_shard_00000", "doc_id": 4557 }, "chunk_id": "train_shard_00000_4557_0", "global_id": 5090 }, { "text": "The aim of the present study was to identify molecular mechanisms involved in liver fat and cholesterol accumulation in ovariectomised (Ovx) rats fed with high-cholesterol diets. VLDL assembly and bile acid metabolism were specifically targeted. After being either Ovx or sham-operated, the rats were fed a standard diet or a high-fat diet containing 0, 0·25 or 0·5 % cholesterol for 6 weeks. Although Ovx rats exposed to dietary cholesterol intake accumulated the greatest amount of hepatic fat and cholesterol, plasma cholesterol levels were lower (P< 0·05) in these animals than in the corresponding control rats. Accompanying this observation, ovariectomy and dietary cholesterol intake resulted in a down-regulation (P< 0·05) of the expression of genes associated with VLDL assembly, including microsomal TAG transfer protein, diacylglycerol acyltransferase 2, acyl-CoA:cholesterol acyltransferase 2 and apoB-100 as well as genes associated with bile acid metabolism including farnesoid X receptor and bile salt export pump (P< 0·01). These results indicate that high-fat/high-cholesterol diets and ovariectomy concomitantly disrupt hepatic lipid output through defects in VLDL assembly and, most probably, secretion. The results also point to a defect in hepatic bile acid secretion. The present study offers novel insights into intrahepatic lipid metabolism, which may be relevant to metabolic complications found in postmenopausal women.\n\nImpaired VLDL assembly: a novel mechanism contributing to hepatic lipid accumulation following ovariectomy and high-fat/high-cholesterol diets?", "token_count": 452, "char_count": 1590, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:21.320593", "source": { "split": "train_shard_00000", "doc_id": 4558 }, "chunk_id": "train_shard_00000_4558_0", "global_id": 5091 }, { "text": "Staphylococcus aureus is a commensal and major pathogen of humans and animals. Comparative genomics of S. aureus populations suggests that colonization of different host species is associated with carriage of mobile genetic elements (MGE), particularly bacteriophages and plasmids capable of encoding virulence, resistance, and immune evasion pathways. Antimicrobial-resistant S. aureus of livestock are a potential zoonotic threat to human health if they adapt to colonize humans efficiently. We utilized the technique of experimental evolution and co-colonized gnotobiotic piglets with both human- and pig-associated variants of the lineage clonal complex 398, and investigated growth and genetic changes over 16 days using whole genome sequencing. The human isolate survived co-colonization on piglets more efficiently than in vitro. During co-colonization, transfer of MGE from the pig to the human isolate was detected within 4 h. Extensive and repeated transfer of two bacteriophages and three plasmids resulted in colonization with isolates carrying a wide variety of mobilomes. Whole genome sequencing of progeny bacteria revealed no acquisition of core genome polymorphisms, highlighting the importance of MGE. Staphylococcus aureus bacteriophage recombination and integration into novel sites was detected experimentally for the first time. During colonization, clones coexisted and diversified rather than a single variant dominating. Unexpectedly, each piglet carried unique populations of bacterial variants, suggesting limited transmission of bacteria between piglets once colonized. Our data show that horizontal gene transfer occurs at very high frequency in vivo and significantly higher than that detectable in vitro.\n\nExtensive horizontal gene transfer during Staphylococcus aureus co-colonization in vivo.", "token_count": 409, "char_count": 1825, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:21.946078", "source": { "split": "train_shard_00000", "doc_id": 4559 }, "chunk_id": "train_shard_00000_4559_0", "global_id": 5092 }, { "text": "In order to gain new insights into the potential of specific dietary fibres to control lipid digestion, the goal of this work is to study the main interactions between commercial cellulose ethers, as dietary fibre, and a bile salt, as an important duodenal component present during the digestibility of lipids. These interactions have been evaluated in two different scenarios found for an oil-in-water emulsion on its transit through the duodenum. Namely, interactions in the continuous phase and competitive adsorption at the oil-water interface have been looked at by means of micro-differential scanning calorimetry (micro-DSC) and interfacial tension (IT). Micro-DSC revealed that the presence of the bile salt affects the thermogelation process of cellulose derivatives, suggesting binding to cellulose ethers. The effect on thermogelation seems to be cellulose type-dependent. IT measurements proved the ability of cellulose ethers to compete for the oil-water interface in the presence of the bile salt. Interactions in the bulk might have an impact on this interfacial scenario. These findings may have implications in the digestion of emulsified lipids, hence providing a springboard to develop new cellulose-based food products with improved functional properties.\n\nInteractions between cellulose ethers and a bile salt in the control of lipid digestion of lipid-based systems.", "token_count": 312, "char_count": 1388, "word_count": 203, "semantic_coherence": 1, "information_density": 0.5961, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:22.504448", "source": { "split": "train_shard_00000", "doc_id": 4560 }, "chunk_id": "train_shard_00000_4560_0", "global_id": 5093 }, { "text": "This report is the summary of presentations at the symposium sponsored by the American Society for Pharmacology and Experimental Therapeutics, April 26-30, at Experimental Biology 2014 in San Diego, CA. The presentations focused on the role of transporters in imaging in health and disease and on assessing transporter function in vivo. Imaging is an important diagnostic tool in clinics and is a novel tool for in vivo visualization of transporter function. Many imaging substrates and endogenous markers for organ function are organic anions. In this symposium, the bile salt transporter sodium taurocholate cotransporting polypeptide and the liver organic anion transporting polypeptides (OATPs) as well as the renal organic anion transporters (OATs) were addressed in detail; e.g., OATPs mediate transport of contrast agents used for magnetic resonance imaging of the liver or transport agents used for hepatobiliary scintigraphy, and OATs transport substances used in renography. In addition, the symposium also focused on the multidrug-resistance transporter 1 (MDR1 or P-gp), which is the most important gatekeeper in epithelial or endothelial barriers for preventing entry of potentially harmful substances into organs. Novel substrates suitable for positron emission tomography (PET) allow the study of such transporters at the blood-brain barrier or while they are mediating uptake of drugs into hepatocytes, and, importantly, PET tracers also now allow renography. Finally, quantitative data on transporter expression in human organs allow the development of improved physiologically based pharmacokinetic (PBPK) models for drug disposition. Hence, the combined efforts using novel substrates for in vivo visualization of transporters and quantification of transporters will lead to a deeper understanding of transporter function in disease and allow development of novel PBPK models for disease states.\n\nRole of (drug) transporters in imaging in health and disease.", "token_count": 475, "char_count": 1977, "word_count": 284, "semantic_coherence": 1, "information_density": 0.5528, "quality_score": 0.7764, "entities": { "genes": [ "MDR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:23.190889", "source": { "split": "train_shard_00000", "doc_id": 4561 }, "chunk_id": "train_shard_00000_4561_0", "global_id": 5094 }, { "text": "Coxiella burnetii is a pathogen causing Q fever. The aim of our work was to study Z3055, a strain that is genotypically related to the strain causing the Netherlands outbreak. We compared Z3055 to 5 other completed genomes available in GenBank. We calculated the blast score ratio (BSR) to analyze genetic differences among the strains. The ratio core genome/pangenome was 98% likely other bacteria with closed pangenomes. Differences between Z3055 and the reference NMI consisted only of point mutations and insertion/deletion (INDELs). Non-synonymous mutations significantly increased in genes coding for membrane proteins (16/156 vs 103/1757, bilateral Chi(2) test, p<0.05), ankyrin repeat domains containing proteins (2/9 vs 117/1904, bilateral Chi(2) test, p<0.05), transcription factors (7/53 vs 112/1860, bilateral Chi(2) test, p<0.05) and translation proteins (15/144 vs 109/1655, bilateral Chi(2) test, p<0.05). The evolution of this strain may have been driven by mutations in critical genes.\n\nThe genome of Coxiella burnetii Z3055, a clone linked to the Netherlands Q fever outbreaks, provides evidence for the role of drift in the emergence of epidemic clones.", "token_count": 362, "char_count": 1172, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:23.786764", "source": { "split": "train_shard_00000", "doc_id": 4562 }, "chunk_id": "train_shard_00000_4562_0", "global_id": 5095 }, { "text": "The feasibility of ethanol production using an enzymatic hydrolysate of pretreated cladodes of Opuntia ficus-indica (prickly pear cactus) as carbohydrate feedstock was investigated, including a comprehensive chemical analysis of the cladode biomass and the effects of limited aeration on the fermentation profiles and sugar utilization. The low xylose and negligible mannose content of the cladode biomass used in this study suggested that the hemicellulose structure of the O. ficus-indica cladode was atypical of hardwood or softwood hemicelluloses. Separate hydrolysis and fermentation and simultaneous saccharification and fermentation procedures using Kluyveromyces marxianus and Saccharomyces cerevisiae at 40 and 35 °C, respectively, gave similar ethanol yields under non-aerated conditions. In oxygen-limited cultures K. marxianus exhibited almost double the ethanol productivity compared to non-aerated cultures, although after sugar depletion utilization of the produced ethanol was evident. Ethanol concentrations of up to 19.5 and 20.6 g l(-1) were obtained with K. marxianus and S. cerevisiae, respectively, representing 66 and 70 % of the theoretical yield on total sugars in the hydrolysate. Because of the low xylan content of the cladode biomass, a yeast capable of xylose fermentation might not be a prerequisite for ethanol production. K. marxianus, therefore, has potential as an alternative to S. cerevisiae for bioethanol production. However, the relatively low concentration of fermentable sugars in the O. ficus-indica cladode hydrolysate presents a technical constraint for commercial exploitation.\n\nOpuntia ficus-indica cladodes as feedstock for ethanol production by Kluyveromyces marxianus and Saccharomyces cerevisiae.", "token_count": 475, "char_count": 1747, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5858, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:24.466611", "source": { "split": "train_shard_00000", "doc_id": 4563 }, "chunk_id": "train_shard_00000_4563_0", "global_id": 5096 }, { "text": "Administration of probiotic Lactobacillus cultures is an important alternative to the use of antibiotic growth promoters and has been demonstrated to improve animal health, growth performance, and preharvest food safety in poultry production. Whereas gastrointestinal colonization is thought to be critical to their probiotic functionality, factors important to Lactobacillus colonization in chickens are not well understood. In this study we investigate epithelial cell adhesion in vitro and colonization of Lactobacillusin vivo in broiler chickens. Adhesion of Lactobacillus cultures to epithelial cells was evaluated using the chicken LMH cell line. Lactobacillus cultures were able adhere effectively to LMH cells relative to Bacillus subtilis and Salmonella Typhimurium. Epithelial cell adhesion was similar for Lactobacillus crispatus TDCC 75, L. cristpatus TDCC 76, and Lactobacillus gallinarum TDCC 77, and all 3 were more adherent than L. gallinarum TDCC 78. However, when colonization was evaluated in the ileum and cecum of broiler chicks, L. crispatus TDCC 75 and L. gallinarum TDCC 77 were more persistent than L. crispatus TDCC 76 and L. gallinarum TDCC 78. The reduction of growth in medium supplemented with oxgal was greater for L. gallinarum TDCC 78 than L. gallinarum TDCC 77, suggesting that whereas adhesion was similar for the 2 strains, the difference in colonization between L. gallinarum strains may be due in part to their bile sensitivity. This study demonstrates that whereas adhesion to epithelial cells may be important in predicting gastrointestinal colonization, other factors including bile tolerance may also contribute to the colonization of Lactobacillus in poultry. Additionally, the chicken LMH cell line is expected to provide a platform for investigating mechanisms of Lactobacillus adhesion to epithelial tissue and evaluating the probiotic potential Lactobacillus in poultry.", "token_count": 514, "char_count": 1917, "word_count": 278, "semantic_coherence": 1, "information_density": 0.4856, "quality_score": 0.7428, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:45:25.133589", "source": { "split": "train_shard_00000", "doc_id": 4564 }, "chunk_id": "train_shard_00000_4564_0", "global_id": 5097 }, { "text": "Epithelial cell adhesion and gastrointestinal colonization of Lactobacillus in poultry.", "token_count": 28, "char_count": 87, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:25.488044", "source": { "split": "train_shard_00000", "doc_id": 4564 }, "chunk_id": "train_shard_00000_4564_1", "global_id": 5098 }, { "text": "Deficiency of the phospholipid flippase ATPase, aminophospholipid transporter, class I, type 8B, member 1 (ATP8B1) causes progressive familial intrahepatic cholestasis type 1 (PFIC1) and benign recurrent intrahepatic cholestasis type 1 (BRIC1). Apart from cholestasis, many patients also suffer from diarrhea of yet unknown etiology. Here we have studied the hypothesis that intestinal ATP8B1 deficiency results in bile salt malabsorption as a possible cause of PFIC1/BRIC1 diarrhea. Bile salt transport was studied in ATP8B1-depleted intestinal Caco-2 cells. Apical membrane localization was studied by a biotinylation approach. Fecal bile salt and electrolyte contents were analyzed in stool samples of PFIC1 patients, of whom some had undergone biliary diversion or liver transplantation. Bile salt uptake by the apical sodium-dependent bile salt transporter solute carrier family 10 (sodium/bile acid cotransporter), member 2 (SLC10A2) was strongly impaired in ATP8B1-depleted Caco-2 cells. The reduced SLC10A2 activity coincided with strongly reduced apical membrane localization, which was caused by impaired apical membrane insertion of SLC10A2. Moreover, we show that endogenous ATP8B1 exists in a functional heterodimer with transmembrane protein 30A (CDC50A) in Caco-2 cells. Analyses of stool samples of post-transplant PFIC1 patients demonstrated that bile salt content was not changed, whereas sodium and chloride concentrations were elevated and potassium levels were decreased. The ATP8B1-CDC50A heterodimer is essential for the apical localization of SLC10A2 in Caco-2 cells. Diarrhea in PFIC1/BRIC1 patients has a secretory origin to which SLC10A2 deficiency may contribute", "token_count": 505, "char_count": 1690, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.806, "entities": { "genes": [ "PFIC1", "BRIC1", "CDC50A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:26.134690", "source": { "split": "train_shard_00000", "doc_id": 4565 }, "chunk_id": "train_shard_00000_4565_0", "global_id": 5099 }, { "text": "This results in elevated luminal bile salt concentrations and consequent enhanced electrolyte secretion and/or reduced electrolyte resorption.\n\nThe lipid flippase heterodimer ATP8B1-CDC50A is essential for surface expression of the apical sodium-dependent bile acid transporter (SLC10A2/ASBT) in intestinal Caco-2 cells.", "token_count": 93, "char_count": 320, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8974, "quality_score": 0.9487, "entities": { "genes": [ "CDC50A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:26.504206", "source": { "split": "train_shard_00000", "doc_id": 4565 }, "chunk_id": "train_shard_00000_4565_1", "global_id": 5100 }, { "text": "Burkholderia pseudomallei (Bp) is the causative agent of the infectious disease melioidosis. To investigate population diversity, recombination, and horizontal gene transfer in closely related Bp isolates, we performed whole-genome sequencing (WGS) on 106 clinical, animal, and environmental strains from a restricted Asian locale. Whole-genome phylogenies resolved multiple genomic clades of Bp, largely congruent with multilocus sequence typing (MLST). We discovered widespread recombination in the Bp core genome, involving hundreds of regions associated with multiple haplotypes. Highly recombinant regions exhibited functional enrichments that may contribute to virulence. We observed clade-specific patterns of recombination and accessory gene exchange, and provide evidence that this is likely due to ongoing recombination between clade members. Reciprocally, interclade exchanges were rarely observed, suggesting mechanisms restricting gene flow between clades. Interrogation of accessory elements revealed that each clade harbored a distinct complement of restriction-modification (RM) systems, predicted to cause clade-specific patterns of DNA methylation. Using methylome sequencing, we confirmed that representative strains from separate clades indeed exhibit distinct methylation profiles. Finally, using an E. coli system, we demonstrate that Bp RM systems can inhibit uptake of non-self DNA. Our data suggest that RM systems borne on mobile elements, besides preventing foreign DNA invasion, may also contribute to limiting exchanges of genetic material between individuals of the same species. Genomic clades may thus represent functional units of genetic isolation in Bp, modulating intraspecies genetic diversity.\n\nBurkholderia pseudomallei sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles.", "token_count": 411, "char_count": 1860, "word_count": 240, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:27.123093", "source": { "split": "train_shard_00000", "doc_id": 4566 }, "chunk_id": "train_shard_00000_4566_0", "global_id": 5101 }, { "text": "Classifications of the Campylobacter fetus subspecies fetus and venerealis were first described in 1959 and were based on the source of isolation (intestinal versus genital) and the ability of the strains to proliferate in the genital tract of cows. Two phenotypic assays (1% glycine tolerance and H2S production) were described to differentiate the subspecies. Multiple molecular assays have been applied to differentiate the C. fetus subspecies, but none of these tests is consistent with the phenotypic identification methods. In this study, we defined the core genome and accessory genes of C. fetus, which are based on the closed genomes of five C. fetus strains. Phylogenetic analysis of the core genomes of 23 C. fetus strains of the two subspecies showed a division into two clusters. The phylogenetic core genome clusters were not consistent with the phenotypic classifications of the C. fetus subspecies. However, they were consistent with the molecular characteristics of the strains, which were determined by multilocus sequence typing, sap typing, and the presence/absence of insertion sequences and a type I restriction modification system. The similarity of the genome characteristics of three of the phenotypically defined C. fetus subsp. fetus strains to C. fetus subsp. venerealis strains, when considering the core genome and accessory genes, requires a critical evaluation of the clinical relevance of C. fetus subspecies identification by phenotypic assays.\n\nInconsistency of phenotypic and genomic characteristics of Campylobacter fetus subspecies requires reevaluation of current diagnostics.", "token_count": 391, "char_count": 1615, "word_count": 237, "semantic_coherence": 1, "information_density": 0.481, "quality_score": 0.7405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:27.738869", "source": { "split": "train_shard_00000", "doc_id": 4567 }, "chunk_id": "train_shard_00000_4567_0", "global_id": 5102 }, { "text": "Bifidobacteria are normal inhabitants of the human gut, and members of which are generally considered to be probiotic. Before exerting their beneficial properties, they must survive and persist in the physiological concentrations (0.05-2%) of bile in the gut. In this work, the functional role of tlyC1 encoding a hemolysin-like protein from Bifidobacterium longum BBMN68 in bile tolerance was tested. Analysis using the program TMHMM and homologous alignment indicated that TlyC1 is a nontransporter membrane protein and is conserved in many bifidobacteria. Heterologous expression of tlyC1 in Lactococcus lactis NZ9000 was shown to confer 45-fold higher tolerance to 0.15% ox-bile. Notably, the recombinant strains showed threefold higher survival when exposed to sublethal concentration of TCA and TDCA, while no significant change was observed when exposed to GCA and GDCA. Furthermore, real-time quantitative PCR demonstrated that the transcription of tlyC1 was up-regulated c. 2.5- and 2.7-fold in B. longum BBMN68 exposed to sublethal concentration of TCA and TDCA, while no significant change was observed with GCA and GDCA challenges. This study indicated that tlyC1 was specifically induced by tauroconjugates, which provided enhanced resistance to sodium taurocholate and sodium taurodeoxycholate.\n\nFunctional role of tlyC1 encoding a hemolysin-like protein from Bifidobacterium longum BBMN68 in bile tolerance.", "token_count": 393, "char_count": 1422, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5792, "quality_score": 0.7896, "entities": { "genes": [ "BBMN68", "NZ9000" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:28.360571", "source": { "split": "train_shard_00000", "doc_id": 4568 }, "chunk_id": "train_shard_00000_4568_0", "global_id": 5103 }, { "text": "Preterm infants often experience suboptimal growth, which can affect organ development. The aim of this study was to improve growth by treatment with bile salt-stimulated lipase (BSSL), naturally present in breast milk, but lost after pasteurization, and absent in formula.\n\nrhBSSL improves growth and LCPUFA absorption in preterm infants fed formula or pasteurized breast milk.", "token_count": 87, "char_count": 378, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8727, "quality_score": 0.9364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:28.737009", "source": { "split": "train_shard_00000", "doc_id": 4569 }, "chunk_id": "train_shard_00000_4569_0", "global_id": 5104 }, { "text": "Wild relatives of crops are an important source of genetic diversity for agriculture, but their gene repertoire remains largely unexplored. We report the establishment and analysis of a pan-genome of Glycine soja, the wild relative of cultivated soybean Glycine max, by sequencing and de novo assembly of seven phylogenetically and geographically representative accessions. Intergenomic comparisons identified lineage-specific genes and genes with copy number variation or large-effect mutations, some of which show evidence of positive selection and may contribute to variation of agronomic traits such as biotic resistance, seed composition, flowering and maturity time, organ size and final biomass. Approximately 80% of the pan-genome was present in all seven accessions (core), whereas the rest was dispensable and exhibited greater variation than the core genome, perhaps reflecting a role in adaptation to diverse environments. This work will facilitate the harnessing of untapped genetic diversity from wild soybean for enhancement of elite cultivars.\n\nDe novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits.", "token_count": 255, "char_count": 1162, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6788, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:29.233613", "source": { "split": "train_shard_00000", "doc_id": 4570 }, "chunk_id": "train_shard_00000_4570_0", "global_id": 5105 }, { "text": "Estrogens can cause liver cholestatic disease. As downregulation of hepatocyte canalicular aquaporin-8 (AQP8) water channels has been involved in estrogen-induced bile secretory failure, we tested whether the archetypal water channel AQP1 improves 17α-ethinylestradiol (EE)-induced cholestasis. EE administration to rats reduced bile flow by 50%. A recombinant adenoviral (Ad) vector encoding human AQP1 (hAQP1), AdhAQP1, or a control vector was administered by retrograde bile ductal infusion. Hepatocyte canalicular hAQP1 expression was confirmed by liver immunostaining and immunoblotting in purified membrane fractions. Accordingly, canalicular osmotic water permeability was markedly increased. Bile flow, either basal or bile salt-stimulated was significantly augmented by over 50%. The choleretic efficiency of endogenous bile salts (that is, volume of bile per μmol of excreted bile salt) was significantly increased by 45% without changes in the biliary bile salt composition. Our data suggest that the adenoviral transfer of hAQP1 gene to the livers of EE-induced cholestatic rats improves bile flow by enhancing the AQP-mediated bile salt-induced canalicular water secretion. This novel finding might have potential therapeutic implications for cholestatic diseases.\n\nAdenoviral transfer of human aquaporin-1 gene to rat liver improves bile flow in estrogen-induced cholestasis.", "token_count": 396, "char_count": 1389, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "AQP8", "AQP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:29.851668", "source": { "split": "train_shard_00000", "doc_id": 4571 }, "chunk_id": "train_shard_00000_4571_0", "global_id": 5106 }, { "text": "The environmental impact of agricultural waste from the processing of food and feed crops is an increasing concern worldwide. Concerted efforts are underway to develop sustainable practices for the disposal of residues from the processing of such crops as coffee, sugarcane, or corn. Coffee is crucial to the economies of many countries because its cultivation, processing, trading, and marketing provide employment for millions of people. In coffee-producing countries, improved technology for treatment of the significant amounts of coffee waste is critical to prevent ecological damage. This mini-review discusses a multi-stage biorefinery concept with the potential to convert waste produced at crop processing operations, such as coffee pulping stations, to valuable biofuels and bioproducts using biochemical and thermochemical conversion technologies. The initial bioconversion stage uses a mutant Kluyveromyces marxianus yeast strain to produce bioethanol from sugars. The resulting sugar-depleted solids (mostly protein) can be used in a second stage by the oleaginous yeast Yarrowia lipolytica to produce bio-based ammonia for fertilizer and are further degraded by Y. lipolytica proteases to peptides and free amino acids for animal feed. The lignocellulosic fraction can be ground and treated to release sugars for fermentation in a third stage by a recombinant cellulosic Saccharomyces cerevisiae, which can also be engineered to express valuable peptide products. The residual protein and lignin solids can be jet cooked and passed to a fourth-stage fermenter where Rhodotorula glutinis converts methane into isoprenoid intermediates. The residues can be combined and transferred into pyrocracking and hydroformylation reactions to convert ammonia, protein, isoprenes, lignins, and oils into renewable gas. Any remaining waste can be thermoconverted to biochar as a humus soil enhancer. The integration of multiple technologies for treatment of coffee waste has the potential to contribute to economic and environmental sustainability.\n\nSustainable conversion of coffee and other crop wastes to biofuels and bioproducts using coupled biochemical and thermochemical processes in a multi-stage biorefinery concept.", "token_count": 507, "char_count": 2226, "word_count": 313, "semantic_coherence": 1, "information_density": 0.6006, "quality_score": 0.8003, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:30.509533", "source": { "split": "train_shard_00000", "doc_id": 4572 }, "chunk_id": "train_shard_00000_4572_0", "global_id": 5107 }, { "text": "The aim of this study was to prepare candesartan cilexetil-loaded niosomes and mixed niosomes to enhance the aqueous solubility of the drug, thus improving its oral bioavailability. The formulations were prepared using various types and combinations of surfactants, copolymers, and charge-inducing agents. The candesartan cilexetil entrapment efficiency, particle size, and zeta potential of these niosomes varied within the range of 99.06 ± 1.74 to 36.26 ± 2.78, 157.3 ± 3.3 to 658.3 ± 12.7 nm, and -14.7 ± 2.8 to -44.5 ± 1.5 mV, respectively. The in vitro drug release from niosomes was improved after niosomal entrapment compared to pure candesartan cilexetil. The sedimentation behavior study and formulation stability tests against bile salt revealed that mixed niosomes prepared by combining Span 60 and Pluronic P85 demonstrated better stability. The differential scanning calorimetry analysis showed the conversion of crystal structure of candesartan cilexetil to the soluble amorphous form after niosomal encapsulation which induced the drug release. Consequently, oral drug delivery by Span 60/Pluronic P85-mixed niosomes seems feasible due to enhanced drug release and stability.\n\nDevelopment and characterization of mixed niosomes for oral delivery using candesartan cilexetil as a model poorly water-soluble drug.", "token_count": 411, "char_count": 1326, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:31.130034", "source": { "split": "train_shard_00000", "doc_id": 4573 }, "chunk_id": "train_shard_00000_4573_0", "global_id": 5108 }, { "text": "Bile salt aggregates incorporate aqueous-insoluble photochromic compounds. The photochromism of a spiropyran (1, 1',3',3'-trimethyl-6-nitrospiro[2H-1]-benzopyran-2,2'-indoline) and a diarylethene derivative (2, 1,2-bis(2,4-dimethyl-5-phenyl-3-thienyl)-3,3,4,4,5,5-hexafluoro-1-cyclopentene) was quantified in different bile salt aggregates. These aggregates act as efficient hosts to solubilize aqueous insoluble photochromic compounds where either both isomers are nonpolar, for example, 2, or compounds where one isomer is hydrophobic and the other is more polar, for example, 1. Methodology was developed to determine molar absorptivity coefficients for solutions containing both isomers and to determine the photoconversion quantum yields under continuous irradiation. The methods were validated by determining parameters in homogeneous solution, which were the same as previously reported. In the case of the colored isomer of 1, the molar extinction coefficient in ethanol at 537 nm ((3.68 ± 0.03) × 10(4) cm(-1) M(-1)) was determined with higher precision. The quantum yields for the photoconversion between the isomers of 2 were shown to be the same in cyclohexane and in the aggregates of sodium cholate (NaCh), deoxycholate (NaDC), and taurocholate (NaTC), showing that bile salt aggregates are not sufficiently rigid to affect the equilibrium between the two possible conformers of the colorless form. In contrast, for 1 the quantum yields for the conversion from the colorless to the colored isomer were higher in bile salts than in ethanol, and the quantum yield was highest in the more hydrophobic aggregates of NaDC, followed by NaCh and then NaTC. The structure of the bile salt had no effect on the quantum yield for the conversion of the colored to the colorless isomer of 1, but these values were higher than in ethanol", "token_count": 518, "char_count": 1838, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5396, "quality_score": 0.7698, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:45:31.789287", "source": { "split": "train_shard_00000", "doc_id": 4574 }, "chunk_id": "train_shard_00000_4574_0", "global_id": 5109 }, { "text": "For all three bile salts, the absorption maximum for the colored form of 1 suggested that this isomer was located in an environment that is more polar than ethanol.\n\nPhotochromism of a spiropyran and a diarylethene in bile salt aggregates in aqueous solution.", "token_count": 68, "char_count": 259, "word_count": 43, "semantic_coherence": 1, "information_density": 0.814, "quality_score": 0.907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:32.155332", "source": { "split": "train_shard_00000", "doc_id": 4574 }, "chunk_id": "train_shard_00000_4574_1", "global_id": 5110 }, { "text": "Methods for error-less gene synthesis are desired because synthesized genes often contain mutations. By cloning PCR-assembled oligonucleotide fragments fused to a selection marker in yeast, we developed a novel method to screen accurate clones in gene synthesis. As a model case, the 555-bp luciferase gene from Gaussia princeps (GLuc) was synthesized to contain yeast-optimized codons (called yGLuc hereafter). After standard PCR-mediated oligonucleotide assembly, many clones showed no luciferase activity. Of these clones, most contained randomly located nucleotide deletions that produced frameshifts and resulted in premature termination. To exclude clones with premature termination, the synthesized yGLuc gene was cloned in-frame to fuse with the URA3 coding sequence, which served as a selection marker in the yeast Kluyveromyces marxianus. Ura(+) transformation selection was expected to eliminate clones with frameshift errors. The results showed that in-frame marker selection increased the frequency of active yGLuc gene to 79%. We used this strategy to synthesize the 1812-bp gene from Rhizopus oryzae that encodes glucoamylase. Five out of seven Ura(+) clones exhibited amylase activity. Of the functional clones, one contained the correct sequence, and four contained sequences with nucleotide changes, suggesting that in-frame selection frequently produced functional mutants. The K. marxianus non-homologous end joining mediated cloning method for gene synthesis will be useful for synthetic biological studies.\n\nScreening of accurate clones for gene synthesis in yeast.", "token_count": 395, "char_count": 1587, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:32.772994", "source": { "split": "train_shard_00000", "doc_id": 4575 }, "chunk_id": "train_shard_00000_4575_0", "global_id": 5111 }, { "text": "The fitness of sensitive and resistant Pseudomonas aeruginosa in different aquatic environments depends on genetic capacities and transcriptional regulation. Therefore, an antibiotic-sensitive isolate PA30 and a multi-resistant isolate PA49 originating from waste waters were compared via whole genome and transcriptome Illumina sequencing after exposure to municipal waste water and tap water. A number of different genomic islands (e.g. PAGIs, PAPIs) were identified in the two environmental isolates beside the highly conserved core genome. Exposure to tap water and waste water exhibited similar transcriptional impacts on several gene clusters (antibiotic and metal resistance, genetic mobile elements, efflux pumps) in both environmental P. aeruginosa isolates. The MexCD-OprJ efflux pump was overexpressed in PA49 in response to waste water. The expression of resistance genes, genetic mobile elements in PA49 was independent from the water matrix. Consistently, the antibiotic sensitive strain PA30 did not show any difference in expression of the intrinsic resistance determinants and genetic mobile elements. Thus, the exposure of both isolates to polluted waste water and oligotrophic tap water resulted in similar expression profiles of mentioned genes. However, changes in environmental milieus resulted in rather unspecific transcriptional responses than selected and stimuli-specific gene regulation.\n\nWhole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water.", "token_count": 354, "char_count": 1584, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5421, "quality_score": 0.771, "entities": { "genes": [ "PA30", "PA49" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:33.355479", "source": { "split": "train_shard_00000", "doc_id": 4576 }, "chunk_id": "train_shard_00000_4576_0", "global_id": 5112 }, { "text": "Hyperuricemia is well known as the cause of gout. In recent years, it has also been recognized as a risk factor for arteriosclerosis, cerebrovascular and cardiovascular diseases, and nephropathy in diabetic patients. Foods high in purine compounds are more potent in exacerbating hyperuricemia. Therefore, the development of probiotics that efficiently degrade purine compounds is a promising potential therapy for the prevention of hyperuricemia. In this study, fifty-five lactic acid bacteria isolated from Chinese sauerkraut were evaluated for the ability to degrade inosine and guanosine, the two key intermediates in purine metabolism. After a preliminary screening based on HPLC, three candidate strains with the highest nucleoside degrading rates were selected for further characterization. The tested biological characteristics of candidate strains included acid tolerance, bile tolerance, anti-pathogenic bacteria activity, cell adhesion ability, resistance to antibiotics and the ability to produce hydrogen peroxide. Among the selected strains, DM9218 showed the best probiotic potential compared with other strains despite its poor bile resistance. Analysis of 16S rRNA sequences showed that DM9218 has the highest similarity (99%) to Lactobacillus plantarum WCFS1. The acclimated strain DM9218-A showed better resistance to 0.3% bile salt, and its survival in gastrointestinal tract of rats was proven by PCR-DGGE. Furthermore, the effects of DM9218-A in a hyperuricemia rat model were evaluated. The level of serum uric acid in hyperuricemic rat can be efficiently reduced by the intragastric administration of DM9218-A (P<0.05). The preventive treatment of DM9218-A caused a greater reduction in serum uric acid concentration in hyperuricemic rats than the later treatment (P<0.05). Our results suggest that DM9218-A may be a promising candidate as an adjunctive treatment in patients with hyperuricemia during the onset period of disease", "token_count": 499, "char_count": 1953, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6137, "quality_score": 0.8069, "entities": { "genes": [ "DM9218", "WCFS1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:34.008320", "source": { "split": "train_shard_00000", "doc_id": 4577 }, "chunk_id": "train_shard_00000_4577_0", "global_id": 5113 }, { "text": "DM9218-A also has potential as a probiotic in the prevention of hyperuricemia in the normal population.\n\nScreening and characterization of purine nucleoside degrading lactic acid bacteria isolated from Chinese sauerkraut and evaluation of the serum uric acid lowering effect in hyperuricemic rats.", "token_count": 77, "char_count": 297, "word_count": 42, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [ "DM9218" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:34.377104", "source": { "split": "train_shard_00000", "doc_id": 4577 }, "chunk_id": "train_shard_00000_4577_1", "global_id": 5114 }, { "text": "The Pseudomonas syringae complex is composed of numerous genetic lineages of strains from both agricultural and environmental habitats including habitats closely linked to the water cycle. The new insights from the discovery of this bacterial species in habitats outside of agricultural contexts per se have led to the revelation of a wide diversity of strains in this complex beyond what was known from agricultural contexts. Here, through Multi Locus Sequence Typing (MLST) of 216 strains, we identified 23 clades within 13 phylogroups among which the seven previously described P. syringae phylogroups were included. The phylogeny of the core genome of 29 strains representing nine phylogroups was similar to the phylogeny obtained with MLST thereby confirming the robustness of MLST-phylogroups. We show that phenotypic traits rarely provide a satisfactory means for classification of strains even if some combinations are highly probable in some phylogroups. We demonstrate that the citrate synthase (cts) housekeeping gene can accurately predict the phylogenetic affiliation for more than 97% of strains tested. We propose a list of cts sequences to be used as a simple tool for quickly and precisely classifying new strains. Finally, our analysis leads to predictions about the diversity of P. syringae that is yet to be discovered. We present here an expandable framework mainly based on cts genetic analysis into which more diversity can be integrated.\n\nA user's guide to a data base of the diversity of Pseudomonas syringae and its application to classifying strains in this phylogenetic complex.", "token_count": 368, "char_count": 1606, "word_count": 246, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:34.984704", "source": { "split": "train_shard_00000", "doc_id": 4578 }, "chunk_id": "train_shard_00000_4578_0", "global_id": 5115 }, { "text": "Pseudomonas aeruginosa PGPR2 is a mung bean rhizosphere strain that produces secondary metabolites and hydrolytic enzymes contributing to excellent antifungal activity against Macrophomina phaseolina, one of the prevalent fungal pathogens of mung bean. Genome sequencing was performed using the Ion Torrent Personal Genome Machine generating 1,354,732 reads (6,772,433 sequenced bases) achieving ~25-fold coverage of the genome. Reference genome assembly using MIRA 3.4.0 yielded 198 contigs. The draft genome of PGPR2 encoded 6803 open reading frames, of which 5314 were genes with predicted functions, 1489 were genes of known functions, and 80 were RNA-coding genes. Strain specific and core genes of P. aeruginosa PGPR2 that are relevant to rhizospheric habitat were identified by pangenome analysis. Genes involved in plant growth promoting function such as synthesis of ACC deaminase, indole-3-acetic acid, trehalose, mineral scavenging siderophores, hydrogen cyanide, chitinases, acyl homoserine lactones, acetoin, 2,3-butanediol, and phytases were identified. In addition, niche-specific genes such as phosphate solubilising 3-phytase, adhesins, pathway-specific transcriptional regulators, a diguanylate cyclase involved in cellulose synthesis, a receptor for ferrienterochelin, a DEAD/DEAH-box helicase involved in stress tolerance, chemotaxis/motility determinants, an HtpX protease, and enzymes involved in the production of a chromanone derivative with potent antifungal activity were identified.\n\nGenome Sequencing of a Mung Bean Plant Growth Promoting Strain of P. aeruginosa with Biocontrol Ability.", "token_count": 467, "char_count": 1615, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [ "PGPR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:35.652860", "source": { "split": "train_shard_00000", "doc_id": 4579 }, "chunk_id": "train_shard_00000_4579_0", "global_id": 5116 }, { "text": "Fungal species play extremely important roles in ecosystems. Clustered at the base of the fungal kingdom are Microsporidia, a group of obligate intracellular eukaryotes infecting multiple animal lineages. Because of their large host spectrum and their implications in host population regulation, they influence food webs, and accordingly, ecosystem structure and function. Unfortunately, their ecological role is not well understood. Present also as highly resistant spores in the environment, their characterisation requires special attention. Different techniques based on direct isolation and/or molecular approaches can be considered to elucidate their role in the ecosystems, but integrating environmental and genomic data (for example, genome architecture, core genome, transcriptional and translational signals) is crucial to better understand the diversity and adaptive capacities of Microsporidia. Here, we review the current status of Microsporidia in trophic networks; the various genomics tools that could be used to ensure identification and evaluate diversity and abundance of these organisms; and how these tools could be used to explore the microsporidian life cycle in different environments. Our understanding of the evolution of these widespread parasites is currently impaired by limited sampling, and we have no doubt witnessed but a small subset of their diversity.\n\nExploiting the architecture and the features of the microsporidian genomes to investigate diversity and impact of these parasites on ecosystems.", "token_count": 306, "char_count": 1533, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:36.249545", "source": { "split": "train_shard_00000", "doc_id": 4580 }, "chunk_id": "train_shard_00000_4580_0", "global_id": 5117 }, { "text": "Butyrate has several beneficial properties that are essential to maintain gastrointestinal health. Therefore butyrate-producing bacteria are seen as the next generation of probiotics. The butyrate-producing bacterium Butyricicoccus pullicaecorum (a clostridial cluster IV strain) is such a promising probiotic candidate for people suffering from inflammatory bowel disease. To exert its beneficial properties, it is crucial that B. pullicaecorum survives the harsh conditions of the upper gastrointestinal tract to arrive in the colon in a viable and metabolically active state. Before developing a stable formulation of B. pullicaecorum for oral administration, it is important to know its intrinsic acid and bile tolerance. We monitored the survival during and short chain fatty acid production after incubation in conditions simulating the stomach and small intestine using in vitro batch experiments. In case of acid conditions (pH 2 and pH 3), B. pullicaecorum was viable and active but not cultivable. Cultivability was restored during subsequent small intestine conditions. Importantly, bile and pancreatic juice had no lethal effect. Milk, as a suspension medium, only had a protective effect on the cultivability during the first hour at pH 2. B. pullicaecorum was still metabolically active after upper gastrointestinal conditions and produced short chain fatty acids, but a shift from butyrate to acetate production was observed. Although the butyrate-producing anaerobe B. pullicaecorum showed good intrinsic acid and bile tolerance in terms of viability and metabolic activity, colonization efficiency and butyrate production under colon conditions is needed to further evaluate its probiotic potential.\n\nButyricicoccus pullicaecorum, a butyrate producer with probiotic potential, is intrinsically tolerant to stomach and small intestine conditions.", "token_count": 439, "char_count": 1862, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5785, "quality_score": 0.7893, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:36.902953", "source": { "split": "train_shard_00000", "doc_id": 4581 }, "chunk_id": "train_shard_00000_4581_0", "global_id": 5118 }, { "text": "Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genome varies from strain to strain and is therefore referred to as \"accessory genome\". Elements within the accessory genome of P. aeruginosa have been associated with differences in virulence and antibiotic resistance. As whole genome sequencing of bacterial strains becomes more widespread and cost-effective, methods to quickly and reliably identify accessory genomic elements in newly sequenced P. aeruginosa genomes will be needed.\n\nCharacterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt.", "token_count": 176, "char_count": 764, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7212, "quality_score": 0.8606, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:37.347206", "source": { "split": "train_shard_00000", "doc_id": 4582 }, "chunk_id": "train_shard_00000_4582_0", "global_id": 5119 }, { "text": "Lactobacillus and Lactococcus strains isolated from food products can be introduced as probiotics because of their health-promoting characteristics and non-pathogenic nature. This study aims to perform the isolation, molecular identification, and probiotic characterization of Lactobacillus and Lactococcus strains from traditional Iranian dairy products. Primary probiotic assessments indicated high tolerance to low pH and high bile salt conditions, high anti-pathogenic activities, and susceptibility to high consumption antibiotics, thus proving that both strains possess probiotic potential. Cytotoxicity assessments were used to analyze the effects of the secreted metabolite on different cancer cell lines, including HT29, AGS, MCF-7, and HeLa, as well as a normal human cell line (HUVEC). Results showed acceptable cytotoxic properties for secreted metabolites (40 μg/ml dry weight) of Lactococcus lactis subsp. Lactis 44Lac. Such performance was similar to that of Taxol against all of the treated cancer cell lines; however, the strain exhibited no toxicity on the normal cell line. Cytotoxic assessments through flow cytometry and fluorescent microscopy demonstrated that apoptosis is the main cytotoxic mechanism for secreted metabolites of L. lactis subsp. Lactis 44Lac. By contrast, the effects of protease-treated metabolites on the AGS cell line verified the protein nature of anti-cancer metabolites. However, precise characterizations and in vitro/in vivo investigations on purified proteins should be conducted before these metabolites are introduced as potential anti-cancer therapeutics.\n\nDifferent effects of two newly-isolated probiotic Lactobacillus plantarum 15HN and Lactococcus lactis subsp. Lactis 44Lac strains from traditional dairy products on cancer cell lines.", "token_count": 459, "char_count": 1793, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [ "HT29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:37.988096", "source": { "split": "train_shard_00000", "doc_id": 4583 }, "chunk_id": "train_shard_00000_4583_0", "global_id": 5120 }, { "text": "Campylobacter jejuni is a leading cause of foodbourne gastroenteritis, despite fragile behaviour under standard laboratory conditions. In the environment, C. jejuni may survive within biofilms, which can impart resident bacteria with enhanced stress tolerance compared to their planktonic counterparts. While C. jejuni forms biofilms in vitro and in the wild, it had not been confirmed that this lifestyle confers stress tolerance. Moreover, little is understood about molecular mechanisms of biofilm formation in this pathogen. We previously found that a ΔcprS mutant, which carries a deletion in the sensor kinase of the CprRS two-component system, forms enhanced biofilms. Biofilms were also enhanced by the bile salt deoxycholate and contained extracellular DNA. Through more in-depth analysis of ΔcprS and WT under conditions that promote or inhibit biofilms, we sought to further define this lifestyle for C. jejuni. Epistasis experiments with ΔcprS and flagellar mutations (ΔflhA, ΔpflA) suggested that initiation is mediated by flagellum-mediated adherence, a process which was kinetically enhanced by motility. Lysis was also observed, especially under biofilm-enhancing conditions. Microscopy suggested adherence was followed by release of eDNA, which was required for biofilm maturation. Importantly, inhibiting biofilm formation by removal of eDNA with DNase decreased stress tolerance. This work suggests the biofilm lifestyle provides C. jejuni with resilience that has not been apparent from observation of planktonic bacteria during routine laboratory culture, and provides a framework for subsequent molecular studies of C. jejuni biofilms.\n\nFlagella-mediated adhesion and extracellular DNA release contribute to biofilm formation and stress tolerance of Campylobacter jejuni.", "token_count": 415, "char_count": 1793, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:38.614519", "source": { "split": "train_shard_00000", "doc_id": 4584 }, "chunk_id": "train_shard_00000_4584_0", "global_id": 5121 }, { "text": "The short-term Crabtree effect is defined as the immediate occurrence of aerobic alcoholic fermentation in response to provision of a pulse of excess sugar to sugar-limited yeast cultures. Here we have characterized ten yeast species with a clearly defined phylogenetic relationship. Yeast species were cultivated under glucose-limited conditions, and we studied their general carbon metabolism in response to a glucose pulse. We generated an extensive collection of data on glucose and oxygen consumption, and ethanol and carbon dioxide generation. We conclude that the Pichia, Debaryomyces, Eremothecium and Kluyveromyces marxianus yeasts do not exhibit any significant ethanol formation, while Kluyveromyces lactis behaves as an intermediate yeast, and Lachancea, Torulaspora, Vanderwaltozyma and Saccharomyces yeasts exhibit rapid ethanol accumulation. Based on the present data and our previous data relating to the presence of the long-term Crabtree effect in over 40 yeast species, we speculate that the origin of the short-term effect may coincide with the origin of the long-term Crabtree effect in the Saccharomycetales lineage, occurring ~ 150 million years ago.\n\nAnalysis of the yeast short-term Crabtree effect and its origin.", "token_count": 305, "char_count": 1239, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6067, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:39.185046", "source": { "split": "train_shard_00000", "doc_id": 4585 }, "chunk_id": "train_shard_00000_4585_0", "global_id": 5122 }, { "text": "The inclusion complexes of glycoconjugated bile salts with β-cyclodextrin (β-CD) and 2-hydroxypropyl-β-cyclodextrins (HP-β-CD) in aqueous solution were investigated by molecular dynamics simulations to provide a molecular explanation of the experimentally observed destabilizing effect of the HP substituents. Good agreement with experimental data was found with respect to penetration depths of CDs. An increased degree of HP substitution (DS) resulted in an increased probability of blocking the cavity opening, thereby hindering the bile salt from entering CD. Further, the residence time of water molecules in the cavity increased with the DS. Release of water from the cavity resulted in a positive enthalpy change, which correlates qualitatively with the experimentally determined increase in complexation enthalpy and contributes to the enthalpy-entropy compensation. The positive change in complexation entropy with DS was not able to compensate for this unfavorable change in enthalpy induced by the HP substituents, resulting in a destabilizing effect. This was found to originate from fixation of the HP substituents and decreased free rotation of the bile salts within the CD cavities.\n\nComputational investigation of enthalpy-entropy compensation in complexation of glycoconjugated bile salts with β-cyclodextrin and analogs.", "token_count": 317, "char_count": 1338, "word_count": 186, "semantic_coherence": 1, "information_density": 0.5538, "quality_score": 0.7769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:39.748405", "source": { "split": "train_shard_00000", "doc_id": 4586 }, "chunk_id": "train_shard_00000_4586_0", "global_id": 5123 }, { "text": "The population genomics of Pseudomonas aeruginosa was analysed by genome sequencing of representative strains of the 15 most frequent clonal complexes in the P. aeruginosa population and of the five most common clones from the environment of which so far no isolate from a human infection has been detected. Gene annotation identified 5892-7187 open reading frame (ORFs; median 6381 ORFs) in the 20 6.4-7.4 Mbp large genomes. The P. aeruginosa pangenome consists of a conserved core of at least 4000 genes, a combinatorial accessory genome of a further 10 000 genes and 30 000 or more rare genes that are present in only a few strains or clonal complexes. Whole genome comparisons of single nucleotide polymorphism synteny indicated unrestricted gene flow between clonal complexes by recombination. Using standardized acute lettuce, Galleria mellonella and murine airway infection models the full spectrum of possible host responses to P. aeruginosa was observed with the 20 strains ranging from unimpaired health following infection to 100% lethality. Genome comparisons indicate that the differential genetic repertoire of clones maintains a habitat-independent gradient of virulence in the P. aeruginosa population.\n\nInterclonal gradient of virulence in the Pseudomonas aeruginosa pangenome from disease and environment.", "token_count": 375, "char_count": 1323, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:40.326992", "source": { "split": "train_shard_00000", "doc_id": 4587 }, "chunk_id": "train_shard_00000_4587_0", "global_id": 5124 }, { "text": "Bile salts are potent olfactory stimuli in fishes; however the biological functions driving such sensitivity remain poorly understood. We provide an integrative review of bile salts as semiochemicals in fish. First, we present characteristics of bile salt structure, metabolism, and function that are particularly relevant to chemical communication. Bile salts display a systematic pattern of structural variation across taxa, are efficiently synthesized, and are stable in the environment. Bile salts are released into the water via the intestine, urinary tract, or gills, and are highly water soluble. Second, we consider the potential role of bile salts as semiochemicals in the contexts of detecting nearby fish, foraging, assessing risk, migrating, and spawning. Lastly, we suggest future studies on bile salts as semiochemicals further characterize release into the environment, behavioral responses by receivers, and directly test the biological contexts underlying olfactory sensitivity.\n\nBile salts as semiochemicals in fish.", "token_count": 228, "char_count": 1034, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:40.798024", "source": { "split": "train_shard_00000", "doc_id": 4588 }, "chunk_id": "train_shard_00000_4588_0", "global_id": 5125 }, { "text": "Acidithiobacillus thiooxidans is a sulfur oxidizing acidophilic bacterium found in many sulfur-rich environments. It is particularly interesting due to its role in bioleaching of sulphide minerals. In this work, we report the genome sequence of At. thiooxidans Licanantay, the first strain from a copper mine to be sequenced and currently used in bioleaching industrial processes. Through comparative genomic analysis with two other At. thiooxidans non-metal mining strains (ATCC 19377 and A01) we determined that these strains share a large core genome of 2109 coding sequences and a high average nucleotide identity over 98%. Nevertheless, the presence of 841 strain-specific genes (absent in other At. thiooxidans strains) suggests a particular adaptation of Licanantay to its specific biomining environment. Among this group, we highlight genes encoding for proteins involved in heavy metal tolerance, mineral cell attachment and cysteine biosynthesis. Several of these genes were located near genetic motility genes (e.g. transposases and integrases) in genomic regions of over 10 kbp absent in the other strains, suggesting the presence of genomic islands in the Licanantay genome probably produced by horizontal gene transfer in mining environments.\n\nA new genome of Acidithiobacillus thiooxidans provides insights into adaptation to a bioleaching environment.", "token_count": 341, "char_count": 1367, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:41.363604", "source": { "split": "train_shard_00000", "doc_id": 4589 }, "chunk_id": "train_shard_00000_4589_0", "global_id": 5126 }, { "text": "The methylotrophic yeast, Hansenula polymorpha is an industrially important microorganism, and belongs to the best studied yeast species with well-developed tools for molecular research. The complete genome sequence of the strain NCYC495 of H. polymorpha is publicly available. Some of the well-studied strains of H. polymorpha are known to ferment glucose, cellobiose and xylose to ethanol at elevated temperature (45 - 50°C) with ethanol yield from xylose significantly lower than that from glucose and cellobiose. Increased yield of ethanol from xylose was demonstrated following directed metabolic changes but, still the final ethanol concentration achieved is well below what is considered feasible for economic recovery by distillation.\n\nMetabolic engineering and classical selection of the methylotrophic thermotolerant yeast Hansenula polymorpha for improvement of high-temperature xylose alcoholic fermentation.", "token_count": 234, "char_count": 920, "word_count": 125, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [ "NCYC495" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:41.836578", "source": { "split": "train_shard_00000", "doc_id": 4590 }, "chunk_id": "train_shard_00000_4590_0", "global_id": 5127 }, { "text": "Probiotic bacteria provide benefits in enhancing host immune responses and protecting against infection. Induction of IgA production by oral administration of probiotic bacteria in the intestine has been considered to be one reason for this beneficial effect, but the mechanisms of the effect are poorly understood. Lactobacillus gasseri SBT2055 (LG2055) is a probiotic bacterium with properties such as bile tolerance, ability to improve the intestinal environment, and it has preventive effects related to abdominal adiposity. In this study, we have found that oral administration of LG2055 induced IgA production and increased the rate of IgA(+) cell population in Peyer's patch and in the lamina propria of the mouse small intestine. The LG2055 markedly increased the amount of IgA in a co-culture of B cells and bone marrow derived dendritic cells (BMDC), and TLR2 signal is critical for it. In addition, it is demonstrated that LG2055 stimulates BMDC to promote the production of TGF-β, BAFF, IL-6, and IL-10, all critical for IgA production from B cells. Combined stimulation of B cells with BAFF and LG2055 enhanced the induction of IgA production. Further, TGF-β signal was shown to be critical for LG2055-induced IgA production in the B cell and BMDC co-culture system, but TGF-β did not induce IgA production in a culture of only B cells stimulated with LG2055. Furthermore, TGF-β was critical for the production of BAFF, IL-6, IL-10, and TGF-β itself from LG2055-stimulated BMDC. These results demonstrate that TGF-β was produced by BMDC stimulated with LG2055 and it has an autocrine/paracrine function essential for BMDC to induce the production of BAFF, IL-6, and IL-10.", "token_count": 483, "char_count": 1685, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5227, "quality_score": 0.7614, "entities": { "genes": [ "SBT2055", "LG2055", "TLR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:42.484219", "source": { "split": "train_shard_00000", "doc_id": 4591 }, "chunk_id": "train_shard_00000_4591_0", "global_id": 5128 }, { "text": "Lactobacillus gasseri SBT2055 induces TGF-β expression in dendritic cells and activates TLR2 signal to produce IgA in the small intestine.", "token_count": 47, "char_count": 138, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [ "SBT2055", "TLR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:42.847595", "source": { "split": "train_shard_00000", "doc_id": 4591 }, "chunk_id": "train_shard_00000_4591_1", "global_id": 5129 }, { "text": "The bacterial core genome is of intense interest and the volume of whole genome sequence data in the public domain available to investigate it has increased dramatically. The aim of our study was to develop a model to estimate the bacterial core genome from next-generation whole genome sequencing data and use this model to identify novel genes associated with important biological functions. Five bacterial datasets were analysed, comprising 2096 genomes in total. We developed a Bayesian decision model to estimate the number of core genes, calculated pairwise evolutionary distances (p-distances) based on nucleotide sequence diversity, and plotted the median p-distance for each core gene relative to its genome location. We designed visually-informative genome diagrams to depict areas of interest in genomes. Case studies demonstrated how the model could identify areas for further study, e.g. 25% of the core genes with higher sequence diversity in the Campylobacter jejuni and Neisseria meningitidis genomes encoded hypothetical proteins. The core gene with the highest p-distance value in C. jejuni was annotated in the reference genome as a putative hydrolase, but further work revealed that it shared sequence homology with beta-lactamase/metallo-beta-lactamases (enzymes that provide resistance to a range of broad-spectrum antibiotics) and thioredoxin reductase genes (which reduce oxidative stress and are essential for DNA replication) in other C. jejuni genomes. Our Bayesian model of estimating the core genome is principled, easy to use and can be applied to large genome datasets. This study also highlighted the lack of knowledge currently available for many core genes in bacterial genomes of significant global public health importance.\n\nDefining the estimated core genome of bacterial populations using a Bayesian decision model.", "token_count": 414, "char_count": 1853, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5699, "quality_score": 0.7849, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:43.469269", "source": { "split": "train_shard_00000", "doc_id": 4592 }, "chunk_id": "train_shard_00000_4592_0", "global_id": 5130 }, { "text": "The primary aim of this work was to investigate the potential of bile salt, sodium taurocholate (NaTC), in improving the bioavailability and anti-tumor efficacy of docetaxel (DCT) upon rectal administration. Poloxamer-based nanomicelles with thermosensitive and mucoadhesive properties were prepared using the cold method. The optimized nanomicellar formulation was evaluated in terms of physicochemical and viscoelastic parameters. Nanomicelles containing bile salt maintained sufficient gelation strength (234×10(2) mPa·s) and mucoadhesive force (17.3×10(2) dyne/cm(2)) to be retained in the upper part of the rectum. They significantly enhanced the DCT internalization across the rectal mucosa and showed a high plasma level during the first 4 hours of the study period, compared to nanomicelles with no bile salt. As a result, a slightly higher rectal bioavailability of ~33% was observed in nanomicelles containing bile salt, compared to ~28% from the latter system. The higher pharmacokinetic parameters for rectally administered DCT/P407/P188/Tween 80/NaTC (0.25%/11%/15%/10%/0.1% by weight, respectively) resulted in significant anti-tumor efficacy. However, the tumor regression rate for the NaTC group was not statistically different from that for nanomicelles without NaTC. Therefore, overall results suggest that thermosensitive nanomicelles could be a potential dosage form for improvement of the bioavailability and chemotherapeutic profile of DCT.\n\nThe influence of bile salt on the chemotherapeutic response of docetaxel-loaded thermosensitive nanomicelles.", "token_count": 423, "char_count": 1573, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:44.101943", "source": { "split": "train_shard_00000", "doc_id": 4593 }, "chunk_id": "train_shard_00000_4593_0", "global_id": 5131 }, { "text": "Inulin is a polyfructan that is abundant in plants such as Jerusalem artichoke, chicory and dahlia. Inulinase can easily hydrolyze inulin to fructose, which is consumed by microorganisms. Generally, Saccharomyces cerevisiae, an industrial workhorse strain for bioethanol production, is known for not having inulinase activity. The inulinase gene from Kluyveromyces marxianus (KmINU), with the ability of converting inulin to fructose, was introduced into S. cerevisiae D452-2. The inulinase gene was fused to three different types of promoter (GPD, PGK1, truncated HXT7) and secretory signal sequence (KmINU, MFα1, SUC2) to generate nine expression cassettes. The inulin fermentation performance of the nine transformants containing different promoter and signal sequence combinations for inulinase production were compared to select an optimized expression system for efficient inulin fermentation. Among the nine inulinase-producing transformants, the S. cerevisiae carrying the PGK1 promoter and MFα1 signal sequence (S. cerevisiae D452-2/p426PM) showed not only the highest specific KmINU activity, but also the best inulin fermentation capability. Finally, a batch fermentation of the selected S. cerevisiae D452-2/p426PM in a bioreactor with 188.2 g/L inulin was performed to produce 80.2 g/L ethanol with 0.43 g ethanol/g inulin of ethanol yield and 1.22 g/L h of ethanol productivity.\n\nOptimizing promoters and secretory signal sequences for producing ethanol from inulin by recombinant Saccharomyces cerevisiae carrying Kluyveromyces marxianus inulinase.", "token_count": 454, "char_count": 1563, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "PGK1", "HXT7", "SUC2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:44.739092", "source": { "split": "train_shard_00000", "doc_id": 4594 }, "chunk_id": "train_shard_00000_4594_0", "global_id": 5132 }, { "text": "Intrahepatic cholestasis of pregnancy (ICP) is defined as pruritus during pregnancy in the absence of primary skin lesions, combined with an increase in serum total bile salts and/or abnormal serum liver tests. This article provides an insight into the diagnostic and therapeutic considerations by presenting two cases. ICP usually presents around 34 weeks of gestation, but can be present early in pregnancy as described in a 32-year-old patient pregnant after in-vitro fertilization. DNA analysis showed a mutation in the ABCB4 gene, causing MDR3 deficiency. Ursodeoxycholic acid treatment seems to alleviate maternal pruritus and possibly reduces perinatal risks related to the severe form of ICP, defined as fasted serum bile salt levels of ≥ 40 μmol/l at any point during the pregnancy. Short-term rifampicin treatment can be considered in patients with persistent pruritus. Induction of labour is advised only after 37 weeks of gestation in patients with severe ICP.\n\n[Risks of intrahepatic cholestasis of pregnancy].", "token_count": 261, "char_count": 1023, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "ABCB4", "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:45.287902", "source": { "split": "train_shard_00000", "doc_id": 4595 }, "chunk_id": "train_shard_00000_4595_0", "global_id": 5133 }, { "text": "Superoxide dismutase (SOD; EC 1.15.1.1) is an antioxidant enzyme that represents the primary cellular defense against superoxide radicals and has interesting applications in the medical and cosmetic industries. In the present work, the partition behavior of SOD in aqueous two-phase systems (ATPS) (using a standard solution and a complex extract from Kluyveromyces marxianus as sample) was characterized on different types of ATPS (polymer-polymer, polymer-salt, alcohol-salt, and ionic liquid (IL)-salt). The systems composed of PEG 3350-potassium phosphate, 45% TLL, 0.5 M NaCl (315 U/mg, 87% recovery, and 15.1-fold purification) and t-butanol-20% ammonium sulfate (205.8 U/mg, 80% recovery and 9.8-fold purification), coupled with a subsequent 100 kDa ultrafiltration stage, allowed the design of a prototype process for the recovery and partial purification of the product of interest. The findings reported herein demonstrate the potential of PEG-salt ATPS for the potential recovery of SOD.\n\nPotential application of aqueous two-phase systems and three-phase partitioning for the recovery of superoxide dismutase from a clarified homogenate of Kluyveromyces marxianus.", "token_count": 346, "char_count": 1176, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6748, "quality_score": 0.8374, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:45.858567", "source": { "split": "train_shard_00000", "doc_id": 4596 }, "chunk_id": "train_shard_00000_4596_0", "global_id": 5134 }, { "text": "The terminal ileum (TI) is important for the active reabsorption of bile salts and is the site of allograft rejection; disruption of enterohepatic circulation (EHC) may give insights to inflammatory and other physiologic processes at the TI.\n\nSelenium homocholic acid taurocholate scanning, selenium-75-labeled bile acid, a novel method for testing the function of the terminal ileum in small bowel transplant recipients: a pilot study.", "token_count": 122, "char_count": 436, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7656, "quality_score": 0.8828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:46.244618", "source": { "split": "train_shard_00000", "doc_id": 4597 }, "chunk_id": "train_shard_00000_4597_0", "global_id": 5135 }, { "text": "An on-line surfactant mediated extraction method in a flow injection analysis format with fluorescence detection was developed for the determination of Rhodamine B (RhB) in food condiments. The sample was extracted using the phase separation behavior exhibited by the bile salt surfactant, sodium cholate (NaC), upon addition of sodium dodecylsulfate (SDS) in the presence of acid at room temperature. The RhB in the sample was incorporated into the NaC/SDS coacervate phase which was then collected on a glass-wool packed mini column from which it was subsequently eluted using a 1.00 mol L(-1) HCl solution. The inherent fluorescence (λex=555 nm; λem=575 nm) of RhB was employed for detection. Good linearity (r(2)=0.9933) was obtained over the concentration range 0.4-4794-479.0 µg L(-1) RhB. The detection (LOD) and quantification (LOQ) limits were 0.12 and 0.40 µg L(-1), respectively. The method was successfully applied for analysis of RhB in food condiments and spiked samples. The average recoveries ranged from 95.3% to 118.9% at spiked concentration levels of 1.19 and 2.39 µg L(-1). Under optimized conditions, a throughput of 50 samples per hour was achieved. The proposed method may be a valuable tool not only for quality control of food condiments and similar food confectioneries but for the analysis of a variety of other RhB-containing samples as well.\n\nFluorescence method using on-line sodium cholate coacervate surfactant mediated extraction for the flow injections analysis of Rhodamine B.", "token_count": 433, "char_count": 1512, "word_count": 230, "semantic_coherence": 1, "information_density": 0.613, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:46.876435", "source": { "split": "train_shard_00000", "doc_id": 4598 }, "chunk_id": "train_shard_00000_4598_0", "global_id": 5136 }, { "text": "The self-assembly of biological surfactants in water is an important topic for study because of its relevance to physiological processes. Two common types of biosurfactants are lecithin (phosphatidylcholine) and bile salts, which are both present in bile and involved in digestion. Previous studies on lecithin-bile salt mixtures have reported the formation of short, rodlike micelles. Here, we show that lecithin-bile salt micelles can be further induced to grow into long, flexible wormlike structures. The formation of long worms and their resultant entanglement into transient networks is reflected in the rheology: the fluids become viscoelastic and exhibit Maxwellian behavior, and their zero-shear viscosity can be up to a 1000-fold higher than that of water. The presence of worms is further confirmed by data from small-angle neutron and X-ray scattering and from cryo-transmission electron microscopy (cryo-TEM). We find that micellar growth peaks at a specific molar ratio (near equimolar) of bile salt:lecithin, which suggests a strong binding interaction between the two species. In addition, micellar growth also requires a sufficient concentration of background electrolyte such as NaCl or sodium citrate that serves to screen the electrostatic repulsion of the amphiphiles and to \"salt out\" the amphiphiles. We postulate a mechanism based on changes in the molecular geometry caused by bile salts and electrolytes to explain the micellar growth.\n\nMixtures of lecithin and bile salt can form highly viscous wormlike micellar solutions in water.", "token_count": 387, "char_count": 1559, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:47.513202", "source": { "split": "train_shard_00000", "doc_id": 4599 }, "chunk_id": "train_shard_00000_4599_0", "global_id": 5137 }, { "text": "This study aimed to evaluate the effects of electroporation on growth, bioconversion of isoflavones, and probiotic properties of parent organisms and subsequent passages of Bifidobacterium longum FTDC 8643. Electroporation with the strength of electric field at 7.5 kV cm(-1) for 3.5 ms was applied on B. longum FTDC 8643. The viability of B. longum FTDC 8643 increased significantly upon treatment with electroporation. Such treatment also enhanced the intracellular and extracellular β-glucosidase activity, leading to enhanced production of bioactive isoflavone aglycones in mannitol-soymilk (P < 0.05). In addition, these treated cells also exhibited better tolerance toward acidic (pH 2 and pH 3) and intestinal bile salt condition compared to the control (P < 0.05). The electroporated cell also possessed better adhesion ability and antimicrobial activity (P < 0.05). However, all these positive effects were only prevalent in the parent cells and were not observed in their subsequent passages of electroporated cells. Our results suggested that electroporation could enhance the bioactive and probiotic potentials of parent cells of B. longum FTDC 8643 and could be used in the production of probiotic foods with enhanced bioactivity.\n\nEffect of electroporation on bioconversion of isoflavones and probiotic properties of parents and subsequent passages of Bifidobacterium longum.", "token_count": 385, "char_count": 1389, "word_count": 201, "semantic_coherence": 1, "information_density": 0.5622, "quality_score": 0.7811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:48.149860", "source": { "split": "train_shard_00000", "doc_id": 4600 }, "chunk_id": "train_shard_00000_4600_0", "global_id": 5138 }, { "text": "This study evaluated the probiotic properties (stability at different pH values and bile salt concentration, auto-aggregation and co-aggregation, survival in the presence of antibiotics and commercial drugs, study of β-galactosidase production, evaluation of the presence of genes encoding MapA and Mub adhesion proteins and EF-Tu elongation factor, and the presence of genes encoding virulence factor) of four LAB strains (Lactobacillus casei SJRP35, Leuconostoc citreum SJRP44, Lactobacillus delbrueckii subsp. bulgaricus SJRP57 and Leuconostoc mesenteroides subsp. mesenteroides SJRP58) which produced antimicrobial substances (antimicrobial peptides). The strains survived the simulated GIT modeled in MRS broth, whole and skim milk. In addition, auto-aggregation and the cell surface hydrophobicity of all strains were high, and various degrees of co-aggregation were observed with indicator strains. All strains presented low resistance to several antibiotics and survived in the presence of commercial drugs. Only the strain SJRP44 did not produce the β-galactosidase enzyme. Moreover, the strain SJRP57 did not show the presence of any genes encoding virulence factors; however, the strain SJRP35 presented vancomycin resistance and adhesion of collagen genes, the strain SJRP44 harbored the ornithine decarboxylase gene and the strain SJRP58 generated positive results for aggregation substance and histidine decarboxylase genes. In conclusion, the strain SJRP57 was considered the best candidate as probiotic cultures for further in vivo studies and functional food products development.\n\nProbiotic properties of lactic acid bacteria isolated from water-buffalo mozzarella cheese.", "token_count": 447, "char_count": 1690, "word_count": 228, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [ "SJRP44", "SJRP57", "SJRP58", "SJRP35" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:49.235703", "source": { "split": "train_shard_00000", "doc_id": 4601 }, "chunk_id": "train_shard_00000_4601_0", "global_id": 5139 }, { "text": "The Gram-positive anaerobic bacterium Propionibacterium acnes is a prevalent member of the normal skin microbiota of human adults. In addition to its suspected role in acne vulgaris it is involved in a variety of opportunistic infections. Multi-locus sequence-typing (MLST) schemes identified distinct phylotypes associated with health and disease. Being based on 8 to 9 house-keeping genes these MLST schemes have a high discriminatory power, but their application is time- and cost-intensive. Here we describe a single-locus sequence typing (SLST) scheme for P. acnes. The target locus was identified with a genome mining approach that took advantage of the availability of representative genome sequences of all known phylotypes of P. acnes. We applied this SLST on a collection of 188 P. acnes strains and demonstrated a resolution comparable to that of existing MLST schemes. Phylogenetic analysis applied to the SLST locus resulted in clustering patterns identical to a reference tree based on core genome sequences. We further demonstrate that SLST can be applied to detect multiple phylotypes in complex microbial communities by a metagenomic pyrosequencing approach. The described SLST strategy may be applied to any bacterial species with a basically clonal population structure to achieve easy typing and mapping of multiple phylotypes in complex microbiotas. The P. acnes SLST database can be found at http://medbac.dk/slst/pacnes.\n\nA novel high-resolution single locus sequence typing scheme for mixed populations of Propionibacterium acnes in vivo.", "token_count": 368, "char_count": 1562, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:49.823045", "source": { "split": "train_shard_00000", "doc_id": 4602 }, "chunk_id": "train_shard_00000_4602_0", "global_id": 5140 }, { "text": "The Bifidobacterium genus currently encompasses 48 recognized taxa, which have been isolated from different ecosystems. However, the current phylogeny of bifidobacteria is hampered by the relative paucity of genotypic data. Here, we reassessed the taxonomy of this bacterial genus using genome-based approaches, which demonstrated that the previous taxonomic view of bifidobacteria contained several inconsistencies. In particular, high levels of genetic relatedness were shown to exist between particular Bifidobacterium taxa which would not justify their status as separate species. The results presented are here based on average nucleotide identity analysis involving the genome sequences for each type strain of the 48 bifidobacterial taxa, as well as phylogenetic comparative analysis of the predicted core genome of the Bifidobacterium genus. The results of this study demonstrate that the availability of complete genome sequences allows the reconstruction of a more robust bifidobacterial phylogeny than that obtained from a single gene-based sequence comparison, thus discouraging the assignment of a new or separate bifidobacterial taxon without such a genome-based validation.\n\nInvestigation of the evolutionary development of the genus Bifidobacterium by comparative genomics.", "token_count": 293, "char_count": 1289, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6648, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:50.385283", "source": { "split": "train_shard_00000", "doc_id": 4603 }, "chunk_id": "train_shard_00000_4603_0", "global_id": 5141 }, { "text": "The nitroderivative 1-nitro-2-phenylethane (NPE) was recently described as a compound possessing heme-dependent soluble guanylyl cyclase (sGC) stimulating properties in vascular smooth muscle cells. In this study, we tested such pharmacological property of NPE in mice pancreatic acinar cells subjected to the bile salt taurocholate, a type of pathological stimulus that simulates pancreatitis. Here, isolated acinar cells were treated with NPE in order to assess the role of sGC on the detrimental effects induced by taurocholate. NPE reduced taurocholate-elicited Ca(2+) overload, production of reactive oxygen species (ROS), apoptosis, necrosis, and exerted a protective effect against mitochondrial membrane potential (ΔΨm) dissipation. These NPE-induced effects were abolished by pretreatment with ODQ and KT 5823, and after the blockade of nitric oxide (NO) synthase with l-NAME, inhibitors of key components of the sGC pathway. Contrarily to cGMP that alone increased ΔΨm collapse and cell damage, the cytoprotective effect of NPE on ΔΨm and cell necrosis was almost reproduced by 8-nitro-cGMP, a second messenger generated by sGC under oxidative stress conditions. In conclusion, putative sGC stimulation with NPE reveals its cytoprotective profile on pancreatic cells subjected to taurocholate. Moreover, ROS and NO conjunctly appear to drive sGC activity in pancreatic acinar cells to implement an adaptive mechanism in response to oxidative and Ca(2+) stress through 8-nitro-cGMPsynthesis.\n\nCytoprotective effect of 1-nitro-2-phenylethane in mice pancreatic acinar cells subjected to taurocholate: putative role of guanylyl cyclase-derived 8-nitro-cyclic-GMP.", "token_count": 495, "char_count": 1670, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:51.034678", "source": { "split": "train_shard_00000", "doc_id": 4604 }, "chunk_id": "train_shard_00000_4604_0", "global_id": 5142 }, { "text": "The objective of this study was to isolate, identify, and characterize some lactic acid bacterial strains from human milk, infant feces, and fermented grapes and dates, as potential probiotics with antimicrobial activity against some human pathogenic strains. One hundred and forty bacterial strains were isolated and, after initial identification and a preliminary screening for acid and bile tolerance, nine of the best isolates were selected and further identified using 16 S rRNA gene sequences. The nine selected isolates were then characterized in vitro for their probiotic characteristics and their antimicrobial activities against some human pathogens. Results showed that all nine isolates belonged to the genus Lactobacillus. They were able to tolerate pH 3 for 3 h, 0.3% bile salts for 4 h, and 1.9 mg/mL pancreatic enzymes for 3 h. They exhibited good ability to attach to intestinal epithelial cells and were not resistant to the tested antibiotics. They also showed good antimicrobial activities against the tested pathogenic strains of humans, and most of them exhibited stronger antimicrobial activity than the reference strain L. casei Shirota. Thus, the nine Lactobacillus strains could be considered as potential antimicrobial probiotic strains against human pathogens and should be further studied for their human health benefits.\n\nProbiotic potential of Lactobacillus strains with antimicrobial activity against some human pathogenic strains.", "token_count": 358, "char_count": 1463, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5674, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:51.611710", "source": { "split": "train_shard_00000", "doc_id": 4605 }, "chunk_id": "train_shard_00000_4605_0", "global_id": 5143 }, { "text": "Numerous drugs have been shown to inhibit the activity of the Bile Salt Export Pump (BSEP in humans, Bsep in animals), and this is now considered to be one of several mechanisms by which idiosyncratic drug-induced liver injury (DILI) may be initiated in susceptible patients. The potential importance of BSEP inhibition by drugs has been recognized by the European Medicines Agency and the International Transporter Consortium, who have recommended that it should be evaluated during drug development when evidence of cholestatic liver injury has been observed in nonclinical safety studies or in human clinical trials. In addition, some pharmaceutical companies have proposed evaluation and minimization of BSEP inhibition during drug discovery, when there is a chemical choice, to help reduce DILI risk. The methods that can be used to assess and quantify BSEP inhibition, and key gaps in our current understanding of the relationship between this process and DILI, are discussed.\n\nCurrent Concepts in Drug-Induced Bile Salt Export Pump (BSEP) Interference.", "token_count": 238, "char_count": 1059, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:52.083996", "source": { "split": "train_shard_00000", "doc_id": 4606 }, "chunk_id": "train_shard_00000_4606_0", "global_id": 5144 }, { "text": "The aim of this work was to purify and characterize the bacteriocin produced by probiotic Lactobacillus plantarum DM5 in order to evaluate its potential as nutraceuticals. Lb. plantarum DM5 exhibited in vitro probiotic properties such as high resistance to gastric juice and bile salt, adherence to human adenocarcinoma (HT-29) cells, bile salt hydrolase and cholesterol assimilation activity. Moreover, Lb. plantarum DM5 showed bacteriocin activity against several major food borne pathogens. Zymogram analysis of purified bacteriocin (plantaricin DM5) showed a molecular size of ∼15.2 kDa. Plantaricin DM5 was sensitive to proteolytic enzymes but stable in the pH range of 2.0-10.0, and it was heat resistant (121 °C for 15 min) and remained active upon treatment with surfactants and detergents. Cytotoxicity analysis of plantaricin DM5 on human embryonic kidney 293 (HEK 293) and human cervical cancer (HeLa) cell lines revealed its nontoxic and biocompatible nature. To the best of our knowledge, this is the first study on the isolated strain expressing probiotic properties and broad antimicrobial activity without any cytotoxic effect on mammalian cells from indigenous fermented beverage Marcha from India, and thus contributes to the food industry as a novel bio-preservant.\n\nCharacterization of a noncytotoxic bacteriocin from probiotic Lactobacillus plantarum DM5 with potential as a food preservative.", "token_count": 397, "char_count": 1414, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [ "DM5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:52.701581", "source": { "split": "train_shard_00000", "doc_id": 4607 }, "chunk_id": "train_shard_00000_4607_0", "global_id": 5145 }, { "text": "Lactobacillus fermentum is a lactic acid bacterium of probiotic importance, which is found ubiquitously in fermented milk products. Bile salt hydrolase (BSH) has a significant role in affording probiotic properties to lactobacilli. In the present study, two bsh genes encoding BSH1 and BSH2 were identified from the draft genome sequence of L. fermentum MTCC 8711. Nucleotide comparison revealed no significant similarity between bsh1 and bsh2 genes, whereas the deduced amino acid sequences showed 26 % sequence similarity between both BSH1 and BSH2. Pfam analysis revealed the presence of cys-2 active site residues in the catalytic pocket of both BSH1 and BSH2 highly essential for catalysis. Phylogentic analysis of BSH1 and BSH2 revealed the possible independent origin of these proteins in Lactobacillus. We cloned these genes in pSLp111.3, a Lactobacillus expression vector with signal peptide A (slpA) and expressed in the native L. fermentum strain for overexpression and extracellular secretion. The bsh1 gene failed to express and to produce promising BSH activity. However, bsh2 gene was overexpressed and the recombinant strain showed improved BSH activity. Induction of the recombinant strain with an optimal 2 % xylose concentration secreted 0.5 U/ml of the BSH into extracellular medium. Furthermore, the recombinant strain was able to completely assimilate the 100-μg/ml cholesterol within 24 h, whereas the native strain took 72 h for the complete assimilation of cholesterol.\n\nIdentification and characterization of bile salt hydrolase genes from the genome of Lactobacillus fermentum MTCC 8711.", "token_count": 446, "char_count": 1614, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5732, "quality_score": 0.7866, "entities": { "genes": [ "BSH1", "BSH2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:53.340392", "source": { "split": "train_shard_00000", "doc_id": 4608 }, "chunk_id": "train_shard_00000_4608_0", "global_id": 5146 }, { "text": "Related species are often used to understand the molecular underpinning of virulence through examination of a shared set of biological features attributable to a core genome of orthologous genes. An important but insufficiently studied issue, however, is the extent to which the regulatory architectures are similarly conserved. A small number of studies have compared the primary transcriptomes of different bacterial species, but few have compared closely related species with clearly divergent evolutionary histories. We addressed the impact of differing modes of evolution within the genus Mycobacterium through comparison of the primary transcriptome of M. marinum with that of a closely related lineage, M. bovis. Both are thought to have evolved from an ancestral generalist species, with M. bovis and other members of the M. tuberculosis complex having subsequently undergone downsizing of their genomes during the transition to obligate pathogenicity. M. marinum, in contrast, has retained a large genome, appropriate for an environmental organism, and is a broad-host-range pathogen. We also examined changes over a shorter evolutionary time period through comparison of the primary transcriptome of M. bovis with that of another member of the M. tuberculosis complex (M. tuberculosis) which possesses an almost identical genome but maintains a distinct host preference. Importance: Our comparison of the transcriptional start site (TSS) maps of M. marinum and M. bovis uncovers a pillar of conserved promoters, noncoding RNA (NCRNA), and a genome-wide signal in the -35 promoter regions of both species. We identify evolutionarily conserved transcriptional attenuation and highlight its potential contribution to multidrug resistance mediated through the transcriptional regulator whiB7. We show that a species population history is reflected in its transcriptome and posit relaxed selection as the main driver of an abundance of canonical -10 promoter sites in M. bovis relative to M. marinum. It appears that transcriptome composition in mycobacteria is driven primarily by the availability of such sites and that their frequencies diverge significantly across the mycobacterial clade. Finally, through comparison of M. bovis and M. tuberculosis, we illustrate that single nucleotide polymorphism (SNP)-driven promoter differences likely underpin many of the transcriptional differences between M", "token_count": 537, "char_count": 2409, "word_count": 346, "semantic_coherence": 1, "information_density": 0.578, "quality_score": 0.789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:45:53.996642", "source": { "split": "train_shard_00000", "doc_id": 4609 }, "chunk_id": "train_shard_00000_4609_0", "global_id": 5147 }, { "text": "tuberculosis complex lineages.\n\nRelaxed selection drives a noisy noncoding transcriptome in members of the Mycobacterium tuberculosis complex.", "token_count": 39, "char_count": 142, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:54.360934", "source": { "split": "train_shard_00000", "doc_id": 4609 }, "chunk_id": "train_shard_00000_4609_1", "global_id": 5148 }, { "text": "Aggregatibacter actinomycetemcomitans is a Gram-negative periodontitis-associated bacterium that expresses a toxin that selectively affects leukocytes. This leukotoxin is encoded by an operon belonging to the core genome of this bacterial species. Variations in the expression of the leukotoxin have been reported, and a well-characterized specific clonal type (JP2) of this bacterium with enhanced leukotoxin expression has been isolated. In particular, the presence of the JP2 genotype significantly increases the risk for the progression of periodontal attachment loss (AL). Based on these findings we hypothesized that variations in the leukotoxicity are linked to disease progression in infected individuals. In the present study, the leukotoxicity of 239 clinical isolates of A. actinomycetemcomitans was analysed with different bioassays, and the genetic peculiarities of the isolates were related to their leukotoxicity based on examination with molecular techniques. The periodontal status of the individuals sampled for the presence of A. actinomycetemcomitans was examined longitudinally, and the importance of the observed variations in leukotoxicity was evaluated in relation to disease progression. Our data show that high leukotoxicity correlates with an enhanced risk for the progression of AL. The JP2 genotype isolates were all highly leukotoxic, while the isolates with an intact leukotoxin promoter (non-JP2 genotypes) showed substantial variation in leukotoxicity. Genetic characterization of the non-JP2 genotype isolates indicated the presence of highly leukotoxic genotypes of serotype b with similarities to the JP2 genotype. Based on these results, we conclude that A. actinomycetemcomitans harbours other highly virulent genotypes besides the previously described JP2 genotype. In addition, the results from the present study further highlight the importance of the leukotoxin as a key virulence factor in aggressive forms of periodontitis.\n\nLeukotoxic activity of Aggregatibacter actinomycetemcomitans and periodontal attachment loss.", "token_count": 508, "char_count": 2062, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5196, "quality_score": 0.7598, "entities": { "genes": [ "JP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:54.994231", "source": { "split": "train_shard_00000", "doc_id": 4610 }, "chunk_id": "train_shard_00000_4610_0", "global_id": 5149 }, { "text": "Inclusion complexes between two bile salts and a range of differently methylated β-cyclodextrins were studied in an attempt to rationalize the complexation thermodynamics of modified cyclodextrins. Calorimetric titrations at a range of temperatures provided precise values of the enthalpies (ΔH°), entropies (ΔS°), and heat capacities (ΔCp) of complexation, while molecular dynamics simulations assisted the interpretation of the obtained thermodynamic parameters. As previously observed for several types of modified cyclodextrins, the substituents at the rims of the cyclodextrin induced large changes in ΔH° and ΔS°, but due to enthalpy-entropy compensation the changes in Gibbs free energy, and the binding constant, were much smaller. For the methylated β-cyclodextrins, the substituent-induced increments in ΔH° and ΔS° were nonmonotonic with an initial strong increase in both ΔH° and ΔS° and then a strong decrease when the degree of substitution exceeded some threshold. Exactly the same trend was observed for ΔCp. The dehydration of nonpolar surface, as quantified by the simulations, can to a large extent explain the variation in the thermodynamic parameters. The methyl substituents form additional hydrophobic contacts with the bile salt, but at high degrees of methylation they also cause significant distortion of the otherwise circular cyclodextrin structure. These two opposing contributions to the dehydration are the major causes for the observed variations in the thermodynamic functions. The structural effects are not expected to be specific for methylated cyclodextrins but should be observed for most modified cyclodextrins. An even more general conclusion is that variations in the extent of hydration are an important underlying reason for the commonly observed phenomenon termed enthalpy-entropy compensation and also for the less frequent reports of entropy convergence around 110 °C.\n\nComplexation thermodynamics of modified cyclodextrins: extended cavities and distorted structures.", "token_count": 473, "char_count": 2014, "word_count": 284, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:55.650468", "source": { "split": "train_shard_00000", "doc_id": 4611 }, "chunk_id": "train_shard_00000_4611_0", "global_id": 5150 }, { "text": "Multiple epidemic diseases have been designated as emerging or reemerging because the numbers of clinical cases have increased. Emerging diseases are often suspected to be driven by increased virulence or fitness, possibly associated with the gain of novel genes or mutations. However, the time period over which humans have been afflicted by such diseases is only known for very few bacterial pathogens, and the evidence for recently increased virulence or fitness is scanty. Has Darwinian (diversifying) selection at the genomic level recently driven microevolution within bacterial pathogens of humans? Salmonella enterica serovar Paratyphi A is a major cause of enteric fever, with a microbiological history dating to 1898. We identified seven modern lineages among 149 genomes on the basis of 4,584 SNPs in the core genome and estimated that Paratyphi A originated 450 y ago. During that time period, the effective population size has undergone expansion, reduction, and recent expansion. Mutations, some of which inactivate genes, have occurred continuously over the history of Paratyphi A, as has the gain or loss of accessory genes. We also identified 273 mutations that were under Darwinian selection. However, most genetic changes are transient, continuously being removed by purifying selection, and the genome of Paratyphi A has not changed dramatically over centuries. We conclude that Darwinian selection is not responsible for increased frequency of enteric fever and suggest that environmental changes may be more important for the frequency of disease.\n\nTransient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever.", "token_count": 374, "char_count": 1695, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6024, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:56.238611", "source": { "split": "train_shard_00000", "doc_id": 4612 }, "chunk_id": "train_shard_00000_4612_0", "global_id": 5151 }, { "text": "Fermentation of xylose-rich and glucose-rich bagasse hydrolysates, obtained from the two-stage acid hydrolysis was studied using the thermotolerant yeast Kluyveromyces sp. IIPE453. The yeast could grow on xylose-rich hydrolysate at 50 °C with the dry cell weight, cell mass yield and maximum specific growth rate of 5.35 g l(-1), 0.58 g g(-1) and 0.13 h(-1), respectively. The yeast was found to be very promising for ethanol as well as xylitol production from the sugars obtained from the lignocellulosic biomass. Batch fermentations of xylose-rich and glucose-rich hydrolysates yielded 0.61 g g(-1) xylitol and 0.43 g g(-1) ethanol in the broth, respectively based on the sugars present in the hydrolysate. Overall ethanol yield of 165 g (210 ml) and 183 g xylitol per kg of bagasse was obtained, when bagasse hydrolysate was used as a substrate. Utilization of both the glucose and xylose sugars makes the process most economical by producing both ethanol and xylitol based on biorefinery concept. On validating the experimental data of ethanol fermentation, the modified Luong kinetic model for product inhibition as well as inhibition due to inhibitory compounds present in hydrolysate, the model was found to be the best fit for ethanol formation from bagasse hydrolysate using Kluyveromyces sp. IIPE453.\n\nBioprocessing of bagasse hydrolysate for ethanol and xylitol production using thermotolerant yeast.", "token_count": 438, "char_count": 1411, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5349, "quality_score": 0.7674, "entities": { "genes": [ "IIPE453" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:56.866291", "source": { "split": "train_shard_00000", "doc_id": 4613 }, "chunk_id": "train_shard_00000_4613_0", "global_id": 5152 }, { "text": "The yeast Kluyveromyces marxianus is a convenient host for industrial synthesis of biomolecules. However, despite its potential, there are few studies reporting the expression of heterologous proteins using this yeast. Here, we report expression of a dengue virus protein in K. marxianus for the first time. The dengue virus type 1 nonstructural protein 1 (NS1) was integrated into the K. marxianus UFV-3 genome at the LAC4 locus using an adapted integrative vector designed for high-level expression of recombinant protein in Kluyveromyces lactis. The NS1 gene sequence was codon-optimized to increase the level of protein expression in yeast. The synthetic gene was cloned in frame with K. lactis α-mating factor signal peptide, and the recombinant plasmid obtained was used to transform K. marxianus UFV-3 by electroporation. The transformed cells, selected in yeast extract peptone dextrose containing 200 μg mL(-1) Geneticin, were mitotically stable. Analysis of recombinant strains by RT-PCR and protein detection using blot analysis confirmed both transcription and expression of extracellular NS1 polypeptide. After induction with galactose, the NS1 protein was analyzed by sodium dodecyl sulfate-PAGE and immunogenic detection. Protein production was investigated under two conditions: with galactose and biotin pulses at 24-h intervals during 96 h of induction and without galactose and biotin supplementation. Protease activity was not detected in post-growth medium. Our results indicate that recombinant K. marxianus is a good host for the production of dengue virus NS1 protein, which has potential for diagnostic applications.\n\nConstruction of recombinant Kluyveromyces marxianus UFV-3 to express dengue virus type 1 nonstructural protein 1 (NS1).", "token_count": 468, "char_count": 1762, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [ "NS1", "LAC4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:57.516391", "source": { "split": "train_shard_00000", "doc_id": 4614 }, "chunk_id": "train_shard_00000_4614_0", "global_id": 5153 }, { "text": "Progressive familial intrahepatic cholestasis type 2 (PFIC2) is an autosomal recessive disease due to mutations in ABCB11. ABCB11 encodes the bile salt export pump (BSEP), the major transporter responsible for biliary bile acid secretion, which expression is restricted to hepatocytes. In some patients, molecular analysis of ABCB11 revealed either exonic or intronic variations - including common polymorphisms - predicted to affect splicing according to in silico analysis or in vitro minigene studies. Transcript analysis in liver tissue is the best way to determine whether the variations predicted to affect splicing are deleterious or not.\n\nLiver transcript analysis reveals aberrant splicing due to silent and intronic variations in the ABCB11 gene.", "token_count": 188, "char_count": 756, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6727, "quality_score": 0.8364, "entities": { "genes": [ "PFIC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:57.955346", "source": { "split": "train_shard_00000", "doc_id": 4615 }, "chunk_id": "train_shard_00000_4615_0", "global_id": 5154 }, { "text": "Probiotic properties are highly strain-dependent but rarely studied in enological lactic acid bacteria (LAB). In this study, the probiotic features of 11 strains of Lactobacillus spp., Pediococcus spp., and Oenococcus oeni, including saliva and acid resistance, bile tolerance and exopolysaccharides' production, were investigated. The assays included two probiotic reference strains (Lactobacillus plantarum CLC 17 and Lactobacillus fermentum CECT5716). The Lactobacillus and Pediococcus strains showed high resistance to lysozyme (>80% resistance to 100 mg/L of lysozyme under conditions simulating the in vivo dilution by saliva) and were capable of surviving at low pH values (pH 1.8) and bile salts, suggesting good adaptation of the wine strains to gastrointestinal conditions. The ability of the strains to adhere to the intestinal mucosa and the inhibition of the adhesion of Escherichia coli to human intestinal cells were also evaluated. Adhesion levels of enological LAB to Caco-2 cells varied from 0.37% to 12.2%, depending on the strain. In particular, Pediococcus pentosaceus CIAL-86 showed a high percentage of adhesion to intestinal cells (>12%), even higher than that shown by the probiotic reference strains, and a high anti-adhesion activity against E. coli CIAL-153 (>30%), all of which support this wine LAB strain as a potential probiotic.\n\nAssessment of probiotic properties in lactic acid bacteria isolated from wine.", "token_count": 417, "char_count": 1441, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "CECT5716" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:58.579240", "source": { "split": "train_shard_00000", "doc_id": 4616 }, "chunk_id": "train_shard_00000_4616_0", "global_id": 5155 }, { "text": "The aim of this study is to prepare a stable phosphatidylcholine/bile salt micelles with Pluronic F127-polyethylenimine conjugates (F127-PEI), d-α-tocopheryl polyethylene glycol 1000 succinate (TPGS), soybean phosphatidylcholine (SPC) and sodium cholate (NaC) and to elucidate the effects and possible mechanism of micelle components on the intestinal absorption of paclitaxel (PTX) in rats. The results of intestinal absorption revealed that the PTX in SPC/NaC micelles displayed superior permeability across intestinal barrier than free drug and PTX in TPGS/SPC/NaC and F127-PEI/TPGS/SPC/NaC mixed micelles exhibited the strongest permeability across intestinal barrier. These results were also proved by the studies on cell uptake tests. The mechanism was demonstrated in connection with inhibition of the efflux mediated by intestinal P-gp and enhancement of the drug transportation across the unstirred water layer to the endothelial lining, thereby promoting the permeation across the intestinal wall. Pharmacokinetic study demonstrated that the area under the plasma concentration-time curve (AUC0→∞) of paclitaxel in F127-PEI/TPGS/SPC/NaC micelles was much greater than that in TPGS/SPC/NaC micelles. This phenomenon deviated from the results of uptake studies by cells and permeability experiments through rat intestine and revealed that the micelle stability had a great effect on intestinal absorption of paclitaxel.\n\nStable phosphatidylcholine-bile salt mixed micelles enhance oral absorption of paclitaxel: preparation and mechanism in rats.", "token_count": 433, "char_count": 1554, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5646, "quality_score": 0.7823, "entities": { "genes": [ "AUC0" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:59.243730", "source": { "split": "train_shard_00000", "doc_id": 4617 }, "chunk_id": "train_shard_00000_4617_0", "global_id": 5156 }, { "text": "Human ileal bile acid-binding protein (I-BABP), a member of the family of intracellular lipid binding proteins plays a key role in the cellular trafficking and metabolic regulation of bile salts. The protein has two internal and, according to a recent study, an additional superficial binding site and binds di- and trihydroxy bile salts with positive cooperativity and a high degree of site-selectivity. Previously, in the apo form, we have identified an extensive network of conformational fluctuations on the millisecond time scale, which cease upon ligation. Additionally, ligand binding at room temperature was found to be accompanied by a slight rigidification of picosecond-nanosecond (ps-ns) backbone flexibility. In the current study, temperature-dependent (15)N NMR spin relaxation measurements were used to gain more insight into the role of dynamics in human I-BABP-bile salt recognition. According to our analysis, residues sensing a conformational exchange in the apo state can be grouped into two clusters with slightly different exchange rates. The entropy-enthalpy compensation observed for both clusters suggests a disorder-order transition between a ground and a sparsely populated higher energy state in the absence of ligands. Analysis of the faster, ps-ns motion of (15)N-(1)H bond vectors indicates an unusual nonlinear temperature-dependence for both ligation states. Intriguingly, while bile salt binding results in a more uniform response to temperature change throughout the protein, the temperature derivative of the generalized order parameter shows different responses to temperature increase for the two forms of the protein in the investigated temperature range. Analysis of both slow and fast motions in human I-BABP indicates largely different energy landscapes for the apo and holo states suggesting that optimization of binding interactions might be achieved by altering the dynamic behavior of specific segments in the protein.\n\nTemperature dependence of backbone dynamics in human ileal bile acid-binding protein: implications for the mechanism of ligand binding.", "token_count": 447, "char_count": 2101, "word_count": 302, "semantic_coherence": 1, "information_density": 0.6026, "quality_score": 0.8013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:45:59.893428", "source": { "split": "train_shard_00000", "doc_id": 4618 }, "chunk_id": "train_shard_00000_4618_0", "global_id": 5157 }, { "text": "Serratia marcescens is an important nosocomial pathogen that can cause an array of infections, most notably of the urinary tract and bloodstream. Naturally, it is found in many environmental niches, and is capable of infecting plants and animals. The emergence and spread of multidrug-resistant strains producing extended-spectrum or metallo beta-lactamases now pose a threat to public health worldwide. Here we report the complete genome sequences of two carefully selected S. marcescens strains, a multidrug-resistant clinical isolate (strain SM39) and an insect isolate (strain Db11). Our comparative analyses reveal the core genome of S. marcescens and define the potential metabolic capacity, virulence, and multidrug resistance of this species. We show a remarkable intraspecies genetic diversity, both at the sequence level and with regards genome flexibility, which may reflect the diversity of niches inhabited by members of this species. A broader analysis with other Serratia species identifies a set of approximately 3,000 genes that characterize the genus. Within this apparent genetic diversity, we identified many genes implicated in the high virulence potential and antibiotic resistance of SM39, including the metallo beta-lactamase and multiple other drug resistance determinants carried on plasmid pSMC1. We further show that pSMC1 is most closely related to plasmids circulating in Pseudomonas species. Our data will provide a valuable basis for future studies on S. marcescens and new insights into the genetic mechanisms that underlie the emergence of pathogens highly resistant to multiple antimicrobial agents.\n\nGenome evolution and plasticity of Serratia marcescens, an important multidrug-resistant nosocomial pathogen.", "token_count": 413, "char_count": 1745, "word_count": 248, "semantic_coherence": 1, "information_density": 0.629, "quality_score": 0.8145, "entities": { "genes": [ "SM39" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:00.552804", "source": { "split": "train_shard_00000", "doc_id": 4619 }, "chunk_id": "train_shard_00000_4619_0", "global_id": 5158 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) types 1 and 3 are severe cholestatic liver diseases caused by deficiency of ATB8B1 and ABCB4, respectively. Mouse models for PFIC display mild phenotypes compared with human patients, and this can be explained by the difference in bile salt pool composition. Mice, unlike humans, have the ability to detoxify hydrophobic bile salts by cytochrome P450-mediated (re)hydroxylation and thus have a less toxic bile salt pool. We have crossed mouse models for PFIC1 and PFIC3 with Hrn mice that have a reduced capacity to (re)hydroxylate bile salts. Double transgenes were obtained by backcrossing Atp8b1(G308V/G308V) and Abcb4(-/-) mice with Hrn mice that have a liver-specific disruption of the cytochrome P450 reductase gene and therefore have markedly reduced P450 activity. In these mice, a more hydrophobic bile salt pool was instilled by cholic acid supplementation of the diet, and bile formation and liver pathology was studied. As opposed to single transgenes, Atp8b1(G308V/G308V)/Hrn and Abcb4(-/-)/Hrn mice rapidly developed strong cholestasis that was evidenced by increased plasma bilirubin and bile salt levels. The bile salt pool was more toxic in both models; Atp8b1(G308V/G308V)/Hrn mice had a more hydrophobic plasma pool compared with the single transgene, whereas Abcb4(-/-)/Hrn mice had a more hydrophobic biliary pool compared with the single transgene. In line with these findings, liver damage was not aggravated in Atp8b1(G308V/G308V)/Hrn but was more severe in Abcb4(-/-)/Hrn mice. These data indicate that bile salt pool composition is a critical determinant in the initiation and progression of cholestasis and liver pathology in PFIC1 and PFIC3", "token_count": 519, "char_count": 1721, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5236, "quality_score": 0.7618, "entities": { "genes": [ "PFIC1", "ABCB4", "PFIC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:46:01.219618", "source": { "split": "train_shard_00000", "doc_id": 4620 }, "chunk_id": "train_shard_00000_4620_0", "global_id": 5159 }, { "text": "Most importantly, our data suggest that the hydrophobicity of the plasma bile salt pool is an important determinant of the severity of cholestasis, whereas the hydrophobicity of the biliary bile salt pool is an important determinant of the severity of liver pathology.\n\nHepatic cytochrome P450 deficiency in mouse models for intrahepatic cholestasis predispose to bile salt-induced cholestasis.", "token_count": 104, "char_count": 394, "word_count": 57, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:01.597061", "source": { "split": "train_shard_00000", "doc_id": 4620 }, "chunk_id": "train_shard_00000_4620_1", "global_id": 5160 }, { "text": "Vibrio harveyi is an opportunistic human pathogen that may cause gastroenteritis, severe necrotizing soft-tissue infections, and primary septicemia, with a potentially high rate of lethality. In this study, we isolated and characterized V. harveyi from seawater collected from the West Sea in Korea, including sites located near shellfish farms. For the initial isolation of putative V. harveyi, isolates were incubated on thiosulfate citrate bile salt sucrose agar plates for 24h, followed by selection of greenish colonies. Gram-negative and oxidase-positive colonies were subsequently confirmed by biochemical assays and the API 20E kit test system. Species-specific 16S rRNA and hemolysin genes were used to design V. harveyi-specific PCR primers. From 840 seawater samples, a total of 2 strains of V. harveyi were isolated from shellfish farm seawater. The two isolates were subjected to profiling against 16 antibiotics and found to be resistant to cephalothin, vancomycin, ampicillin, cefepime, cefotetan, and streptomycin.\n\nAntibiotic resistance of Vibrio harveyi isolated from seawater in Korea.", "token_count": 310, "char_count": 1104, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7278, "quality_score": 0.8639, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:02.172334", "source": { "split": "train_shard_00000", "doc_id": 4621 }, "chunk_id": "train_shard_00000_4621_0", "global_id": 5161 }, { "text": "Bile salts inhibit their own production by inducing the nuclear receptor small heterodimer partner (SHP) (encoded by NR0B2), which contributes to repression of the gene encoding cholesterol 7α-hydroxylase (CYP7A1), a key enzyme for the control of bile salt synthesis. On the other hand, bile salts stimulate hepatic synthesis of nitric oxide. We investigated the role of nitric oxide signaling in the control of CYP7A1 expression and the involvement in this process of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), which participates in intracellular propagation of nitric oxide signals.\n\nA GAPDH-mediated trans-nitrosylation pathway is required for feedback inhibition of bile salt synthesis in rat liver.", "token_count": 206, "char_count": 710, "word_count": 100, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:02.635379", "source": { "split": "train_shard_00000", "doc_id": 4622 }, "chunk_id": "train_shard_00000_4622_0", "global_id": 5162 }, { "text": "The use of liposomes for oral administration of drugs and for food applications is based on their ability to preserve entrapped substances and to increase their bioavailability. Bile salts are one of the agents that affect the liposome structure during intestinal digestion and the main reported studies on liposome/bile salt systems used only one bile salt. The aim of this work is to characterise the interaction of liposomes with a natural bile salt extract (BSE) at physiological pH and temperature. Three types of liposomes (fluid, gel-state and liquid-ordered bilayers) were studied. Phase diagrams were obtained and a very different behaviour was found. Fluid bilayers were completely permeable to an entrapped dye with partial or complete disruption of vesicles (final size 10 nm). Gel-state bilayers released their content but BSE led to the formation of large mixed structures (2000 nm). Liquid-ordered bilayers formed mixed vesicles (1000 nm) and, surprisingly, retained a high percentage of their aqueous content (about 50%). As a consequence, each type of liposome offers singular features to be used in oral applications due to their specific interaction with bile salts.\n\nCharacteristics and behaviour of liposomes when incubated with natural bile salt extract: implications for their use as oral drug delivery systems.", "token_count": 315, "char_count": 1334, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8177, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:03.191351", "source": { "split": "train_shard_00000", "doc_id": 4623 }, "chunk_id": "train_shard_00000_4623_0", "global_id": 5163 }, { "text": "We determined the genome sequence of a thermotolerant yeast, Kluyveromyces marxianus strain DMB1, isolated from sugarcane bagasse hydrolysate, and the sequence provides further insights into the genomic differences between this strain and other reported K. marxianus strains. The genome described here is composed of 11,165,408 bases and has 4,943 protein-coding genes.\n\nDraft Genome Sequence of Kluyveromyces marxianus Strain DMB1, Isolated from Sugarcane Bagasse Hydrolysate.", "token_count": 142, "char_count": 477, "word_count": 64, "semantic_coherence": 1, "information_density": 0.6719, "quality_score": 0.8359, "entities": { "genes": [ "DMB1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:03.616584", "source": { "split": "train_shard_00000", "doc_id": 4624 }, "chunk_id": "train_shard_00000_4624_0", "global_id": 5164 }, { "text": "Streptococcus suis, an important zoonotic pathogen, is a highly diverse species with only a subset of strains that cause disease in humans. Our previous study proposed a minimum core genome (MCG) sequence typing method and defined seven MCG groups, with MCG group 1 as the prevalent group causing human infections. In this study, we identified a set of 10 single nucleotide polymorphisms (SNPs) distributed in six genes that were used to identify the seven MCG groups. The 10 SNPs were typed for 179 S. suis isolates collected from slaughtered pigs. The most prevalent groups among the tested isolates were MCG groups 6 and 7. Most of the isolates (147/179) were genotyped as mrp negative, epf negative, sly negative, and CDS2157 positive. The 179 isolates were also typed by multilocus sequence typing (MLST) and divided into 115 sequence types (STs), 111 of which were new. The 6 serotypes (29, 11, 5, 12, 30, and 2) represented 72.3% of the serotyped isolates. Our data show that the typing assay facilitates the application of genome data to the surveillance of S. suis.\n\nPopulation analysis of Streptococcus suis isolates from slaughtered swine by use of minimum core genome sequence typing.", "token_count": 342, "char_count": 1196, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [ "CDS2157" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:04.197099", "source": { "split": "train_shard_00000", "doc_id": 4625 }, "chunk_id": "train_shard_00000_4625_0", "global_id": 5165 }, { "text": "Bile acids (BAs) are known to regulate their own homeostasis, but the potency of individual bile acids is not known. This study examined the effects of cholic acid (CA), chenodeoxycholic acid (CDCA), deoxycholic acid (DCA), lithocholic acid (LCA) and ursodeoxycholic acid (UDCA) on expression of BA synthesis and transport genes in human primary hepatocyte cultures. Hepatocytes were treated with the individual BAs at 10, 30, and 100μM for 48 h, and RNA was extracted for real-time PCR analysis. For the classic pathway of BA synthesis, BAs except for UDCA markedly suppressed CYP7A1 (70-95%), the rate-limiting enzyme of bile acid synthesis, but only moderately (35%) down-regulated CYP8B1 at a high concentration of 100μM. BAs had minimal effects on mRNA of two enzymes of the alternative pathway of BA synthesis, namely CYP27A1 and CYP7B1. BAs increased the two major target genes of the farnesoid X receptor (FXR), namely the small heterodimer partner (SHP) by fourfold, and markedly induced fibroblast growth factor 19 (FGF19) over 100-fold. The BA uptake transporter Na(+)-taurocholate co-transporting polypeptide was unaffected, whereas the efflux transporter bile salt export pump was increased 15-fold and OSTα/β were increased 10-100-fold by BAs. The expression of the organic anion transporting polypeptide 1B3 (OATP1B3; sixfold), ATP-binding cassette (ABC) transporter G5 (ABCG5; sixfold), multidrug associated protein-2 (MRP2; twofold), and MRP3 (threefold) were also increased, albeit to lesser degrees", "token_count": 483, "char_count": 1517, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6771, "quality_score": 0.8386, "entities": { "genes": [ "MRP2", "MRP3", "FGF19", "ABCG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:04.852202", "source": { "split": "train_shard_00000", "doc_id": 4626 }, "chunk_id": "train_shard_00000_4626_0", "global_id": 5166 }, { "text": "In general, CDCA was the most potent and effective BA in regulating these genes important for BA homeostasis, whereas DCA and CA were intermediate, LCA the least, and UDCA ineffective.\n\nPotency of individual bile acids to regulate bile acid synthesis and transport genes in primary human hepatocyte cultures.", "token_count": 76, "char_count": 308, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:05.219297", "source": { "split": "train_shard_00000", "doc_id": 4626 }, "chunk_id": "train_shard_00000_4626_1", "global_id": 5167 }, { "text": "Nanostructured capsules comprised of the anionic bile salt, sodium taurodeoxycholate (STDC), and the biocompatible cationic polymer, chitosan, were prepared to assess their potential as novel tailored release nanomaterials. For comparison, a previously studied system, sodium dodecyl sulfate (SDS), and polydiallyldimethylammonium chloride (polyDADMAC) was also investigated. Crossed-polarizing light microscopy (CPLM) and small-angle X-ray scattering (SAXS) identified the presence of lamellar and hexagonal phase at the surfactant-polymer interface of the respective systems. The hydrophobic and electrostatic interactions between the oppositely charged components were studied by varying temperature and salt concentration, respectively, and were found to influence the liquid-crystalline nanostructure formed. The hexagonal phase persisted at high temperatures, however the lamellar phase structure was lost above ca. 45 °C. Both mesophases were found to dissociate upon addition of 4% NaCl solution. The rate of release of the model hydrophilic drug, Rhodamine B (RhB), from the lamellar phase significantly increased in response to changes in the solution conditions studied, suggesting that modulating the drug release from these bile salt-chitosan capsules is readily achieved. In contrast, release from the hexagonal phase capsules had no appreciable response to the stimuli applied. These findings provide a platform for these oppositely charged surfactant and polymer systems to function as stimuli-responsive or sustained-release drug delivery systems.\n\nFormation of liquid-crystalline structures in the bile salt-chitosan system and triggered release from lamellar phase bile salt-chitosan capsules.", "token_count": 418, "char_count": 1712, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:05.847114", "source": { "split": "train_shard_00000", "doc_id": 4627 }, "chunk_id": "train_shard_00000_4627_0", "global_id": 5168 }, { "text": "Vitamin C (ascorbic acid, AA) is a water soluble vitamin with many functions including antioxidative properties, haemostasis, hormone synthesis, collagen synthesis, carnitine synthesis, bile salt production and enhancing iron absorption. There is some evidence that there is a negative inverse relationship between plasma vitamin C concentration and the systemic inflammatory response as measured by C-reactive protein (CRP). The aim of the present study was to examine, in the context of a longitudinal study, the change in plasma concentrations of ascorbic acid (AA) and Vitamin E (α-tocopherol, AT) and their relationship to free radical damage during the evolution of the systemic inflammatory response.\n\nThe relationship between acute changes in the systemic inflammatory response and plasma ascorbic acid, alpha-tocopherol and lipid peroxidation after elective hip arthroplasty.", "token_count": 215, "char_count": 884, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6613, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:06.316253", "source": { "split": "train_shard_00000", "doc_id": 4628 }, "chunk_id": "train_shard_00000_4628_0", "global_id": 5169 }, { "text": "This study aims to evaluate the functional and probiotic characteristics of eight indigenous Lactobacillus strains in vitro. The selected lactobacilli include strains of Lactobacillus casei subsp. casei, Lactobacillus salivarius subsp. salicinius, Lactobacillus fermentum, Lactobacillus plantarum, Lactobacillus delbrueckii subsp. lactis, Lactobacillus delbrueckii subsp. bulgaricus, and Lactobacillus rhamnosus. All strains tolerated both pH 2 for 3 h and 1% bile salt for 24 h. The strains CICC 23174 and CGMCC 1.557 were the most adhesive strains producing the highest quantity of EPS. Although a wide variation in the ability of the eight strains to deplete cholesterol and nitrite, antagonize pathogens, scavenge free radical, and stimulate innate immune response were observed, the strains CICC 23174 and CGMCC 1.557 showed the widest range of these useful traits. Taken together, the strains CICC 23174 and CGMCC 1.557 exhibited the best probiotic properties with the potential for use in the production of probiotic fermented foods.\n\nIn vitro evaluation of the probiotic and functional potential of Lactobacillus strains isolated from fermented food and human intestine.", "token_count": 374, "char_count": 1178, "word_count": 168, "semantic_coherence": 1, "information_density": 0.5774, "quality_score": 0.7887, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:06.901232", "source": { "split": "train_shard_00000", "doc_id": 4629 }, "chunk_id": "train_shard_00000_4629_0", "global_id": 5170 }, { "text": "Numerous bacteria in and on its external parts protect the human body from harmful threats. This study aimed to investigate the potential beneficial effects of the vaginal ecosystem microbiota. A type of bacteria was isolated from vaginal secretions of adolescent and young adult women, cultured on an appropriate specific culture medium, and then molecularly identified through 16S rDNA gene sequencing. Results of 16S rDNA sequencing revealed that the isolate belongs to the Lactobacillus plantarum species. The isolated strain exhibited probiotic properties such as low pH and high bile salt concentration tolerance, antibiotic susceptibility and antimicrobial activity against some pathogenic bacteria. The anticancer effects of the strain on human cancer cell lines (cervical, HeLa; gastric, AGS; colon, HT-29; breast, MCF-7) and on a human normal cell line (human umbilical vein endothelial cells [HUVEC]) were investigated. Toxic side effects were assessed by studying apoptosis in the treated cells. The strain exhibited desirable probiotic properties and remarkable anticancer activity against the tested human cancer cell lines (P ≤ 0.05) with no significant cytotoxic effects on HUVEC normal cells (P ≤ 0.05). Overall, the isolated strain showed favorable potential as a bioactive therapeutic agent. Therefore, this strain should be subjected to the other required tests to prove its suitability for clinical therapeutic application.\n\nAssessment of probiotic potential and anticancer activity of newly isolated vaginal bacterium Lactobacillus plantarum 5BL.", "token_count": 384, "char_count": 1568, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:07.514401", "source": { "split": "train_shard_00000", "doc_id": 4630 }, "chunk_id": "train_shard_00000_4630_0", "global_id": 5171 }, { "text": "Pecorino di Farindola is a handicraft cheese made by farmers on small scale using raw ewes' milk and pig rennet. In this study, yeast consortia were evaluated during Pecorino di Farindola making and ripening. Molecular identification of 156 isolates was achieved by a combination of PCR-RFLP of the 5.8S ITS rRNA region and sequencing of the D1/D2 domain of the 26S rRNA gene. Kluyveromyces marxianus was the predominant species, while other species (Pichia kudriavzevii, Candida parapsilosis, Candida glaebosa and Candida zeylanoides) were present only during the early weeks of ripening. Moreover, the isolates were differentiated both by RAPD-PCR and a sequence alignment of D1/D2 26S rRNA gene, revealing different K. marxianus profiles and variants, and suggesting the role of local selective pressure as the origin of distinctive K. marxianus populations. The strains were characterized also on the basis of different dairy properties such as growth temperature, lactose, galactose, lactate and citrate assimilation at different NaCl concentrations, as well as lipolytic and caseinolytic activities. Moreover, 39 selected K. marxianus strains were inoculated in pasteurized whey to evaluate their growth kinetics, besides lactose, lactate and free amino acids metabolism. The growth kinetics distinguished different biotypes and different metabolic behavior were determined. The general picture of K. marxianus population from Pecorino di Farindola shows a high biodiversity at genetic and phenotypic levels that potentially offers many opportunities for new and advanced knowledge at species level, providing in the meantime a good basis to study the relationship between genetic variability and functional diversities.\n\nThe predominance, biodiversity and biotechnological properties of Kluyveromyces marxianus in the production of Pecorino di Farindola cheese.", "token_count": 486, "char_count": 1868, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6053, "quality_score": 0.8026, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:08.160662", "source": { "split": "train_shard_00000", "doc_id": 4631 }, "chunk_id": "train_shard_00000_4631_0", "global_id": 5172 }, { "text": "This study investigated the production of ethanol from unutilized branches pruned from pear trees by steam explosion pretreatment. Steam pressures of 25, 35, and 45 atm were applied for 5 min, followed by enzymatic saccharification of the extracted residues with cellulase (Cellic CTec2). High glucose recoveries, of 93.3, 99.7, and 87.1%, of the total sugar derived from the cellulose were obtained from water- and methanol-extracted residues after steam explosion at 25, 35, and 45 tm, respectively. These values corresponded to 34.9, 34.3, and 27.1 g of glucose per 100 g of dry steam-exploded branches. Simultaneous saccharification and fermentation experiments were done on water-extracted residues and water- and methanol-extracted residues by Kluyveromyces marxianus NBRC 1777. An overall highest theoretical ethanol yield of 76% of the total sugar derived from cellulose was achieved when 100 g/L of water- and methanol-washed residues from 35 atm-exploded pear branches was used as substrate.\n\nSteam explosion treatment for ethanol production from branches pruned from pear trees by simultaneous saccharification and fermentation.", "token_count": 329, "char_count": 1139, "word_count": 165, "semantic_coherence": 1, "information_density": 0.5758, "quality_score": 0.7879, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:08.727008", "source": { "split": "train_shard_00000", "doc_id": 4632 }, "chunk_id": "train_shard_00000_4632_0", "global_id": 5173 }, { "text": "The outer membrane protein K, OmpK first identified in Vibrio parahaemolyticus has been shown to be a receptor for a broad host range vibriophage KVP40 infecting members of the Vibrionaceae. In the study, the effect of culture conditions on the expression of ompK in V. anguillarum was studied using real-time PCR. The expression increased significantly in the presence of bile salts and iron chelating agent 2, 2' bipyridine, suggesting a role for this protein in bile resistance and also in iron acquisition by V. anguillarum. OmpK induction by iron limitation and the presence of bile salts was reconfirmed by western blot technique after growing the cells in trypticase soy broth supplemented with bile salts, blood and 2, 2' bipyridine. We surmise that the expression of OmpK protein of V. anguillarum is bile salt and iron chelating agent-dependent.\n\nIron shortage and bile salts play a major role in the expression of ompK gene in Vibrio anguillarum.", "token_count": 266, "char_count": 957, "word_count": 155, "semantic_coherence": 1, "information_density": 0.5677, "quality_score": 0.7839, "entities": { "genes": [ "KVP40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:09.284650", "source": { "split": "train_shard_00000", "doc_id": 4633 }, "chunk_id": "train_shard_00000_4633_0", "global_id": 5174 }, { "text": "Bile salt transporters directly or indirectly influence biological processes through physicochemical or signalling properties of bile salts. The coordinated action of uptake and efflux transporters in polarized epithelial cells of the liver, biliary tree, small intestine and kidney determine bile salt concentrations in different compartments of the body. Genetic variations of bile salt transporters lead to clinical relevant phenotypes of varying severity ranging from a predisposition for drug-induced liver injury to rapidly progressing end-stage liver disease. This review focuses on the impact of genetic variations of bile salt transporters including BSEP, NTCP, ASBT and OSTα/β and discusses approaches for transporter analysis.\n\nGenetic variations of bile salt transporters.", "token_count": 180, "char_count": 784, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6729, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:09.727495", "source": { "split": "train_shard_00000", "doc_id": 4634 }, "chunk_id": "train_shard_00000_4634_0", "global_id": 5175 }, { "text": "Progressive familial intrahepatic cholestasis type 1 (PFIC1), an inherited liver disease caused by mutations in ATP8B1, progresses to severe cholestasis with a sustained intractable itch. Currently, no effective therapy has been established for PFIC1. Decreased function of the bile salt export pump (BSEP) in hepatocytes is suggested to be responsible for the severe cholestasis observed in PFIC1. We found a previously unidentified pharmacological effect of 4-phenylbutyrate (4PB) that increases the expression and function of BSEP. Here, we tested 4PB therapy in three patients with PFIC1.\n\nIntractable itch relieved by 4-phenylbutyrate therapy in patients with progressive familial intrahepatic cholestasis type 1.", "token_count": 198, "char_count": 718, "word_count": 100, "semantic_coherence": 1, "information_density": 0.69, "quality_score": 0.845, "entities": { "genes": [ "PFIC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:10.178638", "source": { "split": "train_shard_00000", "doc_id": 4635 }, "chunk_id": "train_shard_00000_4635_0", "global_id": 5176 }, { "text": "Hepatocellular carcinoma (HCC) rarely occurs in childhood. We describe a patient with new onset of pruritus at 8 months of age who at 17 months of age was found to have a 2.5 cm HCC. To delineate the possible genetic basis of this tumour, we performed whole exome sequencing (WES) of the germline DNA and identified two novel predictably deleterious missense mutations in ABCB11, encoding bile salt export pump (BSEP), confirmed in the parental DNA as bi-allelic and inherited. Although inherited ABCB11 mutations have previously been linked to HCC in a small number of cases, the molecular mechanisms of hepatocellular carcinogenesis in ABCB11 disease are unknown. WES of the HCC tissue uncovered somatic driver mutations in the beta-catenin (CTNNB1) and nuclear-factor-erythroid-2-related-factor-2 (NFE2L2) genes. Moreover, clonality analysis predicted that the CTNNB1 mutation was clonal and occurred earlier during carcinogenesis, whereas the NFE2L2 mutation was acquired later. Interestingly, background liver parenchyma showed no inflammation or fibrosis and BSEP expression was preserved. This is the first study to identify somatic CTNNB1 and NFE2L2 mutations in early childhood arisen in the setting of inherited bi-allelic ABCB11 mutations. Rapid WES analysis expedited this child's diagnosis and treatment, and likely improved her prognosis.\n\nPaediatric hepatocellular carcinoma due to somatic CTNNB1 and NFE2L2 mutations in the setting of inherited bi-allelic ABCB11 mutations.", "token_count": 407, "char_count": 1489, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6372, "quality_score": 0.8186, "entities": { "genes": [ "ABCB11", "CTNNB1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:10.794202", "source": { "split": "train_shard_00000", "doc_id": 4636 }, "chunk_id": "train_shard_00000_4636_0", "global_id": 5177 }, { "text": "The digestion of dietary components in the human gastrointestinal (GI) tract is a complex, dynamic, inherently heterogeneous process. A key aspect of the digestion of lipid in the GI tract is the combined action of bile salts, lipase and colipase in hydrolysing and solubilising dispersed lipid. The bile salts are a mixture of steroid acid conjugates with surfactant properties. In order to examine whether the different bile salts have different interfacial properties their dynamic interfacial behaviour was characterised. Differences in the adsorption behaviour to solid hydrophobic surfaces of bile salt species were studied using dual polarisation interferometry and atomic force microscopy (AFM) under physiological conditions. Specifically, the cholates adsorbed more slowly and a significant proportion were irreversibly adsorbed following buffer rinsing; whereas the deoxycholates and chenodeoxycholates adsorbed more rapidly and desorbed to a greater extent following buffer rinsing. The conjugating groups (taurine, glycine) did not influence the behaviour. AFM showed that the interfacial structures that remained following buffer rinsing were also different between these two groups. In addition, the adsorption-desorption behaviour affected the adsorption of colipase to a solid surface. This supports the idea that cooperative adsorption occurs between certain bile salts and colipase to facilitate the adsorption and activity of pancreatic lipase in order to restore lipolytic activity in the presence of bile salts. This study provides insights into how differences in bile salt structure could affect lipase activity and solubilisation of lipolysis products and other lipid-soluble bioactive molecules.\n\nThe adsorption-desorption behaviour and structure function relationships of bile salts.", "token_count": 419, "char_count": 1810, "word_count": 250, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:11.442261", "source": { "split": "train_shard_00000", "doc_id": 4637 }, "chunk_id": "train_shard_00000_4637_0", "global_id": 5178 }, { "text": "In order to analyze the correlation between critical residues in the catalytic centre of BSH and the enzyme substrate specificity, seven mutants of Lactobacillus salivarius bile salt hydrolase (BSH1) were constructed by using the Escherichia coli pET-20b(+) gene expression system, rational design and site-directed mutagenesis. These BSH1 mutants exhibited different hydrolytic activities against various conjugated bile salts through substrate specificities comparison. Among the residues being tested, Cys2 and Thr264 were deduced as key sites for BSH1 to catalyze taurocholic acid and glycocholic acid, respectively. Moreover, Cys2 and Thr264 were important for keeping the catalytic activity of BSH1. The high conservative Cys2 was not the only active site, other mutant amino acid sites were possibly involved in substrate binding. These mutant residues might influence the space and shape of the substrate-binding pockets or the channel size for substrate passing through and entering active site of BSH1, thus, the hydrolytic activity of BSH1 was changed to different conjugated bile salt.\n\n[Substrate specificities of bile salt hydrolase 1 and its mutants from Lactobacillus salivarius].", "token_count": 309, "char_count": 1196, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6257, "quality_score": 0.8129, "entities": { "genes": [ "BSH1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:12.024902", "source": { "split": "train_shard_00000", "doc_id": 4638 }, "chunk_id": "train_shard_00000_4638_0", "global_id": 5179 }, { "text": "Bile salt export pump (BSEP) inhibition has been proposed to be an important mechanism for drug-induced liver injury (DILI). Modeling can prioritize knowledge gaps concerning bile acid (BA) homeostasis and thus help guide experimentation. A submodel of BA homeostasis in rats and humans was constructed within DILIsym, a mechanistic model of DILI. In vivo experiments in rats with glibenclamide were conducted, and data from these experiments were used to validate the model. The behavior of DILIsym was analyzed in the presence of a simulated theoretical BSEP inhibitor. BSEP inhibition in humans is predicted to increase liver concentrations of conjugated chenodeoxycholic acid (CDCA) and sulfate-conjugated lithocholic acid (LCA) while the concentration of other liver BAs remains constant or decreases. On the basis of a sensitivity analysis, the most important unknowns are the level of BSEP expression, the amount of intestinal synthesis of LCA, and the magnitude of farnesoid-X nuclear receptor (FXR)-mediated regulation.\n\nMechanistic Modeling Reveals the Critical Knowledge Gaps in Bile Acid-Mediated DILI.", "token_count": 283, "char_count": 1114, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:12.630126", "source": { "split": "train_shard_00000", "doc_id": 4639 }, "chunk_id": "train_shard_00000_4639_0", "global_id": 5180 }, { "text": "Horizontal gene transfer plays an important role in the evolution of bacterial species, conferring new genetic traits on the recipient bacterium that extend its range of phenotypes and plasmids make important contributions to this process. However, the inappropriate expression of newly acquired genes may lead to a loss of competitive fitness, resulting in the elimination of the new gene-bacterium combination. It is thought that transcriptional silencing of horizontally acquired genes offers a route out of this dilemma and that nucleoid-associated proteins, especially those related to the H-NS protein, play a particularly important role in the silencing process. The discovery that many plasmids express orthologues of nucleoid-associated proteins adds an interesting dimension to current models of regulatory integration following lateral transfer of DNA. Other horizontally acquired genetic elements, such as genomic islands, also express nucleoid-associated proteins of their own. Here the interactions of H-NS-like nucleoid-associated proteins encoded by the core genome, genomic islands and plasmids are described.\n\nH-NS-like nucleoid-associated proteins, mobile genetic elements and horizontal gene transfer in bacteria.", "token_count": 256, "char_count": 1233, "word_count": 168, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:13.189033", "source": { "split": "train_shard_00000", "doc_id": 4640 }, "chunk_id": "train_shard_00000_4640_0", "global_id": 5181 }, { "text": "Progressive familial intrahepatic cholestasis (PFIC) type 2 results from a mutation in the bile salt exporter pump, impeding bile acid transport. Patients usually present with jaundice, pruritus, growth failure, and fat soluble vitamin deficiencies. We present two patients diagnosed with PFIC type 2 due to severe coagulopathy and bleeding without jaundice.\n\nTwo Cases of Progressive Familial Intrahepatic Cholestasis Type 2 Presenting with Severe Coagulopathy without Jaundice.", "token_count": 136, "char_count": 479, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7121, "quality_score": 0.8561, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:13.616067", "source": { "split": "train_shard_00000", "doc_id": 4641 }, "chunk_id": "train_shard_00000_4641_0", "global_id": 5182 }, { "text": "Besides reducing gastric acid secretion, proton pump inhibitors (PPIs) suppress Th2-cytokine-stimulated expression of an eosinophil chemoattractant (eotaxin-3) by esophageal epithelial cells through acid-independent, anti-inflammatory mechanisms. To explore acid-inhibitory and acid-independent, anti-inflammatory PPI effects in reducing esophageal eosinophilia, we studied eotaxin-3 expression by the proximal and distal esophagus of children with esophageal eosinophilia before and after PPI therapy. In vitro, we studied acid and bile salt effects on IL-13-stimulated eotaxin-3 expression by esophageal epithelial cells.\n\nProton pump inhibitors decrease eotaxin-3 expression in the proximal esophagus of children with esophageal eosinophilia.", "token_count": 224, "char_count": 745, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6067, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:14.082166", "source": { "split": "train_shard_00000", "doc_id": 4642 }, "chunk_id": "train_shard_00000_4642_0", "global_id": 5183 }, { "text": "Bile components play a significant role in the absorption of dietary fat, by solubilizing the products of fat digestion. The absorption of poorly water-soluble drugs from the gastrointestinal tract is often enhanced by interaction with the pathways of fat digestion and absorption. These processes can enhance drug absorption. Thus, the phase behavior of bile components and digested lipids is of great interest to pharmaceutical scientists who seek to optimize drug solubilization in the gut lumen. This can be achieved by dosing drugs after food or preferably by formulating the drug in a lipid-based delivery system. Phase diagrams of bile salts, lecithin, and water have been available for many years, but here we investigate the association structures that occur in dilute aqueous solution, in concentrations that are present in the gut lumen. More importantly, we have compared these structures with those that would be expected to be present in the intestine soon after secretion of bile. Phosphatidylcholines are rapidly hydrolyzed by pancreatic enzymes to yield equimolar mixtures of their monoacyl equivalents and fatty acids. We constructed phase diagrams that model the association structures formed by the products of digestion of biliary phospholipids. The micelle-vesicle phase boundary was clearly identifiable by dynamic light scattering and nephelometry. These data indicate that a significantly higher molar ratio of lipid to bile salt is required to cause a transition to lamellar phase (i.e., liposomes in dilute solution). Mixed micelles of digested bile have a higher capacity for solubilization of lipids and fat digestion products and can be expected to have a different capacity to solubilize lipophilic drugs. We suggest that mixtures of lysolecithin, fatty acid, and bile salts are a better model of molecular associations in the gut lumen, and such mixtures could be used to better understand the interaction of drugs with the fat digestion and absorption pathway.\n\nDigestion of phospholipids after secretion of bile into the duodenum changes the phase behavior of bile components.", "token_count": 482, "char_count": 2110, "word_count": 321, "semantic_coherence": 1, "information_density": 0.5171, "quality_score": 0.7586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:14.729396", "source": { "split": "train_shard_00000", "doc_id": 4643 }, "chunk_id": "train_shard_00000_4643_0", "global_id": 5184 }, { "text": "The Lipid Formulation Classification System Consortium looks to develop standardized in vitro tests and to generate much-needed performance criteria for lipid-based formulations (LBFs). This article highlights the value of performing a second, more stressful digestion test to identify LBFs near a performance threshold and to facilitate lead formulation selection in instances where several LBF prototypes perform adequately under standard digestion conditions (but where further discrimination is necessary). Stressed digestion tests can be designed based on an understanding of the factors that affect LBF performance, including the degree of supersaturation generated on dispersion/digestion. Stresses evaluated included decreasing LBF concentration (↓LBF), increasing bile salt, and decreasing pH. Their capacity to stress LBFs was dependent on LBF composition and drug type: ↓LBF was a stressor to medium-chain glyceride-rich LBFs, but not more hydrophilic surfactant-rich LBFs, whereas decreasing pH stressed tolfenamic acid LBFs, but not fenofibrate LBFs. Lastly, a new Performance Classification System, that is, LBF composition independent, is proposed to promote standardized LBF comparisons, encourage robust LBF development, and facilitate dialogue with the regulatory authorities. This classification system is based on the concept that performance evaluations across three in vitro tests, designed to subject a LBF to progressively more challenging conditions, will enable effective LBF discrimination and performance grading.\n\nToward the establishment of standardized in vitro tests for lipid-based formulations, part 4: proposing a new lipid formulation performance classification system.", "token_count": 366, "char_count": 1705, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6211, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:15.319212", "source": { "split": "train_shard_00000", "doc_id": 4644 }, "chunk_id": "train_shard_00000_4644_0", "global_id": 5185 }, { "text": "Candida kefyr is an increasingly reported pathogen in patients with hematologic malignancies. We studied a series of bloodstream isolates that exhibited reduced echinocandin susceptibilities (RES). Clinical and surveillance isolates were tested for susceptibilities to all three echinocandins, and those isolates displaying RES to one or more echinocandins were selected for molecular and biochemical studies. The isolates were analyzed for genetic similarities, and a subset was analyzed for mutations in the echinocandin target gene FKS1 and glucan synthase echinocandin sensitivities using biochemical methods. The molecular typing did not indicate strong genetic relatedness among the isolates except for a series of strains recovered from a single patient. Two unrelated isolates with RES had previously uncharacterized FKS1 mutations: R647G and deletion of amino acid 641 (F641Δ). Biochemical analysis of the semipurified R647G glucan synthase generated differential echinocandin sensitivity (resistance to micafungin only), while the deletion of F641 resulted in a glucan synthase highly insensitive to all three echinocandins. The consecutive isolates from a single patient with RES all harbored the common S645P mutation, which conferred resistance to all three echinocandins. The MIC values paralleled the glucan synthase inhibition kinetic data, although the S645P isolates displayed relatively higher susceptibility to caspofungin (2 μg/ml) than the other two echinocandins (>8 μg/ml). These findings highlight novel and common FKS1 mutations in C. kefyr isolates. The observation of differential susceptibilities to echinocandins may provide important mechanistic insights for echinocandin antifungals.\n\nTarget enzyme mutations confer differential echinocandin susceptibilities in Candida kefyr.", "token_count": 473, "char_count": 1808, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5885, "quality_score": 0.7942, "entities": { "genes": [ "FKS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:15.956765", "source": { "split": "train_shard_00000", "doc_id": 4645 }, "chunk_id": "train_shard_00000_4645_0", "global_id": 5186 }, { "text": "Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into \"species groups\". However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.\n\nComparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups.", "token_count": 391, "char_count": 1827, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:16.574065", "source": { "split": "train_shard_00000", "doc_id": 4646 }, "chunk_id": "train_shard_00000_4646_0", "global_id": 5187 }, { "text": "Tibetan kefir grains (TKGs), a kind of natural starter for fermented milk in Tibet, China, host various microorganisms of lactic acid bacteria, yeasts, and occasionally acetic acid bacteria in a polysaccharide/protein matrix. In the present study, the fine structure of TKGs was studied to shed light on this unusual symbiosis with stereomicroscopy and thin sections. The results reveal that TKGs consist of numerous small grain units, which are characterized by a hollow globular structure with a diameter between 2.0 and 9.0 mm and a wall thickness of approximately 200 µm. A polyhedron-like net structure, formed mainly by the bacteria, was observed in the wall of the grain units, which has not been reported previously to our knowledge. Towards the inside of the grain unit, the polyhedron-like net structures became gradually larger in diameter and fewer in number. Such fine structures may play a crucial role in the stability of the grains. Subsequently, the distribution, diversity, and shift of yeasts in TKGs were investigated based on thin section, scanning electron microscopy, cloning and sequencing of D1/D2 of the 26S rRNA gene, real-time quantitative PCR, and in situ hybridization with specific fluorescence-labeled oligonucleotide probes. These show that (i) yeasts appear to localize on the outer surface of the grains and grow normally together to form colonies embedded in the bacterial community; (ii) the diversity of yeasts is relatively low on genus level with three dominant species--Saccharomyces cerevisiae, Kluyveromyces marxianus, and Yarrowia lipolytica; (iii) S. cerevisiae is the stable predominant yeast species, while the composition of Kluyveromyces and Yarrowia are subject to change over time. Our results indicate that TKGs are relatively stable in structure, and culture conditions to some extent shape the microbial community and interaction in kefir grains. These findings pave the way for further study of the specific symbiotic associations between S. cerevisiae and Lactobacillus bacteria in TKGs.", "token_count": 505, "char_count": 2043, "word_count": 308, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:17.229351", "source": { "split": "train_shard_00000", "doc_id": 4647 }, "chunk_id": "train_shard_00000_4647_0", "global_id": 5188 }, { "text": "Fine structure of Tibetan kefir grains and their yeast distribution, diversity, and shift.", "token_count": 21, "char_count": 90, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:17.585733", "source": { "split": "train_shard_00000", "doc_id": 4647 }, "chunk_id": "train_shard_00000_4647_1", "global_id": 5189 }, { "text": "Esophageal adenocarcinoma (EAC) is the most frequent malignancy in the esophagus in the US and its incidence has been rising rapidly in the past few decades. Chronic gastroesophageal reflux disease (GERD), where the esophageal epithelium is abnormally exposed to acid and bile salts, is a pro-inflammatory condition that is the main risk factor for the development of Barrett's esophagus (BE) and its progression to EAC. Glutathione peroxidase 7 (GPX7) is frequently silenced through DNA hypermethylation during Barrett's tumorigenesis. In this study, we investigated the role of GPX7 in regulating the bile salts-induced inflammatory signaling in Barrett's carcinogenesis. Using quantitative real-time PCR (qRT-PCR), we demonstrated a significant induction in the expression levels of pro-inflammatory cytokines (TNF-α, IL-1β, IL-6, and IL-8) and chemokines (CXCL-1 and CXCL-2) in esophageal cells after exposure to acidic (pH4) or neutral (pH7) bile salts. Western blot analysis showed that exposure to acidic and neutral bile salts increased p-NF-κB-p65 (S536) protein levels independent of ROS. Reconstitution of GPX7 expression in EAC cells abolished the increase of p-p65 (S536) protein levels and mRNA expression of cytokines and chemokines upon treatment with acidic and neutral bile salts. Examination of human primary EAC tissues by qRT-PCR demonstrated significant overexpression of cytokines (TNF-α, IL-1β and IL-8) in EAC samples, as compared to normal samples, with significant inverse correlation with GPX7 expression level. Taken together, the loss of GPX7 expression promotes bile salt-induced activation of pro-inflammatory cytokines and chemokines; important contributors to GERD-associated Barrett's carcinogenesis.", "token_count": 509, "char_count": 1735, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5868, "quality_score": 0.7934, "entities": { "genes": [ "GPX7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:18.214505", "source": { "split": "train_shard_00000", "doc_id": 4648 }, "chunk_id": "train_shard_00000_4648_0", "global_id": 5190 }, { "text": "Glutathione Peroxidase 7 Suppresses Bile Salt-Induced Expression of Pro-Inflammatory Cytokines in Barrett's Carcinogenesis.", "token_count": 42, "char_count": 123, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:18.577811", "source": { "split": "train_shard_00000", "doc_id": 4648 }, "chunk_id": "train_shard_00000_4648_1", "global_id": 5191 }, { "text": "Research has suggested that exposure to sub-micellar concentrations of bile salts (BS) increases the permeability of lipid bilayers in a time-dependent manner. In this study, incubation of soy phosphatidylcholine small unilamellar vesicles (liposomes) with sub-micellar concentrations of cholate (C), deoxycholate (DC), 12-monoketocholate (MKC) or taurocholate (TC) in pH 7.2 buffer increased membrane fluidity and negative zeta potential in the order of increasing BS liposome-pH 7.2 buffer distribution coefficients (MKC < C ≈ TC < DC). In liposomes labeled with the dithionite-sensitive fluorescent lipid N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)phosphatidylethanolamine (NBD-PE) in both leaflets and equilibrated with sub-micellar concentrations of BS, fluorescence decline during continuous exposure to dithionite was biphasic involving a rapid initial phase followed by a slower second phase. Membrane permeability to dithionite as measured by the rate of the second phase increased in the order control < MKC < TC ∼ C < DC. In liposomes labeled with NBD-PE in the inner leaflet only and incubated with the same concentrations of C, DC and MKC, membrane permeability to dithionite initially increased very rapidly in the order MKC < C < DC before impermeability to dithionite was restored after which fluorescence decline was consistent with NBD-PE flip-flop. For liposomes incubated with TC, membrane permeability to dithionite was only slightly increased and the decline in fluorescence was mainly the result of NBD-PE flip-flop", "token_count": 496, "char_count": 1532, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5505, "quality_score": 0.7752, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:19.228568", "source": { "split": "train_shard_00000", "doc_id": 4649 }, "chunk_id": "train_shard_00000_4649_0", "global_id": 5192 }, { "text": "These results provide evidence that BS interact with lipid bilayers in a time-dependent manner that is different for conjugated and unconjugated BS. MKC appears to cause least disturbance to liposomal membranes but, when the actual MKC concentration in liposomes is taken into account, MKC is actually the most disruptive.\n\nKinetic and equilibrium studies of bile salt-liposome interactions.", "token_count": 97, "char_count": 391, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:19.601919", "source": { "split": "train_shard_00000", "doc_id": 4649 }, "chunk_id": "train_shard_00000_4649_1", "global_id": 5193 }, { "text": "The entrapment of neutral and cationic species of an anticancer drug, namely ellipticine and their dynamic features in different bile salt aggregates have been investigated for the first time using steady state and time-resolved fluorescence spectroscopy. Because ellipticine exists in various prototropic forms under physiological conditions, we performed comparative photophysical and dynamical studies on these prototropic species in different bile salts varying in their head groups and hydrophobic skeletons. We found that the initial interaction between ellipticine and bile salts is governed by the electrostatic forces where cationic ellipticine is anchored to the head groups of bile salts. Bile salts having conjugated head groups are better candidates to bind with the cationic species than those having the non-conjugated ones. The fact implies that binding of cationic species to different bile salts depends on the pK(a) of the corresponding bile acids. The hydrophobic interaction dominates at higher concentrations of bile salts due to formation of aggregates and results in entrapment of neutral ellipticine molecules according to their hydrophobicity indices. Thus bile salts act as multisite drug carriers. The rotational relaxation parameters of cationic ellipticine were found to be dependent on head groups and the number of hydroxyl groups on the hydrophilic surface of bile salts. Cationic ellipticine exhibits a faster rotational relaxation in the tri-hydroxy bile salt aggregates than in di-hydroxy bile salts. We interpreted this observation from the fact that tri-hydroxy bile salts hold a higher number of water molecules in their hydrophilic surface offering a less viscous environment for ellipticine compared to di-hydroxy bile salts. Surprisingly, the neutral ellipticine molecules display almost the same rotational relaxation in all the bile salts. The observation indicates that after intercalation inside the hydrophobic pocket, neutral ellipticine molecules experience similar confinement in all the bile salts.", "token_count": 481, "char_count": 2049, "word_count": 293, "semantic_coherence": 1, "information_density": 0.4846, "quality_score": 0.7423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:20.249242", "source": { "split": "train_shard_00000", "doc_id": 4650 }, "chunk_id": "train_shard_00000_4650_0", "global_id": 5194 }, { "text": "Partitioning of prototropic species of an anticancer drug ellipticine in bile salt aggregates of different head groups and hydrophobic skeletons: a photophysical study to probe bile salts as multisite drug carriers.", "token_count": 57, "char_count": 215, "word_count": 31, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:20.611659", "source": { "split": "train_shard_00000", "doc_id": 4650 }, "chunk_id": "train_shard_00000_4650_1", "global_id": 5195 }, { "text": "Acinetobacter baumannii has emerged as one of the leading pathogens causing hospital-acquired infection. The success of A. baumannii as a pathogen has to a large extent been attributed to its capacity to remodel its genome. Several major epidemic clonal complexes of A. baumannii spread across different health care facilities around the world, each of which contains a subset of diversified strains. However, little is known about the population dynamics during colonization of A. baumannii within hosts. Here, whole-genome sequencing was used to analyze population dynamics of A. baumannii strains isolated from a group of patients at different time points as well as from different sites of a particular patient. Seven out of nine of the sampled A. baumannii strains belonged to the international clone II (CC92 clonal complex). While the A. baumannii strains were found to be stable in three patients, there was a change of A. baumannii strains in one patient. Comparative genomic analysis revealed that the accessory genome of these strains contained a large set of virulence-encoding genes and these virulence factors might play a role in determining population dynamics. Microscale genome modification has been revealed by analysis of single nucleotide polymorphisms (SNPs) between A. baumannii strains isolated from the same patient. Parallel evolutionary traits have been observed during genome diversification when A. baumannii colonize in different patients. Our study suggested that both antibiotic usage and host environment might impose selective forces that drive the rapid adaptive evolution in colonizing A. baumannii.\n\nPopulation dynamics of an Acinetobacter baumannii clonal complex during colonization of patients.", "token_count": 391, "char_count": 1734, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5898, "quality_score": 0.7949, "entities": { "genes": [ "CC92" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:21.578210", "source": { "split": "train_shard_00000", "doc_id": 4651 }, "chunk_id": "train_shard_00000_4651_0", "global_id": 5196 }, { "text": "Campylobacter spp. are the most common cause of bacterial gastroenteritis worldwide and have been isolated from a wide number of different hosts and environmental sources. Waterfowl is considered a natural reservoir for this zoonotic bacterium and may act as a potential infection source for human campylobacteriosis. In this study, faecal samples from 924 barnacle geese were tested for the presence of C. jejuni and C. coli. The resulting C. jejuni and C. coli populations were characterized by multilocus sequence typing (MLST), structure analysis by BAPS and phylogenetic analysis based on full genome sequences. The prevalences of C. jejuni in barnacle geese faeces were 11.5% and 23.1% in 2011 and 2012, respectively, and only 0.2% of the samples were positive for C. coli in both years. Furthermore, a possible adaption of the clonal complexes (CCs) ST-702 and ST-1034 to the barnacle geese reservoir was found, as these two CCs represented the majority of the typed isolates and were repeatedly isolated from different flocks at several time-points. Further core genome phylogenetic analysis using ClonalFrame revealed a formation of a distinct monophyletic lineage by these two CCs, suggesting a certain degree of clonality of the C. jejuni population adapted to barnacle geese. Therefore, although STs also commonly found in humans patients (e.g. ST-45) were among the barnacle geese C. jejuni isolates, this reservoir is probably an infrequent source for human campylobacteriosis.\n\nCharacterization of the Campylobacter jejuni population in the barnacle geese reservoir.", "token_count": 409, "char_count": 1581, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5858, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:22.203172", "source": { "split": "train_shard_00000", "doc_id": 4652 }, "chunk_id": "train_shard_00000_4652_0", "global_id": 5197 }, { "text": "We report on the first cloning and nucleotide sequencing of an ERG11 allele from a clinical isolate of Candida kefyr cross-resistant to azole antifungals. It was recovered from a stem cell transplant patient, in an oncohematology unit exhibiting unexpected high prevalence of C. kefyr. Two amino acid substitutions were identified: K151E, whose role in fluconazole resistance was already demonstrated in Candida albicans, and E123Q, a new substitution never described so far in azole-resistant Candida yeast.\n\nTwo missense mutations, E123Q and K151E, identified in the ERG11 allele of an azole-resistant isolate of Candida kefyr recovered from a stem cell transplant patient for acute myeloid leukemia.", "token_count": 198, "char_count": 702, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6827, "quality_score": 0.8413, "entities": { "genes": [ "ERG11" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:22.661366", "source": { "split": "train_shard_00000", "doc_id": 4653 }, "chunk_id": "train_shard_00000_4653_0", "global_id": 5198 }, { "text": "The aim of the present study was to describe the identification and characterization (physiological properties) of two strains of lactic acid bacteria (LAB 18 and 48) present in a commercial probiotic culture, FloraMax(®)-B11. Isolates were characterized morphologically, and identified biochemically. In addition, the MIDI System ID, the Biolog ID System, and 16S rRNA sequence analyses for identification of LAB 18 and LAB 48 strains were used to compare the identification results. Tolerance and resistance to acidic pH, high osmotic concentration of NaCl, and bile salts were tested in broth medium. In vitro assessment of antimicrobial activity against enteropathogenic bacteria and susceptibility to antibiotics were also tested. The results obtained in this study showed tolerance of LAB 18 and LAB 48 to pH 3.0, 6.5% NaCl and a high bile salt concentration (0.6%). Both strains evaluated showed in vitro antibacterial activity against Salmonella enterica serovar Enteritidis, Escherichia coli (O157:H7), and Campylobacter jejuni. These are important characteristics of lactic acid bacteria that should be evaluated when selecting strains to be used as probiotics. Antimicrobial activity of these effective isolates may contribute to efficacy, possibly by direct antimicrobial activity in vivo.\n\nIdentification and characterization of lactic Acid bacteria in a commercial probiotic culture.", "token_count": 359, "char_count": 1397, "word_count": 200, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:23.285711", "source": { "split": "train_shard_00000", "doc_id": 4654 }, "chunk_id": "train_shard_00000_4654_0", "global_id": 5199 }, { "text": "Vibrio parahaemolyticus is a halophile that inhabits brackish waters and a wide range of hosts, including crustaceans, fish, mollusks, and humans. In humans, it is the leading cause of bacterial seafood-borne gastroenteritis. The focus of this work was to determine the role of alternative sigma factors in the stress response of V. parahaemolyticus RIMD2210633, an O3:K6 pandemic isolate. Bioinformatics identified five putative extracytoplasmic function (ECF) family of alternative sigma factors: VP0055, VP2210, VP2358, VP2578, and VPA1690. ECF factors typically respond to cell wall/cell envelope stress, iron levels, and the oxidation state of the cell. We have demonstrated here that one such sigma factor, VP2578, a homologue of RpoE from Escherichia coli, is important for survival under a number of cell envelope stress conditions and in gastrointestinal colonization of a streptomycin-treated adult mouse. In this study, we determined that an rpoE deletion mutant strain BHM2578 compared to the wild type (WT) was significantly more sensitive to polymyxin B, ethanol, and high-temperature stresses. We demonstrated that in in vivo competition assays between the rpoE mutant and the WT marked with the β-galactosidase gene lacZ (WBWlacZ), the mutant strain was defective in colonization compared to the WT. In contrast, deletion of the rpoS stress response regulator did not affect in vivo survival. In addition, we examined the role of the outer membrane protein, OmpU, which in V. cholerae is proposed to be the sole activator of RpoE. We found that an ompU deletion mutant was sensitive to bile salt stress but resistant to polymyxin B stress, indicating OmpU is not essential for the cell envelope stress responses or RpoE function. Overall, these data demonstrate that RpoE is a key cell envelope stress response regulator and, similar to E", "token_count": 516, "char_count": 1854, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5825, "quality_score": 0.7912, "entities": { "genes": [ "RIMD2210633", "VP2210", "BHM2578", "VP2578", "VPA1690", "VP0055", "VP2358" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:46:24.937008", "source": { "split": "train_shard_00000", "doc_id": 4655 }, "chunk_id": "train_shard_00000_4655_0", "global_id": 5200 }, { "text": "coli, RpoE may have several factors that stimulate its function.\n\nAlternative sigma factor RpoE is important for Vibrio parahaemolyticus cell envelope stress response and intestinal colonization.", "token_count": 50, "char_count": 195, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:25.293626", "source": { "split": "train_shard_00000", "doc_id": 4655 }, "chunk_id": "train_shard_00000_4655_1", "global_id": 5201 }, { "text": "Eleven uncommon yeast species that are associated with high mortality rates irrespective of antifungal therapy were isolated from 17/187 (201 episodes) pediatric and elderly patients with fungemia from Qatar. The samples were taken over a 6-year period (January 2004-December 2010). Isolated species included Kluyveromyces marxianus, Lodderomyces elongisporus, Lindnera fabianii, Candida dubliniensis, Meyerozyma guilliermondii, Candida intermedia, Pichia kudriavzevii, Yarrowia lipolytica, Clavispora lusitaniae, Candida pararugosa, and Wickerhamomyces anomalus. Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry provided correct identifications compared with molecular analysis testing of the same isolates. Low minimal inhibitory concentrations were found when isavuconazole and voriconazole were used for all uncommon yeast species evaluated in this study. Resistance to antifungal drugs was low and remained restricted to a few species.\n\nUncommon opportunistic yeast bloodstream infections from Qatar.", "token_count": 287, "char_count": 1033, "word_count": 125, "semantic_coherence": 1, "information_density": 0.792, "quality_score": 0.896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:25.857227", "source": { "split": "train_shard_00000", "doc_id": 4656 }, "chunk_id": "train_shard_00000_4656_0", "global_id": 5202 }, { "text": "Targeted gene replacement in the thermotolerant yeast Kluyveromyces marxianus KCTC 17555 has been hampered by its propensity to non-homologous end joining (NHEJ). To enhance homologous recombination (HR) by blocking NHEJ, we identified and disrupted the K. marxianus KU80 gene. The ku80 deletion mutant strain (Kmku80∆) of K. marxianus KCTC 17555 did not show apparent growth defects under several conditions with the exception of exposure to tunicamycin. The targeted disruption of the three model genes, KmLEU2, KmPDC1, and KmPDC5, was increased by 13-70 % in Kmku80∆, although the efficiency was greatly affected by the length of the homologous flanking fragments. In contrast, the double HR frequency was 0-13.7 % in the wild-type strain even with flanking fragments 1 kb long. Therefore, Kmku80∆ promises to be a useful recipient strain for targeted gene manipulation.\n\nDeletion of a KU80 homolog enhances homologous recombination in the thermotolerant yeast Kluyveromyces marxianus.", "token_count": 302, "char_count": 988, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8253, "entities": { "genes": [ "KU80" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:26.423203", "source": { "split": "train_shard_00000", "doc_id": 4657 }, "chunk_id": "train_shard_00000_4657_0", "global_id": 5203 }, { "text": "This study was designed to evaluate the viability, prophage induction, invasive ability, and relative gene expression in lysogenic Salmonella Typhimurium exposed to the simulated gastric juice (SGJ) at pH 2 (SGJ-2), 3 (SGJ-3), 4 (SGJ-4), and 5 (SGJ-5) for 30 min followed by 0.5 % bile salts for 2 h. The susceptibility of lysogenic S. Typhimurium increased with decreasing pH value and increasing bile salt concentration. The lysogenic S. Typhimurium cells were least susceptible to SGJ-4 and SGJ-5, showing <1 log reduction. The highest prophage induction was observed by 3.34 log PFU/ml in lysogenic S. Typhimurium at SGJ-3 in the presence of 0.5 % bile salts. The numbers of invading lysogenic S. Typhimurium treated at SGJ-3, SGJ-4, and SGJ-5 were 3.57, 3.73, and 4.15 log CFU/cm(2), respectively. Most genes (hilA, hilC, hilD, invA, invE, invF, and sirA) were down-regulated in lysogenic S. Typhimurium treated at SGJ-3, SGJ-4, and SGJ-5. This study provides useful information for understanding physiological changes of lysogenic S. Typhimurium in the simulated gastrointestinal conditions.\n\nSurvival, prophage induction, and invasive properties of lysogenic Salmonella Typhimurium exposed to simulated gastrointestinal conditions.", "token_count": 434, "char_count": 1238, "word_count": 182, "semantic_coherence": 1, "information_density": 0.5769, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:27.049202", "source": { "split": "train_shard_00000", "doc_id": 4658 }, "chunk_id": "train_shard_00000_4658_0", "global_id": 5204 }, { "text": "This study aimed at evaluating co-cultures of selected microorganisms for their proteolytic activity and capability to produce fermented milk enriched with ACE-inhibitory (ACEI) peptides. Selected yeasts (Torulaspora delbruekii KL66A, Galactomyces geotrichum KL20B, Pichia kudriavzevii KL84A and Kluyveromyces marxianus KL26A) and lactic acid bacteria strains (Lactobacillus plantarum LAT03, Lb. plantarum KLAT01 and the not virulent Enterococcus faecalis KE06) were screened as single cultures for their capacity of releasing ACEI peptides without producing bitter taste. Three strains cultures (yeast, Lb. plantarum and E. faecalis) were performed to evaluate the combined impact on microbial growth, lactic acid production, citric acid consumption, proteolysis, ACEI activity, and bitter taste after 36 h of fermentation at 28 °C. While G. geotrichum KL20B showed a strong stimulating effect on Lb. plantarum strains and the production of peptides with ACEI activity, the presence of T. delbruekii KL26A in the cultures was deleterious both to ACEI activity and product taste. The most effective combination was P. kudriavzevii KL84A, Lb. plantarum LAT3, E. faecalis KL06, which showed the highest ACEI activity (IC50 = 30.63 ± 1.11 μg ml(-1)) and gave no bitter taste for 7 days at 6 °C. Our results highlight the importance of choosing the strains combination carefully, to obtain a high yield of ACEI activity without bitter taste.\n\nImpact of microbial cultures on proteolysis and release of bioactive peptides in fermented milk.", "token_count": 482, "char_count": 1535, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [ "KE06", "KL06", "KL26A", "KL84A", "KL66A", "LAT3", "LAT03", "IC50", "KLAT01", "KL20B" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:27.696429", "source": { "split": "train_shard_00000", "doc_id": 4659 }, "chunk_id": "train_shard_00000_4659_0", "global_id": 5205 }, { "text": "Burkholderia terrae strain BS001, obtained as an inhabitant of the mycosphere of Laccaria proxima (a close relative of Lyophyllum sp. strain Karsten), actively interacts with Lyophyllum sp. strain Karsten. We here summarize the remarkable ecological behavior of B. terrae BS001 in the mycosphere and add key data to this. Moreover, we extensively analyze the approximately 11.5-Mb five-replicon genome of B. terrae BS001 and highlight its remarkable features. Seventy-nine regions of genomic plasticity (RGP), that is, 16.48% of the total genome size, were found. One 70.42-kb RGP, RGP76, revealed a typical conjugal element structure, including a full type 4 secretion system. Comparative analyses across 24 related Burkholderia genomes revealed that 95.66% of the total BS001 genome belongs to the variable part, whereas the remaining 4.34% constitutes the core genome. Genes for biofilm formation and several secretion systems, under which a type 3 secretion system (T3SS), were found, which is consistent with the hypothesis that T3SSs play a role in the interaction with Lyophyllum sp. strain Karsten. The high number of predicted metabolic pathways and membrane transporters suggested that strain BS001 can take up and utilize a range of sugars, amino acids and organic acids. In particular, a unique glycerol uptake system was found. The BS001 genome further contains genetic systems for the degradation of complex organic compounds. Moreover, gene clusters encoding nonribosomal peptide synthetases (NRPS) and hybrid polyketide synthases/NRPS were found, highlighting the potential role of secondary metabolites in the ecology of strain BS001. The patchwork of genetic features observed in the genome is consistent with the notion that 1) horizontal gene transfer is a main driver of B. terrae BS001 adaptation and 2) the organism is very flexible in its ecological behavior in soil.", "token_count": 501, "char_count": 1891, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6056, "quality_score": 0.8028, "entities": { "genes": [ "BS001", "RGP76" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:28.344695", "source": { "split": "train_shard_00000", "doc_id": 4660 }, "chunk_id": "train_shard_00000_4660_0", "global_id": 5206 }, { "text": "The genome of the fungal-interactive soil bacterium Burkholderia terrae BS001-a plethora of outstanding interactive capabilities unveiled.", "token_count": 36, "char_count": 138, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [ "BS001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:28.703186", "source": { "split": "train_shard_00000", "doc_id": 4660 }, "chunk_id": "train_shard_00000_4660_1", "global_id": 5207 }, { "text": "Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success.", "token_count": 495, "char_count": 1982, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6021, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:29.353325", "source": { "split": "train_shard_00000", "doc_id": 4661 }, "chunk_id": "train_shard_00000_4661_0", "global_id": 5208 }, { "text": "Pangenome evidence for extensive interdomain horizontal transfer affecting lineage core and shell genes in uncultured planktonic thaumarchaeota and euryarchaeota.", "token_count": 38, "char_count": 162, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:29.712311", "source": { "split": "train_shard_00000", "doc_id": 4661 }, "chunk_id": "train_shard_00000_4661_1", "global_id": 5209 }, { "text": "Horizontal gene transfer (HGT) and gene loss are key processes in bacterial evolution. However, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. Here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium Pseudomonas syringae. We apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the accuracy of patterns of gene occurrence among these genomes. We demonstrate a history of extensive genome fluctuation for this species and show that individual lineages could have acquired thousands of genes in the same period in which a 1% amino acid divergence accrues in the core genome. Elucidating the dynamics of genome fluctuation reveals the rapid turnover of gained genes, such that the majority of recently gained genes are quickly lost. Despite high observed rates of fluctuation, a phylogeny inferred from patterns of gene occurrence is similar to a phylogeny based on amino acid replacements within the core genome. Furthermore, the core genome phylogeny suggests that P. syringae should be considered a number of distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. Gained genes are transferred from a variety of sources, reflecting the depth and diversity of the potential gene pool available via HGT. Overall, our results provide further insights into the evolutionary dynamics of genome fluctuation and implicate HGT as a major factor contributing to the diversification of P. syringae lineages.\n\nThe extent of genome flux and its role in the differentiation of bacterial lineages.", "token_count": 375, "char_count": 1755, "word_count": 267, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:30.292191", "source": { "split": "train_shard_00000", "doc_id": 4662 }, "chunk_id": "train_shard_00000_4662_0", "global_id": 5210 }, { "text": "2-Phenylethanol (2-PE) is an aromatic alcohol with a rose scent, which is used in the cosmetics, fragrance and food industries. 2-PE is produced in a few yeast strains by Ehrlich pathway. In this study, Kluyveromyces marxianus was genetically engineered for overproduction of 2-PE from glucose. About 1.0g/L of 2-PE was produced by overexpressing phenylpyruvate decarboxylase (ARO10) and alcohol dehydrogenase (ADH2) genes of Saccharomyces cerevisiae. A similar level of 2-PE was also produced from evolved K. marxianus, which was resistant to the phenylalanine analog, p-fluorophenylalanine. aroG(fbr) from Klebsiella pneumoniae encoding a feedback resistant mutant of 3-deoxy-D-arabino-heptulosonate-7-phosphate (DHAP) synthase was overexpressed in the evolved K. marxianus. Finally, 1.3g/L of 2-PE was produced from 20g/L glucose without addition of phenylalanine in the medium.\n\nBiosynthesis of 2-phenylethanol from glucose with genetically engineered Kluyveromyces marxianus.", "token_count": 337, "char_count": 980, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [ "ADH2", "ARO10" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:30.863566", "source": { "split": "train_shard_00000", "doc_id": 4663 }, "chunk_id": "train_shard_00000_4663_0", "global_id": 5211 }, { "text": "In bacteria, Hfq is a core RNA chaperone that catalyzes the interaction of mRNAs with regulatory small RNAs (sRNAs). To determine in vivo RNA sequence requirements for Hfq interactions, and to study riboregulation in a bacterial pathogen, Hfq was UV crosslinked to RNAs in enterohemorrhagic Escherichia coli (EHEC). Hfq bound repeated trinucleotide motifs of A-R-N (A-A/G-any nucleotide) often associated with the Shine-Dalgarno translation initiation sequence in mRNAs. These motifs overlapped or were adjacent to the mRNA sequences bound by sRNAs. In consequence, sRNA-mRNA duplex formation will displace Hfq, promoting recycling. Fifty-five sRNAs were identified within bacteriophage-derived regions of the EHEC genome, including some of the most abundant Hfq-interacting sRNAs. One of these (AgvB) antagonized the function of the core genome regulatory sRNA, GcvB, by mimicking its mRNA substrate sequence. This bacteriophage-encoded \"anti-sRNA\" provided EHEC with a growth advantage specifically in bovine rectal mucus recovered from its primary colonization site in cattle.\n\nIdentification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli.", "token_count": 349, "char_count": 1163, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7107, "quality_score": 0.8553, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:31.436989", "source": { "split": "train_shard_00000", "doc_id": 4664 }, "chunk_id": "train_shard_00000_4664_0", "global_id": 5212 }, { "text": "Free fatty acids play a vital role as fuel for cells and in lipid metabolism. During lipid digestion in the gastrointestinal tract, triglycerides are hydrolyzed, resulting in free fatty acid and monoglyceride amphiphilic products. These components, together with bile salts, are responsible for the transport of lipids and poorly water-soluble nutrients and xenobiotics from the intestine into the circulatory system of the body. In this study, we show that the self-assembly of digestion products from medium-chain triglycerides (tricaprylin) in combination with bile salt and phospholipid is highly pH-responsive. Individual building blocks of caprylic acid within the mixed colloidal structures are mapped using a combination of small-angle X-ray and neutron scattering combined with both solvent contrast variation and selective deuteration. Modeling of the scattering data shows transitions in the size and shape of the micelles in combination with a transfer of the caprylic acid from the core of the micelles to the shell or into the bulk water upon increasing pH. The results help to understand the process of lipid digestion with a focus on colloidal structure formation and transformation for the delivery of triglyceride lipids and other hydrophobic functional molecules.\n\npH-responsive micelles based on caprylic acid.", "token_count": 316, "char_count": 1330, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:31.998133", "source": { "split": "train_shard_00000", "doc_id": 4665 }, "chunk_id": "train_shard_00000_4665_0", "global_id": 5213 }, { "text": "Next generation sequencing technologies with advanced bioinformatic tools present a unique opportunity to compare genomes from diverse niches. The identification of niche-specific stress-responsive genes can help in characterizing robust strains for multiple applications. In this study, we attempted to compare the stress-responsive genes of a potential probiotic strain, Lactobacillus helveticus MTCC 5463, and a cheese starter strain, Lactobacillus helveticus DPC 4571, from a gut and dairy niche, respectively. Sequencing of MTCC 5463 was done using 454 GS FLX, and contigs were assembled using GS Assembler software. Genome analysis was done using BLAST hits and the prokaryotic annotation server RAST. The MTCC 5463 genome carried multiple orthologs of genes governing stress responses, whereas the DPC 4571 genome lacked in the number of major stress-response proteins. The absence of the bile salt hydrolase gene in DPC 4571 and its presence in MTCC 5463 clearly indicated niche adaptation. Further, MTCC 5463 carried higher copy numbers of genes contributing towards heat, cold, osmotic, and oxidative stress resistance as compared with DPC 4571. Through comparative genomics, we could thus identify stress-responsive gene sets required to adapt to gut and dairy niches.\n\nComparative genome-scale analysis of niche-based stress-responsive genes in Lactobacillus helveticus strains.", "token_count": 361, "char_count": 1390, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6193, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:32.570594", "source": { "split": "train_shard_00000", "doc_id": 4666 }, "chunk_id": "train_shard_00000_4666_0", "global_id": 5214 }, { "text": "Pseudomonas extremaustralis produces mainly polyhydroxybutyrate (PHB), a short chain length polyhydroxyalkanoate (sclPHA) infrequently found in Pseudomonas species. Previous studies with this strain demonstrated that PHB genes are located in a genomic island. In this work, the analysis of the genome of P. extremaustralis revealed the presence of another PHB cluster phbFPX, with high similarity to genes belonging to Burkholderiales, and also a cluster, phaC1ZC2D, coding for medium chain length PHA production (mclPHA). All mclPHA genes showed high similarity to genes from Pseudomonas species and interestingly, this cluster also showed a natural insertion of seven ORFs not related to mclPHA metabolism. Besides PHB, P. extremaustralis is able to produce mclPHA although in minor amounts. Complementation analysis demonstrated that both mclPHA synthases, PhaC1 and PhaC2, were functional. RT-qPCR analysis showed different levels of expression for the PHB synthase, phbC, and the mclPHA synthases. The expression level of phbC, was significantly higher than the obtained for phaC1 and phaC2, in late exponential phase cultures. The analysis of the proteins bound to the PHA granules showed the presence of PhbC and PhaC1, whilst PhaC2 could not be detected. In addition, two phasin like proteins (PhbP and PhaI) associated with the production of scl and mcl PHAs, respectively, were detected. The results of this work show the high efficiency of a foreign gene (phbC) in comparison with the mclPHA core genome genes (phaC1 and phaC2) indicating that the ability of P. extremaustralis to produce high amounts of PHB could be explained by the different expression levels of the genes encoding the scl and mcl PHA synthases.\n\nHigh polyhydroxybutyrate production in Pseudomonas extremaustralis is associated with differential expression of horizontally acquired and core genome polyhydroxyalkanoate synthase genes.", "token_count": 512, "char_count": 1915, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5089, "quality_score": 0.7544, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:33.220559", "source": { "split": "train_shard_00000", "doc_id": 4667 }, "chunk_id": "train_shard_00000_4667_0", "global_id": 5215 }, { "text": "Kluyveromyces marxianus has recently become a species of interest for ethanol production since it can produce ethanol at high temperature and on a wide variety of substrates. However, the reason why this yeast can produce ethanol at high temperature is largely unknown.\n\nAlcohol dehydrogenases from Kluyveromyces marxianus: heterologous expression in Escherichia coli and biochemical characterization.", "token_count": 100, "char_count": 401, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:33.617441", "source": { "split": "train_shard_00000", "doc_id": 4668 }, "chunk_id": "train_shard_00000_4668_0", "global_id": 5216 }, { "text": "The effect of food intake on the release and degradation of peptide drugs from solid lipid particles is unknown and was therefore investigated in vitro using different fed state media in a lipolysis model. Desmopressin was used as a model peptide and incorporated into solid lipid particles consisting of trimyristin (TG14), tripalmitin (TG16), and tristearin (TG18), respectively. Fasted state and fed state media with varying phospholipid and bile salt concentrations, as well as fed state media with milk and oleic acid glycerides, respectively, were used as the release media. The presence of oleic acid glycerides accelerated the release of desmopressin significantly from all solid lipid particles both in the presence and absence of lipase. The presence of oleic acid glycerides also reduced the degradation rate of desmopressin, probably due to the interactions between the lipids and the protease or desmopressin. Addition of a medium chain triglyceride, trilaurin, in combination with drug-loaded lipid particles diminished the food effect on the TG18 particles, and trilaurin is therefore proposed to be a suitable excipient for reduction of the food effect. Overall, the present study shows that strategies to reduce food effect, such as adding trilaurin, for lipid particle formulations should be considered as drug release from such formulations might be influenced by the presence of food in the gastrointestinal tract.\n\nSolid lipid particles for oral delivery of peptide and protein drugs III - the effect of fed state conditions on the in vitro release and degradation of desmopressin.", "token_count": 387, "char_count": 1602, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5061, "quality_score": 0.7531, "entities": { "genes": [ "TG14", "TG18", "TG16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:34.233872", "source": { "split": "train_shard_00000", "doc_id": 4669 }, "chunk_id": "train_shard_00000_4669_0", "global_id": 5217 }, { "text": "The enterohepatic circulation of bile salts is an important physiological route to recycle bile salts and ensure intestinal absorption of dietary lipids. The Na(+)-taurocholate cotransporting polypeptide SLC10A1 (NTCP) plays a key role in this process as the major transporter of conjugated bile salts from the plasma compartment into the hepatocyte. Here we present the first patient with NTCP deficiency, who was clinically characterized by mild hypotonia, growth retardation, and delayed motor milestones. Total bile salts in plasma were extremely elevated (up to 1,500 μM, ref. <16.3) but there were no clinical signs of cholestatic jaundice, pruritis, or liver dysfunction. Bile salt synthesis and intestinal bile salt signaling were not affected, as evidenced by normal plasma 7α-hydroxy-4-cholesten-3-one (C4) and FGF19 levels. Importantly, the presence of secondary bile salts in the circulation suggested residual enterohepatic cycling of bile salts. Sequencing of the SLC10A1 gene revealed a single homozygous nonsynonymous point mutation in the coding sequence of the gene, resulting in an arginine to histidine substitution at position 252. Functional studies showed that this mutation resulted in a markedly reduced uptake activity of taurocholic acid. Immunofluorescence studies and surface biotinylation experiments demonstrated that the mutant protein is virtually absent from the plasma membrane.\n\nSodium taurocholate cotransporting polypeptide (SLC10A1) deficiency: conjugated hypercholanemia without a clear clinical phenotype.", "token_count": 427, "char_count": 1546, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6808, "quality_score": 0.8404, "entities": { "genes": [ "FGF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:34.899127", "source": { "split": "train_shard_00000", "doc_id": 4670 }, "chunk_id": "train_shard_00000_4670_0", "global_id": 5218 }, { "text": "The impact of biological surfactants (bile salts) on the protein (β-lactoglobulin) corona surrounding gold nanoparticles (200 nm) was studied using a variety of analytical techniques at pH 7: dynamic light scattering (DLS); particle electrophoresis (ζ-potential); UV-visible (UV) spectroscopy; transmission electron microscopy (TEM); and surface-enhanced Raman scattering (SERS). The bile salts adsorbed to the protein-coated nanoparticle surfaces and altered their interfacial composition, charge, and structure. SERS spectra of protein-coated nanoparticles after bile salt addition contained bands from both protein and bile salts, indicating that the protein was not fully displaced by the bile salts. UV, DLS and TEM techniques also indicated that the protein coating was not fully displaced from the nanoparticle surfaces. The impact of bile salts could be described by an orogenic mechanism: mixed interfaces were formed that consisted of islands of aggregated proteins surrounded by a sea of bile salts. This knowledge is useful for understanding the interactions of bile salts with protein-coated colloidal particles, which may be important for controlling the fate of colloidal delivery systems in the human gastrointestinal tract, or the gastrointestinal fate of ingested inorganic nanoparticles.\n\nAlterations in nanoparticle protein corona by biological surfactants: impact of bile salts on β-lactoglobulin-coated gold nanoparticles.", "token_count": 358, "char_count": 1444, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:35.500446", "source": { "split": "train_shard_00000", "doc_id": 4671 }, "chunk_id": "train_shard_00000_4671_0", "global_id": 5219 }, { "text": "The purpose of this study was to find a suitable co-surfactant to replace non-food grade bile salts in solid lipid nanoparticle (SLN) formulations. The hypothesis was that the molecular structure and physical properties of co-surfactant modulate the stabilization of SLNs upon polymorphic transition.\n\nInfluence of co-surfactants on crystallization and stability of solid lipid nanoparticles.", "token_count": 96, "char_count": 392, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:35.903703", "source": { "split": "train_shard_00000", "doc_id": 4672 }, "chunk_id": "train_shard_00000_4672_0", "global_id": 5220 }, { "text": "Horizontal gene transfer is an important driver of bacterial evolution, but genetic exchange in the core genome of clonal species, including the major pathogen Staphylococcus aureus, is incompletely understood. Here we reveal widespread homologous recombination in S. aureus at the species level, in contrast to its near-complete absence between closely related strains. We discover a patchwork of hotspots and coldspots at fine scales falling against a backdrop of broad-scale trends in rate variation. Over megabases, homoplasy rates fluctuate 1.9-fold, peaking towards the origin-of-replication. Over kilobases, we find core recombination hotspots of up to 2.5-fold enrichment situated near fault lines in the genome associated with mobile elements. The strongest hotspots include regions flanking conjugative transposon ICE6013, the staphylococcal cassette chromosome (SCC) and genomic island νSaα. Mobile element-driven core genome transfer represents an opportunity for adaptation and challenges our understanding of the recombination landscape in predominantly clonal pathogens, with important implications for genotype-phenotype mapping.\n\nMobile elements drive recombination hotspots in the core genome of Staphylococcus aureus.", "token_count": 300, "char_count": 1236, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [ "ICE6013" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:36.505655", "source": { "split": "train_shard_00000", "doc_id": 4673 }, "chunk_id": "train_shard_00000_4673_0", "global_id": 5221 }, { "text": "We examined the effects of two over-the-counter H1-antihistamines on the progression of fatty liver disease in male C57Bl/6 wild-type and apolipoprotein E (ApoE)-/- mice. Mice were fed a high-fat diet (HFD) for 3 mo, together with administration of either cetirizine (4 mg/kg body wt) or fexofenadine (40 mg/kg body wt) in drinking water. Antihistamine treatments increased body weight gain, gonadal fat deposition, liver weight, and hepatic steatosis in wild-type mice but not in ApoE-/- mice. Lobular inflammation, acute inflammation, and necrosis were not affected by H1-antihistamines in either genotype. Serum biomarkers of liver injury tended to increase in antihistamine-treated wild-type mice. Serum level of glucose was increased by fexofenadine, whereas lipase was increased by cetirizine. H1-antihistamines reduced the mRNA expression of ApoE and carbohydrate response element-binding protein in wild-type mice, without altering the mRNA expression of sterol regulatory element-binding protein 1c, fatty acid synthase, or ApoB100, in either genotype. Fexofenadine increased both triglycerides and cholesterol ester, whereas cetirizine increased only cholesterol ester in liver, with a concomitant decrease in serum triglycerides by both antihistamines in wild-type mice. Antihistamines increased hepatic levels of conjugated bile acids in wild-type mice, with the effect being significant in fexofenadine-treated animals. The increase was associated with changes in the expression of organic anion transport polypeptide 1b2 and bile salt export pump", "token_count": 463, "char_count": 1560, "word_count": 216, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:37.153878", "source": { "split": "train_shard_00000", "doc_id": 4674 }, "chunk_id": "train_shard_00000_4674_0", "global_id": 5222 }, { "text": "These results suggest that H1-antihistamines increase the progression of fatty liver disease in wild-type mice, and there seems to be an association between the severity of disease, presence of ApoE, and increase in hepatic bile acid levels.\n\nH1-antihistamines exacerbate high-fat diet-induced hepatic steatosis in wild-type but not in apolipoprotein E knockout mice.", "token_count": 106, "char_count": 367, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7885, "quality_score": 0.8942, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:37.528433", "source": { "split": "train_shard_00000", "doc_id": 4674 }, "chunk_id": "train_shard_00000_4674_1", "global_id": 5223 }, { "text": "One-step sulfuric acid saccharification of the red alga Pterocladiella capillacea was optimized, and various detoxification methods (neutralization, overliming, and electrodialysis) of the acid hydrolysate were evaluated for fermentation with the thermotolerant yeast Kluyveromyces marxianus. A proximate composition analysis indicated that P. capillacea was rich in carbohydrates. A significant galactose recovery of 81.1 ± 5% was also achieved under the conditions of a 12% (w/v) biomass load, 5% (v/v) sulfuric acid, 121°C, and hydrolysis for 30 min. Among the various detoxification methods, electrodialysis was identified as the most suitable for fermentable sugar recovery and organic acid removal (100% reduction of formic and levulinic acids), even though it failed to reduce the amount of the inhibitor 5-HMF. As a result, K. marxianus fermentation with the electrodialyzed acid hydrolysate of P. capillacea resulted in the best ethanol levels and fermentation efficiency.\n\nSulfuric acid hydrolysis and detoxification of red alga Pterocladiella capillacea for bioethanol fermentation with thermotolerant yeast Kluyveromyces marxianus.", "token_count": 333, "char_count": 1143, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6026, "quality_score": 0.8013, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:38.095212", "source": { "split": "train_shard_00000", "doc_id": 4675 }, "chunk_id": "train_shard_00000_4675_0", "global_id": 5224 }, { "text": "Following a large outbreak of foodborne gastrointestinal (GI) disease, a multiplex PCR approach was used retrospectively to investigate faecal specimens from 88 of the 413 reported cases. Gene targets from a range of bacterial GI pathogens were detected, including Salmonella species, Shigella species and Shiga toxin-producing Escherichia coli, with the majority (75%) of faecal specimens being PCR positive for aggR associated with the Enteroaggregative E. coli (EAEC) group. The 20 isolates of EAEC recovered from the outbreak specimens exhibited a range of serotypes, the most frequent being O104:H4 and O131:H27. None of the EAEC isolates had the Shiga toxin (stx) genes. Multilocus sequence typing and single nucleotide polymorphism analysis of the core genome confirmed the diverse phylogeny of the strains. The analysis also revealed a close phylogenetic relationship between the EAEC O104:H4 strains in this outbreak and the strain of E. coli O104:H4 associated with a large outbreak of haemolytic ureamic syndrome in Germany in 2011. Further analysis of the EAEC plasmids, encoding the key enteroaggregative virulence genes, showed diversity with respect to FIB/FII type, gene content and genomic architecture. Known EAEC virulence genes, such as aggR, aat and aap, were present in all but one of the strains. A variety of fimbrial genes were observed, including genes encoding all five known fimbrial types, AAF/1 to AAF/V. The AAI operon was present in its entirety in 15 of the EAEC strains, absent in three and present, but incomplete, in two isolates. EAEC is known to be a diverse pathotype and this study demonstrates that a high level of diversity in strains recovered from cases associated with a single outbreak. Although the EAEC in this study did not carry the stx genes, this outbreak provides further evidence of the pathogenic potential of the EAEC O104:H4 serotype.", "token_count": 522, "char_count": 1891, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5525, "quality_score": 0.7763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:46:38.751479", "source": { "split": "train_shard_00000", "doc_id": 4676 }, "chunk_id": "train_shard_00000_4676_0", "global_id": 5225 }, { "text": "An investigation of the diversity of strains of enteroaggregative Escherichia coli isolated from cases associated with a large multi-pathogen foodborne outbreak in the UK.", "token_count": 39, "char_count": 171, "word_count": 24, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:39.110142", "source": { "split": "train_shard_00000", "doc_id": 4676 }, "chunk_id": "train_shard_00000_4676_1", "global_id": 5226 }, { "text": "The study was conducted to evaluate the potential of mixed culture of Kluyveromyces marxianus and Candida krusei to enhance COD removal efficiency, minimize contamination at extreme conditions (high temperature 40°C and low pH 3.5) during batch and continuous aerobic fermentation and to obtain improved quality single-cell protein (SCP) using whey as substrate. The batch fermentation of mono-culture and mixed culture result showed that the mixed culture resulted in 8.8% higher COD removal efficacy with 19% higher biomass yield and 33% increased productivity. The maximum COD removal 80.2% (including residual protein) was obtained at 24h HRT with biomass productivity of 0.17 g/L/h; however, maximum biomass productivity of 0.38 g/L/h and 34% COD removal were obtained at 6h HRT. The results showed that the mixed culture of acid resistance and thermo-tolerant yeasts was a potential way to produce SCP (animal feed) and simultaneous COD removal under extreme operating conditions.\n\nMixed culture of Kluyveromyces marxianus and Candida krusei for single-cell protein production and organic load removal from whey.", "token_count": 297, "char_count": 1118, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:39.672835", "source": { "split": "train_shard_00000", "doc_id": 4677 }, "chunk_id": "train_shard_00000_4677_0", "global_id": 5227 }, { "text": "Fucosyltransferase 2 (FUT2) mediates the inclusion of fucose in sugar moieties of glycoproteins and glycolipids. ABO blood group antigens and host-microbe interactions are influenced by FUT2 activity. About 20 % of the population has a \"non-secretor\" status caused by inactivating variants of FUT2 on both alleles. The non-sense mutation G428A and the missense mutation A385T are responsible for the vast majority of the non-secretor status in Caucasians, Africans, and Asians, respectively. Non-secretor individuals do not secrete fucose-positive antigens and lack fucosylation in epithelia. They also appear to be protected against a number of infectious diseases, such as Norovirus and Rotavirus infections. In recent years, genome-wide association studies (GWAS) identified inactivating variants at the FUT2 locus to be associated with primary sclerosing cholangitis (PSC), Crohn's disease (CD), and biochemical markers of biliary damage. These associations are intriguing given the important roles of fucosylated glycans in host-microbe interactions and membrane stability. Non-secretors have a reduced fecal content of Bifidobacteria. The intestinal bacterial composition of CD patients resembles the one of non-secretors, with an increase in Firmicutes and decreases in Proteobacteria and Actinobacteria. Non-secretor individuals lack fucosylated glycans at the surface of biliary epithelium and display a different bacterial composition of bile compared to secretors. Notably, an intact biliary epithelial glycocalix is relevant for a stable 'biliary HCO3 (-) umbrella' to protect against toxic effects of hydrophobic bile salt monomers. Here, the biology of FUT2 will be discussed as well as hypotheses to explain the role of FUT2 in the pathophysiology of PSC and Crohn's disease.", "token_count": 492, "char_count": 1790, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8221, "entities": { "genes": [ "FUT2", "HCO3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:40.326319", "source": { "split": "train_shard_00000", "doc_id": 4678 }, "chunk_id": "train_shard_00000_4678_0", "global_id": 5228 }, { "text": "Fucosyltransferase 2: a genetic risk factor for primary sclerosing cholangitis and Crohn's disease--a comprehensive review.", "token_count": 34, "char_count": 123, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:40.677641", "source": { "split": "train_shard_00000", "doc_id": 4678 }, "chunk_id": "train_shard_00000_4678_1", "global_id": 5229 }, { "text": "Chitosan (CH) is a polymer of glucosamine that is extracted from the shells of several sea fruits. It is well recognized as a nutritional supplement that is used to reduce body weight and blood lipid levels, but its clinical efficacy has not been clearly demonstrated. The true mechanism of action and physiological processes involved in these properties of CH are not yet understood or explained. The most accepted theories assume that CH reduces dietary fat absorption by trapping the fat in the gastric lumen. The very low pH of the gastric lumen induces CH jellification and, therefore, entrapment of the fats. This article describes the most plausible mechanism by which CH interferes with fat absorption in the first part of the enteric tract while interacting with cholic acids. We emphasize the weak points of the classic CH-containing formulations, which are unable to prove this theory. We also report preliminary experimental data of a new CH salt-containing formulation that is capable of effectively interfering with bile salt emulsification processes and, as a result, reducing dietary fat absorption.\n\nNew chitosan salt in gastro-resistant oral formulation could interfere with enteric bile salts emulsification of diet fats: preliminary laboratory observations and physiologic rationale.", "token_count": 292, "char_count": 1303, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6482, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:41.239529", "source": { "split": "train_shard_00000", "doc_id": 4679 }, "chunk_id": "train_shard_00000_4679_0", "global_id": 5230 }, { "text": "Bile salts play crucial roles in allowing the gastrointestinal system to digest, transport and metabolize nutrients. They function as nutrient signaling hormones by activating specific nuclear receptors (FXR, PXR, Vitamin D) and G-protein coupled receptors [TGR5, sphingosine-1 phosphate receptor 2 (S1PR2), muscarinic receptors]. Bile acids and insulin appear to collaborate in regulating the metabolism of nutrients in the liver. They both activate the AKT and ERK1/2 signaling pathways. Bile acid induction of the FXR-α target gene, small heterodimer partner (SHP), is highly dependent on the activation PKCζ, a branch of the insulin signaling pathway. SHP is an important regulator of glucose and lipid metabolism in the liver. One might hypothesize that chronic low grade inflammation which is associated with insulin resistance, may inhibit bile acid signaling and disrupt lipid metabolism. The disruption of these signaling pathways may increase the risk of fatty liver and non-alcoholic fatty liver disease (NAFLD). Finally, conjugated bile acids appear to promote cholangiocarcinoma growth via the activation of S1PR2.\n\nBile acids are nutrient signaling hormones.", "token_count": 317, "char_count": 1172, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [ "TGR5", "ERK1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:41.798621", "source": { "split": "train_shard_00000", "doc_id": 4680 }, "chunk_id": "train_shard_00000_4680_0", "global_id": 5231 }, { "text": "Hepatocellular carcinoma (HCC) is almost invariably associated with an underlying inflammatory state, whose direct contribution to the acquisition of critical genomic changes is unclear. Here we map acquired genomic alterations in human and mouse HCCs induced by defects in hepatocyte biliary transporters, which expose hepatocytes to bile salts and cause chronic inflammation that develops into cancer. In both human and mouse cancer genomes, we find few somatic point mutations with no impairment of cancer genes, but massive gene amplification and rearrangements. This genomic landscape differs from that of virus- and alcohol-associated liver cancer. Copy-number gains preferentially occur at late stages of cancer development and frequently target the MAPK signalling pathway, and in particular direct regulators of JNK. The pharmacological inhibition of JNK retards cancer progression in the mouse. Our study demonstrates that intrahepatic cholestasis leading to hepatocyte exposure to bile acids and inflammation promotes cancer through genomic modifications that can be distinguished from those determined by other aetiological factors.\n\nMassive gene amplification drives paediatric hepatocellular carcinoma caused by bile salt export pump deficiency.", "token_count": 288, "char_count": 1259, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7052, "quality_score": 0.8526, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:42.358498", "source": { "split": "train_shard_00000", "doc_id": 4681 }, "chunk_id": "train_shard_00000_4681_0", "global_id": 5232 }, { "text": "Lactobacillus acidophilus is categorized as a probiotic strain because of its beneficial effects in human health and prevention of disease transmission. This study is aimed to characterize the probiotic potential of L. acidophilus 36YL originally isolated from the vagina of healthy and fertile Iranian women. The L. acidophilus 36YL strain was identified using 16S rDNA gene sequencing and characterized by biochemical methodologies, such as antibiotics susceptibility, antimicrobial activity, and acid and bile resistance. The bioactivity of the secretion of this strain on four human cancer cell lines (AGS, HeLa, MCF-7, and HT-29) and one normal cell line (HUVEC) was evaluated by cytotoxicity assay and apoptosis analysis. This newly isolated strain was found to exhibit notable probiotic properties, such as admirable antibiotic susceptibility, good antimicrobial activity, and favorable resistance to acid and bile salt. The results of bioactivity assessment demonstrated acceptable anticancer effects on the four tested cancer cell lines and negligible side effects on the assayed normal cell line. Our findings revealed that the anticancer effect of L. acidophilus 36YL strain secretions depends on the induction of apoptosis in cancer cells. L. acidophilus 36YL strain is considered as a nutraceutical alternative or a topical medication with a potential therapeutic index because of the absence of cytotoxicity to normal cells, but effective toxicity to cancer cell lines.\n\nProbiotic potential and biotherapeutic effects of newly isolated vaginal Lactobacillus acidophilus 36YL strain on cancer cells.", "token_count": 403, "char_count": 1612, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5302, "quality_score": 0.7651, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:42.970642", "source": { "split": "train_shard_00000", "doc_id": 4682 }, "chunk_id": "train_shard_00000_4682_0", "global_id": 5233 }, { "text": "We induced gallstones in C57L mice fed with a high cholesterol diet and examined the expression of bile salt export pump (BSEP) on the canalicular membrane of hepatocytes and its relation with PKCα and HAX-1.Twenty-four gallstone-prone C57L mice were randomly assigned to receive a high cholesterol diet or a regular diet. Gallstone formation was recorded. BSEP, PKCα and phospho-PKCα expression was examined by immunoblotting assays. Co-expression of BSEP and HAX-1 was studied by immunofluorescent microscopy and immunoprecipitations. Gallstones were formed in all 12 mice fed with the high cholesterol diet. In Gallstone group, BSEP levels on the canalicular membrane of hepatocytes were markedly lower while a significant increase was observed in phosphorylated PKCα. Immunofluorescent microscopy showed that BSEP and HAX-1 were co-localized on the canalicular membrane, which was apparently enhanced by feeding with the high cholesterol diet. The immunoprecipitation assays further demonstrated that BSEP and HAX-1 showed enhanced interaction in the hepatocytes of mice fed with the high cholesterol diet. Cholesterol gallstone formation is associated with downregulation of BSEP expression on the canalicular membrane of hepatocytes with increased phosphorylation of PKCα. BSEP and HAX-1 show enhanced interaction with one another on the canalicular membrane during gallstone formation.\n\nEnhancement of interaction of BSEP and HAX-1 on the canalicular membrane of hepatocytes in a mouse model of cholesterol cholelithiasis.", "token_count": 416, "char_count": 1529, "word_count": 217, "semantic_coherence": 1, "information_density": 0.4378, "quality_score": 0.7189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:43.591401", "source": { "split": "train_shard_00000", "doc_id": 4683 }, "chunk_id": "train_shard_00000_4683_0", "global_id": 5234 }, { "text": "18-Crown-6, one of the most relevant crown ethers, and sodium cholate, a steroidal surfactant classified as a natural bile salt, are components of a novel, synthesized coordination complex: 18-crown-6-sodium cholate (18C6·NaCh). Like crown ethers, bile salts act as building blocks in supramolecular chemistry to design new functionalized materials with a desired structure and properties. In order to obtain thermal behavior of this 1:1 coordination complex, thermogravimetry and differential thermal analysis were used, as well as microscopic observations and differential scanning calorimetry. Temperature dependent infrared (IR) spectroscopy gave a detailed view into phase transitions. The structures during thermal treatment were observed with powder X-ray diffraction, and molecular models of the phases were made. Hard, glassy, colorless compound 18C6·NaCh goes through crystalline-crystalline polymorphic phase transitions at higher temperatures. The room temperature phase is indexed to a triclinic lattice, while in the high temperature phases molecules take randomly one of the two different configurations in the unit cell, resulting in the 2-fold symmetry. The formation of cholesteric liquid crystalline phase occurs simultaneously with partial decomposition, followed by the isotropization with simultaneous and complete decomposition at much higher temperature, as obtained by IR. The results provide valuable information about the relationship between molecular structure, thermal properties, and stability of the complex, indicating the importance of an appropriate choice of cation, amphiphilic, and crown ether unit in order to synthesize compounds with desired behavior.\n\n18-crown-6-sodium cholate complex: thermochemistry, structure, and stability.", "token_count": 403, "char_count": 1771, "word_count": 236, "semantic_coherence": 1, "information_density": 0.661, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:44.220199", "source": { "split": "train_shard_00000", "doc_id": 4684 }, "chunk_id": "train_shard_00000_4684_0", "global_id": 5235 }, { "text": "Acquisition of Elizabethkingia infections in intensive care units (ICUs) has risen in the past decade. Treatment of Elizabethkingia infections is challenging due to the lack of effective therapeutic regimens, leading to a high mortality rate. Elizabethkingia infections have long been attributed to Elizabethkingia meningoseptica. Recently, we used whole-genome sequencing to reveal that E. anophelis is the pathogenic agent for an Elizabethkingia outbreak at two ICUs. We performed comparative genomic analysis of seven hospital-isolated E. anophelis strains with five available Elizabethkingia spp. genomes deposited in the National Center for Biotechnology Information Database. A pan-genomic approach was applied to identify the core- and pan-genome for the Elizabethkingia genus. We showed that unlike the hospital-isolated pathogen E. meningoseptica ATCC 12535 strain, the hospital-isolated E. anophelis strains have genome content and organization similar to the E. anophelis Ag1 and R26 strains isolated from the midgut microbiota of the malaria mosquito vector Anopheles gambiae. Both the core- and accessory genomes of Elizabethkingia spp. possess genes conferring antibiotic resistance and virulence. Our study highlights that E. anophelis is an emerging bacterial pathogen for hospital environments.\n\nComparative genomic analysis of malaria mosquito vector-associated novel pathogen Elizabethkingia anophelis.", "token_count": 354, "char_count": 1421, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6158, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:44.794334", "source": { "split": "train_shard_00000", "doc_id": 4685 }, "chunk_id": "train_shard_00000_4685_0", "global_id": 5236 }, { "text": "Two Kluyveromyces marxianus strains have been tested for their ability to ferment lactose in the medium containing cheese whey powder (CWP) and lactose at different concentrations. The ethanol production by the selected strains was inhibited by the increase in substrate concentration (100 g/l). The strain K. marxianus UCM Y-2096 was found to yield the higher ethanol formation and to be more resistant to ethanol under microaerophilic conditions.\n\nWhey fermentation by yeast strains Kluyveromyces marxianus UCM Y-2096 and UCM Y-2388.", "token_count": 157, "char_count": 535, "word_count": 79, "semantic_coherence": 1, "information_density": 0.6709, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:45.231945", "source": { "split": "train_shard_00000", "doc_id": 4686 }, "chunk_id": "train_shard_00000_4686_0", "global_id": 5237 }, { "text": "Alterations in the gastrointestinal microbiota have been implicated in obesity in mice and humans, but the key microbial functions influencing host energy metabolism and adiposity remain to be determined. Despite an increased understanding of the genetic content of the gastrointestinal microbiome, functional analyses of common microbial gene sets are required. We established a controlled expression system for the parallel functional analysis of microbial alleles in the murine gut. Using this approach we show that bacterial bile salt hydrolase (BSH) mediates a microbe-host dialogue that functionally regulates host lipid metabolism and plays a profound role in cholesterol metabolism and weight gain in the host. Expression of cloned BSH enzymes in the gastrointestinal tract of gnotobiotic or conventionally raised mice significantly altered plasma bile acid signatures and regulated transcription of key genes involved in lipid metabolism (Pparγ, Angptl4), cholesterol metabolism (Abcg5/8), gastrointestinal homeostasis (RegIIIγ), and circadian rhythm (Dbp, Per1/2) in the liver or small intestine. High-level expression of BSH in conventionally raised mice resulted in a significant reduction in host weight gain, plasma cholesterol, and liver triglycerides, demonstrating the overall impact of elevated BSH activity on host physiology. In addition, BSH activity in vivo varied according to BSH allele group, indicating that subtle differences in activity can have significant effects on the host. In summary, we demonstrate that bacterial BSH activity significantly impacts the systemic metabolic processes and adiposity in the host and represents a key mechanistic target for the control of obesity and hypercholesterolemia.\n\nRegulation of host weight gain and lipid metabolism by bacterial bile acid modification in the gut.", "token_count": 434, "char_count": 1836, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5521, "quality_score": 0.7761, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:45.865080", "source": { "split": "train_shard_00000", "doc_id": 4687 }, "chunk_id": "train_shard_00000_4687_0", "global_id": 5238 }, { "text": "Inhibition of bile acid transport by troglitazone (TGZ) and its major metabolite, TGZ sulfate (TS), may lead to hepatocellular accumulation of toxic bile acids; TS accumulation and hepatotoxicity may be associated with impaired TS biliary excretion. This study evaluated the impact of impaired transport of breast cancer resistance protein (Bcrp) and multidrug resistance-associated protein 2 (Mrp2) on the hepatobiliary disposition of generated metabolites, TS and TGZ glucuronide (TG). Sandwich-cultured hepatocytes (SCH) from Mrp2-deficient (TR(-)) rats in combination with Bcrp knockdown using RNA interference were employed. The biliary excretion index (BEI) of generated TS was not significantly altered by impaired Bcrp (20.9 to 21.1%) and/or Mrp2 function (24.4% and 17.5% in WT and TR(-) rat SCH, respectively). Thus, loss-of-function of Mrp2 and/or Bcrp do not appear to be risk factors for increased hepatocellular TS accumulation in rats, potentially because of a compensatory transporter(s) that excretes TS into bile. Further investigations revealed that the compensatory TS biliary transporter was not the bile salt export pump (Bsep) or P-glycoprotein (P-gp). Interestingly, TGZ sulfation was significantly decreased in TR(-) compared with WT rat SCH (total recovery: 2.8 versus 5.0% of TGZ dose), resulting in decreased hepatocellular TS accumulation, even though sulfotransferase activity in TR(-) rat hepatocyte S9 fraction was similar. Hepatocellular TG accumulation was significantly increased in TR(-) compared with WT rat SCH due to increased glucuronidation and negligible TG biliary excretion. These data emphasize that the interplay between metabolite formation and excretion determines hepatocellular exposure to generated metabolites such as TS and TG.", "token_count": 514, "char_count": 1780, "word_count": 250, "semantic_coherence": 1, "information_density": 0.612, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:46:46.526637", "source": { "split": "train_shard_00000", "doc_id": 4688 }, "chunk_id": "train_shard_00000_4688_0", "global_id": 5239 }, { "text": "Hepatocellular exposure of troglitazone metabolites in rat sandwich-cultured hepatocytes lacking Bcrp and Mrp2: interplay between formation and excretion.", "token_count": 45, "char_count": 154, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:46.922341", "source": { "split": "train_shard_00000", "doc_id": 4688 }, "chunk_id": "train_shard_00000_4688_1", "global_id": 5240 }, { "text": "Drug-induced liver injury (DILI) accounts for 20-40% of all instances of clinical hepatic failure and is a common reason for withdrawal of an approved drug or discontinuation of a potentially new drug from clinical/nonclinical development. Numerous individual risk factors contribute to the susceptibility to human DILI and its severity that are either compound- and/or patient-specific. Compound-specific primary mechanisms linked to DILI include: cytotoxicity, reactive metabolite formation, inhibition of bile salt export pump (BSEP), and mitochondrial dysfunction. Since BSEP is an energy-dependent protein responsible for the efflux of bile acids from hepatocytes, it was hypothesized that humans exposed to drugs that impair both mitochondrial energetics and BSEP functional activity are more sensitive to more severe manifestations of DILI than drugs that only have a single liability factor. As annotated in the United States National Center for Toxicological Research Liver Toxicity Knowledge Base (NCTR-LTKB), the inhibitory properties of 24 Most-DILI-, 28 Less-DILI-, and 20 No-DILI-concern drugs were investigated. Drug potency for inhibiting BSEP or mitochondrial activity was generally correlated across human DILI concern categories. However, drugs with dual potency as mitochondrial and BSEP inhibitors were highly associated with more severe human DILI, more restrictive product safety labeling related to liver injury, and appear more sensitive to the drug exposure (Cmax) where more restrictive labeling occurs.\n\nHuman drug-induced liver injury severity is highly associated with dual inhibition of liver mitochondrial function and bile salt export pump.", "token_count": 402, "char_count": 1673, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6137, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:47.575191", "source": { "split": "train_shard_00000", "doc_id": 4689 }, "chunk_id": "train_shard_00000_4689_0", "global_id": 5241 }, { "text": "The lignocellulosic materials are considered promising renewable resources for ethanol production, but improvements in the processes should be studied to reduce operating costs. Thus, the appropriate enzyme loading for cellulose saccharification is critical for process economics. This study aimed at evaluating the concentration of cellulase and β-glucosidase in the production of bioethanol by simultaneous saccharification and fermentation (SSF) of sunflower meal biomass. The sunflower biomass was pretreated with 6% H2SO4 (w/v), at 121 °C, for 20 min, for hemicellulose removal and delignificated with 1% NaOH. SSF was performed with Kluyveromyces marxianus ATCC 36907, at 38 °C, 150 rpm, for 72 h, with different enzyme concentrations (Cellulase Complex NS22086-10, 15 and 20 FPU/gsubstrate and β-Glucosidase NS22118, with a cellulase to β-glucosidase ratio of 1.5:1; 2:1 and 3:1). The best condition for ethanol production was cellulase 20 FPU/gsubstrate and β-glucosidase 13.3 CBU/gsubstrate, resulting in 27.88 g/L ethanol, yield of 0.47 g/g and productivity of 0.38 g/L h. Under this condition the highest enzymatic conversion of cellulose to glucose was attained (87.06%).\n\nEthanol production from sunflower meal biomass by simultaneous saccharification and fermentation (SSF) with Kluyveromyces marxianus ATCC 36907.", "token_count": 446, "char_count": 1328, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [ "NS22118", "NS22086" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:48.276246", "source": { "split": "train_shard_00000", "doc_id": 4690 }, "chunk_id": "train_shard_00000_4690_0", "global_id": 5242 }, { "text": "Whole-genome sequencing (WGS) allows for effective tracing of Mycobacterium tuberculosis complex (MTBC) (tuberculosis pathogens) transmission. However, it is difficult to standardize and, therefore, is not yet employed for interlaboratory prospective surveillance. To allow its widespread application, solutions for data standardization and storage in an easily expandable database are urgently needed. To address this question, we developed a core genome multilocus sequence typing (cgMLST) scheme for clinical MTBC isolates using the Ridom SeqSphere(+) software, which transfers the genome-wide single nucleotide polymorphism (SNP) diversity into an allele numbering system that is standardized, portable, and not computationally intensive. To test its performance, we performed WGS analysis of 26 isolates with identical IS6110 DNA fingerprints and spoligotyping patterns from a longitudinal outbreak in the federal state of Hamburg, Germany (notified between 2001 and 2010). The cgMLST approach (3,041 genes) discriminated the 26 strains with a resolution comparable to that of SNP-based WGS typing (one major cluster of 22 identical or closely related and four outlier isolates with at least 97 distinct SNPs or 63 allelic variants). Resulting tree topologies are highly congruent and grouped the isolates in both cases analogously. Our data show that SNP- and cgMLST-based WGS analyses facilitate high-resolution discrimination of longitudinal MTBC outbreaks. cgMLST allows for a meaningful epidemiological interpretation of the WGS genotyping data. It enables standardized WGS genotyping for epidemiological investigations, e.g., on the regional public health office level, and the creation of web-accessible databases for global TB surveillance with an integrated early warning system.\n\nWhole-genome-based Mycobacterium tuberculosis surveillance: a standardized, portable, and expandable approach.", "token_count": 468, "char_count": 1905, "word_count": 256, "semantic_coherence": 1, "information_density": 0.7031, "quality_score": 0.8516, "entities": { "genes": [ "IS6110" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:48.946368", "source": { "split": "train_shard_00000", "doc_id": 4691 }, "chunk_id": "train_shard_00000_4691_0", "global_id": 5243 }, { "text": "Ethyl acetate is an environmentally friendly solvent with many industrial applications. The production of ethyl acetate currently proceeds by energy-intensive petrochemical processes which are based on natural gas and crude oil without exception. Microbial synthesis of ethyl acetate could become an interesting alternative. The formation of esters as aroma compounds in food has been repeatedly reviewed, but a survey which deals with microbial synthesis of ethyl acetate as a bulk product is missing. The ability of yeasts for producing larger amounts of this ester is known for a long time. In the past, this potential was mainly of scientific interest, but in the future, it could be applied to large-scale ester production from renewable raw materials. Pichia anomala, Candida utilis, and Kluyveromyces marxianus are yeasts which convert sugar into ethyl acetate with a high yield where the latter is the most promising one. Special attention was paid to the mechanism of ester synthesis including regulatory aspects and to the maximum and expectable yield. Synthesis of much ethyl acetate requires oxygen which is usually supplied by aeration. Ethyl acetate is highly volatile so that aeration results in its phase transfer and stripping. This stripping process cannot be avoided but requires adequate handling during experimentation and offers a chance for a cost-efficient process-integrated recovery of the synthesized ester.\n\nPerspectives for the biotechnological production of ethyl acetate by yeasts.", "token_count": 330, "char_count": 1512, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6283, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:49.516323", "source": { "split": "train_shard_00000", "doc_id": 4692 }, "chunk_id": "train_shard_00000_4692_0", "global_id": 5244 }, { "text": "This work explores the potential for the development of a hybrid fermentation-enzymatic process for the production of ethyl lactate from dairy waste. Cheese whey was used in Kluyveromyces marxianus and Lactobacillus bulgaricus batch cultures to produce ethanol and lactic acid respectively. Subsequently, the fermentation products were transferred into an organic phase through liquid-liquid extraction and ethyl lactate was formed in an esterification reaction catalyzed by lipases. The production of ethanol and lactic acid achieved under different conditions was 23gL(-1) and 29gL(-1), respectively. Furthermore, the efficiency of various organic solvents for the esterification reaction was evaluated and toluene was chosen for application in the process. The effect of water content was determined aiming to maximize the product yield and 40mgml(-1) was the optimal enzyme concentration. The bioprocess achieved maximum conversion of 33% constituting a valuable alternative to the application of energy demanding chemically derived methods.\n\nDevelopment of a hybrid fermentation-enzymatic bioprocess for the production of ethyl lactate from dairy waste.", "token_count": 276, "char_count": 1158, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:50.062007", "source": { "split": "train_shard_00000", "doc_id": 4693 }, "chunk_id": "train_shard_00000_4693_0", "global_id": 5245 }, { "text": "In this study, we report the inhibition of Kluyveromyces marxianus TISTR5925 growth and ethanol fermentation in the presence of furan derivatives and weak acids (acetic acid and lactic acid) at high temperatures. Cassava pulp, obtained as the waste from starch processing, was collected from 14 starch factories located in several provinces of Thailand. At a high temperature (42 °C), the cassava pulp hydrolysate from some starch factories strongly inhibited growth and ethanol production of both K. marxianus (strain TISTR5925) and Saccharomyces cerevisiae (strain K3). HPLC detected high levels of lactic acid and acetic acid in the hydrolysates, suggesting that these weak acids impaired the growth of K. marxianus at high temperature. We isolated Trp-requiring mutants that had reduced tolerance to acetic acid compared to the wild-type. This sensitivity to acetic acid was suppressed by supplementation of the medium with tryptophan.\n\nGrowth inhibition of thermotolerant yeast, Kluyveromyces marxianus, in hydrolysates from cassava pulp.", "token_count": 285, "char_count": 1043, "word_count": 152, "semantic_coherence": 1, "information_density": 0.5987, "quality_score": 0.7993, "entities": { "genes": [ "TISTR5925" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:50.610419", "source": { "split": "train_shard_00000", "doc_id": 4694 }, "chunk_id": "train_shard_00000_4694_0", "global_id": 5246 }, { "text": "Treatment of pulmonary arterial hypertension with the endothelin receptor antagonist bosentan has been associated with transient increases in liver transaminases. Mechanistically, bosentan inhibits the bile salt export pump (BSEP) leading to an intrahepatic accumulation of cytotoxic bile salts, which eventually results in hepatocellular damage. BSEP inhibition by bosentan is amplified by its accumulation in the liver as bosentan is a substrate of organic anion-transporting polypeptide (OATP) transport proteins. The novel endothelin receptor antagonist macitentan shows a superior liver safety profile. Introduction of the less acidic sulfamide moiety and increased lipophilicity yield a hepatic disposition profile different from other endothelin receptor antagonists. Passive diffusion rather than OATP-mediated uptake is the driving force for macitentan uptake into the liver. Interaction with the sodium taurocholate cotransporting polypeptide and BSEP transport proteins involved in hepatic bile salt homeostasis is therefore limited due to the low intrahepatic drug concentrations. Evidence for this conclusion is provided by in vitro experiments in drug transporter-expressing cell lines, acute and long-term studies in rats and dogs, absence of plasma bile salt changes in healthy human volunteers after multiple dosing, and finally the liver safety profile of macitentan in the completed phase III morbidity/mortality SERAPHIN (Study with an Endothelin Receptor Antagonist in Pulmonary Arterial Hypertension to Improve Clinical Outcome) trial.\n\nMacitentan does not interfere with hepatic bile salt transport.", "token_count": 409, "char_count": 1622, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:51.236128", "source": { "split": "train_shard_00000", "doc_id": 4695 }, "chunk_id": "train_shard_00000_4695_0", "global_id": 5247 }, { "text": "Hexanoic acid can be used for diverse industrial applications and is a precursor for fine chemistry. Although some natural microorganisms have been screened and evolved to produce hexanoic acid, the construction of an engineered biosynthetic pathway for producing hexanoic acid in yeast has not been reported. Here we constructed hexanoic acid pathways in Kluyveromyces marxianus by integrating 5 combinations of seven genes (AtoB, BktB, Crt, Hbd, MCT1, Ter, and TES1), by which random chromosomal sites of the strain are overwritten by the new genes from bacteria and yeast. One recombinant strain, H4A, which contained AtoB, BktB, Crt, Hbd, and Ter, produced 154mg/L of hexanoic acid from galactose as the sole substrate. However, the hexanoic acid produced by the H4A strain was re-assimilated during the fermentation due to the reverse activity of AtoB, which condenses two acetyl-CoAs into a single acetoacetyl-CoA. This product instability could be overcome by the replacement of AtoB with a malonyl CoA-acyl carrier protein transacylase (MCT1) from Saccharomyces cerevisiae. Our results suggest that Mct1 provides a slow but stable acetyl-CoA chain elongation pathway, whereas the AtoB-mediated route is fast but unstable. In conclusion, hexanoic acid was produced for the first time in yeast by the construction of chain elongation pathways comprising 5-7 genes in K. marxianus.\n\nA biosynthetic pathway for hexanoic acid production in Kluyveromyces marxianus.", "token_count": 408, "char_count": 1467, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [ "MCT1", "TES1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:51.860940", "source": { "split": "train_shard_00000", "doc_id": 4696 }, "chunk_id": "train_shard_00000_4696_0", "global_id": 5248 }, { "text": "Up to 20% of the chromosomal Pseudomonas aeruginosa DNA belong to the so-called accessory genome. Its elements are specific for subgroups or even single strains and are likely acquired by horizontal gene transfer (HGT). Similarities of the accessory genomic elements to DNA from other bacterial species, mainly the DNA of γ- and β-proteobacteria, indicate a role of interspecies HGT. In this study, we analysed the expression of the accessory genome in 150 clinical P. aeruginosa isolates as uncovered by transcriptome sequencing and the presence of accessory genes in eleven additional isolates. Remarkably, despite the large number of P. aeruginosa strains that have been sequenced to date, we found new strain-specific compositions of accessory genomic elements and a high portion (10-20%) of genes without P. aeruginosa homologues. Although some genes were detected to be expressed/present in several isolates, individual patterns regarding the genes, their functions and the possible origin of the DNA were widespread among the tested strains. Our results demonstrate the unaltered potential to discover new traits within the P. aeruginosa population and underline that the P. aeruginosa pangenome is likely to increase with increasing sequence information.\n\nThe extensive set of accessory Pseudomonas aeruginosa genomic components.", "token_count": 320, "char_count": 1337, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:52.427892", "source": { "split": "train_shard_00000", "doc_id": 4697 }, "chunk_id": "train_shard_00000_4697_0", "global_id": 5249 }, { "text": "The present study embarks on the feasibility of GM-bilosomes as a rationally designed vehicle for oral mucosal immunization. Bilosomes containing BSA as a model antigen were found to have vesicle size of 157 +/- 3 nm, PDI of 0.287 +/- 0.045, zeta potential of -21.8 +/- 2.01 mV and entrapment efficiency of 71.3 +/- 4.3%. Bilosomal formulations were freeze dried and entrapped BSA in freeze dried formulations was found to retain its structural and conformational stability as evident by SDS-PAGE and CD analysis. The GM-bilosomes were also found stable in different simulated biological fluids and bile salt solutions of different concentrations. In-vitro drug release revealed that GM-bilosomes were able to sustain drug release up to 24 h. In-vitro cell uptake in RAW 264.7 macrophage cells demonstrated significantly higher uptake of GM-bilosomes in comparison with bilosomes and free antigen. Intestinal uptake studies on excised rat intestinal sections further demonstrated higher uptake of vesicular systems throughout the intestinal region in comparison with free antigen. Significantly higher (p < 0.05) systemic immune response (serum IgG level) was observed in case of GM-bilosomes in comparison with bilosomes and alum adsorbed BSA (BSA-AL) following oral administration. The immune response observed in case of GM-bilosomes was comparable to BSA-AL administered through im route without any significant difference (p > 0.05). More importantly, GM-bilosomes were found capable of inducing mucosal immune response as well as cell mediated immune response which was not induced by im BSA-AL. In conclusion, GM-bilosomes could be considered as promising carrier and adjuvant system for oral mucosal immunization and productively exploited for oral delivery of other candidate antigens.\n\nOral mucosal immunization using glucomannosylated bilosomes.", "token_count": 500, "char_count": 1856, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5941, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:53.080084", "source": { "split": "train_shard_00000", "doc_id": 4698 }, "chunk_id": "train_shard_00000_4698_0", "global_id": 5250 }, { "text": "Background. As whole genome sequence data from bacterial isolates becomes cheaper to generate, computational methods are needed to correlate sequence data with biological observations. Here we present the large-scale BLAST score ratio (LS-BSR) pipeline, which rapidly compares the genetic content of hundreds to thousands of bacterial genomes, and returns a matrix that describes the relatedness of all coding sequences (CDSs) in all genomes surveyed. This matrix can be easily parsed in order to identify genetic relationships between bacterial genomes. Although pipelines have been published that group peptides by sequence similarity, no other software performs the rapid, large-scale, full-genome comparative analyses carried out by LS-BSR. Results. To demonstrate the utility of the method, the LS-BSR pipeline was tested on 96 Escherichia coli and Shigella genomes; the pipeline ran in 163 min using 16 processors, which is a greater than 7-fold speedup compared to using a single processor. The BSR values for each CDS, which indicate a relative level of relatedness, were then mapped to each genome on an independent core genome single nucleotide polymorphism (SNP) based phylogeny. Comparisons were then used to identify clade specific CDS markers and validate the LS-BSR pipeline based on molecular markers that delineate between classical E. coli pathogenic variant (pathovar) designations. Scalability tests demonstrated that the LS-BSR pipeline can process 1,000 E. coli genomes in 27-57 h, depending upon the alignment method, using 16 processors. Conclusions. LS-BSR is an open-source, parallel implementation of the BSR algorithm, enabling rapid comparison of the genetic content of large numbers of genomes. The results of the pipeline can be used to identify specific markers between user-defined phylogenetic groups, and to identify the loss and/or acquisition of genetic information between bacterial isolates. Taxa-specific genetic markers can then be translated into clinical diagnostics, or can be used to identify broadly conserved putative therapeutic candidates.", "token_count": 485, "char_count": 2088, "word_count": 302, "semantic_coherence": 1, "information_density": 0.6258, "quality_score": 0.8129, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:53.735464", "source": { "split": "train_shard_00000", "doc_id": 4699 }, "chunk_id": "train_shard_00000_4699_0", "global_id": 5251 }, { "text": "The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes.", "token_count": 28, "char_count": 123, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:54.088204", "source": { "split": "train_shard_00000", "doc_id": 4699 }, "chunk_id": "train_shard_00000_4699_1", "global_id": 5252 }, { "text": "Bile salt export pump (BSEP) is responsible for biliary secretion of bile acids, a rate-limiting step in the enterohepatic circulation of bile acids and transactivated by nuclear receptor farnesoid X receptor (FXR). Intrahepatic cholestasis of pregnancy (ICP) is the most prevalent disorder among diseases unique to pregnancy and primarily occurs in the third trimester of pregnancy, with a hallmark of elevated serum bile acids. Currently, the transcriptional regulation of BSEP during pregnancy and its underlying mechanisms and involvement in ICP are not fully understood. In this study the dynamics of BSEP transcription in vivo in the same group of pregnant mice before, during, and after gestation were established with an in vivo imaging system (IVIS). BSEP transcription was markedly repressed in the later stages of pregnancy and immediately recovered after parturition, resembling the clinical course of ICP in human. The transcriptional dynamics of BSEP was inversely correlated with serum 17β-estradiol (E2) levels before, during, and after gestation. Further studies showed that E2 repressed BSEP expression in human primary hepatocytes, Huh 7 cells, and in vivo in mice. Such transrepression of BSEP by E2 in vitro and in vivo required estrogen receptor α (ERα). Mechanistic studies with chromatin immunoprecipitation (ChIP), protein coimmunoprecipitation (Co-IP), and bimolecular fluorescence complementation (BiFC) assays demonstrated that ERα directly interacted with FXR in living cells and in vivo in mice.\n\nTranscriptional dynamics of bile salt export pump during pregnancy: mechanisms and implications in intrahepatic cholestasis of pregnancy.", "token_count": 422, "char_count": 1664, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:54.715823", "source": { "split": "train_shard_00000", "doc_id": 4700 }, "chunk_id": "train_shard_00000_4700_0", "global_id": 5253 }, { "text": "Candida species are a common cause of infection in immune-compromised HIV-positive individuals, who are usually treated with the antifungal drug, fluconazole, in public hospitals in Africa. However, information about the prevalence of drug resistance to fluconazole and other antifungal agents on Candida species is very limited. This study examined 128 Candida isolates from South Africa and 126 Cameroonian Candida isolates for determination of species prevalence and antifungal drug susceptibility. The isolates were characterized by growth on chromogenic and selective media and by their susceptibility to 9 antifungal drugs tested using the TREK™ YeastOne9 drug panel (Thermo Scientific, USA). Eighty-three percent (82.8%) of South African isolates were Candida albicans (106 isolates), 9.4% were Candida glabrata (12 isolates), and 7.8% were Candida dubliniensis (10 isolates). Of the Cameroonian isolates, 73.02% were C. albicans (92 isolates); 19.05% C. glabrata (24 isolates); 3.2% Candida tropicalis (4 isolates); 2.4% Candida krusei (3 isolates); 1.59% either Candida kefyr, Candida parapsilopsis, or Candida lusitaneae (2 isolates); and 0.79% C. dubliniensis (1 isolate). Widespread C. albicans resistance to azoles was detected phenotypically in both populations. Differences in drug resistance were seen within C. glabrata found in both populations. Echinocandin drugs were more effective on isolates obtained from the Cameroon than in South Africa. A multiple-drug resistant C. dubliniensis strain isolated from the South African samples was inhibited only by 5-flucytosine in vitro on the YO9 panel. Drug resistance among oral Candida species is common among African HIV patients in these 2 countries. Regional surveillance of Candida species drug susceptibility should be undertaken to ensure effective treatment for HIV-positive patients.", "token_count": 511, "char_count": 1856, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5747, "quality_score": 0.7874, "entities": { "genes": [ "YO9" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:55.731749", "source": { "split": "train_shard_00000", "doc_id": 4701 }, "chunk_id": "train_shard_00000_4701_0", "global_id": 5254 }, { "text": "Multi-drug resistant oral Candida species isolated from HIV-positive patients in South Africa and Cameroon.", "token_count": 25, "char_count": 107, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:56.087356", "source": { "split": "train_shard_00000", "doc_id": 4701 }, "chunk_id": "train_shard_00000_4701_1", "global_id": 5255 }, { "text": "Lactic acid bacteria (LAB) have the potential to degrade intestinal oxalate and this is increasingly being studied as a promising probiotic solution to manage kidney stone disease. In this study, oxalate degrading LAB were isolated from human faeces and south Indian fermented foods, subsequently assessed for potential probiotic property in vitro and in vivo. Based on preliminary characteristics, 251 out of 673 bacterial isolates were identified as LAB. A total of 17 strains were found to degrade oxalate significantly between 40.38% and 62.90% and were subjected to acid and bile tolerance test. Among them, nine strains exhibited considerable tolerance up to pH 3.0 and at 0.3% bile. These were identified as Lactobacillus fermentum and Lactobacillus salivarius using 16S rDNA sequencing. Three strains, Lactobacillus fermentum TY5, Lactobacillus fermentum AB1, and Lactobacillus salivarius AB11, exhibited good adhesion to HT-29 cells and strong antimicrobial activity. They also conferred resistance to kanamycin, rifampicin, and ampicillin, but were sensitive to chloramphenicol and erythromycin. The faecal recovery rate of these strains was observed as 15.16% (TY5), 6.71% (AB1), and 9.3% (AB11) which indicates the colonization ability. In conclusion, three efficient oxalate degrading LAB were identified and their safety assessments suggest that they may serve as good probiotic candidates for preventing hyperoxaluria.\n\nScreening of indigenous oxalate degrading lactic acid bacteria from human faeces and South Indian fermented foods: assessment of probiotic potential.", "token_count": 447, "char_count": 1584, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [ "AB1", "TY5", "AB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:56.717344", "source": { "split": "train_shard_00000", "doc_id": 4702 }, "chunk_id": "train_shard_00000_4702_0", "global_id": 5256 }, { "text": "This study was designed to evaluate the transfer potential of antibiotic resistance genes in antibiotic-resistant Salmonella Typhimurium (S. Typhimurium(R)) in the presence of bile salts. The resistance of S. Typhimurium(R) to ampicillin, kanamycin, and tetracycline was increased by 64-, 64-, and 512-fold, respectively. The highest transfer frequency from S. Typhimurium(R) to Escherichia coli was observed at the bile salt concentration of 160 μg/ml (3.8 × 10(-3) transferrants/cells). The expression of traJ and traY was suppressed in S. Typhimurium(R) by bile salt. This study provides useful information for understanding the conjugative transfer of antibiotic resistance genes in S. Typhimurium under intestinal conditions.\n\nAssessment of conjugal transfer of antibiotic resistance genes in Salmonella Typhimurium exposed to bile salts.", "token_count": 249, "char_count": 843, "word_count": 116, "semantic_coherence": 1, "information_density": 0.5603, "quality_score": 0.7802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:57.204609", "source": { "split": "train_shard_00000", "doc_id": 4703 }, "chunk_id": "train_shard_00000_4703_0", "global_id": 5257 }, { "text": "Following contact with the epithelium, the enteric intracellular bacterial pathogen Shigella flexneri invades epithelial cells and escapes intracellular phagosomal destruction using its type III secretion system (T3SS). The bacterium replicates within the host cell cytosol and spreads between cells using actin-based motility, which is mediated by the virulence factor IcsA (VirG). Whereas S. flexneri invasion is well characterized, adhesion mechanisms of the bacterium remain elusive. We found that IcsA also functions as an adhesin that is both necessary and sufficient to promote contact with host cells. As adhesion can be beneficial or deleterious depending on the host cell type, S. flexneri regulates IcsA-dependent adhesion. Activation of the T3SS in response to the bile salt deoxycholate triggers IcsA-dependent adhesion and enhances pathogen invasion. IcsA-dependent adhesion contributes to virulence in a mouse model of shigellosis, underscoring the importance of this adhesin to S. flexneri pathogenesis.\n\nIcsA is a Shigella flexneri adhesin regulated by the type III secretion system and required for pathogenesis.", "token_count": 303, "char_count": 1130, "word_count": 160, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:57.771134", "source": { "split": "train_shard_00000", "doc_id": 4704 }, "chunk_id": "train_shard_00000_4704_0", "global_id": 5258 }, { "text": "A characterization of the LtrR regulator, an S. Typhi protein belonging to the LysR family is presented. Proteomics, outer membrane protein profiles and transcriptional analyses demonstrated that LtrR is required for the synthesis of OmpR, OmpC and OmpF. DNA-protein interaction analysis showed that LtrR binds to the regulatory region of ompR and then OmpR interacts with the ompC and ompF promoters inducing porin synthesis. LtrR-dependent and independent ompR promoters were identified, and both promoters are involved in the synthesis of OmpR for OmpC and OmpF production. To define the functional role of the ltrR-ompR-ompC-ompF genetic network, mutants in each gene were obtained. We found that ltrR, ompR, ompC and ompF were involved in the control of bacterial transformation, while the two regulators and ompC are necessary for the optimal growth of S. Typhi in the presence of one of the major bile salts found in the gut, sodium deoxycholate. The data presented establish the pivotal role of LtrR in the regulatory network of porin synthesis and reveal new genetic strategies of survival and cellular adaptation to the environment used by Salmonella.\n\nThe Salmonella enterica serovar Typhi ltrR-ompR-ompC-ompF genes are involved in resistance to the bile salt sodium deoxycholate and in bacterial transformation.", "token_count": 342, "char_count": 1323, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5396, "quality_score": 0.7698, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:58.342325", "source": { "split": "train_shard_00000", "doc_id": 4705 }, "chunk_id": "train_shard_00000_4705_0", "global_id": 5259 }, { "text": "The Lactobacillus gasseri SBT2055 (LG2055) is a probiotic lactic acid bacterium with properties such as bile tolerance and ability to improve the intestinal environment. In this study, we established that the oral administration of LG2055 exhibits efficacy to protect mice infected with the influenza virus A/PR8. The body weight losses were lower with the LG2055 administration after the PR8 virus infection. At 5 days after the infection, the virus titer was significantly decreased as was the amount of produced IL-6 in the lung tissue, the number of total cells in the bronchoalveolar lavage fluid was reduced by the LG2055 administration. The expression of the Mx1 and Oas1a genes, critical for the viral clearance in the lung tissues was increased by the pre-treatment with LG2055. These findings suggest that the LG2055 administration is effective for the protection against influenza A virus infection by the down-regulation of viral replication through the induction of antiviral genes expression.\n\nOral administration of Lactobacillus gasseri SBT2055 is effective for preventing influenza in mice.", "token_count": 286, "char_count": 1107, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5928, "quality_score": 0.7964, "entities": { "genes": [ "SBT2055", "LG2055", "PR8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:58.892538", "source": { "split": "train_shard_00000", "doc_id": 4706 }, "chunk_id": "train_shard_00000_4706_0", "global_id": 5260 }, { "text": "Transcriptional coregulators are important components of nuclear receptor (NR) signaling machinery and provide additional mechanisms for modulation of NR activity. Expression of a mutated nuclear corepressor 1 (NCoR1) that lacks 2 NR interacting domains (NCoRΔID) in the liver leads to elevated expression of genes regulated by thyroid hormone receptor (TR) and liver X receptor (LXR), both of which control hepatic cholesterol metabolism. Here, we demonstrate that expression of NCoRΔID in mouse liver improves dietary cholesterol tolerance in an LXRα-independent manner. NCoRΔID-associated cholesterol tolerance was primarily due to diminished intestinal cholesterol absorption as the result of changes in the composition and hydrophobicity of the bile salt pool. Alterations of the bile salt pool were mediated by increased expression of genes encoding the bile acid metabolism enzymes CYP27A1 and CYP3A11 as well as canalicular bile salt pump ABCB11. We have determined that these genes are regulated by thyroid hormone and that TRβ1 is recruited to their regulatory regions. Together, these data indicate that interactions between NCoR1 and TR control a specific pathway involved in regulation of cholesterol metabolism and clearance.\n\nHepatic nuclear corepressor 1 regulates cholesterol absorption through a TRβ1-governed pathway.", "token_count": 338, "char_count": 1336, "word_count": 189, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:46:59.492409", "source": { "split": "train_shard_00000", "doc_id": 4707 }, "chunk_id": "train_shard_00000_4707_0", "global_id": 5261 }, { "text": "Drug-induced cholestasis is a frequently observed side effect of drugs and is often caused by an unexpected interaction with the bile salt export pump (BSEP/ABCB11). BSEP is the key membrane transporter responsible for the transport of bile acids from hepatocytes into bile. Here, we developed a pharmacophore model that describes the molecular features of compounds associated with BSEP inhibitory activity. To generate input and validation data sets, in vitro experiments with membrane vesicles overexpressing human BSEP were used to assess the effect of compounds (50 μM) on BSEP-mediated (3)H-taurocholic acid transport. The model contains two hydrogen bond acceptor/anionic features, two hydrogen bond acceptor vector features, four hydrophobic/aromatic features, and exclusion volumes. The pharmacophore was validated against a set of 59 compounds, including registered drugs. The model recognized 9 out of 12 inhibitors (75%), which could not be identified based on general parameters, such as molecular weight or SlogP, alone. Finally, the model was used to screen a virtual compound database. A number of compounds found via virtual screening were tested and displayed statistically significant BSEP inhibition, ranging from 13 ± 1% to 67 ± 7% of control (P < 0.05). In conclusion, we developed and validated a pharmacophore model that describes molecular features found in BSEP inhibitors. The model may be used as an in silico screening tool to identify potentially harmful drug candidates at an early stage in drug development.\n\nIn silico identification and in vitro validation of potential cholestatic compounds through 3D ligand-based pharmacophore modeling of BSEP inhibitors.", "token_count": 410, "char_count": 1691, "word_count": 250, "semantic_coherence": 1, "information_density": 0.628, "quality_score": 0.814, "entities": { "genes": [ "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:00.143323", "source": { "split": "train_shard_00000", "doc_id": 4708 }, "chunk_id": "train_shard_00000_4708_0", "global_id": 5262 }, { "text": "The yeast Kluyveromyces marxianus features specific traits that render it attractive for industrial applications. These include production of ethanol which, together with thermotolerance and the ability to grow with a high specific growth rate on a wide range of substrates, could make it an alternative to Saccharomyces cerevisiae as an ethanol producer. However, its ability to co-ferment C5 and C6 sugars under oxygen-limited conditions is far from being fully characterized.\n\nEffect of oxygenation and temperature on glucose-xylose fermentation in Kluyveromyces marxianus CBS712 strain.", "token_count": 141, "char_count": 590, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7952, "quality_score": 0.8976, "entities": { "genes": [ "CBS712" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:00.597746", "source": { "split": "train_shard_00000", "doc_id": 4709 }, "chunk_id": "train_shard_00000_4709_0", "global_id": 5263 }, { "text": "Chimeric mice with humanized liver (PXB mice) have been generated by transplantation of urokinase-type plasminogen activator/severe combined immunodeficiency mice with human hepatocytes. The purpose of the present study was to clarify the protein expression levels of metabolizing enzymes and transporters in humanized liver of PXB mice transplanted with hepatocytes from three different donors, and to compare their protein expressions with those of human livers to validate this human liver model. The protein expression levels of metabolizing enzymes and transporters were quantified in microsomal fraction and plasma membrane fraction, respectively, by means of liquid chromatography-tandem mass spectrometry. Protein expression levels of 12 human P450 enzymes, two human UDP-glucuronosyltransferases, eight human ATP binding cassette (ABC) transporters, and eight human solute carrier transporters were determined. The variances of protein expression levels among samples from mice humanized with hepatocytes from all donors were significantly greater than those from samples obtained from mice derived from each individual donor. Compared with the protein expression levels in human livers, all of the quantified metabolizing enzymes and transporters were within a range of 4-fold difference, except for CYP2A6, CYP4A11, bile salt export pump (BSEP), and multidrug resistance protein 3 (MDR3), which showed 4- to 5-fold differences between PXB mouse and human livers. The present study indicates that humanized liver of PXB mice is a useful model of human liver from the viewpoint of protein expression of metabolizing enzymes and transporters, but the results are influenced by the characteristics of the human hepatocyte donor.\n\nValidation of uPA/SCID mouse with humanized liver as a human liver model: protein quantification of transporters, cytochromes P450, and UDP-glucuronosyltransferases by LC-MS/MS.", "token_count": 483, "char_count": 1914, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5206, "quality_score": 0.7603, "entities": { "genes": [ "MDR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:01.247603", "source": { "split": "train_shard_00000", "doc_id": 4710 }, "chunk_id": "train_shard_00000_4710_0", "global_id": 5264 }, { "text": "Rat canalicular membranes contain microdomains enriched in cholesterol and ATP-binding cassette transporters. Cholesterol is known to regulate the activity of transporters. Here, we investigated the effect of membrane cholesterol on the transport kinetics of multidrug resistance-associated protein 2 (MRP2) and of bile salt export pump (BSEP) variants and mutants. MRP2 and BSEP were expressed with baculoviruses in insect cells, followed by vesicle isolation from control and cholesterol-loaded cells (1 mM cholesterol@randomly methylated-β-cyclodextrin) for transport assays. We found that cholesterol stimulates MRP2 transport activity for substrates of different molecular weights: estradiol-17-β-glucuronide (E17βG), prostaglandin E2 (PGE2), cholecystokinin 8 (CCK8), and vasopressin displayed an increase of Vmax and a variable decrease of Km. Kinetics of E17βG showed a sigmoidal shape and a mild cooperativity in Hanes-Woolf plots in control membranes. High cholesterol content shifted E17βG to Michaelis-Menten kinetics. PGE2/glutathione transport followed Michaelis-Menten kinetics irrespective of cholesterol. The MRP2 substrates CCK8 and vasopressin exhibited Michaelis-Menten kinetics independent of membrane cholesterol content. Transport of ochratoxin A was ATP-dependent but was neither mediated by MRP2 nor stimulated by cholesterol. Transport of the two most common BSEP variants p.444V/A showed Michaelis-Menten kinetics irrespective of membrane cholesterol, whereby cholesterol leads to an increased Vmax while Km remains unchanged. The transport activity of the BSEP mutants p.E297G and p.R432T increased at high cholesterol content but did not reach the capacity of normal BSEP", "token_count": 504, "char_count": 1700, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6027, "quality_score": 0.8013, "entities": { "genes": [ "MRP2", "PGE2", "CCK8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:01.906698", "source": { "split": "train_shard_00000", "doc_id": 4711 }, "chunk_id": "train_shard_00000_4711_0", "global_id": 5265 }, { "text": "Hence, changing membrane cholesterol content modulates BSEP and MRP2 transport kinetics differently. Cholesterol increases the transport rates of BSEP and MRP2, but with the latter, may also modify the binding site as for E17βG.\n\nDifferential effects of membrane cholesterol content on the transport activity of multidrug resistance-associated protein 2 (ABCC2) and of the bile salt export pump (ABCB11).", "token_count": 109, "char_count": 404, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [ "MRP2", "ABCC2", "ABCB11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:02.295533", "source": { "split": "train_shard_00000", "doc_id": 4711 }, "chunk_id": "train_shard_00000_4711_1", "global_id": 5266 }, { "text": "Commensal and pathogenic bacteria must deal with many different stress conditions to survive in and colonize the human gastrointestinal tract. One major challenge that bacteria encounter in the gut is the high concentration of bile salts, which not only aid in food absorption but also act as effective physiological antimicrobials. The mechanism by which bile salts limit bacterial growth is still largely unknown. Here, we show that bile salts cause widespread protein unfolding and aggregation, affecting many essential proteins. Simultaneously, the bacterial cytosol becomes highly oxidizing, indicative of disulfide stress. Strains defective in reducing oxidative thiol modifications, restoring redox homeostasis, or preventing irreversible protein aggregation under disulfide stress conditions are sensitive to bile salt treatment. Surprisingly, cholate and deoxycholate, two of the most abundant and very closely related physiological bile salts, vary substantially in their destabilizing effects on proteins in vitro and cause protein unfolding of different subsets of proteins in vivo. Our results provide a potential mechanistic explanation for the antimicrobial effects of bile salts, help explain the beneficial effects of bile salt mixtures, and suggest that we have identified a physiological source of protein-unfolding disulfide stress conditions in bacteria.\n\nBile salts act as effective protein-unfolding agents and instigators of disulfide stress in vivo.", "token_count": 329, "char_count": 1474, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:02.867247", "source": { "split": "train_shard_00000", "doc_id": 4712 }, "chunk_id": "train_shard_00000_4712_0", "global_id": 5267 }, { "text": "One of the main hurdles for the development of an effective and broadly protective vaccine against nonencapsulated isolates of Haemophilus influenzae (NTHi) lies in the genetic diversity of the species, which renders extremely difficult the identification of cross-protective candidate antigens. To assess whether a population structure of NTHi could be defined, we performed genome sequencing of a collection of diverse clinical isolates representative of both carriage and disease and of the diversity of the natural population. Analysis of the distribution of polymorphic sites in the core genome and of the composition of the accessory genome defined distinct evolutionary clades and supported a predominantly clonal evolution of NTHi, with the majority of genetic information transmitted vertically within lineages. A correlation between the population structure and the presence of selected surface-associated proteins and lipooligosaccharide structure, known to contribute to virulence, was found. This high-resolution, genome-based population structure of NTHi provides the foundation to obtain a better understanding, of NTHi adaptation to the host as well as its commensal and virulence behavior, that could facilitate intervention strategies against disease caused by this important human pathogen.\n\nGenome sequencing of disease and carriage isolates of nontypeable Haemophilus influenzae identifies discrete population structure.", "token_count": 296, "char_count": 1441, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6091, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:03.429256", "source": { "split": "train_shard_00000", "doc_id": 4713 }, "chunk_id": "train_shard_00000_4713_0", "global_id": 5268 }, { "text": "The search of robust microorganisms is essential to design sustainable processes of second generation bioethanol. Yeast strains isolated from industrial environments are generally recognised to present an increased stress tolerance but no specific information is available on their tolerance towards inhibitors that come from the pretreatment of lignocellulosic materials. In this work, a strategy for the selection of different yeasts using hydrothermal hydrolysate from Eucalyptus globulus wood, containing different concentrations of inhibitors, was developed. Ten Saccharomyces cerevisiae and four Kluyveromyces marxianus strains isolated from industrial environments and four laboratory background strains were evaluated. Interestingly, a correlation between final ethanol titer and percentage of furfural detoxification was observed. The results presented here highlight industrial distillery environments as a remarkable source of efficient yeast strains for lignocellulosic fermentation processes. Selected strains were able to resourcefully degrade furfural and HMF inhibitors, producing 0.8g ethanol/Lh corresponding to 94% of the theoretical yield.\n\nIndustrial robust yeast isolates with great potential for fermentation of lignocellulosic biomass.", "token_count": 269, "char_count": 1259, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6937, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:03.978069", "source": { "split": "train_shard_00000", "doc_id": 4714 }, "chunk_id": "train_shard_00000_4714_0", "global_id": 5269 }, { "text": "In vitro digestion of isolated milk proteins results in milk peptides with a variety of actions. However, it remains unclear to what degree protein degradation occurs in vivo in the infant stomach and whether peptides previously annotated for bioactivity are released. This study combined nanospray LC separation with time-of-flight mass spectrometry, comprehensive structural libraries, and informatics to analyze milk from 3 human mothers and the gastric aspirates from their 4- to 12-d-old postpartum infants. Milk from the mothers contained almost 200 distinct peptides, demonstrating enzymatic degradation of milk proteins beginning either during lactation or between milk collection and feeding. In the gastric samples, 649 milk peptides were identified, demonstrating that digestion continues in the infant stomach. Most peptides in both the intact milk and gastric samples were derived from β-casein. The numbers of peptides from β-casein, lactoferrin, α-lactalbumin, lactadherin, κ-casein, serum albumin, bile salt-associated lipase, and xanthine dehydrogenase/oxidase were significantly higher in the gastric samples than in the milk samples (P < 0.05). A total of 603 peptides differed significantly in abundance between milk and gastric samples (P < 0.05). Most of the identified peptides have previously identified biologic activity. Gastric proteolysis occurs in the term infant in the first 2 wk of life, releasing biologically active milk peptides with immunomodulatory and antibacterial properties of clinical relevance to the proximal intestinal tract. Data are available via ProteomeXchange (identifier PXD000688).\n\nA peptidomic analysis of human milk digestion in the infant stomach reveals protein-specific degradation patterns.", "token_count": 451, "char_count": 1749, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5861, "quality_score": 0.793, "entities": { "genes": [ "PXD000688" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:04.611408", "source": { "split": "train_shard_00000", "doc_id": 4715 }, "chunk_id": "train_shard_00000_4715_0", "global_id": 5270 }, { "text": "Bile tolerance is a fundamental ability of probiotic bacteria. We examined this property in 56 Lactobacillus brevis strains isolated from Japanese pickles and also evaluated cellular fatty acid composition and cell-bound exopolysaccharide (EPS-b) production. The bile tolerance of these strains was significantly lower in modified de Man - Rogosa - Sharpe (MRS) medium (without Tween 80 or sodium acetate) than in standard MRS medium. Aggregating strains showed significantly higher bile tolerance than nonaggregating strains in MRS medium, but there was no significant difference in the modified MRS media. The relative octadecenoic acid (C18:1) content of the 3 most tolerant aggregating and nonaggregating strains was significantly higher when bile was added to MRS. In MRS without Tween 80, the relative C18:1 content was only marginally affected by addition of bile. In MRS without sodium acetate, only the 3 most tolerant nonaggregating strains increased their relative C18:1 content in the presence of bile. Meanwhile, culture in MRS without sodium acetate reduced EPS-b production in aggregating strains. In conclusion, both EPS-b and cellular fatty acid composition play important roles in bile tolerance of pickle-derived L. brevis.\n\nCellular fatty acid composition and exopolysaccharide contribute to bile tolerance in Lactobacillus brevis strains isolated from fermented Japanese pickles.", "token_count": 355, "char_count": 1400, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5396, "quality_score": 0.7698, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:05.191357", "source": { "split": "train_shard_00000", "doc_id": 4716 }, "chunk_id": "train_shard_00000_4716_0", "global_id": 5271 }, { "text": "Natural resistance to lincosamides and streptogramins A (LSA), which is a species characteristic of Bacillus subtilis and Enterococcus faecalis, has never been documented in the Staphylococcus genus. We investigate here the molecular basis of the LSA phenotype exhibited by seven reference strains of Staphylococcus sciuri, including the type strains of the three described subspecies. By whole-genome sequencing of strain ATCC 29059, we identified a candidate gene that encodes an ATP-binding cassette protein similar to the Lsa and VmlR resistance determinants. Isolation and reverse transcription-quantitative PCR (qRT-PCR) expression studies confirmed that Sal(A) can confer a moderate resistance to lincosamides (8 times the MIC of lincomycin) and a high-level resistance to streptogramins A (64 times the MIC of pristinamycin II). The chromosomal location of sal(A) between two housekeeping genes of the staphylococcal core genome supports the gene's ancient origins and thus innate resistance to these antimicrobials within S. sciuri subspecies.\n\nCharacterization of sal(A), a novel gene responsible for lincosamide and streptogramin A resistance in Staphylococcus sciuri.", "token_count": 314, "char_count": 1179, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:05.749881", "source": { "split": "train_shard_00000", "doc_id": 4717 }, "chunk_id": "train_shard_00000_4717_0", "global_id": 5272 }, { "text": "Public Health England (PHE) holds a collection of Shigella flexneri Type strains isolated between 1949 and 1972 representing 15 established serotypes and one provisional type, E1037. In this study, the genomes of all 16 PHE Type strains were sequenced using the Illumina HiSeq platform. The relationship between core genome phylogeny and serotype was examined.\n\nDraft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence.", "token_count": 142, "char_count": 546, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7407, "quality_score": 0.8704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:06.173651", "source": { "split": "train_shard_00000", "doc_id": 4718 }, "chunk_id": "train_shard_00000_4718_0", "global_id": 5273 }, { "text": "Resistance to high concentrations of bile salts in the human intestinal tract is vital for the survival of enteric bacteria such as Escherichia coli. Although the tripartite AcrAB-TolC efflux system plays a significant role in this resistance, it is purported that other efflux pumps must also be involved. We provide evidence from a comprehensive suite of experiments performed at two different pH values (7.2 and 6.0) that reflect pH conditions that E. coli may encounter in human gut that MdtM, a single-component multidrug resistance transporter of the major facilitator superfamily, functions in bile salt resistance in E. coli by catalysing secondary active transport of bile salts out of the cell cytoplasm. Furthermore, assays performed on a chromosomal ΔacrB mutant transformed with multicopy plasmid encoding MdtM suggested a functional synergism between the single-component MdtM transporter and the tripartite AcrAB-TolC system that results in a multiplicative effect on resistance. Substrate binding experiments performed on purified MdtM demonstrated that the transporter binds to cholate and deoxycholate with micromolar affinity, and transport assays performed on inverted vesicles confirmed the capacity of MdtM to catalyse electrogenic bile salt/H(+) antiport.\n\nA single-component multidrug transporter of the major facilitator superfamily is part of a network that protects Escherichia coli from bile salt stress.", "token_count": 361, "char_count": 1432, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6019, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:06.749572", "source": { "split": "train_shard_00000", "doc_id": 4719 }, "chunk_id": "train_shard_00000_4719_0", "global_id": 5274 }, { "text": "The study was aimed at evaluating the probiotic potential of indigenous autochthonous Lactobacillus rhamnosus strains isolated from infant feces and vaginal mucosa of healthy female. The survival of the selected strains and the two reference strains (L. rhamnosus GG and L. casei Actimel) was 67-81 % at pH 2 and 70-80 % after passage through the simulated gastrointestinal fluid. These strains are able to grow in the presence of 4 % bile salt, 10 % NaCl, and 0.6 % phenol. The cell surface of L. rhamnosus strains is hydrophilic in nature as revealed by bacterial adhesion to hydrocarbons (BATH) assay. Despite this, L. rhamnosus strains showed mucin adherence, autoaggregation and coaggregation properties that are strain-specific. In addition, they produce bile salt hydrolase (BSH) and β-galactosidase activities. L. rhamnosus strains exhibit antimicrobial activity against food spoilage organisms and gastrointestinal pathogens, as well as Candida and Aspergillus spp. L. rhamnosus strains have similar antibiotic susceptibility pattern, and resistance to certain antibiotics is intrinsic or innate. The strains are neither haemolytic nor producer of biogenic amines such as histamine, putrescine, cadaverine and tyramine. Lyophilized cells of L. rhamnosus Fb exhibited probiotic properties demonstrating potential of the strain for technological suitability and in the preparation of diverse probiotic food formulations.\n\nProbiotic attributes of autochthonous Lactobacillus rhamnosus strains of human origin.", "token_count": 430, "char_count": 1515, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:07.380248", "source": { "split": "train_shard_00000", "doc_id": 4720 }, "chunk_id": "train_shard_00000_4720_0", "global_id": 5275 }, { "text": "High temperature ethanol fermentation from sugarcane molasses B using thermophilic Crabtree-positive yeast Kluyveromyces sp. IIPE453 was carried out in batch bioreactor system. Strain was found to have a maximum specific ethanol productivity of 0.688 g/g/h with 92 % theoretical ethanol yield. Aeration and initial sugar concentration were tuning parameters to regulate metabolic pathways of the strain for either cell mass or higher ethanol production during growth with an optimum sugar to cell ratio 33:1 requisite for fermentation. An assessment of ethanol recovery from fermentation broth via simulation study illustrated that distillation-based conventional recovery was significantly better in terms of energy efficiency and overall mass recovery in comparison to coupled solvent extraction-azeotropic distillation technique for the same.\n\nEthanol fermentation from molasses at high temperature by thermotolerant yeast Kluyveromyces sp. IIPE453 and energy assessment for recovery.", "token_count": 241, "char_count": 987, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6866, "quality_score": 0.8433, "entities": { "genes": [ "IIPE453" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:07.859189", "source": { "split": "train_shard_00000", "doc_id": 4721 }, "chunk_id": "train_shard_00000_4721_0", "global_id": 5276 }, { "text": "Traditional tequila fermentation is a complex microbial process performed by different indigenous yeast species. Usually, they are classified in two families: Saccharomyces and Non-Saccharomyces species. Using mixed starter cultures of several yeasts genera and species is nowadays considered to be beneficial to enhance the sensorial characteristics of the final products (taste, odor). However, microbial interactions occurring in such fermentations need to be better understood to improve the process. In this work, we focussed on a Saccharomyces cerevisiae/Kluyveromyces marxianus yeast couple. Indirect interactions due to excreted metabolites, thanks to the use of a specific membrane bioreactor, and direct interaction due to cell-to-cell contact have been explored. Comparison of pure and mixed cultures was done in each case. Mixed cultures in direct contact showed that both yeast were affected but Saccharomyces rapidly dominated the cultures whereas Kluyveromyces almost disappeared. In mixed cultures with indirect contact the growth of Kluyveromyces was decreased compared to its pure culture but its concentration could be maintained whereas the growth of Saccharomyces was enhanced. The loss of viability of Kluyveromyces could not be attributed only to ethanol. The sugar consumption and ethanol production in both cases were similar. Thus the interaction phenomena between the two yeasts are different in direct and indirect contact, Kluyveromyces being always much more affected than Saccharomyces.\n\nInteractions between Kluyveromyces marxianus and Saccharomyces cerevisiae in tequila must type medium fermentation.", "token_count": 366, "char_count": 1634, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5947, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:08.443698", "source": { "split": "train_shard_00000", "doc_id": 4722 }, "chunk_id": "train_shard_00000_4722_0", "global_id": 5277 }, { "text": "Lactobacillus plantarum LD1 was isolated from dosa batter and identified by biochemical, physiological and genetic methods. Species level identification was done by 16S rDNA amplification and sequencing. The probiotic potential of strain LD1 was assessed by different standard parameters. Cell surface hydrophobicity was recorded to be 62% with SAT value <0.007 M. Seventy-eight percent of viable count was found after treatment with simulated gastric juice containing pepsin (pH 2.0). Bile salt tolerance and bile salt hydrolase activity were also demonstrated by strain LD1. The culture supernatant was able to inhibit food-borne as well as clinical pathogenic microorganisms such as Staphylococcus aureus, Salmonella typhimurium, Shigella flexneri, Pseudomonas aeruginosa, urogenic Escherichia coli and Vibrio sp. Strain LD1 was found to be sensitive to most of the antibiotics used in the study. Since strain has been isolated from food source that is most typical of Southern India, it would be safe for further consumption in probiotic products.\n\nProbiotic Potential of Lactobacillus plantarum LD1 Isolated from Batter of Dosa, a South Indian Fermented Food.", "token_count": 315, "char_count": 1164, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [ "LD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:08.998560", "source": { "split": "train_shard_00000", "doc_id": 4723 }, "chunk_id": "train_shard_00000_4723_0", "global_id": 5278 }, { "text": "The increasing availability of hundreds of whole bacterial genomes provides opportunities for enhanced understanding of the genes and alleles responsible for clinically important phenotypes and how they evolved. However, it is a significant challenge to develop easy-to-use and scalable methods for characterizing these large and complex data and relating it to disease epidemiology. Existing approaches typically focus on either homologous sequence variation in genes that are shared by all isolates, or non-homologous sequence variation--focusing on genes that are differentially present in the population. Here we present a comparative genomics approach that simultaneously approximates core and accessory genome variation in pathogen populations and apply it to pathogenic species in the genus Campylobacter. A total of 7 published Campylobacter jejuni and Campylobacter coli genomes were selected to represent diversity across these species, and a list of all loci that were present at least once was compiled. After filtering duplicates a 7-isolate reference pan-genome, of 3,933 loci, was defined. A core genome of 1,035 genes was ubiquitous in the sample accounting for 59% of the genes in each isolate (average genome size of 1.68 Mb). The accessory genome contained 2,792 genes. A Campylobacter population sample of 192 genomes was screened for the presence of reference pan-genome loci with gene presence defined as a BLAST match of ≥ 70% identity over ≥ 50% of the locus length--aligned using MUSCLE on a gene-by-gene basis. A total of 21 genes were present only in C. coli and 27 only in C. jejuni, providing information about functional differences associated with species and novel epidemiological markers for population genomic analyses. Homologs of these genes were found in several of the genomes used to define the pan-genome and, therefore, would not have been identified using a single reference strain approach.\n\nA reference pan-genome approach to comparative bacterial genomics: identification of novel epidemiological markers in pathogenic Campylobacter.", "token_count": 486, "char_count": 2078, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5798, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:09.645822", "source": { "split": "train_shard_00000", "doc_id": 4724 }, "chunk_id": "train_shard_00000_4724_0", "global_id": 5279 }, { "text": "Pseudomonas aeruginosa PA96 is a clinical isolate from Guangzhou, China, that is multiresistant to antibiotics. We previously described the 500-kb IncP-2 plasmid, pOZ176 that encodes many resistance genes including the IMP-9 carbapenemase. Whole-genome sequencing of PA96 enabled characterization of its genomic islands, virulence factors, and chromosomal resistance genes. We filled gaps using PCR and used optical mapping to confirm the correct contig order. We automatically annotated the core genome and manually annotated the genomic islands. The genome is 6 444 091 bp and encodes 5853 ORFs. From the whole-genome sequence, we constructed a physical map and constructed a phylogenetic tree for comparison with sequenced P. aeruginosa strains. Analysis of known core genome virulence factors and resistance genes revealed few differences with other strains, but the major virulence island is closer to that of DK2 than to PA14. PA96 most closely resembles the environmental strain M18, and notably shares a common serotype, pyoverdin type, flagellar operon, type IV pilin, and several genomic islands with M18.\n\nGenomic analysis of Pseudomonas aeruginosa PA96, the host of carbapenem resistance plasmid pOZ176.", "token_count": 338, "char_count": 1215, "word_count": 177, "semantic_coherence": 1, "information_density": 0.661, "quality_score": 0.8305, "entities": { "genes": [ "PA14", "DK2", "PA96" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:10.210678", "source": { "split": "train_shard_00000", "doc_id": 4725 }, "chunk_id": "train_shard_00000_4725_0", "global_id": 5280 }, { "text": "Aliphatic amines, including methylamine, are air-pollutants, due to their intensive use in industry and the natural degradation of proteins, amino acids, and other nitrogen-containing compounds in biological samples. It is necessary to develop systems for removal of methylamine from the air, since airborne methylamine has a negative effect on human health. The primary amine oxidase (primary amine : oxygen oxidoreductase (deaminating) or amine oxidase, AMO; EC 1.4.3.21), a copper-containing enzyme from the thermotolerant yeast Hansenula polymorpha which was overexpressed in baker's yeast Saccharomyces cerevisiae, was tested for its ability to oxidize airborne methylamine. A continuous fluidized bed bioreactor (CFBR) was designed to enable bioconversion of airborne methylamine by AMO immobilized in calcium alginate (CA) beads. The results demonstrated that the bioreactor with immobilized AMO eliminates nearly 97% of the airborne methylamine. However, the enzymatic activity of AMO causes formation of formaldehyde. A two-step bioconversion process was therefore proposed. In the first step, airborne methylamine was fed into a CFBR which contained immobilized AMO. In the second step, the gas flow was passed through another CFBR, with alcohol oxidase from the yeast H. polymorpha immobilized in CA, in order to decompose the formaldehyde formed in the first step. The proposed system provided almost total elimination of the airborne methylamine and the formaldehyde.\n\nBioconversion of airborne methylamine by immobilized recombinant amine oxidase from the thermotolerant yeast Hansenula polymorpha.", "token_count": 428, "char_count": 1612, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:10.839380", "source": { "split": "train_shard_00000", "doc_id": 4726 }, "chunk_id": "train_shard_00000_4726_0", "global_id": 5281 }, { "text": "Whole cells of different yeast species have been widely used for a number of asymmetric transformations. In the present study, the screening of several yeast strains revealed the utility of Debaryomyces etchellsii in acyloin condensation for (R)-(-)-phenylacetylcarbinol production. Some conditions for the efficient biotransformation of benzaldehyde and minimization in the production of by-products were explored: pH of the reaction medium, use of additives (ethanol or acetonitrile), temperature, time, and substrate concentration and dosing. The optimal conditions found allowed the transformation of up to 10 g/L of the starting material in reactions carried out at high scale. Furthermore, the yeast Kluyveromyces marxianus was seen to be a convenient biocatalyst to carry out the kinetic resolution by the bioreduction of racemic (+/-)-phenylacetylcarbinol, resulting in (S)-(+)-phenylacetylcarbinol with excellent stereoselectivity. Finally, the ketone reduction of both isolated stereoisomers (R and S) by D. etchellsii allowed the obtainment of two of the four diastereoisomers of 1-phenyl-1,2-propanediol. All these compounds are key precursors for the production of interesting pharmaceutical and chemical products.\n\nPotential of some yeast strains in the stereoselective synthesis of (R)-(-)-phenylacetylcarbinol and (S)-(+)-phenylacetylcarbinol and their reduced 1,2-dialcohol derivatives.", "token_count": 386, "char_count": 1403, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6576, "quality_score": 0.8288, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:11.492898", "source": { "split": "train_shard_00000", "doc_id": 4727 }, "chunk_id": "train_shard_00000_4727_0", "global_id": 5282 }, { "text": "Aiming to scale up and apply control and optimization strategies, currently is required the development of accurate plant models to forecast the process nonlinear dynamics. In this work, a mathematical model to predict the growth of the Kluyveromyces marxianus and temperature profile in a fixed-bed bioreactor for solid-state fermentation using sugarcane bagasse as substrate was built up. A parameter estimation technique was performed to fit the mathematical model to the experimental data. The estimated parameters and the model fitness were evaluated with statistical analyses. The results have shown the estimated parameters significance, with 95 % confidence intervals, and the good quality of process model to reproduce the experimental data.\n\nModeling the microbial growth and temperature profile in a fixed-bed bioreactor.", "token_count": 165, "char_count": 832, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:11.950278", "source": { "split": "train_shard_00000", "doc_id": 4728 }, "chunk_id": "train_shard_00000_4728_0", "global_id": 5283 }, { "text": "This study aimed to characterize the in vitro hepatic transport mechanisms in primary rat and human hepatocytes of the fluorescent bile acid derivative N-(24-[7-(4-N,N-dimethylaminosulfonyl-2,1,3-benzoxadiazole)]amino-3α,7α,12α-trihydroxy-27-nor-5β-cholestan-26-oyl)-2'-aminoethanesulfonate (tauro-nor-THCA-24-DBD), previously synthesized to study the activity of the bile salt export pump (BSEP). The fluorescent bile acid derivative exhibited saturable uptake kinetics in suspended rat hepatocytes. Hepatic uptake was inhibited in the presence of substrates/inhibitors of the organic anion transporting polypeptide (Oatp) family and Na(+) -taurocholate cotransporting peptide (Ntcp). Concentration-dependent uptake of the fluorescent bile acid was also saturable in Chinese hamster ovary cells transfected with rNtcp, hNTCP, OATP1B1, or OATP1B3. The fluorescent bile acid derivative was actively excreted in the bile canaliculi of sandwich-cultured rat and human hepatocytes (SCRH and SCHH), with a biliary excretion index (BEI) of 26% and 32%, respectively. In SCRH, cyclosporin A significantly decreased the BEI to 5%. Quantification by real-time confocal imaging further confirmed canalicular transport of the fluorescent bile acid derivative (BEI = 75%). We conclude that tauro-nor-THCA-24-DBD is a useful probe to study interference of drugs with NTCP/Ntcp- and BSEP/Bsep-mediated transport in fluorescence-based in vitro assays.\n\nConfocal imaging with a fluorescent bile acid analogue closely mimicking hepatic taurocholate disposition.", "token_count": 496, "char_count": 1544, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5885, "quality_score": 0.7943, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:12.660856", "source": { "split": "train_shard_00000", "doc_id": 4729 }, "chunk_id": "train_shard_00000_4729_0", "global_id": 5284 }, { "text": "Lipolytic activities of Yarrowia lipolytica LIP2 lipase (YLLIP2), human pancreatic (HPL) and dog gastric (DGL) lipases were first compared using lecithin-stabilized triacylglycerol (TAG) emulsions (Intralipid) at various pH and bile salt concentrations. Like DGL, YLLIP2 was able to hydrolyze TAG droplets covered by a lecithin monolayer, while HPL was not directly active on that substrate. These results were in good agreement with the respective kinetics of adsorption on phosphatidylcholine (PC) monomolecular films of the same three lipases, YLLIP2 being the most tensioactive lipase. YLLIP2 adsorption onto a PC monolayer spread at the air/water interface was influenced by pH-dependent changes in the enzyme/lipid interfacial association constant (KAds) which was optimum at pH 6.0 on long-chain egg PC monolayer, and at pH 5.0 on medium chain dilauroylphosphatidylcholine film. Using substrate monolayers (1,2-dicaprin, trioctanoin), YLLIP2 displayed the highest lipolytic activities on both substrates in the 25-35 mN m(-1) surface pressure range. YLLIP2 was active in a large pH range and displayed a pH-dependent activity profile combining DGL and HPL features at pH values found in the stomach (pH 3-5) and in the intestine (pH 6-7), respectively. The apparent maximum activity of YLLIP2 was observed at acidic pH 4-6 and was therefore well correlated with an efficient interfacial binding at these pH levels, whatever the type of interfaces (Intralipid emulsions, substrate or PC monolayers). All these findings support the use of YLLIP2 in enzyme replacement therapy for the treatment of pancreatic exocrine insufficiency, a pathological situation in which an acidification of intestinal contents occurs.", "token_count": 500, "char_count": 1718, "word_count": 250, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [ "LIP2", "YLLIP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:13.327067", "source": { "split": "train_shard_00000", "doc_id": 4730 }, "chunk_id": "train_shard_00000_4730_0", "global_id": 5285 }, { "text": "An interfacial and comparative in vitro study of gastrointestinal lipases and Yarrowia lipolytica LIP2 lipase, a candidate for enzyme replacement therapy.", "token_count": 42, "char_count": 154, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [ "LIP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:13.694425", "source": { "split": "train_shard_00000", "doc_id": 4730 }, "chunk_id": "train_shard_00000_4730_1", "global_id": 5286 }, { "text": "Bile salt hydrolases (BSHs) are gut microbial enzymes that play a significant role in the bile acid modification pathway. Penicillin V acylases (PVAs) are enzymes produced by environmental microbes, having a possible role in pathogenesis or scavenging of phenolic compounds in their microbial habitats. The correct annotation of such physiologically and industrially important enzymes is thus vital. The current methods relying solely on sequence homology do not always provide accurate annotations for these two members of the cholylglycine hydrolase (CGH) family as BSH/PVA enzymes. Here, we present an improved method [binding site similarity (BSS)-based scoring system] for the correct annotation of the CGH family members as BSH/PVA enzymes, which along with the phylogenetic information incorporates the substrate specificity as well as the binding site information. The BSS scoring system was developed through the analysis of the binding sites and binding modes of the available BSH/PVA structures with substrates glycocholic acid and penicillin V. The 198 sequences in the dataset were then annotated accurately using BSS scores as BSH/PVA enzymes. The dataset presented contained sequences from Gram-positive bacteria, Gram-negative bacteria and archaea. The clustering obtained for the dataset using the method described above showed a clear distinction in annotation of Gram-positive bacteria and Gram-negative bacteria. Based on this clustering and a detailed analysis of the sequences of the CGH family in the dataset, we could infer that the CGH genes might have evolved in accordance with the hypothesis stating the evolution of diderms and archaea from the monoderms.\n\nAn improved method for specificity annotation shows a distinct evolutionary divergence among the microbial enzymes of the cholylglycine hydrolase family.", "token_count": 435, "char_count": 1839, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5843, "quality_score": 0.7921, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:14.325851", "source": { "split": "train_shard_00000", "doc_id": 4731 }, "chunk_id": "train_shard_00000_4731_0", "global_id": 5287 }, { "text": "Infections caused by drug-resistant bacteria are a major problem worldwide. Carbapenem-resistant Klebsiella pneumoniae, most notably isolates classified as multilocus sequence type (ST) 258, have emerged as an important cause of hospital deaths. ST258 isolates are predominantly multidrug resistant, and therefore infections caused by them are difficult to treat. It is not known why the ST258 lineage is the most prevalent cause of multidrug-resistant K. pneumoniae infections in the United States and other countries. Here we tested the hypothesis that carbapenem-resistant ST258 K. pneumoniae is a single genetic clone that has disseminated worldwide. We sequenced to closure the genomes of two ST258 clinical isolates and used these genomes as references for comparative genome sequencing of 83 additional clinical isolates recovered from patients at diverse geographic locations worldwide. Phylogenetic analysis of the SNPs in the core genome of these isolates revealed that ST258 K. pneumoniae organisms are two distinct genetic clades. This unexpected finding disproves the single-clone hypothesis. Notably, genetic differentiation between the two clades results from an ∼ 215-kb region of divergence that includes genes involved in capsule polysaccharide biosynthesis. The region of divergence appears to be a hotspot for DNA recombination events, and we suggest that this region has contributed to the success of ST258 K. pneumoniae. Our findings will accelerate research on novel diagnostic, therapeutic, and vaccine strategies designed to prevent and/or treat infections caused by multidrug resistant K. pneumoniae.\n\nMolecular dissection of the evolution of carbapenem-resistant multilocus sequence type 258 Klebsiella pneumoniae.", "token_count": 426, "char_count": 1741, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6025, "quality_score": 0.8012, "entities": { "genes": [ "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:14.954716", "source": { "split": "train_shard_00000", "doc_id": 4732 }, "chunk_id": "train_shard_00000_4732_0", "global_id": 5288 }, { "text": "Plants now supply more than 50 % of protein in Norwegian salmon aquafeeds. The inclusion of plant protein in aquafeeds may be associated with decreased lipid digestibility and cholesterol and bile salt levels, indicating that the replacement of fishmeal with plant protein could result in inadequate supplies of cholesterol in fish. A reduction in feed efficiency, fish growth and pathogen resistance is often observed in parallel to alterations in sterol metabolism. Previous studies have indicated that the negative effects induced by plant components can be attenuated when diets are supplemented with cholesterol. The present study evaluated the effects of dietary cholesterol supplementation (1·5 %) in Atlantic salmon fed a plant-based diet for 77 d. The weights of body, intestines and liver were recorded and blood, tissues, faeces, chyme and bile were sampled for the evaluation of effects on growth, nutrient utilisation and metabolism, and transcriptome and metabolite levels, with particular emphasis on sterol metabolism and organ structure and function. Cholesterol supplementation did not affect the growth or organ weights of Atlantic salmon, but seemed to promote the induction of cholesterol and plant sterol efflux in the intestine while suppressing sterol uptake. Cholesterol biosynthesis decreased correspondingly and conversion into bile acids increased. The marked effect of cholesterol supplementation on bile acid synthesis suggests that dietary cholesterol can be used to increase bile acid synthesis in fish. The present study clearly demonstrated how Atlantic salmon adjusted their metabolic functions in response to the dietary load of cholesterol. It has also expanded our understanding of sterol metabolism and turnover, adding to the existing, rather sparse, knowledge of these processes in fish.\n\nDietary cholesterol supplementation to a plant-based diet suppresses the complete pathway of cholesterol synthesis and induces bile acid production in Atlantic salmon (Salmo salar L.).", "token_count": 464, "char_count": 2014, "word_count": 293, "semantic_coherence": 1, "information_density": 0.57, "quality_score": 0.785, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:15.588224", "source": { "split": "train_shard_00000", "doc_id": 4733 }, "chunk_id": "train_shard_00000_4733_0", "global_id": 5289 }, { "text": "The differences in the interaction of monoglycerides with bile acids or cholesterol have been investigated from a physico-chemical point of view. A Langmuir trough and fluorescence microscope was used to study mixed monolayers of DL-α-palmitin (a monoglyceride) and cholesterol or deoxycholic acid (a bile acid) at the air/aqueous interface. The surface pressure-area per molecule isotherms of the monolayers were analyzed to give the thermodynamic properties. The deoxycholic acid-DL-α-palmitin monolayer showed stronger repulsions between the film components than was observed with the cholesterol acid-DL-α-palmitin monolayer. Mixed monolayers containing DL-α-palmitin and cholesterol or deoxycholic acid phase separated at high surface pressures and high fractions of DL-α-palmitin, the conditions that resulted in the most repulsions between the two components of the monolayer. The mixed cholesterol and DL-α-palmitin monolayer phase separated in a random pattern. The deoxycholic acid and DL-α-palmitin mixed monolayer gave smaller domains that were distributed in a homogeneous fashion within the monolayer at high molecular packing densities. The difference in the cholesterol and deoxycholic acid interactions with DL-α-palmitin were explained by the fact that while both cholesterol and deoxycholic acid molecules do not pack efficiently with the DL-α-palmitin molecules, the attractive interactions between the alcohol groups on DL-α-palmitin and the carboxylic groups on deoxycholic acid cause attractive interactions between the deoxycholic acid and DL-α-palmitin domains, which causes the interaction abilities of deoxycholic acid with DL-α-palmitin to be higher than cholesterol.\n\nDifferences in the interactions of a monoglyceride with cholesterol and with a bile salt.", "token_count": 465, "char_count": 1786, "word_count": 243, "semantic_coherence": 1, "information_density": 0.4609, "quality_score": 0.7305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:16.232428", "source": { "split": "train_shard_00000", "doc_id": 4734 }, "chunk_id": "train_shard_00000_4734_0", "global_id": 5290 }, { "text": "The mechanisms underlying the effect of epigallocatechin gallate (EGCG) on the micellar solubility of cholesterol were examined. EGCG eliminated both cholesterol and phosphatidylcholine (PC) from bile salt micelles in a dose-dependent manner in vitro. When the bile salt micelles contained a phospholipid other than PC, neither cholesterol nor the phospholipid was eliminated following the addition of EGCG. When vesicles comprised of various phospholipids were prepared and, EGCG was added to the vesicles, EGCG effectively and exclusively eliminated only PC. An intermolecular nuclear Overhauser effect (NOE) was observed between PC and EGCG in bile salt micelles with EGCG added, but not between cholesterol and EGCG, by using a NOE-correlated spectroscopy nuclear magnetic resonance method. The results of binding analyses using surface plasmon resonance (SPR) showed that EGCG did not bind to cholesterol. These observations strongly suggest that EGCG decreases the micellar solubility of cholesterol via specific interaction with PC.\n\nEpigallocatechin gallate decreases the micellar solubility of cholesterol via specific interaction with phosphatidylcholine.", "token_count": 309, "char_count": 1165, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5839, "quality_score": 0.7919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:16.807124", "source": { "split": "train_shard_00000", "doc_id": 4735 }, "chunk_id": "train_shard_00000_4735_0", "global_id": 5291 }, { "text": "Lenalidomide is an immunomodulatory agent used for the treatment of myelodysplastic syndromes and multiple myeloma. Renal clearance of lenalidomide is the predominant elimination route and is approximately twofold greater than the glomerular filtration rate (GFR), suggesting the potential contribution of an active secretory mechanism. In vitro studies were conducted to examine whether lenalidomide is a substrate of drug transporters, namely P-glycoprotein (P-gp), human breast cancer resistance protein (BCRP), multidrug resistance proteins (MRP1, MRP2, MRP3), organic anion transporters (OAT1, OAT3), organic cation transporters (OCT1 and OCT2), human organic cation transporter novel 1 and 2 (OCTN1 and OCTN2), multidrug and toxin extrusion (MATE1) and organic anion transporting polypeptide (OATP1B1). Lenalidomide was also evaluated as an inhibitor of P-gp, BCRP, MRP2, OCT2, OAT1, OAT3, OATP1B1, OATP1B3 and bile salt export pump (BSEP). In addition, inhibition of UDP-glucuronosyltransferase 1A1 (UGT1A1) variants by lenalidomide was also assessed.\n\nThe interactions of lenalidomide with human uptake and efflux transporters and UDP-glucuronosyltransferase 1A1: lack of potential for drug-drug interactions.", "token_count": 381, "char_count": 1217, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.8509, "entities": { "genes": [ "OCT1", "MATE1", "OCTN2", "OCT2", "MRP2", "OAT1", "MRP3", "MRP1", "OCTN1", "OAT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:17.385707", "source": { "split": "train_shard_00000", "doc_id": 4736 }, "chunk_id": "train_shard_00000_4736_0", "global_id": 5292 }, { "text": "Candida kefyr is an emerging pathogen among patients with hematologic malignancies (HM). We performed a retrospective study at Johns Hopkins Hospital to evaluate the epidemiology of C. kefyr colonization and infection in HM patients between 2004 and 2010. Eighty-three patients were colonized and/or infected with C. kefyr, with 8 (9.6%) having invasive candidiasis (IC). The yearly incidence of C. kefyr colonization and candidemia increased over the study period (P < 0.01), particularly after 2009. In 2010, C. kefyr caused 16.7% of candidemia episodes. The monthly incidence of C. kefyr was higher during the summer throughout the study. In a cohort of patients with acute myelogenic leukemia receiving induction chemotherapy, risks for C. kefyr colonization included the summer season (odds ratio [OR], 3.1; P = 0.03); administration of an azole (OR, 0.06; P < 0.001) or amphotericin B (OR, 0.35; P = 0.05) was protective. Fingerprinting of 16 isolates by repetitive sequence-based PCR showed that all were different genotypes. The epidemiology of C. kefyr candidemia was evaluated in another hospital in Montreal, Canada; data confirmed higher rates of C. kefyr infection in the summer. C. kefyr appears to be increasing in HM patients, with prominent summer seasonality. These findings raise questions about the effect of antifungal agents and health care exposures (e.g., yogurt) on the epidemiology of this yeast.\n\nEpidemiology of Candida kefyr in patients with hematologic malignancies.", "token_count": 441, "char_count": 1496, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:18.033166", "source": { "split": "train_shard_00000", "doc_id": 4737 }, "chunk_id": "train_shard_00000_4737_0", "global_id": 5293 }, { "text": "Recently, it has been found that Fructus Schisandra Chinensis (FSC), a Chinese herbal medicine, and its related compounds have a profound impact on lipid metabolism process. FSC can be divided into two parts, i.e., seed and pulp. The current study aimed to examine the effect of aqueous extracts of FSC pulp (AqFSC-P) on serum/hepatic lipid and glucose levels in mice fed with a normal diet (ND) or a high cholesterol/bile salt diet (HCBD).\n\nDietary pulp from Fructus Schisandra Chinensis supplementation reduces serum/hepatic lipid and hepatic glucose levels in mice fed a normal or high cholesterol/bile salt diet.", "token_count": 183, "char_count": 616, "word_count": 97, "semantic_coherence": 1, "information_density": 0.701, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:18.496134", "source": { "split": "train_shard_00000", "doc_id": 4738 }, "chunk_id": "train_shard_00000_4738_0", "global_id": 5294 }, { "text": "The present study was conducted to recover the residual soluble protein after cultivation of yeast (K. marxianus) in cheese whey. Cheese whey continuous fermentation with cell recycle system was carried out at 40 °C and pH 3.5. The yeast biomass was separated from the fermented broth by centrifugation and residual soluble protein from fermented whey supernatant was precipitated by heat treatment (at 100 °C, pH 4.5 and 10 min incubation). The maximum soluble protein recovery up to 53 % was achieved at pH 4.5 with 54 % residual COD removal. However, gravity sedimentable precipitates were obtained at pH 3.5 with 47 % protein recovery. Therefore, the reactor (scale up) study was conducted at pH 3.5 with agitation, which resulted in 68 % of residual soluble protein recovery and simultaneously residual COD removal of 62 %. Further precipitation/coagulation of soluble protein was also evaluated using carboxymethylcellulose (CMC) and then two precipitation (thermal followed by CMC precipitation) processes were combined to increase the protein precipitation, which finally reached up to 81 % of total soluble protein recovery from the supernatant. This optimized process could be applied to recover the residual protein left after fermentation of cheese whey without centrifugation.\n\nRecovery of residual soluble protein by two-step precipitation process with concomitant COD reduction from the yeast-cultivated cheese whey.", "token_count": 389, "char_count": 1431, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5488, "quality_score": 0.7744, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:19.109291", "source": { "split": "train_shard_00000", "doc_id": 4739 }, "chunk_id": "train_shard_00000_4739_0", "global_id": 5295 }, { "text": "The objective of this study was to evaluate the probiotic properties of Lactobacillus strains isolated from mother's milk and their effects on cholesterol assimilation. In this study 120 isolates from mother's milk were phenotypically and genotypically characterized. Among these, only 6 predominant strains were identified as Lactobacillus spp. The following parameters were selected as important test variables in model stomach passage survival trials: acid and bile tolerance, antimicrobial activity, antibiotic susceptibility and cholesterol reduction. Results showed that the considerable variation existed among six strains. Moreover, the strain HMI68 is the most acid-tolerant and the HMI28 and HMI74 is the most acid-sensitive of all strains tested. HMI118 did not grow at 0.5% and 1% bile concentration after 5 h but the HMI68 and HMI43 showed some tolerance to such bile concentration. The differences found in the growth rate were not significant (P > 0.05). HMI68 showed resistance to most of the antibiotics as well as antagonistic activity against the tested pathogens. The amount of cholesterol reduction is increased when the media supplemented with bile salts. HMI68 assimilate 61.05 ± 0.05 μg/ml cholesterol with the presence of 0.3% bile salt this could be significantly decreased by 25.41 ± 1.09 μg/ml without bile salt. HMI68 was identified to be Lactobacillus oris HMI68 and 16S rRNA sequence was deposited in the National Center for Biotechnological Information (GenBank). For the first time the cholesterol-reducing property of L. oris isolated from mother's milk were investigated in this study. Therefore the effective L. oris HMI68 strain was regarded as a candidate probiotic.\n\nIsolation of potential probiotic Lactobacillus oris HMI68 from mother's milk with cholesterol-reducing property.", "token_count": 495, "char_count": 1818, "word_count": 268, "semantic_coherence": 1, "information_density": 0.597, "quality_score": 0.7985, "entities": { "genes": [ "HMI28", "HMI74", "HMI118", "HMI68", "HMI43" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:19.758245", "source": { "split": "train_shard_00000", "doc_id": 4740 }, "chunk_id": "train_shard_00000_4740_0", "global_id": 5296 }, { "text": "In the present study bacterial strains were isolated from the rumen fluids of Bos primigenius and investigated their in vitro probiotic properties with potent antibacterial activity and anti-inflammatory effects. 9 g positive bacterial isolates were obtained and three isolates could able to tolerate gastric conditions, high bile salt concentrations and exhibited significant bactericidal effect against the enteric pathogens Vibrio cholera, Enterococcus faecalis, Enterobacter aerogens, Pseudomonas aeruginosa, Escherichia coli and Salmonella typhi. Moreover it showed above 70% cell surface hydrophobicity, significant low-invasion ability and potential adherence capacity in Caco-2 cells when compared with the control. The proinflammatory cytokines (TNF-α) was greatly reduced in rumen bacteria treatment and ARBS-1 modulate the immune response by activating the IL-4 secretion in parallel to TNF-α suppression. The 16s rRNA gene sequence of the active isolates were identified as Enterococcus hirae (ARBS-1), Pediococcus acidilactici (ARBS-4) and Bacillus licheniformis (ARBS-7). This study revealed the probiotic bactericidal properties of E. hirae obtained from the rumen of B. primigenius with potential antibacterial and anti-inflammatory effects. Future studies with the strains may yield some novel probiotic product for livestock's.\n\nAntibacterial, anti-inflammatory and probiotic potential of Enterococcus hirae isolated from the rumen of Bos primigenius.", "token_count": 389, "char_count": 1469, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6598, "quality_score": 0.8299, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:20.377769", "source": { "split": "train_shard_00000", "doc_id": 4741 }, "chunk_id": "train_shard_00000_4741_0", "global_id": 5297 }, { "text": "Kluyveromyces marxianus is a traditional fermentation starter, but the effects of K. marxianus fermentation on tomato remain largely unknown. Here, K. marxianus was employed for tomato puree fermentation under sterile conditions. Sensory evaluation revealed that K. marxianus decreased the unpleasant flavor components in fermented tomato puree (FTP). GC–MS analysis demonstrated that K. marxianus fermentation improved the flavor and aroma, primarily due to increases in alcohols (48.84 %) and esters (43.31 %) and enrichment of aroma-associated metabolites in volatile organic compounds. Widely targeted metabolomics showed that the fermentation significantly increased 37 phenolic compounds, potentially enhancing the antioxidant effects of FTP. The contents of lycopene isomers including cis-lycopene significantly increased in FTP (179.52 μg/g). Notably, FTP showed enrichment of beneficial genera, including Akkermansia and Pediococcus, in fecal microbiota. Collectively, these results indicate that K. marxianus fermentation is a viable approach to improving the sensory profile and potential health benefits of fermented tomato.\n\nKluyveromyces marxianus fermenta tion improves tomato sensory profile, functional metabolites, lycopene bioaccessibility, and human fecal microbiota composition", "token_count": 346, "char_count": 1298, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6407, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:20.962581", "source": { "split": "train_shard_00000", "doc_id": 4742 }, "chunk_id": "train_shard_00000_4742_0", "global_id": 5298 }, { "text": "Abstract

Eukaryotic chromosome segregation requires spindle microtubules to attach to chromosomes through kinetochores. The chromosomal locus that mediates kinetochore assembly is the centromere and is epigenetically specified in most organisms by a centromeric histone H3 variant called CENP-A. An exception to this is budding yeast which have short, sequenced-defined point centromeres. In S. cerevisiae, a single CENP-A nucleosome is formed at the centromere and is sufficient for kinetochore assembly. The thermophilic budding yeast Kluyveromyces marxianus also has a point centromere but its length is nearly double the S. cerevisiae centromere and the number of centromeric nucleosomes and kinetochore attachment sites is unknown. Purification of native kinetochores from K. marxianus yielded a mixed population, with one subpopulation that appeared to consist of doublets, making it unclear whether K. marxianus shares the same attachment architecture as S. cerevisiae. Here, we demonstrate that though the doublet kinetochores have a functional impact on kinetochore strength, kinetochore localization throughout the cell cycle appears conserved between these two yeasts. In addition, whole spindle electron tomography demonstrates that a single microtubule binds to each chromosome. Single-molecule nucleosome mapping analysis suggests the presence of a single centromeric nucleosome. Taken together, we propose that the K. marxianus point centromere assembles a single centromeric nucleosome that mediates attachment to one microtubule.

\n\nCentromeres in the thermotolerant yeast K. marxianus mediate attachment to a single microtubule", "token_count": 487, "char_count": 1785, "word_count": 224, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:21.613690", "source": { "split": "train_shard_00000", "doc_id": 4743 }, "chunk_id": "train_shard_00000_4743_0", "global_id": 5299 }, { "text": "Kluyveromyces marxianus (K. marxianus) has emerged as a prominent microbial platform owing to its exceptional intrinsic properties, demonstrating significant potential for biomanufacturing. A literature search with the keyword 'Kluyveromyces marxianus' in title in the PubMed database indicated that the yeast has been developed as a microbial cell factory for lignocellulosic biomass valorization, heterologous protein production, flavor and fragrance molecule synthesis during the past 10 years. However, the most recent review of K. marxianus application in food industry was 5 years ago. The relatively slow progression is partially due to the paucity of molecular tools and the lagging advancements in process optimization strategies. This review summarizes the physiological characteristics of K. marxianus and its potential industrial applications. Addressing the requirements of industrial-scale production, key limiting factors in high-cell-density fermentation, including carbon source utilization efficiency, dissolved oxygen regulation, and inhibition by metabolic byproducts were analyzed. An integrated approach combining dynamic feeding, metabolic pathway engineering, and fermentation parameter optimization was proposed. Considering the previous reviews, the present work updated the application of K. marxianus in the food industry, including the production of enzymes, sugars, aromatic compounds, single-cell protein, and transformation of food waste, as well as the treatment of wastewater during food processing, and aims to make a comprehensive discussion. Through the systematic construction of the research paradigm from molecular constraints to process hurdles, the work may help the transition of K. marxianus for efficient manufacturing and processing in the food industry.\n\nFrom genetic constraints to process hurdles: A review of <i>Kluyveromyces marxianus</i> for efficient bio-manufacturing and bio-processing in food industry.", "token_count": 484, "char_count": 2040, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:23.075613", "source": { "split": "train_shard_00000", "doc_id": 4744 }, "chunk_id": "train_shard_00000_4744_0", "global_id": 5300 }, { "text": "Monoterpenes are valued for their roles as flavors, fragrances, insecticides, and energy-dense fuels. Microorganisms provide sustainable biosynthesis routes for these important molecules, but production levels remain limited. Here, we introduce a biosensor-driven microbial engineering strategy to enhance monoterpene production, specifically targeting geraniol. Using mutagenized libraries of the PYR1 receptor─a versatile biosensor from plant ABA signaling pathways with a malleable binding pocket─we screened 24 monoterpenes and identified PYR1 variants responsive to eight, including geraniol. A low background, highly selective geraniol-sensitive PYR1 variant was expressed in the thermotolerant yeast Kluyveromyces marxianus as a growth-based biosensor circuit, allowing for rapid strain engineering. By coupling the geraniol-sensitive PYR1 sensor with a genome-wide CRISPR-Cas9 mutagenesis approach, we identified six gene knockouts that enhance geraniol production, achieving up to a 2-fold increase in titer. This study demonstrates the power of the PYR1 biosensor platform to enable rapid strain engineering and the identification of mutants that improve the titer of a desired metabolite.\n\nPYR1 Biosensor-Driven Genome-Wide CRISPR Screens for Improved Monoterpene Production in <i>Kluyveromyces marxianus</i>.", "token_count": 358, "char_count": 1339, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [ "PYR1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:23.685928", "source": { "split": "train_shard_00000", "doc_id": 4745 }, "chunk_id": "train_shard_00000_4745_0", "global_id": 5301 }, { "text": "Kluyveromyces marxianus is a promising thermotolerant yeast for industrial biotechnology, but lacks efficient genome engineering tools. A CRISPR/Cas12a genome editing toolbox for K. marxianus was developed for the first time in this study. A plasmid-free transient system achieved single-gene knockout efficiencies of about 50 %-100 % in Δku70 strain. Even with homology arms as short as 35 bp, the knockout efficiency remained 66.67 %. Chromosomal integration of Cas12a enabled single-to-triple fragment knock-ins efficiency of 82.93-85.70 % and 94.50 % for large fragment (>5 kb) integrations. Applying this system, the roles of succinate dehydrogenase (SDH) genes SDH1-SDH5 were elucidated. Combinatorial SDH genes knockouts redirected carbon flux toward succinic acid (SA), but increased glycerol/acetate byproducts. Subsequent GPD1/ACH1/ADH2A co-knockout in a Δsdh1,3,5,4A,2 strain with NDE1 overexpression (YZH43) yielded a chassis producing 32.38 g/L SA from glucose at 37 °C, which is the highest reported titer in K. marxianus, while reducing ethanol, acetate, and glycerol by 60.79 %, 89.24 %, and 67.5 %, respectively. At 46 °C, YZH43 produced 20.51 g/L SA through simultaneous saccharification and fermentation (SSF) using cellulose as substrate", "token_count": 508, "char_count": 1341, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7865, "quality_score": 0.8933, "entities": { "genes": [ "NDE1", "SDH1", "ACH1", "SDH5", "GPD1", "YZH43", "ADH2A" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:24.371555", "source": { "split": "train_shard_00000", "doc_id": 4746 }, "chunk_id": "train_shard_00000_4746_0", "global_id": 5302 }, { "text": "This work provides a high-efficiency CRISPR/Cas12a platform for K. marxianus, enabling rapid metabolic engineering for value-added chemical production, and demonstrates its utility in developing thermotolerant SA-overproducing strains.\n\nDevelopment of a CRISPR/Cas12a genome editing toolbox in <i>Kluyveromyces marxianus</i> and its application in succinic acid biosynthesis.", "token_count": 124, "char_count": 394, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8409, "quality_score": 0.9205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:24.792987", "source": { "split": "train_shard_00000", "doc_id": 4746 }, "chunk_id": "train_shard_00000_4746_1", "global_id": 5303 }, { "text": "Eukaryotic chromosome segregation requires spindle microtubules to attach to chromosomes through kinetochores. The chromosomal locus that mediates kinetochore assembly is the centromere and is epigenetically specified in most organisms by a centromeric histone H3 variant called CENP-A. An exception to this is budding yeast which have short, sequenced-defined point centromeres. In S. cerevisiae , a single CENP-A nucleosome is formed at the centromere and is sufficient for kinetochore assembly. The thermophilic budding yeast Kluyveromyces marxianus also has a point centromere but its length is nearly double the S. cerevisiae centromere and the number of centromeric nucleosomes and kinetochore attachment sites is unknown. Purification of native kinetochores from K. marxianus yielded a mixed population, with one subpopulation that appeared to consist of doublets, making it unclear whether K. marxianus shares the same attachment architecture as S. cerevisiae. Here, we demonstrate that though the doublet kinetochores have a functional impact on kinetochore strength, kinetochore localization throughout the cell cycle appears conserved between these two yeasts. In addition, whole spindle electron tomography demonstrates that a single microtubule binds to each chromosome. Single-molecule nucleosome mapping analysis suggests the presence of a single centromeric nucleosome. Taken together, we propose that the K. marxianus point centromere assembles a single centromeric nucleosome that mediates attachment to one microtubule.\n\nCentromeres in the thermotolerant yeast K. marxianus mediate attachment to a single microtubule", "token_count": 425, "char_count": 1642, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6205, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:25.423915", "source": { "split": "train_shard_00000", "doc_id": 4747 }, "chunk_id": "train_shard_00000_4747_0", "global_id": 5304 }, { "text": "

ABSTRACT

Organic acids such as fumaric acid are widely used in the food and beverage industry as acidulants and preservatives, while also serving as versatile precursors for industrially relevant compounds. Fumaric acid is still predominantly produced through petroleum-derived processes. To enhance production efficiency and diversify supply, we are engineering Kluyveromyces marxianus as a biosynthetic platform from renewable feedstocks. In previous work, we have established K. marxianus Y-1190 as a host for lactose valorization based on its high growth rate on lactose and its tolerance for acid conditions. Here, we establish a trifunctional genome-wide library for K. marxianus using CRISPR activation, interference, and deletion to allow identification of gene expression perturbations that enhance tolerance to fumaric acid. We determined that deletion of ATP7 , encoding a subunit of the mitochondrial F 1 F 0 ATP synthase, and overexpression of QDR2 and QDR3 , two previously uncharacterized members of the 12-spanner H⁺ antiporter (DHA1) family in K. marxianus, can enhance fumaric acid tolerance. We also found that integrated overexpression of both QDR2 and QDR3 in a Δ FUM1 background strain improved titers of fumaric acid production from 0.26 g L −1 to 2.16 g L −1 . Together, these results highlight roles for membrane transport and mitochondrial function in enabling fumaric acid tolerance and production in K. marxianus .

HIGHLIGHTS

- Trifunctional CRISPR-AID enables gene activation, interference & deletion in K. marxianus . - Genome-wide CRISPR-AID screen identifies guides conferring fumaric acid tolerance. - verexpressing of QDR2 and QDR3 increases fumaric acid tolerance and production. - Deletion of mitochondrial gene ATP7 significantly improves fumaric acid tolerance", "token_count": 495, "char_count": 1818, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5682, "quality_score": 0.7841, "entities": { "genes": [ "DHA1", "FUM1", "ATP7", "QDR3", "QDR2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:26.075747", "source": { "split": "train_shard_00000", "doc_id": 4748 }, "chunk_id": "train_shard_00000_4748_0", "global_id": 5305 }, { "text": "- Fermentation of QDR2 and QDR3 overexpression strain yields 2.16 g L⁻¹ fumaric acid.\n\nTri-Functional CRISPR Screen Reveals Overexpression of QDR2 and QDR3 Transporters Increase Fumaric Acid Production in Kluyveromyces marxianus", "token_count": 97, "char_count": 249, "word_count": 31, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [ "QDR3", "QDR2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:26.454926", "source": { "split": "train_shard_00000", "doc_id": 4748 }, "chunk_id": "train_shard_00000_4748_1", "global_id": 5306 }, { "text": "

Background

Kluyveromyces marxianus, formerly known as Candida kefyr, is an emerging opportunistic yeast increasingly reported in immunocompromised hosts. This review aims to summarize the clinical presentations, diagnostic approaches, treatment strategies, and outcomes of C. kefyr infections among transplantation recipients through an analysis of published case reports. A comprehensive literature search was performed using PubMed, Scopus, and Web of Science for case reports involving transplantation patients infected with C. kefyr. The review included only individual case reports describing invasive fungal infections in solid organ or hematopoietic stem cell transplant recipients. A total of seven case reports were identified. Clinical presentations included fungemia, keratitis and catheter-related bloodstream infections. Median age was 61.0. Most of the case had neutropenia and consumption of dairy products. Also, the ratio of localized organ involvement is higher. C. kefyr should be considered a potential opportunistic pathogen in transplant recipients, particularly in older or neutropenic patients with regular dairy consumption. Early diagnosis and appropriate antifungal therapy are essential for favorable outcomes.\n\nCandida kefyr as an emerging cause of invasive fungal infection in transplant patients: Case report and literature review.", "token_count": 302, "char_count": 1370, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:27.026351", "source": { "split": "train_shard_00000", "doc_id": 4749 }, "chunk_id": "train_shard_00000_4749_0", "global_id": 5307 }, { "text": "Kluyveromyces marxianus exhibits advantages such as strong thermotolerance, rapid growth rate, and high safety, making it an excellent host cell for the production of bio-based products. In this study, two exopolysaccharides, KE1 and KE2, were isolated from the fermentation broth of the strain K. marxianus KM-502, and their hydroxyl radical scavenging, DPPH scavenging, and Fe2+-reducing activities were evaluated. In vitro antioxidant assays demonstrated that exopolysaccharide KE2 exhibited superior antioxidant activity compared to KE1. The fermentation conditions were optimized using single-factor experiments followed by response surface methodology (RSM). The optimized fermentation process revealed that the most suitable fermentation medium consisted of 8% sucrose, 1.99% peptone, and 0.13% CaCl2, while the optimal fermentation conditions were a medium volume of 74 mL in a 300 mL flask, pH 6.7, an inoculum size of 1.99%, a temperature of 30 °C, a shaking speed of 160 r/min, and a cultivation time of 96 h. After optimizing the fermentation conditions of K. marxianus KM-502, the exopolysaccharide (EPS) yield reached 5842.42 mg/L, representing a 22.77-fold increase compared to the yield before optimization. In summary, this study isolated exopolysaccharides KE1 and KE2 from K. marxianus KM-502. These exopolysaccharides demonstrated significant antioxidant activities, and the fermentation conditions for exopolysaccharide production were optimized. The findings of this study will facilitate the further development and utilization of exopolysaccharides from K. marxianus.", "token_count": 502, "char_count": 1648, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [ "KE2", "KE1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:27.677890", "source": { "split": "train_shard_00000", "doc_id": 4750 }, "chunk_id": "train_shard_00000_4750_0", "global_id": 5308 }, { "text": "A Study on the Extraction, Fermentation Condition Optimization, and Antioxidant Activity Assessment of Polysaccharides Derived from <i>Kluyveromyces marxianus</i>.", "token_count": 58, "char_count": 175, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:28.035704", "source": { "split": "train_shard_00000", "doc_id": 4750 }, "chunk_id": "train_shard_00000_4750_1", "global_id": 5309 }, { "text": "Abstract

Background: This study investigated the potential role of solid-state fermentation (SSF) to enhance the in vitro and in vivo antioxidant activities of olive pomace (OP, the environmentally polluting solid residue produced after olive oil extraction) using the GRAS (Generally Recognized As Safe) yeast Kluyveromyces marxianus. Fermented OP (FOP) was produced by SSF of OP by K. marxianus. Both unfermented OP (UFOP) and FOP were extracted using methanol. Results: FOP methanolic extract (FOPME) demonstrated significantly higher antioxidant activity than UFOP methanolic extract (UFOPME) in ABTS radical scavenging, metal chelating, H2O2 scavenging, lipid peroxidation inhibition, reducing power, and total antioxidant capacity. On the other hand, UFOPME demonstrated slightly higher superoxide anion radical scavenging and RBCs-protecting activities than FOPME. Prophylactic and therapeutic antioxidant activities of UFOPME and FOPME were assessed in vivo against oxidative stress associated with diethylnitrosamine (DENA)-induced hepatocellular carcinoma (HCC) in rats. Relative to the normal group, the administration of DENA/CCl4 in the HCC group significantly increased hepatic nitric oxide and malondialdehyde and significantly decreased total antioxidant concentration. Both UFOPME and FOPME protected against and relieved the oxidative stress associated with DENA/CCl4-induced HCC in rats. Conclusion: SSF of OP using the GRAS yeast K", "token_count": 500, "char_count": 1646, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6392, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:29.049130", "source": { "split": "train_shard_00000", "doc_id": 4751 }, "chunk_id": "train_shard_00000_4751_0", "global_id": 5310 }, { "text": "marxianus significantly enhanced most of its in vitro antioxidant activities alongside demonstrating simultaneous protective/therapeutic effects against oxidative stress associated with DENA/CCl4-induced HCC in rats.

\n\nEnhanced in vitro and in vivo antioxidant activities of olive pomace by solid- state fermentation using the yeast Kluyveromyces marxianus", "token_count": 116, "char_count": 396, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8409, "quality_score": 0.9205, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:29.431592", "source": { "split": "train_shard_00000", "doc_id": 4751 }, "chunk_id": "train_shard_00000_4751_1", "global_id": 5311 }, { "text": "Endogenous pathway dysregulation in Kluyveromyces marxianus under nitrogen limitation drives 2-phenylethyl acetate and 2-phenylethanol overproduction.", "token_count": 46, "char_count": 150, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:29.794054", "source": { "split": "train_shard_00000", "doc_id": 4752 }, "chunk_id": "train_shard_00000_4752_0", "global_id": 5312 }, { "text": "Kluyveromyces marxianus is an attractive chassis for microbial cell factories due to its rapid growth, thermotolerance, and wide substrate spectrum. However, gene disruption in this organism is challenging primarily due the prevalence of dominant nonhomologous recombination. AsCas12f1, a hypercompact CRISPR-associated protein consisting of 422 amino acids—approximately one-third the size of Cas9 or Cas12a—enables more efficient packaging into delivery vehicles than its larger counterparts. In this study, a gene disruption method using AsCas12f1 was established in K. marxianus through a transient targeting strategy. The integration of tRNA-gRNA into the gRNA construct increased gene disruption efficiency. Additionally, disrupting KmKU70 or KmLIG4 further increased this efficiency, achieving nearly 100%. By combining the disruption of KmKU70 with the AsCas12f1 system, the length of the homologous arm was shortened to 200 bp while maintaining a disruption efficiency of 87.5%. The implementation of the gRNA-tRNA-array system resulted in the successful generation of three single-gene knockout strains from a single transformation, resulting an overall efficiency of 86.4%. This approach leverages the transient transformation of fragments, eliminates the need for extensive time investment in constructing gRNA expression vectors and negates the requirement for the removal of the CRISPR-AsCas12f1 system after gene disruption. This study presents a novel strategy for gene disruption in K. marxianus and demonstrates the applicability of Cas12f in yeast systems.\n\nGene disruption via a transient hypercompact CRISPR-AsCas12f1 system in Kluyveromyces marxianus", "token_count": 431, "char_count": 1672, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:30.419669", "source": { "split": "train_shard_00000", "doc_id": 4753 }, "chunk_id": "train_shard_00000_4753_0", "global_id": 5313 }, { "text": "Reproductive barriers and genomic structural differences hinder genetic analysis between highly divergent organisms. Here, we examined whether these challenges can be overcome by collinearization, the synthesis of chromosomes that retain the native gene content and organization of a host organism while incorporating the DNA sequences of another organism. We applied collinearization to Kluyveromyces marxianus , a yeast species that is both distantly related to and has a distinct genome structure from the model yeast Saccharomyces cerevisiae . We generated a ∼35-kb K. marxianus DNA segment that was collinear with one-sixth of a S. cerevisiae chromosome and contained 17 protein-coding genes. Although this synthetic chromosome segment successfully substituted for its native counterpart in an S. cerevisiae cell, it imposed a significant growth cost due to the incompatibility of two K. marxianus proteins with the host proteome. We predicted the disrupted protein-protein interactions using AlphaFold and alleviated their cost by supplementing orthologous protein partners from K. marxianus . Furthermore, we completely eliminated the growth cost by replacing the two incompatible K. marxianus genes with their S. cerevisiae orthologs. These findings demonstrate that collinearization can facilitate the creation of chimeric genomes to dissect the genetic basis of incompatibility and traits between organisms that cannot naturally hybridize. They also suggest that hundreds of genetic incompatibilities exist between S. cerevisiae and K. marxianus , reflecting disrupted protein-protein interactions that may be predictable in silico .\n\nSynthetic collinearization of a chromosome segment enables genetic dissection of incompatibility between distant genera", "token_count": 398, "char_count": 1764, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:31.036671", "source": { "split": "train_shard_00000", "doc_id": 4754 }, "chunk_id": "train_shard_00000_4754_0", "global_id": 5314 }, { "text": "The use of genetically modified nonconventional yeast provides significant potential for the bioeconomy by diversifying the tools available for the development of sustainable and novel products. In this study, we sequenced and annotated the genome of Kluyveromyces marxianus Y-1190 to establish it as a platform for lactose valorization. The strain was chosen for rapid growth on lactose-rich dairy permeate, high transformation efficiency, and ease of culturing in bioreactors. Genomic sequencing revealed that K. marxianus Y-1190 possesses single nucleotide polymorphisms associated with efficient lactose metabolism. The strain is diploid with notable genomic heterogeneity, which appears to be critical for its robust growth and acid tolerance. To further exploit this platform strain, we developed protocols for gene and chromosome manipulation using CRISPR editing, constructed and validated a series of promoters compatible with MoClo vectors, and designed synthetically inducible promoters for K. marxianus. These tools enable precise control over gene expression, allowing for the tailored optimization of metabolic pathways and production processes. The synthetic promoters provide flexibility for dynamic expression tuning, while the CRISPR-based editing protocols facilitate targeted genetic modifications with high efficiency. Together, these advancements significantly enhance the genetic toolbox for K. marxianus, positioning it as a versatile platform for industrial biotechnology. These tools open new opportunities for the sustainable production of biobased chemicals, fuels, and high-value products, leveraging lactose-rich feedstocks to contribute to a circular economy.\n\nSequencing of a Dairy Isolate Unlocks <i>Kluyveromyces marxianus</i> as a Host for Lactose Valorization.", "token_count": 439, "char_count": 1836, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6527, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:31.670014", "source": { "split": "train_shard_00000", "doc_id": 4755 }, "chunk_id": "train_shard_00000_4755_0", "global_id": 5315 }, { "text": "The increasing interest in renewable feedstocks for biochemicals production includes the valorization of cheese whey (CW), a by-product of the dairy industry. CW contains a high concentration of lactose, accounting for most of its organic load, making it a major environmental pollutant if untreated. A valorization approach of CW is based on the separation of valuable proteins by ultrafiltration, and the obtainment of a lactose-rich cheese whey permeate (CWP). The conversion of lactose in CWP into bioethanol is considered a sustainable solution for the valorization of this waste. However, lactose is not metabolized by the yeast species Saccharomyces cerevisiae, namely the most industrially used microorganism, to produce bioethanol. Differently, the non-conventional yeast Kluyveromyces marxianus shows high growth rates on a broad range of industrially relevant substrates, including lactose. This study provides a comprehensive physiological characterization of three K. marxianus strains (DSM 5422, DSM 7239, and DSM 5572) to evaluate their potential for lactose hydrolysis and fermentation in order to produce advanced bioethanol from CWP. Microplate growth tests, β-galactosidase activity assays, and flask fermentations were carried out to identify optimal strains for efficient CWP valorization, advancing the applications of K. marxianus in industrial biotechnology. The optimal conditions for lactose utilization and ethanol production were identified as 130 g/L of lactose at 42 °C in semi-synthetic media (SSM)", "token_count": 423, "char_count": 1557, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:32.299293", "source": { "split": "train_shard_00000", "doc_id": 4756 }, "chunk_id": "train_shard_00000_4756_0", "global_id": 5316 }, { "text": "Even though strain DSM 7239 showed the highest β-galactosidase activity of 27.8 ± 0.9 U mg-1, strains DSM 5422 and 5572 were identified as the best performing strains at shake flask experiments in terms of ethanol yield on the substrate, with 0.48 ± 0.03 g/g and 0.50 ± 0.03 g/g, respectively, after 1 day of fermentation.\n\nPhysiological characterization of <i>Kluyveromyces marxianus</i> strains for the development of a microbial platform to obtain bioethanol from cheese whey permeate.", "token_count": 182, "char_count": 511, "word_count": 76, "semantic_coherence": 1, "information_density": 0.8158, "quality_score": 0.9079, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:32.737719", "source": { "split": "train_shard_00000", "doc_id": 4756 }, "chunk_id": "train_shard_00000_4756_1", "global_id": 5317 }, { "text": "This study aimed to investigate the exploitation of Kluyveromyces marxianus FM09 to enhance gamma-aminobutyric acid levels in cheese. Cheese samples were manufactured using a commercial starter of Lacticaseibacillus casei (CC) as the control and a mixed starter culture of CC and K. marxianus FM09. Cheeses were analyzed for GABA content and the concentration of succinic acid. Moreover, the expression of genes related to GABA metabolism was evaluated. A stronger proteolysis and a higher pH characterized cheeses obtained with the mixed-starter culture. Significant increases in cheese GABA content were measured within cheeses obtained with K. marxianus, which reached 512 mg/kg after 30 days, representing an 81 % increase compared with the control. GAD gene expression and GABA accumulation reached their maximum value after 20 days. The sensory analysis revealed that the cheeses obtaiened with K. marxianus showed increased fruity, floral, creamy notes. The obtained data suggested that K. marxianus FM09 could be used for the production of GABA-enriched cheeses featuring improved sensory quality. This work supports K. marxianus as a promising candidate in developing functional fermented dairy products with potential health benefits.\n\nA functional approach to cheese production: Boosting gamma-aminobutyric acid content with Kluyveromyces marxianus", "token_count": 341, "char_count": 1359, "word_count": 194, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [ "FM09" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:33.313301", "source": { "split": "train_shard_00000", "doc_id": 4757 }, "chunk_id": "train_shard_00000_4757_0", "global_id": 5318 }, { "text": "Coffee cherry pulp (CCP), a coffee by-product rich in pectin and phenolic compounds, serves as a valuable substrate for microbial enzyme production, improving the nutritional and antioxidant properties of poultry feed. This study evaluated the potential of Kluyveromyces marxianus ST5 to produce pectin-degrading enzymes using CCP. Under unoptimized conditions, the pectin lyase (PL) and polygalacturonase (PG) activities were 3.29 ± 0.22 and 6.32 ± 0.13 U/mL, respectively. Optimization using a central composite design (CCD) identified optimal conditions at 16.81% (w/v) CCP, 5.87% (v/v) inoculum size, pH 5.24, and 30 °C for 48 h, resulting in PL and PG activities of 9.17 ± 0.20 and 15.78 ± 0.14 U/mL, representing increases of 178.7% and 149.7% over unoptimized conditions. Fermented CCP was further evaluated using an in vitro chicken gastrointestinal digestion model. Peptide release increased by 66.2% compared with unfermented CCP. Antioxidant capacity also improved, with significant increases observed in DPPH (32.4%), ABTS (45.0%), and FRAP (42.3%) assays, along with an 11.1% increase in total phenolic content. These results demonstrate that CCP bioconversion by K. marxianus ST5 enhances digestibility and antioxidant properties, supporting its potential as a sustainable poultry feed additive and contributing to the valorization of agro-industrial waste.", "token_count": 468, "char_count": 1413, "word_count": 197, "semantic_coherence": 1, "information_density": 0.736, "quality_score": 0.868, "entities": { "genes": [ "ST5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:33.956676", "source": { "split": "train_shard_00000", "doc_id": 4758 }, "chunk_id": "train_shard_00000_4758_0", "global_id": 5319 }, { "text": "Valorization of Coffee Cherry Pulp into Potential Functional Poultry Feed Additives by Pectinolytic Yeast <i>Kluyveromyces marxianus</i> ST5.", "token_count": 58, "char_count": 153, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:34.327749", "source": { "split": "train_shard_00000", "doc_id": 4758 }, "chunk_id": "train_shard_00000_4758_1", "global_id": 5320 }, { "text": "Microalgae are promising feedstocks, holding great potential for bioethanol production. However, microalgal bioethanol production requires the use of different approaches in order to optimize the process. In this study, the bioethanol production capacities of local yeasts (Saccharomyces cerevisiae, Candida boidinii and Kluyveromyces marxianus) from Chlorella vulgaris biomass cultivated with 0.5 g/L carrot pomace sugar was investigated. Onion peel, a common waste product, was used for investigating its potential in improving yeast growth and bioethanol production by K. marxianus. Parameters such as biomass loading (50-200 g/L), onion peel waste concentration (1%-5%), and supplement types (nitrogen sources and mineral salts such as peptone, yeast extract, MgSO4, KH2PO4, CaCl2, ZnSO4) were optimized. Among local yeasts, K. marxianus demonstrated the highest bioethanol production and productivity with a measured value of 4.29 ± 0.25 g/L and 0.36 g/L.h, respectively. Bioethanol concentration and productivity increased to 6.98 ± 0.12 g/L and 0.58 g/L.h, respectively, when 200 g/L biomass loading and 3% onion peel concentration was used. This study demonstrates the high potential of K. marxianus in metabolizing microalgal carbohydrates and the utilization potential of food waste as an inexpensive nutrient source in the fermentation medium.", "token_count": 485, "char_count": 1451, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6508, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:34.990560", "source": { "split": "train_shard_00000", "doc_id": 4759 }, "chunk_id": "train_shard_00000_4759_0", "global_id": 5321 }, { "text": "Improvement of third generation bioethanol production from photoheterotrophically cultivated <i>Chlorella vulgaris</i> in the presence of carrot pomace and onion peel waste.", "token_count": 56, "char_count": 185, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:35.391398", "source": { "split": "train_shard_00000", "doc_id": 4759 }, "chunk_id": "train_shard_00000_4759_1", "global_id": 5322 }, { "text": "Engineering a modular pectin-to-lipids bioconversion system using two Kluyveromyces marxianus strains", "token_count": 30, "char_count": 101, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:35.774732", "source": { "split": "train_shard_00000", "doc_id": 4760 }, "chunk_id": "train_shard_00000_4760_0", "global_id": 5323 }, { "text": "Kluyveromyces marxianus is a yeast widely used in the dairy industry and frequently isolated from vineyards and wineries. Its capacity to metabolize diverse sugars makes it highly promising for winemaking applications. We report the draft genome sequence of the K. marxianus strain U848.\n\nDraft genome sequences of Kluyveromyces marxianus strain U848 isolated from Agave sisalana.", "token_count": 127, "char_count": 408, "word_count": 55, "semantic_coherence": 1, "information_density": 0.7818, "quality_score": 0.8909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:36.172720", "source": { "split": "train_shard_00000", "doc_id": 4761 }, "chunk_id": "train_shard_00000_4761_0", "global_id": 5324 }, { "text": "This study investigated the effects of the inoculation of synthetic microbial communities (SynComs), including Staphylococcus carnosus, Lactiplantibacillus plantarum, Bacillus coagulans, and Kluyveromyces marxianus, on the safety, texture, taste, and flavor profiles of slightly fermented dried bonito. The results showed that all slightly fermented samples contained very low levels of total volatile base nitrogen and histamine, the fish proteins underwent acid denaturation and coagulation after fermentation, forming a dense and stable three-dimensional network structure that contributed to the appearance of the final products. A synergistic effect among S. carnosus, L. plantarum, and K. marxianus not only reduced the bitterness scores of the e-tongue, but also enhanced the umami and sweetness taste of dried bonito products by increasing the contents of pleasant tasting amino acids, with the equivalent umami concentration 1.89 times (p < 0.05) higher than control group. In addition, a linear relationship was observed between the amount of flavor compounds produced by lipid oxidation and free fatty acids. The co-inoculation of S. carnosus, L. plantarum, and B. coagulans yielded richer flavor compounds in dried bonito, the upregulation of benzaldehyde, 2, 3-dimethyl-2-cyclopentene-1-one, 1-octen-3-ol and heterocyclic compounds led to the development of intense fruity, sweet, mushroom-like and floral aromas. These findings establish a foundation for the selection of composite fermentation starter cultures, enabling the targeted formulation of SynComs with flavor enhancement and texture improvement functions.\n\nSynthetic microbial communities: A new strategy to enhance texture, taste, and flavor attributes of slightly fermented dried bonito", "token_count": 446, "char_count": 1763, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:36.867370", "source": { "split": "train_shard_00000", "doc_id": 4762 }, "chunk_id": "train_shard_00000_4762_0", "global_id": 5325 }, { "text": "Kluyveromyces marxianus is a rapidly growing thermotolerant yeast that secretes a variety of lytic enzymes, utilizes different sugars, and produces ethanol. The probiotic potential of this yeast has not been well explored. To evaluate its probiotic potential, the yeast strain Kluyveromyces marxianus DMKU3-1042 was analyzed using next-generation sequencing technology. Analysis of the genomes showed that the yeast isolates had a GC content of 40.10-40.59%. The isolates had many genes related to glycerol and mannose metabolism, as well as genes for acetoin and butanediol metabolism, acetolactate synthase subunits, and lactic acid fermentation. The strain isolates were also found to possess genes for the synthesis of different vitamins and Coenzyme A. Genes related to heat and hyperosmotic shock tolerance, as well as protection against reactive oxygen species were also found. Additionally, the isolates contained genes for the synthesis of lysine, threonine, methionine, and cysteine, as well as genes with anticoagulation and anti-inflammatory properties. Based on our analysis, we concluded that the strain DMKU3-1042 possesses probiotic properties that make it suitable for use in food and feed supplementation.\n\nSnapshot of the Probiotic Potential of Kluveromyces marxianus DMKU-1042 Using a Comparative Probiogenomics Approach.", "token_count": 384, "char_count": 1362, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8042, "entities": { "genes": [ "DMKU3" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:37.492419", "source": { "split": "train_shard_00000", "doc_id": 4763 }, "chunk_id": "train_shard_00000_4763_0", "global_id": 5326 }, { "text": "A Study on the Extraction, Fermentation Condition Optimization, and Antioxidant Activity Assessment of Polysaccharides Derived from Kluyveromyces marxianus", "token_count": 42, "char_count": 155, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:37.870594", "source": { "split": "train_shard_00000", "doc_id": 4764 }, "chunk_id": "train_shard_00000_4764_0", "global_id": 5327 }, { "text": "The use of genetically modified non-conventional yeast provides significant potential for the bioeconomy by diversifying the tools available for the development of sustainable and novel products. In this study, we sequenced and annotated the genome of Kluyveromyces marxianus Y-1190 to establish it as a platform for lactose valorization. The strain was chosen for rapid growth on lactose-rich dairy permeate, high transformation efficiency, and ease of culturing in bioreactors. Genomic sequencing revealed that K. marxianus Y-1190 possesses single nucleotide polymorphisms associated with efficient lactose metabolism. The strain is diploid with notable genomic heterogeneity, which appears to be critical for its robust growth and acid tolerance. To further exploit this platform strain, we developed protocols for gene and chromosome manipulation using CRISPR editing, constructed and validated a series of promoters compatible with MoClo vectors, and designed synthetically inducible promoters for K. marxianus . These tools enable precise control over gene expression, allowing for the tailored optimization of metabolic pathways and production processes. The synthetic promoters provide flexibility for dynamic expression tuning, while the CRISPR-based editing protocols facilitate targeted genetic modifications with high efficiency. Together, these advancements significantly enhance the genetic toolbox for K. marxianus , positioning it as a versatile platform for industrial biotechnology. These tools open new opportunities for the sustainable production of bio-based chemicals, fuels, and high-value products, leveraging lactose-rich feedstocks to contribute to a circular economy.\n\nSequencing of a dairy isolate unlocks Kluyveromyces marxianus as a host for lactose valorization", "token_count": 406, "char_count": 1799, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:38.488855", "source": { "split": "train_shard_00000", "doc_id": 4765 }, "chunk_id": "train_shard_00000_4765_0", "global_id": 5328 }, { "text": "One of the most unique non-conventional yeasts, Kluyveromyces marxianus is rapidly gaining ground in biotechnology applications. K. marxianus possesses fast growth, thermotolerance, and a Crabtree negative metabolism, features with a clear advantage over conventional yeasts like Saccharomyces cerevisiae. Additionally, it is diverse in carbon sources utilizing lactate, xylose as well as lignocellulosic materials which becomes critical in waste-utilizing and sustainable production industries. Besides the fact that K. marxianus has been useful in the production of valuable metabolites like β-galactosidase, ethanol, aroma compounds, and organic acids, its GRAS designation makes K. marxianus a prime candidate for pharmaceutical and nutraceutical applications. This review summarizes a detailed description of K. marxianus biochemical and genetic features, its present applications, and future unexplored potentials such as probiotic development, vaccine production, bioremediation, and anticancer therapies. We also describe genetic tools that have been developed with improved metabolic pathways useful for new industry applications, making K. marxianus a resource in modern biotechnology. In sum, due to its unique features, and its thermotolerance and endure under low-pH conditions, K. marxianus appears as a perfect alternative for areas such as biofuel production, biochemical synthesis, enzyme manufacturing, diary industry, and pharmaceuticals.\n\nExpanding Horizons: The Untapped Potential of Kluyveromyces marxianus in Biotechnological Applications", "token_count": 379, "char_count": 1561, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6881, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:39.072448", "source": { "split": "train_shard_00000", "doc_id": 4766 }, "chunk_id": "train_shard_00000_4766_0", "global_id": 5329 }, { "text": "We report the draft genomes of four Kluyveromyces marxianus isolates obtained from the elaboration process of henequen (Agave fourcroydes) mezcal, a Mexican alcoholic beverage. The average nucleotide identity analysis revealed that isolates derived from agave plants are distinct from those from other environments, including agave fermentations.\n\nDraft genomes of four Kluyveromyces marxianus isolates retrieved from the elaboration process of henequen (Agave fourcroydes) mezcal.", "token_count": 147, "char_count": 509, "word_count": 63, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:39.503922", "source": { "split": "train_shard_00000", "doc_id": 4767 }, "chunk_id": "train_shard_00000_4767_0", "global_id": 5330 }, { "text": "Abstract

Weaning in pig production is a stressful event that impacts intestinal biology and increases the risk of infections, impairing piglet development and leading to economic losses. Antibiotic preventive administration has been used to improve the productive parameters, but nowadays this practice has been banned because of its contribution to antimicrobial resistance generation. So, alternatives are urgently needed. Kluyveromyces marxianus CIDCA 9121 has immunomodulatory and convenient biotechnological properties and was studied for preventing post-weaning stress, for which 8 sows were supplemented with 109 CFU per kg of feed from 20 days before piglets´ birth until weaning. Then, piglets were supplemented with 2x109 CFU/ kg of feed for 20 days more. A control group of 8 sows and their piglets not supplemented with yeast was included. Productive parameters were registered from birth to 60 days of age. Five days post-weaning, 5 animals from each group were euthanized; small intestines and blood were taken for histopathology analysis and amino acid analysis respectively. Intestinal content was sampled to determine the main bacterial groups by qPCR. Piglets born from supplemented sows (n = 132) weighed more than controls (n = 130; p < 0,05). During farrowing, there were no differences among groups but 40 days after weaning the supplemented group weighted 10% more than the control group (p < 0,05). We found an increase in citrullinemia and in the small intestine mucosal thickness in supplemented piglets post-weaning indicating better tolerance to post-weaning stress. Our results suggest that K. marxianus CIDCA 9121 is a good candidate for supplementation of gestating sows and postweaning piglets.

", "token_count": 501, "char_count": 1805, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:40.149146", "source": { "split": "train_shard_00000", "doc_id": 4768 }, "chunk_id": "train_shard_00000_4768_0", "global_id": 5331 }, { "text": "Supplementation with Kluyveromyces marxianus probiotic yeasts in sows and their piglets in early post- weaning: effects in biological and productive parameters", "token_count": 38, "char_count": 159, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:40.506833", "source": { "split": "train_shard_00000", "doc_id": 4768 }, "chunk_id": "train_shard_00000_4768_1", "global_id": 5332 }, { "text": "Valorization of Coffee Cherry Pulp into Potential Functional Poultry Feed Additives by Pectinolytic Yeast Kluyveromyces marxianus ST5", "token_count": 42, "char_count": 133, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:40.871194", "source": { "split": "train_shard_00000", "doc_id": 4769 }, "chunk_id": "train_shard_00000_4769_0", "global_id": 5333 }, { "text": "The development of innovative non-alcoholic beer (NAB) with health benefits, with the use of non-conventional potential probiotic yeasts offers an interesting alternative to standard NAB brewing strategies. In this study, potential probiotic non-Saccharomyces yeasts Pichia manshurica, Kluyveromyces lactis, and Kluyveromyces marxianus, along with commercial probiotic yeast Saccharomyces boulardii, were characterized and tested for functional NAB production, whereas P. manshurica was used in NAB production for the first time. Growth and viability were assessed across a range of temperatures, pH, and iso-α-bitter acids. The tested yeasts withstood conditions typical of the beer matrix and human digestive tract and had positive phenolic off-flavour phenotype. Two strains, K. lactis and K. marxianus, showed strong ß-glucosidase activity, which may enhance beverage aroma complexity. Ethanol levels in beers fermented with non-Saccharomyces yeasts remained below the NAB limit (≤0.5% v/v). Analysis of volatile organic compound profiles revealed the potential of these yeasts to produce higher alcohols and esters valuable from a brewer’s perspective. Sensorial evaluation of prepared NAB produced with potential probiotic non-Saccharomyces yeasts revealed floral and clove-like aroma traces. This study provides valuable insight into novel probiotic fermentations and the potential application of unconventional yeasts in functional, aromatic, and health-oriented non-alcoholic beverages.\n\nFunctional Non-Alcoholic Beer Fermented with Potential Probiotic Yeasts", "token_count": 399, "char_count": 1568, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:41.489116", "source": { "split": "train_shard_00000", "doc_id": 4770 }, "chunk_id": "train_shard_00000_4770_0", "global_id": 5334 }, { "text": "Yeasts are widely known for their application in food production, but also because of their clinical significance. As human pathogens, several species of yeasts, mainly of the genus Candida and other closely related genera, are responsible for a great number of life-threatening infections. The occurrence of yeasts in cheeses, including pathogenic species, has been largely studied, yet the antifungal susceptibility of these microorganisms is rarely reported. Here, we identified the species and determined the antifungal susceptibility profile of 45 yeast Candida isolates recovered from artisanal cheeses from 20 cities in Boyacá, Colombia. Among the species, Pichia fermentans (28.9%) prevailed, followed by Pichia kudriavzevii (24.4%), Kluyveromyces marxianus (22.2%), Clavispora lusitaniae (11.1%), Candida inconspicua (6.7%) Candida parapsilosis (4.4%) and Meyerozyma guillermondii (2.2%). Notably, all seven species have been globally reported, to a greater or lesser extent, to cause fungemia and other invasive infections with high mortality rates. Remarkably, together with the intrinsically resistant P. kudriavzevii, most isolates of P. fermentans, C. inconspicua and C. parapsilosis were resistant to fluconazole, one of the most common drugs to treat candidiasis. Our findings highlight the importance of exploring the ecological niches of pathogenic yeasts, together with their antifungal susceptibility, considering that the emergence of resistance in non-commensal opportunistic pathogens poses a serious threat to public health.", "token_count": 488, "char_count": 1632, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7062, "quality_score": 0.8531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:42.131610", "source": { "split": "train_shard_00000", "doc_id": 4771 }, "chunk_id": "train_shard_00000_4771_0", "global_id": 5335 }, { "text": "Occurrence of pathogenic yeast  species in artisanal cheeses from Boyacá, Colombia, including fluconazole resistant isolates.", "token_count": 42, "char_count": 132, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:42.488191", "source": { "split": "train_shard_00000", "doc_id": 4771 }, "chunk_id": "train_shard_00000_4771_1", "global_id": 5336 }, { "text": "There is an increasing interest in yeasts isolated from natural sources to be used as probi-otics. Saccharomyces-based probiotics have been proposed as a valid alternative to the con-ventional drug therapy for the prevention and treatment of vulvovaginal candidiasis, also considering the resistance of some Candida strains to many antifungals. Here we isolated from an artisanal sourdough a new yeast strain which was identified as Kluyveromyces marxianus and assessed its probiotic and safety properties, which resulted comparable at all to those exhibited by the commercial probiotic Saccharomyces boulardii. Then, we checked the antagonistic activity of the new isolate against some clinical fluconazole re-sistant C. albicans strains, showing its ability to inhibit filamentation, biofilm formation, and adhesion of C. albicans to vaginal epithelial A-431 cells. Also, K. marxianus reduced the cell damage provoked by C. albicans and the expression of SAP2 and SAP6 genes. On the whole, our results enlarge the spectrum of the beneficial properties of the food-grade yeast K. marxianus showing for the first time its biotherapeutic potential as anticandidal agent.\n\nBiotherapeutic Potential of a Novel Probiotic Kluyveromyces marxianus Isolated from a Sourdough Starter Against Vaginal C. albicans Strains", "token_count": 350, "char_count": 1328, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.828, "entities": { "genes": [ "SAP2", "SAP6" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:43.072305", "source": { "split": "train_shard_00000", "doc_id": 4772 }, "chunk_id": "train_shard_00000_4772_0", "global_id": 5337 }, { "text": "The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulence, and antibiotic resistance. While it is known that within-MTBC diversity is characterised by large deletions found only in certain lineages (regions of difference [RDs]), a comprehensive pangenomic analysis incorporating both coding and non-coding regions remains unexplored. We utilised a curated dataset representing various MTBC genomes, including under-represented lineages, to quantify the full diversity of the MTBC pangenome. The MTBC was found to have a small, closed pangenome with distinct genomic features and RDs both between lineages (as previously known) and between sub-lineages. The accessory genome was identified to be a product of genome reduction, showing both divergent and convergent deletions. This variation has implications for traits like virulence, drug resistance, and metabolism. The study provides a comprehensive understanding of the MTBC pangenome, highlighting the importance of genome reduction in its evolution, and underlines the significance of genomic variations in determining the pathogenic traits of different MTBC lineages.\n\nThe <i>Mycobacterium tuberculosis</i> complex pangenome is small and shaped by sub-lineage-specific regions of difference.", "token_count": 338, "char_count": 1449, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6462, "quality_score": 0.8231, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:43.642940", "source": { "split": "train_shard_00000", "doc_id": 4773 }, "chunk_id": "train_shard_00000_4773_0", "global_id": 5338 }, { "text": "Milk kefir is a fermented dairy product composed of a complex consortium of microorganisms, including lactic acid bacteria (LAB), yeasts, and acetic acid bacteria. Despite growing interest in its health-promoting properties, the synergistic interactions among the diverse microbial constituents of kefir remain insufficiently characterized. This study investigated the probiotic potential of milk kefir through a multi-omics approach. Two strains, Kluyveromyces marxianus SLAM 005Y and Lentilactobacillus kefiri SLAM 023B, were isolated from Korean household milk kefir. Both strains exhibited key probiotic properties, including antibacterial activity, adherence to intestinal epithelial cells, and resistance in simulated gastrointestinal conditions. Supplementation with SLAM 005Y, SLAM 023B, or their synergistic combination (SYN) significantly enhanced lifespan and immune function in Caenorhabditis elegans. Transcriptomic analysis further revealed upregulation of genes involved in longevity and antimicrobial defense, suggesting the activation of conserved stress-response pathways. In a dextran sulfate sodium (DSS)-induced murine colitis model, SYN administration led to marked improvement in clinical outcomes. SYN also restored the expression of inflammatory and anti-inflammatory cytokines and tight junction proteins, indicating improved intestinal barrier function and immune regulation. Importantly, multi-omics analysis revealed that SYN altered both gut microbial composition and fecal metabolite profiles, supporting a mechanistic link between microbiota modulation and host health. Taken together, milk kefir strains SLAM 005Y and SLAM 023B, particularly in combination, exhibit strong probiotic properties. Our findings highlight the therapeutic potential of milk kefir-originated probiotics as a functional food for improving intestinal health.", "token_count": 476, "char_count": 1887, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7064, "quality_score": 0.8532, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:44.287557", "source": { "split": "train_shard_00000", "doc_id": 4774 }, "chunk_id": "train_shard_00000_4774_0", "global_id": 5339 }, { "text": "Functional evaluation of synbiotic combination of <i>Kluyveromyces marxianus</i> and <i>Lentilactobacillus kefiri</i> derived from milk kefir using multi-omics approaches.", "token_count": 72, "char_count": 195, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:44.653946", "source": { "split": "train_shard_00000", "doc_id": 4774 }, "chunk_id": "train_shard_00000_4774_1", "global_id": 5340 }, { "text": "Biocontrol is one of the most promising alternatives to chemical preservatives for food preservation. This study investigated the biocontrol potential of yeasts isolated from raw milk cheese against spoilage moulds. Eighty-four native yeast strains were screened for antagonistic activity against Penicillium commune, Fusarium verticillioides, and Mucor plumbeus/racemosus via confrontation using a milk-based culture medium. Fifteen strains from the species Pichia jadinii, Kluyveromyces lactis, Kluyveromyces marxianus, and Geotrichum candidum exhibited significant antagonistic activity (inhibition zone > 2 mm) against M. plumbeus/racemosus and F. verticillioides. The modelling of the impact of ripening conditions revealed that temperature was the primary factor influencing yeast antagonism. In addition, notable variability at both species and strain levels was found. The antagonist activity was associated with different mechanisms depending on the species and strains. K. lactis stood out for its proteolytic activity and competition for iron and manganese. Additionally, two strains of this species (KL890 and KL904) were found to produce volatile organic compounds with antifungal properties (phenylethyl alcohol and 1-butanol-3-methyl propionate). G. candidum GC663 exhibited strong competition for space, as well as the ability to parasitise hyphae linked to its pectinase and β-glucanase activity. The latter enzymatic activity was detected in all P. jadinii strains, with P. jadinii PJ433 standing out due to its proteolytic activity. In a cheese matrix, the efficacy of eight yeast strains against three target moulds was assessed, highlighting the potential of G", "token_count": 515, "char_count": 1775, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8312, "entities": { "genes": [ "KL890", "KL904", "PJ433", "GC663" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:47:45.281526", "source": { "split": "train_shard_00000", "doc_id": 4775 }, "chunk_id": "train_shard_00000_4775_0", "global_id": 5341 }, { "text": "candidum GC663 and P. jadinii PJ433 as biocontrol agents, exhibiting high and moderate efficacy, respectively, in controlling the growth of F. verticillioides and M. plumbeus/racemosus. Nonetheless, further research is necessary to elucidate their full spectrum of antifungal mechanisms and to validate their performance under industrial-scale conditions, including their impact on cheese quality.\n\nBiocontrol of Cheese Spoilage Moulds Using Native Yeasts.", "token_count": 140, "char_count": 481, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [ "GC663", "PJ433" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:45.708820", "source": { "split": "train_shard_00000", "doc_id": 4775 }, "chunk_id": "train_shard_00000_4775_1", "global_id": 5342 }, { "text": "Abstract

Astaxanthin (AXT) is a dark-red ketocarotenoid from the xanthophyll group, renowned for its anti-inflammatory, antioxidant, and anti-proliferative properties, which is widely applied in animal feed, food, cosmeceuticals, and pharmaceuticals. Recently, the growing recognition of AXT’s numerous health benefits has significantly boosted both industrial and research interest in this remarkable compound. Synthetic biology represents a cost-effective strategy for the targeted production of specific optical isomers of natural compounds. This study explores the scale-up production of free-form 3S, 3'S astaxanthin (Asta-S) using recombinant probiotic yeast Kluyveromyces marxianus. Among various carbon sources tested, glucose was identified as the most practical substrate due to its cost-effectiveness, although galactose induced higher astaxanthin yields. Increasing glucose concentration from 20 to 80 g/L enhanced biomass but slightly reduced astaxanthin content in flask cultures. In 5 L fermenter trials, biomass growth increased with higher initial glucose levels, with the highest total astaxanthin yield of 41.06 mg/L achieved at 80 g/L glucose. To overcome carbon depletion and enhance productivity, a glucose fed-batch strategy was applied, resulting in the improved astaxanthin yield of 51.22 mg/L with a productivity of 0.711 mg/L/hr. The process was further scaled to a 30 L in-situ fermenter, where pressurized cultivation at 1 atm enhanced dissolved oxygen availability, resulting in higher astaxanthin content (4.38 mg/g) and improved biomass compared to atmospheric pressure fermentation. These results confirm the potential of recombinant K. marxianus 929 Asta strain D56 as a viable host for industrial astaxanthin production, particularly when leveraging fed-batch strategies and controlled pressure fermentation for scalability.

", "token_count": 511, "char_count": 1916, "word_count": 250, "semantic_coherence": 1, "information_density": 0.696, "quality_score": 0.848, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:46.342509", "source": { "split": "train_shard_00000", "doc_id": 4776 }, "chunk_id": "train_shard_00000_4776_0", "global_id": 5343 }, { "text": "Scale up production of astaxanthin by using recombinant yeast-Kluveromyces marxianus", "token_count": 27, "char_count": 84, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:46.701704", "source": { "split": "train_shard_00000", "doc_id": 4776 }, "chunk_id": "train_shard_00000_4776_1", "global_id": 5344 }, { "text": "There is an increasing interest in yeasts isolated from natural sources to be used as probiotics. Saccharomyces-based probiotics have been proposed as a valid alternative to the conventional drug therapy for the prevention and treatment of vulvovaginal candidiasis, also considering the resistance of some Candida strains to many antifungals. Here, we isolated from an artisanal sourdough a new yeast strain which was identified as Kluyveromyces marxianus and assessed its probiotic and safety properties, which resulted in comparable properties to all those exhibited by the commercial probiotic Saccharomyces boulardii. Then, we checked the antagonistic activity of the new isolate against some clinical fluconazole resistant C. albicans strains, showing its ability to inhibit filamentation, biofilm formation, and the adhesion of C. albicans to vaginal epithelial A-431 cells. Also, K. marxianus reduced the cell damage provoked by C. albicans and the expression of SAP2 and SAP6 genes. On the whole, our results enlarge the spectrum of the beneficial properties of the food-grade yeast K. marxianus showing for the first time its biotherapeutic potential against C. albicans.\n\nThe Biotherapeutic Potential of a Novel Probiotic Kluyveromyces marxianus Isolated from a Sourdough Starter Against Vaginal Candida albicans Strains.", "token_count": 423, "char_count": 1429, "word_count": 192, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "SAP2", "SAP6" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:47.367340", "source": { "split": "train_shard_00000", "doc_id": 4777 }, "chunk_id": "train_shard_00000_4777_0", "global_id": 5345 }, { "text": "Green synthesis of silver iodide nanoparticles from Kluyveromyces marxianus M59 beta-glucan: characterization and anticancer activity.", "token_count": 39, "char_count": 134, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:47.749184", "source": { "split": "train_shard_00000", "doc_id": 4778 }, "chunk_id": "train_shard_00000_4778_0", "global_id": 5346 }, { "text": "K. marxianus ( Km ), a stress-tolerant yeast, is closely related to S. cerevisiae ( Sc ). Unlike Sc , Km yeast grows robustly in the presence of proteotoxic stressors, including temperatures up to 45°C and oxidizing agents. Sumoylation, the posttranslational modification with SUMO, plays an important role in the response to proteotoxic stress in the mesophilic yeast Sc . Therefore, we tested the possibility that perturbation of SUMO dynamics may affect Km 's remarkable stress tolerance. Km yeast expresses variants of functionally conserved SUMO pathway genes, and we previously found that the Km SUMO protease KmUlp1 is considerably more tolerant to proteotoxic insults than ScUlp1 (Peek et al., 2018). Here, we tested the possibility that disruption of the non-essential SUMO protease KmUlp2, an isopeptidase related to Ulp1, may negatively affect Km 's remarkable stress tolerance. To this end, we used a Km -specific CRISPR/Cas9 system to generate Kmulp2 truncation mutants in vivo . We then compare the growth properties of these Kmulp2 mutants and their respective WT controls to the Sculp2 knockout mutant after exposure to various cellular stressors. Overall, we find that Kmulp2 mutants recapitulate major phenotypes associated with the Sculp2 mutant. This includes sensitivity to the ribonucleotide reductase inhibitor hydroxyurea and the accumulation of SUMO chains. Our study shows that KmUlp2 is required for Km 's response to hydroxyurea-induced DNA damage stress", "token_count": 513, "char_count": 1615, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:47:48.412947", "source": { "split": "train_shard_00000", "doc_id": 4779 }, "chunk_id": "train_shard_00000_4779_0", "global_id": 5347 }, { "text": "Furthermore, alterations in SUMO dynamics by Ulp2 truncations do not grossly affect the temperature tolerance of K. m. yeast cells.\n\nIdentification and functional analysis of ULP2 SUMO protease mutants of the stress-tolerant yeast <i>Kluyveromyces marxianus</i>.", "token_count": 87, "char_count": 281, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8286, "quality_score": 0.9143, "entities": { "genes": [ "ULP2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:48.838797", "source": { "split": "train_shard_00000", "doc_id": 4779 }, "chunk_id": "train_shard_00000_4779_1", "global_id": 5348 }, { "text": "

Background

With advancements in healthcare services, there has been an increase in the population of immunosuppressed patients and the frequency of opportunistic pathogens including rare yeasts (RY). We aimed to provide data on the distribution of RY causing invasive infections and their antifungal susceptibility profiles. In this retrospective study, the distribution of RYs obtained between January 2015 and January 2023 examined. Antifungal susceptibility analyses of the isolates conducted using the broth microdilution method following European Committee on Antimicrobial Susceptibility Testing (EUCAST) recommendations. The patients' demographics, predisposing factors and outcomes were investigated.

Results

A total of 15 species were identified from 56 clinical samples, including Clavispora lusitaniae, Kluyveromyces marxianus, Magnusiomyces capitatus, Wickerhamomyces anomalus, Meyerozyma guilliermondii, Magnusiomyces clavatus, Candida dubliniensis, Rhodotorula mucilaginosa, Cyberlindnera jadinii, Pichia inconspicua, Candida auris, Yarrowia lipolytica, Trichosporon asahii, Wickerhamiella pararugosa and Saccharomyces cerevisiae. Observed highly heterogenous antifungal susceptibility results depending on the species. Admission to the intensive care unit (ICU), being 65 years or older, and neutropenia increased mortality. Fourteen-day and 30-day mortality rates were 27.8% and 35.2%, respectively.

Conclusions

The variability of RY encountered in various centers and differences in antifungal susceptibility profiles warrant further research on this topic, both regionally and globally.\n\nEpidemiology and antifungal susceptibilities of rare yeast infections in a tertiary care center.", "token_count": 470, "char_count": 1724, "word_count": 204, "semantic_coherence": 1, "information_density": 0.7353, "quality_score": 0.8676, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:49.492405", "source": { "split": "train_shard_00000", "doc_id": 4780 }, "chunk_id": "train_shard_00000_4780_0", "global_id": 5349 }, { "text": "Cell immobilization is a technique that reduces the lag phase of cell growth and improves microbial stress tolerance, resulting in an increased product yield. In this study, a new immobilization carrier was prototyped using 3D printing for thermotolerant Kluyveromyces marxianus to produce bioethanol. Upon coating with soybean meal (SM) waste, new functional groups were introduced and the surface roughness was enhanced significantly (p < 0.05). Fermentation of the immobilized SM-coated templates showed a marked improvement (p < 0.05) of bioethanol production and productivity, from 37 g/L and 1.71 g·L⁻¹·h⁻¹ in a suspension culture to up to 45 g/L and 2.82 g·L⁻¹·h⁻¹, translating to an ¹1 % and 60 % increase in theoretical yield and productivity, respectively. Even after 30 cycles of repeated batch, the yield and productivity remained relatively stable. These findings highlight the physical durability, stability, and commercial potential of 3D-printed templates coated with SM as cell immobilization carrier.\n\nCreating a robust and reusable cell immobilization system for bioethanol production by thermotolerant yeast using 3D printing and soybean waste", "token_count": 339, "char_count": 1163, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:50.065355", "source": { "split": "train_shard_00000", "doc_id": 4781 }, "chunk_id": "train_shard_00000_4781_0", "global_id": 5350 }, { "text": "

Background

Poly lactic acid (PLA) is one of the most promising bioplastics due to its interesting mechanical and physical properties, low carbon footprint, and biodegradability. PLA is produced from lactic acid (LA) that is either sourced from petrochemical industries or obtained through microbial fermentation using lactic acid bacteria, with the latter accounting for 90% of total LA production. While the bio-based production is more sustainable, it requires complex and expensive feedstocks and large amounts of neutralization agents for pH control during fermentation.

Results

We explored the potential of a non-conventional, acid-tolerant yeast Kluyveromyces marxianus for LA production. First, we analyzed 168 genetically diverse K. marxianus strains to identify the best candidate chassis strains and each of the 10 selected strains was genetically engineered to produce LA. The best candidate strain, Km3, was subjected to adaptive laboratory evolution, yielding a further 18% increase in LA production, reaching titers of 120 g L- 1 LA and a yield of 0.81 g g- 1, while requiring less neutralization agent and showing capacity to efficiently ferment xylose-containing feedstocks. Genome sequencing identified a mutation in the general transcription factor gene SUA7 that proved causal for the increased performance of the evolved clone.

Conclusions

Our results highlight the potential of integrating state-of-the-art techniques with the genetic diversity of non-standard microbes to obtain superior microbial cell factories that can ferment xylose-containing media and can be harnessed for sustainable commercial production of fine chemicals through precision fermentation.\n\nMetabolic engineering and adaptive laboratory evolution of Kluyveromyces Marxianus for lactic acid production.", "token_count": 454, "char_count": 1840, "word_count": 247, "semantic_coherence": 1, "information_density": 0.664, "quality_score": 0.832, "entities": { "genes": [ "SUA7" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:50.701446", "source": { "split": "train_shard_00000", "doc_id": 4782 }, "chunk_id": "train_shard_00000_4782_0", "global_id": 5351 }, { "text": "Monoterpenoids are valued for their roles as flavors, fragrances, insecticides, and energy-dense fuels. Microbial biosynthesis offers sustainable biosynthesis routes for these important molecules, but production levels remain limited. Here, we introduce a biosensor-driven microbial engineering strategy to enhance monoterpenoid production, specifically targeting geraniol. Using mutagenized libraries of the PYR1 receptor—a versatile biosensor from plant ABA signaling pathways with a malleable binding pocket—we screened 24 monoterpenoids and identified PYR1 variants responsive to eight, including geraniol. A low background, highly selective geraniol-sensitive PYR1 variant was expressed in the thermotolerant yeast Kluyveromyces marxianus as a growth-based biosensor circuit, allowing for rapid strain engineering. By coupling the geraniol-sensitive PYR1 sensor with a genome-wide CRISPR-Cas9 mutagenesis approach, we identified six gene knockouts that enhance geraniol production, achieving up to a 2-fold increase in titer. This study demonstrates the power of the PYR1 biosensor platform to enable rapid strain engineering and the identification of mutants that improve titer of a desired metabolite.\n\nPYR1 biosensor-driven genome-wide CRISPR screens for improved monoterpenoid production inKluyveromyces marxianus", "token_count": 342, "char_count": 1329, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7066, "quality_score": 0.8533, "entities": { "genes": [ "PYR1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:51.282416", "source": { "split": "train_shard_00000", "doc_id": 4783 }, "chunk_id": "train_shard_00000_4783_0", "global_id": 5352 }, { "text": "

Background

Cystic Fibrosis (CF) Centers worldwide have reported healthcare-associated outbreaks of nontuberculous mycobacteria (NTM). We report a retrospective investigation of shared Mycobacterium abscessus strains among people with cystic fibrosis (pwCF) receiving care at Dell Children's/Ascension combined Pediatric and Adult CF Program (DCMC).

Methods

Whole genome sequencing (WGS) was used to identify genetically similar isolates among 167 NTM isolates from 57 pwCF. Epidemiological investigation, respiratory and environmental isolate comparisons, and watershed mapping were performed.

Results

WGS analysis revealed four M. abscessus clusters, two ssp. abscessus and two ssp. massiliense. One subject was infected with two distinct clustered M. abscessus (ssp. abscessus and ssp. massiliense). Epidemiologic investigation demonstrated opportunities for healthcare-associated transmission within all clusters. Two ssp. massiliense subject pairs had healthcare overlaps and high genomic relatedness, including one cohabitating sibling pair. M. abscessus recovered from DCMC revealed genetic similarity to a respiratory isolate from one patient who was never exposed to the hospital environment.

Conclusions

We identified shared M. abscessus strains via genomic analysis among pwCF at DCMC. None of the clustered patient isolates matched hospital environmental isolates at the genomic level. One hospital environmental isolate had genomic similarity to a respiratory isolate of M. abscessus, but the epidemiologic investigation revealed no evidence of subject exposure to the hospital setting. One ssp. massiliense subject pair had the same level of pangenome relatedness as the sibling pair and epidemiological investigation revealed overlap in the clinic, supporting healthcare-associated person-to-person transmission among the pair within a cluster. One pwCF had polyclonal clustered infections, suggesting multiple environmental sources of acquisition outside the healthcare environment.", "token_count": 495, "char_count": 2026, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5675, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:51.932090", "source": { "split": "train_shard_00000", "doc_id": 4784 }, "chunk_id": "train_shard_00000_4784_0", "global_id": 5353 }, { "text": "Genomic and epidemiologic investigation of Mycobacterium abscessus isolates in a cystic fibrosis center to determine potential routes of transmission.", "token_count": 36, "char_count": 150, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:52.294287", "source": { "split": "train_shard_00000", "doc_id": 4784 }, "chunk_id": "train_shard_00000_4784_1", "global_id": 5354 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) are genetically diverse foodborne pathogens of major global public health concerns. Serogroup-level identification is critical for effective surveillance and outbreak control; however, it is often challenged by STEC's genome plasticity and frequent recombination. In this study, we employed a standardized pangenomic pipeline integrating Roary ILP Bacterial Core Annotation Pipeline (RIBAP) and Panaroo to analyze 160 complete, high-quality STEC genomes representing eight major serogroups at a 95% sequence identity threshold. Candidate serogroup-specific markers were identified using gene presence/absence profiles from RIBAP and Panaroo. Our analysis revealed several high-confidence markers, including metabolic genes (dgcE, fcl_2, dmsA, hisC) and surface polysaccharide-related genes (capD, rfbX, wzzB). Comparative pangenomic evaluation showed that RIBAP predicted a larger pangenome size than Panaroo. Additionally, some genomes from the O104:H1, O145:H28, and O45:H2 serotypes clustered outside their expected clades, indicating sporadic serotype misplacements in phylogenetic reconstructions. Functional annotation suggested that most candidate markers are involved in critical processes such as glucose metabolism, lipopolysaccharide biosynthesis, and cell surface assembly. Notably, approximately 22.9% of the identified proteins were annotated as hypothetical. Overall, this study highlights the utility of pangenomic analysis for potential identification of clinically relevant STEC serogroups markers and phylogenetic interpretation. We also note that pangenome analysis could guide the development of more accurate diagnostic and surveillance tools.", "token_count": 469, "char_count": 1767, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7559, "quality_score": 0.8779, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:52.937395", "source": { "split": "train_shard_00000", "doc_id": 4785 }, "chunk_id": "train_shard_00000_4785_0", "global_id": 5355 }, { "text": "Genomic Markers Distinguishing Shiga Toxin-Producing <i>Escherichia coli</i>: Insights from Pangenome and Phylogenomic Analyses.", "token_count": 53, "char_count": 140, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:53.301119", "source": { "split": "train_shard_00000", "doc_id": 4785 }, "chunk_id": "train_shard_00000_4785_1", "global_id": 5356 }, { "text": "Salmonella enterica is a major public health concern in Africa because of its increasing antimicrobial resistance (AMR) to multiple antibiotics that threatens effective treatment and control. In this study, we analyzed 135 publicly available antimicrobial resistant Salmonella genomes from African food sources. Using a pan genomic analysis approach, we identified a pangenome of 15,269 genes, including a core genome of ∼3.5 Mbp with 3,350 core genes (99-100% prevalence) and a substantial accessory genome comprising 183 soft-core, 1,441 shell, and 10,295 cloud genes. We found substantial genomic diversity among the AMR-positive Salmonella enterica isolates. AMR profiling revealed widespread distribution of resistance genes, with aac(6’)-laa_1 present in nearly all genomes, and tet(A) , sul2 , and fosA71 frequently co-occurring. Core virulence genes such as invA , ssaL , and steA were nearly universally conserved, suggesting essential roles in pathogenesis. Sporadic rare virulence genes like papE , tcpC , and ybtP were present in the genome pointing to lineage-specific patterns. The presence of macrolide inactivation genes ( ereA ) points to a huge risk of resistance to the globally important antibiotic Azithromycin. Quorum-sensing genes, including the AI-2 system ( luxS , lsrA-D , lsrK ) and biofilm formation genes were widely conserved across the isolates, highlighting their potential role in adaptation and the spread of antimicrobial resistance in foodborne Salmonella in Africa. Hierarchical clustering based on core genome multilocus sequence typing (cgMLST) revealed monophyletic clades for major serovars like Enteritidis and Infantis . Shannon diversity indices revealed geographical variation in AMR gene richness, with Burkina Faso, South Africa and Tunisia showing high intra-country diversity. Our analysis identified lineage-associated accessory genes, hence providing potential markers for surveillance", "token_count": 502, "char_count": 1936, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:53.954676", "source": { "split": "train_shard_00000", "doc_id": 4786 }, "chunk_id": "train_shard_00000_4786_0", "global_id": 5357 }, { "text": "This study offers valuable insights into the genomic architecture and AMR landscape of Salmonella in Africa and underscores the need for expanded genomic surveillance across diverse geographic and food production contexts.\n\nPangenome and comparative genomics analysis reveal patterns of quorum sensing and antimicrobial resistance in Salmonella Lineages from African Food Chains", "token_count": 83, "char_count": 385, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:54.330990", "source": { "split": "train_shard_00000", "doc_id": 4786 }, "chunk_id": "train_shard_00000_4786_1", "global_id": 5358 }, { "text": "The growing challenges posed by global warming and the demand for sustainable food and feed resources underscore the need for robust microbial platforms in bioprocessing. Thermotolerant yeasts have emerged as promising candidates due to their ability to thrive at elevated temperatures and other industrially relevant stresses. This review examines the industrial potential of thermotolerant yeasts in the context of climate change, emphasizing how their resilience can lead to more energy-efficient and cost-effective bioprocesses. Particular attention is paid to the thermodynamic implications of yeast metabolism under heat stress, especially in bioethanol production and methanol metabolism in methylotrophic yeasts, where metabolic heat generation plays a critical role. The cellular and molecular mechanisms underlying thermotolerance are also reviewed, including heat shock sensing mechanisms, the protection of biomolecules, and membrane and cell wall integrity. Advances in genetic and metabolic engineering aimed at enhancing these traits are also highlighted. By integrating current insights into the molecular and cellular mechanisms of thermotolerance, along with recent technological advancements, this review outlines the advantages of high-temperature operations and positions thermotolerant yeasts as vital components of future sustainable bioproduction systems.\n\nThermotolerant yeasts promoting climate-resilient bioproduction.", "token_count": 300, "char_count": 1445, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7043, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:54.892766", "source": { "split": "train_shard_00000", "doc_id": 4787 }, "chunk_id": "train_shard_00000_4787_0", "global_id": 5359 }, { "text": "Bacteriophages are rich in genetic diversity, due to frequent horizontal transfer and recombination. This makes traditional microbial phylogenetic analyses, often based on the assumption of vertical inheritance, not suitable for interpreting this diversity. Here, inspired by recent work on bacterial pangenomes, we investigate the evolution of a collection of 3425 actinobacteriophage genomes. We find that synteny is strongly conserved: core genes have a well-defined order, and most accessory genes are localized in a few locations along the core genome backbone. Within the core genome alignment, linkage disequilibrium decays rapidly with distance in some groups, while phylogenetic structure in other groups causes long-range linkage. Our quantitative characterizations extend across many groups of phages and indicate widespread homologous recombination restricted by strong gene order conservation.\n\nSynteny and linkage decay in bacteriophage pangenomes", "token_count": 212, "char_count": 961, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7846, "quality_score": 0.8923, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:55.357768", "source": { "split": "train_shard_00000", "doc_id": 4788 }, "chunk_id": "train_shard_00000_4788_0", "global_id": 5360 }, { "text": "Kluyveromyces marxianus was engineered to mitigate carbon catabolite repression to efficient co-fermenting mixed sugars, which are primary components of cellulosic biomass. Kluyveromyces marxianus KDH1 produced ethanol with 0.42 ± 0.01 g/g yield, and 0.67 ± 0.00 g/L·h productivity for 48 h. RNA sequencing-based transcriptomic analysis showed that genes from the glycolysis pathway, gluconeogenesis pathway, and the citric acid cycle were primarily upregulated when K. marxianus KDH1 fermented mixed sugars. Furthermore, critical genes from the gluconeogenesis pathway, such as fructose-1,6-bisphosphatase and phosphoenolpyruvate carboxykinase, were upregulated by 331.72 and 47.15-fold, respectively. Citrate synthase and malate dehydrogenase, associated with the citric acid cycle, were upregulated by 2284.62 and 7.69-fold, respectively. Enzymatic assays of fructose 1, 6-bisphosphatase indicated that K. marxianus KDH1 showed 1.87-fold higher enzymatic activity than that of the parental strain. These results provide novel information on mixed sugar co-fermentation and a new glucose fermentation process that bypasses the glycolysis pathway.

Supplementary information

The online version contains supplementary material available at 10.1007/s10068-024-01670-5.\n\nUpregulation of the gluconeogenesis pathway was observed by <i>Kluyveromyces marxianus</i> KDH1, mitigating glucose catabolite repression.", "token_count": 511, "char_count": 1453, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7052, "quality_score": 0.8526, "entities": { "genes": [ "KDH1" ], "proteins": [], "pathways": [ "glycolysis", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:56.009436", "source": { "split": "train_shard_00000", "doc_id": 4789 }, "chunk_id": "train_shard_00000_4789_0", "global_id": 5361 }, { "text": "Candida parapsilosis is an opportunistic yeast pathogen that can cause life-threatening infections in immunocompromised humans. Whole-genome sequencing studies of the species have demonstrated remarkably low diversity, with strains typically differing by about 1.5 single nucleotide polymorphisms (SNPs) per 10 kb. However, SNP calling alone does not capture the full extent of genetic variation. Here, we define the pangenome of 372 C. parapsilosis isolates to determine variation in gene content. The pangenome consists of 5,859 genes, of which 48 are not found in the genome of the reference strain. This includes 5,791 core genes (present in ≥99.5% of isolates). Four genes, including the allantoin permease gene DAL4, were present in all isolates but were truncated in some strains. The truncated DAL4 was classified as a pseudogene in the reference strain CDC317. CRISPR-Cas9 gene editing showed that removing the early stop codon (producing the full-length Dal4 protein) is associated with improved use of allantoin as a sole nitrogen source. We find that the accessory genome of C. parapsilosis consists of 68 homologous clusters. This includes 38 previously annotated genes, 27 novel paralogs of previously annotated genes, and 3 uncharacterized open reading frames. Approximately one-third of the accessory genome (24/68 genes) is associated with gene fusions between tandem genes in the major facilitator superfamily. Additionally, we identified two highly divergent C. parapsilosis strains and found that, despite their increased phylogenetic distance (~30 SNPs per 10 kb), both strains have similar gene content to the other 372.IMPORTANCECandida parapsilosis is a human fungal pathogen listed in the high-priority group by the World Health Organization", "token_count": 508, "char_count": 1822, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [ "CDC317", "DAL4" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:56.666597", "source": { "split": "train_shard_00000", "doc_id": 4790 }, "chunk_id": "train_shard_00000_4790_0", "global_id": 5362 }, { "text": "It is an increasing cause of hospital-acquired and drug-resistant infections. Here, we studied the genetic diversity of 372 C. parapsilosis isolates, the largest genomic surveillance of this species to date. We show that there is relatively little genetic variation. However, we identified two more distantly related isolates from Germany, suggesting that even more sampling may yield more diversity. We find that the pangenome (the cumulative gene content of all isolates) is surprisingly small, compared to other fungal species. Many of the non-core genes are involved in transport. We also find that variations in gene content are associated with nitrogen metabolism, which may contribute to the virulence characteristics of this species.\n\nSmall pangenome of <i>Candida parapsilosis</i> reflects overall low intraspecific diversity.", "token_count": 204, "char_count": 861, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:57.132813", "source": { "split": "train_shard_00000", "doc_id": 4790 }, "chunk_id": "train_shard_00000_4790_1", "global_id": 5363 }, { "text": "

Introduction

In lambs, the function of the rumen is incompletely developed at weaning, and the inclusion of yeast cultures in the diet can profoundly influence the morphological and functional development of the rumen.

Methods

In this study, the effects of Saccharomyces cerevisiae and Kluyveromyces marxianus (NM) yeast co-cultures on ruminal histomorphology were assessed, and corresponding transcriptomic changes within the rumen epithelium were identified. In total, 24 lambs were grouped into four groups of six lambs including a control (C) group fed a basal diet, and N, M, and NM groups in which lambs were fed the basal diet, respectively, supplemented with Saccharomyces cerevisiae yeast cultures (30 g/d per head), Kluyveromyces marxianus yeast cultures (30 g/d per head), and co-cultures of both yeasts (30 g/d per head), the experiment lasted for 42 d.

Results

In morphological analyses, lambs from the NM group presented with significant increases in papilla length, papilla width, and epithelial thickness in the rumen relative to lambs in the C group (p < 0.05). Transcriptomic analyses revealed 202 genes that were differentially expressed between samples from the C and NM groups, with the largest proportion of these genes being associated with the oxidative phosphorylation pathway. In a weighted gene coexpression network analysis, a positive correlation was observed between the MEgreen and MEpurple modules and rumen morphology. Of these modules, the MEgreen module was found to be more closely linked to fatty acid metabolism and oxidative phosphorylation, whereas the MEpurple module was linked to oxidative phosphorylation and fatty acid degradation", "token_count": 482, "char_count": 1732, "word_count": 246, "semantic_coherence": 1, "information_density": 0.561, "quality_score": 0.7805, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:57.777116", "source": { "split": "train_shard_00000", "doc_id": 4791 }, "chunk_id": "train_shard_00000_4791_0", "global_id": 5364 }, { "text": "Ultimately, these results suggest that dietary supplementation with NM has driven the degradation of fatty acids, the induction of oxidative phosphorylation, the acceleration of lipid metabolism, the production of ATP to sustain ruminal growth, and the maintenance of intracellular NADH/NAD+ homeostasis on weaned lambs and is superior to single yeast fermentation.

Discussion

These results thus offer a theoretical foundation for further studies examining the mechanisms through which NM cultures can influence ruminal development in lambs.\n\nTranscriptomic characterization of the functional and morphological development of the rumen wall in weaned lambs fed a diet containing yeast co-cultures of Saccharomyces cerevisiae and Kluyveromyces marxianus.", "token_count": 201, "char_count": 774, "word_count": 100, "semantic_coherence": 1, "information_density": 0.73, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:58.235037", "source": { "split": "train_shard_00000", "doc_id": 4791 }, "chunk_id": "train_shard_00000_4791_1", "global_id": 5365 }, { "text": "Background: Whey fermentation could produce bioactive substances with immunomodulatory effects, metabolic syndrome modulation, and antioxidant properties, thereby imparting functional characteristics to products and facilitating the development of novel foods with health-promoting potential. Methods: A non-targeted metabolomics approach using liquid chromatography-mass spectrometry (LC-MS) was employed to investigate changes in the metabolite profiles of whey fermented by Kluyveromyces marxianus strain KM812 over varying fermentation durations. Results: The findings demonstrated a progressive enrichment of metabolites over time. A total of 151 differential metabolites were identified and categorized primarily into amino acids, peptides, and analogues, fatty acids and conjugates, and carbohydrates and conjugates, as well as benzoic acids and derivatives. The highest relative content of whey metabolites was observed at 48 h of fermentation, with a cumulative increase of 1.45-fold, 1.49-fold, 3.39-fold, and 1.24-fold for peptides and amino acids, peptides, and analogues, fatty acids and conjugates, and carbohydrates and conjugates, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed associations with 23 specific metabolites and delineated 9 metabolic pathways, predominantly involved in amino acid and lipid metabolism. Conclusions: Based on the above, KM812 could effectively degrade macromolecular substances in whey into small molecules such as L-isoleucine, ornithine, betaine, α-linolenic acid, and palmitoleic acid, thereby influencing the nutritional and functional properties of whey. In-depth analysis of the metabolic products in KM812-fermented whey could provide a theoretical basis for the development of functional foods derived from small molecules in the future.", "token_count": 507, "char_count": 1857, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6186, "quality_score": 0.8093, "entities": { "genes": [ "KM812" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:58.889260", "source": { "split": "train_shard_00000", "doc_id": 4792 }, "chunk_id": "train_shard_00000_4792_0", "global_id": 5366 }, { "text": "Non-Targeted Metabolomics Analysis Reveals Metabolite Profiles Change During Whey Fermentation with Kluyveromyces marxianus.", "token_count": 41, "char_count": 131, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:59.261106", "source": { "split": "train_shard_00000", "doc_id": 4792 }, "chunk_id": "train_shard_00000_4792_1", "global_id": 5367 }, { "text": "Kluyveromyces marxianus is an attractive thermotolerant yeast species for ethanol production because of its ability to utilize various carbon sources as a fermentation substrate. The use of thermotolerant microbes enables performance of high-temperature ethanol fermentation, which has several advantages including reduction of cooling costs and minimization of contamination risk. To improve K. marxianus for ethanol fermentation under stress conditions, two strains, DMKU 3-1042 and DMKU 3-118, were adapted for heat resistance and toxic substances in pulp wastewater from a paper mill, respectively, resulting in the generation of KMR1042 and KMR118, respectively. Both adapted mutants exhibited clumpy clusters of cells as pseudohyphae and altered colony morphology, and their sedimentation speeds were much faster than those of the corresponding parent strains. The two mutants showed stronger tolerance to various stresses and higher performance for ethanol production than those of the corresponding parent strains at high temperatures or in the presence of toxic substances. Genome sequencing analysis revealed that both mutants had disruption of the same gene, SWI5, despite adaptation under different stress conditions, suggesting that the formation of pseudohyphae is a common strategy of K. marxianus for coping with stresses.\n\nMutants with Enhanced Multi-Stress Tolerance of Kluyveromyces marxianus and Their Ability for Ethanol Fermentation", "token_count": 339, "char_count": 1454, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [ "KMR1042", "SWI5", "KMR118" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:47:59.861898", "source": { "split": "train_shard_00000", "doc_id": 4793 }, "chunk_id": "train_shard_00000_4793_0", "global_id": 5368 }, { "text": "

Objectives

EUCAST has established clinical breakpoints and epidemiological cutoff values (ECOFFs) for Candida spp. However, limited data are available for 5-flucytosine (5-FC). We assessed the in vitro susceptibility of 5-FC against a large collection of clinical Candida species using EUCAST methodology and determined the associated ECOFFs.

Methods

A total of 5622 Candida isolates were collected from patients across the Netherlands between 2008 and 2024. 5-FC MICs were determined using the EUCAST microbroth dilution reference method. Furthermore, MICs were extracted from the EUCAST website. The MICs from this study and those extracted were used to determine ECOFFs and local ECOFFs (L-ECOFFs).

Results

5-FC exhibited potent in vitro activity against C. albicans, N. glabratus and C. parapsilosis, while decreased susceptibility was observed for C. tropicalis, Pichia species, K. marxianus, Y. lipolytica, and C. auris. The ECOFFs (mg/L) and the percentages of WT isolates for 5-FC were: C. albicans: 0.5 (97.2%), N. glabratus: 0.5 (96.6%), C. parapsilosis: 0.5 (99.5%) and P. kudriavzevii: 8 (99.4%). The L-ECOFF (mg/L) and the percentages of WT isolates for 5-FC were: C. dubliniensis: 0.25 (96.8%), C", "token_count": 513, "char_count": 1340, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:00.543406", "source": { "split": "train_shard_00000", "doc_id": 4794 }, "chunk_id": "train_shard_00000_4794_0", "global_id": 5369 }, { "text": "tropicalis: 0.25 (67.2%), K. marxianus: 0.25 (48.0%), C. lusitaniae: 0.25 (86.5%), M. guillermondii: 0.125 (95.9%) and P. norvegiensis: 8 (94.2%).

Conclusions

5-FC remains a valuable drug to manage difficult-to-treat invasive Candida infections. In vitro susceptibility cannot be predicted based on species identification for most Candida species, but requires MIC-testing. ECOFFs will help to interpret the MICs to support treatment decisions.\n\nWild-type MIC distributions and epidemiological cutoff values for 5-flucytosine and Candida species as determined by EUCAST broth microdilution.", "token_count": 256, "char_count": 657, "word_count": 76, "semantic_coherence": 1, "information_density": 0.8684, "quality_score": 0.9342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:01.127023", "source": { "split": "train_shard_00000", "doc_id": 4794 }, "chunk_id": "train_shard_00000_4794_1", "global_id": 5370 }, { "text": "The Bradyrhizobium genus is widely known for encompassing many species capable of forming nodules and establishing the biological nitrogen fixation process with several legumes, significantly contributing to agriculture and environmental sustainability. Despite its importance, questions about the evolution, pangenome, and symbiotic genes of Bradyrhizobium are still poorly understood. In this study, we analyzed the pangenome of a set of Bradyrhizobium symbiotic species using the Roary and GET_HOMOLOGUES tools in strains originated from the Northern and Southern Hemispheres. We also investigated the presence and correlation of the fix, nif, nod, Type III secretion system (T3SS) and their effector proteins, and T4SS genes, trying to find differences between clades, hosts, and biogeographic origin. Pangenome analysis of Bradyrhizobium species from the Northern and Southern Hemispheres provided valuable insights into their diversity, biogeography, origin, and co-evolution with their legume host plants. The genus possesses a relatively small core genome compared to the expanded accessory genome, a key feature that facilitates genetic exchange and acquisition of new genes, allowing adaptation to a variety of environments. Notably, the presence or absence of T3SS effector proteins varied significantly according to the geographic location, suggesting specific environmental adaptations, as well as a direct relationship with nodulation genes. Comparative analysis indicated that symbiotic Bradyrhizobium species originated in the Northern Hemisphere and present a greater diversity of orthologous groups than those from the Southern Hemisphere. These results contribute to our understanding of the evolutionary history of these symbiotic bacteria.\n\nPangenome analysis indicates evolutionary origins and genetic diversity: emphasis on the role of nodulation in symbiotic <i>Bradyrhizobium</i>.", "token_count": 467, "char_count": 1973, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:01.776861", "source": { "split": "train_shard_00000", "doc_id": 4795 }, "chunk_id": "train_shard_00000_4795_0", "global_id": 5371 }, { "text": "

Introduction

The cheese microbiota is very complex and is made up of technologically-relevant, spoilage, opportunistic and pathogenic microorganisms. Among them lactic acid bacteria and yeasts are the main ones. One of the most interesting dairy yeasts is Kluyveromyces marxianus because of its technological properties including the ability to produce aroma compounds.

Methods

This study investigated the contribution of Kluyveromyces marxianus to the gross composition and aroma profile of cow cheeses. Experimental cheeses were prepared by inoculating a co-culture of K. marxianus FM09 and a commercial strain of Lacticaseibacillus casei and compared with cheeses obtained with only L. casei. The gross composition was determined by a FoodScan™ 2 Dairy Analyser, and free amino acids were evaluated at 507 nm after reaction with Cd-ninhydrin. The volatile organic compounds were extracted by head-space solid phase micro-extraction and analyzed by gas chromatography-mass spectrometry coupled with odor activity values. qRT-PCR was applied to determine the expression of genes involved in esters synthesis and degradation.

Results

The inoculation of K. marxianus induced an increase of pH and a reduction of protein content of cheeses, in agreement with the stronger proteolysis detected in these cheeses. K. marxianus influenced the content of aroma compounds both quantitatively and qualitatively. In particular, an increase of higher alcohols, esters and organic acids was observed. Moreover, 12 compounds were detected only in cheeses obtained with the co-culture. These differences were in agreement with the odor activity values (OAV). In fact, only 11 compounds showed OAV > 1 in cheeses obtained with the commercial strain, and 24 in those obtained with the co-culture", "token_count": 504, "char_count": 1850, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5765, "quality_score": 0.7882, "entities": { "genes": [ "FM09" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:02.437114", "source": { "split": "train_shard_00000", "doc_id": 4796 }, "chunk_id": "train_shard_00000_4796_0", "global_id": 5372 }, { "text": "The qPCR analysis revealed an over expression of ATF1, EAT1, and IAH1 genes.

Conclusion

Kluyveromyces marxianus could act as an important auxiliary starter for cheese production through the development and diversification of compounds related to flavor in short-aged cow cheeses.\n\nUnlocking the potential of Kluyveromyces marxianus in the definition of aroma composition of cheeses.", "token_count": 134, "char_count": 424, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:02.870904", "source": { "split": "train_shard_00000", "doc_id": 4796 }, "chunk_id": "train_shard_00000_4796_1", "global_id": 5373 }, { "text": "Kefir is a fermented dairy product that contains many types of lactic acid bacteria and different types of yeast. Yeasts in kefir culture are important in creating the unique properties of kefir. When yeasts are not included in kefir production, the unique properties of kefir do not emerge. In this study, the effects of various yeast microorganisms that can cause negative effects, such as swelling and deformation, in industrial kefir production on product quality characteristics were investigated. For this purpose, a commercial yeast-free kefir culture was supplemented with selected yeasts: Kluyveromyces marxianus (KM), Debaryomyces hansenii (DH), Kluyveromyces lactis (KL), Saccharomyces boulardii (SB), Saccharomyces cerevisiae (SC), Candida colliculosa (CC), Yarrowia lipolytica (YL), and Geotrichum candidum (GC) used in kefir production. Some physicochemical, rheological, microbiological, and sensory properties of the kefirs were examined during 28 days of storage. As a result of the research, the highest hardness and viscosity values (131.00 ± 1.41 g-1236.50 ± 47.38 cp) were observed in kefirs containing G. candidum, while the highest CO2 amount (151.40 ± 1.07 mg/100 mL) was determined in kefirs containing S. cerevisiae (p < 0.05)", "token_count": 477, "char_count": 1340, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:03.519330", "source": { "split": "train_shard_00000", "doc_id": 4797 }, "chunk_id": "train_shard_00000_4797_0", "global_id": 5374 }, { "text": "While serum separation was not determined in any sample, the highest water holding capacity (58.00% ± 00%) was determined in kefirs containing Y. lipolytica. In terms of sensory evaluation, kefir enriched with C. colliculosa received the highest overall acceptance. In general, the use of different yeast types in kefir production is of great importance, especially in terms of gas-carbon dioxide (CO2) formation and product quality.\n\nImpact of Yeast Types on Quality Characteristics and Storage Stability of Industrial Kefir.", "token_count": 151, "char_count": 551, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:03.952732", "source": { "split": "train_shard_00000", "doc_id": 4797 }, "chunk_id": "train_shard_00000_4797_1", "global_id": 5375 }, { "text": "Kluyveromyces marxianus is an emerging yeast cell host for diverse products, but multiple-gene expression in K. marxianus faces challenges due to limited current knowledge of cis-regulatory elements and insertion loci. Our previous study transferred an alien Saccharomyces cerevisiae chromosome I (R1) into K. marxianus, resulting in the creation of the monochromosomal hybrid yeast KS-R1. All R1 genes were actively transcribed, providing a series of loci with varying transcriptional activities. Here, we explore the use of R1 as a novel platform for stable, multi-gene integration and expression. By deleting three essential K. marxianus genes while complementing their functions with orthologs on R1, we achieved stable propagation of R1 in the absence of selective pressure. We characterized several loci on R1 that exhibit stable transcriptional activities under various conditions. GFP inserted in place of genes at six such loci demonstrated varying expression levels. Strains with GFP at two loci exhibited significantly higher expression than those with GFP at a single locus. Furthermore, we replaced five R1 genes with disulfide bond formation genes from Pichia pastoris at distinct loci, resulting in the active expression of all five genes and significantly enhanced production of heterologous glucoamylases BadGLA and TeGlaA. Our findings demonstrate that alien chromosomes offer a stable and versatile platform for the coordinated expression of multiple heterologous genes, serving as valuable tools for metabolic engineering and synthetic biology.\n\nAlien Chromosome Serves as a Novel Platform for Multiple Gene Expression in <i>Kluyveromyces marxianus</i>.", "token_count": 460, "char_count": 1755, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:04.590965", "source": { "split": "train_shard_00000", "doc_id": 4798 }, "chunk_id": "train_shard_00000_4798_0", "global_id": 5376 }, { "text": "Patulin (PAT) is a mycotoxin produced by Penicillium species, which often contaminates fruit and fruit-derived products, posing a threat to human health and food safety. This work aims to investigate the detoxification of PAT by Kluyveromyces marxianus YG-4 (K. marxianus YG-4) and its application in apple juice. The results revealed that the detoxification effect of K. marxianus YG-4 on PAT includes adsorption and degradation. The adsorption binding sites were polysaccharides, proteins, and some lipids on the cell wall of K. marxianus YG-4, and the adsorption groups were hydroxyl groups, amino acid side chains, carboxyl groups, and ester groups, which were combined through strong forces (ion interactions, electrostatic interactions, and hydrogen bonding) and not easily eluted. The degradation active substance was an intracellular enzyme, and the degradation product was desoxypatulinic acid (DPA) without cytotoxicity. K. marxianus YG-4 can also effectively adsorb and degrade PAT in apple juice. The contents of organic acids and polyphenols significantly increased after detoxification, significantly improving the quality of apple juice. The detoxification ability of K. marxianus YG-4 toward PAT would be a novel approach for the elimination of PAT contamination.\n\nDetoxification of Mycotoxin Patulin by the Yeast Kluyveromyces marxianus YG-4 in Apple Juice.", "token_count": 423, "char_count": 1430, "word_count": 197, "semantic_coherence": 1, "information_density": 0.599, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:05.218039", "source": { "split": "train_shard_00000", "doc_id": 4799 }, "chunk_id": "train_shard_00000_4799_0", "global_id": 5377 }, { "text": "γ-Aminobutyric acid (GABA) is a valuable amino acid widely used in food, healthcare, and agriculture. GABA bioproduction by budding yeasts has been commonly reported, but related studies using non-conventional yeasts remain limited. In this study, two non-conventional natural yeast strains, namely, Kluyveromyces marxianus JMY140K and Metschnikowia reukaufii JMY075, were identified as promising GABA producers, and M. reukaufii JMY075 was discovered to be a GABA producer. Enhanced GABA production was observed in the two yeast strains under stress conditions, including high temperature and high ethanol and acetic acid levels. In particular, K. marxianus JMY140K showed 7.93 times higher GABA titers under thermal stress than that of the control. External stress conditions significantly influenced the GABA production of these two yeast strains. The culture filtrate of K. marxianus JMY140K also showed promising activities in human skin cells. In addition, K. marxianus JMY140K could also produce GABA using rice straw hydrolysate, which indicated that it has the potential to produce GABA using renewable biomass. Our studies provide insight for further enhancing the GABA production of natural yeasts and promoting its biotechnology applications.\n\nStress-Driven Production of γ-Aminobutyric Acid Using Non-Conventional Yeast Strains Kluyveromyces marxianus JMY140K and Metschnikowia reukaufii JMY075.", "token_count": 443, "char_count": 1464, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6051, "quality_score": 0.8026, "entities": { "genes": [ "JMY140K", "JMY075" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:05.853050", "source": { "split": "train_shard_00000", "doc_id": 4800 }, "chunk_id": "train_shard_00000_4800_0", "global_id": 5378 }, { "text": "The present work examined the production of single-cell protein (SCP) by a newly isolated strain of Kluyveromyces marxianus EXF-5288 under increased lactose concentration of deproteinized cheese whey (DCW) and different temperatures (in °C: 20.0, 25.0, 30.0 and 35.0). To the best of the authors' knowledge, this is the first report examining the ability of Kluyveromyces marxianus species to produce SCP at T = 20.0 °C. Different culture temperatures led to significant differences in the strain's growth, while maximum biomass and SCP production (14.24 ± 0.70 and 6.14 ± 0.66 g/L, respectively) were observed in the cultivation of K. marxianus strain EXF-5288 in shake-flask cultures at T = 20.0 °C. Increased DCW lactose concentrations (35.0-100.0 g/L) led to increased ethanol production (Ethmax = 35.5 ± 0.2 g/L), suggesting that K. marxianus strain EXF-5288 is \"Crabtree-positive\". Batch-bioreactor trials shifted the strain's metabolism to alcoholic fermentation, favoring ethanol production. Surprisingly, K. marxianus strain EXF-5288 was able to catabolize the produced ethanol under limited carbon presence in the medium. The dominant amino acids in SCP were glutamate (15.5 mg/g), aspartic acid (12.0 mg/g) and valine (9.5 mg/g), representing a balanced nutritional profile.\n\nSingle-Cell Protein and Ethanol Production of a Newly Isolated Kluyveromyces marxianus Strain through Cheese Whey Valorization.", "token_count": 503, "char_count": 1467, "word_count": 204, "semantic_coherence": 1, "information_density": 0.598, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:06.863129", "source": { "split": "train_shard_00000", "doc_id": 4801 }, "chunk_id": "train_shard_00000_4801_0", "global_id": 5379 }, { "text": "

Background

Mycobacterium abscessus (Mab) is a multidrug-resistant bacterial pathogen capable of causing widespread infections, often with a poor prognosis in susceptible populations. Mab comprises three distinct subspecies that exhibit phenotypic diversity and genetic heterogeneity.

Methods

We performed whole-genome sequencing and phenotypic antimicrobial susceptibility testing on 109 Mab isolates collected at zhongshan hospital from 2018 to 2023.

Results

The results indicate that recombination, especially distributed conjugation transfer, promotes the formation and sustained diversity of Mab subspecies. Through pangenome analysis, the synergistic gain/loss of accessory genes was found to contribute to different metabolic profiles and the ability to adapt to oxidative stress, facilitating strain adaptation to host environments. We conducted phenotypic antimicrobial susceptibility testing, revealing resistance to macrolide antibiotics differed among subspecies. We identified 24 genes whose gain or loss may increase the likelihood of macrolide resistance, including those involved in biofilm formation, the stress response, virulence, biotin synthesis, and fatty acid metabolism. Genomic variations within Mab species may have significant implications for disease epidemiology, infection pathogenesis, and host interactions.

Conclusions

Our findings provide a valuable genetic basis for the success of Mab as a highly adaptive and drug-resistant pathogen, informing current efforts to control and treat Mab infections, including strategies targeting specific sequence types or lineages.\n\nWhole-genome recombination and dynamic accessory genomes drive the phenotypic diversity of Mycobacterium abscessus subspecies.", "token_count": 421, "char_count": 1757, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7264, "quality_score": 0.8632, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:07.489427", "source": { "split": "train_shard_00000", "doc_id": 4802 }, "chunk_id": "train_shard_00000_4802_0", "global_id": 5380 }, { "text": "This study introduces the ΔΔG method, a novel approach to analyzing metabolic regulation using relative quantification metabolome data. The method calculates shifts in the Gibbs free energy change (ΔG) in two different metabolic states. Subsequently, key reactions controlling the metabolic flux can be identified by comparing the ΔΔG values to the reaction rates. Two case studies demonstrated the applicability of this method. First, a metabolome data set was obtained from the wild-type and single-gene-deletion mutant strains of Saccharomyces cerevisiae. The ΔΔG values of the glycolytic reactions were calculated between those of the wild-type and each mutant strain. A positive correlation was observed between the ΔΔG values of phosphofructokinase (PFK) and the approximate glycolytic flux levels. These results suggested that PFK regulates glycolytic flux. Moreover, a comparison between S. cerevisiae (Crabtree-positive yeast) and Kluyveromyces marxianus (Crabtree-negative yeast) revealed that S. cerevisiae primarily regulates glycolysis through PFK, whereas K. marxianus employs a more distributed control. The ΔΔG method provides insights into metabolic regulation that are not apparent from metabolite profiles alone and is applicable to various biological systems, particularly for analyzing glycolysis. Furthermore, the simplicity of this method makes it a valuable tool for metabolic engineering and medical research.\n\nΔΔ<i>G</i> Method for Elucidating Key Control Reactions from Relative Quantification Metabolome Data: Comparative Analysis of Yeast Glycolysis.", "token_count": 462, "char_count": 1668, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:08.126476", "source": { "split": "train_shard_00000", "doc_id": 4803 }, "chunk_id": "train_shard_00000_4803_0", "global_id": 5381 }, { "text": "

Introduction

Interest in fermented foods and their purported health benefits has led to increased scientific research investigating the development of starter cultures which maintain the characteristics of traditional products while allowing for industrial scale production. One such fermented food that is gaining steady attention for industrial production is kefir. To improve the ease of use and maintenance of starter cultures without compromising desirable fermentation characteristics and potential health benefits, this study investigated the impact of freeze-drying a previously described reconstituted kefir consortia with two lyoprotectants trehalose and milk.

Methods

5 bacterial species (Lentilactobacillus kefiri, Lactobacillus kefiranofaciens, Lactococcus cremoris, Leuconostoc mesenteroides, and Acetobacter pasteurianus) and 4 yeast species (Saccharomyces cerevisiae, Pichia fermentans, Monosporozyma unispora, and Kluyveromyces marxianus) underwent freeze-drying prior to viability testing and use as starter cultures in kefir fermentations. Completed kefir fermentations were analyzed for pH, microbial composition, volatile compounds, organic acids, and sugar consumption. Freeze-dried starter culture fermentations were compared to kefir made with fresh starter cultures of the same species and pitching rate.

Results

All starter cultures were able to ferment milk to a similar pH, however the freeze-dried cultures prepared with milk took a longer time to complete fermentation. The total bacterial and yeast counts were comparable across the fermentations performed as was the composition of bacteria and yeast present as determined by shotgun metagenomic sequencing. High performance liquid chromatography (HPLC) analysis showed no difference in the levels of lactic acid, acetic acid, ethanol, glucose, and galactose", "token_count": 475, "char_count": 1890, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6695, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:08.777028", "source": { "split": "train_shard_00000", "doc_id": 4804 }, "chunk_id": "train_shard_00000_4804_0", "global_id": 5382 }, { "text": "Additionally, solid-phase microextraction followed by two-dimensional gas chromatography-time-of-flight mass spectrometry (SPME-GC × GC-TOFMS) showed that kefir fermented with freeze-dried starter cultures did not change the volatile profile compared to fresh cultures.

Conclusion

These findings indicate that freeze-dried starter cultures consisting of traditional kefir microorganisms are able to recreate the fresh starter culture version of this product. This provides encouraging evidence for the development of commercially viable starter cultures that are capable of recreating traditional functional fermented foods.\n\nFermentation of kefir with traditional freeze-dried starter cultures successfully recreates fresh culture fermented kefir.", "token_count": 172, "char_count": 755, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8315, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:09.220489", "source": { "split": "train_shard_00000", "doc_id": 4804 }, "chunk_id": "train_shard_00000_4804_1", "global_id": 5383 }, { "text": "Campylobacter is a major foodborne bacterial pathogen that has become increasingly resistant to clinically important antimicrobials. Of particular concern is the emergence of erm(B)-mediated macrolide resistance, which has been increasingly documented across Campylobacter isolates from diverse ecological reservoirs. In this study, we investigated the genomic characteristics and epidemiology of erm(B)-carrying clinical Campylobacter isolates from Shanghai, alongside a globally representative dataset of all publicly available strains. Among clinical isolates obtained from a diarrhoeal outpatient surveillance programme between 2020 and 2023 in Shanghai, China, 16% (80/500) were erythromycin-resistant, with 23.8% (19/80) testing positive for erm(B). The genomes of these isolates were sequenced to identify erm(B) gene alleles. Phylogenetic analyses, pairwise comparisons of core and accessory genomes and examination of shared alleles revealed horizontal gene transfer as the predominant mechanism driving the transmission of erm(B) between isolates from various sources. Poultry was identified as a key reservoir for human infections caused by erm(B)-positive Campylobacter isolates. Comparative pangenome analyses of erm(B)-positive and negative isolates identified multiple accessory elements associated with erm(B) acquisition, among which the IS607 family transposon-associated tnpB gene exhibited sequence and structural homology to functional progenitors of CRISPR-Cas nucleases. These findings expand our understanding of the epidemiology of erm(B)-mediated macrolide resistance in Campylobacter and underscore the urgent need for enhanced antimicrobial stewardship in poultry production and targeted surveillance programmes to curb the spread of resistance.", "token_count": 498, "char_count": 1878, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6637, "quality_score": 0.8318, "entities": { "genes": [ "IS607" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:09.867700", "source": { "split": "train_shard_00000", "doc_id": 4805 }, "chunk_id": "train_shard_00000_4805_0", "global_id": 5384 }, { "text": "Genomic epidemiology and the evolution of <i>erm</i>(B)-mediated macrolide resistance in <i>Campylobacter</i>.", "token_count": 53, "char_count": 134, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:10.233186", "source": { "split": "train_shard_00000", "doc_id": 4805 }, "chunk_id": "train_shard_00000_4805_1", "global_id": 5385 }, { "text": "Increasingly, antimicrobial-resistant (AMR) Salmonella Dublin is a threat to human and animal health, therefore requiring a One Health approach to comprehensively understand pathogen evolution. Moreover, S. Dublin dissemination throughout the United States and the food supply chain is a concern for food safety and security. Here, we leveraged multi-agency biosurveillance data and genomic sequencing of S. Dublin strains to provide a robust analysis of its evolution across human, animal, and environmental reservoirs. This study advances our understanding of AMR S. Dublin, elucidates factors driving AMR emergence, and informs interventions to protect public health. In total, 2,150 strains collected between 2002 and 2023 throughout the United States from clinical bovine (N = 581), clinical human (N = 664), and environmental (N = 905) sources were identified. After uniform quality control, raw reads were assembled de novo followed by genome annotation and characterization of plasmids, antimicrobial resistance genes, and virulence factors. Strain relatedness was evaluated using a core genome maximum-likelihood phylogeny and pairwise core genome single-nucleotide polymorphism (SNP) differences. We identified the highest prevalence of drug-specific antimicrobial resistance genes and multidrug resistance plasmid, IncA/C2 (P < 0.001), in bovine clinical strains, which also had the greatest genetic diversity. Despite source-dependent differences in antimicrobial resistance gene frequency and types, 72% of S. Dublin strains in our study differed with at least one other strain by 20 or fewer SNPs", "token_count": 452, "char_count": 1680, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8473, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:10.873913", "source": { "split": "train_shard_00000", "doc_id": 4806 }, "chunk_id": "train_shard_00000_4806_0", "global_id": 5386 }, { "text": "This high degree of genomic similarity highlights the potential for cross-transmission between humans, animals, and the environment and underscores the importance of considering strain source when assessing and monitoring antimicrobial resistance.IMPORTANCESalmonella Dublin is a zoonotic, sometimes foodborne, pathogen that causes severe illness in cattle and humans. Our study takes a One Health approach to understanding genetic differences in strains within and between different reservoirs in the United States. We identified differences in antimicrobial resistance potential and genome content between clinical bovine, clinical human, and environmental strains. Nonetheless, the U.S. population of S. Dublin is highly related and diverges minimally over time and geography. These findings highlight the importance of the One Health framework when combating zoonotic antimicrobial-resistant pathogens like Salmonella Dublin.\n\nGenomic evolution of <i>Salmonella</i> Dublin in cattle and humans in the United States.", "token_count": 237, "char_count": 1052, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6791, "quality_score": 0.8396, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:11.367502", "source": { "split": "train_shard_00000", "doc_id": 4806 }, "chunk_id": "train_shard_00000_4806_1", "global_id": 5387 }, { "text": "Casein is rich in immunomodulatory peptides. In this study, the release of casein-derived immunomodulatory peptides by Kluyveromyces marxianus JY-1 was investigated for the first time, and an immunosuppressive mouse model was used to evaluate the immunomodulatory activity in the casein hydrolysate. The results showed that the cellular and humoral immunity of immunosuppressed mice could be significantly enhanced by casein hydrolysate. Peptide HPHPHLSF with high immunomodulatory activity from casein hydrolysate was screened using the virtual screening technique. HPHPHLSF possessed strong immunomodulatory activity and significantly upregulated the expression of IL-6, IL-1β, and TNF-α. Next, the interaction of HPHPHLSF with TLR2/4 on the cell surface of RAW264.7 cells was further elucidated by molecular docking and combined analysis of double-stranded small interfering RNA and receptor inhibitors. Further, the results of the highest occupied molecular orbital energy distribution elucidated that the histidine active site C48═O49 played an important role in the immunomodulatory activity of HPHPHLSF. This study confirmed that casein hydrolyzed by K. marxianus JY-1 was a natural immunomodulator, while the structure-activity relationship analysis provided new theoretical and technical support for the targeted preparation and screening of casein-derived immunomodulatory peptides.\n\nNew Insights into the Structure-Activity Relationship of a Novel Immunomodulatory Peptide (HPHPHLSF) from Casein Hydrolyzed by Kluyveromyces marxianus JY-1: Molecular Docking, Interaction Evaluation, and HOMO Analysis.", "token_count": 468, "char_count": 1655, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5782, "quality_score": 0.7891, "entities": { "genes": [ "RAW264", "TLR2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:12.035151", "source": { "split": "train_shard_00000", "doc_id": 4807 }, "chunk_id": "train_shard_00000_4807_0", "global_id": 5388 }, { "text": "Streptococcus uberis is a leading cause of bovine mastitis, resulting in large economic losses and welfare issues for affected cows. However, relatively little is known about the global distribution and emergence of bovine mastitis-causing lineages and dissemination of antimicrobial resistance or virulence genes in the species. Here, we present a global framework for S. uberis based on whole-genome sequencing data from isolates across four continents (n=1,070). Internationally, S. uberis isolates show extensive genetic heterogeneity driven by homologous recombination and high levels of accessory genome content. Within the population, 35% (n=374/1,070) of isolates had at least one acquired antimicrobial resistance gene, while 59% (n=631/1,070) of isolates harboured a mutation in the penicillin-binding proteins (pbp2b or pbp2x) associated with decreased penicillin susceptibility, the front-line antimicrobial for mastitis infections. All described S. uberis virulence factors and currently proposed vaccine candidates were investigated for carriage and sequence heterogeneity to guide potential vaccine development, with two vaccine candidates (GapC and Sua) and seven putative virulence proteins (Fba, FbpS, Vru, GlnA, SUB0888, SUB0241 and haemolysin-like protein) having low naturally occurring sequence variation and high (>99%) coverage. This study will facilitate improved genomic surveillance for the emergence of antimicrobial resistance and virulence in this important mastitis pathogen.\n\nGlobal analysis of the genomic diversity, antimicrobial resistance and potential vaccine candidates carried by the major global bovine pathogen <i>Streptococcus uberis</i>.", "token_count": 499, "char_count": 1755, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [ "SUB0241", "SUB0888" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:12.724301", "source": { "split": "train_shard_00000", "doc_id": 4808 }, "chunk_id": "train_shard_00000_4808_0", "global_id": 5389 }, { "text": "Engineering a modular pectin-to-lipids bioconversion system using two Kluyveromyces marxianus strains.", "token_count": 31, "char_count": 102, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:13.144809", "source": { "split": "train_shard_00000", "doc_id": 4809 }, "chunk_id": "train_shard_00000_4809_0", "global_id": 5390 }, { "text": "Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized to any significant extent. The formation of secondary bile acids is important in the etiology of cancers of the GI tract and in the prevention of Clostridioides difficile infection. We determined the presence and absence of bile acid inducible (bai) and steroid-17,20-desmolase (des) genes among C. scindens strains and the features of the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the C. scindens cultivars have an open pangenome with 12,720 orthologous gene groups and a core genome with 1630 gene families, in addition to 7051 and 4039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The pangenome profile including the MAGs also proved to be open. Our analyses reveal that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, as suggested by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C. scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.", "token_count": 491, "char_count": 1623, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6137, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:13.793224", "source": { "split": "train_shard_00000", "doc_id": 4810 }, "chunk_id": "train_shard_00000_4810_0", "global_id": 5391 }, { "text": "Pangenome Analysis of <i>Clostridium scindens</i>: A Collection of Diverse Bile Acid- and Steroid-Metabolizing Commensal Gut Bacterial Strains.", "token_count": 55, "char_count": 155, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:14.152721", "source": { "split": "train_shard_00000", "doc_id": 4810 }, "chunk_id": "train_shard_00000_4810_1", "global_id": 5392 }, { "text": "The soluble dietary fiber (SDF) was made from separate and co-fermented okara utilizing Lactic acid bacteria (LAB) and Kluyveromyces marxianus C21, and the physicochemical and functional properties of SDF were assessed both before and after modification. The results showed that compared with non-fermented okara, the content of SDF from separate and co-fermented okara utilizing LAB and K. marxianus C21 increased by 16.9%, 19.5%, and 21.6%, respectively. Scanning electron microscopy studies showed that compared to separate and non-fermented okara, co-fermented okara SDF had the most excellent porous surface, the loosest structure, and a greater specific surface area. The ratios of the components of monosaccharides have altered. Additionally, the fermented okara SDFs had reduced particle sizes and spectral patterns similar to those of the non-fermented okara according to particle size distribution and Fourier transform infrared spectroscopy. In addition, co-fermented okara SDF showed increased oil-holding (8.66 g/g), water-swelling (10.33 mL/g), and water-holding (12.87 g/g) capabilities. Additionally, okara SDF's antioxidant, in vitro hypoglycemic, and hypolipidemic properties were all successfully increased by all fermentation treatment groups. In summary, the study's fermented okara SDF offers a high reference value for okara's future use and exploitation, making it a viable functional ingredient.\n\nCharacterization of physicochemical and functional properties of soluble dietary fiber from separate and co-fermented okara by lactic acid bacteria and Kluyveromyces marxianus C21", "token_count": 435, "char_count": 1601, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5734, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:14.777245", "source": { "split": "train_shard_00000", "doc_id": 4811 }, "chunk_id": "train_shard_00000_4811_0", "global_id": 5393 }, { "text": "

Objective

The profile of Candida species and their sensitivity to antifungal drugs isolated from patients in Eastern Poland were analyzed. Identification and drug resistance interpretation issues for clinically significant rare species were investigated.

Methods

A total of 197 yeast isolates were analyzed. Fungal identification was conducted using biochemical tests and MALDI-TOF. Minimum inhibitory concentrations (MICs) were determined for amphotericin B, fluconazole, itraconazole, voriconazole, isavuconazole, posaconazole, caspofungin, micafungin, and anidulafungin. Interpretation of results was based on the EUCAST, CLSI recommendations, and available literature.

Results

The following species were identified: Candida albicans (n=78), C. glabrata (Nakaseomyces glabrata) (n=30), C. dubliniensis (n=23), C. krusei (Pichia kudriavzevii) (n=13), C. parapsilosis (n=13), C. tropicalis (n=7), C. kefyr (Kluyveromyces marxianus) (n=6), C. lusitaniae (Clavispora lusitaniae) (n=6), C. lipolytica (Yarrowia lipolytica) (n=3), C. famata (Debaryomyces hansenii) (n=2), C. intermedia (n=2), C. guillermondii (Meyerozyma guilliermondii) (n=2), C", "token_count": 522, "char_count": 1308, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7687, "quality_score": 0.8843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:15.442666", "source": { "split": "train_shard_00000", "doc_id": 4812 }, "chunk_id": "train_shard_00000_4812_0", "global_id": 5394 }, { "text": "ciferrii (n=1), C. orthopsilosis (n=1), C. pelliculosa (Wickerhamomyces anomalus) (n=1), C. shehatae (n=1), C. fabianii (Cyberlindnera fabianii) (n=1), Cryptococcus humicola (Vanrija humicola) (n=4), and Saccharomyces cerevisiae (n=3). The highest percentage of resistant strains was reported for C. albicans, C. glabrata, C. parapsilosis, C. tropicalis, and C. lusitaniae.

Conclusion

Among the studied isolates, rare Candida species were identified. Their identification in routine diagnostics can be challenging, necessitating the use of MALDI-TOF MS. The wide spectrum of isolated species may complicate the establishment of a targeted antifungal therapy due to the lack of reference MIC ranges for the interpretation of antibiograms. Gradient strips are an accurate, reproducible, and convenient method for MIC determination.\n\nAnalysis of Antifungal Drug Resistance Among <i>Candida</i> Spp. and Other Pathogenic Yeasts Isolated from Patients in Eastern Poland: Diagnostic Problems.", "token_count": 388, "char_count": 1093, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:16.057226", "source": { "split": "train_shard_00000", "doc_id": 4812 }, "chunk_id": "train_shard_00000_4812_1", "global_id": 5395 }, { "text": "Abstract

The bacterial accessory genome, comprised of plasmids, phages, and other mobile elements, underpins the adaptability of bacterial populations. Pangenome (core and accessory) analysis of pathogens can reveal epidemiological relatedness missed by using core-genome methods alone. Employing a k-mer-based Jaccard Index approach to compute pangenome relatedness, we explored the population structure and epidemiology of Salmonella enterica serotype Hadar (Hadar), an emerging zoonotic pathogen in the United States (U.S.) linked to both commercial and backyard poultry. Hadar populations underwent substantial shifts between 2019 and 2020 in the U.S., driven by the expansion of a lineage carrying a previously uncommon prophage-like element. Phylogenetic and pangenomic relatedness, coupled with epidemiological data, suggest this lineage emerged from extant populations circulating in commercial poultry, with subsequent dissemination into backyard poultry environments. We demonstrate the utility of pangenomic approaches for mapping vertical and horizontal diversity and informing complex dynamics of zoonotic bacterial pathogens.

\n\nThe Salmonella enterica serotype Hadar pangenome: Population structure and dynamics of a zoonotic pathogen", "token_count": 320, "char_count": 1304, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:16.623596", "source": { "split": "train_shard_00000", "doc_id": 4813 }, "chunk_id": "train_shard_00000_4813_0", "global_id": 5396 }, { "text": "

Background

N-glycosylation is a prevalent post-translational modification in eukaryotes, essential for regulating protein secretion. In Saccharomyces cerevisiae, glycosylation mutants have been shown to enhance the secretion of heterologous glycosylated proteins. However, whether these mutants can also increase the secretion of non-glycosylated proteins and whether the growth defects associated with glycosylation mutations can be mitigated remains unclear. This study aimed to characterize and optimize enhanced secretory expression in the promising yeast host Kluyveromyces marxianus by deleting MNN11, which encodes a subunit of the mannose polymerase II complex responsible for elongating α-1,6-linked mannose chains.

Results

Compared to wild-type cells, the mnn11Δ cells significantly increased the secretion activities of four glycosylated enzymes and three non-glycosylated enzymes in flasks, with increases ranging from 29 to 668%. Transcriptomic analysis of mnn11Δ mutant revealed upregulation of genes related to essential protein secretion processes, including vesicle coating and tethering, protein folding, translocation, and glycosylation. Additionally, genes involved in vacuolar amino acid transport and amino acid biosynthesis were upregulated, suggesting an amino acid shortage, which might contribute to the observed severe growth defect of the mnn11Δ mutant in a synthetic medium with inorganic nitrogen. Supplementation of the synthetic medium with amino acids or low concentrations of yeast extract alleviated this growth defect, reducing the specific growth rate difference between wild-type strain and mnn11Δ cells from 65% to as little as 2%", "token_count": 429, "char_count": 1684, "word_count": 220, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [ "MNN11" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:17.251848", "source": { "split": "train_shard_00000", "doc_id": 4814 }, "chunk_id": "train_shard_00000_4814_0", "global_id": 5397 }, { "text": "During high-density fermentation, the addition of 0.5% yeast extract substantially reduced the lag phase of mnn11Δ mutants and increased the secretory activities of α-galactosidase, endoxylanase, and β-glucanase, by 11%, 18%, and 36%, respectively, compared to mnn11Δ mutant grown without yeast extract.

Conclusion

In K. marxianus, deletion of MNN11 enhances the secretion of both glycosylated and non-glycosylated proteins by improving key protein secretion processes. The growth defect in the mnn11Δ mutant is closely tied to insufficient amino acid supply. Supplementing the synthetic medium with low concentrations of organic nitrogen sources effectively alleviates this growth defect and enhances secretory expression. This strategy could be applied to optimize the expression of other glycosylation mutants.\n\nCharacterization and optimization of mnn11Δ-mediated enhancement in heterologous protein production in Kluyveromyces marxianus.", "token_count": 253, "char_count": 949, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7131, "quality_score": 0.8566, "entities": { "genes": [ "MNN11" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:17.740246", "source": { "split": "train_shard_00000", "doc_id": 4814 }, "chunk_id": "train_shard_00000_4814_1", "global_id": 5398 }, { "text": "Single-Cell Protein and Ethanol Production of a Newly Isolated Kluyveromyces marxianus Strain through Cheese Whey Valorization", "token_count": 36, "char_count": 126, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:18.102681", "source": { "split": "train_shard_00000", "doc_id": 4815 }, "chunk_id": "train_shard_00000_4815_0", "global_id": 5399 }, { "text": "The demand for controllable fragrance materials is substantial owing to their potential to impart enduring scents in a variety of applications. However, the practical application of such materials has been limited by challenges in tunable morphogenesis, structural variability, and adaptability to diverse conditions. In our study, we introduce a hybrid living material that integrates a genetically engineered strain of Kluyveromyces marxianus CBS6556 with an adaptive hydrogel. The engineered K. marxianus achieved temperature stability in 2-phenylethanol (2-PE) and 2-phenylethyl acetate (2-PEAc) production by expressing relevant genes in the 2-PE metabolic pathway using the high-temperature preferential promoter SSE1. The enhanced water retention capacity supports the metabolic activities of the encapsulated yeast cells, ensuring their survival and functionality over an extended period. Fragrance-releasing living material (FLM) is designed to controllably emit fragrance 2-PE by adjusting the microbial concentration within the hydrogel matrix. The FLM exhibits versatile adhesion capabilities, effectively binding to a spectrum of surfaces such as wood, textiles, and glass as well as to natural substrates like leaves. This adaptability enhances the material's applicability across various settings. Furthermore, FLM can be crafted into various forms, including microbeads, fibers, and films. This research opens up new horizons for controlled fragrance release of living materials.\n\nEngineering Living Material for Controlled Fragrance Release Utilizing <i>Kluyveromyces marxianus</i> CBS6556 and Adaptive Hydrogel.", "token_count": 409, "char_count": 1655, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6977, "quality_score": 0.8488, "entities": { "genes": [ "SSE1", "CBS6556" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:19.401885", "source": { "split": "train_shard_00000", "doc_id": 4816 }, "chunk_id": "train_shard_00000_4816_0", "global_id": 5400 }, { "text": "

Background

Currently, the synthesis of compounds based on microbial cell factories is rapidly advancing, yet it encounters several challenges. During the production process, engineered strains frequently encounter disturbances in the cultivation environment or the impact of their metabolites, such as high temperature, acid-base imbalances, hypertonicity, organic solvents, toxic byproducts, and mechanical damage. These stress factors can constrain the efficiency of microbial fermentation, resulting in slow cell growth, decreased production, significantly increased energy consumption, and other issues that severely limit the application of microbial cell factories.

Results

This study demonstrated that sterol engineering in Kluyveromyces marxianus, achieved by overexpressing or deleting the coding genes for the last five steps of ergosterol synthase (Erg2-Erg6), altered the composition and ratio of sterols in its cell membrane, and affected its multiple tolerance. The results suggest that the knockout of the Erg5 can enhance the thermotolerance of K. marxianus, while the overexpression of the Erg4 can improve its acid tolerance. Additionally, engineering strain overexpressed Erg6 improved its tolerance to elevated temperature, hypertonic, and acid. YZB453, obtained by overexpressing Erg6 in an engineering strain with high efficiency in synthesizing xylitol, produced 101.22 g/L xylitol at 45oC and 75.11 g/L xylitol at 46oC. Using corncob hydrolysate for simultaneous saccharification and fermentation (SSF) at 46oC that xylose released from corncob hydrolysate by saccharification with hemicellulase, YZB453 can produce 45.98 g/L of xylitol, saving 53.72% of the cost of hemicellulase compared to 42oC.

Conclusions

This study elucidates the mechanism by which K", "token_count": 504, "char_count": 1847, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.834, "entities": { "genes": [ "YZB453" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:20.055938", "source": { "split": "train_shard_00000", "doc_id": 4817 }, "chunk_id": "train_shard_00000_4817_0", "global_id": 5401 }, { "text": "marxianus acquires resistance to various antifungal drugs, high temperatures, high osmolarity, acidity, and other stressors, through alterations in the composition and ratio of membrane sterols. By employing sterol engineering, the fermentation temperature of this unconventional thermotolerant K. marxianus was further elevated, ultimately providing an efficient platform for synthesizing high-value-added xylitol from biomass via the SSF process at temperatures exceeding 45 °C.\n\nAltered sterol composition mediates multiple tolerance of Kluyveromyces marxianus for xylitol production.", "token_count": 143, "char_count": 587, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8356, "quality_score": 0.9178, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:20.488020", "source": { "split": "train_shard_00000", "doc_id": 4817 }, "chunk_id": "train_shard_00000_4817_1", "global_id": 5402 }, { "text": "In lambs, weaning imposes stress that can contribute to impaired rumen epithelial barrier functionality and immunological dysregulation. In this study, the effects of a yeast co-culture consisting of Saccharomyces cerevisiae and Kluyveromyces marxianus (NM) on rumen health in lambs was evaluated, with a focus on parameters including growth performance, ruminal fermentation, and epithelial barrier integrity, ruminal metabolic function, and the composition of the ruminal bacteria. In total, 24 lambs were grouped into four groups of six lambs including a control (C) group fed a basal diet, and N, M, and NM groups in which lambs were fed the basal diet respectively supplemented with S. cerevisiae yeast cultures (30 g/d per head), K. marxianus yeast cultures (30 g/d per head), and co-cultures of both yeasts (30 g/d per head), the experiment lasted for 42 d. Subsequent analyses revealed that relative to the C group, the average daily gain (ADG) of lambs in the NM group was significantly greater and exhibited significant increases in a range of mRNA relative expression including monocarboxylate transporter 1 (MCT1), (Na+)/hydrogen (H+) exchanger 1 (NHE1), (Na+)/hydrogen (H+) exchanger 3 (NHE3), proton-coupled amino acid transporter 1 (PAT1), vacuolar H+-ATPase (vH+ ATPase), claudin-1, occludin in the rumen epithelium (P < 0.05)", "token_count": 502, "char_count": 1467, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8144, "entities": { "genes": [ "NHE1", "MCT1", "NHE3", "PAT1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:21.150993", "source": { "split": "train_shard_00000", "doc_id": 4818 }, "chunk_id": "train_shard_00000_4818_0", "global_id": 5403 }, { "text": "Compared with the C group, the pH of the rumen contents in the NM group was significantly decreased , and the concentrations of acetate, propionate, and butyrate were significantly increased (P < 0.05). Analysis of the rumen bacteria showed that the NM group exhibited increases in the relative abundance of Prevotella, Treponema, Moryella, Fibrobacter, CF231 and Ruminococcus (P < 0.05). Metabolomics analyses revealed an increase in the relative content of phthalic acid and cinnamaldehyde in the NM group as compared to the C group (P < 0.05), together with the greater relative content of L-tyrosine, L-dopa, rosmarinic acid, and tyrosol generated by the tyrosine metabolic pathway (P < 0.05). Spearman's correlation analyses revealed relative abundance levels of Fibrobacter and Ruminococcus were positively correlated with the mRNA relative expression levels of PAT1, NHE3, and zonula occluden-1 (ZO-1), as well as with tyrosol, phthalic acid, and cinnamaldehyde levels (P < 0.05). Ultimately, these results suggest that dietary supplementation with NM has a wide range of beneficial effects on weaned lambs and is superior to single bacterial fermentation. These effects include improvements in daily gain and rumen epithelial barrier integrity, as well as improvements in the composition of the rumen microbiome, and alterations in tyrosine metabolic pathways.", "token_count": 476, "char_count": 1480, "word_count": 204, "semantic_coherence": 1, "information_density": 0.549, "quality_score": 0.7745, "entities": { "genes": [ "NHE3", "PAT1", "CF231" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:21.790789", "source": { "split": "train_shard_00000", "doc_id": 4818 }, "chunk_id": "train_shard_00000_4818_1", "global_id": 5404 }, { "text": "Saccharomyces cerevisiae and Kluyveromyces marxianus yeast co-cultures modulate the ruminal microbiome and metabolite availability to enhance rumen barrier function and growth performance in weaned lambs.", "token_count": 68, "char_count": 218, "word_count": 25, "semantic_coherence": 1, "information_density": 0.92, "quality_score": 0.96, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:22.160301", "source": { "split": "train_shard_00000", "doc_id": 4818 }, "chunk_id": "train_shard_00000_4818_2", "global_id": 5405 }, { "text": "Invasive infections with rare yeasts are increasing worldwide and are associated with higher mortality rates due to their resistance to antifungal drugs. Accurate antifungal susceptibility testing (AFST) is crucial for proper management of rare yeast infections. We performed AFST of 74 Candida kefyr isolates by Etest, EUCAST-based MICRONAUT-AM assay (MCN-AM) and reference Clinical and Laboratory Standards Institute broth microdilution method (CLSI). Essential agreement (EA, ±1 two-fold dilution), categorical agreement (CA), major errors (MEs) and very-major errors (VmEs) were determined using epidemiological cut-off values of ≤1.0 µg/mL, ≤0.03 µg/mL, ≤0.5 µg/mL and ≤1 µg/mL, defining wild-type isolates for fluconazole, voriconazole, micafungin and amphotericin B (AMB), respectively. Results for AMB susceptibility were correlated with ERG2/ERG3 mutations and total-cell sterols. CA of ≥97% was recorded between any two methods while EA varied between 72 and 82%, 87 and 92%, and 49 and 76% for fluconazole, voriconazole and micafungin, respectively. For AMB, CAs between CLSI and Etest; CLSI and MCN-AM; MCN-AM and Etest were 95% (4 ME, 0 VmE), 96% (3 ME, 0 VmE) and 99%, respectively, while EA varied from 32% to 69%. Non-synonymous ERG2/ERG3 mutations and no ergosterol were found in seven of eight isolates of non-wild types for AMB by Etest. Our data show that Etest, CLSI and MCN-AM methods are suitable for AFST of C. kefyr for fluconazole, voriconazole and micafungin", "token_count": 518, "char_count": 1513, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6742, "quality_score": 0.8371, "entities": { "genes": [ "ERG2", "ERG3" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:22.788805", "source": { "split": "train_shard_00000", "doc_id": 4819 }, "chunk_id": "train_shard_00000_4819_0", "global_id": 5406 }, { "text": "Excellent CAs for AMB between Etest and MCN-AM with concordant sterol profiles but not with CLSI suggest that Etest is also an excellent alternative for the detection of C. kefyr isolates with reduced susceptibility to AMB.\n\nHead-to-Head Comparison of Etest, MICRONAUT-AM EUCAST and Reference Broth Microdilution-Based CLSI Results for <i>Candida kefyr</i> Antifungal Susceptibility Testing: Implications for Detection of Reduced Susceptibility to Amphotericin B.", "token_count": 146, "char_count": 482, "word_count": 63, "semantic_coherence": 1, "information_density": 0.746, "quality_score": 0.873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:23.227969", "source": { "split": "train_shard_00000", "doc_id": 4819 }, "chunk_id": "train_shard_00000_4819_1", "global_id": 5407 }, { "text": "Patulin (PAT) produced by genus of Penicillium spp attracted more and more concern in view of its widespread contamination in food and toxic effects, which has also promoted the research on the reduction of PAT contamination in food. The use of yeast to remove PAT in food is innovative and promising. In this study, we used the yeast Kluyveromyces marxianus XZ1 to degrade PAT, which can remove 90% of PAT (10 μg/mL) within 48 h. XZ1 exhibits high degradation effect on PAT under the conditions of pH range of 3–6, temperatures of 28–37 °C, and initial PAT concentrations below 50 μg/mL. PAT removing by XZ1 was carried out by intracellular enzymes. XZ1 or intracellular enzyme was able to remove 100% of 10 μg/mL PAT in raw apple juice or commercial apple juice within 60 h. Patulin oxidoreductase (KmPAO) was identified as a potential PTA-degrading enzymes, which degrade PAT to form ascladiol. The degradation products of PAT by XZ1 were identified as ascladiol and desoxypatulinic acid, which was then complete degraded to form unknown final degradation products. Toxic analyses on Caco-2 cells showed that the ascladiol, desoxypatulinic acid and the final degradation products were significantly less toxic compared to PAT, which was mainly manifested in less influence on cell vitality, cell integrity and reactive oxygen species accumulation compared to PAT. Finally, the results revealed the PAT degradation enzyme, as well as the safety of the degradation products, which provide basis for the future application of this yeast to decontamination of PAT in food.\n\nDegradation of patulin by a yeast strain Kluyveromyces marxianus XZ1 and its mechanism", "token_count": 473, "char_count": 1659, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5434, "quality_score": 0.7717, "entities": { "genes": [ "XZ1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:23.888984", "source": { "split": "train_shard_00000", "doc_id": 4820 }, "chunk_id": "train_shard_00000_4820_0", "global_id": 5408 }, { "text": "Campylobacter spp. are the causative agents of campylobacteriosis, a major foodborne illness globally, with millions of cases reported annually. These pathogens pose significant risks to both human and animal health. Conventional culture-based diagnostic methods are labor-intensive and time-consuming, underscoring the need for more efficient molecular detection strategies. This study employed a pangenomic analysis to identify novel gene-specific markers for pathogenic Campylobacter species and subspecies, laying the groundwork for their application in diverse diagnostic assays. A curated dataset of 105 high-quality genomes, representing 33 species and 9 subspecies, was analyzed using the Roary ILP Bacterial Annotation Pipeline. The results revealed substantial genomic diversity within the genus, with core gene counts varying across different nucleotide identity thresholds. Ribosomal genes such as rpsL, rpsJ, rpsS, rpmA, rpsK, rpsU, rpsG, rpmH, and rpsZ were consistently identified in the core genome, whereas accessory genes exhibited marked variability. This study uncovered novel and highly specific genetic markers for various Campylobacter species, including petB, clpX, and carB for C. coli; hypothetical proteins for C. jejuni and C. fetus; porA2 for C. lari; and mdtJ for C. upsaliensis. These markers demonstrated a specificity of at least 90% with minimal cross-reactivity with non-target organisms. The findings underscore the genomic heterogeneity within Campylobacter and provide essential genetic targets for the enhanced molecular detection of its pathogenic species, subspecies, and biovars.", "token_count": 521, "char_count": 1782, "word_count": 220, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:24.566915", "source": { "split": "train_shard_00000", "doc_id": 4821 }, "chunk_id": "train_shard_00000_4821_0", "global_id": 5409 }, { "text": "Identification of Novel Gene-Specific Markers for Differentiating Various Pathogenic <i>Campylobacter</i> Species Using a Pangenome Analysis Approach.", "token_count": 50, "char_count": 162, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:24.959269", "source": { "split": "train_shard_00000", "doc_id": 4821 }, "chunk_id": "train_shard_00000_4821_1", "global_id": 5410 }, { "text": "Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly available complete genomes of Escherichia coli for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of E. coli plus Shigella: A, B1, B2, C, D, E, F, G, and Shigella. The analysis resulted in a detailed structure of the genetic basis of the phylogroups' differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome (consisting of genes found in <6.8% of all strains) consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.

Importance

The comprehensive analysis of the pangenome of Escherichia coli presented in this study marks a significant advancement in understanding bacterial genetic diversity. By employing machine learning techniques to analyze 2,377 complete E. coli genomes, the study provides a detailed mapping of core, accessory, and rare genes. This approach reveals the genetic basis for differential traits across phylogroups, offering insights into pathogenicity, antibiotic resistance, and evolutionary adaptations. The findings enhance the potential for genome-based diagnostics and pave the way for future studies aimed at achieving a global genetic definition of bacterial phylogeny.\n\nDecomposition of the pangenome matrix reveals a structure in gene distribution in the <i>Escherichia coli</i> species.", "token_count": 493, "char_count": 1941, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:25.617934", "source": { "split": "train_shard_00000", "doc_id": 4822 }, "chunk_id": "train_shard_00000_4822_0", "global_id": 5411 }, { "text": "Vibrio parahaemolyticus is an autochthonous marine bacterium that causes gastroenteritis after ingestion of raw or undercooked seafood and, less frequently, wound and tissue infections. Genomic information from northern Australia is scarce, and most sequences to date stem from foodborne outbreaks in southern states. We analysed 24 environmental and 5 clinical isolates (4 wound and 1 gastrointestinal case) collected in the wet-dry tropics from northern Australia and placed them alongside 48 representative public genomes. Core-genome phylogeny showed that the northern Australian strains sit within the broad VppAsia lineage and intermix with Asian and South American isolates, reflecting the limited geographic structuring in the marine environment. A gastrointestinal isolate (RDH3, ST-2901) harboured the trh2-positive VPaI-β pathogenicity island (including vtrAB and hlyDBAC genes) and displayed an A187S change in the TRH2 toxin which was absent in the other TRH-1/-2 sequences of the isolates analysed in this study. Wound isolates lacked tdh and trh genes, suggesting that the species' intrinsic virulome may suffice for tissue colonization; notably, one wound strain carried a plasmid with a Vibrio alginolyticus pilT copy linked to twitching motility which has been associated with wound infections. It remains to be determined whether this additional pilT copy, beyond the core genome copies, confers a selective advantage for tissue colonization. Plasmid diversity amongst clinical isolates and a diseased aquaculture fish, including a putative chimaera plasmid in the gastrointestinal isolate, underscores the role of mobile elements as reservoirs allowing adaptability to changing environments", "token_count": 467, "char_count": 1766, "word_count": 240, "semantic_coherence": 1, "information_density": 0.7042, "quality_score": 0.8521, "entities": { "genes": [ "RDH3", "TRH2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:26.267829", "source": { "split": "train_shard_00000", "doc_id": 4823 }, "chunk_id": "train_shard_00000_4823_0", "global_id": 5412 }, { "text": "Our findings expand the Australian genomic catalogue beyond outbreak strains, reveal extensive accessory-genome variability in tropical waters and underscore the need for One-Health surveillance frameworks that monitor virulence and resistance markers beyond the canonical hemolysin genes.\n\nHigh genomic diversity of <i>Vibrio</i> parahaemolyticus from underexplored tropical northern Australia: a baseline for future surveillance.", "token_count": 102, "char_count": 443, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8654, "quality_score": 0.9327, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:26.638137", "source": { "split": "train_shard_00000", "doc_id": 4823 }, "chunk_id": "train_shard_00000_4823_1", "global_id": 5413 }, { "text": "Salmonella enterica (S. enterica) is a highly ubiquitous and diverse animal and human pathogen. Distinct S. enterica serovars may present varying host-specificity and cause different diseases. While the human-restricted serovars S. Typhi (STY) and S. Paratyphi A (SPA) cause in humans a systemic life-threatening enteric fever, the host-generalist serovar, S. Typhimurium (STM) causes in immunocompetent individuals a self-limited gastroenteritis. Here, we have performed whole-genome sequencing and hybrid assembly of new SPA and STY typhoidal strains and took a comparative genomics approach to examine their phylogeny, pangenome structure and accessory genome content in comparison to the reference non-typhoidal serovar, STM. Our results identified previously uncharacterized lineages of SPA and refined the presence and distribution of core pseudogenes in typhoidal serovars. Pangenome analysis showed that while these serovars have a relatively similar core-genome size, the accessory genome of STM is more than four times larger than those of typhoidal Salmonellae and that STY and SPA display a more closed pangenome than STM. Unexpectedly, we demonstrate that STY and SPA present distinct differences in their pangenome composition, with a noticeable lower number of prophages, conjugative elements and antimicrobial genes per genome in SPA vs. STY. These results suggest that although SPA and STY are closely related at the DNA level, share a similar lifestyle and cause a symptomatic-indistinguishable disease, their genomic evolution and accessory genomes are markedly different. Moreover, these results may provide genomic explanation to phenotypic and epidemiological differences in antimicrobial resistance profiles associated with these serovars globally.", "token_count": 468, "char_count": 1813, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6057, "quality_score": 0.8028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:27.289383", "source": { "split": "train_shard_00000", "doc_id": 4824 }, "chunk_id": "train_shard_00000_4824_0", "global_id": 5414 }, { "text": "Comparative genomics of <i>Salmonella enterica</i> serovars Paratyphi A, Typhi and Typhimurium reveals distinct profiles of their pangenome, mobile genetic elements, antimicrobial resistance and defense systems repertoire.", "token_count": 66, "char_count": 234, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:27.653414", "source": { "split": "train_shard_00000", "doc_id": 4824 }, "chunk_id": "train_shard_00000_4824_1", "global_id": 5415 }, { "text": "In recent years, the development of user-friendly and accessible bioinformatic tools has significantly advanced Gardnerella genome analysis. Despite the taxonomic reclassification of the genus in 2019, many studies continue to rely on subgroups/ clades for species identification. This leads to frequent misidentifications, hindering accurate assessments of species-specific features, such as antimicrobial resistance and pathogenic potential. This study aims to address these gaps by employing precise species-level identification to improve our understanding on Gardnerella and its clinical implications. We performed the most extensive pangenome analysis of Gardnerella to date, analyzing 153 genomes (120 from NCBI and 33 newly sequenced). G. vaginalis, G. leopoldii, G. swidsinskii, and G. pickettii species exhibited open pangenomes. The Gardnerella pangenome is highly diverse, with 90% of its genes belonging to the accessory genome. Carbohydrate transport and metabolism contributed the most for the primary genomic differences observed among Gardnerella species. Additionally, the search for antibiotic resistance genes (ARGs) revealed lsaC gene as the most prevalent ARG, potentially conferring resistance to clindamycin, a commonly prescribed antibiotic for treating bacterial vaginosis (BV). The clustering of Gardnerella genomes mimics the core genome phylogeny, pointing to species specific virulence-associated factors, highlighting important factors such as vaginolysin and sialidases. Our comprehensive pangenome analysis shows that Gardnerella species are well-adapted within the urogenital tract, with identified virulence factors and metabolic capabilities potentially enhancing the pathogenicity of some strains. Future studies should explore Gardnerella ’s ecological interactions and pathogenic mechanisms within the urogenital microbiome.

Importance

In recent years, the availability of user-friendly and accessible bioinformatics tools has led to a surge in studies analyzing the Gardnerella genome. Despite the redefinition of the genus in 2019, many researchers continue to rely on subgroups or clades for Gardnerella identification. Our study builds upon the updated taxonomy of Gardnerella , offering a more comprehensive understanding of its genetic diversity", "token_count": 524, "char_count": 2299, "word_count": 302, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7997, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:28.289484", "source": { "split": "train_shard_00000", "doc_id": 4825 }, "chunk_id": "train_shard_00000_4825_0", "global_id": 5416 }, { "text": "By conducting a pangenome analysis of 153 Gardnerella genomes, we uncover significant genetic variability, species-specific virulence factors, and the widespread presence of antibiotic resistance genes, highlighting the urgent need for precise species-level identification. The identification of novel genomic features and antibiotic resistance profiles not only enhances our understanding of Gardnerella ’s clinical implications but also sheds light on its metabolic and virulence potential. These insights help clarify the pathogenic mechanisms of Gardnerella and provide a more refined understanding of its role in the urogenital microbiome.\n\nUnraveling the Gardnerella Pangenome: Insights into Genetic Diversity, Virulence, and Antibiotic Resistance", "token_count": 174, "char_count": 760, "word_count": 97, "semantic_coherence": 1, "information_density": 0.732, "quality_score": 0.866, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:28.735490", "source": { "split": "train_shard_00000", "doc_id": 4825 }, "chunk_id": "train_shard_00000_4825_1", "global_id": 5417 }, { "text": "This research cloned and expressed the sugar transporter gene KM_SUT5 from Kluyveromyces marxianus GX-UN120, which displayed remarkable sugar transportation capabilities, including pentose sugars. To investigate the impact of point mutations on xylose transport capacity, we selected four sites, predicted the suitable amino acid sites by molecular docking, and altered their codons to construct the corresponding mutants, Q74D, Y195K, S460H, and Q464F, respectively. Furthermore, we conducted site-directed truncation on six sites of KM_SUT5p. The molecular modification resulted in significant changes in mutant growth and the D-xylose transport rate. Specifically, the S460H mutant exhibited a higher growth rate and demonstrated excellent performance across 20 g L-1 xylose, achieving the highest xylose accumulation under xylose conditions (49.94 μmol h-1 gDCW-1, DCW mean dry cell weight). Notably, mutant delA554-, in which the transporter protein SUT5 is truncated at position delA554-, significantly increased growth rates in both D-xylose and D-glucose substrates. These findings offer valuable insights into potential modifications of other sugar transporters and contribute to a deeper understanding of the C-terminal function of sugar transporters.\n\nMolecular Modification Enhances Xylose Uptake by the Sugar Transporter KM_SUT5 of Kluyveromyces marxianus.", "token_count": 380, "char_count": 1405, "word_count": 184, "semantic_coherence": 1, "information_density": 0.712, "quality_score": 0.856, "entities": { "genes": [ "UN120", "SUT5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:29.321400", "source": { "split": "train_shard_00000", "doc_id": 4826 }, "chunk_id": "train_shard_00000_4826_0", "global_id": 5418 }, { "text": "Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous proteins. Improving the yield in K. marxianus remains a challenge and incorporating large-scale functional modules poses a technical obstacle in engineering. To address these issues, linear and circular yeast artificial chromosomes of K. marxianus (KmYACs) were constructed and loaded with disulfide bond formation modules from Pichia pastoris or K. marxianus. These modules contained up to seven genes with a maximum size of 15 kb. KmYACs carried telomeres either from K. marxianus or Tetrahymena. KmYACs were transferred successfully into K. marxianus and stably propagated without affecting the normal growth of the host, regardless of the type of telomeres and configurations of KmYACs. KmYACs increased the overall expression levels of disulfide bond formation genes and significantly enhanced the yield of various heterologous proteins. In high-density fermentation, the use of KmYACs resulted in a glucoamylase yield of 16.8 g/l, the highest reported level to date in K. marxianus. Transcriptomic and metabolomic analysis of cells containing KmYACs suggested increased flavin adenine dinucleotide biosynthesis, enhanced flux entering the tricarboxylic acid cycle, and a preferred demand for lysine and arginine as features of cells overexpressing heterologous proteins. Consistently, supplementing lysine or arginine further improved the yield. Therefore, KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental research. Transferring the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins, and this strategy may be applied to optimize other microbial cell factories.", "token_count": 500, "char_count": 1882, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:29.975954", "source": { "split": "train_shard_00000", "doc_id": 4827 }, "chunk_id": "train_shard_00000_4827_0", "global_id": 5419 }, { "text": "Transfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins in Kluyveromyces marxianus.", "token_count": 42, "char_count": 161, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:30.335193", "source": { "split": "train_shard_00000", "doc_id": 4827 }, "chunk_id": "train_shard_00000_4827_1", "global_id": 5420 }, { "text": "Lactic acid (LA) is a key chemical used in various industries, including food, pharmaceuticals, and bioplastics. Although traditionally produced using lactic acid bacteria, yeasts offer significant advantages, such as higher tolerance to acidic environments, a broader substrate range, and the potential for genetic and metabolic engineering. This review explores the potential use of Lachancea thermotolerans, Saccharomyces cerevisiae, Kluyveromyces marxianus, Kluyveromyces lactis, Candida utilis, and Pichia kudriavzevii as LA producers, highlighting their unique characteristics and industrial applications. S. cerevisiae stands out due to its robust genetic toolkit and acid tolerance, while K. marxianus offers thermotolerance and the efficient utilization of lactose and pentoses, making it ideal for high-temperature fermentations. K. lactis is particularly suited for valorizing dairy by-products like whey, P. kudriavzevii exhibits high tolerance to multiple stresses, while C. utilis demonstrates superior resilience to lignocellulosic inhibitors, enabling its use in biorefineries. Key challenges, including enhancing LA tolerance and optimizing metabolic pathways, are addressed through strategies like heterologous lactate dehydrogenase (LDH) expression, redox balance modification, and adaptive laboratory evolution. The review also discusses industrial applications, particularly in the context of circular economy approaches, where yeasts can convert waste streams into high-value LA. Future research should focus on integrating yeasts into scalable, sustainable bioprocesses to meet the growing demand for renewable and biodegradable materials.\n\nNative and Recombinant Yeast Producers of Lactic Acid: Characteristics and Perspectives.", "token_count": 470, "char_count": 1829, "word_count": 223, "semantic_coherence": 1, "information_density": 0.7399, "quality_score": 0.87, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:30.977528", "source": { "split": "train_shard_00000", "doc_id": 4828 }, "chunk_id": "train_shard_00000_4828_0", "global_id": 5421 }, { "text": "The use of Generally Recognized as Safe (GRAS)-grade microbial cell factories to produce recombinant protein-based nutritional products is a promising trend in developing food and health supplements. In this study, GRAS-grade Kluyveromyces marxianus was employed to express recombinant human heavy-chain ferritin (rhFTH), achieving a yield of 11 g/L in a 5 L fermenter, marking the highest yield reported for ferritin nanoparticle proteins to our knowledge. The rhFTH formed 12 nm spherical nanocages capable of ferroxidase activity, which involves converting Fe2+ to Fe3+ for storage. The rhFTH-containing yeast cell lysates promoted cytokine secretion (tumor necrosis factor-α (TNF-α), interleukin-6 (IL-6), and -1β (IL-1β)) and enhanced locomotion, pharyngeal pumping frequency, egg-laying capacity, and lifespan under heat and oxidative stress in the RAW264.7 mouse cell line and the C. elegans model, respectively, whereas yeast cell lysate alone had no such effects. These findings suggest that rhFTH boosts immunity, holding promise for developing ferritin-based food and nutritional products and suggesting its adjuvant potential for clinical applications of ferritin-based nanomedicine. The high-yield production of ferritin nanoparticles in K. marxianus offers a valuable source of ferritin for the development of ferritin-based products.\n\nHigh-Yield Expressed Human Ferritin Heavy-Chain Nanoparticles in K. marxianus for Functional Food Development.", "token_count": 449, "char_count": 1510, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.846, "entities": { "genes": [ "RAW264" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:31.615076", "source": { "split": "train_shard_00000", "doc_id": 4829 }, "chunk_id": "train_shard_00000_4829_0", "global_id": 5422 }, { "text": "Many desired biobased chemicals exhibit a range of toxicity to microbial cell factories, making industry-level biomanufacturing more challenging. Separating microbial growth and production phases is known to be beneficial for improving production of toxic products. Here, we developed a novel synthetic carbon-responsive promoter for use in the rapidly growing, stress-tolerant yeast Kluyveromyces marxianus, by fusing carbon-source responsive elements of the native ICL1 promoter to the strong S. cerevisiae TDH3 or native NC1 promoter cores. Two hybrids, P IT350 and P IN450 , were validated via EGFP fluorescence and demonstrated exceptional strength, partial repression during growth, and late phase activation in glucose- and lactose-based medium, respectively. Expressing the Gerbera hybrida 2-pyrone synthase (2-PS) for synthesis of the polyketide triacetic acid lactone (TAL) under the control of P IN450 increased TAL more than 50% relative to the native NC1 promoter, and additional promoter engineering further increased TAL titer to 1.39 g/L in tube culture. Expression of the Penicillium griseofulvum 6-methylsalicylic acid synthase (6-MSAS) under the control of P IN450 resulted in a 6.6-fold increase in 6-MSA titer to 1.09 g/L and a simultaneous 1.5-fold increase in cell growth", "token_count": 446, "char_count": 1415, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "ICL1", "NC1", "IN450", "IT350", "TDH3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:32.256842", "source": { "split": "train_shard_00000", "doc_id": 4830 }, "chunk_id": "train_shard_00000_4830_0", "global_id": 5423 }, { "text": "Finally, we used P IN450 to express the Pseudomonas savastanoi IaaM and IaaH proteins and the Salvia pomifera sabinene synthase protein to improve production of the auxin hormone indole-3-acetic acid and the monoterpene sabinene, respectively, both extremely toxic to yeast. The development of carbon-responsive promoters adds to the synthetic biology toolbox and available metabolic engineering strategies for K. marxianus, allowing greater control over heterologous protein expression and improved production of toxic metabolites.\n\nEngineering a carbon source-responsive promoter for improved biosynthesis in the non-conventional yeast Kluyveromyces marxianus.", "token_count": 200, "char_count": 708, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7558, "quality_score": 0.8779, "entities": { "genes": [ "IN450" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:32.702277", "source": { "split": "train_shard_00000", "doc_id": 4830 }, "chunk_id": "train_shard_00000_4830_1", "global_id": 5424 }, { "text": "Extremophiles can be the product of millions of years of evolutionary engineering and refinement. The underlying mechanisms can be quite distinct from the ones operating at earlier stages of trait innovation. In this work, we have developed the compost yeast Kluyveromyces marxianus, which diverged from its closest relative >20 million years ago, as a model for interspecies comparative biology and genomics. We applied a battery of growth assays to species of the Kluyveromyces genus and found that K. marxianus outperformed its relatives in a battery of heat and chemical stress conditions. We then generated and analyzed genomes from across the genus, to find derived genetic features associated with, and potentially causal for, K. marxianus traits. We found robust expansions in gene families in the K. marxianus genome, most notably among genes annotated as transmembrane transporters and in metabolism. In molecular-evolution tests, we identified adaptive protein variants at hundreds of genes, among which plasma membrane transporters were over-represented. Together, these signals enable a model for the molecular mechanisms and evolutionary pressures underlying K. marxianus traits, including gains in transporter function mediating stress resistance, and metabolic variants contributing to its capacity for rapid growth in challenging conditions. Such oligogenic architectures may be the rule rather than the exception in phenotypes that have evolved over long timescales.\n\nGenomic signatures of innovation and selection in the extremotolerant yeast Kluyveromyces marxianus", "token_count": 354, "char_count": 1592, "word_count": 226, "semantic_coherence": 1, "information_density": 0.646, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:33.290257", "source": { "split": "train_shard_00000", "doc_id": 4831 }, "chunk_id": "train_shard_00000_4831_0", "global_id": 5425 }, { "text": "Mycobacterium tuberculosis complex successfully adapts to environmental pressures through mechanisms of rapid adaptation which remain poorly understood despite knowledge gained through decades of research. In this study, we used 110 reference-quality, complete de novo assembled, long-read sequenced clinical genomes to study patterns of structural adaptation through a graph-based pangenome analysis, elucidating rarely studied mechanisms that enable enhanced clinical phenotypes offering a novel perspective to the species' adaptation. Across isolates, we identified a pangenome of 4,325 genes (3,767 core and 558 accessory), revealing 290 novel genes, and a substantially more complete account of difficult-to-sequence esx/pe/pgrs/ppe genes. Seventy-four percent of core genes were deemed non-essential in vitro, 38% of which support the pathogen's survival in vivo, suggesting a need to broaden current perspectives on essentiality. Through information-theoretic analysis, we reveal the ppe genes that contribute most to the species' diversity-several with known consequences for antigenic variation and immune evasion. Construction of a graph pangenome revealed topological variations that implicate genes known to modulate host immunity (Rv0071-73, Rv2817c, cas2), defense against phages/viruses (cas2, csm6, and Rv2817c-2821c), and others associated with host tissue colonization. Here, the prominent trehalose transport pathway stands out for its involvement in caseous granuloma catabolism and the development of post-primary disease. We show paralogous duplications of genes implicated in bedaquiline (mmpL5 in all L1 isolates) and ethambutol (embC-A) resistance, with a paralogous duplication of its regulator (embR) in 96 isolates", "token_count": 505, "char_count": 1826, "word_count": 230, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8543, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:33.951440", "source": { "split": "train_shard_00000", "doc_id": 4832 }, "chunk_id": "train_shard_00000_4832_0", "global_id": 5426 }, { "text": "We provide hypotheses for novel mechanisms of immune evasion and antibiotic resistance through gene dosing that can escape detection by molecular diagnostics.IMPORTANCEM. tuberculosis complex (MTBC) has killed over a billion people in the past 200 years alone and continues to kill nearly 1.5 million annually. The pathogen has a versatile ability to diversify under immune and drug pressure and survive, even becoming antibiotic persistent or resistant in the face of harsh chemotherapy. For proper diagnosis and design of an appropriate treatment regimen, a full understanding of this diversification and its clinical consequences is desperately needed. A mechanism of diversification that is rarely studied systematically is MTBC's ability to structurally change its genome. In this article, we have de novo assembled 110 clinical genomes (the largest de novo assembled set to date) and performed a pangenomic analysis. Our pangenome provides structural variation-based hypotheses for novel mechanisms of immune evasion and antibiotic resistance through gene dosing that can compromise molecular diagnostics and lead to further emergence of antibiotic resistance.\n\nInterred mechanisms of resistance and host immune evasion revealed through network-connectivity analysis of <i>M. tuberculosis</i> complex graph pangenome.", "token_count": 303, "char_count": 1356, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:34.514048", "source": { "split": "train_shard_00000", "doc_id": 4832 }, "chunk_id": "train_shard_00000_4832_1", "global_id": 5427 }, { "text": "Kluyveromyces marxianus is a food-safe yeast with great potential for producing heterologous proteins. Improving the yield in K. marxianus remains a challenge, while incorporating large-scale functional modules poses a technical obstacle in engineering. To address these issues, linear and circular yeast artificial chromosomes of K. marxianus (KmYACs) were constructed and loaded with disulfide bond formation modules from Pichia pastoris or K. marxianus . These modules contained up to 7 genes with a maximum size of 15 kb. KmYACs carried telomeres either from K. marxianus or Tetrahymena . KmYACs were transferred successfully into K. marxianus and stably propagated without affecting the normal growth of the host, regardless of the type of telomeres and configurations of KmYACs. KmYACs increased the overall expressions of disulfide bond formation genes and significantly enhanced the yield of various heterologous proteins. In high-density fermentation, the use of KmYACs resulted in a glucoamylase yield of 16.8 g/L, the highest reported level to date in K. marxianus . Transcriptomic and metabolomic analysis of cells containing KmYACs suggested increased FAD biosynthesis, enhanced flux entering the TCA cycle and a preferred demand for lysine and arginine as features of cells overexpressing heterologous proteins. Consistently, supplementing lysine or arginine further improved the yield. Therefore, KmYAC provides a powerful platform for manipulating large modules with enormous potential for industrial applications and fundamental research. Transferring the disulfide bond formation module via YACs proves to be an efficient strategy for improving the yield of heterologous proteins, and this strategy may be applied to optimize other microbial cell factories.

Impact Statement

In this study, yeast artificial chromosomes of K. marxianus (KmYACs) were constructed and successfully incorporating modules for large-scale disulfide bond formation. KmYACs were stably propagated in K. marxianus without compromising the normal growth of the host, irrespective of the selection of telomeres (either Tetrahymena or K", "token_count": 528, "char_count": 2134, "word_count": 301, "semantic_coherence": 1, "information_density": 0.5249, "quality_score": 0.7625, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:35.172370", "source": { "split": "train_shard_00000", "doc_id": 4833 }, "chunk_id": "train_shard_00000_4833_0", "global_id": 5428 }, { "text": "marxianus ) and configuration (either linear or circular). KmYACs notably enhanced the expressions of various heterologous proteins, with further yield improvement by supplementing lysine or arginine in the medium. Our findings affirm KmYAC as a robust and versatile platform for transferring large-scale function modules, demonstrating immense potential for both industrial applications and fundamental research.\n\nTransfer of disulfide bond formation modules via yeast artificial chromosomes promotes the expression of heterologous proteins inKluyveromyces marxianus", "token_count": 128, "char_count": 574, "word_count": 72, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:35.628023", "source": { "split": "train_shard_00000", "doc_id": 4833 }, "chunk_id": "train_shard_00000_4833_1", "global_id": 5429 }, { "text": "Sourdough fermentation is rarely used for gluten-free flatbread (GFFB), a product that is challenging to produce, especially when using high-fiber ingredients that bring nutritional benefits but lead to physical deterioration. The aim of this study was therefore to evaluate the fermentation performance of carob flour (CSPF), proso millet flour (PMF), and proso millet bran (PMB) individually and in combination with Limosilactobacillus fermentum and Kluyveromyces marxianus (LF + KM) and to compare the performance of LF + KM with a commercial starter (LIVENDO® LV1). A mixture design (n = 13) was used to evaluate the fermentation performance of LF + KM (total titratable acidity (TTA); lactobacilli and yeast growth; acetic and lactic acid, fructose, glucose, and saccharose content) at 35 °C for 16 h. The comparison of LF + KM with LV1 fermentation was based on the acidity rate, fermentation quotient, TTA, and finally by determining the physical properties (texture, shape, color) of a rice-corn GFFB in which 10% of flour was supplemented with the sourdoughs. PMB promoted the growth of lactobacilli and the production of organic acids, especially in combination of CSPF and PMF. The optimum flour ratio was 2.4:1:1.2 (PMB:PMF:CSPF). LF + KM shortened the sourdough fermentation time by 2.5 times compared to LV1. The use of LF + KM sourdough reduced the hardness (32%) and chewiness (28%) of the GFFB, while the volume (35%) was increased compared to LV1 sourdough. This study shows the potential of using local alternative flours in sourdough fermentation for the production of GFFB.", "token_count": 488, "char_count": 1619, "word_count": 250, "semantic_coherence": 1, "information_density": 0.572, "quality_score": 0.786, "entities": { "genes": [ "LV1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:36.299366", "source": { "split": "train_shard_00000", "doc_id": 4834 }, "chunk_id": "train_shard_00000_4834_0", "global_id": 5430 }, { "text": "Fermentation Performance of Carob Flour, Proso Millet Flour and Bran for Gluten-Free Flat-Bread.", "token_count": 30, "char_count": 96, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:36.666275", "source": { "split": "train_shard_00000", "doc_id": 4834 }, "chunk_id": "train_shard_00000_4834_1", "global_id": 5431 }, { "text": "Klebsiella pneumoniae is a rapidly evolving pathogen with a diverse pangenome whose mobilome and resistome remain elusive. Here, we aimed to delineate the pangenome of 198 isolates from Tanzanian regions. Raw Illumina reads retrieved from public repositories were assembled and analyzed using multilocus sequence typing, core-genome single nucleotide polymorphism (SNP)-based phylogeny, and capsular polysaccharide (K-locus) and lipopolysaccharide O-antigen (O-locus) typing. A total of 184 isolates were classified as Klebsiella pneumoniae sensu stricto, while 14 belonged to other species within the Klebsiella pneumoniae complex. We identified 90 sequence types (STs), including global high-risk ST45, ST39, ST336, ST14, ST1552, and ST17. KL24 and KL25 were the most common K-loci, while OL2α.1 and OL2α.2 were dominant O-loci. Pangenome analysis revealed 30,992 gene families, distributed as persistent (13.6%), shell (11.2%), and cloud (75.2%) genes, suggesting an open pangenome structure. Core-genome SNP-based phylogeny confirmed clonal expansion and lineage clustering. Virulence profiling showed yersiniabactin in 44% of isolates. Most genomes carried key fimbrial and iron uptake genes. Resistome analysis revealed near-universal presence of bla_CTX-M-15, oqxA/B, fosA6, sul2, and marA", "token_count": 460, "char_count": 1352, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7803, "quality_score": 0.8902, "entities": { "genes": [ "KL24", "ST1552", "ST17", "ST45", "ST39", "ST336", "ST14", "KL25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:37.362724", "source": { "split": "train_shard_00000", "doc_id": 4835 }, "chunk_id": "train_shard_00000_4835_0", "global_id": 5432 }, { "text": "Plasmid typing identified IncF-type (76%) and Col-type (54%) plasmids, while over 120 mobile genetic elements were detected, whose frequencies were on a huge spectrum of insertion sequences (e.g., IS5075 and MITEYpe1) and transposons (e.g., Tn5403 and Tn6082). Conclusively, Tanzanian K. pneumoniae strains exhibit extensive genomic plasticity, high-risk lineages, and a versatile mobilome, calling for national genomic surveillance to inform intervention strategies.IMPORTANCEThe Klebsiella pneumoniae complex comprises a diverse group of bacterial pathogens adapted to thrive over a wide range of environments. Isolates from clinical and environmental samples are implicated in nosocomial infections and multidrug resistance, with similar genome structures and inherent genes. Our study presents the first pangenome report underlying genomic plasticity of K. pneumoniae isolates from Tanzanian clinical specimens, demonstrating versatile clones, mobilome, and resistome profiles. Combining these profiles with the versatility of K and O structures, our study emphasizes the need for comprehensive multidisciplinary surveillance studies to optimize therapeutic and vaccine development.\n\nPangenome analysis of Tanzanian clinical <i>Klebsiella pneumoniae</i> reveals pandemic clones with high genome plasticity and versatile mobilome, virulome, and resistome profiles.", "token_count": 376, "char_count": 1407, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6954, "quality_score": 0.8477, "entities": { "genes": [ "IS5075" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:37.947524", "source": { "split": "train_shard_00000", "doc_id": 4835 }, "chunk_id": "train_shard_00000_4835_1", "global_id": 5433 }, { "text": "The role of horizontal gene transfer (HGT) in shaping bacterial genomes is well recognized, but constraints on gene exchange and the degree to which these constraints shape genome evolution remain poorly described. In this study, we sought to determine whether geographic and phylogenetic distance constrains HGT within and between bacterial species. To address this question, we isolated strains ( n = 17) of two closely related bacterial species, Streptomyces griseus and Streptomyces pratensis from two ecologically similar sites. We identified homologous recombination events within the core genomes of these species (557 recent and 457 ancient) and determined that patterns of recombination were constrained primarily by phylogeny rather than geography. Notably, shell accessory genes were over three times more likely to be shared between the same species than with non-related geographical neighbors. The richness of secondary metabolite gene clusters is highly variable with an average of 35 – 55 clusters per genome, depending on clade membership. The majority of secondary metabolite gene clusters (60%) are found in all strains, indicating that they were present in the most recent common ancestor of S. griseus and pratensis . We conclude that most HGT in the core and accessory genome is phylogenetically constrained, while HGT of shell genes is more likely constrained by geography. This outcome indicates that the predominant mechanisms of HGT favor high phylogenetic relatedness, and that rapid gene acquisition and loss in the accessory genome could aid with adaptation to contemporary environmental conditions.

Importance

Horizontal gene transfer (HGT) is a vital ecological and evolutionary force in microbiology, but we still lack a precise understanding of how precisely HGT acts on the gene pool of a species or genus. While HGT can complicate phylogenetic analyses and assumptions of homology, its role in adaptation and acquiring secondary metabolites should not be overlooked. Microbial ecologists agree that the pangenome is a shifting collection of genes that can be influenced by both vertical inheritance and ecological factors. This study examines how the Streptomyces pangenome is shaped by these two forces and offers an important quantitative insight into how HGT shapes bacterial genome dynamics.", "token_count": 516, "char_count": 2340, "word_count": 348, "semantic_coherence": 1, "information_density": 0.5718, "quality_score": 0.7859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:38.605573", "source": { "split": "train_shard_00000", "doc_id": 4836 }, "chunk_id": "train_shard_00000_4836_0", "global_id": 5434 }, { "text": "Biogeographical and phylogenetic constraints on horizontal gene transfer and genome evolution in Streptomyces", "token_count": 30, "char_count": 116, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:38.957055", "source": { "split": "train_shard_00000", "doc_id": 4836 }, "chunk_id": "train_shard_00000_4836_1", "global_id": 5435 }, { "text": "The Nocardia genus represents a largely untapped source of valuable secondary metabolites, yet its biosynthetic potential, gene content, and evolutionary history remain underexplored. By analyzing 263 genomes across 88 species, we found that Nocardia varies greatly in genome size and gene content. It exhibits an open pangenome with a small core genome (<900 genes) and high genomic fluidity (0.76), indicating high gene turnover. A large proportion (75%) of its genes are species-specific, indicating high genomic plasticity. Average nucleotide identity (ANI) analysis confirmed taxonomic relationships, with most species showing ANI values (80-85%). N. globerula showed an ANI of ~84% with Rhodococcus erythropolis, supporting its reclassification under Rhodococcus. The biosynthetic capabilities of the Nocardia genus are striking, with the presence of >8,000 biosynthetic gene clusters (BGCs), dominated by type 1 polyketide synthase, terpenes, and non-ribosomal polypeptide synthetases, establishing Nocardia as the Actinomycetota genus that has the largest biosynthetic repertoire. Around 35% of BGCs remain uncharacterized, suggesting Nocardia's high potential for novel natural product discoveries. Our study is the first to identify a prodigiosin BGC in Nocardia. Network analysis revealed complex evolutionary connections between Nocardia's gene cluster families (GCFs) and MIBiG reference BGCs, suggesting evolutionary changes, including gene gains and losses, that may have influenced the genus's BGC diversity and composition. Synteny analysis uncovered conserved and unique gene arrangements across Nocardia and related genera, mostly with core genes conserved in Actinomycetota", "token_count": 506, "char_count": 1770, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6886, "quality_score": 0.8443, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:39.585566", "source": { "split": "train_shard_00000", "doc_id": 4837 }, "chunk_id": "train_shard_00000_4837_0", "global_id": 5436 }, { "text": "Our study addressed unmet clinical and biotechnological challenges while revealing evolutionary mechanisms that shape microbial diversity and adaptability.

Importance

Understanding the genomic diversity and biosynthetic potential of microorganisms is instrumental for addressing issues in microbial evolution, natural product discovery, and host-microbe interactions. Nocardia, a bacterial genus known for its opportunistic pathogenicity, represents an underexplored group of immense genomic diversity and biosynthetic capabilities. This study employed genome mining to reveal the open pangenome of Nocardia and identified an extensive repertoire of BGCs, including novel clusters with the potential to produce therapeutically significant compounds such as prodigiosin-related compounds. By integrating genome mining, phylogenetics, and synteny analysis, this study provides insights into how genomic plasticity, species-specific genes, and evolutionary changes such as gene gains and losses that contribute to Nocardia's biosynthetic diversity and evolution. These findings contribute to advancing microbial genomics, evolution, and biotechnology by uncovering the potential of Nocardia to address challenges in infectious diseases and natural product discovery. This study exemplifies how genome mining can illuminate the ecological and clinical significance of microbial diversity.\n\n<i>Nocardia</i> genomes are a large reservoir of diverse gene content, biosynthetic gene clusters, and species-specific genes.", "token_count": 365, "char_count": 1559, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:40.161947", "source": { "split": "train_shard_00000", "doc_id": 4837 }, "chunk_id": "train_shard_00000_4837_1", "global_id": 5437 }, { "text": "The thermotolerant yeast Kluyveromyces marxianus has great potential for high-temperature ethanol fermentation, but it produces excess acetic acid during high-temperature fermentation, which inhibits ethanol production. The mechanisms of K. marxianus ’s responses to acetic acid have not been fully understood. In this study, the transcriptomic changes of K. marxianus DMKU3-1042 resulted from acetic acid stress during high-temperature ethanol fermentation were investigated based on high-throughput RNA sequencing. We identified 611 differentially expressed genes (DEGs) under acetic acid stress (fold change > 2 or < 0.5, P -adjust <0.05), with 166 up-regulated and 445 down-regulated. GO terms and pathways enriched in these DEGs were identified. Protein-protein interaction (PPI) networks were constructed based on the interactions between proteins coded by the DEGs, and hub genes and key modules in the PPI networks were identified. The results in this study indicated that during high-temperature fermentation, acetic acid stress promoted protein catabolism but repressed protein synthesis, which affected the growth and metabolism of K. marxianus and led to the decrease of ethanol production. The findings in this study provide a better understanding of the response mechanism of K. marxianus to acetic acid stress, and provide a basis for subsequent increase of ethanol production by K. marxianus .\n\nTranscriptomic analysis reveals hub genes and pathways in response to acetic acid stress in Kluyveromyces marxianus during high-temperature ethanol fermentation", "token_count": 402, "char_count": 1578, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [ "DMKU3" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:40.779399", "source": { "split": "train_shard_00000", "doc_id": 4838 }, "chunk_id": "train_shard_00000_4838_0", "global_id": 5438 }, { "text": "The aim of this study was to evaluate the intervention effect of the potential probiotic Kluyveromyces marxianus YG-4 isolated from Tibetan kefir grains on alcoholic liver disease (ALD). Eight-week-old male C57BL/6J mice were fed with a Lieber-DeCarli (LDC) diet containing ethanol with a progressively increasing concentration from 1% to 4% (vol/vol) to establish an ALD mouse model. Our results suggested that K. marxianus treatment improved ALD, as demonstrated by the reduction of serum ALT and AST levels and the suppression of TLR4/NF-κB-mediated inflammatory response in the liver. K. marxianus administration significantly elevated antioxidant activities of SOD, CAT and GSH-Px, and reduced the MDA level in mice. K. marxianus supplementation repaired the gut barrier by increasing tight junction proteins and the number of goblet cells in the colon of ALD mice. In addition, treatment with K. marxianus restored alcohol-induced gut dysbiosis. Specifically, K. marxianus administration depleted the abundance of Lactobacillus, Coriobacteriaceae_UCG-002 and Candida, while increased that of Allobaculum, Dubosiella and Epicoccum in mice. Our findings open new possibilities for K. marxianus application in ALD treatment.\n\nKluyveromyces marxianus supplementation ameliorates alcohol-induced liver injury associated with the modulation of gut microbiota in mice.", "token_count": 466, "char_count": 1472, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6421, "quality_score": 0.8211, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:41.426497", "source": { "split": "train_shard_00000", "doc_id": 4839 }, "chunk_id": "train_shard_00000_4839_0", "global_id": 5439 }, { "text": "Background: Tuberculosis is the second largest public health threat caused by pathogens. Understanding Mycobacterium tuberculosis's transmission, virulence, and resistance profile is crucial for outbreak control. This study aimed to investigate the pangenome composition of Mycobacterium tuberculosis clinical isolates classified as L4 derived from Ecuador. Methods: We analyzed 88 clinical isolates of Mycobacterium tuberculosis by whole-genome sequencing (WGS) and bioinformatic tools for Lineage, Drug-resistance and Pangenome analysis. Results: In our analysis, we identified the dominance of the LAM lineage (44.3%). The pangenomic analysis revealed a core genome of approximately 3200 genes and a pangenome that differed in accessory and unique genes. According to the COG database, metabolism-related genes were the most representative of all partitions. However, differences were found within all lineages analyzed in the metabolic pathways described by KEGG. Isolates from Ecuador showed variations in genomic regions associated with beta-lactamase susceptibility, potentially leading to epistatic resistance to other drugs commonly used in TB treatment, warranting further investigation. Conclusions: Our findings provide valuable insights into the genetic diversity of Mycobacterium tuberculosis populations in Ecuador. These insights may be associated with increasing adaptation within host heterogeneity, variable latency periods, and reduced host damage, collectively contributing to disease spread. The application of WGS is essential to elucidating the epidemiology of TB in the country.\n\nDecoding Ecuadorian Mycobacterium tuberculosis Isolates: Unveiling Lineage-Associated Signatures in Beta-Lactamase Resistance via Pangenome Analysis.", "token_count": 458, "char_count": 1817, "word_count": 225, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:42.065227", "source": { "split": "train_shard_00000", "doc_id": 4840 }, "chunk_id": "train_shard_00000_4840_0", "global_id": 5440 }, { "text": "During fermentation, yeast cells undergo various stresses that inhibit cell growth and ethanol production. Therefore, the ability to tolerate multiple stresses during fermentation is one of the important characteristics for yeast cells that can be used for commercial ethanol production. In the present study, we evaluated the multi-stress tolerance of parent and ethanol adapted Kluyveromyces marxianus MTCC1389 and their relative gene expression analysis. Multi-stress tolerance was confirmed by determining its cell viability, growth, and spot assay under oxidative, osmotic, thermal, and ethanol stress. During oxidative (0.8% H2O2) and osmotic stress (2 M NaCl), there was significant cell viability of 90% and 50%, respectively, by adapted strain. On the other hand, under 45 °C of thermal stress, the adapted strain was 80% viable while the parent strain was 60%. In gene expression analysis, the ethanol stress responsive gene ETP1 was significantly upregulated by 3.5 folds, the osmotic stress gene SLN1 was expressed by 3 folds, and the thermal stress responsive gene MSN2 was expressed by 7 folds. This study shows adaptive evolution for ethanol stress can develop other stress tolerances by changing relative gene expression of osmotic, oxidative, and thermal stress responsive genes.\n\nKluyveromyces marxianus MTCC 1389 Augments Multi-stress Tolerance After Adaptation to Ethanol Stress.", "token_count": 385, "char_count": 1435, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5686, "quality_score": 0.7843, "entities": { "genes": [ "MSN2", "ETP1", "SLN1", "MTCC1389" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:42.682648", "source": { "split": "train_shard_00000", "doc_id": 4841 }, "chunk_id": "train_shard_00000_4841_0", "global_id": 5441 }, { "text": "Streptococcus pneumoniae is a significant cause of bacterial infections, including pneumonia, meningitis and septicemia, primarily affecting children, the elderly and immunocompromised individuals. This study aimed to elucidate the serotype and lineage distribution and molecular mechanisms underlying pneumococcal invasiveness through a comprehensive pangenomic analysis of 1416 isolates from Malawi. Our analysis comprised 810 isolates from asymptomatic carriers and 606 isolates from patients with bacteraemia or meningitis. We identified 58 serotypes, with serotypes 1, 5 and 12F exhibiting significantly higher prevalence among patients. These serotypes likely exhibit reduced nasopharyngeal colonization and demonstrate rapid dissemination to sterile sites. Notably, these serotypes form a distinct lineage with distinct genomic characteristics, including the absence of V-type ATP synthase. The pangenome analysis revealed two highly conserved surface protein complexes, F-type ATP synthase and SecA1-SecY, which deserve further investigation as potential targets for novel therapeutic interventions.\n\nComparative pangenomics of <i>Streptococcus pneumoniae</i> from Malawi: uncovering genetic variability and pathogenicity.", "token_count": 318, "char_count": 1249, "word_count": 151, "semantic_coherence": 1, "information_density": 0.7815, "quality_score": 0.8907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:43.244615", "source": { "split": "train_shard_00000", "doc_id": 4842 }, "chunk_id": "train_shard_00000_4842_0", "global_id": 5442 }, { "text": "Bacterial pathogens of the genus Pectobacterium are responsible for soft-rot and blackleg diseases in a wide range of crops and have a global impact on food production. The emergence of new lineages and their competitive succession is frequently observed in Pectobacterium species, in particular in Pectobacterium brasiliense. With a focus on one such recently emerged P. brasiliense lineage in the Netherlands that causes blackleg in potatoes, we studied genome evolution in this genus using a reference-free graph-based pangenome approach. We clustered 1,977,865 proteins from 454 Pectobacterium spp. genomes into 30,156 homology groups. The Pectobacterium genus pangenome is open, and its growth is mainly contributed by the accessory genome. Bacteriophage genes were enriched in the accessory genome and contributed 16% of the pangenome. Blackleg-causing P. brasiliense isolates had increased genome size with high levels of prophage integration. To study the diversity and dynamics of these prophages across the pangenome, we developed an approach to trace prophages across genomes using pangenome homology group signatures. We identified lineage-specific as well as generalist bacteriophages infecting Pectobacterium species. Our results capture the ongoing dynamics of mobile genetic elements, even in the clonal lineages. The observed lineage-specific prophage dynamics provide mechanistic insights into Pectobacterium pangenome growth and contribution to the radiating lineages of P. brasiliense.\n\nPangenomics to understand prophage dynamics in the <i>Pectobacterium</i> genus and the radiating lineages of <i>Pectobacterium brasiliense</i>.", "token_count": 492, "char_count": 1751, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6044, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:43.889045", "source": { "split": "train_shard_00000", "doc_id": 4843 }, "chunk_id": "train_shard_00000_4843_0", "global_id": 5443 }, { "text": "Staphylococcus argenteus (SARG) was discovered in 2009 as part of the Staphylococcus aureus (SAUR) complex and has been documented from various locations worldwide. In this article, we describe the genomic features of five strains of SARG found in Christchurch, New Zealand. Isolates were first detected in 2019 using MALDI-TOF identification, and their identities were confirmed using whole-genome sequencing. Genomic features, including antimicrobial resistance markers and virulence factors, were compared with other SARG sequences in the NCBI GenBank and well-characterized features in SAUR. Four isolates belonged to ST2250 and one isolate to ST2793. Phylogenetic analysis based on core genome analysis revealed that all five isolates were phylogenetically distinct, with four isolates clustering in the ST2250 clade. Three isolates contained staphylococcal cassette chromosome mec (SCCmec) type IV 2Bc, harbouring the mecA gene conferring resistance to beta-lactam antibiotics. All five strains shared many of the virulence genes found in the global SARG and SAUR isolates; however, no TSST-1 or PVL pathogenic genes were detected. This publication contributes additional data on global occurrences and genomic features of SARG.\n\nCharacterization of Staphylococcus argenteus in Christchurch, New Zealand, and comparison to global strains.", "token_count": 387, "char_count": 1379, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6631, "quality_score": 0.8316, "entities": { "genes": [ "ST2793", "ST2250" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:44.512779", "source": { "split": "train_shard_00000", "doc_id": 4844 }, "chunk_id": "train_shard_00000_4844_0", "global_id": 5444 }, { "text": "The present work addressed the conversion of Agave salmiana leaf juice to ethanol by consolidated bioprocessing (CBP). CBP was tested at 30, 35, and 40 ºC and compared with a conventional fermentation previously subjecting the juices to an acid-thermal pretreatment. An FTIR-DRIFTS analysis was applied on the functional groups of the juice. Fermentation was evaluated by comparing the strains K. marxianus OFF1 and K. marxianus TX4; the latter was isolated in this work from the sap of A. salmiana. In results, the optimal condition pretreatment (H₂SO₄ 0.65% (v/v), 15.7 min, 88 °C) increased the reducing sugars concentration up to 45.15 g/L. FTIR-DRIFTS showed higher peaks of functional groups related to fructose and glucose in the pretreated juice vs the raw. Both strains reached enzymatic activities of up to 2.26 U/mL growing in raw A. salmiana juice. Conventional fermentation showed a similar behavior with both strains, with reducing sugar consumption efficiencies of 98%, 16 g ethanol/L, corresponding to yields of 77%. CBP at different temperatures, showed significant differences, registering the highest ethanol production (22 g/L) and yield (99%) at 40 ºC. The native strain showed a fermentation behavior similar to that of K. marxianus OFF1. Theoretical annual ethanol yields obtained from the results (3828 L/ha/year) were compared to those obtained from other biomass juices such as sweet sorghum and sugarcane bagasse. CBP showed high efficiency in the hydrolysis of polysaccharides from Agave salmiana juice and their conversion to ethanol.\n\nEthanol production from Agave salmiana leaf juices by consolidated bioprocessing comparing two strains of Kluyveromyces marxianus", "token_count": 485, "char_count": 1694, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5748, "quality_score": 0.7874, "entities": { "genes": [ "TX4", "OFF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:45.160805", "source": { "split": "train_shard_00000", "doc_id": 4845 }, "chunk_id": "train_shard_00000_4845_0", "global_id": 5445 }, { "text": "Mycobacterium abscessus is a rapidly growing non-tuberculosis mycobacterium that opportunistically causes pulmonary infections and is notable for its high resistance to antibiotics. While ubiquitous in environmental reservoirs such as soil, water, and biofilms, the genetic factors that enable certain strains to invade and persist in human hosts have remained elusive. To address this gap, we compared whole-genome sequences from 45 environmental isolates— primarily collected on Hawaiʻi Island—with a globally sourced set of clinical isolates retrieved from NCBI RefSeq. Our phylogenetic reconstruction delineated environmental and clinical lineages, and pangenome profiling revealed a conserved core genome of approximately 4,800 genes alongside a large accessory genome. Crucially, we found 20 genes conserved in clinical isolates, but not environmental isolates. Clinical isolates were found to have conserved genes coding for erm(41) , three transcriptional regulators, a pilus synthesis gene, an NADP-dependent oxidoreductase, a carbonic anhydrase, a probable L-ectoine synthase, a ribonuclease P protein component, and 11 hypothetical genes, whereas environmental isolated did not conserve any of these genes. This indicates that clinical isolates have undergone broad changes relating to metabolism, pilus biosynthesis, and transcriptional regulators, which may be necessary for pathogenicity. The candidate virulence markers uncovered here lay the groundwork for experimental validation, rapid diagnostics for non-tuberculous mycobacteria, and targeted surveillance of environmental reservoirs to mitigate the emergence of clinically significant strains.

Importance

Mycobacterium abscessus is an emerging pathogen that causes pulmonary infections in susceptible individuals. Though currently an opportunistic pathogen, M. abscessus may be undergoing evolutionary changes to become an obligate pathogen. Because of this, there is the need to identify markers of virulence in M. abscessus in order to better screen isolates and assess their risk of causing infection", "token_count": 497, "char_count": 2084, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6643, "quality_score": 0.8321, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:45.808391", "source": { "split": "train_shard_00000", "doc_id": 4846 }, "chunk_id": "train_shard_00000_4846_0", "global_id": 5446 }, { "text": "This also provides the opportunity to study a similar pathogenesis to what Mycobacterium tuberculosis may have undergone. This study revealed that clinical isolates of M. abscessus have conserved genes relating to pilus biosynthesis, metabolism, and transcriptional regulators that environmental isolates do not have. These conserved genes may be required for M. abscessus to acquire virulence, and these genes have potential use as biomarkers to screen isolates for possible pathogenicity.\n\nTranscriptional Regulator, Metabolic, and Pilus Biosynthesis Genes as Candidate Virulence Markers in High-Virulence Mycobacterium abscessus", "token_count": 167, "char_count": 638, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7024, "quality_score": 0.8512, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:46.250650", "source": { "split": "train_shard_00000", "doc_id": 4846 }, "chunk_id": "train_shard_00000_4846_1", "global_id": 5447 }, { "text": "In this study, okara was fermented by Lactobacillus plantarum and Kluyveromyces marxianus with single and mixed strains, and the changes in main nutrients and free amino acids before and after fermentation were investigated. Gas-phase ion mobility spectrometry (GC-IMS) was used to examine volatile compound alterations in fermented okara. The impact of fermented okara on Chinese steamed bread (CSB) quality was then assessed. Results showed a rise in soluble dietary fiber in co-fermented okara from 4.2 % to 7.8 %. GC-IMS identified 65 volatile compounds in four fermented okara sourdough samples, with 46 compounds qualitatively confirmed. Aldehyde levels like hexanal and valeraldehyde significantly decreased post-fermentation. CSB formulations substituting wheat flour with 5 %, 10 %, and 15 % okara exhibited decreased specific volume, increased hardness and chewiness, and slight changes in cohesiveness and springiness. Sensory evaluation results indicated that the flavor, appearance, color, internal structure, and texture of CSB made with fermented okara were superior to those of the unfermented group. Co-fermented okara sourdough improved the quality and sensory attributes of okara CSB. Therefore, this study proposes a method for the redevelopment and utilization of okara.\n\nCo-fermentation of okara with Kluyveromyces marxianus and Lactobacillus plantarum and its application in Chinese steamed bread", "token_count": 377, "char_count": 1419, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:46.832395", "source": { "split": "train_shard_00000", "doc_id": 4847 }, "chunk_id": "train_shard_00000_4847_0", "global_id": 5448 }, { "text": "Bacterial genomes primarily diversify via gain, loss, and rearrangement of genetic material in their flexible accessory genome. Yet the dynamics of accessory genome evolution are very poorly understood, in contrast to the core genome where diversification is readily described by mutations and homologous recombination. Here, we tackle this problem for the case of very closely related genomes. We comprehensively describe genome evolution within n=222 genomes of E. coli ST131, which likely shared a common ancestor around one hundred years ago. After removing putative recombinant diversity, the total length of the phylogeny is 6000 core genome mutations. Within this diversity, we find 22 modifications to core genome synteny and estimate around 2000 structural changes within the accessory genome, i.e. one structural change for every 3 core genome mutations. 63% of loci with structural diversity could be resolved into individual gain and loss events with ten-fold more gains than losses, demonstrating a dominance of gains due to insertion sequences and prophage integration. Our results suggest the majority of synteny changes and insertions in bacterial genomes are likely deleterious and only persist for a short time before being removed by purifying selection.\n\nEvolutionary dynamics of genome structure and content among closely related bacteria", "token_count": 303, "char_count": 1359, "word_count": 200, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:47.393455", "source": { "split": "train_shard_00000", "doc_id": 4848 }, "chunk_id": "train_shard_00000_4848_0", "global_id": 5449 }, { "text": "

Objective

Non-albicans Candida species, such as Candida kefyr, are emerging pathogens. Chromogenic media are highly useful for the diagnosis of urinary tract infections (UTIs). The aim was to describe the behavior of this specie on a non-specific chromogenic medium.

Methods

A retrospective study of cases of candiduria detected in the Microbiology laboratory of the Virgen de las Nieves Hospital in Granada (Spain) between 2016 and 2021 (N=2,130). Urine samples were quantitatively seeded on non-selective UriSelect™4 chromogenic agar.

Results

Between 2016 and 2021, C. kefyr was the seventh most frequent Candida species responsible for candiduria in our setting (n=15). The macroscopic appearance of C. kefyr colonies, punctiform and bluish, allowed the direct identification of these microorganisms.

Conclusions

This study provides the first description of the specific behavior of C. kefyr on UriSelect™4 agar, which differentiates it from other Candida species based on its enzymatic characteristics.\n\nConcerning the presumptive identification of Candida kefyr on Uriselect™4 agar.", "token_count": 321, "char_count": 1116, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:47.985354", "source": { "split": "train_shard_00000", "doc_id": 4849 }, "chunk_id": "train_shard_00000_4849_0", "global_id": 5450 }, { "text": "Surface proteins of Gram-positive bacteria are critical for adherence to host tissues, evasion of the immune system, and interaction with the environment. They can be utilized as biomarkers in diagnostics, for vaccine development, and as therapeutic targets due to their accessibility and role in pathogenicity. If utilized as diagnostic targets, surface biomarkers should be highly conserved across different strains of the pathogen, unique to the species to avoid cross-reactivity, abundantly expressed on the bacterial surface, and accessible to antibodies or detection reagents. Mass spectrometry-based proteomics methods have advanced the studies of surface proteins, often in combination with selective enrichment strategies such as tryptic \"shaving\". In this study, 11 clinical strains of Staphylococcus aureus underwent tryptic shaving to identify common surface proteins. Further bioinformatics analysis confirmed that these proteins are encoded in the core genome of S. aureus strains and contain species-specific peptides. In silico analysis identified 26 k-mer peptides in 15 surface proteins with structural accessibility to detection agents, making them the ideal targets for molecular diagnostics or as linear epitope targets for vaccine development or therapeutics. Among the identified candidates were known virulence-associated proteins such as PbpA, Sbi, and Asp23─previously studied in the context of vaccines─as well as uncharacterized proteins encoded by the gene loci SAUSA300_1904 and SAUSA300_1685, whose unique and surface-exposed features suggest unexplored diagnostic potential.\n\nMass Spectrometry-Based Analysis of Surface Proteins in <i>Staphylococcus aureus</i> Clinical Strains: Identification of Promising k-mer Targets for Diagnostics.", "token_count": 445, "char_count": 1795, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6271, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:48.637075", "source": { "split": "train_shard_00000", "doc_id": 4850 }, "chunk_id": "train_shard_00000_4850_0", "global_id": 5451 }, { "text": "Abstract

Background Soybean cyst nematode (SCN) poses a persistent challenge to soybean production. SCN populations repeatedly overcome resistant cultivars, resulting in crop yield loss. Reference-genome driven analysis limits our knowledge of intraspecific diversity, impeding our understanding of virulence evolution and host adaptation. Here, we leverage high-fidelity long-read sequencing and comparative analysis to generate a pangenome from nine SCN populations differing in their pathotypes. Results In this study we compared 9 SCN genomes, including 8 new assemblies at the chromosome level. We identified over 19,000 orthologous gene families, with nearly 50% comprising the conserved core genome. A large portion of the core genome (40%) exhibited signatures of more rapid evolution in a positive selection analysis, particularly in domains related to host interaction and immune evasion. Structural variants in genomic regions under selection suggest population-specific haplotypes that may underlie differential virulence. Furthermore, the secretome, comprising ~ 1,400 genes per genome, revealed dynamic effector content across accessions. Conclusions Our study highlights the power of pangenomics in revealing hidden genetic diversity in SCN. The dynamic nature of both core and accessory genomes, shaped by selection and structural rearrangements, illustrates the genomic evolutionary arms race between SCN and soybean. These insights provide a foundational resource for resistance breeding and pathogen surveillance, with broader implications for managing rapidly evolving crop pathogens.

\n\nPangenome analysis of nine Soybean Cyst Nematode genomes reveal hidden variation contributing to diversity and adaptation", "token_count": 392, "char_count": 1750, "word_count": 231, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:49.737208", "source": { "split": "train_shard_00000", "doc_id": 4851 }, "chunk_id": "train_shard_00000_4851_0", "global_id": 5452 }, { "text": "Kluyveromyces marxianus is an interesting and important yeast because of particular traits like thermotolerance and rapid growth, and applications in food and industrial biotechnology. Knowing how K. marxianus responds and adapts to changing environments is important to achieve a full understanding of the its biology and to develop bioprocesses. For this, a full suite of omics tools to measure and compare global patterns of gene expression and protein synthesis is needed. Whereas transcriptome analysis by RNA-Seq quantifies mRNA abundance, ribosome profiling allows codon-resolution of translation on a genome-wide scale by deep sequencing of ribosome locations on mRNAs and is emerging as a valuable tool to study translation control of gene expression. We report here the development of a ribosome profiling method for K. marxianus and we make the procedure available as a step by step protocol. To aid in the analysis and sharing of ribosome profiling data, we also added the K. marxianus genome as well as transcriptome and ribosome profiling data to the publicly accessible GWIPS-viz and Trips-Viz browsers. Users are able to upload custom ribosome profiling and RNA-Seq data to both browsers, therefore allowing easy analysis and sharing of data. As many studies only focus on the use of RNA-Seq to study K. marxianus in different environments, the availability of ribosome profiling is a powerful addition to the K. marxianus toolbox.

Graphical abstract

Development of a Ribosome Profiling protocol to study gene expression in the thermotolerant yeast Kluyveromyces marxianus .\n\nDevelopment of a Ribosome Profiling Protocol to Study Translation in the yeast Kluyveromyces marxianus", "token_count": 427, "char_count": 1710, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5117, "quality_score": 0.7559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:50.366640", "source": { "split": "train_shard_00000", "doc_id": 4852 }, "chunk_id": "train_shard_00000_4852_0", "global_id": 5453 }, { "text": "This study evaluates Lolium perenne press juice as a sustainable substrate for Single-Cell Protein (SCP) production using Kluyveromyces marxianus. Key fermentation parameters were systematically optimized, including microbial reduction, dilution ratios, temperature, and nutrient supplementation. Pasteurization at 75 °C preserved essential nutrients better than autoclaving, resulting in a 27.8% increase in biomass yield. A 1:2 dilution of press juice enhanced fermentation efficiency, achieving 20.2% higher biomass despite lower initial sugar content. Cultivation at 30 °C enabled sustained substrate utilization and outperformed 40 °C fermentation, increasing final biomass by 43.4%. Nutrient supplementation with yeast extract, peptone, and glucose led to the highest biomass yield, with a 71% increase compared to unsupplemented juice. Press juice from the tetraploid variety Explosion consistently outperformed the diploid Honroso, especially when harvested early, reaching up to 16.62 g·L⁻¹ biomass. Early harvests promoted faster growth, while late harvests exhibited higher biomass yield coefficients due to improved sugar-to-biomass conversion. Compared to conventional YM medium, fermentation with L. perenne press juice achieved up to a threefold increase in biomass yield. These findings highlight the potential of grass-based substrates for efficient SCP production and demonstrate how agricultural parameters like variety and harvest timing influence both quantity and quality. The approach supports circular bioeconomy strategies by valorizing underutilized biomass through microbial fermentation.\n\nEnhancing Single-Cell Protein Yield Through Grass-Based Substrates: A Study of Lolium perenne and Kluyveromyces marxianus", "token_count": 436, "char_count": 1738, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:50.998215", "source": { "split": "train_shard_00000", "doc_id": 4853 }, "chunk_id": "train_shard_00000_4853_0", "global_id": 5454 }, { "text": "Global concern about pathogenic resistance to antibiotics is prompting interest in probiotics as a strategy to prevent or inhibit infections. Fermented beverages are promising sources of probiotic yeasts. This study aimed to evaluate the antagonistic effects of Kluyveromyces marxianus, Wickerhamomyces anomalus, and Pichia manshurica strains from kefir and wine against Salmonella enterica serovar Enteritidis in intestinal epithelial cells. The ability of these yeasts to adhere to Caco-2/TC-7 cells was evaluated, as well as their influence on the ability of Salmonella to associate and invade these cells. The behavior of the pathogen was analyzed by (a) incubation of enterocytes with yeast before adding Salmonella, (b) co-incubation of Salmonella with yeast before contact with the enterocytes, and (c) incubation of Salmonella with yeast metabolites before contact with enterocytes. All yeast strains demonstrated adherence to Caco-2/TC-7 cells (33-100%) and effectively inhibited Salmonella invasion. Among the treatments, co-culture showed the greatest effect, reducing Salmonella association and invasion by more than 50%. Additionally, these yeasts modulated the epithelial immune response, significantly decreasing CCL20-driven luminescence by 60-81% (p < 0.0001). These results highlight the potential of yeasts from fermented beverages as probiotics to counteract Salmonella infections, offering a promising alternative in the fight against antibiotic resistance.\n\nProbiotic Potential of Yeasts Isolated from Fermented Beverages: Assessment of Antagonistic Strategies Against Salmonella enterica Serovar Enteritidis.", "token_count": 502, "char_count": 1722, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [ "CCL20" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:51.652556", "source": { "split": "train_shard_00000", "doc_id": 4854 }, "chunk_id": "train_shard_00000_4854_0", "global_id": 5455 }, { "text": "Enhancing the thermostability of cellulose-degrading enzymes is pivotal for establishing an efficient bioconversion system from cellulosic materials to value-added compounds. Here, by introducing random and saturation mutagenesis into the Thermoascus aurantiacus β-glucosidase gene, we generated a hyperthermostable mutant with five amino acid substitutions. Analysis of temperature-induced unfolding revealed the involvement of each replacement in the increased Tm value. Structural analysis showed that all replacements are located at the periphery of the catalytic pocket. D433N replacement, which had a pronounced thermostabilizing effect (ΔTm ＝ 4.5°C), introduced an additional hydrogen bond with a backbone carbonyl oxygen in a long loop structure. The mutant enzyme expressed in Kluyveromyces marxianus exhibited a Tm of 82°C and hydrolyzed cellobiose with kcat and Km values of 200 s－1 and 1.8 mM, respectively. When combined with a thermostable endoglucanase, the mutant enzyme released 20％ more glucose than wild-type enzyme from cellulosic material. The mutant enzyme is therefore a noteworthy addition to the existing repertoire of thermostable β-glucosidases.\n\nA thermostable and highly active fungal GH3 β-glucosidase generated by random and saturation mutagenesis.", "token_count": 390, "char_count": 1345, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7011, "quality_score": 0.8506, "entities": { "genes": [ "GH3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:52.271936", "source": { "split": "train_shard_00000", "doc_id": 4855 }, "chunk_id": "train_shard_00000_4855_0", "global_id": 5456 }, { "text": "Abstract

Pectin bioconversion from renewable feedstocks represents an appealing and sustainable production route. However, the microbial valorization of pectin is not well developed and requires an efficient expression of key enzymes. Here, a constructed biological system successfully drove pectin-based lipid metabolism by collaborative utilization of two engineered Kluyveromyces marxianus strains. The YKM1013 strain with an overexpression of the PGU1 gene served to break down pectin, resulting in a 65% improvement in conversion rate. And the YKM1015 strain with an additional central D-galacturonic acid (D-galUA) metabolic pathway effectively utilized the available D-galUA components. The developed strategy enabled an effective bioconversion of pectin-based lipid metabolism, with an increasing of 19-fold in medium-chain fatty acid (MCFA) and 6-fold in long-chain fatty acid (LCFA). Collectively, this study provided a feasible and sustainable bioconversion route for transforming pectin into chemicals that can be employed in the construction of a microbial cell factory platform for pectin valorization.

\n\nEngineering a sustainable system for pectin-based lipid metabolism through modular co-utilization of two Kluyveromyces marxianus strains", "token_count": 338, "char_count": 1311, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6826, "quality_score": 0.8413, "entities": { "genes": [ "YKM1015", "YKM1013", "PGU1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:52.852369", "source": { "split": "train_shard_00000", "doc_id": 4856 }, "chunk_id": "train_shard_00000_4856_0", "global_id": 5457 }, { "text": "

Introduction

Staphylococcus chromogenes are commonly found in intramammary infections associated with bovine subclinical mastitis in dairy cattle, yet their genomic diversity and antimicrobial resistance dynamics remain poorly characterized, particularly in African settings.

Methods

This study presents a comparative genomic analysis of 17 S. chromogenes isolates from South Africa, including five newly sequenced bovine mastitis strains and twelve porcine-derived genomes retrieved from GenBank. In-silico analysis using multilocus sequence typing (MLST), virulence genes, antibiotic resistance genes and plasmids replicon types were used to characterise these isolates.

Results and discussion

Pairwise average nucleotide identity (ANI) analysis revealed that bovine isolates SC21, SC28, and SC33 are closely related and likely clonal members of the bovine-adapted ST138 lineage (ANI >99.7%), while SC12 and SC14 are more genetically distinct and show closer similarity (ANI >91%) to porcine-derived strains. This was supported by whole-genome SNP (wgSNP) analysis, whereby the ST138 bovine-derived isolates formed a clonal lineage and displayed a diverse population structure compared to porcine strains. Resistome profiling uncovered antimicrobial resistance gene (ARG) content, bovine isolates reflecting only four core ARGs i.e., dfrC, mgrA, norA, and tet(38), which confer resistance to trimethoprim, fluoroquinolones, and tetracyclines. In contrast, the compared porcine strains harboured a diverse set of resistance determinants, including blaZ, ermC, tet(K), and vgaALC that encode for beta-lactams, macrolides, tetracycline, and lincosamides, respectively", "token_count": 512, "char_count": 1737, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7346, "quality_score": 0.8673, "entities": { "genes": [ "ST138", "SC21", "SC33", "SC28", "SC14", "SC12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:53.506891", "source": { "split": "train_shard_00000", "doc_id": 4857 }, "chunk_id": "train_shard_00000_4857_0", "global_id": 5458 }, { "text": "The five S. chromogenes isolates grouped into two 2 sequence types, namely ST138 and ST62. Pangenome reconstruction of 177 global genomes confirmed that S. chromogenes possesses an open pangenome, with only ~17.5% of genes conserved as core or soft-core elements. Notably, unique strain-specific genes of the ST138 were determined to be associated with trehalose metabolism identified in bovine isolates, potentially reflecting niche-specific adaptation to the mammary environment in the Free State Province of South Africa.

Conclusion

These findings advance our understanding of S. chromogenes population structure and resistance ecology. They underscore the importance of continued genomic surveillance of livestock pathogens to inform targeted intervention strategies and improve animal health in diverse production settings, and further clarify the implications for future antibiotic therapy and prevention of infections associated with this species.\n\nPopulation structure, resistome, and virulome of <i>Staphylococcus chromogenes</i> strains from milk of subclinical bovine mastitis in South Africa.", "token_count": 285, "char_count": 1144, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7534, "quality_score": 0.8767, "entities": { "genes": [ "ST138", "ST62" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:54.059547", "source": { "split": "train_shard_00000", "doc_id": 4857 }, "chunk_id": "train_shard_00000_4857_1", "global_id": 5459 }, { "text": "Exploring drug susceptibility is a critical endeavor in the scientific community, setting the stage for advancements in understanding and combating various pathogens. Candida kefyr has emerged as a significant pathogen, particularly affecting immunocompromised individuals with hematologic malignancies and HIV/AIDS conditions. This study aimed to assess the antifungal susceptibility profile of Candida kefyr isolates obtained from clinical samples and dairy products. A total of 134 Candida kefyr yeast isolates were retrieved from three distinct groups: (1) healthy individuals (n = 41), (2) patients (n = 24) including hematologic malignancy (n = 9), HIV/AIDS (n = 7), and diabetes (n = 8), (3) dairy products (milk, yogurt, and cheese, n = 69) stored at -70°C in the Shiraz University of Medical Science. All Candida kefyr isolates were previously identified using conventional and molecular methods. Susceptibility to antifungal drugs, including caspofungin, fluconazole, itraconazole, voriconazole, and amphotericin B, was determined using the microdilution method following CLSI-M27-A3 protocols, with results interpreted according to CLSI-M27-S4 guidelines. The study emphasizes the clear variation in antifungal susceptibility testing of Candida kefyr strains when compared across different groups, including patients, healthy people, and dairy products. According to the results, across all groups, a high minimum inhibitory concentration of fluconazole is evident, and healthy individuals show the highest minimum inhibitory concentration geometric means (4.0681)", "token_count": 495, "char_count": 1652, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:54.705191", "source": { "split": "train_shard_00000", "doc_id": 4858 }, "chunk_id": "train_shard_00000_4858_0", "global_id": 5460 }, { "text": "Also, 79.1% of the isolates were wild type to amphotericin B, with the lowest minimum inhibitory concentration compared to other antifungals tested. This suggests that amphotericin B was more effective against Candida kefyr. These findings showed fewer susceptibilities of Candida kefyr to both triazole and echinocandin classes of antifungal agents. Additionally, it is noteworthy that individuals without medical conditions exhibited higher minimum inhibitory concentration rates to these antifungal agents in comparison to those with underlying health conditions. Consequently, timely diagnosis and appropriate therapeutic interventions emerge as imperative in the effective management of candidiasis cases.\n\nAntifungal Drug Susceptibility Profile of Candida kefyr Isolated from Clinical Samples and Dairy Products.", "token_count": 204, "char_count": 839, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:55.164161", "source": { "split": "train_shard_00000", "doc_id": 4858 }, "chunk_id": "train_shard_00000_4858_1", "global_id": 5461 }, { "text": "

Background

Non-conventional yeasts and bacteria gain significance in synthetic biology for their unique metabolic capabilities in converting low-cost renewable feedstocks into valuable products. Improving metabolic pathways and increasing bioproduct yields remain dependent on the strategically use of various promoters in these microbes. The development of broad-spectrum promoter libraries with varying strengths for different hosts is attractive for biosynthetic engineers.

Results

In this study, five Yarrowia lipolytica constitutive promoters (yl.hp4d, yl.FBA1in, yl.TEF1, yl.TDH1, yl.EXP1) and five Kluyveromyces marxianus constitutive promoters (km.PDC1, km.FBA1, km.TEF1, km.TDH3, km.ENO1) were selected to construct promoter-reporter vectors, utilizing α-amylase and red fluorescent protein (RFP) as reporter genes. The promoters' strengths were systematically characterized across Y. lipolytica, K. marxianus, Pichia pastoris, Escherichia coli, and Corynebacterium glutamicum. We discovered that five K. marxianus promoters can all express genes in Y. lipolytica and that five Y. lipolytica promoters can all express genes in K. marxianus with variable expression strengths. Significantly, the yl.TEF1 and km.TEF1 yeast promoters exhibited their adaptability in P. pastoris, E. coli, and C. glutamicum. In yeast P. pastoris, the yl.TEF1 promoter exhibited substantial expression of both amylase and RFP. In bacteria E. coli and C. glutamicum, the eukaryotic km.TEF1 promoter demonstrated robust expression of RFP. Significantly, in E", "token_count": 457, "char_count": 1558, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "EXP1", "TDH1", "FBA1", "ENO1", "TDH3", "PDC1", "TEF1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:55.798605", "source": { "split": "train_shard_00000", "doc_id": 4859 }, "chunk_id": "train_shard_00000_4859_0", "global_id": 5462 }, { "text": "coli, The RFP expression strength of the km.TEF1 promoter reached ∼20% of the T7 promoter.

Conclusion

Non-conventional yeast promoters with diverse and cross-domain applicability have great potential for developing innovative and dynamic regulated systems that can effectively manage carbon flux and enhance target bioproduct synthesis across diverse microbial hosts.\n\nScreening of broad-host expression promoters for shuttle expression vectors in non-conventional yeasts and bacteria.", "token_count": 117, "char_count": 492, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8033, "quality_score": 0.9016, "entities": { "genes": [ "TEF1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:56.178357", "source": { "split": "train_shard_00000", "doc_id": 4859 }, "chunk_id": "train_shard_00000_4859_1", "global_id": 5463 }, { "text": "In response to the growing threat posed by the spread of antimicrobial resistance in zoonotic Campylobacter, a One Health approach was used to examine the genomic diversity, phylogenomic relationships, and the distribution of genetic determinants of resistance (GDR) in C. jejuni and C. coli isolates from humans, animals (ruminants, swine, and chickens), and avian food products collected during a regionally (Basque Country, Spain) and temporally (mostly 2021-2022) restricted sampling. Eighty-three C. jejuni and seventy-one C. coli isolates, most exhibiting resistance to ciprofloxacin and/or erythromycin, were whole-genome sequenced using Oxford Nanopore Technologies long-fragment sequencing (ONT). Multilocus sequence typing (MLST) analysis identified a high genomic diversity among isolates. Phylogenomic analysis showed that clustering based on the core genome was aligned with MLST profiles, regardless of the sample source. In contrast, accessory genome content sometimes discriminated isolates within the same STs and occasionally differentiated isolates from different sources. The majority of the identified GDRs were present in isolates from different sources, and a good correlation was observed between GDR distribution and phenotypic susceptibility profiles (based on minimum inhibitory concentrations interpreted according to the EUCAST epidemiological cutoff values). Genotypic resistance profiles were independent of genotypes, indicating no apparent association between resistance and phylogenetic origin. This study demonstrates that ONT sequencing is a powerful tool for molecular surveillance of bacterial pathogens in the One Health framework.\n\nA One Health approach for the genomic characterization of antibiotic-resistant Campylobacter isolates using Nanopore whole-genome sequencing.", "token_count": 451, "char_count": 1855, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:56.812005", "source": { "split": "train_shard_00000", "doc_id": 4860 }, "chunk_id": "train_shard_00000_4860_0", "global_id": 5464 }, { "text": "Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the United States. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction", "token_count": 469, "char_count": 1755, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6079, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:57.454322", "source": { "split": "train_shard_00000", "doc_id": 4861 }, "chunk_id": "train_shard_00000_4861_0", "global_id": 5465 }, { "text": "Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

Importance

Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species. We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in U.S. strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.\n\nMetabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.", "token_count": 343, "char_count": 1508, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:58.022735", "source": { "split": "train_shard_00000", "doc_id": 4861 }, "chunk_id": "train_shard_00000_4861_1", "global_id": 5466 }, { "text": "The Chlamydiaceae are a family of obligate intracellular bacteria known for their unique biphasic developmental cycle. Chlamydial are associated with various host organisms, including humans, and have been proposed as emerging pathogens. Genomic studies have significantly enhanced our understanding of chlamydial biology, host adaptation, and evolutionary processes. In this study, we conducted a complete pangenome association analysis (pan-GWAS) using 101 genomes from the Chlamydiaceae family to identify differentially represented genes in Chlamydia and Chlamydophila, revealing their distinct evolutionary strategies for interacting with eukaryotic hosts. Our analysis identified 289 genes with differential abundance between the two clades: 129 showed a strong association with Chlamydia and 160 with Chlamydophila. Most genes in Chlamydia were related to the type III secretion system, while Chlamydophila genes corresponded to various functional categories, including translation, replication, transport, and metabolism. These findings suggest that Chlamydia has developed a high dependence on mammalian cells for replication, facilitated by a complex T3SS for intracellular manipulation. In contrast, the metabolic and functional diversity in Chlamydophila allows it to colonize a broad range of hosts, such as birds, reptiles, amphibians, and mammals, making it a less specialized clade.\n\nPangenome-Wide Association Study in the Chlamydiaceae Family Reveals Key Evolutionary Aspects of Their Relationship with Their Hosts.", "token_count": 436, "char_count": 1624, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:58.650537", "source": { "split": "train_shard_00000", "doc_id": 4862 }, "chunk_id": "train_shard_00000_4862_0", "global_id": 5467 }, { "text": "Candida parapsilosis is an opportunistic yeast pathogen that can cause life-threatening infections in immunocompromised humans. Whole genome sequencing (WGS) studies of the species have demonstrated remarkably low diversity, with strains typically differing by about 1.5 single nucleotide polymorphisms (SNPs) per 10 kb. However, SNP calling alone does not capture the full extent of genetic variation. Here, we define the pangenome of 372 C. parapsilosis isolates to determine variation in gene content. The pangenome consists of 5,859 genes, of which 48 are not found in the genome of the reference strain. This includes 5,791 core genes (present in ≥ 99.5% of isolates). Four genes, including the allantoin permease gene DAL4 , were present in all isolates but were truncated in some strains. The truncated DAL4 was classified as a pseudogene in the reference strain CDC317. CRISPR-Cas9 gene editing showed that removing the early stop codon (producing the full-length Dal4 protein) is associated with improved use of allantoin as a sole nitrogen source. We find that the accessory genome of C. parapsilosis consists of 68 homologous clusters. This includes 38 previously annotated genes, 27 novel paralogs of previously annotated genes and 3 uncharacterised ORFs. Approximately one-third of the accessory genome (24/68 genes) is associated with gene fusions between tandem genes in the major facilitator superfamily (MFS). Additionally, we identified two highly divergent C. parapsilosis strains and find that, despite their increased phylogenetic distance (∼30 SNPs per 10 kb), both strains have similar gene content to the other 372.

Importance

Candida parapsilosis is a human fungal pathogen, listed in the high priority group by the World Health Organisation. It is an increasing cause of hospital-acquired and drug-resistant infection. Here, we studied the genetic diversity of 372 C. parapsilosis isolates, the largest genomic surveillance of this species to date", "token_count": 526, "char_count": 1983, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.8169, "entities": { "genes": [ "CDC317", "DAL4" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:48:59.316299", "source": { "split": "train_shard_00000", "doc_id": 4863 }, "chunk_id": "train_shard_00000_4863_0", "global_id": 5468 }, { "text": "We show that there is relatively little genetic variation. However, we identified two more distantly-related isolates from Germany, suggesting that even more sampling may yield more diversity. We find that the pangenome (the cumulative gene content of all isolates) is surprisingly small, compared to other fungal species. Many of the non-core genes are involved in transport. We also find that variations in gene content are associated with nitrogen metabolism, which may contribute to the virulence characteristics of this species.\n\nSmall pangenome of Candida parapsilosis reflects overall low intraspecific diversity", "token_count": 134, "char_count": 626, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7416, "quality_score": 0.8708, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:48:59.777090", "source": { "split": "train_shard_00000", "doc_id": 4863 }, "chunk_id": "train_shard_00000_4863_1", "global_id": 5469 }, { "text": "β-Glucans derived from yeast are recognized as beneficial food additives. This study evaluated crude β-glucan extracts from Pichia kudriavzevii DPUL-51-6Y, Kluyveromyces marxianus DPUL-F15, and Saccharomyces cerevisiae DPUL-C6 strains for their anticolitis potential. Chemical analysis revealed that β-glucan was the primary component (71.88-78.47% purity). Notably, the S. cerevisiae extract displayed superior thermal stability and hydration capacity. In RAW264.7 macrophages, β-glucan pretreatment at 100 μg/mL significantly reduced LPS-induced nitric oxide production and pro-inflammatory cytokines by suppressing NF-κB signaling through the reduction of p65 and IκB-α while simultaneously activating the Nrf2 and AHR pathways. In DSS-induced colitis BALB/c mice, oral administration of crude β-glucans alleviated intestinal damage by enhancing tight junction protein expression and restoring gut microbiota composition, characterized by an increased abundance of Lactobacillus and Prevotella. These effects were correlated with the increased production of microbial metabolites, including indole-3-lactic acid, indole-3-β-acrylic acid, tryptophol, and short-chain fatty acids (acetic, propionic, and butyric acids). Mechanistically, β-glucan mitigated colitis through the dual activation of Nrf2/AHR pathways and the inhibition of NF-κB", "token_count": 459, "char_count": 1404, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7831, "quality_score": 0.8916, "entities": { "genes": [ "RAW264" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:00.445919", "source": { "split": "train_shard_00000", "doc_id": 4864 }, "chunk_id": "train_shard_00000_4864_0", "global_id": 5470 }, { "text": "This study suggests that yeast-derived β-glucan plays a significant role in mitigating the inflammatory response and may alleviate ulcerative colitis by reshaping the microbial community and metabolite profiles in the host intestinal tract.\n\nβ-Glucan Extracted from <i>Pichia kudriavzevii</i> DPUL-51-6Y, <i>Kluyveromyces marxianus</i> DPUL-F15, and <i>Saccharomyces cerevisiae</i> DPUL-C6 Shows Ameliorating Effects on DSS-Induced Ulcerative Colitis on BALB/c Mice.", "token_count": 196, "char_count": 502, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8393, "quality_score": 0.9196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:00.913671", "source": { "split": "train_shard_00000", "doc_id": 4864 }, "chunk_id": "train_shard_00000_4864_1", "global_id": 5471 }, { "text": "

Background

The stone-dwelling genus Blastococcus plays a key role in ecosystems facing extreme conditions such as drought, salinity, alkalinity, and heavy metal contamination. Despite its ecological significance, little is known about the genomic factors underpinning its adaptability and resilience in such harsh environments. This study investigates the genomic basis of Blastococcus's adaptability within its specific microniches, offering insights into its potential for biotechnological applications.

Results

Comprehensive pangenome analysis revealed that Blastococcus possesses a highly dynamic genetic composition, characterized by a small core genome and a large accessory genome, indicating significant genomic plasticity. Ecogenomic assessments highlighted the genus's capabilities in substrate degradation, nutrient transport, and stress tolerance, particularly on stone surfaces and archaeological sites. The strains also exhibited plant growth-promoting traits, enhanced heavy metal resistance, and the ability to degrade environmental pollutants, positioning Blastococcus as a candidate for sustainable agriculture and bioremediation. Interestingly, no correlation was found between the ecological or plant growth-promoting traits (PGPR) of the strains and their isolation source, suggesting that these traits are not linked to their specific environments.

Conclusions

This research highlights the ecological and biotechnological potential of Blastococcus species in ecosystem health, soil fertility improvement, and stress mitigation strategies. It calls for further studies on the adaptation mechanisms of the genus, emphasizing the need to validate these findings through wet lab experiments. This study enhances our understanding of microbial ecology in extreme environments and supports the use of Blastococcus in environmental management, particularly in soil remediation and sustainable agricultural practices.\n\nEcogenomic insights into the resilience of keystone Blastococcus Species in extreme environments: a comprehensive analysis.", "token_count": 434, "char_count": 2078, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:01.579614", "source": { "split": "train_shard_00000", "doc_id": 4865 }, "chunk_id": "train_shard_00000_4865_0", "global_id": 5472 }, { "text": "Guanine deaminase (GDA) catalyzes the first step in purine catabolism by converting guanine to xanthine. Despite its significant role in the development of low-purine food, studies on GDA remain limited compared to other metabolic deaminases. To identify a GDA with high enzyme activity and appropriate optimum parameters, GDAs from Kluyveromyces lactis, Kluyveromyces marxianus, Lentilactobacillus kefiri, and Lactobacillus buchneri were heterologously expressed in Escherichia coli. The GDA from Kluyveromyces marxianus (KM-GD) showed the most potent enzyme activity (2.21 IU/mL) at 30 °C and pH 6.5, which is close to the pH of saccharified wort. Furthermore, analyzing the crystal structures of GDAs from different sources revealed that hydrogen bonds could enhance substrate affinity and strengthen enzyme activity. In addition, active pockets with an appropriate size may contribute to high enzyme activity. Finally, KM-GD helped reduce guanine by 80.33% in beer wort and by 80.00% in matured beer, thus suggesting its promise for industrial application in low-purine food production.\n\nCharacterization of Guanine Deaminase from <i>Kluyveromyces marxianus</i> and Its Industrial Application to Reduce Guanine Content in Beer.", "token_count": 393, "char_count": 1285, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:02.203335", "source": { "split": "train_shard_00000", "doc_id": 4866 }, "chunk_id": "train_shard_00000_4866_0", "global_id": 5473 }, { "text": "

Background

The eco-friendly transformation of agro-industrial wastes through microbial bioconversion could address sustainability challenges in line with the United Nations' Sustainable Development Goals. The bulk of agro-industrial waste consists of lignocellulosic materials with fermentable sugars, predominantly cellulose and hemicellulose. A number of pretreatment options have been employed for material saccharification toward successful fermentation into second-generation bioethanol. Biological and/or enzymatic pretreatment of lignocellulosic waste substrates offers eco-friendly and sustainable second-generation bioethanol production opportunities that may also contribute to waste management without affecting food security. In this study, we isolated a promising filamentous bacterium from the guts of cockroaches with commendable cellulolytic activity. The matrices of sequential statistics, from one-factor-at-a-time (OFAT) through significant variable screening by Placket-Burman design (PBD) to Box‒Behnken design of a surface methodology (BBD-RSM), were employed for major medium variable modeling and optimization by solid-state fermentation. The optimized solutions were used to saccharify lignocellulose in real time, and the kinetics of reducing sugar accumulation were subsequently evaluated to determine the maximum concentration of sugars extracted from the lignocellulose. The hydrolysate with the highest reducing sugar concentration was subjected to fermentation by Saccharomyces cerevisiae, Klyuveromyces marxianus and a mixture of both, after which the ethanol yield, concentration and fermentation efficiency were determined.

Results

Sequential statistics revealed that rice husk powder, corn cob powder, peptone and inoculum volume were significant variables for the bioprocess at 59.8% (w/w) rice husk powder, 17.8% (w/w) corn cob powder, 38.8% (v/w; 109 cfu/mL) inoculum volume, and 5.3% (w/w) peptone", "token_count": 500, "char_count": 1962, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6639, "quality_score": 0.832, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "saccharomyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:02.857924", "source": { "split": "train_shard_00000", "doc_id": 4867 }, "chunk_id": "train_shard_00000_4867_0", "global_id": 5474 }, { "text": "These conditions mediated maximum cellulolytic and xylanolytic activities of 219.93 ± 18.64 FPU/mL and 333.44 ± 22.74 U/mL, respectively. The kinetics of saccharification of the lignocellulosic waste under optimized conditions revealed two peaks of reducing sugar accumulation between 16 and 32 h and another between 56 and 64 h.

Conclusions

Although K. marxianus had a significantly greater fermentation efficiency than S. cerevisiae, fermentation with a 50:50 (% v/v) mixture of both yeasts led to 88.32% fermentation efficiency with 55.56 ± 0.19 g/L crude bioethanol, suggesting that inexpensive, eco-friendly and sustainable bioethanol production could be obtained from renewable energy sources.\n\nSaccharification and co-fermentation of lignocellulosic biomass by a cockroach-gut bacterial symbiont and yeast cocktail for bioethanol production.", "token_count": 292, "char_count": 855, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7719, "quality_score": 0.886, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:03.427256", "source": { "split": "train_shard_00000", "doc_id": 4867 }, "chunk_id": "train_shard_00000_4867_1", "global_id": 5475 }, { "text": "Listeria monocytogenes is a bacterial pathogen found in an increasing number of food categories, potentially reflecting an expanding niche and food safety risk profile. In the UK, Listeria monocytogenes sequence type (ST) 121 is more frequently isolated from foods and food environments than from cases of clinical listeriosis, consistent with a relatively low pathogenicity. In this study, we determined the evolution associated with the environmental persistence of a Listeria monocytogenes clone by investigating clone-specific genome features in the context of the ST121 population structure from international sources. To enable unambiguous comparative genomic analysis of ST121 strains, we constructed 16 new high-quality genome assemblies from Listeria monocytogenes isolated from foods, food environments and human clinical sources in the UK from 1987 to 2019. Our dataset was supplemented with additional UK and international genomes from databases held by the Institut Pasteur and the UK Health Security Agency. Time-scaled phylogenetic reconstruction revealed that clade-specific microevolution correlated with key characteristics that may confer adaptations important for success in the environmental niche. For example, a prophage designated LP-13-6 unique to a clade is associated with multi-year persistence in a food production setting. This prophage, observed in a strain that persisted for over a decade, may encode mechanisms facilitating environmental persistence, including the exclusion of other bacteriophages. Pangenome analysis provided insights into other candidate genetic elements associated with persistence and biocide tolerance. The comparative genomic dataset compiled in this study includes an international collection of 482 genome sequences that serve as a valuable resource for future studies to explore conserved genes, regulatory regions, mutations and variations associated with particular traits, such as environmental persistence, pathogenicity or biocide tolerance.\n\nPopulation structure and gene flux of <i>Listeria monocytogenes</i> ST121 reveal prophages as a candidate driver of adaptation and persistence in food production environments.", "token_count": 500, "char_count": 2224, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5966, "quality_score": 0.7983, "entities": { "genes": [ "ST121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:04.080215", "source": { "split": "train_shard_00000", "doc_id": 4868 }, "chunk_id": "train_shard_00000_4868_0", "global_id": 5476 }, { "text": "

Background

Mycobacterium abscessus complex (MABC), an opportunistic nontuberculous mycobacteria, can lead to poor clinical outcomes in pulmonary infections. Conflicting data exist on person-to-person transmission of MABC within and across health care facilities. To investigate further, a comprehensive retrospective study across 5 health care institutions on the Island of Montréal was undertaken.

Methods

We analyzed the genomes of 221 MABC isolates obtained from 115 individuals (2010-2018) to identify possible links. Genetic similarity, defined as ≤25 single-nucleotide polymorphisms (SNPs), was investigated through a blinded epidemiological inquiry.

Results

Bioinformatics analyses identified 28 sequence types, including globally observed dominant circulating clones (DCCs). Further analysis revealed 210 isolate pairs within the SNP threshold. Among these pairs, there was 1 possible laboratory contamination where isolates from different patients processed in the same laboratory differed by only 2 SNPs. There were 37 isolate pairs from patients who had provided specimens from the same hospital; however, epidemiological analysis found no evidence of health care-associated person-to-person transmission between these patients. Additionally, pangenome analysis showed higher discriminatory power than core genome analysis for examining genomic similarity.

Conclusions

Genomics alone is insufficient to establish MABC transmission, particularly considering the genetic similarity and wide distribution of DCCs, although pangenome analysis has the potential to add further insight. Our findings indicate that MABC infections in Montréal are unlikely attributable to health care-associated person-to-person transmission.\n\nGenomic Epidemiology of Mycobacterium abscessus on the Island of Montréal Is Not Suggestive of Health Care-Associated Person-to-Person Transmission.", "token_count": 464, "char_count": 1908, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6983, "quality_score": 0.8491, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:04.724817", "source": { "split": "train_shard_00000", "doc_id": 4869 }, "chunk_id": "train_shard_00000_4869_0", "global_id": 5477 }, { "text": "GCN2 is a conserved receptor kinase activating the Integrated Stress Response (ISR) in eukaryotic cells. The ISR kinases detect accumulation of stress molecules and reprogram translation from basal tasks to preferred production of cytoprotective proteins. GCN2 stands out evolutionarily among all protein kinases due to the presence of a h istidyl t R NA s ynthetase-like (HRSL) domain, which arises only in GCN2 and is located next to the kinase domain. How HRSL contributes to GCN2 signaling remains unknown. Here we report a 3.2 Å cryo-EM structure of HRSL from thermotolerant yeast Kluyveromyces marxianus . This structure shows a constitutive symmetrical homodimer featuring a compact helical-bundle structure at the junction between HRSL and kinase domains, in the core of the receptor. Mutagenesis demonstrates that this junction structure activates GCN2 and indicates that our cryo-EM structure captures the active signaling state of HRSL. Based on these results, we put forward a GCN2 regulation mechanism, where HRSL drives the formation of activated kinase dimers. Remaining domains of GCN2 have the opposite role and in the absence of stress they help keep GCN2 basally inactive. This autoinhibitory activity is relieved upon stress ligand binding. We propose that the opposing action of HRSL and additional GCN2 domains thus yields a regulated ISR receptor.

Significance statement

Regulation of protein synthesis (translation) is a central mechanism by which eukaryotic cells adapt to stressful conditions. In starving cells, this translational adaptation is achieved via the receptor kinase GCN2, which stays inactive under normal conditions, but is switched on under stress. The molecular mechanism of GCN2 switching is not well understood due to the presence of a structurally and biochemically uncharacterized h istidyl t R NA s ynthetase-like domain (HRSL) at the core of GCN2. Here we use single-particle cryo-EM and biochemistry to elucidate the structure and function of HRSL. We identify a structure at the kinase/HRSL interface, which forms crossed helices and helps position GCN2 kinase domains for activation", "token_count": 525, "char_count": 2142, "word_count": 322, "semantic_coherence": 1, "information_density": 0.5745, "quality_score": 0.7873, "entities": { "genes": [ "GCN2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:05.392151", "source": { "split": "train_shard_00000", "doc_id": 4870 }, "chunk_id": "train_shard_00000_4870_0", "global_id": 5478 }, { "text": "These data clarify the molecular mechanism of GCN2 regulation.\n\nCryo-EM Structure of HRSL Domain Reveals Activating Crossed Helices at the Core of GCN2", "token_count": 43, "char_count": 151, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [ "GCN2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:05.752152", "source": { "split": "train_shard_00000", "doc_id": 4870 }, "chunk_id": "train_shard_00000_4870_1", "global_id": 5479 }, { "text": "Mezcal is a traditional Mexican distilled beverage, known for its marked organoleptic profile, which is influenced by several factors, such as the fermentation process, where a wide variety of microorganisms are present. Kluyveromyces marxianus is one of the main yeasts isolated from mezcal fermentations and has been associated with ester synthesis, contributing to the flavors and aromas of the beverage. In this study, we employed CRISPR interference (CRISPRi) technology, using dCas9 fused to the Mxi1 repressor factor domain, to down-regulate the expression of the IAH1 gene, encoding for an isoamyl acetate-hydrolyzing esterase, in K. marxianus strain DU3. The constructed CRISPRi plasmid successfully targeted the IAH1 gene, allowing for specific gene expression modulation. Through gene expression analysis, we assessed the impact of IAH1 down-regulation on the metabolic profile of volatile compounds. We also measured the expression of other genes involved in volatile compound biosynthesis, including ATF1, EAT1, ADH1, and ZWF1 by RT-qPCR. Results demonstrated successful down-regulation of IAH1 expression in K. marxianus strain DU3 using the CRISPRi system. The modulation of IAH1 gene expression resulted in alterations in the production of volatile compounds, specifically ethyl acetate, which are important contributors to the beverage's aroma. Changes in the expression levels of other genes involved in ester biosynthesis, suggesting possible regulatory interactions between these genes. The application of CRISPRi technology in K. marxianus opens the possibility of targeted modulation of gene expression, metabolic engineering strategies, and synthetic biology in this yeast strain.\n\nCRISPRi-Induced Transcriptional Regulation of IAH1 Gene and its Influence on Volatile Compounds Profile in Kluyveromyces marxianus DU3", "token_count": 454, "char_count": 1839, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5938, "quality_score": 0.7969, "entities": { "genes": [ "ATF1", "EAT1", "ADH1", "ZWF1", "IAH1", "DU3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:06.393189", "source": { "split": "train_shard_00000", "doc_id": 4871 }, "chunk_id": "train_shard_00000_4871_0", "global_id": 5480 }, { "text": "Production of 2-phenylethanol (2-PE) via Kluyveromyces marxianus is well-established. However, co-culture with other microbes in combination with in situ product recovery (ISPR) yields improved selectivity and volumetric productivity. Fermentation ofK. marxianus (MUCL 53775) with direct inclusion of absorptive polymer Hytrel3548 achieved ISPR, but accumulation of the byproduct phenylethyl acetate (PEA) was strongly favored. Co-culture of K. marxianus (MUCL 53775) with Meyerozyma guilliermondii (MUCL 28072) with ISPR limited PEA production, thereby improving the 2-PE selectivity from 13 to 90%, compared to a pure culture of K. marxianus (MUCL 53775) under similar conditions. This improved the volumetric productivity by 85% compared to 2-PE ISPR with a pure culture of K. marxianus. This is the first report of co-culture in a two-phase fermentation for 2-PE bioproduction and demonstrates that interactions between co-culture and ISPR techniques can modulate bioproduction between 2-PE and byproduct PEA, and this technique will be explored for other strain combinations and for other high-value molecules of interest.\n\nCo-culture of Kluyveromyces marxianus and Meyerozyma guilliermondii with In Situ Product Recovery of 2-Phenylethanol.", "token_count": 438, "char_count": 1316, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5731, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:07.021807", "source": { "split": "train_shard_00000", "doc_id": 4872 }, "chunk_id": "train_shard_00000_4872_0", "global_id": 5481 }, { "text": "Two immunomodulatory signature peptides (PFPEVFG and SPAQILQW) were obtained from casein hydrolysates produced by Kluyveromyces marxianus JY-1 in our previous studies with the aid of virtual screening. However, their mechanisms for improving the composition of the gut microbiota in immunosuppressed mice remain unknown. The aim of this study was to reveal the mechanisms of immunomodulation and improvement of gut microbiota composition mediated by the casein peptides PFPEVFG and SPAQILQW through a cyclophosphamide (Cy)-induced immunosuppression and intestinal mucosal injury mouse model. The casein peptides PFPEVFG and SPAQILQW reversed Cy-induced intestinal structural damage and could correct for Cy-induced intestinal flora disorders. Importantly, fecal microbiota transplantation (FMT) confirmed that the casein peptides PFPEVFG and SPAQILQW attenuate immunosuppression by targeting participation in the dynamic balance of the gut microbiota. These results indicated that the casein peptides PFPEVFG and SPAQILQW have the potential to be used as natural medicines for the treatment of immunosuppression.\n\nMechanisms of Casein-Derived Immunomodulatory Peptides Maintaining Immune Homeostasis via Regulating Gut Microbiota in a Cyclophosphamide-Induced Mouse Model.", "token_count": 358, "char_count": 1279, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5964, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:07.607198", "source": { "split": "train_shard_00000", "doc_id": 4873 }, "chunk_id": "train_shard_00000_4873_0", "global_id": 5482 }, { "text": "Okara, a natural source of dietary fibre (DF), is recognised as an edible and safe material. In this study, lactic acid bacteria (LAB) and Kluyveromyces marxianus were used to ferment okara in separately or in combination, and the physicochemical and functional characteristics of obtained insoluble dietary fibre (IDF) excluded from okara were compared. The result showed that compared with non‐fermented okara, the content of IDF from co‐fermented okara by LAB and K. marxianus increased by 6.8%, while separate fermentations were 2.4% and 4.0%. Scanning electron microscopy result showed that the structure of co‐fermented okara IDF was looser and porous with the edge disappeared compared to separate and non‐fermented okara. All the fermentation treatment groups effectively reduced the particle size and affected the cellulose and hemicellulose functional groups of IDF. Furthermore, compared with non‐fermented okara, processing performance, and the activities of hypoglycaemic and hypolipidaemic of IDF were greatly improved in fermented okara.\n\nComparison of physicochemical and functional characteristics of insoluble dietary fibre from okara by separate and co‐fermentation with lactic acid bacteria and Kluyveromyces marxianus", "token_count": 317, "char_count": 1238, "word_count": 174, "semantic_coherence": 1, "information_density": 0.546, "quality_score": 0.773, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:08.164963", "source": { "split": "train_shard_00000", "doc_id": 4874 }, "chunk_id": "train_shard_00000_4874_0", "global_id": 5483 }, { "text": "Yeast is a promising source of alternative protein, but the low functionality limits the application of yeast protein in food industry. This paper demonstrated pH-shifting assisted ultrasonication treatment could significantly enhance the solubility of yeast protein from Kluyveromyces marxianus, with protein recovery rate increased from 7.32 % to 81.59 % at pH 12, 900 W for 120 min (pH 12-U900), and with the significant occurrence of higher-molecular-weight yeast proteins as witnessed by SDS-PAGE and SEC. The subsequent acid precipitation resulted in yeast protein with high protein content, increased hydrophobicity and higher disulfide bonds content. pH-shifting assisted ultrasonication increased the relative abundance of 60S/40S ribosomal protein, glycolytic enzymes and elongation factor revealed by proteomic analysis; and significantly improved protein functionality including higher solubility, emulsifying activity, foaming capacity, and superior oil holding capacity. Moreover, the prepared yeast protein was found to be rich in essential amino acids and had a high in vitro gastrointestinal digestibility. Peptidomics characterization further suggested the abundant proteins in yeast could release potentially bioactive peptides, especially with better ACE inhibitory activity (IC₅₀ of 0.92 mg/mL). This study demonstrated pH-shifting assisted ultrasonication could be an effective approach to improve yeast protein and supplied a theoretical basis for better development as an alternative protein.\n\nEnhancing structure, functionality, in vitro digestibility and bioactivity of yeast protein by pH-shifting assisted ultrasonication treatment", "token_count": 405, "char_count": 1659, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6273, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:08.782685", "source": { "split": "train_shard_00000", "doc_id": 4875 }, "chunk_id": "train_shard_00000_4875_0", "global_id": 5484 }, { "text": "Saccharomyces cerevisiae (S. cerevisiae) and Kluyveromyces marxianus (K. marxianus) are often used as fermenters in yogurt and alcohol, and have been less studied within meat products. The yeasts were added to sauce meat, and the uninoculated group served as a control in this study to examine and compare the changing patterns of physicochemical and flavor characteristics of S. cerevisiae and K. marxianus on sauce meat during storage. The changes in moisture content, aw, pH, thiobarbituric acid reactive substances (TBARS), and other flavor characteristics were measured in sauce meat during the first, second, fourth, and sixth months after production. The following factors were examined: moisture content, aw, pH, TBARS, peroxide value (POV), acid value (AV), soluble protein (SP), free amino acid (FAA), and volatile flavoring compounds. With VIP > 1 and p < 0.05 as the screening conditions, the partial least squares model (PLS-DA) was used to assess the distinctive flavor components in the sausages. The findings demonstrated that the three groups' changes in sauce meat were comparable during the first two months of storage but differed significantly between the 4th and 6th months. The moisture content, water activity, and pH of the sauce meat decreased gradually with the storage time; TBARS, AV, and FAA increased significantly; SP decreased significantly from 2.61 to 1.72, while POV increased to 0.03 and then decreased to 0.02. The POV and TBARS values of the yeast-infected meat were substantially lower than those of the control group, and the POV and TBARS values of the meat inoculated with S. cerevisiae were particularly decreased (p < 0.05). The POV and TBARS values of SC (S", "token_count": 511, "char_count": 1769, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5784, "quality_score": 0.7892, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:09.444234", "source": { "split": "train_shard_00000", "doc_id": 4876 }, "chunk_id": "train_shard_00000_4876_0", "global_id": 5485 }, { "text": "cerevisiae group) decreased by 49.09% and 40.15%, respectively, compared to CK (the control group) at the time of storage until June. The experimental group (KM: K. marxianus group) significantly increased the SP and FAA values of the sauce meat (p < 0.05) by 32.4% and 29.84% compared to the CK group, respectively. Esters and olefins as well as alcohols and esters were much greater in meat that had been supplemented with S. cerevisiae and K. marxianus than in meat from the control group. In conclusion, inoculating sauce meat with S. cerevisiae can significantly enhance the quality and flavor of sauce meat while it is being stored.\n\nEffects of Saccharomyces cerevisiae and Kluyveromyces marxianus on the Physicochemical, Microbial, and Flavor Changes of Sauce Meat during Storage.", "token_count": 274, "char_count": 840, "word_count": 125, "semantic_coherence": 1, "information_density": 0.616, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:09.987606", "source": { "split": "train_shard_00000", "doc_id": 4876 }, "chunk_id": "train_shard_00000_4876_1", "global_id": 5486 }, { "text": "Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease, primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide valuable insights into the genetic virulence factors and genomic variations of Xoo strains isolated in Thailand. Furthermore, we present the first complete genomic database of Thai Xoo, offering a comprehensive resource for studying pathogen diversity, tracking virulence evolution and supporting disease management strategies in rice production. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and US strains. Remarkably, the average nt identity values, in comparison with Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99%. These strains can be classified into three assigned ribosomal sequence types. Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30% form the core genome. Notably, all of these genomes exhibit a clustered regularly interspaced short palindromic repeats-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D and E) and the X. oryzae strain AH28 plasmid pAH28 (A97)", "token_count": 505, "char_count": 1722, "word_count": 238, "semantic_coherence": 1, "information_density": 0.7185, "quality_score": 0.8592, "entities": { "genes": [ "BXO1", "AH28", "GX01", "XO35933" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:10.643298", "source": { "split": "train_shard_00000", "doc_id": 4877 }, "chunk_id": "train_shard_00000_4877_0", "global_id": 5487 }, { "text": "This genomic resource will be valuable for advancing research on surveillance, prevention, management and comparative studies of this critical pathogen in the future.\n\nComplete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand.", "token_count": 60, "char_count": 274, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:11.000038", "source": { "split": "train_shard_00000", "doc_id": 4877 }, "chunk_id": "train_shard_00000_4877_1", "global_id": 5488 }, { "text": "

Introduction

The Klebsiella pneumoniae (KP) species complex (KpSC) comprises KP as the predominant species, and six other taxa including two subspecies each of Klebsiella variicola (KV) and Klebsiella quasipneumoniae (KQ), all capable of causing clinical infections and often challenging to differentiate. Among these, KP is by far the most clinically significant, with the emergence of multidrug-resistant and hypervirulent strains leading to severe infections and limited treatment options, underscoring the need to understand the genomic features of KP.

Methods

This study compared globally disseminated KP lineages with less abundant KV strains in synthetic human urine (SHU) across multiple omics levels to identify characteristics differentiating these closely related species. Moreover, a large genomic dataset of over 6,000 publicly available genomes of KP, KV, and KQ was constructed for comparisons to other members of the KpSC.

Results

Among eight clinical KP strains representing four different sequence types (STs), we identified 107 genes comprising the KP-specific core genome, while these genes were absent from two selected KV genomes. Transcriptome and proteome analyses in SHU revealed different regulatory patterns between KP and KV strains, with metabolic responses playing a pivotal role. A total of 193 genes specific to the investigated KP STs were identified, exhibiting differential expression at the transcriptomic and/or proteomic levels. Comparison to the genomic dataset highlighted genes adaptively regulated or uniquely present in KP genomes. For example, certain genes for citrate metabolism are uniquely upregulated in KP and a gene cluster for the cellobiose phosphotransferase system, previously linked to bacterial virulence and biofilm formation, was found exclusively in KP.

Discussion

Our study underscores the metabolic flexibility of KP strains in response to specific environmental conditions, potentially contributing to opportunistic pathogenicity", "token_count": 518, "char_count": 2049, "word_count": 271, "semantic_coherence": 1, "information_density": 0.69, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:11.631838", "source": { "split": "train_shard_00000", "doc_id": 4878 }, "chunk_id": "train_shard_00000_4878_0", "global_id": 5489 }, { "text": "We identified markers enriched in KP STs, providing a foundation for future investigations including their relevance for diagnostics.\n\nMulti-omics investigation reveals unique markers in <i>Klebsiella pneumoniae</i> compared to closely related species.", "token_count": 69, "char_count": 264, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9032, "quality_score": 0.9516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:12.034937", "source": { "split": "train_shard_00000", "doc_id": 4878 }, "chunk_id": "train_shard_00000_4878_1", "global_id": 5490 }, { "text": "

Background and aim

Mycoplasma hominis is a human pathogenic bacterium that causes a wide range of genital infections and reproductive issues. Previously, based on an extended multilocus sequence typing scheme, we provided evidence for the segregation of M. hominis clinical strains into two distinct pathotypes: gynecological infections or infertility. Here, based on whole genome sequencing (WGS) data, we sought to provide a more refined picture of the phylogenetic relationship between these two M. hominis pathotypes, with the aim to delineate the underlying genetic determinants.

Methods

We carried out WGS of 62 Tunisian M. hominis clinical strains collected over a 17-year period. The majority of these clinical strains are associated with infertility (n = 53) and the remaining nine isolates are from gynecological infections cases. An alignment-free distance-based procedure (Jolytree) was used to infer phylogenetic relationships among M. hominis isolates, while the phylogenetic method treeWAS was used to determine the statistical association between pathotypes of interest and genotypes at all loci.

Results

The total pangenome of M. hominis strains was found to contain 1,590 genes including 966 core genes and 592 accessory genes, representing 60 and 37% of the total genome, respectively. Collectively, phylogenetic analyses based on WGS confirmed the distinction between the two M. hominis pathotypes. Strikingly, genome wide association analyses identified 4 virulence genes associated with gynecological infections, mainly involved in nucleotide salvage pathways and tolerance to oxidative stress, while five genes have been associated with infertility cases, two of which are implicated in biofilm formation.

Conclusion

In sum, this study further established the categorization of M", "token_count": 512, "char_count": 1890, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6375, "quality_score": 0.8187, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:12.694237", "source": { "split": "train_shard_00000", "doc_id": 4879 }, "chunk_id": "train_shard_00000_4879_0", "global_id": 5491 }, { "text": "hominis into two pathotypes, and led to the identification of the associated genetic loci, thus holding out promising prospects for a better understanding of the differential interaction of M. hominis with its host.\n\nA genome-wide investigation of <i>Mycoplasma hominis</i> genes associated with gynecological infections or infertility.", "token_count": 94, "char_count": 359, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8043, "quality_score": 0.9022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:13.097118", "source": { "split": "train_shard_00000", "doc_id": 4879 }, "chunk_id": "train_shard_00000_4879_1", "global_id": 5492 }, { "text": "

Background

Clonal complex 180 (CC180) is currently the major clone of serotype 3 Streptococcus pneumoniae (Spn) causing disease among children and adults worldwide. The 13-valent pneumococcal conjugate vaccine (PCV13) does not have significant efficacy against serotype 3 despite polysaccharide inclusion in the vaccine. It was hypothesized that PCV13 may effectively control Clade I of CC180 but that Clades III and IV are resistant, provoking a population shift that enables serotype 3 persistence. This has been observed in the United States, England, and Wales but not Spain. We tested this hypothesis further utilizing a dataset from Portugal to conduct our population genomics and molecular epidemiology comparative study.

Methods

We performed whole-genome sequencing (WGS) of 501 serotype 3 strains from Portugal isolated from patients with pneumococcal infections between 1999 and 2020. The draft genomes underwent phylogenetic analyses, pangenome profiling, and a genome-wide association study (GWAS). We also completed antibiotic susceptibility testing and compiled over 2600 serotype 3 multilocus sequence type 180 (MLST180) WGSs to perform global comparative genomics.

Findings

Relative to strains from all other lineages, CC180 Clades I, II, III, IV, and VI strains trend towards a decreased association with invasive disease cases compared to non-invasive pneumonia cases (binomial logistic regression, odds ratio or OR = 0.59, 95% confidence interval or CI = [0.34, 0.98], P = 0.046) and adult patients compared to paediatric patients (binomial logistic regression, OR = 0.34, 95% CI = [0.098, 0.92], P = 0.054)", "token_count": 490, "char_count": 1648, "word_count": 233, "semantic_coherence": 1, "information_density": 0.7039, "quality_score": 0.8519, "entities": { "genes": [ "MLST180", "PCV13", "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:13.779460", "source": { "split": "train_shard_00000", "doc_id": 4880 }, "chunk_id": "train_shard_00000_4880_0", "global_id": 5493 }, { "text": "The serotype 3 CCs shifted post-PCV13 such that Clades I-VI comprise the majority of post-PCV13 lineages (binomial logistic regression, OR = 7.33, 95% CI = 4.36, 12.80, P < 0.0001), with Clade I representing 54% (220/404) of all post-PCV13 strains. As observed elsewhere, Clade I strains from Portugal are largely antibiotic-sensitive and carry the ΦOXC141 prophage. However, strains from Portugal and Spain, where Clade I remains dominant post-PCV13, have larger pangenomes and are associated with the presence of two genes encoding hypothetical proteins.

Interpretation

Clade I became dominant in Portugal post-PCV13, despite the burden of the prophage and antibiotic sensitivity. The additional accessory genome content may mitigate these fitness costs. Regional differences in Clade I prevalence and pangenome heterogeneity suggest that clade dynamics is not a generalizable approach to understanding serotype 3 vaccine escape.

Funding

National Institute of Child Health and Human Development, Pfizer, and Merck Sharp & Dohme.\n\nCC180 clade dynamics do not universally explain Streptococcus pneumoniae serotype 3 persistence post-vaccine: a global comparative population genomics study.", "token_count": 351, "char_count": 1203, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7256, "quality_score": 0.8628, "entities": { "genes": [ "PCV13", "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:14.353328", "source": { "split": "train_shard_00000", "doc_id": 4880 }, "chunk_id": "train_shard_00000_4880_1", "global_id": 5494 }, { "text": "Cholera is an acute diarrhoeal disease caused by Vibrio cholerae. It remains a major public health challenge worldwide, and particularly in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak. Defining the pool of diversity over finer time-scales is important because the selective pressures that impact V. cholerae, namely antibiotics and phages, are dynamic on these scales. To study the nationwide diversity of V. cholerae, we long-read sequenced 273 V. cholerae genomes from seven hospitals over 1 year (2018) in Bangladesh. Four major V. cholerae lineages were identified: three known lineages, BD-1, BD-2a and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, at which point it had replaced BD-2 as the most common lineage in Bangladesh. We show that, in 2018, BD-1 was already predominant in the five northern regions, including Dhaka, consistent with an origin from northern India. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, yet persisted throughout the sampling period. Genes previously associated with antibiotic resistance in V. cholerae isolated from Bangladesh in the prior decade were entirely absent from all lineages in 2018-2019, suggesting shifting costs and benefits of encoding these genes. Our results highlight the diverse nature of the V", "token_count": 511, "char_count": 1873, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:15.016122", "source": { "split": "train_shard_00000", "doc_id": 4881 }, "chunk_id": "train_shard_00000_4881_0", "global_id": 5495 }, { "text": "cholerae pangenome and geographic structure within a single outbreak season. This diversity provides the raw material for adaptation to antibiotics, phages and other selective pressures.\n\n<i>Vibrio cholerae</i> lineage and pangenome diversity vary geographically across Bangladesh over 1 year.", "token_count": 84, "char_count": 309, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:15.391858", "source": { "split": "train_shard_00000", "doc_id": 4881 }, "chunk_id": "train_shard_00000_4881_1", "global_id": 5496 }, { "text": "Traditional fermented milk from the western Sichuan plateau of China has a unique flavor and rich microbial diversity. This study explored the quality formation mechanism in fermented milk inoculated with Lactobacillus brevis NZ4 and Kluyveromyces marxianus SY11 (MFM), the dominant microorganisms isolated from traditional dairy products in western nan. The results indicated that MFM displayed better overall quality than the milk fermented with L. brevis NZ4 (LFM) and K. marxianus SY11 (KFM), respectively. MFM exhibited good sensory quality, more organic acid types, more free amino acids and esters, and moderate acidity and ethanol concentrations. Non-targeted metabolomics showed a total of 885 metabolites annotated in the samples, representing 204 differential metabolites between MFM and LFM and 163 between MFM and KFM. MFM displayed higher levels of N-acetyl-L-glutamic acid, cysteinyl serine, glaucarubin, and other substances. The differential metabolites were mainly enriched in pathways such as glycerophospholipid metabolism, arginine biosynthesis, and beta-alanine metabolism. This study speculated that L. brevis affected K. marxianus growth via its metabolites, while the mixed fermentation of these strains significantly changed the metabolism pathway of flavor-related substances, especially glycerophospholipid metabolism. Furthermore, mixed fermentation modified the flavor and quality of fermented milk by affecting cell growth and metabolic pathways.\n\nUntargeted Metabolomics and Physicochemical Analysis Revealed the Quality Formation Mechanism in Fermented Milk Inoculated with Lactobacillus brevis and Kluyveromyces marxianus Isolated from Traditional Fermented Milk.", "token_count": 506, "char_count": 1753, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6027, "quality_score": 0.8013, "entities": { "genes": [ "NZ4", "SY11" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:16.025978", "source": { "split": "train_shard_00000", "doc_id": 4882 }, "chunk_id": "train_shard_00000_4882_0", "global_id": 5497 }, { "text": "Introduction People around the world faced the possibility of death during the COVID-19 outbreak, including in India in 2019. Coinfection of oral candidiasis-like symptoms was not uncommon among COVID-19-infected patients undergoing treatment with prolonged broad-spectrum antibiotics or corticosteroid therapy. The present study aims to characterize the prevalence profile of Candida species and their antifungal drug susceptibility patterns among patients with COVID-19. Material and methods A short-term, hospital-based observational study was conducted on patients with Reverse Transcription Polymerase Chain Reaction (RT-PCR)-confirmed COVID-19 infections admitted to the critical care unit of a medical college hospital who presented with oral candidiasis-like symptoms. Oral swab samples were collected and cultured on Sabouraud dextrose agar. Species identification was performed using the VITEK-2 automated system (Biomerieux, France). Results Among 544 patients diagnosed with COVID-19, 20 were microbiologically positive for oral candidiasis. Candida albicans was the predominant species, followed by Candida glabrata, Candida tropicalis, and Candida kefyr. Females (55%) exhibited a slightly higher susceptibility than males (45%). Antifungal susceptibility testing revealed one isolate with multidrug resistance and five additional isolates displaying resistant or intermediate drug sensitivity patterns. COVID-19-related immune suppression and associated overuse of antibiotics and corticosteroids contributed to an increased incidence of oral candidiasis due to opportunistic fungi, including Candida albicans and non-albicans Candida species. Conclusion The candidal species profile associated with oral candidiasis did not significantly alter during the COVID-19 period compared to pre-COVID-19 baselines. Key message There was no occurrence of emerging Candida species during the COVID-19 period.", "token_count": 505, "char_count": 1970, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6803, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:16.690335", "source": { "split": "train_shard_00000", "doc_id": 4883 }, "chunk_id": "train_shard_00000_4883_0", "global_id": 5498 }, { "text": "Oral Candidiasis in COVID-19 Patients Under Critical Care Involving Non-albicans Candida Species Alongside Candida albicans.", "token_count": 37, "char_count": 124, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:17.053777", "source": { "split": "train_shard_00000", "doc_id": 4883 }, "chunk_id": "train_shard_00000_4883_1", "global_id": 5499 }, { "text": "

Abstract

The accuracy of enzyme kinetic parameters, particularly the turnover number ( k cat), is critical for the predictive power of enzyme-constrained genome-scale metabolic models (ecGEMs). However, current kinetic datasets remain sparse and often fail to capture in vivo enzyme behavior, compromising model predictive capacity. To address these challenges, we developed EnzymeTuning——a generative adversarial network (GAN)-based framework for the global kcat optimization. This approach significantly enhances both the accuracy and proteome-level coverage of ecGEM predictions. Moreover, by incorporating literature-derived protein degradation constants ( kdeg ), we inferred the protein synthesis rate and systematically evaluated their impact on model performance. The framework was validated across distinct yeast species, including Saccharomyces cerevisiae , Kluyveromyces lactis , Kluyveromyces marxianus , and Yarrowia lipolytica , demonstrating its generalizability. Further, we found that EnzymeTuning facilitates the identification of context-specific enzyme usage patterns and adaptive catalytic resource allocation under varying carbon-to-nitrogen (C/N) ratios, showcasing the substantial potential of our toolbox for integrative omics analysis. Overall, EnzymeTuning provides a robust and scalable solution for refining kinetic parameters in ecGEMs, thereby promoting the wide applications of these computational models in systems and synthetic biological studies.\n\nEnzymeTuning: a Deep-learning-based Toolbox for Optimizing Enzyme-constrained Metabolic Modeling with Enhanced Proteome Abundance Prediction", "token_count": 384, "char_count": 1636, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7537, "quality_score": 0.8768, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:18.365545", "source": { "split": "train_shard_00000", "doc_id": 4884 }, "chunk_id": "train_shard_00000_4884_0", "global_id": 5500 }, { "text": "

Background

Production of cheese whey in the EU exceeded 55 million tons in 2022, resulting in lactose-rich effluents that pose significant environmental challenges. To address this issue, the present study investigated cheese-whey treatment via membrane filtration and the utilization of its components as fermentation feedstock. A simulation model was developed for an industrial-scale facility located in Italy's Apulia region, designed to process 539 m3/day of untreated cheese-whey. The model integrated experimental data from ethanolic fermentation using a selected strain of Kluyveromyces marxianus in lactose-supplemented media, along with relevant published data.

Results

The simulation was divided into three different sections. The first section focused on cheese-whey pretreatment through membrane filtration, enabling the recovery of 56%w/w whey protein concentrate, process water recirculation, and lactose concentration. In the second section, the recovered lactose was directed towards fermentation and downstream anhydrous ethanol production. The third section encompassed anaerobic digestion of organic residue, sludge handling, and combined heat and power production. Moreover, three different scenarios were produced based on ethanol yield on lactose (YE/L), biomass yield on lactose, and final lactose concentration in the medium. A techno-economic assessment based on the collected data was performed as well as a sensitivity analysis focused on economic parameters, encompassing considerations on cheese-whey by assessing its economical impact as a credit for the simulated facility, dictated by a gate fee, or as a cost by considering it a raw material. The techno-economic analysis revealed different minimum ethanol selling prices across the three scenarios. The best performance was obtained in the scenario presenting a YE/L = 0.45 g/g, with a minimum selling price of 1.43 €/kg", "token_count": 485, "char_count": 1964, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:19.022070", "source": { "split": "train_shard_00000", "doc_id": 4885 }, "chunk_id": "train_shard_00000_4885_0", "global_id": 5501 }, { "text": "Finally, sensitivity analysis highlighted the model's dependence on the price or credit associated with cheese-whey handling.

Conclusions

This work highlighted the importance of policy implementation in this kind of study, demonstrating how a gate fee approach applied to cheese-whey procurement positively impacted the final minimum selling price for ethanol across all scenarios. Additionally, considerations should be made about the implementation of the simulated process as a plug-in addition in to existing processes dealing with dairy products or handling multiple biomasses to produce ethanol.\n\nProcess scale-up simulation and techno-economic assessment of ethanol fermentation from cheese whey.", "token_count": 149, "char_count": 710, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7849, "quality_score": 0.8925, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:19.457581", "source": { "split": "train_shard_00000", "doc_id": 4885 }, "chunk_id": "train_shard_00000_4885_1", "global_id": 5502 }, { "text": "We conducted a comparative genomic analysis of Lactobacillus johnsonii strains isolated from the gastrointestinal tract of diverse vertebrate hosts to explore the genetic basis of host specificity. We then utilized transcriptomics analysis to investigate the expression profile of identified rodent-specific genes in mouse isolate MR1 during in vitro and in vivo growth conditions. There was significant heterogeneity among strains, in both genome sequence and content, with phylogenetic clustering of strains into distinct clades associated with rodent or avian sources. There were not sufficient genomes to identify whether porcine isolates formed their own genetic clade. However, human isolates did not form a distinct clade. Functional enrichment analysis revealed significant enrichment of several genes, including surface proteins and accessory secretory pathway-related genes, as well as tyrosine decarboxylase genes in rodent isolates compared to avian isolates, including in mouse isolate MR1. A total of 40 genes were identified as rodent-associated, and all were transcriptionally active in L. johnsonii MR1. The global transcriptomic analysis of L. johnsonii MR1 was done using cells grown anaerobically, at 37˚C, under both the late-exponential phase and stationary phase, as well as during in vivo growth in the cecum of mono-colonized germ-free mice. Several of these genes were uniquely regulated during late exponential vs stationary phase growth and in vivo colonization in mice, highlighting their potential role in nutrient adaptation and host-microbe interactions.IMPORTANCELactobacillus johnsonii is a well-known probiotic species with health-beneficial properties, including host immunomodulation and pathogen inhibition. Its growing relevance in the medical industry highlights the need to understand its biology, particularly how it adapts to different host environments. In bacteria, niche adaptation is often accompanied by the loss or gain of coding sequences along with changes in the genome size", "token_count": 515, "char_count": 2082, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6184, "quality_score": 0.8092, "entities": { "genes": [ "MR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:20.093425", "source": { "split": "train_shard_00000", "doc_id": 4886 }, "chunk_id": "train_shard_00000_4886_0", "global_id": 5503 }, { "text": "In this study, we explored the genetic diversity of L. johnsonii strains from the gastrointestinal tracts of various vertebrates such as rodents, birds, swine, and humans. We found associations between genome content and host species of origin and could conceptually demonstrate that these genes are being differentially transcribed under varying conditions. Several functions were associated with specific host groups, suggesting that L. johnsonii strains have adapted to their hosts over time.\n\nGenomic and transcriptomic insights into vertebrate host-specific <i>Lactobacillus johnsonii</i> adaptation in the gastrointestinal tract.", "token_count": 166, "char_count": 661, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:20.538644", "source": { "split": "train_shard_00000", "doc_id": 4886 }, "chunk_id": "train_shard_00000_4886_1", "global_id": 5504 }, { "text": "

Background

Built environments (BEs) are typically considered to be oligotrophic and harsh environments for microbial communities under normal, non-damp conditions. However, the metabolic functions of microbial inhabitants in BEs remain poorly understood. This study aimed to shed light on the functional capabilities of microbes in BEs by analyzing 860 representative metagenome-assembled genomes (rMAGs) reconstructed from 738 samples collected from BEs across the city of Hong Kong and from the skin surfaces of human occupants. The study specifically focused on the metabolic functions of rMAGs that are either phylogenetically novel or prevalent in BEs.

Results

The diversity and composition of BE microbiomes were primarily shaped by the sample type, with Micrococcus luteus and Cutibacterium acnes being prevalent. The metabolic functions of rMAGs varied significantly based on taxonomy, even at the strain level. A novel strain affiliated with the Candidatus class Xenobia in the Candidatus phylum Eremiobacterota and two novel strains affiliated with the superphylum Patescibacteria exhibited unique functions compared with their close relatives, potentially aiding their survival in BEs and on human skins. The novel strains in the class Xenobia possessed genes for transporting nitrate and nitrite as nitrogen sources and nitrosative stress mitigation induced by nitric oxide during denitrification. The two novel Patescibacteria strains both possessed a broad array of genes for amino acid and trace element transport, while one of them carried genes for carotenoid and ubiquinone biosynthesis. The globally prevalent M. luteus in BEs displayed a large and open pangenome, with high infraspecific genomic diversity contributed by 11 conspecific strains recovered from BEs in a single geographic region. The versatile metabolic functions encoded in the large accessory genomes of M. luteus may contribute to its global ubiquity and specialization in BEs.

Conclusions

This study illustrates that the microbial inhabitants of BEs possess metabolic potentials that enable them to tolerate and counter different biotic and abiotic conditions", "token_count": 523, "char_count": 2169, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5908, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:21.174954", "source": { "split": "train_shard_00000", "doc_id": 4887 }, "chunk_id": "train_shard_00000_4887_0", "global_id": 5505 }, { "text": "Additionally, these microbes can efficiently utilize various limited residual resources from occupant activities, potentially enhancing their survival and persistence within BEs. A better understanding of the metabolic functions of BE microbes will ultimately facilitate the development of strategies to create a healthy indoor microbiome. Video Abstract.\n\nDiverse and specialized metabolic capabilities of microbes in oligotrophic built environments.", "token_count": 85, "char_count": 451, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:21.553254", "source": { "split": "train_shard_00000", "doc_id": 4887 }, "chunk_id": "train_shard_00000_4887_1", "global_id": 5506 }, { "text": "Multidrug-resistant Klebsiella pneumoniae continues to challenge healthcare services globally. However, our understanding of its occurrence, genomic characteristics, and epidemiology in low- and middle-income countries (LMICs) remains severely limited. In this study, we report the whole-genome sequencing of an extended-spectrum β-lactamase (ESBL)-producing, sequence type (ST) 37 K. pneumoniae isolate (ARM02) recovered from a patient in Armenia. Antibiotic susceptibility testing revealed that ARM02 was resistant to four of the 11 antibiotics tested, including ampicillin, amoxicillin-clavulanic acid, cefepime, and ceftazidime. Genome sequencing analysis identified seven antimicrobial resistance (AMR) genes in ARM02, including blaTEM-1D, blaSHV-11, dfrA14, sul2, strA, strB, and the ESBL-producing gene blaCTX-M-15. In addition, ARM02 harbored 12 virulence genes, including the common pilus fibrillin subunit encoding gene yagZ/ecpA and a complete yersiniabactin siderophore system (irp1, irp2, ybtAEPQSTUX, and fyuA). Moreover, we also detected five insertion sequences and two plasmid replicons in the ARM02 genome. Phylogenetic analysis showed that ARM02 shared a common ancestor with the USA strains SRR5283489 and SRR5973349, diverging around 2007 (95% onfidence interval, 2004 to 2011)", "token_count": 513, "char_count": 1436, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7964, "quality_score": 0.8982, "entities": { "genes": [ "ARM02", "SRR5973349", "SRR5283489" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:22.190135", "source": { "split": "train_shard_00000", "doc_id": 4888 }, "chunk_id": "train_shard_00000_4888_0", "global_id": 5507 }, { "text": "However, ARM02 carried a unique accessory genome, indicating independent evolution and spread. Our findings highlight the co-existence of virulence and resistance genes in the Armenian ST37 strain and emphasize the critical need for genomic surveillance in LMICs. This is crucial for understanding how gram-negative bacterial pathogens, such as ESBL-producing K. pneumoniae, which remain on the WHO's Priority Pathogens list, evolve and spread in LMICs, and how they contribute to the global AMR crisis.IMPORTANCEWe report the first genomic analysis of an extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae ST37 isolate (ARM02) recovered from a hospitalized patient in Armenia. Genome sequencing identified several antimicrobial resistance (AMR) genes, including blaCTX-M-15, blaTEM-1D, and blaSHV-11, which were directly linked to the observed resistance phenotypes. ARM02 also carried a variety of virulence genes, including a complete yersiniabactin siderophore system, which is associated with enhanced pathogenicity. Phylogenetic analysis revealed that ARM02 was closely related to strains from the United States, but it harbored a unique accessory genome, suggesting independent evolution and local spread in Armenia. This highlights the critical need for robust genomic surveillance and targeted interventions in low- and middle-income countries. This study provides crucial insights into the genetic diversity and potential local transmission of ST37 K. pneumoniae in Armenia and calls for larger-scale genomic surveillance to better understand and control its spread.\n\nGenomic characterization of an ESBL-producing <i>Klebsiella pneumoniae</i> ST37 recovered from a hospitalized patient in Armenia.", "token_count": 481, "char_count": 1812, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [ "ARM02", "ST37" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:22.836422", "source": { "split": "train_shard_00000", "doc_id": 4888 }, "chunk_id": "train_shard_00000_4888_1", "global_id": 5508 }, { "text": "β-Glucan (BG), one of the most abundant polysaccharides containing glucose monomers linked by β-glycosidic linkages, is prevalent in yeast biomass that needs to be recovered to obtain this valuable polymer. This study aimed to apply alkaline and enzymatic processes for the recovery of BG from the yeast strain Kluyveromyces marxianus TISTR 5925. For this purpose, the yeast was cultivated to produce the maximum yield of raw material (yeast cells). The effective recovery of BG was then established using either an alkaline or an enzymatic process. BG recovery of 35.45% was obtained by using 1 M NaOH at 90 °C for 1 h, and of 81.15% from 1% (w/v) hydrolytic protease enzyme at 55 °C for 5 h. However, BG recovered by the alkaline process was purer than that obtained by the enzymatic process. Fourier transform infrared (FTIR) and nuclear magnetic resonance (NMR) spectroscopy confirmed the purity, the functional groups, and the linkages of BG obtained from different recovery systems and different raw materials. The results of this study suggest that an alkaline process could be an effective approach for the solubilization and recovery of considerable purity of BG from the yeast cells. In addition, the obtained BG had comparable functional properties with commercially available BG. This study reveals the effectiveness of both chemical and biological recovery of BG obtained from yeast as a potential polymeric material.\n\nFunctionality of Yeast β-Glucan Recovered from Kluyveromyces marxianus by Alkaline and Enzymatic Processes.", "token_count": 435, "char_count": 1567, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5439, "quality_score": 0.772, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:23.469236", "source": { "split": "train_shard_00000", "doc_id": 4889 }, "chunk_id": "train_shard_00000_4889_0", "global_id": 5509 }, { "text": "Engineering identical genetic circuits into different species typically results in large differences in performance due to the unique cellular environmental context of each host, a phenomenon known as the \"chassis-effect\" or \"context-dependency\". A better understanding of how genomic and physiological contexts underpin the chassis-effect will improve biodesign strategies across diverse microorganisms. Here, we combined a pangenomic-based gene expression analysis with quantitative measurements of performance from an engineered genetic inverter device to uncover how genome structure and function relate to the observed chassis-effect across six closely related Stutzerimonas hosts. Our results reveal that genome architecture underpins divergent responses between our chosen non-model bacterial hosts to the engineered device. Specifically, differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed differential genetic device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes involved in denitrification and components of trans-membrane transporter proteins were among the most differentially expressed gene clusters between hosts in response to the genetic device. Our results show that the chassis-effect can be traced along differences among the most conserved genome-encoded functions and that these differences create a unique biodesign space among closely related species.IMPORTANCEContemporary synthetic biology endeavors often default to a handful of model organisms to host their engineered systems. Model organisms such as Escherichia coli serve as attractive hosts due to their tractability but do not necessarily provide the ideal environment to optimize performance. As more novel microbes are domesticated for use as biotechnology platforms, synthetic biologists are urged to explore the chassis-design space to optimize their systems and deliver on the promises of synthetic biology. The consequences of the chassis-effect will therefore only become more relevant as the field of biodesign grows. In our work, we demonstrate that the performance of a genetic device is highly dependent on the host environment it operates within, promoting the notion that the chassis can be considered a design variable to tune circuit function", "token_count": 489, "char_count": 2455, "word_count": 336, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:24.153293", "source": { "split": "train_shard_00000", "doc_id": 4890 }, "chunk_id": "train_shard_00000_4890_0", "global_id": 5510 }, { "text": "Importantly, our results unveil that the chassis-effect can be traced along similarities in genome architecture, specifically the shared core genome. Our study advocates for the exploration of the chassis-design space and is a step forward to empowering synthetic biologists with knowledge for more efficient exploration of the chassis-design space to enable the next generation of broad-host-range synthetic biology.\n\nPangenomic landscapes shape performances of a synthetic genetic circuit across Stutzerimonas species.", "token_count": 118, "char_count": 527, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7571, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:24.562044", "source": { "split": "train_shard_00000", "doc_id": 4890 }, "chunk_id": "train_shard_00000_4890_1", "global_id": 5511 }, { "text": "Pulmonary disease caused by nontuberculous mycobacteria (NTM-PD) is an emerging global health concern. Among NTM, Mycobacterium avium subsp. hominissuis (MAH) is the major causative agent of NTM-PD. Similar to Mycobacterium tuberculosis ( Mtb ), MAH exhibits lineage-specific geographical distributions and host adaptations. Here, we characterized three MAH strains from the residential bathrooms of MAH-PD patients in Japan. A genetic population clustering analysis revealed that the three strains belong to the East Asia (EA) lineages that are predominant in Japan and Korea. Pan-genome analysis using the publicly available complete genome sequences of MAH and the newly sequenced MAH strains identified 3,313 core genes that are conserved among distinct MAH lineages. Identification of essential genes in the three strains was conducted using transposon insertion sequencing (Tn-Seq), and their gene essentiality profiles were compared to those of a previously studied SC3 lineage strain, MAC109. Despite their genetic diversity, nearly all essential genes were derived from the core gene set. In addition, we identified a set of common essential genes for the EA and SC3 lineages, as well as lineage-specific essential genes. Our results highlight the evolutionary and clinical importance of lineage-specific adaptations in MAH.

Importance

By integrating transposon insertion sequencing with pan-genome analysis, we provide the first systematic comparison of essential genes across multiple Mycobacterium avium subsp. hominissuis (MAH) strains. Although MAH strains exhibit remarkable genetic diversity, we found that MAH essential genes are primarily confined to the core genome of MAH. This essential plasticity highlights the evolutionary strategies that underpin MAH survival across diverse environments and patient populations. Recognizing this interplay provides a foundation for identifying robust drug targets and developing lineage-informed therapies for MAH infection.\n\nIntegrated analysis of Tn-Seq and pangenome reveals core and lineage-specific essential genes in Mycobacterium avium subsp. hominissuis", "token_count": 503, "char_count": 2144, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.799, "entities": { "genes": [ "SC3", "MAC109" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:25.262516", "source": { "split": "train_shard_00000", "doc_id": 4891 }, "chunk_id": "train_shard_00000_4891_0", "global_id": 5512 }, { "text": "In a bid to explore the on-site biorefinery approach for conversion of forestry residues, lignocellulosic biomass into value-added products was studied. The bark white pine wood was subjected to the microwave technique of fast and slow hydrolysis under varying acid and biomass concentrations to produce levulinic acid (LA). The HCl (2% v/v) and plant biomass (1% w/v) were identified as the optimum conditions for fast wood hydrolysis (270 ºC for 12 sec), which led to maximum LA yield of 446.68 g/kgPB. The proposed sustainable approach is mild, quick, and utilized a very low concentration of the HCl for the production of LA. The hydrolysate was used as a medium for Kluyveromyces marxianus growth to produce 2-phenylethanol (2-PE). K. marxianus used 74-95% of furfural from hydrolysate as a co-substrate to grow. The proposed model of the integrated biorefinery is an affordable on-site approach of using forest waste into localized solutions to produce LA and 2-PE.\n\nIntegrated biorefinery approach for utilization of wood waste into levulinic acid and 2-Phenylethanol production under mild treatment conditions.", "token_count": 318, "char_count": 1129, "word_count": 172, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:25.868712", "source": { "split": "train_shard_00000", "doc_id": 4892 }, "chunk_id": "train_shard_00000_4892_0", "global_id": 5513 }, { "text": "Soy leghemoglobin, when bound to heme, imparts a meat-like color and flavor and can serve as a substitute for animal-derived proteins. Enhancing cellular heme synthesis improves the recombinant expression of leghemoglobin in yeast. To achieve high-level expression of leghemoglobin A (LBA) in Kluyveromyces marxianus, a food-safe yeast, large-scale heme synthesis modules were transferred into K. marxianus using yeast artificial chromosomes (KmYACs). These modules contained up to 8 native and heterologous genes to promote the supply of heme precursors and downstream synthesis. Next, eight genes inhibiting heme or LBA synthesis were individually or combinatorially deleted, with the lsc1Δssn3Δ mutant yielding the best results. Subsequently, heme synthesis modules were combined with the lsc1Δssn3Δ mutant. In the resulting strains, the module genes were all actively expressed. Among these module genes, heterologous S. cerevisiae genes in the downstream heme synthesis pathway significantly enhanced the expression of their counterparts in K. marxianus, resulting in high heme content and LBA yield. After optimizing the medium recipe by adjusting the concentrations of glucose, glycine, and FeSO4·7H2O, a heme content of 66.32 mg/L and an intracellular LBA titer of 7.27 g/L were achieved in the engineered strain in a 5 L fermentor. This represents the highest intracellular expression of leghemoglobin in microorganisms to date. The leghemoglobin produced by K. marxianus can be utilized as a safe ingredient for plant-based protein products.", "token_count": 492, "char_count": 1636, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5964, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:26.522093", "source": { "split": "train_shard_00000", "doc_id": 4893 }, "chunk_id": "train_shard_00000_4893_0", "global_id": 5514 }, { "text": "High-level expression of leghemoglobin in Kluyveromyces marxianus by remodeling the heme metabolism pathway.", "token_count": 41, "char_count": 115, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:26.878712", "source": { "split": "train_shard_00000", "doc_id": 4893 }, "chunk_id": "train_shard_00000_4893_1", "global_id": 5515 }, { "text": "

Aims

Kluyveromyces marxianus' high production of 2-phenylethyl acetate (2-PEA) via L-phenylalanine (Phe) catabolism makes it relevant for industries relying on the production of aroma compounds through fermentation processes. This study assessed the physiological impact of exogenous supplementation of Phe on cell viability, fermentation performance, and, by extension, on lipid and amino acid metabolism in a wine isolate of this yeast.

Methods and results

The data showed that Phe exerted cytotoxic effects on K. marxianus IWBT Y885, which were minimal on Saccharomyces cerevisiae and impacted amino acid metabolism and aroma production. We demonstrated that K. marxianus strains fermented sugars more effectively in the absence of Phe. While lipid supplementation did not mitigate any deleterious effects of Phe, it supported viability maintenance and fermentation performance in the absence of Phe. Phe supplementation succeeded in augmenting the production of 2-PE and 2-PEA.

Conclusions

The enhanced production of 2-PEA in K. marxianus suggests that this transesterification may be, at least in part, a compensatory detoxification mechanism for this yeast.\n\nComparative impact of exogenous phenylalanine on oenological isolates of Kluyveromyces marxianus and Saccharomyces cerevisiae.", "token_count": 371, "char_count": 1313, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:27.467410", "source": { "split": "train_shard_00000", "doc_id": 4894 }, "chunk_id": "train_shard_00000_4894_0", "global_id": 5516 }, { "text": "Kluyveromyces marxianus yeasts represent a valuable industry alternative due to their biotechnological potential to produce aromatic compounds. 2-phenylethanol and 2-phenylethylacetate are significant aromatic compounds widely used in food and cosmetics due to their pleasant odor. Natural obtention of these compounds increases their value, and because of this, bioprocesses such as de novo synthesis has become of great significance. However, the relationship between aromatic compound production and yeast's genetic diversity has yet to be studied. In the present study, the analysis of the genetic diversity in K. marxianus isolated from the natural fermentation of Agave duranguensis for Mezcal elaboration is presented. The results of strains in a haploid and diploid state added to the direct relationship between the mating type locus MAT with metabolic characteristics are studied. Growth rate, assimilate carbohydrates (glucose, lactose, and chicory inulin), and the production of aromatic compounds such as ethyl acetate, isoamyl acetate, isoamyl alcohol, 2-phenylethyl butyrate and phenylethyl propionate and the diversity in terms of the output of 2-phenylethanol and 2-phenylethylacetate by de novo synthesis were determinate, obtaining maximum concentrations of 51.30 and 60.39 mg/L by ITD0049 and ITD 0136 yeasts respectively.\n\nCharacterization of mating type on aroma production and metabolic properties wild Kluyveromyces marxianus yeasts", "token_count": 392, "char_count": 1456, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.806, "entities": { "genes": [ "ITD0049" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:28.076585", "source": { "split": "train_shard_00000", "doc_id": 4895 }, "chunk_id": "train_shard_00000_4895_0", "global_id": 5517 }, { "text": "Kefir yeast, Kluyveromyces marxianus, has been evaluated for its potential probiotic properties-survivability, non-pathogenicity, and antioxidant and anti-microbial activities. However, host gut microbiota modulation of kefir yeasts remains unclear. Here, we compared kefir yeast strains K. marxianus A4 (Km A4) and K. marxianus A5 (Km A5) with Saccharomyces boulardii ATCC MYA-796 (Sb MYA-796) by investigating their adherence to colorectal adenocarcinoma (Caco-2) cells and gut microbiota modulation in BALB/c mice. The kefir yeast strains exhibited higher intestinal cell adhesion than Sb MYA-796 (p < 0.05). Bacteroidetes, Bacteroidales, and Bacteroides were more abundant in the 1 × 108 CFU/mL of Km A4 treatment group than in the control group (p < 0.05). Moreover, 1 × 108 CFU/mL of Km A5 increased Corynebacteriales and Corynebacterium compared to the 1 × 108 CFU/mL of Km A4 treatment group (p < 0.01). The results showed that Km A4 and Km A5 had good Caco-2 cell adhesion ability and modulated gut microbiota upon short-term administration in healthy mice.

Supplementary information

The online version contains supplementary material available at 10.1007/s10068-023-01268-3.", "token_count": 514, "char_count": 1294, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6529, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:28.733077", "source": { "split": "train_shard_00000", "doc_id": 4896 }, "chunk_id": "train_shard_00000_4896_0", "global_id": 5518 }, { "text": "Gut microbiota modulation via short-term administration of potential probiotic kefir yeast Kluyveromyces marxianus A4 and A5 in BALB/c mice.", "token_count": 52, "char_count": 147, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:29.093167", "source": { "split": "train_shard_00000", "doc_id": 4896 }, "chunk_id": "train_shard_00000_4896_1", "global_id": 5519 }, { "text": "The thermotolerant yeast Kluyveromyces marxianus has gained significant attention in recent years as a promising microbial candidate for industrial biomanufacturing. Despite several contributions to the expanding molecular toolbox for gene expression and metabolic engineering of K. marxianus, there remains a need for a more efficient and versatile genome editing platform. To address this, we developed a CRISPR-based editing system that enables high efficiency marker-less gene disruptions and integrations using only 40 bp homology arms in NHEJ functional and non-functional K. marxianus strains. The use of a strong RNA polymerase II promoter allows efficient expression of gRNAs flanked by the self-cleaving RNA structures, tRNA and HDV ribozyme, from a single plasmid co-expressing a codon optimized Cas9. Implementing this system resulted in nearly 100% efficiency of gene disruptions in both NHEJ-functional and NHEJ-deficient K. marxianus strains, with donor integration efficiencies reaching 50% and 100% in the two strains, respectively. The high gRNA targeting performance also proved instrumental for selection of engineered strains with lower growth rate but improved polyketide biosynthesis by avoiding an extended outgrowth period, a common method used to enrich for edited cells but that fails to recover advantageous mutants with even slightly impaired fitness. Finally, we provide the first demonstration of simultaneous, markerless integrations at multiple loci in K. marxianus using a 2.6 kb and a 7.6 kb donor, achieving a dual integration efficiency of 25.5% in a NHEJ-deficient strain. These results highlight both the ease of use and general robustness of this system for rapid and flexible metabolic engineering in this non-conventional yeast.\n\nRNA polymerase II-driven CRISPR-Cas9 system for efficient non-growth-biased metabolic engineering of Kluyveromyces marxianus.", "token_count": 510, "char_count": 1939, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:29.728454", "source": { "split": "train_shard_00000", "doc_id": 4897 }, "chunk_id": "train_shard_00000_4897_0", "global_id": 5520 }, { "text": "The Mycobacterium tuberculosis complex (MTBC) is a group of bacteria causing tuberculosis (TB) in humans and animals. Understanding MTBC genetic diversity is crucial for insights into its adaptation and traits related to survival, virulence, and antibiotic resistance. While it is known that within-MTBC diversity is characterised by large deletions found only in certain lineages (regions of difference [RDs]), a comprehensive pangenomic analysis incorporating both coding and non-coding regions remains unexplored. We utilised a curated dataset representing various MTBC genomes, including under-represented lineages, to quantify the full diversity of the MTBC pangenome. The MTBC was found to have a small, closed pangenome with distinct genomic features and RDs both between lineages (as previously known) and between sub-lineages. The accessory genome was identified to be a product of genome reduction, showing both divergent and convergent deletions. This variation has implications for traits like virulence, drug resistance, and metabolism. The study provides a comprehensive understanding of the MTBC pangenome, highlighting the importance of genome reduction in its evolution, and underlines the significance of genomic variations in determining the pathogenic traits of different MTBC lineages.\n\nThe Mycobacterium tuberculosis complex pangenome is small and shaped by sub-lineage-specific regions of difference", "token_count": 323, "char_count": 1429, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.8179, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:30.305740", "source": { "split": "train_shard_00000", "doc_id": 4898 }, "chunk_id": "train_shard_00000_4898_0", "global_id": 5521 }, { "text": "Clostridioides difficile infection (CDI) remains a major global health threat due to the emergence of hypervirulent, multidrug-resistant lineages. However, the evolutionary dynamics and resistance profiles of strains circulating in underrepresented regions, such as Mexico, remain poorly characterized. Here, we present a comprehensive genomic and phylogenetic analysis of 77 Mexican C. difficile strains compared with 74 strains from other parts of the world. Using whole-genome sequencing (WGS) and core-genome multilocus sequence typing (cgMLST), we identified 19 sequence types (STs) grouped across three clades, with hypervirulent ST01 dominating clade 2. Virulome analysis showed conserved toxin gene profiles (tcdA, tcdB, cdtAB) across strains, while clade-specific differences were observed in adhesion and survival genes. These variations, particularly pronounced in clade 2 strains from both global and Mexican collections, may contribute to enhanced persistence and transmissibility. Pangenome analysis of 151 genomes highlighted distinct genomic architectures. Clade 2, enriched in ST01 epidemic lineages, contained 5,480 genes (58% core, 42% accessory), showing a compact structure consistent with recent clonal expansion. In contrast, Clade 1 displayed the highest diversity, with 8,584 genes (30% core, 70% accessory), indicative of an open and dynamic pangenome, while Clade 4 showed a smaller, more conserved profile (4,784 genes, 63% core). These findings underscore the contrasting evolutionary strategies among clades. Notably, Mexican ST01 strains exhibited a distinct resistome, including the universal presence of the vanG cluster, the vanR_T115A mutation (94% vs. 23% globally), as well as near complete prevalence of the nimB_T35G mutation associated with metronidazole resistance. This pattern suggests a localized evolutionary trajectory driven by antibiotic selective pressure. Our findings highlight the urgent need to recognize hypervirulent and resistant C. difficile lineages arising outside traditional surveillance regions", "token_count": 517, "char_count": 2056, "word_count": 275, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [ "ST01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:30.962348", "source": { "split": "train_shard_00000", "doc_id": 4899 }, "chunk_id": "train_shard_00000_4899_0", "global_id": 5522 }, { "text": "These Mexican strains not only reflect regional antibiotic usage patterns but also represent a potential reservoir of globally significant resistance traits. This work underscores the importance of integrating genomic surveillance across all continents to refine treatment protocols, prevent outbreaks, and contain the spread of resistant CDI.\n\nComparative Genomic Analysis of Clostridioides difficile Strains in Mexico: Insights into Virulence and Resistance", "token_count": 95, "char_count": 459, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:31.339879", "source": { "split": "train_shard_00000", "doc_id": 4899 }, "chunk_id": "train_shard_00000_4899_1", "global_id": 5523 }, { "text": "In this study, two strains of lactic acid bacteria (Lacticaseibacillus paracasei GL1 and Lactobacillus helveticus SNA12) and one yeast strain of Kluyveromyces marxianus G-Y4 (G-Y4) isolated from Tibetan kefir grains were co-cultured. It was found that the addition of G-Y4 could not only promote the growth of lactic acid bacteria, but also increase the release of metabolites (lactic acid, ethanol, and amino nitrogen). Furthermore, the addition of live cells and cell-free fermentation supernatant (CFS) of G-Y4 could increase the ability of biofilm formation. Morever, the surface characteristics results showed that the addition of G-Y4 live cells could enhance the aggregation ability and hydrophobicity of LAB. Meanwhile, adding live cells and CFS of G-Y4 could promote the release of signaling molecule AI-2 and enhance the expression of the LuxS gene related to biofilm formation. In addition, Fourier-transform infrared spectroscopy and chemical composition analysis were used to investigate the composition of the biofilm, and the results indicated that the biofilm was mainly composed of a small amount of protein but it was rich in polysaccharides including glucose, galactose, and mannose with different ratios. Finally, the formation of biofilm could delay the decline of the number of viable bacteria in storage fermented milk.\n\nThe interaction among Kluyveromyces marxianus G-Y4, Lacticaseibacillus paracasei GL1, and Lactobacillus helveticus SNA12 and signaling molecule AI-2 participate in the formation of biofilm", "token_count": 397, "char_count": 1532, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5561, "quality_score": 0.778, "entities": { "genes": [ "GL1", "SNA12" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:31.961069", "source": { "split": "train_shard_00000", "doc_id": 4900 }, "chunk_id": "train_shard_00000_4900_0", "global_id": 5524 }, { "text": "Bacterial relatedness measured using select chromosomal loci forms the basis of public health genomic surveillance. While approximating vertical evolution through this approach has proven exceptionally valuable for understanding pathogen dynamics, it excludes a fundamental dimension of bacterial evolution-horizontal gene transfer. Incorporating the accessory genome is the logical remediation and has recently shown promise in expanding epidemiological resolution for enteric pathogens. Employing k-mer-based Jaccard index analysis, and a novel genome length distance metric, we computed pangenome (i.e., core and accessory) relatedness for the globally important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both vertical (homology-by-descent) and horizontal (homology-by-admixture) evolutionary relationships in a reticulate network of over 2,200 U.S. Typhi genomes. This analysis revealed non-random structure in the Typhi pangenome that is driven predominantly by the gain and loss of mobile genetic elements, confirming and expanding upon known epidemiological patterns, revealing novel plasmid dynamics, and identifying avenues for further genomic epidemiological exploration. With an eye to public health application, this work adds important biological context to the rapidly improving ways of analyzing bacterial genetic data and demonstrates the value of the accessory genome to infer pathogen epidemiology and evolution.IMPORTANCEGiven bacterial evolution occurs in both vertical and horizontal dimensions, inclusion of both core and accessory genetic material (i.e., the pangenome) is a logical step toward a more thorough understanding of pathogen dynamics. With an eye to public, and indeed, global health relevance, we couple contemporary tools for genomic analysis with decades of research on mobile genetic elements to demonstrate the value of the pangenome, known and unknown, annotated, and hypothetical, for stratification of Salmonella enterica serovar Typhi (Typhi) populations. We confirm and expand upon what is known about Typhi epidemiology, plasmids, and antimicrobial resistance dynamics, and offer new avenues of exploration to further deduce Typhi ecology and evolution, and ultimately to reduce the incidence of human disease.", "token_count": 510, "char_count": 2312, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:32.964684", "source": { "split": "train_shard_00000", "doc_id": 4901 }, "chunk_id": "train_shard_00000_4901_0", "global_id": 5525 }, { "text": "Mobile genetic elements define the non-random structure of the Salmonella enterica serovar Typhi pangenome.", "token_count": 31, "char_count": 114, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:33.321695", "source": { "split": "train_shard_00000", "doc_id": 4901 }, "chunk_id": "train_shard_00000_4901_1", "global_id": 5526 }, { "text": "The effects of single- (Lactobacillus fermentum) or mixed-strain (Lactobacillus fermentum, Kluyveromyces marxianus) fermentation of red bean with or without wheat bran on sourdough bread quality and nutritional aspects were investigated. The results showed that, compared to unfermented controls, the tannins, phytic acid, and trypsin inhibitor levels were significantly reduced, whereas the phytochemical (TPC, TFC, and gallic acid) and soluble dietary fiber were increased in sourdough. Meanwhile, more outstanding changes were obtained in sourdough following a mixed-strain than single-strain fermentation, which might be associated with its corresponding β-glucosidase, feruloyl esterase, and phytase activities. An increased specific volume, reduced crumb firmness, and greater sensory evaluation of bread was achieved after mixed-strain fermentation. Moreover, diets containing sourdough, especially those prepared with mixed-strain-fermented red bean with wheat bran, significantly decreased serum pro-inflammatory cytokines levels, and improved the lipid profile, HDL/LDL ratio, glucose tolerance, and insulin sensitivity of mice. Moreover, gut microbiota diversity increased towards beneficial genera (e.g., Bifidobacterium), accompanied with a greater increase in short-chain fatty acid production in mice fed on sourdough-based bread diets compared to their controls and white bread. In conclusion, mixed-strain fermentation's synergistic effect on high fiber-legume substrate improved the baking, sensory quality, and prebiotic effect of bread, leading to potential health benefits in mice.\n\nThe Effects of Single- or Mixed-Strain Fermentation of Red Bean Sourdough, with or without Wheat Bran, on Bread Making Performance and Its Potential Health Benefits in Mice Model.", "token_count": 472, "char_count": 1811, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.824, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:33.958393", "source": { "split": "train_shard_00000", "doc_id": 4902 }, "chunk_id": "train_shard_00000_4902_0", "global_id": 5527 }, { "text": "

Motivation

Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (the core genome) and measuring the extent of genomic variability as a function of sample size (pangenome growth).

Results

We introduce Panacus (pangenome-abacus), a tool designed to rapidly perform these tasks and visualize the results in interactive plots. Panacus can process GFA files, the accepted standard for pangenome graphs, and is able to analyze a human pangenome graph with 110 million nodes in <1 h.

Availability and implementation

Panacus is implemented in Rust and is published as Open Source software under the MIT license. The source code and documentation are available at https://github.com/marschall-lab/panacus. Panacus can be installed via Bioconda at https://bioconda.github.io/recipes/panacus/README.html.\n\nPanacus: fast and exact pangenome growth and core size estimation.", "token_count": 328, "char_count": 1319, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:34.537076", "source": { "split": "train_shard_00000", "doc_id": 4903 }, "chunk_id": "train_shard_00000_4903_0", "global_id": 5528 }, { "text": "Seven Kluyveromyces marxianus isolates from the elaboration process of pulque and henequen mezcal were characterized. The isolates were identified based on the sequences of the D1/D2 domain of the 26S rRNA gene and the internal transcribed spacer (ITS-5.8S) region. Genetic differences were found between pulque and henequen mezcal isolates and within henequen mezcal isolates, as shown by different branching patterns in the ITS-5.8S phylogenetic tree and (GTG)5 microsatellite profiles, suggesting that sub-strate and process selective conditions may originate different K. marxianus populations. All the isolates fermented and assimilated inulin and lactose and some henequen isolates could also assimilate xylose and cellobiose. Henequen isolates were more thermotolerant than pulque isolates which in contrast presented more tolerance to the cell wall-disturbing agent calcofluor white (CFW) suggesting that they had a different cell wall structure. Additionally, depending on their origin, the isolates presented different maximum specific growth rates (µ max ) patterns at different temperatures. Concerning tolerance to stress factors relevant for lignocellulosic hydrolysates fermentation, tolerance limits were lower at 42 than 30°C except for glucose and furfural. Pulque isolates were less tolerant to ethanol, NaCl, and Cd. Finally, all the isolates could produce ethanol by simultaneous saccharification and fermentation (SSF) of a corncob hydrolysate under laboratory conditions at 42°C.\n\nGenotypic and Phenotypic Diversity ofKluyveromyces marxianusIsolates Obtained from the Elaboration Process of Two Traditional Mexican Alcoholic Beverages Derived from Agave: Pulque and Henequen (Agave fourcroydes) Mezcal", "token_count": 469, "char_count": 1738, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6309, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:35.184250", "source": { "split": "train_shard_00000", "doc_id": 4904 }, "chunk_id": "train_shard_00000_4904_0", "global_id": 5529 }, { "text": "

Background & aims

The adherent-invasive Escherichia coli (AIEC) pathotype is implicated in inflammatory bowel disease (IBD) pathogenesis. AIEC strains are currently defined by phenotypic measurement of their pathogenicity, including invasion of epithelial cells. This broad definition, combined with the genetic diversity of AIEC across patients with IBD, has complicated the identification of virulence determinants. We sought to quantify the invasion phenotype of clinical isolates from patients with IBD and identify the genetic basis for their invasion into epithelial cells.

Methods

A pangenome with core and accessory genes (genotype) was assembled using whole genome sequencing of 168 E coli samples isolated from 13 patients with IBD. A modified assay for invasion of epithelial cells (phenotype) was established with consideration of antibiotic resistance phenotypes. Isolate genotype was correlated to invasiveness phenotype to identify genetic factors that cosegregate with invasion.

Results

Pangenome-wide comparisons of E coli clinical isolates identified accessory genes that can cosegregate with invasion phenotype. These correlations found the acquisition of antibiotic resistance genes in clinical isolates compromised the traditional gentamicin protection assays used to quantify invasion. Therefore, an alternate assay, based on amikacin resistance, identified genes cosegregating with invasion. These genes encode an arylsulfatase, a glycoside hydrolase, and genetic islands carrying propanediol utilization and sulfoquinovose metabolism pathways.

Conclusions

This study highlights the importance of incorporating antibiotic resistance screening for invasion assays used in AIEC identification. Accurately screened invasion phenotypes identified accessory genome elements among E coli IBD isolates that correlate with their ability to invade epithelial cells. These results help explain why single genetic markers for the AIEC phylotype are challenging to identify.\n\nGenetic and Microbial Analysis of Invasiveness for Escherichia coli Strains Associated With Inflammatory Bowel Disease.", "token_count": 511, "char_count": 2135, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7934, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:35.846710", "source": { "split": "train_shard_00000", "doc_id": 4905 }, "chunk_id": "train_shard_00000_4905_0", "global_id": 5530 }, { "text": "

Introduction

Escherichia ruysiae is a newly identified species within the Escherichia genus, yet its presence in domestic animals remains largely unexamined. This study characterizes four isolates detected for the first time in the domestic dog (Canis lupus familiaris), focusing on their phenotypic and genomic features.

Methods

We used culturomic methods to isolate four E. ruysiae isolates that were initially identified as Escherichia coli using MALDI-TOF mass spectrometry. Whole-genome sequencing confirmed that the isolates belonged to E. ruysiae, not E. coli. Phenotypic characterization included enzymatic activity assays and antimicrobial susceptibility testing. Comparative genomic analyses were performed on these four isolates, along with 14 additional E. ruysiae and representative genomes from the five other Escherichia species in order to assess genetic diversity and functional gene distribution.

Results and discussion

All strains exhibited similar enzymatic activities and resistance to clindamycin, erythromycin, and metronidazole. The pangenome analysis revealed that most missing gene orthologs are related to motility followed by metabolism, including synthetases, reductases, phosphatases, permeases, transferases, and epimerases, as well as structural genes like efflux pumps and transporters. Phylogroup typing using the ClermonTyping method identified two main groups within the E. ruysiae species, Clade III and IV. Typical virulence genes associated with E. coli are absent in these strains. The multiple approaches used in this study expand our understanding of the diverse aspects of the recently described species, E. ruysiae.", "token_count": 482, "char_count": 1758, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6968, "quality_score": 0.8484, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:36.540146", "source": { "split": "train_shard_00000", "doc_id": 4906 }, "chunk_id": "train_shard_00000_4906_0", "global_id": 5531 }, { "text": "Comparative genomic and phenotypic description of <i>Escherichia ruysiae</i>: a newly identified member of the gut microbiome of the domestic dog.", "token_count": 50, "char_count": 158, "word_count": 20, "semantic_coherence": 1, "information_density": 0.85, "quality_score": 0.925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:36.912443", "source": { "split": "train_shard_00000", "doc_id": 4906 }, "chunk_id": "train_shard_00000_4906_1", "global_id": 5532 }, { "text": "This study provides a comprehensive analysis of the microbial dynamics involved in the fermentation process of traditional Musalais wine, an intangible cultural heritage of Xinjiang. Utilizing metagenomic sequencing, we identified 2894 microbial species, of which 494 persisted throughout the fermentation process. Saccharomyces cerevisiae was the dominant species, with its prevalence increasing from 97.35% in the early phase to 99.38% in the mid phase, before slightly decreasing to 98.79% in the late phase. Additionally, 24 non-Saccharomyces yeast species, including Hanseniaspora uvarum, Lachancea thermotolerans, and Torulaspora delbrueckii, were detected. Common species associated with other fermented foods, including Wickerhamomyces anomalus, Kluyveromyces marxianus, Saccharomyces eubayanus, and Zygosaccharomyces parabailii, were also identified. Notably, species not previously used in food fermentation, such as Saccharomyces jurei, Sodiomyces alkalinus, Vanrija pseudolonga, and Moesziomyces antarcticus, were also identified in this study. Furthermore, the Kyoto Encyclopedia of Genes and Genomes (KO) and Gene Ontology (GO) revealed notable variations in metabolic pathways and enriched functional genes. In addition, a total of 82 volatile compounds were detected in the final product, with higher alcohols (60.12%), esters (37.80%), and organic acids (1.80%) being the most prevalent. These results offer important insights into microbial interactions and their influence on Musalais wine quality, laying the groundwork for optimizing the fermentation process.", "token_count": 502, "char_count": 1671, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7427, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:37.607448", "source": { "split": "train_shard_00000", "doc_id": 4907 }, "chunk_id": "train_shard_00000_4907_0", "global_id": 5533 }, { "text": "Microbial Dynamics in a Musalais Wine Fermentation: A Metagenomic Study.", "token_count": 22, "char_count": 72, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:37.984487", "source": { "split": "train_shard_00000", "doc_id": 4907 }, "chunk_id": "train_shard_00000_4907_1", "global_id": 5534 }, { "text": "(1) Background: Staphylococcus aureus is a common human respiratory pathogen. Its widespread antimicrobial resistance often leads to severe infections. However, the high genomic diversity among strains frequently causes false negatives in conventional PCR assays. (2) Methods: To address this limitation, we developed a highly sensitive and specific duplex fluorescent quantitative PCR (qPCR) method for S. aureus detection based on pangenome analysis. Conserved core genome sequences of S. aureus were identified using a pangenomic approach. Two highly conserved and species-specific genes—isdA and recQ—were selected as target loci for the duplex qPCR assay. A TaqMan probe-based duplex fluorescent qPCR assay was established, enabling simultaneous detection of both isdA and recQ genes in a single reaction. (3) Results: The assay demonstrated detection sensitivities of 1.335 × 103 copies/μL for isdA and 7.265 × 102 copies/μL for recQ. The intra-assay and inter-assay coefficients of variation (CV) for Ct values were below 1.86% and 2.87%, respectively, indicating excellent reproducibility. Specificity analysis revealed no cross-reactivity with genomic DNA from 14 common respiratory pathogens, including Pseudomonas aeruginosa and Streptococcus pneumoniae. (4) Conclusions: Due to its high specificity and sensitivity, this duplex qPCR assay effectively overcomes limitations of single-target PCR methods, such as missed detections and prolonged turnaround times, and holds significant potential for practical diagnostic applications.\n\nEstablishment of a Duplex Fluorescent Quantitative PCR Assay for Staphylococcus aureus Detection Based on Pangenome Analysis", "token_count": 440, "char_count": 1669, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6756, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:38.615321", "source": { "split": "train_shard_00000", "doc_id": 4908 }, "chunk_id": "train_shard_00000_4908_0", "global_id": 5535 }, { "text": "Horizontal gene transfer (HGT) is a key driver of microbial evolution, promoting genetic diversity and contributing to the emergence of antibiotic resistance. This study explores the pangenome dynamics and HGT in Mycobacterium marinum (M. marinum), a close relative of Mycobacterium tuberculosis. Multiple pangenome datasets were analyzed to quantify gene gain, loss, and pangenome openness, utilizing Panstripe and a Generalized Linear Model (GLM) framework to assess gene presence/absence across strains. Additionally, a comparative benchmarking analysis of gene ontology (GO) annotations were conducted using eggNOG and InterProScan to evaluate their functional annotation accuracy. Our findings demonstrated significant differences in gene gain and loss rates, suggesting variations in annotation accuracy and the presence of mobile genetic elements (MGE). Single nucleotide polymorphisms (SNPs) were also identified, highlighting the genetic variability that may impact strain-specific traits such as pathogenicity and antibiotic resistance. Pangenome of M. marinum was characterized as highly open, with substantial variability in gene content, reflecting ongoing genetic exchange and adaptability. Functional annotation benchmarking demonstrated that eggNOG and InterProScan provided complementary insights, with each tool excelling in distinct strengths of gene function identification. Overall, these findings highlight the complex interplay between HGT, pangenome evolution, and antibiotic resistance in M. marinum, and the analytical framework presented here provides a robust approach for future studies aiming to inform therapeutic interventions and vaccine development.\n\nBenchmarking pangenome dynamics and horizontal gene transfer in <i>Mycobacterium marinum</i> evolution.", "token_count": 420, "char_count": 1835, "word_count": 229, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:39.243732", "source": { "split": "train_shard_00000", "doc_id": 4909 }, "chunk_id": "train_shard_00000_4909_0", "global_id": 5536 }, { "text": "

Background and objectives

Yeasts play a dual role in dairy processing, serving as beneficial fermentative agents that enhance product quality through flavor, texture, and probiotic properties, while also posing spoilage risks if uncontrolled. This study aimed to characterize yeast isolates from industrial and traditional dairy products in Isfahan using PCR-sequencing and phylogenetic analysis.

Materials and methods

A total of 155 dairy samples (fresh/stored, traditional/industrial) were collected. Yeasts were cultured and identified via PCR amplification and sequencing of the ITS1-5.8S rDNA-ITS2 region.

Results

Analysis of ITS sequence data identified 28 yeast strains representing eleven species across seven genera, including Saccharomyces cerevisiae (n=8) Kluyveromyces marxianus (n=6), Pichia kudriavzevii (n=4), Candida orthopsilosis (n=2), Pichia membranifaciens (n=2), Pichia cactophila (n=1), Pichia fermentans (n=1), Galactomyces candidum (n=1), Torulaspora delbrueckii (n=1), Debaryomyces hansenii (n=1), and Kluyveromyces lactis (n=1). Phylogenetic analysis grouped isolates into two clusters. Industrial cheese and both industrial/traditional yogurts showed the highest yeast diversity and counts. Notably, C", "token_count": 449, "char_count": 1330, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7919, "quality_score": 0.896, "entities": { "genes": [ "ITS2", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:39.884512", "source": { "split": "train_shard_00000", "doc_id": 4910 }, "chunk_id": "train_shard_00000_4910_0", "global_id": 5537 }, { "text": "orthopsilosis was found only in industrial milk and cheese, suggesting potential processing-related contamination.

Conclusion

This study highlights the diversity of yeast microbiota in dairy products and underscores the efficacy of ITS sequencing for accurate yeast identification in the dairy industry, aiding quality control and spoilage prevention.\n\nMolecular identification and phylogenetic analysis of yeast strains isolated from dairy products in Isfahan, Iran.", "token_count": 112, "char_count": 478, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7288, "quality_score": 0.8644, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:40.264761", "source": { "split": "train_shard_00000", "doc_id": 4910 }, "chunk_id": "train_shard_00000_4910_1", "global_id": 5538 }, { "text": "

Aims

The aims of this study were to evaluate the potential of Hanseniaspora opuntiae, Meyerozyma caribbica, and Kluyveromyces marxianus for in vitro biocontrol of Aspergillus ochraceus, A. westerdijkiae, and A. carbonarius growth, the ochratoxin A (OTA) effect on yeast growth, and yeast in vitro OTA detoxification ability using an experimental design to predict the combined effects of inoculum size, incubation time, and OTA concentration.

Methods and results

Predictive models were developed using an incomplete Box-Behnken experimental design to predict the combined effects of inoculum size, incubation time, and OTA concentration on OTA detoxification by the yeasts. The yeasts were able to inhibit fungal growth from 13% to 86%. Kluyveromyces marxianus was the most efficient in inhibiting the three Aspergillus species. Furthermore, high OTA levels (100 ng ml-1) did not affect yeast growth over 72 h incubation. The models showed that the maximum OTA detoxification under optimum conditions was 86.8% (H. opuntiae), 79.3% (M. caribbica), and 73.7% (K. marxianus), with no significant difference (P > 0.05) between the values predicted and the results obtained experimentally.

Conclusion

The yeasts showed potential for biocontrol of ochratoxigenic fungi and OTA detoxification, and the models developed are important tools for predicting the best conditions for the application of these yeasts as detoxification agents.\n\nYeasts as sustainable biocontrol agents against ochratoxigenic Aspergillus species and in vitro optimization of ochratoxin A detoxification.", "token_count": 461, "char_count": 1593, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5864, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:40.909821", "source": { "split": "train_shard_00000", "doc_id": 4911 }, "chunk_id": "train_shard_00000_4911_0", "global_id": 5539 }, { "text": "

ABSTRACT

Background

Variation within the prokaryotic pangenome is not random, and natural selection that favours particular combinations of genes appears to dominate over random drift. What is less clear is whether similar phenotypes tend to arise independently within pangenomes, or whether there is a single route through which they evolve. We have previously shown that the wider genomic context is vital to understanding specific phenotypes, such as antimicrobial resistance. Considering the amount of genomic variation we see in many pathogens, the question of routes to resistance and how they arise is particularly urgent.

Methods

We hypothesised that mutually exclusive routes to multidrug antimicrobial resistance evolve through distinct yet predictable pathways dependent upon the species-specific pangenomic background. To test this, we developed an integrated pangenomic and machine learning framework to analyse the emergence of multidrug resistance (MDR) in two clinically significant pathogens, Pseudomonas aeruginosa and Escherichia coli . Machine learning models uncovered genes statistically linked to particular MDR phenotypes. We then examined whether these genes were significantly associated or dissociated with one another in gene co-occurrence networks and evaluated the importance of genomic context on pairs of genes.

Results

We demonstrate three key findings on the evolution of multidrug resistance in our dataset. First, antimicrobial resistance genes (ARGs) were distributed across both the core and accessory genomes, challenging the prevailing view that ARGs are typically confined to the accessory genome. Second, we demonstrate that E. coli possesses mutually exclusive pathways to MDR, with several resistance genes showing distinct dissociation patterns, suggesting alternative evolutionary routes to identical MDR phenotypes. Third, the network of ARG coassociations differed significantly between the P. aeruginosa and E. coli pangenomes with 33 gene pairs showing opposite association patterns between species, revealing species-specific genomic constraints on MDR emergence. These findings emphasise that bacterial evolution is more constrained than previously thought and that designing intervention therapies requires consideration of both historical evolutionary trajectories and the specific genomic context in which the resistance phenotypes arose.", "token_count": 519, "char_count": 2433, "word_count": 325, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:41.567551", "source": { "split": "train_shard_00000", "doc_id": 4912 }, "chunk_id": "train_shard_00000_4912_0", "global_id": 5540 }, { "text": "Genomic constraints shape the evolution of alternative routes to drug resistance in prokaryotes", "token_count": 17, "char_count": 95, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:41.921865", "source": { "split": "train_shard_00000", "doc_id": 4912 }, "chunk_id": "train_shard_00000_4912_1", "global_id": 5541 }, { "text": "Avian necrotic enteritis due to the Gram-positive bacterium Clostridium perfringens has re-emerged following the ban on antibiotic growth promoters in many poultry producing countries. The limited number of previous studies has left important gaps in our understanding of the genetic diversity and virulence traits of the pathogen. To address these knowledge gaps, in this study, we sequenced the genomes of 41 Clostridium perfringens isolates recovered from commercial broiler chicken flocks in Quebec, Canada, including isolates from healthy birds and those affected by necrotic enteritis. We sought to understand the pangenome diversity and interrogated the genomes for key virulence factors involved in necrotic enteritis pathogenesis. On average, the genomes had a GC content of 28% and contained 3206 coding sequences. A variable presence of toxins, degradative hydrolytic enzymes, and collagen-binding proteins was also found. Through pangenome analysis, we revealed a total of 10,223 genes, 652 (6.4%) of which formed the core genome. Additionally, we identified 17 different plasmids, 12 antibiotic resistance genes, and nine prophage regions. Overall, our results demonstrated a relatively high genetic diversity among chicken Clostridium perfringens isolates collected from the same geographical location, offering new insights into potential virulence mechanisms and adaptation of the pathogen within poultry populations.\n\nGenomic Diversity and Virulence Factors of Clostridium perfringens Isolated from Healthy and Necrotic Enteritis-Affected Broiler Chicken Farms in Quebec Province.", "token_count": 410, "char_count": 1625, "word_count": 220, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:42.539937", "source": { "split": "train_shard_00000", "doc_id": 4913 }, "chunk_id": "train_shard_00000_4913_0", "global_id": 5542 }, { "text": "

Background

Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes.

Results

Pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production", "token_count": 435, "char_count": 1678, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8268, "entities": { "genes": [ "NRRL3357", "AF13", "MAT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:43.178787", "source": { "split": "train_shard_00000", "doc_id": 4914 }, "chunk_id": "train_shard_00000_4914_0", "global_id": 5543 }, { "text": "Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites.

Conclusion

In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.\n\nAspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters.", "token_count": 211, "char_count": 912, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:43.637408", "source": { "split": "train_shard_00000", "doc_id": 4914 }, "chunk_id": "train_shard_00000_4914_1", "global_id": 5544 }, { "text": "Prochlorococcus is a cyanobacterial genus that exhibits photosynthetic capacity and remarkable genetic diversity. We analyze how Prochlorococcus genomics relate to high vs. low light environment adaptations, applying traditional comparative genomics and machine learning (ML) approaches to connect genotypes to phenotypes. We downloaded nearly 1,000 Prochlorococcus genomes from NCBI with information on their light adaptation ecotype (high-light/low-light) and depth of isolation using metadata through JGI. Average nucleotide identity analysis and traditional pangenome generation tools struggle to capture the cyanobacterial core genome, but despite its scant conservation, we clearly observe a sharp separation of the taxon by its light utilization preferences — that is, its light ecotypes. A range of classical ML models trained to predict ecotype achieve exceptional binary classification accuracy even when predicting on partial genomes (Matthews Correlation Coefficient = 0.81 – 0.98), while regression models trained to predict the depth of isolation performed poorly, with relatively high root mean square error values (40.8 – 45.3m). For ecotype prediction, top features for the best-performing models included photosynthesis-associated genes and pathways, as well as some novel markers of unknown function. Our research findings recapitulate the extreme genetic versatility in Prochlorococcus and find that variable genetic markers allow excellent classification accuracy, and therefore, ecotype prediction, even for incomplete metagenomic assemblies, emphasizing the specialization and separation among these cyanobacterial ecotypes.\n\nGenotype-phenotype modeling of light ecotypes in Prochlorococcus reveals genomic signatures of ecotypic divergence", "token_count": 405, "char_count": 1770, "word_count": 230, "semantic_coherence": 1, "information_density": 0.7043, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:44.261688", "source": { "split": "train_shard_00000", "doc_id": 4915 }, "chunk_id": "train_shard_00000_4915_0", "global_id": 5545 }, { "text": "This study conducted a comparative genomic investigation of 40 strains of Lentilactobacillus buchneri isolated from various environments-including fermented foods, silage, cattle rumen, and the nasopharynx-to identify species-level diversity and assess their CRISPR immunity. An average genome size of 2.55 ± 0.07 Mb, a GC content of 44.18 ± 0.15%, and 2444 ± 83 coding sequences were identified. Prophages were found in all strains except for two, while 17 strains contained plasmids. No genes associated with bacteriocins were identified. CRISPR analysis revealed the presence of 42 Type II-A and 45 Type I-E systems, with each strain having at least one Type II-A system (~ 2 systems per strain). Among the 33 tested strains, 29 encoded complete LbCas9 proteins, consisting of 1371 amino acids. In-silico analysis of PAM in Type II-A systems revealed a 5'-DNAWDHV-3' motif, with a noted preference for 5'-AAAA-3' at positions 3-6. The spacers found in CRISPR arrays targeted proteins involved in plasmid mobilization as well as components of phage tails, indicating their roles in inhibiting horizontal gene transfer and providing defense against phages. Remarkably, 27 spacers from 24 strains were found to match phages associated with human gut microbiomes, with several showing the ability to cross-target phages from livestock, kefir, and wastewater. This research expands the genomic understanding of L. buchneri from 10 to 40 genomes, uncovering the dynamics of CRISPR-phage co-evolution. The defined PAM preferences of the identified CRISPR systems, together with the broad predicted target range of their spacers, highlight their potential for biotechnological applications-most notably targeted CRISPRization of L. buchneri strains and in-silico-guided phage control during fermentation", "token_count": 512, "char_count": 1798, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6679, "quality_score": 0.834, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:44.917374", "source": { "split": "train_shard_00000", "doc_id": 4916 }, "chunk_id": "train_shard_00000_4916_0", "global_id": 5546 }, { "text": "These findings deepen our understanding of the ecological adaptability of L. buchneri and provide a foundation for future industrial exploitation of its native CRISPR immunity.\n\nComparative genomics of Lentilactobacillus buchneri reveals strain-level hyperdiversity and broad-spectrum CRISPR immunity against human and livestock gut phages.", "token_count": 84, "char_count": 340, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:45.298917", "source": { "split": "train_shard_00000", "doc_id": 4916 }, "chunk_id": "train_shard_00000_4916_1", "global_id": 5547 }, { "text": "Acinetobacter baumannii is a short gram-negative bacillus, notable for its intrinsic multidrug resistance and genomic plasticity, which facilitates the acquisition of additional resistance genes via mobile genetic elements. Due to its increasing carbapenem resistance, the World Health Organization has classified it as a critical priority pathogen. This study performed a comparative genomic analysis of 20 carbapenem-resistant A. baumannii clinical strains isolated from the Hospital Infantil de México Federico Gómez (CRAB-HIMFG), alongside 11 genomes from other Mexican strains. The pangenome was determined to be open, and core genome single-nucleotide polymorphism-based analysis grouped the CRAB-HIMFG strains within CC758/IC5 and CC92/IC2. A novel sequence type (ST) in the MLST-Pasteur scheme was identified, related to STPas156, and in the MLST-Oxford scheme, associated with STOxf758 and STOxf1054. Virulence and resistance genes comprised 0.61% to 2.23% of the pangenome. Oxacillinase genes and efflux pumps primarily mediated carbapenem resistance, while virulence genes included those encoding biofilm and type IV pili. Capsule typing revealed a correlation with established international clones, IC2 and IC5. Plasmids exhibited high diversity, harboring maintenance modules and toxin-antitoxin systems, with the dissemination of resistance genes linked to insertion sequences. Biofilm formation and twitching motility were not always expressed, as they depend on additional environmental factors. Our study shows that comparative genomics is an essential tool to analyze clinically and epidemiologically significant genomes, providing critical insights into gene distribution, genomic architecture, and horizontal gene transfer mechanisms in microbial populations.IMPORTANCEIn recent years, a reported increase in the mortality rate associated with infections caused by A. baumannii, along with a rise in carbapenem resistance, poses a serious clinical challenge", "token_count": 518, "char_count": 2031, "word_count": 262, "semantic_coherence": 1, "information_density": 0.7099, "quality_score": 0.855, "entities": { "genes": [ "IC5", "CC758", "IC2", "CC92" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:45.928954", "source": { "split": "train_shard_00000", "doc_id": 4917 }, "chunk_id": "train_shard_00000_4917_0", "global_id": 5548 }, { "text": "The WHO considered this microorganism critical for research into alternative therapies and epidemiological surveillance. Despite advances in bioinformatics, genomic studies have yet to fully elucidate the structural rearrangements and secretion systems of A. baumannii. This knowledge gap hinders our understanding of its remarkable genomic plasticity and its ability to acquire and spread resistance and virulence genes through horizontal gene transfer.\n\nComparative genomics of carbapenem-resistant <i>Acinetobacter baumannii</i> isolated from pediatric patients in a tertiary care hospital.", "token_count": 146, "char_count": 612, "word_count": 75, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:46.376200", "source": { "split": "train_shard_00000", "doc_id": 4917 }, "chunk_id": "train_shard_00000_4917_1", "global_id": 5549 }, { "text": "

Introduction

Due to the increasing consumer demand for the development and improvement of functional foods containing probiotics, new probiotic candidates need to be explored as well as novel means to enhance their beneficial effects. Lactobacillus kefiranofaciens OSU-BDGOA1 is a strain isolated from kefir grains that has demonstrated probiotic traits. This species is the main inhabitant of kefir grains and is responsible for the production of an exopolysaccharide (EPS) whit vast technological applications and potential bioactivities. Research has shown that interkingdom interactions of yeast and lactic acid bacteria can enhance metabolic activities and promote resistance to environmental stressors.

Methods

Comparative genomic analyses were performed to distinguish OSU-BDGOA1 from other strains of the same species, and the genome was mined to provide molecular evidence for relevant probiotic properties. We further assessed the cumulative effect on the probiotic properties of OSU-BDGOA1 and Kluyveromyces marxianus bdgo-ym6 yeast co-culture compared to monocultures.

Results

Survival during simulated digestion assessed by the INFOGEST digestion model showed higher survival of OSU-BDGOA1 and bdgo-ym6 in co-culture. The adhesion to intestinal cells assessed with the Caco-2 intestinal cell model revealed enhanced adhesion of OSU-BDGOA1 in co-culture. The observed increase in survival during digestion could be associated with the increased production of EPS during the late exponential and early stationary phases of co-culture that, by enhancing co-aggregation between the yeast and the bacterium, protects the microorganisms from severe gastrointestinal conditions as observed by SEM images. Immune modulation and barrier function for recovery and prevention of flagellin-mediated inflammation by Salmonella Typhimurium heat-killed cells (HKSC) in Caco-2 cells were also measured", "token_count": 498, "char_count": 1948, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6324, "quality_score": 0.8162, "entities": { "genes": [ "BDGOA1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:47.038896", "source": { "split": "train_shard_00000", "doc_id": 4918 }, "chunk_id": "train_shard_00000_4918_0", "global_id": 5550 }, { "text": "OSU-BDGOA1 in mono- and co-culture regulated inflammation through downregulation of pro-inflammatory cytokine expression and increased membrane barrier integrity assessed by TEER, FD4 permeability, and expression of tight junctions.

Discussion

The results of the study warrant further research into the application of co-cultures of yeast and LAB in functional probiotic products and the potential to increase EPS production by co-culture strategies.\n\nEnhanced probiotic potential of Lactobacillus kefiranofaciens OSU-BDGOA1 through co-culture with Kluyveromyces marxianus bdgo-ym6.", "token_count": 181, "char_count": 603, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7183, "quality_score": 0.8592, "entities": { "genes": [ "BDGOA1", "FD4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:47.484410", "source": { "split": "train_shard_00000", "doc_id": 4918 }, "chunk_id": "train_shard_00000_4918_1", "global_id": 5551 }, { "text": "Tatum D. Mortimer works in the field of pathogen population genomics and evolution. In this mSphere of Influence article, she reflects on how \"Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae\" by Azarian et al. and \"Contingency, repeatability, and predictability in the evolution of a prokaryotic pangenome\" by Beavan et al. made an impact on her by highlighting the ways in which genomic data can be used to predict pathogen evolution.\n\nmSphere of Influence: Predicting the evolution of pathogen populations.", "token_count": 141, "char_count": 548, "word_count": 80, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:47.909795", "source": { "split": "train_shard_00000", "doc_id": 4919 }, "chunk_id": "train_shard_00000_4919_0", "global_id": 5552 }, { "text": "The aim of this study was to reveal the sites of yeast contamination in dairy production and perform taxonomic characterization of potential yeast spoilers in cheese making. Occurrence of spoilage yeasts was followed throughout the manufacture of white-brined cheese at a Danish dairy, including the areas of milk pasteurization, curd processing, and packaging (26 sites in total). Spoilage yeasts were isolated from whey, old cheese curd, and air samples in viable counts of 1.48-6.27 log CFU/mL, 5.44 log CFU/g, and 1.02 log CFU/m3, respectively. Yeast isolates were genotypically classified using (GTG)5-PCR fingerprinting and identified by sequencing of the D1/D2 region of the 26S rRNA gene. The largest yeast heterogeneity was found in old curd collected under the turning machine of molds, where 11 different yeast species were identified. The most frequently isolated yeast species were Candida intermedia, Kluyveromyces marxianus, and Pichia kudriavzevii. The less abundant yeast species included Candida auris, Candida parapsilosis, Candida pseudoglaebosa, Candida sojae, Cutaneotrichosporon curvatus, Cutaneotrichosporon moniliiforme, Papiliotrema flavescens, Rhodotorula mucilaginosa, Vanrija humicola, and Wickerhamiella sorbophila. The awareness on occurrence and taxonomy of spoilage yeasts in cheese production will contribute to a knowledge-based control of contaminating yeasts and quality management of cheese at the dairies.\n\nOccurrence and Identification of Yeasts in Production of White-Brined Cheese.", "token_count": 510, "char_count": 1636, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:48.562713", "source": { "split": "train_shard_00000", "doc_id": 4920 }, "chunk_id": "train_shard_00000_4920_0", "global_id": 5553 }, { "text": "Mycobacterium abscessus (Mab) is a clinically significant pathogen and a highly genetically diverse species due to its large accessory genome. The functional consequence of this diversity remains unknown mainly because, to date, functional genomic studies in Mab have been primarily performed on reference strains. Given the growing public health threat of Mab infections, understanding the functional genomic differences among Mab clinical isolates can provide more insight into how its genetic diversity influences gene essentiality, clinically relevant phenotypes, and importantly, potential drug targets. To determine the functional genomic diversity among Mab strains, we conducted transposon-sequencing (TnSeq) on 21 genetically diverse clinical isolates, including 15 M. abscessus subsp. abscessus isolates and 6 M. abscessus subsp. massiliense isolates, cataloging all the essential and non-essential genes in each strain. Pan-genome analysis revealed a core set of 3,845 genes and a large accessory genome of 11,507. We identified 259 core essential genes across the 21 clinical isolates and 425 differentially required genes, representing ~10% of the Mab core genome. We also identified genes whose requirements were subspecies, lineage, and isolate-specific. Finally, by correlating TnSeq profiles, we identified 19 previously uncharacterized genetic networks in Mab. Altogether, we find that Mab clinical isolates are not only genetically diverse but functionally diverse as well.

Importance

This study investigates the genetic diversity of Mycobacterium abscessus (Mab), a bacteria known for causing difficult-to-treat infections", "token_count": 487, "char_count": 1761, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:49.254071", "source": { "split": "train_shard_00000", "doc_id": 4921 }, "chunk_id": "train_shard_00000_4921_0", "global_id": 5554 }, { "text": "Researchers performed transposon-sequencing (TnSeq) on 21 different clinical isolates of Mab to identify essential and non-essential genes in each strain. Through this analysis, they identified core genes required for growth across all strains. Interestingly, they also identified genes whose requirement for growth or \"essentiality\" were subspecies, lineage, and isolate-specific. This study reveals that Mab's genetic diversity translates into significant functional differences among clinical isolates. Insights from this paper lay essential groundwork for future studies exploring the biological and clinical implications of genetic diversity in Mab clinical isolates. Understanding this diversity could guide targeted therapies and offer new insights into managing infections caused by Mab, a growing public health concern.\n\nTransposon-sequencing across multiple <i>Mycobacterium abscessus</i> isolates reveals significant functional genomic diversity among strains.", "token_count": 230, "char_count": 1011, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7131, "quality_score": 0.8566, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:49.762605", "source": { "split": "train_shard_00000", "doc_id": 4921 }, "chunk_id": "train_shard_00000_4921_1", "global_id": 5555 }, { "text": "Current large-scale, anaerobic industrial processes for ethanol production from renewable carbohydrates predominantly rely on the mesophilic yeast Saccharomyces cerevisiae . Use of thermotolerant, facultatively fermentative yeasts such as Kluyveromyces marxianus could confer significant economic benefits. However, in contrast to S. cerevisiae , these yeasts cannot grow in the absence of oxygen. Response of K. marxianus and S. cerevisiae to different oxygen-limitation regimes were analyzed in chemostats. Genome and transcriptome analysis, physiological responses to sterol supplementation and sterol-uptake measurements identified absence of a functional sterol-uptake mechanism as a key factor underlying the oxygen requirement of K. marxianus . Heterologous expression of a squalene-tetrahymanol cyclase enabled oxygen-independent synthesis of the sterol surrogate tetrahymanol in K. marxianus . After a brief adaptation under oxygen-limited conditions, tetrahymanol-expressing K. marxianus strains grew anaerobically on glucose at temperatures of up to 45 °C. These results open up new directions in the development of thermotolerant yeast strains for anaerobic industrial applications.\n\nEngineering the thermotolerant industrial yeastKluyveromyces marxianusfor anaerobic growth", "token_count": 335, "char_count": 1293, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6728, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:50.350251", "source": { "split": "train_shard_00000", "doc_id": 4922 }, "chunk_id": "train_shard_00000_4922_0", "global_id": 5556 }, { "text": "This study evaluated potency of antifungals against the rare emerging yeast causing VVC under the influence of acid pH (4.5). The antifungal susceptibility was evaluated by CLSI-M27A4 for 25 isolates represented 11 rare yeast species recovered from VVC patients. Among 11 yeast species (25 isolates), Clavispora lusitaniae (n=9) was the most common species, followed by Cyberlindnera fabianii (n=4) , Kodamaea ohmeri, Candida metapsilosis and Candida bracarensis (n=2, respectively) , Pichia norvegensis, Kluyveromyces marxianus, Diutina rugosa, Tricholoma matsutake, Candida nivariensis and Candida africana (n=1, respectively). The antifungal agents most affected by a lower pH were terconazole (4-fold higher, MIC >0.5-8mg/L) to all 11 yeast species; followed by amphotericin B (3-fold higher, MIC >2mg/L) to 9 species except K. ohmeri and D. rugose ; nystatin (2-fold higher, MIC >2 - 4 mg/L) to 9 species except C. nivariensis and C . africana ; micafungin (2-fold higher, MIC >0.125 - 1 mg/L) to 8 species except C. metapsilosis, D. rugosa and Tricholoma matsutake by acid pH, respectively. 5-flucytosine was not affected by pH to all tested yeast species, and maintained activity at low PH. The rare yeast species tested shared high MICs of terconazole, amphotericin B, nystatin at pH4.5 compared with those at pH7.0. The in vitro antifungal susceptibility at pH 7.0 did not consistently predict the activity of antifungals against those rare yeast species at vaginal acidic pH. Further investigations assessing the clinical utility of antifungal susceptibility testing should take these findings into consideration.", "token_count": 518, "char_count": 1623, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6033, "quality_score": 0.8017, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:51.006953", "source": { "split": "train_shard_00000", "doc_id": 4923 }, "chunk_id": "train_shard_00000_4923_0", "global_id": 5557 }, { "text": "Altered susceptibility of rare yeast species causing vulvovaginal candidiasis at acidic vaginal environment", "token_count": 24, "char_count": 107, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:51.369414", "source": { "split": "train_shard_00000", "doc_id": 4923 }, "chunk_id": "train_shard_00000_4923_1", "global_id": 5558 }, { "text": "The aim of this study was to determine the impact of Kluyveromyces marxianus VM004 culture conditions on the cell wall (CW) structure and its influence on aflatoxin B1 binding. The yeast was inoculated into two types of culture media: yeast extract-peptone-dextrose (YPD) broth and dried distiller's grains with solubles (DDG). The CW was extracted from the biomass produced in these media. AFB1 (150ng/ml) adsorption tests using the biomass (1×107cells/ml) and the CW (0.001g) were performed at pH 2 and pH 8. Transmission electron microscopy (TEM) evaluated the CW thickness, and infrared spectroscopy (IR) determined the CW composition. Biomass production in YPD was higher than that in DDG. Cell diameter (μm) and CW thickness (μm) increased in the DDG medium. The CW percentage obtained in DDG was higher than that in YPD. The absorbance of carbohydrates by IR was higher in YPD. pH influenced AFB1 adsorption, which was lower at pH 8. The proportion of β-glucan and chitin present in CW was higher in the YPD medium. The IR method allowed to study the CW carbohydrate variation under the influence of these carbon sources. In conclusion, the culture media composition influenced the β-glucan and chitin composition and consequently, AFB1 adsorption.\n\nImpact of Kluyveromyces marxianus VM004 culture conditions on the cell wall structure and its influence on aflatoxin B<sub>1</sub> binding.", "token_count": 449, "char_count": 1463, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5138, "quality_score": 0.7569, "entities": { "genes": [ "VM004" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:52.002100", "source": { "split": "train_shard_00000", "doc_id": 4924 }, "chunk_id": "train_shard_00000_4924_0", "global_id": 5559 }, { "text": "Seven Kluyveromyces marxianus isolates from the elaboration process of pulque and henequen mezcal were characterized. The isolates were identified based on the sequences of the D1/D2 domain of the 26S rRNA gene and the internal transcribed spacer (ITS-5.8S) region. Genetic differences were found between pulque and henequen mezcal isolates and within henequen mezcal isolates, as shown by different branching patterns in the ITS-5.8S phylogenetic tree and (GTG)5 microsatellite profiles, suggesting that the substrate and process selective conditions may give rise to different K. marxianus populations. All the isolates fermented and assimilated inulin and lactose and some henequen isolates could also assimilate xylose and cellobiose. Henequen isolates were more thermotolerant than pulque ones, which, in contrast, presented more tolerance to the cell wall-disturbing agent calcofluor white (CFW), suggesting that they had different cell wall structures. Additionally, depending on their origin, the isolates presented different maximum specific growth rate (µmax) patterns at different temperatures. Concerning tolerance to stress factors relevant for lignocellulosic hydrolysates fermentation, their tolerance limits were lower at 42 than 30 °C, except for glucose and furfural. Pulque isolates were less tolerant to ethanol, NaCl, and Cd. Finally, all the isolates could produce ethanol by simultaneous saccharification and fermentation (SSF) of a corncob hydrolysate under laboratory conditions at 42 °C.\n\nGenotypic and Phenotypic Diversity of Kluyveromyces marxianus Isolates Obtained from the Elaboration Process of Two Traditional Mexican Alcoholic Beverages Derived from Agave: Pulque and Henequen (Agave fourcroydes) Mezcal.", "token_count": 497, "char_count": 1788, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:52.647717", "source": { "split": "train_shard_00000", "doc_id": 4925 }, "chunk_id": "train_shard_00000_4925_0", "global_id": 5560 }, { "text": "The Global Panzootic Lineage (GPL) of the amphibian pathogen Batrachochytrium dendrobatidis ( Bd ) has been described as a main driver of amphibian extinctions on nearly every continent. Near complete genomes of three Bd -GPL strains have enabled studies of the pathogen but the genomic features that set Bd- GPL apart from other B. dendrobatidis lineages is not well understood due to a lack of high-quality genome assemblies and annotations from other lineages. We used Oxford Nanopore Technologies (ONT) DNA sequencing to assemble high-quality genomes of three Bd -BRAZIL isolates and one non-pathogen outgroup species Polyrhizophydium stewartii ( Ps ) strain JEL0888 and compared these to genomes of previously sequenced Bd- GPL strains. The Bd -BRAZIL assemblies range in size between 22.0 and 26.1 Mb and encode 8495-8620 protein-coding genes for each strain. A pangenome is defined as all the genes in a species including the core genome, genes found in every strain, and the accessory genome, genes found in only some strains (Brockhurst et al. 2019). To date, a comprehensive analysis identifying the core and accessory genes within B. dendrobatidis has not been conducted. Furthermore, while previous studies have examined the gene transcription profiles of Bd -GPL and Bd -BRAZIL strains (McDonald et al. 2020), they do not account for the genomic differences between these strains. Our pangenome analysis provides insight into shared and lineage-specific gene content and how B. dendrobatidis genotype affects recovery of RNAseq transcripts from different strains. We hypothesize that gene content differences exist between the B. dendrobatidis lineages and genomic differences, such as gene family expansions or gene sequence variation, affect alignment and enumeration of transcriptomic data when relying on a single reference genome", "token_count": 487, "char_count": 1847, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [ "JEL0888" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:53.298946", "source": { "split": "train_shard_00000", "doc_id": 4926 }, "chunk_id": "train_shard_00000_4926_0", "global_id": 5561 }, { "text": "The pangenome analysis revealed a core genome consisting of 6278 conserved gene families, and an accessory genome with 202 Bd -BRAZIL and 172 Bd -GPL specific gene families. We discovered gene copy number differences in five pathogenicity gene families: M36 Peptidase, Crinkler Necrosis Genes (CRN), Aspartyl Peptidase, Carbohydrate-Binding Module-18 (CBM18), and S41 Protease, between Bd- BRAZIL and Bd- GPL strains. However, none of the five families were expanded in Bd -GPL compared to Bd -BRAZIL strains. Comparison between the Batrachochytrium genus and two closely related non-pathogenic saprophytic chytrids identified differences in sequence and protein domain counts. We further test these new Bd -BRAZIL genomes to assess their utility as reference genomes for transcriptome alignment and analysis. Our analysis examines the genomic variation between strains in Bd -BRAZIL and Bd -GPL and offers insights into the application of these genomes as reference genomes for future studies.

Significance

The geographically defined enzootic populations of amphibian pathogen Batrachochytrium dendrobatidis harbor gene context variation revealed in pan-genome analyses. Long read sequencing is required to fully capture this diversity as some recently duplicated and potential virulence gene families are undercounted in short-read only genome assemblies. This genetic variation can impact estimates of gene expression differences between strains if a single genome reference is used. It is necessary to consider the pan-genome diversity of the multiple lineages of this important amphibian pathogen and perhaps other fungal pathogens when engaging in studies of adaptation, virulence, and comparative biology of a species.\n\nComparative genomics reveals intra and inter species variation in the pathogenic fungus Batrachochytrium dendrobatidis", "token_count": 482, "char_count": 1862, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6279, "quality_score": 0.814, "entities": { "genes": [ "CBM18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:53.945298", "source": { "split": "train_shard_00000", "doc_id": 4926 }, "chunk_id": "train_shard_00000_4926_1", "global_id": 5562 }, { "text": "A few genera of diatoms that form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. are widespread in the open ocean. A unique feature of the diatom-Richelia symbioses is the symbiont cellular location spans a continuum of integration (epibiont, periplasmic, and endobiont) that is reflected in the symbiont genome size and content. In this study, we analyzed genomes derived from cultures and environmental metagenome-assembled genomes of Richelia symbionts, focusing on characters indicative of genome evolution. Our results show an enrichment of short-length transposases and pseudogenes in the periplasmic symbiont genomes, suggesting an active and transitionary period in genome evolution. By contrast, genomes of endobionts exhibited fewer transposases and pseudogenes, reflecting advanced stages of genome reduction. Pangenome analyses identified that endobionts streamline their genomes and retain most genes in the core genome, whereas periplasmic symbionts and epibionts maintain larger flexible genomes, indicating higher genomic plasticity compared with the genomes of endobionts. Functional gene comparisons with other N2-fixing cyanobacteria revealed that Richelia endobionts have similar patterns of metabolic loss but are distinguished by the absence of specific pathways (e.g., cytochrome bd ubiquinol oxidase and lipid A) that increase both dependency and direct interactions with their respective hosts. In conclusion, our findings underscore the dynamic nature of genome reduction in N2-fixing cyanobacterial symbionts and demonstrate the diatom-Richelia symbioses as a valuable and rare model to study genome evolution in the transitional stages from a free-living facultative symbiont to a host-dependent endobiont.", "token_count": 461, "char_count": 1795, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6345, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:54.592268", "source": { "split": "train_shard_00000", "doc_id": 4927 }, "chunk_id": "train_shard_00000_4927_0", "global_id": 5563 }, { "text": "Stepwise genome evolution from a facultative symbiont to an endosymbiont in the N<sub>2</sub>-fixing diatom-Richelia symbioses.", "token_count": 55, "char_count": 139, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:54.951266", "source": { "split": "train_shard_00000", "doc_id": 4927 }, "chunk_id": "train_shard_00000_4927_1", "global_id": 5564 }, { "text": "Whey permeate is categorised as hazardous wastewater for aquatic environments, mainly due to its high lactose content. Therefore, it must be valorised before being released into the environment. One pathway for whey permeate management is its use in biotechnological processes. Herein, we present roads for whey permeate valorisation with the K. marxianus WUT240 strain. The established technology is based on two bioprocesses. During first, 2.5 g/L 2-phenylethanol and fermented plant oils enriched with different flavourings are obtained after 48 h biphasic cultures at 30 °C. The second process leads to a maximum of 75 g ethanol/L (YP/S = 0.53 g/g) after 96 h at 30 °C. Moreover, established whey permeate valorisation pathways reduced its biochemical oxygen demand and chemical oxygen demand values by 12- to 3-fold, respectively. Together, the present study reports a complete, effective, and environmentally friendly whey permeate management strategy while simultaneously enabling the acquisition of valuable compounds with substantial application potential.\n\nValorisation of Whey Permeate in Sequential Bioprocesses towards Value-Added Products-Optimisation of Biphasic and Classical Batch Cultures of Kluyveromyces marxianus.", "token_count": 345, "char_count": 1259, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7225, "quality_score": 0.8613, "entities": { "genes": [ "WUT240" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:55.529785", "source": { "split": "train_shard_00000", "doc_id": 4928 }, "chunk_id": "train_shard_00000_4928_0", "global_id": 5565 }, { "text": "Our understanding of the skin microbiome has significantly advanced with the rise of sequencing technologies. While Corynebacterium species are a major component of the human skin microbiome, research has largely centered on other prevalent genera like Staphylococcus and Cutibacterium. Prior to this study, complete genomes for skin-associated Corynebacterium were limited. For instance, only nine were available for the commonly identified species Corynebacterium tuberculostearicum. In this study, we explored Corynebacterium diversity from a single skin site, the axilla, using selective media to enrich for these bacteria. Long-read whole-genome sequencing and bioinformatic analysis of the enriched isolates provided unprecedented insight into the diversity of this genus at a single body site. The study yielded 215 closed genomes, comprising 30 distinct representative genomes following dereplication. These genomes span seven distinct species, including two new species provisionally named Corynebacterium axilliensis and Corynebacterium jamesii, as well as species not previously linked to the skin. Pangenome analysis of these isolates uncovered potential metabolic differences, antimicrobial resistance genes, novel biosynthetic gene clusters, prophages, and phage defense systems. This study represents the most detailed analysis to date of Corynebacterium from a single skin niche and highlights extensive variation even within a single host. Our culture-based Nanopore sequencing approach has expanded the number of publicly available skin Corynebacterium genomes, providing a valuable resource for future studies investigating the diversity and function of this important skin genus.

Importance

This study uncovers the hidden diversity of Corynebacterium, an important yet often overlooked group of bacteria inhabiting human skin. Focusing on the underarm and using advanced sequencing techniques, we identified over 200 complete bacterial genomes", "token_count": 503, "char_count": 2047, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:56.179289", "source": { "split": "train_shard_00000", "doc_id": 4929 }, "chunk_id": "train_shard_00000_4929_0", "global_id": 5566 }, { "text": "This collection includes species not previously known to reside on the skin, as well as two entirely new species, highlighting how little is currently known about this cutaneous genus. Most of these bacteria were isolated from a single individual, underscoring the vast microbial diversity that can exist within one person. By closely examining the corynebacterial community at a single site, we begin to uncover the complex relationships within a true microbial ecosystem. These findings deepen our understanding of the skin microbiome and provide a valuable resource for future research into how these microbes affect skin health, hygiene, and disease.\n\nRevealing the diversity of commensal corynebacteria from a single human skin site.", "token_count": 155, "char_count": 738, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7568, "quality_score": 0.8784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:56.618217", "source": { "split": "train_shard_00000", "doc_id": 4929 }, "chunk_id": "train_shard_00000_4929_1", "global_id": 5567 }, { "text": "Koumiss is a fermented mare's milk beverage with a long history. However, due to the current lack of specialized starters, the product quality is unstable. Therefore, we used dual-omics combined with pure culture technology to screen out strains with excellent fermentation performance for koumiss. The results showed that: (1) The dominant species in koumiss were mainly Lactobacillus and Lactococcus, and metabolites such as arachidonic acid and ascorbic acid were significantly enriched in koumiss. (2) There was a significant correlation between specific microbial species and metabolites. (3) Through preliminary screening using experiments such as milk-based curdling experiments and acid resistance tests, and then rescreening through fermentation tests, five strains with excellent fermentation characteristics were screened out. They are Lacticaseibacillus paracasei SXM-5, Lactobacillus kefianofaciens MGE42-8, Lactobacillus helveticus CFS12-11-1, Saccharomyces cerevisiae PFD-2, and Kluyveromyces marxianus PYM-1. The screened strains supply microbial resources for koumiss products and boost the development of milk beverages.\n\nDual-omics strategy for selecting optimal fermentation strains in traditional koumiss production.", "token_count": 368, "char_count": 1286, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [ "MGE42", "CFS12" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:57.198251", "source": { "split": "train_shard_00000", "doc_id": 4930 }, "chunk_id": "train_shard_00000_4930_0", "global_id": 5568 }, { "text": "Clostridioides difficile has significant clinical importance as a leading cause of healthcare-associated infections, with symptoms ranging from mild diarrhoea to severe colitis, and possible life-threatening complications. C. difficile ribotype (RT) 002, mainly associated with MLST sequence type (ST) 8, is one of the most common RTs found in humans. This study aimed at investigating the genetic characteristics of 537 C. difficile genomes of ST8/RT002. To this end, we sequenced 298 C. difficile strains representing a new European genome collection, with strains from Germany, Denmark, France and Portugal. These sequences were analysed against a global dataset consisting of 1,437 ST8 genomes available through Enterobase. Our results showed close genetic relatedness among the studied ST8 genomes, a diverse array of antimicrobial resistance (AMR) genes and the presence of multiple mobile elements. Notably, the pangenome analysis revealed an open genomic structure. ST8 shows relatively low overall variation. Thus, clonal isolates were found across different One Health sectors (humans, animals, environment and food), time periods, and geographical locations, suggesting the lineage's stability and a universal environmental source. Importantly, this stability did not hinder the acquisition of AMR genes, emphasizing the adaptability of this bacterium to different selective pressures. Although only 2.4 % (41/1,735) of the studied genomes originated from non-human sources, such as animals, food, or the environment, we identified 9 cross-sectoral core genome multilocus sequence typing (cgMLST) clusters. Our study highlights the importance of ST8 as a prominent lineage of C. difficile with critical implications in the context of One Health. In addition, these findings strongly support the need for continued surveillance and investigation of non-human samples to gain a more comprehensive understanding of the epidemiology of C. difficile.", "token_count": 491, "char_count": 2005, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [ "RT002", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:57.848326", "source": { "split": "train_shard_00000", "doc_id": 4931 }, "chunk_id": "train_shard_00000_4931_0", "global_id": 5569 }, { "text": "Genomic study of European Clostridioides difficile ribotype 002/sequence type 8.", "token_count": 31, "char_count": 87, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:58.199797", "source": { "split": "train_shard_00000", "doc_id": 4931 }, "chunk_id": "train_shard_00000_4931_1", "global_id": 5570 }, { "text": "

Background

The 5´ untranslated region (5´ UTR) plays a key role in regulating translation efficiency and mRNA stability, making it a favored target in genetic engineering and synthetic biology. A common feature found in the 5´ UTR is the poly-adenine (poly(A)) tract. However, the effect of 5´ UTR poly(A) on protein production remains controversial. Machine-learning models are powerful tools for explaining the complex contributions of features, but models incorporating features of 5´ UTR poly(A) are currently lacking. Thus, our goal is to construct such a model, using natural 5´ UTRs from Kluyveromyces marxianus, a promising cell factory for producing heterologous proteins.

Results

We constructed a mini-library consisting of 207 5´ UTRs harboring poly(A) and 34 5´ UTRs without poly(A) from K. marxianus. The effects of each 5´ UTR on the production of a GFP reporter were evaluated individually in vivo, and the resulting protein abundance spanned an approximately 450-fold range throughout. The data were used to train a multi-layer perceptron neural network (MLP-NN) model that incorporated the length and position of poly(A) as features. The model exhibited good performance in predicting protein abundance (average R2 = 0.7290). The model suggests that the length of poly(A) is negatively correlated with protein production, whereas poly(A) located between 10 and 30 nt upstream of the start codon (AUG) exhibits a weak positive effect on protein abundance. Using the model as guidance, the deletion or reduction of poly(A) upstream of 30 nt preceding AUG tended to improve the production of GFP and a feruloyl esterase. Deletions of poly(A) showed inconsistent effects on mRNA levels, suggesting that poly(A) represses protein production either with or without reducing mRNA levels.

Conclusion

The effects of poly(A) on protein production depend on its length and position", "token_count": 509, "char_count": 1920, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5851, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:58.831810", "source": { "split": "train_shard_00000", "doc_id": 4932 }, "chunk_id": "train_shard_00000_4932_0", "global_id": 5571 }, { "text": "Integrating poly(A) features into machine-learning models improves simulation accuracy. Deleting or reducing poly(A) upstream of 30 nt preceding AUG tends to enhance protein production. This optimization strategy can be applied to enhance the yield of K. marxianus and other microbial cell factories.\n\nCharacterization and optimization of 5´ untranslated region containing poly-adenine tracts in Kluyveromyces marxianus using machine-learning model.", "token_count": 107, "char_count": 449, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8448, "quality_score": 0.9224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:49:59.217567", "source": { "split": "train_shard_00000", "doc_id": 4932 }, "chunk_id": "train_shard_00000_4932_1", "global_id": 5572 }, { "text": "

Background

Candida species are opportunistic pathogens that can cause local or systemic invasive infections in patients hospitalized in intensive care units (ICUs). The present study aimed to rapidly and precisely identify Candida species, especially Candida auris, from patients hospitalized in high-risk units using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique.

Materials and methods

In this study, 136 clinical samples were prospectively collected from different organs of patients hospitalized in high-risk units recruited from three tertiary care training hospitals in Isfahan. Direct microscopic analysis using potassium hydroxide 10% followed by culturing on Sabouraud dextrose agar and CHROMagar culture media was primarily used to screen Candida species. Molecular detection of clinical isolates was mainly done using the PCR-RFLP method. Then, all the isolates were subjected to confirmatory diagnosis again through amplification of the C. auris-specific PCR.

Results

Candida albicans was the most prevalent isolate (48.8%), followed by Candida glabrata (17.6%), Candida tropicalis (16.1%), Candida parapsilosis (6.6%), Candida krusei (5.8%), Candida famata (4.4%), Candida kefyr (2.9%), and Candida guilliermondii (1.4%). Therefore, the prevalence of non-albicans Candida species was higher than C. albicans isolates. No C. auris isolates were identified among 136 patients. However, according to the positive control, C", "token_count": 518, "char_count": 1615, "word_count": 193, "semantic_coherence": 1, "information_density": 0.7098, "quality_score": 0.8549, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:49:59.852498", "source": { "split": "train_shard_00000", "doc_id": 4933 }, "chunk_id": "train_shard_00000_4933_0", "global_id": 5573 }, { "text": "auris had no restriction enzyme cleavage site for MspI, and its PCR and digestion products were the same size (401 bp).

Conclusions

The simple and reliable PCR-RFLP assay used in the study has the potential to identify rare yeasts such as C. auris. It can reduce turnaround times and costs if applied in developing countries.\n\nMolecular Identification of <i>Candida</i> Species among Iranian Patients: Pursuing <i>Candida auris</i>.", "token_count": 162, "char_count": 481, "word_count": 64, "semantic_coherence": 1, "information_density": 0.9062, "quality_score": 0.9531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:00.335530", "source": { "split": "train_shard_00000", "doc_id": 4933 }, "chunk_id": "train_shard_00000_4933_1", "global_id": 5574 }, { "text": "Paraclostridium bifermentans (P.b) is an emerging human pathogen that is phylogenomically close to Paeniclostridium sordellii (P.s), while their populational genomic features and virulence capacity remain understudied. Here, we performed comparative genomic analyses of P.b and compared their pan-genomic features and virulence coding profiles to those of P.s. Our results revealed that P.b has a more plastic pangenome, a larger genome size, and a higher GC content than P.s. Interestingly, the P.b and P.s share similar core-genomic functions, but P.b encodes more functions in nutrient metabolism and energy conversion and fewer functions in host defense in their accessory-genomes. The P.b may initiate extracellular infection processes similar to those of P.s and Clostridium perfringens by encoding three toxin homologs (i.e., microbial collagenase, thiol-activated cytolysin, phospholipase C, which are involved in extracellular matrices degradation and membrane damaging) in their core-genomes. However, P.b is less toxic than the P.s by encoding fewer secretion toxins in the core-genome and fewer lethal toxins in the accessory-genome. Notably, P.b carries more toxins genes in their accessory-genomes, particularly those of plasmid origin. Moreover, three within-species and highly conserved plasmid groups, encoding virulence, gene acquisition, and adaptation, were carried by 25-33% of P.b strains and clustered by isolation source rather than geography. This study characterized the pan-genomic virulence features of P.b for the first time, and revealed that P. bifermentans is an emerging pathogen that can threaten human health in many aspects, emphasizing the importance of phenotypic and genomic characterizations of in situ clinical isolates.", "token_count": 493, "char_count": 1796, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:01.002399", "source": { "split": "train_shard_00000", "doc_id": 4934 }, "chunk_id": "train_shard_00000_4934_0", "global_id": 5575 }, { "text": "Populational genomic insights of Paraclostridium bifermentans as an emerging human pathogen.", "token_count": 29, "char_count": 99, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:01.374304", "source": { "split": "train_shard_00000", "doc_id": 4934 }, "chunk_id": "train_shard_00000_4934_1", "global_id": 5576 }, { "text": "The laboratory contaminant strain Noodlococcus was named for its coccoid cells and unusual colony morphology, which resembled a pile of noodles. Along with laboratory characterisation and electron microscopy, we generated a complete Noodlococcus genome sequence using Illumina and Oxford Nanopore data. The genome consisted of a single, circular, 2,732,108 bp chromosome that shared 97.5% average nucleotide identity (ANI) with the Kocuria rhizophila type strain TA68. We identified genomic features involved in replication (oriC), carotenoid synthesis (crt) and genome defence (CRISPR-Cas) and discovered four novel mobile elements (ISKrh4-7). Despite its environmental ubiquity and relevance to food production, bioremediation and human medicine, there have been few genomic studies of the Kocuria genus. We conducted a comparative, phylogenetic and pangenomic examination of all 257 publicly available Kocuria genomes, with a particular focus on the 56 that were identified as K. rhizophila. We found that there are two phylogenetically distinct clades of K. rhizophila, with within-clade ANI values of 96.7-100.0% and between-clade values of 89.5-90.4%. The second clade, which we refer to as Kocuria pseudorhizophila, exhibited ANI values of <95% relative to TA68 and should constitute a separate species. Delineation of the two clades would be consistent with the rest of the genus, where all other species satisfy the 95% ANI threshold criteria. Differences in the K. rhizophila and K. pseudorhizophila pangenomes likely reflect phenotypic as well as evolutionary divergence", "token_count": 504, "char_count": 1658, "word_count": 226, "semantic_coherence": 1, "information_density": 0.677, "quality_score": 0.8385, "entities": { "genes": [ "TA68" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:02.065648", "source": { "split": "train_shard_00000", "doc_id": 4935 }, "chunk_id": "train_shard_00000_4935_0", "global_id": 5577 }, { "text": "This distinction is relevant to clinical and industrial settings, as strains and genomes from both clades are currently used interchangeably, which may lead to reproducibility issues and phenotype-genotype discordance. Investigating an innocuous laboratory contaminant has therefore provided useful insights into the understudied species K. rhizophila, prompting an unexpected reassessment of its taxonomy.\n\nThe Kocurious case of Noodlococcus: genomic insights into <i>Kocuria rhizophila</i> from characterisation of a laboratory contaminant.", "token_count": 139, "char_count": 561, "word_count": 68, "semantic_coherence": 1, "information_density": 0.8382, "quality_score": 0.9191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:02.497317", "source": { "split": "train_shard_00000", "doc_id": 4935 }, "chunk_id": "train_shard_00000_4935_1", "global_id": 5578 }, { "text": "In Dutch ICUs patients receive selective digestive decontamination (SDD) as a prophylactic antimicrobial treatment to prevent colonisation with potentially pathogenic microorganisms and subsequent infections, with a beneficial effect on 28-day mortality. In the R-GNOSIS ICU study, conducted outside of The Netherlands, SDD consisted of a mix of an oropharyngeal paste and a gastric suspension containing colistin, tobramycin and nystatin. These topical antimicrobial agents aim to target aerobic Gram-negative bacteria, S. aureus and yeast. SDD improves patient outcome, but its effects on the resistome and pangenome of potentially pathongenic microorganisms have not been extensively studied. In this work, we compared 129 genomes of E. coli isolates from patients that received SDD and patients that did not receive SDD, but standard care only (baseline patients) in five ICUs located across three European countries (R-GNOSIS ICU study). We found that the overall pangenome compositions of E. coli recovered from both patient groups were highly similar. Variations in the accessory genome were strongly associated with the phylogeny of isolates but not with the use of SDD. Similarly, the plasmidome variations were not explained by treatment, but rather by the interaction between ICU location and phylogroup. One antibiotic resistance gene, which confers resistance to tobramycin, was found to be more prevalent in SDD patients. This gene was flanked by IS26 elements and significantly co-occurred with blaCTX-M-15 in various plasmid backbones and chromosomal contexts. Notably, no mcr genes coding for colistin resistance were detected.\n\nImpact of selective digestive decontamination on the pangenome composition of ESBL-E. coli", "token_count": 437, "char_count": 1743, "word_count": 250, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [ "IS26" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:03.127035", "source": { "split": "train_shard_00000", "doc_id": 4936 }, "chunk_id": "train_shard_00000_4936_0", "global_id": 5579 }, { "text": "It is important to understand the basis of thermotolerance in yeasts to broaden their application in industrial biotechnology. The capacity to run bioprocesses at temperatures above 40 °C is of great interest but this is beyond the growth range of most of the commonly used yeast species. In contrast, some industrial yeasts such as Kluyveromyces marxianus can grow at temperatures of 45 °C or higher. Such species are valuable for direct use in industrial biotechnology and as a vehicle to study the genetic and physiological basis of yeast thermotolerance. In previous work, we reported that evolutionarily young genes disproportionately changed expression when yeast were growing under stressful conditions and postulated that such genes could be important for long-term adaptation to stress. Here, we tested this hypothesis in K. marxianus by identifying and studying species-specific genes that showed increased expression during high-temperature growth. Twelve such genes were identified and 11 were successfully inactivated using CRISPR-mediated mutagenesis. One gene, KLMX_70384, is required for competitive growth at high temperature, supporting the hypothesis that evolutionary young genes could play roles in adaptation to harsh environments. KLMX_70384 is predicted to encode an 83 aa peptide, and RNA sequencing and ribo-sequencing were used to confirm transcription and translation of the gene. The precise function of KLMX_70384 remains unknown but some features are suggestive of RNA-binding activity. The gene is located in what was previously considered an intergenic region of the genome, which lacks homologues in other yeasts or in databases. Overall, the data support the hypothesis that genes that arose de novo in K. marxianus after the speciation event that separated K. marxianus and K. lactis contribute to some of its unique traits.", "token_count": 482, "char_count": 1916, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6137, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:03.775248", "source": { "split": "train_shard_00000", "doc_id": 4937 }, "chunk_id": "train_shard_00000_4937_0", "global_id": 5580 }, { "text": "Identification of a novel gene required for competitive growth at high temperature in the thermotolerant yeast Kluyveromyces marxianus.", "token_count": 37, "char_count": 142, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:04.134769", "source": { "split": "train_shard_00000", "doc_id": 4937 }, "chunk_id": "train_shard_00000_4937_1", "global_id": 5581 }, { "text": "

ABSTRACT

The genomic diversity of many fungal pathogens is driven by rapidly evolving regions harbouring significant amounts of transposable elements. Such genomic regions often contain genes important for pathogenicity and may be sequestered from the core genome on accessory chromosomes, which are variably present in isolates of a species. In this study, we present a pangenomic analysis of a fungal insect pathogen, Metarhizium acridum , using seven chromosome-scale genomes from four different continents. We show that approximately 25% of the M. acridum pangenome is comprised of genes only present in one isolate (singletons) or more than one but not all isolates (accessory). These genes are enriched for functions in secondary metabolite production, nutrient transport, and chromosome organization. We also find evidence of functional compartmentalization of the genome, as the core genome of M. acridum is enriched in carbohydrate-active enzymes, while the accessory components are enriched in effectors that are located in gene-sparse regions of the genome. Furthermore, we identified the first naturally recovered accessory chromosome in M. acridum , which does not harbor effector or secondary metabolite proteins related to host-insect interactions but is enriched in functions related to sexual reproduction. Within the genus Metarhizium, M. acridum is one of few species considered to regularly reproduce sexually. We show that the accessory chromosome contains genes from both the MAT1-1 and MAT1-2 idiomorphs, in addition to the MAT locus found on the core chromosomes. Our findings suggest that the presence of this accessory chromosome may facilitate sexual reproduction, possibly even primary homothallism, in the otherwise heterothallic M. acridum . Overall, our study presents a putative novel mechanism whereby this fungal pathogen may acquire gene recombination and ensure maintenance of the accessory chromosome.\n\nGenome compartmentalization in a host-specific fungal insect pathogen reveals a putative mating type locus on an accessory chromosome", "token_count": 499, "char_count": 2083, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5686, "quality_score": 0.7843, "entities": { "genes": [ "MAT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:04.782288", "source": { "split": "train_shard_00000", "doc_id": 4938 }, "chunk_id": "train_shard_00000_4938_0", "global_id": 5582 }, { "text": "Staphylococcus pseudintermedius is a common representative of the normal skin microbiota of dogs and cats but is also a causative agent of a variety of infections. Although primarily a canine/feline bacterium, recent studies suggest an expanded host range including humans. This paper details population genomic analyses of the largest yet assembled and sequenced collection of S. pseudintermedius isolates from across the USA and Canada and assesses these isolates within a larger global population genetic context. We then employ a pan-genome-wide association study analysis of over 1,700 S. pseudintermedius isolates from sick dogs and cats, covering the period 2017-2020, correlating loci at a genome-wide level, with in vitro susceptibility data for 23 different antibiotics. We find no evidence from either core genome phylogenies or accessory genome content for separate lineages colonizing cats or dogs. Some core genome geographic clustering was evident on a global scale, and accessory gene content was noticeably different between various regions, some of which could be linked to known antimicrobial resistance (AMR) loci for certain classes of antibiotics (e.g., aminoglycosides). Analysis of genes correlated with AMR was divided into different categories, depending on whether they were known resistance mechanisms, on a plasmid, or a putatively novel resistance mechanism on the chromosome. We discuss several novel chromosomal candidates for follow-up laboratory experimentation, including, for example, a bacteriocin (subtilosin), for which the same protein from Bacillus subtilis has been shown to be active against Staphylococcus aureus infections, and for which the operon, present in closely related Staphylococcus species, is absent in S. aureus.IMPORTANCEStaphylococcus pseudintermedius is an important causative agent of a variety of canine and feline infections, with recent studies suggesting an expanded host range, including humans", "token_count": 515, "char_count": 2030, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:05.444447", "source": { "split": "train_shard_00000", "doc_id": 4939 }, "chunk_id": "train_shard_00000_4939_0", "global_id": 5583 }, { "text": "This paper presents global population genomic data and analysis of the largest set yet sequenced for this organism, covering the USA and Canada as well as more globally. It also presents analysis of in vitro antibiotic susceptibility testing results for the North American (NA) isolates, as well as genetic analysis for the global set. We conduct a pan-genome-wide association study analysis of over 1,700 S. pseudintermedius isolates from sick dogs and cats from NA to correlate loci at a genome-wide level with the in vitro susceptibility data for 23 different antibiotics. We discuss several chromosomal loci arising from this analysis for follow-up laboratory experimentation. This study should provide insight regarding the development of novel molecular treatments for an organism of both veterinary and, increasingly, human medical concern.\n\nPopulation and pan-genomic analyses of <i>Staphylococcus pseudintermedius</i> identify geographic distinctions in accessory gene content and novel loci associated with AMR.", "token_count": 258, "char_count": 1054, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6871, "quality_score": 0.8435, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:05.992850", "source": { "split": "train_shard_00000", "doc_id": 4939 }, "chunk_id": "train_shard_00000_4939_1", "global_id": 5584 }, { "text": "With rising multidrug-resistant yeast pathogens, conventional antifungals are becoming less effective, urging the need for adjuvants that enhance their activity at lower doses. This study evaluated the synergistic activity of antimicrobial peptidomimetics (TM8 and RK758) or colistin sulphate in combination with conventional antifungals against Candida albicans, C. tropicalis, C. parapsilosis, Meyerozyma guilliermondii, Nakaseomyces glabratus, Pichia kudriavzevii and Kluyveromyces marxianus, and Candidozyma auris using the checkerboard microdilution test. RK758 was synergistic with fluconazole in 78% of isolates, with the remaining 22% of isolates still showing partial synergy; it showed synergy with amphotericin B in 56% of isolates, and with caspofungin, 78% of isolates exhibited either synergy or partial synergy. TM8 showed synergy with fluconazole in 44% (with partial synergy in another 44%) of isolates, with amphotericin B in 67% of isolates, and with caspofungin in 44% (with partial synergy in another 44%) of isolates. Colistin with fluconazole or caspofungin exhibited synergy or partial synergy in 56% of the isolates. No antagonism was observed in any of the combinations. Additionally, a time-kill assay further demonstrated synergistic activity between fluconazole and TM8 or RK758. The effects of these peptidomimetics on cell membrane integrity were demonstrated in an ergosterol binding assay, supported by SYTOX Green and cellular leakage assays, both indicating a lytic effect", "token_count": 499, "char_count": 1563, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7929, "entities": { "genes": [ "TM8", "RK758" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:06.643766", "source": { "split": "train_shard_00000", "doc_id": 4940 }, "chunk_id": "train_shard_00000_4940_0", "global_id": 5585 }, { "text": "These results suggest that peptidomimetics can synergise with conventional antifungals, offering a potential strategy for combination therapy against yeast infections. The membrane lytic activity of the peptidomimetics likely plays a role in their synergistic interaction with antifungals, thereby enhancing the antimicrobial activities of both compounds at sub-MIC levels.\n\nEvaluation of the Synergistic Activity of Antimicrobial Peptidomimetics or Colistin Sulphate with Conventional Antifungals Against Yeasts of Medical Importance.", "token_count": 131, "char_count": 535, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:07.069400", "source": { "split": "train_shard_00000", "doc_id": 4940 }, "chunk_id": "train_shard_00000_4940_1", "global_id": 5586 }, { "text": "

Background

The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represents a limitation when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of sequencing read mapping to the current bovine genome assembly.

Results

In this study, we used long-reads (LR) and bioinformatic tools to construct a comprehensive bovine pangenome, using as a backbone the Hereford ARS-UCD1.2 reference genome assembly, and incorporating genetic diversity of 64 good quality de novo genome assemblies representing 14 French dairy and beef cattle breeds. Using a combination of complementary approaches, we explored the pangenome graph and identified 2.563 Gb of sequences common to all samples, and cumulated 0.295 Gb of variable sequences. Notably, we discovered 0.159 Gb of novel sequences not present in the current reference genome assembly. Our analysis also revealed 109,275 SVs, of which 84,612 were bi-allelic. These included 27,171 insertions and 24,592 deletions, while the remaining 32,849 SVs corresponded to alternate allele sequences defined as sequence substitutions between the reference genome and the sample sequence. Genome-wide association studies using SNPs and a panel of 221 SVs, shared between the pangenome and the EuroGMD chip, revealed well-known QTLs across the genome for the Holstein, Montbéliarde and Normande breeds. Among those, a QTL on chromosome 11 presents an SV with a highly significant effect on stature in the Holstein breed", "token_count": 432, "char_count": 1709, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6598, "quality_score": 0.8299, "entities": { "genes": [ "UCD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:07.695958", "source": { "split": "train_shard_00000", "doc_id": 4941 }, "chunk_id": "train_shard_00000_4941_0", "global_id": 5587 }, { "text": "This SV is a 6.2 kb deletion affecting the 5'UTR, first exon and part of the first intron of the MATN3 gene, suggesting a potential regulatory and coding effect.

Conclusions

Our study provides new insights into the genetic diversity of 14 French dairy and beef breeds and highlights the utility of pangenome graphs in capturing structural variation. The identified SV associated with stature highlights the importance of integrating SVs into GWAS for a more comprehensive understanding of complex traits.\n\nApplication of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes.", "token_count": 143, "char_count": 630, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [ "MATN3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:08.124648", "source": { "split": "train_shard_00000", "doc_id": 4941 }, "chunk_id": "train_shard_00000_4941_1", "global_id": 5588 }, { "text": "

Background

Tidal flats are vital coastal ecosystems that play a significant role in organic carbon accumulation and biogeochemical cycles. Members of the family Flavobacteriaceae is known for its ability to degrade complex organic matter, including polysaccharides. However, the ecological roles and metabolic capabilities of Flavobacteriaceae in tidal flat environments remain underexplored.

Results

In this study, we isolated and characterized a novel bacterium, strain NBU2967T, from the tidal flats of Meishan Island in the East China Sea. Phylogenetic and genomic analyses identified this strain as a new genus and species within the family Flavobacteriaceae, for which we propose the name Meishania litoralis gen. nov., sp. nov. Comprehensive polyphasic characterization, including morphological, physiological, chemotaxonomic, and genomic analyses, confirmed its distinct taxonomic status. Genomic analysis revealed a diverse set of carbohydrate-active enzymes (CAZymes), along with multiple metabolic pathways associated with carbon and sulfur cycling, highlighting the strain's potential adaptation to organic-rich marine environments. Comparative genomic and pangenome analyses further demonstrated significant genetic divergence from related taxa. Environmental distribution data revealed that the newly proposed genus Meishania is widely distributed across global marine ecosystems.

Conclusions

We isolated and characterized a novel bacterium, designated NBU2967T (= KCTC 82912 T = MCCC 1K06391T), for which we propose the name Meishania litoralis gen. nov., sp. nov. This strain is classified as a new genus within the family Flavobacteriaceae. The strain's ability to process both carbon and sulfur compounds underscores its ecological significance in marine ecosystems", "token_count": 476, "char_count": 1849, "word_count": 233, "semantic_coherence": 1, "information_density": 0.618, "quality_score": 0.809, "entities": { "genes": [ "NBU2967" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:08.771519", "source": { "split": "train_shard_00000", "doc_id": 4942 }, "chunk_id": "train_shard_00000_4942_0", "global_id": 5589 }, { "text": "These findings provide novel insights into the ecological functions of the family Flavobacteriaceae in coastal tidal flats environments and enhance our understanding of microbial-mediated degradation and transformation of chemical compounds in dynamic coastal ecosystems.\n\nTaxonomic, genomic, and ecological insights into a novel Flavobacteriaceae strain from coastal tidal flats.", "token_count": 82, "char_count": 380, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:09.146210", "source": { "split": "train_shard_00000", "doc_id": 4942 }, "chunk_id": "train_shard_00000_4942_1", "global_id": 5590 }, { "text": "

Motivation

Much of prokaryotic comparative genomics currently relies on two critical computational tasks: pangenome inference and core genome inference. Pangenome inference involves clustering genes from a set of genomes into gene families, enabling genome-wide association studies and evolutionary history analysis. The core genome represents gene families present in nearly all genomes and is required to infer a high-quality phylogeny. For species-level datasets, fast pangenome inference tools have been developed. However, tools applicable to more diverse datasets are currently slow and scale poorly.

Results

Here, we introduce SCARAP, a program containing three modules for comparative genomics analyses: a fast and scalable pangenome inference module, a direct core genome inference module, and a module for subsampling representative genomes. When benchmarked against existing tools, the SCARAP pan module proved up to an order of magnitude faster with comparable accuracy. The core module was validated by comparing its result against a core genome extracted from a full pangenome. The sample module demonstrated the rapid sampling of genomes with decreasing novelty. Applied to a dataset of over 31 000 Lactobacillales genomes, SCARAP showcased its ability to derive a representative pangenome. Finally, we applied the novel concept of gene fixation frequency to this pangenome, showing that Lactobacillales genes that are prevalent but rarely fixate in species often encode bacteriophage functions.

Availability and implementation

The SCARAP toolkit is publicly available at https://github.com/swittouck/scarap.\n\nSCARAP: scalable cross-species comparative genomics of prokaryotes.", "token_count": 406, "char_count": 1714, "word_count": 227, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:09.766207", "source": { "split": "train_shard_00000", "doc_id": 4943 }, "chunk_id": "train_shard_00000_4943_0", "global_id": 5591 }, { "text": "Traditional cocoa bean fermentation is a spontaneous process and can result in heterogeneous sensory quality. For this reason, yeast-integrated starter cultures may be an option for creating consistent organoleptic profiles. This study proposes the mixture of Hanseniaspora opuntiae and Kluyveromyces marxianus (from non-cocoa fermentation) as starter culture candidates. The microorganisms and volatile compounds were analyzed during the cocoa fermentation process, and the most abundant were correlated with predominant microorganisms. Results showed that Kluyveromyces marxianus, isolated from mezcal fermentation, was identified as the dominant yeast by high-throughput DNA sequencing. A total of 63 volatile compounds identified by HS-SPME-GC–MS were correlated with the more abundant bacteria and yeast using Principal Component Analysis and Agglomerative Hierarchical Clustering. This study demonstrates that yeasts from other fermentative processes can be used as starter cultures in cocoa fermentation and lead to the formation of more aromatic esters, decrease the acetic acid content.\n\nExploring volatile compounds and microbial dynamics: Kluyveromyces marxianus and Hanseniaspora opuntiae reduce Forastero cocoa fermentation time", "token_count": 304, "char_count": 1241, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:10.337651", "source": { "split": "train_shard_00000", "doc_id": 4944 }, "chunk_id": "train_shard_00000_4944_0", "global_id": 5592 }, { "text": "

Background

Salmonella enterica serovar Infantis (Salmonella Infantis) is a zoonotic, ubiquitous and foodborne pathogen of worldwide distribution. Despite Brazil's relevance as a major meat exporter, few studies were conducted to characterize strains of this serovar by genomic analyses in this country. Therefore, this study aimed to assess the diversity of 80 Salmonella Infantis strains isolated from veterinary, food and human sources in Brazil between 2013 and 2018 by comparative genomic analyses. Additional genomes of non-Brazilian countries (n = 18) were included for comparison purposes in some analyses.

Methods

Analyses of whole-genome multi-locus sequence typing (wgMLST), using PGAdb-builder, and of fragmented genomes, using Gegenees, were conducted to compare the 80 Brazilian strains to the 18 non-Brazilian genomes. Pangenome analyses and calculations were performed for all Salmonella Infantis genomes analyzed. The presence of prophages was determined using PHASTER for the 80 Brazilian strains. The genome plasticity using BLAST Ring Image Generator (BRIG) and gene synteny using Mauve were evaluated for 20 selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries. Unique orthologous protein clusters were searched in ten selected Salmonella Infantis genomes from Brazil and ten from non-Brazilian countries.

Results

wgMLST and Gegenees showed a high genomic similarity among some Brazilian Salmonella Infantis genomes, and also the correlation of some clusters with non-Brazilian genomes. Gegenees also showed an overall similarity >91% among all Salmonella Infantis genomes", "token_count": 496, "char_count": 1710, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5701, "quality_score": 0.7851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:10.989426", "source": { "split": "train_shard_00000", "doc_id": 4945 }, "chunk_id": "train_shard_00000_4945_0", "global_id": 5593 }, { "text": "Pangenome calculations revealed an open pangenome for all Salmonella Infantis subsets analyzed and a high gene content in the core genomes. Fifteen types of prophages were detected among 97.5% of the Brazilian strains. BRIG and Mauve demonstrated a high structural similarity among the Brazilian and non-Brazilian isolates. Unique orthologous protein clusters related to biological processes, molecular functions, and cellular components were detected among Brazilian and non-Brazilian genomes.

Conclusion

The results presented using different genomic approaches emphasized the significant genomic similarity among Brazilian Salmonella Infantis genomes analyzed, suggesting wide distribution of closely related genotypes among diverse sources in Brazil. The data generated contributed to novel information regarding the genomic diversity of Brazilian and non-Brazilian Salmonella Infantis in comparison. The different genetically related subtypes of Salmonella Infantis from Brazil can either occur exclusively within the country, or also in other countries, suggesting that some exportation of the Brazilian genotypes may have already occurred.\n\nComparative genomics reveals high genetic similarity among strains of Salmonella enterica serovar Infantis isolated from multiple sources in Brazil.", "token_count": 309, "char_count": 1337, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6369, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:11.558916", "source": { "split": "train_shard_00000", "doc_id": 4945 }, "chunk_id": "train_shard_00000_4945_1", "global_id": 5594 }, { "text": "Abstract

Kluyveromyces marxianus yeasts represent a valuable industry alternative due to their biotechnological potential to produce aromatic compounds. 2-phenylethanol and 2-phenylethylacetate are significant aromatic compounds widely used in food and cosmetics due to their pleasant odor. Natural obtention of these compounds increases their value, and because of this, bioprocesses such as de novo synthesis has become of great significance. However, the relationship between aromatic compound production and yeast's genetic diversity has yet to be studied. In the present study, the analysis of the genetic diversity in K. marxianus isolated from the natural fermentation of Agave duranguensis for Mezcal elaboration is presented. The results of strains in a haploid and diploid state added to the direct relationship between the mating type locus MAT with metabolic characteristics are studied. Growth rate, assimilate carbohydrates (glucose, lactose, and chicory inulin), and the production of aromatic compounds such as ethyl acetate, isoamyl acetate, isoamyl alcohol, 2-phenylethyl butyrate and phenylethyl propionate and the diversity in terms of the output of 2-phenylethanol and 2-phenylethylacetate by de novo synthesis were determinate, obtaining maximum concentrations of 51.30 and 60.39 mg/L by ITD0049 and ITD 0136 yeasts respectively.

\n\nCharacterization of mating type on aroma production and metabolic properties wild Kluyveromyces marxianus yeasts", "token_count": 446, "char_count": 1573, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6238, "quality_score": 0.8119, "entities": { "genes": [ "ITD0049" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:12.207094", "source": { "split": "train_shard_00000", "doc_id": 4946 }, "chunk_id": "train_shard_00000_4946_0", "global_id": 5595 }, { "text": "

Introduction

Dairy farming plays a vital role in agriculture and nutrition; however, the emergence of antimicrobial resistance (AMR) among bacterial pathogens poses significant risks to public health and animal welfare. Multidrug-resistant (MDR) Escherichia coli strains are of particular concern due to their potential for zoonotic transmission and resistance to multiple antibiotics. In this study, we investigated the prevalence of AMR and analyzed the genomes of two MDR E. coli isolated from dairy cows in Shihezi City.

Methods

Fecal samples were collected from dairy cows, and E. coli strains were isolated. Antibiotic susceptibility testing was conducted using the Kirby-Bauer disk diffusion method against 14 antibiotics. Two MDR isolates (E.coli_30 and E.coli_45) were selected for whole-genome sequencing and comparative genomic analysis. The Comprehensive Antibiotic Resistance Database (CARD) was used to identify AMR genes, and virulence factors were analyzed. Phylogenetic analysis was performed to determine the evolutionary relationships of the isolates, and a pangenome analysis of 50 E. coli strains was conducted to assess genetic diversity. The presence of mobile genetic elements (MGEs), including insertion sequences (IS) and transposons, was also examined.

Results

Among the E. coli isolates, 22.9% exhibited MDR, with high resistance to imipenem and ciprofloxacin, while gentamicin and tetracycline remained the most effective antibiotics. Genomic analysis revealed key AMR genes, including mphA, qnrS1, and bla CTX-M-55 (the latter found only in E.coli_45), conferring resistance to macrolides, quinolones, and beta-lactams, respectively", "token_count": 508, "char_count": 1751, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:12.891254", "source": { "split": "train_shard_00000", "doc_id": 4947 }, "chunk_id": "train_shard_00000_4947_0", "global_id": 5596 }, { "text": "Virulence genes encoding type III secretion systems (TTSS) and adhesion factors were identified, indicating pathogenic potential. Phylogenetic analysis showed that E.coli_30 and E.coli_45 originated from distinct ancestral lineages. The presence of two extended-spectrum β-lactamase (ESBL) genes in E.coli_45 was noticeable, so we studied their global and national distribution using evolutionary analysis. We found that they are endemic in E. coli, Salmonella enterica, and Klebsiella pneumoniae. Pangenome analysis revealed significant genetic diversity among E. coli strains, with unique genes related to metabolism and stress response. This indicates the bacteria's adaptation to various environments. MGEs were identified as key contributors to genetic variability and adaptation.

Discussion

This study highlights the growing threat of MDR E. coli in dairy farms, emphasizing the critical role of MGEs in the spread of resistance genes. The genetic diversity observed suggests strong adaptive capabilities, justifying the need for continuous AMR surveillance in livestock. Effective monitoring and mitigation strategies are essential to prevent the dissemination of MDR bacteria, thereby protecting both animal and public health.\n\nGenomic analysis of multidrug-resistant <i>Escherichia coli</i> isolated from dairy cows in Shihezi city, Xinjiang, China.", "token_count": 353, "char_count": 1398, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7444, "quality_score": 0.8722, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:13.495158", "source": { "split": "train_shard_00000", "doc_id": 4947 }, "chunk_id": "train_shard_00000_4947_1", "global_id": 5597 }, { "text": "Antimicrobial resistance (AMR) is a pressing global health issue, intensified by the spread of resistant pathogens like Klebsiella pneumoniae (K. pneumoniae), which frequently causes hospital-acquired infections. This study focuses on a multidrug-resistant K. pneumoniae sequence type (ST) 656 strain, isolated from canal water in Bangladesh. Whole-genome sequencing and comparative genomic analysis revealed extensive resistance mechanisms and genetic elements underlying its adaptability. The strain exhibited resistance to colistin and multiple β-lactam antibiotics, containing key resistance genes such as mcr8.1, blaLAP-2, blaTEM-1, blaSHV-11 and blaOXA-1, alongside genes for copper, zinc, and silver resistance, indicating survival capability in metal-rich environments. Virulence factor analysis identified genes supporting adhesion, biofilm formation, and immune evasion, amplifying its pathogenic potential. Plasmid and phage analyses revealed mobile genetic elements, highlighting the role of horizontal gene transfer in AMR dissemination. The study included a pangenome analysis using a dataset of 32 publicly available K. pneumoniae sequence type (ST) 656 genomes, demonstrating evidence of an expanding pangenome for K. pneumoniae ST656. This study emphasized the role of environmental sources in AMR spread and the importance of continued surveillance, particularly in settings with intensive antibiotic usage, to mitigate the spread of high-risk, multidrug-resistant clones like K. pneumoniae ST656.\n\nComprehensive genomic insights into a highly pathogenic clone ST656 of mcr8.1 containing multidrug-resistant Klebsiella pneumoniae from Bangladesh.", "token_count": 442, "char_count": 1708, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6729, "quality_score": 0.8364, "entities": { "genes": [ "ST656" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:14.158268", "source": { "split": "train_shard_00000", "doc_id": 4948 }, "chunk_id": "train_shard_00000_4948_0", "global_id": 5598 }, { "text": "Bacillus cereus poses a persistent challenge for human milk banks (HMBs) due to its ability to survive Holder pasteurization (HoP; 62.5 °C for 30 min). To ensure neonatal safety, any milk found to be contaminated post-HoP must be discarded, which impacts milk supply and adds to the operational demands of HMBs. In this study, we analyzed 688 B. cereus isolates from human milk (pre- and post-HoP), as well as from patient and environmental sources, to investigate human milk contamination by B. cereus at a Canadian HMB. Despite the limited temporal and geographic scope of the collection, the isolates exhibited remarkable genomic diversity, comparable to global B. cereus collections. Phylogenetic analysis at the core genome level revealed no clear clustering by isolate source, suggesting multifactorial pathways of B. cereus contamination. Isolates surviving HoP displayed gene variants linked to sporulation and cell wall integrity, suggesting a potential basis for HoP tolerance. Our findings emphasize that while genomic analyses offer major valuable insights, they alone are insufficient to address the complexities of B. cereus contamination in HMBs. Addressing this challenge will require combining genomic tools with robust monitoring systems, improved human milk-handling protocols, and pasteurization strategies better-suited to countering B. cereus resilience.\n\nHigh Genetic Diversity Among <i>Bacillus cereus</i> Isolates Contaminating Donated Milk at a Canadian Human Milk Bank.", "token_count": 412, "char_count": 1557, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:14.783183", "source": { "split": "train_shard_00000", "doc_id": 4949 }, "chunk_id": "train_shard_00000_4949_0", "global_id": 5599 }, { "text": "

Background

Genetic discontinuity represents abrupt breaks in genomic identity among species. Advances in genome sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring the degree to which bacterial diversity exists as a continuum or sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aim to quantify the genetic discontinuity ( δ ) and investigate how this metric is related to ecology.

Results

We harness a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which vary depending on the taxa in question. By delving into pangenome characteristics, we uncover a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes are associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis. Additionally, through a machine learning approach, we detect key features such as gene conservation patterns and functional annotations that significantly impact genetic discontinuity prediction.

Conclusions

Our study clarifies bacterial genetic patterns and their ecological impacts, enhancing the delineation of species boundaries and deepening our understanding of microbial diversity.\n\nRelating ecological diversity to genetic discontinuity across bacterial species.", "token_count": 307, "char_count": 1470, "word_count": 184, "semantic_coherence": 1, "information_density": 0.7065, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:16.144481", "source": { "split": "train_shard_00000", "doc_id": 4950 }, "chunk_id": "train_shard_00000_4950_0", "global_id": 5600 }, { "text": "Bacterial pathogens of the genus Pectobacterium are responsible for soft rot and blackleg disease in a wide range of crops and have a global impact on food production. The emergence of new lineages and their competitive succession is frequently observed in Pectobacterium species, in particular in P. brasiliense . With a focus on one such recently emerged P. brasiliense lineage in the Netherlands that causes blackleg in potatoes, we studied genome evolution in this genus using a reference-free graph-based pangenome approach. We clustered 1,977,865 proteins from 454 Pectobacterium spp. genomes into 30,156 homology groups. The Pectobacterium genus pangenome is open and its growth is mainly contributed by the accessory genome. Bacteriophage genes were enriched in the accessory genome and contributed 16% of the pangenome. Blackleg-causing P. brasiliense isolates had increased genome size with high levels of prophage integration. To study the diversity and dynamics of these prophages across the pangenome, we developed an approach to trace prophages across genomes using pangenome homology group signatures. We identified lineage-specific as well as generalist bacteriophages infecting Pectobacterium species. Our results capture the ongoing dynamics of mobile genetic elements, even in the clonal lineages. The observed lineage-specific prophage dynamics provide mechanistic insights into Pectobacterium pangenome growth and contribution to the radiating lineages of P. brasiliense .\n\nPangenomics to understand prophage dynamics in thePectobacteriumgenus and the radiating lineages ofP. Brasiliense", "token_count": 405, "char_count": 1622, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6044, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:17.124308", "source": { "split": "train_shard_00000", "doc_id": 4951 }, "chunk_id": "train_shard_00000_4951_0", "global_id": 5601 }, { "text": "This paper presents results concerning mechanistic modeling to describe the dynamics and interactions between biomass growth, glucose consumption and ethanol production in batch culture fermentation by Kluyveromyces marxianus (K. marxianus). The mathematical model was formulated based on the biological assumptions underlying each variable and is given by a set of three coupled nonlinear first-order Ordinary Differential Equations. The model has ten parameters, and their values were fitted from the experimental data of 17 K. marxianus strains by means of a computational algorithm design in Matlab. The latter allowed us to determine that seven of these parameters share the same value among all the strains, while three parameters concerning biomass maximum growth rate, and ethanol production due to biomass and glucose had specific values for each strain. These values are presented with their corresponding standard error and 95% confidence interval. The goodness of fit of our system was evaluated both qualitatively by in silico experimentation and quantitative by means of the coefficient of determination and the Akaike Information Criterion. Results regarding the fitting capabilities were compared with the classic model given by the logistic, Pirt, and Luedeking-Piret Equations. Further, nonlinear theories were applied to investigate local and global dynamics of the system, the Localization of Compact Invariant Sets Method was applied to determine the so-called localizing domain, i.e., lower and upper bounds for each variable; whilst Lyapunov's stability theories allowed to establish sufficient conditions to ensure asymptotic stability in the nonnegative octant, i.e., R+,03. Finally, the predictive ability of our mechanistic model was explored through several numerical simulations with expected results according to microbiology literature on batch fermentation.\n\nMechanistic Modelling of Biomass Growth, Glucose Consumption and Ethanol Production by Kluyveromyces marxianus in Batch Fermentation.", "token_count": 454, "char_count": 2052, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:17.760487", "source": { "split": "train_shard_00000", "doc_id": 4952 }, "chunk_id": "train_shard_00000_4952_0", "global_id": 5602 }, { "text": "The Cre-loxP system produces structural variations, such as deletion, duplication, inversion and translocation, at specific loci and induces chromosomal rearrangements in the genome. To achieve chromosomal rearrangements in Kluyveromyces marxianus, the positions and sequences of centromeres were identified in this species for the first time. Next, a Cre-loxP system was established in K. marxianus. In this system, the Cre recombinase was expressed from a leaky LAC4 promoter in a plasmid to alleviate the cytotoxicity of Cre, and the unstable plasmid contained a panARS element to facilitate the clearance of the plasmid from the cells. By using LAC4 as a reporter gene, the recombination frequencies between loxP sites or loxPsym sites were 99% and 73%, respectively. A K. marxianus strain containing 16 loxPsym sites in the genome was constructed. The recombination frequency of large-scale chromosomal rearrangements between 16 loxPsym sites was up to 38.9%. Our study provides valuable information and tools for studying chromosomal structures and functions in K. marxianus.\n\nEstablishment of a Cre-loxP System Based on a Leaky LAC4 Promoter and an Unstable panARS Element in Kluyveromyces marxianus.", "token_count": 377, "char_count": 1263, "word_count": 178, "semantic_coherence": 1, "information_density": 0.5506, "quality_score": 0.7753, "entities": { "genes": [ "LAC4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:18.345132", "source": { "split": "train_shard_00000", "doc_id": 4953 }, "chunk_id": "train_shard_00000_4953_0", "global_id": 5603 }, { "text": "Cholera is a diarrhoeal disease caused by Vibrio cholerae . It remains a major public health challenge in the endemic region around the Bay of Bengal. Over decadal time scales, one lineage typically dominates the others and spreads in global pandemic waves. However, it remains unclear to what extent diverse lineages co-circulate during a single outbreak season. Defining the pool of diversity during finer time scales is important because the selective pressures that impact V. cholerae – namely antibiotics and phages – are dynamic on these time scales. To study the nationwide diversity of V. cholerae , we long-read sequenced 273 V. cholerae genomes from seven hospitals over one year (2018) in Bangladesh. Four major V. cholerae lineages were identified: known lineages BD-1, BD-2a, and BD-2b, and a novel lineage that we call BD-3. In 2022, BD-1 caused a large cholera outbreak in Dhaka, apparently outcompeting BD-2 lineages. We show that, in 2018, BD-1 was already dominant in the five northern regions, including Dhaka, consistent with an origin from India in the north. By contrast, we observed a higher diversity of lineages in the two southern regions near the coast. The four lineages differed in pangenome content, including integrative and conjugative elements (ICEs) and genes involved in resistance to bacteriophages and antibiotics. Notably, BD-2a lacked an ICE and is predicted to be more sensitive to phages and antibiotics, but nevertheless persisted throughout the year-long sampling period. Genes associated with antibiotic resistance in V. cholerae from Bangladesh in 2006 were entirely absent from all lineages in 2018-19, suggesting shifting costs and benefits of encoding these genes. Together, our results highlight the dynamic nature of the V. cholerae pangenome and the geographic structure of its lineage diversity.\n\nVibrio choleraelineage and pangenome diversity varies geographically across Bangladesh over one year", "token_count": 508, "char_count": 1956, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:18.998530", "source": { "split": "train_shard_00000", "doc_id": 4954 }, "chunk_id": "train_shard_00000_4954_0", "global_id": 5604 }, { "text": "The Haloferacaceae are a family of extremely halophilic archaea with many species producing enzymes and products beneficial for industrial biotechnology. They are, however, relatively under-characterised with regards to genetics and gene products. This study aims to use existing sequence data to highlight genetic diversity, create pangenomes for three genera, and provide secondary metabolite and pathway analysis. This will establish current knowledge and identify key gaps in research. We show that the Haloferacaceae have significant genetic diversity between genera, with numerous gene gain and loss events in key genera. It also found that the model genus, Haloferax, has relatively low identified secondary metabolites compared to other genera within the family. Additionally, this study has identified potential biotechnology targets for heterologous expression in model organisms.\n\nComparative genomics of the highly halophilic Haloferacaceae.", "token_count": 198, "char_count": 953, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7385, "quality_score": 0.8692, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:19.455777", "source": { "split": "train_shard_00000", "doc_id": 4955 }, "chunk_id": "train_shard_00000_4955_0", "global_id": 5605 }, { "text": "Saline lakes are extreme habitats that host unique microbial communities with high biotechnological potential. In this study, a novel strain, designated Q87T, was isolated from Gaxiukule Lake, a high-altitude magnesium sulfate-type saline lake in the Qaidam Basin, China. A polyphasic taxonomic approach, including morphological, physiological, chemotaxonomic, phylogenetic, and genomic analyses, was applied to characterize the isolate. Strain Q87T is a Gram-stain-negative, non-motile, rod-shaped bacterium showing high tolerance to salinity (0-15.0 %, w/v; optimum 5.0 %) and alkalinity (pH 6.0-10.5; optimum pH 7.0), with a temperature range for growth of 10-40 °C (optimum 32 °C). Phylogenetic and genomic analyses confirmed its affiliation with the genus Gracilimonas and revealed it as a distinct species. The genome of strain Q87T (3.3 Mb, G + C 41.5 %) encodes diverse functional genes associated with nitrogen and sulfur metabolism, stress adaptation, and biosynthesis of secondary metabolites, including terpenoids and polyketides. Comparative analyses with reference Gracilimonas strains demonstrated its unique genomic features and ecological adaptability. Structural modeling confirmed functional conservation of key enzymes involved in nitrogen detoxification and sulfide oxidation. Pangenome analysis highlighted the genetic diversity and open nature of the species of the genus Gracilimonas. Biogeographic assessments suggest a wide distribution of the genus in saline environments, especially in sediments. This study expands our understanding of the genus Gracilimonas taxonomy, physiology, and ecological potential, and underscores the importance of extremophilic bacteria as promising resources for environmental and industrial biotechnology.", "token_count": 516, "char_count": 1838, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:20.114438", "source": { "split": "train_shard_00000", "doc_id": 4956 }, "chunk_id": "train_shard_00000_4956_0", "global_id": 5606 }, { "text": "<i>Gracilimonas qinghaiensis</i> sp. nov., a halophilic bacterium from a high-altitude saline lake exhibiting diverse metabolic potential and ecological adaptation.", "token_count": 57, "char_count": 176, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:20.479761", "source": { "split": "train_shard_00000", "doc_id": 4956 }, "chunk_id": "train_shard_00000_4956_1", "global_id": 5607 }, { "text": "Fusobacterium nucleatum is an anaerobic commensal of the oral cavity associated with periodontitis and extra-oral diseases, including colorectal cancer. Previous studies have shown an increased relative abundance of this bacterium associated with oral dysplasia or within oral tumours. Using direct culture, we found that 75 % of Fusobacterium species isolated from malignant or potentially malignant oral mucosa were F. nucleatum subsp. polymorphum. Whole genome sequencing and pangenome analysis with Panaroo was carried out on 76 F. nucleatum subsp. polymorphum genomes. F. nucleatum subsp. polymorphum was shown to possesses a relatively small core genome of 1604 genes in a pangenome of 7363 genes. Phylogenetic analysis based on the core genome shows the isolates can be separated into three main clades with no obvious genotypic associations with disease. Isolates recovered from healthy and diseased sites in the same patient are generally highly related. A large repertoire of adhesins belonging to the type V secretion system (TVSS) could be identified with major variation in repertoire and copy number between strains. Analysis of intergenic recombination using fastGEAR showed that adhesin complement is shaped by horizontal gene transfer and recombination. Recombination events at TVSS adhesin genes were not only common between lineages of subspecies polymorphum, but also between different subspecies of F. nucleatum. Strains of subspecies polymorphum with low copy numbers of TVSS adhesin encoding genes tended to have the weakest adhesion to oral keratinocytes. This study highlights the genetic heterogeneity of F. nucleatum subsp. polymorphum and provides a new framework for defining virulence in this organism.", "token_count": 513, "char_count": 1830, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6508, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:21.110604", "source": { "split": "train_shard_00000", "doc_id": 4957 }, "chunk_id": "train_shard_00000_4957_0", "global_id": 5608 }, { "text": "Fusobacterium nucleatum subsp. polymorphum recovered from malignant and potentially malignant oral disease exhibit heterogeneity in adhesion phenotypes and adhesin gene copy number, shaped by inter-subspecies horizontal gene transfer and recombination-derived mosaicism.", "token_count": 79, "char_count": 284, "word_count": 31, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:21.490247", "source": { "split": "train_shard_00000", "doc_id": 4957 }, "chunk_id": "train_shard_00000_4957_1", "global_id": 5609 }, { "text": "

Background

Over the past two decades, Corynebacterium striatum has been increasingly isolated from clinical cultures with most isolates showing increased antimicrobial resistance (AMR) to last resort agents. Advances in the field of pan genomics would facilitate the understanding of the clinical significance of such bacterial species previously thought to be among commensals paving the way for identifying new drug targets and control strategies.

Methods

We constructed a pan-genome using 310 genome sequences of C. striatum. Pan-genome analysis was performed using three tools including Roary, PIRATE, and PEPPAN. AMR genes and virulence factors have been studied in relation to core genome phylogeny. Genomic Islands (GIs), Integrons, and Prophage regions have been explored in detail.

Results

The pan-genome ranges between a total of 5253-5857 genes with 2070 - 1899 core gene clusters. Some antimicrobial resistance genes have been identified in the core genome portion, but most of them were located in the dispensable genome. In addition, some well-known virulence factors described in pathogenic Corynebacterium species were located in the dispensable genome. A total of 115 phage species have been identified with only 44 intact prophage regions.

Conclusion

This study presents a detailed comparative pangenome report of C. striatum. The species show a very slowly growing pangenome with relatively high number of genes in the core genome contributing to lower genomic variation. Prophage elements carrying AMR and virulence elements appear to be infrequent in the species. GIs appear to offer a prominent role in mobilizing antibiotic resistance genes in the species and integrons occur at a frequency of 50% in the species. Control strategies should be directed against virulence and resistance determinants carried on the core genome and those frequently occurring in the accessory genome.\n\nPangenome analysis of Corynebacterium striatum: insights into a neglected multidrug-resistant pathogen.", "token_count": 503, "char_count": 2037, "word_count": 286, "semantic_coherence": 1, "information_density": 0.5804, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:22.145643", "source": { "split": "train_shard_00000", "doc_id": 4958 }, "chunk_id": "train_shard_00000_4958_0", "global_id": 5610 }, { "text": "In 2017 an outbreak of Mycoplasma bovis (M. bovis), an infectious agent of cattle, was identified in Aotearoa New Zealand. This study characterizes the genomic population structure of the outbreak in New Zealand and compares it with the known global population structure using multilocus sequence typing (MLST) and genomic analysis. The New Zealand outbreak strain was MLST genotyped as ST21. A comprehensive collection of 840 genomes from the New Zealand outbreak showed a pattern of clonal expansion when characterized by MLST, core genome MLST (cgMLST) and whole genome MLST (wgMLST). A lineage of genomes was found with no in silico identifiable pta2 locus, a housekeeping gene used in the MLST scheme. We compared a sample set of 40 New Zealand genomes to 47 genomes from other countries. This group had 79 ST21 genomes and eight genomes that were single nucleotide polymorphism (SNP) variants within the MLST loci of ST21. Two of the 47 international genomes showed signs of extensive unique recombination. Unique alleles in six genes were identified as present only in the New Zealand genomes. These novel variants were in the genes; haeIIIM encoding for cytosine-specific methyltransferase, cysC encoding for cysteinyl tRNA synthetase, era encoding for GTPase Era, metK encoding for S-adenosylmethionine synthase, parE encoding for DNA topoisomerase, and hisS encoding for histidine-tRNA ligase. This finding could be due to a population bottleneck, genetic drift, or positive selection. The same sample set of 40 New Zealand genomes were compared using MLST to 404 genomes from 15 other countries and 11 genomes without a known country. A FastBAPS analysis of 455 genomes showed a global population structure with 11 clusters", "token_count": 505, "char_count": 1790, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5667, "quality_score": 0.7833, "entities": { "genes": [ "ST21" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:22.802359", "source": { "split": "train_shard_00000", "doc_id": 4959 }, "chunk_id": "train_shard_00000_4959_0", "global_id": 5611 }, { "text": "Some countries, such as Canada, Denmark and Australia contained both internally closely related genomes and some genomes that were more closely related to genomes found in other countries. Our results support the need for Whole Genome Sequencing (WGS) as well as MLST genotyping in M. bovis outbreaks. They also support the importance of understanding the national and international movement patterns of cattle and their genetic material, as possible routes of transmission, when managing the spread of M. bovis.\n\nGenomic analysis of the 2017 Aotearoa New Zealand outbreak of <i>Mycoplasma bovis</i> and its position within the global population structure.", "token_count": 167, "char_count": 682, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7449, "quality_score": 0.8724, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:23.242720", "source": { "split": "train_shard_00000", "doc_id": 4959 }, "chunk_id": "train_shard_00000_4959_1", "global_id": 5612 }, { "text": "Klebsiella pneumoniae sensu stricto (KpI) is an opportunistic pathogen capable of residing as a commensal in both human and bovine intestinal tracts and can cause serious systemic infections in humans and severe clinical mastitis in dairy cattle. It is unclear what role zoonotic and anthroponotic transmission play in the dissemination of KpI. In this study, we use a comparative genomic approach to identify differences between KpI associated with disease in humans and cattle and aimed to identify any potential genetic barriers limiting transmission of KpI between these two hosts. A total of 128 KpI strains (bovine n = 65; human n = 63) were whole genome sequenced and human and bovine strains were compared based on phylogenomics, the pangenome, mobile genetic elements, and differential gene abundance. No obvious phylogenomic differentiation was observed between isolates from these hosts. However, subtle genetic differences exist between bovine and human KpI which likely reflect environmental adaptation to different host niches, including a higher representation of gene clusters encoding ferric citrate uptake transporters, as well as histidine, arginine, and lactose utilization pathways in bovine isolates. These gene clusters may be positively selected due to the unique metabolic environment of the mammary gland, where lactose, citrate-bound iron, and amino acids like histidine and arginine provide growth advantages for KpI during mastitis. Overall, our study identified no obvious genetic barriers to zoonotic transmission of KpI within the dairy environment and provides insight into the development of host-specific therapeutic options for KpI infections in humans and bovine.\n\nSubtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation.", "token_count": 458, "char_count": 1830, "word_count": 261, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:23.881992", "source": { "split": "train_shard_00000", "doc_id": 4960 }, "chunk_id": "train_shard_00000_4960_0", "global_id": 5613 }, { "text": "Kluyveromyces marxianus is an emerging non-conventional food-grade yeast that is generally isolated from diverse habitats, like kefir grain, fermented dairy products, sugar industry sewage, plants, and sisal leaves. A unique set of beneficial traits, such as fastest growth, thermotolerance, and broad substrate spectrum (i.e., hemi-cellulose hydrolysates, xylose, l-arabinose, d-mannose, galactose, maltose, sugar syrup molasses, cellobiose, and dairy industry) makes this yeast a particularly attractive host for applications in a variety of food and biotechnology industries. In contrast to Saccharomyces cerevisiae, most of the K. marxianus strains are apparently Crabtree-negative or having aerobic-respiring characteristics, and unlikely to endure aerobic alcoholic fermentation. This is a desirable phenotype for the large-scale biosynthesis of products associated with biomass formation because the formation of ethanol as an undesirable byproduct can be evaded under aerobic conditions. Herein, we discuss the current insight into the potential applications of K. marxianus as a robust yeast cell factory to produce various industrially pertinent enzymes, bioethanol, cell proteins, probiotic, fructose, and fructo-oligosaccharides, and vaccines, with excellent natural features. Moreover, the biotechnological improvement and development of new biotechnological tools, particularly CRISPR-Cas9-assisted precise genome editing in K. marxianus are delineated. Lastly, the ongoing challenges, concluding remarks, and future prospects for expanding the scope of K. marxianus utilization in modern biotechnology, food, feed, and pharmaceutical industries are also thoroughly vetted. In conclusion, it is critical to apprehend knowledge gaps around genes, metabolic pathways, key enzymes, and regulation for gaining a complete insight into the mechanism for producing relevant metabolites by K. marxianus.", "token_count": 523, "char_count": 1958, "word_count": 249, "semantic_coherence": 1, "information_density": 0.7108, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:24.582891", "source": { "split": "train_shard_00000", "doc_id": 4961 }, "chunk_id": "train_shard_00000_4961_0", "global_id": 5614 }, { "text": "Bioprospecting Kluyveromyces marxianus as a Robust Host for Industrial Biotechnology.", "token_count": 33, "char_count": 92, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:24.952769", "source": { "split": "train_shard_00000", "doc_id": 4961 }, "chunk_id": "train_shard_00000_4961_1", "global_id": 5615 }, { "text": "In humans, Pseudomonas aeruginosa is well known as a prominent opportunistic pathogen associated with antimicrobial resistance (AMR), which presents a major challenge to successful treatment. This is also the case in animals, particularly in companion dogs where P. aeruginosa is a common cause of otitis. Despite its clinical significance, little data are available on the genomics and epidemiology of P. aeruginosa in dogs. To address this, we have genome-sequenced 34 canine otitis P. aeruginosa isolates from a veterinary referral hospital and analysed these along with a further 62 publicly available genomes from canine isolates. Phylogenetic analysis revealed that all three P. aeruginosa phylogroups, A-C, are represented amongst a diverse bacterial population isolated from dogs. We identify examples of persistent or recurrent infection by the same strain of up to 309 days between sampling, demonstrating the difficulty of successfully eradicating infection. Isolates encoded a variety of AMR genes with genomic and phenotypic AMR correlating poorly for β-lactams but showing complete concordance between fluoroquinolone resistance and quinolone resistance-determining regions (QRDRs) of DNA gyrase and topoisomerase IV. Pangenome-wide analysis between 80 canine otitis isolates (34 newly sequenced here and a further 46 publicly available) and a reference collection of 491 human isolates found no genes which were over-represented or specific to either host species, indicating similar strains infect both humans and dogs. This agrees with the sharing of multilocus sequence types between dogs and humans, including the isolation here of ST235 from three dogs, a lineage prominent among the multidrug resistant (MDR) and extensively drug-resistant (XDR) international high-risk clones of P. aeruginosa causing human infections. The presence of such 'high-risk' clones in companion dogs is concerning given their potential impact on animal health and the potential for zoonotic spread", "token_count": 514, "char_count": 2052, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:25.613760", "source": { "split": "train_shard_00000", "doc_id": 4962 }, "chunk_id": "train_shard_00000_4962_0", "global_id": 5616 }, { "text": "These data provide new insight into this difficult-to-treat veterinary pathogen and promote the need for a One Health approach to tackling it.\n\nGenomic characterization of <i>Pseudomonas aeruginosa</i> from canine otitis highlights the need for a One Health approach to this opportunistic pathogen.", "token_count": 79, "char_count": 310, "word_count": 42, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:26.034295", "source": { "split": "train_shard_00000", "doc_id": 4962 }, "chunk_id": "train_shard_00000_4962_1", "global_id": 5617 }, { "text": "Roseburia intestinalis is one of the most abundant and important butyrate-producing human gut anaerobic bacteria that plays an important role in maintaining health and is a potential next-generation probiotic. We investigated the pangenome of 16 distinct strains, isolated over several decades, identifying local and time-specific adaptations. More than 50% of the genes in each individual strain were assigned to the core genome, and 77% of the cloud genes were unique to individual strains, revealing the high level of genome conservation. Co-carriage of the same enzymes involved in carbohydrate binding and degradation in all strains highlighted major pathways in carbohydrate utilization and reveal the importance of xylan, starch and mannose as key growth substrates. A single strain had adapted to use rhamnose as a sole growth substrate, the first time this has been reported. The ubiquitous presence of motility and sporulation gene clusters demonstrates the importance of these phenotypes for gut survival and acquisition of this bacterium. More than half the strains contained functional, potentially transferable, tetracycline resistance genes. This study advances our understanding of the importance of R. intestinalis within the gut ecosystem by elucidating conserved metabolic characteristics among different strains, isolated from different locations. This information will help to devise dietary strategies to increase the abundance of this species providing health benefits.\n\nNovel insights into carbohydrate utilisation, antimicrobial resistance, and sporulation potential in <i>Roseburia intestinalis</i> isolates across diverse geographical locations.", "token_count": 395, "char_count": 1698, "word_count": 231, "semantic_coherence": 1, "information_density": 0.671, "quality_score": 0.8355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:26.657807", "source": { "split": "train_shard_00000", "doc_id": 4963 }, "chunk_id": "train_shard_00000_4963_0", "global_id": 5618 }, { "text": "

Design:

ing CRISPR single guide RNA (sgRNA) libraries targeting entire kingdoms of life will significantly advance genetic research in diverse and underexplored taxa. Current sgRNA design tools are often species-specific and fail to scale to large, phylogenetically diverse datasets, limiting their applicability to comparative genomics, evolutionary studies, and biotechnology. Here, we present ALLEGRO, a combinatorial optimization algorithm able to design minimal, yet highly effective sgRNA libraries targeting thousands of species. Leveraging integer linear programming, ALLEGRO identified compact sgRNA sets simultaneously targeting several genes of interest for over 2,000 species across the fungal kingdom. We experimentally validated the sgRNAs designed by ALLEGRO in Kluyveromyces marxianus, Komagataella phaffii , and Yarrowia lipolytica . In addition, we adopted a generalized Cas9-Ribonucleoprotein delivery system coupled with protoplast transformation to extend ALLEGRO’s sgRNA libraries to other untested fungal genomes, such as Rhodotorula araucariae . Our experimental results, along with cross-validation, show that ALLEGRO enables efficient CRISPR genome editing, supporting the development of universal sgRNA libraries applicable to entire taxonomic groups.\n\nKingdom-Wide CRISPR Guide Design with ALLEGRO", "token_count": 329, "char_count": 1335, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7558, "quality_score": 0.8779, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:27.226332", "source": { "split": "train_shard_00000", "doc_id": 4964 }, "chunk_id": "train_shard_00000_4964_0", "global_id": 5619 }, { "text": "

Background

Microbacterium paraoxydans is known for its potential in bioremediation and biotechnological applications, including promoting plant growth. However, research on this bacterium in Bangladesh has been limited and until now no reported complete genome of M. paraoxydans is available from this country. In this study, we have reported the complete genome of M. paraoxydans BHS25, the first case in Bangladesh, isolated from arsenic-contaminated soil in Bogura.

Results

Complete genome analysis revealed that BHS25 was closely related to Microbacterium paraoxydans LTR1 from Russia, which itself showed similarity to a strain found at the International Space Station, reported to be resistant to extreme conditions. BHS25 possessed a genome of 3.49 Mb with a GC content of 70.12%, comprising 3,415 protein-coding genes, 47 tRNA genes, and 5 rRNA genes. It carried various heavy metal resistance genes and gene islands, such as arsC, arsB, and acr3 for arsenic detoxification/transformation, as well as czcD and copB for resistance to cadmium, zinc, cobalt, and copper. The arrangement of the arsenic resistance genes showed similarity to that in other reported Microbacterium strains, although pangenome and ANI analyses indicated considerable genetic diversity within the species. Additionally, the presence of vanY within the vanB cluster suggested potential vancomycin resistance. Metabolic pathway analyses revealed that BHS25 was well adapted, with different carbohydrate and amino acid metabolism, secondary metabolite biosynthesis, and xenobiotic degradation capabilities", "token_count": 411, "char_count": 1600, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6727, "quality_score": 0.8364, "entities": { "genes": [ "BHS25", "LTR1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:27.852997", "source": { "split": "train_shard_00000", "doc_id": 4965 }, "chunk_id": "train_shard_00000_4965_0", "global_id": 5620 }, { "text": "The unique notable anabolic pathways were streptomycin biosynthesis with 14 associated genes, novobiocin biosynthesis and tropane, piperidine, and pyridine alkaloid biosynthesis (8 genes each), as well as monobactam biosynthesis, prodigiosin biosynthesis, and penicillin and cephalosporin biosynthesis, suggesting a potential for production of antimicrobials. Furthermore, it showed an auxin biosynthesis pathway for plant growth, further demonstrating its biotechnological potential.

Conclusion

This research identified Microbacterium paraoxydans BHS25 as a promising candidate for bioremediation and sustainable environmental management, offering insights into microbial adaptation to challenging environments and potential solutions for pollution encounters.\n\nComparative genomic and functional analyses of Microbacterium paraoxydans BHS25 reveal key metabolic adaptations for survival in arsenic-contaminated soil ecosystems.", "token_count": 241, "char_count": 936, "word_count": 106, "semantic_coherence": 1, "information_density": 0.783, "quality_score": 0.8915, "entities": { "genes": [ "BHS25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:28.333795", "source": { "split": "train_shard_00000", "doc_id": 4965 }, "chunk_id": "train_shard_00000_4965_1", "global_id": 5621 }, { "text": "Bacillus subtilis is central to Asian fermented soybean foods, including Japanese natto. To explore the genomic boundaries of B. subtilis var. natto , we conducted a comparative pangenome analysis of 42 strains, including the core natto clade (n=26) and its closest relatives. Our analysis revealed a striking evolutionary paradox centered on a single strain isolated from Indian bekang. Core-genome phylogenetic analysis places this bekang strain clearly outside the tight natto clade, with a Nepalese kinema strainbeing its closest systematic neighbor. In stark contrast, quantitative analysis of accessory gene profiles revealed this single bekang strain is the functional nearest neighbor to the natto clade, sharing a highly conserved accessory gene repertoire. This shared profile defines a “natto-type” adaptive strategy (the “broad-sense natto group,” n=27), separating it from other related strains. Analysis of this group-specific repertoire revealed an enrichment of transcriptional regulators and metabolic enzymes. This finding provides a compelling case study (n=1) of polygenic adaptation, suggesting complex evolutionary pathways, such as horizontal gene transfer or selective retention, can drive rapid adaptation across disparate lineages.\n\nConserved accessory genes link a phylogenetically distinct Bacillus subtilis strain from Indian bekang to the Japanese natto clade", "token_count": 334, "char_count": 1400, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6911, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:28.905314", "source": { "split": "train_shard_00000", "doc_id": 4966 }, "chunk_id": "train_shard_00000_4966_0", "global_id": 5622 }, { "text": "Ethyl acetate is at present exclusively produced from fossil resources. Microbial synthesis of this ester from sugar-rich waste as an alternative is an aerobic process. Ethyl acetate is highly volatile and therefore stripped with the exhaust gas from the bioreactor which enables in situ product recovery. Previous research on microbial formation of ethyl acetate has focused on the kinetics of ester synthesis and in part on the ester stripping, while the separation of the ester from the exhaust gas has hardly been investigated. A mixed matrix membrane was developed consisting of Silikalite-1 embedded in polydimethylsiloxane which was installed in a radial-symmetrical membrane module. Evaluation of the separation of ethyl acetate was based on the analysis of the composition of the feed and retentate gas by mass spectrometry. The separation efficiency of the membrane was first tested with varied flows of artificial exhaust gas, containing defined amounts of ethyl acetate. A model for describing the separation process was parametrized by the measured data and used to design a real separation experiment. Ethyl acetate produced from delactosed whey permeate by Kluyveromyces marxianus DSM 5422 in a stirred bioreactor gassed with 0.5 vvm air was successfully separated from the exhaust gas by membranes; 93.6% of the stripped ester was separated. Liquid ethyl acetate was recovered by cooling the permeate gas to ‒78°C, whereby 99.75% of the condensed organic compounds were ethyl acetate. This study demonstrates for the first time that microbially produced and stripped ethyl acetate can be effectively separated from the exhaust gas of bioreactors by membrane technology to obtain the ester in high yield and purity.\n\nIn situ Product Recovery of Microbially Synthesized Ethyl Acetate from the Exhaust Gas of a Bioreactor by Membrane Technology.", "token_count": 458, "char_count": 1865, "word_count": 284, "semantic_coherence": 1, "information_density": 0.4965, "quality_score": 0.7482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:29.541851", "source": { "split": "train_shard_00000", "doc_id": 4967 }, "chunk_id": "train_shard_00000_4967_0", "global_id": 5623 }, { "text": "Kluyveromyces marxianus is a yeast capable of fermenting sugars into ethanol and growing at high temperatures (37 degrees C). However, it is less tolerant to ethanol than Saccharomyces cerevisiae, which limits its application in second-generation ethanol production. Since the mechanisms of ethanol stress response are still poorly described, especially compared to S. cerevisiae, we used an integrative multi-omics approach, combining transcriptomics, co-expression networks, gene regulation, and genome-scale metabolic modelling to gain insights about these mechanisms. Through metabolic modelling, we predicted the occurrence of a respiro-fermentative metabolism and its onset as the dilution rate increased. From gene co-expression networks, we detected that the protein quality control system is a main mechanism involved in the ethanol stress response. Further, we identified key regulators in the ethanol stress response, such as HAP3, MET4, and SNF2, and assessed how disturbances in their gene expression affect cellular metabolism. We also found that amino acid metabolism, membrane lipid metabolism, and ergosterol exhibit increased metabolic flux under the explored conditions. These findings provide useful cues to develop and implement genetic and metabolic engineering strategies to enhance ethanol tolerance.\n\nMulti-omics data and model integration reveal the main mechanisms associated with respiro-fermentative metabolism and ethanol stress responses in Kluyveromyces marxianus", "token_count": 347, "char_count": 1495, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6816, "quality_score": 0.8408, "entities": { "genes": [ "SNF2", "HAP3", "MET4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:30.128404", "source": { "split": "train_shard_00000", "doc_id": 4968 }, "chunk_id": "train_shard_00000_4968_0", "global_id": 5624 }, { "text": "Comparative genomics has emerged as a pivotal methodology for elucidating genetic variations in microbial studies. However, conventional analytical approaches for diploid and polyploid microorganisms have demonstrated limited efficacy in discriminating new mutations from background heterozygosity. This study presents an innovative microbial comparative genomics framework adapted from tumor-normal sequencing methodology. Our approach establishes the original strain as the “normal sample” and the derived strain as the “tumor sample”, enabling precise identification of new mutations (“somatic variants”) while filtering pre-existing heterozygous sites (“germline variations”). The analytical pipeline also includes assessment of loss-of-heterozygosity (LOH) events and genome-wide detection of copy number variations (CNVs) with resolution to identify both regional CNV and whole-chromosome aneuploidy through integrated CNV and variant allele frequency analysis. We validated this framework using diploid Saccharomyces cerevisiae strains before successfully extending its application to Kluyveromyces marxianus , Candida spp., and Hortaea werneckii , encompassing haploid, diploid, polyploid, and aneuploid states. The methodology revealed previously undetected variations across experimental evolution studies, demonstrating superior resolution compared to conventional approaches. This adaptable platform establishes a new paradigm for microbial genome studies, particularly for organisms with diploid or polyploid states where traditional comparative genomics methods prove inadequate.\n\nAdvancing Microbial Comparative Genomics Through Tumor-Normal Inspired Framework", "token_count": 378, "char_count": 1675, "word_count": 200, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:30.710260", "source": { "split": "train_shard_00000", "doc_id": 4969 }, "chunk_id": "train_shard_00000_4969_0", "global_id": 5625 }, { "text": "Thermotolerance is an attractive feature for yeast-based industrial ethanol production. However, incompletely understood oxygen requirements of known thermotolerant yeasts are incompatible with process requirements. To study the magnitude and molecular basis of these oxygen requirements in the facultatively fermentative, thermotolerant yeast Ogataea parapolymorpha , chemostat studies were performed under defined oxygen-sufficient and oxygen-limited cultivation regimes. The minimum oxygen requirements of O. parapolymorpha were found to be at least an order of magnitude larger than those of the thermotolerant yeast Kluyveromyces marxianus . This high oxygen requirement coincided with absence of glycerol formation, which plays a key role in NADH reoxidation in oxygen-limited cultures of other facultatively fermentative yeasts. Co-feeding of acetoin, whose reduction to 2,3-butanediol can reoxidize cytosolic NADH, supported a 2.5-fold higher biomass concentration in oxygen-limited cultures. The apparent inability of O. parapolymorpha to produce glycerol correlated with absence of orthologs of the S. cerevisiae genes encoding glycerol-3P phosphatase (Sc GPP1 , Sc GPP2 ). Glycerol production was observed in aerobic batch cultures of a strain in which genes including key enzymes in mitochondrial reoxidation of NADH were deleted. However, transcriptome analysis did not identify a clear candidate for the responsible phosphatase. Expression of Sc GPD2 , encoding NAD + -dependent glycerol-3P dehydrogenase, and Sc GPP1 in O. parapolymorpha resulted in increased glycerol production in oxygen-limited chemostats, but glycerol production rates remained substantially lower than observed in S. cerevisiae and K. marxianus . These results identify a dependency on aerobic respiration for reoxidation of NADH generated in biosynthesis as a key factor in the unexpectedly high oxygen requirements of O. parapolymorpha ", "token_count": 488, "char_count": 1925, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [ "GPP1", "GPP2", "GPD2" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:31.364933", "source": { "split": "train_shard_00000", "doc_id": 4970 }, "chunk_id": "train_shard_00000_4970_0", "global_id": 5626 }, { "text": "

Importance

Thermotolerant yeasts hold great potential for anaerobic fermentation processes but their application is so far hampered by incompletely understood oxygen requirements. Based on quantitative physiological studies in oxygen-limited chemostat cultures, this study shows that the thermotolerant yeast Ogataea parapolymorpha has a much higher oxygen requirement than other, previously investigated facultatively fermentative yeasts. The large oxygen requirement of O. parapolymorpha was linked to an inability of oxygen-limited cultures to efficiently reoxidize NADH formed in biosynthetic processes by glycerol formation. These results provide a basis for reducing the oxygen requirements of O. parapolymorpha by targeted metabolic engineering. In addition, this study shows that diversity of oxygen requirements should be taken into account in selecting yeast species for application in anaerobic or oxygen-limited industrial processes.\n\nRe-oxidation of cytosolic NADH is a major contributor to the high oxygen requirements of the thermotolerant yeastOgataea parapolymorphain oxygen-limited cultures", "token_count": 264, "char_count": 1124, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6643, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:31.908219", "source": { "split": "train_shard_00000", "doc_id": 4970 }, "chunk_id": "train_shard_00000_4970_1", "global_id": 5627 }, { "text": "This study investigated the spoilage potential of yeast strains Kluyveromyces marxianus (Km1, Km2 and Km3), Pichia kudriavzevii Pk1 and Torulaspora delbrueckii Td1 grown in skyr in cold storage. Yeast strains were isolated from skyr and identified by sequencing of the 26S rRNA gene. K. marxianus yeasts were grown in skyr to high numbers, generating large amounts of volatile organic compounds (VOC) associated with off-flavours, among them were alcohols (3-methyl-1-butanol, 2-methyl-1-propanol and 1-hexanol), esters (ethyl acetate and 3-methylbutyl acetate) and aldehydes (hexanal, methylbutanal and methylpropanal). Growth of P. kudriavzevii Pk1 led to moderate increases in several alcohols and esters (mostly, 3-methyl-1-butanol and ethyl acetate), whereas only minor shifts in VOCs were associated with T. delbrueckii Td2. The levels of the key aroma compounds, diacetyl and acetoin, were significantly decreased by all K. marxianus strains and P. kudriavzevii Pk1. In contrast to the other yeast species, K. marxianus was able to utilize lactose, producing ethanol and carbon dioxide. Based on the overall results, K. marxianus was characterised by the highest spoilage potential. The study revealed the differences between the yeast species in fermentative and spoilage activities, and clarified the role of yeast metabolites for off-flavour formation and quality defects in skyr during cold storage.", "token_count": 494, "char_count": 1480, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:32.554444", "source": { "split": "train_shard_00000", "doc_id": 4971 }, "chunk_id": "train_shard_00000_4971_0", "global_id": 5628 }, { "text": "Spoilage Potential of Contaminating Yeast Species Kluyveromyces marxianus, Pichia kudriavzevii and Torulaspora delbrueckii during Cold Storage of Skyr.", "token_count": 69, "char_count": 172, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:32.919949", "source": { "split": "train_shard_00000", "doc_id": 4971 }, "chunk_id": "train_shard_00000_4971_1", "global_id": 5629 }, { "text": "In this study, the effect of mixed-strain fermentation using Kluyveromyces marxianus with either Lactobacillus plantarum or Pediococcus pentosaceus on the physiochemical and nutritional properties of white kidney bean flour sourdough was investigated. The results indicated that mixed-strain fermentation reduced the anti-nutritional factors produced from the white kidney bean flour, especially in the sourdough fermented by L. plantarum and K. marxianus (WKS-LK) compared to that by P. pentosaceus and K. marxianus (WKS-JK). Meanwhile, the content of lactic acid and acetic acid and the proportion of peptides with molecular weights ranging from <500 to 5000 Da were increased in the sourdoughs (WKS-LK > WKS-JK). Compared to the control (WK), microstructural characteristics of the dough seemed to be improved in WKS-LK followed by WKS-JK in terms of their corresponding gluten network consistency. Moreover, mixed fermentation led to a reduced starch digestibility accompanied by a higher content of resistant starch and slowly digestible starch. In contrast, protein digestibility was enhanced in WKS-LK and WKS-JK sourdough breads. More importantly, the changes in gut microbiota composition, short-chain fatty acid (SCFA) production, systemic inflammation, glucose tolerance and liver tissue histopathology following 21-day consumption of the sourdough bread were also evaluated via an animal model. The intake of sourdough breads reduced the abundance of the pathogenic microbiota Escherichia shigella", "token_count": 449, "char_count": 1572, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:33.558493", "source": { "split": "train_shard_00000", "doc_id": 4972 }, "chunk_id": "train_shard_00000_4972_0", "global_id": 5630 }, { "text": "In contrast, the corresponding abundance of Rikenellaceae, Akkermansiaceae, Erysipelotrichaceae, Prevotellaceae and Eubacterium coprostanoligenes was increased, followed by enhanced SCFA generation, with the highest in WKS-LK and then WKS-JK. Meanwhile, a reduced level of pro-inflammatory cytokines IL-1β, IL-6 and TNF-α in the serum and improved glucose tolerance and liver tissue histopathology following the bread consumption were also achieved in the order of WKS-LK, then WKS-JK mice compared to WK.\n\nCharacteristics of the microstructure and the key components of white kidney bean sourdough bread induced by mixed-strain fermentation and its influence on gut microbiota.", "token_count": 210, "char_count": 713, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:34.022078", "source": { "split": "train_shard_00000", "doc_id": 4972 }, "chunk_id": "train_shard_00000_4972_1", "global_id": 5631 }, { "text": "

Background

The lineage 4 (L4) of Mycobacterium tuberculosis (MTB) is not only globally prevalent but also locally dominant, surpassing other lineages, with lineage 2 (L2) following in prevalence. Despite its widespread occurrence, factors influencing the expansion of L4 and its sub-lineages remain poorly understood both at local and global levels. Therefore, this study aimed to conduct a pan-genome and identify genomic signatures linked to the elevated prevalence of L4 sublineages among extrapulmonary TB (EPTB) patients in western Ethiopia.

Methods

A cross-sectional study was conducted at an institutional level involving confirmed cases of extrapulmonary tuberculosis (EPTB) patients from August 5, 2018, to December 30, 2019. A total of 75 MTB genomes, classified under lineage 4 (L4), were used for conducting pan-genome and genome-wide association study (GWAS) analyses. After a quality check, variants were identified using MTBseq, and genomes were de novo assembled using SPAdes. Gene prediction and annotation were performed using Prokka. The pan-genome was constructed using GET_HOMOLOGUES, and its functional analysis was carried out with the Bacterial Pan-Genome Analysis tool (BPGA). For GWAS analysis, Scoary was employed with Benjamini-Hochberg correction, with a significance threshold set at p-value ≤ 0.05.

Results

The analysis revealed a total of 3,270 core genes, predominantly associated with orthologous groups (COG) functions, notably in the categories of '[R] General function prediction only' and '[I] Lipid transport and metabolism'. Conversely, functions related to '[N] Cell motility' and '[Q] Secondary metabolites biosynthesis, transport, and catabolism' were primarily linked to unique and accessory genes. The pan-genome of MTB L4 was found to be open", "token_count": 489, "char_count": 1810, "word_count": 250, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:34.667388", "source": { "split": "train_shard_00000", "doc_id": 4973 }, "chunk_id": "train_shard_00000_4973_0", "global_id": 5632 }, { "text": "Furthermore, the GWAS study identified genomic signatures linked to the prevalence of sublineages L4.6.3 and L4.2.2.2.

Conclusions

Apart from host and environmental factors, the sublineage of L4 employs distinct virulence factors for successful dissemination in western Ethiopia. Given that the functions of these newly identified genes are not well understood, it is advisable to experimentally validate their roles, particularly in the successful transmission of specific L4 sublineages over others.\n\nPangenome and genomic signatures linked to the dominance of the lineage-4 of Mycobacterium tuberculosis isolated from extrapulmonary tuberculosis patients in western Ethiopia.", "token_count": 170, "char_count": 685, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:35.116495", "source": { "split": "train_shard_00000", "doc_id": 4973 }, "chunk_id": "train_shard_00000_4973_1", "global_id": 5633 }, { "text": "This study produced biomass and valuable metabolites through fermentation of electro-activated whey (EA-whey), electro-activated whey permeate, and electro-activated lactose using Kluyveromyces marxianus ATCC 64884. The fermentation process was performed for 96 h at 30 °C and 150 rpm. The results showed that all substrates provided a satisfactory biomass growth and EA-whey achieved a maximum biomass of 4.23 g L⁻¹. Several major organic acids including lactic, acetic, citric, propionic acids were produced during the fermentation of all media, with differences between electro-activated and none-electro-activated substrates. K. marxianus produced various volatile aroma compounds such as ethanol, 2-phenylethanol, and isoamyl alcohol with valued organoleptic properties. The highest ethanol (28.13 g L⁻¹) was produced in the non-electro-activated whey. These findings suggest that electro-activation can be used to improve the performance of K. marxianus driven bioprocesses using whey-based substrates to produce valuable metabolites for different applications, including in foods.\n\nBioconversion of electro-activated lactose, whey and whey permeate to produce single cell protein, ethanol, aroma volatiles, organic acids and fat by Kluyveromyces marxianus", "token_count": 365, "char_count": 1262, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:35.702378", "source": { "split": "train_shard_00000", "doc_id": 4974 }, "chunk_id": "train_shard_00000_4974_0", "global_id": 5634 }, { "text": "Understanding the genetic characteristics of Aeromonas jandaei in Brazilian aquaculture is crucial for developing effective control strategies against this fish pathogen. The present study conducted a genomic analysis of Brazilian A. jandaei strains with the objective of investigating their virulence potential and resistance profiles. Four Brazilian isolates were subjected to sequencing, and comparative genomic analyses were conducted in conjunction with 48 publicly available A. jandaei genomes. The methods employed included quality assessment, de novo assembly, annotation, and analyses of antimicrobial resistance and virulence factors. The results demonstrated the presence of fluoroquinolone resistance genes within the core genome. Notably, these antibiotics are not authorized for use in aquaculture in Brazil, suggesting that their resistance determinants may originate from other selective pressures or horizontal gene transfer unrelated to aquaculture practices. The analysis identified significant virulence mechanisms, including T2SS, T3SS, and notably T6SS (vgrG3 gene), which was more prevalent in Brazilian isolates. Additionally, genes associated with motility, adhesion, and heavy metal resistance were identified. These findings highlight the enhanced adaptability of Brazilian A. jandaei strains and raise concerns about antimicrobial resistance in aquaculture, emphasizing the need for improved regulatory oversight and control strategies.\n\nIn Silico Characterization of Resistance and Virulence Genes in <i>Aeromonas jandaei</i> Strains Isolated from <i>Oreochromis niloticus</i> in Brazil.", "token_count": 408, "char_count": 1675, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:36.340878", "source": { "split": "train_shard_00000", "doc_id": 4975 }, "chunk_id": "train_shard_00000_4975_0", "global_id": 5635 }, { "text": "The aim of this study was to develop and evaluate the bioactive properties and storage stability of microcapsules (MCs) obtained by co‐encapsulation of the potential probiotic yeast Kluyveromyces marxianus VM004 and peanut skin polyphenolic extract (PSE) by spray drying, using whey protein concentrate (WPC) and water‐soluble chitosan (WSCh) as wall materials. The results showed that the selected wall materials provided protection to yeast during spray drying, storage, and simulated gastrointestinal conditions, obtaining better results for WPC and higher concentrations of PSE. Moreover, all formulations demonstrated cytoprotective effects against menadione‐induced oxidative stress in normal rat ileum epithelial cells (IEC‐18) at all concentrations and storage temperatures evaluated. These results suggest that the obtained MCs could be potential functional food ingredients, considering their antioxidant, cytoprotective, and potential probiotic properties.\n\nCo‐encapsulated of potential probiotic yeast Kluyveromyces marxianus and peanut skin polyphenolic extract as a functional ingredient", "token_count": 266, "char_count": 1101, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6901, "quality_score": 0.8451, "entities": { "genes": [ "VM004" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:36.911033", "source": { "split": "train_shard_00000", "doc_id": 4976 }, "chunk_id": "train_shard_00000_4976_0", "global_id": 5636 }, { "text": "Rice (Oryza sativa L.) is a vital global crop with a predominant presence in Asia, including Thailand. However, it faces a significant threat from bacterial blight disease (BB), primarily caused by Xanthomonas oryzae pv. oryzae (Xoo). This research aims to provide an insights into the genetic virulence and variation of Xoo strains isolated in Thailand. Our phylogenetic analysis unveils that the 20 Thai strains align with the Asian strains, setting them apart from African and USA strains. Remarkably, the Average Nucleotide Identity (ANI) values, in comparison to the Xanthomonas oryzae type strain 35933 (XO35933), consistently exceed 99%. These strains can be classified into three assigned ribosomal sequence types (rST). Our investigation into the pangenome and the phylogenetic relationships of these 20 Xoo genomes reveals a diverse genetic landscape, with the pangenome comprising 11,872 orthologous gene clusters, of which roughly 30% form the core genome. Notably, all of these genomes exhibit the presence of a CRISPR-Cas I-C array, indicative of their adaptive immune mechanisms. All strains belonged to BXO1 type LPS cassette with high identity. Furthermore, our analysis identifies two distinct types of plasmids, namely, Xanthomonas oryzae pv. oryzicola strain GX01 plasmid pXOCgx01 (A46, A57, A83, A112, D, and E) and the Xanthomonas oryzae strain AH28 plasmid pAH28 (A97). This genomic resource will be valuable for advancing research on surveillance, prevention, management, and comparative studies of this critical pathogen in the future.\n\nComplete genome and comparative analysis of Xanthomonas oryzae pv. oryzae isolated from northern Thailand", "token_count": 467, "char_count": 1667, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6653, "quality_score": 0.8327, "entities": { "genes": [ "BXO1", "AH28", "GX01", "XO35933" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:37.572568", "source": { "split": "train_shard_00000", "doc_id": 4977 }, "chunk_id": "train_shard_00000_4977_0", "global_id": 5637 }, { "text": "Understanding the origins of variation in agricultural pathogens is of fundamental interest and practical importance, especially for diseases that threaten food security. Fusarium oxysporum is among the most important of soil-borne pathogens, with a global distribution and an extensive host range. The pathogen is considered to be asexual, with horizontal transfer of chromosomes providing an analog of assortment by meiotic recombination. Here, we challenge those assumptions based on the results of population genomic analyses, describing the pathogen's diversity and inferring its origins and functional consequences in the context of a single, long-standing agricultural system. We identify simultaneously low nucleotide distance among strains, and unexpectedly high levels of genetic and genomic variability. We determine that these features arise from a combination of genome-scale recombination, best explained by widespread sexual reproduction, and presence-absence variation consistent with chromosomal rearrangement. Pangenome analyses document an accessory genome more than twice the size of the core genome, with contrasting evolutionary dynamics. The core genome is stable, with low diversity and high genetic differentiation across geographic space, while the accessory genome is paradoxically more diverse and unstable but with lower genetic differentiation and hallmarks of contemporary gene flow at local scales. We suggest a model in which episodic sexual reproduction generates haplotypes that are selected and then maintained through clone-like dynamics, followed by contemporary genomic rearrangements that reassort the accessory genome among sympatric strains. Taken together, these processes contribute unique genome content, including reassortment of virulence determinants that may explain observed variation in pathogenic potential.\n\nHiding in plain sight: Genome-wide recombination and a dynamic accessory genome drive diversity in Fusarium oxysporum f.sp. ciceris.", "token_count": 428, "char_count": 2014, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:38.255358", "source": { "split": "train_shard_00000", "doc_id": 4978 }, "chunk_id": "train_shard_00000_4978_0", "global_id": 5638 }, { "text": "Kluyveromyces marxianus accounts for > 90% of the yeast population of kefir, and recently, its probiotic potential has been actively explored with a focus on its health benefits and safety. Herein, the survivability of five kefir-isolated K. marxianus strains (Km A1-A5) in a simulated gastrointestinal (GI) environment was evaluated and compared with those of commercial probiotic yeast, Saccharomyces boulardii MYA-796. To further explore the potential to survive in the host GI tract, biochemical activities, hydrophobicity assay, biofilm formation, auto-aggregation analysis, and phenol tolerance of the strains were assessed. K. marxianus A4 exhibited the best survivability among all tested strains, including the clinically proven probiotic yeast strain S. boulardii MYA-796 (p = 0.014) in the artificial GI tract ranging from pH 2.0 to 7.5. In addition, the five K. marxianus strains and S. boulardii MYA-796 displayed different assimilation of lactose, xylitol, D-sorbitol, and DL-lactate, indicating that K. marxianus metabolized a wide range of substances and, thus, might be more feasible to nourish themselves in the host GI tract for survival. K. marxianus strains showed a greater hydrophobicity of cell surface, abilities to biofilm formation and auto-aggregation, and phenol tolerance than S. boulardii MYA-796, suggesting greater potential for survival in the host GI tract.\n\nSurvivability of Kluyveromyces marxianus Isolated From Korean Kefir in a Simulated Gastrointestinal Environment.", "token_count": 506, "char_count": 1590, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:38.918282", "source": { "split": "train_shard_00000", "doc_id": 4979 }, "chunk_id": "train_shard_00000_4979_0", "global_id": 5639 }, { "text": "Kluyveromyces marxianus has the ability to contribute to the aroma profile of foods and beverages since it is able to produce several volatile organic compounds (VOCs). In this study, 8 dairy K. marxianus strains, previously selected for their adhesion properties, were tested for VOCs production when grown in different conditions: planktonic, biofilm-detached, and MATS forming-cells. It was shown that biofilm-detached cells were mainly able to produce higher alcohols (64.57 mg/L), while esters were mainly produced by planktonic and MATS forming-cells (117.86 and 94.90 mg/L, respectively). Moreover, K. marxianus biofilm-detached cells were able to produce VOCs with flavor and odor impacts, such as ketons, phenols, and terpenes, which were not produced by planktonic cells. In addition, specific unique compounds were associated to the different conditions tested. Biofilm-detached cells were characterized by the production of 9 unique compounds, while planktonic and MATS forming-cells by 7 and 12, respectively. The obtained results should be exploited to modulate the volatilome of foods and beverages and improve the production of certain compounds at the industrial level. Further studies will be carried out to better understand the genetic mechanisms underlying the metabolic pathways activated under different conditions.\n\nInfluence of Different Aggregation States on Volatile Organic Compounds Released by Dairy Kluyveromyces marxianus Strains.", "token_count": 395, "char_count": 1490, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6117, "quality_score": 0.8058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:39.540484", "source": { "split": "train_shard_00000", "doc_id": 4980 }, "chunk_id": "train_shard_00000_4980_0", "global_id": 5640 }, { "text": "

Background

Mannoproteins, mannose-glycosylated proteins, play an important role in biological processes and have various applications in industries. Several methods have been already used for the extraction of mannoproteins from yeast cell-wall. The aim of this study was to evaluate the extraction and deproteinization of mannan oligosaccharide from the Kluyveromyces (K.) marxianus mannoprotein.

Methods

To acquire crude mannan oligosaccharides, K. marxianus mannoproteins were deproteinized by the Sevage, trichloroacetic acid, and hydrochloric acid (HCL) methods. Total nitrogen, crude protein content, fat, carbohydrate and ash content were measured according to the monograph prepared by the meeting of the Joint FAO/WHO Expert Committee and standard. Mannan oligosaccharide loss, percentage of deproteinization, and chemical composition of the product were assessed to check the proficiency of different methods.

Results

Highly purified (95.4%) mannan oligosaccharide with the highest deproteinization (97.33 ± 0.4%) and mannan oligosaccharide loss (25.1 ± 0.6%) were obtained following HCl method.

Conclusion

HCl, was the most appropriate deproteinization method for the removal of impurities. This preliminary data will support future studies to design scale-up procedures.\n\nOptimal Extraction and Deproteinization Method for Mannoprotein Purification from Kluyveromyces marxianus.", "token_count": 398, "char_count": 1419, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:40.158002", "source": { "split": "train_shard_00000", "doc_id": 4981 }, "chunk_id": "train_shard_00000_4981_0", "global_id": 5641 }, { "text": "Bovine respiratory disease (BRD) is a major economic and animal welfare issue in the beef industry. Mycoplasma bovis is one of the main causal organisms, particularly in chronic cases. Due to the difficulty of isolating M. bovis from clinical isolates, there is a lack of information on the genetic diversity of this pathogen in the Texas panhandle region of the United States. Therefore, our objective was to provide genome-level characterization of M. bovis isolated from the lung lesions of beef and dairy cattle in the Texas panhandle. Fifty-four isolates displaying mycoplasma-like growth were recovered from bovine lung lesions by the Texas Veterinary Medical Diagnostic Laboratory in 2021 and 2022. Of these isolates, 32 were determined to be M. bovis via species-specific qPCR using the uvrC gene. Long-read whole-genome sequencing was used to identify key virulence factors, antimicrobial resistance genes, and to assess the genetic diversity of these isolates. Fisher's exact tests were used to identify associations between isolate characteristics and host metadata, including the state of origin, type of operation, animal age, and animal sex. Our results indicate that there is considerable genetic diversity among the M. bovis isolates, despite their shared geography in the Texas panhandle, though significant clustering based on host metadata was observed. Analysis of the pangenome showed that the M. bovis isolates in this study also harbor a diverse array of virulence genes, but no antimicrobial resistance genes were identified in this study.\n\nThe Pathogenomics of the Respiratory <i>Mycoplasma bovis</i> Strains Circulating in Cattle Around the Texas Panhandle, USA.", "token_count": 456, "char_count": 1749, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5889, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:40.804708", "source": { "split": "train_shard_00000", "doc_id": 4982 }, "chunk_id": "train_shard_00000_4982_0", "global_id": 5642 }, { "text": "Although only Saccharomyces boulardii has been studied for ulcerative colitis (UC), probiotic yeasts have immense therapeutic potential. Herein, we evaluated the kefir yeast Kluyveromyces marxianus A4 (Km A4) and its anti-inflammatory effect with sulfasalazine in BALB/c mice with dextran sulfate sodium (DSS)-induced colitis. Oral administration continued for 7 days after the mice were randomly divided into seven groups: control (CON, normal mice administered with saline), DSS-induced colitis mice administered saline (DSS), and DSS-induced colitis mice administered sulfasalazine only (S), Km A4 only (A4), Km A4 plus sulfasalazine (A4 + S), S. boulardii ATCC MYA-796 (Sb MYA-796) only (Sb), and Sb MYA-796 plus sulfasalazine (Sb + S). The β-glucan content of Km A4 was significantly higher than that of Sb MYA-796 (P < 0.05). Body weight gain (BWG) significantly correlated with colon length, cyclooxygenase-2 (Cox-2) levels, and Bacteroides abundance (P < 0.05). In colitis-induced mice, the A4 + S group had the lowest histological score (6.00) compared to the DSS group (12.67), indicating the anti-inflammatory effects of this combination", "token_count": 426, "char_count": 1204, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7024, "quality_score": 0.8512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:41.432994", "source": { "split": "train_shard_00000", "doc_id": 4983 }, "chunk_id": "train_shard_00000_4983_0", "global_id": 5643 }, { "text": "The A4 + S group showed significantly downregulated expression of interleukin (Il)-6, tumor necrosis factor-α (Tnf-α), and Cox-2 and upregulated expression of Il-10 and occludin (Ocln) compared to the DSS group. Mice treated with A4 + S had enhanced Bacteroides abundance in their gut microbiota compared with the DSS group (P < 0.05). Bacteroides were significantly correlated with all colitis biomarkers (BWG, colon length, Il-6, Tnf-α, Il-10, Cox-2, and Ocln; P < 0.05). The anti-inflammatory effects of Km A4 could be attributed to high β-glucan content and gut microbiota modulation. Thus, treatment with Km A4 and sulfasalazine could alleviate UC.\n\nA comparative evaluation of the kefir yeast Kluyveromyces marxianus A4 and sulfasalazine in ulcerative colitis: anti-inflammatory impact and gut microbiota modulation.", "token_count": 355, "char_count": 934, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6529, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:42.009803", "source": { "split": "train_shard_00000", "doc_id": 4983 }, "chunk_id": "train_shard_00000_4983_1", "global_id": 5644 }, { "text": "

Background:

Bioremediation faces several compounds to recover oil spilled ecosystem. The BTEX (benzene, toluene, ethylbenzene, and xylene) are toxic hydrocarbons requiring efficient microbial degradation for bioremediation. Pseudomonas aeruginosa can degrade hydrocarbons through emulsification ( rhl genes) and tolerance ( mla genes). However, genomic organization of these systems in environmental P. aeruginosa strains remains unclear. This study aimed to investigate the rhl and mla systems in six strains isolated from hydrocarbon-contaminated sites in Peru. Methods Six Pseudomonas aeruginosa strains were evaluated in this study. Each strain were able to degrade hydrocarbon and tolerate heavy metals. DNA extraction, sequencing, and quality-controlled assembly, functional genome annotation was performed using BAKTA. Comparative analysis included high-quality Pseudomonas genomes from RefSeq, with ANI metrics. A phylogenetic tree was built from core gene alignment, revealed evolutionary connections and was visualized with iTOL. Results The assembled genomes ranged from 5.6 to 6.0 Mbp with ~66% GC content. All the strains were confirmed as P. aeruginosa by ANI; placing them within Clade 1 alongside environmental and clinical strains. Pangenome analysis identified 3,544 core genes and a diverse accessory genome. All strains had rhlABRI genes in a conserved 3′-5′ orientation. Most of them contained duplicated rhlB gene, except C1BHIC5 strain. However, rhlG varied in position and orientation, it was often near rhlC , with C1BHIC5 also displaying an exception in rhlG orientation.100% of strains presented mla system, associated with toluene tolerance, with two copies of mlaA , mlaFEDC , and mlaEFD genes arranged with high synteny but variable orientations. In comparison to Pseudomonas putida , where mla genes are positioned between murA and ppcD with an additional toluene tolerance gene ( ttg2D )", "token_count": 504, "char_count": 1929, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:42.668563", "source": { "split": "train_shard_00000", "doc_id": 4984 }, "chunk_id": "train_shard_00000_4984_0", "global_id": 5645 }, { "text": "Conclusions In conclusion, the presence of the rhlABC genes and the BTEX tolerance genes in all of the analyzed strains allowed us to understand the great ability of P. aeruginosa to survive in polluted environments.\n\nComparative Genomics of Rhamnolipid Synthesis and Monoaromatic Hydrocarbon Tolerance Genes in Environmental Pseudomonas aeruginosa strains", "token_count": 92, "char_count": 356, "word_count": 50, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:43.041839", "source": { "split": "train_shard_00000", "doc_id": 4984 }, "chunk_id": "train_shard_00000_4984_1", "global_id": 5646 }, { "text": "This study examined the transcriptional composition and changes in gene expression patterns in citrus fruit tissue treated with Kluyveromyces marxianus and its effects on key defense-related enzyme activities and metabolites. This analysis was carried out by the technique of RNA sequencing, the use of HPLC-MS, and GC–MS equipment. The sequencing data revealed that the induction of K. marxianus in the citrus fruit peel activated the expression of genes in 90 biological pathways. A total of 3785 genes were transcribed between the yeast-treated and control fruits. 1287 genes were expressed significantly, 682 genes were up-regulated representing 52.99 %, and 605 genes were down-regulated representing 47.00 %. Gene expressions in some of the pathways in the treated citrus stimulated an increase in the production of some defense-related enzymes, the synthesis of secondary metabolites such as phenolic compounds, flavonoids, phenolic acids, and an enhanced lignin production. The accumulation of these compounds contributed to the improvement of the antifungal activity and defense responses in the citrus. 8 phenolic acids, 12 sugars, 6 organic acids, and 17 amino acids were detected at varying concentrations. The investigations revealed that the production of the metabolites was significantly enhanced in the K. marxianus-treated fruits as compared to the control fruits. The study provides some fundamental understanding of the induced resistance mechanism in citrus by K. marxianus.\n\nDisease resistance induction by K. marxianus against green mold in citrus via transcriptome analysis and verification based on metabolites", "token_count": 392, "char_count": 1635, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5738, "quality_score": 0.7869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:43.664074", "source": { "split": "train_shard_00000", "doc_id": 4985 }, "chunk_id": "train_shard_00000_4985_0", "global_id": 5647 }, { "text": "Brucella melitensis is a highly infectious zoonotic pathogen responsible for brucellosis, which significantly affects both human and livestock health worldwide. This study employed whole-genome sequencing (WGS) to analyze the genetic diversity of 24 B. melitensis isolates from India. Pangenome analysis revealed a highly conserved nature with the involved strains having very limited accessory genes. Multilocus Sequence Typing (MLST) identified sequence type ST8 as predominant among Indian strains. Analysis of virulence genes revealed a total of 43 virulence-related genes in all strains, emphasizing their critical role in the pathogenicity of B. melitensis. Unique gene profiles and distinct phylogenetic clusters suggest regional adaptations and evolutionary pressures. The comprehensive genomic insights from this study help to elucidate the geographic distribution and interspecies transmission of Indian strains, highlighting the importance of targeted brucellosis control measures in India. Additionally, the identification of conserved virulence genes involved in immune evasion and intracellular survival highlights their importance in the bacterium's pathogenicity. This research contributes to the global understanding of B. melitensis genomic diversity, providing valuable insights for broader epidemiological studies and brucellosis management strategies worldwide.IMPORTANCEB. melitensis is a significant cause of illness in both humans and animals, particularly in India, where the disease remains a major concern. This study highlights that only a few genetic types of the bacteria are circulating in the region, which means control efforts can be better focused on these specific types. By understanding the unique characteristics of Indian strains, and how these strains spread and adapt, this research offers valuable guidance for improving brucellosis prevention strategies. These insights can help in developing more effective diagnostic tools, enhancing vaccination efforts, and strengthening disease control programs to reduce the impact of brucellosis on public health and livestock industries.\n\nGenomic insights into <i>Brucella melitensis</i> in India: stability of ST8 and the role of virulence genes in regional adaptations.", "token_count": 499, "char_count": 2303, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6073, "quality_score": 0.8036, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:44.315906", "source": { "split": "train_shard_00000", "doc_id": 4986 }, "chunk_id": "train_shard_00000_4986_0", "global_id": 5648 }, { "text": "Cells must sense and respond to sudden maladaptive environmental changes-stresses-to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein-a core marker of stress granules-condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.\n\nAn adaptive biomolecular condensation response is conserved across environmentally divergent species.", "token_count": 318, "char_count": 1533, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7263, "quality_score": 0.8632, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:44.879283", "source": { "split": "train_shard_00000", "doc_id": 4987 }, "chunk_id": "train_shard_00000_4987_0", "global_id": 5649 }, { "text": "Introduction: Whole genome sequencing offers great opportunities for linking genotypes to phenotypes aiding in our understanding of human disease and bacterial pathogenicity. However, these analyses often overlook non-coding intergenic regions (IGRs). By disregarding the IGRs, crucial information is lost, as genes have little biological function without expression. Methods/Results: In this study, we present the first complete pangenome of the important human pathogen Streptococcus pneumoniae (pneumococcus), spanning both the genes and IGRs. We show that the pneumococcus species retains a small core genome of IGRs that are present across all isolates. Gene expression is highly dependent on these core IGRs, and often several copies of these core IGRs are found across each genome. Core genes and core IGRs show a clear linkage as 81% of core genes are associated with core IGRs. Additionally, we identify a single IGR within the core genome that is always occupied by one of two highly distinct sequences, scattered across the phylogenetic tree. Discussion: Their distribution indicates that this IGR is transferred between isolates through horizontal regulatory transfer independent of the flanking genes and that each type likely serves different regulatory roles depending on their genetic context.\n\nAdding context to the pneumococcal core genes using bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae.", "token_count": 356, "char_count": 1477, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:45.455609", "source": { "split": "train_shard_00000", "doc_id": 4988 }, "chunk_id": "train_shard_00000_4988_0", "global_id": 5650 }, { "text": "The effect of seasonal and regional changes on the microbial diversity of mares' milk and koumiss in southern Kazakhstan was examined. Samples were collected from farms in Almaty and Zhambyl (eight samples each area) between July and October. Metataxonomic analysis of mares’ milk revealed 85 bacterial species from 38 genera and 84 fungal species from 17 genera. Koumiss samples contained 33 bacterial and 23 fungal species. Lactobacillus was the dominant bacterial genus in mares’ milk, while Kluyveromyces, Dekkera, and Dipodascus were the most prevalent fungal genera. Koumiss showed a similar microbial profile, with dominant species including Lactobacillus gallinarum, Lactococcus cremoris, Kluyveromyces marxianus, and Dekkera bruxellensis. Although both products shared key species, their relative abundances varied across months and regions. While mares’ milk contained pathogens and saprophytes, these were significantly inhibited after 24 h of koumiss fermentation. The findings emphasize the influence of geographic and seasonal factors on fermented dairy microbiota.\n\nEffects of seasonal and regional variations on the bacterial and fungal biodiversity of mares’ milk and koumiss in the Almaty and Zhambyl regions of Kazakhstan", "token_count": 330, "char_count": 1240, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:46.026000", "source": { "split": "train_shard_00000", "doc_id": 4989 }, "chunk_id": "train_shard_00000_4989_0", "global_id": 5651 }, { "text": "The objective was to evaluate the effect of two probiotic yeast strains (Saccharomyces. cerevisiae RC016 and Kluyveromyces marxianus VM004) as a substitute of growth promoter antibiotics on health status and productive parameters in weaned piglets. Commercial line hybrid piglets (Choice n=200), weaned at 21 d age were allotted by sex, and assigned in 4 pens per treatment (2 pens males and 2 pens females), 10 pigs per pen divided into 2 blocks (with or without antibiotics). Dietary treatments included a basal diet (BD) supplemented with probiotic Saccharomyces cerevisiae RC016 and Kluyveromyces marxianus VM004 (100 g, 1 × 1010 CFU/g, respectively), with or without antibiotics, mixed per ton of growth phases diets. Pigs were fed ad libitum with treatments T1) BD with antibiotics (BD); T2) BD with antibiotics + Saccharomyces cerevisiae; T3) BD without antibiotics + Saccharomyces cerevisiae; T4) BD with antibiotics + Kluyveromyces marxianus; T5) BD without antibiotics + Kluyveromyces marxianus. The effects on respiratory tract clinometry, carcass quality, organs weight, blood haematology and productive parameters were evaluated. When clinical signs occurred (diarrhoea, stomach ulcers, respiratory signs), they decreased with both probiotics addition, mainly Saccharomyces cerevisiae. The productive parameters promotion by both probiotics was similar than that using antibiotics. The probiotics inclusion increased the carcass weight and significantly reduced the lumbar fat thickness (P ≤ 0.05)", "token_count": 487, "char_count": 1566, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [ "VM004", "RC016" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:46.681069", "source": { "split": "train_shard_00000", "doc_id": 4990 }, "chunk_id": "train_shard_00000_4990_0", "global_id": 5652 }, { "text": "Supplementation with both probiotics demonstrated their ability to substitute the antibiotics use on clinometry, carcass quality and on the productive parameters promotion of weaned piglets.\n\nRespiratory tract clinometry, fat thickness, haematology and productive parameters associated with direct-fed microbials used as growth promoter antibiotic alternative in weaned piglets.", "token_count": 80, "char_count": 378, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:47.049951", "source": { "split": "train_shard_00000", "doc_id": 4990 }, "chunk_id": "train_shard_00000_4990_1", "global_id": 5653 }, { "text": "Moraxella catarrhalis is an important cause of infectious exacerbations of chronic obstructive pulmonary disease and otitis media. Previously, seroresistant (SR) and serosensitive (SS) lineages that differed in virulence potential were described, which raised questions about their evolutionary relationship and species classification. To investigate the population structure of M. catarrhalis , we developed a core-genome multilocus sequence typing (cgMLST) scheme using 1,319 core genes, and a life identification number (LIN) barcode classification system. Whole-genome analyses of nearly 2,000 genomes confirmed two divergent SR and SS M. catarrhalis lineages with distinct evolutionary trajectories. SR genomes were more conserved, while SS genomes exhibited greater genetic variability. Virulence gene analyses revealed lineage-specific variations in ubiquitous surface proteins (UspA1 and UspA2) and lipooligosaccharide (LOS) types, and SR genomes had more diverse LOS variants. The bro β-lactamase gene, and the mcb bacteriocin cluster, were more common in SR, which suggested different selective pressures and ecological adaptation. This cgMLST scheme and LIN code system provides a robust method for characterising M. catarrhalis , distinguishes between SR and SS lineages, and offers a unified framework for population structure analyses. Implemented within PubMLST, this open-access resource facilitates high-resolution genomic studies and supports the scientific community in understanding the evolutionary complexity of M. catarrhalis .\n\nUnderstanding the population structure of Moraxella catarrhalis using core genome multilocus sequence typing (cgMLST) and a life identification number (LIN) code classification system", "token_count": 413, "char_count": 1742, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:47.676954", "source": { "split": "train_shard_00000", "doc_id": 4991 }, "chunk_id": "train_shard_00000_4991_0", "global_id": 5654 }, { "text": "Enterobacteriaceae are commonly colonizing animal guts and impact health. While strain-specific metabolic features can promote gut colonization, we lack systematic knowledge regarding metabolic diversity and the core metabolism shared among Enterobacteriaceae . To address this gap, we analyzed the pan-genome of nearly 20,000 genomes. We found that genes necessary for monosaccharide-fuelled mixed acid fermentation are part of the Enterobacteriaceae core genome, while most genes for anaerobic respiration and most carbohydrate utilization genes belong to the accessory genome. Understanding Enterobacteriaceae 's metabolic capacity helps clarify the distinction of nutrients consumed by all Enterobacteriaceae , and niche-defining nutrient sources, which are genus-, species- or strain-specific. This knowledge sheds light on bacterial nutrient exploitation during gut colonization in health and disease, aiding in the development of targeted interventions for microbiome research and infectious disease control. The theoretical framework described here can also be adapted to analyze core physiological characteristics of other microbiota taxa.\n\nUnravelling the Core and Accessory Genome Diversity of Enterobacteriaceae in Carbon Metabolism", "token_count": 288, "char_count": 1251, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6975, "quality_score": 0.8488, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation", "respiration" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:48.230230", "source": { "split": "train_shard_00000", "doc_id": 4992 }, "chunk_id": "train_shard_00000_4992_0", "global_id": 5655 }, { "text": "Some budding yeast species contain cytosolic linear DNA plasmids (also called virus-like elements, VLEs) that code for killer toxins that can kill other yeasts. The toxins are anticodon nucleases that cleave a specific tRNA in the cells being attacked, stopping translation. The best known plasmids of this type are the pGKL1/pGKL2 system of Kluyveromyces lactis . pGKL1 is a killer plasmid encoding the toxin zymocin (γ-toxin) which cleaves tRNA-Glu, and pGKL2 is a helper plasmid required for replication and transcription of pGKL1. Here, we investigated similar plasmids in the genus Saccharomycopsis that were originally described in the 1980s. Saccharomycopsis has undergone an evolutionary change of its genetic code, from CUG-Leu to CUG-Ser translation, which we hypothesized could have been driven by a tRNA-cleaving toxin encoded by a cytosolic plasmid. We sequenced a three-plasmid system in S. crataegensis , consisting of apparent killer, immunity, and helper plasmids. The killer plasmid contains genes coding for putative α/β (chitin-binding) and γ (ribonuclease) toxin subunits, but the γ-toxin gene is damaged in all the isolates we examined. We inferred the sequence of the intact S. crataegensis γ-toxin and expressed it in Saccharomyces cerevisiae and Kluyveromyces marxianus , but it did not cause a growth defect. We also identified free plasmids, or plasmids integrated into the nuclear genome, in nine other Saccharomycopsis species, including a case of recent interspecies transfer of a plasmid. Our results show that many yeasts in the CUG-Ser2 clade contain, or have in the past contained, plasmids related to those that carry anticodon nucleases.\n\nCytosolic linear DNA plasmids inSaccharomycopsisspecies", "token_count": 506, "char_count": 1737, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:48.919225", "source": { "split": "train_shard_00000", "doc_id": 4993 }, "chunk_id": "train_shard_00000_4993_0", "global_id": 5656 }, { "text": "We present a case of Kluyveromyces marxianus keratitis nine months after Descement's membrane endothelial keratoplasty (DMEK) in a patient with Fuchs endothelial disease. Endothelial scraping revealed this rare yeast infection at the interface between graft and host cornea. Immediate antifungal treatment with intracameral and corneal intrastromal injections of voriconazole and amphotericin B remained unsuccessful, requiring penetrating keratoplasty. This case highlights the challenging management of keratomycosis in patients with endothelial grafts.\n\nFirst case of Kluyveromyces marxianus (Candida kefyr) late onset keratitis after lamellar endothelial corneal graft.", "token_count": 209, "char_count": 694, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7412, "quality_score": 0.8706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:49.400649", "source": { "split": "train_shard_00000", "doc_id": 4994 }, "chunk_id": "train_shard_00000_4994_0", "global_id": 5657 }, { "text": "Staphylococcus aureus sequence type (ST) 188 is a globally distributed lineage frequently associated with colonization and bloodstream infection in both humans and animals, yet its evolutionary dynamics and genomic adaptations remain poorly understood. In this study, we conducted a comprehensive genomic analysis of 808 ST188 isolates collected from 24 countries between 2004 and 2023. Phylogenetic reconstruction identified seven clades, with clades I and VII showing independent clonal expansions in China. Frequent cross-regional, international, and cross-host transmission events were observed, supporting the emergence of ST188 as a host-generalist lineage. A distinct methicillin-resistant S. aureus subclade within clade VI likely emerged from a methicillin-susceptible ancestor through the acquisition of SCCmec IVa. This event was accompanied by co-acquisition of resistance transposon Tn6636 and fluoroquinolone-resistance mutations, alongside truncation of the adhesion-related gene sraP and loss of the serine protease genes splDE. Preliminary phenotypic assays confirmed reduced adhesion and colonization in clade VI isolates. Comparative analysis revealed clade-specific patterns of mobile genetic elements, including vertical inheritance of SaPI1 and SaPI2 in the Chinese subclade of clade VII. In contrast, the novel prophage φST188-1, found exclusively in clade VII isolates, appeared to have been independently acquired. However, accessory genome variation across clades was limited, and the overall population structure was primarily shaped by core genome single-nucleotide polymorphisms", "token_count": 428, "char_count": 1649, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7488, "quality_score": 0.8744, "entities": { "genes": [ "ST188" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:50.091563", "source": { "split": "train_shard_00000", "doc_id": 4995 }, "chunk_id": "train_shard_00000_4995_0", "global_id": 5658 }, { "text": "These findings provide a detailed view of the evolution and adaptation of ST188, underscore the role of clade-specific resistance and virulence patterns, and highlight the importance of continued genomic surveillance of this emerging lineage.

Importance

The global emergence of Staphylococcus aureus ST188 poses new challenges to public health due to its ability to infect both humans and animals and spread across regions and continents. Despite its growing prevalence, little has been known about its evolutionary history and dissemination patterns. In this study, we analyzed 808 ST188 genomes from 24 countries and found evidence of frequent cross-regional and cross-host transmission. Two major clades, showing clear clonal expansion, were dominated by isolates from China. We also identified a newly emerged methicillin-resistant subclade likely derived from a methicillin-susceptible ancestor, characterized by the acquisition of SCCmec IVa, multiple resistance genes, and fluoroquinolone-resistance mutations. This subclade exhibited reduced adhesion and colonization capacity due to structural loss of key virulence genes. These findings provide new insights into the clade-specific adaptation and global spread of ST188 and underscore the need for genomic surveillance of multidrug-resistant S. aureus emerging from traditionally susceptible lineages.\n\nClade-specific adaptation and global spread of <i>Staphylococcus aureus</i> ST188 with emergence of a multidrug-resistant MRSA sublineage.", "token_count": 384, "char_count": 1541, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [ "ST188" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:50.709462", "source": { "split": "train_shard_00000", "doc_id": 4995 }, "chunk_id": "train_shard_00000_4995_1", "global_id": 5659 }, { "text": "

Introduction

Burkholderia is a rod-shaped aerobic Gram-negative bacteria with considerable genetic and metabolic diversity, which can beused for bioremediation and production applications, and has great biotechnology potential. However, there are few studies on the heavy metal resistance of the Burkholderia genus.

Methods

In this paper, the distribution, characteristics and evolution of heavy metal resistance genes in Burkholderia and the gene island of Tn7-like transposable element associated with heavy metal resistance genes in Burkholderia were studied by comparative genomic method based on the characteristics of heavy metal resistance.

Results and discussion

The classification status of some species of the Burkholderia genus was improved, and it was found that Burkholderia dabaoshanensis and Burkholderia novacaledonica do not belong to the Burkholderia genus.Secondly, comparative genomics studies and pan-genome analysis found that the core genome of Burkholderia has alarger proportion of heavy metal resistance genes and a greater variety of heavy metalresistance genes than the subsidiary genome and strain specific genes. Heavy metal resistance genes are mostly distributed in the genome in the form of various gene clusters (for example, mer clusters, ars clusters, czc/cusABC clusters). At the same time, transposase, recombinase, integrase and other genes were foundupstream and downstream of heavy metal gene clusters, indicating that heavy metal resistance genes may beobtained through horizontal transfer. The analysis of natural selection pressure of heavy metal resistance genes showed that heavy metal resistance genes experienced strong purification selection under purification selection pressure in the genome.The Tn7 like transposable element of Burkholderia was associated with the heavy metal resistance gene island, and there were a large number of Tn7 transposable element insertion events in genomes. At the same time, BGI metal gene islands related to heavy metal resistance genes of Tn7 like transposable element were found, and these gene islands were only distributed in Burkholderia cepacia, Burkholderia polyvora, and Burkholderia contaminant.", "token_count": 513, "char_count": 2238, "word_count": 299, "semantic_coherence": 1, "information_density": 0.4849, "quality_score": 0.7425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:51.368449", "source": { "split": "train_shard_00000", "doc_id": 4996 }, "chunk_id": "train_shard_00000_4996_0", "global_id": 5660 }, { "text": "Distribution, characterization, and evolution of heavy metal resistance genes and Tn7-like associated heavy metal resistance Gene Island of Burkholderia.", "token_count": 36, "char_count": 160, "word_count": 19, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:51.727268", "source": { "split": "train_shard_00000", "doc_id": 4996 }, "chunk_id": "train_shard_00000_4996_1", "global_id": 5661 }, { "text": "Abstract Metabolic heat responses during Carboxypeptidase Y production by Kluyveromyces marxianus was estimated by optimizing the aeration and agitation rates. 1 LPM and 150 RPM was found to be optimum for maximum Carboxypeptidase Y production in a 2L capacity bioreaction calorimeter. The effect of pH on Carboxypeptidase Y production was carried out extensively in this study. Under controlled pH conditions, Kluyveromyces marxianus utilized both the substrate (glucose) and the by-product (ethanol) effectively to yield a maximum of 19 IU/mL compared to 10 IU/mL Carboxypeptidase Y under uncontrolled pH conditions. Biokinetic constants, Oxygen Mass Transfer coefficient, Shear stress and total metabolic heat of the reaction were estimated. For the first time, biocalorimetric coupled respirometric studies have given a maximum Carboxypeptidase Y yield making it attractive for commercial applications.\n\nMetabolic heat response of Kluyveromyces marxianus during Carboxypeptidase Y Production; Effect of Agitation, Aeration and pH control", "token_count": 275, "char_count": 1041, "word_count": 144, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:52.293116", "source": { "split": "train_shard_00000", "doc_id": 4997 }, "chunk_id": "train_shard_00000_4997_0", "global_id": 5662 }, { "text": "Haemophilus influenzae is a major opportunistic human pathogen which causes both non-invasive and invasive disease. The H. influenzae type b (Hib) vaccine has led to a significant reduction of invasive Hib disease, but offers no protection against colonisation or disease by unencapsulated non-typeables (NT) or non-b serotypes, and H. influenzae remains a public health burden worldwide, with increasing reports of multi-drug resistance (MDR). Despite this, there is no comprehensive understanding of the species’ global population structure. To advance understanding about the evolution and epidemiology of the species, we whole-genome sequenced 4,475 isolates of H. influenzae from an unvaccinated paediatric carriage and pneumonia cohort from northwestern Thailand. Despite no Hib immunisation, serotype b was uncommonly found (5.7%), while 91.7% of isolates were NT. We identified a large number of nearly pan-resistant lineages that were mostly NT, and discovered that no lineages were enriched among disease samples, suggesting the ability to cause invasive disease is not restricted to any subpopulation of the species. Extensive population genetic analyses of our data combined with a worldwide collection of 5,976 published genomes revealed a highly admixed population structure, low core genome nucleotide diversity, and evidence of pervasive negative selection. The combined data confirm that MDR lineages are not confined to our cohort, and their establishment globally is an urgent concern.\n\nThe major pathogen Haemophilus influenzae experiences pervasive recombination and purifying selection at local and global scales", "token_count": 386, "char_count": 1641, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:52.912575", "source": { "split": "train_shard_00000", "doc_id": 4998 }, "chunk_id": "train_shard_00000_4998_0", "global_id": 5663 }, { "text": "In this research, the LAB and yeast isolations and identifications of homemade traditional sourdoughs were investigated. Both LAB and yeasts were identified by the PCR method and used in the production of sourdough bread (SDB). Twelve types of SDB were produced from combinations of isolated LAB and yeasts. Eleven LAB and yests were identified from 36 sourdoughs. The most frequently isolated LAB species were Lactobacillus brevis (45.0%), Pediococcus acidilactici (20.0%) and Lactobacillus plantarum (18.3%) while other LAB species were isolated by only 1.7-3.5%. On the other hand, 27.5% of the isolates were Saccharomyces cerevisiae, which was followed by Pichia kudriavzevii (25.0%) and Kluyveromyces marxianus (12.5%). The total titratable acidity and pH of the sourdough ranged from 3.10 to 34.45% and from 4.05 to 4.80 respectively. High acceptable loaf height (7.2 cm), moisture (30.05%), dry matter (69.95%), volume (1370 cm3), specific volume (4.35 cm3 g -1 ) and sensory value (62 scores) were determined for SDB12. Isolated LAB is mainly composed of heterofermentative species (75%). Among the bread produced with the combination of LAB and yeasts, the SDB12 was the most preferred SDB in terms of sensory analysis and other quality characteristics. The use of homofermentative and heterofermentative LAB and yeast combinations provided high-quality SDB. This would be due to the symbiotic growth of these microorganisms. The use of L. plantarum by L", "token_count": 519, "char_count": 1555, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6081, "quality_score": 0.8041, "entities": { "genes": [ "SDB12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:53.565495", "source": { "split": "train_shard_00000", "doc_id": 4999 }, "chunk_id": "train_shard_00000_4999_0", "global_id": 5664 }, { "text": "brevis and by other species resulted in high-quality SDB.\n\nMolecular identification of LAB and yeasts from traditional sourdoughs and their impacts on the sourdough bread quality characteristics.", "token_count": 47, "char_count": 199, "word_count": 27, "semantic_coherence": 1, "information_density": 0.9259, "quality_score": 0.963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:53.928986", "source": { "split": "train_shard_00000", "doc_id": 4999 }, "chunk_id": "train_shard_00000_4999_1", "global_id": 5665 }, { "text": "Abstract

Due to thermotolerance and rapid growth yeast Kluyveromyces marxianus(K.marxianus) is emerging as a new platform organism for production of recombinant proteins. We constructed an expression vector to express exogenous proteins. Firstly, qPCR was used to validate the expression efficiency of endogenous promoters. Selecting PDC1 as the promoter to initiate the expression of EGFP for validation, the vector could successfully express foreign proteins. With Hygromycin in the medium the vector can accumulate in the cell. Further construction the cap of porcine circovirus type 3(PCV3) was carried out on the vector, and soluble PCV3 cap protein was obtained. Under electron microscopy, PCV3 cap formed viral like particles(VLP).This study successfully constructed the expression vector and elements of K.marxianus, which can further promote the research on the expression of exogenous proteins in K.marxianus. The soluble expression of PCV3 cap and formed VLP structure laid the foundation for further developing PCV3 vaccines.

\n\nCharacterization of vector elements and soluble expression of PCV3 cap protein in Kluyveromyces marxianus", "token_count": 293, "char_count": 1167, "word_count": 162, "semantic_coherence": 1, "information_density": 0.5679, "quality_score": 0.784, "entities": { "genes": [ "PDC1", "PCV3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:54.507863", "source": { "split": "train_shard_00001", "doc_id": 0 }, "chunk_id": "train_shard_00001_0_0", "global_id": 5666 }, { "text": "Abstract Kluyveromyces marxianus yeast is often isolated from dairy products and used as probiotic agents in food. As a producer-yeast they must be genetically stable, have simple nutrient requirements, be effective in hostile conditions, grow on inexpensive nutrient media and be easy to store and distribute. Nineteen strains of K. marxianus isolated from natural biotopes were tested for their ability to grow on various carbon sources. For this, the YPD medium (1% yeast extract, 2% peptone, 2% dextrose, pH 5.5) was used with the addition of 20 g/L of one of the following carbon sources: glucose, sucrose, lactose, maltose, mannitol, arabinose, xylose, and galactose. The cultivation was carried out for 1–3 days. All isolates were also tested for their ability to grow in YPD broth at different temperatures (4, 27, 37, 40, 42, 46 and 48 °C) and pH (5; 3 and 2). K. marxianus strains showed widespread use of the substrate and high resistance to elevated incubation temperatures. All tested strains grew at 27 and 37 °C and one strain grew at 46 °C. None of the strains showed active growth at pH 2 and all cultures grew actively at pH 3. At the same time five strains showed growth at pH 5.0. All strains fermented galactose, 16 - xylose, 9 - glucose, 7 - lactose, 12 - maltose, 11 - arabinose, 5 - sucrose, 13 - mannitol. It should be noted that all strains in this study have showed fully restored growth after 2 hours’ incubation at pH 2. It indicates that they could survive when passing through the gastric passage into the intestine. These properties make the use of K. marxianus and its metabolites indispensable in agriculture as a feed additive. This work was supported by the Ministry of Science and Higher Education of Russia.", "token_count": 513, "char_count": 1745, "word_count": 298, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:55.510412", "source": { "split": "train_shard_00001", "doc_id": 1 }, "chunk_id": "train_shard_00001_1_0", "global_id": 5667 }, { "text": "PSX-B-14 Properties of Kluyveromyces marxianus strains isolated from natural biotopes", "token_count": 26, "char_count": 85, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:55.865126", "source": { "split": "train_shard_00001", "doc_id": 1 }, "chunk_id": "train_shard_00001_1_1", "global_id": 5668 }, { "text": "Invasive fungal infections (IFIs) are associated with high mortality rates and mostly affect patients with compromised immunity. The incidence of IFIs is increasing worldwide with the expanding population of susceptible patients. Candida and other yeast infections represent a major component of IFIs. Rare Candida/yeast infections have also increased in recent years and pose considerable diagnostic and management challenges as they are not easily recognized by routine phenotypic characteristic-based diagnostic methods and/or by the automated yeast identification systems. Rare Candida/yeasts also exhibit reduced susceptibility to antifungal drugs making proper management of invasive infections challenging. Here, we review the diagnosis and management of 60 cases of rare Candida/yeast IFIs described so far in Kuwait, an Arabian Gulf country in the Middle East. Interestingly, majority (34 of 60, 56.7%) of these rare Candida/yeast invasive infections occurred among neonates or premature, very-low-birth-weight neonates, usually following prior bacteremia episodes. The clinical details, treatment given, and outcome were available for 28 of 34 neonates. The crude mortality rate among these neonates was 32.2% as 19 of 28 (67.8%) survived the infection and were discharged in healthy condition, likely due to accurate diagnosis and frequent use of combination therapy. Physicians treating patients with extended stay under intensive care, on mechanical ventilation, receiving broad spectrum antibiotics and with gastrointestinal surgery/complications should proactively investigate IFIs. Timely diagnosis and early antifungal treatment are essential to decrease mortality. Understanding the epidemiology and spectrum of rare Candida/yeast invasive infections in different geographical regions, their susceptibility profiles and management will help to devise novel diagnostic and treatment approaches and formulate guidelines for improved patient outcome.\n\nSpectrum and management of rare Candida/yeast infections in Kuwait in the Middle East.", "token_count": 493, "char_count": 2102, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6436, "quality_score": 0.8218, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:56.513509", "source": { "split": "train_shard_00001", "doc_id": 2 }, "chunk_id": "train_shard_00001_2_0", "global_id": 5669 }, { "text": "

Motivation

Metagenome-Assembled Genomes (MAGs) or Single-cell Amplified Genomes (SAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. This presents a particular challenge for the identification of true gene frequencies within a microbial population, as core genes missing in only a few assemblies will be mischaracterized by current pangenome approaches.

Results

Here, we present CELEBRIMBOR, a Snakemake pangenome analysis pipeline which uses a measure of genome completeness to automatically adjust the frequency threshold at which core genes are identified, enabling accurate core gene identification in MAGs and SAGs.

Availability and implementation

CELEBRIMBOR is published under open source Apache 2.0 licence at https://github.com/bacpop/CELEBRIMBOR and is available as a Docker container from this repository. Supplementary material is available in the online version of the article.\n\nCELEBRIMBOR: core and accessory genes from metagenomes.", "token_count": 253, "char_count": 1011, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7154, "quality_score": 0.8577, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:57.009070", "source": { "split": "train_shard_00001", "doc_id": 3 }, "chunk_id": "train_shard_00001_3_0", "global_id": 5670 }, { "text": "Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome multilocus sequence typing (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N = 14) and high-quality draft H. influenzae genomes (N = 2297). The draft genome dataset was divided into a development dataset (N = 921) and a validation dataset (N = 1376). The development dataset was used to identify potential core genes, and the validation dataset was used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all the resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman's correlation and ordinary least square linear regression tests. Preliminary analyses using the development dataset identified 1067 core genes, which were refined to 1037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates (R 2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae, which enhances the genomic analysis of this clinically relevant human pathogen.\n\nDevelopment and implementation of a core genome multilocus sequence typing scheme for <i>Haemophilus influenzae</i>.", "token_count": 514, "char_count": 1952, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5698, "quality_score": 0.7849, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:50:57.666355", "source": { "split": "train_shard_00001", "doc_id": 4 }, "chunk_id": "train_shard_00001_4_0", "global_id": 5671 }, { "text": "Tuberculosis (TB) is one of the leading causes of human deaths worldwide caused by infectious diseases. TB infection by Mycobacterium tuberculosis can occur in the lungs, causing pulmonary tuberculosis (PTB), or in any other organ of the body, resulting in extrapulmonary tuberculosis (EPTB). There is no consensus on the genetic determinants of this pathogen that may contribute to EPTB. In this study, we constructed the M. tuberculosis pangenome and used it as a tool to seek genomic signatures associated with the clinical presentation of TB based on its accessory genome differences. The analysis carried out in the present study includes the raw reads of 490 M. tuberculosis genomes (PTB n = 245, EPTB n = 245) retrieved from public databases that were assembled, as well as ten genomes from Mexican strains (PTB n = 5, EPTB n = 5) that were sequenced and assembled. All genomes were annotated and then used to construct the pangenome with Roary and Panaroo. The pangenome obtained using Roary consisted of 2231 core genes and 3729 accessory genes. On the other hand, the pangenome resulting from Panaroo consisted of 2130 core genes and 5598 accessory genes. Associations between the distribution of accessory genes and the PTB/EPTB phenotypes were examined using the Scoary and Pyseer tools. Both tools found a significant association between the hspR, plcD, Rv2550c, pe_pgrs5, pe_pgrs25, and pe_pgrs57 genes and the PTB genotype", "token_count": 483, "char_count": 1535, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:58.325789", "source": { "split": "train_shard_00001", "doc_id": 5 }, "chunk_id": "train_shard_00001_5_0", "global_id": 5672 }, { "text": "In contrast, the deletion of the aceA, esxR, plcA, and ppe50 genes was significantly associated with the EPTB phenotype. Rv1759c and Rv3740 were found to be associated with the PTB phenotype according to Scoary; however, these associations were not observed when using Pyseer. The robustness of the constructed pangenome and the gene-phenotype associations is supported by several factors, including the analysis of a large number of genomes, the inclusion of the same number of PTB/EPTB genomes, and the reproducibility of results thanks to the different bioinformatic tools used. Such characteristics surpass most of previous M. tuberculosis pangenomes. Thus, it can be inferred that the deletion of these genes can lead to changes in the processes involved in stress response and fatty acid metabolism, conferring phenotypic advantages associated with pulmonary or extrapulmonary presentation of TB. This study represents the first attempt to use the pangenome to seek gene-phenotype associations in M. tuberculosis.\n\nPangenome Reconstruction of Mycobacterium tuberculosis as a Guide to Reveal Genomic Features Associated with Strain Clinical Phenotype.", "token_count": 337, "char_count": 1219, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6369, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:58.895176", "source": { "split": "train_shard_00001", "doc_id": 5 }, "chunk_id": "train_shard_00001_5_1", "global_id": 5673 }, { "text": "Aligning genomes into common coordinates is central to pangenome analysis and construction, but it is also computationally expensive. Multi-sequence maximal unique matches (multi-MUMs) are guideposts for core genome alignments, helping to frame and solve the multiple alignment problem. We introduce Mumemto, a tool that computes multi-MUMs and other match types across large pangenomes. Mumemto allows for visualization of synteny, reveals aberrant assemblies and scaffolds, and highlights pangenome conservation and structural variation. Mumemto computes multi-MUMs across 320 human genome assemblies (960GB) in 25.7 hours with under 800 GB of memory, and over hundreds of fungal genome assemblies in minutes. Mumemto is implemented in C++ and Python and available open-source at https://github.com/vikshiv/mumemto .\n\nMumemto: efficient maximal matching across pangenomes", "token_count": 221, "char_count": 873, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7607, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:50:59.363554", "source": { "split": "train_shard_00001", "doc_id": 6 }, "chunk_id": "train_shard_00001_6_0", "global_id": 5674 }, { "text": "Anbaris is a raw goat milk product naturally fermented in terracotta jars. The aim of this research paper was to follow the dynamics underlying an artisanal production to understand the concomitant evolution of the microbial populations in relation to the chemical changes occurring within the product, make sure of the sanitary conditions prevailing during the production and uncover for the first time its culturable yeast populations. Throughout the fermentation process, Anbaris was endowed with high acidity and included high microbial populations counts of LAB and yeasts that were rapidly installed within the product and maintained as regular new milk additions were made, contributing to lipolytic and proteolytic activities. Salt content varied according to the arbitrary salt additions made during the process but was high in the end product while protein and fat contents varied inversely to moisture. Frequent additions of Enterobacteriaceae and Coliforms contaminated milk samples seemingly fueled a contamination of the product during its manufacturing and in the final fresh Anbaris. Seven species of culturable yeasts, Pichia kudriavzevii, Kluyveromyces marxianus, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, Debaryomyces hansenii, Candida parapsilosis and Kazachstania exigua were found during the production. The first two dominated the process in terms of frequency of occurrence and abundance at the different stages and might be signature species of the product. The same lineage of K. marxianus isolates was maintained throughout the fermentation and sample specific patterns were observed. Strains of this species exhibited low diversity within our product, and more globally in the Lebanese dairy products we studied.\n\nRaw goat's milk fermented Anbaris from Lebanon: insights into the microbial dynamics and chemical changes occurring during artisanal production, with a focus on yeasts.", "token_count": 475, "char_count": 1976, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:00.003740", "source": { "split": "train_shard_00001", "doc_id": 7 }, "chunk_id": "train_shard_00001_7_0", "global_id": 5675 }, { "text": "

Background & Aims

The adherent-invasive Escherichia coli (AIEC) pathotype is implicated in inflammatory bowel disease (IBD) pathogenesis. AIEC strains are currently defined by phenotypic measurement of their pathogenicity, including invasion of epithelial cells. This broad definition, combined with the genetic diversity of AIEC across IBD patients, has complicated the identification of virulence determinants. We sought to quantify the invasion phenotype of clinical isolates from IBD patients and identify the genetic basis for their invasion into epithelial cells.

Methods

A pangenome with core and accessory genes (genotype) was assembled using whole genome sequencing of 168 E. coli samples isolated from 13 IBD patients. A modified assay for invasion of epithelial cells (phenotype) was established with consideration of antibiotic resistance phenotypes. Isolate genotype was correlated to invasiveness phenotype to identify genetic factors that co-segregate with invasion.

Results

Pangenome-wide comparisons of E. coli clinical isolates identified accessory genes that can co-segregate with invasion phenotype. These correlations found the acquisition of antibiotic resistance genes in clinical isolates compromised the traditional gentamicin protection assays used to quantify invasion. Therefore, an alternate assay, based on amikacin resistance, identified genes co-segregating with invasion. These genes encode an arylsulfatase, a glycoside hydrolase, and genetic islands carrying propanediol utilization and sulfoquinovose metabolism pathways.

Conclusions

This study highlights the importance of incorporating antibiotic resistance screening for invasion assays used in AIEC identification. Accurately screened invasion phenotypes identified accessory genome elements among E. coli IBD isolates that correlate with their ability to invade epithelial cells. These results help explain why single genetic markers for the AIEC phylotype are challenging to identify.

Synopsis

We established a pangenome of Escherichia coli isolates from inflammatory bowel disease patients using whole genome sequencing", "token_count": 524, "char_count": 2157, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5683, "quality_score": 0.7842, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:00.692256", "source": { "split": "train_shard_00001", "doc_id": 8 }, "chunk_id": "train_shard_00001_8_0", "global_id": 5676 }, { "text": "The genotypes were correlated with a newly developed measurement of invasion phenotype to identify co-segregating genes.\n\nGenetic and microbial analysis of invasiveness forEscherichia colistrains associated with inflammatory bowel disease", "token_count": 62, "char_count": 245, "word_count": 29, "semantic_coherence": 1, "information_density": 0.931, "quality_score": 0.9655, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:01.075068", "source": { "split": "train_shard_00001", "doc_id": 8 }, "chunk_id": "train_shard_00001_8_1", "global_id": 5677 }, { "text": "

Background

Haemophilus influenzae is a Gram-negative bacterium that can exist as a commensal organism or cause a range of diseases, from ear infections to invasive conditions like meningitis. While encapsulated H. influenzae strains have historically been linked to severe diseases, non-typeable Haemophilus influenzae (NTHi) strains, lacking an intact capsule locus, have emerged as the leading cause of invasive H. influenzae infections, particularly following the widespread use of the H. influenzae serotype b (Hib) vaccine.

Methods

In response to a significant increase in invasive NTHi infections among persons living with HIV in metropolitan Atlanta during 2017-2018, we conducted a comparative genomic analysis of two predominant NTHi clones, C1 and C2, identified during this period. These clones correspond to multilocus sequence types ST164 and ST1714, respectively. We analyzed the genomic characteristics of C1 and C2 using whole genome sequencing data and compared them to a broader pangenome of H. influenzae strains to identify potential virulence factors and genetic adaptations.

Results

Both C1 and C2 isolates were highly related within their clusters, with C1 showing a maximum of 132 SNPs and C2 showing 149 SNPs within their respective core genomes. Genomic analysis revealed significant deletions in known virulence genes, surprisingly suggesting possible attenuation of virulence. No unique accessory genes were identified that distinguished C1 and C2 from other H. influenzae strains, although both clusters exhibited a consistent loss of the pxpB gene (encoding 5-oxoprolinase subunit), replaced by a mobile cassette containing genes potentially involved in sugar metabolism", "token_count": 476, "char_count": 1778, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6695, "quality_score": 0.8347, "entities": { "genes": [ "ST1714", "ST164" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:01.741868", "source": { "split": "train_shard_00001", "doc_id": 9 }, "chunk_id": "train_shard_00001_9_0", "global_id": 5678 }, { "text": "All C1 and C2 isolates showed potential enrichment in accessory genes associated with systemic infections.

Conclusions

Our study suggests that while C1 and C2 clones possess some genetic markers potentially linked to systemic infections, there are no definitive unique genetic factors that distinguish these clones as more virulent than other H. influenzae strains. The expansion of these clones in a vulnerable population may reflect both chance introduction and potential adaptations to the host environment. Further research is needed to understand the implications of these genetic findings on the clinical management and prevention of invasive NTHi infections.\n\nComparative genomic analysis of emerging non-typeable <i>Haemophilus influenzae</i> (NTHi) causing emerging septic arthritis in Atlanta.", "token_count": 194, "char_count": 829, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7706, "quality_score": 0.8853, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:02.229994", "source": { "split": "train_shard_00001", "doc_id": 9 }, "chunk_id": "train_shard_00001_9_1", "global_id": 5679 }, { "text": "

Background

Salmonella Typhi stands as the etiological agent responsible for the onset of human typhoid fever. The pressing demand for innovative therapeutic targets against S. Typhi is underscored by the escalating prevalence of this pathogen and the severe nature of its infections. Consequently, this study employs pangenome analysis to scrutinize 119 S. Typhi-resistant strains, aiming to identify the most promising therapeutic targets originating from its core genome.

Results

Subtractive genomics was employed to systematically eliminate non-homologous (n=1147), essential (n=551), drug-like (n=80), and pathogenicity-related (n=18) proteins from the initial pool of 3351 core genome proteins. Consequently, lipopolysaccharide 1,2-glucosyltransferase RfaJ was designated as the optimal pharmacological target due to its potential versatility. Furthermore, a compendium of 9000 FDA-approved compounds was repurposed for evaluation against the RfaJ drug target, with the specific intent of prioritizing novel, high-potency therapeutic candidates for combating S. Typhi. Ultimately, four compounds, namely DB00549 (Zafirlukast), DB15637 (Fluzoparib), DB15688 (Zavegepant), and DB12411 (Bemcentinib), were singled out as potential inhibitors based on the ligand-protein binding affinity (indicated by the lowest anticipated binding energy) and the overall stability of these compounds. Notably, molecular dynamics simulations, conducted over a 50 nanosecond interval, convincingly demonstrated the stability of these compounds in the context of the RfaJ protein.

Conclusion

In summary, the present findings hold significant promise as an initial stride in the broader drug discovery endeavor against S. Typhi infections. However, the experimental validation of the identified drug target and drug candidate is further required to increase the effectiveness of the applied methodology.", "token_count": 497, "char_count": 1908, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.8361, "entities": { "genes": [ "DB15637", "DB12411", "DB00549", "DB15688" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:02.897231", "source": { "split": "train_shard_00001", "doc_id": 10 }, "chunk_id": "train_shard_00001_10_0", "global_id": 5680 }, { "text": "Pangenome diversification and resistance gene characterization in Salmonella Typhi prioritized RfaJ as a significant therapeutic marker.", "token_count": 30, "char_count": 136, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:03.251050", "source": { "split": "train_shard_00001", "doc_id": 10 }, "chunk_id": "train_shard_00001_10_1", "global_id": 5681 }, { "text": "This research paper addresses the hypotheses that Kluyveromyces marxianus can be cultured with good alcohol production on different whey-derived matrices, and that the fermented product can be used in order to develop alcoholic beverages with acceptable sensory characteristics by mixtures with yeast-fermented fruit-based matrices. Growth and fermentative characteristics of Kluyveromyces marxianus LFIQK1 in different whey-derived matrices were explored by culturing (24 h, 30°C) on reconstituted whey, demineralized whey, heat-treated whey and milk permeate media. High lactose consumption, ethanol production and yield were observed. Reconstituted whey matrix was selected for mixing with orange or strawberry juices fermented using Saccharomyces cerevisiae to obtain alcoholic beverages (W-OR and W-ST, respectively). Consumer evaluation of beverages was performed using acceptability and Check-All-That-Apply (CATA) questions. Good acceptance was observed, significantly higher for W-ST than for W-OR. CATA questions gave information about organoleptic characteristics of beverages. Penalty analysis showed W-R and W-ST were positively associated with smooth/refreshing and fruity/natural, respectively. Liking was represented, accordingly with penalty analysis, by natural/refreshing. A novel alternative for utilization of whey and whey-related matrices by alcoholic beverages production with natural ingredients is presented.\n\nFermentation of whey-derived matrices by Kluyveromyces marxianus: alcoholic beverage development from whey and fruit juice mixes.", "token_count": 406, "char_count": 1593, "word_count": 197, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [ "LFIQK1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:03.872566", "source": { "split": "train_shard_00001", "doc_id": 11 }, "chunk_id": "train_shard_00001_11_0", "global_id": 5682 }, { "text": "

Background

Kluyveromyces marxianus is a thermotolerant yeast with multiple biotechnological potentials for industrial applications, which can metabolize a broad range of carbon sources, including less conventional sugars like lactose, xylose, arabinose and inulin. These phenotypic traits are sustained even up to 45°C, what makes it a relevant candidate for industrial biotechnology applications, such as ethanol production. It is therefore of much interest to get more insight into the metabolism of this yeast. Recent studies suggested, that thermotolerance is achieved by reducing the number of growth-determining proteins or suppressing oxidative phosphorylation. Here we aimed to find related factors contributing to the thermotolerance of K. marxianus .

Results

Here, we reported the first genome-scale metabolic model of Kluyveromyces marxianus , iSM996, using a publicly available Kluyveromyces lactis model as template. The model was manually curated and refined to include missing species-specific metabolic capabilities. The iSM996 model includes 1913 reactions, associated with 996 genes and 1531 metabolites. It performed well to predict the carbon source utilization and growth rates under different growth conditions. Moreover, the model was coupled with transcriptomics data and used to perform simulations at various growth temperatures.

Conclusions

K. marxianus iSM996 represents a well-annotated metabolic model of thermotolerant yeast, which provide new insight into theoretical metabolic profiles at different temperatures of K. marxianus . This could accelerate the integrative analysis of multi-omics data, leading to model-driven strain design and improvement.\n\nReconstruction and Analysis of aKluyveromyces marxianusGenome-scale Metabolic Model", "token_count": 452, "char_count": 1804, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8361, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:04.514077", "source": { "split": "train_shard_00001", "doc_id": 12 }, "chunk_id": "train_shard_00001_12_0", "global_id": 5683 }, { "text": "

Aims

This study aims to systematically characterize the genetic basis and intra-species differentiation of antibiotic resistance/virulence factor genes (ARGs/VFGs) in Enterobacter hormaechei subsp. xiangfangensis.

Methods and results

A high-quality metagenome-assembled genome of E. hormaechei subsp. xiangfangensis bin99 (97.22% completeness, 1.63% contamination) was acquired. Phylogenomic and average nucleotide identity (≥95%) analyses confirmed its taxonomic assignment. Pan-genomic analysis revealed an open configuration (Heap's exponent B = 0.34) with a large accessory genome (approximate 2965 genes) and a stabilized core genome (1139 genes). Critically, a strong positive correlation (r = 0.86, P < 2.2e-16) was observed between mobile genetic elements (MGEs) and accessory gene abundance, probably suggesting horizontal gene transfer (HGT) as a potential driver of genome diversity. Functional annotation highlighted distinct roles: core genes enriched in essential metabolism, while accessory/strain-specific genes were linked to adaptation. Screening identified significant inter-strain variation in ARGs (n = 31) and VFGs (n = 35). Bin99 itself harbored 19 ARGs (e.g. multidrug: soxS, ramA, oqxB) and 40 VFGs (e.g. flagella, T6SS)", "token_count": 390, "char_count": 1260, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7888, "quality_score": 0.8944, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:05.136036", "source": { "split": "train_shard_00001", "doc_id": 13 }, "chunk_id": "train_shard_00001_13_0", "global_id": 5684 }, { "text": "Importantly, MGE abundance showed a significant positive correlation with ARGs (r = 0.67, P < 2.2e-16) but a negative correlation with VFGs (r = -0.29, P < 3.7e-9), suggesting that ARGs were frequently linked to MGEs facilitating HGT-mediated spread, while VFGs might rely less on this route.

Conclusions

The findings provide genome-wide evidence for distinct genetic plasticity underlying ARG and VFG evolution in E. hormaechei subsp. xiangfangensis, highlighting implications for resistance and virulence dissemination.\n\nGenome-wide mining reveals the genetic plasticity of antibiotic resistance/virulence factor genes in Enterobacter hormaechei subsp. xiangfangensis.", "token_count": 199, "char_count": 677, "word_count": 88, "semantic_coherence": 1, "information_density": 0.8068, "quality_score": 0.9034, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:05.586140", "source": { "split": "train_shard_00001", "doc_id": 13 }, "chunk_id": "train_shard_00001_13_1", "global_id": 5685 }, { "text": "Wild plants can contribute valuable genes to their domesticated relatives1. Fertility barriers and a lack of genomic resources have hindered the effective use of crop-wild introgressions. Decades of research into barley's closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes2. Here we construct a pangenome of bulbous barley comprising 10 phased genome sequence assemblies amounting to 32 distinct haplotypes. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster that has been implicated in diverse immune responses in wheat and barley.\n\nA haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum.", "token_count": 297, "char_count": 1225, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7299, "quality_score": 0.8649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:06.150003", "source": { "split": "train_shard_00001", "doc_id": 14 }, "chunk_id": "train_shard_00001_14_0", "global_id": 5686 }, { "text": "A highly efficient methodology for bioactive ingredient 3S,3'S-astaxanthin (3S,3'S-AST) preparation from genetically modified yeast (Kluyveromyces marxianus) with a combination of enzyme-assisted extraction and salt-assisted liquid-liquid extraction (SALLE) was achieved. The highest yield of 3S,3'S-AST indicated that FoodPro® CBL for yeast cell walls hydrolysis could significantly enhance extraction and obtain, with the help of SALLE procedure, quantified 3S,3'S-AST over 99% in purity through cation chelation. In the oxygen radical antioxidant capacity (ORAC) assay, the antioxidant capacity of high-purity 3S,3'S-AST products were 18.3 times higher than that of the original raw material extract. This new combination preparation may replace previous methods and has the potential to be scaled up in the manufacture of high-purity 3S,3'S-AST from low-value bioresources of raw materials to high-value products in the food and/or drug industries with lower cost and simple equipment.\n\nHigh-Purity Bioactive Ingredient-3S,3'S-Astaxanthin: A New Preparation from Genetically Modified Kluyveromyces marxianus without Column Chromatography and Gel Filtration.", "token_count": 426, "char_count": 1284, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:06.775258", "source": { "split": "train_shard_00001", "doc_id": 15 }, "chunk_id": "train_shard_00001_15_0", "global_id": 5687 }, { "text": "

Background

The oceanic microbiome is dominated by members of the SAR11 clade. Despite their abundance, challenges in recovering the full genetic diversity of natural populations have hindered our understanding of the eco-evolutionary mechanisms driving intra-species variation. In this study, we employed a combination of single-amplified genomes and long-read metagenomics to recover the genomic diversity of natural populations within the SAR11 genomospecies Ia.3/VII, the dominant group in the Mediterranean Sea.

Results

The reconstruction of the first complete genome within this genomospecies revealed that the core genome represents a significant proportion of the genome (~ 81%), with highly divergent areas that allow for greater strain-dependent metabolic flexibility. The flexible genome was concentrated in small regions, typically containing a single gene, and was located in equivalent regions within the genomospecies. Each variable region was associated with a specific set of genes that, despite exhibiting some divergence, maintained equivalent biological functionality within the population. The environmental pangenome is large and enriched in genes involved in nutrient transport, as well as cell wall synthesis and modification, showing an extremely high degree of functional redundancy in the flexible genome (i.e. paralogisms).

Conclusions

This genomic architecture promotes polyclonality, preserving genetic variation within the population. This, in turn, mitigates intraspecific competition and enables the population to thrive under variable environmental conditions and selective pressures. Furthermore, this study demonstrates the power of long-read metagenomics in capturing the full genetic diversity of environmental SAR11 populations, overcoming the limitations of second-generation sequencing technologies in genome assembly. Video Abstract.\n\nExtensive paralogism in the environmental pangenome: a key factor in the ecological success of natural SAR11 populations.", "token_count": 442, "char_count": 2019, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:07.412192", "source": { "split": "train_shard_00001", "doc_id": 16 }, "chunk_id": "train_shard_00001_16_0", "global_id": 5688 }, { "text": "The annotated and predicted genomes of five archaeal strains (AS1, AS2, AS8, AS11 and AS19), isolated from Sfax solar saltern sediments (Tunisia) and affiliated with Halobacterium salinarum, were performed by RAST webserver (Rapid Annotation using Subsystem Technology) and NCBI prokaryotic genome annotation pipeline (PGAP). The results showed the ability of strains to use a reduced semi-phosphorylative Entner-Doudoroff pathway for glucose degradation and an Embden-Meyerhof one for gluconeogenesis. They could use glucose, fructose, glycerol, and acetate as sole source of carbon and energy. ATP synthase, various cytochromes and aerobic respiration proteins were encoded. All strains showed fermentation capability through the arginine deiminase pathway and facultative anaerobic respiration using electron acceptors (Dimethyl sulfoxide and trimethylamine N-oxide). Several biosynthesis pathways for many amino acids were identified. Comparative and pangenome analyses between the strains and the well-studied halophilic archaea Halobacterium NRC-1 highlighted a notable dissimilarity. Besides, the strains shared a core genome of 1973 genes and an accessory genome of 767 genes. 129, 94, 67, 15 and 29 unique genes were detected in the AS1, AS2, AS8, AS11 and AS19 genomes, respectively. Most of these unique genes code for hypothetical proteins. The strains displayed plant-growth promoting characteristics under heavy metal stress (Ammonium assimilation, phosphate solubilization, chemotaxis, cell motility and production of indole acetic acid, siderophore and phenazine). Therefore, they could be used as a biofertilizer to promote plant growth", "token_count": 478, "char_count": 1667, "word_count": 225, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [ "AS2", "AS19", "AS8", "AS1", "AS11" ], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:08.063848", "source": { "split": "train_shard_00001", "doc_id": 17 }, "chunk_id": "train_shard_00001_17_0", "global_id": 5689 }, { "text": "The genomes encoded numerous biotechnologically relevant genes responsible for vitamin biosynthesis, including cobalamin, folate, biotin, pantothenate, riboflavin, thiamine, menaquinone, nicotinate, and nicotinamide. The carotenogenetic pathway of the studied strains was also predicted. Consequently, the findings of this study contribute to a better understanding of the halophilic archaea metabolism providing valuable insights into their ecophysiology as well as relevant biotechnological applications.\n\nElucidating metabolic pathways through genomic analysis in highly heavy metal-resistant Halobacterium salinarum strains.", "token_count": 162, "char_count": 635, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8904, "quality_score": 0.9452, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:08.506314", "source": { "split": "train_shard_00001", "doc_id": 17 }, "chunk_id": "train_shard_00001_17_1", "global_id": 5690 }, { "text": "Pea protein is widely used as an alternative protein source in plant-based products. In the current study, we fermented pea protein to reduce off-flavor compounds, such as hexanal, and to produce a suitable fermentate for further processing. Laboratory fermentations using 5% (w/v) pea protein suspension were carried out using four selected lactic acid bacteria (LAB) strains, investigating their growth and acidification capabilities in pea protein. Rapid acidification of pea protein was achieved with Lactococcus lactis subsp. lactis strain LTH 7123. Next, this strain was co-inoculated together with either the yeasts Kluyveromyces lactis LTH 7165, Yarrowia lipolytica LTH 6056, or Kluyveromyces marxianus LTH 6039. Fermentation products of the mixed starter cultures and of the single strains were further analyzed by gas chromatography coupled with mass spectrometry to quantify selected volatile flavor compounds. Fermentation with L. lactis LTH 7123 led to an increase in compounds associated with the \"beany\" off-flavors of peas, including hexanal. However, significant reduction in those compounds was achieved after fermentation with Y. lipolytica LTH 6056 with or without L. lactis LTH 7123. Thus, fermentation using co-cultures of LAB and yeasts strains could prove to be a valuable method for enhancing quality attributes of pea protein-based products.\n\nRapid Acidification and Off-Flavor Reduction of Pea Protein by Fermentation with Lactic Acid Bacteria and Yeasts.", "token_count": 465, "char_count": 1559, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:09.146447", "source": { "split": "train_shard_00001", "doc_id": 18 }, "chunk_id": "train_shard_00001_18_0", "global_id": 5691 }, { "text": "Xiaoqu starter serves as the saccharifying and fermenting agent in the production of Cantonese soybean-flavor (Chi-flavor) Baijiu, and the complex microbial communities determine the flavor and quality of the product. Round-Koji-mechanical starter (produced by using an automated starter-making disk machine) is advantageous as it decreases operator influence, labor costs, and fermentation time, but the product quality is lower compared to traditional starter. Thus, two types of starters (traditional and Round-Koji-mechanical starter) from a Cantonese Baijiu factory were compared in a metagenomic analysis to investigate the differences in microbial community composition and core microbes. The results showed that several core microbes related to carbohydrate metabolism, amino acid metabolism and lipid metabolism, were differentially enriched in the traditional starter. Mucor lusitanicus and Rhizopus delemar were significantly positively correlated with the three key metabolic pathways. Saccharomyces cerevisiae, Cyberlindnera fabianii, Kluyveromyces marxianus, Lactobacillus fermentum, Mucor ambiguous, Rhizopus microspores, Rhizopus azygosporus, Mucor circinelloides, and Ascoidea rubescens were significantly positively correlated with two of the three key metabolic pathways. The results of this study provide a basis for understanding the differential core microbes in traditional and Round-Koji-mechanical starters of Chi-flavor Baijiu, and they also provide guidance for improving Round-Koji-mechanical starter.\n\nMetagenomic analysis of core differential microbes between traditional starter and Round-Koji-mechanical starter of Chi-flavor Baijiu.", "token_count": 486, "char_count": 1728, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7967, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:09.799141", "source": { "split": "train_shard_00001", "doc_id": 19 }, "chunk_id": "train_shard_00001_19_0", "global_id": 5692 }, { "text": "Streptococcus gallolyticus subsp. gallolyticus (SGG) is a bacterial pathogen implicated in bacteremia and endocarditis and is often associated with colon tumors in elderly individuals. The development of colorectal cancer (CRC) has been linked to intestinal dysbiosis, characterized by increased proportions of SGG and other intestinal microbes. In this study, we present the complete nucleotide sequence of five novel clinical isolates of SGG associated with colorectal cancer, revealing unexpected genetic diversity. Sequencing an additional 30 SGG clinical isolates provided a more comprehensive description of this genetic diversity. We did not identify a pathogenicity island specific to CRC-associated SGG isolates. Most of these human-derived SGG isolates exhibit resistance to multiple antibiotics. Our findings also offer additional insights into multilocus sequence typing (MLST), capsular loci, and pilus organization. Analysis of the repertoire of surface proteins reveals high potential for binding and foraging complex polysaccharides. Finally, comparative genomics with the phylogenetically closest non-pathogenic subspecies S. gallolyticus subsp. macedonicus confirmed that SGG pathogenicity-associated factors mostly rely on a large repertoire of surface proteins involved in host colonization, presence of C5a peptidase to avoid innate immunity, bile salt hydrolase to persist in the gut, and of specific bacteriocin and type VII-dependent effectors to colonize the host colon. Additionally, the presence of extracellular polysaccharides in SGG probably helps the bacterium survive in harsher conditions.IMPORTANCEStreptococcus gallolyticus subsp. gallolyticus (SGG) was the first intestinal bacterium associated with colorectal cancer", "token_count": 507, "char_count": 1858, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:10.457887", "source": { "split": "train_shard_00001", "doc_id": 20 }, "chunk_id": "train_shard_00001_20_0", "global_id": 5693 }, { "text": "It is now widely accepted that colonic microbiota dysbiosis contributes to oncogenesis, with a higher relative abundance of several potentially pro-carcinogenic bacteria. For example, the oncogenic role of Escherichia coli pks+ and enterotoxinogenic Bacteroides fragilis in colorectal cancer has been well established, identifying the role of genetic loci encoding toxins. Through the sequencing and analysis of 11 clinical SGG isolates from CRC patients and comparisons with non-CRC isolates, we uncovered a significant diversity among CRC-associated strains. Our findings suggest that SGG association with CRC is complex and is not linked to a specific strain or pathogenicity island, thus highlighting the opportunistic and versatile nature of SGG.\n\nColorectal cancer-associated <i>Streptococcus gallolyticus</i>: a hidden diversity expose.", "token_count": 247, "char_count": 890, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7807, "quality_score": 0.8904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:10.940305", "source": { "split": "train_shard_00001", "doc_id": 20 }, "chunk_id": "train_shard_00001_20_1", "global_id": 5694 }, { "text": "Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods are currently used to cluster together closely- related genomes, potentially leading to inconsistency between studies. Here, we use a global dataset of 26,306 S. pneumoniae genomes to compare four clustering methods: gene-by- gene seven-locus multi-locus sequencing typing (MLST), core genome MLST (cgMLST)- based hierarchical clustering (HierCC) assignments, Life Identification Number (LIN) barcoding, and k-mer-based PopPUNK clustering (known as GPSCs in this species). We compare the clustering results with phylogenetic and pan-genome analyses to assess their relationship with genome diversity and evolution, as we would expect a good clustering method to form a single monophyletic cluster that has high within-cluster similarity of genomic content. We show that the four methods are generally able to accurately reflect the population structure based on these metrics, and that the methods were broadly consistent with each other. We investigated further to study the discrepancies in clusters. The greatest concordance was seen between LIN barcoding and HierCC (Adjusted Mutual Information Score = 0.950), which was expected given that both methods utilise cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods show that the selection of a core genome schema can introduce inconsistencies between studies. GPSC and HierCC assignments were also highly concordant (AMI = 0.946), showing that k-mer based methods which use the whole genome and do not require the careful selection of a core genome schema are just as effective at representing the population structure. Additionally, where there were differences in clustering between these methods, this could be explained by differences in the accessory genome that were not identified in cgMLST. We conclude that for S. pneumoniae , standardised and stable nomenclature is important as the number of genomes available expands", "token_count": 499, "char_count": 2235, "word_count": 325, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:11.595357", "source": { "split": "train_shard_00001", "doc_id": 21 }, "chunk_id": "train_shard_00001_21_0", "global_id": 5695 }, { "text": "Furthermore, the research community should transition away from seven- locus MLST, and cgMLST, GPSC, and LIN assignments should be used more widely. However, to allow for easy comparison between studies and to make previous literature relevant, the reporting of multiple clustering names should be standardised within research.

Data summary

Genome sequences are deposited in the European Nucleotide Archive (ENA); accession numbers. Metadata of the pneumococcal isolates in this study have been submitted as a supplementary file and are also available on the Monocle Database available at https://data.monocle.sanger.ac.uk/ . The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

Impact Statement

Using a global dataset of S. pneumoniae genomes allows us to thoroughly observe and analyse discrepancies between different clustering methods. Whilst all methods in this study are used to cluster S. pneumoniae genomes, no study has yet thoroughly compared the clustering results and discrepancies. This work summarises the strengths and weaknesses of the different methods and highlights the need for consistency between studies.\n\nComparison of gene-by-gene and genome-wide short nucleotide sequence based approaches to define the global population structure ofStreptococcus pneumoniae", "token_count": 319, "char_count": 1389, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6859, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:12.152262", "source": { "split": "train_shard_00001", "doc_id": 21 }, "chunk_id": "train_shard_00001_21_1", "global_id": 5696 }, { "text": "Kluyveromyces marxianus ATCC 26,548 was cultivated in aerobic chemostats with [1-13C] and [U-13C] glucose as carbon source under three different growth conditions (0.10, 0.25, and 0.5 h-1) to evaluate metabolic fluxes. Carbon balances closed always within 97-102%. Growth was carbon limited, and the cell yield on glucose was the same. The extracellular side-product formation was very low, totaling 0.0008 C-mol C-mol-1 substrate at 0.5 h-1. The intracellular flux ratios did not show significant variation for metabolic flux analysis from labelling and biomass composition and metabolic flux ratio analysis from labelling. The observed strictly oxidative metabolism and the stability of the metabolism in terms of fluxes even at high growth rates, without triggering out the synthesis of by-products, is an extremely desired condition that underlines the potential of K. marxianus for biotechnological biomass-related applications and the comprehension of the metabolic pools and pathways is an important step to engineering this organism.

Supplementary information

The online version contains supplementary material available at 10.1007/s13205-022-03324-x.\n\nMetabolic engineering of Kluyveromyces marxianus for biomass-based applications.", "token_count": 412, "char_count": 1324, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6886, "quality_score": 0.8443, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:12.809465", "source": { "split": "train_shard_00001", "doc_id": 22 }, "chunk_id": "train_shard_00001_22_0", "global_id": 5697 }, { "text": "The valorization of cheese whey, a rich by-product of the dairy industry that is rich in lactose (approx. 70%), proteins (14%), and minerals (9%), represents a promising approach for microbial fermentation. With global whey production exceeding 200 million tons annually, the high biochemical oxygen demand underlines the important need for sustainable processing alternatives. This review explores the biotechnological potential of whey as a fermentation medium by examining its chemical composition, microbial interactions, and ability to support the synthesis of valuable metabolites. Functional microorganisms such as lactic acid bacteria (Lactobacillus helveticus, L. acidophilus), yeasts (Kluyveromyces marxianus), actinobacteria, and filamentous fungi (Aspergillus oryzae) have demonstrated the ability to efficiently convert whey into a wide range of bioactive compounds, including organic acids, exopolysaccharides (EPSs), bacteriocins, enzymes, and peptides. To enhance microbial growth and metabolite production, whey fermentation can be carried out using various techniques, including batch, fed-batch, continuous and immobilized cell fermentation, and membrane bioreactors. These bioprocessing methods improve substrate utilization and metabolite yields, contributing to the efficient utilization of whey. These bioactive compounds have diverse applications in food, pharmaceuticals, agriculture, and biofuels and strengthen the role of whey as a sustainable biotechnological resource. Patents and clinical studies confirm the diverse bioactivities of whey-derived metabolites and their industrial potential. Whey peptides provide antihypertensive, antioxidant, immunomodulatory, and antimicrobial benefits, while bacteriocins and EPSs act as natural preservatives in foods and pharmaceuticals. Also, organic acids such as lactic acid and propionic acid act as biopreservatives that improve food safety and provide health-promoting formulations", "token_count": 499, "char_count": 1985, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6976, "quality_score": 0.8488, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:13.503738", "source": { "split": "train_shard_00001", "doc_id": 23 }, "chunk_id": "train_shard_00001_23_0", "global_id": 5698 }, { "text": "These results emphasize whey's significant industrial relevance as a sustainable, cost-efficient substrate for the production of high-quality bioactive compounds in the food, pharmaceutical, agricultural, and bioenergy sectors.\n\nThe Role of Whey in Functional Microorganism Growth and Metabolite Generation: A Biotechnological Perspective.", "token_count": 76, "char_count": 339, "word_count": 41, "semantic_coherence": 1, "information_density": 0.8537, "quality_score": 0.9268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:13.893660", "source": { "split": "train_shard_00001", "doc_id": 23 }, "chunk_id": "train_shard_00001_23_1", "global_id": 5699 }, { "text": "Defining the population structure of a pathogen is a key part of epidemiology, as genomically related isolates are likely to share key clinical features such as antimicrobial resistance profiles and invasiveness. Multiple different methods are currently used to cluster together closely related genomes, potentially leading to inconsistency between studies. Here, we use a global dataset of 26 306 Streptococcus pneumoniae genomes to compare four clustering methods: gene-by-gene seven-locus MLST, core genome MLST (cgMLST)-based hierarchical clustering (HierCC) assignments, life identification number (LIN) barcoding and k-mer-based PopPUNK clustering (known as GPSCs in this species). We compare the clustering results with phylogenetic and pan-genome analyses to assess their relationship with genome diversity and evolution, as we would expect a good clustering method to form a single monophyletic cluster that has high within-cluster similarity of genomic content. We show that the four methods are generally able to accurately reflect the population structure based on these metrics and that the methods were broadly consistent with each other. We investigated further to study the discrepancies in clusters. The greatest concordance was seen between LIN barcoding and HierCC (adjusted mutual information score=0.950), which was expected given that both methods utilize cgMLST, but have different methods for defining an individual cluster and different core genome schema. However, the existence of differences between the two methods shows that the selection of a core genome schema can introduce inconsistencies between studies. GPSC and HierCC assignments were also highly concordant (AMI=0.946), showing that k-mer-based methods which use the whole genome and do not require the careful selection of a core genome schema are just as effective at representing the population structure. Additionally, where there were differences in clustering between these methods, this could be explained by differences in the accessory genome that were not identified in cgMLST. We conclude that for S. pneumoniae, standardized and stable nomenclature is important as the number of genomes available expands", "token_count": 505, "char_count": 2219, "word_count": 315, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:15.320275", "source": { "split": "train_shard_00001", "doc_id": 24 }, "chunk_id": "train_shard_00001_24_0", "global_id": 5700 }, { "text": "Furthermore, the research community should transition away from seven-locus MLST, whilst cgMLST, GPSC and LIN assignments should be used more widely. However, to allow for easy comparison between studies and to make previous literature relevant, the reporting of multiple clustering names should be standardized within the research.\n\nComparison of gene-by-gene and genome-wide short nucleotide sequence-based approaches to define the global population structure of Streptococcus pneumoniae.", "token_count": 112, "char_count": 497, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:15.699523", "source": { "split": "train_shard_00001", "doc_id": 24 }, "chunk_id": "train_shard_00001_24_1", "global_id": 5701 }, { "text": "Yeasts associated with lepidopteran pests have been shown to play a role in their survival, development, and oviposition preference. It has been demonstrated that combining these yeasts with existing biological control agents can enhance their efficacy. The tortricid Thaumatotibia leucotreta is a phytosanitary pest in the South African citrus industry, with the baculovirus Cryptophlebia leucotreta granulovirus (CrleGV) being one of the components that can control this pest. Several yeast species were shown to be associated with T. leucotreta larvae, which affected their behaviour and development. A series of detached fruit bioassays were performed to determine whether the combination of yeast with CrleGV enhances its efficacy. These assays included determining the optimal yeast/virus ratio, testing all isolated yeast species in combination with CrleGV, and further improving yeast/virus formulation by adding an adjuvant. The optimal yeast concentration to use alongside CrleGV was determined to be 106 cells·mL-1. Pichia kluyveri, P. kudriavzevii, Kluyveromyces marxianus, and Saccharomyces cerevisiae in combination with CrleGV reduced larval survival compared to CrleGV alone. The addition of molasses and BREAK-THRU® S 240 to P. kudriavzevii and S. cerevisiae in combination with CrleGV did not notably improve their effectiveness; however, there was an observed decrease in larval survival. In future studies, field trials will be conducted with combinations of CrleGV and P. kudriavzevii or S. cerevisiae to investigate whether these laboratory findings can be replicated in orchard conditions.", "token_count": 518, "char_count": 1736, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6447, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:16.332664", "source": { "split": "train_shard_00001", "doc_id": 25 }, "chunk_id": "train_shard_00001_25_0", "global_id": 5702 }, { "text": "Naturally Occurring Yeasts Associated with Thaumatotibia leucotreta Can Enhance the Efficacy of the Cryptophlebia Leucotreta Granulovirus.", "token_count": 53, "char_count": 145, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:16.696016", "source": { "split": "train_shard_00001", "doc_id": 25 }, "chunk_id": "train_shard_00001_25_1", "global_id": 5703 }, { "text": "Bacillus velezensis, is a bacterium widely recognized for its biocontrol properties and ability to promote plant growth. This study presents the whole genome sequence of B. velezensis B26, a newly identified strain isolated from chicken carcass soil, Udupi, India. The bacterium showed strong activity against fungal pathogens and exhibited diverse enzymatic activities. The whole genome sequencing was executed using Illumina technologies. Assembly revealed that strain B26 possesses a genome of 3,946,698-bp with a G+C content of 46.3%. Genome annotation identified 3776 protein-coding genes, 1 rRNA gene, 50 tRNA genes, 5 ncRNA genes, and 59 pseudogenes. Functional analysis of the B. velezensis B26 genome revealed 216 genes involved in carbohydrate metabolism, 3 genes in potassium metabolism, 148 genes linked for cofactors, vitamins, prosthetic groups and pigments, 10 genes involved in phosphorus metabolism, 24 genes associated with iron acquisition and metabolism, 20 genes for nitrogen metabolism, 6 genes involved in sulfur metabolism, 6 genes in secondary metabolism, 12 genes associated with metabolism of aromatic compounds, 43 genes involved in stress response and 36 genes associated with virulence, disease and defense. The raw sequence data generated in this work has been deposited in the NCBI database and the genome sequence is available under the accession number JAYKOV000000000. This genomic data provides insight into the biocontrol ability and plant-growth promoting capabilities of B. velezensis B26.\n\nThe complete genome sequences of <i>Bacillus velezensis</i> B26: a promising biocontrol agent and biofertilizer.", "token_count": 487, "char_count": 1682, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6213, "quality_score": 0.8106, "entities": { "genes": [ "JAYKOV000000000" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:17.347091", "source": { "split": "train_shard_00001", "doc_id": 26 }, "chunk_id": "train_shard_00001_26_0", "global_id": 5704 }, { "text": "

Background

Clostridioides difficile (C. difficile) exhibiting high linezolid minimum inhibitory concentration (>4 µg/mL) remains infrequently reported in clinical settings. Notably, the prevalence of linezolid-resistant C. difficile is exceptionally low (<3% in Chinese isolates), and the underlying genetic determinants are poorly characterized.

Methods

We conducted a genomic study to investigate the genetic characteristics of C. difficile with high linezolid MIC. To determine the MIC of linezolid and delineate antimicrobial resistance profiles, these isolates were systematically subjected to antimicrobial susceptibility testing. Multilocus sequence typing, antimicrobial resistance genes, and the characteristics of the cfr gene in linezolid-resistant C. difficile strains were analyzed following whole-genome sequencing. Roary was used to construct a pangenome phylogenetic tree, and a Bayesian evolutionary analysis was performed using BEAST.4.

Results

Among 421 screened C. difficile isolates, nine isolates (2.1%) exhibited high-linezolid MICs (≥16 μg/mL), including six ST37 (A-B+) and three ST3 strains (two A-B-). All harbored cfr(B) on Tn6218, sharing homology with E. faecium (NG_050395.1).

Conclusion

This study underscores the risk of cfr(B) dissemination via mobile genetic elements in clinical settings, urging surveillance of co-occurrence in Enterococcus and C. difficile to curb resistance spread.", "token_count": 494, "char_count": 1541, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7022, "quality_score": 0.8511, "entities": { "genes": [ "ST37", "ST3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:18.003824", "source": { "split": "train_shard_00001", "doc_id": 27 }, "chunk_id": "train_shard_00001_27_0", "global_id": 5705 }, { "text": "Characterization of High-Linezolid-MIC <i>Clostridioides difficile</i> Isolated from a Chinese Hospital: First Genomic Evidence of <i>Cfr</i>(B) Transmission and Tn<i>6218</i> Association.", "token_count": 91, "char_count": 224, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:18.382231", "source": { "split": "train_shard_00001", "doc_id": 27 }, "chunk_id": "train_shard_00001_27_1", "global_id": 5706 }, { "text": "Abstract

We previously introduced Giraffe, a short-read-to-pangenome graph mapper available in the vg pangenomics toolkit. Giraffe was fast and accurate for mapping short reads to human-scale pangenomes, but struggled with long reads. Long reads present a unique challenge to pangenome mapping algorithms due to their length and error profile, which allow them to take more topologically complex paths through the pangenome graph and increase the possible search space for the algorithm. We present updates to Giraffe that allow it to quickly and accurately map long reads to pangenome graphs. For both short and long reads, Giraffe mapping to a pangenome containing data from more than 450 human haplotypes, generated by the Human Pangenome Reference Consortium, is comparable in speed to linear mappers to human reference genomes; Giraffe is also over an order of magnitude faster than GraphAligner, the current state-of-the-art long-read-to-pangenome mapper. Its alignments produce similar or improved small and structural variant calling results, compared to those from commonly used graph-based and linear mappers. We additionally demonstrate using Giraffe's long read alignments in a pangenome-guided assembly workflow, which is capable of producing more contiguous local assemblies than Hifiasm in our test regions.

\n\nRapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe", "token_count": 327, "char_count": 1433, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6537, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:18.955821", "source": { "split": "train_shard_00001", "doc_id": 28 }, "chunk_id": "train_shard_00001_28_0", "global_id": 5707 }, { "text": "Abstract

Background Aspergillus flavus is an important agricultural and food safety threat due to its production of carcinogenic aflatoxins. It has high level of genetic diversity that is adapted to various environments. Recently, we reported two reference genomes of A. flavus isolates, AF13 (MAT1-2 and highly aflatoxigenic isolate) and NRRL3357 (MAT1-1 and moderate aflatoxin producer). Where, an insertion of 310 kb in AF13 included an aflatoxin producing gene bZIP transcription factor, named atfC. Observations of significant genomic variants between these isolates of contrasting phenotypes prompted an investigation into variation among other agricultural isolates of A. flavus with the goal of discovering novel genes potentially associated with aflatoxin production regulation. Present study was designed with three main objectives: (1) collection of large number of A. flavus isolates from diverse sources including maize plants and field soils; (2) whole genome sequencing of collected isolates and development of a pangenome; and (3) pangenome-wide association study (Pan-GWAS) to identify novel secondary metabolite cluster genes. Results Pangenome analysis of 346 A. flavus isolates identified a total of 17,855 unique orthologous gene clusters, with mere 41% (7,315) core genes and 59% (10,540) accessory genes indicating accumulation of high genomic diversity during domestication. 5,994 orthologous gene clusters in accessory genome not annotated in either the A. flavus AF13 or NRRL3357 reference genomes. Pan-genome wide association analysis of the genomic variations identified 391 significant associated pan-genes associated with aflatoxin production", "token_count": 504, "char_count": 1846, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6595, "quality_score": 0.8297, "entities": { "genes": [ "NRRL3357", "AF13", "MAT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:19.617299", "source": { "split": "train_shard_00001", "doc_id": 29 }, "chunk_id": "train_shard_00001_29_0", "global_id": 5708 }, { "text": "Interestingly, most of the significantly associated pan-genes (94%; 369 associations) belonged to accessory genome indicating that genome expansion has resulted in the incorporation of new genes associated with aflatoxin and other secondary metabolites. Conclusion In summary, this study provides complete pangenome framework for the species of Aspergillus flavus along with associated genes for pathogen survival and aflatoxin production. The large accessory genome indicated large genome diversity in the species A. flavus, however AflaPan is a closed pangenome represents optimum diversity of species A. flavus. Most importantly, the newly identified aflatoxin producing gene clusters will be a new source for seeking aflatoxin mitigation strategies and needs new attention in research.

\n\nAspergillus flavus pangenome (AflaPan) uncovers novel aflatoxin and secondary metabolite associated gene clusters", "token_count": 228, "char_count": 960, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:20.088790", "source": { "split": "train_shard_00001", "doc_id": 29 }, "chunk_id": "train_shard_00001_29_1", "global_id": 5709 }, { "text": "

ABSTRACT

Clostridium scindens is a commensal gut bacterium capable of forming the secondary bile acids deoxycholic acid and lithocholic acid from the primary bile acids cholic acid and chenodeoxycholic acid, respectively, as well as converting glucocorticoids to androgens. Historically, only two strains, C. scindens ATCC 35704 and C. scindens VPI 12708, have been characterized in vitro and in vivo to any significant extent. The formation of secondary bile acids is important in maintaining normal gastrointestinal function, in regulating the structure of the gut microbiome, in the etiology of such diseases such as cancers of the GI tract, and in the prevention of Clostridium difficile infection. We therefore wanted to determine the pangenome of 34 cultured strains of C. scindens and a set of 200 metagenome-assembled genomes (MAGs) to understand the variability among strains. The results indicate that the 34 strains of C. scindens have an open pangenome with 12,720 orthologous gene groups, and a core genome with 1,630 gene families, in addition to 7,051 and 4,039 gene families in the accessory and unique (i.e., strain-exclusive) genomes, respectively. The core genome contains 39% of the proteins with predicted metabolic function, and, in the unique genome, the function of storage and processing of information prevails, with 34% of the proteins being in that category. The pangenome profile including the MAGs also proved to be open. The presence of bile acid inducible ( bai ) and steroid-17,20-desmolase ( des ) genes was identified among groups of strains. The analysis reveals that C. scindens strains are distributed into two clades, indicating the possible onset of C. scindens separation into two species, confirmed by gene content, phylogenomic, and average nucleotide identity (ANI) analyses. This study provides insight into the structure and function of the C", "token_count": 518, "char_count": 1897, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5724, "quality_score": 0.7862, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:20.745670", "source": { "split": "train_shard_00001", "doc_id": 30 }, "chunk_id": "train_shard_00001_30_0", "global_id": 5710 }, { "text": "scindens pangenome, offering a genetic foundation of significance for many aspects of research on the intestinal microbiota and bile acid metabolism.\n\nPangenome analysis ofClostridium scindens: a collection of diverse bile acid and steroid metabolizing commensal gut bacterial strains", "token_count": 75, "char_count": 291, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:21.119773", "source": { "split": "train_shard_00001", "doc_id": 30 }, "chunk_id": "train_shard_00001_30_1", "global_id": 5711 }, { "text": "Interspecific genetic exchanges caused by natural hybridization or horizontal gene transfer can lead to enhanced phenotypes, which are often of interest for industrial applications and evolutionary research. However, transferring genetic materials between distantly related species, such as intergeneric yeasts, presents technical challenges. In this study, we established a method to transfer individual chromosomes from Saccharomyces cerevisiae ( Sc ) into Kluyveromyces marxianus ( Km ), an emerging model for bioproduction. The Sc chromosome of interest was circularized, genetically modified to carry Km centromeres and replication origins, and transformed into Km via protoplast transformation. Using this method, we generated two synthetic strains, each containing a full set of Km chromosomes and either Sc chromosome I or III. The Sc chromosomes exhibited normal replication, segregation, and active transcription after the transfer. The synthetic strains displayed enhanced phenotypes in flocculation and salt tolerance, which were found to be caused by transgressive expression of FLO9 and SPS22 on the transferred Sc chromosomes, respectively. Transcriptomic analysis revealed that transgressive expression was prevalent among the transferred Sc genes, suggesting evolution of lineage-specific cis- and trans -regulatory interactions across a long evolutionary timescale. Our strategy has potential applications in optimizing cell factories, constructing synthetic genomes, and advancing evolutionary research.\n\nIntergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses", "token_count": 342, "char_count": 1638, "word_count": 215, "semantic_coherence": 1, "information_density": 0.7023, "quality_score": 0.8512, "entities": { "genes": [ "FLO9", "SPS22" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:21.695603", "source": { "split": "train_shard_00001", "doc_id": 31 }, "chunk_id": "train_shard_00001_31_0", "global_id": 5712 }, { "text": "During ethanol fermentation, yeast cells are exposed to various stresses that have negative effects on cell growth, cell survival, and fermentation ability. This study, therefore, aims to develop Kluyveromyces marxianus-adapted strains that are multi-stress tolerant and to increase ethanol production at high temperatures through a novel evolutionary adaptation procedure. K. marxianus DMKU 3-1042 was subjected to repetitive long-term cultivation with gradual increases in temperature (RLCGT), which exposed cells to various stresses, including high temperatures. In each cultivation step, 1% of the previous culture was inoculated into a medium containing 1% yeast extract, 2% peptone, and 2% glucose, and cultivation was performed under a shaking condition. Four adapted strains showed increased tolerance to ethanol, furfural, hydroxymethylfurfural, and vanillin, and they also showed higher production of ethanol in a medium containing 16% glucose at high temperatures. One showed stronger ethanol tolerance. Others had similar phenotypes, including acetic acid tolerance, though genome analysis revealed that they had different mutations. Based on genome and transcriptome analyses, we discuss possible mechanisms of stress tolerance in adapted strains. All adapted strains gained a useful capacity for ethanol fermentation at high temperatures and improved tolerance to multi-stress. This suggests that RLCGT is a simple and efficient procedure for the development of robust strains.\n\nEvolutionary Adaptation by Repetitive Long-Term Cultivation with Gradual Increase in Temperature for Acquiring Multi-Stress Tolerance and High Ethanol Productivity in Kluyveromyces marxianus DMKU 3-1042.", "token_count": 431, "char_count": 1717, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:22.326793", "source": { "split": "train_shard_00001", "doc_id": 32 }, "chunk_id": "train_shard_00001_32_0", "global_id": 5713 }, { "text": "This study explored the application of Kluyveromyces marxianus and Saccharomyces cerevisiae (commercial and wild type) in the alcoholic fermentation of Fuji apple juice under static conditions. Metabolome analyses revealed that ethyl esters, including ethyl hexanoate, ethyl decanoate, ethyl octanoate, octanoic acid and decanoic acid, were the dominant components in ciders fermented by the Saccharomyces yeasts. In the K. marxianus ciders, ethyl acetate, hexyl acetate, propyl acetate and acetic acid were the most abundant volatiles, suggesting that the cider fermented by K. marxianus might have a fruitier smell. Transcriptome analyses were adapted to gain insight into the differential metabolite patterns between K. marxianus and S. cerevisiae during cider fermentation. GO and KEGG enrichments revealed that the metabolic pathways of glucose, organic acids and amino acids during cider fermentation were quite different between these two yeasts. The K. marxianus strain exhibited a higher rate of glycolysis and ethanol fermentation than did Saccharomyces yeasts under oxygen-limited conditions. It also reduced the metabolic flux of acetate into acetyl-CoA and then into the TCA cycle, increasing the syntheses of ethyl acetate and relevant esters, which may affect its cell growth under anaerobic conditions but enriched the taste and variety of aromas in apple cider.\n\nComparative metabolome and transcriptome analyses of the properties of Kluyveromyces marxianus and Saccharomyces yeasts in apple cider fermentation.", "token_count": 489, "char_count": 1619, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:22.973832", "source": { "split": "train_shard_00001", "doc_id": 33 }, "chunk_id": "train_shard_00001_33_0", "global_id": 5714 }, { "text": "Abstract

CAM plants are promising biomasses to assure energy security and biofuel supply in the current changing climate scenario. Their high sugar content and strengthened tolerance to high temperatures and droughts makes them attractive alternatives to classic fuel sources. In Brazil, sisal (Agave sisalana), is cultivated in semiarid regions for fiber production. However, fibers represent only 4% of the plant’s leaves, with the remaining majority being discarded. This work, then, aims to explore this residue’s potential for bioethanol production. For this, low-input fermentations of a fibrous Brazilian agave accession leaves were explored. A maximum ethanol yield of 54.47% (11.64 g.L− 1) was obtained with Kluyveromyces marxianus. Isolating endogenous microbiota activity and fermentation inhibitors (i.e. saponins) revealed major operational challenges. Nevertheless, the results demonstrate that bioethanol production from agave residues is not only attainable but also promising. The unexplored bioethanol potential from this residue in the Brazilian semiarid could yield 489 L.ha− 1.yr− 1, totalizing 639 million liters of fuel, in the last decade.

\n\nFrom Rags to Riches: the Fermentation Potential of Agave Leaf Residues in the Brazilian Semi-arid", "token_count": 376, "char_count": 1352, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7303, "quality_score": 0.8652, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:23.550921", "source": { "split": "train_shard_00001", "doc_id": 34 }, "chunk_id": "train_shard_00001_34_0", "global_id": 5715 }, { "text": "Whey is a dairy residue generated during the production of cheese and yogurt. Whey contains mainly lactose and proteins, contributing to its high chemical oxygen demand (COD). Current environmental regulations request proper whey disposal to avoid environmental pollution. Whey components can be transformed by yeast into ethanol and biomolecules with aroma and flavor properties, for example, 2-phenyethanol (2PE), highly appreciated in the industry due to its organoleptic and biocidal properties. The present study aimed to valorize agri-food residues in 2PE by developing suitable bioprocess. Cheese whey was used as substrate source, whereas crab headshells, residual soy cake, and brewer's spent yeast (BSY) were used as renewable nitrogen sources for the yeasts Kluyveromyces marxianus and Debaryomyces hansenii. The BSYs promoted the growth of both yeasts and the production of 2PE in flask fermentation. The bioprocess scale-up to 2 L bioreactor allowed for obtaining a 2PE productivity of 0.04 g2PE/L·h, twofold better productivity results compared to the literature. The bioprocess can save a treatment unit because the whey COD decreased under the detection limit of the analytical method, which is lower than environmental requirements. In this way, the bioprocess prevents environmental contamination and contributes to the circular economy of the dairy industry.\n\nCo-Fermentation of Agri-Food Residues Using a Co-Culture of Yeasts as a New Bioprocess to Produce 2-Phenylethanol.", "token_count": 399, "char_count": 1518, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:24.168916", "source": { "split": "train_shard_00001", "doc_id": 35 }, "chunk_id": "train_shard_00001_35_0", "global_id": 5716 }, { "text": "

ABSTRACT

Following a whole genome duplication (WGD) event approximately 100 million years ago, the yeast lineage from which the model Saccharomyces cerevisiae derives maintained two copies of genes where it was necessary to synthesise proteoforms with different sub-cellular localisation. In contrast, yeasts that did not undergo the WGD event have a single gene that must encode both proteoforms. We adopted an integrated in silico and experimental approach to study how this is achieved with BAT1 , a gene that encodes mitochondrial and cytosolic forms of a branched chain aminotransferase (BCAT) in pre-WGD yeast such as Kluyveromyces marxianus . We determined that condition-specific regulation of alternative transcription sites gives rise to mRNA isoforms that differ at the 5’end and that, when decoded, generate a mitochondrial or cytosolic proteoform. Furthermore, targeted mutants lacking specific transcription factors were generated to establish how this differentiation was regulated. As in S. cerevisiae , Gcn4 and Leu3 activated expression of the mRNA encoding the mitochondrial proteoform under conditions when branched chain amino acid synthesis was required. Unlike S. cerevisiae , however, K. marxianus lacked tight regulation of the mRNA encoding the cytosolic proteoform supporting the hypothesis that maintaining paralogous genes in post-WGD yeasts facilitated development of more sophisticated expression control mechanisms.\n\nRegulated use of alternative Transcription Start Sites controls the production of cytosolic or mitochondrial forms of branched-chain aminotransferase in Kluyveromyces marxianus", "token_count": 411, "char_count": 1641, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8296, "entities": { "genes": [ "BAT1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:24.825785", "source": { "split": "train_shard_00001", "doc_id": 36 }, "chunk_id": "train_shard_00001_36_0", "global_id": 5717 }, { "text": "

Background

Glucose repression in yeast leads to the sequential or diauxic utilization of mixed sugars and reduces the co-utilization of glucose and xylose from lignocellulosic biomasses. Study of the glucose sensing pathway helps to construct glucose repression-released yeast strains and enhance the utilization of lignocellulosic biomasses.

Results

Herein, the glucose sensor/receptor repressor (SRR) pathway of Kluyveromyces marxianus which mainly consisted of KmSnf3, KmGrr1, KmMth1, and KmRgt1 was studied. The disruption of KmSNF3 led to a release of glucose repression, enhanced xylose consumption and did not result in deficient glucose utilization. Over-expression of glucose transporter gene restored the mild decrease of glucose utilization ability of Kmsnf3 strain to a similar level of the wildtype strain but did not restore glucose repression. Therefore, the repression on glucose transporter is parallel to glucose repression to xylose and other alternative carbon utilization. KmGRR1 disruption also released glucose repression and kept glucose utilization ability, although its xylose utilization ability was very weak with xylose as sole carbon source. The stable mutant of KmMth1-ΔT enabled the release of glucose repression irrespective that the genetic background was Kmsnf3, Kmmth1, or wildtype. Disruption of KmSNF1 in the Kmsnf3 strain or KmMTH1-ΔT overexpression in Kmsnf1 strain kept constitutive glucose repression, indicating that KmSNF1 was necessary to release the glucose repression in both SRR and Mig1-Hxk2 pathway. Finally, overexpression of KmMTH1-ΔT released the glucose repression to xylose utilization in S. cerevisiae.

Conclusion

The glucose repression-released K", "token_count": 498, "char_count": 1725, "word_count": 231, "semantic_coherence": 1, "information_density": 0.4935, "quality_score": 0.7468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:25.503363", "source": { "split": "train_shard_00001", "doc_id": 37 }, "chunk_id": "train_shard_00001_37_0", "global_id": 5718 }, { "text": "marxianus strains constructed via a modified glucose SRR pathway did not lead to a deficiency in the utilization ability of sugar. The obtained thermotolerant, glucose repression-released, and xylose utilization-enhanced strains are good platforms for the construction of efficient lignocellulosic biomass utilization yeast strains.\n\nThe novel properties of Kluyveromyces marxianus glucose sensor/receptor repressor pathway and the construction of glucose repression-released strains.", "token_count": 125, "char_count": 484, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:25.909213", "source": { "split": "train_shard_00001", "doc_id": 37 }, "chunk_id": "train_shard_00001_37_1", "global_id": 5719 }, { "text": "

Background/objectives

Bacteroides fragilis is the pathogenic anaerobe most commonly isolated from intra-abdominal infections, abscesses, and blood. Despite its clinical importance, research on its pan-genome-scale evolution is still limited.

Methods

Herein, we analyzed the pan-genome architecture of 374 B. fragilis strains to explore their intra-species genomic diversity and evolutionary patterns.

Results

Our analysis revealed an open pan-genome with a high proportion of accessory genomes, indicating high genetic variability. Accessory genome genes were substantially enriched in the functions of \"Replication, Recombination, and Repair\" suggesting their roles in gene transfer and divergence. Phylogenomic analysis divided B. fragilis into two distinct clades: divisions I and II, differing in gene content, antimicrobial resistance genes, and mobile genetic elements. Division II revealed higher Tajima's D values, suggesting that it separated after B. fragilis's recent species diversification. The extreme shift in the distribution of gene-wise Hudson's fixation index (Fst) values for each division suggested that several genes are highly differentiated or evolved between the two clades. Average nucleotide identity and 16S rRNA analyses showed that B. fragilis division II represents a distinct species, Bacteroides hominis. Additionally, a considerable depletion of recombination in genes with Fst values > 0.99 was noted, suggesting that the highest Fst genes with little recombination are the basis for differentiation between divisions.

Conclusions

Overall, this study enhances the understanding of B. fragilis's genomic diversity, evolutionary dynamics, and potential role in pathogenesis, shedding light on its adaptation and diversification.\n\nComparative Evolutionary Genomics Reveals Genetic Diversity and Differentiation in Bacteroides fragilis.", "token_count": 498, "char_count": 1952, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6695, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:26.600089", "source": { "split": "train_shard_00001", "doc_id": 38 }, "chunk_id": "train_shard_00001_38_0", "global_id": 5720 }, { "text": "The main goal of wastewater treatment is to significantly reduce organic compounds, micronutrients (nitrogen and phosphorus) and heavy metals and other contaminants (pathogens, pharmaceuticals and industrial chemicals). In this work, the efficiency of removing different contaminants (COD, NO3-, NO2-, NH4+, PO43-, SO42-, Pb2+, Cd2+) from synthetic wastewater was tested using five different yeast strains: Kluyveromyces marxianus CMGBP16 (P1), Saccharomyces cerevisiae S228C (P2), Saccharomyces cerevisiae CM6B70 (P3), Saccharomyces cerevisiae CMGB234 (P4) and Pichia anomala CMGB88 (P5). The results showed a removal efficiency of up to 70% of COD, 97% of nitrate, 80% of nitrite, 93% of phosphate and 70% of sulfate ions for synthetic wastewater contaminated with Pb2+ (43 mg/L) and Cd2+ ions (39 mg/L). In contrast, the results showed an increase in ammonium ions, especially in the presence of Pb2+ ions. The yeast strains showed a high capacity to reduce Pb2+ (up to 96%) and Cd2+ (up to 40%) ions compared to the initial concentrations", "token_count": 473, "char_count": 1264, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6645, "quality_score": 0.8323, "entities": { "genes": [ "CMGBP16", "CMGB234", "CMGB88" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:27.249737", "source": { "split": "train_shard_00001", "doc_id": 39 }, "chunk_id": "train_shard_00001_39_0", "global_id": 5721 }, { "text": "In presence of a crude biosurfactant, the removal efficiency increased up to 99% for Pb2+ and 56% for Cd2+ simultaneously with an increase in yeast biomass of up to 11 times. The results, which were obtained in the absence of aeration and in neutral pH conditions, proved a high potential for practical applications in the biotreatment of the wastewater and the recovery of Pb and Cd ions, with a high benefit-cost ratio.\n\nBioremediation of Wastewater Using Yeast Strains: An Assessment of Contaminant Removal Efficiency.", "token_count": 151, "char_count": 543, "word_count": 84, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:27.684127", "source": { "split": "train_shard_00001", "doc_id": 39 }, "chunk_id": "train_shard_00001_39_1", "global_id": 5722 }, { "text": "

Background

In recent decades, Candida albicans has become a serious issue for public health. The worldwide rapid rise in drug resistance to conventional therapies is the main contributing reason. Moreover, because of their potent activity at low concentrations and apparent lack of toxicity, compounds originating from plants are used in therapeutic treatments because of their potent activity at low concentrations and apparent lack of toxicity. Particularly in immunocompromised people, Candida species can result in a wide range of ailments.

Objectives

Present manuscript describes antifungal activity of an indole derivative 1-(4-((5- methoxy-2-(3,4,5-trimethoxyphenyl)-1H-indol-1-yl) methyl) phenoxy)-N,N-dimethylethan-1- amine (7, 100DL-6) by using in-silico and in-vitro anti-candidal activity against two Candida strains; Candida kefyr-DS-02 (ATCC-204093) and Candida albicans (AI-clinical isolate, AIIMS- Delhi).

Methods

The synthetic strategy for the preparation of indole derivatives was modified through Fischer indole reaction. Antifungal activity of an indole derivative 1-(4-((5-methoxy-2-(3,4,5- trimethoxyphenyl)-1H-indol-1-yl) methyl) phenoxy)-N,N-dimethylethan-1-amine (7, 100DL-6) was done by using in-silico and in-vitro anti-candidal activity against two Candida strains; Candida kefyr-DS-02 (ATCC-204093) and Candida albicans (AI-clinical isolate, AIIMS-Delhi)", "token_count": 513, "char_count": 1475, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:28.317335", "source": { "split": "train_shard_00001", "doc_id": 40 }, "chunk_id": "train_shard_00001_40_0", "global_id": 5723 }, { "text": "Compound 100DL-6 efficacy was determined by Combination synergy study, ergosterol binding assay, MTT toxicity study and Mutagenicity.

Results

Compound 100DL-6 was obtained in 65% yield on desired motifs. Docking scores found were 100DL-6 (-8.7 kcal/mol) and Fluconazole (-7.6 kcal/mol). Further, RMSD were shown for 100DL6 (0.26 ± 0.23 nm) and fluconazole (1.2 ± 0.62 nm). Indole derivative 100DL-6 was active against the tested fungal pathogens and the total zone of inhibition was measured between 13-14 mm in diameter and MIC values between 31.25 μg/mL to 250 μg/mL and MFC values between 62.5 μg/mL to 500 μg/mL. In checkerboard assay synergistic mode of interaction of 100DL-6 with known antifungal drugs was observed. In the presence of ergosterol 100DL-6 and standard drug (s) increased their MIC values, demonstrating a considerable affinity for ergosterol. Compound 100DL-6 was considered to be less-cytotoxic to the cells as determined by MTT assay. Lead compound 100DL-6 was found to be non-mutagenic.

Conclusion

In the present study, 100DL6 (indole derivatives) significantly abrupted the ergosterol biosynthetic pathway and showed moderate anti-candidal effects. These studies suggest that 100DL6 significantly enhances antifungal effect of clinical drug fluconazole synergistically and may be considered as in clinical trial prior to some extensive in-vivo validations.\n\nGallic Acid Derived 1, 2-Diarylindole as a Potential Synergistic Antifungal Agent against Candida Strains.", "token_count": 510, "char_count": 1512, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6493, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:28.951172", "source": { "split": "train_shard_00001", "doc_id": 40 }, "chunk_id": "train_shard_00001_40_1", "global_id": 5724 }, { "text": "K. marxianus is a promising cell factory for producing heterologous proteins. Oxidative stresses were raised during overexpression of heterologous proteins, leading to the shift of the redox state. How to measure the redox state of live K. marxianus cells without perturbing their growth remains a big challenge. Here, a fluorescence lifetime imaging (FLIM)-based method was developed in live K. marxianus cells. During the early exponential growth, K. marxianus cells exhibited an increased mean fluorescence lifetime (τ-mean) of NAD(P)H compared with Saccharomyces cerevisiae cells, which was consistent with the preference for respiration in K. marxianus cells and that for fermentation in S. cerevisiae cells. Upon oxidative stresses induced by high temperature or H2O2, K. marxianus cells exhibited an increased τ-mean in company with decreased intracellular NAD(P)H/NAD(P)+, suggesting a correlation between an increased τ-mean and a more oxidized redox state. The relationship between τ-mean and the expression level of a heterologous protein was investigated. There was no difference between the τ-means of K. marxianus strains which were not producing a heterologous protein. The τ-mean of a strain yielding a high level of a heterologous protein was higher than that of a low-yielding strain. The results suggested the potential application of FLIM in the non-invasive screen of high-yielding cells.\n\nFluorescence lifetime imaging of NAD(P)H upon oxidative stress in Kluyveromyces marxianus.", "token_count": 471, "char_count": 1604, "word_count": 217, "semantic_coherence": 1, "information_density": 0.53, "quality_score": 0.765, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:29.603444", "source": { "split": "train_shard_00001", "doc_id": 41 }, "chunk_id": "train_shard_00001_41_0", "global_id": 5725 }, { "text": "1 We previously introduced Giraffe, a short-read-to-pangenome graph mapper available in the vg pangenomics toolkit. Giraffe was fast and accurate for mapping short reads to human-scale pangenomes, but struggled with long reads. Long reads present a unique challenge to pangenome mapping algorithms due to their length and error profile, which allow them to take more topologically complex paths through the pangenome graph and increase the possible search space for the algorithm. We present updates to Giraffe that allow it to quickly and accurately map long reads to pangenome graphs. For both short and long reads, Giraffe mapping to a pangenome containing data from more than 450 human haplotypes, generated by the Human Pangenome Reference Consortium, is comparable in speed to linear mappers to human reference genomes; Giraffe is also over an order of magnitude faster than GraphAligner, the current state-of-the-art long-read-to-pangenome mapper. Its alignments produce similar or improved small and structural variant calling results, compared to those from commonly used graph-based and linear mappers. We additionally demonstrate using Giraffe’s long read alignments in a pangenome-guided assembly workflow, which is capable of producing more contiguous local assemblies than Hifiasm in our test regions.\n\nRapid, accurate long- and short-read mapping to large pangenome graphs with vg Giraffe", "token_count": 316, "char_count": 1403, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:30.170736", "source": { "split": "train_shard_00001", "doc_id": 42 }, "chunk_id": "train_shard_00001_42_0", "global_id": 5726 }, { "text": "

Background

Streptococcus anginosus has been found to colonize multiple anatomical sites of the human body, including the oral cavity, gastrointestinal tract, skin, vagina, blood, and urinary tract. It is frequently isolated from catheterized urine samples obtained from adult females most often with lower urinary tract symptoms, but also on occasion from those without symptoms. Our prior genome analysis of 166 S. anginosus genomes identified two distinct groups, one - which we here call group Urinae - exhibits a tropism for the urinary tract.

Results

Here we sequenced 100 isolates collected from different urogenital sites, including isolates from urine (both catheterized and voided) samples, urethral swabs, perineal swabs, vaginal swabs, and a foreskin swab. These sequenced isolates, as well as 15 isolates previously sequenced by our group, were collected from 50 unique individuals, with isolates from multiple anatomic sites for 26 of these individuals. The majority (89.57%) of the isolates were representatives of the Urinae group and were found in all sample types. Expanding our prior statistical method, we determined that, for 11 females, the same strain of Urinae was isolated from more than one of the urogenital sites.

Conclusions

The identification of S. anginosus group Urinae strains from all urogenital sites sampled signifies that the tropism of this group is not restricted to the urinary tract. Rather, it seems to be a common constituent of the urogenital tract. The identification of the same strain shared across urogenital sample sites from the same individual suggests that the female urogenital sites in fact have interconnected microbiota.\n\nStreptococcus anginosus of the urogenital tract: evidence of the same strain across anatomical sites of the same females.", "token_count": 454, "char_count": 1820, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5618, "quality_score": 0.7809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:30.805850", "source": { "split": "train_shard_00001", "doc_id": 43 }, "chunk_id": "train_shard_00001_43_0", "global_id": 5727 }, { "text": "Pseudomonas aeruginosa (class Gammaproteobacteria) is a ubiquitous, ecologically widespread, and metabolically versatile species. It is also an opportunistic pathogen that causes a variety of chronic and acute infections in humans. Its ability to thrive in diverse environments and exhibit a wide range of phenotypes lies in part on its large gene pool, but the processes that govern inter-strain genomic variation remain unclear. Here, we aim to characterize the recombination features and accessory genome structure of P. aeruginosa using 840 globally distributed genome sequences. The species can be subdivided into five phylogenetic sequence clusters (corresponding to known phylogroups), two of which are most prominent. Notable epidemic clones are found in the two phylogroups: ST17, ST111, ST146, ST274, and ST395 in phylogroup 1, and ST235 and ST253 in phylogroup 2. The two phylogroups differ in the frequency and characteristics of homologous recombination in their core genomes, including the specific genes that most frequently recombine and the impact of recombination on sequence diversity. Each phylogroup's accessory genome is characterized by a unique gene pool, co-occurrence networks of shared genes, and anti-phage defense systems. Different pools of antimicrobial resistance and virulence genes exist in the two phylogroups and display dissimilar patterns of co-occurrence. Altogether, our results indicate that each phylogroup displays distinct histories and patterns of acquiring exogenous DNA, which may contribute in part to their predominance in the global population. Our study has important implications for understanding the genome dynamics, within-species heterogeneity, and clinically relevant traits of P. aeruginosa.

Importance

The consummate opportunist Pseudomonas aeruginosa inhabits many nosocomial and non-clinical environments, posing a major health burden worldwide. Our study reveals phylogroup-specific differences in recombination features and co-occurrence networks of accessory genes within the species", "token_count": 522, "char_count": 2082, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [ "ST274", "ST17", "ST395", "ST253", "ST146", "ST235", "ST111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:31.461288", "source": { "split": "train_shard_00001", "doc_id": 44 }, "chunk_id": "train_shard_00001_44_0", "global_id": 5728 }, { "text": "This genomic variation partly explains its remarkable ability to exhibit diverse ecological and phenotypic traits, and thus contribute to circumventing clinical and public health intervention strategies to contain it. Our results may help inform efforts to control and prevent P. aeruginosa diseases, including managing transmission, therapeutic efforts, and pathogen circulation in non-clinical environmental reservoirs.\n\nHeterogeneity in recombination rates and accessory gene co-occurrence distinguish <i>Pseudomonas aeruginosa</i> phylogroups.", "token_count": 131, "char_count": 566, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:31.885243", "source": { "split": "train_shard_00001", "doc_id": 44 }, "chunk_id": "train_shard_00001_44_1", "global_id": 5729 }, { "text": "The emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa represents a significant challenge in managing nosocomial infections, particularly in vulnerable populations such as burn patients. This study provides genomic and molecular characterization of MDR and XDR P. aeruginosa strains isolated from burn patients at Sheikh Hasina National Institute of Burn and Plastic Surgery (SHNIBPS) in Dhaka, Bangladesh. Over an 8-month period, 110 wound swabs were collected, with 91 isolates identified as P. aeruginosa. Antimicrobial susceptibility testing demonstrated a multidrug-resistant pattern in 30 isolates and an extensive drug-resistant pattern in the remaining 61 isolates analyzed in this study. PCR assays detected beta-lactamase genes from all four Ambler classes, revealing a notable prevalence of blaNDM-1 (16.48%) and blaVIM-2 (31.87%), with both genes co-occurring in 3.30% of the isolates. Additionally, blaPER-1 (15.38%), blaCTX-M (4.40%), blaOXA-1 (84.62%), and blaOXA-48 (51.65%) genes were detected. Class I integrons were detected in 84 isolates. A total of 21% of the isolates exhibited strong biofilm-forming capabilities. Key biofilm-associated genes (pelB, pilT, rhlB) were detected in most of the isolates. Whole genome sequence analysis of two selected XDR isolates identified different beta-lactamase genes such as blaPDC-98, blaPDC-374, blaOXA-50, blaOXA-677 and blaOXA-847", "token_count": 513, "char_count": 1563, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:32.523800", "source": { "split": "train_shard_00001", "doc_id": 45 }, "chunk_id": "train_shard_00001_45_0", "global_id": 5730 }, { "text": "Virulence factor genes, metal resistance genes, and prophage sequences were also identified in the analysis. The genomic epidemiology analysis of 9,055 P. aeruginosa strains, based on MLST data, revealed the dominance of ST235. The blaPDC and blaOXA genes were found to be notably prominent worldwide. The comparative genomic analysis of P. aeruginosa strains from Bangladesh demonstrated an expanding pangenome as well as high degree of genetic variability. The study emphasized the dynamic nature of the P. aeruginosa pangenome and underscored the necessity for stringent infection control measures in burn units to manage and mitigate the spread of these highly resistant strains.\n\nMolecular and genomic insights into multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa causing burn wound infections in Bangladesh.", "token_count": 220, "char_count": 873, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:32.994029", "source": { "split": "train_shard_00001", "doc_id": 45 }, "chunk_id": "train_shard_00001_45_1", "global_id": 5731 }, { "text": "Paenibacillus polymyxa, a Gram-positive bacterium commonly found in soil and plant roots, plays an important role in the environment due to its nitrogen-fixing ability and is renowned for producing antibiotics like polymyxin. In this study, we present a robust framework for investigating the evolutionary and taxonomic connections of strains belonging to P. polymyxa available at the National Center for Biotechnology Information, as well as five new additional strains isolated at the University of Camerino (Italy), through pangenome analysis. These strains can produce secondary metabolites active against Staphylococcus aureus and Klebsiella pneumoniae. Employing techniques such as digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) estimation, OrthoFinder, and ribosomal multilocus sequence typing, we consistently divided these P. polymyxa strains into four clusters, which differ significantly in terms of ANI and dDDH percentages, both considered as reference indices for separating bacterial species. Moreover, the strains of Cluster 2 were re-classified as belonging to the Paenibacillus ottowii species. By comparing the pangenomes, we identified the core genes of each cluster and analyzed them to recognize distinctive features in terms of biosynthetic/metabolic potential. The comparison of pangenomes also allowed us to pinpoint differences between clusters in terms of genetic variability and the percentage of the genome dedicated to core and accessory genes. In conclusion, the data obtained from our analyses of strains belonging to the P. polymyxa species converge toward a necessary reclassification, which will require a fundamental contribution from microbiologists in the near future.

Importance

The development of sequencing technologies has led to an exponential increase in microbial sequencing data. Accurately identifying bacterial species remains a challenge because of extensive intra-species variability, the need for multiple identification methods, and the rapid rate of taxonomic changes", "token_count": 503, "char_count": 2101, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6738, "quality_score": 0.8369, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:33.656368", "source": { "split": "train_shard_00001", "doc_id": 46 }, "chunk_id": "train_shard_00001_46_0", "global_id": 5732 }, { "text": "A substantial contribution to elucidating the relationships among related bacterial strains comes from comparing their genomic sequences. This comparison also allows for the identification of the \"pangenome,\" which is the set of genes shared by all individuals of a species, as well as the set of genes that are unique to subpopulations. Here, we applied this approach to Paenibacillus polymyxa, a species studied for its potential as a biofertilizer and biocontrol agent and known as an antibiotic producer. Our work highlights the need for a more efficient classification of this bacterial species and provides a better delineation of strains with different properties.\n\nPangenome analysis of Paenibacillus polymyxa strains reveals the existence of multiple and functionally distinct Paenibacillus species.", "token_count": 197, "char_count": 829, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:34.103344", "source": { "split": "train_shard_00001", "doc_id": 46 }, "chunk_id": "train_shard_00001_46_1", "global_id": 5733 }, { "text": "Swine dysentery, caused by the anaerobic spirochete Brachyspira hyodysenteriae, leads to mucohemorrhagic diarrhea in grower-finisher pigs, impacting swine production. Knowledge regarding its genomic epidemiology is limited. We performed a whole-genome sequence analysis for 251 B. hyodysenteriae genomes from 10 countries, including 117 isolates sequenced in this study. Phylogenomic analysis based on core-genome single nucleotide polymorphisms (SNPs) revealed nine lineages, with L7 (72 isolates, 28.69%), L9 (67 isolates, 26.69%), and L2 (53 isolates, 21.12%) predominating. Geographical clustering was observed with distinct lineage distributions. Multilocus sequence typing identified 69 sequence types (STs), including 20 novel STs across 251 genomes. Association between specific lineages, STs, and geographical regions was evident, highlighting evolutionary and regional patterns. The pan-genome analysis identified 5,231 genes, categorized into core (1,648), accessory (2,619), and unique (964) components. Functional annotation linked core genes to essential cellular processes, while accessory and unique genes were enriched in genetic variability, defense mechanisms, and secondary metabolism. The pan-genome exhibited a high proportion of hypothetical genes, necessitating further functional characterization. Antimicrobial resistance (AMR) screening detected the tva(A) and lnu(C) genes associated with tiamulin and lincomycin resistance, respectively, in specific lineages and STs. Virulence factor analysis identified genes linked to hemolysin production, iron uptake, and survival in host environments in most isolates, with a subset of genes demonstrating lineage-specific associations that are further linked to pathogenic potential. This comprehensive genomic epidemiological analysis elucidates the genetic diversity, antimicrobial resistance, and virulence of B", "token_count": 520, "char_count": 1914, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7203, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:34.766412", "source": { "split": "train_shard_00001", "doc_id": 47 }, "chunk_id": "train_shard_00001_47_0", "global_id": 5734 }, { "text": "hyodysenteriae globally, enhancing understanding of its epidemiology and guiding interventions to mitigate swine dysentery.

Importance

Brachyspira hyodysenteriae, the primary causative agent of swine dysentery, remains a less-studied pathogen than other bacterial species that impact animal health. This study uses whole-genome sequencing and advanced phylogenomic approaches to reveal the genetic diversity and geographical distribution of B. hyodysenteriae isolates, focusing on U.S. populations. The identification of nine distinct phylogenetic lineages and associated sublineages highlights the pathogen's complex population structure and regional variation. Importantly, the study detects AMR genes, including tva(A) and lnu(C), linked to tiamulin and lincomycin resistance, that may pose significant challenges to disease management. The analysis also identifies virulence-associated genes, shedding light on molecular mechanisms underlying pathogenicity. By combining core-genome SNP phylogenies with multilocus sequence typing and accessory genome insights, this work provides a robust framework for a better understanding of B. hyodysenteriae evolution. Overall, these findings underscore the importance of genomic surveillance in informing control strategies and improving swine health worldwide.\n\nGenomic insights into the population structure, antimicrobial resistance, and virulence of <i>Brachyspira hyodysenteriae</i> from diverse geographical regions.", "token_count": 380, "char_count": 1525, "word_count": 177, "semantic_coherence": 1, "information_density": 0.7627, "quality_score": 0.8814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:35.359018", "source": { "split": "train_shard_00001", "doc_id": 47 }, "chunk_id": "train_shard_00001_47_1", "global_id": 5735 }, { "text": "Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.\n\nNiche-specific evolution and gene exchange of Salmonella in retail pork and chicken", "token_count": 316, "char_count": 1524, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:35.915242", "source": { "split": "train_shard_00001", "doc_id": 48 }, "chunk_id": "train_shard_00001_48_0", "global_id": 5736 }, { "text": "

ABSTRACT

Background

In the United States, Borrelia burgdorferi ( Bb ) is the principal etiologic agent of Lyme disease. The complex structure of Bb genomes has posed challenges for genomic studies because homology among the bacterium’s many plasmids, which account for ∼40% of the genome by length, has made them difficult to sequence and assemble.

Results

We used long-read sequencing to generate near-complete assemblies of 62 isolates of human-derived Bb and collected public genomes with plasmid sequences. We characterized genetic diversity and population structure in the resulting set of 82 plasmid-complete Borrelia burgdorferi sensu stricto genomes. The Bb core genome is encoded by a chromosome and the conserved plasmids cp26, lp54, and lp17; the accessory genome is encoded by all other plasmids and the distal arm of the chromosome. Near-complete genomes reveal that the most granular Bb genotypes are clonal expansions of complex rearrangements among accessory genome elements. Ribosomal spacer types (RST) represent multiple collections of such genotypes, whereas OspC types are usually clonal. Structural rearrangements are non-randomly distributed throughout the genome, with cp32 plasmids undergoing dense exchanges and most linear plasmids, except lp54, sharing blocks among themselves and with the distal arm of the chromosome. OspC type A strains, known to possess greater virulence in humans, are distinguished by the presence of lp28-1 and lp56. Rearrangements among plasmids tended to preserve gene content, suggesting functional constraints among gene networks. Using k-partite graph decompositions, we identified gene sets with correlation patterns suggestive of conserved functional modules.

Conclusions

Long-read assemblies reveal that Bb population genetic structure results from clonal expansion of lineages that have undergone complex rearrangements among plasmid-encoded accessory genome elements", "token_count": 504, "char_count": 1964, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8007, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:36.570929", "source": { "split": "train_shard_00001", "doc_id": 49 }, "chunk_id": "train_shard_00001_49_0", "global_id": 5737 }, { "text": "Genetic structure is preserved among genes even when plasmid rearrangements occur, suggesting that selection among epistatic loci maintains functional genetic networks. The analysis of near-complete genomes assembled using long-read sequencing methods advances our understanding of Bb biology and Lyme disease pathogenesis by providing the first detailed view of population variation in previously inaccessible areas of the Bb genome.\n\nComplex exchanges among plasmids and clonal expansion of lineages shape the population structure and virulence of Borrelia burgdorferi", "token_count": 127, "char_count": 577, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:36.987004", "source": { "split": "train_shard_00001", "doc_id": 49 }, "chunk_id": "train_shard_00001_49_1", "global_id": 5738 }, { "text": "

Background

High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging.

Results

We developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific long-read amplicons. We focused on the wheat microbiome as a proof-of-principle and demonstrate strain-level resolution for the wheat-associated Pseudomonas microbiome and the ubiquitous fungal pathogen Zymoseptoria tritici. We achieved an order of magnitude higher phylogenetic resolution compared to existing ribosomal amplicons. The designed amplicons accurately capture species and strain diversity outperforming full-length 16S and ITS amplicons. Furthermore, we tracked microbial communities in the wheat phyllosphere across time and space to establish fine-grained species and strain-specific dynamics. To expand the utility of our approach, we generated pangenome-informed amplicon templates for additional key bacterial and fungal genera.

Conclusions

Pangenome-informed microbiome profiling enables the tracking of microbial community dynamics in complex environments and overcomes limitations in phylogenetic resolution. Video Abstract.\n\nHigh-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons.", "token_count": 335, "char_count": 1409, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:37.569950", "source": { "split": "train_shard_00001", "doc_id": 50 }, "chunk_id": "train_shard_00001_50_0", "global_id": 5739 }, { "text": "Yeasts are gaining increasing attention for their potential health benefits as probiotics in recent years. Researchers are actively searching for new yeast strains with probiotic properties (i.e, Debaryomyces hansenii; Kluyveromyces marxianus; Yarrowia lipolytica; Pichia hudriavzevii; and Torulaspora delbrueckii) from various sources, including traditional fermented foods, the human gut, and the environment. This exploration is expanding the pool of potential probiotic yeasts beyond the well-studied Saccharomyces boulardii. Research suggests that specific yeast strains possess properties that could be beneficial for managing conditions like inflammatory bowel disease, irritable bowel syndrome, skin disorders, and allergies. Additionally, probiotic yeasts may compete with pathogenic bacteria for adhesion sites and nutrients, thereby inhibiting their growth and colonization. They might also produce antimicrobial compounds that directly eliminate harmful bacteria. To achieve these goals, the approach that uses probiotics for human health is changing. Next-generation yeast probiotics are emerging as a powerful new approach in the field of live biotherapeutics. By using genetic engineering, scientists are able to equip these tools with specialized capabilities. However, most research on these probiotic yeasts is still in its early stages, and more clinical trials are needed to confirm their efficacy and safety for various health conditions. This review could provide a brief overview of the situation in this field.\n\nProbiotic Yeasts: A Developing Reality?", "token_count": 382, "char_count": 1617, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:38.630506", "source": { "split": "train_shard_00001", "doc_id": 51 }, "chunk_id": "train_shard_00001_51_0", "global_id": 5740 }, { "text": "

Objective

Human brucellosis has re-emerged as a major public health threat in Jiangsu Province, but the sources and transmission dynamics of circulating strains remain poorly understood.

Methods

In this study, we integrated conventional biotyping, whole-genome sequencing single-nucleotide polymorphism (WGS-SNP) analysis, and core genome multilocus sequence typing (cgMLST) to investigate the phylogenetic relationships of Brucella melitensis in the region.

Results

Among 89 isolates analyzed, all were confirmed as B. melitensis (16 as biovar 1 and 73 as biovar 3), with a widespread geographic distribution across 15 cities in Jiangsu and adjacent areas, indicating extensive regional dissemination. All strains belonged to sequence type 8 (ST8) and genotype group II, clustering within the East Mediterranean lineage. Genomic resolution classified these strains into five SNP clades (C-I to C-V) and 17 SNP-based genotypes (STs), revealing a ladder-like phylogenetic structure. The lack of distinct geographic clustering suggests frequent cross-regional transmission, likely facilitated by the movement of infected sheep and goats. Phylogenomic analysis through cgMLST revealed distinct clustering of the 17 STs into two major groups (G-I and G-II), with 15 STs (88.2%) showing high genetic concordance between Jiangsu isolates and strains from China's northeastern and northwestern. This compelling genomic evidence establishes that the current human brucellosis epidemic in Jiangsu is being driven by the nationwide expansion of dominant B. melitensis lineages.

Conclusion

The findings provide crucial insights into the infection sources and interregional transmission dynamics of brucellosis in southern China, highlighting the significant role of domestic animal movement in pathogen dissemination, demanding coordinated cross-regional interventions including strict implementing intervention strategies and enhance disease surveillance.", "token_count": 507, "char_count": 1995, "word_count": 252, "semantic_coherence": 1, "information_density": 0.7024, "quality_score": 0.8512, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:39.292878", "source": { "split": "train_shard_00001", "doc_id": 52 }, "chunk_id": "train_shard_00001_52_0", "global_id": 5741 }, { "text": "Phylogenetic evidence for nationwide expansion <i>Brucella melitensis</i> lineages drives the re-emerging and epidemic of human brucellosis in Jiangsu, China.", "token_count": 55, "char_count": 170, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:39.653026", "source": { "split": "train_shard_00001", "doc_id": 52 }, "chunk_id": "train_shard_00001_52_1", "global_id": 5742 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) are major foodborne pathogens that result in thousands of hospitalizations each year in the United States. Cattle, the natural reservoir, harbor STEC asymptomatically at the recto-anal junction (RAJ). The molecular mechanisms that allow STEC and non-STEC E. coli to adhere to the RAJ are not fully understood, in part because most adherence studies utilize human cell culture models. To identify a set of bovine-specific E. coli adherence factors, we used the primary RAJ squamous epithelial (RSE) cell-adherence assay to coculture RSE cells from healthy Holstein cattle with diverse E. coli strains from bovine and nonbovine sources. We hypothesized that a comparative genomic analysis of the strains would reveal factors associated with RSE adherence. After performing adherence assays with historical strains from the E. coli Reference Center (n = 62) and strains newly isolated from the RAJ (n = 15), we used the bioinformatic tool Roary to create a pangenome of this collection. We classified strains as either low or high adherence and using the Scoary program compiled a list of accessory genes correlated with the \"high adherence\" strains. While none of the correlations were statistically significant, several gene clusters were associated with the high-adherence phenotype, including two that encode uncharacterized proteins. We also demonstrated that non-STEC E. coli strains from the RAJ are more adherent than other isolates and can outcompete STEC in coculture with RSEs. Further analysis of adherence-associated gene clusters may lead to an improved understanding of the molecular mechanisms of RSE adherence and may help develop probiotics targeting STEC in cattle.

Importance

E. coli strains that produce Shiga toxin cause foodborne illness in humans but colonize cattle asymptomatically", "token_count": 523, "char_count": 1927, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:40.290546", "source": { "split": "train_shard_00001", "doc_id": 53 }, "chunk_id": "train_shard_00001_53_0", "global_id": 5743 }, { "text": "The molecular mechanisms that E. coli uses to adhere to cattle cells are largely unknown. Various strategies are used to control E. coli in livestock and limit the risk of outbreaks. These include vaccinating animals against common E. coli strains and supplementing their feed with probiotics to reduce the carriage of pathogens. No strategy is completely effective, and probiotics often fail to colonize the animals. We sought to clarify the genes required for E. coli adherence in cattle by quantifying the attachment to bovine cells in a diverse set of bacteria. We also isolated nonpathogenic E. coli from healthy cows and showed that a representative isolate could outcompete pathogenic strains in cocultures. We propose that the focused study of these strains and their adherence factors will better inform the design of probiotics and vaccines for livestock.\n\nInvestigating the adherence factors of Escherichia coli at the bovine recto-anal junction.", "token_count": 262, "char_count": 999, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:40.843451", "source": { "split": "train_shard_00001", "doc_id": 53 }, "chunk_id": "train_shard_00001_53_1", "global_id": 5744 }, { "text": "Mycobacterium tuberculosis (Mtb) is the causative agent of tuberculosis (TB), an infectious disease that is a major killer worldwide. Due to selection pressure caused by the use of antibacterial drugs, Mtb is characterised by mutational events that have given rise to multi drug resistant (MDR) and extensively drug resistant (XDR) phenotypes. The rate at which mutations occur is an important factor in the study of molecular evolution, and it helps understand gene evolution. Within the same species, different protein-coding genes evolve at different rates. To estimate the rates of molecular evolution of protein-coding genes, a commonly used parameter is the ratio dN/dS, where dN is the rate of non-synonymous substitutions and dS is the rate of synonymous substitutions. Here, we determined the estimated rates of molecular evolution of select biological processes and molecular functions across 264 strains of Mtb. We also investigated the molecular evolutionary rates of core genes of Mtb by computing the dN/dS values, and estimated the pan genome of the 264 strains of Mtb. Our results show that the cellular amino acid metabolic process and the kinase activity function evolve at a significantly higher rate, while the carbohydrate metabolic process evolves at a significantly lower rate for M. tuberculosis. These high rates of evolution correlate well with Mtb physiology and pathogenicity. We further propose that the core genome of M. tuberculosis likely experiences varying rates of molecular evolution which may drive an interplay between core genome and accessory genome during M. tuberculosis evolution.\n\nLarge-scale Pan Genomic Analysis of Mycobacterium tuberculosis Reveals Key Insights Into Molecular Evolutionary Rate of Specific Processes and Functions.", "token_count": 481, "char_count": 1855, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5698, "quality_score": 0.7849, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:41.489179", "source": { "split": "train_shard_00001", "doc_id": 54 }, "chunk_id": "train_shard_00001_54_0", "global_id": 5745 }, { "text": "Abstract

Sorghum is a cereal crop grown for food, feed, and biofuel, yet the genomic diversity of elite commercial lines remains underexplored. Here, we assembled a sorghum pangenome from long-read sequences of 46 U.S. ex-Plant Variety Protection Act (ex-PVP) cultivars and a haplotype-resolved assembly of one wild accession. The pangenome revealed largely conserved genomic architecture across elite lines but identified presence–absence variations (PAVs) in 28% of gene families, including genes involved in stress responses and starch metabolism, such as STARCH BRANCHING ENZYME I (SBE1). Selective sweep analyses detected strong signals at key flowering-time loci (Ma1/SbPRR37, Ma2, Ma6) and circadian/light regulators (PHOT1, DET1, XAP5), with PHYA showing copy number variations (CNVs). Analysis of 24 wild accessions, beyond the core pangenome panel, detected CNVs in MULTIDRUG AND TOXIC COMPOUND EXTRUSION (MATE) transporters, potentially reflecting selection or breeding for enhanced herbicide detoxification. These results highlight breeding-shaped regions and position the pangenome as a resource for sorghum improvement.

\n\nPangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement", "token_count": 364, "char_count": 1289, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7674, "quality_score": 0.8837, "entities": { "genes": [ "PHOT1", "SBE1", "DET1", "XAP5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:42.067493", "source": { "split": "train_shard_00001", "doc_id": 55 }, "chunk_id": "train_shard_00001_55_0", "global_id": 5746 }, { "text": "Investigating the diversity of a given species could give clues for the development of autochthonous starter cultures. However, few studies have focused on the intraspecies diversity of Lactobacillus delbrueckii strains, a technologically important lactic acid bacterium for the dairy industry. For this reason, Lactobacillus delbrueckii strains from the Saint-Nectaire Protected Designation of Origin (PDO) area were isolated and characterized. Genetic diversity was determined based on core genome phylogenetic reconstruction and pangenome analysis, while phenotypic assessments encompassed proteolysis and volatile compound production potential. A total of 15 L. delbrueckii ssp. lactis unique new strains were obtained. The genetic analysis and further proteolytic activities measurement revealed low variability among these Saint-Nectaire strains, while substantial genetic variability was observed within the L. delbrueckii ssp. lactis subspecies as a whole. The volatile compound profiles slightly differed among strains, and some strains produced volatile compounds that could be of particular interest for cheese flavor development. While the genetic diversity among Saint-Nectaire strains was relatively modest compared to overall subspecies diversity, their distinct characteristics and pronounced differentiation from publicly available genomes position them as promising candidates for developing autochthonous starter cultures for cheese production.\n\nGenomic Characterization of Wild Lactobacillus delbrueckii Strains Reveals Low Diversity but Strong Typicity.", "token_count": 387, "char_count": 1623, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:42.684502", "source": { "split": "train_shard_00001", "doc_id": 56 }, "chunk_id": "train_shard_00001_56_0", "global_id": 5747 }, { "text": "

Background

Microbial community played an essential role in ecosystem processes, be it mangrove wetland or other intertidal ecologies. Several enzymatic activities like hydrolases are effective ecological indicators of soil microbial function. So far, little is known on halophilic bacterial contribution and function on a genomic viewpoint of Indian Sundarban Wetland. Considering the above mentioned issues, the aims of this study was to understand the life style, metabolic functionalities and genomic features of the isolated bacterium, Salinicoccus roseus strain RF1H. A comparative genome-based study of S. roseus has not been reported yet. Henceforth, we have considered the inclusion of the intra-species genome comparison of S. roseus to gain insight into the high degree of variation in the genome of strain RF1H among others.

Results

Salinicoccus roseus strain RF1H is a pink-red pigmented, Gram-positive and non-motile cocci. The bacterium exhibited high salt tolerance (up to 15% NaCl), antibiotic resistance, biofilm formation and secretion of extracellular hydrolytic enzymes. The circular genome was approximately 2.62978 Mb in size, encoding 574 predicted genes with GC content 49.5%. Presence of genomic elements (prophages, transposable elements, CRISPR-Cas system) represented bacterial virulence and multidrug-resistance. Furthermore, genes associated with salt tolerance, temperature adaptation and DNA repair system were distributed in 17 genomic islands. Genes related to hydrocarbon degradation manifested metabolic capability of the bacterium for potential biotechnological applications. A comparative pangenome analysis revealed two-component response regulator, modified C4-dicarboxylate transport system and osmotic stress regulated ATP-binding proteins. Presence of genes encoding arginine decarboxylase (ADC) enzyme being involved in biofilm formation was reported from the genome. In silico study revealed the protein is thermostable and made up with ~ 415 amino acids, and hydrophilic in nature", "token_count": 519, "char_count": 2041, "word_count": 272, "semantic_coherence": 1, "information_density": 0.7022, "quality_score": 0.8511, "entities": { "genes": [ "RF1H" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature", "osmotic" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:43.346316", "source": { "split": "train_shard_00001", "doc_id": 57 }, "chunk_id": "train_shard_00001_57_0", "global_id": 5748 }, { "text": "Three motifs appeared to be evolutionary conserved in all Salinicoccus sequences.

Conclusion

The first report of whole genome analysis of Salinicoccus roseus strain RF1H provided information of metabolic functionalities, biofilm formation, resistance mechanism and adaptation strategies to thrive in climate-change induced vulnerable spot like Sundarban. Comparative genome analysis highlighted the unique genome content that contributed the strain's adaptability. The biomolecules produced during metabolism are important sources of compounds with potential beneficial applications in pharmaceuticals.\n\nDelving into the lifestyle of Sundarban Wetland resident, biofilm producing, halotolerant Salinicoccus roseus: a comparative genomics-based intervention.", "token_count": 167, "char_count": 764, "word_count": 89, "semantic_coherence": 1, "information_density": 0.809, "quality_score": 0.9045, "entities": { "genes": [ "RF1H" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:43.784508", "source": { "split": "train_shard_00001", "doc_id": 57 }, "chunk_id": "train_shard_00001_57_1", "global_id": 5749 }, { "text": "Accurate detection of mosaic and somatic structural variants (SVs) provides early diagnostic and therapeutic evidence for cancers. While long-read whole-genome sequencing leads to more accurate SV detection than short read sequencing, existing long-read SV callers only look at alignment against a single reference genome and are susceptible to systematic false discovery caused by germline differences between the individual genome and the reference genome. Here we develop a new SV calling method that jointly considers the alignment against a pangenome and the de novo assembly of the germline genome. It dramatically reduces false positive mosaic SVs in normal samples and somatic SVs in cancer cell lines with little loss in sensitivity. Our study highlights the essential need for pangenome or personal genome assembly to integrate SV calls for both SV discoveries and clinical diagnostics.\n\nImproving long-read somatic structural variant calling with pangenome and de novo personal genome assembly", "token_count": 207, "char_count": 1004, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6463, "quality_score": 0.8231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:44.253482", "source": { "split": "train_shard_00001", "doc_id": 58 }, "chunk_id": "train_shard_00001_58_0", "global_id": 5750 }, { "text": "Kluyveromyces marxianus is an emerging host for metabolic engineering. This thermotolerant yeast is the fastest growing eukaryote, has high flux through the TCA cycle, and can metabolize a broad range of C5, C6, and C12 carbon sources. In comparison to the common host Saccharomyces cerevisiae, this non-conventional yeast suffers from a lack of metabolic engineering tools to control gene expression over a wide transcriptional range. To address this issue, we designed a library of 25 native-derived promoters from K. marxanius CBS6556 that spans 87-fold transcriptional strength under glucose metabolism. Six promoters from the library were further characterized in both glucose and xylose as well as across various temperatures from 30 to 45 ​°C. The temperature study revealed that in most cases EGFP expression decreased with elevating temperature; however, two promoters, P SSA3 and P ADH1 , increased expression above 40 ​°C in both xylose and glucose. The six-promoter set was also validated in xylose for triacetic acid lactone (TAL) production. By controlling the expression level of heterologous 2-pyrone synthase (2-PS), the specific TAL titer increased over 8-fold at 37 ​°C. Cultures at 41 ​°C exhibited a similar TAL biosynthesis capability, while at 30 ​°C TAL levels were lower. Taken together, these results advance the metabolic engineering tool set in K. marxianus and further develop this new host for chemical biosynthesis.\n\nDeveloping a broad-range promoter set for metabolic engineering in the thermotolerant yeast Kluyveromyces marxianus.", "token_count": 489, "char_count": 1635, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [ "SSA3", "CBS6556", "ADH1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:44.898133", "source": { "split": "train_shard_00001", "doc_id": 59 }, "chunk_id": "train_shard_00001_59_0", "global_id": 5751 }, { "text": "Staphylococcus aureus sequence type (ST) 88, encompassing both methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) phenotypes, is globally prevalent and commonly associated with skin and soft tissue infections. Despite its widespread occurrence, comprehensive genomic studies on this clone remain scarce. In this study, we performed detailed genomic analyses on 130 ST88 isolates derived from severe bloodstream infections alongside 275 publicly available ST88 sequences. Our phylogenetic analysis identified four distinct clades, with evidence suggesting independent evolution and significant clonal expansion of ST88 in China, particularly within clade I, which appeared to have emerged circa 1964. We documented notable interregional, international, and even intercontinental transmission of ST88 isolates. Variability in the distribution of SCCmec and spa types was observed across clades. Our in silico analyses indicated distinct patterns in the distribution of resistance genes, virulence genes, and mobile genetic elements among the clades, with clade I notably harboring the highest prevalence of the intact sraP gene and an independently acquired novel prophage, φST88-1. Conversely, clade IV exhibited deletions within the sasC gene, with certain sub-clades lacking the sdrDE and fnbB genes, underscoring the superior adhesive capabilities of clade I. In vitro experiments confirmed enhanced biofilm formation in clade I isolates, although the levels of hemolysis and cytotoxicity were similar across clades. Pan-genome-wide association study revealed that core SNPs, rather than the accessory genome, are the primary contributors to the diversification of the ST88 clades", "token_count": 475, "char_count": 1790, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [ "ST88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:45.544694", "source": { "split": "train_shard_00001", "doc_id": 60 }, "chunk_id": "train_shard_00001_60_0", "global_id": 5752 }, { "text": "These findings enrich our understanding of the genetic foundations underpinning the transmission dynamics and phenotypic diversity of ST88 clones globally.IMPORTANCEUnderstanding the evolution and transmission of Staphylococcus aureus ST88 clones is critically important due to their spread within food, hospital, and community environments, leading to significant health issues. Despite its prevalence, detailed genomic insights into ST88, particularly regarding its diversity and evolutionary dynamics, have been lacking. Our comprehensive genomic analysis of 130 ST88 isolates from severe bloodstream infections, alongside 275 sequences from public databases, significantly advances our understanding of this pathogen. We identified four distinct evolutionary clades, demonstrating the independent evolution and substantial clonal expansion of ST88 in China, as well as its ability to spread across regions and continents. The diversity among the isolates was evident in their unique profiles of SCCmec elements, antibiotic resistance genes, virulence genes, and mobile genetic elements. Our findings underscore the critical role of core genomic variations over accessory elements in driving the diversification of ST88. This enhanced understanding provides new insights that could inform more effective control strategies, crucial for developing interventions to combat the global spread of this formidable pathogen.\n\nDissecting the genetic features and evolution of Staphylococcus aureus sequence type 88: a global perspective.", "token_count": 327, "char_count": 1553, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8342, "entities": { "genes": [ "ST88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:46.112440", "source": { "split": "train_shard_00001", "doc_id": 60 }, "chunk_id": "train_shard_00001_60_1", "global_id": 5753 }, { "text": "

Background

Fruit acidity and color are important quality attributes in peaches. Although there are some exceptions, blood-fleshed peaches typically have a sour taste. However, little is known about the genetic variations linking organic acid and color regulation in peaches.

Results

Here, we report a peach graph-based pangenome constructed from sixteen individual genome assemblies, capturing abundant structural variations and 82.3 Mb of sequences absent in the reference genome. Pangenome analysis reveals a long terminal repeat retrotransposon insertion in the promoter of the NAC transcription factor (TF) PpBL in blood-fleshed peaches, which enhances PpBL expression. Genome-wide association study identifies a significant association between PpBL and malate content. Silencing PpBL in peach fruit and ectopic overexpression of PpBL in tomatoes confirm that PpBL is a positive regulator of malate accumulation. Furthermore, we demonstrate that PpBL works synergistically with another NAC TF, PpNAC1, to activate the transcription of the aluminum-activated malate transporter PpALMT4, leading to increased malate content.

Conclusions

These findings, along with previous research showing that PpBL and PpNAC1 also regulate anthocyanin accumulation, explain the red coloration and sour taste in blood-fleshed peach fruits.\n\nGraph pangenome reveals the regulation of malate content in blood-fleshed peach by NAC transcription factors.", "token_count": 361, "char_count": 1458, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:46.692404", "source": { "split": "train_shard_00001", "doc_id": 61 }, "chunk_id": "train_shard_00001_61_0", "global_id": 5754 }, { "text": "

Background

The conventional method of antigen-based serotyping for Salmonella poses challenges due to the necessity of utilizing over 150 antisera. More recently, in silico Salmonella serotyping has emerged as a predictive alternative. The purpose of this study was to predict the serovars of 62 Salmonella enterica strains isolated from Korean poultry operations and their genetic characteristics using whole genome sequencing. The analysis employed diverse methods, including ribosomal, and core genome multi-locus sequence typing (MLST), based on Salmonella In Silico Typing Resource (SISTR). Pangenome, clusters of orthologous groups (COG) analysis, and identification of virulence and antibiotic resistance genes were conducted.

Results

Salmonella enterica subspecies enterica serovars were observed and clustered based on the pangenome and phylogenetic tree: 21 Salmonella Albany (Albany), 13 Salmonella Bareilly (Bareilly), and 28 Salmonella Mbandaka (Mbandaka). The most frequently observed sequence types for the three serovars were ST292 in Albany, ST203 in Bareilly, and ST413 in Mbandaka. 18 antibiotic resistance genes showed varying presences based on the serovars, including Albany (qacEdelta1, tet(D), CARB-3 (blaCARB-3), and dfrA1) and Bareilly (aac(6')-ly). Intriguingly, a mutated gyrA (Ser83 → Phe, serine to phenylalanine) was observed in all 21 Albany strains, whereas Bareilly and Mbandaka carried the wild-type gyrA", "token_count": 427, "char_count": 1454, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6546, "quality_score": 0.8273, "entities": { "genes": [ "ST413", "ST292", "ST203" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:47.324219", "source": { "split": "train_shard_00001", "doc_id": 62 }, "chunk_id": "train_shard_00001_62_0", "global_id": 5755 }, { "text": "Among 130 virulence genes analyzed, 107 were present in all 62 Salmonella strains, with Mbandaka strains exhibiting a higher prevalence of virulence genes related to fimbrial adherence compared to those of Albany and Bareilly.

Conclusions

The study identified distinct genetic characteristics among the three Salmonella serovars using whole genome sequencing. Albany carried a unique mutation in gyrA, occurring in the quinolone resistance-determining region. Additionally, the virulence gene profile of Mbandaka differed from the other serovars, particularly in fimbrial adherence genes. These findings demonstrate the effectiveness of in silico approaches in predicting Salmonella serovars and highlight genetic differences that may inform strategies for antibiotic resistance and virulence control, such as developing rapid diagnostic tools to detect the AMR (e.g. tet (D), and gyrA) or targeting serovar-specific virulence factors like fimbrial adherence genes in Mbandaka to mitigate pathogenicity.\n\nGenetic characterization and in silico serotyping of 62 Salmonella enterica isolated from Korean poultry operations.", "token_count": 279, "char_count": 1128, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:47.877920", "source": { "split": "train_shard_00001", "doc_id": 62 }, "chunk_id": "train_shard_00001_62_1", "global_id": 5756 }, { "text": "

Summary

Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety in methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. Using Mycobacterium tuberculosis, a clonally evolving bacterium with a small accessory genome, as a model system, we systematically evaluated sources of variability in pan-genome estimates. Our analysis revealed that differences in assembly type (short-read versus hybrid), annotation pipeline, and pan-genome software, significantly impact predictions of core and accessory genome size. Extending our analysis to two additional bacterial species, Escherichia coli and Staphylococcus aureus, we observed consistent tool-dependent biases but species-specific patterns in pan-genome variability. Our findings highlight the importance of integrating nucleotide- and protein-level analyses to improve the reliability and reproducibility of pan-genome studies across diverse bacterial populations.

Availability and implementation

Panqc is freely available under an MIT license at https://github.com/maxgmarin/panqc.\n\nPitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.", "token_count": 303, "char_count": 1294, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6918, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:48.442465", "source": { "split": "train_shard_00001", "doc_id": 63 }, "chunk_id": "train_shard_00001_63_0", "global_id": 5757 }, { "text": "

Background

Kluyveromyces marxianus is a thermotolerant yeast with multiple biotechnological potentials for industrial applications, which can metabolize a broad range of carbon sources, including less conventional sugars like lactose, xylose, arabinose and inulin. These phenotypic traits are sustained even up to 45 °C, what makes it a relevant candidate for industrial biotechnology applications, such as ethanol production. It is therefore of much interest to get more insight into the metabolism of this yeast. Recent studies suggested, that thermotolerance is achieved by reducing the number of growth-determining proteins or suppressing oxidative phosphorylation. Here we aimed to find related factors contributing to the thermotolerance of K. marxianus.

Results

Here, we reported the first genome-scale metabolic model of Kluyveromyces marxianus, iSM996, using a publicly available Kluyveromyces lactis model as template. The model was manually curated and refined to include the missing species-specific metabolic capabilities. The iSM996 model includes 1913 reactions, associated with 996 genes and 1531 metabolites. It performed well to predict the carbon source utilization and growth rates under different growth conditions. Moreover, the model was coupled with transcriptomics data and used to perform simulations at various growth temperatures.

Conclusions

K. marxianus iSM996 represents a well-annotated metabolic model of thermotolerant yeast, which provides a new insight into theoretical metabolic profiles at different temperatures of K. marxianus. This could accelerate the integrative analysis of multi-omics data, leading to model-driven strain design and improvement.\n\nReconstruction and analysis of a Kluyveromyces marxianus genome-scale metabolic model.", "token_count": 450, "char_count": 1800, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8362, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:49.107780", "source": { "split": "train_shard_00001", "doc_id": 64 }, "chunk_id": "train_shard_00001_64_0", "global_id": 5758 }, { "text": "Bacteria infecting the plant phloem represent a growing threat worldwide. While these organisms often resist in vitro culture, they multiply both in plant sieve elements and hemipteran vectors. Such cross-kingdom parasitic lifestyle has emerged in diverse taxa via distinct ecological routes. In the genus Arsenophonus, the phloem pathogens \"Candidatus Arsenophonus phytopathogenicus\" (Ap) and \"Ca. Phlomobacter fragariae\" (Pf) have evolved from insect endosymbionts, but the genetic mechanisms underlying this transition have not been explored. To fill this gap, we obtained the genomes of both strains from insect host metagenomes. The resulting assemblies are highly similar in size and functional repertoire, rich in viral sequences, and closely resemble the genomes of several facultative endosymbiotic Arsenophonus strains of sap-sucking hemipterans. However, a phylogenomic analysis demonstrated distinct origins, as Ap belongs to the \"Triatominarum\" clade, whereas Pf represents a distant species. We identified a set of orthologs encoded only by Ap and Pf in the genus, including hydrolytic enzymes likely targeting plant substrates. In particular, both bacteria encode putative plant cell wall-degrading enzymes and cysteine peptidases related to xylellain, a papain-like peptidase from Xylella fastidiosa, for which close homologs are found in diverse Pseudomonadota infecting the plant vasculature. In silico predictions and gene expression analyses further support a role during phloem colonization for several of the shared orthologs. We conclude that the double emergence of phytopathogenicity in Arsenophonus may have been mediated by a few horizontal gene transfer events, involving genes acquired from other Pseudomonadota, including phytopathogens.

Importance

We investigate the genetic mechanisms of a transition in bacterial lifestyle", "token_count": 519, "char_count": 1939, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6798, "quality_score": 0.8399, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:51:49.780595", "source": { "split": "train_shard_00001", "doc_id": 65 }, "chunk_id": "train_shard_00001_65_0", "global_id": 5759 }, { "text": "We focus on two phloem pathogens belonging to the genus Arsenophonus: \"Candidatus Arsenophonus phytopathogenicus\" and \"Ca. Phlomobacter fragariae.\" Both bacteria cause economically significant pathologies, and they have likely emerged among facultative insect endosymbionts. Our genomic analyses show that both strains are highly similar to other strains of the genus associated with sap-sucking hemipterans, suggesting a recent lifestyle shift. Importantly, although the phytopathogenic Arsenophonus strains belong to distant clades, they share a small set of orthologs unique in the genus pangenome. We provide evidence that several of these genes produce hydrolytic enzymes that are secreted and may target plant substrates. The acquisition and exchange of these genes may thus have played a pivotal role in the lifestyle transition of the phytopathogenic Arsenophonus strains.\n\nFrom insect endosymbiont to phloem colonizer: comparative genomics unveils the lifestyle transition of phytopathogenic <i>Arsenophonus</i> strains.", "token_count": 300, "char_count": 1076, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6812, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:50.392413", "source": { "split": "train_shard_00001", "doc_id": 65 }, "chunk_id": "train_shard_00001_65_1", "global_id": 5760 }, { "text": "Harmful algal blooms (HABs) pose a significant global threat to water ecosystems, prompting extensive research into their inhibition and control strategies. This study presents genomic and bioinformatic analyses to investigate the algicidal potential and elucidate the survival mechanisms in harsh conditions of newly identified Halobacillus species three strains (SSTM10-2T, SSBR10-3T, and SSHM10-5T) isolated from saline environments. Moreover, genomic and bioinformatic analyses were conducted to elucidate their survival mechanisms in harsh conditions. Moreover, comparative genomic analysis revealed a diverse set of orthologous genes, with a core genome primarily associated with metabolism and information processing. Pangenome analysis highlighted accessory and unique genes potentially involved in environmental adaptation and stress response. Functional annotation using KEGG pathways identified genes linked to xenobiotic compound degradation, stress tolerance, and salt adaptation. Additionally, the study elucidated potential mechanisms underlying algicidal activity, implicating Carbohydrate-Active enZYmes (CAZymes), cytochrome P450 oxidases (CYP), and quorum sensing (QS) systems. Finally, analysis of KEGG pathways related to microcystin degradation suggested the strains' capacity to mitigate HABs. Thus, this research enhances understanding of the genomic diversity, phylogeny, and functional characteristics of Halobacillus species, offering insights into their ecological roles and potential applications in biotechnology and environmental management.\n\nComparative Genome Analysis of Three Halobacillus Strains Isolated From Saline Environments Reveal Potential Salt Tolerance and Algicidal Mechanisms.", "token_count": 412, "char_count": 1756, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [ "SSHM10", "SSTM10", "SSBR10" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:51.017348", "source": { "split": "train_shard_00001", "doc_id": 66 }, "chunk_id": "train_shard_00001_66_0", "global_id": 5761 }, { "text": "

Introduction

Free-living amoebae of the Naegleria genus belong to the major protist clade Heterolobosea and are ubiquitously distributed in soil and freshwater habitats. Of the 47 Naegleria species described, N. fowleri is the only one being pathogenic to humans, causing a rare but fulminant primary amoebic meningoencephalitis. Some Naegleria genome sequences are publicly available, but the genetic basis for Naegleria diversity and ability to thrive in diverse environments (including human brain) remains unclear.

Methods

Herein, we constructed a high-quality Naegleria genus pangenome to obtain a comprehensive catalog of genes encoded by these amoebae. For this, we first sequenced, assembled, and annotated six new Naegleria genomes.

Results and discussion

Genome architecture analyses revealed that Naegleria may use genome plasticity features such as ploidy/aneuploidy to modulate their behavior in different environments. When comparing 14 near-to-complete genome sequences, our results estimated the theoretical Naegleria pangenome as a closed genome, with 13,943 genes, including 3,563 core and 10,380 accessory genes. The functional annotations revealed that a large fraction of Naegleria genes show significant sequence similarity with those already described in other kingdoms, namely Animalia and Plantae. Comparative analyses highlighted a remarkable genomic heterogeneity, even for closely related strains and demonstrate that Naegleria harbors extensive genome variability, reflected in different metabolic repertoires", "token_count": 460, "char_count": 1637, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7228, "quality_score": 0.8614, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:51.659238", "source": { "split": "train_shard_00001", "doc_id": 67 }, "chunk_id": "train_shard_00001_67_0", "global_id": 5762 }, { "text": "If Naegleria core genome was enriched in conserved genes essential for metabolic, regulatory and survival processes, the accessory genome revealed the presence of genes involved in stress response, macromolecule modifications, cell signaling and immune response. Commonly reported N. fowleri virulence-associated genes were present in both core and accessory genomes, suggesting that N. fowleri's ability to infect human brain could be related to its unique species-specific genes (mostly of unknown function) and/or to differential gene expression. The construction of Naegleria first pangenome allowed us to move away from a single reference genome (that does not necessarily represent each species as a whole) and to identify essential and dispensable genes in Naegleria evolution, diversity and biology, paving the way for further genomic and post-genomic studies.\n\nNaegleria genus pangenome reveals new structural and functional insights into the versatility of these free-living amoebae.", "token_count": 259, "char_count": 1035, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7338, "quality_score": 0.8669, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:52.200067", "source": { "split": "train_shard_00001", "doc_id": 67 }, "chunk_id": "train_shard_00001_67_1", "global_id": 5763 }, { "text": "Plant adaptation to a terrestrial life 450 million years ago played a major role in the evolution of life on Earth. This shift from an aquatic environment has been mostly studied by focusing on flowering plants. Here, we gathered a collection of 133 accessions of the non-vascular plants Marchantia polymorpha and studied its intraspecific diversity using selection signature analyses, genome-environment association study and a gene-centered pangenome. We identified adaptive features shared with flowering plants, such as peroxidases or nucleotide-binding and leucine-rich repeat (NLR), which likely played a role in the adaptation of the first land plants to the terrestrial habitat. The M. polymorpha pangenome also harbored lineage-specific accessory genes absent from seed plants. We conclude that different land plants lineages still share many elements from the genetic toolkit evolved by their most recent common ancestor to adapt to the terrestrial habitat, refined by lineage specific polymorphisms and gene family evolutions.\n\nTheMarchantiapangenome reveals ancient mechanisms of plant adaptation to the environment", "token_count": 257, "char_count": 1134, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7063, "quality_score": 0.8531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:52.750337", "source": { "split": "train_shard_00001", "doc_id": 68 }, "chunk_id": "train_shard_00001_68_0", "global_id": 5764 }, { "text": "

Background

Clonal complex 180 (CC180) is currently the major clone of serotype 3 Streptococcus pneumoniae (Spn). The 13-valent pneumococcal conjugate vaccine (PCV13) does not have significant efficacy against serotype 3 despite polysaccharide inclusion in the vaccine. It was hypothesized that PCV13 may effectively control Clade I of CC180 but that Clades III and IV are resistant, provoking a population shift that enables serotype 3 persistence. This has been observed in the United States, England, and Wales but not Spain. We tested this hypothesis further utilizing a dataset from Portugal.

Methods

We whole-genome sequenced (WGS) 501 serotype 3 strains from Portugal isolated from patients with pneumococcal infections between 1999-2020. The draft genomes underwent phylogenetic analyses, pangenome profiling, and a genome-wide association study (GWAS). We also completed antibiotic susceptibility testing and compiled over 2,600 serotype 3 multilocus sequence type 180 (MLST180) WGSs to perform global comparative genomics.

Findings

CC180 Clades I, II, III, IV, and VI distributions were similar when comparing non-invasive pneumonia isolates and invasive disease isolates (Fisher’s exact test, P=0.29), and adult and pediatric cases (Fisher’s exact test, P=0.074). The serotype 3 CCs shifted post-PCV13 (Fisher’s exact test, P<0.0001) and Clade I became dominant. Clade I is largely antibiotic-sensitive and carries the ΦOXC141 prophage but the pangenome is heterogenous. Strains from Portugal and Spain, where Clade I remains dominant post-PCV13, have larger pangenomes and are associated with the presence of two genes encoding hypothetical proteins", "token_count": 500, "char_count": 1687, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7021, "quality_score": 0.8511, "entities": { "genes": [ "MLST180", "PCV13", "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:53.404872", "source": { "split": "train_shard_00001", "doc_id": 69 }, "chunk_id": "train_shard_00001_69_0", "global_id": 5765 }, { "text": "

Interpretation

Clade I became dominant in Portugal post-PCV13, despite the burden of the prophage and antibiotic sensitivity. The accessory genome content may mitigate these fitness costs. Regional differences in Clade I prevalence and pangenome heterogeneity suggest that clade dynamics is not a generalizable approach to understanding serotype 3 vaccine escape.

Funding

National Institute of Child Health and Human Development, Pfizer, and Merck Sharp & Dohme.

Research in context

Evidence before this study

We conducted this study because of the mounting interest surrounding the changing prevalence of serotype 3 Streptococcus pneumoniae (Spn) genetic lineages and the potential association with escape from 13-valent pneumococcal conjugate vaccine (PCV13) control. To inform our investigation, we searched the PubMed database using different combinations of the following keywords: “Streptococcus pneumoniae”, “serotype 3”, “CC180”, “PCV13”, “Clade Iα”, “Clade Iβ”, and “Clade II”. The search included all English language primary research articles published before July 1 st , 2024; this language limitation may bias the results of our assessment. Most ST3 isolates belong to clonal complex 180 (CC180), and one study identified three major lineages within CC180: Clade Iα, Clade Iβ, and Clade II. This study observed a global trend of increasing Clade II prevalence with a concomitant decrease in Clade I prevalence over time, which was associated with the introduction of PCV13 in the United States. A report from England and Wales made a similar observation. It was therefore hypothesized that PCV13 may be effective at controlling Clade Iα and that Clade II is driving vaccine escape. Later work refined the clade classification system as follows: Clade I (Clade Iα), Clades II and VI (Clade Iβ), Clades III and IV (Clade II), and Clade V", "token_count": 491, "char_count": 1884, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6727, "quality_score": 0.8363, "entities": { "genes": [ "PCV13", "ST3", "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:54.051524", "source": { "split": "train_shard_00001", "doc_id": 69 }, "chunk_id": "train_shard_00001_69_1", "global_id": 5766 }, { "text": "Clade I strains are marked by a significantly lower recombination rate partly due to the presence of a lineage-specific prophage interfering with competence development, which is a potential mechanism explaining the possible reduced fitness of Clade I. Clade I is also noted to be mostly antibiotic-susceptible. However, a recent study found that Clade I persists as a dominant serotype 3 lineage in Spain, so the generalizability and implications of clade dynamics remain unclear.

Added value of this study

Early work assessing the association between changes in serotype 3 clade prevalence and PCV13 was limited by small sample sizes. In addition, studies investigating differences in clade dynamics did not comprehensively consider patient age or disease manifestations such as non-invasive pneumonia and invasive infections. In this study, we evaluated 501 serotype 3 strains from Portugal to investigate clade dynamics. This must be explored in different geographic contexts for a more robust understanding of changing serotype 3 population genomics. We also sought to define genetic determinants linked to strains from regions in which Clade I remains dominant. This is an important step towards a more mechanistic understanding of the serotype 3 CC180 lineage fitness landscape.

Implications of all the available evidence

Unlike other serotypes covered by PCV13, serotype 3 has evaded vaccine control. It has been suggested that Clade I prevalence has decreased due to PCV13, which has created an expanded niche for strains from other clades and ultimately renders PCV13 less effective against serotype 3. This postulation has important implications for the future design of an improved vaccine, so this hypothesis must be thoroughly tested in diverse contexts. We find that Clade I remains the dominant lineage in Portugal even after the introduction of PCV13. We delineate Clade I pangenome heterogeneity and show that strains from Portugal and Spain share similar pangenome features in contrast to Clade I strains from regions where Clade I decreased in prevalence, which should motivate future studies to elucidate more generalizable population genomics trends that may better inform strategies for the design of an improved vaccine.", "token_count": 502, "char_count": 2262, "word_count": 339, "semantic_coherence": 1, "information_density": 0.5634, "quality_score": 0.7817, "entities": { "genes": [ "PCV13", "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:54.706884", "source": { "split": "train_shard_00001", "doc_id": 69 }, "chunk_id": "train_shard_00001_69_2", "global_id": 5767 }, { "text": "CC180 clade dynamics do not universally explainStreptococcus pneumoniaeserotype 3 persistence post-vaccine: a global comparative population genomics study", "token_count": 48, "char_count": 161, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "CC180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:55.065759", "source": { "split": "train_shard_00001", "doc_id": 69 }, "chunk_id": "train_shard_00001_69_3", "global_id": 5768 }, { "text": "The aim of this study was to evaluate the effectiveness of nine different biological compounds to reduce mycotoxins concentrations. The hypothesis of this study was that a static in vitro gastrointestinal tract model, as an initial screening tool, can be used to simulate the efficacy of Geotrichum fermentans, Rhodotorula rubra, Kluyveromyce marxiamus yeast cell walls and their polysaccharides, red and white clay minerals, and walnuts nutshells claiming to detoxify AFB1, ZEA, DON, and T-2 toxin mycotoxins. Mycotoxin concentrations were analyzed using high-performance liquid chromatography (HPLC) with fluorescent (FLD) and ultraviolet detectors (UV). The greatest effects on reducing mycotoxin concentrations were determined as follows: for AFB1, inserted G. fermentans cell wall polysaccharides and walnut nutshells; for ZEA, inserted R. rubra and G. fermentans cell walls and red clay minerals; for DON, R. rubra cell wall polysaccharides and red clay minerals; and for T-2 toxin, R. rubra cell walls, K. marxianus, and G. fermentans cell wall polysaccharides and walnut nutshells. The present study indicated that selected mycotoxin-detoxifying biological compounds can be used to decrease mycotoxin concentrations.\n\nExploring the Efficacy of Using <i>Geotrichum fermentans</i>, <i>Rhodotorula rubra</i>, <i>Kluyveromyce marxiamus</i>, Clay Minerals, and Walnut Nutshells for Mycotoxin Remediation.", "token_count": 504, "char_count": 1513, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5751, "quality_score": 0.7876, "entities": { "genes": [ "AFB1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:55.725319", "source": { "split": "train_shard_00001", "doc_id": 70 }, "chunk_id": "train_shard_00001_70_0", "global_id": 5769 }, { "text": "

ABSTRACT

The genus Bacillus comprises Gram-positive, endospore-forming rods with a ubiquitous distribution across terrestrial, aquatic, and aerial environments, as well as associations with plants, animals, and food. To explore its diversity, we conducted an integrated phylogenomic and pangenome analysis using 10,839 publicly available RefSeq genomes (67 type strain genomes). Taxonomic delimitation combining genomic-distance metrics (Mash/ANI), network analyses, and a label-propagation algorithm assigned 10,276 genomes to operational communities, revealing novel complexes within B. cereus sensu lato and other clades. A robust phylogeny reconstructed from 103 representative genomes corroborated the ANI-based groupings. Forty-eight communities (≥10 genomes) were further analyzed for pangenome openness, showing a strong negative correlation between the saturation coefficient (α) and genomic fluidity (φ) (ρ = −0.636), indicating that open pangenomes exhibit high gene-content variability. Functional profiling revealed 135 antifungal genes and 15 secondary metabolite clusters, highlighting B. velezensis , B. amyloliquefaciens , and B. subtilis as rich reservoirs of hydrolytic enzymes, NRPS/PKS systems, and nutrient-competition traits. Additionally, 135 resistance determinants and 115 virulence factors were identified, mainly within B. cereus sensu lato. Biofertilization genes related to phosphorus, nitrogen, siderophore, potassium, and sulfur metabolism were broadly conserved, underscoring the genus biotechnological potential.\n\nIntegrative phylogenomic and pangenome landscape of Bacillus : insights from 10,000 genomes into taxonomy, functional potential, and biotechnological applications", "token_count": 476, "char_count": 1735, "word_count": 211, "semantic_coherence": 1, "information_density": 0.782, "quality_score": 0.891, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:56.370273", "source": { "split": "train_shard_00001", "doc_id": 71 }, "chunk_id": "train_shard_00001_71_0", "global_id": 5770 }, { "text": "Insoluble dietary fibre (IDF) accounts for more than 90% of the total dietary fibre in okara and has the potential as a functional ingredient. However, IDF in raw okara has some disadvantages when used in food industries so its modification is needed. This paper focused on IDF in okara modified by fermentation by Kluyveromyces marxianus. Two kinds of modified IDFs, namely, MIDF1 and MIDF2, were obtained through simple fermentation and the combination of fermentation and β-glucosidase hydrolysis at home. The purity of IDF ranged from 75.83 (OIDF) to 81.0 (MIDF1) and 87.70 g/100 g (MIDF2). Colour analysis, scanning electron micrographs, bulk density and viscosity showed positive effects for modification. The functional properties of SC, WHC, OHC, GAC and CAC in MIDF were all increased in modified IDF, but MIDF2 showed a more favourable effect than MIDF1. Overall, the research demonstrated that K. marxianus fermentation can improve the structure and function of IDF from okara, which provides guidance for the development and utilization of okara in the food industry.\n\nInsoluble dietary fibre from okara (soybean residue) modified by yeast Kluyveromyces marxianus", "token_count": 338, "char_count": 1175, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [ "MIDF2", "MIDF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:56.938227", "source": { "split": "train_shard_00001", "doc_id": 72 }, "chunk_id": "train_shard_00001_72_0", "global_id": 5771 }, { "text": "

Motivation

Pangenome indexing is a critical supporting technology in biological sequence analysis such as read alignment applications. The need to accurately identify billions of small sequencing fragments carrying sequencing errors and genomic variants drives the development of scalable and efficient pangenome indexing approach.

Results

We propose a new wavelet tree-based approach, called Panaln, for indexing pangenome and introduce a batch computation approach for fast count query over Panaln. We present a simple and effective seeding strategy and develop a pangenome program that uses the seed-and-extend paradigm for read alignment. Experimental results on simulated and real data demonstrate that Panaln uses significantly less space for the compared pangenome methods with generally higher accuracy. We provide a scalable index construction by representing pangenome with a linear model. Additionally, Panaln brings enhanced accuracy compared to the popular single reference methods.

Availability and implementation

Package: https://anaconda.org/bioconda/panaln and source code: https://github.com/Lilu-guo/Panaln.\n\nPanaln: indexing pangenome for read alignment.", "token_count": 271, "char_count": 1196, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:57.486824", "source": { "split": "train_shard_00001", "doc_id": 73 }, "chunk_id": "train_shard_00001_73_0", "global_id": 5772 }, { "text": "Abstract

Reference data on genomic variation form the basis of genetic research. Limitations in identifying genetic variation from single reference sequences have been recently overcome, as improvements in sequencing technologies have allowed the generation of pangenomic references from multiple accurate, chromosome-level de novo assemblies. Here, we present a comprehensive Emirati telomere-to-telomere (T2T) pangenome generated from 58 individuals, comprising 28 trio-based and 30 single-sample assemblies. The resulting 116 haplotype-resolved assemblies demonstrate high contiguity, with a median continuity of 150 Mb and a median quality value (QV) of 59, achieving T2T-level scaffold status for 71.9% of chromosomes. These assemblies form the foundation of the Emirati T2T pangenome graph. The graph reveals levels of genomic diversity comparable to those reported by the Human Pangenome Reference Consortium, while also capturing regionally enriched and difficult-to-assemble variation, uniquely accessible through the Emirati T2T assemblies. This reference makes a valuable global contribution to human pangenomics and serves as a critical resource for advancing precision medicine in the United Arab Emirates.

\n\nThe Emirati T2T-Level Pangenome: A Graph of 58 Complete Genomes", "token_count": 336, "char_count": 1324, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6994, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:58.056178", "source": { "split": "train_shard_00001", "doc_id": 74 }, "chunk_id": "train_shard_00001_74_0", "global_id": 5773 }, { "text": "The pathogen Nocardia seriolae is responsible for causing chronic granulomatous disease, known as fish nocardiosis, which has been observed in more than 40 species of fish cultured in marine and freshwater environments. Therefore, it is imperative to perform research to address and eradicate this substantial threat to the aquaculture industry. However, quantifying the negative impacts associated with this species is difficult because of insufficient data and underreporting. While several genomes are available in online databases, there is still a lack of comparative genomic analyses and studies on effective treatments, which is particularly important for aquaculture. To gain a deeper understanding of the pathogenic mechanisms associated with various Nocardia strains causing disease outbreaks and their virulence components, as well as the functional enrichment and genetic diversity during infection, it is crucial to develop a dependable and replicable pangenomic dataset. This study quantified Nocardia pangenome openness and discovered the biological processes that drive it. The study also found a substantial association between pangenome openness and numerous parameters such as genomic plasticity, gene synteny, single-copy phylogenomics, and pangenome prediction. The results showed genetic similarity across strains, indicating that the pangenome of this species is moving toward completeness. The diversity was supported by the similarity analysis, which revealed a high percentage of genes in the core genome and close association among the strains. Our findings provide valuable information and emphasize the necessity of sequencing novel genomes of N. serioale isolates to gain a deeper understanding of their diversity and patterns of adaptability.\n\nA comparative genomic and phylogenomic study of Nocardia seriolae strains unveils high genetic homogeneity and open nature of the pangenome ", "token_count": 450, "char_count": 2002, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:58.698040", "source": { "split": "train_shard_00001", "doc_id": 75 }, "chunk_id": "train_shard_00001_75_0", "global_id": 5774 }, { "text": "The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g⁻¹). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers", "token_count": 439, "char_count": 1568, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6845, "quality_score": 0.8422, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:59.330899", "source": { "split": "train_shard_00001", "doc_id": 76 }, "chunk_id": "train_shard_00001_76_0", "global_id": 5775 }, { "text": "Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.\n\nA comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese", "token_count": 200, "char_count": 720, "word_count": 94, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:51:59.783319", "source": { "split": "train_shard_00001", "doc_id": 76 }, "chunk_id": "train_shard_00001_76_1", "global_id": 5776 }, { "text": "Yersinia pestis, the etiological agent of the plague, is considered a genetically homogeneous species. Brazil is currently in a period of epidemiological silence but plague antibodies are still detected in sentinel animals, suggesting disease activity in the sylvatic cycle. The present study deployed an in silico approach to analyze virulence factors among 407 Brazilian genomes of Y. pestis belonging to the Fiocruz Collection (1966-1997). The pangenome analysis associated several known virulence factors of Y. pestis in clades according to the presence or absence of genes. Four main strain clades (C, E, G, and H) exhibited the absence of various virulence genes. Notably, clade G displayed the highest number of absent genes, while clade E showed a significant absence of genes related to the T6SS secretion system and clade H predominantly demonstrated the absence of plasmid-related genes. These results suggest attenuation of virulence in these strains over time. The cgMLST analysis associated genomic and epidemiological data highlighting evolutionary patterns related to the isolation years and outbreaks of Y. pestis in Brazil. Thus, the results contribute to the understanding of the genetic diversity and virulence within Y. pestis and the potential for utilizing genomic data in epidemiological investigations.\n\nGenomic Analysis of Yersinia pestis Strains from Brazil: Search for Virulence Factors and Association with Epidemiological Data.", "token_count": 379, "char_count": 1499, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:00.373478", "source": { "split": "train_shard_00001", "doc_id": 77 }, "chunk_id": "train_shard_00001_77_0", "global_id": 5777 }, { "text": "Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals1, is enriched in human colorectal cancer (CRC) tumours2-5. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis5-8. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.\n\nA distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche.", "token_count": 502, "char_count": 1845, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:01.057870", "source": { "split": "train_shard_00001", "doc_id": 78 }, "chunk_id": "train_shard_00001_78_0", "global_id": 5778 }, { "text": "Citrobacter freundii is a nosocomial pathogen increasingly associated with multidrug resistance and hospital outbreaks. Despite its growing clinical relevance, no standardized core genome multilocus sequence typing (cgMLST) scheme has been available for high-resolution epidemiological analyses. Here, we developed and validated a robust cgMLST scheme for C. freundii comprising 3,250 target loci based on a curated data set of 825 globally distributed genomes representing extensive sequence type and geographic diversity. Validation against published outbreak data sets from hospitals in Finland and Belgium, as well as environmental and patient isolates from two German university hospitals, proved that the scheme possesses high target gene coverage (median 99.6%) and strong discriminatory power. Additionally, we developed a combined cgMLST scheme for C. freundii, C. portucalensis, C. braakii, and C. europaeus, based on 2,307 shared target loci and target gene coverages of ≥99.7%. This scheme proved suitable for cross-species outbreak analysis. Our analyses revealed environments, such as sinks, shower drains, and toilets, as likely reservoirs where Citrobacter species may persist in hospital settings. These findings suggest that environmental sources could play a significant role in transmission events involving patients, while allele-based cluster analyses indicated that direct patient-to-patient transmission was rare. Given the increasing prevalence of multidrug-resistant (MDR) Citrobacter strains, the level of discrimination achieved by these newly developed cgMLST schemes underscores the importance of accurate species identification and environmental screening in understanding the transmission dynamics of opportunistic healthcare-associated pathogens. Ultimately, this makes them valuable tools for genomic surveillance, outbreak investigation, and infection prevention.

Importance

Accurate identification and high-resolution typing of multidrug-resistant bacteria are essential for understanding their transmission dynamics in hospitals, particularly in light of the global spread of resistant strains and the role of environmental reservoirs", "token_count": 509, "char_count": 2234, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:01.758147", "source": { "split": "train_shard_00001", "doc_id": 79 }, "chunk_id": "train_shard_00001_79_0", "global_id": 5779 }, { "text": "The newly developed cgMLST schemes presented here provide standardized, portable tools for both local and global scientific and clinical communities to conduct fine-scale genomic epidemiology across four Citrobacter species. These schemes support detailed outbreak reconstruction, source attribution, and cross-hospital comparisons, capabilities that are critical in an era of increasing antimicrobial resistance and international patient movement. By enabling consistent, species-specific surveillance and comparative analyses, cgMLST enhances infection control and public health responses, facilitating early detection and targeted intervention.\n\nDevelopment and validation of a core genome multilocus sequence typing scheme for <i>Citrobacter freundii</i>: application in outbreak investigations and comparative analysis across the <i>Citrobacter</i> genus.", "token_count": 196, "char_count": 891, "word_count": 102, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:02.225558", "source": { "split": "train_shard_00001", "doc_id": 79 }, "chunk_id": "train_shard_00001_79_1", "global_id": 5780 }, { "text": "

Summary

Most organisms’ traits result from the complex interplay of many genetic and environmental factors, making their prediction from genotypes difficult. Here, we used machine learning models to explore genotype-phenotype connections for 223 life history traits measured across 1011 genome-sequenced Saccharomyces cerevisiae strains. Firstly, we used genome-wide association studies to connect genetic variants with the phenotypes. Next, we benchmarked an automated machine learning pipeline that includes preprocessing, feature selection, and hyperparameters optimization in combination with multiple linear and complex machine learning methods. We determined gradient boosting machines as best performing in 65% of predictions and pangenome as best predictor, suggesting a considerable contribution of the accessory genome in controlling phenotypes. The accuracy broadly varied among the phenotypes (r = 0.2-0.9), consistent with varying levels of complexity, with stress resistance being easier to predict compared to growth across carbon and nitrogen nutrients. While no specific genomic features could be linked to the predictions for most phenotypes, machine learning identifies high-impact variants with established relationships to phenotypes despite being rare in the population. Near-perfect accuracies (r>0.95) were achieved when other phenomics data were used to aid predictions, suggesting shared useful information can be conveyed across phenotypes. Overall, our study underscores the power of machine learning to interpret the functional outcome of genetic variants.\n\nPredicting the natural yeast phenotypic landscape with machine learning", "token_count": 350, "char_count": 1667, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6909, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:02.852857", "source": { "split": "train_shard_00001", "doc_id": 80 }, "chunk_id": "train_shard_00001_80_0", "global_id": 5781 }, { "text": "

Introduction

Data on the prevalence of fungal coinfections/superinfections in patients with COVID-19 are limited.

Objective

To describe the prevalence of fungal coinfections/superinfections in patients with COVID-19, as well as risk factors and demographic, clinical, and microbiological characteristics.

Material and methods

We included patients with a confirmed COVID-19 diagnosis and a confirmed fungal infection hospitalized in the ICU from March 2020 to December 2021. We collected data on age, sex, comorbidities, hospital length of stay (days), laboratory (ferritin) and microbiological results, treatment for COVID-19, antifungal therapy, and outcomes obtained from the clinical records.

Results

Only 11 out of 740 patients met the inclusion criteria. The coinfection rate was 0.3% and the superinfection was 1.2%. The most affected population was male adults. The coinfections/superinfections diagnosed were candiduria and candidemia, caused by Candida albicans, C. tropicalis, C. glabrata, C. lusitaniae, and Kluyveromyces marxianus (C. kefyr). In addition, tracheobronchitis due to Aspergillus fumigatus was found. The most used antifungals were fluconazole and caspofungin. The lethality in patients with fungal coinfections was 50% and superinfections, 22%. The length of hospital stay was 11-65 days. Eight patients required mechanical ventilation and six received corticosteroids. The main comorbidity was diabetes mellitus (81.8%).

Conclusions

The rate of fungal coinfections/superinfections in COVID-19 patients was low, but the lethality found urges for routine fungal screening in patients with severe COVID-19 to timely detect fungal infections that may further compromise the patient’s life.\n\nFungal coinfection/superinfection in COVID-19 patients in a tertiary hospital in Mexico", "token_count": 507, "char_count": 1837, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5983, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:03.509784", "source": { "split": "train_shard_00001", "doc_id": 81 }, "chunk_id": "train_shard_00001_81_0", "global_id": 5782 }, { "text": "We report the draft genomes of four Kluyveromyces marxianus isolates obtained from the elaboration process of henequén ( Agave fourcroydes ) mezcal, a Mexican alcoholic beverage. The average nucleotide identity (ANI) analysis revealed that isolates derived from agave plants are distinct from those from other environments, including agave fermentations.\n\nDraft Genomes of FourKluyveromyces marxianusIsolates Retrieved from the Elaboration Process of Henequén (Agave fourcroydes) Mezcal", "token_count": 140, "char_count": 500, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:03.937386", "source": { "split": "train_shard_00001", "doc_id": 82 }, "chunk_id": "train_shard_00001_82_0", "global_id": 5783 }, { "text": "Staphylococcus pseudintermedius is frequently associated with several bacterial infections in dogs, highlighting a One Health concern due to the zoonotic potential. Given the clinical significance of this pathogen, we performed comprehensive genomic analyses of 28 S. pseudintermedius strains isolated from canine infections throughout whole-genome sequencing using Illumina HiSeq, and compared the genetic features between S. pseudintermedius methicillin-resistant (MRSP) and methicillin-susceptible (MSSP) strains. Our analyses determined that MRSP genomes are larger than MSSP strains, with significant changes in antimicrobial resistance genes and virulent markers, suggesting differences in the pathogenicity of MRSP and MSSP strains. In addition, the pangenome analysis of S. pseudintermedius from canine and human origins identified core and accessory genomes with 1847 and 3037 genes, respectively, which indicates that most of the S. pseudintermedius genome is highly variable. Furthermore, phylogenomic analysis clearly separated MRSP from MSSP strains, despite their infection sites, showing phylogenetic differences according to methicillin susceptibility. Altogether our findings underscore the importance of studying the evolutionary dynamics of S. pseudintermedius, which is crucial for the development of effective prevention and control strategies of resistant S. pseudintermedius infections.\n\nGenomic Analyses of Methicillin-Susceptible and Methicillin-Resistant <i>Staphylococcus pseudintermedius</i> Strains Involved in Canine Infections: A Comprehensive Genotypic Characterization.", "token_count": 440, "char_count": 1663, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6497, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:04.569886", "source": { "split": "train_shard_00001", "doc_id": 83 }, "chunk_id": "train_shard_00001_83_0", "global_id": 5784 }, { "text": "Avian necrotic enteritis due to the Gram-positive bacterium Clostridium perfringens has re-emerged following the ban on antibiotic growth promoters in many poultry producing countries. The limited number of previous studies has left important gaps in our understanding of the genetic diversity and virulence traits of the pathogen. To address these knowledge gaps, in this study, we sequenced the genomes of 41 Clostridium perfringens isolates recovered from commercial broiler chicken flocks in Quebec, Canada, including isolates from healthy birds and those affected by necrotic enteritis. We sought to understand the pangenome diversity and interrogated the genomes for key virulence factors involved in necrotic enteritis pathogenesis. On average, the genomes had a GC content of 28% and contained 3,206 coding sequences. A variable presence of toxins, degradative hydrolytic enzymes, and collagen-binding proteins was also found. Through pangenome analysis, we revealed a total of 10,223 genes, 652 (6.4%) of which formed the core genome. Additionally, we identified 17 different plasmids, 12 antibiotic resistance genes, and nine prophage regions. Overall, our results demonstrated a relatively high genetic diversity among chicken Clostridium perfringens isolates collected from the same geographical location, offering new insights into potential virulence mechanisms and adaptation of the pathogen within poultry populations.\n\nGenomic Diversity and Virulence Factors of Clostridium perfringens Isolated from Healthy andNecrotic Enteritis–Affected Broiler Chicken Farms in Quebec Province", "token_count": 392, "char_count": 1605, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:05.184667", "source": { "split": "train_shard_00001", "doc_id": 84 }, "chunk_id": "train_shard_00001_84_0", "global_id": 5785 }, { "text": "Kluyveromyces marxianus is an ascomycetous yeast which has shown promising results in cellulosic ethanol and renewable chemicals production. It can survive on a variety of carbon sources under industrially favorable conditions due to its fast growth rate, thermotolerance, and acid tolerance. K. marxianus, is generally regarded as a safe (GRAS) microorganism, is widely recognized as a powerhouse for the production of heterologous proteins and is accepted by the US Food and Drug Administration (USFDA) for its pharmaceutical and food applications. Since lignocellulosic hydrolysates are comprised of diverse monomeric sugars, oligosaccharides and potential metabolism inhibiting compounds, this microorganism can play a pivotal role as it can grow on lignocellulosic hydrolysates coping with vegetal cell wall derived inhibitors. Furthermore, advancements in synthetic biology, for example CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, will enable development of an engineered yeast for the production of biochemicals and biopharmaceuticals having a myriad of industrial applications. Genetic engineering companies such as Cargill, Ginkgo Bioworks, DuPont, Global Yeast, Genomatica, and several others are actively working to develop designer yeasts. Given the important traits and properties of K. marxianus, these companies may find it to be a suitable biocatalyst for renewable chemicals and fuel production on the large scale. This paper reviews the recent progress made with K. marxianus biotechnology for sustainable production of ethanol, and other products utilizing lignocellulosic sugars.\n\nKluyveromyces marxianus: a potential biocatalyst of renewable chemicals and lignocellulosic ethanol production.", "token_count": 464, "char_count": 1810, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6695, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:05.825039", "source": { "split": "train_shard_00001", "doc_id": 85 }, "chunk_id": "train_shard_00001_85_0", "global_id": 5786 }, { "text": "Despite its potential as a sustainable feedstock for producing renewable fuels and chemicals, lignocellulosic biomass (LCB) remains largely untapped due to problems associated with its deconstruction and the toxicity of its sugar-rich hydrolysates in microbial conversion processes. Using genetic modification to facilitate inhibitor tolerance, the present study aimed to construct a robust yeast cell factory for cellulosic ethanol bioproduction from non-detoxified LCB. To this effect, two putative nitroreductase genes (KmHBN1 and KmFRM2) hypothesized to be possible mediators of oxidative stress response were separately overexpressed and disrupted in Kluyveromyces marxianus. In contrast to KmFRM2 modified strains (disrupted or overexpressed) with no significant change, the inhibitor tolerance to phenols, furfural, and acetic acid cocktail was improved in YKmHBN1-URA3 strain overexpressing KmHBN1. Although the recombinant KmHBN1 and KmFRM2 had nitroreductase activity, they did not degrade or convert inhibitors. The change of intracellular reactive oxygen species level (ROS) of KmHBN1 disrupted or overexpressed strains indicated that KmHBN1 affected intracellular ROS elimination. Cells with disrupted KmHBN1 failed to respond to ROS created during inhibitor metabolism, and this disruption also led to reduced expression of respiratory chain genes which translates to a decreased inhibitor tolerance. The overexpression of KmHBN1 not only enhanced the ethanol production from glucose in the presence of inhibitors but also improved ethanol productivity (18.75%) from simultaneously-saccharified and co-fermented inhibitor-ladened corn cob. These findings unlock a new pathway for the creation of robust yeast strains to aid in the biorefinery conversion of lignocellulosic feedstock.\n\nEnhancing tolerance of Kluyveromyces marxianus to lignocellulose-derived inhibitors and its ethanol production from corn cob via overexpression of a nitroreductase gene", "token_count": 502, "char_count": 1967, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6374, "quality_score": 0.8187, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:06.484853", "source": { "split": "train_shard_00001", "doc_id": 86 }, "chunk_id": "train_shard_00001_86_0", "global_id": 5787 }, { "text": "

Background

Members of the Klebsiella pneumoniae species complex (KpSC) are opportunistic pathogens that cause severe and difficult-to-treat infections. KpSC are common in non-human niches, but the clinical relevance of these populations is disputed.

Methods

In this study, we analysed 3255 whole-genome sequenced isolates from human, animal and marine sources collected in Norway between 2001 and 2020. We used population genomics in a One Health context to assess the diversity of strains, genes and other clinically relevant genetic features within and between sources. We further explored niche-enriched traits using genome-wide association studies and investigated evidence of spillover and connectivity across the KpSC populations from the three niches.

Results

We found that the KpSC populations in different niches were distinct but overlapping. Overall, there was high genetic diversity both between and within sources, with nearly half (49%) of the genes in the accessory genome overlapping the ecological niches. Further, several sublineages (SLs) including SL17, SL35, SL37, SL45, SL107 and SL3010 were common across sources. There were few niche-enriched traits, except for aerobactin-encoding plasmids and the bacteriocin colicin a, which were associated with KpSC from animal sources. Human infection isolates showed the greatest connectivity with each other, followed by isolates from human carriage, pigs, and bivalves. Nearly 5% of human infection isolates had close relatives (≤22 substitutions) amongst animal and marine isolates, despite temporally and geographically distant sampling of these sources. There were limited but notable recent spillover events, including the movement of plasmids encoding the virulence locus iuc3 between pigs and humans.

Conclusions

Our large One Health genomic study highlights that human-to-human transmission of KpSC is more common than transmission between ecological niches. Still, spillover of clinically relevant strains and genetic features between human and non-human sources does occur and should not be overlooked", "token_count": 512, "char_count": 2105, "word_count": 285, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [ "SL107", "SL45", "SL35", "SL3010", "SL37", "SL17" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:07.146667", "source": { "split": "train_shard_00001", "doc_id": 87 }, "chunk_id": "train_shard_00001_87_0", "global_id": 5788 }, { "text": "Infection prevention measures are essential to limit transmission within human clinical settings and reduce infections. However, preventing transmission that leads to colonisation, e.g. from direct contact with animals or via the food chain, could also play an important role in reducing the KpSC disease burden.\n\nA genome-wide One Health study of Klebsiella pneumoniae in Norway reveals overlapping populations but few recent transmission events across reservoirs.", "token_count": 92, "char_count": 465, "word_count": 65, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:07.525511", "source": { "split": "train_shard_00001", "doc_id": 87 }, "chunk_id": "train_shard_00001_87_1", "global_id": 5789 }, { "text": "Glaesserella (Haemophilus) parasuis, the causative agent of Glässer's disease, is present in most pig farms as an early colonizer of the upper respiratory tract. It exhibits remarkable variability in virulence and antimicrobial resistance (AMR), with virulent strains capable of inducing respiratory or systemic disease. This study aimed to characterize the virulence and the AMR profiles in 65 G. parasuis isolates recovered from Spanish swine farms. Virulence was assessed using multiplex leader sequence (LS)-PCR targeting vtaA genes, with all isolates identified as clinical (presumed virulent). Pathotyping based on ten pangenome genes revealed the virulent HPS_22970 as the most frequent (83.1%). Diverse pathotype profiles were observed, with 29 unique gene combinations and two isolates carrying only potentially non-virulent pangenome genes. AMR phenotyping showed widespread resistance, with 63.3% classified as multidrug resistant, and high resistance to clindamycin (98.3%) and tylosin (93.3%). A very strong association was found between certain pathotype genes and AMR phenotypes, notably between the virulent HPS_22970 and tetracycline resistance (p < 0.001; Φ = 0.58). This study reveals the wide diversity and complexity of G. parasuis pathogenicity and AMR phenotype, emphasizing the need for the targeted characterization of clinical isolates to ensure appropriate antimicrobial treatments and the implementation of prophylactic measures against virulent strains.\n\nVirulence and Antimicrobial Resistance Characterization of Glaesserella parasuis Isolates Recovered from Spanish Swine Farms.", "token_count": 466, "char_count": 1665, "word_count": 218, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:08.170317", "source": { "split": "train_shard_00001", "doc_id": 88 }, "chunk_id": "train_shard_00001_88_0", "global_id": 5790 }, { "text": "Abstract

Here, we report the genome sequence of strain A2. The genome size was 3,855,926 bp, the GC content was 67.4%, and it contains 3509 genes, 62 tRNA, eight rRNA, and four snRNA. Phylogenetic analysis of the 16 S rRNA gene in the RDP, NCBI, and TYGS databases indicates that strain A2 belongs to Halomonas salifodinae. Also, MLSA analysis confirms that A2 is closely related to H. salifodinae. Phylogenomic and comparative genomic analysis using the ANIs and dDDH indicators classify H. salifodinae A2 and Bisbaumannia pacifica NBRC 102220 in a separate phylogenetic group of the genus Halomonas. The phylogenomic and pangenome analysis support the above, placing H. salifodinae A2 in a separate group with B. pacifica NBRC 102220. The pangenomic analysis shows 136,122 genes that comprise the pangenome with 317 core genes, 3457 shell genes, 132,332 accessory genome, and 691 unique genes. We found 29 genes for secretion systems in the genome analysis, 23 for Na + and K + ion transport, 6 BGC groups, a total of 12 genomic islands, an 8.2Kb gene prophage region, 15 regions associated with CRISPR and one CAS-TypeIF cas gene cluster region, 12 genes of biotechnological importance, 38 unique genes essential for adaptability and biotechnological relevance, as well as, 35 genes for the synthesis of compatible solutes", "token_count": 516, "char_count": 1480, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6385, "quality_score": 0.8192, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:08.835634", "source": { "split": "train_shard_00001", "doc_id": 89 }, "chunk_id": "train_shard_00001_89_0", "global_id": 5791 }, { "text": "Furthermore, we propose the reclassification of the species within the genus Bisbaumannia.

\n\nComparative genomic analysis and genome sequence of Halomonas salifodinae strain A2, isolated from the Zapotitlán Salinas Valley Puebla, México", "token_count": 73, "char_count": 256, "word_count": 31, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:09.211222", "source": { "split": "train_shard_00001", "doc_id": 89 }, "chunk_id": "train_shard_00001_89_1", "global_id": 5792 }, { "text": "The Family Borreliaceae contains arthropod-borne spirochetes that cause two widespread human diseases, Lyme disease (LD) and relapsing fever (RF). LD is a subacute, progressive illness with variable stage and tissue manifestations. RF is an acute febrile illness with prominent bacteremia that may recur and disseminate, particularly to the nervous system. Clinical heterogeneity is a hallmark of both diseases. While human clinical manifestations are influenced by a wide variety of factors, including immune status and host genetic susceptibility, there is evidence that Borreliaceae microbial factors influence the clinical manifestations of human disease caused by this Family of spirochetes. Despite these associations, the spirochete genes that influence the severity and manifestations of human disease are, for the most part, unknown. Recent work has identified lineage-specific expansions of lipoproteome-rich accessory genome elements in virulent clones of B. burgdorferi . Using publicly available genome assemblies, I show here that all Borreliaceae lineages for which sufficient sequence data is available harbor a similar pattern of strongly structured, lineage-specific expansions in their accessory genome, particularly among lipoproteins, and that this pattern holds across phylogenetic scales including genera, species, and genotypes. The relationships among pangenome elements suggest that infrequent episodes of marked genomic change followed by clonal expansion in geographically and enzootically structured populations may account for the unique lineage structure of Borreliaceae . This analysis informs future genotype-phenotype studies among Borreliaceae and lays a foundation for studies of individual gene function guided by phylogenetic patterns of conservation, diversification, gain, and/or loss.\n\nAnalysis of theBorreliaceaePangenome Reveals a Conserved Genomic Archictecture Across Phylogenetic Scales", "token_count": 434, "char_count": 1939, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6523, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:09.845189", "source": { "split": "train_shard_00001", "doc_id": 90 }, "chunk_id": "train_shard_00001_90_0", "global_id": 5793 }, { "text": "Mixture designs are employed to systematically change the composition of mixtures and investigate how those changes impact their properties. However, all mixture designs currently available are impractical for analyzing mixtures with relatively large numbers of ingredients. In response, this article presents a novel solution that builds on the construction of a new experimental design called \"fractional mixture design\". The design involves screening the ingredients in mixtures and enables the subsequent construction of a classical mixture design for optimizing mixtures. The design and its accompanying methodology were developed to analyze native strains found in successful spontaneous fermentations with the goal of constructing a mixed starter culture to transition from spontaneous to directed fermentation in the production of agave distillates. The results showed that a starter culture composed of the native strains Kluyveromyces marxianus, Clavispora lusitaniae, and Kluyveromyces marxianus var. drosophilarum, in respective proportions of 35%, 32%, and 33%, enabled the production of a fermented product with 2.1% alcohol and a broad profile of aromatic compounds. Hence, the results show, for the first time, a tool that addresses the technical challenge that allows studying a relatively large number of ingredients in mixtures and a two-stage sequential methodology to construct optimal mixtures.\n\nFractional mixture design: a novel design and methodology for analyzing and optimizing mixtures of several ingredients.", "token_count": 335, "char_count": 1558, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:10.419668", "source": { "split": "train_shard_00001", "doc_id": 91 }, "chunk_id": "train_shard_00001_91_0", "global_id": 5794 }, { "text": "Non-O157 Shiga toxin-producing Escherichia coli (STEC), particularly the O118 serogroup, are emerging pathogens linked to severe foodborne illnesses, including hemolytic uremic syndrome. The hallmark of STEC virulence is the production of a potent phage-borne cytotoxin, often accompanied by the locus of enterocyte effacement (LEE). This study explores the genomic landscape, virulence factors, and resistance traits of O118 STEC. We analyzed 357 publicly available O118 genomes across ten H-antigens and included two clinically significant O118:H16 STEC strains sequenced to closure. Pangenome assessment and core genome multilocus sequence typing (MLST) based on 4,160 shared genes revealed phylogenetic clustering by H-type and delineated distinct STEC-phylogroups, alongside relationships to non-STEC pathovars such as uropathogenic E. coli (UPEC), enteropathogenic E. coli (EPEC), and enterotoxigenic E. coli (ETEC). Identified STEC phylogroups encompassed H6, H12, H16, and H2 strains with diverse Shiga toxin ( stx ) profiles ( stx 1a , stx 2a , stx 2b , stx 2c , stx 2f ). A subset of H2-STEC lacked stx , suggesting potential secondary phage loss. Most STEC groups harbored the locus of enterocyte effacement (LEE). Further, a strong correlation was observed between H-antigens and eae subtypes, with specific pairings such as H6/ eae-ι , H16/ eae-β , and H2/ eae-ε . Horizontally acquired pathogenicity islands—including O-island 122 in H16 strains and a novel pathogenicity-associated island carrying antibiotic resistance—along with other loci related to colonization and interbacterial competition, further enhance these strains’ virulence potential", "token_count": 501, "char_count": 1663, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7288, "quality_score": 0.8644, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:11.072279", "source": { "split": "train_shard_00001", "doc_id": 92 }, "chunk_id": "train_shard_00001_92_0", "global_id": 5795 }, { "text": "Our findings underscore the genetic diversity and virulence potential of O118 STEC. Understanding phylogroup-specific traits and resistance markers is crucial for effective surveillance and public health interventions.

Importance

Shiga toxin-producing Escherichia coli (STEC) are a major public health concern, responsible for illnesses ranging from diarrhea to life-threatening kidney damage. Among non-O157 STEC, serogroup O118 is increasingly recognized as an emerging STEC lineage. This study provides the most comprehensive genomic analysis to date of O118 STEC, offering critical insights into their pathogenome, virulence traits, and antimicrobial resistance inventories. Notably, we identified a novel 74 kb pathogenicity island in clinical strain H16-12089 that encodes a combination of multidrug resistance genes, virulence factors, and interbacterial competition systems. Understanding the genetic makeup and virulence potential of these pathogens is essential for improving surveillance, risk assessment, and public health interventions.\n\nPhylogenomic framework and virulence gene boundaries of emerging Shiga toxin-producing Escherichia coli O118 informed by the comprehensive profiling of 359 O118 genomes", "token_count": 313, "char_count": 1236, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7134, "quality_score": 0.8567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:11.627779", "source": { "split": "train_shard_00001", "doc_id": 92 }, "chunk_id": "train_shard_00001_92_1", "global_id": 5796 }, { "text": "Kluyveromyces marxianus is the fastest-growing eukaryote and a promising host for producing bioethanol and heterologous proteins. To perform a laboratory evolution of thermal tolerance in K. marxianus, diploid, triploid and tetraploid strains were constructed, respectively. Considering the genetic diversity caused by genetic recombination in meiosis, we established an iterative cycle of \"diploid/polyploid - meiosis - selection of spores at high temperature\" to screen thermotolerant strains. Results showed that the evolution of thermal tolerance in diploid strain was more efficient than that in triploid and tetraploid strains. The thermal tolerance of the progenies of diploid and triploid strains after a two-round screen was significantly improved than that after a one-round screen, while the thermal tolerance of the progenies after the one-round screen was better than that of the initial strain. After a two-round screen, the maximum tolerable temperature of Dip2-8, a progeny of diploid strain, was 3°C higher than that of the original strain. Whole-genome sequencing revealed nonsense mutations of PSR1 and PDE2 in the thermotolerant progenies. Deletion of either PSR1 or PDE2 in the original strain improved thermotolerance and two deletions displayed additive effects, suggesting PSR1 and PDE2 negatively regulated the thermotolerance of K. marxianus in parallel pathways. Therefore, the iterative cycle of \"meiosis - spore screening\" developed in this study provides an efficient way to perform the laboratory evolution of heat resistance in yeast.\n\nMeiosis-Based Laboratory Evolution of the Thermal Tolerance in Kluyveromyces marxianus.", "token_count": 477, "char_count": 1732, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5106, "quality_score": 0.7553, "entities": { "genes": [ "PDE2", "PSR1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:12.277950", "source": { "split": "train_shard_00001", "doc_id": 93 }, "chunk_id": "train_shard_00001_93_0", "global_id": 5797 }, { "text": "Effective control of bacterial infections remains a significant challenge in aquaculture. The marine bacterium Piscirickettsia salmonis (P. salmonis), responsible for piscirickettsiosis, causes widespread infections in various salmon species, leading to substantial mortality and economic losses. Despite efforts to genetically characterize P. salmonis, critical gaps persist in understanding its virulence factors, antimicrobial resistance genes, and single-nucleotide polymorphisms (SNPs). This study addresses these gaps through a comparative analysis of the pan-genome and core genomes of 80 P. salmonis strains from different geographical regions and genogroups. P. salmonis had an open pan-genome consisting of 14,564 genes, with a core genome of 1257 conserved genes. Eleven virulence-related genes were identified in the pan-genome, categorized into five functional groups, providing new insights into the pathogenicity of P. salmonis. Unique SNPs were detected in four key genes (gyrA, dnaK, rpoB, and ftsZ), serving as robust molecular markers for distinguishing the LF and EM genogroups. Notably, AMR genes identified in four LF strains suggest evolutionary adaptations under selective pressure. Functional annotation of the core genomes using the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases demonstrated conserved gene clusters linked to essential intracellular survival mechanisms and bacterial pathogenicity. These findings suggest a direct association between core genome features and variations in pathogenesis and host-pathogen interactions across genogroups. Phylogenetic reconstruction further highlighted the influence of AMR genes on strain divergence. Collectively, this study enhances the genomic understanding of P. salmonis and lays the groundwork for improved diagnostic tools and targeted therapeutics to manage piscirickettsiosis in aquaculture.", "token_count": 514, "char_count": 1986, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:12.936973", "source": { "split": "train_shard_00001", "doc_id": 94 }, "chunk_id": "train_shard_00001_94_0", "global_id": 5798 }, { "text": "Pathogenomic Insights into <i>Piscirickettsia salmonis</i> with a Focus on Virulence Factors, Single-Nucleotide Polymorphism Identification, and Resistance Dynamics.", "token_count": 60, "char_count": 177, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:13.338112", "source": { "split": "train_shard_00001", "doc_id": 94 }, "chunk_id": "train_shard_00001_94_1", "global_id": 5799 }, { "text": "Avocado is an economically important perennial tree crop with a complex domestication history, yet modern genomic resources are limited. We present the first high-quality avocado pangenome, spanning seven diverse accessions across Mexican, Guatemalan, and West-Indian lineages. PacBio HiFi, partially phased assemblies deliver near chromosome-level continuity (N50 ~57 Mb; BUSCO >96%), and functional annotations show enrichment of immune-related families. Core-accessory partitioning indicates adaptive functions - pathogen response and secondary metabolism - are overrepresented in accessory genes. Nucleotide-binding Leucine-rich repeat ( NLR ) genes were catalogued (226-256 per accession), showing lineage-specific expansions, diverse domain architectures, and frequent chromosomal clustering. Structural variants concentrate within NLR loci, marking hotspots of pathogen-detection diversification. Comparative analyses show ~54% of NLRs are shared, with extensive functional and sequence diversity among accessions. Together, these results define the avocado NLRome and its core-accessory interplay, providing a graph-based framework to accelerate discovery of resistance loci and breeding for durable disease resistance.\n\nThe avocado pangenome reveals dynamic clustering and lineage-specific diversity of NLR genes", "token_count": 332, "char_count": 1333, "word_count": 163, "semantic_coherence": 1, "information_density": 0.8221, "quality_score": 0.911, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:14.719009", "source": { "split": "train_shard_00001", "doc_id": 95 }, "chunk_id": "train_shard_00001_95_0", "global_id": 5800 }, { "text": "In recent years, prejudice in society against monosodium glutamate (MSG) has directed food manufacturers to alternative sources. Yeast extracts are considered as \"natural\" due to the production process and stand out due to their nutritional properties as well as giving a flavor similar to MSG. In this study, chemical, functional and flavor properties of yeast extract powders produced from Saccharomyces cerevisiae TGM10, Saccharomyces boulardii S11 and Kluyveromyces marxianus TGM66 were evaluated. Results revealed that the most protein-rich sample was S. cerevisiae TGM10 extract (69.17%), followed by S. boulardii S11 (66.16%) and K. marxianus TGM66 (62.42%) extracts, respectively and S. cerevisiae TGM10 extract was also the richest yeast extract for essential amino acids. Additionally, flavor-enhancing amino acids such as glutamic acid, aspartic acid, alanine and glycine were dominant in S. cerevisiae TGM10 extract (47.41 g/100 g protein). Sensorial evaluation of yeast extracts demonstrated that salty taste, umami taste and meaty flavor scores of yeast extracts were lower than MSG whereas for fruity flavor, yeast extracts had the highest scores. These findings revealed the potential of three yeast strains to produce yeast extracts in order to increase the nutritional value and flavor of foods.\n\nProduction and characterization of yeast extracts produced by Saccharomyces cerevisiae, Saccharomyces boulardii and Kluyveromyces marxianus.", "token_count": 475, "char_count": 1532, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.8019, "entities": { "genes": [ "TGM10", "TGM66" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:15.371575", "source": { "split": "train_shard_00001", "doc_id": 96 }, "chunk_id": "train_shard_00001_96_0", "global_id": 5801 }, { "text": "Kluyveromyces marxianus is a yeast that was identified from kefir and can use a broad range of substrates, such as glucose and lactate, as carbon sources. The lactate produced in kefir culture can be a substrate for K. marxianus . However, the complexity of the kefir microbiota makes the traits of K. marxianus difficult to study. In this research, we focused on K. marxianus cultured with lactate as the sole carbon source. The optimal growth and released protein in lactate culture were determined under different pH conditions, and the LC-MS/MS-identified proteins were associated with the tricarboxylic acid cycle, glycolysis pathway, and cellular stress responses in cells, indicating that autolysis of K. marxianus had occurred under the culture conditions. The abundant glyceraldehyde-3-phosphate dehydrogenase (GAP1) was crystallized in the cell-free fraction, and the low transcription level of the GAP1 gene indicated that the protein abundance under autolysis conditions was dependent on protein stability. These results suggest that lactate produced by lactic acid bacteria stimulates the growth and autolysis of K. marxianus , releasing proteins and peptides. These findings can be fundamental for K. marxianus probiotic and kefir studies in the future.\n\nGrowth and Autolysis of Kluyveromyces Marxianus Stimulated with Lactate Provides Insights into Symbiosis", "token_count": 357, "char_count": 1373, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5644, "quality_score": 0.7822, "entities": { "genes": [ "GAP1" ], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:15.954506", "source": { "split": "train_shard_00001", "doc_id": 97 }, "chunk_id": "train_shard_00001_97_0", "global_id": 5802 }, { "text": "The genomic diversity of microbes is commonly parameterized as SNPs relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome, the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the widespread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. In addition to pangenomic approaches that focus on the variation in the sets of genes present in different genomes, complete assemblies allow investigations of the evolution of genome structure and gene order. This latter problem, however, is computationally demanding with few tools available that shed light on these dynamics. Here, we present PanGraph, a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as a path along vertices, which in turn encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into several common formats for either downstream analysis or immediate visualization.\n\nPanGraph: scalable bacterial pan-genome graph construction.", "token_count": 310, "char_count": 1425, "word_count": 198, "semantic_coherence": 1, "information_density": 0.702, "quality_score": 0.851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:16.530085", "source": { "split": "train_shard_00001", "doc_id": 98 }, "chunk_id": "train_shard_00001_98_0", "global_id": 5803 }, { "text": "Methodologies for source attribution (SA) of foodborne illnesses comprise a rapidly expanding suite of techniques for estimating the most important source or sources of human infection. Recently, the increasing availability of whole genome sequencing (WGS) data for a wide range of bacterial strains has led to the development of novel SA methods. These techniques utilize the unique features of bacterial genomes adapted to different host types and hence offer increased resolution of the outputs. Comparative studies of different SA techniques reliant on WGS data are currently lacking. Here, we critically assessed and compared the outputs of three SA methods: a supervised classification random forest machine learning algorithm (RandomForest), an Accessory genes-Based Source Attribution method (AB_SA), and a Bayesian frequency matching method (Bayesian). Each technique was applied to the WGS data of a panel of 902 reservoir host and human monophasic and biphasic Salmonella enterica subsp. enterica serovar Typhimurium isolates sampled in the British Isles (BI) and Denmark from 2012 to 2016. Additionally, for RandomForest and Bayesian, we explored whether utilization of accessory genome features as model inputs improved attribution accuracy of these methods over using the core genome derived features only. Results indicated that this was the case for RandomForest, but for Bayesian the overall attribution estimates varied little regardless of the inclusion or not of the accessory genome features. All three methods attributed the vast majority of human isolates to the Pigs primary source class, which was expected given the known high relative prevalence rates in pigs, and hence routes of infection into the human population, of monophasic and biphasic S. Typhimurium in the BI and Denmark. The accuracy of AB_SA was lower than of RandomForest when attributing the primary source classes to the 120 animal test set isolates with known primary sources. A major advantage of both AB_SA and Bayesian was a much faster execution time as compared to RandomForest. Overall, the SA method comparison presented in this study describes the strengths and weaknesses of each of the three methods applied to attributing potential monophasic and biphasic S", "token_count": 511, "char_count": 2290, "word_count": 340, "semantic_coherence": 1, "information_density": 0.5824, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:17.185041", "source": { "split": "train_shard_00001", "doc_id": 99 }, "chunk_id": "train_shard_00001_99_0", "global_id": 5804 }, { "text": "Typhimurium animal sources to human infections that could be valuable when deciding which SA methodology would be the most applicable to foodborne disease outbreak scenarios involving monophasic and biphasic S. Typhimurium.\n\nComparison of three source attribution methods applied to whole genome sequencing data of monophasic and biphasic Salmonella Typhimurium isolates from the British Isles and Denmark.", "token_count": 106, "char_count": 420, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8214, "quality_score": 0.9107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:17.569199", "source": { "split": "train_shard_00001", "doc_id": 99 }, "chunk_id": "train_shard_00001_99_1", "global_id": 5805 }, { "text": "Aquatic ecosystems serve as crucial reservoirs for pathogens and antimicrobial resistance genes, thus presenting a significant global health risk. Here, we investigated the phylogenomics of Aeromonas veronii from Lake Wilcox in Ontario. Among the 11 bacterial isolates, nine were identified as A. veronii. Notably, 67% of A. veronii isolates were potential human pathogens. Considerable genetic diversity was noted among the A. veronii isolates, suggesting the lake as a reservoir for multiple human pathogenic strains. Comparison of the A. veronii sequenced with global A. veronii genomes highlighted significant genetic diversity and suggests widespread dissemination of strains. All the isolates carried chromosomal genes encoding resistance to β-lactams. Although virulence gene content differed between human and non-human pathogenic strains, type III secretion systems was associated with human pathogenic isolates. The assessment of AMR genes in global isolates showed that β-lactam and tetracycline resistance genes were predominant. Although the machine learning-based pangenome-wide association approach performed did not yield any source-based genes, some genes were enriched in a few isolates from different sources. The mrkABCDF operon that mediates biofilm formation and genes encoding resistance to colistin, chloramphenicol, trimethoprim, and tetracycline were enriched in animal products, whereas macrolide resistance genes and Inc plasmid-types were linked to the aquatic environment. Novel biosynthetic gene clusters were identified, suggesting that A. veronii with varying pathogenic potential could produce unique secondary metabolites. There is a need for continuous tracking of pathogens in aquatic ecosystems to contribute to our understanding of their evolutionary dynamics and the ecological roles of their genetic elements.

Importance

Lakes and other aquatic ecosystems can harbor harmful bacteria that can make people sick and resist antibiotics, posing a significant global health risk", "token_count": 513, "char_count": 2077, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:18.200624", "source": { "split": "train_shard_00001", "doc_id": 100 }, "chunk_id": "train_shard_00001_100_0", "global_id": 5806 }, { "text": "In this study, we investigated Aeromonas veronii, a Gram-negative bacteria found in Lake Wilcox in Ontario. We used various techniques, including whole-genome sequencing (WGS), to analyze the bacteria and found that many of the isolates had the potential to cause human disease. We also discovered significant genetic diversity among the isolates, indicating that the lake may be a reservoir for multiple human pathogenic strains. All isolates carried genes that confer resistance to antibiotics, and some virulence genes were associated with human pathogenic isolates. This study highlights the importance of monitoring aquatic ecosystems for harmful bacteria to better understand their evolution, potential for human pathogenicity, and the ecological roles of their genetic elements. This knowledge can inform strategies for preventing the spread of antibiotic-resistant bacteria and protecting public health.\n\nPhylogenomics of novel clones of Aeromonas veronii recovered from a freshwater lake reveals unique biosynthetic gene clusters.", "token_count": 228, "char_count": 1053, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6759, "quality_score": 0.8379, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:18.679601", "source": { "split": "train_shard_00001", "doc_id": 100 }, "chunk_id": "train_shard_00001_100_1", "global_id": 5807 }, { "text": "Rainbow trout ( Oncorhynchus mykiss ) exhibit extensive genomic diversity shaped by domestication, life history, and geographic origin. To advance the development of a comprehensive pangenome reference, we present new de novo genome assemblies of two genetically and ecologically distinct lines: Whale Rock (WR; wild, landlocked, Central California) and Keithley Creek (KC; wild, resident, interior Columbia Basin), along with the previously published assemblies of the Arlee (domesticated, Northern California) and Swanson (semi-domesticated, resident, Alaska) lines. All assemblies provide nearly complete coverage of known genes (BUSCO 95.8–99.7%) and are similar in genome size (∼2.3 Gb), with scaffold N50 values between 3.4 Mb (KC) and 52.4 Mb (Swanson). Comparative whole-genome alignments revealed high sequence conservation (97–98% identity) among assemblies, but also evidence of extensive structural variation of at least 50 bp in length. Structural variant (SV) profiling identified tens of thousands of deletions, insertions, and complex rearrangements largely in noncoding sequences. In an initial assessment of the utility of having multiple de novo genome assemblies for rainbow trout, we found that two strains (Arlee and Swanson; domesticated) share SVs enriched in genes linked with growth, reproduction, and adaptation to domestication, such as GTP binding and ECM-receptor interaction. In comparison, the other two strains (WR and KC; wild origin) share SVs associated with reproductive timing such as GnRH signaling pathway. Both Arlee and WR also have unique SVs potentially related to their geographic origin and unique life history. Additionally, we identified SVs in key regions, such as a QTL for fillet yield on Omy17 and the maturation-associated SIX6/ERβ-GPHB5 locus on Omy25q, suggesting the importance of considering SVs when investigating the genomics of complex traits", "token_count": 485, "char_count": 1902, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": { "genes": [ "GPHB5", "SIX6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:19.692099", "source": { "split": "train_shard_00001", "doc_id": 101 }, "chunk_id": "train_shard_00001_101_0", "global_id": 5808 }, { "text": "Together, these assemblies and comparative analyses establish a foundation for a rainbow trout pangenome reference, illuminating how they can be utilized to reveal the structural genomic basis of domestication, adaptation, and other complex traits in O. mykiss .\n\nDe novo Genome Assemblies of Four Rainbow Trout Genetic Lines Reveal Structural Variants In Pursuit of a Pangenome Reference", "token_count": 101, "char_count": 395, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:20.066202", "source": { "split": "train_shard_00001", "doc_id": 101 }, "chunk_id": "train_shard_00001_101_1", "global_id": 5809 }, { "text": "

Background

Simultaneous cofermentation of glucose and xylose mixtures would be a cost-effective solution for the conversion of cellulosic biomass to high-value products. However, most yeasts ferment glucose and xylose sequentially due to glucose catabolite repression. A well known thermotolerant yeast, Kluyveromyces marxianus, was selected for this work because it possesses cost-effective advantages over Saccharomyces cerevisiae for biofuel production from cellulosic biomass.

Results

In the present study, we employed a directed evolutionary approach using 2-deoxyglucose to develop a thermotolerant mutant capable of simultaneous cofermentation of glucose and xylose by alleviating catabolite repression. The selected mutant, K. marxianus SBK1, simultaneously cofermented 40 g/L glucose and 28 g/L xylose to produce 23.82 g/L ethanol at 40 °C. This outcome corresponded to a yield of 0.35 g/g and productivity of 0.33 g/L h, representing an 84% and 129% improvement, respectively, over the parental strain. Interestingly, following mutagenesis the overall transcriptome of the glycolysis pathway was highly downregulated in K. marxianus SBK1, except for glucokinase-1 (GLK1) which was 21-fold upregulated. Amino acid sequence of GLK1 from K. marxianus SBK1 revealed three amino acid mutations which led to more than 22-fold lower enzymatic activity compared to the parental strain.

Conclusions

We herein successfully demonstrated that the cofermentation of a sugar mixture is a promising strategy for the efficient utilization of cellulosic biomass by K. marxianus SBK1", "token_count": 511, "char_count": 1639, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [ "GLK1", "SBK1" ], "proteins": [], "pathways": [ "glycolysis", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:20.697900", "source": { "split": "train_shard_00001", "doc_id": 102 }, "chunk_id": "train_shard_00001_102_0", "global_id": 5810 }, { "text": "Through introduction of additional biosynthetic pathways, K. marxianus SBK1 could become a chassis-type strain for the production of fuels and chemicals from cellulosic biomass.\n\nAlleviation of catabolite repression in Kluyveromyces marxianus: the thermotolerant SBK1 mutant simultaneously coferments glucose and xylose.", "token_count": 108, "char_count": 341, "word_count": 40, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [ "SBK1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:21.084202", "source": { "split": "train_shard_00001", "doc_id": 102 }, "chunk_id": "train_shard_00001_102_1", "global_id": 5811 }, { "text": "Two bacterial strains, SP1S1-4T and SP2S1-2T, were isolated from sediment samples collected in the Stockholm archipelago in November 2021. Following whole-genome sequencing, these strains were identified as tentatively belonging to two novel Shewanella genospecies, based on digital DNA-DNA hybridization, as implemented in the Type Strain Genome Server. Shewanella septentrionalis, Shewanella baltica and Shewanella hafniensis were, in this order and within a narrow genomic relatedness range, their closest genotypic relatives. Additional sampling and sequencing efforts led to the retrieval of distinct isolates that were monophyletic with SP1S1-4T and SP2S1-2T, respectively, based on phylogenomic analysis of whole-genome sequences. Comparative analyses of genome sequence data, which included blast-based average nucleotide identity, core genome-based and core proteome-based phylogenomics, in addition to MALDI-TOF MS-based protein profiling, confirmed the distinctness of the putative novel genospecies with respect to their closest genotypic relatives. A comprehensive phenotypic characterisation of SP1S1-4T and SP2S1-2T revealed only minor differences with respect to the type strains of S. septentrionalis, S. baltica and S. hafniensis. Based on the collective phylogenomic, proteomic, and phenotypic evidence presented here, we describe two novel genospecies within the genus Shewanella, for which the names Shewanella scandinavica sp. nov. and Shewanella vaxholmensis sp. nov. are proposed", "token_count": 486, "char_count": 1639, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6396, "quality_score": 0.8198, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:21.741467", "source": { "split": "train_shard_00001", "doc_id": 103 }, "chunk_id": "train_shard_00001_103_0", "global_id": 5812 }, { "text": "The type strains are, respectively, SP2S1-2T (=CCUG 76457T=CECT 30688T), with a draft genome sequence of 5 041 805 bp and a G+C content of 46.3 mol%, and SP1S1-4T (=CCUG 76453T=CECT 30684T), with a draft genome sequence of 4 920147 bp and a G+C content of 46.0 mol%. Our findings suggest the existence of a species complex formed by the species S. baltica, S. septentrionalis, S. scandinavica sp. nov., and S. vaxholmensis sp. nov., with S. hafniensis falling in the periphery, where distinct genomic species clusters could be identified. However, this does not exclude the possibility of a continuum of genomic diversity within this sedimental ecosystem, as discussed herein with additional sequenced isolates.\n\nA hotspot of diversity: novel <i>Shewanella</i> species isolated from Baltic Sea sediments delineate a sympatric species complex.", "token_count": 350, "char_count": 955, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:22.314692", "source": { "split": "train_shard_00001", "doc_id": 103 }, "chunk_id": "train_shard_00001_103_1", "global_id": 5813 }, { "text": "Kluyveromyces marxianus (K. marxianus) is an increasingly popular industrially relevant yeast. It is known to possess a highly efficient non-homologous end joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome. The nature of the integration events was traditionally analyzed by Southern blot hybridization. However, the precise DNA sequence at the insertion sites were not fully explored. We transformed a PCR product of the Saccharomyces cerevisiae URA3 gene (ScURA3) into an uracil auxotroph K. marxianus otherwise wildtype strain and picked 24 stable Ura+ transformants for sequencing analysis. We took advantage of rapid advances in DNA sequencing technologies and developed a method using a combination of Illumina MiSeq and Oxford Nanopore sequencing. This approach enables us to uncover the gross chromosomal rearrangements (GCRs) that are associated with the ScURA3 random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in eukaryotes, which could potentially provide insights for cancer research.\n\nGross Chromosomal Rearrangements in Kluyveromyces marxianus Revealed by Illumina and Oxford Nanopore Sequencing.", "token_count": 339, "char_count": 1254, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7321, "quality_score": 0.8661, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:22.891260", "source": { "split": "train_shard_00001", "doc_id": 104 }, "chunk_id": "train_shard_00001_104_0", "global_id": 5814 }, { "text": "Bran can enrich snacks with dietary fibre but contains fructans that trigger symptoms in people with irritable bowel syndrome (IBS). This study aimed to investigate the bioprocessing of wheat and amaranth bran for degrading fructans and its application (at 20% flour-based) in 3D-printed snacks. Bran was bioprocessed with Saccharomyces cerevisiae alone or combined with inulinase, Kluyveromyces marxianus, Limosilactobacillus fermentum, or commercial starter LV1 for 24 h. Fructans, fructose, glucose, and mannitol in the bran were analysed enzymatically. Dough rheology, snack printing precision, shrinkage in baking, texture, colour, and sensory attributes were determined. The fructan content of wheat bran was 2.64% dry weight, and in amaranth bran, it was 0.96% dry weight. Bioprocessing reduced fructan content (up to 93%) depending on the bran type and bioprocessing agent, while fructose and mannitol remained below the cut-off value for IBS patients. Bran bioprocessing increased the complex viscosity and yield stress of dough (by up to 43 and 183%, respectively) in addition to printing precision (by up to 13%), while it lessened shrinkage in baking (by 20-69%) and the hardness of the snacks (by 20%). The intensity of snack sensory attributes depended on the bran type and bioprocessing agent, but the liking (\"neither like nor dislike\") was similar between samples. In conclusion, snacks can be enriched with fibre while remaining low in fructans by applying bioprocessed wheat or amaranth bran and 3D printing.\n\nBioprocessing of Wheat and Amaranth Bran for the Reduction of Fructan Levels and Application in 3D-Printed Snacks.", "token_count": 502, "char_count": 1664, "word_count": 246, "semantic_coherence": 1, "information_density": 0.561, "quality_score": 0.7805, "entities": { "genes": [ "LV1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:23.545094", "source": { "split": "train_shard_00001", "doc_id": 105 }, "chunk_id": "train_shard_00001_105_0", "global_id": 5815 }, { "text": "The process of domestication has variable consequences on genome evolution leading to different phenotypic signatures. Access to the complete genome sequences of a large number of individuals makes it possible to explore the different facets of this domestication process. Here, we sought to explore the genome evolution of the Kluyveromyces lactis yeast species, a well-known species for its involvement in dairy processes but also present in natural environments. Using a combination of short and long-read sequencing strategies, we investigated the genomic variability of 41 Kluyveromyces lactis isolates and found that the overall genetic diversity of this species is very high (π = 2.9 x 10 -2 ) compared to other species such as Saccharomyces cerevisiae (π = 3 x 10 -3 ). However, the domesticated dairy population shows a reduced level of diversity ( π = 7 x 10 -4 ), probably due to a domestication bottleneck. In addition, this entire population is characterized by the introgression of the LAC4 and LAC12 genes, responsible for lactose fermentation and coming from the closely related species, Kluyveromyces marxianus , as previously described. Our results also highlighted that the LAC4/LAC12 gene cluster was acquired through multiple and independent introgression events. Finally, we also identified several genes that could play a role in adaptation to dairy environments through copy number variation. These genes are involved in sugar consumption, flocculation and drug resistance, and may play a role in dairy processes. Overall, our study illustrates contrasting genomic evolution and sheds new light on the impact of domestication processes on it.\n\nContrasting genomic evolution between domesticated and wild Kluyveromyces lactis yeast populations", "token_count": 411, "char_count": 1773, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8102, "entities": { "genes": [ "LAC12", "LAC4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:24.166900", "source": { "split": "train_shard_00001", "doc_id": 106 }, "chunk_id": "train_shard_00001_106_0", "global_id": 5816 }, { "text": "

Motivation

Using a single linear reference genome poses a limitation to exploring the full genomic diversity of a species. The release of a draft human pangenome underscores the increasing relevance of pangenomics to overcome these limitations. Pangenomes are commonly represented as graphs, which can represent billions of base pairs of sequence. Presently, there is a lack of scalable software able to perform key tasks on pangenomes, such as quantifying universally shared sequence across genomes (the core genome ) and measuring the extent of genomic variability as a function of sample size ( pangenome growth ).

Results

We introduce Panacus (pangenome-abacus), a tool designed to rapidly perform these tasks and visualize the results in interactive plots. Panacus can process GFA files, the accepted standard for pangenome graphs, and is able to analyze a human pangenome graph with 110 million nodes in less than one hour.

Availability

Panacus is implemented in Rust and is published as Open Source software under the MIT license. The source code and documentation are available at https://github.com/marschall-lab/panacus . Panacus can be installed via Bioconda at https://bioconda.github.io/recipes/panacus/README.html .

Contact

Luca Parmigiani ( luca.parmigiani@uni-bielefeld.de ), Daniel Doerr ( daniel.doerr@hhu.de ).\n\nPanacus: fast and exact pangenome growth and core size estimation", "token_count": 374, "char_count": 1432, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:24.761227", "source": { "split": "train_shard_00001", "doc_id": 107 }, "chunk_id": "train_shard_00001_107_0", "global_id": 5817 }, { "text": "Structural variation causes some human haplotypes to align poorly with the linear reference genome, leading to ‘reference bias’. A pangenome reference graph could ameliorate this bias by relating a sample to multiple reference assemblies. However, this approach requires a new definition of a ‘genetic variant.’ We introduce a definition of pangenome variants and a method, pantree , to identify them. Our approach involves a pangenome reference tree which includes all nodes (sequences) of the pangenome graph, but only a subset of its edges; non-reference edges are variant edges . Our variants are biallelic and have well-defined positions. Analyzing the Minigraph-Cactus draft human pangenome reference graph, we identified 29.6 million genetic variants. Most variants (99.2%) are small, and most small variants (73.9%) are SNPs. 3.5 million variants (11.7%) have a reference allele which is not on GRCh38; these variants are difficult to detect without a pangenome reference, or with existing pangenome-based approaches. They tend to be embedded within tangled, multiallelic regions. We analyze two medically relevant regions, around the HLA-A and RHD genes, identifying thousands of small variants embedded within several large insertions, deletions, and inversions. We release an open-source software tool together with a VCF variant catalogue.\n\nDefining and cataloging variants in pangenome graphs", "token_count": 335, "char_count": 1405, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6618, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:25.354197", "source": { "split": "train_shard_00001", "doc_id": 108 }, "chunk_id": "train_shard_00001_108_0", "global_id": 5818 }, { "text": "Fusobacterium nucleatum (Fn) is an oral commensal inhabiting the human gingival plaque that is rarely found in the gut. However, in colorectal cancer (CRC), Fn can be isolated from stool samples and detected in metagenomes. We hypothesized that ecological characteristics of the gut are altered by disease, enabling Fn to colonize. Multiple genomically distinct populations of Fn exist, but their ecological preferences are unstudied. We identified six well-separated populations in 133 Fn genomes and used simulated metagenomes to demonstrate sensitive detection of populations in human oral and gut metagenomes. In 9,560 samples from 11 studies, Fn population C2 animalis is elevated in gut metagenomes from CRC and Crohn's disease patients and is observed more frequently in CRC stool samples than in the gingiva. Polymorphum, the most prevalent gingival Fn population, is significantly increased in Crohn's stool samples; this effect was significantly stronger in male hosts than in female. We find polymorphum genomes are enriched for biosynthetic gene clusters and fluoride exporters, while C2 animalis are high in iron transporters. Fn populations thus associate with specific clinical and demographic phenotypes and harbor distinct functional features. Ecological differences in closely related groups of bacteria inform microbiome impacts on human health.

Importance

Fusobacterium nucleatum is a bacterium normally found in the gingiva. F. nucleatum generally does not colonize the healthy gut, but is observed in approximately a third of colorectal cancer (CRC) patient guts. F. nucleatum's presence in the gut during CRC has been linked to worse prognosis and increased tumor proliferation. Here, we describe the population structure of F. nucleatum in oral and gut microbiomes. We report substantial diversity in gene carriage among six distinct populations of F. nucleatum and identify population disease and body-site preferences", "token_count": 529, "char_count": 2048, "word_count": 282, "semantic_coherence": 1, "information_density": 0.578, "quality_score": 0.789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:26.038669", "source": { "split": "train_shard_00001", "doc_id": 109 }, "chunk_id": "train_shard_00001_109_0", "global_id": 5819 }, { "text": "We find the C2 animalis population is more common in the CRC gut than in the gingiva and is enriched for iron transporters, which support gut colonization in known pathogens. We find that C2 animalis is also enriched in Crohn's disease and type 2 diabetes, suggesting ecological commonalities between the three diseases. Our work shows that closely related bacteria can have different associations with human physiology.\n\nThe physical biogeography of <i>Fusobacterium nucleatum</i> in health and disease.", "token_count": 129, "char_count": 516, "word_count": 76, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:26.498049", "source": { "split": "train_shard_00001", "doc_id": 109 }, "chunk_id": "train_shard_00001_109_1", "global_id": 5820 }, { "text": "This study investigated the fermentability of hemicellulosic hydrolysates obtained by intensified steam explosion pretreatment of switchgrass (Panicum virgatum) and Eucalyptus globulus. Xylitol and carotenoids were the high-value molecules produced by fermentation. The intensified pretreatment allowed to process a large amount of biomass per unit of time and resulted in hydrolysates containing high amount of sugars, among of which, a significant fraction was in the form of oligomers (eucalyptus hydrolysate: 25.0 g/L of oligomers and 50.6 g/L of monomeric sugars; switchgrass hydrolysate: 18.9 g/L of oligomers and 39.6 g/L of monomeric sugars). To be used as fermentation media, a post-hydrolysis step was applied to increase the content of monomeric sugars in the hydrolysates. Then, a detoxification process was carried out to reduce the concentration of inhibitors present. Two evolved yeasts were used for fermentation: Kluyveromyces marxianus for xylitol production, and Rhodosporidium toruloides for carotenoids production. Results revealed that the hydrolysates produced by intensified steam explosion of switchgrass and eucalyptus present good fermentability and can be used to produce valuable compounds such as xylitol, after detoxification. K. marxianus presented better tolerance to inhibitory compounds still present in the detoxified hydrolysates (acetic acid up to 3.94 g/L and phenolic compounds up to 2.28 g/L) than R. toruloides, which favored the production of xylitol. Finally, the intensified pretreatment was found to be a potential strategy to obtain hydrolysates with high concentration of sugars, reducing the need of concentration in a subsequent step. Moreover, the detoxification strategy applied in this study allowed to recover valuable compounds from the hydrolysates, offering extra value to a biorefinery. Altogether, the findings of this study contribute to the advancement of a technology for valorization of hemicellulosic hydrolysates.", "token_count": 519, "char_count": 1978, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5324, "quality_score": 0.7662, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:27.143410", "source": { "split": "train_shard_00001", "doc_id": 110 }, "chunk_id": "train_shard_00001_110_0", "global_id": 5821 }, { "text": "Production of xylitol and carotenoids from switchgrass and Eucalyptus globulus hydrolysates obtained by intensified steam explosion pretreatment", "token_count": 35, "char_count": 144, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:27.506181", "source": { "split": "train_shard_00001", "doc_id": 110 }, "chunk_id": "train_shard_00001_110_1", "global_id": 5822 }, { "text": "Inflammatory diseases of the human gastrointestinal tract are affected by the microbes that reside in the mucosal surfaces. Patients with inflammatory bowel diseases (IBD) have altered bacterial and fungal intestinal compositions, including higher levels of fecal Candida yeasts. Ongoing research indicates that genetic and phenotypic diversity of Candida albicans may be linked with disease severity. Here, we set out to investigate feces-derived C. albicans strains from individuals with IBD and healthy volunteers through microsatellite-based genotyping and phenotypic assays. A seven-locus microsatellite panel was applied, of which six loci were newly developed. It appears that there is no specific lineage of C. albicans that is associated with IBD, but rather that the three study populations (Crohn's disease, ulcerative colitis, healthy volunteers) do have distinguishable distributions of genotypes. In addition, phenotypic characterization by means of enzyme release assays revealed trends between genotypes, virulence-related enzyme activity, and clinical biomarkers. We thus show that microsatellite typing can describe genetic diversity of feces-derived C. albicans strains, and that phenotypic diversity of these strains may indeed correlate with fungal genotype or disease. This study opens further possibilities to investigate fecal fungi in relation to severity of inflammation in IBD or in other (intestinal) diseases.\n\nTyping of feces-derived Candida albicans strains using a novel seven-locus microsatellite panel reveals associations with yeast phenotype in individuals with inflammatory bowel disease.", "token_count": 398, "char_count": 1625, "word_count": 221, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:28.123444", "source": { "split": "train_shard_00001", "doc_id": 111 }, "chunk_id": "train_shard_00001_111_0", "global_id": 5823 }, { "text": "

Objective

This study aimed to investigate the genomic epidemiology of Brucella melitensis in Jiangsu Province, a typical low-endemic region in East China where the incidence of human brucellosis has been increasing in recent years. Accordingly, a molecular epidemiological study was conducted on the 2,552 reported brucellosis patients in Jiangsu province, from 2011 to 2024.

Methods

All B. melitensis isolated from these patients were sequenced using next-generation sequencing (NGS), and 515 strains met the criteria for subsequent analysis. Core genome multi-locus sequence typing (cgMLST), pan-genome analysis and core genome single nucleotide polymorphism (cgSNP) were utilized to analyze genomic characteristics and establish the epidemiological linkages among global strains.

Results

Among 515 isolates, 439 (85.24%) and 505 (98.06%) were identified as B. melitensis biovar 3 and sequence type 8(ST8), respectively. cgMLST further classified them into 28 core gene sequence types (cgSTs), including four novel genotypes (cgST1586-cgST1589) discovered in this study, whose identification expands the global cgMLST database and provides new markers for epidemiological surveillance. According to the cgSNP-based phylogenetic analysis, two distinct clades were persistently circulating within Jiangsu Province. One clade demonstrated significant genetic clustering with the Middle East strains, the other clade was closely linked to the hyper-endemic regions in China. Pan-genome analysis revealed their high homology, with core proteins primarily involved in amino acid transport and metabolism", "token_count": 447, "char_count": 1642, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7251, "quality_score": 0.8626, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:28.760844", "source": { "split": "train_shard_00001", "doc_id": 112 }, "chunk_id": "train_shard_00001_112_0", "global_id": 5824 }, { "text": "Over the past 14 years, these isolates have exhibited limited genetic diversity and may be evolving toward a genotype that is better adapted to the host and environment.

Conclusion

The human brucellosis in Jiangsu is mainly attributed to imported infections through various patterns, which is consistent with the typical epidemiology characteristics observed in low-endemic regions. The identification of four novel cgSTs and evidence of genomic evolutionary changes provide important insights to strengthen surveillance and guide targeted control strategies for brucellosis in East China.\n\nLimited genomic diversity and convergent adaptation of <i>Brucella melitensis</i> isolated from human in East China, from 2011 to 2024.", "token_count": 172, "char_count": 745, "word_count": 100, "semantic_coherence": 1, "information_density": 0.76, "quality_score": 0.88, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:29.202676", "source": { "split": "train_shard_00001", "doc_id": 112 }, "chunk_id": "train_shard_00001_112_1", "global_id": 5825 }, { "text": "The applicability of two lactic acid bacterial strains with probiotic potential and bioprotective properties as additions in the starter culture in yogurt fermentation was examined. The studied strains, Lactobacillus delbrueckii subsp. bulgaricus KZM 2-11-3 and Lactiplantibacillus plantarum KC 5-12, inhibited the growth of Kluyveromyces lactis, Kluyveromyces marxianus, and Saccharomyces cerevisiae. The strain L. delbrueckii subsp. bulgaricus KZM 2-11-3 directly inhibited Escherichia coli. The important characteristics for the quality of the yogurt product, such as physicochemical parameters during fermentation and storage, rheological characteristics, and sensory changes during the storage of samples were determined. The yogurt samples with the strains did not differ in most parameters from the control yogurt with the commercial starter. The added strains showed stable viability in the yogurt samples during storage. The yogurt sample with L. delbrueckii subsp. bulgaricus KZM 2-11-3 and the sample with both strains based on the total evaluation were very similar to the control yogurt with the commercial starter. Using these strains as probiotic supplements to enrich the starter cultures in yogurt production will contribute to developing new products with benefits to human health.\n\nPhysicochemical, Rheological, and Sensory Characteristics of Yogurt Fermented by Lactic Acid Bacteria with Probiotic Potential and Bioprotective Properties.", "token_count": 454, "char_count": 1534, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5377, "quality_score": 0.7688, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:29.839837", "source": { "split": "train_shard_00001", "doc_id": 113 }, "chunk_id": "train_shard_00001_113_0", "global_id": 5826 }, { "text": "Here we review two connected themes in evolutionary microbiology: (a) the nature of gene repertoire variation within species groups (pangenomes) and (b) the concept of metabolite transporters as accessory proteins capable of providing niche-defining \"bolt-on\" phenotypes. We discuss the need for improved sampling and understanding of pangenome variation in eukaryotic microbes. We then review the factors that shape the repertoire of accessory genes within pangenomes. As part of this discussion, we outline how gene duplication is a key factor in both eukaryotic pangenome variation and transporter gene family evolution. We go on to outline how, through functional characterization of transporter-encoding genes, in combination with analyses of how transporter genes are gained and lost from accessory genomes, we can reveal much about the niche range, the ecology, and the evolution of virulence of microbes. We advocate for the coordinated systematic study of eukaryotic pangenomes through genome sequencing and the functional analysis of genes found within the accessory gene repertoire.\n\nTransporter Proteins as Ecological Assets and Features of Microbial Eukaryotic Pangenomes.", "token_count": 278, "char_count": 1199, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:30.401415", "source": { "split": "train_shard_00001", "doc_id": 114 }, "chunk_id": "train_shard_00001_114_0", "global_id": 5827 }, { "text": "The establishment of lignocellulosic biorefineries is dependent on microorganisms being able to cope with the stressful conditions resulting from the release of inhibitory compounds during biomass processing. The yeast Kluyveromyces marxianus has been explored as an alternative microbial factory due to its thermotolerance and ability to natively metabolize xylose. The lignocellulose-derived inhibitors furfural and 5-hydroxymethylfurfural (HMF) are considered promising building-block platforms that can be converted into a wide variety of high-value derivatives. Here, several K. marxianus strains, isolated from cocoa fermentation, were evaluated for xylose consumption and tolerance towards acetic acid, furfural, and HMF. The potential of this yeast to reduce furfural and HMF at high inhibitory loads was disclosed and characterized. Our results associated HMF reduction with NADPH while furfural-reducing activity was higher with NADH. In addition, furans' inhibitory effect was higher when combined with xylose consumption. The furan derivatives produced by K. marxianus in different conditions were identified. Furthermore, one selected isolate was efficiently used as a whole-cell biocatalyst to convert furfural and HMF into their derivatives, furfuryl alcohol and 2,5-bis(hydroxymethyl)furan (BHMF), with high yields and productivities. These results validate K. marxianus as a promising microbial platform in lignocellulosic biorefineries.\n\nEstablishment of Kluyveromyces marxianus as a Microbial Cell Factory for Lignocellulosic Processes: Production of High Value Furan Derivatives.", "token_count": 437, "char_count": 1634, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.831, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:31.047421", "source": { "split": "train_shard_00001", "doc_id": 115 }, "chunk_id": "train_shard_00001_115_0", "global_id": 5828 }, { "text": "Kazakh cheese is a traditional dairy product in Xinjiang, China. The function and potential probiotic characteristics of Saccharomyces cerevisiae DL6-20 and Kluyveromyces marxianus B13-5 in Kazakh cheese and its contribution to cheese fermentation was studied. In this study, the effect of the addition ratio of gamma aminobutyric acid (GABA)-producing S. cerevisiae DL6-20 and K. marxianus B13-5 on cheese quality was investigated. Cheeses were prepared by fermentations with a total of six treatments: comercial culture alone as control (CS), a combination with one yeast, either; K. marxianus B13-5 (CSM); S. cerevisiae DL6-20 (CSS); and three different proportions of this two yeasts (CSM:CSS 1:1, 1:2, 2:1). We measured the GABA content of cheese, as well as basic physical and chemical indicators, microbial content, free amino acid (FAA) content, texture, and flavor compound content. The total FAA content of mixed bacteria fermentation was higher than that of the single bacteria alone. The GABA content CSM:CSS 1:2 GABA content was 0.114 g/100 g, CSM:CSS 2:1 GABA content was 0.12 g/100 g, CSM:CSS1:1 content of GABA produced in the late ripening period of cheese was the highest, reaching 0.189 g/100 g and the number of LAB and yeasts in CSM:CSS 1:1 was higher than that of other cheeses. The mixed-strain fermentation generally produced cheeses with a higher protein content than that of the single-strain fermentation in the late stage of the maturation process, especially the protein content of CSM:CSS 1:1 during the ripening period, when the protein content was highest at day 50", "token_count": 511, "char_count": 1639, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5484, "quality_score": 0.7742, "entities": { "genes": [ "CSS1", "DL6" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:31.708150", "source": { "split": "train_shard_00001", "doc_id": 116 }, "chunk_id": "train_shard_00001_116_0", "global_id": 5829 }, { "text": "CSM:CSS 1:1 had a low moisture content, making it easy to store. With the exception of water and protein content, there is no significant difference in other physical and chemical indicators. CSM:CSS 1:1 contributed to the formation of cheese texture. In addition, multivariate statistical analysis indicated that mixed-strain fermentation was beneficial to the production of cheese aroma, with the aroma production performance of CSM:CSS 1:2 and CSM:CSS 2:1 found to be better than that of CSM: CSS 1:1.\n\nThe Effect of the Ratio of Gamma Aminobutyric Acid-Producing Saccharomyces cerevisiae DL6-20 and Kluyveromyces marxianus B13-5 Addition on Cheese Quality.", "token_count": 196, "char_count": 674, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "DL6" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:32.161390", "source": { "split": "train_shard_00001", "doc_id": 116 }, "chunk_id": "train_shard_00001_116_1", "global_id": 5830 }, { "text": "In recombinant protein-producing yeast strains, cells experience high production-related stresses similar to high temperatures. It is possible to increase recombinant protein production by enhancing thermotolerance, but few studies have focused on this topic. Here we aim to identify cellular regulators that can simultaneously activate thermotolerance and high yield of recombinant protein. Through screening at 46 °C, a heat-resistant Kluyveromyces marxianus (K. marxianus) strain FDHY23 is isolated. It also exhibits enhanced recombinant protein productivity at both 30 °C and high temperatures. The CYR1N1546K mutation is identified as responsible for FDHY23's improved phenotype, characterized by weakened adenylate cyclase activity and reduced cAMP production. Introducing this mutation into the wild-type strain greatly enhances both thermotolerance and recombinant protein yields. RNA-seq analysis reveals that under high temperature and recombinant protein production conditions, CYR1 mutation-induced reduction in cAMP levels can stimulate cells to improve its energy supply system and optimize material synthesis, meanwhile enhance stress resistance, based on the altered cAMP signaling cascades. Our study provides CYR1 mutation as a novel target to overcome the bottleneck in achieving high production of recombinant proteins under high temperature conditions, and also offers a convenient approach for high-throughput screening of recombinant proteins with high yields.\n\nCoupling thermotolerance and high production of recombinant protein by CYR1N1546K mutation via cAMP signaling cascades.", "token_count": 402, "char_count": 1626, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6274, "quality_score": 0.8137, "entities": { "genes": [ "CYR1", "FDHY23" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:32.775741", "source": { "split": "train_shard_00001", "doc_id": 117 }, "chunk_id": "train_shard_00001_117_0", "global_id": 5831 }, { "text": "Corrigendum: A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes", "token_count": 24, "char_count": 113, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:33.139142", "source": { "split": "train_shard_00001", "doc_id": 118 }, "chunk_id": "train_shard_00001_118_0", "global_id": 5832 }, { "text": "Pangenome analysis of Liriodendron reveals presence/absence variations associated with growth traits", "token_count": 20, "char_count": 100, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:33.492211", "source": { "split": "train_shard_00001", "doc_id": 119 }, "chunk_id": "train_shard_00001_119_0", "global_id": 5833 }, { "text": "We identified 23 cases of Mycobacterium immunogenum respiratory acquisition linked to a colonized plumbing system at a new hospital addition. We conducted a genomic and epidemiologic investigation to assess for clonal acquisition of M. immunogenum from hospital water sources and improve understanding of genetic distances between M. immunogenum isolates. We performed whole-genome sequencing on 28 M. immunogenum isolates obtained from August 2013 to July 2021 from patients and water sources on four intensive care and intermediate units at an academic hospital. Study hospital isolates were recovered from 23 patients who experienced de novo respiratory isolation of M. immunogenum and from biofilms obtained from five tap water outlets. We also analyzed 10 M. immunogenum genomes from previously sequenced clinical (n = 7) and environmental (n = 3) external control isolates. The 38-isolate cohort clustered into three clades with pairwise single-nucleotide polymorphism (SNP) distances ranging from 0 to 106,697 SNPs. We identified two clusters of study hospital isolates in Clade 1 and one cluster in Clade 2 for which clinical and environmental isolates differed by fewer than 10 SNPs and had less than 0.5% accessory genome variation. A less restrictive combined threshold of 40 SNPs and 5% accessory genes reliably captured additional isolates that met clinical criteria for hospital acquisition, but 12 (4%) of 310 epidemiologically unrelated isolate pairs also met this threshold. Core and accessory genome analyses confirmed respiratory acquisition of multiple clones of M. immunogenum from hospital water sources to patients. When combined with epidemiologic investigation, genomic thresholds accurately distinguished hospital acquisition.", "token_count": 493, "char_count": 1836, "word_count": 252, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:34.136621", "source": { "split": "train_shard_00001", "doc_id": 120 }, "chunk_id": "train_shard_00001_120_0", "global_id": 5834 }, { "text": "Mycobacterium immunogenum acquisition from hospital tap water: a genomic and epidemiologic analysis.", "token_count": 31, "char_count": 107, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:34.499832", "source": { "split": "train_shard_00001", "doc_id": 120 }, "chunk_id": "train_shard_00001_120_1", "global_id": 5835 }, { "text": "Abstract

The aim of this study was to evaluate the biosynthesis of flavor compounds from rice bran by yeast metabolisms. The microbial growth and flavor biosynthesis of Kluyveromyces marxianus and Debaryomyces hansenii in rice bran by microbial fermentation were investigated. Growth of both yeasts was assessed by the calculation of specific growth rates and doubling time. Their aroma biosynthesis was evaluated by gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS) and Spectrum™ sensory analysis. The specific growth rate (µmax) and doubling time (td) of K. marxianus were calculated as 0.16/h and 4.21 h respectively, D. hansenii had 0.13/h of µmax and 5.33h of td. K. marxianus and D. hansenii significantly produced higher alcohols and acetate esters from rice bran at high levels. Results showed that K. marxianus can produce 827.27 µg/kg of isoamy alcohol, 169.77 µg/kg of phenyl ethyl alcohol and 216.08 µg/kg phenyl ethyl acetate during 24 h batch fermentation. Isovaleric acid was also synthesed by K. marxianus at high level (4013 µg/kg) in the batch fermentation of 96 hours", "token_count": 506, "char_count": 1439, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:35.130028", "source": { "split": "train_shard_00001", "doc_id": 121 }, "chunk_id": "train_shard_00001_121_0", "global_id": 5836 }, { "text": "The highest concentration of of isoamyl alcohol and phenyl ethyl acetate was determined as 415.64 µg/kg and 135.77 µg/kg, respectively at 24 h fermentation of D.hansenii. Fermented cereals and rose were defined as characteristic flavor descriptors for the fermented rice bran samples. Rose flavor term in fermented rice bran samples were found to associate with phenyl ethyl alcohol, phenyl ethyl acetate, isoamyl acetate and guaiacol. The valorization of rice bran can be achieved with the production of natural flavor compounds by yeast metabolisms.

\n\nProduction of Some Higher Alcohols and Acetate Esters from Rice Bran by Yeasts Metabolisms of Kluyveromyces Marxianus and Debaryomyces Hansenii", "token_count": 209, "char_count": 717, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:35.595451", "source": { "split": "train_shard_00001", "doc_id": 121 }, "chunk_id": "train_shard_00001_121_1", "global_id": 5837 }, { "text": "Xylitol production from lignocellulose hydrolysate is a sustainable and environment-friendly process. In this study, a systematic process of converting corncob waste into xylitol is described. First, the corncobs are hydrolyzed with acid to a hydrolysate. Second, Kluyveromyces marxianus YZJQ016 derived from K. marxianus YZJ074, constructed by overexpressing ScGAL2-N376F from Saccharomyces cerevisiae, CtXYL1 from Candida tropicalis, and KmZWF1 from K. marxianus, produces xylitol from the hydrolysate. A total of ten xylose reductase genes were evaluated, and CtXYL1 proved best by showing the highest catalytic activity under the control of the KmGAPDH promoter. A 5 L fermenter at 42°C produced 105.22 g/L xylitol using K. marxianus YZJQ016-the highest production reported to date from corncob hydrolysate. Finally, for crystallization of the xylitol, the best conditions were 50% (v/v) methanol as an antisolvent, at 25°C, with purity and yield of 99%-100% and 74%, respectively-the highest yield reported to date.\n\nLignocellulosic xylitol production from corncob using engineered Kluyveromyces marxianus.", "token_count": 439, "char_count": 1202, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6558, "quality_score": 0.8279, "entities": { "genes": [ "YZJ074", "YZJQ016" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:36.232099", "source": { "split": "train_shard_00001", "doc_id": 122 }, "chunk_id": "train_shard_00001_122_0", "global_id": 5838 }, { "text": "Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H2 and CH4. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and \"Mixed\" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO2, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.", "token_count": 478, "char_count": 2090, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:36.903288", "source": { "split": "train_shard_00001", "doc_id": 123 }, "chunk_id": "train_shard_00001_123_0", "global_id": 5839 }, { "text": "Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman.", "token_count": 38, "char_count": 172, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:37.297176", "source": { "split": "train_shard_00001", "doc_id": 123 }, "chunk_id": "train_shard_00001_123_1", "global_id": 5840 }, { "text": "Arcobacter (A.) butzleri, the most widespread species within the genus Arcobacter, is considered as an emerging pathogen causing gastroenteritis in humans. Here, we performed a comparative genome-wide analysis of 40 A. butzleri strains from Lithuania to determine the genetic relationship, pangenome structure, putative virulence, and potential antimicrobial- and heavy-metal-resistance genes. Core genome single nucleotide polymorphism (cgSNP) analysis revealed low within-group variability (≤4 SNPs) between three milk strains (RCM42, RCM65, RCM80) and one human strain (H19). Regardless of the type of input (i.e., cgSNPs, accessory genome, virulome, resistome), these strains showed a recurrent phylogenetic and hierarchical grouping pattern. A. butzleri demonstrated a relatively large and highly variable accessory genome (comprising of 6284 genes with around 50% of them identified as singletons) that only partially correlated to the isolation source. Downstream analysis of the genomes resulted in the detection of 115 putative antimicrobial- and heavy-metal-resistance genes and 136 potential virulence factors that are associated with the induction of infection in host (e.g., cadF, degP, iamA), survival and environmental adaptation (e.g., flagellar genes, CheA-CheY chemotaxis system, urease cluster). This study provides additional knowledge for a better A. butzleri-related risk assessment and highlights the need for further genomic epidemiology studies in Lithuania and other countries.\n\nGenomic Characterization of Arcobacter butzleri Strains Isolated from Various Sources in Lithuania.", "token_count": 479, "char_count": 1667, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7277, "quality_score": 0.8638, "entities": { "genes": [ "RCM80", "RCM42", "RCM65" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:37.950817", "source": { "split": "train_shard_00001", "doc_id": 124 }, "chunk_id": "train_shard_00001_124_0", "global_id": 5841 }, { "text": "

Background

Studying genomic variation in rapidly evolving pathogens potentially enables identification of genes supporting their \"core biology\", being present, functional and expressed by all strains or \"flexible biology\", varying between strains. Genes supporting flexible biology may be considered to be \"accessory\", whilst the \"core\" gene set is likely to be important for common features of a pathogen species biology, including virulence on all host genotypes. The wheat-pathogenic fungus Zymoseptoria tritici represents one of the most rapidly evolving threats to global food security and was the focus of this study.

Results

We constructed a pangenome of 18 European field isolates, with 12 also subjected to RNAseq transcription profiling during infection. Combining this data, we predicted a \"core\" gene set comprising 9807 sequences which were (1) present in all isolates, (2) lacking inactivating polymorphisms and (3) expressed by all isolates. A large accessory genome, consisting of 45% of the total genes, was also defined. We classified genetic and genomic polymorphism at both chromosomal and individual gene scales. Proteins required for essential functions including virulence had lower-than average sequence variability amongst core genes. Both core and accessory genomes encoded many small, secreted candidate effector proteins that likely interact with plant immunity. Viral vector-mediated transient in planta overexpression of 88 candidates failed to identify any which induced leaf necrosis characteristic of disease. However, functional complementation of a non-pathogenic deletion mutant lacking five core genes demonstrated that full virulence was restored by re-introduction of the single gene exhibiting least sequence polymorphism and highest expression.

Conclusions

These data support the combined use of pangenomics and transcriptomics for defining genes which represent core, and potentially exploitable, weaknesses in rapidly evolving pathogens.\n\nCombined pangenomics and transcriptomics reveals core and redundant virulence processes in a rapidly evolving fungal plant pathogen.", "token_count": 491, "char_count": 2136, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6608, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:38.650520", "source": { "split": "train_shard_00001", "doc_id": 125 }, "chunk_id": "train_shard_00001_125_0", "global_id": 5842 }, { "text": "Astaxanthin (AST), a super antioxidant with coloring and medical properties, renders it a beneficial feed additive for shrimp. This study conducted a white shrimp feeding trial of 3S, 3’S isoform AST, which was derived from metabolic-engineered Kluyveromyces marxianus fermented broth (TB) and its extract (TE) compared to sources from two chemically synthetic ASTs (Carophyll Pink [CP] and Lucantin Pink [LP]), which contain 3S, 3’S, 3R, 3’S (3S, 3’R) and 3R, 3’R isoforms ratio of 1:2:1. The effects on red coloration, immune parameters and resistance to Vibrio infection were evaluated. Four AST sources were incorporated into the diets at concentrations of 0 (control), 100 mg kg − 1 (TB100, TE100, CP100, and LP100), and 200 mg kg − 1 (TB200, TE200, CP200, and LP200). Results revealed that in week 4, shrimps that received AST-supplemented feeds, especially TB100, TB200, and TE200, significantly increased redness (a*) values. Immune responses including phagocytosis activity, superoxide-anion production, phenoloxidase activity, and immune-related genes were examined on days 0, 1, 2, 4, 7, 14, 21, and 28. Generally, shrimps that received AST-supplemented feeds exhibited higher immune responses on days 7 and 14 than the control feed", "token_count": 422, "char_count": 1243, "word_count": 188, "semantic_coherence": 1, "information_density": 0.7553, "quality_score": 0.8777, "entities": { "genes": [ "TE100", "TB200", "CP100", "LP100", "TE200", "TB100", "LP200", "CP200" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:39.289986", "source": { "split": "train_shard_00001", "doc_id": 126 }, "chunk_id": "train_shard_00001_126_0", "global_id": 5843 }, { "text": "Gene expression levels of superoxide dismutase and glutathione peroxidase were significantly upregulated on days 7 and 14 in shrimps that received AST-supplemented feeds, while genes of penaeidins, antilipopolysaccharide factor, and lysozyme were upregulated on days 4, 7, and 14, especially received TB200 and TE200. Furthermore, shrimps that received TB100, TE100, CP100, and LP100 7 days were then challenged with Vibrio parahaemolyticus and the result demonstrated higher survival rates especially TB100 at 168 h than the control feed. In conclusion, incorporating AST into the diets enhanced shrimp red coloration, immune parameters, and resistance against V. parahaemolyticus infection. The K. marxianus -derived AST exhibited higher performance than did chemical AST to be a potential feed additive in shrimp aquaculture.\n\nDietary of astaxanthin derived from a metabolic-engineered yeast to improve red-color performance, immune response and resistance to Vibrio parahaemolyticus on white shrimp Penaeus vannamei.", "token_count": 296, "char_count": 1020, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7021, "quality_score": 0.8511, "entities": { "genes": [ "TE100", "TB200", "CP100", "LP100", "TE200", "TB100" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:39.845894", "source": { "split": "train_shard_00001", "doc_id": 126 }, "chunk_id": "train_shard_00001_126_1", "global_id": 5844 }, { "text": "Thousands of complete genome sequences for strains of a species that are now available enable the advancement of pangenome analytics to a new level of sophistication. We collected 2,377 publicly-available complete genomes of Escherichia coli for detailed pangenome analysis. The core genome and accessory genomes consisted of 2,398 and 5,182 genes, respectively. We developed a machine learning approach to define the accessory genes characterizing the major phylogroups of E. coli plus Shigella: A, B1, B2, C, D, E, F, G, and Shigella. The analysis resulted in a detailed structure of the genetic basis of the phylogroups’ differential traits. This pangenome structure was largely consistent with a housekeeping-gene-based MLST distribution, sequence-based Mash distance, and the Clermont quadruplex classification. The rare genome consisted of 163,619 genes, about 79% of which represented variations of 315 underlying transposon elements. This analysis generated a mathematical definition of the genetic basis for a species.\n\nThe Pangenome ofEscherichia coli", "token_count": 274, "char_count": 1068, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:40.393547", "source": { "split": "train_shard_00001", "doc_id": 127 }, "chunk_id": "train_shard_00001_127_0", "global_id": 5845 }, { "text": "In recent decades, the incidence of Candida infections has increased in immunocompromised patients. This multicenter study aimed to evaluate in vitro antifungal activities of 8 antifungal agents against the Candida species isolated from 10 university hospitals in Iran. During the period from Dec 2019 to Dec 2021, Candida species were collected from clinical samples of patients. The isolates were identified by PCR restriction fragment length polymorphism and sequencing methods. The antifungal susceptibility tests of each isolate to eight antifungal agents were performed according to the microdilution CLSI M27, M59, and M60 standard methods. A total of 598 Candida strains were isolated from clinical samples. The most commonly isolated Candida species was C. albicans, followed by C. glabrata, C. parapsilosis, Debaryomyces hansenii (Candida famata), C. tropicalis, Pichia kudriavzevii (Candida krusei), C. orthopsilosis, Meyerozyma guilliermondii (Candida guilliermondii), Kluyveromyces marxianus (Candida kefyr), and Clavispora lusitaniae (Candida lusitaniae). MIC90 values in all Candida species were as follows: 0.25 μg/mL for caspofungin and voriconazole; 0.5 μg/mL for amphotericin B and isavuconazole; 2 μg/mL for itraconazole, luliconazole, and posaconazole; and 16 μg/mL for fluconazole. Although 30/285 C. albicans, 15/31 C. hansenii, 3/12 M", "token_count": 517, "char_count": 1435, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:41.051627", "source": { "split": "train_shard_00001", "doc_id": 128 }, "chunk_id": "train_shard_00001_128_0", "global_id": 5846 }, { "text": "guilliermondii, 67/125 C. glabrata, 5/15 P. kudriavzevii, 6/60 C. parapsilosis, and 5/23 C. tropicalis isolates were multiazole resistant with resistance to 2 to 4 azoles, pan-azole resistance was not observed. According to our data, Candida albicans and C. glabrata were the most frequent species isolated from clinical samples in Iran. Caspofungin and voriconazole, with lower MIC90 values, are the most effective than other antifungal agents for the treatment of Candida infections in this region. IMPORTANCE Candida species cause severe invasive infections of the heart, brain, eyes, bones, and other parts of the body. Knowledge of regional distributions of causative Candida agents and their antifungal susceptibility patterns can help to monitor resistance to antifungal agents of various species and support local and national surveillance programs. In the present study, C. albicans and C. glabrata were the most frequently isolated species from clinical samples in Iran. Increasing rates of non-albicans Candida isolates from the Iranian population should be looked at as alarming due to various levels of intrinsic MIC values or resistance to various antifungal drugs. Caspofungin and voriconazole are recommended over fluconazole for the treatment of Candida infections in the study region. However, amphotericin B and isavuconazole are also active against the most common Candida species isolated from patients. Pan azole-resistant Candida species were not observed in the present study.\n\nEpidemiology and Antifungal Susceptibility of Candida Species Isolated from 10 Tertiary Care Hospitals in Iran.", "token_count": 487, "char_count": 1698, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5598, "quality_score": 0.7799, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:41.701851", "source": { "split": "train_shard_00001", "doc_id": 128 }, "chunk_id": "train_shard_00001_128_1", "global_id": 5847 }, { "text": "Breakthrough advances in long-read sequencing technologies have opened unprecedented opportunities to study genetic variations through comprehensive pangenome analysis. However, the availability of structural variant (SV) calling tools that can effectively leverage pangenome information is limited. In addition, efficient construction of pangenome graphs becomes increasingly challenging with acquisition of larger number of samples. In this study, we present SVPG, an approach that leverages haplotype-resolved pangenome reference for accurate SV detection and rapid pangenome graph augmentation from long-read sequencing data. Compared to state-of-the-art SV callers, SVPG maintained superior overall performance across different coverages and sequencing technologies. SVPG also achieves notable improvements in calling rare and individual-specific SVs on both simulated and real somatic datasets. Furthermore, in a benchmark involving 20 samples, SVPG accelerated pangenome graph augmentation by nearly 10-fold compared to traditional augmentation strategies. We believe that this novel SVPG method, has the potential to revolutionize SV detection and serve as an effective and essential tool, offering new possibilities for advancing pangenomic research.\n\nSVPG: A pangenome-based structural variant detection approach and rapid augmentation of pangenome graphs with new samples", "token_count": 270, "char_count": 1382, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6949, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:42.255222", "source": { "split": "train_shard_00001", "doc_id": 129 }, "chunk_id": "train_shard_00001_129_0", "global_id": 5848 }, { "text": "Streptococcus canis, a multi-host pathogen commonly isolated from dogs and cats, has been occasionally reported in severe cases of human infection. To address the gap in knowledge on its virulence and host tropism, we investigated S. canis genomic epidemiology and report the results of this analysis for the first time. We analysed 59 S. canis whole genome sequences originating from a variety of host species, comprising 39 newly sequenced isolates from UK sources, along with all (n=20) publicly available genomes. Antimicrobial resistance (AMR) phenotype was determined for all 39 available isolates. Genomes were screened for determinants of resistance and virulence. We created a core SNP phylogeny and compared strain clustering to multi-locus sequence typing (MLST) and S. canis M-like protein (SCM) typing. We investigated the dataset for signals of host adaptation using phylogenetic analysis, accessory genome clustering and pan-genome-wide association study analysis. A total of 23 % (9/39) of isolates exhibited phenotypic resistance to lincosamides, macrolides and/or tetracyclines. This was complemented by the identification of AMR-encoding genes in all genomes: tetracycline (tetO 14 %, 8/59; and tetM 7 %, 4/59) and lincosamide/macrolide (ermB, 7 %, 4/59). AMR was more common in human (36 %, 4/11) compared to companion animal (18 %, 5/28) isolates. We identified 19 virulence gene homologues, 14 of which were present in all strains analysed. In an S. canis strain isolated from a dog with otitis externa we identified a homologue of S. pyogenes superantigen SMEZ", "token_count": 516, "char_count": 1660, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6611, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:42.916815", "source": { "split": "train_shard_00001", "doc_id": 130 }, "chunk_id": "train_shard_00001_130_0", "global_id": 5849 }, { "text": "The MLST and SCM typing schemes were found to be incapable of accurately representing core SNP-based genomic diversity of the S. canis population. No evidence of host adaptation was detected, suggesting the potential for inter-species transmission, including zoonotic transfer.\n\nStreptococcus canis genomic epidemiology reveals the potential for zoonotic transfer.", "token_count": 93, "char_count": 378, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7755, "quality_score": 0.8878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:43.293629", "source": { "split": "train_shard_00001", "doc_id": 130 }, "chunk_id": "train_shard_00001_130_1", "global_id": 5850 }, { "text": "Abstract

The genus Hordeum, which includes cultivated barley and its wild relatives, represents a diverse group of grasses with agricultural, ecological, and evolutionary importance. Here, we present a genus-wide pangenome based on 25 chromosome-scale genome sequences encompassing all known diploid Hordeum species and selected tetraploids. Comparative analysis reveals extensive structural variations, including large-scale inversions and chromosomal rearrangements, which disrupt proximal chromosomal collinearity and reflect lineage-specific genome remodeling. Using single-copy gene phylogenies, we identify multiple deep interspecific hybridization events, segmental exchanges, and introgressions, particularly in regions enriched for conserved inversions. We also uncover widespread horizontal gene transfer from Panicoideae grasses into Hordeum, with functional integration of transferred genes. Transposable element dynamics, especially retrotransposon proliferation, account for much of the observed genome size variation and offer insights into polyploid genome evolution. Whole-genome alignments reveal contrasting evolutionary patterns: while coding genes remain highly conserved, regulatory elements show rapid turnover, providing a substrate for phenotypic diversification. Case studies of vernalization and glume development demonstrate how natural variation in regulatory and coding sequences contributes to flowering time and floral morphology. This comprehensive pangenomic framework establishes Hordeum as a model for studying genome evolution, structural variation, and the genetic basis of adaptive traits, offering new avenues for barley improvement.

\n\nA genus-wide pangenome of Hordeum", "token_count": 374, "char_count": 1731, "word_count": 208, "semantic_coherence": 1, "information_density": 0.7644, "quality_score": 0.8822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:43.880892", "source": { "split": "train_shard_00001", "doc_id": 131 }, "chunk_id": "train_shard_00001_131_0", "global_id": 5851 }, { "text": "Horizontal gene transfer (HGT) plays a critical role in the evolution and diversification of many microbial species. The resulting dynamics of gene gain and loss can have important implications for the development of antibiotic resistance and the design of vaccine and drug interventions. Methods for the analysis of gene presence/absence patterns typically do not account for errors introduced in the automated annotation and clustering of gene sequences. In particular, methods adapted from ecological studies, including the pangenome gene accumulation curve, can be misleading as they may reflect the underlying diversity in the temporal sampling of genomes rather than a difference in the dynamics of HGT. Here, we introduce Panstripe, a method based on Generalised Linear Regression that is robust to population structure, sampling bias and errors in the predicted presence/absence of genes. We demonstrate using simulations that Panstripe can effectively identify differences in the rate and number of genes involved in HGT events, and illustrate its capability by analysing several diverse bacterial genome datasets representing major human pathogens. Panstripe is freely available as an R package at https://github.com/gtonkinhill/panstripe .\n\nRobust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe", "token_count": 270, "char_count": 1332, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6702, "quality_score": 0.8351, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:44.436065", "source": { "split": "train_shard_00001", "doc_id": 132 }, "chunk_id": "train_shard_00001_132_0", "global_id": 5852 }, { "text": "Infectious bursal disease (IBD), caused by the infectious bursal disease virus (IBDV), is a highly contagious and immunosuppressive disease in chickens worldwide. The novel variant IBDV (nvIBDV) has been emerging in Chinese chicken farms since 2017, but there are no available vaccines that can provide effective protection. Herein, the capsid protein VP2 from nvIBDV strain FJ-18 was expressed in Kluyveromyces marxianus with the aim to produce nvIBDV subviral particles (SVPs). Two recombinant strains constructed for expression of nvIBDV VP2 (nvVP2) and His-tagged VP2 (nvHVP2) formed two types of nvIBDV subviral particles (SVPs), namely nvVP2-SVPs and nvHVP2-SVPs. TEM scans showed that both SVPs were about 25 nm in diameter, but there was a large portion of nvVP2-SVPs showing non-spherical particles. Molecular dynamics simulations indicate that an N-terminal His tag strengthened the interaction of the nvHVP2 monomer and contributed to the assembly of SVPs. Vaccination of chicks with the nvHVP2-SVPs provided 100% protection against novel variant IBDV infection when challenged with the FJ-18 strain, as well as the classical strain BC6/85. By contrast, vaccination with the nvVP2-SVPs only provided 60% protection against their parent FJ-18 strain, suggesting that the stable conformation of subviral particles posed a great impact on their protective efficacy. Our results showed that the nvHVP2-SVPs produced by the recombinant K. marxianus strain is an ideal vaccine candidate for IBDV eradication.\n\nA Single Vaccination of IBDV Subviral Particles Generated by Kluyveromyces marxianus Efficiently Protects Chickens against Novel Variant and Classical IBDV Strains.", "token_count": 493, "char_count": 1700, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6116, "quality_score": 0.8058, "entities": { "genes": [ "BC6", "VP2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:45.088737", "source": { "split": "train_shard_00001", "doc_id": 133 }, "chunk_id": "train_shard_00001_133_0", "global_id": 5853 }, { "text": "Cider flavor has a very important impact on the quality. Solid-phase microextraction-gas chromatography-mass spectrometry (SPME-GC-MS) combined with gas chromatography-ion mobility spectrometry (GC-IMS) tested different kinds of non-Saccharomyces yeasts and Saccharomyces cerevisiae (S. cerevisiae) co-inoculated for the fermentation of cider to determine differences in aroma material, and the determination of odor activity value (OAV) is applied less frequently in research. Through Rhodotorula mucilaginosa, Debaryomyces hansenii, Zygosaccharomyces bailii, and Kluyveromyces Marxianus, four different strains of non-Saccharomyces yeast fermented cider, and it was found that, in both the chemical composition and flavor of material things, compared with monoculture-fermented cider using S. cerevisiae, all differences were significant. Co-inoculated fermentation significantly improved the flavor and taste of cider. As in the volatile compounds of OVA > 1, octanoic acid (Sc 633.88 μg/L, co-inoculation fermented group 955.49 μg/L) provides vegetable cheese fragrance and decanoic acid, ethyl ester (Sc 683.19 μg/L, co-inoculation fermented group 694.98 μg/L) a creamy fruity fragrance, etc., and the average content increased after co-inoculated fermentation. Phenylethyl alcohol, which can produce a rose scent, was relatively abundant in cider samples and varied greatly among the groups. Moreover, the contents of ethyl lactate and 1-butanol in the Sc+Rm (ciders fermented by S. cerevisiae and R", "token_count": 506, "char_count": 1578, "word_count": 200, "semantic_coherence": 1, "information_density": 0.71, "quality_score": 0.855, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:45.747754", "source": { "split": "train_shard_00001", "doc_id": 134 }, "chunk_id": "train_shard_00001_134_0", "global_id": 5854 }, { "text": "mucilaginosa) were the highest of all of the cider samples. Different types of non-Saccharomyces yeast produced cider with different flavor characteristics. This study demonstrates that different species of non-Saccharomyces yeast do have an important impact on the characteristics of cider and that co-inoculation with non-Saccharomyces yeast and S. cerevisiae for cider fermentation may be a strategy to improve the flavor of cider.\n\nChemical Composition and Flavor Characteristics of Cider Fermented with Saccharomyces cerevisiae and Non-Saccharomyces cerevisiae.", "token_count": 186, "char_count": 612, "word_count": 76, "semantic_coherence": 1, "information_density": 0.6184, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:46.183563", "source": { "split": "train_shard_00001", "doc_id": 134 }, "chunk_id": "train_shard_00001_134_1", "global_id": 5855 }, { "text": "Clustered regularly interspaced short palindromic repeats (CRISPR)-Cas genome-wide screens are powerful tools for unraveling genotype-phenotype relationships, enabling precise manipulation of genes to study and engineer industrially useful traits. Traditional genetic methods, such as random mutagenesis or RNA interference, often lack the specificity and scalability required for large-scale functional genomic screens. CRISPR systems overcome these limitations by offering precision gene targeting and manipulation, allowing for high-throughput investigations into gene function and interactions. Recent work has shown that CRISPR genome editing is widely adaptable to several yeast species, many of which have natural traits suited for industrial biotechnology. In this review, we discuss recent advances in yeast functional genomics, emphasizing advancements made with CRISPR tools. We discuss how the development and optimization of CRISPR genome-wide screens have enabled a host-first approach to metabolic engineering, which takes advantage of the natural traits of nonconventional yeast-fast growth rates, high stress tolerance, and novel metabolism-to create new production hosts. Lastly, we discuss future directions, including automation and biosensor-driven screens, to enhance high-throughput CRISPR-enabled yeast engineering.\n\nAdvances in CRISPR-enabled genome-wide screens in yeast.", "token_count": 301, "char_count": 1397, "word_count": 177, "semantic_coherence": 1, "information_density": 0.7514, "quality_score": 0.8757, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:46.747553", "source": { "split": "train_shard_00001", "doc_id": 135 }, "chunk_id": "train_shard_00001_135_0", "global_id": 5856 }, { "text": "The bacterial genus Xanthomonas is responsible for disease outbreaks in several hundred plant species, many of them economically important crops. In the era of next-generation sequencing, thousands of strains from this genus have now been sequenced as part of isolated studies that focus on outbreak characterization, host range, diversity, and virulence factor identification. However, these data have not been synthesized and we lack a comprehensive phylogeny for the genus, with some species designations in public databases still relying on phenotypic similarities and representative sequence typing. The extent of genetic cohesiveness among Xanthomonas strains, the distribution of virulence factors across strains, and the impact of evolutionary history on host range across the genus are also poorly understood. In this study, we present a pangenome analysis of 1,910 diverse Xanthomonas genomes, highlighting their evolutionary relationships, the distribution of virulence-associated genes across strains, and rates of horizontal gene transfer. We find a number of broadly conserved classes of virulence factors and considerable diversity in the Type 3 Secretion Systems (T3SSs) and Type 3 Secreted Effector (T3SE) repertoires of different Xanthomonas species. We also use these data to re-assign incorrectly classified strains to phylogenetically informed species designations and find evidence of both monophyletic host specificity and convergent evolution of phylogenetically distant strains to the same host. Finally, we explore the role of recombination in maintaining genetic cohesion within the Xanthomonas genus as a result of both ancestral and recent recombination events. Understanding the evolutionary history of Xanthomonas species and the relationship of key virulence factors with host-specificity provides valuable insight into the mechanisms through which Xanthomonas species shift between hosts and will enable us to develop more robust resistance strategies against these highly virulent pathogens.\n\nPangenome insights into the diversification and disease specificity of worldwide Xanthomonas outbreaks.", "token_count": 503, "char_count": 2186, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:47.395443", "source": { "split": "train_shard_00001", "doc_id": 136 }, "chunk_id": "train_shard_00001_136_0", "global_id": 5857 }, { "text": "Abstract

Evolutionary adaptation provides stability to the strains in the challenging environment. As extension of earlier study, the evolved strains Kluyveromyces marxianus NIRE-K1.1 and K. marxianus NIRE-K3.1 were subjected for secondary adaptation on minimal salt (MS) medium with the aim to enhance xylose utilization for ethanol production together with salt tolerance. Both the strains were adapted till saturated improvement in xylose uptake i.e., 54 generations on MS medium containing xylose. Xylose utilization increased from 14.21 to 45.80% and 10.55 to 45.31%, in evolved strains KmNIRE-K1.2 and KmNIRE-K3.2, respectively. Specific xylose reductase activity has also increased 2.04 and 3.36-folds in KmNIRE-K1.2 and KmNIRE-K3.2, respectively. Xylitol dehydrogenase activity was also increased by 2.82 and 1.35-folds in KmNIRE-K1.2 and KmNIRE-K3.2, respectively. Decrease in redox imbalance was observed in evolved strains, and hence there was a reduction in xylitol production during growth and fermentation. Xylose uptake rate increased by 2.53 and 1.5-folds in KmNIRE-K1.2 and KmNIRE-K3.2, respectively with 2.20 and 6.46-folds higher ethanol concentration, and 2.25 and 5.86-folds higher volumetric productivity, respectively. This study has demonstrated the role of evolutionary adaptation for developing robust yeast strains. KmNIRE-K1.2 and KmNIRE-K3.2 have shown enhanced ethanol production, enzyme activities and less by-product formation like xylitol during xylose metabolism.

", "token_count": 501, "char_count": 1554, "word_count": 201, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:48.053796", "source": { "split": "train_shard_00001", "doc_id": 137 }, "chunk_id": "train_shard_00001_137_0", "global_id": 5858 }, { "text": "Effect of Evolutionary Adaptation on Metabolic Enzyme Activities of Thermotolerant Strain Kluyveromyces Marxianus NIRE-K1 and NIRE-K3 for Bioethanol Production", "token_count": 52, "char_count": 159, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:48.416392", "source": { "split": "train_shard_00001", "doc_id": 137 }, "chunk_id": "train_shard_00001_137_1", "global_id": 5859 }, { "text": "

ABSTRACT

Viral species classification is crucial for understanding viral evolution, epidemiology, and developing effective diagnostics and treatments. Traditional methods often rely on sequence similarity, which can be challenging for rapidly evolving viruses. Pangenomes, offering a comprehensive representation of species’ genomic diversity, provide a richer perspective, but their analysis often requires advanced computational methods. We investigate the use of Hyperdimensional Computing (HDC), also known as Vector-Symbolic Architecture (VSA), an emerging computing paradigm that relies on vectors in high-dimensional spaces to encode a multi-species viral pangenome. We develop a new method for encoding graph-structured viral pangenomes using high-dimensional vectors. Pangenomes are represented as weighted de Bruijn graphs constructed using sequences of consecutive k-mers from the genomes, while information about the genome species (their class) is encoded as specific weights on the edges of the graph. The weighted de Bruijn graph representation is encoded into a single high-dimensional vector. We tested three classification strategies: a flat model at the species level, a flat model at the genus level, and a two-step hierarchical model. We applied our method to a pangenome comprising 542 viral species from NCBI GenBank. Our results reveal a complex relationship between model architecture and classification accuracy. The flat species-level model achieved the highest accuracy, correctly classifying 87.08% of test genomes. Counter-intuitively, simplifying the problem to the genus level or using a hierarchical approach degraded performance, with accuracies dropping to 60.51% and 33.57% respectively. These outcomes highlight critical challenges in alignment-free classification, such as signal dilution in overly broad taxonomic groups and error propagation in multi-step models. The model’s reconstruction rate proved to be a reliable measure of confidence, rather than a direct predictor of correctness. This novel approach offers a promising new direction for viral classification, not only for its predictive power but its ability to reveal underlying challenges in genomic taxonomy.\n\nA novel Vector-Symbolic Architecture for graph encoding and its application to viral pangenome-based species classification", "token_count": 494, "char_count": 2346, "word_count": 317, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:49.099380", "source": { "split": "train_shard_00001", "doc_id": 138 }, "chunk_id": "train_shard_00001_138_0", "global_id": 5860 }, { "text": "Clostridium tyrobutyricum has been recognized as the main cause of late blowing defects (LBD) in cheese leading to considerable economic losses for the dairy industry. Although differences in spoilage ability among strains of this species have been acknowledged, potential links to the genetic diversity and functional traits remain unknown. In the present study, we aimed to investigate and characterize genomic variation, pan-genomic diversity and key traits of C. tyrobutyricum by comparing the genomes of 28 strains. A comparative genomics analysis revealed an \"open\" pangenome comprising 9,748 genes and a core genome of 1,179 genes shared by all test strains. Among those core genes, the majority of genes encode proteins related to translation, ribosomal structure and biogenesis, energy production and conversion, and amino acid metabolism. A large part of the accessory genome is composed of sets of unique, strain-specific genes ranging from about 5 to more than 980 genes. Furthermore, functional analysis revealed several strain-specific genes related to replication, recombination and repair, cell wall, membrane and envelope biogenesis, and defense mechanisms that might facilitate survival under stressful environmental conditions. Phylogenomic analysis divided strains into two clades: clade I contained human, mud, and silage isolates, whereas clade II comprised cheese and milk isolates. Notably, these two groups of isolates showed differences in certain hypothetical proteins, transcriptional regulators and ABC transporters involved in resistance to oxidative stress. To the best of our knowledge, this is the first study to provide comparative genomics of C. tyrobutyricum strains related to LBD. Importantly, the findings presented in this study highlight the broad genetic diversity of C. tyrobutyricum, which might help us understand the diversity in spoilage potential of C. tyrobutyricum in cheese and provide some clues for further exploring the gene modules responsible for the spoilage ability of this species.", "token_count": 485, "char_count": 2075, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:49.774165", "source": { "split": "train_shard_00001", "doc_id": 139 }, "chunk_id": "train_shard_00001_139_0", "global_id": 5861 }, { "text": "Comparative Genomics Provides Insights Into Genetic Diversity of Clostridium tyrobutyricum and Potential Implications for Late Blowing Defects in Cheese.", "token_count": 48, "char_count": 160, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:50.152385", "source": { "split": "train_shard_00001", "doc_id": 139 }, "chunk_id": "train_shard_00001_139_1", "global_id": 5862 }, { "text": "Fungal agents emerged as post-pasteurization contamination are responsible for the spoilage in yogurt drink. In this work, the antifungal effects of some lactic acid bacteria (LAB) on the spoilage yeasts isolated from yogurt drink (Doogh) were evaluated. First, the microbial growth in the yogurt drink samples during the storage time was investigated, and the isolated microorganisms were identified using biochemical methods and sequencing of the specific amplicons. Yeasts (3-7 log CFU ml-1 ) were found to be the most abundant microorganisms (specific spoilage organisms) in several samples. Using the amplification technique of rDNA by ITS1 and ITS4 primers, the dominant yeasts were identified as Pichia kudriavzevii, Kluyveromyces marxianus, and Candida parapsilosis. Then, the antimicrobial activity of 37 strains of LAB against the isolated yeasts was studied using broth microdilution. Eventually, the strains of Lacticplantibacillus plantarum (245, 24, P6, and P7), Lactiplantibacillus pentosus (20), and Levilactobacillus brevis (30) exhibited significant antifungal activity. In the most effective impacts, lag times of C. parapsilosis, K. marxianus, and P. kudriavzevii were increased by almost 12-19 h, 12-19 h, and 2-6 h, respectively, while the area under the growth curve for these yeasts was reduced to lower than 40%, near 16%, and approximately 67%, in the order given. Overall, these bacteria showed high potential as the substituents for chemical preservatives in yogurt drinks. PRACTICAL APPLICATION: Spoilage yeasts were isolated from yogurt drink and identified by molecular method. Isolated yeasts belonged to Pichia, Kluyveromyces, and Candida genera. Inhibitory effects of 37 strains were evaluated against the spoilage yeasts. Cell-free supernatant was used against the isolated fungi in microdilution method", "token_count": 525, "char_count": 1849, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6046, "quality_score": 0.8023, "entities": { "genes": [ "ITS4", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:50.825143", "source": { "split": "train_shard_00001", "doc_id": 140 }, "chunk_id": "train_shard_00001_140_0", "global_id": 5863 }, { "text": "Several LAB strains showed a significant antimicrobial activity.\n\nAntifungal activity of protective cultures against the yogurt drink-specific spoilage yeasts.", "token_count": 39, "char_count": 159, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:51.205404", "source": { "split": "train_shard_00001", "doc_id": 140 }, "chunk_id": "train_shard_00001_140_1", "global_id": 5864 }, { "text": "

Background

Enterococcus faecalis is the most commonly isolated enterococcal species in clinical infection. This bacterium is notorious for its ability to share genetic content within and outside of its species. With this increased proficiency for horizontal gene transfer, tremendous genomic diversity within this species has been identified. Many researchers have hypothesized E. faecalis exhibits niche adaptation to establish infections or colonize various parts of the human body. Here, we hypothesize that E. faecalis strains isolated from the human bladder will carry unique genomic content compared to clinical strains isolated from other sources.

Results

This analysis includes comparison of 111 E. faecalis genomes isolated from bladder, urogenital, blood, and fecal samples. Phylogenomic comparison shows no association between isolation source and lineage; however, accessory genome comparison differentiates blood and bladder genomes. Further gene enrichment analysis identifies gene functions, virulence factors, antibiotic resistance genes, and plasmid-associated genes that are enriched or rare in bladder genomes compared to urogenital, blood, and fecal genomes. Using these findings as training data and 682 publicly available genomes as test data, machine learning classifiers successfully distinguished between bladder and non-bladder strains with high accuracy. Genes identified as important for this differentiation were often related to transposable elements and phage, including 3 prophage species found almost exclusively in bladder and urogenital genomes.

Conclusions

E. faecalis strains isolated from the bladder contain unique genomic content when compared to strains isolated from other body sites. This genomic diversity is most likely due to horizontal gene transfer, as evidenced by lack of phylogenomic clustering and enrichment of transposable elements and prophages. Investigation into how these enriched genes influence host-microbe interactions may elucidate gene functions required for successful bladder colonization and disease establishment.\n\nComparative genomic analysis of clinical Enterococcus faecalis distinguishes strains isolated from the bladder.", "token_count": 495, "char_count": 2216, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5938, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:51.854052", "source": { "split": "train_shard_00001", "doc_id": 141 }, "chunk_id": "train_shard_00001_141_0", "global_id": 5865 }, { "text": "Aligning to a linear reference genome can result in a higher percentage of reads going unmapped or being incorrectly mapped owing to variations not captured by the reference, otherwise known as reference bias. Recently, in efforts to mitigate reference bias, there has been a movement to switch to using pangenomes, a collection of genomes, as the reference. In this paper, we introduce Moni-align, the first short-read pangenome aligner built on the r-index, a variation of the classical FM-index that can index collections of genomes in O(r)-space, where r is the number of runs in the Burrows-Wheeler transform. Moni-align uses a seed-and-extend strategy for aligning reads, utilizing maximal exact matches as seeds, which can be efficiently obtained with the r-index. Using both simulated and real short-read data sets, we demonstrate that Moni-align achieves alignment accuracy comparable to vg map and vg giraffe, the leading pangenome aligners. Although currently best suited for aligning to localized pangenomes owing to computational constraints, Moni-align offers a robust foundation for future optimizations that could further broaden its applicability.\n\nAccurate short-read alignment through <i>r</i>-index-based pangenome indexing.", "token_count": 317, "char_count": 1284, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7039, "quality_score": 0.852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:52.414415", "source": { "split": "train_shard_00001", "doc_id": 142 }, "chunk_id": "train_shard_00001_142_0", "global_id": 5866 }, { "text": "Yeasts are gaining increasing attention for their potential health benefits as probiotics in recent years. Researchers are actively searching for new yeast strains with probiotic properties (i.e, Debaryomyces hansenii; Kluyveromyces marxianus; Yarrowia lipolytica; Pichia hudriavzevii; Torulaspora delbrueckii) from various sources, including traditional fermented foods, the human gut, and the environment. This exploration is expanding the pool of potential probiotic yeasts beyond the well-studied Saccharomyces boulardii. Research suggests that specific yeast strains possess properties that could be beneficial for managing conditions like inflammatory bowel disease, irritable bowel syndrome, skin disorders and allergy. Additionally, probiotic yeasts may compete with pathogenic bacteria for adhesion sites and nutrients, thereby inhibiting their growth and colonization. They might also produce antimicrobial compounds that di-rectly eliminate harmful bacteria. To achieve these goals, the approach that uses probiotics for human health is changing. Next-generation yeast probiotics are emerging as a powerful new approach in the field of live biotherapeutics. By using genetic engineering, scientists are able to give these tools specialized capabilities. However, most research on these probiotic yeasts is still in its early stages, and more clinical trials are needed to confirm their efficacy and safety for various health condi-tions. This review could provide a brief overview of the situation in this field.\n\nProbiotic yeasts: a developing reality?", "token_count": 351, "char_count": 1564, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:52.996896", "source": { "split": "train_shard_00001", "doc_id": 143 }, "chunk_id": "train_shard_00001_143_0", "global_id": 5867 }, { "text": "Infections caused by multidrug-resistant organisms (MDROs) are difficult to treat and often life threatening and place a burden on the healthcare system. Minimizing the transmission of MDROs in hospitals is a global priority with genomics proving to be a powerful tool for identifying the transmission of MDROs. To optimize the utility of genomics for prospective infection control surveillance, results must be available in real time, reproducible and simple to communicate to clinicians. Traditional reference-based approaches suffer from several limitations for prospective genomic surveillance. Whilst reference-free or pairwise genome comparisons avoid some of these limitations, they can be computationally intensive and time consuming. Split k-mer analysis (SKA) offers a viable alternative facilitating rapid reference-free pairwise comparisons of genomic data, but the optimum SKA parameters for the detection of transmission have not been determined. Additionally, the accuracy of SKA-based inferences has not been measured, nor whether modified quality control parameters are required. Here, we explore the performance of 60 SKA parameter combinations across 50 simulations to quantify the false negative and positive SNP proportions for Escherichia coli, Enterococcus faecium, Klebsiella pneumoniae and Staphylococcus aureus. Using the optimum parameter combination, we explore concordance between SKA, multilocus sequence typing (MLST), core genome MLST (cgMLST) and Snippy in a real-world dataset. Lastly, we investigate whether simulated plasmid gain or loss could impact SNP detection with SKA. This work identifies that the use of SKA with sequencing reads, a k-mer length of 19 and a minor allele frequency filter of 0.01 is optimal for MDRO transmission detection. Whilst SNP detection with SKA (when used with sequencing reads) undercalls SNPs compared to Snippy, it is significantly faster, especially with larger datasets. SKA has excellent concordance with MLST and cgMLST and is not impacted by simulated plasmid movement", "token_count": 499, "char_count": 2087, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6586, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:53.652304", "source": { "split": "train_shard_00001", "doc_id": 144 }, "chunk_id": "train_shard_00001_144_0", "global_id": 5868 }, { "text": "We propose that the use of SKA for the detection of bacterial pathogen transmission is superior to traditional methodologies, capable of providing results in a much shorter timeframe.\n\nRapid, reference-free identification of bacterial pathogen transmission using optimized split <i>k</i>-mer analysis.", "token_count": 74, "char_count": 313, "word_count": 40, "semantic_coherence": 1, "information_density": 0.825, "quality_score": 0.9125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:54.018478", "source": { "split": "train_shard_00001", "doc_id": 144 }, "chunk_id": "train_shard_00001_144_1", "global_id": 5869 }, { "text": "A major outbreak of the globally significant Salmonella Enteritidis foodborne pathogen was identified within a large clinical data set by a program of routine WGS of clinical presentations of salmonellosis in New South Wales, Australia. Pangenome analysis helped to quantify and isolate prophage content within the accessory partition of the pangenome. A prophage similar to Gifsy-1 (henceforth GF-1L) was found to occur in all isolates of the outbreak core SNP cluster, and in three other isolates. Further analysis revealed that the GF-1L prophage carried the gogB virulence factor. These observations suggest that GF-1L may be an important marker of virulence for S. Enteritidis population screening and, that anti-inflammatory, gogB-mediated virulence currently associated with Salmonella Typhimurium may also be displayed by S. Enteritidis. IMPORTANCE We examined 5 years of genomic and epidemiological data for the significant global foodborne pathogen, Salmonella enterica. Although Salmonella enterica subspecies enterica serovar Enteritidis (S. Enteritidis) is the leading cause of salmonellosis in the USA and Europe, prior to 2018 it was not endemic in the southern states of Australia. However, in 2018 a large outbreak led to the endemicity of S. Enteritidis in New South Wales, Australia, and a unique opportunity to study this phenomenon. Using pangenome analysis we uncovered that this clone contained a Gifsy-1-like prophage harboring the known virulence factor gogB. The prophage reported has not previously been described in S. Enteritidis isolates.\n\nPangenome Analysis of a Salmonella Enteritidis Population Links a Major Outbreak to a Gifsy-1-Like Prophage Containing Anti-Inflammatory Gene gogB.", "token_count": 479, "char_count": 1759, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:54.668349", "source": { "split": "train_shard_00001", "doc_id": 145 }, "chunk_id": "train_shard_00001_145_0", "global_id": 5870 }, { "text": "Capsicum is one of the most economically significant vegetable crops worldwide, owing to its high content of bioactive compounds with nutritional, pharmacological, and industrial relevance. However, research has focused on C. annuum, often disregarding local diversity and secondary gene pools, which may contain hidden variation for quality traits. Therefore, this study evaluated the genetic and phenotypic diversity of 283 accessions from the Colombian germplasm collection in the agrobiodiversity hotspot of northwest South America, representing all five domesticated species of the genus. A total of 18 morphological, physicochemical, and biochemical fruit traits were assessed, including texture, color, capsaicinoid, and carotenoid content. The phenotypic data were integrated with genomic information obtained through genotyping-by-sequencing (GBS) using the C. annuum reference genome and a multispecies pangenome. Fixed-and-Random-Model-Circulating-Probability-Unification (FarmCPU) and Bayesian-information-and-Linkage-disequilibrium-Iteratively-Nested-Keyway (BLINK) genome-wide association studies (GWAS) were performed on both alignments, respectively, leading to the identification of complex polygenic architectures with 144 and 150 single nucleotide polymorphisms (SNPs) significantly associated with key fruit quality traits. Candidate genes involved in capsaicinoid biosynthesis were identified within associated genomic regions, terpenoid and sterol pathways, and cell wall modifiers. These findings highlight the potential of integrating pangenomic resources with multi-omics approaches to accelerate Capsicum improvement programs and facilitate the development of cultivars with enhanced quality traits and increased agro-industrial value.\n\nPangenomic and Phenotypic Characterization of Colombian <i>Capsicum</i> Germplasm Reveals the Genetic Basis of Fruit Quality Traits.", "token_count": 490, "char_count": 1935, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7181, "quality_score": 0.859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:55.324520", "source": { "split": "train_shard_00001", "doc_id": 146 }, "chunk_id": "train_shard_00001_146_0", "global_id": 5871 }, { "text": "

ABSTRACT

Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineer the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits– thermotolerance, lipid production, and facile transformation with exogenous DNA-into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae , with naturally more robust traits that hold potential for the industrial production of renewable chemicals.\n\nKluyveromyces marxianus as a robust synthetic biology platform host", "token_count": 374, "char_count": 1600, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6217, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:55.902125", "source": { "split": "train_shard_00001", "doc_id": 147 }, "chunk_id": "train_shard_00001_147_0", "global_id": 5872 }, { "text": "Lactobacillus mulieris is a recently described species, reportedly isolated from human urine, vagina, and gut. Previous genomic studies of L. mulieris highlighted significant genetic diversity among its strains. To gain a deeper understanding of this genomic diversity, we conducted a comprehensive genomic comparison of 70 L. mulieris strains from diverse sources. Phylogenomic and genome relatedness analysis identified three distinct clades, each representing a potential subspecies cluster. Pangenome analysis revealed distinct gene clusters shaping the functional characteristics and unique ecological adaptations of each clade. Clade 1 demonstrated a generalist lifestyle, with strains isolated from diverse sources and enriched in serine/threonine protein kinases, suggesting adaptive versatility. Clade 2, predominantly composed of urinary isolates, displayed enrichment in genes facilitating nutrient acquisition and osmotic regulation, enabling survival in the nutrient-limited and high osmolarity conditions of the urinary tract. Clade 3, exclusively composed of vaginal isolates, exhibited significant enrichment in genes supporting glycogen metabolism, carbohydrate transport, and capsular polysaccharide biosynthesis-features indicative of adaptation to the vaginal environment. Collectively, our findings provide essential genomic insights into the ecological specialization of L. mulieris, shedding light on their genetic variability and adaptive traits within their respective ecological niches.IMPORTANCERecognizing the genomic diversity within Lactobacillus mulieris is essential for understanding its ecological specialization and adaptation strategies across distinct human-associated environments. By identifying three distinct clades with unique functional traits, our study highlights the critical role of niche-specific genetic adaptations in microbial survival. The presence of specialized gene functions within each clade underscores how evolutionary pressures shape bacterial resilience in different environments. Despite their coexistence in overlapping environments, these clades exhibit distinct genomic profiles that may influence their colonization potential and interactions with the host and within the host-associated microbiota", "token_count": 504, "char_count": 2306, "word_count": 279, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:56.556749", "source": { "split": "train_shard_00001", "doc_id": 148 }, "chunk_id": "train_shard_00001_148_0", "global_id": 5873 }, { "text": "Our findings emphasize the need for a classification framework that accounts for these genetic and functional differences and the necessity for further investigation to understand their distinct roles and impact on human health.\n\nPangenome analysis of <i>Lactobacillus mulieris</i> strains reveals distinct subspecies clusters with defined ecological adaptations.", "token_count": 80, "char_count": 375, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8723, "quality_score": 0.9362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:56.919629", "source": { "split": "train_shard_00001", "doc_id": 148 }, "chunk_id": "train_shard_00001_148_1", "global_id": 5874 }, { "text": "We report for the first time whole-genome sequencing of four multidrug-resistant sequence type (ST) 307 Klebsiella pneumoniae recovered from patients in two hospitals in Armenia. Comparative genomic analysis revealed that the isolates were closely related, with a maximum of 39 single nucleotide polymorphism (SNP) differences in the core genome. All Armenian isolates carried the integrative and conjugative element ICEKp4, which bears the yersiniabactin locus, and shared a common evolutionary origin, diverging around 2005 (95% CI: 1999 to 2011). Antibiotic susceptibility testing showed resistance to several antibiotics, including ampicillin, amoxicillin-clavulanic acid, cefepime, ceftazidime, norfloxacin, levofloxacin, and chloramphenicol. Specifically, isolates designated as ARM03 and ARM06 were resistant to piperacillin-tazobactam, ARM04 and ARM05 had intermediate resistance to both piperacillin-tazobactam and imipenem, and ARM03 showed intermediate resistance to amikacin. We further identified antimicrobial resistance (AMR) genes in four Armenian isolates, including blaOXA-1, blaTEM-1D, blaSHV-28, dfrA14, tet(A), sul2, qnrB1, aac(6´)-Ib-cr, strA, strB and the extended-spectrum β-lactamase gene blaCTX-M-15", "token_count": 487, "char_count": 1360, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [ "ARM05", "ARM04", "ARM03", "ARM06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:57.566535", "source": { "split": "train_shard_00001", "doc_id": 149 }, "chunk_id": "train_shard_00001_149_0", "global_id": 5875 }, { "text": "Additionally, ARM03 and ARM06 also obtained dfrA5, sul1, sul3, cmlA1, mphA, aph3-Ia and the unique colistin resistance gene mcr-8.1, which was absent in all other publicly available ST307 isolates. These two isolates also acquired aerobactin siderophore-encoding gene clusters (iucABCD-iutA) and the hypermucoidy locus rmpADC (ARM06 had rmpA fragment). ARM04 and ARM05, as well as ARM03 and ARM06, had nearly identical AMR and virulence genes, along with similar plasmid replicon profiles, respectively. Our findings suggest that a transmission event occurred between the two hospitals in Armenia, likely facilitated by patients or community members, during which K. pneumoniae ST307 isolates acquired plasmids carrying AMR and virulence genes.IMPORTANCEMultidrug-resistant (MDR) Klebsiella pneumoniae sequence type (ST) 307 has emerged as a high-risk clone associated with hospital- and community-acquired infections, posing a major threat to global public health. We report in-depth comparative genomics analyses of K. pneumoniae ST307 isolates recovered from patients in Armenia. The unique colistin resistance gene mcr-8.1 identified in ARM03 and ARM06 was absent in all other ST307 isolates obtained from the publicly available data sets. ARM03 and ARM06 also acquired aerobactin siderophore-encoding gene clusters (iucABCD-iutA) and the hypermucoidy locus rmpADC (ARM06 possessed incomplete rmpA fragment). Our findings suggest that a transmission event has occurred between two hospitals in Armenia either through patients or community members", "token_count": 517, "char_count": 1669, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": { "genes": [ "ARM06", "ST307", "ARM03", "ARM05", "ARM04" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:52:58.224719", "source": { "split": "train_shard_00001", "doc_id": 149 }, "chunk_id": "train_shard_00001_149_1", "global_id": 5876 }, { "text": "In addition, the Armenian isolates obtained plasmids carrying virulence and AMR genes during the transmission event. Our study emphasises the importance of genomic surveillance of this emerging MDR-hypervirulent pathogen to provide early interventions.\n\nEmergence of <i>mcr-8.1</i>-bearing MDR-hypervirulent <i>Klebsiella pneumoniae</i> ST307.", "token_count": 115, "char_count": 367, "word_count": 40, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [ "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:58.602653", "source": { "split": "train_shard_00001", "doc_id": 149 }, "chunk_id": "train_shard_00001_149_2", "global_id": 5877 }, { "text": "Sorghum is a cereal crop grown for food, feed, and biofuel, yet the genomic diversity of elite commercial lines remains underexplored. Here, we assembled a sorghum pangenome from long-read sequences of 46 U.S. ex-Plant Variety Protection Act (ex-PVP) cultivars and a haplotype-resolved assembly of one wild accession. The pangenome revealed largely conserved genomic architecture across elite lines but identified presence–absence variations (PAVs) in 28% of gene families, including genes involved in stress responses and starch metabolism, such as STARCH BRANCHING ENZYME I (SBE1) . Selective sweep analyses detected strong signals at key flowering-time loci ( Ma1/SbPRR37, Ma2, Ma6 ) and circadian/light regulators ( PHOT1, DET1, XAP5 ), with PHYA showing copy number variations (CNVs). Analysis of 24 wild accessions, beyond the core pangenome panel, detected CNVs in MULTIDRUG AND TOXIC COMPOUND EXTRUSION (MATE) transporters, potentially reflecting selection or breeding for enhanced herbicide detoxification. These results highlight breeding-shaped regions and position the pangenome as a resource for sorghum improvement.\n\nPangenome of U.S. ex-PVP and Wild Sorghum Reveals Structural Variants and Selective Sweeps Shaping Adaptation and Trait Improvement", "token_count": 351, "char_count": 1262, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7614, "quality_score": 0.8807, "entities": { "genes": [ "PHOT1", "SBE1", "DET1", "XAP5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:52:59.179829", "source": { "split": "train_shard_00001", "doc_id": 150 }, "chunk_id": "train_shard_00001_150_0", "global_id": 5878 }, { "text": "Space-efficient compressed indexing methods are critical for pangenomics and for avoiding reference bias. In the Movi study, we implemented the move structure index, highlighting its locality-of-reference and speed. However, Movi had a high memory footprint compared to other compressed indexes. Here we introduce Movi 2 and describe new methods that greatly reduce size and memory footprint of move structure based indexes. The most compressed version of Movi 2 reduces the Movi index space footprint more than fivefold. We also introduce sampling approaches that enable trade-offs between query and space efficiency. To demonstrate, we show that Movi 2 achieves advantageous time and space tradeoffs when applied to large pangenome collections, including both the first and second releases of the Human Pangenome Reference Consortium (HPRC) collection, the latter of which spans over 460 human haplotyes. We show that Movi 2 dominates prior methods on both speed and memory footprint, including both r-index-based and our previous move structure-based method. The methods we developed for Movi 2 are publicly available at https://github.com/mohsenzakeri/Movi.\n\nMovi 2: Fast and Space-Efficient Queries on Pangenomes", "token_count": 282, "char_count": 1217, "word_count": 176, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:00.077773", "source": { "split": "train_shard_00001", "doc_id": 151 }, "chunk_id": "train_shard_00001_151_0", "global_id": 5879 }, { "text": "De novo genome assembly is challenging in highly repetitive regions; however, reference-guided assemblers often suffer from bias. We propose a framework for pangenome-guided sequence assembly, which can resolve short-read data in complex regions without bias towards a single reference genome. Our method frames assembly as a graph traversal optimisation problem, which can be implemented on quantum computers. The pipeline first annotates pangenome graphs with estimated copy numbers for each node, then finds a path on the graph that best explains those copy numbers. On simulated data, our approach significantly reduces the number of contigs compared to de novo assemblers. While it introduces a small increase in inaccuracies, such as false joins, our optimisation-based methods are competitive with current exhaustive search techniques. They are also designed to scale more efficiently as the problem size grows and will run effectively on future quantum computers.\n\nPangenome-guided sequence assembly via binary optimisation", "token_count": 206, "char_count": 1031, "word_count": 148, "semantic_coherence": 1, "information_density": 0.777, "quality_score": 0.8885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:00.534089", "source": { "split": "train_shard_00001", "doc_id": 152 }, "chunk_id": "train_shard_00001_152_0", "global_id": 5880 }, { "text": "

Summary

Eukaryotic genomes harbor many forms of variation, including nucleotide diversity and structural polymorphisms, which experience natural selection and contribute to genome evolution and biodiversity. However, harnessing this variation for agriculture hinges on our ability to detect, quantify, catalog, and utilize genetic diversity. Here, we explore seven complete genomes of the emerging biofuel crop pennycress ( Thlaspi arvense ) drawn from across the species’s current genetic diversity to catalogue variation in genome structure and content. Across this new pangenome resource, we find contrasting evolutionary modes in different genomic regions. Gene-poor, repeat-rich pericentromeric regions experience frequent rearrangements, including repeated centromere repositioning. In contrast, conserved gene-dense chromosome arms maintain large-scale synteny across accessions, even in fast-evolving immune genes where microsynteny breaks down across species but the macrosynteny of gene cluster positioning is maintained. Our findings highlight that multiple elements of the genome experience dynamic evolution that conserves functional content on the chromosome scale but allows rearrangement and presence-absence variation on a local scale. This diversity is invisible to classical reference-based approaches and highlights the strength and utility of pangenomic resources. These results provide a valuable case study of rapid genomic structural evolution within a species and powerful resources for crop development in an emerging biofuel crop.\n\nStructure and sequence evolution in the pennycress (Thlaspi arvense) pangenome", "token_count": 357, "char_count": 1654, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6869, "quality_score": 0.8435, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:01.134425", "source": { "split": "train_shard_00001", "doc_id": 153 }, "chunk_id": "train_shard_00001_153_0", "global_id": 5881 }, { "text": "During the microbial surveillance of the International Space Station (ISS) in April 2018, four Gram-stain positive bacterial strains, designated as F6_8S_P_2BT, F6_8S_P_3A, F6_8S_P_3B and F6_8S_P_3C, belonging to the genus Microbacterium were isolated from the walls of crew quarters. All four strains exhibited high 16S rRNA gene sequence similarity (> 99%), low average nucleotide identity (93%), and < 49.7% digital DNA: DNA hybridization values with the closest recognized Microbacterium paraoxydans DSM 15019T, delineating new phylogenetic branches within the genus. Further whole-genome sequencing (WGS) and phylogenomic analysis revealed a close genetic relationship (> 98% ANI; > 83% dDDH) between the ISS strains and Microbacterium sp. LTR1 strain isolated from the larva skin of Lissotriton vulgaris from Tula region, Russia, which was misidentified as M. paraoxydans. The pangenomic analysis also shows high correlation between the ISS strains and their proximity to the type strain M. paraoxydans DSM 15019T. These analyses suggest that strain LTR1, previously characterized as M. paraoxydans, should be included in this new Microbacterium clade alongside the four novel ISS strains. Functional genome analysis revealed unique proteins associated with transcription, defense, and metabolism. The genome harbored toxin-antitoxin modules (e.g., VapBC, Phd/YuzE), stress response regulators (FrmR, YhcF), and genes involved in formaldehyde resistance and glycoside hydrolase activity. Secondary metabolite gene clusters included beta-lactone, terpene, and T3PKS. Notably, tetracycline resistance gene tet(42) was present, indicating potential clinical relevance", "token_count": 520, "char_count": 1703, "word_count": 225, "semantic_coherence": 1, "information_density": 0.7378, "quality_score": 0.8689, "entities": { "genes": [ "LTR1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:01.816714", "source": { "split": "train_shard_00001", "doc_id": 154 }, "chunk_id": "train_shard_00001_154_0", "global_id": 5882 }, { "text": "The ISS strains grew at 4-40 °C, 0.5-8% NaCl, and pH 6.0-9.0. Chemotaxonomic features included anteiso-C15:0 and anteiso-C17:0 as major fatty acids, MK-12 as the predominant menaquinone, and ornithine as the diagnostic diamino acid in B2β-type peptidoglycan. The genomic DNA G+C content was 70.03 mol%. The polyphasic taxonomy showed that the ISS isolates along with LTR1 represent distinct strains of a new Microbacterium species, herein named Microbacterium meiriae. The type strain is F6_8S_P_2BT (DSM 115935T = NRRL B-65668T).\n\nGenomic characterization of Microbacterium meiriae sp. nov., a novel bacterium isolated from the International Space Station.", "token_count": 261, "char_count": 690, "word_count": 94, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [ "LTR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:02.397619", "source": { "split": "train_shard_00001", "doc_id": 154 }, "chunk_id": "train_shard_00001_154_1", "global_id": 5883 }, { "text": "The wide adoption of bacterial genome sequencing and encoding both core and accessory genome variation using k-mers has allowed bacterial genome-wide association studies (GWAS) to identify genetic variants associated with relevant phenotypes such as those linked to infection. Significant limitations still remain because of k-mers being duplicated across gene clusters and as far as the interpretation of association results is concerned, which affects the wider adoption of GWAS methods on microbial data sets. We have developed a simple computational method (panfeed) that explicitly links each k-mer to their gene cluster at base-resolution level, which allows us to avoid biases introduced by a global de Bruijn graph as well as more easily map and annotate associated variants. We tested panfeed on two independent data sets, correctly identifying previously characterized causal variants, which demonstrates the precision of the method, as well as its scalable performance. panfeed is a command line tool written in the python programming language and is available at https://github.com/microbial-pangenomes-lab/panfeed.\n\nReduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centric k-mers.", "token_count": 288, "char_count": 1277, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7326, "quality_score": 0.8663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:03.000712", "source": { "split": "train_shard_00001", "doc_id": 155 }, "chunk_id": "train_shard_00001_155_0", "global_id": 5884 }, { "text": "The increasing antimicrobial resistance in Providencia stuartii (P. stuartii) worldwide, particularly concerning for immunocompromised and burn patients, has raised concern in Bangladesh, where the significance of this infectious opportunistic pathogen had been previously overlooked, prompting a need for investigation. The two strains of P. stuartii (P. stuartii SHNIBPS63 and P. stuartii SHNIBPS71) isolated from wound swab of two critically injured burn patients were found to be multidrug-resistant and P. stuartii SHNIBPS63 showed resistance to all the 22 antibiotics tested as well as revealed the co-existence of blaVEB-6 (Class A), blaNDM-1 (Class B), blaOXA-10 (Class D) beta lactamase genes. Complete resistance to carbapenems through the production of NDM-1, is indicative of an alarming situation as carbapenems are considered to be the last line antibiotic to combat this pathogen. Both isolates displayed strong biofilm-forming abilities and exhibited resistance to copper, zinc, and iron, in addition to carrying multiple genes associated with metal resistance and the formation of biofilms. The study also encompassed a pangenome analysis utilizing a dataset of eighty-six publicly available P. stuartii genomes (n = 86), revealing evidence of an open or expanding pangenome for P. stuartii. Also, an extensive genome-wide analysis of all the P. stuartii genomes revealed a concerning global prevalence of diverse antimicrobial resistance genes, with a particular alarm raised over the abundance of carbapenem resistance gene blaNDM-1. Additionally, this study highlighted the notable genetic diversity within P. stuartii, significant informations about phylogenomic relationships and ancestry, as well as potential for cross-species transmission, raising important implications for public health and microbial adaptation across different environments.\n\nGenomic landscape of NDM-1 producing multidrug-resistant Providencia stuartii causing burn wound infections in Bangladesh.", "token_count": 508, "char_count": 2037, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [ "SHNIBPS71", "SHNIBPS63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:03.661319", "source": { "split": "train_shard_00001", "doc_id": 156 }, "chunk_id": "train_shard_00001_156_0", "global_id": 5885 }, { "text": "Abstract

Mycoplasma hyorhinis (homotypic synonym of Mesomycoplasma hyorhinis) is a pathobiont from the upper respiratory tract of pigs. Under unclear circumstances, it can disseminate systemically and cause disease. Although some studies described different infectious capabilities, no factors have been directly linked to virulence. This study aimed to analyze the core and accessory genes of all available M. hyorhinis strains (pangenome) to identify potential virulence factors. We characterized the pangenome of 110 strains, including isolates from healthy (nasal cavity) and diseased (systemic organs, nasal cavity or lung) animals. Comparative analyses were performed according to the clinical background. Although most putative virulence genes were shared, we identified several genes absent in most health-associated strains related to DNA-processing mechanisms, including hsdM-hsdR restriction-modification system and various helicases. Furthermore, the particular analysis of variable lipoprotein (vlp) genes, revealed a similar presence in all strains but higher number of repeats in region III of vlpF and vlpC. Genome-scale metabolic models were used to infer the metabolic capabilities of the strains, showing highly conserved predicted reactomes, including growth capabilities and auxotrophies. In conclusion, although all strains may carry genes enabling disease, nasal strains from healthy animals lacked some DNA-processing genes and showed distinct vlp patterns. Additional genomes especially from strains isolated from healthy animals, would be needed to confirm these findings.

\n\nExploring the pangenome of Mycoplasma hyorhinis in search of potential virulence markers", "token_count": 464, "char_count": 1864, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8473, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:04.311703", "source": { "split": "train_shard_00001", "doc_id": 157 }, "chunk_id": "train_shard_00001_157_0", "global_id": 5886 }, { "text": "Abstract

Vibrio toranzoniae is a marine bacterium belonging to the Splendidus clade, originally isolated from healthy clams in Galicia (NW Spain). Its isolation from different hosts and seawater indicated two lifestyles and wide geographical distribution. The aim of the present study was to determine the differences at genome level among strains, as well as to determine their phylogeny. For this purpose, whole genomes were sequenced by different technologies and the resulting sequences corrected. Genomes were annotated and compared with different online tools. Furthermore, the study of core and pan genome was examined, and the phylogeny was inferred. The content of the core genome ranged from 2,953 to 2,766 genes and that of the pangenome from 6,278 to 6,132, depending on the tool used. The comparison revealed that although the strains shared certain homology, with DDH values ranging from 77.10 to 82.30 and values of OrthoANI higher than 97%,notable differences were found related to motility, capsule synthesis, iron acquisition system or mobile genetic elements. The phylogenetic analysis of the core genome did not reveal a differentiation of the strains according to their lifestyle, but that of the pangenome pointed out certain geographical isolation in the same growing area. The study led to a reclassification of some isolates formerly described as V. toranzoniae and manifested the importance of cured deposited sequences to proper phylogenetic assignment.

\n\nComparative genomics of Vibrio toranzoniae strains", "token_count": 394, "char_count": 1589, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:04.926766", "source": { "split": "train_shard_00001", "doc_id": 158 }, "chunk_id": "train_shard_00001_158_0", "global_id": 5887 }, { "text": "Understanding the evolutionary dynamics of foodborne pathogens throughout host-associated habitats is of utmost importance. Bacterial pan-genomes, as dynamic entities, are strongly influenced by ecological lifestyles. As a phenotypically diverse species in the Bacillus cereus group, Bacillus paranthracis is recognized as an emerging foodborne pathogen and a probiotic simultaneously. This poorly understood species is a suitable study model for adaptive pan-genome evolution. In this study, we determined the biogeographic distribution, abundance, genetic diversity, and genotypic profiles of key genetic elements of B. paranthracis. Metagenomic read recruitment analyses demonstrated that B. paranthracis members are globally distributed and abundant in host-associated habitats. A high-quality pan-genome of B. paranthracis was subsequently constructed to analyze the evolutionary dynamics involved in ecological adaptation comprehensively. The open pan-genome indicated a flexible gene repertoire with extensive genetic diversity. Significant divergences in the phylogenetic relationships, functional enrichment, and degree of selective pressure between the different components demonstrated different evolutionary dynamics between the core and accessory genomes driven by ecological forces. Purifying selection and gene loss are the main signatures of evolutionary dynamics in B. paranthracis pan-genome. The plasticity of the accessory genome is characterized by horizontal gene transfer (HGT), massive gene losses, and weak purifying or positive selection, which might contribute to niche-specific adaptation. In contrast, although the core genome dominantly undergoes purifying selection, its association with HGT and positively selected mutations indicates its potential role in ecological diversification. Furthermore, host fitness-related dynamics are characterized by the loss of secondary metabolite biosynthesis gene clusters (BGCs) and CAZyme-encoding genes and the acquisition of antimicrobial resistance (AMR) and virulence genes via HGT. This study offers a case study of pan-genome evolution to investigate the ecological adaptations reflected by biogeographical characteristics, thereby advancing the understanding of intraspecific diversity and evolutionary dynamics of foodborne pathogens.", "token_count": 521, "char_count": 2354, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6027, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:05.586275", "source": { "split": "train_shard_00001", "doc_id": 159 }, "chunk_id": "train_shard_00001_159_0", "global_id": 5888 }, { "text": "Unveiling intraspecific diversity and evolutionary dynamics of the foodborne pathogen Bacillus paranthracis through high-quality pan-genome analysis.", "token_count": 43, "char_count": 156, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:05.945489", "source": { "split": "train_shard_00001", "doc_id": 159 }, "chunk_id": "train_shard_00001_159_1", "global_id": 5889 }, { "text": "Abstract

Chicken is one of the most popular animal protein sources for humans and serves as an excellent model for genetics and evolutionary research. However, the contribution of structural variations (SVs) to complex trait genetics remains underexplored. Here, we generated eight new telomere-to-telomere (T2T) chicken genome assemblies, including wild, indigenous, broiler, and layer breeds, which resolved 39.23–83.93 Mb of previously unresolved regions (PURs) per breed. By integrating these with five existing references, we constructed a T2T pangenome graph and genotyped 72,147 SVs in 2,021 whole-genome resequenced chickens, with 29.89% of SVs anchored in PURs. Crucially, beyond SNPs/InDels, SVs captured 14.88 Mb of 59.78 Mb (24.89%) selective sweep regions, explained 43,330 of 156,039 (27.76%) gene expression quantitative trait loci (eQTL), and uncovered 37 of 124 (29.84%) complex-trait QTLs. Remarkably, PUR-located SVs contributed 27.02% SV-trait QTL, while 50.99% SV-eQTL localized on the previously unresolved dot chromosomes. In summary, we provide a comprehensive T2T pangenome resource and demonstrate the significant potential of SVs for dissecting complex traits (e.g., production, adaptation) in chickens.

\n\nA telomere-to-telomere pangenome reveals structural variations as key drivers of complex traits in chickens", "token_count": 424, "char_count": 1362, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:06.565773", "source": { "split": "train_shard_00001", "doc_id": 160 }, "chunk_id": "train_shard_00001_160_0", "global_id": 5890 }, { "text": "Mutant sugar transporter ScGAL2-N376F was overexpressed in Kluyveromyces marxianus for efficient utilization of xylose, which is one of the main components of cellulosic biomass. K. marxianus ScGal2_N376F, the ScGAL2-N376F-overexpressing strain, exhibited 47.04 g/l of xylose consumption and 26.55 g/l of xylitol production, as compared to the parental strain (24.68 g/l and 7.03 g/l, respectively) when xylose was used as the sole carbon source. When a mixture of glucose and xylose was used as the carbon source, xylose consumption and xylitol production rates were improved by 195% and 360%, respectively, by K. marxianus ScGal2_N376F. Moreover, the glucose consumption rate was improved by 27% as compared to that in the parental strain. Overexpression of both wild-type ScGAL2 and mutant ScGAL2-N376F showed 48% and 52% enhanced sugar consumption and ethanol production rates, respectively, when a mixture of glucose and galactose was used as the carbon source, which is the main component of marine biomass. As shown in this study, ScGAL2-N376F overexpression can be applied for the efficient production of biofuels or biochemicals from cellulosic or marine biomass.\n\nOverexpression of Mutant Galactose Permease (ScGal2_N376F) Effective for Utilization of Glucose/Xylose or Glucose/ Galactose Mixture by Engineered Kluyveromyces marxianus.", "token_count": 487, "char_count": 1415, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5026, "quality_score": 0.7513, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:07.215459", "source": { "split": "train_shard_00001", "doc_id": 161 }, "chunk_id": "train_shard_00001_161_0", "global_id": 5891 }, { "text": "Distinct evolutionary trajectories in the Escherichia coli pangenome occur within sequence types.", "token_count": 29, "char_count": 104, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:07.571159", "source": { "split": "train_shard_00001", "doc_id": 162 }, "chunk_id": "train_shard_00001_162_0", "global_id": 5892 }, { "text": "Kluyveromyces marxianus is a promising host for producing bioethanol and heterologous proteins. It displays many superior traits to a conventional industrial yeast species, Saccharomyces cerevisiae, including fast growth, thermotolerance and the capacity to assimilate a wider variety of sugars. However, little is known about the mechanisms underlying the fast-growing feature of K. marxianus. In this study, we performed a comparative genomic analysis between K. marxianus and other Saccharomycetaceae species. Genes involved in flocculation, iron transport, and biotin biosynthesis have particularly high copies in K. marxianus. In addition, 60 K. marxianus specific genes were identified, 45% of which were upregulated during cultivation in rich medium and these genes may participate in glucose transport and mitochondrion related functions. Furthermore, the transcriptomic analysis revealed that under aerobic condition, normalized levels of genes participating in TCA cycles, respiration chain and ATP biosynthesis in the lag phase were higher in K. marxianus than those in S. cerevisiae. Levels of highly copied genes, genes involved in the respiratory chain and mitochondrion assembly, were upregulated in K. marxianus, but not in S. cerevisiae, in later time points during cultivation compared with those in the lag phase. Notably, during the fast-growing phase, genes involved in the respiratory chain, ATP synthesis and glucose transport were co-upregulated in K. marxianus. A few shared motifs in upstream sequences of relevant genes might result in the co-upregulation. Specific features in the co-regulations of gene expressions might contribute to the fast-growing phenotype of K. marxianus. Our study underscores the importance of genome-wide rewiring of the transcriptional network during evolution.", "token_count": 510, "char_count": 1901, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:08.202209", "source": { "split": "train_shard_00001", "doc_id": 163 }, "chunk_id": "train_shard_00001_163_0", "global_id": 5893 }, { "text": "Comparative Genomic and Transcriptomic Analysis Reveals Specific Features of Gene Regulation in Kluyveromyces marxianus.", "token_count": 35, "char_count": 127, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:08.564487", "source": { "split": "train_shard_00001", "doc_id": 163 }, "chunk_id": "train_shard_00001_163_1", "global_id": 5894 }, { "text": "The emergence of graph pangenomes has significantly advanced the study of structural variants (SVs) across diverse species. However, the impact of complex polyploidization events, particularly allopolyploidy, on SV landscapes remains poorly explored. Brettanomyces bruxellensis , a yeast species shaped by multiple allopolyploidization events, offers a compelling model due to its well-characterized genomic and phenotypic diversity. Here, we integrated subgenome-resolved assemblies with population-scale genomic and transcriptomic datasets to characterize SVs distribution and their functional impact at the species level. Leveraging a constructed reference graph pangenome, we identified sequences that are unique to each subgenome, and detected 212,177 SVs across 1,060 sequenced isolates. Allopolyploid genomes harbored significantly more SVs (320 on average) than diploid genomes (116 on average), reflecting the extensive impact of hybridization on the genome architecture. A subset of SVs originating from ancestral divergence between subgenomes (hybridization-associated SVs) formed distinct hotspots of structural diversity. Furthermore, functional association analysis revealed that 27.5% of SVs exert local regulatory effects on gene expression. Interestingly, hybridization-associated structural variants disproportionately affect gene expression, with a greater proportion of associated variants and a significantly larger effect size compared to other SVs. Overall, these findings underscore the role of allopolyploidization in driving both structural and functional genomic diversification. Our study also highlights the value of graph-based approaches in dissecting complex genome evolution.\n\nGraph-based pangenome analysis uncovers structural and functional impacts of allopolyploidization events", "token_count": 401, "char_count": 1814, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6814, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:09.178819", "source": { "split": "train_shard_00001", "doc_id": 164 }, "chunk_id": "train_shard_00001_164_0", "global_id": 5895 }, { "text": "Acetic acid, a common weak acid in industrial fermentation processes, occurs naturally in lignocellulosic hydrolysates and is a byproduct of microbial metabolism. As a significant environmental stressor, it triggers the expression of multiple genes involved in various cellular responses, including biological processes, cellular components, and molecular functions. Using the acid-tolerant strain Pichia kudriavzevii PkAC-9, developed through adaptive laboratory evolution under acetic acid stress, we conducted a transcriptional analysis of 70 stress response-associated genes. RT-qPCR analysis revealed significant upregulation of several genes compared with the wild-type strain under acetic acid stress conditions. The most dramatic changes occurred in genes encoding key metabolic enzymes and stress response proteins associated with the TCA cycle (Fum: 18.6-fold, Aco: 17.1-fold, Oxo: 9.0-fold), carbon and energy metabolism (Tdh2: 28.0-fold, Erg2: 2.0-fold), electron transport chain (Gst: 10.6-fold), molecular chaperones (Hsp104: 26.9-fold, Hsp70: 13.0-fold, Sgt2: 10.0-fold), and transcriptional activators. Our findings indicate that the enhanced acetic acid tolerance of P. kudriavzevii PkAC-9 primarily depends on the coordinated upregulation of genes involved in energy metabolism, cellular detoxification mechanisms, and protein quality control systems through heat shock and transcriptional activator proteins.\n\nTranscriptional Regulation Mechanisms in Adaptively Evolved <i>Pichia kudriavzevii</i> Under Acetic Acid Stress.", "token_count": 439, "char_count": 1567, "word_count": 193, "semantic_coherence": 1, "information_density": 0.7098, "quality_score": 0.8549, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:09.814899", "source": { "split": "train_shard_00001", "doc_id": 165 }, "chunk_id": "train_shard_00001_165_0", "global_id": 5896 }, { "text": "Novel traits enable many rodents to thrive in extreme environmental niches. Predatory grasshopper mice (Onychomys sp.) have co-evolved resistance to painful and lethal neurotoxins produced by their scorpion prey. Previous work reported that grasshopper mice have structural and functional modifications in sodium channel Nav1.8 that block the effect of painful toxins. However, key questions remain about the molecular adaptations underlying toxin resistance. We produced the first high-quality reference genomes and annotations for Onychomys species and Peromyscus eremicus. We implemented a comprehensive pipeline to detect positive selection across genome-scale datasets and identified Onychomys-specific mutations in Nav1.3 (Scn3a), a sodium channel gene expressed in the central nervous system and the peripheral sensory system after nerve damage. We detected an Onychomys-specific tandem gene duplication of the Cblif gene, which encodes a glycoprotein crucial for vitamin B12 absorption. This adaptation likely supports the species' dietary specialisation and modified stomach morphology, where parietal cells expressing Cblif are especially numerous. Our study provides a key step for establishing the Onychomys species as a model system for studying toxin resistance, alternative pain phenotypes, and behavioural traits related to predator-prey interactions.\n\nThe Onychomys pangenome reveals the unique molecular adaptations that confer toxin resistance", "token_count": 324, "char_count": 1462, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7128, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:10.380292", "source": { "split": "train_shard_00001", "doc_id": 166 }, "chunk_id": "train_shard_00001_166_0", "global_id": 5897 }, { "text": "Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from 6 countries (Australia, Bosnia and Herzegovina, Brazil, China, France and USA) and 4 host species (domestic sheep, domestic goats, bighorn sheep and caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4 %) of accessory genes (i.e. genes found only in a subset of assemblies) compared to core genes (i.e. genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall, our results suggest that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways", "token_count": 501, "char_count": 2042, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5819, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:11.034963", "source": { "split": "train_shard_00001", "doc_id": 167 }, "chunk_id": "train_shard_00001_167_0", "global_id": 5898 }, { "text": "The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species.\n\nComparative genomic analysis identifies potential adaptive variation in Mycoplasma ovipneumoniae.", "token_count": 82, "char_count": 409, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:11.407573", "source": { "split": "train_shard_00001", "doc_id": 167 }, "chunk_id": "train_shard_00001_167_1", "global_id": 5899 }, { "text": "Global rates of multi-drug resistance continue to rise, posing a significant challenge in the fight against antimicrobial resistance worldwide. Multi-drug efflux pumps are a significant contributor to this burden. Understanding connections between the diverse network of efflux pump genes, and their interactions with other genes, is important for understanding the landscape of multi-drug resistance and devising new interventions to mitigate it. To address this issue, we have investigated how efflux pumps and accessory genes covary across genomes. Using genomic data from 200 publicly available Escherichia coli isolates, we constructed a pangenome and performed coincidence analyses using the bioinformatic tool Coinfinder. On an aggregate level, efflux pumps formed more coincident gene pairs within the accessory genome than avoidant gene pairs. Genes with a functional annotation associated with ‘transport’ had the highest representation for both coincident and avoidant gene pairs. In contrast, when specifically considering gene pairs where both genes were related to efflux pumps, avoidant pairs were more frequent, though some coincident pairs were also found—primarily between subcomponents that make up tripartite pumps, as well as between subcomponents and single unit efflux pumps). Further exploration and understanding on the role the efflux pumps from the accessory genome play and how it expresses itself, would result in developing novel strategies to target increasingly resistant bacteria.\n\nCoincidence analysis of efflux pumps in the Escherichia coli pangenome", "token_count": 341, "char_count": 1585, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.8049, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:12.875773", "source": { "split": "train_shard_00001", "doc_id": 168 }, "chunk_id": "train_shard_00001_168_0", "global_id": 5900 }, { "text": "This study investigates the genomic features and probiotic potential of Lactiplantibacillus plantarum HMX2, isolated from Chinese Sauerkraut, using whole-genome sequencing (WGS) and bioinformatics for the first time. This study also aims to find genetic diversity, antibiotic resistance genes, and functional capabilities to help us better understand its food safety applications and potential as a probiotic. L. plantarum HMX2 was cultured, and DNA was extracted for WGS. Genomic analysis comprised average nucleotide identity (ANI) prediction, genome annotation, pangenome, and synteny analysis. Bioinformatics techniques were used to identify CoDing Sequences (CDSs), transfer RNA (tRNA) and ribosomal RNA (rRNA) genes, and antibiotic resistance genes, as well as to conduct phylogenetic analysis to establish genetic diversity and evolution. The study found a significant genetic similarity (99.17% ANI) between L. plantarum HMX2 and the reference strain. Genome annotation revealed 3,242 coding sequences, 65 tRNA genes, and 16 rRNA genes. Significant genetic variety was found, including 25 antibiotic resistance genes. A phylogenetic study placed L. plantarum HMX2 among closely related bacteria, emphasizing its potential for probiotic and food safety applications. The genomic investigation of L. plantarum showed essential genes, including plnJK and plnEF, which contribute to antibacterial action against foodborne pathogens. Furthermore, genes such as MurA, Alr, and MprF improve food safety and probiotic potential by promoting bacterial survival under stress conditions in food and the gastrointestinal tract. This study introduces the new genomic features of L. plantarum HMX2 about specific genetics and its possibility of relevant uses in food security and technologies. These findings of specific genes involved in antimicrobial activity provide fresh possibilities for exploiting this strain in forming probiotic preparations and food preservation methods", "token_count": 507, "char_count": 2016, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8044, "entities": { "genes": [ "HMX2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:13.558402", "source": { "split": "train_shard_00001", "doc_id": 169 }, "chunk_id": "train_shard_00001_169_0", "global_id": 5901 }, { "text": "The future research should focus on the experimental validation of antibiotic resistance genes, comparative genomics to investigate functional diversity, and the development of novel antimicrobial therapies that take advantage of L. plantarum's capabilities.\n\nUnveiling the whole genomic features and potential probiotic characteristics of novel Lactiplantibacillus plantarum HMX2.", "token_count": 94, "char_count": 395, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8298, "quality_score": 0.9149, "entities": { "genes": [ "HMX2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:13.960551", "source": { "split": "train_shard_00001", "doc_id": 169 }, "chunk_id": "train_shard_00001_169_1", "global_id": 5902 }, { "text": "Abstract

Whey, the main byproduct in cheese manufacturing, has a high organic content, predominantly due to its lactose amount (45-60 g/L). There are three types of residues coming from cheese production: sweet whey (SW), acid whey (AW), and ricotta whey (RW). Each one presents physicochemical particularities that pose challenges when handled by small and medium enterprises, due to their costly treatment. An alternative to address this issue is the fermentation of such substrates to obtain value-added products. The goal of this research was to evaluate the fermentation with Kluyveromyces marxianus in the three types of raw whey for the production of isoamyl acetate, a compound responsible for the banana aroma. Several factors were analyzed: cellular growth, pH variations, reduction in lactose content, ethanol production, and isoamyl acetate generation. Cellular growth showed no significant differences between the three types of whey. Regarding pH, a decrease was recorded during the first 48 hours down to an approximate value of 4.3, then it increased to reach values close to 7. In acid whey, 50.95 g/L of ethanol was obtained at 120 hours. On the other hand, the maximum observed production of isoamyl acetate was 160 mg/L. Finally, the maximum lactose consumption was observed in sweet whey, with an approximate percentage of 76% at 24 hours, higher than that of acid and ricotta whey, which ranged between 56 and 58%.

\n\nComparative Analysis of Three Types of Whey as Substrate for Fermentation by Kluyveromyces marxianus and its Influence on Isoamyl Acetate Synthesis", "token_count": 433, "char_count": 1625, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:14.626079", "source": { "split": "train_shard_00001", "doc_id": 170 }, "chunk_id": "train_shard_00001_170_0", "global_id": 5903 }, { "text": "Population-level structural variant (SV) profiling is crucial in the era of pangenomes. However, identifying SVs from genome assemblies and pangenome graphs remains a significant challenge. Here we present Swave, a sequence-to-image, deep-learning based method that accurately resolves both simple and complex SVs, along with their population characteristics, from assembly-derived pangenome graphs. Swave introduces ‘projection waves’ to summarize the dotplot images that capture mapping patterns between reference and SV-indicating alleles in pangenome. These images are analyzed by a recurrent neural network to distinguishes true SV signals from background noise introduced by genomic repeats. Swave demonstrates superior performance in both SV type classification and genotyping compared to existing methods. When applied to a healthy cohort (n=334) and a rare-disease cohort (n=574), Swave reveals complex and polymorphic SV patterns across human populations and identifies potentially pathogenic SVs. These advancements will facilitate the creation of comprehensive population-level SV catalogs, deepening our understanding of SVs in genetic diversity and disease associations.\n\nPopulation-level structural variant characterization from pangenome graph", "token_count": 269, "char_count": 1259, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7301, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:15.229847", "source": { "split": "train_shard_00001", "doc_id": 171 }, "chunk_id": "train_shard_00001_171_0", "global_id": 5904 }, { "text": "

At the DBCLS BioHackathon 2025, we converted metatranscriptomic analytical shell scripts into Common Workflow Language (CWL) containerized with Docker. Sub-workflows were created for metagenomic assembly, read mapping, and gene annotation, and validated with test datasets. The workflows, released on GitHub and WorkflowHub, improve reproducibility and address issues of reusability and software environment dependency. We also evaluated CWL best practices from the perspective of life scientists, classifying them by difficulty, importance, and applicability to promote FAIR principles and software quality.In parallel, we established a benchmarking framework for pangenome-based structural variant (SV) calling using data from the Dai population. Graph-based references from the Human and Chinese Pangenome Consortia were compared with linear references using minimap2 and vg giraffe. Results showed improved alignment accuracy and variant detection with pangenomes, demonstrating their value for reducing mapping bias and enhancing SV discovery.

\n\nDBCLS BioHackathon 2025 report: Creation and Publication Analytical Workflow of Creators' Interests", "token_count": 258, "char_count": 1156, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7651, "quality_score": 0.8826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:15.779837", "source": { "split": "train_shard_00001", "doc_id": 172 }, "chunk_id": "train_shard_00001_172_0", "global_id": 5905 }, { "text": "This study aims to evaluate the in silico genomic characteristics of five species of the genus Planotetraspora: P. kaengkrachanensis, P. mira, P. phitsanulokensis, P. silvatica, and P. thailandica, with a view to their application in therapeutic research. The 16S rRNA comparison indicated that these species were phylogenetically distinct. Pairwise comparisons of digital DNA-DNA hybridization (dDDH) and OrthoANI values between these studied type strains indicated that dDDH values were below 62.5%, while OrthoANI values were lower than 95.3%, suggesting that the five species represent distinct genomospecies. These results were consistent with the phylogenomic study based on core genes and the pangenome analysis of these five species within the genus Planotetraspora. However, the genome annotation showed some differences between these species, such as variations in the number of subsystem category distributions across whole genomes (ranging between 1979 and 2024). Additionally, the number of CAZYme (Carbohydrate-Active enZYme) genes ranged between 298 and 325, highlighting the potential of these bacteria for therapeutic research applications. The in silico physico-chemical characteristics of cellulases from Planotetraspora species were analyzed. Their 3D structure was modeled, refined, and validated. A molecular docking analysis of this cellulase protein structural model was conducted with cellobiose, cellotetraose, laminaribiose, carboxymethyl cellulose, glucose, and xylose ligand. Our study revealed significant interaction between the Planotetraspora cellulase and cellotetraose substrate, evidenced by stable binding energies. This suggests that this bacterial enzyme holds great potential for utilizing cellotetraose as a substrate in various applications", "token_count": 499, "char_count": 1845, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:16.427386", "source": { "split": "train_shard_00001", "doc_id": 173 }, "chunk_id": "train_shard_00001_173_0", "global_id": 5906 }, { "text": "This study enriches our understanding of the potential applications of Planotetraspora species in therapeutic research.\n\nThe Phylogenomic Characterization of Planotetraspora Species and Their Cellulases for Biotechnological Applications.", "token_count": 69, "char_count": 251, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:16.791199", "source": { "split": "train_shard_00001", "doc_id": 173 }, "chunk_id": "train_shard_00001_173_1", "global_id": 5907 }, { "text": "Mango pangenome reveals dramatic impacts of reference bias on population genomic analyses", "token_count": 17, "char_count": 89, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:17.154453", "source": { "split": "train_shard_00001", "doc_id": 174 }, "chunk_id": "train_shard_00001_174_0", "global_id": 5908 }, { "text": "Population-scale genomics information provides valuable prior knowledge for various genomic analyses, especially variant calling. A notable example of such application is the human pangenome reference released by the Human Pangenome Reference Consortium, which has been shown to improve read mapping and structural variant genotyping. In this work, we introduce pangenome-aware DeepVariant, a variant caller that uses a pangenome reference alongside sample-specific read alignments. It generates pileup images of both reads and pangenome haplotypes near potential variants and uses a Convolutional Neural Network to infer genotypes. This approach allows directly using a pangenome for distinguishing true variant signals from sequencing or alignment noise. We assessed its performance on various short-read sequencing platforms and read mappers. Across all settings, pangenome-aware DeepVariant outperformed the linear-reference-based DeepVariant, reducing errors by up to 25.5%. We also show that Element reads with pangenome-aware DeepVariant can achieve 23.6% more accurate variant calling performance compared to existing methods.\n\nPangenome-aware DeepVariant", "token_count": 247, "char_count": 1163, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7171, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:17.635197", "source": { "split": "train_shard_00001", "doc_id": 175 }, "chunk_id": "train_shard_00001_175_0", "global_id": 5909 }, { "text": "

Background

Escherichia coli is a major cause of bloodstream infections (BSI), which can lead to life-threatening organ dysfunction. We determined the genomic characteristics of E. coli implicated in BSI and the spread of antimicrobial resistance (AMR).

Methods

We carried out in vitro antimicrobial susceptibility testing and whole genome sequencing of 557 E. coli isolates recovered from BSI at Dartmouth-Hitchcock Medical Center, USA.

Results

We identify at least 119 previously recognized sequence types (ST), of which five STs (ST69, ST73, ST95, ST127, ST131) altogether represent 50% of the bloodstream E. coli population. Of the 142 distinct serotypes detected, the most common are O25:H4 and O1:H7. A total of 62 acquired genes are associated with resistance to at least 13 antimicrobial classes. These include the β-lactamase gene families blaTEM, blaSHV, blaOXA, blaCTX-M, and blaCMY, which together can be further classified into 15 variants, including seven genes encoding extended-spectrum β-lactamases (ESBL). A total of 210/557 genomes carry at least one bla gene, with blaTEM-1 being the most prevalent variant. ESBL-related genes are frequently detected in ST131 genomes. Four virulence operons related to iron uptake are differentially distributed among the five dominant STs. The putative IncF-type plasmid is often associated with genes related to AMR and iron uptake. Estimation of core and accessory genome similarity identifies 12 presumptive epidemiological linkages that span anywhere between 2-18 months.

Conclusions

Multiple but genetically distinct E", "token_count": 504, "char_count": 1672, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7104, "quality_score": 0.8552, "entities": { "genes": [ "ST131", "ST73", "ST95", "ST127", "ST69" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:18.293906", "source": { "split": "train_shard_00001", "doc_id": 176 }, "chunk_id": "train_shard_00001_176_0", "global_id": 5910 }, { "text": "coli lineages similarly cause BSI and shape AMR dissemination, emphasizing the opportunistic nature of E. coli in invasive infections.\n\nVariants of β-lactamase-encoding genes are disseminated by multiple genetically distinct lineages of bloodstream Escherichia coli.", "token_count": 71, "char_count": 266, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:18.658479", "source": { "split": "train_shard_00001", "doc_id": 176 }, "chunk_id": "train_shard_00001_176_1", "global_id": 5911 }, { "text": "Camelina sativa is an oilseed crop that has shown strong promise as a biofuel feedstock. The profile of fatty acids greatly influences the oil quality; however, genetic mechanisms that determine the natural variation of fatty acid composition in camelina are not fully understood. A genome wide association study (GWAS) was performed to uncover genetic loci that may contribute to the contents of major fatty acids such as oleic and linolenic acids in camelina seed. Two approaches were taken to improve the GWAS efficiency. First, growing a diversity panel of 212 accessions in four locations and two nitrogen fertilization conditions revealed great variation in fatty acid contents in seeds. Second, using an improved reference genome, abundant markers, including 203,320 single nucleotide polymorphisms (SNPs) and 99,067 insertions/deletions (indels), were developed, which refined the population structure of the diversity panel. GWAS resulted in 118 genetic markers across 31 trait/treatment conditions. Closely linked markers were determined based on linkage decay and by comparing secondarily associated markers when highly associated ones were removed. Candidate genes were examined by comparing the pangenomes of 12 high-quality reference genomes. This study provides new resources to understand seed lipid metabolism and improve camelina oils through molecular breeding.\n\nGenomic Analysis of the Natural Variation of Fatty Acid Composition in Seed Oils of <i>Camelina sativa</i>.", "token_count": 367, "char_count": 1508, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:19.247895", "source": { "split": "train_shard_00001", "doc_id": 177 }, "chunk_id": "train_shard_00001_177_0", "global_id": 5912 }, { "text": "Pangenomes are increasingly critical for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here, we report a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated near-gapless genomes representing all seven watermelon species. The super-pangenome captures approximately one million structural variants (SVs), enabling accurate variant genotyping across ~900 watermelon accessions and substantially expanding variant discovery both across and within species. Broader sampling within the pangenome provides insights into genome evolution among watermelon species and sheds light on the origin of cultivated watermelon. SV-inclusive genome-wide association studies enhance trait mapping resolution and identify a copy number variation upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, our findings and genomic resources establish a foundational framework for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crop species.\n\nPopulation-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon", "token_count": 308, "char_count": 1448, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7486, "quality_score": 0.8743, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:19.814911", "source": { "split": "train_shard_00001", "doc_id": 178 }, "chunk_id": "train_shard_00001_178_0", "global_id": 5913 }, { "text": "

Background

Future expansion of corn-derived ethanol raises concerns of sustainability and competition with the food industry. Therefore, cellulosic biofuels derived from agricultural waste and dedicated energy crops are necessary. To date, slow and incomplete saccharification as well as high enzyme costs have hindered the economic viability of cellulosic biofuels, and while approaches like simultaneous saccharification and fermentation (SSF) and the use of thermotolerant microorganisms can enhance production, further improvements are needed. Cellulosic emulsions have been shown to enhance saccharification by increasing enzyme contact with cellulose fibers. In this study, we use these emulsions to develop an emulsified SSF (eSSF) process for rapid and efficient cellulosic biofuel production and make a direct three-way comparison of ethanol production between S. cerevisiae, O. polymorpha, and K. marxianus in glucose and cellulosic media at different temperatures.

Results

In this work, we show that cellulosic emulsions hydrolyze rapidly at temperatures tolerable to yeast, reaching up to 40-fold higher conversion in the first hour compared to microcrystalline cellulose (MCC). To evaluate suitable conditions for the eSSF process, we explored the upper temperature limits for the thermotolerant yeasts Kluyveromyces marxianus and Ogataea polymorpha, as well as Saccharomyces cerevisiae, and observed robust fermentation at up to 46, 50, and 42 °C for each yeast, respectively. We show that the eSSF process reaches high ethanol titers in short processing times, and produces close to theoretical yields at temperatures as low as 30 °C. Finally, we demonstrate the transferability of the eSSF technology to other products by producing the advanced biofuel isobutanol in a light-controlled eSSF using optogenetic regulators, resulting in up to fourfold higher titers relative to MCC SSF.

Conclusions

The eSSF process addresses the main challenges of cellulosic biofuel production by increasing saccharification rate at temperatures tolerable to yeast", "token_count": 516, "char_count": 2084, "word_count": 286, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:20.475335", "source": { "split": "train_shard_00001", "doc_id": 179 }, "chunk_id": "train_shard_00001_179_0", "global_id": 5914 }, { "text": "The rapid hydrolysis of these emulsions at low temperatures permits fermentation using non-thermotolerant yeasts, short processing times, low enzyme loads, and makes it possible to extend the process to chemicals other than ethanol, such as isobutanol. This transferability establishes the eSSF process as a platform for the sustainable production of biofuels and chemicals as a whole.\n\nCellulosic biofuel production using emulsified simultaneous saccharification and fermentation (eSSF) with conventional and thermotolerant yeasts.", "token_count": 127, "char_count": 532, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:20.859841", "source": { "split": "train_shard_00001", "doc_id": 179 }, "chunk_id": "train_shard_00001_179_1", "global_id": 5915 }, { "text": "With the current speed of sequencing, there is a desire for standardised and automated genome assembly and annotation to produce high-quality genomes as input for comparative (pan)genomics. Therefore, we created a convenience pipeline using existing tools that creates annotated genome assemblies from HiFi (and optionally ultra-long ONT and/or Hi-C) reads for a set of related accessions as well as a related reference genome. Our pipeline is species-agnostic and generates an extensive quality assessment report that can be used for manual filtering and refinement of the assembly and annotation. It includes statistics for individual completeness and contamination assessments as well as a concise pangenome view. The pipeline is implemented in Snakemake and available with a GPLv3 license at GitHub under github.com/dirkjanvw/MoGAAAP and at Zenodo under doi.org/10.5281/zenodo.14833021.\n\nMoGAAAP: A modular Snakemake workflow for automated genome assembly and annotation with quality assessment", "token_count": 246, "char_count": 998, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:21.385646", "source": { "split": "train_shard_00001", "doc_id": 180 }, "chunk_id": "train_shard_00001_180_0", "global_id": 5916 }, { "text": "Species belonging to the Mycobacterium kansasii complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species M. kansasii (sensu stricto), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC. Many genomic aspects of the MKC that relate to these broad phenotypes are not well elucidated. Here, we performed genomic analyses from a collection of 665 MKC strains, isolated from environmental, animal and human sources. We inferred the MKC pangenome, mobilome, resistome, virulome and defence systems and show that the MKC species harbours unique and shared genomic signatures. High frequency of presence of prophages and different types of defence systems were observed. We found that the M. kansasii species splits into four lineages, of which three are lowly represented and mainly in Brazil, while one lineage is dominant and globally spread. Moreover, we show that four sub-lineages of this most distributed M. kansasii lineage emerged during the twentieth century. Further analysis of the M. kansasii genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the M. kansasii's increased virulence and drug resistance.\n\nPhylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species.", "token_count": 424, "char_count": 1607, "word_count": 226, "semantic_coherence": 1, "information_density": 0.615, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:22.012315", "source": { "split": "train_shard_00001", "doc_id": 181 }, "chunk_id": "train_shard_00001_181_0", "global_id": 5917 }, { "text": "For several decades, scientists relied on unique reference genomes as the basis for various genomic studies. This methodology presents multiple drawbacks, particularly for variation studies, often yielding unrepresentative and incomplete observations regarding the diversity of the species or group under study. Pangenomes are collections of genomic sequences from several individuals of a species or population, which allow to overcome the limitations of studies based on a single reference genome. In this study, we produced a 93-assembly pangenome of the model plant Arabidopsis thaliana using the reference-free method PanGenome Graph Builder (PGGB). The aim was to investigate the diversity within this species using this novel methodology, encompassing genomic sequences, genes, and pseudogenes. The pangenome exhibited a total length of 488.78 Mb, consisting of 30,391,243 nodes and 7,189,634 edges. We mapped a total of 2,325,577 genes and 23,894 pseudogenes across 93 assemblies, of which 36% and 0.9%, respectively, were classified as core. The observed variation in terms of genes and especially pseudogenes related to the geographical distance between sampling sites. Since the simulated pangenome growth curve based on gene did not reach a plateau, new accessions could potentially expand the represented diversity. This study enriches our understanding of intra-specific variation in A. thaliana and provides a new viewpoint on the potential applications of pangenomes in diversity research.\n\nThe reference-free pangenome of Arabidopsis thaliana", "token_count": 372, "char_count": 1566, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8213, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:22.601805", "source": { "split": "train_shard_00001", "doc_id": 182 }, "chunk_id": "train_shard_00001_182_0", "global_id": 5918 }, { "text": "

Background:

Gut microbiomes are crucial for host nutrition due to their feed energy-harvesting capacity. In the rumen microbiome Butyrivibrio and Pseudobutyrivibrio dominate and play a key role in harvesting dietary energy. Within these genera, five rumen species have been classified ( Butyrivibrio fibrisolvens , B. hungatei , B. proteoclasticus , Pseudobutyrivibrio ruminis and P. xylanivorans ) and more recently an additional sixth Butyrivibrio sp. group was added. Nonetheless, in recent years the explosion in available metagenomically assembled genomes (MAGs) offer a new insight into their taxonomy and function. Consequently, in this study we analysed the pangenome and function of 64 MAGs and 71 culture representatives of Butyrivibrio and Pseudobutyrivibrio . Results Using MASH and ANI we demonstrate that the 135 Butyrivibrio and Pseudobutyrivibrio genomes from MAGs and pure culture cluster into 59 genera and 75 species. Pangenome analysis of 8 groups containing > 4 strains showed average core genome percentages of between 38.49–76.67%. In turn, the accessory genome percentages for the 8 groups were between 23.33% and 65.39%. The most abundant GH families found in the 8 groups were GH13, GH3, GH43, GH2, GH25, GH31, GH36, and GH5 in descending order. Dendograms of the GH families show extensive variation, and expression of 20.45–47.11% of the genes is observed in metatranscriptome datasets. Conclusions Our findings demonstrate that Butyrivibrio and Pseudobutyrivibrio genomes cluster into 59 genera and 75 species. The 8 groups containing 4 or more genomes that were carried forward possess open genomes with extensive genomic diversity", "token_count": 501, "char_count": 1673, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "GH2", "GH5", "GH25", "GH43", "GH31", "GH3", "GH36", "GH13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:23.256402", "source": { "split": "train_shard_00001", "doc_id": 183 }, "chunk_id": "train_shard_00001_183_0", "global_id": 5919 }, { "text": "The MAGs, alongside genomes for cultured isolates, contained an expansive repertoire of glycosyl hydrolase isoforms, which likely facilitate the symbiotic breakdown of plant matter under dietary perturbations allowing a competitive advantage and driving niche specialisation. This study has enabled a substantial enhancement in our understanding of the functional capacity and taxonomy of the dominant rumen isolates, Butyrivibrio and Pseudobutyrivibrio by utilising all recently published rumen MAGs.\n\nPhylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio pure culture and metagenomically assembled genomes suggest existence of 59 genera and 75 species, alongside possession of open pangenomes with an abundance of carbohydrate-active enzyme family isoforms", "token_count": 185, "char_count": 768, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7677, "quality_score": 0.8838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:23.694895", "source": { "split": "train_shard_00001", "doc_id": 183 }, "chunk_id": "train_shard_00001_183_1", "global_id": 5920 }, { "text": "

Background

The marine environment boasts distinctive physical, chemical, and biological characteristics. While numerous studies have delved into the microbial ecology and biological potential of the marine environment, exploration of genetically encoded, deep-sea sourced secondary metabolites remains scarce. This study endeavors to investigate marine bioproducts derived from deep-sea water samples at a depth of 1,000 m in the Java Trench, Indonesia, utilizing both culture-dependent and whole-genome sequencing methods.

Results

Our efforts led to the successful isolation and cultivation of a bacterium Priestia flexa JT4 from the water samples, followed by comprehensive genome sequencing. The resultant high-quality draft genome, approximately 4 Mb, harbored 5185 coding sequences (CDSs). Notably, 61.97% of these CDSs were inadequately characterized, presenting potential novel CDSs. This study is the first to identify the \"open-type\" (α < 1) pangenome within the genus Priestia. Moreover, our analysis uncovered eight biosynthetic gene clusters (BGCs) using the common genome mining pipeline, antiSMASH. Two non-ribosomal peptide synthetase (NRPS) BGCs within these clusters exhibited the potential to generate novel biological compounds. Noteworthy is the confirmation that the terpene BGC in P. flexa JT4 can produce lycopene, a compound in substantial industrial demand. The presence of lycopene in the P. flexa JT4 cells was verified using Ultra-performance liquid chromatography-mass spectrometry (UPLC-MS/MS) in multiple reaction modes.

Conclusions

This study highlights the bioprospecting opportunity to explore novel bioproducts and lycopene compounds from P. flexa JT4. It marks the pioneering exploration of deep-sea bacterium bioprospecting in Indonesia, seeking to unveil novel bioproducts and lycopene compounds through a genome mining approach.", "token_count": 490, "char_count": 1889, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.836, "entities": { "genes": [ "JT4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:24.345809", "source": { "split": "train_shard_00001", "doc_id": 184 }, "chunk_id": "train_shard_00001_184_0", "global_id": 5921 }, { "text": "From the depths of the Java Trench: genomic analysis of Priestia flexa JT4 reveals bioprospecting and lycopene production potential.", "token_count": 35, "char_count": 132, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [ "JT4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:24.699489", "source": { "split": "train_shard_00001", "doc_id": 184 }, "chunk_id": "train_shard_00001_184_1", "global_id": 5922 }, { "text": "The use of probiotics has been considered as a new therapy option for ulcerative colitis (UC), and yeast has recently received widespread recommendation for human health. In this study, the probiotic characteristics of four yeast strains, Saccharomyces boulardii CNCMI-745, Kluyveromyces marxianus QHBYC4L2, Saccharomyces cerevisiae QHNLD8L1, and Debaryomyces hansenii QSCLS6L3, were evaluated in vitro; their ability to ameliorate dextran sulfate sodium (DSS)-induced colitis was investigated. Among these, S. cerevisiae QHNLD8L1 protected against colitis, which was reflected by increased body weight, colon length, histological injury relief, decreased gut inflammation markers, and intestinal barrier restoration. The abundance of the pathogenic bacteria Escherichia-Shigella and Enterococcaceae in mice with colitis decreased after S. cerevisiae QHNLD8L1 treatment. Moreover, S. cerevisiae QHNLD8L1 enriched beneficial bacteria Lactobacillus, Faecalibaculum, and Butyricimonas, enhanced carbon metabolism and fatty acid biosynthesis function, and increased short chain fatty acid (SCFAs) production. Taken together, our results indicate the great potential of S. cerevisiae QHNLD8L1 supplementation for the prevention and alleviation of UC.\n\nAnti-Inflammatory, Barrier Maintenance, and Gut Microbiome Modulation Effects of Saccharomyces cerevisiae QHNLD8L1 on DSS-Induced Ulcerative Colitis in Mice.", "token_count": 503, "char_count": 1502, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7102, "quality_score": 0.8551, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:25.386252", "source": { "split": "train_shard_00001", "doc_id": 185 }, "chunk_id": "train_shard_00001_185_0", "global_id": 5923 }, { "text": "Long-read sequencing and pangenomics are revolutionizing crop research by providing more complete genome information and revealing crucial structural variations linked to important agricultural traits. Building on recent advances in intraspecific pangenome construction, this study addresses the challenge of creating broader, cross-taxon pangenomes, using the Armeniaca taxonomic section as a model. Leveraging a diverse panel of genome assemblies, we constructed a pangenome graph and cataloged associated single nucleotide polymorphisms (SNPs) and structural variants. We characterized the diversity of these variants and assessed the extent to which different taxa contribute to overall pangenome expansion. Additionally, we evaluated the performance of low-depth sample mapping to the graph-based reference, highlighting key technical limitations that may affect the quality of downstream analyses. We further identified specific subsets of SVs that exhibit associations with particular classes of transposable elements. As a case study illustrating the potential functional and phenotypic relevance of graph-derived SVs, we examined the genomic configuration of the DAM locus within the Armeniaca pangenome.\n\nBuilding pangenomes for domesticated and wild tree species: genomic complexity and strategies", "token_count": 266, "char_count": 1308, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7384, "quality_score": 0.8692, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:25.956212", "source": { "split": "train_shard_00001", "doc_id": 186 }, "chunk_id": "train_shard_00001_186_0", "global_id": 5924 }, { "text": "Fermenting grape juice provides a habitat for a well-mapped and evolutionarily relevant microbial ecosystem consisting of many natural or inoculated strains of yeasts and bacteria. The molecular nature of many of the ecological interactions within this ecosystem remains poorly understood, with the partial exception of interactions of a metabolic nature such as competition for nutrients and production of toxic metabolites/peptides. Data suggest that physical contact between species plays a significant role in the phenotypic outcome of interspecies interactions. However, the molecular nature of the mechanisms regulating these phenotypes remains unknown. Here, we present a transcriptomic analysis of physical versus metabolic contact between two wine relevant yeast species, Saccharomyces cerevisiae and Lachancea thermotolerans. The data show that these species respond to the physical presence of the other species. In S. cerevisiae, physical contact results in the upregulation of genes involved in maintaining cell wall integrity, cell wall structural components, and genes involved in the production of H2S. In L. thermotolerans, HSP stress response genes were the most significantly upregulated gene family. Both yeasts downregulated genes belonging to the FLO family, some of which play prominent roles in cellular adhesion. qPCR analysis indicates that the expression of some of these genes is regulated in a species-specific manner, suggesting that yeasts adjust gene expression to specific biotic challenges or interspecies interactions. These findings provide fundamental insights into yeast interactions and evolutionary adaptations of these species to the wine ecosystem.IMPORTANCEWithin the wine ecosystem, yeasts are the most relevant contributors to alcoholic fermentation and wine organoleptic characteristics. While some studies have described yeast-yeast interactions during alcoholic fermentation, such interactions remain ill-defined, and little is understood regarding the molecular mechanisms behind many of the phenotypes observed when two or more species are co-cultured. In particular, no study has investigated transcriptional regulation in response to physical interspecies cell-cell contact, as opposed to the generally better understood/characterized metabolic interactions", "token_count": 497, "char_count": 2362, "word_count": 311, "semantic_coherence": 1, "information_density": 0.5691, "quality_score": 0.7846, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:26.647088", "source": { "split": "train_shard_00001", "doc_id": 187 }, "chunk_id": "train_shard_00001_187_0", "global_id": 5925 }, { "text": "These data are of direct relevance to our understanding of microbial ecological interactions in general while also creating opportunities to improve ecosystem-based biotechnological applications such as wine fermentation. Furthermore, the presence of competitor species has rarely been considered an evolutionary biotic selection pressure. In this context, the data reveal novel gene functions. This, and further such analysis, is likely to significantly enlarge the genome annotation space.\n\nPhysical cell-cell contact elicits specific transcriptomic responses in wine yeast species.", "token_count": 113, "char_count": 584, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:27.063675", "source": { "split": "train_shard_00001", "doc_id": 187 }, "chunk_id": "train_shard_00001_187_1", "global_id": 5926 }, { "text": "Eukaryotic autonomously replicating sequences (ARSs) are composed of three domains, A, B, and C. Domain A is comprised of an ARS consensus sequence (ACS), while the B domain has the DNA unwinding element and the C domain is important for DNA-protein interactions. In Saccharomyces cerevisiae and Kluyveromyces lactis ARS101, the ACS is commonly composed of 11 bp, 5'-(A/T)AAA(C/T)ATAAA(A/T)-3'. This core sequence is essential for S. cerevisiae and K. lactis ARS activity. In this study, we identified ARS-containing sequences from genomic libraries of the yeast Kluyveromyces marxianus DMKU3-1042 and validated their replication activities. The identified K. marxianus DMKU3-1042 ARSs (KmARSs) have very effective replication ability but their sequences are divergent and share no common consensus. We have carried out point mutations, deletions, and base pairs substitutions within the sequences of some of the KmARSs to identify the sequence(s) that influence the replication activity. Consensus sequences same as the 11 bp ACS of S. cerevisiae and K. lactis were not found in all minimum functional KmARSs reported here except KmARS7. Moreover, partial sequences from different KmARSs are interchangeable among each other to retain the ARS activity. We have also specifically identified the essential nucleotides, which are indispensable for replication, within some of the KmARSs. Our deletions analysis revealed that only 21 bp in KmARS18 could retain the ARS activity", "token_count": 506, "char_count": 1579, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6037, "quality_score": 0.8018, "entities": { "genes": [ "ARS101", "ARS18", "DMKU3", "ARS7" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:27.707059", "source": { "split": "train_shard_00001", "doc_id": 188 }, "chunk_id": "train_shard_00001_188_0", "global_id": 5927 }, { "text": "The identified KmARSs in this study are unique compared to other yeasts' ARSs, do not share common ACS, and are interchangeable.\n\nVarious short autonomously replicating sequences from the yeast Kluyveromyces marxianus seemingly without canonical consensus.", "token_count": 77, "char_count": 270, "word_count": 35, "semantic_coherence": 1, "information_density": 0.9429, "quality_score": 0.9714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:28.081076", "source": { "split": "train_shard_00001", "doc_id": 188 }, "chunk_id": "train_shard_00001_188_1", "global_id": 5928 }, { "text": "The American mink ( Neogale vison ), a semi-aquatic Mustelidae carnivoran with broad ecological range across North America, includes several putative subspecies of conservation concern. To investigate the evolutionary history and adaptive signatures of mink subspecies, chromosome-scale genome assemblies were generated for six individuals representing three southern subspecies: N. vison evergladensis , N. vison vulgivaga , and N. vison lutensis . Genomes were assembled using Illumina short reads, scaffolded with Oxford Nanopore long reads, and aligned to the phased N. vison reference genome. Assemblies ranged from 75.9% to 97.8% completeness, with five meeting thresholds for pangenome construction. A reference-free pangenome revealed an open architecture, highlighting considerable subspecies diversity. Subspecies-specific gene enrichment reflected adaptation: N. vison evergladensis showed enrichment in traits related to reproduction and sensory function; N. vison vulgivaga in cytoskeletal remodeling and oxidative stress; and N. vison lutensis in neuronal development, synaptic plasticity and cellular stress pathways. Assessment of the mitogenomes resolved N. vison lutensis as a distinct lineage, while nuclear data supported broader subspecies divergence but lacked fine scale resolution. N. vison evergladensis showed multiple signatures of small population size, including inbreeding coefficients (F ROH ) above 0.5, and displayed consistent population decline over time via demographic inference. Our findings support evergladensis as a distinct subspecies, supported by both the mitogenome phylogeny, and significant functional differentiation. As the first pangenome for Mustelidae, this study demonstrates the power of integrating cross-platform sequencing with natural history specimens to improve the resolution on signatures of adaptation and inform conservation policy and management of threatened populations.\n\nMink by mink: stitching together signatures of subspecies adaptation through a pangenome of threatened mustelids", "token_count": 479, "char_count": 2051, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:28.732218", "source": { "split": "train_shard_00001", "doc_id": 189 }, "chunk_id": "train_shard_00001_189_0", "global_id": 5929 }, { "text": "European Ash (Fraxinus excelsior) is a keystone forest tree species, whose populations are being decimated by Ash Dieback disease (ADB). Uncovering the genetic basis of low susceptibility to this devastating disease relies on a comprehensive understanding of genetic variation present in F. excelsior. A linear reference genome from a single individual cannot contain the total sequence variability within a species, including its genic regions; a pangenome more fully captures total sequence content. In this study, we developed a F. excelsior pangenome reference using a new chromosomal-level phased linear reference genome, and de novo assemblies and long-read data from a geographically diverse set of fifty F. excelsior samples. We identified 362,965 structural variants (SVs), including 174Mb of sequence absent from the linear reference genome (22% of the linear reference size). We demonstrated that failing to explicitly link SVs with gene sequences can lead to substantial overestimation of dispensable genes (those that vary in their presence/absence between individuals) due to variability in the annotation process. Controlling for this, we identified 3,065 dispensable genes including 133 with gene ontologies associated with low disease susceptibility. We used the pangenome to analyse existing genomic data from over 1,200 individuals to identify loci associated with reduced susceptibility to ADB. This analysis revealed that different genetic backgrounds harbour distinct sets of loci associated with low susceptibility, highlighting the complexity of this trait but also the potential benefits of combining variants from different genetic backgrounds to boost efforts to ensure the future survival of F. excelsior.\n\nEuropean ash pangenome reveals widespread structural variation and a diverse genetic basis for low ash dieback susceptibility", "token_count": 405, "char_count": 1860, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5811, "quality_score": 0.7906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:29.354036", "source": { "split": "train_shard_00001", "doc_id": 190 }, "chunk_id": "train_shard_00001_190_0", "global_id": 5930 }, { "text": "Bacterial species often consist of strains with variable gene content, collectively referred to as the pangenome. Variations in the genetic makeup of strains can alter bacterial physiology and fitness. To define biologically relevant genes of a genome, genome-wide transposon mutant libraries have been used to identify genes essential for survival or virulence in a given strain. Such phenotypic studies have been conducted in four different genotypes of the human pathogen Streptococcus pyogenes, yet challenges exist in comparing results across studies conducted in different genetic backgrounds and conditions. To advance genotype to phenotype inferences across different S. pyogenes strains, we built a pangenome database of 249 S. pyogenes reference genomes. We systematically re-analyzed publicly available transposon sequencing datasets from S. pyogenes using a transposon sequencing-specific analysis pipeline, Transit. Across four genetic backgrounds and nine phenotypic conditions, 355 genes were essential for survival, corresponding to ~24% of the core genome. Clusters of Orthologous Genes (COG) categories related to coenzyme and lipid transport and growth functions were overrepresented as essential. Finally, essential operons across S. pyogenes genotypes were defined, with an increased number of essential operons detected under in vivo conditions. This study provides an extendible database to which new studies can be added, and a searchable html-based resource to direct future investigations into S. pyogenes biology.IMPORTANCEStreptococcus pyogenes is a human-adapted pathogen occupying restricted ecological niches. Understanding the essentiality of genes across different strains and experimental conditions is important to direct research questions and efforts to prevent the large burden of disease caused by S. pyogenes. To this end we systematically reanalyzed transposon sequencing studies in S. pyogenes using transposon sequencing-specific methods, integrating them into an extendible meta-analysis framework. This provides a repository of gene essentiality in S", "token_count": 527, "char_count": 2175, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:30.008455", "source": { "split": "train_shard_00001", "doc_id": 191 }, "chunk_id": "train_shard_00001_191_0", "global_id": 5931 }, { "text": "pyogenes which was used to highlight specific genes of interest and for the community to guide future phenotypic studies.\n\nPangenome evaluation of gene essentiality in Streptococcus pyogenes.", "token_count": 54, "char_count": 202, "word_count": 27, "semantic_coherence": 1, "information_density": 0.9259, "quality_score": 0.963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:30.367855", "source": { "split": "train_shard_00001", "doc_id": 191 }, "chunk_id": "train_shard_00001_191_1", "global_id": 5932 }, { "text": "The present study aims to deepen the knowledge of the microbiota, gross composition, physico-chemical and morpho-textural features, biogenic amines content and volatilome of Njeguški cheese, one of the most popular indigenous cheeses produced in Montenegro. Cheese samples were collected in duplicate from three different batches produced by three Montenegrin artisan producers. For the first time, the microbiota of Njeguški cheese was investigated using both culture-dependent techniques and metagenomic analysis. Coagulase positive staphylococci viable counts were below the detection limit of the analysis (<1 log cfu g-1). Salmonella spp., Listeria monocytogenes and staphylococcal enterotoxins were absent. However, relatively high viable counts of Enterobacteriaceae, Escherichia coli, Pseudomonadaceae and eumycetes were detected. Metataxonomic analysis revealed a core microbiome composed of Lactococcus lactis, Streptococcus thermophilus, Debaryomyces hansenii, and Kluyveromyces marxianus. Furthermore, the detection of opportunistic pathogenic yeasts such as Magnusiomyces capitatus and Wickerhamiella pararugosa, along with the variable content of biogenic amines, suggests the need for increased attention to hygienic conditions during Njeguški cheese production. Significant variability was observed in humidity (ranging from 38.37 to 45.58 %), salt content (ranging from 0.70 to 1.78 %), proteins content (ranging from 21.42 to 25.08 %), ash content (ranging from 2.97 to 4.05 %), hardness, springiness, and color among samples from different producers", "token_count": 443, "char_count": 1579, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6845, "quality_score": 0.8422, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:31.004297", "source": { "split": "train_shard_00001", "doc_id": 192 }, "chunk_id": "train_shard_00001_192_0", "global_id": 5933 }, { "text": "Gas chromatography-mass spectrometry analysis showed a well-defined and complex volatilome profile of the Njeguški cheese, with alcohols (ethanol, isoamyl alcohol, phenetyl alcol), esters and acetates (ethyl acetate, ethyl butanoate, isoamyl acetate), ketones (acetoin, 2-butanone), and acids (acetic, butanoic, hexanoic acids) being the main chemical groups involved in aroma formation. This research will provide new insights into the still poorly explored identity of Njeguški cheese, thus serving as a first baseline for future studies aimed at protecting its tradition.\n\nA comprehensive study on the autochthonous microbiota, volatilome, physico-chemical, and morpho-textural features of Montenegrin Njeguški cheese.", "token_count": 201, "char_count": 721, "word_count": 94, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:31.465937", "source": { "split": "train_shard_00001", "doc_id": 192 }, "chunk_id": "train_shard_00001_192_1", "global_id": 5934 }, { "text": "Comparative metatranscriptomics of bacterial and yeast communities of two milk kefir beverages (MKAA1 and MKAA2) obtained by fermentation with two different frozen stocks of the kefir grain CIDCA AGK1, and differing in rheological features and organic acid amounts production was carried out to figure out the relation between differences in physicochemical and rheological properties of kefir and the microbial active profile associated with each product. The dominance of lactic acid bacteria and yeast and a marginal amount of acetic acid bacteria marked the microbiome. The bacterial families Lactobacillaceae and Streptococcaceae account for almost all bacterial gene transcripts, with Lactobacillus helveticus, L. kefiranofaciens, L. gallinarum and Lactococcus lactis being most frequent in the microbiome of MKAA1 beverage, and L. kefiranofaciens, Lc. lactis and Leuconostoc mesenteroides being most prevalent in the MKAA2. Dipodascaceae and Saccharomycetaceae were the leading yeast families represented by Yarrowia lipolytica, Saccharomyces unisporus, and Kluyveromyces marxianus. The MKAA1 and MKAA2 shared >75% KEGG Ortologs (KO) in bacteria and yeast libraries. Considerable decreases in total expressed genes (KEGG Ortolog) assigned to Lactobacillus helveticus and L. gallinarum might be related to the variations in rheological features of the beverages, probably by compromising the interrelations with L. kefiranofaciens which might explain the variations in rheological features of the beverages.\n\nMetatranscriptomic Analysis of Argentinian Kefirs Varying in Apparent Viscosity", "token_count": 437, "char_count": 1597, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6019, "quality_score": 0.8009, "entities": { "genes": [ "AGK1", "MKAA2", "MKAA1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:32.094095", "source": { "split": "train_shard_00001", "doc_id": 193 }, "chunk_id": "train_shard_00001_193_0", "global_id": 5935 }, { "text": "

Background

Gardnerella is a genus of gram variable anaerobic bacteria that is commonly present in the female urogenital tract, especially during bacterial vaginosis (BV). BV is linked with increased risk of urinary tract infections (UTI) and Gardnerella has been frequently detected in urine collected directly from the bladder. Understanding the contribution of Gardnerella to urogenital pathogenesis has been complicated by its genetic heterogeneity and a shortage of data from in vivo models. Recently, a clinical isolate of Gardnerella displayed covert pathogenesis in a mouse urinary tract inoculation model, triggering urothelial exfoliation and promoting UTI by uropathogenic E. coli . Data from clinical studies suggests differential association of Gardnerella phylogenetic clades with BV or urogenital infections. In vitro data has demonstrated heterogeneity in the presence and expression of putative virulence determinants between Gardnerella strains. This study was designed to compare diverse Gardnerella strains in vivo to identify genomic variation associated with urinary tract persistence and pathogenesis.

Methods

Eighteen Gardnerella clinical isolates from each of the four main phylogenetic clades were individually inoculated transurethrally into female C57BL/6 mice. Bacteriuria was monitored by quantitative culturing of Gardnerella in urine. Pathologic features were assessed by immunofluorescent and histological staining of bladder tissues. Pan-genome phylogenetic analyses were performed on the 18 Gardnerella isolates used for mouse infections to identify accessory genes that were associated with observable in vivo phenotypes, including long and short-term persistence, urothelial exfoliation and bladder edema. Genes that were significantly associated to phenotype were then matched against a pangenome analysis of 291 publicly available Gardnerella genomes to determine the conservation of these putative colonization and virulence factors across the genus.

Results

Gardnerella strains displayed clear differences in persistence and pathogenesis in the mouse bladder that were congruent with phylogeny", "token_count": 521, "char_count": 2163, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5819, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:32.758952", "source": { "split": "train_shard_00001", "doc_id": 194 }, "chunk_id": "train_shard_00001_194_0", "global_id": 5936 }, { "text": "Clade 2 strains were more persistent in the urinary tract whereas strains from the other three clades either caused transient bacteriuria or were undetectable. Strains from clade 2 and 4 induced urothelial exfoliation while edema was triggered by strains from clades 2, 3 and 4. Pangenome analyses revealed 45 genes that were associated with in vivo persistence and pathogenicity. Among the wider 291 publicly available genomes, clade 2 strains encoded more of the genes associated with bacteriuria phenotypes compared to strains in the other three clades. Exfoliation-associated genes were present in most clade 4 strains. Clade 3 strains lack most of the in vivo -associated genes, whereas clade 1 strains were more heterogenous.

Conclusions

This study provides in vivo evidence for differential urinary tract colonization and pathogenesis by strains from different clades/species within the genus Gardnerella and identifies new putative persistence and virulence factors. Utilizing the in vivo data from tested strains, pangenome analyses predicts that clade 2 Gardnerella are the most likely to persist in the urinary tract and that clades 2 and 4 have the highest uropathogenic potential. These findings inform future targeted screening and treatment approaches aimed at limiting harmful Gardnerella urinary tract exposures\n\nStrain-level differences in Gardnerella urinary tract persistence and pathogenesis are consistent with comparative phylogenomic analyses", "token_count": 371, "char_count": 1483, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5472, "quality_score": 0.7736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:33.343574", "source": { "split": "train_shard_00001", "doc_id": 194 }, "chunk_id": "train_shard_00001_194_1", "global_id": 5937 }, { "text": "

Background

Breeding of lettuce (Lactuca sativa L.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on four Lactuca species (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines.

Results

With the super-pangenome we find substantial presence/absence variation (PAV) and copy-number variation (CNV). Functional enrichment analyses of core and variable genes show that transcriptional regulators are conserved whereas disease resistance genes are variable. PAV-genome-wide association studies (GWAS) and CNV-GWAS are largely congruent with single-nucleotide polymorphism (SNP)-GWAS. Importantly, they also identify several major novel quantitative trait loci (QTL) for resistance against Bremia lactucae in variable regions not present in the reference lettuce genome. The usability of the super-pangenome is demonstrated by identifying the likely origin of non-reference resistance loci from the wild relatives Lactuca serriola, Lactuca saligna and Lactuca virosa.

Conclusions

The super-pangenome offers a broader view on the gene repertoire of lettuce, revealing relevant loci that are not in the reference genome(s). The provided methodology and data provide a strong basis for research into PAVs, CNVs and other variation underlying important biological traits of lettuce and other crops.\n\nLactuca super-pangenome reduces bias towards reference genes in lettuce research.", "token_count": 429, "char_count": 1726, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:33.984213", "source": { "split": "train_shard_00001", "doc_id": 195 }, "chunk_id": "train_shard_00001_195_0", "global_id": 5938 }, { "text": "The aim of this paper was to examine the effect of different OTA concentrations on the parameters of oxidative stress (glutathione (GSH) and malondialdehyde (MDA) concentrations) and glucose utilization in ethanol production by wine yeasts. In addition to the above, artificial neural networks (ANN) were used to predict the effects of different OTA concentrations on the fermentation ability of yeasts and oxidative stress parameters. The obtained results indicate a negative influence of OTA (4 µg mL-1) on ethanol production after 12 h. For example, K. marxianus produced 1.320 mg mL-1 of ethanol, while in the control sample 1.603 µg mL-1 of ethanol was detected. However, after 24 h, OTA had no negative effect on ethanol production, since it was higher (7.490 and 3.845 mg mL-1) in comparison to control samples. Even low concentrations of OTA affect GSH concentrations, with the highest being detected after 12 and 24 h (up to 16.54 µM), while MDA concentrations are affected by higher OTA concentrations, with the highest being detected at 24 h (1.19 µM). The obtained results with the use of ANNs showed their potential for quantification purposes based on experimental data, while the results of ANN prediction models have shown to be useful for predictions of what outcomes different concentrations of OTA that were not part of experiment will have on the fermentation capacity and oxidative stress parameters of yeasts.\n\nA Predictive Assessment of Ochratoxin A's Effects on Oxidative Stress Parameters and the Fermentation Ability of Yeasts Using Neural Networks.", "token_count": 447, "char_count": 1626, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5403, "quality_score": 0.7702, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:34.618989", "source": { "split": "train_shard_00001", "doc_id": 196 }, "chunk_id": "train_shard_00001_196_0", "global_id": 5939 }, { "text": "

Motivation

Antimicrobial resistance is increasingly recognized as one of the most significant global health threats, with profound implications for human, animal, and environmental health. Genome analysis represents a very useful tool that provides accurate and reproducible results allowing for the advancement of knowledge regarding antimicrobial resistance diagnosis, therapeutics, surveillance, transmission, and evolution. However, due to increasing complexity of bacterial genome analysis and computational power required for genomic approaches, there is a continuous need for comprehensive, user-friendly tools for data analysis. We developed Pangenome and Genomic Analysis Suite (PeGAS), to address some of these challenges by offering an all-in-one pipeline that performs a range of analyses.

Results

PeGAS integrates key genomic analysis features of bacteria whole genome sequencing, including the prediction of antimicrobial resistance profiles, sorted by various categories of antibiotics, VF detection, and plasmid replicon assignment. The pipeline also performs pangenome analysis, multilocus sequence typing, genome assembly quality control (by reporting statistics such as GC content, contig length, the number of contigs, as well as variation from certain GC thresholds) providing a comprehensive genomic overview. PeGAS also offers the ability to restart seamlessly from any sporadic interruptions that might occur during long or resource-intensive runs.

Availability and implementation

PeGAS is available at: https://github.com/liviurotiul/PeGAS.\n\nPeGAS: a versatile bioinformatics pipeline for antimicrobial resistance, virulence and pangenome analysis.", "token_count": 377, "char_count": 1695, "word_count": 210, "semantic_coherence": 1, "information_density": 0.7095, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:35.214448", "source": { "split": "train_shard_00001", "doc_id": 197 }, "chunk_id": "train_shard_00001_197_0", "global_id": 5940 }, { "text": "Abstract

The roots of three Cynanchum species—Cynanchum wilfordii (CW), C. auriculatum (CA), and C. rostellatum (CR)—are widely used for medicinal purposes in Northeast Asia. Unlike CW and CA, CR lacks storage roots and features long, slender roots. To explore these species' genomes and support breeding efforts, we assembled nearly complete pseudo-haploid reference genomes with centromere and telomere repeats for all three, along with 28 haplotype-resolved genomes from nine CW, three CA, and two CR accessions. Graph-based pangenome integration and association scans identified key genes involved in root diversity in CW. Additionally, the Cynanchum pangenome and expression data indicated lower abscisic acid (ABA) biosynthesis in CR due to structural variation in ABSCISIC ALDEHYDE OXIDASE 3. ABA deficiency hampers stomatal control, while extremely long roots likely adapt to water loss. Our findings offer insights into root development and aid genomics-based breeding of these valuable root crops.

\n\nGraph-based Pangenome Analysis Reveals the Genetic Control of Root Development in Cynanchum Species", "token_count": 295, "char_count": 1131, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7389, "quality_score": 0.8694, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:35.767947", "source": { "split": "train_shard_00001", "doc_id": 198 }, "chunk_id": "train_shard_00001_198_0", "global_id": 5941 }, { "text": "Bioethanol has been considered as an excellent alternative to fossil fuels since it importantly contributes to the reduced consumption of the crude oil and to the alleviation of environmental pollution [1]. Up to now, the baker yeast Saccharomyces cerevisiae is the most common eukaryotic microorganism used in ethanol production. The inability of S. cerevisiae to grow on pentoses, however, hinders its effective growth on plant biomass hydrolysates, which contain large amounts of C5 and C12 sugars. The industrial-scale bioprocessing requires high temperature bioreactors, diverse carbon sources, and the high titer production of volatile compounds [2]. These criteria indicate that the search for alternative microbes possessing useful traits that meet the required standards of bioethanol production is necessary. Compared to other yeasts, Kluyveromyces marxianus has several advantages over the others, e.g. it could grow on a broad spectrum of substrates (C5, C6 and C12 sugars) [3], tolerate to high temperature, toxin [4,5] and a wide range of pH values [6], and produce volatile short-chain ester [2]. K. marxianus also shows a high ethanol production rate at high temperature and is a Crabtree-negative species [7]. These attributes make K. marxianus a promise as an industrial host for the biosynthesis of biofuels and other valuable chemicals.\n\nKluyveromyces marxianus: Current State of Omics Studies, Strain Improvement Strategy and Potential Industrial Implementation", "token_count": 368, "char_count": 1482, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:36.350694", "source": { "split": "train_shard_00001", "doc_id": 199 }, "chunk_id": "train_shard_00001_199_0", "global_id": 5942 }, { "text": "

Introduction

Mycobacterium orygis, a member of MTBC has been identified in higher numbers in the recent years from animals of South Asia. Comparative genomics of this important zoonotic pathogen is not available which can provide data on the molecular difference between other MTBC members. Hence, the present study was carried out to isolate, whole genome sequence M. orygis from different animal species (cattle, buffalo and deer) and to identify molecular marker for the differentiation of M. orygis from other MTBC members.

Methods

Isolation and whole genome sequencing of M. orygis was carried out for 9 samples (4 cattle, 4 deer and 1 buffalo) died due to tuberculosis. Comparative genomics employing 53 genomes (44 from database and 9 newly sequenced) was performed to identify SNPs, spoligotype, pangenome structure, and region of difference.

Results

M. orygis was isolated from water buffalo and sambar deer which is the first of its kind report worldwide. Comparative pangenomics of all M. orygis strains worldwide (n= 53) showed a closed pangenome structure which is also reported for the first time. Pairwise SNP between TANUVAS_2, TANUVAS_4, TANUVAS_5, TANUVAS_7 and NIRTAH144 was less than 15 indicating that the same M. orygis strain may be the cause for infection. Region of difference prediction showed absence of RD7, RD8, RD9, RD10, RD12, RD301, RD315 in all the M. orygis analyzed. SNPs in virulence gene, PE35 was found to be unique to M. orygis which can be used as marker for identification.

Conclusion

The present study is yet another supportive evidence that M", "token_count": 509, "char_count": 1680, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8082, "entities": { "genes": [ "RD315", "PE35", "RD8", "RD12", "NIRTAH144", "RD301", "RD10", "RD9", "RD7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:37.010693", "source": { "split": "train_shard_00001", "doc_id": 200 }, "chunk_id": "train_shard_00001_200_0", "global_id": 5943 }, { "text": "orygis is more prevalent among animals in South Asia and the zoonotic potential of this organism needs to be evaluated.\n\nWhole genome sequencing and comparative genomics of Mycobacterium orygis isolated from different animal hosts to identify specific diagnostic markers.", "token_count": 70, "char_count": 282, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8974, "quality_score": 0.9487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:37.409828", "source": { "split": "train_shard_00001", "doc_id": 200 }, "chunk_id": "train_shard_00001_200_1", "global_id": 5944 }, { "text": "

A bstract

Bacterial secondary metabolites are a major source of therapeutics and play key roles in microbial ecology. These compounds are encoded by biosynthetic gene clusters (BGCs), which show extensive genetic diversity across microbial genomes. While recent advances have enabled clustering of BGCs into gene cluster families (GCFs), there is still a lack of frameworks for systematically analysing their internal diversity at a population scale. Here, we introduce PanBGC , a pangenome-inspired framework that treats each GCF as a population of related BGCs. This enables classification of biosynthetic genes into core, accessory, and unique categories and provides openness metrics to quantify compositional diversity. Applied to over 250 000 BGCs from more than 35 000 genomes, PanBGC maps biosynthetic diversity of more than 80 000 GCFs. To facilitate exploration, we present PanBGC-DB ( https://panbgc-db.cs.uni-tuebingen.de ), an interactive web platform for comparative BGC analysis. PanBGC-DB offers gene- and domain-level visualizations, phylogenetic tools, openness metrics, and custom query integration. Together, PanBGC and PanBGC-DB provide a scalable framework for exploring biosynthetic gene clusters at population resolution and for contextualizing newly discovered BGCs within the global landscape of secondary metabolism.\n\nPanBGC: A Pangenome-inspired framework for comparative analysis of biosynthetic gene clusters", "token_count": 372, "char_count": 1449, "word_count": 197, "semantic_coherence": 1, "information_density": 0.7005, "quality_score": 0.8503, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:38.427539", "source": { "split": "train_shard_00001", "doc_id": 201 }, "chunk_id": "train_shard_00001_201_0", "global_id": 5945 }, { "text": "Huanglongbing (HLB) is a bacterial disease that affects citrus trees and is considered the most severe citrus disease in the world. The three HLB-associated \"Ca. Liberibacter\" species harbor prophage regions which have been described to play critical roles in their evolution and biology. In this study, using infected insect vectors, we assembled and characterized the accessory genome of the first circular de novo \"Candidatus Liberibacter asiaticus\" (CLas) assembly (V1R1) from Réunion, one of the sparse areas worldwide hosting CLas and \"Ca. Liberibacter africanus\" (CLaf). This 1.272 Mb-long whole-genome harbored 1,129 coding sequences and two complete prophages, including a 37,934 bp-long Type 1 prophage, frequently present in CLas genomes, and a 40,501 bp-long undescribed CLas prophage designated as P-V1R1-5. Comparative genomic approaches suggested that P-V1R1-5 has all the genetic elements to produce new viral particles and revealed that it likely belongs to a new CLas Type 5 prophage. While P-V1R1-5-like prophages had been identified previously in CLaf genomes, our study demonstrates the first lysogenic conversion of these prophages in CLas, suggesting a positive selection of prophage-like sequences among HLB-associated \"Ca. Liberibacter\" species. Using PCR amplifications targeting P-V1R1-5, we also showed that 85.7% of the tested CLas strains from Réunion and all tested CLaf strains from Madagascar and Réunion harbored a Type 5-like prophage", "token_count": 443, "char_count": 1504, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:39.119355", "source": { "split": "train_shard_00001", "doc_id": 202 }, "chunk_id": "train_shard_00001_202_0", "global_id": 5946 }, { "text": "The identification of CLas Type 5-like prophages not only expanded our knowledge of CLas genomic diversity in Réunion but also provided new insights into the role of horizontally transferred elements in the evolution of the sympatric HLB-associated bacteria.IMPORTANCEHuanglongbing (HLB) is the most severe citrus disease worldwide. The disease is associated with three \"Candidatus Liberibacter\" species harboring prophage regions that have been described to play critical roles in their biology. In this study, using infected insect vectors, we assembled and characterized the accessory genome of the first circular de novo \"Ca. Liberibacter asiaticus\" (CLas) assembly from Réunion, one of the very few areas in the world where both of CLas and \"Ca. Liberibacter africanus\" (CLaf) coexist. Comparative genomic approaches demonstrated that this genome harbored two complete prophages, including a new CLas Type 5 prophage that was previously identified in CLaf but was reported for the first time in a CLas strain. This first evidence of shared prophage-like sequences among HLB-associated species expands our knowledge of CLas genomic diversity but also provides new insights into the role of the accessory genome in the evolution of these bacteria.\n\nGenomic footprint of a shared Type 5 prophage in <i>\"Candidatus</i> Liberibacter asiaticus\" and \"<i>Candidatus</i> Liberibacter africanus,\" two destructive bacterial pathogens of citrus Huanglongbing.", "token_count": 395, "char_count": 1504, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:39.735821", "source": { "split": "train_shard_00001", "doc_id": 202 }, "chunk_id": "train_shard_00001_202_1", "global_id": 5947 }, { "text": "Public health genomic surveillance systems typically measure genome relatedness and infer molecular epidemiological relationships using chromosomal loci alone – an approximation of vertical evolution, or homology-by-descent. The accessory genome, composed of plasmids and other mobile genetic elements, reflects horizontal gene transfer and serves as an important mechanism of bacterial evolution, enabling rapid adaptation. Measuring homology in the accessory genome – homology-by-admixture – could offer important molecular epidemiological information for public health application. We applied Jaccard Index and a novel genome length distance metric to compute pangenome relatedness for the globally-important pathogen Salmonella enterica serotype Typhi (Typhi), and graphically express both homology-by-descent and homology-by-admixture in a reticulate network. Jaccard Index Network Analysis revealed structure in the Typhi pangenome that can be harnessed to enhance discriminatory power for surveillance, track antimicrobial resistance, and refine our understanding of homology for outbreak management and prevention. This offers a more intricate, multidimensional framework for understanding pathogen evolution.

Significance Statement

Bacterial relatedness is often measured and visualized using chromosomal comparison and phylogenetic trees. While valuable, this approach captures only the vertical evolutionary dimension and excludes genetic material acquired or lost through horizontal gene transfer. We present an approach for measuring and visualizing bacterial relatedness using all core and accessory genetic material and discuss the interpretation of resulting reticulate networks of bacterial genomes. In application to Salmonella Typhi, Jaccard Index Network Analysis revealed structure in populations of this pathogen that may be harnessed for public health applications. This approach captures both vertical and horizontal evolutionary dimensions, offering an intricate genetic framework for exploring pathogen evolution.\n\nHarnessing the pangenome for genomic surveillance:Salmonella entericaserotype Typhi as a paradigm", "token_count": 445, "char_count": 2154, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5688, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:40.370393", "source": { "split": "train_shard_00001", "doc_id": 203 }, "chunk_id": "train_shard_00001_203_0", "global_id": 5948 }, { "text": "Staphylococcus aureus causes both hospital- and community-acquired infections in humans worldwide. Due to the high incidence of infection, S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole-genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of average nucleotide identity revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10%-95% of genomes) could be divided into those closely linked to strain background (\"strain-concentrated\") and those highly variable within strains (\"strain-diffuse\"). Non-core genes had different patterns of chromosome location. Notably, strain-diffuse genes were associated with prophages; strain-concentrated genes were associated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic resistance genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core, and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.

Importance

We analyzed the genomic diversity of Staphylococcus aureus, a globally prevalent bacterial species that causes serious infections in humans. Our goal was to build a genetic picture of the different strains of S. aureus and which genes may be associated with them. We reprocessed >84,000 genomes and subsampled to remove redundancy. We found that individual samples sharing >99.5% of their genome could be grouped into strains", "token_count": 510, "char_count": 1993, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:41.029398", "source": { "split": "train_shard_00001", "doc_id": 204 }, "chunk_id": "train_shard_00001_204_0", "global_id": 5949 }, { "text": "We also showed that a portion of genes that are present in intermediate frequency in the species are strongly associated with some strains but completely absent from others, suggesting a role in strain specificity. This work lays the foundation for understanding individual gene histories of the S. aureus species and also outlines strategies for processing large bacterial genomic data sets.\n\nAverage nucleotide identity-based Staphylococcus aureus strain grouping allows identification of strain-specific genes in the pangenome.", "token_count": 120, "char_count": 544, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7733, "quality_score": 0.8867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:41.415135", "source": { "split": "train_shard_00001", "doc_id": 204 }, "chunk_id": "train_shard_00001_204_1", "global_id": 5950 }, { "text": "We investigated the phylogeny of biofilm forming (BF) and nonbiofilm forming (NBF) Escherichia coli (n = 114) from a beef processing environment as well as genetic elements in their BF and persistence via a comparative genomic analysis. Phylogroup B1 made up the largest proportion of both the BF (73.8%) and NBF (50.9%) groups. E. coli from all of the sources that were examined had mixed phylogroups, except for those that were recovered from equipment after cleaning, which were exclusively from phylogroup B1. Both the core genome and gene content trees showed a tree-wide spread of BF strains, with clusters, including both BF and NBF strains. Genome-wide association studies (GWAS) via Scoary or Pyseer did not find any genes or mutations that were overrepresented in the BF group. A retrospective analysis of phenotypes found a significant correlation (P < 0.05) between BF ability and curli production, cellulose synthesis, and/or mobility. However, the BF group also included strains that were negative for curli and cellulose and/or missing encoding genes for the two traits. All curli and cellulose encoding genes were present in most genomes, regardless of their BF status. The degree of motility was correlated with both curli and cellulose production, and 80 common genes were overrepresented in all three of the trait-positive groups. A PTS enzyme II, a subsidiary gluconate catabolism pathway, and an iron-dicitrate transport system were more abundant in the persisting E. coli group. These findings suggest gene function redundancy in E. coli for biofilm formation as well as additional substrate utilization and iron acquisition in its persistence. IMPORTANCE The persistence of potentially hazardous bacteria is a major challenge for meat processing environments, which are conducive for biofilm formation. Marker genes/phenotypes are commonly used to differentiate biofilm forming E. coli strains from their nonbiofilm forming counterparts. We took a comparative genomic analysis approach to analyze E", "token_count": 521, "char_count": 2042, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:42.048490", "source": { "split": "train_shard_00001", "doc_id": 205 }, "chunk_id": "train_shard_00001_205_0", "global_id": 5951 }, { "text": "coli strains that were from the same environment but were differentiated by their biofilm forming ability. A diversification of the genes involved in the biofilm formation of E. coli was observed. Even though there is a correlation on the population level between biofilm formation and the expression of curli and cellulose, uncertainties exist on the individual strain level. Novel substrate utilization and iron acquisition could contribute to the persistence of E. coli. These findings not only advance our understanding of the ecology of E. coli with respect to its persistence but also show that a marker gene/phenotype driven approach for the biofilm control of E. coli may not be prudent.\n\nComparative Genomic Analyses of Escherichia coli from a Meat Processing Environment in Relation to Their Biofilm Formation and Persistence.", "token_count": 187, "char_count": 836, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:42.494385", "source": { "split": "train_shard_00001", "doc_id": 205 }, "chunk_id": "train_shard_00001_205_1", "global_id": 5952 }, { "text": "Tomato pomace (TP) is generated as a natural by product in a significant amount in the tomato processing industry, and it is a good source of lignocelluloses to produce some high-value products from fermentable sugars (FS). The present study was performed to produce FS by using either ultrasound-assisted dilute acid (UADA) or heat-treated dilute acid (HTDA) pretreatments of TP followed by enzymatic hydrolysis (EH). When HTDA and UADA were compared in terms of FS (g/L) concentration, HTDA pretreatment generally produced more FS content than UADA. The optimum conditions for HTDA pretreatment were the application of 2.5% H₂SO₄, 10% (w/v) solution of TP, and heating at 121 °C for 6 min, which yielded 31 g/L FS concentration. Beside the optimized conditions for EH of HTDA, pretreated TP required 1.5% of enzyme concentration and 6 h of hydrolysis time. In conclusion, the most abundant volatile organic compounds (VOCs) produced by K. marxianus in final tomato pomace hydrolysate (TPH) were isoamyl alcohol, phenyl ethyl alcohol, ethyl acetate and phenyl ethyl acetate in a 5-L bioreactor. Nine descriptive sensory terms were developed to characterize fermented TPH. The rose and sweet floral aromas were defined as aroma characteristics for TPH fermented by K. marxianus.\n\nOptimization of pretreatment and enzymatic hydrolysis conditions of tomato pomace for production of alcohols and esters by Kluyveromyces marxianus", "token_count": 416, "char_count": 1426, "word_count": 218, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:43.117755", "source": { "split": "train_shard_00001", "doc_id": 206 }, "chunk_id": "train_shard_00001_206_0", "global_id": 5953 }, { "text": "

Background

Thermotolerance is a highly desirable trait of microbial cell factories and has been the focus of extensive research. Yeast usually tolerate only a narrow temperature range and just two species, Kluyveromyces marxianus and Ogataea polymorpha have been described to grow at reasonable rates above 40 °C. However, the complex mechanisms of thermotolerance in yeast impede its full comprehension and the rare physiological data at elevated temperatures has so far not been matched with corresponding metabolic analyses.

Results

To elaborate on the metabolic network response to increased fermentation temperatures of up to 49 °C, comprehensive physiological datasets of several Kluyveromyces and Ogataea strains were generated and used for 13C-metabolic flux analyses. While the maximum growth temperature was very similar in all investigated strains, the metabolic network response to elevated temperatures was not conserved among the different species. In fact, metabolic flux distributions were remarkably irresponsive to increasing temperatures in O. polymorpha, while the K. marxianus strains exhibited extensive flux rerouting at elevated temperatures.

Conclusions

While a clear mechanism of thermotolerance is not deducible from the fluxome level alone, the generated data can be valued as a knowledge repository for using temperature to modulate the metabolic activity towards engineering goals.\n\nElevated temperatures do not trigger a conserved metabolic network response among thermotolerant yeasts.", "token_count": 366, "char_count": 1550, "word_count": 207, "semantic_coherence": 1, "information_density": 0.628, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:43.701467", "source": { "split": "train_shard_00001", "doc_id": 207 }, "chunk_id": "train_shard_00001_207_0", "global_id": 5954 }, { "text": "Unravelling the genetic basis of the remarkable phenotypic diversity observed in natural populations remains a central challenge in biology1-4. Despite major advances5-19, no species has yet been characterized with a truly comprehensive atlas of genetic variation. Here we present an extensive genomic and phenotypic resource for the yeast Saccharomyces cerevisiae based on near telomere-to-telomere assemblies of 1,086 natural isolates. Leveraging these high-contiguity assemblies, we generated a highly complete species-wide structural variant atlas, gene-based pangenome and graph pangenome. By incorporating the full spectrum of genetic variation captured across the species, we conducted genome-wide association studies across 8,391 molecular and organismal traits19-22. The inclusion of structural variants and small insertion-deletion mutations improved heritability estimates by an average of 14.3% compared with analyses based only on single-nucleotide polymorphisms. Structural variants were more frequently associated with traits and exhibited greater pleiotropy than other variant types. Notably, the genetic architecture of molecular and organismal traits differed markedly. Together, this work provides a unique dataset that illuminates how diverse forms of genetic variation shape phenotypic diversity and lays the groundwork for integrative, genome-scale studies in other eukaryotic systems.\n\nFrom genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes.", "token_count": 367, "char_count": 1520, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6979, "quality_score": 0.849, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:44.285092", "source": { "split": "train_shard_00001", "doc_id": 208 }, "chunk_id": "train_shard_00001_208_0", "global_id": 5955 }, { "text": "Two-component systems are key signal-transduction systems that enable bacteria to respond to a wide variety of environmental stimuli. The human pathogen, Streptococcus pneumoniae (pneumococcus) encodes 13 two-component systems and a single orphan response regulator, most of which are significant for pneumococcal pathogenicity. Mapping the regulatory networks governed by these systems is key to understand pneumococcal host adaptation. Here we employ a novel bioinformatic approach to predict the regulons of each two-component system based on publicly available whole-genome sequencing data. By employing pangenome-wide association studies (panGWAS) to predict genotype-genotype associations for each two-component system, we predicted regulon genes of 11 of the pneumococcal two-component systems. Through validation via next-generation RNA-sequencing on response regulator overexpression mutants, several top candidate genes predicted by the panGWAS analysis were confirmed as regulon genes. The present study presents novel details on multiple pneumococcal two-component systems, including an expansion of regulons, identification of candidate response regulator binding motifs, and identification of candidate response regulator-regulated small non-coding RNAs. We also demonstrate a use for panGWAS as a complementary tool in target gene identification via identification of genotype-to-genotype links. Expanding our knowledge on two-component systems in pathogens is crucial to understanding how these bacteria sense and respond to their host environment, which could prove useful in future drug development.\n\nA comprehensive analysis of pneumococcal two-component system regulatory networks.", "token_count": 374, "char_count": 1708, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:44.865619", "source": { "split": "train_shard_00001", "doc_id": 209 }, "chunk_id": "train_shard_00001_209_0", "global_id": 5956 }, { "text": "

Background

Transposable elements are major components of plant genomes and major drivers of plant genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization, speciation, domestication, and crop improvement. Here, we implement genome and pangenome analyses to study in detail the dynamics of LTR-retrotransposons during the cotton evolution.

Results

We show that some LTR-retrotransposon lineages amplified in tetraploid cotton compared to their diploid progenitors, whereas others stayed stable or amplified but were removed through solo-LTR formation. Using species-level pangenomes we show that only a few lineages (CRM, Tekay, Ivana, and Tork) remained active after polyploidization and are still transposing. Tekay and CRM elements have re-shaped the centromeric and pericentromeric regions of tetraploid cottons in a subgenome specific manner, through new insertions but also selective eliminations through solo-LTR formation. On the other hand, Ivana and Tork have actively inserted within or close to genes affecting their expression. Finally, population-level analyses using the two pangenomes and data from 283 and 223 varieties of G. hirsutum and G. barbadense reveal changes in Transposon Insertion Polymorphism frequencies accompanying domestication and improvement of both species, suggesting the possibility of selection on linked regions.

Conclusions

Our findings reveal that LTR-retrotransposon lineages followed differential dynamics during cotton evolution, displaying differences among species and the two coresident genomes of allopolyploid cotton. A handful of the LTR-retrotransposon lineages that expanded after polyploidization helped shape the genomes of both G. hirsutum and G. barbadense, impacting their centromere and pericentromeric regions as well as protein-coding genes.\n\nDifferential LTR-retrotransposon dynamics across polyploidization, speciation, domestication, and improvement of cotton (Gossypium).", "token_count": 499, "char_count": 2003, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:45.516363", "source": { "split": "train_shard_00001", "doc_id": 210 }, "chunk_id": "train_shard_00001_210_0", "global_id": 5957 }, { "text": "Diarrhoea is a serious cause of mortality worldwide that can lead to dehydration, gut barrier function impairment, nutrient malabsorption, and alterations of the gut microbiota (dysbiosis). Current solutions for its management, such as oral rehydration salts (ORS), inhibitors of the gut motility, antibiotics, and living probiotics only partially counteract the mechanisms of the disease and do not provide a full coverage of the problem. Potential risks of the use of living probiotic strains, particularly in immunocompromised patients, can be eliminated with the use of tyndallized (heat-killed) postbiotic bacteria and yeast. ABB C22® is a postbiotic combination of three tyndallized yeasts, namely Saccharomyces boulardii, Saccharomyces cerevisiae, and Kluyveromyces marxianus. To assess the action of the postbiotic combination on diarrhoea, immune and gut epithelial cell signaling assays, gut barrier formation assay and rotavirus gene expression assay were performed. ABB C22® showed a strong anti-inflammatory effect, an induction of the build-up of the gut epithelium, and a degree of protection against rotavirus infection. These experimental studies support the use of the postbiotic ABB C22® as a solution for the management of diarrhoea and gastrointestinal conditions, alone or in combination with existing but incomplete treatments.\n\nSynergistic effect of postbiotic yeast ABB C22® on gut in-flammation, barrier function and protection from Rotavirus in-fection", "token_count": 378, "char_count": 1479, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:46.097550", "source": { "split": "train_shard_00001", "doc_id": 211 }, "chunk_id": "train_shard_00001_211_0", "global_id": 5958 }, { "text": "Structural variants (SVs) represent a significant yet underexplored component of plant genome diversity. Analyzing SV dynamics is essential for understanding their contributions to phenotypic variation and their influence on genome evolution. Here, we present a graph-based pangenome for cucumber, constructed from 39 reference-level genome assemblies. The pangenome captures 171,892 high-confidence SVs and enables genotyping of these SVs across 443 cucumber accessions, representing diverse geographic origins and spanning wild progenitors, landraces, and modern cultivars. Our analyses reveal that during cucumber domestication, a substantial portion of mildly deleterious SNPs are retained, whereas SVs are consistently purged, highlighting their potentially highly deleterious nature. During the geographic expansion of cucumber, a reduction in SV burden and a younger age of SVs than SNPs were observed, suggesting stronger purifying selection acting on SVs. Additionally, notable gene flow from wild population to African and European populations was detected, resulting in an increased SV burden, potentially due to hitchhiking effects. Importantly, incorporating SV burden into genomic prediction models improved the prediction accuracy for several agronomically important traits. This study illuminates the dynamics of SVs during cucumber domestication and improvement, highlights the complex interplay between SVs and selection pressures, and underscores the extensive implications of SVs for future cucumber breeding.\n\nGraph pangenome reveals structural variation dynamics during cucumber breeding", "token_count": 351, "char_count": 1609, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:46.673337", "source": { "split": "train_shard_00001", "doc_id": 212 }, "chunk_id": "train_shard_00001_212_0", "global_id": 5959 }, { "text": "Diarrhoea is a serious cause of mortality worldwide that can lead to dehydration, gut barrier function impairment, nutrient malabsorption, and alterations of the gut microbiota (dysbiosis). Current solutions for its management, such as oral rehydration salts (ORS), inhibitors of the gut motility, antibiotics, and living probiotics only partially counteract the mechanisms of the disease and do not provide a full coverage of the problem. Potential risks of the use of living probiotic strains, particularly in immunocompromised patients, can be eliminated with the use of tyndallized (heat-killed) postbiotic bacteria and yeast. ABB C22® is a postbiotic combination of three tyndallized yeasts, namely Saccharomyces boulardii, Saccharomyces cerevisiae, and Kluyveromyces marxianus. To assess the action of the postbiotic combination on diarrhoea, immune and gut epithelial cell signaling assays, gut barrier formation assay and rotavirus gene expression assay were performed. ABB C22® showed a strong anti-inflammatory effect, an induction of the build-up of the gut epithelium, and a degree of protection against rotavirus infection. These experimental studies support the use of the postbiotic ABB C22® as a solution for the management of diarrhoea and gastrointestinal conditions, alone or in combination with existing but incomplete treatments.\n\nSynergistic Effect of Postbiotic Yeast ABB C22® on Gut Inflammation, Barrier Function and Protection from Rotavirus Infection", "token_count": 378, "char_count": 1477, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:47.258590", "source": { "split": "train_shard_00001", "doc_id": 213 }, "chunk_id": "train_shard_00001_213_0", "global_id": 5960 }, { "text": "Streptococcus suis serotype 2 (SS2) is a Gram-positive bacterium. It is a common and significant pathogen in pigs and a common cause of zoonotic meningitis in humans. It can lead to sepsis, endocarditis, arthritis, and pneumonia. If not diagnosed and treated promptly, it has a high mortality rate. The pan-genome of SS2 is open, and with an increasing number of genes, the core genome and accessory genome may exhibit more pronounced differences. Due to the diversity of SS2, the genes related to its virulence and resistance are still unclear. In this study, a strain of SS2 was isolated from a pig farm in Sichuan Province, China, and subjected to whole-genome sequencing and characterization. Subsequently, we conducted a Pan-Genome-Wide Association Study (Pan-GWAS) on 230 strains of SS2. Our analysis indicates that the core genome is composed of 1,458 genes related to the basic life processes of the bacterium. The accessory genome, consisting of 4,337 genes, is highly variable and a major contributor to the genetic diversity of SS2. Furthermore, we identified important virulence and resistance genes in SS2 through pan-GWAS. The virulence genes of SS2 are mainly associated with bacterial adhesion. In addition, resistance genes in the core genome may confer natural resistance of SS2 to fluoroquinolone and glycopeptide antibiotics. This study lays the foundation for further research on the virulence and resistance of SS2, providing potential new drug and vaccine targets against SS2.\n\nPan-genome analysis of Streptococcus suis serotype 2 highlights genes associated with virulence and antibiotic resistance.", "token_count": 424, "char_count": 1637, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5565, "quality_score": 0.7782, "entities": { "genes": [ "SS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:47.879547", "source": { "split": "train_shard_00001", "doc_id": 214 }, "chunk_id": "train_shard_00001_214_0", "global_id": 5961 }, { "text": "

Background

Pneumococcal genomes are highly dynamic with varying core genome sizes. The genotype classification system, Global Pneumococcal Sequence Clusters, identified patterns within genotype and antibiotic resistance. Few genotypes like GPSC10 are frequently associated with antimicrobial resistance and high rates of non-vaccine serotypes.

Objective

To identify and annotate the differences in the core genomes of major GPSC in India, and construct and analyse the Indian Pneumococcal Pangenome (IPPG).

Methods

Using existing dataset from the Global Pneumococcal Sequencing Project, 618 strains were included. The most frequent GPSCs: GPSC1, GOSC2, GPSC8, GPSC9 and GPSC10 were analyzed separately. Pangenomes were constructed using Panaroo with tuning the family threshold parameter. Differences in protein clusters were identified using Orthovenn3 webserver. Functional annotations were performed by eggNOG, Uniprot and STRING database searches.

Results

The IPPG core genome size (1615 genes) was similar to those reported previously, with similar distribution of metabolic categories across the five GPSC types. The GPSC10 (1619 genes) and GPSC1 (1909 genes) had the lowest and highest core genome sizes respectively, and these core genomes possessed genes encoding for macrolide and tetracycline resistance. Virulence genes ply, psaA, pce (cbpE), pavA, nanB, lytA, and hysA are detected among all the core genomes.

Conclusions

There is a genotype specific variation within the core genomes of major GPSCs in India. The presence of antibiotic resistance genes among GPSC1 and GPSC10 core genomes explain widespread drug resistance due to these genotypes. The core virulence genes identified among all the genotypes indicate conserved pathogenesis mechanisms, and can be targets for vaccine development or therapy.\n\nComparative pangenome analysis of major pneumococcal genotypes from India", "token_count": 508, "char_count": 1940, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [ "GPSC10", "GPSC8", "GPSC1", "GOSC2", "GPSC9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:48.545439", "source": { "split": "train_shard_00001", "doc_id": 215 }, "chunk_id": "train_shard_00001_215_0", "global_id": 5962 }, { "text": "The famous model organism Saccharomyces cerevisiae is widely present in a variety of natural and human-associated habitats. Despite extensive studies of this organism, the metabolic mechanisms driving its adaptation to varying niches remain elusive. We here gathered genomic resources from 1,807 S. cerevisiae strains and assembled them into a high-quality pangenome, facilitating the comprehensive characterization of genetic diversity across isolates. Utilizing the pangenome, 1,807 strain-specific genome-scale metabolic models (ssGEMs) were generated, which performed well in quantitative predictions of cellular phenotypes, thus helping to examine the metabolic disparities among all S. cerevisiae strains. Integrative analyses of fluxomics and transcriptomics with ssGEMs showcased ubiquitous transcriptional regulation of metabolic flux in specific pathways (i.e., amino acid synthesis) at a population level. Additionally, the gene/reaction inactivation analysis through the ssGEMs refined by transcriptomics showed that S. cerevisiae strains from various ecological niches had undergone reductive evolution at both the genomic and metabolic network levels when compared to wild isolates. Finally, the compiled analysis of the pangenome, transcriptome, and metabolic fluxome revealed remarkable metabolic differences among S. cerevisiae strains originating from distinct oxygen-limited niches, including human gut and cheese environments, and identified convergent metabolic evolution, such as downregulation of oxidative phosphorylation pathways. Together, these results illustrate how yeast adapts to distinct niches modulated by genomic and metabolic reprogramming, and provide computational resources for translating yeast genotype to fitness in future studies.\n\nYeast adapts to diverse ecological niches driven by genomics and metabolic reprogramming.", "token_count": 465, "char_count": 1899, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:49.187177", "source": { "split": "train_shard_00001", "doc_id": 216 }, "chunk_id": "train_shard_00001_216_0", "global_id": 5963 }, { "text": "

Background

A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multicopy gene families, which are recognizable by synteny conservation, and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes.

Results

Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, allowing robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables.

Conclusions

Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.\n\nComparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses.", "token_count": 437, "char_count": 2030, "word_count": 255, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:49.835952", "source": { "split": "train_shard_00001", "doc_id": 217 }, "chunk_id": "train_shard_00001_217_0", "global_id": 5964 }, { "text": "

Background

Mastitis poses a significant threat to dairy industry and public health due to the emergence of multidrug-resistant (MDR) Escherichia coli . This study provides a genomic characterization of two MDR E. coli strains, MBBL4 and MBBL5, from bovine mastitis in Bangladesh, highlighting their evolutionary relationships, resistome, and virulome.

Methods

Species-level identification of MBBL4 and MBBL5 was confirmed using biochemical assays, VITEK-2 system, and 16S rRNA gene sequencing. Antimicrobial susceptibility profiling was conducted to determine their resistance patterns. Whole genome sequencing (WGS) and comprehensive genomic analysis were performed for phylogenetic, comparative genomics, mobile genetic elements (MGEs), antimicrobial resistance genes (ARGs), and virulence factor genes (VFGs) analyses.

Results

Both isolates exhibited extensive MDR patterns, showing resistance to ten antibiotics. Phylogenetic and ANI analyses showed that MBBL4 clustered with mastitis-associated and human bacteremia strains of E. coli , while MBBL5 was closely related to wildlife-associated strains, reflecting divergent evolutionary lineages. Pangenome analysis revealed an open pangenome structure, indicating high genetic diversity, with MBBL4 harboring 21 unique genes and MBBL5 possessing nine unique genes. Both genomes harbored numerous ARGs spanning over 11 antibiotic classes, and VFGs, predominantly associated with adherence and secretion systems, underscoring their extensive resistome, virulome, and adaptive potentials. Abundant MGEs (plasmids, prophages, insertion sequence elements and genomic islands) further underscored the role of horizontal gene transfer in driving resistance and virulence in these strains.

Conclusion

This study highlights the zoonotic potential and adaptive capacity of MDR E. coli from bovine mastitis in Bangladesh driven by resistome, virulome, and mobile genetic elements", "token_count": 519, "char_count": 1967, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6773, "quality_score": 0.8386, "entities": { "genes": [ "MBBL5", "MBBL4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:50.519848", "source": { "split": "train_shard_00001", "doc_id": 218 }, "chunk_id": "train_shard_00001_218_0", "global_id": 5965 }, { "text": "These findings highlight the urgent need for One Health-based genomic surveillance to mitigate MDR E. coli transmission from dairy farms to humans and the environment.\n\nGenomic insights into multidrug resistant Escherichia coli from bovine mastitis in Bangladesh", "token_count": 70, "char_count": 272, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8919, "quality_score": 0.9459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:50.932431", "source": { "split": "train_shard_00001", "doc_id": 218 }, "chunk_id": "train_shard_00001_218_1", "global_id": 5966 }, { "text": "

Background

Despite widespread implementation of exome and genome sequencing, a substantial proportion of rare disease patients remain undiagnosed due to inherent limitations in detecting structural, repetitive, and regulatory variants.

Methods

We applied long-read sequencing (LRS) to 40 individuals from 33 previously undiagnosed Korean families. De novo assemblies were integrated into a graph-based pangenome workflow, enabling sensitive detection of single-nucleotide, structural, and tandem-repeat variants and direct profiling of CpG methylation.

Results

Pathogenic or likely pathogenic variants were identified in 9 (27.3%) families that had remained unsolved despite prior short-read sequencing. The discoveries comprised deep intronic splice-altering SNVs, non-coding regulatory deletions, complex rearrangements, large deletions, tandem repeat expansions, and aberrant methylation profiles. We also implicate CXXC1 as a novel disease-associated gene, potentially contributing to a global DNA methylation defects, and revealed novel pathogenic variants in established disease genes such as HEXB and NGLY1 , providing insights into underrecognized genetic contributors to rare diseases.

Conclusions

LRS coupled with pangenome-based, graph-driven analysis closed a sizable diagnostic gap, broadened the mutational spectra of several Mendelian genes and brought epigenomic evidence into rare disease investigation. These findings support the adoption of long-read, graph-based workflows as a front-line strategy for comprehensive genomic and epigenomic diagnosis.\n\nPangenome-based identification of cryptic pathogenic variants in undiagnosed rare disease patients", "token_count": 413, "char_count": 1709, "word_count": 209, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [ "NGLY1", "CXXC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:51.588757", "source": { "split": "train_shard_00001", "doc_id": 219 }, "chunk_id": "train_shard_00001_219_0", "global_id": 5967 }, { "text": "Helcococcus ovis (H. ovis) is an opportunistic bacterial pathogen of a wide range of animal hosts including domestic ruminants, swine, avians, and humans. In this study, we sequenced the genomes of 35 Helcococcus sp. clinical isolates from the uterus of dairy cows and explored their antimicrobial resistance and biochemical phenotypes in vitro. Phylogenetic and average nucleotide identity analyses classified four Helcococcus isolates within a cryptic clade representing an undescribed species, for which we propose the name Helcococcus bovis sp. nov. By establishing this new species clade, we also resolve the longstanding question of the classification of the Tongji strain responsible for a confirmed human conjunctival infection. This strain did not neatly fit into H. ovis and is instead a member of H. bovis. We applied whole genome comparative analyses to explore the pangenome, resistome, virulome, and taxonomic diversity of the remaining 31 H. ovis isolates. An overwhelming 97% of H. ovis strains (30 out of 31) harbor mobile tetracycline resistance genes and displayed significantly increased minimum inhibitory concentrations of tetracyclines in vitro. The high prevalence of mobile tetracycline resistance genes makes H. ovis a significant antimicrobial resistance gene reservoir in our food chain. Finally, the phylogenetic distribution of co-occurring high-virulence determinant genes of H. ovis across unlinked and distant loci highlights an instance of convergent gene loss in the species. In summary, this study showed that mobile genetic element-mediated tetracycline resistance is widespread in H. ovis, and that there is evidence of co-occurring virulence factors across clades suggesting convergent gene loss in the species", "token_count": 514, "char_count": 1847, "word_count": 254, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:52.249962", "source": { "split": "train_shard_00001", "doc_id": 220 }, "chunk_id": "train_shard_00001_220_0", "global_id": 5968 }, { "text": "Finally, we introduced a novel Helcococcus species closely related to H. ovis, called H. bovis sp. nov., which has been reported to cause infection in humans.\n\nPangenomic and biochemical analyses of Helcococcus ovis reveal widespread tetracycline resistance and a novel bacterial species, Helcococcus bovis.", "token_count": 112, "char_count": 342, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:52.631715", "source": { "split": "train_shard_00001", "doc_id": 220 }, "chunk_id": "train_shard_00001_220_1", "global_id": 5969 }, { "text": "

ABSTRACT

Autism spectrum disorders (ASDs) are genetically and phenotypically heterogeneous and the majority of cases still remain genetically unresolved. To better understand large-effect pathogenic variation, we generated long-read sequencing data to construct phased and near-complete genome assemblies (average contig N50=43 Mbp, QV=56) for 189 individuals from 51 families with unsolved cases of autism. We applied read- and assembly-based strategies to facilitate comprehensive characterization of de novo mutations (DNMs), structural variants (SVs), and DNA methylation profiles. Merging common SVs obtained from long-read pangenome controls, we efficiently filtered >97% of common SVs exclusive to 87 offspring. We find no evidence of increased autosomal SV burden for probands when compared to unaffected siblings yet note a trend for an increase of SV burden on the X chromosome among affected females. We establish a workflow to prioritize potential pathogenic variants by integrating autism risk genes and putative noncoding regulatory elements defined from ATAC-seq and CUT&Tag data from the developing cortex. In total, we identified three pathogenic variants in TBL1XR1 , MECP2 , and SYNGAP1 , as well as nine candidate de novo and biparental homozygous SVs, most of which were missed by short-read sequencing. Our work highlights the potential of phased genomes to discover complex more pathogenic mutations and the power of the pangenome to restrict the focus on an increasingly smaller number of SVs for clinical evaluation.\n\nPangenome discovery of missing autism variants", "token_count": 393, "char_count": 1599, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6739, "quality_score": 0.837, "entities": { "genes": [ "MECP2", "SYNGAP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:53.251625", "source": { "split": "train_shard_00001", "doc_id": 221 }, "chunk_id": "train_shard_00001_221_0", "global_id": 5970 }, { "text": "Ralstonia solanacearum species complex (RSSC) is a diverse group of plant pathogens that attack a wide range of hosts and cause devastating losses worldwide. In this study, we conducted a comprehensive analysis of 131 RSSC strains to detect their genetic diversity, pathogenicity, and evolution dynamics. Average nucleotide identity analysis was performed to explore the genomic relatedness among these strains, and finally obtained an open pangenome with 32,961 gene families. To better understand the diverse evolution and pathogenicity, we also conducted a series of analyses of virulence factors (VFs) and horizontal gene transfer (HGT) in the pangenome and at the single genome level. The distribution of VFs and mobile genetic elements (MGEs) showed significant differences among different groups and strains, which were consistent with the new nomenclatures of the RSSC with three distinct species. Further functional analysis showed that most HGT events conferred from Burkholderiales and played a great role in shaping the genomic plasticity and genetic diversity of RSSC genomes. Our work provides insights into the genetic polymorphism, evolution dynamics, and pathogenetic variety of RSSC and provides strong supports for the new taxonomic classification, as well as abundant resources for studying host specificity and pathogen emergence.\n\nComprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification.", "token_count": 360, "char_count": 1526, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:53.838812", "source": { "split": "train_shard_00001", "doc_id": 222 }, "chunk_id": "train_shard_00001_222_0", "global_id": 5971 }, { "text": "Papillomaviruses (PVs) are groups of ubiquitous DNA viruses infecting a wide range of vertebrate hosts, including human. The infection of some human PVs (i.e., HPVs) are strongly associated with cancers, but it remains elusive how such pathogenicity evolved at the genomic level. Here we performed a super-pangenome analysis on a compendium of well-curated 3562 human and animal PV genomes. We found their global genomic diversity being strongly associated with their body sites and tissue origins, but not with their host, geographical, or disease specificity. By reconciling time-resolved phylogenies of PVs and their hosts, we revealed a high-resolution view on how virus-host cospeciation, horizontal host switches, and duplication/loss turnovers collectively shaped the evolution of PVs. We identified key selection-driven mutations that defined the genus-specific divergence of PVs, with those underlying the rise of Alpha-PVs highly enriched in the N-terminal domain of E1 gene. Especially, we identified a group of risk-defining variant sites showing contrasting genotypes between low-risk and high-risk HPVs. With four independent PV genome cohorts, we further validated their high sensitivity and specificity on HPV risk classification even at single site level, underscoring their application values in large-scale HPV screening tests. Finally, with cervical and oropharyngeal cancer patient cohorts assembled by this study, we also evaluated the prognostic value of specific HPV16 variants in predicting patient survival. Taken together, such illumination on the genome and pathogenicity evolution of PVs paves the road for better prevention, control, and treatment of PV-related cancers.

Significance statement

Papillomaviruses (PVs) are ancient and widespread DNA viruses co-evolved with many vertebrate hosts, including human. Some human PVs (e.g., HPV16 and HPV18) bear strong association with cancers, raising a pressing public health challenge. A better understanding of how such pathogenicity evolved holds the key in addressing this challenge", "token_count": 513, "char_count": 2072, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6426, "quality_score": 0.8213, "entities": { "genes": [ "HPV16", "HPV18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:54.492543", "source": { "split": "train_shard_00001", "doc_id": 223 }, "chunk_id": "train_shard_00001_223_0", "global_id": 5972 }, { "text": "Here we systematically investigated the genomic and evolutionary diversity of PVs via a pangenome study on over 3500 human and animal PV isolates, which revealed key selection-driven mutations shaping their genome and pathogenicity evolution. With independently acquired HPV-associated cancer cohorts, we further demonstrated how some of these important HPV variants can serve as clinically informative predictive and prognostic biomarkers. Such comprehensive characterization on PVs’ genome diversity, pathogenicity evolution, and clinical implication paves the road for better prevention, control, and treatment of PV-related cancers.\n\nSuper-pangenome analysis of 3562 human and animal papillomavirus isolates illuminates their genome and pathogenicity evolution", "token_count": 176, "char_count": 764, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:54.934901", "source": { "split": "train_shard_00001", "doc_id": 223 }, "chunk_id": "train_shard_00001_223_1", "global_id": 5973 }, { "text": "The yeast Kluyveromyces marxianus offers unique potential for industrial biotechnology because of useful features like rapid growth, thermotolerance and a wide substrate range. As an emerging alternative platform, K. marxianus requires the development and validation of metabolic engineering strategies to best utilize its metabolism as a basis for bio-based production. To illustrate the synthetic biology strategies to be followed and showcase its potential, we describe a comprehensive approach to rationally engineer a metabolic pathway in K. marxianus . We use the phenylalanine biosynthetic pathway both as a prototype and because phenylalanine is a precursor for commercially valuable secondary metabolites. First, we modify and overexpress the pathway to be resistant to feedback inhibition so as to overproduce phenylalanine de novo from synthetic minimal medium. Second, we assess native and heterologous means to increase precursor supply to the biosynthetic pathway. Finally, we eliminate branch points and competing reactions in the pathway and rebalance precursors to redirect metabolic flux to a specific product, 2-phenylethanol (2-PE). As a result, we are able to construct robust strains capable of producing over 800 mg L −1 2-PE from minimal medium. The strains we constructed are a promising platform for the production of aromatic amino acid-based biochemicals, and our results illustrate challenges with attempting to combine individually beneficial modifications in an integrated platform.\n\nRational engineering ofKluyveromyces marxianusto create a chassis for the production of aromatic products", "token_count": 375, "char_count": 1627, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:55.522511", "source": { "split": "train_shard_00001", "doc_id": 224 }, "chunk_id": "train_shard_00001_224_0", "global_id": 5974 }, { "text": "

Motivation

Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses. The construction of a variation graph from a collection of chromosome-size genome sequences is a difficult task that is generally addressed using a number of heuristics. The question that arises is to what extent the construction method influences the resulting graph, and the characterization of variability.

Results

We aim to characterize the differences between variation graphs derived from the same set of genomes with a metric which expresses and pinpoint differences. We designed a pairwise variation graph comparison algorithm, which establishes an edit distance between variation graphs, threading the genomes through both graphs. We applied our method to pangenome graphs built from yeast and human chromosome collections, and demonstrate that our method effectively characterizes discordances between pangenome graph construction methods and scales to real datasets.

Availability and implementation

pancat compare is published as free Rust software under the AGPL3.0 open source license. Source code and documentation are available at https://github.com/dubssieg/rs-pancat-compare. Snapshot available on Software Heritage at swh:1:dir:61acda8ba3dac1709ed60530147d3871831be629.\n\nPairwise graph edit distance characterizes the impact of the construction method on pangenome graphs.", "token_count": 344, "char_count": 1484, "word_count": 192, "semantic_coherence": 1, "information_density": 0.599, "quality_score": 0.7995, "entities": { "genes": [ "AGPL3" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:56.092586", "source": { "split": "train_shard_00001", "doc_id": 225 }, "chunk_id": "train_shard_00001_225_0", "global_id": 5975 }, { "text": "Bradyrhizobium is known for fixing atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight natural variants of the parental strains, Bradyrhizobium japonicum SEMIA 586 (=CNPSo 17) or Bradyrhizobium diazoefficiens SEMIA 566 (=CNPSo 10). CNPSo 17 and CNPSo 10 were used as commercial inoculants for soybean crops in Brazil at the beginning of the crop expansion in the southern region in the 1960s-1970s. Variants derived from these parental strains were obtained in the late 1980s through a strain selection program aimed at identifying elite strains adapted to a new cropping frontier in the central-western Cerrado region, with a higher capacity of biological nitrogen fixation (BNF) and competitiveness. Here, we aimed to detect genetic variations possibly related to BNF, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains. The core genome phylogeny revealed that strains of each group are closely related, as confirmed by high average nucleotide identity values. However, variants accumulated divergences resulting from horizontal gene transfer, genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, possibly due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed considering the observed differences in their BNF capacity, competitiveness for nodule occupancy, and environmental adaptation.IMPORTANCEToday, Brazil is a global leader in the study and use of biological nitrogen fixation with soybean crops", "token_count": 513, "char_count": 1921, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:53:56.750385", "source": { "split": "train_shard_00001", "doc_id": 226 }, "chunk_id": "train_shard_00001_226_0", "global_id": 5976 }, { "text": "As Brazilian soils are naturally void of soybean-compatible bradyrhizobia, strain selection programs were established, starting with foreign isolates. Selection searched for adaptation to the local edaphoclimatic conditions, higher efficiency of nitrogen fixation, and strong competitiveness for nodule occupancy. We analyzed the genomes of two parental strains of Bradyrhizobium japonicum and Bradyrhizobium diazoefficiens and eight variant strains derived from each parental strain. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation. Our analysis contributes to new insights into the evolution of Bradyrhizobium, and some of the identified differences may be applied as genetic markers to assist strain selection programs.\n\nComparative genomic analysis of Bradyrhizobium strains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions.", "token_count": 280, "char_count": 1177, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:57.296769", "source": { "split": "train_shard_00001", "doc_id": 226 }, "chunk_id": "train_shard_00001_226_1", "global_id": 5977 }, { "text": "In microbiome research, considerable effort has been invested in finding core microbiomes, which have been hypothesized to contain the species most important for host function. Much less attention has been paid to microbiome members that are present in only a subset of hosts. Such accessory microbiomes must in large part consist of species that have no effect on fitness, but some will have deleterious effects on fitness (pathogens), and it is also possible that some accessory microbiome members benefit an ecologically distinct subset of hosts. This short paper discusses what we know about accessory microbiomes, specifically by comparing it with the concept of accessory genomes.\n\nAccessory microbiomes.", "token_count": 148, "char_count": 710, "word_count": 107, "semantic_coherence": 1, "information_density": 0.729, "quality_score": 0.8645, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:57.729412", "source": { "split": "train_shard_00001", "doc_id": 227 }, "chunk_id": "train_shard_00001_227_0", "global_id": 5978 }, { "text": "This study aimed to isolate and identify yeast species from kefir samples and to determine their probiotic characteristics in comparison with commercial probiotic yeast Saccharomyces boulardii. The microbial flora of traditional kefir samples were dominated by Saccharomyces cerevisiae and Kluyveromyces marxianus. Kefir isolates demonstrated higher auto‐aggregation, hydrophobicity and antioxidant properties compared to S. boulardii although S. boulardii demonstrated the highest survival rate under in␣vitro gastrointestinal digestion conditions followed by two kefir yeasts K. marxianus and Kazachstania unispora. Importantly, kefir isolates revealed strong antifungal activities against mould species except Penicillium roqueforti. These findings suggest probiotic and functional roles of yeast strains isolated from traditional kefir samples.\n\nCharacterisation of probiotic properties of yeast strains isolated from kefir samples", "token_count": 231, "char_count": 935, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6724, "quality_score": 0.8362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:58.202042", "source": { "split": "train_shard_00001", "doc_id": 228 }, "chunk_id": "train_shard_00001_228_0", "global_id": 5979 }, { "text": "Homologous recombination plays a key function in the evolution of bacterial genomes. Within Xylella fastidiosa, an emerging plant pathogen with increasing host and geographic ranges, it has been suggested that homologous recombination facilitates host switching, speciation, and the development of virulence. We used 340 whole-genome sequences to study the relationship between inter- and intrasubspecific homologous recombination, random mutation, and natural selection across individual X. fastidiosa genes. Individual gene orthologs were identified and aligned, and a maximum likelihood (ML) gene tree was generated. Each gene alignment and tree pair were then used to calculate gene-wide and branch-specific r/m values (relative effect of recombination to mutation), gene-wide and branch-site nonsynonymous over synonymous substitution rates (dN/dS values; episodic selection), and branch length (as a proxy for mutation rate). The relationships between these variables were evaluated at the global level (i.e., for all genes among and within a subspecies), among specific functional classes (i.e., COGs), and between pangenome components (i.e., accessory versus core genes). Our analysis showed that r/m varied widely among genes as well as across X. fastidiosa subspecies. While r/m and dN/dS values were positively correlated in some instances (e.g., core genes in X. fastidiosa subsp. fastidiosa and both core and accessory genes in X. fastidiosa subsp. multiplex), low correlation coefficients suggested no clear biological significance. Overall, our results indicate that, in addition to its adaptive role in certain genes, homologous recombination acts as a homogenizing and a neutral force across phylogenetic clades, gene functional groups, and pangenome components. IMPORTANCE There is ample evidence that homologous recombination occurs frequently in the economically important plant pathogen Xylella fastidiosa", "token_count": 505, "char_count": 1996, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:58.851809", "source": { "split": "train_shard_00001", "doc_id": 229 }, "chunk_id": "train_shard_00001_229_0", "global_id": 5980 }, { "text": "Homologous recombination has been known to occur among sympatric subspecies and is associated with host-switching events and virulence-linked genes. As a consequence, is it generally assumed that recombinant events in X. fastidiosa are adaptive. This mindset influences expectations of how homologous recombination acts as an evolutionary force as well as how management strategies for X. fastidiosa diseases are determined. Yet, homologous recombination plays roles beyond that of a source for diversification and adaptation. Homologous recombination can act as a DNA repair mechanism, as a means to facilitate nucleotide compositional change, as a homogenization mechanism within populations, or even as a neutral force. Here, we provide a first assessment of long-held beliefs regarding the general role of recombination in adaptation for X. fastidiosa. We evaluate gene-specific variations in homologous recombination rate across three X. fastidiosa subspecies and its relationship to other evolutionary forces (e.g., natural selection, mutation, etc.). These data were used to assess the role of homologous recombination in X. fastidiosa evolution.\n\nThe Multifaceted Role of Homologous Recombination in a Fastidious Bacterial Plant Pathogen.", "token_count": 286, "char_count": 1246, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:53:59.409716", "source": { "split": "train_shard_00001", "doc_id": 229 }, "chunk_id": "train_shard_00001_229_1", "global_id": 5981 }, { "text": "Crop breeding has entered the pangenomics era, unlocking a far more comprehensive view of genetic diversity than a single reference genome can capture. In rice (Oryza sativa), a staple crop critical to global food security, the construction of pangenome resources has uncovered extensive structural variations (SVs), novel genes, and presence/absence variations (PAVs) that underpin key agronomic traits. As the rice pangenome matures from a research resource into a practical breeding tool, it promises to accelerate the development of higher-yielding, stress-resilient, and disease-resistant varieties. This transition represents a pivotal advance toward sustainable agriculture and enhanced global food security, while also establishing a model for applying pangenomics to other crops. Here, we review how rice pangenome research, encompassing both cultivated and wild species, has advanced trait discovery (from yield improvement and disease resistance to stress tolerance) and enabled new molecular breeding strategies. Despite these advances, several challenges remain before pangenomic data can be routinely integrated into breeding pipelines. The complexity of graph-based data structures, difficulties in detecting multiallelic variants from population-wide resequencing data, and the lack of breeder-friendly genotyping tools are significant barriers. Additionally, while artificial intelligence (AI) and machine learning (ML) approaches show great promise for interpreting complex pangenomic data and accelerating trait discovery, their practical adoption is hindered by the absence of breeder-oriented interfaces, integration challenges with phenotypic and environmental data, and high computational demands. Overcoming these issues will require interdisciplinary collaboration, robust infrastructure, and innovations focused on practical breeding needs across diverse crop species.\n\nChallenges in Bringing Pangenome Research into Breeding: A Case Study in Rice", "token_count": 401, "char_count": 1973, "word_count": 257, "semantic_coherence": 1, "information_density": 0.7237, "quality_score": 0.8619, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:00.030769", "source": { "split": "train_shard_00001", "doc_id": 230 }, "chunk_id": "train_shard_00001_230_0", "global_id": 5982 }, { "text": "Kluyveromyces marxianus (K. marxianus) is a newly emerging industrially relevant yeast. It is known to possess a highly efficient Non-Homologous End Joining (NHEJ) pathway that promotes random integration of non-homologous DNA fragments into its genome. The nature of the integration events was traditionally analyzed by Southern blot hybridization. However, the precise DNA sequence at the insertion sites were not fully explored. We transformed a PCR product of the Saccharomyces cerevisiae URA3 gene (ScURA3) into an uracil auxotroph K. marxianus wildtype strain and picked 24 stable Ura+ transformants for sequencing analysis. We took advantage of rapid advances in DNA sequencing technologies and developed a method using a combination of Illumina MiSeq and Oxford Nanopore sequencing. This approach enables us to uncover the Gross Chromosomal Rearrangements (GCRs) that are associated with the ScURA3 random integration. Moreover, it will shine a light on understanding DNA repair mechanisms in Eukaryotes, which could potentially provide insights for cancer research.\n\nGross Chromosomal Rearrangements in Kluyveromyces Marxianus Revealed by Illumina and Oxford Nanopore Sequencing", "token_count": 297, "char_count": 1187, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7305, "quality_score": 0.8653, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:00.590304", "source": { "split": "train_shard_00001", "doc_id": 231 }, "chunk_id": "train_shard_00001_231_0", "global_id": 5983 }, { "text": "In contrast to other human-associated bifidobacteria, Bifidobacterium dentium is commonly classified as an opportunistic pathogen as its presence in the oral cavity has been associated with the development of dental caries. While B. dentium is frequently isolated from the oral cavity of children with caries, recent microbiome investigations and preliminary genomic analyses have suggested that this species is also adapted to colonize the gastrointestinal tract. Understanding the genetic and metabolic adaptations that enable this flexible colonization ability is crucial to clarify its role in human health and disease. To assess B. dentium genomic diversity and metabolic potential, the current study presents analysis and characterization of 10 complete genome sequences from recently isolated B. dentium strains obtained from human fecal samples together with 48 publicly available genome sequences. We investigated genetic loci predicted to be involved in host interaction and carbohydrate utilization in this species by means of comparative genomics, pan-genome analysis, and gene-trait matching. These analyses identified gene clusters involved in the utilization of plant-derived glycans and, for the first time, revealed B. dentium strains capable of utilizing human milk oligosaccharides (HMOs) through a fucosyllactose utilization cluster homologous to the one found in several infant-derived bifidobacterial species. Moreover, additional investigations of strain-specific genetic features highlighted a taxon that is evolved to colonize multiple niches and to compete with other colonizers. These findings challenge the narrow classification of B. dentium as an opportunist and underscore its ecological versatility.\n\nGene-trait matching among <i>Bifidobacterium dentium</i> strains reveals various glycan metabolism loci including a strain-specific fucosyllactose utilization cluster.", "token_count": 464, "char_count": 1954, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:01.234332", "source": { "split": "train_shard_00001", "doc_id": 232 }, "chunk_id": "train_shard_00001_232_0", "global_id": 5984 }, { "text": "DNA foundation models offer a new approach to interpret genetic variation, but their potential in population-scale genomics remains untapped. We introduce a novel analytical framework that integrates a genomic foundation model with human population genomics studies. We employed the Evo2 DNA foundation model to systematically score the functional impact of a variant and haplotype across diverse cohorts including people with Alzheimer’s Disease Neuroimaging Initiative (ADNI), the Human Pangenome Project, and the UK Biobank. As proof-of-concept, the analysis of the APOE locus confirmed the approach’s validity, with model-derived scores can help to prioritize putatively functional variants and quantify effects of both variants and haplotype onto Alzheimer’s Disease susceptibility or associated endophenotypes, including cognitive performance, brain structural change and amyloid load. Specifically, scoring multi-ancestry assembly sequences from the Human Pangenome Project revealed, for the first time, that genetic variation could nicely explains ancestry-specific differences in APOE expression and the impact of APOE -ε4 on Alzheimer’s disease risk. Overall, this study provides a scalable framework for mapping functional genetic variation, complementing conventional population-genomics approaches, enabling better interpretation of genetic effects in complex genomic regions at population scale.\n\nAdvancing Human Population Genomics with DNA Foundation Models", "token_count": 311, "char_count": 1473, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:01.826408", "source": { "split": "train_shard_00001", "doc_id": 233 }, "chunk_id": "train_shard_00001_233_0", "global_id": 5985 }, { "text": "

Aims

Kluyveromyces marxianus dairy strains were tested for γ-aminobutyric acid (GABA) production. The genes involved in GABA catabolism (UGA1 and UGA2) and anabolism (GAD1) were found in K. marxianus genome. Their relative expression was evaluated with primer designed ad hoc.

Methods and results

Strains were grouped on the basis of GAD1 gene sequence. Representative strains for each group were tested for GABA production by high-performance liquid chromatography. All strains produced it at low levels. qRT-PCR showed the absence of a relation between GABA production and GAD1 gene expression. UGA1 and UGA2 genes were not upregulated and low amounts of succinic acid were detected.

Conclusions

All strains released a low amount of GABA suggesting that probably it was stored within cells. The different behaviour of strains in terms of GABA and succinic acid production as well as gene expression highlighted the genetic and phenotypic biodiversity of this species.

Significance and impact of the study

GABA production and genes involved in its catabolism and anabolism were described in a population of dairy K. marxianus for the first time. The variability observed in terms of genetic and phenotypic biodiversity is important especially to exploit this non-conventional yeast as microbial platform.\n\nγ-aminobutyric acid production by Kluyveromyces marxianus strains.", "token_count": 378, "char_count": 1402, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5584, "quality_score": 0.7792, "entities": { "genes": [ "GAD1", "UGA1", "UGA2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:02.428917", "source": { "split": "train_shard_00001", "doc_id": 234 }, "chunk_id": "train_shard_00001_234_0", "global_id": 5986 }, { "text": "

Motivation

The first step when working with DNA sequence data of human-derived microbiomes is usually to remove human contamination for two reasons. First, many countries have strict privacy and data protection guidelines for human sequence data, so microbiome data containing partly human data cannot be easily further processed or published. Second, human contamination may cause problems in downstream analysis steps, such as genome assembly and binning. For large-scale metagenomics projects, fast and accurate removal of human contamination is hence critical.

Results

We introduce Cleanifier, a fast and memory frugal alignment-free tool for detecting and removing human contamination based on gapped k -mers, or spaced seeds. Cleanifier uses a pangenome index of all human gapped k -mers, but the creation and use of alternative references is also possible. Reads are filtered based on the gapped k -mers present in the index. Cleanifier supports two filtering modes: one that queries all gapped k -mers and one that queries only a sample of them. A comparison of Cleanifier with other state-of-the-art tools shows that our sampling mode makes Cleanifier the fastest method with comparable accuracy. Because we store the gapped k -mers in a probabilistic Cuckoo filter, Cleanifier has similar memory requirements to methods that use a minimizer index. At the same time, Cleanifier is more flexible, because it can use different sampling methods on the same index.

Availability and Implementation

The Cleanifier tool is available via gitlab ( https://gitlab.com/rahmannlab/cleanifier ), PyPi ( https://pypi.org/project/cleanifier/ ) and Bioconda ( https://anaconda.org/bioconda/cleanifier ). The pre-computed human pangenome index is available for download at https://doi.org/10.5281/zenodo.15639519 .

Contact

rahmann@cs.uni-saarland.de\n\nCleanifier: Contamination removal from microbial sequences using spaced seeds of a human pangenome index", "token_count": 489, "char_count": 1987, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:03.137005", "source": { "split": "train_shard_00001", "doc_id": 235 }, "chunk_id": "train_shard_00001_235_0", "global_id": 5987 }, { "text": "Whole genome sequencing has revolutionized infectious disease surveillance for tracking and monitoring the spread and evolution of pathogens. However, using a linear reference genome for genomic analyses may introduce biases, especially when studies are conducted on highly variable bacterial genomes of the same species. Pangenome graphs provide an efficient model for representing and analyzing multiple genomes and their variants as a graph structure that includes all types of variations. In this study, we present a practical bioinformatics pipeline that employs the PanGenome Graph Builder and the Variation Graph toolkit to build pangenomes from assembled genomes, align whole genome sequencing data and call variants against a graph reference. The pangenome graph enables the identification of structural variants, rearrangements, and small variants (e.g., single nucleotide polymorphisms and insertions/deletions) simultaneously. We demonstrate that using a pangenome graph, instead of a single linear reference genome, improves mapping rates and variant calling for both simulated and real datasets of the pathogen Neisseria meningitidis. Overall, pangenome graphs offer a promising approach for comparative genomics and comprehensive genetic variation analysis in infectious disease. Moreover, this innovative pipeline, leveraging pangenome graphs, can bridge variant analysis, genome assembly, population genetics, and evolutionary biology, expanding the reach of genomic understanding and applications.\n\nPangenome graphs in infectious disease: a comprehensive genetic variation analysis of Neisseria meningitidis leveraging Oxford Nanopore long reads.", "token_count": 354, "char_count": 1678, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:03.720768", "source": { "split": "train_shard_00001", "doc_id": 236 }, "chunk_id": "train_shard_00001_236_0", "global_id": 5988 }, { "text": "The molecular basis of reduced susceptibility to amphotericin B (rs-AMB) among any yeasts is poorly defined. Genetic alterations in genes involved in ergosterol biosynthesis and total cell sterols were investigated among clinical Candida kefyr isolates. C. kefyr isolates (n = 81) obtained from 74 patients in Kuwait and identified by phenotypic and molecular methods were analyzed. An Etest was initially used to identify isolates with rs-AMB. Specific mutations in ERG2 and ERG6 involved in ergosterol biosynthesis were detected by PCR sequencing. Twelve selected isolates were also tested by the SensiTitre Yeast One (SYO), and total cell sterols were evaluated by gas chromatography-mass spectrometry and ERG3 and ERG11 sequencing. Eight isolates from 8 patients showed rs-AMB by Etest, including 2 isolates with additional resistance to fluconazole or to all three antifungals. SYO correctly identified 8 of 8 rs-AMB isolates. A nonsynonymous mutation in ERG2 was detected in 6 of 8 rs-AMB isolates but also in 3 of 73 isolates with a wild-type AMB pattern. One rs-AMB isolate contained a deletion (frameshift) mutation in ERG2. One or more nonsynonymous mutations was detected in ERG6 in 11 of 81 isolates with the rs-AMB or wild-type AMB pattern. Among 12 selected isolates, 2 and 2 isolates contained a nonsynonymous mutation(s) in ERG3 and ERG11, respectively", "token_count": 454, "char_count": 1438, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5498, "quality_score": 0.7749, "entities": { "genes": [ "ERG2", "ERG11", "ERG6", "ERG3" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:04.362562", "source": { "split": "train_shard_00001", "doc_id": 237 }, "chunk_id": "train_shard_00001_237_0", "global_id": 5989 }, { "text": "Ergosterol was undetectable in 7 of 8 rs-AMB isolates, and the total cell sterol profiles were consistent with loss of ERG2 function in 6 rs-AMB isolates and loss of ERG3 activity in another rs-AMB isolate. Our data showed that ERG2 is a major target conferring rs-AMB in clinical C. kefyr isolates. IMPORTANCE Some yeast species exhibit intrinsic resistance or rapidly acquire resistance to azole antifungals. Despite >50 years of clinical use, resistance to amphotericin B (AMB) among yeast species has been extremely rarely reported until recently. Reduced susceptibility to AMB (rs-AMB) among yeast species is, therefore, a matter of serious concern due to the availability of only four classes of antifungal drugs. Recent studies in Candida glabrata, Candida lusitaniae, and Candida auris have identified ERG genes involved in ergosterol biosynthesis as the major targets conferring rs-AMB. The results of this study also show that nonsynonymous mutations in ERG2 impair its function, abolish ergosterol from C. kefyr, and confer rs-AMB. Thus, rapid detection of rs-AMB among clinical isolates will help in proper management of invasive C. kefyr infections.\n\nMolecular Characterization and Sterol Profiles Identify Nonsynonymous Mutations in ERG2 as a Major Mechanism Conferring Reduced Susceptibility to Amphotericin B in Candida kefyr.", "token_count": 404, "char_count": 1391, "word_count": 200, "semantic_coherence": 1, "information_density": 0.635, "quality_score": 0.8175, "entities": { "genes": [ "ERG2", "ERG3" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:04.976183", "source": { "split": "train_shard_00001", "doc_id": 237 }, "chunk_id": "train_shard_00001_237_1", "global_id": 5990 }, { "text": "Mammalian tuberculosis (TB) is a zoonotic disease mainly due to Mycobacterium bovis (M. bovis). A current challenge for its eradication is understanding its transmission within multi-host systems. Improvements in long-read sequencing technologies have made it possible to obtain complete bacterial genomes that provide a comprehensive view of species-specific genomic features. In the context of TB, new genomic references based on complete genomes genetically close to field strains are also essential to perform precise field molecular epidemiological studies. A total of 10 M. bovis strains representing each genetic lineage identified in France and in other countries were selected for performing complete assembly of their genomes. Pangenome analysis revealed a \"closed\" pangenome composed of 3900 core genes and only 96 accessory genes. Whole genomes-based alignment using progressive Mauve showed remarkable conservation of the genomic synteny except that the genomes have a variable number of copies of IS6110. Characteristic genomic traits of each lineage were identified through the discovery of specific indels. Altogether, these results provide new genetic features that improve the description of M. bovis lineages. The availability of new complete representative genomes of M. bovis will be useful to epidemiological studies and better understand the transmission of this clonal-evolving pathogen.\n\nFeatures of Mycobacterium bovis Complete Genomes Belonging to 5 Different Lineages.", "token_count": 373, "char_count": 1545, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6476, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:05.557503", "source": { "split": "train_shard_00001", "doc_id": 238 }, "chunk_id": "train_shard_00001_238_0", "global_id": 5991 }, { "text": "

Aims

Isolation, characterization and assessment of inhibitor tolerance of thermotolerant yeasts associated with distillery effluent and molasses, and their use in high-temperature ethanol production from alkali-treated rice straw.

Methods and results

A total of 92 thermotolerant yeasts were isolated from seven different distillery effluent and molasses samples. Based on MSP-PCR, 34 yeasts were selected and identified by sequencing the D1/D2 domain of LSU rDNA. These yeasts belonged to eight genera and nine different species. We assessed the inhibitor tolerance of these 34 well-characterized yeasts against various pre-treatment-generated inhibitors (furfural, 5-hydroxymethyl furfural and acetic acid) and also evaluated their ethanol yields at 40, 45 and 50℃. Among selected strains, Pichia kudriavzevii DSA3.2 exhibited the highest ethanol production (24.5 g l-1 ) with an efficiency of 95.7% at 40℃ using 5% glucose. At 45℃, P. kudriavzevii DSA3.2 and Kluyveromyces marxianus MSS6.3 yielded maximum ethanol titres; 22.3 and 23 g l-1 with 87.4% and 90% efficiency, respectively. While using alkali-treated RS at 45℃, K. marxianus MSS6.3 produced 10.5 g l-1 of ethanol with 84.5% fermentation efficiency via separate hydrolysis and fermentation, and 10.9 g l-1 of ethanol with 85% efficiency via simultaneous saccharification and fermentation. Pichia kudriavzevii DSA3.2, DSA3.1 and K", "token_count": 502, "char_count": 1451, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [ "MSS6", "DSA3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:06.216486", "source": { "split": "train_shard_00001", "doc_id": 239 }, "chunk_id": "train_shard_00001_239_0", "global_id": 5992 }, { "text": "marxianus MSS6.3 also exhibited significant tolerance against multiple inhibitors.

Conclusions

Yeast isolates P. kudriavzevii DSA3.2 and K. marxianus MSS6.3 exhibited significant inhibitor tolerance and proved to be suitable for high-temperature ethanol fermentation. After additional optimization and scale-up experiments, these isolates can be exemplary candidates for industrial-scale ethanol production from lignocellulosic biomass.

Significance and impact of the study

Our study recognizes distillery effluents and molasses as specialized niches for yeasts with a broad substrate range, capable of tolerating multiple inhibitors and yielding high levels of ethanol at elevated temperatures. These yeasts can further be exploited for bioethanol production through SSF/SHF at a larger scale.\n\nBioprospecting thermotolerant yeasts from distillery effluent and molasses for high-temperature ethanol production.", "token_count": 239, "char_count": 925, "word_count": 111, "semantic_coherence": 1, "information_density": 0.6847, "quality_score": 0.8423, "entities": { "genes": [ "MSS6", "DSA3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:06.684149", "source": { "split": "train_shard_00001", "doc_id": 239 }, "chunk_id": "train_shard_00001_239_1", "global_id": 5993 }, { "text": "Jaccard Index Network Analysis (JINA) is a comprehensive workflow designed to explore bacterial genome relationships through an integrated network-based approach. This workflow combines existing tools such as Jaccard Index (1), Gephi (2) and Pangraph (3). By integrating these methodologies into a unified framework, JINA enables efficient visualization and stratification of genomic data, facilitating the identification of meaningful patterns, groups, and associations within bacterial populations. The use of JINA ensures precision in capturing genomic variation including single nucleotide polymorphisms, insertions and deletions. While JINA does not implement Gephi, BLAST, and PanGraph directly in a single software, it guides their coordinated use to analyze and interpret genomic data effectively.\n\nJaccard Index Network Analysis for pangenome analysis", "token_count": 186, "char_count": 860, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7544, "quality_score": 0.8772, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:07.133743", "source": { "split": "train_shard_00001", "doc_id": 240 }, "chunk_id": "train_shard_00001_240_0", "global_id": 5994 }, { "text": "Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations from DeepFRI. This is the first approach to apply deep learning-based functional annotations in metagenomics. We validate DeepFRI functional annotations by comparing them to orthology-based annotations from eggNOG on a set of 1,070 infant metagenomes from the DIABIMMUNE cohort. Using this workflow, we generated a sequence catalogue of 1.9 million nonredundant microbial genes. The functional annotations revealed 70% concordance between Gene Ontology annotations predicted by DeepFRI and eggNOG. DeepFRI improved the annotation coverage, with 99% of the gene catalogue obtaining Gene Ontology molecular function annotations, although they are less specific than those from eggNOG. Additionally, we constructed pangenomes in a reference-free manner using high-quality metagenome-assembled genomes (MAGs) and analyzed the associated annotations. eggNOG annotated more genes on well-studied organisms, such as Escherichia coli, while DeepFRI was less sensitive to taxa. Further, we show that DeepFRI provides additional annotations in comparison to the previous DIABIMMUNE studies. This workflow will contribute to novel understanding of the functional signature of the human gut microbiome in health and disease as well as guiding future metagenomics studies. IMPORTANCE The past decade has seen advancement in high-throughput sequencing technologies resulting in rapid accumulation of genomic data from microbial communities. While this growth in sequence data and gene discovery is impressive, the majority of microbial gene functions remain uncharacterized. The coverage of functional information coming from either experimental sources or inferences is low. To solve these challenges, we have developed a new workflow to computationally assemble microbial genomes and annotate the genes using a deep learning-based model DeepFRI", "token_count": 502, "char_count": 2235, "word_count": 299, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:07.796112", "source": { "split": "train_shard_00001", "doc_id": 241 }, "chunk_id": "train_shard_00001_241_0", "global_id": 5995 }, { "text": "This improved microbial gene annotation coverage to 1.9 million metagenome-assembled genes, representing 99% of the assembled genes, which is a significant improvement compared to 12% Gene Ontology term annotation coverage by commonly used orthology-based approaches. Importantly, the workflow supports pangenome reconstruction in a reference-free manner, allowing us to analyze the functional potential of individual bacterial species. We therefore propose this alternative approach combining deep-learning functional predictions with the commonly used orthology-based annotations as one that could help us uncover novel functions observed in metagenomic microbiome studies.\n\nComprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method.", "token_count": 161, "char_count": 785, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7677, "quality_score": 0.8838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:08.240516", "source": { "split": "train_shard_00001", "doc_id": 241 }, "chunk_id": "train_shard_00001_241_1", "global_id": 5996 }, { "text": "The Escherichia coli species contains a diverse set of sequence types and there remain important questions regarding differences in genetic content within this population that need to be addressed. Pangenomes are useful vehicles for studying gene content within sequence types. Here, we analyse 21 E. coli sequence type pangenomes using comparative pangenomics to identify variance in both pangenome structure and content. We present functional breakdowns of sequence type core genomes and identify sequence types that are enriched in metabolism, transcription and cell membrane biogenesis genes. We also uncover metabolism genes that have variable core classification depending on which allele is present. Our comparative pangenomics approach allows for detailed exploration of sequence type pangenomes within the context of the species. We show that pangenome evolution is independent of phylogenetic signal at the phylogroup level, which may be a consequence of distinct sequence type-specific driving factors relating to ecology and pathogenic phenotype.

Data Summary

Supporting data and code have been provided within the article or through Supplementary Data files available at https://doi.org/10.6084/m9.figshare.19793758 . Custom Python scripts used to perform analyses are available at github.com/lillycummins/InterPangenome unless otherwise stated in the text.\n\nPangenome evolution in Escherichia coli is sequence type, not phylogroup, specific", "token_count": 339, "char_count": 1470, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6734, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:08.810768", "source": { "split": "train_shard_00001", "doc_id": 242 }, "chunk_id": "train_shard_00001_242_0", "global_id": 5997 }, { "text": "

Background

Kluyveromyces marxianus is a promising cell factory for producing bioethanol and that raised a demand for a high yield of heterologous proteins in this species. Expressions of heterologous proteins usually lead to the accumulation of misfolded or unfolded proteins in the lumen of the endoplasmic reticulum (ER) and then cause ER stress. To cope with this problem, a group of ER stress response target genes (ESRTs) are induced, mainly through a signaling network called unfolded protein response (UPR). Characterization and modulation of ESRTs direct the optimization of heterologous expressions. However, ESRTs in K. marxianus have not been identified so far.

Results

In this study, we characterized the ER stress response in K. marxianus for the first time, by using two ER stress-inducing reagents, dithiothreitol (DTT) and tunicamycin (TM). Results showed that the Kar2-Ire1-Hac1 pathway of UPR is well conserved in K. marxianus. About 15% and 6% of genes were upregulated during treatment of DTT and TM, respectively. A total of 115 upregulated genes were characterized as ESRTs, among which 97 genes were identified as UPR target genes and 37 UPR target genes contained UPR elements in their promoters. Genes related to carbohydrate metabolic process and actin filament organization were identified as new types of UPR target genes. A total of 102 ESRTs were overexpressed separately in plasmids and their effects on productions of two different lignocellulolytic enzymes were systematically evaluated. Overexpressing genes involved in carbohydrate metabolism, including PDC1, PGK and VID28, overexpressing a chaperone gene CAJ1 or overexpressing a reductase gene MET13 substantially improved secretion expressions of heterologous proteins", "token_count": 474, "char_count": 1772, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [ "PDC1", "VID28", "CAJ1", "MET13" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:09.463119", "source": { "split": "train_shard_00001", "doc_id": 243 }, "chunk_id": "train_shard_00001_243_0", "global_id": 5998 }, { "text": "Meanwhile, overexpressing a novel gene, KLMA_50479 (named ESR1), as well as overexpressing genes involved in ER-associated protein degradation (ERAD), including HRD3, USA1 andYET3, reduced the secretory expressions. ESR1 and the aforementioned ERAD genes were deleted from the genome. Resultant mutants, except the yet3Δ mutant, substantially improved secretions of three different heterologous proteins. During the fed-batch fermentation, extracellular activities of an endoxylanase and a glucanase in hrd3Δ cells improved by 43% and 28%, respectively, compared to those in wild-type cells.

Conclusions

Our results unveil the transcriptional scope of the ER stress response in K. marxianus and suggest efficient ways to improve productions of heterologous proteins by manipulating expressions of ESRTs.\n\nCharacterization and modulation of endoplasmic reticulum stress response target genes in Kluyveromyces marxianus to improve secretory expressions of heterologous proteins.", "token_count": 259, "char_count": 983, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [ "HRD3", "ESR1", "USA1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:10.002089", "source": { "split": "train_shard_00001", "doc_id": 243 }, "chunk_id": "train_shard_00001_243_1", "global_id": 5999 }, { "text": "Biotechnology requires efficient microbial cell factories. The budding yeast Saccharomyces cerevisiae is a vital cell factory, but more diverse cell factories are essential for the sustainable use of natural resources. Here, we benchmarked nonconventional yeasts Kluyveromyces marxianus and Rhodotorula toruloides against S. cerevisiae strains CEN.PK and W303 for their responses to potassium and sodium salt stress. We found an inverse relationship between the maximum growth rate and the median cell volume that was responsive to salt stress. The supplementation of K+ to CEN.PK cultures reduced Na+ toxicity and increased the specific growth rate 4-fold. The higher K+ and Na+ concentrations impaired ethanol and acetate metabolism in CEN.PK and acetate metabolism in W303. In R. toruloides cultures, these salt supplementations induced a trade-off between glucose utilization and cellular aggregate formation. Their combined use increased the beta-carotene yield by 60% compared with that of the reference. Neural network-based image analysis of exponential-phase cultures showed that the vacuole-to-cell volume ratio increased with increased cell volume for W303 and K. marxianus but not for CEN.PK and R. toruloides in response to salt stress. Our results provide insights into common salt stress responses in yeasts and will help design efficient bioprocesses. IMPORTANCE Characterization of microbial cell factories under industrially relevant conditions is crucial for designing efficient bioprocesses. Salt stress, typical in industrial bioprocesses, impinges upon cell volume and affects productivity. This study presents an open-source neural network-based analysis method to evaluate volumetric changes using yeast optical microscopy images. It allows quantification of cell and vacuole volumes relevant to cellular physiology", "token_count": 463, "char_count": 1890, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:11.305307", "source": { "split": "train_shard_00001", "doc_id": 244 }, "chunk_id": "train_shard_00001_244_0", "global_id": 6000 }, { "text": "On applying salt stress in yeasts, we found that the combined use of K+ and Na+ improves the cellular fitness of Saccharomyces cerevisiae strain CEN.PK and increases the beta-carotene productivity in Rhodotorula toruloides, a commercially important antioxidant and a valuable additive in foods.\n\nPotassium and Sodium Salt Stress Characterization in the Yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and Rhodotorula toruloides.", "token_count": 143, "char_count": 467, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7458, "quality_score": 0.8729, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:11.728343", "source": { "split": "train_shard_00001", "doc_id": 244 }, "chunk_id": "train_shard_00001_244_1", "global_id": 6001 }, { "text": "In many countries, whey from the dairy industry is an abundant waste that generates an important environmental impact. Alternative processes to use the whey and minimize the environmental impact are needed. This work considered six formulations with different ammonium sulfate and L-phenylalanine (L-Phe) concentrations to produce bioethanol in sweet whey fermentation by Kluyveromyces marxianus . The results showed a maximum bioethanol concentration equal to 25.13 ± 0.37 g L -1 (p < 0.05) for formulation F6, with 1 g L -1 of L-Phe and 1.350 g L -1 of ammonium sulfate (96 h). For these conditions, the chemical oxygen demand removal percent (CODR%) was 67%. The maximum CODR% obtained was 97.5% for formulation F3 (1 g L -1 of L-Phe) at 96 hours; however, a significant decrease in bioethanol concentration (14.33 ± 2.58 g L -1 ) was observed. On the other hand, for formulation, F3, at 48 hours of fermentation time, a bioethanol concentration of 23.71 ± 1.26 g L -1 was observed, with 76.5% CODR%. Based on these results, we suggest that the best conditions to obtain a significant bioethanol concentration and CODR% value are those used on the configuration F3 at 48 hours.\n\nConversion of sweet whey to bioethanol: a bioremediation alternative for dairy industry", "token_count": 383, "char_count": 1269, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:12.312345", "source": { "split": "train_shard_00001", "doc_id": 245 }, "chunk_id": "train_shard_00001_245_0", "global_id": 6002 }, { "text": "

Background

Schaalia species are primarily found among the oral microbiota of humans and other animals. They have been associated with various infections through their involvement in biofilm formation, modulation of host responses, and interaction with other microorganisms. In this study, two strains previously indicated as Actinomyces spp. were found to be novel members of the genus Schaalia based on their whole genome sequences.

Results

Whole-genome sequencing revealed both strains with a genome size of 2.3 Mbp and GC contents of 65.5%. Phylogenetics analysis for taxonomic placement revealed strains NCTC 9931 and C24 as distinct species within the genus Schaalia. Overall genome-relatedness indices including digital DNA-DNA hybridization (dDDH), and average nucleotide/amino acid identity (ANI/AAI) confirmed both strains as distinct species, with values below the species boundary thresholds (dDDH < 70%, and ANI and AAI < 95%) when compared to nearest type strain Schaalia odontolytica NCTC 9935 T. Pangenome and orthologous analyses highlighted their differences in gene properties and biological functions compared to existing type strains. Additionally, the identification of genomic islands (GIs) and virulence-associated factors indicated their genetic diversity and potential adaptive capabilities, as well as potential implications for human health", "token_count": 349, "char_count": 1393, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7166, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:12.908114", "source": { "split": "train_shard_00001", "doc_id": 246 }, "chunk_id": "train_shard_00001_246_0", "global_id": 6003 }, { "text": "Notably, CRISPR-Cas systems in strain NCTC 9931 underscore its adaptive immune mechanisms compared to strain C24.

Conclusions

Based on these findings, strain NCTC 9931T (= ATCC 17982T = DSM 43331T = CIP 104728T = CCUG 18309T = NCTC 14978T = CGMCC 1.90328T) represents a novel species, for which the name Schaalia dentiphila subsp. dentiphila sp. nov. subsp. nov. is proposed, while strain C24T (= NCTC 14980T = CGMCC 1.90329T) represents a distinct novel subspecies, for which the name Schaalia dentiphila subsp. denticola. subsp. nov. is proposed. This study enriches our understanding of the genomic diversity of Schaalia species and paves the way for further investigations into their roles in oral health.

Significance

This research reveals two Schaalia strains, NCTC 9931 T and C24T, as novel entities with distinct genomic features. Expanding the taxonomic framework of the genus Schaalia, this study offers a critical resource for probing the metabolic intricacies and resistance patterns of these bacteria. This work stands as a cornerstone for microbial taxonomy, paving the way for significant advances in clinical diagnostics.", "token_count": 477, "char_count": 1283, "word_count": 169, "semantic_coherence": 1, "information_density": 0.645, "quality_score": 0.8225, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:13.578954", "source": { "split": "train_shard_00001", "doc_id": 246 }, "chunk_id": "train_shard_00001_246_1", "global_id": 6004 }, { "text": "Genome characterisation and comparative analysis of Schaalia dentiphila sp. nov. and its subspecies, S. dentiphila subsp. denticola subsp. nov., from the human oral cavity.", "token_count": 48, "char_count": 172, "word_count": 24, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:13.954858", "source": { "split": "train_shard_00001", "doc_id": 246 }, "chunk_id": "train_shard_00001_246_2", "global_id": 6005 }, { "text": "Abstract

Background: Recently, more chemical and biotechnological applications have been found in Kluyveromyces marxianus than Saccharomyces cerevisiae in the food field because they show advantageous metabolism features in the production of flavor components of interest. However, most of study demonstrated Kluyveromyces marxianus involved in ethanol synthesis in the dairy products in food fields. Our study aims to clarify the formation mechanism of ethyl acetate and organic acids in acid rice soup inoculated with Kluyveromyces marxianus.Results: The higher concentration of ethyl acetate than ethanol and organic acids in fermented acid rice soup inoculated with Kluyveromyces marxianus. Up-regulated genes/proteins, including ADH1, ADH2, ADH6, ATF1, ACCT, and TES1, and down-regulated ALD family involved in glycolysis/gluconeogenesis and pyruvate metabolism played the crucial roles in the formation of ethyl acetate and other esters. In addition, up-regulated genes/proteins involved in starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, TCA cycle, and pyruvate metabolism played the important roles in the formation of organic acids, ethanol and esters.Conclusion: Our results reveals the formation mechanism of ethyl acetate and organic acids in acid rice soup inoculated with K. marxianus L1-1. This study provides the basis for improving aroma and taste of fermented foods and reveals the formation mechanisms of flavors in no-dairy products.

", "token_count": 477, "char_count": 1690, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5604, "quality_score": 0.7802, "entities": { "genes": [ "ATF1", "ADH1", "TES1", "ADH6", "ADH2" ], "proteins": [], "pathways": [ "glycolysis", "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:14.612323", "source": { "split": "train_shard_00001", "doc_id": 247 }, "chunk_id": "train_shard_00001_247_0", "global_id": 6006 }, { "text": "Complementary analyses of transcriptome and proteome revealed the formation mechanism of ethyl acetate, ethanol and organic acids in Kluyveromyces marxianus L1-1 in Chinese fermented acid rice soup", "token_count": 52, "char_count": 197, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:15.008830", "source": { "split": "train_shard_00001", "doc_id": 247 }, "chunk_id": "train_shard_00001_247_1", "global_id": 6007 }, { "text": "Salmonella enterica non-typhoidal is a major contributor to diarrheal diseases, with over 2600 serovars identified across diverse environments. In Mexico, serovars Newport and Anatum have shown a marked increase, especially in foodborne disease, posing a public health problem. We conducted a cross-sectional study from 2021 to 2023 using active epidemiological surveillance to assess contamination in ground beef and pork at butcher shops nationwide. It involved isolation, phenotypic antimicrobial resistance, comparative genomics, spatial distribution, antimicrobial-resistance genes, and pangenome analysis. A total of 402 non-typhoidal S. enterica strains were isolated, including 59 Newport and 50 Anatum. After curating for redundancy, 45 Newport and 32 Anatum strains remained. We found that 75% of Newport strains exhibited multidrug resistance (MDR), compared to 25% of Anatum strains. Salmonella Newport also showed a broader distribution and stronger antibiotic-resistance capacity, particularly due to genes such as mphA and ramA. Our pangenome analysis showed a predominance of cell maintenance and survival-process genes in the accessory genome of both serotypes. Considering unique genes, Salmonella Anatum and Newport showed a notorious abundance of genes with functions related to replication, recombination, and repair. The substantial rise of Anatum and Newport strains in meat samples for human consumption presents an epidemiological alert, highlighting the critical need for stringent surveillance programs to mitigate human and ecosystem health risks.\n\nGeography, Antimicrobial Resistance, and Genomics of Salmonella enterica (Serotypes Newport and Anatum) from Meat in Mexico (2021-2023).", "token_count": 477, "char_count": 1762, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6638, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:15.659738", "source": { "split": "train_shard_00001", "doc_id": 248 }, "chunk_id": "train_shard_00001_248_0", "global_id": 6008 }, { "text": "Enterobacteriaceae produce an arsenal of antimicrobial compounds including microcins, ribosomally produced antimicrobial peptides showing diverse structures and mechanisms of action. Microcins target close relatives of the producing strain to promote its survival. Their narrow spectrum of antibacterial activity makes them a promising alternative to conventional antibiotics, as it should decrease the probability of resistance dissemination and collateral damage to the host's microbiota. To assess the therapeutic potential of microcins, there is a need to understand the mechanisms of resistance to these molecules. In this study, we performed genomic analyses of the resistance to four microcins [microcin C, a nucleotide peptide; microcin J25, a lasso peptide; microcin B17, a linear azol(in)e-containing peptide; and microcin E492, a siderophore peptide] on a collection of 54 Enterobacteriaceae from three species: Escherichia coli, Salmonella enterica and Klebsiella pneumoniae. A gene-targeted analysis revealed that about half of the microcin-resistant strains presented mutations of genes involved in the microcin mechanism of action, especially those involved in their uptake (fhuA, fepA, cirA and ompF). A genome-wide association study did not reveal any significant correlations, yet relevant genetic elements were associated with microcin resistance. These were involved in stress responses, biofilm formation, transport systems and acquisition of immunity genes. Additionally, microcin-resistant strains exhibited several mutations within genes involved in specific metabolic pathways, especially for S. enterica and K. pneumoniae.\n\nExploring the genetic basis of natural resistance to microcins.", "token_count": 469, "char_count": 1790, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6769, "quality_score": 0.8384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:16.300946", "source": { "split": "train_shard_00001", "doc_id": 249 }, "chunk_id": "train_shard_00001_249_0", "global_id": 6009 }, { "text": "Pangenome graphs offer a compact and comprehensive representation of genomic diversity, improving tasks such as variant calling, genotyping, and other downstream analyses. Although the underlying graph structures scale sublinearly with the number of haplotypes, the widely used GFA file format suffers from rapidly growing file sizes due to the explicit and repetitive encoding of haplotype paths. In this work, we introduce an extension to the GFA format that enables efficient grammar-based compression of haplotype paths while retaining human readability. In addition, grammar-based encoding provides an efficient in-memory data structure that does not require decompression, but conversely improves the runtime of many computational tasks that involve haplotype comparisons. We present sqz , a method that makes use of the proposed format extension to encode haplotype paths using byte pair encoding, a grammar-based compression scheme. We evaluate sqz on recent human pangenome graphs from Heumos et al . and the Human Pangenome Reference Consortium (HPRC), comparing it to existing compressors bgzip , gbz , and sequitur . sqz scales sublinearly with the number of haplotypes in a pangenome graph and consistently achieves higher compression ratios than sequitur and up to 5 times better compression than bgzip in HPRC graphs and up to 10 times in the graph from Heumos et al .. When combined with bgzip , sqz matches or excels the compression ratio of gbz across all our datasets. These results demonstrate the potential of our proposed extension of the GFA format in reducing haplotype path redundancy and improving storage efficiency for pangenome graphs.\n\nHuman readable compression of GFA paths using grammar-based code", "token_count": 385, "char_count": 1730, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5687, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:16.920497", "source": { "split": "train_shard_00001", "doc_id": 250 }, "chunk_id": "train_shard_00001_250_0", "global_id": 6010 }, { "text": "Eukaryotic chromosome segregation requires kinetochores, multi-megadalton protein machines that assemble on the centromeres of chromosomes and mediate attachments to dynamic spindle microtubules. Kinetochores are built from numerous complexes, and understanding how they are arranged is key to understanding how kinetochores perform their multiple functions. However, an integrated understanding of kinetochore architecture has not yet been established. To address this, we purified functional, native kinetochores from Kluyveromyces marxianus and examined them by electron microscopy, cryo-electron tomography and atomic force microscopy. The kinetochores are extremely large, flexible assemblies that exhibit features consistent with prior models. We assigned kinetochore polarity by visualizing their interactions with microtubules and locating the microtubule binder Ndc80c. This work shows that isolated kinetochores are more dynamic and complex than what might be anticipated based on the known structures of recombinant subassemblies, and provides the foundation to study the global architecture and functions of kinetochores at a structural level.\n\nArchitecture and flexibility of native kinetochores revealed by structural studies utilizing a thermophilic yeast", "token_count": 281, "char_count": 1270, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:17.828820", "source": { "split": "train_shard_00001", "doc_id": 251 }, "chunk_id": "train_shard_00001_251_0", "global_id": 6011 }, { "text": "The genomic representation of populations across the globe is critical to ensuring a comprehensive and equitable human reference. Constructing a pangenome graph reference for different populations is the best approach to addressing local genomic diversities. Although major initiatives across continents are underway to construct pangenome graph references, the field lacks the necessary toolsets for tertiary analysis to characterize telomere-to-telomere (T2T) assemblies and the complexity of haplotypes. PanScan is a bioinformatics software package developed for human pangenome tertiary analysis. It includes multiple modules designed to detect duplicated gene sets from T2T assemblies, identify novel variants and sequences, as well as detect and visualize complex genomic regions through pangenome graph haplotype loops. We have used multiple pangenomes across different populations to assess the tertiary analysis and their accuracy. The tool is designed to streamline tertiary analysis and is compatible with multiple pangenome graph construction algorithms. PanScan is freely available on GitHub ( https://github.com/CATG-Github/panscan ), where users can provide human pangenome assemblies or VCF files as inputs for automated analyses through command-line operations on Linux systems.

Graphical Abstract

\n\nPanScan: A tertiary analysis tool for pangenome graph", "token_count": 305, "char_count": 1378, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:18.398090", "source": { "split": "train_shard_00001", "doc_id": 252 }, "chunk_id": "train_shard_00001_252_0", "global_id": 6012 }, { "text": "

Background

The purpose of this study was to characterize Corynebacterium isolated from the ocular surface of dry eye disease patients and healthy controls. We aimed to investigate the pathogenic potential of these isolates in relation to ocular surface health. To this end, we performed whole genome sequencing in combination with biochemical, enzymatic, and antibiotic susceptibility tests. In addition, we employed deferred growth inhibition assays to examine how Corynebacterium isolates may impact the growth of potentially competing microorganisms including the ocular pathogens Pseudomonas aeruginosa and Staphylococcus aureus, as well as other Corynebacterium present on the eye.

Results

The 23 isolates were found to belong to 8 different species of Corynebacterium with genomes ranging from 2.12 mega base pairs in a novel Corynebacterium sp. to 2.65 mega base pairs in C. bovis. Whole genome sequencing revealed the presence of a range of antimicrobial targets present in all isolates. Pangenome analysis showed the presence of 516 core genes and that the pangenome is open. Phenotypic characterization showed variously urease, lipase, mucinase, protease and DNase activity in some isolates. Attention was particularly drawn to a potentially new or novel Corynebacterium species which had the smallest genome, and which produced a range of hydrolytic enzymes. Strikingly the isolate inhibited in vitro the growth of a range of possible pathogenic bacteria as well as other Corynebacterium isolates. The majority of Corynebacterium species included in this study did not seem to possess canonical pathogenic activity.

Conclusions

This study is the first reported genomic and biochemical characterization of ocular Corynebacterium. A number of potential virulence factors were identified which may have direct relevance for ocular health and contribute to the finding of our previous report on the ocular microbiome, where it was shown that DNA libraries were often dominated by members of this genus", "token_count": 508, "char_count": 2030, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5808, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:19.050678", "source": { "split": "train_shard_00001", "doc_id": 253 }, "chunk_id": "train_shard_00001_253_0", "global_id": 6013 }, { "text": "Particularly interesting in this regard was the observation that some Corynebacterium, particularly new or novel Corynebacterium sp. can inhibit the growth of other ocular Corynebacterium as well as known pathogens of the eye.\n\nWhole genome sequencing and characterization of Corynebacterium isolated from the healthy and dry eye ocular surface.", "token_count": 86, "char_count": 345, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7755, "quality_score": 0.8878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:19.427186", "source": { "split": "train_shard_00001", "doc_id": 253 }, "chunk_id": "train_shard_00001_253_1", "global_id": 6014 }, { "text": "Haemophilus seminalis is a newly proposed species that is phylogenetically related to Haemophilus haemolyticus. The distribution of H. seminalis in the human population, its genomic diversity, and its pathogenic potential are still unclear. This study reports the finding of our comparative genomic analyses of four newly isolated Haemophilus strains (SZY H8, SZY H35, SZY H36, and SZY H68) from human sputum specimens (Guangzhou, China) along with the publicly available genomes of other phylogenetically related Haemophilus species. Based on pairwise comparisons of the 16S rRNA gene sequences, the four isolates showed <98.65% sequence identity to the type strains of all known Haemophilus species but were identified as belonging to H. seminalis, based on comparable phenotypic and genotypic features. Additionally, the four isolates showed high genome-genome relatedness indices (>95% ANI values) with 17 strains that were previously identified as either \"Haemophilus intermedius\" or hemin (X-factor)-independent H. haemolyticus and therefore required a more detailed classification study. Phylogenetically, these isolates, along with the two previously described H. seminalis isolates (a total of 23 isolates), shared a highly homologous lineage that is distinct from the clades of the main H. haemolyticus and Haemophilus influenzae strains. These isolates present an open pangenome with multiple virulence genes. Notably, all 23 isolates have a functional heme biosynthesis pathway that is similar to that of Haemophilus parainfluenzae. The phenotype of hemin (X-factor) independence and the analysis of the ispD, pepG, and moeA genes can be used to distinguish these isolates from H. haemolyticus and H. influenzae", "token_count": 519, "char_count": 1779, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6194, "quality_score": 0.8097, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:54:20.059286", "source": { "split": "train_shard_00001", "doc_id": 254 }, "chunk_id": "train_shard_00001_254_0", "global_id": 6015 }, { "text": "Based on the above findings, we propose a reclassification for all \"H. intermedius\" and two H. haemolyticus isolates belonging to H. seminalis with an emended description of H. seminalis. This study provides a more accurate identification of Haemophilus isolates for use in the clinical laboratory and a better understanding of the clinical significance and genetic diversity in human environments. IMPORTANCE As a versatile opportunistic pathogen, the accurate identification of Haemophilus species is a challenge in clinical practice. In this study, we characterized the phenotypic and genotypic features of four H. seminalis strains that were isolated from human sputum specimens and propose the \"H. intermedius\" and hemin (X-factor)-independent H. haemolyticus isolates as belonging to H. seminalis. The prediction of virulence-related genes indicates that H. seminalis isolates carry several virulence genes that are likely to play an important role in its pathogenicity. In addition, we depict that the genes ispD, pepG, and moeA can be used as biomarkers for distinguishing H. seminalis from H. haemolyticus and H. influenzae. Our findings provide some insights into the identification, epidemiology, genetic diversity, pathogenic potential, and antimicrobial resistance of the newly proposed H. seminalis.\n\nComparative Genomic Analysis Reveals Genetic Diversity and Pathogenic Potential of Haemophilus seminalis and Emended Description of Haemophilus seminalis.", "token_count": 445, "char_count": 1581, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5825, "quality_score": 0.7913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:20.701071", "source": { "split": "train_shard_00001", "doc_id": 254 }, "chunk_id": "train_shard_00001_254_1", "global_id": 6016 }, { "text": "Pseudomonas aeruginosa is an opportunistic pathogen and a major driver of morbidity and mortality in people with Cystic Fibrosis (CF). The Type VI secretion system (T6SS) is a molecular nanomachine that translocates effectors across the bacterial membrane into target cells or the extracellular environment enabling intermicrobial interaction. P. aeruginosa encodes three T6SS clusters, the H1-, H2- and H3-T6SS, and numerous orphan islands. Genetic diversity of T6SS-associated effectors in P. aeruginosa has been noted in reference strains but has yet to be explored in clinical isolates. Here, we perform a comprehensive bioinformatic analysis of the pangenome and T6SS effector genes in 52 high-quality clinical P. aeruginosa genomes isolated from CF patients and housed in the Personalised Approach to P. aeruginosa strain repository. We confirm that the clinical CF isolate pangenome is open and principally made up of accessory and unique genes that may provide strain-specific advantages. We observed genetic variability in some effector/immunity encoding genes and show that several well-characterised vgrG and PAAR islands are absent from numerous isolates. Our analysis shows clear evidence of disruption to T6SS genomic loci through transposon, prophage, and mobile genetic element insertions. We identified an orphan vgrG island in P. aeruginosa strain PAK and five clinical isolates using in silico analysis which we denote vgrG7, predicting a gene within this cluster to encode a Tle2 lipase family effector. Close comparison of T6SS loci in clinical isolates compared to reference P. aeruginosa strain PAO1 revealed the presence of genes encoding eight new T6SS effectors with the following putative functions: cytidine deaminase, lipase, metallopeptidase, NADase, and pyocin", "token_count": 509, "char_count": 1875, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [ "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:21.360846", "source": { "split": "train_shard_00001", "doc_id": 255 }, "chunk_id": "train_shard_00001_255_0", "global_id": 6017 }, { "text": "Finally, the prevalence of characterised and putative T6SS effectors were assessed in 532 publicly available P. aeruginosa genomes, which suggests the existence of accessory effectors. Our in silico study of the P. aeruginosa T6SS exposes a level of genetic diversity at T6SS genomic loci not seen to date within P. aeruginosa, particularly in CF isolates. As understanding the effector repertoire is key to identifying the targets of T6SSs and its efficacy, this comprehensive analysis provides a path for future experimental characterisation of these mediators of intermicrobial competition and host manipulation.\n\nDiversity and prevalence of type VI secretion system effectors in clinical <i>Pseudomonas aeruginosa</i> isolates.", "token_count": 209, "char_count": 771, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7404, "quality_score": 0.8702, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:21.838514", "source": { "split": "train_shard_00001", "doc_id": 255 }, "chunk_id": "train_shard_00001_255_1", "global_id": 6018 }, { "text": "

Background

Thermotolerance is a critical trait for yeasts employed in industrial settings, and the utilization of unconventional yeasts has gained notable attention in recent years. However, the mechanisms underlying thermotolerance in unconventional yeasts, particularly Pichia spp., remain insufficiently elucidated.

Results

This study focuses on the thermotolerance of a non-traditional yeast strain Pichia kudriavzevii LC375240, renowned for its remarkable thermotolerance. Through transcriptomic analysis of both short-term and long-term heat shock exposures, we uncovered an intricate regulatory response in P. kudriavzevii. During long-term heat treatment, the yeast exhibited elevated expression of genes involved in the tricarboxylic acid (TCA) cycle and suppressed expression of genes in the pentose phosphate pathway (PPP). Additionally, long-term heat treatment led to an upregulation of heat shock proteins (HSPs) and an increase in trehalose, glutathione (GSH), and superoxide dismutase (SOD) levels, along with a reduction in the intracellular NADPH/NADP+ ratio and pyruvate content. These changes collectively contribute to the thermotolerance of P. kudriavzevii. CRISPR-Cas9-mediated knockout experiments further highlighted the critical roles of HSPs, antioxidases, and the trehalose metabolic pathway in the yeast's response to high temperatures.

Conclusions

Taken together, this study demonstrates that P. kudriavzevii adapts to thermal stress through a combination of enhanced TCA cycle, reduced PPP, increased HSPs, trehalose, GSH, and SOD levels. These findings provide a comprehensive understanding of the molecular mechanisms underlying thermotolerance in P. kudriavzevii.\n\nUnveiling the thermotolerance mechanism of Pichia kudriavzevii LC375240 through transcriptomic and genetic analyses.", "token_count": 508, "char_count": 1848, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [ "LC375240" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:22.493894", "source": { "split": "train_shard_00001", "doc_id": 256 }, "chunk_id": "train_shard_00001_256_0", "global_id": 6019 }, { "text": "The zoonotic pathogen Streptococcus equi subspecies zooepidemicus (SEZ) frequently colonizes equines harmlessly but can occasionally cause disease or cross species barriers. Currently, growing evidence suggests SEZ can lead to severe clinical manifestations in horses and other animals, posing a threat to human and companion animal health. In this study, we sequenced the complete genome of the SEZ strain HT321, a novel sequence type 420 isolated from a donkey with a respiratory infection in China. Subsequently, we conducted comparative genomics, core genome single nucleotide polymorphisms (cgSNP), phylogenetic analysis multilocus sequence typing (MLST), and in vitro pathogenic analysis of this isolate. 118 genes in HT321 were annotated as antibiotic resistance genes (ARGs) and comparative genomics revealed that HT321 contained more lincosamide ARGs compared to other strains. The genomic island of HT321 carried more defensive virulence genes than that in the horse strain JMC111. Furthermore, compared to the reference equine strain JMC111, HT321 exhibited superior antimicrobial resistance and biofilm formation capability but lower pathogenicity. Interestingly, core genome single-nucleotide polymorphism phylogenetic analysis of 51 SEZ strains demonstrated that HT321 clustered with horse and donkey SEZ strains as well as S. canis strains. Notably, MLST analysis of the HT321 and 116 SEZ strains indicated that the HT321 donkey strain was related to SEZ canis isolates. These findings provide valuable insights for understanding, tracking, controlling, and preventing diseases caused by SEZ in donkeys.\n\nComparative genomic and virulence analyses of a novel sequence type 420 <i>Streptococcus equi</i> subspecies <i>zooepidemicus</i> isolated from donkey.", "token_count": 508, "char_count": 1823, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": { "genes": [ "HT321", "JMC111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:23.144249", "source": { "split": "train_shard_00001", "doc_id": 257 }, "chunk_id": "train_shard_00001_257_0", "global_id": 6020 }, { "text": "The recent adaptation of the cereal crop sorghum to a global aphid outbreak was a fortuitous case of evolutionary rescue, but the pangenomic and molecular basis is not known. We show that RMES1 disrupts phloem feeding via activation of conserved immunity networks, with a growth-to-defense transition mediated by phytohormone signaling and activated by nucleotide-binding site-leucine-rich repeat receptor (NLR) resistance genes on a structural variant. The causative NLRs [resistance to Melanaphis sorghi 1A (RMES1A) and RMES1B] lack signaling domains and have adenosine triphosphatase mutations expected to abrogate function, suggesting that RMES1 NLRs regulate immunity via a noncanonical mechanism. The RMES1 NLR family is ancient, orthologous to phloem-feeding resistance genes in rice and syntenic across the grass superpangenome. Thus, gene birth-and-death processes at an ancient gene cluster created rare standing variation and provided the adaptive allele for evolutionary rescue.\n\nAncient pangenomic origins of noncanonical NLR genes underlying the recent evolutionary rescue of a staple crop.", "token_count": 306, "char_count": 1125, "word_count": 153, "semantic_coherence": 1, "information_density": 0.719, "quality_score": 0.8595, "entities": { "genes": [ "RMES1A", "RMES1B", "RMES1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:23.711288", "source": { "split": "train_shard_00001", "doc_id": 258 }, "chunk_id": "train_shard_00001_258_0", "global_id": 6021 }, { "text": "The purpose of the study was to evaluate the inhibitory effect of garlic (GEO) and peppermint (PEO) essential oils on Kluyveromyces marxianus (K. marxianus) in zucchini bouranee and also to assess the product's functional physicochemical properties during storage. The results showed that the combined use of the GEO and PEO caused a faster decrease in the yeast count. The growth rate of K. marxianus reduced significantly with increasing the EOs concentration (p < .05). No significant difference was found between amounts of the dry matter of the treatments until the 14th day. The syneresis percentages were significantly different between the treatments during storage. Meanwhile, the GEO treatments had a higher syneresis rate compared with the PEO treatments (p < .05). The organoleptic assays showed that the GEO 0.05% treatment obtained the highest score. As a result, the antimicrobial properties of the EOs, especially GEO, could increase the zucchini bouranee shelf life.\n\nSynergistic effect of peppermint and garlic essential oil on fate of Kluyveromyces marxianus in Zucchini Bouranee", "token_count": 290, "char_count": 1098, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5808, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:24.270905", "source": { "split": "train_shard_00001", "doc_id": 259 }, "chunk_id": "train_shard_00001_259_0", "global_id": 6022 }, { "text": "Identifying genetic variants associated with bacterial phenotypes, such as virulence, host preference and antimicrobial resistance, has great potential for a better understanding of the mechanisms involved in these traits. The availability of large collections of bacterial genomes has made genome-wide association studies (GWAS) a common approach for this purpose. The need to employ multiple software tools for data pre- and postprocessing limits the application of these methods by experienced bioinformaticians. To address this issue, we have developed a pipeline to perform bacterial GWAS from a set of assemblies and annotations, with multiple phenotypes as targets. The associations are run using five sets of genetic variants: unitigs, gene presence/absence, rare variants (i.e. gene burden test), gene-cluster-specific k-mers and all unitigs jointly. All variants passing the association threshold are further annotated to identify overrepresented biological processes and pathways. The results can be further augmented by generating a phylogenetic tree and predicting the presence of antimicrobial resistance and virulence-associated genes. We tested the microGWAS pipeline on a previously reported dataset on Escherichia coli virulence, successfully identifying the causal variants and providing further interpretation of the association results. The microGWAS pipeline integrates state-of-the-art tools to perform bacterial GWAS into a single, user-friendly and reproducible pipeline, allowing for the democratization of these analyses. The pipeline, together with its documentation, can be accessed at https://github.com/microbial-pangenomes-lab/microGWAS.\n\nmicroGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies.", "token_count": 409, "char_count": 1786, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:24.890448", "source": { "split": "train_shard_00001", "doc_id": 260 }, "chunk_id": "train_shard_00001_260_0", "global_id": 6023 }, { "text": "Acid whey is a by-product generated in large quantities during dairy processing, and is characterized by its low pH and high chemical oxygen demand. Due to a lack of reliable disposal pathways, acid whey currently presents a major sustainability challenge to the dairy industry. The study presented in this paper proposes a solution to this issue by transforming yogurt acid whey (YAW) into potentially palatable and marketable beverages through yeast fermentation. In this study, five prototypes were developed and fermented by Kluyveromyces marxianus, Brettanomyces bruxellensis, Brettanomyces claussenii, Saccharomyces cerevisiae (strain: Hornindal kveik), and IOC Be Fruits (IOCBF) S. cerevisiae, respectively. Their fermentation profiles were characterized by changes in density, pH, cell count, and concentrations of ethanol and organic acids. The prototypes were also evaluated on 26 sensory attributes, which were generated through a training session with 14 participants. While S. cerevisiae (IOCBF) underwent the fastest fermentation (8 days) and B. claussenii the slowest (21 days), K. marxianus and S. cerevisiae (Hornindal kveik) showed similar fermentation rates, finishing on day 20. The change in pH of the fermentate was similar for all five strains (from around 4.45 to between 4.25 and 4.31). Cell counts remained stable throughout the fermentation for all five strains (at around 6 log colony-forming units (CFU)/mL) except in the case of S. cerevisiae (Hornindal kveik), which ultimately decreased by 1.63 log CFU/mL. B. bruxellensis was the only strain unable to utilize all of the sugars in the substrate, with residual galactose remaining after fermentation", "token_count": 525, "char_count": 1758, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6478, "quality_score": 0.8239, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:54:25.559600", "source": { "split": "train_shard_00001", "doc_id": 261 }, "chunk_id": "train_shard_00001_261_0", "global_id": 6024 }, { "text": "While both S. cerevisiae (IOCBF)- and B. claussenii-fermented samples were characterized by a fruity apple aroma, the former also had an aroma characteristic of lactic acid, dairy products, bakeries and yeast. A chemical odor characteristic of petroleum, gasoline or solvents, was perceived in samples fermented by B. bruxellensis and K. marxianus. An aroma of poorly aged or rancid cheese or milk also resulted from B. bruxellensis fermentation. In terms of appearance and mouthfeel, the S. cerevisiae (IOCBF)-fermented sample was rated the cloudiest, with the heaviest body. This study provides a toolkit for product development in a potential dairy-based category of fermented alcoholic beverages, which can increase revenue for the dairy industry by upcycling the common waste product YAW.\n\nCharacterization of the Fermentation and Sensory Profiles of Novel Yeast-Fermented Acid Whey Beverages.", "token_count": 275, "char_count": 940, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8473, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:26.133487", "source": { "split": "train_shard_00001", "doc_id": 261 }, "chunk_id": "train_shard_00001_261_1", "global_id": 6025 }, { "text": "

Background

Kluyveromyces marxianus is a potentially excellent host for microbial cell factories using lignocellulosic biomass, due to its thermotolerance, high growth rate, and wide substrate spectrum. However, its tolerance to inhibitors derived from lignocellulosic biomass pretreatment needs to be improved. The prefoldin complex assists the folding of cytoskeleton which relates to the stress tolerance, moreover, several subunits of prefoldin have been verified to be involved in gene expression regulation. With the presence of inhibitors, the expression of a gene coding the subunit 4 of prefoldin (KmPFD4), a possible transcription factor, was significantly changed. Therefore, KmPFD4 was selected to evaluate its functions in inhibitors tolerance.

Results

In this study, the disruption of the prefoldin subunit 4 gene (KmPFD4) led to increased concentration of intracellular reactive oxygen species (ROS) and disturbed the assembly of actin and tubulin in the presence of inhibitors, resulting in reduced inhibitor tolerance. Nuclear localization of KmPFD4 indicated that it could regulate gene expression. Transcriptomic analysis showed that upregulated gene expression related to ROS elimination, ATP production, and NAD+ synthesis, which is a response to the presence of inhibitors, disappeared in KmPFD4-disrupted cells. Thus, KmPFD4 impacts inhibitor tolerance by maintaining integration of the cytoskeleton and directly or indirectly affecting the expression of genes in response to inhibitors. Finally, overexpression of KmPFD4 enhanced ethanol fermentation with a 46.27% improvement in productivity in presence of the inhibitors.

Conclusion

This study demonstrated that KmPFD4 plays a positive role in the inhibitor tolerance and can be applied for the development of inhibitor-tolerant platform strains.\n\nInfluence of prefoldin subunit 4 on the tolerance of Kluyveromyces marxianus to lignocellulosic biomass-derived inhibitors.", "token_count": 500, "char_count": 1979, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:26.804725", "source": { "split": "train_shard_00001", "doc_id": 262 }, "chunk_id": "train_shard_00001_262_0", "global_id": 6026 }, { "text": "

Background

The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data showed that none of the Salmonella isolates collected from the farm regions were linked to the clinical isolates-preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to horizontal transfer.

Results

SNP analysis confirmed that the clinical isolates formed a single, nearly-clonal clade with evidence for ancestry in California going back a decade. The clinical clade had a large core genome (4,399 genes) and a large and sparsely distributed accessory genome (2,577 genes, at least 64% on plasmids). At least 20 plasmid types occurred in the clinical clade, more than were found in the literature for Salmonella Newport. A small number of plasmids, 14 from 13 clinical isolates and 17 from 8 farm isolates, were found to be highly similar (> 95% identical)-indicating they might be related by horizontal transfer. Phylogenetic analysis was unable to determine the geographic origin, isolation source, or time of transfer of the plasmids, likely due to their promiscuous and transient nature. However, our resampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within the NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation.

Conclusion

Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak", "token_count": 496, "char_count": 2142, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5375, "quality_score": 0.7687, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:27.491955", "source": { "split": "train_shard_00001", "doc_id": 263 }, "chunk_id": "train_shard_00001_263_0", "global_id": 6027 }, { "text": "Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution.\n\nAssessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation.", "token_count": 83, "char_count": 409, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8596, "quality_score": 0.9298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:27.861181", "source": { "split": "train_shard_00001", "doc_id": 263 }, "chunk_id": "train_shard_00001_263_1", "global_id": 6028 }, { "text": "Abstract

BackgroundHemicelluloses act as one factor contributing to the recalcitrance of lignocelluloses that prevent cellulases to degrade the cellulose efficiently even in low quantities. Supplement of hemicellulases can enhance performance of commercial cellulases in the enzymatic hydrolyses of lignocellulose. Kluyveromyce marxianu is an attractive yeast for cellulosic ethanol fermentation, as well as a promising host for heterologous protein production, since it has remarkable thermotolerance, high growth rate, and broad substrate spectrum etc. In this study, we attempted to coordinately express multiple hemicellulases in K. marxianus through a 2A-mediated ribosomes skipping to self-cleave polyproteins, and investigated their capabilities for saccharification and ethanol production from corncobs.ResultsTwo polycistronic genes IMPX and IMPαX were constructed to test the self-cleavage of P2A sequence from Foot and Mouth Disease virus (FMDV) in K. marxianus. The IMPX gene consisted of a β-mannanase gene M330 (without the stop codon), a P2A sequence and a β-xylanase gene Xyn-CDBFV in turn, while in the IMPαX gene there was an additional α-factor signal sequence in frame with the N-terminus of Xyn-CDBFV. The extracellular β-mannanase activities of IMPX and IMPαX strains were 21.34 and 15.50 U/mL repectively", "token_count": 487, "char_count": 1576, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7135, "quality_score": 0.8568, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:28.511806", "source": { "split": "train_shard_00001", "doc_id": 264 }, "chunk_id": "train_shard_00001_264_0", "global_id": 6029 }, { "text": "By contrast, the IMPαX strain secreted 136.17 U/mLof the β-xylanase, which was much higher than that of IMPX strain 42.07 U/mL. Based on these, two recombinant strains, the IXαR and IMPαXPαR, were constructed to coordinately and secretorily express two xylantic enzymes a β-D-xylosidase RuXyn1 and Xyn-CDBFV, or three hemicellulolytic enzymes including M330, Xyn-CDBFV and RuXyn1. In fed-batch fermentations, extracellular activities of β-xylanase and β-xylosidase in the IMPαX strain were 1664.2 and 0.90 U/mL, while productions of secretory β-mannanase, β-xylanase, and β-xylosidase in the IMPαXPαR strain were 159.8, 2210.5, and 1.25 U/ml of respectively. Hemicellulolytic enzymes of these two strains enhanced the yields of both glucose and xylose from diluted acid pretreated (DAP) corncobs when acted synergistically with commercial cellulases. In hybrid saccharification and fermentation (HSF) of DAP corncobs, hemicellulases of the IMPαXPαR strain increased the ethanol yields by 8.7% at 144 h. When using aqueous ammonia pretreated (AAP) corncobs as HSF feedstocks, the IMPαXPαR strain increased both ethanol and xylose yields, which were about 12.7% and 18.2% more than that of the control at 120 h. Our results indicated that coordinately expression of hemicellulolytic enzymes in K", "token_count": 477, "char_count": 1314, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:29.150230", "source": { "split": "train_shard_00001", "doc_id": 264 }, "chunk_id": "train_shard_00001_264_1", "global_id": 6030 }, { "text": "marxianus could promote the saccharification and ethanol production from corncobs.ConclusionsThe FMDV P2A sequence showed high efficiency in self-cleavage of polyproteins in K. marxianus, and could be used for secretory expression of multiple enzymes in present of their own signal sequences. The IMPαXPαR strain that coexpressed three hemicellulolytic enzymes improved the saccharification and ethanol production from corncobs, and could be used as a promising strain for ethanol production from lignocelluloses.

\n\nCoordinately Express Hemicellulolytic Enzymes in Kluyveromyces Marxianus to Improve the Saccharification and Ethanol Production from Corncobs", "token_count": 198, "char_count": 716, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:29.594517", "source": { "split": "train_shard_00001", "doc_id": 264 }, "chunk_id": "train_shard_00001_264_2", "global_id": 6031 }, { "text": "A polyphasic study was undertaken to characterize strain G32T, an actinomycete isolated from soil collected on Giresun Island (Black Sea, Turkey). 16S rRNA phylogeny placed the strain within the genus Nonomuraea, but ≤99.1% similarity to its nearest type strains, Nonomuraea turkmeniaca DSM 43926T, Nonomuraea aridisoli KC333T, Nonomuraea candida NRRL B-24552T, Nonomuraea polychroma DSM 43925T and Nonomuraea endophytica DSM 45385T, suggested that it potentially represents a novel taxon. The total genome size is about 12.66 Mb, and the digital G+C content is 69.6 mol%. The high-quality draft genome shared ≤92.16% average nucleotide identity and ≤47.0% digital DNA-DNA hybridization with the closest related type strains, corroborating species-level distinctness. Comparative genomics against four type strains, N. turkmeniaca DSM 43926T, N. polychrom DSM 43925T, N. aridisoli KC333T and N. endophytica DSM 45385T, revealed an open pangenome of 24,056 orthologous families, of which G32T contributed 2,785 singletons", "token_count": 490, "char_count": 1211, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7394, "quality_score": 0.8697, "entities": { "genes": [ "KC333" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:30.251380", "source": { "split": "train_shard_00001", "doc_id": 265 }, "chunk_id": "train_shard_00001_265_0", "global_id": 6032 }, { "text": "Copy-number expansion of aqpZ with four paralogues and efeB with three paralogues, together with the sole genome-wide occurrence of ACC-deaminase and an additional fhuDBC siderophore transporter, highlights adaptations to periodic salinity, iron limitation and rhizosphere contact in island soil. Chemotaxonomic markers (meso-diaminopimelic, madurose, MK-9(H4), iso-C16 : 0, iso-C16 : 0 2OH and C17 : 0 10-methyl) of the strain were consistent with the genus Nonomuraea, but phenotypic traits further differentiated the isolate from its relatives. Based on the evidence presented here, strain G32T represents a novel species of the genus Nonomuraea, for which the name Nonomuraea turcica sp. nov. is proposed. The type strain of the species is G32T (=KCTC 49887T=CGMCC 4.7873T).\n\nComparative genomics and ecological insights into <i>Nonomuraea turcica</i> sp. nov., an actinomycete from Black Sea island soil.", "token_count": 406, "char_count": 1079, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7287, "quality_score": 0.8643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:30.865990", "source": { "split": "train_shard_00001", "doc_id": 265 }, "chunk_id": "train_shard_00001_265_1", "global_id": 6033 }, { "text": "

Background

While fungal infections of the bovine uterus are well-known diseases in pregnant cattle, very limited knowledge exists on the presence and significance of fungi in the uterus of non-pregnant cows. Presence of fungi in the uterine lumen of postpartum (pp) cows has been reported, but little attention has been paid to this as most studies of the bovine pp uterus have focused on bacteria.

Case presentation

Microscopy of uterine lavage cytology slides of three cows from one herd revealed the presence of numerous yeast-like organisms, which were located either free in the fluid or within macrophages. Two of the cows were around 30 days pp, while the third was 7 months pp. None of the cows had been treated with antibiotics. Culturing of the flush samples was unsuccessful, but Sanger sequencing of DNA extracted from an endometrial biopsy of one of the cows revealed the presence of Candida kefyr (Kluyveromyces marxianus). Fluorescence in situ hybridization examination of endometrial tissue sections of two cows using probes targeting 18S rRNA of the K. marxianus group was performed and revealed the presence of yeast cells on the endometrium. Histology was performed and demonstrated hyphal and non-hyphal yeast-like organisms on the surface of endometrium and in the crypts. Tissue invasion was restricted to the superficial part of the epithelium and although endometrial inflammation was present, this was mild and considered as not being caused by the fungi. One of the cows became pregnant and delivered a normal calf at term, while the two others were not bred.

Conclusions

Candida kefyr is commonly isolated from milk of cows with mastitis, but has not been reported in association with other diseases of cattle. The infection was present as a monoculture in all three cows, but the fungi had only colonized the uterine lumen and the endometrial surface", "token_count": 493, "char_count": 1900, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5488, "quality_score": 0.7744, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:31.517004", "source": { "split": "train_shard_00001", "doc_id": 266 }, "chunk_id": "train_shard_00001_266_0", "global_id": 6034 }, { "text": "Only a mild non-suppurative endometrial inflammation was present, but within the uterine luminal content, many macrophages having phagocytized yeast cells were present. Re-examination of the cows did not reveal a persistent infection, so the infection probably resolved spontaneously.\n\nColonization of the bovine uterus by Candida kefyr.", "token_count": 87, "char_count": 337, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8913, "quality_score": 0.9457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:31.886859", "source": { "split": "train_shard_00001", "doc_id": 266 }, "chunk_id": "train_shard_00001_266_1", "global_id": 6035 }, { "text": "Abiotic and biotic stresses increasingly threaten plant health and productivity, causing substantial yield losses in vital crops. In this study, 99 rhizobacteria isolated from Moroccan olive rhizospheres, OM-41 was selected as the most potent strain, exhibiting exceptional drought tolerance (thriving at Aw 0.859), thermotolerance (up to 55 °C), and halotolerance (15% NaCl), alongside plant growth-promoting (PGP) traits such as phosphate solubilization, indole-acetic acid (IAA), gibberellic acid, siderophore production, and hydrolytic enzyme secretion. The strain suppressed V. dahliae via diffusible and volatile antifungal compounds, achieving 76% and 69% inhibition rates, respectively. Whole-genome sequencing revealed a 4.2 Mbp genome (43.5% GC content) with 4362 protein-coding genes. Phylogenetic analyses confirmed its classification as B. halotolerans. Genomic annotation identified 11 secondary metabolite clusters and stress-related genes, including those linked to phosphate solubilization (phy, pho, pst family), IAA synthesis (dhaS, trp operon), siderophores (dhb cluster), nitrogen fixation (nif, suf, urt genes), ammonia production (gudB, nasD/E), biofilm formation (tasA, bsl genes), antifungal volatiles (alsD, ilv operon), hydrolytic enzymes (e.g., amyE, eglS), and vitamin biosynthesis (thiamine/riboflavin operons). Pangenome analysis of 79 B. halotolerans strains highlighted an open pangenome with 12,679 total genes (2270 core, 2382 accessory and 8027 unique); OM-41 harbored 98 unique genes", "token_count": 483, "char_count": 1520, "word_count": 197, "semantic_coherence": 1, "information_density": 0.8782, "quality_score": 0.9391, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:32.534167", "source": { "split": "train_shard_00001", "doc_id": 267 }, "chunk_id": "train_shard_00001_267_0", "global_id": 6036 }, { "text": "These findings underscore potential of OM-41 as a biofertilizer and biocontrol agent, leveraging antibiosis, resource competition, and plant defense induction to mitigate pathogens and abiotic stresses. Up to our knowledge, this is the first work that evaluates the pangenome features of B. halotolerans, offering insights into its genomic plasticity and adaptive traits. The strain’s multifunctional PGP capabilities and stress resilience position it as a promising solution for sustainable agriculture in challenging environments.\n\nComprehensive genomic and pan-genomic analysis of the drought-tolerant Bacillus halotolerans strain OM-41 isolated from Olive rhizosphere, reveals potential plant growth-promoting and biocontrol traits", "token_count": 177, "char_count": 735, "word_count": 95, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:32.971684", "source": { "split": "train_shard_00001", "doc_id": 267 }, "chunk_id": "train_shard_00001_267_1", "global_id": 6037 }, { "text": "White-Nose Syndrome (WNS) has devastated insectivorous bat populations, particularly in North America, leading to severe ecological and economic consequences. Despite extensive research, many aspects of the evolutionary history, mitochondrial genome organization, and metabolic adaptations of its etiological agent, Pseudogymnoascus destructans, remain unexplored. Here, we present a multi-scale genomic analysis integrating pangenome reconstruction, phylogenetic inference, Bayesian divergence dating, comparative mitochondrial genomics, and refined functional annotation. Our divergence dating analysis reveals that P. destructans separated from its Antarctic relatives approximately 141 million years ago, before adapting to bat hibernacula in the Northern Hemisphere. Additionally, our refined functional annotation significantly expands the known functional landscape of P. destructans, revealing an extensive repertoire of previously uncharacterized proteins involved in carbohydrate metabolism and secondary metabolite biosynthesis-key processes that likely contribute to its pathogenic success. By providing new insights into the genomic basis of P. destructans adaptation and pathogenicity, our study refines the evolutionary framework of this fungal pathogen and creates the foundation for future research on WNS mitigation strategies.\n\nBeyond White-Nose Syndrome: Mitochondrial and Functional Genomics of <i>Pseudogymnoascus destructans</i>.", "token_count": 362, "char_count": 1492, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8764, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:33.550635", "source": { "split": "train_shard_00001", "doc_id": 268 }, "chunk_id": "train_shard_00001_268_0", "global_id": 6038 }, { "text": "

Background

Breeds genetically distant from the reference genome often show considerable differences in DNA fragments, making it difficult to achieve accurate mappings. The genetic differences between pig reference genome (Sscrofa11.1) and Chinese indigenous pigs may lead to mapping bias and affect subsequent analyses.

Results

Our analysis revealed that pangenome exhibited superior mapping accuracy to the Sscrofa11.1, reducing false-positive mappings by 1.4% and erroneous mappings by 0.8%. Furthermore, the pangenome yielded more accurate genotypes of SNP (F1: 0.9660 vs. 0.9607) and INDEL (F1: 0.9226 vs. 0.9222) compared to Sscrofa11.1. In real sequencing data, the inconsistent SNPs called from the pangenome exhibited lower genome heterozygosity compared to those identified by the Sscrofa11.1, including observed heterozygosity and nucleotide diversity. The same reduction of heterozygosity overestimation was also found in the chicken pangenome.

Conclusions

This study quantifies the mapping bias of Sscrofa11.1 in Chinese indigenous pigs, demonstrating that mapping bias can lead to an overestimation of heterozygosity in Chinese indigenous pig breeds. The adoption of a pig pangenome mitigates this bias and provides a more accurate representation of genetic diversity in these populations.\n\nPangenome graph mitigates heterozygosity overestimation from mapping bias: a case study in Chinese indigenous pigs.", "token_count": 395, "char_count": 1441, "word_count": 189, "semantic_coherence": 1, "information_density": 0.5767, "quality_score": 0.7884, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:34.166330", "source": { "split": "train_shard_00001", "doc_id": 269 }, "chunk_id": "train_shard_00001_269_0", "global_id": 6039 }, { "text": "Bacterial genomes differ in both gene content and sequence mutations, which can cause important clinical phenotypic differences such as vaccine escape or antimicrobial resistance. To identify and quantify important variants, all genes within a population must be predicted, functionally annotated and clustered, representing the ‘pangenome’. Despite the volume of genome data available, gene prediction and annotation are currently conducted in isolation on individual genomes, which is computationally inefficient and frequently inconsistent across genomes. Here, we introduce the open-source software graph-gene-caller (ggCaller; https://github.com/samhorsfield96/ggCaller ). ggCaller combines gene prediction, functional annotation and clustering into a single step using population-wide de Bruijn Graphs, removing redundancy in gene annotation, and resulting in more accurate gene predictions and orthologue clustering. We applied ggCaller to simulated and real-world bacterial genome datasets, comparing it to current state-of-the-art tools. ggCaller is ~50x faster with equivalent or greater accuracy, particularly in datasets with complex sources of error, such as assembly contamination or fragmentation. ggCaller is also an important extension to bacterial genome-wide association studies, enabling querying of annotated graphs for functional analyses. We highlight this application by functionally annotating DNA sequences with significant associations to tetracycline and macrolide resistance in Streptococcus pneumoniae , identifying key resistance determinants that were missed when using only a single reference genome. ggCaller is a novel bacterial genome analysis tool with applications in bacterial epidemiology and evolutionary study.\n\nAccurate and fast graph-based pangenome annotation and clustering with ggCaller", "token_count": 404, "char_count": 1833, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:34.783629", "source": { "split": "train_shard_00001", "doc_id": 270 }, "chunk_id": "train_shard_00001_270_0", "global_id": 6040 }, { "text": "The challenge facing Helicobacter pylori (H. pylori) infection management in some parts of Africa is the evolution of drug-resistant species, the lack of gold standard in diagnostic methods, and the ineffectiveness of current vaccines against the bacteria. It is being established that even though clinical consequences linked to the bacteria vary geographically, there is rather a generic approach to treatment. This situation has remained problematic in the successful fight against the bacteria in parts of Africa. As a result, this study compared the genomes of selected H. pylori isolates from selected areas of Africa and evaluated their virulence and antibiotic drug resistance, those that are highly pathogenic and are associated with specific clinical outcomes and those that are less virulent and rarely associated with clinical outcomes. 146 genomes of H. pylori isolated from selected locations of Africa were sampled, and bioinformatic tools such as Abricate, CARD RGI, MLST, Prokka, Roary, Phandango, Google Sheets, and iTOLS were used to compare the isolates and their antibiotic resistance or susceptibility. Over 20 k virulence and AMR genes were observed. About 95% of the isolates were genetically diverse, 90% of the isolates harbored shell genes, and 50% harbored cloud and core genes. Some isolates did not retain the cagA and vacA genes. Clarithromycin, metronidazole, amoxicillin, and tinidazole were resistant to most AMR genes (vacA, cagA, oip, and bab). Conclusion. This study found both virulence and AMR genes in all H. pylori strains in all the selected geographies around Africa with differing quantities. MLST, Pangenome, and ORF analyses showed disparities among the isolates. This in general could imply diversities in terms of genetics, evolution, and protein production. Therefore, generic administration of antibiotics such as clarithromycin, amoxicillin, and erythromycin as treatment methods in the African subregion could be contributing to the spread of the bacterium's antibiotic resistance.", "token_count": 501, "char_count": 2040, "word_count": 301, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:35.442449", "source": { "split": "train_shard_00001", "doc_id": 271 }, "chunk_id": "train_shard_00001_271_0", "global_id": 6041 }, { "text": "Pangenome Analysis of Helicobacter pylori Isolates from Selected Areas of Africa Indicated Diverse Antibiotic Resistance and Virulence Genes.", "token_count": 45, "char_count": 148, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:35.795625", "source": { "split": "train_shard_00001", "doc_id": 271 }, "chunk_id": "train_shard_00001_271_1", "global_id": 6042 }, { "text": "

ABSTRACT

Understanding how pangenomes originate and evolve is crucial for predicting evolutionary trajectories and uncovering ecological interactions of bacterial pathogens. Pangenome fluidity has been attributed to adaptive evolution, yet the underlying ecological drivers for bacterial pathogens persisting in natural reservoirs remain poorly understood. Listeria monocytogenes ( Lm ), a foodborne pathogen causing fatal listeriosis, serves as an ideal model for investigating the ecological mechanisms underlying pangenome fluidity in bacterial pathogens due to its high evolutionary divergence, broad ecological versatility, and significant public health concern. Through pangenome analysis of 177 Lm isolates representing three evolutionary lineages (I, II, and III) that we isolated from soils across the United States, we found that substantial genome variation was strongly associated with climatic factors (e.g. precipitation and temperature), soil properties (e.g. aluminum, pH, and molybdenum), and bacterial community composition, particularly Nitrospirae, Planctomycetes, Acidobacteria, and Cyanobacteria. These factors exerted selective pressure across many gene functions, with pronounced effects on genes involved in cell envelope synthesis, defense mechanisms, and replication, recombination, and repair. Among Lm lineages occupying varied habitats, distinct pangenome properties were observed. Lineage III exhibited a highly fluid pangenome, which was attributed to local adaptation to nutrient-limited conditions and strong dispersal limitation. In contrast, lineage I maintained a conserved pangenome, likely due to frequent homogenizing dispersal. Consistent with these dispersal patterns, we identified an elevated risk of soil-to-human transmission in lineage I, evidenced by epidemiological links between three soil-derived and 17 clinical isolates. Collectively, this study reveals the pivotal role of environmental selection imposed by both abiotic factors and bacterial communities in governing the adaptive pangenome evolution in bacterial pathogens. It also highlights significant differences in pangenome flexibility, ecological niches, and transmission dynamics across lineages of the same pathogen species, underscoring the need for tailored source tracking strategies", "token_count": 506, "char_count": 2309, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6973, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:36.436143", "source": { "split": "train_shard_00001", "doc_id": 272 }, "chunk_id": "train_shard_00001_272_0", "global_id": 6043 }, { "text": "

AUTHOR SUMMARY

Studying the full set of genes found in different strains of a bacterium (i.e. pangenome) helps us understand how bacterial pathogens develop and adapt to changes in the environment. Here, we focused on Listeria monocytogenes ( Lm ), a pathogen capable of spreading through food and surviving in diverse environments, to understand how environmental factors and the way that bacteria move across locations can influence the pangenome content in this important bacterium. By analyzing the genomes of 177 Lm strains representing three evolutionary lineages (I, II, and III) collected from soils across the United States, we found that variation in climate, soil chemistry, and surrounding bacteria (e.g., Nitrospirae) was closely linked to genetic differences among strains. These environmental conditions seemed to affect genes that help build the cell envelop, protect the bacteria from harm, and fix damaged DNA. We also observed different levels of genome flexibility across Lm lineages which were found to be related to how they move across different locations. Lineage III showed evidence of barriers to spreading, which may enhance genetic differentiation across populations, leading to a more flexible pangenome. In contrast, lineage I appeared to spread more readily and was epidemiologically linked to human clinical cases, which may facilitate genetic exchange that reduce pangenome diversity. This study shows that both non-living environmental conditions—like precipitation and pH—and nearby groups of bacteria play a big role in shaping how bacterial pathogens change their genes to survive. It also highlights that different subtypes of the same pathogen can have different gene flexibility and spread in different ways, calling for specific biocontrol measures.\n\nDisentangling the impacts of abiotic and biotic environmental factors and dispersal dynamics on the pangenome fluidity of bacterial pathogens", "token_count": 411, "char_count": 1942, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:37.067492", "source": { "split": "train_shard_00001", "doc_id": 272 }, "chunk_id": "train_shard_00001_272_1", "global_id": 6044 }, { "text": "While the green revolution adapted a handful of crops to homogenous and high-input industrialized agriculture, much of the global population still relies on local food production from low-input smallholder farms that grow highly variable crop cultivars. The high diversity of the grain and bioenergy crop sorghum, and many other crops that were not homogenized during the green revolution, not only provides the raw materials for breeders to make substantial gains in cultivar improvement, but also constrains breeding efforts due to highly specialized locally adapted plant phenotypes. Here, we construct a 33-member pangenome and identify trait-associated variants in 1,988 cultivars and landraces. We then apply these resources to explore the complex interplay between historical contingency, ongoing adaptation, and the potential for future gains through climate-aware genome-enabled breeding. Specifically, our analyses conclusively demonstrate that multiple nested, deeply diverged, and previously uncharacterized structural variants in the domestication gene SHATTERING1 distinguish the previously established multicentric origin of sorghum. We then apply landscape genomics tests to reveal how gene flow, adaptation, and secondary contact created the complex genetic mosaic in current global breeding networks. Further analysis of climate-gene associations highlights candidate loci underlying adaptation, including the biosynthetic gene cluster for the cyanogenic glucoside dhurrin. Combined, the pangenome-informed variants developed here will enable both trait discovery and subsequent marker assays to accelerate breeding and provide a framework for similar applications in other diverse and non-model crops.\n\nDeveloping future resilience from signatures of adaptation across the sorghum pangenome", "token_count": 372, "char_count": 1809, "word_count": 241, "semantic_coherence": 1, "information_density": 0.7054, "quality_score": 0.8527, "entities": { "genes": [ "SHATTERING1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:37.690759", "source": { "split": "train_shard_00001", "doc_id": 273 }, "chunk_id": "train_shard_00001_273_0", "global_id": 6045 }, { "text": "

Background

India harbors the world's largest cattle population, encompassing over 50 distinct Bos indicus breeds. This rich genetic diversity underscores the inadequacy of a single reference genome to fully capture the genomic landscape of Indian cattle. To comprehensively characterize the genomic variation within Bos indicus and, specifically, dairy breeds, we aim to identify non-reference sequences and construct a comprehensive pangenome.

Results

Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics 'linked-read' technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb, comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-reference Unique Insertions (NUIs) spanning 7.57 Mb was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs encompassing ~ 2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (lncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis", "token_count": 498, "char_count": 1806, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6855, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:38.360266", "source": { "split": "train_shard_00001", "doc_id": 274 }, "chunk_id": "train_shard_00001_274_0", "global_id": 6046 }, { "text": "The protein-coding genes were found in various prominent quantitative trait locus (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly Long Interspersed Nuclear Elements (LINEs). Additionally, 70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.

Conclusions

This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.\n\nAdvancing the Indian cattle pangenome: characterizing non-reference sequences in Bos indicus.", "token_count": 204, "char_count": 812, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:38.841549", "source": { "split": "train_shard_00001", "doc_id": 274 }, "chunk_id": "train_shard_00001_274_1", "global_id": 6047 }, { "text": "Shiga-toxin-producing E. coli (STEC) is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Whole-genome sequencing (WGS) is a powerful tool used in public health and microbiology for the detection, surveillance, and outbreak investigation of STEC. In this study, we applied three WGS-based subtyping methods, high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multi-locus sequence typing using chromosome-associated loci [wgMLST (chrom)], and core genome multi-locus sequence typing (cgMLST), to isolate sequences from 11 STEC outbreaks. For each outbreak, we evaluated the concordance between subtyping methods using pairwise genomic differences (number of SNPs or alleles), linear regression models, and tanglegrams. Pairwise genomic differences were highly concordant between methods for all but one outbreak, which was associated with international travel. The slopes of the regressions for hqSNP vs. allele differences were 0.432 (cgMLST) and 0.966 wgMLST (chrom); the slope was 1.914 for cgMLST vs. wgMLST (chrom) differences. Tanglegrams comprised of outbreak and sporadic sequences showed moderate clustering concordance between methods, where Baker's Gamma Indices (BGIs) ranged between 0.35 and 0.99 and Cophenetic Correlation Coefficients (CCCs) were ≥0.88 across all outbreaks. The K-means analysis using the Silhouette method showed the clear separation of outbreak groups with average silhouette widths ≥0.87 across all methods. This study validates the use of cgMLST for the national surveillance of STEC illness clusters using the PulseNet 2.0 system and demonstrates that hqSNP or wgMLST can be used for further resolution.", "token_count": 472, "char_count": 1696, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6638, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:39.522749", "source": { "split": "train_shard_00001", "doc_id": 275 }, "chunk_id": "train_shard_00001_275_0", "global_id": 6048 }, { "text": "Validation of Core and Whole-Genome Multi-Locus Sequence Typing Schemes for Shiga-Toxin-Producing <i>E. coli</i> (STEC) Outbreak Detection in a National Surveillance Network, PulseNet 2.0, USA.", "token_count": 74, "char_count": 205, "word_count": 24, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:39.893640", "source": { "split": "train_shard_00001", "doc_id": 275 }, "chunk_id": "train_shard_00001_275_1", "global_id": 6049 }, { "text": "Mycobacterium abscessus is a rapid growing, free-living species of bacterium that also causes lung infections in humans. Human infections are usually acquired from the environment; however, dominant circulating clones (DCCs) have emerged recently in both M. abscessus subsp. massiliense and subsp. abscessus that appear to be transmitted among humans and are now globally distributed. These recently emerged clones are potentially informative about the ecological and evolutionary mechanisms of pathogen emergence and host adaptation. The geographical distribution of DCCs has been reported, but the genomic processes underlying their transition from environmental bacterium to human pathogen are not well characterized. To address this knowledge gap, we delineated the structure of M. abscessus subspecies abscessus and massiliense using genomic data from 200 clinical isolates of M. abscessus from seven geographical regions. We identified differences in overall patterns of lateral gene transfer (LGT) and barriers to LGT between subspecies and between environmental and host-adapted bacteria. We further characterized genome reorganization that accompanied bacterial host adaptation, inferring selection pressures acting at both genic and intergenic loci. We found that both subspecies encode an expansive pangenome with many genes at rare frequencies. Recombination appears more frequent in M. abscessus subsp. massiliense than in subsp. abscessus, consistent with prior reports. We found evidence suggesting that phage are exchanged between subspecies, despite genetic barriers evident elsewhere throughout the genome. Patterns of LGT differed according to niche, with less LGT observed among host-adapted DCCs versus environmental bacteria. We also found evidence suggesting that DCCs are under distinct selection pressures at both genic and intergenic sites. Our results indicate that host adaptation of M. abscessus was accompanied by major changes in genome evolution, including shifts in the apparent frequency of LGT and impacts of selection", "token_count": 516, "char_count": 2137, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:54:40.529896", "source": { "split": "train_shard_00001", "doc_id": 276 }, "chunk_id": "train_shard_00001_276_0", "global_id": 6050 }, { "text": "Differences were evident among the DCCs as well, which varied in the degree of gene content remodelling, suggesting they were placed differently along the evolutionary trajectory toward host adaptation. These results provide insight into the evolutionary forces that reshape bacterial genomes as they emerge into the pathogenic niche.\n\nGenome reorganization during emergence of host-associated Mycobacterium abscessus.", "token_count": 98, "char_count": 425, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8214, "quality_score": 0.9107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:40.913535", "source": { "split": "train_shard_00001", "doc_id": 276 }, "chunk_id": "train_shard_00001_276_1", "global_id": 6051 }, { "text": "Bovine tuberculosis (bTB) is a respiratory disease caused by Mycobacterium bovis, posing a significant threat to animal health and the livestock industry. Current control strategies for bTB rely on diagnostic tests and slaughter policies. However, the limitations of existing diagnostic methods, which depend on PPD antigens, necessitate the exploration of alternative antigens to enhance the accuracy and reliability of bTB diagnosis. This study aimed to identify, produce, and evaluate novel antigens for use in the intradermal skin test for bTB diagnosis. A pangenome analysis of four Mycobacterium species identified 12 unique genes specific to M. bovis SP38. Further integrated bioinformatic analysis revealed 224 genomic islands associated with virulence and pathogenesis. Among these, a highly antigenic protein, termed HP28, was selected for in vivo testing. The recombinant HP28 protein (rHP28) was expressed in E. coli and assessed for its ability to induce intradermal skin reactions in guinea pigs. The rHP28 protein elicited a skin reaction of 6.6 mm at 72 h post-injection, whereas negative controls showed no reaction. This study presents a pipeline for the selection of antigens using integrated bioinformatic analysis to identify diagnostic targets that can effectively distinguish between sensitized and non-sensitized animals, offering a promising approach for improving bTB diagnostics.\n\nIntegrated Bioinformatics Analysis for Target Identification and Evaluation of Recombinant Protein as an Antigen for Intradermal Skin Test in Bovine Tuberculosis Diagnosis.", "token_count": 409, "char_count": 1608, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6741, "quality_score": 0.8371, "entities": { "genes": [ "HP28", "SP38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:41.535850", "source": { "split": "train_shard_00001", "doc_id": 277 }, "chunk_id": "train_shard_00001_277_0", "global_id": 6052 }, { "text": "Molecular surveillance of methicillin-resistant Staphylococcus aureus (MRSA) isolated from Hospital Canselor Tuanku Muhriz (HCTM), a Malaysian teaching hospital revealed clonal replacement events of SCCmec type III-SCCmercury to SCCmec type IV strains before the year 2017; however, the reasons behind this phenomenon are still unclear. This study aimed to identify factors associated with the clonal replacement using genomic sequencing and phenotypic investigations (antibiogram profiling, growth rate and desiccation tolerance determination, survival in vancomycin sub-minimum inhibitory concentration (MIC) determination) of representative HCTM MRSA strains isolated in four-year intervals from 2005 - 2017 (n = 16). HCTM Antimicrobial Stewardship (AMS) and Infection Prevention and Control (IPC) policies were also reviewed. Phylogenetic analyses revealed the presence of 3 major MRSA lineages: ST239-III, ST22-IV and ST6-IV; MRSAs with the same STs shared similar core and accessory genomes. Majority of the ST239-III strains isolated in earlier years of the surveillance (2005, 2009 and 2013) were resistant to many antibiotics and harboured multiple AMR and virulence genes compared to ST22-IV and ST6-IV strains (isolated in 2013 and 2017). Interestingly, ST22-IV and ST6-IV MRSAs grew significantly faster and were more resistant to desiccation than ST239-III (p < 0.05), even though the later clone survived better post-vancomycin exposure. Intriguingly, ST22-IV was outcompeted by ST239-III in broth co-cultures; though it survived better when desiccated together with ST239-III", "token_count": 467, "char_count": 1590, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7005, "quality_score": 0.8502, "entities": { "genes": [ "ST6", "ST22", "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:42.175520", "source": { "split": "train_shard_00001", "doc_id": 278 }, "chunk_id": "train_shard_00001_278_0", "global_id": 6053 }, { "text": "Higher desiccation tolerance and fewer carriage of AMR genes by ST22-IV, together with reduction of antibiotic selection pressure in HCTM (due to AMS and IPC policies) during 2005 - 2017 may have provided the clone a competitive edge in replacing the previously dominant ST239-III in HCTM. This study highlights the importance of MRSA surveillance for a clearer picture of circulating clones and clonal changes. To our knowledge, this is the first genomic epidemiology study of MRSA in Malaysia, which will serve as baseline genomic data for future surveillance.\n\nDesiccation tolerance and reduced antibiotic resistance: Key drivers in ST239-III to ST22-IV MRSA clonal replacement at a Malaysian teaching hospital.", "token_count": 175, "char_count": 714, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7315, "quality_score": 0.8657, "entities": { "genes": [ "ST239", "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:42.622901", "source": { "split": "train_shard_00001", "doc_id": 278 }, "chunk_id": "train_shard_00001_278_1", "global_id": 6054 }, { "text": "This study aimed to address the need for effective probiotics and antibacterial agents to combat American foulbrood disease in honeybees, caused by Paenibacillus larvae. In the context of declining honeybee populations due to pathogens, we isolated eight lactic acid bacteria (LAB) strains from honeybee larvae (Apis mellifera L.) and evaluated their probiotic potential and inhibitory effects against P. larvae. Methods included probiotic property assessments, such as acid and bile salt resistance, hydrophobicity, auto-aggregation, co-aggregation with P. larvae, antioxidant capacities, osmotolerance to 50% sucrose, and antibiotic susceptibility. Results indicated that the GL3 strain exhibited superior probiotic attributes and potent inhibitory effects on P. larvae. Whole-genome sequencing revealed GL3 to be an Enterococcus lactis strain with genetic features tailored to the honeybee larval gut environment. Pangenome analysis highlighted genetic diversity among E. lactis strains, while molecular docking analysis identified aborycin, a lasso peptide produced by GL3, as a promising inhibitor of bacterial cell wall synthesis. These findings suggested that GL3 was a promising probiotic candidate and antibacterial agent for honeybee health management, warranting further investigation into its in vivo efficacy and potential applications in beekeeping practices.\n\nProbiotic Potential of Enterococcus lactis GL3 Strain Isolated from Honeybee (Apis mellifera L.) Larvae: Insights into Its Antimicrobial Activity Against Paenibacillus larvae.", "token_count": 450, "char_count": 1620, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6796, "quality_score": 0.8398, "entities": { "genes": [ "GL3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:43.265672", "source": { "split": "train_shard_00001", "doc_id": 279 }, "chunk_id": "train_shard_00001_279_0", "global_id": 6055 }, { "text": "Extensive genomic analyses of Enterococcus cecorum isolates from sepsis outbreaks in broilers suggest a polyphyletic origin, likely arising from core genome mutations rather than gene acquisition. This species is a normal intestinal flora of avian species with particular isolates associated with osteomyelitis. More recently, this species has been associated with sepsis outbreaks affecting broilers during the first 3 weeks post-hatch. Understanding the genetic and management basis of this new phenotype is critical for developing strategies to mitigate this emerging problem. Phylogenomic analyses of 227 genomes suggest that sepsis isolates are polyphyletic and closely related to both commensal and osteomyelitis isolate genomes. Pangenome analyses detect no gene acquisitions that distinguish all the sepsis isolates. Core genome single nucleotide polymorphism analyses have identified a number of mutations, affecting the protein-coding sequences, that are enriched in sepsis isolates. The analysis of the protein substitutions supports the mutational origins of sepsis isolates.\n\nMolecular Genomic Analyses of Enterococcus cecorum from Sepsis Outbreaks in Broilers.", "token_count": 292, "char_count": 1188, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:43.831545", "source": { "split": "train_shard_00001", "doc_id": 280 }, "chunk_id": "train_shard_00001_280_0", "global_id": 6056 }, { "text": "To explore the influence of γ-Aminobutyric acid (GABA)-producing yeast on the quality of cheese, Pichia kudriavzevii 1–21, Kluyveromyces marxianus B13-5, Saccharomyces cerevisiae DL6-20, Kluyveromyces lactis DY1-10, and a commercial starter were used to make cheese, with only the commercial starter used as a control. The results showed that K. marxianus B13-5 produced cheese had the highest GABA content (up to 489 mg/kg) and a relatively good texture, and K. lactis DY1-10 increased the production of amino acids. Principal component analysis and orthogonal partial least squares discrimination analysis were performed to distinguish the different substances in the yeast-produced cheeses from those of the control cheese. Headspace solid phase microextraction-gas chromatography-mass spectrometry of aroma compounds demonstrated that the four cheeses had strong fruity, apple, and pineapple aromas, and the yeasts all produced butanoic acid, ethyl ester, acetic acid ethyl ester, hexanoic acid, ethyl ester, and octanoic acid, ethyl ester. Compared with the control group, the different substances in the yeast-produced cheeses were 2-heptanol, 1-propanol, 2-methyl-, benzene ethanol, isoamyl alcohol; propanoic acid, 2-methyl-, acetic acid; 2-butanone; 3-hydroxy-, octanoic acid ethyl ester, and acetic acid ethyl ester. Cheese made by GABA-producing yeast could have potential probiotic effects and improved flavor.\n\nInfluence of GABA-producing yeasts on cheese quality, GABA content, and the volatilome", "token_count": 457, "char_count": 1510, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [ "DY1", "DL6" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:44.475483", "source": { "split": "train_shard_00001", "doc_id": 281 }, "chunk_id": "train_shard_00001_281_0", "global_id": 6057 }, { "text": "The growing interest in health-promoting diets has brought fermented foods into the spotlight due to their unique microbial compositions and bioactive metabolites. Fermented foods and their beneficial microbiota are expected to stimulate the overall industry's expansion over the next few years as their beneficial health effects become established. This narrative review explores the evolving dynamics of fermented food microbiota and their interactions with the gut microenvironment, emphasizing strategic pathways to enhance human health. Fermented foods, both industrially produced and traditionally prepared, serve as carriers of beneficial microorganisms such as lactic acid bacteria, yeasts, and certain fungi that transform food substrates into bioactive compounds including short-chain fatty acids (SCFAs), exopolysaccharides, and bioactive peptides. Simultaneously, their bioactive metabolites are the subject of passionate investigation by the scientific community, uncovering novel beneficial aspects that have not been elucidated until now. These metabolites contribute to improved gut barrier function, modulation of immune responses, and overall metabolic health. Notably, microbial fermentation can reshape the intrinsic properties of food, offering therapeutic potential beyond basic nutrition. The interactions between food-derived microbes and the host gut microbiota suggest a synergistic mechanism influencing gastrointestinal and systemic health outcomes. Nevertheless, there remains a significant gap in the comprehensive evaluation of the existing literature in this specific research area. Further research is needed to standardize fermented food formulations, validate the effects of individual microbial strains, and optimize their application in personalized nutrition and functional food development. Accordingly, this review highlights the association between the microbiota of fermented foods and their metabolites with the gut microenvironment, emphasizing their potential health-promoting properties.\n\nEvolving Dynamics of Fermented Food Microbiota and the Gut Microenvironment: Strategic Pathways to Enhance Human Health.", "token_count": 439, "char_count": 2155, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:45.111083", "source": { "split": "train_shard_00001", "doc_id": 282 }, "chunk_id": "train_shard_00001_282_0", "global_id": 6058 }, { "text": "Bacillus subtilis YZ01, a novel strain isolated from the feces of a healthy individual, demonstrated potent in vitro biodegradation of uric acid (54.13%) and nucleosides (41.21%). Phylogenomic analysis of 2,198 single-copy orthologous genes confirmed strain YZ01's taxonomic identity, while genome mining uncovered five circular antimicrobial peptide clusters. B. subtilis has been extensively utilized in the food industry for decades and is on the U.S. Food and Drug Administration's GRAS (Generally Recognized as Safe) list. Integrated genomic and phenotypic characterization revealed the probiotic properties and safety profile of B. subtilis YZ01, and proposed pathways for its biodegradation of uric acid and nucleosides. In vitro assays indicated that B. subtilis YZ01 exhibits excellent acid and bile salt tolerance as well as good adhesion, supported by the presence of stress-response genes, adhesion-associated surface proteins, and bile salt hydrolase genes. Antibiotic resistance genes and virulence factors were identified and confirmed to be safe through associated tests (antibiotic resistance, hemolytic assay, cytotoxicity assay and biogenic amine production). Furthermore, pilot-scale fermentation in a 100 L fermenter achieved high-density biomass production (6.12 × 1010 CFU/mL) under optimized culture conditions, underscoring its industrial scalability. These findings highlight B. subtilis YZ01's bioactive properties, food-safe profile, industrial feasibility, and promising potential as a probiotic candidate for the development of functional foods aimed at improving hyperuricemia.", "token_count": 480, "char_count": 1668, "word_count": 215, "semantic_coherence": 1, "information_density": 0.7395, "quality_score": 0.8698, "entities": { "genes": [ "YZ01" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:45.767962", "source": { "split": "train_shard_00001", "doc_id": 283 }, "chunk_id": "train_shard_00001_283_0", "global_id": 6059 }, { "text": "From indigenous screening to pilot fermentation: comprehensive characterization of <i>Bacillus subtilis</i> YZ01 as a novel food-grade probiotic candidate.", "token_count": 50, "char_count": 167, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "YZ01" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:46.126350", "source": { "split": "train_shard_00001", "doc_id": 283 }, "chunk_id": "train_shard_00001_283_1", "global_id": 6060 }, { "text": "

Background

Filamentous plant pathogens secrete effectors to successfully establish host infections. In resistant crop varieties, plant immunity can be triggered by immune receptors that recognize these effectors. Resistant crop varieties are grown in large-scale monocultures imposing strong selection pressure on pathogens, driving rapid evolution of effector repertoires resulting in the frequent breakdowns of resistance within just a few growing seasons. The oomycete Peronospora effusa , responsible for downy mildew on spinach, is an example of a rapidly adapting pathogen, but it is yet unknown how P. effusa can successfully overcome resistance of spinach by genomic adaptations.

Results

To close this knowledge gap, we here generated genome assemblies and constructed a pangenome graph for 19 isolates corresponding to 19 officially denominated resistance-breaking P. effusa races, which can cause disease on a differential set of spinach cultivars. Haplotype-resolved pangenome graph analyses revealed that many isolates emerged from recent sexual recombination, yet others evolved via prolonged asexual reproduction and loss of heterozygosity. By phasing effector candidates to determine their allelic variation, we identified effector candidates associated to resistance breaking of spinach varieties and reconstructed the evolutionary events that led to their diversification.

Conclusions

The here developed and applied computational genomics approaches offer unparalleled insights into the molecular mechanisms of the rapid evolution of P. effusa , and points to potential targets for future resistance breading.\n\nEvolution of resistance breaking in spinach downy mildew revealed through pangenome graph analysis", "token_count": 385, "char_count": 1753, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6638, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:46.744643", "source": { "split": "train_shard_00001", "doc_id": 284 }, "chunk_id": "train_shard_00001_284_0", "global_id": 6061 }, { "text": "Lignocellulosic biomass is an attractive raw material for the sustainable production of chemicals and materials using microbial cell factories. Most of the existing bioprocesses focus on second-generation ethanol production using genetically modified Saccharomyces cerevisiae, however, this microorganism is naturally unable to consume xylose. Moreover, extensive metabolic engineering has to be carried out to achieve high production levels of industrially relevant building blocks. Hence, the use of non-Saccharomyces species, or non-conventional yeasts, bearing native metabolic routes, allows conversion of a wide range of substrates into different products, and higher tolerance to inhibitors improves the efficiency of biorefineries. In this study, nine non-conventional yeast strains were selected and screened on a diluted hemicellulosic hydrolysate from Birch. Kluyveromyces marxianus CBS 6556, Scheffersomyces stipitis CBS 5773, Lipomyces starkeyi DSM 70295, and Rhodotorula toruloides CCT 7815 were selected for further characterization, where their growth and substrate consumption patterns were analyzed under industrially relevant substrate concentrations and controlled environmental conditions in bioreactors. K. marxianus CBS 6556 performed poorly under higher hydrolysate concentrations, although this yeast was determined among the fastest-growing yeasts on diluted hydrolysate. S. stipitis CBS 5773 demonstrated a low growth and biomass production while consuming glucose, while during the xylose-phase, the specific growth and sugar co-consumption rates were among the highest of this study (0.17 h-1 and 0.37 g/gdw*h, respectively). L. starkeyi DSM 70295 and R", "token_count": 500, "char_count": 1759, "word_count": 222, "semantic_coherence": 1, "information_density": 0.7027, "quality_score": 0.8514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:47.404849", "source": { "split": "train_shard_00001", "doc_id": 285 }, "chunk_id": "train_shard_00001_285_0", "global_id": 6062 }, { "text": "toruloides CCT 7815 were the fastest to consume the provided sugars at high hydrolysate conditions, finishing them within 54 and 30 h, respectively. R. toruloides CCT 7815 performed the best of all four studied strains and tested conditions, showing the highest specific growth (0.23 h-1), substrate co-consumption (0.73 ± 0.02 g/gdw*h), and xylose consumption (0.22 g/gdw*h) rates. Furthermore, R. toruloides CCT 7815 was able to produce 10.95 ± 1.37 gL-1 and 1.72 ± 0.04 mgL-1 of lipids and carotenoids, respectively, under non-optimized cultivation conditions. The study provides novel information on selecting suitable host strains for biorefinery processes, provides detailed information on substrate consumption patterns, and pinpoints to bottlenecks possible to address using metabolic engineering or adaptive evolution experiments.\n\nScreening and Growth Characterization of Non-conventional Yeasts in a Hemicellulosic Hydrolysate.", "token_count": 308, "char_count": 989, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7519, "quality_score": 0.876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:47.977823", "source": { "split": "train_shard_00001", "doc_id": 285 }, "chunk_id": "train_shard_00001_285_1", "global_id": 6063 }, { "text": "

Background

Cumulative sequencing efforts have yielded enough genomes to construct pangenomes for dozens of bacterial species and elucidate intraspecies gene conservation. Given the diversity of organisms for which this is achievable, similar analyses for ancestral species are feasible through the integration of pangenomics and phylogenetics, promising deeper insights into the nature of ancient life.

Results

We construct pangenomes for 183 bacterial species from 54,085 genomes and identify their core genomes using a novel statistical model to estimate genome-specific error rates and underlying gene frequencies. The core genomes are then integrated into a phylogenetic tree to reconstruct the core genome of the last bacterial common ancestor (LBCA), yielding three main results: First, the gene content of modern and ancestral core genomes are diverse at the level of individual genes but are similarly distributed by functional category and share several poorly characterized genes. Second, the LBCA core genome is distinct from any individual modern core genome but has many fundamental biological systems intact, especially those involving translation machinery and biosynthetic pathways to all major nucleotides and amino acids. Third, despite this metabolic versatility, the LBCA core genome likely requires additional non-core genes for viability, based on comparisons with the minimal organism, JCVI-Syn3A.

Conclusions

These results suggest that many cellular systems commonly conserved in modern bacteria were not just present in ancient bacteria but were nearly immutable with respect to short-term intraspecies variation. Extending this analysis to other domains of life will likely provide similar insights into more distant ancestral species.\n\nReconstruction of the last bacterial common ancestor from 183 pangenomes reveals a versatile ancient core genome.", "token_count": 421, "char_count": 1898, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:48.601990", "source": { "split": "train_shard_00001", "doc_id": 286 }, "chunk_id": "train_shard_00001_286_0", "global_id": 6064 }, { "text": "Background/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacterales (CPE). However, the recent emergence of resistance in clinical settings raises important concerns regarding its long-term effectiveness. This study aims to investigate the genomic determinants associated with cefiderocol resistance in CPE isolates of human origin. Methods: Comparative genomic analyses were conducted between cefiderocol-susceptible and -resistant CPE isolates recovered from human clinical and epidemiological samples at a tertiary care hospital. Whole-genome sequencing, variant annotation, structural modelling, and pangenome analysis were performed to characterize resistance mechanisms. Results: A total of 59 isolates (29 resistant and 30 susceptible) were analyzed, predominantly comprising Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae. The most frequent carbapenemase gene among the resistant isolates was blaNDM, which was also present in a subset of susceptible strains. The resistant isolates exhibited a significantly higher burden of non-synonymous mutations in their siderophore receptor genes, notably within fecR, fecA, fiu, and cirA. Structural modelling predicted deleterious effects for mutations such as fecR:G104S and fecA:A190T. Additionally, porin loss and loop 3 insertions (e.g., GD/TD) in OmpK36, as well as OmpK35 truncations, were more frequent in the resistant isolates, particularly in high-risk clones such as ST395 and ST512", "token_count": 484, "char_count": 1701, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7184, "quality_score": 0.8592, "entities": { "genes": [ "ST395", "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:49.249481", "source": { "split": "train_shard_00001", "doc_id": 287 }, "chunk_id": "train_shard_00001_287_0", "global_id": 6065 }, { "text": "Genes associated with toxin-antitoxin systems (chpB2, pemI) and a hypothetical metalloprotease (group_2577) were uniquely found in the resistant group. Conclusions: Cefiderocol resistance in CPE appears to be multifactorial. NDM-type metallo-β-lactamases and missense mutations in siderophore uptake systems-especially in those encoded by fec, fhu, and cir operons-play a central role. These may be further potentiated by alterations in membrane permeability, such as porin disruption and efflux deregulation. The integration of genomic and structural approaches provides valuable insights into emerging resistance mechanisms and may support the development of diagnostic tools and therapeutic strategies.\n\nMechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacterales: Insights from Comparative Genomics.", "token_count": 247, "char_count": 866, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:49.762947", "source": { "split": "train_shard_00001", "doc_id": 287 }, "chunk_id": "train_shard_00001_287_1", "global_id": 6066 }, { "text": "Transmission of antimicrobial-resistant bacteria among humans, animals, and the environment is a growing concern worldwide. The distribution of an international high-risk fluoroquinolone-resistant Escherichia coli clone, ST131, has been documented in clinical settings. However, the transmission of ST131 from humans to surrounding environments remains poorly elucidated. To comprehend the current situation and identify the source of ST131 in nature, we analyzed the genetic features of ST131 isolates from the aquatic environment (lake/river water) and wildlife (fox, raccoon, raccoon dog, and deer) and compared them with the features of isolates from humans in Japan using accessory and core genome single nucleotide polymorphism (SNP) analyses. We identified ST131 isolates belonging to the same phylotype and genome clusters (four of eight clusters were concomitant) with low SNP distance between the human isolates and those from the aquatic environment and wildlife. These findings warn of ST131 transmission between humans and the surrounding environment in Japan.\n\nTraces of pandemic fluoroquinolone-resistant Escherichia coli clone ST131 transmitted from human society to aquatic environments and wildlife in Japan.", "token_count": 299, "char_count": 1240, "word_count": 169, "semantic_coherence": 1, "information_density": 0.5799, "quality_score": 0.7899, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:50.349883", "source": { "split": "train_shard_00001", "doc_id": 288 }, "chunk_id": "train_shard_00001_288_0", "global_id": 6067 }, { "text": "

Background

Pangenome graphs integrate multiple assemblies to represent non-redundant genetic diversity. However, current evaluations of pangenome graphs rely primarily on technical parameters (e.g., total length, number of nodes/edges, growth curves), which fail to assess how effectively the graph represents homologous stretches across the integrated assemblies.

Results

We introduce a novel method to quantitatively assess how well a pangenome graph represents its integrated assemblies. Our method quantifies how many single-copy and universal k-mers from the source assemblies are uniquely and completely represented within the graph nodes. Implemented in the open-source tool PG-SCUnK, this approach identifies the fractions of unique, duplicated, and split k-mers, which correlate with short read mapping rates to the pangenome graph.

Conclusions

Insights provided by PG-SCUnK facilitate the selection of appropriate parameters to build optimal pangenome graphs.

Availability and implementation

A bash implementation of the PG-SCUnK workflow is freely available under the GNU GPLv3 license at https://github.com/cumtr/PG-SCUnK/ .\n\nPG-SCUnK: measuring pangenome graph representativeness using single-copy and universal K-mers", "token_count": 310, "char_count": 1271, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7125, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:50.953675", "source": { "split": "train_shard_00001", "doc_id": 289 }, "chunk_id": "train_shard_00001_289_0", "global_id": 6068 }, { "text": "

Background

The yeast Kluyveromyces marxianus offers unique potential for industrial biotechnology because of useful features like rapid growth, thermotolerance and a wide substrate range. As an emerging alternative platform, K. marxianus requires the development and validation of metabolic engineering strategies to best utilise its metabolism as a basis for bio-based production.

Results

To illustrate the synthetic biology strategies to be followed and showcase its potential, we describe a comprehensive approach to rationally engineer a metabolic pathway in K. marxianus. We use the phenylalanine biosynthetic pathway both as a prototype and because phenylalanine is a precursor for commercially valuable secondary metabolites. First, we modify and overexpress the pathway to be resistant to feedback inhibition so as to overproduce phenylalanine de novo from synthetic minimal medium. Second, we assess native and heterologous means to increase precursor supply to the biosynthetic pathway. Finally, we eliminate branch points and competing reactions in the pathway and rebalance precursors to redirect metabolic flux to a specific product, 2-phenylethanol (2-PE). As a result, we are able to construct robust strains capable of producing over 800 mg L-1 2-PE from minimal medium.

Conclusions

The strains we constructed are a promising platform for the production of aromatic amino acid-based biochemicals, and our results illustrate challenges with attempting to combine individually beneficial modifications in an integrated platform.\n\nRational engineering of Kluyveromyces marxianus to create a chassis for the production of aromatic products.", "token_count": 404, "char_count": 1685, "word_count": 227, "semantic_coherence": 1, "information_density": 0.63, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:51.609505", "source": { "split": "train_shard_00001", "doc_id": 290 }, "chunk_id": "train_shard_00001_290_0", "global_id": 6069 }, { "text": "Mango ( Mangifera spp.) is a major tropical fruit crop of global economic importance, but advanced genomic resources are needed to support its breeding, conservation, and sustainable cultivation. In this study, a mango pangenome was constructed using high-quality, telomere-to-telomere genomes of four cultivated mango ( M. indica ) accessions representing distinct genetic origins, and one wild relative, M. odorata . Genome-wide analyses revealed a significant reduction in heterozygosity among elite commercial cultivars, indicating a genetic bottleneck resulting from long-term artificial selection. Core genes were enriched in fundamental biological pathways, including primary metabolism, photosynthesis, transcriptional regulation, and cellular signaling. Variable genes were primarily associated with secondary metabolite biosynthesis, reflecting local environmental adaptations. Pangenome and comparative genomic analyses identified structural variations among accessions. Additionally, 10,482 high-confidence single nucleotide polymorphisms (SNPs) were detected and utilized for population genomic analysis of 197 mango accessions, delineating four genetically distinct groups. Southeast Asian accessions exhibited unique genetic diversity and divergence from Caribbean, Indian, and U.S. groups. Comparative analyses revealed differentiation in specialized metabolic pathways, particularly alkaloid and diterpenoid biosynthesis, likely reflecting adaptive responses to the complex ecological interactions and high biodiversity of Southeast Asian tropical rainforests. Genomic analysis of the MiRWP gene, associated with apomixis, provided comprehensive insights into this important mango trait, demonstrating the potential of the pangenome for future mango breeding efforts. The genomic resources generated in this study establish a critical foundation for advancing mango genetic research, facilitating trait improvement, and informing conservation strategies.\n\nPangenome analysis provides insights into the evolution of mango ( Mangifera spp.)", "token_count": 450, "char_count": 2062, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6838, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:52.259819", "source": { "split": "train_shard_00001", "doc_id": 291 }, "chunk_id": "train_shard_00001_291_0", "global_id": 6070 }, { "text": "Genome annotation, alignment, and phylogenetics are at the center of most work in evolutionary genomics. These techniques function best when rooted in prior work. Genes are mined from new genomes using evidence from old gene models. These genomes are aligned to well-worn references to create matrices for tree reconstruction. And trees are often populated with well characterized genomes to add context to the newly sequenced. Genome inference traces a line back to model organisms, yoking the analysis of new genomes to layers of previous knowledge. We instead highlight methods that use unannotated and unaligned sequence to understand the information diversity of sequence ensembles. Any set of genomes can comprise our sequence ensemble. In a pandemic context, a sequence ensemble might be clinically isolated strains from one day. In a systematic context, a sequence ensemble could be the pangenome available for a clade. The normal bioinformatics playbook would have us align. But we instead compress. A sequence ensemble that compresses easily contains lower information diversity. For pandemics, we can use curves of information diversity to trace genomic novelty and monitor selective sweeps in new strains. For systematics, we can calculate compressibility quickly across all known bacterial taxa, leveling the criteria for species across clades. If we tolerate data loss, we can go one step further and capture structural evolution as we compress. Our approach sacrifices a lot. We skip many of the products of modern bioinformatics like variation anchored to known genes or genome alignment to prescribed references or pangenome graphs. But we gain speed, breadth, and the ability to respond to novelty.\n\nWhat we talk about when we talk about species", "token_count": 370, "char_count": 1763, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:52.845274", "source": { "split": "train_shard_00001", "doc_id": 292 }, "chunk_id": "train_shard_00001_292_0", "global_id": 6071 }, { "text": "Pangenomics, the identification of shared genes across a taxonomic range, is essential for understanding microbial genetic diversity. Yet, gene clustering and pangenome tools often operate as one-size-fits-all black boxes whose outputs are difficult to validate and interpret. This study introduces PyamilySeq, not a replacement, but a diagnostic framework to expose and quantify hidden limitations and guide the development of more robust methodologies. By evaluating widely used gene clustering and pangenome tools, we observe how clustering thresholds (often hard-coded and provided without explanation) and paralog handling impact gene family composition. Parameters unrelated to clustering thresholds, such as decimal precision (0.8 vs. 0.80), output selection, and even CPU and memory allocation, are demonstrated to alter gene family assignments, in striking contrast to the standard assumption that broadly the same parameter values will yield consistent results. Additionally, tools often fail to report biologically meaningful or representative sequences for gene families, leading to misguided downstream analyses. This work highlights key limitations in current gene clustering and pangenome methodologies, demonstrating their potential to influence biological interpretations. To advance the field, we must prioritise adaptable and transparent approaches and move beyond rigid, one-size-fits-all tools and parameter choices.\n\nPyamilySeq: Exposing the fragility of conventional gene (re)clustering and pangenomic inference methods", "token_count": 318, "char_count": 1542, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7291, "quality_score": 0.8645, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:53.413559", "source": { "split": "train_shard_00001", "doc_id": 293 }, "chunk_id": "train_shard_00001_293_0", "global_id": 6072 }, { "text": "The effective utilization of okara (soybean residue) has become a considerable challenge in recent years. In this paper, the potential advantages of β-glucosidase production from okara fermented by Kluyveromyces marxianus were evaluated and the properties of the β-glucosidase were also characterized. The results showed that okara can significantly induce the production of β-glucosidase from K. marxianus. The β-glucosidase activity was up to 4.5 U/mg under optimized fermentation conditions. The optimal parameters were as follows: fermentation temperature 35 °C, cultivation time 98 h, inoculum concentration 10%, and 30 g/L of okara. After two steps of purification using ammonium sulfate precipitation and Sephadex G-75 column chromatography, the activity of β-glucosidase was 71.4 U/mg. The native enzyme was an approximately 66 kDa dimer consisting of two different subunits (22 and 44 kDa). The kinetic parameters of the K. marxianus β-glucosidase, using pNPG as substrate, were V max 8.34 μmol min-1 mg-1 and K m 7.42 mM. The β-glucosidase showed high thermostability and acid-alkali tolerance as well as low inhibition by DMSO (10-50%). In conclusion, this study supports the notion that okara fermentation by K. marxianus could be a useful process to produce β-glucosidase.", "token_count": 512, "char_count": 1448, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6737, "quality_score": 0.8368, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:54.070333", "source": { "split": "train_shard_00001", "doc_id": 294 }, "chunk_id": "train_shard_00001_294_0", "global_id": 6073 }, { "text": "Production of β-glucosidase from okara fermentation using Kluyveromyces marxianus.", "token_count": 38, "char_count": 96, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:54.431959", "source": { "split": "train_shard_00001", "doc_id": 294 }, "chunk_id": "train_shard_00001_294_1", "global_id": 6074 }, { "text": "This study presents three genome assemblies within the Capsicum genus, enabling comprehensive comparative analyses for the Annuum and Baccatum complexes within the genus. We produced highly continuous assemblies of the nuclear genomes and complete chloroplast assemblies. Subsequent genome annotation identified 34,580 genes in non-pungent C. annuum cv. ECW, and 32,704 and 33,994 genes in pungent C. chacoense and C. galapagoense , respectively. These assemblies, including the first complete genomes for C. chacoense and C. galapagoense , provide additional genomic resolution within the Capsicum genus. The novel genomes were analyzed within a pangenomic framework, integrating 16 Capsicum genomes across the Annuum, Baccatum , and Pubescens complexes. Homology grouping was used to identify core, accessory and unique genes and showed a wide spectrum of genetic diversity, particularly in homology groups exclusive to C. chacoense and C. galapagoense . Out of 79,267 homology groups identified, 13% were core groups, present in all accessions, corresponding to approximately 30% of core genes per genome. Comparative analyses revealed distinct species and genus specific genomic characteristics. Additionally, we used the graph pangenome to illustrate locus-level exploration by examining the Pun1 locus associated with capsaicinoid biosynthesis, identifying multiple Pun1 -like genes including their genomic position and homology information. The integration of these new resources into a dynamic Capsicum pangenome framework provides a versatile platform for extracting genetic information relevant to both fundamental research and breeding applications.\n\nThree novel genomes broaden the wild side of the Capsicum pangenome", "token_count": 426, "char_count": 1736, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:55.056483", "source": { "split": "train_shard_00001", "doc_id": 295 }, "chunk_id": "train_shard_00001_295_0", "global_id": 6075 }, { "text": "In this work, the newly isolated thermotolerant Kluyveromyces marxianus DBKKUY-103 exhibited a high ethanol fermentation efficiency at high temperatures using sweet sorghum juice (SSJ). The highest ethanol concentrations and productivities achieved under the optimum conditions using thermotolerant K. marxianus DBKKUY-103 were 85.16 g/l and 1.42 g/l.h at 37 °C and 83.46 g/l and 1.39 g/l.h at 40 °C, respectively. The expression levels of genes during ethanol fermentation at 40 °C were evaluated and the results found that the transcriptional levels of the RAD10, RAD14, RAD33, RAD50, ATPH, ATP4, ATP16, and ATP20 genes were up-regulated compared with those at 30 °C, suggesting that the high growth and high ethanol production efficiencies of K. marxianus DBKKUY-103 during high-temperature ethanol production associated with the genes involved in DNA repair and ATP production.\n\nThe potential of the newly isolated thermotolerant Kluyveromyces marxianus for high-temperature ethanol production using sweet sorghum juice.", "token_count": 393, "char_count": 1108, "word_count": 146, "semantic_coherence": 1, "information_density": 0.5548, "quality_score": 0.7774, "entities": { "genes": [ "RAD50", "RAD10", "ATP4", "ATP20", "RAD33", "ATP16", "RAD14" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:55.671846", "source": { "split": "train_shard_00001", "doc_id": 296 }, "chunk_id": "train_shard_00001_296_0", "global_id": 6076 }, { "text": "Enterococcus raffinosus is an understudied member of its genus possessing a characteristic megaplasmid contributing to a large genome size. Although less commonly associated with human infection compared to other enterococci, this species can cause disease and persist in diverse niches such as the gut, urinary tract, blood and environment. Few complete genome assemblies have been published to date for E. raffinosus . In this study, we report the complete assembly of the first clinical urinary E. raffinosus strain, Er676, isolated from a postmenopausal woman with history of recurrent urinary tract infection. We additionally completed the assembly of clinical type strain ATCC49464. Comparative genomic analyses reveal inter-species diversity driven by large accessory genomes. The presence of a conserved megaplasmid indicates it is a ubiquitous and vital genetic feature of E. raffinosus . We find that the E. raffinosus chromosome is enriched for DNA replication and protein biosynthesis genes while the megaplasmid is enriched for transcription and carbohydrate metabolism genes. Prophage analysis suggests that diversity in the chromosome and megaplasmid sequences arises, in part, from horizontal gene transfer. Er676 demonstrated the largest genome size reported to date for E. raffinosus and the highest probability of human pathogenicity. Er676 also possesses multiple antimicrobial resistance genes, of which all but one are encoded on the chromosome, and has the most complete prophage sequences. Complete assembly and comparative analyses of the Er676 and ATCC49464 genomes provide important insight into the inter-species diversity of E. raffinosus that gives it its ability to colonize and persist in the human body. Investigating genetic factors that contribute to the pathogenicity of this species will provide valuable tools to combat diseases caused by this opportunistic pathogen.", "token_count": 491, "char_count": 1954, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [ "ATCC49464" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:56.336455", "source": { "split": "train_shard_00001", "doc_id": 297 }, "chunk_id": "train_shard_00001_297_0", "global_id": 6077 }, { "text": "Inter-species diversity and functional genomic analyses of closed genome assemblies of clinically isolated, megaplasmid-containing Enterococcus raffinosus Er676 and ATCC49464.", "token_count": 58, "char_count": 182, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [ "ATCC49464" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:56.695948", "source": { "split": "train_shard_00001", "doc_id": 297 }, "chunk_id": "train_shard_00001_297_1", "global_id": 6078 }, { "text": "Infections caused by antibiotic-resistant Staphylococcus are a global concern. This is true in the Middle East, where increasingly resistant Staphylococcus aureus and Staphylococcus haemolyticus strains have been detected. While extensive surveys have revealed the prevalence of infections caused by antibiotic-resistant staphylococci in Europe, Asia, and North America, the population structure of antibiotic-resistant staphylococci recovered from patients and clinical settings in Egypt remains uncharacterized. We performed whole-genome sequencing of 56 S. aureus and 10 S. haemolyticus isolates from Alexandria Main University Hospital; 46 of the S. aureus genomes and all 10 of the S. haemolyticus genomes carry mecA, which confers methicillin resistance. Supplemented with additional publicly available genomes from the other parts of the Middle East (34 S. aureus and 6 S. haemolyticus), we present the largest genomic study to date of staphylococcal isolates from the Middle East. These genomes include 20 S. aureus multilocus sequence types (MLST), including 3 new ones. They also include 9 S. haemolyticus MLSTs, including 1 new one. Phylogenomic analyses of each species' core genome largely mirrored those of the MLSTs, irrespective of geographical origin. The hospital-acquired spa t037/ST239-SCCmec III/MLST CC8 clone represented the largest clade, comprising 22% of the S. aureus isolates. Like S. aureus genome surveys of other regions, these isolates from the Middle East have an open pangenome, a strong indicator of gene exchange of virulence factors and antibiotic resistance genes with other reservoirs. Our genome analyses will inform antibiotic stewardship and infection control plans in the Middle East. IMPORTANCE Staphylococci are understudied despite their prevalence within the Middle East", "token_count": 532, "char_count": 1873, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [ "CC8", "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:54:57.335776", "source": { "split": "train_shard_00001", "doc_id": 298 }, "chunk_id": "train_shard_00001_298_0", "global_id": 6079 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is endemic to hospitals in Egypt, as are other antibiotic-resistant strains of S. aureus and S. haemolyticus. To provide insight into the strains circulating in Egypt, we performed whole-genome sequencing of 56 S. aureus and 10 S. haemolyticus isolates from Alexandria Main University Hospital. Through analysis of these genomes, as well as all available S. aureus and S. haemolyticus genomes from the Middle East (n = 40), we were able to produce a picture of the diversity in this region more complete than those afforded by traditional molecular typing strategies. For example, we identified 4 new MLSTs. Most strains harbored genes associated with multidrug resistance, toxin production, biofilm formation, and immune evasion. These data provide invaluable insight for future antibiotic stewardship and infection control within the Middle East.\n\nWhole-Genome Sequencing of Staphylococcus aureus and Staphylococcus haemolyticus Clinical Isolates from Egypt.", "token_count": 309, "char_count": 1053, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:57.912317", "source": { "split": "train_shard_00001", "doc_id": 298 }, "chunk_id": "train_shard_00001_298_1", "global_id": 6080 }, { "text": "

Background:

Using yeast fermentation to produce bioethanol, is an economic and renewable way to tackle the rapid increase in fuel consumption. Faster cell growth rate guarantees the superior result of fermentation course. The “non-conventional” yeast Kluyveromyces marxianus is the known fastest-growing eukaryote on the earth. Although its wide application in industry, the molecular mechanisms for its fast growth have seldom been discovered.Results We first carried out a comparative genome content analysis for K. marxianus evolution in Saccharomycetaceae and identified the gain/lost genes as well as highly copied genes during K. marxianus speciation. Then RNA-seq analyses for K. marxianus and S. cerevisiae at different time points along cultivation were performed, to infer the function of K. marxianus-specific genes and to find out the difference in homologous gene expression patterns between the two species. RNA-seq results were further validated with RT-qPCR analysis. Genome content analysis shows the highly intense events of genes’ gain/loss happened at the occurrence of Saccharomycetaceae and Kluyveromyces, and K. marxianus has particularly high copy numbers of genes participating in iron transport and biotin biosynthesis. The RNA-seq analysis reveals 40% of K. marxianus-specific genes were up-regulated and may participate in glucose transport and mitochondrial function. Furthermore, compared to S. cerevisiae, K. marxianus has developed two features in homologous gene expressions to ensure its fast growth: (1) enhanced fundamental expressions of TCA cycle and respiratory chain genes at the beginning of cultivation; (2) tightly co-up-regulated expressions of respiratory chain, F0F1 ATPase, and glucose transporter genes at its fastest growth phase. Those co-expressions are mainly ascribed to the higher number of significant motifs in the upstream sequences of involved genes in K. marxianus than in S. cerevisiae, indicating the importance of transcriptional network remodelling during evolution.Conclusions This study gives insights into the possible mechanisms of K", "token_count": 505, "char_count": 2110, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6115, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:58.571791", "source": { "split": "train_shard_00001", "doc_id": 299 }, "chunk_id": "train_shard_00001_299_0", "global_id": 6081 }, { "text": "marxianus’ fast growth trait, via efficiently supplying sufficient energy for cell growth, meanwhile reinforcing glucose transport to guarantee the competition for environmental resources. Our findings present a theoretical support for K. marxianus’ prospective application in industry, and give clues for further rational construction of fast-growing yeast strains.\n\nComparative genomic analysis reveals metabolic mechanisms for Kluyveromyces marxianus’ fast growth during evolution", "token_count": 101, "char_count": 483, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:58.947450", "source": { "split": "train_shard_00001", "doc_id": 299 }, "chunk_id": "train_shard_00001_299_1", "global_id": 6082 }, { "text": "The K. marxianus has emerged as a potential yeast strain for various biotechnological applications. However, the limited number of available genetic tools has hindered the widespread usage of this yeast. In the current study we have expanded the molecular tool box by identifying novel sets of promoters and terminators for increased recombinant protein expression in K. marxianus. The previously available transcriptomic data were analyzed to identify top 10 promoters of highest gene expression activity. We further characterized and compared strength of these identified promoters using eGFP as a reporter protein, at different temperatures and carbon sources. To examine the regulatory region driving protein expression, serially truncated shorter versions of two selected strong promoters were designed, and examined for their ability to drive eGFP protein expression. The activities of these two promoters were further enhanced using different combinations of native transcription terminators of K. marxianus. We further utilized the identified DNA cassette encoding strong promoter in metabolic engineering of K. marxianus for enhanced β-galactosidase activity. The present study thus provides novel sets of promoters and terminators as well as engineered K. marxianus strain for its wider utility in applications requiring lactose degradation such as in cheese whey and milk.\n\nThe identification of novel promoters and terminators for protein expression and metabolic engineering applications in Kluyveromyces marxianus.", "token_count": 348, "char_count": 1570, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:54:59.535126", "source": { "split": "train_shard_00001", "doc_id": 300 }, "chunk_id": "train_shard_00001_300_0", "global_id": 6083 }, { "text": "Rosa , belonging to the family Rosaceae, encompasses more than 150 species which are widely distributed in the northern hemisphere. Renowned for their beauty, roses are cultivated throughout the world for ornamental purposes and the production of essential oils and perfumes. Despite their cultural and commercial significance, the genomic resources of wild Rosa species have not been studied comprehensively, hampering the understanding of their genetic diversity, evolutionary history, and breeding potential. Here we report on high-quality de novo genomes for Rosa sericea and Rosa rugosa . By integrating these two de novo genomes with existing public genomic resources, we have built a Rosaceae panproteome and a Rosa pangenome (spanning wild, traditional garden, and modern rose lineages) using a De Bruijn graph (DBG)-based approach. A maximum likelihood (ML) phylogeny of 18 Rosa haplotypes based on 4,367 single-copy core homology groups (genes) provided robust evolutionary inference, confirming the basal position of R. sericea , and enabled a gene-based macrosynteny analysis across the pangenome. Our analyses revealed significant genomic diversity among species, extensive variation in core gene content, and lineage-specific transposable element (TE) expansion patterns that contribute to the variation in Rosa genome size and to species-specific adaptations. The pangenome also revealed biased diversification of homology groups potentially linked to phenotypic plasticity in Rosa . Specifically, our analysis of the rose scent-related gene family, NUDX1 , uncovered its evolutionary trajectory in Rosa , in which TEs insertions provided putative novel regulatory elements that facilitated adaptive evolution in metabolic pathways. This pangenomic study deepens our understanding of the genetic diversity and evolution of traits within the Rosa genus. In addition, the findings lay the foundation for future efforts to understand the genetic mechanisms driving trait evolution, which can support rose breeding.\n\nTwo high-quality rose genomes underpin a novel Rosa pangenome to advance rose genomics, phylogenetics, and breeding", "token_count": 475, "char_count": 2150, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [ "NUDX1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:00.521083", "source": { "split": "train_shard_00001", "doc_id": 301 }, "chunk_id": "train_shard_00001_301_0", "global_id": 6084 }, { "text": "Short-read genome assemblies typically consist of many contigs of variable lengths and their putative connections represented as an assembly graph. Assembly graphs produced by different tools from the same data may differ significantly, posing a challenge to tools for downstream processing tasks. One such task is plasmid binning, that is identifying plasmids in sequenced bacterial isolates, which is crucial for monitoring the spread of antimicrobial resistance. When plasmid binning tools are applied to assembly graphs produced by different tools, they may exhibit different performance, and choosing the best results a priori can be difficult. To address the above issue, we propose the use of a pangenome graph, built from assembly graphs produced by assembling short reads of the same sample with different assemblers. The resulting pangenome-assembly graph highlights similarities between contigs from different assemblies while retaining information on contigs that appear only in one of the input assemblies. We then used the PlasBin-flow plasmid binning tool customized to take into account pangenome information to identify plasmid bins. The results for pangenome-assemblies built by Unicycler and Skesa show an increase in accuracy measures compared to the mean results obtained on single assemblies, leading to an overall more accurate prediction than a blind choice of assemblers. The source code of the pipeline is available at https://github.com/AlgoLab/pangebin along with the dataset used in this study.\n\nPangebin: improving plasmid binning in bacterial isolates using pangenome-assembly graphs", "token_count": 346, "char_count": 1614, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:01.095071", "source": { "split": "train_shard_00001", "doc_id": 302 }, "chunk_id": "train_shard_00001_302_0", "global_id": 6085 }, { "text": "Repeats are the most diverse and dynamic but also the least well-understood component of microbial genomes. For all we know, repeat-associated mutations such as duplications, deletions, inversions and gene conversion might be as common as point mutations, but because of short-read myopia and methodological bias, they have received much less attention. Long-read DNA sequencing opens the perspective of resolving repeats and systematically investigating the mutations they induce. For this study, we assembled the genomes of 16 closely related strains of the bacterial pathogen Mycobacterium tuberculosis from Pacific Biosciences HiFi reads, with the aim of characterizing the full spectrum of DNA polymorphisms. We found that complete and accurate genomes can be assembled from HiFi reads, with read size being the main limitation in the presence of duplications. By combining a reference-free pangenome graph with extensive repeat annotation, we identified 110 variants, 58 of which could be assigned to repeat-associated mutational mechanisms such as strand slippage and homologous recombination. Whilst recombination events were less frequent than point mutations, they affected large regions and introduced multiple variants at once, as shown by three gene conversion events and a duplication of 7.3 kb that involved ppe18 and ppe57, two genes possibly involved in immune subversion. The vast majority of variants were present in single isolates, such that phylogenetic resolution was only marginally increased when estimating a tree from complete genomes. Our study shows that the contribution of repeat-associated mechanisms of mutation can be similar to that of point mutations at the microevolutionary scale of an outbreak. A large reservoir of unstudied genetic variation in this 'monomorphic' bacterial pathogen awaits investigation.\n\nGene conversion and duplication contribute to genetic variation in an outbreak of <i>Mycobacterium tuberculosis</i>.", "token_count": 465, "char_count": 1996, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6214, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:01.754215", "source": { "split": "train_shard_00001", "doc_id": 303 }, "chunk_id": "train_shard_00001_303_0", "global_id": 6086 }, { "text": "Abstract

Background: Porcine Parvovirus (PPV) is a Parvovirinae virus that can cause embryonic and fetal loss and death and mummification in affected fetal pigs. Unlike conventional vaccines, virus-like particles (VLPs) inherit the natural structure of their authentic virions and highly immunostimulatory that can induce strong humoral immune and T cell responses with no risk of pathogenicity. The production of PPV VLPs is still a challenge based on traditional expression platforms due to their low yields and high culture costs. Kluyveromyces marxianus is a safe and fast-growing eukaryote that can get high biomass with low-cost cultures. In this study, we investigated the expression and downstream processes of PPV VLPs in K. marxianus, and the potential for effective stand-alone vaccines.Results: After optimization according to the codon bias of K.marxianus, the VP2 protein from Kresse strain was highly expressed. In a 5 L fermentator, the yield of PPV VLPs reached 2.5 g/L, quantified by HPLC, using a defined mineral medium after 48 h fermentation. Two strategies were established to purify intracellular PPV VLPs: i) Using the cation exchange chromatography coupled with Sephacryl® S-500 HR chromatography to purify VLPs from the supernatants of pH adjusted cell lysates. ii) Using anion exchange chromatography followed by cross-flow diafiltration to recover the VLPs precipitated in pH adjusted cell lysates. The purity of PPV VLPs reached about 95%, and total recovery was more than 60%. Vaccination of mice with the purified PPV VLPs induced high titers of specific IgG antibodies in sera, and showed hemagglutination inhibitions on both swine and guinea pig erythrocytes", "token_count": 507, "char_count": 1821, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8314, "entities": { "genes": [ "VP2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:02.453313", "source": { "split": "train_shard_00001", "doc_id": 304 }, "chunk_id": "train_shard_00001_304_0", "global_id": 6087 }, { "text": "Spleen lymphocyte proliferation and cytokines detection suggested the PPV VLPs produced by K.marxianus provoked the cellular immune and humoral immunity responses in mice.Conclusion: This is the highest production of recombinant PPV VLPs achieved to date. The superiorities, Generally Recognized As Safe (GRAS), high production, short lead time, and low cost, make K. marxianus a greatly competitive platform for bioproduction of PPV VLPs vaccine.

\n\nInvestigation of Kluyveromyces marxianus as a novel host for large-scale production of porcine parvovirus virus-like particles", "token_count": 178, "char_count": 626, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:02.903073", "source": { "split": "train_shard_00001", "doc_id": 304 }, "chunk_id": "train_shard_00001_304_1", "global_id": 6088 }, { "text": "Citrobacter werkmanii is an emerging and opportunistic human pathogen found in developing countries and is a causative agent of wound, urinary tract, and blood infections. The present study conducted comparative genomic analyses of a C. werkmanii strain collection from diverse geographical locations and sources to identify the relevant virulence and antimicrobial resistance genes. Pangenome analyses divided the examined C. werkmanii strains into five distinct clades; the subsequent classification identified genes with functional roles in carbohydrate and general metabolism for the core genome and genes with a role in secretion, adherence, and the mobilome for the shell and cloud genomes. A maximum-likelihood phylogenetic tree with a heatmap, showing the virulence and antimicrobial genes' presence or absence, demonstrated the presence of genes with functional roles in secretion systems, adherence, enterobactin, and siderophore among the strains belonging to the different clades. C. werkmanii strains in clade V, predominantly from clinical sources, harbored genes implicated in type II and type Vb secretion systems as well as multidrug resistance to aminoglycoside, beta-lactamase, fluoroquinolone, phenicol, trimethoprim, macrolides, sulfonamide, and tetracycline. In summary, these comparative genomic analyses have demonstrated highly pathogenic and multidrug-resistant genetic profiles in C. werkmanii strains, indicating a virulence potential for this commensal and opportunistic human pathogen.\n\nComparative Genomic Analyses of Virulence and Antimicrobial Resistance in Citrobacter werkmanii, an Emerging Opportunistic Pathogen.", "token_count": 439, "char_count": 1691, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5826, "quality_score": 0.7913, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:03.583580", "source": { "split": "train_shard_00001", "doc_id": 305 }, "chunk_id": "train_shard_00001_305_0", "global_id": 6089 }, { "text": "Whey is the main by-product of the dairy industry and contains sugars (lactose) and proteins (especially serum proteins and, at lesser extent, residual caseins), which can be valorized by the fermentative action of yeasts. In the present study, we characterized the spoilage yeast fraction inhabiting natural whey starter (NWS), the undefined starter culture of thermophilic lactic acid bacteria used in Parmigiano Reggiano (PR) cheesemaking, and evaluated thermotolerance, mating type, and the aptitude to produce ethanol and bioactive peptides from whey lactose and proteins, respectively, in a selected pool of strains. We found that PR NWS yeast population consists of other species (Saccharomyces cerevisiae, Wickerhamiella pararugosa, and Torulaspora delbrueckii) in addition to the well-documented Kluyveromyces marxianus, with multiple biotypes scored within each species. Haploid and diploid K. marxianus strains were identified through MAT genotyping, while thermotolerance assay allowed the selection of strains suitable to grow up to 48 °C. In whey fermentation assay, one thermotolerant strain was suitable to release ethanol with yield of 86.5%, while another candidate was able to produce the highest amounts of both ethanol and bioactive peptides with potentially anti-hypertensive function. The present work demonstrated that PR NWS is a reservoir of ethanol and bioactive peptides producer yeasts, which can be exploited to valorize whey, in agreement with the principles of circularity and sustainability.\n\nCharacterization of Yeasts Isolated From Parmigiano Reggiano Cheese Natural Whey Starter: From Spoilage Agents to Potential Cell Factories for Whey Valorization", "token_count": 440, "char_count": 1690, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6555, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:04.223481", "source": { "split": "train_shard_00001", "doc_id": 306 }, "chunk_id": "train_shard_00001_306_0", "global_id": 6090 }, { "text": "

ABSTRACT

The increasing worldwide spread of multidrug-resistant (MDR) Kp is largely driven by high-risk sublineages, some of them well-characterised such as Clonal Group (CG) 258, CG147 or CG307. MDR Kp Sequence-Type (ST) 14 and ST15 have been described worldwide causing frequent outbreaks of CTX-M-15 and/or carbapenemase producers. However, their phylogeny, population structure and global dynamics remain unclear. Here, we clarify the phylogenetic structure and evolvability of CG14 and CG15 Kp by analysing the CG14 and CG15 genomes available in public databases (n=481, November 2019) and de novo sequences representing main sublineages circulating in Portugal (n=9). Deduplicated genomes (n=235) were used to infer temporal phylogenetic evolution and to compare their capsular locus (KL), resistome, virulome and plasmidome using high-resolution tools. Phylogenetic analysis supported independent evolution of CG14 and CG15 within two distinct clades and 4 main subclades which are mainly defined according to the KL and the accessory genome. Within CG14, two large monophyletic subclades, KL16 (14%) and KL2 (86%), presumptively emerged around 1937 and 1942, respectively. Sixty-five percent of CG14 carried genes encoding ESBL, AmpC and/or carbapenemases and, remarkably, they were mainly observed in the KL2 subclade. The CG15 clade was segregated in two major subclades. One was represented by KL24 (42%) and KL112 (36%), the latter one diverging from KL24 around 1981, and the other comprised KL19 and other KL-types (16%)", "token_count": 490, "char_count": 1543, "word_count": 222, "semantic_coherence": 1, "information_density": 0.7162, "quality_score": 0.8581, "entities": { "genes": [ "KL19", "KL2", "KL24", "CG307", "CG15", "KL112", "KL16", "CG14", "ST15", "CG147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:04.877789", "source": { "split": "train_shard_00001", "doc_id": 307 }, "chunk_id": "train_shard_00001_307_0", "global_id": 6091 }, { "text": "Of note, most CG15 genomes contained genes encoding ESBL, AmpC and/or carbapenemases (n=148, 87%) and displayed a characteristic set of mutations in regions encoding quinolone resistance (QRDR, GyrA83F/GyrA87A/ParC80I). Plasmidome analysis revealed 2463 plasmids grouped in 27 predominant plasmid groups (PG) with a high degree of recombination, including particularly pervasive F-type (n=10) and Col (n=10) plasmids. Whereas bla CTX-M-15 was linked to a high diversity of mosaic plasmids, other ARGs were confined to particular plasmids (e.g. bla OXA-48 -IncL; bla CMY/TEM-24 -IncC). This study firstly demonstrates an independent evolutionary trajectory for CG15 and CG14, and suggests how the acquisition of specific KL, QRDR mutations (CG15) and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-KL2, CG15-KL24/KL112).

IMPORTANCE

Klebsiella pneumoniae ( Kp ) represents a major threat in the burden of antimicrobial resistance (AMR). Phylogenetic approaches to explain the phylogeny, emergence and evolution of certain multidrug resistant populations have mainly focused on core-genome approaches while variation in the accessory genome and the plasmidome have been long overlooked. In this study, we provide unique insights into the phylogenetic evolution and plasmidome of two intriguing and yet uncharacterized clonal groups (CGs), the CG14 and CG15, which have contributed to the global dissemination of contemporaneous β-lactamases. Our results point-out an independent evolution of these two CGs and highlight the existence of different clades structured by the capsular-type and the accessory genome", "token_count": 506, "char_count": 1687, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8433, "entities": { "genes": [ "KL2", "KL24", "CG15", "KL112", "CG14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:05.527412", "source": { "split": "train_shard_00001", "doc_id": 307 }, "chunk_id": "train_shard_00001_307_1", "global_id": 6092 }, { "text": "Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome, reflect the exposure and adaptation of Kp under different selective pressures.\n\nPhylogenomics of globally spread Clonal Groups 14 and 15 of Klebsiella pneumoniae", "token_count": 99, "char_count": 357, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:05.903561", "source": { "split": "train_shard_00001", "doc_id": 307 }, "chunk_id": "train_shard_00001_307_2", "global_id": 6093 }, { "text": "

Background

Pseudomonas aeruginosa is an opportunistic pathogen responsible for complicated UTIs and exhibits high antibiotic resistance, leading to increased mortality rates, especially in cases of multidrug-resistant strains. This study aimed to investigate the antibiotic susceptibility patterns and genomic characterization of XDR strains identified in end-stage liver disease patients who underwent liver transplants.

Methods

In this study, a number of 30 individuals who underwent liver transplants were registered. Ninety urine and 60 wound site swab samples were collected and processed for culturing, identification, and antimicrobial sensitivity. Extensively drug-resistant strain EMARA01 was confirmed through Sanger sequencing and was then processed for whole genome sequencing to characterize the genomic pattern. Sequencing data were processed for de novo assembly using various tools and databases, including genome annotation, serotype identification, virulence factor genes, and antimicrobial resistance gene. Pangenome analysis of randomly selected 147 reference strains and EMAR01 sequenced strain was performed using the Bacterial Pan Genome Analysis (BPGA) software.

Results

Of these total examined samples, nosocomial infection due to P. aeruginosa was detected in twelve patients' samples. AST analysis showed that P. aeruginosa strains exhibit resistance to tobramycin, erythromycin, and gentamicin, followed by piperacillin and ofloxacin, and no strains exhibit resistance to meropenem and imipenem. The CARD database identified 59 AMR genes similar to the EMAR01 strain genome and mostly belong to the family involved in the resistance-nodulation-cell division (RND) antibiotic efflux pump. Five genes; nalC, nalD, MexR, MexA, and MexB, exhibit resistance to 14 classes of antibiotics, while two AMR; CpxR, and OprM, exhibit resistance to 15 classes of drugs. Pangenome analysis revealed that the pan-genome remained open, suggesting the potential for acquiring accessory and unique genes", "token_count": 502, "char_count": 2035, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8284, "entities": { "genes": [ "EMARA01", "EMAR01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:06.561118", "source": { "split": "train_shard_00001", "doc_id": 308 }, "chunk_id": "train_shard_00001_308_0", "global_id": 6094 }, { "text": "Notably, the genes predominantly involved in amino acid transport metabolism were identified using the KEGG database.

Conclusions

This study provides valuable insights into the antimicrobial resistance profile, genetic features, and genomic evolution of P. aeruginosa strains causing UTIs in liver transplant patients. The findings emphasize the significance of comprehending AMR mechanisms and genetic diversity in P. aeruginosa for developing effective treatment strategies and infection control measures.\n\nMicrobiological and molecular studies on a multidrug-resistant Pseudomonas aeruginosa from a liver transplant patient with urinary tract infection in Egypt.", "token_count": 146, "char_count": 672, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7738, "quality_score": 0.8869, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:06.991188", "source": { "split": "train_shard_00001", "doc_id": 308 }, "chunk_id": "train_shard_00001_308_1", "global_id": 6095 }, { "text": "

Background

Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism. Xenorhabdus play a central role in all aspects of the Steinernema lifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications.

Results

Here, we report a comparative genomics analysis of Xenorhabdus griffiniae, including the symbiont of Steinernema hermaphroditum nematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for three Xenorhabdus strains: HGB2511, ID10 and TH1. We then determined their relationships to other Xenorhabdus and delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 are Xenorhabdus griffiniae while TH1 is a novel species. These additions to the existing X. griffiniae landscape further allowed for the identification of two subspecies within the clade. Consistent with other Xenorhabdus, the analysed X. griffiniae genomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation in X. griffiniae is contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within the X. griffiniae species.

Conclusions

Our findings suggest that phage-related genes drive the genomic diversity in closely related Xenorhabdus symbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships between X", "token_count": 524, "char_count": 2022, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [ "HGB2511", "TH1", "ID10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:07.625352", "source": { "split": "train_shard_00001", "doc_id": 309 }, "chunk_id": "train_shard_00001_309_0", "global_id": 6096 }, { "text": "griffiniae species and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.\n\nAnalyses of Xenorhabdus griffiniae genomes reveal two distinct sub-species that display intra-species variation due to prophages.", "token_count": 68, "char_count": 256, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9062, "quality_score": 0.9531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:07.996274", "source": { "split": "train_shard_00001", "doc_id": 309 }, "chunk_id": "train_shard_00001_309_1", "global_id": 6097 }, { "text": "

Introduction

Fusarium wilt, caused by Fusarium oxysporum f. sp. cubense (Foc), poses a significant global threat to banana cultivation. Conventional methods of disease management are increasingly challenged, thus making it necessary to explore alternative strategies. Bacterial endophytes, particularly from resistant genotypes, are gaining attention as potential biocontrol agents. Sphingobacterium thalpophilum, isolated from the resistant banana cultivar Pisang lilin (JALHSB010000001-JALHSB010000029), presents an intriguing prospect for combating Fusarium wilt. However, its underlying biocontrol mechanisms remain poorly understood. This study aimed to elucidate the antifungal efficacy of S. thalpophilum NMS02 S296 against Foc and explore its biocontrol mechanisms at the genomic level.

Methods

Whole genome sequencing of S. thalpophilum NMS02 S296 was conducted using next-generation sequencing technologies and bioinformatics analyses were performed to identify genes associated with antifungal properties. In vitro assays were used to assess the inhibitory effects of the bacterial isolate on the mycelial growth of Foc. To explore the biomolecules responsible for the observed antagonistic activity, metabolites diffused into the agar at the zone of inhibition between Foc S16 and S. thalpophilum NMS02 S296 were extracted and identified.

Results

Whole genome sequencing revealed an array of genes encoding antifungal enzymes and secondary metabolites in S. thalpophilum NMS02 S296", "token_count": 514, "char_count": 1620, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8446, "entities": { "genes": [ "NMS02", "JALHSB010000001", "JALHSB010000029" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:08.630193", "source": { "split": "train_shard_00001", "doc_id": 310 }, "chunk_id": "train_shard_00001_310_0", "global_id": 6098 }, { "text": "In vitro experiments demonstrated significant inhibition of Foc mycelial growth by the bacterial endophyte. Comparative genomic analysis highlighted unique genomic features in S. thalpophilum linked to its biocontrol potential, setting it apart from other bacterial species.

Discussion

The study underscores the remarkable antifungal efficacy of S. thalpophilum NMS02 S296 against Fusarium wilt. The genetic basis for its biocontrol potential was elucidated through whole genome sequencing, shedding light on the mechanisms behind its antifungal activity. This study advanced our understanding of bacterial endophytes as biocontrol agents and offers a promising avenue for plant growth promotion towards sustainable strategies to mitigate Fusarium wilt in banana cultivation.\n\nInsights on mining the pangenome of Sphingobacterium thalpophilum NMS02 S296 from the resistant banana cultivar Pisang lilin confirms the antifungal action against Fusarium oxysporum f. sp. cubense.", "token_count": 313, "char_count": 1045, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7364, "quality_score": 0.8682, "entities": { "genes": [ "NMS02" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:09.188587", "source": { "split": "train_shard_00001", "doc_id": 310 }, "chunk_id": "train_shard_00001_310_1", "global_id": 6099 }, { "text": "Streptococcus dysgalactiae (SD) is capable of infecting both humans and animals and causing a wide range of invasive and non-invasive infections. With two subspecies, the taxonomic status of subspecies of SD remains controversial. Subspecies equisimilis (SDSE) is an important human pathogen, while subspecies dysgalactiae (SDSD) has been considered a strictly animal pathogen; however, occasional human infections by this subspecies have been reported in the last few years. Moreover, the differences between the adaptation of SDSD within humans and other animals are still unknown. In this work, we provide a phylogenomic analysis based on the single-copy core genome of 106 isolates from both the subspecies and different infected hosts (animal and human hosts). The accessory genome of this species was also analyzed for screening of genes that could be specifically involved with adaptation to different hosts. Additionally, we searched putatively adaptive traits among prophage regions to infer the importance of transduction in the adaptation of SD to different hosts. Core genome phylogenetic relationships segregate all human SDSE in a single cluster separated from animal SD isolates. The subgroup of bovine SDSD evolved from this later clade and harbors a specialized accessory genome characterized by the presence of specific virulence determinants (e.g., cspZ) and carbohydrate metabolic functions (e.g., fructose operon). Together, our results indicate a host-specific SD and the existence of an SDSD group that causes human-animal cluster infections may be due to opportunistic infections, and that the exact incidence of SDSD human infections may be underestimated due to failures in identification based on the hemolytic patterns. However, more detailed research into the isolation of human SD is needed to assess whether it is a carrier phenomenon or whether the species can be permanently integrated into the human microbiome, making it ready to cause opportunistic infections.\n\nPhylogenetic analysis and accessory genome diversity reveal insight into the evolutionary history of Streptococcus dysgalactiae.", "token_count": 504, "char_count": 2154, "word_count": 309, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:10.595749", "source": { "split": "train_shard_00001", "doc_id": 311 }, "chunk_id": "train_shard_00001_311_0", "global_id": 6100 }, { "text": "

Introduction

Next-generation sequencing (NGS) has played a pivotal role in the advancement of taxonomics, allowing for the accurate identification, differentiation, and reclassification of several bacteria species. Bacillus velezensis is a Gram-positive, facultatively aerobic, spore-forming bacterium known for its antimicrobial and antifungal properties. Strains of this species are highly relevant in agriculture, biotechnology, the food industry, and biomedicine.

Methods

In this study, we characterized the genomes of nine Bacillus strains isolated from soil in the state of Bahia (Brazil) using NGS with Illumina platform. Identification was performed by Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (dDDH) analyses, which revealed a match between the genomic information of the isolates and B. velezensis NRRL B-41580, with a variation of 89.3% to 91.8% by dDDH in TYGS and 95% to 98.04% by ANI in GTDBtk.

Results and discussion

Two strains, BAC144 and BAC1273, exhibited high similarity to B. amyloliquefaciens subsp. plantarum FZB42. However, the latter strain was subsequently reclassified as B. velezensis. The division pattern observed during identification was confirmed in the phylogenomic analysis, where BAC144 and BAC1273 clustered with Bacillus amyloliquefaciens subsp. plantarum, while the other strains clustered with B. velezensis NRRL B-41580, forming a clade with high genetic similarity, with a bootstrap value of 100%. Furthermore, a synteny analysis demonstrated greater conservation among the strains from this study compared to the reference strain, with the formation of distinct collinear groups", "token_count": 517, "char_count": 1719, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [ "BAC144", "FZB42", "BAC1273" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:11.249707", "source": { "split": "train_shard_00001", "doc_id": 312 }, "chunk_id": "train_shard_00001_312_0", "global_id": 6101 }, { "text": "The pangenome analysis revealed an open pangenome, highlighting the genetic diversity within the species. Based on this analysis, a functional annotation was performed to compare exclusive gene repertoires across groups, uncovering distinct adaptations and functional profiles. The identification of bacterial strains belonging to this species is of great importance due to their high applicability. The strains identified in this study underscore the need for more robust taxonomic technologies to accurately classify prokaryotes, which are subject to constant evolutionary changes, requiring the reclassification of several species within the genus Bacillus, many of which are heterotypic synonyms of B. velezensis like Bacillus oryzicola, B. amyloliquefaciens subsp. plantarum and Bacillus methylotrophicus.\n\nThe research on the identification, taxonomy, and comparative genomics analysis of nine <i>Bacillus velezensis</i> strains significantly contributes to microbiology, genetics, bioinformatics, and biotechnology.", "token_count": 263, "char_count": 1055, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7405, "quality_score": 0.8702, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:11.798852", "source": { "split": "train_shard_00001", "doc_id": 312 }, "chunk_id": "train_shard_00001_312_1", "global_id": 6102 }, { "text": "Interpretation of whole-genome sequencing (WGS) data for foodborne outbreak investigations is complex, as the genetic diversity within processing plants and transmission events need to be considered. In this study, we analyzed 92 food-associated Listeria monocytogenes isolates by WGS-based methods. We aimed to examine the genetic diversity within meat and fish production chains and to assess the applicability of suggested thresholds for clustering of potentially related isolates. Therefore, meat-associated isolates originating from the same samples or processing plants as well as fish-associated isolates were analyzed as distinct sets. In silico serogrouping, multilocus sequence typing (MLST), core genome MLST (cgMLST), and pangenome analysis were combined with screenings for prophages and genetic traits. Isolates of the same subtypes (cgMLST types (CTs) or MLST sequence types (STs)) were additionally compared by SNP calling. This revealed the occurrence of more than one CT within all three investigated plants and within two samples. Analysis of the fish set resulted in predominant assignment of isolates from pangasius catfish and salmon to ST2 and ST121, respectively, potentially indicating persistence within the respective production chains. The approach not only allowed the detection of distinct subtypes but also the determination of differences between closely related isolates, which need to be considered when interpreting WGS data for surveillance.\n\nWhole-Genome Sequence Comparisons of Listeria monocytogenes Isolated from Meat and Fish Reveal High Inter- and Intra-Sample Diversity.", "token_count": 371, "char_count": 1627, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6295, "quality_score": 0.8147, "entities": { "genes": [ "ST2", "ST121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:12.385255", "source": { "split": "train_shard_00001", "doc_id": 313 }, "chunk_id": "train_shard_00001_313_0", "global_id": 6103 }, { "text": "Metagenomic and metatranscriptomic functional profiling is crucial for understanding microbial community capabilities, yet current tools often face challenges in computational efficiency, scalability, and integrated genome-resolved references. Here, I introduce Leviathan , an open-source software package designed to address these limitations. Leviathan implements taxonomic profiling via Sylph and a novel highly optimized functional profiling workflow. The functional profiling workflow uniquely combines the speed of PyHMMER for feature annotation, the accuracy of Salmon for read quantification against genome-resolved reference gene catalogs, and graph-based pathway completeness assessment. I demonstrate Leviathan’s capabilities using the CAMI low, medium, and high complexity datasets. Compared to the widely used tool HUMAnN, Leviathan exhibits significantly reduced runtimes (up to ~72-fold faster) and memory usage (up to ~14-fold lower), while achieving competitive or superior accuracy gains (up to 12%) in identifying functional features at both individual genome and pangenome levels. Notably, Leviathan natively supports and streamlines pangenome-level analysis, a critical aspect for understanding functional redundancy and diversity within microbial communities. Leviathan is available as an open-source software package offering a powerful and accessible solution for comprehensive genome-resolved metagenomic profiling.\n\nLeviathan: A fast, memory-efficient, and scalable taxonomic and pathway profiler for (pan)genome-resolved metagenomics and metatranscriptomics", "token_count": 351, "char_count": 1591, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7077, "quality_score": 0.8538, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:12.971360", "source": { "split": "train_shard_00001", "doc_id": 314 }, "chunk_id": "train_shard_00001_314_0", "global_id": 6104 }, { "text": "

Introduction

The Population Health Management (PHM) Genomic Newborn Screens (GNBS) and Multi-Omics Intercepts for Human Phenotype Ontology (HPO) using Federated Data Platforms (FDP) represent a groundbreaking innovation in global health. This reform, supported by the UK's Genomic Medical Services (GMS) through \"The Generation Study,\" aims to significantly reduce infant mortality by identifying and managing over 200 rare diseases from birth, paving the way for personalised health planning.

Methods

Using an ecosystem approach, this study evaluates a diverse pangenome to predict health outcomes or confirm diagnoses prior to symptomatic manifestations. GNBS standardises care by integrating diagnostic techniques such as blood spot analysis and full blood cell diagnostics to stratify risk. The approach enhances the understanding of rare diseases in primary care medicine, with biomedical and haematology diagnoses re-evaluated. Scientific proof of concept and fit-for-purpose technology align multi-omics in pre-eXams (X = Gen AI).

Recommendations

The Digital Regulation Service (DRS) assembles an agile group of experts to enhance medical science through human phenotype ontology (HPO) for precise disease segmentation, scheduling accurate eXam intercepts where needed. This team strategically plans regulation services for digital HPO eXam assurance and implements Higher Expert Medical Science Safety (HEMSS) frameworks. The DRS is responsible for overseeing gene, oligonucleotide, and recombinant protein intercepts; commissioning blood pathology HPO eXam intercepts; and monitoring preliminary eXams with advanced imaging techniques.

Discussion

In pursuit of excellence in PHM of HPO, HEMSS with Agile Group Development leverages the Genomic Newborn Screens (GNBS) and multi-omics to create personalised health plans integrated with NHS England Genomics and AI-driven DRS. The discourse extends to examining GNBS predictors and intercepts, focusing on their impact on public health and patient safety", "token_count": 496, "char_count": 2040, "word_count": 266, "semantic_coherence": 1, "information_density": 0.688, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:13.628360", "source": { "split": "train_shard_00001", "doc_id": 315 }, "chunk_id": "train_shard_00001_315_0", "global_id": 6105 }, { "text": "Discussions encompass structured HPO knowledge addressing newborn health, ethical considerations, family privacy, and the benefits and limitations of pre-eXam screenings and life eXam intercepts. These debates involve stakeholders in adopting HPO-enhanced clinical pathways through Alliances for Health Systems Networking-Genomic Enterprise Partnerships (AHSN-GEP).

Conclusion

\"The Generation Study\" represents a paradigm in digital child health management using an HPO-X-Gen-AI framework, transitioning from trusted research to evidence-based discovery. This approach sets a standard for personalised healthcare practices, incorporating ontology risk stratification and future-ready analytics as outlined in the NHS Constitution. The discourse on higher expert medical science safety governance will continue in the forthcoming manuscript, \"PHM Fit Lifecycles in Future Analytics,\" which will further explore developing localised health solutions for \"Our Future Health.\"\n\nPopulation health management genomic new-born screens and multi-omics intercepts.", "token_count": 232, "char_count": 1062, "word_count": 127, "semantic_coherence": 1, "information_density": 0.8346, "quality_score": 0.9173, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:14.135188", "source": { "split": "train_shard_00001", "doc_id": 315 }, "chunk_id": "train_shard_00001_315_1", "global_id": 6106 }, { "text": "

ABSTRACT

The presence of Vibrio parahaemolyticus ( Vp ) at various stages of seafood production has adversely affected public health and threatened the sustainability of the industry. To address the critical public health threats posed by this prevalent seafood-borne pathogen, this research applied advanced machine learning (ML) and deep learning (DL) algorithms to predict the pathogenic potential of Vp using pangenome data. Utilizing comprehensive pangenomic assemblies and sophisticated ML/DL models, this study achieved robust and precise pathogenic potential prediction of Vp based on source attribution, which provides a novel reliable diagnostic tool facilitating conventional serotyping and virulence gene combination approaches. Based on results, non-core regions in Vp pangenome exhibited useful signals ML models can utilize in pathogenic potential determination process. Tree-based ensemble learning methods (Random Forest and Gradient Boosting Trees) have shown the distinguished performance with AUC score 0.97 based on selected pangenome matrix. Furthermore, Convolutional Neural Network successfully predicted the pathogenic potential of isolates with slightly better performance with AUC score 0.98 based on full pangenome. Critical biological insights revealing critical pathogenic potential-associated genes were retrieved from established ML/DL models: the gene feature weight analysis from Random Forest revealed the importance of accessory genes during Vp evolution (similarly highlighted by Gram-cam analysis of Convolutional Neural Network), which provided potential guidance for future research direction.\n\nPathogenic potential prediction of Vibrio parahaemolyticus by using pangenome data with high performance machine learning algorithms", "token_count": 374, "char_count": 1784, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:14.739052", "source": { "split": "train_shard_00001", "doc_id": 316 }, "chunk_id": "train_shard_00001_316_0", "global_id": 6107 }, { "text": "

Background

The current cattle reference genome assembly, a pseudo-linear sequence produced using sequences from a single Hereford cow, represent a limit when performing genetic studies, especially when investigating the whole spectrum of genetic variations within the species. Detecting structural variations (SVs) poses significant challenges when relying solely on conventional methods of short or long-read sequence mapping to the current bovine genome assembly.

Results

In this study, we used long-reads (LR) and bioinformatic tools to construct a comprehensive bovine pangenome incorporating genetic diversity of 64 good quality de novo genome assemblies representing 14 French dairy and beef cattle breeds. Using a combination of complementary approaches, we explored the pangenome graph and identified 2.563 Gb of sequences common to all samples, and cumulated 0.295 Gb of variable sequences. Notably, we discovered 0.159 Gb of novel sequences not present in the current Hereford reference genome assembly. Our analysis also revealed 109,275 SVs, of which 84,612 were bi-allelic, including 21,840 insertions and 21,340 deletions. Genome-wide association studies using SNPs and a panel of 221 SVs, shared between the pangenome and the EuroGMD chip, revealed several well-known QTLs across the genome for the Holstein, Montbéliarde and Normande breeds. Among those, a QTL on chromosome 11 presents an SV with a highly significant effect on stature in the Holstein breed. This SV is a 6.2 kb deletion affecting the 5’UTR, first exon and part of first intron of MATN3 gene, suggesting a potential regulatory and coding effect.

Conclusions

Our study provides new insights into the genetic diversity of 14 French dairy and beef breeds and highlights the utility of pangenome graphs in capturing structural variation. The identified SV associated with stature highlights the importance of integrating SVs into GWAS for a more comprehensive understanding of complex traits.", "token_count": 496, "char_count": 1999, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6289, "quality_score": 0.8144, "entities": { "genes": [ "MATN3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:15.430780", "source": { "split": "train_shard_00001", "doc_id": 317 }, "chunk_id": "train_shard_00001_317_0", "global_id": 6108 }, { "text": "Application of a French cattle pangenome, from structural variant discovery to association studies on key phenotypes", "token_count": 21, "char_count": 116, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:15.813211", "source": { "split": "train_shard_00001", "doc_id": 317 }, "chunk_id": "train_shard_00001_317_1", "global_id": 6109 }, { "text": "Acinetobacter pittii has increasingly been associated with several types of hospital-acquired severe infections. Genes implicated in carbapenem resistance, tigecycline resistance, or genes encoding extended spectrum cephalosporinases, such as blaADC, are commonly found in isolates implicated in these infections. A. pittii strains that are pandrug resistant have occasionally been identified. Food for human consumption, animals and plants are environmental sources of this pathogen. An alarming situation is that A. pitti has been identified as responsible for outbreaks in different regions worldwide. In this study, 384 genomes of A. pittii were analyzed, comprising sequences from clinical and non-clinical origins from 32 countries. The objective was to investigate if clinical strains possess genetic traits facilitating hospital adaptation. Results indicate significant genomic variability in terms of size and gene content among A. pittii isolates. The core genome represents a small portion (25-36%) of each isolate's genome, while genes associated with antibiotic resistance and virulence predominantly belong to the accessory genome. Notably, antibiotic resistance genes are encoded by a diverse array of plasmids. As the core genome between environmental and hospital isolates is the same, we can assume that hospital isolates acquired ARGs due to a high selective pressure in these settings. The strain's phylogeographic distribution indicates that there is no geographical bias in the isolate distribution; isolates from different geographic regions are dispersed throughout a core genome phylogenetic tree. A single clade may include isolates from extremely distant geographical areas. Furthermore, strains isolated from the environment or animal, or plant sources frequently share the same clade as hospital isolates. Our analysis showed that the clinical isolates do not already possess specific genes, other than antibiotic-resistant genes, to thrive in the hospital setting.\n\nAcinetobacter pittii: the emergence of a hospital-acquired pathogen analyzed from the genomic perspective.", "token_count": 500, "char_count": 2151, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6254, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:16.463719", "source": { "split": "train_shard_00001", "doc_id": 318 }, "chunk_id": "train_shard_00001_318_0", "global_id": 6110 }, { "text": "2. Haemophilus influenzae is part of the human nasopharyngeal microbiota and a pathogen causing invasive disease. The extensive genetic diversity observed in H. influenzae necessitates discriminatory analytical approaches to evaluate its population structure. This study developed a core genome MLST (cgMLST) scheme for H. influenzae using pangenome analysis tools and validated the cgMLST scheme using datasets consisting of complete reference genomes (N=14) and high-quality draft H. influenzae genomes (N=2,297). The draft genome dataset was divided into a development (N=921) and a validation dataset (N=1,376). The development dataset was used to identify potential core genes with the validation dataset used to refine the final core gene list to ensure the reliability of the proposed cgMLST scheme. Functional classifications were made for all resulting core genes. Phylogenetic analyses were performed using both allelic profiles and nucleotide sequence alignments of the core genome to test congruence, as assessed by Spearman’s correlation and Ordinary Least Square linear regression tests. Preliminary analyses using the development dataset identified 1,067 core genes, which were refined to 1,037 with the validation dataset. More than 70% of core genes were predicted to encode proteins essential for metabolism or genetic information processing. Phylogenetic and statistical analyses indicated that the core genome allelic profile accurately represented phylogenetic relatedness among the isolates ( R 2 = 0.945). We used this cgMLST scheme to define a high-resolution population structure for H. influenzae , which enhances the genomic analysis of this clinically relevant human pathogen. 3.

Impact statement

Discriminating H. influenzae variants and evaluating population structure has been challenging and largely unstandardised. To address this, we have developed a cgMLST scheme for H. influenzae. Since an accurate typing approach relies on precise reflection of the underlying population structure, we explored various methods to define the scheme. The core genes included in this scheme were predicted to encode functions in essential biological pathways, such as metabolism and genetic information processing, and could be reliably assembled from short-read sequence data", "token_count": 528, "char_count": 2304, "word_count": 324, "semantic_coherence": 1, "information_density": 0.5864, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:17.130405", "source": { "split": "train_shard_00001", "doc_id": 319 }, "chunk_id": "train_shard_00001_319_0", "global_id": 6111 }, { "text": "Single-linkage clustering, based on core genome allelic profiles, showed high congruence to genealogy reconstructed by Maximum-Likelihood (ML) methods from the core genome nucleotide alignment. The cgMLST scheme v1 enables rapid and accurate depiction of high-resolution H. influenzae population structure, and making this scheme accessible via the PubMLST database, ensures that microbiology reference laboratories and public health authorities worldwide can use it for genomic surveillance. 4.

Data summary

The H. influenzae cgMLST scheme is accessible via https://pubmlst.org/organisms/haemophilus-influenzae . The list of isolate IDs available publicly from pubmlst.org is provided in Supplementary File 1. The pipeline for cgMLST scheme development and validation is published at https://www.protocols.io/private/EF6DB7FE429311EEB8630A58A9FEAC02 . All in-house R and Python scripts for data processing and analysis are available from https://gitfront.io/r/user-4399403/ZHt8DArALHcY/cgmlst-hinf/ .\n\nDevelopment and Implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme forHaemophilusinfluenzae", "token_count": 334, "char_count": 1134, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7239, "quality_score": 0.8619, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:17.709841", "source": { "split": "train_shard_00001", "doc_id": 319 }, "chunk_id": "train_shard_00001_319_1", "global_id": 6112 }, { "text": "Combatting Clostridioides difficile infections, a dominant cause of hospital-associated infections with incidence and resulting deaths increasing worldwide, is complicated by the frequent emergence of new virulent strains. Here, we employ whole-genome sequencing, high-throughput phenotypic screenings, and genome-scale models of metabolism to evaluate the genetic diversity of 451 strains of C. difficile. Constructing the C. difficile pangenome based on this set revealed 9,924 distinct gene clusters, of which 2,899 (29%) are defined as core, 2,968 (30%) are defined as unique, and the remaining 4,057 (41%) are defined as accessory. We develop a strain typing method, sequence typing by accessory genome (STAG), that identifies 176 genetically distinct groups of strains and allows for explicit interrogation of accessory gene content. Thirty-five strains representative of the overall set were experimentally profiled on 95 different nutrient sources, revealing 26 distinct growth profiles and unique nutrient preferences; 451 strain-specific genome scale models of metabolism were constructed, allowing us to computationally probe phenotypic diversity in 28,864 unique conditions. The models create a mechanistic link between the observed phenotypes and strain-specific genetic differences and exhibit an ability to correctly predict growth in 76% of measured cases. The typing and model predictions are used to identify and contextualize discriminating genetic features and phenotypes that may contribute to the emergence of new problematic strains.\n\nSystems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power.", "token_count": 406, "char_count": 1704, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6478, "quality_score": 0.8239, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:18.338346", "source": { "split": "train_shard_00001", "doc_id": 320 }, "chunk_id": "train_shard_00001_320_0", "global_id": 6113 }, { "text": "Robiola di Roccaverano is a Protected Designation of Origin (PDO) cheese from the Piedmont region of Italy. In this study, the mycobiota occurring during Robiola di Roccaverano production was elucidated. Samples of milk, Natural Milk Cultures (NMC), curd, 5- and 15-days ripened cheese were collected from one dairy plant and the mycobiota was analyzed by the metataxonomic approach. Milk samples showed a high diversity and Cladosporium, Kluyveromyces marxianus, Geotrichum candidum and Debaryomyces hansenii were found with higher relative abundance. This mycobiota remains quite stable in NMC and curd matrices although the relative abundance of K. marxianus and G. candidum yeasts increased significantly and shaped the fungal composition of 5- and 15-day ripened cheese.\n\nMycobiota Composition of Robiola di Roccaverano Cheese along the Production Chain.", "token_count": 269, "char_count": 901, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:18.885271", "source": { "split": "train_shard_00001", "doc_id": 321 }, "chunk_id": "train_shard_00001_321_0", "global_id": 6114 }, { "text": "Abstract

Lactic acid bacteria (LAB), including many well-known beneficial bacteria, have seen a rise in the number of applications with specific strains across various areas, including live biotherapeutic products (LBPs). The most extensively researched strains belong to the Lactobacillaceae. Assessing the survival and persistence of specific strains in different niches is still an important challenge, while selective monitoring techniques are often lacking at strain level. Here, we show a robust pangenome-based approach for detecting singletons, which can be used to develop strain-specific primers. We developed selective and specific primers for six strains across different LAB species. The primers for the widely-used probiotic L. rhamnosus GG and L. plantarum WCFS1 were validated in in vivo studies and showed that these strains can persist in and on other habitats such as the human skin, upper respiratory tract and fermented vegetables. In conclusion, the selection of unique genes derived from the pangenome of a species resulted in a specific and sensitive method based on qPCR to detect and monitor strains in different habitats. This approach can be readily extended to other bacterial strains on other families for any type applications in research and industry.

\n\nPangenome-based design of strain-specific primers allows the specific monitoring of engraftment in different habitats", "token_count": 318, "char_count": 1425, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [ "WCFS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:19.448780", "source": { "split": "train_shard_00001", "doc_id": 322 }, "chunk_id": "train_shard_00001_322_0", "global_id": 6115 }, { "text": "Oat grain is a traditional human food that is rich in dietary fibre and contributes to improved human health1,2. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogues3. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales4. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oat lines, along with an atlas of gene expression across 6 tissues of different developmental stages in 23 of these lines. We construct an atlas of gene-expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory upregulation of the remaining homeologues, but this process is constrained by subgenome divergence. Chromosomal rearrangements have substantially affected recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semi-dwarf mutant has risen to prominence in Australian elite varieties. The oat pangenome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.\n\nA pangenome and pantranscriptome of hexaploid oat.", "token_count": 387, "char_count": 1584, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:20.061827", "source": { "split": "train_shard_00001", "doc_id": 323 }, "chunk_id": "train_shard_00001_323_0", "global_id": 6116 }, { "text": "Recent technological advances have accelerated the production of high-quality genome assemblies within species, driving the growing use of pangenome graphs in genetic diversity analyses. These graphs reduce reference bias in read mapping and enhance variant discovery and genotyping from SNPs to Structural Variants (SVs). In pangenome graphs, variants appear as bubbles, which can be detected by dedicated bubble calling tools. Although these tools report essential information on the variant bubbles, such as their position and allele walks in the graph, they do not annotate the type of the detected variants. While simple SNPs, insertions, and deletions are easily distinguishable by allele size, large balanced variants like inversions are harder to differentiate among the large number of unannotated bubbles. In fact, inversions and other types of large variants remain underexplored in pangenome graph benchmarks and analyses. In this work we focused on inversions, which have been drawing renewed attention in evolutionary genomics studies in the past years, and aimed to assess how this type of variant is handled by state of the art pangenome graphs pipelines. We identified two distinct topological motifs for inversion bubbles: one path-explicit and one alignment-rescued, and developed a tool to annotate them from bubble-caller outputs. We constructed pangenome graphs with both simulated data and real data using four state of the art pipelines, and assessed the impact of inversion size, punctual genome divergence and haplotype number on inversion representation and accuracy. Our results reveal substantial differences between pipelines, with many inversions either mis-represented or lost. Most notably, recovery rates remain strikingly low, even with the most simple simulated genome sets, highlighting major challenges in analyzing inversions in pangenomic approaches.\n\nInvestigating the topological motifs of inversions in pangenome graphs", "token_count": 419, "char_count": 1962, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6277, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:20.684242", "source": { "split": "train_shard_00001", "doc_id": 324 }, "chunk_id": "train_shard_00001_324_0", "global_id": 6117 }, { "text": "

Background

Porcine Parvovirus (PPV) is a Parvovirinae virus that can cause embryonic and fetal loss and death and mummification in affected fetal pigs. Unlike conventional vaccines, virus-like particles (VLPs) inherit the natural structure of their authentic virions and highly immunostimulatory that can induce strong humoral immune and T cell responses with no risk of pathogenicity. The production of PPV VLPs is still a challenge based on traditional expression platforms due to their low yields and high culture costs. Kluyveromyces marxianus is a safe and fast-growing eukaryote that can get high biomass with low-cost cultures. In this study, we investigated the expression and downstream processes of PPV VLPs in K. marxianus, and the potential for effective stand-alone vaccines.

Results

After optimization according to the codon bias of K. marxianus, the VP2 protein from Kresse strain was highly expressed. In a 5 L fermentator, the yield of PPV VLPs reached 2.5 g/L, quantified by HPLC, using a defined mineral medium after 48 h fermentation. Two strategies were established to purify intracellular PPV VLPs: (i) Using the cation exchange chromatography coupled with Sephacryl® S-500 HR chromatography to purify VLPs from the supernatants of pH adjusted cell lysates. (ii) Using anion exchange chromatography followed by cross-flow diafiltration to recover the VLPs precipitated in pH adjusted cell lysates. The purity of PPV VLPs reached about 95%, and total recovery was more than 60%. Vaccination of mice with the purified PPV VLPs induced high titers of specific IgG antibodies in sera, and showed hemagglutination inhibitions on both swine and guinea pig erythrocytes. Spleen lymphocyte proliferation and cytokines detection suggested the PPV VLPs produced by K", "token_count": 496, "char_count": 1793, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6504, "quality_score": 0.8252, "entities": { "genes": [ "VP2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:21.347202", "source": { "split": "train_shard_00001", "doc_id": 325 }, "chunk_id": "train_shard_00001_325_0", "global_id": 6118 }, { "text": "marxianus provoked the cellular immune and humoral immunity responses in mice.

Conclusions

This is the highest production of recombinant PPV VLPs achieved to date. The superiorities, Generally Recognized As Safe (GRAS), high production, short lead time, and low cost, make K. marxianus a greatly competitive platform for bioproduction of PPV VLPs vaccine.\n\nInvestigation of Kluyveromyces marxianus as a novel host for large-scale production of porcine parvovirus virus-like particles.", "token_count": 135, "char_count": 491, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:21.769075", "source": { "split": "train_shard_00001", "doc_id": 325 }, "chunk_id": "train_shard_00001_325_1", "global_id": 6119 }, { "text": "Microbes are omnipresent, thriving in a range of habitats, from oceans to soils, and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently, understanding the diversity in terms of strains in microbial communities is crucial, as variations between strains can lead to different phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several limitations, including their reliance solely on species resolution, support for either short or long reads, or their confinement to a given single species. Most notably, most existing strain-level taxonomic classifiers rely on the sequence representation of multiple linear reference genomes, which fails to capture the sequence correlations among these genomes, potentially introducing ambiguity and biases in metagenomic profiling. Here, we present PanTax, a pangenome graph-based taxonomic profiler that overcomes the short-comings of sequence-based approaches, because pangenome graphs possess the capability to depict the full range of genetic variability present across multiple evolutionarily or environmentally related genomes. PanTax provides a comprehensive solution to taxonomic classification for strain resolution, compatibility with both short and long reads, and compatibility with single or multiple species. Extensive benchmarking results demonstrate that PanTax drastically outperforms state-of-the-art approaches, primarily evidenced by its significantly higher precision or recall at strain level, while maintaining comparable or better performance in other aspects across various datasets. PanTax is an open-source user-friendly tool that is publicly available at https://github.com/LuoGroup2023/PanTax .\n\nStrain-level metagenomic profiling using pangenome graphs with PanTax", "token_count": 390, "char_count": 1931, "word_count": 250, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:22.385920", "source": { "split": "train_shard_00001", "doc_id": 326 }, "chunk_id": "train_shard_00001_326_0", "global_id": 6120 }, { "text": "Probiotics are vital and beneficial organisms which offers the health benefits to the host organisms. The fungal probiotic field is one of the developing fields nowadays. Yeast has an enormous and diverse group of microorganisms that is attracting and expanding the attention from researchers and industries. Saccharomyces boulardii, the only patented strain belonging to yeast genera for the human use, has been broadly evaluated for its probiotic effect. Yeasts belonging to the genera Debaryomyces, Pichia, Yarrowia, Meyerozyma, Kluyveromyces etc.., have attained more interest because of their beneficial and probable probiotic features. These yeast probiotics produce VOCs (Volatile organic compounds), mycocins and antimicrobials which shows the antagonistic effect against pathogenic fungi and bacteria. Additionally, those yeasts have been recorded as good plant growth promoting microorganisms. Yeast has an important role in environmental applications such as bioremediation and removal of metals like chromium, mercury, lead etc., from waste water. Probiotic yeasts with their promising antimicrobial, antioxidant, anticancer properties, cholesterol assimilation and immunomodulatory effects can also be utilized as biotherapeutics. In this review article we have made an attempt to address important yeast probiotic attributes.\n\nExploring biotechnological and functional characteristics of probiotic yeasts: A review.", "token_count": 346, "char_count": 1443, "word_count": 192, "semantic_coherence": 1, "information_density": 0.7135, "quality_score": 0.8568, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:22.958130", "source": { "split": "train_shard_00001", "doc_id": 327 }, "chunk_id": "train_shard_00001_327_0", "global_id": 6121 }, { "text": "Bacterial transformation is an important mode of horizontal gene transfer that helps spread genetic material across species boundaries. Yet, the factors that pose barriers to genome-wide cross-species gene transfer are poorly characterized. Here, we develop a replacement accumulation assay to study the effects of genomic distance on transfer dynamics. Using Bacillus subtilis as recipient and various species of the genus Bacillus as donors, we find that the rate of orthologous replacement decreases exponentially with the divergence of their core genomes. We reveal that at least 96% of the B. subtilis core genes are accessible to replacement by alleles from Bacillus spizizenii. For the more distantly related Bacillus atrophaeus, gene replacement events cluster at genomic locations with high sequence identity and preferentially replace ribosomal genes. Orthologous replacement also creates mosaic patterns between donor and recipient genomes, rearranges the genome architecture, and governs gain and loss of accessory genes. We conclude that cross-species gene transfer is dominated by orthologous replacement of core genes which occurs nearly unrestricted between closely related species. At a lower rate, the exchange of accessory genes gives rise to more complex genome dynamics.\n\nGenome-wide transformation reveals extensive exchange across closely related Bacillus species.", "token_count": 292, "char_count": 1387, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:23.517753", "source": { "split": "train_shard_00001", "doc_id": 328 }, "chunk_id": "train_shard_00001_328_0", "global_id": 6122 }, { "text": "Klebsiella pneumoniae sequence type 14 (ST14) and ST15 caused outbreaks of CTX-M-15 and/or carbapenemase producers worldwide, but their phylogeny and global dynamics remain unclear. We clarified the evolution of K. pneumoniae clonal group 14 (CG14) and CG15 by analyzing the capsular locus (KL), resistome, virulome, and plasmidome of public genomes (n = 481) and de novo sequences (n = 9) representing main sublineages circulating in Portugal. CG14 and CG15 evolved independently within 6 main subclades defined according to the KL and the accessory genome. The CG14 (n = 65) clade was structured in two large monophyletic subclades, CG14-I (KL2, 86%) and CG14-II (KL16, 14%), whose emergences were dated to 1932 and 1911, respectively. Genes encoding extended-spectrum β-lactamase (ESBL), AmpC, and/or carbapenemases were mostly observed in CG14-I (71% versus 22%). CG15 clade (n = 170) was segregated into subclades CG15-IA (KL19/KL106, 9%), CG15-IB (variable KL types, 6%), CG15-IIA (KL24, 43%) and CG15-IIB (KL112, 37%). Most CG15 genomes carried specific GyrA and ParC mutations and emerged from a common ancestor in 1989", "token_count": 482, "char_count": 1162, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8765, "entities": { "genes": [ "KL19", "KL2", "KL24", "CG15", "KL106", "KL112", "KL16", "CG14", "ST14", "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:24.159515", "source": { "split": "train_shard_00001", "doc_id": 329 }, "chunk_id": "train_shard_00001_329_0", "global_id": 6123 }, { "text": "CTX-M-15 was especially prevalent in CG15 (68% CG15 versus 38% CG14) and in CG15-IIB (92%). Plasmidome analysis revealed 27 predominant plasmid groups (PG), including particularly pervasive and recombinant F-type (n = 10), Col (n = 10), and new plasmid types. While blaCTX-M-15 was acquired multiple times by a high diversity of F-type mosaic plasmids, other antibiotic resistance genes (ARGs) were dispersed by IncL (blaOXA-48) or IncC (blaCMY/TEM-24) plasmids. We first demonstrate an independent evolutionary trajectory for CG15 and CG14 and how the acquisition of specific KL, quinolone-resistance determining region (QRDR) mutations (CG15), and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-I and CG15-IIA/IIB). IMPORTANCE Klebsiella pneumoniae represents a major threat in the burden of antibiotic resistance (ABR). Available studies to explain the origin, the diversity, and the evolution of certain ABR K. pneumoniae populations have mainly been focused on a few clonal groups (CGs) using phylogenetic analysis of the core genome, the accessory genome being overlooked. Here, we provide unique insights into the phylogenetic evolution of CG14 and CG15, two poorly characterized CGs which have contributed to the global dissemination of genes responsible for resistance to first-line antibiotics such as β-lactams. Our results point out an independent evolution of these two CGs and highlight the existence of different subclades structured by the capsular type and the accessory genome", "token_count": 507, "char_count": 1640, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6814, "quality_score": 0.8407, "entities": { "genes": [ "CG15", "CG14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:24.806451", "source": { "split": "train_shard_00001", "doc_id": 329 }, "chunk_id": "train_shard_00001_329_1", "global_id": 6124 }, { "text": "Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome reflect the exposure and adaptation of K. pneumoniae under different selective pressures.\n\nPhylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae.", "token_count": 98, "char_count": 361, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8039, "quality_score": 0.902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:25.182614", "source": { "split": "train_shard_00001", "doc_id": 329 }, "chunk_id": "train_shard_00001_329_2", "global_id": 6125 }, { "text": "Pangenome graphs represent the genomic variation by encoding multiple haplotypes within a unified graph structure. However, efficient and lossless indexing of such structures remains challenging due to the scale and complexity of pangenomic data. We present a practical and scalable indexing framework based on tag arrays, which annotate positions in the Burrows–Wheeler transform (BWT) with graph coordinates. Our method extends the FM-index with a run-length compressed tag structure that enables efficient retrieval of all unique graph locations where a query pattern appears. We introduce a novel construction algorithm that combines unique k -mers, graph-based extensions, and haplotype traversal to compute the tag array in a memory-efficient manner. To support large genomes, we process each chromosome independently and then merge the results into a unified index using properties of the multi-string BWT and r-index. Our evaluation on the HPRC graphs demonstrates that the tag array structure compresses effectively, scales well with added haplotypes, and preserves accurate mapping information across diverse regions of the genome. This indexing method enables lossless and haplotype-aware querying in complex pangenomes and offers a practical indexing layer to develop scalable aligners and downstream graph-based analysis tools.\n\nLossless Pangenome Indexing Using Tag Arrays", "token_count": 290, "char_count": 1386, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6564, "quality_score": 0.8282, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:25.747478", "source": { "split": "train_shard_00001", "doc_id": 330 }, "chunk_id": "train_shard_00001_330_0", "global_id": 6126 }, { "text": "

Background

Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named A, B, and C). Here, we assessed phylogroup-specific evolutionary dynamics across available and also new P. aeruginosa genomes.

Methods

In this genomic analysis, we first generated new genome assemblies for 18 strains of the major P. aeruginosa clone type (mPact) panel, comprising a phylogenetically diverse collection of clinical and environmental isolates for this species. Thereafter, we combined these new genomes with 1991 publicly available P. aeruginosa genomes for a phylogenomic and comparative analysis. We specifically explored to what extent antimicrobial resistance (AMR) genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and \"masked\" (RGP-free) genomes, and to what extent this variation differs among the phylogroups.

Findings

We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, inter- and intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events. Finally, we provide here the mPact panel of diverse P. aeruginosa strains that may serve as a valuable reference for functional analyses.

Interpretation

Altogether, our results highlight distinct pangenome characteristics of the P", "token_count": 429, "char_count": 1705, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6816, "quality_score": 0.8408, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:26.410456", "source": { "split": "train_shard_00001", "doc_id": 331 }, "chunk_id": "train_shard_00001_331_0", "global_id": 6127 }, { "text": "aeruginosa phylogroups, which are possibly influenced by variation in the abundance of CRISPR-Cas systems and are shaped by the differential distribution of other defence systems and AMR genes.

Funding

German Science Foundation, Max-Planck Society, Leibniz ScienceCampus Evolutionary Medicine of the Lung, BMBF program Medical Infection Genomics, Kiel Life Science Postdoc Award.\n\nPhylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity in Pseudomonas aeruginosa.", "token_count": 139, "char_count": 556, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7536, "quality_score": 0.8768, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:26.841971", "source": { "split": "train_shard_00001", "doc_id": 331 }, "chunk_id": "train_shard_00001_331_1", "global_id": 6128 }, { "text": "Comparative genomic analysis of Vibrio harveyi, a leading pathogen in Mediterranean aquaculture, was conducted to assess the genomic plasticity of the species. V. harveyi is responsible for vibriosis outbreaks during the warmer months, resulting in significant economic losses that impact Greek aquaculture. Over a span of six years, we curated a diverse collection of bacterial strains associated with these outbreaks. Whole-genome sequencing was employed in 21 strains to uncover their evolutionary relationships and virulence factors. Pangenome analysis revealed significant gene gain/loss, with numerous unique genes within the strains. The core genome featured genes associated with pathogenicity, including secretion systems, flagella, pili, siderophores, and toxins. Furthermore, we examined the phenotypic traits and virulence of these strains using in vivo testing with gilthead seabream larvae. Our findings indicated variant metabolic profiles and virulence among the strains during these in vivo assays. By integrating genomic and phenotypic data, our study highlights the ongoing evolution of disease-associated V. harveyi strains, which pose a growing challenge to the aquaculture industry.\n\nVirulence and pangenome analysis of Vibrio harveyi strains from Greek and Red Sea marine aquaculture", "token_count": 306, "char_count": 1306, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6611, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:27.449658", "source": { "split": "train_shard_00001", "doc_id": 332 }, "chunk_id": "train_shard_00001_332_0", "global_id": 6129 }, { "text": "Ethyl acetate is currently produced from fossil carbon resources. This ester could also be microbially synthesized from sugar-rich wastes of the food industry. Wild-type strains with GRAS status are preferred for such applications. Production of ethyl acetate by wild-type yeasts has been repeatedly reported, but comparative studies with several strains at various induction modes are largely missing. Here, synthesis of ethyl acetate by three yeasts with GRAS status, Kluyveromyces marxianus DSM 5422, Cyberlindnera jadinii DSM 2361 and Wickerhamomyces anomalus DSM 6766, was studied under identical and well-defined conditions in an aerated bioreactor, by inducing the ester synthesis via iron or oxygen limitation. Balancing the ester synthesis was based on measured concentrations of ethyl acetate in the exhaust gas, delivering masses of synthesized ester and synthesis rates in a high temporal resolution. All tested yeasts synthesized ethyl acetate under these conditions, but the intensity varied with the strain and induction mode. The highest yields were achieved under iron limitation with K. marxianus (0.182 g g-1) and under oxygen limitation with W. anomalus (0.053 g g-1). Iron limitation proved to be the better inducer for ester synthesis while oxygen limitation favored ethanol formation. K. marxianus DSM 5422 was the most potent producer of ethyl acetate exhibiting the highest biomass-specific synthesis rate of 0.5 g g-1h-1 under moderate iron limitation.", "token_count": 454, "char_count": 1564, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6083, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:28.094328", "source": { "split": "train_shard_00001", "doc_id": 333 }, "chunk_id": "train_shard_00001_333_0", "global_id": 6130 }, { "text": "Synthesis of ethyl acetate from glucose by Kluyveromyces marxianus, Cyberlindnera jadinii and Wickerhamomyces anomalus depending on the induction mode.", "token_count": 69, "char_count": 172, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:28.464502", "source": { "split": "train_shard_00001", "doc_id": 333 }, "chunk_id": "train_shard_00001_333_1", "global_id": 6131 }, { "text": "Lipids are essential energy storage compounds and are the core structural elements of all biological membranes. During wine alcoholic fermentation, the ability of yeasts to adjust the lipid composition of the plasma membrane partly determines their ability to cope with various fermentation-related stresses, including elevated levels of ethanol and the presence of weak acids. In addition, the lipid composition of grape juice also impacts the production of many wine-relevant aromatic compounds. Several studies have evaluated the impact of lipids and of their metabolism on fermentation performance and aroma production in the dominant wine yeast Saccharomyces cerevisiae, but limited information is available on other yeast species. Thus, the aim of this study was to evaluate the influence of specific fatty acid and sterol mixtures on various non-Saccharomyces yeast fermentation rates and the production of primary fermentation metabolites. The data show that the response to different lipid mixtures is species-dependent. For Metschnikowia pulcherrima, a slight increase in carbon dioxide production was observed in media enriched with unsaturated fatty acids whereas Kluyveromyces marxianus fermented significantly better in synthetic media containing a higher concentration of polyunsaturated fatty acids than monounsaturated fatty acids. Torulaspora delbrueckii fermentation rate increased in media supplemented with lipids present at an equimolar concentration. The data indicate that these different responses may be linked to variations in the lipid profile of these yeasts and divergent metabolic activities, in particular the regulation of acetyl-CoA metabolism. Finally, the results suggest that the yeast metabolic footprint and ultimately the wine organoleptic properties could be optimized via species-specific lipid adjustments.\n\nSpecies-Dependent Metabolic Response to Lipid Mixtures in Wine Yeasts.", "token_count": 462, "char_count": 1963, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6098, "quality_score": 0.8049, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:29.107050", "source": { "split": "train_shard_00001", "doc_id": 334 }, "chunk_id": "train_shard_00001_334_0", "global_id": 6132 }, { "text": "As well as undergoing mutational selection, bacterial genomes are shaped by a complex evolutionary interplay among diverse accessory genome elements (AGEs). In this study we define AGEs as encompassing both autonomous elements including phage, plasmids, integrative conjugative elements (ICEs) and carried elements such as defence systems (DSs) and antimicrobial resistance genes (ARGs). Genomic studies can facilitate our better understanding of the relationships among these AGEs within microbial genomes, offering deeper insights into their roles in bacterial adaptation and evolution. Emerging evidence suggests that bacterial DSs can interact both synergistically and antagonistically with each other, and ecological studies describe non-random patterns of co-occurrence and avoidance of DSs in bacterial populations. Here, we analysed the distributions of DSs and other AGEs in a recently curated dataset of 4,288 Pseudomonas aeruginosa genomes. Genomic DS content varied by ecological niche, with higher numbers per genome in non-CF isolates (average n=7.9) compared to CF isolates (average n=6.9). We observed multiple phylogenetically independent associations (n=426) and dissociations (n=50) among DSs, and among other AGEs, many of which had a plausible biological basis. We further explored the relative importance of interactions among different AGEs, revealing that DSs and anti-defence systems engage in the most significant interactions with other AGEs and, most notably, with each other. Ultimately, these patterns of DS interactions and their variation across ecological niches reveals the evolutionary conflicts shaping bacterial accessory genomes and provides a significant public resource for downstream studies on DS and other AGE interactions.\n\nDefence systems drive accessory genome interactions in Pseudomonas aeruginosa", "token_count": 426, "char_count": 1852, "word_count": 252, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:29.741407", "source": { "split": "train_shard_00001", "doc_id": 335 }, "chunk_id": "train_shard_00001_335_0", "global_id": 6133 }, { "text": "

Background

The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation.

Results

Starting with the output of standard pangenome analysis tools, we describe the generation and analysis of interactive, 3D network graphs to explore the structure of bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur, in the new open-source network analysis platform, Graphia. Both the analysis and the visualisation are scalable to datasets of thousands of genome sequences.

Conclusions

We anticipate that the approaches presented here will be of great utility to the microbial research community, allowing faster, more intuitive, and flexible interaction with pangenome datasets, thereby enhancing interpretation of these complex data.\n\nA graph-based approach for the visualisation and analysis of bacterial pangenomes.", "token_count": 240, "char_count": 1146, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6603, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:30.218918", "source": { "split": "train_shard_00001", "doc_id": 336 }, "chunk_id": "train_shard_00001_336_0", "global_id": 6134 }, { "text": "

Background

DNA methylation (DNAm) plays an important functional role and is influenced by genetic variants known as methylation QTLs (meQTLs). The majority of meQTL studies have been conducted in human blood. Despite its unique landscape, the genetic regulation of sperm DNAm remains largely unexplored. In this study, we leveraged DNAm measured in sperm from 405 Holstein bulls using reduced representation bisulfite sequencing (RRBS) and performed sequence-level genome-wide association studies for 166,985 variable CpGs (s.d. >5%). We reported heritability estimates and have mapped both cis-meQTLs and trans-meQTLs.

Results

Heritability estimates ranged from 0 to 1 and averaged 0.26 across all selected CpGs, with 76% of estimates above 0.1. The meQTL mapping revealed that 32.9% of the CpGs had a cis-meQTL, 3.6% had a trans-meQTL and 1.0% had both cis- and trans-meQTLs. The cis-CpGs were located on average 261 kb (absolute mean) from their cis-meQTL top SNPs (defined by the most significant association). MeQTLs were enriched in featured genomic annotations, including regions surrounding transcription start sites and ATAC-seq peaks. We also identified spurious trans-associations by analyzing data across multiple genome assemblies, including the construction of a partial pangenome. Additionally, eight trans-meQTL hotspots, defined as variants associated with at least 30 trans-CpGs, were identified and overlapped with genes involved in epigenetic regulation", "token_count": 424, "char_count": 1488, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7379, "quality_score": 0.8689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:30.845809", "source": { "split": "train_shard_00001", "doc_id": 337 }, "chunk_id": "train_shard_00001_337_0", "global_id": 6135 }, { "text": "Using peripheral blood mononuclear cell DNAm from 54 out of the 405 bulls, we did not observe a similar effect of the trans-meQTL hotspots to that one observed in sperm.

Conclusions

For the first time, meQTLs have been detected and characterized in bovine sperm, contributing to a better understanding of the transmission of paternally inherited DNAm marks. These findings provide useful information for further research aimed at integrating epigenetic information into the prediction of performance traits.\n\nGenetic regulation of sperm DNA methylation in cattle through meQTL mapping.", "token_count": 141, "char_count": 592, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:31.273881", "source": { "split": "train_shard_00001", "doc_id": 337 }, "chunk_id": "train_shard_00001_337_1", "global_id": 6136 }, { "text": "

Background

2-phenylethanol (2-PE) is a rose-scented flavor and fragrance compound that is used in food, beverages, and personal care products. Compatibility with gasoline also makes it a potential biofuel or fuel additive. A biochemical process converting glucose or other fermentable sugars to 2-PE can potentially provide a more sustainable and economical production route than current methods that use chemical synthesis and/or isolation from plant material.

Results

We work toward this goal by engineering the Shikimate and Ehrlich pathways in the stress-tolerant yeast Kluyveromyces marxianus. First, we develop a multigene integration tool that uses CRISPR-Cas9 induced breaks on the genome as a selection for the one-step integration of an insert that encodes one, two, or three gene expression cassettes. Integration of a 5-kbp insert containing three overexpression cassettes successfully occurs with an efficiency of 51 ± 9% at the ABZ1 locus and was used to create a library of K. marxianus CBS 6556 strains with refactored Shikimate pathway genes. The 33-factorial library includes all combinations of KmARO4, KmARO7, and KmPHA2, each driven by three different promoters that span a wide expression range. Analysis of the refactored pathway library reveals that high expression of the tyrosine-deregulated KmARO4K221L and native KmPHA2, with the medium expression of feedback insensitive KmARO7G141S, results in the highest increase in 2-PE biosynthesis, producing 684 ± 73 mg/L. Ehrlich pathway engineering by overexpression of KmARO10 and disruption of KmEAT1 further increases 2-PE production to 766 ± 6 mg/L", "token_count": 493, "char_count": 1671, "word_count": 236, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [ "ABZ1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:31.922313", "source": { "split": "train_shard_00001", "doc_id": 338 }, "chunk_id": "train_shard_00001_338_0", "global_id": 6137 }, { "text": "The best strain achieves 1943 ± 63 mg/L 2-PE after 120 h fed-batch operation in shake flask cultures.

Conclusions

The CRISPR-mediated multigene integration system expands the genome-editing toolset for K. marxianus, a promising multi-stress tolerant host for the biosynthesis of 2-PE and other aromatic compounds derived from the Shikimate pathway.\n\nCRISPR-mediated multigene integration enables Shikimate pathway refactoring for enhanced 2-phenylethanol biosynthesis in Kluyveromyces marxianus.", "token_count": 167, "char_count": 502, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8065, "quality_score": 0.9032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:32.363907", "source": { "split": "train_shard_00001", "doc_id": 338 }, "chunk_id": "train_shard_00001_338_1", "global_id": 6138 }, { "text": "Extra-intestinal pathogenic E. coli (ExPEC) can cause a variety of infections outside of the intestine and are a major causative agent of urinary tract infections. Treatment of these infections is increasingly frustrated by antimicrobial resistance (AMR) diminishing the number of effective therapies available to clinicians. Incidence of multi-drug resistance (MDR) is not uniform across the phylogenetic spectrum of E. coli . Instead AMR is concentrated in select lineages, such as ST131, which are MDR pandemic clones that have spread AMR globally. Using a gnotobiotic mouse model we demonstrate that an MDR E. coli ST131 is capable out-competing and displacing non-MDR E. coli from the gut in vivo . This is achieved in the absence of antibiotic treatment mediating a selective advantage. In mice colonised with non-MDR E. coli strains, challenge with MDR E. coli either by oral gavage or co-housing with MDR E. coli colonized mice results in displacement and dominant intestinal colonization by MDR E. coli ST131. To investigate the genetic basis of this superior gut colonization ability by MDR E. coli , we used a functional pangenomic analysis of 19,571 E. coli genomes revealing that carriage of AMR genes is associated with increased diversity in carbohydrate metabolism genes. The data presented here demonstrate that independent of antibiotic selective pressures, MDR E. coli display a competitive advantage to colonise the mammalian gut and points to a vital role of metabolism in the evolution and success of MDR lineages of E. coli via carriage and spread.\n\nMulti-drug resistantE. colidisplace commensalE. colifrom the intestinal tract, a trait associated with elevated levels of genetic diversity in carbohydrate metabolism genes", "token_count": 461, "char_count": 1759, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5618, "quality_score": 0.7809, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:32.999396", "source": { "split": "train_shard_00001", "doc_id": 339 }, "chunk_id": "train_shard_00001_339_0", "global_id": 6139 }, { "text": "The adaptive immune receptor repertoire (AIRR), composed of V(D)J-recombined T cell receptors (TR) and immunoglobulins (IG), is central to adaptive immunity. Accurate AIRR profiling depends on a comprehensive and diverse germline gene set encoding AIRR (gAIRR). Furthermore, gAIRR alleles themselves are associated with immune-related phenotypes and diseases. However, for TR genes, the IMGT database - the primary gAIRR reference - has not been updated since 2020 and lacks sufficient population diversity and complete flanking sequences. To address these limitations, we investigated 47 high-quality genomes from the Human Pangenome Reference Consortium (HPRC) using the gAIRR Suite and identified 335 novel TR alleles - 305 TRV and 30 TRJ - representing 91.6% and 30.9% increases over IMGT records. All novel alleles were crosschecked using two orthogonal pipelines. We also established a comprehensive flanking sequence database, including recombination signal sequences (RSS). We have made all resources publicly available to support immunogenomics research and clinical applications.\n\nUnmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite", "token_count": 323, "char_count": 1231, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7093, "quality_score": 0.8547, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:33.565641", "source": { "split": "train_shard_00001", "doc_id": 340 }, "chunk_id": "train_shard_00001_340_0", "global_id": 6140 }, { "text": "Consumption of high FODMAP (Fermentable Oligo-, Di-, and Monosaccharides and Polyols) diet is the leading cause of alteration in the human gut microbiome, thereby, causing irritable bowel syndrome (IBS). Therefore, sourdough technology can be exploited for reduction of FODMAPs in various foods to alleviate the symptoms of IBS. Several microorganisms viz. Pichia fermentans, Lactobacillus fetmentum, Saccharomyces cerevisiae, Torulaspora delbrueckii, Kluyveromyces marxianus etc. have been identified for the production of low FODMAP type II sourdough fermented products. However, more research on regulation of end-product and volatilome profile is required for maximal exploitation of FODMAP-reducing microorganisms. Therefore, the present review is focused on utilisation of lactic acid bacteria and yeasts, alone and in synergy, for the production of low FODMAP sourdough foods. Moreover, the microbial bioprocessing of cereal and non-cereal based low FODMAP fermented sourdough products along with their nutritional and therapeutic benefits have been elaborated. The challenges and future prospects for the production of sourdough fermented low FODMAP foods, thereby, bringing out positive alterations in gut microbiome, have also been discussed.\n\nUnlocking the potential of low FODMAPs sourdough technology for management of irritable bowel syndrome", "token_count": 345, "char_count": 1356, "word_count": 184, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:34.136711", "source": { "split": "train_shard_00001", "doc_id": 341 }, "chunk_id": "train_shard_00001_341_0", "global_id": 6141 }, { "text": "New representatives of the phylum Nucleocytoviricota have been rapidly described in the last decade. Despite this, not all viruses of this phylum are allocated to recognized taxonomic families, as is the case for orpheovirus, pithovirus, and cedratvirus, which form the proposed family Pithoviridae. In this study, we performed comprehensive comparative genomic analyses of 8 pithovirus-like isolates, aiming to understand their common traits and evolutionary history. Structural and functional genome annotation was performed de novo for all the viruses, which served as a reference for pangenome construction. The synteny analysis showed substantial differences in genome organization between these viruses, with very few and short syntenic blocks shared between orpheovirus and its relatives. It was possible to observe an open pangenome with a significant increase in the slope when orpheovirus was added, alongside a decrease in the core genome. Network analysis placed orpheovirus as a distant and major hub with a large fraction of unique clusters of orthologs, indicating a distant relationship between this virus and its relatives, with only a few shared genes. Additionally, phylogenetic analyses of strict core genes shared with other viruses of the phylum reinforced the divergence of orpheovirus from pithoviruses and cedratviruses. Altogether, our results indicate that although pithovirus-like isolates share common features, this group of ovoid-shaped giant viruses presents substantial differences in gene contents, genomic architectures, and the phylogenetic history of several core genes. Our data indicate that orpheovirus is an evolutionarily divergent viral entity, suggesting its allocation to a different viral family, Orpheoviridae. IMPORTANCE Giant viruses that infect amoebae form a monophyletic group named the phylum Nucleocytoviricota. Despite being genomically and morphologically very diverse, the taxonomic categories of some clades that form this phylum are not yet well established. With advances in isolation techniques, the speed at which new giant viruses are described has increased, escalating the need to establish criteria to define the emerging viral taxa", "token_count": 521, "char_count": 2226, "word_count": 312, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:34.794994", "source": { "split": "train_shard_00001", "doc_id": 342 }, "chunk_id": "train_shard_00001_342_0", "global_id": 6142 }, { "text": "In this work, we performed a comparative genomic analysis of representatives of the putative family Pithoviridae. Based on the dissimilarity of orpheovirus from the other viruses of this putative family, we propose that orpheovirus be considered a member of an independent family, Orpheoviridae, and suggest criteria to demarcate families consisting of ovoid-shaped giant viruses.\n\nAnalysis of the Genomic Features and Evolutionary History of Pithovirus-Like Isolates Reveals Two Major Divergent Groups of Viruses.", "token_count": 128, "char_count": 514, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:35.216271", "source": { "split": "train_shard_00001", "doc_id": 342 }, "chunk_id": "train_shard_00001_342_1", "global_id": 6143 }, { "text": "Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream of the KIT gene has been proposed. Here, we construct a graph pangenome from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white-head-associated locus for the first time based on long-read sequencing data and pangenome analyses. We introduce a pangenome-wide association mapping approach that examines assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant (SV) 66 kb upstream of KIT and facial depigmentation. The complex SV contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs, and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pangenome graph, further validating that the alleles of the SV segregate with head depigmentation. We estimate an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference genome, which had fewer copies. Our work shows that exploiting assembly path similarities within graph pangenomes can reveal trait-associated complex SVs.\n\nTaurine pangenome uncovers a segmental duplication upstream of <i>KIT</i> associated with depigmentation in white-headed cattle.", "token_count": 434, "char_count": 1812, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6454, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:35.849336", "source": { "split": "train_shard_00001", "doc_id": 343 }, "chunk_id": "train_shard_00001_343_0", "global_id": 6144 }, { "text": "Breeding of lettuce ( Lactuca sativa L.), the most important leafy vegetable worldwide, for enhanced disease resistance and resilience relies on multiple wild relatives to provide the necessary genetic diversity. In this study, we constructed a super-pangenome based on four Lactuca species (representing the primary, secondary and tertiary gene pools) and comprising 474 accessions. We include 68 newly sequenced accessions to improve cultivar coverage and add important foundational breeding lines. With the super-pangenome we find substantial presence/absence variation (PAV) and copy-number variation (CNV). Functional enrichment analyses of core and variable genes show that transcriptional regulators are conserved whereas disease resistance genes are variable. PAV-genome-wide association studies (GWAS) and CNV-GWAS are largely congruent with single-nucleotide polymorphism (SNP)-GWAS. Importantly, they also identify several major novel quantitative trait loci (QTL) for resistance against Bremia lactucae in variable regions not present in the reference lettuce genome. The usability of the super-pangenome is demonstrated by identifying the likely origin of non-reference resistance loci from the wild relatives Lactuca serriola, Lactuca saligna and Lactuca virosa . The provided methodology and data provide a strong basis for research into PAVs, CNVs and other variation underlying important biological traits of lettuce and other crops.\n\nLactucasuper-pangenome reduces bias towards reference genes in lettuce research", "token_count": 372, "char_count": 1538, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6878, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:36.427205", "source": { "split": "train_shard_00001", "doc_id": 344 }, "chunk_id": "train_shard_00001_344_0", "global_id": 6145 }, { "text": "

Background

From July 23 to 24, 2022, Qingxu People's Hospital in Taiyuan reported an increase in acute gastroenteritis cases among individuals who had dined together.An investigation was initiated to identify factors associated with acute intestinal infection and to prevent further illness.

Methods

To isolate, cultivate, and identify pathogens, we collected samples from patients, food, and the environment. The isolated strains underwent multiple tests, including antimicrobial susceptibility testing, pulsed-field gel electrophoresis (PFGE), and whole-genome sequencing (WGS). Based on the WGS data, analyses were conducted, including serotype prediction, resistance gene prediction, multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST), single nucleotide polymorphism (SNP) analysis, and phylogenetic analysis.

Results

A total of 11 samples were collected from Patient 1's residence and the supermarket. These included 2 samples of leftover food from a family gathering, 4 samples of the supermarket environment, and 5 stool samples from 5 patients. Among these, two strains of Salmonella were isolated from the food, and three strains were isolated from the patients' stools. All five strains of Salmonella were identified as Salmonella Agona (S. Agona) and were susceptible to the 15 antibiotics tested. The PFGE banding patterns were identical among the strains. Bioinformatics analysis revealed that the isolated strains were all S. Agona of sequence type ST13 and cgMLST type cgST164980. They all carried the resistance genes aac(6')-laa and fosA7. SNP disparities ranged from 0 to 2. In the phylogenetic tree, the five strains of S. Agona isolated clustered closely together.

Conclusions

In this investigation of a food poisoning outbreak caused by S. Agona, we employed two key molecular techniques: Pulsed-Field Gel Electrophoresis (PFGE) and Whole Genome Sequencing (WGS)", "token_count": 519, "char_count": 1944, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6302, "quality_score": 0.8151, "entities": { "genes": [ "ST13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:37.088821", "source": { "split": "train_shard_00001", "doc_id": 345 }, "chunk_id": "train_shard_00001_345_0", "global_id": 6146 }, { "text": "PFGE provided initial high-resolution DNA fingerprinting to identify bacterial strains and establish their clonal relatedness, offering preliminary but crucial insights into understanding the microbial causes of the epidemic. Subsequently, WGS delivered comprehensive genetic information with unparalleled precision, confirming that the pathogen was S. Agona and revealing its genomic characteristics. The integration of PFGE and WGS results provided strong evidence proving the epidemic was related to S. Agona. This comprehensive approach not only confirmed the etiology of the food poisoning event but also highlighted the power of molecular and genomic tools in modern epidemiological investigations. Our findings emphasize the importance of these techniques in rapidly and accurately identifying pathogens, thereby enabling timely public health interventions and reinforcing food safety measures to prevent similar outbreaks in the future.\n\nEpidemiological and molecular investigation of a Salmonella Agona-associated foodborne outbreak in Taiyuan, Shanxi Province, China, 2022.", "token_count": 221, "char_count": 1083, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7465, "quality_score": 0.8732, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:37.553855", "source": { "split": "train_shard_00001", "doc_id": 345 }, "chunk_id": "train_shard_00001_345_1", "global_id": 6147 }, { "text": "

Background

Hemicellulose acts as one factor contributing to the recalcitrance of lignocellulose that prevents cellulases to degrade the cellulose efficiently even in low quantities. Supplement of hemicellulases can enhance the performance of commercial cellulases in the enzymatic hydrolyses of lignocellulose. Kluyveromyce marxianus is an attractive yeast for cellulosic ethanol fermentation, as well as a promising host for heterologous protein production, since it has remarkable thermotolerance, high growth rate, and broad substrate spectrum etc. In this study, we attempted to coordinately express multiple hemicellulases in K. marxianus through a 2A-mediated ribosome skipping to self-cleave polyproteins, and investigated their capabilities for saccharification and ethanol production from corncobs.

Results

Two polycistronic genes IMPX and IMPαX were constructed to test the self-cleavage of P2A sequence from the Foot-and-Mouth Disease virus (FMDV) in K. marxianus. The IMPX gene consisted of a β-mannanase gene M330 (without the stop codon), a P2A sequence and a β-xylanase gene Xyn-CDBFV in turn. In the IMPαX gene, there was an additional α-factor signal sequence in frame with the N-terminus of Xyn-CDBFV. The extracellular β-mannanase activities of the IMPX and IMPαX strains were 21.34 and 15.50 U/mL, respectively, but the extracellular β-xylanase activity of IMPαX strain was much higher than that of the IMPX strain, which was 136.17 and 42.07 U/mL, respectively", "token_count": 444, "char_count": 1496, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:38.217388", "source": { "split": "train_shard_00001", "doc_id": 346 }, "chunk_id": "train_shard_00001_346_0", "global_id": 6148 }, { "text": "Subsequently, two recombinant strains, the IXPαR and IMPαXPαR, were constructed to coordinately and secretorily express two xylantic enzymes, Xyn-CDBFV and β-D-xylosidase RuXyn1, or three hemicellulolytic enzymes including M330, Xyn-CDBFV and RuXyn1. In fed-batch fermentation, extracellular activities of β-xylanase and β-xylosidase in the IXPαR strain were 1664.2 and 0.90 U/mL. Similarly, the IMPαXPαR strain secreted the three enzymes, β-mannanase, β-xylanase, and β-xylosidase, with the activities of 159.8, 2210.5, and 1.25 U/mL, respectively. Hemicellulolases of both strains enhanced the yields of glucose and xylose from diluted acid pretreated (DAP) corncobs when acted synergistically with commercial cellulases. In hybrid saccharification and fermentation (HSF) of DAP corncobs, hemicellulases of the IMPαXPαR strain increased the ethanol yield by 8.7% at 144 h compared with the control. However, both ethanol and xylose yields were increased by 12.7 and 18.2%, respectively, at 120 h in HSF of aqueous ammonia pretreated (AAP) corncobs with this strain. Our results indicated that coordinate expression of hemicellulolytic enzymes in K. marxianus promoted the saccharification and ethanol production from corncobs.

Conclusions

The FMDV P2A sequence showed high efficiency in self-cleavage of polyproteins in K. marxianus and could be used for secretory expression of multiple enzymes in the presence of their signal sequences", "token_count": 488, "char_count": 1446, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:38.873445", "source": { "split": "train_shard_00001", "doc_id": 346 }, "chunk_id": "train_shard_00001_346_1", "global_id": 6149 }, { "text": "The IMPαXPαR strain coexpressed three hemicellulolytic enzymes improved the saccharification and ethanol production from corncobs, and could be used as a promising strain for ethanol production from lignocelluloses.\n\nCoordinately express hemicellulolytic enzymes in Kluyveromyces marxianus to improve the saccharification and ethanol production from corncobs.", "token_count": 100, "char_count": 359, "word_count": 44, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:39.284121", "source": { "split": "train_shard_00001", "doc_id": 346 }, "chunk_id": "train_shard_00001_346_2", "global_id": 6150 }, { "text": "

Background

Escherichia coli (E. coli) has been one of the most studied model organisms in the history of life sciences. Initially thought just to be commensal bacteria, E. coli has shown wide phenotypic diversity including pathogenic isolates with great relevance to public health. Though pangenome analysis has been attempted several times, there is no systematic functional characterization of the E. coli subgroups according to the gene profile.

Results

Systematically scanning for optimal parametrization, we have built the E. coli pangenome from 1324 complete genomes. The pangenome size is estimated to be ~25,000 gene families (GFs). Whereas the core genome diminishes as more genomes are added, the softcore genome (≥95% of strains) is stable with ~3000 GFs regardless of the total number of genomes. Apparently, the softcore genome (with a 92% or 95% generation threshold) can define the genome of a bacterial species listing the critically relevant, evolutionarily most conserved or important classes of GFs. Unsupervised clustering of common E. coli sequence types using the presence/absence GF matrix reveals distinct characteristics of E. coli phylogroups B1, B2, and E. We highlight the bi-lineage nature of B1, the variation of the secretion and of the iron acquisition systems in ST11 (E), and the incorporation of a highly conserved prophage into the genome of ST131 (B2). The tail structure of the prophage is evolutionarily related to R2-pyocin (a tailocin) from Pseudomonas aeruginosa PAO1. We hypothesize that this molecular machinery is highly likely to play an important role in protecting its own colonies; thus, contributing towards the rapid rise of pandemic E. coli ST131.

Conclusions

This study has explored the optimized pangenome development in E. coli. We provide complete GF lists and the pangenome matrix as supplementary data for further studies. We identified biological characteristics of different E. coli subtypes, specifically for phylogroups B1, B2, and E", "token_count": 519, "char_count": 2017, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6208, "quality_score": 0.8104, "entities": { "genes": [ "ST131", "PAO1", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:39.931717", "source": { "split": "train_shard_00001", "doc_id": 347 }, "chunk_id": "train_shard_00001_347_0", "global_id": 6151 }, { "text": "We found an operon-like genome region coding for a tailocin specific for ST131 strains. The latter is a potential killer weapon providing pandemic E. coli ST131 with an advantage in inter-bacterial competition and, suggestively, explains their dominance as human pathogen among E. coli strains.\n\nTo kill or to be killed: pangenome analysis of Escherichia coli strains reveals a tailocin specific for pandemic ST131.", "token_count": 109, "char_count": 415, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:40.319744", "source": { "split": "train_shard_00001", "doc_id": 347 }, "chunk_id": "train_shard_00001_347_1", "global_id": 6152 }, { "text": "In the present work the effect of three factors: pH, temperature and type of microorganism using a factorial design 32x2 was evaluated on: growth, total cellulases hydrolytic activity (FPases), endoglucanases hydrolytic activity (CMCases), free reducing sugars (FRS), glucose, sucrose, and alcohol production using a culture medium based on mineral salts added with cladodes flour of Opuntia ficus-indica at 20% as the unique carbon source. Two wild microorganisms were used, Acinetobacter pittii a bacteria isolated from decaying cladodes, and Kluyveromyces marxianus a yeast isolated from termite stomach. The maximum hydrolytic activities were obtained with Acinetobacter pittii at 37 °C and pH 6.5 for total cellulases (0.67 ± 0.02 IU/ml) and for endoglucanases (0.23 ± 0.02 IU/ml) at 24 and 4 h. The maximum production of alcohol was 12.98 ± 0.06 g/L obtained with Kluyveromyces marxianus at 4 h with conditions of 40 °C and pH 5.5.\n\nEnzymatic hydrolysis of Opuntia ficus-indica cladode by Acinetobacter pittii and alcohol fermentation by Kluyveromyces marxianus: pH, temperature and microorganism effect.", "token_count": 438, "char_count": 1177, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:40.950537", "source": { "split": "train_shard_00001", "doc_id": 348 }, "chunk_id": "train_shard_00001_348_0", "global_id": 6153 }, { "text": "The strain Gordonia polyisoprenivorans 135 is able to utilize a wide range of aromatic compounds. The aim of this work was to study the features of genetic organization and biotechnological potential of the strain G. polyisoprenivorans 135 as a degrader of aromatic compounds. The study of the genome of the strain 135 and the pangenome of the G. polyisoprenivorans species revealed that some genes, presumably involved in PAH catabolism, are atypical for Gordonia and belong to the pangenome of Actinobacteria. Analyzing the intergenic regions of strain 135 alongside the \"panIGRome\" of G. polyisoprenivorans showed that some intergenic regions in strain 135 also differ from those located between the same pairs of genes in related strains. The strain G. polyisoprenivorans 135 in our work utilized naphthalene (degradation degree 39.43%) and grew actively on salicylate. At present, this is the only known strain of G. polyisoprenivorans with experimentally confirmed ability to utilize these compounds.\n\nGenomic, Phylogenetic and Physiological Characterization of the PAH-Degrading Strain Gordonia polyisoprenivorans 135.", "token_count": 370, "char_count": 1188, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5427, "quality_score": 0.7713, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:41.534375", "source": { "split": "train_shard_00001", "doc_id": 349 }, "chunk_id": "train_shard_00001_349_0", "global_id": 6154 }, { "text": "

Motivation

Constructing and studying pangenome variation graphs (PVG) supports new insights into viral genomic diversity. This is because such pangenomes are less prone to reference bias, which affects mutation detection. Interpreting the information arising from this is challenging, so automating these processes to allow exploratory investigations for PVG optimisation is essential. Moreover, existing methods do not scale well to the smaller virus genome sizes and to facilitate analysis in laptop environments. To address this, we developed an easily deployable pipeline to facilitate the rapid creation of virus PVGs that applies a broad range of analyses to these PVGs.

Results

We present panalyze, a scalable and unbiased virus PVG construction, analysis and annotation tool implemented in NextFlow and containerised in Docker. Panalyze uses NextFlow to efficiently complete tasks across multiple compute nodes and in diverse high-performance computing environments. Panalyze can also operate on a single thread on a standard laptop, and analyse sequences lengths are of any size. We illustrate how Panalyze works and the valuable outputs it can generate using a range of common viral pathogens.

Availability

Panalyze is released under a MIT open-source license, available on GitHub with documentation accessible at https://github.com/downingtim/Panalyze/ .

Contact

Chandana.tennakoon@pirbright.ac.uk , tim.downing@pibright.ac.uk

Supplementary information

Supplementary data are available online.\n\nPanalyze: automated virus pangenome variation graph construction, analysis and annotation", "token_count": 396, "char_count": 1645, "word_count": 215, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:42.158241", "source": { "split": "train_shard_00001", "doc_id": 350 }, "chunk_id": "train_shard_00001_350_0", "global_id": 6155 }, { "text": "Somatic mosaicism is increasingly recognized as a fundamental feature of human biology, yet the detection of somatic mutations remains challenging. The SMaHT Network conducted four large-scale benchmarking experiments to evaluate sequencing technologies, experimental approaches, and computational methods for detecting diverse somatic mutations. Cumulative sequencing coverage exceeded 1,000× with short reads and 100-400× with long reads for each of nine analyzed samples. We defined optimal strategies for integrating bulk short- and long-read sequencing for mutation detection and demonstrated that using donor-specific assemblies and human pangenome improved variant calling and extended mutation catalogs to challenging genomic regions. We benchmarked six duplex-seq technologies and showed that single-cell sequencing resolves cell type-specific mutational patterns and heterogeneity. Our results indicate that bulk, single-cell, and duplex analyses are complementary – and leveraging all three provides comprehensive characterization of mosaicism within a tissue. Together, these findings provide a roadmap for accurate, genome-wide somatic mutation discovery and analysis.\n\nComprehensive benchmarking of somatic mutation detection by the SMaHT Network", "token_count": 265, "char_count": 1260, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7125, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:43.062093", "source": { "split": "train_shard_00001", "doc_id": 351 }, "chunk_id": "train_shard_00001_351_0", "global_id": 6156 }, { "text": "Pangenomes are becoming increasingly popular data structures for genomics analyses due to their ability to compactly represent the genetic diversity within populations. Constructing a pangenome graph, however, is still a time-consuming and expensive process. A promising approach for pangenome construction consists of progressively augmenting a pangenome graph with additional high-quality assemblies. Currently, there is no approach to augment a pangenome graph using unassembled reads from newly sequenced samples that does not require to align them and genotype the new individuals. In this work, we present the first assembly-free and mapping-free approach for augmenting an existing pangenome graph using unassembled long reads from an individual not already present in the pangenome. Our approach consists of finding sample specific sequences in reads using efficient indexes, clustering reads corresponding to the same novel variant(s), and then building a consensus sequence to be added to the pangenome graph for each variant separately. Using simulated reads based on Human Pangenome Reference Consortium (HPRC) assemblies, we demonstrate the effectiveness of the proposed approach for progressively augmenting the pangenome with long reads, without the need for de novo assembly or predicting genetic variants of the new sample. The software is freely available at https://github.com/ldenti/palss .\n\nPangenome graph augmentation from unassembled long reads", "token_count": 300, "char_count": 1468, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:43.625883", "source": { "split": "train_shard_00001", "doc_id": 352 }, "chunk_id": "train_shard_00001_352_0", "global_id": 6157 }, { "text": "Genes and other genomic elements have variable presence absence patterns across most bacterial species. Pangenome fluidity is often invoked to measure this genome flux. Fluid pangenomes contain genes found only in subsets of species strains. Tighter pangenomes contain more genes that define a shared core. Species definitions are often tied to this pangenome diversity. In any global comparative framework, pangenomes must be calculated across all known species. But defining pangenomes is fraught with computational and biological challenges, requiring assembly, annotation, alignment, and phylogenetics of millions of orthologs. We offer an alternate view that de-centers the gene and emphasizes the raw information content of sequences. Information is data that reduces uncertainty. Tight pangenomes, with elements repeated across every strain in a species ensemble, contain more complete information. In contrast, fluid pangenomes have more uncertainty, higher complexity, and higher information diversity. Bacterial lifestyle has been shown to drive this information diversity. For example, challenging environments often increase information diversity by encouraging the accrual of auxiliary genes. Here, we employ agile complexity metrics to quantify this increase. Ensembles of free-living, motile, and non-pathogenic species have high genomic complexity. Ensemble complexity decreases in species bound to specific hosts. Because we eliminate annotation and alignment, our method is fast enough to evaluate species across all known bacterial genomes. The approach democratizes classification and our results highlight how broad the term “species” has become.\n\nThe information content of species: formal definitions of pangenome complexity track with bacterial lifestyle", "token_count": 351, "char_count": 1778, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6281, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:44.210958", "source": { "split": "train_shard_00001", "doc_id": 353 }, "chunk_id": "train_shard_00001_353_0", "global_id": 6158 }, { "text": "

Background

Pseudomonas syringae pv. actinidiae (Psa) is an important bacterial plant pathogen that causes severe damage to the kiwifruit industry worldwide. Three Psa strains were recently obtained from different kiwifruit orchards in Anhui Province, China. The present study mainly focused on the variations in virulence and genome characteristics of these strains based on the pathogenicity assays and comparative genomic analyses.

Results

Three strains were identified as biovar 3 (Psa3), along with strain QSY6 showing higher virulence than JZY2 and YXH1 in pathogenicity assays. The whole genome assembly revealed that each of the three strains had a circular chromosome and a complete plasmid. The chromosome sizes ranged from 6.5 to 6.6 Mb with a GC content of approximately 58.39 to 58.46%, and a predicted number of protein-coding sequences ranging from 5,884 to 6,019. The three strains clustered tightly with 8 Psa3 reference strains in terms of average nucleotide identity (ANI), whole-genome-based phylogenetic analysis, and pangenome analysis, while they were evolutionarily distinct from other biovars (Psa1 and Psa5). Variations were observed in the repertoire of effectors of the type III secretion system among all 15 strains. Moreover, synteny analysis of the three sequenced strains revealed eight genomic regions containing 308 genes exclusively present in the highly virulent strain QSY6. Further investigation of these genes showed that 16 virulence-related genes highlight several key factors, such as effector delivery systems (type III secretion systems) and adherence (type IV pilus), which might be crucial for the virulence of QSY6.

Conclusion

Three Psa strains were identified and showed variant virulence in kiwifruit plant. Complete genome sequences and comparative genomic analyses further provided a theoretical basis for the potential pathogenic factors responsible for kiwifruit bacterial canker.", "token_count": 504, "char_count": 1954, "word_count": 274, "semantic_coherence": 1, "information_density": 0.635, "quality_score": 0.8175, "entities": { "genes": [ "QSY6", "JZY2", "YXH1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:44.862893", "source": { "split": "train_shard_00001", "doc_id": 354 }, "chunk_id": "train_shard_00001_354_0", "global_id": 6159 }, { "text": "Comparative genomic analyses provide insight into the pathogenicity of three Pseudomonas syringae pv. actinidiae strains from Anhui Province, China.", "token_count": 40, "char_count": 148, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:45.226222", "source": { "split": "train_shard_00001", "doc_id": 354 }, "chunk_id": "train_shard_00001_354_1", "global_id": 6160 }, { "text": "Abstract

Background Staphylococcus aureus is a major pathogen that causes hospital- and community-acquired infections, with increasing antimicrobial resistance (AMR) posing a global threat. East Africa remains an understudied region concerning the genomic epidemiology of S. aureus. This study provides a comprehensive genomic characterization of S. aureus genomes from hospital settings in East Africa, focusing on AMR, virulence determinants, mobile genetic elements (MGEs), and population structure. Methods We analyzed a total of 496 S. aureus whole-genome sequences (WGSs) from Tanzania, Kenya and Uganda retrieved from the NCBI Sequence Read Archive (SRA). Bioinformatics pipelines were employed for quality control, genome assembly, annotation and comparative genomics. In-silico multi-Locus Sequence Typing (MLST), spa & SCCmec typing and pangenome assessment were conducted. AMR and virulence genes, as well as plasmid and prophage diversity, were identified via curated databases. Results MLST analysis revealed 45 sequence types (STs), including 18 novel allelic profiles, with CC152 (ST152) being the most prevalent (26.7%). Spa typing identified 67 distinct types, with t355 (24.4%) and t1476 (17.8%) dominating. SCCmec typing revealed Type V (78.1%) as the predominant methicillin resistance determinant, particularly in Tanzania (91.3%)", "token_count": 451, "char_count": 1523, "word_count": 183, "semantic_coherence": 1, "information_density": 0.776, "quality_score": 0.888, "entities": { "genes": [ "CC152", "ST152" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:45.871813", "source": { "split": "train_shard_00001", "doc_id": 355 }, "chunk_id": "train_shard_00001_355_0", "global_id": 6161 }, { "text": "AMR profiling revealed 94 resistance genes, with a high prevalence of blaZ (β-lactamase), tet(38) (tetracycline efflux), and dfrG (trimethoprim resistance). Virulence gene analysis revealed 147 loci, including Panton-Valentine leukocidin (lukF-PV; 2.1%) and biofilm-associated genes (icaD). Plasmid analysis revealed high diversity, with Tanzania exhibiting the highest replicon complexity (mean = 4.2 plasmids/isolate). The phage sequence (n = 934) was predominantly Siphoviridae (94.1%), with no significant geographic structuring. Pangenome analysis revealed extreme diversity, with only five core genes conserved across all the isolates and 68,759 strain-specific cloud genes. Conclusion This study highlights the dynamic genomic landscape of S. aureus in East Africa, characterized by regional clonal expansion, extensive AMR, and diverse virulence profiles. The dominance of community-associated MRSA (Type V SCCmec) in Tanzania contrasts with Kenya’s co-circulation of hospital and community strains, whereas Uganda harbors rare SCCmec Type VI strains, suggesting potential zoonotic origins. These findings emphasize the need for region-specific surveillance and tailored AMR stewardship programs to mitigate the spread of resistant and virulent S. aureus clones in East Africa.

\n\nUnraveling the Genomic Landscape of Staphylococcus aureus in Hospital Settings of East Africa", "token_count": 459, "char_count": 1537, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7473, "quality_score": 0.8736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:46.514913", "source": { "split": "train_shard_00001", "doc_id": 355 }, "chunk_id": "train_shard_00001_355_1", "global_id": 6162 }, { "text": "Fungal infections are difficult to prevent and treat in large part due to strain heterogeneity, which confounds diagnostic predictability. Yet, the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined the extent to which Starships-giant transposons capable of mobilizing numerous fungal genes-generate genetic and phenotypic variability in the opportunistic human pathogen Aspergillus fumigatus. We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology and multiple isolates of the same reference strain, to reveal 20 distinct Starships that are generating genomic heterogeneity over timescales relevant for experimental reproducibility. Starship-mobilized genes encode diverse functions, including known biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal evolution wherein Starships help generate variation in genome structure, gene content, and expression among fungal strains. Together, our results demonstrate that Starships are a previously hidden mechanism generating genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen.IMPORTANCENo \"one size fits all\" option exists for treating fungal infections in large part due to genetic and phenotypic variability among strains. Accounting for strain heterogeneity is thus fundamental for developing efficacious treatments and strategies for safeguarding human health. Here, we report significant progress toward achieving this goal by uncovering a previously hidden mechanism generating heterogeneity in the human fungal pathogen Aspergillus fumigatus: giant transposons, called Starships, that span dozens of kilobases and mobilize fungal genes as cargo. By conducting a systematic investigation of these unusual transposons in a single fungal species, we demonstrate their contributions to population-level variation at the genome, pangenome, and transcriptome levels", "token_count": 489, "char_count": 2148, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:47.165051", "source": { "split": "train_shard_00001", "doc_id": 356 }, "chunk_id": "train_shard_00001_356_0", "global_id": 6163 }, { "text": "The Starship compendium we develop will not only help predict variation introduced by these elements in laboratory experiments but will serve as a foundational resource for determining how Starships impact clinically relevant phenotypes, such as antifungal resistance and pathogenicity.\n\nGiant transposons promote strain heterogeneity in a major fungal pathogen.", "token_count": 86, "char_count": 376, "word_count": 49, "semantic_coherence": 1, "information_density": 0.9184, "quality_score": 0.9592, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:47.543153", "source": { "split": "train_shard_00001", "doc_id": 356 }, "chunk_id": "train_shard_00001_356_1", "global_id": 6164 }, { "text": "

Background

The concept of pangenomics and the importance of structural variants is gaining recognition within the plant genomics community. Due to advancements in sequencing and computational technology, it has become feasible to sequence the entire genome of numerous individuals of a single species at a reasonable cost. Pangenomes have been constructed for many major diploid crops, including rice, maize, soybean, sorghum, pearl millet, peas, sunflower, grapes, and mustards. However, pangenomes for polyploid species are relatively scarce and are available in only few crops including wheat, cotton, rapeseed, and potatoes.

Main body

In this review, we explore the various methods used in crop pangenome development, discussing the challenges and implications of these techniques based on insights from published pangenome studies. We offer a systematic guide and discuss the tools available for constructing a pangenome and conducting downstream analyses. Alfalfa, a highly heterozygous, cross pollinated and autotetraploid forage crop species, is used as an example to discuss the concerns and challenges offered by polyploid crop species. We conducted a comparative analysis using linear and graph-based methods by constructing an alfalfa graph pangenome using three publicly available genome assemblies. To illustrate the intricacies captured by pangenome graphs for a complex crop genome, we used five different gene sequences and aligned them against the three graph-based pangenomes. The comparison of the three graph pangenome methods reveals notable variations in the genomic variation captured by each pipeline.

Conclusion

Pangenome resources are proving invaluable by offering insights into core and dispensable genes, novel gene discovery, and genome-wide patterns of variation. Developing user-friendly online portals for linear pangenome visualization has made these resources accessible to the broader scientific and breeding community. However, challenges remain with graph-based pangenomes including compatibility with other tools, extraction of sequence for regions of interest, and visualization of genetic variation captured in pangenome graphs. These issues necessitate further refinement of tools and pipelines to effectively address the complexities of polyploid, highly heterozygous, and cross-pollinated species.", "token_count": 506, "char_count": 2364, "word_count": 317, "semantic_coherence": 1, "information_density": 0.6088, "quality_score": 0.8044, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:48.175128", "source": { "split": "train_shard_00001", "doc_id": 357 }, "chunk_id": "train_shard_00001_357_0", "global_id": 6165 }, { "text": "A stepwise guide for pangenome development in crop plants: an alfalfa (Medicago sativa) case study.", "token_count": 27, "char_count": 99, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:48.540271", "source": { "split": "train_shard_00001", "doc_id": 357 }, "chunk_id": "train_shard_00001_357_1", "global_id": 6166 }, { "text": "Staphylococcus pseudintermedius is the foremost cause of opportunistic canine skin and mucosal infections worldwide. Multidrug-resistant (MDR) and methicillin-resistant Staphylococcus pseudintermedius (MRSP) lineages have disseminated globally in the last decade and present significant treatment challenges. However, little is known regarding the factors that contribute to the success of MDR lineages. In this study, we compared the genome sequence of 110 UK isolates of S. pseudintermedius with 2166 genomes of S. pseudintermedius populations from different continents. A novel core genome multi-locus typing scheme was generated to allow large-scale, rapid and detailed analysis of S. pseudintermedius phylogenies and was used to show that the S. pseudintermedius population structure is broadly segregated into an MDR population and a non-MDR population. MRSP lineages are predicted to encode certain resistance genes either chromosomally or on plasmids, and this is associated with their MLST sequence type. A comparison of lineages most frequently implicated in disease, ST-45 and ST-71, with the phylogenetically related ST-496 lineage that has a comparatively low disease rate, revealed that ST-45 and ST-71 genomes encode distinct combinations of phage-defence systems and concurrently encode a high number of intact prophages. In contrast, ST-496 genomes encode a wider array of phage defence systems and lack intact and complete prophages. These findings indicate that MRSP lineages have significant structural genomic differences and that prophage integration and differential antiviral systems correlate with the emergence of successful genotypes.\n\nGlobal phylogenomic analysis of <i>Staphylococcus pseudintermedius</i> reveals genomic and prophage diversity in multidrug-resistant lineages.", "token_count": 485, "char_count": 1859, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6214, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:49.184801", "source": { "split": "train_shard_00001", "doc_id": 358 }, "chunk_id": "train_shard_00001_358_0", "global_id": 6167 }, { "text": "Objectives: When COVID-19 emerged as a global pandemic, invasive yeast infections (IYIs) also presented a risk of developing super-infections as another cause of mortality. Our research is to identify the most common Candida species among COVID-19 patients in the Duhok City/Kurdistan region of Iraq.

Methods: All confirmed COVID-19 cases were tested by real-time RT-PCR on nasal and oral samples. Culture-based techniques and DNA sequencing of ITS region were used to identify and analyze Candida species.

Results: As a result of culture-based techniques, 45 positive Candida isolates were identified out of 100 samples grown on chromogenic Candida agar. The highest percentage belongs to Candida albicans 37.77 %, followed by C. krusei 28.88 %, C. glabrata 20 %, and C. tropicalis 13.33 %. A DNA study revealed new species of Candida africana, C. dublinensis, Kluyveromyces marxianus, Cyberlindnera fabianii, Rhodotorula mucilaginosa, and Purpureocillium lilacinum.

Conclusion: To better diagnose, manage, and prescribe the correct antifungal to COVID-19 patients, DNA-based techniques should be used.\n\nPrevalence, Molecular Identification, and Genetic Relationships of Oral and Nasal Candidiasis in COVID-19 Patients", "token_count": 362, "char_count": 1245, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:49.759800", "source": { "split": "train_shard_00001", "doc_id": 359 }, "chunk_id": "train_shard_00001_359_0", "global_id": 6168 }, { "text": "Abstract

This study aimed to conduct a phylogenetic and functional analysis of Ureibacillus thermophilus LM102. The phylogeny using the TYGS web server revealed that Ureibacillus thermophilus LM102 shares both mesophilic and thermophilic strain traits. Digital DNA-DNA hybridization values ranged from 19.1% to 37.4%, confirming the strain unique taxonomic classification. BlastKOALA identified genes involved in complete biotin, riboflavin, and cobalamin biosynthesis pathways, highlighting its industrial relevance. The P2RP web tool identified stress-response mechanisms including WalRK (YycFG), DesKR, LiaRS, BceRS, and ResDE adaptations to temperature fluctuations, low oxygen levels, and antibiotic stresses through TCS mechanisms. The pangenome analysis using the power-law regression based on Heaps' law revealed the BP = 0.65, indicating the Ureibacillus genus has an open pangenome nature. Furthermore, the pan-genomic analysis using Roary revealed the stains possess 1006 genes encoding for hypothetical proteins. The gene ontology and physicochemical properties of the HPs were carried out using UPIMAPI and ExPASy. Of the total hypothetical protein, 49.36% is involved in molecular function, 41.71% in biological processes, and 6.36% in cellular components. Notably, 500 HPs exhibited known protein domains, and the average Aliphatic Index of these proteins is as high as 105.08, suggesting the high thermostability of the proteins", "token_count": 483, "char_count": 1630, "word_count": 197, "semantic_coherence": 1, "information_density": 0.731, "quality_score": 0.8655, "entities": { "genes": [ "LM102" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:50.430035", "source": { "split": "train_shard_00001", "doc_id": 360 }, "chunk_id": "train_shard_00001_360_0", "global_id": 6169 }, { "text": "These findings suggest that Ureibacillus thermophilus LM102 has significant potential for applications in biotechnology and industrial processes.

\n\nExploring the Functional Potential of Ureibacillus thermophilus LM102 through comprehensive and comparative Genome Analysis", "token_count": 75, "char_count": 291, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9032, "quality_score": 0.9516, "entities": { "genes": [ "LM102" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:50.812788", "source": { "split": "train_shard_00001", "doc_id": 360 }, "chunk_id": "train_shard_00001_360_1", "global_id": 6170 }, { "text": "Some biotechnological strategies have succeeded in the attempt to imitate natural fermentation, and bioprocesses have been efficiently designed when the product is the result of a unique biological reaction. However, when the process requires more than one biological reaction, few bioprocesses have been successfully designed because the available tools to construct multi-strain starter cultures are not yet well defined. In this work, a novel experimental strategy to construct multi-strain starter cultures with selected native microorganisms from natural fermentation is proposed. The strategy analyses, selects, and defines the number and proportion of each strain that should form a starter culture to be used in directed fermentations. It was applied to evolve natural fermentation to directed fermentation in distilled agave production. The results showed that a starter culture integrated by Kluyveromyces marxianus, Clavispora lusitaniae, and Kluyveromyces marxianus var. drosophilarum in proportions of 35, 32, and 33%, respectively, allows obtaining fermented agave juice containing a 2.1% alcohol yield and a distilled product with a broad profile of aromatic compounds. Hence, the results show, for the first time, a tool that addresses the technical challenge for multi-strain starter culture construction, offering the possibility of preserving the typicity and genuineness of the original traditional product.\n\nA novel strategy to construct multi-strain starter cultures: an insight to evolve from natural to directed fermentation.", "token_count": 365, "char_count": 1577, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6037, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:51.437754", "source": { "split": "train_shard_00001", "doc_id": 361 }, "chunk_id": "train_shard_00001_361_0", "global_id": 6171 }, { "text": "

Background:

The RCCX locus, resulting from segmental duplication, exhibits extensive sequence identity and modular variations because of unequal crossover events, leading to copy number variations and the formation of chimeric genes between active and pseudogenes. Precise characterization of this locus is essential for molecular diagnosis, because aberrations within this region can cause congenital adrenal hyperplasia (CAH), an autosomal recessive disorder. However, the intricate modular structures, comprising mono-, bi-, and tri-modular haplotypes, have posed challenges to accurate analysis using conventional sequencing technologies. Methods In this study, we analyzed the segmentally duplicated RCCX locus using a pangenome-based approach. High-fidelity long-read sequencing data were produced to generate high-quality personalized genome assemblies from patients with CAH. Their RCCX haplotypes were fully resolved at the single-nucleotide level, and compared with those from non-patient populations. Results We generated high-fidelity long-read sequencing data and constructed 26 phased genome assemblies from 13 Korean patients with CAH, achieving single-nucleotide resolution analysis of the RCCX locus. Furthermore, by integrating human draft pangenome reference data, we analyzed non-patient cohorts and identified characteristic variations unique to the Korean patient population and novel structural variants formed through DNA damage and homologous recombination. Conclusions Our findings provide a key methodological framework for resolving segmentally duplicated genomic regions associated with genetic disorders. This study is expected to serve as a foundation for the precise molecular diagnosis of patients with CAH.\n\nHigh-fidelity long-read sequencing reveals a complex RCCX locus at the single-nucleotide level in Korean patients with congenital adrenal hyperplasia", "token_count": 432, "char_count": 1904, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:52.066297", "source": { "split": "train_shard_00001", "doc_id": 362 }, "chunk_id": "train_shard_00001_362_0", "global_id": 6172 }, { "text": "2-Phenylethanol (2-PE) is an alcohol with a rosy scent and antimicrobial activity, and therefore, it is widely used in the food and cosmetic industries as an aroma and preservative. This work was aimed to draw up a technology for 2-PE bioproduction on whey permeate, which is waste produced by the dairy industry, rich in lactase and proteins. Its composition makes it a harmful waste to dispose of; however, with a properly selected microorganism, it could be converted to a value-added product. Herein, two yeast Kluyveromyces marxianus strains and one Kluyveromyces lactis, isolated from dairy products, were tested for 2-PE production, firstly on standard media and then on whey permeate based media in batch cultures. Thereafter, the 2-PE bioproduction in a continuous system in a 4.8 L bioreactor was developed, and subsequently, the final product was recovered from culture broth. The results showed that the yield of 2-PE production increased by 60% in the continuous culture compared to batch culture. Together with a notable reduction of chemical oxygen demand for whey permeate, the present study reports a complete, effective, and environmentally friendly strategy for 2-PE bioproduction with a space-time yield of 57.5 mg L-1 h-1.\n\nDevelopment of a Continuous System for 2-Phenylethanol Bioproduction by Yeast on Whey Permeate-Based Medium.", "token_count": 376, "char_count": 1389, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:52.650279", "source": { "split": "train_shard_00001", "doc_id": 363 }, "chunk_id": "train_shard_00001_363_0", "global_id": 6173 }, { "text": "

Introduction

As a highly adaptable opportunistic pathogen, Pseudomonas aeruginosa presents a significant threat to people with weakened immune systems. This is because it naturally resists antibiotics and can form biofilms. These factors complicate treatment and underscore the urgent need for innovative therapeutic strategies, such as vaccines, to combat this pathogen.

Methods

A pangenome analysis of P. aeruginosa genomes was performed to identify conserved core genes critical for bacterial survival and virulence. LptF, an outer membrane protein, was prioritized as a target for vaccine development. B-cell and T-cell epitopes were predicted from LptF using immunoinformatics tools, and a multi-epitope peptide vaccine was designed. The interaction between the vaccine candidate and Toll-like receptors (TLRs) was investigated through molecular docking and molecular dynamics simulations. Codon optimization and in-silico cloning were carried out to validate the vaccine's expression potential in E. coli. Immune response simulations evaluated the vaccine's immunogenicity.

Results

Our pangenome analysis identified highly conserved core genes, including LptF, which proved crucial for bacterial virulence. A multi-epitope peptide vaccine was designed using the most immunogenic B-cell and T-cell epitopes derived from LptF. Studies using molecular docking and dynamic simulation have shown stable interactions between the vaccine and TLRs, with the POA_V_RS09 construct exhibiting the highest stability. Codon optimization indicated high expression efficiency in E. coli. Immune simulations revealed robust adaptive immune responses, including sustained IgG production, the formation of memory B cells, and the activation of T-cell responses.

Discussion

The POA_V_RS09 vaccine candidate exhibited excellent stability, immunogenic potential, and expression efficiency, making it a promising candidate for combating P. aeruginosa infections. This study provides a strong foundation for developing effective therapeutic strategies to address the growing issue of antimicrobial resistance in P. aeruginosa", "token_count": 524, "char_count": 2179, "word_count": 273, "semantic_coherence": 1, "information_density": 0.63, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:55:53.307271", "source": { "split": "train_shard_00001", "doc_id": 364 }, "chunk_id": "train_shard_00001_364_0", "global_id": 6174 }, { "text": "More experimental validation is needed to verify its effectiveness in preclinical and clinical environments.\n\nRational design of an epitope-centric vaccine against <i>Pseudomonas aeruginosa</i> using pangenomic insights and immunoinformatics approach.", "token_count": 67, "char_count": 263, "word_count": 29, "semantic_coherence": 1, "information_density": 0.9655, "quality_score": 0.9828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:53.677129", "source": { "split": "train_shard_00001", "doc_id": 364 }, "chunk_id": "train_shard_00001_364_1", "global_id": 6175 }, { "text": "1. Agroindustrial by-products and residues can be transformed into valuable compounds in biorefineries. Here we present a new concept: production of fuel ethanol, whey protein and probiotic yeast from cheese whey. An initial screening under industrially relevant conditions, involving thirty Kluyveromyces marxianus strains, was carried out using spot assays to evaluate their capacity to grow on cheese whey or on whey permeate (100 g lactose/L), under aerobic or anaerobic conditions, in the absence or presence of 5% ethanol, at pH 5.8 or pH 2.5. The four best growing K. marxianus strains were selected and further evaluated in a miniaturized industrial fermentation process using reconstituted whey permeate (100 g lactose/L) with cell recycling (involving sulfuric acid treatment). After five consecutive fermentation cycles, the ethanol yield on sugar reached 90% of the theoretical maximum in the best cases, with 90% cell viability. Cells harvested at this point displayed probiotic properties such as capacity to survive the passage through the gastrointestinal tract and capacity to modulate innate immune response of intestinal epithelium, both in vitro . Furthermore, the CIDCA 9121 strain was able to protect against histopathological damage in an animal model of acute colitis. Our findings demonstrate that K. marxianus CIDCA 9121 is capable of efficiently fermenting the lactose present in whey permeate to ethanol and that the remaining yeast biomass has probiotic properties, enabling an integrated process for the obtainment of whey protein, fuel ethanol and probiotics from cheese whey. 2.

Importance

Cheese whey is the liquid remaining following the precipitation and removal of milk casein during cheese-making. This by-product represents about 85-95% of the milk volume and retains 55% of milk nutrients so it can be exploited as a source of valuable end products", "token_count": 493, "char_count": 1896, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:54.330716", "source": { "split": "train_shard_00001", "doc_id": 365 }, "chunk_id": "train_shard_00001_365_0", "global_id": 6176 }, { "text": "However, at a global level around 50% of cheese whey is wasted, representing an important environmental impact and indicating the need to develop alternative processes to recover value. Kluyveromyces marxianus is capable of fermenting lactose, generally regarded as safe, and has been explored separately as an ethanol producer and as a viable bioactive microorganism. The significance of our research is to establish the proof of concept that a biorefinery for fuel ethanol production using whey and K. marxianus can also be exploited to obtain viable probiotic biomass, conferring an added value to the process and providing an alternative to reduce environmental impact.\n\nA biorefinery concept for the production of fuel ethanol, probiotic yeast and whey protein from a by-product of the cheese industry", "token_count": 181, "char_count": 806, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:54.778044", "source": { "split": "train_shard_00001", "doc_id": 365 }, "chunk_id": "train_shard_00001_365_1", "global_id": 6177 }, { "text": "Kefir, a fermented milk beverage, is recognized for its potential health benefits, including its cholesterol-lowering properties. This study demonstrated that selected kefir starter cultures, including Lactococcus strains and yeasts, significantly reduce cholesterol-binding capacity under simulated gastrointestinal conditions, underscoring the challenges of probiotic delivery. We compared the performance of these cultures under laboratory conditions (growth broths) and simulated digestive juice models. Lactococcus strains showed significant differences in cholesterol binding between the two environments, highlighting the limitations of relying solely on laboratory testing. Yeast cultures also exhibited greater cholesterol binding in their native broths, but their survival was limited in digestive models. Our findings suggest that effective probiotic formulations should prioritize strains with high cholesterol-binding capacity and robust survival rates throughout the digestive tract. This study provides valuable insights for future research on the mechanisms behind these functionalities and the potential of kefir yeast strains for use in human digestive models. Our results can be used to inform the development of improved probiotic formulations for cholesterol management.\n\nIn Vitro Cholesterol Uptake by the Microflora of Selected Kefir Starter Cultures.", "token_count": 304, "char_count": 1388, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6554, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:55.342041", "source": { "split": "train_shard_00001", "doc_id": 366 }, "chunk_id": "train_shard_00001_366_0", "global_id": 6178 }, { "text": "

Background

The construction of a pangenome graph is a fundamental task in pangenomics. A natural theoretical question is how to formalize the computational problem of building an optimal pangenome graph, making explicit the underlying optimization criterion and the set of feasible solutions. Current approaches build a pangenome graph with some heuristics, without assuming some explicit optimization criteria. Thus it is unclear how a specific optimization criterion affects the graph topology and downstream analysis, like read mapping and variant calling.

Results

In this paper, by leveraging the notion of maximal block in a Multiple Sequence Alignment (MSA), we reframe the pangenome graph construction problem as an exact cover problem on blocks called Minimum Weighted Block Cover (MWBC). Then we propose an Integer Linear Programming (ILP) formulation for the MWBC problem that allows us to study the most natural objective functions for building a graph. We provide an implementation of the ILP approach for solving the MWBC and we evaluate it on SARS-CoV-2 complete genomes, showing how different objective functions lead to pangenome graphs that have different properties, hinting that the specific downstream task can drive the graph construction phase.

Conclusion

We show that a customized construction of a pangenome graph based on selecting objective functions has a direct impact on the resulting graphs. In particular, our formalization of the MWBC problem, based on finding an optimal subset of blocks covering an MSA, paves the way to novel practical approaches to graph representations of an MSA where the user can guide the construction.\n\nPangeBlocks: customized construction of pangenome graphs via maximal blocks.", "token_count": 378, "char_count": 1759, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5608, "quality_score": 0.7804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:55.929678", "source": { "split": "train_shard_00001", "doc_id": 367 }, "chunk_id": "train_shard_00001_367_0", "global_id": 6179 }, { "text": "

Background

To explore the genetic characteristics of the Mycobacterium abscessus complex (MABC) population in China, given its rising clinical importance among nontuberculous mycobacteria.

Methods

We conducted population genetic analyses on 360 MABC genomes from China, focusing on core genome multilocus sequence typing (cgMLST), pan-genome characterization, population genetics, and antimicrobial resistance gene profiling.

Results

Our analysis identified 273 M. abscessus subsp. abscessus (MabA) and 87 M. abscessus subsp. massiliense (MabM) isolates, uncovering 68 sequence types (STs), with ST5 being the most common. cgMLST classified 33.3% of isolates into six dominant circulating clones (DCCs) and 49.4% into 59 genomic clusters at a threshold of 25 different alleles, including 18 international clusters linking Chinese isolates with seven other countries. The MABC pan-genome is open, with MabA exhibiting greater accessory gene diversity and higher gene turnover compared to MabM. Mobile genetic elements (MGEs), such as prophages and genomic islands, were prevalent across all genomes. 139 to 151 virulence factors (VFs) were identified per genome, with distinct accessory VFs in MabA and MabM affecting immune modulation and metabolism. Resistance gene profiling revealed ubiquitous mtrA, RbpA, and bla MAB, with MabA-specific erm(41) conferring resistance to macrolides and β-lactams", "token_count": 509, "char_count": 1571, "word_count": 187, "semantic_coherence": 1, "information_density": 0.754, "quality_score": 0.877, "entities": { "genes": [ "ST5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:56.585622", "source": { "split": "train_shard_00001", "doc_id": 368 }, "chunk_id": "train_shard_00001_368_0", "global_id": 6180 }, { "text": "Common rrs and rrl gene mutations indicated widespread resistance to aminoglycosides and macrolides, while gyrA mutations suggested emerging fluoroquinolone resistance. An acquired erm(46) gene, likely obtained via phage-mediated horizontal gene transfer, was detected in one MabA strain.

Conclusion

This study provides key genetic insights into the dynamics of MABC in China. The widespread distribution of DCCs, high genomic clustering rates, open pan-genome, and distinct resistance patterns between MabA and MabM, along with MGEs, highlight the need for targeted surveillance and tailored therapies to address emerging challenges in MABC infections.\n\nPopulation genetic analysis of clinical <i>Mycobacterium abscessus</i> complex strains in China.", "token_count": 234, "char_count": 831, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:57.050572", "source": { "split": "train_shard_00001", "doc_id": 368 }, "chunk_id": "train_shard_00001_368_1", "global_id": 6181 }, { "text": "Abstract

The Burkholderia cepacia complex (BCC) is a Gram-negative bacterial, including Burkholderia contaminans species. Although the plain Burkholderia is pervasive from taxonomic and genetic perspectives, a common characteristic is that they may use the quorum-sensing (QS) system. In our previous study, we generated the complete genome sequence of Burkholderia contaminans SK875 isolated from the respiratory tract. To our knowledge, this is the first study to report functional genomic features of B. contaminans SK875 for understanding the pathogenic characteristics. In addition, comparative genomic analysis for five B. contaminans genomes was performed to provide comprehensive information on the disease potential of B. contaminans species. Analysis of average nucleotide identity (ANI) showed that the genome has high similarity (> 96%) with other B. contaminans strains. Five B. contaminans genomes yielded a pangenome of 8,832 coding genes, a core genome of 5,452 genes, the accessory genome of 2,128 genes, and a unique genome of 1,252 genes. The 186 genes were specific to B. contaminans SK875, including toxin higB-2, oxygen-dependent choline dehydrogenase, and hypothetical proteins. Genotypic analysis of the antimicrobial resistance of B. contaminans SK875 verified resistance to tetracycline, fluoroquinolone, and aminoglycoside", "token_count": 511, "char_count": 1657, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "SK875" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:57.707458", "source": { "split": "train_shard_00001", "doc_id": 369 }, "chunk_id": "train_shard_00001_369_0", "global_id": 6182 }, { "text": "Compared with the virulence factor database, we identified 79 promising virulence genes such as adhesion system, invasions, antiphagocytic, and secretion systems. Moreover, 45 genes of 57 QS-related genes that were identified in B. contaminans SK875 indicated high sequence homology with other B. contaminans strains. Our results will help to gain insight into virulence, antibiotic resistance, and quorum sensing for B. contaminans species.

\n\nComprehensive genome analysis of Burkholderia contaminans SK875, a quorum-sensing strain isolated from the swine", "token_count": 175, "char_count": 610, "word_count": 76, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [ "SK875" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:58.145908", "source": { "split": "train_shard_00001", "doc_id": 369 }, "chunk_id": "train_shard_00001_369_1", "global_id": 6183 }, { "text": "

Background

Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations.

Results

Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which are phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce's disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes.

Conclusions

This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.\n\nA super-pangenome of the North American wild grape species.", "token_count": 359, "char_count": 1634, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:58.722958", "source": { "split": "train_shard_00001", "doc_id": 370 }, "chunk_id": "train_shard_00001_370_0", "global_id": 6184 }, { "text": "

Background

Mycoplasma bovis mastitis is an important disease of dairy cows that causes substantial economic losses. However, its prevalence in different states in the United States (US), including Tennessee, is not well known. Furthermore, recent studies showed a high prevalence of bovine hemotropic mycoplasmas in US dairy farms.

Objectives

Determine the prevalence of M. bovis in bulk tank milk (BTM) of dairy farms in Tennessee and evaluate the genetic diversity, virulence factors, and antimicrobial resistance genes of the identified isolates. In addition, the prevalence of Mycoplasma wenyonii and Candidatus Mycoplasma haemobos in the bulk tank milk was determined.

Methods

Seventy-five BTM samples were collected from 59 dairy farms. Of the 59 farms, 56 are in Tennessee and the remaining 3 farms are in the neighboring states, Georgia (n = 2) and Alabama (n = 1). Milk samples were tested using bacterial culture, PCR, and qPCR. M. bovis isolates were genetically characterized by pangenome analysis.

Results

Of the 56 farms, 3 (5.3%) were positive for M. bovis by bacterial culture and 43 (76.7%) were positive by PCR. Pangenome analysis showed clustering of current isolates with mastitis isolates from the US, Israel, and Europe. Of 75 BTM samples tested by qPCR, 42 (56%) and 51 (68%) were positive for M. wenyonii and C. M. haemobos, respectively.

Conclusions

M. bovis intramammary infection is prevalent in Tennessee dairy farms.\n\nPrevalence and Whole Genome Sequence Analysis of Mycoplasma bovis Isolates From Bulk Tank Milk of Dairy Farms in Tennessee, USA.", "token_count": 484, "char_count": 1611, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5381, "quality_score": 0.7691, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:55:59.368788", "source": { "split": "train_shard_00001", "doc_id": 371 }, "chunk_id": "train_shard_00001_371_0", "global_id": 6185 }, { "text": "Mixed fermentation improves the flavor quality of food. Untargeted metabolomics were used to evaluate the impact of mixed fermentation and single-strain fermentation on the volatile and non-volatile compound profiles of Kazak cheese. Lacticaseibacillus paracasei SMN-LBK and Kluyveromyces marxianus SMN-S7-LBK were used to make mixed-fermentation cheese (M), while L. paracasei SMN-LBK was applied in single-strain-fermentation cheese (S). A higher abundances of acids, alcohols, and esters were produced via mixed fermentation. Furthermore, 397 differentially expressed non-volatile metabolites were identified between S and M during ripening. The flavor compounds in mixed-fermentation cheese mainly resulted from ester production (ethyl butanoate, ethyl acetate, ethyl octanoate, and ethyl hexanoate) and amino acid biosynthesis (Asp, Glu, Gln, and Phe). The metabolites were differentially expressed in nitrogen metabolism, D-glutamine and D-glutamate metabolism, phenylalanine metabolism, D-alanine metabolism, and other metabolic pathways. The amount of flavor compounds was increased in M, indicating that L. paracasei SMN- LBK and K. marxianus SMN-S7-LBK had synergistic effects in the formation of flavor compounds. This study comprehensively demonstrated the difference in metabolites between mixed-fermentation and single-strain-fermentation cheese and provided a basis for the production of Kazak cheese with diverse flavor characteristics.\n\nDifferences between Kazak Cheeses Fermented by Single and Mixed Strains Using Untargeted Metabolomics.", "token_count": 462, "char_count": 1591, "word_count": 200, "semantic_coherence": 1, "information_density": 0.605, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:00.017096", "source": { "split": "train_shard_00001", "doc_id": 372 }, "chunk_id": "train_shard_00001_372_0", "global_id": 6186 }, { "text": "Water buffalo is a cornerstone livestock species in many low- and middle-income countries, yet major gaps persist in its genomic characterization—complicated by the divergent karyotypes of its two sub-species (swamp and river). Such genomic complexity makes water buffalo a particularly good candidate for the use of graph genomics, which can capture variation missed by linear reference approaches. However, the utility of this approach to improve water buffalo has been largely unexplored. We present a comprehensive pangenome that integrates four newly generated, highly contiguous assemblies of Pakistani river buffalo with available assemblies from both sub- species. This doubles the number of accessible high-quality river buffalo genomes and provides the most contiguous assemblies for the sub-species to date. Using the pangenome to assay variation across 711 global samples, we uncovered extensive genomic diversity, including thousands of large structural variants absent from the reference genome, spanning over 140 Mb of additional sequence. We demonstrate the utility of these data by identifying putative functional indels and structural variants linked to selective sweeps in key genes involved in productivity and immune response across 26 populations. This study represents one of the first successful applications of graph genomics in water buffalo and offers valuable insights into how integrating assemblies can transform analyses of water buffalo and other species with complex evolutionary histories. We anticipate that these assemblies, and the pangenome and putative functional structural variants we have released, will accelerate efforts to unlock water buffalo’s genetic potential, improving productivity and resilience in this economically important species.\n\nA comprehensive water buffalo pangenome reveals extensive structural variation linked to population specific signatures of selection", "token_count": 391, "char_count": 1921, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6165, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:00.634142", "source": { "split": "train_shard_00001", "doc_id": 373 }, "chunk_id": "train_shard_00001_373_0", "global_id": 6187 }, { "text": "Graph pangenome references can address single-reference bias, thereby enhancing the accuracy of variant genotyping and empowering downstream applications in population genetics and quan-titative genetics. However, existing pangenome-based genotyping methods struggle with large or complex pangenome graphs, particularly in polyploid genomes. Here, we introduce Varigraph, an algorithm that leverages the comparison of unique and repetitive k-mers between variant sites and short reads for genotyping both small and large variants. Varigraph outperforms current state-of-the-art linear and graph-based genotypers across non-human genomes while maintaining comparable accuracy in human genomes. By employing an efficient data structure, Varigraph achieves higher accuracy in repetitive regions while managing computational costs for large da-tasets. Notably, Varigraph is the first tool capable of effectively utilizing pangenome graphs for genotyping autopolyploids, enabling precise determination of allele dosage. This work provides a robust and accurate solution for genotyping non-human genomes and will facilitate genomic studies of polyploid crops.\n\nVarigraph: an accurate and widely applicable pangenome graph-based variant genotyper for diploid and polyploid genomes", "token_count": 283, "char_count": 1273, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6975, "quality_score": 0.8488, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:01.184900", "source": { "split": "train_shard_00001", "doc_id": 374 }, "chunk_id": "train_shard_00001_374_0", "global_id": 6188 }, { "text": "Yeasts are important microorganisms used for ethanol production; however, they are not equally efficient in the amount of ethanol production under different environmental conditions. It is, therefore, necessary to screen for elite strains to utilize them for commercial production of these commodities. In this study, yeasts were isolated from different Ethiopian traditional fermented alcoholic beverages (teji, tella, shamiata and areqe tinisis), milk and ergo, teff and maize dough, soil and compost, flowers, and fruits to evaluate their potential use for ethanol fermentation process. Isolates were screened for efficient ethanol production and the selected ones were identified using phenotypic and genetic characters using D1/D2 region of LSU rDNA sequence analysis. The yeast isolates were evaluated based on their growth and fermentation of different carbon sources. Response surface methodology (RSM) was applied to optimize temperature, pH and incubation time using central composite design (CCD) in Design-Expert 7.0.0. A total of 211 yeasts colonies were isolated of which 60% were ethanologenic yeasts (ethanol producers) and 40% were non-ethanol producers. The yeast population detected from various sources was in the range of 10 5 CFU from traditional foods and beverages to that of 10 3 CFU from fruits and soil samples. The data also showed that the number of colony types (diversity) did not correlate with population density. The highly fermentative isolates were taxonomically characterized into four genera, of which 65% of the isolates (ETP37, ETP50; ETP53, ETP89, ETP94) were categorized under Saccharomyces cerevisiae, and the remaining were Pichia fermentans ETP22, Kluyveromyces marxianus ETP87, and Candida humilis ETP122. The S", "token_count": 506, "char_count": 1831, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.832, "entities": { "genes": [ "ETP22", "ETP89", "ETP87", "ETP122", "ETP37", "ETP50", "ETP94", "ETP53" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:01.865895", "source": { "split": "train_shard_00001", "doc_id": 375 }, "chunk_id": "train_shard_00001_375_0", "global_id": 6189 }, { "text": "cerevisiae isolates produced ethanol (7.6-9.0 g/L) similar with K. marxianus ETP87 producing 7.97 g/L; comparable to the ethanol produced from commercial baker's yeast (8.43 g/L) from 20 g/L dextrose; whereas C. humilis ETP122 and P. fermentans ETP22 produced 5.37 g/L and 6.43 g/L ethanol, respectively. S. cerevisiae ETP53, K. marxianus ETP87, P. fermentans ETP22 and C. humilis ETP122 tolerated 10% extraneous ethanol but the percentage of ethanol tolerance considerably decreased upon 15%. S. cerevisiae ETP53 produced ethanol optimally at pH 5.0, 60 h, and 34 o C. pH 4.8, temperature 36 o C, and 65 h of time were optimal growth conditions of ethanol fermentation by K. marxianus ETP87. The ethanol fermentation conditions of P. fermentans ETP22 was similar to S. cerevisiae ETP53 though the ethanol titer of S. cerevisiae ETP53 was higher than P. fermentans ETP22. Therefore, S. cerevisiae ETP53, K. marxianus and P. fermentans ETP22 are good candidates for ethanol production.\n\nOptimization of ethanol production using newly isolated ethanologenic yeasts.", "token_count": 482, "char_count": 1187, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8086, "entities": { "genes": [ "ETP22", "ETP87", "ETP122", "ETP53" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:02.534931", "source": { "split": "train_shard_00001", "doc_id": 375 }, "chunk_id": "train_shard_00001_375_1", "global_id": 6190 }, { "text": "Aerobic fermentation, also referred to as the Crabtree effect in yeast, is a well-studied phenomenon that allows many eukaryal cells to attain higher growth rates at high glucose availability. Not all yeasts exhibit the Crabtree effect, and it is not known why Crabtree-negative yeasts can grow at rates comparable to Crabtree-positive yeasts. Here, we quantitatively compared two Crabtree-positive yeasts, Saccharomyces cerevisiae and Schizosaccharomyces pombe, and two Crabtree-negative yeasts, Kluyveromyces marxianus and Scheffersomyces stipitis, cultivated under glucose excess conditions. Combining physiological and proteome quantification with genome-scale metabolic modeling, we found that the two groups differ in energy metabolism and translation efficiency. In Crabtree-positive yeasts, the central carbon metabolism flux and proteome allocation favor a glucose utilization strategy minimizing proteome cost as proteins translation parameters, including ribosomal content and/or efficiency, are lower. Crabtree-negative yeasts, however, use a strategy of maximizing ATP yield, accompanied by higher protein translation parameters. Our analyses provide insight into the underlying reasons for the Crabtree effect, demonstrating a coupling to adaptations in both metabolism and protein translation.\n\nAdaptations in metabolism and protein translation give rise to the Crabtree effect in yeast.", "token_count": 359, "char_count": 1430, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:03.143173", "source": { "split": "train_shard_00001", "doc_id": 376 }, "chunk_id": "train_shard_00001_376_0", "global_id": 6191 }, { "text": "Objective: To analyze the pangenome, pan drug resistance genes, pan virulence genes, pan replicons, and others of the plasmids carried by hypervirulent Klebsiella pneumoniae (hvKP) in the world and their evolutionary trends over time, and provide evidence for more comprehensive understanding of the evolution of genetic diversity, drug resistance genes, and virulence genes of the plasmids. Methods: From the National Center for Biotechnology Information database, a total 1 738 plasmids were screened from 524 strains with completed genome sequences in 2 136 strains of hvKP carrying plasmids. Through pangenome, pan drug resistance gene, and pan-virulence gene composition and functional analyses, the curves of pangenome size and new gene size against plasmid isolation time were established, revealing the diversity of the plasmid pangenome and its evolutionary patterns. Results: The homologous genes, homologous drug resistance genes, homologous virulence genes, and replicons of the plasmids carried by hvKP comprised of 12 906, 149, 107 and 89 types, respectively. The fitting curves for the number of new genes, new drug resistance genes and new replicons increased with the increase of plasmids in an open state, while the curve for novel virulence genes was in a closed state. A obvious increase in new drug resistance genes was observed during 2018-2019. Among the newly added drug resistance genes during 2021-2023, beside those conferring aminoglycoside resistance, they were mainly new subtypes conferring carbapenem resistance. Conclusions: The pangenome of plasmids carried by hvKP exhibited high diversity, with the plasmid pan genes, pan drug resistance genes, and pan replicon types gradually expanding, while the pan virulence genes remains stable", "token_count": 472, "char_count": 1804, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5115, "quality_score": 0.7558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:03.822165", "source": { "split": "train_shard_00001", "doc_id": 377 }, "chunk_id": "train_shard_00001_377_0", "global_id": 6192 }, { "text": "The increase in novel drug resistance genes in specific years and the emergence of new carbapenem-resistant gene subtypes during 2021-2023 suggested the need for strengthened drug resistance surveillance and prevention efforts, with particular attention to carbapenem resistance.\n\n[Pangenome analysis on plasmids carried by hypervirulent <i>Klebsiella pneumoniae</i>].", "token_count": 100, "char_count": 380, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:04.200824", "source": { "split": "train_shard_00001", "doc_id": 377 }, "chunk_id": "train_shard_00001_377_1", "global_id": 6193 }, { "text": "CCT motif genes play a key role in barley development and flowering, yet their genetic diversity remains underexplored. Leveraging a barley pangenome (76 genotypes) and pan-transcriptome (subset of 20 genotypes), we examined CCT gene variation and evolutionary dynamics. Motif-based searches, combined with genome assembly validation, revealed annotation limitations and novel frameshift variants (e.g., HvCO10), indicating active diversification. Pangenome-wide phylogenetic analysis identified clade-specific domain expansions, including B-box domain additions in HvCO clades. Tissue-specific expression patterns further supported functional divergence among paralogs. Notably, VRN2, a canonical floral repressor associated with winter growth, was retained in spring genotypes, challenging its presumed exclusive role in vernalization. Discrepancies between VRN1 expression, VRN2 deletion, and growth habits implicated additional regulatory mechanisms. These findings highlight the power of pangenomes in resolving gene family complexity, refining annotations, and advancing the understanding of CCT genes to enhance barley resilience and adaptability.\n\nPangenome insights into structural variation and functional diversification of barley CCT motif genes", "token_count": 290, "char_count": 1257, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7871, "quality_score": 0.8935, "entities": { "genes": [ "VRN1", "VRN2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:04.773853", "source": { "split": "train_shard_00001", "doc_id": 378 }, "chunk_id": "train_shard_00001_378_0", "global_id": 6194 }, { "text": "

Background

Elizabethkingia is emerging as an opportunistic pathogen in humans. The aim of this study was to investigate the clinical epidemiology, antimicrobial susceptibility, virulence factors, and genome features of Elizabethkingia spp.

Methods

Clinical data from 71 patients who were diagnosed with Elizabethkingia-induced pneumonia and bacteremia between August 2019 and September 2021 were analyzed. Whole-genome sequencing was performed on seven isolates, and the results were compared with a dataset of 83 available Elizabethkingia genomes. Genomic features, Kyoto Encyclopedia of Genes and Genomes (KEGG) results and clusters of orthologous groups (COGs) were analyzed.

Results

The mean age of the patients was 56.9 ± 20.7 years, and the in-hospital mortality rate was 29.6% (21/71). Elizabethkingia strains were obtained mainly from intensive care units (36.6%, 26/71) and emergency departments (32.4%, 23/71). The majority of the strains were isolated from respiratory tract specimens (85.9%, 61/71). All patients had a history of broad-spectrum antimicrobial exposure. Hospitalization for invasive mechanical ventilation or catheter insertion was found to be a risk factor for infection. The isolates displayed a high rate of resistance to cephalosporins and carbapenems, but all were susceptible to minocycline and colistin", "token_count": 387, "char_count": 1358, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7072, "quality_score": 0.8536, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:05.390831", "source": { "split": "train_shard_00001", "doc_id": 379 }, "chunk_id": "train_shard_00001_379_0", "global_id": 6195 }, { "text": "Genomic analysis identified five β-lactamase genes (blaGOB, blaBlaB, blaCME, blaOXA, and blaTEM) responsible for β-lactam resistance and virulence genes involved in stress adaptation (ureB/G, katA/B, and clpP), adherence (groEL, tufA, and htpB) and immune modulation (gmd, tviB, cps4J, wbtIL, cap8E/D/G, and rfbC). Functional analysis of the COGs revealed that \"metabolism\" constituted the largest category within the core genome, while \"information storage and processing\" was predominant in both the accessory and unique genomes. The unique genes in our 7 strains were mostly enriched in KEGG pathways related to microRNAs in cancer, drug resistance (β-lactam and vancomycin), ABC transporters, biological metabolism and biosynthesis, and nucleotide excision repair mechanisms.

Conclusion

The Elizabethkingia genus exhibits multidrug resistance and carries carbapenemase genes. This study presents a comparative genomic analysis of Elizabethkingia, providing knowledge that facilitates a better understanding of this microorganism.\n\nClinical manifestations, antimicrobial resistance and genomic feature analysis of multidrug-resistant Elizabethkingia strains.", "token_count": 355, "char_count": 1223, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7397, "quality_score": 0.8699, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:05.961303", "source": { "split": "train_shard_00001", "doc_id": 379 }, "chunk_id": "train_shard_00001_379_1", "global_id": 6196 }, { "text": "[This corrects the article DOI: 10.3389/fmicb.2022.820431.].\n\nCorrigendum: <i>Pseudomonas aeruginosa</i> detection using conventional PCR and quantitative real-time PCR based on species-specific novel gene targets identified by pangenome analysis.", "token_count": 91, "char_count": 259, "word_count": 27, "semantic_coherence": 1, "information_density": 0.963, "quality_score": 0.9815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:06.342214", "source": { "split": "train_shard_00001", "doc_id": 380 }, "chunk_id": "train_shard_00001_380_0", "global_id": 6197 }, { "text": "Abstract

The Bacillus genus includes plant growth-promoting rhizobacteria (PGPR), and the discovery of new strains within this group is of great biotechnological interest due to their ability to produce antimicrobial compounds (AMCs), vitamins, enzymes, and heterologous proteins. Among these, Bacillus paralicheniformis is a recently described species whose phylogeny remains poorly resolved, highlighting the need for further investigation. This study aimed to identify and characterize the isolates BAC30 and BAC220 using whole-genome sequencing (WGS). Both were confirmed as B. paralicheniformis and included in phylogenomic and comparative analyses with 28 other strains to assess the species’ genetic structure and inter-strain similarity. Functional annotation of BAC30 and BAC220 was also performed, focusing on biotechnological potential. Comparative analysis revealed high genomic similarity among strains, including the two isolates. Pangenome analysis showed a low proportion of core genes relative to accessory genes (shell and cloud), and the rarefaction curve suggested an open pangenome, indicating the species’ ubiquity and co-evolution with other organisms. Functional analysis identified genes of defense mechanisms related to beta-lactam resistance. Regarding secondary metabolite production, genes involved in the biosynthesis of vitamins (e.g., riboflavin) and AMCs (e.g., bacitracin) were detected. Although further in vitro and in vivo assays are needed to confirm gene expression, the findings support the biotechnological relevance of these isolates as potential biocontrol agents and/or producers of industrially valuable compounds.

\n\nComparative, Pangenomic and Functional Analyses of two Bacillus paralicheniformis Soil- Isolated Strains from Bahia Sequenced by WGS Reveal Species Homogeneity and Bioactive Metabolites with Biotechnological Potential", "token_count": 513, "char_count": 1986, "word_count": 246, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [ "BAC220", "BAC30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:06.971996", "source": { "split": "train_shard_00001", "doc_id": 381 }, "chunk_id": "train_shard_00001_381_0", "global_id": 6198 }, { "text": "

Background

Mycoplasma spp. are wall-less bacteria with small genomes (usually 0.5-1.5 Mb). Many Mycoplasma (M.) species are known to colonize the respiratory tract of both humans and livestock animals, where they act as primary pathogens or opportunists. M. equirhinis was described for the first time in 1975 in horses but has been poorly studied since, despite regular reports of around 14% prevalence in equine respiratory disorders. We recently showed that M. equirhinis is not a primary pathogen but could play a role in co-infections of the respiratory tract. This study was a set up to propose the first genomic characterization to better our understanding of the M. equirhinis species.

Results

Four circularized genomes, two of which were generated here, were compared in terms of synteny, gene content, and specific features associated with virulence or genome plasticity. An additional 20 scaffold-level genomes were used to analyse intra-species diversity through a pangenome phylogenetic approach. The M. equirhinis species showed consistent genomic homogeneity, pointing to potential clonality of isolates despite their varied geographical origins (UK, Japan and various places in France). Three different classes of mobile genetic elements have been detected: insertion sequences related to the IS1634 family, a putative prophage related to M. arthritidis and integrative conjugative elements related to M. arginini. The core genome harbours the typical putative virulence-associated genes of mycoplasmas mainly involved in cytoadherence and immune escape.

Conclusion

M. equirhinis is a highly syntenic, homogeneous species with a limited repertoire of mobile genetic elements and putative virulence genes.\n\nUnravelling the main genomic features of Mycoplasma equirhinis.", "token_count": 467, "char_count": 1807, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [ "IS1634" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:07.616460", "source": { "split": "train_shard_00001", "doc_id": 382 }, "chunk_id": "train_shard_00001_382_0", "global_id": 6199 }, { "text": "The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene, suggesting that cooperation is more common than conflict in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

Data summary

All Supplementary Data files and the Python scripts used in the analyses are available at doi.org/10.17639/nott.7103.

Impact statement

The pangenome of a species encompasses the core genes encoded by all genomes, as well as the accessory genes found in only a subset. Much remains to be understood about the relationships and interactions between accessory genes; in particular, what drives pairs of genes to appear together in the same genome, or what prevents them from being in the same genome together, more often than expected by chance. How these co-occurrence and avoidance relationships develop, and what effect they have on the dynamics and evolution of the pangenome as a whole, is largely unknown. Here, we present a springboard for understanding prokaryote pangenome evolution by uncovering significant gene relationships in a model Escherichia coli pangenome. We identify mobile genetic elements and the sharing of common function as possible driving forces behind the co-occurrence of accessory genes. Furthermore, this work offers an extensive dataset from which gene relationships could be identified for any gene of interest in this E", "token_count": 518, "char_count": 2368, "word_count": 364, "semantic_coherence": 1, "information_density": 0.4918, "quality_score": 0.7459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:08.998718", "source": { "split": "train_shard_00001", "doc_id": 383 }, "chunk_id": "train_shard_00001_383_0", "global_id": 6200 }, { "text": "coli accessory genome, providing a rich resource for the community.\n\nGene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility", "token_count": 48, "char_count": 175, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9583, "quality_score": 0.9792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:09.364099", "source": { "split": "train_shard_00001", "doc_id": 383 }, "chunk_id": "train_shard_00001_383_1", "global_id": 6201 }, { "text": "Xylella fastidiosa causes diseases in many plant species. Originally confined to the Americas, infecting mainly grapevine, citrus, and coffee, X. fastidiosa has spread to several plant species in Europe causing devastating diseases. Many pathogenicity and virulence factors have been identified, which enable the various X. fastidiosa strains to successfully colonize the xylem tissue and cause disease in specific plant hosts, but the mechanisms by which this happens have not been fully elucidated. Here we present thorough comparative analyses of 94 whole-genome sequences of X. fastidiosa strains from diverse plant hosts and geographic regions. Core-genome phylogeny revealed clades with members sharing mostly a geographic region rather than a host plant of origin. Phylogenetic trees for 1605 orthologous CDSs were explored for potential candidates related to host specificity using a score of mapping metrics. However, no candidate host-specificity determinants were strongly supported using this approach. We also show that X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, including a diversity of prophage regions. Our findings provide a better understanding of the diversity of phylogenetically close genomes and expand the knowledge of X. fastidiosa mobile genetic elements and immunity systems.\n\nComparative Genomics of Xylella fastidiosa Explores Candidate Host-Specificity Determinants and Expands the Known Repertoire of Mobile Genetic Elements and Immunity Systems.", "token_count": 390, "char_count": 1571, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:09.977226", "source": { "split": "train_shard_00001", "doc_id": 384 }, "chunk_id": "train_shard_00001_384_0", "global_id": 6202 }, { "text": "The E. coli strains harboring the polyketide synthase (pks) island encode the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involves whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organisms. Fifteen E. coli strains isolated from patients with ulcerative colitis (UC) were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks-positive (pks+) isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158 + 13) pks+ isolates belonged to phylogroup B2, and most of the isolates belong to sequence types ST73 and ST95. One isolate from a UC patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks+ isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the0020preponderance of virulence genes and a reduced number of antimicrobial genes in pks+ isolates. This study significantly contributes to understanding the evolution of pks islands in E. coli.\n\nGenomic characterization of Escherichia coli with a polyketide synthase (pks) island isolated from ulcerative colitis patients.", "token_count": 422, "char_count": 1495, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [ "ST95", "ST8303", "ST73" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:10.598897", "source": { "split": "train_shard_00001", "doc_id": 385 }, "chunk_id": "train_shard_00001_385_0", "global_id": 6203 }, { "text": "Cells often localize pathway enzymes in close proximity to reduce substrate loss via diffusion and to ensure that carbon flux is directed toward the desired product. To emulate this strategy for the biosynthesis of heterologous products in yeast, we have taken advantage of the highly specific Cas6-RNA interaction and the predictability of RNA hybridizations to demonstrate Cas6-mediated RNA-guided protein assembly within the yeast cytosol. The feasibility of this synthetic scaffolding technique for protein localization was first demonstrated using a split luciferase reporter system with each part fused to a different Cas6 protein. In Saccharomyces cerevisiae, the luminescence signal increased 3.6- to 20-fold when the functional RNA scaffold was also expressed. Expression of a trigger RNA, designed to prevent the formation of a functional scaffold by strand displacement, decreased the luminescence signal by nearly 2.3-fold. Temporal control was also possible, with induction of scaffold expression resulting in an up to 11.6-fold increase in luminescence after 23 h. Cas6-mediated assembly was applied to create a two-enzyme metabolon to redirect a branch of the violacein biosynthesis pathway. Localizing VioC and VioE together increased the amount of deoxyviolacein (desired) relative to prodeoxyviolacein (undesired) by 2-fold. To assess the generality of this colocalization method in other yeast systems, the split luciferase reporter system was evaluated in Kluyveromyces marxianus; RNA scaffold expression resulted in an increase in the luminescence signal of up to 1.9-fold. The simplicity and flexibility of the design suggest that this strategy can be used to create metabolons in a wide range of recombinant hosts of interest.\n\nAssembly of Metabolons in Yeast Using Cas6-Mediated RNA Scaffolding.", "token_count": 469, "char_count": 1833, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5856, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:11.250208", "source": { "split": "train_shard_00001", "doc_id": 386 }, "chunk_id": "train_shard_00001_386_0", "global_id": 6204 }, { "text": "Population genomics using short-read resequencing captures single nucleotide polymorphisms and small insertions and deletions but struggles with structural variants (SVs), leading to a loss of heritability in genome-wide association studies. In recent years, long-read sequencing has improved pangenome construction for key eukaryotic species, addressing this issue to some extent. Sufficient-coverage high-fidelity (HiFi) data for population genomics is often prohibitively expensive, limiting its use in large-scale populations and broader eukaryotic species and creating an urgent need for robust ultra-low coverage assemblies. However, current assemblers underperform in such conditions. To address this, we propose HiFiCCL, the first assembly framework specifically designed for ultra-low-coverage high-fidelity reads, using a reference-guided, chromosome-by-chromosome assembly approach. We demonstrate that HiFiCCL improves ultra-low-coverage assembly performance of existing assemblers and outperforms the state-of-the-art assemblers on human and plant datasets. Tested on 45 human datasets (~5x coverage), HiFiCCL combined with hifiasm reduces the length of misassembled contigs relative to hifiasm by an average of 21.19% and up to 38.58%. These improved assemblies enhance germline structural variant detection, reduce chromosome-level mis-scaffolding, enable more accurate pangenome graph construction, and improve the detection of rare and somatic structural variants based on the pangenome graph under ultra-low-coverage conditions.\n\nReference-guided genome assembly at scale using ultra-low-coverage high-fidelity long-reads with HiFiCCL", "token_count": 397, "char_count": 1652, "word_count": 205, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:11.874615", "source": { "split": "train_shard_00001", "doc_id": 387 }, "chunk_id": "train_shard_00001_387_0", "global_id": 6205 }, { "text": "Pangenome collections are growing to hundreds of high-quality genomes. This necessitates scalable methods for constructing pangenome alignments that can incorporate newly-sequenced assemblies. We previously developed Mumemto, which computes maximal unique matches (multi-MUMs) across pangenomes using compressed indexing. In this work, we extend Mumemto by introducing two new partitioning and merging strategies. Both strategies enable highly parallel, memory efficient, and updateable computation of multi-MUMs. One of the strategies, called string-based merging, is also capable of conducting the merges in a way that follows the shape of a phylogenetic tree, naturally yielding the multi-MUM for the tree’s internal nodes as well as the root. With these strategies, Mumemto now scales to 474 human haplo-types, the only multi-MUM method able to do so. It also introduces a time-memory tradeoff that allows Mumemto to be tailored to more scenarios, including in resource-limited settings.\n\nPartitioned Multi-MUM finding for scalable pangenomics", "token_count": 247, "char_count": 1047, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7655, "quality_score": 0.8828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:12.368658", "source": { "split": "train_shard_00001", "doc_id": 388 }, "chunk_id": "train_shard_00001_388_0", "global_id": 6206 }, { "text": "We present the first mouse pangenome consisting of 17 high-quality inbred mouse strain genomes with complete annotation. This collection includes 12 widely used classical laboratory strains and 5 wild-derived strains. We have fully resolved previously incomplete genomic regions, including the major histocompatibility complex (MHC), the defensin cluster, T-cell receptor, and Ly49 complexes. Hundreds of non-reference genes identified in previous publications not found in GRCm39, like Defa1, Raet1a , and Klra20 ( Ly49T ), were localised in the new reference genomes. We conducted the first genome-wide scan of variable number tandem repeats (VNTRs) within the coding regions of mice, identifying over 400 genes with VNTR polymorphisms up to more than 600 repeat copies and repeat units reaching 990 nucleotides. Our strain-specific annotations enhance RNA-Seq analyses, as demonstrated in PWK/PhJ, where we observed a 5.1% improvement in read mapping and expression level differences in 2.1% of coding genes compared to using GRCm39.\n\nThe mouse pangenome reveals the structural complexity of the murine protein-coding landscape", "token_count": 289, "char_count": 1130, "word_count": 162, "semantic_coherence": 1, "information_density": 0.784, "quality_score": 0.892, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:12.927938", "source": { "split": "train_shard_00001", "doc_id": 389 }, "chunk_id": "train_shard_00001_389_0", "global_id": 6207 }, { "text": "Traditional Wagashi cheese and fermented cow milk are among the most popular dairy products appreciated by people from Benin, Niger, and the neighboring region. These products are the main source of protein in the diet of the low-income population in the region. The fermented milk is prepared by spontaneous fermentation without back-slopping. Whereas, the leaf extract of Calotropis procera is used for curdling the milk to prepare the soft Wagashi cheese. The present study aims to provide in-depth analysis of yeast communities associated with these traditional milk products by high-throughput Illumina MiSeq amplicon sequencing of internal transcribed spacer (ITS) region of fungal rRNA genes. A total of 60 samples, 20 samples of fermented milk each from Benin and Niger, and 20 samples of Wagashi cheese from Benin were used for analysis. The metagenomic investigation revealed that Kluyveromyces marxianus, Saccharomyces cerevisiae, Candida parapsilosis, and Sagenomella keratitidis were the predominant yeast species present in the traditional milk products. Furthermore, we noticed a high presence of K. marxianus (61.1% relative abundance) in the Wagashi cheese and S. cerevisiae (28.4% relative abundance) in the fermented milk of Niger. The presence of potential pathogenic yeast C. parapsilosis and S. keratitidis in these African milk products calls for further investigation to assess their safety. The predominant yeast K. marxianus and S. cerevisiae, recognized with generally regarded as safe (GRAS) status, could be further selected as starter culture along with lactic acid bacteria for developing controlled fermentation processes with enhanced product quality and safety.", "token_count": 498, "char_count": 1800, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:13.578929", "source": { "split": "train_shard_00001", "doc_id": 390 }, "chunk_id": "train_shard_00001_390_0", "global_id": 6208 }, { "text": "High-Throughput Illumina MiSeq Amplicon Sequencing of Yeast Communities Associated With Indigenous Dairy Products From Republics of Benin and Niger.", "token_count": 37, "char_count": 148, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:13.972657", "source": { "split": "train_shard_00001", "doc_id": 390 }, "chunk_id": "train_shard_00001_390_1", "global_id": 6209 }, { "text": "Salmonella enterica subsp. enterica serovar Infantis (S. Infantis), a major cause of human salmonellosis, is commonly associated with transmission via contaminated chicken meat. This study, as part of the national Salmonella monitoring program, assessed the prevalence of S. enterica, including S. Infantis, in chicken slaughterhouses across South Korea from 2014-2022. The presence of a megaplasmid, known as plasmid of emerging S. Infantis (pESI), was confirmed. This confirmation was based on multidrug-resistant and third-generation cephalosporin-resistant S. Infantis isolates using whole-genome sequencing. Phenotypic and genotypic characterization involved antimicrobial susceptibility tests, pulsed-field gel electrophoresis, polymerase chain reaction to screen for pESI plasmids, plasmid profiling, and conjugation assays. S. Infantis was identified in 9.3% of Salmonella-positive samples in 2014, undetected from 2015-2020, but re-emerged as the predominant serovar in 2021 (54.7%) and 2022 (75.5%). The isolates in 2014 were antibiotic susceptible, whereas most isolates from 2021 to 2022 exhibited multidrug-resistance, including resistance to third-generation cephalosporins. All isolates were sequence type 32 (ST32), with core genome multilocus sequence typing demonstrating pESI plasmid-based clustering", "token_count": 455, "char_count": 1389, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7262, "quality_score": 0.8631, "entities": { "genes": [ "ST32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:14.639450", "source": { "split": "train_shard_00001", "doc_id": 391 }, "chunk_id": "train_shard_00001_391_0", "global_id": 6210 }, { "text": "The pESI+ isolates harbored genes, such as aadA1, dfrA14, sul1, and tetA, and three multidrug-resistant pESI+ isolates harbored blaCTX-M-65. The plasmids were genetically similar to those observed in S. Infantis from broilers, chicken meat, and human clinical samples across various countries. This study highlights the spread of multidrug-resistant S. Infantis harboring the pESI plasmid with blaCTX-M-65 during early chicken production in South Korea. Continuous monitoring and control of resistant S. Infantis throughout the food chain is essential to inform public health initiatives.IMPORTANCEThis study highlights the critical emergence of multidrug-resistant (MDR) Salmonella enterica serovar Infantis (S. Infantis) in South Korea's chicken slaughterhouses, driven by the acquisition of the pESI megaplasmid harboring the extended-spectrum beta-lactamase (ESBL) determinant blaCTX-M-65. Using whole-genome sequencing and comprehensive phenotypic-genotypic analyses, the findings reveal that pESI+ isolates in South Korea are genetically similar to strains from broilers, chicken meat, and human clinical cases worldwide. This underscores the transboundary nature of S. Infantis and its potential as a global public health threat.\n\nEmergence and characteristics of multidrug-resistant <i>Salmonella enterica</i> subspecies <i>enterica</i> serovar Infantis harboring the pESI plasmid in chicken slaughterhouses in South Korea.", "token_count": 510, "char_count": 1612, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:15.321615", "source": { "split": "train_shard_00001", "doc_id": 391 }, "chunk_id": "train_shard_00001_391_1", "global_id": 6211 }, { "text": "Despite the notable clinical impact, recent molecular epidemiology regarding third-generation-cephalosporin-resistant (3GC-R) Klebsiella pneumoniae in the USA remains limited. We performed whole-genome sequencing of 3GC-R K. pneumoniae bacteraemia isolates collected from March 2016 to May 2022 at a tertiary care cancer centre in Houston, TX, USA, using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics and pan-genomic signatures of our 3GC-R K. pneumoniae population. Of the 178 3GC-R K. pneumoniae bacteraemias that occurred during our study time frame, we were able to analyse 153 (86 %) bacteraemia isolates, 126 initial and 27 recurrent isolates. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant CG, 307, accounted for 37 (29 %) index isolates and displayed a significant correlation (Pearson correlation test P value=0.03) with the annual frequency of 3GC-R K. pneumoniae bacteraemia. Interestingly, only 11 % (4/37) of CG307 isolates belonged to the commonly detected 'Texas-specific' clade that has been observed in previous Texas-based K. pneumoniae antimicrobial-resistance surveillance studies. We identified nearly half of our CG307 isolates (n=18) belonged to a novel, monophyletic CG307 sub-clade characterized by the chromosomally encoded bla SHV-205 and unique accessory genome content", "token_count": 506, "char_count": 1568, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7389, "quality_score": 0.8695, "entities": { "genes": [ "CG307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:15.993283", "source": { "split": "train_shard_00001", "doc_id": 392 }, "chunk_id": "train_shard_00001_392_0", "global_id": 6212 }, { "text": "This CG307 sub-clade was detected in various regions of the USA, with genome sequences from 24 additional strains becoming recently available in the National Center for Biotechnology Information (NCBI) SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R K. pneumoniae bacteraemia among cancer patients seen in Houston, TX, and has recently been isolated throughout the USA.\n\nIdentification of a novel CG307 sub-clade in third-generation-cephalosporin-resistant Klebsiella pneumoniae causing invasive infections in the USA.", "token_count": 185, "char_count": 639, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8765, "entities": { "genes": [ "CG307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:16.441446", "source": { "split": "train_shard_00001", "doc_id": 392 }, "chunk_id": "train_shard_00001_392_1", "global_id": 6213 }, { "text": "

Background

LTR-retrotransposons (LTR-RT) are a major component of plant genomes and important drivers of genome evolution. Most LTR-RT copies in plant genomes are defective elements found as truncated copies, nested insertions or as part of more complex structures. The recent availability of highly contiguous plant genome assemblies based on long-read sequences now allows to perform detailed characterization of these complex structures and to evaluate their importance for plant genome evolution.

Results

The detailed analysis of two rice loci containing complex LTR-RT structures showed that they consist of tandem arrays of LTR copies sharing internal LTRs. Our analyses suggests that these LTR-RT tandems are the result of a single insertion and not of the recombination of two independent LTR-RT elements. Our results also suggest that gypsy elements may be more prone to form these structures. We show that these structures are highly polymorphic in rice and therefore have the potential to generate genetic variability. We have developed a computational pipeline (IDENTAM) that scans genome sequences and identifies tandem LTR-RT candidates. Using this tool, we have detected 266 tandems in a pangenome built from the genomes of 76 accessions of cultivated and wild rice, showing that tandem LTR-RT structures are frequent and highly polymorphic in rice. Running IDENTAM in the Arabidopsis, almond and cotton genomes showed that LTR-RT tandems are frequent in plant genomes of different size, complexity and ploidy level. The complexity of differentiating intra-element variations at the nucleotide level among haplotypes is very high, and we found that graph-based pangenomic methodologies are appropriate to resolve these structures.

Conclusions

Our results show that LTR-RT elements can form tandem arrays. These structures are relatively abundant and highly polymorphic in rice and are widespread in the plant kingdom. Future studies will contribute to understanding how these structures originate and whether the variability that they generate has a functional impact.\n\nTandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes.", "token_count": 499, "char_count": 2196, "word_count": 312, "semantic_coherence": 1, "information_density": 0.5385, "quality_score": 0.7692, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:17.087727", "source": { "split": "train_shard_00001", "doc_id": 393 }, "chunk_id": "train_shard_00001_393_0", "global_id": 6214 }, { "text": "

Background

Isabel Island is a Mexican volcanic island primarily composed of basaltic stones. It features a maar known as Laguna Fragatas, which is classified as a meromictic thalassohaline lake. The constant deposition of guano in this maar results in increased levels of phosphorus, nitrogen, and carbon. The aim of this study was to utilize high-quality genomes from the genus Halomonas found in specialized databases as a reference for genome mining of moderately halophilic bacteria isolated from Laguna Fragatas. This research involved genomic comparisons employing phylogenetic, pangenomic, and metabolic-inference approaches.

Results

The Halomonas genus exhibited a large open pangenome, but several genes associated with salt metabolism and homeostatic regulation (ectABC and betABC), nitrogen intake through nitrate and nitrite transporters (nasA, and narGI), and phosphorus uptake (pstABCS) were shared among the Halomonas isolates.

Conclusions

The isolated bacteria demonstrate consistent adaptation to high salt concentrations, and their nitrogen and phosphorus uptake mechanisms are highly optimized. This optimization is expected in an extremophile environment characterized by minimal disturbances or abrupt seasonal variations. The primary significance of this study lies in the dearth of genomic information available for this saline and low-disturbance environment. This makes it important for ecosystem conservation and enabling an exploration of its biotechnological potential. Additionally, the study presents the first two draft genomes of H. janggokensis.\n\nGenome analysis of haloalkaline isolates from the soda saline crater lake of Isabel Island; comparative genomics and potential metabolic analysis within the genus Halomonas.", "token_count": 417, "char_count": 1775, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:17.716121", "source": { "split": "train_shard_00001", "doc_id": 394 }, "chunk_id": "train_shard_00001_394_0", "global_id": 6215 }, { "text": "

Background

Klebsiella pneumoniae is the major cause of nosocomial infections worldwide and is related to a worsening increase in Multidrug-Resistant Bacteria (MDR) and virulence genes that seriously affect immunosuppressed patients, long-stay intensive care patients, elderly individuals, and children. Whole-Genome Sequencing (WGS) has resulted in a useful strategy for characterizing the genomic components of clinically important bacteria, such as K. pneumoniae, enabling them to monitor genetic changes and understand transmission, highlighting the risk of dissemination of resistance and virulence associated genes in hospitals. In this study, we report on WGS 14 clinical isolates of K. pneumoniae from a pediatric hospital biobank of Guayaquil, Ecuador.

Results

The main findings revealed pronounced genetic heterogeneity among the isolates. Multilocus sequencing type ST45 was the predominant lineage among non-KPC isolates, whereas ST629 was found more frequently among KPC isolates. Phylogenetic analysis suggested local transmission dynamics. Comparative genomic analysis revealed a core set of 3511 conserved genes and an open pangenome in neonatal isolates. The diversity of MLSTs and capsular types, and the high genetic diversity among these isolates indicate high intraspecific variability. In terms of virulence factors, we identified genes associated with adherence, biofilm formation, immune evasion, secretion systems, multidrug efflux pump transporters, and a notably high number of genes related to iron uptake. A large number of these genes were detected in the ST45 isolate, whereas iron uptake yersiniabactin genes were found exclusively in the non-KPC isolates. We observed high resistance to commonly used antibiotics and determined that these isolates exhibited multidrug resistance including β-lactams, aminoglycosides, fluoroquinolones, quinolones, trimetropins, fosfomycin and macrolides; additionally, resistance-associated point mutations and cross-resistance genes were identified in all the isolates. We also report the first K", "token_count": 507, "char_count": 2077, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [ "ST629", "ST45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:18.369627", "source": { "split": "train_shard_00001", "doc_id": 395 }, "chunk_id": "train_shard_00001_395_0", "global_id": 6216 }, { "text": "pneumoniae KPC-3 gene producers in Ecuador.

Conclusions

Our WGS results for clinical isolates highlight the importance of MDR in neonatal K. pneumoniae infections and their genetic diversity. WGS will be an imperative strategy for the surveillance of K. pneumoniae in Ecuador, and will contribute to identifying effective treatment strategies for K. pneumoniae infections in critical units in patients at stratified risk.\n\nWhole-genome sequencing of Klebsiella pneumoniae MDR circulating in a pediatric hospital setting: a comprehensive genome analysis of isolates from Guayaquil, Ecuador.", "token_count": 154, "char_count": 596, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:18.811636", "source": { "split": "train_shard_00001", "doc_id": 395 }, "chunk_id": "train_shard_00001_395_1", "global_id": 6217 }, { "text": "Streptococcus agalactiae (Group B Streptococcus , GBS) is a major pathogen of humans and animals, posing a threat to human health as well as food security. Here, we investigate the role of genomic mechanisms, including homologous recombination and horizontal gene transfer, in shaping the population structure of GBS and its adaptation to three major host groups (humans, cattle, fishes). We demonstrate that the GBS population comprises host-specialist, host-adapted lineages as well as host generalists, and that these categories differ in their level or recombination. Although the accessory genome at large varies by lineage rather than host, genome wide association studies show that host association is driven by three accessory genome clusters, regardless of lineage or breadth of the host spectrum. These genomic clusters ( scpB in human GBS, lactose operon in bovine GBS, Locus 3 in fish GBS) are known ( scpB , Lac.2) or shown here (Locus 3) to be functionally relevant and are shared with other streptococcal species occupying the same host niche. These findings demonstrate the importance of considering the role of non-human host species in the evolution of GBS, including high risk clones that may lead to interspecies transmission and affect efficacy of future GBS vaccines.\n\nThree Accessory Gene Clusters Drive Host-Adaptation in Group BStreptococcus", "token_count": 336, "char_count": 1373, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:19.380121", "source": { "split": "train_shard_00001", "doc_id": 396 }, "chunk_id": "train_shard_00001_396_0", "global_id": 6218 }, { "text": "Currently, invasive infections caused by Staphylococcus argenteus, which is a recently named staphylococcal species, are increasingly reported worldwide. However, only a few genomic studies of S. argenteus have offered comprehensive information regarding its genetic diversity, epidemiological characteristics, antimicrobial resistance genes (ARGs), virulence genes and other profiles. Here, we describe a comparative genomic analysis by population structure, pangenome, panmobilome, region-specific accessory genes confer an adaptive advantage in 153 S. argenteus strains which comprised 24 strains sequenced in this study and 129 strains whose genome sequences were available from GenBank. As a result, the population of S. argenteus comprised seven genetically distinct clades, including two major clades (C1 and C2), with distinct isolation source patterns. Pangenome analysis revealed that S. argenteus has an open pangenome composed of 7,319 genes and a core genome composed of 1,508 genes. We further determined the distributions of 75 virulence factors (VFs) and 30 known ARGs and identified at least four types of plasmids and 93 complete or partial putative prophages. It indicate that S. argenteus may show a similar level of pathogenicity to that of S. aureus. This study also provides insights into the evolutionary divergence of this pathogen, indicating that the geographical distribution was a potential driving force behind the evolutionary divergence of S. argenteus. The preferential horizontal acquisition of particular elements, such as staphylococcal cassette chromosome mec elements and plasmids, was observed in specific regions, revealing potential gene exchange between S. argenteus strains and local S", "token_count": 509, "char_count": 1861, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:20.033895", "source": { "split": "train_shard_00001", "doc_id": 397 }, "chunk_id": "train_shard_00001_397_0", "global_id": 6219 }, { "text": "aureus strains. Moreover, multiple specific genes related to environmental adaptation were identified in strains isolated from East Asia. However, these findings may help promote our understanding of the evolutionary divergence of this bacterium at a high genetic resolution by providing insights into the epidemiology of S. argenteus and may help combat its spread.\n\nEvolutionary Divergence of the Novel Staphylococcal Species Staphylococcus argenteus.", "token_count": 122, "char_count": 481, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8548, "quality_score": 0.9274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:20.418593", "source": { "split": "train_shard_00001", "doc_id": 397 }, "chunk_id": "train_shard_00001_397_1", "global_id": 6220 }, { "text": "

Background

In fungal plant pathogens, genome rearrangements followed by selection pressure for adaptive traits have facilitated the co-evolutionary arms race between hosts and their pathogens. Pyrenophora tritici-repentis (Ptr) has emerged recently as a foliar pathogen of wheat worldwide and its populations consist of isolates that vary in their ability to produce combinations of different necrotrophic effectors. These effectors play vital roles in disease development. Here, we sequenced the genomes of a global collection (40 isolates) of Ptr to gain insights into its gene content and genome rearrangements.

Results

A comparative genome analysis revealed an open pangenome, with an abundance of accessory genes (~ 57%) reflecting Ptr's adaptability. A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around effector coding genes, were detailed using long-read assemblies (PacBio RS II) generated in this work in addition to previously assembled genomes. We also discovered the involvement of large mobile elements associated with Ptr's effectors: ToxA, the gene encoding for the necrosis effector, was found as a single copy within a 143-kb 'Starship' transposon (dubbed 'Horizon') with a clearly defined target site and target site duplications. 'Horizon' was located on different chromosomes in different isolates, indicating mobility, and the previously described ToxhAT transposon (responsible for horizontal transfer of ToxA) was nested within this newly identified Starship. Additionally, ToxB, the gene encoding the chlorosis effector, was clustered as three copies on a 294-kb element, which is likely a different putative 'Starship' (dubbed 'Icarus') in a ToxB-producing isolate. ToxB and its putative transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and 'Icarus' were both present in a different non-coding isolate", "token_count": 513, "char_count": 2037, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:21.053598", "source": { "split": "train_shard_00001", "doc_id": 398 }, "chunk_id": "train_shard_00001_398_0", "global_id": 6221 }, { "text": "This suggests that ToxB may have been mobile at some point during the evolution of the Ptr genome which is contradictory to the current assumption of ToxB vertical inheritance. Finally, the genome architecture of Ptr was defined as 'one-compartment' based on calculated gene distances and evolutionary rates.

Conclusions

These findings together reflect on the highly plastic nature of the Ptr genome which has likely helped to drive its worldwide adaptation and has illuminated the involvement of giant transposons in facilitating the evolution of virulence in Ptr.\n\nThe pangenome of the wheat pathogen Pyrenophora tritici-repentis reveals novel transposons associated with necrotrophic effectors ToxA and ToxB.", "token_count": 172, "char_count": 718, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7157, "quality_score": 0.8578, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:21.505964", "source": { "split": "train_shard_00001", "doc_id": 398 }, "chunk_id": "train_shard_00001_398_1", "global_id": 6222 }, { "text": "Thiopseudomonas alkaliphila, an organism recently classified within the Pseudomonadaceae family, has been detected in diverse sources such as human tissues, animal guts, industrial fermenters, and decomposition environments, suggesting a diverse ecological role. However, a large knowledge gap exists in how T. alkaliphila functions. In this comparative genomic analysis, adaptations indicative of habitat specificity among strains and genomic similarity to known opportunistic pathogens are revealed. Genomic investigation reveals a core metabolic utilization of multiple oxidative and non-oxidative catabolic pathways, suggesting adaptability to varied environments and carbon sources. The genomic repertoire of T. alkaliphila includes secondary metabolites, such as antimicrobials and siderophores, indicative of its involvement in microbial competition and resource acquisition. Additionally, the presence of transposases, prophages, plasmids, and Clustered Regularly Interspaced Short Palindromic Repeats-Cas systems in T. alkaliphila genomes suggests mechanisms for horizontal gene transfer and defense against viral predation. This comprehensive genomic analysis expands our understanding on the ecological functions, community interactions, and potential virulence of T. alkaliphila, while emphasizing its adaptability and diverse capabilities across environmental and host-associated ecosystems.IMPORTANCEAs the microbial world continues to be explored, new organisms will emerge with beneficial and/or pathogenetic impact. Thiopseudomonas alkaliphila is a species originally isolated from clinical human tissue and fluid samples but has not been attributed to disease. Since its classification, T. alkaliphila has been found in animal guts, animal waste, decomposing remains, and biogas fermentation reactors. This is the first study to provide an in-depth view of the metabolic potential of publicly available genomes belonging to this species through a comparative genomics and draft pangenome calculation approach. It was found that T. alkaliphila is metabolically versatile and likely adapts to diverse energy sources and environments, which may make it useful for bioremediation and in industrial settings", "token_count": 527, "char_count": 2276, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:22.142633", "source": { "split": "train_shard_00001", "doc_id": 399 }, "chunk_id": "train_shard_00001_399_0", "global_id": 6223 }, { "text": "A range of virulence factors and antibiotic resistances were also detected, suggesting T. alkaliphila may operate as an undescribed opportunistic pathogen.\n\nComparative genomic analysis of an emerging Pseudomonadaceae member, Thiopseudomonas alkaliphila.", "token_count": 76, "char_count": 268, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9355, "quality_score": 0.9677, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:22.529937", "source": { "split": "train_shard_00001", "doc_id": 399 }, "chunk_id": "train_shard_00001_399_1", "global_id": 6224 }, { "text": "Lactococcus garvieae is an emerging zoonotic pathogen, but there are few reports regarding bovine mastitis. The prevalence of L. garvieae represents an increasing disease threat and global public health risk. Thirty-nine L. garvieae isolates were obtained from 2,899 bovine clinical mastitis milk samples in 6 provinces of China from 2017 to 2021. Five clonal complexes were determined from 32 multilocus sequence types (MLSTs) of L. garvieae: sequence type 46 (ST46) was the predominant sequence type, and 13 novel MLSTs were identified. All isolates were resistant to chloramphenicol and clindamycin, but susceptible to penicillin, ampicillin, amoxicillin-clavulanic acid, imipenem, ceftiofur, enrofloxacin, and marbofloxacin. Based on genomic analyses, L. garvieae had 6,310 genes, including 1,015 core, 3,641 accessory, and 1,654 unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase, and NADH oxidase. Most isolates had lsaD and mdtA antimicrobial resistance (AMR) genes. Based on COG (Clusters of Orthologous Genes database) results, the functions of defense, transcription and replication, and recombination and repair were enhanced in unique genes, whereas functions of translation, ribosomal structure, and biogenesis were enhanced in core genes. The KEGG functional categories enriched in unique genes included human disease and membrane transport, whereas COG functional categories enriched in core genes included energy metabolism, nucleotide metabolism, and translation. No gene was significantly associated with host specificity. In addition, analysis of core genome single nucleotide polymorphisms (SNPs) implied potential host adaptation of some isolates in several sequence types", "token_count": 521, "char_count": 1819, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6612, "quality_score": 0.8306, "entities": { "genes": [ "ST46" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:23.160252", "source": { "split": "train_shard_00001", "doc_id": 400 }, "chunk_id": "train_shard_00001_400_0", "global_id": 6225 }, { "text": "In conclusion, this study characterized L. garvieae isolated from mastitis and detected potential adaptations of L. garvieae to various hosts. IMPORTANCE This study provides important genomic insights into a bovine mastitis pathogen, Lactococcus garvieae. Comprehensive genomic analyses of L. garvieae from dairy farms have not been reported. This study is a detailed and comprehensive report of novel features of isolates of L. garvieae, an important but poorly characterized bacterium, recovered in the past 5 years in 6 Chinese provinces. We documented diverse genetic features, including predominant sequence type ST46 and 13 novel MLSTs. Lactococcus garvieae had 6,310 genes, including 1,015 core, 3,641 accessory, and 1,654 unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase, and NADH oxidase and resistance to chloramphenicol and clindamycin. Most isolates had lsaD and mdtA antimicrobial resistance genes. However, no gene was significantly associated with host specificity. This is the first report that characterized L. garvieae isolates from bovine mastitis and revealed potential host adaptations of L. garvieae to various hosts.\n\nComparative Genomic Analyses of Lactococcus garvieae Isolated from Bovine Mastitis in China.", "token_count": 390, "char_count": 1368, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.8071, "entities": { "genes": [ "ST46" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:23.782323", "source": { "split": "train_shard_00001", "doc_id": 400 }, "chunk_id": "train_shard_00001_400_1", "global_id": 6226 }, { "text": "

Background

The thermotolerant yeast Kluyveromyces marxianus is a potential candidate for high-temperature fermentation. When K. marxianus was used for high-temperature ethanol fermentation, a fermentation arrest was observed during the late fermentation stage and the stress responses have been investigated based on the integration of RNA-Seq and metabolite data. In order to bring new insights into the cellular responses of K. marxianus after the fermentation arrest during high-temperature ethanol fermentation, quantitative proteomic profiling and integrated analysis with transcriptomic data were performed in this study.

Results

Samples collected at 14, 16, 18, 20 and 22 h during high-temperature fermentation were subjected to isobaric tags for relative and absolute quantitation (iTRAQ)-based proteomic profiling and integrated analysis with transcriptomic data. The correlations between transcripts and proteins for the comparative group 16 h vs 14 h accounted for only 4.20% quantified proteins and 3.23% differentially expressed proteins (DEPs), respectively, much higher percentages of correlations (30.56%-59.11%) were found for other comparative groups (i.e., 18 h vs 14 h, 20 h vs 14 h, and 22 h vs 14 h)", "token_count": 374, "char_count": 1257, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:24.712627", "source": { "split": "train_shard_00001", "doc_id": 401 }, "chunk_id": "train_shard_00001_401_0", "global_id": 6227 }, { "text": "According to Spearman correlation tests between transcriptome and proteome (the absolute value of a correlation coefficient between 0.5 and 1 indicates a strong correlation), poor correlations were found for all quantified proteins (R = - 0.0355 to 0.0138), DEPs (R = - 0.0079 to 0.0233) and the DEPs with opposite expression trends to corresponding differentially expressed genes (DEGs) (R = - 0.0478 to 0.0636), whereas stronger correlations were observed in terms of the DEPs with the same expression trends as the correlated DEGs (R = 0.5593 to 0.7080). The results of multiple reaction monitoring (MRM) verification indicate that the iTRAQ results were reliable. After the fermentation arrest, a number of proteins involved in transcription, translation, oxidative phosphorylation and fatty acid metabolism were down-regulated, some molecular chaperones and proteasome proteins were up-regulated, the ATPase activity significantly decreased, and the total fatty acids gradually accumulated. In addition, the contents of palmitic acid, oleic acid, C16, C18, C22 and C24 fatty acids increased by 16.77%, 28.49%, 14.14%, 26.88%, 628.57% and 125.29%, respectively.

Conclusions

This study confirmed some biochemical and enzymatic alterations provoked by the stress conditions in the specific case of K. marxianus: such as decreases in transcription, translation and oxidative phosphorylation, alterations in cellular fatty acid composition, and increases in the abundance of molecular chaperones and proteasome proteins. These findings provide potential targets for further metabolic engineering towards improvement of the stress tolerance in K. marxianus.", "token_count": 503, "char_count": 1705, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:25.361556", "source": { "split": "train_shard_00001", "doc_id": 401 }, "chunk_id": "train_shard_00001_401_1", "global_id": 6228 }, { "text": "Proteomic profiling and integrated analysis with transcriptomic data bring new insights in the stress responses of Kluyveromyces marxianus after an arrest during high-temperature ethanol fermentation.", "token_count": 51, "char_count": 207, "word_count": 25, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:25.717919", "source": { "split": "train_shard_00001", "doc_id": 401 }, "chunk_id": "train_shard_00001_401_2", "global_id": 6229 }, { "text": "Extensive genomic analyses of Enterococcus cecorum isolates from sepsis outbreaks in broilers suggests a polyphyletic origin likely arising from core genome mutations rather than gene acquisition. This species is normal intestinal flora in avian species with particular isolates associated with osteomyelitis. More recently, the species has been associated with sepsis outbreaks affecting broilers during the first 3 weeks post hatch. Understanding the genetic and management basis of this new phenotype is critical for developing strategies to mitigate this emerging problem. Phylogenomic analyses of 227 genomes suggest that sepsis isolates are polyphyletic and closely related to both commensal and osteomyelitis isolate genomes. Pangenome analyses detect no gene acquisitions that distinguish all sepsis isolates. Core genome SNP analyses identify a number of mutations, affecting protein coding sequence, that are enriched in sepsis isolates. Analysis of the protein substitutions supports mutational origins of sepsis isolates.\n\nMolecular genomic analyses of Enterococcus cecorum from sepsis outbreaks in broilers", "token_count": 261, "char_count": 1119, "word_count": 153, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:26.291004", "source": { "split": "train_shard_00001", "doc_id": 402 }, "chunk_id": "train_shard_00001_402_0", "global_id": 6230 }, { "text": "As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only 27 species have been described to date. In this study, a novel Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 - this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils - were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70 % of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1 and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70 % of species-specific genes encoded unknown functions. Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae ", "token_count": 523, "char_count": 1676, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": { "genes": [ "VH1", "XN45", "BG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:26.982368", "source": { "split": "train_shard_00001", "doc_id": 403 }, "chunk_id": "train_shard_00001_403_0", "global_id": 6231 }, { "text": "The functions encoded by most species-specific genes in the X. griffiniae clade remain unknown.\n\nDraft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil-dwelling nematodes in Kenya.", "token_count": 76, "char_count": 262, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:27.385260", "source": { "split": "train_shard_00001", "doc_id": 403 }, "chunk_id": "train_shard_00001_403_1", "global_id": 6232 }, { "text": "Diabetic foot infections (DFI) are a major complication of diabetes, often leading to lower limb amputations. Escherichia coli is a predominant Gram-negative pathogen in DFI, yet its genomic and pathogenic features remain poorly characterised. Here, we present a whole genome sequence-based analysis of diabetic foot-associated E. coli (DFEC) isolates from diverse geographical locations. Phylogenetic reconstruction revealed substantial diversity, with strains spanning seven phylogroups and 28 sequence types. Capsule biosynthesis loci linked to invasive infections, such as K1, K2ab, and K5, were also detected. The DFEC pangenome comprised 18,263 gene clusters, indicating high genomic plasticity. The plasmid repertoire was also varied and contributed to the genomic diversity of the strains. Approximately 78% of isolates were multidrug-resistant (MDR) or extensively drug-resistant (XDR), with resistance to last-resort antibiotics such as colistin and carbapenems also observed. High frequencies of virulence factors involved in host cell adherence, iron metabolism, serum survival, as well as toxins and type 3 secretion system (T3SS) genes were also detected. In contrast, metabolic modelling showed conserved biochemical profiles. Clustering based on accessory metabolic functions did not mirror phylogeny, suggesting metabolic convergence among distinct lineages. Collectively, these findings reveal that DFEC are versatile pathogens with a repertoire of antimicrobial resistance and virulence determinants. These traits make them functionally distinct from commensal E. coli strains and highlight the potential of DFEC to cause severe and invasive infections.\n\nPopulation structure, antimicrobial resistance, and virulence factors of diabetic foot-associated E. coli", "token_count": 453, "char_count": 1779, "word_count": 237, "semantic_coherence": 1, "information_density": 0.7089, "quality_score": 0.8544, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:28.039350", "source": { "split": "train_shard_00001", "doc_id": 404 }, "chunk_id": "train_shard_00001_404_0", "global_id": 6233 }, { "text": "Traditionally, variations from a linear reference genome were used to represent large sets of haplotypes compactly. In the linear reference genome based paradigm, the positional Burrows-Wheeler transform (PBWT) has traditionally been used to perform efficient haplotype matching. Pangenome graphs have recently been proposed as an alternative to linear reference genomes for representing the full spectrum of variations in the human genome. However, haplotype matches in pangenome graph based haplotype sets are not trivially generalizable from haplotype matches in the linear reference genome based haplotype sets. Work has been done to represent large sets of haplotypes as paths through a pangenome graph. The graph Burrows-Wheeler transform (GBWT) is one such work. The GBWT essentially stores the haplotype paths in a run length compressed BWT with compressed local alphabets. Although efficient in practice count and locate queries on the GBWT were provided by the original authors, the efficient haplotype matching capabilities of the PBWT have never been shown on the GBWT. In this paper, we formally define the notion of haplotype matches in pangenome graph-based haplotype sets by generalizing from haplotype matches in linear reference genome-based haplotype sets. We also describe the relationship between set maximal matches, long matches, locally maximal matches, and text maximal matches on the GBWT, PBWT, and the BWT. We provide algorithms for outputting some of these matches by applying the data structures of the r-index (introduced by Gagie et al.) to the GBWT. We show that these structures enable set maximal match and long match queries on the GBWT in almost linear time and in space close to linear in the number of runs in the GBWT. We also provide multiple versions of the query algorithms for different combinations of the available data structures. The long match query algorithms presented here even run on the BWT in the same time complexity as the GBWT due to their similarity.\n\nHaplotype Matching with GBWT for Pangenome Graphs", "token_count": 463, "char_count": 2060, "word_count": 318, "semantic_coherence": 1, "information_density": 0.4748, "quality_score": 0.7374, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:28.683697", "source": { "split": "train_shard_00001", "doc_id": 405 }, "chunk_id": "train_shard_00001_405_0", "global_id": 6234 }, { "text": "Enterococcus faecalis is a commensal bacterium that colonizes the gut of humans and animals and is a major opportunistic pathogen, known for causing multidrug-resistant healthcare-associated infections (HAIs). Its ability to thrive in diverse environments and disseminate antimicrobial resistance genes (ARGs) across ecological niches highlights the importance of understanding its ecological, evolutionary, and epidemiological dynamics. The CRISPR2 locus has been used as a valuable marker for assessing clonality and phylogenetic relationships in E. faecalis. In this study, we identified a group of E. faecalis strains lacking CRISPR2, forming a distinct, well-supported clade. We demonstrate that this clade meets the genomic criteria for classification as a novel subspecies, here referred to as \"subspecies B.\" Through a comprehensive pangenome analysis and comparative genomics, we explored the adaptive ecological traits underlying this diversification process, identifying clade-specific features and their predicted functional roles. Our findings suggest that the frequent isolation of subspecies B from meat products and processing facilities may reflect dissemination routes involving environmental contamination (e.g., water, plants, soil) from avian species. The absence of key virulence traits required for pathogenicity in mammals, particularly humans, and the lack of clinically relevant resistance determinants indicate that subspecies B currently poses minimal threat to public health compared with the broadly disseminated \"subspecies A.\" Nevertheless, the unclear potential for genetic exchange between these subspecies and the frequent association of subspecies B with food sources calls for continued genomic surveillance of E. faecalis from a One Health perspective to detect and mitigate the emergence of high-risk variants in advance.IMPORTANCEExploring intraspecific genetic variability in generalist bacteria with pathogenic potential, such as Enterococcus faecalis, is a key to uncovering stable evolutionary trends. By screening the CRISPR2 locus across a representative set of genomes from diverse sources, this study reveals a previously unrecognized lineage within the population structure of E", "token_count": 506, "char_count": 2265, "word_count": 299, "semantic_coherence": 1, "information_density": 0.6689, "quality_score": 0.8344, "entities": { "genes": [ "CRISPR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:29.338470", "source": { "split": "train_shard_00001", "doc_id": 406 }, "chunk_id": "train_shard_00001_406_0", "global_id": 6235 }, { "text": "faecalis, associated with underexplored nonhuman and nonhospital reservoirs. These findings broaden our knowledge of the species' genetic landscape and shed light on its adaptive strategies and patterns of ecological dissemination. By bridging phylogenetic patterns with variation in genetic defense systems and accessory traits, the study generates testable hypotheses about the genomic determinants and corresponding selective pressures that shape the species' behavior and long-term dissemination. This work offers new perspectives on the eco-evolutionary dynamics of E. faecalis and highlights the value of genomic surveillance beyond clinical settings, in alignment with One Health principles.\n\nHidden diversity in <i>Enterococcus faecalis</i> revealed by CRISPR2 screening: eco-evolutionary insights into a novel subspecies.", "token_count": 199, "char_count": 853, "word_count": 107, "semantic_coherence": 1, "information_density": 0.757, "quality_score": 0.8785, "entities": { "genes": [ "CRISPR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:29.785929", "source": { "split": "train_shard_00001", "doc_id": 406 }, "chunk_id": "train_shard_00001_406_1", "global_id": 6236 }, { "text": "Apple pomace was studied as a raw material for the production of xylitol and 2G ethanol, since this agroindustrial residue has a high concentration of carbohydrate macromolecules, but is still poorly studied for the production of fermentation bioproducts, such as polyols. The dry biomass was subjected to dilute-acid hydrolysis with H2SO4 to obtain the hemicellulosic hydrolysate, which was concentrated, detoxified and fermented. The hydrolyzate after characterization was submitted to submerged fermentations, which were carried out in Erlenmeyer flasks using, separately, the yeasts Candida guilliermondii and Kluyveromyces marxianus. High cellulose (32.62%) and hemicellulose (23.60%) contents were found in this biomass, and the chemical hydrolysis yielded appreciable quantities of fermentable sugars, especially xylose. Both yeasts were able to metabolize xylose, but Candida guilliermondii produced only xylitol (9.35 g L-1 in 96 h), while K. marxianus produced ethanol as the main product (10.47 g L-1 in 24 h) and xylitol as byproduct (9.10 g L-1 xylitol in 96 h). Maximum activities of xylose reductase and xylitol dehydrogenase were verified after 24 h of fermentation with C. guilliermondii (0.23 and 0.53 U/mgprot, respectively) and with K. marxianus (0.08 e 0.08 U/mgprot, respectively). Apple pomace has shown potential as a raw material for the fermentation process, and the development of a biotechnological platform for the integrated use of both the hemicellulosic and cellulosic fraction could add value to this residue and the apple production chain.", "token_count": 516, "char_count": 1650, "word_count": 230, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:30.439501", "source": { "split": "train_shard_00001", "doc_id": 407 }, "chunk_id": "train_shard_00001_407_0", "global_id": 6237 }, { "text": "Valorization of apple pomace using bio-based technology for the production of xylitol and 2G ethanol.", "token_count": 27, "char_count": 101, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:30.793104", "source": { "split": "train_shard_00001", "doc_id": 407 }, "chunk_id": "train_shard_00001_407_1", "global_id": 6238 }, { "text": "Clostridioides difficile infections (CDI) cause almost 300,000 hospitalizations per year, of which ~15%-30% are the result of recurring infections. The prevalence and persistence of CDI in hospital settings have resulted in an extensive collection of C. difficile clinical isolates and their classification, typically by ribotype. While much of the current literature focuses on one or two prominent epidemic ribotypes (e.g., RT027), recent years have seen several other ribotypes dominate the clinical landscape (e.g., RT106 and RT078). Some ribotypes are associated with severe disease and/or increased recurrence rates, but why certain ribotypes are more prominent or harmful than others remains unknown. Because C. difficile has a large, open pan-genome, this observed relationship between ribotype and clinical outcome could be a result of the genetic diversity of C. difficile. Thus, we hypothesize that the core biological processes of C. difficile are conserved across ribotypes/clades. We tested this hypothesis by observing the growth kinetics, sporulation, germination, production of toxin A and toxin B, bile acid sensitivity, bile salt hydrolase activity, and surface motility of 15 strains belonging to various ribotypes spanning each known C. difficile clade. In viewing these phenotypes across each strain, we see that core phenotypes (growth, germination, sporulation, and resistance to bile salt toxicity) are remarkably consistent across clades/ribotypes. This suggests that variations observed in the clinical setting may be due to unidentified factors in the accessory genome or due to unknown host factors.IMPORTANCEClostridioides difficile infections impact thousands of individuals every year, many of whom experience recurring infections. Clinical studies have reported an unexplained correlation between some clades/ribotypes of C. difficile and disease severity/recurrence. Here, we demonstrate that C", "token_count": 511, "char_count": 1987, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [ "RT106", "RT078", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:31.421777", "source": { "split": "train_shard_00001", "doc_id": 408 }, "chunk_id": "train_shard_00001_408_0", "global_id": 6239 }, { "text": "difficile strains across major clades/ribotypes are consistent in their core phenotypes. This suggests that such phenotypes are not responsible for variations in disease severity/recurrence and are ideal targets for the development of therapeutics meant to treat C. difficile-related infections.\n\nPhenotypic analysis of various <i>Clostridioides difficile</i> ribotypes reveals consistency among core processes.", "token_count": 116, "char_count": 434, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:31.806555", "source": { "split": "train_shard_00001", "doc_id": 408 }, "chunk_id": "train_shard_00001_408_1", "global_id": 6240 }, { "text": "Environmental perturbations shape the structure and function of microbial communities. Oil spills are a major perturbation and resolving spills often requires active measures like dispersant application that can exacerbate the initial disturbance. Species-specific responses of microorganisms to oil and dispersant exposure during such perturbations remain largely unknown. We merged metatranscriptomic libraries with pangenomes to generate Core-Accessory Metatranscriptomes (CA-Metatranscriptomes) for two microbial hydrocarbon degraders that played important roles in the aftermath of the Deepwater Horizon oil spill. The Colwellia CA-Metatranscriptome illustrated pronounced dispersant-driven acceleration of core (~41%) and accessory gene (~59%) transcription, suggesting an opportunistic strategy. Marinobacter responded to oil exposure by expressing mainly accessory genes (~93%), suggesting an effective hydrocarbon-degrading lifestyle. The CA-Metatranscriptome approach offers a robust way to identify the underlying mechanisms of key microbial functions and highlights differences of specialist-vs-opportunistic responses to environmental disturbance.\n\nSpecies-specific responses of marine bacteria to environmental perturbation.", "token_count": 263, "char_count": 1238, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:32.361703", "source": { "split": "train_shard_00001", "doc_id": 409 }, "chunk_id": "train_shard_00001_409_0", "global_id": 6241 }, { "text": "Abstract

Morganella morganii is a bacterium with open pangenomes, where genes move intra- and interspecies via horizontal gene transfer. Through pangenome analysis, the study maps three agriculture isolates; M. morganii with strong PGP activity, along with 78 publicly available genomes from clinical, food, wastewater, and animal sources. The analysis showed 23,829 gene clusters with only 8.52% core genes and discriminating distribution of 78.34% cloud genes across different niches. KEGG analysis showed 33, 12, and 38 genes related to nutrient solubilization in M. morganii isolates HM01, HM02, and HM04, respectively. Chemotaxis genes, crucial for stress response, were most abundant in HM04 (30), followed by HM01 (17) and HM02 (11). Additionally, numerous biosynthetic gene clusters encoding antibacterial and antifungal metabolites were identified. Clinical and wastewater isolates harboured a higher number of mobile genetic element (MGE) linked antimicrobial resistance (AMR) genes that confer resistance to 15 antibiotic classes. These AMR genes were predominantly plasmid-borne and found to transfer in M. morganii from clinical pathogens such as E. coli and A. baumannii. This study indicates that habitat pressure creates the scenario for selection of functional traits which enables the ecosystem specific survival of M. morganii. Together, the present investigation provides important insight into the genomic diversity and remarkable PGP potential of M. morganii strains for sustainable agriculture. The pangenome analysis proposes that detailed investigation is needed to confirm their efficacy as PGP bacterium and to distinguish them from pathogenic strains.

", "token_count": 488, "char_count": 1838, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7076, "quality_score": 0.8538, "entities": { "genes": [ "HM02", "HM01", "HM04" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:33.009185", "source": { "split": "train_shard_00001", "doc_id": 410 }, "chunk_id": "train_shard_00001_410_0", "global_id": 6242 }, { "text": "Pan-genome analysis of Morganella Morganii reveals niche-specific selection of functional traits: Friend or Foe?", "token_count": 25, "char_count": 112, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:33.375586", "source": { "split": "train_shard_00001", "doc_id": 410 }, "chunk_id": "train_shard_00001_410_1", "global_id": 6243 }, { "text": "

Background

Candidatus Ornithobacterium hominis (O. hominis), which was identified in nasopharyngeal swabs from Egypt, has been associated with respiratory disorders in humans. O. hominis, a recently identified member of the Flavobacteriaceae family, belongs to the largest family within the Bacteroidetes phylum. This family includes hundreds of species and 90 genera, including major human pathogens such as Capnocytophaga canimorsus and Elizabethkingia meningoseptica. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The alignment of reads against the O. hominis genome was accomplished using BLASTN, and the reads with significant hits were extracted using Seqtk and assembled using SPAdes. The primary goal of this study was to obtain a more profound understanding of the genomic landscape of O. hominis, with an emphasis on identifying the associated virulence, antimicrobial genes, and distinct defense mechanisms to shed light on the potential role of O. hominis in human respiratory infections.

Results

The genome size was estimated to be 1.84 Mb, including 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G+C content of 35.62%. Genes encoding gliding motility, antibiotic resistance (20 genes), and the toxA gene were all included in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique genes encoding proteins, such as the ParE1 toxin that defend against the actions of quinolone and other antibiotics. The cobalt-zinc-cadmium resistance gene encoding the protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected", "token_count": 498, "char_count": 1928, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6407, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:34.033384", "source": { "split": "train_shard_00001", "doc_id": 411 }, "chunk_id": "train_shard_00001_411_0", "global_id": 6244 }, { "text": "Several multidrug resistance genes encoding proteins were identified, such as MexB, MdtK, YheI, and VanC.

Conclusion

Our study focused on identifying virulence factors, and antimicrobial resistance genes present in the core genome of O. hominis. These findings provide valuable insights into the potential pathogenicity and antibiotic susceptibility of O. hominis.\n\nDraft genome sequence of novel Candidatus Ornithobacterium hominis carrying antimicrobial resistance genes in Egypt.", "token_count": 122, "char_count": 489, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7742, "quality_score": 0.8871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:34.421300", "source": { "split": "train_shard_00001", "doc_id": 411 }, "chunk_id": "train_shard_00001_411_1", "global_id": 6245 }, { "text": "Glaesserella parasuis is a gram-negative bacterium that causes fibrotic polyserositis and arthritis in pig, significantly affecting the pig industry. The pan-genome of G. parasuis is open. As the number of genes increases, the core and accessory genomes may show more pronounced differences. The genes associated with virulence and biofilm formation are also still unclear due to the diversity of G. parasuis. Therefore, we have applied a pan-genome-wide association study (Pan-GWAS) to 121 strains G. parasuis. Our analysis revealed that the core genome consists of 1,133 genes associated with the cytoskeleton, virulence, and basic biological processes. The accessory genome is highly variable and is a major cause of genetic diversity in G. parasuis. Furthermore, two biologically important traits (virulence, biofilm formation) of G. parasuis were studied via pan-GWAS to search for genes associated with the traits. A total of 142 genes were associated with strong virulence traits. By affecting metabolic pathways and capturing the host nutrients, these genes are involved in signal pathways and virulence factors, which are beneficial for bacterial survival and biofilm formation. This research lays the foundation for further studies on virulence and biofilm formation and provides potential new drug and vaccine targets against G. parasuis.\n\nPan-genome wide association study of Glaesserella parasuis highlights genes associated with virulence and biofilm formation.", "token_count": 391, "char_count": 1538, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5728, "quality_score": 0.7864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:35.043099", "source": { "split": "train_shard_00001", "doc_id": 412 }, "chunk_id": "train_shard_00001_412_0", "global_id": 6246 }, { "text": "Brucella melitensis causes small ruminant brucellosis and a zoonotic pathogen prevalent worldwide. Whole genome phylogeny of all available B. melitensis genomes (n = 355) revealed that all Indian isolates (n = 16) clustered in the East Mediterranean lineage except the ADMAS-GI strain. Pangenome analysis indicated the presence of limited accessory genomes with few clades showing specific gene presence/absence pattern. A total of 43 virulence genes were predicted in all the Indian strains of B. melitensis except 2007BM-1 (ricA and wbkA are absent). Multilocus sequence typing (MLST) analysis indicated all except one Indian strain (ADMAS-GI) falling into sequence type (ST 8). In comparison with MLST, core genome phylogeny indicated two major clusters (>70% bootstrap support values) among Indian strains. Clusters with <70% bootstrap support values represent strains with diverse evolutionary origins present among animal and human hosts. Genetic relatedness among animal (sheep and goats) and human strains with 100% bootstrap values shows its zoonotic transfer potentiality. SNP-based analysis indicated similar clustering to that of core genome phylogeny. Among the Indian strains, the highest number of unique SNPs (112 SNPs) were shared by a node that involved three strains from Tamil Nadu. The node SNPs involved several peptidase genes like U32, M16 inactive domain protein, clp protease family protein, and M23 family protein and mostly represented non-synonymous (NS) substitutions. Vaccination has been followed in several parts of the world to prevent small ruminant brucellosis but not in India. Comparison of Indian strains with vaccine strains showed that M5 is genetically closer to most of the Indian strains than Rev.1 strain", "token_count": 484, "char_count": 1798, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:35.688696", "source": { "split": "train_shard_00001", "doc_id": 413 }, "chunk_id": "train_shard_00001_413_0", "global_id": 6247 }, { "text": "The presence of most of the virulence genes among all Indian strains and conserved core genome compositions suggest the use of any circulating strain/genotypes for the development of a vaccine candidate for small ruminant brucellosis in India.\n\nGenome Sequencing and Comparative Genomics of Indian Isolates of Brucella melitensis.", "token_count": 84, "char_count": 337, "word_count": 48, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:36.057824", "source": { "split": "train_shard_00001", "doc_id": 413 }, "chunk_id": "train_shard_00001_413_1", "global_id": 6248 }, { "text": "The red seaweed Gracilaria verrucosa has been used for the production of bioethanol. Pretreatment for monosaccharide production was carried out with 12% (w/v) G. verrucosa slurry and 500 mM HNO3 at 121°C for 90 min. Enzymatic hydrolysis was performed with a mixture of commercial enzymes (Cellic C-Tec 2 and Celluclast 1.5 L; 16 U/ml) at 50°C and 150 rpm for 48 h. G. verrucosa was composed of 66.9% carbohydrates. In this study, 61.0 g/L monosaccharides were obtained from 120.0 g dw/l G. verrucosa. The fermentation inhibitors such as hydroxymethylfurfural (HMF), levulinic acid, and formic acid were produced during pretreatment. Activated carbon was used to remove HMF. Wildtype and adaptively evolved Saccharomyces cerevisiae, Candida lusitaniae, and Kluyveromyces marxianus were used for fermentation to evaluate ethanol production.\n\nComparison of Ethanol Yield Coefficients Using Saccharomyces cerevisiae, Candida lusitaniae, and Kluyveromyces marxianus Adapted to High Concentrations of Galactose with Gracilaria verrucosa as Substrate.", "token_count": 433, "char_count": 1132, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7047, "quality_score": 0.8523, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:36.683678", "source": { "split": "train_shard_00001", "doc_id": 414 }, "chunk_id": "train_shard_00001_414_0", "global_id": 6249 }, { "text": "The increasing availability of genome sequences has highlighted the limitations of using a single reference genome to represent the diversity within a species. Pangenomes, encompassing the genomic information from multiple genomes, thus offer a more comprehensive representation of intraspecific diversity. However, pangenomes in form of a variation graph often lack annotation information and tools for, which limits their utility for downstream analyses. We introduce here GrAnnoT, a tool designed for an efficient and reliable integration of annotation information in such variation graphs. It projects existing annotations from a source genome to the variation graph and subsequently to other embedded genomes. GrAnnoT was benchmarked against state-of-the-art tools on pangenome variation graphs and linear genomes for Asian rice, and tested on human and E. coli data. The results demonstrate that GrAnnoT is consensual, conservative, and fast. It provides informative outputs, such as presence-absence matrices for genes, and alignments of transferred features between source and target genomes, helping in the study of genomic variations and evolution. GrAnnoT's robustness and replicability across different species make it a valuable tool for enhancing pangenome analyses. GrAnnoT is available under the GNU GPLv3 licence athttps://forge.ird.fr/diade/dynadiv/grannot.\n\nGrAnnoT, a tool for efficient and reliable annotation transfer through pangenome graph", "token_count": 319, "char_count": 1463, "word_count": 200, "semantic_coherence": 1, "information_density": 0.645, "quality_score": 0.8225, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:37.248670", "source": { "split": "train_shard_00001", "doc_id": 415 }, "chunk_id": "train_shard_00001_415_0", "global_id": 6250 }, { "text": "The present study aimed to identify the mechanisms underlying the survival of an environmental bacterium originally isolated from the waste-contaminated soil of Jhiri, Ranchi, India. Based on 16S rRNA, ANI (average nucleotide identity), and BLAST Ring Image Generator (BRIG) analysis, the isolated strain was identified as Pseudomonas aeruginosa. The present study extends the characterization of this bacterium through genomic and comparative genomic analysis to understand the genomic features pertaining to survival in stressed environments. The sequencing of the bacterium at Illumina HiSeq platform revealed that it possessed a 6.8 Mb circular chromosome with 65.9% GC content and 63 RNAs sequence. The genome also harbored several genes associated to plant growth promotion i.e. phytohormone and siderophore production, phosphate solubilization, motility, and biofilm formation, etc. The genomic analysis with online tools unraveled the various genes belonging to the bacterial secretion system, antibiotic resistance, virulence, and efflux pumps, etc. The presence of biosynthetic gene clusters (BCGs) indicated that large numbers of genes were associated to non-ribosomal synthesized peptide synthetase, polyketide synthetase, and other secondary metabolite production. Additionally, its genomes encode various CAZymes such as glycoside hydrolases and other genes associated with lignocellulose breakdown, suggesting that strain S-8 have strong biomass degradation potential. Furthermore, pan-genome analysis based on a comparison of whole genomes showed that core genome represented the largest part of the gene pools. Therefore, genome and comparative genome analysis of Pseudomonas strains is valuable for understanding the mechanism of resistance to metal stress, genome evolution, HGT events, and therefore, opens a new perspective to exploit a newly isolated bacterium for biotechnological applications.\n\nIn-depth genome and comparative genome analysis of a metal-resistant environmental isolate <i>Pseudomonas aeruginosa</i> S-8.", "token_count": 511, "char_count": 2077, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:37.927198", "source": { "split": "train_shard_00001", "doc_id": 416 }, "chunk_id": "train_shard_00001_416_0", "global_id": 6251 }, { "text": "The NAC transcription factor family is pivotal in regulating plant development and stress responses, yet its diversity and evolutionary dynamics in barley (Hordeum vulgare) remain underexplored. In this study, we performed a comprehensive pan-genome analysis to identify and characterize the HvNACs across 20 barley accessions. A ranging from 127 to 149 HvNACs were identified in each genome, in which the Morex genome harbored the highest count. These HvNACs were classified into 201 orthogroups, further stratified into core (102), soft-core (18), shell (25), and lineage-specific (56) categories. Phylogenetic analysis delineated them into 12 subfamilies, of which the core genes have undergone strong purifying selection, by contrast, the shell and lineage-specific genes were under relaxed selection constraint, suggesting functional diversification in barley. Genomic variation, such as PAVs and CNVs, largely driven by TEs, highlighted the dynamic nature of NAC loci. Furthermore, transcriptome profiling of the HvNACs demonstrated diverse tissue expression patterns and different response characteristics under salt stress. These findings elucidate the evolutionary and functional dynamics of HvNACs, offering valuable insights for genetic improvement of breeding programs in barley as well as in other crops.\n\nThe evolution, variation, and expression patterns under development and stress responses of the NAC gene family in the barley pan-genome.", "token_count": 384, "char_count": 1498, "word_count": 203, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:38.577168", "source": { "split": "train_shard_00001", "doc_id": 417 }, "chunk_id": "train_shard_00001_417_0", "global_id": 6252 }, { "text": "Paratuberculosis is a chronic infection of the intestine, mainly the ileum, caused by Mycobacterium avium subsp. paratuberculosis in cattle and other ruminants. This enzootic disease is present worldwide and has a negative impact on the dairy cattle industry. For this subspecies, the current genotyping tools do not provide the needed resolution to investigate the genetic diversity of closely related strains. These limitations can be overcome by the application of whole-genome sequencing (WGS), particularly for clonal populations such as M. avium subsp. paratuberculosis. The purpose of the present study was to undertake a WGS analysis with a panel of 200 animal field M. avium subsp. paratuberculosis strains selected based on a previous large-scale longitudinal study of Prim'Holstein and Normande dairy breeds naturally infected with M. avium subsp. paratuberculosis in the West of France. The pangenome analysis revealed that M. avium subsp. paratuberculosis has a closed pangenome. The phylogeny, based on alignment of 2,786 nonhomoplasic single nucleotide polymorphisms (SNPs), showed that the strain population is structured into three clades independently of the cattle breed or geographic distribution. The increased resolution of phylogeny obtained by WGS confirmed the homoplasic nature of the markers variable-number tandem repeat (VNTR) and short sequence repeat (SSR) used for M. avium subsp. paratuberculosis genotyping. These phylogenetic data also revealed independent introductions of the different genotypes in two main waves since at least 2003. WGS applied to this sampling demonstrated the presence of mixed infections in herds and at the individual animal level. Collectively, the phylogeny results inferred with French isolates compared to M. avium subsp. paratuberculosis isolates from around the world suggest introductions of M", "token_count": 533, "char_count": 1954, "word_count": 267, "semantic_coherence": 1, "information_density": 0.618, "quality_score": 0.809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:39.267195", "source": { "split": "train_shard_00001", "doc_id": 418 }, "chunk_id": "train_shard_00001_418_0", "global_id": 6253 }, { "text": "avium subsp. paratuberculosis genotypes through the animal trade. Relationships between genetic traits and epidemiological data can now be investigated to better understand transmission dynamics of the disease. IMPORTANCE Mycobacterium avium subsp. paratuberculosis causes Johne's disease in ruminants, which is present worldwide and has significant negative impacts on the dairy cattle industry and animal welfare. Prevention and control of M. avium subsp. paratuberculosis infection are hampered by knowledge gaps in strain virulence, genotype distribution, and transmission dynamics. This work has revealed new insights into M. avium subsp. paratuberculosis strains currently circulating in western France and how they are related to strains circulating globally. We applied whole-genome sequencing (WGS) to obtain comprehensive information on genome evolution and discrimination of closely related strains. This approach revealed the history of M. avium subsp. paratuberculosis infection in France, refined the pangenomic characteristics of M. avium subsp. paratuberculosis, and demonstrated the existence of mixed infection in animals. Finally, this study identified predominant genotypes, which allow a better understanding of disease transmission dynamics. This information will facilitate tracking of this pathogen on farms and across agricultural regions, thus informing transmission pathways and disease control points.\n\nGenetic Features of Mycobacterium avium subsp. paratuberculosis Strains Circulating in the West of France Deciphered by Whole-Genome Sequencing.", "token_count": 414, "char_count": 1663, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6019, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:39.909947", "source": { "split": "train_shard_00001", "doc_id": 418 }, "chunk_id": "train_shard_00001_418_1", "global_id": 6254 }, { "text": "

ABSTRACT

Huanglongbing (HLB) is a bacterial disease that affects citrus trees and is considered the most severe citrus disease in the world. The three HLB-associated ‘ Ca. Liberibacter’ species harbor prophage regions which have been described to play critical roles in their evolution and biology. In this study, we assembled and characterized the accessory genome of the first circular de novo ‘ Candidatus Liberibacter asiaticus’ (CLas) assembly (V1R1) from Réunion, one of the sparse areas worldwide hosting CLas and ‘ Ca. Liberibacter africanus’ (CLaf). This 1,272 Mb-long whole-genome harbored 1,129 coding sequences and two complete prophages, including a 37,934 bp-long Type 1 prophage, frequently present in CLas genomes, and a 40,501 bp-long undescribed CLas prophage designated as P-V1R1-5. Comparative genomic approaches suggested that P-V1R1-5 have all the genetic elements to produce new viral particles and revealed that it likely belongs to a new CLas Type 5 prophage. While being reported for the first time in a CLas strain, P-V1R1-5-like prophages were previously identified in CLaf genomes, making it the first evidence of shared prophage-like sequence among HLB-associated ‘ Ca , Liberibacter’ species. Using PCR amplifications targeting P-V1R1-5, we also showed that 85.7% of the tested CLas strains from Réunion and all tested CLaf strains from Madagascar and Réunion harbored a Type 5-like prophage. The identification of CLas Type 5-like prophages not only expanded our knowledge of CLas genomic diversity in Réunion, but also provided new insights into the role of horizontally transferred elements in the evolution of the sympatric HLB-associated bacteria.

IMPORTANCE

Huanglongbing (HLB) is the most severe citrus disease worldwide", "token_count": 503, "char_count": 1778, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:40.564029", "source": { "split": "train_shard_00001", "doc_id": 419 }, "chunk_id": "train_shard_00001_419_0", "global_id": 6255 }, { "text": "The disease is associated with three ‘ Candidatus Liberibacter’ species harboring prophage regions that have been described to play critical roles in their biology. In this study, we assembled and characterized the accessory genome of the first circular de novo ‘ Ca. Liberibacter asiaticus’ (CLas) assembly from Réunion, one of the very few areas in the world where both of CLas and ‘ Ca. Liberibacter africanus’ (CLaf) coexist. Comparative genomic approaches demonstrated that this genome harbored two complete prophages, including a new CLas Type 5 prophage that was previously identified in CLaf but was reported for the first time in a CLas strain. This first evidence of shared prophage-like sequences among HLB-associated species expands our knowledge of CLas genomic diversity, but also provides new insights into the role of the accessory genome in the evolution of these bacteria.\n\nGenomic footprint of a shared Type 5 prophage in ‘ Candidatus Liberibacter asiaticus’ and ‘ Candidatus Liberibacter africanus’, two destructive bacterial pathogens of citrus huanglongbing", "token_count": 278, "char_count": 1093, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6319, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:41.114104", "source": { "split": "train_shard_00001", "doc_id": 419 }, "chunk_id": "train_shard_00001_419_1", "global_id": 6256 }, { "text": "Kluyveromyces marxianus and Saccharomyces paradoxus, which are the native microorganisms found in aguamiel, were used successfully for exo- and endo-fructanase synthesis to hydrolyze agave fructans important in agave sap production. We studied culture media for enzyme synthesis, as well as the physicochemical properties and enzyme activity, and we optimized the bioprocess parameters and the enzyme extract mixture to maximize agave fructan hydrolysis. The results showed that the best culture medium for fructanase synthesis contained 14.0, 20.0, and 1.0 (g-L⁻¹) of sucrose, peptone, and K2HPO4, respectively. The best enzyme-to-substrate ratio for agave juice containing 90 g-L⁻¹ of fructans was 10:1. Under constant operating conditions of 45.25 °C, 65.47 rpm, and pH 4.28, a product with 93.62 g-L⁻¹of total reducing sugars (TRS) and fructooligosaccharides (FOS) with a polymerization degree (PD) from 3 to 10 hexose units was obtained using a mixture of 98.4% K. marxianus and 1.6% S. paradoxus enzyme extracts. The resulting agave sap preserves the natural flavor and tastes closest to natural agave sap (aguamiel); hence, the results show, for the first time, a resolution of the technical challenge for stable agave sap production and confirm the importance of using native strains to evolve from spontaneous to directed fermentation.\n\nNovel process to obtain agave sap (aguamiel) by directed enzymatic hydrolysis of agave juice fructans", "token_count": 442, "char_count": 1447, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:41.749563", "source": { "split": "train_shard_00001", "doc_id": 420 }, "chunk_id": "train_shard_00001_420_0", "global_id": 6257 }, { "text": "Barley (Hordeum vulgare) is widely cultivated, ranking fourth in cultivation area among cereal crops worldwide. Many wild and cultivated barley accessions have been collected and preserved in crop genebanks throughout the world. Barley has a large genome (~5 Gbp) that has recently been sequenced and assembled at the chromosome level by the international research community. The community also is sequencing accessions representing the diversity of both domesticated and wild barley to provide genome-wide genotyping information for pangenome analysis. Given that the pangenome represents the universe of genome sequences existing in a species, the long-term goal of this project is to obtain high-quality genome sequences of the major barley accessions worldwide. As each accession is annotated, the capacity to explore structural differences is enhanced by the increased understanding of the diversity of the barley genome, which will facilitate efficient development of cultivars for human consumption. This review describes our current knowledge of barley genome diversity and proposes future directions for basic and applied research of the barley pangenome.\n\nGenetic resources and pangenome analysis of barley.", "token_count": 256, "char_count": 1224, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:42.297787", "source": { "split": "train_shard_00001", "doc_id": 421 }, "chunk_id": "train_shard_00001_421_0", "global_id": 6258 }, { "text": "Phased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia", "token_count": 20, "char_count": 92, "word_count": 14, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:42.654509", "source": { "split": "train_shard_00001", "doc_id": 422 }, "chunk_id": "train_shard_00001_422_0", "global_id": 6259 }, { "text": "

ABSTRACT

Evolutionary rescue occurs when populations in deteriorating environments avoid extinction by rapid adaptation. The recent evolutionary rescue of the cereal crop sorghum via RMES1 aphid resistance is among a few known in situ cases, but its pangenomic origins and molecular basis is not yet known. Here, we describe the behavioral effects, molecular endophenotypes, and pangenomic evolution underlying this evolutionary rescue. Analysis of near-isogenic lines show that RMES1 disrupts phloem feeding via global immunity activation of conserved defense networks. A growth-to-defense transition is evidenced by extensive transcriptome remodeling (>15% of expressed genes) and mediated by salicylic acid signaling. Nucleotide-binding leucine-rich repeat (NLR) immune receptor genes at the RMES1 locus harbored on a large tandem duplication have extensive copy number variation across the sorghum pangenome. The likely causative NLRs (RMES1A and RMES1B) were inferred from expression and structural variation. The NLRs encoded at RMES1 lack an N-terminal signaling domain and have nucleotide-binding domain sequence variation expected to result in a loss of ATP binding, suggesting RMES1 NLRs function via a noncanonical mechanism. The RMES1 NLR family is shared across the grass super-pangenome and includes the brown planthopper resistance gene BPH40 in Oryza sativa , which is syntenic to RMES1 . Finally, k-mer analysis of RMES1 haplotypes in the sorghum pangenome established the East African origin of rare standing variation for resistance. Thus, the birth-and-death process at an ancient gene cluster generated pangenomic variation that was recruited to activate coordinated defense pathways and provide evolutionary rescue.\n\nAncient pangenomic origins of noncanonical NLR genes underlying the recent evolutionary rescue of a staple crop", "token_count": 461, "char_count": 1859, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [ "BPH40", "RMES1A", "RMES1B", "RMES1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:43.291948", "source": { "split": "train_shard_00001", "doc_id": 423 }, "chunk_id": "train_shard_00001_423_0", "global_id": 6260 }, { "text": "Pangenomes are collections of annotated genome sequences of multiple individuals of a species1. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants2. Here we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that are rich in gene copy number variation. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that allelic diversity at structurally complex loci may have helped crop plants to adapt to new selective regimes in agricultural ecosystems.\n\nStructural variation in the pangenome of wild and domesticated barley.", "token_count": 310, "char_count": 1338, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6546, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:43.864275", "source": { "split": "train_shard_00001", "doc_id": 424 }, "chunk_id": "train_shard_00001_424_0", "global_id": 6261 }, { "text": "

ABSTRACT

Sequenced genomes for thousands of strains of a bacterial species allow for a comprehensive analysis of its pangenome. We present a pangenome study of Escherichia coli ’s metabolism by formulating ‘gene-to-protein-to-reaction associations’ (GPRs) for about 2,700 metabolic reactions in 2,377 fully sequenced strains. On one hand, these GPRs reconstruct strain–specific networks that allow computational predictions (and experimental validation) of metabolic phenotypes, while on the other hand, they give the genetic basis for a given metabolic reaction in every strain. A pangenome-wide analysis of GPRs shows that: 1) We can reveal the genetic basis for a specific metabolic property at the species level; 2) The genetic basis for many metabolic reactions is diverse; 3) Many rare genes show variation in the gene’s genomic neighborhood which often contain genes from transposable elements, 4) Many rare genes show large-scale fragmentation and horizontal gene transfer (>11,000 rare genes in 2,377 strains); and 5) The aromatic amino acids and branched chain amino acids pathways are enriched with rare genes, with Acetolactate synthase having 29 distinct genes. Thus, analysis of GPRs across the pangenome reveals a complex dynamic evolutionary history of metabolism, revealing the role of conserved, fragmented, and horizontally transferred metabolic genes.\n\nA Diverse Genetic Basis for Metabolic Reactions is Revealed Through Pangenome analysis", "token_count": 384, "char_count": 1468, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:44.484740", "source": { "split": "train_shard_00001", "doc_id": 425 }, "chunk_id": "train_shard_00001_425_0", "global_id": 6262 }, { "text": "Speciation is a continuous process driven by genetic, geographic, and ecological barriers to gene flow. It is widely investigated in multicellular eukaryotes, yet we are only beginning to comprehend the relative importance of mechanisms driving the emergence of barriers to gene flow in microbial populations. Here, we explored the diversification of the nearly ubiquitous soil cyanobacterium Microcoleus. Our dataset consisted of 291 genomes, of which 202 strains and eight herbarium specimens were sequenced for this study. We found that Microcoleus represents a global speciation continuum of at least 12 lineages, which radiated during Eocene/Oligocene aridification and exhibit varying degrees of divergence and gene flow. The lineage divergence has been driven by selection, geographical distance, and the environment. Evidence of genetic divergence and selection was widespread across the genome, but we identified regions of exceptional differentiation containing candidate genes associated with stress response and biosynthesis of secondary metabolites.\n\nThe global speciation continuum of the cyanobacterium Microcoleus.", "token_count": 249, "char_count": 1130, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6968, "quality_score": 0.8484, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:44.974208", "source": { "split": "train_shard_00001", "doc_id": 426 }, "chunk_id": "train_shard_00001_426_0", "global_id": 6263 }, { "text": "

Key message

Pangenome graphs enable population-scale genotyping and improve expression analysis, revealing that structural variations (SVs), particularly transposable elements (TEs), significantly contribute to gene expression variation in winter oilseed rape. Structural variations (SVs) impact important traits, from yield to flowering behaviour and stress responses. Pangenome graphs capture population-level diversity, including SVs, within a single data structure and provide a robust framework for downstream applications. They have the potential to serve as unbiased references for SV genotyping, pan-transcriptomic analyses, and association studies, offering significant advantages over single reference genomes. However, their full potential for expression quantitative trait locus (eQTL) analysis is yet to be explored. We combined long and short-read whole genome sequencing data with expression profiling of Brassica napus (oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. Over 90,000 SVs were discovered from 57 long-read datasets. Pangenome graph as reference was evaluated and used for SV genotyping with short reads and transcript expression quantification. Using SVs genotyped from the graph and 100 expression datasets, we identified 267 gene proximal (cis) SV-eQTLs. Over 70% of eQTL-SVs had similarity to transposable elements (TEs), especially Helitrons. The highest proportion of cis-eQTL-SVs were found in promoter regions. About a third of transcripts whose expression was associated with SVs, had no associated SNPs, suggesting that including SVs allows capturing of relationship which would be missed in SNP-only analyses. This study demonstrated that pangenome graphs provide a unifying framework for eQTL analysis by allowing population-scale SV genotyping and gene expression quantification. We also showed that SVs make an appreciable contribution to gene expression variation in winter oilseed rape.\n\nGraphical pangenomics-enabled characterization of structural variant impact on gene expression in Brassica napus.", "token_count": 483, "char_count": 2140, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6146, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:45.616660", "source": { "split": "train_shard_00001", "doc_id": 427 }, "chunk_id": "train_shard_00001_427_0", "global_id": 6264 }, { "text": "The search for efficient oleaginous microorganisms, which can be an alternative to fossil fuels and biofuels obtained from oilseed crops, has been going on for many years. The suitability of microorganisms in this regard is determined by their ability to biosynthesize lipids with preferred fatty acid profile along with the concurrent utilization of energy-rich industrial waste. In this study, we isolated, characterized, and identified kefir yeast strains using molecular biology techniques. The yeast isolates identified were Candida inconspicua, Debaryomyces hansenii, Kluyveromyces marxianus, Kazachstania unispora, and Zygotorulaspora florentina. We showed that deproteinated potato wastewater, a starch processing industry waste, supplemented with various carbon sources, including lactose and glycerol, is a suitable medium for the growth of yeast, which allows an accumulation of over 20% of lipid substances in its cells. Fatty acid composition primarily depended on the yeast strain and the carbon source used, and, based on our results, most of the strains met the criteria required for the production of biodiesel. In particular, this concerns a significant share of saturated fatty acids, such as C16:0 and C18:0, and unsaturated fatty acids, such as C18:1 and C18:2. The highest efficiency in lipid biosynthesis exceeded 6.3 g L-1. Kazachstania unispora was able to accumulate the high amount of palmitoleic acid.\n\nIdentification and Characterization of Oleaginous Yeast Isolated from Kefir and Its Ability to Accumulate Intracellular Fats in Deproteinated Potato Wastewater with Different Carbon Sources.", "token_count": 473, "char_count": 1674, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:46.255629", "source": { "split": "train_shard_00001", "doc_id": 428 }, "chunk_id": "train_shard_00001_428_0", "global_id": 6265 }, { "text": "Abstract

Decoding the genome of cultivated species is one of the key starting points for supporting marker-assisted selection to accelerate breeding programmes. To date, five to six flax genotypes, including fiber flax, linseed and related wild flax, mainly from Canada, China and Russia, have been sequenced and assembled. But no genome assembly was available for Western European flax cultivar, although France is the world's leading producer of fiber flax (85% of world production). The Canadian oilseed flax cultivars CDC Bethune have been mainly used as reference for studies and breeding activities. The best assembly to date was the Chinese fiber Yiya5 assembly, which had the best metric of all the flax genome assemblies available. Recent analyses have shown that up to 30% of fiber flax reads from different origins do not map to the oilseed genome. Thus, much genetic information could be neglected using the oilseed genome as a reference. The aim of this study is to sequence, assemble and annotate the genomes of four European flax cultivars (two fiber Bolchoï and Idéo; two oilseed Marquise and Attila) and provide flax pangenome for genotype characterization and breeding. From 21 to 46 Gb of ONT Minion long reads sequence data were -sequenced for the four genotypes, - assembled using Flye, -polished, validated and organised into hybrid scaffolds using 100 to 197 Gb optical map data (Bionano Genomics), and finally anchored into fifteen T2T pseudomolecules for each genotype using the fiber flax Yiya5 assembly. The final genome size reached 437, 441, 442 and 453 Mb for Idéo, Marquise, Attila and Bolchoï respectively. The four assemblies were annotated using ab initio predictions of genomic sequences and evidence from transcriptomic data", "token_count": 464, "char_count": 1796, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:46.907197", "source": { "split": "train_shard_00001", "doc_id": 429 }, "chunk_id": "train_shard_00001_429_0", "global_id": 6266 }, { "text": "A pangenome graph were constructed for ten cultivars, including the four previous assemblies and six publicly available assemblies (CDC Bethune, Longya10 and Line 3896, Heiya-14, Yiya5 and Atlant). The total pangenome graph size was 835.77 Mbp (74,123 non-redundant orthologous proteins) with the core pangenome size of 172.2 Mbp. The resources generated could be used for the development of genomic tools useful for breeders to improve the efficiency of breeding and variety evaluation.

\n\nChromosome-scale assembly of European flax (Linum usitatissimum L.) genotypes and pangenomic analysis provide genomic tools to improve breeding", "token_count": 179, "char_count": 636, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:47.350045", "source": { "split": "train_shard_00001", "doc_id": 429 }, "chunk_id": "train_shard_00001_429_1", "global_id": 6267 }, { "text": "Proteus mirabilis is a leading cause of urinary tract infections and a common commensal of the gastrointestinal tract. Our recent study (JB) showed that P. mirabilis strain BL95 employs a novel contact-dependent killing system against enteric bacteria in the mouse gut and in vitro. To uncover the genetic determinants of this system, we performed whole-genome sequencing of BL95 and compared it with 98 complete genomes of P. mirabilis. BL95 carries 56 coding sequences (CDSs) not found in other P. mirabilis. Over half of these unique genes are located on a novel integrative conjugative element (ICE) named ICEPm2, inserted in tRNA-Phe and exclusive to BL95. ICEPm2 has integration, conjugation, and DNA replication modules nearly identical to ICEPm1 (common in P. mirabilis), but ICEPm2 of BL95 carries two unique operons for P. mirabilis-a phenazine biosynthesis and a contact-dependent growth inhibition (CDI) system. ICEPm2 is absent in the P. mirabilis (AR_0156) closest to BL95 and it is present in the genomes of several Escherichia coli from mouse intestines, indicating its recent horizontal mobilization. BL95 shares over 100 genes of five different secretion systems with other P. mirabilis, mostly poorly studied, making a large pool of candidate genes for the contact-dependent growth inhibition.\n\nPangenome Analysis Reveals Novel Contact-Dependent Growth Inhibition System and Phenazine Biosynthesis Operons in <i>Proteus mirabilis</i> BL95 That Are Located in An Integrative and Conjugative Element.", "token_count": 506, "char_count": 1627, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6161, "quality_score": 0.808, "entities": { "genes": [ "BL95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:47.984097", "source": { "split": "train_shard_00001", "doc_id": 430 }, "chunk_id": "train_shard_00001_430_0", "global_id": 6268 }, { "text": "Pangenome analysis is a computational method for identifying genes that are present or absent from a group of genomes, which helps to understand evolutionary relationships and to identify essential genes. While current state-of-the-art approaches for calculating pangenomes comprise various software tools and algorithms, these methods can have limitations such as low sensitivity, specificity, and poor performance on specific genome compositions. A common task is the identification of core genes, i.e., genes that are present in (almost) all input genomes. However, especially for species with high sequence diversity, e.g., higher taxonomic orders like genera or families, identifying core genes is challenging for current methods. We developed RIBAP (Roary ILP Bacterial core Annotation Pipeline) to specifically address these limitations. RIBAP utilizes an integer linear programming (ILP) approach that refines the gene clusters initially predicted by the pangenome pipeline Roary. Our approach performs pairwise all-versus-all sequence similarity searches on all annotated genes for the input genomes and translates the results into an ILP formulation. With the help of these ILPs, RIBAP has successfully handled the complexity and diversity of Chlamydia, Klebsiella, Brucella, and Enterococcus genomes, even when genomes of different species are part of the analysis. We compared the results of RIBAP with other established and recent pangenome tools (Roary, Panaroo, PPanGGOLiN) and showed that RIBAP identifies all-encompassing core gene sets, especially at the genus level. RIBAP is freely available as a Nextflow pipeline under the GPL3 license: https://github.com/hoelzer-lab/ribap .\n\nPangenome calculation beyond the species level using RIBAP: A comprehensive bacterial core genome annotation pipeline based on Roary and pairwise ILPs", "token_count": 417, "char_count": 1849, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [ "GPL3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:48.611347", "source": { "split": "train_shard_00001", "doc_id": 431 }, "chunk_id": "train_shard_00001_431_0", "global_id": 6269 }, { "text": "As redesigning organisms using engineering principles is one of the purposes of synthetic biology (SynBio), the standardization of experimental methods and DNA parts is becoming increasingly a necessity. The synthetic biology community focusing on the engineering of Saccharomyces cerevisiae has been in the foreground in this area, conceiving several well-characterized SynBio toolkits widely adopted by the community. In this review, the molecular methods and toolkits developed for S. cerevisiae are discussed in terms of their contributions to the required standardization efforts. In addition, the toolkits designed for emerging nonconventional yeast species including Yarrowia lipolytica, Komagataella phaffii, and Kluyveromyces marxianus are also reviewed. Without a doubt, the characterized DNA parts combined with the standardized assembly strategies highlighted in these toolkits have greatly contributed to the rapid development of many metabolic engineering and diagnostics applications among others. Despite the growing capacity in deploying synthetic biology for common yeast genome engineering works, the yeast community has a long journey to go to exploit it in more sophisticated and delicate applications like bioautomation.\n\nStandardization of Synthetic Biology Tools and Assembly Methods for <i>Saccharomyces cerevisiae</i> and Emerging Yeast Species.", "token_count": 330, "char_count": 1418, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6196, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:49.175205", "source": { "split": "train_shard_00001", "doc_id": 432 }, "chunk_id": "train_shard_00001_432_0", "global_id": 6270 }, { "text": "The selection of a reference sequence in genome analysis is critical, as it serves as the foundation for all downstream analyses. Recently, the pangenome graph has been proposed as a data model that incorporates haplotypes from multiple individuals. Here we present JaSaPaGe, a pangenome graph reference for Saudi Arabian and Japanese populations, both of which have been significantly underrepresented in previous genomic studies. We constructed JaSaPaGe from high-quality phased diploid assemblies which were made utilizing PacBio high-fidelity long reads, Nanopore long reads, and Hi-C short reads of 9 Saudi and 10 Japanese individuals. Quality evaluation of the pangenome graph by variant calling showed that our pangenome outperformed earlier linear reference genomes (GRCh38 and T2T-CHM13) and showed comparable performance to the pangenome graph provided by the Human Pangenome Reference Consortium (HPRC), with more variants found in Japanese and Saudi samples using their population-specific pangenomes. This pangenome reference will serve as a valuable resource for both the research and clinical communities in Japan and Saudi Arabia.\n\nPhased genome assemblies and pangenome graphs of human populations of Japan and Saudi Arabia", "token_count": 279, "char_count": 1240, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6236, "quality_score": 0.8118, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:49.726888", "source": { "split": "train_shard_00001", "doc_id": 433 }, "chunk_id": "train_shard_00001_433_0", "global_id": 6271 }, { "text": "Exopolysaccharides (EPSs), a constitutive part of bacterial biofilm, act as a protecting sheath to the extremophilic bacteria and are of high industrial value. In this study, we elucidate a new EPS produced by thermotolerant (growth from 34-44 °C) strain Pseudomonas alcaligenes Med1 from Medano hot spring (39.1 °C surface temperature, pH 7.1) located in the Central Andean Mountains of Chile. Bacterial growth was screened for temperature tolerance (10-60 °C) to confirm the thermotolerance behaviour. Physicochemical properties of the EPS were characterized by different techniques: Scanning Electron Microscopy- Energy Dispersive X-ray Spectroscopy (SEM-EDS), Atomic Force Microscopy (AFM), High-Performance Liquid Chromatography (HPLC), Gel permeation chromatography (GPC), Fourier Transform Infrared Spectroscopy (FTIR), Nuclear Magnetic Resonance (NMR), and Thermogravimetric analysis (TGA). Whole genome of P. alcaligenes Med1 has also been studied in detail to correlate the structural and functional characteristics with genomic insight. The EPS demonstrated amorphous surface roughness composed of evenly distributed macromolecular lumps composed of mainly carbon and oxygen. The monosaccharide analysis has shown the presence of glucose, galactose, and mannose sugars at different ratios. TGA revealed the high thermal stability (315.3 °C) of the polysaccharide. The GPC has shown that Med1 is a low molecular weight polysaccharide (34.8 kDa) with low PI. The 2D-NMR linkage analysis suggests a diverse array of glycosidic bonds within the exopolysaccharide structure. The functional properties of the EPS were evaluated for food industry applications, specifically for antioxidant (DPPH, FRAP an H2O2)", "token_count": 489, "char_count": 1736, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7234, "quality_score": 0.8617, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:50.404701", "source": { "split": "train_shard_00001", "doc_id": 434 }, "chunk_id": "train_shard_00001_434_0", "global_id": 6272 }, { "text": "Extracted Med1 EPS revealed significant emulsification activity against different food grade vegetative oils (Coconut oil, Corn oil, Canola oil, Avocado oil, Sunflower oil, Olive oil, and Sesame oil). The highest 33.9% flocculation activity was observed with 60 mg L-1 EPS concentration. It showed water-holding (WHC) of 107.6% and oil-holding (OHC) capacity of 110.8%. The functional EPS produced by Pseudomonas alcaligenes Med1 from Central Andean Chilean hot spring of central Chile can be a useful additive for the food-processing industry.\n\nUnveiling a novel exopolysaccharide produced by Pseudomonas alcaligenes Med1 isolated from a Chilean hot spring as biotechnological additive.", "token_count": 206, "char_count": 698, "word_count": 97, "semantic_coherence": 1, "information_density": 0.732, "quality_score": 0.866, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:50.880732", "source": { "split": "train_shard_00001", "doc_id": 434 }, "chunk_id": "train_shard_00001_434_1", "global_id": 6273 }, { "text": "Abstract

Background: Understanding the chloroplast genome is pivotal to unravel evolutionary relationships within plant species and facilitate accurate species identification by utilizing conserved yet diverse sequences. Genus Aconitum consists of around 300 traditional Indian and Chinese medicinal plant species, many native to mountainous regions. Despite their medicinal value, several species are known to be highly poisonous due to the presence of toxic diterpene alkaloids. Therefore, accurate identification and classification of these species is vital for traditional medicine systems especially for their safe usage. Results: Our investigation revealed a consistent quadripartite structure across all chloroplast genomes, comprising the typical large single copy (LSC), small single copy (SSC), and two inverted repeats (IR) regions. Using the available annotations, pangenome analysis unveiled 72 core and nine accessory genes, indicating an open pangenome characteristic. In-depth nucleotide-level homology analysis revealed that homologous genes of all accessory genes are present in all other genomes, implying the requisite for better chloroplast genome annotation tools that can identify all putative genes from such conserved genomes. Notably, the order of all core and accessory genes remained highly conserved across all analysed genomes, underscoring overall evolutionary stability with the diversity of accessory genes. Members of some core pathways are relatively absent on the chloroplast genome, suggesting its potential presence on the nuclear genome, which will be revealed after their nuclear genome sequencing. Furthermore, codon usage analysis demonstrated a preference for A/T ending codons over G/C ending codons, consistent with chloroplast genomes across species. Our phylogenetic results largely supported the morphological classification, with distinct Lycoctonum and Aconitum subgenera clustering. This validated the gross accuracy except for A. tanguticum and A. flavum, which clustered in wrong subgenus clades, suggesting discrepancy in morphological classification of the species or inaccurate classification", "token_count": 513, "char_count": 2278, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6446, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:51.576595", "source": { "split": "train_shard_00001", "doc_id": 435 }, "chunk_id": "train_shard_00001_435_0", "global_id": 6274 }, { "text": "Conclusion: This comprehensive comparative analysis of 73 Aconitum chloroplast genomes elucidated their diversity at gene and genome architecture levels along with showcasing their evolutionary relationships with each other. Leveraging morphological classifications, we investigated the concordance between traditional taxonomy and molecular data through core gene-based and whole-genome phylogeny. The observed phylogenetic incongruences, such as non-monophyly of conspecific accessions and unexpected clustering patterns, likely reflect the combined effects of incomplete lineage sorting and historical hybridization events, both of which appear to be prominent evolutionary forces shaping the genomic architecture of Aconitum.

\n\nComprehensive chloroplast genome analysis of 73 genus Aconitum members of family Ranunculaceae reveals insights into genome structure, codon usage polymorphism, and phylogenetic relationships", "token_count": 230, "char_count": 973, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:52.067095", "source": { "split": "train_shard_00001", "doc_id": 435 }, "chunk_id": "train_shard_00001_435_1", "global_id": 6275 }, { "text": "Abstract

The advent of low cost, high throughput DNA sequencing has led to the availability of thousands of complete genome sequences for a wide variety of bacterial species. Examining and interpreting genetic variation on this scale represents a significant challenge to existing methods of data analysis and visualisation. Starting with the output of standard pangenome analysis tools, we provide scripts to generate input files for a new open-source network analysis platform called Graphia. We describe the generation and analysis of interactive, 3D network graphs to explore the structure of a bacterial populations, the distribution of genes across a population, and the syntenic order in which those genes occur. Both the analysis and the visualisation are scalable to datasets of thousands of genome sequences. We anticipate that the approaches presented here will be of great utility to the microbial research community, allowing faster, more intuitive, and flexible interaction with pangenomes datasets, thereby enhancing interpretation of these complex data.

\n\nA graph-based approach for the visualisation and analysis of bacterial pangenomes", "token_count": 232, "char_count": 1175, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:52.541128", "source": { "split": "train_shard_00001", "doc_id": 436 }, "chunk_id": "train_shard_00001_436_0", "global_id": 6276 }, { "text": "

Abstract

Many flavoring agents on the market are extracted from natural sources or synthesized chemically. Due to the disadvantages of both methods, biotechnology is becoming a promising alternative. In this study, short chain ethyl esters with fruity notes were biosynthesized in UHT whole milk via coupling ethanolic fermentation with lipase (Palatase®) transesterification. Kluyveromyces marxianus, Lactobacillus fermentum and Lb. paracasei were used for fermentation. Milk fat was esterified with in situ produced ethanol by adding lipase at 0, 8 and 24 h of fermentation. Viable cell counts and pH were monitored during 48 h fermentation period. Flavor active ethyl esters, ethanol and free fatty acids were analyzed using headspace SPME-GC. Free fatty acid levels were lower in K. marxianus samples than lactobacilli. K. marxianus produced higher amounts of ethanol and esters than lactic acid bacteria. Viable cell counts decreased after lipase application at 0 and 8 h, possibly due to fatty acid production. Addition of lipase at 24 h resulted in improved cell counts as well as ethanol and ester production in the case of K. marxianus. This study demonstrated that fermenting milk with alcohol producing cultures in conjunction with lipase application can be an alternative to artificial flavorings in fermented milks.

Graphic abstract

\n\nNatural flavor biosynthesis by lipase in fermented milk using in situ produced ethanol.", "token_count": 428, "char_count": 1492, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:53.173265", "source": { "split": "train_shard_00001", "doc_id": 437 }, "chunk_id": "train_shard_00001_437_0", "global_id": 6277 }, { "text": "The genomic diversity of microbes is commonly parameterized as single nucleotide polymorphisms relative to a reference genome of a well-characterized, but arbitrary, isolate. However, any reference genome contains only a fraction of the microbial pangenome , the total set of genes observed in a given species. Reference-based approaches are thus blind to the dynamics of the accessory genome, as well as variation within gene order and copy number. With the wide-spread usage of long-read sequencing, the number of high-quality, complete genome assemblies has increased dramatically. Traditional computational approaches towards whole-genome analysis either scale poorly with the number of genomes, or treat genomes as dissociated “bags of genes”, and thus are not suited for this new era. Here, we present PanGraph , a Julia-based library and command line interface for aligning whole genomes into a graph. Each genome is represented as an undirected path along vertices, which in turn, encapsulate homologous multiple sequence alignments. The resultant data structure succinctly summarizes population-level nucleotide and structural polymorphisms and can be exported into a several common formats for either downstream analysis or immediate visualization.\n\nPanGraph: scalable bacterial pan-genome graph construction", "token_count": 285, "char_count": 1318, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7204, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:53.731849", "source": { "split": "train_shard_00001", "doc_id": 438 }, "chunk_id": "train_shard_00001_438_0", "global_id": 6278 }, { "text": "Escherichia coli carrying IncK-blaCMY-2 plasmids mediating resistance to extended-spectrum cephalosporins (ESC) has been frequently described in food-producing animals and in humans. This study aimed to characterize IncK-blaCMY-2-positive ESC-resistant E. coli isolates from poultry production systems in Denmark, Finland, and Germany, as well as from Danish human blood infections, and further compare their plasmids. Whole-genome sequencing (Illumina) of all isolates (n = 46) confirmed the presence of the blaCMY-2 gene. Minimum inhibitory concentration (MIC) testing revealed a resistant phenotype to cefotaxime as well as resistance to ≥3 antibiotic classes. Conjugative transfer of the blaCMY-2 gene confirmed the resistance being on mobile plasmids. Pangenome analysis showed only one-third of the genes being in the core with the remainder being in the large accessory gene pool. Single nucleotide polymorphism (SNP) analysis on sequence type (ST) 429 and 1286 isolates showed between 0-60 and 13-90 SNP differences, respectively, indicating vertical transmission of closely related clones in the poultry production, including among Danish, Finnish, and German ST429 isolates. A comparison of 22 ST429 isolates from this study with 80 ST429 isolates in Enterobase revealed the widespread geographical occurrence of related isolates associated with poultry production. Long-read sequencing of a representative subset of isolates (n = 28) allowed further characterization and comparison of the IncK-blaCMY-2 plasmids with publicly available plasmid sequences. This analysis revealed the presence of highly similar plasmids in ESC-resistant E", "token_count": 514, "char_count": 1768, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8084, "entities": { "genes": [ "ST429" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:54.396124", "source": { "split": "train_shard_00001", "doc_id": 439 }, "chunk_id": "train_shard_00001_439_0", "global_id": 6279 }, { "text": "coli from Denmark, Finland, and Germany pointing to the existence of common sources. Moreover, the analysis presented evidence of global plasmid transmission and evolution. Lastly, our results indicate that IncK-blaCMY-2 plasmids and their carriers had been circulating in the Danish production chain with an associated risk of spreading to humans, as exemplified by the similarity of the clinical ST429 isolate to poultry isolates. Its persistence may be driven by co-selection since most IncK-blaCMY-2 plasmids harbor resistance factors to drugs used in veterinary medicine.\n\nComparison of IncK-blaCMY-2 Plasmids in Extended-Spectrum Cephalosporin-Resistant Escherichia coli Isolated from Poultry and Humans in Denmark, Finland, and Germany.", "token_count": 232, "char_count": 808, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7255, "quality_score": 0.8627, "entities": { "genes": [ "ST429" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:54.864743", "source": { "split": "train_shard_00001", "doc_id": 439 }, "chunk_id": "train_shard_00001_439_1", "global_id": 6280 }, { "text": "Clostridium butyricum is an anaerobic bacterium that inhabits broad niches. Clostridium butyricum is known for its production of butyrate, 1,3-propanediol, and hydrogen. This study aimed to present a comparative pangenome analysis of 24 strains isolated from different niches. We sequenced and annotated the genome of C. butyricum 3-3 isolated from the Chinese baijiu ecosystem. The pangenome of C. butyricum was open. The core genome, accessory genome, and strain-specific genes comprised 1011, 4543, and 1473 genes, respectively. In the core genome, Carbohydrate metabolism was the largest category, and genes in the biosynthetic pathway of butyrate and glycerol metabolism were conserved (in the core or soft-core genome). Furthermore, the 1,3-propanediol operon existed in 20 strains. In the accessory genome, numerous mobile genetic elements belonging to the Replication, recombination, and repair (L) category were identified. In addition, genome islands were identified in all 24 strains, ranging from 2 (strain KNU-L09) to 53 (strain SU1), and phage sequences were found in 17 of the 24 strains. This study provides an important genomic framework that could pave the way for the exploration of C. butyricum and future studies on the genetic diversification of C. butyricum.\n\nAnalysis of the core genome and pangenome of Clostridium butyricum.", "token_count": 432, "char_count": 1399, "word_count": 200, "semantic_coherence": 1, "information_density": 0.585, "quality_score": 0.7925, "entities": { "genes": [ "SU1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:55.492651", "source": { "split": "train_shard_00001", "doc_id": 440 }, "chunk_id": "train_shard_00001_440_0", "global_id": 6281 }, { "text": "Enterobacter asburiae (E. asburiae) is a gram-negative rod-shaped bacterium which has emerging significance as an opportunistic pathogen having high virulence pattern and drug resistant properties. In this study, we present the detailed analysis of the whole genome sequence of a multidrug-resistant (MDR) E. asburiae strain BDW1M3 from Bangladesh. The isolate was collected from an infected foot wound of a diabetic foot ulcer patient. Through sophisticated genomic techniques encompassing whole genome sequencing and in-depth bioinformatic analyses, this research unveils a profound understanding of the isolate's antimicrobial resistance patterns, virulence determinants, biosynthetic gene clusters, metabolic pathways and pathogenic potential. The isolate displayed resistance to Ampicillin, Fosfomycin, Cefoxitin, Tigecycline, Meropenem, Linezolid, Vancomycin antibiotics and demonstrated the capacity for biofilm formation. Several antimicrobial resistance genes such as blaACT-2,fosA2, baeR, qnrE2, vanA and numbers of virulence genes including ybaJ, csrA, barA, uvrY, pgaD, hlyD, hlyC, terC, purD were detected. Metal resistance genes investigation revealed the presence of cusCFBA operon system, and many other genes including zntA, zitB, czrB. Prophage region of Myoviridae was detected. Comparative genomics with 47 whole genome sequence (n = 47) shed light on the genetic diversity of E. asburiae strains from diverse sources and countries, with a notable observation that strains from both human and non-human origins exhibited significant pathogenicity potential, genomic and phylogenomic relations hinting at potential cross-species transmission. Pangenome analysis indicated toward an expanding pangenome of E. asburiae. Further research and in-depth comprehensive studies are required to investigate the prevalence of E", "token_count": 483, "char_count": 1847, "word_count": 243, "semantic_coherence": 1, "information_density": 0.7202, "quality_score": 0.8601, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:56.149186", "source": { "split": "train_shard_00001", "doc_id": 441 }, "chunk_id": "train_shard_00001_441_0", "global_id": 6282 }, { "text": "asburiae in Bangladesh and emphasize towards unraveling the bacterium's inherent pathogenic potential and the intricate molecular mechanisms that underlie its resistance traits and virulence properties.\n\nFirst report on comprehensive genomic analysis of a multidrug-resistant Enterobacter asburiae isolated from diabetic foot infection from Bangladesh.", "token_count": 78, "char_count": 352, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8837, "quality_score": 0.9419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:56.518901", "source": { "split": "train_shard_00001", "doc_id": 441 }, "chunk_id": "train_shard_00001_441_1", "global_id": 6283 }, { "text": "

Motivation

We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.

Results

PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20-30× times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Finally, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.

Availabilityand implementation

The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nPATO: Pangenome Analysis Toolkit.", "token_count": 302, "char_count": 1267, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7063, "quality_score": 0.8531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:57.085134", "source": { "split": "train_shard_00001", "doc_id": 442 }, "chunk_id": "train_shard_00001_442_0", "global_id": 6284 }, { "text": "Pannagram is a toolkit for unbiased pangenome alignment and Mobilome detection based on full-genome assemblies. It consists of two components: a command-line interface for performing the multiple genome alignment in different modes, extracting features such as structural variants (SVs), and searching sequences between datasets; and an R library that provides tools for analyzing alignments and SVs, as well as visualizing every step of the Mobilome analysis pipeline. As a proof of concept, we applied Pannagram to 12 Cucumis sativus genomes, identified SVs, and constructed the graph of nestedness for these variants. Within this graph, we identified families of actually mobile elements belonging to known transposable element families (LINEs, LTRs, and TIRs) and uncovered candidates for a novel type of mobile elements. Our results highlight the power of Pannagram in Mobilome discovery while ensuring an unbiased approach to pangenome analysis.\n\nPannagram: unbiased pangenome alignment and the Mobilome calling", "token_count": 232, "char_count": 1017, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6803, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:57.551950", "source": { "split": "train_shard_00001", "doc_id": 443 }, "chunk_id": "train_shard_00001_443_0", "global_id": 6285 }, { "text": "Prochlorococcus is the most numerically abundant photosynthetic organism in the oceans and plays a role in global carbon cycling. Despite its ecological significance and the availability of over a thousand assembled genomes, progress in understanding gene function has been limited by the lack of genetic tools. Here, we report a reproducible electroporation-based protocol to introduce replicative plasmids into two strains of Prochlorococcus representing different ecotypes: MIT9313 (low-light adapted) and MED4 (high-light adapted). Using plasmids carrying a spectinomycin resistance cassette, we achieved transformation in ~33% of MED4 and ~10% of MIT9313 attempts, with greatest success when electroporating cells in late exponential phase. Transformed cells stably retained plasmids and expressed resistance genes, demonstrating functional uptake and gene expression. We also delivered a modified 13 kb plasmid carrying a CRISPR-Cpf1 system into MED4. While no targeted edits were observed, cpf1 and specR were expressed, indicating successful delivery of large constructs and active transcription. These findings represent a key step toward genetic manipulation of Prochlorococcus , enabling future optimization of gene editing approaches and deeper functional analysis of its vast and largely uncharacterized pangenome.\n\nTransformation of plasmid DNA into Prochlorococcus via electroporation", "token_count": 329, "char_count": 1406, "word_count": 188, "semantic_coherence": 1, "information_density": 0.7234, "quality_score": 0.8617, "entities": { "genes": [ "MIT9313", "MED4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:58.117602", "source": { "split": "train_shard_00001", "doc_id": 444 }, "chunk_id": "train_shard_00001_444_0", "global_id": 6286 }, { "text": "Aspergillus oryzae is an industrially important fungus used to produce traditional fermented foods and beverages in Korea and other East Asian countries. Conversely, A. flavus, which exhibits approximately 99.5 % of genomic similarity to A. oryzae, is a species that endangers food safety due to aflatoxin production. This study involved the genome sequences of A. oryzae KBP3 and KSS2 isolated from nuruk, a traditional Korean fermentation starter, assembled at the chromosomal level. To investigate differences among closely related species concerning food safety, compartive genome analysis was conducted on 30 strains of Aspergillus section Flavi, including nuruk strains and 28 genome sequences sourced from additional sequencing and the GenBank database. A detailed interspecific diversity was compared by examining the composition and chromosomal locations of annotated genes across 30 strains. A phylogenetic tree based on whole genome sequences, orthologous genes, and single nucleotide polymorphisms of core genes across 30 strains divided A. oryzae and A. flavus into two separate clades with some exceptions. This study presents two high-quality whole genome sequences of A. oryzae, providing significant genetic insights for this species and its closely related species. Our study confirmed the wide range of enzyme-related genes in A. oryzae isolated from nuruk, and its intraspecific genomic diversity. Our findings also systematically organize the pangenome analysis data of closely related species within Aspergillus section Flavi at the chromosomal level, enhancing the understanding of the genetic information relevant to food safety-related species.\n\nComparative genome analyses of Aspergillus oryzae and Aspergillus flavus originated from a Korean fermentation starter, nuruk", "token_count": 433, "char_count": 1796, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5889, "quality_score": 0.7945, "entities": { "genes": [ "KSS2", "KBP3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:58.746024", "source": { "split": "train_shard_00001", "doc_id": 445 }, "chunk_id": "train_shard_00001_445_0", "global_id": 6287 }, { "text": "Modified okara insoluble dietary fiber (OIDF) has attracted great interest as a promising Pickering emulsifier. At present, the modification methods are mainly physicochemical methods, and the research on microbial modified OIDF as stabilizer is not clear. In this work, modified OIDF was prepared by yeast Kluyveromyces marxianus fermentation. The potential of modified OIDF as a Pickering emulsifier and the formation and stability of OIDF-Pickering emulsions stabilized by modified OIDF were characterized, respectively. The results showed that the specific surface area, hydrophilicity, and electronegativity of the modified OIDF were all enhanced compared with the unmodified OIDF. The existence of the network structure between droplets is the key to maintain the stability of the emulsions, as indicated by Croy-Scanning Electron Microscope (Croy-SEM) and rheological properties measurements. The stability of OIDF-Pickering emulsions was evaluated in terms of storage time, centrifugal force, pH value, and ionic strength (NaCl). Moreover, the OIDF-Pickering emulsions stabilized by modified OIDF showed better stability. These results will contribute to the development of efficient OIDF-based emulsifiers, expand the application of emulsions in more fields, and will greatly improve the high-value utilization of okara by-products.\n\nPreparation and Characterization of Pickering Emulsions with Modified Okara Insoluble Dietary Fiber.", "token_count": 361, "char_count": 1450, "word_count": 196, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:56:59.328341", "source": { "split": "train_shard_00001", "doc_id": 446 }, "chunk_id": "train_shard_00001_446_0", "global_id": 6288 }, { "text": "

Background

Lignocellulosic biomass is an attractive, inexpensive source of potentially fermentable sugars. However, hydrolysis of lignocellulose results in a complex mixture containing microbial inhibitors at variable composition. A single microbial species is unable to detoxify or even tolerate these non-sugar components while converting the sugar mixtures effectively to a product of interest. Often multiple substrates are metabolized sequentially because of microbial regulatory mechanisms. To overcome these problems, we engineered strains of Acinetobacter baylyi ADP1 to comprise a consortium able to degrade benzoate and 4-hydroxybenzoate simultaneously under batch and continuous conditions in the presence of sugars. We furthermore used a thermotolerant yeast, Kluyveromyces marxianus, to convert the glucose remaining after detoxification to ethanol.

Results

The two engineered strains, one unable to metabolize benzoate and another unable to metabolize 4-hydroxybenzoate, when grown together removed these two inhibitors simultaneously under batch conditions. Under continuous conditions, a single strain with a deletion in the gcd gene metabolized both inhibitors in the presence of sugars. After this batch detoxification using ADP1-derived mutants, K. marxianus generated 36.6 g/L ethanol.

Conclusions

We demonstrated approaches for the simultaneous removal of two aromatic inhibitors from a simulated lignocellulosic hydrolysate. A two-stage batch process converted the residual sugar into a non-growth-associated product, ethanol. Such a two-stage process with bacteria (A. baylyi) and yeast (K. marxianus) is advantageous, because the yeast fermentation occurs at a higher temperature which prevents growth and ethanol consumption of A. baylyi. Conceptually, the process can be extended to other inhibitors or sugars found in real hydrolysates", "token_count": 514, "char_count": 1933, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": { "genes": [ "ADP1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:56:59.977615", "source": { "split": "train_shard_00001", "doc_id": 447 }, "chunk_id": "train_shard_00001_447_0", "global_id": 6289 }, { "text": "That is, additional strains which degrade components of lignocellulosic hydrolysates could be made substrate-selective and targeted for use with specific complex mixtures found in a hydrolysate.\n\nRemoval of aromatic inhibitors produced from lignocellulosic hydrolysates by Acinetobacter baylyi ADP1 with formation of ethanol by Kluyveromyces marxianus.", "token_count": 107, "char_count": 366, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [ "ADP1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:00.355767", "source": { "split": "train_shard_00001", "doc_id": 447 }, "chunk_id": "train_shard_00001_447_1", "global_id": 6290 }, { "text": "

ABSTRACT

The coding potential of the eukaryotic genome can be greatly expanded by the regulated use of mechanisms that generate more than one protein product from a gene. We combined techniques for mapping 5’ and 3’ ends of RNA transcripts with ribosome profiling to study the organisation of protein coding gene expression in the yeast Kluyveromyces marxianus . We uncovered over 1000 cases of novel proteoforms due to use of alternative transcription or translation start sites, identified 800 translated upstream open reading frames, observed surprising translation of antisense RNAs, and discovered a novel case of programmed ribosomal frameshifting. In some cases, features are conserved across yeast species, whereas others are species-specific. This offers new possibilities to explore the evolution of genomes and gene regulation in budding yeasts. Our analysis also enabled us to improve the genome annotation of K. marxianus by adding or correcting annotations of over 300 protein coding genes. The processed data has been made available on the GWIPS-viz and Trips-Viz browsers, thus providing an accurate data-driven annotation of transcripts and their protein coding regions along with quantitative information on their transcription and translation.\n\nTranscriptional and translational profiling in yeast reveals the use of diverse genome decoding mechanisms to generate functionally distinct proteoforms", "token_count": 319, "char_count": 1425, "word_count": 205, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:00.922352", "source": { "split": "train_shard_00001", "doc_id": 448 }, "chunk_id": "train_shard_00001_448_0", "global_id": 6291 }, { "text": "Enterococcus species are used as One Health indicators of antimicrobial resistance (AMR) in humans, animals, and the environment. A surveillance study in beef cows and calves isolated Enterococcus casseliflavus along with E. faecium, E. faecalis, and E. hirae. Given the high prevalence of E. casseliflavus, we elected to characterize this species to better understand its role in the antimicrobial resistance of enterococci in cows and calves. Almost 12% of E. casseliflavus isolates exhibited multidrug resistance with the majority being resistant to lincomycin (99%), followed by quinupristin-dalfopristin (34%), ciprofloxacin (9.6%), tylosin (4.5%), erythromycin (2.7%), tetracycline (1.8%), tigecycline (1.5%), daptomycin (0.6%), streptomycin (0.3%), and kanamycin (0.3%). All E. casseliflavus were susceptible to chloramphenicol, penicillin, streptomycin, nitrofurantoin, gentamicin, and linezolid. Whole genome antimicrobial resistance gene profiling identified vanC-type intrinsic vancomycin resistance genes in all E. casseliflavus, with the vanC4XYT gene cluster being dominant (67%) followed by vanC2XYT (31%) and vanC3XYT (1.5%). Resistance genes for erythromycin (ermB) and tetracycline (tetM) were rarely identified (2.1% and 1.2%, respectively) within E. casseliflavus genomes", "token_count": 519, "char_count": 1403, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6766, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:57:01.583256", "source": { "split": "train_shard_00001", "doc_id": 449 }, "chunk_id": "train_shard_00001_449_0", "global_id": 6292 }, { "text": "No resistance genes were identified to explain either the quinupristin-dalfopristin or ciprofloxacin resistance in these isolates. A core genome phylogenetic tree revealed two clades that exhibited no distinct association with the age of the host, time of sample collection, or the farm sampled. The open nature of the E. casseliflavus pan-genome highlighted its intraspecies diversity. These findings suggest that E. casseliflavus is likely a low-risk species in terms of contributing to antimicrobial resistance in the cow-calf sector.\n\nGenomic Characterization of <i>Enterococcus casseliflavus</i> Isolated from Beef Cows and Calves.", "token_count": 189, "char_count": 662, "word_count": 88, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:02.059567", "source": { "split": "train_shard_00001", "doc_id": 449 }, "chunk_id": "train_shard_00001_449_1", "global_id": 6293 }, { "text": "

Purpose

Fungal keratitis caused by Aspergillus flavus (A. flavus) can result in severe inflammation and corneal stromal melting, leading to visual impairment. This study aimed to identify virulent genes correlated with the severity of A. flavus keratitis using whole-genome sequencing.

Methods

Whole-genome sequencing of 21 clinical A. flavus strains from cornea was performed to elucidate the pathogenesis of A. flavus in infectious keratitis, followed by pan-genome analysis and virulence analysis. To further understand the results from the previous analyses, growth phenotypes and virulence effect of mutant strains were validated experimentally, including the spore counting, growth pattern under different conditions, and clinical and pathological evaluation of A. flavus keratitis in mice models.

Results

The A. flavus pan-genome was composed of 17,326 gene clusters with a core genome of 5378 (31.0% of the pan-genome) orthogroups in all 21 isolates. Virulence gene analysis revealed 183 genes contributing to A. flavus pathogenesis and mutation of the kexB gene was associated with the severity of keratitis. The kexB mutant (ΔkexB) strains showed significantly reduced conidia formation and lower growth rates in the presence of the cell-wall perturbing agents. Further, the mice models validated that clinical score, and corneal perforation rates significantly decreased in the group infected by ΔkexB strains. Infiltration of immune cells, gene expression of cytokines, and matrix metalloproteinase (MMP) were also decreased in the mutant group.

Conclusions

The role of kexB gene in A. flavus keratitis was identified through whole-genome sequencing. Its mutation impairs conidia formation, cell wall integrity, and invasion, leading to milder clinical symptoms.\n\nkexB Gene Correlates With Aspergillus flavus Keratitis Severity: A Whole-Genome Analysis.", "token_count": 511, "char_count": 1894, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5564, "quality_score": 0.7782, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:02.710941", "source": { "split": "train_shard_00001", "doc_id": 450 }, "chunk_id": "train_shard_00001_450_0", "global_id": 6294 }, { "text": "Clostridium perfringens causes a variety of human and animal enteric diseases including food poisoning, antibiotic-associated diarrhea, and necrotic enteritis. Yet, the reservoirs of enteropathogenic enterotoxin-producing strains remain unknown. We conducted a genomic comparison of 290 strains and a heat resistance phenotyping of 30 C. perfringens strains to elucidate the population structure and ecology of this pathogen. C. perfringens genomes shared a conserved genetic backbone with more than half of the genes of an average genome conserved in >95% of strains. The cpe-carrying isolates were found to share genetic context: the cpe-carrying plasmids had different distribution patterns within the genetic lineages and the estimated pan genome of cpe-carrying isolates had a larger core genome and a smaller accessory genome compared to that of 290 strains. We characterize cpe-negative strains related to chromosomal cpe-carrying strains elucidating the origin of these strains and disclose two distinct groups of chromosomal cpe-carrying strains with different virulence characteristics, spore heat resistance properties, and, presumably, ecological niche. Finally, an antibiotic-associated diarrhea isolate carrying two copies of the enterotoxin cpe gene and the associated genetic lineage with the potential for the emergence of similar strains are outlined. With C. perfringens as an example, implications of input genome quality for pan genome analysis are discussed. Our study furthers the understanding of genome epidemiology and population structure of enteropathogenic C. perfringens and brings new insight into this important pathogen and its reservoirs.", "token_count": 473, "char_count": 1756, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5905, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:03.836238", "source": { "split": "train_shard_00001", "doc_id": 451 }, "chunk_id": "train_shard_00001_451_0", "global_id": 6295 }, { "text": "Comparative Genome Analysis and Spore Heat Resistance Assay Reveal a New Component to Population Structure and Genome Epidemiology Within Clostridium perfringens Enterotoxin-Carrying Isolates.", "token_count": 56, "char_count": 199, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:04.206859", "source": { "split": "train_shard_00001", "doc_id": 451 }, "chunk_id": "train_shard_00001_451_1", "global_id": 6296 }, { "text": "Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis, posing increasing public health challenges globally. We conducted a large-scale molecular epidemiological analysis of 7932 clinical isolates collected from seafood-associated diarrheal patients in 69 sentinel hospitals across 11 prefecture-level cities in Zhejiang Province between 2016 and 2023. Whole-genome sequencing (WGS) was performed on 1261 representative isolates, supplemented by 11,555 publicly available genomes. We analyzed temporal serotype dynamics, antimicrobial resistance genes (ARGs), virulence factors, and pangenomic diversity, with an emphasis on the globally prevalent ST3 lineage. Notably, the O10:K4 serotype emerged as the second most common within ST3, increasing in prevalence from 40.0 % to 65.6 % over the study period. O10:K4 isolates exhibited a significantly higher frequency of tdh (96.3 % vs. 78.2 %) and complete T3SS2 effector gene clusters. Nearly all isolates harbored tet(35) and blaCARB₋₂₂, indicating widespread resistance. Comparative pangenome analysis revealed O10:K4-specific acquisitions in chemotaxis and LPS synthesis (e.g., per, mcpQ, fcl) and loss of key polyamine metabolism genes (aguA, puu operon). These findings suggest that the emergence and clonal expansion of the O10:K4 serotype represent a significant epidemiological shift characterized by enhanced virulence and multidrug resistance. Sustained genomic surveillance is imperative to guide seafood safety management and clinical interventions.\n\nEmergence and genomic characterization of Vibrio parahaemolyticus serotype O10:K4 from seafood-linked diarrheal cases in Zhejiang, China (2016–2023)", "token_count": 478, "char_count": 1686, "word_count": 219, "semantic_coherence": 1, "information_density": 0.7443, "quality_score": 0.8721, "entities": { "genes": [ "ST3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:04.850323", "source": { "split": "train_shard_00001", "doc_id": 452 }, "chunk_id": "train_shard_00001_452_0", "global_id": 6297 }, { "text": "Mannheimia haemolytica is an opportunistic bacterial pathogen associated with the economically costly bovine respiratory disease. Two genotypes have been described, of which genotype 2 is more strongly associated with disease. Several previous studies have investigated the genomic differences between the genotypes and/or the major serotypes (1, 2 and 6) of M. haemolytica , however we still lack a clear basis for the greater disease association of genotype 2 (serotypes 1 and 6) and demonstrations of phenotypic differences are scarce. This work builds upon previous investigations to identify genes that differentiate the two genotypes with a particular focus on genes that may play a role in virulence and fitness in the respiratory tract microbiome. We identified 422 genotype differentiating genes in a collection of 206 unique M. haemolytica genomes (61 genotype 1, 145 genotype 2). Genotype differentiating genes included genotype-associated variants of a TonB-dependent siderophore receptor homolog, transferrin binding protein B, leukotoxin A, and IgA1 proteases. We also identified a genotype 1 associated lytic transglycosylase, and a genotype 2 specific highly immunogenic outer membrane lipoprotein. Genotype 2 genomes were significantly larger in size and contained more predicted protein coding genes than genotype 1 genomes. These results expand our knowledge of what differentiates the genotypes 1 and 2 of M. haemolytica and provides information that can be used as the basis for laboratory investigations of corresponding phenotypic differences.\n\nIdentification of genes that differentiate Mannheimia haemolytica genotypes 1 and 2 using a pangenome approach", "token_count": 425, "char_count": 1685, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6017, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:05.475547", "source": { "split": "train_shard_00001", "doc_id": 453 }, "chunk_id": "train_shard_00001_453_0", "global_id": 6298 }, { "text": "

Background

Shewanella xiamenensis, widely distributed in natural environments, has long been considered as opportunistic pathogen. Recently, significant changes in the resistance spectrum have been observed in S. xiamenensis, due to acquired antibiotic resistance genes. Therefore, a pan-genome analysis was conducted to illuminate the genomic changes in S. xiamenensis.

Results

Phylogenetic analysis revealed three major clusters and three singletons, among which close relationship between several strains was discovered, regardless of their host and niches. The \"open\" genomes with diversity of accessory and strain-specific genomes took advantage towards diversity environments. The purifying selection pressure was the main force on genome evolution, especially in conservative genes. Only 53 gene families were under positive selection pressure. Phenotypic resistance analysis revealed 21 strains were classified as multi-drug resistance (MDR). Ten types of antibiotic resistance genes and two heavy metal resistance operons were discovered in S. xiamenensis. Mobile genetic elements and horizontal gene transfer increased genome diversity and were closely related to MDR strains. S. xiamenensis carried a variety of virulence genes and macromolecular secretion systems, indicating their important roles in pathogenicity and adaptability. Type IV secretion system was discovered in 15 genomes with various sequence structures, indicating it was originated from different donors through horizontal gene transfer.

Conclusions

This study provided with a detailed insight into the changes in the pan-genome of S. xiamenensis, highlighting its capability to acquire new mobile genetic elements and resistance genes for its adaptation to environment and pathogenicity to human and animals.\n\nPangenome analysis of Shewanella xiamenensis revealed important genetic traits concerning genetic diversity, pathogenicity and antibiotic resistance.", "token_count": 413, "char_count": 1962, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6126, "quality_score": 0.8063, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:06.095625", "source": { "split": "train_shard_00001", "doc_id": 454 }, "chunk_id": "train_shard_00001_454_0", "global_id": 6299 }, { "text": "

Background

With the exponential growth of publicly available genome sequences, pangenome analyses have provided increasingly complete pictures of genetic diversity for many microbial species. However, relatively few studies have scaled beyond single pangenomes to compare global genetic diversity both within and across different species. We present here several methods for \"comparative pangenomics\" that can be used to contextualize multi-pangenome scale genetic diversity with gene function for multiple species at multiple resolutions: pangenome shape, genes, sequence variants, and positions within variants.

Results

Applied to 12,676 genomes across 12 microbial pathogenic species, we observed several shared resolution-specific patterns of genetic diversity: First, pangenome openness is associated with species' phylogenetic placement. Second, relationships between gene function and frequency are conserved across species, with core genomes enriched for metabolic and ribosomal genes and accessory genomes for trafficking, secretion, and defense-associated genes. Third, genes in core genomes with the highest sequence diversity are functionally diverse. Finally, certain protein domains are consistently mutation enriched across multiple species, especially among aminoacyl-tRNA synthetases where the extent of a domain's mutation enrichment is strongly function-dependent.

Conclusions

These results illustrate the value of each resolution at uncovering distinct aspects in the relationship between genetic and functional diversity across multiple species. With the continued growth of the number of sequenced genomes, these methods will reveal additional universal patterns of genetic diversity at the pangenome scale.\n\nComparative pangenomics: analysis of 12 microbial pathogen pangenomes reveals conserved global structures of genetic and functional diversity.", "token_count": 402, "char_count": 1895, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6229, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:07.434839", "source": { "split": "train_shard_00001", "doc_id": 455 }, "chunk_id": "train_shard_00001_455_0", "global_id": 6300 }, { "text": "Oryza rufipogon, the wild progenitor of Asian cultivated rice Oryza sativa, is an important resource for rice breeding1. Here we present a wild-cultivated rice pangenome based on 145 chromosome-level assemblies, comprising 129 genetically diverse O. rufipogon accessions and 16 diverse varieties of O. sativa. This pangenome contains 3.87 Gb of sequences that are absent from the O. sativa ssp. japonica cv. Nipponbare reference genome. We captured alternate assemblies that include heterozygous information missing in the primary assemblies, and identified a total of 69,531 pan-genes, with 28,907 core genes and 13,728 wild-rice-specific genes. We observed a higher abundance and a significantly greater diversity of resistance-gene analogues in wild rice than in cultivars. Our analysis indicates that two cultivated subpopulations, intro-indica and basmati, were generated through gene flows among cultivars in South Asia. We also provide strong evidence to support the theory that the initial domestication of all Asian cultivated rice occurred only once. Furthermore, we captured 855,122 differentiated single-nucleotide polymorphisms and 13,853 differentiated presence-absence variations between indica and japonica, which could be traced to the divergence of their respective ancestors and the existence of a larger genetic bottleneck in japonica. This study provides reference resources for enhancing rice breeding, and enriches our understanding of the origins and domestication process of rice.\n\nA pangenome reference of wild and cultivated rice.", "token_count": 408, "char_count": 1568, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6743, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:08.054891", "source": { "split": "train_shard_00001", "doc_id": 456 }, "chunk_id": "train_shard_00001_456_0", "global_id": 6301 }, { "text": "

Introduction

Most SV studies in livestock rely on short-read sequencing, posing challenges in accurately characterizing large genomic variants due to their limited read length.

Objectives

Our goal is to reveal structural variation and novel sequences specific to Holstein and Jersey cattle breeds using long-read and pan-genome analyses.

Methods

We sequenced 20 Holsteins and 8 Jersey cattle using PacBio HiFi to 20×, and integrated five read-based and one assembly-based SV caller to determine SVs.

Results

We assembled the 28 genomes averaging 3.25 Gb with a contig N50 of 69.36 Mb and using the ARS-UCD1.2 reference, we acquired Holstein/Jersey SV catalogs with 74,068/54,689 events spanning 202/135 Mb (7.43 %/4.97 % of the genome). SVs were enriched in less conserved, non-coding, and non-regulatory regions. Comparing Holsteins with differing feed efficiency (FE), SVs unique to high FE were linked to energy metabolism and olfactory receptors, while those specific to low FE were associated with material transport. We constructed Holstein/Jersey pangenome graphs with 148,598/105,875 nodes and 208,891/147,990 edges, representing 47,028/37,137 biallelic and multi-allelic events, and 63.75/42.34 Mb of novel sequence. We observed SV count saturation with 20 Holsteins, while adding Jerseys significantly increased the SV count, highlighting breed-specific SV events.

Conclusion

Our long-read data and SV catalogs are valuable resources, revealing that the cattle genome is more complex than previously thought.", "token_count": 494, "char_count": 1554, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7101, "quality_score": 0.8551, "entities": { "genes": [ "UCD1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:08.708252", "source": { "split": "train_shard_00001", "doc_id": 457 }, "chunk_id": "train_shard_00001_457_0", "global_id": 6302 }, { "text": "Long read and preliminary pangenome analyses reveal breed-specific structural variations and novel sequences in Holstein and Jersey cattle.", "token_count": 26, "char_count": 139, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:09.062907", "source": { "split": "train_shard_00001", "doc_id": 457 }, "chunk_id": "train_shard_00001_457_1", "global_id": 6303 }, { "text": "Methanogens are strictly anaerobic archaea capable of energy conservation by methane production, yet their presence in oxic and arid environments challenges existing paradigms. In this study, we enriched and genomically characterised seven methanogenic cultures from desert biocrusts, affiliated with the genera Methanobacterium , Methanosarcina , and Methanocella . Six of these new cultures represent new species. Nonetheless, phylogenomic analyses revealed close genetic relationships with organisms from anoxic environments, indicating the absence of an evolutionary distinction. Comparative genomics exposed diverse though non-unique repertories of antioxidant (e.g. catalase, superoxide dismutase and desulfoferrodoxin), and desiccation-resistance genes (including genes for maintaining osmotic pressure and repair of cell wall and membrane), with Methanobacterium spp. possessing the lowest gene abundance and diversity for oxygen and desiccation tolerance. Nevertheless, the occurrence of a Class I methanogen such as Methanobacterium in arid soils challenges the notion that members of this class are less oxygen tolerant than Class II. Pangenome analysis further uncovered unique genes enriched in membrane-associated functions and potentially non-functional stress-related genes. Via a global metagenomic survey, we find that methanogens are underdetected in dryland soils, likely due to sequencing depth limitations. Our findings highlight previously overlooked methanogen diversity and ecological plasticity in oxic and desiccated habitats, and emphasise the need for further studies to elucidate their survival strategies.\n\nCultivation and genomic characterisation of novel methanogens from a desert biocrust", "token_count": 397, "char_count": 1722, "word_count": 223, "semantic_coherence": 1, "information_density": 0.7085, "quality_score": 0.8543, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:09.676503", "source": { "split": "train_shard_00001", "doc_id": 458 }, "chunk_id": "train_shard_00001_458_0", "global_id": 6304 }, { "text": "Vibrio cholerae remains a major public health threat worldwide, causing millions of cholera cases each year. Although much is known about the evolution and pathogenicity of the O1/O139 serogroups of V. cholerae, information is lacking on the molecular epidemiology of non‒O1/O139 strains isolated from patients who have diarrheal illnesses. We performed whole-genome sequence analysis and in vivo infections to investigate characteristics of V. cholerae O141 isolated from sporadic diarrheal cases in 4 countries. The strains formed a distinct phylogenetic clade distinguishable from other serogroups and a unique multilocus sequence type 42, but interstrain variation suggests that O141 isolates are not clonal. These isolates encode virulence factors including cholera toxin and the toxin-coregulated pilus, as well as a type 3 secretion system. They had widely variable capacities for intestinal colonization in the infant mouse model. We propose that O141 isolates comprise a distinct clade of V. cholerae non‒O1/O139, and their continued surveillance is warranted.\n\nGenomic and Phenotypic Insights for Toxigenic Clinical Vibrio cholerae O141.", "token_count": 310, "char_count": 1147, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6994, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:10.251262", "source": { "split": "train_shard_00001", "doc_id": 459 }, "chunk_id": "train_shard_00001_459_0", "global_id": 6305 }, { "text": "

Aim

This study was designed to isolate and identify yeast species from milk and meat products, and to test their antimicrobial activity against some bacterial species.

Materials and methods

A total of 160 milk and meat products samples were collected from random sellers and super markets in New Damietta city, Damietta, Egypt. Samples were subjected to yeast isolation procedures and tested for its antimicrobial activity against Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli. In addition, all yeast species isolates were subjected to polymerase chain reaction (PCR) for detection of khs (kievitone hydratase) and pelA (pectate degrading enzyme)genes.

Results

The recovery rate of yeasts from sausage was 20% (2/10) followed by kareish cheese, processed cheese, and butter 10% (1/10) each as well as raw milk 9% (9/100), and fruit yoghurt 30% (6/20). Different yeast species were recovered, namely, Candida kefyr (5 isolates), Saccharomyces cerevisiae (4 isolates), Candida intermedia (3 isolates), Candida tropicalis (2 isolates), Candida lusitaniae (2 isolates), and Candida krusei (1 isolate). khs gene was detected in all S. cerevisiae isolates, however, pelA gene was not detected in all identified yeast species. Antimicrobial activity of recovered yeasts against the selected bacterial species showed high activity with C. intermedia against S. aureus and E", "token_count": 511, "char_count": 1524, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:10.911964", "source": { "split": "train_shard_00001", "doc_id": 460 }, "chunk_id": "train_shard_00001_460_0", "global_id": 6306 }, { "text": "coli, C. kefyr against E. coli, and C. lusitaniae against S. aureus. Moderate activities were obtained with C. tropicalis, C. lusitaniae, and S. cerevisiae against E. coli; meanwhile, all the tested yeasts revealed a very low antimicrobial activity against P. aeruginosa.

Conclusion

The obtained results confirmed that some kinds of yeasts have the ability to produce antimicrobial compounds that could inhibit some pathogenic and spoilage bacteria and these antimicrobial activity of yeasts enables them to be one of the novel agents in controlling spoilage of food.\n\nAntimicrobial activity of yeasts against some pathogenic bacteria.", "token_count": 228, "char_count": 709, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:11.380331", "source": { "split": "train_shard_00001", "doc_id": 460 }, "chunk_id": "train_shard_00001_460_1", "global_id": 6307 }, { "text": "

Motivation

With more and more telomere-to-telomere genomes assembled, pangenomes make it possible to capture the genomic diversity of a species. Because they introduce less biases, pangenomes, represented as graphs, tend to supplant the usual linear representation of a reference genome, augmented with variations. However, this major change requires new tools adapted to this data structure. Among the numerous questions that can be addressed to a pangenome graph is the search for conserved or divergent genes.

Results

In this article, we present a new tool, named PanSel, which computes a conservation score for each segment of the genome, and finds genomic regions that are significantly conserved, or divergent. PanSel can be used on prokaryotes and eukaryotes, with a sequence identity not less than 98%.

Availability and implementation

PanSel, written in C++11 with no dependency, is available at https://github.com/mzytnicki/pansel.\n\nAssessing genome conservation on pangenome graphs with PanSel.", "token_count": 262, "char_count": 1026, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7429, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:11.932946", "source": { "split": "train_shard_00001", "doc_id": 461 }, "chunk_id": "train_shard_00001_461_0", "global_id": 6308 }, { "text": "

Background

The opportunistic bacterium Escherichia coli can invade normally sterile sites in the human body, potentially leading to life-threatening organ dysfunction and even death. However, our understanding of the evolutionary processes that shape its genetic diversity in this sterile environment remains limited. Here, we aim to quantify the frequency and characteristics of homologous recombination in E. coli from bloodstream infections.

Results

Analysis of 557 short-read genome sequences revealed that the propensity to exchange DNA by homologous recombination varies within a distinct population (bloodstream) at narrow geographic (Dartmouth Hitchcock Medical Center, New Hampshire, USA) and temporal (years 2016 - 2022) scope. We identified the four largest monophyletic sequence clusters in the core genome phylogeny that are represented by prominent sequence types (ST): BAPS1 (mainly ST95), BAPS4 (mainly ST73), BAPS10 (mainly ST131), BAPS14 (mainly ST58). We show that the four dominant clusters vary in different characteristics of recombination: number of single nucleotide polymorphisms due to recombination, number of recombination blocks, cumulative bases in recombination blocks, ratio of probabilities that a given site was altered through recombination and mutation (r/m), and ratio of rates at which recombination and mutation occurred (ρ/θ). Each sequence cluster contains a unique set of antimicrobial resistance (AMR) and virulence genes that have experienced recombination. Common among the four sequence clusters were the recombined virulence genes with functions associated with the Curli secretion channel (csgG) and ferric enterobactin transport (entEF, fepEG). We did not identify any one recombined AMR gene that was present in all four sequence clusters. However, AMR genes mdtABC, baeSR, emrKY and tolC had experienced recombination in sequence clusters BAPS4, BAPS10, and BAPS14", "token_count": 495, "char_count": 1930, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "ST131", "BAPS10", "ST73", "BAPS1", "ST95", "BAPS4", "ST58", "BAPS14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:12.594508", "source": { "split": "train_shard_00001", "doc_id": 462 }, "chunk_id": "train_shard_00001_462_0", "global_id": 6309 }, { "text": "These differences lie in part on the contributions of vertically inherited ancestral recombination and contemporary branch-specific recombination, with some genomes having relatively higher proportions of recombined DNA.

Conclusions

Our results highlight the variation in the propensity to exchange DNA via homologous recombination within a distinct population at narrow geographic and temporal ranges. Understanding the sources of the genetic variation in invasive E. coli will help inform the implementation of effective strategies to reduce the burden of disease and AMR.\n\nLineage-specific variation in frequency and hotspots of recombination in invasive Escherichia coli.", "token_count": 144, "char_count": 682, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7303, "quality_score": 0.8652, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:13.028179", "source": { "split": "train_shard_00001", "doc_id": 462 }, "chunk_id": "train_shard_00001_462_1", "global_id": 6310 }, { "text": "

Motivation

Pangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGenome Graph Builder (PGGB) addresses these issues. To date, though, there is no state-of-the-art pipeline allowing for easy deployment, efficient and dynamic use of available resources, and scalable usage at the same time.

Results

To overcome these limitations, we present nf-core/pangenome, a reference-unbiased approach implemented in Nextflow following nf-core's best practices. Leveraging biocontainers ensures portability and seamless deployment in High-Performance Computing (HPC) environments. Unlike PGGB, nf-core/pangenome distributes alignments across cluster nodes, enabling scalability. Demonstrating its efficiency, we constructed pangenome graphs for 1000 human chromosome 19 haplotypes and 2146 Escherichia coli sequences, achieving a two to threefold speedup compared to PGGB without increasing greenhouse gas emissions.

Availability and implementation

nf-core/pangenome is released under the MIT open-source license, available on GitHub and Zenodo, with documentation accessible at https://nf-co.re/pangenome/docs/usage.\n\nCluster-efficient pangenome graph construction with nf-core/pangenome.", "token_count": 340, "char_count": 1367, "word_count": 156, "semantic_coherence": 1, "information_density": 0.8269, "quality_score": 0.9135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:13.598192", "source": { "split": "train_shard_00001", "doc_id": 463 }, "chunk_id": "train_shard_00001_463_0", "global_id": 6311 }, { "text": "Tea plants, one of the world's most economically significant beverage crops, exhibit extensive genetic diversity and a rich array of secondary metabolites. While structural variations (SVs) are key drivers of phenotypic innovation, their regulatory roles in transcriptional networks and agronomic trait diversification remain underexplored in this perennial crop. We constructed a pangenome from 21 representative tea accessions and their wild relatives. Comparative analysis revealed that wild relatives harbor a greater abundance of gibberellin-related genes, whereas cultivated accessions exhibit an expansion of defense-related genes. We identified 522,428 non-redundant SVs, primarily insertions/deletions (73.56%), which were enriched in promoter regions. These SVs influenced the expression of genes governing flavor compounds, including those involved in flavonoid, amino acid, and terpenoid biosynthesis. Population SV analysis of 275 tea accessions uncovered three haplotypes in the ANS3 gene promoter region, with Hap1, containing a 192 bp insertion, predominantly found in wild relatives but largely lost in modern cultivars. This insertion enhanced CtANS3 expression, increasing anthocyanin accumulation. Additionally, a 159 bp insertion in the CtLRR1 promoter reduced resistance to Colletotrichum gloeosporioides in wild relatives. Our findings underscore SVs as pivotal regulators of genomic diversity, flavor differentiation, and adaptive evolution in tea plant domestication.\n\nPangenome analyses of tea plant reveal structural variations driven gene expression alterations and agronomic trait diversification", "token_count": 382, "char_count": 1625, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7156, "quality_score": 0.8578, "entities": { "genes": [ "ANS3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:14.206887", "source": { "split": "train_shard_00001", "doc_id": 464 }, "chunk_id": "train_shard_00001_464_0", "global_id": 6312 }, { "text": "The global emergence of extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-E. coli), mainly causing urinary tract infections (UTI), is a major threat to human health. ESBL-E. coli sequence type (ST) 131 is the dominating clone worldwide, especially its subclade C2. Patients developing recurrent UTI (RUTI) due to ST131 subclade C2 appear to have an increased risk of recurrent infections. We have thus compared the whole genome of ST131 subclade C2 isolates from 14 patients with RUTI to those from 14 patients with sporadic UTI (SUTI). We aimed to elucidate if isolates causing RUTI can be associated with specific genomic features. Paired isolates from patients with RUTI were identical, presenting 2-18 single nucleotide polymorphism (SNP) differences for all six patients investigated. Comparative genomic analyses, including virulence factors, antibiotic resistance, pangenome and SNP analyses did not find any pattern associated with isolates causing RUTI. Despite extensive whole genome analyses, an increased risk of recurrences seen in patients with UTI due to ST131 subclade C2 isolates could not be explained by bacterial genetic differences in the two groups of isolates. Hence, additional factors that could aid in identifying bacterial properties contributing to the increased risk of RUTI due to ESBL-E. coli ST131 subclade C2 remains to be explored.\n\nComparative Genomic Analysis of ST131 Subclade C2 of ESBL-Producing E. coli Isolates from Patients with Recurrent and Sporadic Urinary Tract Infections.", "token_count": 442, "char_count": 1570, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:14.859198", "source": { "split": "train_shard_00001", "doc_id": 465 }, "chunk_id": "train_shard_00001_465_0", "global_id": 6313 }, { "text": "The study aimed to explore the effects of fortified fermented rice-acid on the antioxidant capacity of mouse serum and the gut microbiota. Hair characteristics, body mass index, intestinal villus height, intestinal crypt depth, serum antioxidant capacity, and gut microbiota of mice were first measured and the correlation between the antioxidant capacity of mouse serum and the gut microbiota was then explored. The mice in the lactic acid bacteria group (L-group), the mixed bacteria group (LY-group), and the rice soup group (R-group) kept their weight well and had better digestion. The mice in the L-group had the better hair quality (dense), but the hair quality in the R-group and the yeast group (Y-group) was relatively poor (sparse). In addition, the inoculation of Lactobacillus paracasei H4-11 (L. paracasei H4-11) and Kluyveromyces marxianus L1-1 (K. marxianus L1-1) increased the villus height/crypt depth of the mice (3.043 ± 0.406) compared to the non-inoculation group (R-group) (2.258 ± 0.248). The inoculation of L. paracasei H4-11 and K. marxianus L1-1 in fermented rice-acid enhanced the blood antioxidant capacity of mouse serum (glutathione 29.503 ± 6.604 umol/L, malonaldehyde 0.687 ± 0.125 mmol/L, catalase 15.644 ± 4.618 U/mL, superoxide dismutase 2.292 ± 0.201 U/mL)", "token_count": 482, "char_count": 1335, "word_count": 196, "semantic_coherence": 1, "information_density": 0.5612, "quality_score": 0.7806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:15.540512", "source": { "split": "train_shard_00001", "doc_id": 466 }, "chunk_id": "train_shard_00001_466_0", "global_id": 6314 }, { "text": "In the gut microbiota of L-group and LY-group, beneficial microorganisms (Lactobacillus and Blautia) increased, but harmful microorganisms (Candidatus Arthromitus and Erysipelotrichales) decreased. L. paracasei H4-11 and K. marxianus L1-1 might have a certain synergistic effect on the improvement in antibacterial function since they reduced harmful microorganisms in the gut microbiota of mice. The study provides the basis for the development of fortified fermented rice-acid products for regulating the gut microbiota and improving the antioxidant capacity.\n\nFortified Fermented Rice-Acid Can Regulate the Gut Microbiota in Mice and Improve the Antioxidant Capacity.", "token_count": 222, "char_count": 712, "word_count": 90, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:16.041794", "source": { "split": "train_shard_00001", "doc_id": 466 }, "chunk_id": "train_shard_00001_466_1", "global_id": 6315 }, { "text": "Nearly 50 years after the ground-breaking isolation of the primary Comptonia peregrina microsymbiont under axenic conditions, efforts to isolate a substantial number of Protofrankia and Frankia strains continue with enduring challenges and complexities. This study aimed to streamline genomic insights through comparative and predictive tools to extract traits crucial for isolating specific Frankia in axenic conditions. Pangenome analysis unveiled significant genetic diversity, suggesting untapped potential for cultivation strategies. Shared metabolic strategies in cellular components, central metabolic pathways, and resource acquisition traits offered promising avenues for cultivation. Ecological trait extraction indicated that most uncultured strains exhibit no apparent barriers to axenic growth. Despite ongoing challenges, potential caveats, and errors that could bias predictive analyses, this study provides a nuanced perspective. It highlights potential breakthroughs and guides refined cultivation strategies for these yet-uncultured strains. We advocate for tailored media formulations enriched with simple carbon sources in aerobic environments, with atmospheric nitrogen optionally sufficient to minimize contamination risks. Temperature adjustments should align with strain preferences-28-29°C for Frankia and 32-35°C for Protofrankia-while maintaining an alkaline pH. Given potential extended incubation periods (predicted doubling times ranging from 3.26 to 9.60 days, possibly up to 21.98 days), patience and rigorous contamination monitoring are crucial for optimizing cultivation conditions.\n\nMAGs-centric crack: how long will, spore-positive Frankia and most Protofrankia, microsymbionts remain recalcitrant to axenic growth?", "token_count": 452, "char_count": 1808, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7569, "quality_score": 0.8784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:16.677419", "source": { "split": "train_shard_00001", "doc_id": 467 }, "chunk_id": "train_shard_00001_467_0", "global_id": 6316 }, { "text": "

Aims

The antifungal effect of the yeast species Kluyveromyces marxianus, Meyerozyma caribbica, and Wickerhamomyces anomalus was evaluated against two Fusarium graminearum strains (FRS 26 and FSP 27) in vitro and on corn seeds.

Methods and results

The antifungal effect of the yeasts against F. graminearum was evaluated using scanning electron microscopy and extracellular chitinase and glucanase production to further elucidate the biocontrol mode of action. In addition, the germination percentage and vigor test were investigated after applying yeast on corn seeds. All the yeast strains inhibited fungal growth in vitro (57.4%-100.0%) and on corn seeds (18.9%-87.2%). In co-culture with antagonistic yeasts, F. graminearum showed collapsed hyphae and turgidity loss, which could be related to the ability of yeasts to produce chitinases and glucanases. The three yeasts did not affect the seed corn germination, and W. anomalus and M. caribbica increased corn seed growth parameters (germination percentage, shoot and root length, and shoot dry weight).

Conclusion

Meyerozyma caribbica and W. anomalus showed satisfactory F. graminearum growth inhibition rates and did not affect seed growth parameters. Further studies are required to evaluate the application of these yeasts to the crop in the field.\n\nPotential of yeasts as biocontrol agents against Fusarium graminearum in vitro and on corn.", "token_count": 406, "char_count": 1421, "word_count": 200, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:17.308210", "source": { "split": "train_shard_00001", "doc_id": 468 }, "chunk_id": "train_shard_00001_468_0", "global_id": 6317 }, { "text": "Mycobacterium avium subsp. paratuberculosis (MAP) is the aetiological agent of paratuberculosis (Johne's disease) in both domestic and wild ruminants. In the present study, using a whole-genome sequence (WGS) approach, we investigated the genetic diversity of 15 Mycobacterium avium field strains isolated in the last 10 years from red deer inhabiting the Stelvio National Park and affected by paratuberculosis. Combining de novo assembly and a reference-based method, followed by a pangenome analysis, we highlight a very close relationship among 13 MAP field isolates, suggesting that a single infecting event occurred in this population. Moreover, two isolates have been classified as Mycobacterium avium subsp. hominissuis, distinct from the other MAPs under comparison but close to each other. This is the first time that this subspecies has been found in Italy in samples without evident epidemiological correlations, having been isolated in two different locations of the Stelvio National Park and in different years. Our study highlights the importance of a multidisciplinary approach incorporating molecular epidemiology and ecology into traditional infectious disease knowledge in order to investigate the nature of infectious disease in wildlife populations.\n\nHigh clonality of Mycobacterium avium subsp. paratuberculosis field isolates from red deer revealed by two different methodological approaches of comparative genomic analysis.", "token_count": 381, "char_count": 1502, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:17.890853", "source": { "split": "train_shard_00001", "doc_id": 469 }, "chunk_id": "train_shard_00001_469_0", "global_id": 6318 }, { "text": "Benzo[a]pyrene (B[a]P) is a five-ring polycyclic aromatic hydrocarbon (PAH) recognized as a potent carcinogen and persistent environmental pollutant, highly resistant to microbial degradation. In this study, a B[a]P-degrading and biosurfactant producing bacterium, Bacillus altitudinis AR19 , was isolated from the Digboi oil refinery site in Assam, India. The isolate was screened using the spray plate technique, and its morphological features and cell viability were examined by scanning electron microscopy (SEM) and flow cytometry. Biosurfactant production was confirmed through drop collapse, oil spreading, and emulsification assays. Taxonomic identity was established using average nucleotide identity (ANI), and comparative pangenome analysis was performed among B. altitudinis (Taxonomy ID: 1178544), Bacillus pumilus (Taxonomy ID: 1408), Mycolicibacterium vanbaalenii (Taxonomy ID: 110539), and B. altitudinis AR19. The results highlight that several mechanisms including osmolyte accumulation, biosurfactant production, and mechanosensitive ion channels play key roles in enabling B. altitudinis AR19 to tolerate and degrade B[a]P. This study demonstrates the potential of B. altitudinis AR19 as a promising candidate for bioremediation of PAH-contaminated environments.

Importance of the work

This manuscript describes the morphological and genomic characterization of Bacillus altitudinis AR19, a bacterium capable of degrading benzo[a]pyrene. Benzo[a]pyrene is a five-ring polycyclic aromatic hydrocarbon that is highly recalcitrant to bacterial remediation, making this work important for advancing bioremediation strategies.\n\nBenzo[a]pyrene degrading Bacillus altitudinis AR19 isolated from Digboi oil refinery soil (India)", "token_count": 498, "char_count": 1757, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [ "AR19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:18.540836", "source": { "split": "train_shard_00001", "doc_id": 470 }, "chunk_id": "train_shard_00001_470_0", "global_id": 6319 }, { "text": "Adverse environmental conditions are severely limiting the use of microorganisms in food systems, such as probiotic delivery, where low pH causes a rapid decrease in the survival of ingested bacteria, and mixed-culture fermentation, where stepwise changes and/or metabolites of individual microbial groups can hinder overall growth and production. In our study, model probiotic lactic acid bacteria (L. plantarum ATCC 8014, L. rhamnosus GG) and yeasts native to dairy mixed cultures (K. marxianus ZIM 1868) were entrapped in an optimized (cell, alginate and hardening solution concentration, electrostatic working parameters) Ca-alginate system. Encapsulated cultures were examined for short-term survival in the absence of nutrients (lactic acid bacteria) and long-term performance in acidified conditions (yeasts). In particular, the use of encapsulated yeasts in these conditions has not been previously examined. Electrostatic manufacturing allowed for the preparation of well-defined alginate microbeads (180-260 µm diameter), high cell-entrapment (95%) and viability (90%), and uniform distribution of the encapsulated cells throughout the hydrogel matrix. The entrapped L. plantarum maintained improved viabilities during 180 min at pH 2.0 (19% higher when compared to the free culture), whereas, L. rhamnosus appeared to be less robust. The encapsulated K. marxianus exhibited double product yields in lactose- and lactic acid-modified MRS growth media (compared to an unfavorable growth environment for freely suspended cells). Even within a conventional encapsulation system, the pH responsive features of alginate provided superior protection and production of encapsulated yeasts, allowing several applications in lacto-fermented or acidified growth environments, further options for process optimization, and novel carrier design strategies based on inhibitor charge expulsion.\n\nPolysaccharide Hydrogels for the Protection of Dairy-Related Microorganisms in Adverse Environmental Conditions.", "token_count": 509, "char_count": 2046, "word_count": 268, "semantic_coherence": 1, "information_density": 0.694, "quality_score": 0.847, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:19.195886", "source": { "split": "train_shard_00001", "doc_id": 471 }, "chunk_id": "train_shard_00001_471_0", "global_id": 6320 }, { "text": "

ABSTRACT

The vaginal microbiome plays a central role in reproductive health. Vaginal microbiome dysbiosis increases risk of many adverse reproductive health outcomes, but most studies have focused on associations at the species level. The potential contribution of intraspecies microbial variation, especially gene content differences across bacterial strains, remains underexplored in reproductive health contexts. The Metagenomic Intra-Species Diversity Analysis (MIDAS) framework enables such analyses but depends on comprehensive reference databases. We constructed a MIDAS-compatible pangenome database from over 18,000 genomes in the Vaginal Microbiome Genome Collection (VMGC). Compared to the Genome Taxonomy Database (GTDB)-derived reference, the VMGC database expanded pangenomes of prevalent vaginal species, better capturing vaginal-specific intraspecies diversity. Applying this database to a cervical dysplasia cohort, we identified thirteen Lactobacillus crispatus accessory genes significantly associated with increased risk of cervical dysplasia, including a HicAB toxin-antitoxin system, three transcriptional regulators, and three phage-derived genes. These findings highlight the utility of body site-specific reference resources for uncovering intraspecies microbial variation relevant to reproductive health.\n\nExpanding vaginal microbiome pangenomes via a custom MIDAS database reveals Lactobacillus crispatus accessory genes associated with cervical dysplasia", "token_count": 366, "char_count": 1499, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7056, "quality_score": 0.8528, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:19.778523", "source": { "split": "train_shard_00001", "doc_id": 472 }, "chunk_id": "train_shard_00001_472_0", "global_id": 6321 }, { "text": "Potato (Solanum sp., family Solanaceae) is the most important noncereal food crop globally. It has over 100 wild relatives in the Solanum section Petota, which features species with both sexual and asexual reproduction and varying ploidy levels. A pangenome of Solanum section Petota composed of 296 accessions was constructed including diploids and polyploids compared via presence/absence variation (PAV). The Petota core (genes shared by at least 97% of the accessions) and shell genomes (shared by 3 to 97%) are enriched in basic molecular and cellular functions, while the cloud genome (genes present in less than 3% of the member accessions) showed enrichment in transposable elements (TEs). Comparison of PAV in domesticated vs. wild accessions was made, and a phylogenetic tree was constructed based on PAVs, grouping accessions into different clades, similar to previous phylogenies produced using DNA markers. A cladewise pangenome approach identified abiotic stress response among the core genes in clade 1+2 and clade 3, and flowering/tuberization among the core genes in clade 4. The TE content differed between the clades, with clade 1+2, which is composed of species from North and Central America with reproductive isolation from species in other clades, having much lower TE content compared to other clades. In contrast, accessions with in vitro propagation history were identified and found to have high levels of TEs. Results indicate a role for TEs in adaptation to new environments, both natural and artificial, for Solanum section Petota.\n\nPangenome analyses reveal impact of transposable elements and ploidy on the evolution of potato species.", "token_count": 460, "char_count": 1723, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.8169, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:20.424912", "source": { "split": "train_shard_00001", "doc_id": 473 }, "chunk_id": "train_shard_00001_473_0", "global_id": 6322 }, { "text": "Understanding adaptation to the local environment is a central tenet and a major focus of evolutionary biology. But this is only part of the adaptionist story. In addition to the external environment, one of the main drivers of genome composition is genetic background. In this perspective, I argue that there is a growing body of evidence that intra-genomic selective pressures play a significant part in the composition of prokaryotic genomes and play a significant role in the origin, maintenance and structuring of prokaryotic pangenomes.\n\nProkaryotic Pangenomes Act as Evolving Ecosystems.", "token_count": 132, "char_count": 594, "word_count": 90, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:20.850009", "source": { "split": "train_shard_00001", "doc_id": 474 }, "chunk_id": "train_shard_00001_474_0", "global_id": 6323 }, { "text": "Tropheryma whipplei the causative agent of Whipple disease, presents a diagnostic challenge due to its diverse symptomatology, including weight loss, abdominal pain, diarrhea, joint pain, fever, and occasionally neurological manifestations. Its resistance to fluoroquinolones complicates treatment further. Traditional methods for antibiotic susceptibility testing are ineffective as Tropheryma whipplei cannot be cultured in axenic media. To address this, we explored potential drug targets within its core genome as no drug targets from this bacterium have been studied so far. murE, a macrolide-resistant enzyme, emerged as a promising candidate exhibiting both resistance and drug target characteristics. We screened over 1,000 lead-like Ayurvedic compounds against the target enzyme UDP-N-acetylmuramyl-tripeptide synthetase and identified three promising candidates: (1) Ergost-5-en-3-ol (3beta,24xi), (2) [6]-Gingerdiol 3-monoacetate, and (3) Valtrate. DiffDock and GNINA rescoring yielded consistent binding strength rankings. Molecular dynamics simulations over 100 nanoseconds confirmed stable interactions with these compounds. ADMET analysis indicated low water solubility, but coupling with cyclodextrin SBE-β-CD improved solubility. None of the compounds showed hepatotoxic effects, though Valtrate exhibited AMES toxicity. Based on the favorable properties, we propose scaffold hopping and further in vitro/in vivo studies on [6]-Gingerdiol 3-monoacetate. Our findings offer potential avenues for combating T. whipplei infections, addressing the limitations posed by antibiotic resistance.", "token_count": 459, "char_count": 1639, "word_count": 202, "semantic_coherence": 1, "information_density": 0.8119, "quality_score": 0.9059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:21.493709", "source": { "split": "train_shard_00001", "doc_id": 475 }, "chunk_id": "train_shard_00001_475_0", "global_id": 6324 }, { "text": "Exploring <i>murE</i> protein inhibitors of <i>Tropheryma whipplei</i> through pharmacoinformatic approaches incorporating solubility-enhancing formulation insights.", "token_count": 65, "char_count": 189, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:21.860647", "source": { "split": "train_shard_00001", "doc_id": 475 }, "chunk_id": "train_shard_00001_475_1", "global_id": 6325 }, { "text": "Constructing and personalizing population pangenome graphs.", "token_count": 11, "char_count": 59, "word_count": 6, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:22.213663", "source": { "split": "train_shard_00001", "doc_id": 476 }, "chunk_id": "train_shard_00001_476_0", "global_id": 6326 }, { "text": "Artisanal mezcal is produced by the natural fermentation of maguey juice, which frequently results in a process that becomes stuck or is sluggish. Using selected indigenous starter inoculums of Saccharomyces and non-Saccharomyces yeasts is considered beneficial in overcoming these problems and thereby preserving the essence of the artisanal process. In this work, three hundred and four yeast isolates were recovered from 17 distilleries and then grouped by the ARDRA analysis, their restriction profiles were clustered in 15 groups. Four of them included 90% of all isolates, and these were identified using the sequence of the D1/D2 domain of the large-subunit rDNA. Pichia kudriavzevii, Pichia manshurica, Saccharomyces cerevisiae, and Kluyveromyces marxianus were detected as predominant species. Both species belonging to the Pichia genus were detected in 88% of the distilleries, followed by S. cerevisiae (70%) and K. marxianus (50%). In order to evaluate the fermentative capacity, one strain of each species was assessed in a pure and mixed culture in two culture media, filtered maguey juice (MJ) and maguey juice including its bagasse (MJB). Findings demonstrated that non-Saccharomyces yeast presented better growth than that of S. cerevisiae. K. marxianus PA16 was more efficient for ethanol production than S. cerevisiae DI14. It produced 32 g/L of ethanol with a yield of 0.47 g/g and efficient of 90%. While, P. kudriavzevii produced more ethyl acetate (280 mg/L) than the others species. All fermentations were characterized by the presence of isobutyl and isoamyl alcohol", "token_count": 521, "char_count": 1682, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6583, "quality_score": 0.8292, "entities": { "genes": [ "DI14", "PA16" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:57:22.850672", "source": { "split": "train_shard_00001", "doc_id": 477 }, "chunk_id": "train_shard_00001_477_0", "global_id": 6327 }, { "text": "The presence of K. marxianus in a mixed culture, improved the ethanol production and volatile compounds increased using co-cultures.\n\nPredominant Yeasts During Artisanal Mezcal Fermentation and Their Capacity to Ferment Maguey Juice.", "token_count": 68, "char_count": 240, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:23.240201", "source": { "split": "train_shard_00001", "doc_id": 477 }, "chunk_id": "train_shard_00001_477_1", "global_id": 6328 }, { "text": "The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.\n\nGene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility.", "token_count": 280, "char_count": 1243, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5573, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:23.796371", "source": { "split": "train_shard_00001", "doc_id": 478 }, "chunk_id": "train_shard_00001_478_0", "global_id": 6329 }, { "text": "Acinetobacter species are emerging as major nosocomial pathogens, aided by their ability to acquire resistance to all classes of antibiotics. A key factor leading to their multi-drug resistance phenotypes is the acquisition of a wide variety of mobile genetic elements, particularly large conjugative plasmids. Here, we characterize a family of 21 multi-drug resistance mega-plasmids in 11 different Acinetobacter species isolated from various locations across the globe. The plasmid family exhibits a highly dynamic and diverse accessory genome, including 221 antibiotic resistance genes (ARGs) that confer resistance to 13 classes of antibiotics. We show that plasmids isolated within the same geographic region are often evolutionarily divergent members of this family based on their core-genome, yet they exhibit a more similar accessory genome. Individual plasmids, therefore, can disseminate to different locations around the globe, where they then appear to acquire diverse sets of accessory genes from their local surroundings. Further, we show that plasmids from several geographic regions were enriched with location-specific functional traits. Together, our findings show that these mega-plasmids can transmit across species boundaries, have the capacity for global dissemination, can accumulate a diverse suite of location-specific accessory genes, and can confer multi-drug resistance phenotypes of significant concern for human health. We therefore highlight this previously undescribed plasmid family as a serious threat to healthcare systems worldwide. These findings also add to the growing concern that mega-plasmids are key disseminators of antibiotic resistance and require global surveillance.\n\nA Novel Family of Acinetobacter Mega-Plasmids Are Disseminating Multi-Drug Resistance Across the Globe While Acquiring Location-Specific Accessory Genes.", "token_count": 427, "char_count": 1890, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5843, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:24.427894", "source": { "split": "train_shard_00001", "doc_id": 479 }, "chunk_id": "train_shard_00001_479_0", "global_id": 6330 }, { "text": "To date, the only probiotic yeast with evidence of health-promoting effects is Saccharomyces cerevisiae var. boulardii. The expanded market including dietary supplements and functional foods supplemented with Saccharomyces cerevisiae var. boulardii creates an environment conductive to food adulterations, necessitating rapid testing to verify product probiotic status. Herein, qPCR-HRM analysis was tested for probiotic yeast identification. The effectiveness of the primer pairs' set was examined, designed to amplify heterogeneous regions in (a) rDNA sequences previously designed to identify food-derived yeast and (b) genes associated with physiological and genotypic divergence of Saccharomyces cerevisiae var. boulardii. Preliminary tests of amplicons' differentiation power enabled the selection of interspecies sequences for 18SrRNA and ITS and genus-specific sequences HO, RPB2, HXT9 and MAL11. The multi-fragment qPCR-HRM analysis was sufficient for culture-dependent Saccharomyces cerevisiae var. boulardii identification and proved effective in the authentication of dietary supplements' probiotic composition. The identification of S. cerevisiae var. boulardii in complex microbial mixtures of kefir succeeded with more specific intragenus sequences HO and RPB2. The predominance of S. cerevisiae var. boulardii in the tested matrices, quantitatively corresponded to the probiotic-enriched food, was crucial for identification with qPCR-HRM analysis. Considering the reported assumptions, qPCR-HRM analysis is an appropriate tool for verifying probiotic-enriched food.", "token_count": 504, "char_count": 1715, "word_count": 201, "semantic_coherence": 1, "information_density": 0.5871, "quality_score": 0.7935, "entities": { "genes": [ "MAL11", "HXT9", "RPB2" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:25.073636", "source": { "split": "train_shard_00001", "doc_id": 480 }, "chunk_id": "train_shard_00001_480_0", "global_id": 6331 }, { "text": "High-Resolution Melting Analysis Potential for Saccharomyces cerevisiae var. boulardii Authentication in Probiotic-Enriched Food Matrices.", "token_count": 51, "char_count": 152, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:25.436546", "source": { "split": "train_shard_00001", "doc_id": 480 }, "chunk_id": "train_shard_00001_480_1", "global_id": 6332 }, { "text": "

Background

The development of pangenomes has revolutionized genomic studies by capturing the complete genetic diversity within a species. Pangenome assembly integrates data from multiple individuals to construct a comprehensive genomic landscape, revealing both core and accessory genomic elements. This approach enables the identification of novel genes, structural variations, and gene presence-absence variations, providing insights into species evolution, adaptation, and trait variation. Representing pangenomes requires innovative visualization formats that effectively convey the complex genomic structures and variations.

Aim

This review delves into contemporary methodologies and recent advancements in constructing pangenomes, particularly in plant genomes. It examines the structure of pangenome representation, including format comparison, conversion, visualization techniques, and their implications for enhancing crop improvement strategies.

Key scientific concepts of review

Earlier comparative studies have illuminated novel gene sequences, copy number variations, and presence-absence variations across diverse crop species. The concept of a pan-genome, which captures multiple genetic variations from a broad spectrum of genotypes, offers a holistic perspective of a species' genetic makeup. However, constructing a pan-genome for plants with larger genomes poses challenges, including managing vast genome sequence data and comprehending the genetic variations within the germplasm. To address these challenges, researchers have explored cost-effective alternatives to encapsulate species diversity in a single assembly known as a pangenome. This involves reducing the volume of genome sequences while focusing on genetic variations. With the growing prominence of the pan-genome concept in plant genomics, several software tools have emerged to facilitate pangenome construction. This review sheds light on developing and utilizing software tools tailored for constructing pan-genomes in plants. It also discusses representation formats suitable for downstream analyses, offering valuable insights into the genetic landscape and evolutionary dynamics of plant species. In summary, this review underscores the significance of pan-genome construction and representation formats in resolving the genetic architecture of plants, particularly those with complex genomes. It provides a comprehensive overview of recent advancements, aiding in exploring and understanding plant genetic diversity.\n\nDeveloping pangenomes for large and complex plant genomes and their representation formats.", "token_count": 493, "char_count": 2624, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5872, "quality_score": 0.7936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:26.084917", "source": { "split": "train_shard_00001", "doc_id": 481 }, "chunk_id": "train_shard_00001_481_0", "global_id": 6333 }, { "text": "Extreme environments like arid and semi-arid deserts harbor unique microbial diversity, offering rich sources of specialized microbial metabolites. This study explores Bacillus velezensis RVMD2, a strain isolated from rock varnish in the Ma'an Desert, Jordan. The genome was sequenced using the Illumina NextSeq 2000 platform, resulting in a 4,212,579 bp assembly with a GC content of 45.94%. The assembled genome comprises 112 contigs and encodes 4,250 proteins, 77 tRNA genes, and 4 rRNA genes. Phylogenetic analysis of the 16S rRNA gene indicated a 99.84% similarity to previously identified B. velezensis strains. Whole-genome phylogeny using EzBiome, MiGA, and TYGS confirmed its classification as B. velezensis. Functional annotation identified genes involved in carbohydrate metabolism, including 324 carbohydrate-active enzyme (CAZyme) genes, stress response, and secondary metabolite biosynthesis. The genome also contains 50 genes associated with heavy metal resistance and plant growth promotion. Analysis using AntiSMASH identified 12 biosynthetic gene clusters involved in the production of secondary metabolites, including fengycin, surfactin, polyketides, terpenes, and bacteriocins. Notably, several clusters did not match any known sequences, suggesting the presence of potentially novel antimicrobial compounds. The genomic features of RVMD2 highlight its adaptability to extreme environments and its potential for biotechnological applications, including bioremediation and the discovery of novel bioactive metabolites.\n\nGenomic insights into the taxonomic status and bioactive gene cluster profiling of Bacillus velezensis RVMD2 isolated from desert rock varnish in Ma'an, Jordan.", "token_count": 460, "char_count": 1700, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [ "RVMD2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:26.742901", "source": { "split": "train_shard_00001", "doc_id": 482 }, "chunk_id": "train_shard_00001_482_0", "global_id": 6334 }, { "text": "

Summary

Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thousands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k-mers and their presence-absence values in each genome. These are stored in an efficient k-mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k-mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k-mers can be \"anchored\" in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias.

Availability and implementation

PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer. Full documentation is available at https://salk-tm.gitlab.io/pankmer/.\n\nPanKmer: k-mer-based and reference-free pangenome analysis.", "token_count": 427, "char_count": 1826, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6844, "quality_score": 0.8422, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:27.392152", "source": { "split": "train_shard_00001", "doc_id": 483 }, "chunk_id": "train_shard_00001_483_0", "global_id": 6335 }, { "text": "

Background

Water buffalo is a cornerstone livestock species in many low- and middle-income countries, yet major gaps persist in its genomic characterization-complicated by the divergent karyotypes of its two subspecies (swamp and river). Such genomic complexity makes water buffalo a particularly good candidate for the use of graph genomics, which can capture variation missed by linear reference approaches. However, the utility of this approach to improve water buffalo has been largely unexplored.

Results

We present a comprehensive pangenome that integrates 4 newly generated, highly contiguous assemblies of Pakistani river buffalo with 8 publicly available assemblies from both subspecies. This doubles the number of accessible high-quality river buffalo genomes and provides the most contiguous assemblies for the subspecies to date. Using the pangenome to assay variation across 711 global samples, we uncovered extensive genomic diversity, including thousands of large structural variants absent from the reference genome, spanning over 140 Mb of additional sequence. We demonstrate the utility of these data by identifying putative functional indels and structural variants linked to selective sweeps in key genes involved in productivity and immune response across 26 populations.

Conclusions

This study represents one of the first successful applications of graph genomics in water buffalo and offers valuable insights into how integrating assemblies can transform analyses of water buffalo and other species with complex evolutionary histories. We anticipate that these assemblies, as well as the pangenome and putative functional structural variants we have released, will accelerate efforts to unlock water buffalo's genetic potential, improving productivity and resilience in this economically important species.\n\nA comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection.", "token_count": 424, "char_count": 1986, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:28.055848", "source": { "split": "train_shard_00001", "doc_id": 484 }, "chunk_id": "train_shard_00001_484_0", "global_id": 6336 }, { "text": "Accessory chromosomes, found in some but not all individuals of a species, play an important role in pathogenicity and host specificity in fungal plant pathogens. However, their variability complicates reference-based analysis, especially when chromosomes are missing from reference genomes. Pangenome variation graphs offer a reference-free alternative for studying these chromosomes. Here, we constructed a pangenome variation graph for Fusarium oxysporum , a major fungal plant pathogen with a compartmentalized genome. To study accessory chromosomes, we constructed a chromosome similarity network and identified eleven conserved core chromosomes and many highly variable accessory chromosomes. Some of these are host-specific and are likely involved in determining host range, which we corroborate by analyzing nearly 600 F. oxysporum assemblies. By a reconstruction of pangenome variation graph per homologous chromosomes, we show that these evolve due to extensive structural variation as well as the exchange of genetic material between accessory chromosomes giving rise to these mosaic accessory chromosomes. Furthermore, we show that accessory chromosomes are horizontally transferred in natural populations. We demonstrate that pangenome variation graphs are a powerful approach to elucidate the evolutionary dynamics of accessory chromosomes in F. oxysporum and provides a computational framework for similar analyses in other species that encode accessory chromosomes.\n\nReference-free identification and pangenome analysis of accessory chromosomes in a major fungal plant pathogen", "token_count": 344, "char_count": 1593, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5767, "quality_score": 0.7884, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:28.642939", "source": { "split": "train_shard_00001", "doc_id": 485 }, "chunk_id": "train_shard_00001_485_0", "global_id": 6337 }, { "text": "The objective of this study was to determine the effect of supplementing Kluyveromyces marxianus CPY1, K. marxianus RSY5 and Pichia kudriavzevii YSY2 isolated from ruminal fluid of dairy cows on transfer of aflatoxin B1 (AFB1) from feed into aflatoxin M1 (AFM1) in milk, DMI, milk production and nutrient digestibility. Four multiparous Holsteins in mid-lactation were used in a 4 × 4 Latin square design trial consisting of 14 days in each experimental period for sample collection. Between each period, 14 clearance days prior to the next treatment were allowed to minimize carryover effects. In each treatment, subsequent supplementation of isolated yeast was compared, i.e., (1) control (without yeast supplementation), (2) K. marxianus CPY1 (K1Y), (3) K. marxianus RSY5 (K2Y) and (4) P. kudriavzevii YSY2 (PY). All diets contained 22.28 µg of AFB1/kg. Treatments were individually fed at the rate of 2 g/day (1 × 109 CFU/g) of yeast biomass or corn meal in the control group. Concentrations of AFM1 in milk was reduced with yeast and averaged 1.54, 0.36, 0.43 and 0.51 µg/L for control, K1Y, K2Y and PY, respectively (p < 0.01). The transfer of AFB1 from feed into AFM1 in milk was higher in control compared with K1Y, K2Y and PY (7.26% vs", "token_count": 507, "char_count": 1392, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6634, "quality_score": 0.8317, "entities": { "genes": [ "CPY1", "RSY5", "YSY2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:29.300900", "source": { "split": "train_shard_00001", "doc_id": 486 }, "chunk_id": "train_shard_00001_486_0", "global_id": 6338 }, { "text": "1.18%, 1.44% and 1.69% respectively, p < 0.01). Supplementation of yeast also improved DMI and milk compositions, but no differences were observed in nutrient digestibility or milk yield among treatments. Concentration and yield of milk protein, fat, lactose, solid-not-fat (SNF) and total solids were greater in cows fed yeast compared with the control (p < 0.01). These results indicate that K. marxianus CPY1, RSY5 and P. kudriavzevii YSY2 shows promise as a dietary supplementation to detoxify AFB1 and improve DMI and yield of milk components.\n\nEffect of Supplemental Kluyveromyces marxianus and Pichia kudriavzevii on Aflatoxin M1 Excretion in Milk of Lactating Dairy Cows.", "token_count": 264, "char_count": 743, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7379, "quality_score": 0.8689, "entities": { "genes": [ "CPY1", "RSY5", "YSY2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:29.854403", "source": { "split": "train_shard_00001", "doc_id": 486 }, "chunk_id": "train_shard_00001_486_1", "global_id": 6339 }, { "text": "Abstract

Klebsiella pneumoniae , a major bovine clinical mastitis (CM) pathogen, carries multidrug resistance (MDR) and virulence factor genes (VFGs), posing serious animal and public health threats. This study screened 27 K. pneumoniae isolates (19 from CM milk and 8 from feces) through culture, biochemical tests, and 16S rRNA -gene sequencing. An overall prevalence of K. pneumoniae was 22.5% (27/120), with a higher rate in milk (27.14%) than feces (16.0%). Antibiogram profiling revealed that all isolates were multidrug-resistant, with high resistance to doxycycline, tetracycline, nalidixic acid, and ampicillin. Three highly resistant isolates (MBBL2, MNH_G2C5, MNH_G2C5F) underwent whole-genome sequencing for comprehensive genomic analysis. Sequence typing (ST), phylogenetic and pangenome analyses assigned MBBL2 and MNH_G2C5F to ST273 and MNH_G2C5 to ST101, clustering with global human- and animal-derived K. pneumoniae strains, and carrying notable strain-specific accessory genes (MNH_G2C5:123; MBBL2/MNH_G2C5F:826). Functional annotation identified abundant genes for carbohydrate metabolism (~ 10%), amino acid transport (~ 9%), and transcription (~ 9%). Resistome analysis identified 29–41 resistance genes, covering 12 antibiotic classes, metals, biocides, and acid stress", "token_count": 500, "char_count": 1407, "word_count": 171, "semantic_coherence": 1, "information_density": 0.8012, "quality_score": 0.9006, "entities": { "genes": [ "MBBL2", "ST273", "ST101" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:30.507302", "source": { "split": "train_shard_00001", "doc_id": 487 }, "chunk_id": "train_shard_00001_487_0", "global_id": 6340 }, { "text": "Virulence profiling identified 44–60 VFGs involved in adherence, biofilm formation, effector delivery, immune modulation, and metabolism. Genomic plasticity analysis revealed 27–34 variable regions, multiple prophages, 46–58 insertion sequences, and four plasmid replicons. Conserved exopolysaccharide/capsule clusters, secondary metabolites, and high pathogenicity scores (> 0.9) underscored both animal and human pathogenic potential. This study demonstrates that dairy cattle are a reservoir for high-risk MDR clones of K. pneumoniae carrying an extensive resistome and virulome arsenal, highlighting the urgent need for strengthened surveillance and control measures.

\n\nGenomic Characterization of Multidrug-Resistant Klebsiella pneumoniae Strains from Bovine Mastitis Reveals Extensive Resistome and Virulome Arsenals", "token_count": 234, "char_count": 845, "word_count": 100, "semantic_coherence": 1, "information_density": 0.88, "quality_score": 0.94, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:30.973677", "source": { "split": "train_shard_00001", "doc_id": 487 }, "chunk_id": "train_shard_00001_487_1", "global_id": 6341 }, { "text": "As sequencing costs decrease, short-read and long-read technologies are indispensable tools for uncovering the genetic drivers behind bacterial pathogen resistance. This study explores the differences between the use of short-read (Illumina) and long-read (Oxford Nanopore Technologies, ONT) sequencing in detecting antimicrobial resistance (AMR) genes in ESKAPE pathogens ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter cloacae ). Utilizing a dataset of 1,385 whole genome sequences and applying commonly used bioinformatic methods in bacterial genomics, we assessed the differences in genomic completeness, pangenome structure, and AMR gene and point mutation identification. Illumina presented higher genome completeness, while ONT identified a broader pangenome. Hybrid assembly outperformed both Illumina and ONT at identifying key AMR genetic determinants, presented results closer to Illumina’s completeness, and revealed ONT-like pangenomic content. Notably, Illumina consistently detected more AMR-related point mutations than its counterparts. This highlights the importance of method selection based on research goals. Differences were also observed for specific gene classes and bacterial species, underscoring the need for a nuanced understanding of technology limitations. Overall, this study reveals the strengths and limitations of each approach, advocating for the use of Illumina for common AMR analysis; ONT for studying complex genomes and novel species, and hybrid assembly for a more comprehensive characterization, leveraging the benefits of both technologies.

Impact Statement

This study provides a comprehensive comparison of short-read (Illumina) and long-read (Oxford Nanopore Technologies, ONT) sequencing technologies in the context of antimicrobial resistance (AMR) detection in ESKAPE pathogens. By analyzing a large dataset of 1,385 whole genome sequences, the research offers valuable insights into the strengths and limitations of each approach, as well as the benefits of the novel approach of hybrid assembly. These findings have broad utility across microbiology, genomics, and infectious disease research", "token_count": 522, "char_count": 2239, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8003, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:57:31.632913", "source": { "split": "train_shard_00001", "doc_id": 488 }, "chunk_id": "train_shard_00001_488_0", "global_id": 6342 }, { "text": "In particular, they apply to the work of researchers and clinicians dealing with AMR surveillance, investigation into outbreaks, and bacterial genome analysis. Given the nuance with which technological differences in genomic completeness, pangenome structure, and AMR determinant detection have been explored in this study, it is a good basis for informed method selection for future research. While the output represents an incremental advance, its significance lies in its practical implications. It thus enables researchers to take more reasonable decisions in designing genomic studies of bacterial pathogens by showing the complementarity of various sequencing approaches and their specific strengths. This could lead to more accurate and comprehensive detection of AMR, which would contribute ultimately to improved antibiotic stewardship and public health strategies.

Data Summary

The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.

Repositories

All the sequences used for this study are publicly accessible from GenBank, and their individual IDs are disclosed in Supplementary Table 1.\n\nInfluence of Sequencing Technology on Pangenome-level Analysis and Detection of Antimicrobial Resistance Genes in ESKAPE Pathogens", "token_count": 270, "char_count": 1326, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7198, "quality_score": 0.8599, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:32.182894", "source": { "split": "train_shard_00001", "doc_id": 488 }, "chunk_id": "train_shard_00001_488_1", "global_id": 6343 }, { "text": "

Background

Opportunistic infections due to Candida species occur frequently in cancer patients because of their inherent immunosuppression. The aim of the present study was to investigate the epidemiology of yeast species from the oral cavity of patients during treatment for oncological and haematological malignancies.

Methods

MALDI-TOF was performed to identify yeasts isolated from the oral cavity of 350 cancer patients. Moreover, antifungal susceptibility testing was performed in according to CLSI guidelines (M27-A3).

Results

Among 162 yeasts and yeast-like fungi isolated from the oral cavity of cancer patients, Candida albicans was the most common species (50.6%), followed by Candida glabrata (24.7%), Pichia kudriavzevii (Candida krusei (9.9%)), Candida tropicalis (4.3%), Candida dubliniensis (3.7%), Kluyveromyces marxianus (Candida kefyr (3.7%)) and Candida parapsilosis (1%). In addition, uncommon yeast species i.e., Saprochaete capitata, Saccharomyces cerevisiae, Clavispora lusitaniae (C. lusitaniae) and Pichia kluyveri (C. eremophila) were recovered from oral lesions. Oral colonization by C. albicans, non-albicans Candida species and uncommon yeasts were as follow; 55%, 44% and 1%, whereas oral infection due to C. albicans was 33.3%, non-albicans Candida species 60.6%, and uncommon yeasts 6.1%. Poor oral hygiene and xerostomia were identified as independent risk factors associated with oral yeast colonization. The overall resistance to fluconazole was 11.7% (19/162)", "token_count": 476, "char_count": 1518, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:32.831885", "source": { "split": "train_shard_00001", "doc_id": 489 }, "chunk_id": "train_shard_00001_489_0", "global_id": 6344 }, { "text": "Low MIC values were observed for anidulafungin for all Candida and uncommon yeast species.

Conclusions

This current study provides insight into the prevalence and susceptibility profiles of Candida species, including emerging Candida species and uncommon yeasts, isolated from the oral cavity of Iranian cancer patients. The incidence of oral candidiasis was higher amongst patients with hematological malignancies. The majority of oral infections were caused by non-albicans Candida species which were often more resistant to anti-fungal agents. Our findings suggest that anidulafungin should be used as antifungal of choice for prophylaxis in clinically high-risk patients with documented oral colonization or infection.\n\nIdentification of uncommon oral yeasts from cancer patients by MALDI-TOF mass spectrometry.", "token_count": 192, "char_count": 822, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:33.281151", "source": { "split": "train_shard_00001", "doc_id": 489 }, "chunk_id": "train_shard_00001_489_1", "global_id": 6345 }, { "text": "

Background

Wickerhamomyces anomalus (W. anomalus) is a kind of non-Saccharomyces yeast that has a variety of unique physiological characteristics and metabolic features and is widely used in many fields, such as food preservation, biomass energy, and aquaculture feed protein production. However, the mechanism of W. anomalus response to ethanol stress is still unclear, which greatly limits its application in the production of ethanol beverages and ethanol fuels. Therefore, we checked the effects of ethanol stress on the morphology, the growth, and differentially expressed genes (DEGs) and metabolites (DEMs) of W. anomalus.

Results

High concentrations of ethanol (9% ethanol and 12% ethanol) remarkably inhibited the growth of W. anomalus. Energy metabolism, amino acid metabolism, fatty acids metabolism, and nucleic acid metabolism were significantly influenced when exposing to 9% ethanol and 12% ethanolstress, which maybe universal for W. anomalus to response to different concentrations of ethanol stressl Furthermore, extracellular addition of aspartate, glutamate, and arginine significantly abated ethanol damage and improved the survival rate of W. anomalus.

Conclusions

The results obtained in this study provide insights into the mechanisms involved in W. anomalus response to ethanol stress. Therefore, new strategies can be realized to improve the ethanol tolerance of W. anomalus through metabolic engineering.\n\nAnalysis of the ethanol stress response mechanism in Wickerhamomyces anomalus based on transcriptomics and metabolomics approaches.", "token_count": 415, "char_count": 1586, "word_count": 213, "semantic_coherence": 1, "information_density": 0.615, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:33.903778", "source": { "split": "train_shard_00001", "doc_id": 490 }, "chunk_id": "train_shard_00001_490_0", "global_id": 6346 }, { "text": "

Background and aim

Pseudomonas aeruginosa is a multidrug-resistant (MDR) zoonotic pathogen increasingly implicated in infections in both humans and animals, including avian species. Raptors, particularly peregrine falcons, are vulnerable due to their exposure to diverse environments and intensive management practices. This study aimed to identify P. aeruginosa isolates from peregrine falcons in Saudi Arabia and to characterize their genomic features, phylogenetic relationships, and antimicrobial resistance (AMR) profiles using whole-genome sequencing (WGS).

Materials and methods

Eighty cloacal swabs were collected from adult peregrine falcons showing clinical signs of gastrointestinal distress and housed in falconry facilities in Eastern Saudi Arabia between 2022 and 2024. Samples underwent bacteriological culture, biochemical identification using the Vitek 2 system, and WGS of a representative isolate. Multilocus sequence typing (MLST) analysis, phylogenetic comparison, and resistance gene profiling were conducted using standard bioinformatic tools and the Comprehensive Antibiotic Resistance Database and PubMLST databases.

Results

Sixteen isolates (20%) were confirmed as P. aeruginosa through biochemical identification and BLAST analysis. One representative isolate underwent WGS and revealed a 6.0 Mbp genome with close phylogenetic relatedness (92% bootstrap) to a human-derived P. aeruginosa strain (CP050326), with a 4% genetic divergence. The MLST profile included allele numbers acsA (23), aroE (29), guaA (1), mutL (3), nuoD (1), ppsA (15), and trpE (9)", "token_count": 508, "char_count": 1680, "word_count": 205, "semantic_coherence": 1, "information_density": 0.722, "quality_score": 0.861, "entities": { "genes": [ "CP050326" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:34.565034", "source": { "split": "train_shard_00001", "doc_id": 491 }, "chunk_id": "train_shard_00001_491_0", "global_id": 6347 }, { "text": "Resistance genes identified included β-lactamase PAO-type (blaPAO), Class Dβ -lactamase OXA-type (variants 485 and 488) (blaOXA-485/488), aminoglycoside 3'-phosphotransferase type IIb (aph(3')-IIb), glutathione transferase FosA (fosA), and chloramphenicol acetyltransferase type B7 (catB7), indicating MDR to beta-lactams, aminoglycosides, fosfomycin, and chloramphenicol.

Conclusion

This is the first report of WGS-characterized, MDR P. aeruginosa in falcons from Saudi Arabia. The genomic similarity to human strains highlights the zoonotic potential and One Health implications. These findings emphasize the urgent need for integrated AMR surveillance in wildlife, especially in regions with widespread falconry practices. WGS offers valuable molecular insights for pathogen tracking, resistance monitoring, and epidemiological risk assessment. Broader genomic surveillance across bird species and regions is necessary to guide control strategies and reduce the risks of zoonotic transmission.\n\nGenomic characterization and multidrug resistance of <i>Pseudomonas aeruginosa</i> isolated from peregrine falcons in Saudi Arabia: A One Health perspective.", "token_count": 367, "char_count": 1216, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7571, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:35.141498", "source": { "split": "train_shard_00001", "doc_id": 491 }, "chunk_id": "train_shard_00001_491_1", "global_id": 6348 }, { "text": "Clostridia are a polyphyletic group of Gram-positive, spore-forming anaerobes in the Firmicutes phylum that significantly impact metabolism and functioning of the human gastrointestinal tract. Recently, Clostridia were divided into two separate classes, Clostridia and Erysipelotrichia, based on phenotypic and 16S rRNA gene-based differences. While Clostridia include many well-known pathogenic bacteria, Erysipelotrichia remain relatively uncharacterized, particularly regarding their role as a pathogen versus commensal. Despite wide recognition as a commensal, the erysipelotrichial species Clostridium innocuum has recently been associated with various disease states. To further understand the ecological and potential virulent role of C. innocuum, we conducted a genomic comparison across 38 C. innocuum isolates and 194 publicly available genomes. Based on colony morphology, we isolated multiple C. innocuum cultivars from the feces of healthy human volunteers (n = 5). Comparison of the 16S rRNA gene of our isolates against publicly available microbiota data sets in healthy individuals suggests a high prevalence of C. innocuum across the human population (>80%). Analysis of single nucleotide polymorphisms (SNPs) across core genes and average nucleotide identify (ANI) revealed the presence of four clades among all available genomes (n = 232 total). Investigation of carbohydrate and protein utilization pathways, including comparison against the carbohydrate-activating enzyme (CAZyme) database, demonstrated inter- and intraclade differences that were further substantiated in vitro. Collectively, these data indicate genetic variance within the C. innocuum species that may help clarify its role in human disease and health", "token_count": 488, "char_count": 1811, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6851, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:35.792320", "source": { "split": "train_shard_00001", "doc_id": 492 }, "chunk_id": "train_shard_00001_492_0", "global_id": 6349 }, { "text": "IMPORTANCE Clostridia are a group of medically important anaerobes as both commensals and pathogens. Recently, a new class of Erysipelotrichia containing a number of reassigned clostridial species has emerged, including Clostridium innocuum. Recent studies have implicated C. innocuum as a potential causative agent of diarrhea in patients from whom Clostridioides difficile could not be isolated. Using genomic and in vitro comparison, this study sought to characterize C. innocuum in the healthy human gut. Our analyses suggest that C. innocuum is a highly prevalent and diverse species, demonstrating clade-specific differences in metabolism and potential virulence. Collectively, this study is the first investigation into a broader description of C. innocuum as a human gut inhabitant.\n\nDiversity and Prevalence of Clostridium innocuum in the Human Gut Microbiota.", "token_count": 234, "char_count": 897, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7016, "quality_score": 0.8508, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:36.262446", "source": { "split": "train_shard_00001", "doc_id": 492 }, "chunk_id": "train_shard_00001_492_1", "global_id": 6350 }, { "text": "Staphylococcus pseudintermedius, an opportunistic pathogen of veterinary and zoonotic concern, harbors diverse biosynthetic gene clusters (BGCs) that may contribute to its ecological fitness and virulence. In this study, we performed a comparative genomic analysis of 6815 S. pseudintermedius isolates. Using Roary, we identified core and accessory genomes, revealing the subtilosin A gene (sboA) as part of the accessory genome, present in a subset of S. pseudintermedius isolates from clinical (n = 657), environmental (n = 1031), and unclassified sources (n = 487). AntiSMASH v8.0.0 analysis confirmed the presence of subtilosin A BGCs annotated as a sactipeptide with low similarity confidence to Bacillus subtilis subsp. spizizenii ATCC 6633 subtilosin A cluster. Further characterization using BAGEL4 identified multiple genes homologous to the Bacillus subtilis subtilosin A biosynthetic machinery (sbo-albABCDEFG), although albB, albG, and sboX were not annotated, raising questions about cluster completeness and functionality. BLAST v2.12.0 analysis of the full BGC identified by BAGEL4, revealing high conservation (99.6-100% pairwise identity) of gene content and order in 395 clinical, 593 environmental, and 417 unclassified S. pseudintermedius isolates. Incomplete clusters were identified in 763 clinical, 942 environmental, and 201 unclassified S. pseudintermedius isolates", "token_count": 496, "char_count": 1495, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6614, "quality_score": 0.8307, "entities": { "genes": [ "BAGEL4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:36.925127", "source": { "split": "train_shard_00001", "doc_id": 493 }, "chunk_id": "train_shard_00001_493_0", "global_id": 6351 }, { "text": "The discrepancy between the number of isolates containing sboA and those harboring the full cluster may reflect evolutionary divergence or could be attributed to limitations in assembly quality. The functional implications of the identified cluster in S. pseudintermedius remain to be elucidated; however, its potential role in conferring competitive fitness by inhibiting closely related species is supported by previous findings in other staphylococci.\n\nGenome Mining Reveals a Sactipeptide Biosynthetic Cluster in <i>Staphylococcus pseudintermedius</i>.", "token_count": 150, "char_count": 582, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8082, "quality_score": 0.9041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:37.360839", "source": { "split": "train_shard_00001", "doc_id": 493 }, "chunk_id": "train_shard_00001_493_1", "global_id": 6352 }, { "text": "Scaffold protein Ste5 and associated kinases, including Ste11, Ste7, and Fus3, are core components of the mating pheromone pathway, which is required to induce a mating response. Orthologs of these proteins are widely present in fungi, but to which extent one protein can be replaced by its ortholog is less well understood. Here, interspecies complementation was carried out to evaluate the functional homology of Ste5 and associated kinases in Kluyveromyces lactis, K. marxianus, and Saccharomyces cerevisiae. These three species occupy important positions in the evolution of hemiascomycetes. Results indicated that Ste5 and associated kinases in K. lactis and K. marxianus could be functionally replaced by their orthologs to different extents. However, the extent of sequence identity, either between full-length proteins or between domains, did not necessarily indicate the extent of functional replaceability. For example, Ste5, the most unconserved protein in sequence, achieved the highest average functional replaceability. Notably, swapping Ste5 between K. lactis and K. marxianus significantly promoted mating in both species and the weakened interaction between the Ste5 and Ste7 might contribute to this phenotype. Consistently, chimeric Ste5 displaying a higher affinity for Ste7 decreased the mating efficiency, while chimeric Ste5 displaying a lower affinity for Ste7 improved the mating efficiency. Furthermore, the length of a negatively charged segment in the Ste7-binding domain of Ste5 was negatively correlated with the mating efficiency in K. lactis and K. marxianus. Extending the length of the segment in KlSte5 improved its interaction with Ste7 and that might contribute to the reduced mating efficiency. Our study suggested a novel role of Ste5-Ste7 interaction in the negative regulation of the pheromone pathway", "token_count": 490, "char_count": 1919, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5522, "quality_score": 0.7761, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:38.013261", "source": { "split": "train_shard_00001", "doc_id": 494 }, "chunk_id": "train_shard_00001_494_0", "global_id": 6353 }, { "text": "Meanwhile, Ste5 mutants displaying improved mating efficiency facilitated the breeding and selection of Kluyveromyces strains for industrial applications.\n\nCorrelation Between Improved Mating Efficiency and Weakened Scaffold-Kinase Interaction in the Mating Pheromone Response Pathway Revealed by Interspecies Complementation.", "token_count": 85, "char_count": 333, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8378, "quality_score": 0.9189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:38.422196", "source": { "split": "train_shard_00001", "doc_id": 494 }, "chunk_id": "train_shard_00001_494_1", "global_id": 6354 }, { "text": "The Human Pangenome Reference Consortium (HPRC) aims to construct a comprehensive and representative human pangenome reference to better illustrate the genomic landscape of diverse human populations. In this webinar, we will guide you on how to access HPRC data via the Ensembl genome browser. We will explore the available gene annotation and genetic variation data of the sequence assemblies produced by the project.\n\nExplore Human Pangenome Reference Consortium (HPRC) data in Ensembl", "token_count": 109, "char_count": 487, "word_count": 72, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:38.815303", "source": { "split": "train_shard_00001", "doc_id": 495 }, "chunk_id": "train_shard_00001_495_0", "global_id": 6355 }, { "text": "The tetraploid genome and clonal propagation of the cultivated potato (Solanum tuberosum L.)1,2 dictate a slow, non-accumulative breeding mode of the most important tuber crop. Transitioning potato breeding to a seed-propagated hybrid system based on diploid inbred lines has the potential to greatly accelerate its improvement3. Crucially, the development of inbred lines is impeded by manifold deleterious variants; explaining their nature and finding ways to eliminate them is the current focus of hybrid potato research4-10. However, most published diploid potato genomes are unphased, concealing crucial information on haplotype diversity and heterozygosity11-13. Here we develop a phased potato pangenome graph of 60 haplotypes from cultivated diploids and the ancestral wild species, and find evidence for the prevalence of transposable elements in generating structural variants. Compared with the linear reference, the graph pangenome represents a broader diversity (3,076 Mb versus 742 Mb). Notably, we observe enhanced heterozygosity in cultivated diploids compared with wild ones (14.0% versus 9.5%), indicating extensive hybridization during potato domestication. Using conservative criteria, we identify 19,625 putatively deleterious structural variants (dSVs) and reveal a biased accumulation of deleterious single nucleotide polymorphisms (dSNPs) around dSVs in coupling phase. Based on the graph pangenome, we computationally design ideal potato haplotypes with minimal dSNPs and dSVs. These advances provide critical insights into the genomic basis of clonal propagation and will guide breeders to develop a suite of promising inbred lines.\n\nLeveraging a phased pangenome for haplotype design of hybrid potato.", "token_count": 469, "char_count": 1772, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:39.491153", "source": { "split": "train_shard_00001", "doc_id": 496 }, "chunk_id": "train_shard_00001_496_0", "global_id": 6356 }, { "text": "Phytic acid is an anti-nutritional compound able to chelate proteins and ions. For this reason, the food industry is looking for a convenient method which allows its degradation. Phytases are a class of enzymes that catalyze the degradation of phytic acid and are used as additives in feed-related industrial processes. Due to their industrial importance, our goal was to identify new activities that exhibit best performances in terms of tolerance to high temperature and acidic pH. As a result of an initial screening on 21 yeast species, we focused our attention on phytases found in Cyberlindnera jadinii, Kluyveromyces marxianus, and Torulaspora delbrueckeii. In particular, C. jadinii showed the highest secreted and cell-bound activity, with optimum of temperature and pH at 50°C and 4.5, respectively. These characteristics suggest that this enzyme could be successfully used for feed as well as for food-related industrial applications.\n\nScreening For Yeast Phytase Leads to the Identification of a New Cell-Bound and Secreted Activity in Cyberlindnera jadinii CJ2.", "token_count": 304, "char_count": 1109, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [ "CJ2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:40.112217", "source": { "split": "train_shard_00001", "doc_id": 497 }, "chunk_id": "train_shard_00001_497_0", "global_id": 6357 }, { "text": "Leuconostoc species are important microorganisms in food fermentation but also cause food spoilage. Although these species are commercially important, their taxonomy is still based on inaccurate identification methods. Here, we used computational pangenome analysis to develop a real-time PCR-based method for identifying and differentiating the 12 major Leuconostoc species found in food. Analysis of pan and core-genome phylogenies showed clustering of strains into 12 distinct groups according to the species. Pangenome analysis of 130 Leuconostoc genomes from these 12 species enabled the identification of each species-specific gene. In silico testing of the species-specific genes against 143 publicly available Leuconostoc and 100 other lactic acid bacterial genomes showed that all the assays had 100% inclusivity/exclusivity. We also verified the specificity for each primer pair targeting each specific gene using 23 target and 124 non-target strains and found high specificity (100%). The sensitivity of the real-time PCR method was 102 colony forming units (CFUs)/ml in pure culture and spiked food samples. All standard curves showed good linear correlations, with an R 2 value of ≥0.996, suggesting that screened targets have good specificity and strong anti-interference ability from food sample matrices and non-target strains. The real-time PCR method can be potentially used to determine the taxonomic status and identify the Leuconostoc species in foods.\n\nIdentification of Leuconostoc species based on novel marker genes identified using real-time PCR via computational pangenome analysis.", "token_count": 458, "char_count": 1694, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:40.761949", "source": { "split": "train_shard_00001", "doc_id": 498 }, "chunk_id": "train_shard_00001_498_0", "global_id": 6358 }, { "text": "

Motivation

Pangenome variation graphs are an increasingly used tool to perform genome analysis, aiming to replace a linear reference in a wide variety of genomic analyses. The construction of a variation graph from a collection of chromosome-size genome sequences is a difficult task that is generally addressed using a number of heuristics. The question that arises is to what extent the construction method influences the resulting graph, and the characterization of variability.

Results

We aim to characterize the differences between variation graphs derived from the same set of genomes with a metric which expresses and pinpoint differences. We designed a pairwise variation graph comparison algorithm, which establishes an edit distance between variation graphs, threading the genomes through both graphs. We applied our method to pangenome graphs built from yeast and human chromosome collections, and demonstrate that our method effectively characterizes discordances between pangenome graph construction methods and scales to real datasets.

Availability

pancat compare is published as free Rust software under the AGPL3.0 open source license. Source code and documentation are available at https://github.com/dubssieg/rs-pancat-compare .

Contact

siegfried.dubois@inria.fr

Supplementary information

Supplementary data are available online at https://doi.org/10.5281/zenodo.10932490 . Code to replicate figures and analysis is available online at https://github.com/dubssieg/pancat_paper .\n\nPairwise graph edit distance characterizes the impact of the construction method on pangenome graphs", "token_count": 390, "char_count": 1643, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [ "AGPL3" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:41.387480", "source": { "split": "train_shard_00001", "doc_id": 499 }, "chunk_id": "train_shard_00001_499_0", "global_id": 6359 }, { "text": "Bacterial vaginosis (BV) is a prevalent condition characterized by an imbalance in the vaginal microbiota, often involving the presence of Gardnerella species. The taxonomic complexity and inconsistent nomenclature of Gardnerella have impeded progress in understanding the role of this genus in health and disease. In this study, we obtained genomes from 392 Gardnerella isolates from asymptomatic individuals and those with BV. With stringent curation of these and additional publicly-available genomes, we conducted a comprehensive genomic analysis (final dataset: n=312). We resolve taxonomic ambiguities using current species thresholds and propose updated Gardnerella nomenclature to facilitate formal naming of these twenty-one identified lineages (eleven species, fifteen subspecies). Syntenic pangenome analysis revealed lineage-specific genetic factors and putative operons associated with virulence, metabolism, and genetic defense mechanisms. We also report on the first cryptic plasmids naturally present within the Gardnerella genus, which should serve to advance mechanistic studies within these species. Our findings provide a unified framework for Gardnerella taxonomy and nomenclature, and advance our understanding of species-specific functional capabilities, with implications for Gardnerella research, diagnostics, and targeted therapeutics in BV.\n\nA Syntenic Pangenome for Gardnerella Reveals Taxonomic Boundaries and Stratification of Metabolic and Virulence Potential across Species", "token_count": 333, "char_count": 1505, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:41.957398", "source": { "split": "train_shard_00001", "doc_id": 500 }, "chunk_id": "train_shard_00001_500_0", "global_id": 6360 }, { "text": "We describe here a new NHGRI Sample Repository for Human Genetic Research collection of induced pluripotent stem cell (iPSC) lines reprogrammed from whole blood derived peripheral blood mononuclear cells (PBMCs). The PBMCs were reprogrammed using Sendai viral vectors carrying transcription factors OCT4, SOX2, KLF4, and c-MYC. The iPSC lines exhibit a normal karyotype, express common stemness and pluripotency markers, and demonstrate the ability to differentiate into cell types representing all three germ layers. These iPSCs (n=5) will have accompanying public, near telomere to telomere genomic data through the Human Pangenome Reference Consortium, and will provide an invaluable in vitro resource for studying common genetic and genomic variation and its functional implications.\n\nA new NHGRI Sample Repository for Human Genetic Research collection of induced pluripotent stem cell lines.", "token_count": 221, "char_count": 896, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7165, "quality_score": 0.8583, "entities": { "genes": [ "SOX2", "KLF4", "OCT4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:42.786886", "source": { "split": "train_shard_00001", "doc_id": 501 }, "chunk_id": "train_shard_00001_501_0", "global_id": 6361 }, { "text": "Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum's chromosomal structure, pangenome, and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites, including one RM system hot spot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms. IMPORTANCE Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections", "token_count": 526, "char_count": 2127, "word_count": 301, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:57:43.446855", "source": { "split": "train_shard_00001", "doc_id": 502 }, "chunk_id": "train_shard_00001_502_0", "global_id": 6362 }, { "text": "Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the United States across a 20-year span. We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation, and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.\n\nGenomic Stability and Genetic Defense Systems in Dolosigranulum pigrum, a Candidate Beneficial Bacterium from the Human Microbiome.", "token_count": 178, "char_count": 669, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7802, "quality_score": 0.8901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:43.887330", "source": { "split": "train_shard_00001", "doc_id": 502 }, "chunk_id": "train_shard_00001_502_1", "global_id": 6363 }, { "text": "

Background

Rare actinomycetes, particularly Gordoni spp., are emerging as critical sources of bioactive metabolites and opportunistic pathogens.

Results

In this study, we isolated three novel Gordonia strains from soil samples and characterized their taxonomic status using a polyphasic taxonomic approach. Phylogenetic analysis of 16S rRNA genes and whole-genome comparisons indicated that strains CPCC 205333 T, CPCC 205515 T, and CPCC 206044 T represent three distinct novel species. The overall genome relatedness indices of average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) between these studied strains and their related type strains of the genus Gordonia were all below the established thresholds for species delineation, confirming the classification of these three as novel species, for which we propose the names Gordonia altitudinis sp. nov., Gordonia ligustrum sp. nov., and Gordonia pistacia sp. nov., respectively. Functional annotation revealed their ecological versatility, with Gordonia spp. contributing significantly to soil microbiome functionality through plant growth-promoting traits (e.g., nitrogen fixation, siderophore production) and biosynthetic gene clusters (BGCs), while also harboring virulence factors. Pan-genomic analysis of 225 Gordonia strains delineated an open gene pool (α = 0.82; 22% fluidity), reflecting adaptive plasticity. Core genomes were enriched in conserved metabolic pathways, whereas accessory and strain-specific genes showed niche-driven functional diversification, suggesting ecological specialization.

Conclusion

These findings expand the genomic and functional understanding of Gordonia, highlighting its dual role in environmental resilience and pathogenicity, with potential applications in biotechnology and microbiome engineering.", "token_count": 492, "char_count": 1871, "word_count": 229, "semantic_coherence": 1, "information_density": 0.7293, "quality_score": 0.8646, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:44.534450", "source": { "split": "train_shard_00001", "doc_id": 503 }, "chunk_id": "train_shard_00001_503_0", "global_id": 6364 }, { "text": "Genomic insights into Gordonia diversity: proposal of three novel species (Gordonia. altitudinis sp. nov., Gordonia. ligustrum sp. nov., and Gordonia. pistacia sp. nov.) with distinct environmental and biomedical traits.", "token_count": 57, "char_count": 220, "word_count": 29, "semantic_coherence": 1, "information_density": 0.8276, "quality_score": 0.9138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:44.903702", "source": { "split": "train_shard_00001", "doc_id": 503 }, "chunk_id": "train_shard_00001_503_1", "global_id": 6365 }, { "text": "Abstract

Quercus infectoria is one of the most abundant native oak species in the Kurdistan region of Iraq. This study focused on utilizing leaves of Quercus infectoria for ethanol production in the region. A typical three-step conversion process of acid pretreatment, enzymatic hydrolysis, and yeast fermentation was investigated to produce ethanol from the leaves. Under the selected acid pretreatment and enzymatic hydrolysis conditions, the glucose and xylose concentrations in the hydrolysates reached 11.4 g/L and 16.8 g/L, respectively, with the corresponding sugar conversions of 42.8% and 99.8%. A yeast strain, Kluyveromyces marxianus, was used to ferment mono-sugars in the hydrolysates for ethanol production. The ethanol production rate and conversion of K. marxianus in the fermentation were 0.17 g/L/h and 27%. The techno-economic analysis further concluded that a regional ethanol biorefinery can be established in the Zawita sub-district, Iraq to utilize Q. infectoria leaves to produce 200,000,000 kg ethanol/year with a positive energy balance of 745,052,623 MJ/year. The net annual revenue of the biorefinery is $123,692,804. The payback period of the biorefinery is 10 years.

\n\nBioethanol Production From Leaves of Quercus Infectoria in Kurdistan Region", "token_count": 427, "char_count": 1381, "word_count": 184, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:45.531235", "source": { "split": "train_shard_00001", "doc_id": 504 }, "chunk_id": "train_shard_00001_504_0", "global_id": 6366 }, { "text": "

Summary

To what extent gut bacteria respond to the distinct ecological pressures imposed by human lifestyle remains unclear. Here, we investigate how genomic adaptation in gut bacteria differ between industrialized and non-industrialized human populations. We generated a broad collection of isolate genomes spanning diverse host geographies, lifestyles, species, and strains. We first found that compared to MAGs, paired isolate genomes recover more functional elements and signals of horizontal gene transfers (HGTs). Leveraging isolate genomes from multiple species, we find that strains from industrialized hosts experience an expansion of proteome size and harbor greater pangenome fluidity, driven by recent events of HGTs. Gene- and variant-level analyses reveal convergent patterns of lifestyle-specific adaptation in functions that are critical for ecological adaptation, such as stress response, cell envelope remodeling and central metabolism. Our results demonstrate that industrialization imprints evolutionary signatures on gut bacterial genomes, illuminating the effects of rapidly changing environments on human biology.\n\nConvergent genomic responses of human gut bacteria to variations in industrialization", "token_count": 254, "char_count": 1233, "word_count": 162, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:46.018612", "source": { "split": "train_shard_00001", "doc_id": 505 }, "chunk_id": "train_shard_00001_505_0", "global_id": 6367 }, { "text": "In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil.\n\nHybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil.", "token_count": 343, "char_count": 1317, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5737, "quality_score": 0.7868, "entities": { "genes": [ "SE3", "SE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:46.589099", "source": { "split": "train_shard_00001", "doc_id": 506 }, "chunk_id": "train_shard_00001_506_0", "global_id": 6368 }, { "text": "Populations of bacterial pathogens are made of strains that often have variable gene content, termed the pangenome. Variations in the genetic makeup of a single strain can alter bacterial physiology and fitness in response to different environmental stimuli. To define biologically relevant genes within a genome, genome-wide knockout transposon mutant libraries have been used to identify genes essential for survival or virulence in a particular strain. Such phenotypic studies have been applied in four different genotypes of the major human pathogen Streptococcus pyogenes , yet challenges exist in comparing results across studies conducted in different genetic backgrounds and conditions. To advance genotype-phenotype inferences within a population genomic framework of 250 S. pyogenes reference genomes, we systematically re-analysed publicly available transposon sequencing datasets from S. pyogenes using a transposon sequencing specific analysis pipeline, Transit. Across 4 genetic backgrounds and 9 phenotypic conditions, 311 genes were highly essential for survival, corresponding to ∼22% of the core genome. Among the 311 genes, functions related to information storage, and processing were overrepresented. Genes associated with cellular processing and signalling were of significantly higher essentiality under in vivo conditions (animal models with differing disease manifestation and site of colonisation) compared to in vitro (varying types of culture media). Finally, essential operons across S. pyogenes genotypes were defined, with an increased number of essential operons detected under in vivo conditions. This study provides an extendible database to which new studies can be added, and a searchable html-based resource to direct future investigations into S. pyogenes population biology.

Importance

Streptococcus pyogenes is a human adapted pathogen occupying restricted ecological niches. Understanding essentiality of genes across different strains and experimental conditions is important to direct research questions and efforts to prevent the large burden of disease caused by S. pyogenes . To this end we systematically reanalysed transposon sequencing studies in S. pyogenes using transposon sequencing specific methods, integrating them into an extendible meta-analysis framework. This provides a repository of gene essentiality in S. pyogenes for the community to guide future phenotypic studies.", "token_count": 528, "char_count": 2440, "word_count": 335, "semantic_coherence": 1, "information_density": 0.5791, "quality_score": 0.7896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:57:47.241408", "source": { "split": "train_shard_00001", "doc_id": 507 }, "chunk_id": "train_shard_00001_507_0", "global_id": 6369 }, { "text": "Pangenome evaluation of gene essentiality inStreptococcus pyogenes", "token_count": 24, "char_count": 73, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:47.599622", "source": { "split": "train_shard_00001", "doc_id": 507 }, "chunk_id": "train_shard_00001_507_1", "global_id": 6370 }, { "text": "Accurate annotation of germline immunoglobulin (IG) and T cell receptor (TCR) loci is critical for understanding adaptive immunity. VDJ-Insights provides a user-friendly software package for characterizing these complex immune regions. In addition, it assesses gene segment functionality, identifies recombination signal sequences (RSS), and annotates complementary-determining regions 1 and 2 (CDR1, CDR2). VDJ-Insights achieved over 99% concordance with curated annotations from multiple species, outperforming existing annotation tools. When applied to 95 haplotypes from the Human Pangenome Reference Consortium, VDJ-Insights identified 652 and 275 novel IG and TCR alleles, respectively, highlighting its scalability for large immunogenetic studies.\n\nVDJ-Insights: simplifying the annotation of genomic IG and TCR regions", "token_count": 219, "char_count": 826, "word_count": 105, "semantic_coherence": 1, "information_density": 0.8381, "quality_score": 0.919, "entities": { "genes": [ "CDR2", "CDR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:48.062116", "source": { "split": "train_shard_00001", "doc_id": 508 }, "chunk_id": "train_shard_00001_508_0", "global_id": 6371 }, { "text": "Black quarter caused by Clostridium (C.) chauvoei is an important bacterial disease that affects cattle and sheep with high mortality. A comparative genomics analysis of 64 C. chauvoei strains, most of European origin and a few of non-European and unknown origin, was performed. The pangenome analysis showed limited new gene acquisition for the species. The accessory genome involved prophages and genomic islands, with variations in gene composition observed in a few strains. This limited accessory genome may indicate that the species replicates only in the host or that an active CRISPR/Cas system provides immunity to foreign genetic elements. All strains contained a CRISPR type I-B system and it was confirmed that the unique spacer sequences therein can be used to differentiate strains. Homologous recombination events, which may have contributed to the evolution of this pathogen, were less frequent compared to other related species from the genus. Pangenome single nucleotide polymorphism (SNP) based phylogeny and clustering indicate diverse clusters related to geographical origin. Interestingly the identified SNPs were mostly non-synonymous. The study demonstrates the possibility of the existence of polymorphic populations in one host, based on strain variability observed for strains from the same animal and strains from different animals of one outbreak. The study also demonstrates that new outbreak strains are mostly related to earlier outbreak strains from the same farm/region. This indicates the last common ancestor strain from one farm can be crucial to understand the genetic changes and epidemiology occurring at farm level. Known virulence factors for the species were highly conserved among the strains. Genetic elements involved in Nicotinamide adenine dinucleotide (NAD) precursor synthesis (via nadA, nadB, and nadC metabolic pathway) which are known as potential anti-virulence loci are completely absent in C. chauvoei compared to the partial inactivation in C. septicum. A novel core-genome MLST based typing method was compared to sequence typing based on CRISPR spacers to evaluate the usefulness of the methods for outbreak investigations.", "token_count": 510, "char_count": 2210, "word_count": 321, "semantic_coherence": 1, "information_density": 0.6044, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:48.715601", "source": { "split": "train_shard_00001", "doc_id": 509 }, "chunk_id": "train_shard_00001_509_0", "global_id": 6372 }, { "text": "Genome Sequence Analysis of Clostridium chauvoei Strains of European Origin and Evaluation of Typing Options for Outbreak Investigations.", "token_count": 39, "char_count": 144, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:49.070445", "source": { "split": "train_shard_00001", "doc_id": 509 }, "chunk_id": "train_shard_00001_509_1", "global_id": 6373 }, { "text": "Lipoxygenase-based and lipoxygenase-deficient okara were modified by Kluyveromyces marxianus fermentation, then adding modified okara back to the corresponding soymilk to prepare soy yogurt. The physicochemical properties, texture, and volatile components of soy yogurt were characterized. The results showed that okara modified by Kluyveromyces marxianus fermentation was rich in soluable dietary fiber and was imparted better water-holding capacity, swelling capacity, and oil-holding capacity. The soy yogurt with the modified okara was greatly enhanced in its appearance, texture and was relatively stable during storage. Moreover, lipoxygenase-based soy yogurt had a unique soybean flavor while lipoxygenase-deficient soy yogurt had a slight beany flavor and soybean flavor. This article guides a bio-modified method for okara and provides a theoretical basis for the further development and application of soy yogurt with high dietary fiber as well as lipoxygenase-deficient soy yogurt.

Supplementary information

The online version contains supplementary material available at 10.1007/s10068-021-01003-w.\n\nCharacteristics of lipoxygenase-based and lipoxygenase-deficient soy yogurt with modified okara.", "token_count": 337, "char_count": 1229, "word_count": 154, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:49.638277", "source": { "split": "train_shard_00001", "doc_id": 510 }, "chunk_id": "train_shard_00001_510_0", "global_id": 6374 }, { "text": "Rice-acid has abundant taste substances and health protection function due to the various bioactive compounds it contains, including organic acids. L-lactic acid is the most abundant organic acid in rice-acid, but the regulatory mechanisms of L-lactic acid accumulation in rice-acid are obscure. In this study, we analyzed the dynamic changes in organic acids and taste substances in rice-acid in various fermentation phases and different inoculation methods. We identified the key genes involved in taste substance biosynthesis by RNA-Seq analysis and compared the data of four experimental groups. We found that the interaction of the differences in key functional genes (L-lactate dehydrogenase and D-lactate dehydrogenase) and key metabolism pathways (glycolysis, pyruvate metabolism, TCA cycle, amino acid biosynthesis, and metabolism) might interpret the accumulation of L-lactic acid, other organic acids, and taste substances in rice-acid fermented with Lacticaseibacillus paracasei. The experimental data provided the basis for exploring regulatory mechanisms of taste substance accumulation in rice-acid.\n\nRegulatory Mechanisms of L-Lactic Acid and Taste Substances in Chinese Acid Rice Soup (Rice-Acid) Fermented With a Lacticaseibacillus paracasei and Kluyveromyces marxianus.", "token_count": 346, "char_count": 1309, "word_count": 175, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:50.209756", "source": { "split": "train_shard_00001", "doc_id": 511 }, "chunk_id": "train_shard_00001_511_0", "global_id": 6375 }, { "text": "

Background

Lentilactobacillus parabuchneri is of particular concern in fermented food bioprocessing due to causing unwanted gas formation, cracks, and off-flavor in fermented dairy foods. This species is also a known culprit of histamine poisonings because of decarboxylating histidine to histamine in ripening cheese. Twenty-eight genomes in NCBI GenBank were evaluated via comparative analysis to determine genomic diversity within this species and identify potential avenues for reducing health associated risks and economic losses in the food industry caused by these organisms.

Result

Core genome-based phylogenetic analysis revealed four distinct major clades. Eight dairy isolates, two strains from an unknown source, and a saliva isolate formed the first clade. Three out of five strains clustered on clade 2 belonged to dairy, and the remaining two strains were isolated from the makgeolli and Korean effective microorganisms (KEM) complex. The third and fourth clade members were isolated from Tete de Moine and dairy-associated niches, respectively. Whole genome analysis on twenty-eight genomes showed ~ 40% of all CDS were conserved across entire strains proposing a considerable diversity among L. parabuchneri strains analyzed. After assigning CDS to their corresponding function, ~ 79% of all strains were predicted to carry putative intact prophages, and ~ 43% of the strains harbored at least one plasmid; however, all the strains were predicted to encode genomic island, insertion sequence, and CRISPR-Cas system. A type I-E CRISPR-Cas subgroup was identified in all the strains, with the exception of DSM15352, which carried a type II-A CRISPR-Cas system. Twenty strains were predicted to encode histidine decarboxylase gene cluster that belongs to not only dairy but also saliva, KEM complex, and unknown source. No bacteriocin-encoding gene(s) or antibiotic resistome was found in any of the L", "token_count": 503, "char_count": 1930, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6523, "quality_score": 0.8262, "entities": { "genes": [ "DSM15352" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:50.889755", "source": { "split": "train_shard_00001", "doc_id": 512 }, "chunk_id": "train_shard_00001_512_0", "global_id": 6376 }, { "text": "parabuchneri strains screened.

Conclusion

The findings of the present work provide in-depth knowledge of the genomics of L. parabuchneri by comparing twenty-eight genomes available to date. For example, the hdc gene cluster was generally reported in cheese isolates; however, our findings in the current work indicated that it could also be encoded in those strains isolated from saliva, KEM complex, and unknown source. We think prophages are critical mobile elements of L. parabuchneri genomes that could pave the way for developing novel tools to reduce the occurrence of this unwanted species in the food industry.\n\nComparative Genomics of Lentilactobacillus parabuchneri isolated from dairy, KEM complex, Makgeolli, and Saliva Microbiomes.", "token_count": 187, "char_count": 751, "word_count": 107, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:51.351610", "source": { "split": "train_shard_00001", "doc_id": 512 }, "chunk_id": "train_shard_00001_512_1", "global_id": 6377 }, { "text": "Homologous recombination is a major force mechanism driving bacterial evolution, host adaptability and acquisition of novel virulence traits. Pectobacterium parmentieri is a plant bacterial pathogen distributed worldwide, primarily affecting potatoes, by causing soft rot and blackleg diseases. The goal of this investigation was to understand the impact of homologous recombination on the genomic evolution of P. parmentieri . Analysis of P. parmentieri genomes using Roary revealed a dynamic pan-genome with 3,742 core genes and over 55% accessory genome variability. Bayesian population structure analysis identified seven lineages, indicating species heterogeneity. ClonalFrameML analysis displayed 5,125 recombination events, with the lineage 4 exhibiting the highest events. FastGEAR analysis identified 486 ancestral and 941 recent recombination events ranging 43 bp - 119 kb and 36 bp - 13.96 kb, respectively, suggesting ongoing adaptation. Notably, 11% (412 genes) of the core genome underwent recent recombination, with lineage 1 as the main donor. The prevalence of recent recombination (double compared to ancient) events implies continuous adaptation, possibly driven by global potato trade. Recombination events were found in vital cellular processes (DNA replication, DNA repair, RNA processing, homeostasis, and metabolism), pathogenicity determinants (type secretion systems, cell-wall degrading enzymes, iron scavengers, lipopolysaccharides, flagellum, etc.), antimicrobial compounds (phenazine and colicin) and even CRISPR-Cas genes. Overall, these results emphasize the role of homologous recombination in P. parmentieri ’s evolutionary dynamics, influencing host colonization, pathogenicity, adaptive immunity, and ecological fitness.

Significance

This study explores the influence of homologous recombination on the genomic evolution of the globally distributed plant pathogen P. parmentieri , characterized by highly heterogenous strains from various global locations. Our findings reveal diverse recombinogenic patterns within the core genomes of P", "token_count": 512, "char_count": 2082, "word_count": 272, "semantic_coherence": 1, "information_density": 0.7022, "quality_score": 0.8511, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:52.031545", "source": { "split": "train_shard_00001", "doc_id": 513 }, "chunk_id": "train_shard_00001_513_0", "global_id": 6378 }, { "text": "parmentieri isolates, notably in genomic loci associated with vital cell functions, pathogenicity determinants, and CRISPR-Cas genes. These findings highlight the role of homologous recombination in shaping the genomes of P. parmentieri and impacting its phytopathogenic lifestyle. Additionally, the data suggest a potential role of recombination in the ecological adaptation of this species across different climates, providing insights into the worldwide presence of P. parmentieri . This study represents a pioneering exploration of the impact of homologous recombination on the dynamic evolutionary genomics of the soft rot-causing bacterium P. parmentieri .\n\nImpact of homologous recombination on core genome evolution and host adaptation ofPectobacterium parmentieri", "token_count": 181, "char_count": 779, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:52.499463", "source": { "split": "train_shard_00001", "doc_id": 513 }, "chunk_id": "train_shard_00001_513_1", "global_id": 6379 }, { "text": "The hypersaline soils of the Odiel Saltmarshes Natural Area are an extreme environment with high levels of some heavy metals; however, it is a relevant source of prokaryotic diversity that we aim to explore. In this study, six strains related to the halophilic genus Pseudidiomarina were isolated from this habitat. The phylogenetic study based on the 16S rRNA gene sequence and the fingerprinting analysis suggested that they constituted a single new species within the genus Pseudidiomarina. Comparative genomic analysis based on the OGRIs indices and the phylogeny inferred from the core genome were performed considering all the members of the family Idiomarinaceae. Additionally, a completed phenotypic characterization, as well as the fatty acid profile, were also carried out. Due to the characteristics of the habitat, genomic functions related to salinity and high heavy metal concentrations were studied, along with the global metabolism of the six isolates. Last, the ecological distribution of the isolates was studied in different hypersaline environments by genome recruitment. To sum up, the six strains constitute a new species within the genus Pseudidiomarina, for which the name Pseudidiomarina terrestris sp. nov. is proposed. The low abundance in all the studied hypersaline habitats indicates that it belongs to the rare biosphere in these habitats. In silico genome functional analysis suggests the presence of heavy metal transporters and pathways for nitrate reduction and nitrogen assimilation in low availability, among other metabolic traits.\n\nThe Hypersaline Soils of the Odiel Saltmarshes Natural Area as a Source for Uncovering a New Taxon: Pseudidiomarina terrestris sp. nov.", "token_count": 437, "char_count": 1748, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:53.141380", "source": { "split": "train_shard_00001", "doc_id": 514 }, "chunk_id": "train_shard_00001_514_0", "global_id": 6380 }, { "text": "

ABSTRACT

Corynebacterium is a predominant genus in the skin microbiome, yet its genetic diversity on skin is incompletely characterized and lacks a comprehensive set of reference genomes. Our work aims to investigate the distribution of Corynebacterium species on the skin, as well as to expand the existing genome reference catalog to enable more complete characterization of skin metagenomes. We used V1-V3 16S rRNA gene sequencing data from 14 body sites of 23 healthy volunteers to characterize Corynebacterium diversity and distribution across healthy human skin. Corynebacterium tuberculostearicum is the predominant species found on human skin and we identified two distinct C. tuberculostearicum ribotypes (A & B) that can be distinguished by variation in the 16S rRNA V1-V3 sequence. One is distributed across all body sites and the other found primarily on the feet. We performed whole genome sequencing of 40 C. tuberculostearicum isolates cultured from the skin of five healthy individuals across seven skin sites. We generated five closed genomes of diverse C. tuberculostearicum which revealed that C. tuberculostearicum isolates are largely syntenic and carry a diversity of methylation patterns, plasmids and CRISPR/Cas systems. The pangenome of C. tuberculostearicum is open with a core genome size of 1806 genes and a pangenome size of 5451 total genes. This expanded pangenome enabled the mapping of 24% more C. tuberculostearicum reads from shotgun metagenomic datasets derived from skin body sites. Finally, while the genomes from this study all fall within a C. tuberculostearicum species complex, the ribotype B isolates may constitute a new species.

IMPORTANCE

Amplicon sequencing data combined with isolate whole genome sequencing has expanded our understanding of Corynebacterium on the skin. Human skin is characterized by a diverse collection of Corynebacterium species but C. tuberculostearicum predominates many sites. Our work supports the emerging idea that C", "token_count": 516, "char_count": 2009, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5254, "quality_score": 0.7627, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:57:53.800794", "source": { "split": "train_shard_00001", "doc_id": 515 }, "chunk_id": "train_shard_00001_515_0", "global_id": 6381 }, { "text": "tuberculostearicum is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex including a potentially new species which we are calling C. hallux based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomics and growth in skin-like media. This isolate collection and high-quality genome resource sets the stage for developing engineered strains for both basic and translational clinical studies. Microbiomes are shaped by taxa that are both characteristic to those sites and functionally important to that community. The genus Corynebacterium is one such taxa for the human skin and nares. Foundational studies using 16S rRNA gene sequencing and shotgun metagenomics by our lab (1, 2) and others (3) have established Corynebacterium as common members of the skin microbiome. While Corynebacterium have been positively correlated with the resolution of dysbiosis associated with eczema flares (4), the importance of the Corynebacterium spp. is less defined for skin disease severity in primary immune deficient patients (5, 6). Corynebacterium spp. are predominant members of the human aerodigestive tract microbiome (nares, oral cavity and respiratory tract) (3) and participate in microbe-microbe interactions with members of nasal microbiome (7, 8). Corynebacterium have been shown to engage with the host immune system, specifically C. accolens -promoted IL23-dependent inflammation in mice on a high-fat diet (9). C. bovis and C. mastiditis have been shown to predominate the microbiome of a ADAM10-deficient mouse model (10) as well as an ADAM17-deficient mouse model of eczema (11). Finally, C. tuberculostearicum has been shown to induce inflammation in human epidermal keratinocyte cell cultures (12). These studies establish Corynebacterium spp. as key members of the skin microbiome capable of both microbe-microbe and microbe-host interactions", "token_count": 506, "char_count": 1957, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [ "ADAM10", "IL23", "ADAM17" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:54.456923", "source": { "split": "train_shard_00001", "doc_id": 515 }, "chunk_id": "train_shard_00001_515_1", "global_id": 6382 }, { "text": "A critical resource for understanding the biology of Corynebacterium on the skin is a robust collection of complete reference genomes, including isolates collected from a variety of individuals and body sites. Previously published genome collections from skin- or nares-resident species include Staphylococcus epidermidis (13), Cutibacterium acnes (14) and the recent comparative analysis of Dolosigranulum pigrum (15). Of note, while emerging bioinformatic methods and pipelines are now being employed to extract nearly-complete genomes (MAGs) from metagenomic assemblies of skin samples (16), MAGs are not yet a substitute for genomes from cultured isolates to understand strain level or pangenomic diversity. In addition to functional prediction, comparative genomics is increasingly being used to augment conventional microbiological methods to define or redefine taxonomic boundaries (17, 18), as well as describe the full extent of diversity within these boundaries (19). A pangenome, which encompasses the complete set of genes present within a set of genome sequences, enables the characterization of gene-level heterogeneity within a taxonomic group. The pangenome is commonly subdivided into the ‘core’ genome, referring to genes present in all strains, and the ‘accessory’ or ‘dispensable’ genome, referring to those present in only one or some isolates. (The accessory pangenome can be further subdivided to reflect a wider range of gene uniqueness, e.g. singletons.) Thorough characterization of taxa is limited by the availability of representative and high-quality genome assemblies. Unfortunately, with the exceptions of clinically relevant Corynebacterium spp. ( e.g. , C. diphtheriae , C. striatum and C. pseudotuberculosis ), the genus is inadequately sequenced, with 75% of species having fewer than six genomes. This includes common skin-associated species like C. tuberculostearicum with just five unique isolate genomes, only two of which are from skin. This work seeks first to characterize the distribution of Corynebacterium across 14 skin sites from 23 healthy volunteers", "token_count": 505, "char_count": 2098, "word_count": 299, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:55.106895", "source": { "split": "train_shard_00001", "doc_id": 515 }, "chunk_id": "train_shard_00001_515_2", "global_id": 6383 }, { "text": "The second goal of this work focuses on what we identify as the predominant skin Corynebacterium species, C. tuberculostearicum . We have sequenced 23 distinct C. tuberculostearicum strains (n=40 genomes before dereplication), a five-fold increase in the number of publicly available, unique genomes (n=5). In addition to short-read assemblies, we generated five complete genomes which, along with the type strain (DSM44922), demonstrate that C. tuberculostearicum genomes are largely syntenic and carry a number of methylation systems as well as a CRISPR/Cas system. Genes from the C. tuberculostearicum genomes in our collection fall into 5451 gene clusters comprising the species pangenome. This expanded pangenome, as compared to existing public references, improved the mapping of C. tuberculostearicum metagenomic reads from unrelated healthy volunteers. In addition, we have identified a distinct C. tuberculostearicum clade that is highly enriched on the feet that may represent a new species, tentatively designated Corynebacterium hallux .\n\nGenomic characterization of theC. tuberculostearicumspecies complex, a ubiquitous member of the human skin microbiome", "token_count": 313, "char_count": 1175, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [ "DSM44922" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:55.670157", "source": { "split": "train_shard_00001", "doc_id": 515 }, "chunk_id": "train_shard_00001_515_3", "global_id": 6384 }, { "text": "Members of the lactic acid bacillus group are well-known probiotics and primarily isolated from fermented food, dairy products, intestinal and gut environment of human. Since probiotics from the human source are preferred, there exists a huge repertoire of lactobacilli in the human oral cavity which could prove a much better niche to be exploited for these beneficial microorganisms. Therefore, in this study, four lactobacilli strains, including strain DISK7, reported earlier, isolated from dental plaque samples of a healthy humans were evaluated for their probiotic potential. Strains displayed 99.9% of 16S rRNA gene sequence identity with species of the genera Lactobacillus and Limosilactobacillus. All strains showed lactic acid production, tolerance to low pH and antibiotic sensitivity. Variations were observed among strains in their aggregation ability, biofilm formation, bile salt resistance and cholesterol degradation. Further, we analyzed the interaction of strains with other oral commensals and opportunistic pathogens in co-culture experiments. Isolates DISK7 and DISK26 exhibited high co-aggregation (> 70%) with secondary colonizers, Streptococcus pyogenes and Veillonella parvula, respectively, but their aggregation ability was decreased with opportunistic pathogens. Furthermore, strains showed a substantial increase in biofilm in co-culture with other Lactobacillus isolates, indicating their ability to proliferate commensal bacteria in the oral environment. These microbes continually evolve in terms of niche adaptation as evidenced in genome analysis. The highlight of the investigation is the isolation and evaluation of the probiotic lactobacilli from the human oral cavity, which could prove a much better niche to be exploited for the effective commercialization of these beneficial microbes", "token_count": 463, "char_count": 1863, "word_count": 252, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [ "DISK26", "DISK7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:56.312518", "source": { "split": "train_shard_00001", "doc_id": 516 }, "chunk_id": "train_shard_00001_516_0", "global_id": 6385 }, { "text": "Taken together, probiotic properties and interaction with commensal bacteria, these isolates exhibit the huge potential to be developed as alternative bioresource agents for maintenance of oral health.

Supplementary information

The online version contains supplementary material available at 10.1007/s12088-023-01108-2.\n\nEvaluation of Human Dental Plaque Lactic Acid Bacilli for Probiotic Potential and Functional Analysis in Relevance to Oral Health.", "token_count": 122, "char_count": 458, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8727, "quality_score": 0.9364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:56.701219", "source": { "split": "train_shard_00001", "doc_id": 516 }, "chunk_id": "train_shard_00001_516_1", "global_id": 6386 }, { "text": "Reference data on genomic variation form the basis of genetic research. Limitations in identifying genetic variation from single reference sequences have been recently overcome, as improvements in sequencing technologies have allowed the generation of pangenomic references from multiple accurate, chromosome-level de novo assemblies. Here, we present a comprehensive Emirati telomere-to-telomere (T2T) pangenome generated from 58 individuals, comprising 28 trio-based and 30 single-sample assemblies. The resulting 116 haplotype-resolved assemblies demonstrate high contiguity, with a median continuity of 150 Mb and a median quality value (QV) of 59, achieving T2T-level scaffold status for 71.9% of chromosomes. These assemblies form the foundation of the Emirati T2T pangenome graph. The graph reveals levels of genomic diversity comparable to those reported by the Human Pangenome Reference Consortium, while also capturing regionally enriched and difficult-to-assemble variation, uniquely accessible through the Emirati T2T assemblies. This reference makes a valuable global contribution to human pangenomics and serves as a critical resource for advancing precision medicine in the United Arab Emirates.\n\nThe Emirati T2T-Level Pangenome: A Graph of 58 Complete Genomes", "token_count": 315, "char_count": 1275, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:57.265181", "source": { "split": "train_shard_00001", "doc_id": 517 }, "chunk_id": "train_shard_00001_517_0", "global_id": 6387 }, { "text": "A pangenome analysis offers a unique exploration of the metabolic and genetic diversity, range of ecological niches, and evolution of a particular genus or species. However, such pangenomic analyses are uncommon among environmentally relevant genera. Here, we present freshwater pangenomes of three environmentally relevant genera, Limnohabitans, Aquabacterium, and Novosphingobium. These genera had been detected in hydrocarbon degrading cultures in previous research by our group. Using pangenomic tools we attempted to characterize the extent of hydrocarbon degradation potential within each pangenome and determine what ecological niche each genus occupies within hydrocarbon degradation. In total 46 Limnohabitans, 10 Aquabacterium, and 32 Novosphingobium freshwater genomes were collected from various databases and compiled into pangenomes. We found that each pangenome harbours downstream hydrocarbon degrading potential and unexpected genetic diversity within its core and accessory pangenomes possibly stemming from geographic and metagenomic data processing influences. This work was the first to explore pangenomes of these environmentally relevant genera.\n\nPangenomic analysis of three putative hydrocarbon degrading genera <i>Limnohabitans, Aquabacterium</i>, and <i>Novosphingobium</i> collected from freshwater sources.", "token_count": 363, "char_count": 1394, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6568, "quality_score": 0.8284, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:57.843077", "source": { "split": "train_shard_00001", "doc_id": 518 }, "chunk_id": "train_shard_00001_518_0", "global_id": 6388 }, { "text": "While graph-based pangenomes have become a standard and interoperable foundation for comparisons across multiple reference genomes, integrating protein-coding gene annotations across pangenomes in a single ‘pangene set’ remains challenging, both because of methodological inconsistency and biological presence-absence variation (PAV). Here, we review and experimentally evaluate the root of genome annotation and pangene set inconsistency using two polyploid plant pangenomes: cotton and soybean, which were chosen because of their existing diverse high-quality genomic resources and the known importance of gene presence-absence variation in their respective breeding programs. We first demonstrate that building pangene sets across different genome resources is highly error prone: PAV calculated directly from the genome annotations hosted on public repositories recapitulates structure in annotation methods and not biological sequence differences. Re-annotation of all genomes with a single identical pipeline largely resolves the broadest stroke issues; however, substantial challenges remain, including a surprisingly common case where exactly identical sequences have different gene model structural annotations. Combined, these results clearly show that pangenome gene model annotations must be carefully integrated before any biological inference can be made regarding sequence evolution, gene copy-number, or presence-absence variation.\n\nEvolutionary and methodological considerations when interpreting gene presence-absence variation in pangenomes", "token_count": 302, "char_count": 1559, "word_count": 196, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:58.405424", "source": { "split": "train_shard_00001", "doc_id": 519 }, "chunk_id": "train_shard_00001_519_0", "global_id": 6389 }, { "text": "

Background

Leptospirosis is a complex zoonotic disease mostly caused by a group of eight pathogenic species (L. interrogans, L. borgpetersenii, L. kirschneri, L. mayottensis, L. noguchii, L. santarosai, L. weilii, L. alexanderi), with a wide spectrum of animal reservoirs and patient outcomes. Leptospira interrogans is considered as the leading causative agent of leptospirosis worldwide and it is the most studied species. However, the genomic features and phylogeography of other Leptospira pathogenic species remain to be determined.

Methodology/principal findings

Here we investigated the genome diversity of the main pathogenic Leptospira species based on a collection of 914 genomes from strains isolated around the world. Genome analyses revealed species-specific genome size and GC content, and an open pangenome in the pathogenic species, except for L. mayottensis. Taking advantage of a new set of genomes of L. santarosai strains isolated from patients in Costa Rica, we took a closer look at this species. L. santarosai strains are largely distributed in America, including the Caribbean islands, with over 96% of the available genomes originating from this continent. Phylogenetic analysis showed high genetic diversity within L. santarosai, and the clonal groups identified by cgMLST were strongly associated with geographical areas. Serotype identification based on serogrouping and/or analysis of the O-antigen biosynthesis gene loci further confirmed the great diversity of strains within the species.

Conclusions/significance

In conclusion, we report a comprehensive genome analysis of pathogenic Leptospira species with a focus on L. santarosai. Our study sheds new light onto the genomic diversity, evolutionary history, and epidemiology of leptospirosis in America and globally. Our findings also expand our knowledge of the genes driving O-antigen diversity. In addition, our work provides a framework for understanding the virulence and spread of L. santarosai and for improving its surveillance in both humans and animals.", "token_count": 523, "char_count": 2069, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5986, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:57:59.061696", "source": { "split": "train_shard_00001", "doc_id": 520 }, "chunk_id": "train_shard_00001_520_0", "global_id": 6390 }, { "text": "Phylogenomics of Leptospira santarosai, a prevalent pathogenic species in the Americas.", "token_count": 29, "char_count": 87, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:57:59.417444", "source": { "split": "train_shard_00001", "doc_id": 520 }, "chunk_id": "train_shard_00001_520_1", "global_id": 6391 }, { "text": "Listeria monocytogenes is a major foodborne pathogen associated with fresh produce contamination, posing a significant public health risk due to its adaptability and virulence. This study investigates the genomic diversity and distribution of L. monocytogenes strains isolated from imported and domestic fresh produce in Mexico between 2014 and 2018. A total of 113 L. monocytogenes strains were isolated from produce commodities and subjected to whole-genome sequencing. The analysis focused on identifying lineages, serogroups, clonal complexes (CCs), antimicrobial resistance genes, virulence factors, prophage-associated regions, and SNP clusters, while the pangenome was characterized to assess both core and accessory gene diversity. Two main lineages (I and II) were identified, with lineage I predominantly associated with imported produce. Thirty-two CCs were detected, with CC4, CC11, and CC20 being the most prevalent. The pangenome analysis revealed 2188 core genes and 3739 accessory genes. Antimicrobial resistance genes, including fosX, lin, norB, and sul, were present in all strains. Virulence analysis identified 78 virulence genes, with notable differences among serogroups. Prophage analysis revealed 189 prophage-associated regions, with common phages such as A118 and LP-101 detected predominantly in serogroup IIa. The SNP cluster analysis grouped the strains into 33 clusters, with 48 % of the strains from imported produce concentrated in only three major clusters, indicating potential common sources or similar environmental exposures. The significant genomic diversity and SNP clustering of L. monocytogenes strains underscore the pathogen's adaptability and widespread dissemination potential in the global food supply chain. The presence of virulent CCs and antimicrobial resistance genes highlights an ongoing public health risk, emphasizing the need for enhanced surveillance and targeted interventions to prevent listeriosis outbreaks.\n\nGenomic diversity and distribution of Listeria monocytogenes strains isolated from imported and national fresh produce in Mexico from 2014 to 2018", "token_count": 512, "char_count": 2116, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5828, "quality_score": 0.7914, "entities": { "genes": [ "CC11", "CC20", "CC4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:00.042958", "source": { "split": "train_shard_00001", "doc_id": 521 }, "chunk_id": "train_shard_00001_521_0", "global_id": 6392 }, { "text": "

Background

While benchmarks on short-read variant calling suggest a low error rate below 0.5%, they are only applicable to predefined confident regions. For a human sample without such regions, the error rate could be 10 times higher. Although multiple sets of easy regions have been identified to alleviate the issue, they fail to consider nonreference samples or are biased toward existing short-read data or aligners.

Results

Here, using hundreds of high-quality human assemblies, we derived a set of sample-agnostic easy regions where short-read variant calling reaches high accuracy. These regions cover 88.2% of GRCh38, 92.2% of coding regions, and 96.3% of ClinVar pathogenic variants. They achieve a good balance between coverage and easiness and can be generated for other human assemblies or species with multiple well-assembled genomes.

Conclusions

This resource provides a convenient and powerful way to filter spurious variant calls for clinical or research human samples.\n\nFinding easy regions for short-read variant calling from pangenome data.", "token_count": 258, "char_count": 1081, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:00.595580", "source": { "split": "train_shard_00001", "doc_id": 522 }, "chunk_id": "train_shard_00001_522_0", "global_id": 6393 }, { "text": "

Introduction

The gut microbiota plays a crucial role in maintaining human health, and probiotics have gained significant attention for their potential benefits. Among the diverse array of gut bacteria, Akkermansia muciniphila, and Lactobacillus spp. have emerged as promising candidates for their putative probiotic properties.

Methods

In this study, we conducted a comprehensive comparative in silico analysis of the genomes of A. muciniphila and Lactobacillus to decipher their probiotic potential. Utilizing a range of bioinformatics tools, we evaluated various genomic attributes, including functional gene content, metabolic pathways, antimicrobial peptide production, adhesion factors, and stress response elements. These findings revealed distinctive genomic signatures between the two genera. A. muciniphila genomes exhibited a high prevalence of mucin-degrading enzymes, suggesting a specialized adaptation for mucin utilization in the gut environment.

Results

Additionally, the presence of specific pathways for short-chain fatty acid production highlighted its potential impact on host health. Lactobacillus genomes, on the other hand, demonstrated a diverse repertoire of functional genes associated with probiotic attributes, including the production of antimicrobial peptides and adhesion factors, indicating potential for host-microbe interactions and immune modulation. Furthermore, this analysis unveiled the genetic basis of stress tolerance in both genera, revealing conserved mechanisms for surviving the dynamic conditions of the gut ecosystem.

Conclusion

This study also shed light on the distribution of antibiotic-resistance genes, allowing us to assess safety concerns associated with their potential use as probiotics. Overall, this comparative in silico exploration provides valuable insights into the genomic foundation of A. muciniphila and Lactobacillus probiotic potential", "token_count": 499, "char_count": 2002, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6446, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:01.250103", "source": { "split": "train_shard_00001", "doc_id": 523 }, "chunk_id": "train_shard_00001_523_0", "global_id": 6394 }, { "text": "These findings contribute to the understanding of their respective roles within the gut microbiota and offer a foundation for further experimental investigations. As probiotic applications continue to expand, this study advances our knowledge of the genetic underpinnings that govern their functionality and highlights promising avenues for future therapeutic interventions and personalized health strategies.\n\nGenomic Face-off: An <i>In Silico</i> Comparison of the Probiotic Potential of <i>Lactobacillus</i> spp. and <i>Akkermansia muciniphila</i>.", "token_count": 154, "char_count": 587, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8116, "quality_score": 0.9058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:01.692103", "source": { "split": "train_shard_00001", "doc_id": 523 }, "chunk_id": "train_shard_00001_523_1", "global_id": 6395 }, { "text": "Bacillus sp. THPS1 is a novel strain isolated from a high-temperature hot spring in Thailand, exhibiting distinctive genomic features that enable adaptation to an extreme environment. This study aimed to characterize the genomic and functional attributes of Bacillus sp. THPS1 to understand its adaptation strategies and evaluate its potential for biotechnological applications. The draft genome is 5.38 Mbp with a GC content of 35.67%, encoding 5606 genes, including those linked to stress response and sporulation, which are essential for survival in high-temperature conditions. Phylogenetic analysis and average nucleotide identity (ANI) values confirmed its classification as a distinct species within the Bacillus genus. Pangenome analysis involving 19 others closely related thermophilic Bacillus species identified 1888 singleton genes associated with heat resistance, sporulation, and specialized metabolism, suggesting adaptation to nutrient-deficient, high-temperature environments. Genomic analysis revealed 12 biosynthetic gene clusters (BGCs), including those for polyketides and non-ribosomal peptides, highlighting its potential for synthesizing secondary metabolites that may facilitate its adaptation. Additionally, the presence of three Siphoviridae phage regions and 96 mobile genetic elements (MGEs) suggests significant genomic plasticity, whereas the existence of five CRISPR arrays implies an advanced defense mechanism against phage infections, contributing to genomic stability. The distinctive genomic features and functional capacities of Bacillus sp. THPS1 make it a promising candidate for biotechnological applications, particularly in the production of heat-stable enzymes and the development of resilient bioformulations.\n\nGenomic Characterization of Bacillus sp. THPS1: A Hot Spring-Derived Species with Functional Features and Biotechnological Potential.", "token_count": 468, "char_count": 1938, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [ "THPS1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:02.340479", "source": { "split": "train_shard_00001", "doc_id": 524 }, "chunk_id": "train_shard_00001_524_0", "global_id": 6396 }, { "text": "

SUMMARY

Somatic mosaicism is essential in human biology and disease, yet robust benchmarks are scarce. The SMaHT Consortium mixed six HapMap cell lines to create artificial somatic variants spanning 0.25% to 16.5% variant allele fractions. We developed a technology-agnostic method that builds pangenome graphs from individual assemblies to create unified benchmarking sets: > 6M single-nucleotide variants, 1.8M small insertions/deletions, 49K structural variations, and 10K mobile element insertions across autosomes, X, and mitochondrial chromosomes. We validated the variants using ultra-deep simulated reads and developed a binomial-based model to estimate coverage requirements for variant detection. Evaluating multiple callers showed CHM13 alignment improves structural variant detection and offers advantages in difficult-to-map regions compared to GRCh38. Systematic characterization showed regions with low detection rate are enriched in centromeres, satellite sequences, tandem repeats, and falsely duplicated genes. This accurate, versatile resource enables systematic evaluation of somatic variant detection technologies.\n\nA Pangenomic Method for Establishing a Somatic Variant Detection Resource in HapMap Mixtures", "token_count": 302, "char_count": 1239, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7516, "quality_score": 0.8758, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:02.938806", "source": { "split": "train_shard_00001", "doc_id": 525 }, "chunk_id": "train_shard_00001_525_0", "global_id": 6397 }, { "text": "Clostridium septicum is a Gram-positive, toxin-producing, and spore-forming bacterium that is recognized, together with C. perfringens, as the most important etiologic agent of progressive gas gangrene. Clostridium septicum infections are almost always fatal in humans and animals. Despite its clinical and agricultural relevance, there is currently limited knowledge of the diversity and genome structure of C. septicum. This study presents the complete genome sequence of C. septicum DSM 7534T type strain as well as the first comparative analysis of five C. septicum genomes. The taxonomy of C. septicum, as revealed by 16S rRNA analysis as well as by genomic wide indices such as protein-based phylogeny, average nucleotide identity, and digital DNA-DNA hybridization indicates a stable clade. The composition and presence of prophages, CRISPR elements and accessory genetic material was variable in the investigated genomes. This is in contrast to the limited genetic variability described for the phylogenetically and phenotypically related species Clostridium chauvoei. The restriction-modification (RM) systems between two C. septicum genomes were heterogeneous for the RM types they encoded. C. septicum has an open pangenome with 2,311 genes representing the core genes and 1,429 accessory genes. The core genome SNP divergence between genome pairs varied up to 4,886 pairwise SNPs. A vast arsenal of potential virulence genes was detected in the genomes studied. Sequence analysis of these genes revealed that sialidase, hemolysin, and collagenase genes are conserved compared to the α-toxin and hyaluronidase genes. In addition, a conserved gene found in all C", "token_count": 490, "char_count": 1756, "word_count": 244, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:03.611495", "source": { "split": "train_shard_00001", "doc_id": 526 }, "chunk_id": "train_shard_00001_526_0", "global_id": 6398 }, { "text": "septicum genomes was predicted to encode a leucocidin homolog (beta-channel forming cytolysin) similar (71.10% protein identity) to Clostridium chauvoei toxin A (CctA), which is a potent toxin. In conclusion, our results provide first, valuable insights into strain relatedness and genomic plasticity of C. septicum and contribute to our understanding of the virulence mechanisms of this important human and animal pathogen.\n\nFirst Comparative Analysis of Clostridium septicum Genomes Provides Insights Into the Taxonomy, Species Genetic Diversity, and Virulence Related to Gas Gangrene.", "token_count": 177, "char_count": 612, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7531, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:04.103304", "source": { "split": "train_shard_00001", "doc_id": 526 }, "chunk_id": "train_shard_00001_526_1", "global_id": 6399 }, { "text": "Lactiplantibacillus plantarum is a beneficial bacterium commonly found in fermented foods, including fermented milk products. In the present study, we reported the whole genome sequence of L. plantarum LPJBC5. The complete genome sequence of LPJBC5 was 3.23Mb, and the average GC% was found to be 44.55% encoding a total of 3016 genes. A comprehensive analysis of the LPJBC5 genome detected major carbohydrate-active enzymes, exopolysaccharide synthesis genes (eps), and the presence of genes related to stress response and antioxidant activity. Longevity regulating genes including katE, CAT (chloramphenicol acetyltransferase), catB and their regulating pathways (MAPK signaling pathway) were detected in the LPJBC5 genome. The genome was found to contain plantaracin (pln) operon for the production of antimicrobial bacteriocin and various regions of secondary metabolite biosynthetic gene clusters, including the type III polyketide synthases (T3PKS), Ribosomally synthesized and post-translationally modified peptide product (Ripp-Like), which exhibit specific antimicrobial activity. A comparative pangenome analysis was performed to further evaluate the metabolic framework of L. plantarum JBC5, including the complete L. plantarum genome (N=30) retrieved from publicly available repositories. The core/soft-core genome was found to harbor probiotic associated marker genes. Functional analysis revealed the presence of genes majorly enriched in cell wall/membrane/envelop biogenesis, carbohydrate metabolism and transport, amino acid metabolism and transport, translational mechanism, and transcription processes. Identification of probiotic and longevity associated genes suggests that LPJBC5 holds potential as a probiotic candidate with multifaceted applications in the food industries.", "token_count": 467, "char_count": 1797, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.812, "entities": { "genes": [ "JBC5", "LPJBC5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:05.564598", "source": { "split": "train_shard_00001", "doc_id": 527 }, "chunk_id": "train_shard_00001_527_0", "global_id": 6400 }, { "text": "Exploring the probiotic potential, antioxidant capacity, and healthy aging based on whole genome analysis of Lactiplantibacillus plantarum LPJBC5 isolated from fermented milk product", "token_count": 47, "char_count": 182, "word_count": 23, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "LPJBC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:05.923109", "source": { "split": "train_shard_00001", "doc_id": 527 }, "chunk_id": "train_shard_00001_527_1", "global_id": 6401 }, { "text": "Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations and as an additional source of information when detecting possible transmission events. Due to their variable gene content and order, reference-free methods offer more sensitive detection of genetic differences, especially among closely related samples found in outbreaks. However, across longer genetic distances, frequent recombination can make calculation and interpretation of these differences more challenging, requiring significant bioinformatic expertise and manual intervention during the analysis process. Here, we present a Population analysis PIPEline (PopPIPE) which combines rapid reference-free genome analysis methods to analyse bacterial genomes across these two scales, splitting whole populations into subclusters and detecting plausible transmission events within closely related clusters. We use k-mer sketching to split populations into strains, followed by split k-mer analysis and recombination removal to create alignments and subclusters within these strains. We first show that this approach creates high-quality subclusters on a population-wide dataset of Streptococcus pneumoniae. When applied to nosocomial vancomycin-resistant Enterococcus faecium samples, PopPIPE finds transmission clusters that are more epidemiologically plausible than core genome or multilocus sequence typing (MLST) approaches. Our pipeline is rapid and reproducible, creates interactive visualizations and can easily be reconfigured and re-run on new datasets. Therefore, PopPIPE provides a user-friendly pipeline for analyses spanning species-wide clustering to outbreak investigations.\n\nIntegrated population clustering and genomic epidemiology with PopPIPE.", "token_count": 382, "char_count": 1814, "word_count": 226, "semantic_coherence": 1, "information_density": 0.708, "quality_score": 0.854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:06.512253", "source": { "split": "train_shard_00001", "doc_id": 528 }, "chunk_id": "train_shard_00001_528_0", "global_id": 6402 }, { "text": "

ABSTRACT

The NPIP (nuclear pore interacting protein) gene family has expanded to high copy number in humans and African apes where it has been subject to an excess of amino acid replacement consistent with positive selection (1). Due to the limitations of short-read sequencing, NPIP human genetic diversity has been poorly understood. Using highly accurate assemblies generated from long-read sequencing as part of the human pangenome, we completely characterize 169 human haplotypes (4,665 NPIP paralogs and alleles). Of the 28 NPIP paralogs, just three ( NPIPB2 , B11 , and B14 ) are fixed at a single copy, and only a single locus, B2 , shows no structural variation. Four NPIP paralogs map to large segmental duplication blocks that mediate polymorphic inversions (355 kbp–1.6 Mbp) corresponding to microdeletions associated with developmental delay and autism. Haplotype-based tests of positive selection and selective sweeps identify two paralogs, B9 and B15 , within the top percentile for both tests. Using full-length cDNA data from 101 tissue/cell types, we construct paralog-specific gene models and show that 56% (31/55 most abundant isoforms) have not been previously described in RefSeq. We define six distinct translation start sites and other protein structural features that distinguish paralogs, including a variable number tandem repeat that encodes a beta helix of variable size that emerged ∼3.1 million years ago in human evolution. Among the 28 NPIP paralogs, we identify distinct tissue and developmental patterns of expression with only a few maintaining the ancestral testis-enriched expression. A subset of paralogs ( NPIPA1 , A5 , A6-9 , B3-5 , and B12/B13 ) show increased brain expression. Our results suggest ongoing positive selection in the human population and rapid diversification of NPIP gene models.\n\nStructural variation, selection, and diversification of the NPIP gene family from the human pangenome", "token_count": 506, "char_count": 1957, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [ "NPIPB2", "NPIPA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:07.170564", "source": { "split": "train_shard_00001", "doc_id": 529 }, "chunk_id": "train_shard_00001_529_0", "global_id": 6403 }, { "text": "

Objectives

The worldwide dissemination of carbapenem-resistant Klebsiella pneumoniae co-producing KPC and NDM (KPC-NDM-CRKP) poses a substantial clinical challenge.

Methods

This study characterized 5 KPC-NDM-CRKP isolates from a tertiary hospital in southern China and integrated 460 global isolates genomes to demonstrate the population framework of this epidemic pathogen.

Results

5 clinical isolates were multidrug resistance, exhibiting high level resistance to first-line drugs including carbapenems and ceftazidime/avibactam. Globally, KPC-2-NDM-1 (50.3%) were the most common and an increasing trend of ST11-KL64 (20%) isolates carrying iucA and rmpA / A2 . Resistance and virulence genes were positively associated with specific mobile elements including bla KPC-3 with Tn 4401, iucABC with IncHI1B, iroBCDN with IncQ1. The phylogenetic analysis revealed distinct lineage-specific mutations and pan-genome enrichments synergistically promoted adaptive evolution: cluster 1 had membrane transport and secretion but enhanced immune evasion and horizontal gene transfer, cluster 3 adapted metabolically for nutrient-limited niches; cluster 4 reprogrammed metabolism for host adaptation, cluster 6 displayed membrane repair and reduced virulence (e.g., KC187). High-risk iucA/rmpA -positive isolates in cluster 2 acquired enhanced virulence and metabolic adaptive capacity through recombination hotspots (ABC transporters DdpABCD, efflux systems MdtABCD, metabolic enzymes XylB and MtlD, regulators BaeR and OmpR) and pan-genome enrichment (siderophore biosynthesis, toxin–antitoxin VapC and restriction-modification systems)", "token_count": 491, "char_count": 1659, "word_count": 205, "semantic_coherence": 1, "information_density": 0.7659, "quality_score": 0.8829, "entities": { "genes": [ "KC187", "KL64", "ST11" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:07.823288", "source": { "split": "train_shard_00001", "doc_id": 530 }, "chunk_id": "train_shard_00001_530_0", "global_id": 6404 }, { "text": "Functionally, these traits correlated with high mucoviscosity, serum resistance, siderophore production and lower survival rates in G. mellonella that contribute to epidemiological success.

Conclusions

These findings demonstrated the discrete mutation, horizontal transfer, and accessory genome plasticity collectively drove the epidemiological success of KPC-NDM-CRKP.\n\nGlobal Insights into Evolution and Adaptation in KPC and NDM Coproducing Carbapenem-Resistant Klebsiella pneumoniae", "token_count": 137, "char_count": 503, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8772, "quality_score": 0.9386, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:08.252512", "source": { "split": "train_shard_00001", "doc_id": 530 }, "chunk_id": "train_shard_00001_530_1", "global_id": 6405 }, { "text": "

Background

Probiotic milk-fermented microorganism mixtures (e.g., yogurt, kefir) are perceived as contributing to human health, and possibly capable of protecting against bacterial infections. Co-existence of probiotic microorganisms are likely maintained via complex biomolecular mechanisms, secreted metabolites mediating cell-cell communication, and other yet-unknown biochemical pathways. In particular, deciphering molecular mechanisms by which probiotic microorganisms inhibit proliferation of pathogenic bacteria would be highly important for understanding both the potential benefits of probiotic foods as well as maintenance of healthy gut microbiome.

Results

The microbiome of a unique milk-fermented microorganism mixture was determined, revealing a predominance of the fungus Kluyveromyces marxianus. We further identified a new fungus-secreted metabolite-tryptophol acetate-which inhibits bacterial communication and virulence. We discovered that tryptophol acetate blocks quorum sensing (QS) of several Gram-negative bacteria, particularly Vibrio cholerae, a prominent gut pathogen. Notably, this is the first report of tryptophol acetate production by a yeast and role of the molecule as a signaling agent. Furthermore, mechanisms underscoring the anti-QS and anti-virulence activities of tryptophol acetate were elucidated, specifically down- or upregulation of distinct genes associated with V. cholerae QS and virulence pathways.

Conclusions

This study illuminates a yet-unrecognized mechanism for cross-kingdom inhibition of pathogenic bacteria cell-cell communication in a probiotic microorganism mixture. A newly identified fungus-secreted molecule-tryptophol acetate-was shown to disrupt quorum sensing pathways of the human gut pathogen V. cholerae. Cross-kingdom interference in quorum sensing may play important roles in enabling microorganism co-existence in multi-population environments, such as probiotic foods and the gut microbiome", "token_count": 498, "char_count": 1984, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6611, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:08.903008", "source": { "split": "train_shard_00001", "doc_id": 531 }, "chunk_id": "train_shard_00001_531_0", "global_id": 6406 }, { "text": "This discovery may account for anti-virulence properties of the human microbiome and could aid elucidating health benefits of probiotic products against bacterially associated diseases. Video Abstract.\n\nCross-kingdom inhibition of bacterial virulence and communication by probiotic yeast metabolites.", "token_count": 66, "char_count": 300, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8919, "quality_score": 0.9459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:09.275897", "source": { "split": "train_shard_00001", "doc_id": 531 }, "chunk_id": "train_shard_00001_531_1", "global_id": 6407 }, { "text": "

Motivation

Realising the value of large DNA sequence collections demands efficient search and extraction of sequences of interest. Search queries may vary in size from short gene sequences to multiple whole genomes that are too large to fit in computer memory. In microbial genomics, a routine search application involving both large queries and large collections is the removal of contaminating host genome sequences from microbial (meta)genomes. Where the host is human, sensitive classification and excision of host sequences is usually necessary to protect host genetic information. Precise classification is also critical in order to retain microbial sequences and permit accurate microbial genomic analysis. While human pangenomes have been shown to increase sensitivity of human sequence classification, existing bioinformatic host depletion approaches have either limited precision when used with metagenomes or large computing resource requirements.

Results

We present Deacon, an efficient and versatile sequence filter for raw sequence files and streams. We demonstrate its leading accuracy for the task of host depletion, using less computing resource than existing approaches. By querying a human pangenome index for minimizers contained in each input sequence, Deacon is able to accurately classify and discard diverse human sequences from long reads at over 250Mbp/s with a commodity laptop. We present validation of classification sensitivity, specificity and speed with simulated short and long reads for diverse catalogues of human, bacterial and viral genomes alongside existing methods. Beyond host depletion, Deacon is well suited to common sequence search and filtering applications, particularly those involving large queries. Capable of indexing a human genome in under 30s, Deacon is equipped to rapidly compose custom minimizer indexes using set operations, facilitating efficient search and filtering of massive sequence datasets using gigabase queries.

Availability and implementation

Deacon is implemented as an MIT-licensed command line tool written in Rust and packaged with Bioconda. Code is available from https://github.com/bede/deacon .\n\nDeacon: fast sequence filtering and contaminant depletion", "token_count": 462, "char_count": 2256, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:09.914240", "source": { "split": "train_shard_00001", "doc_id": 532 }, "chunk_id": "train_shard_00001_532_0", "global_id": 6408 }, { "text": "Predominantly used human reference genomes, including GRCh38 and the gapless T2T-CHM13 references, remain limited in their representation of African genomic diversity. We analyzed African Pan- Genome (APG) contig sequences representing 296.5 Mb of African-ancestry-specific sequence not represented in GRCh38 to assess their representation and functional potential in newer long-read assemblies. Alignments to T2T-CHM13 and the 47 Human Pangenome Reference Consortium (HPRC) linear assemblies positioned 40% and 83% of APG contigs, respectively, with high identity and coverage. Most T2T-CHM13 placements corresponded to sequences absent from GRCh38 (94.5%) and were enriched in centromeric and satellite repeats (94.2%). Functional overlap included annotated genes (2.6%) and CpG islands (3.6%), with enrichment in immune, synaptic and intracellular signaling pathways. HPRC alignments revealed ancestry-associated patterns, with African and Admixed American genomes showing the highest numbers of unique contig placements and shared alignments. A subset of 742 APG contigs showed weak or no mapping to any of the reference assemblies. These contigs were not enriched for repeat elements, and ∼58% showed predicted gene content. These findings highlight persistent gaps in even the most complete reference genomes and underscore the importance of incorporating ancestry-enriched sequences into future genome frameworks to reduce reference bias and advance equitable discovery in genomics.\n\nUncovering Functional Sequence Gaps in Human Reference Genomes using African Pan Genome Contig Sequences", "token_count": 400, "char_count": 1595, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:10.526821", "source": { "split": "train_shard_00001", "doc_id": 533 }, "chunk_id": "train_shard_00001_533_0", "global_id": 6409 }, { "text": "The current reference genome is the backbone of diverse and rich annotations. Simple text formats, like VCF or BED, have been widely adopted and helped the critical exchange of genomic information. There is a dire need for tools and formats enabling pangenomic annotation to facilitate such enrichment of pangenomic references. The Graph Alignment Format (GAF) is a text format, tab-delimited like BED/VCF files, which was proposed to represent alignments. GAF could also be used to store paths representing annotations in a pangenome graph, but there are no tools to index and query them efficiently. Here, we present extensions to vg and HTSlib that provide efficient sorting, indexing, and querying for GAF files. With this approach, annotations overlapping a subgraph can be extracted quickly. Paths are sorted based on the IDs of traversed nodes, compressed with BGZIP, and indexed with HTSlib/tabix via our extensions for the GAF format. Compared to the binary GAM format, GAF files are easier to edit or inspect because they are plain text, and we show that they are twice as fast to sort and half as large on disk. In addition, we updated vg annotate , which takes BED or GFF3 annotation files relative to linear sequences and projects them into the pangenome. It can now produce GAF files representing these annotations’ paths through the pangenome. We showcase these new tools on several applications. We projected annotations for all Human Pangenome Reference Consortium Year 1 haplotypes, including genes, segmental duplications, tandem repeats and repeats annotations, into the Minigraph-Cactus pangenome (GRCh38-based v1.1). We also projected known variants from the GWAS Catalog and expression QTLs from the GTEx project into the pangenome. Finally, we reanalyzed ATAC-seq data from ENCODE to demonstrate what a coverage track could look like in a pangenome graph. These rich annotations can be quickly queried with vg and visualized using existing tools like the Sequence Tube Map or Bandage.\n\nEfficient indexing and querying of annotations in a pangenome graph", "token_count": 497, "char_count": 2077, "word_count": 325, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [ "GFF3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:11.174114", "source": { "split": "train_shard_00001", "doc_id": 534 }, "chunk_id": "train_shard_00001_534_0", "global_id": 6410 }, { "text": "Bartonella grahamii is one of the most prevalent Bartonella species in wild rodents and has been associated with human cases of neuroretinitis. The structure and distribution of genomic diversity in natural B. grahamii is largely unexplored. Here, we have applied a comprehensive population genomic and phylogenomic analysis to 172 strains of B. grahamii to unravel the genetic differences and influencing factors that shape its populations. The findings reveal a remarkable genomic diversity within the species, primarily in the form of single- nucleotide polymorphisms. The open pangenome of B. grahamii indicates a dynamic genomic evolution influenced by its ecological niche. Whole-genome data allowed us to decompose B. grahamii diversity into six phylogroups, each characterized by a unique \"mosaic pattern\" of hosts and biogeographic regions. This suggests a complex interplay between host specificity and biogeography. In addition, our study suggests a possible origin of European strains from Asian lineages, and host factors have a more significant impact on the genetic differentiation of B. grahamii than geographical factors. These insights contribute to understanding the evolutionary history of this pathogen and provide a foundation for future epidemiological research and public health strategies.

Importance

Bartonella grahamii has been reported worldwide and shown to infect humans. Up to now, an effective transmission route of B. grahamii to humans has not been confirmed. The genetic evolution of B. grahamii and the relationship between B. grahamii and its host need to be further studied. The factors driving the genetic diversity of B. grahamii are still controversial. The results showed that the European isolates shared a common ancestor with the Chinese isolates. Host factors were shown to play an important role in driving the genetic diversity of B. grahamii. When host factors were fixed, geographic barriers drove B. grahamii microevolution", "token_count": 515, "char_count": 2079, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5813, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:11.827873", "source": { "split": "train_shard_00001", "doc_id": 535 }, "chunk_id": "train_shard_00001_535_0", "global_id": 6411 }, { "text": "Our study emphasizes the importance of characterizing isolate genomes derived from hosts and geographical locations and provides a new reference for the origin of B. grahamii.\n\nMicroevolution of Bartonella grahamii driven by geographic and host factors.", "token_count": 68, "char_count": 267, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8611, "quality_score": 0.9306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:12.191028", "source": { "split": "train_shard_00001", "doc_id": 535 }, "chunk_id": "train_shard_00001_535_1", "global_id": 6412 }, { "text": "Redefining genomic view of Clostridioides difficile through pangenome analysis and identification of drug targets from its core genome.", "token_count": 37, "char_count": 142, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:12.549111", "source": { "split": "train_shard_00001", "doc_id": 536 }, "chunk_id": "train_shard_00001_536_0", "global_id": 6413 }, { "text": "Targeted gene replacement in the thermotolerant yeast Kluyveromyces marxianus KCTC 17555 has been hampered by its propensity to non-homologous end joining (NHEJ). To enhance homologous recombination (HR) by blocking NHEJ, we identified and disrupted the K. marxianus KU80 gene. The ku80 deletion mutant strain (Kmku80∆) of K. marxianus KCTC 17555 did not show apparent growth defects under several conditions with the exception of exposure to tunicamycin. The targeted disruption of the three model genes, KmLEU2, KmPDC1, and KmPDC5, was increased by 13–70 % in Kmku80∆, although the efficiency was greatly affected by the length of the homologous flanking fragments. In contrast, the double HR frequency was 0–13.7 % in the wild-type strain even with flanking fragments 1 kb long. Therefore, Kmku80∆ promises to be a useful recipient strain for targeted gene manipulation.\n\nDeletion of a KU80 homolog enhances homologous recombination in the thermotolerant yeast Kluyveromyces marxianus", "token_count": 303, "char_count": 987, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [ "KU80" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:13.107684", "source": { "split": "train_shard_00001", "doc_id": 537 }, "chunk_id": "train_shard_00001_537_0", "global_id": 6414 }, { "text": "

Introduction

Phenylalanine ammonia-lyase (PAL), as the rate-limiting enzyme in plant phenylpropanoid metabolism, catalyzes the conversion of L-phenylalanine to trans-cinnamic acid and plays a pivotal role in plant-insect resistance mechanisms.

Methods

Utilizing a maize pangenome constructed from 26 high-quality genomes, we systematically identified the ZmPAL gene family members. Evolutionary pressure and structural variation (SV) analyses were conducted, alongside reanalysis of publicly available RNA-seq datasets under lepidopteran stress conditions. Temporal expression patterns were further validated via qRT-PCR.

Results

This investigation identified 29 ZmPAL genes, comprising 7 core, 2 near-core, 12 dispensable, and 8 private genes, revealing substantial limitations of single-reference genome-based studies. Evolutionary analysis indicated positive selection of ZmPAL8 in specific germplasms, while SV-affected ZmPAL5 exhibited significantly divergent expression patterns. Conserved expression profiles were observed among ZmPAL members under diverse lepidopteran stresses. Temporal-specific regulation was established: ZmPAL7, ZmPAL10, and ZmPAL23 dominated early defense responses, whereas ZmPAL10 and ZmPAL23 maintained predominance during mid-late phases.

Discussion

This pangenome-based study provides novel insights into PAL-mediated phytoprotective mechanisms against lepidopteran pests and establishes a theoretical framework for understanding maize's molecular adaptation to biotic stressors.\n\nAnalysis of maize PAL pan gene family and expression pattern under lepidopteran insect stress.", "token_count": 481, "char_count": 1702, "word_count": 185, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:13.751854", "source": { "split": "train_shard_00001", "doc_id": 538 }, "chunk_id": "train_shard_00001_538_0", "global_id": 6415 }, { "text": "

Background

Low ethanol tolerance of Kluyveromyces marxianus limits its application in high-temperature ethanol fermentation. As a complex phenotype, ethanol tolerance involves synergistic actions of many genes that are widely distributed throughout the genome, thereby being difficult to engineer. TATA-binding protein is the most common target of global transcription machinery engineering for improvement of complex phenotypes.

Results

A random mutagenesis library of K. marxianus TATA-binding protein Spt15 was constructed and subjected to screening under ethanol stress. Two mutant strains with improved ethanol tolerance were identified, one of which (denoted as M2) exhibited increased ethanol productivity. The mutant of Spt15 in strain M2 (denoted as Spt15-M2) has a single amino acid substitution at position 31 (Lys → Glu). RNA-Seq-based transcriptomic analysis revealed cellular transcription profile changes resulting from Spt15-M2. Spt15-M2 caused changes in transcriptional level of most of the genes in the central carbon metabolism network. Compared with control strain, 444 differentially expressed genes (DEGs) were identified in strain M2 (fold change > 2, Padj < 0.05), including 48 up-regulated and 396 down-regulated. The up-regulated DEGs are involved in amino acid transport, long-chain fatty acid biosynthesis and MAPK signaling pathway, while the down-regulated DEGs are related to ribosome biogenesis, translation and protein synthesis. Five candidate genes (GAP1, GNP1, FAR1, STE2 and TEC1), which were found to be up-regulated in M2 strain, were overexpressed for a gain-of-function assay", "token_count": 508, "char_count": 1699, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6847, "quality_score": 0.8423, "entities": { "genes": [ "GAP1", "STE2", "FAR1", "TEC1", "GNP1" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:14.431320", "source": { "split": "train_shard_00001", "doc_id": 539 }, "chunk_id": "train_shard_00001_539_0", "global_id": 6416 }, { "text": "However, the overexpression of no single gene helped improve ethanol tolerance as SPT15-M2 did.

Conclusions

This work demonstrates that ethanol tolerance of K. marxianus can be improved by engineering its TATA-binding protein. A single amino acid substitution (K31E) of TATA-binding protein Spt15 is able to bring differential expression of hundreds of genes that acted as an interconnected network for the phenotype of ethanol tolerance. Future perspectives of this technique in K. marxianus were discussed.\n\nEngineering TATA-binding protein Spt15 to improve ethanol tolerance and production in Kluyveromyces marxianus.", "token_count": 185, "char_count": 655, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [ "SPT15" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:14.889861", "source": { "split": "train_shard_00001", "doc_id": 539 }, "chunk_id": "train_shard_00001_539_1", "global_id": 6417 }, { "text": "Affordable genotyping methods are essential in genomics. Commonly used genotyping methods primarily support single nucleotide variants and short indels but neglect structural variants. Additionally, accuracy of read alignments to a reference genome is unreliable in highly polymorphic and repetitive regions, further impacting genotyping performance. Recent works highlight the advantage of haplotype-resolved pangenome graphs in addressing these challenges. Building on these developments, we propose a rigorous alignment-free genotyping framework. Our formulation seeks a path through the pangenome graph that maximizes the matches between the path and substrings of sequencing reads (e.g., k -mers) while minimizing recombination events (haplotype switches) along the path. We prove that this problem is NP-Hard and develop efficient integer-programming solutions. We benchmarked the algorithm using downsampled short-read datasets from homozygous human cell lines with coverage ranging from 0.1× to 10×. Our algorithm accurately estimates complete major histocompatibility complex (MHC) haplotype sequences with small edit distances from the ground-truth sequences, providing a significant advantage over existing methods on low-coverage inputs. Although our algorithm is designed for haploid samples, we discuss future extensions to diploid samples.

Implementation

https://github.com/at-cg/PHI\n\nInteger programming framework for pangenome-based genome inference", "token_count": 333, "char_count": 1475, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7688, "quality_score": 0.8844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:15.493779", "source": { "split": "train_shard_00001", "doc_id": 540 }, "chunk_id": "train_shard_00001_540_0", "global_id": 6418 }, { "text": "Non-conventional yeasts such as Yarrowia lipolytica, Pichia pastoris, Kluyveromyces marxianus, Rhodosporidium toruloides and Hansenula polymorpha have proven to be efficient cell factories in producing a variety of natural products due to their wide substrate utilization spectrum, strong tolerance to environmental stresses and other merits. With the development of synthetic biology and gene editing technology, metabolic engineering tools and strategies for non-conventional yeasts are expanding. This review introduces the physiological characteristics, tool development and current application of several representative non-conventional yeasts, and summarizes the metabolic engineering strategies commonly used in the improvement of natural products biosynthesis. We also discuss the strengths and weaknesses of non-conventional yeasts as natural products cell factories at current stage, and prospects future research and development trends.\n\n[Biosynthesis of natural products by non-conventional yeasts].", "token_count": 251, "char_count": 1046, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6772, "quality_score": 0.8386, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:16.011418", "source": { "split": "train_shard_00001", "doc_id": 541 }, "chunk_id": "train_shard_00001_541_0", "global_id": 6419 }, { "text": "Listeria monocytogenes is a foodborne pathogen that causes listeriosis worldwide. In México, L. monocytogenes has been identified as a hazard of deli-meats. However, the genomic analysis that supports the transmission of L. monocytogenes strains via deli-meats and its role as a source for virulence and resistance genes is lacking. Here, we present four high-quality genome drafts of L. monocytogenes strains isolated from deli-meats in Mexico. In silico typing was used to determine the serotype, lineage, clonal complexes (CC), and multilocus sequence (ST). Also, comparative genomics were performed to explore the diversity, virulence, mobile elements, antimicrobial resistant and stress survival traits. The genome sequence size of these strains measured 3.05 ± 0.07 Mb with a mean value of 37.9%G+C. All strains belonged to linage I, which was divided into two groups: 4b, CC2, ST1 (n = 3) and 1/2b, CC5, ST5 (n = 1). The pangenome and core genome contained 3493 and 2625 genes, respectively. The strains harbor the L. monocytogenes pathogenicity island-1 (LIPI-1) and the same multidrug resistance pattern (fosX, norB, mprF, lin) via in silico analysis. Comparative analysis delineated the genomes as essentially syntenic, whose genomic differences were due to phage insertion. These results expand what is known about the biology of the L. monocytogenes strains isolated from deli-meats in Mexico and warns of the risk that these strains belong to epidemic linage and harbor virulence genes linked to human disease.\n\nGenomic Approach of Listeria monocytogenes Strains Isolated from Deli-Meats in Mexico.", "token_count": 482, "char_count": 1622, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8086, "entities": { "genes": [ "ST5", "CC2", "CC5", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:16.666072", "source": { "split": "train_shard_00001", "doc_id": 542 }, "chunk_id": "train_shard_00001_542_0", "global_id": 6420 }, { "text": "The search for the genetic basis of phenotypes has primarily focused on single nucleotide polymorphisms, often overlooking structural variants (SVs). SVs can significantly affect gene function, but detecting and characterizing them is challenging, even with long-read sequencing. Moreover, traditional single-reference methods can fail to capture many genetic variants. Using long-reads, we generated a Capuchino Seedeater ( Sporophila ) pangenome, including 16 individuals from seven species, to investigate how SVs contribute to species and coloration differences. Leveraging this pangenome, we mapped short-read data from 127 individuals to perform FST scans and genome-wide association studies. Species divergence primarily arises from SNPs and indels (< 50 bp) in non-coding regions of melanin-related genes, as larger SVs rarely overlap with divergence peaks. One exception was a 55 bp deletion near the OCA2 and HERC2 genes, associated with feather pheomelanin content. These findings support the hypothesis that the reshuffling of small regulatory alleles, rather than larger species-specific mutations, accelerated plumage evolution leading to prezygotic isolation in Capuchinos.\n\nA pangenomic approach reveals the sources of genetic variation fueling the rapid radiation of Capuchino Seedeaters", "token_count": 306, "char_count": 1304, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7809, "quality_score": 0.8904, "entities": { "genes": [ "HERC2", "OCA2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:17.238401", "source": { "split": "train_shard_00001", "doc_id": 543 }, "chunk_id": "train_shard_00001_543_0", "global_id": 6421 }, { "text": "We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex specificity, the functional potential of the Phascolarctobacterium species, and their interaction with other microbial species. We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing, and species-specific qPCR, using 2350 samples from three Norwegian cohorts-CRCAhus, NORCCAP, and CRCbiome-and a large publicly available data set, curatedMetagenomicData. Using metagenome-assembled genomes from the CRCbiome study, we explore the genomic characteristics and functional potential of the Phascolarctobacterium pangenome. Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for Phascolarctobacterium succinatutens and negative associations were shown for Phascolarctobacterium faecium and adenoma in curatedMetagenomicData. Men show a higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species shows distinct microbial composition and forms distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P", "token_count": 521, "char_count": 1824, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:17.897315", "source": { "split": "train_shard_00001", "doc_id": 544 }, "chunk_id": "train_shard_00001_544_0", "global_id": 6422 }, { "text": "faecium.IMPORTANCEUntil now Phascolarctobacterium has been going under the radar as a CRC-associated genus despite having been noted, but overseen, as such for over a decade. We found not just one, but two species of Phascolarctobacterium to be associated with CRC-Phascolarctobacterium succinatutens was more abundant in adenoma/CRC, while Phascolarctobacterium faecium was less abundant in adenoma. Each of them represents distinct communities, constituted by specific microbial partners and metabolic capacities-and they rarely occur together in the same patients. We have verified that P. succinatutens is increased in adenoma and CRC and this species should be recognized among the most important CRC-associated bacteria.\n\nSpecies-level verification of Phascolarctobacterium association with colorectal cancer.", "token_count": 244, "char_count": 861, "word_count": 108, "semantic_coherence": 1, "information_density": 0.787, "quality_score": 0.8935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:18.378677", "source": { "split": "train_shard_00001", "doc_id": 544 }, "chunk_id": "train_shard_00001_544_1", "global_id": 6423 }, { "text": "Many diverse bacterial phytopathogens deploy type III secreted effectors (T3SEs) to promote virulence by interrupting host immunity and other critical plant processes. However, the virulence of T3SEs has been countered on the host side through the evolution of a multitude of resistance genes (R genes) capable of recognizing the presence of T3SEs and eliciting a response termed effector-triggered immunity. This dynamic sets up an evolutionary arms race that has led to enormous diversification of both bacterial T3SEs and plant R genes. Over the past decade, efforts to document and characterize the pangenome T3SE profiles of individual pathogens have generated indispensable resources that have facilitated collaborative research progress on these focal pathogens. However, despite the deeply integrated evolutionary history of T3SEs, the lack of a concerted effort to synthesize T3SE conventions across diverse pathosystems has resulted in a lack of connectivity across the literature. Here, we catalog the distribution of T3SEs across six of the most globally significant genera of bacterial phytopathogens. We show that the number of T3SEs per genome varies dramatically within and between genera and that many T3SE families are present in multiple genera despite their sparse distributions across closely related strains. We also document all inter-genera evolutionary relationships for each T3SE family and propose integrated nomenclature conventions for all phytopathogen T3SEs. Ultimately, our expanded T3SE collection includes thousands of newly classified alleles, catalogs several previously unestablished homologies between distinct genera, and will enable more comprehensive studies on the implications of T3SE diversification for virulence and immunity.\n\nUnified Classification of the Type III Secreted Effectors of Bacterial Plant Pathogens to Advance Phytopathology Research.", "token_count": 439, "char_count": 1909, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:19.009488", "source": { "split": "train_shard_00001", "doc_id": 545 }, "chunk_id": "train_shard_00001_545_0", "global_id": 6424 }, { "text": "

ABSTRACT

Gene panels represent a widely used strategy for genetic testing in a vast range of Mendelian disorders. While this approach aids reliable bioinformatic detection of short coding variants, it fails to detect most larger variants. Recent studies have recommended the adoption of pangenomes to augment detection of large variants from targeted sequencing, potentially providing diagnostic laboratories with the possibility to streamline diagnostic work-ups and reduce costs. Here, we analyze a large-scale cohort comprising 1,952 cardiomyopathy cases and 1,805 technically matched controls and show that a pangenome-based workflow, GRAF, conjugates higher precision and recall (F1 score 0.86) compared with conventional orthogonal methods (F1 0-0.57) in detecting potentially pathogenic ≥20bp variants from short-read panel data. Our results indicate that pangenome-based workflows aid precise and cost-effective detection of large variants from targeted sequencing data in the clinical context. This will be particularly relevant for conditions in which these variants explain a high proportion of the disease burden.\n\nPANGENOMES AID ACCURATE DETECTION OF LARGE INSERTION AND DELETIONS FROM GENE PANEL DATA: THE CASE OF CARDIOMYOPATHIES", "token_count": 310, "char_count": 1253, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7151, "quality_score": 0.8576, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:19.580553", "source": { "split": "train_shard_00001", "doc_id": 546 }, "chunk_id": "train_shard_00001_546_0", "global_id": 6425 }, { "text": "

Background

Campylobacter jejuni is a pervasive pathogen of major public health concern with a complex ecology requiring accurate and informative approaches to define pathogen diversity during outbreak investigations. Source attribution analysis may be confounded if the genetic diversity of a C. jejuni population is not adequately captured in a single specimen. The aim of this study was to determine the genomic diversity of C. jejuni within individual stool specimens from four campylobacteriosis patients. Direct plating and pre-culture filtration of one stool specimen per patient was used to culture multiple isolates per stool specimen. Whole genome sequencing and pangenome level analysis were used to investigate genomic diversity of C. jejuni within a patient.

Results

A total 92 C. jejuni isolates were recovered from four patients presenting with gastroenteritis. The number of isolates ranged from 13 to 30 per patient stool. Three patients yielded a single C. jejuni multilocus sequence type: ST-21 (n = 26, patient 4), ST-61 (n = 30, patient 1) and ST-2066 (n = 23, patient 2). Patient 3 was infected with two different sequence types [ST-51 (n = 12) and ST-354 (n = 1)]. Isolates belonging to the same sequence type from the same patient specimen shared 12-43 core non-recombinant SNPs and 0-20 frameshifts with each other, and the pangenomes of each sequence type consisted of 1406-1491 core genes and 231-264 accessory genes. However, neither the mutation nor the accessory genes were connected to a specific functional gene category.

Conclusions

Our findings show that the C. jejuni population recovered from an individual patient's stool are genetically diverse even within the same ST and may have shared common ancestors before specimens were obtained", "token_count": 501, "char_count": 1795, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5762, "quality_score": 0.7881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:20.242131", "source": { "split": "train_shard_00001", "doc_id": 547 }, "chunk_id": "train_shard_00001_547_0", "global_id": 6426 }, { "text": "The population is unlikely to have evolved from a single isolate at the time point of initial patient infection, leading us to conclude that patients were likely infected with a heterogeneous C. jejuni population. The diversity of the C. jejuni population found within individual stool specimens can inform future methodological approaches to attribution and outbreak investigations.\n\nComparative genomics of Campylobacter jejuni from clinical campylobacteriosis stool specimens.", "token_count": 98, "char_count": 479, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:20.621523", "source": { "split": "train_shard_00001", "doc_id": 547 }, "chunk_id": "train_shard_00001_547_1", "global_id": 6427 }, { "text": "

Background

Corynebacterium silvaticum is a pathogenic, gram-positive bacterial species that causes caseous lymphadenitis in wild boars, domestic pigs and roe deer in Western Europe. It can affect animal production and cause zoonosis. Genome analysis has suggested that one strain from Portugal and one from Austria could probably produce the diphtheria toxin (DT), which inhibits protein synthesis and can cause death.

Methods

To further investigate the species genetic diversity and probable production of DT by Portuguese strains, eight isolates from this country were sequenced and compared to 38 public ones.

Results

Strains from Portugal are monophyletic, nearly identical, form a unique cluster and have 27 out of 36 known Corynebacterium virulence or niche factors. All of them lack a frameshift in the tox gene and were suggested to produce DT. A phylogenetic analysis shows that the species has diverged into two clades. Clade 1 is composed of strains that were suggested to have the ability to produce DT, represented by the monophyletic strains from Portugal and strain 05-13 from Austria. Clade 2 is composed of strains unable to produce DT due to a frameshifted tox gene. The second clade is represented by strains from Austria, Germany and Switzerland. Ten genome clusters were detected, in which strains from Germany are the most diverse. Strains from Portugal belong to an exclusive cluster. The pangenome has 2,961 proteins and is nearly closed (α = 0.968). Exclusive genes shared by clusters 1 and 2, and Portuguese strains are probably not related to disease manifestation as they share the same host but could play a role in their extra-host environmental adaptation. These results show the potential of the species to cause zoonosis, possibly diphtheria. The identified clusters, exclusively shaded genes, and exclusive STs identified in Portugal could be applied in the identification and epidemiology of the species.", "token_count": 501, "char_count": 1996, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5845, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:21.279588", "source": { "split": "train_shard_00001", "doc_id": 548 }, "chunk_id": "train_shard_00001_548_0", "global_id": 6428 }, { "text": "Analysis of Corynebacterium silvaticum genomes from Portugal reveals a single cluster and a clade suggested to produce diphtheria toxin.", "token_count": 41, "char_count": 143, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:21.638048", "source": { "split": "train_shard_00001", "doc_id": 548 }, "chunk_id": "train_shard_00001_548_1", "global_id": 6429 }, { "text": "Uricase as an important healthcare-related protein is extensively used in the treatment of tumor lysis syndrome and in the manufacture of serum uric-acid diagnostic kits. In this study, a gene of a new thermostable uricase (KmUOX) was cloned from thermotolerant yeast Kluyveromyces marxianus. The uricase was fused with a self-cleaving intein and cellulose-binding affinity tag and expressed in Escherichia coli BL21 (DE3). Through the binding to inexpensive cellulose and in situ intein cleavage induced by a pH change, tag-free uricase (KmUOX) was efficiently purified with a 77.11% yield via a single-step column purification strategy. This tag-free uricase showed Km, Vmax, and Kcat values of 67.60 µM, 56.35 µM/(min mg), and 32.74 S-1, respectively. Furthermore, this pure uricase was relatively thermostable and retained 79.75% of activity when incubated at 40 °C for 90 h. Thus, this pH-induced self-cleavable intein system combined with a cellulose matrix for affinity chromatography is proven here to be an effective and low-cost method for recombinant-uricase purification. Moreover, the stability of KmUOX makes it useful for clinical applications.\n\nEfficient purification of a recombinant tag-free thermostable Kluyveromyces marxianus uricase by pH-induced self-cleavage of intein and expression in Escherichia coli.", "token_count": 469, "char_count": 1421, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [ "BL21", "DE3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:22.282777", "source": { "split": "train_shard_00001", "doc_id": 549 }, "chunk_id": "train_shard_00001_549_0", "global_id": 6430 }, { "text": "Kefir yeasts were investigated for their possible virulence using an in vitro system. Unweighted pair group method with arithmetic mean (UPGMA) cluster analysis of 46 biochemical traits showed that all kefir isolates formed clusters distinct from Candida albicans. No isolate showed N‐acetylglucosaminidase activity, which is involved in resistance against host immune systems. All Kluyveromyces marxianus isolates formed pseudohyphae and grew at 42 °C, whereas Saccharomyces unisporus isolates did not. None of the kefir yeasts had proteolytic or haemolytic activities. All K. marxianus isolates were susceptible to fluconazole, whereas S. unisporus isolates were classified as resistant.\n\nBiochemical characteristics, virulence traits and antifungal resistance of two major yeast species isolated from kefir: Kluyveromyces marxianus and Saccharomyces unisporus", "token_count": 240, "char_count": 862, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:22.762369", "source": { "split": "train_shard_00001", "doc_id": 550 }, "chunk_id": "train_shard_00001_550_0", "global_id": 6431 }, { "text": "In the study, Lactobacillus paracasei H4-11, Lactobacillus fermentum D1-1, Lactobacillus casei H1-8, Lactobacillus reuteri H2-12, and Kluyveromyces marxianus L1-1 were screened from traditional fermented rice acid based on several indicators: L-lactic acid production capacity (13.46 ~ 19.69 g/kg), antioxidant capacity (DPPH clearance ability of 35.36 ~ 56.89%), and savory flavor indicators. Glutinous rice, quinoa, barley rice, and brown rice were selected to carry out rice acid fermentation. Different viable lactic acid bacteria and yeasts were screened, respectively, in the saccharification, acidification, alcoholization, and late acidification stages. Rice acid fermented with L. paracasei H4-11 and K. marxianus L1-1 in glutinous rice showed the high L-lactic acid content (23.09 g/kg). The DPPH free radical scavenging ability in rice acid fermented with L. fermentum D1-1 and L. paracasei H4-11, respectively, reached 34.27% and 33.05% in 96 hr. Although quinoa rice acid had the highest L-lactic acid content (33.74 g/kg) and the DPPH free radical scavenging ability (60.10%), it had the poor taste due to the high astringency intensity and bitter intensity. Rice acid fermented with both L. paracasei H4-11 and K. marxianus L1-1 in glutinous rice showed the highest savory flavor and had the lowest astringency and bitter. L", "token_count": 519, "char_count": 1419, "word_count": 196, "semantic_coherence": 1, "information_density": 0.5357, "quality_score": 0.7679, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:23.774695", "source": { "split": "train_shard_00001", "doc_id": 551 }, "chunk_id": "train_shard_00001_551_0", "global_id": 6432 }, { "text": "paracasei H4-11 and K. marxianus L1-1 were the potential strains for the fermentation of rice acid. These results promote the industrial development of Chinese rice acid.

Practical applications

Rice acid as a functional nondairy fermented product is widely accepted by Chinese consumers. However, rice acid fermentation is still a traditional spontaneous process, which causes instability in its flavor and quality. Lactobacillus paracasei H4-11 and Kluyveromyces marxianus L1-1 screened in this study contributed to the improvements in the flavor and antioxidant capacity of rice acid. In addition, glutinous rice was confirmed as the suitable fermentation material of rice acid in the study.\n\nScreening and application of lactic acid bacteria and yeasts with l-lactic acid-producing and antioxidant capacity in traditional fermented rice acid.", "token_count": 238, "char_count": 877, "word_count": 119, "semantic_coherence": 1, "information_density": 0.605, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:24.246082", "source": { "split": "train_shard_00001", "doc_id": 551 }, "chunk_id": "train_shard_00001_551_1", "global_id": 6433 }, { "text": "Recent listeriosis outbreaks linked to fresh produce suggest the need to better understand and mitigate L. monocytogenes contamination in packing and processing environments. Using whole genome sequencing (WGS) and phenotype screening assays for sanitizer tolerance, we characterized 48 L. monocytogenes isolates previously recovered from environmental samples in five produce handling facilities. Within the studied population there were 10 sequence types (STs) and 16 cgMLST types (CTs). Pairwise single nucleotide polymorphisms (SNPs) ranged from 0 to 3047 SNPs within a CT, revealing closely and distantly related isolates indicative of both sporadic and continuous contamination events within the facility. Within Facility 1, we identified a closely related cluster (0-2 SNPs) of isolates belonging to clonal complex 37 (CC37; CT9492), with isolates recovered during sampling events 1-year apart and in various locations inside and outside the facility. The accessory genome of these CC37 isolates varied from 94 to 210 genes. Notable genetic elements and mutations amongst the isolates included the bcrABC cassette (2/48), associated with QAC tolerance; mutations in the actA gene on the Listeria pathogenicity island (LIPI) 1 (20/48); presence of LIPI-3 (21/48) and LIPI-4 (23/48). This work highlights the potential use of WGS in tracing the pathogen within a facility and understanding properties of L. monocytogenes in produce settings.\n\nApplication of Whole Genome Sequencing to Understand Diversity and Presence of Genes Associated with Sanitizer Tolerance in Listeria monocytogenes from Produce Handling Sources.", "token_count": 479, "char_count": 1698, "word_count": 229, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "CT9492", "CC37" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:24.890934", "source": { "split": "train_shard_00001", "doc_id": 552 }, "chunk_id": "train_shard_00001_552_0", "global_id": 6434 }, { "text": "Legionella pneumophila is ubiquitous and sporadically infects humans causing Legionnaire's disease (LD). Globally, reported cases of LD have risen fourfold from 2000 to 2014. In 2016, Sydney, Australia was the epicenter of an outbreak caused by L. pneumophila serogroup 1 (Lpsg1). Whole-genome sequencing was instrumental in identifying the causal clone which was found in multiple locations across the city. This study examined the epidemiology of Lpsg1 in an urban environment, assessed typing schemes to classify resident clones, and investigated the association between local climate variables and LD outbreaks. Of 223 local Lpsg1 isolates, we identified dominant clones with one clone isolated from patients in high frequency during outbreak investigations. The core genome multi-locus sequence typing scheme was the most reliable in identifying this Lpsg1 clone. While an increase in humidity and rainfall was found to coincide with a rise in LD cases, the incidence of the major L. pneumophila outbreak clone did not link to weather phenomena. These findings demonstrated the role of high-resolution typing and weather context assessment in determining source attribution for LD outbreaks in urban settings, particularly when clinical isolates remain scarce.IMPORTANCEWe investigated the genomic and meteorological influences of infections caused by Legionella pneumophila in Sydney, Australia. Our study contributes to a knowledge gap of factors that drive outbreaks of legionellosis compared to sporadic infections in urban settings. In such cases, clinical isolates can be rare, and thus, other data are needed to inform decision-making around control measures. The study revealed that core genome multi-locus sequence typing is a reliable and adaptable technique when investigating Lpsg1 outbreaks. In Sydney, the genomic profile of Lpsg1 was dominated by a single clone, which was linked to numerous community cases over a period of 40 years. Interestingly, the peak in legionellosis cases during Autumn was not associated with this prevalent outbreak clone", "token_count": 498, "char_count": 2097, "word_count": 302, "semantic_coherence": 1, "information_density": 0.5861, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:25.545076", "source": { "split": "train_shard_00001", "doc_id": 553 }, "chunk_id": "train_shard_00001_553_0", "global_id": 6435 }, { "text": "Incorporating meteorological data with Lpsg1 genomics can support risk assessment strategies for legionellosis in urban environments, and this approach may be relevant for other densely populated regions globally.\n\nCan genomics and meteorology predict outbreaks of legionellosis in urban settings?", "token_count": 68, "char_count": 297, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8205, "quality_score": 0.9103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:25.913328", "source": { "split": "train_shard_00001", "doc_id": 553 }, "chunk_id": "train_shard_00001_553_1", "global_id": 6436 }, { "text": "

Introduction

Vibrio parahaemolyticus is a foodborne pathogen commonly found in seafood, and drug resistance poses significant challenges to its control. This study aimed to identify novel drug targets for antibacterial drug discovery.

Methods

To identify drug targets, we performed a pan-genome analysis on 58 strains of V. parahaemolyticus genomes to obtain core genes. Subsequently, subtractive proteomics and physiochemical checks were conducted on the core proteins to identify potential therapeutic targets. Molecular docking was then employed to screen for anti-V. parahaemolyticus compounds using a in-house compound library of Streptomyces parvus, chosen based on binding energy. The anti-V. parahaemolyticus efficacy of the identified compounds was further validated through a series of experimental tests.

Results and discussion

Pangenome analysis of 58 V. parahaemolyticus genomes revealed that there were 1,392 core genes. After Subtractive proteomics and physiochemical checks, Flagellar motor switch protein FliN was selected as a therapeutic target against V. parahaemolyticus. FliN was modeled and docked with Streptomyces parvus source compounds, and Actinomycin D was identified as a potential anti-V. parahaemolyticus agent with a strong binding energy. Experimental verification confirmed its effectiveness in killing V. parahaemolyticus and significantly inhibiting biofilm formation and motility. This study is the first to use pan-genome and subtractive proteomics to identify new antimicrobial targets for V. parahaemolyticus and to identify the anti-V. parahaemolyticus effect of Actinomycin D. These findings suggest potential avenues for the development of new antibacterial drugs to control V. parahaemolyticus infections.", "token_count": 526, "char_count": 1863, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5628, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:26.580585", "source": { "split": "train_shard_00001", "doc_id": 554 }, "chunk_id": "train_shard_00001_554_0", "global_id": 6437 }, { "text": "Anti-Vibrio parahaemolyticus compounds from Streptomyces parvus based on Pan-genome and subtractive proteomics.", "token_count": 48, "char_count": 125, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:26.967634", "source": { "split": "train_shard_00001", "doc_id": 554 }, "chunk_id": "train_shard_00001_554_1", "global_id": 6438 }, { "text": "SUN-413 Generic Heterogeneity of the RCCX Module Copy Number Variations Using Long-Read Sequencing in the Human Pangenome Data", "token_count": 34, "char_count": 126, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:27.374334", "source": { "split": "train_shard_00001", "doc_id": 555 }, "chunk_id": "train_shard_00001_555_0", "global_id": 6439 }, { "text": "Lactic acid bacteria has been extensively used in food industry because of widespread properties and Pediococcus is among one of them. This study aims to conduct a comprehensive genomic analysis of Pediococcus acidilactici strain BCB1H to elucidate its genetic composition, functional elements, and potential biotechnological applications. The objectives include identifying key genomic features such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, which will highlight the adaptability and potential of P. acidilactici strain BCB1H for use in a variety of industrial and therapeutic applications. P. acidilactici strain BCB1H was analyzed using whole-genome sequencing, which used advanced sequencing technologies to obtain comprehensive genomic data. Key genomic features, such as coding sequences, tRNA and rRNA genes, antibiotic resistance genes, and secondary metabolite biosynthetic gene clusters, were identified through bioinformatics analyses. The genomic analysis of P. acidilactici strain BCB1H revealed a genome size of approximately 1.92 million base pairs with a GC content of 42.4%. The annotation identified 1,895 genes across 192 subsystems, highlighting the metabolic pathways and functional categories. Notably, specialty genes associated with carbohydrate metabolism, stress response, pathogenicity, and amino acid synthesis were identified, underscoring the versatility and potential applications in food technology and medicine. These findings shed light on the genetic makeup and functional potential of P. acidilactici strain BCB1H, highlighting its flexibility and industrial importance. The genetic traits discovered suggest its prospective use in probiotics, food preservation, and biotechnological advancements.\n\nGenomic profiling of pediococcus acidilactici BCB1H and identification of its key features for Biotechnological innovation, food technology and medicine.", "token_count": 447, "char_count": 1970, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5581, "quality_score": 0.7791, "entities": { "genes": [ "BCB1H" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:28.056741", "source": { "split": "train_shard_00001", "doc_id": 556 }, "chunk_id": "train_shard_00001_556_0", "global_id": 6440 }, { "text": "Escherichia coli contain a high level of genetic diversity and are generally associated with the guts of warm-blooded animals but have also been isolated from secondary habitats outside hosts. We used E. coli isolates from previous in situ microcosm experiments conducted under actual beach conditions and performed population-level genomic analysis to identify accessory genes associated with survival within the beach sand environment. E. coli strains capable of surviving had been selected for by seeding isolates originating from sand, sewage, and gull waste (n = 528; 176 from each source) into sand, which was sealed in microcosm chambers and buried for 45 days in the backshore beach of Lake Michigan. In the current work, survival-associated genes were identified by comparing the pangenome of viable E. coli populations at the end of the microcosm experiment with the original isolate collection and identifying loci enriched in the out put samples. We found that environmental survival was associated with a wide variety of genetic factors, with the majority corresponding to metabolism enzymes and transport proteins. Of the 414 unique functions identified, most were present across E. coli phylogroups, except B2 which is often associated with human pathogens. Gene modules that were enriched in surviving populations included a betaine biosynthesis pathway, which produces an osmoprotectant, and the GABA (gamma-aminobutyrate) biosynthesis pathway, which aids in pH homeostasis and nutrient use versatility. Overall, these results demonstrate that the genetic flexibility within this species allows for survival in the environment for extended periods. IMPORTANCE Escherichia coli is commonly used as an indicator of recent fecal pollution in recreational water despite its known ability to survive in secondary environments, such as beach sand. These long-term survivors from sand reservoirs can be introduced into the water column through wave action or runoff during precipitation events, thereby impacting the perception of local water quality. Current beach monitoring methods cannot differentiate long-term environmental survivors from E. coli derived from recent fecal input, resulting in inaccurate monitoring results and unnecessary beach closures", "token_count": 510, "char_count": 2290, "word_count": 329, "semantic_coherence": 1, "information_density": 0.6292, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:28.722400", "source": { "split": "train_shard_00001", "doc_id": 557 }, "chunk_id": "train_shard_00001_557_0", "global_id": 6441 }, { "text": "This work identified the genetic factors that are associated with long-term survivors, providing insight into the mechanistic basis for E. coli accumulation in beach sand. A greater understanding of the intrinsic ability of E. coli to survive long-term and conditions that promote such survival will provide evidence of the limitations of beach water quality assessments using this indicator.\n\nGenetic Determinants of Escherichia coli Survival in Beach Sand.", "token_count": 96, "char_count": 458, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7164, "quality_score": 0.8582, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:29.103707", "source": { "split": "train_shard_00001", "doc_id": 557 }, "chunk_id": "train_shard_00001_557_1", "global_id": 6442 }, { "text": "Vibrio parahaemolyticus is the leading cause of illnesses and outbreaks linked to seafood consumption across the globe. Understanding how this pathogen may be adapted to persist along the farm-to-table supply chain has applications for addressing food safety. This study utilized machine learning to develop robust models classifying genomic diversity of V. parahaemolyticus that was isolated from environmental (n = 176), seafood (n = 975), and clinical (n = 865) sample origins. We constructed a pangenome of the respective genome assemblies and employed random forest algorithm to develop predictive models to identify gene clusters encoding metabolism, virulence, and antibiotic resistance that were associated with isolate source type. Comparison of genomes of all seafood-clinical isolates showed high balanced accuracy (≥0.80) and Area Under the Receiver Operating Characteristics curve (≥0.87) for all of these functional features. Major virulence factors including tdh, trh, type III secretion system-related genes, and four alpha-hemolysin genes (hlyA, hlyB, hlyC, and hlyD) were identified as important differentiating factors in our seafood-clinical virulence model, underscoring the need for further investigation. Significant patterns for AMR genes differing among seafood and clinical samples were revealed from our model and genes conferring to tetracycline, elfamycin, and multidrug (phenicol antibiotic, diaminopyrimidine antibiotic, and fluoroquinolone antibiotic) resistance were identified as the top three key variables. These findings provide crucial insights into the development of effective surveillance and management strategies to address the public health threats associated with V. parahaemolyticus.", "token_count": 484, "char_count": 1813, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:29.754097", "source": { "split": "train_shard_00001", "doc_id": 558 }, "chunk_id": "train_shard_00001_558_0", "global_id": 6443 }, { "text": "Bioinformatics combined with machine learning unravels differences among environmental, seafood, and clinical isolates of <i>Vibrio parahaemolyticus</i>.", "token_count": 47, "char_count": 165, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:30.116386", "source": { "split": "train_shard_00001", "doc_id": 558 }, "chunk_id": "train_shard_00001_558_1", "global_id": 6444 }, { "text": "Human microbiota form a biofilm with substantial consequences for health and disease. Numerous studies have indicated that microbial communities produce functional amyloids as part of their biofilm extracellular scaffolds. The overlooked interplay between bacterial amyloids and the host may have detrimental consequences for the host, including neurodegeneration. This work gives an overview of the biofilm-associated amyloids expressed by the gut microbiota and their potential role in neurodegeneration. It discusses the biofilm-associated proteins (BAPs) of the gut microbiota, maps the amyloidogenic domains of these proteins, and analyzes the presence of bap genes within accessory genomes linked with transposable elements. Furthermore, the evidence supporting the existence of amyloids in the gut are presented. Finally, it explores the potential interactions between BAPs and α-synuclein, extending the literature on amyloid cross-kingdom interactions. Based on these findings, this study propose that BAP amyloids act as transmissible catalysts, facilitating the misfolding, accumulation, and spread of α-synuclein aggregates. This review contributes to the understanding of complex interactions among the microbiota, transmissible elements, and host, which is crucial for developing novel therapeutic approaches to combat microbiota-related diseases and improve overall health outcomes.\n\nBiofilm-associated proteins: from the gut biofilms to neurodegeneration.", "token_count": 346, "char_count": 1478, "word_count": 192, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:30.697720", "source": { "split": "train_shard_00001", "doc_id": 559 }, "chunk_id": "train_shard_00001_559_0", "global_id": 6445 }, { "text": "

Background

Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for a wide range of compounds. Ethyl acetate is an industrial solvent that is used in several applications, mainly as a biodegradable organic solvent with low toxicity. While ethyl acetate is produced by several natural yeast species, the main mechanism of production has remained elusive until the discovery of Eat1 in Wickerhamomyces anomalus. Unlike other yeast alcohol acetyl transferases (AATs), Eat1 is located in the yeast mitochondria, suggesting that the coding sequence contains a mitochondrial pre-sequence. For expression in prokaryotic hosts such as E. coli, expression of heterologous proteins with eukaryotic signal sequences may not be optimal.

Results

Unprocessed and synthetically truncated eat1 variants of Kluyveromyces marxianus and Wickerhamomyces anomalus have been compared in vitro regarding enzyme activity and stability. While the specific activity remained unaffected, half-life improved for several truncated variants. The same variants showed better performance regarding ethyl acetate production when expressed in E. coli.

Conclusion

By analysing and predicting the N-terminal pre-sequences of different Eat1 proteins and systematically trimming them, the stability of the enzymes in vitro could be improved, leading to an overall improvement of in vivo ethyl acetate production in E. coli. Truncated variants of eat1 could therefore benefit future engineering approaches towards efficient ethyl acetate production.\n\nFrom Eat to trEat: engineering the mitochondrial Eat1 enzyme for enhanced ethyl acetate production in Escherichia coli.", "token_count": 464, "char_count": 1761, "word_count": 229, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:31.340327", "source": { "split": "train_shard_00001", "doc_id": 560 }, "chunk_id": "train_shard_00001_560_0", "global_id": 6446 }, { "text": "

Background

High temperature inhibits cell growth and ethanol fermentation of Saccharomyces cerevisiae. As a complex phenotype, thermotolerance usually involves synergistic actions of many genes, thereby being difficult to engineer. The overexpression of either endogenous or exogenous stress-related transcription factor genes in yeasts was found to be able to improve relevant stress tolerance of the hosts.

Results

To increase ethanol yield of high-temperature fermentation, we constructed a series of strains of S. cerevisiae by expressing 8 transcription factor genes from S. cerevisiae and 7 transcription factor genes from thermotolerant K. marxianus in S. cerevisiae. The results of growth curve measurements and spotting test show that KmHsf1 and KmMsn2 can enhance cell growth of S. cerevisiae at 40-42 °C. According to the results of batch fermentation at 43 °C with an initial glucose concentration of 104.8 g/l, the fermentation broths of KmHSF1 and KmMSN2-expressing strains could reach final ethanol concentrations of 27.2 ± 1.4 and 27.6 ± 1.2 g/l, respectively, while the control strain just produced 18.9 ± 0.3 g/l ethanol. Transcriptomic analysis found that the expression of KmHSF1 and KmMSN2 resulted in 55 (including 31 up-regulated and 24 down-regulated) and 50 (including 32 up-regulated and 18 down-regulated) genes with different expression levels, respectively (padj < 0.05)", "token_count": 495, "char_count": 1498, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:31.993014", "source": { "split": "train_shard_00001", "doc_id": 561 }, "chunk_id": "train_shard_00001_561_0", "global_id": 6447 }, { "text": "The results of transcriptomic analysis also reveal that KmHsf1 might increase ethanol production by regulating genes related to transporter activity to limit excessive ATP consumption and promote the uptake of glucose; while KmMsn2 might promote ethanol fermentation by regulating genes associated with glucose metabolic process and glycolysis/gluconeogenesis. In addition, KmMsn2 might also help to cope with high temperature by regulating genes associated with lipid metabolism to change the membrane fluidity.

Conclusions

The transcription factors KmHsf1 and KmMsn2 of thermotolerant K. marxianus can promote both cell growth and ethanol fermentation of S. cerevisiae at high temperatures. Different mechanisms of KmHsf1 and KmMsn2 in promoting high-temperature ethanol fermentation of S. cerevisiae were revealed by transcriptomic analysis.\n\nThe transcription factors Hsf1 and Msn2 of thermotolerant Kluyveromyces marxianus promote cell growth and ethanol fermentation of Saccharomyces cerevisiae at high temperatures.", "token_count": 346, "char_count": 1113, "word_count": 134, "semantic_coherence": 1, "information_density": 0.5373, "quality_score": 0.7687, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:32.565060", "source": { "split": "train_shard_00001", "doc_id": 561 }, "chunk_id": "train_shard_00001_561_1", "global_id": 6448 }, { "text": "Beijing sub-lineage of Mycobacterium tuberculosis has been reported to have increased transmissibility and drug resistance. This led us to get insights of genomic landscape of modern Beijing sub-lineages in comparison with other lineages of M. tuberculosis utilizing pan-genomics approach. Pangenome analysis was performed using software Spine (v0.2.3), AGEnt (v0.2.3) and ClustAGE (v0.7.6). The average pangenome size was 45,40,849 bp with 4,391 coding sequences (CDS), with a GC content of 65.4%. The size of the core genome was 36,83,161 bp, contained 3,698 CDS and had an average GC content of 65.1%. The average accessory genome size was 6,96,320.9 bp, with 539.4 CDS and GC content of 67.9%. Among the accessory elements complete deletion of CRISPR-associated endoribonuclease cas1 ( Rv2817c ), cas2 ( Rv2816c ), CRISPR type III-a/mtube-associated protein csm6 ( Rv2818c ), CRISPR type III-a/mtube-associated ramp protein csm5 ( Rv2819c ) and partial deletion (61.5%) CRISPR type III-a/mtube-associated ramp protein csm4 ( Rv2820c ) sequences was found specifically in modern Beijing lineages taken in assortment. The sequences were validated using conventional PCR method, which precisely amplified the corresponding targets of sequence elements with 100% sensitivity and specificity. Deletion of accessory CRISPR sequence elements amongst the modern Beijing sub-lineage of M. tuberculosis suggest more defective DNA-repair in these strains which may enhance virulence of the strains. Further, the developed conventional PCR approach for detection of virulent modern Beijing lineage may be of interest to public health and outbreak control organizations for rapid detection of modern Beijing lineage.", "token_count": 499, "char_count": 1707, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:33.215324", "source": { "split": "train_shard_00001", "doc_id": 562 }, "chunk_id": "train_shard_00001_562_0", "global_id": 6449 }, { "text": "Pan-genome analysis of Mycobacterium tuberculosis identifies accessory genome sequences deleted in modern Beijing lineage", "token_count": 34, "char_count": 128, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:33.578472", "source": { "split": "train_shard_00001", "doc_id": 562 }, "chunk_id": "train_shard_00001_562_1", "global_id": 6450 }, { "text": "Group B Streptococcus (GBS) literature largely focuses on humans and neonatal disease, but GBS also affects numerous animals, with significant impacts on health and productivity. Spill-over events occur between humans and animals and may be followed by amplification and evolutionary adaptation in the new niche, including changes in the core or accessory genome content. Here, we describe GBS from one-humped camels (Camelus dromedarius), a relatively poorly studied GBS host of increasing importance for food security in arid regions. Genomic analysis shows that virtually all GBS from camels in East Africa belong to a monophyletic clade, sublineage (SL)609. Capsular types IV and VI, including a new variant of type IV, were over-represented compared to other host species. Two genomic islands with signatures of mobile elements contained most camel-associated genes, including genes for metal and carbohydrate utilisation. Lactose fermentation genes were associated with milk isolates, albeit at lower prevalence in camel than bovine GBS. The presence of a phage with high identity to Streptococcus pneumoniae and Streptococcus suis suggests lateral gene transfer between GBS and bacterial species that have not been described in camels. The evolution of camel GBS appears to combine host restriction with the sharing of accessory genome content across pathogen and host species.\n\nHow GBS Got Its Hump: Genomic Analysis of Group B Streptococcus from Camels Identifies Host Restriction as well as Mobile Genetic Elements Shared across Hosts and Pathogens.", "token_count": 401, "char_count": 1594, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:34.196819", "source": { "split": "train_shard_00001", "doc_id": 563 }, "chunk_id": "train_shard_00001_563_0", "global_id": 6451 }, { "text": "Agrobacterium fabrum has been critical for the development of plant genetic engineering and agricultural biotechnology due to its ability to transform eukaryotic cells. However, the gene composition, evolutionary dynamics, and niche adaptation of this species is still unknown. Therefore, we established a comparative genomic analysis based on a pan-chromosome data set to evaluate the genetic diversity of A. fabrum. Here, 25 A. fabrum genomes were selected for analysis by core genome phylogeny combined with the average nucleotide identity (ANI), amino acid identity (AAI), and in silico DNA-DNA hybridization (DDH) values. An open pan-genome of A. fabrum exhibits genetic diversity with variable accessorial genes as evidenced by a consensus pan-genome of 12 representative genomes. The genomic plasticity of A. fabrum is apparent in its putative sequences for mobile genetic elements (MGEs), limited horizontal gene transfer barriers, and potentially horizontally transferred genes. The evolutionary constraints and functional enrichment in the pan-chromosome were measured by the Clusters of Orthologous Groups (COG) categories using eggNOG-mapper software, and the nonsynonymous/synonymous rate ratio (dN/dS) was determined using HYPHY software. Comparative analysis revealed significant differences in the functional enrichment and the degree of purifying selection between the core genome and non-core genome. We demonstrate that the core gene families undergo stronger purifying selection but have a significant bias to contain one or more positively selected sites. Furthermore, although they shared similar genetic diversity, we observed significant differences between chromosome 1 (Chr I) and the chromid in their functional features and evolutionary constraints. We demonstrate that putative genetic elements responsible for plant infection, ecological adaptation, and speciation represent the core genome, highlighting their importance in the adaptation of A. fabrum to plant-related niches. Our pan-chromosome analysis of A. fabrum provides comprehensive insights into the genetic properties, evolutionary patterns, and niche adaptation of the species", "token_count": 516, "char_count": 2231, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6081, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:34.856533", "source": { "split": "train_shard_00001", "doc_id": 564 }, "chunk_id": "train_shard_00001_564_0", "global_id": 6452 }, { "text": "IMPORTANCE Agrobacterium spp. live in diverse plant-associated niches such as soil, the rhizosphere, and vegetation, which are challenged by multiple stressors such as diverse energy sources, plant defenses, and microbial competition. They have evolved the ability to utilize diverse resources, escape plant defenses, and defeat competitors. However, the underlying genetic diversity and evolutionary dynamics of Agrobacterium spp. remain unexplored. We examined the phylogeny and pan-genome of A. fabrum to define intraspecies evolutionary relationships. Our results indicate an open pan-genome and numerous MGEs and horizontally transferred genes among A. fabrum genomes, reflecting the flexibility of the chromosomes and the potential for genetic exchange. Furthermore, we observed significant differences in the functional features and evolutionary constraints between the core and accessory genomes and between Chr I and the chromid, respectively.\n\nPan-Chromosome and Comparative Analysis of Agrobacterium fabrum Reveal Important Traits Concerning the Genetic Diversity, Evolutionary Dynamics, and Niche Adaptation of the Species.", "token_count": 292, "char_count": 1177, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6733, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:35.423900", "source": { "split": "train_shard_00001", "doc_id": 564 }, "chunk_id": "train_shard_00001_564_1", "global_id": 6453 }, { "text": "This study aims to utilize the microbial resources found within Laphet-so, a traditional fermented tea in Myanmar. A total of 18 isolates of thermotolerant yeasts were obtained from eight samples of Laphet-so collected from southern Shan state, Myanmar. All isolates demonstrated the tannin tolerance, and six isolates were resistant to 5% (w/v) tannin concentration. All 18 isolates were capable of carboxy-methyl cellulose (CMC) degrading, but only the isolate DK showed ethanol production at 45 °C noticed by gas formation. This ethanol producing yeast was identified to be Cyberlindnera rhodanensis based on the sequence analysis of the D1/D2 domain on rRNA gene. C. rhodanensis DK produced 1.70 ± 0.01 U of thermostable extracellular β-glucosidase when cultured at 37 °C for 24 h using 0.5% (w/v) CMC as a carbon source. The best two carbon sources for extracellular β-glucosidase production were found to be either xylose or xylan, with β-glucosidase activity of 3.07-3.08 U/mL when the yeast was cultivated in the yeast malt extract (YM) broth containing either 1% (w/v) xylose or xylan as a sole carbon source at 37 °C for 48 h", "token_count": 404, "char_count": 1191, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:36.043089", "source": { "split": "train_shard_00001", "doc_id": 565 }, "chunk_id": "train_shard_00001_565_0", "global_id": 6454 }, { "text": "The optimal medium compositions for enzyme production predicted by Plackett-Burman design and central composite design (CCD) was composed of yeast extract 5.83 g/L, peptone 10.81 g/L and xylose 20.20 g/L, resulting in a production of 7.96 U/mL, while the medium composed (g/L) of yeast extract 5.79, peptone 13.68 and xylan 20.16 gave 9.45 ± 0.03 U/mL for 48 h cultivation at 37 °C. Crude β-glucosidase exhibited a remarkable stability of 100%, 88% and 75% stable for 3 h at 35, 45 and 55 °C, respectively.\n\nA Thermotolerant Yeast Cyberlindnera rhodanensis DK Isolated from Laphet-so Capable of Extracellular Thermostable β-Glucosidase Production.", "token_count": 262, "char_count": 654, "word_count": 100, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:36.591913", "source": { "split": "train_shard_00001", "doc_id": 565 }, "chunk_id": "train_shard_00001_565_1", "global_id": 6455 }, { "text": "Korea, being surrounded by the sea, provides a rich habitat for marine sponges, which have been a prolific source of bioactive natural products. Although a diverse array of structurally novel natural products has been isolated from Korean marine sponges, their biosynthetic origins remain largely unknown. To explore the biosynthetic potential of Korean marine sponges, we conducted metagenomic analyses of sponges inhabiting the East Sea of Korea. This analysis revealed a symbiotic association of Candidatus Entotheonella bacteria with Halichondria sponges. Here, we report a new chemically rich Entotheonella variant, which we named Ca. Entotheonella halido. Remarkably, this symbiont makes up 69% of the microbial community in the sponge Halichondira dokdoensis. Genome-resolved metagenomics enabled us to obtain a high-quality Ca. E. halido genome, which represents the largest (12 Mb) and highest quality among previously reported Entotheonella genomes. We also identified the biosynthetic gene cluster (BGC) of the known sponge-derived Halicylindramides from the Ca. E. halido genome, enabling us to determine their biosynthetic origin. This new symbiotic association expands the host diversity and biosynthetic potential of metabolically talented bacterial genus Ca. Entotheonella symbionts.IMPORTANCEOur study reports the discovery of a new bacterial symbiont Ca. Entotheonella halido associated with the Korean marine sponge Halichondria dokdoensis. Using genome-resolved metagenomics, we recovered a high-quality Ca. E. halido MAG (Metagenome-Assembled Genome), which represents the largest and most complete Ca. Entotheonella MAG reported to date. Pangenome and BGC network analyses revealed a remarkably high BGC diversity within the Ca", "token_count": 508, "char_count": 1833, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5875, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:37.254143", "source": { "split": "train_shard_00001", "doc_id": 566 }, "chunk_id": "train_shard_00001_566_0", "global_id": 6456 }, { "text": "Entotheonella pangenome, with almost no overlapping BGCs between different MAGs. The cryptic and genetically unique BGCs present in the Ca. Entotheonella pangenome represents a promising source of new bioactive natural products.\n\nMetagenomic insights and biosynthetic potential of Candidatus Entotheonella symbiont associated with Halichondria marine sponges.", "token_count": 110, "char_count": 380, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8444, "quality_score": 0.9222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:37.635274", "source": { "split": "train_shard_00001", "doc_id": 566 }, "chunk_id": "train_shard_00001_566_1", "global_id": 6457 }, { "text": "Throughout history, the yeast Saccharomyces cerevisiae has played a central role in human society due to its use in food production and more recently as a major industrial and model microorganism, because of the many genetic and genomic tools available to probe its biology. However, S. cerevisiae has proven difficult to engineer to expand the carbon sources it can utilize, the products it can make, and the harsh conditions it can tolerate in industrial applications. Other yeasts that could solve many of these problems remain difficult to manipulate genetically. Here, we engineered the thermotolerant yeast Kluyveromyces marxianus to create a new synthetic biology platform. Using CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats with Cas9)-mediated genome editing, we show that wild isolates of K. marxianus can be made heterothallic for sexual crossing. By breeding two of these mating-type engineered K. marxianus strains, we combined three complex traits-thermotolerance, lipid production, and facile transformation with exogenous DNA-into a single host. The ability to cross K. marxianus strains with relative ease, together with CRISPR-Cas9 genome editing, should enable engineering of K. marxianus isolates with promising lipid production at temperatures far exceeding those of other fungi under development for industrial applications. These results establish K. marxianus as a synthetic biology platform comparable to S. cerevisiae, with naturally more robust traits that hold potential for the industrial production of renewable chemicals.IMPORTANCE The yeast Kluyveromyces marxianus grows at high temperatures and on a wide range of carbon sources, making it a promising host for industrial biotechnology to produce renewable chemicals from plant biomass feedstocks. However, major genetic engineering limitations have kept this yeast from replacing the commonly used yeast Saccharomyces cerevisiae in industrial applications", "token_count": 513, "char_count": 2048, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:38.278541", "source": { "split": "train_shard_00001", "doc_id": 567 }, "chunk_id": "train_shard_00001_567_0", "global_id": 6458 }, { "text": "Here, we describe genetic tools for genome editing and breeding K. marxianus strains, which we use to create a new thermotolerant strain with promising fatty acid production. These results open the door to using K. marxianus as a versatile synthetic biology platform organism for industrial applications.\n\nEngineering Kluyveromyces marxianus as a Robust Synthetic Biology Platform Host.", "token_count": 105, "char_count": 400, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8036, "quality_score": 0.9018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:38.706505", "source": { "split": "train_shard_00001", "doc_id": 567 }, "chunk_id": "train_shard_00001_567_1", "global_id": 6459 }, { "text": "Mucous membrane pemphigoid (MMP) is an autoimmune-based bullous disease affecting the mucous membranes, mainly oral and ocular. One of the most common clinical manifestations is desquamative gingivitis (DG), characterized by intense symptoms and functional limitations. The dentist is among the first specialists to observe DG and, therefore, must be able to diagnose it. In this regard, the purpose of the present study was to evaluate the efficacy and safety of a clinical protocol for the topical management of patients with DG and MMP buccal lesions. Thirteen patients with clinical and histologic diagnoses of MMP-localized DG in the oral cavity were retrospectively enrolled. Each patient received topical treatment with clobetasol propionate oral gel 0.05%; nicotinamide; oral probiotic (contains Bifidobacterium lactis HN019, Kluyveromyces marxianus fragilis B0399, colostrum, and biotin); and doxycycline. Before and after 3 months of therapy, clinic records were collected for each patient. Seven patients (53.8%) had a complete response to treatment; four patients (30.8%) had a partial response to treatment; and, finally, two patients (15.4%) had no benefit from therapy. Dental management of patients presenting solely with oral manifestations of MMP may involve the use of topical corticosteroids, doxycycline, vitamin supplements, and probiotics and associating professional oral hygiene procedures.\n\nAnalysis of a Combination Therapy Protocol for the Treatment of Oral Mucous Membrane Pemphigoid: A Retrospective Case Series Study.", "token_count": 407, "char_count": 1562, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [ "HN019" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:39.356599", "source": { "split": "train_shard_00001", "doc_id": 568 }, "chunk_id": "train_shard_00001_568_0", "global_id": 6460 }, { "text": "It has recently been shown that patients from non-European ancestries are at a higher risk of inappropriate clinical intervention because of inaccurate biomarker estimation, arising from the reference bias inherent in standard methods for determining the tumor genome from sequencing data. Here we demonstrate that these inaccuracies can be reduced by using a pangenome reference appropriate for the patient’s population. We constructed a novel secondary analysis workflow where the pangenome reference serves as a scaffold for mapping the sequencing reads, and is also included in the relevant ‘panel of normals’ needed to discriminate between germline and somatic mutations in tumor-only sequencing. This approach detects known somatic mutations in tumor-only sequencing more accurately than the standard GATK somatic calling workflow, prevalent in diagnostic settings for analysis of sequencing data from tumor-only assays, on a standard benchmark tumor sample, HCC1395 (33% relative increase in F1 score). We also assessed the expected clinical impact of our approach by comparing the Tumor Mutational Burden (TMB) calculated from missense somatic mutations called in tumor/normal samples from 6 patients self-reported as belonging to African, 1 to Asian and 3 to European populations respectively. We find that the TMB values calculated from the tumor-only sequencing data analyzed by our workflow more closely approximate the TMB values calculated from the tumor-normal analysis of the same sample, being 35% higher on average, whereas GATK tumor-only analysis generates TMB values 56% higher on average than the tumor-normal analysis of the same sample. Tumor-normal TMB values calculated by the two methods do not vary as drastically, GATK generated values being 13% higher on average, indicating that GATK tumor-only analysis leads to significant overestimation of TMB values, which can be largely corrected by using our workflow when tumor-normal sequencing is not available. These results indicate that pangenome based analysis has the potential to become the new standard for unbiased processing of somatic sequencing samples, following on from its increased adoption for germline sequencing analysis.\n\nPangenome References Improve Biomarker Estimation from Tumor Sequencing Data", "token_count": 508, "char_count": 2291, "word_count": 331, "semantic_coherence": 1, "information_density": 0.5287, "quality_score": 0.7644, "entities": { "genes": [ "HCC1395" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:40.051080", "source": { "split": "train_shard_00001", "doc_id": 569 }, "chunk_id": "train_shard_00001_569_0", "global_id": 6461 }, { "text": "Edwardsiella ictaluri continues to pose a significant risk to the health and production of striped catfish (Pangasianodon hypophthalmus) in Vietnam. Whilst recent advances in genomic sequencing provide an insight into the global genomic diversity of this important fish pathogen, genome-wide analysis of Vietnamese isolates recovered over time is lacking. In this study, we used a whole-genome sequencing approach to compare the genomes of 31 E. ictaluri isolates recovered over a 20-year period (2001-2021) and performed comparative genomic analysis to explore temporal changes in genome diversity, population structure and mechanisms driving pathogenesis and antimicrobial resistance. Our findings revealed an open pan-genome with 4148 genes and a core genome (3 060 genes) accounting for over two-thirds of the genome. Moreover, we found the genomes sequenced to classify into two distinct lineages and estimated the ancestral origin of these lineages within Vietnam to date back to the 1950s. Plasmids were highly prevalent in Vietnamese E. ictaluri, with isolates harbouring up to four plasmids within their genome. Further, a diverse mobilome was observed with nine different plasmid types detected across the genome collection. Exploration of putative plasmids revealed a diverse set of antimicrobial resistance genes (ARGs) against key antibiotics used in Vietnamese aquaculture and virulence genes associated with protein secretion systems. Correlation analysis revealed the total number of ARGs detected in genomes to increase with isolate recovery time. Whilst the number of virulence genes remained relatively stable, temporal variation was noted in several virulence factors related to motility and immune system modulation. Findings from this study highlight the need for continued genomic surveillance to monitor changes in antimicrobial resistance and pathogenesis, to help inform the development of disease control and management strategies.", "token_count": 470, "char_count": 1986, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6151, "quality_score": 0.8076, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:40.713922", "source": { "split": "train_shard_00001", "doc_id": 570 }, "chunk_id": "train_shard_00001_570_0", "global_id": 6462 }, { "text": "Genomic diversity and evolutionary patterns of <i>Edwardsiella ictaluri</i> affecting farmed striped catfish (<i>Pangasianodon hypophthalmus</i>) in Vietnam over 20 years.", "token_count": 70, "char_count": 195, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:41.079943", "source": { "split": "train_shard_00001", "doc_id": 570 }, "chunk_id": "train_shard_00001_570_1", "global_id": 6463 }, { "text": "

Background

Fermented foods harbour the bacterium Weissella confusa , which has probiotic properties but can potentially act as an opportunistic pathogen in humans and animals. Using pangenome analysis, our study aimed to improve the classification and identify functional traits of publicly available W. confusa genomes, focusing on evaluating their potential as probiotics.

Method

The genomic sequence of 120 strains of W. confusa was acquired from the NCBI RefSeq database. The downloaded sequences underwent a quality verification and filtering process. Ultimately, the chosen genomes were examined for comparative genomic analysis. We employed Roary to investigate the pangenome of W. confusa . Fisher’s exact test was utilised to analyse contingency tables, with a significance threshold of p < 0.05 (two-tailed).

Results

Our investigation revealed that the pangenome of W. confusa comprises 1100 core genes, 184 soft-core genes, 1407 shell genes, and 7006 cloud genes. This finding emphasises the “open” aspect of the W. confusa pangenome. The comparison of genomes showed that there were no acquired antibiotic resistance genes. However, the strains had different amounts of prophage regions, CRISPR arrays, and plasmids. Our research identified probiotic marker genes (PMGs), with the majority (78%) found in the core and soft-core genomes of various strains of W. confusa .

Conclusions

An extensive investigation of the W. confusa pangenome has concluded that it could be useful as a probiotic. Additional research is necessary to thoroughly evaluate the potential risks.\n\nA Comprehensive Pangenome Approach to Exploring the Probiotic Potential ofWeissella Confusa", "token_count": 436, "char_count": 1716, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:41.711951", "source": { "split": "train_shard_00001", "doc_id": 571 }, "chunk_id": "train_shard_00001_571_0", "global_id": 6464 }, { "text": "Escherichia albertii is an emerging foodborne pathogen. To better understand the pathogenesis and health risk of this pathogen, comparative genomics and phenotypic characterization were applied to assess the pathogenicity potential of E. albertii strains isolated from wild birds in a major agricultural region in California. Shiga toxin genes stx2f were present in all avian strains. Pangenome analyses of 20 complete genomes revealed a total of 11,249 genes, of which nearly 80% were accessory genes. Both core gene-based phylogenetic and accessory gene-based relatedness analyses consistently grouped the three stx2f-positive clinical strains with the five avian strains carrying ST7971. Among the three Stx2f-converting prophage integration sites identified, ssrA was the most common one. Besides the locus of enterocyte effacement and type three secretion system, the high pathogenicity island, OI-122, and type six secretion systems were identified. Substantial strain variation in virulence gene repertoire, Shiga toxin production, and cytotoxicity were revealed. Six avian strains exhibited significantly higher cytotoxicity than that of stx2f-positive E. coli, and three of them exhibited a comparable level of cytotoxicity with that of enterohemorrhagic E. coli outbreak strains, suggesting that wild birds could serve as a reservoir of E. albertii strains with great potential to cause severe diseases in humans.\n\nGenomic and Phenotypic Characterization of Shiga Toxin-Producing Escherichia albertii Strains Isolated from Wild Birds in a Major Agricultural Region in California.", "token_count": 481, "char_count": 1692, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5991, "quality_score": 0.7995, "entities": { "genes": [ "ST7971" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:42.359527", "source": { "split": "train_shard_00001", "doc_id": 572 }, "chunk_id": "train_shard_00001_572_0", "global_id": 6465 }, { "text": "The attempts toward addition of biocontrol agents in dairy products have gained popularity. Here, we worked on analysing the antifungal activity of binary and ternary combinations of three Lactic Acid Bacteria (LAB) against five spoilage yeasts in yogurt. The yogurt samples were characterized in terms of pH, acidity, WHC, textural parameters, viscosity, survivability and antifungal activity of LAB and sensorial properties during cold storage. The results showed that the inoculation of LAB in yogurt gave rise in significant reduction of pH throughout cold storage while titrable acidity and WHC decreased (p < .05). Inoculation of LAB resulted in significant increase in hardness and adhesiveness while springiness remained constant. On the other hand, apparent viscosity of all samples experienced a profound increase up to the 10th day of storage followed by a reduction trend for the rest of storage period. Analysis of inhibitory activity of LAB showed an efficient barrier against all five yeasts, in which the most activity was recorded for Lactobacillus reuteri followed by Lactobacillus acidophilus. On the other hand, the most resistance yeast was Kluyveromyces marxianus followed by Rhodotorula mucilaginosa. Sensorial analysis revealed that addition of LAB in yogurt brought about a profound improvement in textural quality of samples. Inoculation of LAB cultures in yogurt at 5% (v/v) not only could improve the physicochemical and sensorial properties of yogurt, but also could introduce a strategy toward substituting of chemical preservatives with biocontrol agents.\n\nEvaluation of the bioprotectivity of Lactobacillus binary/ternary cultures in yogurt.", "token_count": 446, "char_count": 1715, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:42.992511", "source": { "split": "train_shard_00001", "doc_id": 573 }, "chunk_id": "train_shard_00001_573_0", "global_id": 6466 }, { "text": "Robiola di Roccaverano is an artisanal Protected Designation of Origin (PDO) soft cheese made with raw goat's milk and by the addition of Natural Milk Culture (NMC) to drive the fermentation process. Cheeses collected from five different dairy plants were analyzed for their bacterial and fungal microbiota diversity. Lactococcus lactis and Leuconostoc mesenteroides were the main bacterial population, while Galactomyces candidum and Kluyveromyces marxianus constituted the core mycobiota but many other minor taxa were observed, suggesting a high level of complexity in fungal composition by these cheeses compared to bacteria population.\n\nThe Bacterial and Fungal Microbiota of \"Robiola di Roccaverano\" Protected Designation of Origin Raw Milk Cheese.", "token_count": 219, "char_count": 782, "word_count": 107, "semantic_coherence": 1, "information_density": 0.729, "quality_score": 0.8645, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:43.462554", "source": { "split": "train_shard_00001", "doc_id": 574 }, "chunk_id": "train_shard_00001_574_0", "global_id": 6467 }, { "text": "The Bacillus subtilis group (Bs group), with Bacillus subtilis as its core species, holds significant research and economic value in various fields, including science, industrial production, food, and pharmaceuticals. However, most studies have been confined to comparative genomics analyses and exploration within individual genomes at the level of species, with few conducted within groups across different species. This study focused on Bacillus subtilis, the model of Gram-positive bacteria, and 14 other species with significant research value, employing comparative pangenomics as well as population enrichment analysis to ascertain the functional enrichment and diversity. Through the quantification of pangenome openness, this work revealed the underlying biological drivers and significant correlation between pangenome openness and various factors, including the distribution of toxin-antitoxin- and integrase-related genes, as well as the number of endonucleases, recombinases, repair system-related genes, prophages, integrases, and transfer mobile elements. Furthermore, the functional enrichment results indicated the potential for secondary metabolite, probiotic, and antibiotic exploration in Bacillus licheniformis, Bacillus paralicheniformis, and Bacillus spizizenii, respectively. In general, this work systematically exposed the quantification of pangenome openness, biological drivers, the pivotal role of genomic instability factors, and mobile elements, providing targeted exploration guidance for the Bs group.\n\nComparative Genomics Unveils Functional Diversity, Pangenome Openness, and Underlying Biological Drivers among Bacillus subtilis Group.", "token_count": 414, "char_count": 1720, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6077, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:44.088164", "source": { "split": "train_shard_00001", "doc_id": 575 }, "chunk_id": "train_shard_00001_575_0", "global_id": 6468 }, { "text": "This paper presents a new data structure, GIN-TONIC (Graph INdexing Through Optimal Near Interval Compaction), designed to index arbitrary string-labelled directed graphs representing, for instance, pangenomes or transcriptomes. GIN-TONIC provides several capabilities not offered by other graph-indexing methods based on the FM-Index. It is non-hierarchical, handling a graph as a monolithic object; it indexes at nucleotide resolution all possible walks in the graph without the need to explicitly store them; it supports exact substring queries in polynomial time and space for all possible walk roots in the graph, even if there are exponentially many walks corresponding to such roots. Specific ad-hoc optimizations, such as precomputed caches, allow GIN-TONIC to achieve excellent performance for input graphs of various topologies and sizes. Robust scalability capabilities and a querying performance close to that of a linear FM-Index are demonstrated for two real-world applications on the scale of human pangenomes and transcriptomes. Source code and associated benchmarks are available on GitHub.\n\nGIN-TONIC: non-hierarchical full-text indexing for graph genomes.", "token_count": 310, "char_count": 1223, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:44.668397", "source": { "split": "train_shard_00001", "doc_id": 576 }, "chunk_id": "train_shard_00001_576_0", "global_id": 6469 }, { "text": "

Main conclusion

Next-generation molecular tools with AI integration can accelerate genetic gain in sugarcane by enhancing variation, accuracy, and efficiency, enabling rapid development of high-yielding, high-quality, and climate-resilient varieties. Enhancing genetic gain is essential for sustainable sugar and bioenergy production, especially amid growing global reliance on renewable energy sources. Sugarcane and its byproducts serve as important feedstocks for both first and second-generation biofuels, and face several breeding challenges due to its genetic complexity, extended breeding cycles, and strong environmental interactions. The breeder's equation offers a quantitative framework to accelerate genetic improvement by optimizing four key components: additive genetic variation (σa), heritability (h2), selection intensity (i), and breeding cycle length (L). Additive genetic variation can be enhanced through genome-wide exploration, including genome, pan-genome, and super pangenome analyses, gene discovery, characterization, and the induction of novel variations. Precise estimation of heritability in sugarcane can be achieved through the large-scale characterization of germplasm, high-throughput phenotyping, and detailed genotype × environment interaction (G × E) studies. Selection intensity can be increased by expanding population sizes via genotypic, genomic, and in vitro selection, leveraging the law of large numbers, and adopting technologies that provide greater throughput, precision, and cost efficiency. Breeding cycle time can be significantly reduced using tools, such as marker-assisted selection, genomic selection, emerging doubled haploid strategies (though still challenging in polyploid crops like sugarcane), speed breeding, transgenic approaches, and genome editing technologies like CRISPR/Cas9 (including base and prime editing), TALENs. This review provides a comprehensive overview of each component of the breeder's equation in sugarcane breeding and highlights next-generation molecular strategies and tools aligned to these components. The integration of these advanced tools with artificial intelligence holds immense potential to enhance genetic gain and accelerate the development of high-yielding, high-quality, and climate-resilient sugarcane varieties.", "token_count": 515, "char_count": 2341, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:45.330443", "source": { "split": "train_shard_00001", "doc_id": 577 }, "chunk_id": "train_shard_00001_577_0", "global_id": 6470 }, { "text": "Next-generation molecular breeding tools to harness higher genetic gains in sugarcane.", "token_count": 19, "char_count": 86, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:45.683107", "source": { "split": "train_shard_00001", "doc_id": 577 }, "chunk_id": "train_shard_00001_577_1", "global_id": 6471 }, { "text": "

Background

Actinomyces strains are commonly found as part of the normal microflora on human tissue surfaces, including the oropharynx, gastrointestinal tract, and female genital tract. Understanding the diversity and characterization of Actinomyces species is crucial for human health, as they play an important role in dental plaque formation and biofilm-related infections. Two Actinomyces strains ATCC 49340 T and ATCC 51655 T have been utilized in various studies, but their accurate species classification and description remain unresolved.

Results

To investigate the genomic properties and taxonomic status of these strains, we employed both 16S rRNA Sanger sequencing and whole-genome sequencing using the Illumina HiSeq X Ten platform with PE151 (paired-end) sequencing. Our analyses revealed that the draft genome of Actinomyces acetigenes ATCC 49340 T was 3.27 Mbp with a 68.0% GC content, and Actinomyces stomatis ATCC 51655 T has a genome size of 3.08 Mbp with a 68.1% GC content. Multi-locus (atpA, rpoB, pgi, metG, gltA, gyrA, and core genome SNPs) sequence analysis supported the phylogenetic placement of strains ATCC 51655 T and ATCC 49340 T as independent lineages. Digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI), and average amino acid identity (AAI) analyses indicated that both strains represented novel Actinomyces species, with values below the threshold for species demarcation (70% dDDH, 95% ANI and AAI)", "token_count": 475, "char_count": 1535, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [ "PE151" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:46.330202", "source": { "split": "train_shard_00001", "doc_id": 578 }, "chunk_id": "train_shard_00001_578_0", "global_id": 6472 }, { "text": "Pangenome analysis identified 5,731 gene clusters with strains ATCC 49340 T and ATCC 51655 T possessing 1,515 and 1,518 unique gene clusters, respectively. Additionally, genomic islands (GIs) prediction uncovered 24 putative GIs in strain ATCC 49340 T and 16 in strain ATCC 51655 T, contributing to their genetic diversity and potential adaptive capabilities. Pathogenicity analysis highlighted the potential human pathogenicity risk associated with both strains, with several virulence-associated factors identified. CRISPR-Cas analysis exposed the presence of CRISPR and Cas genes in both strains, indicating these strains might evolve a robust defense mechanism against them.

Conclusion

This study supports the classification of strains ATCC 49340 T and ATCC 51655 T as novel species within the Actinomyces, in which the name Actinomyces acetigenes sp. nov. (type strain ATCC 49340 T = VPI D163E-3 T = CCUG 34286 T = CCUG 35339 T) and Actinomyces stomatis sp. nov. (type strain ATCC 51655 T = PK606T = CCUG 33930 T) are proposed.\n\nGenome characterization and taxonomy of Actinomyces acetigenes sp. nov., and Actinomyces stomatis sp. nov., previously isolated from the human oral cavity.", "token_count": 484, "char_count": 1339, "word_count": 177, "semantic_coherence": 1, "information_density": 0.5989, "quality_score": 0.7994, "entities": { "genes": [ "PK606" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:46.977828", "source": { "split": "train_shard_00001", "doc_id": 578 }, "chunk_id": "train_shard_00001_578_1", "global_id": 6473 }, { "text": "Plant Growth-Promoting Rhizobacteria (PGPR) are emerging as a sustainable alternative in agriculture due to their environmentally friendly properties and their ability to enhance crop productivity. Among these, Pantoea agglomerans has gained attention for its versatility as both a biofertilizer and a biocontrol agent. In this study, we use comparative genomics to gain insight into the genetic diversity and functional specialization of members of this species. The pan-genome analysis of 20 representative P. agglomerans strains revealed that 32% of the genes constitute the core genome (2856 out of 8899), while the remaining 68% are classified as accessory or singleton genes, indicating a high level of genomic diversity within the species. Functional annotation showed that core genes are predominantly involved in central metabolic processes, whereas genes associated with specialized metabolic functions are found within the accessory and singleton categories. The comparative analysis demonstrated a mosaic distribution of genes related to nitrogen and sulfur metabolism, heavy metal resistance, defense mechanisms, and oligopeptide uptake, suggesting niche-specific adaptations and metabolic capabilities within this species. Exometabolome profiling of strains associated with different hosts, specifically plant (C1) or human (DSM3493T), demonstrated that omics-centered approaches can be utilized to select P. agglomerans strains tailored to specific agronomic requirements.\n\nIntegrative Genomics and Metabolomics Analyses Provide New Insights into the Molecular Basis of Plant Growth Promotion by <i>Pantoea agglomerans</i>.", "token_count": 412, "char_count": 1682, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "DSM3493" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:47.599880", "source": { "split": "train_shard_00001", "doc_id": 579 }, "chunk_id": "train_shard_00001_579_0", "global_id": 6474 }, { "text": "This study aimed to overexpress an inulinase gene in Kluyveromyces marxianus to achieve the inulinase overproduction and preparation of ultra-high-fructose syrup. First, the inulinase gene (INU1 gene) was overexpressed through codon optimization and selection of a suitable promoter. Then, the inulinase was overproduced by high-cell-density fermentation. Finally, ultra-high-fructose syrup was prepared. It was found that optimization of the codons of the native INU1 gene encoding inulinase from Kluyveromyces marxianus KM-0 made a recombinant strain KM-N70 carrying the optimized INU1N gene produce 251.4 U/mL of the inulinase activity. Furthermore, inulinase activity produced by a recombinant KM-KN16 strain carrying the optimized INU1N gene directed by the native TPS1 promoter from K. marxianus KM-0 reached 338.5 U/mL and expression level of the optimized INU1N gene in the recombinant KM-KN16 strain was also greatly enhanced. During a 10-L fermentation, the recombinant KM-KN16 strain could produce 374.3 U/mL of inulinase activity within 24 h, while during a high-cell-density fed-batch fermentation, the recombinant KM-KN16 strain could produce 896.1 U/mL of inulinase activity and OD₆₀₀ₙₘ value of its culture reached 108. The crude inulinase preparation obtained in this study had an inulinase activity of 18,699.8 ± 736.4 U/g of the crude preparation", "token_count": 444, "char_count": 1365, "word_count": 195, "semantic_coherence": 1, "information_density": 0.4974, "quality_score": 0.7487, "entities": { "genes": [ "TPS1", "INU1", "INU1N", "KN16" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:48.239062", "source": { "split": "train_shard_00001", "doc_id": 580 }, "chunk_id": "train_shard_00001_580_0", "global_id": 6475 }, { "text": "It was found that 90.3% of 332.4 g/L of inulin was hydrolyzed to produce 41.0 g/L of glucose and 256.0 g/L of fructose and 91.1% of 328.2 g/L of inulin in the extract of the tubers of Jerusalem artichoke was hydrolyzed to produce 48.3 g/L of glucose and 250.5 g/L of fructose by the crude inulinase preparation (75 U/g of the substrate) within 8 h. The hydrolysates contained major monosaccharides and a trace amount of trisaccharides and the monosaccharides were composed of around 85% fructose and 15% glucose. So far, any other yeasts available have produced only up to 120 U/mL of inulinase activity. Together, this made the recombinant KM-KN16 strain be the best inulinase producer at this moment. The inulinase activity of 18,699.8 ± 736.4 U/g of the crude preparation and the ultra-high-fructose syrup with 41.0 g/L of glucose and 256.0 g/L of fructose were obtained. The inulinase activity obtained in this study was the highest among all the inulinase activities produced by yeast, fungal, and bacterial strains obtained so far.\n\nInulinase hyperproduction by Kluyveromyces marxianus through codon optimization, selection of the promoter, and high-cell-density fermentation for efficient inulin hydrolysis", "token_count": 415, "char_count": 1213, "word_count": 191, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [ "KN16" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:48.866104", "source": { "split": "train_shard_00001", "doc_id": 580 }, "chunk_id": "train_shard_00001_580_1", "global_id": 6476 }, { "text": "

Motivation

Comparative genomics is a growing field but one that will be eventually overtaken by sample size studies and the increase of available genomes in public databases. We present the Pangenome Analysis Toolkit (PATO) designed to simultaneously analyze thousands of genomes using a desktop computer. The tool performs common tasks of pangenome analysis such as core-genome definition and accessory genome properties and includes new features that help characterize population structure, annotate pathogenic features and create gene sharedness networks. PATO has been developed in R to integrate with the large set of tools available for genetic, phylogenetic and statistical analysis in this environment.

Results

PATO can perform the most demanding bioinformatic analyses in minutes with an accuracy comparable to state-of-the-art software but 20–30x times faster. PATO also integrates all the necessary functions for the complete analysis of the most common objectives in microbiology studies. Lastly, PATO includes the necessary tools for visualizing the results and can be integrated with other analytical packages available in R.

Availability

The source code for PATO is freely available at https://github.com/irycisBioinfo/PATO under the GPLv3 license.

Contact

val.fernandez@salud.madrid.org

Supplementary information

Supplementary data are available at Bioinformatics online\n\nPATO: Pangenome Analysis Toolkit", "token_count": 358, "char_count": 1465, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6856, "quality_score": 0.8428, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:49.439730", "source": { "split": "train_shard_00001", "doc_id": 581 }, "chunk_id": "train_shard_00001_581_0", "global_id": 6477 }, { "text": "Most new pathogens of humans and animals arise via switching events from distinct host species. However, our understanding of the evolutionary and ecological drivers of successful host adaptation, expansion, and dissemination are limited. Staphylococcus aureus is a major bacterial pathogen of humans and a leading cause of mastitis in dairy cows worldwide. Here we trace the evolutionary history of bovine S. aureus using a global dataset of 10,254 S. aureus genomes including 1,896 bovine isolates from 32 countries in 6 continents. We identified 7 major contemporary endemic clones of S. aureus causing bovine mastitis around the world and traced them back to 4 independent host-jump events from humans that occurred up to 2,500 y ago. Individual clones emerged and underwent clonal expansion from the mid-19th to late 20th century coinciding with the commercialization and industrialization of dairy farming, and older lineages have become globally distributed via established cattle trade links. Importantly, we identified lineage-dependent differences in the frequency of host transmission events between humans and cows in both directions revealing high risk clones threatening veterinary and human health. Finally, pangenome network analysis revealed that some bovine S. aureus lineages contained distinct sets of bovine-associated genes, consistent with multiple trajectories to host adaptation via gene acquisition. Taken together, we have dissected the evolutionary history of a major endemic pathogen of livestock providing a comprehensive temporal, geographic, and gene-level perspective of its remarkable success.\n\nMulticlonal human origin and global expansion of an endemic bacterial pathogen of livestock.", "token_count": 417, "char_count": 1756, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:50.066036", "source": { "split": "train_shard_00001", "doc_id": 582 }, "chunk_id": "train_shard_00001_582_0", "global_id": 6478 }, { "text": "

Introduction

The genus Alistipes consists of anaerobic, Gram-negative bacteria with 13 species that colonize the entire gastrointestinal tract and are a serious health concern. They contribute to gut dysbiosis, intestinal inflammation, colorectal cancer, and depression.

Methods

To explore potential therapeutic targets and inhibitors, we filtered the core genome of Alistipes strains through subtractive genomics for non-host homology, gene essentiality, PPI, KEGG pathways, virulence, cellular localization, and druggability. The potential targets were docked against two drug-like libraries (ZINC, n = 11,993) and TCM (n = 36,043). ADMET profiling for best hits and MD simulation for apo/complex structures were performed, followed by physicochemical and pharmacokinetic evaluation and complex stabilities.

Results and discussion

A set of 39 potential proteins was drastically reduced to only two targets after sequential data mining. The 3D structures of the selected targets (LpxA and KdsB) revealed good druggability scores. The top hits (ZINC85530940, ZINC05161112, ZINC95911713, and ZINC05566415) for both targets showed maximum H-bond interactions. The RMSD and RMSF values exhibited compactness with minimum fluctuation in ligand-bound complexes. The β-factor of ZINC05161112 at 327th residue and 352nd residue exhibited higher thermal instability, consistent with the RMSF results. The globularity of the complexes and apo structures remained consistent, whereas the LpxA complexes exhibited lower solvent-accessible surface area", "token_count": 481, "char_count": 1597, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7376, "quality_score": 0.8688, "entities": { "genes": [ "ZINC05161112", "ZINC95911713", "ZINC05566415", "ZINC85530940" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:50.745552", "source": { "split": "train_shard_00001", "doc_id": 583 }, "chunk_id": "train_shard_00001_583_0", "global_id": 6479 }, { "text": "For the KdsB, the surface area for ZINC5566415 increased significantly, with a steep decrease for ZINC95911713, establishing rather stable protein-ligand complexes. The results highlight the importance of identifying novel inhibitors and therapeutic targets. They are crucial for establishing better treatment regimes for human health and to aid in controlling the pathogenicity of Alistipes species.\n\nDruggable proteins of <i>Alistipes</i> reveal promising antimicrobial targets against chronic intestinal inflammation.", "token_count": 147, "char_count": 546, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [ "ZINC5566415", "ZINC95911713" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:51.204809", "source": { "split": "train_shard_00001", "doc_id": 583 }, "chunk_id": "train_shard_00001_583_1", "global_id": 6480 }, { "text": "

Background

The thermotolerant yeast Kluyveromyces marxianus shows promise as an industrial host for the biochemical production of fuels and chemicals. Wild-type strains are known to ferment high titers of ethanol and can effectively convert a wide range of C5, C6, and C12 sugars into the volatile short-chain ester ethyl acetate. Strain engineering, however, has been limited due to a lack of advanced genome-editing tools and an incomplete understanding of ester and ethanol biosynthesis.

Results

Enabled by the design of hybrid RNA polymerase III promoters, this work adapts the CRISPR-Cas9 system from Streptococcus pyogenes for use in K. marxianus. The system was used to rapidly create functional disruptions to alcohol dehydrogenase (ADH) and alcohol-O-acetyltransferase (ATF) genes with putative function in ethyl acetate and ethanol biosynthesis. Screening of the KmATF disrupted strain revealed that Atf activity contributes to ethyl acetate biosynthesis, but the knockout reduced ethyl acetate titers by only ~15%. Overexpression experiments revealed that KmAdh7 can catalyze the oxidation of hemiacetal to ethyl acetate. Finally, analysis of the KmADH2 disrupted strain showed that the knockout almost completely eliminated ethanol production and resulted in the accumulation of acetaldehyde.

Conclusions

Newly designed RNA polymerase III promoters for sgRNA expression in K. marxianus enable a CRISPR-Cas9 genome-editing system for the thermotolerant yeast", "token_count": 488, "char_count": 1580, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8177, "entities": { "genes": [ "ADH2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:51.887058", "source": { "split": "train_shard_00001", "doc_id": 584 }, "chunk_id": "train_shard_00001_584_0", "global_id": 6481 }, { "text": "This system was used to disrupt genes involved in ethyl acetate biosynthesis, specifically KmADH1-7 and KmATF. KmAdh2 was found to be critical for aerobic and anaerobic ethanol production. Aerobically produced ethanol supplies the biosynthesis of ethyl acetate catalyzed by KmAtf. KmAdh7 was found to exhibit activity toward the oxidation of hemiacetal, a possible alternative route for the synthesis of ethyl acetate.\n\nCRISPR-Cas9-enabled genetic disruptions for understanding ethanol and ethyl acetate biosynthesis in Kluyveromyces marxianus.", "token_count": 204, "char_count": 586, "word_count": 74, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [ "ADH1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:52.386689", "source": { "split": "train_shard_00001", "doc_id": 584 }, "chunk_id": "train_shard_00001_584_1", "global_id": 6482 }, { "text": "Unveiling horizontal gene transfer in the gut microbiome: bioinformatic strategies and challenges in metagenomics analysis.", "token_count": 27, "char_count": 123, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:52.770134", "source": { "split": "train_shard_00001", "doc_id": 585 }, "chunk_id": "train_shard_00001_585_0", "global_id": 6483 }, { "text": "

Objectives

Catheter-associated urinary tract infections (CAUTIs) are among the most common healthcare-associated infections in low- and middle-income countries (LMICs), but there are few resistome data available for relevant uropathogens. The goal of this study was to characterize the antimicrobial resistance (AMR) phenotypes and genotypes of a large collection of Gram-negative bacteria recovered from CAUTIs in a hospital in Mansoura, Egypt.

Methods

Phenotypic AMR profiles and whole-genome sequence data were generated for 132 isolates. Resistomes were predicted using ResFinder, CARD and AMRFinder. Similarity of uropathogen genomic data was determined using sourmash (kmer signatures). Escherichia coli genomic data were subject to a pangenome analysis using Panaroo.

Results

Sixty-seven E. coli (Phylogroup B2; 53.7%, 36/67), 14 Pseudomonas aeruginosa, 11 Klebsiella pneumoniae, 9 Proteus mirabilis, 8 Providencia spp., 5 Enterobacter hormaechei and 18 rare CAUTI-associated isolates were identified. Several (22/132) isolates were multidrug-resistant, while almost half (62/132) were extensively drug-resistant. Phenotype-genotype discordance was found to be an important consideration in resistome studies in Egypt, with a total concordance of 91% (1115/1225), 85.7% (1273/1485) and 80.5% (1196/1485) for ResFinder, CARD and AMRFinder, respectively. Pseudomonas, at the species level, exhibited the greatest discordance. At the antimicrobial level, meropenem was subject to greatest discordance", "token_count": 484, "char_count": 1526, "word_count": 192, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:53.421156", "source": { "split": "train_shard_00001", "doc_id": 586 }, "chunk_id": "train_shard_00001_586_0", "global_id": 6484 }, { "text": "New AMR variants were found for Egypt for Pseudomonas (blaOXA-486, blaOXA-488, blaOXA-905, blaIMP-43, blaPDC-35, blaPDC-45, blaPDC-201) and E. coli (blaTEM-176, blaTEM-190).

Conclusions

This study shows that there is phenotype-genotype discordance in AMR profiling among CAUTI isolates, highlighting the need for comprehensive approaches in resistome studies. We also show the genomic diversity of Gram-negative uropathogens contributing to disease burden in a little-studied LMIC setting.\n\nPhenotype-genotype discordance in antimicrobial resistance profiles of Gram-negative uropathogens recovered from catheter-associated urinary tract infections in Egypt.", "token_count": 226, "char_count": 665, "word_count": 78, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:53.889147", "source": { "split": "train_shard_00001", "doc_id": 586 }, "chunk_id": "train_shard_00001_586_1", "global_id": 6485 }, { "text": "In this paper, we developed a novel approach to utilize the human pangenome to improve peptide and protein identification from proteomic data (MS/MS spectra). We propose a new data structure called panproteome graph (PPG), in which nodes are tryptic peptides, to represent the human pangenome. The PPG can be built in linear time and can be utilized via graph traversal using a depth-first search algorithm to generate potential peptides for peptide identification in proteomics. The PPG built using the 47 human proteomes from the Human Pangenome Reference Consortium (HPRC) coupled with UniProt human proteins resulted in more than 4.2M tryptic peptides, a 26% increase as compared to when only the UniProt proteins were included. Graph-based analysis of the PPG revealed a giant disconnected component with about 3M nodes, suggesting substantial sharing of tryptic peptides among proteins. We applied tryptic peptides derived from PPG to characterize three collections of human proteomic and metaproteomic datasets, and our results showed that by exploiting the human pangenome, we were able to increase the number of identified peptides on all datasets we tested (about 8% increase across all three collections). We also showed that using more complete human proteome would be useful for reducing potential misidentification of human peptides as microbial peptides, a problem that was previously studied but based on genomic sequencing data. Our tool for building PPG is available in a GitHub repo PPGpep, and PPG-derived tryptic peptides can be utilized by MetaProD, a pipeline for both human and bacterial peptide and protein identification from (meta)proteomics datasets.\n\nLeveraging the Human Panproteome to Enhance Peptide and Protein Identification in Proteomics and Metaproteomics", "token_count": 421, "char_count": 1791, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5634, "quality_score": 0.7817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:54.515882", "source": { "split": "train_shard_00001", "doc_id": 587 }, "chunk_id": "train_shard_00001_587_0", "global_id": 6486 }, { "text": "Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon, which differentiates into two genomospecies termed divisions I and II. Through a comprehensive collection of 694 B. fragilis whole genome sequences, we identify novel features distinguishing these divisions. Our study reveals a distinct geographic distribution with division I strains predominantly found in North America and division II strains in Asia. Additionally, division II strains are more frequently associated with bloodstream infections, suggesting a distinct pathogenic potential. We report differences between the two divisions in gene abundance related to metabolism, virulence, stress response, and colonization strategies. Notably, division II strains harbor more antimicrobial resistance (AMR) genes than division I strains. These findings offer new insights into the functional roles of division I and II strains, indicating specialized niches within the intestine and potential pathogenic roles in extraintestinal sites.

Importance

Understanding the distinct functions of microbial species in the gut microbiome is crucial for deciphering their impact on human health. Classifying division II strains as Bacteroides fragilis can lead to erroneous associations, as researchers may mistakenly attribute characteristics observed in division II strains to the more extensively studied division I B. fragilis. Our findings underscore the necessity of recognizing these divisions as separate species with distinct functions. We unveil new findings of differential gene prevalence between division I and II strains in genes associated with intestinal colonization and survival strategies, potentially influencing their role as gut commensals and their pathogenicity in extraintestinal sites. Despite the significant niche overlap and colonization patterns between these groups, our study highlights the complex dynamics that govern strain distribution and behavior, emphasizing the need for a nuanced understanding of these microorganisms.\n\nPangenome comparison of Bacteroides fragilis genomospecies unveils genetic diversity and ecological insights.", "token_count": 465, "char_count": 2199, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5854, "quality_score": 0.7927, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:55.157672", "source": { "split": "train_shard_00001", "doc_id": 588 }, "chunk_id": "train_shard_00001_588_0", "global_id": 6487 }, { "text": "

ABSTRACT

Most of the rich genetic diversity observed in cultivated citrus results from a reticulate evolution involving four ancestral taxa, C. medica , C. reticulata , C. maxima and C. micrantha , whose radiation occurred in allopatry. In such an evolutive context, genome diversity studies, GWAS analysis and transcriptomic studies will be significantly enhanced through pangenome approaches. We report the implementation of a super-pangenome for cultivated citrus, established with de novo assemblies in pseudochromosomes of C. medica (346 Mb), C. reticulata (332 Mb) and C. micrantha (333 Mb), released for the first time alongside a previously published chromosome-scale assembly of C. maxima . Gene annotation of these four genome assemblies revealed 28,090, 29,477, 29,258 and 30,101 genes, respectively, with a focus on pattern recognition receptors. Repetitive element annotation revealed that nearly half of each genome consisted of transposable elements or DNA-satellites. The 3 new genome assemblies display strong synteny and collinearity, while significant discrepancies are observed with the C. maxima assembly. Resequencing information (single nucleotide polymorphisms [SNPs], small indels and gene presence-absence variation [PAV]) from 55 accessions were used to explore the intra- and interspecific diversity of the four ancestral taxa and their relationships with the main horticultural groups resulting from reticulate evolution. Diagnostic SNPs of the ancestral taxa, all over the four genomes assemblies, revealed interspecific introgressions in several accessions representative of C. reticulata , C. maxima and C. medica as well as insights into the origin and phylogenomic structures of modern horticultural groups. PAV analysis revealed a gene whose absence or presence was specific to one of the ancestral taxa (dPAV). Interestingly, diagnostic PAV (dPAV) analysis uncovered a large chloroplastic introgression in chromosome 4 of C. medica , inherited in horticultural groups and recent hybrids having this species as the male parent", "token_count": 532, "char_count": 2070, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6088, "quality_score": 0.8044, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:55.812567", "source": { "split": "train_shard_00001", "doc_id": 589 }, "chunk_id": "train_shard_00001_589_0", "global_id": 6488 }, { "text": "Implementing the super-pangenome combined the identification of orthologous genes across the four genome assemblies and the PAV information from the resequencing data. Significant inter- and intraspecific variations were highlighted, including 25,291 core, 2,431 soft-core and 5,171 dispensable genes. The analysis of the functional enrichment and species-specific adaptations in the citrus super-pangenome revealed distinct functional specializations. This highlights the evolutionary paths that have shaped each species, contributing to the diversity in the citrus super-pangenome while maintaining a shared foundation of essential biological processes. The development of this super-pangenome is a significant milestone in citrus genomics, providing a comprehensive resource that captures the extensive genetic diversity of modern cultivated citrus. Additionally, we established a dedicated Genome Hub, offering a platform for continuous genomic research and allowing for ongoing updates and future inclusion of additional ancestral species.\n\nA super-pangenome for cultivated citrus reveals evolutive features during the allopatric phase of their reticulate evolution", "token_count": 246, "char_count": 1170, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:56.297625", "source": { "split": "train_shard_00001", "doc_id": 589 }, "chunk_id": "train_shard_00001_589_1", "global_id": 6489 }, { "text": "

Aims

Clostridioides difficile is a major cause of antibiotic-associated diarrhea. This study investigated the diversity, clonality, and antimicrobial resistance of C. difficile isolates from Mexican children and adults with diarrhea.

Methods

Between 2014 and 2016, we isolated 37 C. difficile strains in three hospitals in Mexico City. C. difficile strains were typed by PCR-ribotyping and pulsed-field gel electrophoresis (PFGE). Antimicrobial susceptibility to eleven antibiotics was determined. Whole-genome sequencing (WGS) was used to investigate the presence of antimicrobial resistance genes (ARG) and perform a pangenome analysis of 53 genomes from Mexico and 137 publicly available C. difficile genomes.

Results

Toxigenic strains comprised six isolates from children and 31 from adults. While NAP1/RT027 isolates were found in three children, they were predominant in adults (n = 31, 90.3%) and showed the 1058 and 008 PFGE macrorestriction patterns. All isolates were susceptible to vancomycin and metronidazole but resistant to ciprofloxacin, and over 90% of the isolates were resistant to linezolid and carried cfr(E). The pangenome of these isolates contained 4,852 genes, of which 3,455 (81.2%) were categorized as core genes and 801 (18.8%) as accessory genes. In addition, our isolates demonstrated a close relationship with strains from the United States, Canada, and France.

Conclusions

Our work provides, for the first time, genomic insights into C. difficile strains present in Mexico. In our hospital setting, the predominant strains were primarily NAP1/RT027 and exhibited resistance to linezolid, a pattern observed in both pediatric and adult populations. This unique combination of characteristics has not been previously reported in Latin America.", "token_count": 520, "char_count": 1802, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8117, "entities": { "genes": [ "NAP1", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:58:56.956304", "source": { "split": "train_shard_00001", "doc_id": 590 }, "chunk_id": "train_shard_00001_590_0", "global_id": 6490 }, { "text": "Predominance of FQR1 NAP1/RT027 Clostridioides difficile Among Mexican Children and Adult Patients, and its Resistance to Eleven Antibiotics.", "token_count": 44, "char_count": 141, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [ "FQR1", "NAP1", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:57.325218", "source": { "split": "train_shard_00001", "doc_id": 590 }, "chunk_id": "train_shard_00001_590_1", "global_id": 6491 }, { "text": "Kluyveromyces marxianus is a non-conventional yeast whose physiology and metabolism lends itself to diverse biotechnological applications. While the wild-type yeast is already in use for producing fragrances and fermented products, the lack of standardised tools for its genetic and metabolic engineering prevent it from being used as a next-generation cell factory for bio-based chemicals. In this paper, we bring together and characterise a set of native K. marxianus parts for the expression of multiple genes for metabolic engineering and synthetic biology. All parts are cloned and stored according to the MoClo/Yeast Tool Kit standard for quick sharing and rapid construction. Using available genomic and transcriptomic data, we have selected promoters and terminators to fine-tune constitutive and inducible gene expression. The collection includes a number of known centromeres and autonomously replication sequences (ARS). We also provide a number of chromosomal integration sites selected for efficiency or visible phenotypes for rapid screening. Finally, we provide a single-plasmid CRISPR/Cas9 platform for genome engineering and facilitated gene targeting, and rationally create auxotrophic strains to expand the common range of selection markers available to K. marxianus. The curated and characterised tools we have provided in this kit will serve as a base to efficiently build next-generation cell factories from this alternative yeast. Plasmids containing all parts are available at Addgene for public distribution.\n\nBiological Parts for Kluyveromyces marxianus Synthetic Biology.", "token_count": 388, "char_count": 1626, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6311, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:57.940914", "source": { "split": "train_shard_00001", "doc_id": 591 }, "chunk_id": "train_shard_00001_591_0", "global_id": 6492 }, { "text": "

Background

Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype.

Results

The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa.

Conclusions

The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan invasive isolates.\n\nWhole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco.", "token_count": 499, "char_count": 1860, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5637, "quality_score": 0.7819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:58.592116", "source": { "split": "train_shard_00001", "doc_id": 592 }, "chunk_id": "train_shard_00001_592_0", "global_id": 6493 }, { "text": "Microbes are omnipresent, thriving in a range of habitats from oceans to soils and even within our gastrointestinal tracts. They play a vital role in maintaining ecological equilibrium and promoting the health of their hosts. Consequently, understanding the strain diversity within microbial communities is crucial, as variations between strains can lead to distinct phenotypic expressions or diverse biological functions. However, current methods for taxonomic classification from metagenomic sequencing data have several limitations, including their reliance solely on species resolution, support for either short or long reads, or their confinement to a given single species. Most notably, the majority of existing taxonomic classifiers rely solely on a single linear representative genome as a reference, which fails to capture the strain diversity, thereby introducing single-reference biases. Here, we present PanTax, a pangenome graph-based taxonomic classification method that overcomes the shortcomings of single-reference genome-based approaches, because pangenome graphs possess the capability to depict the genetic variability present across multiple evolutionarily or environmentally related genomes. PanTax provides a comprehensive solution to taxonomic classification for strain resolution, compatibility with both short and long reads, and compatibility with single or multiple species. Extensive benchmarking results demonstrate that PanTax drastically outperforms state-of-the-art approaches, primarily evidenced by its significantly higher precision or recall (at both species and strain levels), while maintaining comparable or better performance in other aspects across various datasets. PanTax is a user-friendly open-source tool that is publicly accessible at https://github.com/LuoGroup2023/PanTax .\n\nPanTax: Strain-level taxonomic classification of metagenomic data using pangenome graphs", "token_count": 381, "char_count": 1913, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:59.175897", "source": { "split": "train_shard_00001", "doc_id": 593 }, "chunk_id": "train_shard_00001_593_0", "global_id": 6494 }, { "text": "Abstract

Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation. Indexes based on k-mers and de Bruijn graphs are limited to answering questions at a specific substring length k. We present Maximal Exact Match Ordered (MEMO), a pangenome indexing method based on maximal exact matches (MEMs) between sequences. A single MEMO index can handle arbitrary-length queries over pangenomic windows. MEMO enables both queries that test k-mer presence/absence (membership queries) and that count the number of genomes containing k-mers in a window (conservation queries). MEMO's index for a pangenome of 89 human autosomal haplotypes fits in 2.04 GB, 8.8X smaller than a comparable KMC3 index and 11.4X smaller than a PanKmer index. MEMO indexes can be made smaller by sacrificing some counting resolution, with our decile-resolution HPRC index reaching 0.67 GB. MEMO can conduct a conservation query for 31-mers over the human leukocyte antigen locus in 13.89 seconds, 2.5X faster than other approaches. MEMO's small index size, lack of k-mer length dependence, and efficient queries make it a flexible tool for studying and visualizing substring conservation in pangenomes.

\n\nMEM-based pangenome indexing for k-mer queries", "token_count": 385, "char_count": 1530, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.8311, "entities": { "genes": [ "KMC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:58:59.792245", "source": { "split": "train_shard_00001", "doc_id": 594 }, "chunk_id": "train_shard_00001_594_0", "global_id": 6495 }, { "text": "

Background

Staphylococcus aureus can infect and adapt to multiple host species. However, our understanding of the genetic and evolutionary drivers of its generalist lifestyle remains inadequate. This is particularly important when considering local populations of S. aureus, where close physical proximity between bacterial lineages and between host species may facilitate frequent and repeated interactions between them. Here, we aim to elucidate the genomic differences between human- and animal-derived S. aureus from 437 isolates sampled from disease cases in the northeast region of the United States.

Results

Multi-locus sequence typing revealed the existence of 75 previously recognized sequence types (ST). Our population genomic analyses revealed heterogeneity in the accessory genome content of three dominant S. aureus lineages (ST5, ST8, ST30). Genes related to antimicrobial resistance, virulence, and plasmid types were differentially distributed among isolates according to host (human versus non-human) and among the three major STs. Across the entire population, we identified a total of 1,912 recombination events that occurred in 765 genes. The frequency and impact of homologous recombination were comparable between human- and animal-derived isolates. Low-frequency STs were major donors of recombined DNA, regardless of the identity of their host. The most frequently recombined genes (clfB, aroA, sraP) function in host infection and virulence, which were also frequently shared between the rare lineages.

Conclusions

Taken together, these results show that frequent but variable patterns of recombination among co-circulating S. aureus lineages, including the low-frequency lineages, that traverse host barriers shape the structure of local gene pool and the reservoir of host-associated genetic variants. Our study provides important insights to the genetic and evolutionary factors that contribute to the ability of S. aureus to colonize and cause disease in multiple host species. Our study highlights the importance of continuous surveillance of S. aureus circulating in different ecological host niches and the need to systematically sample from them. These findings will inform development of effective measures to control S", "token_count": 513, "char_count": 2276, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [ "ST5", "ST30", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:00.459554", "source": { "split": "train_shard_00001", "doc_id": 595 }, "chunk_id": "train_shard_00001_595_0", "global_id": 6496 }, { "text": "aureus colonization, infection, and transmission across the One Health continuum.\n\nMulti-host infection and phylogenetically diverse lineages shape the recombination and gene pool dynamics of Staphylococcus aureus.", "token_count": 53, "char_count": 214, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:00.817569", "source": { "split": "train_shard_00001", "doc_id": 595 }, "chunk_id": "train_shard_00001_595_1", "global_id": 6497 }, { "text": "Interactions of isavuconazole and colistin were evaluated against 57 common Candida strains belonging to the species Candida albicans (n = 10), Candida glabrata (n = 10), Candida kefyr (n = 8), Candida krusei (n = 10), Candida parapsilosis (n = 9), and Candida tropicalis (n = 10) by a broth microdilution checkerboard technique based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) reference methodology for antifungal susceptibility testing. Results were analyzed with the fractional inhibitory concentration index and by the response surface analysis. Interpretation by the fractional inhibitory concentration index showed synergy for 50%, 80%, 90%, and 90% of the C. kefyr, C. krusei, C. glabrata, and C. tropicalis strains, respectively. Combination of isavuconazole with colistin against C. albicans and C. parapsilosis exhibited only indifference for 100% and 90% of the strains, respectively. The results were confirmed by response surface analysis for all species except for C. glabrata, for which an indifferent interaction was found for the majority of strains. Antagonistic interaction was never seen regardless of the interpretation model was used.\n\nIn Vitro Synergy of Isavuconazole Combined With Colistin Against Common Candida Species.", "token_count": 456, "char_count": 1390, "word_count": 185, "semantic_coherence": 1, "information_density": 0.5297, "quality_score": 0.7649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:01.461443", "source": { "split": "train_shard_00001", "doc_id": 596 }, "chunk_id": "train_shard_00001_596_0", "global_id": 6498 }, { "text": "

Background

The emergence and spread of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) is a potential epidemiological threat that needs to be monitored. However, the transmission and pathogenic characteristics of hv-CRKP in China remain unclear. We investigated the epidemiological characteristics of gut colonized hv-CRKP in a hospital in Guangdong Province, China.

Methods

A total of 46 gut colonized hv-CRKP isolates were collected from Sun Yat-Sen Memorial Hospital (Guangzhou, China) from August 31st to December 31st, 2021. Minimum inhibitory concentrations (MICs) were obtained for 15 antibiotics for 46 hv-CRKP isolates. BALB/C mice infection model and mucoviscosity assay was used to evaluate the virulence of the isolates. The characteristics of genome, phylogenetic relationship and the structure of the plasmid of 46 gut colonized hv-CRKP isolates were compared with pathogenic isolates from GeneBank based on whole-genome data.

Results

The hv-CRKP isolation rate of all gut colonized carbapenem-resistant Klebsiella pneumoniae was 17% (46/270), and the intestinal colonization rate of hv-CRKP was irrelevant to the sex, age, department of hospitalization, and history of antibiotic use of the host. The gut colonized hv-CRKP showed pandrug resistance and hypervirulence. The gut colonized hv-CRKP and pathogenic hv-CRKP prevalent in China were mainly ST11 hv-CRKP and had two major epidemic clades. The similarities in genomic characteristics between gut colonized hv-CRKP and pathogenic hv-CRKP were consistent. The gut colonized hv-CRKP carried an incomplete structure pK2044 virulence plasmid from hypervirulent K", "token_count": 520, "char_count": 1687, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5471, "quality_score": 0.7735, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:02.122750", "source": { "split": "train_shard_00001", "doc_id": 597 }, "chunk_id": "train_shard_00001_597_0", "global_id": 6499 }, { "text": "pneumoniae NTUH-K2044 by analyzing the virulence plasmid structure.

Conclusion

Our results suggest that the gut colonized ST11 hv-CRKP may serve as a reservoir for the clinical pathogenic ST11 HV-CRKP. It is necessary to further strengthen the monitoring of gut colonized hv-CRKP and research the potential mechanism of infection caused by gut colonized hv-CRKP.\n\nComparative Genomic Analysis of Hypervirulence Carbapenem-Resistant Klebsiella pneumoniae from Inpatients with Infection and Gut Colonization, China.", "token_count": 165, "char_count": 531, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:02.568518", "source": { "split": "train_shard_00001", "doc_id": 597 }, "chunk_id": "train_shard_00001_597_1", "global_id": 6500 }, { "text": "Structure and conformational behaviour of a putative β-1,4-glucosidase of glycoside hydrolase family 3 (PsGH3) from Pseudopedobacter saltans was predicted by using in-silico tools. PsGH3 modeled structure constructed using Phyre2 displayed multidomain architecture comprising an N-terminal (β/α)8-fold domain followed by (α/β)6-sandwich domain, PA14 domain, and a C-terminal domain resembling an immunoglobulin fold. Ramachandran plot displayed 99.3% of amino acids in the allowed region and 0.7% residues in the disallowed region. Multiple sequence alignment (MSA) and structure superposition of PsGH3 with other homologues from GH3 family revealed the conserved residues, Asp274 and Glu624 present in loops LA and LB, respectively originating from N-terminal domain act as catalytic residues. The volume and area calculated for PsGH3 displayed a deep active-site conformation comparable with its homologues, β-1,4-glucosidases (GH3) of Kluyveromyces marxianus and Streptomyces venezuelae. Molecular dynamic (MD) simulation of PsGH3 structure for 80 ns suggested stable and compact structure. Molecular docking studies revealed deeper active site conformation of PsGH3 that could house larger cellooligosaccharides up to 7° of polymerization (DP7). The amino acid residues, Ala86, Leu88, Cys275, Pro483, Phe493, Asn417, Asn491, Pro492, and Leu495 created a binding pocket near the catalytic cleft, crucial for ligand binding. MD simulation of PsGH3 in the presence of cellooligosaccharides, viz., cellobiose and celloheptaose showed stability in terms of RMSD, Rg, and SASA values till 80 ns", "token_count": 516, "char_count": 1625, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [ "PA14", "DP7", "GH3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:03.216715", "source": { "split": "train_shard_00001", "doc_id": 598 }, "chunk_id": "train_shard_00001_598_0", "global_id": 6501 }, { "text": "The calculation of average number of hydrogen bond (H-bond), interaction energy, and binding free energy confirmed the stronger binding affinity of the larger cellooligosaccharides such as celloheptaose in the binding cavity of PsGH3.\n\nStructure and dynamics analysis of multi-domain putative β-1,4-glucosidase of family 3 glycoside hydrolase (PsGH3) from Pseudopedobacter saltans.", "token_count": 108, "char_count": 381, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:03.623216", "source": { "split": "train_shard_00001", "doc_id": 598 }, "chunk_id": "train_shard_00001_598_1", "global_id": 6502 }, { "text": "

Objectives

This is the first study conducted in southern Spain to determine i) the population structure (PS) of carbapenem-resistant (CR) Acinetobacter baumannii isolates by multilocus sequencing typing (MLST) and core genome MLST (cgMLST) and ii) the association between the sequence type ST and the blaOXA-51 variant, capsule polysaccharide locus (KL) and lipooligosaccharide outer core locus (OCL) types.

Methods

Of 336 isolates submitted to the Andalusian reference laboratory (PIRASOA; December 2017-2020), 73 were subjected to WGS (MiSeq). The following analyses were performed: bacterial identification (ribosomal MLST), carbapenemase gene detection (Resfinder 4.0), PS delineation (MLST by MLSTfinder 2.0 and cgMLST by Ridom SeqSphere+), and KL types and OCL types (Kaptive tool).

Results

The carbapenemases detected were blaOXA-23 (n = 41), blaOXA-58 (n = 26), blaOXA-24 (n = 5), blaOXA-72 (n = 1) and blaNDM-1 (n = 2). The PS revealed one major ST2 clone (n = 54) and seven minor ST clones by MLST, and 41 lineages by cgMLST. Thirty-five lineages were detected only in a single hospital whereas five lineages were observed in several hospitals and provinces", "token_count": 485, "char_count": 1277, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:04.316968", "source": { "split": "train_shard_00001", "doc_id": 599 }, "chunk_id": "train_shard_00001_599_0", "global_id": 6503 }, { "text": "blaOXA-66 was the most frequent blaOXA-51 variant and was mainly associated with the ST2 clone. Eleven KL types and 3 OCL types were assigned, with KL2 (n = 27), KL7 (n = 16) and OCL1 being the most frequent.

Conclusions

The PS of CR A. baumannii in Andalusia is characterized by a dominant ST2/blaOXA-23 clone and several lineages, showing local spread of lineages in most hospitals, and intercenter or interregional spread of a few lineages. Single-locus blaOXA-51-like typing and KL typing may be useful as complementary preliminary typing tool.\n\nRegional distribution of carbapenemase-producing Acinetobacter baumannii isolates in southern Spain (Andalusia).", "token_count": 243, "char_count": 713, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7449, "quality_score": 0.8724, "entities": { "genes": [ "ST2", "OCL1", "KL2", "KL7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:04.819955", "source": { "split": "train_shard_00001", "doc_id": 599 }, "chunk_id": "train_shard_00001_599_1", "global_id": 6504 }, { "text": "Thirty-three Kluyveromyces marxianus strains were tested for the ability to form biofilm and mat structures in YPD and whey and for cell surface hydrophobicity. To identify genes potentially involved in adhesion properties, a RT-qPCR analysis was performed. Eight strains were able to adhere on polystyrene plates in both media and formed a mature mat structure. These strains showed a different level of hydrophobicity ranging from 55 to 66% in YPD and from 69 to 81% in whey. Four K. marxianus orthologs genes (FLO11, STE12, TPK3, and WSC4), known from studies in other yeast to be involved in biofilm formation, have been studied. FLO11 and STE12 showed the highest fold changes in all conditions tested and especially in whey: 15.05 and 11.21, respectively. TPK3 was upregulated only in a strain, and WSC4 in 3 strains. In YPD, fold changes were lower than in whey with STE12 and FLO11 genes showing the highest fold changes. In mat structures FLO11 and STE12 fold changes ranged from 3.6-1.3 to 2-1.17, respectively. Further studies are necessary to better understand the role of these genes in K. marxianus adhesion ability.\n\nCell Wall Surface Properties of Kluyveromyces marxianus Strains From Dairy-Products.", "token_count": 445, "char_count": 1328, "word_count": 194, "semantic_coherence": 1, "information_density": 0.567, "quality_score": 0.7835, "entities": { "genes": [ "FLO11", "STE12", "WSC4", "TPK3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:05.454963", "source": { "split": "train_shard_00001", "doc_id": 600 }, "chunk_id": "train_shard_00001_600_0", "global_id": 6505 }, { "text": "To overcome the economic losses associated with fungi and their toxic metabolites, environmentally safe and efficient approaches are needed. To this end, biological control using yeasts and safe bacterial strains and their products are being explored to replace synthetic fungicides. In the present study, the biocontrol effect of a yeast strain of Kluyveromyces marxianus, QKM-4, against the growth and mycotoxin synthesis potential of key toxigenic fungi was evaluated. In vitro assays were performed to find the application of yeast volatile organic compounds (VOCs) against fungal contamination on important agricultural commodities. The removal of ochratoxin A (OTA) and deoxynivalenol (DON) by living and heat-inactivated yeast cells was also explored. VOCs produced by strain QKM-4 were able to significantly limit the fungal growth of 17 fungal species belonging to genera Aspergillus, Penicillium, and Fusarium. Yeast VOCs were able to reduce OTA biosynthesis potential of Penicillium verrucosum and Aspergillus carbonarius by 99.6 and 98.7%, respectively. In vivo application of QKM-4 VOCs against Fusarium oxysporum and A. carbonarius infection on tomatoes and grapes, respectively, determined a complete inhibition of fungal spore germination. GC/MS-based analysis of yeast VOCs identified long-chain alkanes, including nonadecane, eicosane, docosane, heptacosane, hexatriacontane, and tetracosane. In vitro testing of the mycotoxin-binding potential of the living and heat-inactivated QKM-4 cells showed a reduction of OTA and DON up to 58 and 49%, respectively, from artificially contaminated buffers. Our findings clearly demonstrate the strong antifungal potential of K", "token_count": 518, "char_count": 1765, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:06.471946", "source": { "split": "train_shard_00001", "doc_id": 601 }, "chunk_id": "train_shard_00001_601_0", "global_id": 6506 }, { "text": "marxianus QKM-4 and propose this strain as a strong candidate for application in agriculture to safeguard food and feed products.\n\nIsolation of a Novel Kluyveromyces marxianus Strain QKM-4 and Evidence of Its Volatilome Production and Binding Potentialities in the Biocontrol of Toxigenic Fungi and Their Mycotoxins.", "token_count": 102, "char_count": 327, "word_count": 46, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:06.856613", "source": { "split": "train_shard_00001", "doc_id": 601 }, "chunk_id": "train_shard_00001_601_1", "global_id": 6507 }, { "text": "The sunflower, an important oilseed crop and food source across the world, is susceptible to several pathogens, which cause severe losses in sunflower production. The utilization of genetic resistance is the most economical, effective measure to prevent infectious diseases. Based on the sunflower pangenome, in this study, we explored the variability of resistance gene analogs (RGAs) within the species. According to a comparative analysis of RGA candidates in the sunflower pangenome using the RGAugury pipeline, a total of 1344 RGAs were identified, comprising 1107 conserved, 199 varied, and 38 rare RGAs. We also identified RGAs associated with resistance against Sclerotinia sclerotiorum (S. sclerotiorum) in sunflower at the quantitative trait locus (QTL). A total of 61 RGAs were found to be located at four quantitative trait loci (QTLs). Through a detailed expression analysis of RGAs in one susceptible and two tolerant sunflower inbred lines (ILs) across various time points post inoculation, we discovered that 348 RGAs exhibited differential expression in response to Sclerotinia head rot (SHR), with 17 of these differentially expressed RGAs being situated within the QTL regions. In addition, 15 RGA candidates had gene introgression. Our data provide a better understanding of RGAs, which facilitate genomics-based improvements in disease resistance in sunflower.\n\nPangenome Data Analysis Reveals Characteristics of Resistance Gene Analogs Associated with Sclerotinia sclerotiorum Resistance in Sunflower.", "token_count": 410, "char_count": 1544, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:07.480940", "source": { "split": "train_shard_00001", "doc_id": 602 }, "chunk_id": "train_shard_00001_602_0", "global_id": 6508 }, { "text": "

Background

Salmonella enterica subsp. enterica serovar Schwarzengrund (S. Schwarzengrund) is most frequently isolated from commensals humans or poultry. Here we report S. Schwarzengrund strain S16, the first sequenced genome in the Republic of Korea. Additionally, genome sequencing for strain S16 was performed and compared with other S. Schwarzengrund genomes obtained from public database.

Results

Strain S16 was isolated from chicken feces. The complete genome consists of one chromosome and one plasmid. The genome size is 4,822,755 bp with 4852 coding sequences. Strain S16 was determined as serovar Schwarzengrund by in silico serotyping and typed as sequence type (ST) 96. Forty-six S. Schwarzengrund genomes yielded a pangenome of 7112 genes, core-genome of 3374 genes, accessory-genome of 2906 genes, and unique-genome of 835 genes. Eighty-one genes were unique to strain S16, including hypothetical proteins and transcriptional regulators. Genotypic analysis of antibiotic resistance of strain S16 confirmed resistance to amikacin, ciprofloxacin, sulfamethoxazole, streptomycin, and tetracycline. Unlike other S. Schwarzengrund genomes, strain S16 had a mutation of gyrB. Moreover, similar to other S. Schwarzengrund genomes reported in other countries, strain S16 was harbored for 153 virulence genes including Saf operon and cdtB gene. All the antibiotic resistance genes and virulence genes were present in the core- or accessory-genomes.

Conclusions

Complete genome of strain S16 was sequenced. Comparative genomic analysis revealed several genes responsible for antibiotic resistance and specific genomic features of strain S16 and identified virulence factors that might contribute to the human and animal pathogenicity of other S. Schwarzengrund genomes.", "token_count": 511, "char_count": 1794, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5661, "quality_score": 0.7831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:08.129852", "source": { "split": "train_shard_00001", "doc_id": 603 }, "chunk_id": "train_shard_00001_603_0", "global_id": 6509 }, { "text": "Genomic characteristics and comparative genomics of Salmonella enterica subsp. enterica serovar Schwarzengrund strain S16 isolated from chicken feces.", "token_count": 36, "char_count": 150, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:08.486324", "source": { "split": "train_shard_00001", "doc_id": 603 }, "chunk_id": "train_shard_00001_603_1", "global_id": 6510 }, { "text": "

Background

The new complete telomere-to-telomere human genome assembly, T2T-CHM13, and the first draft of the human pangenome reference provide unique opportunities to update the reference genome for epigenetics investigations and clinical research. However, it is largely unclear how these reference genome updates may impact DNA methylation (DNAm) analysis.

Results

Compared to the previous GRCh38 assembly, we found an average increase of 7.4% (range 5.4%–9.9% across samples and sequencing methods) in the number of CpGs genome-wide using T2T-CHM13 with data from four commonly used short-read sequencing DNAm profiling methods. The increase in number of CpGs facilitated discovery of 88 new differentially methylated CpGs within cancer driver genes in an epigenome-wide association study (EWAS) of colon cancer. Further, by aligning probe sequences from the commonly used and recently released Illumina DNAm arrays to T2T-CHM13 and GRCh38, we showed the enhanced utility of T2T-CHM13 for evaluation of potential probe cross-reactivity (i.e., where probes match multiple regions) and mismatch (i.e., where probes do not perfectly match the target region), resulting in the identification of new and more reproducible sets of unambiguous probes (i.e., probes uniquely mapping to the target region) (HM450K, n = 430,719; EPIC, n = 777,491; EPICv2, n = 859,216). In EWASs of 24 cancer types, an average of 945 additional differentially methylated CpG sites were identified in the new unambiguous probe set rather than in the GRCh38-based unambiguous probe set, with enrichments in cancer driver genes and cancer signaling pathways", "token_count": 469, "char_count": 1649, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": { "genes": [ "CHM13", "HM450K" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:09.127712", "source": { "split": "train_shard_00001", "doc_id": 604 }, "chunk_id": "train_shard_00001_604_0", "global_id": 6511 }, { "text": "Moreover, the pangenome called 4.5% more CpGs on average in short-read sequencing data than T2T-CHM13 and identified cross-population and population-specific unambiguous probes in DNAm arrays, owing to its improved representation of genetic diversity. These additional CpGs were overlapped with the promoters and gene bodies of various biologically and medically relevant genes and pangenome-based unambiguous probes can potentially facilitate the discovery of DNAm alterations in more than 200 cancer driver genes in each cancer type.

Conclusions

Use of T2T-CHM13 and pangenome references can benefit epigenome-wide association studies by including CpGs previously unobserved in short-read sequencing data and by improving the identification of unambiguous probes for DNAm arrays, thus expanding biologically relevant information. This study highlights the practical applications of T2T-CHM13 and pangenome for genome biology and provides a basis for expansion of epigenetics investigations.\n\nComplete Reference Genome and Pangenome Expand Biologically Relevant Information for Genome-Wide DNA Methylation Analysis Using Short-Read Sequencing and Array Data", "token_count": 276, "char_count": 1167, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8105, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:09.674779", "source": { "split": "train_shard_00001", "doc_id": 604 }, "chunk_id": "train_shard_00001_604_1", "global_id": 6512 }, { "text": "

Background

The construction of a pangenome graph is a fundamental task in pangenomics. A natural theoretical question is how to formalize the computational problem of building an optimal pangenome graph, making explicit the underlying optimization criterion and the set of feasible solutions. Current approaches build a pangenome graph with some heuristics, without assuming some explicit optimization criteria. Thus it is unclear how a specific optimization criterion affects the graph topology and downstream analysis, like read mapping and variant calling.

Methods

In this paper, by leveraging the notion of maximal block in a Multiple Sequence Alignment (MSA), we reframe the pangenome graph construction problem as an exact cover problem on blocks called Minimum Weighted Block Cover (MWBC). Then we propose an Integer Linear Programming (ILP) formulation for the MWBC problem that allows us to study the most natural objective functions for building a graph.

Results

We provide an implementation of the ILP approach for solving the MWBC and we evaluate it on SARS-CoV-2 complete genomes, showing how different objective functions lead to pangenome graphs that have different properties, hinting that the specific downstream task can drive the graph construction phase.

Conclusion

We show that a customized construction of a pangenome graph based on selecting objective functions has a direct impact on the resulting graphs. In particular, our formalization of the MWBC problem, based on finding an optimal subset of blocks covering an MSA, paves the way to novel practical approaches to graph representations of an MSA where the user can guide the construction.\n\nPangeBlocks: customized construction of pangenome graphs via maximal blocks", "token_count": 388, "char_count": 1780, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:10.300927", "source": { "split": "train_shard_00001", "doc_id": 605 }, "chunk_id": "train_shard_00001_605_0", "global_id": 6513 }, { "text": "The aim of the study was to evaluate the impact of probiotics obtained from agro-industrial substrates fermented with lactic acid bacteria and/or yeasts on the health and changes in the microbiota of the digestive tract of guinea pigs. Eighty male guinea pigs, Kuri breed, 30 days old and 250 g live weight, were randomly selected and divided into four groups of 20 animals each. T0, Control, T1, Lactobacillus acidophilus and L. bulgaricus. T2, Saccharomyces cerevisiae and Kluyveromyces fragilis and T3. L acidophilus, L bulgariccus, S cerevisiae and K. fragilis. T1, T2 and T3 contained molasses-vinasse substrate in their base, the dose administered was 0.75 mL/animal orally. The parameters evaluated were weight gain, occurrence of diarrhea and mortality, blood profile, macroscopic lesions in the digestive tract organs and changes in the microbiota of the stomach, caecum, small and large intestine. Treatments T1, T2 and T3 improved weight gain (p<0.05) and reduced the presence of guinea pigs with diarrhea (p<0.05) and there was no mortality; hematic indices did not vary significantly (p>0.05) between treatments; animals in the control group presented a greater amount (p<0.05) of macroscopic lesions in the digestive tract organs; in the T1, T2 and T3 group there was an improvement in the natural microbiota. It is concluded that the inclusion of microbial additive in young guinea pigs improves intestinal health, consequently, improves weight gain, reduces diarrhea and deaths, and normalizes the natural microbiota of the gastrointestinal tract.\n\nEffect of Agro-Industrial Substrates Fermented with Lactic Acid Bacteria and Yeasts on the Intestinal Microbiota of Guinea Pigs (Cavia porcellus)", "token_count": 497, "char_count": 1722, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:10.959760", "source": { "split": "train_shard_00001", "doc_id": 606 }, "chunk_id": "train_shard_00001_606_0", "global_id": 6514 }, { "text": "

ABSTRACT

The 17q21.31 locus in humans harbors several complex structural haplotypes including a ∼970kb inversion. Different inversion haplotypes have been associated with susceptibility to microdeletions causing Koolen-de Vries syndrome and variation in fecundity and recombination rates. Here, using 210 haplotype-resolved human genome assemblies and pangenome graph-based approaches we characterize 11 distinct structural haplotypes, several of which have not been previously described. Extending our analyses to a set of haplotype-resolved great-ape genomes, we characterize the structure of an independent inversion in chimpanzees which extends an additional 650kb, encompasses 5 additional genes, and is ∼2 million years younger than the human inversion. We further determine that gorillas exhibit an independent duplication of the KANSL1 gene which may predispose them to Koolen-de Vries syndrome causing microdeletions. Using short read sequencing data we characterize 17q21.31 haplotype diversity worldwide in ∼5174 individuals from 107 populations finding increased frequencies of KANSL1 duplication-containing haplotypes in both European and South Asian populations as well as 8 double recombination events between inverted and non-inverted haplotypes ranging in size from 20-180kb. Finally, using 626 ancient Eurasian human genomes we show the frequency of haplotypes containing KANSL1 duplications has increased ∼6-fold over the past 12 thousand years in Europe. Together, our results highlight the dynamics, complexity, and recurrent, independent evolution of a medically relevant locus across humans and great apes.\n\nRecurrent structural variation and recent turnover at the 17q21.31 locus in humans and great apes", "token_count": 449, "char_count": 1738, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [ "KANSL1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:11.595222", "source": { "split": "train_shard_00001", "doc_id": 607 }, "chunk_id": "train_shard_00001_607_0", "global_id": 6515 }, { "text": "Individual genes from microbiomes can drive host-level phenotypes. To help identify such candidate genes, several recent tools estimate microbial gene copy numbers directly from metagenomes. These tools rely on alignments to pangenomes, which in turn are derived from the set of all individual genomes from one species. While large-scale metagenomic assembly efforts have made pangenome estimates more complete, mixed communities can also introduce contamination into assemblies, and it is unknown how robust pangenome-based metagenomic analyses are to these errors. To gain insight into this problem, we re-analyzed a case-control study of the gut microbiome in cirrhosis, focusing on commensal Clostridia previously implicated in this disease. We tested for differentially prevalent genes in the Lachnospiraceae , then investigated which were likely to be contaminants using sequence similarity searches. Out of 86 differentially prevalent genes, we found that 33 (38%) were probably contaminants originating in taxa such as Veillonella and Haemophilus , unrelated genera that were independently correlated with disease status. Our results demonstrate that even small amounts of contamination in metagenome assemblies, below typical quality thresholds, can threaten to overwhelm gene-level metagenomic analyses. However, we also show that such contaminants can be accurately identified using a method based on gene-to-species correlation. After removing these contaminants, we observe that several flagellar motility gene clusters in the Lachnospira eligens pangenome are associated with cirrhosis status. We have integrated our analyses into an analysis and visualization pipeline, PanSweep, that can automatically identify cases where pangenome contamination may bias the results of gene-resolved analyses.

Importance

Metagenome-assembled genomes, or MAGs, can be constructed without pure cultures of microbes. Large scale efforts to build MAGs have yielded more complete pangenomes (i.e., sets of all genes found in one species). Pangenomes allow us to measure strain variation in gene content, which can strongly affect phenotype. However, because MAGs come from mixed communities, they can contaminate pangenomes with unrelated DNA, and how much this impacts downstream analyses has not been studied", "token_count": 519, "char_count": 2315, "word_count": 322, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:12.253860", "source": { "split": "train_shard_00001", "doc_id": 608 }, "chunk_id": "train_shard_00001_608_0", "global_id": 6516 }, { "text": "Using a metagenomic study of gut microbes in cirrhosis as our test case, we investigate how contamination affects analyses of microbial gene content. Surprisingly, even small, typical amounts of MAG contamination (<5%) result in disproportionately high levels of false positive associations (38%). Fortunately, we show that most contaminants can be automatically flagged, and provide a simple method for doing so. Furthermore, applying this method reveals a new association between cirrhosis and gut microbial motility.\n\nSmall amounts of misassembly can have disproportionate effects on pangenome-based metagenomic analyses", "token_count": 142, "char_count": 623, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7907, "quality_score": 0.8953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:12.677857", "source": { "split": "train_shard_00001", "doc_id": 608 }, "chunk_id": "train_shard_00001_608_1", "global_id": 6517 }, { "text": "Woody ornamentals are an integral part of home gardens and urban landscapes and are key to the economic vitality of the nursery industry. Movement of plants infected with emerging pathogens can quickly lead to wide geographic spread of new diseases impacting ecosystem health and leading to economic losses. Using metagenomic sequencing, we investigated the microbial species associated with vascular streak dieback (VSD), an emerging disease of woody ornamentals in the United States, analyzing 106 samples obtained from 34 different species in seven states. The fastidious fungal pathogen Ceratobasidium sp. ( Csp ), previously found to be associated with VSD, was the only putative pathogen consistently identified. Assembly of 17 high quality draft genomes followed by phylogenetic and pangenome analyses revealed Csp to form a tight genetic cluster closely related to, yet distinct in gene content, from genomes of Ceratobasidium theobromae , a pathogen of cacao, avocado, and cassava in Southeast Asia. These results reveal the unparalleled ability of metagenomics for identification and characterization of fastidious fungal pathogens and suggest the recent introduction of a single genetic lineage of Csp into the U.S., possibly from Southeast Asia, that is characterized by a wide host range and that quickly spread geographically.\n\nInsights gained into Vascular Streak Dieback, an Emerging Disease of Woody Ornamentals in the United States, using Metagenomic Sequencing", "token_count": 340, "char_count": 1479, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:13.243556", "source": { "split": "train_shard_00001", "doc_id": 609 }, "chunk_id": "train_shard_00001_609_0", "global_id": 6518 }, { "text": "The higher adaptation of landraces to local agroclimatic conditions resulting from natural and moderate artificial selection by farmers within specific environments makes them a crucial source of alleles and genotypes for cultivation and breeding programs. Unlike modern cultivars, which have been developed under more intense artificial selective pressures, landraces exhibit a broader genetic base that has been documented in landrace collections for many crops. This review provides an overview of the importance of genetic resource valorisation in legume species, focusing on cultivated species of the Lupinus genus, particularly white lupin (Lupinus albus). On the one hand, legumes, including Lupins, are considered a crucial alternative source of protein within the framework of more sustainable agriculture. On the other hand, they are often neglected species in terms of breeding efforts, despite receiving increasing attention in recent years. Here, we also report on the latest advances in the development of genomic tools, such as the novel pangenome of white lupin and the identification of markers and loci for target adaptation traits, such as tolerance to alkaline soils, which can effectively support the breeding of Lupinus albus, especially for the introgression of desirable alleles from locally adapted varieties.\n\nRecent Advances in Molecular Tools and Pre-Breeding Activities in White Lupin (<i>Lupinus albus</i>).", "token_count": 327, "char_count": 1470, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:13.814299", "source": { "split": "train_shard_00001", "doc_id": 610 }, "chunk_id": "train_shard_00001_610_0", "global_id": 6519 }, { "text": "Sustainable economy drives increasing demand for raw biomass-decomposing enzymes. Microbial expression platforms exploited as cellular factories of such biocatalysts meet requirements of large-volume production. Previously, we developed Yarrowia lipolytica recombinant strains able to grow on raw starch of different plant origin. In the present study, we used the most efficient amylolytic strain as a microbial cell factory of raw-starch-digesting (RSD) amylolytic preparation composed of two enzymes. The RSD-preparation was produced in fed-batch bioreactor cultures. Concentrated and partly purified preparation was then tested in simultaneous saccharification and fermentation (SSF) processes with thermotolerant Kluyveromyces marxianus for ethanol production and Lactobacillus plantarum for production of lactic acid. These processes were conducted as a proof-of-concept that application of the novel RSD-preparation supports sufficient starch hydrolysis enabling microbial growth and production of targeted molecules, as the selected strains were confirmed to lack amylolytic activity. Doses of the preparation and thermal conditions were individually adjusted for the two processes. Additionally, ethanol production was tested under different aeration strategies; and lactic acid production process was tested in thermally pre-treated substrate, as well. Conducted studies demonstrated that the novel RSD-preparation provides satisfactory starch hydrolyzing activity for ethanol and lactic acid production from starch by non-amylolytic microorganisms.\n\nProduction of Raw Starch-Digesting Amylolytic Preparation in Yarrowia lipolytica and Its Application in Biotechnological Synthesis of Lactic Acid and Ethanol.", "token_count": 436, "char_count": 1747, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8005, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:14.442390", "source": { "split": "train_shard_00001", "doc_id": 611 }, "chunk_id": "train_shard_00001_611_0", "global_id": 6520 }, { "text": "As the name of the genus Pantoea (\"of all sorts and sources\") suggests, this genus includes bacteria with a wide range of provenances, including plants, animals, soils, components of the water cycle, and humans. Some members of the genus are pathogenic to plants, and some are suspected to be opportunistic human pathogens; while others are used as microbial pesticides or show promise in biotechnological applications. During its taxonomic history, the genus and its species have seen many revisions. However, evolutionary and comparative genomics studies have started to provide a solid foundation for a more stable taxonomy. To move further toward this goal, we have built a 2,509-gene core genome tree of 437 public genome sequences representing the currently known diversity of the genus Pantoea. Clades were evaluated for being evolutionarily and ecologically significant by determining bootstrap support, gene content differences, and recent recombination events. These results were then integrated with genome metadata, published literature, descriptions of named species with standing in nomenclature, and circumscriptions of yet-unnamed species clusters, 15 of which we assigned names under the nascent SeqCode. Finally, genome-based circumscriptions and descriptions of each species and each significant genetic lineage within species were uploaded to the LINbase Web server so that newly sequenced genomes of isolates belonging to any of these groups could be precisely and accurately identified.\n\nGenomic delineation and description of species and within-species lineages in the genus <i>Pantoea</i>.", "token_count": 369, "char_count": 1639, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6724, "quality_score": 0.8362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:15.073739", "source": { "split": "train_shard_00001", "doc_id": 612 }, "chunk_id": "train_shard_00001_612_0", "global_id": 6521 }, { "text": "Genome structural variants (SVs) comprise a sizable portion of functionally important genetic variation in all organisms; yet, many SVs evade discovery using short reads. While long-read sequencing can find the hidden SVs, the role of SVs in variation in organismal traits remains largely unclear. To address this gap, we investigate the molecular basis of 50 classical phenotypes in 11 Drosophila melanogaster strains using highly contiguous de novo genome assemblies generated with Oxford Nanopore long reads. These assemblies enabled the creation of a pangenome graph containing comprehensive, nucleotide-resolution maps of SVs, including complex rearrangements such as the interchromosomal inverted duplication Dp(2;4)eyD and large tandem duplications at the Bar locus. We uncovered new candidate causal mutations for 15 phenotypes and new molecular alleles for 2 mutations comprising tandem duplications, transposable element (TE) insertions, and indels. For example, we mapped the tarsal joint defect Ablp eyD to an 8 kb Roo retrotransposon insertion into an intergenic enhancer, a finding validated via CRISPR-Cas9. The wing vein phenotype plexus (px 1 ) was linked to a 1.5 kb partial tandem gene duplication, and the century-old Curved (c 1 ) wing phenotype was linked to a 7.5 kb DM412 retrotransposon inserted into the coding sequence of the muscle protein gene Strn-Mlck . We also unveiled 8 SV alleles of previously identified causal genes, including previously uncharacterized SVs underlying the extensively studied white and yellow phenotypes. Overall, 67.4% of the genes causing phenotypic changes harbored candidate SVs over 100 bp, whereas only 28% is expected based on euchromatic SVs. Our data, based on the 50 Drosophila phenotypes, 44 of which are strongly deleterious, suggests a disproportionately larger contribution of SVs to deleterious changes in visible phenotypes in Drosophila .", "token_count": 511, "char_count": 1909, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6915, "quality_score": 0.8457, "entities": { "genes": [ "DM412" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:15.739589", "source": { "split": "train_shard_00001", "doc_id": 613 }, "chunk_id": "train_shard_00001_613_0", "global_id": 6522 }, { "text": "Structural variants are enriched in deleterious visible phenotypes in Drosophila", "token_count": 28, "char_count": 87, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:16.130380", "source": { "split": "train_shard_00001", "doc_id": 613 }, "chunk_id": "train_shard_00001_613_1", "global_id": 6523 }, { "text": "

Background

Acinetobacter baumannii (A. baumannii) has emerged as a major public health threat in low- and middle-income countries (LMICs), particularly in Egypt, due to its remarkable ability to acquire and transfer resistance genes, as highlighted in the WHO bacterial Priority Pathogens List 2024 classification. This pilot study aimed to characterize 18 A. baumannii isolates from Egyptian healthcare settings, focusing on clonal lineages, antibiotic resistance determinants, horizontal gene transfer potential, and the presence of virulence factors and chromosomal mutations.

Methods

Antimicrobial susceptibility testing was performed to determine resistance profiles using minimum inhibitory concentrations. Whole-genome sequencing was used to identify β-lactamase, carbapenemase, and other antibiotic resistance genes (ARGs), as well as mobile genetic elements (MGEs). Clonal relationships among isolates were assessed via core genome multilocus sequence typing (cgMLST).

Results

Phenotypic analysis revealed that 72% of the isolates were extensively drug-resistant (XDR), exhibiting resistance to all tested antibiotics except colistin. Clonal diversity analysis identified 11 Oxford sequence types (STs), including two novel STs (ST3309OXF and ST3321OXF), and six international clonal (IC) groups, with IC2 being the most prevalent. Additionally, eight Pasteur STs were detected, with ST570PAS being the most frequent. The cgMLST analysis showed that two Egyptian ST570PAS isolates clustered with a strain from Saudi Arabia, suggesting potential regional transmission. Genomic analysis revealed the widespread dissemination of ARGs via MGEs, particularly rep plasmids and insertion sequence elements, which contributed significantly to genomic diversity and antibiotic resistance.

Conclusions

This pilot study highlights the clonal diversity of A. baumannii in Egypt and underscores the critical role of MGEs in the spread of resistance genes", "token_count": 515, "char_count": 2023, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [ "IC2", "ST3321", "ST3309", "ST570" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:16.789648", "source": { "split": "train_shard_00001", "doc_id": 614 }, "chunk_id": "train_shard_00001_614_0", "global_id": 6524 }, { "text": "Targeted genomic surveillance and infection control are essential to curb the spread of high-risk resistant A. baumannii clones in Egyptian clinical settings.\n\nComparative genomics of Acinetobacter baumannii from Egyptian healthcare settings reveals high-risk clones and resistance gene mobilization.", "token_count": 67, "char_count": 300, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:17.167410", "source": { "split": "train_shard_00001", "doc_id": 614 }, "chunk_id": "train_shard_00001_614_1", "global_id": 6525 }, { "text": "

Background

Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution.

Results

Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes.

Conclusions

Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.\n\nPangenome analysis reveals transposon-driven genome evolution in cotton.", "token_count": 473, "char_count": 1971, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6732, "quality_score": 0.8366, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:17.820331", "source": { "split": "train_shard_00001", "doc_id": 615 }, "chunk_id": "train_shard_00001_615_0", "global_id": 6526 }, { "text": "According to the latest WHO estimates (2015) of the global burden of foodborne diseases, Listeria monocytogenes is responsible for one of the most serious foodborne infections and commonly results in severe clinical outcomes. The 2013 French MONALISA prospective cohort identified that women born in Africa has a 3-fold increase in the risk of maternal neonatal listeriosis. One of the largest L. monocytogenes outbreaks occurred in South Africa in 2017-2018 with over 1,000 cases. Moreover, recent findings identified L. monocytogenes in human breast milk in Mali and Senegal with its relative abundance positively correlated with severe acute malnutrition. These observations suggest that the carriage of L. monocytogenes in Africa should be further explored, starting with the existing literature. For that purpose, we searched the peer-reviewed and grey literature published dating back to 1926 to date using six databases. Ultimately, 225 articles were included in this review. We highlighted that L. monocytogenes is detected in various sample types including environmental samples, food samples as well as animal and human samples. These studies were mostly conducted in five east African countries, four west African countries, four north African countries, and two Southern African countries. Moreover, only ≈ 0.2% of the Listeria monocytogenes genomes available on NCBI were obtained from African samples, contracted with its detection. The pangenome resulting from the African Listeria monocytogenes samples revealed three clusters including two from South-African strains as well as one consisting of the strains isolated from breast milk in Mali and Senegal and, a vaginal post-miscarriage sample. This suggests there was a clonal complex circulating in Mali and Senegal. As this clone has not been associated to infections, further studies should be conducted to confirm its circulation in the region and explore its association with foodborne infections. Moreover, it is apparent that more resources should be allocated to the detection of L", "token_count": 511, "char_count": 2108, "word_count": 305, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:18.483673", "source": { "split": "train_shard_00001", "doc_id": 616 }, "chunk_id": "train_shard_00001_616_0", "global_id": 6527 }, { "text": "monocytogenes as only 15/54 countries have reported its detection in the literature. It seems paramount to map the presence and carriage of L. monocytogenes in all African countries to prevent listeriosis outbreaks and the related miscarriages and confirm its association with severe acute malnutrition.\n\nA review of the literature of Listeria monocytogenes in Africa highlights breast milk as an overlooked human source.", "token_count": 113, "char_count": 439, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7581, "quality_score": 0.879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:18.860812", "source": { "split": "train_shard_00001", "doc_id": 616 }, "chunk_id": "train_shard_00001_616_1", "global_id": 6528 }, { "text": "Pigs are among the most essential sources of high-quality protein in human diets. Structural variants (SVs) are a major source of genetic variants associated with diverse traits and evolutionary events. However, the current linear reference genome of pigs limits the presentation of position information for SVs. In this study, we generated a pangenome of pigs and a genome variation map of 599 deep-sequenced genomes across Eurasia. Moreover, a section-wide gene repertoire was constructed, which indicated that core genes were more evolutionarily conserved than variable genes. Subsequently, we identified 546,137 SVs, their enrichment regions, and relationships with genomic features and found significant divergence across Eurasian pigs. More importantly, the pangenome-detected SVs could complement heritability estimates and genome-wide association studies based only on single nucleotide polymorphisms. Among the SVs shaped by selection, we identified an insertion in the promoter region of the TBX19 gene, which may be related to the development, growth, and timidity traits of Asian pigs and may affect the gene expression. Our constructed pig pangenome and the identified SVs provide rich resources for future functional genomic research on pigs.\n\nPangenome Reveals Gene Content Variations and Structural Variants Contributing to Pig Characteristics", "token_count": 304, "char_count": 1359, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [ "TBX19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:19.442101", "source": { "split": "train_shard_00001", "doc_id": 617 }, "chunk_id": "train_shard_00001_617_0", "global_id": 6529 }, { "text": "Abstract

Background: Lignocellulosic biomass is a promising renewable and sustainable resource for biofuels and chemicals. However, the inhibitors generated during lignocellulosic biomass pretreatment hinder microbial growth and interfere with fermentation. Studies on the tolerance to inhibitors, especially multiple inhibitors, are important in the construction of robust strains that can utilize lignocellulosic biomass.

Results:

The expression of an uncharted α/β hydrolase (ABHD) from Kluyveromyces marxianus was found to be up-regulated in the presence of single or multiple inhibitors; this enzyme was termed KmYME in this study. Disruption of KmYME made the yeast more susceptible to inhibitors, particularly to acetic acid, furfural and 5-hydroxymethylfurfural. KmYME was located in the mitoplast of mitochondria with targeting signals in the N-terminal 1-40 amino acid residues. Under inhibitor stress, the intracellular concentration of ATP, NAD(P) in the KmYME disrupted strain decreased. In addition, the KmYME disrupted strain lost more mitochondrial membrane potential, showed increased plasma membrane permeability, a more severe redox imbalance, and increased ROS accumulation, compared with those of the non-disrupted strain in the presence of the same inhibitors. The recombinant KmYME possessed esterase/thioesterase activity and preferred short-chain pNP aliphatic esters, long-chain acyl-CoA, and succinyl-CoA as substrates. The retro-complementation results indicated that the enzymatic activity of KmYME was necessary for the resistance to inhibitors. In addition, KmYME was also required for the resistance to other stresses including ethanol, temperature, and osmotic pressure. Disruption of two possible homologous genes in S. cerevisiae also reduced its tolerance to inhibitors", "token_count": 500, "char_count": 1867, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:20.094279", "source": { "split": "train_shard_00001", "doc_id": 618 }, "chunk_id": "train_shard_00001_618_0", "global_id": 6530 }, { "text": "

Conclusion:

As an uncharted α/β hydrolase, KmYME which had esterase/thioesterase activity and located in mitochondrial matrix was identified for the first time. The esterase/thioesterase activity was necessary for the tolerance to lignocellulosic biomass derived inhibitors in K. marxianus. Disruption of KmYME reduced the tolerance to inhibitors by interfering with ATP, NAD and NADP synthesis. KmYME also correlated with tolerance to other stresses such as osmotic, ethanol, and temperature. This study may provide useful information for better understanding the resistance mechanism of multiple inhibitors, which is important in the creation of a robust strain for industrial fermentation that can use cellulosic biomass as substrate.

\n\nEffect of a novel alpha/beta hydrolase domain protein on tolerance of K. marxianus to lignocellulosic biomass derived inhibitors", "token_count": 235, "char_count": 897, "word_count": 121, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus" ], "conditions": [ "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:20.569772", "source": { "split": "train_shard_00001", "doc_id": 618 }, "chunk_id": "train_shard_00001_618_1", "global_id": 6531 }, { "text": "Pasteurella multocida causes acute/chronic pasteurellosis in porcine, resulting in considerable economic losses globally. The draft genomes of two Indian strains NIVEDIPm17 (serogroup D) and NIVEDIPm36 (serogroup A) were sequenced. A total of 2182-2284 coding sequences (CDSs) were predicted along with 5-6 rRNA and 45-46 tRNA genes in the genomes. Multilocus sequence analysis and LPS genotyping showed the presence of ST50: genotype 07 and ST74: genotype 06 in NIVEDIPm17 and NIVEDIPm36, respectively. Pangenome analysis of 61 strains showed the presence of 1653 core genes, 167 soft core genes, 750 shell genes, and 1820 cloud genes. Analysis of virulence-associated genes in 61 genomes indicated the presence of nanB, exbB, exbD, ptfA, ompA, ompH, fur, plpB, fimA, sodA, sodC, tonB, and omp87 in all strains. The 61 genomes contained genes encoding tetracycline (54%), streptomycin (48%), sulphonamide (28%), tigecycline (25%), chloramphenicol (21%), amikacin (7%), cephalosporin (5%), and trimethoprim (5%) resistance. Multilocus sequence type revealed that ST50 was the most common (34%), followed by ST74 (26%), ST13 (24%), ST287 (5%), ST09 (5%), ST122 (3%), and ST07 (2%). Single-nucleotide polymorphism and core genome-based phylogenetic analysis clustered the strains into three major clusters", "token_count": 491, "char_count": 1324, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7151, "quality_score": 0.8575, "entities": { "genes": [ "ST122", "ST13", "ST74", "ST07", "ST287", "ST50", "ST09" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:21.216940", "source": { "split": "train_shard_00001", "doc_id": 619 }, "chunk_id": "train_shard_00001_619_0", "global_id": 6532 }, { "text": "In conclusion, we described the various virulence factors, mobile genetic elements, and antimicrobial resistance genes in the pangenome of P. multocida of porcine origin, besides the rare presence of LPS genotype 7 in serogroup D.\n\nComparative genome analysis of Pasteurella multocida strains of porcine origin.", "token_count": 93, "char_count": 325, "word_count": 45, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:21.596623", "source": { "split": "train_shard_00001", "doc_id": 619 }, "chunk_id": "train_shard_00001_619_1", "global_id": 6533 }, { "text": "Lateral gene transfer (LGT) is widespread in eukaryotes, including in animals and plants where it can fuel adaptive evolution and innovation. However, the factors that influence the integration and long-term retention of transferred genes remain poorly understood. The pangenome of the grass Alloteropsis has a high turnover of laterally acquired genes, and here we combine expression, methylation and genomic data to identify factors promoting their long-term persistence. Most transferred genes appear to be degenerating, showing lower expression levels and/or greater sequence truncation compared to their vertically inherited homologs. These degenerating genes also show significantly higher levels of DNA methylation, potentially indicating transcriptional silencing. The likelihood of a transferred gene being retained will be influenced by how easily it can be expressed in the recipient genome. In Alloteropsis , putatively functional laterally acquired genes had expression levels significantly more similar to their donor xenolog than to their vertically inherited homolog. This pattern suggests that transferred genes may carry cis-regulatory elements encoded on the fragment of DNA that moves between species, facilitating their expression in the new genomic context. Evolutionary novelty may also increase the likelihood that selection retains a transferred gene. However, only a significant difference in expression level, not sequence divergence, between donor and recipient orthologs is associated with successful lateral gene transfer. Overall, our results show that most transferred genes degrade over time. However, those capable of regulating their own expression are more likely to persist and contribute to long-term evolutionary innovation.

Significance Statement

Lateral gene transfer (LGT) can introduce novel traits into plant genomes, yet most transferred genes are only transient residents and are degenerating, with reduced expression, truncation, and elevated DNA methylation. However, a minority persist and are more likely to resemble their donor counterparts in expression, suggesting co-transfer of cis-regulatory elements. These findings indicate that regulatory compatibility is key to their long-term survival.\n\nRegulatory features determine the evolutionary fate of laterally acquired genes in plants", "token_count": 461, "char_count": 2348, "word_count": 319, "semantic_coherence": 1, "information_density": 0.5674, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:22.245358", "source": { "split": "train_shard_00001", "doc_id": 620 }, "chunk_id": "train_shard_00001_620_0", "global_id": 6534 }, { "text": "The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.\n\nCore genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex.", "token_count": 446, "char_count": 1952, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:22.880910", "source": { "split": "train_shard_00001", "doc_id": 621 }, "chunk_id": "train_shard_00001_621_0", "global_id": 6535 }, { "text": "Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits but remain less explored compared to mRNA and classical phenotypes. This study systematically analyzed brain proteomes in a rat family using tandem mass tag (TMT)-based quantitative mass spectrometry. We quantified 8,119 proteins across two parental strains (SHR/Olalpcv and BN-Lx/Cub) and 29 HXB/BXH recombinant inbred (RI) strains, identifying 597 proteins with differential expression and 464 proteins linked to cis-acting quantitative trait loci (pQTLs). Proteogenomics identified 95 variant peptides, and sex-specific analyses revealed both shared and distinct cis-pQTLs. We improved the ability to pinpoint candidate genes underlying pQTLs by utilizing the rat pangenome and explored the connections between pQTLs in rats and human disorders. Collectively, this study highlights the value of large proteo-genetic datasets in elucidating protein modulation in the brain and its links to complex central nervous system (CNS) traits.\n\nGenetic modulation of protein expression in rat brain.", "token_count": 293, "char_count": 1120, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:23.454447", "source": { "split": "train_shard_00001", "doc_id": 622 }, "chunk_id": "train_shard_00001_622_0", "global_id": 6536 }, { "text": "Parvimonas micra is a Gram-positive, anaerobic bacterium commonly found in the oral cavity, skin and gastrointestinal tract. While typically a harmless organism, it can cause infections in individuals with weakened immune systems, leading to conditions like periodontitis and deep-tissue abscesses. This study focuses on the comparative genomic analysis of P. micra to explore its evolutionary relationships, antimicrobial resistance profiles and functional diversity by assessing phylogenetic analyses, resistance genes, virulence factors, mobile genetic elements, carbohydrate-active enzymes and pan-genome analysis. Comparative genomic analysis of 11 P. micra strains reveals significant functional variations among the strains, indicating notable interspecies diversity. Phylogenetic and comparative genome analysis revealed that strain JM503A is taxonomically distinct from the P. micra species, with genome similarity ranging from 54% to 61%. The 16S rRNA sequence similarity of strain JM503A is 98.28%, indicating a distinct phylogenetic position. The average nucleotide identity value ranging from 91.32% to 91.7% and digital DNA-DNA hybridization values ranging from 43.00% to 44.00% of JM503A with other strains are below the cutoff values <95% and <70%, respectively, which confirms JM503A as a novel species. Based on its evolutionary relationships, strain JM503A is identified as a potential new species of Parvimonas, providing important evidence for its reclassification as a new species within the genus Parvimonas.", "token_count": 443, "char_count": 1573, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [ "JM503A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:24.088117", "source": { "split": "train_shard_00001", "doc_id": 623 }, "chunk_id": "train_shard_00001_623_0", "global_id": 6537 }, { "text": "Comparative genome analysis of human pathogen <i>Parvimonas micra</i> revealed strain JM503A as potential novel species in the genus <i>Parvimonas</i> and high intra-species functional diversity.", "token_count": 74, "char_count": 219, "word_count": 24, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "JM503A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:24.460247", "source": { "split": "train_shard_00001", "doc_id": 623 }, "chunk_id": "train_shard_00001_623_1", "global_id": 6538 }, { "text": "

ABSTRACT

Microbial inoculants that integrate plant growth promotion, pathogen suppression, and pollutant degradation are central to sustainable agriculture. Here, we report the genomic and phenotypic characterization of Lysinibacillus capsici BCSIR-Raj-01, an endophyte isolated from citrus leaves in Bangladesh. The 4.62 Mb genome encodes 4,699 coding sequences and displays an open pangenome with loci linked to stress adaptation, xenobiotic degradation, and secondary metabolite biosynthesis. Genome mining revealed complete pathways for indole-3-acetic acid (IAA) production, siderophore biosynthesis, and phosphate metabolism, alongside gene clusters for bacteriocins, lantibiotics, terpenes, and polyketides. Nitrogen cycling genes indicated diazotrophic growth potential and a truncated denitrification pathway. Phenotypic assays validated these predictions: L. capsici BCSIR-Raj-01 solubilized phosphate, produced IAA and siderophores, grew on hydrocarbons, and exhibited diazotrophic activity. Notably, the strain showed potent larvicidal activity against Culex and Anopheles larvae, suggesting ecological roles beyond plant association. Together, these results establish L. capsici BCSIR-Raj-01 as a multifunctional bacterium with potential applications in crop improvement, bioremediation, and biological vector control.

IMPORTANCE

The challenges of modern agriculture and environmental sustainability demand microbial solutions that deliver multiple functions. Lysinibacillus species are increasingly recognized for such versatility, but their genomic basis remains poorly resolved. Our study provides the first genome-enabled framework for understanding multifunctionality in L. capsici ", "token_count": 451, "char_count": 1720, "word_count": 204, "semantic_coherence": 1, "information_density": 0.7892, "quality_score": 0.8946, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:25.101654", "source": { "split": "train_shard_00001", "doc_id": 624 }, "chunk_id": "train_shard_00001_624_0", "global_id": 6539 }, { "text": "By combining whole-genome sequencing with phenotypic validation, we show that BCSIR-Raj-01 harbors biosynthetic clusters, stress adaptation loci, and xenobiotic degradation genes while also expressing experimentally confirmed traits, including phosphate solubilization, IAA and siderophore production, nitrogen fixation, hydrocarbon utilization, and larvicidal activity. This integration of plant growth promotion, biocontrol potential, and pollutant degradation positions L. capsici BCSIR-Raj-01 as a next-generation bioinoculant. Beyond broadening the functional scope of Lysinibacillus , our findings highlight how genome-guided approaches can identify microbes with cross-sectoral applications in agriculture, bioremediation, and vector management.\n\nMetabolic Versatility of Lysinibacillus capsici BCSIR-Raj-01 Underpins Its Multifunctionality in Biocontrol, Bioremediation, and Plant Growth Promotion", "token_count": 249, "char_count": 912, "word_count": 102, "semantic_coherence": 1, "information_density": 0.8529, "quality_score": 0.9265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:25.590022", "source": { "split": "train_shard_00001", "doc_id": 624 }, "chunk_id": "train_shard_00001_624_1", "global_id": 6540 }, { "text": "Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of P. mirabilis genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related P. mirabilis genomes, and pan-genome annotation to identify genes of interest not present in the model P. mirabilis strain HI4320. Within our cohort, Proteus is composed of 10 named species and 5 uncharacterized genomospecies. P. mirabilis can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The P. mirabilis pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain P. mirabilis HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome", "token_count": 524, "char_count": 1807, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6397, "quality_score": 0.8198, "entities": { "genes": [ "HI4320" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:26.250345", "source": { "split": "train_shard_00001", "doc_id": 625 }, "chunk_id": "train_shard_00001_625_0", "global_id": 6541 }, { "text": "IMPORTANCE Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on P. mirabilis, but similar to other Gram-negative bacteria, P. mirabilis has a mosaic genome with a linkage between phylogenetic position and accessory genome content. P. mirabilis encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection.\n\nUncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape.", "token_count": 250, "char_count": 1028, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8417, "entities": { "genes": [ "HI4320" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:26.738995", "source": { "split": "train_shard_00001", "doc_id": 625 }, "chunk_id": "train_shard_00001_625_1", "global_id": 6542 }, { "text": "

Background

Indian cattle known as desi cattle, renowned for their adaptability to harsh environments and diverse phenotypic traits, represent a valuable genetic resource. While reference genome assemblies have been instrumental in advancing cattle genomics, they often fail to capture the full spectrum of genetic variation present within diverse populations. To address this limitation, we aimed to construct a pangenome for desi cattle by identifying and characterizing Non-Reference Novel Sequences (NRNS).

Findings

We sequenced 68 desi cattle genomes representing seven distinct breeds, generating 48.35 billion short reads. A PanGenome Analysis (PanGA) pipeline was developed in Bash scripts to process these data to identify NRNS missing in the reference genome. A total of 13,065 NRNS with a cumulative length of ∼41 Mbp were identified that exhibited substantial variation across the population. These NRNS were found to be exclusive to Indian desi cattle, matching only 4.1% with the Chinese indicine pangenome. However, a significant proportion (∼40%) of NRNS displayed ancestral origins within the Bos genus. These sequences were enriched in genic regions, suggesting functional roles, and were associated with quantitative trait loci (QTLs), particularly for milk production. Compared to a single reference genome, the pangenome approach significantly enhanced read mapping accuracy, reduced spurious SNP calls, and facilitated the discovery of novel genetic variants.

Conclusions

This study has successfully established a within-species cattle pangenome specifically focused on desi cattle breeds from India. Our findings highlight the importance of pangenome based analyses for understanding the complex genetic architecture of desi cattle.\n\nConstructing a Draft Indian Cattle Pangenome Using Short-Read Sequencing", "token_count": 416, "char_count": 1855, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:27.386279", "source": { "split": "train_shard_00001", "doc_id": 626 }, "chunk_id": "train_shard_00001_626_0", "global_id": 6543 }, { "text": "

Background

Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or nearly complete Streptomyces genome sequences are now available, affording the opportunity to deeply investigate the biosynthetic potential within these organisms and to advance natural product discovery initiatives.

Results

We perform pangenome analysis on 2371 Streptomyces genomes, including approximately 1200 complete assemblies. Employing a data-driven approach based on genome similarities, the Streptomyces genus was classified into 7 primary and 42 secondary Mash-clusters, forming the basis for comprehensive pangenome mining. A refined workflow for grouping biosynthetic gene clusters (BGCs) redefines their diversity across different Mash-clusters. This workflow also reassigns 2729 known BGC families to only 440 families, a reduction caused by inaccuracies in BGC boundary detections. When the genomic location of BGCs is included in the analysis, a conserved genomic structure, or synteny, among BGCs becomes apparent within species and Mash-clusters. This synteny suggests that vertical inheritance is a major factor in the diversification of BGCs.

Conclusions

Our analysis of a genomic dataset at a scale of thousands of genomes refines predictions of BGC diversity using Mash-clusters as a basis for pangenome analysis. The observed conservation in the order of BGCs' genomic locations shows that the BGCs are vertically inherited. The presented workflow and the in-depth analysis pave the way for large-scale pangenome investigations and enhance our understanding of the biosynthetic potential of the Streptomyces genus.\n\nPangenome mining of the Streptomyces genus redefines species' biosynthetic potential.", "token_count": 447, "char_count": 1870, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:28.041517", "source": { "split": "train_shard_00001", "doc_id": 627 }, "chunk_id": "train_shard_00001_627_0", "global_id": 6544 }, { "text": "

Background

Tuberculosis is a serious infectious disease affecting millions of people. In spite of efforts to reduce the disease, increasing antibiotic resistance has contributed to persist in the top 10 causes of death worldwide. In fact, the increased cases of multi (MDR) and extreme drug resistance (XDR) worldwide remains the main challenge for tuberculosis control. Whole genome sequencing is a powerful tool for predicting drug resistance-related variants, studying lineages, tracking transmission, and defining outbreaks. This study presents the identification and characterization of resistant clinical isolates of Mycobacterium tuberculosis including a phylogenetic and molecular resistance profile study by sequencing the complete genome of 24 strains from different provinces of Ecuador.

Results

Genomic sequencing was used to identify the variants causing resistance. A total of 15/21 isolates were identified as MDR, 4/21 as pre-XDR and 2/21 as XDR, with three isolates discarded due to low quality; the main sub-lineage was LAM (61.9%) and Haarlem (19%) but clades X, T and S were identified. Of the six pre-XDR and XDR strains, it is noteworthy that five come from females; four come from the LAM sub-lineage and two correspond to the X-class sub-lineage. A core genome of 3,750 genes, distributed in 295 subsystems, was determined. Among these, 64 proteins related to virulence and implicated in the pathogenicity of M. tuberculosis and 66 possible pharmacological targets stand out. Most variants result in nonsynonymous amino acid changes and the most frequent genotypes were identified as conferring resistance to rifampicin, isoniazid, ethambutol, para-aminosalicylic acid and streptomycin. However, an increase in the resistance to fluoroquinolones was detected.

Conclusion

This work shows for the first time the variability of circulating resistant strains between men and women in Ecuador, highlighting the usefulness of genomic sequencing for the identification of emerging resistance", "token_count": 516, "char_count": 2030, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:28.743353", "source": { "split": "train_shard_00001", "doc_id": 628 }, "chunk_id": "train_shard_00001_628_0", "global_id": 6545 }, { "text": "In this regard, we found an increase in fluoroquinolone resistance. Further sampling effort is needed to determine the total variability and associations with the metadata obtained to generate better health policies.\n\nComparative genomics of drug-resistant strains of Mycobacterium tuberculosis in Ecuador.", "token_count": 67, "char_count": 306, "word_count": 41, "semantic_coherence": 1, "information_density": 0.878, "quality_score": 0.939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:29.109557", "source": { "split": "train_shard_00001", "doc_id": 628 }, "chunk_id": "train_shard_00001_628_1", "global_id": 6546 }, { "text": "

Background

The high prevalence and rapid emergence of antibiotic resistance in high-risk Klebsiella pneumoniae (KP) ST147 clones is a global health concern and warrants molecular surveillance.

Methods

A pangenome analysis was performed using publicly available ST147 complete genomes. The characteristics and evolutionary relationships among ST147 members were investigated through a Bayesian phylogenetic analysis.

Results

The large number of accessory genes in the pangenome indicates genome plasticity and openness. Seventy-two antibiotic resistance genes were found to be linked with antibiotic inactivation, efflux, and target alteration. The exclusive detection of the blaOXA-232 gene within the ColKp3 plasmid of KP_SDL79 suggests its acquisition through horizontal gene transfer. The association of seventy-six virulence genes with the acrAB efflux pump, T6SS system and type I secretion system describes its pathogenicity. The presence of Tn6170, a putative Tn7-like transposon in KP_SDL79 with an insertion at the flanking region of the tnsB gene, establishes its transmission ability. The Bayesian phylogenetic analysis estimates ST147's initial divergence in 1951 and the most recent common ancestor for the entire KP population in 1621.

Conclusions

Present study highlights the genetic diversity and evolutionary dynamics of high-risk clones of K. pneumoniae. Further inter-clonal diversity studies will help us understand its outbreak more precisely and pave the way for therapeutic interventions.\n\nUnravelling the Evolutionary Dynamics of High-Risk Klebsiella pneumoniae ST147 Clones: Insights from Comparative Pangenome Analysis.", "token_count": 498, "char_count": 1741, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6759, "quality_score": 0.838, "entities": { "genes": [ "ST147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:29.770050", "source": { "split": "train_shard_00001", "doc_id": 629 }, "chunk_id": "train_shard_00001_629_0", "global_id": 6547 }, { "text": "The objective of this work was to deliver a comprehensive genetic characterization of a collection of E. coli strains isolated from raw sheep milk. To complete our purpose, the technique of whole-genome sequencing, coupled with bioinformatics and phenotypic characterization of antimicrobial resistance, was performed. These Gram-negative, facultative anaerobic bacteria belong to the family Enterobacteriaceae, together with other intestinal pathogens, such as Shigella spp. and Salmonella spp. Genetic analysis was carried out on all strains (phylogram, sequence types, VFs, AMR genes, and pangenome). The results showed the presence of various genetic traits that are related to virulence factors contributing to their pathogenic potential. In addition, genes conferring resistance to antibiotics were also detected and confirmed using phenotypic tests. Finally, the genome of the E. coli strains was characterized by the presence of several mobile genetic elements, thus facilitating the exchange of various genetic elements, associated with virulence and antimicrobial resistance, within and beyond the species, through horizontal gene transfer. Contaminated raw sheep milk with pathogenic E. coli strains is particularly alarming for cheese production in artisan dairies.\n\n<i>Escherichia coli</i> Strains Originating from Raw Sheep Milk, with Special Reference to Their Genomic Characterization, Such as Virulence Factors (VFs) and Antimicrobial Resistance (AMR) Genes, Using Whole-Genome Sequencing (WGS).", "token_count": 402, "char_count": 1566, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:30.390030", "source": { "split": "train_shard_00001", "doc_id": 630 }, "chunk_id": "train_shard_00001_630_0", "global_id": 6548 }, { "text": "Proteus mirabilis, a significant pathogenic bacterium within the Enterobacteriaceae family, is widely distributed across various natural environments. This study conducted a genomic comparison analysis of 1,267 strains of P. mirabilis using extensive genome data from public databases. The objective was to elucidate the pan-genomic structure of P. mirabilis, revealing the composition and distribution of core and accessory gene families among different strains. Additionally, an attempt was made to construct a core genome multilocus sequence typing scheme specific to this species in order to enhance the precision of describing genetic diversity and evolutionary relationships. Furthermore, the study delved into the mechanisms of resistance of P. mirabilis to carbapenems and quinolones. Our findings underscore significant challenges posed by P. mirabilis in terms of antibiotic resistance, with widespread resistance observed particularly against beta-lactams and an increasing trend in resistance to carbapenems and quinolones. These results highlight the severity of P. mirabilis as a pathogen and underscore its rapid evolution and adaptability in developing resistance. This study aims to deepen our understanding of the antibiotic resistance of P. mirabilis, providing important insights for the development of future antimicrobial drugs, promoting effective treatment and control of this pathogen, and mitigating its threat to human health.

Importance

The bacterium Proteus mirabilis is a common pathogenic bacterium that is known to cause a variety of human infections. The drug-resistant genes carried by P. mirabilis present a significant challenge to clinical treatment, particularly in regard to the organism's notable resistance to commonly used beta-lactam and quinolone drugs. Furthermore, the prevalence of the urease gene cluster of P. mirabilis at the urease gene level may be associated with the formation of kidney stones. The objective of the study is to analyze the bacterium's drug resistance, urease gene clusters, and gene distribution in genomes in order to facilitate the development of antimicrobial drugs and improve the treatment and control of P", "token_count": 530, "char_count": 2262, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5469, "quality_score": 0.7735, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:31.048701", "source": { "split": "train_shard_00001", "doc_id": 631 }, "chunk_id": "train_shard_00001_631_0", "global_id": 6549 }, { "text": "mirabilis infections.\n\nGenomic insights on cgMLST markers, drug resistance, and urease cluster of Proteus mirabilis strains.", "token_count": 45, "char_count": 135, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:31.418844", "source": { "split": "train_shard_00001", "doc_id": 631 }, "chunk_id": "train_shard_00001_631_1", "global_id": 6550 }, { "text": "The porcine gut microbiome is crucial for pig health and key to its production performance. However, genome-level analysis across multiple kingdoms remains limited. Here, we reconstructed the unified pig gastrointestinal genome (UPGG), including bacterial, archaeal, and annotated over 78 million non-redundant protein-coding genes using 5784 metagenome samples. We identified antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs), and the distribution of 72,056 metabolic gene clusters within existing populations. We have constructed pan-genomes of 436 high-quality microbial species and, using these as references, discovered intraspecies genomic variations that revealed 23,350,975 single-nucleotide variants (SNVs). Finally, through comparative analysis of gut microbiome genomes conducted in this study, we observed that pigs may serve as a more suitable model than other animals for investigating human gut microbiota composition and functional patterns. In summary, we constructed a comprehensive reference catalog of the porcine gut microbiome and enhanced the understanding of the host-microbe coevolution.\n\nUPGG: expanding the taxonomic and functional diversity of the pig gut microbiome with an enhanced genome catalog.", "token_count": 299, "char_count": 1247, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7349, "quality_score": 0.8675, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:31.988427", "source": { "split": "train_shard_00001", "doc_id": 632 }, "chunk_id": "train_shard_00001_632_0", "global_id": 6551 }, { "text": "

Background

Long-read sequencing (LRS) enables high-quality structural variant (SV) discovery. SV genotypers utilize these precise call sets to improve the recall and precision of genotyping in short-read sequencing (SRS) samples. With the extensive growth in publicly available SRS datasets, it is now possible to calculate accurate population allele frequencies of SVs. However, reprocessing hundreds of terabytes of raw SRS data to genotype new variants is impractical for population-scale studies, a computational challenge known as the N+1 problem (i.e., the challenge of re-genotyping an entire cohort for one additional variant). Overcoming this computational bottleneck is essential for analyzing new SVs from the growing number of pangenomes, public genomic databases, and pathogenic variant discovery studies.

Results

We propose the Great Genotyper, a population-scale genotyping workflow to address the N+1 problem. Applied to a human dataset, the workflow begins by preprocessing 4.2k short-read samples of a total of 183 TB raw data to create an 867-GB Counting Colored de Bruijn Graph (CCDG). The Great Genotyper uses this CCDG to genotype a list of phased or unphased variants, leveraging the CCDG population information to increase both precision and recall. The Great Genotyper offers the same accuracy as the state-of-the-art genotypers while achieving unprecedented performance. It took about 100 hours to genotype 4.5M variants across the 4.2k samples and calculate their population allele frequencies using 1 server with 32 cores and 145 GB of memory. The Great Genotyper opens the door to new ways to study SVs. For example, using the premade index, we demonstrate the Great Genotyper's application in finding pathogenic variants by calculating accurate allele frequency for novel SVs. Also, we used it to create a 4k reference panel by genotyping variants from the Human Pangenome Reference Consortium (HPRC). The new reference panel allows for SV imputation from genotyping microarrays", "token_count": 516, "char_count": 2023, "word_count": 294, "semantic_coherence": 1, "information_density": 0.5986, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:32.647178", "source": { "split": "train_shard_00001", "doc_id": 633 }, "chunk_id": "train_shard_00001_633_0", "global_id": 6552 }, { "text": "Moreover, we genotype the human GWAS Catalog and merge its variants with the 4k reference panel. We show 6,253 events of high linkage between the HPRC's SVs and nearby GWAS single-nucleotide polymorphisms, which can help in interpreting the effect of these SVs on gene functions. This analysis uncovers the detailed haplotype structure of the human fibrinogen locus and revives the pathogenic association of a 28-bp insertion in the FGA gene with thromboembolic disorders.

Conclusion

The Great Genotyper solves the N+1 problem for population-scale genotyping of small and structural variants, offering both high accuracy and efficiency. Its ability to rapidly re-genotype large cohorts paves the road for several new studies of SVs.\n\nThe Great Genotyper: a graph-based method for population genotyping of small and structural variants.", "token_count": 228, "char_count": 842, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:33.115641", "source": { "split": "train_shard_00001", "doc_id": 633 }, "chunk_id": "train_shard_00001_633_1", "global_id": 6553 }, { "text": "

Motivation

Since novel long read sequencing technologies allow for de novo assembly of many individuals of a species, high-quality assemblies are becoming widely available. For example, the recently published draft human pangenome reference was based on assemblies composed of contigs. There is an urgent need for a software-tool that is able to generate a multiple alignment of genomes of the same species because current multiple sequence alignment programs cannot deal with such a volume of data.

Results

We show that the combination of a well-known anchor-based method with the technique of prefix-free parsing yields an approach that is able to generate multiple alignments on a pangenomic scale, provided that large-scale structural variants are rare. Furthermore, experiments with real world data show that our software tool PANgenomic Anchor-based Multiple Alignment significantly outperforms current state-of-the art programs.

Availability and implementation

Source code is available at: https://gitlab.com/qwerzuiop/panama, archived at swh:1:dir:e90c9f664995acca9063245cabdd97549cf39694.\n\nGenerating multiple alignments on a pangenomic scale.", "token_count": 296, "char_count": 1174, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:33.677451", "source": { "split": "train_shard_00001", "doc_id": 634 }, "chunk_id": "train_shard_00001_634_0", "global_id": 6554 }, { "text": "

ABSTRACT

Bradyrhizobium is known for its ability to fix atmospheric nitrogen in symbiosis with agronomically important crops. This study focused on two groups of strains, each containing eight putative natural variants of B. japonicum SEMIA 586 (=CNPSo 17) or B. diazoefficiens SEMIA 566 (=CNPSo 10), previously used as commercial inoculants for soybean crops in Brazil. We aimed to detect genetic variations that might be related to biological nitrogen fixation, competitiveness for nodule occupancy, and adaptation to the stressful conditions of the Brazilian Cerrado soils. High-quality genome assemblies were produced for all strains and used for comparative genomic analyses. The core genome phylogeny revealed that strains of each group are closely related, confirmed by high average nucleotide identity (ANI) values. However, variants accumulated divergences resulting from horizontal gene transfer (HGT), genomic rearrangements, and nucleotide polymorphisms. The B. japonicum group presented a larger pangenome and a higher number of nucleotide polymorphisms than the B. diazoefficiens group, probably due to its longer adaptation time to the Cerrado soil. Interestingly, five strains of the B. japonicum group carry two plasmids. The genetic variability found in both groups is discussed in light of the observed differences in their nitrogen fixation capacity, competitiveness for nodule occupancy, and environmental adaptation.

SIGNIFICANCE

The two main reference strains for soybean inoculation in Brazil, B. japonicum CPAC 15 (=SEMIA 5079) and B. diazoefficiens CPAC 7 (=SEMIA 5080), have been considered highly competitive and highly efficient in nitrogen fixation, respectively. In this study, we obtained and analyzed the genomes of the parental and variant strains. We detected two plasmids in five strains and several genetic differences that might be related to adaptation to the stressful conditions of the soils of the Brazilian Cerrado biome. We also detected genetic variations in specific regions that may impact symbiotic nitrogen fixation", "token_count": 531, "char_count": 2082, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5825, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:34.338147", "source": { "split": "train_shard_00001", "doc_id": 635 }, "chunk_id": "train_shard_00001_635_0", "global_id": 6555 }, { "text": "Our analysis contributes to new insights into evolution of Bradyrhizobium , and some of the identified differences may be applied as genetic markers to assist strain selection programs.\n\nComparative genomic analysis ofBradyrhizobiumstrains with natural variability in the efficiency of nitrogen fixation, competitiveness, and adaptation to stressful edaphoclimatic conditions", "token_count": 87, "char_count": 382, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8542, "quality_score": 0.9271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:34.710565", "source": { "split": "train_shard_00001", "doc_id": 635 }, "chunk_id": "train_shard_00001_635_1", "global_id": 6556 }, { "text": "

Background

A key step for comparative genomics is to group open reading frames into functionally and evolutionarily meaningful gene clusters. Gene clustering is complicated by intraspecific duplications and horizontal gene transfers, that are frequent in prokaryotes. In consequence, gene clustering methods must deal with a trade-off between identifying vertically transmitted representatives of multi-copy gene families (recognizable by synteny conservation) and retrieving complete sets of species-level orthologs. We studied the implications of adopting homology, orthology, or synteny conservation as formal criteria for gene clustering by performing comparative analyses of 125 prokaryotic pangenomes.

Results

Clustering criteria affect pangenome functional characterization, core genome inference, and reconstruction of ancestral gene content to different extents. Species-wise estimates of pangenome and core genome sizes change by the same factor when using different clustering criteria, which allows for robust cross-species comparisons regardless of the clustering criterion. However, cross-species comparisons of genome plasticity and functional profiles are substantially affected by inconsistencies among clustering criteria. Such inconsistencies are driven not only by mobile genetic elements, but also by genes involved in defense, secondary metabolism, and other accessory functions. In some pangenome features, the variability attributed to methodological inconsistencies can even exceed the effect sizes of ecological and phylogenetic variables.

Conclusions

Choosing an appropriate criterion for gene clustering is critical to conduct unbiased pangenome analyses. We provide practical guidelines to choose the right method depending on the research goals and the quality of genome assemblies, and a benchmarking dataset to assess the robustness and reproducibility of future comparative studies.\n\nComparison of gene clustering criteria reveals intrinsic uncertainty in pangenome analyses", "token_count": 438, "char_count": 2034, "word_count": 260, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:35.351077", "source": { "split": "train_shard_00001", "doc_id": 636 }, "chunk_id": "train_shard_00001_636_0", "global_id": 6557 }, { "text": "BACKGROUND AND OBJECTIVES: In this study, Kluyveromyces marxianus with ability to produce β‐glucosidase was used to preferment wheat bran (WB) and release a mixture of natural enzymes for improving dough performance and bread quality. Five different enzyme activities were analyzed. The effect of the prefermented WB with enzyme mixture on stickiness and microstructure of dough, ferulic acid release in bread, and molecular weight distribution of arabinoxylan were evaluated using Texture Analyzer, scanning electron microscopy (SEM), HPLC, and high‐performance gel filtration chromatography (HPGFC). FINDINGS: Kluyveromyces marxianus exhibited abundant extracellular β‐glucosidase activity (up to 6.98 U/g). The main enzymes released in prefermented bran were endoglucanase and exoglucanase, β‐glucosidase, xylanase, and ferulate esterases. These enzymes were active during bread making (only prefermented bran added as improver or combined with xylanase) and affected solubility and molecular weight distribution of dietary fiber, which resulted in positive improvement of dough performance, release of phenolic acid, and overall quality of the breads. The changes observed were attributed to the extracellular enzymes from K. marxianus and endogenous enzymes activated during prefermentation, thus enhancing the WB functionality in bread. CONCLUSIONS: Wheat bran bioprocessing using high enzyme producing yeasts increases functional application of wheat bran in baked products. SIGNIFICANCE AND NOVELTY: This study added new knowledge for developing a natural enzyme‐based improver for bran‐enriched baked products in the food industry.\n\nUse of Kluyveromyces marxianus prefermented wheat bran as a source of enzyme mixture to improve dough performance and bread biochemical properties", "token_count": 467, "char_count": 1788, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6017, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:35.994981", "source": { "split": "train_shard_00001", "doc_id": 637 }, "chunk_id": "train_shard_00001_637_0", "global_id": 6558 }, { "text": "Seven strains of selected probiotic bacteria were separately combined with Kluyveromyces marxianus LAF4 to ferment 12% reconstituted skim milk (RSM) at 37 °C for 0–12 h. The growth characteristics of the probiotic strains and K. marxianus, pH levels, proteolytic activity and angiotensin‐converting enzyme inhibitory (ACE‐I) activity of the fermented RSM were measured. The highest ACE‐I activity of 60% was for K. marxianus at 37 °C for 12 h (P < 0.005) when compared to K. marxianus in combination with the probiotic bacterial strains.\n\nEffects of fermented skim milk drink by Kluyveromyces marxianus LAF4 co‐cultured with lactic acid bacteria to release angiotensin‐converting enzyme inhibitory activities", "token_count": 233, "char_count": 708, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [ "LAF4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:36.468188", "source": { "split": "train_shard_00001", "doc_id": 638 }, "chunk_id": "train_shard_00001_638_0", "global_id": 6559 }, { "text": "Nowadays, biofuels, especially bioethanol, are becoming increasingly popular as an alternative to fossil fuels. Zymomonas mobilis is a desirable species for bioethanol production due to its unique characteristics, such as low biomass production and high-rate glucose metabolism. However, several factors can interfere with the fermentation process and hinder microbial activity, including lignocellulosic hydrolysate inhibitors, high temperatures, an osmotic environment, and high ethanol concentration. Overcoming these limitations is critical for effective bioethanol production. In this review, the stress response mechanisms of Z. mobilis are discussed in comparison to other ethanol-producing microbes. The mechanism of stress response is divided into physiological (changes in growth, metabolism, intracellular components, and cell membrane structures) and molecular (up and down-regulation of specific genes and elements of the regulatory system and their role in expression of specific proteins and control of metabolic fluxes) changes. Systemic metabolic engineering approaches, such as gene manipulation, overexpression, and silencing, are successful methods for building new metabolic pathways. Therefore, this review discusses systems metabolic engineering in conjunction with systems biology and synthetic biology as an important method for developing new strains with an effective response mechanism to fermentation stresses during bioethanol production. Overall, understanding the stress response mechanisms of Z. mobilis can lead to more efficient and effective bioethanol production.\n\nComprehensive network of stress-induced responses in Zymomonas mobilis during bioethanol production: from physiological and molecular responses to the effects of system metabolic engineering.", "token_count": 382, "char_count": 1793, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:37.057353", "source": { "split": "train_shard_00001", "doc_id": 639 }, "chunk_id": "train_shard_00001_639_0", "global_id": 6560 }, { "text": "

Background

After introduction of pneumococcal conjugate vaccines (PCVs), serotype replacement occurred in the population of Streptococcus pneumoniae. Predicting which pneumococcal clones and serotypes will become more common in carriage after vaccination can enhance vaccine design and public health interventions, while also improving our understanding of pneumococcal evolution. We sought to use invasive disease data to assess how well negative frequency-dependent selection (NFDS) models could explain pneumococcal carriage population evolution in the post-PCV13 epoch by weighting invasive data to approximate strain proportions in the carriage population.

Methods

Invasive pneumococcal isolates were collected and sequenced during 1998–2018 by the Active Bacterial Core surveillance (ABCs) from the Centers for Disease Control and Prevention (CDC). To predict the post-PCV13 population dynamics in the carriage population using a NFDS model, all genomic data were processed under a bioinformatic pipeline of assembly, annotation, and pangenome analysis to define genetically similar sequence clusters (i.e., strains) and a set of accessory genes present in 5% to 95% of the isolates. The NFDS model predicted the strain proportion by calculating the post-vaccine strain composition in the weighted invasive disease population that would best match pre-vaccine accessory gene frequencies. To overcome the biases of invasive disease data, serotype-specific inverse-invasiveness weights were defined as the ratio of the proportion of the serotype in the carriage data to the proportion in the invasive data, using data from 1998–2001 in the United States, before conjugate vaccine introduction. The weights were applied to adjust both the observed strain proportion and the accessory gene frequencies.

Results

Inverse-invasiveness weighting increased the correlation of accessory gene frequencies between invasive and carriage data with reduced residuals in linear or logit scale for pre-vaccine, post-PCV7, and post-PCV13. Similarly, weighting increased the correlation of accessory gene frequencies between different time periods in the invasive data", "token_count": 510, "char_count": 2182, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5593, "quality_score": 0.7797, "entities": { "genes": [ "PCV13", "PCV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:37.718085", "source": { "split": "train_shard_00001", "doc_id": 640 }, "chunk_id": "train_shard_00001_640_0", "global_id": 6561 }, { "text": "By weighting the invasive data, we were able to use the NFDS model to predict strain proportions in the carriage population in the post-PCV13 epoch, with the adjusted R-squared between predicted and observed strain proportions increasing from 0.176 to 0.544 after weighting.

Conclusions

The weighting system adjusted the invasive disease surveillance data to better represent the carriage population of S. pneumoniae . The NFDS mechanism predicted the strain proportions in the projected carriage population as estimated from the weighted invasive disease frequencies in the post-PCV13 epoch. Our methods enrich the value of genomic sequences from invasive disease surveillance, which is readily available, easy to collect, and of direct interest to public health.

IMPORTANCE

Streptococcus pneumoniae , a common colonizer in the human nasopharynx, can cause invasive diseases including pneumonia, bacteremia, and meningitis mostly in children under 5 years or older adults. The PCV7 was introduced in 2000 in the United States within the pediatric population to prevent disease and reduce deaths, followed by PCV13 in 2010, PCV15 in 2022, and PCV20 in 2023. After the removal of vaccine serotypes, the prevalence of carriage remained stable as the vacated pediatric ecological niche was filled with certain non-vaccine serotypes. Predicting which pneumococcal clones, and which serotypes, will be most successful in colonization after vaccination can enhance vaccine design and public health interventions, while also improving our understanding of pneumococcal evolution. While carriage data, which are collected from the pneumococcal population that is competing to colonize and transmit, are most directly relevant to evolutionary studies, invasive disease data are often more plentiful. Previously, evolutionary models based on negative frequency-dependent selection (NFDS) on the accessory genome were shown to predict which non-vaccine strains and serotypes were most successful in colonization following the introduction of PCV7", "token_count": 488, "char_count": 2053, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5773, "quality_score": 0.7887, "entities": { "genes": [ "PCV20", "PCV13", "PCV15", "PCV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:38.367389", "source": { "split": "train_shard_00001", "doc_id": 640 }, "chunk_id": "train_shard_00001_640_1", "global_id": 6562 }, { "text": "Here, we show that an inverse-invasiveness weighting system applied to invasive disease surveillance data allows the NFDS model to predict strain proportions in the projected carriage population in the post-PCV13/pre-PCV15 and -PCV20 epoch. The significance of our research lies in using a sample of invasive disease surveillance data to extend the use of NFDS as an evolutionary mechanism to predict post-PCV13 population dynamics. This has shown that we can correct for biased sampling that arises from differences in virulence and can enrich the value of genomic data from disease surveillance and advances our understanding of how NFDS impacts carriage population dynamics after both PCV7 and PCV13 vaccination.\n\nPrediction of post-PCV13 pneumococcal evolution using invasive disease data enhanced by inverse-invasiveness weighting", "token_count": 190, "char_count": 835, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [ "PCV20", "PCV13", "PCV15", "PCV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:38.817931", "source": { "split": "train_shard_00001", "doc_id": 640 }, "chunk_id": "train_shard_00001_640_2", "global_id": 6563 }, { "text": "Kluyveromyces marxianus is a multifaceted yeast used in the dairy, biotechnological, and probiotic industries, and has been implicated in the spoilage of dairy products. Currently, K. marxianus detection involves laborious and time-consuming culture methods. To develop a rapid and reliable detection method for K. marxianus in pure cultures and dairy products, we designed a novel real-time PCR primer/probe set, KM55, which targets the internal transcribed spacer (ITS) rRNA gene. In the inclusivity and exclusivity tests, 11 K. marxianus strains tested positive, while 28 closely related microorganisms tested negative; this confirmed 100% sensitivity and specificity of the assay. Further, the KM55 set enabled a linear K. marxianus detection in the range of 100–105 colony-forming units (CFU) per reaction in phosphate-buffered saline, 10% skim milk, and commercial yogurts, with no cross-reactivity with microorganisms of kefir origin. The enumeration of K. marxianus in kefir revealed 5.1 to 6.9 logCFU ml−1 of kefir, depending on the fermentation time, temperature, and grain-milk ratio. K. marxianus was successfully detected in artificially contaminated yogurt samples within 2 h. These results suggest that this method could be an effective and sensitive presumptive screening tool for detecting and enumerating K. marxianus in dairy products.\n\nDevelopment of a rapid and reliable TaqMan probe-based real-time PCR assay for the detection and enumeration of the multifaceted yeast Kluyveromyces marxianus in dairy products", "token_count": 432, "char_count": 1532, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "KM55" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:39.467821", "source": { "split": "train_shard_00001", "doc_id": 641 }, "chunk_id": "train_shard_00001_641_0", "global_id": 6564 }, { "text": "

Background

The rapid expansion of Whole-Genome Sequencing has revolutionized the fields of clinical and food microbiology. However, its implementation as a routine laboratory technique remains challenging due to the growth of data at a faster rate than can be effectively analyzed and critical gaps in bioinformatics knowledge.

Results

To address both issues, CamPype was developed as a new bioinformatics workflow for the genomics analysis of sequencing data of bacteria, especially Campylobacter, which is the main cause of gastroenteritis worldwide making a negative impact on the economy of the public health systems. CamPype allows fully customization of stages to run and tools to use, including read quality control filtering, read contamination, reads extension and assembly, bacterial typing, genome annotation, searching for antibiotic resistance genes, virulence genes and plasmids, pangenome construction and identification of nucleotide variants. All results are processed and resumed in an interactive HTML report for best data visualization and interpretation.

Conclusions

The minimal user intervention of CamPype makes of this workflow an attractive resource for microbiology laboratories with no expertise in bioinformatics as a first line method for bacterial typing and epidemiological analyses, that would help to reduce the costs of disease outbreaks, or for comparative genomic analyses. CamPype is publicly available at https://github.com/JoseBarbero/CamPype .\n\nCamPype: an open-source workflow for automated bacterial whole-genome sequencing analysis focused on Campylobacter.", "token_count": 360, "char_count": 1622, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7056, "quality_score": 0.8528, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:40.069676", "source": { "split": "train_shard_00001", "doc_id": 642 }, "chunk_id": "train_shard_00001_642_0", "global_id": 6565 }, { "text": "Tuberculosis is a major public health threat demanding more than one million lives every year. Many challenges exist to defeat this deadly infectious disease which address the importance of a thorough understanding of the biology of the causative agent Mycobacterium tuberculosis (MTB). We generated a non-redundant pangenome of 420 epidemic MTB strains from China. We estimate that MTB strains have a pangenome of 4,278 genes encoding 4,183 proteins, of which 3,438 of which are core genes. However, due to 99,694 interruptions in 2,447 coding genes, only 1,651 may be translated in all samples, which dramatically reduces the number of active core genes. Of these interruptions, 67,315 (67.52%) could be classified by various genetic variations detected by currently available tools, and more than half of them are due to structure variations, mostly small indels. We further describe differential evolutionary patterns of genes under the influences of selective pressure, population structure and background selection. While selective pressure is ubiquitous among these coding genes, evolutionary adaptations primarily occur in 1,313 genes. Genes located in the cell wall and membrane region are under the strongest selective pressure, while biological processes including regulation of transcription, translation and regulation of growth are under strongest background selection in MTB. The metabolism of fatty acids may be an outstanding example of evolutionary adaption for MTB under current selective pressure. This study provides a comprehensive view on the genetic diversity and evolution patterns of coding genes in MTB which may deepen our understanding of its epidemiology and pathogenicity.\n\nUnderstanding the epidemiology and pathogenesis ofMycobacterium tuberculosiswith non-redundant pangenome and population genetics", "token_count": 424, "char_count": 1840, "word_count": 261, "semantic_coherence": 1, "information_density": 0.613, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:40.729179", "source": { "split": "train_shard_00001", "doc_id": 643 }, "chunk_id": "train_shard_00001_643_0", "global_id": 6566 }, { "text": "In this study, a high-throughput sequencing technique was used to analyze bacterial and fungal diversity of two traditional Tibetan kefir grains from Linzhi (K1) and Naqu (K2) regions. Comparative bioinformatic analyses indicated that Lactobacillus kefiranofaciens, L. kefiri and Kluyveromyces marxianus were the main dominant strains in K1 and K2. In order to research the relationship of the growth of kefir grains, the biofilm and the extracellular polysaccharides (EPS) produced by microorganisms, the proliferation rate of kefir grains, the yield and chemical structure of EPS and the optimal days for biofilm formation were determined. The results showed that the growth rate, the yield of EPS and the biofilm formation ability of K1 were higher than K2, and the optimal day of their biofilm formation was the same in 10th day. Additionally, the live cells, dead cells and EPS in biofilm formation of K1 and K2 were observed by fluorescence microscope to clarify the formation process of kefir grains. To determine the influence of microbial interactions on biofilm and the formation of kefir grains, the essential role of microbial quorum sensing needs further attention.\n\nThe Microbial Diversity and Biofilm-Forming Characteristic of Two Traditional Tibetan Kefir Grains.", "token_count": 346, "char_count": 1300, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5464, "quality_score": 0.7732, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:41.321257", "source": { "split": "train_shard_00001", "doc_id": 644 }, "chunk_id": "train_shard_00001_644_0", "global_id": 6567 }, { "text": "

ABSTRACT

A variety of marine invertebrates are known to form associations with chemosynthetic bacteria, but to the best of our knowledge this has not been documented in fishes. Here, we apply genome-resolved metagenomics to the hamlets ( Hypoplectrus spp), a model system for the study of speciation in the sea. The analysis of 304 gill samples from 12 hamlet species collected at six locations over 13 years revealed a stark contrast between the gill microbiota and ambient water microbial communities. One novel lineage in the Burkholderiaceae-B family was particularly prevalent across host species, sampling locations and years. Its genome encoded highly complete metabolic modules for carbon fixation and sulfur oxidation, indicating chemosynthetic potential. Its pangenome revealed large-scale geographic structure (western Caribbean, eastern Caribbean and Gulf of Mexico), paralleling the phylogenomic pattern observed in the hamlet radiation. Our survey also identified genomes of multiple novel gill-associated lineages related to known fish gill pathogens, fish gut microbes and free-living seawater taxa. These lineages harbor diverse metabolic modules, involved notably in nitrogen cycling, antibiotic production and biofilm formation, revealing a highly dynamic microbial ecosystem. Overall, our findings suggest complex host-microbe and microbe-microbe eco-evolutionary interactions that may influence fish physiology, homeostasis and immune response.\n\nProteobacteria with chemosynthetic potential are highly enriched in the gills of Hypoplectrus reef fishes", "token_count": 385, "char_count": 1589, "word_count": 214, "semantic_coherence": 1, "information_density": 0.743, "quality_score": 0.8715, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:41.933667", "source": { "split": "train_shard_00001", "doc_id": 645 }, "chunk_id": "train_shard_00001_645_0", "global_id": 6568 }, { "text": "Milk beer is a new type of milk beverage produced by two‐step fermentation of lactic acid bacteria and yeast and created first in China. Yeast is the key strain of milk beer fermentation, which determines the flavor and quality of milk beer. In this study, the preparation process of high‐quality yeast strain MJ1 active freeze‐dried powder suitable for milk beer fermentation was optimized. Results showed that the optimal freeze‐dried protective agent was used: sucrose 11.27%, mannitol 4.88%, maltodextrin 15.43%, skimmed milk powder 7.82%, and applying the optimal freeze‐drying conditions: rotation speed 6,000 rpm, centrifugation time 15 min, the mixing ratio of centrifugal bacterial sludge and the protective agent is 1:1.5, the mixing equilibrium time is 30 min, the cell survival rate of strain MJ1 can reach 90.21% ± 1.04%. It laid the foundation for the preparation of active freeze‐dried yeast powder and the industrial production of milk beer. NOVELTY IMPACT STATEMENT: (1) The formulation and conditions of the freeze‐dried protectant of Kluyveromyces marxianus yeast strain MJ1 were optimized to improve the cell survival rate of the freeze‐dried yeast powder, (2) the optimal storage conditions of the freeze‐dried yeast powder of strain MJ1 were screened to provide theoretical reference for the long‐term storage of freeze‐dried yeast powder, and (3) the fermentation performance of the freeze‐dried yeast powder of strain MJ1 was verified, which provided a reliable basis for the industrial production of milk beer.\n\nScreening of the freeze‐drying protective agent for high‐quality milk beer yeast (Kluyveromyces marxianus) and optimization of freeze‐drying process conditions", "token_count": 448, "char_count": 1696, "word_count": 252, "semantic_coherence": 1, "information_density": 0.4802, "quality_score": 0.7401, "entities": { "genes": [ "MJ1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:42.567262", "source": { "split": "train_shard_00001", "doc_id": 646 }, "chunk_id": "train_shard_00001_646_0", "global_id": 6569 }, { "text": "Probiotics are health-beneficial microorganisms with mainly immunomodulatory and anti-inflammatory properties. Lactobacillus delbrueckii species is a common bacteria used in the dairy industry, and their benefits to hosting health have been reported. This study analyzed the core genome of nine strains of L. delbrueckii species with documented probiotic properties, focusing on genes related to their host health benefits. For this, a combined methodology including several software and databases (BPGA, SPAAN, BAGEL4, BioCyc, KEEG, and InterSPPI) was used to predict the most important characteristics related to L. delbrueckii strains probiose. Comparative genomics analyses revealed that L. delbrueckii probiotic strains shared essential genes related to acid and bile stress response and antimicrobial activity. Other standard features shared by these strains are surface layer proteins and extracellular proteins-encoding genes, with high adhesion profiles that interacted with human proteins of the inflammatory signaling pathways (TLR2/4-MAPK, TLR2/4-NF-κB, and NOD-like receptors). Among these, the PrtB serine protease appears to be a strong candidate responsible for the anti-inflammatory properties reported for these strains. Furthermore, genes with high proteolytic and metabolic activity able to produce beneficial metabolites, such as acetate, bioactive peptides, and B-complex vitamins were also identified. These findings suggest that these proteins can be essential in biological mechanisms related to probiotics' beneficial effects of these strains in the host.\n\nGenomic Characterization of Lactobacillus delbrueckii Strains with Probiotics Properties.", "token_count": 442, "char_count": 1707, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [ "BAGEL4", "TLR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:43.201537", "source": { "split": "train_shard_00001", "doc_id": 647 }, "chunk_id": "train_shard_00001_647_0", "global_id": 6570 }, { "text": "Language Models (LM) have been extensively utilized for learning DNA sequence patterns and generating synthetic sequences. In this paper, we present a novel approach for the generation of synthetic DNA data using pangenomes in combination with LM. We introduce three innovative pangenome-based tokenization schemes, including two that can decouple from private data, while enhance long DNA sequence generation. Our experimental results demonstrate the superiority of pangenome-based tokenization over classical methods in generating high-utility synthetic DNA sequences, highlighting a promising direction for the public sharing of genomic datasets.\n\nPangenome-Informed Language Models for Synthetic Genome Sequence Generation", "token_count": 140, "char_count": 726, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:43.634230", "source": { "split": "train_shard_00001", "doc_id": 648 }, "chunk_id": "train_shard_00001_648_0", "global_id": 6571 }, { "text": "Multipartite genomes are thought to confer evolutionary advantages to bacteria by providing greater metabolic flexibility in fluctuating environments and enabling rapid adaptation to new ecological niches and stress conditions. This genome architecture is commonly found in plant symbionts, including nitrogen-fixing rhizobia, such as Rhizobium leguminosarum bv. trifolii TA1 (RtTA1), whose genome comprises a chromosome and four extrachromosomal replicons (ECRs). In this study, the transcriptomic responses of RtTA1 to partial nutrient limitation and low acidic pH were analyzed using high-throughput RNA sequencing. RtTA1 growth under these conditions resulted in the differential expression of 1035 to 1700 genes (DEGs), which were assigned to functional categories primarily related to amino acid and carbohydrate metabolism, ribosome and cell envelope biogenesis, signal transduction, and transcription. These results highlight the complexity of the bacterial response to stress. Notably, the distribution of DEGs among the replicons indicated that ECRs played a significant role in the stress response. The transcriptomic data align with the Rhizobium pangenome analysis, which revealed an over-representation of functional categories related to transport, metabolism, and regulatory functions on ECRs. These findings confirm that ECRs contribute substantially to the ability of rhizobia to adapt to challenging environmental conditions.\n\nTranscriptomic Response of Rhizobium leguminosarum to Acidic Stress and Nutrient Limitation Is Versatile and Substantially Influenced by Extrachromosomal Gene Pool.", "token_count": 410, "char_count": 1638, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6714, "quality_score": 0.8357, "entities": { "genes": [ "TA1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:44.254116", "source": { "split": "train_shard_00001", "doc_id": 649 }, "chunk_id": "train_shard_00001_649_0", "global_id": 6572 }, { "text": "As Arctic soil ecosystems warm due to climate change, enhanced microbial activity is projected to increase the rate of soil organic matter degradation. Delineating the diversity and activity of Arctic tundra microbial communities active in decomposition is thus of keen interest. Here, we describe novel cold-adapted bacteria in the genus Mucilaginibacter (Bacteroidota) isolated from Artic tundra soils in Finland. These isolates are aerobic chemoorganotrophs and appear well adapted to the low-temperature environment, where they are also exposed to desiccation and a wide regime of annual temperature variation. Initial 16S ribosomal RNA (rRNA)-based phylogenetic analysis suggested that five isolated strains represent new species of the genus Mucilaginibacter, confirmed by whole genome-based phylogenomic and average nucleotide identity. Five novel species are described: Mucilaginibacter geliditolerans sp. nov., Mucilaginibacter tundrae sp. nov., Mucilaginibacter empetricola sp. nov., Mucilaginibacter saanensis sp. nov., and Mucilaginibacter cryoferens sp. nov. Genome and phenotype analysis showed their potential in complex carbon degradation, nitrogen assimilation, polyphenol degradation, and adaptation to their tundra heath habitat. A pangenome analysis of the newly identified species alongside known members of the Mucilaginibacter genus sourced from various environments revealed the distinctive characteristics of the tundra strains. These strains possess unique genes related to energy production, nitrogen uptake, adaptation, and the synthesis of secondary metabolites that aid in their growth, potentially accounting for their prevalence in tundra soil. By uncovering novel species and strains within the Mucilaginibacter, we enhance our understanding of this genus and elucidate how environmental fluctuations shape the microbial functionality and interactions in Arctic tundra ecosystems.", "token_count": 519, "char_count": 1983, "word_count": 252, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:44.911610", "source": { "split": "train_shard_00001", "doc_id": 650 }, "chunk_id": "train_shard_00001_650_0", "global_id": 6573 }, { "text": "Genome analysis reveals diverse novel psychrotolerant <i>Mucilaginibacter</i> species in Arctic tundra soils.", "token_count": 41, "char_count": 121, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:45.271409", "source": { "split": "train_shard_00001", "doc_id": 650 }, "chunk_id": "train_shard_00001_650_1", "global_id": 6574 }, { "text": "The enteric, pathogenic spirochaete Brachyspira pilosicoli colonizes and infects a variety of birds and mammals, including humans. However, there is a paucity of genomic data available for this organism. This study introduces 12 newly sequenced draft genome assemblies, boosting the cohort of examined isolates by fourfold and cataloguing the intraspecific genomic diversity of the organism more comprehensively. We used several in silico techniques to define a core genome of 1751 genes and qualitatively and quantitatively examined the intraspecific species boundary using phylogenetic analysis and average nucleotide identity, before contextualizing this diversity against other members of the genus Brachyspira. Our study revealed that an additional isolate that was unable to be species typed against any other Brachyspira lacked putative virulence factors present in all other isolates. Finally, we quantified that homologous recombination has as great an effect on the evolution of the core genome of the B. pilosicoli as random mutation (r/m=1.02). Comparative genomics has informed Brachyspira diversity, population structure, host specificity and virulence. The data presented here can be used to contribute to developing advanced screening methods, diagnostic assays and prophylactic vaccines against this zoonotic pathogen.\n\nEvidence of homologous recombination as a driver of diversity in Brachyspira pilosicoli.", "token_count": 390, "char_count": 1488, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6768, "quality_score": 0.8384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:46.255066", "source": { "split": "train_shard_00001", "doc_id": 651 }, "chunk_id": "train_shard_00001_651_0", "global_id": 6575 }, { "text": "

Background

Although Escherichia coli (E. coli) is the most studied prokaryote organism in the history of life sciences, many molecular mechanisms and gene functions encoded in its genome remain to be discovered. This work aims at quantifying the illumination of the E. coli gene function space by the scientific literature and how close we are towards the goal of a complete list of E. coli gene functions.

Results

The scientific literature about E. coli protein-coding genes has been mapped onto the genome via the mentioning of names for genomic regions in scientific articles both for the case of the strain K-12 MG1655 as well as for the 95%-threshold softcore genome of 1324 E. coli strains with known complete genome. The article match was quantified with the ratio of a given gene name's occurrence to the mentioning of any gene names in the paper. The various genome regions have an extremely uneven literature coverage. A group of elite genes with ≥ 100 full publication equivalents (FPEs, FPE = 1 is an idealized publication devoted to just a single gene) attracts the lion share of the papers. For K-12, ~ 65% of the literature covers just 342 elite genes; for the softcore genome, ~ 68% of the FPEs is about only 342 elite gene families (GFs). We also find that most genes/GFs have at least one mentioning in a dedicated scientific article (with the exception of at least 137 protein-coding transcripts for K-12 and 26 GFs from the softcore genome). Whereas the literature growth rates were highest for uncharacterized or understudied genes until 2005-2010 compared with other groups of genes, they became negative thereafter. At the same time, literature for anyhow well-studied genes started to grow explosively with threshold T10 (≥ 10 FPEs). Typically, a body of ~ 20 actual articles generated over ~ 15 years of research effort was necessary to reach T10", "token_count": 515, "char_count": 1886, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7977, "entities": { "genes": [ "MG1655" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:46.912591", "source": { "split": "train_shard_00001", "doc_id": 652 }, "chunk_id": "train_shard_00001_652_0", "global_id": 6576 }, { "text": "Lineage-specific co-occurrence analysis of genes belonging to the accessory genome of E. coli together with genomic co-localization and sequence-analytic exploration hints previously completely uncharacterized genes yahV and yddL being associated with osmotic stress response/motility mechanisms.

Conclusion

If the numbers of scientific articles about uncharacterized and understudied genes remain at least at present levels, full gene function lists for the strain K-12 MG1655 and the E. coli softcore genome are in reach within the next 25-30 years. Once the literature body for a gene crosses 10 FPEs, most of the critical fundamental research risk appears overcome and steady incremental research becomes possible.\n\nAbout the dark corners in the gene function space of Escherichia coli remaining without illumination by scientific literature.", "token_count": 202, "char_count": 853, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7179, "quality_score": 0.859, "entities": { "genes": [ "MG1655" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:47.373323", "source": { "split": "train_shard_00001", "doc_id": 652 }, "chunk_id": "train_shard_00001_652_1", "global_id": 6577 }, { "text": "Individuals of Pacific ancestry suffer some of the highest rates of health disparities yet remain vastly underrepresented in genomic research, including currently available linear and pangenome references. To begin addressing this, we developed the first Pacific ancestry pangenome reference using 23 individuals with diverse Pacific ancestry. We assembled 46 haploid genomes from these 23 individuals, resulting in highly accurate and contiguous genome assemblies with an average quality value of 55.0 and an average N50 of 40.7 Mb, marking the first de novo assembly of highly accurate Pacific ancestry genomes. We combined these assemblies to create a pangenome reference, which added 30.6 Mb of novel sequence missing from the Human Pangenome Reference Consortium (HPRC) reference. Mapping short reads to this pangenome reduced variant call errors and yielded more true-positive variants compared to the HPRC and T2T-CHM13 references. This Pacific ancestry pangenome reference serves as a resource to enhance genetic analyses for this underserved population.\n\nA Draft Pacific Ancestry Pangenome Reference", "token_count": 260, "char_count": 1108, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.827, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:47.922292", "source": { "split": "train_shard_00001", "doc_id": 653 }, "chunk_id": "train_shard_00001_653_0", "global_id": 6578 }, { "text": "Cytosine methylation, a crucial epigenetic modification, plays a vital role in genomic regulation. Leveraging the advancements in third-generation sequencing, we investigated the methylation patterns of non-reference insertions of human lymphoblastoid cell lines (LCLs), particularly polymorphic transposable elements (TEs). We validated the high concordance between long-read methylation calls and conventional whole genome bisulfite sequencing (WGBS) method. By characterizing thousands of polymorphic TE insertions genome-wide using long reads from the draft Human Pangenome Reference, we aimed to establish general rules of TE methylation by addressing three key questions: 1) what is the methylation profile of each insertion? 2) do newly inserted TEs adopt the methylation pattern of their genomic context? and 3) do new TE insertions affect the methylation of their flanking regions? While most non-TE insertions exhibit DNA methylation patterns consistent with their genomic context, TE insertions are generally highly methylated, exhibiting distinct, class-specific patterns, and with profound variation within TE bodies. A small percentage of Alu insertions are hypomethylated, particularly those inserted within hypomethylated CpG islands. By comparing DNA methylation of flanking regions of TE insertions between individuals with and without the TE insertions, we revealed that majority of TEs exhibited minimal impact on nearby regions, although numerous exceptions exist where the methylation status of both L1 and Alu insertions leak into nearby regions, leading to either methylation spreading or hypomethylation sloping shores. In conclusion, we demonstrated the methylation calling capability of third-generation sequencing and its unique advantage in characterizing epigenomic features within non-reference positions. While TE insertions primarily exhibit methylation patterns restricted within their boundaries, some TEs are able to engage in context-dependent complex interactions with genomic neighborhood.\n\nCharacterizing cytosine methylation of polymorphic human transposable element insertions using human pangenome resources", "token_count": 468, "char_count": 2150, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:48.568238", "source": { "split": "train_shard_00001", "doc_id": 654 }, "chunk_id": "train_shard_00001_654_0", "global_id": 6579 }, { "text": "Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates, FSP34 and KS17. Multi-sample variant calling identified a total of 461,683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. The variant density was higher on the sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets that were affected by high impact variants. A core genome representing genomic elements that were conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements were present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help to inform novel disease management strategies against the pathogen.\n\nIntra-Species Genomic Variation in the Pine Pathogen Fusarium circinatum.", "token_count": 379, "char_count": 1494, "word_count": 215, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [ "FSP34", "KS17" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:49.150285", "source": { "split": "train_shard_00001", "doc_id": 655 }, "chunk_id": "train_shard_00001_655_0", "global_id": 6580 }, { "text": "

Background and objectives

Probiotics are defined as live micro-organisms conferring a health benefit on the host. Although most probiotics are bacteria, some yeasts such as Saccharomyces and Kluyveromyces, has been found to have effective probiotic properties. The objective of this study was to isolate and identify indigenous Saccharomyces and Kluyveromyces yeast strains and to compare some probiotic characteristics between these two strains in vitro.

Materials and methods

Strains were isolated on yeast glucose chloramphenicol agar medium from 205 samples and identified by morphological, physiological and biochemical assays. The effects of different conditions such as pH and temperature on the survival and growth of the isolates were studied. In addition, resistance to acidic pH (1.5, 2, 3 and 5), pepsin and different concentrations of bile salts (1%, 3% and 5%), as well as proteolytic, lipolytic and hemolytic activity of selected isolates were assessed. Finally, the best isolates were selected for investigation of their viability in samples of dairy products.

Results

126 isolates were identified using biochemical and molecular techniques as yeast strains. Five isolates were found to have effective probiotic properties, belonging to Kluyveromyces marxianus (S97, S101 and S106) and Saccharomyces cerevisiae (S28, S34). These isolates were able to grow at 37°C, pH=1.5, withstand to concentration of 5% oxbile and pepsin and exhibit the proteolytic activity. The isolates of K. marxianus showed better viability in dairy (yogurt).

Conclusion

In the in-vitro comparative experiments, the isolates of K", "token_count": 520, "char_count": 1714, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:49.798641", "source": { "split": "train_shard_00001", "doc_id": 656 }, "chunk_id": "train_shard_00001_656_0", "global_id": 6581 }, { "text": "marxianus showed better probiotic potentials.\n\nScreening and characterization of in-vitro probiotic criteria of Saccharomyces and Kluyveromyces strains.", "token_count": 67, "char_count": 177, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:50.162304", "source": { "split": "train_shard_00001", "doc_id": 656 }, "chunk_id": "train_shard_00001_656_1", "global_id": 6582 }, { "text": "Terpene synthases (TPSs), key gatekeepers in the biosynthesis of herbivore-induced terpenes, are pivotal in the diversity of terpene chemotypes across and within plant species. Here, we constructed a gene-based pangenome of the Gossypium genus by integrating the genomes of 17 diploid and 10 tetraploid species. Within this pangenome, 208 TPS syntelog groups (SGs) were identified, comprising 2 core SGs (TPS5 and TPS42) present in all 27 analyzed genomes, 6 softcore SGs (TPS11, TPS12, TPS13, TPS35, TPS37, and TPS47) found in 25 to 26 genomes, 131 dispensable SGs identified in 2 to 24 genomes, and 69 private SGs exclusive to a single genome. The mutational load analysis of these identified TPS genes across 216 cotton accessions revealed a great number of splicing variants and complex splicing patterns. The nonsynonymous/synonymous Ka/Ks value for all 52 analyzed TPS SGs was less than one, indicating that these genes were subject to purifying selection. Of 208 TPS SGs encompassing 1795 genes, 362 genes derived from 102 SGs were identified as atypical and truncated. The structural analysis of TPS genes revealed that gene truncation is a major mechanism contributing to the formation of atypical genes. An integrated analysis of three RNA-seq datasets from cotton plants subjected to herbivore infestation highlighted nine upregulated TPSs, which included six previously characterized TPSs in G", "token_count": 471, "char_count": 1464, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6698, "quality_score": 0.8349, "entities": { "genes": [ "TPS11", "TPS35", "TPS37", "TPS47", "TPS42", "TPS13", "TPS5", "TPS12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:50.808172", "source": { "split": "train_shard_00001", "doc_id": 657 }, "chunk_id": "train_shard_00001_657_0", "global_id": 6583 }, { "text": "hirsutum (AD1_TPS10, AD1_TPS12, AD1_TPS40, AD1_TPS42, AD1_TPS89, and AD1_TPS104), two private TPSs (AD1_TPS100 and AD2_TPS125), and one atypical TPS (AD2_TPS41). Also, a TPS-associated coexpression module of eight genes involved in the terpenoid biosynthesis pathway was identified in the transcriptomic data of herbivore-infested G. hirsutum. These findings will help us understand the contributions of TPS family members to interspecific terpene chemotypes within Gossypium and offer valuable resources for breeding insect-resistant cotton cultivars.\n\nPangenome Identification and Analysis of Terpene Synthase Gene Family Members in Gossypium.", "token_count": 298, "char_count": 754, "word_count": 82, "semantic_coherence": 1, "information_density": 0.8171, "quality_score": 0.9085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:51.386688", "source": { "split": "train_shard_00001", "doc_id": 657 }, "chunk_id": "train_shard_00001_657_1", "global_id": 6584 }, { "text": "

Motivation

As genomics data analysis becomes increasingly intricate, researchers face the challenge of mastering various software tools. The rise of Pangenomics analysis, which examines the complete set of genes in a group of genomes, is particularly transformative in understanding genetic diversity. Our interdisciplinary team of biologists and mathematicians developed a short Pangenomics Workshop covering Bash, Python scripting, Pangenome, and Topological Data Analysis. These skills provide deeper insights into genetic variations and their implications in Evolutionary Biology. The workshop uses a Conda environment for reproducibility and accessibility. Developed in The Carpentries Incubator infrastructure, the workshop aims to equip researchers with essential skills for Pangenomics research. By emphasizing the role of a community of practice, this work underscores its significance in empowering multidisciplinary professionals to collaboratively develop training that adheres to best practices.

Results

Our workshop delivers tangible outcomes by enhancing the skill sets of Computational Biology professionals. Participants gain hands-on experience using real data from the first described pangenome. We share our paths toward creating an open-source, multidisciplinary, and public resource where learners can develop expertise in Pangenomic Analysis. This initiative goes beyond advancing individual capabilities, aligning with the broader mission of addressing educational needs in Computational Biology.

Availability and implementation

https://carpentries-incubator.github.io/pangenomics-workshop/.\n\nMeeting the challenge of genomic analysis: a collaboratively developed workshop for pangenomics and topological data analysis.", "token_count": 372, "char_count": 1765, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6934, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:51.987375", "source": { "split": "train_shard_00001", "doc_id": 658 }, "chunk_id": "train_shard_00001_658_0", "global_id": 6585 }, { "text": "Abstract

Staphylococcus aureus ST398 is a typical ‘One Health’ pathobiont exemplifying multiple-host tropisms. Here we traced the evolutionary trajectory of the global accessory genome (an assembly of accessory genes) of S. aureus ST398 over 20 years, with the aim of identifying the mechanisms linking accessory genomes with multiple-host tropisms and the phylogenomic traits associated with severe human infections. We analyzed 1079 high-quality genomes of ST398 from 13 host species, spanning 23 years (1998–2021) and 25 countries across 5 continents, and showed that accessory gene pools of ST398 substantially expanded in the early period before 2010, aligning with the increase in the host-species spectrum. The more recent shifts of accessory genomes were mainly driven by stochastic processes. Accessory genes transferred widely across ST398 from different host-species and barely formed host-specific accessory gene pools, indicating that a host-jump of ST398 was followed shortly by another host-switch rather than a long-term co-evolution with a new host species to generate host-specific gene pools. Human-ST398 was a major recipient of accessory gene transfer, with more common gene transfer with ST398 from pig than other animals. Life-threatening exotoxin genes separately encoding Panton-Valentine Leukocidin and the staphylococcal enterotoxin B were abundant and exclusive to human-ST398 that showed a higher evolution rate than animal-ST398. Both accessory and core genome analyses implied nutrient metabolism as a major force for ST398 evolution. Analyses of clinical data revealed a conserved evolution of ST398 along infection development within a patient, and identified a novel subtype ST398-9 (a relatively recent phylogenetic branch) and phages StauST398_5 and StauST398_1 to be closely associated with human infections", "token_count": 508, "char_count": 1897, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:52.703397", "source": { "split": "train_shard_00001", "doc_id": 659 }, "chunk_id": "train_shard_00001_659_0", "global_id": 6586 }, { "text": "Our findings elucidate mechanisms underlying the distribution and evolution of accessory gene pools of ST398, which determine the development of multiple-host tropisms and pathogenicity.

\n\nFrequent host-switch and gene exchange shape the evolution of Staphylococcus aureus ST398", "token_count": 69, "char_count": 281, "word_count": 36, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:53.088276", "source": { "split": "train_shard_00001", "doc_id": 659 }, "chunk_id": "train_shard_00001_659_1", "global_id": 6587 }, { "text": "One approach to sustainable agricultural production in a changing global environment is the effective utilization of unutilized germplasms. Among these, crop wild relatives (CWRs) represent valuable germplasms that retain the diversity lost during domestication. The genus Oryza has two cultivated species and 22 wild species. One of the cultivated species, Oryza sativa, produces the rice that is the staple food for half of the world's population. We are responsible for the maintenance and distribution of wild Oryza genetic resources held by Japan's National Institute of Genetics (NIG). The NIG has collected the genome sequences of numerous wild Oryza accessions, aiming at understanding and promoting the utilization of Oryza germplasm for both basic and applied sciences, such as breeding. The genome information of many wild Oryza germplasms deciphered by multiple groups is publicly available in databases, allowing for pangenome analysis. This review mainly introduces the wild Oryza genetic resources held by the NIG, discusses the genome diversity revealed through genome sequencing, presents new attempts to utilize wild Oryza germplasm as novel resources enabled by genome sequencing, and discusses the challenges in further effectively utilizing wild Oryza germplasm in breeding.\n\nUsage of wild <i>Oryza</i> germplasms for breeding in pan-genomics era.", "token_count": 373, "char_count": 1443, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:53.674498", "source": { "split": "train_shard_00001", "doc_id": 660 }, "chunk_id": "train_shard_00001_660_0", "global_id": 6588 }, { "text": "Bacterial typing at whole-genome scales is now feasible owing to decreasing costs in high-throughput sequencing and the recent advances in computation. The unprecedented resolution of whole-genome typing is achieved by genotyping the variable segments of bacterial genomes that can fluctuate significantly in gene content. However, due to the transient and hypervariable nature of many accessory elements, the value of the added resolution in outbreak investigations remains disputed. To assess the analytical value of bacterial accessory genomes in clustering epidemiologically related cases, we trained classifiers on a set of genomes collected from 24 Salmonella enterica outbreaks of food, animal, or environmental origin. The models demonstrated high precision and recall on unseen test data with near-perfect accuracy in classifying clonal and short-term outbreaks. Annotating the genomic features important for cluster classification revealed functional enrichment of molecular fingerprints in genes involved in membrane transportation, trafficking, and carbohydrate metabolism. Importantly, we discovered polymorphisms in mobile genetic elements (MGEs) and gain/loss of MGEs to be informative in defining outbreak clusters. To quantify the ability of MGE variations to cluster outbreak clones, we devised a reference-free tree-building algorithm inspired by colored de Bruijn graphs, which enabled topological comparisons between MGE and standard typing methods. Systematic evaluation of clustering MGEs on an unseen dataset of 34 Salmonella outbreaks yielded mixed results that exemplified the power of accessory sequence variations when core genomes of unrelated cases are insufficiently discriminatory, as well as the distortion of outbreak signals by microevolution events or the incomplete assembly of MGEs.

Importance

Gene-by-gene typing is widely used to detect clusters of foodborne illnesses that share a common origin. It remains actively debated whether the inclusion of accessory sequences in bacterial typing schema is informative or deleterious for cluster definitions in outbreak investigations due to the potential confounding effects of horizontal gene transfer. By training machine learning models on a curated set of historical Salmonella outbreaks, we revealed an enriched presence of outbreak distinguishing features in a wide range of mobile genetic elements", "token_count": 521, "char_count": 2416, "word_count": 327, "semantic_coherence": 1, "information_density": 0.6147, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:54.348091", "source": { "split": "train_shard_00001", "doc_id": 661 }, "chunk_id": "train_shard_00001_661_0", "global_id": 6589 }, { "text": "Systematic comparison of the efficacy of clustering different accessory elements against standard sequence typing methods led to our cataloging of scenarios where accessory sequence variations were beneficial and uninformative to resolving outbreak clusters. The presented work underscores the complexity of the molecular trends in enteric outbreaks and seeks to inspire novel computational ways to exploit whole-genome sequencing data in enteric disease surveillance and management.\n\nMachine learning reveals the dynamic importance of accessory sequences for <i>Salmonella</i> outbreak clustering.", "token_count": 124, "char_count": 610, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7532, "quality_score": 0.8766, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:54.734430", "source": { "split": "train_shard_00001", "doc_id": 661 }, "chunk_id": "train_shard_00001_661_1", "global_id": 6590 }, { "text": "A comprehensive water buffalo pangenome reveals extensive structural variation linked to population-specific signatures of selection", "token_count": 21, "char_count": 132, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:55.109734", "source": { "split": "train_shard_00001", "doc_id": 662 }, "chunk_id": "train_shard_00001_662_0", "global_id": 6591 }, { "text": "

Introduction

Cutibacterium acnes can both be a helpful colonizer of the human skin as well as the causative agent of acne and purulent infections. Until today, it is a moot point whether there are C. acnes strains exclusively devoted to be part of the skin microbiome and others, that carry special features enabling them to cause disease. So far, the search for the molecular background of such diverse behavior has led to inconsistent results.

Methods

In the present study, we prospectively collected C. acnes strains from 27 infected persons and 18 healthy controls employing rigid selection criteria to ensure their role as infectious agent or colonizer. The genome sequences from these strains were obtained and carefully controlled for quality.

Results

Deduced traditional phylotyping assigned almost all superficial isolates to type IA1, while the clinical strains were evenly distributed between types IA1, IB, and II. Single locus sequence typing (SLST) showed a predominance of A1 type for the control strains, whereas 56% of the clinical isolates belonged to types A1, H1 and K8. Pangenome analysis from all the present strains and 30 published genomes indicated the presence of an open pangenome. Except for three isolates, the colonizing strains clustered in clades separate from the majority of clinical strains, while 4 clinical strains clustered with the control strains. Identical results were obtained by a single nucleotide polymorphism (SNP) analysis. However, there were no significant differences in virulence gene contents in both groups.

Discussion

Genome-wide association studies (GWAS) from both the pangenome and SNP data consistently showed genomic differences between both groups located in metabolic pathway and DNA repair genes. Thus, the different behavior of colonizing and infectious C. acnes strains could be due to special metabolic capacities or flexibilities rather than specific virulence traits.\n\nWhole genome sequencing distinguishes skin colonizing from infection-associated Cutibacterium acnes isolates.", "token_count": 513, "char_count": 2103, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [ "IA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T05:59:55.743417", "source": { "split": "train_shard_00001", "doc_id": 663 }, "chunk_id": "train_shard_00001_663_0", "global_id": 6592 }, { "text": "Invasive gastric candidiasis is a rare fungal infection of the stomach, often arising in the setting of immunosuppression, critical illness, mucosal barrier disruption, gut microbial alterations, or antibiotic use. Though Candida spp. are normal flora within the gastrointestinal tract, compromised host defenses can contribute to overgrowth and invasion of the fungal species into deeper tissues. We report a case of an 89-year-old man presenting with concurrent upper gastrointestinal bleeding from diffuse gastric ulcers secondary to invasive gastric candidiasis and diarrhea resulting from Clostridioides difficile colitis. The pathophysiology, diagnosis, and management of invasive candidiasis as well as interactions between gastrointestinal candidiasis and Clostridioides difficile infection are discussed. Overall, this case highlights the interplay between antibiotic use, gut barrier translocation, interactions between microorganisms, and worsening infectious disease in an elderly patient. Similarly, it stresses the importance of maintaining a high index of suspicion for fungal infections in patients with large atypical appearing gastric ulcers, even in the absence of overt immunosuppression.\n\nInvasive Gastric Candidiasis With Concurrent Clostridioides difficile Colitis: A Case Report and Review of the Literature.", "token_count": 341, "char_count": 1353, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:56.330605", "source": { "split": "train_shard_00001", "doc_id": 664 }, "chunk_id": "train_shard_00001_664_0", "global_id": 6593 }, { "text": "

Background

Long-read technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT. Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges.

Results

Our study evaluates recommended data types and volumes required to establish a robust de novo genome assembly pipeline for population-level pangenome projects, extensively examining performance between ONT's Duplex and PacBio HiFi datasets in the context of achieving high-quality phased genomes with enhanced contiguity and completeness. The results show that achieving chromosome-level haplotype-resolved assembly requires 20 × high-quality long reads such as PacBio HiFi or ONT Duplex, combined with 15-20 × of ultra-long ONT per haplotype and 10 × of long-range data such as Omni-C or Hi-C. High-quality long reads from both platforms yield assemblies with comparable contiguity, with HiFi excelling in phasing accuracies, while Duplex generates more T2T contigs.

Conclusion

Our study provides insights into optimal data types and volumes for robust de novo genome assembly in population-level pangenome projects. Reassessing the recommended data types and volumes in this study and aligning them with practical economic limitations are vital to the pangenome research community, contributing to their efforts and pushing genomic studies with broader impacts.\n\nEvaluating data requirements for high-quality haplotype-resolved genomes for creating robust pangenome references.", "token_count": 482, "char_count": 2010, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:56.983579", "source": { "split": "train_shard_00001", "doc_id": 665 }, "chunk_id": "train_shard_00001_665_0", "global_id": 6594 }, { "text": "Prophages play a crucial role in shaping host physiology, influencing traits such as virulence and antimicrobial resistance. In Salmonella enterica , prophages can constitute up to 30% of the accessory genome, contributing significantly to its genetic diversity and adaptability. In this study, we employed an in-silico approach to identify prophages within S. enterica genomes obtained poultry and clinical isolates. A total of 151 S. enterica sequences were assembled using SPAdes and subsequently quality-filtered with Abyss and BUSCO. Prophage sequences were detected using Phigaro and CheckV, followed by quality assessment with PHASTEST. The identification was performed using a custom database comprising 60 S. enterica prophages from previous studies. Comparative genomics, including gene annotation and recombination detection, were performed on representative prophages. Virulence genes were identified using VFDB and VirulenceFinder databases. Lastly, phylogenetic analysis of the prophages was carried out based on terminase and integrase sequences. We obtained 142 S. enterica genomes to analyze their prophage content. Peduovirus pro483 was highly prevalent among S. Infantis isolates and carried two cargo proteins: an Imma/Irre metalloendopeptidase and a fimbrial protein. In contrast, a related S. Enteritidis isolate also harboring Peduovirus pro483 carried a different set of cargo genes—HEPN-MAE-28990 and a cytosine-specific methyltransferase—suggesting horizontal transfer or a recent phage acquisition event. Enterobacteria phage ST104 , found in S. Typhimurium, exhibited nearly complete identity to its reference and encoded superinfection exclusion proteins (SieA, SieB), enhancing phage resistance. Phylogenetic analyses supported their classification and revealed distinct evolutionary relationships tied to host serovar and environment. To our knowledge, this is the first study to describe prophage diversity in S. enterica strains isolated from Ecuadorian poultry farms, providing insights into their potential role in strain adaptation and public health relevance.", "token_count": 509, "char_count": 2096, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.831, "entities": { "genes": [ "ST104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:57.640627", "source": { "split": "train_shard_00001", "doc_id": 666 }, "chunk_id": "train_shard_00001_666_0", "global_id": 6595 }, { "text": "Exploring prophages in Salmonella enterica: an in-silico approach", "token_count": 29, "char_count": 79, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:57.995423", "source": { "split": "train_shard_00001", "doc_id": 666 }, "chunk_id": "train_shard_00001_666_1", "global_id": 6596 }, { "text": "Bacterial exopolysaccharides (EPS) have emerged as one of the key players in the field of heavy metal-contaminated environmental bioremediation. This study aimed to characterize and evaluate the metal biosorption potential of EPS produced by a novel Psychrobacillus strain, NEAU-3TGS, isolated from an iron ore deposit at Tamra iron mine, northern Tunisia. Genomic and pan-genomic analysis of NEAU-3TGS bacterium with nine validated published Psychrobacillus species was also performed. The results showed that the NEAU-3TGS genome (4.48 Mb) had a mean GC content of 36%, 4,243 coding sequences and 14 RNA genes. Phylogenomic analysis and calculation of nucleotide identity (ANI) values (less than 95% for new species with all strains) confirmed that NEAU-3TGS represents a potential new species. Pangenomic analysis revealed that Psychrobacillus genomic diversity represents an \"open\" pangenome model with 33,091 homologous genes, including 65 core, 3,738 shell, and 29,288 cloud genes. Structural EPS characterization by attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy showed uronic acid and α-1,4-glycosidic bonds as dominant components of the EPS. X-ray diffraction (XRD) analysis revealed the presence of chitin, chitosan, and calcite CaCO3 and confirmed the amorphous nature of the EPS. Heavy metal bioabsorption assessment showed that iron and lead were more adsorbed than copper and cadmium. Notably, the optimum activity was observed at 37°C, pH=7 and after 3 h contact of EPS with each metal. Genomic insights on iron acquisition and metabolism in Psychrobacillus sp", "token_count": 487, "char_count": 1647, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6913, "quality_score": 0.8457, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:58.646146", "source": { "split": "train_shard_00001", "doc_id": 667 }, "chunk_id": "train_shard_00001_667_0", "global_id": 6597 }, { "text": "NEAU-3TGS suggested that no genes involved in siderophore biosynthesis were found, and only the gene cluster FeuABCD and trilactone hydrolase genes involved in the uptake of siderophores, iron transporter and exporter are present. Molecular modelling and docking of FeuA (protein peptidoglycan siderophore-binding protein) and siderophores ferrienterobactine [Fe+3 (ENT)]-3 and ferribacillibactine [Fe+3 (BB)]-3 ligand revealed that [Fe+3 (ENT)]-3 binds to Phe122, Lys127, Ile100, Gln314, Arg215, Arg217, and Gln252. Almost the same for [Fe+3 (ENT)]-3 in addition to Cys222 and Tyr229, but not Ile100.To the best of our knowledge, this is the first report on the characterization of EPS and the adsorption of heavy metals by Psychrobacillus species. The heavy metal removal capabilities may be advantageous for using these organisms in metal remediation.\n\nGenome and pan-genome analysis of a new exopolysaccharide-producing bacterium Pyschrobacillus sp. isolated from iron ores deposit and insights into iron uptake.", "token_count": 401, "char_count": 1132, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7254, "quality_score": 0.8627, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:59.262724", "source": { "split": "train_shard_00001", "doc_id": 667 }, "chunk_id": "train_shard_00001_667_1", "global_id": 6598 }, { "text": "Bacterial genomes exhibit significant variation in gene content and sequence identity. Pangenome analyses explore this diversity by classifying genes into core and accessory clusters of orthologous groups (COGs). However, strict sequence identity cutoffs can misclassify divergent alleles as different genes, inflating accessory gene counts. CLARC (Connected Linkage and Alignment Redefinition of COGs) [ https://github.com/IndraGonz/CLARC ] improves pangenome analyses by condensing accessory COGs using functional annotation and linkage information. Through this approach, orthologous groups are consolidated into more practical units of selection. Analyzing 8,000+ Streptococcus pneumoniae genomes, CLARC reduced accessory gene estimates by more than 30% and improved evolutionary predictions based on accessory gene frequencies. By refining COG definitions, CLARC offers critical insights into bacterial evolution, aiding genetic studies across diverse populations.\n\nLinkage-based ortholog refinement in bacterial pangenomes with CLARC", "token_count": 242, "char_count": 1039, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7519, "quality_score": 0.876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T05:59:59.746799", "source": { "split": "train_shard_00001", "doc_id": 668 }, "chunk_id": "train_shard_00001_668_0", "global_id": 6599 }, { "text": "Bacterial genome analysis provides valuable insights into the identification of potential biomolecules for diverse biotechnological and therapeutic applications. Particularly, bacteria isolated from extreme environments such as mud volcanoes possess unique physiological and genetic traits that may offer novel opportunities for both in vitro studies and in silico drug target discovery. In this study, a total of 10 bacteria were isolated from Baratang mud volcano, located in Andaman and Nicobar Islands of India; of which strain BRTN was selected for further study based on its best ferrous sulfate (FeSO4 MTC value 600 mg L-1) tolerance capability and antibiotic sensitivity profile (resistant to Gentamycin, Streptomycin, Ceftriaxone, and Sulphatriad). Optimum growth of BRTN was found at pH 8.0 and it could tolerate up to 16% NaCl. The whole genome sequencing, assembly, and annotation identified that BRTN had the most proximity with Bacillus genera. The bacterium was associated with 3.35 Mb genome with 35.9% of GC content and harbored 3514 genes. Genome analysis revealed that Sulfur Utilization Factor (SUF) proteins was present in the accessory genome. Genome analyses confirmed the presence of SufB, SufC, SufD, SufE2, etc. SUF genes (non-homologous to human genome) that could be considered as potent targets to develop antimicrobial compounds. Furthermore, in silico analysis including homology modeling and receptor-ligand docking were carried out to characterize the selected SUF proteins and to assess their potentiality for functional inhibition by candidate ligands. Among all interactions, SufD showed best Vina score (-14.0) when it interacted with ChEMBL3921511, suggesting SufD protein as a potential drug target. Thus, the SUF system genes identified in this study may serve as promising targets for the development of novel antibacterial therapies.", "token_count": 489, "char_count": 1897, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:01.273130", "source": { "split": "train_shard_00001", "doc_id": 669 }, "chunk_id": "train_shard_00001_669_0", "global_id": 6600 }, { "text": "Physiological and genomic insights into Bacillus sp. BRTN from Baratang mud volcano with emphasis on SUF system proteins.", "token_count": 34, "char_count": 121, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:01.634243", "source": { "split": "train_shard_00001", "doc_id": 669 }, "chunk_id": "train_shard_00001_669_1", "global_id": 6601 }, { "text": "

Introduction

Outbreak investigation of foodborne salmonellosis is hindered when the food source is contaminated by multiple strains of Salmonella, creating difficulties matching an incriminated organism recovered from patients with the specific strain in the suspect food. An outbreak of the rare Salmonella Adjame was caused by multiple strains of the organism as revealed by single-nucleotide polymorphism (SNP) variation. The use of highly discriminatory prophage analysis to characterize strains of Salmonella should enable a more precise strain characterization and aid the investigation of foodborne salmonellosis.

Methods

We have carried out genomic analysis of S. Adjame strains recovered during the course of a recent outbreak and compared them with other strains of the organism (n = 38 strains), using SNPs to evaluate strain differences present in the core genome, and prophage sequence typing (PST) to evaluate the accessory genome. Phylogenetic analyses were performed using both total prophage content and conserved prophages.

Results

The PST analysis of the S. Adjame isolates showed a high degree of strain heterogeneity. We observed small clusters made up of 2-6 isolates (n = 27) and singletons (n = 11) in stark contrast with the three clusters observed by SNP analysis. In total, we detected 24 prophages of which only four were highly prevalent, namely: Entero_p88 (36/38 strains), Salmon_SEN34 (35/38 strains), Burkho_phiE255 (33/38 strains) and Edward_GF (28/38 strains)", "token_count": 466, "char_count": 1572, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:02.282506", "source": { "split": "train_shard_00001", "doc_id": 670 }, "chunk_id": "train_shard_00001_670_0", "global_id": 6602 }, { "text": "Despite the marked strain diversity seen with prophage analysis, the distribution of the four most common prophages matched the clustering observed using core genome.

Discussion

Mutations in the core and accessory genomes of S. Adjame have shed light on the evolutionary relationships among the Adjame strains and demonstrated a convergence of the variations observed in both fractions of the genome. We conclude that core and accessory genomes analyses should be adopted in foodborne bacteria outbreak investigations to provide a more accurate strain description and facilitate reliable matching of isolates from patients and incriminated food sources. The outcomes should translate to a better understanding of the microbial population structure and an 46 improved source attribution in foodborne illnesses.\n\nApplication of prophage sequence analysis to investigate a disease outbreak involving Salmonella Adjame, a rare serovar and implications for the population structure.", "token_count": 209, "char_count": 998, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6788, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:02.751182", "source": { "split": "train_shard_00001", "doc_id": 670 }, "chunk_id": "train_shard_00001_670_1", "global_id": 6603 }, { "text": "Antimicrobial resistance (AMR) in livestock represents a significant and growing One Health concern, with Escherichia coli acting as a major reservoir of resistance and virulence determinants. The present study analysed the whole-genome sequences of 172 E. coli strains of dairy cattle origin from 7 countries, which included ESBL (Extended-Spectrum β-Lactamase) (n = 63) and non-ESBL (n = 109) strains. The isolates showed high genetic diversity across 64 sequence types (STs) and seven phylogroups, with A (34.88 %) and B1 (34.30 %) being the most prevalent. The STs, ST10 (14.53 %) and ST224 (9.30 %), were the most dominant. Among the 86 distinct antimicrobial resistance genes (ARGs) identified, ESBL genes were prevalent, with blaCTX-M-1 (15.86 %) and blaCTX-M-15 (11.71 %) being most common. ESBL strains showed enriched ARG profiles, whereas non-ESBL strains exhibited greater ARG diversity. Among the 163 virulence-associated genes identified, terC (7.39 %, Tellurium ion resistance protein) and fdeC (6.18 %, intimin-like adhesin FdeC) were the most widespread, with phylogroups C and D exhibiting the highest cumulative virulence scores. Notably, ESBL-producing E. coli strains showed marginally higher virulence gene frequencies than their non-ESBL counterparts. The accessory genome was enriched with mobile genetic elements (MGEs), notably IS26 and IS5075 (linked to 26 and 13 ARGs), Tn2 (blaTEM variants), Tn1721/Tn6303 (tetA), and Tn801 (β-lactams)", "token_count": 506, "char_count": 1497, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [ "IS26", "ST224", "ST10", "IS5075" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:03.440156", "source": { "split": "train_shard_00001", "doc_id": 671 }, "chunk_id": "train_shard_00001_671_0", "global_id": 6604 }, { "text": "IncQ1 and IncF were the predominant plasmid vectors, with IncQ1 accounting for over 60 % of ARG-plasmid linkages. These findings provide important genomic associations of E. coli in dairy animals, highlighting the interplay of AMR gene mobility and virulence, and the importance of genomic surveillance in the dairy environment to prevent E. coli pathogen transmission into the human food chain.\n\nGenetic comparison of virulence and resistance factors in phylogenetically diverse Escherichia coli from dairy cattle.", "token_count": 128, "char_count": 515, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:03.883668", "source": { "split": "train_shard_00001", "doc_id": 671 }, "chunk_id": "train_shard_00001_671_1", "global_id": 6605 }, { "text": "

ABSTRACT

Sepsis (blood stream infection) caused by multidrug-resistant (MDR) bacteria, particularly Escherichia coli , represents a significant global health threat due to high morbidity, mortality, and limited treatment options. E. coli , a major causative agent of bloodstream infections, has evolved highly virulent and MDR strains, which contribute to the increasing burden of antimicrobial resistance (AMR), complicating clinical management and reducing the efficacy of conventional antibiotic therapies. In this study, we characterised the genomic and phenotypic drug resistance mechanism of E. coli 266631E isolated from a sepsis patient, highlighting the negative implications of MDR E. coli in sepsis. Antimicrobial susceptibility testing and minimum inhibitory concentration analysis revealed resistance to multiple antibiotics, including amoxicillin, cefotaxime, ciprofloxacin, gentamicin, and tobramycin. Whole genome sequencing identified a broad array of AMR genes encoding resistance to various antibiotic classes, such as macrolides, fluoroquinolones, aminoglycosides, carbapenems, and cephalosporins. Notably, the CTX-M-15 gene, a key extended-spectrum β-lactamase determinant, was found in both the bacterial chromosome and an IncF-type plasmid, emphasizing the potential for horizontal gene transfer and rapid dissemination of resistance. Confirming the taxonomy of the novel and unidentified bacterial strain through querying its 16S rRNA sequence and genome in recognised bacterial taxonomic databases presented a challenge. The isolate showed genetic similarity to E. coli, E. fergusonii , and Shigella species despite their phenotypic differences and variations in their pathogenic traits. However, a simple phenotypic laboratory procedure, based on the biochemical and cultural differences among these bacteria in Coliform ChromoSelect Agar, confirmed the isolate as E. coli . This study underscores the critical importance of integrating phenotypic methods with genomic tools for the accurate identification of clinically significant bacteria", "token_count": 516, "char_count": 2077, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6949, "quality_score": 0.8474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:04.565679", "source": { "split": "train_shard_00001", "doc_id": 672 }, "chunk_id": "train_shard_00001_672_0", "global_id": 6606 }, { "text": "It also highlights the need for both phenotypic and genetic surveillance of key MDR variants in healthcare settings to enable timely, precise diagnosis and targeted treatment of life-threatening infections such as sepsis.

DATA SUMMARY

The outputs of the MALDI-TOF analysis, AMR analysis using AMRFinderPlus, starAMR, and RGI, the query of bacterial 16S rRNA in the NCBI, Greengenes2, and SILVA databases, as well as Sourmash and pangenome analyses, are available in the supplementary material. The bacterial 16S rRNA gene sequence has been deposited in the NCBI GenBank database under accession number PQ871642 . The isolate’s complete genome sequence has been submitted to the NCBI Genome database under BioProject accession PRJNA1220687 and BioSample accession SAMN46722626. The chromosome is available under GenBank accession number CP183489 , while plasmids and other contigs are available under accession numbers CP183490 – CP183498 . The scripts used in the following bioinformatics analysis – Sourmash, Roary, and Prokka (for pangenome analysis) are available at: https://github.com/LucyDillon/MDR_isolate .

IMPACT STATEMENT

This study presents a comprehensive genomic and phenotypic characterization of a multidrug-resistant Escherichia coli strain implicated in sepsis, uncovering extensive antimicrobial resistance genes across both the chromosome and plasmids. It exposes taxonomic ambiguity with closely related species such as E. coli, Shigella , and E. fergusonii , underscoring gaps in current genomic databases and reinforcing the necessity of phenotypic testing. By integrating whole-genome sequencing with biochemical differentiation, the research strengthens diagnostic precision and informs clinical decision-making for life-threatening infections", "token_count": 496, "char_count": 1787, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [ "PRJNA1220687", "CP183498", "CP183490", "PQ871642", "SAMN46722626", "CP183489" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:05.239639", "source": { "split": "train_shard_00001", "doc_id": 672 }, "chunk_id": "train_shard_00001_672_1", "global_id": 6607 }, { "text": "Overall, it advances AMR and bacterial taxonomy research by demonstrating the value of an integrated genomic-phenotypic framework to accurately identify and guide the treatment and surveillance of emerging MDR pathogens in clinical settings.\n\nWhole-Genome Sequencing, Annotation and Phenotypic Taxonomic Confirmation of a Multidrug-Resistant Escherichia coli Strain Isolated from the Blood of a Sepsis Patient", "token_count": 109, "char_count": 416, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:05.619583", "source": { "split": "train_shard_00001", "doc_id": 672 }, "chunk_id": "train_shard_00001_672_2", "global_id": 6608 }, { "text": "

ABSTRACT

Genetic introgression from Neanderthals and Denisovan has shaped modern human genomes; however, introgressed structural variants (SVs ≥50 base pairs) remain challenging to discover. We integrated high-quality phased assemblies from four new Papua New Guinea (PNG) genomes with 94 published assemblies of diverse ancestry to infer an archaic introgressed SV map. Introgressed SVs are overall enriched in genes (44%, n=1,592), including critical genomic disorder regions, and most abundant in PNG. We identify 11 centromeres likely derived from archaic hominins, adding unexplored diversity to centromere genomics. Pangenome genotyping across 1,363 samples reveals 16 candidate adaptive SVs, many associated with immune-related genes and their expression, in the PNG. We hypothesize that archaic SV introgression contributed to reproductive success, underscoring introgression as a significant force in human adaptive evolution.\n\nA global map for introgressed structural variation and selection in humans", "token_count": 265, "char_count": 1020, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7737, "quality_score": 0.8869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:06.171223", "source": { "split": "train_shard_00001", "doc_id": 673 }, "chunk_id": "train_shard_00001_673_0", "global_id": 6609 }, { "text": "Effects of wine and dairy yeast fermentation on chemical constituents of tilapia fish head hydrolysate supplemented with glucose in an unsalted and acidic environment were investigated. Three wine yeasts (Torulaspora delbrueckii Biodiva, Saccharomyces cerevisiae Lalvin EC-1118 and Pichia kluyveri Frootzen) and one dairy yeast (Kluyveromyces marxianus NCYC1425) were employed as single starter cultures, respectively, and were compared with one soy sauce yeast (Candida versatilis NCYC1433). Each yeast showed different growth kinetics and fermentation performance. Compared with C. versatilis NCYC1433, other yeasts presented a significant higher rate of glucose consumption (P < 0.05). Besides, K. marxianus NCYC1425 and P. kluyveri Frootzen produced more citric acid and succinic acid, respectively, while S. cerevisiae Lalvin EC-1118 exhibited higher pyruvic acid production. Significant lower levels of total free amino acids were observed in samples inoculated with wine yeasts relative to other yeasts (P < 0.05). Non-soy sauce yeasts produced increased various levels of esters and alcohols without traditional fish sauce unpleasant odorants, especially K. marxianus NCYC1425 and P. kluyveri Frootzen. The results confirmed that non-soy sauce yeasts are suitable for fish sauce flavor compound modification and to develop a fast fermentation process for saltless fish sauce from fish head, which could increase the acceptability of fish sauce and improve the utilization of fish by-products.", "token_count": 493, "char_count": 1591, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6238, "quality_score": 0.8119, "entities": { "genes": [ "NCYC1425", "NCYC1433" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:06.828960", "source": { "split": "train_shard_00001", "doc_id": 674 }, "chunk_id": "train_shard_00001_674_0", "global_id": 6610 }, { "text": "Use of Wine and Dairy Yeasts as Single Starter Cultures for Flavor Compound Modification in Fish Sauce Fermentation.", "token_count": 31, "char_count": 116, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:07.185709", "source": { "split": "train_shard_00001", "doc_id": 674 }, "chunk_id": "train_shard_00001_674_1", "global_id": 6611 }, { "text": "

ABSTRACT

Yeasts are a diverse group of fungal microorganisms that are widely used to produce fermented foods and beverages. In Mexico, open fermentations are used to obtain spirits from agave plants. Despite the prevalence of this traditional practice throughout the country, yeasts have only been isolated and studied from a limited number of distilleries. To systematically describe the diversity of yeast species from open agave fermentations, here we generate the YMX.1.0 culture collection by isolating 4,524 strains from 68 sites in diverse climatic, geographical, and biological contexts. We used MALDI-TOF mass spectrometry for taxonomic classification and a subset of the strains was verified by ITS and D1/D2 sequencing. The most abundant species isolated from all producing regions were Saccharomyces cerevisiae , Pichia kudriavzevii , Pichia manshurica , and Kluyveromyces marxianus . Despite the great diversity of environmental conditions and production practices the composition of yeast communities remained largely homogeneous throughout locations and fermentation stages, even if less abundant but commonly occurring yeasts were considered. Furthermore, ITS and D1/D2 sequencing revealed two candidate new species of Saccharomycetales. To explore the intraspecific variation of the yeasts from agave fermentations, we conducted genome sequencing on four isolates of the non-conventional yeast Kazachstania humilis . The genomes of these four strains were considerably distinct from other genomes of the same species, suggesting that they belong to a different population. Our work contributes to the understanding and conservation of an open fermentation system of great cultural and economic importance, providing a valuable resource to study the biology and genetic diversity of microorganisms living at the interface of natural and human-associated environments.

TAKE AWAY

We isolated and identified 4,524 yeast strains from open agave fermentations in Mexico. Yeast communities remained largely homogeneous throughout diverse locations. Kazachstania humilis genomes differed significantly from isolates in other regions of the world. We report two candidate new species related to the Pichia clade.", "token_count": 507, "char_count": 2238, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5591, "quality_score": 0.7796, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:07.815251", "source": { "split": "train_shard_00001", "doc_id": 675 }, "chunk_id": "train_shard_00001_675_0", "global_id": 6612 }, { "text": "Yeast diversity in open agave fermentations across Mexico", "token_count": 12, "char_count": 57, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:08.163650", "source": { "split": "train_shard_00001", "doc_id": 675 }, "chunk_id": "train_shard_00001_675_1", "global_id": 6613 }, { "text": "Clostridium perfringens is the causative agent of many enterotoxic diseases in humans and animals, and it is present in diverse environments (soil, food, sewage, and water). Multilocus Sequence Typing (MLST) and Whole Genome Sequencing (WGS) have provided a general approach about genetic diversity of C. perfringens; however, those studies are limited to specific locations and often include a reduced number of genomes. In this study, 372 C. perfringens genomes from multiple locations and sources were used to assess the genetic diversity and phylogenetic relatedness of this pathogen. In silico MLST was used for typing the isolates, and the resulting sequence types (ST) were assigned to clonal complexes (CC) based on allelic profiles that differ from its founder by up to double-locus variants. A pangenome analysis was conducted, and a core genome-based phylogenetic tree was created to define phylogenetic groups. Additionally, key virulence factors, toxinotypes, and antibiotic resistance genes were identified using ABRicate against Virulence Factor Database (VFDB), TOXiper, and Resfinder, respectively. The majority of the C. perfringens genomes found in publicly available databases were derived from food (n = 85) and bird (n = 85) isolates. A total of 195 STs, some of them shared between sources such as food and human, horses and dogs, and environment and birds, were grouped in 25 CC and distributed along five phylogenetic groups. Fifty-three percent of the genomes were allocated to toxinotype A, followed by F (32%) and G (7%)", "token_count": 441, "char_count": 1597, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6751, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:08.794005", "source": { "split": "train_shard_00001", "doc_id": 676 }, "chunk_id": "train_shard_00001_676_0", "global_id": 6614 }, { "text": "The most frequently found virulence factors based on > 70% coverage and 99.95% identity were plc (100%), nanH (99%), ccp (99%), and colA (98%), which encode an alpha-toxin, a sialidase, an alpha-clostripain, and a collagenase, respectively, while tetA (39.5%) and tetB (36.2%), which mediate tetracycline resistance determinants, were the most common antibiotic resistance genes detected. The analyses conducted here showed a better view of the presence of this pathogen across several host species. They also confirm that the genetic diversity of C. perfringens is based on a large number of virulence factors that vary among phylogroups, and antibiotic resistance markers, especially to tetracyclines, aminoglycosides, and macrolides. Those characteristics highlight the importance of C. perfringens as a one of the most common causes of foodborne illness.\n\nIntra-species diversity of Clostridium perfringens: A diverse genetic repertoire reveals its pathogenic potential.", "token_count": 321, "char_count": 1037, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:09.362507", "source": { "split": "train_shard_00001", "doc_id": 676 }, "chunk_id": "train_shard_00001_676_1", "global_id": 6615 }, { "text": "This study investigated the interaction among Kluyveromyces marxianus G-Y4 (G-Y4), Lacticaseibacillus paracasei GL1 (GL1) and Lactobacillus helveticus SNA12 (SNA12) that isolated from Tibetan kefir grains. Additionally, the effects of G-Y4 on the growth and biofilm formation of GL1 and SNA12 were determined. The results indicated that G-Y4 promoted the growth of GL1 and SNA12 and improved their biofilm-forming ability. Furthermore, the dead cells of G-Y4 were found that could enhance bacterial biofilm formation, and the cell wall polysaccharide (CWPS) produced by G-Y4 was performed to be key substances that promote the formation of bacterial biofilms. Moreover, the structure of soluble cell wall polysaccharides (SCWP) and insoluble cell wall polysaccharide (NCWP) of G-Y4 were studied to determine their contribution to biofilm formation. Results showed that G-Y4-SCWP was α-mannan with the main chain of a →6)-α-d-Manp-(1→ unit and the branch structure of →2)-α-d-Manp-(1. At the same time, G-Y4-NCWP was a glucan rich in β-(1→3), β-(1→2), or β-(1→4) linkages.\n\nYeast cell wall polysaccharides in Tibetan kefir grains are key substances promoting the formation of bacterial biofilm", "token_count": 365, "char_count": 1192, "word_count": 173, "semantic_coherence": 1, "information_density": 0.5838, "quality_score": 0.7919, "entities": { "genes": [ "GL1", "SNA12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:09.943219", "source": { "split": "train_shard_00001", "doc_id": 677 }, "chunk_id": "train_shard_00001_677_0", "global_id": 6616 }, { "text": "Linear reference genomes are ubiquitously used in genomics research, despite known biases associated with their use. In recent years, there has a been a shift towards using graph-based reference genomes to address some of these biases, which has required new algorithms and file formats to be developed. This has created the need to develop new tools capable of utilizing these formats and performing operations similar to those carried out by traditional methods.In this paper we present “gaftools”, a multi-purpose tool that introduces several utilities for processing graph alignments in GAF format. Gaftools enables users to index and sort alignments, with graph ordering serving as a necessary step for the sorting process. Additionally it allows users to view subsets of alignments and perform realignment using the wavefront alignment algorithm, among other useful features. Many of these functionalities are inspired by SAMtools, which provide similar operations for linear genomes, while gaftools adapts and extends them for pangenomes.

Availability

gaftools is available under MIT license at https://github.com/marschall-lab/gaftools .\n\ngaftools: a toolkit for analyzing and manipulating pangenome alignments", "token_count": 266, "char_count": 1227, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:10.502409", "source": { "split": "train_shard_00001", "doc_id": 678 }, "chunk_id": "train_shard_00001_678_0", "global_id": 6617 }, { "text": "

Introduction

Bacteria of genus Pectobacterium, encompassing economically significant pathogens affecting various plants, includes the species P. betavasculorum, initially associated with beetroot infection. However, its host range is much broader. It causes diseases of sunflower, potato, tomato, carrots, sweet potato, radish, squash, cucumber, and chrysanthemum. To explain this phenomenon, a comprehensive pathogenomic and phenomic characterisation of P. betavasculorum species was performed.

Methods

Genomes of P. betavasculorum strains isolated from potato, sunflower, and artichoke were sequenced and compared with those from sugar beet isolates. Metabolic profiling and pathogenomic analyses were conducted to assess virulence determinants and adaptation potential. Pathogenicity assays were performed on potato tubers and chicory leaves to confirm in silico predictions of disease symptoms. Phenotypic assays were also conducted to assess the strains ability to synthesise homoserine lactones and siderophores.

Results

The genome size ranged from 4.675 to 4.931 kbp, and GC % was between 51.0% and 51.2%. The pangenome of P. betavasculorum is open and comprises, on average, 4,220 gene families. Of these, 83% of genes are the core genome, and 2% of the entire pangenome are unique genes. Strains isolated from sugar beet have a smaller pangenome size and a higher number of unique genes than those from other plants. Interestingly, genomes of strains from artichoke and sunflower share 391 common CDS that are not present in the genomes of other strains from sugar beet or potato. Those strains have only one unique gene. All strains could use numerous sugars as building materials and energy sources and possessed a high repertoire of virulence determinants in the genomes. P", "token_count": 516, "char_count": 1852, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8137, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:11.157083", "source": { "split": "train_shard_00001", "doc_id": 679 }, "chunk_id": "train_shard_00001_679_0", "global_id": 6618 }, { "text": "betavasculorum strains were able to cause disease symptoms on potato tubers and chicory leaves. They were also able to synthesise homoserine lactones and siderophores.

Discussion

The findings underscore the adaptability of P. betavasculorum to diverse hosts and environments. Strains adapted to plants with high sugar content in tissues have a different composition of fatty acids in membranes and a different mechanism of replenishing nitrogen in case of deficiency of this compound than strains derived from other plant species. Extensive phenomics and genomic analyses performed in this study have shown that P. betavasculorum species is an agronomically relevant pathogen.\n\nComparative genomics, pangenomics, and phenomic studies of Pectobacterium betavasculorum strains isolated from sugar beet, potato, sunflower, and artichoke: insights into pathogenicity, virulence determinants, and adaptation to the host plant.", "token_count": 248, "char_count": 953, "word_count": 125, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:11.640920", "source": { "split": "train_shard_00001", "doc_id": 679 }, "chunk_id": "train_shard_00001_679_1", "global_id": 6619 }, { "text": "A prevalent food-borne pathogen, Salmonella enterica serotypes Typhi, is responsible for gastrointestinal and systemic infections globally. Salmonella vaccines are the most effective, however, producing a broad-spectrum vaccine remains challenging due to Salmonella's many serotypes. Efforts are urgently required to develop a novel vaccine candidate that can tackle all S. Typhi strains because of their high resistance to multiple kinds of antibiotics (particularly the XDR H58 strain). In this work, we used a computational pangenome-based vaccine design technique on all available (n = 119) S. Typhi reference genomes and identified one TonB-dependent siderophore receptor (WP_001034967.1) as highly conserved and prospective vaccine candidates from the predicted core genome (n = 3,351). The applied pan-proteomics and Immunoinformatic approaches help in the identification of four epitopes that may trigger adequate host body immune responses. Furthermore, the proposed vaccine ensemble demonstrates a stable binding conformation with the examined immunological receptor (HLAs and TRL2/4) and has large interaction energy determined via molecular docking and molecular dynamics simulation techniques. Eventually, an expression vector for the Escherichia. coli K12 strain was constructed from the vaccine sequence. Additional analysis revealed that the vaccine may help to elicit strong immune responses for typhoid infections, however, experimental analysis is required to verify the vaccine's effectiveness based on these results. Moreover, the applied computer-assisted vaccine design may considerably decrease vaccine development costs and speed up the process. The study's findings are intriguing, but they must be evaluated in the experimental labs to confirm the developed vaccine's biological efficiency against XDR S. Typhi.Communicated by Ramaswamy H. Sarma.", "token_count": 488, "char_count": 1943, "word_count": 254, "semantic_coherence": 1, "information_density": 0.7165, "quality_score": 0.8583, "entities": { "genes": [ "TRL2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:12.287065", "source": { "split": "train_shard_00001", "doc_id": 680 }, "chunk_id": "train_shard_00001_680_0", "global_id": 6620 }, { "text": "A therapeutic epitopes-based vaccine engineering against Salmonella enterica XDR strains for typhoid fever: a Pan-vaccinomics approach.", "token_count": 43, "char_count": 142, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:12.649063", "source": { "split": "train_shard_00001", "doc_id": 680 }, "chunk_id": "train_shard_00001_680_1", "global_id": 6621 }, { "text": "Amphotericin-B-liposomal/dexamethasone/methylprednisolone : Invasive candida kefyr infection, off label use and drug resistance: case report", "token_count": 47, "char_count": 140, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:13.006596", "source": { "split": "train_shard_00001", "doc_id": 681 }, "chunk_id": "train_shard_00001_681_0", "global_id": 6622 }, { "text": "Genetic distances between bacterial DNA sequences can be used to cluster populations into closely related subpopulations, and as an additional source of information when detecting possible transmission events. Due to their variable gene content and order, reference-free methods offer more sensitive detection of genetic differences, especially among closely related samples found in outbreaks. However, across longer genetic distances, frequent recombination can make calculation and interpretation of these differences more challenging, requiring significant bioinformatic expertise and manual intervention during the analysis process. Here we present a Pop ulation analysis PIPE line (PopPIPE) which combines rapid reference-free genome analysis methods to analyse bacterial genomes across these two scales, splitting whole populations into subclusters and detecting plausible transmission events within closely related clusters. We use k-mer sketching to split populations into strains, followed by split k-mer analysis and recombination removal to create alignments and subclusters within these strains. We first show that this approach creates high quality subclusters on a population-wide dataset of Streptococcus pneumoniae . When applied to nosocomial vancomycin resistant Enterococcus faecium samples, PopPIPE finds transmission clusters which are more epidemiologically plausible than core genome or MLST-based approaches. Our pipeline is rapid and reproducible, creates interactive visualisations, and can easily be reconfigured and re-run on new datasets. Therefore PopPIPE provides a user-friendly pipeline for analyses spanning species-wide clustering to outbreak investigations.

Impact statement

As time passes, bacterial genomes accumulate small changes in their sequence due to mutations, or larger changes in their content due to horizontal gene transfer. Using their genome sequences, it is possible to use phylogenetics to work out the most likely order in which these changes happened, and how long they took to happen. Then, one can estimate the time that separates any two bacterial samples – if it is short then they may have been directly transmitted or acquired from the same source; but if it is long they must have been acquired separately. This information can be used to determine transmission chains, in conjunction with dates and locations of infections. Understanding transmission chains enables targeted infection control measures", "token_count": 491, "char_count": 2474, "word_count": 342, "semantic_coherence": 1, "information_density": 0.6374, "quality_score": 0.8187, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:13.660264", "source": { "split": "train_shard_00001", "doc_id": 682 }, "chunk_id": "train_shard_00001_682_0", "global_id": 6623 }, { "text": "However, correctly calculating the genetic evidence for transmission is made difficult by correctly distinguishing different types of sequence changes, dealing with large amounts of genome data, and the need to use multiple complex bioinformatic tools. We addressed this gap by creating a computational workflow, PopPIPE, which automates the process of detecting possible transmissions using genome sequences. PopPIPE applies state-of-the-art tools and is fast and easy to run – making this technology will be available to a wider audience of researchers.

Data summary

The code for this pipeline is available at https://github.com/bacpop/PopPIPE and as a docker image https://hub.docker.com/r/poppunk/poppipe . Raw sequencing reads for Enterococcus faecium isolates have been deposited at the NCBI under BioProject accession number PRJNA997588.\n\nIntegrated population clustering and genomic epidemiology with PopPIPE", "token_count": 221, "char_count": 925, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7742, "quality_score": 0.8871, "entities": { "genes": [ "PRJNA997588" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:14.118677", "source": { "split": "train_shard_00001", "doc_id": 682 }, "chunk_id": "train_shard_00001_682_1", "global_id": 6624 }, { "text": "The core perturbome is defined as a central response to multiple disturbances, functioning as a complex molecular network to overcome the disruption of homeostasis under stress conditions, thereby promoting tolerance and survival under stress conditions. Based on the biological and clinical relevance of Escherichia coli and Staphylococcus aureus, we characterized their molecular responses to multiple perturbations. Gene expression data from E. coli (8815 target genes-based on a pangenome-across 132 samples) and S. aureus (3312 target genes across 156 samples) were used. Accordingly, this study aimed to identify and describe the functionality of the core perturbome of these two prokaryotic models using a machine learning approach. For this purpose, feature selection and classification algorithms (KNN, RF and SVM) were implemented to identify a subset of genes as core molecular signatures, distinguishing control and perturbation conditions. After verifying effective dimensional reduction (with median accuracies of 82.6% and 85.1% for E. coli and S. aureus, respectively), a model of molecular interactions and functional enrichment analyses was performed to characterize the selected genes. The core perturbome was composed of 55 genes (including nine hubs) for E. coli and 46 (eight hubs) for S. aureus. Well-defined interactomes were predicted for each model, which are jointly associated with enriched pathways, including energy and macromolecule metabolism, DNA/RNA and protein synthesis and degradation, transcription regulation, virulence factors, and other signaling processes. Taken together, these results may support the identification of potential therapeutic targets and biomarkers of stress responses in future studies.\n\nCore Perturbomes of <i>Escherichia coli</i> and <i>Staphylococcus aureus</i> Using a Machine Learning Approach.", "token_count": 498, "char_count": 1939, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:14.776865", "source": { "split": "train_shard_00001", "doc_id": 683 }, "chunk_id": "train_shard_00001_683_0", "global_id": 6625 }, { "text": "The uncontrolled growth of potential spoilage microorganisms in cheese surfaces can deteriorate cheese quality, especially filamentous fungi. This study aimed to evaluate the effect of several gaseous ozone treatments during the ripening of soft cheese on the growth of cheese rind microorganisms at different production scales. On a pilot plant scale, the cheeses were inoculated with potential spoilage microorganisms (Mucor plumbeus, Kluyveromyces marxianus, and Pseudomonas fluorescens), while on an industrial scale, naturally present microorganisms were evaluated. Ozone treatments showed a considerable fungistatic effect on cheese surface molds at both pilot and industrial scale. However, the effect of ozone on yeast growth was only observed at pilot plant scale, while Pseudomonas ssp. was not affected by the ozone concentrations used in this study. The sensory quality of the cheese was also assessed. Cheese typicality was not affected by gaseous ozone. However, the ozonized samples had significantly higher scores than the control samples for rind appearance and color. Hence, ozonation can be considered an alternative approach to control mold growth in soft cheese during ripening and prevent cheese rind discoloration.\n\nUse of gaseous ozone in soft cheese ripening: Effect on the rind microorganisms and the sensorial quality", "token_count": 307, "char_count": 1344, "word_count": 195, "semantic_coherence": 1, "information_density": 0.5333, "quality_score": 0.7667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:15.396459", "source": { "split": "train_shard_00001", "doc_id": 684 }, "chunk_id": "train_shard_00001_684_0", "global_id": 6626 }, { "text": "Plant genome sequences catalogue genes and the genetic elements that regulate their expression. Such inventories further research aims as diverse as mapping the molecular basis of trait diversity in domesticated plants or inquiries into the origin of evolutionary innovations in flowering plants millions of years ago. The transformative technological progress of DNA sequencing in the past two decades has enabled researchers to sequence ever more genomes with greater ease. Pangenomes - complete sequences of multiple individuals of a species or higher taxonomic unit - have now entered the geneticists' toolkit. The genomes of crop plants and their wild relatives are being studied with translational applications in breeding in mind. But pangenomes are applicable also in ecological and evolutionary studies, as they help classify and monitor biodiversity across the tree of life, deepen our understanding of how plant species diverged and show how plants adapt to changing environments or new selection pressures exerted by human beings.\n\nPlant pangenomes for crop improvement, biodiversity and evolution.", "token_count": 218, "char_count": 1110, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7055, "quality_score": 0.8528, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:15.875326", "source": { "split": "train_shard_00001", "doc_id": 685 }, "chunk_id": "train_shard_00001_685_0", "global_id": 6627 }, { "text": "In Bangladesh, Vibrio cholerae lineages are undergoing genomic evolution, with increased virulence and spreading ability. However, our understanding of the genomic determinants influencing lineage transmission and disease severity remains incomplete. Here, we developed a computational framework using machine-learning, genome scale metabolic modelling (GSSM) and 3D structural analysis, to identify V. cholerae genomic traits linked to lineage transmission and disease severity. We analysed in-patients isolates from six Bangladeshi regions (2015-2021), and uncovered accessory genes and core SNPs unique to the most recent dominant lineage, with virulence, motility and bacteriophage resistance functions. We also found a strong correlation between V. cholerae genomic traits and disease severity, with some traits overlapping those driving lineage transmission. GSMM and 3D structure analysis unveiled a complex interplay between transcription regulation, protein interaction and stability, and metabolic networks, associated to lifestyle adaptation, intestinal colonization, acid tolerance and symptom severity. Our findings support advancing therapeutics and targeted interventions to mitigate cholera spread.\n\nCore and accessory genomic traits of Vibrio cholerae O1 drive lineage transmission and disease severity.", "token_count": 297, "char_count": 1320, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6805, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:16.455417", "source": { "split": "train_shard_00001", "doc_id": 686 }, "chunk_id": "train_shard_00001_686_0", "global_id": 6628 }, { "text": "Mycoplasma ovipneumoniae is associated with respiratory disease in wild and domestic Caprinae globally, with wide variation in disease outcomes within and between host species. To gain insight into phylogenetic structure and mechanisms of pathogenicity for this bacterial species, we compared M. ovipneumoniae genomes for 99 samples from six countries (Australia, Bosnia and Herzegovina, Brazil, China, France, USA) and four host species (domestic sheep, domestic goats, bighorn sheep, caribou). Core genome sequences of M. ovipneumoniae assemblies from domestic sheep and goats fell into two well-supported phylogenetic clades that are divergent enough to be considered different bacterial species, consistent with each of these two clades having an evolutionary origin in separate host species. Genome assemblies from bighorn sheep and caribou also fell within these two clades, indicating multiple spillover events, most commonly from domestic sheep. Pangenome analysis indicated a high percentage (91.4%) of accessory genes (i.e., genes found only in a subset of assemblies) compared to core genes (i.e., genes found in all assemblies), potentially indicating a propensity for this pathogen to adapt to within-host conditions. In addition, many genes related to carbon metabolism, which is a virulence factor for Mycoplasmas, showed evidence for homologous recombination, a potential signature of adaptation. The presence or absence of annotated genes was very similar between sheep and goat clades, with only two annotated genes significantly clade-associated. However, three M. ovipneumoniae genome assemblies from asymptomatic caribou in Alaska formed a highly divergent subclade within the sheep clade that lacked 23 annotated genes compared to other assemblies, and many of these genes had functions related to carbon metabolism. Overall our results provide evidence that adaptation of M. ovipneumoniae has involved evolution of carbon metabolism pathways and virulence mechanisms related to those pathways. The genes involved in these pathways, along with other genes identified as potentially involved in virulence in this study, are potential targets for future investigation into a possible genomic basis for the high variation observed in disease outcomes within and between wild and domestic host species", "token_count": 521, "char_count": 2319, "word_count": 331, "semantic_coherence": 1, "information_density": 0.5408, "quality_score": 0.7704, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:17.150390", "source": { "split": "train_shard_00001", "doc_id": 687 }, "chunk_id": "train_shard_00001_687_0", "global_id": 6629 }, { "text": "

Data Summary

Raw sequence data and genome assemblies generated for this study have been deposited with the National Center for Biotechnology Information (NCBI) under BioProject number PRJNA1070810. Assemblies are also currently available for download through Dryad with the following link: https://datadryad.org/stash/share/aNet7o-xag3PTjJ0_A_BDoOPUpHHshArGW1eJMfLYl4 NCBI accession numbers and associated metadata for each assembly are available in the Supplemental Materials. DNA sequences extracted from these assemblies for four genetic markers (gyrB, rpoB, 16S, IGS) are available in the Supplemental Materials. Analysis code is available at https://github.com/kimandrews/Movi and an interactive phylogeny is available at https://nextstrain.org/community/narratives/kimandrews/Movi

Impact statement

Mycoplasma ovipneumoniae causes respiratory disease in wild and domestic sheep and goats around the world, resulting in economic losses for the domestic sheep industry and severe population declines for wild species. Disease outcomes vary widely within and between host species, and this variation could be influenced by genomic differences across bacterial strains. We compared M. ovipneumoniae genomes from six countries and four host species and found species-level divergence for strains from domestic goats versus domestic sheep, indicating separate evolutionary origins in these two host species. All wildlife strains fell within these two groups, providing evidence that these strains originated by transmission from domestic populations. We identified genes potentially involved in adaptation to hosts, which could be responsible for differences in disease outcomes across bacterial strains and host species. Many of these genes had functions related to carbon metabolism, a potential virulence factor for Mycoplasmas.\n\nComparative genomic analysis identifies potential adaptive variation and virulence factors inMycoplasma ovipneumoniae", "token_count": 470, "char_count": 1974, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [ "PRJNA1070810" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:17.794820", "source": { "split": "train_shard_00001", "doc_id": 687 }, "chunk_id": "train_shard_00001_687_1", "global_id": 6630 }, { "text": "

Introduction

An elastic-degenerate (ED) string is a sequence of sets of strings. It can also be seen as a directed acyclic graph whose edges are labeled by strings. The notion of ED strings was introduced as a simple alternative to variation and sequence graphs for representing a pangenome, that is, a collection of genomic sequences to be analyzed jointly or to be used as a reference.

Methods

In this study, we define notions of matching statistics of two ED strings as similarity measures between pangenomes and, consequently infer a corresponding distance measure. We then show that both measures can be computed efficiently, in both theory and practice, by employing the intersection graph of two ED strings.

Results

We also implemented our methods as a software tool for pangenome comparison and evaluated their efficiency and effectiveness using both synthetic and real datasets.

Discussion

As for efficiency, we compare the runtime of the intersection graph method against the classic product automaton construction showing that the intersection graph is faster by up to one order of magnitude. For showing effectiveness, we used real SARS-CoV-2 datasets and our matching statistics similarity measure to reproduce a well-established clade classification of SARS-CoV-2, thus demonstrating that the classification obtained by our method is in accordance with the existing one.\n\nPangenome comparison via ED strings.", "token_count": 325, "char_count": 1465, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6143, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:18.361806", "source": { "split": "train_shard_00001", "doc_id": 688 }, "chunk_id": "train_shard_00001_688_0", "global_id": 6631 }, { "text": "

Background

Sunflower (Helianthus annuus) is one of the most important economic crops in oilseed production worldwide. The different cultivars exhibit variability in their resistance genes. The NAC transcription factor (TF) family plays diverse roles in plant development and stress responses. With the completion of the H. annuus genome sequence, the entire complement of genes coding for NACs has been identified. However, the reference genome of a single individual cannot cover all the genetic information of the species.

Results

Considering only a single reference genome to study gene families will miss many meaningful genes. A pangenome-wide survey and characterization of the NAC genes in sunflower species were conducted. In total, 139 HaNAC genes are identified, of which 114 are core and 25 are variable. Phylogenetic analysis of sunflower NAC proteins categorizes these proteins into 16 subgroups. 138 HaNACs are randomly distributed on 17 chromosomes. SNP-based haplotype analysis shows haplotype diversity of the HaNAC genes in wild accessions is richer than in landraces and modern cultivars. Ten HaNAC genes in the basal stalk rot (BSR) resistance quantitative trait loci (QTL) are found. A total of 26 HaNAC genes are differentially expressed in response to Sclerotinia head rot (SHR). A total of 137 HaNAC genes are annotated in Gene Ontology (GO) and are classified into 24 functional groups. GO functional enrichment analysis reveals that HaNAC genes are involved in various functions of the biological process.

Conclusions

We identified NAC genes in H. annuus (HaNAC) on a pangenome-wide scale and analyzed S. sclerotiorum resistance-related NACs. This study provided a theoretical basis for further genomic improvement targeting resistance-related NAC genes in sunflowers.\n\nPangenome characterization and analysis of the NAC gene family reveals genes for Sclerotinia sclerotiorum resistance in sunflower (Helianthus annuus).", "token_count": 509, "char_count": 1968, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:19.018035", "source": { "split": "train_shard_00001", "doc_id": 689 }, "chunk_id": "train_shard_00001_689_0", "global_id": 6632 }, { "text": "

ABSTRACT

In prokaryotes lateral gene transfer (LGT) is a key mechanism leading to intra-species variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that include Aureococcus anophagefferens – a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and within Aureococcus anophagefferens , we used long-read sequencing to produce high-quality genome assemblies for five strains of Ac. anophagefferens (52-54 megabase-pairs; Mbp), a telomere-to-telomere assembly for Pelagomonas calceolata (32 Mbp), and the first reference genome for Aureoumbra lagunensis (41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain level genetic variation in Ac. anophagefferens with a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation within Ac. anophagefferens does not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found in P. calceolata or Au. lagunensis . 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.\n\nPangenome biology and evolution in harmful algal-bloom-forming pelagophyte algae", "token_count": 480, "char_count": 1637, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6577, "quality_score": 0.8288, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:19.664421", "source": { "split": "train_shard_00001", "doc_id": 690 }, "chunk_id": "train_shard_00001_690_0", "global_id": 6633 }, { "text": "Priestia megaterium strain AB-S79 isolated from active gold mine soil previously expressed in vitro heavy metal resistance and has a 5.7 Mb genome useful for biotechnological exploitation. This study used web-based bioinformatic resources to analyze P. megaterium AB-S79 genomic relatedness, decipher its secondary metabolite biosynthetic gene clusters (BGCs), and better comprehend its taxa. Genes were highly conserved across the 14 P. megaterium genomes examined here. The pangenome reflected a total of 61,397 protein-coding genes, 59,745 homolog protein family hits, and 1,652 singleton protein family hits. There were also 7,735 protein families, including 1,653 singleton families and 6,082 homolog families. OrthoVenn3 comparison of AB-S79 protein sequences with 13 other P. megaterium strains, 7 other Priestia spp., and 6 other Bacillus spp. highlighted AB-S79's unique genomic and evolutionary trait. antiSMASH identified two key transcription factor binding site regulators in AB-S79's genome: zinc-responsive repressor (Zur) and antibiotic production activator (AbrC3), plus putative enzymes for the biosynthesis of terpenes and ranthipeptides. AB-S79 also harbors BGCs for two unique siderophores (synechobactins and schizokinens), phosphonate, dienelactone hydrolase family protein, and phenazine biosynthesis protein (phzF), which is significant for this study. Phosphonate particularly showed specificity for the P. megaterium sp. validating the effect of gene family expansion and contraction. P. megaterium AB-S79 looks to be a viable source for value-added compounds", "token_count": 523, "char_count": 1656, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7336, "quality_score": 0.8668, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:20.322044", "source": { "split": "train_shard_00001", "doc_id": 691 }, "chunk_id": "train_shard_00001_691_0", "global_id": 6634 }, { "text": "Thus, this study contributes to the theoretical framework for the systematic metabolic and genetic exploitation of the P. megaterium sp., particularly the value-yielding strains.

Importance

This study explores microbial natural product discovery using genome mining, focusing on Priestia megaterium. Key findings highlight the potential of P. megaterium, particularly strain AB-S79, for biotechnological applications. The research shows a limited output of P. megaterium genome sequences from Africa, emphasizing the importance of the native strain AB-S79. Additionally, the study underlines the strain's diverse metabolic capabilities, reinforcing its suitability as a model for microbial cell factories and its foundational role in future biotechnological exploitation.\n\nUnveiling novel features and phylogenomic assessment of indigenous <i>Priestia megaterium</i> AB-S79 using comparative genomics.", "token_count": 249, "char_count": 948, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7257, "quality_score": 0.8628, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:20.805113", "source": { "split": "train_shard_00001", "doc_id": 691 }, "chunk_id": "train_shard_00001_691_1", "global_id": 6635 }, { "text": "During pretreatment of lignocellulosic biomass, toxic compounds were released and inhibited the growth and fermentation of microorganisms. Here the global transcriptional response of K. marxianus to multiple inhibitors including acetic acid, phenols, furfural and HMF, at 42 °C, was studied, via RNA-seq technology. Genes involved in the glycolysis pathway, fatty acid metabolism, ergosterol metabolism and vitamin B6 and B1 metabolic process were enriched in the down-regulated gene set, while genes involved in TCA cycle, respiratory chain, ROS detoxification and transporter coding genes were enriched in the up-regulated gene set in response to the multiple inhibitors stress. Further real time-PCR results with three single inhibitor stress conditions showed that different transporters responded quite differently to different inhibitor stress. Coenzyme assay results showed that the level of NAD+ was increased and both NADH/NAD+ and NADPH/NADP+ ratio decreased. Furthermore, genes involved with transcription factors related to carbohydrate metabolism, sulfur amino acids metabolism, lipid metabolism or those directly involved in the transcriptional process were significantly regulated. Though belonging to different GO categories or KEGG pathway, many differentially expressed genes were enriched in maintaining the redox balance, NAD(P)+/NAD(P)H homeostasis or NAD+ synthesis, energy production, and iron transportation or metabolism. These results suggest that engineering these aspects represents a possible strategy to develop more robust strains for industrial fermentation from cellulosic biomass.\n\nTranscriptomic analysis of thermotolerant yeast Kluyveromyces marxianus in multiple inhibitors tolerance.", "token_count": 464, "char_count": 1797, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:21.447690", "source": { "split": "train_shard_00001", "doc_id": 692 }, "chunk_id": "train_shard_00001_692_0", "global_id": 6636 }, { "text": "

Background

Borrelia afzelii and Borrelia garinii are the leading causes of Lyme borreliosis (LB) in Europe. Persistent LB forms may involve biofilms, potentially contributing to antibiotic tolerance.

Methods

Whole genome sequencing (WGS) was conducted on 7 B. afzelii and 5 B. garinii isolates from erythema migrans skin biopsies. Biofilms were analyzed for extracellular DNA (eDNA) content and biomass. A phenol red metabolic assay assessed the minimum inhibitory concentration (MIC) and minimum biofilm inhibitory concentration (MBIC) of amoxicillin, azithromycin, ceftriaxone, and doxycycline.

Results

Phylogenetic analysis revealed B. afzelii and B. garinii formed distinct clades, while B. burgdorferi B31 clustered separately. Core genome analysis showed 38.9% of genes were shared between B. afzelii and B. garinii, decreasing to 26.1% with B. burgdorferi. The cloud genome expanded from 34.4% to 53.4% with the addition of B. burgdorferi. No antimicrobial resistance genes were detected. Surface adhesion gene profiles exhibited significant variation across species, suggesting potential functional differences in host adaptation. B. afzelii and B. garinii species exhibited biofilms, with biomass correlating significantly with eDNA production. MIC values were 0.25 μg/mL (amoxicillin, ceftriaxone), 0.125 μg/mL (azithromycin), and 0.5 μg/mL (doxycycline), with no significant interspecies differences", "token_count": 525, "char_count": 1523, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:22.108937", "source": { "split": "train_shard_00001", "doc_id": 693 }, "chunk_id": "train_shard_00001_693_0", "global_id": 6637 }, { "text": "However, MBIC values were considerably higher: 2 μg/mL (amoxicillin, azithromycin), 16 μg/mL (ceftriaxone), and 32 μg/mL (doxycycline).

Conclusions

Biofilms in B. afzelii and B. garinii significantly reduce antibiotic efficacy, particularly ceftriaxone and doxycycline. These in vitro findings highlight the need for targeted therapeutic strategies and suggest biofilms may impact treatment outcomes in LB.\n\nGenomic characterization and antibiotic susceptibility of biofilm-forming <i>Borrelia afzelii</i> and <i>Borrelia garinii</i> from patients with erythema migrans.", "token_count": 225, "char_count": 622, "word_count": 68, "semantic_coherence": 1, "information_density": 0.8382, "quality_score": 0.9191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:22.572901", "source": { "split": "train_shard_00001", "doc_id": 693 }, "chunk_id": "train_shard_00001_693_1", "global_id": 6638 }, { "text": "Acinetobacter baumannii is a common cause of multidrug-resistant (MDR) nosocomial infections around the world. However, little is known about the persistence and dynamics of A. baumannii in a healthy community. This study investigated the role of the community as a prospective reservoir for A. baumannii and explored possible links between hospital and community isolates. A total of 12 independent A. baumannii strains were isolated from human faecal samples from the community in Segamat, Malaysia, in 2018 and 2019. Another 15 were obtained in 2020 from patients at the co-located tertiary public hospital. The antimicrobial resistance profile and biofilm formation ability were analysed, and the relatedness of community and hospital isolates was determined using whole-genome sequencing (WGS). Antibiotic profile analysis revealed that 12 out of 15 hospital isolates were MDR, but none of the community isolates were MDR. However, phylogenetic analysis based on single-nucleotide polymorphisms (SNPs) and a pangenome analysis of core genes showed clustering between four community and two hospital strains. Such clustering of strains from two different settings based on their genomes suggests that these strains could persist in both. WGS revealed 41 potential resistance genes on average in the hospital strains, but fewer (n=32) were detected in the community strains. In contrast, 68 virulence genes were commonly seen in strains from both sources. This study highlights the possible transmission threat to public health posed by virulent A. baumannii present in the gut of asymptomatic individuals in the community.\n\nMolecular characterization and comparative genomic analysis of Acinetobacter baumannii isolated from the community and the hospital: an epidemiological study in Segamat, Malaysia.", "token_count": 478, "char_count": 1856, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5611, "quality_score": 0.7805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:23.220602", "source": { "split": "train_shard_00001", "doc_id": 694 }, "chunk_id": "train_shard_00001_694_0", "global_id": 6639 }, { "text": "

Background

India, with the world’s largest cattle population and more than 50 registered breeds of Bos indicus , stands as a vital reservoir of genetic diversity. However, the abundant diversity among Indian cattle breeds highlights the inadequacy of a single reference sequence to represent the entire genomic content of desi cattle. We recognize the need to capture the genomic differences within the Bos indicus population as a whole, and specifically within the dairy cattle subset by identifying non-reference sequences and constructing a pangenome.

Finding

Five representative genomes of prominent dairy breeds, including Gir, Kankrej, Tharparkar, Sahiwal, and Red Sindhi, were sequenced using 10X Genomics ’Linked-Read’ technology. Assemblies generated from these linked-reads ranged from 2.70 Gb to 2.77 Gb,comparable to the Bos indicus Brahman reference genome. A pangenome of Bos indicus cattle was constructed by comparing the newly assembled genomes with the reference using alignment and graph-based methods, revealing 8 Mb and 17.7 Mb of novel sequence respectively. A confident set of 6,844 Non-Reference Unique Insertions (NUIs) spanning 7.57 Mbs was identified through both methods, representing the pangenome of Indian Bos indicus breeds. Comparative analysis with previously published pangenomes unveiled 2.8 Mb (37%) commonality with the Chinese indicine pangenome and only 1% commonality with the Bos taurus pangenome. Among these, 2,312 NUIs - encompassing ∼2 Mb, were commonly found in 98 samples of the 5 breeds and designated as Bos indicus Common Insertions (BICIs) in the population. Furthermore, 926 BICIs were identified within 682 protein-coding genes, 54 long non-coding RNAs (LncRNA), and 18 pseudogenes. These protein-coding genes were enriched for functions such as chemical synaptic transmission, cell junction organization, cell-cell adhesion, and cell morphogenesis", "token_count": 507, "char_count": 1920, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:23.879055", "source": { "split": "train_shard_00001", "doc_id": 695 }, "chunk_id": "train_shard_00001_695_0", "global_id": 6640 }, { "text": "The protein-coding genes were found in various prominent Quantitative Trait Loci (QTL) regions, suggesting potential roles of BICIs in traits related to milk production, reproduction, exterior, health, meat, and carcass. Notably, 63.21% of the bases within the BICIs call set contained interspersed repeats, predominantly LINEs. Additionally,70.28% of BICIs are shared with other domesticated and wild species, highlighting their evolutionary significance.

Conclusion

This is the first report unveiling a robust set of NUIs defining the pangenome of Bos indicus breeds of India. The analyses contribute valuable insights into the genomic landscape of desi cattle breeds.\n\nAdvancing the Indian Cattle Pangenome: Characterizing Non-Reference Sequences inBos indicus", "token_count": 202, "char_count": 779, "word_count": 104, "semantic_coherence": 1, "information_density": 0.8173, "quality_score": 0.9087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:24.340415", "source": { "split": "train_shard_00001", "doc_id": 695 }, "chunk_id": "train_shard_00001_695_1", "global_id": 6641 }, { "text": "In 2020, an outbreak of Salmonella Hadar illnesses was linked to contact with non-commercial, privately owned (backyard) poultry including live chickens, turkeys, and ducks, resulting in 848 illnesses. From late 2020 to 2021, this Salmonella Hadar strain caused an outbreak that was linked to ground turkey consumption. Core genome multilocus sequence typing (cgMLST) analysis determined that the Salmonella Hadar isolates detected during the outbreak linked to backyard poultry and the outbreak linked to ground turkey were closely related genetically (within 0-16 alleles). Epidemiological and traceback investigations were unable to determine how Salmonella Hadar detected in backyard poultry and ground turkey were linked, despite this genetic relatedness. Enhanced molecular characterization methods, such as analysis of the pangenome of Salmonella isolates, might be necessary to understand the relationship between these two outbreaks. Similarly, enhanced data collection during outbreak investigations and further research could potentially aid in determining whether these transmission vehicles are truly linked by a common source and what reservoirs exist across the poultry industries that allow Salmonella Hadar to persist. Further work combining epidemiological data collection, more detailed traceback information, and genomic analysis tools will be important for monitoring and investigating future enteric disease outbreaks.\n\nSalmonella Hadar linked to two distinct transmission vehicles highlights challenges to enteric disease outbreak investigations.", "token_count": 376, "char_count": 1618, "word_count": 210, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:24.918501", "source": { "split": "train_shard_00001", "doc_id": 696 }, "chunk_id": "train_shard_00001_696_0", "global_id": 6642 }, { "text": "The high diversity and global distribution of heterotrophic bacterial diazotrophs (HBDs) in the ocean has recently become apparent. However, understanding the role these largely uncultured microorganisms play in marine N2 fixation poses a challenge due to their undefined growth requirements and the complex regulation of the nitrogenase enzyme. We isolated and characterized Candidatus Thalassolituus haligoni, a member of a widely distributed clade of HBD belonging to the Oceanospirillales. Analysis of its nifH gene via amplicon sequencing revealed the extensive distribution of Cand. T. haligoni across the Pacific, Atlantic, and Arctic Oceans. Pangenome analysis indicates that the isolate shares >99% identity with an uncultured metagenome-assembled genome called Arc-Gamma-03, recently recovered from the Arctic Ocean. Through combined genomic, proteomic, and physiological approaches, we confirmed that the isolate fixes N2 gas. However, the mechanisms governing nitrogenase regulation in Cand. T. haligoni remain unclear. We propose Cand. T. haligoni as a globally distributed, cultured HBD model species within this understudied clade of Oceanospirillales.\n\nNitrogen fixation in the widely distributed marine γ-proteobacterial diazotroph <i>Candidatus</i> Thalassolituus haligoni.", "token_count": 370, "char_count": 1360, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6725, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:25.508836", "source": { "split": "train_shard_00001", "doc_id": 697 }, "chunk_id": "train_shard_00001_697_0", "global_id": 6643 }, { "text": "Bacteria use gene regulation to dynamically adapt to changes in their environment, including resistance to stress and the occupation of new niches. Gene expression is known to vary within a species pangenome, but the extent to which these changes could be explained by genetic variants in cis non-coding regions has so far been poorly investigated. Statistical genetics offers a hypothesis-free approach to this problem, as opposed to mechanistic models, which can be used only for reference isolates that are not representative of the whole species. In this study, we assembled two genomic and transcriptomic datasets for Escherichia coli (N=117) and Pseudomonas aeruginosa (N=413) and identified associations between genetic variants in cis non-coding regions and recorded gene expression variation. We identified at least one associated variant in up to 39% of the tested genes in both species. We partly validated the associations in-silico and in-vitro for E. coli , reinforcing the difficulty of identifying a single mechanism generating gene expression diversity. We then investigated the relevance of non-coding variants in explaining the variability in antimicrobial resistance in both species using two additional publicly available datasets, identifying a large number of these variants across antimicrobial compounds. This work confirms the role of genetic variation in often overlooked regions of bacterial genomes in influencing molecular and clinically relevant phenotypes.\n\nCis non-coding genetic variation drives gene expression changes in the E. coli and P. aeruginosa pangenomes", "token_count": 366, "char_count": 1618, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:26.092365", "source": { "split": "train_shard_00001", "doc_id": 698 }, "chunk_id": "train_shard_00001_698_0", "global_id": 6644 }, { "text": "Anti-phage defense systems are widespread in bacteria due to the latter continuous adaptation to infection by bacteriophages (phages). Stenotrophomonas maltophilia has a high degree of intrinsic antibiotic resistance, which makes phage therapy relevant for the treatment of infections caused by this species. Studying the array of anti-phage defense systems that could be found in S. maltophilia helps in better adapting the phages to the systems present in the pathogenic bacteria. Pangenome analysis of the available S. maltophilia strains with complete genomes that were downloaded from GenBank, including five local genomes, indicated a wide set of 72 defense systems and subsystems that varied between the strains. Seven of these systems were present in more than 20% of the studied genomes and the proteins encoded by the systems were variable in most of the cases. A total of 27 defense islands were revealed where defense systems were found; however, more than 60% of the instances of systems were found in four defense islands. Several elements linked to the transfer of these systems were found. No obvious associations between the pattern of distribution of the anti-phage defense systems of S. maltophilia and the phylogenetic features or the isolation site were found.\n\nGenome Analysis of Anti-Phage Defense Systems and Defense Islands in <i>Stenotrophomonas maltophilia</i>: Preservation and Variability.", "token_count": 355, "char_count": 1458, "word_count": 213, "semantic_coherence": 1, "information_density": 0.554, "quality_score": 0.777, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:26.664314", "source": { "split": "train_shard_00001", "doc_id": 699 }, "chunk_id": "train_shard_00001_699_0", "global_id": 6645 }, { "text": "

Motivation

The increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human-readable graph layout: a graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph's potential excessive size, this is a significant challenge.

Results

In response, we introduce a novel graph layout algorithm: the Path-Guided Stochastic Gradient Descent (PG-SGD). PG-SGD uses the genomes, represented in the pangenome graph as paths, as an embedded positional system to sample genomic distances between pairs of nodes. This avoids the quadratic cost seen in previous versions of graph drawing by SGD. We show that our implementation efficiently computes the low-dimensional layouts of gigabase-scale pangenome graphs, unveiling their biological features.

Availability and implementation

We integrated PG-SGD in ODGI which is released as free software under the MIT open source license. Source code is available at https://github.com/pangenome/odgi.\n\nPangenome graph layout by Path-Guided Stochastic Gradient Descent.", "token_count": 304, "char_count": 1275, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:27.232912", "source": { "split": "train_shard_00001", "doc_id": 700 }, "chunk_id": "train_shard_00001_700_0", "global_id": 6646 }, { "text": "

ABSTRACT

A novel giant virus was isolated from a freshwater sample collected in Pará de Minas city, Minas Gerais state, Brazil. The new isolate, named BR-AMG2, is a chlorovirus infecting the microalga Chlorella variabilis . Members of the family Phycodnaviridae , the chloroviruses have large linear dsDNA genomes (285–410 kbp), encoding hundreds of proteins and tRNAs. Despite their ecological and evolutionary importance, chloroviruses remain poorly studied, especially in South America. This study aimed to expand the understanding of this viral group by isolating and fully characterizing new chloroviruses in Brazil. After inoculating alga cultures with environmental samples, cytopathic effects, marked by lysis plaque formation, were observed 72 hours post-sampling. Chlorovirus BR-AMG2 remained stable across a temperature range of - 30 °C to 37 °C, yet was highly sensitive to UV exposure. This virus has a 160 nm icosahedral capsid and establishes a large viral factory in the host cytoplasm. Whole genome sequencing revealed a 338,043 bp genome, containing 11 tRNAs and 388 protein-coding sequences. We observed an extensive DNA methylation machinery, accounting for ∼5% of gene content in this isolate, suggesting a highly methylated genome. Phylogenetic reconstruction and Average Nucleotide Identity analyses confirmed that BR-AMG2 is a new member of the species Chlorovirus americanus , the first isolate recovered from a tropical region of the planet. Additionally, we observed a slight expansion of the species pangenome, suggesting ongoing genetic innovation with new isolates. Altogether, our results expand our knowledge about the viral diversity in Brazil and provide valuable insights into the biology of giant algae-infecting viruses.\n\nBiological and genomic characterization of a new chlorovirus isolate expands the diversity and complexity of giant algal viruses in Brazil", "token_count": 488, "char_count": 1907, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6812, "quality_score": 0.8406, "entities": { "genes": [ "AMG2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:28.358176", "source": { "split": "train_shard_00001", "doc_id": 701 }, "chunk_id": "train_shard_00001_701_0", "global_id": 6647 }, { "text": "Air flow rate and agitation speed for inulinase production by Kluyveromyces marxianus were optimized based on metabolic heat release profiles. Shear stress and oxygen transfer (kLa) values were compared to assess the effects of aeration and agitation. At agitation rates of ≤ 100 rpm, the oxygen mass transfer rates were small and eventually led to less inulinase production, but at agitation rates > 150 rpm, loss of biomass resulted in less inulinase activity. Bio-reaction calorimeter (BioRc1e) experiment with aeration rates ≤ 0.5 lpm showed low kLa while at 1.5 lpm frothing of reactor contents caused loss of biomass and inulinase activity. The optimum conditions for aeration and agitation rate for K. marxianus in BioRc1e were 1 lpm and 150 rpm. Heat yield values obtained for the substrate, product and biomass reinstated the ongoing metabolic process. The heat release pattern could be a promising tool for optimization of bioprocess and in situ monitoring, with a possibility of interventions during the biotransformation process. At optimized aeration and agitation conditions, a two-fold increase in inulinase activity could be noticed.\n\nEffect of aeration and agitation on yeast inulinase production: a biocalorimetric investigation.", "token_count": 342, "char_count": 1269, "word_count": 188, "semantic_coherence": 1, "information_density": 0.5638, "quality_score": 0.7819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:28.975643", "source": { "split": "train_shard_00001", "doc_id": 702 }, "chunk_id": "train_shard_00001_702_0", "global_id": 6648 }, { "text": "Leuconostoc carnosum is a known colonizer of meat-related food matrices. It reaches remarkably high loads during the shelf life in packaged meat products and plays a role in spoilage, although preservative effects have been proposed for some strains. In this study, the draft genomes of 17 strains of L. carnosum (i.e., all the strains that have been sequenced so far) were compared to decipher their metabolic and functional potential and to determine their role in food transformations. Genome comparison and pathway reconstruction indicated that L. carnosum is a compact group of closely related heterofermentative bacteria sharing most of the metabolic features. Adaptation to a nitrogen-rich environment, such as meat, is evidenced by 23 peptidase genes identified in the core genome and by the autotrophy for nitrogen compounds including several amino acids, vitamins, and cofactors. Genes encoding the decarboxylases yielding biogenic amines were not present. All the strains harbored 1-4 of 32 different plasmids, bearing functions associated to proteins hydrolysis, transport of amino acids and oligopeptides, exopolysaccharides, and various resistances (e.g., to environmental stresses, bacteriophages, and heavy metals). Functions associated to bacteriocin synthesis, secretion, and immunity were also found in plasmids. While genes for lactococcin were found in most plasmids, only three harbored the genes for leucocin B, a class IIa antilisterial bacteriocin. Determinants of antibiotic resistances were absent in both plasmids and chromosomes.\n\nComparative Genomics of Leuconostoc carnosum.", "token_count": 436, "char_count": 1633, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8311, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:29.613549", "source": { "split": "train_shard_00001", "doc_id": 703 }, "chunk_id": "train_shard_00001_703_0", "global_id": 6649 }, { "text": "

Background

Ethyl acetate is a widely used industrial solvent that is currently produced by chemical conversions from fossil resources. Several yeast species are able to convert sugars to ethyl acetate under aerobic conditions. However, performing ethyl acetate synthesis anaerobically may result in enhanced production efficiency, making the process economically more viable.

Results

We engineered an E. coli strain that is able to convert glucose to ethyl acetate as the main fermentation product under anaerobic conditions. The key enzyme of the pathway is an alcohol acetyltransferase (AAT) that catalyses the formation of ethyl acetate from acetyl-CoA and ethanol. To select a suitable AAT, the ethyl acetate-forming capacities of Atf1 from Saccharomyces cerevisiae, Eat1 from Kluyveromyces marxianus and Eat1 from Wickerhamomyces anomalus were compared. Heterologous expression of the AAT-encoding genes under control of the inducible LacI/T7 and XylS/Pm promoters allowed optimisation of their expression levels.

Conclusion

Engineering efforts on protein and fermentation level resulted in an E. coli strain that anaerobically produced 42.8 mM (3.8 g/L) ethyl acetate from glucose with an unprecedented efficiency, i.e. 0.48 C-mol/C-mol or 72% of the maximum pathway yield.\n\nMultilevel optimisation of anaerobic ethyl acetate production in engineered Escherichia coli.", "token_count": 455, "char_count": 1452, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6223, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:30.258127", "source": { "split": "train_shard_00001", "doc_id": 704 }, "chunk_id": "train_shard_00001_704_0", "global_id": 6650 }, { "text": "Mycobacterium ulcerans, an environmental opportunistic pathogen, causes necrotic cutaneous and subcutaneous lesions, named Buruli ulcers, in tropical countries. PCR-derived tests used to detect M. ulcerans in environmental and clinical samples do not allow one-shot detection, identification, and typing of M. ulcerans among closely related Mycobacterium marinum complex mycobacteria. We established a 385-member M. marinum/M. ulcerans complex whole-genome sequence database by assembling and annotating 341 M. marinum/M. ulcerans complex genomes and added 44 M. marinum/M. ulcerans complex whole-genome sequences already deposited in the NCBI database. Pangenome, core genome, and single-nucleotide polymorphism (SNP) distance-based comparisons sorted the 385 strains into 10 M. ulcerans taxa and 13 M. marinum taxa, correlating with the geographic origin of strains. Aligning conserved genes identified one PPE (proline-proline-glutamate) gene sequence to be species and intraspecies specific, thereby genotyping the 23 M. marinum/M. ulcerans complex taxa. PCR sequencing of the PPE gene correctly genotyped nine M. marinum/M. ulcerans complex isolates among one M. marinum taxon and three M. ulcerans taxa in the African taxon (T2.4). Further, successful PPE gene PCR sequencing in 15/21 (71.4%) swabs collected from suspected Buruli ulcer lesions in Côte d'Ivoire exhibited positive M. ulcerans IS2404 real-time PCR and identified the M. ulcerans T2.4.1 genotype in eight swabs and M. ulcerans T2.4.1/T2.4.2 mixed genotypes in seven swabs. PPE gene sequencing could be used as a proxy for whole-genome sequencing for the one-shot detection, identification, and typing of clinical M", "token_count": 537, "char_count": 1720, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:30.914524", "source": { "split": "train_shard_00001", "doc_id": 705 }, "chunk_id": "train_shard_00001_705_0", "global_id": 6651 }, { "text": "ulcerans strains, offering an unprecedented tool for identifying M. ulcerans mixed infections. IMPORTANCE We describe a new targeted sequencing approach that characterizes the PPE gene to disclose the simultaneous presence of different variants of a single pathogenic microorganism. This approach has direct implications on the understanding of pathogen diversity and natural history and potential therapeutic implications when dealing with obligate and opportunistic pathogens, such as Mycobacterium ulcerans presented here as a prototype.\n\nPPE Barcoding Identifies Biclonal Mycobacterium ulcerans Buruli Ulcer, Côte d'Ivoire.", "token_count": 162, "char_count": 648, "word_count": 82, "semantic_coherence": 1, "information_density": 0.8049, "quality_score": 0.9024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:31.359166", "source": { "split": "train_shard_00001", "doc_id": 705 }, "chunk_id": "train_shard_00001_705_1", "global_id": 6652 }, { "text": "Co-cultures of Bacillus subtilis and Kluyveromyces marxianus were investigated in submerged fermentation for xylanase production at shake-flask scale. Xylanase production markedly increased when arabinose, xylose, or hazelnut shells were used as the single carbon source. Maximal xylanase of 49.5 IU/mL was achieved with 4% B. subtilis, 4% K. marxianus, 40% solid load of hazelnut shells, and pH 7.0. Overall, xylanase was enhanced by 4.4-fold compared to initial un-optimized monoculture production and 2.8-fold compared to initial un-optimized co-cultured production, after optimization by response surface method.\n\nAssessment and optimization of xylanase production using co-cultures of Bacillus subtilis and Kluyveromyces marxianus.", "token_count": 259, "char_count": 778, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7041, "quality_score": 0.852, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:31.907197", "source": { "split": "train_shard_00001", "doc_id": 706 }, "chunk_id": "train_shard_00001_706_0", "global_id": 6653 }, { "text": "Wolbachia is a maternally inherited intracellular bacterium that infects a wide range of arthropods including mosquitoes. The endosymbiont is widely used in biocontrol strategies due to its capacity to modulate arthropod reproduction and limit pathogen transmission. Wolbachia infections in Culex spp. are generally assumed to be monoclonal but the potential presence of genetically distinct Wolbachia subpopulations within and between individual organs has not been investigated using whole genome sequencing. Here we reconstructed Wolbachia genomes from ovary and midgut metagenomes of single naturally infected Culex pipiens mosquitoes from Southern France to investigate patterns of intra- and inter-individual differences across mosquito organs. Our analyses revealed a remarkable degree of intra-individual conservancy among Wolbachia genomes from distinct organs of the same mosquito both at the level of gene presence-absence signal and single-nucleotide polymorphisms (SNPs). Yet, we identified several synonymous and non-synonymous substitutions between individuals, demonstrating the presence of some level of genomic heterogeneity among Wolbachia that infect the same C. pipiens field population. Overall, the absence of genetic heterogeneity within Wolbachia populations in a single individual confirms the presence of a dominant Wolbachia that is maintained under strong purifying forces of evolution.\n\nWolbachia populations across organs of individual Culex pipiens: highly conserved intra-individual core pangenome with inter-individual polymorphisms.", "token_count": 450, "char_count": 1658, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:32.549214", "source": { "split": "train_shard_00001", "doc_id": 707 }, "chunk_id": "train_shard_00001_707_0", "global_id": 6654 }, { "text": "Microcystis, a common harmful algal bloom (HAB) taxon, threatens water supplies and human health, yet species delimitation is contentious in this taxon, leading to challenges in research and management of this threat. Historical and common morphology-based classifications recognize multiple morphospecies, most with variable and diverse ecologies, while DNA sequence-based classifications indicate a single species with multiple ecotypes. To better delimit Microcystis species, we conducted a pangenome analysis of 122 genomes. Core- and non-core gene phylogenetic analyses placed 113 genomes into 23 monophyletic clusters containing at least two genomes. Overall, genome-related indices revealed that Microcystis contains at least 16 putative genospecies. Fifteen genospecies included at least one Microcystis aeruginosa morphospecies, and 10 genospecies included two or more morphospecies. This classification system will enable consistent taxonomic identification of Microcystis and thereby aid in resolving some of the complexities and controversies that have long characterized eco-evolutionary research and management of this important HAB taxon.\n\nMicrocystis pangenome reveals cryptic diversity within and across morphospecies.", "token_count": 332, "char_count": 1277, "word_count": 160, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:33.114181", "source": { "split": "train_shard_00001", "doc_id": 708 }, "chunk_id": "train_shard_00001_708_0", "global_id": 6655 }, { "text": "

Background

Streptococcus pneumoniae Serotype 3 (SPN3) remains a significant cause of morbidity and mortality worldwide despite of pneumococcal conjugate vaccine (PCV) implementation. We explored genomic profile of SPN3 from children and adult groups to understand population structure and evolution dynamics of SPN3 in Indonesia.

Methods

We undertook whole genome sequencing (WGS) from 19 isolates of SPN3 in Indonesia between 2017 and 2021 prior to PCV introduction. This study assessed sequence types (STs), global pneumococcal sequence cluster (GPSC), genome prediction of antimicrobial resistance (AMR) profile, pangenome analysis, phylogenetic tree, and genome comparative of capsular polysaccharide (cps) locus.

Results

We identified ST451-GPSC234 (n = 5) and ST180-GPSC12 (n = 4), ST458-GPSC51 (n = 2), ST3805-GPSC12 (n = 2), ST4909-GPSC363 (n = 2), ST700-GPSC10 (n = 1), ST5292-GPSC309 (n = 1), ST505-GPSC12 (n = 1), and ST4233 (n = 1). Genome prediction of AMR discover isolates were resistant to tetracycline (n = 5); co-resistant of chloramphenicol and tetracycline (n = 2); co-trimoxazole and tetracycline (n = 1). We observed SPN3 possess closed pangenome characteristic, indicates more stable genetic repertoire", "token_count": 450, "char_count": 1247, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6433, "quality_score": 0.8216, "entities": { "genes": [ "GPSC10", "GPSC309", "ST3805", "GPSC234", "GPSC363", "GPSC51", "ST180", "ST700", "ST5292", "ST505" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:33.749774", "source": { "split": "train_shard_00001", "doc_id": 709 }, "chunk_id": "train_shard_00001_709_0", "global_id": 6656 }, { "text": "We found 5 absent genes in cps locus including cpsABCD and tnp in ST700-GPSC10 lineage.

Conclusions

SPN3 has potential genomic profile to enhance the ability of this strain to endure selective pressure such as PCV introduction.\n\nAn insight of Streptococcus pneumoniae serotype 3 genomic profile in Indonesia.", "token_count": 93, "char_count": 315, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [ "ST700", "GPSC10", "SPN3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:34.124034", "source": { "split": "train_shard_00001", "doc_id": 709 }, "chunk_id": "train_shard_00001_709_1", "global_id": 6657 }, { "text": "Ralstonia solanacearum species complex (RSSC) cause several phytobacteriosis in many economically important crops around the globe, especially in the tropics. In Brazil, phylotypes I and II cause bacterial wilt (BW) and are indistinguishable by classical microbiological and phytopathological methods, while Moko disease is caused only by phylotype II strains. Type III effectors of RSSC (Rips) are key molecular actors regarding pathogenesis and are associated with specificity to some hosts. In this study, we sequenced and characterized 14 newly RSSC isolates from Brazil's Northern and Northeastern regions, including BW and Moko ecotypes. Virulence and resistance sequences were annotated, and the Rips repertoire was predicted. Confirming previous studies, RSSC pangenome is open as α≅0.77. Genomic information regarding these isolates matches those for R. solanacearum in NCBI. All of them fit in phylotype II with a similarity above 96%, with five isolates in phylotype IIB and nine in phylotype IIA. Almost all R. solanacearum genomes in NCBI are actually from other species in RSSC. Rips repertoire of Moko IIB was more homogeneous, except for isolate B4, which presented ten non-shared Rips. Rips repertoire of phylotype IIA was more diverse in both Moko and BW, with 43 common shared Rips among all 14 isolates. New BW isolates shared more Rips with Moko IIA and Moko IIB than with other public BW genome isolates from Brazil. Rips not shared with other isolates might contribute to individual virulence, but commonly shared Rips are good avirulence candidates. The high number of Rips shared by new Moko and BW isolates suggests they are actually Moko isolates infecting solanaceous hosts. Finally, infection assays and Rips expression on different hosts are needed to better elucidate the association between Rips repertoire and host specificities.", "token_count": 505, "char_count": 1883, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5972, "quality_score": 0.7986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:34.778064", "source": { "split": "train_shard_00001", "doc_id": 710 }, "chunk_id": "train_shard_00001_710_0", "global_id": 6658 }, { "text": "Characterization and Association of Rips Repertoire to Host Range of Novel Ralstonia solanacearum Strains by In Silico Approaches.", "token_count": 40, "char_count": 137, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:35.131612", "source": { "split": "train_shard_00001", "doc_id": 710 }, "chunk_id": "train_shard_00001_710_1", "global_id": 6659 }, { "text": "Kefir grains are a unique symbiotic association of different microbiota, including a variety of bacterial and fungal species. The microbiota in kefir grains is strongly influenced by the geographical origin and sub-culturing environment. After sub-culturing in goat milk for 2 to 4 months, amplicon sequencing (16S rRNA and ITS1 region) was applied for the identification of bacterial and fungal autogenic succession of three kefir grains collected from China (CN, Asia), Germany (DE, Europe) and United States of America (USA, America). Taxonomic analysis displayed three main bacterial and fungal species in kefir grains from different origins during sub-culturing process (Lactobacillus helveticus, Lactobacillus kefiranofaciens and Lactobacillus kefiri for bacteria, Kazachstania unispora, Kluyveromyces marxianus and Saccharomyces cerevisiae for fungi). Based on the results of beta diversity analysis, microbiota in kefir grains from CN and DE would be stable when sub-cultured in goat milk for more than three months. Differently, a highly microbial stability has been found for the sample from USA during the whole sub-culturing process. These results helped to understand the composition and stability of microbiota in kefir grains when sub-cultured in goat milk.\n\nAutogenic successions of bacteria and fungi in kefir grains from different origins when sub-cultured in goat milk", "token_count": 368, "char_count": 1387, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:35.713270", "source": { "split": "train_shard_00001", "doc_id": 711 }, "chunk_id": "train_shard_00001_711_0", "global_id": 6660 }, { "text": "Several mutations of the sorghum [Sorghum bicolor (L.) Moench] GRANULE-BOUND STARCH SYNTHASE (GBSS) gene [Sobic.010G022600; commonly known as Waxy (Wx)] result in a low amylose:amylopectin starch ratio. Recessive waxy (wx) alleles improve starch digestibility in ethanol production, human foods and beverages, and animal feed. However, breeding waxy sorghum is challenging due to reliance on traditional PCR markers for genotyping, which are not amenable to next-generation sequencing (NGS). Most commercial breeding programs use high-throughput genotyping and genomic selection in large, segregating populations prior to flowering. This study provides the first published NGS markers for the two most commonly used waxy (wx) alleles of sorghum and is the first to fully sequence the large insertion that is causal of the wxa allele. In the absence of a pangenome including wxa genotypes, we constructed an in silico B.Tx623 wxa genome assembly from the B.Tx623 reference genome (v3.1.1) including the insertion, a ~ 5-kb-long terminal repeat (LTR) retrotransposon of the copia superfamily. The in silico wxa assembly improved read mapping at Sobic.010G022600 in wxa individuals, identified 78 new uniquely mapped reads, and made it possible to distinguish different Waxy genotypes using short-read sequencing data. Functional PACE-PCR markers, suitable for marker-assisted selection and multiplexed, low-to-mid-density genomic selection, were developed for Wx, wxa, and wxb alleles. The PACE markers were validated in segregating populations of three public and private breeding programs", "token_count": 491, "char_count": 1665, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8356, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:36.365745", "source": { "split": "train_shard_00001", "doc_id": 712 }, "chunk_id": "train_shard_00001_712_0", "global_id": 6661 }, { "text": "These new molecular breeding resources comprise a toolkit that will improve the efficiency of developing commercial waxy sorghum hybrids using genomics-assisted approaches.\n\nAn updated molecular toolkit for genomics-assisted breeding of waxy sorghum [Sorghum bicolor (L.) Moench].", "token_count": 71, "char_count": 280, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8056, "quality_score": 0.9028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:36.736527", "source": { "split": "train_shard_00001", "doc_id": 712 }, "chunk_id": "train_shard_00001_712_1", "global_id": 6662 }, { "text": "Aligning DNA sequences retrieved from fossils or other paleontological artifacts, referred to as ancient DNA, is particularly challenging due to the short sequence length and chemical damage which creates a specific pattern of substitution (C→T and G→A) in addition to the heightened divergence between the sample and the reference genome thus exacerbating reference bias. This bias can be mitigated by aligning to pangenome graphs to incorporate documented organismic variation, but this approach still suffers from substitution patterns due to chemical damage. We introduce a novel methodology introducing the RYmer index, a variant of the commonly-used minimizer index which represents purines (A,G) and pyrimidines (C,T) as R and Y respectively. This creates an indexing scheme robust to the aforementioned chemical damage. We implemented SAFARI , an ancient DNA damage-aware version of the pangenome aligner vg giraffe which uses RYmers to rescue alignments containing deaminated seeds. We show that our approach produces more correct alignments from ancient DNA sequences than current approaches while maintaining a tolerable rate of spurious alignments. In addition, we demonstrate that our algorithm improves the estimate of the rate of ancient DNA damage, especially for highly damaged samples. Crucially, we show that this improved alignment can directly translate into better insights gained from the data by showcasing its integration with a number of extant pangenome tools.\n\nSAFARI: Pangenome Alignment of Ancient DNA Using Purine/Pyrimidine Encodings", "token_count": 340, "char_count": 1565, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6608, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:37.318806", "source": { "split": "train_shard_00001", "doc_id": 713 }, "chunk_id": "train_shard_00001_713_0", "global_id": 6663 }, { "text": "

ABSTRACT

Genomic and metagenomic explorations of the oceans have identified well-structured microbial assemblages showing endemic genomic adaptations with increasing depth. However, deep water column surveys have been limited, especially of the Gulf of Mexico (GoM) basin, despite its importance for human activities. To fill this gap, we report on 19 deeply sequenced [∼5 Gbp/sample] shotgun metagenomes collected along a vertical gradient, from the surface to about 2,000m deep, at three GoM stations. Beta diversity analysis revealed strong clustering by depth, and not by station, even when including previously determined samples from other ocean basins. However, a community level pangenome style gene content analysis revealed ∼54% of predicted gene sequences to be station specific within our GoM samples. Of the 154 high-quality MAGs recovered, 145 represent novel species compared to NCBI genomes and TARA MAGs databases. Two of these MAGs were relatively abundant at both surface and deep samples, revealing remarkable versatility across the water column. A few MAGs of freshwater origin (∼6% of total detected) were relatively abundant at 600m deep and 270 miles from the coast at one station, revealing that the effects of freshwater input in the GoM can sometimes be far-reaching and long-lasting. Notably, 1,447/16,068 of the total COGs detected were positively (Pearson’s r ≥ 0.5) or negatively (Pearson’s r ≤ −0.5) correlated with depth including beta-lactamases, dehydrogenase, and CoA-associated oxidoreductases. Taken together our results reveal substantial novel genome and gene diversity across the GoM’s water column, and testable hypotheses for some of the diversity patterns observed.

IMPORTANCE

To what extent microbial communities are similar between different ocean basins at similar depths and what the impact of freshwater input by major rivers may be on these communities remain poorly understood issues with potentially important implications for modeling and managing marine biodiversity", "token_count": 507, "char_count": 2040, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6803, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:37.973113", "source": { "split": "train_shard_00001", "doc_id": 714 }, "chunk_id": "train_shard_00001_714_0", "global_id": 6664 }, { "text": "In this study, we performed metagenomic sequencing and recovered 154 high-quality metagenome-assembled genomes (MAGs) from three stations in the Gulf of Mexico (GoM) and from various depths up to about 2000m. Comparison to similar data from other ocean basins highlight the unique diversity harbored by the GoM, which could be driven by more substantial input by the Mississippi River and by human activities, including offshore oil drilling. The data and results provided by this study should be useful for future comparative analysis of marine biodiversity and contribute toward its more complete characterization.\n\nMetagenome-based vertical profiling of the Gulf of Mexico highlights its uniqueness and far-reaching effects of freshwater input", "token_count": 165, "char_count": 746, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7248, "quality_score": 0.8624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:38.414465", "source": { "split": "train_shard_00001", "doc_id": 714 }, "chunk_id": "train_shard_00001_714_1", "global_id": 6665 }, { "text": "Antioxidant peptide obtained from Kluyveromyces marxianus protein hydrolysate, VLSTSFPPK (VL-9) and peptide analogues were synthesized chemically and analyzed for in vitro and cellular antioxidant activity. VLSTSFCPK (VCK-9), VLSTSFYPK (VYK-9), VLSTSFPPY (VY-9) and VLSTSFPPW(VW-9) showed the highest DPPH radical, ABTS radical cation scavenging and ferric reducing activities. VCK-9, VYK-9 and STSFPPK (SK-7) showed cytoprotective effects against Caco2 cells under H₂O₂-induced oxidative stress. The positive role of peptides in the protection of cells was shown to be due to scavenging free radicals, activation of Keap1-Nrf2 signaling pathway that may lead to overexpression of antioxidant enzyme genes and also increasing the activity of antioxidant enzymes including catalase (CAT), superoxide dismutase (SOD) and glutathione peroxidase (GPX) due to direct interaction with enzymes and changing their conformation. Altogether, pretreatment of cells under oxidative stress with VCK-9, VYK-9 and SK-7 led to decreasing the level of lipid and protein oxidation and cell apoptosis and increasing the cell viability.\n\nAntioxidant and cytoprotective effects of synthetic peptides identified from Kluyveromyces marxianus protein hydrolysate: Insight into the molecular mechanism", "token_count": 392, "char_count": 1276, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:39.030223", "source": { "split": "train_shard_00001", "doc_id": 715 }, "chunk_id": "train_shard_00001_715_0", "global_id": 6666 }, { "text": "Elizabethkingia anophelis is an emerging pathogen that causes life-threatening infections in neonates and immunocompromised patients. In this study, we performed next-generation sequencing (NGS) to characterize 10 E. anophelis strains isolated from clinical patients in Nantong, China. Core, accessory, and unique genomes were composed of 2,891, 1,633, and 498 genes, respectively. Based on genetic screening for antimicrobial resistance genes (AMRs), all E. anophelis strains carried the same AMRs, including blaB, blaCME, and blaGOB. The virulence factors (VFs) in the 10 strains were classified into 13 functional categories, and the differences between strains were mainly in immune modulation and nutritional/metabolic factor. We further analyzed the genomic features of one of ten strains, NT06 strain. The capsule type of NT06 was X, which is rare among E. anophelis strains. Based on comparative analyses, we first found that NT06 carried the YclNOPQ-like operon, which is the complete transporter for petrobactin, to acquire iron. The genomic features are important for further investigations of epidemiology, resistance, virulence, and to identify appropriate treatments.IMPORTANCEElizabethkingia anophelis strains are opportunistic pathogens causing meningitis, bloodstream infections, and endophthalmitis in vulnerable populations. There is a lack of knowledge of the genetic diversity, presence of antimicrobial resistance genes (AMRs), and virulence factors (VFs) in E. anophelis isolated from clinical patients in China. Based on next-generation sequencing (NGS) and comparative genomic analyses, we determined the genomic features, phylogeny, and diversity of E", "token_count": 517, "char_count": 1783, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [ "NT06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:39.735134", "source": { "split": "train_shard_00001", "doc_id": 716 }, "chunk_id": "train_shard_00001_716_0", "global_id": 6667 }, { "text": "anophelis strains isolated from patients and identified a large accessory genome, intrinsic AMRs, and variable VFs. Based on comparative analyses, we identified a key strain, NT06, that carried a unique capsule type of X and the siderophore-mediated iron acquisition system (yclNOPQ-like genes). These findings advance our understanding of the genomic plasticity, evolution, and pathogenicity determinants of E. anophelis.\n\nComparative genomic analysis of ten Elizabethkingia anophelis isolated from clinical patients in China.", "token_count": 155, "char_count": 559, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7887, "quality_score": 0.8944, "entities": { "genes": [ "NT06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:40.191716", "source": { "split": "train_shard_00001", "doc_id": 716 }, "chunk_id": "train_shard_00001_716_1", "global_id": 6668 }, { "text": "Diversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, these functions include disease suppression and pathogen inhibition. However, limited effort has been given to defining the importance of rhizosphere intragenus microdiversity, despite the increasing homogeneity of agricultural systems. Through an integrative approach combining culture-dependent and -independent methods, we generated a strain library of 373 pseudomonads, benchmarked to long-read 16S rRNA amplicon sequencing, from two modern winter wheat cultivars. Representative isolates were genome sequenced to provide a Pseudomonas pangenome of 112 genomes. The isolates were used to demonstrate cultivar-dependent taxonomic and functional microdiversity between two closely related winter wheat cultivars. A Fusarium-resistant cultivar demonstrated increased Pseudomonas taxonomic diversity but not biosynthetic diversity when compared to the susceptible cultivar, coinciding with a thinner root diameter of the resistant cultivar. We found enrichment of Pseudomonas isolates capable of antagonizing Fusarium as well as chitinase-encoding genes and pyoverdine gene clusters in the resistant cultivar. Across closely related Pseudomonas isolates from the two cultivars, there were differences in genomic content and biosynthetic gene clusters. Ultimately, we highlight the need for fine-scale analysis to uncover the hidden microdiversity within rhizosphere Pseudomonas.\n\nPseudomonas taxonomic and functional microdiversity in the wheat rhizosphere is cultivar-dependent and links to disease resistance profile and root diameter", "token_count": 392, "char_count": 1683, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:40.844326", "source": { "split": "train_shard_00001", "doc_id": 717 }, "chunk_id": "train_shard_00001_717_0", "global_id": 6669 }, { "text": "Genome expansion and contraction are reportedly driven by transposable element (TE) activity, but the underlying dynamics remain enigmatic due to a lack of historical records tracing these changes. Here, we present PrinTE for versatile, forward-time simulation of whole-genome sequences with highly customizable transposon dynamics. Through simulations, we confirm that the distribution of TE sequence divergence reflects their historical insertion and deletion dynamics, which can be used to infer TE dynamic parameters through PrinTE simulations. We analyzed the pangenome of Pucciniomycotina , a subdivision of fungi containing myrtle rust ( Austropuccinia psidii ), which drastically expanded its genome size to 1018 Mb. Our analyses reveal that the best strategy for controlling genome size is to avoid the invasion of LTR retrotransposons (LTR-RTs). While illegitimate recombination (IR) is considered the most effective counteraction of LTR-RT invasions leaving only solo LTR remnants, we observed a strong positive correlation between solo:intact LTR ratio (strength of LTR-RT removal) and genome size ( r = 0.65), and a near-linear correlation between solo LTR count and genome size ( r = 0.98). This result suggests that IR alone may not effectively prevent genome obesity. Through simulation of Pucciniomycotina genomes, we proposed that A. psidii might experience a prolonged period of genome expansion followed by a short, potent, and likely ongoing period of contraction. PrinTE is freely available at https://github.com/cwb14/PrinTE.git .\n\nPrinTE: A Forward Simulation Framework for Studying the Role of Transposable Elements in Genome Expansion and Contraction", "token_count": 405, "char_count": 1676, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6625, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:41.499060", "source": { "split": "train_shard_00001", "doc_id": 718 }, "chunk_id": "train_shard_00001_718_0", "global_id": 6670 }, { "text": "

Background

Bioremediation faces several compounds to recover oil spilled ecosystem. The BTEX (benzene, toluene, ethylbenzene, and xylene) are toxic hydrocarbons requiring efficient microbial degradation for bioremediation. Pseudomonas aeruginosa can degrade hydrocarbons through emulsification ( rhl genes) and tolerance ( mla genes). However, genomic organization of these systems in environmental P. aeruginosa strains remains unclear. This study aimed to investigate the rhl and mla systems in six strains isolated from hydrocarbon-contaminated sites in Peru.

Methods

Six Pseudomonas aeruginosa strains were evaluated in this study. Each strain were able to degrade hydrocarbon and tolerate heavy metals. DNA extraction, sequencing, and quality-controlled assembly, functional genome annotation was performed using BAKTA. Comparative analysis included high-quality Pseudomonas genomes from RefSeq, with ANI metrics. A phylogenetic tree was built from core gene alignment, revealed evolutionary connections and was visualized with iTOL.

Results

The assembled genomes ranged from 5.6 to 6.0 Mbp with ~66% GC content. All the strains were confirmed as P. aeruginosa by ANI; placing them within Clade 1 alongside environmental and clinical strains. Pangenome analysis identified 3,544 core genes and a diverse accessory genome. All strains had rhlABRI genes in a conserved 3'-5' orientation. Most of them contained duplicated rhlB gene, except C1BHIC5 strain", "token_count": 455, "char_count": 1556, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:42.139033", "source": { "split": "train_shard_00001", "doc_id": 719 }, "chunk_id": "train_shard_00001_719_0", "global_id": 6671 }, { "text": "However, rhlG varied in position and orientation, it was often near rhlC, with C1BHIC5 also displaying an exception in rhlG orientation.100% of strains presented mla system, associated with toluene tolerance, with two copies of mlaA, mlaFEDC, and mlaEFD genes arranged with high synteny but variable orientations. In comparison to Pseudomonas putida, where mla genes are positioned between murA and ppcD with an additional toluene tolerance gene ( ttg2D).

Conclusions

In conclusion, the presence of the rhlABC genes and the BTEX tolerance genes in all of the analyzed strains allowed us to understand the great ability of P. aeruginosa to survive in polluted environments.\n\nComparative Genomics of Rhamnolipid Synthesis and Monoaromatic Hydrocarbon Tolerance Genes in Environmental <i>Pseudomonas aeruginosa</i> strains.", "token_count": 318, "char_count": 937, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6983, "quality_score": 0.8491, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:42.695236", "source": { "split": "train_shard_00001", "doc_id": 719 }, "chunk_id": "train_shard_00001_719_1", "global_id": 6672 }, { "text": "Salmonella enterica is a leading cause of bacterial foodborne and zoonotic illnesses in the United States. For this study, we applied four different whole genome sequencing (WGS)-based subtyping methods: high quality single-nucleotide polymorphism (hqSNP) analysis, whole genome multilocus sequence typing using either all loci [wgMLST (all loci)] and only chromosome-associated loci [wgMLST (chrom)], and core genome multilocus sequence typing (cgMLST) to a dataset of isolate sequences from 9 well-characterized Salmonella outbreaks. For each outbreak, we evaluated the genomic and epidemiologic concordance between hqSNP and allele-based methods. We first compared pairwise genomic differences using all four methods. We observed discrepancies in allele difference ranges when using wgMLST (all loci), likely caused by inflated genetic variation due to loci found on plasmids and/or other mobile genetic elements in the accessory genome. Therefore, we excluded wgMLST (all loci) results from any further comparisons in the study. Then, we created linear regression models and phylogenetic tanglegrams using the remaining three methods. K-means analysis using the silhouette method was applied to compare the ability of the three methods to partition outbreak and sporadic isolate sequences. Our results showed that pairwise hqSNP differences had high concordance with cgMLST and wgMLST (chrom) allele differences. The slopes of the regressions for hqSNP vs. allele pairwise differences were 0.58 (cgMLST) and 0.74 [wgMLST (chrom)], and the slope of the regression was 0.77 for cgMLST vs. wgMLST (chrom) pairwise differences", "token_count": 443, "char_count": 1640, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:43.333917", "source": { "split": "train_shard_00001", "doc_id": 720 }, "chunk_id": "train_shard_00001_720_0", "global_id": 6673 }, { "text": "Tanglegrams showed high clustering concordance between methods using two statistical measures, the Baker's gamma index (BGI) and cophenetic correlation coefficient (CCC), where 9/9 (100%) of outbreaks yielded BGI values ≥ 0.60 and CCCs were ≥ 0.97 across all nine outbreaks and all three methods. K-means analysis showed separation of outbreak and sporadic isolate groups with average silhouette widths ≥ 0.87 for outbreak groups and ≥ 0.16 for sporadic groups. This study demonstrates that Salmonella isolates clustered in concordance with epidemiologic data using three WGS-based subtyping methods and supports using cgMLST as the primary method for national surveillance of Salmonella outbreak clusters.\n\nEvaluation of whole and core genome multilocus sequence typing allele schemes for Salmonella enterica outbreak detection in a national surveillance network, PulseNet USA.", "token_count": 245, "char_count": 899, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7258, "quality_score": 0.8629, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:43.815606", "source": { "split": "train_shard_00001", "doc_id": 720 }, "chunk_id": "train_shard_00001_720_1", "global_id": 6674 }, { "text": "Streptococcus halichoeri is an emerging pathogen with a variety of host species and zoonotic potential. It has been isolated from grey seals and other marine mammals as well as from human infections. Beginning in 2010, two concurrent epidemics were identified in Finland, in fur animals and domestic dogs, respectively. The fur animals suffered from a new disease fur animal epidemic necrotic pyoderma (FENP) and the dogs presented with ear infections with poor treatment response. S. halichoeri was isolated in both studies, albeit among other pathogens, indicating a possible role in the disease etiologies. The aim was to find a possible common origin of the fur animal and dog isolates and study the virulence factors to assess pathogenic potential. Isolates from seal, human, dogs, and fur animals were obtained for comparison. The whole genomes were sequenced from 20 different strains using the Illumina MiSeq platform and annotated using an automatic annotation pipeline RAST. The core and pangenomes were formed by comparing the genomes against each other in an all-against-all comparison. A phylogenetic tree was constructed using the genes of the core genome. Virulence factors were assessed using the Virulence Factor Database (VFDB) concentrating on the previously confirmed streptococcal factors. A core genome was formed which encompassed approximately half of the genes in Streptococcus halichoeri. The resulting core was nearly saturated and would not change significantly by adding more genomes. The remaining genes formed the pangenome which was highly variable and would still evolve after additional genomes. The results highlight the great adaptability of this bacterium possibly explaining the ease at which it switches hosts and environments. Virulence factors were also analyzed and were found primarily in the core genome. They represented many classes and functions, but the largest single category was adhesins which again supports the marine origin of this species.\n\nStreptococcus halichoeri: Comparative Genomics of an Emerging Pathogen.", "token_count": 468, "char_count": 2074, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:44.458800", "source": { "split": "train_shard_00001", "doc_id": 721 }, "chunk_id": "train_shard_00001_721_0", "global_id": 6675 }, { "text": "

Introduction

The spread of antibiotic resistance genes among Campylobacter jejuni (C. jejuni) is a serious problem, and the effects of the restriction-modification (R-M) system on the transmission dynamics of these genes in C. jejuni remain poorly understood.

Materials and methods

Complete genome sequences of C. jejuni strains were extracted from the BV-BRC database until March 25, 2024. The phylogenetic and the resistance analysis were used to analyze the distribution of resistance genes in C. jejuni. The impacts of the R-M systems on the AMR genes transmission between C. jejuni strains and the possible mechanisms were explored through recombination, pangenome and mobile genetic elements analysis.

Results

C. jejuni strains carrying the Type III R-M system have a significantly lower number of antimicrobial resistance (AMR) genes compared to strains without this system (p < 0.0001), with covariance value being -0.0526. The recombination analysis also shows that the median number of the number of AMR genes in the strains not possessing the Type III R-M system increases by 19.38% compared to strains carrying that system (p < 0.0001). We also find that the horizontal gene transfer frequency might have limited relationship with the Type III R-M system in C. jejuni through pangenome and mobile genetic elements analysis.

Conclusion

Our research indicates that the Type III R-M system might restrict the transmission of AMR genes potentially by affecting recombination in C. jejuni, which provides a theoretical basis for addressing the drug resistance problem.\n\nThe restriction impacts of the Type III restriction-modification system on the transmission dynamics of antimicrobial resistance genes in <i>Campylobacter jejuni</i>.", "token_count": 514, "char_count": 1861, "word_count": 252, "semantic_coherence": 1, "information_density": 0.4881, "quality_score": 0.744, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:45.116788", "source": { "split": "train_shard_00001", "doc_id": 722 }, "chunk_id": "train_shard_00001_722_0", "global_id": 6676 }, { "text": "The genus Streptomyces has consistently been found to be enriched in drought-stressed plant root microbiomes, yet the ecological basis and functional variation underlying this enrichment at the strain and isolate level remain unclear. Using two 16S rRNA sequencing methods with different levels of taxonomic resolution, we confirmed drought-associated enrichment of Streptomyces in field-grown sorghum roots and identified five closely related but distinct ASVs belonging to the genus with variable drought enrichment patterns. From a culture collection of sorghum root endophytes, we selected 12 Streptomyces isolates representing these ASVs for phenotypic and genomic characterization. Whole-genome sequencing revealed substantial variation in gene content, even among closely related isolates, and exometabolomic profiling showed distinct metabolic responses to media supplemented with drought- versus well-watered root tissue. Traits linked to drought survival, including osmotic stress tolerance, siderophore production, and carbon utilization, varied widely among isolates and were not phylogenetically conserved. Using a broader panel of 48 Streptomyces, we demonstrate that drought enrichment (DE) scores, determined through mono-association experiments in gnotobiotic sorghum systems, showed high variability and lacked correlation with plant growth promotion. Pangenome-wide association identified gene clusters involved in osmolyte transport (e.g., proP) and membrane biosynthesis (e.g., fabG) as positively associated with DE, though most associations lacked phylogenetic signal. Collectively, these results demonstrate that Streptomyces enrichment under drought is not a conserved genus-level trait but is instead strain-specific and functionally heterogeneous. Furthermore, enrichment in the root microbiome does not predict beneficial effects on plant growth. This work underscores the need to resolve functional traits at the strain level and highlights the complexity of microbe-host-environment interactions under abiotic stress.\n\nUncovering the hidden diversity and functional roles of root endophytic Streptomyces under drought stress", "token_count": 485, "char_count": 2154, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:45.762336", "source": { "split": "train_shard_00001", "doc_id": 723 }, "chunk_id": "train_shard_00001_723_0", "global_id": 6677 }, { "text": "Kluyveromyces marxianus is a thermotolerant yeast that has been explored for potential use in biotechnological applications, such as production of biofuels, single-cell proteins, enzymes, and other heterologous proteins. Here, we present the high-quality draft of the 10.9-Mb genome of K. marxianus var. marxianus KCTC 17555 (= CBS 6556 = ATCC 26548).\n\nGenome sequence of the thermotolerant yeast Kluyveromyces marxianus var. marxianus KCTC 17555.", "token_count": 156, "char_count": 447, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:46.201300", "source": { "split": "train_shard_00001", "doc_id": 724 }, "chunk_id": "train_shard_00001_724_0", "global_id": 6678 }, { "text": "A strain of the opportunistic pathogenic yeast Candida lusitaniae was genetically modified for use as a cellular model for assessing by allele replacement the impact of lanosterol C14α-demethylase ERG11 mutations on azole resistance. Candida lusitaniae was chosen because it is susceptible to azole antifungals, it belongs to the CTG clade of yeast, which includes most of the Candida species pathogenic for humans, and it is haploid and easily amenable to genetic transformation and molecular modeling. In this work, allelic replacement is targeted at the ERG11 locus by the reconstitution of a functional auxotrophic marker in the 3' intergenic region of ERG11 Homologous and heterologous ERG11 alleles are expressed from the resident ERG11 promoter of C. lusitaniae, allowing accurate comparison of the phenotypic change in azole susceptibility. As a proof of concept, we successfully expressed in C. lusitaniae different ERG11 alleles, either bearing or not bearing mutations retrieved from a clinical context, from two phylogenetically distant yeasts, C. albicans and Kluyveromyces marxianusCandida lusitaniae constitutes a high-fidelity expression system, giving specific Erg11p-dependent fluconazole MICs very close to those observed with the ERG11 donor strain. This work led us to characterize the phenotypic effect of two kinds of mutation: mutation conferring decreased fluconazole susceptibility in a species-specific manner and mutation conferring fluconazole resistance in several yeast species", "token_count": 484, "char_count": 1613, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [ "ERG11" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:46.843327", "source": { "split": "train_shard_00001", "doc_id": 725 }, "chunk_id": "train_shard_00001_725_0", "global_id": 6679 }, { "text": "In particular, a missense mutation affecting amino acid K143 of Erg11p in Candida species, and the equivalent position K151 in K. marxianus, plays a critical role in fluconazole resistance.\n\nA CTG Clade Candida Yeast Genetically Engineered for the Genotype-Phenotype Characterization of Azole Antifungal Resistance in Human-Pathogenic Yeasts.", "token_count": 110, "char_count": 356, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8298, "quality_score": 0.9149, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:47.221451", "source": { "split": "train_shard_00001", "doc_id": 725 }, "chunk_id": "train_shard_00001_725_1", "global_id": 6680 }, { "text": "Abstract

Large structural variants (SVs) underlying important agronomic traits remain largely unexplored in Solanaceae crops. Eggplant (Solanum melongena L.) is a globally important horticultural crop worldwide, belonging to the Solanaceae family. Here, we first present population genomic analyses of a diversity panel of 201 eggplant accessions, largely representing genetic diversity from one of the main eggplant domestication centers, Southeast Asia. We revealed that genetic relationships are highly correlated with geographic origin. We then de novo generated the chromosome-scale genomes of nine representative accessions, plus five previously published assemblies, to construct a graph-based pangenome. With the aid of this resource in association scans, we identified a 12.4 Mb inversion at a high frequency (53.7%) within the population, which is associated with fruit color, likely the result of artificial selection favoring purple peel. We also discovered multiple mutations linked to bacterial wilt resistance, including a premature stop codon in SmCYP82D47 and copy number variations of SmEPS1 and SmRoq1 homologs. This study provides insights into the evolution and biology of large SVs in Solanaceae crops, as well as provides fundamental genomic resources accessible to genetic analyses and breeding in eggplant.

\n\nPangenome analysis uncovers large hidden structural variants underlying fruit color and bacterial wilt resistance in eggplant", "token_count": 337, "char_count": 1481, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7044, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:47.798363", "source": { "split": "train_shard_00001", "doc_id": 726 }, "chunk_id": "train_shard_00001_726_0", "global_id": 6681 }, { "text": "

Motivation

Burrows-Wheeler Transform (BWT) is a common component in full-text indices. Initially developed for data compression, it is particularly powerful for encoding redundant sequences such as pangenome data. However, BWT construction is resource intensive and hard to be parallelized, and many methods for querying large full-text indices only report exact matches or their simple extensions. These limitations have hampered the biological applications of full-text indices.

Results

We developed ropebwt3 for efficient BWT construction and query. Ropebwt3 indexed 320 assembled human genomes in 65 h and indexed 7.3 terabases of commonly studied bacterial assemblies in 26 days. This was achieved using up to 170 gigabytes of memory at the peak without working disk space. Ropebwt3 can find maximal exact matches and inexact alignments under affine-gap penalties, and can retrieve similar local haplotypes matching a query sequence. It demonstrates the feasibility of full-text indexing at the terabase scale.

Availability and implementation

https://github.com/lh3/ropebwt3.\n\nBWT construction and search at the terabase scale.", "token_count": 300, "char_count": 1154, "word_count": 153, "semantic_coherence": 1, "information_density": 0.732, "quality_score": 0.866, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:48.369191", "source": { "split": "train_shard_00001", "doc_id": 727 }, "chunk_id": "train_shard_00001_727_0", "global_id": 6682 }, { "text": "Global surveys of soil bacteria have identified several taxa that are nearly ubiquitous and often the most abundant members of soil bacterial communities. However, it remains unclear why these taxa are so dominant across a wide range of soil types and environmental conditions. Here we use genome-resolved metagenomics to test the hypothesis that strain-level differences exist in these taxa that are not adequately captured with standard marker gene sequencing, and that distinct strains harbor unique traits that reflect adaptations to different soil environments. We analyzed data from 331 natural soils spanning Australia to assess strain differentiation in Bradyrhizobium , a dominant soil bacterial genus of ecological importance. We developed a workflow for strain-level bacterial analyses of complex soil metagenomes, combining genomes from pre-existing databases with new genomes generated via targeted assembly from metagenomes to detect 181 Bradyrhizobium strains across the soil collection. In addition to a high degree of phylogenetic variation, we observed substantial variation in pangenome content and inferred traits, highlighting the breadth of diversity within this widespread genus. While members of the genus Bradyrhizobium were detected in > 80% of samples, most individual strains were restricted in their distributions. The overall strain-level community composition of Bradyrhizobium varied significantly across geographic space and environmental gradients, and was particularly associated with differences in temperature, soil pH, and soil nitrate and metal concentrations. Our work provides a general framework and methodology for studying the strain-level ecology of soil bacteria and highlights the ecological and pangenomic diversity within this dominant soil bacterial genus.\n\nContinent-wide assessment of the strain-level diversity of Bradyrhizobium , a dominant soil bacterial genus", "token_count": 400, "char_count": 1922, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:48.993282", "source": { "split": "train_shard_00001", "doc_id": 728 }, "chunk_id": "train_shard_00001_728_0", "global_id": 6683 }, { "text": "

Background

Understanding genetic diversity is crucial for enhancing crop productivity. This study explores species-wide genome structural variation and its role in intraspecific and ecogeographical diversification of Brassica napus , a recently evolved, globally important allopolyploid crop.

Results

We performed whole-genome long-read DNA-sequencing and constructed reference-guided genome assemblies for 94 diverse, homozygous accessions, including winter-type, spring-type, and East Asian oilseed, along with kale forms and swedes/rutabagas. We investigated pangenomic patterns of genomic structural variants (SV) and determined pangenome-wide distributions and frequencies of inversions, gene presence-absence variants, and collective SV including insertions and deletions. Results revealed pangenome-wide patterns for insertions, deletions, inversions, and large chromosomal deletions/duplications, reflecting evolutionary diversification across morphotypes and ecotypes. Collective SV were unevenly distributed and biased toward subgenome A, with asymmetrical selection pattern favoring subgenome C. Selection signatures for inversions exhibited no subgenome asymmetry; however, selection signal strength and frequency increased in paracentric chromosome regions, highlighting their evolutionary significance. Selective sweep analysis identified regions for collective SV and inversions, harboring genes for organ formation, cell division and expansion in swede, and stress responses in East Asian oilseed rape. Large chromosomal duplications and deletions distinguished swede from oilseed rape, particularly in subgenome C, including copy-number variation in flowering-time genes BnFLC.C09 and BnATX2.C08 , and cell wall development gene BnCEL2.C08 .

Conclusions

These findings underscore functional and evolutionary significance of pangenomic SV formation during B. napus diversification. Information on SV patterns with putative functional relevance, provides breeding insights, particularly for developing molecular markers to optimize performance of B. napus and other Brassica crops.\n\nPangenomic structural variant patterns reflect evolutionary diversification inBrassica napus", "token_count": 511, "char_count": 2224, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6832, "quality_score": 0.8416, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:49.654273", "source": { "split": "train_shard_00001", "doc_id": 729 }, "chunk_id": "train_shard_00001_729_0", "global_id": 6684 }, { "text": "Bacterial leaf spot of pepper (BSP), primarily caused by Xanthomonas euvesicatoria (Xe), poses a significant challenge to pepper production worldwide. Despite its impact, the genetic diversity of this pathogen remains underexplored, which limits our understanding of its population structure. To bridge this knowledge gap, we conducted a comprehensive analysis using 103 Xe strains isolated from pepper in southwest Florida to characterize genomic and type III effector (T3E) variation in this population. Phylogenetic analysis of core genomes revealed a major distinct genetic lineage associated with amylolytic activity. This amylolytic lineage was represented in Xe strains globally. Molecular clock analysis dated the emergence of amylolytic strains in Xe to around 1972. Notably, non-amylolytic strains possessed a single base pair frameshift deletion in the ⍺-amylase gene yet retained a conserved C-terminus. GUS assay revealed the expression of two open reading frames in non-amylolytic strains, one at the N-terminus and another that starts 136 base pairs upstream of the ⍺-amylase gene. Analysis of T3Es in the Florida Xe population identified variation in 12 effectors, including two classes of mutations in avrBs2 that prevent AvrBs2 from triggering a hypersensitive response in Bs2-resistant pepper plants. Knowledge of T3E variation could be used for effector-targeted disease management. This study revealed previously undescribed population structure in this economically important pathogen.IMPORTANCEBacterial leaf spot (BSP), a significant threat to pepper production globally, is primarily caused by Xanthomonas euvesicatoria (Xe). Limited genomic data has hindered detailed studies on its population diversity. This study analyzed the whole-genome sequences of 103 Xe strains from peppers in southwest Florida, along with additional global strains, to explore the pathogen's diversity", "token_count": 524, "char_count": 1974, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:50.313322", "source": { "split": "train_shard_00001", "doc_id": 730 }, "chunk_id": "train_shard_00001_730_0", "global_id": 6685 }, { "text": "The study revealed two major distinct genetic groups based on their amylolytic activity, the ability to break down starch, with non-amylolytic strains having a mutation in the ⍺-amylase gene. Additionally, two classes of mutations in the avrBs2 gene were found, leading to susceptibility in pepper plants with the Bs2 resistance gene, a commercially available resistance gene for BSP. These findings highlight the need to forecast the emergence of such strains, identify genetic factors for innovative disease management, and understand how this pathogen evolves and spreads.\n\nAmylase-associated genetic pattern in <i>Xanthomonas euvesicatoria</i> on pepper.", "token_count": 180, "char_count": 684, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7634, "quality_score": 0.8817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:50.754373", "source": { "split": "train_shard_00001", "doc_id": 730 }, "chunk_id": "train_shard_00001_730_1", "global_id": 6686 }, { "text": "

Background

Kluyveromyces marxianus, the known fastest-growing eukaryote on the earth, has remarkable thermotolerance and capacity to utilize various agricultural residues to produce low-cost bioethanol, and hence is industrially important to resolve the imminent energy shortage crisis. Currently, the poor ethanol tolerance hinders its operable application in the industry, and it is necessary to improve K. marxianus' ethanol resistance and unravel the underlying systematical mechanisms. However, this has been seldom reported to date.

Results

We carried out a wild-type haploid K. marxianus FIM1 in adaptive evolution in 6% (v/v) ethanol. After 100-day evolution, the KM-100d population was obtained; its ethanol tolerance increased up to 10% (v/v). Interestingly, DNA analysis and RNA-seq analysis showed that KM-100d yeasts' ethanol tolerance improvement was not due to ploidy change or meaningful mutations, but founded on transcriptional reprogramming in a genome-wide range. Even growth in an ethanol-free medium, many genes in KM-100d maintained their up-regulation. Especially, pathways of ethanol consumption, membrane lipid biosynthesis, anti-osmotic pressure, anti-oxidative stress, and protein folding were generally up-regulated in KM-100d to resist ethanol. Notably, enhancement of the secretory pathway may be the new strategy KM-100d developed to anti-osmotic pressure, instead of the traditional glycerol production way in S. cerevisiae. Inferred from the transcriptome data, besides ethanol tolerance, KM-100d may also develop the ability to resist osmotic, oxidative, and thermic stresses, and this was further confirmed by the cell viability test. Furthermore, under such environmental stresses, KM-100d greatly improved ethanol production than the original strain. In addition, we found that K", "token_count": 520, "char_count": 1863, "word_count": 246, "semantic_coherence": 1, "information_density": 0.7114, "quality_score": 0.8557, "entities": { "genes": [ "FIM1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "osmotic" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:51.386682", "source": { "split": "train_shard_00001", "doc_id": 731 }, "chunk_id": "train_shard_00001_731_0", "global_id": 6687 }, { "text": "marxianus may adopt distinct routes to resist different ethanol concentrations. Trehalose biosynthesis was required for low ethanol, while sterol biosynthesis and the whole secretory pathway were activated for high ethanol.

Conclusions

This study reveals that ethanol-driven laboratory evolution could improve K. marxianus' ethanol tolerance via significant up-regulation of multiple pathways including anti-osmotic, anti-oxidative, and anti-thermic processes, and indeed consequently raised ethanol yield in industrial high-temperature and high-ethanol circumstance. Our findings give genetic clues for further rational optimization of K. marxianus' ethanol production, and also partly confirm the positively correlated relationship between yeast's ethanol tolerance and production.\n\nKluyveromyces marxianus developing ethanol tolerance during adaptive evolution with significant improvements of multiple pathways.", "token_count": 237, "char_count": 947, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:51.897999", "source": { "split": "train_shard_00001", "doc_id": 731 }, "chunk_id": "train_shard_00001_731_1", "global_id": 6688 }, { "text": "To investigate the effect of yeasts on Kazak cheese quality and flavor, three isolated yeasts (Kluyveromyces marxianus A2, Pichia kudriavzevii A11, and Pichia fermentans A19) were used to ferment cheeses and designated as StC, LhC, and WcC, respectively. The cheese fermented with a commercial lactic acid starter without adding yeast was used as control named LrC. The results showed that the texture of cheese added with yeasts were more brittle. K. marxianus A2 contributed to the formation of free amino acids and organic acids, especially glutamate and lactic acid. Moreover, K. marxianus A2 provides cheese with onion, oily, and floral aromas. Furthermore, P. kudriavzevii A11 promotes a strong brandy, herbaceous, and onion flavor. Although no significant aroma change was observed in PfC, it promoted the production of acetic acid, isoamyl acetate, and phenethyl acetate. These results indicate that yeasts are important auxiliary starters for cheese production.\n\nEvaluation of the Effect of Auxiliary Starter Yeasts With Enzyme Activities on Kazak Cheese Quality and Flavor.", "token_count": 335, "char_count": 1125, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6626, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:52.490639", "source": { "split": "train_shard_00001", "doc_id": 732 }, "chunk_id": "train_shard_00001_732_0", "global_id": 6689 }, { "text": "The three Gram-negative, catalase- and oxidase-positive bacterial strains RS43T, HBC28, and HBC61T, were isolated from fresh water and subjected to a polyphasic study. Comparison of 16S rRNA gene sequence initially indicated that strains RS43T, HBC28, and HBC61T were closely related to species of genus Curvibacter and shared the highest sequence similarity of 98.14%, 98.21%, and 98.76%, respectively, with Curvibacter gracilis 7-1T. Phylogenetic analysis based on genome sequences placed all strains within the genus Curvibacter. The average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values between the three strains and related type strains supported their recognition as two novel genospecies in the genus Curvibacter. Comparative genomic analysis revealed that the genus possessed an open pangenome. Based on KEGG BlastKOALA analyses, Curvibacter species have the potential to metabolize benzoate, phenylacetate, catechol, and salicylate, indicating their potential use in the elimination of these compounds from the water systems. The results of polyphasic characterization indicated that strain RS43T and HBC61T represent two novel species, for which the name Curvibacter microcysteis sp. nov. (type strain RS43T =KCTC 92793T=LMG 32714T) and Curvibacter cyanobacteriorum sp. nov", "token_count": 480, "char_count": 1470, "word_count": 180, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [ "RS43", "HBC28", "HBC61" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:53.178140", "source": { "split": "train_shard_00001", "doc_id": 733 }, "chunk_id": "train_shard_00001_733_0", "global_id": 6690 }, { "text": "(type strain HBC61T =KCTC 92794T =LMG 32713T) are proposed.\n\nComparative Genome analysis of the Genus Curvibacter and the Description of Curvibacter microcysteis sp. nov. and Curvibacter cyanobacteriorum sp. nov., Isolated from Fresh Water during the Cyanobacterial Bloom Period.", "token_count": 131, "char_count": 333, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [ "HBC61" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:53.623246", "source": { "split": "train_shard_00001", "doc_id": 733 }, "chunk_id": "train_shard_00001_733_1", "global_id": 6691 }, { "text": "CRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign DNA by encoding CRISPR spacers that help target DNA if it re-enters the cell. In this way, CRISPR spacers are a type of molecular tape recorder of foreign DNA encountered by the host microorganism. Here, we extracted ∼8,000 CRISPR spacers from a collection of over three hundred Streptococcus mutans genomes. Phage DNA is a major target of S. mutans spacers. S. mutans strains have also generated immunity against mobile DNA elements such as plasmids and integrative and conjugative elements. There may also be considerable immunity generated against bacterial DNA, although the relative contribution of self-targeting versus bona fide intra- or inter-species targeting needs to be investigated further. While there was clear evidence that these systems have acquired immunity against foreign DNA, there appeared to be minimal impact on horizontal gene transfer (HGT) constraints on a species-level. There was little or no impact on genome size, GC content and 'openness' of the pangenome when comparing between S. mutans strains with low or high CRISPR spacer loads. In summary, while there is evidence of CRISPR spacer acquisition against self and foreign DNA, CRISPR-Cas does not act as a barrier on the expansion of the S. mutans accessory genome.\n\nInvestigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans.", "token_count": 388, "char_count": 1534, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:54.247684", "source": { "split": "train_shard_00001", "doc_id": 734 }, "chunk_id": "train_shard_00001_734_0", "global_id": 6692 }, { "text": "The Gram-negative bacterium Xylella fastidiosa colonizes plant xylem vessels and is obligately vectored by xylem sap-feeding hemipteran insects. X. fastidiosa causes diseases in many plant species but in a variety of its plant hosts this bacterium behaves as a commensal endophyte. Originally confined to the Americas, infecting mainly grapevine, citrus and coffee plants, X. fastidiosa has spread to several plant species in Europe, causing devastating crop diseases. Although many pathogenicity and virulence factors have been identified in X. fastidiosa which enable the bacterium to successfully establish in the xylem tissue, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in specific plant hosts have not been fully elucidated. Here we present comparative analyses of 94 publicly available whole-genome sequences of X. fastidiosa strains with the goal of providing insights into plant host specificity determinants for this phytopathogen as well as of expanding the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results revealed a pangenome of 4,549 protein coding sequences (CDSs) which is still open. The core- and accessory genomes comprise 954 and 2,219 CDSs, respectively. Phylogenetic tree construction using all core genome CDSs grouped the strains in three major clades of subspecies fastidiosa, multiplex and pauca , with subclades related to the strains’ sequence type (ST) obtained from multi-locus sequence typing (MLST). The geographic region where the strains were collected showed stronger association with the clades of X. fastidiosa strains rather than the plant species from which they were isolated. Among the CDS related to virulence and pathogenicity found in the core genome, those related to lipopolysaccharide (LPS) synthesis and trimeric autotransporter adhesins (TAA) are somewhat related with the plant host of a given strain according to phylogenetic inference. The X. fastidiosa accessory genome is represented by an abundant and heterogeneous mobilome, which includes a diversity of prophage regions", "token_count": 519, "char_count": 2102, "word_count": 306, "semantic_coherence": 1, "information_density": 0.6144, "quality_score": 0.8072, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:54.907503", "source": { "split": "train_shard_00001", "doc_id": 735 }, "chunk_id": "train_shard_00001_735_0", "global_id": 6693 }, { "text": "In summary, the genome comparisons reported here will enable a better understanding of the diversity of phylogenetically close genomes and warrant further investigation of LPS and TAAs as potential X. fastidiosa host-specificity determinants.

Impact statement

The bacterium Xylella fastidiosa is a pathogen that infects many plant species and has caused devastating diseases in grapevine, citrus, coffee, and olive plants. This phytopathogen X. fastidiosa is original from the Americas and has emerged in Europe where it is causing severe economic losses for olive producers, mainly in Italy. Although many pathogenicity and virulence factors have been identified in X. fastidiosa , which enable this bacterium to successfully establish in the xylem vessels network, the mechanisms by which distinct X. fastidiosa strains colonize and cause disease in the different plant host species have not been fully elucidated. The comparative analyses of 94 whole-genome sequences from X. fastidiosa strains from diverse hosts and geographic regions provide insights into host specificity determinants for this phytopathogen as well as expand the knowledge of its mobile genetic elements (MGE) content, mainly prophages. Our results contribute for a better understanding of the diversity of phylogenetically close genomes and warrant further experimental investigation of lipopolysaccharide and trimeric autotransporter adhesins as potential host-specificity determinants for X. fastidiosa .

Data summary

All genomic sequences were accessed from publicly available GenBank RefSeq database at NCBI (National Center for Biotechnology Information). A full listing of NCBI accession numbers for X. fastidiosa strains described in this paper is available in Table S1 (available in the online version of this article).\n\nComparative genomics of Xylella fastidiosa suggests determinants of host-specificity and expands its mobile genetic elements repertoire", "token_count": 453, "char_count": 1964, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5919, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:55.540856", "source": { "split": "train_shard_00001", "doc_id": 735 }, "chunk_id": "train_shard_00001_735_1", "global_id": 6694 }, { "text": "Ethyl acetate is an organic solvent with many industrial applications, currently produced by energy-intensive chemical processes based on fossil carbon resources. Ethyl acetate can be synthesized from renewable sugars by yeasts like Kluyveromyces marxianus in aerobic processes. However, ethyl acetate is highly volatile and thus stripped from aerated cultivation systems which complicate the quantification of the produced ester. Synthesis of volatile metabolites is commonly monitored by repeated analysis of metabolite concentrations in both the gas and liquid phase. In this study, a model-based method for quantifying the synthesis and degradation of volatile metabolites was developed. This quantification of volatiles is solely based on repeatedly measured gas-phase concentrations and allows calculation of reaction rates and yields in high temporal resolution. Parameters required for these calculations were determined in abiotic stripping tests. The developed method was validated for ethyl acetate, ethanol and acetaldehyde which were synthesized by K. marxianus DSM 5422 during an iron-limited batch cultivation; it was shown that the presented method is more precise and less time-consuming than the conventional method. The biomass-specific synthesis rate and the yield of ethyl acetate varied over time and exhibited distinct momentary maxima of 0.50 g g‒1h‒1 and 0.38 g g‒1 at moderate iron limitation.\n\nA new approach for balancing the microbial synthesis of ethyl acetate and other volatile metabolites during aerobic bioreactor cultivations.", "token_count": 399, "char_count": 1608, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:56.160597", "source": { "split": "train_shard_00001", "doc_id": 736 }, "chunk_id": "train_shard_00001_736_0", "global_id": 6695 }, { "text": "Vibrio parahaemolyticus is a leading cause of seafood-associated gastroenteritis, posing increasing public health challenges globally. We conducted a large-scale molecular epidemiological analysis of 7932 clinical isolates collected from seafood-associated diarrheal patients in 69 sentinel hospitals across 11 prefecture-level cities in Zhejiang Province between 2016 and 2023. Whole-genome sequencing (WGS) was performed on 1261 representative isolates, supplemented by 11,555 publicly available genomes. We analyzed temporal serotype dynamics, antimicrobial resistance genes (ARGs), virulence factors, and pangenomic diversity, with an emphasis on the globally prevalent ST3 lineage. Notably, the O10:K4 serotype emerged as the second most common within ST3, increasing in prevalence from 40.0 % to 65.6 % over the study period. O10:K4 isolates exhibited a significantly higher frequency of tdh (96.3 % vs. 78.2 %) and complete T3SS2 effector gene clusters. Nearly all isolates harbored tet(35) and blaCARB-22, indicating widespread resistance. Comparative pangenome analysis revealed O10:K4-specific acquisitions in chemotaxis and LPS synthesis (e.g., per, mcpQ, fcl) and loss of key polyamine metabolism genes (aguA, puu operon). These findings suggest that the emergence and clonal expansion of the O10:K4 serotype represent a significant epidemiological shift characterized by enhanced virulence and multidrug resistance. Sustained genomic surveillance is imperative to guide seafood safety management and clinical interventions.\n\nEmergence and genomic characterization of Vibrio parahaemolyticus serotype O10:K4 from seafood-linked diarrheal cases in Zhejiang, China (2016-2023).", "token_count": 481, "char_count": 1698, "word_count": 219, "semantic_coherence": 1, "information_density": 0.7443, "quality_score": 0.8721, "entities": { "genes": [ "ST3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:56.807039", "source": { "split": "train_shard_00001", "doc_id": 737 }, "chunk_id": "train_shard_00001_737_0", "global_id": 6696 }, { "text": "Members of the Pseudomonas syringae species complex are heterogeneous bacteria that are the most abundant bacterial plant pathogens in the plant phyllosphere, with strong abilities to exist on and infect different plant hosts and survive in/outside agroecosystems. In this study, the draft genome sequences of two pathogenic P. syringae pv. aptata strains with different in planta virulence capacities isolated from the phyllosphere of infected sugar beet were analyzed to evaluate putative features of survival strategies and to determine the pathogenic potential of the strains. The draft genomes of P. syringae pv. aptata strains P16 and P21 are 5,974,057 bp and 6,353,752 bp in size, have GC contents of 59.03% and 58.77%, respectively, and contain 3,439 and 3,536 protein-coding sequences, respectively. For both average nucleotide identity and pangenome analysis, P16 and P21 largely clustered with other pv. aptata strains from the same isolation source. We found differences in the repertoire of effectors of the type III secretion system among all 102 selected strains, suggesting that the type III secretion system is a critical factor in the different virulent phenotypes of P. syringae pv. aptata. During genome analysis of the highly virulent strain P21, we discovered genes for T3SS effectors (AvrRpm1, HopAW1, and HopAU1) that were not previously found in genomes of P. syringae pv. aptata. We also identified coding sequences for pantothenate kinase, VapC endonuclease, phospholipase, and pectate lyase in both genomes, which may represent novel effectors of the type III secretion system. IMPORTANCE Genome analysis has an enormous effect on understanding the life strategies of plant pathogens", "token_count": 502, "char_count": 1760, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:57.463786", "source": { "split": "train_shard_00001", "doc_id": 738 }, "chunk_id": "train_shard_00001_738_0", "global_id": 6697 }, { "text": "Comparing similarities with pathogens involved in other epidemics could elucidate the pathogen life cycle when a new outbreak happens. This study represents the first in-depth genome analysis of Pseudomonas syringae pv. aptata, the causative agent of leaf spot disease of sugar beet. Despite the increasing number of disease reports in recent years worldwide, there is still a lack of information about the genomic features, epidemiology, and pathogenic life strategies of this particular pathogen. Our findings provide advances in disease etiology (especially T3SS effector repertoire) and elucidate the role of environmental adaptations required for prevalence in the pathobiome of the sugar beet. From the perspective of the very heterogeneous P. syringae species complex, this type of analysis has specific importance in reporting the characteristics of individual strains.\n\nGenome Analysis of Two Pseudomonas syringae pv. <i>aptata</i> Strains with Different Virulence Capacity Isolated from Sugar Beet: Features of Successful Pathogenicity in the Phyllosphere Microbiome.", "token_count": 261, "char_count": 1096, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:58.010244", "source": { "split": "train_shard_00001", "doc_id": 738 }, "chunk_id": "train_shard_00001_738_1", "global_id": 6698 }, { "text": "Streptococcus anginosus is a prevalent member of the human flora. While it has been found in the microbiota of \"healthy\" asymptomatic individuals, it has also been associated with genitourinary tract infections and bacteremia. Based upon multilocus sequence analysis, two subspecies and two genomosubspecies have been characterized for the species. We previously conducted whole-genome sequencing of 85 S. anginosus isolates from the urinary tract. Here, we present genomic analysis of this species, including isolates from the urinary tract as well as gut and fecal, vaginal, oral, respiratory, and blood and heart samples. Average nucleotide identity and core genome analysis revealed that these strains form two distinct groups. Group 1 is comprised of the S. anginosus type strain and other previously identified S. anginosus subspecies and genomosubspecies, including isolates from throughout the human body. In contrast, group 2 consists of predominantly urinary streptococci (n = 77; 85.6%). Both of these S. anginosus groups are distinct from other members of the Streptococcus anginosus group (SAG) species S. intermedius and S. constellatus. Genes conserved among all strains of one group but not in any strains in the other group were next identified. Group 1 strains included genes found in S. intermedius and S. constellatus, suggesting that they were lost within the ancestor of the group 2 strains. In contrast, genes unique to the group 2 strains were homologous to more distant streptococci, indicative of acquisition via horizontal gene transfer. These genes are ideal candidates for use as marker genes to distinguish between the two groups in the human microbiota. IMPORTANCE Whole-genome analysis of S. anginosus strains provides greater insight into the diversity of this species than from marker genes alone. Our investigation of 166 publicly available S", "token_count": 503, "char_count": 1936, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5689, "quality_score": 0.7845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:58.672739", "source": { "split": "train_shard_00001", "doc_id": 739 }, "chunk_id": "train_shard_00001_739_0", "global_id": 6699 }, { "text": "anginosus genomes via average nucleotide identity and core genome analysis revealed two phylogenomically distinct groups of this species, with one group almost exclusively consisting of isolates from the urinary tract. In contrast, only 8 urinary strains were identified within the other group, which contained the S. anginosus type strain, as well as all identified subspecies and genomosubspecies. While genomic analysis suggested that this urinary group of S. anginosus is genomically different from the previously characterized S. anginosus subspecies, phenotypic characterization is still needed. Given prior reports of the prevalence of S. anginosus in the urinary tract of both continent and incontinent females, future studies are needed to investigate if the symptom state of the urinary tract is associated with these two different groups.\n\nComparative Genomic Study of Streptococcus anginosus Reveals Distinct Group of Urinary Strains.", "token_count": 237, "char_count": 978, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:00:59.143645", "source": { "split": "train_shard_00001", "doc_id": 739 }, "chunk_id": "train_shard_00001_739_1", "global_id": 6700 }, { "text": "Gardnerella spp. are pathognomonic for bacterial vaginosis, which increases the risk of preterm birth and the transmission of sexually transmitted infections. Gardnerella spp. are genetically diverse, comprising what have recently been defined as distinct species with differing functional capacities. Disease associations with Gardnerella spp. are not straightforward: patients with BV are usually infected with multiple species, and Gardnerella spp. are also found in the vaginal microbiome of healthy women. Genome comparisons of Gardnerella spp. show evidence of lateral gene transfer (LGT), but patterns of LGT have not been characterized in detail. Here we sought to define the role of LGT in shaping the genetic structure of Gardnerella spp. We analyzed whole genome sequencing data for 106 Gardnerella strains and used these data for pan genome analysis and to characterize LGT in the core and accessory genomes, over recent and remote timescales. In our diverse sample of Gardnerella strains, we found that both the core and accessory genomes are clearly differentiated in accordance with newly defined species designations. We identified putative competence and pilus assembly genes across most species; we also found them to be differentiated between species. Competence machinery has diverged in parallel with the core genome, with selection against deleterious mutations as a predominant influence on their evolution. By contrast, the virulence factor vaginolysin, which encodes a toxin, appears to be readily exchanged among species. We identified five distinct prophage clusters in Gardnerella genomes, two of which appear to be exchanged between Gardnerella species. Differences among species are apparent in their patterns of LGT, including their exchange with diverse gene pools. Despite frequent LGT and co-localization in the same niche, our results show that Gardnerella spp. are clearly genetically differentiated and yet capable of exchanging specific genetic material. This likely reflects complex interactions within bacterial communities associated with the vaginal microbiome", "token_count": 531, "char_count": 2179, "word_count": 302, "semantic_coherence": 1, "information_density": 0.5695, "quality_score": 0.7848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:00:59.802935", "source": { "split": "train_shard_00001", "doc_id": 740 }, "chunk_id": "train_shard_00001_740_0", "global_id": 6701 }, { "text": "Our results provide insight into how such interactions evolve and are maintained, allowing these multi-species communities to colonize and invade human tissues and adapt to antibiotics and other stressors.\n\nLateral Gene Transfer Shapes Diversity of Gardnerella spp.", "token_count": 66, "char_count": 272, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8919, "quality_score": 0.9459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:00.177381", "source": { "split": "train_shard_00001", "doc_id": 740 }, "chunk_id": "train_shard_00001_740_1", "global_id": 6702 }, { "text": "

Background

Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains with different lifestyles in foods.

Methods

We selected as diverse a set of strains as possible in terms of sources, previous genotyping results and geographical distribution, and included also 10 publicly available genomes in our analyses. We studied genomic taxonomy using pairwise average nucleotide identity (ANI) and calculation of digital DNA-DNA hybridisation (dDDH) scores. Phylogeny analyses were done using the core gene set of 1141 single-copy genes and a set of housekeeping genes commonly used for lactic acid bacteria. In addition, the pangenome and core genome sizes as well as some properties, such as acquired antimicrobial resistance (AMR), important due to the growth in foods, were analysed.

Results

Genome relatedness indices and phylogenetic analyses supported the recently suggested classification that restores the taxonomic position of L. gelidum subsp. gasicomitatum back to the species level as L. gasicomitatum. Genome properties, such as size and coding potential, revealed limited intraspecies variation and showed no attribution to the source of isolation. The distribution of the unique genes between species and subspecies was not associated with the previously documented lifestyle in foods. None of the strains carried any acquired AMR genes or genes associated with any known form of virulence.

Conclusion

Genome-wide examination of strains confirms that the proposition to restore the taxonomic position of L. gasicomitatum is justified. It further confirms that the distribution and lifestyle of L. gelidum and L", "token_count": 519, "char_count": 2149, "word_count": 310, "semantic_coherence": 1, "information_density": 0.5774, "quality_score": 0.7887, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:00.803554", "source": { "split": "train_shard_00001", "doc_id": 741 }, "chunk_id": "train_shard_00001_741_0", "global_id": 6703 }, { "text": "gasicomitatum in foods have not been driven by the evolution of functional and phylogenetic diversification detectable at the genome level.\n\nPangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum.", "token_count": 65, "char_count": 234, "word_count": 31, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:01.171541", "source": { "split": "train_shard_00001", "doc_id": 741 }, "chunk_id": "train_shard_00001_741_1", "global_id": 6704 }, { "text": "Shigellosis, a major cause of diarrheal death, is predominantly caused by Shigella flexneri and Shigella sonnei . Notably, S. sonnei has begun to overtake S. flexneri in incidence worldwide. We conducted a comparative pangenome and transcriptomic analysis of these two species using the well-established model Caenorhabditis elegans as an infection model to explore this shift. Pangenome analysis of 46 S. sonnei and 111 S. flexneri strains revealed that S. sonnei has more core genes (44%) than S. flexneri (13.6%). Additionally, S. sonnei, but not S. flexneri, has core virulence genes. The transcriptomic study during C. elegans infection showed that S. sonnei significantly upregulates the ferric enterobactin outer membrane transporter ( fepA ) and other metabolic processes (sulfur, thiamine and arginine). In contrast, S. flexneri upregulates regulatory genes involved in biofilm formation, transcription, cellular processes, and cell communication. These findings suggest that S. sonnei ’s ability to upregulate specific genes, including fepA, may confer a competitive advantage over S. flexneri . These findings provide a comprehensive understanding of the genetic and functional adaptations that may contribute to the global epidemiological shift from S. flexneri to S. sonnei , underscoring the need for further research into the mechanisms driving S. sonnei ’s increased virulence and adaptability.\n\nPangenome and Transcriptomic Analysis Revealed Distinct Virulence Genes Profiles and Infection Responses inShigella SonneiandShigella Flexneri", "token_count": 418, "char_count": 1568, "word_count": 219, "semantic_coherence": 1, "information_density": 0.621, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:01.796416", "source": { "split": "train_shard_00001", "doc_id": 742 }, "chunk_id": "train_shard_00001_742_0", "global_id": 6705 }, { "text": "

Motivation

Pangenome graphs offer a comprehensive way of capturing genomic variability across multiple genomes. However, current construction methods often introduce biases, excluding complex sequences or relying on references. The PanGenome Graph Builder (PGGB) addresses these issues. To date, though, there is no state-of-the-art pipeline allowing for easy deployment, efficient and dynamic use of available resources, and scalable usage at the same time.

Results

To overcome these limitations, we present nf-core/pangenome , a reference-unbiased approach implemented in Nextflow following nf-core’s best practices. Leveraging biocontainers ensures portability and seamless deployment in HPC environments. Unlike PGGB, nf-core/pangenome distributes alignments across cluster nodes, enabling scalability. Demonstrating its efficiency, we constructed pangenome graphs for 1000 human chromosome 19 haplotypes and 2146 E. coli sequences, achieving a two to threefold speedup compared to PGGB without increasing greenhouse gas emissions.

Availability

nf-core/pangenome is released under the MIT open-source license, available on GitHub and Zenodo, with documentation accessible at https://nf-co.re/pangenome/1.1.2/docs/usage .

Contact

simon.heumos@qbic.uni-tuebingen.de , sven.nahnsen@qbic.uni-tuebingen.de\n\nCluster efficient pangenome graph construction with nf-core/pangenome", "token_count": 382, "char_count": 1411, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7927, "quality_score": 0.8963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:02.384059", "source": { "split": "train_shard_00001", "doc_id": 743 }, "chunk_id": "train_shard_00001_743_0", "global_id": 6706 }, { "text": "The effects of yeast Kluyveromyces marxianus S-2-05, of cheese origin, were assessed on the intestine anaerobe symbiont Bacteroides thetaiotaomicron ATCC 29741 to unveil any changes in its antioxidant properties. To this end, these microorganisms were grown and incubated either separately, or co-incubated, under anaerobic atmosphere. Afterwards, the microbial cells were recovered and washed, and extracts were prepared using a sterile detergent solution to mimic the intestine detergent content. The extracts prepared from K. marxianus S-2-05 and reference strain K. marxianus MUCL 29917, grown under different conditions, were assessed for their antioxidant properties against superoxide anion and hydrogen peroxide. Extracts from both yeasts showed antioxidative effects, which were particularly important for K. marxianus S-02-5 after anaerobic incubation. Moreover, K. marxianus S-02-5 displayed a high level of activity against the aforementioned reactive oxygen species, enhancing that of B. thetaiotaomicron ATCC 29741, after the co-incubation process. Two-dimensional polyacrylamide gel electrophoresis was used to separate the proteins extracted. Superoxide dismutase, thiol peroxidase, rubrerythrin -intensively produced by B. thetaiotaomicron induced by the yeast-were identified by mass spectrometry. The antioxidative potential evidenced for K. marxianus S-02-5 is another advantage which could justify the utilization of this strain as a probiotic for countering intestinal inflammatory processes.\n\nInteractions between Kluyveromyces marxianus from cheese origin and the intestinal symbiont Bacteroides thetaiotaomicron: Impressive antioxidative effects", "token_count": 483, "char_count": 1670, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:03.028045", "source": { "split": "train_shard_00001", "doc_id": 744 }, "chunk_id": "train_shard_00001_744_0", "global_id": 6707 }, { "text": "Many commonly studied species now have more than one chromosome-scale genome assembly, revealing a large amount of genetic diversity previously missed by approaches that map short reads to a single reference. However, many species still lack multiple reference genomes and correctly aligning references to build pangenomes can be challenging for many species, limiting our ability to study this missing genomic variation in population genetics. Here, we argue that k-mers are a very useful but underutilized tool for bridging the reference-focused paradigms of population genetics with the reference-free paradigms of pangenomics. We review current literature on the uses of k-mers for performing three core components of most population genetics analyses: identifying, measuring, and explaining patterns of genetic variation. We also demonstrate how different k-mer-based measures of genetic variation behave in population genetic simulations according to the choice of k, depth of sequencing coverage, and degree of data compression. Overall, we find that k-mer-based measures of genetic diversity scale consistently with pairwise nucleotide diversity (π) up to values of about π=0.025 (R2=0.97) for neutrally evolving populations. For populations with even more variation, using shorter k-mers will maintain the scalability up to at least π=0.1. Furthermore, in our simulated populations, k-mer dissimilarity values can be reliably approximated from counting bloom filters, highlighting a potential avenue to decreasing the memory burden of k-mer-based genomic dissimilarity analyses. For future studies, there is a great opportunity to further develop methods to identifying selected loci using k-mers.\n\nK-mer-based Approaches to Bridging Pangenomics and Population Genetics.", "token_count": 384, "char_count": 1779, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6734, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:03.671442", "source": { "split": "train_shard_00001", "doc_id": 745 }, "chunk_id": "train_shard_00001_745_0", "global_id": 6708 }, { "text": "The first documented nosocomial outbreak caused by Serratia marcescens in Spain occurred in 1969 at the neonatal intensive care unit (NICU) of the tertiary La Paz Children's Hospital in Madrid, Spain, and based on the available phenotyping techniques at this time, it was considered as a monoclonal outbreak. Only 47 years later, another S. marcescens outbreak of an equivalent dimension occurred at the same NICU. The aim of the present study was to study isolates from these historical and contemporary outbreaks by phenotypic analysis and whole-genome sequencing techniques and to position these strains along with 444 publicly available S. marcescens genomes, separately comparing core genome and accessory genome contents. Clades inferred by both approaches showed high correlation, indicating that core and accessory genomes seem to evolve in the same manner for S. marcescens. Nine S. marcescens clusters were identified, and isolates were grouped in two of them according to sampling year. One exception was isolate 13F-69, the most genetically distant strain, located in a different cluster. Categorical functions in the annotated accessory genes of both collections were preserved among all isolates. No significant differences in frequency of insertion sequences in historical (0.18-0.20)-excluding the outlier strain-versus contemporary isolates (0.11-0.19) were found despite the expected resting effect. The most dissimilar isolate, 13F-69, contains a highly preserved plasmid previously described in Bordetella bronchiseptica. This strain exhibited a few antibiotic resistance genes not resulting in a resistant phenotype, suggesting the value of gene down expression in adaptation to long-term starvation.\n\nGenomics of Serratia marcescens Isolates Causing Outbreaks in the Same Pediatric Unit 47 Years Apart: Position in an Updated Phylogeny of the Species.", "token_count": 505, "char_count": 1922, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6431, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:04.352611", "source": { "split": "train_shard_00001", "doc_id": 746 }, "chunk_id": "train_shard_00001_746_0", "global_id": 6709 }, { "text": "Eucheuma denticulatum is a red macroalgae with a high carbohydrate content. The fermentable sugars from E. denticulatum were obtained through sequential thermal acid hydrolysis, enzymatic saccharification, and detoxification. Thermal acid hydrolysis of E. denticulatum was optimized under the condition of 10% (w/v) slurry content and 300 mM HNO3 at 121 ℃ for 90 min. The maximum monosaccharide concentration after thermal acid hydrolysis was 31.0 g/L with an efficiency (ETAH) of 44.7%. By further enzymatic hydrolysis of pretreated biomass solution under 20 U/mL Cellic CTec2 at 50 ℃ and 160 rpm for 72 h, the maximum monosaccharide concentration reached 79.9 g/L with an efficiency of 66.2% (ES). To remove 5-hydroxymethylfurfural (5-HMF), a fermentation inhibitor, absorption using 2% activated carbon was performed for 2 min. Ethanol fermentation was performed using wild-type and high galactose-adapted strains of Saccharomyces cerevisiae, Kluyveromyces marxianus, and Candida lusitaniae. As a result, galactose-adapted strains showed higher ethanol production than wild-type strains. Especially, the fermentation result by adaptively evolved S. cerevisiae produced the highest ethanol of 37.6 g/L and with YEtOH of 0.48 g/g. Moreover, the transcript level of MIG1 in the galactose-adapted strain was slightly lower than that in the wild-type strain. The application of adaptive evolution of microorganisms was efficient for bioethanol production.", "token_count": 488, "char_count": 1497, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [ "MIG1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:05.023908", "source": { "split": "train_shard_00001", "doc_id": 747 }, "chunk_id": "train_shard_00001_747_0", "global_id": 6710 }, { "text": "Enhancement of galactose uptake for bioethanol production from Eucheuma denticulatum hydrolysate using galactose-adapted yeasts.", "token_count": 41, "char_count": 128, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:05.423276", "source": { "split": "train_shard_00001", "doc_id": 747 }, "chunk_id": "train_shard_00001_747_1", "global_id": 6711 }, { "text": "Bacteriophages (hereafter \"phages\") are ubiquitous predators of bacteria in the natural world, but interest is growing in their development into antibacterial therapy as complement or replacement for antibiotics. However, bacteria have evolved a huge variety of antiphage defense systems allowing them to resist phage lysis to a greater or lesser extent. In addition to dedicated phage defense systems, some aspects of the general stress response also impact phage susceptibility, but the details of this are not well known. In order to elucidate these factors in the opportunistic pathogen Pseudomonas aeruginosa, we used the laboratory-conditioned strain PAO1 as host for phage infection experiments as it is naturally poor in dedicated phage defense systems. Screening by transposon insertion sequencing indicated that the uncharacterized operon PA3040-PA3042 was potentially associated with resistance to lytic phages. However, we found that its primary role appeared to be in regulating biofilm formation, particularly in a clinical isolate of P. aeruginosa in which it also altered tobramycin resistance. Its expression was highly growth-phase dependent and responsive to phage infection and cell envelope stress. Our results suggest that this operon may be a cryptic but important locus for P. aeruginosa stress tolerance.

Importance

An important category of bacterial stress response systems is bacteriophage defense, where systems are triggered by bacteriophage infection and activate a response which may either destroy the phage genome or destroy the infected cell so that the rest of the population survives. In some bacteria, the cell envelope stress response is activated by bacteriophage infection, but it is unknown whether this contributes to the survival of the infection. We have found that a conserved uncharacterized operon (PA3040-PA3042) of the cell envelope stress regulon in Pseudomonas aeruginosa, which has very few dedicated phage defense systems, responds to phage infection and stationary phase as well as envelope stress and is important for growth and biofilm formation in a clinical isolate of P. aeruginosa, even in the absence of phages", "token_count": 506, "char_count": 2213, "word_count": 319, "semantic_coherence": 1, "information_density": 0.5329, "quality_score": 0.7665, "entities": { "genes": [ "PA3040", "PAO1", "PA3042" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:06.065286", "source": { "split": "train_shard_00001", "doc_id": 748 }, "chunk_id": "train_shard_00001_748_0", "global_id": 6712 }, { "text": "As homologs of these genes are found in other bacteria, they may be a novel component of the general stress response.\n\nThe uncharacterized PA3040-3042 operon is part of the cell envelope stress response and a tobramycin resistance determinant in a clinical isolate of Pseudomonas aeruginosa.", "token_count": 79, "char_count": 298, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [ "PA3040" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:06.444374", "source": { "split": "train_shard_00001", "doc_id": 748 }, "chunk_id": "train_shard_00001_748_1", "global_id": 6713 }, { "text": "Mycobacterium abscessus (Mab) is a clinically significant pathogen and a highly genetically diverse species due to its large accessory genome. The functional consequence of this diversity remains unknown mainly because, to date, functional genomic studies in Mab have been primarily performed on reference strains. Given the growing public health threat of Mab infections, understanding the functional genomic differences among Mab clinical isolates can provide more insight into how its genetic diversity influences gene essentiality, clinically relevant phenotypes, and importantly, potential drug targets. To determine the functional genomic diversity among Mab strains, we conducted transposon-sequencing (TnSeq) on 21 genetically diverse clinical isolates, including 15 M. abscessus subsp. abscessus isolates and 6 M. abscessus subsp. massiliense isolates, cataloging all the essential and non-essential genes in each strain. Pan-genome analysis revealed a core set of 3845 genes and a large accessory genome of 11,507. We identified 259 core essential genes across the 21 clinical isolates and 425 differentially required genes, representing ~10% of the Mab core genome. We also identified genes whose requirements were sub-species, lineage, and isolate-specific. Finally, by correlating TnSeq profiles, we identified 19 previously uncharacterized genetic networks in Mab. Altogether, we find that Mab clinical isolates are not only genetically diverse but functionally diverse as well.\n\nTransposon-sequencing across multiple Mycobacterium abscessus isolates reveals significant functional genomic diversity among strains", "token_count": 382, "char_count": 1627, "word_count": 219, "semantic_coherence": 1, "information_density": 0.621, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:07.040396", "source": { "split": "train_shard_00001", "doc_id": 749 }, "chunk_id": "train_shard_00001_749_0", "global_id": 6714 }, { "text": "In yeasts, proteins of the Major Superfamily Transporter selectively bind and allow the uptake of sugars to permit growth on varied substrates. The genome of brewer's yeast, Saccharomyces cerevisiae, encodes multiple hexose transporters (Hxt) to transport glucose and other MFS proteins for maltose, galactose, and other monomers. For sugar uptake, the dairy yeast, Kluyveromyces lactis, uses Rag1p for glucose, Hgt1 for glucose and galactose, and Lac12 for lactose. In the related industrial species Kluyveromyces marxianus, there are four genes encoding Lac12-like proteins but only one of them, Lac12, can transport lactose. In this study, which initiated with efforts to investigate possible functions encoded by the additional LAC12 genes in K. marxianus, a genome-wide survey of putative MFS sugar transporters was performed. Unexpectedly, it was found that the KHT and the HGT genes are present as tandem arrays of five to six copies, with the precise number varying between isolates. Heterologous expression of individual genes in S. cerevisiae and mutagenesis of single and multiple genes in K. marxianus was performed to establish possible substrates for these transporters. The focus was on the sugar galactose since it was already reported in K. lactis that this hexose was a substrate for both Lac12 and Hgt1. It emerged that three of the four copies of Lac12, four Hgt-like proteins and one Kht-like protein have some capacity to transport galactose when expressed in S. cerevisiae and inactivation of all eight genes was required to completely abolish galactose uptake in K. marxianus", "token_count": 494, "char_count": 1683, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5772, "quality_score": 0.7886, "entities": { "genes": [ "LAC12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:07.690096", "source": { "split": "train_shard_00001", "doc_id": 750 }, "chunk_id": "train_shard_00001_750_0", "global_id": 6715 }, { "text": "Analysis of the amino acid sequence of all known yeast galactose transporters failed to identify common residues that explain the selectivity for galactose. Instead, the capacity to transport galactose has arisen three different times in K. marxianus via polymorphisms in proteins that are probably ancestral glucose transporters. Although, this is analogous to S. cerevisiae, in which Gal2 is related to glucose transporters, there are not conserved amino acid changes, either with Gal2, or among the K. marxianus galactose transporters. The data highlight how gene duplication and functional diversification has provided K. marxianus with versatile capacity to utilise sugars for growth.\n\nExpansion and Diversification of MFS Transporters in Kluyveromyces marxianus.", "token_count": 220, "char_count": 803, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:08.153002", "source": { "split": "train_shard_00001", "doc_id": 750 }, "chunk_id": "train_shard_00001_750_1", "global_id": 6716 }, { "text": "Gene expression is known to vary among individuals, and this variability can impact the phenotypic diversity observed in natural populations. While the transcriptome and proteome have been extensively studied, little is known about the translation process itself. Here, we therefore performed ribosome and transcriptomic profiling on a genetically and ecologically diverse set of natural isolates of the Saccharomyces cerevisiae yeast. Interestingly, we found that the Euclidean distances between each profile and the expression fold changes in each pairwise isolate comparison were higher at the transcriptomic level. This observation clearly indicates that the transcriptional variation observed in the different isolates is buffered through a phenomenon known as post-transcriptional buffering at the translation level. Furthermore, this phenomenon seemed to have a specific signature by preferentially affecting essential genes as well as genes involved in complex-forming proteins, and low transcribed genes. We also explored the translation of the S. cerevisiae pangenome and found that the accessory genes related to introgression events displayed similar transcription and translation levels as the core genome. By contrast, genes acquired through horizontal gene transfer events tended to be less efficiently translated. Together, our results highlight both the extent and signature of the post-transcriptional buffering.\n\nTranslation variation across genetic backgrounds reveals a post-transcriptional buffering signature in yeast", "token_count": 297, "char_count": 1540, "word_count": 208, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:09.065296", "source": { "split": "train_shard_00001", "doc_id": 751 }, "chunk_id": "train_shard_00001_751_0", "global_id": 6717 }, { "text": "Enterococci are lactic acid bacteria (LAB) that, as their name implies, often are found in the gastrointestinal tract of animals. Like many other gut-dwelling LAB, for example, various lactobacilli, they are frequently found in other niches as well, including plants and fermented foods from all over the world. In fermented foods, they contribute to flavor and other organoleptic properties, help extend shelf life, and some even possess probiotic properties. There are many positive attributes of enterococci; however, they have been overshadowed by the occurrence of antibiotic-resistant and virulent strains, often reported for the two species, Enterococcus faecalis and Enterococcus faecium. More than 40,000 whole-genome sequences covering 64 Enterococcus type species are currently available in the National Center for Biotechnology Information repository. Closer inspection of these sequences revealed that most represent the two gut-dwelling species E. faecalis and E. faecium. The remaining 62 species, many of which have been isolated from plants, are thus quite underrepresented. Of the latter species, we found that most carried no potential virulence and antibiotic resistance genes, an observation that is aligned with these species predominately occupying other niches. Thus, the culprits found in the Enterococcus genus mainly belong to E. faecalis, and a biased characterization has resulted in the opinion that enterococci do not belong in food. Since enterococci possess many industrially desirable traits and frequently are found in other niches besides the gut of animals, we suggest that their use as food fermentation microorganisms is reconsidered.IMPORTANCEWe have retrieved a large number of Enterococcus genome sequences from the National Center for Biotechnology Information repository and have scrutinized these for the presence of virulence and antibiotic resistance genes", "token_count": 482, "char_count": 1959, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5919, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:09.715765", "source": { "split": "train_shard_00001", "doc_id": 752 }, "chunk_id": "train_shard_00001_752_0", "global_id": 6718 }, { "text": "Our results show that such genes are prevalently found in the two species Enterococcus faecalis and Enterococcus faecium. Most other species do not harbor any virulence and antibiotic resistance genes and display great potential for use as food fermentation microorganisms or as probiotics. The study contributes to the current debate on enterococci and goes against the mainstream perception of enterococci as potentially dangerous microorganisms that should not be associated with food and health.\n\nGenome analysis reveals a biased distribution of virulence and antibiotic resistance genes in the genus <i>Enterococcus</i> and an abundance of safe species.", "token_count": 166, "char_count": 684, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7158, "quality_score": 0.8579, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:10.157446", "source": { "split": "train_shard_00001", "doc_id": 752 }, "chunk_id": "train_shard_00001_752_1", "global_id": 6719 }, { "text": "FetchM is a Python-based tool for fetching, analyzing, and combining bacterial genomic metadata from the NCBI Genome database and associated sample metadata from NCBI BioSample records. When working with bulk-genome analyses, such as comparative genomics or pangenome studies, you often require a unified dataset that captures the full context of a particular bacterial species population. You can obtain genomic metadata by downloading the ncbi_dataset.tsv file from the NCBI Genome database for a specific bacterial species. However, this file lacks key metadata fields such as Collection Date, Host, Geographic Location, and Isolation Source. FetchM fills this gap by automatically retrieving these missing fields, linking genome accessions to their corresponding BioSample records via the NCBI Entrez API. FetchM not only helps you compile a complete, metadata-rich dataset but also provides visualizations and summaries of both genomic and contextual metadata features. You can filter and download sequences based on specific criteria such as year, host, isolation source, country, continent, and subcontinent, making it a flexible and powerful companion for large-scale genomic studies. FetchM is available as an open-source tool at: https://github.com/Tasnimul-Arabi-Anik/FetchM . It can also be downloaded as a PyPI package.\n\nFetchM: Streamlining Genome and Metadata Integration for Microbial Comparative Genomics", "token_count": 322, "char_count": 1421, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:10.721382", "source": { "split": "train_shard_00001", "doc_id": 753 }, "chunk_id": "train_shard_00001_753_0", "global_id": 6720 }, { "text": "

Key message

Many plant cells can be induced to regenerate in vitro. We show that successful regeneration during microspore-derived embryo culture relies in part on the ability of embryogenic cells to resolve tissue culture-induced ER stress. During Brassica napus microspore embryogenesis, the immature male gametophyte is induced by a heat stress treatment to develop into a haploid embryo. Different multicellular embryogenic structures develop in response to heat stress, each with a different potential to complete embryo development. The underlying factors that determine the ability of these initially embryogenic structures to successfully complete embryo development are not known. We show that all embryogenic structures exhibit elements of endoplasmic reticulum (ER) stress, like ER expansion and protein-filled ER cisternae, but that the ER stress response is amplified in embryogenic structures with a low potential to complete embryo development. ER stress was amplified even further by treating heat-stressed cultures with trichostatin A, a histone deacetylase inhibitor epidrug that promotes embryogenic cell formation. Pharmacological treatment of microspore-derived embryo cultures with small molecule modulators of ER stress provided further evidence for the role of ER stress in microspore embryo development. Our results suggest that (1) the inability of certain embryogenic structures to resolve their ER stress responses restricts their ability to complete embryo development, and (2) histone deacetylation enhances microspore embryogenesis in B. napus, in part through its activity as an abiotic stress inducer.\n\nUnresolved ER stress restricts in vitro plant cell totipotency.", "token_count": 401, "char_count": 1707, "word_count": 237, "semantic_coherence": 1, "information_density": 0.557, "quality_score": 0.7785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:11.343147", "source": { "split": "train_shard_00001", "doc_id": 754 }, "chunk_id": "train_shard_00001_754_0", "global_id": 6721 }, { "text": "Staphylococcus aureus integrate the list of highly virulent and antibiotic resistant pathogens, mainly due to the mecA gene, associated with methicillin resistance. Given the ubiquity of this species, the aim of this study was to investigate whether closely related mecA+S. aureus found in the environment can be also thrive as clinical isolates and if the respective accessory genome may suggest bacterial adaptation. The genomes of environmental (water, animal facilities, food products, n = 111) isolates were compared with closely related genomes of clinical origin (human patients, n = 103). These genomes, available in the public database NCBI, were analysed for phylogeny, accessory genome, and presence of selected clinically relevant genes (n = 104). The genomes of environmental isolates belonged to 18 multi-locus sequence types (MLSTs), 11 of which also included clinical genomes, a result confirmed based on core-genome analysis. Genes significantly (p ≤ 0.05) more frequent among environmental genomes were related with resistance to β-lactams (blaI, blaPCI), aminoglycosides (ant(6)-Ia), macrolides (mph(C), erm(B)), enterotoxins (seg, sei, sem, sen, seo, seu) and serine protease functions (splB), among others. Genes significantly more frequent among clinical genomes were associated with resistance to macrolides (erm(C)), phenicols (fexA), fosfomycin (murA), the leucocidin virulence gene (lukS-PV), and serine protease functions (splA, splE). It is suggested that mecA+S. aureus can be exchanged between clinical and environmental settings, with accessory traits (particularly antibiotic resistance, virulence and stress response) possibly being associated with the habitat. The interplay between phylogeny and accessory genome is an interesting contribution to better understanding the ecology and evolution of mecA+S. aureus.", "token_count": 505, "char_count": 1880, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:11.998676", "source": { "split": "train_shard_00001", "doc_id": 755 }, "chunk_id": "train_shard_00001_755_0", "global_id": 6722 }, { "text": "Searching for links between environmental and clinical mecA+Staphylococcus aureus: A comparative genomics study.", "token_count": 35, "char_count": 123, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:12.353581", "source": { "split": "train_shard_00001", "doc_id": 755 }, "chunk_id": "train_shard_00001_755_1", "global_id": 6723 }, { "text": "

Purpose of review

The advancement of molecular techniques such as whole-genome sequencing (WGS) has revolutionized the field of bacterial strain typing, with important implications for epidemiological surveillance and outbreak investigations. This review summarizes state-of-the-art techniques in strain typing and examines barriers faced by clinical and public health laboratories in implementing these new methodologies.

Recent findings

WGS-based methodologies are on track to become the new 'gold standards' in bacterial strain typing, replacing traditional methods like pulsed-field gel electrophoresis and multilocus sequence typing. These new techniques have an improved ability to identify genetic relationships among organisms of interest. Further, advances in long-read sequencing approaches will likely provide a highly discriminatory tool to perform pangenome analyses and characterize relevant accessory genome elements, including mobile genetic elements carrying antibiotic resistance determinants in real time. Barriers to widespread integration of these approaches include a lack of standardized workflows and technical training.

Summary

Genomic bacterial strain typing has facilitated a paradigm shift in clinical and molecular epidemiology. The increased resolution that these new techniques provide, along with epidemiological data, will facilitate the rapid identification of transmission routes with high confidence, leading to timely and effective deployment of infection control and public health interventions in outbreak settings.\n\nTechniques in bacterial strain typing: past, present, and future.", "token_count": 327, "char_count": 1643, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6814, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:12.920112", "source": { "split": "train_shard_00001", "doc_id": 756 }, "chunk_id": "train_shard_00001_756_0", "global_id": 6724 }, { "text": "Transposable elements (TEs) significantly influence genomic diversity and gene regulation in plants. Brassica rapa and B. oleracea, with their distinct domestication histories, offer excellent models to explore TE dynamics. Here, we developed a refined TE classification method and systematically analyzed TEs across 12 B. rapa and B. oleracea genomes, identifying 1878 TE families. Approximately half (49.5%) of these TE families were shared between the two species, reflecting a common evolutionary origin, whereas species-specific expansions, particularly among long-terminal repeat (LTR) retrotransposons, underscore their roles in genomic differentiation. We notably characterized a heat-responsive Ty1-copia family (Copia0035) in B. oleracea roots, distinguished by low GC content and the absence of CG and CHG methylation motifs, sharing regulatory similarities with the Arabidopsis heat-induced ONSEN element. Syntenic analyses of gene-TE associations highlighted significant intraspecies TE insertion variability, with more accession-specific insertions in B. rapa and more conserved insertions, often associated with distinct morphotypes in B. oleracea. Gene ontology enrichment indicated TE involvement in developmental, reproductive, and stress response pathways. Transcriptome analysis across diverse accessions revealed that genes proximal to TEs, particularly those regulating floral development and flowering time, exhibit increased expression variability. These findings advance our understanding of TE-mediated genome evolution in Brassica species and underscore their potential utility in breeding and genome engineering strategies for crop improvement.\n\nTransposable elements drive evolution and perturb gene expression in Brassica rapa and B. oleracea.", "token_count": 401, "char_count": 1773, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7093, "quality_score": 0.8546, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:13.542166", "source": { "split": "train_shard_00001", "doc_id": 757 }, "chunk_id": "train_shard_00001_757_0", "global_id": 6725 }, { "text": "Streptococcus uberis is a globally endemic and poorly controlled cause of bovine mastitis impacting the sustainability of the modern dairy industry. A core genome was derived from 579 newly sequenced S. uberis isolates, along with 305 publicly available genome sequences of S. uberis isolated from 11 countries around the world and used to develop a core genome multi-locus sequence typing (cgMLST) scheme. The S. uberis core genome comprised 1475 genes, and these were used to identify 1447 curated loci that were indexed into the cgMLST scheme. This was able to type 1012 of 1037 (>97  %) isolates used and differentiated the associated sequences into 932 discrete core genome sequence types (cgSTs). Analysis of the phylogenetic relationships of cgSTs revealed no clear clustering of isolates based on metadata such as disease status or year of isolation. Geographical clustering of cgSTs was limited to identification of a UK-centric clade, but cgSTs from UK isolates were also dispersed with those originating from other geographical regions across the entire phylogenetic topology. The cgMLST scheme offers a new tool for the detailed analysis of this globally important pathogen of dairy cattle. Initial analysis has re-emphasized and exemplified the genetically diverse nature of the global population of this opportunistic pathogen.\n\nA core genome multi-locus sequence typing scheme for Streptococcus uberis: an evolution in typing a genetically diverse pathogen.", "token_count": 409, "char_count": 1507, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5991, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:14.167223", "source": { "split": "train_shard_00001", "doc_id": 758 }, "chunk_id": "train_shard_00001_758_0", "global_id": 6726 }, { "text": "Kariba weed (Salvinia molesta) was used as biomass feedstock for ethanol production by separate hydrolysis and fermentation (SHF). Monosaccharides from Kariba weed hydrolysate were produced using thermal acid hydrolysis, sonication, and enzymatic saccharification. The optimal conditions for thermal acid hydrolysis of 12% (w/v) Kariba weed slurry were evaluated as 200 mM HNO3 at 121 °C for 60 min yielding 10.2 g/L monosaccharides. Sonication for 45 min before enzymatic saccharification yielded more monosaccharides to 18.7 g/L. Enzymatic saccharification with 16 U/mL Cellic CTec2 produced 35.4 g/L monosaccharides. Fermentation was performed using Saccharomyces cerevisiae, Kluyveromyces marxianus, or Pichia stipitis with sonicated Kariba weed hydrolysate. The control fermentations were carried out using Kariba weed hydrolysate without sonication. The improvement of ethanol production from sonicated Kariba weed hydrolysate using P. stipitis produced 15.9 g/L ethanol with ethanol yield coefficient YEtOH = 0.45, K. marxianus produced 14.7 g/L ethanol with YEtOH = 0.41. S. cerevisiae produced the lowest yield of 13.2 g/L ethanol with YEtOH = 0.37 as it utilized only glucose not xylose. Sonication of Kariba weed was essential in the ethanol production to enhance the productivity of monosaccharides. P. stipitis was determined as the best yeast species using hydrolysates with the mixture of glucose and xylose to produce ethanol.", "token_count": 503, "char_count": 1486, "word_count": 206, "semantic_coherence": 1, "information_density": 0.568, "quality_score": 0.784, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:14.820084", "source": { "split": "train_shard_00001", "doc_id": 759 }, "chunk_id": "train_shard_00001_759_0", "global_id": 6727 }, { "text": "Enhanced Bioethanol Fermentation by Sonication Using Three Yeasts Species and Kariba Weed (Salvinia molesta) as Biomass Collected from Lake Victoria, Uganda.", "token_count": 45, "char_count": 157, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:15.180956", "source": { "split": "train_shard_00001", "doc_id": 759 }, "chunk_id": "train_shard_00001_759_1", "global_id": 6728 }, { "text": "Pretreatments with different concentrations of sulfuric acid (0, 0.5, and 1% v/v) and temperatures (28 and 121 °C at 103 kPa in an autoclave) were performed on banana peels (BP) milled by mechanical grinding and grinding in a blender as well as without grinding. Cellulose, hemicellulose, lignin, ash, and total and reducing sugar contents were evaluated. The highest yields of cellulose enzymatic hydrolysis (99%) were achieved with liquefied autoclaved BP treated with 0.5 and 1% acid after 48 h of hydrolysis. Ethanol production by Kluyveromyces marxianus fermentation was assayed using hydrolyzed BP at 10, 15, and 20% (w/w). The highest ethanol level (21 g/L) was reached after 24 h of fermentation with 20% (w/w) BP. Kinetics of the consumption of reducing sugars under this fermentation condition demonstrates the presence of a lag period (about 8 h). Thus, BP are a good source for ethanol production.\n\nComparison of physicochemical pretreatments of banana peels for bioethanol production.", "token_count": 328, "char_count": 1011, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:15.756352", "source": { "split": "train_shard_00001", "doc_id": 760 }, "chunk_id": "train_shard_00001_760_0", "global_id": 6729 }, { "text": "As natural environments degrade and extreme weather events become more frequent, humanity increasingly faces the challenge of producing crops under various complex and adverse conditions. Improving crop adaptability has become crucial. Universal stress proteins (USPs) are a class of small molecular proteins widely found in plants, capable of withstanding various biotic and abiotic environmental stresses, including temperature stress, drought, nutrient deficiency, oxidative imbalance, salt and heavy ion toxicity, and pathogenic infections. Enhancing our understanding of USPs holds significant potential for improving plant stress resilience. This study focuses on 13 species of Solanum, including cultivated and wild tomatoes, and systematically identified 438 members of the USP gene family through bioinformatics approaches. Phylogenetic analysis reveals that major USP members are conserved within Solanum, with interspecies differences in USP numbers primarily attributed to copy number variation (CNV). Through synteny and homology analyses, we found that USP27 and USP28 are unique to tomatoes, while the homologous gene of USP19 is absent in cultivated tomatoes. Notably, five unique USP genes are present in S. pennellii, which is characterized by its early differentiation and resistance advantages. Ka/Ks analysis indicates that only the USP10/21 homologous gene pair has undergone positive selection in wild tomatoes, while all other genes are subject to strong negative selection. The USPs in Solanum exhibit high consistency in domain characteristics, sequence conservation, and types of promoter regulatory elements, although there are substantial differences in the number of these elements. Utilizing publicly available data, we identified eight USPs that have undergone domestication or improvement selection, particularly noting the tissue-specific expression patterns of domesticated SolycUSP3/28/30", "token_count": 478, "char_count": 2008, "word_count": 260, "semantic_coherence": 1, "information_density": 0.7115, "quality_score": 0.8558, "entities": { "genes": [ "USP19", "USP28", "USP27", "USP10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:16.440902", "source": { "split": "train_shard_00001", "doc_id": 761 }, "chunk_id": "train_shard_00001_761_0", "global_id": 6730 }, { "text": "Through graph pangenome analysis, we screened 12 USPs covered by high-confidence structural variants, which primarily disrupt the intron regions of USPs, leading to significant differences in their expression responses to salt stress. We anticipate that these findings will provide a theoretical foundation and prior knowledge for further understanding and application of USP in plants.\n\nThe Evolution and expression analysis of USP gene family in <i>Solanum</i>.", "token_count": 116, "char_count": 489, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8308, "quality_score": 0.9154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:16.835812", "source": { "split": "train_shard_00001", "doc_id": 761 }, "chunk_id": "train_shard_00001_761_1", "global_id": 6731 }, { "text": "Variations in metabolite accumulation particularly anthocyanins have been of keen interest to the global tea industry due to their potential health benefits. Previous studies on tea genome, transcriptome, and metabolome provided an integrated spectrum of bioactive metabolites biosynthesis in tea plants. However, comprehending knowledge of anthocyanin biosynthesis and its accumulation in tea plants needed to be unified with multi-omics approaches that can build a complete depiction of the regulatory genomic machinery for improving quality characteristics in tea. Furthermore, true visualization, interpretation, and precise dissection of key traits required significant enrichment of multi-omics data for integration of machine learning. This review emphasizes the role of genetics, epigenetics, and transcriptional regulation of early (EBG) and late biosynthetic genes (LBG) involved in anthocyanin biosynthesis and accumulation in purple tea. Additionally, other factors including key transcription factors, transporters, photosynthesis, vacuole pH, and co-biosynthesis of other flavonoids were discussed. We envision an integration of pangenome and genome-wide strategies (GWAS, mGWAS, EWAS) which can offer new insights for the breeding of anthocyanin-rich tea cultivars to fetch better trade revenue and nutraceutical benefits.\n\nRevolutionizing Speciality Teas: Multi-omics prospective to breed anthocyanin-rich tea", "token_count": 332, "char_count": 1425, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7135, "quality_score": 0.8568, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:17.464132", "source": { "split": "train_shard_00001", "doc_id": 762 }, "chunk_id": "train_shard_00001_762_0", "global_id": 6732 }, { "text": "RNA regulators are often found in regulatory networks and mediate growth and virulence in bacteria. Small RNAs (sRNAs) are non-coding RNAs that modulate translation initiation and mRNA degradation by base pairing. To better understand the role of sRNAs in pathogenicity, several studies identified sRNAs in Streptococcus pneumoniae; however, little functional characterization has followed. This study's goals are to (i) survey putative sRNAs in S. pneumoniae; (ii) assess the conservation of these sRNAs; and (iii) examine their predicted targets. Three previous studies in S. pneumoniae identified 287 putative sRNAs by high-throughput sequencing. This study narrows the candidates down to 58 putative sRNAs. BLAST analysis indicates that the 58 sequences are highly conserved across the S. pneumoniae pangenome, and 25 are identified sporadically in other Streptococcus species. However, only two have corresponding sequences identified across several Streptococcus species. We used four RNA-target prediction programs to predict targets for each of the 58 putative sRNAs. Across all probable predictions, six sRNAs have overlapping targets predicted by multiple programs, four targeting numerous transposase-encoding transcripts. sRNAs targeting transposase-encoding transcripts display nearly identical and perfect base pairing. One sRNA, M63 (Spd_sr37), has several probable targets in the CcpA regulon, a network responsible for global catabolite repression, suggesting a possible biological function in carbon metabolism control. Each M63-target interaction exhibits unique base pairing, increasing confidence in the biological relevance of the result. This study produces a list of S", "token_count": 449, "char_count": 1727, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:18.103635", "source": { "split": "train_shard_00001", "doc_id": 763 }, "chunk_id": "train_shard_00001_763_0", "global_id": 6733 }, { "text": "pneumoniae putative sRNAs whose predicted targets suggest functional significance in transposon and carbon metabolism regulation.

Importance

Previous studies identified many small RNA candidates in Streptococcus pneumoniae, several of which were hypothesized to play a role in S. pneumoniae virulence. Due to the differing sequencing methods, diverse inclusion criteria, S. pneumoniae strain differences, as well as limited follow-up, it is unclear to what extent candidates identified in different studies have overlapping sequences and functions, and their biological relevance remains ambiguous. This research aims to consolidate the candidate sRNAs across these studies and focuses attention on those that are likely to be regulatory and associated with virulence. This study's findings enhance our knowledge of the conservation of small regulatory RNAs across the many Streptococcus pneumoniae strains and highlight a handful that appear likely to have a role in growth or virulence.\n\nAssessing the conservation and targets of putative sRNAs in <i>Streptococcus pneumoniae</i>.", "token_count": 289, "char_count": 1136, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6622, "quality_score": 0.8311, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:18.658304", "source": { "split": "train_shard_00001", "doc_id": 763 }, "chunk_id": "train_shard_00001_763_1", "global_id": 6734 }, { "text": "2. Solirubrobacter , a genus within the Actinobacteriota phylum, is commonly found in soils and rhizospheres yet remains unexplored despite its widespread presence and diversity, as revealed through metagenomic studies. Previously recognized as a prevalent soil bacterium, our study delved into phylogenomics, pangenomics, environmental diversity, and bacterial interactions of Solirubrobacter . Analyzing the limited genomic sequences available for this genus, we uncovered a pangenome consisting of 19,645 protein families, with 2,644 constituting a strict core genome. While reported isolates do not exhibit motility, we intriguingly discovered the presence of flagellin genes, albeit with an incomplete flagellum assembly pathway. Our examination of 16S ribosomal genes unveiled a considerable diversity (3,166 operational taxonomic units OTUs) of Solirubrobacter in Mexican soils, and co-occurrence network analysis indicated its extensive connectivity with other bacterial taxa. Through phylogenomic analysis, we delved into the relatedness of sequenced strains and notably dismissed ASM999324v1 as a member of this genus. Our investigation extended to the metagenomic diversity of Solirubrobacter across various environments, affirming its pervasive presence in rhizospheres and certain soils. This broader pangenomic view revealed genes linked to transcription, signal transduction, defense mechanisms, and carbohydrate metabolism, highlighting Solirubrobacter’s adaptability. We observed that Solirubrobacter’s prevalence in rhizospheres is geographically indiscriminate, prompting intriguing questions about its potential interactions with plants and the biotic and abiotic determinants of its soil occurrence. Given its richness and diversity, Solirubrobacter might be a versatile yet overlooked keystone species in its environments, meriting further recognition and study. 3.

Impact statement

This study explored the enigmatic world of Solirubrobacter , a widespread microbe commonly found in soils and plants across various regions. Despite its prevalence, little is known about its genetic diversity and functionality and how it thrives in diverse environments", "token_count": 520, "char_count": 2183, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6456, "quality_score": 0.8228, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:19.326964", "source": { "split": "train_shard_00001", "doc_id": 764 }, "chunk_id": "train_shard_00001_764_0", "global_id": 6735 }, { "text": "Our research unveils the genetic secrets of Solirubrobacter , shedding light on its adaptability and ecological interactors and roles. We showed that Solirubrobacter environmental prevalence makes it a good candidate for studying the genetic basis of being a successful microbe associated with soil and plants. 4.

Data summary

Data, scripts and statistical analysis available in GitHub: https://github.com/genomica-fciencias-unam/Solirubrobacter Sequences, phylogenetic analysis, raw data structures: https://doi.org/10.6084/m9.figshare.24446521 16S rRNA gene raw data: https://www.ncbi.nlm.nih.gov/sra/PRJNA603586 https://www.ncbi.nlm.nih.gov/sra/PRJNA603590 Shotgun metagenomes: https://www.ncbi.nlm.nih.gov/bioproject/603603 All supporting data, code, and protocols are within the article, supplementary files, and described repositories.\n\nUnraveling the Genomic and Environmental Diversity of the UbiquitousSolirubrobacter", "token_count": 309, "char_count": 942, "word_count": 98, "semantic_coherence": 1, "information_density": 0.8163, "quality_score": 0.9082, "entities": { "genes": [ "PRJNA603586", "PRJNA603590" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:19.893128", "source": { "split": "train_shard_00001", "doc_id": 764 }, "chunk_id": "train_shard_00001_764_1", "global_id": 6736 }, { "text": "

Objective

Studies investigating the relationship between the gut microbiome and osteoarthritis have increased in recent years. However, data on the relationship between joints and the gut microbiome are limited. The aim of this study was to determine whether there is a relation between knee joint fluid and gut microbiota in patients with knee osteoarthritis.

Methods

This study included 40 individuals, 20 of whom were diagnosed with knee osteoarthritis and 20 of whom were considered healthy controls. Joint-fluid and stool samples were taken from the participants. Bacteria isolated from the samples were identified using a matrix-assisted laser desorption ionization-time of flight-mass spectrometry device.

Results

Twenty-nine different bacteria were isolated from the stool samples and five bacteria were isolated from the joint-fluid samples. In our study, the same types of microorganisms (Enterococcus faecium and Staphylococcus hominis) were isolated from the stool and joint-fluid samples.

Conclusion

The data obtained in our study shed light on the uncertainty of how microorganisms, especially those identified in the knee and hip in the literature, reach these regions. The presence of intestinal bacteria in the knee joint fluid of osteoarthritis patients indicates that intestinal bacteria, especially in individuals with a weak immune system, malnutrition, and obesity, pass through the intestinal wall and reach other parts of the body via the bloodstream, a condition also known as \"leaky gut.\"\n\nA new approach to osteoarthritis: gut microbiota.", "token_count": 386, "char_count": 1594, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5475, "quality_score": 0.7738, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:20.511470", "source": { "split": "train_shard_00001", "doc_id": 765 }, "chunk_id": "train_shard_00001_765_0", "global_id": 6737 }, { "text": "

Purpose

The purpose of this study was to highlight the clinical and molecular features of 13 Raoultella ornithinolytica strains isolated from clinical environments in Ecuador, and to perform comparative genomics with previously published genomes of Raoultella spp. As Raoultella is primarily found in environmental, clinical settings, we focused our work on identifying mechanisms of resistance that can provide this bacterium an advantage to establish and persist in hospital environments.

Methods

We analyzed 13 strains of Raoultella ornithinolytica isolated from patients with healthcare associated infections (HAI) in three hospitals in Quito and one in Santo Domingo de Los Tsáchilas, Ecuador, between November 2017 and April 2018. These isolates were subjected to phenotypic antimicrobial susceptibility testing, end-point polymerase chain reaction (PCR) to detect the presence of carbapenemases and whole-genome sequencing.

Results

Polymerase chain reaction revealed that seven isolates were positive isolates for blaOXA-48 and one for blaKPC-2 gene. Of the seven strains that presented the blaOXA-48 gene, six harbored it on an IncFII plasmid, one was inserted into the bacterial chromosome. The blaKPC gene was detected in an IncM2/IncR plasmid. From the bioinformatics analysis, nine genomes had the gene blaOXA-48, originating from Ecuador. Moreover, all R. ornithinolytica strains contained the ORN-1 gene, which confers resistance for β-lactams, such as penicillins and cephalosporins", "token_count": 509, "char_count": 1644, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6537, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:21.173112", "source": { "split": "train_shard_00001", "doc_id": 766 }, "chunk_id": "train_shard_00001_766_0", "global_id": 6738 }, { "text": "Comparative genome analysis of the strains showed that the pangenome of R. ornithinolytica is considered an open pangenome, with 27.77% of core genes, which could be explained by the fact that the antibiotic resistance genes in the ancestral reconstruction are relatively new, suggesting that this genome is constantly incorporating new genes.

Conclusion

These results reveal the genome plasticity of R. ornithinolytica, particularly in acquiring antibiotic-resistance genes. The genomic surveillance and infectious control of these uncommon species are important since they may contribute to the burden of antimicrobial resistance and human health.\n\nEmergence of Raoultella ornithinolytica in human infections from different hospitals in Ecuador with OXA-48-producing resistance.", "token_count": 217, "char_count": 815, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:21.647887", "source": { "split": "train_shard_00001", "doc_id": 766 }, "chunk_id": "train_shard_00001_766_1", "global_id": 6739 }, { "text": "

Background

Carbapenem resistant Acinetobacter baumannii (CRAb) is categorised by the World Health Organization (WHO) as a pathogen of critical concern. However, little is known about CRAb transmission within the Oceania region. This study addresses this knowledge gap by using molecular epidemiology to characterise the phylogenetic relationships of CRAb isolated in hospitals in Fiji, Samoa, and other countries within the Oceania region including Australia and New Zealand, and India from South Asia.

Methods

In this multicountry cohort study, we analysed clinical isolates of CRAb collected from the Colonial War Memorial Hospital (CWMH) in Fiji from January through December 2019 (n = 64) and Tupua Tamasese Mea'ole Hospital (TTMH) in Samoa from November 2017 through June 2021 (n = 32). All isolates were characterised using mass spectrometry, antimicrobial susceptibility testing, and whole-genome sequencing. For CWMH, data were collected on clinical and demographic characteristics of patients with CRAb, duration of hospital stay, mortality and assessing the appropriateness of meropenem use from the treated patients who had CRAb infections. To provide a broader geographical context, CRAb strains from Fiji and Samoa were compared with CRAb sequences from Australia collected in 2016-2018 (n = 22), New Zealand in 2018-2021 (n = 13), and India in 2019 (n = 58), a country which has close medical links with Fiji", "token_count": 446, "char_count": 1500, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:22.290284", "source": { "split": "train_shard_00001", "doc_id": 767 }, "chunk_id": "train_shard_00001_767_0", "global_id": 6740 }, { "text": "Phylogenetic relationships of all these CRAb isolates were determined using differences in core genome SNPs.

Findings

Of CRAb isolates, 49 (77%) of 64 from Fiji and all 32 (100%) from Samoa belonged to CRAb sequence type 2 (ST2). All ST2 isolates from both countries harboured blaOXA-23, blaOXA-66 and ampC-2 genes, mediating resistance to β-lactam antimicrobials, including cephalosporins and carbapenems. The blaOXA-23 gene was associated with two copies of ISAba1 insertion element, forming the composite transposon Tn2006, on the chromosome. Two distinct clusters (group 1 and group 2) of CRAb ST2 were detected in Fiji. The first group shared common ancestral linkage to all CRAb ST2 collected from Fiji's historic outbreak in 2016/2017, Samoa, Australia and 54% of total New Zealand isolates; they formed a single cluster with a median (range) SNP difference of 13 (0-102). The second group shared common ancestral linkage to 3% of the total CRAb ST2 isolated from India. Fifty eight of the 64 patients with CRAb infections at the CWMH had their first positive CRAb sample collected 72 h or more following admission. Meropenem use was deemed inappropriate in 15 (48%) of the 31 patients that received treatment with meropenem in Fiji", "token_count": 485, "char_count": 1395, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6649, "quality_score": 0.8325, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:22.935716", "source": { "split": "train_shard_00001", "doc_id": 767 }, "chunk_id": "train_shard_00001_767_1", "global_id": 6741 }, { "text": "Other strains of CRAb ST1, ST25, ST107, and ST1112 were also detected in Fiji.

Interpretation

We identified unrecognised outbreaks of CRAb ST2 in Fiji and Samoa that linked to strains in other parts of Oceania and South Asia. The existence of Tn2006, containing the blaOXA-23 and ISAba1 insertion element, within CRAb ST2 from Fiji and Samoa indicates the potential for high mobility and dissemination. This raises concerns about unmitigated prolonged outbreaks of CRAb ST2 in the two major hospitals in Fiji and Samoa. Given the magnitude of this problem, there is a need to re-evaluate the current strategies used for infection prevention and control, antimicrobial stewardship, and public health measures locally and internationally. Moreover, a collaborative approach to AMR surveillance within the Oceania region with technical, management and budgetary support systems is required to prevent introduction and control transmission of these highly problematic strains within the island nation health systems.

Funding

This project was funded by an Otago Global Health Institute seed grant and Maurice Wilkins Centre of Research Excellence (CoREs) grant (SC0000169653, RO0000002300).\n\nMolecular and clinical epidemiology of carbapenem resistant Acinetobacter baumannii ST2 in Oceania: a multicountry cohort study.", "token_count": 403, "char_count": 1396, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "ST1112", "ST2", "ST25", "SC0000169653", "ST1", "ST107", "RO0000002300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:23.556116", "source": { "split": "train_shard_00001", "doc_id": 767 }, "chunk_id": "train_shard_00001_767_2", "global_id": 6742 }, { "text": "Klebsiella pneumoniae sensu stricto (KpI) is an opportunistic pathogen capable of residing as a commensal in both human and bovine intestinal tracts and can cause serious systemic infections in humans and severe clinical mastitis in dairy cattle. It is unclear what role zoonotic and anthroponotic transmission play in the dissemination of KpI. In this study, we use a comparative genomic approach to identify differences between KpI associated with disease in humans and cattle and aimed to identify any potential genetic barriers limiting transmission of KpI between these two hosts. A total of 128 KpI strains (bovine n = 65; human n = 63) were whole genome sequenced and human and bovine strains were compared based on phylogenomics, the pangenome, mobile genetic elements, and differential gene abundance. No obvious phylogenomic differentiation was observed between isolates from these hosts. However, subtle genetic differences exist between bovine and human KpI which likely reflect environmental adaptation to different host niches, including a higher representation of gene clusters encoding ferric citrate uptake transporters, as well as histidine, arginine, and lactose utilization pathways in bovine isolates. These gene clusters may be positively selected due to the unique metabolic environment of the mammary gland, where lactose, citrate-bound iron, and amino acids like histidine and arginine provide growth advantages for KpI during mastitis. Overall, our study identified no obvious genetic barriers to zoonotic transmission of KpI within the dairy environment and provides insight into the development of host-specific therapeutic options for KpI infections in humans and bovine.\n\nSubtle genomic differences in Klebsiella pneumoniae sensu stricto isolates indicate host adaptation", "token_count": 431, "char_count": 1801, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:24.181414", "source": { "split": "train_shard_00001", "doc_id": 768 }, "chunk_id": "train_shard_00001_768_0", "global_id": 6743 }, { "text": "Listeria monocytogenes is an opportunistic food-borne bacterium that is capable of infecting humans with high rates of hospitalization and mortality. Natural populations are genotypically and phenotypically variable, with some lineages being responsible for most human infections. The success of L. monocytogenes is linked to its capacity to persist on food and in the environment. Biofilms are an important feature that allow these bacteria to persist and infect humans, so understanding the genetic basis of biofilm formation is key to understanding transmission. We sought to investigate the biofilm-forming ability of L. monocytogenes by identifying genetic variation that underlies biofilm formation in natural populations using genome-wide association studies (GWAS). Changes in gene expression of specific strains during biofilm formation were then investigated using RNA sequencing (RNA-seq). Genetic variation associated with enhanced biofilm formation was identified in 273 genes by GWAS and differential expression in 220 genes by RNA-seq. Statistical analyses show that the number of overlapping genes flagged by either type of experiment is less than expected by random sampling. This novel finding is consistent with an evolutionary scenario where rapid adaptation is driven by variation in gene expression of pioneer genes, and this is followed by slower adaptation driven by nucleotide changes within the core genome.\n\nContrasting genes conferring short- and long-term biofilm adaptation in Listeria.", "token_count": 341, "char_count": 1544, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6186, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:24.761351", "source": { "split": "train_shard_00001", "doc_id": 769 }, "chunk_id": "train_shard_00001_769_0", "global_id": 6744 }, { "text": "Mannheimia haemolytica is a major contributor to bovine respiratory disease (BRD), which causes substantial economic losses to the beef industry, and there is an urgent need for rapid and accurate diagnostic tests to provide evidence for treatment decisions and support antimicrobial stewardship. Diagnostic sequencing can provide information about antimicrobial resistance genes in M. haemolytica more rapidly than conventional diagnostics. Realizing the full potential of diagnostic sequencing requires a comprehensive understanding of the genetic markers of antimicrobial resistance. We identified genetic markers of resistance in M. haemolytica to macrolide class antibiotics commonly used for control of BRD. Genome sequences were determined for 99 M. haemolytica isolates with six different susceptibility phenotypes collected over 2 years from a feedlot in Saskatchewan, Canada. Known macrolide resistance genes estT, msr(E), and mph(E) were identified in most resistant isolates within predicted integrative and conjugative elements (ICEs). ICE sequences lacking antibiotic resistance genes were detected in 10 of 47 susceptible isolates. No resistance-associated polymorphisms were detected in ribosomal RNA genes, although previously unreported mutations in the L22 and L23 ribosomal proteins were identified in 12 and 27 resistant isolates, respectively. Pangenome analysis led to the identification of 79 genes associated with resistance to gamithromycin, of which 95% (75 of 79) had no functional annotation. Most of the observed phenotypic resistance was explained by previously identified antibiotic resistance genes, although resistance to the macrolides gamithromycin and tulathromycin was not explained in 39 of 47 isolates, demonstrating the need for continued surveillance for novel determinants of macrolide resistance.IMPORTANCEBovine respiratory disease is the costliest disease of beef cattle in North America and the most common reason for injectable antibiotic use in beef cattle", "token_count": 507, "char_count": 2054, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5876, "quality_score": 0.7938, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:25.418253", "source": { "split": "train_shard_00001", "doc_id": 770 }, "chunk_id": "train_shard_00001_770_0", "global_id": 6745 }, { "text": "Metagenomic sequencing offers the potential to make economically significant reductions in turnaround time for diagnostic information for evidence-based selection of antibiotics for use in the feedlot. The success of diagnostic sequencing depends on a comprehensive catalog of antimicrobial resistance genes and other genome features associated with reduced susceptibility. We analyzed the genome sequences of isolates of Mannheimia haemolytica, a major bovine respiratory disease pathogen, and identified both previously known and novel genes associated with reduced susceptibility to macrolide class antimicrobials. These findings reinforce the need for ongoing surveillance for markers of antimicrobial resistance to support improved diagnostics and antimicrobial stewardship.\n\nIdentification of genetic markers of resistance to macrolide class antibiotics in Mannheimia haemolytica isolates from a Saskatchewan feedlot.", "token_count": 208, "char_count": 937, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:25.877370", "source": { "split": "train_shard_00001", "doc_id": 770 }, "chunk_id": "train_shard_00001_770_1", "global_id": 6746 }, { "text": "Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives", "token_count": 456, "char_count": 1742, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6034, "quality_score": 0.8017, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:26.513418", "source": { "split": "train_shard_00001", "doc_id": 771 }, "chunk_id": "train_shard_00001_771_0", "global_id": 6747 }, { "text": "Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.\n\nInsights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut.", "token_count": 268, "char_count": 1022, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7132, "quality_score": 0.8566, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:27.060230", "source": { "split": "train_shard_00001", "doc_id": 771 }, "chunk_id": "train_shard_00001_771_1", "global_id": 6748 }, { "text": "Bacillus velezensis, a key microorganism in traditional Korean soybean-fermented foods such as Meju, contributes to flavor and food safety. In this study, B. velezensis strains were isolated from Meju, and their morphological characteristics and biosynthetic gene clusters were analyzed using whole-genome sequencing. Pangenome analysis identified core and accessory genes, with MJ06 showing the highest number of genes associated with secondary metabolite biosynthesis, transport, and catabolism. Antimicrobial assays against six foodborne pathogenic bacteria and six fungi revealed MJ06 had the strongest antimicrobial activity, correlating with its enriched secondary metabolite biosynthetic gene clusters. Active antimicrobial compounds were extracted using C18 cartridges and anion exchange chromatography, and liquid chromatography-mass spectrometry analysis identified surfactin and bacillomycin D as major bioactive metabolites. This study highlights the power of comparative genomics in linking genetic potential to functional antimicrobial traits, facilitating the targeted selection of industrially valuable strains for food safety applications.

Supplementary information

The online version contains supplementary material available at 10.1007/s10068-025-01901-3.\n\nHarnessing genomic insights to identify antimicrobial traits in <i>Bacillus velezensis</i> MJ06 from Korean soybean-fermented Meju.", "token_count": 380, "char_count": 1440, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7396, "quality_score": 0.8698, "entities": { "genes": [ "MJ06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:27.648273", "source": { "split": "train_shard_00001", "doc_id": 772 }, "chunk_id": "train_shard_00001_772_0", "global_id": 6749 }, { "text": "

Background

Vulvovaginal candidiasis (VVC) is an important health problem caused by Candida spp. The aim of this study was molecular identification, phylogenetic analysis, and evaluation of antifungal susceptibility of non-albicans Candida isolates from VVC.

Methods

Vaginal secretion samples were collected from 550 vaginitis patients at Sayyad Shirazi Medical and Educational Center of Gorgan (Golestan Province, Iran) from May to October 2015. Samples were analyzed using conventional mycological and molecular approaches. Clinical isolates were analyzed with specific PCR using CGL primers, and the internal transcribed spacer region and the D1-D2 domain of the large-subunit rRNA gene were amplified and sequenced. Susceptibility to amphotericin B, fluconazole, itraconazole, and clotrimazole was determined by the guidelines of the Clinical and Laboratory Standard Institute.

Results

In total, 35 non-albicans Candida isolates were identified from VVC patients. The isolates included 27 strains of Candida glabrata (77.1%), 5 Candida krusei (Pichia kudriavzevii; 14.3%), 2 Candida kefyr (Kluyveromyces marxianus; 5.7%), and 1 Candida lusitaniae (Clavispora lusitaniae; 2.9%). The fungicides itraconazole and amphotericin B were effective against all species. One isolate of C. glabrata showed resistance to fluconazole and clotrimazole, and 26 isolates of C. glabrata indicated dose-dependent susceptibility to fluconazole. C. lusitaniae was susceptible in a dose-dependent manner to fluconazole and resistant to clotrimazole.

Conclusion

Non-albicans Candida spp. are common agents of vulvovaginitis, and C. glabrata is the most common species in the tested patients.", "token_count": 518, "char_count": 1701, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:28.326727", "source": { "split": "train_shard_00001", "doc_id": 773 }, "chunk_id": "train_shard_00001_773_0", "global_id": 6750 }, { "text": "Molecular Identification and Antifungal Susceptibility Pattern of Non-albicans Candida Species Isolated from Vulvovaginal Candidiasis", "token_count": 38, "char_count": 133, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:28.720823", "source": { "split": "train_shard_00001", "doc_id": 773 }, "chunk_id": "train_shard_00001_773_1", "global_id": 6751 }, { "text": "

Summary

Background

Pseudomonas aeruginosa is an opportunistic pathogen consisting of three phylogroups (hereafter named A, B, and C) of unevenly distributed size. Here, we assessed phylogroup-specific evolutionary dynamics in a collection of P. aeruginosa genomes.

Methods

In this genomic analysis, using phylogenomic and comparative genomic analyses, we generated 18 hybrid assemblies from a phylogenetically diverse collection of clinical and environmental P. aeruginosa isolates, and contextualised this information with 1991 publicly available genomes of the same species. We explored to what extent antimicrobial resistance (AMR) genes, defence systems, and virulence genes vary in their distribution across regions of genome plasticity (RGPs) and “masked” (RGP-free) genomes, and to what extent this variation differs among the phylogroups.

Findings

We found that members of phylogroup B possess larger genomes, contribute a comparatively larger number of pangenome families, and show lower abundance of CRISPR-Cas systems. Furthermore, AMR and defence systems are pervasive in RGPs and integrative and conjugative/mobilizable elements (ICEs/IMEs) from phylogroups A and B, and the abundance of these cargo genes is often significantly correlated. Moreover, inter- and intra-phylogroup interactions occur at the accessory genome level, suggesting frequent recombination events. Finally, we provide here a panel of diverse P. aeruginosa strains to be used as reference for functional analyses.

Interpretation

Altogether, our results highlight distinct pangenome characteristics of the P. aeruginosa phylogroups, which are possibly influenced by variation in the abundance of CRISPR-Cas systems and that are shaped by the differential distribution of other defence systems and AMR genes.

Funding

German Science Foundation, Max-Planck Society, Leibniz ScienceCampus Evolutionary Medicine of the Lung, BMBF program Medical Infection Genomics, Kiel Life Science Postdoc Award", "token_count": 517, "char_count": 2030, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6679, "quality_score": 0.834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:29.394906", "source": { "split": "train_shard_00001", "doc_id": 774 }, "chunk_id": "train_shard_00001_774_0", "global_id": 6752 }, { "text": "

Research in context

Evidence before this study

To date, pangenome studies exploring the epidemiology and evolution dynamics of bacterial pathogens have been limited due to the use of gene frequencies across whole species dataset without accounting for biased sampling or the population structure of the genomes in the dataset. We searched PubMed without language restrictions for articles published before September 1, 2021, that investigated the phylogroup-specific evolutionary dynamics across bacterial species. In this literature search we used the search terms “pangenome” and “phylogroup” or “uneven”, which returned 14 results. Of these, only one study used a population structure-aware approach to explore pangenome dynamics in a bacterial species consisting of multiple phylogroups with unevenly distributed members.

Added value of this study

To our knowledge, this study is the first to assess phylogroup-specific evolutionary dynamics in a collection of genomes belonging to the nosocomial pathogen P. aeruginosa. Using a refined approach that challenges traditional pangenome analyses, we found specific signatures for each of the three phylogroups, and we demonstrate that members of phylogroup B contribute a comparatively larger number of pangenome families, have larger genomes, and have a lower prevalence of CRISPR-Cas systems. Additionally, we observed that antibiotic resistance and defence systems are pervasive in regions of genome plasticity and integrative and conjugative/mobilizable elements from phylogroups A and B, and that antibiotic resistance and defence systems are often significantly correlated in these mobile genetic elements.

Implications of all the available evidence

These results indicate that biases inherent to traditional pangenome approaches can obscure the real distribution of important cargo genes in a bacterial species with a complex population structure. Furthermore, our findings pave the way to new pangenome approaches that are currently under-explored in comparative genomics and, crucially, shed a new light on the role that integrative and conjugative/mobilizable elements may play in protecting the host against foreign DNA.\n\nPhylogroup-specific variation shapes the clustering of antimicrobial resistance genes and defence systems across regions of genome plasticity", "token_count": 518, "char_count": 2361, "word_count": 324, "semantic_coherence": 1, "information_density": 0.5772, "quality_score": 0.7886, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:30.040273", "source": { "split": "train_shard_00001", "doc_id": 774 }, "chunk_id": "train_shard_00001_774_1", "global_id": 6753 }, { "text": "ST15 Klebsiella pneumoniae (Kpn) is a growing public health concern in China and worldwide, yet its genomic and evolutionary dynamics in this region remain poorly understood. This study comprehensively elucidates the population genomics of ST15 Kpn in China by analyzing 287 publicly available genomes. The proportion of the genomes increased sharply from 2012 to 2021, and 92.3% of them were collected from the Yangtze River Delta (YRD) region of eastern China. Carbapenemase genes, including OXA-232, KPC-2, and NDM, were detected in 91.6% of the studied genomes, and 69.2% of which were multidrug resistant (MDR) and hypervirulent (hv). Phylogenetic analysis revealed four clades, C1 (KL112, 59.2%), C2 (mainly KL19, 30.7%), C3 (KL48, 0.7%) and C4 (KL24, 9.4%). C1 appeared in 2007 and was OXA-232-producing and hv; C2 and C4 appeared between 2005 and 2007, and both were KPC-2-producing but with different levels of virulence. Transmission clustering detected 86.1% (n = 247) of the enrolled strains were grouped into 55 clusters (2-159 strains) and C1 was more transmissible than others. Plasmid profiling revealed 88 plasmid clusters (PCs) that were highly heterogeneous both between and within clades. 60.2% (n = 53) of the PCs carrying AMR genes and 7 of which also harbored VFs. KPC-2, NDM and OXA-232 were distributed across 14, 4 and 1 PCs, respectively", "token_count": 495, "char_count": 1378, "word_count": 214, "semantic_coherence": 1, "information_density": 0.715, "quality_score": 0.8575, "entities": { "genes": [ "KL19", "KL24", "KL112", "ST15", "KL48" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:30.698904", "source": { "split": "train_shard_00001", "doc_id": 775 }, "chunk_id": "train_shard_00001_775_0", "global_id": 6754 }, { "text": "The MDR-hv strains all carried one of two homologous PCs encoding iucABCD and rmpA2 genes. Pangenome analysis revealed two major coinciding accessory components predominantly located on plasmids. One component, associated with KPC-2, encompassed 15 additional AMR genes, while the other, linked to OXA-232, involved seven more AMR genes. This study provides essential insights into the genomic evolution of the high-risk ST15 CP-Kpn strains in China and warrants rigorous monitoring.\n\nPopulation genomic analysis of clinical ST15 Klebsiella pneumoniae strains in China.", "token_count": 171, "char_count": 590, "word_count": 80, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:31.139695", "source": { "split": "train_shard_00001", "doc_id": 775 }, "chunk_id": "train_shard_00001_775_1", "global_id": 6755 }, { "text": "

Background

Arsenic (As), found in diverse ecosystems, poses major public health risks in various parts of the world. Arsenotrophic bacteria in contaminated environments help reduce toxicity by converting arsenite (AsIII) to less harmful arsenate (AsV). We assumed that Achromobacter aegrifaciens strains from As-contaminated tubewell water and soil would share similar genomic characteristics associated with arsenic detoxification and bioremediation. To investigate this, we employed both culture-dependent and culture-independent viz. whole genome sequencing (WGS) methods to thoroughly elucidate the phenotypic and genotypic features of two A. aegrifaciens strains isolated from As-contaminated tubewell water (BAW48) and soil (BAS32) samples collected in the Bogura district of Bangladesh.

Results

Both BAW48 and BAS32 isolates demonstrated As(III) oxidation in the KMNO4 test, which was corroborated by molecular analysis confirming the presence of aioA and arsB genes in both strains. These strains were found to be phylogenetically related to many strains of Achromobacter spp., isolated from biological inorganic reactors, environmental soils, sediments and human clinical samples across diverse geographical regions. Moreover, both strains possessed distinct heavy metal resistance genes conferring resistance to Co, Zn, Cu, Cd, Hg, As, and Cr. Three As gene clusters such as As(III) oxidizing aioBA, As(III) reducing arsRCDAB and the MMA(III) oxidizing ars resistance gene (arsHCsO) cluster were predicted in both genomes of A. aegrifaciens. Further genomic analyses revealed similar profiles in both strains, with mobile genetic elements, antimicrobials and heavy metal resistance genes, virulence genes, and metabolic features. Pangenome and synteny analysis showed that the two genomes are evolutionary distinct from other strains, but closely related to one another.

Conclusion

The genomic data confirmed that A", "token_count": 503, "char_count": 1947, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [ "BAS32", "BAW48", "KMNO4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:31.791853", "source": { "split": "train_shard_00001", "doc_id": 776 }, "chunk_id": "train_shard_00001_776_0", "global_id": 6756 }, { "text": "aegrifaciens strains can oxidize As(III) and detoxify heavy metals like As, suggesting their potential for As detoxification and bioremediation. These findings align with our assumption and provide a basis for developing sustainable solutions for bioremediation efforts in As-contaminated environments.\n\nArsenotrophic Achromobacter aegrifaciens strains isolated from arsenic contaminated tubewell water and soil sources shared similar genomic potentials.", "token_count": 108, "char_count": 454, "word_count": 56, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:32.169846", "source": { "split": "train_shard_00001", "doc_id": 776 }, "chunk_id": "train_shard_00001_776_1", "global_id": 6757 }, { "text": "The geographically isolated region of the Yaghnob Valley, Tajikistan, has allowed its inhabitants to maintain a unique culture and lifestyle. Their fermented goat milk constitutes one of the staple foods for the Yaghnob population, and is produced by backslopping, i.e., using the previous fermentation batch to inoculate the new one. This study addresses the yeast composition of the fermented milk, assessing genotypic, and phenotypic properties. The 52 isolates included in this study revealed small species diversity, belonging to Kluyveromyces marxianus, Pichia fermentans, Saccharomyces cerevisiae, and one Kazachstania unispora. The K. marxianus strains showed two different genotypes, one of which never described previously. The two genetically different groups also differed significantly in several phenotypic characteristics, such as tolerance toward high temperatures, low pH, and presence of acid. Microsatellite analysis of the S. cerevisiae strains from this study, compared to 350 previously described strains, attributed the Yaghnobi S. cerevisiae to two different ancestry origins, both distinct from the wine and beer strains, and similar to strains isolated from human and insects feces, suggesting a peculiar origin of these strains, and the existence of a gut reservoir for S. cerevisiae. Our work constitutes a foundation for strain selection for future applications as starter cultures in food fermentations. This work is the first ever on yeast diversity from fermented milk of the previously unexplored area of the Yaghnob Valley.\n\nIsolation, Identification and Characterization of Yeasts from Fermented Goat Milk of the Yaghnob Valley in Tajikistan.", "token_count": 444, "char_count": 1719, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6224, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:32.806480", "source": { "split": "train_shard_00001", "doc_id": 777 }, "chunk_id": "train_shard_00001_777_0", "global_id": 6758 }, { "text": "Pseudomonas aeruginosa TBCF10839 is a highly virulent strain that can persist and replicate in human neutrophils. Screening of a signature-tagged mutagenesis (STM) TBCF10839 transposon library in phagocytosis tests identified a mutant that carried the transposon in the VirB4 homolog 5PG21 of an integrative and conjugative element (ICE)-associated type IV secretion system of the pKLC102 subtype. 5P21 TBCF10839 insertion mutants were deficient in metabolic versatility, secretion, quorum sensing, and virulence. The mutants were efficiently killed in phagocytosis tests in vitro and were avirulent in an acute murine airway infection model in vivo. The inactivation of 5PG21 silenced the rhl, las, and pqs operons and the gene expression for the synthesis of hydrogen cyanide, the antimetabolite l-2-amino-4-methoxy-trans-3-butenoic acid, and the H2- and H3-type VI secretion systems and their associated effectors. The mutants were impaired in the utilization of carbon sources and stored compounds that are not funneled into intermediary metabolism. This showcase demonstrates that a single gene of the mobile accessory genome can become an essential element to operate the core genome-encoded features of metabolism and virulence.\n\nA VirB4 ATPase of the mobile accessory genome orchestrates core genome-encoded features of physiology, metabolism, and virulence of Pseudomonas aeruginosa TBCF10839.", "token_count": 451, "char_count": 1458, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [ "TBCF10839" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:33.446298", "source": { "split": "train_shard_00001", "doc_id": 778 }, "chunk_id": "train_shard_00001_778_0", "global_id": 6759 }, { "text": "

Summary

Pangenomes represent a significant shift from relying on a single reference sequence to a robust set of assemblies, Arab populations remain significantly underrepresented; hence, we present the first Arab Pangenome Reference (APR) utilizing 53 individuals of diverse Arab ethnicities. We assembled nuclear and mitochondrial pangenomes using 35.27X high-fidelity long reads, 54.22X ultralong reads and 65.46X Hi-C reads yielded contiguous haplotype-phased de novo assemblies of exceptional quality, with an average N50 of 124.28 Mb. We discovered 111.96 million base pairs of novel euchromatic sequences absent from existing human pangenomes, the T2T-CHM13, GRCh38 reference human genomes, and other public datasets. We identified 8.94 million population-specific small variants and 235,195 structural variants within the Arab pangenome. We detected 883 gene duplications including 15.06% associated with recessive diseases and 1,436 bp of novel mitochondrial pangenome sequence. Our study provides a valuable resource for future genomic medicine initiatives in Arab population and other global populations.\n\nA draft Arab pangenome reference", "token_count": 314, "char_count": 1157, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:34.010134", "source": { "split": "train_shard_00001", "doc_id": 779 }, "chunk_id": "train_shard_00001_779_0", "global_id": 6760 }, { "text": "In this paper the effect of aflatoxin B1, ochratoxin A and zearalenon on morphology, growth parameters and metabolic activity of yeasts Saccharomyces cerevisiae, Saccharomyces uvarum, Candida utilis and Kluyveromyces marxianus was determined. The results showed that the three mycotoxins affected the morphology of all these yeasts, primarily the cell diameter, but not their final cell count. Fourier transform infrared spectroscopy showed that the yeast membranes bound the mycotoxins, C. utilis in particular. The cell membranes of most yeasts underwent denaturation, except S. uvarum exposed to ochratoxin A and zearalenone. In the early stage of fermentation, all mycotoxin-exposed yeasts had lower metabolic activity and biomass growth than controls, but fermentation products and biomass concentrations reached the control levels by the end of the fermentation, except for C. utilis exposed to 20 µg/mL of zearalenone. The adaptive response to mycotoxins suggests that certain yeasts could be used to control mycotoxin concentrations in the production of fermented food and beverages.\n\nProperties and Fermentation Activity of Industrial Yeasts Saccharomyces cerevisiae, S. uvarum, Candida utilis and Kluyveromyces marxianus Exposed to AFB1, OTA and ZEA.", "token_count": 409, "char_count": 1345, "word_count": 179, "semantic_coherence": 1, "information_density": 0.5922, "quality_score": 0.7961, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:34.631186", "source": { "split": "train_shard_00001", "doc_id": 780 }, "chunk_id": "train_shard_00001_780_0", "global_id": 6761 }, { "text": "Microorganisms are effective platforms for the production of a variety of chemicals including biofuels, commodity chemicals, polymers and other natural products. However, deep cellular understanding is required for improvement of current biofuel cell factories to truly transform the Bioeconomy. Modifications in microbial metabolic pathways and increased resistance to various types of stress caused by the production of these chemicals are crucial in the generation of robust and efficient production hosts. Recent advances in systems and synthetic biology provide new tools for metabolic engineering to design strategies and construct optimal biocatalysts for the sustainable production of desired chemicals, especially in the case of ethanol and fatty acid production. Yeast is an efficient producer of bioethanol and most of the available synthetic biology tools have been developed for the industrial yeast Saccharomyces cerevisiae. Non-conventional yeast systems have several advantageous characteristics that are not easily engineered such as ethanol tolerance, low pH tolerance, thermotolerance, inhibitor tolerance, genetic diversity and so forth. Currently, synthetic biology is still in its initial steps for studies in non-conventional yeasts such as Yarrowia lipolytica, Kluyveromyces marxianus, Issatchenkia orientalis and Pichia pastoris. Therefore, the development and application of advanced synthetic engineering tools must also focus on these underexploited, non-conventional yeast species. Herein, we review the basic synthetic biology tools that can be applied to the standard S. cerevisiae model strain, as well as those that have been developed for non-conventional yeasts. In addition, we will discuss the recent advances employed to develop non-conventional yeast strains that are efficient for the production of a variety of chemicals through the use of metabolic engineering and synthetic biology.\n\nThe Model System Saccharomyces cerevisiae Versus Emerging Non-Model Yeasts for the Production of Biofuels.", "token_count": 474, "char_count": 2082, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:35.276817", "source": { "split": "train_shard_00001", "doc_id": 781 }, "chunk_id": "train_shard_00001_781_0", "global_id": 6762 }, { "text": "

Background

The red junglefowl, the wild outgroup of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single-nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.

Methods

We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines.

Results

We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K feathering locus using short reads, which would not be possible using a linear reference.

Conclusions

We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.\n\nA pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants.", "token_count": 396, "char_count": 1766, "word_count": 250, "semantic_coherence": 1, "information_density": 0.612, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:35.894320", "source": { "split": "train_shard_00001", "doc_id": 782 }, "chunk_id": "train_shard_00001_782_0", "global_id": 6763 }, { "text": "Corynebacterium striatum, present in the microbiota of human skin and nasal mucosa, has recently emerged as a causative agent of hospital-acquired infections, notable for its resistance to multiple antimicrobials. Its mobilome comprises several mobile genetic elements, such as plasmids, transposons, insertion sequences and integrons, which contribute to the acquisition of antimicrobial resistance genes. This study analyzes the contribution of the C. striatum mobilome in the transfer and dissemination of resistance genes. In addition, integrative and conjugative elements (ICEs), essential in the dissemination of resistance genes between bacterial populations, whose role in C. striatum has not yet been studied, are examined. This study examined 365 C. striatum genomes obtained from the NCBI Pathogen Detection database. Phylogenetic and pangenome analyses were performed, the resistance profile of the bacterium was recognized, and mobile elements, including putative ICE, were detected. Bioinformatic analyses identified 20 antimicrobial resistance genes in this species, with the Ermx gene being the most predominant. Resistance genes were mainly associated with plasmid sequence regions and class 1 integrons. Although an ICE was detected, no resistance genes linked to this element were found. This study provided valuable information on the geographic spread and prevalence of outbreaks observed through phylogenetic and pangenome analyses, along with identifying antimicrobial resistance genes and mobile genetic elements that carry many of the resistance genes and may be the subject of future research and therapeutic approaches.\n\nContribution of the Mobilome to the Configuration of the Resistome of Corynebacterium striatum.", "token_count": 426, "char_count": 1785, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6017, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:36.522013", "source": { "split": "train_shard_00001", "doc_id": 783 }, "chunk_id": "train_shard_00001_783_0", "global_id": 6764 }, { "text": "

Background

A microorganism engineered for non-native tasks may suffer stresses it never met before. Therefore, we examined whether a Kluyveromyces marxianus strain engineered with a carotenoid biosynthesis pathway can serve as an anti-stress chassis for building cell factories.

Results

Carotenoids, a family of antioxidants, are valuable natural products with high commercial potential. We showed that the free radical removal ability of carotenoids can confer the engineered host with a higher tolerance to ethanol, so that it can produce more bio-ethanol than the wild type. Moreover, we found that this engineered strain has improved tolerance to other toxic effects including furfurals, heavy metals such as arsenate (biomass contaminant) and isobutanol (end product). Furthermore, the enhanced ethanol tolerance of the host can be applied to bioconversion of a natural medicine that needs to use ethanol as the delivery solvent of hydrophobic precursors. The result suggested that the engineered yeast showed enhanced tolerance to ethanol-dissolved hydrophobic 10-deacetylbaccatin III, which is considered a sustainable precursor for paclitaxel (taxol) bioconversion.

Conclusions

The stress tolerances of the engineered yeast strain showed tolerance to several toxins, so it may serve as a chassis for cell factories to produce target products, and the co-production of carotenoids may make the biorefinary more cost-effective.\n\nCharacterizing an engineered carotenoid-producing yeast as an anti-stress chassis for building cell factories.", "token_count": 399, "char_count": 1567, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:37.150137", "source": { "split": "train_shard_00001", "doc_id": 784 }, "chunk_id": "train_shard_00001_784_0", "global_id": 6765 }, { "text": "We analyzed the pan-genome and gene content modulation of the most diverse genome data set of the Mycobacterium tuberculosis complex (MTBC) gathered to date. The closed pan-genome of the MTBC was characterized by reduced accessory and strain-specific genomes, compatible with its clonal nature. However, significantly fewer gene families were shared between MTBC genomes as their phylogenetic distance increased. This effect was only observed in inter-species comparisons, not within-species, which suggests that species-specific ecological characteristics are associated with changes in gene content. Gene loss, resulting from genomic deletions and pseudogenization, was found to drive the variation in gene content. This gene erosion differed among MTBC species and lineages, even within M. tuberculosis, where L2 showed more gene loss than L4. We also show that phylogenetic proximity is not always a good proxy for gene content relatedness in the MTBC, as the gene repertoire of Mycobacterium africanum L6 deviated from its expected phylogenetic niche conservatism. Gene disruptions of virulence factors, represented by pseudogene annotations, are mostly not conserved, being poor predictors of MTBC ecotypes. Each MTBC ecotype carries its own accessory genome, likely influenced by distinct selective pressures such as host and geography. It is important to investigate how gene loss confer new adaptive traits to MTBC strains; the detected heterogeneous gene loss poses a significant challenge in elucidating genetic factors responsible for the diverse phenotypes observed in the MTBC. By detailing specific gene losses, our study serves as a resource for researchers studying the MTBC phenotypes and their immune evasion strategies.IMPORTANCEIn this study, we analyzed the gene content of different ecotypes of the Mycobacterium tuberculosis complex (MTBC), the pathogens of tuberculosis. We found that changes in their gene content are associated with their ecological features, such as host preference. Gene loss was identified as the primary driver of these changes, which can vary even among different strains of the same ecotype. Our study also revealed that the gene content relatedness of these bacteria does not always mirror their evolutionary relationships", "token_count": 523, "char_count": 2301, "word_count": 329, "semantic_coherence": 1, "information_density": 0.5805, "quality_score": 0.7903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:37.811554", "source": { "split": "train_shard_00001", "doc_id": 785 }, "chunk_id": "train_shard_00001_785_0", "global_id": 6766 }, { "text": "In addition, some genes of virulence can be variably lost among strains of the same MTBC ecotype, likely helping them to evade the immune system. Overall, our study highlights the importance of understanding how gene loss can lead to new adaptations in these bacteria and how different selective pressures may influence their genetic makeup.\n\nDiversification of gene content in the Mycobacterium tuberculosis complex is determined by phylogenetic and ecological signatures.", "token_count": 109, "char_count": 480, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8143, "quality_score": 0.9071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:38.193052", "source": { "split": "train_shard_00001", "doc_id": 785 }, "chunk_id": "train_shard_00001_785_1", "global_id": 6767 }, { "text": "Background: New chemotherapeutics are urgently required to treat Candida infections caused by drug-resistant strains. Methods: The effects of 16 1,10-phenanthroline (phen)/1,10-phenanthroline-5,6-dione/dicarboxylate complexed with Mn(II), Cu(II) and Ag(I) were evaluated against ten different Candida species. Results: Proliferation of Candida albicans, Candida dubliniensis, Candida famata, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida lusitaniae, Candida parapsilosis and Candida tropicalis was inhibited by three of six Cu(II) (MICs 1.52-21.55 μM), three of three Ag(I) (MICs 0.11-12.74 μM) and seven of seven Mn(II) (MICs 0.40-38.06 μM) complexes. Among these [Mn2(oda)(phen)4(H2O)2][Mn2(oda)(phen)4(oda)2].4H2O, where oda = octanedioic acid, exhibited effective growth inhibition (MICs 0.4-3.25 μM), favorable activity indexes, low toxicity against Vero cells and good/excellent selectivity indexes (46.88-375)", "token_count": 501, "char_count": 1144, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7411, "quality_score": 0.8705, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:38.846520", "source": { "split": "train_shard_00001", "doc_id": 786 }, "chunk_id": "train_shard_00001_786_0", "global_id": 6768 }, { "text": "Conclusion: [Mn2(oda)(phen)4(H2O)2][Mn2(oda)(phen)4(oda)2].4H2O represents a promising chemotherapeutic option for emerging, medically relevant and drug-resistant Candida species.\n\nManganese(II), copper(II) and silver(I) complexes containing 1,10-phenanthroline/1,10-phenanthroline-5,6-dione against Candida species.", "token_count": 181, "char_count": 425, "word_count": 25, "semantic_coherence": 1, "information_density": 0.88, "quality_score": 0.94, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:39.291161", "source": { "split": "train_shard_00001", "doc_id": 786 }, "chunk_id": "train_shard_00001_786_1", "global_id": 6769 }, { "text": "Inversions are a unique type of balanced structural variants (SVs) with important consequences in multiple organisms. However, despite considerable effort, this and other complex SVs remain poorly characterized due to the presence of large repeats. New techniques are finally allowing us to identify the full spectrum of human inversions, but the number of individuals analyzed is still quite limited. Here, we take advantage of Oxford Nanopore Technologies (ONT) long reads to characterize an exhaustive catalogue of 612 candidate inversions between 197 bp and 4.4 Mb of length and flanked by <190-kb long inverted repeats (IRs). For that, we developed a bioinformatic package to identify inversion alleles reliably from long read data. Next, using a combination of different DNA extraction, library preparation, and ONT sequencing protocols, we showed that ultra-long reads (50-100 kb) and adaptive sampling are an efficient method to detect most human inversions. Lastly, by analyzing ONT data from 54 diverse individuals, 87-99% of the inversions could be genotyped in each sample, depending mainly on read and IR length and genome coverage. Both orientations were observed for 155 of the analyzed regions (frequency 0.01-0.49), which multiplies by three the polymorphic IR-mediated inversions studied in detail so far. Moreover, we found more than 300 additional independent SVs in the studied regions and resolved several complex rearrangements. Our work therefore provides an accurate benchmark of those inversions that typically escape most analyses, improving existing resources, such as the Pangenome. In addition, it demonstrates the potential of nanopore sequencing to determine the functional impact of missing human genomic variation.\n\nResolving the full set of human polymorphic inversions and other complex variants from ultra-long read data", "token_count": 428, "char_count": 1857, "word_count": 273, "semantic_coherence": 1, "information_density": 0.685, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:39.932432", "source": { "split": "train_shard_00001", "doc_id": 787 }, "chunk_id": "train_shard_00001_787_0", "global_id": 6770 }, { "text": "

Motivation

The gene content regulates the biology of an organism. It varies between species and between individuals of the same species. Although tools have been developed to identify gene content changes in bacterial genomes, none is applicable to collections of large eukaryotic genomes such as the human pangenome.

Results

We developed pangene, a computational tool to identify gene orientation, gene order and gene copy-number changes in a collection of genomes. Pangene aligns a set of input protein sequences to the genomes, resolves redundancies between protein sequences and constructs a gene graph with each genome represented as a walk in the graph. It additionally finds subgraphs, which we call bibubbles, that capture gene content changes. Applied to the human pangenome, pangene identifies known gene-level variations and reveals complex haplotypes that are not well studied before. Pangene also works with high-quality bacterial pangenome and reports similar numbers of core and accessory genes in comparison to existing tools.

Availability and implementation

Source code at https://github.com/lh3/pangene; pre-built pangene graphs can be downloaded from https://zenodo.org/records/8118576 and visualized at https://pangene.bioinweb.org.\n\nExploring gene content with pangene graphs.", "token_count": 323, "char_count": 1319, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:40.520311", "source": { "split": "train_shard_00001", "doc_id": 788 }, "chunk_id": "train_shard_00001_788_0", "global_id": 6771 }, { "text": "Abstract

The phenolic antioxidant 2,6-Di-tert-butyl-p-cresol (BHT) has been detected in various environments and is considered a potential threat to aquatic organisms. Algal-bacterial interactions are crucial for maintaining ecosystem balance and elemental cycling, but their response to BHT remains to be investigated. This study analyzed the physiological and biochemical responses of the microalga Isochrysis galbana and the changes of associated bacterial communities under different concentrations of BHT stress. Results showed that the biomass of I. galbana exhibited a decreasing trend with increasing BHT concentrations up to 40 mg/L. The reduction in chlorophyll, carotenoid, and soluble protein content of microalgal cells was also observed under BHT stress. The production of malondialdehyde and the activities of superoxide dismutase, peroxidase, and catalase were further determined. Scanning electron microscopy analysis revealed that BHT caused surface rupture of the algal cells and loss of intracellular nutrients. Proteomic analysis demonstrated the upregulation of photosynthesis and citric acid cycle pathways as a response to BHT stress. Additionally, BHT significantly increased the relative abundance of specific bacteria in the phycosphere, including Marivita, Halomonas, Marinobacter, and Alteromonas. Further experiments confirmed that these bacteria had the ability to utilize BHT as the sole carbon resource for growth, and genes related to the degradation of phenolic compounds were detected through pangenome analysis.

\n\nIntegrated proteome and pangenome analysis revealed the variation of microalga Isochrysis galbana and associated bacterial community to 2,6-Di- tert-butyl-p-cresol (BHT) stress", "token_count": 472, "char_count": 1851, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6537, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:41.190153", "source": { "split": "train_shard_00001", "doc_id": 789 }, "chunk_id": "train_shard_00001_789_0", "global_id": 6772 }, { "text": "Fermented foods represent an intricate ecosystem that delivers live microbes and numerous metabolites, influencing gut health. In this review, we explore how complex microbial communities and metabolites generated during food fermentation modulate the gut microbiome and affect human health. We discuss fermentation-induced biochemical transformations, including enhanced fiber fermentability; nutrient availability; and the synthesis of bioactive metabolites such as short-chain fatty acids, exopolysaccharides, bacteriocins, and modified polyphenols. We describe the dynamic microbial ecology of fermented foods, influenced by ingredient variations, highlighting its effect on health-related metabolic outcomes. Fermented products when consumed transiently introduce beneficial microbes and bioactive compounds into the gut, thereby boosting microbial diversity, resilience, and barrier function. We review clinical and preclinical studies to substantiate the roles of fermented foods in immune regulation, metabolic homeostasis, cognitive function, and inflammation mitigation. Individual variability in response to fermented foods has been emphasized, underscoring the potential for personalized nutrition strategies informed by advanced omics technologies. By integrating microbial ecology, metabolomics, and clinical evidence, this review positions fermented food intake as a strategic dietary intervention for microbiome modulation and health promotion.\n\nFermented Foods as Functional Systems: Microbial Communities and Metabolites Influencing Gut Health and Systemic Outcomes.", "token_count": 345, "char_count": 1584, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:41.809078", "source": { "split": "train_shard_00001", "doc_id": 790 }, "chunk_id": "train_shard_00001_790_0", "global_id": 6773 }, { "text": "

Introduction

Coaggregation may reduce the abundance of bacteria in physiological fluids, such as saliva, as aggregated bacteria are cleared more easily than planktonic cells. This study aimed to identify Lactobacillus strains that coaggregate with oral pathogens with the perspective of using this approach to improve oral health.

Material and methods

Coaggregation of 719 postbiotic Lactobacillus strains with target pathogens Fusobacterium nucleatum, Porphyromonas gingivalis, and Prevotella intermedia was quantified by absorbance. Coaggregation efficacy of selected strains with clinical isolates and in the presence of other salivary bacteria was determined by flow cytometry. Brightfield and confocal microscopy were applied to characterize the size and structure of coaggregates. Pangenome analysis was used to identify genomic regions potentially involved in the coaggregation activity.

Results

Two strains, Lacticaseibacillus rhamnosus 1B06 and Lacticaseibacillus paracasei 8A12, coaggregated efficiently with all three target pathogens and clinical isolates of the same species even in the presence of other salivary bacteria. The coaggregation capability of the selected Lactobacillus strains was unique and could not be reproduced with other genetically similar lactic acid bacteria of the same species.

Conclusion

Lactobacillus strains capable of coaggregating oral pathogens were identified as promising candidates for the development of new postbiotic ingredients for oral hygiene products.\n\nCoaggregation of oral pathogens by postbiotic lactobacilli.", "token_count": 428, "char_count": 1623, "word_count": 201, "semantic_coherence": 1, "information_density": 0.592, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:42.448145", "source": { "split": "train_shard_00001", "doc_id": 791 }, "chunk_id": "train_shard_00001_791_0", "global_id": 6774 }, { "text": "Lentinula is a broadly distributed group of fungi that contains the cultivated shiitake mushroom, L. edodes. We sequenced 24 genomes representing eight described species and several unnamed lineages of Lentinula from 15 countries on four continents. Lentinula comprises four major clades that arose in the Oligocene, three in the Americas and one in Asia-Australasia. To expand sampling of shiitake mushrooms, we assembled 60 genomes of L. edodes from China that were previously published as raw Illumina reads and added them to our dataset. Lentinula edodes sensu lato (s. lat.) contains three lineages that may warrant recognition as species, one including a single isolate from Nepal that is the sister group to the rest of L. edodes s. lat., a second with 20 cultivars and 12 wild isolates from China, Japan, Korea, and the Russian Far East, and a third with 28 wild isolates from China, Thailand, and Vietnam. Two additional lineages in China have arisen by hybridization among the second and third groups. Genes encoding cysteine sulfoxide lyase (lecsl) and γ-glutamyl transpeptidase (leggt), which are implicated in biosynthesis of the organosulfur flavor compound lenthionine, have diversified in Lentinula. Paralogs of both genes that are unique to Lentinula (lecsl 3 and leggt 5b) are coordinately up-regulated in fruiting bodies of L. edodes. The pangenome of L. edodes s. lat. contains 20,308 groups of orthologous genes, but only 6,438 orthogroups (32%) are shared among all strains, whereas 3,444 orthogroups (17%) are found only in wild populations, which should be targeted for conservation.", "token_count": 526, "char_count": 1712, "word_count": 250, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:43.106891", "source": { "split": "train_shard_00001", "doc_id": 792 }, "chunk_id": "train_shard_00001_792_0", "global_id": 6775 }, { "text": "A global phylogenomic analysis of the shiitake genus Lentinula.", "token_count": 24, "char_count": 70, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:43.480055", "source": { "split": "train_shard_00001", "doc_id": 792 }, "chunk_id": "train_shard_00001_792_1", "global_id": 6776 }, { "text": "Bacterial genomic surveillance requires balancing computational efficiency with genetic resolution for effective outbreak investigation. Traditional cgMLST distance calculations treat all allelic differences as equivalent units, potentially obscuring nucleotide-level variation critical for source attribution. While SNP-based methods provide enhanced resolution, their computational requirements limit routine deployment in surveillance laboratories. We present cgDist, an algorithm that bridges this resolution gap by calculating nucleotide-level distances directly from cgMLST allelic profiles. The unified cache architecture stores comprehensive alignment statistics, enabling multiple distance calculation modes without redundant computation and supporting both dataset-specific and schema-complete cache generation. This design transforms genomic surveillance from batch processing to continuous streaming analysis, with cumulative performance benefits as laboratories accumulate alignment data. cgDist functions optimally as a precision “zoom lens” for the detailed investigation of clusters identified through initial cgMLST screening. Rather than restructuring entire population relationships, this targeted approach maximizes epidemiological insight precisely where enhanced resolution is most valuable. The algorithm ensures that cgDist distances are always greater than or equal to corresponding cgMLST distances, preserving epidemiological interpretability while adding critical genetic discrimination. The system includes integrated recombination detection capabilities that leverage cached alignment statistics to identify potential horizontal gene transfer events through mutation density analysis. This multi-scale analytical framework—from population screening through cluster zoom analysis to recombination detection—provides comprehensive surveillance capabilities within the computational constraints of routine public health practice.\n\ncgDist: An Enhanced Algorithm for Efficient Calculation of pairwise SNP and InDel differences from Core Genome Multilocus Sequence Typing", "token_count": 360, "char_count": 2095, "word_count": 241, "semantic_coherence": 1, "information_density": 0.7427, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:44.058192", "source": { "split": "train_shard_00001", "doc_id": 793 }, "chunk_id": "train_shard_00001_793_0", "global_id": 6777 }, { "text": "Provided here is a study of large language models (LLMs) and retrieval augmented generation (RAG) frameworks in air-gapped environments for genome research on small grain crops. We developed two main applications: (1) a RAG-based system for contextual analysis of scientific literature, collecting over 5,000 PDFs on wheat pathogens, and (2) a GFF3 file analysis tool called Genoma that enables exploration of genome annotation through an interactive interface. Using the open-source framework Ollama, we compared the performance of multiple LLMs including Llama3.1, Deepseek-r1, and Qwen2.5 for biological data analysis. A LightRAG approach provided semantic visualization of document relationships, while the Genoma tool offered chromosome-level insights into genome annotations. These tools demonstrate the viability of powerful AI assistance for sensitive research environments, with potential applications for pangenome analysis and gene discovery. The code provides researchers with practical solutions for implementing AI in secure settings without sacrificing analytical power.\n\nContextual Science and Genome Analysis for Air-Gapped AI Research", "token_count": 245, "char_count": 1152, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7355, "quality_score": 0.8677, "entities": { "genes": [ "GFF3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:44.549263", "source": { "split": "train_shard_00001", "doc_id": 794 }, "chunk_id": "train_shard_00001_794_0", "global_id": 6778 }, { "text": "Exposure of lactic acid bacteria (LAB) and yeasts to adverse fluctuations during fermentation causes stress; consequently, microbes develop adaptive responses. In this study, we investigated the physiological and proteomic responses of LAB and yeast to acid stress and their application in food fermentation. The physiological and proteomic responses of Lactobacillus amylovorus LS07 and Candida kefyr YS12 to acid stress were measured using turbidimetry, SDS-PAGE, and LC-MS/MS. The technique previously reported by the Association of Official Analytical Chemists (AOAC) was employed to evaluate the physicochemical and organoleptic properties of sorghum gruel fermented using LAB and yeast alone and in combination as starter cultures and spontaneous fermentation as a control. The growth of L. amylovorus LS07 was optimal at pH 1.0, and that of C. kefyr YSI2 was optimal at pH 4. An increased intensity of 30S ribosomal protein S2 (L. amylovorus LS07) and 6-phosphogluconate dehydrogenase (C. kefyr YS12) was observed at pH 1 and 4, respectively, suggesting increased microbial metabolism, thereby reducing the stress. Sorghum gruel produced with combined starters had the highest crude protein (10.94%), iron content (0.0085%), and organoleptic acceptability (7.29), which was significantly different from the products produced with the single starters and the control. The combined starter (L. amylovorus LS07 and C. kefyr YSI2) adapted to stress yielded foods with improved sensory properties, minerals, and reduced anti-nutrient contents.", "token_count": 474, "char_count": 1601, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": { "genes": [ "LS07", "YSI2", "YS12" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:45.194179", "source": { "split": "train_shard_00001", "doc_id": 795 }, "chunk_id": "train_shard_00001_795_0", "global_id": 6779 }, { "text": "Acid stress responses of Lactobacillus amylovorus and Candida kefyr isolated from fermented sorghum gruel and their application in food fermentation.", "token_count": 53, "char_count": 163, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:45.558428", "source": { "split": "train_shard_00001", "doc_id": 795 }, "chunk_id": "train_shard_00001_795_1", "global_id": 6780 }, { "text": "Previous reviews have already explored the safety and bioavailability of astaxanthin, as well as its beneficial effects on human body. The great commercial potential in a variety of industries, such as the pharmaceutical and health supplement industries, has led to a skyrocketing demand for natural astaxanthin. In this study, we have successfully optimized the astaxanthin yield up to 12.8 mg/g DCW in a probiotic yeast and purity to 97%. We also verified that it is the desired free-form 3S, 3'S configurational stereoisomer by NMR and FITR that can significantly increase the bioavailability of astaxanthin. In addition, we have proven that our extracted astaxanthin crystals have higher antioxidant capabilities compared with natural esterified astaxanthin from H. pluvialis. We also screened for potential adverse effects of the pure astaxanthin crystals extracted from the engineered probiotic yeast by dosing SD rats with 6, 12, and 24 mg/kg/day of astaxanthin crystals via oral gavages for a 13-week period and have found no significant biological differences between the control and treatment groups in rats of both genders, further confirming the safety of astaxanthin crystals. This study demonstrates that developing metabolically engineered microorganisms provides a safe and feasible approach for the bio-based production of many beneficial compounds, including astaxanthin.\n\nSafety Assessment of 3S, 3'S Astaxanthin Derived from Metabolically Engineered K. marxianus.", "token_count": 380, "char_count": 1497, "word_count": 215, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:46.145385", "source": { "split": "train_shard_00001", "doc_id": 796 }, "chunk_id": "train_shard_00001_796_0", "global_id": 6781 }, { "text": "In this study, the thermotolerant yeast Kluyveromyces marxianus CECT 10875 was compared to the industrial strain Saccharomyces cerevisiae Ethanol Red for lignocellulosic ethanol production. For it, whole slurry from steam-exploded wheat straw was used as raw material, and two process configurations, simultaneous saccharification and fermentation (SSF) and presaccharification and simultaneous saccharification and fermentation (PSSF), were evaluated. Compared to S. cerevisiae, which was able to produce ethanol in both process configurations, K. marxianus was inhibited, and neither growth nor ethanol production occurred during the processes. However, laccase treatment of the whole slurry removed specifically lignin phenols from the overall inhibitory compounds present in the slurry and triggered the fermentation by K. marxianus, attaining final ethanol concentrations and yields comparable to those obtained by S. cerevisiae.\n\nComparing cell viability and ethanol fermentation of the thermotolerant yeast Kluyveromyces marxianus and Saccharomyces cerevisiae on steam-exploded biomass treated with laccase.", "token_count": 285, "char_count": 1114, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:46.704891", "source": { "split": "train_shard_00001", "doc_id": 797 }, "chunk_id": "train_shard_00001_797_0", "global_id": 6782 }, { "text": "Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes", "token_count": 523, "char_count": 2036, "word_count": 289, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:47.365854", "source": { "split": "train_shard_00001", "doc_id": 798 }, "chunk_id": "train_shard_00001_798_0", "global_id": 6783 }, { "text": "This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.\n\nOpen pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes.", "token_count": 133, "char_count": 506, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8143, "quality_score": 0.9071, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:47.784915", "source": { "split": "train_shard_00001", "doc_id": 798 }, "chunk_id": "train_shard_00001_798_1", "global_id": 6784 }, { "text": "

Objective

Recent research has suggested that fungemia may demonstrate an epidemiologic shift in etiologic agents. This study focuses on the agents causing fungemia and antifungal resistance in a tertiary hospital.

Patients and methods

We evaluated all-age fungemia cases admitted to Balikesir Ataturk City Hospital in 2017-2021. Blood cultures (BC) were studied using BacT/Alert® 3D (bioMérieux, Marcyl'Etoile, France) and Render BC128 System (Render Biotech Co. Ltd., Shenzhen, China). On the data, we explored only the first fungal positive samples or the first isolates in different episodes of the same patients. Upon The Clinical and Laboratory Standards Institute (CLSI) disk diffusion guidelines, conventional methods and the Phoenix™ 100 System (Becton Dickinson, Franklin Lakes, NJ, USA) were utilized for antifungal susceptibility identifications.

Results

The findings showed that 325 (0.84%) of 38,682 BC sets were positive for fungal growth. Except for four cases (1.2%) [Saprochaete capitata (n = 2); Trichosporon asahii (n = 1), and Saccharomyces cerevisiae (n = 1)], all positive cases yielded Candida spp. (98.8%) growth. In these patients, the following Candida spp. were isolated: Candida albicans complex (n = 155; 47.7%), Candida parapsilosis complex (n = 127; 39.1%), Candida glabrata complex (n = 19; 5.85%), Candida tropicalis (n = 12; 3.7%), Candida kefyr (n = 5; 1.54%), Candida krusei (n = 2; 0.62%), and Candida guilliermondii complex (n = 1; 0.31%). We also realized that while none of the Candida spp", "token_count": 515, "char_count": 1551, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6844, "quality_score": 0.8422, "entities": { "genes": [ "BC128" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:48.420539", "source": { "split": "train_shard_00001", "doc_id": 799 }, "chunk_id": "train_shard_00001_799_0", "global_id": 6785 }, { "text": "had echinocandin resistance, 8 C. parapsilosis complex isolates were resistant to fluconazole, and 17 C. parapsilosis complex and 2 C. tropicalis isolates were susceptible dose-dependent to fluconazole.

Conclusions

In brief, antifungal resistance is more likely to restrict therapeutic options, albeit it is, fortunately, not prevalent in Turkey despite a few recent reports. Yet, a robust detection or management of antifungal resistance requires species-level identification and strict compliance with relevant management guidelines. Besides, challenges in research may be compensated with a national data set built with data from local laboratories.\n\nDistribution of fungemia agents in five years and antifungal resistance.", "token_count": 176, "char_count": 733, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7629, "quality_score": 0.8814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:48.865365", "source": { "split": "train_shard_00001", "doc_id": 799 }, "chunk_id": "train_shard_00001_799_1", "global_id": 6786 }, { "text": "In the model yeast Saccharomyces cerevisiae, Trk1 is the main K+ importer. It is involved in many important physiological processes, such as the maintenance of ion homeostasis, cell volume, intracellular pH, and plasma-membrane potential. The ScTrk1 protein can be of great interest to industry, as it was shown that changes in its activity influence ethanol production and tolerance in S. cerevisiae and also cell performance in the presence of organic acids or high ammonium under low K+ conditions. Nonconventional yeast species are attracting attention due to their unique properties and as a potential source of genes that encode proteins with unusual characteristics. In this work, we aimed to study and compare Trk proteins from Debaryomyces hansenii, Hortaea werneckii, Kluyveromyces marxianus, and Yarrowia lipolytica, four biotechnologically relevant yeasts that tolerate various extreme environments. Heterologous expression in S. cerevisiae cells lacking the endogenous Trk importers revealed differences in the studied Trk proteins' abilities to support the growth of cells under various cultivation conditions such as low K+ or the presence of toxic cations, to reduce plasma-membrane potential or to take up Rb+ . Examination of the potential of Trks to support the stress resistance of S. cerevisiae wild-type strains showed that Y. lipolytica Trk1 is a promising tool for improving cell tolerance to both low K+ and high salt and that the overproduction of S. cerevisiae's own Trk1 was the most efficient at improving the growth of cells in the presence of highly toxic Li+ ions.\n\nHeterologous expression reveals unique properties of Trk K+ importers from nonconventional biotechnologically relevant yeast species together with their potential to support Saccharomyces cerevisiae growth.", "token_count": 474, "char_count": 1881, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5672, "quality_score": 0.7836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:49.510521", "source": { "split": "train_shard_00001", "doc_id": 800 }, "chunk_id": "train_shard_00001_800_0", "global_id": 6787 }, { "text": "Abstract

Background

Fungi are ubiquitous in the environment, and for patients with risk factors, they can present as pathogens. Unusual fungi often pose a diagnostic challenge and when encountered in practice, albeit infrequently, can delay diagnosis and treatment.

Methods

Over a period of three years (2018-2020), such cases were followed up till death or discharge and all details were noted down. All patients were diagnosed to have invasive fungal disease according to the EORTC/MSG criteria. Species identification was performed using MALDI-TOF MS and antifungal susceptibility testing (AFST) was done using standard CLSI guidelines.

Results

A total of 14 cases of rare yeasts were noted out of a total of 155 infections due to yeasts. Among these 5 presented with fungemia and 9 with invasive fungal infections (IFI). Of the IFI clinical isolates, there were 2 pus samples and 7 sterile fluids. The majority of these 14 patients were male (11) and belonged to extremes of age (8). The risk factors included CKD (2), prior history of tuberculosis (2), CLD (1), congenital heart disease (2), and type 2 diabetes mellitus (1). Pathogens isolated were Candida guilliermondii (2), Candida pelliculosa (2), Lodderomyces elongisporus (1) from the blood samples, and Trichosporon asahii (6), Candida guilliermondii (1), Candida kefyr (1), and Geotrichum spp. (1) from the other samples. Certain Candida species showed higher MICs to azoles and echinocandins. Trichosporon and Geotrichum showed higher MICs to azoles. Unfortunately, half of the patients (7) received no antifungals. Of those who did, 4 received mono therapy with azoles or Amphotericin B, while other 3 received combination or sequential therapy with azoles, echinocandins and Amphotericin B. Of the 14 patients, 3 patients expired", "token_count": 520, "char_count": 1823, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:50.518795", "source": { "split": "train_shard_00001", "doc_id": 801 }, "chunk_id": "train_shard_00001_801_0", "global_id": 6788 }, { "text": "The etiological agents in these cases were Candida pelliculosa (fungemia) and Trichosporon asahii (IFI, 2 cases).

Conclusion

This study aims to highlight the clinical presentation of uncommon yeasts, presenting both as bloodstream infections (BSI) and as invasive disease. Improved methods of detection will help us improve our diagnostic accuracy of uncommon pathogens. The clinician should liaise closely with the laboratory, and treatment should be instituted according to the AFST data.

Disclosures

All Authors: No reported disclosures.\n\n479. Predisposing factors and outcomes of infections due to rare yeasts: a study from an apex medical center in India (2018-2020).", "token_count": 186, "char_count": 690, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8144, "quality_score": 0.9072, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:50.964043", "source": { "split": "train_shard_00001", "doc_id": 801 }, "chunk_id": "train_shard_00001_801_1", "global_id": 6789 }, { "text": "The aim of the study was to check the integument and alimentary tract of Theromyzon for the occurrence of fungi. Moreover, the mycological purity of water sources from which leeches were collected was analyzed. The potential role of the duck leech Theromyzon maculosum in transmitting pathogenic fungi has not been studied until now. Mycological analyses were performed according to the procedure approved in mycological diagnostic laboratories, using classical diagnostic methods (macro- and microcultures, microscopic observations). In total, 22 species of yeasts were detected. The specimens belong to eight genera: Candida, Citeromyces, Debaryomyces, Kluyveromyces, Lodderomyces, Pichia, Saccharomyces and Saccharomycodes. Overall, 18 species of fungi were isolated from leeches Theromyzon maculosum, including seven species from the integument and 11 species from the gastrointestinal system. Among fungi isolated from body integument, fungi of the genus Candida were dominant, whereas in the gastrointestinal system, the genus Saccharomyces dominated. From the river waters, nine fungi species were isolated, and yeasts of the genera Candida and Kluyveromyces dominated. Isolation of the same species of microfungi from the integument of leeches and the river water suggests that Theromyzon maculosum may be a potential vector of pathogenic yeasts for vertebrates living in the same ecosystems and for humans.\n\nTheromyzon maculosum (Rathke, 1862) as a vector of potentially pathogenic fungi in aquatic ecosystems.", "token_count": 492, "char_count": 1638, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5421, "quality_score": 0.771, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:51.616115", "source": { "split": "train_shard_00001", "doc_id": 802 }, "chunk_id": "train_shard_00001_802_0", "global_id": 6790 }, { "text": "Recent studies suggest that Wohlfahrtiimonas chitiniclastica may be the cause of several diseases in humans including sepsis and bacteremia making the bacterium as a previously underappreciated human pathogen. However, very little is known about the pathogenicity and genetic potential of W. chitiniclastica; therefore, it is necessary to conduct systematic studies to gain a deeper understanding of its virulence characteristics and treatment options. In this study, the entire genetic repertoire of all publicly available W. chitiniclastica genomes was examined including in silico characterization of bacteriophage content, antibiotic resistome, and putative virulence profile. The pan-genome of W. chitiniclastica comprises 3819 genes with 1622 core genes (43%) indicating a putative metabolic conserved species. Furthermore, in silico analysis indicated presumed resistome expansion as defined by the presence of genome-encoded transposons and bacteriophages. While macrolide resistance genes macA and macB are located within the core genome, additional antimicrobial resistance genotypes for tetracycline (tetH, tetB, and tetD), aminoglycosides (ant(2'')-Ia, aac(6')-Ia,aph(3'')-Ib, aph(3')-Ia, and aph(6)-Id)), sulfonamide (sul2), streptomycin (strA), chloramphenicol (cat3), and beta-lactamase (blaVEB) are distributed among the accessory genome", "token_count": 476, "char_count": 1479, "word_count": 172, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:52.293166", "source": { "split": "train_shard_00001", "doc_id": 803 }, "chunk_id": "train_shard_00001_803_0", "global_id": 6791 }, { "text": "Notably, our data indicate that the type strain DSM 18708T does not encode any additional clinically relevant antibiotic resistance genes, whereas drug resistance is increasing within the W. chitiniclastica clade. This trend should be monitored with caution. To the best of our knowledge, this is the first comprehensive genome analysis of this species, providing new insights into the genome of this opportunistic human pathogen.\n\nComparative Genomic Analysis of the Human Pathogen Wohlfahrtiimonas Chitiniclastica Provides Insight Into the Identification of Antimicrobial Resistance Genotypes and Potential Virulence Traits.", "token_count": 168, "char_count": 651, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7442, "quality_score": 0.8721, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:52.759322", "source": { "split": "train_shard_00001", "doc_id": 803 }, "chunk_id": "train_shard_00001_803_1", "global_id": 6792 }, { "text": "

ABSTRACT

Endosymbiotic bacteria extensively impact phenotypes of their eukaryotic hosts, while experiencing dramatic changes to their own genome as they become more host-restricted in lifestyle. Understanding the trajectory of such a genome has largely been done through study of animal-associated bacteria, especially insect endosymbionts. Yet, endofungal bacteria provide another natural experimental model for investigating how microbial genomes change when living inside of a host cell. Mycetohabitans spp. are culturable bacterial endosymbionts of the Mucoromycota fungus Rhizopus microsporus . To investigate the genome dynamics resulting from the endohyphal nature of this emerging model genus, we long-read sequenced and assembled new complete genomes to combine with previous assemblies, creating a global dataset of 28 complete Mycetohabitans genomes. All genomes were between 3.3 and 3.9 Mbp in size and were multipartite, structured into two conserved replicons with some strains having an additional plasmid. Based on evolutionary rate and gene content analysis of the different replicons, we termed the two major ones a chromosome and chromid. The differential presence of a third, mobilome-rich plasmid in some strains and the proliferation of transposable elements provide putative mechanisms for recombination or gene loss. The conservation of intact prophage and putative toxin-antitoxin systems, and extensive enrichment of secondary metabolite clusters in the Mycetohabitans genomes highlight the dynamic nature of this reducing genome. With fungal-bacterial symbioses becoming increasingly apparent phenomena, lessons learned from this symbiosis will inform our understanding of bacterial adaptation to novel hosts, and the process of microbe-microbe coevolution.

SIGNIFICANCE

Genomes change when organisms become closely associated, as bacterial partners undergo less opportunities for genetic exchange and become more reliant on their hosts. Our pangenome analysis of the endofungal genus Mycetohabitans shows a snapshot of evolution where the bacteria are moving from a facultative towards an obligate relationship with their host fungi", "token_count": 519, "char_count": 2180, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:53.423481", "source": { "split": "train_shard_00001", "doc_id": 804 }, "chunk_id": "train_shard_00001_804_0", "global_id": 6793 }, { "text": "We find that Mycetohabitans genomes are marked by transposable elements, pseudogenes, a large biosynthetic repertoire, and novel bacteriophage. We provide a genomic resource to match publicly accessible strains for future work on endosymbiotic genetics and evolution.\n\nComparative genomics reveals multipartite genomes undergoing loss in the fungal endosymbiotic genus Mycetohabitans", "token_count": 106, "char_count": 390, "word_count": 49, "semantic_coherence": 1, "information_density": 0.898, "quality_score": 0.949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:53.856895", "source": { "split": "train_shard_00001", "doc_id": 804 }, "chunk_id": "train_shard_00001_804_1", "global_id": 6794 }, { "text": "The PA7-clade (or group 3) of Pseudomonas aeruginosa is now recognized as a distinct species, Pseudomonas paraeruginosa. We report here the genomic sequences of six new strains of P. paraeruginosa: Zw26 (the first complete genome of a cystic fibrosis isolate of P. paraeruginosa), draft genomes of four burn and wound strains from Argentina very closely related to PA7, and of Pa5196, the strain in which arabinosylation of type IV pili was documented. We compared the genomes of 82 strains of P. paraeruginosa and confirmed that the species is divided into two sub-clades. Core genomes are very similar, while most differences are found in \"regions of genomic plasticity\" (RGPs). Several genomic deletions were identified, and most are common to the CR1 sub-clade that includes Zw26 and Pa5196. All strains lack the type 3 secretion system (T3SS) and instead use an alternative virulence strategy involving an exolysin, a characteristic shared with group 5 P. aeruginosa. All strains tend to be multiresistant like PA7, with a significant proportion of carbapenem-resistant strains, either oprD mutants or carrying carbapenemase genes. Although P. paraeruginosa is still relatively rare, it has a worldwide distribution. Its multiresistance and its alternative virulence strategy need to be considered in future therapeutic development.IMPORTANCEPseudomonas aeruginosa is an important opportunistic pathogen causing respiratory infections, notably in cystic fibrosis, and burn and wound infections. Our study reports six new genomes of Pseudomonas paraeruginosa, a new species recently reported as distinct from P. aeruginosa. The number of sequenced genomes of P. paraeruginosa is only about 1% that of P", "token_count": 521, "char_count": 1807, "word_count": 254, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [ "CR1", "PA7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:54.500181", "source": { "split": "train_shard_00001", "doc_id": 805 }, "chunk_id": "train_shard_00001_805_0", "global_id": 6795 }, { "text": "aeruginosa. We compare the genomic content of nearly all strains of P. paraeruginosa in GenBank, highlighting the differences in core and accessory genomes, antimicrobial resistance genes, and virulence factors. This novel species is very similar in environmental spectrum to P. aeruginosa but is notably resistant to last-line antibiotics and uses an alternative virulence strategy based on exolysin-this strategy being shared with some P. aeruginosa outliers.\n\nComparative genomics of <i>Pseudomonas paraeruginosa</i>.", "token_count": 159, "char_count": 557, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:54.955352", "source": { "split": "train_shard_00001", "doc_id": 805 }, "chunk_id": "train_shard_00001_805_1", "global_id": 6796 }, { "text": "

Background

Salmonella is a bacterium that causes foodborne infections. This study characterized two strains isolated from cheese and beef in Brazil using whole-genome sequencing (WGS).

Objectives

We evaluated their antimicrobial resistance profiles, virulence factors, plasmid content, serotypes and phylogenetic relationships.

Methods

DNA was extracted and sequenced on the NovaSeq 6000 platform; the pangenome was assembled using the Roary tool; and the phylogenetic tree was constructed via IQ-TREE.

Results and discussion

For contextualization and comparison, 3493 Salmonella genomes of Brazilian origin from NCBI were analyzed. In our isolates, both strains carried the aac(6')-Iaa_1 gene, while only Schwarzengrund harbored the qnrB19_1 gene and the Col440I_1 plasmid. Cerro presented the islands SPI-1, SPI-2, SPI-3, SPI-4, SPI-5 and SPI-9, while Schwarzengrund also possessed SPI-13 and SPI-14. Upon comparison with other Brazilian genomes, we observed that Cerro and Schwarzengrund represented only 0.40% and 2.03% of the national database, respectively. Furthermore, they revealed that Schwarzengrund presented higher levels of antimicrobial resistance, a finding supported by the higher frequency of plasmids in this serovar. Furthermore, national data corroborated our findings that SPI-13 and SPI-14 were absent in Cerro. A virulence analysis revealed distinct profiles: the cdtB and pltABC genes were present in the Schwarzengrund isolates, while the sseK and tldE1 family genes were exclusive to Cerro. The results indicated that the sequenced strains have pathogenic potential but exhibit low levels of antimicrobial resistance compared to national data", "token_count": 513, "char_count": 1761, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6413, "quality_score": 0.8206, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:01:55.589860", "source": { "split": "train_shard_00001", "doc_id": 806 }, "chunk_id": "train_shard_00001_806_0", "global_id": 6797 }, { "text": "The greater diversity of SPIs in Schwarzengrund explains their prevalence and higher virulence potential.

Conclusions

Finally, the serovars exhibit distinct virulence profiles, which results in different clinical outcomes.\n\nIntegrated Whole-Genome Sequencing and In Silico Characterization of <i>Salmonella</i> Cerro and Schwarzengrund from Brazil.", "token_count": 98, "char_count": 367, "word_count": 40, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:55.984470", "source": { "split": "train_shard_00001", "doc_id": 806 }, "chunk_id": "train_shard_00001_806_1", "global_id": 6798 }, { "text": "To assess the genomic diversity of Fusarium oxysporum f. sp. lini strains and compile a comprehensive gene repertoire, we constructed a pangenome using 13 isolates from four different clonal lineages, each exhibiting distinct levels of virulence. Syntenic analyses of two selected genomes revealed significant chromosomal rearrangements unique to each genome. A comprehensive examination of both core and accessory pangenome content and diversity points at an open genome state. Additionally, Gene Ontology (GO) enrichment analysis indicated that non-core pangenome genes are associated with pathogen recognition and immune signaling. Furthermore, the Folini pansecterome, encompassing secreted proteins critical for fungal pathogenicity, primarily consists of three functional classes: effector proteins, CAZYmes, and proteases. These three classes account for approximately 3.5% of the pangenome. Each functional class within the pansecterome was meticulously annotated and characterized with respect to pangenome category distribution, PFAM domain frequency, and strain virulence assessment. This analysis revealed that highly virulent isolates have specific types of PFAM domains that are exclusive to them. Upon examining the repertoire of SIX genes known for virulence in other formae speciales, it was found that all isolates had a similar gene content except for two, which lacked SIX genes entirely.\n\nPangenomics of flax fungal parasite Fusarium oxysporum f. sp. lini.", "token_count": 384, "char_count": 1526, "word_count": 204, "semantic_coherence": 1, "information_density": 0.7108, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:56.602460", "source": { "split": "train_shard_00001", "doc_id": 807 }, "chunk_id": "train_shard_00001_807_0", "global_id": 6799 }, { "text": "Background: Vancomycin-resistant Enterococcus faecium (VREfm) is a successful nosocomial pathogen. The current molecular method recommended in the Netherlands for VREfm typing is based on core genome Multilocus sequence typing (cgMLST), however, the rapid emergence of specific VREfm lineages challenges distinguishing outbreak isolates solely based on their core genome. Here, we explored if a detailed molecular characterisation of mobile genetic elements (MGEs) and accessory genes could support and expand the current molecular typing of VREfm isolates sharing the same genetic background, enhancing the discriminatory power of the analysis. Materials/Methods: The genomes of 39 VREfm and three vancomycin-susceptible E. faecium (VSEfm) isolates belonging to ST117/CT24, as assessed by cgMLST, were retrospectively analysed. The isolates were collected from patients and environmental samples from 2011 to 2017, and their genomes were analysed using short-read sequencing. Pangenome analysis was performed on de novo assemblies, which were also screened for known predicted virulence factors, antimicrobial resistance genes, bacteriocins, and prophages. Two representative isolates were also sequenced using long-read sequencing, which allowed a detailed analysis of their plasmid content. Results: The cgMLST analysis showed that the isolates were closely related, with a minimal allelic difference of 10 between each cluster's closest related isolates. The vanB-carrying transposon Tn1549 was present in all VREfm isolates. However, in our data, we observed independent acquisitions of this transposon. The pangenome analysis revealed differences in the accessory genes related to prophages and bacteriocins content, whilst a similar profile was observed for known predicted virulence and resistance genes", "token_count": 470, "char_count": 1860, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": { "genes": [ "CT24", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:57.909762", "source": { "split": "train_shard_00001", "doc_id": 808 }, "chunk_id": "train_shard_00001_808_0", "global_id": 6800 }, { "text": "Conclusion: In the case of closely related isolates sharing a similar genetic background, a detailed analysis of MGEs and the integration point of the vanB-carrying transposon allow to increase the discriminatory power compared to the use of cgMLST alone. Thus, enabling the identification of epidemiological links amongst hospitalised patients.\n\nMolecular Characterisation of Vancomycin-Resistant Enterococcus faecium Isolates Belonging to the Lineage ST117/CT24 Causing Hospital Outbreaks.", "token_count": 137, "char_count": 512, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7656, "quality_score": 0.8828, "entities": { "genes": [ "CT24", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:58.332895", "source": { "split": "train_shard_00001", "doc_id": 808 }, "chunk_id": "train_shard_00001_808_1", "global_id": 6801 }, { "text": "

Summary

Rationale

The mechanisms controlling lateral root emergence in monocots, particularly the role of the exodermis, are poorly understood. We investigated how natural variation in the Brachypodium distachyon stress response shapes root system architecture by modulating cell wall dynamics.

Methods

We used root tip excision to synchronize lateral root development across natural accessions. The resulting phenotypes were analysed using comparative transcriptomics, biochemical lignin quantification, confocal Raman spectroscopy, and chemical inhibition of lignin biosynthesis.

Key Results

Two distinct root system architectures, ’pine tree’ and ’fishbone’, were identified. The ’fishbone’ phenotype results from an emergence-specific defect caused by the premature and intense lignification of the exodermis. This was driven by the transcriptional upregulation of lignin biosynthesis genes and was rescued by a lignin inhibitor.

Main Conclusion

Stress-induced exodermal lignification acts as a mechanical ’brake’ on lateral root emergence. This positions the exodermis as a key regulatory hub that integrates environmental cues with developmental programs to control RSA plasticity in grasses.\n\nExodermis lignification impacts lateral root emergence in Brachypodium distachyon", "token_count": 352, "char_count": 1338, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7186, "quality_score": 0.8593, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:58.908972", "source": { "split": "train_shard_00001", "doc_id": 809 }, "chunk_id": "train_shard_00001_809_0", "global_id": 6802 }, { "text": "The growing prevalence of antibiotic-resistant Staphylococcus aureus strains mandates selective susceptibility testing and epidemiological investigations. It also draws attention to an efficient typing strategy. Whole genome sequencing helps in genetic comparison, strain differentiation, and typing; however, it is not that cost-effective. In comparison, Multi-Locus Sequence Typing (MLST) is an efficient typing method employed for bacterial strain typing and characterizations. In this paper, a comprehensive pangenome and phylogenetic analysis of 502/1279 S. aureus genomes is carried out to understand the species divergence. Additionally, the current Multi-Locus Sequence Typing (MLST) scheme was evaluated, and genes were excluded or substituted by alternative genes based on reported shortcomings, genomic data, and statistical scores calculated. The data generated were helpful in devising a new Multi-Locus Sequence Typing (MLST) scheme for the efficient typing of S. aureus strains. The revised scheme is now a blend of previously used genes and new candidate genes. The genes yQil, aroE, and gmk are replaced with better gene candidates, opuCC, aspS, and rpiB, based on their genome localization, representation, and statistical scores. Therefore, the proposed Multi-Locus Sequence Typing (MLST) method offers a greater resolution with 58 sequence types (STs) in comparison to the prior scheme's 42 STs.\n\nComparative Pan-Genomic Analysis Revealed an Improved Multi-Locus Sequence Typing Scheme for Staphylococcus aureus.", "token_count": 426, "char_count": 1602, "word_count": 210, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:01:59.541844", "source": { "split": "train_shard_00001", "doc_id": 810 }, "chunk_id": "train_shard_00001_810_0", "global_id": 6803 }, { "text": "

Background

The C-type lectin family 18 (CLEC18) with lipid and glycan binding capabilities is important to metabolic regulation and innate immune responses against viral infection. However, human CLEC18 comprises three paralogous genes with highly similar sequences, making it challenging to distinguish genetic variations, expression patterns, and biological functions of individual CLEC18 paralogs. Additionally, the evolutionary relationship between human CLEC18 and its counterparts in other species remains unclear.

Methods

To identify the sequence variation and evolutionary divergence of human CLEC18 paralogs, we conducted a comprehensive analysis using various resources, including human and non-human primate reference genome assemblies, human pangenome assemblies, and long-read-based whole-genome and -transcriptome sequencing datasets.

Results

We uncovered paralogous sequence variants (PSVs) and polymorphic variants (PVs) of human CLEC18 proteins, and identified distinct signatures specific to each CLEC18 paralog. Furthermore, we unveiled a novel segmental duplication for human CLEC18A gene. By comparing CLEC18 across human and non-human primates, our research showed that the CLEC18 paralogy probably occurred in the common ancestor of human and closely related non-human primates, and the lipid-binding CAP/SCP/TAPS domain of CLEC18 is more diverse than its glycan-binding CTLD. Moreover, we found that certain amino acids alterations at variant positions are exclusive to human CLEC18 paralogs.

Conclusions

Our findings offer a comprehensive profiling of the intricate variations and evolutionary characteristics of human CLEC18.\n\nCharacterization of the genetic variation and evolutionary divergence of the CLEC18 family.", "token_count": 453, "char_count": 1773, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6622, "quality_score": 0.8311, "entities": { "genes": [ "CLEC18", "CLEC18A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:00.186764", "source": { "split": "train_shard_00001", "doc_id": 811 }, "chunk_id": "train_shard_00001_811_0", "global_id": 6804 }, { "text": "Mycobacteroides abscessus (Mab) is a clinically significant non-tuberculous mycobacterium. It comprises three distinct subspecies being considered to have different macrolide susceptibilities, transmission patterns, and treatment outcomes. In this study, systematic analysis was conducted on 2,006 Mab genomes deposited in the National Center for Biotechnology Information genome database, and the taxonomic classification of their subspecies was revised accordingly. The findings revealed that: (i) in terms of three distinct subspecies classification, the analysis based on core genes and average nucleotide identity (ANI) values was completely consistent; (ii) ANI was a reliable criterion for Mab species and subspecies classification, with defined thresholds of 95% ANI for species-level and 98% ANI for subspecies-level differentiations; and (iii) the integrity of the erm(41) gene or the similarity of the rpoB gene was an unreliable characteristic for Mab subspecies, and the assertions that subspecies massiliense lack inducible resistance to macrolides also cannot be sustained. Moreover, through a subspecies re-classification of genomes and pangenome analysis, Mab subspecies-specific genes were successfully identified, and a novel single-gene test with enhanced clinical applicability was developed. Additionally, the impact of reference genome selection on taxonomic classification highlighted the importance of adopting a standardized set of reference genomes in species/subspecies identification to significantly enhance the comparability across different studies.IMPORTANCEMycobacteroides abscessus (Mab) is a clinically challenging non-tuberculous mycobacteria species. The accurate identification of subspecies is of utmost importance for clinical diagnosis and treatment, as well as for research on pathogenicity, drug resistance, and other related aspects. This study provided a clear average nucleotide identity threshold for Mab subspecies classification, as well as revised options of the three Mab subspecies, new and accurate Mab subspecies-special biomarker, and a detection technique with practical clinical application.", "token_count": 514, "char_count": 2184, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5842, "quality_score": 0.7921, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:00.843342", "source": { "split": "train_shard_00001", "doc_id": 812 }, "chunk_id": "train_shard_00001_812_0", "global_id": 6805 }, { "text": "Genomic-enabled classification of three <i>Mycobacteroides abscessus</i> subspecies and an effective subspecies-specific identification method.", "token_count": 45, "char_count": 155, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:01.205606", "source": { "split": "train_shard_00001", "doc_id": 812 }, "chunk_id": "train_shard_00001_812_1", "global_id": 6806 }, { "text": "Brucellosis represents a significant global health concern that is endemic in many regions of the world, especially in Maghreb (Tunisia, Morocco and Algeria). In Tunisia the diagnosis of human brucellosis is primarily based on serological tests and cultivation of the causative pathogen, without the knowledge of the underlying Brucella species or biovar. In addition, the scarcity of laboratories with adequate biosecurity measures to handle suspected specimens constitutes a significant challenge. Furthermore, the absence of full genome data limits our understanding of the genetic diversity of Brucella in Tunisia in comparison to the strains circulating in the North African region and the world. In the present study, a total of 36 bacterial isolates derived from human patients diagnosed with brucellosis in Tunisia were subjected to examination. Real-time PCR confirmed all isolates as B. melitensis. In the subsequent core genome-based MLST analysis (cgMLST) based on 2706 target genes, the isolates formed two separate but closely related clusters with a distance of 140 alleles. The intra-cluster diversity was one to six alleles. In the larger geographical context and in comparison to almost 1000 other Brucella genomes, the isolates showed the highest genetic relationship to B. melitensis isolates from Italy and Egypt with distances of 130 and 150 alleles, respectively. All the isolates were most similar to the biovar 3 genotype. Markedly, strains from a reported brucellosis outbreak in Austria were grouped closely (26 and 27 alleles, respectively) together with strains from Tunisia, suggesting that this country may represent their geographical origin. This research represents a significant advancement in our understanding of B. melitensis strains circulating in the Maghreb region, as it is the first study to elucidate the molecular characterization of strains isolated from humans in Tunisia. The cgMLST analysis of the strains provided information on the regional distribution of the strains and the association with neighboring countries and significant outbreaks in the region", "token_count": 513, "char_count": 2148, "word_count": 311, "semantic_coherence": 1, "information_density": 0.5595, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:01.841673", "source": { "split": "train_shard_00001", "doc_id": 813 }, "chunk_id": "train_shard_00001_813_0", "global_id": 6807 }, { "text": "The data will form the basis of a future reference framework for strains circulating in the Mediterranean region.\n\nA Genomic Characterization of Clinical Brucella melitensis Isolates from Tunisia: Integration into the Global Population Structure.", "token_count": 62, "char_count": 253, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8529, "quality_score": 0.9265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:02.211709", "source": { "split": "train_shard_00001", "doc_id": 813 }, "chunk_id": "train_shard_00001_813_1", "global_id": 6808 }, { "text": "Salmonella enterica serovar Enteritidis (SE) remains a frequent cause of foodborne illnesses associated with the consumption of contaminated hen eggs. Such a food-pathogen association has been demonstrated epidemiologically, but the molecular basis for this association has not been explored. Comparative genomic analysis was implemented to decipher the phylogenomic characteristics, antimicrobial resistance, and virulence potential of eggs-associated SE. Analyzing 1,002 genomes belonging to 841 sequence types of food-isolated SE strains suggests a high genomic similarity within the egg-related lineage, which is phylogenetically close to SE strains isolated from poultry but is different from those isolated from beef. Core genome- and single nucleotide polymorphism (SNP)-based phylogeny of 74 SE strains of egg origin showcased two distinct sublineages. Time-scaled phylogeny supported the possibility of a common ancestor of egg-related SE lineages. Additionally, genome mining revealed frequent antibiotic resistance due to the presence of aac(6')-Iaa and mdsAB encoded on the genomes of egg-associated SE strains. For virulence gene profiling, 103-113 virulence determinants were identified in the egg-associated SE, which were comparable to 112 determinants found in human-associated SE, emphasizing the capacity of egg-associated strains to infect humans and cause diseases. The findings of this study proved the genomic similarity of egg-associated SE strains, and these were closely related to poultry strains. The egg-associated strains also harbor virulence genes equivalent to those found in human-associated SE strains. The analysis provided critical insights into the genetic structure, phylogenomics, dynamics of virulence, and antibiotic resistance of Salmonella Enteritidis, circulating in eggs and emphasizing the necessity of implementing anti-Salmonella intervention strategies, starting at the production stage of the poultry supply chain.", "token_count": 500, "char_count": 2000, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:02.868272", "source": { "split": "train_shard_00001", "doc_id": 814 }, "chunk_id": "train_shard_00001_814_0", "global_id": 6809 }, { "text": "Egg-associated Salmonella enterica serovar Enteritidis: comparative genomics unveils phylogenetic links, virulence potential, and antimicrobial resistance traits.", "token_count": 52, "char_count": 169, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:03.230139", "source": { "split": "train_shard_00001", "doc_id": 814 }, "chunk_id": "train_shard_00001_814_1", "global_id": 6810 }, { "text": "

Background

Candidemia is a pervasive problem associated with significant morbidity and mortality in health care settings. This study aimed to determine the changing distribution of Candida species and the emergence of uncommon species.

Methods

This was a cross-sectional study performed in two Cairo University hospitals between 2019 and 2020. All Candida species isolates recovered from blood cultures of adults and pediatrics patients admitted to the hospitals were included. Candida isolates were identified by chromogenic Candida agar and Vitek2 YST identification card. Candida kefyr was confirmed by chip array.

Results

Candida species were responsible for 1.6% of bloodstream infections in adults and 10.8% in pediatric patients. C. albicans was the most prevalent species representing 27.8% in adults and 48.3% in pediatrics. Non-albicans species (NAC) represented the most isolated Candida species among adults and pediatrics (72.2% and 51.6%, respectively) with the predominance of C. tropicalis (27.8% and 22.5%, respectively) followed by C. parapsilosis (16.7% and 10.8%, respectively). The uncommon Candida, which is Candida species other than C. albicans, C. parapsilosis, C. tropicalis, C. glabrata, and C. krusei, represents 16.6% and 14% of all candidemia in adults and pediatrics, respectively. Only one of each of C. lusitaniae, C. utilis, and C. kefyr were detected in adults. C. lusitaniae was the most frequently recovered uncommon Candida among pediatrics resulting in 6.4% of candidemia followed by C. famata (4.3%), C. utilis (2.2%), and C. kefyr (1.1%).

Conclusions

C. albicans is still the primary species isolated from pediatrics and adults with candidemia despite the considerable shift to the non-albicans species. C. tropicalis and C. parapsilosis are the most prevalent NAC", "token_count": 533, "char_count": 1834, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5253, "quality_score": 0.7626, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:03.859100", "source": { "split": "train_shard_00001", "doc_id": 815 }, "chunk_id": "train_shard_00001_815_0", "global_id": 6811 }, { "text": "The increased prevalence of uncommon Candida species is alarming and necessitates a prompt stewardship program.\n\nPrevalence and species distribution of Candida bloodstream infection in children and adults in two teaching university hospitals in Egypt: first report of Candida kefyr.", "token_count": 59, "char_count": 282, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:04.282321", "source": { "split": "train_shard_00001", "doc_id": 815 }, "chunk_id": "train_shard_00001_815_1", "global_id": 6812 }, { "text": "Next generation of \"magic bullets\", solutions from the microbial pangenome.", "token_count": 19, "char_count": 75, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:04.654428", "source": { "split": "train_shard_00001", "doc_id": 816 }, "chunk_id": "train_shard_00001_816_0", "global_id": 6813 }, { "text": "The genomics landscape is evolving with the emergence of pangenomes, challenging the conventional single-reference genome model. The new human pangenome reference provides an extra dimension by incorporating variations observed in different human populations. However, the increasing use of pangenomes in human reference databases poses challenges for proteomics, which currently relies on UniProt canonical/isoform-based reference proteomics. Including more variant information in human proteomes, such as small and long open reading frames and pseudogenes, prompts the development of complex proteogenomics pipelines for analysis and validation. This study explores the advantages of pangenomes, particularly the human reference pangenome, on proteomics, and large-scale proteogenomics studies. We reanalyze two large human tissue datasets using the quantms workflow to identify novel peptides and variant proteins from the pangenome samples. Using three search engines SAGE, COMET, and MSGF+ followed by Percolator we analyzed 91,833,481 MS/MS spectra from more than 30 normal human tissues. We developed a robust deep-learning framework to validate the novel peptides based on DeepLC, MS2PIP and pyspectrumAI. The results yielded 170142 novel peptide spectrum matches, 4991 novel peptide sequences, and 3921 single amino acid variants, corresponding to 2367 genes across five population groups, demonstrating the effectiveness of our proteogenomics approach using the recent pangenome references.\n\nProteogenomics analysis of human tissues using pangenomes", "token_count": 363, "char_count": 1559, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:05.257249", "source": { "split": "train_shard_00001", "doc_id": 817 }, "chunk_id": "train_shard_00001_817_0", "global_id": 6814 }, { "text": "Genomic structural variants (SVs) play a crucial role in adaptive evolution, yet their average fitness effects and characterization with pangenome tools are understudied in wild animal populations. We constructed a pangenome for House Finches, a model for studies of host-pathogen coevolution, using long-read sequence data on 16 individuals (32 de novo- assembled haplotypes) and one outgroup. We identified 643,207 SVs larger than 50 base pairs, mostly (60%) involving repetitive elements, with reduced SV diversity in the eastern US as a result of its introduction by humans. The distribution of fitness effects of genome-wide SVs was estimated using maximum likelihood approaches and showed SVs in both coding and non-coding regions to be on average more deleterious than smaller indels or single nucleotide polymorphisms. The reference-free pangenome facilitated discovery of a 10-million-year-old, 11-megabase-long pericentric inversion on chromosome 1. We found that the genotype frequencies of the inversion, estimated from 135 birds widely sampled geographically and temporally, increased steadily over the 25 years since House Finches were first exposed to the bacterial pathogen Mycoplasma gallispecticum and showed signatures of balancing selection, capturing genes related to immunity and telomerase activity. We also observed shorter telomeres in populations with a greater number of years exposure to Mycoplasma . Our study illustrates the utility of applying pangenome methods to wild animal populations, helps estimate fitness effects of genome-wide SVs, and advances our understanding of adaptive evolution through structural variation.

Significance Statement

Prevailing genomic research on adaptive and neutral evolution has focused primarily on single nucleotide polymorphisms (SNPs). However, structural variation (SV) plays a critical role in animal adaptive evolution, often directly underlying fitness-relevant traits, although their average effects on fitness are less well understood. Our study constructs a pangenome for the House Finch using long-read sequencing, capturing the full spectrum of genomic diversity without use of a reference genome", "token_count": 496, "char_count": 2183, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:05.956098", "source": { "split": "train_shard_00001", "doc_id": 818 }, "chunk_id": "train_shard_00001_818_0", "global_id": 6815 }, { "text": "In addition to detecting over half a million SVs, we also document a large inversion that shows evidence of contributing to disease resistance. Our use of long-read sequencing and pangenomic approaches in a wild bird population presents a compelling approach to understanding the complexities of molecular ecology and adaptive evolution.

Graphical abstract

\n\nFitness consequences of structural variation inferred from a House Finch pangenome", "token_count": 93, "char_count": 449, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8254, "quality_score": 0.9127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:06.337218", "source": { "split": "train_shard_00001", "doc_id": 818 }, "chunk_id": "train_shard_00001_818_1", "global_id": 6816 }, { "text": "We analyzed antimicrobial resistance and virulence traits in multidrug-resistant (MDR) E. coli isolates obtained from imported shrimp using whole-genome sequences (WGSs). Antibiotic resistance profiles were determined phenotypically. WGSs identified key characteristics, including their multilocus sequence type (MLST), serotype, virulence factors, antibiotic resistance genes, and mobile elements. Most of the isolates exhibited resistance to gentamicin, streptomycin, ampicillin, chloramphenicol, nalidixic acid, ciprofloxacin, tetracycline, and trimethoprim/sulfamethoxazole. Multilocus sequence type (MLST), serotype, average nucleotide identity (ANI), and pangenome analysis showed high genomic similarity among isolates, except for EC15 and ECV01. The EC119 plasmid contained a variety of efflux pump genes, including those encoding the acid resistance transcriptional activators (gadE, gadW, and gadX), resistance-nodulation-division-type efflux pumps (mdtE and mdtF), and a metabolite, H1 symporter (MHS) family major facilitator superfamily transporter (MNZ41_23075). Virulence genes displayed diversity, particularly EC15, whose plasmids carried genes for adherence (faeA and faeC-I), invasion (ipaH and virB), and capsule (caf1A and caf1M). This comprehensive analysis illuminates antimicrobial resistance, virulence, and plasmid dynamics in E. coli from imported shrimp and has profound implications for public health, emphasizing the need for continued surveillance and research into the evolution of these important bacterial pathogens.", "token_count": 508, "char_count": 1648, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7354, "quality_score": 0.8677, "entities": { "genes": [ "ECV01", "EC15", "EC119" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:06.971270", "source": { "split": "train_shard_00001", "doc_id": 819 }, "chunk_id": "train_shard_00001_819_0", "global_id": 6817 }, { "text": "Whole-Genome Sequence Analysis of Antibiotic Resistance, Virulence, and Plasmid Dynamics in Multidrug-Resistant E. coli Isolates from Imported Shrimp.", "token_count": 53, "char_count": 157, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:07.340074", "source": { "split": "train_shard_00001", "doc_id": 819 }, "chunk_id": "train_shard_00001_819_1", "global_id": 6818 }, { "text": "Yersinia ruckeri is the causative agent of enteric redmouth disease (ERM), a serious infection that affects global aquaculture with high economic impact. The present study used whole genome sequences to perform a comparative analysis on 10 Y. ruckeri strains and to explore their genetic relatedness to other members of the genus. Y. ruckeri, Yersinia entomophaga, and Yersinia nurmii formed a species complex that constitutes the most basal lineage of the genus. The results showed that the taxonomy of Y. ruckeri strains is better defined by using a core genome alignment and phylogenetic analysis. The distribution of accessory genes in all Yersinia species revealed the presence of 303 distinctive genes in Y. ruckeri. Of these, 169 genes were distributed in 17 genomic islands potentially involved in the pathogenesis of ERM via (1) encoding virulence factors such as Afp18, Yrp1, phage proteins and (2) improving the metabolic capabilities by enhancing utilization and metabolism of iron, amino acids (specifically, arginine and histidine), and carbohydrates. The genome of Y. ruckeri is highly conserved regarding gene structure, gene layout and functional categorization of genes. It contains various components of mobile genetic elements but lacks the CRISPR-Cas system and possesses a stable set of virulence genes possibly playing a critical role in pathogenicity. Distinct virulence plasmids were exclusively restricted to a specific clonal group of Y. ruckeri (CG4), possibly indicating a selective advantage. Phylogenetic analysis of Y. ruckeri genomes revealed the co-presence of multiple genetically distant lineages of Y. ruckeri strains circulating in Germany. Our results also suggest a possible dissemination of a specific group of strains in the United States, Peru, Germany, and Denmark", "token_count": 517, "char_count": 1899, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8123, "entities": { "genes": [ "CG4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:07.971235", "source": { "split": "train_shard_00001", "doc_id": 820 }, "chunk_id": "train_shard_00001_820_0", "global_id": 6819 }, { "text": "In conclusion, this study provides new insights into the taxonomy and evolution of Y. ruckeri and contributes to a better understanding of the pathogenicity of ERM in aquaculture. The genomic analysis presented here offers a framework for the development of more efficient control strategies for this pathogen.\n\nPhylogenetic Relatedness and Genome Structure of Yersinia ruckeri Revealed by Whole Genome Sequencing and a Comparative Analysis.", "token_count": 112, "char_count": 455, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:08.358255", "source": { "split": "train_shard_00001", "doc_id": 820 }, "chunk_id": "train_shard_00001_820_1", "global_id": 6820 }, { "text": "Structural variants (SVs) are increasingly recognized as key drivers of bacterial evolution, yet their role has not been explored thoroughly. This is due to limitations in traditional short-read sequencing and linear reference-based analyses, which can miss complex structural changes. Tuberculosis (TB), a disease caused by Mycobacterium tuberculosis ( Mtb ), remains a major global health concern. In this study, we harness long-read sequencing technologies and genome graph tools to construct a Mtb pangenome reference graph (PRG) from 859 high-quality, diverse, long-read assemblies. To enable accurate genotyping of SVs leveraging the PRG, we developed miniwalk , a tool that outperforms a traditional linear genome-based approach in precision for SV detection. We characterize patterns of structural variation genome-wide, revealing a virulence-associated ESX-5 deletion to be recurrent across the phylogeny, and fixed in a sub-lineage of L4. Systematic screens for additional genes that are recurrently affected by SVs implicated those related to metal homeostasis, including a copper exporter fixed in the widely distributed L1.2.1 sub-lineage. Lastly, we genotyped 41,134 isolates and found SVs putatively associated with resistance to various first and second-line drugs. These findings underscore the broader role of SVs in shaping Mtb diversity, highlighting their importance in both understanding evolution and designing strategies to combat drug-resistant TB.\n\nGenome graphs reveal the importance of structural variation in Mycobacterium tuberculosis evolution and drug resistance", "token_count": 376, "char_count": 1601, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:08.944403", "source": { "split": "train_shard_00001", "doc_id": 821 }, "chunk_id": "train_shard_00001_821_0", "global_id": 6821 }, { "text": "

Background

Streptococcus intermedius, a member of the S. anginosus group, is a commensal bacterium present in the normal microbiota of human mucosal surfaces of the oral, gastrointestinal, and urogenital tracts. However, it has been associated with various infections such as liver and brain abscesses, bacteremia, osteo-articular infections, and endocarditis. Since 2005, high throughput genome sequencing methods enabled understanding the genetic landscape and diversity of bacteria as well as their pathogenic role. Here, in order to determine whether specific virulence genes could be related to specific clinical manifestations, we compared the genomes from 27 S. intermedius strains isolated from patients with various types of infections, including 13 that were sequenced in our institute and 14 available in GenBank.

Results

We estimated the theoretical pangenome size to be of 4,020 genes, including 1,355 core genes, 1,054 strain-specific genes and 1,611 accessory genes shared by 2 or more strains. The pangenome analysis demonstrated that the genomic diversity of S. intermedius represents an \"open\" pangenome model. We identified a core virulome of 70 genes and 78 unique virulence markers. The phylogenetic clusters based upon core-genome sequences and SNPs were independent from disease types and sample sources. However, using Principal Component analysis based on presence/ absence of virulence genes, we identified the sda histidine kinase, adhesion protein LAP and capsular polysaccharide biosynthesis protein cps4E as being associated to brain abscess or broncho-pulmonary infection. In contrast, liver and abdominal abscess were associated to presence of the fibronectin binding protein fbp54 and capsular polysaccharide biosynthesis protein cap8D and cpsB.

Conclusions

Based on the virulence gene content of 27 S", "token_count": 492, "char_count": 1856, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:09.594274", "source": { "split": "train_shard_00001", "doc_id": 822 }, "chunk_id": "train_shard_00001_822_0", "global_id": 6822 }, { "text": "intermedius strains causing various diseases, we identified putative disease-specific genetic profiles discriminating those causing brain abscess or broncho-pulmonary infection from those causing liver and abdominal abscess. These results provide an insight into S. intermedius pathogenesis and highlights putative targets in a diagnostic perspective.\n\nPangenome analysis and virulence profiling of Streptococcus intermedius.", "token_count": 92, "char_count": 425, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8627, "quality_score": 0.9314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:09.967300", "source": { "split": "train_shard_00001", "doc_id": 822 }, "chunk_id": "train_shard_00001_822_1", "global_id": 6823 }, { "text": "Notifications of Salmonella Strathcona infections increased in Europe in 2023 prompting a multi-country outbreak investigation. We aimed to describe the epidemiology of S. Strathcona infections in 17 European countries 2011-2024, investigate the genetic relatedness of S. Strathcona isolates and identify the vehicle. Cases were persons residing in the study area and with a laboratory-confirmed S. Strathcona infection 2011-2024. Confirmed cases had a S. Strathcona isolate clustering with the outbreak reference strain in core genome multilocus sequence typing (cgMLST) within 7 allelic differences (AD) and possible cases within 8-13 AD. Probable cases had an epidemiological link to a confirmed case and non-outbreak cases had an isolate > 13 AD from the outbreak reference strain. Since 2011, 662 S. Strathcona infections have been identified: 469 confirmed, 161 probable, 13 possible and 19 non-outbreak cases. Median age of the cases was 34 years (IQR: 19-58 years) and 306 (47.5%) were notified in 2023-2024. Most sequenced isolates (469/496; 94.5%) were highly genetically related (≤ 7 AD) over time and across countries, compatible with a common source. Epidemiological and traceback investigations identified small tomatoes from Sicily as the suspect food vehicle. Stringent control measures at the source are needed to stop the contamination and prevent future cases.\n\nInsights into recurring multi-country outbreaks of <i>Salmonella</i> Strathcona associated with tomatoes, Europe, 2011 to 2024.", "token_count": 497, "char_count": 1562, "word_count": 217, "semantic_coherence": 1, "information_density": 0.659, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:10.624387", "source": { "split": "train_shard_00001", "doc_id": 823 }, "chunk_id": "train_shard_00001_823_0", "global_id": 6824 }, { "text": "

Introduction

Bacterial spot, caused by diverse xanthomonads classified into four lineages within three species, poses a significant threat to global pepper and tomato production. In Taiwan, tomato bacterial spot xanthomonads phylogenetically related to an atypical Xanthomonas euvesicatoria pv. perforans (Xep) strain NI1 from Nigeria were found.

Methods

To investigate the genetic structure of Taiwanese Xep strains and determine the phylogenetic position of the atypical strains, we completed high-quality, gap-free, circularized genomes of seven Taiwanese Xep strains and performed comparative genomic analyses with genomes of X. euvesicatoria pathovars. Average nucleotide identity, core genome analysis, and phylogenomic analysis were conducted.

Results

Three sequenced strains were identified as typical Xep, while four clustered with the atypical strain NI1, forming a distinct genomovar within X. euvesicatoria, proposed as X. euvesicatoria genomovar taiwanensis (Xet). This new lineage likely originated in Taiwan and spread to Nigeria through global seed trade. At the genomovar level, chromosomes remained conserved among Taiwanese strains, while plasmids likely contributed to bacterial virulence, avirulence, and field fitness. Gap-free genomes revealed associations between the evolution of type III effectors, horizontal gene transfer events, plasmid diversity, and recombination.

Discussion

This study highlights the critical roles of horizontal gene transfer and plasmids in shaping the genetic makeup, evolution, and environmental adaptation of plant pathogenic xanthomonads. The identification of a new genomovar, X. euvesicatoria genomovar taiwanensis, provides insights into the diversity and global spread of bacterial spot pathogens through seed trade.", "token_count": 505, "char_count": 1881, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8268, "entities": { "genes": [ "NI1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:11.280740", "source": { "split": "train_shard_00001", "doc_id": 824 }, "chunk_id": "train_shard_00001_824_0", "global_id": 6825 }, { "text": "Comparative genomic analysis uncovered phylogenetic diversity, evolution of virulence factors, and horizontal gene transfer events in tomato bacterial spot Xanthomonas euvesicatoria.", "token_count": 46, "char_count": 189, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:11.644185", "source": { "split": "train_shard_00001", "doc_id": 824 }, "chunk_id": "train_shard_00001_824_1", "global_id": 6826 }, { "text": "Lyme disease is the most common vector-borne disease in North America and Europe. The clinical manifestations of Lyme disease vary based on the genospecies of the infecting Borrelia burgdorferi spirochete, but the microbial genetic elements underlying these associations are not known. Here, we report the whole genome sequence (WGS) and analysis of 299 patient-derived B. burgdorferi sensu stricto ( Bbss ) isolates from patients in the Eastern and Midwestern US and Central Europe. We develop a WGS-based classification of Bbss isolates, confirm and extend the findings of previous single- and multi-locus typing systems, define the plasmid profiles of human-infectious Bbss isolates, annotate the core and strain-variable surface lipoproteome, and identify loci associated with disseminated infection. A core genome consisting of ∼800 open reading frames and a core set of plasmids consisting of lp17, lp25, lp36, lp28-3, lp28-4, lp54, and cp26 are found in nearly all isolates. Strain-variable (accessory) plasmids and genes correlate strongly with phylogeny. Using genetic association study methods, we identify an accessory genome signature associated with dissemination and define the individual plasmids and genes that make up this signature. Strains within the RST1/WGS A subgroup, particularly a subset marked by the OspC type A genotype, are associated with increased rates of dissemination. OspC type A strains possess a unique constellation of strongly linked genetic changes including the presence of lp56 and lp28-1 plasmids and a cluster of genes that may contribute to their enhanced virulence compared to other genotypes. The patterns of OspC type A strains typify a broader paradigm across Bbss isolates, in which genetic structure is defined by correlated groups of strain-variable genes located predominantly on plasmids, particularly for expression of surface-exposed lipoproteins. These clusters of genes are inherited in blocks through strain-specific patterns of plasmid occupancy and are associated with the probability of invasive infection.", "token_count": 497, "char_count": 2068, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5967, "quality_score": 0.7983, "entities": { "genes": [ "RST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:12.295177", "source": { "split": "train_shard_00001", "doc_id": 825 }, "chunk_id": "train_shard_00001_825_0", "global_id": 6827 }, { "text": "Whole genome sequencing ofBorrelia burgdorferiisolates reveals linked clusters of plasmid-borne accessory genome elements associated with virulence", "token_count": 45, "char_count": 154, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:12.656823", "source": { "split": "train_shard_00001", "doc_id": 825 }, "chunk_id": "train_shard_00001_825_1", "global_id": 6828 }, { "text": "Bacterial hyaluronate lyases (Hys) are enzymes that degrade hyaluronic acid in their host and are known to contribute to the pathogenesis of several illnesses. The first two identified Hys genes in Staphylococcus aureus were registered as hysA1 and hysA2. However, their annotations have been mistakenly reversed in some registered assembly data, and different abbreviations (hysA and hysB) in some reports complicates comparative analysis of Hys proteins. We investigated the hys loci of S. aureus genome sequences registered in public databases, analyzed the homology, and defined hysA as hys located in the core genome surrounded by a lactose metabolic operon and a ribosomal protein cluster present in almost all strains and hysB as that located on the genomic island νSaβ of the accessory genome. Homology analysis of the amino acid sequences of HysA and HysB revealed that they are conserved among clonal complex (CC) groups with a few exceptions. Thus, we propose a new nomenclature for S. aureus Hys subtypes: HysACC*** for HysA and HysBCC*** for HysB, with the asterisks representing the clonal complex number of the S. aureus strain producing the Hys subtype. The application of this proposed nomenclature will facilitate the intuitive, straightforward, and unambiguous designation of Hys subtypes and contribute to enhancing comparative studies in this regard. IMPORTANCE Numerous whole-genome sequence data for Staphylococcus aureus harboring two hyaluronate lyase (Hys) genes have been registered", "token_count": 456, "char_count": 1594, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:13.305769", "source": { "split": "train_shard_00001", "doc_id": 826 }, "chunk_id": "train_shard_00001_826_0", "global_id": 6829 }, { "text": "However, the assigned gene names for hysA1 and hysA2 are incorrect in some assembled data, and in some cases, the genes are annotated differently as hysA and hysB. This creates confusion with respect to the nomenclature of Hys subtypes and complicates analysis involving Hys. In this study, we compared the homology of Hys subtypes and observed that to some extent, their amino acid sequences are conserved in each clonal complex group. Hys has been implicated as an important virulence factor, but relative sequence heterogeneity among S. aureus clones raises the question of whether Hys activities are different among these clones. Our proposed Hys nomenclature will facilitate comparison of the virulence of Hys, as well as discussions of the subject.\n\nDiversity and Standard Nomenclature of Staphylococcus aureus Hyaluronate Lyases HysA and HysB.", "token_count": 234, "char_count": 878, "word_count": 131, "semantic_coherence": 1, "information_density": 0.687, "quality_score": 0.8435, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:13.776700", "source": { "split": "train_shard_00001", "doc_id": 826 }, "chunk_id": "train_shard_00001_826_1", "global_id": 6830 }, { "text": "Thermotolerance is a required characteristic for biofuel production by yeast. Here, we report the draft genome sequence of thermotolerant Saccharomyces cerevisiae AH465, which was originally isolated by the authors. A hybrid assembly approach using MinION Mk1b and MiSeq sequencers was conducted. The assembled sequence comprises 13.4 Mb in 26 contigs.\n\nDraft genome sequence of thermotolerant Saccharomyces cerevisiae AH465, isolated from Mt. Tatsuda, Kumamoto, Japan.", "token_count": 148, "char_count": 483, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7656, "quality_score": 0.8828, "entities": { "genes": [ "AH465" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:14.213118", "source": { "split": "train_shard_00001", "doc_id": 827 }, "chunk_id": "train_shard_00001_827_0", "global_id": 6831 }, { "text": "Vibrio parahaemolyticus is a significant cause of foodborne illness, and its incidence worldwide is on the rise. It is thus imperative to develop a straightforward and efficient method for typing strains of this pathogen. In this study, we conducted a pangenome analysis of 75 complete genomes of V. parahaemolyticus and identified the core gene mtlA with the highest degree of variation, which distinguished 44 strains and outperformed traditional seven-gene-based MLST when combined with aer, another core gene with high degree of variation. The mtlA gene had higher resolution to type strains with a close relationship compared to the traditional MLST genes in the phylogenetic tree built by core genomes. Strong positive selection was also detected in the gene mtlA (ω > 1), representing adaptive and evolution in response to the environment. Therefore, the panel of gene mtlA and aer may serve as a tool for the typing of V. parahaemolyticus, potentially contributing to the prevention and control of this foodborne disease.\n\nAdvance typing of Vibrio parahaemolyticus through the mtlA and aer gene: A high-resolution, cost-effective approach.", "token_count": 342, "char_count": 1231, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6023, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:14.788454", "source": { "split": "train_shard_00001", "doc_id": 828 }, "chunk_id": "train_shard_00001_828_0", "global_id": 6832 }, { "text": "Plant pathogens adapt at speeds that challenge contemporary disease management strategies like the deployment of disease resistance genes. The strong evolutionary pressure to adapt, shapes pathogens’ genomes, and comparative genomics has been instrumental in characterizing this process. With the aim to capture genomic variation at high resolution and study the processes contributing to adaptation, we here leverage and expand on an innovative, multi-genome method to construct, annotate, and analyse the first pangenome graph of an oomycete plant pathogen. We generated telomere-to-telomere genome assemblies of six genetically diverse isolates of the oomycete pathogen Peronospora effusa , the economically most important disease in cultivated spinach worldwide. The pangenome graph demonstrates that P. effusa genomes are highly conserved, both in chromosomal structure and gene content, and revealed the continued activity of transposable elements which are directly responsible for 80% of the observed variation between the isolates. While most genes are generally conserved, pathogenicity related genes are highly variable between the isolates. Most of the variation is found in large gene clusters resulting from extensive copy-number expansion. Pangenome graph-based discovery can thus be effectively used to capture genomic variation at exceptional resolution, thereby providing a framework to study the biology and evolution of plant pathogens.

Author Summary

Plant pathogens are known to evolve rapidly and overcome disease resistance of newly introduced crop varieties. This swift adaptation is visible in the genomes of these pathogens, which can be highly variable. Such genomic variation cannot be captured with contemporary comparative genomic methods that rely on a single reference genome or focus solely on protein coding genes. To overcome these limitations and compare multiple genomes in a robust and scalable method, we constructed the first pangenome graph for an oomycete filamentous plant pathogen with six telomere-to-telomere genome assemblies of Peronospora effusa . This high-resolution pangenomic framework enabled detailed comparisons of the genomes at any level, from the nucleotide to the chromosome, and for any subset of protein-coding genes or transposable elements, to discover novel biology and potential mechanisms for the rapid evolution of this devastating pathogen.", "token_count": 510, "char_count": 2419, "word_count": 339, "semantic_coherence": 1, "information_density": 0.5634, "quality_score": 0.7817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:15.440044", "source": { "split": "train_shard_00001", "doc_id": 829 }, "chunk_id": "train_shard_00001_829_0", "global_id": 6833 }, { "text": "Pangenome graph analysis reveals extensive effector copy-number variation in spinach downy mildew", "token_count": 21, "char_count": 97, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:15.796404", "source": { "split": "train_shard_00001", "doc_id": 829 }, "chunk_id": "train_shard_00001_829_1", "global_id": 6834 }, { "text": "As a result of the increasing use of sensitive nucleic acid amplification tests, Kingella kingae is being recognized as a common pathogen of early childhood, causing medical conditions ranging from asymptomatic oropharyngeal colonization to bacteremia, osteoarthritis, and life-threatening endocarditis. However, the genomic determinants associated with the different clinical outcomes are unknown. Employing whole-genome sequencing, we studied 125 international K. kingae isolates derived from 23 healthy carriers and 102 patients with invasive infections, including bacteremia (n = 23), osteoarthritis (n = 61), and endocarditis (n = 18). We compared their genomic structures and contents to identify genomic determinants associated with the different clinical conditions. The mean genome size of the strains was 2,024,228 bp, and the pangenome comprised 4,026 predicted genes, of which 1,460 (36.3%) were core genes shared by >99% of the isolates. No single gene discriminated between carried and invasive strains; however, 43 genes were significantly more frequent in invasive isolates, compared to asymptomatically carried organisms, and a few showed a significant differential distribution among isolates from skeletal system infections, bacteremia, and endocarditis. The gene encoding the iron-regulated protein FrpC was uniformly absent in all 18 endocarditis-associated strains but was present in one-third of other invasive isolates. Similar to other members of the Neisseriaceae family, the K. kingae differences in invasiveness and tropism for specific body tissues appear to depend on combinations of multiple virulence-associated determinants that are widely distributed throughout the genome. The potential role of the absence of the FrpC protein in the pathogenesis of endocardial invasion deserves further investigation", "token_count": 486, "char_count": 1864, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:16.480532", "source": { "split": "train_shard_00001", "doc_id": 830 }, "chunk_id": "train_shard_00001_830_0", "global_id": 6835 }, { "text": "IMPORTANCE The wide range of clinical severities exhibited by invasive Kingella kingae infections strongly suggests that isolates differ in their genomic contents, and strains associated with life-threatening endocarditis may harbor distinct genomic determinants that result in cardiac tropism and severe tissue damage. The results of the present study show that no single gene discriminated between asymptomatically carried isolates and invasive strains. However, 43 putative genes were significantly more frequent among invasive isolates than among pharyngeal colonizers. In addition, several genes displayed a significant differential distribution among isolates from bacteremia, skeletal system infections, and endocarditis, suggesting that the virulence and tissue tropism of K. kingae are multifactorial and polygenic, depending on changes in the allele content and genomic organization. Further analysis of these putative genes may identify genomic determinants of the invasiveness of K. kingae and its affinity for specific body tissues and potential targets for a future protective vaccine.\n\nWhole-Genome Sequencing Reveals Differences among Kingella kingae Strains from Carriers and Patients with Invasive Infections.", "token_count": 269, "char_count": 1234, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:17.049830", "source": { "split": "train_shard_00001", "doc_id": 830 }, "chunk_id": "train_shard_00001_830_1", "global_id": 6836 }, { "text": "Engineered strains of the yeast Saccharomyces cerevisiae are intensively studied as production platforms for aromatic compounds such as hydroxycinnamic acids, stilbenoids and flavonoids. Heterologous pathways for production of these compounds use l-phenylalanine and/or l-tyrosine, generated by the yeast shikimate pathway, as aromatic precursors. The Ehrlich pathway converts these precursors to aromatic fusel alcohols and acids, which are undesirable by-products of yeast strains engineered for production of high-value aromatic compounds. Activity of the Ehrlich pathway requires any of four S. cerevisiae 2-oxo-acid decarboxylases (2-OADCs): Aro10 or the pyruvate-decarboxylase isoenzymes Pdc1, Pdc5, and Pdc6. Elimination of pyruvate-decarboxylase activity from S. cerevisiae is not straightforward as it plays a key role in cytosolic acetyl-CoA biosynthesis during growth on glucose. In a search for pyruvate decarboxylases that do not decarboxylate aromatic 2-oxo acids, eleven yeast and bacterial 2-OADC-encoding genes were investigated. Homologs from Kluyveromyces lactis (KlPDC1), Kluyveromyces marxianus (KmPDC1), Yarrowia lipolytica (YlPDC1), Zymomonas mobilis (Zmpdc1) and Gluconacetobacter diazotrophicus (Gdpdc1.2 and Gdpdc1.3) complemented a Pdc- strain of S", "token_count": 511, "char_count": 1387, "word_count": 163, "semantic_coherence": 1, "information_density": 0.681, "quality_score": 0.8405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:17.744661", "source": { "split": "train_shard_00001", "doc_id": 831 }, "chunk_id": "train_shard_00001_831_0", "global_id": 6837 }, { "text": "cerevisiae for growth on glucose. Enzyme-activity assays in cell extracts showed that these genes encoded active pyruvate decarboxylases with different substrate specificities. In these in vitro assays, ZmPdc1, GdPdc1.2 or GdPdc1.3 had no substrate specificity towards phenylpyruvate. Replacing Aro10 and Pdc1,5,6 by these bacterial decarboxylases completely eliminated aromatic fusel-alcohol production in glucose-grown batch cultures of an engineered coumaric acid-producing S. cerevisiae strain. These results outline a strategy to prevent formation of an important class of by-products in 'chassis' yeast strains for production of non-native aromatic compounds.\n\nElimination of aromatic fusel alcohols as by-products of Saccharomyces cerevisiae strains engineered for phenylpropanoid production by 2-oxo-acid decarboxylase replacement.", "token_count": 278, "char_count": 885, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7524, "quality_score": 0.8762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:18.314651", "source": { "split": "train_shard_00001", "doc_id": 831 }, "chunk_id": "train_shard_00001_831_1", "global_id": 6838 }, { "text": "

Background:

/Objectives: Cefiderocol is a novel siderophore cephalosporin with potent in vitro activity against a broad spectrum of Gram-negative bacteria, including carbapenemase-producing Enterobacteriaceae CPE). However, the recent emergence of re-sistance in clinical settings raises important concerns regarding its long-term effective-ness. This study aims to investigate the genomic determinants associated with cefiderocol resistance in CPE isolates of human origin.

Methods:

Comparative genomic analyses were conducted between cefiderocol-susceptible and -resistant CPE isolates recovered from human clinical and epidemiological samples at a tertiary care hospital. Whole-genome sequencing, variant annotation, structural modeling, and pangenome analysis were performed to characterize resistance mechanisms.

Results:

A total of 59 isolates (29 resistant and 30 susceptible) were analyzed, predominantly comprising Klebsiella pneumoniae, Escherichia coli, and Enterobacter cloacae. The most frequent car-bapenemase among resistant isolates was blaNDM, which was also present in a subset of susceptible strains. Resistant isolates exhibited a significantly higher burden of non-synonymous mutations in siderophore receptor genes, notably within fecR, fecA, fiu, and cirA. Structural modeling predicted deleterious effects for mutations such as fecR:G104S and fecA:A190T. Additionally, porin loss and loop 3 insertions (e.g., GD/TD) in OmpK36, as well as OmpK35 truncations, were more frequent in resistant isolates, partic-ularly in high-risk clones such as ST395 and ST512. Genes associated with toxin–antitoxin systems (chpB2, pemI) and a hypothetical metalloprotease (group_2577) were uniquely found in the resistant group.

Conclusions:

Cefiderocol resistance in CPE appears to be multifactorial", "token_count": 520, "char_count": 1849, "word_count": 231, "semantic_coherence": 1, "information_density": 0.71, "quality_score": 0.855, "entities": { "genes": [ "ST395", "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:18.978263", "source": { "split": "train_shard_00001", "doc_id": 832 }, "chunk_id": "train_shard_00001_832_0", "global_id": 6839 }, { "text": "NDM-type metallo-β-lactamases and mutations in siderophore up-take systems—especially in the fec, fhu, and cir operons—play a central role. These may be further potentiated by alterations in membrane permeability, such as porin disruption and efflux deregulation. The integration of genomic and structural approaches provides valuable insight into emerging resistance mechanisms and may support the development of diagnostic tools and therapeutic strategies.\n\nMechanisms of Cefiderocol Resistance in Carbapenemase-Producing Enterobacteriaceae: Insights from Comparative Genomics", "token_count": 154, "char_count": 604, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7887, "quality_score": 0.8944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:19.415399", "source": { "split": "train_shard_00001", "doc_id": 832 }, "chunk_id": "train_shard_00001_832_1", "global_id": 6840 }, { "text": "Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years later. An increase in the number of described Thiothrix species at the beginning of the 21st century shows that the classical phylogenetic marker, 16S rRNA gene, is not informative for species differentiation, which is possible based on genome analysis. Pangenome analysis of the genus Thiothrix showed that the core genome includes genes for dissimilatory sulfur metabolism and central metabolic pathways, namely the Krebs cycle, Embden-Meyerhof-Parnas pathway, glyoxylate cycle, Calvin-Benson-Bassham cycle, and genes for phosphorus metabolism and amination. The shell part of the pangenome includes genes for dissimilatory nitrogen metabolism and nitrogen fixation, for respiration with thiosulfate. The dispensable genome comprises genes predicted to encode mainly hypothetical proteins, transporters, transcription regulators, methyltransferases, transposases, and toxin-antitoxin systems.\n\nHistory of the Study of the Genus Thiothrix: From the First Enrichment Cultures to Pangenomic Analysis.", "token_count": 355, "char_count": 1319, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:19.996371", "source": { "split": "train_shard_00001", "doc_id": 833 }, "chunk_id": "train_shard_00001_833_0", "global_id": 6841 }, { "text": "With advances in long-read sequencing and assembly techniques, haplotype-resolved (phased) genome assemblies are becoming more common, also in the field of plant genomics. Computational tools to effectively explore these phased genomes, particularly for polyploid genomes are currently limited. Here we describe a new strategy adopting a pangenome approach. To analyze both intra- and intergenomic variation in phased genome assemblies, we have made the software package PanTools ploidy-aware by updating the pangenome graph representation and adding several novel functionalities to assess synteny and gene retention, profile repeats and calculate synonymous and nonsynyonymous mutation rates. Using PanTools, we constructed and analyzed a pangenome comprising of one diploid and four tetraploid potato cultivars, and a pangenome of five diploid apple species. Both pangenomes show high intra- and intergenomic allelic diversity in terms of gene absence/presence, SNPs, indels and larger structural variants. Our findings show that the new functionalities and visualizations are useful to discover introgressions and detect likely misassemblies in phased genomes. PanTools is available at https://git.wur.nl/bioinformatics/pantools.\n\nExploring intra- and intergenomic variation in haplotype-resolved pangenomes", "token_count": 308, "char_count": 1311, "word_count": 172, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:20.558689", "source": { "split": "train_shard_00001", "doc_id": 834 }, "chunk_id": "train_shard_00001_834_0", "global_id": 6842 }, { "text": "Shigellosis is a gastrointestinal illness caused by bacteria belonging to one of four species of Shigella . Sexually transmissible shigellosis was first reported in 1974, but recently there has been a global increase in the transmission of extensively drug-resistant strains. Here, we sought to characterise the natural history of sexually transmissible shigellosis through literature review and genomic epidemiological analysis of early outbreaks. The literature review revealed a significant gap in reporting of sexually transmissible shigellosis between the first report in 1974 and the early 2000s after which reporting increased. To better understand this sustained emergence of sexually transmissible shigellosis in the 21 st century, we explored potential pathogen factors and linked these with changes in host populations. Specifically, we analysed the genomic epidemiology of preserved strains from outbreaks in both Berlin (2000 - 2002) and London (2004 - 2006). Both outbreaks were S. sonnei Genotype 3.1, an ancestral branch of the globally disseminated Lineage III subtype, which is distinct from the currently extensively drug-resistant forms (Genotypes 3.6.1.1.2 and 3.6.1.1) circulating in sexual transmission networks. We also describe the variable antimicrobial resistance, conserved colicin genes, and differing virulence and plasmid profiles between the London and Berlin outbreaks. Finally, we conducted temporal reconstruction of Genotype 3.1 and found that the most recent common ancestor occurred in 1999 (95% HPD 1998 - 2000) which is coincident with the introduction of highly active antiretroviral therapy (HAART) for HIV. This suggests that changes associated with the introduction of HAART likely contributed to the re-emergence of sexually transmissible shigellosis in the 21 st Century.\n\nThe natural history of the emergence of sexually transmissible shigellosis", "token_count": 474, "char_count": 1893, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:21.200491", "source": { "split": "train_shard_00001", "doc_id": 835 }, "chunk_id": "train_shard_00001_835_0", "global_id": 6843 }, { "text": "Background: Chryseobacterium indologenes, an environmental bacterium, is increasingly recognized as an emerging nosocomial pathogen, particularly in Asia, and is often characterized by multidrug resistance. Objectives: This study aimed to investigate the genomic features of clinical C. indologenes isolates from Maharaj Nakorn Chiang Mai Hospital, Thailand, to understand their mechanisms of multidrug resistance, virulence factors, and mobile genetic elements (MGEs). Methods: Twelve C. indologenes isolates were identified, and their antibiotic susceptibility profiles were determined. Whole genome sequencing (WGS) was performed using a hybrid approach combining Illumina short-reads and Oxford Nanopore long-reads to generate complete bacterial genomes. The hybrid assembled genomes were subsequently analyzed to detect antimicrobial resistance (AMR) genes, virulence factors, and MGEs. Results: C. indologenes isolates were primarily recovered from urine samples of hospitalized elderly male patients with underlying conditions. These isolates generally exhibited extensive drug resistance, which was subsequently explored and correlated with genomic determinants. With one exception, CMCI13 showed a lower resistance profile (Multidrug resistance, MDR). Genomic analysis revealed isolates with genome sizes of 4.83-5.00 Mb and GC content of 37.15-37.35%. Genomic characterization identified conserved resistance genes (blaIND-2, blaCIA-4, adeF, vanT, and qacG) and various virulence factors. Phylogenetic and pangenome analysis showed 11 isolates clustering closely with Chinese strain 3125, while one isolate (CMCI13) formed a distinct branch", "token_count": 473, "char_count": 1763, "word_count": 210, "semantic_coherence": 1, "information_density": 0.7286, "quality_score": 0.8643, "entities": { "genes": [ "CMCI13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:21.850827", "source": { "split": "train_shard_00001", "doc_id": 836 }, "chunk_id": "train_shard_00001_836_0", "global_id": 6844 }, { "text": "Importantly, each isolate, except CMCI13, harbored a large genomic island (approximately 94-100 kb) carrying significant resistance genes (blaOXA-347, tetX, aadS, and ermF). The absence of this genomic island in CMCI13 correlated with its less resistant phenotype. No plasmids, integrons, or CRISPR-Cas systems were detected in any isolate. Conclusions: This study highlights the alarming emergence of multidrug-resistant C. indologenes in a hospital setting in Thailand. The genomic insights into specific resistance mechanisms, virulence factors, and potential horizontal gene transfer (HGT) events, particularly the association of a large genomic island with the XDR phenotype, underscore the critical need for continuous genomic surveillance to monitor transmission patterns and develop effective treatment strategies for this emerging pathogen.\n\nGenomic Insights into Emerging Multidrug-Resistant <i>Chryseobacterium indologenes</i> Strains: First Report from Thailand.", "token_count": 287, "char_count": 1039, "word_count": 125, "semantic_coherence": 1, "information_density": 0.744, "quality_score": 0.872, "entities": { "genes": [ "CMCI13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:22.407207", "source": { "split": "train_shard_00001", "doc_id": 836 }, "chunk_id": "train_shard_00001_836_1", "global_id": 6845 }, { "text": "

Background

β-Nicotinamide mononucleotide (NMN) is the direct precursor of nicotinamide coenzymes such as NAD+ and NADP+, which are widely applied in industrial biocatalysis especially involving cofactor-dependent oxidoreductases. Moreover, NMN is a promising candidate for medical uses since it is considered to be beneficial for improving health of aged people who usually suffer from an insufficient level of NAD+. To date, various methods have been developed for the synthesis of NMN. Chemical phosphorylation of nicotinamide riboside (NR) to NMN depends on excessive phosphine oxychloride and delicate temperature control, while fermentation of NMN is limited by low product titers, making it unsuitable for industrial-scale NMN production. As a result, the more efficient synthesis process of NMN is still challenging.

Aim

This work attempted to construct an eco-friendly and cost-effective biocatalytic process for transforming the chemically synthesized NR into the highly value-added NMN.

Results

A new nicotinamide riboside kinase (Klm-NRK) was identified from Kluyveromyces marxianus. The specific activity of purified Klm-NRK was 7.9 U·mg-1 protein, ranking the highest record among the reported NRKs. The optimal pH of Klm-NRK was 7.0 in potassium phosphate buffer. The purified Klm-NRK retained a half activity after 7.29 h at 50 °C. The catalytic efficiencies (kcat/KM) toward ATP and nicotinamide riboside (NR) were 57.4 s-1·mM-1 and 84.4 s-1·mM-1, respectively", "token_count": 509, "char_count": 1608, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7184, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:23.072440", "source": { "split": "train_shard_00001", "doc_id": 837 }, "chunk_id": "train_shard_00001_837_0", "global_id": 6846 }, { "text": "In the presence of an external ATP regeneration system (AcK/AcP), as much as 100 g·L-1 of NR could be completely phosphorylated to NMN in 8 h with Klm-NRK, achieving a molar isolation yield of 84.2% and a space-time yield of 281 g·L-1·day-1. These inspiring results indicated that Klm-NRK is a promising biocatalyst which provides an efficient approach for the bio-manufacturing of NMN in a high titer.\n\nEnzymatic synthesis of high-titer nicotinamide mononucleotide with a new nicotinamide riboside kinase and an efficient ATP regeneration system.", "token_count": 195, "char_count": 580, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7262, "quality_score": 0.8631, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:23.512797", "source": { "split": "train_shard_00001", "doc_id": 837 }, "chunk_id": "train_shard_00001_837_1", "global_id": 6847 }, { "text": "The application of pan-genomics in understanding Mycobacterium tuberculosis complex (MTBC) transmission remains understudied, particularly in high-burden settings such as China. We constructed an M. tuberculosis complex pan-genome (MTB_pan) using 307 complete genomes representing all eight lineages from the National Center for Biotechnology Information (NCBI). Core and accessory genomes were analysed, lineage-associated genes were identified and functional annotations were assessed using Pfam domains. Transmission dynamics were evaluated by comparing pan-genome- and H37Rv-based approaches for isolates collected from China, focusing on alignment rates, clustering efficiency and SNP distances. The MTB_pan (5.75 Mb) consisted of 3,893 core and 958 accessory genes, with 176 accessory genes significantly associated with specific lineages. These genes were enriched in PE/PPE/PGRS families, mobile genetic elements (e.g. IS6110) and pentapeptide repeats. The median alignment rate based on MTB_pan reached 99.8%, which was significantly higher than that based on H37Rv. The clustering rate of isolates based on MTB_pan (19.93%) was higher than that based on H37Rv (18.90%). The pairwise SNP distances below 50 SNPs within lineage 2 decreased significantly, while those within lineage 4 showed no significant differences. Compared to a single reference genome, clustering using the pan-genome improved the identification of same-province transmission events. Therefore, the pan-genomic analysis is a more powerful analytical tool that enables the establishment of a high-resolution picture of tuberculosis transmission in different epidemiological settings, which will enable more precise outbreak mapping and support data-driven tuberculosis control strategies.\n\nPan- and core genome analysis of <i>Mycobacterium tuberculosis</i> in high-resolution transmission and genetic diversity studies.", "token_count": 492, "char_count": 1924, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6734, "quality_score": 0.8367, "entities": { "genes": [ "IS6110" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:24.165326", "source": { "split": "train_shard_00001", "doc_id": 838 }, "chunk_id": "train_shard_00001_838_0", "global_id": 6848 }, { "text": "Enterococcus faecium is a major human opportunistic bacterial pathogen and a close relative of the recently established species Enterococcus lactis. As a species, commensal E. lactis remains relatively understudied, and its genetic connectivity with E. faecium is not thoroughly understood. Here, we introduce a large collection of whole-genome sequenced isolates comprising 894 E. faecium and 392 E. lactis genomes. Using these genomes to complement publicly available data, we studied the genome content and the evolutionary relationship between these species. A wider range of host species was observed in E. faecium; in particular, there is a radiation of E. faecium clades specialized to domesticated and pet animals among which E. lactis is uncommon. Of note, pangenome analyses reveal that E. lactis has significantly more allelic variation and lower recombination rates in core genes compared with E. faecium. These observations suggest that E. lactis represents a population that has occupied its ecological niche longer than E. faecium has. This study enhances understanding of the evolutionary histories of these species and highlights the importance of sampling and studying closely related commensal bacteria in addition to clinically relevant opportunistic pathogens.\n\n<i>Enterococcus lactis</i> is ecologically and genetically distinct from the major opportunistic pathogen <i>Enterococcus faecium</i>.", "token_count": 424, "char_count": 1532, "word_count": 200, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:24.790005", "source": { "split": "train_shard_00001", "doc_id": 839 }, "chunk_id": "train_shard_00001_839_0", "global_id": 6849 }, { "text": "Consumer demands for plant-based products have increased in recent years. However, their consumption is still limited due to the presence of off-flavor compounds, primarily beany and green notes, which are mainly associated with the presence of aldehydes, ketones, furans, and alcohols. To overcome this problem, fermentation is used as a lever to reduce off-flavors. A starter culture of lactic acid bacteria (LAB) was tested in a 4% pea protein solution with one of the following yeasts: Kluyveromyces lactis, Kluyveromyces marxianus, or Torulaspora delbrueckii. The fermented samples were evaluated by a sensory panel. Non-fermented and fermented matrices were analyzed by gas chromatography coupled with mass spectrometry to identify and quantify the volatile compounds. The sensory evaluation showed a significant reduction in the green/leguminous attributes of pea proteins and the generation of new descriptors in the presence of yeasts. Compared to the non-fermented matrix, fermentations with LAB or LAB and yeasts led to the degradation of many off-flavor compounds. Moreover, the presence of yeasts triggered the generation of esters. Thus, fermentation by a co-culture of LAB and yeasts can be used as a powerful tool for the improvement of the sensory perception of a pea protein-based product.\n\nSensory Improvement of a Pea Protein-Based Product Using Microbial Co-Cultures of Lactic Acid Bacteria and Yeasts.", "token_count": 374, "char_count": 1444, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:25.373685", "source": { "split": "train_shard_00001", "doc_id": 840 }, "chunk_id": "train_shard_00001_840_0", "global_id": 6850 }, { "text": "The locus of heat resistance (LHR) can confer heat resistance to Escherichia coli to various extents. This study investigated the phylogenetic relationships and the genomic and phenotypic characteristics of E. coli with or without LHR recovered from beef by direct plating or from enrichment broth at 42°C. LHR-positive E. coli isolates (n = 24) were subjected to whole-genome sequencing by short and long reads. LHR-negative isolates (n = 18) from equivalent sources as LHR-positive isolates were short-read sequenced. All isolates were assessed for decimal reduction time at 60°C (D60°C) and susceptibility to the sanitizers E-SAN and Perox-E. Selected isolates were evaluated for growth at 42°C. The LHR-positive and -negative isolates were well separated on the core genome tree, with 22/24 positive isolates clustering into three clades. Isolates within clade 1 and 2, despite their different D60°C values, were clonal, as determined by subtyping (multilocus sequence typing [MLST], core genome MLST, and serotyping). Isolates within each clade are of one serotype. The LHR-negative isolates were genetically diverse. The LHR-positive isolates had a larger (P < 0.001) median genome size by 0.3 Mbp (5.0 versus 4.7 Mbp) and overrepresentation of genes related to plasmid maintenance, stress response, and cryptic prophages but underrepresentation of genes involved in epithelial attachment and virulence. All LHR-positive isolates harbored a chromosomal copy of LHR, and all clade 2 isolates had an additional partial copy of LHR on conjugative plasmids", "token_count": 500, "char_count": 1615, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:26.023865", "source": { "split": "train_shard_00001", "doc_id": 841 }, "chunk_id": "train_shard_00001_841_0", "global_id": 6851 }, { "text": "The growth rates at 42°C were 0.71 ± 0.02 and 0.65 ± 0.02 log(OD) h-1 for LHR-positive and -negative isolates, respectively. No meaningful difference in sanitizer susceptibility was noted between LHR-positive and -negative isolates. IMPORTANCE Resistant bacteria are serious food safety and public health concerns. Heat resistance conferred by the LHR varies largely among different strains of E. coli. The findings in this study show that genomic background and composition of LHR, in addition to the presence of LHR, play an important role in the degree of heat resistance in E. coli and that strains with certain genetic backgrounds are more likely to acquire and maintain the LHR. Also, caution should be exercised when recovering E. coli at elevated temperatures, as the presence of LHR may confer growth advantages to some strains. Interestingly, the LHR-harboring strains seem to have evolved further from their primary animal host to adapt to their secondary habitat, as reflected by fewer genes involved in virulence and epithelial attachment. The phylogenetic relationships among the isolates point toward multiple mechanisms for acquisition of LHR by E. coli, likely prior to its being deposited on meat.\n\nGenomic and Phenotypic Analysis of Heat and Sanitizer Resistance in Escherichia coli from Beef in Relation to the Locus of Heat Resistance.", "token_count": 361, "char_count": 1388, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:26.597565", "source": { "split": "train_shard_00001", "doc_id": 841 }, "chunk_id": "train_shard_00001_841_1", "global_id": 6852 }, { "text": "Streptomyces is a genus of Gram-positive bacteria with high GC content. It remains attractive for studying and discovering new antibiotics, antifungals, and chemotherapeutics. Streptomyces genomes can contain more than 30 cryptic and expressed biosynthetic gene clusters (BGC) encoding secondary metabolites. In this study, three Streptomyces strains isolated from jungle rhizospheric soil exhibited supernatants that can inhibit sensitive and fluconazole-resistant Candida spp. The genomes of the strains Streptomyces sp. A1, J25, J29 ori2 were sequenced, assembled de novo, and analyzed. The genome assemblies revealed that the size of the genomes was 6.9 Mb, with linear topology and 73.5% GC. A phylogenomic approach identified the strains with high similitudes between 98.5 and 98.7% with Streptomyces albidoflavus SM254 and R-53649 strains, respectively. Pangenomic analysis of eight genomes of S. albidoflavus strains deposited in the Genomes database recognized 4707 core protein orthogroups and 745 abundant accessory and exclusive protein orthogroups, suggesting an open pangenome in this species. The antiSMASH software detected candicidin and surugamide BGC-encoding polyene and octapeptide antifungal secondary metabolites in other S. albidoflavus. CORASON software was used to compare the synteny, and the abundance of genes harbored in the clusters was used. In conclusion, although the three strains belong to the same species, each possesses a distinct genome, as evidenced by the different phenotypes, including antifungal and extracellular enzymatic activities.", "token_count": 483, "char_count": 1636, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8463, "entities": { "genes": [ "SM254" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:27.252606", "source": { "split": "train_shard_00001", "doc_id": 842 }, "chunk_id": "train_shard_00001_842_0", "global_id": 6853 }, { "text": "Comparative Genomics and Biosynthetic Cluster Analysis of Antifungal Secondary Metabolites of Three Strains of Streptomyces albidoflavus Isolated from Rhizospheric Soils.", "token_count": 56, "char_count": 177, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:27.611474", "source": { "split": "train_shard_00001", "doc_id": 842 }, "chunk_id": "train_shard_00001_842_1", "global_id": 6854 }, { "text": "Type IV secretion systems (T4SSs) are versatile machines with variable functions including DNA uptake and release, protein translocation, and DNA conjugation. However, the diversity, distribution, and functional roles of the T4SS in the Ralstonia genus remain poorly understood. The Ralstonia solanacearum species complex (RSSC) comprises three species of plant-pathogenic bacteria that cause bacterial wilt disease. The Ralstonia genus also includes non-RSSC species that are primarily environmental bacteria and rare opportunistic human pathogens. This study compared the diversity and phylogenetic distribution of T4SSs in the RSSC phytopathogens vs. non-RSSC environmentals. Phylogenetic analysis of VirB4 sequences and synteny analysis revealed 16 distinct T4SS clusters in Ralstonia , with ten clusters found in RSSC phytopathogen genomes, twelve in non-RSSC environmental genomes, and six clusters in both groups. Collectively, these gene clusters were more prevalent in non-RSSC environmental genomes. The presence of type IV coupling protein and relaxase genes suggests that at least 14 of these T4SS gene clusters could be putative DNA conjugation systems. The clusters were encoded on accessory plasmids of various sizes or as integrative and conjugative elements (ICEs) on the chromosome or megaplasmid. The putative regions of transfer for T4SS gene clusters in the RSSC phytopathogen genomes often contained type III effectors, type VI secretion toxin/antitoxin clusters, and hemagglutinin gene clusters. In contrast, the non-RSSC environmentals were enriched in heavy metal metabolism and resistance genes. One of the 16 T4SS clusters, cluster i, exhibited evidence of specialization for the RSSC phytopathogens. These findings shed light on the eco-evolutionary differences in the Ralstonia genus.

Impact statement

The Ralstonia genus contains the Ralstonia solanacearum species complex (RSSC), a group of globally important plant pathogens that impact food security. These pathogens are known to have an expansive, open pangenome with high levels of gene flow", "token_count": 527, "char_count": 2086, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:28.264753", "source": { "split": "train_shard_00001", "doc_id": 843 }, "chunk_id": "train_shard_00001_843_0", "global_id": 6855 }, { "text": "To shed light on the eco-evolutionary differences between RSSC phytopathogens and closely related environmental species, we explored the potential role of type IV secretion systems (T4SSs) in horizontal gene flow within the Ralstonia genus. Surprisingly, these mobile genetic elements were less common in the phytopathogens than the environmentals. Nevertheless, we identified a particular T4SS gene cluster encoded on an accessory plasmid that appears to be specialized to the pathogenic lifestyle of the RSSC. This specialized cluster harbors genes that drive RSSC host range (type III effectors) and others that likely allow these pathogens to antagonize the plant microbiota (type VI secretion toxins and hemagglutinin two partner secretion systems). Moreover, this study sheds light on the cryptic lifestyles of the poorly studied environmental Ralstonia species, revealing that their conjugative T4SSs frequently carry heavy metal metabolism and resistance genes. Overall, this study provides a foundation to investigate the functional roles of T4SS clusters and their cargo genes in the fitness of phytopathogenic and environmental Ralstonia .

Data summary

Supplemental Table S1 lists details of the RSSC phytopathogen, non-RSSC environmental, and Burkholderiaceae family genomes used in this study. Supplemental Table S2A is the final list of 503 VirB4 sequences collectively identified in 644 RSSC phytopathogen genomes and 143 non-RSSC environmental genomes. Supplemental Table S2B includes the annotations and NCBI accessions for every gene and protein sequence in reference clusters a-p. Supplemental Table S2C is the list of putative T4SS cargo genes identified in complete Ralstonia genomes. Supplemental Table S2D is the list of putative T4SS cargo genes identified in cluster i regions from draft and complete Ralstonia genomes. Supplemental File S1 is the multiple sequence alignment (MSA) input for HMMER, made from the 753 VirB4 protein sequences from the Burkholderiaceae family genomes", "token_count": 498, "char_count": 2016, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5675, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:28.936615", "source": { "split": "train_shard_00001", "doc_id": 843 }, "chunk_id": "train_shard_00001_843_1", "global_id": 6856 }, { "text": "Supplemental Files S2 and S3 are the species trees displaying the presence of T4SS gene clusters in RSSC phytopathogens and non-RSSC environmentals, respectively. Supplemental File S4 is the species tree displaying the presence of RSp0179 and RSp1521 in the Ralstonia genus. Supplemental File S5 is the MSA input for FastTree 2, made from the VirB4 protein sequences from Ralstonia genomes. Supplemental Files S6-S9 are various formats of the VirB4 protein tree in Figure 1. Supplemental Files S10-S25 are the GBK files for reference clusters a-p. Supplemental File S26 is the clinker output comparing the reference clusters. Supplemental Files S27-S36 are the clinker outputs comparing the putative regions of transfer of T4SSs in complete Ralstonia genomes. Supplemental File S37 is the clustered ANI matrix for the putative regions of transfer of cluster i T4SSs in draft and complete Ralstonia genomes. Supplemental File S38 is the clinker output comparing the cluster i regions in draft and complete Ralstonia genomes. All Supplemental Tables and Files are available through Zenodo (DOI: 10.5281/zenodo.14873519). This study’s newly sequenced genomes, Gazipur 4 and Gazipur 5, are available on NCBI with the following accessions: GCF_049860735.1 and GCF_049860725.1, respectively. The two contigs containing the cluster j T4SS were submitted to NCBI through the Third Party Annotation (TPA) section of the DDBJ/ENA/ GenBank databases with the following accessions: BK072068 - BK072069 . These contigs were assembled from SRA reads under the accession: SRR18649448.\n\nLifestyle-associated variation in type IV secretion systems between phytopathogenic and environmental Ralstonia", "token_count": 511, "char_count": 1689, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5224, "quality_score": 0.7612, "entities": { "genes": [ "BK072068", "BK072069", "SRR18649448" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:29.611873", "source": { "split": "train_shard_00001", "doc_id": 843 }, "chunk_id": "train_shard_00001_843_2", "global_id": 6857 }, { "text": "BACKGROUND: Exoinulinase catalyzes the successive removal of individual fructose moiety from the non‐reducing end of the inulin molecule, which is useful for biotechnological applications like producing fructan‐based non‐grain biomass energy and high‐fructose syrup. In this study, an exoinulinase (KmINU) from Kluyveromyces marxianus DSM 5418 was tailored for increased catalytic activity and acidic adaptation for inulin hydrolysis processes by rational site‐directed mutagenesis. RESULTS: Three mutations, S124Y, N158S and Q215V distal to the catalytic residues of KmINU were designed and heterologously expressed in Pichia pastoris GS115. Compared to the wild‐type, S124Y shifted the pH‐activity profile towards acidic pH values and increased the catalytic activity and catalytic efficiency by 59% and 99% to 688.4 ± 17.03 s⁻¹ and 568.93 L mmol⁻¹ s⁻¹, respectively. N158S improved the catalytic activity under acidic pH conditions, giving a maximum value of 464.06 ± 14.06 s⁻¹ on inulin at pH 4.5. Q215V markedly improved the substrate preference for inulin over sucrose by 5.56‐fold, and showed catalytic efficiencies of 208.82 and 6.88 L mmol⁻¹ s⁻¹ towards inulin and sucrose, respectively. Molecular modeling and computational docking indicated that structural reorientation may underlie the increased catalytic activity, acidic adaptation and substrate preference. CONCLUSIONS: The KmINU mutants may serve as industrially promising candidates for inulin hydrolysis", "token_count": 492, "char_count": 1472, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "GS115" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:30.286234", "source": { "split": "train_shard_00001", "doc_id": 844 }, "chunk_id": "train_shard_00001_844_0", "global_id": 6858 }, { "text": "Protein engineering of exoinulinase here provides a successful example of the extent to which mutating non‐conserved substrate recognition and binding residues distal to the active site can be used for industrial enzyme improvements. © 2020 Society of Chemical Industry\n\nEngineering better catalytic activity and acidic adaptation into Kluyveromyces marxianus exoinulinase using site‐directed mutagenesis", "token_count": 94, "char_count": 404, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8679, "quality_score": 0.934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:30.658372", "source": { "split": "train_shard_00001", "doc_id": 844 }, "chunk_id": "train_shard_00001_844_1", "global_id": 6859 }, { "text": "The exponential increase in sequencing data calls for conceptual and computational advances to extract useful biological insights. One such advance, minimizers, allows for reducing the quantity of data handled while maintaining some of its key properties. We provide a basic introduction to minimizers, cover recent methodological developments, and review the diverse applications of minimizers to analyze genomic data, including de novo genome assembly, metagenomics, read alignment, read correction, and pangenomes. We also touch on alternative data sketching techniques including universal hitting sets, syncmers, or strobemers. Minimizers and their alternatives have rapidly become indispensable tools for handling vast amounts of data.\n\nWhen less is more: sketching with minimizers in genomics.", "token_count": 158, "char_count": 799, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7982, "quality_score": 0.8991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:31.099596", "source": { "split": "train_shard_00001", "doc_id": 845 }, "chunk_id": "train_shard_00001_845_0", "global_id": 6860 }, { "text": "

Background

Lignocellulosic biomass is one of the most abundant materials for biochemicals production. However, efficient co-utilization of glucose and xylose from the lignocellulosic biomass is a challenge due to the glucose repression in microorganisms. Kluyveromyces marxianus is a thermotolerant and efficient xylose-utilizing yeast. To realize the glucose-xylose co-utilization, analyzing the glucose repression of xylose utilization in K. marxianus is necessary. In addition, a glucose-xylose co-utilization platform strain will facilitate the construction of lignocellulosic biomass-utilizing strains.

Results

Through gene disruption, hexokinase 1 (KmHXK1) and sucrose non-fermenting 1 (KmSNF1) were proved to be involved in the glucose repression of xylose utilization while disruption of the downstream genes of cyclic AMP-protein kinase A (cAMP-PKA) signaling pathway or sucrose non-fermenting 3 (SNF3) glucose-sensing pathway did not alleviate the repression. Furthermore, disruption of the gene of multicopy inhibitor of GAL gene expression (KmMIG1) alleviated the glucose repression on some nonglucose sugars (galactose, sucrose, and raffinose) but still kept glucose repression of xylose utilization. Real-time PCR analysis of the xylose utilization related genes transcription confirmed these results, and besides, revealed that xylitol dehydrogenase gene (KmXYL2) was the critical gene for xylose utilization and stringently regulated by glucose repression. Many other genes of candidate targets interacting with SNF1 were also evaluated by disruption, but none proved to be the key regulator in the pathway of the glucose repression on xylose utilization. Therefore, there may exist other signaling pathway(s) for glucose repression on xylose consumption", "token_count": 508, "char_count": 1785, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5641, "quality_score": 0.7821, "entities": { "genes": [ "SNF1", "SNF3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:31.733317", "source": { "split": "train_shard_00001", "doc_id": 846 }, "chunk_id": "train_shard_00001_846_0", "global_id": 6861 }, { "text": "Based on these results, a thermotolerant xylose-glucose co-consumption platform strain of K. marxianus was constructed. Then, exogenous xylose reductase and xylose-specific transporter genes were overexpressed in the platform strain to obtain YHY013. The YHY013 could efficiently co-utilized the glucose and xylose from corncob hydrolysate or xylose mother liquor for xylitol production (> 100 g/L) even with inexpensive organic nitrogen sources.

Conclusions

The analysis of the glucose repression in K. marxianus laid the foundation for construction of the glucose-xylose co-utilizing platform strain. The efficient xylitol production strain further verified the potential of the platform strain in exploitation of lignocellulosic biomass.\n\nRelease of glucose repression on xylose utilization in Kluyveromyces marxianus to enhance glucose-xylose co-utilization and xylitol production from corncob hydrolysate.", "token_count": 260, "char_count": 917, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6325, "quality_score": 0.8162, "entities": { "genes": [ "YHY013" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:32.288883", "source": { "split": "train_shard_00001", "doc_id": 846 }, "chunk_id": "train_shard_00001_846_1", "global_id": 6862 }, { "text": "

Background

Transposable Elements (TEs) are segments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility.

Results

We develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera, that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies.

Conclusions

Our results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.\n\nIdentification of transposable element families from pangenome polymorphisms.", "token_count": 304, "char_count": 1393, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6878, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:32.854337", "source": { "split": "train_shard_00001", "doc_id": 847 }, "chunk_id": "train_shard_00001_847_0", "global_id": 6863 }, { "text": "Yeasts are generally recognized as contaminants in the production of white-brined cheeses, such as Feta and Feta-type cheeses. The most predominant yeasts species are Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces marxianus, Kluyveromyces lactis, Rhodotorula mucilaginosa, and Trichosporon spp. Although their spoilage potential varies at both species and strain levels, yeasts will, in case of excessive growth, present a microbiological hazard, effecting cheese quality. To evaluate the hazard and trace routes of contamination, the exact taxonomic classification of yeasts is required. Today, identification of dairy yeasts is mainly based on DNA sequencing, various genotyping techniques, and, to some extent, advanced phenotypic identification technologies. Even though these technologies are state of the art at the scientific level, they are only hardly implemented at the industrial level. Quality defects, caused by yeasts in white-brined cheese, are mainly linked to enzymatic activities and metabolism of fermentable carbohydrates, leading to production of metabolites (CO2, fatty acids, volatile compounds, amino acids, sulfur compounds, etc.) and resulting in off-flavors, texture softening, discoloration, and swelling of cheese packages. The proliferation of spoilage yeast depends on maturation and storage conditions at each specific dairy, product characteristics, nutrients availability, and interactions with the co-existing microorganisms. To prevent and control yeast contamination, different strategies based on the principles of HACCP and Good Manufacturing Practice (GMP) have been introduced in white-brined cheese production. These strategies include milk pasteurization, refrigeration, hygienic sanitation, air filtration, as well as aseptic and modified atmosphere packaging. Though a lot of research has been dedicated to yeasts in dairy products, the role of yeast contaminants, specifically in white-brined cheeses, is still insufficiently understood", "token_count": 507, "char_count": 2046, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:33.514946", "source": { "split": "train_shard_00001", "doc_id": 848 }, "chunk_id": "train_shard_00001_848_0", "global_id": 6864 }, { "text": "This review aims to summarize the current knowledge on the identification of contaminant yeasts in white-brined cheeses, their occurrence and spoilage potential related to different varieties of white-brined cheeses, their interactions with other microorganisms, as well as guidelines used by dairies to prevent cheese contamination.\n\nOccurrence of Yeasts in White-Brined Cheeses: Methodologies for Identification, Spoilage Potential and Good Manufacturing Practices.", "token_count": 107, "char_count": 467, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:33.891988", "source": { "split": "train_shard_00001", "doc_id": 848 }, "chunk_id": "train_shard_00001_848_1", "global_id": 6865 }, { "text": "The pangenome of a species is the set of all genes carried by at least one member of the species. In bacteria, pangenomes can be much larger than the set of genes carried by a single organism. Many questions remain unanswered regarding the evolutionary forces shaping the patterns of presence/absence of genes in pangenomes of a given species. We introduce a new model for bacterial pangenome evolution along a species phylogeny that explicitly describes the timing of appearance of each gene in the species and accounts for three generic types of gene evolutionary dynamics: persistent genes that are present in the ancestral genome, private genes that are specific to a given clade, and mobile genes that are imported once into the gene pool and then undergo frequent horizontal gene transfers. We call this model the Persistent-Private-Mobile (PPM) model. We develop an algorithm fitting the PPM model and apply it to a dataset of 902 Salmonella enterica genomes. We show that the best fitting model is able to reproduce the global pattern of some multivariate statistics like the gene frequency spectrum and the parsimony vs. frequency plot. Moreover, the gene classification induced by the PPM model allows us to study the position of accessory genes on the chromosome depending on their category, as well as the gene functions that are most present in each category. This work paves the way for a mechanistic understanding of pangenome evolution, and the PPM model developed here could be used for dynamics-aware gene classification.\n\nPersistent, Private and Mobile genes: a model for gene dynamics in evolving pangenomes", "token_count": 346, "char_count": 1627, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5496, "quality_score": 0.7748, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:34.479378", "source": { "split": "train_shard_00001", "doc_id": 849 }, "chunk_id": "train_shard_00001_849_0", "global_id": 6866 }, { "text": "The rise of antifungal resistance is a global challenge for both human health and food security, because resistance emergence easily outpaces the antifungal development pipeline. Furthermore, resistance arises often in parallel and through alternative mechanisms creating challenges to predict emergence. In agriculture, where vast areas are sprayed by diverse cocktails, antifungal resistance gains are particularly complex. Despite broad efforts, knowledge of resistance mechanisms is often limited to model genotypes and empirical evidence from the field is lacking. Here, we define and validate a high- throughput pipeline for antifungal resistance discovery informed by emerging resistance gains at continental scale. We analyzed a thousand-genome European diversity panel of the major wheat pathogen Zymoseptoria tritici and assessed resistance levels against over 29 fungicides covering all major classes. We optimized high-throughput phenotyping assays to comprehensively capture emerging resistance phenotypes. Pangenome-informed genotyping techniques revealed a total of 2192 genes associated with antifungal resistance. This expands by an order of magnitude the current knowledge and establishes a refined atlas of resistance mutations. We generated mutants to recapitulate several of the discovered resistance factors. Hence, our approach captures in-field resistance gains across Europe for all major fungicide classes and can define exact molecular targets. Broad knowledge of resistance gains will guide more sustainable fungicide development pipelines.\n\nHigh-throughput discovery of emerging antifungal resistance in crop pathogens", "token_count": 332, "char_count": 1647, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:35.050713", "source": { "split": "train_shard_00001", "doc_id": 850 }, "chunk_id": "train_shard_00001_850_0", "global_id": 6867 }, { "text": "The pangenome of lactic acid bacteria (LAB) was constructed with five bacterial strains isolated from oat silage produced by smallholder farmers from a region in the highlands of the Colombian Andes. The goal of this work was to use genome mining to elucidate some potential mechanisms of action associated with plant growth promotion and biocontrol in LAB. Multiple genes were uncovered, including those associated with antibiosis and antimicrobial compound production, genes that induce plant defense and phytohormone activation. Additionally, genome sequencing suggested mechanisms for LAB to protect against abiotic and biotic stress. Furthermore, genes that may improve phosphorus availability and those that might stimulate root growth were present. We then tested some of these findings in vitro. For instance, the biocontrol activity of these strains was evaluated against the fungal pathogens Fusarium oxsyporum f. sp. cubense (Foc R1 and Foc TR4) and the bacterial pathogen Ralstonia solanacearum (Rs). All tested strains showed the ability to significantly inhibit pathogen growth in vitro. The capability of LAB to grow at high concentrations of fusaric acid was demonstrated, suggesting that LAB might have detoxification mechanisms to compete with other microorganisms. Also, the ability of LAB to solubilize phosphate and produce IAA was demonstrated. These two properties might be involved in plant-growth promotion. Here we show that genomic sequencing can be an efficient tool to identify putative biocontrol or plant-growth promoting related sequences for genome mining.\n\nGenome mining to elucidate antimicrobial and plant growth promoting potentials in Lactic acid bacteria", "token_count": 387, "char_count": 1693, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6057, "quality_score": 0.8028, "entities": { "genes": [ "TR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:36.024693", "source": { "split": "train_shard_00001", "doc_id": 851 }, "chunk_id": "train_shard_00001_851_0", "global_id": 6868 }, { "text": "

Background

Ralstonia solanacearum species complex (RSSC) strains are destructive plant pathogenic bacteria and the causative agents of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, their virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape RSSC virulence, the global diversity, distribution, and wider functional gene content of RSSC prophages are unknown. In this study, prophages were identified in a diverse collection of 192 RSSC draft genome assemblies originating from six continents.

Results

Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distributions were characterised using metadata on RSSC strain geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 313 intact prophages were identified, forming ten genetically distinct clusters. These included six prophage clusters with similarity to the Inoviridae, Myoviridae, and Siphoviridae phage families, and four uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distributions, being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained many auxiliary genes involved in metabolism and virulence of both phage and bacteria.

Conclusions

Our results show that while RSSC prophages are highly diverse globally, they make lineage-specific contributions to the RSSC accessory genome, which could have resulted from shared coevolutionary history.\n\nGlobal diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum species complex.", "token_count": 502, "char_count": 2177, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6716, "quality_score": 0.8358, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:36.679326", "source": { "split": "train_shard_00001", "doc_id": 852 }, "chunk_id": "train_shard_00001_852_0", "global_id": 6869 }, { "text": "There is widespread concern about the increase in cases of human and animal infections caused by pathogenic Vibrio species due to the emergence of epidemic lineages. In Colombia, active surveillance by the National Institute of Health (INS) has confirmed the presence of Vibrio; however, in routine surveillance, these isolates are not genomically characterized. This study focused on the pangenome analysis of six Vibrio species: V. parahaemolyticus, V. vulnificus, V. alginolyticus, V. fluvialis, V. diabolicus and V. furnissii to determine the genetic architectures of potentially virulent and antimicrobial resistance traits. Isolates from environmental and clinical samples were genome sequenced, assembled and annotated. The most important species in public health were further characterized by multilocus sequence typing and phylogenomics. For V. parahaemolyticus, we found the virulent ST3 and ST120 genotypes. For V. vulnificus, we identified isolates belonging to lineages 1 and 2. Virulence gene homologues between species were found even in non-pathogenic species such as V. diabolicus. Annotations related to the mobilome, integrative mobile and conjugative elements and resistance genes were obtained from environmental and clinical isolates. This study contributes genomic information to the intensified surveillance program implemented by the INS to establish potential sources of vibriosis in Colombia.\n\nComparative Genomics of Clinical and Environmental Isolates of Vibrio spp. of Colombia: Implications of Traits Associated with Virulence and Resistance.", "token_count": 436, "char_count": 1664, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6267, "quality_score": 0.8134, "entities": { "genes": [ "ST3", "ST120" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:37.317527", "source": { "split": "train_shard_00001", "doc_id": 853 }, "chunk_id": "train_shard_00001_853_0", "global_id": 6870 }, { "text": "Highlighting the Distinguished Speakers Symposium on \"The Future of Human Genetics and Genomics,\" this collection of articles is based on presentations at the ASHG 2023 Annual Meeting in Washington, DC, in celebration of all our field has accomplished in the past 75 years, since the founding of ASHG in 1948.\n\nFrom complete genomes to pangenomes.", "token_count": 92, "char_count": 347, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:37.701846", "source": { "split": "train_shard_00001", "doc_id": 854 }, "chunk_id": "train_shard_00001_854_0", "global_id": 6871 }, { "text": "The reported human infections with the emerging zoonotic pathogen Streptococcus parasuis are steadily rising. Rapid and standardized genotyping tools specific to S. parasuis are critically needed for epidemiological surveillance and identification of strains with zoonotic potential. This study developed a whole-genome sequence (WGS)-based typing strategy, encompassing average nucleotide identity, a minimum core genome (MCG) typing scheme, and a multilocus sequence typing (MLST) scheme using 255 S. parasuis genomes isolated from eight countries between the 1980s and 2024. The S. parasuis population was categorized into 12 MCG clusters based on 72,172 SNPs in non-recombining regions distributed across an MCG comprising 607 genes, forming two distinct lineages. The rapid MCG typing program accurately assigned 92.5% of S. parasuis genomes to their corresponding MCG clusters by identifying 4,509 cluster/subcluster-specific SNPs. To elucidate the clonal relationships among S. parasuis genomes, an MLST scheme was developed, defining 161 sequence types (STs) based on the allelic profiles of seven housekeeping loci (aroA, cpn60, gki, mutS, sdhA, recA, and thrA). Thirty-two STs that shared identical alleles at 6 loci were assigned to 10 complex clones, whereas 100 STs that shared identical alleles at 4 or more loci were grouped into 9 ST clades. The MCG typing scheme and the MLST scheme demonstrated sufficient discriminatory power, with Simpson's diversity index values of 0.8864 and 0.9821, respectively. This study characterized the S", "token_count": 516, "char_count": 1672, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:38.339320", "source": { "split": "train_shard_00001", "doc_id": 855 }, "chunk_id": "train_shard_00001_855_0", "global_id": 6872 }, { "text": "parasuis population and provided a rapid, reproducible, and expandable WGS-based typing strategy for taxonomic identification, epidemiological surveillance, and evaluation of the zoonotic potential of S. parasuis.IMPORTANCEOur study provides valuable insights for developing effective prevention and control strategies for Streptococcus parasuis infections, by revealing the structural characteristics and phylogenetic relationship of S. parasuis population, by developing a whole-genome sequence-based typing strategy applicable for epidemiological surveillance, transmission investigation, and zoonotic potential evaluation.\n\nDeveloping genome typing strategies for the emerging zoonotic pathogen <i>Streptococcus parasuis</i>.", "token_count": 181, "char_count": 766, "word_count": 81, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:38.791177", "source": { "split": "train_shard_00001", "doc_id": 855 }, "chunk_id": "train_shard_00001_855_1", "global_id": 6873 }, { "text": "Campylobacter jejuni is a leading cause of bacterial gastroenteritis in humans around the world. The emergence of bacterial resistance is becoming more serious; therefore, development of new vaccines is considered to be an alternative strategy against drug-resistant pathogen. In this study, we investigated the pangenome of 173 C. jejuni strains and analyzed the phylogenesis and the virulence factor genes. In order to acquire a high-quality pangenome, genomic relatedness was firstly performed with average nucleotide identity (ANI) analyses, and an open pangenome of 8,041 gene families was obtained with the correct taxonomy genomes. Subsequently, the virulence property of the core genome was analyzed and 145 core virulence factor (VF) genes were obtained. Upon functional genomics and immunological analyses, five core VF proteins with high antigenicity were selected as potential core vaccine targets for humans. Furthermore, functional annotations indicated that these proteins are involved in important molecular functions and biological processes, such as adhesion, regulation, and secretion. In addition, transcriptome analysis in human cells and pig intestinal loop proved that these vaccine target genes are important in the virulence of C. jejuni in different hosts. Comprehensive pangenome and relevant animal experiments will facilitate discovering the potential core vaccine targets with improved efficiency in reverse vaccinology. Likewise, this study provided some insights into the genetic polymorphism and phylogeny of C. jejuni and discovered potential vaccine candidates for humans. Prospective development of new vaccines using the targets will be an alternative to the use of antibiotics and prevent the development of multidrug-resistant C. jejuni in humans and even other animals.\n\nMulti-Omics Approach Reveals the Potential Core Vaccine Targets for the Emerging Foodborne Pathogen Campylobacter jejuni.", "token_count": 462, "char_count": 1974, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5904, "quality_score": 0.7952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:39.432473", "source": { "split": "train_shard_00001", "doc_id": 856 }, "chunk_id": "train_shard_00001_856_0", "global_id": 6874 }, { "text": "The genus Hanseniaspora includes apiculate yeasts commonly found in fruit- and fermentation-associated environments. Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and enological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated from wine environments, focusing on Hanseniaspora uvarum , the most abundant non- Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow- (SEL) and fast-evolving (FEL) lineages that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting specifically in the FEL lineage. Pangenome analysis within H. uvarum identified extensive copy number variation (CNV), particularly in genes related to xenobiotic tolerance, nutrient transport and metabolism. Investigation into the selective landscape following the FEL/SEL divergence identified diversifying selection in 229 genes in the Hanseniaspora FEL lineage, with significant enrichment in genes within the lysine biosynthetic pathway, suggesting a key role for this amino acid in early FEL adaptation. In H. uvarum , signatures of recent positive selection were detected in genes linked to sulphur assimilation, sterol biosynthesis and glycerol production, indicating potential adaptation to the stresses imposed by grape and wine fermentation. Furthermore, phenotypic screening of 113 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO₂, and cold tolerance. These findings provide novel insights into the genomic evolution and functional diversity of Hanseniaspora , expanding our understanding of yeast adaptation to wine fermentation and laying the foundation for targeted gene investigations within this important genus.\n\nGenetic and phenotypic diversity of wine-associated Hanseniaspora species", "token_count": 512, "char_count": 2258, "word_count": 289, "semantic_coherence": 1, "information_density": 0.6678, "quality_score": 0.8339, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:40.085266", "source": { "split": "train_shard_00001", "doc_id": 857 }, "chunk_id": "train_shard_00001_857_0", "global_id": 6875 }, { "text": "Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates the treatment of S. aureus infections. Understanding the population structure and distribution of genetic lineages of S. aureus is central to understanding the biology, epidemiology and pathogenesis of this organism. This study exploited a large, publicly available dataset of nearly 27,000 S. aureus genomes to (i) develop a core genome multilocus sequence typing (cgMLST) scheme, (ii) stratify hierarchical clusters based on allelic similarity thresholds, and (iii) define the clusters with a life identification number (LIN) code classification system. The cgMLST scheme characterised allelic variation at 1,716 core gene loci, and 13 classification thresholds were defined, which discriminated S. aureus variants across a range of genetic similarity thresholds. LIN code 'lineages' and clonal complexes defined by seven-locus multilocus sequence typing were highly concordant, but the LIN codes permitted a wider range of genetic discrimination among S. aureus genomes. This S. aureus cgMLST scheme and LIN code system is a high-resolution, stable genotyping tool that enables detailed genomic analyses of S. aureus.\n\nDevelopment of a core genome multilocus sequence typing scheme and life identification number code classification system for <i>Staphylococcus aureus</i>.", "token_count": 417, "char_count": 1480, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6218, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:40.736803", "source": { "split": "train_shard_00001", "doc_id": 858 }, "chunk_id": "train_shard_00001_858_0", "global_id": 6876 }, { "text": "

Summary

Prefix free parsing [Boucher et al., Alg. Mol. Biol., 2019], is a highly effective heuristic for computing text indexes for very large amounts of biological data. The algorithm constructs a data structure, the prefix-free parse (PFP) of the input, consisting of a dictionary and a parse, which is then used to speed up computation of the final index. In this paper, we study the size of the PFP, which we refer to as π , and show that it is a powerful theoretical tool in its own right. To show this, we present two use cases. We first study the application of π as a repetitiveness measure of the input text, and compare it to other currently used repetitiveness measures, including z, r , and δ . We then turn to the use of π as a measure for pangenome openness . In both applications, our results are similar to existing measures, but our tool, in almost all cases, is more efficient than those computing the other measures, both in terms of time and space, sometimes by an order of magnitude. We close the paper with the first systematic study of the parameter choice for PFP (window size w and modulus p ). This gives rise to interesting open questions.

Availability and implementation

The source code is available at https://github.com/simolucaa/piPFP , the accession codes for all the datasets used at https://github.com/simolucaa/piPFP_experiments .\n\nMeasuring Genomic Data with PFP", "token_count": 352, "char_count": 1416, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:41.336489", "source": { "split": "train_shard_00001", "doc_id": 859 }, "chunk_id": "train_shard_00001_859_0", "global_id": 6877 }, { "text": "Pangenomes are growing in number and size, thanks to the prevalence of high-quality long-read assemblies. However, current methods for studying sequence composition and conservation within pangenomes have limitations. Methods based on graph pangenomes require a computationally expensive multiple-alignment step, which can leave out some variation. Indexes based on k -mers and de Bruijn graphs are limited to answering questions at a specific substring length k . We present Maximal Exact Match Ordered (MEMO), a pangenome indexing method based on maximal exact matches (MEMs) between sequences. A single MEMO index can handle arbitrary-length queries over pangenomic windows. MEMO enables both queries that test k -mer presence/absence (membership queries) and that count the number of genomes containing k -mers in a window (conservation queries). MEMO’s index for a pangenome of 89 human autosomal haplotypes fits in 2.04 GB, 8.8 × smaller than a comparable KMC3 index and 11.4 × smaller than a PanKmer index. MEMO indexes can be made smaller by sacrificing some counting resolution, with our decile-resolution HPRC index reaching 0.67 GB. MEMO can conduct a conservation query for 31-mers over the human leukocyte antigen locus in 13.89 seconds, 2.5x faster than other approaches. MEMO’s small index size, lack of k -mer length dependence, and efficient queries make it a flexible tool for studying and visualizing substring conservation in pangenomes.\n\nMEM-based pangenome indexing fork-mer queries", "token_count": 378, "char_count": 1511, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6518, "quality_score": 0.8259, "entities": { "genes": [ "KMC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:41.972968", "source": { "split": "train_shard_00001", "doc_id": 860 }, "chunk_id": "train_shard_00001_860_0", "global_id": 6878 }, { "text": "With antimicrobial resistance (AMR) rapidly evolving in pathogens, quick and accurate identification of genetic determinants of phenotypic resistance is essential for improving surveillance, stewardship, and clinical mitigation. Machine learning (ML) models show promise for AMR prediction in diagnostics but require a deep understanding of internal processes to use effectively. Our study utilised AMR gene, pangenomic, and predicted plasmid features from 647 Enterococcus faecium and Enterococcus faecalis genomes across the One Health continuum, along with corresponding resistance phenotypes, to develop interpretive ML classifiers. Vancomycin resistance could be predicted with 99% accuracy with AMR gene features, 98% with pangenome features, and 96% with plasmid clusters. Top pangenome features overlapped with the resistance genes of the vanA operon, which are often laterally transmitted via plasmids. Doxycycline resistance prediction achieved approximately 92% accuracy with pangenome features, with the top feature being elements of Tn916 conjugative transposon, a tet(M) carrier. Erythromycin resistance prediction models achieved about 90% accuracy, but top features were negatively correlated with resistance due to the confounding effect of population structure. This work demonstrates the importance of reviewing ML models' features to discern biological relevance even when achieving high-performance metrics. Our workflow offers the potential to propose hypotheses for experimental testing, enhancing the understanding of AMR mechanisms, which are crucial for combating the AMR crisis.\n\nIdentification of key drivers of antimicrobial resistance in Enterococcus using machine learning.", "token_count": 419, "char_count": 1753, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:42.605887", "source": { "split": "train_shard_00001", "doc_id": 861 }, "chunk_id": "train_shard_00001_861_0", "global_id": 6879 }, { "text": "Raw starch and raw cassava tuber powder were directly and efficiently fermented at elevated temperatures to produce ethanol using the thermotolerant yeast Kluyveromyces marxianus that expresses α-amylase from Aspergillus oryzae as well as α-amylase and glucoamylase from Debaryomyces occidentalis. Among the constructed K. marxianus strains, YRL 009 had the highest efficiency in direct starch fermentation. Raw starch from corn, potato, cassava, or wheat can be fermented at temperatures higher than 40°C. At the optimal fermentation temperature 42°C, YRL 009 produced 66.52 g/L ethanol from 200 g/L cassava starch, which was the highest production among the selected raw starches. This production increased to 79.75 g/L ethanol with a 78.3% theoretical yield (with all cassava starch were consumed) from raw cassava starch at higher initial cell densities. Fermentation was also carried out at 45 and 48°C. By using 200 g/L raw cassava starch, 137.11 and 87.71 g/L sugar were consumed with 55.36 and 32.16 g/L ethanol produced, respectively. Furthermore, this strain could directly ferment 200 g/L nonsterile raw cassava tuber powder (containing 178.52 g/L cassava starch) without additional nutritional supplements to produce 69.73 g/L ethanol by consuming 166.07 g/L sugar at 42°C. YRL 009, which has consolidated bioprocessing ability, is the best strain for fermenting starches at elevated temperatures that has been reported to date.\n\nDirect fermentation of raw starch using a Kluyveromyces marxianus strain that expresses glucoamylase and alpha-amylase to produce ethanol.", "token_count": 503, "char_count": 1580, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5584, "quality_score": 0.7792, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:43.261686", "source": { "split": "train_shard_00001", "doc_id": 862 }, "chunk_id": "train_shard_00001_862_0", "global_id": 6880 }, { "text": "The D4Z4 locus is a macrosatellite array on chromosome 4q that normally comprises 8 to >100 3.3-kb repeat units. Its size and repetitiveness render it refractory to most sequencing technologies; consequently its genetic and epigenetic architectures remain incompletely understood despite their relevance to human health, in particular facioscapulohumeral muscular dystrophy (FSHD). Molecular diagnosis for FSHD following clinical description currently involves complex, multi-step and low resolution assays, aiming at identifying contractions on permissive haplotypes (FSHD type 1) or epigenetic reactivation (FSHD type 2) due to pathogenic variants in the epigenetic machinery (most often in SMCHD1 ). Here we leverage ultra-long whole-genome and Cas9-targeted sequencing to develop a fast and accurate workflow, D4Z4End2End, to comprehensively charactere the genetics and methylation of D4Z4 alleles. We apply it to samples from patients affected by FSHD1, FSHD2, and another disease caused by SMCHD1 variants, Bosma arhinia microphthalmia syndrome (BAMS), as well as publicly-available data from the 1000 Genomes Project and Human Pangenome Reference Consortium. We attain high read depth sequencing of full-length D4Z4 arrays of up to 40 repeat units (~132 kb), accurately capture contracted arrays, genetic mosaicism, and pathogenic SMCHD1 variants, and generate accurate consensus sequences of the full set of D4Z4 alleles for variant analysis. Moreover, we identify new allelic variants, analyse complex D4Z4 rearrangements including in- cis duplications, and reveal striking length- and SMCHD1 status-dependent methylation patterns across the D4Z4 array. Our findings provide new insights into human macrosatellite genetics and epigenetics, and demonstrate the potential of long-read nanopore sequencing to accelerate FSHD research and diagnostics.", "token_count": 488, "char_count": 1856, "word_count": 254, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8543, "entities": { "genes": [ "FSHD1", "SMCHD1", "FSHD2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:43.917169", "source": { "split": "train_shard_00001", "doc_id": 863 }, "chunk_id": "train_shard_00001_863_0", "global_id": 6881 }, { "text": "D4Z4End2End: complete genetic and epigenetic architecture of D4Z4 macrosatellites in FSHD, BAMS and reference cohorts", "token_count": 38, "char_count": 117, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:44.276623", "source": { "split": "train_shard_00001", "doc_id": 863 }, "chunk_id": "train_shard_00001_863_1", "global_id": 6882 }, { "text": "Open burning of agricultural residues causes numerous complications including particulate matter pollution in the air, soil degradation, global warming and many more. Since they possess bio-conversion potential, agro-industrial residues including sugarcane bagasse (SCB), rice straw (RS), corncob (CC) and sweet sorghum bagasse (SSB) were chosen for the study. Yeast strains, Candida tropicalis , C. shehatae , Saccharomyces cerevisiae , and Kluyveromyces marxianus var. marxianus were compared for their production potential of bioethanol and phenylacetylcarbinol (PAC), an intermediate in the manufacture of crucial pharmaceuticals, namely, ephedrine, and pseudoephedrine. Among the substrates and yeasts evaluated, RS cultivated with C. tropicalis produced significantly (p ≤ 0.05) higher ethanol concentration at 15.3 g/L after 24 h cultivation. The product per substrate yield ( Y eth/s ) was 0.38 g/g with the volumetric productivity ( Q p ) of 0.64 g/L/h and fermentation efficiency of 73.6% based on a theoretical yield of 0.51 g ethanol/g glucose. C. tropicalis grown in RS medium produced 0.303 U/mL pyruvate decarboxylase (PDC), a key enzyme that catalyzes the production of PAC, with a specific activity of 0.400 U/mg protein after 24 h cultivation. This present study also compared the whole cells biomass of C. tropicalis with its partially purified PDC preparation for PAC biotransformation. The whole cells C. tropicalis PDC at 1.29 U/mL produced an overall concentration of 62.3 mM PAC, which was 68.4% higher when compared to partially purified enzyme preparation. The results suggest that the valorization of lignocellulosic residues into bioethanol and PAC will not only aid in mitigating the environmental challenge posed by their surroundings but also has the potential to improve the bioeconomy.", "token_count": 518, "char_count": 1818, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6679, "quality_score": 0.834, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:44.908625", "source": { "split": "train_shard_00001", "doc_id": 864 }, "chunk_id": "train_shard_00001_864_0", "global_id": 6883 }, { "text": "Valorization of rice straw, sugarcane bagasse and sweet sorghum bagasse for the production of bioethanol and phenylacetylcarbinol", "token_count": 36, "char_count": 129, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:45.278175", "source": { "split": "train_shard_00001", "doc_id": 864 }, "chunk_id": "train_shard_00001_864_1", "global_id": 6884 }, { "text": "Arthropods, the most diverse phylum on Earth, are hosts to a plethora of bacterial parasites that secrete various effectors of unknown function during infection. The most prevalent of these is the intracellular bacterium Wolbachia pipientis . The microbe infects between 40-60% of insect species, causes important reproductive manipulations, and limits virus replication in arthropod vectors, becoming a promising biocontrol agent. Understanding the molecular basis of Wolbachia infection and Wolbachia- induced phenotypes is critical to the use of Wolbachia in vector control. These Wolbachia ankyrin repeat proteins (WARPs) represent a highly dynamic and diverse part of the Wolbachia pangenome and remain thus far, largely uncharacterized. Here, we perform molecular and genetic screens to identify interactions between Wolbachia w Mel WARPs and their target host proteins in Drosophila melanogaster . Our results identify strong interactions of two Wolbachia proteins, WARP434 and WARP754, with two host targets (CG11327 and Ptp61F, respectively). Heterologous expression of these two WARPs is extremely toxic in Drosophila tissues and the toxicity is dependent on the ankyrin repeat domain of each WARP. Importantly, knockdown of the host targets alleviates toxicity, confirming WARP/target interactions. Finally, antibodies targeting both WARPs show expression by Wolbachia during infection of Drosophila cells. Understanding how Wolbachia manipulates its host biology and which host pathways it targets during infection will help us divine how the most prevalent intracellular bacterial parasite on Earth interacts with its insect hosts at the molecular level. Our screen is the first step towards that goal.

Importance

Molecular interactions drive co-evolutionary arms races between hosts and pathogens. These interactions shape the structure and function of both host and parasite proteins, enabling immunity or virulence during infection. Understanding the molecular details that unfold during these events illustrates not only how hosts and parasites co-evolve at the molecular level but also may help characterize the function of poorly understood proteins", "token_count": 504, "char_count": 2178, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5719, "quality_score": 0.7859, "entities": { "genes": [ "WARP434", "WARP754", "CG11327" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:45.936735", "source": { "split": "train_shard_00001", "doc_id": 865 }, "chunk_id": "train_shard_00001_865_0", "global_id": 6885 }, { "text": "The most prevalent intracellular infection on earth is Wolbachia pipientis, with between 40-60% of insects harboring the bacterial symbiont. Understanding how Wolbachia infects host cells and the molecular tools it uses to alter cell biology is critical to the use of the microbe in vector control. Here, we identify Wolbachia proteins used by the symbiont to interface with specific host proteins. Understanding the molecular mechanisms underlying this host-microbe interaction will shed light on how an important symbiont, used in the control of vector populations and disease transmission, uses WARPs to interact with host targets and how targeting this host protein contributes to infection.\n\nWolbachia uses ankyrin repeats to target specific fly proteins", "token_count": 181, "char_count": 766, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:46.386007", "source": { "split": "train_shard_00001", "doc_id": 865 }, "chunk_id": "train_shard_00001_865_1", "global_id": 6886 }, { "text": "Bifidobacterium species are well-established members of the human gut microbiome, particularly prominent during infancy, contributing to host health. Within this genus, Bifidobacterium longum ( BL. ) is a widespread species found in both infant and adult guts, known for its complexity and functional diversity among its known subspecies: BL. longum , BL. infantis and BL. suis . Here, using genomic and phylogenetic tools we propose a novel subspecies within the BL. species, Bifidobacterium longum subsp. nexti subspecies novel. We analyzed 435 BL. genomes using a polyphasic taxonomic approach comprising average nucleotide identity (ANI), digital DNA–DNA hybridization (dDDH), and pangenome analysis. We identified nine BL. strains, isolated from human infants and adults stool samples, as members of a distinct lineage within the BL. species. The type strain, LL6991, was isolated from the stool of a two-week-old Dutch infant in the Lifelines NEXT birth cohort. Phenotypically, BL. nexti exhibits a distinct morphological pattern, predominantly forming rod-shaped cells, often in chains with visible septa, contrasting with the Y-shaped morphology commonly observed for other BL. subspecies. Furthermore, BL. nexti demonstrates unique metabolic capabilities, including efficient utilization of fructose, and starch, carbohydrates not metabolized well by other tested BL. subspecies. This ability may be attributed to specific genes, such as a gene predicted to encode an extracellular amylopullulanase. This characterization expands the known diversity within the BL. species and provides insights into BL. nexti ’s unique adaptations and potential ecological roles within the human gut, especially in infants. Based on the consistent results from genotypic, phylogenetic, and phenotypic analyses, a novel subspecies with the name Bifidobacterium longum subsp. nexti , with type strain LL6991 (=NCCB 101085 =DSM 120337), is proposed.", "token_count": 501, "char_count": 1939, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8236, "entities": { "genes": [ "LL6991" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:47.041345", "source": { "split": "train_shard_00001", "doc_id": 866 }, "chunk_id": "train_shard_00001_866_0", "global_id": 6887 }, { "text": "Bifidobacterium longum subsp. nexti subsp. nov., a novel subspecies isolated from infant stool", "token_count": 40, "char_count": 108, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:47.401866", "source": { "split": "train_shard_00001", "doc_id": 866 }, "chunk_id": "train_shard_00001_866_1", "global_id": 6888 }, { "text": "Staphylococcus aureus is a ubiquitous commensal and opportunistic bacterial pathogen that can cause a wide gamut of infections, which are exacerbated by the presence of multidrug-resistant and methicillin-resistant S. aureus. S. aureus is genetically heterogeneous and consists of numerous distinct lineages. Using 558 complete genomes of S. aureus, we aim to determine how the accessory genome content among phylogenetic lineages of S. aureus is structured and has evolved. Bayesian hierarchical clustering identified 10 sequence clusters, of which seven contained major sequence types (ST 1, 5, 8, 30, 59, 239, and 398). The seven sequence clusters differed in their accessory gene content, including genes associated with antimicrobial resistance and virulence. Focusing on the two largest clusters, BAPS8 and BAPS10, and each consisting mostly of ST5 and ST8, respectively, we found that the structure and connected components in the co-occurrence networks of accessory genomes varied between them. These differences are explained, in part, by the variation in the rates at which the two sequence clusters gained and lost accessory genes, with the highest rate of gene accumulation occurring recently in their evolutionary histories. We also identified a divergent group within BAPS10 that has experienced high gene gain and loss early in its history. Together, our results show highly variable and dynamic accessory genomes in S. aureus that are structured by the history of the specific lineages that carry them.IMPORTANCEStaphylococcus aureus is an opportunistic, multi-host pathogen that can cause a variety of benign and life-threatening infections. Our results revealed considerable differences in the structure and evolution of the accessory genomes of major lineages within S. aureus. Such genomic variation within a species can have important implications on disease epidemiology, pathogenesis of infection, and interactions with the vertebrate host", "token_count": 514, "char_count": 2018, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5895, "quality_score": 0.7947, "entities": { "genes": [ "BAPS8", "ST5", "ST8", "BAPS10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:48.037262", "source": { "split": "train_shard_00001", "doc_id": 867 }, "chunk_id": "train_shard_00001_867_0", "global_id": 6889 }, { "text": "Our findings provide important insights into the underlying genetic basis for the success of S. aureus as a highly adaptable and resistant pathogen, which will inform current efforts to control and treat staphylococcal diseases.\n\nEvolutionary dynamics of the accessory genomes of <i>Staphylococcus aureus</i>.", "token_count": 90, "char_count": 328, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8837, "quality_score": 0.9419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:48.416448", "source": { "split": "train_shard_00001", "doc_id": 867 }, "chunk_id": "train_shard_00001_867_1", "global_id": 6890 }, { "text": "A few genera of diatoms are widespread in the oceans and form stable partnerships with N2-fixing filamentous cyanobacteria Richelia spp. A unique feature of the diatom-Richelia symbioses is the symbiont cellular location spans a continuum of integration (epibiont, periplasmic, endobiont) that is reflected in the symbiont genome size and content. In this study we analyzed genomes derived from cultures and environmental metagenome-assembled genomes focusing on characters indicative of genome evolution. Our results show an enrichment of short length transposable elements (TEs) and pseudogenes in the periplasmic endosymbiont genomes, suggesting an active and transitionary period in genome evolution. In contrast, genomes of endobionts exhibited fewer TEs and pseudogenes, reflecting advanced stages of genome reduction and increased host dependency in the endobionts. Pangenome analyses identified that endobionts streamline their genomes and conserve a majority of their genes in the core, whereas periplasmic endobionts and epibionts maintain larger flexible genomes, suggesting increased genomic plasticity. Functional gene comparisons with other N2-fixing cyanobacteria revealed that Richelia endobionts have similar patterns of metabolic loss but are distinguished by absence of specific pathways (e.g. cytochrome bd ubiquinol oxidase, lipid-A) that increase dependency and direct interaction with their respective hosts. In conclusion, our findings underscore the dynamic nature of genome reduction in N2-fixing cyanobacterial symbionts and demonstrate the diatom-Richelia symbioses as a valuable and rare model to study genome evolution in the transitional stages from a free-living facultative symbiont to a host-dependent endobiont.\n\nThe path to dependence: stepwise genome evolution from a facultative symbiont to an endosymbiont in the N2-fixing diatom-Richelia symbioses", "token_count": 485, "char_count": 1887, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5945, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:49.064085", "source": { "split": "train_shard_00001", "doc_id": 868 }, "chunk_id": "train_shard_00001_868_0", "global_id": 6891 }, { "text": "Hydrogen sulfide (H 2 S) is a gas produced endogenously in organisms from the three domains of life. In mammals, it is involved in diverse physiological processes, including the regulation of blood pressure, and its effects on memory. In contrast, in unicellular organisms the physiological role of H 2 S has not been studied in detail. In yeast, for example, in the winemaking industry H 2 S is an undesirable byproduct because of its rotten egg smell; however, its biological relevance during fermentation is not well understood. The effect of H 2 S in cells is linked to a posttranslational modification in cysteine residues known as S-persulfidation. We evaluated S-persulfidation in the Saccharomyces cerevisiae proteome. We screened S-persulfidated proteins from cells growing in fermentable carbon sources and we identified several glycolytic enzymes as S-persulfidation targets. Pyruvate kinase, catalyzing the last irreversible step of glycolysis, increased its activity in the presence of a H 2 S donor. Yeast cells treated with H 2 S increased ethanol production; moreover, mutant cells that endogenously accumulated H 2 S produced more ethanol and ATP during the exponential growth phase. This mechanism of the regulation of the metabolism seems to be evolutionarily conserved in other yeast species, because H 2 S induces ethanol production in the pre-Whole Genome Duplication species Kluyveromyces marxianus and Meyerozyma guilliermondii . Our results suggest a new role of H 2 S in the regulation of the metabolism during fermentation.\n\nSelf-produced hydrogen sulfide improves ethanol fermentation by Saccharomyces cerevisiae and other yeast species", "token_count": 437, "char_count": 1671, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5794, "quality_score": 0.7897, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:49.705561", "source": { "split": "train_shard_00001", "doc_id": 869 }, "chunk_id": "train_shard_00001_869_0", "global_id": 6892 }, { "text": "In the fermentation process of distilled spirits from Agave sugars, saponins inhibit the growth of yeasts during this procedure. This type of compound is present in the must, and the mechanisms of the cell growth inhibition are poorly understood. The fundamental objective of this work was to study the effect of saponins on the cell walls of the fermentative yeasts Saccharomyces cerevisiae and Kluyveromyces marxianus. This study was performed in batch and continuous cultures, adding pulses of saponins extracted from the leaves of Agave durangensis and Agave salmiana ssp. crassispina. The saponin extract from A. durangensis exhibited a stronger growth inhibitory effect in both yeast strains than A. salmiana saponin extract due to the structure of the saponins. However, in K. marxianus growth recovery was observed, because these strain showed saponinase activity that performed the saponin hydrolysis. Finally, microscopic observations confirmed the changes in the wall cell of S. cerevisiae and K. marxianus.\n\nEffect of steroidal saponins from Agave on the polysaccharide cell wall composition of Saccharomyces cerevisiae and Kluyveromyces marxianus", "token_count": 294, "char_count": 1159, "word_count": 171, "semantic_coherence": 1, "information_density": 0.538, "quality_score": 0.769, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:50.270723", "source": { "split": "train_shard_00001", "doc_id": 870 }, "chunk_id": "train_shard_00001_870_0", "global_id": 6893 }, { "text": "

Background

Taking into account its thermotolerance, high growth rate, and broad substrate spectrum, Kluyveromyces marxianus can be considered an ideal consolidated bioprocessing (CBP). A major obstacle to ethanol production using K. marxianus is the low production of lignocellulolytic enzymes, which reduces the cellulose hydrolysis and ethanol production. Thus, further improvement of enzyme expression and secretion is essential.

Results

To improve the expression of lignocellulolytic enzymes, the inulinase promoter and signal sequence from K. marxianus was optimized through mutagenesis. A T(-361)A mutation inside the promoter, a deletion of AT-rich region inside 5'UTR (UTR∆A), and a P10L substitution in the signal sequence increased the secretory expression of the feruloyl esterase Est1E by up to sixfold. T(-361)A and UTR∆A increased the mRNA expression, while the P10L substitution extended the hydrophobic core of signal sequence and promoted secretion of mature protein. P10L and T(-361)A mutations increased secretory expressions of other types of lignocellulolytic enzymes by up to threefold, including endo-1,4-β-glucanase RuCelA, endo-1,4-β-endoxylanase Xyn-CDBFV, and endo-1,4-β-mannanase MAN330. During the fed-batch fermentation of strains carrying optimized modules, the peak activities of RuCelA, Xyn-CDBFV, MAN330, and Est1E reached 24 U/mL, 25,600 U/mL, 10,200 U/mL, and 1220 U/mL, respectively", "token_count": 490, "char_count": 1455, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6223, "quality_score": 0.8112, "entities": { "genes": [ "MAN330" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:50.916505", "source": { "split": "train_shard_00001", "doc_id": 871 }, "chunk_id": "train_shard_00001_871_0", "global_id": 6894 }, { "text": "Importantly, higher yield of enzymes by optimized promoter and signal sequence were achieved in all tested carbon sources, including the major end products of lignocellulose saccharification and fermentation, with growth on xylose resulting in the highest production.

Conclusions

The engineered promoter and signal sequence presented increased secretory expressions of different lignocellulolytic enzymes in K. marxianus by means of various carbon resources. Activities of lignocellulolytic enzymes in fed-batch fermentation were the highest activities reported for K. marxianus so far. Our engineered modules are valuable in producing lignocellulolytic enzymes by K. marxianus and in constructing efficient CBP strains for cellulosic ethanol production.\n\nImproved secretory expression of lignocellulolytic enzymes in Kluyveromyces marxianus by promoter and signal sequence engineering.", "token_count": 250, "char_count": 921, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6018, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:51.409496", "source": { "split": "train_shard_00001", "doc_id": 871 }, "chunk_id": "train_shard_00001_871_1", "global_id": 6895 }, { "text": "

ABSTRACT

Campylobacter concisus comprises two distinct genomospecies (GS) based on core genome analysis. Here we conducted further analysis and demonstrated that C. concisus GS2 strains belong to a novel Campylobacter species. A total of 245 C. concisus genomes including 85 GS1 and 160 GS2 strains were analysed. DNA-DNA hybridization (DDH) values between strains of GS1 and GS2 C. concisus were from 42.8% to 66%. Average Nucleotide Identity (ANI) between GS1 and GS2 C. concisus strains were from 87.8% to 89.7%. The average GC contents of GS1 and GS2 C. concisus strains were 37.3% and 39.2% respectively. GS1 and GS2 specific genes have been identified. GS1 and GS2 C. concisus strains can also be differentiated based on core genome, 23S rRNA polymorphisms and protein profiles. Their morphology appears different under certain conditions. In conclusion, ANI and DDH values clearly support that C. concisus GS2 as a novel Campylobacter species, for which we propose the name Campylobacter oralis. The identification of C. concisus and C. oralis specific genes, along with differences in their protein profiles, morphology, core genome and 23S rRNA phylogeny, further support this classification.\n\nGenomic analysis identifies Campylobacter concisus genomospecies 2 as a novel species and proposes the name Campylobacter oralis", "token_count": 416, "char_count": 1355, "word_count": 201, "semantic_coherence": 1, "information_density": 0.5622, "quality_score": 0.7811, "entities": { "genes": [ "GS1", "GS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:52.033206", "source": { "split": "train_shard_00001", "doc_id": 872 }, "chunk_id": "train_shard_00001_872_0", "global_id": 6896 }, { "text": "Members of the genus Chryseobacterium have attracted great interest as beneficial bacteria that can promote plant growth and biocontrol. Given the recent risks of climate change, it is important to develop tolerance strategies for efficient applications of plant-beneficial bacteria in saline environments. However, the genetic determinants of plant-growth-promoting and halotolerance effects in Chryseobacterium have not yet been investigated at the genomic level. Here, a comparative genomic analysis was conducted with seven Chryseobacterium species. Phylogenetic and phylogenomic analyses revealed niche-specific evolutionary distances between soil and freshwater Chryseobacterium species, consistent with differences in genomic statistics, indicating that the freshwater bacteria have smaller genome sizes and fewer genes than the soil bacteria. Phosphorus- and zinc-cycling genes (required for nutrient acquisition in plants) were universally present in all species, whereas nitrification and sulphite reduction genes (required for nitrogen- and sulphur-cycling, respectively) were distributed only in soil bacteria. A pan-genome containing 6842 gene clusters was constructed, which reflected the general features of the core, accessory and unique genomes. Halotolerant species with an accessory genome shared a Kdp potassium transporter and biosynthetic pathways for branched-chain amino acids and the carotenoid lycopene, which are associated with countermeasures against salt stress. Protein-protein interaction network analysis was used to define the genetic determinants of Chryseobacterium salivictor NBC122 that reduce salt damage in bacteria and plants. Sixteen hub genes comprised the aromatic compound degradation and Por secretion systems, which are required to cope with complex stresses associated with saline environments. Horizontal gene transfer and CRISPR-Cas analyses indicated that C. salivictor NBC122 underwent more evolutionary events when interacting with different environments. These findings provide deep insights into genomic adaptation to dynamic interactions between plant-growth-promoting Chryseobacterium and salt stress.", "token_count": 514, "char_count": 2207, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6462, "quality_score": 0.8231, "entities": { "genes": [ "NBC122" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:52.722026", "source": { "split": "train_shard_00001", "doc_id": 873 }, "chunk_id": "train_shard_00001_873_0", "global_id": 6897 }, { "text": "Comparative genomic analysis of Chryseobacterium species: deep insights into plant-growth-promoting and halotolerant capacities.", "token_count": 38, "char_count": 135, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:53.093602", "source": { "split": "train_shard_00001", "doc_id": 873 }, "chunk_id": "train_shard_00001_873_1", "global_id": 6898 }, { "text": "The genetic diversity of the gut microbiota has a central role in host health. Here, we created pangenomes for 728 human gut prokaryotic species, quadrupling the genes of strain-specific genomes. Each of these species has a core set of a thousand genes, differing even between closely related species, and an accessory set of genes unique to the different strains. Functional analysis shows high strain variability associates with sporulation, whereas low variability is linked with antibiotic resistance. We further map the antibiotic resistome across the human gut population and find 237 cases of extreme resistance even to last-resort antibiotics, with a predominance among Enterobacteriaceae. Lastly, the presence of specific genes in the microbiota relates to host age and sex. Our study underscores the genetic complexity of the human gut microbiota, emphasizing its significant implications for host health. The pangenomes and antibiotic resistance map constitute a valuable resource for further research.\n\nPangenomes of human gut microbiota uncover links between genetic diversity and stress response.", "token_count": 242, "char_count": 1110, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:53.591075", "source": { "split": "train_shard_00001", "doc_id": 874 }, "chunk_id": "train_shard_00001_874_0", "global_id": 6899 }, { "text": "Arthrobacter arilaitensis is a food-related bacterial species under investigation for its involvement in the coloration of surface-ripened cheeses. Presently, information about this species in association with the development of appropriate cheese coloration is still lacking. This study was performed in order to investigate-with the use of spectrocolorimetry-the influence of pH, NaCl, and deacidifying yeasts on the pigmentation of Arthrobacter arilaitensis biofilms. Three types of cheese-based (curd) solid media were prepared by using different deacidification methods: (i) chemical deacidification by NaOH (CMNaOH); (ii) biological deacidification by the yeast strain Debaryomyces hansenii 304 (CMDh304); and (iii) biological deacidification by the yeast strain Kluyveromyces marxianus 44 (CMKm44). Each medium was prepared with initial pH values of 5.8, 7.0, and 7.5. After pasteurization, agar was incorporated and NaCl was added in varying concentrations (0%, 2%, 4%, and 8% (w/v)). A. arilaitensis Po102 was then inoculated on the so prepared \"solid-curd\" media, and incubated at 12 °C under light conditions for 28 days. According to the data obtained by spectrocolorimetry in the Compagnie Internationale de l'Eclairage (CIE) L*a*b* color system, all controlled factors appeared to affect the pigments produced by the A. arilaitensis strain. NaCl content in the media showed distinct inhibitory effects on the development of color by this strain when the initial pH was at 5.8", "token_count": 484, "char_count": 1585, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6526, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:55.264152", "source": { "split": "train_shard_00001", "doc_id": 875 }, "chunk_id": "train_shard_00001_875_0", "global_id": 6900 }, { "text": "By contrast, when the initial pH of the media was higher (7.0, 7.5), only the highest concentration of NaCl (8%) had this effect, while the coloring capacity of this bacterial species was always higher when D. hansenii 304 was used for deacidification compared to K. marxianus 44.\n\nThe Influence of pH, NaCl, and the Deacidifying Yeasts Debaryomyces hansenii and Kluyveromyces marxianus on the Production of Pigments by the Cheese-Ripening Bacteria Arthrobacter arilaitensis.", "token_count": 175, "char_count": 510, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:55.714222", "source": { "split": "train_shard_00001", "doc_id": 875 }, "chunk_id": "train_shard_00001_875_1", "global_id": 6901 }, { "text": "

Background

The genetic diversity of yak, a key domestic animal on the Qinghai-Tibetan Plateau (QTP), is a vital resource for domestication and breeding efforts. This study presents the first yak pangenome obtained through the de novo assembly of 16 yak genomes.

Results

We discovered 290 Mb of nonreference sequences and 504 new genes. Our pangenome-wide presence and absence variation (PAV) analysis revealed 5,120 PAV-related genes, highlighting a wide range of variety-specific genes and genes with varying frequencies across yak populations. Principal component analysis (PCA) based on binary gene PAV data classified yaks into three new groups: wild, domestic, and Jinchuan. Moreover, we proposed a 'two-haplotype genomic hybridization model' for understanding the hybridization patterns among breeds by integrating gene frequency, heterozygosity, and gene PAV data. A gene PAV-GWAS identified a novel gene (BosGru3G009179) that may be associated with the multirib trait in Jinchuan yaks. Furthermore, an integrated transcriptome and pangenome analysis highlighted the significant differences in the expression of core genes and the mutational burden of differentially expressed genes between yaks from high and low altitudes. Transcriptome analysis across multiple species revealed that yaks have the most unique differentially expressed mRNAs and lncRNAs (between high- and low-altitude regions), especially in the heart and lungs, when comparing high- and low-altitude adaptations.

Conclusions

The yak pangenome offers a comprehensive resource and new insights for functional genomic studies, supporting future biological research and breeding strategies.\n\nPangenome and multi-tissue gene atlas provide new insights into the domestication and highland adaptation of yaks.", "token_count": 441, "char_count": 1801, "word_count": 242, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:56.347064", "source": { "split": "train_shard_00001", "doc_id": 876 }, "chunk_id": "train_shard_00001_876_0", "global_id": 6902 }, { "text": "Legionella pneumophila typing, based on SBT analysis, has been allowing to identify sequence types (ST) responsible for many Legionnaires’ disease cases. ST901 has so far been identified only in a town of the northern Italy, where it caused numerous travel-associated Legionnaires’ disease cases over a 32-year period. In this study, ST901 were analyzed by whole genome sequencing in looking for both differences and similarities inside this ST and with other unrelated Legionella strains. To this aim core genome multi locus sequence type, single nucleotide polymorphisms and pangenome analyses were performed. ST901 resulted highly similar each other, characterized by I-C CRISPR-cas system, located on the chromosome and by a putative plasmid, highly similar to that found in Lp strain Lens, which contains I-F CRISPR-cas system. Accessory genomic islands, either already described or specifically found in ST901, were also shown. In conclusion ST901 has been quite preserved over the time. The co-occurrence of two phage resistance systems and genomic islands of virulence could have made the ST901 enough virulent to cause such a high number of cases.

Summary blurb

ST901 appears as endemic of the Northern Italy, with virulence traits similar to those in Alcoy and Corby, and with two CRISPR-cas systems which probably preserved them in their environmental niche.\n\nGenome analysis ofLegionella pneumophilaST901 an Italian endemic strain", "token_count": 369, "char_count": 1458, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "ST901" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:56.931407", "source": { "split": "train_shard_00001", "doc_id": 877 }, "chunk_id": "train_shard_00001_877_0", "global_id": 6903 }, { "text": "

Background

The emergence and spread of third-generation cephalosporins (3GC) and carbapenem-resistant Klebsiella pneumoniae pose a global critical challenge. Understanding the transmission dynamics within and between hospital environments is crucial to develop effective control strategies.

Methods

From 2017 to 2019, we conducted a genomic surveillance program in eight hospitals of the Comunitat Valenciana, Spain, collecting and sequencing 1,768 3GC- and carbapenem-resistant isolates. We quantified the overall transmission using core genomes and assessed the contribution of national and global isolates to the spread of AMR in the region by including 11,967 database genomes in the analysis.

Results

The local collection was highly diverse, involving 188 lineages, including global high-risk clones such as ST307 and ST11, and 3GC and carbapenem resistance determinants. Half of the isolates were involved in transmission, with 70.5% occurring within hospitals.

Conclusions

Different transmission patterns characterized the spread of 3GC- and carbapenem resistance in the region. While inter-hospital transmission played a significant role in the spread of 3GC-resistance, this was only sporadic for carbapenem resistance. Moreover, the factors behind inter-hospital spread for each type of resistance differed: while 3GC-resistance likely disseminated between hospitals through intermediate steps, carbapenem resistance was driven by more direct transmission routes. The burden of national and global cases on the ongoing regional AMR dissemination was low. Moreover, we revealed the rapid expansion in the region and globally of lineage ST307 carrying the blaCTX-M-15 gene, a main driver of local transmissions, providing a deeper understanding of the successful spread of this high-risk clone.\n\nGenomic surveillance reveals different transmission patterns between third-generation cephalosporin and carbapenem resistance in Klebsiella pneumoniae in the Comunidad Valenciana (Spain), 2018-2020.", "token_count": 512, "char_count": 2042, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5747, "quality_score": 0.7874, "entities": { "genes": [ "ST11", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:57.588944", "source": { "split": "train_shard_00001", "doc_id": 878 }, "chunk_id": "train_shard_00001_878_0", "global_id": 6904 }, { "text": "The processing of dairy products currently generates significant amounts of waste, particularly in the form of liquid whey. The disposal of whey poses a challenge to the environment due to its high organic content and biological oxygen demand. Whey contains lactose, soluble proteins, lipids, and minerals. While Saccharomyces cerevisiae can efficiently utilize glucose, they are unable to metabolize lactose. In contrast, Kluyveromyces spp. encode two genes, Lac12 and Lac4 that enable conversion of lactose to other by-products such as ethanol. Here, we selected five Kluyveromyces yeast inoculated into three different types of whey substrates, cheddar sweet whey, cream cheese acid whey, and yogurt acid whey that could be used to convert lactose into ethanol. We demonstrate that differences exist in ethanol production across different whey substrates inoculated with Kluyveromyces yeast. In sweet whey, K. lactis, K. lactis Y-1205 and K. lactis Y-1564 were the highest ethanol producing strains. The highest amount of ethanol produced was 24.85 ± 3.5 g/L achieved by Y-1564 in sweet whey (96.8% efficiency). K. lactis Y-1205 produced 22.39 ± 5.6 g/L ethanol in yogurt acid whey. In cream cheese acid whey, K. lactis strains produced significantly higher ethanol levels compared to S. cerevisiae and K. marxianus (p < 0.05). Outcomes from this study could provide a simple and cheap solution for small-to medium-sized dairy processing facilities to ferment lactose in whey into ethanol using lactose-consuming yeasts.", "token_count": 518, "char_count": 1614, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6348, "quality_score": 0.8174, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:02:58.247737", "source": { "split": "train_shard_00001", "doc_id": 879 }, "chunk_id": "train_shard_00001_879_0", "global_id": 6905 }, { "text": "Evaluation of Kluyveromyces spp. for conversion of lactose in different types of whey from dairy processing waste into ethanol.", "token_count": 40, "char_count": 134, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:58.608798", "source": { "split": "train_shard_00001", "doc_id": 879 }, "chunk_id": "train_shard_00001_879_1", "global_id": 6906 }, { "text": "The use of 16S rRNA metabarcoding for functional prediction is limited by several biases. Shallow shotgun sequencing is a cost-effective and taxonomically high-resolution alternative to 16S rRNA metabarcoding, but the low sequencing depth limits functional inference. Our BioSIFTR tool maps shallow shotgun sequencing reads against single-biome databases and extrapolates into their precalculated functional profiles. We used three datasets from red junglefowl, mice, and human gut, containing matched deep shotgun metagenomic and 16S rRNA metabarcoding data for taxonomic and functional benchmarking. An additional human gut deep shotgun sequencing data set was subsampled to 1 M reads and analysed with BioSIFTR to replicate previously obtained results. BioSIFTR taxonomic and functional profiles closely agree with the results of the full deep sequencing data in all biomes. We also replicated differences in the human gut microbiome between high and low trimethylamine N-oxide producing participants, using only < 2 % of the original deep sequencing data. The BioSIFTR tool is a powerful approach which approximates the functional information of a deep-sequenced metagenome while using only a fraction of the data. Shallow shotgun sequencing combined with BioSIFTR could be a stand-in replacement for 16S rRNA metabarcoding with an increased taxonomic and functional resolution, and lower bias.

Graphical abstract

\n\nBiome-specific genome catalogues reveal functional potential of shallow sequencing", "token_count": 361, "char_count": 1510, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5877, "quality_score": 0.7938, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:59.187586", "source": { "split": "train_shard_00001", "doc_id": 880 }, "chunk_id": "train_shard_00001_880_0", "global_id": 6907 }, { "text": "Achromobacter xylosoxidans is an emerging pathogen characterized by high levels of antibiotic resistance and increasing infection rates worldwide. This motile, opportunistic pathogen is widely distributed in the environment and can cause various infections, including pneumonia, bacteremia, endocarditis, meningitis, and others. In this study, we analyzed the population structure, antibiotic resistance profiles, and virulence factors of over 200 publicly available genomes. Core genome analysis revealed that A. xylosoxidans is highly adaptable, possessing a relatively small core genome. Antibiotic susceptibility testing of isolates from the United States revealed high resistance to multiple antibiotics including ceftolozane/tazobactam, aztreonam, cefepime, and ciprofloxacin. Our data show that imipenem/relebactam (IMR) is not more effective against A. xylosoxidans than imipenem (IMI) alone, indicating that relebactam does not inhibit β-lactamase activity in Achromobacter. The species features multiple secretion systems, including the Type III secretion system (T3SS) of the YscN family, which is similar to those found in Bordetella pertussis and Pseudomonas aeruginosa . Isolates collected from the same patients showed dynamic changes in cytotoxicity, flagella motility, biofilm and antibiotic resistance suggesting its dynamic adaptation to host environment. Intra-host evolved isolates, NIH-010 and NIH-016, demonstrated the loss of flagella motility and variable cytotoxicity while exhibiting increased antibiotic resistance and enhanced biofilm formation. Sequence analysis suggests that NIH-016-3 has tyrosine to histidine mutation at position 330 (Y330H) near the FlhF Guanosine triphosphate (GTP)-binding domain that may affect flagellar assembly. Interestingly, virulence assays showed significant variation in the ability of different A. xylosoxidans isolates to induce cell death in in vitro models, suggesting its dynamic adaptation to host environment", "token_count": 501, "char_count": 1978, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6848, "quality_score": 0.8424, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:02:59.847222", "source": { "split": "train_shard_00001", "doc_id": 881 }, "chunk_id": "train_shard_00001_881_0", "global_id": 6908 }, { "text": "These findings highlight the complexity of this pathogen group and underscore the urgent need for further research into its mechanisms of antibiotic resistance and virulence.

Impact statement

This study provides a comprehensive examination of Achromobacter xylosoxidans , an emerging pathogen of global concern due to its high antibiotic resistance and increasing clinical relevance. By analyzing over 200 genomes, we offer critical insights into the population structure, resistance mechanisms, and virulence factors of this species. The identification of a relatively small core genome underscores the adaptability of A. xylosoxidans and its potential for genomic plasticity. The existence of multiple secretion systems (T1SS to T6SS) highlights the great capacity of A. xylosoxidans as a pathogen. Variations in virulence among A. xylosoxidans isolates indicate the complexity of this pathogen and underscore the need for further studies on its virulence mechanisms. The dynamic within-host evolution including the loss of motility-associated systems and the acquisition of enhanced antibiotic resistance and biofilm formation, adds new dimensions to our understanding of its pathogenesis. Flagella, an important virulence mechanism, exhibit variable motility in different isolates, suggesting the bacteria use flagella as an adaptive mechanism. This work also showed that A. xylosoxidans are resistant to relebactam, which are effective in other bacteria. These findings emphasize the urgent need for targeted therapeutic strategies to combat this opportunistic pathogen.\n\nAchromobacter xylosoxidans isolates exhibit genome diversity, variable virulence, high levels of antibiotic resistance and potential intrahost evolution", "token_count": 388, "char_count": 1746, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5957, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:00.465103", "source": { "split": "train_shard_00001", "doc_id": 881 }, "chunk_id": "train_shard_00001_881_1", "global_id": 6909 }, { "text": "Background: Oral candidiasis (OC) has a profound effect on the life quality of immunocompromised patients, such as those undergoing chemotherapy. Objective: Systematic investigation of clinical outcome and microbiological features of yeast isolates recovered from the oral cavity of 150 Iranian patients with hematological malignancies. Design: MALDI-TOF MS, 21-plex PCR, and rDNA sequencing were used for identification. Antifungal susceptibility testing (broth microdilution, CLSI M27-A3/S4) and genotypic diversity of yeast isolates (amplified fragment length polymorphism) were assessed. Results: Nystatin treatment resulted in 70% therapeutic failure and administration of 150 mg fluconazole (FLZ) + nystatin for patients with OC relapse showed 70% clinical failure. Previous history of OC was significantly correlated with FLZ treatment requirement and nystatin failure (P = 0.005, α < 0.05). Candida albicans (80.3%) and Kluyveromyces marxianus (C. kefyr) (12.7%) were the two most prevalent yeast species isolated. FLZ and AMB exhibited the highest geometric mean values. 21-PCR showed 98.9% agreement with MALDI-TOF MS. K. marxianus isolates had the same genotype, while C. albicans isolates grouped in 15 genotypes. Conclusions: Marked rate of therapeutic failure of nystatin necessitated OC treatment with systemic antifungals. K. marxianus was the second most prevalent yeast and 21-plex PCR could be considered as an inexpensive identification tool.", "token_count": 517, "char_count": 1546, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7129, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:01.119682", "source": { "split": "train_shard_00001", "doc_id": 882 }, "chunk_id": "train_shard_00001_882_0", "global_id": 6910 }, { "text": "Incidence and spectrum of yeast species isolated from the oral cavity of Iranian patients suffering from hematological malignancies.", "token_count": 27, "char_count": 132, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:01.475712", "source": { "split": "train_shard_00001", "doc_id": 882 }, "chunk_id": "train_shard_00001_882_1", "global_id": 6911 }, { "text": "Long-read (LR) technologies from Pacific Biosciences (PacBio) and Oxford Nanopore Technologies (ONT) have transformed genomics research by providing diverse data types like HiFi, Duplex, and ultra-long ONT (ULONT). Despite recent strides in achieving haplotype-phased gapless genome assemblies using long-read technologies, concerns persist regarding the representation of genetic diversity, prompting the development of pangenome references. However, pangenome studies face challenges related to data types, volumes, and cost considerations for each assembled genome, while striving to maintain sensitivity. The absence of comprehensive guidance on optimal data selection exacerbates these challenges. To fill this gap, our study evaluates available data types, their significance, and the required volumes for robust de novo assembly in population-level pangenome projects. The results show that achieving chromosome-level haplotype-resolved assembly requires 20x high-quality long reads (HQLR) such as PacBio HiFi or ONT duplex, combined with 15-20x of ULONT per haplotype and 30x of long-range data such as Omni-C. High-quality long reads from both platforms yield assemblies with comparable contiguity, with HiFi excelling in NG50 and phasing accuracies, while usage of duplex generates more T2T contigs. As Long-Read Technologies advance, our study reevaluates recommended data types and volumes, providing practical guidelines for selecting sequencing platforms and coverage. These insights aim to be vital to the pangenome research community, contributing to their efforts and pushing genomic studies with broader impacts.\n\nThe Hitchhiker’s Guide to Sequencing Data Types and Volumes for Population-Scale Pangenome Construction", "token_count": 399, "char_count": 1735, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6724, "quality_score": 0.8362, "entities": { "genes": [ "NG50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:02.095081", "source": { "split": "train_shard_00001", "doc_id": 883 }, "chunk_id": "train_shard_00001_883_0", "global_id": 6912 }, { "text": "Listeria monocytogenes is an opportunistic food-borne bacterium that is capable of infecting humans with high rates of hospitalisation and mortality. Natural populations are genotypically and phenotypically variable, with some lineages being responsible for most human infections. The success of L. monocytogenes is linked to its capacity to persist on food and in the environment. Biofilms are an important feature that allow these bacteria to persist and infect humans, therefore, understanding the genetic basis of biofilm formation is key to understanding transmission. We sought to investigate the biofilm forming ability of L. monocytogenes by identifying genetic variation that underlies biofilm formation in natural populations using genome-wide association studies. Changes in gene expression of specific strains during biofilm formation were then investigated using RNAseq. Genetic variation associated with enhanced biofilm formation was identified in 273 genes by GWAS and differential expression in 220 genes by RNAseq. Statistical analyses show that number of overlapping genes flagged by either type of experiment is less than expected by random sampling. This is consistent with an evolutionary scenario where rapid adaptation is driven by variation in gene expression of pioneer genes, and this is followed by slower adaptation driven by nucleotide changes within the core genome.

Impact statement

Listeria monocytogenes is a problematic food-borne bacterium that can cause severe illness and even death in humans. Some strains are known to be more common in disease and biofilms are crucial for survival in the environment and transmission to humans. To unravel the genetic basis of biofilm formation, we undertook a study employing genome-wide association studies (GWAS) and gene transcription profiling. We identified 273 genes associated with robust biofilm formation through GWAS and discovered differential expression in 220 genes through RNAseq. Statistical analysis revealed fewer overlapping genes than expected by chance, supporting an evolutionary scenario where initial adaptation relies on gene expression variation, followed by slower adaptation through genetic changes within the core genome", "token_count": 459, "char_count": 2232, "word_count": 316, "semantic_coherence": 1, "information_density": 0.5158, "quality_score": 0.7579, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:02.743618", "source": { "split": "train_shard_00001", "doc_id": 884 }, "chunk_id": "train_shard_00001_884_0", "global_id": 6913 }, { "text": "

Data summary

Short read genome data are available from the NCBI (National Center for Biotechnology Information) SRA (Sequence Read Archive), associated with BioProject PRJNA971143 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA971143 ). Assembled genomes and supplementary material are available from FigShare: doi: 10.6084/m9.figshare.23148029. RNA sequence data and differential gene expression profiles have been deposited in the NCBI Gene Expression Omnibus.\n\nContrasting genes conferring short and long-term biofilm adaptation inListeria", "token_count": 174, "char_count": 558, "word_count": 64, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [ "PRJNA971143" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:03.184710", "source": { "split": "train_shard_00001", "doc_id": 884 }, "chunk_id": "train_shard_00001_884_1", "global_id": 6914 }, { "text": "

ABSTRACT

Dolosigranulum pigrum is positively associated with indicators of health in multiple epidemiological studies of human nasal microbiota. Knowledge of the basic biology of D. pigrum is a prerequisite for evaluating its potential for future therapeutic use; however, such data are very limited. To gain insight into D. pigrum ’s chromosomal structure, pangenome and genomic stability, we compared the genomes of 28 D. pigrum strains that were collected across 20 years. Phylogenomic analysis showed closely related strains circulating over this period and closure of 19 genomes revealed highly conserved chromosomal synteny. Gene clusters involved in the mobilome and in defense against mobile genetic elements (MGEs) were enriched in the accessory genome versus the core genome. A systematic analysis for MGEs identified the first candidate D. pigrum prophage and insertion sequence. A systematic analysis for genetic elements that limit the spread of MGEs, including restriction modification (RM), CRISPR-Cas, and deity-named defense systems, revealed strain-level diversity in host defense systems that localized to specific genomic sites including one RM system hotspot. Analysis of CRISPR spacers pointed to a wealth of MGEs against which D. pigrum defends itself. These results reveal a role for horizontal gene transfer and mobile genetic elements in strain diversification while highlighting that in D. pigrum this occurs within the context of a highly stable chromosomal organization protected by a variety of defense mechanisms.

IMPORTANCE

Dolosigranulum pigrum is a candidate beneficial bacterium with potential for future therapeutic use. This is based on its positive associations with characteristics of health in multiple studies of human nasal microbiota across the span of human life. For example, high levels of D. pigrum nasal colonization in adults predicts the absence of Staphylococcus aureus nasal colonization. Also, D. pigrum nasal colonization in young children is associated with healthy control groups in studies of middle ear infections. Our analysis of 28 genomes revealed a remarkable stability of D. pigrum strains colonizing people in the U.S. across a 20-year span", "token_count": 524, "char_count": 2222, "word_count": 324, "semantic_coherence": 1, "information_density": 0.5648, "quality_score": 0.7824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:03.825405", "source": { "split": "train_shard_00001", "doc_id": 885 }, "chunk_id": "train_shard_00001_885_0", "global_id": 6915 }, { "text": "We subsequently identified factors that can influence this stability, including genomic stability, phage predators, the role of MGEs in strain-level variation and defenses against MGEs. Finally, these D. pigrum strains also lacked predicted virulence factors. Overall, these findings add additional support to the potential for D. pigrum as a therapeutic bacterium.\n\nGenomic Stability and Genetic Defense Systems inDolosigranulum pigruma Candidate Beneficial Bacterium from the Human Microbiome", "token_count": 122, "char_count": 501, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8788, "quality_score": 0.9394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:04.255274", "source": { "split": "train_shard_00001", "doc_id": 885 }, "chunk_id": "train_shard_00001_885_1", "global_id": 6916 }, { "text": "Coxiella burnetii is the etiological agent of Q fever, a worldwide zoonosis able to cause large outbreaks. The disease is polymorphic. Symptomatic primary infection is named acute Q fever and is associated with hepatitis, pneumonia, fever, and auto-immune complications while persistent focalized infections, mainly endocarditis, and vascular infections, occur in a minority of patients but are potentially lethal. In order to evaluate the genomic features, genetic diversity, evolution, as well as genetic determinants of antibiotic resistance, pathogenicity, and ability to cause outbreaks of Q fever, we performed a pangenomic analysis and genomic comparison of 75 C. burnetii strains including 63 newly sequenced genomes. Our analysis demonstrated that C. burnetii has an open pangenome, unique genes being found in many strains. In addition, pathogenicity islands were detected in all genomes. In consequence C. burnetii has a high genomic plasticity, higher than that of other intracellular bacteria. The core- and pan-genomes are made of 1,211 and 4,501 genes, respectively (ratio 0.27). The core gene-based phylogenetic analysis matched that obtained from multi-spacer typing and the distribution of plasmid types. Genomic characteristics were associated to clinical and epidemiological features. Some genotypes were associated to specific clinical forms and countries. MST1 genotype strains were associated to acute Q fever. A significant association was also found between clinical forms and plasmids. Strains harboring the QpRS plasmid were never found in acute Q fever and were only associated to persistent focalized infections. The QpDV and QpH1 plasmids were associated to acute Q fever. In addition, the Guyanese strain CB175, the most virulent strain to date, exhibited a unique MST genotype, a distinct COG profile and an important variation in gene number that may explain its unique pathogenesis. Therefore, strain-specific factors play an important role in determining the epidemiological and clinical manifestations of Q fever alongside with host-specific factors (valvular and vascular defects notably).", "token_count": 526, "char_count": 2154, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [ "CB175", "MST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:04.923514", "source": { "split": "train_shard_00001", "doc_id": 886 }, "chunk_id": "train_shard_00001_886_0", "global_id": 6917 }, { "text": "Pangenomic analysis of Coxiella burnetii unveils new traits in genome architecture.", "token_count": 28, "char_count": 90, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:05.296186", "source": { "split": "train_shard_00001", "doc_id": 886 }, "chunk_id": "train_shard_00001_886_1", "global_id": 6918 }, { "text": "

Background

Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate [1] those genomic signatures that characterize a habitat-specific ecotype and [2] the source of genomic variation within this ecotype.

Results

We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~ 90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype.

Conclusion

We conclude that all nine V. alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype", "token_count": 478, "char_count": 1972, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5575, "quality_score": 0.7787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:05.991998", "source": { "split": "train_shard_00001", "doc_id": 887 }, "chunk_id": "train_shard_00001_887_0", "global_id": 6919 }, { "text": "The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.\n\nGenomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements.", "token_count": 88, "char_count": 393, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8276, "quality_score": 0.9138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:06.368158", "source": { "split": "train_shard_00001", "doc_id": 887 }, "chunk_id": "train_shard_00001_887_1", "global_id": 6920 }, { "text": "

ABSTRACT

Enterococcus faecalis is a commensal bacterium that colonizes the gut of humans and animals, and a major opportunistic pathogen, known for causing multidrug-resistant healthcare-associated infections (HAIs). Its ability to thrive in diverse environments and disseminate antimicrobial resistance genes (ARGs) across ecological niches highlights the importance of understanding its ecological, evolutionary, and epidemiological dynamics. The CRISPR2 locus has been used as a valuable marker for assessing clonality and phylogenetic relationships in E. faecalis . In this study, we identified a group of E. faecalis strains lacking CRISPR2, forming a distinct, well-supported clade. We demonstrate that this clade meets the genomic criteria for classification as a novel subspecies, here referred to as “subspecies B”. Through a comprehensive pangenome analysis and comparative genomics, we explored the adaptive ecological traits underlying this diversification process, identifying clade-specific features and their predicted functional roles. Our findings suggest that the frequent isolation of subspecies B from meat products and processing facilities may reflect dissemination routes involving environmental contamination (e.g., water, plants, soil) from avian species. The absence of key virulence traits required for pathogenicity in mammals, particularly in humans, and the lack of clinically relevant resistance determinants indicate that subspecies B may currently pose minimal threat to public health compared to the broadly disseminated “subspecies A”. Nevertheless, the unclear potential for genetic exchange between these subspecies, and the frequent association of subspecies B with food sources, calls for continued genomic surveillance of E. faecalis from a One Health perspective to detect and mitigate the emergence of high-risk variants in advance.\n\nHidden Diversity in Enterococcus faecalis Revealed by CRISPR2 Screening: Eco-evolutionary Insights into a Novel Subspecies", "token_count": 456, "char_count": 2015, "word_count": 269, "semantic_coherence": 1, "information_density": 0.684, "quality_score": 0.842, "entities": { "genes": [ "CRISPR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:07.016064", "source": { "split": "train_shard_00001", "doc_id": 888 }, "chunk_id": "train_shard_00001_888_0", "global_id": 6921 }, { "text": "Mosquitoes transmit medically important human pathogens, including viruses like dengue virus and parasites such as Plasmodium spp., the causative agent of malaria. Mosquito microbiomes are critically important for the ability of mosquitoes to transmit disease-causing agents. However, while large collections of bacterial isolates and genomic data exist for vertebrate microbiomes, the vast majority of work in mosquitoes to date is based on 16S rRNA gene amplicon data that provides limited taxonomic resolution and no functional information. To address this gap and facilitate future studies using experimental microbiome manipulations, we generated a bacterial Mosquito-Associated Isolate Collection (MosAIC) consisting of 392 bacterial isolates with extensive metadata and high-quality draft genome assemblies that are publicly available, both isolates and sequence data, for use by the scientific community. MosAIC encompasses 142 species spanning 29 bacterial families, with members of the Enterobacteriaceae comprising 40% of the collection. Phylogenomic analysis of 3 genera, Enterobacter, Serratia, and Elizabethkingia, reveal lineages of mosquito-associated bacteria isolated from different mosquito species in multiple laboratories. Investigation into species' pangenomes further reveals clusters of genes specific to these lineages, which are of interest for future work to test for functions connected to mosquito host association. Altogether, we describe the generation of a physical collection of mosquito-associated bacterial isolates, their genomic data, and analyses of selected groups in context of genome data from closely related isolates, providing a unique, highly valuable resource for research on bacterial colonisation and adaptation within mosquito hosts. Future efforts will expand the collection to include broader geographic and host species representation, especially from individuals collected from field populations, as well as other mosquito-associated microbes, including fungi, archaea, and protozoa.\n\nMosAIC: An annotated collection of mosquito-associated bacteria with high-quality genome assemblies.", "token_count": 483, "char_count": 2138, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6596, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:07.660141", "source": { "split": "train_shard_00001", "doc_id": 889 }, "chunk_id": "train_shard_00001_889_0", "global_id": 6922 }, { "text": "Bacteria of the genera Xenorhabdus and Photorhabdus are symbionts of entomopathogenic nematodes. Despite their close phylogenetic relationship, they show differences in their pathogenicity and virulence mechanisms in target insects. These differences were explored by the analysis of the pangenome, as it provides a framework for characterizing and defining the gene repertoire. We performed the first pangenome analysis of 91 strains of Xenorhabdus and Photorhabdus; the analysis showed that the Photorhabdus genus has a higher number of genes associated with pathogenicity. However, biological tests showed that whole cells of X. nematophila SC 0516 were more virulent than those of P. luminescens HIM3 when both were injected into G. mellonella larvae. In addition, we cloned and expressed the GroEL proteins of both bacteria, as this protein has been previously indicated to show insecticidal activity in the genus Xenorhabdus. Among these proteins, Cpn60-Xn was found to be the most toxic at all concentrations tested, with an LC50 value of 102.34 ng/larva. Sequence analysis suggested that the Cpn60-Xn toxin was homologous to Cpn60-Pl; however, Cpn60-Xn contained thirty-five differentially substituted amino acid residues that could be responsible for its insecticidal activity.\n\nComparative Genomics and Pathogenicity Analysis of Two Bacterial Symbionts of Entomopathogenic Nematodes: The Role of the GroEL Protein in Virulence.", "token_count": 441, "char_count": 1500, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [ "HIM3", "LC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:08.293863", "source": { "split": "train_shard_00001", "doc_id": 890 }, "chunk_id": "train_shard_00001_890_0", "global_id": 6923 }, { "text": "The exponential growth of microbial genome data presents unprecedented opportunities for mining the potential of microorganisms. The burgeoning field of pangenomics offers a framework for extracting insights from this big biological data. Recent advances in microbial pangenomic research have generated substantial data and literature, yielding valuable knowledge across diverse microbial species. PanKB (pankb.org), a knowledgebase designed for microbial pangenomics research and biotechnological applications, was built to capitalize on this wealth of information. PanKB currently includes 51 pangenomes on 8 industrially relevant microbial families, comprising 8, 402 genomes, over 500, 000 genes, and over 7M mutations. To describe this data, PanKB implements four main components: 1) Interactive pangenomic analytics to facilitate exploration, intuition, and potential discoveries; 2) Alleleomic analytics, a pangenomic- scale analysis of variants, providing insights into intra-species sequence variation and potential mutations for applications; 3) A global search function enabling broad and deep investigations across pangenomes to power research and bioengineering workflows; 4) A bibliome of 833 open- access pangenomic papers and an interface with an LLM that can answer in-depth questions using their knowledge. PanKB empowers researchers and bioengineers to harness the full potential of microbial pangenomics and serves as a valuable resource bridging the gap between pangenomic data and practical applications.

Graphical Abstract

\n\nPanKB: An interactive microbial pangenome knowledgebase for research, biotechnological innovation, and knowledge mining", "token_count": 391, "char_count": 1675, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:08.911935", "source": { "split": "train_shard_00001", "doc_id": 891 }, "chunk_id": "train_shard_00001_891_0", "global_id": 6924 }, { "text": "Abstract

Cannabis sativa is a globally significant seed-oil, fiber, and drug-producing plant species. However, a century of prohibition has severely restricted legal breeding and germplasm resource development, leaving potential hemp-based nutritional and fiber applications unrealized. Existing cultivars are highly heterozygous and lack competitiveness in the overall fiber and grain markets, relegating hemp to less than 200,000 hectares globally1. The relaxation of drug laws in recent decades has generated widespread interest in expanding and reincorporating cannabis into agricultural systems, but progress has been impeded by the limited understanding of genomics and breeding potential. No studies to date have examined the genomic diversity and evolution of cannabis populations using haplotype-resolved, chromosome-scale assemblies from publicly available germplasm. Here we present a cannabis pangenome, constructed with 181 new and 12 previously released genomes from a total of 156 biological samples from both male (XY) and female (XX) plants, including 42 trio phased and 36 haplotype-resolved, chromosome-scale assemblies. We discovered widespread regions of the cannabis pangenome that are surprisingly diverse for a single species, with high levels of genetic and structural variation, and propose a novel population structure and hybridization history. Conversely, the cannabinoid synthase genes contain very low levels of diversity, despite being embedded within a variable region containing multiple pseudogenized paralogs and distinct transposable element arrangements. Additionally, we identified variants of acyl-lipid thioesterase (ALT) genes2 that are associated with fatty acid chain length variation and the production of the rare cannabinoids, tetrahydrocannabinol varin (THCV) and cannabidiol varin (CBDV). We conclude the Cannabis sativa gene pool has only been partially characterized, and that the existence of wild relatives in Asia remains likely, while its potential as a crop species remains largely unrealized.

\n\nDomesticated cannabinoid synthases amid a wild mosaic cannabis pangenome", "token_count": 495, "char_count": 2146, "word_count": 287, "semantic_coherence": 1, "information_density": 0.7178, "quality_score": 0.8589, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:09.562125", "source": { "split": "train_shard_00001", "doc_id": 892 }, "chunk_id": "train_shard_00001_892_0", "global_id": 6925 }, { "text": "The production of Greek-style yogurts requires more processing steps than traditional yogurt, which increases the possibility of microbial contamination by pathogens or spoilage organisms. The growth and survival during storage of two microbial contaminants (Escherichia coli and Kluyveromyces marxianus) in Greek-style yogurt, produced by centrifugation or ultrafiltration, was compared with that in regular stirred yogurt. E. coli strain ATCC® BAA-1430™ was shown to be a suitable surrogate for pathogenic O157:H7 in yogurt. The increased buffering capacity of the Greek-style yogurts produced from ultrafiltered milk led to lower E. coli viability during storage. On the other hand, the Greek-style yogurt seems to promote faster growth of the dairy yeast K. marxianus at a storage temperature of 4 °C.\n\nFate of Escherichia coli and Kluyveromyces marxianus contaminants during storage of Greek-style yogurt produced by centrifugation or ultrafiltration", "token_count": 267, "char_count": 955, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:10.116380", "source": { "split": "train_shard_00001", "doc_id": 893 }, "chunk_id": "train_shard_00001_893_0", "global_id": 6926 }, { "text": "As a mycotoxin, aflatoxin B1 (AFB1) has attracted increasing attention due to its highly toxic effects, such as teratogen, carcinogen, and mutagen. AFB1-producing fungi have been found in both terrestrial and marine sources. Over the last two years, the marine-derived bacteria Kocuria rosea has shown the ability to degrade AFB1. However, no studies have yet explored the aflatoxin degradation potential in the genus Kocuria, and the molecular basis of aflatoxin metabolisms by strain has not yet been investigated. In this study, we first compared and analyzed the genomic features of 13 bacteria of the genus Kocuria by comparative genomic analysis and investigated the evolutionary patterns (evolutionary selection pressure analysis and gene family expansion analysis) and pan and core genomes of Kocuria strains. It was found that Kocuria genus strains showed high potential in the bioremediation of aromatic compounds and aflatoxin degradation. In addition, this study revealed 1421 differentially expressed genes and 752 upregulated genes between the aflatoxin group and the control group through transcriptome analysis and conducted functional annotation and analysis of functional enrichment. According to the expression and functional analysis of upregulated genes, the enzymes and genes (cytochrome P450, oxidoreductase, intradiol ring-cleavage dioxygenase, hydrolase, and monooxygenase) involved in the aflatoxin degradation of Kocuria rosea were screened. These findings indicate the potential of Kocuria rosea in the remediation of aflatoxin contamination and provide a foundation and direction for the further excavation of novel degradation genes, exploration of degradation mechanisms, and genomic modification.", "token_count": 477, "char_count": 1821, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:10.762198", "source": { "split": "train_shard_00001", "doc_id": 894 }, "chunk_id": "train_shard_00001_894_0", "global_id": 6927 }, { "text": "Comparative Genomic and Transcriptomic Analysis Provides New Insights into the Aflatoxin B<sub>1</sub> Biodegradability by <i>Kocuria rosea</i> from Deep Sea.", "token_count": 64, "char_count": 182, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:11.127622", "source": { "split": "train_shard_00001", "doc_id": 894 }, "chunk_id": "train_shard_00001_894_1", "global_id": 6928 }, { "text": "

Background

Koumiss is a naturally fermented mare's milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile.

Results

A total of 119 bacterial and 36 yeast species were identified among the 14 koumiss samples. The dominant bacterial species in koumiss were Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactococcus raffinolactis, and Citrobacter freundii. The main yeast species were Dekkera anomala, Kazachstania unispora, Meyerozyma caribbica, Pichia sp.BZ159, Kluyveromyces marxianus, and uncultured Guehomyces. The bacterial and yeast Shannon diversity of the Xilinhaote-urban group were higher than those of the Xilingol-rural group. The most dominant organic acids were lactic, acetic, tartaric, and malic acids. Lactic acid bacteria species were mostly responsible for the accumulation of those organic acids, although Kazachstania unispora, Dekkera anomala, and Meyerozyma caribbica may also have contributed. Redundancy analysis suggested that both bacteria and yeast respond to koumiss flavor, such as Lactobacillus helveticus and Dekkera anomala are associated with sourness, astringency, bitterness, and aftertaste, whereas Lactococcus lactis and Kazachstania unispora are associated with umami.

Conclusions

Our results suggest that differences were observed in koumiss microbiota of Xilinhaote-urban and Xilingol-rural samples. The biodiversity of the former was higher than the latter group. Positive or negative correlations between bacteria and yeast species and taste also were found.\n\nProfiling of koumiss microbiota and organic acids and their effects on koumiss taste.", "token_count": 505, "char_count": 1793, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [ "BZ159" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:11.786701", "source": { "split": "train_shard_00001", "doc_id": 895 }, "chunk_id": "train_shard_00001_895_0", "global_id": 6929 }, { "text": "Cannabis sativa is a globally significant seed-oil, fiber, and drug-producing plant species. However, a century of prohibition has severely restricted legal breeding and germplasm resource development, leaving potential hemp-based nutritional and fiber applications unrealized. Existing cultivars are highly heterozygous and lack competitiveness in the overall fiber and grain markets, relegating hemp to less than 200,000 hectares globally1. The relaxation of drug laws in recent decades has generated widespread interest in expanding and reincorporating cannabis into agricultural systems, but progress has been impeded by the limited understanding of genomics and breeding potential. No studies to date have examined the genomic diversity and evolution of cannabis populations using haplotype-resolved, chromosome-scale assemblies from publicly available germplasm. Here we present a cannabis pangenome, constructed with 181 new and 12 previously released genomes from a total of 156 biological samples from both male (XY) and female (XX) plants, including 42 trio phased and 36 haplotype-resolved, chromosome-scale assemblies. We discovered widespread regions of the cannabis pangenome that are surprisingly diverse for a single species, with high levels of genetic and structural variation, and propose a novel population structure and hybridization history. Conversely, the cannabinoid synthase genes contain very low levels of diversity, despite being embedded within a variable region containing multiple pseudogenized paralogs and distinct transposable element arrangements. Additionally, we identified variants of acyl-lipid thioesterase (ALT) genes that are associated with fatty acid chain length variation and the production of the rare cannabinoids, tetrahydrocannabinol varin (THCV) and cannabidiol varin (CBDV). We conclude the Cannabis sativa gene pool has only been partially characterized, and that the existence of wild relatives in Asia remains likely, while its potential as a crop species remains largely unrealized.\n\nDomesticated cannabinoid synthases amid a wild mosaic cannabis pangenome", "token_count": 480, "char_count": 2113, "word_count": 286, "semantic_coherence": 1, "information_density": 0.7063, "quality_score": 0.8531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:12.435050", "source": { "split": "train_shard_00001", "doc_id": 896 }, "chunk_id": "train_shard_00001_896_0", "global_id": 6930 }, { "text": "Abstract

Background Transposable elements (TEs) are major components of plant genomes and major drivers of plant genome evolution. The cotton genus (Gossypium) is an excellent evolutionary model for polyploidization, speciation, domestication and crop improvement. Here, we implement genome and pangenome analyses to study in detail the dynamics of LTR-retrotransposons (LTR-RT) during the cotton evolution. Results We show that some LTR-RT lineages amplified in tetraploid cotton compared to their diploid progenitors, whereas others stayed stable or amplified but were removed through solo-LTR formation. Using species-level pangenomes we show that only a few lineages (CRM, Tekay, Ivana and Tork) remained active after polyploidization and are still transposing. Tekay and CRM elements have re-shaped the centromeric and pericentromeric regions of tetraploid cottons in a subgenome specific manner, through new insertions but also selective eliminations through solo-LTR formation. On the other hand, Ivana and Tork have actively inserted within or close to genes. Finally, population-level analyses using the two pangenomes and data from 283 and 223 varieties of G. hirsutum and G. barbandense reveal changes in Transposon Insertion Polymorphism (TIP) frequencies accompanying domestication and improvement of both species, suggesting the possibility of selection on linked regions. Conclusions Our findings reveal that LTR-RT lineages followed differential dynamics during cotton evolution, displaying differences among species and the two coresident genomes of allopolyploid cotton. A handful of the LTR-RT lineages that expanded after polyploidisation helped shape the genomes of both G. hirstutum and G. barbadense, impacting their centromere and pericentromeric regions as well as protein- coding genes.

", "token_count": 489, "char_count": 1923, "word_count": 250, "semantic_coherence": 1, "information_density": 0.644, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:13.084215", "source": { "split": "train_shard_00001", "doc_id": 897 }, "chunk_id": "train_shard_00001_897_0", "global_id": 6931 }, { "text": "Differential LTR-retrotransposon dynamics across polyploidization, speciation, domestication and improvement of cotton (Gossypium)", "token_count": 34, "char_count": 130, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:13.441933", "source": { "split": "train_shard_00001", "doc_id": 897 }, "chunk_id": "train_shard_00001_897_1", "global_id": 6932 }, { "text": "Mycobacterium avium comprises four subspecies that contain both human and veterinary pathogens. At the inception of this study, twenty-eight M. avium genomes had been annotated as RefSeq genomes, facilitating direct comparisons. These genomes represent strains from around the world and provided a unique opportunity to examine genome dynamics in this species. Each genome was confirmed to be classified correctly based on SNP genotyping, nucleotide identity and presence/absence of repetitive elements or other typing methods. The Mycobacterium avium subspecies paratuberculosis (Map) genome size and organization was remarkably consistent, averaging 4.8 Mb with a variance of only 29.6 kb among the 13 strains. Comparing recombination events along with the larger genome size and variance observed among Mycobacterium avium subspecies avium (Maa) and Mycobacterium avium subspecies hominissuis (Mah) strains (collectively termed non-Map) suggests horizontal gene transfer occurs in non-Map, but not in Map strains. Overall, M. avium subspecies could be divided into two major sub-divisions, with the Map type II (bovine strains) clustering tightly on one end of a phylogenetic spectrum and Mah strains clustering more loosely together on the other end. The most evolutionarily distinct Map strain was an ovine strain, designated Telford, which had >1,000 SNPs and showed large rearrangements compared to the bovine type II strains. The Telford strain clustered with Maa strains as an intermediate between Map type II and Mah", "token_count": 510, "char_count": 1673, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:14.072080", "source": { "split": "train_shard_00001", "doc_id": 898 }, "chunk_id": "train_shard_00001_898_0", "global_id": 6933 }, { "text": "SNP analysis and genome organization analyses repeatedly demonstrated the conserved nature of Map versus the mosaic nature of non-Map M. avium strains. Finally, core and pangenomes were developed for Map and non-Map strains. A total of 80% Map genes belonged to the Map core genome, while only 40% of non-Map genes belonged to the non-Map core genome. These genomes provide a more complete and detailed comparison of these subspecies strains as well as a blueprint for how genetic diversity originated.\n\nGenetic Diversity Among Mycobacterium avium Subspecies Revealed by Analysis of Complete Genome Sequences.", "token_count": 204, "char_count": 672, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6237, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:14.534237", "source": { "split": "train_shard_00001", "doc_id": 898 }, "chunk_id": "train_shard_00001_898_1", "global_id": 6934 }, { "text": "Fusarium graminearum, the primary cause of Fusarium head blight (FHB) in small-grain cereals, demonstrates remarkably variable levels of aggressiveness in its host, producing different infection dynamics and contrasted symptom severity. While the secreted proteins, including effectors, are thought to be one of the essential components of aggressiveness, our knowledge of the intra-species genomic diversity of F. graminearum is still limited. In this work, we sequenced eight European F. graminearum strains of contrasting aggressiveness to characterize their respective genome structure, their gene content and to delineate their specificities. By combining the available sequences of 12 other F. graminearum strains, we outlined a reference pangenome that expands the repertoire of the known genes in the reference PH-1 genome by 32%, including nearly 21,000 non-redundant sequences and gathering a common base of 9250 conserved core-genes. More than 1000 genes with high non-synonymous mutation rates may be under diverse selection, especially regarding the trichothecene biosynthesis gene cluster. About 900 secreted protein clusters (SPCs) have been described. Mostly localized in the fast sub-genome of F. graminearum supposed to evolve rapidly to promote adaptation and rapid responses to the host's infection, these SPCs gather a range of putative proteinaceous effectors systematically found in the core secretome, with the chloroplast and the plant nucleus as the main predicted targets in the host cell. This work describes new knowledge on the intra-species diversity in F. graminearum and emphasizes putative determinants of aggressiveness, providing a wealth of new candidate genes potentially involved in the Fusarium head blight disease.\n\nComparative Genomics of Eight Fusarium graminearum Strains with Contrasting Aggressiveness Reveals an Expanded Open Pangenome and Extended Effector Content Signatures.", "token_count": 503, "char_count": 1973, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:15.188502", "source": { "split": "train_shard_00001", "doc_id": 899 }, "chunk_id": "train_shard_00001_899_0", "global_id": 6935 }, { "text": "Species clustering within Dickeya zeae has been recently identified as complex, encompassing validly published names, including Dickeya oryzae and Dickeya parazeae, with some strains potentially delineating new species. In this study, genomes of strains isolated from bacterial heart rot of pineapple (Ananas comosus var. comosus) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93 to 99.9% and 91.8 to 99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae and D. oryzae ranged from 94.4-95.9% to 57.2-66.5%, respectively. These values fall below the proposed boundaries for species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA, multi-locus sequence analysis of ten housekeeping genes, whole genome and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the 7 pineapple strains", "token_count": 475, "char_count": 1524, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:15.835329", "source": { "split": "train_shard_00001", "doc_id": 900 }, "chunk_id": "train_shard_00001_900_0", "global_id": 6936 }, { "text": "Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological and phylogenomic analyses, we propose the reclassification into a new species of the five pineapple strains from Hawaii A5391, A5410T, A5611, A6136 and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae. We propose the name Dickeya ananatis sp. nov. for this taxon, represented by the type strain A5410T (=ICMP 25020T=LMG 33197T).\n\n<i>Dickeya ananatis</i> sp. nov., pectinolytic bacterium isolated from pineapple (<i>Ananas comosus</i>).", "token_count": 261, "char_count": 667, "word_count": 82, "semantic_coherence": 1, "information_density": 0.8171, "quality_score": 0.9085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:16.431027", "source": { "split": "train_shard_00001", "doc_id": 900 }, "chunk_id": "train_shard_00001_900_1", "global_id": 6937 }, { "text": "Abstract

Transposable element (TE) annotation is crucial for understanding genetics, genomics and evolution, yet current methods struggle to identify TEs in graph-based pangenomes. We developed a framework PanTE to construct accurate and representative TE libraries for both single genomes and graph pangenomes. PanTE is the first of its kind capable of being directly applied to graph-based pangenomes to build population-level TE libraries. By partially reimplementing RepeatModeler2 and integrating key innovations, including graph pangenome disassembly, alignment-free LTR structure detection, a machine learning-based classifier and efficiency-boosting strategies, PanTE outperformed RepeatModeler2 by efficiently handling large genomes, detecting high-abundance TEs and LTR-retrotransposons, and providing robust TE classification with superior computational efficiency. Compared to EDTA, it annotated ~ 26% more TEs in the grapevine genome and achieved up to 13 times faster runtimes in the wheat genome. PanTE represents a significant advancement in population-wide TE discovery, making it particularly valuable for pangenomic studies.

\n\nPanTE: A Comprehensive Framework for Transposable Element Discovery in Graph-based Pangenomes", "token_count": 288, "char_count": 1261, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7233, "quality_score": 0.8616, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:17.454606", "source": { "split": "train_shard_00001", "doc_id": 901 }, "chunk_id": "train_shard_00001_901_0", "global_id": 6938 }, { "text": "Legionella pneumophila serogroup 1 (Lp1) sequence type (ST) 23 is one of the most commonly detected STs in Italy where it currently causes all investigated outbreaks. ST23 has caused both epidemic and sporadic cases between 1995 and 2018 and was analysed at genomic level and compared with ST23 isolated in other countries to determine possible similarities and differences. A core genome multi-locus sequence typing (cgMLST), based on a previously described set of 1,521 core genes, and single-nucleotide polymorphisms (SNPs) approaches were applied to an ST23 collection including genomes from Italy, France, Denmark and Scotland. DNAs were automatically extracted, libraries prepared using NextEra library kit and MiSeq sequencing performed. Overall, 63 among clinical and environmental Italian Lp1 isolates and a further seven and 11 ST23 from Denmark and Scotland, respectively, were sequenced, and pangenome analysed. Both cgMLST and SNPs analyses showed very few loci and SNP variations in ST23 genomes. All the ST23 causing outbreaks and sporadic cases in Italy and elsewhere, were phylogenetically related independent of year, town or country of isolation. Distances among the ST23s were further shortened when SNPs due to horizontal gene transfers were removed. The Lp1 ST23 isolated in Italy have kept their monophyletic origin, but they are phylogenetically close also to ST23 from other countries. The ST23 are quite widespread in Italy, and a thorough epidemiological investigation is compelled to determine sources of infection when this ST is identified in both LD sporadic cases and outbreaks.\n\nGenome analysis of Legionella pneumophila ST23 from various countries reveals highly similar strains.", "token_count": 437, "char_count": 1727, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6575, "quality_score": 0.8287, "entities": { "genes": [ "ST23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:18.119012", "source": { "split": "train_shard_00001", "doc_id": 902 }, "chunk_id": "train_shard_00001_902_0", "global_id": 6939 }, { "text": "Antimicrobial resistance (AMR) gene cassettes comprise an AMR gene flanked by short recombination sites (attI and attC or attC and attC). Integrons are genetic elements able to capture, excise and shuffle these cassettes, providing 'adaptation on demand', and can be found on both chromosomes and plasmids. Understanding the patterns of integron diversity may help to understand the epidemiology of AMR genes. As a case study, we examined the clinical resistance gene bla GES-5, an integron-associated class A carbapenemase first reported in Greece in 2004 and since observed worldwide, which to our knowledge has not been the subject of a previous global analysis. Using a dataset comprising all de-duplicated NCBI contigs containing bla GES-5 (n=104), we developed a pangenome graph-based workflow to characterize and cluster the diversity of bla GES-5-associated integrons. We demonstrate that bla GES-5-associated integrons on plasmids are different to those on chromosomes. Chromosomal integrons were almost all identified in Pseudomonas aeruginosa ST235, with a consistent gene cassette content and order. We observed instances where insertion sequence IS110 disrupted attC sites, which might immobilize the gene cassettes and explain the conserved integron structure despite the presence of intI1 integrase promoters, which would typically facilitate capture or excision and rearrangement. The plasmid-associated integrons were more diverse in their gene cassette content and order, which could be an indication of greater integrase activity and 'shuffling' of integrons on plasmids.", "token_count": 495, "char_count": 1725, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8268, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:18.768753", "source": { "split": "train_shard_00001", "doc_id": 903 }, "chunk_id": "train_shard_00001_903_0", "global_id": 6940 }, { "text": "Global genomic epidemiology of bla GES-5 carbapenemase-associated integrons.", "token_count": 36, "char_count": 94, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:19.126534", "source": { "split": "train_shard_00001", "doc_id": 903 }, "chunk_id": "train_shard_00001_903_1", "global_id": 6941 }, { "text": "Grass powdery mildews ( Blumeria spp.) include economically important fungal crop pathogens with complex and highly repetitive genomes. To investigate the diversity and genome evolution in Blumeria graminis , we combined population genetic and pangenomic analyses using a worldwide sample of 399 wheat powdery mildew isolates. Additionally, we produced high-quality genome assemblies for seven isolates from wheat and one from rye powdery mildew. Using these, we compiled the first grass powdery mildew pangenome comprising 11 Blumeria graminis isolates. We found multiple chromosomal rearrangements between the isolates that grow on wheat, rye and/or triticale hosts. Interestingly, chr-11 showed some characteristics of accessory chromosomes such as presence/absence of large chromosomal segments and higher sequence diversity. Additionally, we identified nearly 67,000 cases of copy number variations (CNVs), which were highly enriched within effector gene families. Furthermore, we found evidence for recent and high transposable element (TE) activity, such as high numbers of TE insertion polymorphisms. Analyses of TE families showed enrichment 1 kb to 2 kb up- and downstream of effector genes, and we also found high levels of TE insertion polymorphisms between populations. Our results demonstrate that chromosomal variations, gene family expansions and contractions, and TE activity are important sources of genome diversification and diversity in grass powdery mildews. Our findings indicate that a combination of pangenomic and population genetics analyses is needed to understand drivers of evolution in plant pathogenic fungi in a comprehensive way.

Author Summary

Fungi are a diverse group of organisms, with some of them (e.g. powdery mildews) having at times a devastating impact on important crops like wheat. Studying the genomes of these grass powdery mildew fungi can improve our understanding the pathogen’s patterns of genome evolution and virulence in order to find more efficient ways to protect crops", "token_count": 478, "char_count": 2035, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:19.769088", "source": { "split": "train_shard_00001", "doc_id": 904 }, "chunk_id": "train_shard_00001_904_0", "global_id": 6942 }, { "text": "Using high quality genomes of a worldwide dataset of wheat and rye powdery mildews, we found multiple re-arrangements in chromosomes, as well as presence and absence of large chromosomal segments in different mildew strains. Along with some genes, important for making these pathogens infectious on various crop lines, some genomic regions may be deleted or duplicated, potentially affecting how the fungus survives and spreads. Additionally, we found that transposable elements are highly active in powdery mildews and that they are enriched near so-called effector genes, which are associated with fungal virulence. Our study shows how powdery mildew genomes have diversified during recent evolution, which has implications for future breeding of crops toward better resistance to fungal diseases.\n\nCombining pangenomics and population genetics finds chromosomal re-arrangements, accessory-like chromosome segments, copy number variations and transposon polymorphisms in wheat and rye powdery mildew", "token_count": 228, "char_count": 1001, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7571, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:20.233546", "source": { "split": "train_shard_00001", "doc_id": 904 }, "chunk_id": "train_shard_00001_904_1", "global_id": 6943 }, { "text": "

Background

Identification of human leukocyte antigen (HLA) types from DNA-sequenced human samples is important in organ transplantation and cancer immunotherapy and remains a challenging task considering sequence homology and extreme polymorphism of HLA genes.

Results

We present Orthanq, a novel statistical model and corresponding application for transparent and uncertainty-aware quantification of haplotypes. We utilize our approach to perform HLA typing while, for the first time, reporting uncertainty of predictions and transparently observing mutations beyond reported HLA types. Using 99 gold standard samples from 1000 Genomes, Illumina Platinum Genomes and Genome In a Bottle projects, we show that Orthanq can provide overall superior accuracy and shorter runtimes than state-of-the-art HLA typers.

Conclusions

Orthanq is the first approach that allows to directly utilize existing pangenome alignments and type all HLA loci. Moreover, it can be generalized for usages beyond HLA typing, e.g. for virus lineage quantification. Orthanq is available under https://orthanq.github.io .\n\nOrthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing.", "token_count": 296, "char_count": 1216, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7226, "quality_score": 0.8613, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:20.804096", "source": { "split": "train_shard_00001", "doc_id": 905 }, "chunk_id": "train_shard_00001_905_0", "global_id": 6944 }, { "text": "Abstract

Natural variations are the basis of crop improvement. However, genomic variability remains largely understudied. We present the full-spectrum panvariome and pangenome of 1,020 peach accessions, including 10.5 million SNPs, indels, SVs, CNVs, TIPs, PAVs, uncovering 70.6% novel variants and 3,289 novel genes. Analysis of the panvariome reconstructs the globally evolutionary history of peach and identifies several trait-causally rare variants. Landraces and improved accessions encode more genes than wild accessions, suggesting gene gains during evolution. Global introgression patterns reveal its new utilizations in phenotype prediction and gene mining and suggest that the most likely wild progenitor of domesticated peach is Prunus mira and almond was involved in the origin of Prunus davidiana. We develop a novel panvariome-based solution for association study, GWASPV, that achieves rapid and precise identification of trait-conferring genes using only one-step GWAS. Our study provides a novel solution for gene mining, with important implications in accelerating plant breeding.

\n\nPanvariome and pangenome of 1,020 global peach accessions shed light on evolution pattern, hidden natural variation and efficient gene discovery", "token_count": 316, "char_count": 1267, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7251, "quality_score": 0.8626, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:21.367563", "source": { "split": "train_shard_00001", "doc_id": 906 }, "chunk_id": "train_shard_00001_906_0", "global_id": 6945 }, { "text": "Exploring Brevibacterium strains from various ecosystems may lead to the discovery of new antibiotic-producing strains. Brevibacterium sp. H-BE7, a strain isolated from marine sediments from Northern Patagonia, Chile, exhibited antimicrobial activity against Salmonella enterica and Listeria monocytogenes . Chemical dereplication identified bioactive compounds, such as 1-methoxyphenazine in the crude extracts of strain H-BE7, which could be responsible of the observed antibacterial activity. The genome of Brevibacterium sp. H-BE7 was sequenced and a phenazine-like biosynthetic gene clusters (BGCs) is not present within the genome. To study the biosynthetic potential of strain H-BE7 and Brevibacterium genus, the genome sequences of 98 Brevibacterium strains, including strain H-BE7, were selected for a genomic analysis. A phylogenomic cladogram was generated, which divided the Brevibacterium strains into four major clades. A total of 25 strains are potentially unique new species according to Average Nucleotide Identity (ANIb) values. These strains were isolated from various environments, emphasizing the importance of exploring diverse ecosystems to discover the full diversity of Brevibacterium . Pangenome analysis of Brevibacterium strains revealed that only 2.5% of gene clusters are included within the core genome, and most gene clusters occur either as singletons or as cloud genes present in less than ten strains. Brevibacterium strains from various phylogenomic clades exhibit diverse BGCs. Specific groups of BGCs show clade-specific distribution patterns, such as siderophore BGCs and carotenoid-related BGCs. A group of clade IV-A Brevibacterium strains possess a clade-specific Polyketide synthase (PKS) BGCs that connects with phenazine-related BGCs and could be related to the production of 1-methoxyphenazine in HBE-7’s crude extract", "token_count": 492, "char_count": 1864, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5961, "quality_score": 0.798, "entities": { "genes": [ "BE7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:22.017139", "source": { "split": "train_shard_00001", "doc_id": 907 }, "chunk_id": "train_shard_00001_907_0", "global_id": 6946 }, { "text": "Within the PKS BGC, five genes, including the biosynthetic PKS gene, participate in the mevalonate pathway and exhibit similarities with the phenazine A BGC. However, additional core biosynthetic phenazine genes were exclusively discovered in nine Brevibacterium strains, primarily isolated from cheese. While strain H-BE7 lacks the core phenazine biosynthetic genes, it produces 1-methoxyphenazine, indicating the presence of an unknown biosynthetic pathway for this compound. This suggests the existence of alternative biosynthetic pathways or promiscuous enzymes within H-BE7's genome.\n\nExploring the Biosynthetic Gene Clusters in Brevibacterium: A Comparative Genomic Analysis of Diversity and Distribution", "token_count": 184, "char_count": 710, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7204, "quality_score": 0.8602, "entities": { "genes": [ "BE7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:22.465493", "source": { "split": "train_shard_00001", "doc_id": 907 }, "chunk_id": "train_shard_00001_907_1", "global_id": 6947 }, { "text": "

Background

Fuel ethanol from lignocellulose could be important source of renewable energy. However, to make the process feasible, more efficient microbial fermentation of pentose sugars, mainly xylose, should be achieved. The native xylose-fermenting thermotolerant yeast Ogataea polymorpha is a promising organism for further development. Efficacy of xylose alcoholic fermentation by O. polymorpha was significantly improved by metabolic engineering. Still, genes involved in regulation of xylose fermentation are insufficiently studied.

Results

We isolated an insertional mutant of O. polymorpha with impaired ethanol production from xylose. The insertion occurred in the gene HXS1 that encodes hexose transporter-like sensor, a close homolog of Saccharomyces cerevisiae sensors Snf3 and Rgt2. The role of this gene in xylose utilization and fermentation was not previously elucidated. We additionally analyzed O. polymorpha strains with the deletion and overexpression of the corresponding gene. Strains with deletion of the HXS1 gene had slower rate of glucose and xylose consumption and produced 4 times less ethanol than the wild-type strain, whereas overexpression of HXS1 led to 10% increase of ethanol production from glucose and more than 2 times increase of ethanol production from xylose. We also constructed strains of O. polymorpha with overexpression of the gene AZF1 homologous to S. cerevisiae AZF1 gene which encodes transcription activator involved in carbohydrate sensing. Such transformants produced 10% more ethanol in glucose medium and 2.4 times more ethanol in xylose medium. Besides, we deleted the AZF1 gene in O. polymorpha. Ethanol accumulation in xylose and glucose media in such deletion strains dropped 1.5 and 1.8 times respectively. Overexpression of the HXS1 and AZF1 genes was also obtained in the advanced ethanol producer from xylose", "token_count": 511, "char_count": 1886, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5261, "quality_score": 0.7631, "entities": { "genes": [ "HXS1", "AZF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:23.101722", "source": { "split": "train_shard_00001", "doc_id": 908 }, "chunk_id": "train_shard_00001_908_0", "global_id": 6948 }, { "text": "The corresponding strains were characterized by 20-40% elevated ethanol accumulation in xylose medium. To understand underlying mechanisms of the observed phenotypes, specific enzymatic activities were evaluated in the isolated recombinant strains.

Conclusions

This paper shows the important role of hexose sensor Hxs1 and transcription factor Azf1 in xylose and glucose alcoholic fermentation in the native xylose-fermenting yeast O. polymorpha and suggests potential importance of the corresponding genes for construction of the advanced ethanol producers from the major sugars of lignocellulose.\n\nThe role of hexose transporter-like sensor hxs1 and transcription activator involved in carbohydrate sensing azf1 in xylose and glucose fermentation in the thermotolerant yeast Ogataea polymorpha.", "token_count": 205, "char_count": 803, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:23.571301", "source": { "split": "train_shard_00001", "doc_id": 908 }, "chunk_id": "train_shard_00001_908_1", "global_id": 6949 }, { "text": "This study presents the assembly and comparative genomic analysis of luminous Photobacterium strains isolated from the light organs of 12 fish species using Oxford Nanopore Technologies (ONT) sequencing. The majority of assemblies achieved chromosome-level continuity, consisting of one large (>3 Mbp) and one small (~1.5 Mbp) contig, with near complete BUSCO scores along with varying plasmid sequences. Leveraging this dataset, this study significantly expanded the available genomes for P. leiognathi and its subspecies P. 'mandapamensis', enabling a comparative genomic analysis between the two lineages. An analysis of the large and small chromosomes unveiled distinct patterns of core and accessory genes, with a larger fraction of the core genes residing on the large chromosome, supporting the hypothesis of secondary chromosome evolution from megaplasmids in Vibrionaceae. In addition, we discovered a proposed new species, Photobacterium acropomis sp. nov., isolated from an acropomatid host, with an average nucleotide identify (ANI) of 93 % compared to the P. leiognathi and P. 'mandapamensis' strains. A comparison of the P. leiognathi and P. 'mandapamensis' lineages revealed minimal differences in gene content, yet highlighted the former's larger genome size and potential for horizontal gene transfer. An investigation of the lux-rib operon, responsible for light production, indicated congruence between the presence of luxF and host family, challenging its role in differentiating P. 'mandapamensis' from P. leiognathi. Further insights were derived from the identification of metabolic differences, such as the presence of the NADH:quinone oxidoreductase respiratory complex I in P", "token_count": 500, "char_count": 1788, "word_count": 241, "semantic_coherence": 1, "information_density": 0.639, "quality_score": 0.8195, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:24.224023", "source": { "split": "train_shard_00001", "doc_id": 909 }, "chunk_id": "train_shard_00001_909_0", "global_id": 6950 }, { "text": "leiognathi as well as variations in the type II secretion system (T2S) genes between the lineages, potentially impacting protein secretion and symbiosis. In summary, this study advances our understanding of Photobacterium genome evolution, highlighting subtle differences between closely related lineages, specifically P. leiognathi and P. 'mandapamensis'. These findings highlight the benefit of long read sequencing for bacterial genome assembly and pangenome analysis and provide a foundation for exploring early bacterial speciation processes of these facultative light organ symbionts.\n\nComparative genomics of symbiotic Photobacterium using highly contiguous genome assemblies from long read sequences.", "token_count": 186, "char_count": 740, "word_count": 92, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:24.672887", "source": { "split": "train_shard_00001", "doc_id": 909 }, "chunk_id": "train_shard_00001_909_1", "global_id": 6951 }, { "text": "Escherichia coli ST131 is a major cause of infection with extensive antimicrobial resistance (AMR) facilitated by widespread beta-lactam antibiotic use. This drug pressure has driven extended-spectrum beta-lactamase (ESBL) gene acquisition and evolution in pathogens, so a clearer resolution of ST131’s origin, adaptation and spread is essential. E. coli ST131’s ESBL genes are typically embedded in mobile genetic elements (MGEs) that aid transfer to new plasmid or chromosomal locations, which are mobilised further by plasmid conjugation and recombination, resulting in a flexible ESBL, MGE and plasmid composition with a conserved core genome. We used population genomics to trace the evolution of AMR in ST131 more precisely by extracting all available high-quality Illumina HiSeq read libraries to investigate 4,071 globally-sourced genomes, the largest ST131 collection examined so far. We applied rigorous quality-control, genome de novo assembly and ESBL gene screening to resolve ST131’s population structure across three genetically distinct Clades (A, B, C) and abundant subclades from the dominant Clade C. We reconstructed their evolutionary relationships across the core and accessory genomes using published reference genomes, long read assemblies and k-mer-based methods to contextualise pangenome diversity. The three main C subclades have co-circulated globally at relatively stable frequencies over time, suggesting attaining an equilibrium after their origin and initial rapid spread. This contrasted with their ESBL genes, which had stronger patterns across time, geography and subclade, and were located at distinct locations across the chromosomes and plasmids between isolates. Within the three C subclades, the core and accessory genome diversity levels were not correlated due to plasmid and MGE activity, unlike patterns between the three main clades, A, B and C. This population genomic study highlights the dynamic nature of the accessory genomes in ST131, suggesting that surveillance should anticipate genetically variable outbreaks with broader antibiotic resistance levels", "token_count": 495, "char_count": 2106, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6655, "quality_score": 0.8328, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:25.324527", "source": { "split": "train_shard_00001", "doc_id": 910 }, "chunk_id": "train_shard_00001_910_0", "global_id": 6952 }, { "text": "Our findings emphasise the potential of evolutionary pangenomics to improve our understanding of AMR gene transfer, adaptation and transmission to discover accessory genome changes linked to novel subtypes.\n\nAn Escherichia coli ST131 pangenome atlas reveals population structure and evolution across 4,071 isolates", "token_count": 78, "char_count": 321, "word_count": 42, "semantic_coherence": 1, "information_density": 0.881, "quality_score": 0.9405, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:25.699462", "source": { "split": "train_shard_00001", "doc_id": 910 }, "chunk_id": "train_shard_00001_910_1", "global_id": 6953 }, { "text": "Bacteroides fragilis is among the most abundant and pathogenic bacterial species in the gut microbiota and is associated with diarrheal disease in children, inflammatory bowel disease, and the development of colorectal cancer. It is increasingly resistant to potent antimicrobial agents such as carbapenems and metronidazole, making it among the most resistant anaerobic bacteria. These factors combined call for increased monitoring of B. fragilis and its population structure on a worldwide scale. Here, we present a possible solution through the development of a multilocus sequence typing scheme (MLST). The scheme is based on seven core gene fragments: groL (hsp60), rpoB, recA, dnaJ, rprX, prfA, and fusA. These gene fragments possess high discriminatory power while retaining concordance with whole core genome-based phylogenetic analysis. The scheme proved capable of differentiating B. fragilis isolates at the strain level. It offers a standardized method for molecular typing and can be applied to isolates from various sampling backgrounds, such as patient isolates, environmental samples, and strains obtained from food and animal sources. In total, 567 B. fragilis genomes were sequence typed and their isolate data collected. The MLST scheme clearly divided the B. fragilis population into two divisions based on the presence of the cfiA and cepA resistance genes. However, no other specific subpopulations within the analyzed genomes were found to be associated with any specific diseases or geographical location. With this MLST scheme, we hope to provide a powerful tool for the study and monitoring of B. fragilis on an international scale. IMPORTANCE Here, we present the first MLST scheme for Bacteroides fragilis, one of the most abundant pathogenic bacteria in the human gut microbiota. The scheme enables standard classification and monitoring of B. fragilis on a worldwide scale and groups the majority of current isolate data in one place. A more unified approach to the collection and analysis of B", "token_count": 516, "char_count": 2102, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:26.329842", "source": { "split": "train_shard_00001", "doc_id": 911 }, "chunk_id": "train_shard_00001_911_0", "global_id": 6954 }, { "text": "fragilis data could provide crucial insights into how the pathogen operates and develops as a species. Close monitoring of B. fragilis is especially relevant, as it is increasingly resistant to potent antimicrobial agents and engages in horizontal gene transfer with other bacteria. Hopefully, this approach will guide new discoveries into how B. fragilis evolves and interacts with its human host. Additionally, the scheme could potentially be applied to other species of the genus Bacteroides.\n\nDevelopment and Clinical Application of a Multilocus Sequence Typing Scheme for Bacteroides fragilis Based on Whole-Genome Sequencing Data.", "token_count": 152, "char_count": 650, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7826, "quality_score": 0.8913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:26.775876", "source": { "split": "train_shard_00001", "doc_id": 911 }, "chunk_id": "train_shard_00001_911_1", "global_id": 6955 }, { "text": "Structural variants (SVs) are widespread in vertebrate genomes, yet their evolutionary dynamics remain poorly understood. Using 45 long-read de novo genome assemblies and pangenome tools, we analyze SVs within three closely related species of North American jays (Aphelocoma, scrub-jays) displaying a 60-fold range in effective population size. We find rapid evolution of genome architecture, including ~100 Mb variation in genome size driven by dynamic satellite landscapes with unexpectedly long (> 10 kb) repeat units and widespread variation in gene content, influencing gene expression. SVs exhibit slightly deleterious dynamics modulated by variant length and population size, with strong evidence of adaptive fixation only in large populations. Our results demonstrate how population size shapes the distribution of SVs and the importance of pangenomes to characterizing genomic diversity.\n\nComparative population pangenomes reveal unexpected complexity and fitness effects of structural variants", "token_count": 215, "char_count": 1003, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7664, "quality_score": 0.8832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:27.242603", "source": { "split": "train_shard_00001", "doc_id": 912 }, "chunk_id": "train_shard_00001_912_0", "global_id": 6956 }, { "text": "The boll weevil, Anthonomus grandis grandis Boheman, and thurberia weevil, Anthonomus grandis thurberiae Pierce, together comprise a species complex that ranges throughout Mexico, the southwestern regions of the United States and parts of South America. The boll weevil is a historically damaging and contemporaneously threatening pest to commercial upland cotton, Gossypium hirsutum L. (Malvales: Malvaceae), whereas the thurberia weevil is regarded as an innocuous non-pest subspecies that is mostly found on non-cultivated Thurber's or Arizona cotton, Gossypium thurberi L., throughout its native range in western Mexico and the southwestern United States. Recent independent analyses, using mitochondrial and whole-genome markers, have suggested the independent evolution of these lineages is more attributable to geographic isolation than biotic factors. We suggest a combination of drivers after employing comparative genomic, population genetic and pangenome methodologies to identify large and small polymorphisms. By leveraging genetic differences, we determined 39,310 diagnostic loci between the subspecies, find genes under selection, and model the subspecies' shared and unique evolutionary history. Interestingly, structural variations capture a large proportion of genes at the population level and demographic reconstruction suggests a split between approximately 3,320-16,300 before present (YBP), which coincides with cotton cultivation in Mesoamerica, approximately 3,000-5,000 YBP. Observed polymorphisms are enriched for reproductive, regulatory, and metabolic genes, which may be attributed to the subspecies split and coevolution with cultivated cotton. Our results demonstrate the utility of a holistic, comparative framework utilising small and large polymorphisms to reconstruct demography and identify genetic novelty via pangenomics.\n\nPangenomics Links Boll Weevil Divergence With Ancient Mesoamerican Cotton Cultivation", "token_count": 471, "char_count": 1948, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6929, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:27.882258", "source": { "split": "train_shard_00001", "doc_id": 913 }, "chunk_id": "train_shard_00001_913_0", "global_id": 6957 }, { "text": "1

Motivation

With more and more telomere-to-telomere genomes assembled, pangenomes make it possible to capture the genomic diversity of a species. Because they introduce less biases, pangenomes, represented as graphs, tend to supplant the usual linear representation of a reference genome, augmented with variations. However, this major change requires new tools adapted to this data structure. Among the numerous questions that can be addressed to a pangenome graph is the search for conserved or divergent genes.

Results

In this article, we present a new tool, named PanSel, which computes a conservation score for each segment of the genome, and finds genomic regions that are significantly conserved, or divergent.

Availability

PanSel, written in C++11 with no dependency, is available at https://github.com/mzytnicki/pansel .

Contact

matthias.zytnicki@inrae.fr\n\nAssessing genome conservation on pangenome graphs with PanSel", "token_count": 257, "char_count": 964, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7634, "quality_score": 0.8817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:28.463991", "source": { "split": "train_shard_00001", "doc_id": 914 }, "chunk_id": "train_shard_00001_914_0", "global_id": 6958 }, { "text": "As Arctic shipping increases due to climate change, characterised by rising temperatures and decreasing sea-ice coverage, the risk of oil spills through the Northwest Passage in this fragile ecosystem grows, necessitating effective bioremediation strategies. Research on bioremediation using Arctic coastal sediment bacteria has gained attention, particularly Rhodococcus species that play key roles in hydrocarbon degradation under extreme conditions. This study investigates the hydrocarbon degradation capabilities of a novel cryophilic Arctic Rhodococcus sp. strain R1B_2T isolated from Canadian high Arctic beach sediment in Resolute Bay, exposed to ultra-low sulphur fuel oil for 3 months at 5°C. Comparative transcriptomics analyses revealed dynamic responses and metabolic plasticity, with upregulation of genes for aliphatic, aromatic, and polycyclic aromatic hydrocarbons, biosurfactant production (e.g., rhamnolipid), cold adaptation, and stress responses. The strain possesses several key alkane degradation genes (alkB, almA, CYP153, ladA), with co-expression network analysis highlighting synergistic mechanisms between alkB and CYP153 that target different chain-length alkanes (alkB: ~C5-C20; CYP153: ~C5-C12 and > C30), demonstrating complementary degradation strategies. The findings reveal adaptive mechanisms and degradation kinetics of native Arctic bacteria, highlighting the potential of Arctic cryophilic and halotolerant Rhodococcus species for oil spill remediation in polar marine environments.\n\nTranscriptomic Analyses Unveil Hydrocarbon Degradation Mechanisms in a Novel Polar Rhodococcus sp. Strain R1B_2T From a High Arctic Intertidal Zone Exposed to Ultra-Low Sulphur Fuel Oil.", "token_count": 452, "char_count": 1709, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [ "CYP153" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:29.116416", "source": { "split": "train_shard_00001", "doc_id": 915 }, "chunk_id": "train_shard_00001_915_0", "global_id": 6959 }, { "text": "Few studies have assessed the probiotic characteristics and antioxidant activity of the kefir-derived yeast, Kluyveromyces marxianus, and its synergistic interactions with polyphenol-rich grape seed flour (GSF)/extract (GSE). We examined several probiotic characteristics (gastric resistance, intestinal resistance, cholesterol reduction, adhesiveness to intestinal cells) of four K. marxianus strains. Each of the yeasts showed 5–25% greater intestinal cell adhesiveness than that of Lactobacillus acidophilus. Among the four yeast strains, K. marxianus KU140723-02 (KM2) exhibited the greatest antioxidant activity. When incubated with GSF/GSE, its antioxidant activity was synergistically increased by two-fold. In conclusion, a combination of kefir-derived yeast KM2 and GSF/GSEs may be a novel functional food ingredient with antioxidant properties targeting gut health.\n\nCharacterization of yeasts isolated from kefir as a probiotic and its synergic interaction with the wine byproduct grape seed flour/extract", "token_count": 290, "char_count": 1016, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7023, "quality_score": 0.8511, "entities": { "genes": [ "KU140723", "KM2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:29.712312", "source": { "split": "train_shard_00001", "doc_id": 916 }, "chunk_id": "train_shard_00001_916_0", "global_id": 6960 }, { "text": "

Background

Ongoing studies have revealed the global prevalence of severe infections caused by the hypervirulent strains of Klebsiella pneumoniae (K. pneumoniae). Meanwhile, the World Health Organization and the Centers for Disease Control declared carbapenem-resistant K. pneumoniae as an urgent public health threat, requiring swift and effective action to mitigate its spread. Low- and middle-income countries are severely impacted by such devastating infectious diseases owing to the ill implementation of antimicrobial practices and infection control policies. Having both hypervirulence and carbapenemase gene determinants, the emergence of convergent hypervirulent carbapenem-resistant K. pneumoniae is now being reported worldwide.

Methods

In this study, we sequenced 19 carbapenemase-producing K. pneumoniae strains recovered from various clinical specimens. Additionally, we evaluated the phenotypic antimicrobial susceptibility to multiple antimicrobial classes using the VITEK2 automated system. Utilizing the sequencing data, we characterized the sequence types, serotypes, pangenome, resistance profiles, virulence profiles, and mobile genetic elements of the examined isolates. We highlighted the emergence of high-risk clones carrying hypervirulence genetic determinants among the screened isolates.

Results

Our findings revealed that all carbapenem-resistant isolates exhibited either extensive- or pan-drug resistance and harbored multiple variants of resistance genes spanning nearly all the antimicrobial classes. The most prevalent carbapenemase genes detected within the isolates were blaNDM-5 and blaOXA-48. We identified high-risk clones, such as ST383-K30, ST147-K64, ST11-K15, and ST14-K2, which may have evolved into putative convergent strains by acquiring the full set of hypervirulence-associated genetic determinants (iucABCD, rmpA and/ or rmpA2, putative transporter peg-344)", "token_count": 515, "char_count": 1950, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [ "VITEK2", "ST383", "ST11", "ST14", "ST147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:30.395646", "source": { "split": "train_shard_00001", "doc_id": 917 }, "chunk_id": "train_shard_00001_917_0", "global_id": 6961 }, { "text": "Additionally, this study identified ST709-K9 as a high-risk clone for the first time and uncovered that capsule types K15 and K9 carried hypervirulence genetic determinants. The most frequent Inc types found in these isolates were Col440I, IncHI1B, and Inc FII(K).

Conclusion

This study highlights the emergence of high-risk, extensively carbapenem-resistant K. pneumoniae strains co-carrying hypervirulence determinants in Egyptian clinical settings. This poses an imminent threat not only to Egypt but also to the global community, underscoring the urgent need for enhanced surveillance and control strategies to combat this pathogen.\n\nGenomic dynamics of high-risk carbapenem-resistant klebsiella pneumoniae clones carrying hypervirulence determinants in Egyptian clinical settings.", "token_count": 204, "char_count": 792, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7353, "quality_score": 0.8676, "entities": { "genes": [ "ST709" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:30.852840", "source": { "split": "train_shard_00001", "doc_id": 917 }, "chunk_id": "train_shard_00001_917_1", "global_id": 6962 }, { "text": "Oceanobacter-related bacteria (ORB) are a group of oligotrophic marine bacteria play an underappreciated role in carbon cycling. They have been frequently described as one of the dominant bacterial groups with a wide distribution in coastal and deep seawater of global oceans. To clarify their taxonomic affiliation in relation to alkane utilization, phylogenomic and comparative genomics analyses were performed based on currently available genomes from GenBank and four newly isolated strains, in addition to phenotypic and chemotaxonomic characteristics. Consistently, phylogenomic analysis robustly separated them into two groups, which are accordingly hydrocarbon-degrading (HD, Thalassolituus and Oleibacter) and non-HD (NHD, Oceanobacter). In addition, the two groups can also be readily distinguished by several polyphasic taxonomic characteristics. Furthermore, both AAI and POCP genomic indices within the HD group support the conclusion that the members of the genus Oleibacter should be transferred into the genus Thalassolituus. Moreover, HD and NHD bacteria differed significantly in terms of genome size, G + C content and genes involved in alkane utilization. All HD bacteria contain the key gene alkB encoding an alkane monooxygenase, which can be used as a marker gene to distinguish the members of closely related genera Oceanobacter and Thalassolituus", "token_count": 377, "char_count": 1434, "word_count": 194, "semantic_coherence": 1, "information_density": 0.701, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:31.456155", "source": { "split": "train_shard_00001", "doc_id": 918 }, "chunk_id": "train_shard_00001_918_0", "global_id": 6963 }, { "text": "Pangenome analysis revealed that the larger accessory genome may endow Thalassolituus with the flexibility to cope with the dynamics of marine environments and thrive therein, although they possess smaller pan, core- and unique-genomes than Oceanobacter. Within the HD group, twelve species were clearly distinguished from each other by both dDDH and ANI genomic indices, including two novel species represented by the newly isolated strains alknpb1M-1 T and 59MF3M-4 T , for which the names Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. are proposed. Collectively, these findings build a phylogenetic framework for the ORB and contribute to understanding of their role in marine carbon cycling.\n\nGenome-based taxonomic rearrangement of Oceanobacter-related bacteria including the description of Thalassolituus hydrocarbonoclasticus sp. nov. and Thalassolituus pacificus sp. nov. and emended description of the genus Thalassolituus.", "token_count": 317, "char_count": 1062, "word_count": 132, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:32.015869", "source": { "split": "train_shard_00001", "doc_id": 918 }, "chunk_id": "train_shard_00001_918_1", "global_id": 6964 }, { "text": "Lactobacilli are dominant members of the \"healthy\" female urogenital microbiota. One of these species, Lactobacillus jensenii, is routinely identified in the urinary microbiota of women both with and without urinary tract symptoms. In March 2020, the new bacterial species Lactobacillus mulieris was introduced, and phylogenetic and average nucleotide identity analysis identified eight L. jensenii strains that should be classified as members of the L. mulieris species. This prompted our phylogenomic study of all publicly available L. jensenii and L. mulieris genome sequences. While there is little variation in the 16S rRNA gene sequences, the core genome shows a clear distinction between genomes of the two species. We find eight additional strains of the species L. mulieris among these genomes. Furthermore, one strain, currently classified as L. mulieris UMB7784, is distinct from both L. jensenii and L. mulieris strains. As part of our comparative genomic study, we also investigated the genetic content that distinguishes these two species. Unique to the L. jensenii genomes are several genes related to catabolism of disaccharides. In contrast, L. mulieris genomes encode several cell surface and secreted proteins that are not found within the L. jensenii genomes. These L. jensenii-specific and L. mulieris-specific loci provide insight into phenotypic differences of these two species.IMPORTANCELactobacillus species play a key role in the health of the urinary tract. For instance, Lactobacillus crispatus and L. jensenii have been found to inhibit uropathogenic Escherichia coli growth. While L", "token_count": 535, "char_count": 1756, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5865, "quality_score": 0.7932, "entities": { "genes": [ "UMB7784" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:32.674116", "source": { "split": "train_shard_00001", "doc_id": 919 }, "chunk_id": "train_shard_00001_919_0", "global_id": 6965 }, { "text": "crispatus is typically found only within the microbiota of women without lower urinary tract symptoms (LUTS), L. jensenii has been found in the microbiota of women both with and without LUTS. With the recent introduction of the new species Lactobacillus mulieris, several strains of L. jensenii were reclassified as L. mulieris based upon gene marker and average nucleotide identity. We took a phylogenomic and comparative genomic approach to ascertain the genetic determinants of these two species. Looking at a larger data set, we identified additional L. mulieris strains, including one distinct from other members of the species-L. mulieris UMB7784. Furthermore, we identified unique loci in each species that may have clinical implications.\n\nComparative Genomic Study of Lactobacillus jensenii and the Newly Defined Lactobacillus mulieris Species Identifies Species-Specific Functionality.", "token_count": 260, "char_count": 940, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [ "UMB7784" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:33.223989", "source": { "split": "train_shard_00001", "doc_id": 919 }, "chunk_id": "train_shard_00001_919_1", "global_id": 6966 }, { "text": "Salmonella enterica is a bacterial pathogen known to cause gastrointestinal infections in diverse hosts, including humans and animals. Despite extensive knowledge of virulence mechanisms, understanding the factors driving host specificity remains limited. In this study, we performed a comprehensive pangenome-wide analysis of S. enterica to identify potential loci determining preference towards certain hosts. We used a dataset of high-quality genome assemblies grouped into 300 reference clusters with a special focus on four host groups: humans, pigs, cattle, and birds. The reconstructed pangenome was shown to be open and enriched with the accessory component implying high genetic diversity. Notably, phylogenetic inferences did not correspond to the distribution of affected hosts, as large compact phylogenetic groups were absent. By performing a pangenome-wide association study, we identified potential host specificity determinants. These included multiple genes encoding proteins involved in distinct infection stages, e.g., secretion systems, surface structures, transporters, transcription regulators, etc. We also identified antibiotic resistance loci in host-adapted strains. Functional annotation corroborated the results obtained with significant enrichments related to stress response, antibiotic resistance, ion transport, and surface or extracellular localization. We suggested categorizing the revealed specificity factors into three main groups: pathogenesis, resistance to antibiotics, and propagation of mobile genetic elements (MGEs).\n\nFor Someone, You Are the Whole World: Host-Specificity of Salmonella enterica.", "token_count": 368, "char_count": 1662, "word_count": 212, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:33.800125", "source": { "split": "train_shard_00001", "doc_id": 920 }, "chunk_id": "train_shard_00001_920_0", "global_id": 6967 }, { "text": "The aim of the study was to evaluate the impact of probiotics obtained from an agroindustrial waste substrate fermented with lactic acid bacteria and/or yeasts on the health and changes in the microbiota of the digestive tract of guinea pigs. Eighty male guinea pigs, Kuri breed, 30 days old and 250 g live weight, were randomly selected and divided into four groups of 20 animals each: T0, control; T1, Lactobacillus acidophilus and L. bulgaricus; T2, Saccharomyces cerevisiae and Kluyveromyces fragilis; and T3. L. acidophilus, L. bulgariccus, S. cerevisiae and K. fragilis. T1, T2 and T3 contained molasses-vinasse substrate in their base, the dose administered was 1.00 mL/animal orally every 3 days. The indicators evaluated were weight gain, occurrence of diarrhea and mortality, macroscopic lesions in the digestive tract organs and changes in the microbiota of the stomach, caecum, small and large intestine. Treatments T1, T2 and T3 improved weight gain (p < 0.05) and reduced the presence of guinea pigs with diarrhea (p < 0.05) and there was no mortality; animals in the control group presented a greater amount (p < 0.05) of macroscopic lesions in the digestive tract organs; in the T1, T2 and T3 groups there was an improvement in the natural microbiota. It is concluded that the inclusion of a microbial additive in young guinea pigs improves intestinal health and consequently improves weight gain, reduces diarrhea and deaths and normalizes the natural microbiota of the gastrointestinal tract.", "token_count": 491, "char_count": 1580, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5792, "quality_score": 0.7896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:34.448100", "source": { "split": "train_shard_00001", "doc_id": 921 }, "chunk_id": "train_shard_00001_921_0", "global_id": 6968 }, { "text": "Effect of Agroindustrial Waste Substrate Fermented with Lactic Acid Bacteria and Yeast on Changes in the Gut Microbiota of Guinea Pigs.", "token_count": 40, "char_count": 135, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:34.807933", "source": { "split": "train_shard_00001", "doc_id": 921 }, "chunk_id": "train_shard_00001_921_1", "global_id": 6969 }, { "text": "Plasticity of Pseudomonas aeruginosa chromosomes is mainly driven by an extended accessory genome that is shaped by insertion and deletion events. Further modification of the genome composition can be induced by chromosomal inversion events which lead to relocation of genes in the affected genomic DNA segments, modify the otherwise highly conserved core genome synteny and could even alter the location of the replication terminus. Although the genome of the first sequenced strain, PAO1, displayed such a large genomic inversion, knowledge on such recombination events in the P. aeruginosa population is limited. Several large inversions had been discovered in the late 1990s in cystic fibrosis isolates of the major clonal lineage C by physical genome mapping, and subsequent work on these examples led to the characterization of the DNA at the recombination breakpoints and a presumed recombination mechanism. Since then, the topic was barely addressed in spite of the compilation of thousands of P. aeruginosa genome sequences that are deposited in databases. Due to the use of second-generation sequencing, genome contig assembly had usually followed synteny blueprints provided by the existing reference genome sequences. Inversion detection was not feasible by these approaches, as the respective read lengths did not allow reliable resolution of sequence repeats that are typically found at the borders of inverted segments. In this study, we applied PacBio and MinION long-read sequencing to isolates of the mentioned clone C collection. Confirmation of inversions predicted from the physical mapping data demonstrated that unbiased sequence assembly of such read datasets allows the detection of genomic inversions and the resolution of the recombination breakpoint regions. Additional long-read sequencing of representatives of the other major clonal lineage, PA14, revealed large inversions in several isolates, from cystic fibrosis origin as well as from other sources. These findings indicated that inversion events are not restricted to strains from chronic infection background, but could be widespread in the P. aeruginosa population and contribute to genome plasticity. Moreover, the monitored examples emphasized the role of small mobile DNA units, such as IS elements or transposons, and accessory DNA elements in the inversion-related recombination processes.", "token_count": 524, "char_count": 2410, "word_count": 348, "semantic_coherence": 1, "information_density": 0.5546, "quality_score": 0.7773, "entities": { "genes": [ "PA14", "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:35.440382", "source": { "split": "train_shard_00001", "doc_id": 922 }, "chunk_id": "train_shard_00001_922_0", "global_id": 6970 }, { "text": "Structural genome variants of Pseudomonas aeruginosa clone C and PA14 strains.", "token_count": 29, "char_count": 85, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:35.795786", "source": { "split": "train_shard_00001", "doc_id": 922 }, "chunk_id": "train_shard_00001_922_1", "global_id": 6971 }, { "text": "An industrial process is profitable when its individual unit operations are efficient and thus, this work shows a guideline for designing efficient fermentation-industrial processes for agave distilled production based on a sequential approach of optimization, beginning in the laboratory and followed by the adjustment of the variable values using the evolutionary operation method for successful process scaling. The results at the laboratory showed that a starter inoculum containing a 5 × 106 cells/mL mixture of Kluyveromyces marxianus, Clavispora lusitaniae, and Kluyveromyces marxianus var. drosophilarum strains in a bioreactor containing agave syrup with 120 g/L fermented sugar, processed at a constant temperature of 33 °C and 1.0 VVM aeration for 1.6 h, led to a fermented product with a 4.18% (v/v) alcohol content after 72 h of processing time. The scale-up process results showed that the best operating conditions at the pilot-plant level were a temperature of 35 °C and aeration at 1.0 VVM for 1.2 h, which led to a fermented product with a 4.22% (v/v) total alcohol content after 72 h of processing time. These represent similar performance values for both production processes, but each one worked with their specific values of process variables, which demonstrates that each level of production had its own specific values for process variables. The volatile compound analysis shows that both distilled products contained a similar profile of volatile components that provide fruity and ethereal aromatic notes pleasant to the palate. Therefore, the process design for agave spirit production at the semi-industrial level was successfully achieved.\n\nA validated strategy to design efficient fermentation-industrial processes: agave spirit production.", "token_count": 430, "char_count": 1781, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5703, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:36.418579", "source": { "split": "train_shard_00001", "doc_id": 923 }, "chunk_id": "train_shard_00001_923_0", "global_id": 6972 }, { "text": "Pangenomics and long reads bring the promise of integrating read mapping with variant calling, since a pangenome encodes a reference genome that incorporates evolutionary or population aspects, while even a single long read can provide a good evidence of different kinds of variants (not only the single nucleotide variants that can be easily observed by short reads). This promise needs to be fulfilled by the development of new read mapping approaches that are tailored for that purpose. This paper focuses on integrating recombination events, that are key in bacteria, into read mapping. A first approach in that direction [ACBC + 24] provides an exact dynamic programming algorithm that is too slow to manage multiple recombinations or long reads. We present a novel A* algorithm for recombination-aware sequence-to-graph mapping that significantly reduces running time by incorporating haplotype information and an efficient heuristic function. Our tool, RecAlign , demonstrates up to a two-order magnitude improvement in time and space complexity over [ACBC + 24] and efficiently handles multiple recombinations.\n\nRecAlign: A* recombination-aware sequence to graph mapping", "token_count": 249, "char_count": 1178, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:36.909309", "source": { "split": "train_shard_00001", "doc_id": 924 }, "chunk_id": "train_shard_00001_924_0", "global_id": 6973 }, { "text": "By random integrative mutagenesis with a kanMX4 cassette in Kluyveromyces marxianus DMKU 3-1042, we obtained three mutants of COX15, ATP25 and CYC3 encoding a cytochrome oxidase assembly factor (singleton), a transcription factor required for assembly of the Atp9p subunit of mitochondrial ATP synthase and cytochrome c heme lyase, respectively, as mutants lacking growth capability on xylose and/or arabinose. They exhibited incapability of growth on non-fermentable carbon sources, such as acetate or glycerol, and thermosensitiveness. Their biomass formation in glucose medium was reduced, but ethanol yields were increased with a high ethanol level in the medium, compared to those of the parental strain. Experiments with respiratory inhibitors showed that cox15 and cyc3, but not atp25, were able to grow in glucose medium containing antimycin A and that the atp25 mutant was KCN-resistant. Activities of NADH and ubiquinol oxidases in membrane fractions of each mutant became a half of that of the parent and negligible, respectively, and their remaining NADH oxidase activities were found to be resistant to KCN. Absolute absorption spectral analysis revealed that the peak corresponding to a + a 3 was very small in atp25 and negligible in cox15 and cyc3. These findings suggest that the K. marxianus strain possesses an alternative KCN-resistant oxidase that is located between primary dehydrogenases and the ubiquinone pool and that the respiratory activity is essential for utilization of pentoses.\n\nEssentiality of respiratory activity for pentose utilization in thermotolerant yeast Kluyveromyces marxianus DMKU 3-1042.", "token_count": 450, "char_count": 1633, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6208, "quality_score": 0.8104, "entities": { "genes": [ "COX15", "CYC3", "ATP25" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:37.544116", "source": { "split": "train_shard_00001", "doc_id": 925 }, "chunk_id": "train_shard_00001_925_0", "global_id": 6974 }, { "text": "

Background

The yeast Kluyveromyces marxianus is an emerging cell factory for heterologous protein biosynthesis and its use holds tremendous advantages for multiple applications. However, which genes influence the productivity of desired proteins in K. marxianus has so far been investigated by very few studies.

Results

In this study, we constructed a K. marxianus recombinant (FIM1/Est1E), which expressed the heterologous ruminal feruloyl esterase Est1E as reporter. UV-60Co-γ irradiation mutagenesis was performed on this recombinant, and one mutant (be termed as T1) was screened and reported, in which the productivity of heterologous Est1E was increased by at least tenfold compared to the parental FIM1/Est1E recombinant. Transcriptional perturbance was profiled and presented that the intracellular vesicle trafficking was enhanced while autophagy be weakened in the T1 mutant. Moreover, whole-genome sequencing combined with CRISPR/Cas9 mediated gene-editing identified a novel functional protein Mtc6p, which was prematurely terminated at Tyr251 by deletion of a single cytosine at 755 loci of its ORF in the T1 mutant. We found that deleting C755 of MTC6 in FIM1 led to 4.86-fold increase in the production of Est1E compared to FIM1, while the autophagy level decreased by 47%; on the contrary, when reinstating C755 of MTC6 in the T1 mutant, the production of Est1E decreased by 66% compared to T1, while the autophagy level increased by 124%", "token_count": 428, "char_count": 1480, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6262, "quality_score": 0.8131, "entities": { "genes": [ "FIM1", "MTC6" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:38.175880", "source": { "split": "train_shard_00001", "doc_id": 926 }, "chunk_id": "train_shard_00001_926_0", "global_id": 6975 }, { "text": "Additionally, in the recombinant with attenuated autophagy (i.e., FIM1 mtc6C755Δ and T1) or interdicted autophagy (i.e., FIM1 atg1Δ and T1 atg1Δ), the productivity of three other heterologous proteins was also increased, specifically the heterologous mannase Man330, the β-1,4-endoxylanase XynCDBFV or the conventional EGFP.

Conclusions

Our results demonstrated that Mtc6p was involved in regulating autophagy; attenuating or interdicting autophagy would dramatically improve the yields of desired proteins in K. marxianus, and this modulation could be achieved by focusing on the premature mutation of Mtc6p target.\n\nMutational Mtc6p attenuates autophagy and improves secretory expression of heterologous proteins in Kluyveromyces marxianus.", "token_count": 233, "char_count": 760, "word_count": 96, "semantic_coherence": 1, "information_density": 0.6979, "quality_score": 0.849, "entities": { "genes": [ "FIM1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:38.641614", "source": { "split": "train_shard_00001", "doc_id": 926 }, "chunk_id": "train_shard_00001_926_1", "global_id": 6976 }, { "text": "Structural variants (SVs, eg. insertions and deletions) are genomic variations > 50 bp that are known to be associated with a range of crop traits, from yield to flowering behaviour and stress responses. Recently, pangenome graphs have emerged as a powerful framework for analysing genomic data by encoding population- or species-level diversity in one data structure. Pangenome graphs have the potential to serve as unbiased references for downstream applications, including SV genotyping and pan-transcriptomic analyses. In this work, we hypothesized that extensive variation affects transcript quantification and expression quantitative trait locus (eQTL) analysis when relying on a single reference, and that using pangenome graphs can mitigate reference sequence bias. We combined long and short read whole genome sequencing data with expression profiling of Brassica napus (oilseed rape) to assess the impact of SVs on gene expression regulation and explored the utility of pangenome graphs for eQTL analysis. We demonstrate that pangenome graphs provides a superior framework for eQTL analysis by eliminating single reference bias in gene expression quantification. Combined with the graph-based genotyping of SVs, we identified 240 eQTL-SVs found in close proximity of target loci. These SVs affect expression of genes related to important traits, are often not in linkage with SNPs and represent diversity unaccounted for in classical SNP-based analyses. This study highlights the multiple advantages of graph-based approaches in population-scale studies and provides novel insight into gene expression regulation in an important crop.\n\nGraphical pangenomics-enabled characterisation of structural variant impact on gene expression in Brassica napus", "token_count": 375, "char_count": 1758, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:39.236775", "source": { "split": "train_shard_00001", "doc_id": 927 }, "chunk_id": "train_shard_00001_927_0", "global_id": 6977 }, { "text": "

Background

Exoinulinase catalyzes the successive removal of individual fructose moiety from the non-reducing end of the inulin molecule, which is useful for biotechnological applications like producing fructan-based non-grain biomass energy and high-fructose syrup. In this study, an exoinulinase (KmINU) from Kluyveromyces marxianus DSM 5418 was tailored for increased catalytic activity and acidic adaptation for inulin hydrolysis processes by rational site-directed mutagenesis.

Results

Three mutations, S124Y, N158S and Q215V distal to the catalytic residues of KmINU were designed and heterologously expressed in Pichia pastoris GS115. Compared to the wild-type, S124Y shifted the pH-activity profile towards acidic pH values and increased the catalytic activity and catalytic efficiency by 59% and 99% to 688.4 ± 17.03 s-1 and 568.93 L mmol-1 s-1 , respectively. N158S improved the catalytic activity under acidic pH conditions, giving a maximum value of 464.06 ± 14.06 s-1 on inulin at pH 4.5. Q215V markedly improved the substrate preference for inulin over sucrose by 5.56-fold, and showed catalytic efficiencies of 208.82 and 6.88 L mmol-1 s-1 towards inulin and sucrose, respectively", "token_count": 463, "char_count": 1275, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8314, "entities": { "genes": [ "GS115" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:39.875430", "source": { "split": "train_shard_00001", "doc_id": 928 }, "chunk_id": "train_shard_00001_928_0", "global_id": 6978 }, { "text": "Molecular modeling and computational docking indicated that structural reorientation may underlie the increased catalytic activity, acidic adaptation and substrate preference.

Conclusions

The KmINU mutants may serve as industrially promising candidates for inulin hydrolysis. Protein engineering of exoinulinase here provides a successful example of the extent to which mutating non-conserved substrate recognition and binding residues distal to the active site can be used for industrial enzyme improvements. © 2020 Society of Chemical Industry.\n\nEngineering better catalytic activity and acidic adaptation into Kluyveromyces marxianus exoinulinase using site-directed mutagenesis.", "token_count": 161, "char_count": 689, "word_count": 84, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:40.337377", "source": { "split": "train_shard_00001", "doc_id": 928 }, "chunk_id": "train_shard_00001_928_1", "global_id": 6979 }, { "text": "The ability of Kluyveromyces marxianus for converting lactose into ethyl acetate offers a chance for the economical reuse of whey. Iron plays a significant role in this process as ester synthesis requires a low intracellular iron content, xFe . The iron content in turn is decreased by growth due to cell expansion and increased by iron uptake. Thus, the iron-uptake rate, ψ, is important for the considered process. Iron uptake by K. marxianus DSM 5422 was studied in aerobic cultivation on a whey-borne medium with varied initial iron content, in part combined with a feed of iron under intensive growth conditions. A possible precipitation of iron that would pretend iron uptake was verified not to have occurred. Regularly measured dissolved iron concentrations, CFe,L , allowed the xFe and ψ parameters to be obtained by model-based iron balancing. The achieved data were used for establishing a ψ(CFe,L , xFe ) model. Mathematical simulations based on this iron-uptake model reproduced the performed cultivation processes. The created iron-uptake model allows for a future predictive system to be developed for the optimization of biotechnological ester production.\n\nUptake of iron by Kluyveromyces marxianus DSM 5422 cultivated in a whey-based medium.", "token_count": 401, "char_count": 1390, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:40.974153", "source": { "split": "train_shard_00001", "doc_id": 929 }, "chunk_id": "train_shard_00001_929_0", "global_id": 6980 }, { "text": "Campylobacteriosis, a prevalent foodborne gastrointestinal infection in Europe, is primarily caused by Campylobacter jejuni and Campylobacter coli, with rising global concerns over antimicrobial resistance in these species. This study comprehensively investigates 133 human-origin Campylobacter spp. strains (102 C. jejuni and 31 C. coli) collected in Italy from 2013 to 2021. The predominant Multilocus Sequence Typing Clonal complexes (CCs) were ST-21 CC and ST-206 CC in C. jejuni and ST-828 CC in C. coli. Ciprofloxacin and tetracycline resistance, mainly attributed to GyrA (T86I) mutation and tet(O) presence, were prevalent, while erythromycin resistance was associated with 23S rRNA gene mutation (A2075G), particularly in C. coli exhibiting multidrug-resistant pattern CipTE. Notable disparities in virulence factors among strains were observed, with C. jejuni exhibiting a higher abundance compared to C. coli. Notably, specific C. jejuni sequence types, including ST-21, ST-5018, and ST-1263, demonstrated significantly elevated counts of virulence genes. This finding underscores the significance of considering both the species and strain-level variations in virulence factor profiles, shedding light on potential differences in the pathogenicity and clinical outcomes associated with distinct C. jejuni lineages. Campylobacter spp. plasmids were classified into three groups comprising pVir-like and pTet-like plasmids families, exhibiting diversity among Campylobacter spp", "token_count": 500, "char_count": 1592, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6869, "quality_score": 0.8434, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:41.661290", "source": { "split": "train_shard_00001", "doc_id": 930 }, "chunk_id": "train_shard_00001_930_0", "global_id": 6981 }, { "text": "The study underscores the importance of early detection through Whole Genome Sequencing to identify potential emergent virulence, resistance/virulence plasmids, and new antimicrobial resistance markers. This approach provides actionable public health data, supporting the development of robust surveillance programs in Italy.\n\nAntibiotic resistance, plasmids, and virulence-associated markers in human strains of Campylobacter jejuni and Campylobacter coli isolated in Italy.", "token_count": 120, "char_count": 489, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8103, "quality_score": 0.9052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:42.097103", "source": { "split": "train_shard_00001", "doc_id": 930 }, "chunk_id": "train_shard_00001_930_1", "global_id": 6982 }, { "text": "Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot on foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onions. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onions and millets or on millets only, respectively. In the current study, we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n = 4) and pv. setariae (n = 13)]. The full spectrum of the pan-genome contained 7030 genes. Among these, 3546 (present in genomes of all 17 strains) were the core genes that were a subset of 3682 soft-core genes (present in ≥16 strains). The accessory genome included 1308 shell genes and 2040 cloud genes (present in ≤2 strains). The pan-genome showed a clear linear progression with >6000 genes, suggesting that the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison with core genome SNPs-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study using Psi strains from both pathovars along with strains from other Pantoea species, namely, P. stewartii subsp", "token_count": 530, "char_count": 1535, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:42.735017", "source": { "split": "train_shard_00001", "doc_id": 931 }, "chunk_id": "train_shard_00001_931_0", "global_id": 6983 }, { "text": "stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfer events occurring between Psi pv. cepacicola and Psi pv. setariae. Pan-GWAS analysis predicted a total of 154 genes, including seven gene-clusters, which were associated with the pathogenicity phenotype (necrosis on seedling) on onions. One of the gene-clusters contained 11 genes with known functions and was found to be chromosomally located.\n\nPan-Genome of Novel Pantoea stewartii subsp. indologenes Reveals Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer.", "token_count": 294, "char_count": 782, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7624, "quality_score": 0.8812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:43.303063", "source": { "split": "train_shard_00001", "doc_id": 931 }, "chunk_id": "train_shard_00001_931_1", "global_id": 6984 }, { "text": "

Background

Although pneumococcal conjugate vaccines (PCVs) effectively prevent invasive pneumococcal disease (IPD), serotype replacement has occurred.

Objectives

We studied the pangenome, antibiotic resistance mechanisms and presence of mobile elements in predominant non-PCV13 serotypes causing adult IPD after PCV13 vaccine introduction in Spain.

Methods

We conducted a multicentre study comparing three periods in six Spanish hospitals and analysed through whole genome sequencing representative strains collected in the pre-PCV13, early-PCV13 and late-PCV13 periods.

Results

Among 2197 cases of adult IPD identified, 110 pneumococci expressing non-PCV13 capsules were sequenced. Seven predominant serotypes accounted for 42.6% of IPD episodes in the late-PCV13 period: serotypes 8 (14.4%), 12F (7.5%), 9N (5.2%), 11A (4.1%), 22F (3.9%), 24F (3.9%) and 16F (3.6%). All predominant non-PCV13 serotypes were highly clonal, comprising one or two clonal complexes (CC). In general, CC538, CC4048, CC3016F, CC43322F and CC669N, related to predominant non-PCV13 serotypes, were antibiotic susceptible. CC15611A was associated with resistance to co-trimoxazole, penicillin and amoxicillin. CC23024F was non-susceptible to penicillin and resistant to erythromycin, clindamycin, and tetracycline. Six composite transposon structures of the Tn5252-family were found in CC23024F, CC98912F and CC3016F carrying different combinations of erm(B), tet(M), and cat", "token_count": 516, "char_count": 1480, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7418, "quality_score": 0.8709, "entities": { "genes": [ "PCV13", "CC23024F", "CC538", "CC4048", "CC15611A", "CC98912F", "CC43322F", "CC669N", "CC3016F" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:43.959546", "source": { "split": "train_shard_00001", "doc_id": 932 }, "chunk_id": "train_shard_00001_932_0", "global_id": 6985 }, { "text": "Pangenome analysis revealed differences in accessory genomes among the different CC, with most variety in CC3016F (23.9%) and more conservation in CC15611A (8.5%).

Conclusions

We identified highly clonal predominant serotypes responsible for IPD in adults. The detection of not only conjugative elements carrying resistance determinants but also clones previously associated with vaccine serotypes (CC15611A and CC23024F) highlights the importance of the accessory genome.\n\nGenomic features of predominant non-PCV13 serotypes responsible for adult invasive pneumococcal disease in Spain.", "token_count": 159, "char_count": 594, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7733, "quality_score": 0.8867, "entities": { "genes": [ "PCV13", "CC15611A", "CC23024F", "CC3016F" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:44.404640", "source": { "split": "train_shard_00001", "doc_id": 932 }, "chunk_id": "train_shard_00001_932_1", "global_id": 6986 }, { "text": "The bacterial pangenome encodes an immense array of antiphage systems, yet much of their diversity remains uncharted. In this study, we developed language models to predict novel antiphage proteins in two ways: first via fine-tuning ESM2, a protein language model capable of detecting distant homology to known defense proteins, second via a genomic language model with ALBERT architecture which predicts defensive function based on genomic context. We demonstrate that applying these approaches to Actinomycetota - a phylum largely unexplored for antiphage defenses, can accurately predict previously unknown functional defense mechanisms, leading to the discovery and experimental validation of six defense systems with novel antiphage proteins. Analysis of over 30,000 bacterial genomes predicted more than 45,000 uncharacterized protein families potentially involved in antiphage defense, underscoring the vast, untapped diversity of these systems.\n\nProtein and genomic language models chart a vast landscape of antiphage defenses", "token_count": 224, "char_count": 1034, "word_count": 143, "semantic_coherence": 1, "information_density": 0.7133, "quality_score": 0.8566, "entities": { "genes": [ "ESM2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:44.874321", "source": { "split": "train_shard_00001", "doc_id": 933 }, "chunk_id": "train_shard_00001_933_0", "global_id": 6987 }, { "text": "Enterotoxigenic Escherichia coli (ETEC) is the primary aetiologic agent of traveller's diarrhoea and a significant cause of diarrhoeal disease and death in developing countries. ETEC O169:H41 strains are known to cause both traveller's diarrhoea and foodborne outbreaks in developed countries and are cause for concern. Here, whole-genome sequencing (WGS) was used to assemble 46 O169:H41 (ST182) E. coli draft genomes derived from two airplane waste samples sourced from a German international airport. The ST182 genomes were compared with all 84 publicly available, geographically diverse ST182 genomes to construct a core genome-based phylogenetic tree. ST182 isolates were all phylogroup E, the majority serotype O169:H41 (n = 121, 93%) and formed five major clades. The airplane waste isolates differed by an average of 15 core SNPs (range 0-45) but their accessory genome content was diverse", "token_count": 286, "char_count": 918, "word_count": 133, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [ "ST182" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:45.438190", "source": { "split": "train_shard_00001", "doc_id": 934 }, "chunk_id": "train_shard_00001_934_0", "global_id": 6988 }, { "text": "While uncommon in other ST182 genomes, all airplane-derived ST182 isolates carried: (i) extended-spectrum β-lactamase gene bla CTX-M- 15 notably lacking the typical adjacent ISEcp1; (ii) qnrS1 and the S83L mutation in gyrA, both conferring resistance to fluoroquinolones; and (iii) a class 1 integron structure (IS26-intI1 Δ 648-dfrA17-aadA5-qacEΔ1-sul1-ORF-srpC-padR-IS6100-mphR-mrx-mphA-IS26) identified previously in major extraintestinal pathogenic E. coli STs but not in ETEC. ST182 isolates carried ETEC-specific virulence factors STp + CS6. Adhesin/invasin tia was identified in 89% of aircraft ST182 isolates (vs 23%) and was located on a putative genomic island within a hotspot region for various insertions including PAI I536 and plasmid-associated transposons. The most common plasmid replicons in this collection were IncFII (100%; F2:A-:B-) and IncB/O/K/Z (89%). Our data suggest that potentially through travel, E. coli ST182 are evolving a multidrug-resistant profile through the acquisition of class 1 integrons and different plasmids.", "token_count": 517, "char_count": 1254, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7887, "quality_score": 0.8944, "entities": { "genes": [ "ST182", "CS6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:46.084322", "source": { "split": "train_shard_00001", "doc_id": 934 }, "chunk_id": "train_shard_00001_934_1", "global_id": 6989 }, { "text": "Multidrug-Resistant Lineage of Enterotoxigenic Escherichia coli ST182 With Serotype O169:H41 in Airline Waste.", "token_count": 48, "char_count": 117, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST182" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:46.440848", "source": { "split": "train_shard_00001", "doc_id": 934 }, "chunk_id": "train_shard_00001_934_2", "global_id": 6990 }, { "text": "Determining the intricate tapestry of human genetic relationships is a central challenge in population genetics and precision medicine. We propose that the principles of lexical connectivity, which words derive meaning from their contextual interactions, can be adapted to genetic data, enabling transformer models to reveal that individuals with higher genetic similarity form stronger latent connections. We explored this by transposing KING kinship-related matrices into the (query, key, value) QKV latent space within transformer models and determined that attention mechanisms can capture genetic relatedness in an unsupervised fashion. We found that individuals had an attention weight connectivity of 85.34% (p<0.05) if they were from within the same continent, compared to if they were from other continents. Surprisingly, we found that some encoder layers required inversion of their latent representations for this connectivity to become obvious. Lastly, we used BERTViz to create human-readable hyper-dense connectivity patterns among individuals. Our approach is purely based on attention, which yields a non-discrete spectrum of relatedness, and thus uncovers patterns on first principles. Seq2KING addresses the significant challenge of discovering population structures to construct a global human relatedness map, without relying on predefined labels. Our excavation into the latent space is a paradigm shift from legacy-supervised genetic methodologies, which presents a new way to understand the human pangenome as well as discern population substructures for creating precision genetic medicines.

Non-Expert Description

Is it possible to build artificial intelligence (AI) to read the human genome as a first language. Why would one want such AI. We at Ecotone believe that such AI will provide the genetic coordinates needed to manufacture CRISPRs medications to cure about ∼10,000 genetic diseases. How does one build such AI. Our recently released model dnaSORA proposed a means to assign meaning to every single token (typically referred to as a base) of all 3 billion tokens in the human genome (Koreniuk & Njie, 2025). This builds the vocabulary for reading the human genome as a first language. For dnaSORA to work, it needs to know the heritages of people that are in its model of our genetics", "token_count": 518, "char_count": 2330, "word_count": 344, "semantic_coherence": 1, "information_density": 0.6134, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:47.072443", "source": { "split": "train_shard_00001", "doc_id": 935 }, "chunk_id": "train_shard_00001_935_0", "global_id": 6991 }, { "text": "We mostly rely on country, culture and geography to determine our heritages, but this is too error-prone for dnaSORA. Also error-prone in our experience are legacy genetic approaches such as those used by 23andMe. Our research here introduces Seq2KING, a new artificial intelligence method that is based on excavating the insides of transformers to uncover hidden patterns of genetic relatedness among people around the world—without needing any prior labels or categorizations. The key innovation of Seq2KING is applying the principles of lexical connectivity— how words derive meaning through their relationships to other words—to genetic data. Just as “dog” gains meaning through its connections to words like “pet,” “animal,” and “loyal,” we show that individuals’ genomes can be understood through their genetic connections to others. We start by converting raw genetic data into a compact kinship matrix (using a tool called KING) that summarizes how closely everyone is related. We then feed these kinship values into a transformer model—the same kind of AI behind cutting-edge language tools like ChatGPT. Inside the transformer, special components called “attention heads” learn which individuals are most similar, strengthening links between people from the same region and showing subtler connections across continents. Unlike legacy approaches that rely on discrete pre-defined categories, Seq2KING provides continuous measures of relatedness, allowing us to visualize connections between any individual and all other humans. Additionally, because Seq2KING operates directly within the transformer’s internal reasoning system, it can be seamlessly integrated as a component within larger genome interpretation systems—essentially functioning like high-speed cache memory for heritage assignments, dramatically improving both efficiency and scalability. By examining these attention patterns, we can reconstruct familiar population groupings—such as European, African, and Asian heritage—entirely by the model’s internal logic. Finally, we use a visualization technique (BERTViz) to turn these dense connection maps into intuitive diagrams that highlight population connections between individuals. Because our approach doesn’t rely on pre-assigned labels, it offers a truly unbiased way to explore human population structure. This could help scientists trace migration routes that resulted in the peopling of the continents, find subtle subgroups within larger populations, and remove “background noise” in genetic studies of disease", "token_count": 514, "char_count": 2545, "word_count": 354, "semantic_coherence": 1, "information_density": 0.6836, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:47.713684", "source": { "split": "train_shard_00001", "doc_id": 935 }, "chunk_id": "train_shard_00001_935_1", "global_id": 6992 }, { "text": "Ultimately, Seq2KING paves the way for more precise genetic maps of all humans, revealing the natural “family trees” hidden in our DNA and bringing us one step closer to reading the human genome as a first language.\n\nSeq2KING: An unsupervised internal transformer representation of global human heritages", "token_count": 70, "char_count": 304, "word_count": 47, "semantic_coherence": 1, "information_density": 0.9149, "quality_score": 0.9574, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:48.083275", "source": { "split": "train_shard_00001", "doc_id": 935 }, "chunk_id": "train_shard_00001_935_2", "global_id": 6993 }, { "text": "Bacterial spot disease, caused by Xanthomonas species, is a significant threat to tomato and pepper production worldwide. This study aims to characterise these pathogens and evaluate their genomic diversity in Thailand. Sixty bacterial strains were isolated from symptomatic tomatoes and peppers across Thailand from 1987 to 2022. Morphological, physiological, biochemical, pathological and species‐specific PCR analyses identified these strains as X. euvesicatoria pv. euvesicatoria (Xee) and X. euvesicatoria pv. perforans (Xep). Genome sequence analysis, including pairwise average nucleotide identity (ANI) and in silico DNA–DNA hybridisation (isDDH), revealed high genetic similarity to Xee‐ and Xep‐type strains, with ANI values above 98.6% and isDDH values higher than 97%. ANI values exceeding 99% supported distinguishing pathovars within X. euvesicatoria. Core genome phylogeny of 60 Thai Xanthomonas genomes and 121 Xanthomonas genomes from GenBank (NCBI) showed that 30 Thai strains clustered with Xee strains, while 29 clustered with Xep strains. The pan‐genome analysis of these Xanthomonas strains further supported the core genome phylogeny. Additionally, individual core genome phylogeny categorised the Thai strains into three groups within Xee and three groups within Xep, some of which correlate to geographical location. The pan‐genome of individual Xee and Xep strains contains 8222 and 8413 predicted genes, respectively, with 61.3% and 61.8% identified as accessory genes, reflecting the genetic diversity within species. These findings offer valuable insights into the genetic diversity of Xee and Xep strains in Thailand, contributing to the development of more effective disease management strategies.\n\nCharacterisation and Genomic Diversity of Xanthomonas Species Causing Bacterial Spot Disease of Tomato and Pepper in Thailand", "token_count": 495, "char_count": 1855, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:48.738757", "source": { "split": "train_shard_00001", "doc_id": 936 }, "chunk_id": "train_shard_00001_936_0", "global_id": 6994 }, { "text": "Clostridioides difficile, a zoonotic pathogen causing enteric diseases in different animals and humans. A comprehensive study on the presence of toxin genes and antimicrobial resistance genes based on genome data of C. difficile in animals is scanty. In the present study, a total of 15 C. difficile isolates were recovered from dogs and isolates with toxin genes (D1, CD15 and CD26) along with two other non-toxigenic strains (CD28, CD32) were used for whole genome sequencing and comparative genomics. Sequence type-based clustering was noted in the whole genome phylogeny with 4 known multi-locus sequence typing (MLST) clades namely I, II, IV, and V and a cryptic clade. ST11 and ST54 were reported for the 2nd time worldwide in dogs. Out of 109 genomes used in the study, 29 genomes were predicted with all four toxin genes (toxA, toxB, cdtA, cdtB) while 22 did not have any of the toxin genes. ST11 of MLST clade V had the maximum number of 46 genomes predicted with at least one toxin gene. Among the genomes sequenced in this study, CD26 had a maximum of 5 AMR genes (aac(6')-aph(2″), ant(6)-Ia, catP, erm(B)_18, and tet(M)_11) and CD15 was predicted with 2 AMR genes (aac(6')-aph(2″), erm(B)_18). Tetracycline resistance genes were predicted most in the ST11 genome", "token_count": 482, "char_count": 1383, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5981, "quality_score": 0.799, "entities": { "genes": [ "ST54", "CD28", "CD26", "CD15", "ST11", "CD32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:49.390075", "source": { "split": "train_shard_00001", "doc_id": 937 }, "chunk_id": "train_shard_00001_937_0", "global_id": 6995 }, { "text": "Of the 22 non-toxigenic strains, 9 genomes (ST48 = 5, ST3 = 2, ST109 = 1, ST15 = 1) were predicted with a minimum of one AMR gene. Pangenome analysis indicated that the Bpan value is 0.12 showing that C. difficile has an open pangenome structure. This indicates that the organism can evolve by the addition of new genes. This study reports the circulation of clinically important ST11 and multidrug-resistant non-toxigenic strains among animals.

Supplementary information

The online version contains supplementary material available at 10.1007/s13205-024-04102-7.\n\nComparative genomics of zoonotic pathogen <i>Clostridioides difficile</i> of animal origin to understand its diversity.", "token_count": 257, "char_count": 717, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8247, "quality_score": 0.9124, "entities": { "genes": [ "ST3", "ST48", "ST109", "ST11", "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:49.931797", "source": { "split": "train_shard_00001", "doc_id": 937 }, "chunk_id": "train_shard_00001_937_1", "global_id": 6996 }, { "text": "Streptococci are one of the predominant and the most diverse genus in the human lung. Previously, we isolated human distal lung Streptococci from bronchoalvolear lavage fluid (BALF) as part of the human Lung Microbiota culture Collection (LuMiCol). Here, we performed whole genome sequencing, comparative phylogenomics and phenotypic characterization of six Streptococcal isolates representing the phylogenetic diversity of the genus in distal human lung. Here, we report five new species and one new subspecies including phylogenetic intermediates of commonly found Streptococci not limited to human lung. Pangenome analysis reveals gene content, evolutionary relationships, and metabolic functions shedding light on contribution of these Streptococci to lung microbial metabolism. Antimicrobial resistance gene analysis followed by MIC determination revealed macrolide, lincosamide and tetracycline resistance in lung Streptococci. We show the presence of capsular genes in lung streptococci both matching to the prototypical capsular genes ( cps ) and unique genes. Interestingly, the new Streptococcus isolate sp. nov. P2E5, genetically identical to the most prevalent Streptococcus in the human distal lung was revealed to be a phylogenetic intermediate between the S. mitis group and S. pneumoniae. It also harbors the pneumolysin ( ply ) gene and was found to have the serotype 21E. Finally, core genome phylogeny reveals that lung Streptococci the are evolutionary distinct from oral Streptococcal isolates in expanded Human Oral Microbiome Database (eHOMD). Hence, these findings we reveal new phylogenetically distinct Streptococcal species from the human distal lung microbiota and its genetic diversity and metabolism to understand the microbial ecology of human lung.

Importance

A healthy human distal lung harbour characteristic microbial communities mostly composed of oropharyngeal taxa, which are facultative or obligative anaerobes despite lung being the medium of oxygen intake", "token_count": 513, "char_count": 2005, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5679, "quality_score": 0.7839, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:03:50.589792", "source": { "split": "train_shard_00001", "doc_id": 938 }, "chunk_id": "train_shard_00001_938_0", "global_id": 6997 }, { "text": "However, little is known about the genetic and functional diversity of these bacteria owing to the lack of resources including availability of primary lung isolate from human samples. Therefore, we have established a large bacterial collection that covers all major phyla by cultivating human bronchoalveolar lavage fluid (BALF) under various conditions. Streptococcus is the most prevalent and diverse genera in the human lung microbiota. Using genetic and biochemical approaches, we studied six diverse lung isolates from our collection representing the actual Streptococcal diversity and identify these as new species and subspecies. We hypothesize that learning about the phylogenetic genetic diversity, preferred metabolism and molecular structures of these Streptococci will provide with new insights on the understudied microbial ecosystem of the human lung.\n\nComparative genomic analysis reveals novel phylogenetically intermediate Streptococci with high phenotypic diversity in the human distal lung microbiota", "token_count": 217, "char_count": 1019, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:51.050668", "source": { "split": "train_shard_00001", "doc_id": 938 }, "chunk_id": "train_shard_00001_938_1", "global_id": 6998 }, { "text": "This study provides an in-depth genome analysis of Bacillus paralicheniformis AA1, a bacterial strain isolated from a traditional milpa farming system in Sonora, Mexico. The genomic investigation revealed a high level of completeness, demonstrated by the presence of a diverse and functionally significant repertoire of genes associated with fundamental biological processes, including nutrient assimilation, stress response, and cellular regulation. Notably, the genome also contains genes responsible for the biosynthesis of secondary metabolites, highlighting its potential for biotechnological applications. Taxonomic classification was rigorously conducted using integrated genome-wide approaches, which definitively confirmed the identification of isolate AA1 as belonging to the species Bacillus paralicheniformis. Comparative genomic analysis further established a high degree of genetic similarity between AA1 and other B. paralicheniformis strains with well-characterized biotechnological capabilities. This similarity strongly suggests that AA1 harbors genetic elements responsible for the synthesis of antimicrobial compounds, enzymes with industrial relevance, and metabolites that promote plant growth. The findings underscore the potential of Bacillus paralicheniformis AA1 as a valuable resource for biotechnology and sustainable agriculture. By enhancing our understanding of microbial diversity within traditional agroecosystems, this study contributes to the broader knowledge base required for the development of innovative agricultural practices. Future research should focus on functional validation of key genes to fully unlock AA1 potential as a bioresource for antimicrobial production, enzyme synthesis, and crop enhancement, paving the way for its application in environmentally sustainable farming systems.\n\nGenome Analysis of Bacillus paralicheniformis AA1 isolated from a conventional milpa farming system in the northwestern region of Sonora, Mexico", "token_count": 405, "char_count": 1980, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [ "AA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:51.672394", "source": { "split": "train_shard_00001", "doc_id": 939 }, "chunk_id": "train_shard_00001_939_0", "global_id": 6999 }, { "text": "

Aims

We aimed to determine the genetic relatedness among β-lactamase-producing Escherichia coli isolated from soil, lake water, and feces of geese, pigs, dogs, cattle, coyotes, wild hogs, and horses at one health interface in West Texas.

Methods and results

Previously isolated 56 β-lactamase-producing E. coli isolates from the feces of geese, pigs, horses, coyotes, dogs, cattle, and wild hogs, and soil and lake water from different locations in West Texas were analyzed for genetic relatedness using whole-genome sequencing, core genome multilocus sequence typing, and phylogenetic single-nucleotide polymorphism (SNP) analysis using the publicly available bioinformatic platforms. Among 56 β-lactamase-producing E. coli isolates, 82.1% carried blaCTX-M genes, 42.86% carried blaTEM genes, 7.14% carried blaOXA-10, and 3.57% contained blaCMY-2 genes. Nine different types of phylogroups, 35 serotypes and 36 sequence types, 32 distinct plasmid groups, 75 types of virulence genes, and 46 core genome multilocus sequence types were identified. Using 100 maximum of SNPs between the isolates to define a clone, 14 clones were identified in 13 E. coli isolates from animal feces and environmental samples. The clonally related E. coli isolates were clustered based on the phylogenetic tree.

Conclusion

The findings from this study provide limited evidence of clonal dissemination of β-lactamase-producing E. coli between different animal sources.\n\nGenetic relatedness and antimicrobial resistance profiles of β-lactamase-producing Escherichia coli from environmental and animal sources in West Texas: a One Health approach.", "token_count": 494, "char_count": 1646, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5695, "quality_score": 0.7848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:53.033116", "source": { "split": "train_shard_00001", "doc_id": 940 }, "chunk_id": "train_shard_00001_940_0", "global_id": 7000 }, { "text": "Yeast is one of the microorganisms widely used in fermentation industry, and its high temperature resistance plays an important role in fermentation. However, the complex regulatory process of cell tolerance to heat stress has not been fully understood. Therefore, this study carried out basic research on high temperature resistant yeast at 28℃, 37℃ and 43℃, including morphological observation, determination of trehalose content and cell membrane permeability, and combined with RNA-seq technology to screen differentially expressed genes in yeast responding to high temperature stress at the transcriptome level. The results showed that under heat treatment conditions, the macroscopic and microscopic morphology of yeast cells were changed, the selective permeability of cell membrane was changed, and the intracellular trehalose was accumulated. Different nitrogen sources and inorganic salt ions can improve the high temperature tolerance of yeast ZG-3. In addition, a total of 517 differentially expressed genes were screened by comparing the temperature resistant yeast at 28℃ with that at 37℃, among which 435 genes were up-regulated and 82 genes were down-regulated. A total of 632 differentially expressed genes were screened at 37℃ compared with that at 43℃, among which 393 genes were up-regulated and 239 genes were down-regulated. Among them, SSA3 , SSA4 , HSP82 , SSE1 , KAR2 , FES1 , HSP26 , HSP42 genes of the heat shock protein family were significantly up-regulated, which improved the basic and acquired heat tolerance of yeast. This study combined physical and chemical properties analysis and transcriptome analysis to preliminarily explore the differentially expressed genes in yeast in response to high temperature stress, which provides a theoretical basis for further study of yeast high temperature tolerance.\n\nTranscriptome research on differentially expressed genes in a thermotolerant yeast strain from Daqu of Luzhou-flavor liquors", "token_count": 462, "char_count": 1964, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5208, "quality_score": 0.7604, "entities": { "genes": [ "SSA4", "SSA3", "HSP82", "HSP26", "FES1", "SSE1", "KAR2", "HSP42" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:53.711149", "source": { "split": "train_shard_00001", "doc_id": 941 }, "chunk_id": "train_shard_00001_941_0", "global_id": 7001 }, { "text": "Acinetobacter baumannii is an opportunistic bacterium that causes hospital-acquired infections with a high mortality and morbidity, since there are strains resistant to virtually any kind of antibiotic. The chase to find novel strategies to fight against this microbe can be favoured by knowledge of the complete catalogue of genes of the species, and their relationship with the specific characteristics of different isolates. In this work, we performed a genomics analysis of almost 2500 strains. Two different groups of genomes were found based on the number of shared genes. One of these groups rarely has plasmids, and bears clustered regularly interspaced short palindromic repeat (CRISPR) sequences, in addition to CRISPR-associated genes (cas genes) or restriction-modification system genes. This fact strongly supports the lack of plasmids. Furthermore, the scarce plasmids in this group also bear CRISPR sequences, and specifically contain genes involved in prokaryotic toxin-antitoxin systems that could either act as the still little known CRISPR type IV system or be the precursors of other novel CRISPR/Cas systems. In addition, a limited set of strains present a new cas9-like gene, which may complement the other cas genes in inhibiting the entrance of new plasmids into the bacteria. Finally, this group has exclusive genes involved in biofilm formation, which would connect CRISPR systems to the biogenesis of these bacterial resistance structures.\n\nPangenome of Acinetobacter baumannii uncovers two groups of genomes, one of them with genes involved in CRISPR/Cas defence systems associated with the absence of plasmids and exclusive genes for biofilm formation.", "token_count": 415, "char_count": 1716, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6265, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:54.360014", "source": { "split": "train_shard_00001", "doc_id": 942 }, "chunk_id": "train_shard_00001_942_0", "global_id": 7002 }, { "text": "To investigate the use of yeasts and lactic acid bacteria from natural kefir grain in bread making and its effects on dough and bread quality. The kefir grains were treated with different food‐based solutions to enrich the yeast content. Three kefir samples were produced with the treated grains (KAL and SIT) and the control (KEF) kefir grains (untreated). The yeasts isolated from the kefir samples were identified as Saccharomyces cerevisiae and Kluyveromyces marxianus. The microbial and chemical properties were compared with the sourdough sample made with baker's yeast (CON). The amounts of lactic acid and acetic acid varied from 0.51 to 2.99 and 0.20 to 1.0 g/kg, respectively. The concentration of aromatic substances such as ethanol, acetaldehyde, and acetone were determined. The SIT bread achieved the highest sensory score. The kefir grains could be an important natural source in sourdough bread making. NOVELTY IMPACT STATEMENT: It was determined that kefir produced from kefir grains can be an important natural source in sourdough bread making. Microbial and sensory properties of sourdough breads were improved. It was shown that some microorganisms in kefir grain natural microbiota could be used for different food fermentations.\n\nThe use of yeast‐rich kefir grain as a starter culture in bread making", "token_count": 343, "char_count": 1322, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5196, "quality_score": 0.7598, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:54.941444", "source": { "split": "train_shard_00001", "doc_id": 943 }, "chunk_id": "train_shard_00001_943_0", "global_id": 7003 }, { "text": "Streptococcus gallolyticus, formerly known as Streptococcus bovis, is a Gram-positive coccus bacterium that is a facultative anaerobe. Although it was previously considered a commensal bacterium that caused secondary disease because of a stressor, S. gallolyticus can now be considered a causative agent of disease associated with a variety of infections in both humans and animals. Streptococcus gallolyticus has become an emerging pathogen in the poultry industry, particularly in turkey poults, causing acute mortality, usually without any premonitory signs. In the southern portion of the United States, there has been an influx of S. gallolyticus infections occurring predominately in July and August. A majority of turkey poults most susceptible to this disease range in age between 1.5 and 2.5 wk of age. It is suggested that virulence capability relies on accessory genome components that may not be core to all S. gallolyticus strains. In this review, we aim to provide an overview of the nomenclature changes, identification, and emergence of S. gallolyticus in turkeys.\n\nThe Emergence of <i>Streptococcus gallolyticus</i> as a Pathogen in Turkeys.", "token_count": 349, "char_count": 1219, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6358, "quality_score": 0.8179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:55.515322", "source": { "split": "train_shard_00001", "doc_id": 944 }, "chunk_id": "train_shard_00001_944_0", "global_id": 7004 }, { "text": "FIM-1 is an acquired metallo-β-lactamase identified in a multidrug-resistant Pseudomonas aeruginosa (index strain FI-14/157) of clinical origin isolated in 2007 in Florence, Italy. Here we report on a second case of infection by FIM-1-positive P. aeruginosa (FI-17645), which occurred in 2020 in the same hospital. Both FIM-1-positive strains exhibited resistance to all anti-Pseudomonas antibiotics except colistin and cefiderocol. Comparative genomic characterization revealed that the two FIM-positive strains were closely related [core genome difference, 16 single nucleotide polymorphisms (SNPs)], suggesting a local circulation of similar strains. In the FI-14/157 index strain, the blaFIM-1 gene was associated with an ISCR19-like element that likely contributed to its capture downstream an integron platform inserted aboard a Tn21-like transposon, named Tn7703.1, which was associated with a large integrative and conjugative element (ICE) named ICE7705.1, integrated into an att site located within the 3'-end of tRNAGly CCC gene of the P. aeruginosa chromosome. In strain FI-17645, blaFIM-1 was associated with a closely related ICE, named ICE7705.2, integrated in the same chromosomal site. Similar ICE platforms, lacking the blaFIM-1-containing region, were detected in other ST235 P", "token_count": 490, "char_count": 1441, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6983, "quality_score": 0.8492, "entities": { "genes": [ "CR19", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:56.166992", "source": { "split": "train_shard_00001", "doc_id": 945 }, "chunk_id": "train_shard_00001_945_0", "global_id": 7005 }, { "text": "aeruginosa strains from different geographic areas, suggesting a common ancestry and underscoring the role of these elements in the dissemination of resistance genes in P. aeruginosa. Sequence database mining revealed two draft P. aeruginosa genomes, one from Italy and one from the USA (both isolated in 2012), including a contig with blaFIM-1, suggesting that this resistance gene could have a broader distribution than originally anticipated.\n\nNovel resistance ICEs carrying the <i>bla</i><sub>FIM-1</sub> metallo-β-lactamase gene from an ST235 <i>Pseudomonas aeruginosa</i> sublineage.", "token_count": 208, "char_count": 661, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7595, "quality_score": 0.8797, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:56.625749", "source": { "split": "train_shard_00001", "doc_id": 945 }, "chunk_id": "train_shard_00001_945_1", "global_id": 7006 }, { "text": "

Background

To date genomic studies on Map have concentrated on Type C strains with only a few Type S strains included for comparison. In this study the entire pan-genome of 261 Map genomes (205 Type C, 52 Type S and 4 Type B) and 7 Mycobacterium avium complex (Mac) genomes were analysed to identify genomic similarities and differences between the strains and provide more insight into the evolutionary relationship within this Mycobacterial species.

Results

Our analysis of the core genome of all the Map isolates identified two distinct lineages, Type S and Type C Map that is consistent with previous phylogenetic studies of Map. Pan-genome analysis revealed that Map has a larger accessory genome than Mycobacterium avium subsp. avium (Maa) and Type C Map has a larger accessory genome than Type S Map. In addition, we found large rearrangements within Type S strains of Map and little to none in Type C and Type B strains. There were 50 core genes identified that were unique to Type S Map and there were no unique core genes identified between Type B and Type C Map strains. In Type C Map we identified an additional CE10 CAZyme class which was identified as an alpha/beta hydrolase and an additional polyketide and non-ribosomal peptide synthetase cluster. Consistent with previous analysis no plasmids and only incomplete prophages were identified in the genomes of Map. There were 45 hypothetical CRISPR elements identified with no associated cas genes.

Conclusion

This is the most comprehensive comparison of the genomic content of Map isolates to date and included the closing of eight Map genomes. The analysis revealed that there is greater variation in gene synteny within Type S strains when compared to Type C indicating that the Type C Map strain emerged after Type S. Further analysis of Type C and Type B genomes revealed that they are structurally similar with little to no genetic variation and that Type B Map may be a distinct clade within Type C Map and not a different strain type of Map. The evolutionary lineage of Maa and Map was confirmed as emerging after M. hominissuis.", "token_count": 509, "char_count": 2124, "word_count": 348, "semantic_coherence": 1, "information_density": 0.4339, "quality_score": 0.717, "entities": { "genes": [ "CE10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:57.276382", "source": { "split": "train_shard_00001", "doc_id": 946 }, "chunk_id": "train_shard_00001_946_0", "global_id": 7007 }, { "text": "The pan-genome of Mycobacterium avium subsp. paratuberculosis (Map) confirms ancestral lineage and reveals gene rearrangements within Map Type S.", "token_count": 43, "char_count": 145, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:57.635860", "source": { "split": "train_shard_00001", "doc_id": 946 }, "chunk_id": "train_shard_00001_946_1", "global_id": 7008 }, { "text": "

Background

Streptomyces is a highly diverse genus known for the production of secondary or specialized metabolites with a wide range of applications in the medical and agricultural industries. Several thousand complete or nearly-complete Streptomyces genome sequences are now available, affording the opportunity to deeply investigate the biosynthetic potential within these organisms and to advance natural product discovery initiatives.

Result

We performed pangenome analysis on 2,371 Streptomyces genomes, including approximately 1,200 complete assemblies. Employing a data-driven approach based on genome similarities, the Streptomyces genus was classified into 7 primary and 42 secondary MASH-clusters, forming the basis for a comprehensive pangenome mining. A refined workflow for grouping biosynthetic gene clusters (BGCs) redefined their diversity across different MASH-clusters. This workflow also reassigned 2,729 known BGC families to only 440 families, a reduction caused by inaccuracies in BGC boundary detections. When the genomic location of BGCs is included in the analysis, a conserved genomic structure (synteny) among BGCs becomes apparent within species and MASH-clusters. This synteny suggests that vertical inheritance is a major factor in the acquisition of new BGCs.

Conclusion

Our analysis of a genomic dataset at a scale of thousands of genomes refined predictions of BGC diversity using MASH-clusters as a basis for pangenome analysis. The observed conservation in the order of BGCs’ genomic locations showed that the BGCs are vertically inherited. The presented workflow and the in-depth analysis pave the way for large-scale pangenome investigations and enhance our understanding of the biosynthetic potential of the Streptomyces genus.\n\nPangenome mining of theStreptomycesgenus redefines their biosynthetic potential", "token_count": 456, "char_count": 1880, "word_count": 254, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:58.273011", "source": { "split": "train_shard_00001", "doc_id": 947 }, "chunk_id": "train_shard_00001_947_0", "global_id": 7009 }, { "text": "

Background

Multiple sequence alignment (MSA) has proven extremely useful in computational biology, especially in inferring evolutionary relationships via phylogenetic analysis and providing insight into protein structure and function. An alternative to the standard MSA model is partial order alignment (POA), in which aligned sequences are represented as paths in a graph rather than rows in a matrix. While the POA model has proven useful in several applications (e.g. sequencing reads assembly and pangenome structure exploration), we lack efficient visualization tools that could highlight its advantages.

Results

We propose Sequence Flow - a web application designed to address the above problem. Sequence Flow presents the POA as a Sankey diagram, a kind of graph visualisation typically used for graphs representing flowcharts. Sequence Flow enables interactive alignment exploration, including fragment selection, highlighting a selected group of sequences, modification of the position of graph nodes, structure simplification etc. After adjustment, the visualization can be saved as a high-quality graphic file. Thanks to the use of SanKEY.js - a JavaScript library for creating Sankey diagrams, designed specifically to visualize POAs, Sequence Flow provides satisfactory performance even with large alignments.

Conclusions

We provide Sankey diagram-based POA visualization tools for both end users (Sequence Flow) and bioinformatic software developers (SanKEY.js). Sequence Flow webservice is available at https://sequenceflow.mimuw.edu.pl/ . The source code for SanKEY.js is available at https://github.com/Krzysiekzd/SanKEY.js and for Sequence Flow at https://github.com/Krzysiekzd/SequenceFlow .\n\nSequence Flow: interactive web application for visualizing partial order alignments.", "token_count": 395, "char_count": 1818, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:58.889203", "source": { "split": "train_shard_00001", "doc_id": 948 }, "chunk_id": "train_shard_00001_948_0", "global_id": 7010 }, { "text": "The World Health Organization included Cryptococcus neoformans and Cryptococcus gattii in its priority fungal pathogen list due to their high mortality rates and frequent treatment failures. These facts have driven research toward the discovery of new compounds for the treatment of cryptococcosis. In this study, we investigated the therapeutic potential of two complexes, [Cu(phendione)3](ClO4)2·4H2O (Cu-phendione) and [Ag(phendione)2]ClO4 (Ag-phendione), against drug-resistant clinical isolates of C. gattii and C. neoformans. Both complexes demonstrated anti-Cryptococcus activity, with Cu-phendione exhibiting minimum inhibitory concentration (MIC) values of 6.25 μM for C. gattii and 3.125 μM for C. neoformans, while Ag-phendione showed an MIC of 1.56 μM for both Cryptococcus species. Notably, both Cu-phendione and Ag-phendione complexes exhibited enhanced antifungal activity against reference strains of C. neoformans and C. gattii. In silico analysis identified both complexes as highly promising, exhibiting good oral bioavailability, high gastrointestinal absorption, and moderate skin permeability. Moreover, neither complex demonstrated toxicity toward sheep erythrocytes at concentrations up to 62.5 μM, with a selectivity index (SI) exceeding 10 for Cu-phendione and 40 for Ag-phendione", "token_count": 470, "char_count": 1442, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6959, "quality_score": 0.848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:03:59.531288", "source": { "split": "train_shard_00001", "doc_id": 949 }, "chunk_id": "train_shard_00001_949_0", "global_id": 7011 }, { "text": "In vivo testing using the Galleria mellonella model demonstrated that both complexes were non-toxic, with 100% larval survival at concentrations up to 1000 μM and SI exceeding 160 following a single administration. Interestingly, larvae exposed to Cu-phendione at concentrations of 15.6-31.25 μM exhibited a significant increase in the density of hemocytes, the immune cells responsible for defense in invertebrates. Furthermore, multiple treatments with 62.5 μM of complexes caused either no larval mortality, hemocyte alterations, or changes in silk production or coloration, indicating a lack of toxicity. These findings suggest that Cu-phendione and Ag-phendione may serve as promising antifungal alternatives against Cryptococcus, with minimal host toxicity.\n\nToxicity Assessment and Antifungal Potential of Copper(II) and Silver(I) Complexes with 1,10-Phenanthroline-5,6-dione Against Drug-Resistant Clinical Isolates of <i>Cryptococcus gattii</i> and <i>Cryptococcus neoformans</i>.", "token_count": 318, "char_count": 1027, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7323, "quality_score": 0.8661, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:00.087336", "source": { "split": "train_shard_00001", "doc_id": 949 }, "chunk_id": "train_shard_00001_949_1", "global_id": 7012 }, { "text": "Wild Malus species flourished in North America long before Europeans introduced domesticated apples. Malus coronaria and M. ioensis are native to the mid-western and eastern USA, while M. angustifolia and M. fusca grow in the southeast and west, respectively. They offer disease resistance, climate and soil adaptability, and horticultural traits for apple breeding. However, their utilization remains limited due to insufficient genomic resources and specific genetics. We report high-quality phased chromosome-scale assemblies of M. coronaria and M. ioensis , generated using long-read and conformation capture sequencing. Phylogenetic and synteny analysis indicated high relatedness between these two genomes and previously-published genome of M. angustifolia , and lower relatedness with M. fusca . Gene family-based pangenome of North American Malus identified 60,211 orthogroups containing 340,087 genes. Genes involved in basic cellular and metabolic processes, growth, and development were core to the existence of these species, whereas genes involved in secondary metabolism, stress response, and interactions with other organisms were accessory and are likely associated with adaptation to specific environments. Structural variation hotspots were mostly overlapping with high gene density. This study offers novel native North American Malus genome resources that can be used to identify genes for apple breeding and understand their evolution and adaptation.\n\nAdvancing apple genetics research:Malus coronariaandMalus ioensisgenomes and a gene family-based pangenome of native North American apples", "token_count": 366, "char_count": 1625, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6575, "quality_score": 0.8288, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:00.671320", "source": { "split": "train_shard_00001", "doc_id": 950 }, "chunk_id": "train_shard_00001_950_0", "global_id": 7013 }, { "text": "

Background

Transposable Elements (TEs) are fragments of DNA, typically a few hundred base pairs up to several tens of thousands bases long, that have the ability to generate new copies of themselves in the genome. Most existing methods used to identify TEs in a newly sequenced genome are based on their repetitive character, together with detection based on homology and structural features. As new high quality assemblies become more common, including the availability of multiple independent assemblies from the same species, an alternative strategy for identification of TE families becomes possible in which we focus on the polymorphism at insertion sites caused by TE mobility.

Results

We develop the idea of using the structural polymorphisms found in pangenomes to create a library of the TE families recently active in a species, or in a closely related group of species. We present a tool, pantera , that achieves this task, and illustrate its use both on species with well-curated libraries, and on new assemblies.

Conclusions

Our results show that pantera is sensitive and accurate, tending to correctly identify complete elements with precise boundaries, and is particularly well suited to detect larger, low copy number TEs that are often undetected with existing de novo methods.\n\nIdentification of transposable element families from pangenome polymorphisms", "token_count": 305, "char_count": 1399, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6777, "quality_score": 0.8389, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:01.590209", "source": { "split": "train_shard_00001", "doc_id": 951 }, "chunk_id": "train_shard_00001_951_0", "global_id": 7014 }, { "text": "Whole-genome sequencing (WGS) has become the key approach for molecular surveillance of Listeria monocytogenes. Genome comparison analysis can reveal transmission routes that cannot be found with classic epidemiology. A widespread standard for use in genome comparison analysis involves data from short-read sequencing, generated on Illumina or Ion Torrent devices. To date, little is known about the compatibility of data from both platforms. This knowledge is essential when it comes to the central analysis of data, for example, in the case of outbreaks. We used WGS data from 47 L. monocytogenes isolates of the strain collection of the German National Reference Laboratory for L. monocytogenes, generated on either Illumina or Ion Torrent devices, to analyse the impact of the sequencing technology on downstream analyses. In our study, only the assembler SPAdes delivered qualitatively comparable results. In the gene-based core genome multilocus sequence typing (cgMLST), the same-strain allele discrepancy between the platforms was 14.5 alleles on average, which is well above the threshold of 7 alleles routinely used for cluster detection in L. monocytogenes. An application of a strict frameshift filter in cgMLST analysis could push the mean discrepancy below this threshold but reduced discriminatory power. The impact of the platform on the read-based single nucleotide polymorphism analysis was lower than that on the cgMLST. Overall, it was possible to improve compatibility in various ways, but perfect compatibility could not be achieved.\n\nCompatibility of whole-genome sequencing data from Illumina and Ion Torrent technologies in genome comparison analysis of <i>Listeria monocytogenes</i>.", "token_count": 430, "char_count": 1757, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:02.225083", "source": { "split": "train_shard_00001", "doc_id": 952 }, "chunk_id": "train_shard_00001_952_0", "global_id": 7015 }, { "text": "The linear human reference genome that we use today does not represent the haplotypic diversity of the global human population. This raises bias in genomic read alignment and limits our ability to call large structural variations (SV), especially at highly polymorphic loci. Thus, many SV alleles remain unresolved. Recent efforts to transition to a graph-based reference genome resulted in the generation of the first draft human pangenome reference, but tools to call SVs relative to the pangenome reference are presently lacking. In this study, we present the SVarp algorithm, aiming to discover haplotype resolved SVs on top of a pangenome reference using long sequencing reads. SVarp outputs local assemblies of SV alleles, termed svtigs, instead of a VCF file of SV breakpoints, which we propose as a general exchange format allowing for flexible downstream analyses. In order to assess the accuracy of svtigs, we used simulated and real human genomes. Simulations allowed us to make exact breakpoint comparisons against the true callsets. We observed ~96% recall with deletions, insertions and duplications larger than 1,000bp, showing that SVarp can reliably detect genomic structural variants not yet represented in the graph. On the other hand, we compared SVarp output for ONT sequencing data at 20X coverage against independent genome assemblies of the same samples and found that ~82% of our svtig predictions are validated by the assemblies by a match with more than 85% sequence identity. SVarp was implemented using C++ and its source code is available at https://github.com/asylvz/SVarp under MIT license.\n\nSVarp: pangenome-based structural variant discovery", "token_count": 385, "char_count": 1675, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:02.839864", "source": { "split": "train_shard_00001", "doc_id": 953 }, "chunk_id": "train_shard_00001_953_0", "global_id": 7016 }, { "text": "tRNAs are encoded by a large gene family, usually with several isogenic tRNAs interacting with the same codon. Mutations in the anticodon region of other tRNAs can overcome specific tRNA deficiencies. Phylogenetic analysis suggests that such mutations have occurred in evolution, but the driving force is unclear. We show that in yeast suppressor mutations in other tRNAs are able to overcome deficiency of the essential TRT2-encoded tRNAThrCGU at high temperature (40°C). Surprisingly, these tRNA suppressor mutations were obtained after whole-genome transformation with DNA from thermotolerant Kluyveromyces marxianus or Ogataea polymorpha strains but from which the mutations did apparently not originate. We suggest that transient presence of donor DNA in the host facilitates proliferation at high temperature and thus increases the chances for occurrence of spontaneous mutations suppressing defective growth at high temperature. Whole-genome sequence analysis of three transformants revealed only four to five nonsynonymous mutations of which one causing TRT2 anticodon stem stabilization and two anticodon mutations in non-threonyl-tRNAs, tRNALysCUU and tRNAeMetCAU, were causative. Both anticodon mutations suppressed lethality of TRT2 deletion and apparently caused the respective tRNAs to become novel substrates for threonyl-tRNA synthetase. Liquid chromatography-tandem mass spectrometry (LC-MS/MS) data could not detect any significant mistranslation, and reverse transcription-quantitative PCR results contradicted induction of the unfolded protein response", "token_count": 466, "char_count": 1673, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [ "TRT2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:03.490513", "source": { "split": "train_shard_00001", "doc_id": 954 }, "chunk_id": "train_shard_00001_954_0", "global_id": 7017 }, { "text": "We suggest that stress conditions have been a driving force in evolution for the selection of anticodon-switching mutations in tRNAs as revealed by phylogenetic analysis.IMPORTANCE In this work, we have identified for the first time the causative elements in a eukaryotic organism introduced by applying whole-genome transformation and responsible for the selectable trait of interest, i.e., high temperature tolerance. Surprisingly, the whole-genome transformants contained just a few single nucleotide polymorphisms (SNPs), which were unrelated to the sequence of the donor DNA. In each of three independent transformants, we have identified a SNP in a tRNA, either stabilizing the essential tRNAThrCGU at high temperature or switching the anticodon of tRNALysCUU or tRNAeMetCAU into CGU, which is apparently enough for in vivo recognition by threonyl-tRNA synthetase. LC-MS/MS analysis indeed indicated absence of significant mistranslation. Phylogenetic analysis showed that similar mutations have occurred throughout evolution and we suggest that stress conditions may have been a driving force for their selection. The low number of SNPs introduced by whole-genome transformation may favor its application for improvement of industrial yeast strains.\n\nWhole-Genome Transformation Promotes tRNA Anticodon Suppressor Mutations under Stress.", "token_count": 361, "char_count": 1424, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6324, "quality_score": 0.8162, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:04.067339", "source": { "split": "train_shard_00001", "doc_id": 954 }, "chunk_id": "train_shard_00001_954_1", "global_id": 7018 }, { "text": "Cultivar Désirée is an important model for potato functional genomics studies to assist breeding strategies. Here, we present a haplotype-resolved genome assembly of Désirée, achieved by assembling PacBio HiFi reads and Hi-C scaffolding, resulting in a high-contiguity chromosome-level assembly. We implemented a comprehensive annotation pipeline incorporating gene models and functional annotations from the Solanum tuberosum Phureja DM reference genome alongside RNA-seq reads to provide high-quality gene and transcript annotations. Additionally, we provide a genome-wide DNA methylation profile using Oxford Nanopore reads, enabling insights into potato epigenetics. The assembled genome, annotations, methylation and expression data are visualised in a publicly accessible genome browser, providing a valuable resource for the potato research community.\n\nHaplotype-resolved genome assembly of the tetraploid potato cultivar Désirée.", "token_count": 221, "char_count": 937, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7417, "quality_score": 0.8708, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:04.577910", "source": { "split": "train_shard_00001", "doc_id": 955 }, "chunk_id": "train_shard_00001_955_0", "global_id": 7019 }, { "text": "Enterococcus spp. some of which are pathogenic, are common gut microbiota members, including also infants. Infants may be more susceptible to Enterococcus due to their developing gut ecosystems. It is unclear whether antibiotic resistance genes (ARGs) and certain genomic traits in enterococci are restricted to the human subpopulation or more widespread. Furthermore, the correlation between these traits and geographic variation is poorly understood. Therefore, we sequenced 100 strains isolated from full-term healthy infants' fecal samples from two geographically distant European cohorts (MAMI in Spain and LucKi from the Netherlands) to explore the diversity of Enterococcus spp. within the infant's gut microbiome and assess cohort-specific traits such as ARGs. Most isolates were E. faecalis and E. gallinarum, with a total of 11 species identified. We found a rich reservoir of ARGs, plasmids, prophages and virulence factors in the infant strains, with minimal cohort-specific differences in resistome profiles. In addition, Epx, a pore-forming toxin associated with pathogenicity, was found in E. hirae strains. While metabolic profiles were similar across cohorts, E. faecalis strains harbored more virulence genes and prophages compared to other species. An analysis of public Enterococcus genomes revealed that multi-drug resistant (MDR) strains exist without any significant geographic or temporal pattern. Phenotypic resistance analysis indicated that 28% of MAMI strains were gentamicin resistant, compared to 5% of the strains from the LucKi cohort, though LucKi isolates were also resistant to other antibiotics. We also selected ten E", "token_count": 468, "char_count": 1720, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6624, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:05.252539", "source": { "split": "train_shard_00001", "doc_id": 956 }, "chunk_id": "train_shard_00001_956_0", "global_id": 7020 }, { "text": "faecalis isolates with varying virulence gene repertoires for phenotypic virulence testing in Caenorhabditis elegans and found them killing at various rates, however no clear pattern emerged in correlation with any specific genetic determinant. Overall, our results suggest that Enterococcus spp. including ARGs, are highly mobile across Europe and beyond. Their adaptability likely facilitates long-distance dissemination, with strains being acquired early in life from community environments.\n\nComprehensive analysis of <i>Enterococcus</i> spp. from two European healthy infant cohorts shows stable genomic traits including antimicrobial resistance (AMR).", "token_count": 176, "char_count": 687, "word_count": 84, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:05.705480", "source": { "split": "train_shard_00001", "doc_id": 956 }, "chunk_id": "train_shard_00001_956_1", "global_id": 7021 }, { "text": "A large library based on a Tn5 minitransposon carrying a thermostable kanamycin resistance gene was prepared using Thermus thermophilus HB27 genomic DNA as target. To increase the yield of transformants, DNA from the in vitro transposition reaction was amplified using isothermal multiple displacement amplification. The resulting product was first transformed into the high-transformation efficiency ΔaddAB/ppol strain and then into a wild-type HB27 strain. Tn-seq analysis of the libraries showed that almost all genes contained insertions and the distribution of the number of insertions per gene was unimodal, unlike the bimodal distribution reported in most Tn-seq analyses, thus hindering the discrimination of required or essential genes. Upon comparing the Tn-seq results with gene conservation in pangenomic analysis from Thermus thermophilus to Deiococcota levels, as well as with available HB27 RNA-seq data, we observed a very low correlation between core genes or gene transcription levels and Tn-seq insertion frequency. Notably, many genes largely deemed part of the essential bacterial core, supporting critical cellular pathways, showed relatively high transposon insertion numbers. In the case of DNA repair routes, which are essential but somewhat redundant, our results align well with previously published essentiality data, indicating that many genes are dispensable and permissive to insertions. The analysis of these striking results in the context of Thermus biology suggests that the polyploidy of the Thermus genome and the differential stability of proteins may explain the apparent non-essentiality of key genes.

Importance

The Tn-seq technique, random insertion of transposons into an organism’s genome followed by deep sequencing of the resulting population, has enabled precise identification of genes necessary for that organism to live under specified conditions. We have performed Tn-seq on the extremophilic bacterium Thermus thermophilus to gain information on the genes required for thriving at high temperature. Unexpectedly, we detected transposon insertions in the practical totality of the genes of this organism, hindering a clear discrimination of essential genes", "token_count": 491, "char_count": 2217, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5911, "quality_score": 0.7955, "entities": { "genes": [ "HB27" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:06.424492", "source": { "split": "train_shard_00001", "doc_id": 957 }, "chunk_id": "train_shard_00001_957_0", "global_id": 7022 }, { "text": "Furthermore, a comparison with core genes derived from a pangenome analysis, spanning from the Thermus genus up to the phylum level, failed to establish a correlation between gene conservation and Tn-seq results. The polyploidy of the genome of this organism, along with potential regulatory mechanisms, may explain why commonly essential bacterial genes tolerate transposon insertions, a characteristic that appears particular for this organism.\n\nTn-seq of Thermus thermophilus genome reveals unexpected tolerance to insertions in bacterial common essential genes", "token_count": 126, "char_count": 571, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7564, "quality_score": 0.8782, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:06.811881", "source": { "split": "train_shard_00001", "doc_id": 957 }, "chunk_id": "train_shard_00001_957_1", "global_id": 7023 }, { "text": "Whole genome sequencing of bacterial pathogens can positively impact infectious disease management in clinical contexts, both in individual settings and assisting infection prevention efforts. However, logistical issues have often prevented its translation into clinical settings. Oxford Nanopore Technologies (ONT) platforms are flexible, affordable, and now offer accuracy comparable to other sequencing platforms, making them uniquely well-suited for clinical bacterial isolate sequencing. We sought to determine the best methods for implementing ONT sequencing into clinical settings by benchmarking multi-locus sequence typing (MLST), core genome MLST (cgMLST), antimicrobial resistance (AMR) and core genome single nucleotide polymorphism (cgSNP) typing against the genomic gold standard. We sequenced 199 Enterobacterales isolates with Illumina and ONT platforms and assessed performance based on sequencing chemistry, basecaller, basecalling model, assembly status, assembly polishing and sequencing depth. Modern ONT data generated perfect MLST and AMR allelic variant calls, and correctly classified a median of 99.5% of cgMLST loci. Illumina and kmer-based SNP typing failed to call 9-68 SNPs per 1000 sites due to poor sensitivity in repetitive regions of the reference genome, while ONT’s long reads generated perfect SNP calls across the entire genome using simulated readsets. Using real sequencing data to identify putative transmission pairs, ONT read-based methods were concordant with traditional Illumina approaches in 155-158/158 (98.1-100%) of isolate pairs. We also provide specific recommendations on sequencing depth and basecalling model based on the time and computational resources available to the user. This study demonstrates the viability of modern ONT data for highly accurate characterisation of bacterial pathogens while providing an actionable framework for clinical implementation.\n\nNanopore sequencing enables highly accurate genotyping and identification of resistance determinants in key nosocomial pathogens", "token_count": 467, "char_count": 2048, "word_count": 273, "semantic_coherence": 1, "information_density": 0.674, "quality_score": 0.837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:07.462589", "source": { "split": "train_shard_00001", "doc_id": 958 }, "chunk_id": "train_shard_00001_958_0", "global_id": 7024 }, { "text": "

Background

Neisseria meningitidis serogroup Y, especially ST-23 clonal complex (Y:cc23), represents a larger proportion of invasive meningococcal disease (IMD) in older adults compared to younger individuals. This study explored the meningococcal genetic variation underlying this association.

Methods

Maximum-likelihood phylogenies and the pangenome were analyzed using whole-genome sequence (WGS) data from 200 Y:cc23 isolates in the Neisseria PubMLST database. Genome-wide association studies (GWAS) were performed on WGS data from 250 Y:cc23 isolates from individuals with IMD aged ≥65 years versus < 65 years.

Results

Y:cc23 meningococcal variants did not cluster by age group or disease phenotype in phylogenetic analyses. Pangenome comparisons found no differences in presence or absence of genes in IMD isolates from the different age groups. GWAS identified differences in nucleotide polymorphisms within the transferrin-binding protein B (tbpB) gene in isolates from individuals ≥65 years of age. TbpB structure modelling suggests these may impact binding of human transferrin.

Conclusions

These data suggest differential iron scavenging capacity amongst Y:cc23 meningococci isolated from older compared to younger patients. Iron acquisition is essential for many bacterial pathogens including the meningococcus. These polymorphisms may facilitate colonization, thereby increasing the risk of disease in vulnerable older people with altered nasopharyngeal microbiomes and nutritional status.\n\nGenome-Wide Association Studies Identify an Association of Transferrin Binding Protein B Variation and Invasive Serogroup Y Meningococcal Disease in Older Adults.", "token_count": 443, "char_count": 1694, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6729, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:08.091466", "source": { "split": "train_shard_00001", "doc_id": 959 }, "chunk_id": "train_shard_00001_959_0", "global_id": 7025 }, { "text": "Carbapenem-resistant Klebsiella pneumoniae (CRKp) is an urgent public health threat. Worldwide dissemination of CRKp has been largely attributed to clonal group (CG) 258. However, recent evidence indicates the global emergence of a CRKp CG307 lineage. Houston, TX, is the first large city in the United States with detected cocirculation of both CRKp CG307 and CG258. We sought to characterize the genomic and clinical factors contributing to the parallel endemic spread of CG258 and CG307. CRKp isolates were collected as part of the prospective, Consortium on Resistance against Carbapenems in Klebsiella and other Enterobacterales 2 (CRACKLE-2) study. Hybrid short-read and long-read genome assemblies were generated from 119 CRKp isolates (95 originated from Houston hospitals). A comprehensive characterization of phylogenies, gene transfer, and plasmid content with pan-genome analysis was performed on all CRKp isolates. Plasmid mating experiments were performed with CG307 and CG258 isolates of interest. Dissection of the accessory genomes suggested independent evolution and limited horizontal gene transfer between CG307 and CG258 lineages. CG307 contained a diverse repertoire of mobile genetic elements, which were shared with other non-CG258 K. pneumoniae isolates. Three unique clades of Houston CG307 isolates clustered distinctly from other global CG307 isolates, indicating potential selective adaptation of particular CG307 lineages to their respective geographical niches. CG307 strains were often isolated from the urine of hospitalized patients, likely serving as important reservoirs for genes encoding carbapenemases and extended-spectrum β-lactamases. Our findings suggest parallel cocirculation of high-risk lineages with potentially divergent evolution", "token_count": 516, "char_count": 1835, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [ "CG258", "CG307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:08.747512", "source": { "split": "train_shard_00001", "doc_id": 960 }, "chunk_id": "train_shard_00001_960_0", "global_id": 7026 }, { "text": "IMPORTANCE The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKp) infections in nosocomial settings remains a public health challenge. High-risk clones such as clonal group 258 (CG258) are particularly concerning due to their association with blaKPC carriage, which can severely complicate antimicrobial treatments. There is a recent emergence of clonal group 307 (CG307) worldwide with little understanding of how this successful clone has been able to adapt while cocirculating with CG258. We provide the first evidence of potentially divergent evolution between CG258 and CG307 with limited sharing of adaptive genes. Houston, TX, is home to the largest medical center in the world, with a large influx of domestic and international patients. Thus, our unique geographical setting, where two pandemic strains of CRKp are circulating, provides an indication of how differential accessory genome content can drive stable, endemic populations of CRKp. Pan-genomic analyses such as these can reveal unique signatures of successful CRKp dissemination, such as the CG307-associated plasmid (pCG307_HTX), and provide invaluable insights into the surveillance of local carbapenem-resistant Enterobacterales (CRE) epidemiology.\n\nAccessory Genomes Drive Independent Spread of Carbapenem-Resistant Klebsiella pneumoniae Clonal Groups 258 and 307 in Houston, TX.", "token_count": 398, "char_count": 1426, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7112, "quality_score": 0.8556, "entities": { "genes": [ "CG258", "CG307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:09.360420", "source": { "split": "train_shard_00001", "doc_id": 960 }, "chunk_id": "train_shard_00001_960_1", "global_id": 7027 }, { "text": "Candidiasis is an acute or subacute fungal infection caused by fungi that belongs to candida genus, with Candida albicansbeing the most frequent causative agent. Candida kefyr is a rare cause of candidiasis which has been reported in systemic candidiasis and deep infections. However, to date, it has never been reported as a cause in dermatophytosis. We report a case of candidiasis caused by Candida kefyr in a 72-year-old woman with a chief complaint of pruritic erythematous rash on the back from one day prior to admission. Diagnosis was established based on clinical features, direct microscopic examination with 10% potassium hydroxide solution, gram staining. The fungal species was determined by carbohydrate fermentation test which showed a positive result for Candida kefyr. The patient was treated with miconazole cream and fusidic cream and showed significant clinical improvement.\n\nCutaneous candidiasis caused by Candida kefyr.", "token_count": 242, "char_count": 949, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6738, "quality_score": 0.8369, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:09.842138", "source": { "split": "train_shard_00001", "doc_id": 961 }, "chunk_id": "train_shard_00001_961_0", "global_id": 7028 }, { "text": "

Summary

Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past methods for signal-based classification do not scale efficiently to large, repetitive references like pangenomes, limiting their utility to partial references or individual genomes. We introduce Sigmoni: a rapid, multiclass classification method based on the r-index that scales to references of hundreds of Gbps. Sigmoni quantizes nanopore signal into a discrete alphabet of picoamp ranges. It performs rapid, approximate matching using matching statistics, classifying reads based on distributions of picoamp matching statistics and co-linearity statistics, all in linear query time without the need for seed-chain-extend. Sigmoni is 10-100× faster than previous methods for adaptive sampling in host depletion experiments with improved accuracy, and can query reads against large microbial or human pangenomes. Sigmoni is the first signal-based tool to scale to a complete human genome and pangenome while remaining fast enough for adaptive sampling applications.

Availability and implementation

Sigmoni is implemented in Python, and is available open-source at https://github.com/vshiv18/sigmoni.\n\nSigmoni: classification of nanopore signal with a compressed pangenome index.", "token_count": 329, "char_count": 1465, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:10.417065", "source": { "split": "train_shard_00001", "doc_id": 962 }, "chunk_id": "train_shard_00001_962_0", "global_id": 7029 }, { "text": "

Background

In recent years, the detection of Klebsiella pneumoniae (KLPN) producing New Delhi metallo-β-lactamase (NDM), particularly NDM-1, has increased in Germany. Plasmids play a crucial role in the dissemination of NDM-1, facilitating its persistence in both clinical and environmental reservoirs. Between 2021 and 2024, a substantial number of NDM-1-producing KLPN isolates were detected across multiple hospital sites in Berlin. This study aimed to investigate a potential multi-site outbreak involving NDM-1-producing KLPN, and to assess the role of clonal versus plasmid-mediated dissemination.

Methods

We performed short-read sequencing for all isolates, complemented by long-read sequencing for a subset (Illumina and Oxford Nanopore Technologies). Core genome multi locus sequence typing (cgMLST) was conducted using SeqSphere+. NDM-1 plasmids were characterized with the MOB-suite tools. Reference plasmids were reconstructed from hybrid assemblies using TaDReP. Short-read sequences from all isolates were aligned against these reference plasmids to assess genetic relatedness.

Results

Analysis of 57 NDM-1 plasmid carrying KLPN isolates at the clonal level revealed three distinct outbreak clusters (O1-O3). These corresponded to three unique NDM-1 reference plasmids: p1 (54.0 kb IncFIB(pQil)), p2 (54.3 kb IncR), and p3 (355.5 kb; no Inc type specified). Plasmid clustering from short-reads was consistent with the clonal clusters.

Conclusions

Both plasmid-level analysis and cgMLST yielded congruent results, effectively ruling out the possibility of multi-site, plasmid-mediated NDM-1 transmission. The detection of a globally disseminated NDM-1 plasmid within one of the clonal clusters highlights its potential role in the spread of resistance during the recent surge of NDM-1 carrying KLPN isolates in Germany.", "token_count": 516, "char_count": 1861, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:11.072809", "source": { "split": "train_shard_00001", "doc_id": 963 }, "chunk_id": "train_shard_00001_963_0", "global_id": 7030 }, { "text": "NDM-1 plasmid clustering reflects clonal transmission of Klebsiella pneumoniae ST147 in four hospitals in Berlin, Germany.", "token_count": 35, "char_count": 122, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [ "ST147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:11.432443", "source": { "split": "train_shard_00001", "doc_id": 963 }, "chunk_id": "train_shard_00001_963_1", "global_id": 7031 }, { "text": "Studies of bacterial adaptation and evolution are hampered by the difficulty of measuring traits such as virulence, drug resistance and transmissibility in large populations. In contrast, it is now feasible to obtain high-quality complete assemblies of many bacterial genomes thanks to scalable and affordable long-read sequencing technology. To exploit this opportunity we introduce a phenotype- and alignment-free method for discovering co-selected and epistatically interacting genomic variation from genome assemblies covering both core and accessory parts of genomes. Our approach uses a compact coloured de Bruijn graph to approximate the intra-genome distances between pairs of loci for a collection of bacterial genomes to account for the impacts of linkage disequilibrium (LD). We demonstrate the versatility of our approach to efficiently identify associations between loci linked with drug resistance and adaptation to the hospital niche in the major human bacterial pathogens Streptococcus pneumoniae and Enterococcus faecalis .\n\nPAN-GWES: Pangenome-spanning epistasis and co-selection analysis via de Bruijn graphs", "token_count": 246, "char_count": 1127, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6968, "quality_score": 0.8484, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:11.916902", "source": { "split": "train_shard_00001", "doc_id": 964 }, "chunk_id": "train_shard_00001_964_0", "global_id": 7032 }, { "text": "Acetogens are anaerobes using Wood-Ljungdahl pathway (WLP) as the terminal electron acceptor for both assimilation and dissimilation of CO2 and widely distributed in diverse habitats. However, their habitat adaptation is often unclear. Given that bacterial genome evolution is often the result of environmental selective pressure, hereby we analysed gene copy number, phylogeny and selective pressure of genes involved in WLP within known genomes of 43 species to study the habitat adaption of gastrointestinal acetogens. The gene copy number of formate dehydrogenase (FDH) in gastrointestinal acetogens was much lower than that of non-gastrointestinal acetogens, and in five cases, no FDH genes were found in the genomes of five gastrointestinal acetogens, but that of the other WLP genes showed no difference. The evolutionary pattern of FDH genes was significantly different from that of the other enzymes. Additionally, seven positively selected sites were only identified in the fdhF genes, which means fdhF mutations favoured their adaptation. Collectively, reduction or loss of FDH genes and their evolutionary pattern as well as positive selection in gastrointestinal acetogens indicated their adaptation to formate-rich habitats, implying that FDH genes catalysing CO2 reduction to formate as the first step of methyl branch of WLP may have evolved independently.\n\nReduction, evolutionary pattern and positive selection of genes encoding formate dehydrogenase in Wood-Ljungdahl pathway of gastrointestinal acetogens suggests their adaptation to formate-rich habitats.", "token_count": 398, "char_count": 1598, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5561, "quality_score": 0.778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:12.530152", "source": { "split": "train_shard_00001", "doc_id": 965 }, "chunk_id": "train_shard_00001_965_0", "global_id": 7033 }, { "text": "Overweight and obesity are associated with increased intestinal permeability, characterized by loss of gut epithelial integrity, resulting in unregulated passage of lipopolysaccharide (LPS) and other inflammatory triggers into circulation, i.e., metabolic endotoxemia. In obesity, shifts in the gut microbiome negatively impact intestinal permeability. Probiotics are an intervention that can target the gut microbiome by introducing beneficial microbial species, potentially restoring gut barrier integrity. Currently, the role of probiotic supplementation in ameliorating obesity- and overweight-associated increases in gut permeability has not been reviewed. This systematic review aimed to summarize findings from both animal and clinical studies that evaluated the effect of probiotic supplementation on obesity-induced impairment in intestinal permeability (International Prospective Register of Systematic Reviews, CRD42022363538). A literature search was conducted using PubMed (Medline), Web of Science, and CAB Direct from origin until August 2023 using keywords of intestinal permeability, overweight or obesity, and probiotic supplementation. Of 920 records, 26 eligible records were included, comprising 12 animal and 14 clinical studies. Clinical trials ranged from 3 to 26 wk and were mostly parallel-arm (n = 13) or crossover (n = 1) design. In both animal and clinical studies, plasma/serum LPS was the most common measure of intestinal permeability. Eleven of 12 animal studies reported a positive effect of probiotic supplementation in reducing intestinal permeability. However, results from clinical trials were inconsistent, with half reporting reductions in serum LPS and half reporting no differences after probiotic supplementation. Bifidobacterium, Lactobacillus, and Akkermansia emerged as the most common genera in probiotic formulations among the animal and clinical studies that yielded positive results, suggesting that specific bacteria may be more effective at reducing intestinal permeability and improving gut barrier function", "token_count": 496, "char_count": 2060, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8055, "entities": { "genes": [ "CRD42022363538" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:13.184007", "source": { "split": "train_shard_00001", "doc_id": 966 }, "chunk_id": "train_shard_00001_966_0", "global_id": 7034 }, { "text": "However, better standardization of strain use, dosage, duration, and the delivery matrix is needed to fully understand the probiotic impact on intestinal permeability in individuals with overweight and obesity.\n\nEffect of Probiotic Supplementation on Intestinal Permeability in Overweight and Obesity: A Systematic Review of Randomized Controlled Trials and Animal Studies.", "token_count": 85, "char_count": 373, "word_count": 50, "semantic_coherence": 1, "information_density": 0.76, "quality_score": 0.88, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:13.560246", "source": { "split": "train_shard_00001", "doc_id": 966 }, "chunk_id": "train_shard_00001_966_1", "global_id": 7035 }, { "text": "Flavobacteria are widely dispersed in a variety of environments and produce various polysaccharide-degrading enzymes. Here, we report the complete genome of Flavobacterium faecale WV33T, an agar-degrading bacterium isolated from the stools of Antarctic penguins. The sequenced genome of F. faecale WV33T represents a single circular chromosome (4,621,116 bp, 35.2% G + C content), containing 3984 coding DNA sequences and 85 RNA-coding genes. The genome of F. faecale WV33T contains 154 genes that encode carbohydrate-active enzymes (CAZymes). Among the CAZymes, seven putative genes encoding agarases have been identified in the genome. Transcriptional analysis revealed that the expression of these putative agarases was significantly enhanced by the presence of agar in the culture medium, suggesting that these proteins are involved in agar hydrolysis. Pangenome analysis revealed that the genomes of the 27 Flavobacterium type strains, including F. faecale WV33T, tend to be very plastic, and Flavobacterium strains are unique species with a tiny core genome and a large non-core region. The average nucleotide identity and phylogenomic analysis of the 27 Flavobacterium-type strains showed that F. faecale WV33T was positioned in a unique clade in the evolutionary tree.\n\nComparative Genomic Analysis of Agarolytic Flavobacterium faecale WV33T.", "token_count": 484, "char_count": 1486, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6373, "quality_score": 0.8187, "entities": { "genes": [ "WV33" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:14.215831", "source": { "split": "train_shard_00001", "doc_id": 967 }, "chunk_id": "train_shard_00001_967_0", "global_id": 7036 }, { "text": "Bacteria of the Thiothrix morphotype, comprising the genera Thiothrix, Thiolinea and Thiofilum, are frequently encountered in domestic and industrial wastewater treatment systems, but they are usually not clearly differentiated due to the marked similarity in their morphologies. Methods ranging from light microscopy, FISH and PCR to modern high-throughput sequencing are used to identify them. The development of these bacteria in wastewater treatment systems has both advantages and disadvantages. On the one hand, the explosive growth of these bacteria can lead to activated sludge bulking or clogging of the treatment system's membranes, with a consequent decrease in the water treatment efficiency. On the other hand, members of the Thiothrix morphotype can improve the quality of granular sludge and increase the water treatment efficiency. This may be due to their capacity for sulfide oxidation, denitrification combined with the oxidation of reduced sulfur compounds, enhanced biological phosphate removal and possibly denitrifying phosphate removal. The recently obtained pangenome of the genus Thiothrix allows the explanation, at the genomic level, of the experimental results of various studies. Moreover, this review summarizes the data on the factors affecting the proliferation of representatives of the Thiothrix morphotype.\n\nWastewater Treatment with Bacterial Representatives of the Thiothrix Morphotype.", "token_count": 357, "char_count": 1480, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:14.802100", "source": { "split": "train_shard_00001", "doc_id": 968 }, "chunk_id": "train_shard_00001_968_0", "global_id": 7037 }, { "text": "A variety of yeast species have been considered ideal hosts for metabolic engineering to produce value-added chemicals, including the model organism Saccharomyces cerevisiae, as well as non-conventional yeasts including Yarrowia lipolytica, Kluyveromyces marxianus, and Pichia pastoris. However, the metabolic capacity of these microbes is not simply dictated or implied by genus or species alone. Within the same species, yeast strains can display distinct variations in their phenotypes and metabolism, which affect the performance of introduced pathways and the production of interesting compounds. Moreover, it is unclear how this metabolic potential corresponds to function upon rewiring these organisms. These reports thus point out a new consideration for successful metabolic engineering, specifically: what are the best strains to utilize and how does one achieve effective metabolic engineering? Understanding such questions will accelerate the host selection and optimization process for generating yeast cell factories. In this review, we survey recent advances in studying yeast strain variations and utilizing non-type strains in pathway production and metabolic engineering applications. Additionally, we highlight the importance of employing portable methods for metabolic rewiring to best access this metabolic diversity. Finally, we conclude by highlighting the importance of considering strain diversity in metabolic engineering applications.\n\nConsidering Strain Variation and Non-Type Strains for Yeast Metabolic Engineering Applications.", "token_count": 343, "char_count": 1586, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:15.380455", "source": { "split": "train_shard_00001", "doc_id": 969 }, "chunk_id": "train_shard_00001_969_0", "global_id": 7038 }, { "text": "

Background:

Leuconostoc gelidum and Leuconostoc gasicomitatum have dual roles in foods. They may spoil cold-stored packaged foods but can also be beneficial in kimchi fermentation. The impact in food science as well as the limited number of publicly available genomes prompted us to create pangenomes and perform genomic taxonomy analyses starting from de novo sequencing of the genomes of 37 L. gelidum/L. gasicomitatum strains from our culture collection. Our aim was also to evaluate the recently proposed change in taxonomy as well as to study the genomes of strains that had have different lifestyles in foods.

Methods:

We selected as diverse a set of strains as possible in terms of sources, previously conducted genotyping results and geographical distribution, and included also 10 publicly available genomes in our analyses. We studied genomic taxonomy using pairwise average nucleotide identity (ANI) and calculation of digital DNA-DNA hybridisation (dDDH) scores. Phylogeny analyses were done using the core gene set of 1141 single-copy genes and a set of housekeeping genes commonly used for lactic acid bacteria. In addition, the pangenome and core genome sizes as well as some properties, such as acquired antimicrobial resistance (AMR), important due to the growth in foods, were analysed.

Results:

Genome relatedness indices and phylogenetic analyses supported the recently suggested classification that restores the taxonomic position of L. gelidum subsp. gasicomitatum back to the species level as L. gasicomitatum. Genome properties, such as size and coding potential, revealed limited intraspecies variation and showed no attribution to the source of isolation. Distribution of the unique genes between species and subspecies was not associated with the previously documented lifestyle in foods. None of the strains carried any acquired AMR genes or genes associated with any known form of virulence.

Conclusion:

Genome-wide examination of strains confirms that the proposition to restore the taxonomic position of L. gasicomitatum is justified. It further confirms that the distribution of L. gelidum and L", "token_count": 523, "char_count": 2164, "word_count": 318, "semantic_coherence": 1, "information_density": 0.5786, "quality_score": 0.7893, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:16.035472", "source": { "split": "train_shard_00001", "doc_id": 970 }, "chunk_id": "train_shard_00001_970_0", "global_id": 7039 }, { "text": "gasicomitatum between different foods or lifestyles is not a result of functional and phylogenetic diversification at the genome level. Thus, we consider that the distribution and lifestyle of L. gelidum and L. gasicomitatum in foods has not been driven by the evolution of functional and phylogenetic diversification detectable at the genome level.\n\nPangenome and genomic taxonomy analyses of Leuconostoc gelidum and Leuconostoc gasicomitatum", "token_count": 114, "char_count": 443, "word_count": 63, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:16.419142", "source": { "split": "train_shard_00001", "doc_id": 970 }, "chunk_id": "train_shard_00001_970_1", "global_id": 7040 }, { "text": "The positive impact of certain non-Saccharomyces yeasts on the aromatic profile of wines has been well documented in literature and their industrial use in association with S. cerevisiae is now recommended. Competition between non-Saccharomyces species and Saccharomyces cerevisiae for various nutrients, especially nitrogen sources, greatly impacts the production of aroma compounds. In this study, we further explored the impact of different nitrogen nutrition strategies on the production of carbon and sulphur volatile compounds of three non-Saccharomyces strains, namely Pichia burtonii, Kluyveromyces marxianus, Zygoascus meyerae sequentially inoculated with S. cerevisiae in Sauvignon blanc and Shiraz grape musts. Nitrogen additions were implemented according the specific requirement of each species. At the end of fermentation, we observed specific metabolic signatures for each strain in response to the nature of the nitrogen source suggesting strain-specific metabolic fluxes present. Overall, these results confirmed and further explored the interconnection between nitrogen sources and aroma metabolism (including that of higher alcohols, fatty acids, esters and volatile sulphur compounds), and their variations according to species and the nature of the nitrogen source. The knowledge generated provides new insights to modulate the aroma profile of wines produced with non-Saccharomyces species.\n\nNitrogen metabolism in three non-conventional wine yeast species: A tool to modulate wine aroma profiles", "token_count": 348, "char_count": 1519, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6068, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:17.026184", "source": { "split": "train_shard_00001", "doc_id": 971 }, "chunk_id": "train_shard_00001_971_0", "global_id": 7041 }, { "text": "Salmonella enterica serotype Enteritidis is a generalist serotype that adapts to different hosts and transmission niches. It has significant epidemiological relevance and is among the most prevalent serotypes distributed in several countries. Salmonella Enteritidis causes self-limited gastroenteritis in humans, which can progress to systemic infection in immunocompromised individuals. The Salmonella pathogenicity mechanism is multifactorial and complex, including the presence of virulence factors that are encoded by virulence genes. Poultry products are considered significant reservoirs of many Salmonella serotypes, and Salmonella Enteritidis infections are often related to the consumption of chicken meat and eggs. This study reports the whole-genome sequence of Salmonella Enteritidis PT4 strain 578. A total of 165 genes (3.66%) of the 4506 coding sequences (CDS) predicted in its genome are virulence factors associated with cell invasion, intestinal colonization, and intracellular survival. The genome harbours twelve Salmonella pathogenicity islands (SPIs), with the SPI-1 and SPI-2 genes encoding type III secretion systems (T3SS) showing high conservation. Six prophage-related sequences were found, with regions of intact prophages corresponding to Salmon_118970_sal3 and Gifsy-2. The genome also contains two CRISPR systems. Comparative genome analysis with Salmonella Enteritidis ATCC 13076, Salmonella Typhimurium ATCC 13311, and Salmonella Typhimurium ATCC 14028 demonstrates that most unshared genes are related to metabolism, membrane, and hypothetical proteins", "token_count": 481, "char_count": 1670, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [ "PT4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:17.689150", "source": { "split": "train_shard_00001", "doc_id": 972 }, "chunk_id": "train_shard_00001_972_0", "global_id": 7042 }, { "text": "Finally, the phenotypic characterization evidenced differences among Salmonella Enteritidis PT4 578 and the other three serotypes regarding the expression of the red, dry, and rough (rdar) morphotype and biofilm formation. Overall, the genomic characterization and phenotypic properties expand knowledge of the mechanisms of pathogenicity in Salmonella Enteritidis PT4 578.\n\nGenome sequencing and analysis of Salmonella enterica subsp. enterica serotype Enteritidis PT4 578: insights into pathogenicity and virulence.", "token_count": 147, "char_count": 531, "word_count": 67, "semantic_coherence": 1, "information_density": 0.6716, "quality_score": 0.8358, "entities": { "genes": [ "PT4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:18.156337", "source": { "split": "train_shard_00001", "doc_id": 972 }, "chunk_id": "train_shard_00001_972_1", "global_id": 7043 }, { "text": "Kluyveromyces marxianus is traditionally associated with fermented dairy products, but can also be isolated from diverse non-dairy environments. Because of thermotolerance, rapid growth and other traits, many different strains are being developed for food and industrial applications but there is, as yet, little understanding of the genetic diversity or population genetics of this species. K. marxianus shows a high level of phenotypic variation but the only phenotype that has been clearly linked to a genetic polymorphism is lactose utilisation, which is controlled by variation in the LAC12 gene. The genomes of several strains have been sequenced in recent years and, in this study, we sequenced a further nine strains from different origins. Analysis of the Single Nucleotide Polymorphisms (SNPs) in 14 strains was carried out to examine genome structure and genetic diversity. SNP diversity in K. marxianus is relatively high, with up to 3% DNA sequence divergence between alleles. It was found that the isolates include haploid, diploid, and triploid strains, as shown by both SNP analysis and flow cytometry. Diploids and triploids contain long genomic tracts showing loss of heterozygosity (LOH). All six isolates from dairy environments were diploid or triploid, whereas 6 out 7 isolates from non-dairy environment were haploid. This also correlated with the presence of functional LAC12 alleles only in dairy haplotypes. The diploids were hybrids between a non-dairy and a dairy haplotype, whereas triploids included three copies of a dairy haplotype.\n\nPloidy Variation in Kluyveromyces marxianus Separates Dairy and Non-dairy Isolates.", "token_count": 459, "char_count": 1691, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [ "LAC12" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:18.801405", "source": { "split": "train_shard_00001", "doc_id": 973 }, "chunk_id": "train_shard_00001_973_0", "global_id": 7044 }, { "text": "Aspergillus flavus and Aspergillus oryzae are closely related fungal species with contrasting roles in food safety and fermentation. To comprehensively investigate their phylogenetic, genomic, and metabolic characteristics, we conducted an extensive comparative pangenome analysis using complete, dereplicated genome sets for both species. Phylogenetic analyses, employing both the entirety of the identified single-copy orthologous genes and six housekeeping genes commonly used for fungal classification, did not reveal clear differentiation between A. flavus and A. oryzae genomes. Upon analyzing the aflatoxin biosynthesis gene clusters within the genomes, we observed that non-aflatoxin-producing strains were dispersed throughout the phylogenetic tree, encompassing both A. flavus and A. oryzae strains. This suggests that aflatoxin production is not a distinguishing trait between the two species. Furthermore, A. oryzae and A. flavus strains displayed remarkably similar genomic attributes, including genome sizes, gene contents, and G + C contents, as well as metabolic features and pathways. The profiles of CAZyme genes and secondary metabolite biosynthesis gene clusters within the genomes of both species further highlight their similarity. Collectively, these findings challenge the conventional differentiation of A. flavus and A. oryzae as distinct species and highlight their phylogenetic, genomic, and metabolic homogeneity, potentially indicating that they may indeed belong to the same species.\n\nComparative pangenome analysis of Aspergillus flavus and Aspergillus oryzae reveals their phylogenetic, genomic, and metabolic homogeneity", "token_count": 400, "char_count": 1654, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5845, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:19.423652", "source": { "split": "train_shard_00001", "doc_id": 974 }, "chunk_id": "train_shard_00001_974_0", "global_id": 7045 }, { "text": "

Motivation

Identification of complete sets of transcription factors (TFs) is a foundational step in the inference of genetic regulatory networks. With the availability of high-quality predictions of protein three-dimensional structures (3D), it has become possible to use structural comparisons for the inference of homology beyond what is possible from sequence analyses alone. This work explores the potential to use predicted 3D structures for the identification of TFs in the Escherichia coli pangenome.

Results

Comparisons between predicted structures and their experimentally confirmed counterparts confirmed the high-quality of predicted structures, with most 3D structural alignments showing TM-scores well above established structural similarity thresholds, though the quality seemed slightly lower for TFs than for other proteins. As expected, structural similarity decreased with sequence similarity, though most TM-scores still remained above the structural similarity threshold. This was true regardless of the aligned structures being experimental or predicted. Results at the lowest sequence identity levels revealed potential for 3D structural comparisons to extend homology inferences below the “twilight zone” of sequence-based methods. The body of predicted 3D structures covered 99.7% of available proteins from the E. coli pangenome, missing only two of those matching TF domain sequence profiles. Structural analyses increased the inferred TFs in the E. coli pangenome by 18% above the amount obtained with sequence profiles alone.\n\nTranscription factors across theEscherichia colipangenome: a 3D perspective", "token_count": 364, "char_count": 1655, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5946, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:20.006403", "source": { "split": "train_shard_00001", "doc_id": 975 }, "chunk_id": "train_shard_00001_975_0", "global_id": 7046 }, { "text": "Bacterial clades are often ecologically distinct, despite extensive horizontal gene transfer (HGT). How selection works on different parts of bacterial pan-genomes to drive and maintain the emergence of clades is unclear. Focusing on the three largest clades in the diverse and well-studied Bacillus cereus sensu lato group, we identified clade-specific core genes (present in all clade members) and then used clade-specific allelic diversity to identify genes under purifying and diversifying selection. Clade-specific accessory genes (present in a subset of strains within a clade) were characterized as being under selection using presence/absence in specific clades. Gene ontology analyses of genes under selection revealed that different gene functions were enriched in different clades. Furthermore, some gene functions were enriched only amongst clade-specific core or accessory genomes. Genes under purifying selection were often clade-specific, while genes under diversifying selection showed signs of frequent HGT. These patterns are consistent with different selection pressures acting on both the core and the accessory genomes of different clades and can lead to ecological divergence in both cases. Examining variation in allelic diversity allows us to uncover genes under clade-specific selection, allowing ready identification of strains and their ecological niche.\n\nSignatures of selection in core and accessory genomes indicate different ecological drivers of diversification among Bacillus cereus clades.", "token_count": 320, "char_count": 1523, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5619, "quality_score": 0.781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:20.572079", "source": { "split": "train_shard_00001", "doc_id": 976 }, "chunk_id": "train_shard_00001_976_0", "global_id": 7047 }, { "text": "

Introduction

Extended-spectrum beta-lactamase (ESBL) producing Escherichia coli have become prevalent worldwide, with E. coli of sequence type 131 (ST131) as the dominant genotype. E. coli ST131 predominantly exhibits the serotype O25, is associated with the ESBL CTX-M-15 and belongs to a well-defined subclade within the FimH30-R clade, FimH30-Rx/C2. Multidrug resistance may have fitness costs for the bacteria. The aim of the current study was to investigate the fitness burden compared to a susceptible ST131 isolate without resistance genes in vitro and in vivo and describe genetic differences between fit and less fit isolates.

Materials and methods

From a collection of clinical ESBL and non-ESBL E. coli isolates from urinary tract infection, we selected 16 bla CTX-M-15-positive isolates of ST131. The in vitro fitness was examined, and relative bacterial fitness (fit t ) was determined by direct competition with a fully susceptible ST131 isolate and illustrated in percent, with <100% resulting in a lower fitness, compared to the susceptible reference isolate. The isolates were subjected to whole-genome sequencing and analyzed for resistance markers, plasmids, phage content, and serotype. In vivo competition was tested in a mouse colonization model.

Results

The majority (12 out of 16) of the CTX-M-15-producing isolates had a slightly lower relative fitness compared to the susceptible ST131 isolate (mean, 97.6%; range, 82.6-108%) in vitro", "token_count": 509, "char_count": 1595, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:21.236184", "source": { "split": "train_shard_00001", "doc_id": 977 }, "chunk_id": "train_shard_00001_977_0", "global_id": 7048 }, { "text": "Three isolates had a better fitness than the susceptible ST131 isolate, and one isolate had an identical fitness to the susceptible ST131 isolate. The in vitro fitness showed no correlation to the number of plasmids, number of phages, number of resistances, or genome size. For the in vivo competition assays, all three ESBL-producing isolates showed better colonization of the ESBL-resistant ST131 isolates compared to the susceptible ST131 isolate.

Conclusion

This study shows that ESBL-producing ST131/H30-Rx are not necessarily burdened by multidrug resistance, however, have a better in vitro fitness than the susceptible isolate. These data contribute to the understanding of the success of ST131/H30-Rx, although they do not indicate ways to overcome this highly fit, virulent, and antimicrobial-resistant clone.\n\nIn vitro Relative Fitness, in vivo Intestinal Colonization and Genomic Differences of Escherichia coli of ST131 Carrying bla CTX-M-15.", "token_count": 325, "char_count": 1036, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:21.797797", "source": { "split": "train_shard_00001", "doc_id": 977 }, "chunk_id": "train_shard_00001_977_1", "global_id": 7049 }, { "text": "Assessment of the pathogenic potential (virulence and toxicity) in non-pathogenic bacterial species is a challenge as it relies on methods developed for assessment of species known to be pathogenic. Here we have applied and evaluated some of these methods on industrially relevant bacteria to differentiate between “true” virulence factors applying only to pathogens and niche factors being defined as promoting colonization and survival rather than pathogenicity and as being present also in non-pathogenic bacteria. We examined the pathogenicity of 49 strains from nine industrially relevant bacterial species (Lactobacillus gasseri, Lactobacillus jensenii, Lactobacillus delbrueckii, Lacticaseibacillus rhamnosus, Limosilactobacillus fermentum, Latilactobacillus curvatus, Ligilactobacillus salivarius, Staphylococcus carnosus, and Staphylococcus xylosus), including 14 clinical isolates of the same species, through genomic screening and phenotypically through assays established for pathogenic bacteria. The genomes were screened against the Virulence Factor Database (VFDB) and thresholds (>80% nucleotide or protein identity, >70% coverage) provided by the European Food Safety Authority (EFSA) were adopted to differentiate between genes of potential concern and genes of no concern. Core genome analysis was performed to determine whether the clinical isolates were phylogenetically related to the industrial isolates. The genotypic assessment did not reveal the presence of true virulence factors in the examined strains, and in the core genome analysis the clinical isolates could not be distinguished from the industrial strains. Furthermore, cytotoxicity toward Vero cells, negative impact on Caco-2 cell viability, and hemolytic activity on blood agar plates were examined, and none of the tested strains exhibited any activity in these assays. Overall, the results suggest that VFDB screening with the EFSA thresholds can be used to differentiate between true virulence factors and niche factors", "token_count": 486, "char_count": 2010, "word_count": 272, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:22.442446", "source": { "split": "train_shard_00001", "doc_id": 978 }, "chunk_id": "train_shard_00001_978_0", "global_id": 7050 }, { "text": "Furthermore, the use of phenotypic assays supports the genotypic assessments and Caco-2 cell viability and hemolysis assays are useful to determine the presence of acquired virulence genes, albeit expert knowledge is required to interpret the results.\n\nAssessment of pathogenic potential in non-pathogenic bacterial species for industrial production of live bacteria", "token_count": 81, "char_count": 366, "word_count": 50, "semantic_coherence": 1, "information_density": 0.82, "quality_score": 0.91, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:22.814965", "source": { "split": "train_shard_00001", "doc_id": 978 }, "chunk_id": "train_shard_00001_978_1", "global_id": 7051 }, { "text": "

Aims

Hypervirulent and carbapenem-resistant pathogens posed a significant and growing threat to global public health. This study focused on the rapid spread of a hypervirulent carbapenem-resistant E. coli (hv-CREC) subclone and its genomic resembles with hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP), driven by recombination impacting both chromosomal and plasmid gene content.

Methods

A multicenter molecular epidemiological study was conducted on 653 CREC clinical isolates collected across China (2013-2022), integrated with public genomic data. Pangenome-wide and phylogeographical analyses were performed to uncover recombination events, define the epidemic clone, and trace its evolutionary history. Growth advantage and virulence were evaluated through competition assays and Galleria mellonella infection models.

Results

Sequence types (ST) 167, ST410, ST617, and ST361 collectively accounted for 53.8 % (351/653) of the CREC isolates, with ST167 showing a sharp increase in prevalence after 2017. Among these, subclone named KpnK48 emerged as the primary driver of the increase in ST167 CREC prevalence. Traced to a European origin, KpnK48 rapidly expanded globally, particularly in China. The remarkable success of KpnK48 could plausibly be attributed to enhanced survival and virulence, driven by the acquisition of a ∼492 kb recombinant genomic region which mirrored the genomic architecture underlying the hv-CRKP ST11-K64 clone, reflecting a Klebsiella-like evolutionary path", "token_count": 446, "char_count": 1525, "word_count": 198, "semantic_coherence": 1, "information_density": 0.7172, "quality_score": 0.8586, "entities": { "genes": [ "ST410", "ST167", "ST361", "ST11", "ST617" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:23.448053", "source": { "split": "train_shard_00001", "doc_id": 979 }, "chunk_id": "train_shard_00001_979_0", "global_id": 7052 }, { "text": "Additionally, plasmid shift in KpnK48 clone from the prevalent NDM-IncX3 plasmid to Klebsiella-common NDM-IncF plasmid expanded its resistance spectrum and virulence gene repertoire, likely further amplifying its pathogenicity and success.

Conclusions

The KpnK48 subclone combined the features of hypervirulence and carbapenem resistance, bridging genomic traits of E. coli and K. pneumoniae, signifying a broader evolutionary trend with profound global health implications.\n\nKpnK48 clone driving hypervirulent carbapenem-resistant Escherichia coli epidemics: Insights into its evolutionary trajectory similar to Klebsiella pneumoniae.", "token_count": 181, "char_count": 642, "word_count": 76, "semantic_coherence": 1, "information_density": 0.8026, "quality_score": 0.9013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:23.885808", "source": { "split": "train_shard_00001", "doc_id": 979 }, "chunk_id": "train_shard_00001_979_1", "global_id": 7053 }, { "text": "

Aims

Yeasts produce 2-phenylethanol (2-PE) from sugars via de novo synthesis; however, its synthesis is limited due to feedback inhibition on the isofunctional 3-deoxy-d-arabino-heptulosonate-7-phosphate (DAHP) synthases (Aro3p and Aro4p). This work aimed to select Kluyveromyces marxianus mutant strains with improved capacity to produce 2-PE from sugars.

Methods and results

Kluyveromyces marxianus CCT 7735 mutant strains were selected from UV irradiation coupled with screening of p-fluoro-dl-phenylalanine (PFP) tolerant strains on culture medium without l-Phe addition. Most of them produced 2-PE titres higher than the parental strain and the Km_PFP41 mutant strain stood out for displaying the highest 2-PE specific production rate. Moreover it showed higher activity of DAHP synthase than the parental strain. We sequenced both ARO3 and ARO4 genes of Km_PFP41 mutant and identified mutations in ARO4 which caused changes in both size and conformation of the Aro4p. These changes seem to be associated with the enhanced activity of DAHP synthase and improved production of 2-PE exhibited by that mutant strain.

Conclusions

The Km_PFP41 mutant strain presented improved 2-PE production via de novo synthesis and enhanced DAHP synthase activity.

Significance and impact of the study

The mutant strain obtained in this work may be exploited as a yeast cell factory for high-level synthesis of 2-PE.\n\nObtainment, selection and characterization of a mutant strain of Kluyveromyces marxianus that displays improved production of 2-phenylethanol and enhanced DAHP synthase activity.", "token_count": 472, "char_count": 1612, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5727, "quality_score": 0.7864, "entities": { "genes": [ "ARO3", "ARO4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:24.527350", "source": { "split": "train_shard_00001", "doc_id": 980 }, "chunk_id": "train_shard_00001_980_0", "global_id": 7054 }, { "text": "

Introduction

Species of genus Candida are part of the common microbiota of humans; however, some of the Candida species are known opportunistic pathogens. Formation of biofilms, resistance to antifungal drugs, and increase in asymptomatic infections demands more studies on isolation, identification and characterization of Candida from clinical samples.

Methods

The present manuscript deals with assessment of authentic yeast identification by three methods viz., DNA sequencing of 28S rRNA gene, protein profiles using MALDI-TOF MS, and colony coloration on chromogenic media. Antifungal susceptibility and in vitro cell invasion assays were performed to further characterize these isolates.

Results

Comparison of three methods showed that DNA sequence analysis correctly identified more than 99.4% of the isolates up to species level as compared to 89% by MALDI-TOF MS. In this study, we isolated a total of 176 yeasts from clinical samples and preliminary morphological characters indicated that these yeast isolates belong to the genus Candida. The species distribution of isolates was as follows: 75 isolates of Candida albicans (42.61%), 50 of C. tropicalis (28.40%), 22 of C. glabrata (12.5%), 14 of C. parapsilosis (7.95%) and 4 of Clavispora lusitaniae (2.27%). Other species like Cyberlindnera fabianii, Issatchenkia orientalis, Kluyveromyces marxianus, Kodamaea ohmeri, Lodderomyces sp., and Trichosporon asahii were less than 2%", "token_count": 492, "char_count": 1547, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6965, "quality_score": 0.8483, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:25.184400", "source": { "split": "train_shard_00001", "doc_id": 981 }, "chunk_id": "train_shard_00001_981_0", "global_id": 7055 }, { "text": "Antifungal susceptibility assay performed with 157 isolates showed that most of the isolates were resistant to the four azoles viz., clotrimazole, fluconazole, itraconazole, and ketoconazole, and the frequency of resistance was more in non-albicans Candida isolates. The susceptibility to azole drugs ranged from 7% to 48%, while 75% of the tested yeasts were susceptible to nystatin. Moreover, 88 isolates were also tested for their capacity to invade human cells using HeLa cells. In vitro invasion assay showed that most of the C. albicans isolates showed epithelial cell invasion as compared to isolates belonging to C. glabrata, C. parapsilosis and C. tropicalis.

Discussion

The identification of yeasts of clinical origin by sequencing of 28S rRNA gene performed better than MALDI-TOF MS. The present study reiterates the world scenario wherein there is a shift from Candida strains to emerging opportunistic pathogens which were earlier regarded as environmental strains. The present study enlightens the current understanding of identification methods for clinical yeast isolates, increased antifungal drug resistance, epithelial cell invasion as a virulence factor, and diversity of yeasts in Indian clinical samples.\n\nDistribution of Pathogenic Yeasts in Different Clinical Samples: Their Identification, Antifungal Susceptibility Pattern, and Cell Invasion Assays.", "token_count": 385, "char_count": 1424, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6186, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:25.795472", "source": { "split": "train_shard_00001", "doc_id": 981 }, "chunk_id": "train_shard_00001_981_1", "global_id": 7056 }, { "text": "

Background

Decreasing sea ice coverage across the Arctic Ocean due to climate change is expected to increase shipping activity through previously inaccessible shipping routes, including the Northwest Passage (NWP). Changing weather conditions typically encountered in the Arctic will still pose a risk for ships which could lead to an accident and the uncontrolled release of hydrocarbons onto NWP shorelines. We performed a metagenomic survey to characterize the microbial communities of various NWP shorelines and to determine whether there is a metabolic potential for hydrocarbon degradation in these microbiomes.

Results

We observed taxonomic and functional gene evidence supporting the potential of NWP beach microbes to degrade various types of hydrocarbons. The metagenomic and metagenome-assembled genome (MAG) taxonomy showed that known hydrocarbon-degrading taxa are present in these beaches. Additionally, we detected the presence of biomarker genes of aerobic and anaerobic degradation pathways of alkane and aromatic hydrocarbons along with complete degradation pathways for aerobic alkane degradation. Alkane degradation genes were present in all samples and were also more abundant (33.8 ± 34.5 hits per million genes, HPM) than their aromatic hydrocarbon counterparts (11.7 ± 12.3 HPM). Due to the ubiquity of MAGs from the genus Rhodococcus (23.8% of the MAGs), we compared our MAGs with Rhodococcus genomes from NWP isolates obtained using hydrocarbons as the carbon source to corroborate our results and to develop a pangenome of Arctic Rhodococcus. Our analysis revealed that the biodegradation of alkanes is part of the core pangenome of this genus. We also detected nitrogen and sulfur pathways as additional energy sources and electron donors as well as carbon pathways providing alternative carbon sources", "token_count": 470, "char_count": 1845, "word_count": 264, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:26.440613", "source": { "split": "train_shard_00001", "doc_id": 982 }, "chunk_id": "train_shard_00001_982_0", "global_id": 7057 }, { "text": "These pathways occur in the absence of hydrocarbons allowing microbes to survive in these nutrient-poor beaches.

Conclusions

Our metagenomic analyses detected the genetic potential for hydrocarbon biodegradation in these NWP shoreline microbiomes. Alkane metabolism was the most prevalent type of hydrocarbon degradation observed in these tidal beach ecosystems. Our results indicate that bioremediation could be used as a cleanup strategy, but the addition of adequate amounts of N and P fertilizers, should be considered to help bacteria overcome the oligotrophic nature of NWP shorelines.\n\nMetagenomic survey reveals hydrocarbon biodegradation potential of Canadian high Arctic beaches.", "token_count": 167, "char_count": 696, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7527, "quality_score": 0.8763, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:26.878218", "source": { "split": "train_shard_00001", "doc_id": 982 }, "chunk_id": "train_shard_00001_982_1", "global_id": 7058 }, { "text": "Escherichia coli is a gram-negative bacterium commonly found in mammals and birds’ intestinal microbiota. It can be easily isolated and has been studied for more than nine decades, making it an ideal model organism. It is mainly commensal but occasionally pathogenic, expressing virulence factors, antibiotic-resistance and acid-resistance genes, which contribute to its ability to persist and colonize diverse environments. Its multi-resistance, combined with the virulence of certain pathotypes (e.g. STEC), poses a recurring threat to public health, as treatment for clinical infections is not always straightforward. The remarkable propensity of E. coli for diversification and genomic variability is often referred to as an open pangenome. This project’s objective was to create the ‘Escobase’ database ( Es cherichia co li data base ), which is comprised exclusively of Escherichia coli isolates from cattle farms, allowing us to generate a reference set of genomes that can be used for comparative genomics on samples from cattle and cattle farms. Using the annotated E. coli genomes, we further built a catalog of predicted proteins that help E. coli survive in low pH environments, often encountered when the bacteria traverse through the intestine. We believe these two databases will be of great help to the community, and we plan to keep improving them and publish updated versions in the future.\n\nEscobase and AcR:Escherichia coli databases of genomes and acid resistance genes from isolates from cattle farms", "token_count": 359, "char_count": 1529, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6883, "quality_score": 0.8442, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:27.461000", "source": { "split": "train_shard_00001", "doc_id": 983 }, "chunk_id": "train_shard_00001_983_0", "global_id": 7059 }, { "text": "Pantoea ananatis is a member of a Pantoea species complex that causes center rot of bulb onions (A. cepa) and also infects other Allium crops like leeks (Allium porrum), chives (Allium schoenoprasum), bunching onion or Welsh onion (Allium fistulosum), and garlic (Allium sativum). This pathogen relies on a chromosomal phosphonate biosynthetic gene cluster (HiVir) and a plasmid-borne thiosulfinate tolerance cluster (alt) for onion pathogenicity and virulence, respectively. However, pathogenicity and virulence factors associated with other Allium species remain unknown. We used phenotype-dependent genome-wide association (GWAS) and phenotype-independent gene-pair coincidence (GPC) analyses on a panel of diverse 92 P. ananatis strains, which were inoculated on A. porrum and A. fistulosum × A. cepa under greenhouse conditions. Phenotypic assays showed that, in general, these strains were more aggressive on A. fistulosum × A. cepa as opposed to A. porrum. Of the 92 strains, only six showed highly aggressive foliar lesions on A. porrum compared to A. fistulosum × A. cepa. Conversely, nine strains showed highly aggressive foliar lesions on A. fistulosum × A. cepa compared to A. porrum. These results indicate that there are underlying genetic components in P", "token_count": 518, "char_count": 1433, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:28.116807", "source": { "split": "train_shard_00001", "doc_id": 984 }, "chunk_id": "train_shard_00001_984_0", "global_id": 7060 }, { "text": "ananatis that may drive pathogenicity in these two Allium spp. Based on GWAS for foliar pathogenicity, 835 genes were associated with P. ananatis' pathogenicity on A. fistulosum × A. cepa whereas 243 genes were associated with bacterial pathogenicity on A. porrum. The Hivir as well as the alt gene clusters were identified among these genes. Besides the 'HiVir' and the alt gene clusters that are known to contribute to pathogenicity and virulence from previous studies, genes annotated with functions related to stress responses, a potential toxin-antitoxin system, flagellar-motility, quorum sensing, and a previously described phosphonoglycan biosynthesis (pgb) cluster were identified. The GPC analysis resulted in the identification of 165 individual genes sorted into 39 significant gene-pair association components and 255 genes sorted into 50 significant gene-pair dissociation components. Within the coincident gene clusters, several genes that occurred on the GWAS outputs were associated with each other but dissociated with genes that did not appear in their respective GWAS output. To focus on candidate genes that could explain the difference in virulence between hosts, a comparative genomics analysis was performed on five P. ananatis strains that were differentially pathogenic on A. porrum or A. fistulosum × A. cepa. Here, we found a putative type III secretion system, and several other genes that occurred on both GWAS outputs of both Allium hosts. Further, we also demonstrated utilizing mutational analysis that the pepM gene in the HiVir cluster is important than the pepM gene in the pgb cluster for P. ananatis pathogenicity in A. fistulosum × A", "token_count": 526, "char_count": 1791, "word_count": 254, "semantic_coherence": 1, "information_density": 0.563, "quality_score": 0.7815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:28.803554", "source": { "split": "train_shard_00001", "doc_id": 984 }, "chunk_id": "train_shard_00001_984_1", "global_id": 7061 }, { "text": "cepa and A. porrum. Overall, our results support that P. ananatis may utilize a common set of genes or gene clusters to induce symptoms on A. fistulosum × A. cepa foliar tissue as well as A. cepa but implicates additional genes for infection on A. porrum.\n\nGenome-wide association and dissociation studies in Pantoea ananatis reveal potential virulence factors affecting Allium porrum and Allium fistulosum  ×  Allium cepa hybrid.", "token_count": 177, "char_count": 497, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:29.274888", "source": { "split": "train_shard_00001", "doc_id": 984 }, "chunk_id": "train_shard_00001_984_2", "global_id": 7062 }, { "text": "Gram-negative bloodstream infections (GNBSI) carry a significant global health burden. Escherichia coli and Klebsiella pneumoniae are the two most common causes of healthcare-associated GNBSI, which may arise from gastrointestinal tract (GIT) colonisation. Understanding genomic and phenotypic adaptations that underpin transition from GIT colonisation to invasive bloodstream infection could improve understanding of pathogenesis. This study identified ‘linked’ faecal and blood isolates from children with healthcare-associated GNBSI caused by E. coli and K. pneumoniae . Linked pairs were compared for antimicrobial resistance, biofilm formation, and underwent comparative genomic analysis via whole-genome sequencing, comparative average nucleotide identity (ANI) and core genome single nucleotide polymorphism (SNP) analysis. Five isolate pairs (three E. coli , two K. pneumoniae ) showed high relatedness, supporting GIT origin of bloodstream infection. Isolates within pairs had identical virulence genes whereas phenotypic assays revealed changes in antimicrobial susceptibility, with one pair undergoing changes in resistance gene profiles, and increased biofilm formation in 4/5 isolates. This study provides insight into within-host evolution from gastrointestinal colonisation to bloodstream invasion in Gram-negative pathogens. Convergence on metabolic adaptation and biofilm formation suggests these traits may be advantageous in healthcare-associated GNBSI. Further studies involving larger cohorts alongside functional validation of mutations are needed to better understand GNBSI pathogenesis.\n\nFrom Colonisation to Invasion: Genomic and Phenotypic Comparison of Faecal and Bloodstream Isolates from the same patients", "token_count": 406, "char_count": 1734, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6909, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:29.917105", "source": { "split": "train_shard_00001", "doc_id": 985 }, "chunk_id": "train_shard_00001_985_0", "global_id": 7063 }, { "text": "Pangenomics is an emerging field that uses a collection of genomes of a species instead of a single reference genome to overcome reference bias and study the within-species genetic diversity. Future pangenomics applications will require analyzing large and ever-growing collections of genomes. Therefore, the choice of data representation is a key determinant of the scope, as well as the computational and memory performance of pangenomic analyses. Current pangenome formats, while capable of storing genetic variations across multiple genomes, fail to capture the shared evolutionary and mutational histories among them, thereby limiting their applications. They are also inefficient for storage, and therefore face significant scaling challenges. In this manuscript, we propose PanMAN, a novel data structure that is information-wise richer than all existing pangenome formats – in addition to representing the alignment and genetic variation in a collection of genomes, PanMAN represents the shared mutational and evolutionary histories inferred between those genomes. By using “evolutionary compression”, PanMAN achieves 5.2 to 680-fold compression over other variation-preserving pangenomic formats. PanMAN’s relative performance generally improves with larger datasets and it is compatible with any method for inferring phylogenies and ancestral nucleotide states. Using SARS-CoV-2 as a case study, we show that PanMAN offers a detailed and accurate portrayal of the pathogen’s evolutionary and mutational history, facilitating the discovery of new biological insights. We also present panmanUtils , a software toolkit that supports common pangenomic analyses and makes PanMANs interoperable with existing tools and formats. PanMANs are poised to enhance the scale, speed, resolution, and overall scope of pangenomic analyses and data sharing.\n\nCompressive Pangenomics Using Mutation-Annotated Networks", "token_count": 407, "char_count": 1909, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:30.589350", "source": { "split": "train_shard_00001", "doc_id": 986 }, "chunk_id": "train_shard_00001_986_0", "global_id": 7064 }, { "text": "Uropathogenic Escherichia coli (UPEC) is one of the most common causes of urinary tract infections. Here, we report for the first time the whole-genome sequencing (WGS) and analysis of four extended-spectrum β-lactamase (ESBL), UPEC sequence type (ST) 127 isolates that were recovered from patients in five hospitals in Armenia from January to August of 2019. A phylogenetic comparison revealed that our isolates were closely related to each other by their core and accessory genomes, despite having been isolated from different regions and hospitals in Armenia. We identified unique genes in our isolates and in a closely related isolate recovered in France. The unique genes (hemolysin E virulence gene, lactate utilization operon lutABC, and endonuclease restriction modification operon hsdMSR) were identified in three separate genomic regions that were adjacent to prophage genes, including one region containing the TonB-dependent iron siderophore receptor gene ireA, which was only found in 5 other ST127 isolates from the European Nucleotide Archive (ENA). We further identified that these isolates possessed unique virulence and metabolic genes and harbored antibiotic resistance genes, including the ESBL genes blaCTX-M-3 (n = 3), blaCTX-M-236 (n = 1), and blaTEM-1 (n = 1), in addition to a quinolone resistance protein gene qnrD1 (n = 1), which was absent in the ST127 isolates obtained from the ENA", "token_count": 478, "char_count": 1521, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8107, "entities": { "genes": [ "ST127" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:31.244095", "source": { "split": "train_shard_00001", "doc_id": 987 }, "chunk_id": "train_shard_00001_987_0", "global_id": 7065 }, { "text": "Moreover, a plasmid replicon gene IncI2 (n = 1) was unique to ARM88 of the Armenian isolates. Our findings demonstrate that at the time of this study, E. coli ST127 was a cause of urinary tract infections in patients in different regions of Armenia, with a possibility of cross-country transmission between Armenia and France. IMPORTANCE Whole-genome sequencing studies of pathogens causing infectious diseases are seriously lacking in Armenia, hampering global efforts to track, trace and contain infectious disease outbreaks. In this study, we report for the first-time the whole-genome sequencing and analysis of ESBL UPEC ST127 isolates recovered from hospitalized patients in Armenia and compare them with other E. coli ST127 retrieved from the ENA. We found close genetic similarities of the Armenian isolates, indicating that E. coli ST127 was potentially a dominant lineage causing urinary tract infections in Armenia. Furthermore, we identified unique genes that were horizontally acquired in the clusters of Armenian and French isolates that were absent in other ST127 isolates obtained from the ENA. Our findings highlight a possible cross-country transmission between Armenia and France and the idea that the implementation of WGS surveillance could contribute to global efforts in tackling antibiotic resistance, as bacteria carrying antimicrobial resistance (AMR) genes do not recognize borders.\n\nAn Emerging Lineage of Uropathogenic Extended Spectrum β-Lactamase Escherichia coli ST127.", "token_count": 372, "char_count": 1515, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5936, "quality_score": 0.7968, "entities": { "genes": [ "ARM88", "ST127" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:31.826245", "source": { "split": "train_shard_00001", "doc_id": 987 }, "chunk_id": "train_shard_00001_987_1", "global_id": 7066 }, { "text": "Vibrio cholerae O1 causes the diarrheal disease cholera, and the small intestine is the site of active infection. During cholera, cholera toxin is secreted from V. cholerae and induces a massive fluid influx into the small intestine, which causes vomiting and diarrhea. Typically, V. cholerae genomes are sequenced from bacteria passed in stool, but rarely from vomit, a fluid that may more closely represents the site of active infection. We hypothesized that V. cholerae O1 population bottlenecks along the gastrointestinal tract would result in reduced genetic variation in stool compared to vomit. To test this, we sequenced V. cholerae genomes from 10 cholera patients with paired vomit and stool samples. Genetic diversity was low in both vomit and stool, consistent with a single infecting population rather than coinfection with divergent V. cholerae O1 lineages. The amount of single-nucleotide variation decreased from vomit to stool in four patients, increased in two, and remained unchanged in four. The variation in gene presence/absence decreased between vomit and stool in eight patients and increased in two. Pangenome analysis of assembled short-read sequencing demonstrated that the toxin-coregulated pilus operon more frequently contained deletions in genomes from vomit compared to stool. However, these deletions were not detected by PCR or long-read sequencing, indicating that interpreting gene presence or absence patterns from short-read data alone may be incomplete. Overall, we found that V. cholerae O1 isolated from stool is genetically similar to V. cholerae recovered from the upper intestinal tract.

Importance

Vibrio cholerae O1, the bacterium that causes cholera, is ingested in contaminated food or water and then colonizes the upper small intestine and is excreted in stool. Shed V", "token_count": 520, "char_count": 1890, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5572, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:32.488332", "source": { "split": "train_shard_00001", "doc_id": 988 }, "chunk_id": "train_shard_00001_988_0", "global_id": 7067 }, { "text": "cholerae genomes from stool are usually studied, but V. cholerae isolated from vomit may be more representative of where V. cholerae colonizes in the upper intestinal epithelium. V. cholerae may experience bottlenecks, or large reductions in bacterial population sizes and genetic diversity, as it passes through the gut. Passage through the gut may select for distinct V. cholerae mutants that are adapted for survival and gut colonization. We did not find strong evidence for such adaptive mutations, and instead observed that passage through the gut results in modest reductions in V. cholerae genetic diversity, and only in some patients. These results fill a gap in our understanding of the V. cholerae life cycle, transmission, and evolution.\n\nVibrio cholerae O1 experiences mild bottlenecks through the gastrointestinal tract in some but not all cholera patients.", "token_count": 254, "char_count": 923, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:32.977946", "source": { "split": "train_shard_00001", "doc_id": 988 }, "chunk_id": "train_shard_00001_988_1", "global_id": 7068 }, { "text": "Understanding the forces shaping genomic diversity within bacterial species is essential for interpreting microbiome evolution, ecology, and host associations. Here, we analyze over one hundred prevalent gut bacterial species using the Unified Human Gut Genome (UHGG) collection to characterize patterns of intra-specific genomic variability. Gene content divergence scales predictably with divergence in core genome single nucleotide polymorphisms (SNPs), though there is substantial variability in evolutionary dynamics across species. Overall, accessory genes exhibit consistently faster linkage decay compared to core SNPs, highlighting the fluidity of functional repertoires within species boundaries. This signal is strongest for mobile genetic elements, which show minimal linkage to core genome SNPs. Together, our findings reveal species-specific recombination regimes in the gut microbiome, underscoring the importance of accounting for horizontal gene transfer and genome plasticity in microbiome-wide association studies and evolutionary models.\n\nLinkage of nucleotide and functional diversity varies across gut bacteria", "token_count": 229, "char_count": 1132, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7172, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:33.449707", "source": { "split": "train_shard_00001", "doc_id": 989 }, "chunk_id": "train_shard_00001_989_0", "global_id": 7069 }, { "text": "β-galactosidase from dairy yeast was immobilized on silicon dioxide based nanoparticles for the hydrolysis of whey. The biocatalyst was checked for the optimal thermal and pH stability. Consequently, the immobilized β-galactosidase was recycled 15 times for the hydrolysis of lactose (37 °C and pH 7.0) without loss of a significant amount of catalytic activity. Almost 91% of lactose hydrolysis was obtained from using concentrated cheese whey. Considering the available approaches for efficient bioconversion of hydrolyzed whey into ethanol, co-immobilization strategy was used using Saccharomyces cerevisiae and Kluyveromyces marxianus for fermentation. Same vessel hydrolysis and fermentation process was employed using silicon dioxide nanoparticles based enzyme immobilization along with co-immobilized yeast cell and provided a maximum ethanol titer of 63.9 g/L on concentrated cheese whey (150 g/L). Hence, the nano-biocatalytic system along with immobilized S.cerevisiae could improve the viability of ethanol production from cheese whey.\n\nUse of silicon dioxide nanoparticles for β-galactosidase immobilization and modulated ethanol production by co-immobilized K. marxianus and S. cerevisiae in deproteinized cheese whey", "token_count": 357, "char_count": 1230, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5723, "quality_score": 0.7861, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:34.026001", "source": { "split": "train_shard_00001", "doc_id": 990 }, "chunk_id": "train_shard_00001_990_0", "global_id": 7070 }, { "text": "Pangenomes, by including genetic diversity, should reduce reference bias by better representing new samples compared to them. Yet when comparing a new sample to a pangenome, variants in the pangenome that are not part of the sample can be misleading, for example, causing false read mappings. These irrelevant variants are generally rarer in terms of allele frequency, and have previously been dealt with using allele frequency filters. However, this is a blunt heuristic that both fails to remove some irrelevant variants and removes many relevant variants. We propose a new approach, inspired by local ancestry inference methods, that imputes a personalized pangenome subgraph based on sampling local haplotypes according to k -mer counts in the reads. Our approach is tailored for the Giraffe short read aligner, as the indexes it needs for read mapping can be built quickly. We compare the accuracy of our approach to state-of-the-art methods using graphs from the Human Pangenome Reference Consortium. The resulting personalized pangenome pipelines provide faster pangenome read mapping than comparable pipelines that use a linear reference, reduce small variant genotyping errors by 4x relative to the Genome Analysis Toolkit (GATK) best-practice pipeline, and for the first time make short-read structural variant genotyping competitive with long-read discovery methods.\n\nPersonalized Pangenome References", "token_count": 310, "char_count": 1412, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6779, "quality_score": 0.8389, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:34.604776", "source": { "split": "train_shard_00001", "doc_id": 991 }, "chunk_id": "train_shard_00001_991_0", "global_id": 7071 }, { "text": "The human gut microbiota has been the subject of many studies, establishing its central role in host health and disease. Interplay between mutations, horizontal gene transfer, natural selection, and genetic drift, lead to genetic diversity within these species, resulting in different phenotypes and effects on the host. Pangenome represents the collective gene pool of different strains of the same species. Here, we created pangenomes for 728 human gut prokaryotic species, holding four times more genes than the highest quality individual genome, showcasing the genetic diversity inherent in the human gut population. We find these species have a core set of about a thousand genes that defines them, distinct even between closely related species, and an accessory set of genes that are unique to the different strains. Furthermore, we show a spectrum of microbial behavior, while some species exhibit a saturated or “closed” pangenome, suggesting a limited set of genetic capabilities, others maintain an “open” pangenome, indicating elevated adaptability through genetic diversity. We discover that high strain variability is associated with the capacity of species to undergo sporulation, whereas low strain variability is associated with carrying genes that facilitate antibiotic resistances, suggesting different evolutionary strategies for survival taken by these microbes. We further map the landscape of antibiotic resistance genes across the human gut population, and find 237 cases of extreme resistance, predominantly of Enterobacteriaceae species, even to last resort antibiotics kept for cases where traditional treatments have failed. Lastly, we associate microbial strain level differences with human age and sex, exemplifying how the presence of specific genes in Akkermansia muciniphila and Phocaeicola vulgatus relate to host characteristics. Overall, our research provides a comprehensive overview of the evolution, genetic complexity and functional potential of the human gut microbiota, emphasizing its significant implications for human health and disease. The pangenomes and the antibiotic resistances map constitute a valuable resource for further scientific research and therapeutic advancements.\n\nPangenomes of Human Gut Microbiota Uncover Links Between Genetic Diversity and Stress Response", "token_count": 466, "char_count": 2320, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:35.251530", "source": { "split": "train_shard_00001", "doc_id": 992 }, "chunk_id": "train_shard_00001_992_0", "global_id": 7072 }, { "text": "Pseudomonas aeruginosa is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic diversity and the functional metabolic landscape of P. aeruginosa clinical isolates. To better understand the metabolic repertoire of P. aeruginosa in infection, we deeply profiled a representative set from a library of 971 clinical P. aeruginosa isolates with corresponding patient metadata and bacterial phenotypes. The genotypic clustering based on whole-genome sequencing of the isolates, multilocus sequence types, and the phenotypic clustering generated from a multi-parametric analysis were compared to each other to assess the genotype-phenotype correlation. Genome-scale metabolic network reconstructions were developed for each isolate through amendments to an existing PA14 network reconstruction. These network reconstructions show diverse metabolic functionalities and enhance the collective P. aeruginosa pangenome metabolic repertoire. Characterizing this rich set of clinical P. aeruginosa isolates allows for a deeper understanding of the genotypic and metabolic diversity of the pathogen in a clinical setting and lays a foundation for further investigation of the metabolic landscape of this pathogen and host-associated metabolic differences during infection.\n\nModel-driven characterization of functional diversity of <i>Pseudomonas aeruginosa</i> clinical isolates with broadly representative phenotypes.", "token_count": 377, "char_count": 1563, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5567, "quality_score": 0.7784, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:35.837518", "source": { "split": "train_shard_00001", "doc_id": 993 }, "chunk_id": "train_shard_00001_993_0", "global_id": 7073 }, { "text": "Genetic markers currently used for the discrimination of Lactobacillus delbrueckii subspecies have low efficiency for identification at subspecies level. Therefore, our objective in this study was to select novel genetic markers for accurate identification and discrimination of six L. delbrueckii subspecies based on pangenome analysis. We evaluated L. delbrueckii genomes to avoid making incorrect conclusions in the process of selecting genetic markers due to mislabeled genomes. Genome analysis showed that two genomes of L. delbrueckii subspecies deposited at NCBI were misidentified. Based on these results, subspecies-specific genetic markers were selected by comparing the core and pangenomes. Genetic markers were confirmed to be specific for 59,196,562 genome sequences via in silico analysis. They were found in all strains of the same subspecies, but not in other subspecies or bacterial strains. These genetic markers also could be used to accurately identify genomes at the subspecies level for genomes known at the species level. A real-time PCR method for detecting three main subspecies (L. delbrueckii subsp. delbrueckii, lactis, and bulgaricus) was developed to cost-effectively identify them using genetic markers. Results showed 100% specificity for each subspecies. These genetic markers could differentiate each subspecies from 44 other lactic acid bacteria. This real-time PCR method was then applied to monitor 26 probiotics and dairy products. It was also used to identify 64 unknown strains isolated from raw milk samples and dairy products. Results confirmed that unknown isolates and subspecies contained in the product could be accurately identified using this real-time PCR method.\n\nIdentification and Monitoring of Lactobacillus delbrueckii Subspecies Using Pangenomic-Based Novel Genetic Markers.", "token_count": 492, "char_count": 1892, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5367, "quality_score": 0.7683, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:36.501028", "source": { "split": "train_shard_00001", "doc_id": 994 }, "chunk_id": "train_shard_00001_994_0", "global_id": 7074 }, { "text": "Ascites is a common complication in patients with decompensated liver cirrhosis. Spontaneous bacterial peritonitis (SBP) is the most frequent infection, affecting up to 30% of hospitalized patients with ascites. Multidrug-resistant bacteria in patients with liver cirrhosis are becoming more common, particularly in nosocomial infections. With early detection and adequate antibiotic therapy, the mortality rate of SBP can be reduced from over 90% to 15-20%. However, the etiologic agent remains undetected by conventional pathogen diagnostics from ascites in more than half of the patients. Here, we describe a robust workflow combining long read metagenome sequencing with best practices for low microbial biomass sample processing and bioinformatic analytics, to detect and characterize pathogens from the cirrhotic ascites of SBP patients, as a complement to routine microbiological diagnostics. This approach identified Paracoccus yeei as a likely etiologic agent for a patient who developed a fever after successful treatment of an Escherichia coli infection. Analysis of the genome of P. yeei recovered directly from ascites delineated pathogenicity-related features and an antimicrobial resistance profile consistent with the patient’s treatment. Pangenome phylogenetics placed the P. yeei strain closest to isolates associated with abdominal infections. Our study underscores the utility of metagenomics for a rapid and comprehensive assessment of infectious agents, suggesting a novel and rarely reported pathogen contributing to SBP with potential implications for diagnostics and therapeutic strategies.

Importance

Our study demonstrates the clinical utility of real-time, long-read metagenomics in identifying elusive pathogens in Spontaneous Bacterial Peritonitis (SBP), a condition with high mortality and frequently inconclusive conventional diagnostics. By uncovering Paracoccus yeei as a likely secondary etiologic agent and characterizing its pathogenicity and AMR profile, our findings expand the known etiology of SBP and emphasize the potential of metagenomics to improve diagnostic accuracy, guide targeted treatment, and ultimately reduce mortality rates in infectious diseases. This approach could shape future clinical practice for managing complex infections.", "token_count": 518, "char_count": 2295, "word_count": 309, "semantic_coherence": 1, "information_density": 0.6214, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:37.155580", "source": { "split": "train_shard_00001", "doc_id": 995 }, "chunk_id": "train_shard_00001_995_0", "global_id": 7075 }, { "text": "Detection of Paracoccus yeei in Spontaneous Bacterial Peritonitis using Rapid, Long Read Sequencing", "token_count": 35, "char_count": 106, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:37.513174", "source": { "split": "train_shard_00001", "doc_id": 995 }, "chunk_id": "train_shard_00001_995_1", "global_id": 7076 }, { "text": "

Introduction

Serratia marcescens is most commonly known as an opportunistic pathogen causing nosocomial infections. It, however, was shown to infect a wide range of hosts apart from vertebrates such as insects or plants as well, being either pathogenic or growth-promoting for the latter. Despite being extensively studied in terms of virulence mechanisms during human infections, there has been little evidence of which factors determine S. marcescens host specificity. On that account, we analyzed S. marcescens pangenome to reveal possible specificity factors.

Methods

We selected 73 high-quality genome assemblies of complete level and reconstructed the respective pangenome and reference phylogeny based on core genes alignment. To find an optimal pipeline, we tested current pangenomic tools and obtained several phylogenetic inferences. The pangenome was rich in its accessory component and was considered open according to the Heaps' law. We then applied the pangenome-wide associating method (pan-GWAS) and predicted positively associated gene clusters attributed to three host groups, namely, humans, insects, and plants.

Results

According to the results, significant factors relating to human infections included transcriptional regulators, lipoproteins, ABC transporters, and membrane proteins. Host preference toward insects, in its turn, was associated with diverse enzymes, such as hydrolases, isochorismatase, and N-acetyltransferase with the latter possibly exerting a neurotoxic effect. Finally, plant infection may be conducted through type VI secretion systems and modulation of plant cell wall synthesis. Interestingly, factors associated with plants also included putative growth-promoting proteins like enzymes performing xenobiotic degradation and releasing ammonium irons. We also identified overrepresented functional annotations within the sets of specificity factors and found that their functional characteristics fell into separate clusters, thus, implying that host adaptation is represented by diverse functional pathways. Finally, we found that mobile genetic elements bore specificity determinants", "token_count": 497, "char_count": 2174, "word_count": 281, "semantic_coherence": 1, "information_density": 0.7153, "quality_score": 0.8577, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:38.163878", "source": { "split": "train_shard_00001", "doc_id": 996 }, "chunk_id": "train_shard_00001_996_0", "global_id": 7077 }, { "text": "In particular, prophages were mainly associated with factors related to humans, while genetic islands-with insects and plants, respectively.

Discussion

In summary, functional enrichments coupled with pangenomic inferences allowed us to hypothesize that the respective host preference is carried out through distinct molecular mechanisms of virulence. To the best of our knowledge, the presented research is the first to identify specific genomic features of S. marcescens assemblies isolated from different hosts at the pangenomic level.\n\nThe man, the plant, and the insect: shooting host specificity determinants in Serratia marcescens pangenome.", "token_count": 156, "char_count": 668, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7816, "quality_score": 0.8908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:38.598502", "source": { "split": "train_shard_00001", "doc_id": 996 }, "chunk_id": "train_shard_00001_996_1", "global_id": 7078 }, { "text": "

Background

Discerning genes crucial to antimicrobial resistance (AMR) mechanisms is becoming more and more important to accurately and swiftly identify AMR pathogenic strains. Pangenome-wide association studies (e.g. Scoary) identified numerous putative AMR genes. However, only a tiny proportion of the putative resistance genes are annotated by AMR databases or Gene Ontology. In addition, many putative resistance genes are of unknown function (termed hypothetical proteins). An annotation tool is crucially needed in order to reveal the functional organization of the resistome and expand our knowledge of the AMR gene repertoire.

Results

We developed an approach (PangenomeNet) for building co-functional networks from pan-genomes to infer functions for hypothetical genes. Using Escherichia coli as an example, we demonstrated that it is possible to build co-functional network from its pan-genome using co-inheritance, domain-sharing, and protein-protein-interaction information. The investigation of the network revealed that it fits the characteristics of biological networks and can be used for functional inferences. The subgraph consisting of putative meropenem resistance genes consists of clusters of stress response genes and resistance gene acquisition pathways. Resistome subgraphs also demonstrate drug-specific AMR genes such as beta-lactamase, as well as functional roles shared among multiple classes of drugs, mostly in the stress-related pathways.

Conclusions

By demonstrating the idea of pan-genome-based co-functional network on the E. coli species, we showed that the network can infer functional roles of the genes, including those without functional annotations, and provides holistic views on the putative antimicrobial resistomes. We hope that the pan-genome network idea can help formulate hypothesis for targeted experimental works.\n\nPangenomeNet: a pan-genome-based network reveals functional modules on antimicrobial resistome for Escherichia coli strains.", "token_count": 465, "char_count": 2012, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5817, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:39.244395", "source": { "split": "train_shard_00001", "doc_id": 997 }, "chunk_id": "train_shard_00001_997_0", "global_id": 7079 }, { "text": "The adoption of agriculture triggered a rapid shift towards starch-rich diets in human populations1. Amylase genes facilitate starch digestion, and increased amylase copy number has been observed in some modern human populations with high-starch intake2, although evidence of recent selection is lacking3,4. Here, using 94 long-read haplotype-resolved assemblies and short-read data from approximately 5,600 contemporary and ancient humans, we resolve the diversity and evolutionary history of structural variation at the amylase locus. We find that amylase genes have higher copy numbers in agricultural populations than in fishing, hunting and pastoral populations. We identify 28 distinct amylase structural architectures and demonstrate that nearly identical structures have arisen recurrently on different haplotype backgrounds throughout recent human history. AMY1 and AMY2A genes each underwent multiple duplication/deletion events with mutation rates up to more than 10,000-fold the single-nucleotide polymorphism mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome-based approach, we infer structural haplotypes across thousands of humans identifying extensively duplicated haplotypes at higher frequency in modern agricultural populations. Leveraging 533 ancient human genomes, we find that duplication-containing haplotypes (with more gene copies than the ancestral haplotype) have rapidly increased in frequency over the past 12,000 years in West Eurasians, suggestive of positive selection. Together, our study highlights the potential effects of the agricultural revolution on human genomes and the importance of structural variation in human adaptation.\n\nRecurrent evolution and selection shape structural diversity at the amylase locus.", "token_count": 413, "char_count": 1821, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6456, "quality_score": 0.8228, "entities": { "genes": [ "AMY2A", "AMY1", "AMY2B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:39.871958", "source": { "split": "train_shard_00001", "doc_id": 998 }, "chunk_id": "train_shard_00001_998_0", "global_id": 7080 }, { "text": "Fosfomycin has gained attention as a combination therapy for methicillin-resistant Staphylococcus aureus infections. Hence, the detection of novel fosfomycin-resistance mechanisms in S. aureus is important. Here, the minimal inhibitory concentrations (MICs) of fosfomycin in CC1 methicillin-resistant S. aureus were determined. The pangenome analysis and comparative genomics were used to analyse CC1 MRSA. The gene function was confirmed by cloning the gene into pTXΔ. A phylogenetic tree was constructed to determine the clustering of the CC1 strains of S. aureus. We identified a novel gene, designated fosY, that confers fosfomycin resistance in S. aureus. The FosY protein is a putative bacillithiol transferase enzyme sharing 65.9-77.5% amino acid identity with FosB and FosD, respectively. The function of fosY in decreasing fosfomycin susceptibility was confirmed by cloning it into pTXΔ. The pTX-fosY transformant exhibited a 16-fold increase in fosfomycin MIC. The bioinformatic analysis showed that fosY is in a novel genomic island designated RIfosY (for \"resistance island carrying fosY\") that originated from other species. The global phylogenetic tree of ST1 MRSA displayed this fosY-positive ST1 clone, originating from different regions, in the same clade. The novel resistance gene in the fos family, fosY, and a genomic island, RIfosY, can promote cross-species gene transfer and confer resistance to CC1 MRSA causing the failure of clinical treatment. This emphasises the importance of genetic surveillance of resistance genes among MRSA isolates.", "token_count": 509, "char_count": 1687, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "CC1", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:40.530268", "source": { "split": "train_shard_00001", "doc_id": 999 }, "chunk_id": "train_shard_00001_999_0", "global_id": 7081 }, { "text": "The novel fosfomycin resistance gene fosY is present on a genomic island in CC1 methicillin-resistant Staphylococcus aureus.", "token_count": 42, "char_count": 131, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:40.941197", "source": { "split": "train_shard_00001", "doc_id": 999 }, "chunk_id": "train_shard_00001_999_1", "global_id": 7082 }, { "text": "Cellulosomes, which are multienzyme complexes from anaerobic bacteria, are considered nature's finest cellulolytic machinery. Thus, constructing a cellulosome in an industrial yeast has long been a goal pursued by scientists. However, it remains highly challenging due to the size and complexity of cellulosomal genes. Here, we overcame the difficulties by synthesizing the Clostridium thermocellum scaffoldin gene (CipA) and the anchoring protein gene (OlpB) using advanced synthetic biology techniques. The engineered Kluyveromyces marxianus, a probiotic yeast, secreted a mixture of dockerin-fused fungal cellulases, including an endoglucanase (TrEgIII), exoglucanase (CBHII), β-glucosidase (NpaBGS), and cellulase boosters (TaLPMO and MtCDH). The confocal microscopy results confirmed the cell-surface display of OlpB-ScGPI and fluorescence-activated cell sorting analysis results revealed that almost 81% of yeast cells displayed OlpB-ScGPI. We have also demonstrated the cellulosome complex formation using purified and crude cellulosomal proteins. Native polyacrylamide gel electrophoresis and mass spectrometric analysis further confirmed the cellulosome complex formation. Our engineered cellulosome can accommodate up to 63 enzymes, whereas the largest engineered cellulosome reported thus far could accommodate only 12 enzymes and was expressed by a plasmid instead of chromosomal integration. Interestingly, CipA 2B9C (with two cellulose binding modules, CBM) released significantly higher quantities of reducing sugars compared with other CipA variants, thus confirming the importance of cohesin numbers and CBM domain on cellulosome complex", "token_count": 496, "char_count": 1731, "word_count": 215, "semantic_coherence": 1, "information_density": 0.7535, "quality_score": 0.8767, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:41.623757", "source": { "split": "train_shard_00001", "doc_id": 1000 }, "chunk_id": "train_shard_00001_1000_0", "global_id": 7083 }, { "text": "The engineered yeast host efficiently degraded cellulosic substrates and released 3.09 g/L and 8.61 g/L of ethanol from avicel and phosphoric acid-swollen cellulose, respectively, which is higher than any previously constructed yeast cellulosome.\n\nConstructing a yeast to express the largest cellulosome complex on the cell surface.", "token_count": 88, "char_count": 332, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8478, "quality_score": 0.9239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:42.026677", "source": { "split": "train_shard_00001", "doc_id": 1000 }, "chunk_id": "train_shard_00001_1000_1", "global_id": 7084 }, { "text": "Campylobacter hyointestinalis is an emerging pathogen currently divided in two subspecies: C. hyointestinalis subsp. lawsonii which is restricted to pigs, and C. hyointestinalis subsp. hyointestinalis which can be found in a much wider range of mammalian hosts. Despite C. hyointestinalis has been reported as an emerging pathogen, its evolutionary and host-associated diversification patterns are still vastly unexplored. For this reason, we whole-genome sequenced 13 C. hyointestinalis subsp. hyointestinalis strains and performed a comprehensive comparative analysis including publicly available genomes of C. hyointestinalis subsp. hyointestinalis and C. hyointestinalis subsp. lawsonii to gain insight into the genomic variation of these differentially-adapted subspecies. Both subspecies are distinct phylogenetic lineages which present a barrier to homologous recombination, suggesting genetic isolation. This is further supported by accessory gene patterns that recapitulate the core genome phylogeny. Additionally, C. hyointestinalis subsp. hyointestinalis presents a bigger and more diverse accessory genome, which probably reflects its capacity to colonize different mammalian hosts unlike C. hyointestinalis subsp. lawsonii that is host-restricted. This greater plasticity in the accessory genome of C. hyointestinalis subsp. hyointestinalis correlates to a higher incidence of genome-wide recombination events, that may be the underlying mechanism driving its diversification. Concordantly, both subspecies present distinct patterns of gene families involved in genome plasticity and DNA repair like CRISPR-associated proteins and restriction-modification systems. Together, our results provide an overview of the genetic mechanisms shaping the genomes of C. hyointestinalis subspecies, contributing to understand the biology of Campylobacter species that are increasingly found as emerging pathogens.\n\nPangenome analysis reveals genetic isolation inCampylobacter hyointestinalissubspecies adapted to different mammalian hosts", "token_count": 496, "char_count": 2046, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5759, "quality_score": 0.7879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:43.150636", "source": { "split": "train_shard_00001", "doc_id": 1001 }, "chunk_id": "train_shard_00001_1001_0", "global_id": 7085 }, { "text": "Bacterial soft rot is a devastating disease for a wide range of crops, vegetables, and ornamental plants including konjac (Amorphophallus konjac). However, the pangenome and genomic plasticity of the konjac soft rot pathogens is little explored. In this study, we reported the complete genome sequences of 11 bacterial isolates that can cause typical soft rot symptoms in konjac by in vitro and in vivo pathogenicity tests. Based on in silico DNA-DNA hybridization, average nucleotide identity and phylogenomic analysis, all 11 isolates were determined to be Pectobacterium aroidearum. In addition, synteny analysis of these genomes revealed considerable chromosomal inversions, one of which is triggered by homologous recombination of ribose operon. Pangenome analysis and COG enrichment analysis showed that the pangenome of P. aroidearum is open and that accessory genes are enriched in replication, recombination, and repair. Variations in type IV secretion system and type VI secretion system were found, while plant cell wall degrading enzymes were conserved. Furthermore, sequence analyses also provided evidence for the presence of a type V secretion system in Pectobacterium. These findings advance our understanding of the pathogenicity determinants, genomic plasticity, and evolution of P. aroidearum.\n\nAnalysis of the Taxonomy, Synteny, and Virulence Factors for Soft Rot Pathogen <i>Pectobacterium aroidearum</i> in <i>Amorphophallus konjac</i> Using Comparative Genomics.", "token_count": 452, "char_count": 1579, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6603, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:43.787620", "source": { "split": "train_shard_00001", "doc_id": 1002 }, "chunk_id": "train_shard_00001_1002_0", "global_id": 7086 }, { "text": "Acinetobacter baumannii, a notorious opportunistic pathogen, presents a formidable challenge in both clinical and environmental fields due to its resilience and ability to acquire resistance. This study undertook a comprehensive analysis of 183 A. baumannii isolates collected between 2019 and 2022 from intra-hospital infections (IHI), hospital sewages (Hs), wastewater treatment plants (WWTP), and adjacent river waters from two Southern cities, focusing on their resistome, virulome, and mobilome through isolation on chromogenic media, identification by MALDI-TOF-MS and antibiotic susceptibility testing by disk diffusion) followed by genotypic characterization [Whole Genome Sequencing (WGS), 3rd generation sequencing through the MinION (ONT) platform, pangenome description, and respectively horizontal gene transfer through conjugation assays]. Our findings reveal significant genomic plasticity and the prevalence of high-risk international clones, underlining the potential of these isolates to act as reservoirs for antibiotic resistance genes (ARGs) that could be dynamically exchanged between clinical and environmental settings through mobile genetic elements (MGEs) such as the pMAL1 plasmids and the critical role of WWTPs in the persistence and spread of A. baumannii. Moreover, our study presents the first report of the co-occurrence of bla OXA-23 and bla OXA-72 in A. baumannii ST2 clone. Thus, our research underscores the necessity for integrated surveillance and targeted interventions across healthcare and environmental sectors to mitigate the risk posed by this adaptable pathogen.\n\nDecoding the resistome, virulome and mobilome of clinical versus aquatic Acinetobacter baumannii in southern Romania.", "token_count": 474, "char_count": 1805, "word_count": 232, "semantic_coherence": 1, "information_density": 0.694, "quality_score": 0.847, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:44.436304", "source": { "split": "train_shard_00001", "doc_id": 1003 }, "chunk_id": "train_shard_00001_1003_0", "global_id": 7087 }, { "text": "Microbial genomes have highly variable gene content, and the evolutionary history of microbial populations is shaped by gene gain and loss mediated by horizontal gene transfer and selection. To evaluate the influence of selection on gene content variation in hydrothermal vent microbial populations, we examined 22 metagenome-assembled genomes (MAGs) (70 to 97% complete) from the ubiquitous vent Epsilonbacteraeota genus Sulfurovum that were recovered from two deep-sea hydrothermal vent regions, Axial Seamount in the northeastern Pacific Ocean (13 MAGs) and the Mid-Cayman Rise in the Caribbean Sea (9 MAGs). Genes involved in housekeeping functions were highly conserved across Sulfurovum lineages. However, genes involved in environment-specific functions, and in particular phosphate regulation, were found mostly in Sulfurovum genomes from the Mid-Cayman Rise in the low-phosphate Atlantic Ocean environment, suggesting that nutrient limitation is an important selective pressure for these bacteria. Furthermore, genes that were rare within the pangenome were more likely to undergo positive selection than genes that were highly conserved in the pangenome, and they also appeared to have experienced gene-specific sweeps. Our results suggest that selection is a significant driver of gene gain and loss for dominant microbial lineages in hydrothermal vents and highlight the importance of factors like nutrient limitation in driving microbial adaptation and evolution.IMPORTANCE Microbes can alter their gene content through the gain and loss of genes. However, there is some debate as to whether natural selection or neutral processes play a stronger role in molding the gene content of microbial genomes. In this study, we examined variation in gene content for the Epsilonbacteraeota genus Sulfurovum from deep-sea hydrothermal vents, which are dynamic habitats known for extensive horizontal gene transfer within microbial populations. Our results show that natural selection is a strong driver of Sulfurovum gene content and that nutrient limitation in particular has shaped the Sulfurovum genome, leading to differences in gene content between ocean basins", "token_count": 517, "char_count": 2219, "word_count": 310, "semantic_coherence": 1, "information_density": 0.5258, "quality_score": 0.7629, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:04:45.100615", "source": { "split": "train_shard_00001", "doc_id": 1004 }, "chunk_id": "train_shard_00001_1004_0", "global_id": 7088 }, { "text": "Our results also suggest that recently acquired genes undergo stronger selection than genes that were acquired in the more distant past. Overall, our results highlight the importance of natural selection in driving the evolution of microbial populations in these dynamic habitats.\n\nSelection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents.", "token_count": 103, "char_count": 451, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7231, "quality_score": 0.8615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:45.481907", "source": { "split": "train_shard_00001", "doc_id": 1004 }, "chunk_id": "train_shard_00001_1004_1", "global_id": 7089 }, { "text": "

Design:

ing minimal bacterial genomes remains a key challenge in synthetic biology. There is currently a lack of efficient tools for the rapid generation of streamlined bacterial genomes, limiting research in this area. Here, using a pangenome dataset for Escherichia coli , we explore how generation of minimal genomes can be achieved using variational autoencoders. Our results show that variational autoencoders can successfully create minimised genomes retaining the essential genes identified in the literature. This study proposes a rapid, machine learning-based approach for bacterial sequence generation, that could accelerate the genomic design process.\n\nDesigning minimalE. coligenomes using variational autoencoders", "token_count": 166, "char_count": 743, "word_count": 100, "semantic_coherence": 1, "information_density": 0.74, "quality_score": 0.87, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:45.932303", "source": { "split": "train_shard_00001", "doc_id": 1005 }, "chunk_id": "train_shard_00001_1005_0", "global_id": 7090 }, { "text": "

Background

As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses. Several data structures have been proposed for representing collections of genomes as pangenomes, in particular graphs.

Results

In this work, we collect all publicly available high-quality human haplotypes and construct the largest human pangenome graphs to date, incorporating 52 individuals in addition to two synthetic references (CHM13 and GRCh38). We build variation graphs and de Bruijn graphs of this collection using five of the state-of-the-art tools: Bifrost, mdbg, Minigraph, Minigraph-Cactus and pggb. We examine differences in the way each of these tools represents variations between input sequences, both in terms of overall graph structure and representation of specific genetic loci.

Conclusion

This work sheds light on key differences between pangenome graph representations, informing end-users on how to select the most appropriate graph type for their application.\n\nComparing methods for constructing and representing human pangenome graphs.", "token_count": 265, "char_count": 1217, "word_count": 162, "semantic_coherence": 1, "information_density": 0.716, "quality_score": 0.858, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:46.480744", "source": { "split": "train_shard_00001", "doc_id": 1006 }, "chunk_id": "train_shard_00001_1006_0", "global_id": 7091 }, { "text": "The current availability of complete genome sequences has allowed knowing that bacterial genomes can bear genes not present in the genome of all the strains from a specific species. So, the genes shared by all the strains comprise the core of the species, but the pangenome can be much greater and usually includes genes appearing in one only strain. Once the pangenome of a species is estimated, other studies can be undertaken to generate new knowledge, such as the study of the evolutionary selection for protein-coding genes. Most of the genes of a pangenome are expected to be subject to purifying selection that assures the conservation of function, especially those in the core group. However, some genes can be subject to selection pressure, such as genes involved in virulence that need to escape to the host immune system, which is more common in the accessory group of the pangenome. We analyzed 180 strains of Helicobacter pylori, a bacterium that colonizes the gastric mucosa of half the world population and presents a low number of genes (around 1500 in a strain and 3000 in the pangenome). After the estimation of the pangenome, the evolutionary selection for each gene has been calculated, and we found that 85% of them are subject to purifying selection and the remaining genes present some grade of selection pressure. As expected, the latter group is enriched with genes encoding for membrane proteins putatively involved in interaction to host tissues. In addition, this group also presents a high number of uncharacterized genes and genes encoding for putative spurious proteins. It suggests that they could be false positives from the gene finders used for identifying them. All these results propose that this kind of analyses can be useful to validate gene predictions and functionally characterize proteins in complete genomes.\n\nProtein-Coding Genes of Helicobacter pylori Predominantly Present Purifying Selection though Many Membrane Proteins Suffer from Selection Pressure: A Proposal to Analyze Bacterial Pangenomes.", "token_count": 463, "char_count": 2060, "word_count": 323, "semantic_coherence": 1, "information_density": 0.5263, "quality_score": 0.7632, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:47.133182", "source": { "split": "train_shard_00001", "doc_id": 1007 }, "chunk_id": "train_shard_00001_1007_0", "global_id": 7092 }, { "text": "Staphylococcus epidermidis is found naturally on the skin but is a common cause of persistent orthopaedic device-related infections (ODRIs). This study used a pan-genome and gene-by-gene approach to analyse the clonality of whole genome sequences (WGS) of 115 S. epidermidis isolates from 55 patients with persistent ODRIs. Analysis of the 522 gene core genome revealed that the isolates clustered into three clades, and MLST analysis showed that 83% of the isolates belonged to clonal complex 2 (CC2). Analysis also found 13 isolate pairs had different MLST types and less than 70% similarity within the genes; hence, these were defined as re-infection by a different S. epidermidis strain. Comparison of allelic diversity in the remaining 102 isolates (49 patients) revealed that 6 patients had microevolved infections (>7 allele differences), and only 37 patients (77 isolates) had a 'true' persistent infection. Analysis of the core genomes of isolate pairs from 37 patients found 110/841 genes had variations; mainly in metabolism associated genes. The accessory genome consisted of 2936 genes; with an average size of 1515 genes. To conclude, this study demonstrates the advantage of using WGS for identifying the accuracy of a persistent infection diagnosis. Hence, persistent infections can be defined as 'true' persistent infections if the core genome of paired isolates has ≤7 allele differences; microevolved persistent infection if the paired isolates have >7 allele differences but same MLST type; and polyclonal if they are the same species but a different MLST type.\n\nTemporal Changes in Patient-Matched Staphylococcus epidermidis Isolates from Infections: towards Defining a 'True' Persistent Infection.", "token_count": 472, "char_count": 1747, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5681, "quality_score": 0.784, "entities": { "genes": [ "CC2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:47.771882", "source": { "split": "train_shard_00001", "doc_id": 1008 }, "chunk_id": "train_shard_00001_1008_0", "global_id": 7093 }, { "text": "Grapevine (Vitis) is the oldest domesticated fruit crop with great cultural and economic importance. Here, we assemble and annotate haplotype-resolved genomes of 72 Vitis accessions including 25 wild and 47 cultivated grapevines, and a haplotype-resolved complete genome of V. vinifera. Coalescent phylogenomics of 142 haplotype genomes disentangles the mysterious hybridization history of grapevines, revealing enormous genetic diversity among species. Pangenome analysis together with phenotyping data reveals that European cultivars, more susceptible to the most destructive disease downy mildew (DM), had a smaller repertoire of disease resistance genes of NLR family. Through extensive structural variation (SV) characterization, phenotyping, transcriptome profiling of 113 Vitis accessions, and SV-eQTL analysis, we have identified over 79 SVs and their relevant genes significantly associated with DM resistance, exemplified by a lysine histidine transporter, VvLHT8. This haplotype-resolved complete genome and pangenome of Vitis genus will accelerate grapevine breeding and enrich our understanding of the evolution and biology of grapevines.\n\nSuper Pangenome of Grapevines Empowers Improvement of the Oldest Domesticated Fruit", "token_count": 313, "char_count": 1236, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7301, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:48.332018", "source": { "split": "train_shard_00001", "doc_id": 1009 }, "chunk_id": "train_shard_00001_1009_0", "global_id": 7094 }, { "text": "Cattle have been selectively bred for coat color, spotting, and depigmentation patterns. The assumed autosomal dominant inherited genetic variants underlying the characteristic white head of Fleckvieh, Simmental, and Hereford cattle have not been identified yet, although the contribution of structural variation upstream the KIT gene has been proposed. Here, we construct a graph pangenome from 24 haplotype assemblies representing seven taurine cattle breeds to identify and characterize the white head-associated locus for the first time based on long-read sequencing data and pangenome analyses. We introduce a pangenome-wide association mapping approach which examines assembly path similarities within the graph to reveal an association between two most likely serial alleles of a complex structural variant 66 kb upstream KIT and facial depigmentation. The complex structural variant contains a variable number of tandemly duplicated 14.3 kb repeats, consisting of LTRs, LINEs, and other repetitive elements, leading to misleading alignments of short and long reads when using a linear reference. We align 250 short-read sequencing samples spanning 15 cattle breeds to the pangenome graph, further validating that the alleles of the structural variant segregate with head depigmentation. We estimate an increased count of repeats in Hereford relative to Simmental and other white-headed cattle breeds from the graph alignment coverage, suggesting a large under-assembly in the current Hereford-based cattle reference genome which had fewer copies. We show that exploiting assembly path similarities within graph pangenomes can reveal trait-associated complex structural variants.\n\nTaurine pangenome uncovers a segmental duplication upstream ofKITassociated with depigmentation in white-headed cattle", "token_count": 409, "char_count": 1813, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6265, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:48.952311", "source": { "split": "train_shard_00001", "doc_id": 1010 }, "chunk_id": "train_shard_00001_1010_0", "global_id": 7095 }, { "text": "

Background

The international disclosure of Chinese human genetic data continues to be a contentious issue in China, generating public debates in both traditional and social media channels. Concerns have intensified after Chinese scientists' research on pangenome data was published in the prestigious journal Nature.

Methods

This study scrutinized microblogs posted on Weibo, a popular Chinese social media site, in the two months immediately following the publication (June 14, 2023-August 21, 2023). Content analysis was conducted to assess the nature of public responses, justifications for positive or negative attitudes, and the users' overall knowledge of how Chinese human genetic information is regulated and managed in China.

Results

Weibo users displayed contrasting attitudes towards the article's public disclose of pangenome research data, with 18% positive, 64% negative, and 18% neutral. Positive attitudes came primarily from verified government and media accounts, which praised the publication. In contrast, negative attitudes originated from individual users who were concerned about national security and health risks and often believed that the researchers have betrayed China. The benefits of data sharing highlighted in the commentaries included advancements in disease research and scientific progress. Approximately 16% of the microblogs indicated that Weibo users had misunderstood existing regulations and laws governing data sharing and stewardship.

Conclusions

Based on the predominantly negative public attitudes toward scientific data sharing established by our study, we recommend enhanced outreach by scientists and scientific institutions to increase the public understanding of developments in genetic research, international data sharing, and associated regulations. Additionally, governmental agencies can alleviate public fears and concerns by being more transparent about their security reviews of international collaborative research involving Chinese human genetic data and its cross-border transfer.\n\nPublic perceptions of international genetic information sharing for biomedical research in China: a case study of the social media debate on the article \"A Pangenome Reference of 36 Chinese Populations\" published in Nature.", "token_count": 460, "char_count": 2295, "word_count": 302, "semantic_coherence": 1, "information_density": 0.606, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:49.591066", "source": { "split": "train_shard_00001", "doc_id": 1011 }, "chunk_id": "train_shard_00001_1011_0", "global_id": 7096 }, { "text": "The H30Rx subclade of Escherichia coli ST131 is a clinically important, globally dispersed pathogenic lineage that typically displays resistance to fluoroquinolones and extended spectrum β-lactams. Isolates EC233 and EC234, variants of ST131-H30Rx with a novel sequence type (ST) 8196, isolated from unrelated patients presenting with bacteraemia at a Sydney Hospital in 2014 are characterised here. EC233 and EC234 are phylogroup B2, serotype O25:H4A, and resistant to ampicillin, amoxicillin, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, norfloxacin and gentamicin and are likely clonal. Both harbour an IncFII_2 plasmid (pSPRC_Ec234-FII) that carries most of the resistance genes on an IS26 associated translocatable unit, two small plasmids and a novel IncI1 plasmid (pSPRC_Ec234-I). SNP-based phylogenetic analysis of the core genome of representatives within the ST131 clonal complex places both isolates in a subclade with three clinical Australian ST131-H30Rx clade-C isolates. A MrBayes phylogeny analysis of EC233 and EC234 indicates ST8196 share a most recent common ancestor with ST131-H30Rx strain EC70 isolated from the same hospital in 2013. Our study identified genomic hallmarks that define the ST131-H30Rx subclade in the ST8196 isolates and highlights a need for unbiased genomic surveillance approaches to identify novel high-risk MDR E. coli pathogens that impact healthcare facilities.", "token_count": 508, "char_count": 1477, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6735, "quality_score": 0.8367, "entities": { "genes": [ "ST131", "EC70", "EC233", "ST8196", "EC234" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:50.245095", "source": { "split": "train_shard_00001", "doc_id": 1012 }, "chunk_id": "train_shard_00001_1012_0", "global_id": 7097 }, { "text": "Escherichia coli ST8196 is a novel, locally evolved, and extensively drug resistant pathogenic lineage within the ST131 clonal complex.", "token_count": 46, "char_count": 142, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST131", "ST8196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:50.599721", "source": { "split": "train_shard_00001", "doc_id": 1012 }, "chunk_id": "train_shard_00001_1012_1", "global_id": 7098 }, { "text": "The dairy yeast Kluyveromyces marxianus represents a promising industrial strain useful for the production of bioethanol from cheese whey. Physiology of the five K. marxianus strains on galactose was examined during batch cultivation under controlled aerobic conditions on minimal media and one of the strains designated K. marxianus strain 6C17 which presented the highest specific galactose consumption rate. A maximum specific growth rate of 0.34 and 0.37 h-1, respectively, was achieved using batch cultivation in a minimal medium and a complex medium amended with galactose (50 g/L) at 37 °C. The sugar was metabolized for the production of ethanol as the chief metabolite with a maximum ethanol yield of 0.39 g/g of galactose. Different growth behaviors were observed when galactose was used with other sugar such as glucose, lactose and fructose. The growth rates on hydrolyzed cheese whey were also measured, and a maximum specific growth rate of 0.39 and 0.32 h-1 was observed with glucose and galactose, respectively, with the maximum flux diverted toward ethanol production. This approach of studying the physiology of thermotolerant K. marxianus on hydrolyzed whey during fermentation would be helpful in achieving higher yields of ethanol.\n\nPhysiological growth and galactose utilization by dairy yeast Kluyveromyces marxianus in mixed sugars and whey during fermentation.", "token_count": 408, "char_count": 1442, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:51.225115", "source": { "split": "train_shard_00001", "doc_id": 1013 }, "chunk_id": "train_shard_00001_1013_0", "global_id": 7099 }, { "text": "Raw transgalactosylated oligosaccharides (raw TOS) obtained by enzymatic synthesis with Aspergillus oryzae β-galactosidase were purified by selective bioconversion with Saccharomyces cerevisiae ATCC4126 and Kluyveromyces marxianus NRLLY-1109. Monosaccharides were completely removed by S. cerevisiae and K. marxianus from raw TOS without any nutrient supplementation. The effect of the biomass to carbohydrate mass ratio on the purity and specific productivity of removal of sugars was assessed with S. cerevisiae, where both effects were significant. Purity obtained with a collection strain of S. cerevisiae and bakers’ yeast was compared, the latter being higher after 24 h of bioconversion. A product free of monosaccharides was obtained with a purity (0.48; 28% lactulose and 20% oligosaccharides), similar to that of commercial galacto-oligosaccharide preparations. The possibility of yeast recovery and reuse in sequential batch operation was assessed: two batches could be performed before a significant reduction in monosaccharide removal was seen.\n\nSelective bioconversion with yeast for the purification of raw lactulose and transgalactosylated oligosaccharides", "token_count": 338, "char_count": 1172, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6392, "quality_score": 0.8196, "entities": { "genes": [ "ATCC4126" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:52.477301", "source": { "split": "train_shard_00001", "doc_id": 1014 }, "chunk_id": "train_shard_00001_1014_0", "global_id": 7100 }, { "text": "In the province of Alberta, Canada, invasive disease caused by Streptococcus pneumoniae serogroup 20 (serotypes 20A/20B) has been increasing in incidence. Here, we characterize provincial invasive serogroup 20 isolates collected from 1993 to 2019 alongside invasive and non-invasive serogroup 20 isolates from the Global Pneumococcal Sequencing (GPS) Project collected from 1998 to 2015. Trends in clinical metadata and geographic location were evaluated, and serogroup 20 isolate genomes were subjected to molecular sequence typing, virulence and antimicrobial resistance factor mining, phylogenetic analysis and pangenome calculation. Two hundred and seventy-four serogroup 20 isolates from Alberta were sequenced, and analysed along with 95 GPS Project genomes. The majority of invasive Alberta serogroup 20 isolates were identified after 2007 in primarily middle-aged adults and typed predominantly as ST235, a sequence type that was rare among GPS Project isolates. Most Alberta isolates carried a full-length whaF capsular gene, suggestive of serotype 20B. All Alberta and GPS Project genomes carried molecular resistance determinants implicated in fluoroquinolone and macrolide resistance, with a few Alberta isolates exhibiting phenotypic resistance to azithromycin, clindamycin, erythromycin, tetracycline and trimethoprim-sulfamethoxazole, as well as non-susceptibility to tigecycline. All isolates carried multiple virulence factors including those involved in adherence, immune modulation and nutrient uptake, as well as exotoxins and exoenzymes. Phylogenetically, Alberta serogroup 20 isolates clustered with predominantly invasive GPS Project isolates from the USA, Israel, Brazil and Nepal. Overall, this study highlights the increasing incidence of invasive S", "token_count": 498, "char_count": 1792, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:53.159550", "source": { "split": "train_shard_00001", "doc_id": 1015 }, "chunk_id": "train_shard_00001_1015_0", "global_id": 7101 }, { "text": "pneumoniae serogroup 20 disease in Alberta, Canada, and provides insights into the genetic and clinical characteristics of these isolates within a global context.\n\nGenomic analysis of Streptococcus pneumoniae serogroup 20 isolates in Alberta, Canada from 1993-2019.", "token_count": 85, "char_count": 276, "word_count": 36, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:53.549943", "source": { "split": "train_shard_00001", "doc_id": 1015 }, "chunk_id": "train_shard_00001_1015_1", "global_id": 7102 }, { "text": "Escherichia coli (E. coli) ST1193 is an emerging fluoroquinolones-resistant and virulent lineage. Large gaps remain in our understanding of the evolutionary processes and differences of this lineage. Therefore, we used 76 E. coli ST1193 genomes to detect strain-level genetic diversity and phylogeny of this lineage globally. All E. coli ST1193 possessed fimH64, filCH5, and fumC14. There was 94.7% of isolates classified as O-type O75. There was 9.33% of E. coli ST1193 that possessed K5 capsular, while 90.67% of isolates possessed K1 capsular. The core genome analysis revealed that all isolates were divided into two phylogenetic clades (clade A and B). Clade A included 25 non-Chinese E. coli ST1193, and clade B contained all isolates collected from Fuzhou, China, respectively. The results of comparative genomics indicated Indels were identified in 150 clade-specific genes, which were enriched into the biological process and molecular function. Accessory genome phylogenetic tree showed a high degree of correlation between accessory genome clusters and core genome clades", "token_count": 361, "char_count": 1145, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [ "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:54.159165", "source": { "split": "train_shard_00001", "doc_id": 1016 }, "chunk_id": "train_shard_00001_1016_0", "global_id": 7103 }, { "text": "There was significant difference in antibiotic resistance genes (ARGs) [bla CTX-M-55 , bla TEM-1 , sul2, tet(B), tet(R), APH(6)-Id, and AAC(3)-IId], virulence factors (cia, neuC, gad, and traT), and plasmid replicon types (IncQ1, Col156, and IncB/O/K/Z) between clade A (non-Chinese isolates) and clade B (Chinese isolates) (p < 0.05). Further analysis of the genetic environments of bla CTX-M-55 demonstrated that the flanking contexts of bla CTX-M-55 were diverse. In conclusion, our results reveal the distinct evolutionary trajectories of the spread of E. coli ST1193 in Fuzhou, China and non-China regions. This supports both global transmission and localized lineage expansion of this lineage following specific introductions into a geographic locality.\n\nPhylogenetic Analysis Reveals Distinct Evolutionary Trajectories of the Fluoroquinolones-Resistant Escherichia coli ST1193 From Fuzhou, China.", "token_count": 415, "char_count": 1087, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7177, "quality_score": 0.8589, "entities": { "genes": [ "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:54.798484", "source": { "split": "train_shard_00001", "doc_id": 1016 }, "chunk_id": "train_shard_00001_1016_1", "global_id": 7104 }, { "text": "In this study, a multi-starters fermentation system involved lactic acid bacteria and yeasts was applied to obtain a novel acidified goat milk (AGM). Significant differences were found in the volatile flavor profile among goat milk, goat yogurt, and AGM reflected by principal component analysis of electronic nose (E-nose) data. Gas chromatography-mass spectrometry (GC-MS) results indicated that the relative content of free octanoic acid decreased, and more aromas were formed in AGM, which were considered to mask the goaty smell and give AGM a pleasant flavor. Rheological analysis indicated that AGM had higher apparent viscosity and G' and G'' moduli than goat yogurt and goat milk. Therefore, the goat yogurt fermented by lactic acid bacteria and K. marxianus exhibits a new method to alleviate the goaty flavor in goat milk and provides a novel option for those who were allergic to milk protein and dislike goaty flavor in goat milk.\n\nEffect of Co-Fermentation with Lactic Acid Bacteria and K. marxianus on Physicochemical and Sensory Properties of Goat Milk.", "token_count": 284, "char_count": 1083, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:55.354024", "source": { "split": "train_shard_00001", "doc_id": 1017 }, "chunk_id": "train_shard_00001_1017_0", "global_id": 7105 }, { "text": "The FTF (Fusarium Transcription Factor) gene family is composed of two members (FTF1 and FTF2) with high sequence homology. Both genes encode Zn(II)2Cys6 binuclear zinc finger transcription factors involved in the modulation of virulence in the F. oxysporum species complex (FOSC). While FTF1 is a multicopy gene exclusive of highly virulent strains of FOSC and is located in the accessory genome, FTF2 is a single copy gene, located in the core genome, and well conserved in all filamentous ascomycete fungi, except yeast. The involvement of FTF1 in the colonization of the vascular system and regulation of the expression of SIX effectors has been stablished. To address the role of FTF2 we generated and characterized null FTF2 mutants in a F. oxysporum f. sp. phaseoli weakly virulent strain and analyzed them together with the equivalent mutants formerly obtained in a highly virulent strain. The results obtained highlight a role for FTF2 as a negative regulator of the production of macroconidia and demonstrate that it is required for full virulence and positive regulation of SIX effectors. In addition, gene expression analyses provide compelling evidence that FTF2 is involved in the regulation of hydrophobins likely required for plant colonization.\n\nThe Role of the Fusarium oxysporum FTF2 Transcription Factor in Host Colonization and Virulence", "token_count": 338, "char_count": 1367, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5667, "quality_score": 0.7833, "entities": { "genes": [ "FTF2", "FTF1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:55.927454", "source": { "split": "train_shard_00001", "doc_id": 1018 }, "chunk_id": "train_shard_00001_1018_0", "global_id": 7106 }, { "text": "Oryza sativa (rice) is a major staple food targeted for increased production to achieve food security. However, increased production is threatened by several biotic and abiotic factors, of which bacterial blight disease caused by Xanthomonas oryzae pathovar oryzae is severe. Developing effective control strategies requires an up-to-date understanding of its pathogenomics. This study analyzes the genomes of 30 X. oryzae strains collected from rice-producing regions across five continents to identify genetic elements critical for its pathogenicity and adaptability and for an intraspecific diversity assessment using advanced genomics and bioinformatics tools. Resistome analysis revealed 28 distinct types of antibiotic resistance genes (ARGs), both innate and acquired, indicating a growing threat from multidrug-resistant X. oryzae strains. Sixteen virulent genes, including type III and VI secretion systems, motility genes, and effector proteins, were identified. A unique 'MexCD-OprJ' multidrug efflux system was detected in the Tanzanian strains, conferring resistance to multiple antibiotic classes. To curb further ARG emergence, there is a need to regulate the use of antibiotics for X. oryzae control and adopt resistant rice varieties. Transposable elements were also discovered to contribute to X. oryzae pathogenicity, facilitating the horizontal transfer of virulence genes. Pangenome analysis revealed intraspecific variation among the population, with 112 unique CDS having diverse functional roles. Strains registered in the Philippines had the most unique genes. Phylogenetic analysis confirmed the divergent evolution of X. oryzae. This study's results will aid in identifying more effective management strategies and biocontrol alternatives for sustainable rice production.", "token_count": 463, "char_count": 1861, "word_count": 244, "semantic_coherence": 1, "information_density": 0.7049, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:56.576284", "source": { "split": "train_shard_00001", "doc_id": 1019 }, "chunk_id": "train_shard_00001_1019_0", "global_id": 7107 }, { "text": "Pathogenomic Insights into Xanthomonas oryzae pv. oryzae's Resistome, Virulome, and Diversity for Improved Rice Blight Management.", "token_count": 53, "char_count": 144, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:56.939052", "source": { "split": "train_shard_00001", "doc_id": 1019 }, "chunk_id": "train_shard_00001_1019_1", "global_id": 7108 }, { "text": "Alfalfa (Medicago sativa L.), a perennial legume forage, has been broadly cultivated owing to a variety of favorable characteristics, including comprehensive ecological adaptability, superior nutritive value and palatability, and nitrogen fixation capacity. The productivity traits of alfalfa, specifically its biomass yield and forage quality, are significantly influenced by a series of determinants, including internal developmental factors and external environmental cues. However, the regulatory mechanisms underlying the fundamental biological problems of alfalfa remain elusive. Here, we conducted a comprehensive review focusing on the genomics of alfalfa, advancements in gene-editing technologies, and the identification of genes that control pivotal agronomic characteristics, including biomass formation, nutritional quality, flowering time, and resistance to various stresses. Moreover, a molecular design roadmap for the 'ideal alfalfa' has been proposed and the potential of pangenomes, self-incompatibility mechanisms, de novo domestication, and intelligent breeding strategies to enhance alfalfa's yield, quality, and resilience were further discussed. This review will provide comprehensive information on the basic biology of alfalfa and offer new insights for the cultivation of ideal alfalfa.\n\nAdvances in basic biology of alfalfa (<i>Medicago sativa L.</i>): a comprehensive overview.", "token_count": 330, "char_count": 1432, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6961, "quality_score": 0.8481, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:57.513199", "source": { "split": "train_shard_00001", "doc_id": 1020 }, "chunk_id": "train_shard_00001_1020_0", "global_id": 7109 }, { "text": "The presence of intermittently dispersed insertion sequences and transposases in the Mycobacterium tuberculosis (Mtb) genome makes intra-genome recombination events inevitable. Understanding their effect on the gene repertoires (GR), which may contribute to the development of drug-resistant Mtb, is critical. In this study, publicly available WGS data of clinical Mtb isolates (endemic region n = 2,601; non-endemic region n = 1,130) were de novo assembled, filtered, scaffolded into assemblies, and functionally annotated. Out of 2,601 Mtb WGS data sets from endemic regions, 2,184 (drug resistant/sensitive: 1,386/798) qualified as high quality. We identified 3,784 core genes, 123 softcore genes, 224 shell genes, and 762 cloud genes in the pangenome of Mtb clinical isolates from endemic regions. Sets of 33 and 39 genes showed positive and negative associations (P < 0.01) with drug resistance status, respectively. Gene ontology clustering showed compromised immunity to phages and impaired DNA repair in drug-resistant Mtb clinical isolates compared to the sensitive ones. Multidrug efflux pump repressor genes (Rv3830c and Rv3855c) and CRISPR genes (Rv2816c-19c) were absent in the drug-resistant Mtb. A separate WGS data analysis of drug-resistant Mtb clinical isolates from the Netherlands (n = 1130) also showed the absence of CRISPR genes (Rv2816c-17c)", "token_count": 449, "char_count": 1407, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6751, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:58.148622", "source": { "split": "train_shard_00001", "doc_id": 1021 }, "chunk_id": "train_shard_00001_1021_0", "global_id": 7110 }, { "text": "This study highlights the role of CRISPR genes in drug resistance development in Mtb clinical isolates and helps in understanding its evolutionary trajectory and as useful targets for diagnostics development.IMPORTANCEThe results from the present Pan-GWAS study comparing gene sets in drug-resistant and drug-sensitive Mtb clinical isolates revealed intricate presence-absence patterns of genes encoding DNA-binding proteins having gene regulatory as well as DNA modification and DNA repair roles. Apart from the genes with known functions, some uncharacterized and hypothetical genes that seem to have a potential role in drug resistance development in Mtb were identified. We have been able to extrapolate many findings of the present study with the existing literature on the molecular aspects of drug-resistant Mtb, further strengthening the relevance of the results presented in this study.\n\nPangenome-wide association study reveals the selective absence of CRISPR genes (Rv2816c-19c) in drug-resistant Mycobacterium tuberculosis.", "token_count": 229, "char_count": 1042, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6294, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:58.613937", "source": { "split": "train_shard_00001", "doc_id": 1021 }, "chunk_id": "train_shard_00001_1021_1", "global_id": 7111 }, { "text": "Mycobacterium abscessus complex (MABC) is an important pathogen of immunocompromised patients. Accurate and rapid determination of MABC at the subspecies level is vital for optimal antibiotic therapy. Here we have used comparative genomics to design MABC subspecies-specific PCR assays. Analysis of single nucleotide polymorphisms and core genome multilocus sequence typing showed clustering of genomes into three distinct clusters representing the MABC subspecies M. abscessus, M. bolletii and M. massiliense. Pangenome analysis of 318 MABC genomes from the three subspecies allowed for the identification of 15 MABC subspecies-specific genes. In silico testing of primer sets against 1,663 publicly available MABC genomes and 66 other closely related Mycobacterium genomes showed that all assays had >97% sensitivity and >98% specificity. Subsequent experimental validation of two subspecies-specific genes each showed the PCR assays worked well in individual and multiplex format with no false-positivity with 5 other mycobacteria of clinical importance. In conclusion, we have developed a rapid, accurate, multiplex PCR-assay for discriminating MABC subspecies that could improve their detection, diagnosis and inform correct treatment choice.\n\nThe Use of Comparative Genomic Analysis for the Development of Subspecies-Specific PCR Assays for <i>Mycobacterium abscessus</i>.", "token_count": 394, "char_count": 1432, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6738, "quality_score": 0.8369, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:59.231404", "source": { "split": "train_shard_00001", "doc_id": 1022 }, "chunk_id": "train_shard_00001_1022_0", "global_id": 7112 }, { "text": "Polycystic Ovary Syndrome (PCOS), which is common among women of reproductive age, is characterized by low-grade chronic inflammation and is associated with several health problems and dysbiosis. Kefir has been shown to have many beneficial health effects; however, its effect on PCOS is unknown. This study aimed to examine the effect of kefir on the intestinal microbiota and health outcomes in PCOS. In this intervention study, 17 women with PCOS consumed 250 mL/day of kefir (containing Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactobacillus kefiranofaciens subsp. kefirgranum, Lactobacillus kefiri, Lactobacillus acidophilus, Lactobacillus parakefiri, Lactobacillus bulgaricus, Lactobacillus reuteri, Lactobacillus casei, Lactobacillus fermentum, Lactobacillus helveticus, Lactococcus lactis, Leuconostoc mesentereoides, Bifidobacterium bifidum, Streptococcus thermophilus, Kluyveromyces marxianus, Kluyveromyces lactis, Acetobacter pasteurianus, and Saccharomyces cerevisiae) for 8 weeks. Food consumption and physical activity records, anthropometrical measurements, quality of life, and fecal and blood samples were taken at the study's beginning and end", "token_count": 487, "char_count": 1315, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:04:59.881290", "source": { "split": "train_shard_00001", "doc_id": 1023 }, "chunk_id": "train_shard_00001_1023_0", "global_id": 7113 }, { "text": "Quality of life in mental health (58.8 ± 15.08; 64.0 ± 15.23, respectively) and physical function (95.00 and 100.00, respectively) categories showed a significant increase after kefir intervention (p < .05). Additionally, Interleukin-6 (IL-6), one of the inflammatory cytokines, significantly decreased (174.00 and 109.10 ng/L, respectively) (p < .05). The intestinal barrier permeability was evaluated with zonulin, and no significant change was observed. Gut microbiota analysis showed that while the relative abundance of the class Bacilli and genus Lactococcus significantly increased, the genus Holdemania decreased with kefir consumption (p < .05). In conclusion, kefir appears to be beneficial for improving the microbiota and some health outcomes, like reducing inflammation and improving quality of life in PCOS. Therefore, kefir may be useful in the treatment of PCOS.\n\nEffects of kefir consumption on gut microbiota and health outcomes in women with polycystic ovary syndrome.", "token_count": 338, "char_count": 1022, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:00.449853", "source": { "split": "train_shard_00001", "doc_id": 1023 }, "chunk_id": "train_shard_00001_1023_1", "global_id": 7114 }, { "text": "

Background

Escherichia coli has an extensive accessory genome, though its role in impacting patient mortality is unknown.

Methods

We performed whole genome sequencing with E. coli bloodstream infection isolates from inpatients at Duke University. Pan-genome analysis was used to identify flexible genomic islands associated with in-hospital attributable mortality (death due to infection). The functions of the flexible genomic islands of interest were investigated with serum growth assays and bacterial-host cell interaction assays.

Results

We included 193 E. coli genomes. Two separate genomic islands were co-present within 41 (21%) E. coli isolates and associated with increased attributable mortality (22% [9/41]) vs. 11% [17/152]) in an adjusted analysis (Mortality odds ratio 3.0; 95% confidence interval 1.1-7.9; p=0.03). The two genomic islands together contain genes homologous to a type III secretion system (T3SS): 1) E. coli type III secretion system 2 (ETT2), encoding 35 genes homologous to a T3SS basal body and needle complex, and 2) an ETT2 accessory region (ETT2-AR) encoding six genes homologous to a T3SS needle tip, translocases, and adhesin. ETT2/ETT2-AR altered bacterial virulence through two mechanisms. First, ETT2/ETT2-AR increased resistance to complement-mediated growth restriction by inhibiting classical complement pathway activation. Second, ETT2/ETT2-AR influenced E. coli-host cell interactions by increasing adhesion to and death of mammalian cells.

Conclusions

Genomic islands ETT2 and ETT2-AR are homologous to a T3SS, co-localize within specific E. coli lineages, associate with increased mortality in patients with E. coli bloodstream infection, and increase bacterial virulence through resistance to complement and enhanced host cell adhesion and death.", "token_count": 507, "char_count": 1825, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8086, "entities": { "genes": [ "ETT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:01.103071", "source": { "split": "train_shard_00001", "doc_id": 1024 }, "chunk_id": "train_shard_00001_1024_0", "global_id": 7115 }, { "text": "Escherichia coli Type III Secretion System 2 (ETT2) is Associated with Patient Mortality in Bloodstream Infections.", "token_count": 33, "char_count": 115, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ETT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:01.465194", "source": { "split": "train_shard_00001", "doc_id": 1024 }, "chunk_id": "train_shard_00001_1024_1", "global_id": 7116 }, { "text": "The gut microbiome plays a key role in the pathogenesis and disease activity of inflammatory bowel disease (IBD). While research has focused on the bacterial microbiome, recent studies have shifted towards host genetics and host-fungal interactions. The mycobiota is a vital component of the gastrointestinal microbial community and plays a significant role in immune regulation. Among fungi, Candida species, particularly Candida albicans (C. albicans), have been extensively studied due to their dual role as gut commensals and invasive pathogens. Recent findings indicate that various strains of C. albicans exhibit considerable differences in virulence factors, impacting IBD's pathophysiology. Intestinal fungal dysbiosis and antifungal mucosal immunity may be associated to IBD, especially Crohn's disease (CD). This article discusses intestinal fungal dysbiosis and antifungal immunity in healthy individuals and CD patients. It discusses factors influencing the mycobiome's role in IBD pathogenesis and highlights significant contributions from the scientific community aimed at enhancing understanding of the mycobiome and encouraging further research and targeted intervention studies on specific fungal populations. Our article also provided insights into a recent study by Wu et al in the World Journal of Gastroenterology regarding the role of the gut microbiota in the pathogenesis of CD.\n\nRole of Candida species in pathogenesis, immune regulation, and prognostic tools for managing ulcerative colitis and Crohn's disease.", "token_count": 398, "char_count": 1586, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:02.078874", "source": { "split": "train_shard_00001", "doc_id": 1025 }, "chunk_id": "train_shard_00001_1025_0", "global_id": 7117 }, { "text": "Salmonella enterica serovar Typhimurium ST213 is an emergent multidrug-resistant sequence type associated with the food chain, and gastrointestinal and invasive infections in North America. Here, we applied genomic and phenotypic analyses to illustrate the diversity and evolution of sequence type ST213. The population structure and evolutionary history of ST213 strains, particularly the North American isolates (NA-ST213) distinguish them from other S. Typhimurium sequence types, including European ST213 strains. NA-ST213 isolates were distributed in four co-circulating lineages with distinct multidrug resistance profiles and unique phage and CRISPR spacers patterns that could have shaped their local microevolution. Compared to the SL1344 reference strain, NA-ST213 demonstrated reduced adherence and internalization in cultured eukaryotic cell lines but exhibited more efficient replication and intracellular survival. This study underscores the relevance of studying an emergent S. Typhimurium sequence type and the events leading to its diversification beyond the well-characterized reference strains and worldwide predominant sequence types. However, it must also serve as a cautionary tale of the potential health risk the NA-ST213 may represent; particularly when there is a close relationship with pandemic sequence types such as the monophasic ST34.\n\nPopulation structure and ongoing microevolution of the emerging multidrug-resistant Salmonella Typhimurium ST213.", "token_count": 353, "char_count": 1481, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6888, "quality_score": 0.8444, "entities": { "genes": [ "ST34", "SL1344", "ST213" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:02.660914", "source": { "split": "train_shard_00001", "doc_id": 1026 }, "chunk_id": "train_shard_00001_1026_0", "global_id": 7118 }, { "text": "Staphylococcus aureus chronic airway infection in patients with cystic fibrosis (CF) allows this pathogen to adapt over time in response to different selection pressures. We have previously shown that the main sequence types related to community-acquired methicillin-resistant S. aureus (MRSA) infections in Argentina - ST5 and ST30 - are also frequently isolated from the sputum of patients with CF, but in these patients they usually display multi-drug antimicrobial resistance. In this study, we sequenced the genomes of MRSA from four paediatric CF patients with the goal of identifying mutations among sequential isolates, especially those possibly related to antimicrobial resistance and virulence, which might contribute to the adaptation of the pathogen in the airways of patients with CF. Our results revealed genetic differences in sequential MRSA strains isolated from patients with CF in both their core and accessory genomes. Although the genetic adaptation of S. aureus was distinct in different hosts, we detected independent mutations in thyA, htrA, rpsJ and gyrA - which are known to have crucial roles in S. aureus virulence and antimicrobial resistance - in isolates recovered from multiple patients. Moreover, we identified allelic variants that were detected in all of the isolates recovered after a certain time point; these non-synonymous mutations were in genes associated with antimicrobial resistance, virulence, iron scavenging and oxidative stress resistance. In conclusion, our results provide evidence of genetic variability among sequential MRSA isolates that could be implicated in the adaptation of these strains during chronic CF airway infection.\n\nComparative genomics of ST5 and ST30 methicillin-resistant Staphylococcus aureus sequential isolates recovered from paediatric patients with cystic fibrosis.", "token_count": 468, "char_count": 1889, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5341, "quality_score": 0.767, "entities": { "genes": [ "ST5", "ST30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:03.304262", "source": { "split": "train_shard_00001", "doc_id": 1027 }, "chunk_id": "train_shard_00001_1027_0", "global_id": 7119 }, { "text": "Fundamental to effective Legionnaires' disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, Legionella pneumophila. Genomics has revolutionized pathogen surveillance, but L. pneumophila has a complex ecology and population structure that can limit source inference based on standard core genome phylogenetics. Here, we present a powerful machine learning approach that assigns the geographical source of Legionnaires' disease outbreaks more accurately than current core genome comparisons. Models were developed upon 534 L. pneumophila genome sequences, including 149 genomes linked to 20 previously reported Legionnaires' disease outbreaks through detailed case investigations. Our classification models were developed in a cross-validation framework using only environmental L. pneumophila genomes. Assignments of clinical isolate geographic origins demonstrated high predictive sensitivity and specificity of the models, with no false positives or false negatives for 13 out of 20 outbreak groups, despite the presence of within-outbreak polyclonal population structure. Analysis of the same 534-genome panel with a conventional phylogenomic tree and a core genome multi-locus sequence type allelic distance-based classification approach revealed that our machine learning method had the highest overall classification performance-agreement with epidemiological information. Our multivariate statistical learning approach maximizes the use of genomic variation data and is thus well-suited for supporting Legionnaires' disease outbreak investigations.IMPORTANCEIdentifying the sources of Legionnaires' disease outbreaks is crucial for effective control. Current genomic methods, while useful, often fall short due to the complex ecology and population structure of Legionella pneumophila, the causative agent. Our study introduces a high-performing machine learning approach for more accurate geographical source attribution of Legionnaires' disease outbreaks. Developed using cross-validation on environmental L. pneumophila genomes, our models demonstrate excellent predictive sensitivity and specificity", "token_count": 491, "char_count": 2217, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:03.957777", "source": { "split": "train_shard_00001", "doc_id": 1028 }, "chunk_id": "train_shard_00001_1028_0", "global_id": 7120 }, { "text": "Importantly, this new approach outperforms traditional methods like phylogenomic trees and core genome multi-locus sequence typing, proving more efficient at leveraging genomic variation data to infer outbreak sources. Our machine learning algorithms, harnessing both core and accessory genomic variation, offer significant promise in public health settings. By enabling rapid and precise source identification in Legionnaires' disease outbreaks, such approaches have the potential to expedite intervention efforts and curtail disease transmission.\n\nHigh performance Legionella pneumophila source attribution using genomics-based machine learning classification.", "token_count": 132, "char_count": 669, "word_count": 81, "semantic_coherence": 1, "information_density": 0.8642, "quality_score": 0.9321, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:04.380672", "source": { "split": "train_shard_00001", "doc_id": 1028 }, "chunk_id": "train_shard_00001_1028_1", "global_id": 7121 }, { "text": "The multiple inhibitors tolerance of microorganism is important in bioconversion of lignocellulosic biomass which is a promising renewable and sustainable source for biofuels and other chemicals. The disruption of an unknown α/β hydrolase, which was termed KmYME and located in mitochondria in this study, resulted in the yeast more susceptible to lignocellulose-derived inhibitors, particularly to acetic acid, furfural and 5-HMF. The KmYME disrupted strain lost more mitochondrial membrane potential, showed increased plasma membrane permeability, severer redox ratio imbalance, and increased ROS accumulation, compared with those of the non-disrupted strain in the presence of the same inhibitors. The intracellular concentration of ATP, NAD and NADP in the KmYME disrupted strain was decreased. However, disruption of KmYME did not result in a significant change of gene expression at the transcriptional level. The KmYME possessed esterase/thioesterase activity which was necessary for the resistance to inhibitors. In addition, KmYME was also required for the resistance to other stresses including ethanol, temperature, and osmotic pressure. Disruption of two possible homologous genes in S. cerevisiae also reduced its tolerance to inhibitors.\n\nEffect of a Novel Alpha/Beta Hydrolase Domain Protein on Tolerance of K. marxianus to Lignocellulosic Biomass Derived Inhibitors.", "token_count": 377, "char_count": 1410, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6218, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid", "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:04.998741", "source": { "split": "train_shard_00001", "doc_id": 1029 }, "chunk_id": "train_shard_00001_1029_0", "global_id": 7122 }, { "text": "Genome assembly databases are growing rapidly. The redundancy of sequence content between a new assembly and previous ones is neither conceptually nor algorithmically easy to measure. We introduce pertinent methods and DandD, a tool addressing how much new sequence is gained when a sequence collection grows. DandD can describe how much structural variation is discovered in each new human genome assembly and when discoveries will level off in the future. DandD uses a measure called δ (\"delta\"), developed initially for data compression and chiefly dependent on k-mer counts. DandD rapidly estimates δ using genomic sketches. We propose δ as an alternative to k-mer-specific cardinalities when computing the Jaccard coefficient, thereby avoiding the pitfalls of a poor choice of k. We demonstrate the utility of DandD's functions for estimating δ, characterizing the rate of pangenome growth, and computing all-pairs similarities using k-independent Jaccard.\n\nDandD: Efficient measurement of sequence growth and similarity.", "token_count": 254, "char_count": 1061, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:05.504581", "source": { "split": "train_shard_00001", "doc_id": 1030 }, "chunk_id": "train_shard_00001_1030_0", "global_id": 7123 }, { "text": "Pan-genome analysis is a fundamental tool for studying bacterial genome evolution; however, the variety of methods used to define and measure the pan-genome poses challenges to the interpretation and reliability of results. To quantify sources of bias and error related to common pan-genome analysis approaches, we evaluated different approaches applied to curated collection of 151 Mycobacterium tuberculosis ( Mtb ) isolates. Mtb is characterized by its clonal evolution, absence of horizontal gene transfer, and limited accessory genome, making it an ideal test case for this study. Using a state-of-the-art graph-genome approach, we found that a majority of the structural variation observed in Mtb originates from rearrangement, deletion, and duplication of redundant nucleotide sequences. In contrast, we found that pan-genome analyses that focus on comparison of coding sequences (at the amino acid level) can yield surprisingly variable results, driven by differences in assembly quality and the softwares used. Upon closer inspection, we found that coding sequence annotation discrepancies were a major contributor to inflated Mtb accessory genome estimates. To address this, we developed panqc, a software that detects annotation discrepancies and collapses nucleotide redundancy in pan-genome estimates. When applied to Mtb and E. coli pan-genomes, panqc exposed distinct biases influenced by the genomic diversity of the population studied. Our findings underscore the need for careful methodological selection and quality control to accurately map the evolutionary dynamics of a bacterial species.\n\nAnalysis of the limitedM. tuberculosisaccessory genome reveals potential pitfalls of pan-genome analysis approaches", "token_count": 382, "char_count": 1734, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6529, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:06.113715", "source": { "split": "train_shard_00001", "doc_id": 1031 }, "chunk_id": "train_shard_00001_1031_0", "global_id": 7124 }, { "text": "Various bovine species have been domesticated and bred for thousands of years, and they provide adequate animal-derived products, including meat, milk, and leather, to meet human requirements. Despite the review studies on economic traits in cattle, the genetic basis of traits has only been partially explained by phenotype and pedigree breeding methods, due to the complexity of genomic regulation during animal development and growth. With the advent of next-generation sequencing technology, genomics projects, such as the 1000 Bull Genomes Project, Functional Annotation of Animal Genomes project, and Bovine Pangenome Consortium, have advanced bovine genomic research. These large-scale genomics projects gave us a comprehensive concept, technology, and public resources. In this review, we summarize the genomics research progress of the main bovine species during the past decade, including cattle (Bos taurus), yak (Bos grunniens), water buffalo (Bubalus bubalis), zebu (Bos indicus), and gayal (Bos frontalis). We mainly discuss the development of genome sequencing and functional annotation, focusing on how genomic analysis reveals genetic variation and its impact on phenotypes in several bovine species.\n\nResearch Progress and Applications of Bovine Genome in the Tribe Bovini.", "token_count": 331, "char_count": 1333, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6612, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:06.712466", "source": { "split": "train_shard_00001", "doc_id": 1032 }, "chunk_id": "train_shard_00001_1032_0", "global_id": 7125 }, { "text": "

Background

A substantial and rapid increase, followed by a sharp decline in vanB -type vancomycin-resistant E. faecium (VRE), occurred in Germany in the late 2010s. This unusual epidemiological trend prompted detailed genomic investigations to explore the underlying dynamics at a German university hospital.

Methods

We retrospectively analyzed E. faecium bloodstream infection (BSI) isolates collected between 2017 and 2022. Isolates were classified as vanA -positive, vanB -positive, or van- negative. Molecular typing included multilocus sequence typing (MLST), core genome MLST (cgMLST), and split k-mer analysis (SKA). Clonal relationships and potential patient-to-patient transmission events were assessed by integrating genomic data with machine-aided analysis of available longitudinal patient movement data.

Results

High-resolution genomic analysis of BSI isolates revealed an oligoclonal scenario involving multiple epidemic lineages (e.g., sequence type (ST)117/complex type (CT)71, ST117/CT929, ST117/CT2505, ST80, and ST262) with distinct van genotypes and dynamic changes over time. Overall, genomic overlap between vanA -positive, vanB -positive, and van -negative populations was minimal. The vanB surge, peaking in late 2018-early 2019, was mainly driven by ST117/CT71, ST117/CT36, and ST117/CT1917. SKA provided enhanced discriminatory power over cgMLST. Prolonged intervals between infection onsets and frequent intra-hospital transfers were characteristic of potential transmission events.

Conclusions

Accurate characterization of the transient vanB -type VRE peak required an integrated genomic approach combining cgMLST, high-resolution SKA, and epidemiological data. These comprehensive methods enable infection prevention and control (IPC) teams to distinguish true outbreaks from numerical clusters of polyclonal isolates", "token_count": 517, "char_count": 1886, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [ "CT71", "ST262", "CT929", "CT1917", "ST117", "CT36", "CT2505", "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:07.374713", "source": { "split": "train_shard_00001", "doc_id": 1033 }, "chunk_id": "train_shard_00001_1033_0", "global_id": 7126 }, { "text": "This allows for accurate interpretation and precisely targeted interventions where evidence supports transmission.

Importance

Vancomycin-resistant Enterococcus faecium is an increasingly important nosocomial pathogen worldwide. Understanding its epidemiology and transmission dynamics is critical to effectively control its spread. This study documents shifting E. faecium populations within a high-risk hospital environment, including both vancomycin-resistant and vancomycin-susceptible bloodstream isolates. Detailed genomic analyses, combining core genome multilocus sequence typing with high-resolution split k-mer analysis, integrated with comprehensive epidemiological tracking, were critical to accurately depict complex epidemiological dynamics. This combined approach allows precise differentiation between monoclonal outbreaks and oligoclonal transmission, enabling more targeted infection prevention and control strategies.\n\nGenomic Epidemiology of Enterococcus faecium Bloodstream Infections During a VanB-type VRE Peak Reveals an Oligoclonal Scenario: An Observational Study at a German University Hospital (2017–2022)", "token_count": 256, "char_count": 1149, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7891, "quality_score": 0.8945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:07.923804", "source": { "split": "train_shard_00001", "doc_id": 1033 }, "chunk_id": "train_shard_00001_1033_1", "global_id": 7127 }, { "text": "Oat grain is a traditional human food rich in dietary fiber that contributes to improved human health. Interest in the crop has surged in recent years owing to its use as the basis for plant-based milk analogs. Oat is an allohexaploid with a large, repeat-rich genome that was shaped by subgenome exchanges over evolutionary timescales. In contrast to many other cereal species, genomic research in oat is still at an early stage, and surveys of structural genome diversity and gene expression variability are scarce. Here, we present annotated chromosome-scale sequence assemblies of 33 wild and domesticated oats along with an atlas of gene expression across six tissues of different developmental stages in 23 accessions. We describe the interplay of gene expression diversity across subgenomes, accessions and tissues. Gene loss in the hexaploid is accompanied by compensatory up-regulation of the remaining homeologs, but this process is constrained by subgenome divergence. Chromosomal rearrangements have significantly impacted recent oat breeding. A large pericentric inversion associated with early flowering explains distorted segregation on chromosome 7D and a homeologous sequence exchange between chromosomes 2A and 2C in a semidwarf mutant has risen to prominence in Australian elite varieties. The oat pangeome will promote the adoption of genomic approaches to understanding the evolution and adaptation of domesticated oats and will accelerate their improvement.\n\nA pangenome and pantranscriptome of hexaploid oat", "token_count": 359, "char_count": 1530, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:08.502375", "source": { "split": "train_shard_00001", "doc_id": 1034 }, "chunk_id": "train_shard_00001_1034_0", "global_id": 7128 }, { "text": "Kluyveromyces marxianus is thermotolerant yeast that is able to utilize a wider range of substrates and has greater thermal tolerance than most other yeast species. K. marxianus can assimilate xylose, but its ability to produce ethanol from xylose in oxygen-limited environments is poor. In the present study, the K. marxianus xylose reductase (KmXR) gene (Kmxyl1) was cloned and the recombinant enzyme was characterized to clarify the factors that limit xylose fermentation in K. marxianus NBRC1777. KmXR is a key enzyme in the xylose metabolism of K. marxianus, which was verified by disruption of the Kmxyl1 gene. The Km of the recombinant KmXR for NADPH is 65.67 μM and KmXR activity is 1.295 U/mg, which is lower than those of most reported yeast XRs, and the enzyme has no activity with coenzyme NADH. This result demonstrates that the XR from K. marxianus is highly coenzyme specific; combined with the extremely low XDH activity of K. marxianus with NADP+, the limitation of xylose fermentation is due to a redox imbalance under anaerobic conditions and low KmXR activity.\n\nIdentification of a xylose reductase gene in the xylose metabolic pathway of Kluyveromyces marxianus NBRC1777.", "token_count": 372, "char_count": 1192, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5421, "quality_score": 0.7711, "entities": { "genes": [ "NBRC1777" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:09.085458", "source": { "split": "train_shard_00001", "doc_id": 1035 }, "chunk_id": "train_shard_00001_1035_0", "global_id": 7129 }, { "text": "Staphylococcus haemolyticus is an important cause of sepsis in preterm infants, with gut colonization being recognized as a risk factor for infection. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n = 140) from 44 stool samples of 22 preterm infants from four hospitals in England. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 78/85 (91.7%) strains having Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were prevalent in the genomes. There was a strong association between the presence of mecA and phenotypic resistance to oxacillin, and the aacA-aphD gene and phenotypic resistance to gentamicin. While mecA was near-ubiquitous, none of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCCmec) element. The aacA-aphD gene was associated with the transposon Tn4001 in multiple chromosomal and plasmid contexts. Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonize the gut of preterm infants, and widespread horizontal gene transfer and recombination among this frequent colonizer of the preterm infant gut.\n\n<i>Staphylococcus haemolyticus</i> is a reservoir of antibiotic resistance genes in the preterm infant gut.", "token_count": 514, "char_count": 1591, "word_count": 215, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:09.736727", "source": { "split": "train_shard_00001", "doc_id": 1036 }, "chunk_id": "train_shard_00001_1036_0", "global_id": 7130 }, { "text": "

Objective

Candida kefyr causes invasive candidiasis in immunocompromised patients, particularly among those with oncohematological diseases. This study determined the prevalence of C. kefyr among yeast isolates collected during 2011-2018 in Kuwait. Antifungal susceptibility testing (AST) and genotypic heterogeneity among C. kefyr was also studied.

Methods

Clinical C. kefyr isolates recovered from bloodstream and other specimens during 2011 to 2018 were retrospectively analyzed. All C. kefyr isolates were identified by CHROMagar Candida, Vitek2 and PCR amplification of rDNA. AST was performed by Etest. Molecular basis of resistance to fluconazole and echinocandins was studied by PCR-sequencing of ERG11 and FKS1, respectively. Genotypic heterogeneity was determined with microsatellite-/minisatellite-based primers and for 27 selected isolates by PCR-sequencing of IGS1 region of rDNA.

Results

Among 8257 yeast strains, 69 C. kefyr (including four bloodstream) isolates were detected by phenotypic and molecular methods. Isolation from urine and respiratory samples from female and male patients was significantly different (P = 0.001). Four isolates showed reduced susceptibility to amphotericin B and one isolate to all (amphotericin B, fluconazole, voriconazole and caspofungin/micafungin) antifungals tested. Fluconazole-resistant isolate contained only synonymous mutations in ERG11. Echinocandin-resistant isolate contained wild-type hotspot-1 and hotspot-2 of FKS1. Fingerprinting with microsatellite-/minisatellite-based primers identified only three types. IGS1 sequencing identified seven haplotypes among 27 selected isolates.

Conclusions

The overall prevalence of C", "token_count": 518, "char_count": 1714, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [ "FKS1", "ERG11", "IGS1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:10.389293", "source": { "split": "train_shard_00001", "doc_id": 1037 }, "chunk_id": "train_shard_00001_1037_0", "global_id": 7131 }, { "text": "kefyr among clinical yeast isolates and among candidemia cases was recorded as 0.83% and 0.32%, respectively. The frequency of isolation of C. kefyr from bloodstream and other invasive samples was stable during the study period. The C. kefyr isolates grown from invasive (bloodstream, bronchoalveolar lavage, abdominal drain fluid, peritonial fluid and gastric fluid) samples and amphotericin B-resistant isolates were genotypically heterogeneous strains.\n\nCandida kefyr in Kuwait: Prevalence, antifungal drug susceptibility and genotypic heterogeneity.", "token_count": 154, "char_count": 553, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7397, "quality_score": 0.8699, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:10.826130", "source": { "split": "train_shard_00001", "doc_id": 1037 }, "chunk_id": "train_shard_00001_1037_1", "global_id": 7132 }, { "text": "This study describes the first complete genomic sequence of an NDM-19 and QnrS11-producing multidrug-resistant (MDR) Escherichia coli isolate collected from a fecal swab from a poultry farm in 2019 in Egypt. The blaNDM-19 was identified by PCR screening and DNA sequencing. The isolate was then subjected to antimicrobial susceptibility testing, conjugation and transformation experiments, and complete genome sequencing. The chromosome of strain M2-13-1 measures 4,738,278 bp and encodes 4557 predicted genes, with an average G + C content of 50.8%. M2-13-1 is classified under ST167, serotype O101:H5, phylogroup A, and shows an MDR phenotype, having minimum inhibitory concentrations (MICs) of 64 mg/L for both meropenem and doripenem. The genes blaNDM-19 and qnrS11 are present on 49,816 bp IncX3 and 113,285 bp IncFII: IncFIB plasmids, respectively. M2-13-1 harbors genes that impart resistance to sulfonamides (sul1), trimethoprim (dfrA14), β-lactams (blaTEM-1B), aminoglycosides (aph(6)-Id, aph(3')-Ia, aph(3″)-Ib, aac(3)-IV, and aph(4)-Ia), tetracycline (tet(A)), and chloramphenicol (floR)", "token_count": 500, "char_count": 1229, "word_count": 150, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [ "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:11.479321", "source": { "split": "train_shard_00001", "doc_id": 1038 }, "chunk_id": "train_shard_00001_1038_0", "global_id": 7133 }, { "text": "It was susceptible to aztreonam, colistin, fosfomycin, and tigecycline. The genetic context surrounding blaNDM-19 includes ISAba125-IS5-blaNDM-19-bleMBL-trpF-hp1-hp2-IS26. Hierarchical clustering of the core genome MLST (HierCC) indicated M2-13-1 clusters with global ST167 E. coli lineages, showing HC levels of 100 (HC100) core genome allelic differences. Plasmids of the IncX3 group and the insertion sequence (ISAba125) are critical vehicles for the dissemination of blaNDM and its related variants. To our knowledge, this is the first genomic report of a blaNDM-19/IncX3-carrying E. coli isolate of animal origin globally.\n\nDetection and Genomic Characteristics of NDM-19- and QnrS11-Producing O101:H5 <i>Escherichia coli</i> Strain Phylogroup A: ST167 from a Poultry Farm in Egypt.", "token_count": 398, "char_count": 952, "word_count": 105, "semantic_coherence": 1, "information_density": 0.781, "quality_score": 0.8905, "entities": { "genes": [ "HC100", "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:12.099315", "source": { "split": "train_shard_00001", "doc_id": 1038 }, "chunk_id": "train_shard_00001_1038_1", "global_id": 7134 }, { "text": "

Summary

The HXB/BXH family of recombinant inbred rat strains is a unique genetic resource that has been extensively phenotyped over 25 years, resulting in a vast dataset of quantitative molecular and physiological phenotypes. We built a pangenome graph from 10x Genomics Linked-Read data for 31 recombinant inbred rats to study genetic variation and association mapping. The pangenome includes 0.2Gb of sequence that is not present the reference mRatBN7.2, confirming the capture of substantial additional variation. We validated variants in challenging regions, including complex structural variants resolving into multiple haplotypes. Phenome-wide association analysis of validated SNPs uncovered variants associated with glucose/insulin levels and hippocampal gene expression. We propose an interaction between Pirl1l1 , chromogranin expression, TNF-α levels, and insulin regulation. This study demonstrates the utility of linked-read pangenomes for comprehensive variant detection and mapping phenotypic diversity in a widely used rat genetic reference panel.\n\nPangenome reconstruction in rats enhances genotype-phenotype mapping and novel variant discovery", "token_count": 282, "char_count": 1170, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:12.655475", "source": { "split": "train_shard_00001", "doc_id": 1039 }, "chunk_id": "train_shard_00001_1039_0", "global_id": 7135 }, { "text": "Clostridium perfringens is associated with a variety of diseases in both humans and animals. Recent advances in genomic sequencing make it timely to re-visit this important pathogen. Although the genome sequence of C. perfringens was first determined in 2002, large-scale comparative genomics with isolates of different origins is still lacking. In this study, we used whole-genome sequencing of 45 C. perfringens isolates with isolation time spanning an 80-year period and performed comparative analysis of 173 genomes from worldwide strains. We also conducted phylogenetic lineage analysis and introduced an openness index (OI) to evaluate the openness of bacterial genomes. We classified all these genomes into five lineages and hypothesized that the origin of C. perfringens dates back to ~80 000 years ago. We showed that the pangenome of the 173 C. perfringens strains contained a total of 26 954 genes, while the core genome comprised 1020 genes, accounting for about a third of the genome of each isolate. We demonstrated that C. perfringens had the highest OI compared with 51 other bacterial species. Intact prophage sequences were found in nearly 70.0 % of C. perfringens genomes, while CRISPR sequences were found only in ~40.0 %. Plasmids were prevalent in C. perfringens isolates, and half of the virulence genes and antibiotic resistance genes (ARGs) identified in all the isolates could be found in plasmids. ARG-sharing network analysis showed that C. perfringens shared its 11 ARGs with 55 different bacterial species, and a high frequency of ARG transfer may have occurred between C. perfringens and species in the genera Streptococcus and Staphylococcus", "token_count": 523, "char_count": 1771, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:13.319283", "source": { "split": "train_shard_00001", "doc_id": 1040 }, "chunk_id": "train_shard_00001_1040_0", "global_id": 7136 }, { "text": "Correlation analysis showed that the ARG number in C. perfringens strains increased with time, while the virulence gene number was relative stable. Our results, taken together with previous studies, revealed the high genome openness and genetic diversity of C. perfringens and provide a comprehensive view of the phylogeny, genomic features, virulence gene and ARG profiles of worldwide strains.\n\nPhylogenetic and genomic analysis reveals high genomic openness and genetic diversity of Clostridium perfringens.", "token_count": 132, "char_count": 531, "word_count": 72, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:13.743554", "source": { "split": "train_shard_00001", "doc_id": 1040 }, "chunk_id": "train_shard_00001_1040_1", "global_id": 7137 }, { "text": "Genome shuffling is a process to combine advantage traits by the recombination of the entire genome and it has been successfully applied in the laboratory evolution of various industrial microorganisms. However, genome shuffling has not been described in Kluyveromyces marxianus (KM), a promising yeast host for the expression of heterologous proteins. In this protocol, genome shuffling in KM is performed by sexual reproduction and is combined with high-throughput screening to obtain high-yielding strains. Notably, the screening of diploid clones risen from one mating mixture is carried out to improve the effectiveness of evolution. Mating-sporulation-mating cycles are repeated to obtain KM strain with ideal traits. •The method combines genome shuffling with high-throughput to achieve strains displaying high yielding of heterologous proteins.•This method can be applied to the genome shuffling of other species when only a few starting strains are available for sexual reproduction.\n\nA protocol of rapid laboratory evolution by genome shuffling in Kluyveromyces marxianus.", "token_count": 264, "char_count": 1096, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:14.300477", "source": { "split": "train_shard_00001", "doc_id": 1041 }, "chunk_id": "train_shard_00001_1041_0", "global_id": 7138 }, { "text": "The Pseudomonas syringae species complex is a heterogeneous group of plant pathogenic bacteria associated with a wide distribution of plant species. Advances in genomics are revealing the complex evolutionary history of this species complex and the wide array of genetic adaptations underpinning their diverse lifestyles. Here, we genomically characterize two P. syringae isolates collected from diseased Callery pears (Pyrus calleryana) in Berkeley, California in 2019 and 2022. We also isolated a lytic bacteriophage, which we characterized and evaluated for biocontrol efficiency. Using a multilocus sequence analysis and core genome alignment, we classified the P. syringae isolates as members of phylogroup 2, related to other strains previously isolated from Pyrus and Prunus. An analysis of effector proteins demonstrated an evolutionary conservation of effectoromes across isolates classified in PG2 and yet uncovered unique effector profiles for each, including the two newly identified isolates. Whole-genome sequencing of the associated phage uncovered a novel phage genus related to Pseudomonas syringae pv. actinidiae phage PHB09 and the Flaumdravirus genus. Finally, using in planta infection assays, we demonstrate that the phage was equally useful in symptom mitigation of immature pear fruit regardless of the Pss strain tested. Overall, this study demonstrates the diversity of P. syringae and their viruses associated with ornamental pear trees, posing spill-over risks to commercial pear trees and the possibility of using phages as biocontrol agents to reduce the impact of disease.IMPORTANCEGlobal change exacerbates the spread and impact of pathogens, especially in agricultural settings. There is a clear need to better monitor the spread and diversity of plant pathogens, including in potential spillover hosts, and for the development of novel and sustainable control strategies. In this study, we characterize the first described strains of Pseudomonas syringae pv", "token_count": 522, "char_count": 2075, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5895, "quality_score": 0.7947, "entities": { "genes": [ "PG2", "PHB09" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:14.958149", "source": { "split": "train_shard_00001", "doc_id": 1042 }, "chunk_id": "train_shard_00001_1042_0", "global_id": 7139 }, { "text": "syringae isolated from Callery pear in Berkeley, California from diseased tissues in an urban environment. We show that these strains have divergent virulence profiles from previously described strains and that they can cause disease in commercial pears. Additionally, we describe a novel bacteriophage that is associated with these strains and explore its potential to act as a biocontrol agent. Together, the data presented here demonstrate that ornamental pear trees harbor novel P. syringae pv. syringae isolates that potentially pose a risk to local fruit production, or vice versa-but also provide us with novel associated phages, effective in disease mitigation.\n\nGenomic characterization of Pseudomonas syringae pv. syringae from Callery pear and the efficiency of associated phages in disease protection.", "token_count": 207, "char_count": 848, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6949, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:15.422285", "source": { "split": "train_shard_00001", "doc_id": 1042 }, "chunk_id": "train_shard_00001_1042_1", "global_id": 7140 }, { "text": "

Importance

The findings of this study are significant, as N4-like viruses represent a unique viral lineage with a distinct replication mechanism and a conserved core genome. This work has resulted in a comprehensive global map of the entire N4-like viral lineage, including information on their distribution in different biomes, evolutionary divergence, genomic diversity, and the potential for viral-mediated host metabolic reprogramming. As such, this work significantly contributes to our understanding of the ecological function and viral-host interactions of bacteriophages.\n\nIdentification of hidden N4-like viruses and their interactions with hosts.", "token_count": 149, "char_count": 664, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:15.858231", "source": { "split": "train_shard_00001", "doc_id": 1043 }, "chunk_id": "train_shard_00001_1043_0", "global_id": 7141 }, { "text": "Here, the draft genome sequence of a multi-drug resistant (MDR) Serratia marcescens strain BMD28, isolated from a clinical source from Dhaka, Bangladesh, has been reported. The sequence raw read files were generated using Illumina sequencing technology utilizing genomic DNA from the pure culture of this strain. The strain has a genome size of around 5.4 million base pairs, a GC content of 59.70 %, and 5,141 coding sequences. We conducted genomic studies using several bioinformatics tools focusing on resistance genes, virulence factors, toxin-antitoxin systems, and pangenome analysis. Strain BMD28 harbored the blaNDM-7 gene in an IncX3 plasmid. A phylogenomic study with S. marcescens strains isolated worldwide revealed that our strain is in the same clade as other strains reported in Bangladesh. The data can be used primarily to understand the genomic content, epidemiology, and evolution of S. marcescens in Bangladesh. The genome sequence data of BMD28 has been deposited in the NCBI database under BioSample accession number SAMN41260295.\n\nDraft genome sequence data of Serratia marcescens strain harboring blaNDM-7 from Dhaka, Bangladesh.", "token_count": 363, "char_count": 1217, "word_count": 171, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "BMD28", "SAMN41260295" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:16.438096", "source": { "split": "train_shard_00001", "doc_id": 1044 }, "chunk_id": "train_shard_00001_1044_0", "global_id": 7142 }, { "text": "

Aims

To explore the pathogenic mechanisms of Candida albicans (C. albicans), focusing on its impact on human health, particularly through invasive infections in the gastrointestinal and respiratory tracts.

Methods

In this study, we evaluated the demographic and clinical profiles of 7 pneumonia patients. Meanwhile, we used Gene Set Enrichment Analysis (GSEA) and Evolutionary Dynamics method to analyze the role of candidalysin in C. albicans pathogenicity.

Results

By analyzing genomic data and conducting biomedical text mining, we identified novel mutation sites in the candidalysin coding gene ECE1-III, shedding light into the genetic diversity within C. albicans strains and their potential implications for antifungal resistance. Our results revealed significant associations between C. albicans and respiratory as well as gastrointestinal diseases, emphasizing the fungus's role in the pathogenesis of these diseases. Additionally, we identified a new mutation site in the C. albicans strain YF2-5, isolated from patients with pneumonia. This mutation may be associated with its heightened pathogenicity.

Conclusion

Our research advances the understanding of C. albicans pathogenicity and opens new avenues for developing targeted antifungal therapies. By focusing on the molecular basis of fungal virulence, we aim to contribute to the development of more effective treatment strategies, addressing the challenge of multidrug resistance in invasive fungal infections.\n\nExploring the role of candidalysin in the pathogenicity of Candida albicans by gene set enrichment analysis and evolutionary dynamics.", "token_count": 455, "char_count": 1705, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.8111, "entities": { "genes": [ "ECE1", "YF2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:17.110008", "source": { "split": "train_shard_00001", "doc_id": 1045 }, "chunk_id": "train_shard_00001_1045_0", "global_id": 7143 }, { "text": "Bee bread has received attention due to its high nutritional value, especially its phenolic composition, which enhances life quality. The present study aimed to evaluate the chemical and antimicrobial properties of bee bread (BB) samples from Romania. Initially, the bee bread alcoholic extracts (BBEs) were obtained from BB collected and prepared by Apis mellifera carpatica bees. The chemical composition of the BBE was characterized by Fourier Transform Infrared Spectroscopy (FTIR) and the total phenols and flavonoid contents were determined. Also, a UHPLC-DAD-ESI/MS analysis of phenolic compounds (PCs) and antioxidant activity were evaluated. Furthermore, the antimicrobial activity of BBEs was evaluated by qualitative and quantitative assessments. The BBs studied in this paper are provided from 31 families of plant species, with the total phenols content and total flavonoid content varying between 7.10 and 18.30 mg gallic acid equivalents/g BB and between 0.45 and 1.86 mg quercetin equivalents/g BB, respectively. Chromatographic analysis revealed these samples had a significant content of phenolic compounds, with flavonoids in much higher quantities than phenolic acids. All the BBEs presented antimicrobial activity against all clinical and standard pathogenic strains tested. Salmonella typhi, Candida glabrata, Candida albicans, and Candida kefyr strains were the most sensitive, while BBEs' antifungal activity on C. krusei and C. kefyr was not investigated in any prior research. In addition, this study reports the BBEs' inhibitory activity on microbial (bacterial and fungi) adhesion capacity to the inert substratum for the first time.\n\nBee Bread: A Promising Source of Bioactive Compounds with Antioxidant Properties-First Report on Some Antimicrobial Features.", "token_count": 505, "char_count": 1837, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.8169, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:17.783368", "source": { "split": "train_shard_00001", "doc_id": 1046 }, "chunk_id": "train_shard_00001_1046_0", "global_id": 7144 }, { "text": "Modern pangenome graphs are built using haplotype-resolved genome assemblies. During read mapping to a pangenome graph, prioritizing alignments that are consistent with the known haplotypes has been shown to improve genotyping accuracy. However, the existing rigorous formulations for sequence-to-graph co-linear chaining and alignment problems do not consider the haplotype paths in a pangenome graph. This often leads to spurious read alignments to those paths that are unlikely recombinations of the known haplotypes. In this paper, we develop novel formulations and algorithms for haplotype-aware sequence alignment to an acyclic pangenome graph. We consider both sequence-to-graph chaining and sequence-to-graph alignment problems. Drawing inspiration from the commonly used models for genotype imputation, we assume that a query sequence is an imperfect mosaic of the reference haplotypes. Accordingly, we extend previous chaining and alignment formulations by introducing a recombination penalty for a haplotype switch. First, we solve haplotype-aware sequence-to-graph alignment in O(|Q||E||H|) time, where Q is the query sequence, E is the set of edges, and H is the set of haplotypes represented in the graph. To complement our solution, we prove that an algorithm significantly faster than O(|Q||E||H|) is impossible under the Strong Exponential Time Hypothesis (SETH). Second, we propose a haplotype-aware chaining algorithm that runs in O(|H|N log |H|N) time after graph preprocessing, where N is the count of input anchors. We then establish that a chaining algorithm significantly faster than O(|H|N) is impossible under SETH. As a proof-of-concept of our algorithmic solutions, we implemented the chaining algorithm in the Minichain aligner (https://github.com/at-cg/minichain). We demonstrate the advantage of the algorithm by aligning sequences sampled from human major histocompatibility complex (MHC) to a pangenome graph of 60 MHC haplotypes. The proposed algorithm offers better consistency with ground-truth recombinations when compared to a haplotype-agnostic algorithm.", "token_count": 506, "char_count": 2094, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5567, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:18.478886", "source": { "split": "train_shard_00001", "doc_id": 1047 }, "chunk_id": "train_shard_00001_1047_0", "global_id": 7145 }, { "text": "Haplotype-aware sequence alignment to pangenome graphs", "token_count": 13, "char_count": 54, "word_count": 6, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:18.868664", "source": { "split": "train_shard_00001", "doc_id": 1047 }, "chunk_id": "train_shard_00001_1047_1", "global_id": 7146 }, { "text": "The genotoxin colibactin is a secondary metabolite produced by the polyketide synthase (pks) island harbored by extraintestinal pathogenic E. coli (ExPEC) and other members of the Enterobacteriaceae that has been increasingly reported to have critical implications in human health. The present study entails a high-throughput whole-genome comparison and phylogenetic analysis of such pathogenic E. coli isolates to gain insights into the patterns of distribution, horizontal transmission, and evolution of the island. For the current study, 23 pks-positive ExPEC genomes were newly sequenced, and their virulome and resistome profiles indicated a preponderance of virulence encoding genes and a reduced number of genes for antimicrobial resistance. In addition, 4,090 E. coli genomes from the public domain were also analyzed for large-scale screening for pks-positive genomes, out of which a total of 530 pks-positive genomes were studied to understand the subtype-based distribution pattern(s). The pks island showed a significant association with the B2 phylogroup (82.2%) and a high prevalence in sequence type 73 (ST73; n = 179) and ST95 (n = 110) and the O6:H1 (n = 110) serotype. Maximum-likelihood (ML) phylogeny of the core genome and intergenic regions (IGRs) of the ST95 model data set, which was selected because it had both pks-positive and pks-negative genomes, displayed clustering in relation to their carriage of the pks island", "token_count": 497, "char_count": 1549, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [ "ST95", "ST73" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:19.537695", "source": { "split": "train_shard_00001", "doc_id": 1048 }, "chunk_id": "train_shard_00001_1048_0", "global_id": 7147 }, { "text": "Prevalence patterns of genes encoding RM systems in the pks-positive and pks-negative genomes were also analyzed to determine their potential role in pks island acquisition and the maintenance capability of the genomes. Further, the maximum-likelihood phylogeny based on the core genome and pks island sequences from 247 genomes with an intact pks island demonstrated horizontal gene transfer of the island across sequence types and serotypes, with few exceptions. This study vitally contributes to understanding of the lineages and subtypes that have a higher propensity to harbor the pks island-encoded genotoxin with possible clinical implications.IMPORTANCE Extraintestinal pathologies caused by highly virulent strains of E. coli amount to clinical implications with high morbidity and mortality rates. Pathogenic E. coli strains are evolving with the horizontal acquisition of mobile genetic elements, including pathogenicity islands such as the pks island, which produces the genotoxin colibactin, resulting in severe clinical outcomes, including colorectal cancer progression. The current study encompasses high-throughput comparative genomics and phylogenetic analyses to address the questions pertaining to the acquisition and evolution pattern of the genomic island in different E. coli subtypes. It is crucial to gain insights into the distribution, transfer, and maintenance of pathogenic islands, as they harbor multiple virulence genes involved in pathogenesis and clinical implications of the infection.\n\nEvolutionary Dynamics Based on Comparative Genomics of Pathogenic Escherichia coli Lineages Harboring Polyketide Synthase (pks) Island.", "token_count": 433, "char_count": 1740, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:20.159584", "source": { "split": "train_shard_00001", "doc_id": 1048 }, "chunk_id": "train_shard_00001_1048_1", "global_id": 7148 }, { "text": "Basidiomycetes like rust fungi have complex reproductive cycles and dikaryotic life stages which influence their population structure and evolution. Puccinia coronata f. sp. avenae ( Pca ), the causal agent of oat crown rust, is a pathogen of global economic importance. To investigate the genetic diversity of the species, as well as the role of mating type system and nuclear exchange (somatic hybridization) in host adaptation of Pca we acquired whole genome sequencing data of Taiwanese and Australian isolates, adding to existing data for USA and South African populations. An atlas of 30 chromosome-level, fully-phased nuclear haplotypes from six USA isolates and nine Australian isolates was generated to capture the genomic composition of key oat crown rust lineages. This study provides evidence of nuclear exchange and recombination of haplotypes in both the USA and Australian Pca populations as mechanisms for the introduction of genetic diversity. The limitations of assuming clonal evolutionary history from virulence phenotyping is demonstrated by the detection of either sexual or cryptic genetic recombination in the Pca Australian population. Overall, the characterization of intercontinental migration of Pca at the haplotype level provides further impetus for molecular monitoring of rust pathogen populations on a global scale.\n\nA high-resolution haplotype pangenome uncovers somatic hybridization, recombination and intercontinental migration in oat crown rust", "token_count": 322, "char_count": 1482, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:20.727768", "source": { "split": "train_shard_00001", "doc_id": 1049 }, "chunk_id": "train_shard_00001_1049_0", "global_id": 7149 }, { "text": "Multichromosomal mitochondrial genomes (mtDNAs) in eukaryotes exhibit remarkable structural diversity, yet intraspecific variability and the origin of the individual chromosomes remain poorly understood. We focus on a holoparasitic angiosperm with an mtDNA consisting of 65 chromosomes largely composed of foreign DNA acquired by horizontal gene transfer (HGT) from its mimosoid hosts. The frequency, timing and population dynamics of these HGT events have not been examined. Here, we sampled different individuals of the holoparasite Lophophytum mirabile, along with their host plants, to assess mtDNA intraspecific variability and capture recent events that may bring insights into the HGT process. We also gathered mitochondrial data from 43 mimosoids to identify older and recent HGT events and assess precisely the proportion of foreign DNA. Through comparative genomic and evolutionary analyses, we uncovered great intraspecific variability in chromosome content and defined the mitochondrial pangenome of L. mirabile with 105 distinct chromosomes. The estimated foreign content reaches 93.5% of the mtDNA, including 73 fully foreign chromosomes that support the circle‐mediated HGT model as a key mechanism for their acquisition. We inferred recurrent DNA transfers from the host plants, leading to new mitochondrial chromosomes that replicate autonomously. Our results emphasize the importance of adopting a pangenomic approach to fully capture the genetic diversity and evolution of multichromosomal mitochondrial genomes. This study shows that HGT can strongly influence the mtDNA content and generate enormous intraspecific variability even in geographically close individuals.\n\nHighly variable mitochondrial chromosome content in a holoparasitic plant due to recurrent gains of foreign circular DNA", "token_count": 419, "char_count": 1810, "word_count": 250, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:21.352109", "source": { "split": "train_shard_00001", "doc_id": 1050 }, "chunk_id": "train_shard_00001_1050_0", "global_id": 7150 }, { "text": "

Motivation

Pangenomics evolved since its first applications on bacteria, extending from the study of genes for a given population to the study of all of its sequences available. While multiple methods are being developed to construct pangenomes in eukaryotic species there is still a gap for efficient and user-friendly visualization tools. Emerging graph representations come with their own challenges, and linearity remains a suitable option for user-friendliness.

Results

We introduce Panache, a tool for the visualization and exploration of linear representations of gene-based and sequence-based pangenomes. It uses a layout similar to genome browsers to display presence absence variations and additional tracks along a linear axis with a pangenomics perspective.

Availability and implementation

Panache is available at github.com/SouthGreenPlatform/panache under the MIT License.\n\nPanache: a web browser-based viewer for linearized pangenomes.", "token_count": 217, "char_count": 972, "word_count": 125, "semantic_coherence": 1, "information_density": 0.728, "quality_score": 0.864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:22.172411", "source": { "split": "train_shard_00001", "doc_id": 1051 }, "chunk_id": "train_shard_00001_1051_0", "global_id": 7151 }, { "text": "E. grandis is a hardwood tree used worldwide as pure species or hybrid partner to breed fast-growing plantation forestry crops that serve as feedstocks of timber and lignocellulosic biomass for pulp, paper, biomaterials and biorefinery products. The current v2.0 genome reference for the species (Bartholome et al., 2015; Myburg et al., 2014) served as the first reference for the genus and has helped drive the development of molecular breeding tools for eucalypts. Using PacBio HiFi long reads and Omni-C proximity ligation sequencing, we produced an improved, haplotype phased assembly (v4.0) for TAG0014, an early-generation selection of E. grandis. The two haplotypes are 571 Mbp (HAP1) and 552 Mbp (HAP2) in size and consist of 37 and 46 contigs scaffolded onto 11 chromosomes (contig N50 of 28.9 and 16.7 Mbp), respectively. These haplotype assemblies are 70 to 90 Mbp smaller than the diploid v2.0 assembly but capture all except one of the 22 telomeres, suggesting that substantial redundant sequence was included in the previous assembly. A total of 35,929 (HAP1) and 35,583 (HAP2) gene models were annotated, of which 438 and 472 contain long introns (>10 kbp) in gene models previously (v2.0) identified as multiple smaller genes. These and other improvements have increased gene annotation completeness levels from 93.8% to 99.4% in the v4.0 assembly. We found that 6,493 and 6,346 genes are within tandem duplicate arrays (HAP1 and HAP2, respectively, 18.4% and 17.8% of the total) and >43.8% of the haplotype assemblies consists of repeat elements. Analysis of synteny between the haplotypes and the E", "token_count": 511, "char_count": 1616, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": { "genes": [ "TAG0014", "HAP1", "HAP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:22.827374", "source": { "split": "train_shard_00001", "doc_id": 1052 }, "chunk_id": "train_shard_00001_1052_0", "global_id": 7152 }, { "text": "grandis v2.0 reference genome revealed extensive regions of collinearity, but also some major rearrangements, and provided a preview of population and pan-genome variation in the species.

Paper summary

We assembled a haplotype-phased genome for Eucalyptus grandis that will serve as reference for the most widely planted hardwood crop globally. It includes more than 430 new gene models with long introns and has 6% higher annotation completeness. The phased assembly provides a more accurate look at genome variation at DNA and transcript level and will better support future studies of genome structure and function. The improved assembly contains more tandem duplicate genes compared to the previous unphased reference. Finally, major genomic rearrangements between the two phased genomes provide a preview of pangenome and structural variation in E. grandis .\n\nA haplotype-resolved reference genome for Eucalyptus grandis", "token_count": 224, "char_count": 941, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7111, "quality_score": 0.8556, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:23.296110", "source": { "split": "train_shard_00001", "doc_id": 1052 }, "chunk_id": "train_shard_00001_1052_1", "global_id": 7153 }, { "text": "

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen causing ear infections. However, genomic epidemiology and determinants influencing transmission of ear infections associated MRSA (EIA-MRSA) in community remain unknown.

Methods

In 2020-2021, 105 EIA-MRSA isolates were collected and sequenced from outpatients across different households in Shanghai, China. Antimicrobial susceptibility testing, core genome MLST, and phylodynamic analyses were conducted to characterize EIA-MRSA dissemination.

Results

Quinolone resistance was identified as a risk factor for EIA-MRSA spread (OR 9, [95% CI 3-31]). The ST764 clone and two subclones of ST22-PT hypervirulent clone have developed an extensive quinolone-resistant (eQR) phenotype, conferring additional resistance to advanced quinolones due to the accumulation of four mutations in gyrA (S84L and either S85P, E88K, or E88G) and parC (S80F and either E84K or E84G). These ST764- and ST22-PT-eQR isolates were highly transmissible and showed increased resistance to other commonly used antimicrobials, posing potential high-risk clones. The eQR phenotype may be inherent to the ST764 lineage, which emerged in the late 1980s, coinciding with the widespread fluoroquinolone usage. The ST22-PT-eQR subclones emerged in around 2017 and are accumulating resistance genes.

Conclusion

Vigilance is crucial for eQR high-risk clones, particularly the convergent ST22-PT-eQR subclones that accumulate resistance and virulence traits, posing risks for ear infections.

Clinical trial number

Not applicable.", "token_count": 498, "char_count": 1610, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [ "ST764", "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:23.942116", "source": { "split": "train_shard_00001", "doc_id": 1053 }, "chunk_id": "train_shard_00001_1053_0", "global_id": 7154 }, { "text": "Genomic insights into the spread of methicillin-resistant Staphylococcus aureus involved in ear infections.", "token_count": 29, "char_count": 107, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:24.295604", "source": { "split": "train_shard_00001", "doc_id": 1053 }, "chunk_id": "train_shard_00001_1053_1", "global_id": 7155 }, { "text": "Bacteriophages are the most prevalent biological entities in the biosphere. However, limitations in both medical relevance and sequencing technologies have led to a systematic underestimation of the genetic diversity within phages. This underrepresentation not only creates a significant gap in our understanding of phage roles across diverse biosystems but also introduces biases in computational models reliant on these data for training and testing. In this study, we focused on publicly available genomes of bacteriophages infecting high-priority ESKAPE pathogens to show the extent and impact of this underrepresentation. First, we demonstrate a stark underrepresentation of ESKAPE phage genomes within the public genome and protein databases. Next, a pangenome analysis of these ESKAPE phages reveals extensive sharing of core genes among phages infecting the same host. Furthermore, genome analyses and clustering highlight close nucleotide-level relationships among the ESKAPE phages, raising concerns about the limited diversity within current public databases. Lastly, we uncover a scarcity of unique lytic phages and phage proteins with antimicrobial activities against ESKAPE pathogens. This comprehensive analysis of the ESKAPE phages underscores the severity of underrepresentation and its potential implications. This lack of diversity in phage genomes may restrict the resurgence of phage therapy and cause biased outcomes in data-driven computational models due to incomplete and unbalanced biological datasets.\n\nA pangenome analysis of ESKAPE bacteriophages: the underrepresentation may impact machine learning models", "token_count": 357, "char_count": 1635, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:24.868527", "source": { "split": "train_shard_00001", "doc_id": 1054 }, "chunk_id": "train_shard_00001_1054_0", "global_id": 7156 }, { "text": "Syphilis cases have been consistently rising since its near elimination in the late 1990s. This resurgence, along with increasing rates of macrolide resistance and congenital syphilis, has triggered renewed efforts to better understand and control the disease. We analyzed 827 Treponema pallidum genomes and created a new genome-based hierarchical lineage framework, recapitulating the major T. pallidum lineages and characterizing sub-lineages. An updated pangenome was constructed, revealing that T. pallidum subsp. pallidum lineages are determined by a single hypothetical major outer sheath C-terminal domain-containing gene, while no significant genetic difference was observed between T. pallidum subsp. pertenue and T. pallidum subsp. endemicum. This study introduces an integrated genomic approach to characterize T. pallidum and highlights the significance of pangenomes in supporting public health.\n\nIntegrated genomic approaches improve <i>Treponema pallidum</i> phylogenetics and lineage classification.", "token_count": 317, "char_count": 1090, "word_count": 132, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:25.423194", "source": { "split": "train_shard_00001", "doc_id": 1055 }, "chunk_id": "train_shard_00001_1055_0", "global_id": 7157 }, { "text": "

Introduction

Bovine Genital Campylobacteriosis (BGC), caused by Campylobacter fetus subsp. venerealis, is a sexually transmitted bacterium that significantly impacts cattle reproductive performance. However, current detection methods lack consistency and reliability due to the close genetic similarity between C. fetus subsp. venerealis and C. fetus subsp. fetus. Therefore, this study aimed to utilize complete genome analysis to distinguish genetic features between C. fetus subsp. venerealis and other subspecies, thereby enhancing BGC detection for routine screening and epidemiological studies.

Methods and results

This study reported the complete genomes of four C. fetus subsp. fetus and five C. fetus subsp. venerealis, sequenced using long-read sequencing technologies. Comparative whole-genome analyses (n = 25) were conducted, incorporating an additional 16 complete C. fetus genomes from the NCBI database, to investigate the genomic differences between these two closely related C. fetus subspecies. Pan-genomic analyses revealed a core genome consisting of 1,561 genes and an accessory pangenome of 1,064 genes between the two C. fetus subspecies. However, no unique predicted genes were identified in either subspecies. Nonetheless, whole-genome single nucleotide polymorphisms (SNPs) analysis identified 289 SNPs unique to one or the C. fetus subspecies. After the removal of SNPs located on putative genomic islands, recombination sites, and those causing synonymous amino acid changes, the remaining 184 SNPs were functionally annotated. Candidate SNPs that were annotated with the KEGG \"Peptidoglycan Biosynthesis\" pathway were recruited for further analysis due to their potential association with the glycine intolerance characteristic of C. fetus subsp. venerealis and its biovar variant", "token_count": 532, "char_count": 1909, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:26.076580", "source": { "split": "train_shard_00001", "doc_id": 1056 }, "chunk_id": "train_shard_00001_1056_0", "global_id": 7158 }, { "text": "Verification with 58 annotated C. fetus genomes, both complete and incomplete, from RefSeq, successfully classified these seven SNPs into two groups, aligning with their phenotypic identification as CFF (Campylobacter fetus subsp. fetus) or CFV/CFVi (Campylobacter fetus subsp. venerealis and its biovar variant). Furthermore, we demonstrated the application of mraY SNPs for detecting C. fetus subspecies using a quantitative PCR assay.

Discussion

Our results highlighted the high genetic stability of C. fetus subspecies. Nevertheless, Campylobacter fetus subsp. venerealis and its biovar variants encoded common SNPs in genes related to glycine intolerance, which differentiates them from C. fetus subsp. fetus. This discovery highlights the potential of employing a multiple-SNP assay for the precise differentiation of C. fetus subspecies.\n\nWhole-genome comparison using complete genomes from Campylobacter fetus strains revealed single nucleotide polymorphisms on non-genomic islands for subspecies differentiation.", "token_count": 322, "char_count": 1091, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:26.644270", "source": { "split": "train_shard_00001", "doc_id": 1056 }, "chunk_id": "train_shard_00001_1056_1", "global_id": 7159 }, { "text": "

ABSTRACT

Vietnam, the 16th most populated nation, remains profoundly underrepresented in global genomic databases. Here, we present VN1K, a first-ever comprehensive and well-curated resource of multi-omics data with a wide-range of phenotypic information of 1,011 unrelated Vietnamese individuals. High-depth short-read whole-genome sequencing data were generated for all samples along with various - omic data, including microarray, long-read whole-genome sequencing, and RNA sequencing. Using a high-sensitivity variant detection pipeline, which included a pangenome graph reference and a deep-learning framework, we identified nearly 40 million variants of which 8.5 million are novel with nearly 900 thousand short insertions/deletions and 39 thousand structural variants. Specifically, VN1K featured a first-ever whole-genome methylation profile based on long read sequencing. A genotype imputation panel was also created with the highest accuracy on the Vietnamese population. Variants with significantly different allele frequencies in the Vietnamese population compared to others were found to be functionally significant, especially in genes associated with immune diseases ( HLA-B, KIR3DL3, KIR2DL1, KIR2DL4 ) or drug responses ( CYP2C19, CYP2D6, VKORC1, CYP2B6 ). We were also able to map various loci related to hepatitis B virus infection as well as six disease traits, including triglyceride levels, LDL-C, serum glucose levels, HbA1c, and levels of two liver enzymes (ALT and AST). VN1K dataset is accessible via genome.vinbigdata.org, an integrated platform with both linear and graph-based genome browser for facilitating data exploration, research, and applications in precision medicine.\n\nVN1K: a genome graph-based and function-driven multi-omics and phenomics resource for the Vietnamese population", "token_count": 476, "char_count": 1829, "word_count": 247, "semantic_coherence": 1, "information_density": 0.7206, "quality_score": 0.8603, "entities": { "genes": [ "VN1K", "VKORC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:27.289852", "source": { "split": "train_shard_00001", "doc_id": 1057 }, "chunk_id": "train_shard_00001_1057_0", "global_id": 7160 }, { "text": "

Background

This study aimed to determine, at the phenotypic and molecular levels, resistance and virulence markers in Candida spp. isolated from community-acquired infections in Bucharest outpatients during 2021, and to demonstrate the efficiency of alternative solutions against them based on silver nanoparticles (AgNPs).

Methods

A total of 62 Candida spp. strains were isolated from dermatomycoses and identified using chromogenic culture media and MALDI-TOF MS, and then investigated for their antimicrobial resistance and virulence markers (VMs), as well as for metabolic enzymes using enzymatic tests for the expression of soluble virulence factors, their biofilm formation and adherence capacity on HeLa cells, and PCR assays for the detection of virulence markers and the antimicrobial activity of alternative solutions based on AgNPs.

Results

Of the total of 62 strains, 45.16% were Candida parapsilosis; 29.03% Candida albicans; 9.67% Candida guilliermondii; 3.22% Candida lusitaniae, Candia pararugosa, and Candida tropicalis; and 1.66% Candida kefyr, Candida famata, Candida haemulonii, and Candida metapsilosis. Aesculin hydrolysis, caseinase, and amylase production were detected in the analyzed strains. The strains exhibited different indices of adherence to HeLa cells and were positive in decreasing frequency order for the LIP1, HWP1, and ALS1,3 genes (C", "token_count": 510, "char_count": 1510, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [ "ALS1", "LIP1", "HWP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:27.943624", "source": { "split": "train_shard_00001", "doc_id": 1058 }, "chunk_id": "train_shard_00001_1058_0", "global_id": 7161 }, { "text": "tropicalis/C. albicans). An inhibitory effect on microbial growth, adherence capacity, and on the production of virulence factors was obtained using AgNPs.

Conclusions

The obtained results in C. albicans and Candida non-albicans circulating in Bucharest outpatients were characterized by moderate-to-high potential to produce VMs, necessitating epidemiological surveillance measures to minimize the chances of severe invasive infections.\n\nPhenotypic and Genotypic Characterization of Resistance and Virulence Markers in Candida spp. Isolated from Community-Acquired Infections in Bucharest, and the Impact of AgNPs on the Highly Resistant Isolates.", "token_count": 202, "char_count": 694, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7654, "quality_score": 0.8827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:28.402171", "source": { "split": "train_shard_00001", "doc_id": 1058 }, "chunk_id": "train_shard_00001_1058_1", "global_id": 7162 }, { "text": "Synthetic biology seeks to engineer microbial cells for sustainable efficient production of value-added biofuels and bioproducts from low-cost renewable feedstocks. In order to resolve the conflicts of carbon flux between cell growth and bioproducts synthesis, the dynamic up-regulation on the bioproduct synthesis pathways and down-regulation on the competitive pathways simultaneously could be adjusted by promoter sets with diverse strengths. The development of broad-spectrum promoter libraries comprising promoters of varying strengths for different hosts without tedious reconstruction processes are attractive for biosynthetic engineers. In this study, we observed that five K. marxianus promoters ( km.PDC1, km.FBA1, km.TEF1, km.TDH3, km.ENO1 ) can all express genes in Y. lipolytica and that five Y. lipolytica promoters ( yl.hp4d, yl.FBA1in, yl.TEF1, yl.TDH1, yl.EXP1 ) can all express genes in K. marxianus with variable expression strengths. Interestingly, we also found two yeast promoters could shuttle express reporter genes in P. pastoris, E. coli and C. glutamicum . The yl . TEF1 promoter can also strongly express amylase and RFP in yeast P. pastoris and the eukaryotic promoter km . TEF1 can constitutively strong express RFP in bacterium E. coli and C. glutamicum. The RFP expression strength of the promoter km . TEF1 reached ∼20% to that of the T7 promoter in E. coli and was much stronger (more than 10 times) than in K. marxianus . Our work will expand the future development of broad host acceptable dynamic regulated systems with these broad-spectrum promoters for dynamically orchestrate the carbon flux to maximize target bioproduct synthesis.\n\nDesign and construction of shuttle expression vectors for non- conventional yeasts and bacteria", "token_count": 468, "char_count": 1769, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [ "EXP1", "TDH1", "FBA1", "ENO1", "TDH3", "PDC1", "TEF1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:29.055873", "source": { "split": "train_shard_00001", "doc_id": 1059 }, "chunk_id": "train_shard_00001_1059_0", "global_id": 7163 }, { "text": "Asgard archaea played a key role in the origin of the eukaryotic cell. While previous studies found that Asgard genomes encode diverse eukaryotic signature proteins (ESPs), representing homologs of proteins that play important roles in the complex organization of eukaryotic cells, the cellular characteristics and complexity of the Asgard archaeal ancestor of eukaryotes remain unclear. Here, we used de novo protein structure modeling and sensitive sequence similarity detection algorithms within an expanded Asgard archaeal genomic dataset to build a structural catalogue of the Asgard archaeal pangenome and identify 908 new ‘isomorphic’ ESPs (iESPs), representing clusters of protein structures most similar to eukaryotic proteins and that likely underwent extensive sequence divergence. While most previously identified ESPs were involved in cellular processes and signaling, iESPs are enriched in information storage and processing functions, with several being potentially implicated in facilitating cellular complexity. By expanding the complement of eukaryotic proteins in Asgard archaea, this study indicates that the archaeal ancestor of eukaryotes was more complex than previously assumed.\n\nStructure-based inference of eukaryotic complexity in Asgard archaea", "token_count": 277, "char_count": 1272, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6358, "quality_score": 0.8179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:29.623365", "source": { "split": "train_shard_00001", "doc_id": 1060 }, "chunk_id": "train_shard_00001_1060_0", "global_id": 7164 }, { "text": "The pangenome is the set of all genes present in a prokaryotic species. Most pangenomes contain many accessory genes that are present in only some of the species members. Genes need to function together, and it has been suggested that selection for certain gene combinations affects the structure of prokaryotic pangenomes. Nevertheless, genes might also co-occur simply due to being linked on the genome, and efficient tools are needed to distinguish linkage from co-selection. Here we present Goldfinder, an approach to infer co-occurrence and co-avoidance between gene pairs by taking the phylogenetic relationships of the species into account. The approach is implemented in an efficient Python script available at https://github.com/fbaumdicker/goldfinder . We also provide scripts for clustering co-occurring genes and for visualizing the resulting co-occurrence and co-avoidance networks in Cytoscape. In comparison to the co-occurrence inference tool Coinfinder, Goldfinder finds fewer co-occurring pairs in a real species pangenome, suggesting that fewer spurious associations due to phylogenetic dependencies are detected. We conclude that Goldfinder is a fast and accurate tool to infer gene co-occurrence and co-avoidance, which will enable large-scale analyses to infer co-selected genes across bacterial pangenomes.\n\nGoldfinder: Unraveling Networks of Gene Co-occurrence and Avoidance in Bacterial Pangenomes", "token_count": 336, "char_count": 1429, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:30.200960", "source": { "split": "train_shard_00001", "doc_id": 1061 }, "chunk_id": "train_shard_00001_1061_0", "global_id": 7165 }, { "text": "Cotton production faces challenges in fluctuating environmental conditions due to limited genetic variation in cultivated cotton species. To enhance the genetic diversity crucial for this primary fiber crop, it is essential to augment current germplasm resources. High-throughput sequencing has significantly impacted cotton functional genomics, enabling the creation of diverse mutant libraries and the identification of mutant functional genes and new germplasm resources. Artificial mutation, established through physical or chemical methods, stands as a highly efficient strategy to enrich cotton germplasm resources, yielding stable and high-quality raw materials. In this paper, we discuss the good foundation laid by high-throughput sequencing of cotton genome for mutant identification and functional genome, and focus on the construction methods of mutant libraries and diverse sequencing strategies based on mutants. In addition, the important functional genes identified by the cotton mutant library have greatly enriched the germplasm resources and promoted the development of functional genomes. Finally, an innovative strategy for constructing a cotton CRISPR mutant library was proposed, and the possibility of high-throughput screening of cotton mutants based on a UAV phenotyping platform was discussed. The aim of this review was to expand cotton germplasm resources, mine functional genes, and develop adaptable materials in a variety of complex environments.\n\nAdvances in genome sequencing and artificially induced mutation provides new avenues for cotton breeding.", "token_count": 304, "char_count": 1585, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:30.811302", "source": { "split": "train_shard_00001", "doc_id": 1062 }, "chunk_id": "train_shard_00001_1062_0", "global_id": 7166 }, { "text": "

ABSTRACT

Introduction

One third of people with CF in the UK are co-infected by both Staphylococcus aureus and Pseudomonas aeruginosa . Chronic bacterial infection in CF contributes to the gradual destruction of lung tissue, and eventually respiratory failure in this group.

Gap Statement

The contribution of S. aureus to cystic fibrosis (CF) lung decline in the presence or absence of P. aeruginosa is unclear. Defining the molecular and phenotypic characteristics of a range of S. aureus clinical isolates will help further understand its pathogenic capabilities.

Aim

Our objective was to use molecular and phenotypic tools to characterise twenty-five clinical S. aureus isolates collected from mono- and coinfection with P. aeruginosa from people with CF at the Royal Victoria Infirmary, Newcastle upon Tyne.

Methodology

Genomic DNA was extracted and sequenced. Multilocus sequence typing was used to construct phylogeny from the seven housekeeping genes. A pangenome was calculated using Roary. and cluster of Orthologous groups were assigned using eggNOG-mapper which were used to determine differences within core, accessory, and unique genomes. Characterisation of sequence type, clonal complex, agr and spa types was carried out using PubMLST, eBURST, AgrVATE and spaTyper, respectively. Antibiotic resistance was determined using Kirby Bauer disk diffusion tests. Phenotypic testing of haemolysis was carried out using ovine red blood cell agar plates and mucoid phenotypes visualised using Congo red agar.

Results

Clinical strains clustered closely based on agr type, sequence type and clonal complex. COG analysis revealed statistically significant enrichment of COG families between core, accessory and unique pangenome groups. The unique genome was significantly enriched for replication, recombination and repair, and defence mechanisms. The presence of known virulence genes and toxins were high within this group, and unique genes were identified in 11 strains", "token_count": 514, "char_count": 2029, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6469, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:31.475642", "source": { "split": "train_shard_00001", "doc_id": 1063 }, "chunk_id": "train_shard_00001_1063_0", "global_id": 7167 }, { "text": "Strains which were isolated from the same patient all surpassed average nucleotide identity thresholds, however, differed in phenotypic traits. Antimicrobial resistance to macrolides was significantly higher in the coinfection group.

Conclusion

There is huge variation in genetic and phenotypic capabilities of S. aureus strains. Further studies on how these may differ in relation to other species in the CF lung may give insight into inter-species interactions.

Data summary

The assembled GenBank (gbk) files for all clinical isolates in this study have been deposited in ENA under the study accession PRJEB56184, accession numbers for each of the twenty-five clinical isolates have been provided in Table S1. The reference strains were collected from the NCBI BioSample database ( www.ncbi.nlm.nih.gov/biosample ): MRSA_252 (NC_002952.2), HO 5096 0412 (NC_017763.1), ST398 (NC_017333.1) and NCTC8325 (NC_007795.1).\n\nCharacterisation of key genotypic and phenotypic traits of clinical cystic fibrosisStaphylococcus aureusisolates", "token_count": 328, "char_count": 1056, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7518, "quality_score": 0.8759, "entities": { "genes": [ "PRJEB56184", "ST398", "NCTC8325" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:32.041936", "source": { "split": "train_shard_00001", "doc_id": 1063 }, "chunk_id": "train_shard_00001_1063_1", "global_id": 7168 }, { "text": "

Background

The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been extensively studied.

Results

In this study, we constructed a pig pangenome graph using 21 pig assemblies and identified 23,831 NRSs with a total length of 105 Mb. Our findings revealed that NRSs were more prevalent in breeds exhibiting greater genetic divergence from the reference genome. Furthermore, we observed that NRSs were rarely found within coding sequences, while NRS insertions were enriched in immune-related Gene Ontology terms. Notably, our investigation also unveiled a close association between novel genes and the immune capacity of pigs. We observed substantial differences in terms of frequencies of NRSs between Eastern and Western pigs, and the heat-resistant pigs exhibited a substantial number of NRS insertions in an 11.6 Mb interval on chromosome X. Additionally, we discovered a 665 bp insertion in the fourth intron of the TNFRSF19 gene that may be associated with the ability of heat tolerance in Southern Chinese pigs.

Conclusions

Our findings demonstrate the potential of a graph genome approach to reveal important functional features of NRSs in pig populations.\n\nPig pangenome graph reveals functional features of non-reference sequences.", "token_count": 341, "char_count": 1458, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6618, "quality_score": 0.8309, "entities": { "genes": [ "TNFRSF19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:32.613360", "source": { "split": "train_shard_00001", "doc_id": 1064 }, "chunk_id": "train_shard_00001_1064_0", "global_id": 7169 }, { "text": "Whole genome sequencing offers great opportunities for linking genotypes to phenotypes aiding in our understanding of human disease and bacterial pathogenicity. However, these analyses often overlook non-coding intergenic regions (IGRs). By disregarding the IGRs, crucial information is lost, as genes have little biological function without expression. In this study, we present the first complete pangenome of the important human pathogen Streptococcus pneumoniae (pneumococcus), spanning both the genes and IGRs. We show that the pneumococcus species retains a small core genome of IGRs that are present across all isolates. Gene expression is highly dependent on these core IGRs, and often several copies of these core IGRs are found across each genome. Core genes and core IGRs show a clear linkage as 81% of core genes are associated with core IGRs. Additionally, we identify a single IGR within the core genome that is always occupied by one of two highly distinct sequences, scattered across the phylogenetic tree. Their distribution indicates that this IGR is transferred between isolates through horizontal regulatory transfer independent of the flanking genes and that each type likely serves different regulatory roles depending on their genetic context.\n\nAdding context to the pneumococcal core genes – a bioinformatic analysis of the intergenic pangenome of Streptococcus pneumoniae", "token_count": 326, "char_count": 1403, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:33.190221", "source": { "split": "train_shard_00001", "doc_id": 1065 }, "chunk_id": "train_shard_00001_1065_0", "global_id": 7170 }, { "text": "Species of the Bacteroidales order are among the most abundant and stable bacterial members of the human gut microbiome, with diverse impacts on human health. We cultured and sequenced the genomes of 408 Bacteroidales isolates from healthy human donors representing nine genera and 35 species and performed comparative genomic, gene-specific, metabolomic, and horizontal gene transfer analyses. Families, genera, and species could be grouped based on many distinctive features. We also observed extensive DNA transfer between diverse families, allowing for shared traits and strain evolution. Inter- and intra-species diversity is also apparent in the metabolomic profiling studies. This highly characterized and diverse Bacteroidales culture collection with strain-resolved genomic and metabolomic analyses represents a valuable resource to facilitate informed selection of strains for microbiome reconstitution.\n\nComprehensive analyses of a large human gut Bacteroidales culture collection reveal species- and strain-level diversity and evolution.", "token_count": 220, "char_count": 1049, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:33.680218", "source": { "split": "train_shard_00001", "doc_id": 1066 }, "chunk_id": "train_shard_00001_1066_0", "global_id": 7171 }, { "text": "Campylobacter is a leading causing of bacterial foodborne and zoonotic illnesses in the USA. Pulsed-field gene electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST) have been historically used to differentiate sporadic from outbreak Campylobacter isolates. Whole genome sequencing (WGS) has been shown to provide superior resolution and concordance with epidemiological data when compared with PFGE and 7-gene MLST during outbreak investigations. In this study, we evaluated epidemiological concordance for high-quality SNP (hqSNP), core genome (cg)MLST and whole genome (wg)MLST to cluster or differentiate outbreak-associated and sporadic Campylobacter jejuni and Campylobacter coli isolates. Phylogenetic hqSNP, cgMLST and wgMLST analyses were also compared using Baker's gamma index (BGI) and cophenetic correlation coefficients. Pairwise distances comparing all three analysis methods were compared using linear regression models. Our results showed that 68/73 sporadic C. jejuni and C. coli isolates were differentiated from outbreak-associated isolates using all three methods. There was a high correlation between cgMLST and wgMLST analyses of the isolates; the BGI, cophenetic correlation coefficient, linear regression model R 2 and Pearson correlation coefficients were >0.90. The correlation was sometimes lower comparing hqSNP analysis to the MLST-based methods; the linear regression model R 2 and Pearson correlation coefficients were between 0.60 and 0.86, and the BGI and cophenetic correlation coefficient were between 0.63 and 0.86 for some outbreak isolates. We demonstrated that C. jejuni and C. coli isolates clustered in concordance with epidemiological data using WGS-based analysis methods", "token_count": 518, "char_count": 1820, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5574, "quality_score": 0.7787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:34.345306", "source": { "split": "train_shard_00001", "doc_id": 1067 }, "chunk_id": "train_shard_00001_1067_0", "global_id": 7172 }, { "text": "Discrepancies between allele and SNP-based approaches may reflect the differences between how genomic variation (SNPs and indels) are captured between the two methods. Since cgMLST examines allele differences in genes that are common in most isolates being compared, it is well suited to surveillance: searching large genomic databases for similar isolates is easily and efficiently done using allelic profiles. On the other hand, use of an hqSNP approach is much more computer intensive and not scalable to large sets of genomes. If further resolution between potential outbreak isolates is needed, wgMLST or hqSNP analysis can be used.\n\nEvaluation of core genome and whole genome multilocus sequence typing schemes for Campylobacter jejuni and Campylobacter coli outbreak detection in the USA.", "token_count": 190, "char_count": 809, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7395, "quality_score": 0.8697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:34.789219", "source": { "split": "train_shard_00001", "doc_id": 1067 }, "chunk_id": "train_shard_00001_1067_1", "global_id": 7173 }, { "text": "The increase of Vancomycin-resistant Enterococcus faecium (VREfm) in recent years has been partially attributed to the rise of specific clonal lineages, which have been identified throughout Germany. To date, there is no gold standard for the interpretation of genomic data for outbreak analyses. New genomic approaches such as split k-mer analysis (SKA) could support cluster attribution for routine outbreak investigation. The aim of this project was to investigate frequent clonal lineages of VREfm identified during suspected outbreaks across different hospitals, and to compare genomic approaches including SKA in routine outbreak investigation. We used routine outbreak laboratory data from seven hospitals and three different hospital networks in Berlin, Germany. Short-read libraries were sequenced on the Illumina MiSeq system. We determined clusters using the published Enterococcus faecium-cgMLST scheme (threshold ≤20 alleles), and assigned sequence and complex types (ST, CT), using the Ridom SeqSphere+ software. For each cluster as determined by cgMLST, we used pairwise core-genome SNP-analysis and SKA at thresholds of ten and seven SNPs, respectively, to further distinguish cgMLST clusters. In order to investigate clinical relevance, we analysed to what extent epidemiological linkage backed the clusters determined with different genomic approaches. Between 2014 and 2021, we sequenced 693 VREfm strains, and 644 (93 %) were associated within cgMLST clusters. More than 74 % (n=475) of the strains belonged to the six largest cgMLST clusters, comprising ST117, ST78 and ST80. All six clusters were detected across several years and hospitals without apparent epidemiological links. Core SNP analysis identified 44 clusters with a median cluster size of three isolates (IQR 2-7, min-max 2-63), as well as 197 singletons (41.4 % of 475 isolates)", "token_count": 477, "char_count": 1885, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [ "ST80", "ST78", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:35.439139", "source": { "split": "train_shard_00001", "doc_id": 1068 }, "chunk_id": "train_shard_00001_1068_0", "global_id": 7174 }, { "text": "SKA identified 67 clusters with a median cluster size of two isolates (IQR 2-4, min-max 2-19), and 261 singletons (54.9 % of 475 isolates). Of the isolate pairs attributed to clusters, 7 % (n=3064/45 596) of pairs in clusters determined by standard cgMLST, 15 % (n=1222/8500) of pairs in core SNP-clusters and 51 % (n=942/1880) of pairs in SKA-clusters showed epidemiological linkage. The proportion of epidemiological linkage differed between sequence types. For VREfm, the discriminative ability of the widely used cgMLST based approach at ≤20 alleles difference was insufficient to rule out hospital outbreaks without further analytical methods. Cluster assignment guided by core genome SNP analysis and the reference free SKA was more discriminative and correlated better with obvious epidemiological linkage, at least recently published thresholds (ten and seven SNPs, respectively) and for frequent STs. Besides higher overall discriminative power, the whole-genome approach implemented in SKA is also easier and faster to conduct and requires less computational resources.\n\nSplit k-mer analysis compared to cgMLST and SNP-based core genome analysis for detecting transmission of vancomycin-resistant enterococci: results from routine outbreak analyses across different hospitals and hospitals networks in Berlin, Germany.", "token_count": 373, "char_count": 1349, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6984, "quality_score": 0.8492, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:36.029242", "source": { "split": "train_shard_00001", "doc_id": 1068 }, "chunk_id": "train_shard_00001_1068_1", "global_id": 7175 }, { "text": "

ABSTRACT

Motivation

Strain-level microbiome profiling has revealed key insights into microbial community composition and strain dynamics. However, accurate strain-level analysis remains challenging due to limited linkage information, ambiguous read mapping, and complicating factors such as genome similarity, sequencing depth, and community complexity. These challenges are especially pronounced for short-read metagenomic data when estimating the relative abundances of multiple strains, a task critical for genotype-phenotype association studies.

Results

To address this gap, we present Strainify, which enables accurate strain-level abundance estimation from short-read metagenomes with as little as 1% genome coverage. Specifically, Strainify combines (1) identification of informative variants via core genome alignment, (2) filtering of confounding variants via a window-based test, and (3) maximum likelihood estimation of strain abundances. A Shannon entropy-weighted version of the model further improves robustness in noisy, low-coverage settings by downweighting sites with low information content. Across simulated communities of varying complexity, Strainify consistently outperformed existing approaches. On mock community sequencing data, Strainify’s estimates aligned more closely with reference abundances. When applied to a longitudinal gut microbiome dataset, Strainify successfully recapitulated the reported temporal dynamics of Bacteroides ovatus strain groups, demonstrating its ability to recover biologically meaningful patterns from real-world metagenomes. Together, these results establish Strainify as a robust and versatile solution for accurate strain-level abundance estimation in short-read, low-coverage microbiome studies.

Availability

The Strainify code and results are available at: https://github.com/treangenlab/Strainify\n\nStrainify: Strain-Level Microbiome Profiling for Low-Coverage Short-Read Metagenomic Datasets", "token_count": 454, "char_count": 1995, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7106, "quality_score": 0.8553, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:36.671402", "source": { "split": "train_shard_00001", "doc_id": 1069 }, "chunk_id": "train_shard_00001_1069_0", "global_id": 7176 }, { "text": "Abstract

Background The Borreliaceae family includes many obligate parasitic bacterial species which are etiologically associated with a myriad of zoonotic borrelioses including Lyme disease and vector-borne relapsing fevers. Infections by the Borreliaceae are difficult to detect by both direct and indirect methods, often leading to delayed and missed diagnoses. Efforts to improve diagnoses center around the development of molecular diagnostics (MDx), but due to deep tissue sequestration of the causative spirochaetes and the lack of persistent bacteremias, even MDx assays suffer from a lack of sensitivity. Additionally, the highly extensive genomic heterogeneity among isolates, even within the same species, contributes to the lack of assay sensitivity as single target assays cannot provide universal coverage. This within-species heterogeneity is partly due to differences in replicon repertoires and genomic structures that have likely arisen to support the complex Borreliaceae lifecycle in which these parasites have to survive in multiple hosts each with unique immune responses. Results We constructed a Borreliaceae family-level pangenome and characterized the phylogenetic relationships among the constituent taxa which supports the recent taxonomy of splitting the family into at least two genera. Gene content profiles were created for the majority of the Borreliaceae replicons, providing for the first time their unambiguous molecular typing. Conclusion Our characterization of the Borreliaceae pan-genome supports the splitting of the former Borrelia genus into two genera and provides for the phylogenetic placement of several non-species designated isolates. Mining this family-level pangenome will enable precision diagnostics corresponding to gene content-driven clinical outcomes while also providing targets for interventions.

\n\nCharacterization of the family-level Borreliaceae pan-genome and development of an episomal typing protocol", "token_count": 489, "char_count": 2109, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:37.317399", "source": { "split": "train_shard_00001", "doc_id": 1070 }, "chunk_id": "train_shard_00001_1070_0", "global_id": 7177 }, { "text": "

Introduction

Salmonella enterica serovar Typhi (S. Typhi) is a major cause of morbidity and mortality in developing countries, contributing significantly to the global disease burden.

Methods

In this study, S. Typhi strains were isolated from 100 patients exhibiting symptoms of typhoid fever at a tertiary care hospital in Pakistan. Antimicrobial testing of all isolates was performed to determine the sensitivity and resistance pattern. Three MDR strains, namely QS194, QS430, and QS468, were subjected to whole genome sequencing for genomic characterization.

Results and discussion

MLST analysis showed that QS194, belonged to ST19, which is commonly associated with Salmonella enterica serovar typhimurium. In contrast, QS430 and QS468, belonged to ST1, a sequence type frequently associated with S. Typhi. PlasmidFinder identified the presence of IncFIB(S) and IncFII(S) plasmids in QS194, while IncQ1 was found in QS468. No plasmid was detected in QS430. CARD-based analysis showed that the strains were largely resistant to a variety of antibiotics and disinfecting agents/antiseptics, including fluoroquinolones, cephalosporins, monobactams, cephamycins, penams, phenicols, tetracyclines, rifamycins, aminoglycosides, etc. The S. Typhi strains possessed various virulence factors, such as Vi antigen, Agf/Csg, Bcf, Fim, Pef, etc. The sequencing data indicated that the strains had antibiotic resistance determinants and shared common virulence factors. Pangenome analysis of the selected S", "token_count": 503, "char_count": 1596, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7015, "quality_score": 0.8507, "entities": { "genes": [ "ST19", "ST1", "QS430", "QS468", "QS194" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:37.973609", "source": { "split": "train_shard_00001", "doc_id": 1071 }, "chunk_id": "train_shard_00001_1071_0", "global_id": 7178 }, { "text": "Typhi strains identified 13,237 genes, with 3,611 being core genes, 2,093 shell genes, and 7,533 cloud genes. Genome-based typing and horizontal gene transfer analysis revealed that the strains had different evolutionary origins and may have adapted to distinct environments or host organisms. These findings provide important insights into the genetic characteristics of S. Typhi strains and their potential association with various ecological niches and host organisms.\n\nWhole-genome sequencing of multidrug resistance Salmonella Typhi clinical strains isolated from Balochistan, Pakistan.", "token_count": 148, "char_count": 605, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:38.409658", "source": { "split": "train_shard_00001", "doc_id": 1071 }, "chunk_id": "train_shard_00001_1071_1", "global_id": 7179 }, { "text": "Compressed full-text indexes enable efficient sequence classification against a pangenome or tree-of-life index. Past work on compressed-index classification used matching statistics or pseudo-matching lengths to capture the fine-grained co-linearity of exact matches. But these fail to capture coarse-grained information about whether seeds appear co-linearly in the reference. We present a novel approach that additionally obtains coarse-grained co-linearity (“chain”) statistics. We do this without using a chaining algorithm, which would require superlinear time in the number of matches. We start with a collection of strings, avoiding the multiple-alignment step required by graph approaches. We rapidly compute multi-maximal unique matches (multi-MUMs) and identify BWT sub-runs that correspond to these multi-MUMs. From these, we select those that can be “tunneled,” and mark these with the corresponding multi-MUM identifiers. This yields an ℴ( r + n/d )-space index for a collection of d sequences having a length- n BWT consisting of r maximal equal-character runs. Using the index, we simultaneously compute fine-grained matching statistics and coarse-grained chain statistics in linear time with respect to query length. We found that this substantially improves classification accuracy compared to past compressed-indexing approaches and reaches the same level of accuracy as less efficient alignmentbased methods.\n\nImproved pangenomic classification accuracy with chain statistics", "token_count": 320, "char_count": 1495, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:38.974910", "source": { "split": "train_shard_00001", "doc_id": 1072 }, "chunk_id": "train_shard_00001_1072_0", "global_id": 7180 }, { "text": "The most common approach to sampling the bacterial populations within an infected or colonized host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. Sequencing a mixture of several colonies (pool-seq) is a better approach to detect population heterogeneity, but it is more complex to analyse due to different types of heterogeneity, such as within-clone polymorphisms, multi-strain mixtures, multi-species mixtures and contamination. Here, we compared 8 single-colony isolates (singles) and pool-seq on a set of 2286 Staphylococcus aureus culture samples to identify features that can distinguish pure samples, samples undergoing intraclonal variation and mixed strain samples. The samples were obtained by swabbing 3 body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to those for the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of intra-clonal polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.\n\nComparison of genomic diversity between single and pooled Staphylococcus aureus colonies isolated from human colonization cultures.", "token_count": 462, "char_count": 2046, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6448, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:39.612198", "source": { "split": "train_shard_00001", "doc_id": 1073 }, "chunk_id": "train_shard_00001_1073_0", "global_id": 7181 }, { "text": "The underlying factors that lead to specific strains within a species to emerge as human pathogens remain mostly enigmatic. The diarrheal disease cholera is caused by strains from a phylogenetically confined group within the Vibrio cholerae species, the pandemic cholera group (PCG), making it an ideal model system to tackle this puzzling phenomenon. Comprehensive analyses of over 1,840 V. cholerae genomes, including environmental isolates from this study, reveal that the species consists of eleven groups, with the PCG belonging to the largest and located within a lineage shared with environmental strains. This hierarchical classification provided us with a framework to unravel the ecoevolutionary dynamics of the genetic determinants associated with the emergence of toxigenic V. cholerae. Our analyses indicate that this phenomenon is largely dependent on the acquisition of unique modular gene clusters and allelic variations that confer a competitive advantage during intestinal colonization. We determined that certain PCG-associated alleles are essential for successful colonization whereas others provide a nonlinear competitive advantage, acting as a critical bottleneck that clarifies the isolated emergence of PCG. For instance, toxigenic strains encoding non-PCG alleles of a) tcpF or b) a sextuple allelic exchange mutant for genes tcpA, toxT, VC0176, VC1791, rfbT, and ompU, lose their ability to colonize the intestine. Interestingly, these alleles do not play a role in the colonization of newly established model environmental reservoirs. Our study uncovers the evolutionary roots of toxigenic V. cholerae offering a tractable approach for investigating the emergence of pathogenic clones within an environmental population.\n\nAllelic variations and gene cluster modularity act as nonlinear bottlenecks for cholera emergence.", "token_count": 490, "char_count": 1925, "word_count": 262, "semantic_coherence": 1, "information_density": 0.645, "quality_score": 0.8225, "entities": { "genes": [ "VC0176", "VC1791" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:40.271813", "source": { "split": "train_shard_00001", "doc_id": 1074 }, "chunk_id": "train_shard_00001_1074_0", "global_id": 7182 }, { "text": "Various fermented whey‐based beverages have been developed to reduce waste. However, approaches to increase the preference of whey‐based beverages are required because of the low sensory acceptability of whey. Here, we identified the better starting material (whey type), between raw whey (RW) and demineralised whey (DMW), and determined the optimal initial concentration using multiple sensory evaluations to develop acceptable fermented beverages made from sole whey with pure cultured Kluyveromyces marxianus (i.e. without additional ingredients and processing methods). Acceptance tests showed that fermented beverages made from DMW were superior to RW as the starting material. The amounts of ethanol produced were 5.0%, 7.6% and 9.5% v/v from the different initial DMW concentrations of 10%, 15% and 20% w/v, respectively. We observed a significant positive correlation (rₛ = 0.32, P < 0.05) between the assessment attributes, strength of taste as alcohol beverage and overall acceptability, indicating that higher concentrations of DMW yielded a more desirable product.\n\nApplication of multiple sensory evaluations to produce fermented beverages made from sole whey using Kluyveromyces marxianus", "token_count": 303, "char_count": 1203, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:40.835046", "source": { "split": "train_shard_00001", "doc_id": 1075 }, "chunk_id": "train_shard_00001_1075_0", "global_id": 7183 }, { "text": "Efficient pangenome indexes are promising tools for many applications, including rapid classification of nanopore sequencing reads. Recently, a compressed-index data structure called the “move structure” was proposed as an alternative to other BWT-based indexes like the FM index and r-index. The move structure uniquely achieves both O(r) space and O(1)-time queries, where r is the number of runs in the pangenome BWT. We implemented Movi, an efficient tool for building and querying move-structure pangenome indexes. While the size of the Movi’s index is larger than the r-index, it scales at a smaller rate for pangenome references, as its size is exactly proportional to r, the number of runs in the BWT of the reference. Movi can compute sophisticated matching queries needed for classification – such as pseudo-matching lengths and backward search – at least ten times faster than the fastest available methods, and in some cases more than 30-fold faster. Movi achieves this speed by leveraging the move structure’s strong locality of reference, incurring close to the minimum possible number of cache misses for queries against large pangenomes. We achieve still further speed improvements by using memory prefetching to attain a degree of latency hiding that would be difficult with other index structures like the r-index. Movi’s fast constant-time query loop makes it well suited to real-time applications like adaptive sampling for nanopore sequencing, where decisions must be made in a small and predictable time interval.\n\nMovi: a fast and cache-efficient full-text pangenome index", "token_count": 356, "char_count": 1595, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:41.457284", "source": { "split": "train_shard_00001", "doc_id": 1076 }, "chunk_id": "train_shard_00001_1076_0", "global_id": 7184 }, { "text": "Diverse sets of complete human genomes are required to construct a pangenome reference and to understand the extent of complex structural variation. Here, we sequence 65 diverse human genomes and build 130 haplotype-resolved assemblies (130 Mbp median continuity), closing 92% of all previous assembly gaps and reaching telomere-to-telomere (T2T) status for 39% of the chromosomes. We highlight complete sequence continuity of complex loci, including the major histocompatibility complex (MHC), SMN1/SMN2, NBPF8, and AMY1/AMY2, and fully resolve 1,852 complex structural variants (SVs). In addition, we completely assemble and validate 1,246 human centromeres. We find up to 30-fold variation in α-satellite high-order repeat (HOR) array length and characterize the pattern of mobile element insertions into α-satellite HOR arrays. While most centromeres predict a single site of kinetochore attachment, epigenetic analysis suggests the presence of two hypomethylated regions for 7% of centromeres. Combining our data with the draft pangenome reference significantly enhances genotyping accuracy from short-read data, enabling whole-genome inference to a median quality value (QV) of 45. Using this approach, 26,115 SVs per sample are detected, substantially increasing the number of SVs now amenable to downstream disease association studies.\n\nComplex genetic variation in nearly complete human genomes", "token_count": 365, "char_count": 1403, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7128, "quality_score": 0.8564, "entities": { "genes": [ "SMN2", "AMY1", "NBPF8", "SMN1", "AMY2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:42.059706", "source": { "split": "train_shard_00001", "doc_id": 1077 }, "chunk_id": "train_shard_00001_1077_0", "global_id": 7185 }, { "text": "

Objectives

To investigate the epidemiology of fosB-positive Staphylococcus aureus in waterfowl farms in the Pearl River tributaries in Guangdong Province, China in 2020.

Methods

A total of 63 S. aureus were recovered from 315 samples collected from six duck farms and one goose farm. PFGE, WGS and analysis were performed on 19 fosB-positive S. aureus.

Results

The fosfomycin resistance rate of the strains was as high as 52.4% (33/63), and 30.1% (19/63) of the strains carried fosB. Resistance gene prediction results showed that duck farm environment-derived strains contained the oxazolidinone drug resistance gene optrA. All fosB-positive S. aureus were MRSA and most of them were MDR, mainly ST9-t899 and ST164-t899. PFGE showed that fosB-positive S. aureus from humans and ducks could be clustered into the same clade. In addition, core-genome SNP analysis showed that clonal transmission of S. aureus occurred between humans and water. Pan-genome analysis showed that S. aureus had an open pangenome. The fosB gene was located on 2610-2615 bp plasmids, which all contained a broad host-range plasmid replication protein family 13. Small plasmids carrying the fosB gene could be found in different multilocus STs of S. aureus.

Conclusions

This study indicated that duck farms in Guangdong, China could be an important reservoir of fosB-positive S. aureus. The spread of drug-resistant bacteria in waterfowl farms requires further monitoring.\n\nPrevalence and genetic characteristics of fosB-positive Staphylococcus aureus in duck farms in Guangdong, China in 2020.", "token_count": 494, "char_count": 1598, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5764, "quality_score": 0.7882, "entities": { "genes": [ "ST164", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:42.753241", "source": { "split": "train_shard_00001", "doc_id": 1078 }, "chunk_id": "train_shard_00001_1078_0", "global_id": 7186 }, { "text": "Probiotic fermented foods are perceived as contributing to human health, however solid evidence for their presumptive therapeutic systemic benefits is generally lacking. Here we report that tryptophol acetate and tyrosol acetate, small molecule metabolites secreted by the probiotic milk-fermented yeast Kluyveromyces marxianus inhibit hyperinflammation (e.g., “cytokine storm”). Comprehensive in vivo and in vitro analyses, employing LPS-induced hyperinflammation models, reveal dramatic effects of the molecules, added in tandem, on mice morbidity, laboratory parameters, and mortality. Specifically, we observed attenuated levels of the pro-inflammatory cytokines IL-6, IL-1α, IL-1β and TNF-α, and reduced reactive oxygen species. Importantly, tryptophol acetate and tyrosol acetate did not completely suppress pro-inflammatory cytokine generation, rather brought their concentrations back to baseline levels thus maintaining core immune functions, including phagocytosis. The anti-inflammatory effects of tryptophol acetate and tyrosol acetate were mediated through downregulation of TLR4, IL-1R, and TNFR signaling pathways and increased A20 expression, leading to NF-kB inhibition. Overall, this work illuminates phenomenological and molecular details underscoring anti-inflammatory properties of small molecules identified in a probiotic mixture, pointing to potential therapeutic avenues against severe inflammation.\n\nTryptophol acetate and tyrosol acetate, small molecule metabolites identified in a probiotic mixture, inhibit hyperinflammation", "token_count": 406, "char_count": 1553, "word_count": 191, "semantic_coherence": 1, "information_density": 0.7068, "quality_score": 0.8534, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:43.385747", "source": { "split": "train_shard_00001", "doc_id": 1079 }, "chunk_id": "train_shard_00001_1079_0", "global_id": 7187 }, { "text": "The FTF (Fusarium Transcription Factor) gene family is composed of two members (FTF1 and FTF2) with high-sequence homology that encode transcription factors involved in the modulation of virulence in the F. oxysporum species complex (FOSC). While FTF1 is a multicopy gene exclusive of highly virulent strains of FOSC and is located in the accessory genome, FTF2 is a single-copy gene, located in the core genome, and well-conserved in all filamentous ascomycete fungi, except yeast. The involvement of FTF1 in the colonization of the vascular system and regulation of the expression of SIX effectors has been stablished. To address the role of FTF2, we generated and characterized mutants defective in FTF2 in a F. oxysporum f. sp. phaseoli weakly virulent strain and analyzed them together with the equivalent mutants formerly obtained in a highly virulent strain. The results obtained highlight a role for FTF2 as a negative regulator of the production of macroconidia and demonstrate that it is required for full virulence and the positive regulation of SIX effectors. In addition, gene expression analyses provided compelling evidence that FTF2 is involved in the regulation of hydrophobins likely required for plant colonization.\n\nThe Role of the Fusarium oxysporum FTF2 Transcription Factor in Host Colonization and Virulence in Common Bean Plants (Phaseolus vulgaris L.).", "token_count": 431, "char_count": 1490, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5592, "quality_score": 0.7796, "entities": { "genes": [ "FTF2", "FTF1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:44.009295", "source": { "split": "train_shard_00001", "doc_id": 1080 }, "chunk_id": "train_shard_00001_1080_0", "global_id": 7188 }, { "text": "Vancomycin-resistant enterococci (VRE) are major opportunistic pathogens and the causative agents of serious diseases, such as urinary tract infections and endocarditis. VRE strains mainly include species of Enterococcus faecium and E. faecalis which can colonise the gastrointestinal tract (GIT) of patients and, following growth and persistence in the gut, can transfer to blood resulting in systemic dissemination in the body. Advancements in genomics have revealed that hospital-associated VRE strains are characterised by increased numbers of mobile genetic elements, higher numbers of antibiotic resistance genes and often lack active CRISPR-Cas systems. Additionally, comparative genomics have increased our understanding of dissemination routes among patients and healthcare workers. Since the efficiency of currently available antibiotics is rapidly declining, new measures to control infection and dissemination of these persistent pathogens are urgently needed. These approaches include combinatory administration of antibiotics, strengthening colonisation resistance of the gut microbiota to reduce VRE proliferation through commensals or probiotic bacteria, or switching to non-antibiotic bacterial killers, such as bacteriophages or bacteriocins. In this review, we discuss the current knowledge of the genomics of VRE isolates and state-of-the-art therapeutic advances against VRE infections.\n\nPromiscuous, persistent and problematic: insights into current enterococcal genomics to guide therapeutic strategy.", "token_count": 340, "char_count": 1524, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:44.587124", "source": { "split": "train_shard_00001", "doc_id": 1081 }, "chunk_id": "train_shard_00001_1081_0", "global_id": 7189 }, { "text": "Climate change poses significant challenges to our ability to keep a growing global population fed, clothed, and fuelled. This review sets the scene by summarizing the impacts of climate change on production of the major grain crop species rice, wheat, and maize, with a focus on yield reductions due to abiotic stresses and altered disease pressures. We discuss efforts to improve resilience, emphasizing traits such as water use efficiency, heat tolerance, and disease resistance. We move on to exploring production trends of established, re-emerging, and new crops, highlighting the challenges of developing and maintaining new arrivals in the global market. We analyse the potential of wild relatives for improving domesticated crops, or as candidates for de novo domestication. The importance of pangenomes for uncovering genetic variation for crop improvement is also discussed. We examine the impact of climate change on non-cereals, including fruit, nut, and fibre crops, and the potential of alternative multiuse crops to increase global sustainability and address climate change-related challenges. Agave is used as an exemplar to demonstrate the strategic pathway for developing a robust new crop option. There is a need for sustained investment in research and development across the entire value chain to facilitate the exploration of diverse species and genetic resources to enhance crop resilience and adaptability to future environmental conditions.\n\nNew crops on the block: effective strategies to broaden our food, fibre, and fuel repertoire in the face of increasingly volatile agricultural systems.", "token_count": 321, "char_count": 1618, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6292, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:45.149236", "source": { "split": "train_shard_00001", "doc_id": 1082 }, "chunk_id": "train_shard_00001_1082_0", "global_id": 7190 }, { "text": "Salmonella Weltevreden is increasingly reported from aquatic environments, seafood, and patients in several Southeast Asian countries. Using genome-wide analysis, we characterized S. Weltevreden isolated from cultured shrimp and tilapia from Vietnam and China to study their genetic characteristics and relatedness to clinical isolates of S. Weltevreden ST-365. The phylogenetic analysis revealed up to 312 single-nucleotide polymorphism (SNP) difference between tilapia isolates, whereas isolates from shrimp were genetically more closely related. Epidemiologically unrelated isolates from Vietnam were closely related to isolates from China, e.g., 20 SNPs differences between strains 28V and 75C. In comparison with strains from other parts of the world, our environmental isolates predominantly clustered within the continental South Asia lineage, constituted mostly of strains from human stool with as low as seven SNPs difference, e.g., 30V versus Cont_ERR495254. All sequenced isolates were MLST type ST-365 and contained the major virulence-related genes encoded by the Salmonella Pathogenicity Islands 1-5. Ten of the isolates harbored the IncFII(S) plasmid similar to the virulence genes-mediated plasmid pSPCV of S. Paratyphi C, and one isolate had the IncQ1 plasmid on the same contig with strA/B, sul2, and tetA resistance genes similar to the IncQ1 type, pNUC of S. Typhimurium. A pangenomic analysis yielded 7891 genes including a core genome of 4892 genes, with a closely related accessory genome content between clinical and environmental isolates (Benjamini p > 0.05)", "token_count": 512, "char_count": 1675, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6489, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:45.803128", "source": { "split": "train_shard_00001", "doc_id": 1084 }, "chunk_id": "train_shard_00001_1084_0", "global_id": 7191 }, { "text": "In a search for differences that could explain the higher prevalence of S. Weltevreden in aquatic samples, genomes were compared with those of other Salmonella enterica serovars. S. Weltevreden revealed specific regions harboring glpX (Fructose-1;6-bisphosphatase; class II), rfbC (dTDP-4-dehydrorhamnose 3;5-epimerase), and cmtB (PTS Mannitol-specific cryptic phosphotransferase enzyme IIA component) involved in carbohydrate biosynthesis pathways. Our study builds grounds for future experiments to determine genes or pathways that are essential when S. Weltevreden are in aquatic environments and microbial interactions providing survival advantages to S. Weltevreden in such environments.\n\nMolecular Characteristics and Zoonotic Potential of Salmonella Weltevreden From Cultured Shrimp and Tilapia in Vietnam and China.", "token_count": 282, "char_count": 886, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7905, "quality_score": 0.8952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:46.365718", "source": { "split": "train_shard_00001", "doc_id": 1084 }, "chunk_id": "train_shard_00001_1084_1", "global_id": 7192 }, { "text": "Klebsiella pneumoniae is a leading cause of antibiotic-resistant-associated deaths in the world. Here, we report the deposition of 14 structures of enzymes from both the core and accessory genomes of sequence type 23 (ST23) K1 hypervirulent K. pneumoniae.\n\nA Structural Systems Biology Approach to High-Risk CG23 Klebsiella pneumoniae.", "token_count": 103, "char_count": 335, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [ "ST23", "CG23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:46.748531", "source": { "split": "train_shard_00001", "doc_id": 1085 }, "chunk_id": "train_shard_00001_1085_0", "global_id": 7193 }, { "text": "Abstract

Fleshy fruits are classified as ethylene dependent or ethylene independent according to the ethylene production rate at the onset of ripening. However, the mechanism regulating ethylene production in fruits is unclear. Pears (Pyrus spp.) contain both types of fruits. Analyses of 5 Pyrus genomes and 109 resequenced pear accessions revealed an important chromosomal locus closely associated with ethylene-producing phenotype. This locus was closely linked to a novel long noncoding RNA (lncRNA). Interestingly, the expression of this lncRNA showed an opposite pattern to ethylene production. Fruits overexpressing this lncRNA displayed extremely low ethylene production and a late ripening phenotype, which was observed for both tomatoes and pears. Therefore, this lncRNA was termed Ethylene Inhibiting Factor (EIF). Variable deletions of 3.8 kb and 1.1 kb regions altered EIF expression and enabled the categorization of pears into six genotypes. The huge number of transposable elements (TEs) were observed and they probably drove fragment rearrangement, generating the EIF, which repressed the ethylene production, resulting in ethylene-independent pear fruit. These findings provide new insights into the molecular basis of ethylene-producing phenotype in Maloideae fruits.

\n\nPangenome Analyses of Pyrus Unravel the Mechanism of Ethylene-Dependent and Ethylene-Independent Fruit Formation", "token_count": 418, "char_count": 1525, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:47.378541", "source": { "split": "train_shard_00001", "doc_id": 1086 }, "chunk_id": "train_shard_00001_1086_0", "global_id": 7194 }, { "text": "

Background

Ethyl acetate is a bulk chemical traditionally produced via energy intensive chemical esterification. Microbial production of this compound offers promise as a more sustainable alternative process. So far, efforts have focused on using sugar-based feedstocks for microbial ester production, but extension to one-carbon substrates, such as CO and CO2/H2, is desirable. Acetogens present a promising microbial platform for the production of ethyl esters from these one-carbon substrates.

Results

We engineered the acetogen C. autoethanogenum to produce ethyl acetate from CO by heterologous expression of an alcohol acetyltransferase (AAT), which catalyzes the formation of ethyl acetate from acetyl-CoA and ethanol. Two AATs, Eat1 from Kluyveromyces marxianus and Atf1 from Saccharomyces cerevisiae, were expressed in C. autoethanogenum. Strains expressing Atf1 produced up to 0.2 mM ethyl acetate. Ethyl acetate production was barely detectable (< 0.01 mM) for strains expressing Eat1. Supplementation of ethanol was investigated as potential boost for ethyl acetate production but resulted only in a 1.5-fold increase (0.3 mM ethyl acetate). Besides ethyl acetate, C. autoethanogenum expressing Atf1 could produce 4.5 mM of butyl acetate when 20 mM butanol was supplemented to the growth medium.

Conclusions

This work offers for the first time a proof-of-principle that autotrophic short chain ester production from C1-carbon feedstocks is possible and offers leads on how this approach can be optimized in the future.\n\nMetabolic engineering of Clostridium autoethanogenum for ethyl acetate production from CO.", "token_count": 485, "char_count": 1666, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:48.025286", "source": { "split": "train_shard_00001", "doc_id": 1087 }, "chunk_id": "train_shard_00001_1087_0", "global_id": 7195 }, { "text": "Enterohemorrhagic Escherichia coli continues to be a significant public health risk. With the onset of next generation sequencing, whole genome sequences require a new paradigm of analysis relevant for epidemiology and drug discovery. A large-scale bacterial population genomic analysis was applied to 702 isolates of serotypes associated with EHEC resulting in five pangenome clusters. Serotype incongruence with pangenome types suggests recombination clusters. Core genome analysis was performed to determine the population wide distribution of sdiA as potential drug target. Protein modelling revealed nonsynonymous variants are notably absent in the ligand binding site for quorum sensing, indicating that population wide conservation of the sdiA ligand site can be targeted for potential prophylactic purposes. Applying pathotype-wide pangenomics as a guide for determining evolution of pharmacophore sites is a potential approach in drug discovery.\n\nLarge scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target.", "token_count": 251, "char_count": 1118, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:48.511747", "source": { "split": "train_shard_00001", "doc_id": 1088 }, "chunk_id": "train_shard_00001_1088_0", "global_id": 7196 }, { "text": "Pangenome indexes reduce reference bias in sequencing data analysis. However, bias can be reduced further by using a personalized reference, e.g. a diploid human reference constructed to match a donor individual’s alleles. We present a novel impute-first alignment framework that combines elements of genotype imputation and pangenome alignment. It begins by genotyping the individual using only a subsample of the input reads. It next uses a reference panel and efficient imputation algorithm to impute a personalized diploid reference. Finally, it indexes the personalized reference and applies a read aligner, which could be a linear or graph aligner, to align the full read set to the personalized reference. This framework achieves higher variant-calling recall (99.54% vs. 99.37%), precision (99.36% vs. 99.18%), and F1 (99.45% vs. 99.28%) compared to a graph pangenome aligner. The personalized reference is also smaller and faster to query compared to a pangenome index, making it an overall advantageous choice for whole-genome DNA sequencing experiments.\n\nMinimizing Reference Bias with an Impute-First Approach", "token_count": 282, "char_count": 1121, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:49.066178", "source": { "split": "train_shard_00001", "doc_id": 1089 }, "chunk_id": "train_shard_00001_1089_0", "global_id": 7197 }, { "text": "

Background

The honey bee reference genome, HAv3.1, was produced from a commercial line sample that was thought to have a largely dominant Apis mellifera ligustica genetic background. Apis mellifera mellifera, often referred to as the black bee, has a separate evolutionary history and is the original type in western and northern Europe. Growing interest in this subspecies for conservation and non-professional apicultural practices, together with the necessity of deciphering genome backgrounds in hybrids, triggered the necessity for a specific genome assembly. Moreover, having several high-quality genomes is becoming key for taking structural variations into account in pangenome analyses.

Results

Pacific Bioscience technology long reads were produced from a single haploid black bee drone. Scaffolding contigs into chromosomes was done using a high-density genetic map. This allowed for re-estimation of the recombination rate, which was over-estimated in some previous studies due to mis-assemblies, which resulted in spurious inversions in the older reference genomes. The sequence continuity obtained was very high and the only limit towards continuous chromosome-wide sequences seemed to be due to tandem repeat arrays that were usually longer than 10 kb and that belonged to two main families, the 371 and 91 bp repeats, causing problems in the assembly process due to high internal sequence similarity. Our assembly was used together with the reference genome to genotype two structural variants by a pangenome graph approach with Graphtyper2. Genotypes obtained were either correct or missing, when compared to an approach based on sequencing depth analysis, and genotyping rates were 89 and 76% for the two variants.

Conclusions

Our new assembly for the Apis mellifera mellifera honey bee subspecies demonstrates the utility of multiple high-quality genomes for the genotyping of structural variants, with a test case on two insertions and deletions. It will therefore be an invaluable resource for future studies, for instance by including structural variants in GWAS", "token_count": 497, "char_count": 2106, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6205, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:49.722768", "source": { "split": "train_shard_00001", "doc_id": 1090 }, "chunk_id": "train_shard_00001_1090_0", "global_id": 7198 }, { "text": "Having used a single haploid drone for sequencing allowed a refined analysis of very large tandem repeat arrays, raising the question of their function in the genome. High quality genome assemblies for multiple subspecies such as presented here, are crucial for emerging projects using pangenomes.\n\nThe black honey bee genome: insights on specific structural elements and a first step towards pangenomes.", "token_count": 88, "char_count": 404, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8689, "quality_score": 0.9344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:50.092795", "source": { "split": "train_shard_00001", "doc_id": 1090 }, "chunk_id": "train_shard_00001_1090_1", "global_id": 7199 }, { "text": "Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CRhvKP) poses a significant global health threat due to its enhanced virulence and resistance. This study analyzed 5,036 publicly available K. pneumoniae genomes from China (2005-2023), identifying 1,538 CRhvKP genomes, accounting for 44.6% of carbapenem-resistant isolates and 69.5% of hypervirulent isolates. Predominant carbapenemases included bla KPC (92.1%), with an increasing prevalence of bla NDM and bla OXA-48-like genes. Most isolates (93.6%) carried both aerobactin and yersiniabactin genes. The genetic background showed high diversity, characterized by 36 sequence types (STs) and 22 capsule types, with high-risk endemic STs such as ST11, ST15, and ST23 being predominant. ST23 demonstrated enhanced virulence, whereas ST11 carried more resistance genes but showed minimal presence of iroBCDN genes. A core genome MLST analysis revealed that 89.0% of CRhvKP isolates clustered into 131 clonal groups, indicating widespread dissemination, particularly in eastern China. CR and hv plasmids, primarily IncF, IncH, and IncR types, showed distinct community structures, with CR plasmids demonstrating higher mobility and diversity. Crucially, we identified 40 CR-hv convergent plasmids across five STs, likely resulting from plasmid fusions, which have become increasingly prevalent in eastern China over the last decade. Furthermore, chromosomal integration of hv genes and bla KPC-2 was detected, underscoring the stable inheritance of these traits", "token_count": 496, "char_count": 1611, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7816, "quality_score": 0.8908, "entities": { "genes": [ "ST15", "ST23", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:51.598796", "source": { "split": "train_shard_00001", "doc_id": 1091 }, "chunk_id": "train_shard_00001_1091_0", "global_id": 7200 }, { "text": "Class 1 Integrons were present in 84.5% of CRhvKP strains, most notably in ST11 and least in ST23. These integrons harbored genes that confer resistance to various antibiotics, including bla IMP and bla VIM, with their content varying across different STs. This study highlights the genetic complexity, rapid dissemination, and increasing prevalence of CRhvKP in China, emphasizing the urgent need for enhanced genomic surveillance and targeted interventions to mitigate the threat posed by these multidrug-resistant and hypervirulent strains.\n\nMolecular epidemiology and genetic dynamics of carbapenem-resistant hypervirulent <i>Klebsiella pneumoniae</i> in China.", "token_count": 203, "char_count": 713, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [ "ST23", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:52.059407", "source": { "split": "train_shard_00001", "doc_id": 1091 }, "chunk_id": "train_shard_00001_1091_1", "global_id": 7201 }, { "text": "Halophilic sulfur-oxidizing bacteria belonging to the genus Guyparkeria occur at both marine and terrestrial habitats. Common physiological characteristics displayed by Guyparkeria isolates have not yet been linked to the metabolic potential encoded in their genetic inventory. To provide a genetic basis for understanding the metabolism of Guyparkeria, nine genomes were compared to reveal the metabolic capabilities and adaptations. A detailed account is given on Guyparkeria's ability to assimilate carbon by fixation, to oxidize reduced sulfur, to oxidize thiocyanate, and to cope with salinity stress.\n\nMetabolism of the Genus Guyparkeria Revealed by Pangenome Analysis.", "token_count": 190, "char_count": 710, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:52.500295", "source": { "split": "train_shard_00001", "doc_id": 1092 }, "chunk_id": "train_shard_00001_1092_0", "global_id": 7202 }, { "text": "Ethanol fermentation ability of the thermotolerant yeast Kluyveromyces marxianus, which is able to utilize various sugars including glucose, mannose, galactose, xylose, and arabinose, was examined under shaking and static conditions at high temperatures. The yeast was found to produce ethanol from all of these sugars except for arabinose under a shaking condition but only from hexose sugars under a static condition. Growth and sugar utilization rate under a static condition were slower than those under a shaking condition, but maximum ethanol yield was slightly higher. Even at 40°C, a level of ethanol production similar to that at 30°C was observed except for galactose under a static condition. Glucose repression on utilization of other sugars was observed, and it was more evident at elevated temperatures. Consistent results were obtained by the addition of 2-deoxyglucose. The glucose effect was further examined at a transcription level, and it was found that KmGAL1 for galactokinase and KmXYL1 for xylose reductase for galactose and xylose/arabinose utilization, respectively, were repressed by glucose at low and high temperatures, but KmHXK2 for hexokinase was not repressed. We discuss the possible mechanism of glucose repression and the potential for utilization of K. marxianus in high-temperature fermentation with mixed sugars containing glucose.\n\nGrowth and ethanol fermentation ability on hexose and pentose sugars and glucose effect under various conditions in thermotolerant yeast Kluyveromyces marxianus.", "token_count": 392, "char_count": 1533, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5247, "quality_score": 0.7623, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:53.118470", "source": { "split": "train_shard_00001", "doc_id": 1093 }, "chunk_id": "train_shard_00001_1093_0", "global_id": 7203 }, { "text": "The genus Escherichia has been extensively studied and it is known to encompass a range of commensal and pathogenic bacteria that primarily inhabit the gastrointestinal tracts of warm-blooded vertebrates. However, the presence of E. coli as a model organism and potential pathogen has diverted attention away from commensal strains and other species in the genus. To investigate the diversity of Escherichia in healthy chickens, we collected fecal samples from antibiotic-free Lohmann Brown layer hens and determined the genome sequences of 100 isolates, 81 of which were indistinguishable at the HC0 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing scheme. Despite initial selection on CHROMagar Orientation medium, which is considered selective for E. coli, in silico phylotyping and core genome single nucleotide polymorphism analysis revealed the presence of at least one representative of all major clades of Escherichia, except for E. albertii, Shigella, and E. coli phylogroup B2 and cryptic clade I. The most frequent phylogenomic groups were E. coli phylogroups A and B1 and E. ruysiae (clades III and IV). We compiled a collection of reference strains isolated from avian sources (predominantly chicken), representing every Escherichia phylogroup and species, and used it to confirm the phylogeny and diversity of our isolates. Overall, the isolates carried low numbers of the virulence and antibiotic resistance genes typically seen in avian pathogenic E. coli. Notably, the clades not recovered are ones that have been most strongly associated with virulence by other studies.\n\nRemarkable genomic diversity among Escherichia isolates recovered from healthy chickens.", "token_count": 506, "char_count": 1800, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [ "HC0" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:53.787191", "source": { "split": "train_shard_00001", "doc_id": 1094 }, "chunk_id": "train_shard_00001_1094_0", "global_id": 7204 }, { "text": "CRISPR-Cas is a bacterial immune system that restricts the acquisition of mobile DNA elements. These systems provide immunity against foreign DNA by encoding CRISPR spacers that help target DNA if it re-enters the cell. In this way, CRISPR spacers are a type of molecular tape recorder of foreign DNA encountered by the host microorganism. Here, we extracted ∼8,000 CRISPR spacers from a collection of over three hundred Streptococcus mutans genomes. Phage DNA is a major target of S. mutans spacers. Strains have also generated immunity against mobile DNA elements such as plasmids and integrative and conjugative elements. There may also be considerable immunity generated against bacterial DNA, although the relative contribution of self-targeting versus bona fide intra- or inter-species targeting needs to be investigated further. While there was clear evidence that these systems have acquired immunity against foreign DNA, there appeared to be minimal impact on horizontal gene transfer (HGT) constraints on a species-level. There was little or no impact on genome size, GC content and ‘openness’ of the pangenome when comparing between S. mutans strains with low or high CRISPR spacer loads. In summary, while there is evidence of CRISPR spacer acquisition against self and foreign DNA, CRISPR-Cas does not act as a barrier on the expansion of the S. mutans accessory genome.

Impact Statement

CRISPR-Cas is a widespread bacterial immune system that has been repurposed as a molecular biology tool. This study investigates the role of these systems in the biology and evolution of the dental caries pathogen Streptococcus mutans . CRISPR spacers, that encode immunity against foreign DNA, were extracted from over three hundred S. mutans isolates. Sequence analysis showed that the CRISPR spacers match against phage, mobile element, and bacterial DNA. This shows that S. mutans is actively acquiring immunity against horizontally acquired DNA. However, additional analysis revealed little to no impact of CRISPR-Cas systems on diversification of the S. mutans genome. This suggests that while these systems are actively acquiring CRISPR spacers to defend against foreign DNA, the overall impact on the S. mutans genome might be small", "token_count": 529, "char_count": 2250, "word_count": 343, "semantic_coherence": 1, "information_density": 0.4898, "quality_score": 0.7449, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:05:54.473076", "source": { "split": "train_shard_00001", "doc_id": 1095 }, "chunk_id": "train_shard_00001_1095_0", "global_id": 7205 }, { "text": "

Data Summary

Supporting data provided on the Github platform: https://github.com/theshieldslab/Streptococcus-mutans-CRISPR-Spacers-Analysis The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.\n\nInvestigating CRISPR spacer targets and their impact on genomic diversification of Streptococcus mutans", "token_count": 110, "char_count": 395, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:54.893279", "source": { "split": "train_shard_00001", "doc_id": 1095 }, "chunk_id": "train_shard_00001_1095_1", "global_id": 7206 }, { "text": "A pangenome graph can serve as a better reference for genomic studies because it allows a compact representation of multiple genomes within a species. Aligning sequences to a graph is critical for pangenome-based resequencing. The seed-chain-extend heuristic works by finding short exact matches between a sequence and a graph. In this heuristic, colinear chaining helps identify a good cluster of exact matches that can be combined to form an alignment. Colinear chaining algorithms have been extensively studied for aligning two sequences with various gap costs, including linear, concave, and convex cost functions. However, extending these algorithms for sequence-to-graph alignment presents significant challenges. Recently, Makinen et al. introduced a sparse dynamic programming framework that exploits the small path cover property of acyclic pangenome graphs, enabling efficient chaining. However, this framework does not consider gap costs, limiting its practical effectiveness. We address this limitation by developing novel problem formulations and provably good chaining algorithms that support a variety of gap cost functions. These functions are carefully designed to enable fast chaining algorithms whose time requirements are parameterized in terms of the size of the minimum path cover. Through an empirical evaluation, we demonstrate the superior performance of our algorithm compared with existing aligners. When mapping simulated long reads to a pangenome graph comprising 95 human haplotypes, we achieved 98.7% precision while leaving <2% of reads unmapped.\n\nGap-Sensitive Colinear Chaining Algorithms for Acyclic Pangenome Graphs.", "token_count": 341, "char_count": 1659, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:55.478794", "source": { "split": "train_shard_00001", "doc_id": 1096 }, "chunk_id": "train_shard_00001_1096_0", "global_id": 7207 }, { "text": "The airway fluids of cystic fibrosis (CF) patients contain local pH gradients and are more acidic than those of healthy individuals. pH is a critical factor that is often overlooked in studies seeking to recapitulate the infection microenvironment. We sought to determine the impact of pH on the physiology of a ubiqituous yet understudied microbe, Stenotrophomonas maltophilia Phylogenomics was first used to reconstruct evolutionary relationships between 74 strains of S. maltophilia (59 from CF patients). Neither the core genome (2,158 genes) nor the accessory genome (11,978 genes) distinguish the CF and non-CF isolates; however, strains from similar isolation sources grouped into the same subclades. We grew two human and six CF S. maltophilia isolates from different subclades at a range of pH values and observed impaired growth and altered antibiotic tolerances at pH 5. Transcriptomes revealed increased expression of both antibiotic resistance and DNA repair genes in acidic conditions. Although the gene expression profiles of S. maltophilia in lab cultures and CF sputum were distinct, we found that the same genes associated with low pH were also expressed during infection, and the higher pH cultures were more similar to sputum metatranscriptomes. Our findings suggest that S. maltophilia is not well adapted to acidity and may cope with low pH by expressing stress response genes and colonizing less acidic microenvironments. As a whole, our study underlines the impact of microenvironments on bacterial colonization and adaptation in CF infections.IMPORTANCE Understanding bacterial responses to physiological conditions is an important priority for combating opportunistic infections. The majority of CF patients succumb to inflammation and necrosis in the airways, arising from chronic infection due to ineffective mucociliary clearance. Steep pH gradients characterize the CF airways but are not often incorporated in standard microbiology culture conditions", "token_count": 497, "char_count": 2023, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:56.132107", "source": { "split": "train_shard_00001", "doc_id": 1097 }, "chunk_id": "train_shard_00001_1097_0", "global_id": 7208 }, { "text": "Stenotrophomonas maltophilia is a prevalent CF opportunistic pathogen also found in many disparate environments, yet this bacterium's contribution to CF lung damage and its response to changing environmental factors remain largely understudied. Here, we show that pH impacts the physiology and antibiotic susceptibility of S. maltophilia, with implications for the development of relevant in vitro models and assessment of antibiotic sensitivity.\n\nCystic Fibrosis-Associated Stenotrophomonas maltophilia Strain-Specific Adaptations and Responses to pH.", "token_count": 153, "char_count": 573, "word_count": 71, "semantic_coherence": 1, "information_density": 0.8592, "quality_score": 0.9296, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:56.565283", "source": { "split": "train_shard_00001", "doc_id": 1097 }, "chunk_id": "train_shard_00001_1097_1", "global_id": 7209 }, { "text": "Staphylococcus aureus infects both humans and animals, and antimicrobial resistance, including multidrug resistance, complicates treatment of S. aureus infections. Understanding S. aureus population structure and the distribution of genetic lineages is central to understanding the biology, epidemiology, and pathogenesis of this organism. This study exploited a large, publicly available dataset of nearly 27,000 S. aureus genomes to: i) develop a core genome multilocus sequence type (cgMLST) scheme; ii) stratify hierarchical clusters based on allelic similarity thresholds; and iii) define the clusters with a life identification number (LIN) code classification system. The cgMLST scheme characterised allelic variation at 1,716 core gene loci, and 13 classification thresholds were defined, which discriminated S. aureus variants across a range of genetic similarity thresholds. LIN code ‘lineages’ and clonal complexes defined by seven-locus multilocus sequence typing were highly concordant, but the LIN codes permitted a wider range of genetic discrimination among S. aureus genomes. This S. aureus cgMLST scheme and LIN code system is a high-resolution, stable genotyping tool that enables detailed genomic analyses of S. aureus .\n\nDevelopment of a core genome multilocus sequence typing (cgMLST) scheme and life identification number (LIN) code classification system for Staphylococcus aureus", "token_count": 359, "char_count": 1410, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6186, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:57.160429", "source": { "split": "train_shard_00001", "doc_id": 1098 }, "chunk_id": "train_shard_00001_1098_0", "global_id": 7210 }, { "text": "[This corrects the article DOI: 10.3389/fmicb.2023.1119226.].\n\nCorrigendum: Pangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants.", "token_count": 74, "char_count": 201, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:57.531538", "source": { "split": "train_shard_00001", "doc_id": 1099 }, "chunk_id": "train_shard_00001_1099_0", "global_id": 7211 }, { "text": "Ancient environmental DNA (aeDNA) is becoming a powerful tool to gain insights about past ecosystems. However, several methodological challenges remain, particularly for classifying the DNA to species level and conducting phylogenetic placement. Current methods, primarily tailored for modern datasets, fail to capture several idiosyncrasies of aeDNA, including species mixtures from closely related species and ancestral divergence. We introduce soibean , a novel tool that utilises pangenomic graphs for identifying species from ancient environmental mitochondrial reads. It outperforms existing methods in accurately identifying species from multiple sources within a sample, enhancing phylogenetic analysis for aeDNA. soibean employs a damage-aware likelihood model for precise identification at low-coverage with high damage rate, demonstrating effectiveness through simulated data tests and empirical validation. Notably, our method uncovered new empirical results in published datasets, including using porpoise whales as food in a Mesolithic community in Sweden, demonstrating its potential to reveal previously unrecognised findings in aeDNA studies.\n\nsoibean: High-resolution Taxonomic Identification of Ancient Environmental DNA Using Mitochondrial Pangenome Graphs", "token_count": 267, "char_count": 1276, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7362, "quality_score": 0.8681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:58.087227", "source": { "split": "train_shard_00001", "doc_id": 1100 }, "chunk_id": "train_shard_00001_1100_0", "global_id": 7212 }, { "text": "Conventional breeding approaches have played a significant role in meeting the food demand remarkably well until now. However, the increasing population, yield plateaus in certain crops, and limited recombination necessitate using genomic resources for genomics-assisted crop improvement programs. As a result of advancements in the next-generation sequence technology, GABs have developed dramatically to characterize allelic variants and facilitate their rapid and efficient incorporation in crop improvement programs. Genomics-assisted breeding (GAB) has played an important role in harnessing the potential of modern genomic tools, exploiting allelic variation from genetic resources and developing cultivars over the past decade. The availability of pangenomes for major crops has been a significant development, albeit with varying degrees of completeness. Even though adopting these technologies is essentially determined on economic grounds and cost-effective assays, which create a wealth of information that can be successfully used to exploit the latent potential of crops. GAB has been instrumental in harnessing the potential of modern genomic resources and exploiting allelic variation for genetic enhancement and cultivar development. GAB strategies will be indispensable for designing future crops and are expected to play a crucial role in breeding climate-smart crop cultivars with higher nutritional value.\n\nTriumphs of genomic-assisted breeding in crop improvement.", "token_count": 292, "char_count": 1485, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:59.005196", "source": { "split": "train_shard_00001", "doc_id": 1101 }, "chunk_id": "train_shard_00001_1101_0", "global_id": 7213 }, { "text": "

Motivation

Bacterial genomes present more variability than human genomes, which requires important adjustments in computational tools that are developed for human data. In particular, bacteria exhibit a mosaic structure due to homologous recombinations, but this fact is not sufficiently captured by standard read mappers that align against linear reference genomes. The recent introduction of pangenomics provides some insights in that context, as a pangenome graph can represent the variability within a species. However, the concept of sequence-to-graph alignment that captures the presence of recombinations has not been previously investigated.

Results

In this paper, we present the extension of the notion of sequence-to-graph alignment to a variation graph that incorporates a recombination, so that the latter are explicitly represented and evaluated in an alignment. Moreover, we present a dynamic programming approach for the special case where there is at most a recombination-we implement this case as RecGraph. From a modelling point of view, a recombination corresponds to identifying a new path of the variation graph, where the new arc is composed of two halves, each extracted from an original path, possibly joined by a new arc. Our experiments show that RecGraph accurately aligns simulated recombinant bacterial sequences that have at most a recombination, providing evidence for the presence of recombination events.

Availability and implementation

Our implementation is open source and available at https://github.com/AlgoLab/RecGraph.\n\nRecGraph: recombination-aware alignment of sequences to variation graphs.", "token_count": 356, "char_count": 1654, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:05:59.578021", "source": { "split": "train_shard_00001", "doc_id": 1102 }, "chunk_id": "train_shard_00001_1102_0", "global_id": 7214 }, { "text": "Microbiota comprise the bulk of life's diversity, yet we know little about how populations of microbes accumulate adaptive diversity across natural landscapes. Adaptation to stressful soil conditions in plants provides seminal examples of adaptation in response to natural selection via allelic substitution. For microbes symbiotic with plants however, horizontal gene transfer allows for adaptation via gene gain and loss, which could generate fundamentally different evolutionary dynamics. We use comparative genomics and genetics to elucidate the evolutionary mechanisms of adaptation to physiologically stressful serpentine soils in rhizobial bacteria in western North American grasslands. In vitro experiments demonstrate that the presence of a locus of major effect, the nre operon, is necessary and sufficient to confer adaptation to nickel, a heavy metal enriched to toxic levels in serpentine soil, and a major axis of environmental soil chemistry variation. We find discordance between inferred evolutionary histories of the core genome and nreAXY genes, which often reside in putative genomic islands. This suggests that the evolutionary history of this adaptive variant is marked by frequent losses, and/or gains via horizontal acquisition across divergent rhizobium clades. However, different nre alleles confer distinct levels of nickel resistance, suggesting allelic substitution could also play a role in rhizobium adaptation to serpentine soil. These results illustrate that the interplay between evolution via gene gain and loss and evolution via allelic substitution may underlie adaptation in wild soil microbiota. Both processes are important to consider for understanding adaptive diversity in microbes and improving stress-adapted microbial inocula for human use.\n\nThe evolutionary genomics of adaptation to stress in wild rhizobium bacteria.", "token_count": 402, "char_count": 1886, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:00.199707", "source": { "split": "train_shard_00001", "doc_id": 1103 }, "chunk_id": "train_shard_00001_1103_0", "global_id": 7215 }, { "text": "Two Gram-reaction-positive bacterial strains, designated BWT-B31T and BWR-S6Y, were isolated from larvae of Allomyrina dichotoma, and their taxonomic positions were examined by a polyphasic approach. Both strains were found to be Gram-reaction-positive, strictly aerobic, short rods and grew at 10-37 °C, pH 5.0-10.0 and in the presence of up to 5% (w/v) NaCl concentration (optimum, 0-1%). Strain BWT-B31T showed the highest 16S rRNA gene sequence similarity (98.1%) with Microbacterium mangrovi, followed by 97.9% with Microbacterium immunditiarum, while strain BWR-S6Y shared 100% sequence identity with Microbacterium hydrothermale, followed by 99.9% sequence similarity with Microbacterium galbum. In the core genome-based phylogenetic tree, strain BWT-B31T formed a clade with Microbacterium immunditiarum and Microbacterium mangrovi, with orthologous average nucleotide identities of 81.1% and 76.2%, respectively. Strain BWR-S6Y showed the same topology with that of 16S rRNA gene phylogeny, with an orthologous average nucleotide identity of 96.8% and a digital DNA-DNA hybridization value of 72.0% with Microbacterium hydrothermale. A combination of the phenotypic distinctness and overall genomic relatedness indices supports that strain BWR-S6Y is a strain of Microbacterium hydrothermale, while strain BWT-B31T represents a new species of the genus Microbacterium, for which the name Microbacterium insectihabitans sp. nov", "token_count": 483, "char_count": 1479, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:00.845197", "source": { "split": "train_shard_00001", "doc_id": 1104 }, "chunk_id": "train_shard_00001_1104_0", "global_id": 7216 }, { "text": "(type strain, BWT-B31T = KACC 22261T = DSM 112528T = NBRC 115128T) is proposed.\n\nMicrobacterium insectihabitans sp. nov., Isolated from Larvae of Allomyrina dichotoma.", "token_count": 121, "char_count": 211, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:01.230331", "source": { "split": "train_shard_00001", "doc_id": 1104 }, "chunk_id": "train_shard_00001_1104_1", "global_id": 7217 }, { "text": "Congenital Adrenal Hyperplasia (CAH), one of the most common inherited disorders, is caused by defects in adrenal steroidogenesis. It is potentially lethal if untreated and is associated with multiple comorbidities, including fertility issues, obesity, insulin resistance, and dyslipidemia. CAH can result from variants in multiple genes, but the most frequent cause is deletions and conversions in the segmentally duplicated RCCX module, which contains the CYP21A2 gene and a pseudogene. The molecular genetic test to identify pathogenic alleles is cumbersome, incomplete, and available from a limited number of laboratories. It requires testing parents for accurate interpretation, leading to healthcare inequity. Less severe forms are frequently misdiagnosed, and phenotype/genotype correlations incompletely understood. We explored whether emerging technologies could be leveraged to identify all pathogenic alleles of CAH, including phasing in proband-only cases. We targeted long-read sequencing outputs that would be practical in a clinical laboratory setting. Both HiFi-based and nanopore-based whole-genome long-read sequencing datasets could be mined to accurately identify pathogenic single-nucleotide variants, full gene deletions, fusions creating non-functional hybrids between the gene and pseudogene (“30-kb deletion”), as well as count the number of RCCX modules and phase the resulting multimodular haplotypes. On the Hi-Fi data set of 6 samples, the PacBio Paraphase tool was able to distinguish nine different mono-, bi-, and tri-modular haplotypes, as well as the 30-kb and whole gene deletions. To do the same on the ONT-Nanopore dataset, we designed a tool, Parakit, which creates an enriched local pangenome to represent known haplotype assemblies and map ClinVar pathogenic variants and fusions onto them. With few labels in the region, optical genome mapping was not able to reliably resolve module counts or fusions, although designing a tool to mine the dataset specifically for this region may allow doing so in the future", "token_count": 493, "char_count": 2051, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6928, "quality_score": 0.8464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:01.893148", "source": { "split": "train_shard_00001", "doc_id": 1105 }, "chunk_id": "train_shard_00001_1105_0", "global_id": 7218 }, { "text": "Both sequencing techniques yielded congruent results, matching clinically identified variants, and offered additional information above the clinical test, including phasing, count of RCCX modules, and status of the other module genes, all of which may be of clinical relevance. Thus long-read sequencing could be used to identify variants causing multiple forms of CAH in a single test.\n\nLong-read sequencing resolves the clinically relevantCYP21A2locus, supporting a new clinical test for Congenital Adrenal Hyperplasia", "token_count": 124, "char_count": 527, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:02.280194", "source": { "split": "train_shard_00001", "doc_id": 1105 }, "chunk_id": "train_shard_00001_1105_1", "global_id": 7219 }, { "text": "Contamination of soil by antibiotics and heavy metals originating from hospital facilities has emerged as a major cause for the development of resistant microbes. We collected soil samples surrounding a hospital effluent and measured the resistance of bacterial isolates against multiple antibiotics and heavy metals. One strain BMCSI 3 was found to be sensitive to all tested antibiotics. However, it was resistant to many heavy metals and metalloids like cadmium, chromium, copper, mercury, arsenic, and others. This strain was motile and potentially spore-forming. Whole-genome shotgun assembly of BMCSI 3 produced 4.95 Mb genome with 4,638 protein-coding genes. The taxonomic and phylogenetic analysis revealed it, to be a Bordetella petrii strain. Multiple genomic islands carrying mobile genetic elements; coding for heavy metal resistant genes, response regulators or transcription factors, transporters, and multi-drug efflux pumps were identified from the genome. A comparative genomic analysis of BMCSI 3 with annotated genomes of other free-living B. petrii revealed the presence of multiple transposable elements and several genes involved in stress response and metabolism. This study provides insights into how genomic reorganization and plasticity results in evolution of heavy metals resistance by acquiring genes from its natural environment.\n\nGenomic, morphological, and biochemical analyses of a multi-metal resistant but multi-drug susceptible strain of Bordetella petrii from hospital soil.", "token_count": 361, "char_count": 1511, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:02.862396", "source": { "split": "train_shard_00001", "doc_id": 1106 }, "chunk_id": "train_shard_00001_1106_0", "global_id": 7220 }, { "text": "Objective: To investigate the pathogenetic characteristics of clinical isolates of Streptococcus suis in Henan Province from 2020 to 2023. Methods: Eight clinical isolates of S. suis in Henan Province from 2020 to 2023 were identified using matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) and real-time fluorescence polymerase chain reaction (PCR). Serotype and virulence genes were detected by the serum agglutination test and PCR, and antibiotic susceptibility was evaluated using the microbroth dilution method. Multilocus sequence typing (MLST), minimum core genome (MCG), identification of antibiotic resistance genes, and core genome single nucleotide polymorphism (cgSNP) analysis were conducted using whole genome sequencing. Results: The results showed that eight S. suis strains isolated from humans were mainly serotype 2 (75.0%), while the rest were serotype 14 (25.0%). ST353 (62.5%) was the predominant genotype, followed by ST1 (25.0%) and ST7 (12.5%). All isolates belonged to the MCG1 group. The virulence genotypes of these isolates were primarily mrp(NA2)/sly+/ef+/gapdh+(75.0%), while the remaining were mrp(EU)/sly+/ef+/gapdh+(25.0%)", "token_count": 441, "char_count": 1296, "word_count": 160, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [ "NA2", "MCG1", "ST7", "ST1", "ST353" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:03.502461", "source": { "split": "train_shard_00001", "doc_id": 1107 }, "chunk_id": "train_shard_00001_1107_0", "global_id": 7221 }, { "text": "These isolates carried tetracycline, macrolide, lincosamide and aminoglycoside resistance genes, and their resistance rates to tetracycline, erythromycin and clindamycin were 100.0%, 87.5% and 87.5%, respectively, and 62.5% strains were intermediate-resistant to penicillin. The cgSNP analysis indicated that these isolates were closer to the isolates from Guangdong, Zhejiang and Guangxi Provinces, with five ST353 strains and one ST7 strain belonging to Clade Ⅰ, and two ST1 strains belonging to Clade Ⅱ. Conclusion: The human isolates of S. suis in Henan Province are mainly ST353, harboring multiple virulence and antibiotic resistance genes.\n\n[Pathogenetic characteristics of human isolates of <i>Streptococcus suis</i> in Henan Province from 2020 to 2023].", "token_count": 265, "char_count": 788, "word_count": 105, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [ "ST353", "ST7", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:04.046831", "source": { "split": "train_shard_00001", "doc_id": 1107 }, "chunk_id": "train_shard_00001_1107_1", "global_id": 7222 }, { "text": "Background: Pseudomonas aeruginosa is an opportunistic pathogen that exhibits a strong resistance ability to antibiotics. Methods: The complete genome of P. aeruginosa CYZ was sequenced using a PacBio RS II system. The functions of all the predicted genes and proteins were classified and annotated using the Clusters of Orthologous Groups of proteins, Gene Ontology, and Kyoto Encyclopedia of Genes and Genomes databases. Furthermore, the antimicrobial resistance genes were also analyzed via the Comprehensive Antibiotic Resistance Database, and several types of antibiotics were selected to test the antimicrobial susceptibility. Phylogenetic relationships were investigated using the single nucleotide polymorphisms (SNPs) from 228 clinically isolated P. aeruginosa strains. Results: The genome size of P. aeruginosa CYZ is 6,382,603 bp and contains 5,807 protein-coding genes, with an average G + C content of 66.44%. Functional genomic analysis via the annotations of the databases identified a total of 499 antimicrobial resistance genes. P. aeruginosa CYZ showed resistance to 14 types of antibiotics. The phylogenetic analysis revealed that P. aeruginosa CYZ was closely related to P. aeruginosa PAO1. The P. aeruginosa strains exhibited no geographical specificity, and the variation in core genome SNPs was nonrandomly distributed. Conclusion: Our findings give valuable insight into the genetic antimicrobial-resistant features of P. aeruginosa as well as provide a genetic basis for the further study of the phenotype.", "token_count": 489, "char_count": 1650, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [ "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:04.697052", "source": { "split": "train_shard_00001", "doc_id": 1108 }, "chunk_id": "train_shard_00001_1108_0", "global_id": 7223 }, { "text": "Whole Genome Features and Analysis of Antibiotic Resistance Determinants in <i>Pseudomonas aeruginosa</i> Strain CYZ.", "token_count": 46, "char_count": 129, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:05.056160", "source": { "split": "train_shard_00001", "doc_id": 1108 }, "chunk_id": "train_shard_00001_1108_1", "global_id": 7224 }, { "text": "Lactobacillaceae represent a large family of important microbes that are foundational to the food industry. Many genome sequences of Lactobacillaceae strains are now available, enabling us to conduct a comprehensive pangenome analysis of this family. We collected 3591 high-quality genomes from public sources and found that: 1) they contained enough genomes for 26 species to perform a pangenomic analysis, 2) the normalized Heap's coefficient λ (a measure of pangenome openness) was found to have an average value of 0.27 (ranging from 0.07 to 0.37), 3) the pangenome openness was correlated with the abundance and genomic location of transposons and mobilomes, 4) the pangenome for each species was divided into core, accessory, and rare genomes, that highlight the species-specific properties (such as motility and restriction-modification systems), 5) the pangenome of Lactiplantibacillus plantarum (which contained the highest number of genomes found amongst the 26 species studied) contained nine distinct phylogroups, and 6) genome mining revealed a richness of detected biosynthetic gene clusters, with functions ranging from antimicrobial and probiotic to food preservation, but ∼93% were of unknown function. This study provides the first in-depth comparative pangenomics analysis of the Lactobacillaceae family.\n\nPangenome analysis reveals the genetic basis for taxonomic classification of the Lactobacillaceae family", "token_count": 358, "char_count": 1429, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:05.664287", "source": { "split": "train_shard_00001", "doc_id": 1109 }, "chunk_id": "train_shard_00001_1109_0", "global_id": 7225 }, { "text": "The origin and evolution of genes are central themes in evolutionary biology and genomics, shedding light on how molecular innovations shape biological complexity and adaptation. This review explores the principal mechanisms underlying gene emergence in eukaryotes, including gene duplication, de novo gene birth, horizontal gene transfer, viral gene domestication, and exon shuffling. We examine the population dynamics that govern the fixation of new genes, their functional integration, and the selective forces acting upon them-from purifying selection to adaptive innovation. Examples such as NOTCH2NL and SRGAP2C, which originated through recent segmental duplications followed by neofunctionalization, illustrate how duplicate-derived de novo genes can play a key role in human brain development. In addition, we highlight the emerging relevance of nuclear architecture in determining the evolutionary fate of new genes, offering a spatial dimension to gene innovation. We also discuss methodological approaches for detecting new genes and inferring selection, and finally, we highlight the emerging role of the human pangenome in revealing hidden gene diversity and its implications for evolutionary and biomedical research. Understanding gene innovation not only enhances our grasp of evolutionary processes but also informs clinical studies on disease susceptibility and human uniqueness.\n\nOrigin and Evolution of Genes in Eukaryotes: Mechanisms, Dynamics, and Functional Implications.", "token_count": 311, "char_count": 1509, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "SRGAP2C" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:06.250181", "source": { "split": "train_shard_00001", "doc_id": 1110 }, "chunk_id": "train_shard_00001_1110_0", "global_id": 7226 }, { "text": "The intracellular pathogens of the genus Brucella are phylogenetically close to Ochrobactrum, a diverse group of free-living bacteria with a few species occasionally infecting medically compromised patients. A group of taxonomists recently included all Ochrobactrum organisms in the genus Brucella based on global genome analyses and alleged equivalences with genera such as Mycobacterium. Here, we demonstrate that such equivalencies are incorrect because they overlook the complexities of pathogenicity. By summarizing Brucella and Ochrobactrum divergences in lifestyle, structure, physiology, population, closed versus open pangenomes, genomic traits, and pathogenicity, we show that when they are adequately understood, they are highly relevant in taxonomy and not unidimensional quantitative characters. Thus, the Ochrobactrum and Brucella differences are not limited to their assignments to different \"risk-groups\", a biologically (and hence, taxonomically) oversimplified description that, moreover, does not support ignoring the nomen periculosum rule, as proposed. Since the epidemiology, prophylaxis, diagnosis, and treatment are thoroughly unrelated, merging free-living Ochrobactrum organisms with highly pathogenic Brucella organisms brings evident risks for veterinarians, medical doctors, and public health authorities who confront brucellosis, a significant zoonosis worldwide. Therefore, from taxonomical and practical standpoints, the Brucella and Ochrobactrum genera must be maintained apart. Consequently, we urge researchers, culture collections, and databases to keep their canonical nomenclature.\n\nPathogenicity and Its Implications in Taxonomy: The Brucella and Ochrobactrum Case.", "token_count": 496, "char_count": 1816, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6898, "quality_score": 0.8449, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:06.945454", "source": { "split": "train_shard_00001", "doc_id": 1111 }, "chunk_id": "train_shard_00001_1111_0", "global_id": 7227 }, { "text": "Klebsiella pneumoniae is an opportunistic pathogen causing diseases ranging from gastrointestinal disorders to severe liver abscesses. While clinical isolates of K. pneumoniae have been extensively studied, less is known about asymptomatic variants colonizing the human gut across diverse populations. Genome-resolved metagenomics has offered unprecedented access to metagenome-assembled genomes (MAGs) from diverse host states and geographical locations, opening opportunities to explore health-associated microbial features. Here we analysed 662 human gut-derived K. pneumoniae genomes (319 MAGs, 343 isolates) from 29 countries to investigate the population structure and genomic diversity of K. pneumoniae in carriage and disease. Only 9% of sequence types were found to be shared between healthy and disease states, highlighting distinct diversity across health conditions. Integrating MAGs nearly doubled gut-associated K. pneumoniae phylogenetic diversity, and uncovered 86 lineages without representation among >20,000 Klebsiella isolate genomes from various sources. Genomic signatures linked to pathogenicity and carriage included those involved in antibiotic resistance, iron regulation, restriction modification systems and polysaccharide biosynthesis. Notably, machine learning models integrating MAGs and isolates more accurately classified disease and carriage states compared to isolates alone. These findings showcase the value of metagenomics to understand pathogen evolution with implications for public health surveillance strategies.\n\nIntegration of metagenome-assembled genomes with clinical isolates reveals genomic signatures ofKlebsiella pneumoniaein carriage and disease", "token_count": 390, "char_count": 1703, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7062, "quality_score": 0.8531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:07.571748", "source": { "split": "train_shard_00001", "doc_id": 1112 }, "chunk_id": "train_shard_00001_1112_0", "global_id": 7228 }, { "text": "

Background

Brachyspira (B.) hyodysenteriae is a fastidious anaerobe spirochete that can cause swine dysentery, a severe mucohaemorragic colitis that affects pig production and animal welfare worldwide. In Switzerland, the population of B. hyodysenteriae is characterized by the predominance of macrolide-lincosamide-resistant B. hyodysenteriae isolates of sequence type (ST) ST196, prompting us to obtain deeper insights into the genomic structure and variability of ST196 using pangenome and whole genome variant analyses.

Results

The draft genome of 14 B. hyodysenteriae isolates of ST196, sampled during a 7-year period from geographically distant pig herds, was obtained by whole-genome sequencing (WGS) and compared to the complete genome of the B. hyodysenteriae isolate Bh743-7 of ST196 used as reference. Variability results revealed the existence of 30 to 52 single nucleotide polymorphisms (SNPs), resulting in eight sublineages of ST196. The pangenome analysis led to the identification of a novel prophage, pphBhCH20, of the Siphoviridae family in a single isolate of ST196, which suggests that horizontal gene transfer events may drive changes in genomic structure.

Conclusions

This study contributes to the catalogue of publicly available genomes and provides relevant bioinformatic tools and information for further comparative genomic analyses for B. hyodysenteriae. It reveals that Swiss B. hyodysenteriae isolates of the same ST may have evolved independently over time by point mutations and acquisition of larger genetic elements. In line with this, the third type of mobile genetic element described so far in B. hyodysenteriae, the novel prophage pphBhCH20, has been identified in a single isolate of B. hyodysenteriae of ST196.", "token_count": 490, "char_count": 1772, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8117, "entities": { "genes": [ "ST196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:08.218468", "source": { "split": "train_shard_00001", "doc_id": 1113 }, "chunk_id": "train_shard_00001_1113_0", "global_id": 7229 }, { "text": "Whole-genome analyses reveal a novel prophage and cgSNPs-derived sublineages of Brachyspira hyodysenteriae ST196.", "token_count": 41, "char_count": 113, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:08.574735", "source": { "split": "train_shard_00001", "doc_id": 1113 }, "chunk_id": "train_shard_00001_1113_1", "global_id": 7230 }, { "text": "

Summary

The Saccharomyces cerevisiae Irc3 protein is a mitochondrial Superfamily II DNA helicase that, according to genomic data, is conserved in different yeast species. Here we characterize Irc3 helicase from the thermotolerant yeast Ogataea polymorpha (Irc3 op ) that throughout its helicase motor domain has approximately 82% similarity with the S. cerevisiae protein. Irc3 op retains enzymatic activity at considerably higher temperatures than Irc3 sc , displaying the fastest rate of ATP hydrolysis at 41 °C and a Tm of 45.3 °C for its secondary structure melting. We demonstrate that Irc3 op is a structure-specific DNA helicase translocating on both single- and double-stranded DNA molecules. Like the homolog of S. cerevisiae , Irc3 op can unwind only DNA molecules that contain branched structures. Different DNA molecules containing three- and four-way branches are utilized by Irc3 op as unwinding substrates. Importantly, the preferred unwinding substrate of Irc3 op is a DNA fork containing the nascent lagging strand, suggesting a possible role in replication restart following a block in leading strand polymerization. A lower unwinding efficiency of four-way branched DNA molecules could explain why Irc3 op only partially complements the irc3 Δ phenotype in S. cerevisiae .\n\nIrc3 of the thermotolerant yeast Ogataea polymorpha is a branched-DNA-specific mitochondrial helicase", "token_count": 379, "char_count": 1410, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:09.154797", "source": { "split": "train_shard_00001", "doc_id": 1114 }, "chunk_id": "train_shard_00001_1114_0", "global_id": 7231 }, { "text": "

Background

Multiple lignocellulose-derived inhibitors represent great challenges for bioethanol production from lignocellulosic materials. These inhibitors that are related to the levels of intracellular reactive oxidative species (ROS) make oxidoreductases a potential target for an enhanced tolerance in yeasts.

Results

In this study, the thioredoxin and its reductase from Kluyveromyces marxianus Y179 was identified, which was subsequently achieved over-expression in Saccharomyces cerevisiae 280. In spite of the negative effects by expression of thioredoxin gene (KmTRX), the thioredoxin reductase (KmTrxR) helped to enhance tolerance to multiple lignocellulose-derived inhibitors, such as formic acid and acetic acid. In particular, compared with each gene expression, the double over-expression of KmTRX2 and KmTrxR achieved a better ethanol fermentative profiles under a mixture of formic acid, acetic acid, and furfural (FAF) with a shorter lag period. At last, the mechanism that improves the tolerance depended on a normal level of intracellular ROS for cell survival under stress.

Conclusions

The synergistic effect of KmTrxR and KmTRX2 provided the potential possibility for ethanol production from lignocellulosic materials, and give a general insight into the possible toxicity mechanisms for further theoretical research.\n\nSynergistic effect of thioredoxin and its reductase from Kluyveromyces marxianus on enhanced tolerance to multiple lignocellulose-derived inhibitors.", "token_count": 403, "char_count": 1511, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6134, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:09.778183", "source": { "split": "train_shard_00001", "doc_id": 1115 }, "chunk_id": "train_shard_00001_1115_0", "global_id": 7232 }, { "text": "

Background

Surveillance of Neisseria gonorrhoeae strains, their antimicrobial resistance (AMR) profiles, and transmission dynamics is essential in the prevention and control of gonococcal infections. In Kenya, gonococcal molecular surveillance remains limited, leaving gaps in understanding circulating sequence types (STs). This study characterized Kenyan N. gonorrhoeae isolates using multiple molecular typing schemes.

Methods

Illumina MiSeq generated paired-end sequence reads prepared from 35 N. gonorrhoeae isolates recovered from males and females from four different regions in Kenya were analyzed. Assemblies were analyzed using PubMLST tools for multi-locus sequence typing (MLST) and the N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) scheme. Multi-antigen sequence typing (NG-MAST) was carried out using the NG-MAST database. Phylogenetic relationships were assessed using concatenated NG-STAR loci and core genome-based analyses.

Results

Twenty-two MLST STs were identified, including eight novel STs; ST-1932 was most frequent. NG-MAST revealed 29 STs, of which 26 were novel, with a newly described ST-19168 predominating in Nyanza region. NG-STAR identified 23 STs with variation across mtrR , penA , 23S rRNA , gyrA , parC, ponA , and porB. Phylogenetic analyses showed clustering of isolates into distinct groups with diverse AMR profiles. One cluster comprised isolates resistant to tetracycline and ciprofloxacin. No clear association was observed between MLST, NG-MAST, or NG-STAR types and specific AMR patterns.

Conclusion

Kenyan N. gonorrhoeae strains are genetically diverse, with high numbers of novel NG-MAST and MLST STs", "token_count": 506, "char_count": 1722, "word_count": 229, "semantic_coherence": 1, "information_density": 0.69, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:10.432315", "source": { "split": "train_shard_00001", "doc_id": 1116 }, "chunk_id": "train_shard_00001_1116_0", "global_id": 7233 }, { "text": "The lack of regional clustering and varied AMR profiles suggest widespread transmission of heterogeneous gonococcal populations. These findings underscore the importance of strengthened genomic surveillance to inform gonorrhea control strategies in Kenya.\n\nGenomic Diversity of Neisseria gonorrhoeae Isolates in Kenya Revealed by MLST, NG-MAST, and NG-STAR Typing", "token_count": 101, "char_count": 372, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:10.816557", "source": { "split": "train_shard_00001", "doc_id": 1116 }, "chunk_id": "train_shard_00001_1116_1", "global_id": 7234 }, { "text": "Our understanding of the skin microbiome has dramatically improved since the pioneering studies and the improvements in sequencing technologies. Species of the genus Corynebacterium are known to form a major part of the human skin microbiome but most detailed studies have focussed on other similarly prevalent genera like Staphylococcus and Cutibacteria . Prior to this study, there were few complete genomes for skin commensals of the genus Corynebacterium , with only 9 complete genomes available for the most commonly identified species C. tuberculostearicum . In this study we explored the genus Corynebacterium from a single body site by swabbing the axilla/underarm of 4 individuals and using a selective media to enrich for corynebacteria. We then generated whole genome sequencing data of these corynebacteria enriched isolates using long-read sequencing and subsequent bioinformatics analysis to reveal an unparalleled diversity of this genus from a single skin site. Through this approach, we obtained the closed genomes of 215 isolates, 154 derived from a single individual. With this genetic information, we were able to identify 7 different species including species previously not associated to the skin and two novel species provisionally named C. axilliensis and C. jamesii . We used pangenome analysis on 30 genetically distinct isolates spanning the 7 species to identify putative metabolic differences, antimicrobial resistance profiles, novel biosynthetic gene clusters (BGCs), prophages and phage defence systems. Our culture-based Nanopore sequencing approach has dramatically improved our overall knowledge of skin corynebacteria, and uniquely here also providing in-depth analysis from a single skin site, revealing a multitude of differences between the isolates. Here we not only improved our knowledge of axillary corynebacteria but also greatly expanded the publicly available number of cutaneous corynebacterial genomes complementing recent studies seeking to understand the diversity of skin corynebacteria.\n\nRevealing the diversity of commensal corynebacteria from a single human skin site", "token_count": 490, "char_count": 2121, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5592, "quality_score": 0.7796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:11.466774", "source": { "split": "train_shard_00001", "doc_id": 1117 }, "chunk_id": "train_shard_00001_1117_0", "global_id": 7235 }, { "text": "Low-abundance members of microbial communities are difficult to study in their native habitats. This includes Escherichia coli , a minor, but common inhabitant of the gastrointestinal tract and opportunistic pathogen, including of the urinary tract, where it is the primary pathogen. While multi-omic analyses have detailed critical interactions between uropathogenic Escherichia coli (UPEC) and the bladder that mediate UTI outcome, comparatively little is known about UPEC in its pre-infection reservoir, partly due to its low abundance there (<1% relative abundance). To accurately and sensitively explore the genomes and transcriptomes of diverse E. coli in gastrointestinal communities, we developed E. coli PanSelect which uses a set of probes designed to specifically recognize and capture E. coli ’s broad pangenome from sequencing libraries. We demonstrated the ability of E. coli PanSelect to enrich, by orders of magnitude, sequencing data from diverse E. coli using a mock community and a set of human stool samples collected as part of a cohort study investigating drivers of recurrent urinary tract infections (rUTI). Comparisons of genomes and transcriptomes between E. coli residing in the gastrointestinal tracts of women with and without a history of rUTI suggest that rUTI gut E. coli are responding to increased levels of oxygen and nitrate, suggestive of mucosal inflammation, which may have implications for recurrent disease. E. coli PanSelect is well suited for investigations of native in vivo biology of E. coli in other environments where it is at low relative abundance, and the framework described here has broad applicability to other highly diverse, low abundance organisms.\n\nDistinctEscherichia colitranscriptional profiles in the guts of recurrent UTI sufferers revealed by pangenome hybrid selection", "token_count": 439, "char_count": 1840, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:12.094966", "source": { "split": "train_shard_00001", "doc_id": 1118 }, "chunk_id": "train_shard_00001_1118_0", "global_id": 7236 }, { "text": "Clostridioides difficile infections (CDI) cause almost 300,000 hospitalizations per year of which ∼15-30% are the result of recurring infections. The prevalence and persistence of CDI in hospital settings has resulted in an extensive collection of C. difficile clinical isolates and their classification, typically by ribotype. While much of the current literature focuses on one or two prominent ribotypes ( e.g ., RT027), recent years have seen several other ribotypes dominate the clinical landscape ( e.g. , RT106 and RT078). Some ribotypes are associated with severe disease and / or increased recurrence rates, but why are certain ribotypes more prominent or harmful than others remains unknown. Because C. difficile has a large, open pan-genome, this observed relationship between ribotype and clinical outcome could be a result of the genetic diversity of C. difficile . Thus, we hypothesize that core biological processes of C. difficile are conserved across ribotypes / clades. We tested this hypothesis by observing the growth kinetics, sporulation, germination, bile acid sensitivity, bile salt hydrolase activity, and surface motility of fifteen strains belonging to various ribotypes spanning each known C. difficile clade. In viewing these phenotypes across each strain, we see that core phenotypes (growth, germination, sporulation, and resistance to bile salt toxicity) are remarkably consistent across clades / ribotypes. This suggests that variations observed in the clinical setting may be due to unidentified factors in the accessory genome or due to unknown host-factors.

Importance

C. difficile infections impact thousands of individuals every year many of whom experience recurring infections. Clinical studies have reported an unexplained correlation between some clades / ribotypes of C. difficile and disease severity / recurrence. Here, we demonstrate that C. difficile strains across the major clades / ribotypes are consistent in their core phenotypes. This suggests that such phenotypes are not responsible for variations in disease severity / recurrence and are ideal targets for the development of therapeutics meant to treat C. difficile related infections.", "token_count": 516, "char_count": 2200, "word_count": 321, "semantic_coherence": 1, "information_density": 0.5763, "quality_score": 0.7882, "entities": { "genes": [ "RT106", "RT078", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:12.754757", "source": { "split": "train_shard_00001", "doc_id": 1119 }, "chunk_id": "train_shard_00001_1119_0", "global_id": 7237 }, { "text": "Phenotypic analysis of various Clostridioides difficile ribotypes reveals consistency among core processes", "token_count": 30, "char_count": 113, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:13.113313", "source": { "split": "train_shard_00001", "doc_id": 1119 }, "chunk_id": "train_shard_00001_1119_1", "global_id": 7238 }, { "text": "

Motivation

The increasing availability of complete genomes demands for models to study genomic variability within entire populations. Pangenome graphs capture the full genomic similarity and diversity between multiple genomes. In order to understand them, we need to see them. For visualization, we need a human readable graph layout: A graph embedding in low (e.g. two) dimensional depictions. Due to a pangenome graph’s potential excessive size, this is a significant challenge.

Results

In response, we introduce a novel graph layout algorithm: the Path-Guided Stochastic Gradient Descent (PG-SGD). PG-SGD uses the genomes, represented in the pangenome graph as paths, as an embedded positional system to sample genomic distances between pairs of nodes. This avoids the quadratic cost seen in previous versions of graph drawing by Stochastic Gradient Descent (SGD). We show that our implementation efficiently computes the low dimensional layouts of gigabase-scale pangenome graphs, unveiling their biological features.

Availability

We integrated PG-SGD in ODGI which is released as free software under the MIT open source license. Source code is available at https://github.com/pangenome/odgi .

Contact

egarris5@uthsc.edu\n\nPangenome graph layout by Path-Guided Stochastic Gradient Descent", "token_count": 327, "char_count": 1327, "word_count": 181, "semantic_coherence": 1, "information_density": 0.674, "quality_score": 0.837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:13.693979", "source": { "split": "train_shard_00001", "doc_id": 1120 }, "chunk_id": "train_shard_00001_1120_0", "global_id": 7239 }, { "text": "Abstract El objetivo de este estudio fue evaluar el posible efecto probiótico del sustrato de residuos agroindustriales fermentado con BAL y levaduras sobre los indicadores productivos, reproductivos y de salud de cobayas primíparas y su descendencia. Se utilizaron 80 cuyes nulíparas distribuidas en 4 grupos de 20 hembras nulíparas cada uno, de 120 ± 5 días de edad, 1450 ± 25 g de peso vivo, todas sometidas al mismo sistema de manejo y alimentación actual de la granja. Se aplicaron con una dosis de 1 mL del bioaditivo / animal. Los tratamientos suministrados fueron las siguientes variantes: T1. control. T2, Sustrato (residuos agroindustriales) fermentado con L. acidophilus ATCC® 4356 ™. T3, sustrato más Kluyveromyces fragilis L4 (UCLV). T4, sustrato fermentado con microorganismos T2 y T3.En el experimento se utilizó un diseño completamente al azar, donde se evaluaron los indicadores reproductivos, productivos y de salud. Weight gain in pregnancy was greater (P < 0.05) in T4 in this same group, weight loss was less (P < 0.05) in lactation; the age at first conception and at delivery decreased (P < 0.05) in T4; fertility, the number of live-born animals and the weight at birth and at weaning were higher (P < 0.05) in T4 compared to the other groups; Likewise, blood parameters notably improved in the animals of treatment 4. The treaties with bioaditive were the ones whit the best behavior as reflected in table 1. In the experiment, the beneficial effect as a probiotic was confirmed by the treatments (T2, T3 and T4) of these with the best performance was T4", "token_count": 486, "char_count": 1579, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6782, "quality_score": 0.8391, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:14.345819", "source": { "split": "train_shard_00001", "doc_id": 1121 }, "chunk_id": "train_shard_00001_1121_0", "global_id": 7240 }, { "text": "The inclusion of substrates fermented with LAB and yeasts significantly improves the productive, reproductive and health indicators of primiparous guinea pigs and their offspring.\n\nPSVI-7 Effect of substrates of agroindustrial wastes fermented with LAB and yeasts on productive, reproductive and health indicators in primiparous guinea pigs", "token_count": 86, "char_count": 340, "word_count": 46, "semantic_coherence": 1, "information_density": 0.5652, "quality_score": 0.7826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:14.716500", "source": { "split": "train_shard_00001", "doc_id": 1121 }, "chunk_id": "train_shard_00001_1121_1", "global_id": 7241 }, { "text": "Abstract

Bacteria of the genera Xenorhabdus and Photorhabdus are symbionts of entomopathogenic nematodes. Despite their close phylogenetic relationship, they show differences in their pathogenicity and virulence mechanisms in target insects. These differences can be explored by the analysis of the pangenome, as it provides a framework for characterizing and defining the gene repertoire. Here, we report the genome of strain SC 0516. In addition, we performed the first pangenome analysis of 91 strains of Xenorhabdus and Photorhabdus, obtaining a total of 23,603 gene clusters and a core genome of 348 genes. Phylogenetic analysis performed with the core genome showed that our strain belonged to the X. nematophila group. Biological tests showed that whole cells of X. nematophila SC 0516 were more virulent than those of P. luminescens HIM3 when both were injected into Galleria mellonella larvae. In addition, we cloned and expressed the GroEL proteins of both bacteria, as this protein has been previously indicated to show insecticidal activity in the genus Xenorhabdus. Cpn60-Xn was found to be the most toxic at all concentrations tested, with an LC50 value of 102.34 ng/larva. Sequence analysis suggested that the Cpn60-Xn toxin was homologous to Cpn60-Pl; however, Cpn60-Xn contained thirty-five differentially substituted amino acid residues that could be responsible for its insecticidal activity.

", "token_count": 477, "char_count": 1598, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.831, "entities": { "genes": [ "HIM3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:15.363632", "source": { "split": "train_shard_00001", "doc_id": 1122 }, "chunk_id": "train_shard_00001_1122_0", "global_id": 7242 }, { "text": "Comparative Genomics and Pathogenicity Analysis of Two Bacterial Symbionts of Entomopathogenic Nematodes: The Role of The GroEL Protein in Virulence", "token_count": 41, "char_count": 148, "word_count": 20, "semantic_coherence": 1, "information_density": 0.85, "quality_score": 0.925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:15.717306", "source": { "split": "train_shard_00001", "doc_id": 1122 }, "chunk_id": "train_shard_00001_1122_1", "global_id": 7243 }, { "text": "Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Two emerging challenges for the C. sativa research community are to 1) comprehensively capture the genomic diversity of the species and 2) reconcile and leverage the large amounts of genomic data to make meaningful contributions to fundamental research and commercial production systems. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We used a kmer-based pangenome analysis to place these new assemblies in the context of more than 200 existing assemblies. We leveraged linkage maps constructed from F2 progeny of two of the assembled genotypes to characterize the recombination rate across the genome. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts.\n\nComparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in Cannabis sativa Using Seven De Novo Genome Assemblies", "token_count": 338, "char_count": 1485, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:16.289080", "source": { "split": "train_shard_00001", "doc_id": 1123 }, "chunk_id": "train_shard_00001_1123_0", "global_id": 7244 }, { "text": "The human gastrointestinal tract harbors a vast array of microorganisms, which play essential roles in maintaining metabolic balance and immune function. While bacteria dominate the gut microbiome, fungi represent a much smaller, often overlooked fraction. Despite their relatively low abundance, fungi may significantly influence both health and disease. Advances in next-generation sequencing, metagenomics, metatranscriptomics, metaproteomics, metabolomics, and computational biology have provided novel opportunities to study the gut mycobiome, shedding light on its composition, functional genes, and metabolite interactions. Emerging evidence links fungal dysbiosis to various diseases, including inflammatory bowel disease, colorectal cancer, metabolic disorders, and neurological conditions. The gut mycobiome also presents a promising avenue for precision medicine, particularly in biomarker discovery, disease diagnostics, and targeted therapeutics. Nonetheless, significant challenges remain in effectively integrating gut mycobiome knowledge into clinical practice. This review examines gut fungal microbiota, highlighting analytical methods, associations with human diseases, and its potential role in precision medicine. It also discusses pathways for clinical translation, particularly in diagnosis and treatment, while addressing key barriers to implementation.\n\nThe Gut Mycobiome for Precision Medicine.", "token_count": 300, "char_count": 1420, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:16.853378", "source": { "split": "train_shard_00001", "doc_id": 1124 }, "chunk_id": "train_shard_00001_1124_0", "global_id": 7245 }, { "text": "Jellified materials were observed in spoiled pasteurized apple juice that contained dimethyl dicarbonate (DMDC). Microbiological analysis showed a high microbial load (4-5 log CFU/mL) in the sample. Acetobacter spp. was identified as the spoilage microorganism by 16S rRNA gene sequencing. Metataxonomic analysis showed Acetobacter represented 99 % of the bacterial community. Three Acetobacter isolates (LX5, LX9 and LX16) were selected for whole genome sequencing and characterized for their susceptibility to DMDC. Genome-based phylogeny supported the species-level classification of LX5 as A. fabarum. It also suggested LX9 and LX16 are the same microorganisms from a potentially novel species closely related to A. lovaniensis. The minimum inhibitory concentrations (MICs) of DMDC for Acetobacter isolates in sterile apple juice (pH ∼3) at 30 °C were 46 ppm and 329 ppm for A. fabarum LX5 and Acetobacter LX9/LX16, respectively. The minimum bactericidal concentrations (MBCs) were 250 and 500 ppm for A. fabarum LX5 and Acetobacter LX9/LX16, respectively. The inoculum concentration for the MIC assay was approximately 6 log10 CFU/mL, representing the \"worst-case\" scenario. When the contamination level was reduced to 500 CFU/mL per US federal regulation (21 CFR 172.133) and the apple juice was refrigerated, Acetobacter isolates did not grow and were completely inhibited by 238 ppm DMDC. Pangenome analysis identified gene clusters that potentially play a role in biofilm development, carbohydrate metabolism, and oxidative stress tolerance, but it also ruled out the involvement of Acetobacter in apple juice gel formation. The investigation concluded that post-pasteurization contamination, high microbial load and ambient storage were factors leading to this spoilage incident.", "token_count": 526, "char_count": 1800, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6289, "quality_score": 0.8145, "entities": { "genes": [ "LX9", "LX16", "LX5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:17.554016", "source": { "split": "train_shard_00001", "doc_id": 1125 }, "chunk_id": "train_shard_00001_1125_0", "global_id": 7246 }, { "text": "Spoilage investigation of pasteurized apple juice with visual defects identifies a potentially novel Acetobacter species as the primary spoilage agent.", "token_count": 33, "char_count": 151, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:17.937518", "source": { "split": "train_shard_00001", "doc_id": 1125 }, "chunk_id": "train_shard_00001_1125_1", "global_id": 7247 }, { "text": "Pangenome analyses are increasingly being utilized to study the evolution of eukaryotic organisms, which is often governed by variable gene content. While pangenomes can provide insight into polymorphic gene content, inferences about the ecological and adaptive potential of such organisms also need to be accompanied by additional supportive genomic analyses. In this study we constructed a pangenome of Claviceps purpurea from 24 genomes and examined the positive selection and recombination landscape of an economically important fungal organism for pharmacology and agricultural research. Together, these analyses revealed that C. purpurea has a relatively large accessory genome (∼ 38%) that is likely maintained by high recombination rates (ρ = 0.044) and transposon mediated gene duplication. However, due to observations of relatively low transposable element (TE) content (8.8%) and a lack of variability in genome sizes, prolific TE expansion is likely controlled by these high recombination rates, which may additionally be influencing the overall trend of purifying selection across the genome. Despite this trend, we observed a strong positive selection pressure on secondary metabolite genes, particularly within the ergoline biosynthetic cluster where we also revealed that the lpsA1 and lpsA2 genes were the result of a recombination event. These results indicate that secondary metabolites are primary factors affecting the diversification of the species into new ecological niches and help maintain its global distribution and broad host range. These results showcase the use of selection and recombination landscapes to identify mechanisms contributing to pangenome structure and primary factors influencing the evolution of an organism.

Author Summary

The use of genomic data to better understand the lifestyle of a pathogen and its relationship with its host has expanded our ability to investigate the evolutionary history of these organisms. This in turn has allowed us to decipher and understand the ambiguity surrounding the true nature of the fungal plant pathogen Claviceps purpurea . By combining three different types of broad genomic analyses we identified primary factors affecting the evolution and adaptive potential of this pathogen; particularly a large accessory genome, high recombination rates, and positive selection of genes associated with stress tolerance. These factors likely contribute to the pathogen’s global distribution and broad host range", "token_count": 519, "char_count": 2498, "word_count": 359, "semantic_coherence": 1, "information_density": 0.5627, "quality_score": 0.7813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:18.606790", "source": { "split": "train_shard_00001", "doc_id": 1126 }, "chunk_id": "train_shard_00001_1126_0", "global_id": 7248 }, { "text": "Furthermore, these findings will influence the direction of future research into optimal control methods.\n\nA large accessory genome, high recombination rates, and selection of secondary metabolite genes help maintain global distribution and broad host range of the fungal plant pathogenClaviceps purpurea", "token_count": 68, "char_count": 311, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9024, "quality_score": 0.9512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:19.028227", "source": { "split": "train_shard_00001", "doc_id": 1126 }, "chunk_id": "train_shard_00001_1126_1", "global_id": 7249 }, { "text": "Abstract

Wild plants can contribute valuable genes to their domesticated relatives. Fertility barriers and a lack of genomic resources have hindered the effective use of crop-wild introgressions. Decades of research into barley’s closest wild relative, Hordeum bulbosum, a grass native to the Mediterranean basin and Western Asia, have yet to manifest themselves in the release of a cultivar bearing alien genes. Here, we construct a pangenome of bulbous barley comprising ten haplotype-resolved genome sequence assemblies. Autotetraploid cytotypes, among which the donors of resistance-conferring introgressions are found, arose at least twice, and are connected among each other and to diploid forms through gene flow. The differential amplification of transposable elements after barley and H. bulbosum diverged from each other is responsible for genome size differences between them. We illustrate the translational value of our resource by mapping non-host resistance to a viral pathogen to a structurally diverse multigene cluster implicated in diverse immune responses in wheat and barley.

\n\nA haplotype-resolved pangenome of the barley wild relative Hordeum bulbosum", "token_count": 319, "char_count": 1295, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7305, "quality_score": 0.8653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:19.598277", "source": { "split": "train_shard_00001", "doc_id": 1127 }, "chunk_id": "train_shard_00001_1127_0", "global_id": 7250 }, { "text": "Small RNAs (sRNAs) exert their regulation posttranscriptionally by base pairing with their target mRNAs, often in association with the RNA chaperone protein Hfq. Here, integrating RNA-seq–based technologies and bioinformatics, we deciphered the Hfq-mediated sRNA-target interactome of enteropathogenic Escherichia coli (EPEC). The emerging network comprises hundreds of sRNA-mRNA pairs, including mRNAs of virulence-associated genes interacting with known sRNAs encoded within the core genome, as well as with newly found sRNAs encoded within pathogenicity islands. Some of the sRNAs affect multiple virulence genes, suggesting they function as hubs of virulence control. We further analyzed one such sRNA hub, MgrR, and one of its targets identified here, the major virulence-associated chaperon, cesT. We show that MgrR adjusts the level of EPEC cytotoxicity via regulation of CesT expression. Our results reveal an elaborate sRNA-mRNA interactome controlling the pathogenicity of EPEC and reinforce a role for sRNAs in the control of pathogen-host interaction.\n\nThe impact of Hfq-mediated sRNA-mRNA interactome on the virulence of enteropathogenic Escherichia coli.", "token_count": 342, "char_count": 1189, "word_count": 161, "semantic_coherence": 1, "information_density": 0.677, "quality_score": 0.8385, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:20.173246", "source": { "split": "train_shard_00001", "doc_id": 1128 }, "chunk_id": "train_shard_00001_1128_0", "global_id": 7251 }, { "text": "Escherichia coli is a facultative anaerobe found in a wide range of environments. Commonly described as the laboratory workhorse, E. coli is one of the best characterized bacterial species to date, however much of our understanding comes from studies involving the laboratory strain E. coli K-12. Resistance-nodulation-division efflux pumps are found in Gram-negative bacteria and can export a diverse range of substrates, including antibiotics. E. coli K-12 has six RND pumps; AcrB, AcrD, AcrF, CusA, MdtBC and MdtF, and it is frequently reported that all E. coli strains possess these six pumps. However, this is not true of E. coli ST11, a lineage of E. coli, which is primarily composed of the highly virulent important human pathogen, E. coli O157:H7. Here we show that acrF is absent from the pangenome of ST11 and that this lineage of E. coli has a highly conserved insertion within the acrF gene, which when translated encodes 13 amino acids and two stop codons. This insertion was found to be present in 97.59 % of 1787 ST11 genome assemblies. Non-function of AcrF in ST11 was confirmed in the laboratory as complementation with acrF from ST11 was unable to restore AcrF function in E. coli K-12 substr. MG1655 ΔacrB ΔacrF. This shows that the complement of RND efflux pumps present in laboratory bacterial strains may not reflect the situation in virulent strains of bacterial pathogens.", "token_count": 494, "char_count": 1502, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [ "MG1655", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:20.826554", "source": { "split": "train_shard_00001", "doc_id": 1129 }, "chunk_id": "train_shard_00001_1129_0", "global_id": 7252 }, { "text": "E. coli ST11 (O157:H7) does not encode a functional AcrF efflux pump.", "token_count": 35, "char_count": 76, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:21.188653", "source": { "split": "train_shard_00001", "doc_id": 1129 }, "chunk_id": "train_shard_00001_1129_1", "global_id": 7253 }, { "text": "Candida kefyr has been considered both a food-spoiling agent and a type of yeast with fermentation properties. In this study, the authors have evaluated the antimicrobial activity of a coconut oil-in-water emulsion associated to the presence of C. kefyr. Fresh coconut kernels were used to obtain the coconut oil-in-water emulsion, the sterile coconut oil-in-water emulsion by decantation, and the coconut oil by means of a heating process. Commercial virgin coconut oil was also used. Agar diffusion, minimal inhibitory concentration and minimal bactericidal concentration (MIC/MBC) techniques were employed to evaluate antimicrobial activity against E. coli and S. epidermidis. The C. kefyr isolate was identified and confirmed. Coconut milk-derived fatty acids were characterized by acid index and thin layer chromatography. Scanning electronic microscopy was performed to evaluate the morphology of the microorganisms. Lipase activity of C. kefyr isolate was also detected. Coconut oil-in-water emulsion associated to C. kefyr was active against both bacteria. Thin layer chromatography confirmed the presence of triglycerides and free fatty acids. The acid index showed higher acidity potential for the coconut oil-in-water emulsion. The microscopic images showed antibacterial action through the formation of membrane holes' and demonstrated yeast shape. All the above show new potentials for C. kefyr and coconut oil-in-water emulsion in food technology.\n\nAntimicrobial activity of coconut oil-in-water emulsion on Staphylococcus epidermidis and Escherichia coli EPEC associated to Candida kefyr.", "token_count": 478, "char_count": 1680, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5402, "quality_score": 0.7701, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:21.835139", "source": { "split": "train_shard_00001", "doc_id": 1130 }, "chunk_id": "train_shard_00001_1130_0", "global_id": 7254 }, { "text": "To understand the prevalence and phylogeny of methicillin-resistant Staphylococcus aureus (MRSA) in Chinese hospitals and identify the dominant MRSA lineages causing hospital infections, we collected 101 S. aureus isolates from multiple centers across China, tested their antibiotic sensitivity, and performed whole-genome sequencing. Using our group's database, a core genome-based phylogenetic analysis of 204 S. aureus isolates was conducted. The results revealed an interspersed distribution of MRSA and MSSA without distinct clade separation. CC59-ST59-t437-SCCmec IV was identified as the predominant community-associated MRSA (CA-MRSA) clone widely distributed across cities, while hospital-associated MRSA (HA-MRSA) was mainly composed of CC5-ST5-SCCmec II and CC8-ST239-SCCmec III, forming significant phylogenetic clusters. In contrast, MSSA strains were more diverse, with no clear clustering patterns. No regional clustering was observed, suggesting a widespread dissemination of major clones nationwide. Notably, some sequence types (e.g., ST45 and ST59) were shared by both MRSA and MSSA, and closely related strains with and without SCCmec elements suggested that smaller SCCmec types may be more readily gained or lost during evolution. Our findings indicate that CA-MRSA has a significant presence in hospitals with diverse subtypes, highlighting the need for increased attention to CA-MRSA in S. aureus control and prevention.IMPORTANCEThe aim of this study was to identify the molecular epidemiological characteristics of S. aureus in Chinese hospitals, especially the dominant typing changes of MRSA during transmission. This study found that CA-MRSA appeared in the hospital environment with high diversity, suggesting that clinical attention should be paid to CA-MRSA in the prevention and diagnosis of S", "token_count": 521, "char_count": 1913, "word_count": 250, "semantic_coherence": 1, "information_density": 0.664, "quality_score": 0.832, "entities": { "genes": [ "CC8", "ST239", "ST45", "ST5", "CC5", "ST59", "CC59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:22.494470", "source": { "split": "train_shard_00001", "doc_id": 1131 }, "chunk_id": "train_shard_00001_1131_0", "global_id": 7255 }, { "text": "aureus infection.\n\nUnveiling the emergence of community-acquired methicillin-resistant <i>Staphylococcus aureus</i> (CA-MRSA) in Chinese hospitals with remarkable genetic diversity: a multicenter molecular epidemiological investigation.", "token_count": 76, "char_count": 252, "word_count": 23, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:22.860216", "source": { "split": "train_shard_00001", "doc_id": 1131 }, "chunk_id": "train_shard_00001_1131_1", "global_id": 7256 }, { "text": "Abstract

Human pangenomes provide a comprehensive portrayal of genetic diversity of humans, yet it lacks representation of Arab populations. We constructed the Arab Pangenome Reference (APR) from 43 individuals with diverse Arab ethnicities. Nuclear and mitochondrial pangenomes were constructed utilizing 35.52X High fidelity long reads and 53.54X ultra-long reads. This yielded high-quality contiguous (average N50=106.81 Mb) de novo assemblies that used over 99% of the sequences constructing haplotype phased diploid genome assemblies with 88% exhibited larger genome length (average 3.01 gigabase) than the prevailing human reference GRCh38. We discovered 100.93 million base pairs of novel euchromatic sequences that were not present in recent human pangenomes and in the human genome references (T2T-CHM13 and GRCh38). We identified 10.68 million population-specific small variants, 108,709 structural variants, and 838 genes (13.24% recessive disease genes) duplication from the Arab pangenome. On exploring the mitochondria pangenome, we uncovered 718 bp of novel sequences. Our study provides a valuable resource for future genetic research and genomic medicine initiatives in the Arab populations and other populations with similar genetic backgrounds.

\n\nA draft Arab pangenome reference", "token_count": 368, "char_count": 1337, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7022, "quality_score": 0.8511, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:23.443492", "source": { "split": "train_shard_00001", "doc_id": 1132 }, "chunk_id": "train_shard_00001_1132_0", "global_id": 7257 }, { "text": "Abstract

Background LTR-retrotransposons (LTR-RT) are a major component of plant genomes and are a major driver of genome evolution. Most LTR-RT copies in plant genomes are defective elements, found as truncated copies, nested insertions or being part of more complex structures. With the availability of highly contiguous plant genome assemblies based on long-read sequences it has become feasible the detailed characterization of these complex structures and the evaluation of their importance for plant genome evolution. Results The detailed analysis of two rice loci containing complex LTR-RT structures showed that they consist of tandem arrays of LTR copies sharing internal LTRs. Our analysis show that the tandems are not the result of a single insertion and not of the recombination of two independent LTR-RT elements. Our results suggest that gypsy elements may be more prone to form these structures. We show that these structures are highly polymorphic in rice and have therefore the potential to generate genetic and phenotypic variability. We developed a computational pipeline, IDENTAM, that scans genome sequences and identifies tandem LTR-RT candidates and detected 307 tandems in a pangenome built from the genomes of 75 accessions of cultivated and wild rice, showing that tandem LTR-RT structures are frequent in the rice genome and are highly polymorphic in the species. Running IDENTAM in the Arabidopsis, almond and cotton genomes showed that LTR-RT tandems are frequent in plant genomes of different size, complexity and ploidy levels. The complexity of differentiating intra-element variations at the nucleotide level among haplotypes is very high, and we found that graph-based pangenomic methodologies are appropriate to resolve these structures. Conclusions Our results show that LTR-RTs can form tandem arrays of elements. These structures are relatively abundant and highly polymorphic in rice and are widespread in the plant kingdom. Future studies will contribute to understand how these structures originate and if the variability that they generate has a functional impact.

\n\nTandem LTR-retrotransposon structures are common and highly polymorphic in plant genomes", "token_count": 501, "char_count": 2223, "word_count": 325, "semantic_coherence": 1, "information_density": 0.5046, "quality_score": 0.7523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:24.108131", "source": { "split": "train_shard_00001", "doc_id": 1133 }, "chunk_id": "train_shard_00001_1133_0", "global_id": 7258 }, { "text": "This research provides an extensive genomic analysis of Weissella paramesenteroides WP12, a strain with significant potential for food fermentation. The 2.07 Mb genome comprises a circular chromosome and two plasmids, encoding 2301 protein-coding sequences, 25 rRNA genes, 77 tRNA genes, and one tmRNA gene. Functional annotation identified essential genes involved in carbohydrate metabolism, aminopeptidase activity, and maltose transport, emphasizing the fermentative abilities of this strain. Key metabolic pathways, such as glycolysis, pentose phosphate pathway, and pyruvate metabolism, are well-represented, highlighting the robust capacity of the strain for sugar utilization and energy production. Safety evaluations performed in silico indicate the absence of antibiotic resistance and virulence genes. Moreover, the comparative analysis of secondary metabolite gene clusters across 47 W. paramesenteroides showed that most strains, including WP12, predominantly encode Type III Polyketide Synthase (T3PKS), confirming its safety for use in food products. The genome also lacks genes associated with biogenic amine production, reducing the risk of foodborne toxicity. Pangenome analysis of 47 strains revealed a unique gene repertoire of WP12, including pepN and malK which are important for efficient fermentation. Additionally, the presence of a cold shock RNA helicase gene suggests its capability to withstand environmental stresses, especially in diverse fermentation conditions. Comparative genomics demonstrated that the WP12 harbors unique carbohydrate-active enzymes (CAZymes) not found in other strains, potentially enhancing its fermentative performance. The analysis identified 1929 genes shared across all strains, representing core genes essential for fundamental biological functions. The strain also possesses genes linked to exopolysaccharide (EPS) production, a feature absent in some other strains. These EPS-related genes enhance the ability of this strain to improve the texture and stability of fermented foods", "token_count": 488, "char_count": 2042, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8407, "entities": { "genes": [ "WP12" ], "proteins": [], "pathways": [ "glycolysis", "metabolism", "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:24.756076", "source": { "split": "train_shard_00001", "doc_id": 1134 }, "chunk_id": "train_shard_00001_1134_0", "global_id": 7259 }, { "text": "The phenotypic analysis demonstrated that WP12 exhibits strong probiotic characteristics, including tolerance to gastrointestinal conditions such as low pH and bile salts. The strain showed robust auto-aggregation and co-aggregation abilities, achieving up to 70% co-aggregation with foodborne pathogens, which suggests its potential to inhibit pathogen colonization. WP12 also exhibited broad-spectrum antibacterial activity, primarily through acid-mediated inhibition of various foodborne pathogens. These findings highlight W.paramesenteroides WP12 as a promising candidate for biotechnological applications in the food industry, particularly for the development of innovative and enhanced fermented food products.\n\nGenomic and phenotypic characterization of Weissella paramesenteroides WP12 from fermented fish sauce (Budu) reveals promising strain for food fermentation and probiotic applications", "token_count": 204, "char_count": 901, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7523, "quality_score": 0.8761, "entities": { "genes": [ "WP12" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:25.213627", "source": { "split": "train_shard_00001", "doc_id": 1134 }, "chunk_id": "train_shard_00001_1134_1", "global_id": 7260 }, { "text": "

Background

The KT/HAK/KUP is the largest K+ transporter family in plants, playing crucial roles in K+ absorption, transport, and defense against environmental stress. Sweet watermelon is an economically significant horticultural crop belonging to the genus Citrullus, with a high demand for K+ during its growth process. However, a comprehensive analysis of the KT/HAK/KUP gene family in watermelon has not been reported.

Results

14 KT/HAK/KUP genes were identified in the genomes of each of seven Citrullus species. These KT/HAK/KUPs in watermelon were unevenly distributed across seven chromosomes. Segmental duplication is the primary driving force behind the expansion of the KT/HAK/KUP family, subjected to purifying selection during domestication (Ka/Ks < 1), and all KT/HAK/KUPs exhibit conserved motifs and could be phylogenetically classified into four groups. The promoters of KT/HAK/KUPs contain numerous cis-regulatory elements related to plant growth and development, phytohormone response, and stress response. Under K+ deficiency, the growth of watermelon seedlings was significantly inhibited, with cultivated watermelon experiencing greater impacts (canopy width, redox enzyme activity) compared to the wild type. All KT/HAK/KUPs in C. lanatus and C. amarus exhibit specific expression responses to K+-deficiency and drought stress by qRT-PCR. Notably, ClG42_07g0120700/CaPI482276_07g014010 were predominantly expressed in roots and were further induced by K+-deficiency and drought stress", "token_count": 469, "char_count": 1587, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6766, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:25.857328", "source": { "split": "train_shard_00001", "doc_id": 1135 }, "chunk_id": "train_shard_00001_1135_0", "global_id": 7261 }, { "text": "Additionally, the K+ transport capacity of ClG42_07g0120700 under low K+ stress was confirmed by yeast functional complementation assay.

Conclusions

KT/HAK/KUP genes in watermelon were systematically identified and analyzed at the pangenome level and provide a foundation for understanding the classification and functions of the KT/HAK/KUPs in watermelon plants.\n\nGenome-wide survey of KT/HAK/KUP genes in the genus Citrullus and analysis of their involvement in K+-deficiency and drought stress responses in between C. lanatus and C. amarus.", "token_count": 172, "char_count": 583, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7123, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:26.302400", "source": { "split": "train_shard_00001", "doc_id": 1135 }, "chunk_id": "train_shard_00001_1135_1", "global_id": 7262 }, { "text": "The permanent organs of grapevines (Vitis vinifera L.), like those of other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata, Neofusicoccum parvum, and Phaeoacremonium minimum, causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced 50 isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examination of genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection and recent gene family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, carbohydrate active enzymes (CAZymes) were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum. The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthase genes in E. lata and P. minimum, glycosyltransferases in N. parvum). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.", "token_count": 525, "char_count": 2006, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:26.930868", "source": { "split": "train_shard_00001", "doc_id": 1136 }, "chunk_id": "train_shard_00001_1136_0", "global_id": 7263 }, { "text": "Comparative Pangenomic Insights into the Distinct Evolution of Virulence Factors Among Grapevine Trunk Pathogens.", "token_count": 31, "char_count": 113, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:27.308276", "source": { "split": "train_shard_00001", "doc_id": 1136 }, "chunk_id": "train_shard_00001_1136_1", "global_id": 7264 }, { "text": "Staphylococcus aureus causes both hospital and community acquired infections in humans worldwide. Due to the high incidence of infection S. aureus is also one of the most sampled and sequenced pathogens today, providing an outstanding resource to understand variation at the bacterial subspecies level. We processed and downsampled 83,383 public S. aureus Illumina whole genome shotgun sequences and 1,263 complete genomes to produce 7,954 representative substrains. Pairwise comparison of core gene Average Nucleotide Identity (ANI) revealed a natural boundary of 99.5% that could be used to define 145 distinct strains within the species. We found that intermediate frequency genes in the pangenome (present in 10-95% of genomes) could be divided into those closely linked to strain background (“strain-concentrated”) and those highly variable within strains (“strain-diffuse”). Non-core genes had different patterns of chromosome location; notably, strain-diffuse associated with prophages, strain-concentrated with the vSaβ genome island and rare genes (<10% frequency) concentrated near the origin of replication. Antibiotic genes were enriched in the strain-diffuse class, while virulence genes were distributed between strain-diffuse, strain-concentrated, core and rare classes. This study shows how different patterns of gene movement help create strains as distinct subspecies entities and provide insight into the diverse histories of important S. aureus functions.

Importance

We analyzed the genomic diversity of Staphylococcus aureus , a globally prevalent bacterial species that causes serious infections in humans. Our goal was to build a genetic picture of the different strains of S. aureus and which genes may be associated with them. We used a large public dataset (>84,000 genomes) that was re-processed and subsampled to remove redundancy. We found that individual genomes could be grouped into strains by sharing > 99.5% identical nucleotide sequence of the core part of their genome", "token_count": 492, "char_count": 2013, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6237, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:27.959300", "source": { "split": "train_shard_00001", "doc_id": 1137 }, "chunk_id": "train_shard_00001_1137_0", "global_id": 7265 }, { "text": "We also showed that a portion of genes that are present in intermediate frequency in the species are strongly associated with some strains but completely absent from others, suggesting a role in strain-specificity. This work lays the foundation for understanding individual gene histories of the S. aureus species and also outlines strategies for processing large bacterial genomic datasets.\n\nAverage Nucleotide Identity basedStaphylococcus aureusstrain grouping allows identification of strain-specific genes in the pangenome", "token_count": 115, "char_count": 533, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:28.338001", "source": { "split": "train_shard_00001", "doc_id": 1137 }, "chunk_id": "train_shard_00001_1137_1", "global_id": 7266 }, { "text": "A pangenome is the complete set of genes (core and accessory) present in a phylogenetic clade. We hypothesize that a pangenome’s accessory gene content is structured and maintained by selection. To test this hypothesis, we interrogated the genomes of 40 Pseudomonas genomes for statistically significant coincident (i.e. co-occurring/avoiding) gene patterns. We found that 86.7% of common accessory genes are involved in ≥1 coincident relationship. Further, genes that co-occur and/or avoid each other - but are not vertically or horizontally co-inherited - are more likely to share Gene Ontology categories, are more likely to be simultaneously transcribed, and are more likely to produce interacting proteins, than would be expected by chance. These results are not due to coincident genes being adjacent to one another on the chromosome. Together, these findings suggest that the accessory genome is structured into interacting sets of genes co-selected to function together within a given strain. Given the simi larity of the Pseudomonas pangenome with open pangenomes of other prokaryotic species, we speculate that these results are generalizable.\n\nEvidence for selection in a prokaryote pangenome", "token_count": 289, "char_count": 1203, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6124, "quality_score": 0.8062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:28.899755", "source": { "split": "train_shard_00001", "doc_id": 1138 }, "chunk_id": "train_shard_00001_1138_0", "global_id": 7267 }, { "text": "The conversion of lignocellulose into fermentable sugars is considered a promising alternative for increasing ethanol production. Higher fermentation yield has been achieved through the process of simultaneous saccharification and fermentation (SSF). In this study, a comparison was performed between the yeast species Saccharomyces cerevisiae and Kluyveromyces marxianus for their potential use in SSF process. Three strains of S. cerevisiae were evaluated: two are widely used in the Brazilian ethanol industry (CAT-1 and PE-2), and one has been isolated based on its capacity to grow and ferment at 42 °C (LBM-1). In addition, we used thermotolerant strains of K. marxianus. Two strains were obtained from biological collections, ATCC 8554 and CCT 4086, and one strain was isolated based on its fermentative capacity (UFV-3). SSF experiments revealed that S. cerevisiae industrial strains (CAT-1 and PE-2) have the potential to produce cellulosic ethanol once ethanol had presented yields similar to yields from thermotolerant strains. The industrial strains are more tolerant to ethanol and had already been adapted to industrial conditions. Moreover, the study shows that although the K. marxianus strains have fermentative capacities similar to strains of S. cerevisiae, they have low tolerance to ethanol. This characteristic is an important target for enhancing the performance of this yeast in ethanol production.\n\nPhysiological characterization of thermotolerant yeast for cellulosic ethanol production.", "token_count": 379, "char_count": 1513, "word_count": 217, "semantic_coherence": 1, "information_density": 0.576, "quality_score": 0.788, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:29.522366", "source": { "split": "train_shard_00001", "doc_id": 1139 }, "chunk_id": "train_shard_00001_1139_0", "global_id": 7268 }, { "text": "

Background

Clostridioides difficile is an anaerobic enteropathogen of clinical relevance in hospital and community settings. Its ubiquitous presence in pets, livestock, food and the environment, together with its ability to form spores, facilitates its survival and spread. Hypervirulent and multi-drug-resistant genotypes have been reported previously from Central America.

Aim

To characterize 31 isolates from patients of two major hospitals in Honduras.

Methods

Second- and third-generation whole-genome sequencing and phenotypic antimicrobial susceptibility testing.

Findings

Two toxigenic polymerase chain reaction ribotypes RT027 (ST1) and RT002 (ST8) were detected. All RT027/ST1 isolates (N=29) were resistant to moxifloxacin, tetracycline and linezolid, whereas RT002/ST8 isolates (N=2) were susceptible. In addition, a number of mobile genetic elements associated with antimicrobial resistance were found in all RT027 isolates. Notably, core genome multi-locus sequence typing and core genome single nucleotide polymorphism analysis demonstrated the close genetic relationship among RT027/ST1 isolates, their persistence since 2016, and an interhospital transfer event with unknown sanitary and economic consequences. In addition, RT002, a genotype with known implications for community-acquired C. difficile infection and possible zoonotic implications, is a remarkable finding in the national epidemiologic context.

Conclusions

Taken together, these findings highlight the presence of persistent and community-relevant C. difficile strains, and the consequent need to adopt and develop interventions to control and prevent CDI in the Honduran national health system within a One Health research approach.\n\nClostridioides difficile in Honduras: a genomic and phenotypic characterization of the persistent RT027 and emergent RT002 genotypes.", "token_count": 507, "char_count": 1887, "word_count": 232, "semantic_coherence": 1, "information_density": 0.681, "quality_score": 0.8405, "entities": { "genes": [ "ST8", "RT002", "ST1", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:30.192807", "source": { "split": "train_shard_00001", "doc_id": 1140 }, "chunk_id": "train_shard_00001_1140_0", "global_id": 7269 }, { "text": "Extraintestinal pathogenic Escherichia coli (ExPEC) is a pathogen that causes host extraintestinal diseases. The ST95 E. coli lineage is one of the dominant ExPEC lineages in humans and poultry. In this study, we took advantage of extensive E. coli genomes available through public open-access databases to construct a detailed understanding of the phylogeny and evolution of ST95. We used a high variability of accessory genomes to highlight the diversity and dynamic traits of ST95. Isolates from diverse hosts and geographic sources were randomly located on the phylogenetic tree, which suggested that there is no host specificity for ST95. The time-scaled phylogeny showed that ST95 is an ancient and long-lasting lineage. The virulence genes, resistance genes, and pathogenicity islands (PAIs) were characterized in ST95 pan-genomes to provide novel insights into the pathogenicity and multidrug resistance (MDR) genotypes. We found that a pool of large plasmids drives virulence and MDR. Based on the unique genes in the ST95 pan-genome, we designed a novel multiplex PCR reaction to rapidly detect ST95. Overall, our study addressed a gap in the current understanding of ST95 ExPEC genomes, with significant implications for recognizing the success and spread of ST95.\n\nGenomics Analysis to Identify Multiple Genetic Determinants That Drive the Global Transmission of the Pandemic ST95 Lineage of Extraintestinal Pathogenic Escherichia coli (ExPEC).", "token_count": 395, "char_count": 1484, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6065, "quality_score": 0.8032, "entities": { "genes": [ "ST95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:30.845190", "source": { "split": "train_shard_00001", "doc_id": 1141 }, "chunk_id": "train_shard_00001_1141_0", "global_id": 7270 }, { "text": "Specific virulence factors that likely influence C. acnes invasion into deep tissues remain to be elucidated. Herein, we describe the frequency of C. acnes identification in deep tissue specimens of patients undergoing clean shoulder surgery and assess its phenotypic and genetic traits associated with virulence and antibiotic resistance patterns, compared with isolates from the skin of healthy volunteers. Multiple deep tissue specimens from the bone fragments, tendons, and bursa of 84 otherwise healthy patients undergoing primary clean-open and arthroscopic shoulder surgeries were aseptically collected. The overall yield of tissue sample cultures was 21.5% (55/255), with 11.8% (30/255) identified as C. acnes in 27.3% (23/84) of patients. Antibiotic resistance rates were low, with most strains expressing susceptibility to first-line antibiotics, while a few were resistant to penicillin and rifampicin. Phylotypes IB (73.3%) and II (23.3%) were predominant in deep tissue samples. Genomic analysis demonstrated differences in the pangenome of the isolates from the same clade. Even though strains displayed a range of pathogenic markers, such as biofilm formation, patients did not evolve to infection during the 1-year follow-up. This suggests that the presence of polyclonal C. acnes in multiple deep tissue samples does not necessarily indicate infection.\n\nPhenotypic and Genotypic Characterization of Cutibacterium acnes Isolated from Shoulder Surgery Reveals Insights into Genetic Diversity.", "token_count": 415, "char_count": 1542, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:31.485395", "source": { "split": "train_shard_00001", "doc_id": 1142 }, "chunk_id": "train_shard_00001_1142_0", "global_id": 7271 }, { "text": "Milk beer is a new type of dairy beverage in China and increasingly popular with consumers. The strain FXJ1 isolated in our laboratory was an excellent strain for the production of milk beer with alcohol content of 0.48%. Our research verified that the strain FXJ1 was superior to the commercial strain MJ for milk beer production and got the optimal medium formula (67.37 g/L sucrose, 29.7 g/L yeast extract, 15.61 g/L corn steep liquor, 4.13 g/L KH₂PO₄ and 0.3 g/L MgSO₄) which allowed the biomass production of strain FXJ1 to achieve 8.88 ± 0.08 g/L and increase 2.94‐fold as compared with yeast extract peptone dextrose base medium.\n\nComparative analysis of the fermentation performance of high‐quality milk beer strains (Kluyveromyces marxianus) and optimisation of medium formula for high‐density fermentation", "token_count": 246, "char_count": 815, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6328, "quality_score": 0.8164, "entities": { "genes": [ "FXJ1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:31.970033", "source": { "split": "train_shard_00001", "doc_id": 1143 }, "chunk_id": "train_shard_00001_1143_0", "global_id": 7272 }, { "text": "Bacteria from the genus Sulfitobacter are distributed across various marine habitats and play a significant role in sulfur cycling. However, the metabolic features of Sulfitobacter inhabiting marine biofilms are still not well understood. Here, complete genomes and paired metatranscriptomes of eight Sulfitobacter strains, isolated from biofilms on subtidal stones, have been analyzed to explore their central energy metabolism and potential of secondary metabolite biosynthesis. Based on average nucleotide identity and phylogenetic analysis, the eight strains were classified into six novel species and two novel strains. The reconstruction of the metabolic pathways indicated that all strains had a complete Entner-Doudoroff pathway, pentose phosphate pathway, and diverse pathways for amino acid metabolism, suggesting the presence of an optimized central carbon metabolism. Pangenome analysis further revealed the differences between the gene cluster distribution patterns among the eight strains, suggesting significant functional variation. Moreover, a total of 47 biosynthetic gene clusters were discovered, which were further classified into 37 gene cluster families that showed low similarity with previously documented clusters. Furthermore, metatranscriptomic analysis revealed the expressions of key functional genes involved in the biosynthesis of ribosomal peptides in in situ marine biofilms. Overall, this study sheds new light on the metabolic features, adaptive strategies, and value of genome mining in this group of biofilm-associated Sulfitobacter bacteria.\n\nGenomic Analysis of Novel Sulfitobacter Bacterial Strains Isolated from Marine Biofilms.", "token_count": 404, "char_count": 1705, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6547, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:32.590502", "source": { "split": "train_shard_00001", "doc_id": 1144 }, "chunk_id": "train_shard_00001_1144_0", "global_id": 7273 }, { "text": "Members of Phytobacter , a recently described genus within the family Enterobacteriaceae, are still frequently misclassified as species of other genera. Here, we present genomic evidence that the taxa “Citrobacter bitternis” and “Kluyvera intestini” , as cited in the literature and listed in NCBI databases, are heterotypic synonyms of Phytobacter diazotrophicus . Comparative analyses of 16S rRNA gene phylogeny, core genome phylogeny, average nucleotide identity (ANI), and digital DNA–DNA hybridization (dDDH) consistently place the type strains of both “C. bitternis” and “K. intestini” within the species P. diazotrophicus . Recognizing these taxa as synonyms will help resolve persistent taxonomic inconsistencies and reduce misidentification in clinical and environmental microbiology.\n\n“Citrobacter bitternis” Ko et al., 2015 and “Kluyvera intestini” Tetz and Tetz, 2016 are heterotypic synonyms of Phytobacter diazotrophicus Zhang et al., 2017", "token_count": 306, "char_count": 974, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7176, "quality_score": 0.8588, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:33.156315", "source": { "split": "train_shard_00001", "doc_id": 1145 }, "chunk_id": "train_shard_00001_1145_0", "global_id": 7274 }, { "text": "The disease erysipelas caused by Erysipelothrix rhusiopathiae (ER) is a major concern in pig production. In the present study the genomes of ER from pigs (n=87), wild boars (n=71) and other sources (n=85) were compared in terms of whole-genome SNP variation, accessory genome content and the presence of genetic antibiotic resistance determinants. The aim was to investigate if genetic features among ER were associated with isolate origin in order to better estimate the risk of transmission of porcine-adapted strains from wild boars to free-range pigs and to increase our understanding of the evolution of ER. Pigs and wild boars carried isolates representing all ER clades, but clade one only occurred in healthy wild boars and healthy pigs. Several accessory genes or gene variants were found to be significantly associated with the pig and wild boar hosts, with genes predicted to encode cell wall-associated or extracellular proteins overrepresented. Gene variants associated with serovar determination and capsule production in serovars known to be pathogenic for pigs were found to be significantly associated with pigs as hosts. In total, 30 % of investigated pig isolates but only 6 % of wild boar isolates carried resistance genes, most commonly tetM (tetracycline) and lsa(E) together with lnu(B) (lincosamides, pleuromutilin and streptogramin A). The incidence of variably present genes including resistance determinants was weakly linked to phylogeny, indicating that host adaptation in ER has evolved multiple times in diverse lineages mediated by recombination and the acquisition of mobile genetic elements. The presented results support the occurrence of host-adapted ER strains, but they do not indicate frequent transmission between wild boars and domestic pigs. This article contains data hosted by Microreact.", "token_count": 470, "char_count": 1881, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6022, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:33.801907", "source": { "split": "train_shard_00001", "doc_id": 1146 }, "chunk_id": "train_shard_00001_1146_0", "global_id": 7275 }, { "text": "Comparative genome analysis of Erysipelothrix rhusiopathiae isolated from domestic pigs and wild boars suggests host adaptation and selective pressure from the use of antibiotics.", "token_count": 48, "char_count": 186, "word_count": 24, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:34.159354", "source": { "split": "train_shard_00001", "doc_id": 1146 }, "chunk_id": "train_shard_00001_1146_1", "global_id": 7276 }, { "text": "One of the fascinating outcomes of human microbiome studies adopting multi-omics technology is its ability to decipher millions of microbial encoded functions in the most complex and crowded microbial ecosystem, including the human gastrointestinal (GI) tract without cultivating the microbes. It is well established that several functions that modulate the human metabolism, nutrient assimilation, immunity, infections, disease severity and therapeutic efficacy of drugs are mostly of microbial origins. In addition, these microbial functions are dynamic and can disseminate between microbial taxa residing in the same ecosystem or other microbial ecosystems through horizontal gene transfer. For clinicians and researchers alike, understanding the toxins, virulence factors and drug resistance traits encoded by the microbes associated with the human body is of utmost importance. Nevertheless, when such traits are genetically linked with mobile genetic elements (MGEs) that make them transmissible, it creates an additional burden to public health. This review mainly focuses on the functions of gut commensals and the dynamics and crosstalk between commensal and pathogenic bacteria in the gut. Also, the review summarises the plethora of MGEs linked with virulence genes present in the genomes of various enteric bacterial pathogens, which are transmissible among other pathogens and commensals.\n\nToxin-linked mobile genetic elements in major enteric bacterial pathogens.", "token_count": 324, "char_count": 1477, "word_count": 206, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:34.729019", "source": { "split": "train_shard_00001", "doc_id": 1147 }, "chunk_id": "train_shard_00001_1147_0", "global_id": 7277 }, { "text": "Thermotolerant yeast strains were isolated from nuruk, a traditional Korean fermentation starter in which variety of microorganisms are present. Among the isolates, the MBY1358 identified as yeast Pichia kudriavzevii showed significantly higher growth rate (0.59 ± 0.00 1/h) at 44 °C than other strains. Maximum ethanol concentration of 8.35 ± 0.03 g/L was obtained from 20 g/L glucose with yield of 0.44 ± 0.01 g/g at 44 °C, which is 1.14 times ethanol production of the control strain of P. kudriavzevii. The MBY1358, which was significantly more thermotolerant than the control strain and fermented 200 g/L glucose to 107.33 ± 5.03 g/L ethanol at 44 °C, was deposited to Korean Collection for Type Cultures (KCTC) under the accession number 27654.\n\nIsolation of thermotolerant yeast Pichia kudriavzevii from nuruk.", "token_count": 330, "char_count": 852, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6719, "quality_score": 0.8359, "entities": { "genes": [ "MBY1358" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:35.302080", "source": { "split": "train_shard_00001", "doc_id": 1148 }, "chunk_id": "train_shard_00001_1148_0", "global_id": 7278 }, { "text": "At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined “species”, whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species‐level niche adaptation among others) and accessory regions (present only in some, and responsible for intra‐species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome‐assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non‐redundant, preserve gene ordering and contain both coding and non‐coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra‐species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.\n\nExploring environmental intra‐species diversity through non‐redundant pangenome assemblies", "token_count": 400, "char_count": 1875, "word_count": 257, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:35.920173", "source": { "split": "train_shard_00001", "doc_id": 1149 }, "chunk_id": "train_shard_00001_1149_0", "global_id": 7279 }, { "text": "Salmonella enterica is a pathogenic bacterium known for causing severe typhoid fever in humans, making it important to study due to its potential health risks and significant impact on public health. This study provides evolutionary classification of proteins from Salmonella enterica pangenome. We classified 17,238 domains from 13,147 proteins from 79,758 Salmonella enterica strains and studied in detail domains of 272 proteins from fourteen characterized Salmonella pathogenicity islands (SPIs). Among SPIs-related proteins, 90 proteins function in the secretion machinery. 41% domains of SPI proteins have no previous sequence annotation. By comparing clinical and environmental isolates, we identified 3682 proteins that are overrepresented in clinical group that we consider as potentially pathogenic. 69 of them overlap with SPI proteins. Among domains of potentially pathogenic proteins only 50% domains were annotated by sequence methods previously. Moreover, 36% (1330 out of 3682) of potentially pathogenic proteins cannot be classified into Evolutionary Classification of Protein Domains database (ECOD). Among classified domains of potentially pathogenic proteins the most populated homology groups include helix-turn-helix (HTH), Immunoglobulin-related, and P-loop domains-related. Functional analysis revealed overrepresentation of these protein in biological processes related to viral entry into host cell, antibiotic biosynthesis, DNA metabolism and conformation change, and underrepresentation in translational processes. Analysis of the potentially pathogenic proteins indicates that they form 119 clusters (islands) within the Salmonella genome, suggesting their potential contribution to the bacterium’s virulence. Overall, our analysis revealed that identified potentially pathogenic proteins are poorly studied. ECOD hierarchy of classified Salmonella enterica domains is available online: http://prodata.swmed.edu/ecod/index_salm.php

Author Summary

Salmonella enterica is a dangerous bacterium known for causing severe typhoid fever in humans, posing significant health risks", "token_count": 500, "char_count": 2111, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:36.575177", "source": { "split": "train_shard_00001", "doc_id": 1150 }, "chunk_id": "train_shard_00001_1150_0", "global_id": 7280 }, { "text": "Our study focuses on understanding the proteins of this bacterium’s genetic composition, unraveling their evolutionary classification. Analyzing a vast collection of strains, we identified and classified over 17,000 protein domains, with special focus on 272 proteins within Salmonella pathogenicity islands (SPIs). By comparing strains from clinical and environmental sources, we pinpointed 3,682 proteins overrepresented in clinical samples, signifying potential pathogenicity. Surprisingly, half of these proteins’ domains were not identified previously using sequence-based approaches. Our analysis identified these proteins forming 119 clusters within the Salmonella genome, suggesting their involvement in its virulence. Our study underscores the insufficient understanding of these potentially pathogenic proteins, highlighting the need for further investigation into their roles and implications in Salmonella -related illnesses.\n\nStructure classification of the proteins fromSalmonella entericapangenome revealed novel potential pathogenicity islands", "token_count": 230, "char_count": 1066, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7287, "quality_score": 0.8643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:37.036693", "source": { "split": "train_shard_00001", "doc_id": 1150 }, "chunk_id": "train_shard_00001_1150_1", "global_id": 7281 }, { "text": "Sellimonas intestinalis is a Gram-positive and anaerobic bacterial species previously considered as uncultivable. Although little is known about this Lachnospiraceae family member, its increased abundance has been reported in patients who have recovered from intestinal homeostasis after dysbiosis events. In this context, the aim of the present study was to take advantage of a massive in vitro culture protocol that allowed the recovery of extremely oxygen-sensitive species from faecal samples, which led to isolation of S. intestinalis. Whole genome analyses of 11 S. intestinalis genomes revealed that this species has a highly conserved genome with 99.7 % 16S rRNA gene sequence similarity, average nucleotide polymorphism results >95, and 50.1 % of its coding potential being part of the core genome. Despite this, the variable portion of its genome was informative enough to reveal the existence of three lineages (lineage-I including isolates from Chile and France, lineage-II from South Korea and Finland, and lineage-III from China and one isolate from the USA) and evidence of some recombination signals. The identification of a cluster of orthologous groups revealed a high number of genes involved in metabolism, including amino acid and carbohydrate transport as well as energy production and conversion, which matches with the metabolic profile previously reported for microbiota from healthy individuals. Additionally, virulence factors and antimicrobial resistance genes were found (mainly in lineage-III), which could favour their survival during antibiotic-induced dysbiosis. These findings provide the basis of knowledge about the potential of S. intestinalis as a bioindicator of intestinal homeostasis recovery and contribute to advancing the characterization of gut microbiota members with beneficial potential.\n\nComprehensive genome analyses of Sellimonas intestinalis, a potential biomarker of homeostasis gut recovery.", "token_count": 508, "char_count": 2001, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:38.043389", "source": { "split": "train_shard_00001", "doc_id": 1151 }, "chunk_id": "train_shard_00001_1151_0", "global_id": 7282 }, { "text": "Cefotaxime-resistant Haemophilus influenzae (CRHI) are a global concern, but little is known about their molecular epidemiology. The goal of this study was to perform genomic profiling of 191 CRHI from Norway (n = 183) or Sweden (n = 8) (2006-2018) and assess clonal spread using core genome multilocus sequence typing (cgMLST)-based Life Identification Number (LIN) codes based on whole genome sequencing (Ion Torrent). Cefotaxime resistance was confirmed with broth microdilution minimal inhibitory concentration (MIC), interpreted with the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. 35.7% of isolates with cefotaxime gradient MIC of 0.25 mg/L were falsely resistant. All but two isolates (blood) were non-invasive, and all but two (serotype f) were non-typeable. Characterization included calling of resistance determinants, ftsI typing (penicillin-binding protein 3, PBP3), and classification of PBP3-mediated beta-lactam resistance (rPBP3), with assignment to rPBP3 stage and group. All isolates had rPBP3-defining substitutions, and 78.5% were stage 3 (L389F positive). Beta-lactam MICs correlated well with rPBP3 genotypes. Significant proportions of stage 3 isolates were cross-resistant to ceftriaxone (86.0%) and meropenem (meningitis breakpoints, 26.0%). The CRHI prevalence in Norway doubled during the study period and approached 1%. A shift from stage 2 to stage 3 rPBP3 in 2011-2012 led to emergence of CRHI with higher beta-lactam MICs and co-resistance to multiple non-beta-lactams, including extensively drug-resistant (XDR) strains", "token_count": 509, "char_count": 1616, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6959, "quality_score": 0.8479, "entities": { "genes": [ "PBP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:38.701001", "source": { "split": "train_shard_00001", "doc_id": 1152 }, "chunk_id": "train_shard_00001_1152_0", "global_id": 7283 }, { "text": "The shift was driven by transformation with two distinct variants of the transpeptidase region and multiclonal expansion. 66.0% of the isolates belonged to 27 clusters. Ten clusters or singletons belonged to international CRHI clones represented in the PubMLST database. The study provides new insight into CRHI evolution, resistance profiles, and clonal dynamics in a period when this phenotype went from exceptional to unusual in Europe. International CRHI clones are described for the first time, including eight high-risk clones associated with invasive disease, calling for enhanced genomic surveillance. LIN coding, supplemented with ftsI typing and rPBP3 staging, is well-suited for definition of CRHI clones. LIN9, defined by ≤ 10 allelic differences, offered the highest resolution level fully supported by maximum likelihood core genome phylogeny and is proposed as a global standard for genomic surveillance of H. influenzae.\n\nGenomic profiling of cefotaxime-resistant <i>Haemophilus influenzae</i> from Norway and Sweden reveals extensive expansion of virulent multidrug-resistant international clones.", "token_count": 278, "char_count": 1140, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7403, "quality_score": 0.8701, "entities": { "genes": [ "LIN9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:39.254595", "source": { "split": "train_shard_00001", "doc_id": 1152 }, "chunk_id": "train_shard_00001_1152_1", "global_id": 7284 }, { "text": "

Objective

Whole genome sequencing (WGS) is increasingly being used to guide infection prevention and control measures. However, the value of regional prospective WGS surveillance for vancomycin-resistant Enterococcus faecium (VREfm) remains uncertain. The objective of this study is to investigate the value of routine centralised multicentre WGS in regional outbreak detection and analysis of transmission of VREfm within and between healthcare facilities.

Methods

VREfm isolates identified from patient samples in five different hospitals in the Netherlands during a one-year period were whole genome sequenced and typed using core genome multilocus sequence typing (cgMLST). Sequence data were correlated with admission data of the year prior to the first positive VREfm culture of the respective patients. By combining epidemiological and sequence data within and between hospital transmission events were identified.

Results

57 VREfm isolates were detected during the study period. 38/57 (66.7%) isolates clustered with at least one other isolate. Based on our definitions, intrahospital transmission could be demonstrated in 37 of 38 cases and interhospital transmission in 3 of 38 cases. Using this approach, a multicenter outbreak and two local outbreaks were detected.

Conclusions

Routine whole genome sequencing of VRE is a powerful tool for detecting, tracing and delineating outbreaks. When integrated into a centralised surveillance system spanning collaborative healthcare networks, it becomes an essential tool for unravelling the complex transmission dynamics of VRE within and between hospitals, ultimately strengthening infection control strategies.\n\nSurveillance of interhospital VRE transmission using routine centralised, multicentre whole genome sequencing", "token_count": 408, "char_count": 1818, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:39.877210", "source": { "split": "train_shard_00001", "doc_id": 1153 }, "chunk_id": "train_shard_00001_1153_0", "global_id": 7285 }, { "text": "Human Pangenome Reference Consortium (HPRC) and Chinese Pangenome Consortium (CPC) have pronounced the finish of the pilot work of the Human Pangenome Project, which aimed to build worldwide population-representative high-quality haplotype-resolved reference graph genomes. Graph-based gapless pangenome reference genomes with enriched genomic diversity and higher completeness and contiguity possessed the potential for a new beginning for third-generation sequencing (TGS)-based genomic research and high-performance mapping rate and variant genotyping for traditional short-read sequencing platforms. With the new pangenome reference coordinates and corresponding computation algorithms and methods, forensic integrative genomics fields will benefit in new-marker identification, highly-accurate marker genotyping, high-resolution panel development and corresponding statistical algorithm updates. Here, we discussed the past advances and new challenges of pangenome-based genomic research and their integrative genomics applications for variant identification and new forensic genomic, epigenetic, transcriptomic, and microbiome practices. We highlighted the necessity and importance of including the forensic TGS-based platforms, pangenome-based entire landscape of genomic diversity, pangenome-based study design and graph-based pangenome reference in short-read NGS mapping and TGS-based innovations to achieve forensic precision medicine.\n\nPerspective and Opportunity for forensic integrative genomics in the Human Pangenome Reference sequence era", "token_count": 331, "char_count": 1555, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6022, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:40.441906", "source": { "split": "train_shard_00001", "doc_id": 1154 }, "chunk_id": "train_shard_00001_1154_0", "global_id": 7286 }, { "text": "

Background

High-temperature fermentation technology with thermotolerant microbes has been expected to reduce the cost of bioconversion of cellulosic biomass to fuels or chemicals. Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. These capabilities have been found to exceed those of the traditional ethanol producer Saccharomyces cerevisiae or lignocellulose-bioconvertible ethanologenic Scheffersomyces stipitis.

Results

The complete genome sequence of K. marxianus DMKU 3-1042 as one of the most thermotolerant strains in the same species has been determined. A comparison of its genomic information with those of other yeasts and transcriptome analysis revealed that the yeast bears beneficial properties of temperature resistance, wide-range bioconversion ability, and production of recombinant proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature, and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30°C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions.

Conclusions

This study reveals many gene resources for the ability to assimilate various sugars in addition to species-specific genes in K. marxianus, and the molecular basis of its attractive traits for industrial applications including high-temperature fermentation. Especially, the thermotolerance trait may be achieved by an integrated mechanism consisting of various strategies. Gene resources and transcriptome data of the yeast are particularly useful for fundamental and applied researches for innovative applications.\n\nGenetic basis of the highly efficient yeast Kluyveromyces marxianus: complete genome sequence and transcriptome analyses.", "token_count": 456, "char_count": 1999, "word_count": 255, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:41.084996", "source": { "split": "train_shard_00001", "doc_id": 1155 }, "chunk_id": "train_shard_00001_1155_0", "global_id": 7287 }, { "text": "

Introduction

In Eragrostis curvula, commonly known as weeping lovegrass, a synthetic diploidization event of the facultative apomictic tetraploid Tanganyika INTA cv. originated from the sexual diploid Victoria cv. Apomixis is an asexual reproduction by seeds in which the progeny is genetically identical to the maternal plant.

Methods

To assess the genomic changes related to ploidy and to the reproductive mode occurring during diploidization, a mapping approach was followed to obtain the first E. curvula pangenome assembly. In this way, gDNA of Tanganyika INTA was extracted and sequenced in 2x250 Illumina pair-end reads and mapped against the Victoria genome assembly. The unmapped reads were used for variant calling, while the mapped reads were assembled using Masurca software.

Results

The length of the assembly was 28,982,419 bp distributed in 18,032 contigs, and the variable genes annotated in these contigs rendered 3,952 gene models. Functional annotation of the genes showed that the reproductive pathway was differentially enriched. PCR amplification in gDNA and cDNA of Tanganyika INTA and Victoria was conducted to validate the presence/absence variation in five genes related to reproduction and ploidy. The polyploid nature of the Tanganyika INTA genome was also evaluated through the variant calling analysis showing the single nucleotide polymorphism (SNP) coverage and allele frequency distribution with a segmental allotetraploid pairing behavior.

Discussion

The results presented here suggest that the genes were lost in Tanganyika INTA during the diploidization process that was conducted to suppress the apomictic pathway, affecting severely the fertility of Victoria cv.\n\nFrom tetraploid to diploid, a pangenomic approach to identify genes lost during synthetic diploidization of Eragrostis curvula.", "token_count": 500, "char_count": 1879, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5938, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:41.766723", "source": { "split": "train_shard_00001", "doc_id": 1156 }, "chunk_id": "train_shard_00001_1156_0", "global_id": 7288 }, { "text": "

Background

The increasing availability of microbial genomes and environmental shotgun metagenomes provides unprecedented access to the genomic differences within related bacteria. The human oral microbiome with its diverse habitats and abundant, relatively well-characterized microbial inhabitants presents an opportunity to investigate bacterial population structures at an ecosystem scale.

Results

Here, we employ a metapangenomic approach that combines public genomes with Human Microbiome Project (HMP) metagenomes to study the diversity of microbial residents of three oral habitats: tongue dorsum, buccal mucosa, and supragingival plaque. For two exemplar taxa, Haemophilus parainfluenzae and the genus Rothia, metapangenomes reveal distinct genomic groups based on shared genome content. H. parainfluenzae genomes separate into three distinct subgroups with differential abundance between oral habitats. Functional enrichment analyses identify an operon encoding oxaloacetate decarboxylase as diagnostic for the tongue-abundant subgroup. For the genus Rothia, grouping by shared genome content recapitulates species-level taxonomy and habitat preferences. However, while most R. mucilaginosa are restricted to the tongue as expected, two genomes represent a cryptic population of R. mucilaginosa in many buccal mucosa samples. For both H. parainfluenzae and the genus Rothia, we identify not only limitations in the ability of cultivated organisms to represent populations in their native environment, but also specifically which cultivar gene sequences are absent or ubiquitous.

Conclusions

Our findings provide insights into population structure and biogeography in the mouth and form specific hypotheses about habitat adaptation. These results illustrate the power of combining metagenomes and pangenomes to investigate the ecology and evolution of bacteria across analytical scales.\n\nMetapangenomics of the oral microbiome provides insights into habitat adaptation and cultivar diversity.", "token_count": 458, "char_count": 2021, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:42.422908", "source": { "split": "train_shard_00001", "doc_id": 1157 }, "chunk_id": "train_shard_00001_1157_0", "global_id": 7289 }, { "text": "

Background

Structural variation contributes substantially to polymorphism within species. Chromosomal rearrangements that impact genes can lead to functional variation among individuals and influence the expression of phenotypic traits. Genomes of fungal pathogens show substantial chromosomal polymorphism that can drive virulence evolution on host plants. Assessing the adaptive significance of structural variation is challenging, because most studies rely on inferences based on a single reference genome sequence.

Results

We constructed and analyzed the pangenome of Zymoseptoria tritici, a major pathogen of wheat that evolved host specialization by chromosomal rearrangements and gene deletions. We used single-molecule real-time sequencing and high-density genetic maps to assemble multiple genomes. We annotated the gene space based on transcriptomics data that covered the infection life cycle of each strain. Based on a total of five telomere-to-telomere genomes, we constructed a pangenome for the species and identified a core set of 9149 genes. However, an additional 6600 genes were exclusive to a subset of the isolates. The substantial accessory genome encoded on average fewer expressed genes but a larger fraction of the candidate effector genes that may interact with the host during infection. We expanded our analyses of the pangenome to a worldwide collection of 123 isolates of the same species. We confirmed that accessory genes were indeed more likely to show deletion polymorphisms and loss-of-function mutations compared to core genes.

Conclusions

The pangenome construction of a highly polymorphic eukaryotic pathogen showed that a single reference genome significantly underestimates the gene space of a species. The substantial accessory genome provides a cradle for adaptive evolution.\n\nPangenome analyses of the wheat pathogen Zymoseptoria tritici reveal the structural basis of a highly plastic eukaryotic genome.", "token_count": 459, "char_count": 1969, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5704, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:43.110305", "source": { "split": "train_shard_00001", "doc_id": 1158 }, "chunk_id": "train_shard_00001_1158_0", "global_id": 7290 }, { "text": "Metagenomics has greatly expanded our understanding of the human gut microbiome by revealing a vast diversity of bacterial species within and across individuals. Even within a single species, different strains can have highly divergent gene content, affecting traits such as antibiotic resistance, metabolism, and virulence. Methods that harness metagenomic data to resolve strain-level differences in functional potential are crucial for understanding the causes and consequences of this intraspecific diversity. The enormous size of pangenome references, strain mixing within samples, and inconsistent sequencing depth present challenges for existing tools that analyze samples one at a time. To address this gap, we updated the MIDAS pangenome profiler, now released as version 3, and developed StrainPGC, an approach to strain-specific gene content estimation that combines strain tracking and correlations across multiple samples. We validate our integrated analysis using a complex synthetic community of strains from the human gut and find that StrainPGC outperforms existing approaches. Analyzing a large, publicly available metagenome collection from inflammatory bowel disease patients and healthy controls, we catalog the functional repertoires of thousands of strains across hundreds of species, capturing extensive diversity missing from reference databases. Finally, we apply StrainPGC to metagenomes from a clinical trial of fecal microbiota transplantation for the treatment of ulcerative colitis. We identify two Escherichia coli strains from two different donors that are both frequently transmitted to patients, but have notable differences in functional potential. StrainPGC and MIDAS v3 together enable precise, intraspecific pangenomic investigations using large collections of metagenomic data without microbial isolation or de novo assembly.\n\nAccurate estimation of intraspecific microbial gene content variation in metagenomic data with MIDAS v3 and StrainPGC", "token_count": 411, "char_count": 1984, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6519, "quality_score": 0.8259, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:43.736621", "source": { "split": "train_shard_00001", "doc_id": 1159 }, "chunk_id": "train_shard_00001_1159_0", "global_id": 7291 }, { "text": "The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.\n\nArcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness.", "token_count": 408, "char_count": 1993, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6236, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:44.360848", "source": { "split": "train_shard_00001", "doc_id": 1160 }, "chunk_id": "train_shard_00001_1160_0", "global_id": 7292 }, { "text": "

Objective

This study aimed to investigate the epidemiological characteristics and genomic evolutionary mechanisms of pks-positive Klebsiella pneumoniae (pks + KPN), providing theoretical insights for infection prevention and control strategies.

Methods

A total of 873 non-duplicate K. pneumoniae isolates collected between 2016 and 2022 at the Fifth Affiliated Hospital of Wenzhou Medical University were screened for pks + strains via PCR targeting clbA, clbB, clbN, and clbQ. Clonal structures of pks+ and pks- strains were determined by MLST and KL typing, and virulence gene profiles (peg344, iucA, rmpA, rmpA2, iroB) were analyzed to compare the two populations. Global distribution patterns of pks + KPN were analyzed using data from the Bacterial and Viral Bioinformatics Resource Center (BV-BRC). Pan-genomic analysis via the IPGA platform and a phylogenetic tree was constructed. Core-genome comparative analysis identified lineage-specific genes in dominant pks+ strains, and KEGG enrichment revealed their putative biological functions. Statistical analyses were performed using SPSS 26.0, with p < 0.05 considered statistically significant.

Results

Among 873 clinical isolates, 105 (12.03 %) were pks + KPN, predominantly isolated from infectious disease and surgical departments. The pks island prevalence was significantly higher in non-carbapenem-resistant strains (25.45 %) than in carbapenem-resistant strains (1.04 %) (χ2 = 125.57, p < 0.001)", "token_count": 498, "char_count": 1570, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7487, "quality_score": 0.8744, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:45.011121", "source": { "split": "train_shard_00001", "doc_id": 1161 }, "chunk_id": "train_shard_00001_1161_0", "global_id": 7293 }, { "text": "pks + strains exhibited higher virulence gene carriage rates (p < 0.05) and infected younger patients (57.97 ± 14.90 vs. 64.18 ± 17.29 years, t = 3.46, p = 0.001). pks + isolates showed a conserved clonal structure dominated by ST23-KL1 (66.7 %), while pks- strains displayed greater heterogeneity with 37 distinct ST-KL types. Analysis of 706 global pks + KPN revealed that ST23 (45.18 %), ST11 (15.72 %), and ST258 (15.16 %) are the predominant clonal lineages. Phylogenetic construction delineated five evolutionarily distinct clades among pks+ strains. Comparative core genome analysis identified 245 lineage-associated genes, of which 96 were shared among dominant strains. Functional enrichment (KEGG) demonstrated that these conserved genes are significantly enriched in the galactose metabolism.

Conclusion

This study systematically elucidates the clinical epidemiology, clonal dissemination patterns, and genomic evolution of pks + KPN, identifying ST23-KL1 as the dominant clone. The findings reveal that galactose metabolism may enhance the adaptability of dominant strains, thereby driving their global spread.\n\nEvolution and epidemiology of pks<sup>+</sup>Klebsiella pneumoniae: Global and local insights.", "token_count": 437, "char_count": 1303, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7574, "quality_score": 0.8787, "entities": { "genes": [ "ST23", "KL1", "ST11", "ST258" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:45.638642", "source": { "split": "train_shard_00001", "doc_id": 1161 }, "chunk_id": "train_shard_00001_1161_1", "global_id": 7294 }, { "text": "Streptococcus pyogenes, also known as group A Streptococcus (GAS), is a Gram-positive bacterial pathogen responsible for approximately 500,000 deaths globally per year. Therefore, surveillance of invasive GAS infections is of critical importance in understanding societal transmission. In this study, we propose an optical DNA mapping (ODM)-based assay for strain-level typing of S. pyogenes. Fluorescently labeled DNA molecules of lengths >150 kbp are stretched in nanochannels and imaged to reveal genomic information. A core genome alignment-based typing scheme is then utilized for identification at the strain level. Although our technique lacks the nucleotide-level resolution of whole-genome sequencing, it excels at detecting patterns across long stretches of DNA that remain inaccessible to short-read sequencing methods. Using clinical isolates, we demonstrate that the ODM assay can identify S. pyogenes at both the species level and at even higher taxonomic resolutions with high accuracy. Our typing scheme also shows a high correlation with standard emm subtyping for the analyzed samples. We conclude that ODM has the potential to deliver timely and cost-efficient strain-level bacterial identification.\n\nStrain-Level Typing of <i>Streptococcus pyogenes</i> Using Optical DNA Mapping.", "token_count": 346, "char_count": 1346, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:46.223398", "source": { "split": "train_shard_00001", "doc_id": 1162 }, "chunk_id": "train_shard_00001_1162_0", "global_id": 7295 }, { "text": "\"Candidatus Accumulibacter\" is a unique and pivotal genus of polyphosphate-accumulating organisms prevalent in wastewater treatment plants and plays mainstay roles in the global phosphorus cycle. However, the efforts to fully understand their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods. Here, we reported an integrated approach combining pangenome analysis, protein structure prediction and clustering, and meta-omic characterization, to uncover genetic and metabolic traits previously unexplored for Ca. Accumulibacter. The identification of a previously overlooked pyrophosphate-fructose 6-phosphate 1-phosphotransferase gene (pfp) suggested that all Ca. Accumulibacter encoded a complete Embden-Meyerhof-Parnas pathway. A homologue of the phosphate-specific transport system accessory protein (PhoU) was suggested to be an inorganic phosphate transport (Pit) accessory protein (Pap) conferring effective and efficient phosphate transport. Additional lineage members were found to encode complete denitrification pathways. A pipeline was built, generating a pan-Ca. Accumulibacter annotation reference database, covering >200,000 proteins and their encoding genes. Benchmarking on 27 Ca. Accumulibacter genomes showed major improvement in the average annotation coverage from 51% to 82%. This pipeline is readily applicable to diverse cultured and uncultured bacteria to establish high-coverage annotation reference databases, facilitating the exploration of genomic dark matter in the bacterial domain.\n\nFrom Gene to Structure: Unraveling Genomic Dark Matter in Ca. Accumulibacter.", "token_count": 444, "char_count": 1716, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6938, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:46.855920", "source": { "split": "train_shard_00001", "doc_id": 1163 }, "chunk_id": "train_shard_00001_1163_0", "global_id": 7296 }, { "text": "

Background

Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Advances in whole genome sequencing technologies have led to a vast expansion in the amount of bacterial genomes deposited in public databases. There is a pressing need for software solutions which are able to cluster, catalogue and characterise genes, or other features, in increasingly large genomic datasets.

Results

Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement and Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino acid or nucleotide identity thresholds and uses the clustering information to rapidly identify paralogous gene families and putative fission/fusion events. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation, and estimates sequence divergence for each gene family.

Conclusions

We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.\n\nPIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria.", "token_count": 374, "char_count": 1692, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:47.439559", "source": { "split": "train_shard_00001", "doc_id": 1164 }, "chunk_id": "train_shard_00001_1164_0", "global_id": 7297 }, { "text": "Pangenomes are becoming a powerful framework to perform many bioinformatics analyses taking into account the genetic variability of a population, thus reducing the bias introduced by a single reference genome. With the wider diffusion of pangenomes, integrating genetic variability with transcriptome diversity is becoming a natural extension that demands specific methods for its exploration. In this work, we extend the notion of spliced pangenomes to that of annotated spliced pangenomes ; this allows us to introduce a formal definition of Alternative Splicing (AS) events on a graph structure. To investigate the usage of graph pangenomes for the quantification of AS events across conditions, we developed pantas , the first pangenomic method for the detection and differential analysis of AS events from short RNA-Seq reads. A comparison with state-of-the-art linear reference-based approaches proves that pantas achieves competitive accuracy, making spliced pangenomes effective for conducting AS events quantification and opening future directions for the analysis of population-based transcriptomes. pantas is open-source and freely available at github.com/algolab/pantas .

Author summary

The ever increasing availability of complete genomes is advancing our comprehension of many biological mechanisms and is enhancing the knowledge we can extract from sequencing data. Pange3PM ESTnome graphs are a convenient way to represent multiple genomes and the genetic variability within a population. Integrating genetic variability with transcriptome diversity can improve our understanding of alternative splicing, a regulation mechanism which allows a single gene to code for multiple proteins. However, many unanswered questions are limiting our comprehension of the relationship between genetic and trancriptomic variations. With this work, we start to fill this gap by introducing pantas , the first approach based on pangenome graphs for the detection and differential quantification of alternative splicing events. A comparison with state-of-the-art approaches based on linear genome prove that pangenome graphs can be effectively used to perform such an analysis. By integrating genetic and transcriptome variability in a single structure, pantas can pave the way to next generation bioinformatic approaches for the accurate analysis of the relations between genetic variations and alternative splicing aberrations.", "token_count": 494, "char_count": 2437, "word_count": 339, "semantic_coherence": 1, "information_density": 0.5221, "quality_score": 0.7611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:48.086038", "source": { "split": "train_shard_00001", "doc_id": 1165 }, "chunk_id": "train_shard_00001_1165_0", "global_id": 7298 }, { "text": "Differential quantification of alternative splicing events on spliced pangenome graphs", "token_count": 19, "char_count": 86, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:48.438375", "source": { "split": "train_shard_00001", "doc_id": 1165 }, "chunk_id": "train_shard_00001_1165_1", "global_id": 7299 }, { "text": "Escherichia coli is frequently associated with mastitis in cattle. \"Pathogenic\" and \"commensal\" isolates appear to be genetically similar. With a few exceptions, no notable genotypic differences have been found between commensal and mastitis-associated E. coli. In this study, 24 E. coli strains were isolated from dairy cows with clinical mastitis in three geographic regions of Australia (North Queensland, South Queensland, and Victoria), sequenced, then genomically surveyed. There was no observed relationship between sequence type (ST) and region (p = 0.51). The most common Multi Locus Sequence Type was ST10 (38%), then ST4429 (13%). Pangenomic analysis revealed a soft-core genome of 3,463 genes, including genes associated with antibiotic resistance, chemotaxis, motility, adhesion, biofilm formation, and pili. A total of 36 different plasmids were identified and generally found to have local distributions (p = 0.02). Only 2 plasmids contained antibiotic resistance genes, a p1303_5-like plasmid encoding multidrug-resistance (trimethoprim, quaternary ammonium, beta-lactam, streptomycin, sulfonamide, and kanamycin) from two North Queensland isolates on the same farm, while three Victorian isolates from the same farm contained a pCFSAN004177P_01-like plasmid encoding tetracycline-resistance. This pattern is consistent with a local spread of antibiotic resistance through plasmids of bovine mastitis cases. Notably, co-occurrence of plasmids containing virulence factors/antibiotic resistance with putative mobilization was rare, though the multidrug resistant p1303_5-like plasmid was predicted to be conjugative and is of some concern. This survey has provided greater understanding of antibiotic resistance within E. coli-associated bovine mastitis which will allow greater prediction and improved decision making in disease management.", "token_count": 523, "char_count": 1898, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6653, "quality_score": 0.8327, "entities": { "genes": [ "ST4429", "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:49.744206", "source": { "split": "train_shard_00001", "doc_id": 1166 }, "chunk_id": "train_shard_00001_1166_0", "global_id": 7300 }, { "text": "Survey and Sequence Characterization of Bovine Mastitis-Associated Escherichia coli in Dairy Herds.", "token_count": 35, "char_count": 106, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:50.104564", "source": { "split": "train_shard_00001", "doc_id": 1166 }, "chunk_id": "train_shard_00001_1166_1", "global_id": 7301 }, { "text": "Strains across the Lactobacillaceae family form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly available Lactobacillaceae genomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in the Lactobacillaceae family and a collection of predictive computational metabolic models that enable a variety of practical uses.IMPORTANCELactobacillaceae, a bacterial family foundational to a trillion-dollar industry, is increasingly relevant to biosustainability initiatives. Our study, leveraging approximately 2,400 genome sequences, provides a pangenomic analysis of Lactobacillaceae metabolism, creating over 2,400 curated and validated genome-scale models (GEMs). These GEMs successfully predict (i) unique, species-specific metabolic reactions; (ii) niche-enriched reactions that increase organism fitness; (iii) essential media components, offering insights into the global amino acid essentiality of Lactobacillaceae; and (iv) fermentation capabilities across the family, shedding light on the metabolic basis of Lactobacillaceae-based commercial products. This quantitative understanding of Lactobacillaceae metabolic properties and their genomic basis will have profound implications for the food industry and biosustainability, offering new insights and tools for strain selection and manipulation.", "token_count": 486, "char_count": 1949, "word_count": 238, "semantic_coherence": 1, "information_density": 0.605, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:50.749547", "source": { "split": "train_shard_00001", "doc_id": 1167 }, "chunk_id": "train_shard_00001_1167_0", "global_id": 7302 }, { "text": "Pangenome reconstruction of Lactobacillaceae metabolism predicts species-specific metabolic traits.", "token_count": 30, "char_count": 106, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:51.101359", "source": { "split": "train_shard_00001", "doc_id": 1167 }, "chunk_id": "train_shard_00001_1167_1", "global_id": 7303 }, { "text": "Accurate genome assemblies are essential for biological research, but even the highest quality assemblies retain errors caused by the technologies used to construct them. Base-level errors are typically fixed with an additional polishing step that uses reads aligned to the draft assembly to identify necessary edits. However, current methods struggle to find a balance between over- and under-polishing. Here, we present an encoder-only transformer model for assembly polishing called DeepPolisher, which predicts corrections to the underlying sequence using Pacbio HiFi read alignments to a diploid assembly. Our pipeline introduces a method, PHARAOH (Phasing Reads in Areas Of Homozygosity), which uses ultra-long ONT data to ensure alignments are accurately phased and to correctly introduce heterozygous edits in falsely homozygous regions. We demonstrate that the DeepPolisher pipeline can reduce assembly errors by half, with a greater than 70% reduction in indel errors. We have applied our DeepPolisher-based pipeline to 180 assemblies from the next Human Pangenome Reference Consortium (HPRC) data release, producing an average predicted Quality Value (QV) improvement of 3.4 (54% error reduction) for the majority of the genome.\n\nHighly accurate assembly polishing with DeepPolisher", "token_count": 295, "char_count": 1293, "word_count": 184, "semantic_coherence": 1, "information_density": 0.7011, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:51.662156", "source": { "split": "train_shard_00001", "doc_id": 1168 }, "chunk_id": "train_shard_00001_1168_0", "global_id": 7304 }, { "text": "Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. Besides the well-known and tested lactic acid bacteria, yeasts may also be probiotics. The subject of probiotic and potentially probiotic yeasts has been developing and arising potential for new probiotic products with novel properties, which are not offered by bacteria-based probiotics available on the current market. The paper reviews the first probiotic yeast Saccharomyces cerevisiae var. boulardii, its characteristics, pro-healthy activities and application in functional food production. This species offers such abilities as improving digestion of certain food ingredients, antimicrobial activities and even therapeutic properties. Besides Saccharomyces cerevisiae var. boulardii, on this background, novel yeasts with potentially probiotic features are presented. They have been intensively investigated for the last decade and some species have been observed to possess probiotic characteristics and abilities. There are yeasts from the genera Debaryomyces, Hanseniaspora, Pichia, Meyerozyma, Torulaspora, etc. isolated from food and environmental habitats. These potentially probiotic yeasts can be used for production of various fermented foods, enhancing its nutritional and sensory properties. Because of the intensively developing research on probiotic yeasts in the coming years, we can expect many discoveries and possibly even evolution in the segment of probiotics available on the market.\n\nProbiotic and Potentially Probiotic Yeasts-Characteristics and Food Application.", "token_count": 402, "char_count": 1671, "word_count": 215, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:52.280553", "source": { "split": "train_shard_00001", "doc_id": 1169 }, "chunk_id": "train_shard_00001_1169_0", "global_id": 7305 }, { "text": "To exploit cellulosic materials for fuel ethanol production, a microorganism capable of high temperature and simultaneous saccharification-fermentation has been required. However, a major drawback is the optimum temperature for the saccharification and fermentation. Most ethanol-fermenting microbes have an optimum temperature for ethanol fermentation ranging between 28 degrees C and 37 degrees C, while the activity of cellulolytic enzymes is highest at around 50 degrees C and significantly decreases with a decrease in temperature. Therefore, in the present study, a thermotolerant yeast, Kluyveromyces marxianus, which has high growth and fermentation at elevated temperatures, was used as a producer of ethanol from cellulose. The strain was genetically engineered to display Trichoderma reesei endoglucanase and Aspergillus aculeatus beta-glucosidase on the cell surface, which successfully converts a cellulosic beta-glucan to ethanol directly at 48 degrees C with a yield of 4.24 g/l from 10 g/l within 12 h. The yield (in grams of ethanol produced per gram of beta-glucan consumed) was 0.47 g/g, which corresponds to 92.2% of the theoretical yield. This indicates that high-temperature cellulose fermentation to ethanol can be efficiently accomplished using a recombinant K. marxianus strain displaying thermostable cellulolytic enzymes on the cell surface.\n\nDirect ethanol production from cellulosic materials at high temperature using the thermotolerant yeast Kluyveromyces marxianus displaying cellulolytic enzymes.", "token_count": 409, "char_count": 1529, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:52.900396", "source": { "split": "train_shard_00001", "doc_id": 1170 }, "chunk_id": "train_shard_00001_1170_0", "global_id": 7306 }, { "text": "The aim of this study was to evaluate the effect of the microencapsulation (by spray drying) of the whey-native probiotic yeast Kluyveromyces marxianus VM004 in matrices of whey protein concentrate (WPC) and water-soluble chitosan (WSCh) on the viability of the yeast during drying and storage and in simulated gastrointestinal conditions. The optimized outlet drying temperature was 68 °C. This temperature allowed obtaining an encapsulation efficiency of 91% for a suspension of 10% (w/v) WPC. Yeasts microencapsulated in WSCh showed a significantly improved tolerance to simulated gastrointestinal conditions in comparison to free yeasts and yeasts microencapsulated in WPC. Besides, the solids content showed a significant influence on the probiotic viability during storage, with a suspension with 30% (w/v) solids (29:1 WPC:WSCh) showing 95% of viability after passing through gastrointestinal conditions. The results allow expanding the development of mixtures of encapsulating materials to improve the probiotic aptitude of a food ingredient powder.\n\nEffect of microencapsulation in whey protein and water-soluble chitosan derivative on the viability of the probiotic Kluyveromyces marxianus VM004 during storage and in simulated gastrointestinal conditions", "token_count": 332, "char_count": 1265, "word_count": 176, "semantic_coherence": 1, "information_density": 0.5227, "quality_score": 0.7614, "entities": { "genes": [ "VM004" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:53.501137", "source": { "split": "train_shard_00001", "doc_id": 1171 }, "chunk_id": "train_shard_00001_1171_0", "global_id": 7307 }, { "text": "Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.\n\nGenomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota.", "token_count": 333, "char_count": 1248, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [ "PRL2012" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:54.101809", "source": { "split": "train_shard_00001", "doc_id": 1172 }, "chunk_id": "train_shard_00001_1172_0", "global_id": 7308 }, { "text": "Salmonella enterica remains one of the leading causes of foodborne bacterial disease. Retail meat is a major source of human salmonellosis. However, comparative genomic analyses of S. enterica isolates from retail meat from different sources in China are lacking. A total of 341 S. enterica strains were isolated from retail meat in sixteen districts of Beijing, China, at three different time points (January 1st, May 1st, and October 1st) in 2017. Comparative genomics was performed to investigate the genetic diversity, virulence and antimicrobial resistance gene (ARG) profiles of these isolates. The most common serotype was S. Enteritidis (203/341, 59.5%), which dominated among isolates from three different time points during the year. Laboratory retesting confirmed the accuracy of the serotyping results predicted by the Salmonella In Silico Typing Resource (SISTR) (96.5%). The pangenome of the 341 S. enterica isolates contained 13,931 genes, and the core genome contained 3,635 genes. Higher Salmonella phage 118970 sal3 (219/341, 64.2%) and Gifsy-2 (206/341, 60.4%) prevalence contributed to the diversity of the accessory genes, especially those with unknown functions. IncFII(S), IncX1, and IncFIB(S) plasmid replicons were more common in these isolates and were major sources of horizontally acquired foreign genes. The virulence gene profile showed fewer virulence genes associated with type III secretion systems in certain isolates from chicken. A total of 88 different ARGs were found in the 341 isolates", "token_count": 470, "char_count": 1581, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6267, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:54.789938", "source": { "split": "train_shard_00001", "doc_id": 1173 }, "chunk_id": "train_shard_00001_1173_0", "global_id": 7309 }, { "text": "Three beta-lactamases, namely, bla CTX - M - 55 (n = 15), bla CTX - M - 14 (n = 11), and bla CTX - M - 65 (n = 11), were more prevalent in retail meats. The emergence of qnrE1 and bla CTX - M - 123 indicated a potential increase in the prevalence of retail meats. After the prohibition of colistin in China, three and four isolates were positive for the colistin resistance genes mcr-1.1 and mcr-9, respectively. Thus, we explored the evolution and genomic features of S. enterica isolates from retail meats in Beijing, China. The diverse ARGs of these isolates compromise food security and are a clinical threat.\n\nGenomic Characterization of Salmonella enterica Isolates From Retail Meat in Beijing, China.", "token_count": 427, "char_count": 1067, "word_count": 124, "semantic_coherence": 1, "information_density": 0.5645, "quality_score": 0.7823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:55.438168", "source": { "split": "train_shard_00001", "doc_id": 1173 }, "chunk_id": "train_shard_00001_1173_1", "global_id": 7310 }, { "text": "

Background:

and aims: We have previously demonstrated an association between increased abundance of Phascolarctobacterium and colorectal cancer (CRC) and adenomas in two independent Norwegian cohorts. Here we seek to verify our previous findings using new cohorts and methods. In addition, we characterize lifestyle and sex-specificity, the functional potential of the Phascolarctobacterium species and their interaction with other microbial species.

Methods:

We analyze Phascolarctobacterium with 16S rRNA sequencing, shotgun metagenome sequencing and species-specific qPCR, using 2350 samples from three Norwegian cohorts - CRCAhus, NORCCAP and CRCbiome - and a large publicly available dataset, Curatedmetagenomedata. Using metagenome assembled genomes from the CRCbiome study we explore genomic characteristics and functional potential of the Phascolarctobacterium pangenome.

Results:

Three species of Phascolarctobacterium associated with adenoma/CRC were consistently detected by qPCR and sequencing. Positive associations with adenomas/CRC were verified for P. succinatutens and negative associations were shown for P. faecium and adenoma in Curatedmetagenomedata. Men show higher prevalence of P. succinatutens across cohorts. Co-occurrence among Phascolarctobacterium species was low (<6%). Each of the three species show distinct microbial composition and form distinct correlation networks with other bacterial taxa, although Dialister invisus was negatively correlated to all investigated Phascolarctobacterium species. Pangenome analyses showed P. succinatutens to be enriched for genes related to porphyrin metabolism and degradation of complex carbohydrates, whereas glycoside hydrolase enzyme 3 was specific to P. faecium.

Conclusion:

We have verified that P. succinatutens is increased in adenoma and CRC and this species should therefore be recognised among the most important CRC-associated bacteria.", "token_count": 508, "char_count": 1956, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6265, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:56.094653", "source": { "split": "train_shard_00001", "doc_id": 1174 }, "chunk_id": "train_shard_00001_1174_0", "global_id": 7311 }, { "text": "Species-level verification of Phascolarctobacterium association to colorectal cancer", "token_count": 21, "char_count": 84, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:56.446754", "source": { "split": "train_shard_00001", "doc_id": 1174 }, "chunk_id": "train_shard_00001_1174_1", "global_id": 7312 }, { "text": "

Background

Members of the Bacillus pumilus group (abbreviated as the Bp group) are quite diverse and ubiquitous in marine environments, but little is known about correlation with their terrestrial counterparts. In this study, 16 marine strains that we had isolated before were sequenced and comparative genome analyses were performed with a total of 52 Bp group strains. The analyses included 20 marine isolates (which included the 16 new strains) and 32 terrestrial isolates, and their evolutionary relationships, differentiation, and environmental adaptation.

Results

Phylogenomic analysis revealed that the marine Bp group strains were grouped into three species: B. pumilus, B. altitudinis and B. safensis. All the three share a common ancestor. However, members of B. altitudinis were observed to cluster independently, separating from the other two, thus diverging from the others. Consistent with the universal nature of genes involved in the functioning of the translational machinery, the genes related to translation were enriched in the core genome. Functional genomic analyses revealed that the marine-derived and the terrestrial strains showed differences in certain hypothetical proteins, transcriptional regulators, K+ transporter (TrK) and ABC transporters. However, species differences showed the precedence of environmental adaptation discrepancies. In each species, land specific genes were found with possible functions that likely facilitate survival in diverse terrestrial niches, while marine bacteria were enriched with genes of unknown functions and those related to transcription, phage defense, DNA recombination and repair.

Conclusion

Our results indicated that the Bp isolates show distinct genomic features even as they share a common core. The marine and land isolates did not evolve independently; the transition between marine and non-marine habitats might have occurred multiple times. The lineage exhibited a priority effect over the niche in driving their dispersal", "token_count": 516, "char_count": 2097, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6057, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:57.080746", "source": { "split": "train_shard_00001", "doc_id": 1175 }, "chunk_id": "train_shard_00001_1175_0", "global_id": 7313 }, { "text": "Certain intra-species niche specific genes could be related to a strains adaptation to its respective marine or terrestrial environment(s). In summary, this report describes the systematic evolution of 52 Bp group strains and will facilitate future studies toward understanding their ecological role and adaptation to marine and/or terrestrial environments.\n\nBacillus pumilus Group Comparative Genomics: Toward Pangenome Features, Diversity, and Marine Environmental Adaptation.", "token_count": 118, "char_count": 492, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8226, "quality_score": 0.9113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:57.477987", "source": { "split": "train_shard_00001", "doc_id": 1175 }, "chunk_id": "train_shard_00001_1175_1", "global_id": 7314 }, { "text": "Clostridium baratii strains are rare opportunistic pathogens associated with botulism intoxication. They have been isolated from foods, soil and be carried asymptomatically or cause botulism outbreaks. Is not taxonomically related to Clostridium botulinum, but some strains are equipped with BoNT/F7 cluster. Despite their relationship with diseases, our knowledge regarding the genomic features and phylogenetic characteristics is limited. We analyzed the pangenome of C. baratii to understand the diversity and genomic features of this species. We compared existing genomes in public databases, metagenomes, and one newly sequenced strain isolated from an asymptomatic subject. The pangenome was open, indicating it comprises genetically diverse organisms. The core genome contained 28.49% of the total genes of the pangenome. Profiling virulence factors confirmed the presence of phospholipase C in some strains, a toxin capable of disrupting eukaryotic cell membranes. Furthermore, the genomic analysis indicated significant horizontal gene transfer (HGT) events as defined by the presence of prophage genomes. Seven strains were equipped with BoNT/F7 cluster. The active site was conserved in all strains, identifying a missing 7-aa region upstream of the active site in C. baratii genomes. This analysis could be important to advance our knowledge regarding opportunistic clostridia and better understand their contribution to disease.\n\nComparative Genomics of Clostridium baratii Reveals Strain-Level Diversity in Toxin Abundance.", "token_count": 390, "char_count": 1572, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:58.102738", "source": { "split": "train_shard_00001", "doc_id": 1176 }, "chunk_id": "train_shard_00001_1176_0", "global_id": 7315 }, { "text": "Nontuberculous mycobacteria, including those in the Mycobacterium avium complex (MAC), constitute an increasingly urgent threat to global public health. Ubiquitous in soil and water worldwide, MAC members cause a diverse array of infections in humans and animals that are often multidrug resistant, intractable, and deadly. MAC lung disease is of particular concern and is now more prevalent than tuberculosis in many countries, including the United States. Although the clinical importance of these microorganisms continues to expand, our understanding of their genomic diversity is limited, hampering basic and translational studies alike. Here, we leveraged a unique collection of genomes to characterize MAC population structure, gene content, and within-host strain dynamics in unprecedented detail. We found that different MAC species encode distinct suites of biomedically relevant genes, including antibiotic resistance genes and virulence factors, which may influence their distinct clinical manifestations. We observed that M. avium isolates from different sources-human pulmonary infections, human disseminated infections, animals, and natural environments-are readily distinguished by their core and accessory genomes, by their patterns of horizontal gene transfer, and by numerous specific genes, including virulence factors. We identified highly similar MAC strains from distinct patients within and across two geographically distinct clinical cohorts, providing important insights into the reservoirs which seed community acquisition. We also discovered a novel MAC genomospecies in one of these cohorts. Collectively, our results provide key genomic context for these emerging pathogens and will facilitate future exploration of MAC ecology, evolution, and pathogenesis. IMPORTANCE Members of the Mycobacterium avium complex (MAC), a group of mycobacteria encompassing M. avium and its closest relatives, are omnipresent in natural environments and emerging pathogens of humans and animals. MAC infections are difficult to treat, sometimes fatal, and increasingly common. Here, we used comparative genomics to illuminate key aspects of MAC biology. We found that different MAC species and M. avium isolates from different sources encode distinct suites of clinically relevant genes, including those for virulence and antibiotic resistance. We identified highly similar MAC strains in patients from different states and decades, suggesting community acquisition from dispersed and stable reservoirs, and we discovered a novel MAC species", "token_count": 523, "char_count": 2559, "word_count": 350, "semantic_coherence": 1, "information_density": 0.5743, "quality_score": 0.7871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:06:58.760341", "source": { "split": "train_shard_00001", "doc_id": 1177 }, "chunk_id": "train_shard_00001_1177_0", "global_id": 7316 }, { "text": "Our work provides valuable insight into the genomic features underlying these versatile pathogens.\n\nComparative Genomics of Mycobacterium avium Complex Reveals Signatures of Environment-Specific Adaptation and Community Acquisition.", "token_count": 53, "char_count": 232, "word_count": 27, "semantic_coherence": 1, "information_density": 0.963, "quality_score": 0.9815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:59.118609", "source": { "split": "train_shard_00001", "doc_id": 1177 }, "chunk_id": "train_shard_00001_1177_1", "global_id": 7317 }, { "text": "Structural variants (SVs) are omnipresent in human DNA, yet their genotype and methylation status is rarely characterized due to previous limitations in genome assembly and detection of modified nucleotides. Because of this, the extent to which these regions act as quantitative-trait loci is also largely unknown. Here, we generated a pangenome graph summarizing the SVs in 782 de novo assembled genomes obtained from the Genomic Answers for Kids rare disease cohort, that captures 14.6 million CpGs in DNA segments that are absent from the CHM13v2 assembly (SV-CpGs), expanding their number by 43.6%. Next, using 435 methylomes from the same samples, we genotyped a total of 7.99 million SV-CpGs, of which 5.18 million (64.8%) were found to be methylated (SV-5mCpGs) in at least one sample. To understand the provenance and impact of these novel SV-CpGs, we noted that non-repeat sequences were the leading contributor of SV-CpGs (3.3 × 10 6 ), followed by centromeric satellites (1.58 × 10 6 ), simple repeats (1.19 × 10 6 ), Alus (0.67 × 10 6 ), satellites (0.39 × 10 6 ), L1s (0.27 × 10 6 ), and SVAs (0.19 × 10 6 ). Meanwhile, the methylation rate of SV-CpGs was the highest in repeat sequences. Moreover, in contrast to Alus and L1s, centromeric satellites, simple repeats and SVA sequences were overrepresented in SV-5mCpGs compared to reference CpGs. Similarly, we established that non-reference CpGs were more than twice (37% vs. 15%) as likely to be variable, showing intermediate methylation levels in the population", "token_count": 477, "char_count": 1528, "word_count": 250, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:06:59.767039", "source": { "split": "train_shard_00001", "doc_id": 1178 }, "chunk_id": "train_shard_00001_1178_0", "global_id": 7318 }, { "text": "Lastly, to explore if SVs detected in this pangenome are potentially causal for functional variation in population we measured methylation quantitative trait loci (SV-mQTLs) using CHM13v2 as a backbone. This revealed over 230,464 methylation bins within 100 kbp of a common SV (>5% MAF) showing significant association (at 5% FDR) with methylation variation. Finally, we assessed how many of these SVs-mQTLs were the leading QTL variant compared to SNVs and identified 65,659 methylation bins (28.5%) where the leading variant was an SV. In conclusion, our results demonstrate that graph genome references providing full SV structures in combination with the associated methylation variation reveal tens-of-thousands of QTLs that are more accurately mapped in personal genomes, underscoring the importance of assembly-based analyses of human traits.\n\nExpanded methylome and quantitative trait loci detection by long-read profiling of personal DNA", "token_count": 243, "char_count": 946, "word_count": 136, "semantic_coherence": 1, "information_density": 0.7574, "quality_score": 0.8787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:00.245059", "source": { "split": "train_shard_00001", "doc_id": 1178 }, "chunk_id": "train_shard_00001_1178_1", "global_id": 7319 }, { "text": "Fusobacterium necrophorum is a Gram-negative, filamentous anaerobe prevalent in the mucosal flora of animals and humans. It causes necrotic infections in cattle, resulting in a substantial economic impact on the cattle industry. Although infection severity and management differ within F. necrophorum species, little is known about F. necrophorum speciation and the genetic virulence determinants between strains. To characterize the clinical isolates, we performed whole-genome sequencing of four bovine isolates (8L1, 212, B17, and SM1216) and one human isolate (MK12). To determine the phylogenetic relationship and evolution pattern and investigate the presence of antimicrobial resistance genes (ARGs) and potential virulence genes of F. necrophorum, we also performed comparative genomics with publicly available Fusobacterium genomes. Using up-to-date bacterial core gene (UBCG) set analysis, we uncovered distinct Fusobacterium species and F. necrophorum subspecies clades. Pangenome analyses revealed a high level of diversity among Fusobacterium strains down to species levels. The output also identified 14 and 26 genes specific to F. necrophorum subsp. necrophorum and F. necrophorum subsp. funduliforme, respectively, which could be essential for bacterial survival under different environmental conditions. ClonalFrameML-based recombination analysis suggested that extensive recombination among accessory genes led to species divergence. Furthermore, the only strain of F. necrophorum with ARGs was F. necrophorum subsp. funduliforme B35, with acquired macrolide and tetracycline resistance genes. Our custom search revealed common virulence genes, including toxins, adhesion proteins, outer membrane proteins, cell envelope, type IV secretion system, ABC (ATP-binding cassette) transporters, and transporter proteins. A focused study on these genes could help identify major virulence genes and inform effective vaccination strategies against fusobacterial infections", "token_count": 528, "char_count": 2024, "word_count": 260, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [ "SM1216", "MK12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:00.913788", "source": { "split": "train_shard_00001", "doc_id": 1179 }, "chunk_id": "train_shard_00001_1179_0", "global_id": 7320 }, { "text": "IMPORTANCE Fusobacterium necrophorum is an anaerobic bacterium that causes liver abscesses in cattle with an annual incidence rate of 10% to 20%, resulting in a substantial economic impact on the cattle industry. The lack of definite biochemical tests makes it difficult to distinguish F. necrophorum subspecies phenotypically, where genomic characterization plays a significant role. However, due to the lack of a good reference genome for comparison, F. necrophorum subspecies-level identification represents a significant challenge. To overcome this challenge, we used comparative genomics to validate clinical test strains for subspecies-level identification. The findings of our study help predict specific clades of previously uncharacterized strains of F. necrophorum. Our study identifies both general and subspecies-specific virulence genes through a custom search-based analysis. The virulence genes identified in this study can be the focus of future studies aimed at evaluating their potential as vaccine targets to prevent fusobacterial infections in cattle.\n\nComparative Genomic Analysis of Fusobacterium necrophorum Provides Insights into Conserved Virulence Genes.", "token_count": 273, "char_count": 1187, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7125, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:01.469791", "source": { "split": "train_shard_00001", "doc_id": 1179 }, "chunk_id": "train_shard_00001_1179_1", "global_id": 7321 }, { "text": "

Background

Urinary tract infection (UTI) in children is a common bacterial infection. The emergence of extended-spectrum beta-lactamases (ESBLs) poses a major challenge against the treatment of uropathogens. We aimed to characterize the E. coli isolates recovered from children with UTI for their resistance profile and circulating sequence types (ST).

Methods

Children (> 1.5-18 years of age) from different community health centres of India with symptoms of UTI were enrolled. Isolates causing significant bacteriuria were identified by Matrix-Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) and tested for antimicrobial susceptibility by the automated system, VITEK-2 (Biomeriux, Durhum, US). Nineteen E. coli isolates (15 ESBL positive and 4 ESBL negative) were sequenced in Oxford Nanopore platform followed by core-genome phylogeny, accessory genome cluster analysis, identification of sequence types, mobile genetic elements, genetic antimicrobial resistance markers. The correlation between detection of antimicrobial resistance genes with phenotypic resistance profiles was also investigated.

Results

Eleven percent of children had significant bacteriuria [male:female-1:1, > 50% were 11-18 years of age group]. E. coli was predominant (86%) followed by K. pneumoniae (11%). Susceptibility of E. coli was highest against fosfomycin (100%) followed by carbapenems (90.7%) and nitrofurantoin (88.8%). ST131 (15.8%) and ST167 (10.5%) found as high-risk clones with the presence of plasmid [IncFIB (63.1%), IncFIA (52.6%)], and composite transposon [Tn2680 (46.6%)] in many isolates", "token_count": 503, "char_count": 1646, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6977, "quality_score": 0.8488, "entities": { "genes": [ "ST131", "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:02.122172", "source": { "split": "train_shard_00001", "doc_id": 1180 }, "chunk_id": "train_shard_00001_1180_0", "global_id": 7322 }, { "text": "Few isolates coharboured multiple beta-lactamases including blaNDM-5 (33.3%), blaOXA-1 (53.3%), blaCTX-M-15 (60%) and blaTEM-4 (60%).

Conclusions

This study highlights horizontal transmission of resistance genes and plasmids in paediatric patients at community centers across the nation harbouring multidrug-resistant genes such as blaNDM-5 and blaCTX-M-15 associated with high-risk clones ST131 and ST167. The data is alarming and emphasizes the need for rapid identification of resistance markers to reduce the spread in community. To our knowledge, this is the first multicentric study targeting paediatric UTI patients from the community setting of India.\n\nGenome profiling of uropathogenic E. coli from strictly defined community-acquired UTI in paediatric patients: a multicentric study.", "token_count": 274, "char_count": 866, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [ "ST131", "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:02.670176", "source": { "split": "train_shard_00001", "doc_id": 1180 }, "chunk_id": "train_shard_00001_1180_1", "global_id": 7323 }, { "text": "Speciation models and the concept of speciation continuum have been well established in multicellular eukaryotes. However, the mechanisms underlying population differentiation and their environmental drivers in prokaryotes remain elusive. Here, we explored the population diversification of the filamentous cyanobacterium Microcoleus vaginatus , a photoautotrophic edificator with significant importance for dryland ecosystems worldwide. By constructing a 132-genome dataset spanning multiple climate zones across four continents, we integrated intraspecific genomics with environmental association analyses to elucidate the population genetic structure and molecular mechanisms underlying the divergence of the M. vaginatus continuum. Our findings reveal that adaptive differentiation is driven by the combined effects of natural selection, homologous recombination, and gene family turnover, with varying contributions across different phylogroups. The evolution of core and accessory genomes exhibits complementary patterns, with genome-wide association studies demonstrating the predominant role of the core genome in population divergence. Selection, followed by neutral evolution and recombination, mediates trade-offs in life-history strategies, while environmental factors shape these evolutionary processes. Notably, while local edaphic variables exert direct influences on Tajima’s D values, they demonstrate predominantly indirect modulation through alterations in the selection-to-gene gain ratio (S/G). pH emerges as the principal abiotic driver governing population genetic signatures, operating through coordinated effects on both S/G and the proportion of selected genes undergoing recombination (SUR). This study offers novel insights into the diversification mechanisms of cosmopolitan, dominant cyanobacteria, thereby advancing our understanding of prokaryotic speciation in complex natural settings and providing a framework for predicting microbial adaptation in a changing world.\n\npH-driven evolutionary divergence and ongoing speciation in the cosmopolitan cyanobacterium Microcoleus vaginatus", "token_count": 441, "char_count": 2123, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6962, "quality_score": 0.8481, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:03.304530", "source": { "split": "train_shard_00001", "doc_id": 1181 }, "chunk_id": "train_shard_00001_1181_0", "global_id": 7324 }, { "text": "The haploid malaria parasite, Plasmodium falciparum, evolved a unique cohort of DNA repair pathways enabling the parasite to survive in a vertebrate host red blood cell and the mosquito vector. P. falciparum chromosomes are partitioned into a highly conserved core genome and remarkably diverse, largely subtelomeric regions that contain genes encoding important parasite virulence factors. The molecular mechanisms that maintain this chromosomal structure have not been identified. Here, we describe specific DNA repair pathways that differentiate between hypervariable subtelomeric and conserved core regions of the genome. Based on our previous work, we hypothesized that there are potentially important interactions between translesion (TLS) and homologous recombination (HR) pathways for the diversification of multicopy gene families in P. falciparum. Thus, we created knockout parasite lines of the DNA repair enzymes: PfRad51 and the TLS polymerases PfPol ζ and PfRev1 . We identified that irradiation hypersensitivity varied across the cell cycle for TLSΔ parasites and was uniform across the erythrocytic cycle for PfRad51 Δ parasites, highlighting the variable roles of these pathways. However, important interactions between these pathways were found when we studied directed double strand break (DSB) repair, which revealed a difference in the DNA damage response according to chromosomal location. PfRad51 was essential for HR-mediated repair in the core genome. In contrast, we identified a Rad51 independent homology-directed repair in all three of our knockout lines when a DSB was made in the subtelomeric region of the chromosome. We propose that this differential DNA damage response maintains the distinction in diversification across the chromosome.\n\nPlasmodium falciparum DNA repair dynamics reveal unique roles for TLS polymerases and PfRad51 in genome diversification", "token_count": 448, "char_count": 1899, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5762, "quality_score": 0.7881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:03.947099", "source": { "split": "train_shard_00001", "doc_id": 1182 }, "chunk_id": "train_shard_00001_1182_0", "global_id": 7325 }, { "text": "Lactobacillus delbrueckii has been considered a very rare cause of human urinary tract infections (UTIs). However, little is known about its clinical significance and antimicrobial susceptibility, and genomic data from clinical isolates are lacking. This study aimed at analyzing clinical, microbiological, and genomic data of L. delbrueckii urinary isolates. All L. delbrueckii isolates collected from patients hospitalized in a French university hospital from 2014 to 2016 were included. Clinical and biological data were gathered. Species identification was performed by matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry, and MICs were determined using the broth microdilution method. Whole genome sequencing (WGS) was conducted (Illumina MiSeq 2 × 300 bp), and genomes were compared using three approaches (multilocus sequence typing [MLST], average nucleotide identity [ANI], and core genome single nucleotide polymorphism [SNP]). From 2014 to 2016, 48 isolates of L. delbrueckii were recovered from the urine of 48 patients (mean age = 84 years; sex ratio M/F = 0.04). Nearly half (44%) of patients were diagnosed with a UTI, and all had significant cultures (≥105 CFU/mL) with a positive direct examination in >90% of cases. The majority of isolates were susceptible to most antibiotics (especially β-lactams), whereas they seemed intrinsically resistant to fosfomycin and metronidazole. Subspecies identification was consistent across the three approaches, showing that most L. delbrueckii isolates belonged to subspecies allosunkii (n = 40; 83%), followed by subspecies lactis (n = 8; 17%)", "token_count": 520, "char_count": 1711, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6853, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:04.601382", "source": { "split": "train_shard_00001", "doc_id": 1183 }, "chunk_id": "train_shard_00001_1183_0", "global_id": 7326 }, { "text": "Two isolates were resistant to tetracycline (MIC >16 mg/L) and both harbored the tet(W) gene. This study demonstrates the uropathogenic role of L. delbruekii subspecies allosunkii and lactis, particularly in elderly female patients.IMPORTANCEThis largest case series of urinary tract infections (UTIs) caused by Lactobacillus delbrueckii clearly demonstrates the uropathogenic role of this species (especially the subspecies allosunkii) in human UTIs, particularly in elderly female patients and those with underlying comorbidities. This study may change practice in two ways: (i) clinical laboratories, which typically consider lactobacilli from urine samples as contaminants, may need to reassess this practice; (ii) patient care can be improved by prescribing appropriate antibiotics for these underdiagnosed UTIs. L. delbrueckii should be considered an actual pathogen when it is significantly found in the urine of predisposed patients with clinical and/or biological signs of infection. While matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry allows reliable identification of L. delbrueckii, there is also a need for better discrimination between subspecies (especially allosunkii and lactis). Since L. delbrueckii isolates are usually susceptible to many antibiotics, we recommend β-lactams (especially aminopenicillins) for the treatment of those UTIs.\n\n<i>Lactobacillus delbrueckii</i> subsp. <i>allosunkii</i> and <i>lactis</i> as emerging human uropathogens in elderly patients.", "token_count": 503, "char_count": 1642, "word_count": 198, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:05.252852", "source": { "split": "train_shard_00001", "doc_id": 1183 }, "chunk_id": "train_shard_00001_1183_1", "global_id": 7327 }, { "text": "Susceptibility testing is an important tool in the clinical setting; its utility is based on the availability of categorical endpoints, breakpoints (BPs), or epidemiological cutoff values (ECVs/ECOFFs). CLSI and EUCAST have developed antifungal susceptibility testing, BPs, and ECVs for some fungal species. Although the concentration gradient strip bioMérieux Etest is useful for routine testing in the clinical laboratory, ECVs are not available for all agent/species; the lack of clinical data precludes development of BPs. We reevaluated and consolidated Etest data points from three previous studies and included new data. We defined ECOFFinder Etest ECVs for three sets of species-agent combinations: fluconazole, posaconazole, and voriconazole and 9 Candida spp.; amphotericin B and 3 nonprevalent Candida spp.; and caspofungin and 4 Aspergillus spp. The total of Etest MICs from 23 laboratories (Europe, the Americas, and South Africa) included (antifungal agent dependent): 17,242 Candida albicans, 244 C. dubliniensis, 5,129 C. glabrata species complex (SC), 275 C. guilliermondii (Meyerozyma guilliermondii), 1,133 C. krusei (Pichia kudriavzevii), 933 C. kefyr (Kluyveromyces marxianus), 519 C. lusitaniae (Clavispora lusitaniae), 2,947 C. parapsilosis SC, 2,214 C. tropicalis, 3,212 Aspergillus fumigatus, 232 A. flavus, 181 A. niger, and 267 A. terreus SC isolates", "token_count": 480, "char_count": 1398, "word_count": 193, "semantic_coherence": 1, "information_density": 0.7306, "quality_score": 0.8653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:05.925010", "source": { "split": "train_shard_00001", "doc_id": 1184 }, "chunk_id": "train_shard_00001_1184_0", "global_id": 7328 }, { "text": "Triazole MICs for 66 confirmed non-wild-type (non-WT) Candida isolates were available (ERG11 point mutations). Distributions fulfilling CLSI ECV criteria were pooled, and ECOFFinder Etest ECVs were established for triazoles (9 Candida spp.), amphotericin B (3 less-prevalent Candida spp.), and caspofungin (4 Aspergillus spp.). Etest fluconazole ECVs could be good detectors of Candida non-WT isolates (59/61 non-WT, 4 of 6 species).\n\nEtest ECVs/ECOFFs for Detection of Resistance in Prevalent and Three Nonprevalent Candida spp. to Triazoles and Amphotericin B and Aspergillus spp. to Caspofungin: Further Assessment of Modal Variability.", "token_count": 256, "char_count": 681, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [ "ERG11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:06.480230", "source": { "split": "train_shard_00001", "doc_id": 1184 }, "chunk_id": "train_shard_00001_1184_1", "global_id": 7329 }, { "text": "Multidrug-resistant Acinetobacter baumannii ABU3 was isolated from a tracheal suction specimen from a 76-year-old female patient in Thailand. The draft genome was sequenced using Illumina NextSeq 550. The genome comprised 95 contigs totaling 3826,273 base pairs with an N50 of 112,717 bp and GC content of 38.89. Digital DNA-DNA hybridisation with A. baumannii ATCC 19606T revealed 80.3 % similarity. MLST assigned the isolate to ST-164, whereas MLST of the core genome showed 99.0 % similarity to cgST-4302. Resistance gene analysis identified bla OXA-23, bla CARB variants, bla ADC-25, and tet(39). Antimicrobial susceptibility testing showed resistance to carbapenems, fluoroquinolones, beta-lactam combinations, extended-spectrum cephalosporins, and penicillins, with sensitivity to aminoglycosides and folate pathway inhibitors. Two intact prophage regions (23.5 and 26.3 kb) were identified containing structural and functional components. Data are available at NCBI under BioProject PRJNA550309.\n\nDraft genome sequence and intact prophage characterisation of multidrug-resistant <i>Acinetobacter baumannii</i> isolate ABU3 from a tracheal suction specimen in Thailand.", "token_count": 445, "char_count": 1273, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7161, "quality_score": 0.8581, "entities": { "genes": [ "ABU3", "PRJNA550309" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:07.147534", "source": { "split": "train_shard_00001", "doc_id": 1185 }, "chunk_id": "train_shard_00001_1185_0", "global_id": 7330 }, { "text": "

Summary

KmerSV is a visualization and annotation tool for structural variants ( SVs ). It can be applied to assembly contigs or long-read sequences. Using k-mers it rapidly generates images and provides genome features of SVs. As an important feature, it utilizes the new Human Pangenome reference which provide haploid specific assemblies, addresses limitations in prior references and improves the discovery of SVs.

Availability and implementation

KmerSV is implemented in Python and available at github.com/sgtc-stanford/kmerSV\n\nKmerSV: a visualization and annotation tool for structural variants using Human Pangenome derived k-mers", "token_count": 161, "char_count": 654, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7303, "quality_score": 0.8652, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:07.605117", "source": { "split": "train_shard_00001", "doc_id": 1186 }, "chunk_id": "train_shard_00001_1186_0", "global_id": 7331 }, { "text": "OBJECTIVES: Development of a system for direct lactose to ethanol fermentation provides a market for the massive amounts of underutilized whey permeate made by the dairy industry. For this system, glucose and galactose metabolism were uncoupled in Saccharomyces cerevisiae by deleting two negative regulatory genes, GAL80 and MIG1, and introducing the essential lactose hydrolase LAC4 and lactose transporter LAC12, from the native but inefficient lactose fermenting yeast Kluyveromyces marxianus. RESULTS: Previously, integration of the LAC4 and LAC12 genes into the MIG1 and NTH1 loci was achieved to construct strain AY-51024M. Low rates of lactose conversion led us to generate the Δmig1Δgal80 diploid mutant strain AY-GM from AY-5, which exhibited loss of diauxic growth and glucose repression, subsequently taking up galactose for consumption at a significantly higher rate and yielding higher ethanol concentrations than strain AY-51024M. Similarly, in cheese whey permeate powder solution (CWPS) during three, repeated, batch processes in a 5L bioreactor containing either 100 g/L or 150 g/L lactose, the lactose uptake and ethanol productivity rates were both significantly greater than that of AY-51024M, while the overall fermentation times were considerably lower. CONCLUSIONS: Using the Cre-loxp system for deletion of the MIG1 and GAL80 genes to relieve glucose repression, and LAC4 and LAC12 overexpression to increase lactose uptake and conversion provides an efficient basis for yeast fermentation of whey permeate by-product into ethanol.\n\nUncoupling glucose sensing from GAL metabolism for heterologous lactose fermentation in Saccharomyces cerevisiae", "token_count": 479, "char_count": 1670, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6034, "quality_score": 0.8017, "entities": { "genes": [ "NTH1", "LAC12", "LAC4", "MIG1", "GAL80" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:08.253284", "source": { "split": "train_shard_00001", "doc_id": 1187 }, "chunk_id": "train_shard_00001_1187_0", "global_id": 7332 }, { "text": "Abstract

Background Acidobacteriota are abundant in soil, peatlands and sediments, but there are so far only a few studies on those in freshwater environments. Genome streamlined bacteria have reduced genomes as an evolutionary process to adapt to oligotrophic environments such as oceans and lakes. UBA12189, an Acidobacteriota genus under the family Holophagaceae, is an uncultivated lineage with ultra-small genome size found in aquatic environments. So far, no detailed genomic analyses were done on this genome streamlined lineage. Here, we analyzed 66 MAGs of UBA12189 (metagenome assembled genomes; including 2 complete genomes) from freshwater lakes and rivers in Europe, North America and Asia, which is the first genome streamlined Acidobacteriota reported. Results UBA12189 have extremely small genome sizes (< 1.4Mbp), low GC content and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to 300 meters depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis, and there is no concrete evidence of host association. Comparative genome analysis shows that compared to other genome streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur and nitrogen metabolisms, as well as a higher degree of auxotrophy to various amino acids, vitamins and reduced sulfur. UBA12189 also have very limited numbers of membrane transporters", "token_count": 485, "char_count": 1685, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [ "UBA12189" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:08.911483", "source": { "split": "train_shard_00001", "doc_id": 1188 }, "chunk_id": "train_shard_00001_1188_0", "global_id": 7333 }, { "text": "Interestingly, UBA12189 has a higher proportion of unannotated genes (10% – 14%) and a diverse pangenome, suggesting an unknown trove of metabolic potential for environmental adaptation. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, cbb3-type cytochrome c oxidases and complete biosynthesis pathways for heme, vitamin K2 and vitamin B2 (riboflavin). These genes may give a selective advantage during the genome streamlining process. We propose a new genus ‘Ca. Acidiparvus’ within the family Holophagaceae, with two new species named ‘A. lacustris’ and ‘A. fluvialis’. Acidiparvus is the first described genome streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments. Conclusion This study explores the ecology and genomics of yet another genome streamlined freshwater bacterium. With limited metabolic repertoires and no co-occurring microorganisms observed, future studies on cultivated Acidiparvus are crucial. Metagenomics studies alone cannot identify non-canonical metabolic pathways, especially considering high numbers of unannotated genes in Acidiparvus.

\n\nUbiquitous genome streamlined Acidobacteriota in freshwater environments", "token_count": 431, "char_count": 1432, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7532, "quality_score": 0.8766, "entities": { "genes": [ "UBA12189" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:09.538023", "source": { "split": "train_shard_00001", "doc_id": 1188 }, "chunk_id": "train_shard_00001_1188_1", "global_id": 7334 }, { "text": "With increasing application of yeast in fermented milk, in order to study the effect of yeast on milk protein during the fermentation process, the effects of the presence of Kluyveromyces marxianus in milk fermented by Streptococcus thermophilus and Lactobacillus bulgaricus were investigated. After fermentation, the amino acid, protein, and peptide contents were analyzed by ultra-performance liquid chromatography, two-dimensional gel electrophoresis, and liquid chromatography-mass spectrometry, respectively. After the addition of K. marxianus for fermentation, 25 protein spots changed significantly. These were mostly caseins and bovine serum proteins, and the content of total free amino acids increased by 16.30%; ten types of bioactive peptides were identified. Furthermore, the number of peptide types in milk fermented by K. marxianus increased significantly compared with milk fermented by Lactobacillus. K. marxianus is considered to promote proteometabolism in milk when added with Lactobacillus, generate flavor compounds, and improve the digestion and absorption character of milk.\n\nInfluence of Kluyveromyces marxianus on proteins, peptides, and amino acids in Lactobacillus-fermented milk.", "token_count": 373, "char_count": 1278, "word_count": 162, "semantic_coherence": 1, "information_density": 0.5864, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:10.126046", "source": { "split": "train_shard_00001", "doc_id": 1189 }, "chunk_id": "train_shard_00001_1189_0", "global_id": 7335 }, { "text": "Developing an effective method to improve the quality of Pu-erh tea is of great scientific and commercial interest. In this work, Penicillium chrysogenum P1 isolated from Pu-erh tea was inoculated in sterilized or unsterilized sun-dreid green tea leaves to develop pure-culture fermentation (PF) and enhanced fermentation (EF) of Pu-erh tea. Spectrophotometry and high performance liquid chromatography determined that contents of free amino acids (FAA), total tea polyphenols and eight polyphenolic compounds in PF were significantly lower than these in non-inoculation control test (CK) (P < 0.05), whereas the contents of soluble sugars and theabrownins (TB) in PF were significantly higher (P < 0.05) than in CK. A total of 416 volatile compounds were detected by headspace solid-phase micro-extraction combined with gas chromatography-mass spectrometry. Comparison to CK, 124 compounds in PF were degraded or decreased significantly [Variable importance in projection [(VIP) > 1.0, P < 0.05, fold change (FC) < 0.5], whereas 110 compounds in PF were formed or increased significantly (VIP > 1.0, P < 0.05, FC > 2). Compared with normal fermentation (NF), the levels of gallic acid, (+)-catechin, (−)-epicatechin and 64 volatile compounds in EF were significantly lower (VIP > 1.0, P < 0.05, FC < 0.5), whereas the levels of FAA and 39 volatile compounds were significantly higher (VIP > 1.0, P < 0.05, FC > 2). Amplicon sequencing of fungal internal transcribed spacer 1 (ITS1) revealed that P", "token_count": 467, "char_count": 1498, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:10.772167", "source": { "split": "train_shard_00001", "doc_id": 1190 }, "chunk_id": "train_shard_00001_1190_0", "global_id": 7336 }, { "text": "chrysogenum P1 didn’t become the dominant fungus in EF; while the fungal communities in EF were different from those in NF, in that the relative abundances of Blastobotrys bambusae and P. chrysogenum in EF were higher, and the relative abundances of Aspergillus niger and Kluyveromyces marxianus in EF were lower. Overall, inoculation of P. chrysogenum in unsterilized sun-dreid green tea leaves changed the the fungal communities in fermentation of Pu-erh tea, and chemical compounds in fermented tea leaves, i.e., the levels of TB and the compounds responsible for the stale flavor, e.g., 2-amino-4-methoxybenzothiazole were increased, resulting in improvement of the sensory quality, including mellower taste and stronger stale flavor.\n\nEffect of inoculation with Penicillium chrysogenum on chemical components and fungal communities in fermentation of Pu-erh tea", "token_count": 241, "char_count": 866, "word_count": 126, "semantic_coherence": 1, "information_density": 0.5635, "quality_score": 0.7817, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:11.258582", "source": { "split": "train_shard_00001", "doc_id": 1190 }, "chunk_id": "train_shard_00001_1190_1", "global_id": 7337 }, { "text": "

Background

The initial colonization of the infant gut is a complex process that defines the foundation for a healthy microbiome development. Bifidobacterium longum is one of the first colonizers of newborns' gut, playing a crucial role in the healthy development of both the host and its microbiome. However, B. longum exhibits significant genomic diversity, with subspecies (e.g., Bifidobacterium longum subsp. infantis and subsp. longum) displaying distinct ecological and metabolic strategies including differential capabilities to break down human milk glycans (HMGs). To promote healthy infant microbiome development, a good understanding of the factors governing infant microbiome dynamics is required.

Methodology

We analyzed newly sequenced gut microbiome samples of mother-infant pairs from the Amsterdam Infant Microbiome Study (AIMS) and four publicly available datasets to identify important environmental and bifidobacterial features associated with the colonization success and succession outcomes of B. longum subspecies. Metagenome-assembled genomes (MAGs) were generated and assessed to identify characteristics of B. longum subspecies in relation to early-life gut colonization. We further implemented machine learning tools to identify significant features associated with B. longum subspecies abundance.

Results

B. longum subsp. longum was the most abundant and prevalent gut Bifidobacterium at one month, being replaced by B. longum subsp. infantis at six months of age. By utilizing metagenome-assembled genomes (MAGs), we reveal significant differences between and within B. longum subspecies in their potential to break down HMGs. We further combined strain-tracking, meta-pangenomics and machine learning to understand these abundance dynamics and found an interplay of priority effects, milk-feeding type and HMG-utilization potential to govern them across the first six months of life", "token_count": 528, "char_count": 2031, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:11.910580", "source": { "split": "train_shard_00001", "doc_id": 1191 }, "chunk_id": "train_shard_00001_1191_0", "global_id": 7338 }, { "text": "We find higher abundances of B. longum subsp. longum in the maternal gut microbiome, vertical transmission, breast milk and a broader range of HMG-utilizing genes to promote its abundance at one month of age. Eventually, we find B. longum subsp. longum to be replaced by B. longum subsp. infantis at six months of age due to a combination of nutritional intake, HMG-utilization potential and a diminishment of priority effects.

Discussion

Our results establish a strain-level ecological framework explaining early-life abundance dynamics of B. longum subspecies. We highlight the role of priority effects, nutrition and significant variability in HMG-utilization potential in determining the predictable colonization and succession trajectories of B. longum subspecies, with potential implications for promoting infant health and well-being.\n\nPriority effects, nutrition and milk glycan-metabolic potential drive <i>Bifidobacterium longum</i> subspecies dynamics in the infant gut microbiome.", "token_count": 293, "char_count": 1067, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:12.476561", "source": { "split": "train_shard_00001", "doc_id": 1191 }, "chunk_id": "train_shard_00001_1191_1", "global_id": 7339 }, { "text": "

ABSTRACT

Recently, species clustering within Dickeya zeae has been identified as complex, encompassing validly published names, including D. oryzae and D. parazeae , with some strains potentially delineating new species. In this study, genomes of strains isolated from a bacterial heart rot outbreak in pineapple ( Ananas comosus var. comosus ) on Oahu, Hawaii, along with two strains from pineapple in Malaysia, were sequenced. Orthologous average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values among the sequenced genomes ranged from 98.93-99.9% and 91.8-99.9%, respectively, supporting the classification of seven strains within the same species. Comparisons of ANI and dDDH values between these seven strains and type strains of D. zeae, D. parazeae, and D. oryzae ranged from 94.4-95.9% and 57.2-66.5%, respectively. These values fall below the proposed boundaries for new species designation, supporting the delineation of a novel species. Phylogenetic analyses, including 16S rRNA, gapA , multi-locus sequence analysis (MLSA) of 10 housekeeping genes, whole-genome, and pangenome analyses, were concordant and revealed a distinct monophyletic clade, separating these strains from other members of the D. zeae complex, with D. oryzae as the closest relative. Notably, a nitrogen fixation gene cluster comprising 28 genes, similar to the Klebsiella spp. nitrogenase gene cluster, was found in the genome of the seven pineapple strains", "token_count": 418, "char_count": 1475, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:13.100756", "source": { "split": "train_shard_00001", "doc_id": 1192 }, "chunk_id": "train_shard_00001_1192_0", "global_id": 7340 }, { "text": "Based on polyphasic approaches, including ANI, dDDH, biochemical, physiological, and phylogenomic analyses, we propose the reclassification in a new species of the five pineapple strains from Hawaii A5391, A5410 T , A5611, A6136, and A6137, together with the two pineapple strains from Malaysia CFBP 1272 and CFBP 1278, previously classified as D. zeae . We propose the name Dickeya ananae sp. nov. for this taxon, represented by the type strain A5410 T (= ICMP 25020 T = LMG 33197 T ).\n\nDickeya ananaesp. nov., pectinolytic bacterium isolated from pineapple (Ananas comosus)", "token_count": 214, "char_count": 589, "word_count": 91, "semantic_coherence": 1, "information_density": 0.8022, "quality_score": 0.9011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:13.566438", "source": { "split": "train_shard_00001", "doc_id": 1192 }, "chunk_id": "train_shard_00001_1192_1", "global_id": 7341 }, { "text": "Acinetobacter baumannii is one of the most important nosocomial pathogens able to rapidly develop extensive drug resistance. Here, we study the role of accessory genome in the success of the globally disseminated clone 1 (GC1) with functional and genomic approaches. Comparative genomics was performed with available GC1 genomes (n = 106) against other A. baumannii high-risk and sporadic clones. Genetic traits related to accessory genome were found common and conserved along time as two novel regions of genome plasticity, and a CRISPR-Cas system acquired before clonal diversification located at the same loci as \"sedentary\" modules. Although identified within hotspot for recombination, other block of accessory genome was also \"sedentary\" in lineage 1 of GC1 with signs of microevolution as the AbaR0-type genomic island (GI) identified in A144 and in A155 strains which were maintained one month in independent experiments without antimicrobial pressure. The prophage YMC/09/02/B1251_ABA_BP was found to be \"mobile\" since, although it was shared by all GC1 genomes, it showed high intrinsic microevolution as well as mobility to different insertion sites. Interestingly, a wide variety of Insertion Sequences (IS), probably acquired by the flow of plasmids related to Rep_3 superfamily was found. These IS showed dissimilar genomic location amongst GC1 genomes presumably associated with promptly niche adaptation. On the other hand, a type VI secretion system and three efflux pumps were subjected to deep processes of genomic loss in A. baumannii but not in GC1. As a whole, these findings suggest that preservation of some genetic modules of accessory genome harbored by strains from different continents in combination with great plasticity of IS and varied flow of plasmids, may be central features of the genomic structure of GC1", "token_count": 480, "char_count": 1870, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6272, "quality_score": 0.8136, "entities": { "genes": [ "GC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:14.212813", "source": { "split": "train_shard_00001", "doc_id": 1193 }, "chunk_id": "train_shard_00001_1193_0", "global_id": 7342 }, { "text": "Competition of A144 and A155 versus A118 (ST 404/ND) without antimicrobial pressure suggested a higher ability of GC1 to grow over a clone with sporadic behavior which explains, from an ecological perspective, the global achievement of this successful pandemic clone in the hospital habitat. Together, these data suggest an essential role of still unknown properties of \"mobile\" and \"sedentary\" accessory genome that is preserved over time under different antibiotic or stress conditions.\n\nCrucial Role of the Accessory Genome in the Evolutionary Trajectory of Acinetobacter baumannii Global Clone 1.", "token_count": 154, "char_count": 607, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [ "GC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:14.646055", "source": { "split": "train_shard_00001", "doc_id": 1193 }, "chunk_id": "train_shard_00001_1193_1", "global_id": 7343 }, { "text": "

Background

Bioethanol from lignocellulosic materials is of great significance to the production of renewable fuels due to its wide sources. However, multiple inhibitors generated from pretreatments represent great challenges for its industrial-scale fermentation. Despite the complex toxicity mechanisms, lignocellulose-derived inhibitors have been reported to be related to the levels of intracellular reactive oxygen species (ROS), which makes oxidoreductase a potential target for the enhancement of the tolerance of yeasts to these inhibitors.

Results

A typical 2-Cys peroxiredoxin from Kluyveromyces marxianus Y179 (KmTPX1) was identified, and its overexpression was achieved in Saccharomyces cerevisiae 280. Strain TPX1 with overexpressed KmTPX1 gene showed an enhanced tolerance to oxidative stresses. Serial dilution assay indicated that KmTPX1 gene contributed to a better cellular growth behavior, when the cells were exposed to multiple lignocellulose-derived inhibitors, such as formic acid, acetic acid, furfural, ethanol, and salt. In particular, KmTPX1 expression also possessed enhanced tolerance to a mixture of formic acid, acetic acid, and furfural (FAF) with a shorter lag period. The maximum glucose consumption rate and ethanol generation rate in KmTPX1-expressing strain were significantly improved, compared with the control. The mechanism of improved tolerance to FAF depends on the lower level of intracellular ROS for cell survival under stress.

Conclusion

A new functional gene KmTPX1 from K. marxianus is firstly associated with the enhanced tolerance to multiple lignocellulose-derived inhibitors in S. cerevisiae", "token_count": 490, "char_count": 1735, "word_count": 220, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [ "TPX1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:15.299765", "source": { "split": "train_shard_00001", "doc_id": 1194 }, "chunk_id": "train_shard_00001_1194_0", "global_id": 7344 }, { "text": "We provided a possible detoxification mechanism of the KmTPX1 for further theoretical research; meanwhile, we provided a powerful potential for application of the KmTPX1 overexpressing strain in ethanol production from lignocellulosic materials.\n\nEnhanced fermentative performance under stresses of multiple lignocellulose-derived inhibitors by overexpression of a typical 2-Cys peroxiredoxin from Kluyveromyces marxianus.", "token_count": 125, "char_count": 443, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7843, "quality_score": 0.8922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:15.684705", "source": { "split": "train_shard_00001", "doc_id": 1194 }, "chunk_id": "train_shard_00001_1194_1", "global_id": 7345 }, { "text": "Blautia, a genus established in 2008, is a relevantly abundant taxonomic group present in the microbiome of human and other mammalian gastrointestinal (GI) tracts. Several described (or proposed) Blautia species are available at this date. However, despite the increasing level of knowledge about Blautia, its diversity is still poorly understood. The increasing availability of Blautia genomic sequences in the public databases opens the possibility to study this genus from a genomic perspective. Here we report the pangenome analysis and the phylogenomic study of 225 Blautia genomes available in RefSeq. We found 33 different potential species at the genomic level, 17 of them previously undescribed; we also confirmed by genomic standards the status of 4 previously proposed new Blautia species. Comparative genomic analyses suggest that the Blautia pangenome is open, with a relatively small core genome (∼ 700-800 gene families). Utilizing a set of representative genomes, we performed a gene family gain/loss model for the genus, showing that despite terminal nodes suffered more massive gene gain events than internal nodes (i.e., predicted ancestors), some ancestors were predicted to have gained an important number of gene families, some of them associated with the possible acquisition of metabolic abilities. Gene loss events remained lower than gain events in most cases. General aspects regarding pangenome composition and gene gain/loss events are discussed, as well as the proposition of changes in the taxonomic assignment of B. coccoides TY and the proposition of a new species, \"B. pseudococcoides.\".\n\nInsights on the Evolutionary Genomics of the Blautia Genus: Potential New Species and Genetic Content Among Lineages.", "token_count": 458, "char_count": 1821, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:16.326463", "source": { "split": "train_shard_00001", "doc_id": 1195 }, "chunk_id": "train_shard_00001_1195_0", "global_id": 7346 }, { "text": "

Background

Nucleotide-binding domain Leucine-rich Repeat (NLR) proteins are a key component of the plant innate immune system. In plant genomes NLRs exhibit considerable presence/absence variation and sequence diversity. Recent advances in sequencing technologies have made the generation of high-quality novel plant genome assemblies considerably more straightforward. Accurately identifying NLRs from these genomes is a prerequisite for improving our understanding of NLRs and identifying potential novel sources of disease resistance.

Results

Whilst several tools have been developed to predict NLRs, they are hampered by low accuracy, speed, and availability. Here, the NLR annotation tool Resistify is presented. Resistify is an easy-to-use, rapid, and accurate tool to identify and classify NLRs from protein sequences. Applying Resistify to the RefPlantNLR database demonstrates that it can correctly identify NLRs from a diverse range of species. Applying Resistify in combination with tools to identify transposable elements to a panel of Solanaceae genomes reveals a previously undescribed association between NLRs and Helitron transposable elements.

Conclusion

Resistify can rapidly identify NLRs within plant genomes and provides accurate structural classifications. Its ease of use and accessibility allows easy integration into bioinformatic workflows and projects, enhancing the study of this important group of genes. Applying Resistify to a Solanaceae pangenome reveals an undescribed association between NLRs and transposable elements. Availability: https://github.com/SwiftSeal/resistify\n\nResistify - A rapid and accurate annotation tool to identify NLRs and study their genomic organisation", "token_count": 403, "char_count": 1737, "word_count": 228, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:16.945752", "source": { "split": "train_shard_00001", "doc_id": 1196 }, "chunk_id": "train_shard_00001_1196_0", "global_id": 7347 }, { "text": "INTRODUCTION: The participation of non-Saccharomyces yeasts in fermentation processes is of great importance due to their participation in the formation of esters and superior alcohols, which confer characteristic aromas to beverages such as wine and mescal. THE AIM: The aim of this study was identify and evaluate the potential aroma production of yeast native of Agave fermentation by the mescal production in Durango, Mexico. Isolated yeasts were molecularly identified by 5.8s ribosomal gene; the potential production of aromas was carried out in fermentations with the addition of L-phenylalanine and evaluated after 24 h of fermentation. Extraction and quantification of aromatic compounds by headspace solid-phase micro-extraction (HS-SPME) and gas chromatograph mass spectrometry (GC-MS). RESULTS: The isolated non-Saccharomyces yeasts could be classified into six different genera Saccharomyces cerevisiae, Clavispora lusitaniae, Torulaspora delbrueckii, Kluyveromyces dobzhanskii, Kluyveromyces marxianus, and Kluyveromyces sp. All probed strains presented a potential aroma production (ethyl acetate, isoamyl acetate, isoamyl alcohol, benzaldehyde, 2-phenylethyl butyrate, and phenylethyl propionate), particularly 2-phenylethanol and 2-phenylethylacetate; the levels found in the Kluyveromyces marxianus ITD0211 yeast have the highest 2-phenylethylacetate production at 203 mg/L and Kluyveromyces marxianus ITD0090 with a production of 2-phenylethanol at 1024 mg/L. CONCLUSION: Non-Saccharomyces yeasts were isolated from the mescal fermentation in Durango; the Kluyveromyces genus is the most predominant", "token_count": 484, "char_count": 1618, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [ "ITD0211", "ITD0090" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:17.609191", "source": { "split": "train_shard_00001", "doc_id": 1197 }, "chunk_id": "train_shard_00001_1197_0", "global_id": 7348 }, { "text": "For the production of aromas, highlighting two strains of Kluyveromyces marxianus produces competitive quantities of compounds of great biotechnological interest such as 2-phenylethanol and 2-phenylethylacetate, without resorting to the genetic modification of yeasts or the optimization of the culture medium.\n\nPotential production of 2-phenylethanol and 2-phenylethylacetate by non-Saccharomyces yeasts from Agave durangensis", "token_count": 119, "char_count": 427, "word_count": 52, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:18.012111", "source": { "split": "train_shard_00001", "doc_id": 1197 }, "chunk_id": "train_shard_00001_1197_1", "global_id": 7349 }, { "text": "

Background

Enterococci are gut commensal microorganisms, which can however cause life-threatening infections especially in patients suffering from intestinal barrier disorders. Treatment of these enterococcal infections is challenging due to a variety of intrinsic and acquired antibiotic resistances. In this context, linezolid is applied as last-resort antibiotic. Our study aimed at determining linezolid-resistant enterococci (LRE) long-term carriage (≥ 10 weeks), since this is a risk factor for the development of LRE infection.

Methods

In a one-year cohort study, all patients on hemato-oncology, intensive and intermediate care units were screened for LRE. To determine the molecular epidemiology, all detected LRE isolates were subjected to whole genome sequencing-based typing to investigate whether in-host selection or pathogen transmission was causative for LRE occurrence. Clinical and demographic data were recorded to identify risk factors for LRE clearance and persistence.

Results

Long-term LRE carriage was identified in 7 of 46 (15%) patients. Duration of hospitalization differed significantly between LRE persistence (mean: 110 days; range 28-225 days) and clearance group (mean: 53 days; range 5-213 days). LRE strains mostly exhibited a high genetic core genome diversity, indicating that transmission events played a minor role.

Conclusions

Our study shows that the duration of hospitalization increases the risk for long-term carriage of LRE. In contrast to other multi drug resistant bacteria, LRE carriage was rarely caused by transmission events. Thus, future infection prevention measures should focus on antimicrobial stewardship approaches next to classical hygiene strategies.\n\nDuration of hospitalization increases the risk for long-term carriage of linezolid-resistant enterococci in critically ill patients.", "token_count": 463, "char_count": 1872, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6735, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:18.670302", "source": { "split": "train_shard_00001", "doc_id": 1198 }, "chunk_id": "train_shard_00001_1198_0", "global_id": 7350 }, { "text": "Latilactobacillus sakei, a lactic acid bacterium in diverse environments such as fermented foods, meat and the human gastrointestinal tract, exhibits significant genetic diversity and niche-specific adaptations. This study conducts a comprehensive comparative genomic analysis of 29 complete L. sakei genomes to uncover the genetic mechanisms underlying these adaptations. Phylogenetic analysis divided the species into three distinct clades that did not correlate with the source of isolation and did not suggest any niche-specific evolutionary direction. The pan-genome analysis revealed a substantial core genome alongside a diverse genetic repertoire, indicating both high genetic conservation and adaptability. Predicted growth rates based on codon use bias analysis suggest that L. sakei strains have an overall faster growth rate and may be able to efficiently dominate in competitive environments. Plasmid analysis revealed a variety of plasmids carrying genes essential for carbohydrate metabolism, enhancing L. sakei's ability to thrive in various fermentation substrates. It was also found that the number of genes belonging to the GH1 family amongst sugar metabolism-related genes present on chromosomes and plasmids varies between strains and that AA1, which is involved in alcohol oxidation, has been acquired from plasmids. blast analysis revealed that some strains have environmental adaptation gene clusters of cell surface polysaccharides that may mediate attachment to food and mucosa. The knowledge gleaned from this study lays a solid foundation for future research aimed at harnessing the genetic traits of L. sakei strains for industrial and health-related applications.\n\nComparative genomic analysis of <i>Latilactobacillus sakei</i> strains provides new insights into their association with different niche adaptations.", "token_count": 434, "char_count": 1891, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [ "AA1", "GH1" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:19.339070", "source": { "split": "train_shard_00001", "doc_id": 1199 }, "chunk_id": "train_shard_00001_1199_0", "global_id": 7351 }, { "text": "Active surveillance for methicillin-resistant Staphylococcus aureus (MRSA) is a component of our neonatal intensive care unit (NICU) infection prevention efforts. Recent atypical trends prompted review of 42 suspected MRSA isolates. Species identification was confirmed by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and methicillin resistance was reevaluated by PBP2a lateral flow assay, cefoxitin/oxacillin susceptibility testing, mecA and mecC PCR, and six commercially available MRSA detection agars. All isolates were confirmed S. aureus, but only eight were MRSA (cefoxitin resistant, PBP2a positive, mecA positive, growth on all MRSA screening agars). One MRSA isolate was cefoxitin susceptible but PBP2a and mecA positive, and the remaining 33 were cefoxitin susceptible, PBP2a negative, and mecA negative; interestingly, these isolates grew inconsistently across MRSA screening agars and had susceptibility profiles consistent with that of borderline oxacillin-resistant S. aureus (BORSA). Comparative genomic analyses found these BORSA isolates to be phylogenetically diverse and not representative of clonal expansion or shared gene content, though clones of two NICU strains were infrequently observed over 8 months. We identified 6 features-substitutions and truncations in PBP2, PBP4, and GdpP and beta-lactamase hyperproduction-that were used to generate a random forest classifier to distinguish BORSA from methicillin-susceptible S. aureus (MSSA) in our cohort. Our model demonstrated a robust ability to predict the BORSA phenotype among isolates collected across two continents (validation area under the curve [AUC], 0.902)", "token_count": 492, "char_count": 1727, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7225, "quality_score": 0.8612, "entities": { "genes": [ "PBP4", "PBP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:20.000139", "source": { "split": "train_shard_00001", "doc_id": 1200 }, "chunk_id": "train_shard_00001_1200_0", "global_id": 7352 }, { "text": "Taking these findings together, we observed an unexpected prevalence of BORSA in our NICU, BORSA misclassification by existing MRSA screening methods, and markers that are together discriminatory for BORSA and MSSA within our cohort. This work has implications for epidemiological reporting of MRSA rates for centers using different screening methods. IMPORTANCE In this study, we found a high prevalence of Staphylococcus aureus isolates exhibiting a borderline oxacillin resistance phenotype (BORSA) in our neonatal intensive care unit (NICU) serendipitously due to the type of MRSA screening agar used by our laboratory for active surveillance cultures. Subsequent phenotypic and molecular characterization highlighted an unexpected prevalence and variability of BORSA isolates. Through whole-genome sequencing, we interrogated core and accessory genome content and generated a random forest classification model to identify mutations and truncations in the PBP2, PBP4, and GdpP proteins and beta-lactamase hyperproduction, which correlated with BORSA and MSSA phenotypes among S. aureus clinical isolates collected across two continents. In consideration of these findings, this work will help clinical microbiology laboratories and clinicians identify MRSA screening shortfalls and draw attention to the non-mecA-mediated BORSA phenotype.\n\nComparative Genomics of Borderline Oxacillin-Resistant Staphylococcus aureus Detected during a Pseudo-outbreak of Methicillin-Resistant S. aureus in a Neonatal Intensive Care Unit.", "token_count": 387, "char_count": 1539, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8227, "entities": { "genes": [ "PBP4", "PBP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:20.609810", "source": { "split": "train_shard_00001", "doc_id": 1200 }, "chunk_id": "train_shard_00001_1200_1", "global_id": 7353 }, { "text": "Francisella tularensis , the causative agent for tularaemia, is a Tier 1 select agent, and a pan-species pathogen of global significance due to its zoonotic potential. Consistent genome characterization of the pathogen is essential to identify novel genes, virulence factors, antimicrobial resistance genes, for studying phylogenetics and other features of interest. This study was conducted to understand the genetic variations among genomes of F. tularensis isolated from two felines and one human source. Pan-genome analysis revealed that 97.7 % of genes were part of the core genome. All three F. tularensis isolates were assigned to sequence type A based on single nucleotide polymorphisms (SNPs) in sdhA. Most of the virulence genes were part of the core genome. An antibiotic resistance gene coding for class A beta-lactamase was detected in all three isolates. Phylogenetic analysis showed that these isolates clustered with other isolates reported from Central and South-Central USA. Assessment of large sets of the F. tularensis genome sequences is essential in understanding pathogen dynamics, geographical distribution and potential zoonotic implications.\n\nCharacterization of three Francisella tularensis genomes from Oklahoma, USA.", "token_count": 341, "char_count": 1287, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6257, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:21.540934", "source": { "split": "train_shard_00001", "doc_id": 1201 }, "chunk_id": "train_shard_00001_1201_0", "global_id": 7354 }, { "text": "Banana is an important fruit and staple crop, which is vital for food and income security in developing countries. A genomics initiative was undertaken as part of the Global Alliance against TR4 (Tropical Race 4 of Fusarium Wilt of Banana) Alliance, with Bayer Crop Science, International Institute of Tropical Agriculture, and University of Queensland to collectively accelerate the breeding efforts in Eastern Africa. The goal of this project is to develop genomics resources to improve banana breeding, productivity, and quality traits amid a changing climate and shifting disease pressures for breeding. Here, we present the PacBio HiFi sequencing, assembly, and comparative analysis of seven genomes of wild and edible diploid banana accessions belonging to subspecies considered important progenitors to cultivated banana varieties and part of breeding programs. This banana genome resource will help power genome editing, a pangenome effort, and conventional breeding programs for germplasm improvement.\n\nLong read sequencing and assembly of wild diploid relatives and cultivars in support of banana breeding programs", "token_count": 241, "char_count": 1124, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6871, "quality_score": 0.8436, "entities": { "genes": [ "TR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:22.022695", "source": { "split": "train_shard_00001", "doc_id": 1202 }, "chunk_id": "train_shard_00001_1202_0", "global_id": 7355 }, { "text": "Abstract

The increasing prevalence of Ralstonia pseudosolanacearum phylotype I (phy I) in agricultural regions across Europe highlights the need for heightened awareness and preventive measures. Recent detections in multiple European countries spam a range of agricultural systems, host plants, and natural aquatic environments. These findings have been linked either to infected plant material at import (interceptions) or to plants cultivated in specific European regions, often after importation of infected plant material. To investigate the genetic diversity of these emerging populations, we analysed whole-genome sequence (WGS) data from a collection of 62 R. pseudosolanacearum phy I isolates, including those recently obtained in various European countries, using average nucleotide analysis (ANI) and and core genome multilocus sequence typing (cgMLST). ANI analysis revealed two distinct major clades: the \"rose clade\", comprising isolates from rose, potato, surface water, and bittersweet, most closely matching with sequevar 33, and the \"ginger clade\", including isolates from members of the Zingiberaceae family, with the best match to sequevar 30. A third smaller clade was also identified consisting of two R. pseudosolanacearum phy I isolates from tomato corresponding to sequevar 18 (\"tomato clade\"). Pathogenicity assays were performed on tomato to deduce information on the biological relevance of the genetic diversity observed among these R. pseudosolanacearum phy I isolates. Our findings suggest at least three independent introduction events of virulent R. pseudosolanacearum phy I populations into Europebetween 2015 and 2024. Given the pathogen’s ability to systemically infect a broad range of host plants and persist in diverse agricultural and environmental niches, the implementation of stringent import control measures for plant material entering the European Union is strongly recommended.

\n\nExploring the genetic diversity of recent Ralstonia pseudosolanacearum phylotype I findings in Europe", "token_count": 502, "char_count": 2134, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:22.675759", "source": { "split": "train_shard_00001", "doc_id": 1203 }, "chunk_id": "train_shard_00001_1203_0", "global_id": 7356 }, { "text": "RNA regulators are often found in regulatory networks and mediate growth and virulence in bacteria. Small RNAs (sRNAs) are non-coding RNAs that modulate translation initiation and mRNA degradation by base-pairing. To better understand the role of sRNAs in pathogenicity several studies identified sRNAs in Streptococcus pneumoniae ; however, little functional characterization has followed. This study’s goals are: 1) survey putative sRNAs in S. pneumoniae ; 2) assess the conservation of these sRNAs; and 3) examine their predicted targets. Three previous studies in S. pneumoniae identified 287 putative sRNAs by high-throughput sequencing. This study narrows the candidates to a list of 58 putative sRNAs. BLAST analysis indicates that the 58 sequences are highly conserved across the S. pneumoniae pangenome, and 25 of them are identified sporadically in other Streptococcus species. However, only 2 have corresponding sequences identified across several Streptococcus species. We used four RNA-target prediction programs to predict targets for each of the 58 putative sRNAs. Across all probable predictions, six sRNAs have overlapping targets predicted by multiple programs, four of which target numerous transposase encoding transcripts. sRNAs targeting transposase genes display nearly identical and perfect base-pairing. One sRNA, M63 (Spd_sr37), has several probable targets in the CcpA regulon, a network responsible for global catabolite repression, suggesting a possible biological function in carbon metabolism control. Each M63-target interaction exhibits unique base-pairing increasing confidence in the biological relevance of the result. This study produces a list of S . pneumoniae putative sRNAs whose predicted targets suggest functional significance in transposon and carbon metabolism regulation.

Importance

Previous studies identified many small RNA candidates in Streptococcus pneumoniae , several of which were hypothesized to play a role in S. pneumoniae virulence. Due to the differing sequencing methods, diverse inclusion criteria, S", "token_count": 515, "char_count": 2071, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5903, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:23.334022", "source": { "split": "train_shard_00001", "doc_id": 1204 }, "chunk_id": "train_shard_00001_1204_0", "global_id": 7357 }, { "text": "pneumoniae strain differences, as well as limited follow-up since, it is unclear to what extent candidates identified in different studies have overlapping sequences and functions, and their biological relevance remains ambiguous. This research aims to consolidate the candidate sRNAs across these studies and focuses attention on those that are likely to be regulatory and associated with virulence. This study’s findings enhance our knowledge of the conservation of small regulatory RNAs across the many Streptococcus pneumoniae strains and highlights a handful that appear likely to have a role in growth or virulence.\n\nAssessing the conservation and targets of putative sRNAs in Streptococcus pneumoniae", "token_count": 159, "char_count": 714, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7255, "quality_score": 0.8627, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:23.777571", "source": { "split": "train_shard_00001", "doc_id": 1204 }, "chunk_id": "train_shard_00001_1204_1", "global_id": 7358 }, { "text": "Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available strains and nine new strains sequenced here. Genomic analyses conducted include phylogenetics of the core genome as well as biosynthetic gene cluster analysis and metabolic pathway analyses. Urinary strains of both species were assayed for their ability to utilize four simple carbohydrates. We found that L. jensenii strains can efficiently catabolize maltose, trehalose, and glucose, but not ribose, and L. mulieris strains can utilize maltose and glucose, but not trehalose and ribose. Metabolic pathway analysis clearly shows the lack of treB within L. mulieris strains, indicative of its inability to catabolize external sources of trehalose. While genotypic and phenotypic observations provide insight into the differences between these two species, we did not find any association with urinary symptom status. Through this genomic and phenotypic investigation, we identify markers that can be leveraged to clearly distinguish these two species in investigations of the female urogenital microbiota. IMPORTANCE We have expanded upon our prior genomic analysis of L. jensenii and L. mulieris strains, including nine new genome sequences", "token_count": 527, "char_count": 1925, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5611, "quality_score": 0.7805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:24.408362", "source": { "split": "train_shard_00001", "doc_id": 1205 }, "chunk_id": "train_shard_00001_1205_0", "global_id": 7359 }, { "text": "Our bioinformatic analysis finds that L. jensenii and L. mulieris cannot be distinguished by short-read 16S rRNA gene sequencing alone. Thus, to discriminate between these two species, future studies of the female urogenital microbiome should employ metagenomic sequencing and/or sequence species-specific genes, such as those identified here. Our bioinformatic examination also confirmed our prior observations of differences between the two species related to genes associated with carbohydrate utilization, which we tested here. We found that the transport and utilization of trehalose are key distinguishing traits of L. jensenii, which is further supported by our metabolic pathway analysis. In contrast with other urinary Lactobacillus species, we did not find strong evidence for either species, nor particular genotypes, to be associated with lower urinary tract symptoms (or the lack thereof).\n\nExploring the genotypic and phenotypic differences distinguishing Lactobacillus jensenii and Lactobacillus mulieris.", "token_count": 271, "char_count": 1062, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7286, "quality_score": 0.8643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:24.975888", "source": { "split": "train_shard_00001", "doc_id": 1205 }, "chunk_id": "train_shard_00001_1205_1", "global_id": 7360 }, { "text": "Staphylococcus aureus in the bloodstream causes high morbidity and mortality, exacerbated by the spread of multidrug-resistant and methicillin-resistant S. aureus (MRSA). We aimed to characterize the circulating lineages of S. aureus from bloodstream infections and the contribution of individual lineages to resistance over time. Here, we generated 852 high-quality short-read draft genome sequences of S. aureus isolates from patient blood cultures in a single hospital from 2010 to 2022. A total of 80 previously recognized sequence types (ST) and five major clonal complexes are present in the population. Two frequently detected lineages, ST5 and ST8 exhibited fluctuating demographic structures throughout their histories. The rise and fall in their population growth coincided with the acquisition of antimicrobial resistance, mobile genetic elements, and superantigen genes, thus shaping the accessory genome structure across the entire population. These results reflect undetected selective events and changing ecology of multidrug-resistant S. aureus in the bloodstream.\n\nDemographic fluctuations in bloodstream Staphylococcus aureus lineages configure the mobile gene pool and antimicrobial resistance.", "token_count": 327, "char_count": 1255, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6646, "quality_score": 0.8323, "entities": { "genes": [ "ST5", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:25.542238", "source": { "split": "train_shard_00001", "doc_id": 1206 }, "chunk_id": "train_shard_00001_1206_0", "global_id": 7361 }, { "text": "As numerous industrial bioprocesses rely on yeast fermentation, developing CO2-fixing yeast strains can be an attractive option toward sustainable industrial processes and carbon neutrality. Recent studies have shown that the expression of ribulose-1,5-bisphosphate carboxylase-oxygenase (RuBisCO) in yeasts, such as Saccharomyces cerevisiae and Kluyveromyces marxianus, enables mixotrophic CO2 fixation and production of biofuels. Also, the expression of a synthetic Calvin-Benson-Bassham (CBB) cycle including RuBisCO in Pichia pastoris enables autotrophic growth on CO2. This review highlights recent advances in metabolic engineering strategies to enable CO2 fixation in yeasts. Also, we discuss the potentials of other natural and synthetic metabolic pathways independent of RuBisCO for developing CO2-fixing yeast strains capable of producing value-added biochemicals.\n\nYeast metabolic engineering for carbon dioxide fixation and its application.", "token_count": 275, "char_count": 1007, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:26.096796", "source": { "split": "train_shard_00001", "doc_id": 1207 }, "chunk_id": "train_shard_00001_1207_0", "global_id": 7362 }, { "text": "

Objectives

To explore a comprehensive genomic analysis of Clostridium perfringens type A strains from diverse regions in China, investigating their virulence genes, antibiotic resistance genes, and mobile genetic elements (MGEs) to inform strategies for infection control and resistance gene surveillance.

Methods

We conducted whole-genome sequencing on 168 C. perfringens type A strains from nine provinces in China (2016-2021). Previously described alpha-toxin (PLC) sequence typing for C. perfringens was used for comparisons with core genome multilocus sequence typing. Virulence genes, antibiotic resistance genes, and MGEs, including CRISPR/Cas, prophages, and plasmids of C. perfringens type A were investigated by molecular and bioinformatic methods.

Results

PLC type II contained the largest number of isolates (n = 44). The same type strains were largely clustered in the same branches. Tetracycline resistance genes tetA(P) and tetB(P) had high prevalence in type A isolates. 395 prophages were predicted including 265 \"incomplete,\" 55 \"questionable,\" and 75 \"intact\" prophages. CRISPR/Cas systems were more common in isolates from humans (63 %) than in those from animals and food (52 % and 46 %, respectively). Fifty-seven percent of strains likely had the tcp conjugation locus (tcpC to tcpH), and 12 isolates likely carried the conjugative pCW3 plasmid. Type A strains exhibited fewer plasmid-encoded toxins.

Conclusions

cgMLST analysis demonstrated some micro-evolution and regional transmission trends within type A, which exhibited partial correlated with PLC typing. This study highlights the need for enhanced surveillance of antimicrobial resistance and pathogenicity-associated MGEs in C. perfringens type A.\n\nGenomic analysis and mobile genetic elements carriage of Clostridium perfringens type A.", "token_count": 506, "char_count": 1849, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6331, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:26.746473", "source": { "split": "train_shard_00001", "doc_id": 1208 }, "chunk_id": "train_shard_00001_1208_0", "global_id": 7363 }, { "text": "Clostridium neonatale is a potential opportunistic pathogen recovered from faecal samples in cases of necrotizing enterocolitis (NEC), a gastrointestinal disease affecting preterm neonates. Although the C. neonatale species description and name validation were published in 2018, comparative genomics are lacking. In the present study, we provide the closed genome assembly of the C. neonatale ATCC BAA-265T (=250.09) reference strain with a manually curated functional annotation of the coding sequences. Pan-, core- and accessory genome analyses were performed using the complete 250.09 genome (4.7 Mb), three new assemblies (4.6-5.6 Mb), and five publicly available draft genome assemblies (4.6-4.7 Mb). The C. neonatale pan-genome contains 6840 genes, while the core-genome has 3387 genes. Pan-genome analysis revealed an 'open' state and genomic diversity. The strain-specific gene families ranged from five to 742 genes. Multiple mobile genetic elements were predicted, including a total of 201 genomic islands, 13 insertion sequence families, one CRISPR-Cas type I-B system and 15 predicted intact prophage signatures. Primary virulence classes including offensive, defensive, regulation of virulence-associated genes and non-specific virulence factors were identified. The presence of a tet(W/N/W) gene encoding a tetracycline resistance ribosomal protection protein and a 23S rRNA methyltransferase ermQ gene were identified in two different strains. Together, our results revealed a genetic diversity and plasticity of C. neonatale genomes and provide a comprehensive view of this species genomic features, paving the way for the characterization of its biological capabilities.", "token_count": 501, "char_count": 1748, "word_count": 233, "semantic_coherence": 1, "information_density": 0.7082, "quality_score": 0.8541, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:27.398358", "source": { "split": "train_shard_00001", "doc_id": 1209 }, "chunk_id": "train_shard_00001_1209_0", "global_id": 7364 }, { "text": "Core-, pan- and accessory genome analyses of Clostridium neonatale: insights into genetic diversity.", "token_count": 31, "char_count": 107, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:27.765206", "source": { "split": "train_shard_00001", "doc_id": 1209 }, "chunk_id": "train_shard_00001_1209_1", "global_id": 7365 }, { "text": "

Background

Low-abundance microorganisms of the gut microbiome are often referred to as a reservoir for antibiotic resistance genes. Unfortunately, these less-abundant bacteria can be overlooked by deep shotgun sequencing. In addition, it is a challenge to associate the presence of resistance genes with their risk of acquisition by pathogens. In this study, we used liquid culture enrichment of stools to assemble the genome of lower-abundance bacteria from fecal samples. We then investigated the gene content recovered from these culture-enriched and culture-independent metagenomes in relation with their taxonomic origin, specifically antibiotic resistance genes. We finally used a pangenome approach to associate resistance genes with the core or accessory genome of Enterobacteriaceae and inferred their propensity to horizontal gene transfer.

Results

Using culture-enrichment approaches with stools allowed assembly of 187 bacterial species with an assembly size greater than 1 million nucleotides. Of these, 67 were found only in culture-enriched conditions, and 22 only in culture-independent microbiomes. These assembled metagenomes allowed the evaluation of the gene content of specific subcommunities of the gut microbiome. We observed that differentially distributed metabolic enzymes were associated with specific culture conditions and, for the most part, with specific taxa. Gene content differences between microbiomes, for example, antibiotic resistance, were for the most part not associated with metabolic enzymes, but with other functions. We used a pangenome approach to determine if the resistance genes found in Enterobacteriaceae, specifically E. cloacae or E. coli, were part of the core genome or of the accessory genome of this species. In our healthy volunteer cohort, we found that E. cloacae contigs harbored resistance genes that were part of the core genome of the species, while E. coli had a large accessory resistome proximal to mobile elements.

Conclusion

Liquid culture of stools contributed to an improved functional and comparative genomics study of less-abundant gut bacteria, specifically those associated with antibiotic resistance", "token_count": 500, "char_count": 2197, "word_count": 304, "semantic_coherence": 1, "information_density": 0.523, "quality_score": 0.7615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:28.420681", "source": { "split": "train_shard_00001", "doc_id": 1210 }, "chunk_id": "train_shard_00001_1210_0", "global_id": 7366 }, { "text": "Defining whether a gene is part of the core genome of a species helped in interpreting the genomes recovered from culture-independent or culture-enriched microbiomes.\n\nCulture-enriched human gut microbiomes reveal core and accessory resistance genes.", "token_count": 59, "char_count": 250, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8529, "quality_score": 0.9265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:28.786200", "source": { "split": "train_shard_00001", "doc_id": 1210 }, "chunk_id": "train_shard_00001_1210_1", "global_id": 7367 }, { "text": "The COVID-19 pandemic has highlighted the critical role of genomic surveillance for guiding policy and control. Timeliness is key, but sequence alignment and phylogeny slow most surveillance techniques. Millions of SARS-CoV-2 genomes have been assembled. Phylogenetic methods are ill equipped to handle this sheer scale. We introduce a pangenomic measure that examines the information diversity of a k-mer library drawn from a country's complete set of clinical, pooled, or wastewater sequence. Quantifying diversity is central to ecology. Hill numbers, or the effective number of species in a sample, provide a simple metric for comparing species diversity across environments. The more diverse the sample, the higher the Hill number. We adopt this ecological approach and consider each k-mer an individual and each genome a transect in the pangenome of the species. Structured in this way, Hill numbers summarize the temporal trajectory of pandemic variants, collapsing each day's assemblies into genome equivalents. For pooled or wastewater sequence, we instead compare days using survey sequence divorced from individual infections. Across data from the UK, USA, and South Africa, we trace the ascendance of new variants of concern as they emerge in local populations well before these variants are named and added to phylogenetic databases. Using data from San Diego wastewater, we monitor these same population changes from raw, unassembled sequence. This history of emerging variants senses all available data as it is sequenced, intimating variant sweeps to dominance or declines to extinction at the leading edge of the COVID-19 pandemic.\n\nRapid SARS-CoV-2 surveillance using clinical, pooled, or wastewater sequence as a sensor for population change.", "token_count": 399, "char_count": 1774, "word_count": 262, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:29.401717", "source": { "split": "train_shard_00001", "doc_id": 1211 }, "chunk_id": "train_shard_00001_1211_0", "global_id": 7368 }, { "text": "Pangenome reference graphs are useful in genomics because they compactly represent the genetic diversity within a species, a capability that linear references lack. However, efficiently aligning sequences to these graphs with complex topology and cycles can be challenging. The seed-chain-extend based alignment algorithms use co-linear chaining as a standard technique to identify a good cluster of exact seed matches that can be combined to form an alignment. Recent works show how the co-linear chaining problem can be efficiently solved for acyclic pangenome graphs by exploiting their small width [Makinen et al ., TALG’19] and how incorporating gap cost in the scoring function improves alignment accuracy [Chandra and Jain, RECOMB’23]. However, it remains open on how to effectively generalize these techniques for general pangenome graphs which contain cycles. Here we present the first practical formulation and an exact algorithm for co-linear chaining on cyclic pangenome graphs. We rigorously prove the correctness and computational complexity of the proposed algorithm. We evaluate the empirical performance of our algorithm by aligning simulated long reads from the human genome to a cyclic pangenome graph constructed from 95 publicly available haplotype-resolved human genome assemblies. While the existing heuristic-based algorithms are faster, the proposed algorithm provides a significant advantage in terms of accuracy.

Implementation

https://github.com/at-cg/PanAligner\n\nCo-linear Chaining on Pangenome Graphs", "token_count": 332, "char_count": 1539, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:30.019697", "source": { "split": "train_shard_00001", "doc_id": 1212 }, "chunk_id": "train_shard_00001_1212_0", "global_id": 7369 }, { "text": "

Objectives

In this study, we report the complete genome sequence of a multidrug-resistant Escherichia coli LD91-1 recovered from a 57-year-old hepatitis B patient in Myanmar.

Methods

E. coli LD91-1 was subjected to antimicrobial susceptibility testing. Extracted genomic DNA from the E. coli LD91-1 clone was sequenced using a Nanopore PromethION sequencer (ONT, UK) and the high-throughput Illumina HiSeq 2500 platform. The clean reads were de novo assembled using Flye (v.2.9). The complete genome was annotated using MLST, phylogeny, serotyping, plasmid replicons, fimH typing, chromosomal point mutations, antibiotic resistance, and virulence genes using web tools available at the Center for Genomic Epidemiology.

Results

E. coli LD91-1 had a circular genome of 4,838,891 bp. In silico analysis revealed that E. coli LD91-1 comprised plasmid pLD91-1 and belonged to the ST1737-O22:H16 serotype carrying a fimH32 variant that had not been reported in such strains. Core genome phylogeny demonstrated clear divergence among major E. coli clades. Mutations in the quinolone resistance-determining regions gyrA, gyrB, parC, and parE conferred fluoroquinolone resistance; mutations in pmrA and pmrB conferred colistin resistance. Cephalosporin, fluoroquinolone, and tetracycline resistance genes were located on plasmid pLD91-1. Notably, several virulence genes, including 12 encoding yersiniabactin and yersiniabactin siderophores were also revealed in the E. coli LD91-1 genome.

Conclusions

To our knowledge, this is the first complete genome report of a new E", "token_count": 519, "char_count": 1591, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [ "LD91", "ST1737" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:30.699118", "source": { "split": "train_shard_00001", "doc_id": 1213 }, "chunk_id": "train_shard_00001_1213_0", "global_id": 7370 }, { "text": "coli LD91-1 carrying the fimH32 variant in Myanmar. This MDR E. coli isolate may pose potential risks to human and animal health, highlighting the urgent need for control and preventive strategies.\n\nComplete genome sequence of a novel fimH32 variant Escherichia coli LD91-1 ST1737, recovered from a hepatitis B patient in Yangon, Myanmar.", "token_count": 102, "char_count": 338, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8077, "quality_score": 0.9038, "entities": { "genes": [ "LD91", "ST1737" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:31.107373", "source": { "split": "train_shard_00001", "doc_id": 1213 }, "chunk_id": "train_shard_00001_1213_1", "global_id": 7371 }, { "text": "

Background

Enterococcus faecium and E. lactis are phylogenetically closely related lactic acid bacteria that are ubiquitous in nature and are known to be beneficial or pathogenic. Despite their considerable industrial and clinical importance, comprehensive studies on their evolutionary relationships and genomic, metabolic, and pathogenic traits are still lacking. Therefore, we conducted comparative pangenome analyses using all available dereplicated genomes of these species.

Results

E. faecium was divided into two subclades: subclade I, comprising strains derived from humans, animals, and food, and the more recent phylogenetic subclade II, consisting exclusively of human-derived strains. In contrast, E. lactis strains, isolated from diverse sources including foods, humans, animals, and the environment, did not display distinct clustering based on their isolation sources. Despite having similar metabolic features, noticeable genomic differences were observed between E. faecium subclades I and II, as well as E. lactis. Notably, E. faecium subclade II strains exhibited significantly larger genome sizes and higher gene counts compared to both E. faecium subclade I and E. lactis strains. Furthermore, they carried a higher abundance of antibiotic resistance, virulence, bacteriocin, and mobile element genes. Phylogenetic analysis of antibiotic resistance and virulence genes suggests that E. faecium subclade II strains likely acquired these genes through horizontal gene transfer, facilitating their effective adaptation in response to antibiotic use in humans.

Conclusions

Our study offers valuable insights into the adaptive evolution of E. faecium strains, enabling their survival as pathogens in the human environment through horizontal gene acquisitions.\n\nComparative pangenome analysis of Enterococcus faecium and Enterococcus lactis provides new insights into the adaptive evolution by horizontal gene acquisitions.", "token_count": 456, "char_count": 1960, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6342, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:31.767288", "source": { "split": "train_shard_00001", "doc_id": 1214 }, "chunk_id": "train_shard_00001_1214_0", "global_id": 7372 }, { "text": "In this work, by comparing genomes of closely related individuals of Streptomyces isolated at a spatial microscale (millimeters or centimeters), we investigated the extent and impact of horizontal gene transfer in the diversification of a natural Streptomyces population. We show that despite these conspecific strains sharing a recent common ancestor, all harbored significantly different gene contents, implying massive and rapid gene flux. The accessory genome of the strains was distributed across insertion/deletion events (indels) ranging from one to several hundreds of genes. Indels were preferentially located in the arms of the linear chromosomes (ca. 12 Mb) and appeared to form recombination hot spots. Some of them harbored biosynthetic gene clusters (BGCs) whose products confer an inhibitory capacity and may constitute public goods that can favor the cohesiveness of the bacterial population. Moreover, a significant proportion of these variable genes were either plasmid borne or harbored signatures of actinomycete integrative and conjugative elements (AICEs). We propose that conjugation is the main driver for the indel flux and diversity in Streptomyces populations.IMPORTANCE Horizontal gene transfer is a rapid and efficient way to diversify bacterial gene pools. Currently, little is known about this gene flux within natural soil populations. Using comparative genomics of Streptomyces strains belonging to the same species and isolated at microscale, we reveal frequent transfer of a significant fraction of the pangenome. We show that it occurs at a time scale enabling the population to diversify and to cope with its changing environment, notably, through the production of public goods.\n\nMassive Gene Flux Drives Genome Diversity between Sympatric Streptomyces Conspecifics.", "token_count": 438, "char_count": 1846, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:32.398518", "source": { "split": "train_shard_00001", "doc_id": 1215 }, "chunk_id": "train_shard_00001_1215_0", "global_id": 7373 }, { "text": "Investigation of the traditional cheeses and bringing them to the industry contributes to the development of dairy technology in terms of quality and diversity. For this purpose, traditional Turkish mouldy Civil cheese, which has a rich microbial diversity and is lovingly consumed, was studied and its yeast flora revealed. Samples were evaluated in terms of aerobic plate count, psychrotrophic bacteria, proteolytic bacteria, yeast, mould, coliform, enterococci, presumptive lactobacilli, presumptive lactococci, Staphylococcus aureus and Enterobacteriaceae counts. Seventy isolates were characterised by RAPD-PCR with M13 primer. Six diverse species were detected: Yarrowia lipolytica, Kluyveromyces marxianus, Pichia membranifaciens, Debaryomyces hansenii, Pichia fermentans and Candida zeylanoides. As a result, yeast diversity in mouldy Civil cheese may have an important role on development of characteristic blue cheese flavour and selected yeast strains could be used as adjunct culture to improve the quality of the final product.\n\nMicrobiological characteristics and identification of yeast microbiota of traditional mouldy civil cheese", "token_count": 289, "char_count": 1147, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7124, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:32.957481", "source": { "split": "train_shard_00001", "doc_id": 1216 }, "chunk_id": "train_shard_00001_1216_0", "global_id": 7374 }, { "text": "Lactiplantibacillus plantarum SPS109, an isolated strain of lactic acid bacteria (LAB) from fermented foods, showed remarkable potential as a probiotic with dual capabilities in γ-aminobutyric acid (GABA) production and cholesterol reduction. This study employs genomic and comparative analyses to search into the strain's genetic profile, safety features, and probiotic attributes. The safety assessment reveals the absence of virulence factors and antimicrobial resistance genes, while the genome uncovers bacteriocin-related elements, including sactipeptides and a cluster for putative plantaricins, strengthening its ability to combat diverse pathogens. Pangenome analysis revealed unique bacteriocin-related genes, specifically lcnD and bcrA, distinguishing SPS109 from four other L. plantarum strains producing GABA. In addition, genomic study emphasizes SPS109 strain distinctive features, two GABA-related genes responsible for GABA production and a bile tolerance gene (cbh) crucial for cholesterol reduction. Additionally, the analysis highlights several genes of potential probiotic properties, including stress tolerance, vitamin production, and antioxidant activity. In summary, L. plantarum SPS109 emerges as a promising probiotic candidate with versatile applications in the food and beverage industries, supported by its unique genomic features and safety profile.\n\nProbiogenomic analysis of Lactiplantibacillus plantarum SPS109: A potential GABA-producing and cholesterol-lowering probiotic strain.", "token_count": 413, "char_count": 1564, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6684, "quality_score": 0.8342, "entities": { "genes": [ "SPS109" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:33.583467", "source": { "split": "train_shard_00001", "doc_id": 1217 }, "chunk_id": "train_shard_00001_1217_0", "global_id": 7375 }, { "text": "The COVID-19 outbreak has caused significant global changes and increased public awareness of SARS-CoV-2. Substantial progress in developing vaccines, enhancing sanitation practices, and implementing various measures to combat the virus, including the utilization of probiotics has been made. This comprehensive review examined the medical impact of clinically proven probiotics on infectious diseases, considering three crucial time periods: before (pre-), during (mid-), and after (post-) COVID-19 pandemic era. This review also showed a perspective on the use of probiotics to stimulate the innate immune system and prevent infectious diseases. In pre-COVID-19 era, several probiotic strains were found to be clinically effective in addressing gastrointestinal infectious diseases, the common cold and flu. However, the mechanism by which probiotics exerted their antiviral effects remained relatively unclear during that period. Nevertheless, probiotics, Lactococcus lactis strain Plasma (LC-Plasma), and others have gained attention for their unique ability to modulate the immune system and demonstrate antiviral properties. While some probiotics have shown promise in alleviating gastrointestinal symptoms linked to COVID-19, their direct effectiveness in treating or preventing COVID-19 progression has not yet been conclusively established. As we transition into the post-COVID-19 era, the relationship between COVID-19 and plasmacytoid dendritic cells (pDCs), a vital component of the innate immune system, has been gradually elucidated. These findings are now being applied in developing novel vaccines and treatments involving interferons and in immune activation research using probiotics as adjuvants, comparable to CpG-DNA through TLR9. The role of the local innate immune system, including pDCs, as the first line of defense against viral infections has gained increasing interest. Moving forward, insight of the immune system and the crosstalk between probiotics and the innate immune system is expected to highlight the role of probiotics in adjunctive immunoregulatory therapy. In combination with drug treatments, probiotics may play a more substantial role in enhancing immune responses", "token_count": 496, "char_count": 2214, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8201, "entities": { "genes": [ "TLR9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:34.238131", "source": { "split": "train_shard_00001", "doc_id": 1218 }, "chunk_id": "train_shard_00001_1218_0", "global_id": 7376 }, { "text": "The immunoregulatory approach using probiotics such as LC-Plasma, which can induce anti-infectious factors such as interferons, holds promise as a viable therapeutic and prophylactic option against viral infectious diseases due to their good safety profile and protective efficacy.\n\nOverview of anti-viral effects of probiotics via immune cells in pre-, mid- and post-SARS-CoV2 era.", "token_count": 102, "char_count": 382, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8679, "quality_score": 0.934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:34.621830", "source": { "split": "train_shard_00001", "doc_id": 1218 }, "chunk_id": "train_shard_00001_1218_1", "global_id": 7377 }, { "text": "

Background

The drug resistance development in Mycobacterium tuberculosis (Mtb) is attributed to the acquisition of mutations in the drug target genes. However, the role of the differential presence of non-essential accessory genes is relatively unexplored and Pan Genome-Wide Association Study (Pan-GWAS) can identify these gene sets that could contribute to drug resistance development in Mtb.

Methodology

Publicly available Whole Genome Sequencing (WGS) data of clinical Mtb isolates (n=2601) from TB endemic countries (India, China, Zambia, Pakistan) were used in this study. The Mtb WGS data was de novo assembled, filtered for contamination, scaffolded into longer contigs, and functionally annotated. All analyses, including Gene repertoire and Pan-GWAS, were conducted using open-source tools, and the Benjamin Hochberg test was applied to identify genes having significant association with drug-resistant Mtb isolates.

Results

Out of 2601 Mtb WGS data sets, 2184 qualified as high-quality and were used for Pan-GWAS analysis (drug-resistant n=1386; drug-sensitive n=798). A set of 3784 core genes, 123 softcore genes, 224 shell genes, and 762 cloud genes were identified. Sets of 33 and 39 genes showed a positive and a negative association with drug-resistant isolates, respectively, with high significance (p-value < 0.01). Gene ontology cluster analysis indicated a compromised bacterial immune system and impaired DNA repair in drug-resistant compared to the sensitive isolates. Multidrug efflux pump repressor genes (Rv3830c and Rv3855c) were also absent in the drug-resistant Mtb isolates. The absence of CRISPR-associated genes (Rv2816c-19c) is reported in other drug-resistant microbes, and a similar pattern is observed in Mtb", "token_count": 496, "char_count": 1770, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6613, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:35.277543", "source": { "split": "train_shard_00001", "doc_id": 1219 }, "chunk_id": "train_shard_00001_1219_0", "global_id": 7378 }, { "text": "

Conclusions

This study sheds light on Mtb genes involved in drug resistance emergence and could be helpful in better understanding of host-pathogen interactions, identification of novel drug targets and diagnostics.\n\nPangenome-wide association study reveals selective absence of CRISPR genes (Rv2816c-19c) in drug-resistantMycobacterium tuberculosis", "token_count": 100, "char_count": 365, "word_count": 43, "semantic_coherence": 1, "information_density": 0.814, "quality_score": 0.907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:35.651992", "source": { "split": "train_shard_00001", "doc_id": 1219 }, "chunk_id": "train_shard_00001_1219_1", "global_id": 7379 }, { "text": "The killer-cell immunoglobulin-like receptor (KIR) gene complex, a highly polymorphic region of the human genome that encodes proteins involved in immune responses, poses strong challenges in genotyping due to its remarkable genetic diversity and structural intricacy. Accurate analysis of KIR alleles, including their structural variations, is crucial for understanding their roles in various immune responses. Leveraging the high-quality genome assemblies from the Human Pangenome Reference Consortium (HPRC), we present a novel bioinformatic tool, the Structural KIR annoTator (SKIRT), to investigate gene diversity and facilitate precise KIR allele analysis. We applied SKIRT on 47 HPRC-phased assemblies and identified a recurrent novel KIR2DS4/3DL1 fusion gene in the paternal haplotype of HG02630 and maternal haplotype of NA19240. Additionally, SKIRT accurately identifies eight structural variants and 17 novel nonsynonymous alleles, all of which were independently validated using short-read data or quantitative polymerase chain reaction. Our study has discovered a total of 570 novel alleles, among which eight haplotypes harbor at least one KIR gene duplication, six haplotypes have lost at least one framework gene, and 75 out of 94 haplotypes (79.8%) carry at least five novel alleles, thus confirming KIR genetic diversity. These findings are pivotal in providing insights into KIR gene diversity and serve as a solid foundation for understanding the functional consequences of KIR structural variations. High-resolution genome assemblies offer unprecedented opportunities to explore polymorphic regions that are challenging to investigate using short-read sequencing methods. The SKIRT pipeline emerges as a highly efficient tool, enabling the comprehensive detection of the complete spectrum of KIR alleles within human genome assemblies.\n\nGenetic Diversity and Structural Complexity of the Killer-Cell Immunoglobulin-Like Receptor Gene Complex: A Comprehensive Analysis Using Human Pangenome Assemblies", "token_count": 490, "char_count": 2021, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [ "NA19240", "HG02630" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:36.300410", "source": { "split": "train_shard_00001", "doc_id": 1220 }, "chunk_id": "train_shard_00001_1220_0", "global_id": 7380 }, { "text": "

Objectives

To characterize carbapenem-resistant Acinetobacter baumannii isolates associated with healthcare-associated infections (HAIs) in Colombia using whole-genome sequencing (WGS).

Methods

A total of 83 A. baumannii isolates collected between 2012 and 2015 were sequenced using the Illumina platform. Raw reads were assembled by SPAdes and classified via multilocus sequence typing (MLST), using the Pasteur, Oxford, and core genome MLST (cgMLST) schemes. Antimicrobial resistance determinants, capsule types, and outer core (OC) serotypes were identified. Phylogenetic relationships were inferred through single nucleotide polymorphism (SNP) analysis using IQ-TREE.

Results

MLST analysis assigned isolates to 10 sequence types (STs) in the Pasteur scheme and 20 STs in the Oxford scheme. The most prevalent types were ST79 P (68.7%) and ST124 ° (25.3%). IC5 (ST79 P ) and IC7 (ST25 P /ST945 P ) were the predominant ICs, confirming their endemic presence in Colombia and highlighting the genetic diversity of emerging clonal variants. cgMLST identified 13 minimum spanning trees (MSTSs), with MST1 grouping 19 isolates. Carbapenem resistance was primarily driven by the presence of the class D β-lactamase gene bla OXA-23. The most common K locus types were KL9 and KL151, while the dominant OC locus was OCL10. Phylogenetic analysis revealed two major clades and seven minor clusters.

Conclusions

This study provides a comprehensive genomic overview of carbapenem-resistant A. baumannii isolates circulating in Colombia, highlighting key resistance determinants and population structure. These findings can inform public health strategies to mitigate the spread of high-risk clones and improve antimicrobial resistance surveillance.", "token_count": 511, "char_count": 1779, "word_count": 244, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [ "KL151", "IC7", "OCL10", "MST1", "IC5", "ST25", "KL9", "ST124", "ST945", "ST79" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:36.963143", "source": { "split": "train_shard_00001", "doc_id": 1221 }, "chunk_id": "train_shard_00001_1221_0", "global_id": 7381 }, { "text": "DISTRIBUTION AND GENOMIC CHARACTERIZATION OF COLOMBIAN CARBAPENEM-RESISTANT Acinetobacter baumannii ISOLATES", "token_count": 48, "char_count": 115, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:37.323373", "source": { "split": "train_shard_00001", "doc_id": 1221 }, "chunk_id": "train_shard_00001_1221_1", "global_id": 7382 }, { "text": "Capturing the genetic diversity of wild relatives is crucial for improving crops because wild species are valuable sources of agronomic traits that are essential to enhance the sustainability and adaptability of domesticated cultivars. Genetic diversity across a genus can be captured in super-pangenomes, which provide a framework for interpreting genomic variations. Here we report the sequencing, assembly, and annotation of nine wild North American grape genomes, which were phased and scaffolded at chromosome scale. We generate a reference-unbiased super-pangenome using pairwise whole-genome alignment methods, revealing the extent of the genomic diversity among wild grape species from sequence to gene level. The pangenome graph captures genomic variation between haplotypes within a species and across the different species, and it accurately assesses the similarity of hybrids to their parents. The species selected to build the pangenome are a great representation of the genus, as illustrated by capturing known allelic variants in the sex-determining region and for Pierce’s disease resistance loci. Using pangenome-wide association analysis, we demonstrate the utility of the super-pangenome by effectively mapping short-reads from genus-wide samples and identifying loci associated with salt tolerance in natural populations of grapes. This study highlights how a reference-unbiased super-pangenome can reveal the genetic basis of adaptive traits from wild relatives and accelerate crop breeding research.\n\nA super-pangenome of the North American wild grape species", "token_count": 333, "char_count": 1581, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:37.898714", "source": { "split": "train_shard_00001", "doc_id": 1222 }, "chunk_id": "train_shard_00001_1222_0", "global_id": 7383 }, { "text": "Abstract

The genus Apiospora has been relatively understudied in comparison to other filamentous fungi species, despite indications from previous research that this genus could yield valuable discoveries of novel enzymes and secondary metabolites applicable to various practical uses. In this investigation, we conducted sequencing of 16 previously uncharacterized Apiospora genomes. Seven are distantly related to previously known genomes and are the first genome assembly available for these species. In conjunction with five existing genome assemblies, we conducted an examination of the genetic composition and diversity within this genus. A deeper analysis of the genomes revealed a genus rich in genes associated with carbohydrate-active enzymes (CAZymes) and secondary metabolites. We identified the synthesis potential of CAZymes to be a core genome feature of the genus. In addition, clustering of polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) core genes into gene families, revealed a highly diverse specialized metabolite synthesis potential within the genus. Surprisingly, we also found that certain Apiospora species completely lack the gene cluster responsible for the synthesis of 3-nitropropionic acid (3-NPA), a compound previously associated with this genus. Taken together, this study’s results elucidate an unusually high potential for the discovery of new enzymes and compounds within the Apiospora genus.

\n\nAnalysis of 21 Apiospora genomes reveals a genus with tremendous synthesis potential for carbohydrate-active enzymes and secondary metabolites", "token_count": 405, "char_count": 1684, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7977, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:38.524812", "source": { "split": "train_shard_00001", "doc_id": 1223 }, "chunk_id": "train_shard_00001_1223_0", "global_id": 7384 }, { "text": "The family Marseilleviridae was the second family of giant viruses that was described in 2013, after the family Mimiviridae. Marseillevirus marseillevirus, isolated in 2007 by coculture on Acanthamoeba polyphaga, is the prototype member of this family. Afterward, the worldwide distribution of marseilleviruses was revealed through their isolation from samples of various types and sources. Thus, 62 were isolated from environmental water, one from soil, one from a dipteran, one from mussels, and two from asymptomatic humans, which led to the description of 67 marseillevirus isolates, including 21 by the IHU Méditerranée Infection in France. Recently, five marseillevirus genomes were assembled from deep sea sediment in Norway. Isolated marseilleviruses have ≈250 nm long icosahedral capsids and 348-404 kilobase long mosaic genomes that encode 386-545 predicted proteins. Comparative genomic analyses indicate that the family Marseilleviridae includes five lineages and possesses a pangenome composed of 3,082 clusters of genes. The detection of marseilleviruses in both symptomatic and asymptomatic humans in stool, blood, and lymph nodes, and an up-to-30-day persistence of marseillevirus in rats and mice, raise questions concerning their possible clinical significance that are still under investigation.\n\nMarseilleviruses: An Update in 2021.", "token_count": 401, "char_count": 1387, "word_count": 189, "semantic_coherence": 1, "information_density": 0.672, "quality_score": 0.836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:39.144725", "source": { "split": "train_shard_00001", "doc_id": 1224 }, "chunk_id": "train_shard_00001_1224_0", "global_id": 7385 }, { "text": "Serotype surveillance of Streptococcus pneumoniae (the pneumococcus) is critical for understanding the effectiveness of current vaccination strategies. However, existing methods for serotyping are limited in their ability to identify co-carriage of multiple pneumococci and detect novel serotypes. To develop a scalable and portable serotyping method that overcomes these challenges, we employed Nanopore Adaptive Sampling (NAS), an on-sequencer enrichment method which selects for target DNA in real-time, for direct detection of S. pneumoniae in complex samples. Whereas NAS targeting the whole S. pneumoniae genome was ineffective in the presence of non-pathogenic streptococci, the method was both specific and sensitive when targeting the capsular biosynthetic locus (CBL), the operon that determines S. pneumoniae serotype. NAS significantly improved coverage and yield of the CBL relative to sequencing without NAS, and accurately quantified the relative prevalence of serotypes in samples representing co-carriage. To maximise the sensitivity of NAS to detect novel serotypes, we developed and benchmarked a new pangenome-graph algorithm, named GNASTy. We show that GNASTy outperforms the current NAS implementation, which is based on linear genome alignment, when a sample contains a serotype absent from the database of targeted sequences. The methods developed in this work provide an improved approach for novel serotype discovery and routine S. pneumoniae surveillance that is fast, accurate and feasible in low resource settings. GNASTy therefore has the potential to increase the density and coverage of global pneumococcal surveillance.

One sentence summary

Pangenome graph-based Nanopore Adaptive Sampling, presented in our tool GNASTy, is a sensitive, portable and cost-effective method for Streptococcus pneumoniae surveillance.\n\nGraph-based Nanopore Adaptive Sampling with GNASTy enables sensitive pneumococcal serotyping in complex samples", "token_count": 467, "char_count": 1969, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:39.782766", "source": { "split": "train_shard_00001", "doc_id": 1225 }, "chunk_id": "train_shard_00001_1225_0", "global_id": 7386 }, { "text": "Corynebacterium jeikeium is an opportunistic human pathogen with high genomic diversity. In the past, multi-drug resistance has been considered a hallmark of C. jeikeium. However, some strains of C. jeikeium are fully susceptible and thus, their reclassification would avoid the empirical therapy with glycopeptides. One hundred eighty-six clinical isolates and four reference isolates identified as C. jeikeium between 1994-1999 and 2012-2019, respectively, were analyzed by matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS) and 16S ribosomal RNA (16S rRNA) gene sequence analysis. A total of 153 confirmed C. jeikeium isolates was further analyzed by whole genome sequencing (WGS) and by disk diffusion antimicrobial susceptibility testing (AST). WGS and subsequent core genome single nucleotide polymorphism-based phylogenetic analysis segregated the isolates into seven phylogenetic clusters. The average nucleotide identity between the clusters was <95%, qualifying them as separate C. jeikeium genomospecies. Overall, AST profiles of all 153 isolates were heterogeneous for six of the 16 antibiotics tested. Notably, genomospecies 6 and 7 displayed mainly comparably small inhibition zones. For the other 10 antibiotics, all genomospecies displayed either small or large inhibition zones, respectively. Our study of C. jeikeium clinical isolates revealed a relatively complex phylogenetic structure", "token_count": 430, "char_count": 1502, "word_count": 196, "semantic_coherence": 1, "information_density": 0.7194, "quality_score": 0.8597, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:40.408238", "source": { "split": "train_shard_00001", "doc_id": 1226 }, "chunk_id": "train_shard_00001_1226_0", "global_id": 7387 }, { "text": "As soon as clear phenotypic traits can be attributed to the seven genomospecies by routine diagnostic tests, genomospecies encompassing mainly antibiotic-susceptible strains should be reclassified to fine-tune potential treatment strategies.IMPORTANCECorynebacterium jeikeium isolates typically display multi-drug resistance (MDR), frequently triggering empirical therapies with glycopeptides. However, some strains are susceptible to a broad range of antibiotics. In our study, analysis of a large collection of C. jeikeium by whole genome sequencing (WGS) and antibiotic resistance testing revealed genomic diversity, and some correlations between MDR phenotypes and specific genomospecies. While WGS is not yet a routine method, identification of MDR genomospecies may confirm the need for glycopeptide therapy. Identification of a less-resistant genomospecies would have even a higher clinical impact, as unnecessary therapies with glycopeptides are avoided, thereby reducing the selection for vancomycin-resistant enterococci. In the future, databases of diagnostic tools, e.g., MALDI-TOF, may be expanded to allow for the differentiation of genomospecies. Furthermore, rational taxonomic reclassification of some C. jeikeium genomospecies would help clinicians to fine-tune potential treatment strategies.\n\nAntibiotic resistance profiles of seven genomospecies of <i>Corynebacterium jeikeium</i> analyzed by whole genome sequencing.", "token_count": 377, "char_count": 1471, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6575, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:40.985014", "source": { "split": "train_shard_00001", "doc_id": 1226 }, "chunk_id": "train_shard_00001_1226_1", "global_id": 7388 }, { "text": "

Background

A significant surge in pertussis cases since early 2023 has raised serious public health concerns. To investigate the potential mechanisms contributing to this increased prevalence, we collected throat swab specimens from children exhibiting pertussis symptoms and conducted detailed molecular characterization.

Methods

All Bordetella pertussis (B. pertussis) isolates underwent whole-genome sequencing using the Illumina HiSeq platform (Illumina, San Diego, CA). Genome annotation was conducted with Prokka (https://github.com/tseemann/prokka/). Allele typing of key antigens and 23S rRNA mutations was determined using the Bordetella BIGSdb database. A phylogenetic tree was constructed using the maximum likelihood method based on core genome single-nucleotide polymorphisms.

Results

A total of 118 nasopharyngeal swab specimens were collected from patients diagnosed with B. pertussis infection. Of these, 48 isolates were successfully cultured and subjected to whole-genome sequencing. Genotyping revealed that 47 of these isolates shared the allelic profile ptxA1-ptxB1-ptxC4-ptxD1-ptxE4-ptxP3-fim2-1/fim3-1. All isolates exhibited bapC1 and brkA1/tcfA2//vag8/fhaB2 profiles, and belonged to the prn150 allele. Notably, approximately half of the isolates possessed an intact prn gene due to the insertion of IS481. A high prevalence of macrolide resistance was observed, with 97.5% of isolates carrying the A2047G mutation in the 23S rRNA gene. Phylogenetic analysis demonstrated significant genetic diversity between the circulating B. pertussis strains in Jiangsu Province and vaccine strains.

Conclusions

The increasing prevalence of macrolide-resistant B. pertussis strains exhibiting ptxP3-prn150 genotype poses a significant challenge to both disease control and treatment", "token_count": 522, "char_count": 1824, "word_count": 224, "semantic_coherence": 1, "information_density": 0.692, "quality_score": 0.846, "entities": { "genes": [ "IS481" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:41.642391", "source": { "split": "train_shard_00001", "doc_id": 1227 }, "chunk_id": "train_shard_00001_1227_0", "global_id": 7389 }, { "text": "The high virulence associated with these strains, coupled with antibiotic resistance, underscores the urgent need for the development of novel vaccine strategies to effectively combat this emerging threat.\n\nHigh Prevalence of Macrolide-resistant ptxP3-prn150 Bordetella pertussis in Jiangsu Province, China, 2024.", "token_count": 82, "char_count": 313, "word_count": 40, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:42.045176", "source": { "split": "train_shard_00001", "doc_id": 1227 }, "chunk_id": "train_shard_00001_1227_1", "global_id": 7390 }, { "text": "

Objectives

Melioidosis, caused by Burkholderia pseudomallei, is an environmentally acquired disease endemic to Southeast Asia and northern Australia, and increasingly recognised as an important but underdiagnosed tropical infection. In Taiwan, the spatial distribution and environmental reservoirs of this pathogen remain poorly understood.

Methods

We analysed 796 melioidosis cases reported between 2003 and 2024 and identified a recurrent, statistically significant cluster zone using SaTScan, especially during 2009-2013 and again in 2024. To investigate environmental persistence, we conducted long-term surveillance across 46 GIS-defined grid squares within the cluster zone from 2012 to 2024.

Results

This zone accounted for 61%-72% of national cases, with annual incidence rates ranging from 0.3 to 4.0 per 100,000 people. Three adjacent squares (31-33) consistently showed high soil PCR positivity (68.4%-85.5%). During rainy seasons, DNA concentrations in aerosols and stagnant surface water followed similar temporal patterns, influenced by rainfall and wind gusts. A heavy rainfall event in 2024 increased soil PCR positivity from 77.7% to 97.4%. Seventeen viable B. pseudomallei isolates were cultured from soil, surface water, aerosols and cattle shed wastewater. All belonged to ST58, ST1115 or ST1354, with ST58 prevalent across environmental sources. Core genome single nucleotide polymorphism (SNP) analysis revealed close phylogenetic relatedness between environmental and clinical ST58 isolates, indicating localised environmental-to-human transmission.

Conclusions

These findings provide insights into the environmental persistence and transmission dynamics of B. pseudomallei, supporting more effective risk assessment and public health strategies for melioidosis in endemic tropical regions.", "token_count": 487, "char_count": 1842, "word_count": 231, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [ "ST1354", "ST58", "ST1115" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:42.722399", "source": { "split": "train_shard_00001", "doc_id": 1228 }, "chunk_id": "train_shard_00001_1228_0", "global_id": 7391 }, { "text": "Long-Term Environmental Persistence and Phylogenetic Evidence of Burkholderia pseudomallei in a Melioidosis Case Cluster in Taiwan.", "token_count": 35, "char_count": 131, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:43.104867", "source": { "split": "train_shard_00001", "doc_id": 1228 }, "chunk_id": "train_shard_00001_1228_1", "global_id": 7392 }, { "text": "Bifidobacterium longum subsp. longum is a prevalent group in the human gut microbiome. Its persistence in the intestinal microbial community suggests a close host-microbe relationship according to age. The subspecies adaptations are related to metabolic capabilities and genomic and functional diversity. In this study, 154 genomes from public databases and four new Chilean isolates were genomically compared through an in silico approach to identify genomic divergence in genes associated with carbohydrate consumption and their possible adaptations to different human intestinal niches. The pangenome of the subspecies was open, which correlates with its remarkable ability to colonize several niches. The new genomes homogenously clustered within subspecies longum, as observed in phylogenetic analysis. B. longum SC664 was different at the sequence level but not in its functions. COG analysis revealed that carbohydrate use is variable among longum subspecies. Glycosyl hydrolases participating in human milk oligosaccharide use were found in certain infant and adult genomes. Predictive genomic analysis revealed that B. longum M12 contained an HMO cluster associated with the use of fucosylated HMOs but only endowed with a GH95, being able to grow in 2-fucosyllactose as the sole carbon source. This study identifies novel genomes with distinct adaptations to HMOs and highlights the plasticity of B. longum subsp. longum to colonize the human gut microbiota.\n\nComparative Genomic Analysis of Novel Bifidobacterium longum subsp. longum Strains Reveals Functional Divergence in the Human Gut Microbiota.", "token_count": 458, "char_count": 1681, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5844, "quality_score": 0.7922, "entities": { "genes": [ "SC664", "GH95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:43.763714", "source": { "split": "train_shard_00001", "doc_id": 1229 }, "chunk_id": "train_shard_00001_1229_0", "global_id": 7393 }, { "text": "The sequential inoculation of non-Saccharomyces yeasts and Saccharomyces cerevisiae in grape juice is becoming an increasingly popular practice to diversify wine styles and/or to obtain more complex wines with a peculiar microbial footprint. One of the main interactions is competition for nutrients, especially nitrogen sources, that directly impacts not only fermentation performance but also the production of aroma compounds. In order to better understand the interactions taking place between non-Saccharomyces yeasts and S. cerevisiae during alcoholic fermentation, sequential inoculations of three yeast species (Pichia burtonii, Kluyveromyces marxianus, Zygoascus meyerae) with S. cerevisiae were performed individually in a synthetic medium. Different species-dependent interactions were evidenced. Indeed, the three sequential inoculations resulted in three different behaviors in terms of growth. P. burtonii and Z. meyerae declined after the inoculation of S. cerevisiae which promptly outcompeted the other two species. However, while the presence of P. burtonii did not impact the fermentation kinetics of S. cerevisiae, that of Z. meyerae rendered the overall kinetics very slow and with no clear exponential phase. K. marxianus and S. cerevisiae both declined and became undetectable before fermentation completion. The results also demonstrated that yeasts differed in their preference for nitrogen sources. Unlike Z. meyerae and P. burtonii, K. marxianus appeared to be a competitor for S. cerevisiae (as evidenced by the uptake of ammonium and amino acids), thereby explaining the resulting stuck fermentation. Nevertheless, the results suggested that competition for other nutrients (probably vitamins) occurred during the sequential inoculation of Z", "token_count": 525, "char_count": 1878, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:44.423170", "source": { "split": "train_shard_00001", "doc_id": 1230 }, "chunk_id": "train_shard_00001_1230_0", "global_id": 7394 }, { "text": "meyerae with S. cerevisiae. The metabolic footprint of the non-Saccharomyces yeasts determined after 48 h of fermentation remained until the end of fermentation and combined with that of S. cerevisiae. For instance, fermentations performed with K. marxianus were characterized by the formation of phenylethanol and phenylethyl acetate, while those performed with P. burtonii or Z. meyerae displayed higher production of isoamyl alcohol and ethyl esters. When considering sequential inoculation of yeasts, the nutritional requirements of the yeasts used should be carefully considered and adjusted accordingly. Finally, our chemical data suggests that the organoleptic properties of the wine are altered in a species specific manner.\n\nAltered Fermentation Performances, Growth, and Metabolic Footprints Reveal Competition for Nutrients between Yeast Species Inoculated in Synthetic Grape Juice-Like Medium.", "token_count": 263, "char_count": 951, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7177, "quality_score": 0.8589, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:44.968801", "source": { "split": "train_shard_00001", "doc_id": 1230 }, "chunk_id": "train_shard_00001_1230_1", "global_id": 7395 }, { "text": "New high-quality human genome assemblies derived from lymphoblastoid cell lines (LCLs) provide reference genomes and pangenomes for genomics studies. However, the characteristics of LCLs pose technical challenges to profiling immunoglobulin (IG) genes. IG loci in LCLs contain a mixture of germline and somatically recombined haplotypes, making them difficult to genotype or assemble accurately. To address these challenges, we introduce IGLoo , a software tool that implements novel methods for analyzing sequence data and genome assemblies derived from LCLs. IGLoo characterizes somatic V(D)J recombination events in the sequence data and identifies the breakpoints and missing IG genes in the LCL-based assemblies. Furthermore, IGLoo implements a novel reassembly framework to improve germline assembly quality by integrating information about somatic events and population structural variantions in the IG loci. We applied IGLoo to study the assemblies from the Human Pangenome Reference Consortium, providing new insights into the mechanisms, gene usage, and patterns of V(D)J recombination, causes of assembly fragmentation in the IG heavy chain (IGH) locus, and improved representation of the IGH assemblies.\n\nIGLoo: Profiling the Immunoglobulin Heavy chain locus in Lymphoblastoid Cell Lines with PacBio High-Fidelity Sequencing reads", "token_count": 327, "char_count": 1342, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:45.541286", "source": { "split": "train_shard_00001", "doc_id": 1231 }, "chunk_id": "train_shard_00001_1231_0", "global_id": 7396 }, { "text": "Variation in the genome of Pseudomonas aeruginosa, an important pathogen, can have dramatic impacts on the bacterium's ability to cause disease. We therefore asked whether it was possible to predict the virulence of P. aeruginosa isolates based on their genomic content. We applied a machine learning approach to a genetically and phenotypically diverse collection of 115 clinical P. aeruginosa isolates using genomic information and corresponding virulence phenotypes in a mouse model of bacteremia. We defined the accessory genome of these isolates through the presence or absence of accessory genomic elements (AGEs), sequences present in some strains but not others. Machine learning models trained using AGEs were predictive of virulence, with a mean nested cross-validation accuracy of 75% using the random forest algorithm. However, individual AGEs did not have a large influence on the algorithm's performance, suggesting instead that virulence predictions are derived from a diffuse genomic signature. These results were validated with an independent test set of 25 P. aeruginosa isolates whose virulence was predicted with 72% accuracy. Machine learning models trained using core genome single-nucleotide variants and whole-genome k-mers also predicted virulence. Our findings are a proof of concept for the use of bacterial genomes to predict pathogenicity in P. aeruginosa and highlight the potential of this approach for predicting patient outcomes.IMPORTANCEPseudomonas aeruginosa is a clinically important Gram-negative opportunistic pathogen. P. aeruginosa shows a large degree of genomic heterogeneity both through variation in sequences found throughout the species (core genome) and through the presence or absence of sequences in different isolates (accessory genome). P. aeruginosa isolates also differ markedly in their ability to cause disease. In this study, we used machine learning to predict the virulence level of P. aeruginosa isolates in a mouse bacteremia model based on genomic content. We show that both the accessory and core genomes are predictive of virulence", "token_count": 524, "char_count": 2165, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5197, "quality_score": 0.7599, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:46.199232", "source": { "split": "train_shard_00001", "doc_id": 1232 }, "chunk_id": "train_shard_00001_1232_0", "global_id": 7397 }, { "text": "This study provides a machine learning framework to investigate relationships between bacterial genomes and complex phenotypes such as virulence.\n\nA Genome-Based Model to Predict the Virulence of Pseudomonas aeruginosa Isolates.", "token_count": 54, "char_count": 228, "word_count": 30, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:46.560937", "source": { "split": "train_shard_00001", "doc_id": 1232 }, "chunk_id": "train_shard_00001_1232_1", "global_id": 7398 }, { "text": "Pediococcus pentosaceus is a lactic acid bacterium used inter alia for the fermentation of milk, meat, vegetables, fruits, and even for brewing beer. Several health-promoting effects, such as antibacterial and antifungal activities or microphage and immune system stimulation, have been attributed. Apart from refining foods during the fermentation process, P. pentosaceus strains are added to meat and meat products as protective cultures to improve food safety, while leaving the organoleptic properties untouched. Since knowledge on the latter issue is still limited, we investigated 32 isolates from milk samples and teat canal biofilms regarding their antibacterial efficacy as a prerequisite for possible application as protective cultures. P. pentosaceus strains were unequivocally identified by DNA sequencing of the rrnA gene encoding 16S rRNA. Binary matrices obtained from random amplification of polymorphic DNA experiments showed that all isolates differed by more than 5% and thus represented subspecies. The antibacterial profiles against eight food-borne pathogens and food spoilage bacteria were determined. They efficiently combatted, although to various extents, Gram-negative bacteria such as Pseudomonas aeruginosa or Salmonella enterica, and Gram-positive bacteria such as Staphylococcus aureus and Listeria monocytogenes. Interestingly, acid production was dependent on the presence of the challenged pathogen and did not correlate with the extent of inhibition. Bioinformatic analyses of the genomes of the three top-ranked isolates revealed a pronounced genomic plasticity with a core genome of 1460 genes and additional 91, 130, and 161 unique genes, respectively. Each strain included a set of three, five, or six plasmids and was equipped with different genes encoding bacteriocins. The data suggest that multiple strains of P. pentosaceus should be included in order to optimize the selection of a culture for food preservation. The approach could also be applicable to other bacterial species.", "token_count": 524, "char_count": 2086, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:47.192167", "source": { "split": "train_shard_00001", "doc_id": 1233 }, "chunk_id": "train_shard_00001_1233_0", "global_id": 7399 }, { "text": "Comparative Analyses of <i>Pediococcus pentosaceus</i> Strains Isolated from Milk Cattle Reveal New Insights for Screening Food-Protective Cultures.", "token_count": 57, "char_count": 160, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:47.561750", "source": { "split": "train_shard_00001", "doc_id": 1233 }, "chunk_id": "train_shard_00001_1233_1", "global_id": 7400 }, { "text": "Vibrio mimicus is an emerging pathogen, mainly associated with contaminated seafood consumption. However, little is known about its evolution, biodiversity, and pathogenic potential. This study analyzes the pan-, core, and accessory genomes of nine V. mimicus strains. The core genome yielded 2424 genes in chromosome I (ChI) and 822 genes in chromosome II (ChII), with an accessory genome comprising an average of 10.9% of the whole genome for ChI and 29% for ChII. Core genome phylogenetic trees were obtained, and V. mimicus ATCC-33654 strain was the closest to the outgroup in both chromosomes. Additionally, a phylogenetic study of eight conserved genes (ftsZ, gapA, gyrB, topA, rpoA, recA, mreB, and pyrH), including Vibrio cholerae, Vibrio parilis, Vibrio metoecus, and Vibrio caribbenthicus, clearly showed clade differentiation. The main virulence genes found in ChI corresponded with type I secretion proteins, extracellular components, flagellar proteins, and potential regulators, while, in ChII, the main categories were type-I secretion proteins, chemotaxis proteins, and antibiotic resistance proteins. The accessory genome was characterized by the presence of mobile elements and toxin encoding genes in both chromosomes. Based on the genome atlas, it was possible to characterize differential regions between strains. The pan-genome of V. mimicus encompassed 3539 genes for ChI and 2355 genes for ChII. These results give us an insight into the virulence and gene content of V", "token_count": 516, "char_count": 1608, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:48.196534", "source": { "split": "train_shard_00001", "doc_id": 1234 }, "chunk_id": "train_shard_00001_1234_0", "global_id": 7401 }, { "text": "mimicus, as well as constitute the first approach to its diversity.\n\nCore and Accessory Genome Analysis of Vibrio mimicus.", "token_count": 38, "char_count": 133, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:48.559790", "source": { "split": "train_shard_00001", "doc_id": 1234 }, "chunk_id": "train_shard_00001_1234_1", "global_id": 7402 }, { "text": "Tuberculosis (TB) is an airborne communicable disease with high morbidity and mortality rates, especially in developing countries. The causal agents of TB belong to the complex Mycobacterium tuberculosis (MTBc), which is composed of different human and animal TB associated species. Some animal associated species have zoonotic potential and add to the burden of TB management. The BCG (\"Bacillus Calmette-Guérin\") vaccine is widely used for the prevention against TB, but its use is limited in immunocompromised patients and animals due to the adverse effects and disseminated life-threatening complications. In this study, we aimed to carry out a comparative genome analysis between the human adapted species including BCG vaccine strains to identify and pinpoint the conserved genes related to the virulence across all the species, which could add a new value for vaccine development. For this purpose, the sequences of 183 Mycobacterium tuberculosis (MTB) strains were retrieved from the freely available WGS dataset at NCBI. The species included: 168 sensu stricto MTB species with other human MTB complex associated strains: M. tuberculosis var. africanum (3), M. tuberculosis var. bovis (2 draft genomes) and 10 BCG species, which enabled the analysis of core genome which contains the conserved genes and some virulence factor determinants. Further, a phylogenetic tree was constructed including the genomes of human (183); animals MTB adapted strains (6) and the environmental Mycobacterium strain \"M. canettii\". Our results showed that the core genome consists of 1166 conserved genes among these species, which represents a small portion of the pangenome (7036 genes). The remaining genes in the pangenome (5870) are accessory genes, adding a high inter-species diversity", "token_count": 496, "char_count": 1845, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6113, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:49.210945", "source": { "split": "train_shard_00001", "doc_id": 1235 }, "chunk_id": "train_shard_00001_1235_0", "global_id": 7403 }, { "text": "Further, the core genome includes several virulence-associated genes and this could explain the rare infectiousness potential of some attenuated vaccine strains in some patients. This study reveals that low number of conserved genes in human adapted MTBc species and high inter-species diversity of the pan-genome could be considered for vaccine candidate development.\n\nPan and Core Genome Analysis of 183 Mycobacterium tuberculosis Strains Revealed a High Inter-Species Diversity among the Human Adapted Strains.", "token_count": 126, "char_count": 520, "word_count": 72, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:49.597042", "source": { "split": "train_shard_00001", "doc_id": 1235 }, "chunk_id": "train_shard_00001_1235_1", "global_id": 7404 }, { "text": "Difructose anhydride III (DFA III), a functional sweetener, is enzymatically produced from inulin by inulin fructotransferase (IFTase; EC 4.2.2.18). Here, a recombinant yeast strain hyper-secreting IFTase from Arthrobacter aurescens was developed by employing the translational fusion partner technique, and the recombinant yeast produced 77.5 g (64.6% yield) of DFA III from 200 g of crude extract of Jerusalem artichoke tuber powder containing 120 g of inulin during direct fermentation. The sugar purity of DFA III was increased up to 95% by additional incubation with Kluyveromyces marxianus. This study is the first report of the secretory production of recombinant IFTase in Saccharomyces cerevisiae, and the direct conversion of DFA III from crude extract of Jerusalem artichoke tuber powder by microbial fermentation.\n\nMicrobial production of difructose anhydride III from Jerusalem artichoke tuber powder by recombinant yeast Saccharomyces cerevisiae and Kluyveromyces marxianus", "token_count": 298, "char_count": 987, "word_count": 139, "semantic_coherence": 1, "information_density": 0.554, "quality_score": 0.777, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:50.162520", "source": { "split": "train_shard_00001", "doc_id": 1236 }, "chunk_id": "train_shard_00001_1236_0", "global_id": 7405 }, { "text": "Pangenome analysis is an indispensable step in bacterial genomics to address the high variability of bacteria genomes. However, speed and scalability remain a challenge for pangenome inference software tools to cope with the fast-growing genomic collections. We present PanTA, a software package for constructing the pangenomes of large bacterial collections. We show that PanTA exhibits an unprecedented multiple times more efficient than the current state-of-the-arts while maintaining a similar pangenome accuracy. In addition, PanTA introduces a novel mechanism to construct the pangenome progressively where new samples are added into an existing pangenome without rebuilding the accumulated collection from scratch. In the progressive mode, PanTA is demonstrated to consume orders of magnitude less computational resource than existing solutions in managing the pangenomes of growing microbial datasets. We further show that PanTA can build the pangenome of the entire collection of >28000 Escherichia coli genomes from the RefSeq database on a laptop computer in 32 hours, highlighting the scalability and practicality of PanTA.The software is open source and is publicly available at https://github.com/amromics/panta under an MIT license.\n\nEfficient inference of large pangenomes with PanTA", "token_count": 285, "char_count": 1299, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6374, "quality_score": 0.8187, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:50.719865", "source": { "split": "train_shard_00001", "doc_id": 1237 }, "chunk_id": "train_shard_00001_1237_0", "global_id": 7406 }, { "text": "Water caltrop (Trapa spp., Lythraceae) is a traditional but currently underutilized non-cereal crop. Here, we generated chromosome-level genome assemblies for the two diploid progenitors of allotetraploid Trapa. natans (4x, AABB), i.e., diploid T. natans (2x, AA) and Trapa incisa (2x, BB). In conjunction with four published (sub)genomes of Trapa, we used gene-based and graph-based pangenomic approaches and a pangenomic transposable element (TE) library to develop Trapa genomic resources. The pangenome displayed substantial gene-content variation with dispensable and private gene clusters occupying a large proportion (51.95%) of the total cluster sets in the six (sub)genomes. Genotyping of presence-absence variation (PAVs) identified 40 453 PAVs associated with 2570 genes specific to A- or B-lineages, of which 1428 were differentially expressed, and were enriched in organ development process, organic substance metabolic process and response to stimulus. Comparative genome analyses showed that the allotetraploid T. natans underwent asymmetric subgenome divergence, with the B-subgenome being more dominant than the A-subgenome. Multiple factors, including PAVs, asymmetrical amplification of TEs, homeologous exchanges (HEs), and homeolog expression divergence, together affected genome evolution after polyploidization. Overall, this study sheds lights on the genome architecture and evolution of Trapa, and facilitates its functional genomic studies and breeding program.\n\nPangenome of water caltrop reveals structural variations and asymmetric subgenome divergence after allopolyploidization.", "token_count": 493, "char_count": 1679, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7393, "quality_score": 0.8697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:51.368818", "source": { "split": "train_shard_00001", "doc_id": 1238 }, "chunk_id": "train_shard_00001_1238_0", "global_id": 7407 }, { "text": "

ABSTRACT

Klebsiella pneumoniae causes life-threatening nosocomial infections and is featured by a remarkable propensity for multidrug resistance acquisition. Infections caused by multidrug- (MDR) and extensively drug-resistant (XDR) strains lead to a limitation of therapeutic options and an increase in persistent infections, and they are usually represented by high-risk lineages. Based on these features and their relevance to global public health, most of the studies focused on such high-risk clones, and little is known about the epidemiological and evolutionary dynamics of new/geographically restricted lineages. This study aimed to unveil the antimicrobial resistance and virulence genetic repertoire of a clinical XDR K. pneumoniae (Kp199) strain belonging to geographically-restricted ST, not linked to any known clonal complex. Its intrinsic ( gyrA, parC, ramR, soxR and soxS mutations) and acquired resistome agreed with the observed XDR phenotype. An extensive arsenal of both antibiotic and heavy metal resistance genes was observed, as well as genes involved with resistance to several antiseptics currently used in clinical settings. The co-occurrence of bla KPC-2 and bla NDM-1 carbapenemase genes in Kp199 was an alarming finding since it could contribute to increased carbapenem resistance. Kp199 virulome was associated with bacterial survival and replication during infections. This study raises concern about a novel, geographically restricted K. pneumoniae lineage harbouring a huge resistome and virulome, which may strongly contribute to its successful establishment as an epidemic lineage. Therefore, our findings underscore the importance of vigilant surveillance and control measures to mitigate the threat posed by the potential emergence of new high-risk pandemic clones.\n\nGenomic insights on the potential role of the accessory genome in the emergence of a novel geographically restrictedK. pneumoniaelineage as a high-risk clone", "token_count": 486, "char_count": 1977, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:52.022508", "source": { "split": "train_shard_00001", "doc_id": 1239 }, "chunk_id": "train_shard_00001_1239_0", "global_id": 7408 }, { "text": "

Background

Salmonella spp. is a major foodborne pathogen with a wide variety of serovars associated with human cases and food sources. Nevertheless, in Europe a panel of ten serovars is responsible for up to 80% of confirmed human cases. Clustering studies by single nucleotide polymorphism (SNP) core-genome phylogenetic analysis of outbreaks due to these major serovars are simplified by the availability of many complete genomes in the free access databases. This is not the case for outbreaks due to less common serovars, such as Welikade, for which no reference genomes are available. In this study, we propose a method to solve this problem. We propose to perform a core genome MLST (cgMLST) analysis based on hierarchical clustering using the free-access EnteroBase to select the most suitable genome to use as a reference for SNP phylogenetic analysis. In this study, we applied this protocol to a retrospective analysis of a Salmonella enterica serovar Welikade (S. Welikade) foodborne outbreak that occurred in France in 2016. Finally, we compared the cgMLST and SNP analyses. SNP phylogenetic reconstruction was carried out considering the effect of recombination events identified by the ClonalFrameML tool. The accessory genome was also explored by phage content and virulome analyses.

Results

Our findings revealed high clustering concordance using cgMLST and SNP analyses. Nevertheless, SNP analysis allowed for better assessment of the genetic distance among strains. The results revealed epidemic clones of S. Welikade circulating within the poultry and dairy sectors in France, responsible for sporadic and non-sporadic human cases between 2012 and 2019.

Conclusions

This study increases knowledge on this poorly described serovar and enriches public genome databases with 42 genomes from human and non-human S. Welikade strains, including the isolate collected in 1956 in Sri Lanka, which gave the name to this serovar. This is the first genomic analysis of an outbreak due to S. Welikade described to date.", "token_count": 524, "char_count": 2048, "word_count": 305, "semantic_coherence": 1, "information_density": 0.577, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:52.681270", "source": { "split": "train_shard_00001", "doc_id": 1240 }, "chunk_id": "train_shard_00001_1240_0", "global_id": 7409 }, { "text": "Salmonella enterica subsp. enterica Welikade: guideline for phylogenetic analysis of serovars rarely involved in foodborne outbreaks.", "token_count": 35, "char_count": 133, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:53.041581", "source": { "split": "train_shard_00001", "doc_id": 1240 }, "chunk_id": "train_shard_00001_1240_1", "global_id": 7410 }, { "text": "Kluyveromyces marxianus DMKU3-1042 is a thermotolerant yeast strain suitable for high-temperature ethanol fermentation and genetic engineering with linear DNA. We have developed a highly efficient random gene integration method with a frequency that exceeds 2.5 x 10(6) transformants/microg linear DNA, a figure comparable to what is observed with autonomously replicating plasmid transformation in Saccharomyces cerevisiae. To establish the mechanism of random integration in DMKU3-1042, we identified and deleted the K. marxianus KU70 gene, which is known to be involved in the non-homologous end-joining (NHEJ) pathway. In yeast lacking KU70, high-frequency non-homologous gene integration was abolished and the Kmku70 mutants showed 82-95% homologous gene targeting efficiencies using homologous sequences of 40-1000 bp. These results indicate that the highly efficient NHEJ pathway can be utilized with random gene disruption techniques such as transposon mutagenesis and plasmid-free gene manipulations in K. marxianus.\n\nRandom and targeted gene integrations through the control of non-homologous end joining in the yeast Kluyveromyces marxianus.", "token_count": 313, "char_count": 1152, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "KU70", "DMKU3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:53.597049", "source": { "split": "train_shard_00001", "doc_id": 1241 }, "chunk_id": "train_shard_00001_1241_0", "global_id": 7411 }, { "text": "Ralstonia mannitolilytica, primarily recognized as an environmental bacterium, has emerged as an opportunistic pathogen associated with nosocomial infections. R. mannitolilytica is well-adapted to oligotrophic and humid environments, harbors intrinsic resistance to both disinfection measures and antimicrobial therapies and possesses the ability to bypass 0.2 µm filters, thereby facilitating its persistence in clinical and environmental reservoirs. In this study, 11 R. mannitolilytica isolates were isolated from bloodstream infection cases at a tertiary hospital in Liaocheng City, China, between November 2019 and November 2021. Clinical data, antimicrobial susceptibility profiles, and whole-genome sequencing were analyzed to investigate the resistance mechanisms, genomic characteristics, and clonal dissemination patterns. All isolates exhibited multidrug resistance, exhibiting resistance to ceftazidime, amikacin, gentamicin, imipenem, meropenem, polymyxin B, ceftazidime/avibactam, and chloramphenicol, while retaining susceptibility to minocycline, cefotaxime, cefepime, trimethoprim/sulfamethoxazole, tigecycline, and tetracycline. Core genome multilocus sequence typing and average nucleotide identity analyzes revealed two distinct clades, suggesting independent nosocomial transmission events. Genomic characterization uncovered the presence of intrinsic blaOXA-22-like and blaOXA-60-like carbapenemase genes, along with efflux pump genes (qacJ, adeF), contributing to resistance. Although the infection sources remain unresolved, this study demonstrates the utility of genomic surveillance in tracking hospital-acquired R. mannitolilytica outbreaks and advocates for stringent infection control measures to mitigate the spread of this opportunistic pathogen", "token_count": 521, "char_count": 1861, "word_count": 208, "semantic_coherence": 1, "information_density": 0.7452, "quality_score": 0.8726, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:07:54.277125", "source": { "split": "train_shard_00001", "doc_id": 1242 }, "chunk_id": "train_shard_00001_1242_0", "global_id": 7412 }, { "text": "This report provides novel comparative genomic insights into R. mannitolilytica, enhancing understanding of its resistance mechanisms and evolutionary adaptability.

Importance

Ralstonia mannitolilytica, an environmental bacterium increasingly linked to hospital-acquired infections, poses significant treatment challenges due to its resistance to common antibiotics. This study investigates 11 bloodstream infection cases caused by R. mannitolilytica in a Chinese hospital, revealing two distinct transmission clusters through genomic analysis. The findings highlight the bacterium's ability to persist in clinical settings and its resistance to critical antibiotics like carbapenems, likely driven by intrinsic genes and efflux pumps. By combining patient data and genomic surveillance, this work underscores the urgent need for enhanced infection control measures to curb outbreaks. It also provides novel comparative genomic insights into R. mannitolilytica, advancing our understanding of its evolution and resistance mechanisms, which is vital for guiding future clinical management and public health strategies.\n\nEpidemiological and genomic characteristics of <i>Ralstonia mannitolilytica</i> isolated from bloodstream in Liaocheng City, Shandong Province, China.", "token_count": 305, "char_count": 1316, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7134, "quality_score": 0.8567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:54.861814", "source": { "split": "train_shard_00001", "doc_id": 1242 }, "chunk_id": "train_shard_00001_1242_1", "global_id": 7413 }, { "text": "The principal objective of this study was to isolate and identify the microorganisms present in commercial kefir grains, a novel kefir-fermented coconut water (CWK) and a novel coconut water kefir-fermented sourdough using phenotypic identification and Sanger sequencing and examine the microbial diversity of CWK and CWK-fermented sourdough throughout the fermentation process using the MiSeq Illumina sequencing method. The phenotypic characterisation based on morphology identified ten isolates of LAB, five AAB and seven yeasts from kefir (K), CWK and CWK-fermented sourdough (CWKS). The results confirm the presence of the LAB species Limosilactobacillus fermentum, Lactobacillus. plantarum, L. fusant, L. reuteri and L. kunkeei; the AAB species Acetobacter aceti, A. lovaniensis and A. pasteurianus; and the yeast species Candida kefyr, Rhodotorula mucilaginosa, Saccharomyces cerevisiae, C. guilliermondii and C. colliculosa. To the best of our knowledge, the identification of Rhodotorula from kefir is being reported for the first time. This study provides important insights into the relative abundances of the microorganisms in CWKS. A decrease in pH and an increase in the titratable acidity for CWK- and CWK-fermented sourdough corresponded to the increase in D- and L-lactic acid production after 96 h of fermentation. Significant reductions in the pHs of CWK and CWKS were observed between 48 and 96 h of fermentation, indicating that the kefir microorganisms were able to sustain highly acidic environments", "token_count": 506, "char_count": 1613, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:55.559476", "source": { "split": "train_shard_00001", "doc_id": 1243 }, "chunk_id": "train_shard_00001_1243_0", "global_id": 7414 }, { "text": "There was also increased production of L-lactic acid with fermentation, which was almost twice that of D-lactic acid in CWK.\n\nIdentification of the Microbiota in Coconut Water, Kefir, Coconut Water Kefir and Coconut Water Kefir-Fermented Sourdough Using Culture-Dependent Techniques and Illumina-MiSeq Sequencing.", "token_count": 93, "char_count": 313, "word_count": 42, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:55.938358", "source": { "split": "train_shard_00001", "doc_id": 1243 }, "chunk_id": "train_shard_00001_1243_1", "global_id": 7415 }, { "text": "Tuberculosis, caused by Mycobacterium tuberculosis (M. tuberculosis), is one of the leading causes of human deaths globally according to the WHO TB 2019 report. The continuous rise in multi- and extensive-drug resistance in M. tuberculosis broadens the challenges to control tuberculosis. The availability of a large number of completely sequenced genomes of M. tuberculosis has provided an opportunity to explore the pangenome of the species along with the pan-phylogeny and to identify potential novel drug targets leading to drug discovery. We attempt to calculate the pangenome of M. tuberculosis that comprises a total of 150 complete genomes and performed the phylo-genomic classification and analysis. Further, the conserved core genome (1251 proteins) is subjected to various sequential filters (non-human homology, essentiality, virulence, physicochemical parameters, and pathway analysis) resulted in identification of eight putative broad-spectrum drug targets. Upon molecular docking analyses of these targets with ligands available at the DrugBank database shortlisted a total of five promising ligands with projected inhibitory potential; namely, 2'deoxy-thymidine-5'-diphospho-alpha-d-glucose, uridine diphosphate glucose, 2'-deoxy-thymidine-beta-l-rhamnose, thymidine-5'-triphosphate, and citicoline. We are confident that with further lead optimization and experimental validation, these lead compounds may provide a sound basis to develop safe and effective drugs against tuberculosis disease in humans.\n\nPangenome Analysis of Mycobacterium tuberculosis Reveals Core-Drug Targets and Screening of Promising Lead Compounds for Drug Discovery.", "token_count": 459, "char_count": 1701, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6574, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:56.576155", "source": { "split": "train_shard_00001", "doc_id": 1244 }, "chunk_id": "train_shard_00001_1244_0", "global_id": 7416 }, { "text": "Strains across the Lactobacillaceae family form the basis for a trillion-dollar industry. Our understanding of the genomic basis for their key traits is fragmented, however, including the metabolism that is foundational to their industrial uses. Pangenome analysis of publicly available Lactobacillaceae genomes allowed us to generate genome-scale metabolic network reconstructions for 26 species of industrial importance. Their manual curation led to more than 75,000 gene-protein-reaction associations that were deployed to generate 2,446 genome-scale metabolic models. Cross-referencing genomes and known metabolic traits allowed for manual metabolic network curation and validation of the metabolic models. As a result, we provide the first pangenomic basis for metabolism in the Lactobacillaceae family and a collection of predictive computational metabolic models that enable a variety of practical uses.\n\nPangenome reconstruction ofLactobacillaceaemetabolism predicts species-specific metabolic traits", "token_count": 242, "char_count": 1015, "word_count": 130, "semantic_coherence": 1, "information_density": 0.5923, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:57.055769", "source": { "split": "train_shard_00001", "doc_id": 1245 }, "chunk_id": "train_shard_00001_1245_0", "global_id": 7417 }, { "text": "Evolutionary events leading to organismal preference for a specific growth temperature, as well as genes whose products are needed for a proper function at that temperature, are poorly understood. Using 64 bacteria from phylum Thermotogota as a model system, we examined how optimal growth temperature changed throughout Thermotogota history. We inferred that Thermotogota ’s last common ancestor was a thermophile and that some Thermotogota evolved the mesophilic and hyperthermophilic lifestyles secondarily. By modeling gain and loss of genes throughout Thermotogota history and by reconstructing their phylogenies, we demonstrated that adaptations to lower and higher growth temperature require both the acquisition of necessary genes and loss of unnecessary genes. Via a pangenome-wide association study, we correlated presence/absence of 68 gene families with specific optimal growth temperature intervals. While some of these genes are poorly characterized, most are involved in metabolism of amino acids, nucleotides, carbohydrates, and lipids, as well as in signal transduction and regulation of transcription. Most of the 68 genes have a history of horizontal gene transfer to/from other bacteria and archaea, suggesting that parallel acquisitions of genes likely promote independent adaptations of different Thermotogota species to specific growth temperatures.

Significance

While the currently known range of life-permitting temperatures spans from −15°C to +122°C, most living organisms, including microbes, can grow only in a narrow temperature interval around their optimal growth temperature. The genetic and genomic determinants of such preference remain poorly understood. Using genomes from Thermotogota , a group of bacteria that collectively can grow between 20° and 90°C, we detected 68 genes, presence of which strongly correlates with growth at specific optimal growth temperature. Our findings dramatically expand a list of genes that are likely important for both lowering and increasing preferred growth temperature of a microorganism. We also demonstrated that these genes were usually horizontally acquired from other bacteria and archaea that likely share environment with Thermotogota , highlighting the importance of gene exchange in microbial adaptation.\n\nBacterial growth temperature as a horizontally acquired polygenic trait", "token_count": 509, "char_count": 2369, "word_count": 330, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:57.709280", "source": { "split": "train_shard_00001", "doc_id": 1246 }, "chunk_id": "train_shard_00001_1246_0", "global_id": 7418 }, { "text": "Vibrio cincinnatiensis is a poorly understood pathogenic Vibrio species, and the underlying mechanisms of its genetic diversity, genomic plasticity, evolutionary dynamics, and pathogenicity have not yet been comprehensively investigated. Here, a comparative genomic analysis of V. cincinnatiensis was constructed. The open pan-genome with a flexible gene repertoire exhibited genetic diversity. The genomic plasticity and stability were characterized by the determinations of diverse mobile genetic elements (MGEs) and barriers to horizontal gene transfer (HGT), respectively. Evolutionary divergences were exhibited by the difference in functional enrichment and selective pressure between the different components of the pan-genome. The evolution on the Chr I and Chr II core genomes was mainly driven by purifying selection. Predicted essential genes in V. cincinnatiensis were mainly found in the core gene families on Chr I and were subject to stronger evolutionary constraints. We identified diverse virulence-related elements, including the gene clusters involved in encoding flagella, secretion systems, several pili, and scattered virulence genes. Our results indicated the pathogenic potential of V. cincinnatiensis and highlighted that HGT events from other Vibrio species promoted pathogenicity. This pan-genome study provides comprehensive insights into this poorly understood species from the genomic perspective.\n\nComparative Genomic Analysis of Vibrio cincinnatiensis Provides Insights into Genetic Diversity, Evolutionary Dynamics, and Pathogenic Traits of the Species.", "token_count": 383, "char_count": 1635, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:58.295846", "source": { "split": "train_shard_00001", "doc_id": 1247 }, "chunk_id": "train_shard_00001_1247_0", "global_id": 7419 }, { "text": "As the mobile cassette carrier of the methicillin resistance gene mecA that is transported across staphylococci species, the evolution and origin of Staphylococcal Cassette Chromosome mec (SCCmec)-and in particular, the composition of mecA and SCCmec-have been extensively discussed in the scientific literature; however, information regarding its dissemination across geographical limits and evolution over decades remains limited. In addition, whole-genome sequencing-based macro-analysis was unable to provide sufficiently detailed evolutionary information on SCCmec. Herein, the cassette chromosome recombinase genes ccrAB/C, as essential components of SCCmec, were employed to explore the evolution of SCCmec. This work established the basic taxonomy of 33 staphylococci species. The CUB of mecA, ccrAB/C of 12 SCCmec types and core genome of 33 staphylococci species were subsequently compared; the phylogenetic relationship of ccrAB/C was observed via SCCmec typing on a temporal and geographical scale; and the duplicate appearance of ccrAB/C was illustrated by comparing SCCmec compositions. The results highlighted a deviation in the CUB of mecA and ccrAB/C, which evidenced their exogenous characteristics to staphylococci, and provided theological support for the phylogenetic analysis of ccrAB/C as representative of SCCmec", "token_count": 460, "char_count": 1476, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:58.939507", "source": { "split": "train_shard_00001", "doc_id": 1248 }, "chunk_id": "train_shard_00001_1248_0", "global_id": 7420 }, { "text": "Importantly, the phylogenetic relationship of ccrAB/C did not exhibit centralization over time; instead, similarly to mecA, ccrAB/C with similar identities had close clades across decades and geographical limits and different SCCmec types, which enabled us to discriminate SCCmec based on the sequence identity of ccrAB/C. In addition, the duplicate appearance of ccrAB/C and fixed composition of the ccrAB/C complex among different strains were indicative of more complicated transmission mechanisms than targeting direct repeats of SCCmec.\n\nIn Silico Exploration of Staphylococcal Cassette Chromosome mec (SCCmec) Evolution Based on Phylogenetic Relationship of ccrAB/C.", "token_count": 241, "char_count": 756, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7363, "quality_score": 0.8681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:07:59.424755", "source": { "split": "train_shard_00001", "doc_id": 1248 }, "chunk_id": "train_shard_00001_1248_1", "global_id": 7421 }, { "text": "Barley (Hordeum vulgare L.) is a major cereal grain with uses in the feed, food, and malting industries. Growth habit, seed dormancy, and disease resistance are important considerations when selecting germplasm for production or release. With the ever-increasing availability of sequencing technologies, a deeper understanding of the genes underlying these key traits is within reach. In the present case study, the VRN-H1 (HvBM5A), SD2 (HvMKK3), and the novel stem and stripe rust resistance quantitative trait locus (QTL) described by Hernandez et al. (Hernandez et al. Phytopathology 110:1082–1092, 2020b) were investigated. These loci in three advanced barley inbred genotypes were the focus of the present study using next-generation sequencing. The intent behind the study was the identification and exploration of possible causal sequence variation in the genotypes within the context of the whole gene or QTL region. The sequence data was used to identify an intron one deletion in the HvBM5A sequence of the spring genotype that was conserved in the winter and facultative genotypes. Interestingly, a tandem duplication of the HvMKK3 sequence was identified in one of the genotypes, Thunder, that merits further investigation. Finally, 13 high confidence genes were identified within the Morex V3 reference genome in proximity to the rust QTL identified previously. Sequence variation between all tested genotypes was identified for 11 of the genes. This study explored structural and sequence variation of key genes in barley development and outlined directions for future research. The remaining, unexplored genome sequence will be a resource for identifying allelic variation and will contribute to the growing barley pangenome.\n\nExploratory genomic sequence analysis reveals structural differences at key loci for growth habit, seed dormancy, and rust resistance in barley", "token_count": 446, "char_count": 1885, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5863, "quality_score": 0.7932, "entities": { "genes": [ "SD2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:00.051420", "source": { "split": "train_shard_00001", "doc_id": 1249 }, "chunk_id": "train_shard_00001_1249_0", "global_id": 7422 }, { "text": "

Aims

Avian pathogenic Escherichia coli (APEC) causes colibacillosis, requiring effective vaccines to prevent this devastating disease in poultry. Current strain-specific vaccines show limited protection against diverse APEC strains, highlighting the need to identify conserved antigens for broad-protective vaccine development. This study combines reverse vaccinology (RV) analysis of APEC whole-genome sequences with host-pathogen interaction studies to identify universal vaccine candidates, their expression, and effect on host immune responses. These complementary approaches aim to identify and select potential antigens for the development of broad-spectrum vaccines against APEC infections in poultry.

Methods and results

A total of 3061 core genome protein coding sequences were predicted from 25 APEC isolates, including 44 proteins that met the criteria of subcellular localization (extracellular and outer membrane), number of transmembrane helix (0 or 1), and adhesion probability score (≥ 0.5). Among them, 32 proteins were antigenic (antigen score ≥ 0.5) and highly conserved across the E. coli database. Finally, 13 vaccine candidates were predicted to have the immunogenicity potential. During the host-pathogen interaction studies, selected E. coli isolates induced a host immune reaction (all with P ≤ 0.01), and among the 13 predicted vaccine candidates, pagP showed a highly upregulated expression level during the interaction (P ≤ 0.01).

Conclusions

In this study, pagP was identified as having the most potential for future development of recombinant vaccines against APEC.\n\nReverse vaccinology and host-pathogen analysis reveal pagP as a potential universal vaccine candidate against avian pathogenic Escherichia coli in poultry.", "token_count": 452, "char_count": 1774, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:00.684969", "source": { "split": "train_shard_00001", "doc_id": 1250 }, "chunk_id": "train_shard_00001_1250_0", "global_id": 7423 }, { "text": "The fungus Fusarium oxysporum (Fo) is widely known for causing wilt disease in over 100 different plant species. Endophytic interactions of Fo with plants are much more common, and strains pathogenic on one plant species can even be beneficial endophytes on another species. However, endophytic and beneficial interactions have been much less investigated at the molecular level, and the genetic basis that underlies endophytic versus pathogenic behavior is unknown. To investigate this, 44 Fo strains from non-cultivated Australian soils, grass roots from Spain, and tomato stems from United States were characterized genotypically by whole genome sequencing, and phenotypically by examining their ability to symptomlessly colonize tomato plants and to confer resistance against Fusarium Wilt. Comparison of the genomes of the validated endophytic Fo strains with those of 102 pathogenic strains revealed that both groups have similar genomes sizes, with similar amount of accessory DNA. However, although endophytic strains can harbor homologs of known effector genes, they have typically fewer effector gene candidates and associated non-autonomous transposons (mimps) than pathogenic strains. A pathogenic 'lifestyle' is associated with extended effector gene catalogs and a set of \"host specific\" effectors. No candidate effector genes unique to endophytic strains isolated from the same plant species were found, implying little or no host-specific adaptation. As plant-beneficial interactions were observed to be common for the tested Fo isolates, the propensity for endophytism and the ability to confer biocontrol appears to be a predominant feature of this organism. These findings allow prediction of the lifestyle of a Fo strain based on its genome sequence as a potential pathogen or as a harmless or even beneficial endophyte by determining its effectorome and mimp number.\n\nNumber of Candidate Effector Genes in Accessory Genomes Differentiates Pathogenic From Endophytic Fusarium oxysporum Strains.", "token_count": 496, "char_count": 2042, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5842, "quality_score": 0.7921, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:01.682473", "source": { "split": "train_shard_00001", "doc_id": 1251 }, "chunk_id": "train_shard_00001_1251_0", "global_id": 7424 }, { "text": "Industrial manufacturing of bioproducts, especially bioethanol, can benefit from high-temperature fermentation, which requires the use of thermotolerant yeast strains. Mitochondrial activity in yeast is closely related to its overall metabolism. However, the mitochondrial respiratory changes in response to adaptive thermotolerance are still poorly understood and have been rarely utilized for developing thermotolerant yeast cell factories. Here, adaptive evolution and transcriptional sequencing, as well as whole-genome-level gene knockout, were used to obtain a thermotolerant strain of Saccharomyces cerevisiae. Furthermore, thermotolerance and bioethanol production efficiency of the engineered strain were examined. Physiological evaluation showed the boosted fermentation capacity and suppressed mitochondrial respiratory activity in the thermotolerant strain. The improved fermentation produced an increased supply of adenosine triphosphate required for more active energy-consuming pathways. Transcriptome analysis revealed significant changes in the expression of the genes involved in the mitochondrial respiratory chain. Evaluation of mitochondria-associated gene knockout confirmed that ADK1, DOC1, or MET7 were the key factors for the adaptive evolution of thermotolerance in the engineered yeast strain. Intriguingly, overexpression of DOC1 with TEF1 promoter regulation led to a 10.1% increase in ethanol production at 42 °C. The relationships between thermotolerance, mitochondrial activity, and respiration were explored, and a thermotolerant yeast strain was developed by altering the expression of mitochondrial respiration-related genes. This study provides a better understanding on the physiological mechanism of adaptive evolution of thermotolerance in yeast.\n\nElucidation and engineering mitochondrial respiratory-related genes for improving bioethanol production at high temperature in Saccharomyces cerevisiae.", "token_count": 486, "char_count": 1981, "word_count": 241, "semantic_coherence": 1, "information_density": 0.61, "quality_score": 0.805, "entities": { "genes": [ "MET7", "DOC1", "TEF1", "ADK1" ], "proteins": [], "pathways": [ "metabolism", "fermentation", "respiration" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:02.336520", "source": { "split": "train_shard_00001", "doc_id": 1252 }, "chunk_id": "train_shard_00001_1252_0", "global_id": 7425 }, { "text": "Hydrothermolysis pretreated switchgrass at 200 degrees C for 10min was used in a simultaneous saccharification and fermentation (SSF) process using five thermotolerant yeast strains Kluyveromyces marxianus IMB 1, IMB 2, IMB 3, IMB 4, and IMB 5 at 45 degrees C and Saccharomyces cerevisiae D(5)A at 37 degrees C. SSF was carried out for 7d using 5, 10, and 15FPU/g glucan to determine the effect of decreasing cellulase loading on ethanol yield. The effect of initial pH on SSF by S. cerevisiae D(5)A was also investigated. Fermentation by K. marxianus IMB 1, IMB 2, IMB 4, and IMB 5 ceased by 72 h and fermentation by K. marxianus IMB 3 ceased by 96 h, while fermentation S. cerevisiae D(5)A continued for 7d. At 96 and 120 h, IMB 3 and S. cerevisiae D(5)A had similar ethanol yields while the other K. marxianus strains were lower at a 95% confidence level. Final ethanol yields for IMB 3, IMB 1, IMB 5 strains were similar to one another, however, ethanol yield for S. cerevisiae D(5)A (92% maximum theoretical) was greater than all of the IMB strains except IMB 3 at a 95% confidence level. Reducing enzyme loading reduced ethanol yields for both K. marxianus IMB 3 and S. cerevisiae D(5)A. Reducing buffer pH from 5.5 to 4.8 reduced ethanol yields for S. cerevisiae D(5)A. This study shows that K. marxianus IMB 3 has potential for commercial use for ethanol production from cellulose in SSF processes with further improvement of its thermotolerance.", "token_count": 509, "char_count": 1454, "word_count": 249, "semantic_coherence": 1, "information_density": 0.4819, "quality_score": 0.741, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:03.001699", "source": { "split": "train_shard_00001", "doc_id": 1253 }, "chunk_id": "train_shard_00001_1253_0", "global_id": 7426 }, { "text": "Ethanol production through simultaneous saccharification and fermentation of switchgrass using Saccharomyces cerevisiae D(5)A and thermotolerant Kluyveromyces marxianus IMB strains.", "token_count": 51, "char_count": 181, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:03.364586", "source": { "split": "train_shard_00001", "doc_id": 1253 }, "chunk_id": "train_shard_00001_1253_1", "global_id": 7427 }, { "text": "High-throughput sequencing technologies have greatly advanced our understanding of microbiomes, but resolving microbial communities at species and strain levels remains challenging. Here, we developed and validated a pipeline for designing, multiplexing, and sequencing highly polymorphic taxon-specific long-read amplicons. We focused on the wheat microbiome as a proof-of-principle and demonstrate unprecedented resolution for the wheat-associated Pseudomonas microbiome and the ubiquitous fungal pathogen Zymoseptoria tritici . We achieved an order of magnitude higher phylogenetic resolution compared to existing ribosomal amplicons. The designed amplicons accurately capture species and strain diversity outperforming full-length 16S and ITS amplicons. Furthermore, we tracked microbial communities in the wheat phyllosphere across time and space to establish fine-grained species and strain-specific dynamics. To expand the utility of our approach, we generated pangenome-informed amplicon templates for additional key bacterial and fungal genera. Pangenome-informed microbiome profiling enables the tracking of microbial community dynamics in complex environments and overcomes limitations in phylogenetic resolution.\n\nHigh-resolution profiling of bacterial and fungal communities using pangenome-informed taxon-specific long-read amplicons", "token_count": 306, "char_count": 1347, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6503, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:03.935398", "source": { "split": "train_shard_00001", "doc_id": 1254 }, "chunk_id": "train_shard_00001_1254_0", "global_id": 7428 }, { "text": "

Background

Hospital wastewater is a reservoir of antimicrobial resistance (AMR), yet the genetic diversity and resistance mechanisms of environmental Escherichia coli in such settings remain underexplored. This study aimed to investigate the genomic characteristics, resistance profiles, and virulence potential of E. coli isolates recovered from a hospital wastewater in Jakarta, Indonesia.

Methods and results

Six Escherichia coli isolates from hospital wastewater were sequenced using short-read next-generation sequencing (NGS). Raw reads were quality-checked and assembled with SPAdes, with five genomes retained for downstream analysis. Antimicrobial resistance (AMR) genes were identified using Staramr and the CARD database, while virulence factors were predicted using Abricate against the Virulence Factors Database (VFDB). Plasmid replicons were detected with PlasmidFinder. Phylogroup assignment followed the Clermont typing method, and phylogenetic analysis was conducted using a neighbor-joining tree based on core genome MLST (cgMLST) generated with chewBBACA v3.3.10. Multilocus sequence typing (MLST) revealed five distinct sequence types (ST744, ST156, ST1196, ST38, and ST10) across three phylogroups (A, B1, and D). A total of 57 AMR genes were detected, including blaCTX-M-15, blaCMY-2, and blaOXA-1 along with plasmid-mediated and chromosomal mutations conferring resistance to fluoroquinolones, aminoglycosides, and tetracyclines.

Conclusions

E. coli from hospital wastewater in Jakarta exhibited high genomic diversity, multidrug resistance, and variable virulence profiles. The findings support the role of untreated hospital effluents as a hotspot for AMR emergence and horizontal gene transfer. This showed the need for routine environmental surveillance to mitigate the public health risks associated with environmental reservoirs of resistant pathogens.", "token_count": 497, "char_count": 1904, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6722, "quality_score": 0.8361, "entities": { "genes": [ "ST1196", "ST10", "ST156", "ST744", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:04.591429", "source": { "split": "train_shard_00001", "doc_id": 1255 }, "chunk_id": "train_shard_00001_1255_0", "global_id": 7429 }, { "text": "Genomic characterization of multidrug-resistant Escherichia coli isolates from hospital wastewater in Jakarta, Indonesia.", "token_count": 30, "char_count": 121, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:04.943642", "source": { "split": "train_shard_00001", "doc_id": 1255 }, "chunk_id": "train_shard_00001_1255_1", "global_id": 7430 }, { "text": "The rat, Rattus norvegicus, has provided an important model for investigation of a range of characteristics of biomedical importance. Here we survey the origins of this species, its introduction into laboratory research, and the emergence of genetic and genomic methods that utilize this model organism. Genomic studies have yielded important progress and provided new insight into several biologically important traits. However, some studies have been impeded by the lack of a complete and accurate reference genome for this species. New sequencing and genome assembly methods applied to the rat have resulted in a new reference genome assembly, GRCr8, which is a near telomere-to-telomere assembly of high base-level accuracy that incorporates several elements not captured in prior assemblies. As genome assembly methods continue to advance and production costs become a less significant obstacle, genome assemblies for multiple inbred rat strains are emerging. These assemblies will allow a rat pangenome assembly to be constructed that captures all the genetic variations in strains selected for their utility in research and will overcome reference bias, a limitation associated with reliance on a single reference assembly. By this means, the full utility of this model organism to genomic studies will begin to be revealed.\n\nThree decades of rat genomics: approaching the finish(ed) line.", "token_count": 291, "char_count": 1403, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:05.503960", "source": { "split": "train_shard_00001", "doc_id": 1256 }, "chunk_id": "train_shard_00001_1256_0", "global_id": 7431 }, { "text": "Staphylococcus aureus (S. aureus) ST22 is considered a clinically important clone because an epidemic strain EMRSA-15 belongs to ST22, and several outbreaks of this clone have been documented worldwide. We performed genomic analysis of an S. aureus strain Lr2 ST22 from Pakistan and determined comparative analysis with other ST22 strains. The genomic data show that Lr2 belongs to spa-type t2986 and harbors staphylococcal cassette chromosome mec (SCCmec) type IVa(2B), one complete plasmid, and seven prophages or prophage-like elements. The strain harbors several prophage-associated virulence factors, including Panton-Valentine leukocidin (PVL) and toxic shock syndrome toxin (TSST). The single nucleotide polymorphism (SNPs)-based phylogenetic relationship inferred from whole genome and core genome revealed that strain Lr2 exhibits the nearest identities to a South African community-acquired methicillin-resistant S. aureus (CA-MRSA) ST22 strain and makes a separate clade with an Indian CA-MRSA ST22 strain. Although most ST22 strains carry blaZ, mecA, and mutations in gyrA, the Lr2 strain does not have the blaZ gene but, unlike other ST22 strains, carries the antibiotic resistance genes erm(C) and aac(6')-Ie-aph(2″)-Ia. Among ST22 strains analyzed, only the strain Lr2 possesses both PVL and TSST genes. The functional annotation of genes unique to Lr2 revealed that mobilome is the third-largest Cluster of Orthologous Genes (COGs) category, which encodes genes associated with prophages and transposons", "token_count": 515, "char_count": 1610, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [ "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:06.189011", "source": { "split": "train_shard_00001", "doc_id": 1257 }, "chunk_id": "train_shard_00001_1257_0", "global_id": 7432 }, { "text": "This possibly makes methicillin-resistant S. aureus (MRSA) Lr2 ST22 strain highly virulent, and this study would improve the knowledge of MRSA ST22 strains in Pakistan. However, further studies are needed on a large collection of MRSA to comprehend the genomic epidemiology and evolution of this clone in Pakistan.\n\nComparative Genomic Analysis of a Panton-Valentine Leukocidin-Positive ST22 Community-Acquired Methicillin-Resistant Staphylococcus aureus from Pakistan.", "token_count": 141, "char_count": 483, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7258, "quality_score": 0.8629, "entities": { "genes": [ "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:06.640590", "source": { "split": "train_shard_00001", "doc_id": 1257 }, "chunk_id": "train_shard_00001_1257_1", "global_id": 7433 }, { "text": "Clostridium perfringens is an important cause of animal and human infections, however information about the genetic makeup of this pathogenic bacterium is currently limited. In this study, we sought to understand and characterise the genomic variation, pangenomic diversity, and key virulence traits of 56 C. perfringens strains which included 51 public, and 5 newly sequenced and annotated genomes using Whole Genome Sequencing. Our investigation revealed that C. perfringens has an \"open\" pangenome comprising 11667 genes and 12.6% of core genes, identified as the most divergent single-species Gram-positive bacterial pangenome currently reported. Our computational analyses also defined C. perfringens phylogeny (16S rRNA gene) in relation to some 25 Clostridium species, with C. baratii and C. sardiniense determined to be the closest relatives. Profiling virulence-associated factors confirmed presence of well-characterised C. perfringens-associated exotoxins genes including α-toxin (plc), enterotoxin (cpe), and Perfringolysin O (pfo or pfoA), although interestingly there did not appear to be a close correlation with encoded toxin type and disease phenotype. Furthermore, genomic analysis indicated significant horizontal gene transfer events as defined by presence of prophage genomes, and notably absence of CRISPR defence systems in >70% (40/56) of the strains. In relation to antimicrobial resistance mechanisms, tetracycline resistance genes (tet) and anti-defensins genes (mprF) were consistently detected in silico (tet: 75%; mprF: 100%)", "token_count": 508, "char_count": 1674, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7512, "quality_score": 0.8756, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:07.321367", "source": { "split": "train_shard_00001", "doc_id": 1258 }, "chunk_id": "train_shard_00001_1258_0", "global_id": 7434 }, { "text": "However, pre-antibiotic era strain genomes did not encode for tet, thus implying antimicrobial selective pressures in C. perfringens evolutionary history over the past 80 years. This study provides new genomic understanding of this genetically divergent multi-host bacterium, and further expands our knowledge on this medically and veterinary important pathogen.\n\nProbing Genomic Aspects of the Multi-Host Pathogen <i>Clostridium perfringens</i> Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.", "token_count": 159, "char_count": 554, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:07.795039", "source": { "split": "train_shard_00001", "doc_id": 1258 }, "chunk_id": "train_shard_00001_1258_1", "global_id": 7435 }, { "text": "CRISPR-Cas systems are prokaryotic acquired immunity mechanisms, which are found in 40% of bacterial genomes. They prevent viral infections through small DNA fragments called spacers. However, the vast majority of these spacers have not yet been associated with the virus they recognize, and it has been named CRISPR dark matter. By analyzing the spacers of tens of thousands of genomes from six bacterial species, we have been able to reduce the CRISPR dark matter from 80% to as low as 15% in some of the species. In addition, we have observed that, when a genome presents CRISPR-Cas systems, this is accompanied by particular sets of membrane proteins. Our results suggest that when bacteria present membrane proteins that make it compete better in its environment and these proteins are, in turn, receptors for specific phages, they would be forced to acquire CRISPR-Cas.\n\nAnalysis of bacterial pangenomes reduces CRISPR dark matter and reveals strong association between membranome and CRISPR-Cas systems.", "token_count": 243, "char_count": 1010, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7025, "quality_score": 0.8513, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:08.275877", "source": { "split": "train_shard_00001", "doc_id": 1259 }, "chunk_id": "train_shard_00001_1259_0", "global_id": 7436 }, { "text": "

Background

Typhoid fever, caused by Salmonella enterica serovar Typhi, is a significant public health concern due to the escalating of antimicrobial resistance (AMR), with limited treatment options for extensively drug-resistant (XDR) S. Typhi strains pose a serious threat to disease management and control. This study aimed to investigate the genomic characteristics, epidemiology and AMR genes of XDR S. Typhi strains from typhoid fever patients in Pakistan.

Methodology

We assessed 200 patients with enteric fever symptoms, confirming 65 S. Typhi cases through culturing and biochemical tests. Subsequent antimicrobial susceptibility testing revealed 40 cases of extensively drug-resistant (XDR) and 25 cases of multi-drug resistance (MDR). Thirteen XDR strains were selected for whole-genome sequencing, to analyze their sequence type, phylogenetics, resistance genes, pathogenicity islands, and plasmid sequences using variety of data analysis resources. Pangenome analysis was conducted for 140 XDR strains, including thirteen in-house and 127 strains reported from other regions of Pakistan, to assess their genetic diversity and functional annotation.

Results

MLST analysis classified all isolates as sequence type 1 (ST-1) with 4.3.1.1. P1 genotype characterization. Prophage and Salmonella Pathogenicity Island (SPI) analysis identified intact prophages and eight SPIs involved in Salmonella's invasion and replication within host cells. Genome data analysis revealed numerous AMR genes including dfrA7, sul1, qnrS1, TEM-1, Cat1, and CTX-M-15, and SNPs associated with antibiotics resistance. IncY, IncQ1, pMAC, and pAbTS2 plasmids, conferring antimicrobial resistance, were detected in a few XDR S. Typhi strains. Phylogenetic analysis inferred a close epidemiological linkage among XDR strains from different regions of Pakistan", "token_count": 492, "char_count": 1863, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:08.929607", "source": { "split": "train_shard_00001", "doc_id": 1260 }, "chunk_id": "train_shard_00001_1260_0", "global_id": 7437 }, { "text": "Pangenome was noted closed among these strains and functional annotation highlighted genes related to metabolism and pathogenesis.

Conclusion

This study revealed a uniform genotypic background among XDR S. Typhi strains in Pakistan, signifying a persistence transmission of a single, highly antibiotic-resistant clone. The closed pan-genome observed underscores limited genetic diversity and highlights the importance of genomic surveillance for combating drug-resistant typhoid infections.\n\nWhole-genome sequencing of extensively drug-resistant Salmonella enterica serovar Typhi clinical isolates from the Peshawar region of Pakistan.", "token_count": 149, "char_count": 642, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:09.363166", "source": { "split": "train_shard_00001", "doc_id": 1260 }, "chunk_id": "train_shard_00001_1260_1", "global_id": 7438 }, { "text": "

Background

Ibrexafungerp (SCY-078) is the newest oral and intravenous antifungal drug with broad activity, currently undergoing clinical trials for invasive candidiasis.

Objective

The aim of this study was to assess the in vitro activity of ibrexafungerp and comparators against a collection of 434 European blood isolates of Candida.

Methods

Ibrexafungerp, caspofungin, fluconazole, and micafungin minimum inhibitory concentrations (MICs) were collected from 12 European laboratories for 434 blood isolates, including 163 Candida albicans, 108 Candida parapsilosis, 60 Candida glabrata, 40 Candida tropicalis, 29 Candida krusei, 20 Candida orthopsilosis, 6 Candida guilliermondii, 2 Candida famata, 2 Candida lusitaniae, and 1 isolate each of Candida bracarensis, Candida catenulata, Candida dubliniensis, and Candida kefyr. MICs were determined by the EUCAST broth microdilution method, and isolates were classified according to recommended clinical breakpoints and epidemiological cutoffs. Additionally, 22 Candida auris from different clinical specimens were evaluated.

Results

Ibrexafungerp MICs ranged from 0.016 to ≥8 mg/L. The lowest ibrexafungerp MICs were observed for C", "token_count": 486, "char_count": 1317, "word_count": 151, "semantic_coherence": 1, "information_density": 0.702, "quality_score": 0.851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:10.014136", "source": { "split": "train_shard_00001", "doc_id": 1261 }, "chunk_id": "train_shard_00001_1261_0", "global_id": 7439 }, { "text": "albicans (geometric MIC 0.062 mg/L, MIC range 0.016-0.5 mg/L) and the highest ibrexafungerp MICs were observed for C. tropicalis (geometric MIC 0.517 mg/L, MIC range 0.06-≥8 mg/L). Modal MICs/MIC50s (mg/L) against Candida spp. were 0.125/0.06 for C. albicans, 0.5/0.5 for C. parapsilosis, 0.25/0.25 for C. glabrata, 0.5/0.5 for C. tropicalis, 1/1 for C. krusei, 4/2 for C. orthopsilosis, and 0.5/0.5 for C. auris. Ibrexafungerp showed activity against fluconazole- and echinocandin-resistant isolates. If adopting wild-type upper limits, a non-wild-type phenotype for ibrexafungerp was only observed for 16/434 (3.7%) isolates: 11 (4.6%) C. parapsilosis, 4 (5%) C. glabrata, and 1 (2.5%) C. tropicalis.

Conclusion

Ibrexafungerp showed a potent in vitro activity against Candida.\n\nIn Vitro Antifungal Activity of Ibrexafungerp (SCY-078) Against Contemporary Blood Isolates From Medically Relevant Species of Candida: A European Study.", "token_count": 500, "char_count": 1067, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6279, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:10.662062", "source": { "split": "train_shard_00001", "doc_id": 1261 }, "chunk_id": "train_shard_00001_1261_1", "global_id": 7440 }, { "text": "Gioddu is the sole variety of fermented milk originating in Italy. Despite the long history of consumption, Gioddu still represents an undisclosed source of microbial diversity. The present study was aimed to get an insight into the bacterial and fungal diversity of Gioddu samples collected from two artisan producers located in Sardinia. To this end 3 batches of Gioddu were collected from each producer and subjected to Polymerase Chain Reaction-Denaturing Gradient Gel Electrophoresis (PCR-DGGE) analyses. Gioddu was produced with sheep milk in accordance with the local tradition. Regarding the bacterial population, a low biodiversity emerged. In more detail, the sole species Lactobacillus delbrueckii subsp. bulgaricus was detected in all the samples, irrespective of the producer or the batch. A more ample microbial diversity was highlighted for the fungal population that included closest relatives to Pichia cactophila, Kluyveromyces marxianus and Galactomyces candidum. Based on the results, the detected bacterial and fungal species generally clustered in accordance with the producer, irrespective of the batch considered. It is noteworthy that, Gioddu revealed several microbiological similarities with kefir beverage, thus suggesting, by analogy, potential health benefits related to its consumption. More research is needed to better clarify the microbiota composition of Gioddu by using more powerful metagenomic techniques.\n\nBacterial and Fungal Communities of Gioddu as Revealed by PCR-DGGE Analysis.", "token_count": 443, "char_count": 1612, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:11.296255", "source": { "split": "train_shard_00001", "doc_id": 1262 }, "chunk_id": "train_shard_00001_1262_0", "global_id": 7441 }, { "text": "Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This paper introduces BAKIR (Biologically-informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community.\n\nBiologically-informed Killer cell immunoglobulin-like receptor (KIR) gene annotation tool", "token_count": 406, "char_count": 1882, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:11.921228", "source": { "split": "train_shard_00001", "doc_id": 1263 }, "chunk_id": "train_shard_00001_1263_0", "global_id": 7442 }, { "text": "

Background

In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool).

Methods

Simulations of short-read sequencing were conducted for 5 genomes of 27 pathogens of interest in animal, plant, and human health to evaluate the repeatability and reproducibility of cgMLST. Various quality parameters, such as read quality and depth of sequencing were applied, and several read simulations and genome assemblies were repeated using three tools: SPAdes, Unicycler and Shovill. In vitro sequencing were also used to evaluate assembly impact on cgMLST results, for six bacterial species: Bacillus thuringiensis, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, Vibrio parahaemolyticus and Xylella fastidiosa.

Results

The results highlighted variability in cgMLST, which not only related to the assembly tools, but also induced by the intrinsic composition of the genomes themselves. This variability observed in simulated sequencing was further validated with real data for six of the bacterial pathogens studied.

Conclusion

This highlights that the intrinsic genome composition affects assembly and resulting cgMLST profiles, and that variability in bioinformatics tools can induce a bias in cgMLST profiles. In conclusion, we propose that the completeness of cgMLST schemes should be considered when clustering strains.\n\nUnraveling the impact of genome assembly on bacterial typing: a one health perspective.", "token_count": 435, "char_count": 1778, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6596, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:12.549357", "source": { "split": "train_shard_00001", "doc_id": 1264 }, "chunk_id": "train_shard_00001_1264_0", "global_id": 7443 }, { "text": "An accurate diagnostic method for Salmonella serovars is fundamental to preventing the spread of associated diseases. A diagnostic polymerase chain reaction (PCR)-based method has proven to be an effective tool for detecting pathogenic bacteria. However, the gene markers currently used in real-time PCR to detect Salmonella serovars have low specificity and are developed for only a few serovars. Therefore, in this study, we explored the novel unique gene markers for 60 serovars that share similar antigenic formulas and show high prevalence using pangenome analysis and developed a real-time PCR to detect them. Before exploring gene markers, the 535 Salmonella genomes were evaluated, and some genomes had serovars different from the designated serovar information. Based on these analyses, serovar-specific gene markers were explored. These markers were identified as genes present in all strains of target serovar genomes but absent in strains of other serovar genomes. Serovar-specific primer pairs were designed from the gene markers, and a real-time PCR method that can distinguish between 60 of the most common Salmonella serovars in a single 96-well plate assay was developed. As a result, real-time PCR showed 100% specificity for 199 Salmonella and 29 non-Salmonella strains. Subsequently, the method developed was applied successfully to both strains with identified serovars and an unknown strain, demonstrating that real-time PCR can accurately detect serovars of strains compared with traditional serotyping methods, such as antisera agglutination. Therefore, our method enables rapid and economical Salmonella serotyping compared with the traditional serotyping method.\n\nRapid Real-Time Polymerase Chain Reaction for Salmonella Serotyping Based on Novel Unique Gene Markers by Pangenome Analysis.", "token_count": 483, "char_count": 1871, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5462, "quality_score": 0.7731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:13.191570", "source": { "split": "train_shard_00001", "doc_id": 1265 }, "chunk_id": "train_shard_00001_1265_0", "global_id": 7444 }, { "text": "The deployment of omics technologies has obtained an incredible boost over the past few decades with the advances in next-generation sequencing (NGS) technologies, innovative bioinformatics tools, and the deluge of available biological information. The major omics technologies in the limelight are genomics, transcriptomics, proteomics, metabolomics, and phenomics. These biotechnological advances have modernized crop breeding and opened new horizons for developing crop varieties with improved traits. The genomes of several crop species are sequenced, and a huge number of genes associated with crucial economic traits have been identified. These identified genes not only provide insights into the understanding of regulatory mechanisms of crop traits but also decipher practical grounds to assist in the molecular breeding of crops. This review discusses the potential of omics technologies for the acquisition of biological information and mining of the genes associated with important agronomic traits in important food and fiber crops, such as wheat, rice, maize, potato, tomato, cassava, and cotton. Different functional genomics approaches for the validation of these important genes are also highlighted. Furthermore, a list of genes discovered by employing omics approaches is being represented as potential targets for genetic modifications by the latest genome engineering methods for the development of climate-resilient crops that would in turn provide great impetus to secure global food security.\n\nOmics-driven exploration and mining of key functional genes for the improvement of food and fiber crops.", "token_count": 314, "char_count": 1621, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:13.759093", "source": { "split": "train_shard_00001", "doc_id": 1266 }, "chunk_id": "train_shard_00001_1266_0", "global_id": 7445 }, { "text": "Streptococcus pneumoniae is an opportunistic human pathogen responsible for high morbidity and mortality rates. Extensive genome sequencing revealed its large pangenome, serotype diversity, and provided insight into genome dynamics. However, functional genome analysis has lagged behind, as that requires detailed and time-consuming manual curation of genome annotations, and integration of genomic and phenotypic data. To remedy this, PneumoBrowse was presented in 2018; a user-friendly interactive online platform, which provided the detailed annotation of the S. pneumoniae D39V genome, alongside transcriptomic data. Since 2018, many new studies on S. pneumoniae genome biology and protein functioning have been performed. Here, we present PneumoBrowse 2 ( https://veeninglab.com/pneumobrowse ) , fully rebuilt in JBrowse 2. We updated annotations for transcribed and transcriptional regulatory features in the D39V genome. We added genome-wide data tracks for high-resolution chromosome conformation capture (Hi-C) data, chromatin immunoprecipitation coupled to high-throughput sequencing (ChIP-Seq), ribosome profiling, CRISPRi-seq gene essentiality data and more. Additionally, we included 18 phylogenetically diverse S. pneumoniae genomes and their annotations. By providing easy access to diverse high-quality genome annotations, and links to other databases (including UniProt and AlphaFold), PneumoBrowse 2 will further accelerate research and development into preventive and treatment strategies, through increased understanding of the pneumococcal genome.

Graphical abstract

\n\nPneumoBrowse 2: An integrated visual platform for curated genome annotation and multiomics data analysis ofStreptococcus pneumoniae", "token_count": 453, "char_count": 1736, "word_count": 219, "semantic_coherence": 1, "information_density": 0.7306, "quality_score": 0.8653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:14.394119", "source": { "split": "train_shard_00001", "doc_id": 1267 }, "chunk_id": "train_shard_00001_1267_0", "global_id": 7446 }, { "text": "Since the discovery of the urinary microbiome, including the identification of Escherichia coli in healthy hosts, its involvement in UTI development has been a subject of high interest. We explored the population diversity and antimicrobial resistance of E. coli (n = 22) in the urogenital microbiome of ten asymptomatic women (representing 50% of the sample tested). We evaluated their genomic relationship with extraintestinal pathogenic E. coli (ExPEC) strains from healthy and diseased hosts, including the ST131 lineage. E. coli prevalence was higher in vaginal samples than in urine samples, and occasionally different lineages were observed in the same individual. Furthermore, B2 was the most frequent phylogenetic group, with the most strains classified as ExPEC. Resistance to antibiotics of therapeutic relevance (e.g., amoxicillin-clavulanate conferred by blaTEM-30) was observed in ExPEC widespread lineages sequence types (ST) 127, ST131, and ST73 and ST95 clonal complexes. Phylogenomics of ST131 and other ExPEC lineages revealed close relatedness with strains from gastrointestinal tract and diseased host. These findings demonstrate that healthy urogenital microbiome is a source of potentially pathogenic and antibiotic resistant E. coli strains, including those causing UTI, e.g., ST131. Importantly, diverse E. coli lineages can be observed per individual and urogenital sample type which is relevant for future studies screening for this uropathogen.\n\nThe Darkest Place Is under the Candlestick-Healthy Urogenital Tract as a Source of Worldwide Disseminated Extraintestinal Pathogenic Escherichia coli Lineages.", "token_count": 484, "char_count": 1700, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6332, "quality_score": 0.8166, "entities": { "genes": [ "ST95", "ST131", "ST73" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:15.042776", "source": { "split": "train_shard_00001", "doc_id": 1268 }, "chunk_id": "train_shard_00001_1268_0", "global_id": 7447 }, { "text": "Fusarium circinatum is an important global pathogen of pine trees. Genome plasticity has been observed in different isolates of the fungus, but no genome comparisons are available. To address this gap, we sequenced and assembled to chromosome level five isolates of F. circinatum. These genomes were analysed together with previously published genomes of F. circinatum isolates FSP34 and KS17. Multi-sample variant calling identified a total of 461683 micro variants (SNPs and small indels) and a total of 1828 macro structural variants of which 1717 were copy number variants and 111 were inversions. Variant density was higher on sub-telomeric regions of chromosomes. Variant annotation revealed that genes involved in transcription, transport, metabolism and transmembrane proteins were overrepresented in gene sets affected by high impact variants. A core genome representing genomic elements conserved in all the isolates and a non-redundant pangenome representing all genomic elements is presented. Whole genome alignments showed that an average of 93% of the genomic elements are present in all isolates. The results of this study reveal that some genomic elements are not conserved within the isolates and some variants are high impact. The described genome-scale variations will help inform novel disease management strategies against the pathogen.\n\nIntra-Species Genomic Variation in the Pine Pathogen Fusarium Circinatum", "token_count": 354, "char_count": 1440, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [ "FSP34", "KS17" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:15.624794", "source": { "split": "train_shard_00001", "doc_id": 1269 }, "chunk_id": "train_shard_00001_1269_0", "global_id": 7448 }, { "text": "As a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses. Several data structures have been proposed for representing collections of genomes as pangenomes, in particular graphs. In this work we collect all publicly available high-quality human haplotypes and constructed the largest human pangenome graphs to date, incorporating 52 individuals in addition to two synthetic references (CHM13 and GRCh38). We build variation graphs and de Bruijn graphs of this collection using five of the state-of-the-art tools: Bifrost , mdbg , Minigraph , Minigraph-Cactus and pggb . We examine differences in the way each of these tools represents variations between input sequences, both in terms of overall graph structure and representation of specific genetic loci. This work sheds light on key differences between pangenome graph representations, informing end-users on how to select the most appropriate graph type for their application.\n\nConstruction and representation of human pangenome graphs", "token_count": 234, "char_count": 1152, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6807, "quality_score": 0.8404, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:16.105839", "source": { "split": "train_shard_00001", "doc_id": 1270 }, "chunk_id": "train_shard_00001_1270_0", "global_id": 7449 }, { "text": "The recent re-emergence of multidrug-resistant pathogens has exacerbated their threat to worldwide public health. The evolution of the genomics era has led to the generation of huge volumes of sequencing data at an unprecedented rate due to the ever-reducing costs of whole-genome sequencing (WGS). We have developed the Rapid Microbial Analysis Pipeline (rMAP), a user-friendly pipeline capable of profiling the resistomes of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter species) using WGS data generated from Illumina's sequencing platforms. rMAP is designed for individuals with little bioinformatics expertise, and automates the steps required for WGS analysis directly from the raw genomic sequence data, including adapter and low-quality sequence read trimming, de novo genome assembly, genome annotation, single-nucleotide polymorphism (SNP) variant calling, phylogenetic inference by maximum likelihood, antimicrobial resistance (AMR) profiling, plasmid profiling, virulence factor determination, multi-locus sequence typing (MLST), pangenome analysis and insertion sequence characterization (IS). Once the analysis is finished, rMAP generates an interactive web-like html report. rMAP installation is very simple, it can be run using very simple commands. It represents a rapid and easy way to perform comprehensive bacterial WGS analysis using a personal laptop in low-income settings where high-performance computing infrastructure is limited.\n\nrMAP: the Rapid Microbial Analysis Pipeline for ESKAPE bacterial group whole-genome sequence data.", "token_count": 443, "char_count": 1709, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:16.737303", "source": { "split": "train_shard_00001", "doc_id": 1271 }, "chunk_id": "train_shard_00001_1271_0", "global_id": 7450 }, { "text": "Prokaryotes demonstrate tremendous variation in gene content, even within individual bacterial clones or lineages. This diversity is made possible by the ability of bacteria to horizontally transfer DNA through a variety of mechanisms, and the extent of such transfer sets them apart from eukaryotes. What has become evident through interrogation of thousands of bacterial genomes is that gene variation is directly related to the ecology of the organism and is driven by continual processes of niche exploration, diversification, and adaptation. Of course, the acquisition of new genes is not necessarily beneficial, resulting in either the removal of that individual through purifying selection or the occurrence of compensatory mutations in the genomic “backbone” (i.e., core genes) that become epistatically linked to the presence accessory genes. There are now numerous examples of relationship between gene variation and niche adaptation. We explore some of those examples here as well as the population genomic footprint left by the dynamics of gene flow, diversification, and adaptation.\n\nStructure and Dynamics of Bacterial Populations: Pangenome Ecology", "token_count": 232, "char_count": 1163, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6272, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:17.214286", "source": { "split": "train_shard_00001", "doc_id": 1272 }, "chunk_id": "train_shard_00001_1272_0", "global_id": 7451 }, { "text": "Lawsonia intracellularis is a Gram-negative obligate intracellular bacterium that is the aetiological agent of proliferative enteropathy (PE), a common intestinal disease of major economic importance in pigs and other animal species. To date, progress in understanding the biology of L. intracellularis for improved disease control has been hampered by the inability to culture the organism in vitro. In particular, our understanding of the genomic diversity and population structure of clinical L. intercellularis is very limited. Here, we utilized a metagenomic shotgun approach to directly sequence and assemble 21 L. intracellularis genomes from faecal and ileum samples of infected pigs and horses across three continents. Phylogenetic analysis revealed a genetically monomorphic clonal lineage responsible for infections in pigs, with distinct subtypes associated with infections in horses. The genome was highly conserved, with 94 % of genes shared by all isolates and a very small accessory genome made up of only 84 genes across all sequenced strains. In part, the accessory genome was represented by regions with a high density of SNPs, indicative of recombination events importing novel gene alleles. In summary, our analysis provides the first view of the population structure for L. intracellularis, revealing a single major lineage associated with disease of pigs. The limited diversity and broad geographical distribution suggest the recent emergence and clonal expansion of an important livestock pathogen.\n\nMetagenomic sequencing of clinical samples reveals a single widespread clone of Lawsonia intracellularis responsible for porcine proliferative enteropathy.", "token_count": 427, "char_count": 1735, "word_count": 240, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:17.849374", "source": { "split": "train_shard_00001", "doc_id": 1273 }, "chunk_id": "train_shard_00001_1273_0", "global_id": 7452 }, { "text": "We constructed a xylose-fermenting recombinant strain of thermotolerant yeast Kluyveromyces marxianus, DMB3-7. Both xylose consumption and ethanol production were remarkably increased in DMB3-7 compared to the control strain at 30°C. Furthermore, DMB3-7 produced ethanol from xylose at both 42°C and 45°C, above which xylose metabolic activity decreased.\n\nEthanol fermentation from xylose by metabolically engineered strains of Kluyveromyces marxianus.", "token_count": 142, "char_count": 452, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7759, "quality_score": 0.8879, "entities": { "genes": [ "DMB3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:18.326774", "source": { "split": "train_shard_00001", "doc_id": 1274 }, "chunk_id": "train_shard_00001_1274_0", "global_id": 7453 }, { "text": "Lactococcus garvieae is a well-known pathogen of fish, but is rarely involved in infections in humans and other mammals. In humans, the main clinical manifestation of L. garvieae infections is endocarditis usually related to the ingestion of contaminated food, such as undercooked fish and shellfish. This study presents the first complete genomic sequence of a clinical L. garvieae strain isolated from a patient with endocarditis and its comparative analysis with other genomes. This human isolate contains a circular chromosome of 2 099 060 bp and one plasmid of 50 557 bp. In comparison with other fully sequenced L. garvieae strains, the chromosomal DNA of L. garvieae Lg-Granada carries a low proportion of insertion sequence elements and a higher number of putative prophages. Our results show that, in general, L. garvieae is a highly recombinogenic species with an open pangenome in which almost 30 % of its genome has undergone horizontal transfers. Within the genus Lactococcus, L. lactis is the main donor of genetic components to L. garvieae but, taking Lg-Granada as a representative, this bacterium tends to import more genes from Bacilli taxa than from other Lactococcus species.\n\nComparative genomics and evolutionary analysis of Lactococcus garvieae isolated from human endocarditis.", "token_count": 424, "char_count": 1378, "word_count": 200, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:18.967481", "source": { "split": "train_shard_00001", "doc_id": 1275 }, "chunk_id": "train_shard_00001_1275_0", "global_id": 7454 }, { "text": "A Streptococcus suis strain isolated from the blood of a patient in Zhejiang Province, China, was analysed using whole-genome sequencing and tested for antimicrobial resistance. The isolated strain was identified as S. suis serotype 2, and classified to ST25 on multilocus sequence typing (MLST). The minimum core genome group of the strain was identified as Group 4, and multilocus variable-number tandem-repeat analysis (MLVA) assigned it as type 2, 4.4, 0, 9, 3, 2, 0, 0. An antimicrobial resistance analysis showed that the strain was resistant to clindamycin, tetracycline, azithromycin, and erythromycin but sensitive to 11 other antibiotics. In a genomic evolution analysis, this isolate clustered on the same branch as North American pig isolate, Chinese pig isolates from Tianjin, and Hubei pig isolates.\n\nGenomic and Antimicrobial Resistance Analysis of an ST25 <i>Streptococcus suis</i> Strain Isolated from a Human in Zhejiang Province, China.", "token_count": 301, "char_count": 981, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [ "ST25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:19.578110", "source": { "split": "train_shard_00001", "doc_id": 1276 }, "chunk_id": "train_shard_00001_1276_0", "global_id": 7455 }, { "text": "

Background

Lignocellulosic hydrolysates contain a mixture of hexose (C6)/pentose (C5) sugars and pretreatment-generated inhibitors (furans, weak acids and phenolics). Therefore, robust yeast isolates with characteristics of C6/C5 fermentation and tolerance to pretreatment-derived inhibitors are pre-requisite for efficient lignocellulosic material based biorefineries. Moreover, use of thermotolerant yeast isolates will further reduce cooling cost, contamination during fermentation, and required for developing simultaneous saccharification and fermentation (SSF), simultaneous saccharification and co-fermentation (SScF), and consolidated bio-processing (CBP) strategies.

Results

In this study, we evaluated thirty-five yeast isolates (belonging to six genera including Saccharomyces, Kluyveromyces, Candida, Scheffersomyces, Ogatea and Wickerhamomyces) for pretreatment-generated inhibitors {furfural, 5-hydroxymethyl furfural (5-HMF) and acetic acid} and thermotolerant phenotypes along with the fermentation performances at 40 °C. Among them, a sugarcane distillery waste isolate, Saccharomyces cerevisiae NGY10 produced maximum 49.77 ± 0.34 g/l and 46.81 ± 21.98 g/l ethanol with the efficiency of 97.39% and 93.54% at 30 °C and 40 °C, respectively, in 24 h using glucose as a carbon source", "token_count": 445, "char_count": 1341, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7532, "quality_score": 0.8766, "entities": { "genes": [ "NGY10" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:20.223933", "source": { "split": "train_shard_00001", "doc_id": 1277 }, "chunk_id": "train_shard_00001_1277_0", "global_id": 7456 }, { "text": "Furthermore, isolate NGY10 produced 12.25 ± 0.09 g/l and 7.18 ± 0.14 g/l of ethanol with 92.81% and 91.58% efficiency via SHF, and 30.22 g/l and 25.77 g/l ethanol with 86.43% and 73.29% efficiency via SSF using acid- and alkali-pretreated rice straw as carbon sources, respectively, at 40 °C. In addition, isolate NGY10 also produced 92.31 ± 3.39 g/l (11.7% v/v) and 33.66 ± 1.04 g/l (4.26% v/v) ethanol at 40 °C with the yields of 81.49% and 73.87% in the presence of 30% w/v glucose or 4× concentrated acid-pretreated rice straw hydrolysate, respectively. Moreover, isolate NGY10 displayed furfural- (1.5 g/l), 5-HMF (3.0 g/l), acetic acid- (0.2% v/v) and ethanol-(10.0% v/v) tolerant phenotypes.

Conclusion

A sugarcane distillery waste isolate NGY10 demonstrated high potential for ethanol production, C5 metabolic engineering and developing strategies for SSF, SScF and CBP.\n\nEvaluation of divergent yeast genera for fermentation-associated stresses and identification of a robust sugarcane distillery waste isolate Saccharomyces cerevisiae NGY10 for lignocellulosic ethanol production in SHF and SSF.", "token_count": 477, "char_count": 1119, "word_count": 163, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [ "NGY10" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:20.864996", "source": { "split": "train_shard_00001", "doc_id": 1277 }, "chunk_id": "train_shard_00001_1277_1", "global_id": 7457 }, { "text": "

Background

Environmentally sensitive pathogens exhibit ecological and evolutionary responses to climate change that result in the emergence and global expansion of well-adapted variants. It is imperative to understand the mechanisms that facilitate pathogen emergence and expansion, as well as the drivers behind the mechanisms, to understand and prepare for future pandemic expansions.

Objective

The unique, rapid, global expansion of a clonal complex of Vibrio parahaemolyticus (a marine bacterium causing gastroenteritis infections) named Vibrio parahaemolyticus sequence type 3 (VpST3) provides an opportunity to explore the eco-evolutionary drivers of pathogen expansion.

Methods

The global expansion of VpST3 was reconstructed using VpST3 genomes, which were then classified into metrics characterizing the stages of this expansion process, indicative of the stages of emergence and establishment. We used machine learning, specifically a random forest classifier, to test a range of ecological and evolutionary drivers for their potential in predicting VpST3 expansion dynamics.

Results

We identified a range of evolutionary features, including mutations in the core genome and accessory gene presence, associated with expansion dynamics. A range of random forest classifier approaches were tested to predict expansion classification metrics for each genome. The highest predictive accuracies (ranging from 0.722 to 0.967) were achieved for models using a combined eco-evolutionary approach. While population structure and the difference between introduced and established isolates could be predicted to a high accuracy, our model reported multiple false positives when predicting the success of an introduced isolate, suggesting potential limiting factors not represented in our eco-evolutionary features. Regional models produced for 2 countries reporting the most VpST3 genomes had varying success, reflecting the impacts of class imbalance.

Conclusions

These novel insights into evolutionary features and ecological conditions related to the stages of VpST3 expansion showcase the potential of machine learning models using genomic data and will contribute to the future understanding of the eco-evolutionary pathways of climate-sensitive pathogens.", "token_count": 498, "char_count": 2296, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:21.517903", "source": { "split": "train_shard_00001", "doc_id": 1278 }, "chunk_id": "train_shard_00001_1278_0", "global_id": 7458 }, { "text": "Eco-Evolutionary Drivers of Vibrio parahaemolyticus Sequence Type 3 Expansion: Retrospective Machine Learning Approach.", "token_count": 35, "char_count": 119, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:21.874998", "source": { "split": "train_shard_00001", "doc_id": 1278 }, "chunk_id": "train_shard_00001_1278_1", "global_id": 7459 }, { "text": "Introduction. Bacteroides fragilis is a Gram-negative anaerobe that is a member of the human gastrointestinal microbiota and is frequently found as an extra-intestinal opportunistic pathogen. B. fragilis comprises two distinct groups - divisions I and II - characterized by the presence/absence of genes [cepA and ccrA (cfiA), respectively] that confer resistance to β-lactam antibiotics by either serine or metallo-β-lactamase production. No large-scale analyses of publicly available B. fragilis sequence data have been undertaken, and the resistome of the species remains poorly defined.Hypothesis/Gap Statement. Reclassification of divisions I and II B. fragilis as two distinct species has been proposed but additional evidence is required.Aims. To investigate the genomic diversity of GenBank B. fragilis genomes and establish the prevalence of division I and II strains among publicly available B. fragilis genomes, and to generate further evidence to demonstrate that B. fragilis division I and II strains represent distinct genomospecies.Methodology. High-quality (n=377) genomes listed as B. fragilis in GenBank were included in pangenome and functional analyses. Genome data were also subject to resistome profiling using The Comprehensive Antibiotic Resistance Database.Results. Average nucleotide identity and phylogenetic analyses showed B. fragilis divisions I and II represent distinct species: B. fragilis sensu stricto (n=275 genomes) and B. fragilis A (n=102 genomes; Genome Taxonomy Database designation), respectively. Exploration of the pangenome of B. fragilis sensu stricto and B", "token_count": 523, "char_count": 1767, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5611, "quality_score": 0.7805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:22.511252", "source": { "split": "train_shard_00001", "doc_id": 1279 }, "chunk_id": "train_shard_00001_1279_0", "global_id": 7460 }, { "text": "fragilis A revealed separation of the two species at the core and accessory gene levels.Conclusion. The findings indicate that B. fragilis A, previously referred to as division II B. fragilis, is an individual species and distinct from B. fragilis sensu stricto. The B. fragilis pangenome analysis supported previous genomic, phylogenetic and resistome screening analyses collectively reinforcing that divisions I and II are two separate species. In addition, it was confirmed that differences in the accessory genes of B. fragilis divisions I and II are primarily associated with carbohydrate metabolism and suggest that differences other than antimicrobial resistance could also be used to distinguish between these two species.\n\nGenomic analyses of Bacteroides fragilis: subdivisions I and II represent distinct species.", "token_count": 220, "char_count": 876, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6639, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:22.979908", "source": { "split": "train_shard_00001", "doc_id": 1279 }, "chunk_id": "train_shard_00001_1279_1", "global_id": 7461 }, { "text": "Abstract

In Bangladesh, Vibrio cholerae lineages are undergoing genomic evolution, causing pandemics and outbreaks with increased virulence, resistance, spreading ability and disease severity. However, our understanding of the genomic determinants influencing transmission and disease severity patterns, as well as their interplay, remains incomplete. Here, we developed a computational framework based on machine-learning, genome scale metabolic modelling (GSSM) and 3D structural analysis, to identify V. cholerae signatures genomic traits linked to lineage transmission dynamics and disease severity. We analysed isolates collected from in-patients across six regions in Bangladesh from 2015 to 2021, and uncovered a core set of accessory genes, coding, and intergenic SNPs uniquely present in the most recent dominant lineage and underlying lineage transmission, with virulence, motility, colonization, biofilm formation, acid tolerance and bacteriophage resistance functions. Furthermore, we uncovered the existence of a strong correlation between a core set of V. cholerae genomic determinants and disease severity patterns (diarrhoeal duration, number of stools, abdominal pain, vomit, and dehydration). A subset of these determinants overlapped with those driving lineage transmission dynamics. Through GSMM and 3D structure analysis, we inferred the mechanistic bases underlying their selection and unveiled a complex interplay between transcription regulation, protein interactions and stability, and metabolic networks leading to severe symptoms. These connections influence lifestyle adaptation, intestinal colonization, oxidative stress and acid tolerance through modulation of ribosome, fatty acid and peptide biosynthesis, bacterial efflux systems, virulence, and resistant genes. Our computational framework allows to uncover signature traits which can provide insights for advancing therapeutics and developing targeted interventions to mitigate cholera spread.

\n\nSignature genomic traits of the core and accessory genome of Vibrio Cholerae O1 drive lineage transmission and disease severity", "token_count": 477, "char_count": 2130, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:23.625163", "source": { "split": "train_shard_00001", "doc_id": 1280 }, "chunk_id": "train_shard_00001_1280_0", "global_id": 7462 }, { "text": "Staphylococcus epidermidis is a commensal skin organism and leading cause of medical-device associated infections. Although previous research has investigated the phylogenetic diversity of the species, the level of positive selection on the core genome has yet to be explored. Here, we present the first core genome-wide screen of positive selection in the species. A curated dataset of 1003 whole-genome sequences (WGS) was created which represented the global diversity of the species, including all previously identified clades and genetic clusters (GCs). A 100-strain subset, which retained the diversity of the collection, was created by pruning the species-level tree with treemmer; core genes present in all genomes were extracted with Roary and used for positive selection analysis (n = 826). Site-level analysis was performed using PAML with omegaMap for confirmation. Selection along branches separating clades A and B were also investigated using PAML branch-site models and HyPhy. PAML site analysis revealed 17 genes under selection, including six hypothetical genes, most of which were linked to metabolism or transport. Several genes were associated with antimicrobial resistance, such as ileS which confers resistance to mupirocin. cysG and sirC , which catalyse the first two steps in the synthesis of siroheme, were also under selection. Two genes were found to be under selection at the branch-site level by both PAML and HyPhy, of which only one, rhtC , has been functionally characterised. Our analysis reveals the extent to which positive selection is operating on the core genome and identifies candidate genes which may have important roles in the fitness of the species.\n\nDetection of positive selection driving antimicrobial resistance in the core genome ofStaphylococcus epidermidis", "token_count": 424, "char_count": 1816, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5593, "quality_score": 0.7796, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:24.257640", "source": { "split": "train_shard_00001", "doc_id": 1281 }, "chunk_id": "train_shard_00001_1281_0", "global_id": 7463 }, { "text": "Members of the genus Qipengyuania are heterotrophic bacteria frequently isolated from marine environments with great application potential in areas such as carotenoid production. However, the genomic diversity, metabolic function, and adaption of this genus remain largely unclear. Here, 16 isolates related to the genus Qipengyuania were recovered from coastal samples and their genomes were sequenced. The phylogenetic inference of these isolates and reference type strains of this genus indicated that the 16S rRNA gene was insufficient to distinguish them at the species level; instead, the phylogenomic reconstruction could provide the reliable phylogenetic relationships and confirm 15 new well-supported branches, representing 15 putative novel genospecies corroborated by the digital DNA-DNA hybridization and average nucleotide identity analyses. Comparative genomics revealed that the genus Qipengyuania had an open pangenome and possessed multiple conserved genes and pathways related to metabolic functions and environmental adaptation, despite the presence of divergent genomic features and specific metabolic potential. Genetic analysis and pigment detection showed that the members of this genus were identified as carotenoid producers, while some proved to be potentially aerobic anoxygenic photoheterotrophs. Collectively, the first insight into the genetic diversity and metabolic potentials of the genus Qipengyuania will contribute to better understanding of the speciation and adaptive evolution in natural environments. IMPORTANCE The deciphering of the phylogenetic diversity and metabolic features of the abundant bacterial taxa is critical for exploring their ecological importance and application potential. Qipengyuania is a genus of frequently isolated heterotrophic microorganisms with great industrial application potential. Numerous strains related to the genus Qipengyuania have been isolated from diverse environments, but their genomic diversity and metabolic functions remain unclear. Our study revealed a high degree of genetic diversity, metabolic versatility, and environmental adaptation of the genus Qipengyuania using comparative genomics", "token_count": 518, "char_count": 2235, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5799, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:24.913806", "source": { "split": "train_shard_00001", "doc_id": 1282 }, "chunk_id": "train_shard_00001_1282_0", "global_id": 7464 }, { "text": "Fifteen novel species of this genus have been established using a polyphasic taxonomic approach, expanding the number of described species to almost double. This study provided an overall view of the genus Qipengyuania at the genomic level and will enable us to better uncover its ecological roles and evolutionary history.\n\nComparative Genomics Reveals Genetic Diversity and Metabolic Potentials of the Genus Qipengyuania and Suggests Fifteen Novel Species.", "token_count": 121, "char_count": 472, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7463, "quality_score": 0.8731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:25.299559", "source": { "split": "train_shard_00001", "doc_id": 1282 }, "chunk_id": "train_shard_00001_1282_1", "global_id": 7465 }, { "text": "Staphylococcus aureus is a colonizing opportunistic pathogen and a leading cause of bloodstream infection with high morbidity and mortality. S. aureus carriage frequency is reportedly between 20 and 40 % among healthy adults, with S. aureus colonization considered to be a risk factor for S. aureus bacteraemia. It is unknown whether a genetic component of the bacterium is associated with S. aureus bacteraemia in comparison to nasal carriage strains. Previous association studies primarily focusing on the clinical outcome of an S. aureus infection have produced conflicting results, often limited by study design challenged by sample collections and the clonal diversity of S. aureus. To date, no study has investigated whether genomic features separate nasal carriage isolates from S. aureus bacteraemia isolates within a single clonal lineage. Here we have investigated whether genomic features, including single-nucleotide polymorphisms (SNPs), genes, or kmers, distinguish S. aureus nasal carriage isolates from bacteraemia isolates that all belong to the same clonal lineage [clonal complex 45 (CC45)] using whole-genome sequencing (WGS) and a genome-wide association (GWA) approach. From CC45, 100 isolates (50 bacteraemia and 50 nasal carriage, geographically and temporally matched) from Denmark were whole-genome sequenced and subjected to GWA analyses involving gene copy number variation, SNPs, gene content, kmers and gene combinations, while correcting for lineage effects. No statistically significant association involving SNPs, specific genes, gene variants, gene copy number variation, or a combination of genes was identified that could distinguish bacteraemia isolates from nasal carriage isolates. The presented results suggest that all S. aureus nasal CC45 isolates carry the potential to cause invasive disease, as no core or accessory genome content or variations were statistically associated with invasiveness.", "token_count": 524, "char_count": 2008, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5949, "quality_score": 0.7974, "entities": { "genes": [ "CC45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:25.936920", "source": { "split": "train_shard_00001", "doc_id": 1283 }, "chunk_id": "train_shard_00001_1283_0", "global_id": 7466 }, { "text": "Genomic analyses of Staphylococcus aureus clonal complex 45 isolates does not distinguish nasal carriage from bacteraemia.", "token_count": 41, "char_count": 129, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:26.305554", "source": { "split": "train_shard_00001", "doc_id": 1283 }, "chunk_id": "train_shard_00001_1283_1", "global_id": 7467 }, { "text": "Recurrent urinary tract infection (rUTI) remains a major problem for many women and therefore the pursuit for genomic and phenotypic traits which could define rUTI has been ongoing. The present study applied a genomic approach to investigate recurrent urinary tract infections by comparative analyses of recurrent and non-recurrent Escherichia coli isolates from general practice. From whole-genome sequencing data, phylogenetic clustering and genomic traits were studied on a collection of isolates which caused recurrent infection compared to non-recurrent isolates. In addition, genomic variation between the 1st and following infection was studied on a subset of the isolates. Evidence of limited adaptation between the recurrent infections based on single nucleotide polymorphism analyses with a range of 0-13 non-synonymous single nucleotide polymorphisms (SNPs) between the paired isolates. This included an overrepresentation of SNPs in metabolism genes. We identified several genes which were more common in rUTI isolates, including nine fimbrial genes, however, not significantly after false-discovery rate. Finally, the results show that recurrent isolates of the present dataset are not distinctive by variation in the core genome, and thus, did not cluster distinct from non-rUTI isolates in a SNP phylogeny.\n\nEscherichia coli Causing Recurrent Urinary Tract Infections: Comparison to Non-Recurrent Isolates and Genomic Adaptation in Recurrent Infections.", "token_count": 362, "char_count": 1482, "word_count": 204, "semantic_coherence": 1, "information_density": 0.598, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:26.885651", "source": { "split": "train_shard_00001", "doc_id": 1284 }, "chunk_id": "train_shard_00001_1284_0", "global_id": 7468 }, { "text": "In September 2024, a school-aged child (P1), unvaccinated against diphtheria, was hospitalised with severe respiratory diphtheria caused by toxigenic Corynebacterium diphtheriae. P1 subsequently died from the disease. The child's mother (P2) had pharyngitis 9 days before the onset of symptoms of P1 and subsequently tested positive for C. diphtheriae. In multilocus sequence typing (MLST), the C. diphtheriae isolates from P1 and P2 were of sequence type (ST) 574. In core genome (cg)MLST, they were clonal, suggesting recent human-to-human transmission. This indicates the first autochthonous respiratory diphtheria outbreak by toxigenic C. diphtheriae in Germany since 1984 with epidemiologically- and molecularly-confirmed transmission. Furthermore, the isolates were close to isolates from patients with cutaneous diphtheria among people experiencing homelessness in two major German cities in 2023 and 2024, and to isolates from an outbreak among newly arriving migrants across several European countries, including Germany, detected in 2022. This indicates transmission beyond vulnerable groups. Our findings illustrate the potential of C. diphtheriae spreading further from patients with cutaneous diphtheria and even causing outbreaks of respiratory diphtheria. Given the potentially serious complications of respiratory diphtheria, including death, equitably achieving and maintaining high vaccination coverage among the whole population, especially among vulnerable people is essential.\n\nAutochthonous outbreak of respiratory diphtheria caused by <i>Corynebacterium diphtheriae</i>, Germany, September 2024.", "token_count": 453, "char_count": 1665, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:27.528505", "source": { "split": "train_shard_00001", "doc_id": 1285 }, "chunk_id": "train_shard_00001_1285_0", "global_id": 7469 }, { "text": "

Background

A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools.

Methods

We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: 1) indels creating early stop codons and new start codons; 2) interruption by a selfish genetic element; and 3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees.

Results

We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g. T4), the Studiervirinae (e.g. T7), and the Pbunaviruses (e.g. PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny", "token_count": 482, "char_count": 1911, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [ "PB1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:28.191329", "source": { "split": "train_shard_00001", "doc_id": 1286 }, "chunk_id": "train_shard_00001_1286_0", "global_id": 7470 }, { "text": "The Rephine.r pipeline is provided through GitHub ( https://www.github.com/coevoeco/Rephine.r ) as a single script for automated analysis and with utility functions and a walkthrough for researchers with specific use cases for each type of correction.\n\nRephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies", "token_count": 90, "char_count": 357, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:28.569347", "source": { "split": "train_shard_00001", "doc_id": 1286 }, "chunk_id": "train_shard_00001_1286_1", "global_id": 7471 }, { "text": "The adaptation of versatile multi-host pathogens to various hosts and various niches within hosts is often still poorly understood. The alternative Sigma factor B (SigB) is the master regulator of the general stress response of most gram-positive bacteria, which is a classic case of adaptive plasticity. In Staphylococcus aureus , SigB appears co-opted to function as a switch between intracellular and extracellular niches. During bovine mastitis, low SigB-activity confers an advantage in the milk-rich extracellular niche of the bovine udder. We show that narrowly adapted SigB-deficient strains evolved repeatedly from phenotypically plastic SigB-wildtype strains during persistent mastitis. This genetic assimilation appears driven by the cost of phenotypic plasticity: long time lags in adapting to milk and slow growth. Surprisingly, we observe that mutations causing SigB-deficiency allow even human isolates to grow in milk. While host adaptation often proceeds by mobile genetic elements exchanged between strains, we show how a master regulator in the core genome can drive niche adaptation.\n\nA single transcriptional regulator is crucial for the adaptation of Staphylococcus aureus to diverse niches", "token_count": 296, "char_count": 1219, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7011, "quality_score": 0.8506, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:29.135681", "source": { "split": "train_shard_00001", "doc_id": 1287 }, "chunk_id": "train_shard_00001_1287_0", "global_id": 7472 }, { "text": "

ABSTRACT

The standard workhorse for genomic analysis of the evolution of bacterial populations is phylogenetic modelling of mutations in the core genome. However, in the current era of population genomics, a notable amount of information about evolutionary and transmission processes in diverse populations can be lost unless the accessory genome is also taken into consideration. Here we introduce PANINI, a computationally scalable method for identifying the neighbours for each isolate in a data set using unsupervised machine learning with stochastic neighbour embedding. PANINI is browser-based and integrates with the Microreact platform for rapid online visualisation and exploration of both core and accessory genome evolutionary signals together with relevant epidemiological, geographic, temporal and other metadata. Several case studies with single-and multi-clone pneumococcal populations are presented to demonstrate ability to identify biologically important signals from gene content data. PANINI is available at http://panini.wgsa.net/ and code at http://gitlab.com/cgps/panini\n\nPANINI: Pangenome Neighbor Identification for Bacterial Populations", "token_count": 258, "char_count": 1171, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7171, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:29.682226", "source": { "split": "train_shard_00001", "doc_id": 1288 }, "chunk_id": "train_shard_00001_1288_0", "global_id": 7473 }, { "text": "

Background

A pangenome is the collection of all genes found in a set of related genomes. For microbes, these genomes are often different strains of the same species, and the pangenome offers a means to compare gene content variation with differences in phenotypes, ecology, and phylogenetic relatedness. Though most frequently applied to bacteria, there is growing interest in adapting pangenome analysis to bacteriophages. However, working with phage genomes presents new challenges. First, most phage families are under-sampled, and homologous genes in related viruses can be difficult to identify. Second, homing endonucleases and intron-like sequences may be present, resulting in fragmented gene calls. Each of these issues can reduce the accuracy of standard pangenome analysis tools.

Methods

We developed an R pipeline called Rephine.r that takes as input the gene clusters produced by an initial pangenomics workflow. Rephine.r then proceeds in two primary steps. First, it identifies three common causes of fragmented gene calls: (1) indels creating early stop codons and new start codons; (2) interruption by a selfish genetic element; and (3) splitting at the ends of the reported genome. Fragmented genes are then fused to create new sequence alignments. In tandem, Rephine.r searches for distant homologs separated into different gene families using Hidden Markov Models. Significant hits are used to merge families into larger clusters. A final round of fragment identification is then run, and results may be used to infer single-copy core genomes and phylogenetic trees.

Results

We applied Rephine.r to three well-studied phage groups: the Tevenvirinae (e.g., T4), the Studiervirinae (e.g., T7), and the Pbunaviruses (e.g., PB1). In each case, Rephine.r recovered additional members of the single-copy core genome and increased the overall bootstrap support of the phylogeny", "token_count": 480, "char_count": 1912, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.817, "entities": { "genes": [ "PB1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:30.371051", "source": { "split": "train_shard_00001", "doc_id": 1289 }, "chunk_id": "train_shard_00001_1289_0", "global_id": 7474 }, { "text": "The Rephine.r pipeline is provided through GitHub (https://www.github.com/coevoeco/Rephine.r) as a single script for automated analysis and with utility functions to assist in building single-copy core genomes and predicting the sources of fragmented genes.\n\nRephine.r: a pipeline for correcting gene calls and clusters to improve phage pangenomes and phylogenies.", "token_count": 95, "char_count": 364, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:30.768929", "source": { "split": "train_shard_00001", "doc_id": 1289 }, "chunk_id": "train_shard_00001_1289_1", "global_id": 7475 }, { "text": "The pear ( Pyrus spp .) is a remarkable fruit, well known for its diverse flavors, textures, culinary versatility, and global horticultural importance. However, the genetic diversity responsible for its extensive phenotypic variations remains largely unexplored. Here, we de novo assembled and annotated the genomes of the maternal (PsbM) and paternal (PsbF) lines of the hybrid ‘Yuluxiang’ pear and constructed the first pear pangenome of 1.15Gb by combining these two genomes with five previously published pear genomes. Using the constructed pangenome, we identified 21,224 gene PAVs and 1,158,812 SNPs in the non-reference genome that were absent in the PsbM reference genome. Compared with SNP markers, we found that PAV-based analysis provides additional insights into the pear population structure. In addition, we also revealed that some genes associated with pear fruit quality traits have differential occurrence frequencies and differential gene expression between Asian and European populations. Moreover, our analysis of the pear pangenome revealed a mutated SNP and an insertion in the promoter region of the gene PsbMGH3.1 potentially enhances sepal shedding in ‘Xuehuali’ which is vital for pear quality. This research helps further capture the genetic diversity of pear populations and provides valuable genomic resources for accelerating pear breeding.\n\nPan-genome of pear provides insights into the fruit quality traits differentiation between Asian and European pears", "token_count": 347, "char_count": 1487, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:31.396611", "source": { "split": "train_shard_00001", "doc_id": 1290 }, "chunk_id": "train_shard_00001_1290_0", "global_id": 7476 }, { "text": "Fourteen lactose-fermenting strains of Kluyveromyces marxianus, including its anamorph, Candida kefyr, were grown in two media containing 20% (w/v) sugar as either beet molasses or cheese whey. Strain NBRC 1963 of K. marxianus converted sucrose and lactose to ethanol in both media most efficiently. However, ethanol was produced from sucrose and not from lactose by strain NBRC 1963 in the medium containing equal amounts of sugar from beet molasses and cheese whey. The spontaneous mutants resistant to 2-deoxyglucose in the minimal medium composed of galactose as the sole carbon source were isolated from strain NBRC 1963. Among them, strain KD-15 vigorously produced ethanol in the media containing beet molasses, cheese whey, or both. The mutant strain KD-15 was insensitive to catabolite repression, as shown by the observation that beta-galactosidase was not repressed in the presence of sucrose from beet molasses.\n\nProduction of ethanol from the mixture of beet molasses and cheese whey by a 2-deoxyglucose-resistant mutant of Kluyveromyces marxianus.", "token_count": 313, "char_count": 1061, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5472, "quality_score": 0.7736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:31.970600", "source": { "split": "train_shard_00001", "doc_id": 1291 }, "chunk_id": "train_shard_00001_1291_0", "global_id": 7477 }, { "text": "

Key message

Comparative genomic analysis of two all-stage stripe rust resistance loci from Vavilov wheat landrace accession, AGG40807WHEA1, using Chinese Spring and 10 + hexaploid wheat genomes and validation of closely linked KASP markers. The ongoing occurrence and spread of wheat stripe rust, caused by the fungal pathogen Puccinia striiformis f. sp. tritici, threatens the global food security. Cultivation of varieties with effective sources of resistance is often followed by the appearance of virulent pathotypes at various times after their introduction. This requires an ongoing search for new sources. Tests of 296 accessions from the Vavilov wheat landrace collection identified numerous lines with broadly effective all-stage stripe rust resistance. Genetic analysis of one of these accessions (Australian Grains Genebank number AGG40807WHEA1) identified two all-stage resistance genes, temporarily named YrV1 and YrV2. The YRV1 and YRV2 loci were mapped to 3.48-3.98 and 730.2-731.2 Mb intervals in the short arm of chromosome 3B and the long arm of chromosome 7B, respectively. A comparative genomic analysis of the YRV1 locus in the Chinese Spring and the 10 + wheat pangenome databases revealed genomic rearrangements and lack of sequences encoding a nucleotide-binding and leucine-rich repeat (NLR) domain protein. Sequences belonging to NLR-like genes were present in the YRV2 region. Kompetitive allele-specific PCR (KASP) markers designed from SNPs IWB71814 and IWB69562, located at 0.4 cM and 0.5 cM distal to YrV1 and YrV2, respectively, were validated for marker-assisted selection using 123 hexaploid and 15 tetraploid wheat and 14 triticale cultivars", "token_count": 504, "char_count": 1684, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8197, "entities": { "genes": [ "YRV1", "IWB69562", "IWB71814", "YRV2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:32.618634", "source": { "split": "train_shard_00001", "doc_id": 1292 }, "chunk_id": "train_shard_00001_1292_0", "global_id": 7478 }, { "text": "YrV1 and YrV2 genes are potentially valuable resources, and use of the closely linked molecular markers will expedite their deployment in breeding.\n\nGenomic analysis of two all-stage stripe rust resistance genes in the Vavilov wheat landrace AGG40807WHEA1.", "token_count": 70, "char_count": 256, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:32.984830", "source": { "split": "train_shard_00001", "doc_id": 1292 }, "chunk_id": "train_shard_00001_1292_1", "global_id": 7479 }, { "text": "Although prokaryotic DNA methylation investigations have long focused on immunity against exogenous DNA, it has been recently recognized that DNA methylation impacts gene expression and phase variation in Streptococcus pneumoniae and Streptococcus suis. A comprehensive analysis of DNA methylation is lacking for beta-hemolytic streptococci, and thus we sought to examine DNA methylation in the major human pathogen group A Streptococcus (GAS). Using a database of 224 GAS genomes encompassing 80 emm types, we found that nearly all GAS strains encode a type I restriction modification (RM) system that lacks the hsdS' alleles responsible for impacting gene expression in S. pneumoniae and S. suis. The GAS type I system is located on the core chromosome, while sporadically present type II orphan methyltransferases were identified on prophages. By combining single-molecule real-time (SMRT) analyses of 10 distinct emm types along with phylogenomics of 224 strains, we were able to assign 13 methylation patterns to the GAS population. Inactivation of the type I RM system, occurring either naturally through phage insertion or through laboratory-induced gene deletion, abrogated DNA methylation detectable via either SMRT or MinION sequencing. Contrary to a previous report, inactivation of the type I system did not impact transcript levels of the gene (mga) encoding the key multigene activator protein (Mga) or Mga-regulated genes. Inactivation of the type I system significantly increased plasmid transformation rates. These data delineate the breadth of the core chromosomal type I RM system in the GAS population and clarify its role in immunity rather than impacting Mga regulon expression. IMPORTANCE The advent of whole-genome approaches capable of detecting DNA methylation has markedly expanded appreciation of the diverse roles of epigenetic modification in prokaryotic physiology. For example, recent studies have suggested that DNA methylation impacts gene expression in some streptococci", "token_count": 521, "char_count": 2040, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:33.618420", "source": { "split": "train_shard_00001", "doc_id": 1293 }, "chunk_id": "train_shard_00001_1293_0", "global_id": 7480 }, { "text": "The data described herein are from the first systematic analysis of DNA methylation in a beta-hemolytic streptococcus and one of the few analyses to comprehensively characterize DNA methylation across hundreds of strains of the same bacterial species. We clarify that DNA methylation in group A Streptococcus (GAS) is primarily due to a type I restriction modification (RM) system present in the core genome and does not impact mga-regulated virulence gene expression, but does impact immunity against exogenous DNA. The identification of the DNA motifs recognized by each type I RM system may assist with optimizing methods for GAS genetic manipulation and help us understand how bacterial pathogens acquire exogenous DNA elements.\n\nCharacterization of the Type I Restriction Modification System Broadly Conserved among Group A Streptococci.", "token_count": 199, "char_count": 849, "word_count": 125, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:34.071051", "source": { "split": "train_shard_00001", "doc_id": 1293 }, "chunk_id": "train_shard_00001_1293_1", "global_id": 7481 }, { "text": "

Abstract

The demand for preservative-free food products is rising, and biopreservation is a potential alternative to replace or reduce the use of chemical preservatives. The objectives of this study were to assess the antifungal activity of lactic acid bacteria (LAB; n = 98) and the efficacy and applicability of the chosen bioprotective cultures against fungal spoilers in dairy products. First, 14 antifungal strains were preliminarily screened by in vitro tests against Pichia pastoris D3, Aspergillus niger D1, Geotrichum candidum N1, Kluyveromyces marxianus W1, and Penicillium chrysogenum B1 and validated by challenge tests in yogurt, indicating that the fungal-inhibiting activity of LAB was species specific and yogurt fermented with antifungal LAB cultures was more effective in extending shelf life. Second, the chosen 14 LAB strains were identified by the 16S rDNA sequence analysis and carbohydrate fermentation test. The results were as follows: nine strains were Lactobacillus plantarum, three were Lactobacillus paracasei, one was Enterococus faecium, and one was Lactobacillus rhamnosus. Among them, active L. plantarum N7 was the chosen and studied factor affecting antifungal activity by using the response surface methodology. Finally, in situ tests were conducted to validate the activity of L. plantarum N7 in actual dairy products (whey beverages). Physicochemical and microbial indices of whey beverages during storage indicated that antifungal L. plantarum N7 could slow yeast growth and be candidates of interest for industrial applications.

Highlights

\n\nScreening of Antifungal Lactic Acid Bacteria as Bioprotective Cultures in Yogurt and a Whey Beverage.", "token_count": 465, "char_count": 1698, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:34.708313", "source": { "split": "train_shard_00001", "doc_id": 1294 }, "chunk_id": "train_shard_00001_1294_0", "global_id": 7482 }, { "text": "

Introduction

Kodamaea ohmeri is a rare but significant emerging human pathogen, particularly in neonates, with high mortality rates. While most K. ohmeri infections are sporadic, they can be underestimated during hospital outbreaks owing to challenges with traditional identification methods. We conducted a retrospective study to determine the diagnostic accuracy of detecting K. ohmeri in candidemia.

Methods

Six non-duplicated isolates (initially misidentified as Candida dubliniensis) were collected from four patients in a single department over 1 month. Clinical and whole-genome sequencing data of the outbreak strains were evaluated to identify possible outbreaks.

Results

All patients presented atypical features at diagnosis, and isolates had a low minimum inhibitory concentration (MIC) for amphotericin B, 5-fluorocytosine, and echinocandins, except for fluconazole with a high MIC. Notably, Patient 4 had a high MIC for triazoles. The isolates were grouped into three clades based on core genome single-nucleotide polymorphisms and single-copy orthologous genes. Clade 1 contained isolates from Patients 1 and 2, suggesting a common infection source.

Conclusion

This study underscores the need for improved awareness of K. ohmeri infections, which, although rare, involve emerging fluconazole-resistant strains. Kodamaea ohmeri should be considered a potential nosocomial pathogen capable of causing outbreaks; overlooking these emerging human pathogens may have serious consequences.\n\nEmerging pathogens: the underestimated risk of <i>Kodamaea ohmeri</i> infection in hospitals.", "token_count": 467, "char_count": 1675, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7295, "quality_score": 0.8647, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:35.360157", "source": { "split": "train_shard_00001", "doc_id": 1295 }, "chunk_id": "train_shard_00001_1295_0", "global_id": 7483 }, { "text": "Abstract

Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into GEMs was first enabled by the GECKO method, allowing the study of phenotypes constrained by protein limitations. Here, we upgraded the GECKO toolbox in order to enhance models with enzyme and proteomics constraints for any organism with an available GEM reconstruction. With this, enzyme-constrained models (ecModels) for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus were generated, aiming to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions revealed that upregulation and high saturation of enzymes in amino acid metabolism were found to be common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO was further developed by the implementation of an automated framework for continuous and version-controlled update of ecModels, which was validated by producing additional high-quality ecModels for Escherichia coli and Homo sapiens. These efforts aim to facilitate the utilization of ecModels in basic science, metabolic engineering and synthetic biology purposes.

\n\nReconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0", "token_count": 414, "char_count": 1694, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:35.985220", "source": { "split": "train_shard_00001", "doc_id": 1296 }, "chunk_id": "train_shard_00001_1296_0", "global_id": 7484 }, { "text": "Hansenula polymorpha DL-1 is a thermotolerant yeast capable of utilizing multiple renewable carbon sources, making it a promising microbial cell factory for sustainable manufacturing. However, advanced metabolic engineering efforts have been constrained by its strong non-homologous end joining (NHEJ) mechanism and limited choice of suitable genetic tools. This study presents an optimized synthetic biology toolkit to address these limitations. A high-efficiency CRISPR-Cas9-based genome editing system was established, achieving an editing efficiency of 97.2 %. To further enhance homologous recombination (HR), the NHEJ pathway was partially suppressed by knocking out KU80 and overexpressing HR-related genes from Saccharomyces cerevisiae. This increased HR rates to 88.9 %. In addition, 36 neutral sites were identified for stable single-copy gene integration without disrupting native gene expression cassettes. Finally, multi-copy integration tools were developed by targeting rDNA and Ty elements, leading to a ∼60-fold increase in β-carotene production compared with single-copy integrants. Furthermore, squalene titers were increased from 0.1 mg/L in the wild-type strain to 187.2 mg/L through iterative multi-copy integration. These advances significantly expand the genetic tractability of H. polymorpha DL-1, underscoring its potential as a versatile platform for efficient and sustainable production of value-added compounds.\n\nDevelopment of precise genome editing and multi-copy integration tools in <i>Hansenula polymorpha</i> DL-1.", "token_count": 410, "char_count": 1589, "word_count": 204, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "KU80" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:36.606536", "source": { "split": "train_shard_00001", "doc_id": 1297 }, "chunk_id": "train_shard_00001_1297_0", "global_id": 7485 }, { "text": "The allotetraploid wild grass Aegilops ventricosa (2n = 4x = 28, genome DvDvNvNv) has been recognized as an important germplasm resource for wheat improvement owing to its ability to tolerate biotic stresses. In particular, the 2NvS segment from Ae. ventricosa, as a stable and effective resistance source, has contributed greatly to wheat improvement. The 2NvS/2AS translocation is a prevalent chromosomal translocation between common wheat and wild relatives, ranking just behind the 1B/1R translocation in importance for modern wheat breeding. Here, we assembled a high-quality chromosome-level reference genome of Ae. ventricosa RM271 with a total length of 8.67 Gb. Phylogenomic analyses revealed that the progenitor of the Dv subgenome of Ae. ventricosa is Ae. tauschii ssp. tauschii (genome DD); by contrast, the progenitor of the D subgenome of bread wheat (Triticum aestivum L.) is Ae. tauschii ssp. strangulata (genome DD). The oldest polyploidization time of Ae. ventricosa occurred ∼0.7 mya. The Dv subgenome of Ae. ventricosa is less conserved than the D subgenome of bread wheat. Construction of a graph-based pangenome of 2AS/6NvL (originally known as 2NvS) segments from Ae. ventricosa and other genomes in the Triticeae enabled us to identify candidate resistance genes sourced from Ae. ventricosa. We identified 12 nonredundant introgressed segments from the Dv and Nv subgenomes using a large winter wheat collection representing the full diversity of the European wheat genetic pool, and 29.40% of European wheat varieties inherit at least one of these segments", "token_count": 529, "char_count": 1713, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [ "RM271" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:37.262603", "source": { "split": "train_shard_00001", "doc_id": 1298 }, "chunk_id": "train_shard_00001_1298_0", "global_id": 7486 }, { "text": "The high-quality RM271 reference genome will provide a basis for cloning key genes, including the Yr17-Lr37-Sr38-Cre5 resistance gene cluster in Ae. ventricosa, and facilitate the full use of elite wild genetic resources to accelerate wheat improvement.\n\nGenome architecture of the allotetraploid wild grass Aegilops ventricosa reveals its evolutionary history and contributions to wheat improvement.", "token_count": 102, "char_count": 400, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [ "RM271" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:37.639608", "source": { "split": "train_shard_00001", "doc_id": 1298 }, "chunk_id": "train_shard_00001_1298_1", "global_id": 7487 }, { "text": "

Background

Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown.

Results

We create multi-species super-pangenomes using pggb, cactus, and minigraph with the Bos taurus taurus reference sequence and eleven haplotype-resolved assemblies from taurine and indicine cattle, bison, yak, and gaur. We recover 221 k nonredundant structural variations (SVs) from the pangenomes, of which 135 k (61%) are common to all three. SVs derived from assembly-based calling show high agreement with the consensus calls from the pangenomes (96%), but validate only a small proportion of variations private to each graph. Pggb and cactus, which also incorporate base-level variation, have approximately 95% exact matches with assembly-derived small variant calls, which significantly improves the edit rate when realigning assemblies compared to minigraph. We use the three pangenomes to investigate 9566 variable number tandem repeats (VNTRs), finding 63% have identical predicted repeat counts in the three graphs, while minigraph can over or underestimate the count given its approximate coordinate system. We examine a highly variable VNTR locus and show that repeat unit copy number impacts the expression of proximal genes and non-coding RNA.

Conclusions

Our findings indicate good consensus between the three pangenome methods but also show their individual strengths and weaknesses that need to be considered when analysing different types of variants from multiple input assemblies.\n\nGraph construction method impacts variation representation and analyses in a bovine super-pangenome.", "token_count": 418, "char_count": 1744, "word_count": 238, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:38.267320", "source": { "split": "train_shard_00001", "doc_id": 1299 }, "chunk_id": "train_shard_00001_1299_0", "global_id": 7488 }, { "text": "Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. lncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only a few model fungi have well-documented inventories of lncRNA. In this study, we apply a recent computational pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyse genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host defence signals, such as oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling future molecular genetics and functional analyses in an important pathogen.\n\nThe expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogen Zymoseptoria tritici.", "token_count": 443, "char_count": 1799, "word_count": 252, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:38.903637", "source": { "split": "train_shard_00001", "doc_id": 1300 }, "chunk_id": "train_shard_00001_1300_0", "global_id": 7489 }, { "text": "Nonstarter lactic acid bacteria (NSLAB) are major contributors to the unique characteristics (e.g., aroma, flavor, texture) of dairy and nondairy fermented products. Lc. paracasei SRX10 is an NSLAB strain originally isolated from a traditional Greek cheese and previously shown to exhibit favorable biotechnological characteristics. More specifically, the strain showed tolerance to simulated gastrointestinal conditions, exopolysaccharide (EPS) biosynthetic capacity, and lack of hemolytic activity and was used in the production of yoghurt and feta cheese with distinct organoleptic characteristics. The aim of the present study was to investigate these traits at the genome level through whole-genome sequencing (WGS), annotation, and comparative genomics. Functional annotation of the genome revealed that Lc. paracasei SRX10 can utilize different carbon sources, leading to the generation of flavor compounds, including lactic acid, acetate, ethanol, and acetoin. Similarly, full clusters for fatty acid biosynthesis, protein and peptide degradation, as well as genes related to survival under extreme temperatures, osmotic shock, and oxidative stress were annotated. Importantly, no transferable antibiotic resistance genes or virulence factors were identified. Finally, strain-specific primers based on genome-wide polymorphisms were designed for the efficient and rapid identification of Lc. paracasei SRX10 via multiplex PCR in fermented products.\n\nDissecting the Genetic Basis of the Technological, Functional, and Safety Characteristics of Lacticaseibacillus paracasei SRX10.", "token_count": 413, "char_count": 1614, "word_count": 209, "semantic_coherence": 1, "information_density": 0.7321, "quality_score": 0.866, "entities": { "genes": [ "SRX10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:39.879121", "source": { "split": "train_shard_00001", "doc_id": 1301 }, "chunk_id": "train_shard_00001_1301_0", "global_id": 7490 }, { "text": "Understanding the underlying mechanisms between genome evolution and phenotypic and adaptive innovations is a key goal of evolutionary studies. Poplars are the world’s most widely distributed and cultivated trees, with extensive phenotypic diversity and environmental adaptability. Here we report a genus-level super-pangenome of 19 Populus genomes. After integrating pan-genomes with transcriptomes, methylomes and chromatin accessibility mapping, we reveal that the evolutionary fate of pan-genes and duplicated genes are largely associated with local genomic landscapes of regulatory and epigenetic architectures. Further comparative genomic analyses enabled to identify 142,202 structural variations (SVs) across species, which overlap with substantial genes and play key roles in both phenotypic and adaptive divergence. We experimentally validated a ∼180 bp presence/absence variant located in the promoter of the CUC2 gene, which contributed critically to leaf serration divergence between species. Together, this first super-pangenome resource in forest trees will not only accelerate molecular functional studies and genetic breeding of this globally important tree genus, but also lays a foundation for our understanding of tree biology.\n\nThe super-pangenome ofPopulusunveil genomic facets for adaptation and diversification in widespread forest trees", "token_count": 305, "char_count": 1368, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7111, "quality_score": 0.8556, "entities": { "genes": [ "CUC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:40.450556", "source": { "split": "train_shard_00001", "doc_id": 1302 }, "chunk_id": "train_shard_00001_1302_0", "global_id": 7491 }, { "text": "

Background

Staphylococcus pseudintermedius is the main aetiological agent of canine pyoderma. Whole genome sequencing is the most comprehensive way of obtaining relevant genomic information about micro-organisms.

Hypothesis/objectives

Oxford Nanopore technology enables quality sequencing and de novo assembly of the whole genome of S. pseudintermedius. Whole genome analysis of S. pseudintermedius may help to better understand the pathogenesis of canine pyodermas.

Methods and materials

Twenty-two strains of S. pseudintermedius isolated from the skin of five healthy dogs and 33 strains isolated from skin of 33 dogs with pyoderma were analysed. DNA was extracted and sequenced using Oxford Nanopore MinION, a new technology that delivers longer reads in a hand-held device. The pangenome was analysed and visualised with Anvi'o 6.1.

Results

Nanopore technology allowed the sequencing and de novo assembly of the genomes of 55 S. pseudintermedius strains isolated from healthy dogs and from dogs with pyoderma. The average genome size of S. pseudintermedius was 2.62 Mbp, with 48% being core genome. Pyoderma isolates contained a higher number of antimicrobial resistance genes, yet the total number of virulence factors genes did not change between isolates from healthy dogs and from dogs with pyoderma. Genomes of meticillin-resistant S. pseudintermedius (MRSP) strains were larger than those of meticillin-susceptible (MSSP) strains (2.80 Mbp versus 2.59 Mbp), as a consequence of a greater presence of antimicrobial resistance genes, phages and prophages.

Conclusions and clinical importance

This technique allows much more precise and easier characterisation of canine S. pseudintermedius populations and may lead to a better understanding of the pathogenesis of canine pyodermas.", "token_count": 502, "char_count": 1825, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5344, "quality_score": 0.7672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:41.109793", "source": { "split": "train_shard_00001", "doc_id": 1303 }, "chunk_id": "train_shard_00001_1303_0", "global_id": 7492 }, { "text": "Whole genome sequencing and de novo assembly of Staphylococcus pseudintermedius: a pangenome approach to unravelling pathogenesis of canine pyoderma.", "token_count": 42, "char_count": 149, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:41.471917", "source": { "split": "train_shard_00001", "doc_id": 1303 }, "chunk_id": "train_shard_00001_1303_1", "global_id": 7493 }, { "text": "Introduction: Previous studies, including our research, provide critical insights on the contamination of food, water and environment in the Southern African Development Community (SADC) with diarrhoeagenic Escherichia coli (DEC). This study used whole-genome sequencing to investigate the genetic diversity, virulence-associated factors and antimicrobial resistance (AMR) patterns of DEC isolated from children under 5 years old and food sources in Maputo and compared these findings with publicly available DEC genome assemblies from the Southern Africa region. Methods: Whole-genome sequence data from 11 DEC isolates from food, children under 5 and water sources in Maputo, Mozambique, were analysed alongside 125 publicly available DEC genomic assemblies from the SADC region. The latter were retrieved from the EnteroBase database (http://enterobase.warwick.ac.uk) and included isolates previously collected from food, animals and environmental sources. Genomic analyses were performed using the online pipelines provided by the Centre for Genomic Epidemiology (CGE), Denmark. Unsupervised hierarchical clustering was applied to visualize patterns in genetic diversity, AMR, virulence-associated genes and plasmid content using the R software. Results: Clustering based on single nucleotide polymorphism (SNP) and core genome multilocus sequence typing (cgMLST) alleles revealed associations based on geographic locations, sample niche, pathovar and O:H antigen, pointing to evolutionary relatedness between the clades with principal coordinate analysis uncovering this accounted for 27.55% of the genetic diversity. Virulence-associated genes encoding for attaching and effacing (eae) (63.97%), heat-labile toxin (LT) (25.00%) and Shiga toxin 1 (Stx1) (15.44%) were most abundant, with an inverse association between genes encoding for the presence of LT and eae", "token_count": 480, "char_count": 1897, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6586, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:42.167909", "source": { "split": "train_shard_00001", "doc_id": 1304 }, "chunk_id": "train_shard_00001_1304_0", "global_id": 7494 }, { "text": "Resistance to folate pathway antagonists (sulfamethoxazole-55.9%), β-lactamases (amoxicillin, ampicillin and piperacillin-all 54.4%) and aminoglycoside (streptomycin-55.1%) was most abundant. Conclusions: The study revealed region-specific lineages, evidence of horizontal gene transfer and the clustering patterns suggest both localized and cross-border transmission. The study provides insightful evidence on DEC transmission patterns associated with antimicrobial and disinfectant resistance and associated virulence factors.\n\nExploring the Genetic Diversity, Virulence and Antimicrobial Resistance of Diarrhoeagenic <i>Escherichia coli</i> From Southern Africa Using Whole-Genome Data.", "token_count": 212, "char_count": 708, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:42.644252", "source": { "split": "train_shard_00001", "doc_id": 1304 }, "chunk_id": "train_shard_00001_1304_1", "global_id": 7495 }, { "text": "

Unlabelled

The human gastrointestinal epithelium makes up the largest barrier separating the body from the external environment. Whereas invasive pathogens cause epithelial barrier disruption, probiotic micro-organisms modulate tight junction regulation and improve epithelial barrier function. In addition, probiotic strains may be able to reduce epithelial barrier disruption caused by pathogenic species. The aim of this study was to explore non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Benchmarking against established probiotic strains, we evaluated the ability of four nonpathogenic yeast species to modulate transepithelial electrical resistance (TER) across a monolayer of differentiated human colonocytes (Caco-2 cells). Further, we assessed yeast modulation of a Salmonella Typhimurium-induced epithelial cell barrier function insult. Our findings demonstrate distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function. While the established probiotic yeast Saccharomyces boulardii increased TER across a Caco-2 monolayer by 30%, Kluyveromyces marxianus exhibited significantly stronger properties of TER enhancement (50% TER increase). In addition, our data demonstrate significant yeast-mediated modulation of Salmonella-induced epithelial cell barrier disruption and identify K. marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion.

Significance and impact of the study

This study demonstrates distinct patterns of non-Saccharomyces yeast modulation of epithelial cell barrier function in vitro. Further, our data demonstrate significant yeast-mediated modulation of Salmonella Typhimurium-induced epithelial cell barrier disruption and identify Kluyveromyces marxianus and Metschnikowia gruessii as two non-Saccharomyces yeasts capable of protecting human epithelial cells from pathogen invasion", "token_count": 501, "char_count": 1977, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5042, "quality_score": 0.7521, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:43.326889", "source": { "split": "train_shard_00001", "doc_id": 1305 }, "chunk_id": "train_shard_00001_1305_0", "global_id": 7496 }, { "text": "This study is the first to demonstrate significant non-Saccharomyces yeast-mediated epithelial cell barrier protection from Salmonella invasion, thus encouraging future efforts aimed at confirming the observed effects in vivo and driving further strain development towards novel yeast probiotics.\n\nNon-Saccharomyces yeasts protect against epithelial cell barrier disruption induced by Salmonella enterica subsp. enterica serovar Typhimurium.", "token_count": 102, "char_count": 441, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8704, "quality_score": 0.9352, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:43.738767", "source": { "split": "train_shard_00001", "doc_id": 1305 }, "chunk_id": "train_shard_00001_1305_1", "global_id": 7497 }, { "text": "

Background

Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk of patient DNA leakage. To mitigate this risk, we need near-comprehensive removal of human DNA sequences at the point of sequencing, typically involving the use of resource-constrained devices. Existing benchmarks have largely focused on the use of standardized databases and largely ignored the computational requirements of depletion pipelines as well as the impact of human genome diversity.

Results

We benchmarked host removal pipelines on simulated and artificial real Illumina and Nanopore metagenomic samples. We found that construction of a custom kraken database containing diverse human genomes results in the best balance of accuracy and computational resource usage. In addition, we benchmarked pipelines using kraken and minimap2 for taxonomic classification of Mycobacterium reads using standard and custom databases. With a database representative of the Mycobacterium genus, both tools obtained improved specificity and sensitivity, compared to the standard databases for classification of Mycobacterium tuberculosis. Computational efficiency of these custom databases was superior to most standard approaches, allowing them to be executed on a laptop device.

Conclusions

Customized pangenome databases provide the best balance of accuracy and computational efficiency when compared to standard databases for the task of human read removal and M. tuberculosis read classification from metagenomic samples. Such databases allow for execution on a laptop, without sacrificing accuracy, an especially important consideration in low-resource settings. We make all customized databases and pipelines freely available.\n\nPangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.", "token_count": 410, "char_count": 1955, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5771, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:44.369086", "source": { "split": "train_shard_00001", "doc_id": 1306 }, "chunk_id": "train_shard_00001_1306_0", "global_id": 7498 }, { "text": "Bread wheat ( Triticum aestivum ) is a globally dominant crop and major source of calories and proteins for the human diet. Compared to its wild ancestors, modern bread wheat shows lower genetic diversity caused by polyploidisation, domestication, and breeding bottlenecks 1,2 . Wild wheat relatives represent genetic reservoirs, harbouring diversity and beneficial alleles that have not been incorporated into bread wheat. Here, we establish and analyse pangenome resources for Tausch’s goatgrass, Aegilops tauschii , the donor of the bread wheat D genome. This new pangenome facilitated the cloning of a disease resistance gene and haplotype analysis across a complex disease resistance locus, allowing us to discern alleles from paralogous gene copies. We also reveal the complex genetic composition and history of the bread wheat D genome, involving previously unreported contributions from genetically and geographically discrete Ae. tauschii subpopulations. Together, our results reveal the complex history of the bread wheat D genome and demonstrate the potential of wild relatives in crop improvement.\n\nOrigin and evolution of the bread wheat D genome", "token_count": 259, "char_count": 1159, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:44.912155", "source": { "split": "train_shard_00001", "doc_id": 1307 }, "chunk_id": "train_shard_00001_1307_0", "global_id": 7499 }, { "text": "Genome-scale metabolic models (GEMs) have been widely used for quantitative exploration of the relation between genotype and phenotype. Streamlined integration of enzyme constraints and proteomics data into GEMs was first enabled by the GECKO method, allowing the study of phenotypes constrained by protein limitations. Here, we upgraded the GECKO toolbox in order to enhance models with enzyme and proteomics constraints for any organism with an available GEM reconstruction. With this, enzyme-constrained models (ecModels) for the budding yeasts Saccharomyces cerevisiae, Yarrowia lipolytica and Kluyveromyces marxianus were generated, aiming to study their long-term adaptation to several stress factors by incorporation of proteomics data. Predictions revealed that upregulation and high saturation of enzymes in amino acid metabolism were found to be common across organisms and conditions, suggesting the relevance of metabolic robustness in contrast to optimal protein utilization as a cellular objective for microbial growth under stress and nutrient-limited conditions. The functionality of GECKO was further developed by the implementation of an automated framework for continuous and version-controlled update of ecModels, which was validated by producing additional high-quality ecModels for Escherichia coli and Homo sapiens. These efforts aim to facilitate the utilization of ecModels in basic science, metabolic engineering and synthetic biology purposes.\n\nReconstruction of a catalogue of genome-scale metabolic models with enzymatic constraints using GECKO 2.0", "token_count": 361, "char_count": 1577, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6589, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:46.235021", "source": { "split": "train_shard_00001", "doc_id": 1308 }, "chunk_id": "train_shard_00001_1308_0", "global_id": 7500 }, { "text": "

ABSTRACT

Bacteroides fragilis is a Gram-negative commensal bacterium commonly found in the human colon that differentiates into two genomospecies termed division I and II. We leverage a comprehensive collection of 694 B. fragilis whole genome sequences and report differential gene abundance to further support the recent proposal that divisions I and II represent separate species. In division I strains, we identify an increased abundance of genes related to complex carbohydrate degradation, colonization, and host niche occupancy, confirming the role of division I strains as gut commensals. In contrast, division II strains display an increased prevalence of plant cell wall degradation genes and exhibit a distinct geographic distribution, primarily originating from Asian countries, suggesting dietary influences. Notably, division II strains have an increased abundance of genes linked to virulence, survival in toxic conditions, and antimicrobial resistance, consistent with a higher incidence of these strains in bloodstream infections. This study provides new evidence supporting a recent proposal for classifying divisions I and II B. fragilis strains as distinct species, and our comparative genomic analysis reveals their niche-specific roles.\n\nPangenome comparison ofBacteroides fragilisgenomospecies unveil genetic diversity and ecological insights", "token_count": 300, "char_count": 1380, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:46.792395", "source": { "split": "train_shard_00001", "doc_id": 1309 }, "chunk_id": "train_shard_00001_1309_0", "global_id": 7501 }, { "text": "

Background

Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. The composition of kefir can vary by geographic localization and weather, and this paper focuses on a Brazilian sample and continues previous work that has successful anti-Alzheimer properties. In this study, we employed shotgun metagenomics and peptidomics approaches to characterize Brazilian kefir further.

Results

We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silico prospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting β-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties.

Conclusions

These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.\n\nUnveiling the Brazilian kefir microbiome: discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties.", "token_count": 404, "char_count": 1553, "word_count": 198, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:47.418357", "source": { "split": "train_shard_00001", "doc_id": 1310 }, "chunk_id": "train_shard_00001_1310_0", "global_id": 7502 }, { "text": "Currently, Fusarium oxysporum f. sp. apii (Foa) race 4 in celery and F. oxysporum f. sp. coriandrii (Foci) in coriander have the characteristics of emerging infectious plant diseases in coastal southern California: the pathogens are spreading, yield losses can be severe, and there are currently no economical solutions for their control. Celery, and possibly coriander, production in these regions is are likely to have more severe disease from projected warmer conditions in the historically cool, coastal regions. Experimental evidence shows that Foa race 4 causes much higher disease severity when temperatures exceed 21°C. A phylogenomic analysis indicated that Foa race 4, an older, less virulent, and uncommon Foa race 3, and two Foci are closely related in their conserved genomes. These closely related genotypes are somatically compatible. Foa race 4 can also cause disease in coriander and the two organisms readily form \"hetero\" conidial anastomosis tubes (CAT), further increasing the likelihood of parasexual recombination and the generation of novel pathotypes. A horizontal chromosome transfer event likely accounts for the difference in host range between Foci versus Foa races 4 and 3 because they differ primarily in one or two accessory chromosomes. How Foa race 4 evolved its hyper-virulence is unknown. Although the accessory chromosomes of Foa races 3 and 4 are highly similar, there is no evidence that Foa race 4 evolved directly from race 3, and races 3 and 4 probably only have a common ancestor", "token_count": 465, "char_count": 1634, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:48.059537", "source": { "split": "train_shard_00001", "doc_id": 1311 }, "chunk_id": "train_shard_00001_1311_0", "global_id": 7503 }, { "text": "Foa race 2, which is in a different clade within the Fusarium oxysporum species complex (FOSC) than the other Foa, did not contribute to the evolution of race 4, and does not form CATs with Foa race 4; consequently, while inter-isolate CAT formation is genetically less restrictive than somatic compatibility, it might be more restricted between FOSC clades than currently known. Other relatively new F. oxysporum in coastal California include F. oxysporum f. sp. fragariae on strawberry (Fof). Curiously, Fof \"yellows-fragariae\" isolates also have similar core genomes to Foa races 4 and 3 and Foci, perhaps suggesting that there may be core genome factors in this lineage that favor establishment in these soils.\n\nThe Emergence of Fusarium oxysporum f. sp. apii Race 4 and Fusarium oxysporum f. sp. coriandrii Highlights Major Obstacles Facing Agricultural Production in Coastal California in a Warming Climate: A Case Study.", "token_count": 340, "char_count": 1032, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7103, "quality_score": 0.8552, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:48.622381", "source": { "split": "train_shard_00001", "doc_id": 1311 }, "chunk_id": "train_shard_00001_1311_1", "global_id": 7504 }, { "text": "Porcine blood is an important by-product from slaughterhouses and an abundant source of proteins. Indeed, cruor, the solid part of blood, is mainly composed of hemoglobin. Its enzymatic hydrolysis with pepsin generates a diversity of peptides, particularly antimicrobials. One of the downsides of using these hydrolysates as food bio-preservatives is the color brought by the heme, which can be removed by discoloration. Nonetheless, the effects of this procedure on the antimicrobial peptide population have not been completely investigated. In this study, its impacts were evaluated on the final antibacterial and antifungal activities of a cruor hydrolysate. The results demonstrated that 38 identified and characterized peptides showed a partial or total decrease in the hydrolysate, after discoloration. Antifungal activities were observed for the raw and discolored hydrolysates: MICs vary between 0.1 and 30.0 mg/mL of proteins, and significant differences were detected between both hydrolysates for the strains S. boulardii, C. guilliermondii, K. marxianus, M. racemosus and P. chrysogenum. The raw hydrolysate showed up to 12 times higher antifungal activities. Hence, peptides with the highest relative abundance decrease after discoloration were synthesized and tested individually. In total, eight new antifungal peptides were characterized as active and promising. To our knowledge, this is the first time that effective antifungal peptide sequences have been reported from porcine cruor hydrolysates.\n\nHow Discoloration of Porcine Cruor Hydrolysate Allowed the Identification of New Antifungal Peptides.", "token_count": 437, "char_count": 1653, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6447, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:49.253600", "source": { "split": "train_shard_00001", "doc_id": 1312 }, "chunk_id": "train_shard_00001_1312_0", "global_id": 7505 }, { "text": "

Background:

The red junglefowl, the wild progenitor of domestic chickens, has historically served as a reference for genomic studies of domestic chickens. These studies have provided insight into the etiology of traits of commercial importance. However, the use of a single reference genome does not capture diversity present among modern breeds, many of which have accumulated molecular changes due to drift and selection. While reference-based resequencing is well-suited to cataloging simple variants such as single nucleotide changes and short insertions and deletions, it is mostly inadequate to discover more complex structural variation in the genome.

Results:

. We present a pangenome for the domestic chicken consisting of thirty assemblies of chickens from different breeds and research lines. We demonstrate how this pangenome can be used to catalog structural variants present in modern breeds and untangle complex nested variation. We show that alignment of short reads from 100 diverse wild and domestic chickens to this pangenome reduces reference bias by 38%, which affects downstream genotyping results. This approach also allows for the accurate genotyping of a large and complex pair of structural variants at the K ‘feathering’ locus using short reads, which would not be possible using a linear reference.

Conclusions:

. We expect that this new paradigm of genomic reference will allow better pinpointing of exact mutations responsible for specific phenotypes, which will in turn be necessary for breeding chickens that meet new sustainability criteria and are resilient to quickly evolving pathogen threats.\n\nA pangenome graph reference of 30 chicken genomes allows genotyping of large and complex structural variants", "token_count": 394, "char_count": 1769, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:49.870007", "source": { "split": "train_shard_00001", "doc_id": 1313 }, "chunk_id": "train_shard_00001_1313_0", "global_id": 7506 }, { "text": "Genome sequences of the three strains of L. monocytogenes, which are the first core genome multi-locus sequence types (cgMLST) 2050 and 2051 were reviewed and compared with 21 close relatives and reference genomes. Using a pan-genomic approach to analyse whole genome sequences, it was found that the strains consisted of approximately 2200 shared genes and a much greater pool of genes present as an accessory genome. An unknown transmissible sequence of approximately 91 kb harbouring bacitracin resistance genes found in strain LmNG2 (1/2b) was revealed to be an Inc18 plasmid. The CT2051, strain LmNG3 (1/2a) haboured more unique genes (252 vs 230) than the well-known reference strain LmEGD-e (1/2a). More studies to monitor new strains can help reduce food-borne outbreaks.\n\nComparative genome analysis of the first Listeria monocytogenes core genome multi-locus sequence types CT2050 AND CT2051 strains with their close relatives.", "token_count": 280, "char_count": 951, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.844, "entities": { "genes": [ "CT2051", "CT2050" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:50.429402", "source": { "split": "train_shard_00001", "doc_id": 1314 }, "chunk_id": "train_shard_00001_1314_0", "global_id": 7507 }, { "text": "

Background

Portugal is one of the main producers of industrial tomato and tomato paste, an important intermediate ingredient used in many added-value foods. The tomato processing industry rigorously selects the fruits by colour during mechanical harvest, picking only completely ripe fruits to produce high quality tomato paste. The latest available data shows that about 1.12 × 108 kg yr-1 of non-red/not-ripe tomatoes are left in the field, representing a major side product/field residue with great impact on the environment and for tomato producers.

Results

The aim of the work was to use fermentation by a consortium of yeast and lactic acid bacteria to improve the nutritional quality of unripe tomato paste. A consortium of Lactobacillus plantarum, Leuconostoc mesenteroides and Kluyveromyces marxianus was selected, producing an acidic paste with olive-like flavours after 4 days of fermentation. Nutritional characterization revealed a significant improvement (P < 0.05) in the content of ascorbic acid and antioxidant potential. In addition, ultrahigh-performance liquid chromatography tandem mass spectrometry (UHPLC-MS/MS) analysis showed that the fermented green tomato paste content in glycoalkaloid α-tomatine represents no hazard to the consumer.

Conclusion

Therefore, the obtained fermented green tomato paste can be further used to produce new food products, such as salad dressings and sauces. © 2021 Society of Chemical Industry.\n\nImproving nutritional quality of unripe tomato through fermentation by a consortium of yeast and lactic acid bacteria.", "token_count": 442, "char_count": 1613, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:51.059163", "source": { "split": "train_shard_00001", "doc_id": 1315 }, "chunk_id": "train_shard_00001_1315_0", "global_id": 7508 }, { "text": "The taxonomic composition and spatial localization of yeast and bacteria in kefir grains (KG) obtained for study from different regions of the planet were investigated. The diversity of their microbiome has been demonstrated by high-throughput sequencing of bacterial 16S rRNA genes and the ITS1 region of the 18S-ITS1-5.8S-ITS2-28S complex of yeast rRNA. It has been established that the main representatives of the complex community of KG from different regions are lactic acid bacteria (LAB; lactobacilli, lactococci, and Leuconostoc spp. in different ratios) and different types of yeast of the genus Kazachstania (family Saccharomycetaceae). Acetic acid bacteria and a small percentage of yeast Kluyveromyces marxianus were detected in the KG from Tibet, and yeast Pichia kluyveri was detected in the KG from Ossetia.\n\nAnalysis of Kefir Grains from Different Regions of the Planet Using High-Throughput Sequencing.", "token_count": 283, "char_count": 954, "word_count": 135, "semantic_coherence": 1, "information_density": 0.563, "quality_score": 0.7815, "entities": { "genes": [ "ITS2", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:51.616097", "source": { "split": "train_shard_00001", "doc_id": 1316 }, "chunk_id": "train_shard_00001_1316_0", "global_id": 7509 }, { "text": "The permanent organs of grapevines ( V. vinifera L.), like other woody perennials, are colonized by various unrelated pathogenic ascomycete fungi secreting cell wall-degrading enzymes and phytotoxic secondary metabolites that contribute to host damage and disease symptoms. Trunk pathogens differ in the symptoms they induce and the extent and speed of damage. Isolates of the same species often display a wide virulence range, even within the same vineyard. This study focuses on Eutypa lata , Neofusicoccum parvum , and Phaeoacremonium minimum , causal agents of Eutypa dieback, Botryosphaeria dieback, and Esca, respectively. We sequenced fifty isolates from viticulture regions worldwide and built nucleotide-level, reference-free pangenomes for each species. Through examining genomic diversity and pangenome structure, we analyzed intraspecific conservation and variability of putative virulence factors, focusing on functions under positive selection, and recent gene-family dynamics of contraction and expansion. Our findings reveal contrasting distributions of putative virulence factors in the core, dispensable, and private genomes of each pangenome. For example, CAZymes were prevalent in the core genomes of each pangenome, whereas biosynthetic gene clusters were prevalent in the dispensable genomes of E. lata and P. minimum . The dispensable fractions were also enriched in Gypsy transposable elements and virulence factors under positive selection (polyketide synthases genes in E. lata and P. minimum glycosyltransferases in N. parvum ). Our findings underscore the complexity of the genomic architecture in each species and provide insights into their adaptive strategies, enhancing our understanding of the underlying mechanisms of virulence.\n\nComparative pangenomic insights into the distinct evolution of virulence factors among grapevine trunk pathogens", "token_count": 445, "char_count": 1876, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:52.252698", "source": { "split": "train_shard_00001", "doc_id": 1317 }, "chunk_id": "train_shard_00001_1317_0", "global_id": 7510 }, { "text": "The Liverpool epidemic strain (LES) is an important transmissible clonal lineage of Pseudomonas aeruginosa that chronically infects the lungs of people with cystic fibrosis (CF). Previous studies have focused on the genomics of the LES in a limited number of isolates, mostly from one CF centre in the UK, and from studies highlighting identification of the LES in Canada. Here we significantly extend the current LES genome database by genome sequencing 91 isolates from multiple CF centres across the UK, and we describe the comparative genomics of this large collection of LES isolates from the UK and Canada. Phylogenetic analysis revealed that the 145 LES genomes analysed formed a distinct clonal lineage when compared with the wider P. aeruginosa population. Notably, the isolates formed two clades: one associated with isolates from Canada, and the other associated with UK isolates. Further analysis of the UK LES isolates revealed clustering by clinic geography. Where isolates clustered closely together, the association was often supported by clinical data linking isolates or patients. When compared with the earliest known isolate, LESB58 (from 1988), many UK LES isolates shared common loss-of-function mutations, such as in genes gltR and fleR. Other loss-of-function mutations identified in previous studies as common adaptations during CF chronic lung infections were also identified in multiple LES isolates. Analysis of the LES accessory genome (including genomic islands and prophages) revealed variations in the carriage of large genomic regions, with some evidence for shared genomic island/prophage complement according to clinic location. Our study reveals divergence and adaptation during the spread of the LES, within the UK and between continents.\n\nTransmission, adaptation and geographical spread of the Pseudomonas aeruginosa Liverpool epidemic strain.", "token_count": 455, "char_count": 1917, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5632, "quality_score": 0.7816, "entities": { "genes": [ "LESB58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:52.891835", "source": { "split": "train_shard_00001", "doc_id": 1318 }, "chunk_id": "train_shard_00001_1318_0", "global_id": 7511 }, { "text": "Gram-negative, rod-shaped, and aerobic bacteria designated chi1T and chi5T were isolated from the root of Suaeda japonica Makino. Phylogenetics utilizing 16S rRNA and whole-genome sequences of the two novel strains chi1T and chi5T confirmed that they were related to the genera Marinobacter and Wenyingzhuangia, respectively. For the novel strains chi1T and chi5T, the digital DNA-DNA hybridization values (19-20% and 22.1-36.6%, respectively) and average nucleotide identity values (74.4-76.5% and 79.1-88.9%, respectively) fell within the range for the genera Marinobacter and Wenyingzhuangia, respectively. Pangenome analyses of the novel strains chi1T and chi5T revealed 357 and 368 singletons genes, respectively. The genomic DNA G + C contents of the strains chi1T and chi5T were 57.2% and 31.5%, respectively. The major fatty acids of strain chi1T were C12:0, C16:0, and summed feature 3 (C16:1ω6c and/or C16:1ω7c), while those of the strain chi5T were iso-C15:0 3OH, iso-C17:0 3OH, and iso-C15:0", "token_count": 515, "char_count": 1275, "word_count": 145, "semantic_coherence": 1, "information_density": 0.5793, "quality_score": 0.7897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:53.555430", "source": { "split": "train_shard_00001", "doc_id": 1319 }, "chunk_id": "train_shard_00001_1319_0", "global_id": 7512 }, { "text": "Data from the phylogenetic, phylogenomic, pangenome, genomic, physiological, and biochemical analyses indicated that the novel strains were distinct. Therefore, we propose the names Marinobacter suadae (type strain chi1T = KACC 23259T = TBRC 17652T) and Wenyingzhangia gilva (type strain chi5T = KACC 23262T = TBRC 17900T) for the studied bacterial strains.\n\nDraft Genome Sequence Analyses of Two Novel Marinobacter suadae sp. nov. and Wenyingzhuangia gilva sp. nov. Isolated from the Root of Suaeda japonica Makino.", "token_count": 250, "char_count": 617, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:54.050081", "source": { "split": "train_shard_00001", "doc_id": 1319 }, "chunk_id": "train_shard_00001_1319_1", "global_id": 7513 }, { "text": "In recent years, Salmonella Infantis has become a predominant serovariant in clinical and poultry isolates, thereby imposing a substantial economic burden on both public health and the livestock industry. With the aim of coping with the steep increase in serovar Infantis prevalence, a polymerase chain reaction (PCR)-based rapid and accurate diagnostic assay was developed in this study through pangenome profiling of 60 Salmonella serovars. A gene marker, SIN_02055, was identified, which is present in the S. Infantis genome but not in the pangenome of the other serovars. Primers specific to SIN_02055 were used to accurately detect serovar Infantis, and to successfully differentiate Infantis from the other 59 serovars in real-time PCR with a R2 of 0.999 and an efficiency of 95.76%. The developed method was applied to 54 Salmonella strains belonging to eight dominant serovars, and distinguished Infantis from the other seven serovars with an accuracy of 100%. The diagnostic primer set also did not show false positive amplification with 32 strains from eight non-Salmonella bacterial species. This cost-effective and rapid method can be considered an alternative to the classic serotyping using antisera.\n\nDevelopment of a Genoserotyping Method for Salmonella Infantis Detection on the Basis of Pangenome Analysis.", "token_count": 386, "char_count": 1377, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6212, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:54.696140", "source": { "split": "train_shard_00001", "doc_id": 1320 }, "chunk_id": "train_shard_00001_1320_0", "global_id": 7514 }, { "text": "The isolation and application of auxotrophic mutants for gene manipulations, such as genetic transformation, mating selection and tetrad analysis, form the basis of yeast genetics. For the development of these genetic methods in the thermotolerant fermentative yeast Kluyveromyces marxianus, we isolated a series of auxotrophic mutants with defects in amino acid or nucleic acid metabolism. To identify the mutated genes, linear DNA fragments of nutrient biosynthetic pathway genes were amplified from Saccharomyces cerevisiae chromosomal DNA and used to directly transform the K. marxianus auxotrophic mutants by random integration into chromosomes through non-homologous end joining (NHEJ). The appearance of transformant colonies indicated that the specific S. cerevisiae gene complemented the K. marxianus mutant. Using this interspecific complementation approach with linear PCR-amplified DNA, we identified auxotrophic mutations of ADE2, ADE5,7, ADE6, HIS2, HIS3, HIS4, HIS5, HIS6, HIS7, LYS1, LYS2, LYS4, LYS9, LEU1, LEU2, MET2, MET6, MET17, TRP3, TRP4 and TRP5 without the labour-intensive requirement of plasmid construction. Mating, sporulation and tetrad analysis techniques for K. marxianus were also established. With the identified auxotrophic mutant strains and S. cerevisiae genes as selective markers, NHEJ-mediated integrative transformation with PCR-amplified DNA is an attractive system for facilitating genetic analyses in the yeast K. marxianus.\n\nIdentification of auxotrophic mutants of the yeast Kluyveromyces marxianus by non-homologous end joining-mediated integrative transformation with genes from Saccharomyces cerevisiae.", "token_count": 470, "char_count": 1651, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8196, "entities": { "genes": [ "LYS9", "MET17", "MET2", "ADE6", "HIS2", "HIS7", "MET6", "ADE2", "HIS4", "LEU2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:55.374222", "source": { "split": "train_shard_00001", "doc_id": 1321 }, "chunk_id": "train_shard_00001_1321_0", "global_id": 7515 }, { "text": "Blood stream infections (BSIs) are a major cause of hospitalisation and death for children under the age of five in sub-Saharan Africa with members of the Gram-negative bacteria Enterobacterales such as Klebsiella pneumoniae and Escherichia coli among the most common causative agents. These bacteria usually colonise the human gastrointestinal (GI) tract which has been identified as a reservoir for invasive infections into extra-intestinal environments such as the urinary tract and bloodstream. In this study we used comparative genomics to compare hybrid genome assemblies of blood and faecal isolates taken from the same patients (all neonates under 19 days old) to determine if the BSI associated bacterial isolates originated in their GI tract. We show that both E. coli and K. pneumoniae likely translocated from the GI tract to the blood in multiple cases of BSI. We also highlight key virulence genes and acquired mutations that are indicative of pathogenic strains capable of BSI. These findings expand our understanding of BSI pathogenesis and could help guide targeted interventions to prevent future BSI infections in neonates.\n\nGenomic comparison of highly related pairs of E. coli and K. pneumoniae isolated from faeces and blood of the same neonatal patients hospitalized with fever in Dar es Salaam, Tanzania", "token_count": 328, "char_count": 1341, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:55.971775", "source": { "split": "train_shard_00001", "doc_id": 1322 }, "chunk_id": "train_shard_00001_1322_0", "global_id": 7516 }, { "text": "Xylella fastidiosa is an economically important bacterial plant pathogen. With insights gained from 72 genomes, this study investigated differences among the three main subspecies, which have allopatric origins: X. fastidiosa subsp. fastidiosa, multiplex, and pauca The origin of recombinogenic X. fastidiosa subsp. morus and sandyi was also assessed. The evolutionary rate of the 622 genes of the species core genome was estimated at the scale of an X. fastidiosa subsp. pauca subclade (7.62 × 10-7 substitutions per site per year), which was subsequently used to estimate divergence time for the subspecies and introduction events. The study characterized genes present in the accessory genome of each of the three subspecies and investigated the core genome to detect genes potentially under positive selection. Recombination is recognized to be the major driver of diversity in X. fastidiosa, potentially facilitating shifts to novel plant hosts. The relative effect of recombination in comparison to point mutation was calculated (r/m = 2.259). Evidence of recombination was uncovered in the core genome alignment; X. fastidiosa subsp. fastidiosa in the United States was less prone to recombination, with an average of 3.22 of the 622 core genes identified as recombining regions, whereas a specific clade of X. fastidiosa subsp. multiplex was found to have on average 9.60 recombining genes, 93.2% of which originated from X. fastidiosa subsp. fastidiosa Interestingly, for X. fastidiosa subsp", "token_count": 529, "char_count": 1651, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5689, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:56.639592", "source": { "split": "train_shard_00001", "doc_id": 1323 }, "chunk_id": "train_shard_00001_1323_0", "global_id": 7517 }, { "text": "morus, which was initially thought to be the outcome of genome-wide recombination between X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex, intersubspecies homologous recombination levels reached 15.30% in the core genome. Finally, there is evidence of X. fastidiosa subsp. pauca strains from citrus containing genetic elements acquired from strains infecting coffee plants as well as genetic elements from both X. fastidiosa subsp. fastidiosa and X. fastidiosa subsp. multiplex In summary, our data provide new insights into the evolution and epidemiology of this plant pathogen.IMPORTANCEXylella fastidiosa is an important vector-borne plant pathogen. We used a set of 72 genomes that constitutes the largest assembled data set for this bacterial species so far to investigate genetic relationships and the impact of recombination on phylogenetic clades and to compare genome content at the subspecies level, and we used a molecular dating approach to infer the evolutionary rate of X. fastidiosa The results demonstrate that recombination is important in shaping the genomes of X. fastidiosa and that each of the main subspecies is under different selective pressures. We hope insights from this study will improve our understanding of X. fastidiosa evolution and biology.\n\nGenomic Diversity and Recombination among Xylella fastidiosa Subspecies.", "token_count": 430, "char_count": 1479, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:57.264982", "source": { "split": "train_shard_00001", "doc_id": 1323 }, "chunk_id": "train_shard_00001_1323_1", "global_id": 7518 }, { "text": "Rhodococcus equi (R. equi) is a zoonotic opportunistic pathogen that can cause life-threatening infections. The rapid evolution of multidrug-resistant R. equi and the fact that there is no currently licensed effective vaccine against R. equi warrant the need for vaccine development. Reverse vaccinology (RV), which involves screening a pathogen's entire genome and proteome using various web-based prediction tools, is considered one of the most effective approaches for identifying vaccine candidates. Here, we performed a pangenome analysis to determine the core proteins of R. equi. We then used the RV approach to examine the subcellular localization, host and gut flora homology, antigenicity, transmembrane helices, physicochemical properties, and immunogenicity of the core proteins to select potential vaccine candidates. The vaccine candidates were then subjected to epitope mapping to predict the exposed antigenic epitopes that possess the ability to bind with major histocompatibility complex I/II (MHC I/II) molecules. These vaccine candidates and epitopes will form a library of elements for the development of a polyvalent or universal vaccine against R. equi. Sixteen R. equi complete proteomes were found to contain 6,238 protein families, and the core proteins consisted of 3,969 protein families (∼63.63% of the pangenome), reflecting a low degree of intraspecies genomic variability. From the pool of core proteins, 483 nonhost homologous membrane and extracellular proteins were screened, and 12 vaccine candidates were finally identified according to their antigenicity, physicochemical properties and other factors. These included four cell wall/membrane/envelope biogenesis proteins; four amino acid transport and metabolism proteins; one cell cycle control, cell division and chromosome partitioning protein; one carbohydrate transport and metabolism protein; one secondary metabolite biosynthesis, transport and catabolism protein; and one defense mechanism protein", "token_count": 513, "char_count": 2041, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6218, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:08:57.924906", "source": { "split": "train_shard_00001", "doc_id": 1324 }, "chunk_id": "train_shard_00001_1324_0", "global_id": 7519 }, { "text": "All 12 vaccine candidates have an experimentally validated 3D structure available in the protein data bank (PDB). Epitope mapping of the candidates showed that 16 MHC I epitopes and 13 MHC II epitopes with the strongest immunogenicity were exposed on the protein surface, indicating that they could be used to develop a polypeptide vaccine. Thus, we utilized an analytical strategy that combines pangenome analysis and RV to generate a peptide antigen library that simplifies the development of multivalent or universal vaccines against R. equi and can be applied to the development of other vaccines.\n\nIdentification of vaccine candidates against rhodococcus equi by combining pangenome analysis with a reverse vaccinology approach.", "token_count": 180, "char_count": 747, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:58.383731", "source": { "split": "train_shard_00001", "doc_id": 1324 }, "chunk_id": "train_shard_00001_1324_1", "global_id": 7520 }, { "text": "Abstract

Most in silico evolutionary studies commonly assumed that core genes are essential for cellular function, while accessory genes are dispensable, particularly in nutrient-rich environments. However, this assumption is seldom tested genetically within the pangenome context. Here we conducted a robust pangenomic Tn-seq analysis of fitness genes in a nutrient-rich medium for Sinorhizobium strains with a canonical open pangenome. The Hidden Markov Model-based method is the most robust to variations among mutant libraries per strain and non-sensitive to data size. Fitness genes, categorized as essential (ES), advantage (GA) and disadvantage (GD) for growth, are enriched in core genes, while nonessential genes (NE) are over-represented in accessory genes. Connectivity degrees in predicted protein-protein interaction networks decline in the order of ES, GA, GD and NE, and those in the co-fitness network decreases from ES to GA/GD to NE. Notably, 1599 out of 3284 core genes display differential essentiality across test strains. Within pangenome core, both shared quasi-essential (ES and GA) and strain-dependent fitness genes are enriched in similar functional categories. Our analysis demonstrates a considerable fuzzy essential zone determined by co-fitness connectivity degrees in Sinorhizobium pangenome, and highlights the power of co-fitness network in understanding genetic basis of ever-increasing prokaryotic pangenome data.

\n\nCo-fitness network connectivity determines a fuzzy essential zone in Sinorhizobium of canonical open pangenome", "token_count": 379, "char_count": 1584, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6372, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:58.965208", "source": { "split": "train_shard_00001", "doc_id": 1325 }, "chunk_id": "train_shard_00001_1325_0", "global_id": 7521 }, { "text": "

Background

Salmonella Paratyphi C is an infrequent etiological agent of enteric fever, with sporadic cases primarily reported in Asia and Africa. Documented outbreaks remain exceedingly rare, and epidemiological data on such events are notably scarce.

Methods

This study investigated a paratyphoid fever outbreak caused by S. Paratyphi C at a secondary school in China in 2023. Comprehensive field epidemiological investigations were conducted, including environmental sampling and the collection of clinical specimens. All outbreak-associated isolates underwent antimicrobial susceptibility testing, whole-genome sequencing, and in-depth bioinformatics analysis. Single-nucleotide polymorphism profiling and core genome multilocus sequence typing were employed to elucidate the genetic relatedness of the isolates.

Results

A total of 11 S. Paratyphi C strains, characterized by the antigenic formula 6,7:c:1,5, were recovered from a variety of sample sources. Genomic analyses revealed striking homogeneity across all isolates, with uniform multilocus sequence types, identical antimicrobial resistance patterns, and shared virulence-associated genes. Phylogenetic reconstruction demonstrated a tightly clustered lineage, corroborated by highly similar circular genome structures, suggesting a common source of infection.

Conclusions

This investigation offered critical insights into a rare foodborne outbreak caused by S. Paratyphi C, bridging significant knowledge gaps regarding its epidemiology and genetic characteristics. The findings underscored the global diversity and potential public health threat of S. Paratyphi C, reinforcing the urgent need to enhance food safety monitoring and improve outbreak preparedness strategies both in China and internationally.\n\nA foodborne outbreak of <i>Salmonella</i> Paratyphi C in a Chinese middle school: Genomic tracing and epidemiological characterization.", "token_count": 487, "char_count": 1983, "word_count": 237, "semantic_coherence": 1, "information_density": 0.7131, "quality_score": 0.8565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:08:59.612766", "source": { "split": "train_shard_00001", "doc_id": 1326 }, "chunk_id": "train_shard_00001_1326_0", "global_id": 7522 }, { "text": "

Objectives

P. aeruginosa is one of the most metabolically versatile bacteria having the ability to survive in multiple environments through its accessory genome. An important hallmark of P. aeruginosa is the high level of antibiotic resistance, which often makes eradication difficult and sometimes impossible. Evolutionary forces have led to this bacterium to develop high antimicrobial resistance with a variety of elements contributing to both intrinsic and acquired resistance. The objectives were to genetically and phenotypically characterizer P. aeruginosa strains isolated from companion animals of different species.

Methods

We characterized a collection of 39 P. aeruginosa strains isolated from infected animals. The genetic characterization was in relation to chromosomal profile by PFGE; content of virulence gene; presence of genomic islands (GIs); genes of the cytotoxins exported by T3SS: exoU, exoS, exoT and exoY; and type IV pili allele. The phenotypic characterization was based on patterns of susceptibility to different antimicrobials.

Results

Each strain had a PFGE profile, a high virulence genes content, and a large accessory genome. However, most of the strains presented high sensitivity to almost all antimicrobials tested, showing no acquired resistance (no β-lactamases). The exception to this lack of resistance was seen with penicillin.

Conclusions

P. aeruginosa could be a naturally sensitive bacterium to standard antimicrobials but could rapidly develop intrinsic and acquired resistance when the bacterium is exposed to pressure exerted by antibiotics, as observed in hospital settings.\n\nPseudomonas aeruginosa strains isolated from animal with high virulence genes content and highly sensitive to antimicrobials.", "token_count": 429, "char_count": 1779, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6083, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:00.248354", "source": { "split": "train_shard_00001", "doc_id": 1327 }, "chunk_id": "train_shard_00001_1327_0", "global_id": 7523 }, { "text": "

Background

The cladodes of Opuntia ficus-indica (prickly pear cactus) have a low protein content; for use as a balanced feed, supplementation with other protein sources is therefore desirable. We investigated protein enrichment by cultivation of the yeasts Candida utilis and Kluyveromyces marxianus in an enzymatic hydrolysate of the cladode biomass.

Results

Dilute acid pretreatment and enzymatic hydrolysis of sun-dried cladodes resulted in a hydrolysate containing (per litre) 45.5 g glucose, 6.3 g xylose, 9.1 g galactose, 10.8 g arabinose and 9.6 g fructose. Even though K. marxianus had a much higher growth rate and utilized l-arabinose and d-galactose more completely than C. utilis, its biomass yield coefficient was lower due to ethanol and ethyl acetate production despite aerobic cultivation. Yeast cultivation more than doubled the protein content of the hydrolysate, with an essential amino acid profile superior to sorghum and millet grains.

Conclusions

This K. marxianus strain was weakly Crabtree positive. Despite its low biomass yield, its performance compared well with C. utilis. This is the first report showing that the protein content and quality of O. ficus-indica cladode biomass could substantially be improved by yeast cultivation, including a comparative evaluation of C. utilis and K. marxianus.\n\nProtein enrichment of an Opuntia ficus-indica cladode hydrolysate by cultivation of Candida utilis and Kluyveromyces marxianus.", "token_count": 427, "char_count": 1477, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:00.878044", "source": { "split": "train_shard_00001", "doc_id": 1328 }, "chunk_id": "train_shard_00001_1328_0", "global_id": 7524 }, { "text": "P. brasiliense is an important bacterial pathogen causing blackleg (BL) in potatoes. Nevertheless, P. brasiliense is often detected in seed lots that do not develop any of the typical blackleg symptoms in the potato crop when planted. Field bioassays identified that P. brasiliense strains can be categorized into two distinct classes, some able to cause blackleg symptoms and some unable to do it. A comparative pangenomic approach was performed on 116 P. brasiliense strains, of which 15 were characterized as BL-causing strains and 25 as non-causative. In a genetically homogeneous clade comprising all BL-causing P. brasiliense strains, two genes only present in the BL-causing strains were identified, one encoding a predicted lysozyme inhibitor Lprl (LZI) and one encoding a putative Toll/interleukin-1 receptor (TIR) domain-containing protein. TaqMan assays for the specific detection of BL-causing P. brasiliense were developed and integrated with the previously developed generic P. brasiliense assay into a triplex TaqMan assay. This simultaneous detection makes the scoring more efficient as only a single tube is needed, and it is more robust as BL-causing strains of P. brasiliense should be positive for all three assays. Individual P. brasiliense strains were found to be either positive for all three assays or only for the P. brasiliense assay. In potato samples, the mixed presence of BL-causing and not BL-causing P. brasiliense strains was observed as shown by the difference in Ct value of the TaqMan assays. However, upon extension of the number of strains, it became clear that in recent years additional BL-causing lineages of P. brasiliense were detected for which additional assays must be developed.", "token_count": 507, "char_count": 1810, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5303, "quality_score": 0.7652, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:01.539921", "source": { "split": "train_shard_00001", "doc_id": 1329 }, "chunk_id": "train_shard_00001_1329_0", "global_id": 7525 }, { "text": "An Efficient Triplex TaqMan Quantitative PCR to Detect a Blackleg-Causing Lineage of Pectobacterium brasiliense in Potato Based on a Pangenome Analysis.", "token_count": 49, "char_count": 159, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:01.902747", "source": { "split": "train_shard_00001", "doc_id": 1329 }, "chunk_id": "train_shard_00001_1329_1", "global_id": 7526 }, { "text": "The grape genome is the basis for grape studies and breeding, and is also important for grape industries. In the last two decades, more than 44 grape genomes have been sequenced. Based on these genomes, researchers have made substantial progress in understanding the mechanism of biotic and abiotic resistance, berry quality formation, and breeding strategies. In addition, this work has provided essential data for future pangenome analyses. Apart from de novo assembled genomes, more than six whole-genome sequencing projects have provided datasets comprising almost 5000 accessions. Based on these datasets, researchers have explored the domestication and origins of the grape and clarified the gene flow that occurred during its dispersed history. Moreover, genome-wide association studies and other methods have been used to identify more than 900 genes related to resistance, quality, and developmental phases of grape. These findings have benefited grape studies and provide some basis for smart genomic selection breeding. Moreover, the grape genome has played a great role in grape studies and the grape industry, and the importance of genomics will increase sharply in the future.\n\nBiography of Vitis genomics: recent advances and prospective.", "token_count": 281, "char_count": 1267, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:02.463243", "source": { "split": "train_shard_00001", "doc_id": 1330 }, "chunk_id": "train_shard_00001_1330_0", "global_id": 7527 }, { "text": "The incidence of fungal infections particularly Candida species, is increasing gradually as a result of the increased life expectancy associated with the advances in the diagnosis and treatment of diseases, and increased number of patients in the risk group over the years. In addition, the incidence of fungal infection types that are resistant to antifungal drugs has been increasing, and rare fungal species have been reported to be isolated more frequently. For this reason, it is indicated that identification to the species level will contribute to the early initiation of an accurate and effective treatment. In this study, it was aimed to define the Candida species isolated from various clinical specimens and to document the performance of antifungal sensitivity tests. The Candida isolates sent to the central mycology laboratory in 2019 for identification and antifungal susceptibility tests were included in the study. The definition of the fungi to the species level was carried out using matrix-assisted laser desorption ionization-time of fl ight mass spectrometry (MALDI-TOF MS) and conventional methods. In vitro antifungal drug susceptibilities were analyzed using the The Clinical and Laboratory Standarts Institute (CLSI, M27-A3) reference broth microdilution method. The minimum inhibitory concentration (MIC) results were interpreted in accordance with the species-specific clinical breakpoints (CBPs) cited in the CLSI-M60 guidelines, and according to the epidemiological cut-off value (ECV) when no CBP was mentioned", "token_count": 333, "char_count": 1541, "word_count": 224, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:03.036657", "source": { "split": "train_shard_00001", "doc_id": 1331 }, "chunk_id": "train_shard_00001_1331_0", "global_id": 7528 }, { "text": "The distribution of the species of the total 813 Candida isolates included in the study were as follows: Candida albicans (n= 312 ), Candida parapsilosis (n= 202), Candida tropicalis (n= 92), Candida glabrata (n= 71), Candida dubliniensis (n=28), Candida lusitaniae (n= 26), Candida kefyr (n= 22), Candida utilis (n= 17), Candida krusei (n= 14), Candida orthopsilosis (n= 7), Candida inconspicua (n= 7), Candida guilliermondii (n= 5), Candida metapsilosis (n= 4), Candida norvegensis (n= 4), Candida lambica (n= 1) and Candida lipolytica (n= 1). The evaluation of the results of the antifungal susceptibility tests according to the CBPs revealed that one C.albicans isolate and 60 C.parapsilosis (29.7%) isolates were resistant, and seven C.parapsilosis (3.5%) isolates were dose-dependent susceptible to fluconazole; 32 C.parapsilosis (15.8%) isolates were intermediately susceptible to voriconazole; one C.parapsilosis (0.5%) was resistant and one C.krusei (7.1%) was intermediately susceptible to anidulafungin; and one C.parapsilosis (0.5%) was resistant and one C.krusei (7.1%) isolate was intermediately susceptible to micafungin. In terms of ECVs, one C.lusitaniae isolate for fluconazole and one of each C.lusitaniae and C.kefyr isolates were evaluated as a non-wild type", "token_count": 465, "char_count": 1279, "word_count": 181, "semantic_coherence": 1, "information_density": 0.5028, "quality_score": 0.7514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:03.665378", "source": { "split": "train_shard_00001", "doc_id": 1331 }, "chunk_id": "train_shard_00001_1331_1", "global_id": 7529 }, { "text": "In the present study, 61 of 813 isolates were found to be resistant to fluconazole and seven were dose dependently susceptible, 32 were intermediately susceptible to voriconazole, one was resistant to anidulafungin, one was intermediately susceptible, and one was resistant to micafungin and one was intermediately susceptible to micafungin. In conclusion, the increased number of non- albicans Candida species and increased levels of resistance to antifungal drugs further establish the importance of early diagnosis at a species level alongside antifungal susceptibility tests.\n\n[One-Year Candida Data of the Central Mycology Laboratory: Which Sample, Which Species, How Resistant?]", "token_count": 172, "char_count": 684, "word_count": 96, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:04.113175", "source": { "split": "train_shard_00001", "doc_id": 1331 }, "chunk_id": "train_shard_00001_1331_2", "global_id": 7530 }, { "text": "Pangenome graphs provide a powerful way to present both sequence and structural features in a given genome relative to the typical features of a population. There are different methods of building pangenome graphs, but few tools are available to visualize them. To address this problem, we developed PanGraphViewer, which is written in Python 3 and runs on all major operating systems. The PanGraphViewer package contains two separate versions: a desktop-based application and a web-based application. Compared to other graph viewers that are initially designed to visualize individual genome graphs, PanGraphViewer targets pangenome graphs and allows the viewing of pangenome graphs built from multiple genomes in either the (reference) graphical fragment assembly format or the variant call format (VCF). Apart from visualization of different types of structural variations (SV), PanGraphViewer also integrates genome annotations with graph nodes to analyze insertions or deletions in a particular gene model. The graph node shapes in PanGraphViewer can represent different types of genomic variations when a VCF file is used. Notably, PanGraphViewer displays subgraphs from a chromosome or sequence segment based on any given coordinates. This function is absent from most genome graph viewers. PanGraphViewer is freely available at https://github.com/TF-Chan-Lab/panGraphViewer to facilitate pangenome analysis.\n\nPanGraphViewer: A Versatile Tool to Visualize Pangenome Graphs", "token_count": 314, "char_count": 1479, "word_count": 207, "semantic_coherence": 1, "information_density": 0.628, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:04.669493", "source": { "split": "train_shard_00001", "doc_id": 1332 }, "chunk_id": "train_shard_00001_1332_0", "global_id": 7531 }, { "text": "Sweet watermelon ( Citrullus lanatus subsp. vulgaris ) is among the most important vegetable crops in the world. Wild relatives are important resources for watermelon breeding. Here we report high-quality reference genomes of three wild watermelons, C. mucosospermus, C. amarus and C. colocynthis , and the divergence and genome evolution of different Citrullus species. Using genomic data from 547 watermelon accessions spanning four Citrullus species, we construct a super-pangenome to represent the Citrullus gene repertoire and provide a catalogue of orthologous relationships among species. Gene presence/absence variation analysis uncovers many disease resistance genes that are missing in cultivated watermelons, as well as genes with significantly different occurrence frequencies between populations that might underlie watermelon evolution and domestication. We revisit watermelon domestication using the recently identified wild progenitor, Kordofan melon, which provides insights into the domestication of fruit bitterness, sweetness and flesh coloration. The Citrullus super-pangenome provides a valuable resource for breeding and biological discovery, and our comparative genomic analyses shed additional light on watermelon evolution and domestication.\n\nACitrullusgenus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication", "token_count": 332, "char_count": 1429, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:05.240906", "source": { "split": "train_shard_00001", "doc_id": 1333 }, "chunk_id": "train_shard_00001_1333_0", "global_id": 7532 }, { "text": "

Background

Heterozygous variants in GBA1 are the commonest genetic risk factor for Parkinson's disease (PD), but penetrance is incomplete. GBA1 dysfunction can cause gastrointestinal disturbances and microbiome changes in preclinical models. Mounting evidence suggests that the microbiota-gut-brain axis is potentially implicated in PD pathogenesis. Whether the gut microbiome composition is influenced by host GBA1 genetics in heterozygosis has never been explored.

Objectives

This study aimed to evaluate whether heterozygosity for the GBA1 pathogenic L444P variant can cause perturbations in gut microbiome composition.

Methods

Faecal samples collected from GBA1 L444P/WT and GBA1 WT/WT mice at 3 and 6 months of age were analysed through shotgun metagenomic sequencing.

Results

No differences in α- and β-diversities were detected between genotyped groups, at either time point. Overall, we found a little variation in the gut microbiome composition and functional potential between GBA1 L444P/WT and GBA1 WT/WT mice over time.

Conclusion

Host GBA1 genotype does not impact gut microbiome structure and composition in the presented GBA1 L444P/WT mouse model. Studies investigating the effect of a second hit on gut physiology and microbiome composition could explain the partial penetrance of GBA1 variants in PD.", "token_count": 483, "char_count": 1499, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6536, "quality_score": 0.8268, "entities": { "genes": [ "GBA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:05.886237", "source": { "split": "train_shard_00001", "doc_id": 1334 }, "chunk_id": "train_shard_00001_1334_0", "global_id": 7533 }, { "text": "Exploring the relationship between <i>GBA1</i> host genotype and gut microbiome in the <i>GBA1</i> <sup>L444P/WT</sup> mouse model: implications for Parkinson's disease pathogenesis.", "token_count": 84, "char_count": 218, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [ "GBA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:06.300948", "source": { "split": "train_shard_00001", "doc_id": 1334 }, "chunk_id": "train_shard_00001_1334_1", "global_id": 7534 }, { "text": "Thermophilic organisms have evolved a proteome that resists thermal denaturation. While the evolution of their complete proteome would require multiple generations, early on, organisms would need to develop strategies to survive at high temperatures despite their thermolabile proteome. We hypothesized that the organisms would do this by reinforcing their proteostasis capacity. We tested this hypothesis using adaptive laboratory evolution of thermotolerance in Saccharomyces cerevisiae and found that the cells reproducibly evolved better proteostasis capacity in short-term evolution experiments. However, rather than improving the global proteostasis capacity, most of the evolved strains demonstrated enhanced capacity to tackle misfolding in the Endoplasmic Reticulum (ER), specifically by increasing their capacity for ER-associated degradation (ERAD). Given the strong selective advantage of these strains, we posit that protein folding in the ER may be exquisitely sensitive to chronic thermal stress and may act as an early indicator for adaptation to higher temperatures.\n\nLaboratory adaptive evolution of thermotolerance is linked to the evolution of a robust proteostasis in S. cerevisiae", "token_count": 251, "char_count": 1202, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6463, "quality_score": 0.8232, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:06.807370", "source": { "split": "train_shard_00001", "doc_id": 1335 }, "chunk_id": "train_shard_00001_1335_0", "global_id": 7535 }, { "text": "The foliar disease net form net blotch (NFNB), caused by the necrotrophic fungal pathogen Pyrenophora teres f. teres (Ptt), causes significant yield and quality losses of barley worldwide. Dominant resistance conferred by the Resistance to Pyrenophora teres 5 (Rpt5) gene from barley line CI5791 is the broadest and most effective resistance reported in this pathosystem. The Rpt5 locus was identified in multiple independent genetic studies utilizing diverse host populations and Ptt isolates, and harbors both dominant Rpt5 resistance and isolate-specific susceptibility genes/alleles that are dominant in the absence of Rpt5, designated susceptibility to Pyrenophora teres 1 (Spt1). Ptt virulence and avirulence effectors from diverse pathogen isolates genetically interact with the Rpt5/Spt1 locus, suggesting a complex locus with a function targeted by the evolution of a diversity of pathogen effectors. High-resolution mapping utilizing 1,920 recombinant gametes from a CI5791 x Tifang biparental population, identified 12 candidate genes in an ~4.6 Mb delimited region in the cv Morex V3 genome assembly, but is 1.1 − 2.2 Mb in the pangenome assemblies, containing 5−12 genes. Analysis revealed a strong correlation between the CI5791 allele of a receptor-like protein (RLP), provisionally designated Rpt5 candidate gene 1, (Rcg1), and broad Rpt5−mediated resistance. Two independent transformants of the CI5791 Rcg1 allele in the susceptible cv Golden Promise background showed significantly increased resistance when challenged with Rpt5 avirulent Ptt isolates 6A, 15A, and 0−1 compared to the Golden Promise wildtype. Thus, Rpt5, encodes an RLP and is the first net blotch resistance gene cloned in barley.\n\nRpt5 encodes a receptor-like protein that provides broad and effective net form net blotch (Pyrenophora teres f. teres) resistance in barley", "token_count": 507, "char_count": 1859, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5889, "quality_score": 0.7944, "entities": { "genes": [ "CI5791" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:07.514732", "source": { "split": "train_shard_00001", "doc_id": 1336 }, "chunk_id": "train_shard_00001_1336_0", "global_id": 7536 }, { "text": "The negative ecological impact of industrialization, which involves the use of petroleum products and dyes in the environment, has prompted research into effective, sustainable, and economically beneficial green technologies. For green remediation primarily based on active microbial metabolites, these microbes are typically from relevant sources. Active microbial metabolite production and genetic systems involved in xenobiotic degradation provide these microbes with the advantage of survival and proliferation in polluted ecological niches. In this study, we evaluated the ability of wheat root-associated L. fusiformis MGMM7 to degrade xenobiotic contaminants such as crude oil, phenol, and azo dyes. We sequenced the whole genome of MGMM7 and provided insights into the genomic structure of related strains isolated from contaminated sources. The results revealed that influenced by its isolation source, L. fusiformis MGMM7 demonstrated remediation and plant growth-promoting abilities in soil polluted with crude oil. Lysinibacillus fusiformis MGMM7 degraded up to 44.55 ± 5.47% crude oil and reduced its toxicity in contaminated soil experiments with garden cress (Lepidium sativum L.). Additionally, L. fusiformis MGMM7 demonstrated a significant ability to degrade Congo Red azo dye (200 mg/L), reducing its concentration by over 60% under both static and shaking cultivation conditions. However, the highest degradation efficiency was observed under shaking conditions. Genomic comparison among L. fusiformis strains revealed almost identical genomic profiles associated with xenobiotic assimilation. Genomic relatedness using Average Nucleotide Identity (ANI) and digital DNA-DNA hybridization (DDH) revealed that MGMM7 is distantly related to TZA38, Cu-15, and HJ.T1", "token_count": 470, "char_count": 1823, "word_count": 242, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [ "TZA38", "MGMM7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:08.194307", "source": { "split": "train_shard_00001", "doc_id": 1337 }, "chunk_id": "train_shard_00001_1337_0", "global_id": 7537 }, { "text": "Furthermore, subsystem distribution and pangenome analysis emphasized the distinctive features of MGMM7, including functional genes in its chromosome and plasmid, as well as the presence of unique genes involved in PAH assimilation, such as phnC/T/E, which is involved in phosphonate biodegradation, and nemA, which is involved in benzoate degradation and reductive degradation of N-ethylmaleimide. These findings highlight the potential properties of petroleum-degrading microorganisms isolated from non-contaminated rhizospheres and offer genomic insights into their functional diversity for xenobiotic remediation.\n\nGenomic Insights of Wheat Root-Associated Lysinibacillus fusiformis Reveal Its Related Functional Traits for Bioremediation of Soil Contaminated with Petroleum Products.", "token_count": 217, "char_count": 809, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "MGMM7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:08.657659", "source": { "split": "train_shard_00001", "doc_id": 1337 }, "chunk_id": "train_shard_00001_1337_1", "global_id": 7538 }, { "text": "

Background

Campylobacter is a genus of bacteria that has been isolated from the gastrointestinal tract of humans and animals, and the environments they inhabit around the world. Campylobacter adapt to new environments by changes in their gene content and expression, but little is known about how they adapt to long-term human colonization. In this study, the genomes of 31 isolates from a New Zealand patient and 22 isolates from a United Kingdom patient belonging to Campylobacter jejuni sequence type 45 (ST45) were compared with 209 ST45 genomes from other sources to identify the mechanisms by which Campylobacter adapts to long-term human colonization. In addition, the New Zealand patient had their microbiota investigated using 16S rRNA metabarcoding, and their level of inflammation and immunosuppression analyzed using biochemical tests, to determine how Campylobacter adapts to a changing gastrointestinal tract.

Results

There was some evidence that long-term colonization led to genome degradation, but more evidence that Campylobacter adapted through the accumulation of non-synonymous single nucleotide polymorphisms (SNPs) and frameshifts in genes involved in cell motility, signal transduction and the major outer membrane protein (MOMP). The New Zealand patient also displayed considerable variation in their microbiome, inflammation and immunosuppression over five months, and the Campylobacter collected from this patient could be divided into two subpopulations, the proportion of which correlated with the amount of gastrointestinal inflammation.

Conclusions

This study demonstrates how genomics, phylogenetics, 16S rRNA metabarcoding and biochemical markers can provide insight into how Campylobacter adapts to changing environments within human hosts. This study also demonstrates that long-term human colonization selects for changes in Campylobacter genes involved in cell motility, signal transduction and the MOMP; and that genetically distinct subpopulations of Campylobacter evolve to adapt to the changing gastrointestinal environment.", "token_count": 501, "char_count": 2087, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5374, "quality_score": 0.7687, "entities": { "genes": [ "ST45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:09.312802", "source": { "split": "train_shard_00001", "doc_id": 1338 }, "chunk_id": "train_shard_00001_1338_0", "global_id": 7539 }, { "text": "Genomic adaptations of Campylobacter jejuni to long-term human colonization.", "token_count": 19, "char_count": 76, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:09.660689", "source": { "split": "train_shard_00001", "doc_id": 1338 }, "chunk_id": "train_shard_00001_1338_1", "global_id": 7540 }, { "text": "Beneath the seafloor, microbial life subsists in isolation from the surface world under persistent energy limitation. The nature and extent of genomic evolution in subseafloor microbes have been unknown. Here, we show that the genomes of Thalassospira bacterial populations cultured from million-year-old subseafloor sediments evolve in clonal populations by point mutation, with a relatively low rate of homologous recombination and elevated numbers of pseudogenes. Ratios of nonsynonymous to synonymous substitutions correlate with the accumulation of pseudogenes, consistent with a role for genetic drift in the subseafloor strains but not in type strains of Thalassospira isolated from the surface world. Consistent with this, pangenome analysis reveals that the subseafloor bacterial genomes have a significantly lower number of singleton genes than the type strains, indicating a reduction in recent gene acquisitions. Numerous insertion-deletion events and pseudogenes were present in a flagellar operon of the subseafloor bacteria, indicating that motility is nonessential in these million-year-old subseafloor sediments. This genomic evolution in subseafloor clonal populations coincided with a phenotypic difference: all subseafloor isolates have a lower rate of growth under laboratory conditions than the Thalassospira xiamenensis type strain. Our findings demonstrate that the long-term physical isolation of Thalassospira, in the absence of recombination, has resulted in clonal populations whereby reduced access to novel genetic material from neighbors has resulted in the fixation of new mutations that accumulate in genomes over millions of years. IMPORTANCE The nature and extent of genomic evolution in subseafloor microbial populations subsisting for millions of years below the seafloor are unknown. Subseafloor populations have ultralow metabolic rates that are hypothesized to restrict reproduction and, consequently, the spread of new traits", "token_count": 461, "char_count": 1994, "word_count": 270, "semantic_coherence": 1, "information_density": 0.563, "quality_score": 0.7815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:10.304976", "source": { "split": "train_shard_00001", "doc_id": 1339 }, "chunk_id": "train_shard_00001_1339_0", "global_id": 7541 }, { "text": "Our findings demonstrate that genomes of cultivated bacterial strains from the genus Thalassospira isolated from million-year-old abyssal sediment exhibit greatly reduced levels of homologous recombination, elevated numbers of pseudogenes, and genome-wide evidence of relaxed purifying selection. These substitutions and pseudogenes are fixed into the population, suggesting that the genome evolution of these bacteria has been dominated by genetic drift. Thus, reduced recombination, stemming from long-term physical isolation, resulted in small clonal populations of Thalassospira that have accumulated mutations in their genomes over millions of years.\n\nGenome Evolution in Bacteria Isolated from Million-Year-Old Subseafloor Sediment.", "token_count": 178, "char_count": 752, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7234, "quality_score": 0.8617, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:10.741864", "source": { "split": "train_shard_00001", "doc_id": 1339 }, "chunk_id": "train_shard_00001_1339_1", "global_id": 7542 }, { "text": "

Background

A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, bioinformatics analysis tools for graph format genomes are lacking.

Results

To overcome this problem, we develop a novel strategy for pangenome construction and a downstream pangenome analysis pipeline (PSVCP) that captures genetic variants' position information while maintaining a linearized layout. Using PSVCP, we construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome as the reference. We show that PSVCP successfully identifies causal structural variations for rice grain weight and plant height. Our results provide insights into rice population structure and genomic diversity. We characterize a new locus (qPH8-1) associated with plant height on chromosome 8 undetected by the SNP-based genome-wide association study (GWAS).

Conclusions

Our results demonstrate that the pangenome constructed by our pipeline combined with a presence and absence variation-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and the associated genome sequence and genetic variants data provide valuable genomic resources for rice genomics research and improvement in future.\n\nA pangenome analysis pipeline provides insights into functional gene identification in rice.", "token_count": 364, "char_count": 1725, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6052, "quality_score": 0.8026, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:11.322449", "source": { "split": "train_shard_00001", "doc_id": 1340 }, "chunk_id": "train_shard_00001_1340_0", "global_id": 7543 }, { "text": "The production of ethanol and beta‐galactosidase by Kluyveromyces marxianus and Saccharomyces fragilis strains grown in cheese whey was evaluated. The conditions for fermentation in 50 g/L (3.3% lactose) and 150 g/L (8.8% lactose) cheese whey were 100 rpm for 24 h at 30, 35 and 40 °C. Saccharomyces fragilis IZ 275 in 8.8% lactose at 40 °C resulted in 3.90% ethanol. Kluyveromyces marxianus CCT 3172 showed higher beta‐galactosidase, 1.10 U/mg, at 30 °C. Therefore, the choice of cultivation conditions and the most suitable species is important for obtaining high yields of the products of interest.\n\nComparison of bioethanol and beta‐galactosidase production by Kluyveromyces and Saccharomyces strains grown in cheese whey", "token_count": 259, "char_count": 725, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:11.863996", "source": { "split": "train_shard_00001", "doc_id": 1341 }, "chunk_id": "train_shard_00001_1341_0", "global_id": 7544 }, { "text": "Newly isolated yeasts from different Tunisian microhabitats, such as soil, milk, olive brine, vinegar, and from olive mill wastewater-contaminated biotopes were extensively studied for their biochemical arsenal and morphological features, i.e. cell, ascospore, and lipid body morphology. All strains were classified into the Ascomycota phylum. However, they showed great functional diversity, including different morphological and biochemical features, lipid production ability, and fatty acid profiles. Accordingly, the strains were placed in three different groups: Group I, which includes Candida species; Group II (Pichia and related); and Group III (Kluyveromyces marxianus strain CC1). Group I and II were characterized by a high percentage of oleic acid (41.6-65.3% of total lipids) while in Group III, linoleic acid was the major fatty acid (37.2%). Members of Group I and II were further grouped into subgroups according to their fatty acid composition. Among the newly isolated strains, Pichia etchellsii BM1 was able to accumulate around 25% wt/wt lipid per dry cell mass and thus characterized as oleaginous. Some other strains, such as Candida metapsilosis strain EL2, C. parapsilosis strain LV2, C. pararugosa strain BM24, and K. marxianus strain CC1, which are able to produce extracellular lipases, may be of interest for specific environmental applications and/or for the production of novel lipases.\n\nNewly isolated yeasts from Tunisian microhabitats: Lipid accumulation and fatty acid composition.", "token_count": 446, "char_count": 1572, "word_count": 218, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [ "LV2", "BM1", "EL2", "CC1", "BM24" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:12.502194", "source": { "split": "train_shard_00001", "doc_id": 1342 }, "chunk_id": "train_shard_00001_1342_0", "global_id": 7545 }, { "text": "The human genome contains numerous structurally-variable polymorphic loci, including several hundred disease-associated genes, almost inaccessible for accurate variant calling. Here we present Locityper, a tool capable of genotyping such challenging genes using short and long-read whole genome sequencing. For each target, Locityper recruits and aligns reads to locus haplotypes, for instance extracted from a pangenome, and finds the likeliest haplotype pair by optimizing read alignment, insert size and read depth profiles. Locityper accurately genotypes up to 194 of 256 challenging medically relevant loci (95% haplotypes at QV33), an 8.8-fold gain compared to 22 genes achieved with standard variant calling pipelines. Furthermore, Locityper provides access to hyperpolymorphic HLA genes and other gene families, including KIR, MUC and FCGR. With its low running time of 1h10m per sample at 8 threads, Locityper is scalable to biobank-sized cohorts, enabling association studies for previously intractable disease-relevant genes.\n\nLocityper: targeted genotyping of complex polymorphic genes", "token_count": 278, "char_count": 1097, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7867, "quality_score": 0.8933, "entities": { "genes": [ "QV33" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:13.055765", "source": { "split": "train_shard_00001", "doc_id": 1343 }, "chunk_id": "train_shard_00001_1343_0", "global_id": 7546 }, { "text": "The development of technologies for cellulosic ethanol production by simultaneous saccharification and fermentation (SSF) depends on the use of microorganisms with high fermentative rates and thermotolerance. In this study, the ability of five Kluyveromyces marxianus strains to produce ethanol from glucose at 45 °C was investigated. The highest fermentative parameters were observed with K. marxianus NRRL Y-6860, which was then further studied. An initial evaluation of the oxygen supply on ethanol production by the selected yeast and a comparison of SSF process from acid pretreated rice straw between K. marxianus NRRL Y-6860 and Saccharomyces cerevisiae at 30 and 45 °C were carried out. Under the lowest evaluated conditions of aeration and agitation, K. marxianus NRRL Y-6860 produced 21.5 g/L ethanol from 51.3 g/L glucose corresponding to YP/S of 0.44 g/g and QP of 3.63 g/L h. In the SSF experiments, K. marxianus NRRL Y-6860 was more efficient than S. cerevisiae at both evaluated temperatures (30 and 45 °C), attained at the highest temperature an ethanol yield of 0.24 g/g and productivity of 1.44 g/L h.\n\nSelection of a thermotolerant Kluyveromyces marxianus strain with potential application for cellulosic ethanol production by simultaneous saccharification and fermentation.", "token_count": 383, "char_count": 1293, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5722, "quality_score": 0.7861, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:13.641166", "source": { "split": "train_shard_00001", "doc_id": 1344 }, "chunk_id": "train_shard_00001_1344_0", "global_id": 7547 }, { "text": "Commentary: Probing Genomic Aspects of the Multi-Host Pathogen Clostridium perfringens Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.", "token_count": 56, "char_count": 176, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:14.004734", "source": { "split": "train_shard_00001", "doc_id": 1345 }, "chunk_id": "train_shard_00001_1345_0", "global_id": 7548 }, { "text": "As a group, the genus Dehalococcoides dehalogenates a wide range of organohalide pollutants, but the range of organohalide compounds that can be utilized for reductive dehalogenation differs among Dehalococcoides strains. Dehalococcoides lineages cannot be reliably disambiguated in mixed communities using typical phylogenetic markers, which often confounds bioremediation efforts. Here, we describe a computational approach to identify Dehalococcoides genetic markers with improved discriminatory resolution. Screening core genes from the Dehalococcoides pangenome for degree of similarity and frequency of 100% identity found a candidate genetic marker encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function. This gene exhibits the fewest completely identical amino acid sequences and has among the lowest average amino acid sequence identity in the core pangenome. Primers targeting BNR could effectively discriminate between 40 available BNR sequences (in silico) and 10 different Dehalococcoides isolates (in vitro). Amplicon sequencing of BNR fragments generated from 22 subsurface soil samples revealed a total of 109 amplicon sequence variants, suggesting a high diversity of Dehalococcoides distributed in the environment. Therefore, the BNR gene can serve as an alternative genetic marker to differentiate strains of Dehalococcoides in complicated microbial communities. IMPORTANCE The challenge of discriminating between phylogenetically similar but functionally distinct bacterial lineages is particularly relevant to the development of technologies seeking to exploit the metabolic or physiological characteristics of specific members of bacterial genera. A computational approach was developed to expedite screening of potential genetic markers among phylogenetically affiliated bacteria", "token_count": 494, "char_count": 1932, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6639, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:14.660445", "source": { "split": "train_shard_00001", "doc_id": 1346 }, "chunk_id": "train_shard_00001_1346_0", "global_id": 7549 }, { "text": "Using this approach, a gene encoding a bacterial neuraminidase repeat (BNR)-containing protein of unknown function was selected and evaluated as a genetic marker to differentiate strains of Dehalococcoides, an environmentally relevant genus of bacteria whose members can transform and detoxify a range of halogenated organic solvents and persistent organic pollutants, in complex microbial communities to demonstrate the validity of the approach. Moreover, many apparently phylogenetically distinct, currently uncharacterized Dehalococcoides were detected in environmental samples derived from contaminated sites.\n\nDifferentiating Closely Affiliated Dehalococcoides Lineages by a Novel Genetic Marker Identified via Computational Pangenome Analysis.", "token_count": 182, "char_count": 770, "word_count": 93, "semantic_coherence": 1, "information_density": 0.8172, "quality_score": 0.9086, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:15.100565", "source": { "split": "train_shard_00001", "doc_id": 1346 }, "chunk_id": "train_shard_00001_1346_1", "global_id": 7550 }, { "text": "

Background

The fungal community of the gastrointestinal tract has recently become of interest, and knowledge of its relationship with the development of obesity is scarce. The present study aimed to evaluate the cultivable fungal fraction from the microbiota and to analyze its relationship with obesity.

Methods

Samples were taken from 99 participants with normal weight, overweight and obesity (n = 31, 34 and 34, respectively) and were cultivated in selective medium, and the cultivable yeasts were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Anthropometric and biochemical measures were also evaluated.

Results

Eutrophic, overweight and obese groups presented concentrations of 1.6, 2.16 and 2.19 log10  colony-forming units g-1 yeast, respectively. Ascomycota and Basidiomycota were the two identified phyla. At the genus level, Candida spp. showed a relatively high prevalence, and 10 different species were detected: Candida glabrata, Candida orthopsilosis, Candida lambica, Candida kefyr, Candida albicans, Candida krusei, Candida valida, Candida parapsilosis, Candida utilis and Candida humilis (with relative abundances of 71.72%, 5.05%, 21.21%, 6.06%, 29.29%, 27.27%, 8.08%, 16.16%, 1.01% and 2.02%, respectively).

Conclusions

The obese group presented a higher prevalence of Candida albicans. Furthermore, Candida albicans, Candida kefyr and Rhodotorula mucilaginosa showed a high positive correlation with obesity, weight gain and fat mass and showed a negative correlation with high-density lipoprotein and lean mass, parameters related to weight loss.", "token_count": 510, "char_count": 1665, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:15.730620", "source": { "split": "train_shard_00001", "doc_id": 1347 }, "chunk_id": "train_shard_00001_1347_0", "global_id": 7551 }, { "text": "The intestinal mycobiota and its relationship with overweight, obesity and nutritional aspects.", "token_count": 24, "char_count": 95, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:16.091572", "source": { "split": "train_shard_00001", "doc_id": 1347 }, "chunk_id": "train_shard_00001_1347_1", "global_id": 7552 }, { "text": "Although microorganisms are known to dominate Earth's biospheres and drive biogeochemical cycling, little is known about the geographic distributions of microbial populations or the environmental factors that pattern those distributions. We used a global-level hierarchical sampling scheme to comprehensively characterize the evolutionary relationships and distributional limitations of the nitrogen-fixing bacterial symbionts of the crop chickpea, generating 1,027 draft whole-genome sequences at the level of bacterial populations, including 14 high-quality PacBio genomes from a phylogenetically representative subset. We find that diverse Mesorhizobium taxa perform symbiosis with chickpea and have largely overlapping global distributions. However, sampled locations cluster based on the phylogenetic diversity of Mesorhizobium populations, and diversity clusters correspond to edaphic and environmental factors, primarily soil type and latitude. Despite long-standing evolutionary divergence and geographic isolation, the diverse taxa observed to nodulate chickpea share a set of integrative conjugative elements (ICEs) that encode the major functions of the symbiosis. This symbiosis ICE takes 2 forms in the bacterial chromosome-tripartite and monopartite-with tripartite ICEs confined to a broadly distributed superspecies clade. The pairwise evolutionary relatedness of these elements is controlled as much by geographic distance as by the evolutionary relatedness of the background genome. In contrast, diversity in the broader gene content of Mesorhizobium genomes follows a tight linear relationship with core genome phylogenetic distance, with little detectable effect of geography. These results illustrate how geography and demography can operate differentially on the evolution of bacterial genomes and offer useful insights for the development of improved technologies for sustainable agriculture.\n\nGlobal-level population genomics reveals differential effects of geography and phylogeny on horizontal gene transfer in soil bacteria.", "token_count": 464, "char_count": 2072, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:16.734132", "source": { "split": "train_shard_00001", "doc_id": 1348 }, "chunk_id": "train_shard_00001_1348_0", "global_id": 7553 }, { "text": "Purpose. The prevalence of multidrug-resistant (MDR) Shigella sonnei is increasing globally, raising concerns for public health. In 2022, an outbreak of MDR S. sonnei was observed in Tunisia. We aimed to evaluate the genetic profile of S. sonnei isolates during the outbreak, including their clonal relationship, antimicrobial determinants and connection to international strains.Methods. In this study, we sequenced the whole genome of 24 S. sonnei strains collected from South Tunisia between July 2022 and November 2023. Bioinformatic analysis was conducted to confirm species identification, assign sequence types, determine core genome sequence types, analyse phylogenetic relationships and identify antimicrobial resistance determinants. Phylodynamic and phylogeographic analyses were performed to trace the spatiotemporal spread of the outbreak genotype.Results. Our investigation revealed that 23 out of 24 isolates were grouped into the HC10-20662 genotype within the 3.6.3 subclade. All isolates carried the blaCTX-M-15 gene associated with extended-spectrum beta-lactamase production, as well as the dfrA1 and qnrS1 genes, along with the D87G mutation in gyrA. Additionally, the sul2, tet(A) and mph(A) resistance genes were present in most isolates (96%, 96 and 83, respectively). Phylogeographic analysis suggested that the outbreak genotype likely spread in Europe before being introduced into Tunisia.Conclusion. To the best of our knowledge, this is the first MDR S. sonnei outbreak in the country. The HC10-20662 genotype appears to be responsible for a multi-country outbreak, affecting both Tunisia and Europe", "token_count": 520, "char_count": 1733, "word_count": 227, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [ "HC10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:09:17.391194", "source": { "split": "train_shard_00001", "doc_id": 1349 }, "chunk_id": "train_shard_00001_1349_0", "global_id": 7554 }, { "text": "Continued genomic surveillance efforts, both nationally and internationally, are essential for monitoring the dynamic evolution and global spread of MDR S. sonnei.\n\nMolecular epidemiology of a multidrug-resistant <i>Shigella sonnei</i> outbreak in Tunisia (2022-2023) using whole-genome sequencing.", "token_count": 98, "char_count": 317, "word_count": 36, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:17.773292", "source": { "split": "train_shard_00001", "doc_id": 1349 }, "chunk_id": "train_shard_00001_1349_1", "global_id": 7555 }, { "text": "

Background

Ethanol production from non-crop materials, such as Jerusalem artichokes, would make a great contribution to the energy industry. The non-conventional yeast, Kluyveromyces marxianus, is able to carry out ethanol fermentation of sugar molecules obtained from inulin-containing materials by consolidated bioprocessing. Lower inulin concentrations and micro-aeration can lead to a relatively fast and ideal fermentation process; however, it is unclear what causes the inhibition of higher concentrations of inulin and the promotion effect of aeration.

Results

Next-generation sequencing technology was used to study the global transcriptional response of K. marxianus Y179 under three fermentation conditions, including 120 g/L inulin without aeration (120-N), 230 g/L inulin without aeration (230-N), 230 g/L inulin with aeration by ORP controlling at -130 mV (230-130mV). A total of 35.55 million clean reads were generated from three samples, of which 4,820 predicted that open reading frames were annotated. For differential expression analysis, 950 and 1,452 differentially expressed genes were discovered under the conditions of 230-130mV and 120-N, respectively, and the sample 230-N was used as the control. These genes are mainly associated with the pathways of central carbon metabolism and ethanol formation. Increased expression of inulinase and the low activity of the autophagy-related gene, ATG8, ensured fast and ideal fermentation processes.

Conclusions

Despite being reported as the \"crabtree-negative\" species, K. marxianus Y179 could achieve favorable ethanol fermentation profiles under micro-aeration and high inulin concentrations. K. marxianus Y179 cells responded to inulin concentrations and micro-aeration that is involved in the whole ethanol metabolism network", "token_count": 505, "char_count": 1819, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "ATG8" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:18.503582", "source": { "split": "train_shard_00001", "doc_id": 1350 }, "chunk_id": "train_shard_00001_1350_0", "global_id": 7556 }, { "text": "These results will serve as an important foundation for further exploration of the regulatory mechanisms involved in ethanol fermentation from inulin by consolidated bioprocessing and also provide a valuable reference for future studies on optimization and reconstruction of the metabolism network in K. marxianus.\n\nTranscriptional analysis of Kluyveromyces marxianus for ethanol production from inulin using consolidated bioprocessing technology.", "token_count": 95, "char_count": 447, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7931, "quality_score": 0.8966, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:18.899898", "source": { "split": "train_shard_00001", "doc_id": 1350 }, "chunk_id": "train_shard_00001_1350_1", "global_id": 7557 }, { "text": "Streptococcus suis is an emerging zoonotic pathogen. Over 100 putative virulence factors have been described, but it is unclear to what extent these virulence factors could contribute to zoonotic potential of S. suis. We identified all S. suis virulence factors studied in experimental models of human origin in a systematic review and assessed their contribution to zoonotic potential in a subsequent genomic meta-analysis. PubMed and Scopus were searched for English-language articles that studied S. suis virulence published until 31 March 2021. Articles that analyzed a virulence factor by knockout mutation, purified protein, and/or recombinant protein in a model of human origin, were included. Data on virulence factor, strain characteristics, used human models and experimental outcomes were extracted. All publicly available S. suis genomes with available metadata on host, disease status and country of origin, were included in a genomic meta-analysis. We calculated the ratio of the prevalence of each virulence factor in human and pig isolates. We included 130 articles and 1703 S. suis genomes in the analysis. We identified 53 putative virulence factors that were encoded by genes which are part of the S. suis core genome and 26 factors that were at least twice as prevalent in human isolates as in pig isolates. Hhly3 and NisK/R were particularly enriched in human isolates, after stratification by genetic lineage and country of isolation. This systematic review and genomic meta-analysis have identified virulence factors that are likely to contribute to the zoonotic potential of S. suis.\n\nIdentification of Streptococcus suis putative zoonotic virulence factors: A systematic review and genomic meta-analysis.", "token_count": 465, "char_count": 1792, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5058, "quality_score": 0.7529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:20.010503", "source": { "split": "train_shard_00001", "doc_id": 1351 }, "chunk_id": "train_shard_00001_1351_0", "global_id": 7558 }, { "text": "Salmonella enterica subsp. enterica (S.) serovar Cerro is rarely isolated from human clinical cases of salmonellosis but represents the most common serovar isolated from cattle without clinical signs of illness in the United States. In this study, using a large, diverse set of 316 isolates, we utilized genomic methods to further elucidate the evolutionary history of S. Cerro and to identify genomic features associated with its apparent virulence attenuation in humans. Phylogenetic analyses showed that within this polyphyletic serovar, 98.4% of isolates (311/316) represent a monophyletic clade within section Typhi and the remaining 1.6% of isolates (5/316) form a monophyletic clade within subspecies enterica Clade A1. Of the section Typhi S. Cerro isolates, 93.2% of isolates (290/311) clustered into a large clonal clade comprised of predominantly sequence type (ST) 367 cattle and environmental isolates, while the remaining 6.8% of isolates (21/311), primarily from human clinical sources, clustered outside of this clonal clade. A tip-dated phylogeny of S. Cerro ST367 identified two major clades (I and II), one of which overwhelmingly consisted of cattle isolates that share a most recent common ancestor that existed circa 1975. Gene presence/absence and rarefaction curve analyses suggested that the pangenome of section Typhi S. Cerro is open, potentially reflecting the gain/loss of prophage; human isolates contained the most open pangenome, while cattle isolates had the least open pangenome", "token_count": 458, "char_count": 1575, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5964, "quality_score": 0.7982, "entities": { "genes": [ "ST367" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:20.657479", "source": { "split": "train_shard_00001", "doc_id": 1352 }, "chunk_id": "train_shard_00001_1352_0", "global_id": 7559 }, { "text": "Hypothetically disrupted coding sequences (HDCs) displayed clade-specific losses of intact speC and sopA virulence genes within the large clonal S. Cerro clade, while loss of intact vgrG, araH, and vapC occurred in all section Typhi S. Cerro isolates. Further phenotypic analysis suggested that the presence of a premature stop codon in speC does not abolish ornithine decarboxylase activity in S. Cerro, likely due to the activity of the second ornithine decarboxylase encoded by speF, which remained intact in all isolates. Overall, our study identifies specific genomic features associated with S. Cerro's infrequent isolation from humans and its apparent adaptation to cattle, which has broader implications for informing our understanding of the evolutionary events facilitating host adaptation in Salmonella.\n\nSalmonella enterica serovar Cerro displays a phylogenetic structure and genomic features consistent with virulence attenuation and adaptation to cattle.", "token_count": 303, "char_count": 1059, "word_count": 137, "semantic_coherence": 1, "information_density": 0.708, "quality_score": 0.854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:21.224117", "source": { "split": "train_shard_00001", "doc_id": 1352 }, "chunk_id": "train_shard_00001_1352_1", "global_id": 7560 }, { "text": "

Purpose

Polygala tenuifolia Willd. (PT), a traditional Chinese medicinal plant extensively employed in managing Alzheimer's disease, exhibits notable gastrointestinal side effects as highlighted by prior investigations. In contrast, Magnolia officinalis Rehd. et Wils (MO), a traditional remedy for gastrointestinal ailments, shows promising potential for ameliorating this adverse effect of PT. The objective of this study is to examine the underlying mechanism of MO in alleviating the side effects of PT.

Methods

Hematoxylin-eosin (H&E) staining was used to observe the structural damage of zebrafish intestine, and enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of inflammatory factors and oxidative stress. The integrity of the intestinal tight junctions was examined using transmission electron microscope (TEM). Moreover, the expression of intestinal barrier genes and PI3K/AKT/NF-κB signaling pathway-related genes was determined through quantitative real-time PCR. The changes in intestinal microbial composition were analyzed using 16S rRNA and metagenomic techniques.

Results

MO effectively ameliorated intestinal pathological damage and barrier gene expression, and significantly alleviated intestinal injury by reducing the expression of inflammatory cytokines IL-1β, IL-6, TNF-α, and inhibiting the activation of PI3K/AKT/NF-κB pathway", "token_count": 383, "char_count": 1410, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6971, "quality_score": 0.8486, "entities": { "genes": [ "PI3K" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:21.814534", "source": { "split": "train_shard_00001", "doc_id": 1353 }, "chunk_id": "train_shard_00001_1353_0", "global_id": 7561 }, { "text": "Furthermore, MO could significantly increase the relative abundance of beneficial microorganisms (Lactobacillus, Blautia and Saccharomyces cerevisiae), and reduce the relative abundance of pathogenic bacteria (Plesiomonas and Aeromonas).

Conclusion

MO alleviated PT-induced intestinal injury, and its mechanism may be related to the inhibition of PI3K/AKT/NF-κB pathway activation and regulation of intestinal flora.\n\nMagnolia Officinalis Alcohol Extract Alleviates the Intestinal Injury Induced by Polygala Tenuifolia Through Regulating the PI3K/AKT/NF-κB Signaling Pathway and Intestinal Flora.", "token_count": 199, "char_count": 631, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "PI3K" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:22.258463", "source": { "split": "train_shard_00001", "doc_id": 1353 }, "chunk_id": "train_shard_00001_1353_1", "global_id": 7562 }, { "text": "Primary sludge from a Portuguese pulp and paper mill, containing 60% of carbohydrates, and unbleached pulp (as reference material), with 93% of carbohydrates, were used to produce ethanol by simultaneous saccharification and fermentation (SSF). SSF was performed in batch or fed-batch conditions without the need of a pretreatment. Cellic® CTec2 was the cellulolytic enzymatic complex used and Saccharomyces cerevisiae (baker's yeast or ATCC 26602 strain) or the thermotolerant yeast Kluyveromyces marxianus NCYC 1426 were employed. Primary sludge was successfully converted to ethanol and the best results in SSF efficiency were obtained with S. cerevisiae. An ethanol concentration of 22.7 g L-1 was produced using a content of 50 g L-1 of carbohydrates from primary sludge, in batch conditions, with a global conversion yield of 81% and a production rate of 0.94 g L-1 h-1. Fed-batch operation enabled higher solids content (total carbohydrate concentration of 200 g L-1, equivalent to a consistency of 33%) and a reduction of three-quarters of cellulolytic enzyme load, leading to an ethanol concentration of 40.7 g L-1, although with lower yield and productivity. Xylitol with a concentration up to 7 g L-1 was also identified as by-product in the primary sludge bioconversion process.\n\nBatch and fed-batch simultaneous saccharification and fermentation of primary sludge from pulp and paper mills.", "token_count": 482, "char_count": 1491, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5519, "quality_score": 0.7759, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:22.906338", "source": { "split": "train_shard_00001", "doc_id": 1354 }, "chunk_id": "train_shard_00001_1354_0", "global_id": 7563 }, { "text": "

Background

The genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. However, the evolutionary factors that define the specific shape of this distribution are not thoroughly understood.

Results

We investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genome intersections for 33 groups of closely related bacterial genomes. A model with an infinite external gene pool available for gene acquisition and constant genome size (IGP-CGS model), and two gene turnover rates, one for slow- and the other one for fast-evolving genes, allows two approaches to estimate the parameters for gene content dynamics. One is by fitting the model prediction to the distribution of the number of genes shared by precisely k genomes (gene commonality distribution) and another by analyzing the distribution of the number of genes common for k genome sets (k-cores). Both approaches produce a comparable overall quality of fit, although the former significantly overestimates the number of the universally conserved genes, while the latter overestimates the number of singletons. We further explore the effect of dropping each of the assumptions of the IGP-CGS model on the fit to the gene commonality distributions and show that models with either a finite gene pool or unequal rates of gene loss and gain (greater gene loss rate) eliminate the overestimate of the number of singletons or the core genome size.

Conclusions

We examine the assumptions that are usually adopted for modeling the evolution of the U-shaped gene commonality distributions in prokaryote genomes, namely, those of infinitely many genes and constant genome size. The combined analysis of genome intersections and gene commonality suggests that at least one of these assumptions is invalid. The violation of both these assumptions reflects the limited ability of prokaryotes to gain new genes. This limitation seems to stem, at least partly, from the horizontal gene transfer barrier, i.e., the cost of accommodation of foreign genes by prokaryotes. Further development of models taking into account the complexity of microbial evolution is necessary for an improved understanding of the evolution of prokaryotes.", "token_count": 516, "char_count": 2445, "word_count": 364, "semantic_coherence": 1, "information_density": 0.5027, "quality_score": 0.7514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:09:23.567152", "source": { "split": "train_shard_00001", "doc_id": 1355 }, "chunk_id": "train_shard_00001_1355_0", "global_id": 7564 }, { "text": "Assessment of assumptions underlying models of prokaryotic pangenome evolution.", "token_count": 16, "char_count": 79, "word_count": 9, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:23.922345", "source": { "split": "train_shard_00001", "doc_id": 1355 }, "chunk_id": "train_shard_00001_1355_1", "global_id": 7565 }, { "text": "Introduction. The global spread of extended-spectrum cephalosporinase-producing Escherichia coli (producing extended-spectrum β-lactamase or plasmid-borne AmpC, hereafter ESC-Ec) is a major public health concern. Whilst extensively studied in high-income countries, the transmission pathways between humans and animals in low- and middle-income countries (LMICs) remain unclear. In rural Cambodia, the asymptomatic carriage and transmission dynamics of ESC-Ec between humans and animals living in close proximity are poorly understood, highlighting the need for targeted research in this area.Gap statement. An enhanced understanding of the genetic epidemiology of ESC-Ec can enable mitigation strategies to reduce the burden of disease and drug-resistant infections in LMIC settings.Aim. This study aimed to investigate the genetic relatedness and genotypic antibiotic resistance profiles of ESC-Ec strains from humans and livestock in rural Cambodia and to identify patterns of antimicrobial resistance (AMR) gene transmission between hosts and across households and villages.Methodology. Faecal samples were collected from 307 humans and 285 livestock in 100 households in or near Kampong Cham Province in rural Cambodia. From these samples, 108 ESC-Ec strains were subjected to whole-genome sequencing. Core genome MLST (cgMLST) and phylogenetic analysis determined genetic relationships between strains. All strains were screened for the presence of antibiotic resistance genes and plasmids.Results. Human and livestock isolates were assigned to six phylogroups, with phylogroup A being the most common (56.5%). MLST identified 50 sequence types (STs), 17 of which were shared between humans and animals, with ST155 being the most prevalent. cgMLST revealed 97 distinct cgMLST sequence types (cgST), indicating strain sharing between humans and animals", "token_count": 497, "char_count": 1906, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8175, "entities": { "genes": [ "ST155" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:24.575885", "source": { "split": "train_shard_00001", "doc_id": 1356 }, "chunk_id": "train_shard_00001_1356_0", "global_id": 7566 }, { "text": "Additionally, AMR gene analysis showed widespread resistance, with genes from the bla CTX-M group detected in 84.2% of isolates. Notably, AMR genes such as aph(3'')-Ib-sul2 co-occurred in 50% of isolates. Finally, plasmid analysis identified IncF plasmids in 75.9% of isolates, likely facilitating AMR gene transmission across hosts.Conclusions. Our findings demonstrate that ESC-Ec strains and their AMR genes are transmitted between humans and livestock in rural Cambodia, likely driven by both clonal spread and plasmid-mediated horizontal gene transfer. These results highlight the urgent need for antimicrobial stewardship and infection control strategies to mitigate the spread of multidrug-resistant pathogens in both human and animal populations.\n\nGenomic insights into extended-spectrum <i>β</i>-lactamase- and plasmid-borne AmpC-producing <i>Escherichia coli</i> transmission between humans and livestock in rural Cambodia.", "token_count": 292, "char_count": 989, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:25.126738", "source": { "split": "train_shard_00001", "doc_id": 1356 }, "chunk_id": "train_shard_00001_1356_1", "global_id": 7567 }, { "text": "A long-standing question is to what degree genetic drift and selection drive the divergence in rare accessory gene content between closely related bacteria. Rare genes, including singletons, make up a large proportion of pangenomes (the set of all genes in a set of genomes), but it remains unclear how many such genes are adaptive, deleterious, or neutral to their host genome. Estimates of species’ effective population sizes (N e ) are positively associated with pangenome size and fluidity, which has independently been interpreted as evidence for both neutral and adaptive pangenome models. We hypothesised that pseudogenes, used as a neutral reference, could be used to distinguish these models. We find that most functional categories are depleted for rare pseudogenes when a genome encodes only a single intact copy of a gene family. In contrast, transposons are enriched in pseudogenes, suggesting they are mostly neutral or deleterious to the host genome. Thus, even if individual rare accessory genes vary in their effects on host fitness, we can confidently reject a model of entirely neutral or deleterious rare genes. We also define the ratio of singleton intact genes to singleton pseudogenes (s i /s p ) within a pangenome, compare this measure across 668 prokaryotic species, and detect a signal consistent with the adaptive value of many rare accessory genes. Taken together, our work demonstrates that comparing to pseudogenes can improve inferences of the evolutionary forces driving pangenome variation.\n\nPseudogenes as a neutral reference for detecting selection in prokaryotic pangenomes", "token_count": 358, "char_count": 1610, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6331, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:25.707484", "source": { "split": "train_shard_00001", "doc_id": 1357 }, "chunk_id": "train_shard_00001_1357_0", "global_id": 7568 }, { "text": "Abstract

Pseudomonas aeruginosa is a bacterium with increasing relevance in clinical settings and among the most common bacteria occupying the cystic fibrosis (CF) lung niche. Its ability to colonize and persist in diverse niches is attributed to this bacterium’s large accessory genome. In P. aeruginosa, prophages represent a common feature of a strain’s accessory genome. Hence, we hypothesized that prophages play a role in the bacterium’s fitness and persistence in CF. We focused on the CF niche and used longitudinal isolates of patients persistently infected by P. aeruginosa. Via in silico analysis we predicted intact prophages in the genomes of each longitudinal isolate group and scored their long-term persistence. We then confirmed whether they are inducible and where they reside by induction experiments and lysate sequencing. Lastly, we performed comparative genomics to evaluate prophage diversity and confirm their predicted long-term persistence and level of genomic maintenance. In concurrence with other studies, our findings support that most P. aeruginosa harbour prophages, some of which can self-induce. We also found ciprofloxacin, an antibiotic commonly used for P. aeruginosa treatment in CF, to induce prophages. The induced prophage genomes displayed a high degree of diversity and instances of genomic novelty. Finally, we discovered that all induced prophages persisted long-term with their genomes virtually unchanged, suggesting that they likely assist host persistence. In addition to elucidating the role of prophages in P. aeruginosa, we expect our findings to aid in developing novel diagnostics and phage-based therapies for P. aeruginosa infections.

\n\nPseudomonas aeruginosa maintains an inducible array of novel and diverse prophages over lengthy persistence in CF lungs", "token_count": 501, "char_count": 1970, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:26.362950", "source": { "split": "train_shard_00001", "doc_id": 1358 }, "chunk_id": "train_shard_00001_1358_0", "global_id": 7569 }, { "text": "Lysogeny was frequently detected in marine ecosystems, while how temperate phage genomes (prophages) impact marine microbial population or individual dynamics remained poorly understood. Using marine Citromicrobium strain collection as a model system, we revealed that 58% (22/38) were lysogens harboring 31 prophages that can be grouped into five novel genera (φA-φE). Prophage-encoded genes constituted 9% of host accessory genome, significantly expanding the microdiversity among citromicrobial clonal strains. Metagenomic abundance correlations indirectly supported the \"Piggyback-the-Winner\" dynamics for φA/φE, evidenced by their sublinear growth pattern with increasing host abundance. Most prophages were capable of spontaneous induction and exhibited high lytic activity when triggered by mitomycin C. Importantly, host-range profiling revealed these prophages deployed a dual \"Kill-the-Relatives\" and \"Colonize-the-Relatives\" strategy, and meanwhile, they protected parental host strains through superinfection immunity and enhanced phage resistance with greater prophage carriage. Sequencing data showed the dominance of Mu-like phages over non-Mu-like partners upon induced from the double lysogens. Our analysis further hinted at a unique Mu-type within-host competitive strategy: selectively targeting genes of co-resident prophages and host hypothetical genes, while avoiding self-damage and host metabolic genes potentially essential for phage lytic growth or progeny release. Collectively, this work establishes prophages as key architects of bacterial adaptation and provides new perspectives for prophage-driven evolution in marine bacterial hosts.\n\nProphages in marine <i>Citromicrobium</i>: diversity, activity, and interaction with the host.", "token_count": 448, "char_count": 1782, "word_count": 222, "semantic_coherence": 1, "information_density": 0.7703, "quality_score": 0.8851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:27.004954", "source": { "split": "train_shard_00001", "doc_id": 1359 }, "chunk_id": "train_shard_00001_1359_0", "global_id": 7570 }, { "text": "Secondary active transporters shuttle substrates across eukaryotic and prokaryotic membranes, utilizing different electrochemical gradients. They are recognized as one of the antimicrobial efflux pumps among pathogens. While primary active transporters within the genome of C. difficile 630 have been completely cataloged, the systematical study of secondary active transporters remains incomplete. Here, we not only identify secondary active transporters but also disclose their evolution and role in drug resistance in C. difficile 630. Our analysis reveals that C. difficile 630 carries 147 secondary active transporters belonging to 27 (super)families. Notably, 50 (34%) of them potentially contribute to antimicrobial resistance (AMR). AMR-secondary active transporters are structurally classified into five (super)families: the p-aminobenzoyl-glutamate transporter (AbgT), drug/metabolite transporter (DMT) superfamily, major facilitator (MFS) superfamily, multidrug and toxic compound extrusion (MATE) family, and resistance-nodulation-division (RND) family. Surprisingly, complete RND genes found in C. difficile 630 are likely an evolutionary leftover from the common ancestor with the diderm. Through protein structure comparisons, we have potentially identified six novel AMR-secondary active transporters from DMT, MATE, and MFS (super)families. Pangenome analysis revealed that half of the AMR-secondary transporters are accessory genes, which indicates an important role in adaptive AMR function rather than innate physiological homeostasis. Gene expression profile firmly supports their ability to respond to a wide spectrum of antibiotics. Our findings highlight the evolution of AMR-secondary active transporters and their integral role in antibiotic responses. This marks AMR-secondary active transporters as interesting therapeutic targets to synergize with other antibiotic activity.", "token_count": 500, "char_count": 1938, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6626, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:27.659395", "source": { "split": "train_shard_00001", "doc_id": 1360 }, "chunk_id": "train_shard_00001_1360_0", "global_id": 7571 }, { "text": "The complete catalog of antimicrobial resistance secondary active transporters in Clostridioides difficile: evolution and drug resistance perspective.", "token_count": 36, "char_count": 157, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:28.018052", "source": { "split": "train_shard_00001", "doc_id": 1360 }, "chunk_id": "train_shard_00001_1360_1", "global_id": 7572 }, { "text": "Klebsiellapneumoniae (Kp) is one of the most important etiological factors of urinary tract infections in renal transplant (RTx) recipients. We described the antimicrobial susceptibility phenotypes and genomic features of two hypermucoviscous (HM) Kp isolates recovered from RTx recipients with asymptomatic bacteriuria (ABU). Using whole genome sequencing (WGS) data, we showed that the strains belong to the ST152 lineage with the KL149 capsular serotype, but without rmpA/magA genes, which is typical for HM+ hypervirulent Kp. These new strains carried virulence-associated genes that predispose for urinary tract infections (UTIs). Likewise, both strains carried the ecp gene encoding pilus common for extended-spectrum β-lactamase (ESBL) Escherichiacoli. Although the two ST152 isolates were closely related and differed by only nine single nucleotide polymorphisms (SNPs) in their chromosomes, they had different plasmid compositions and chromosomal elements, with isolate KP28872 carrying an ESBL plasmid and an integrative conjugative element. These two isolates are an example of the high plasticity of the K. pneumoniae accessory genome. The identification of patients with ABU matched with the correct epidemiological profiling of isolates could facilitate interventions to prevent or rapidly treat K. pneumoniae infections.\n\nThe New Klebsiellapneumoniae ST152 Variants with Hypermucoviscous Phenotype Isolated from Renal Transplant Recipients with Asymptomatic Bacteriuria-Genetic Characteristics by WGS.", "token_count": 480, "char_count": 1593, "word_count": 202, "semantic_coherence": 1, "information_density": 0.698, "quality_score": 0.849, "entities": { "genes": [ "ST152", "KL149", "KP28872" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:28.675752", "source": { "split": "train_shard_00001", "doc_id": 1361 }, "chunk_id": "train_shard_00001_1361_0", "global_id": 7573 }, { "text": "Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 30% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli, sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding coevolution. They also reveal broad host ranges in P4-like elements, as almost identical elements can be found in distinct bacterial genera. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites. This article is part of the theme issue 'The secret lives of microbial mobile genetic elements'.\n\nTo catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites.", "token_count": 348, "char_count": 1583, "word_count": 228, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:29.273487", "source": { "split": "train_shard_00001", "doc_id": 1362 }, "chunk_id": "train_shard_00001_1362_0", "global_id": 7574 }, { "text": "Acinetobacter nosocomialis is a prevalent opportunistic pathogen that causes hospital-acquired infections. The increasing threats from A. nosocomialis infections have led to attention from the scientific and medical communities. Metagenomic next-generation sequencing (mNGS) was performed for an exudate specimen collected from an ICU patient with wound infection, followed by sepsis, in Tongji Hospital. Three assembly strategies were employed to recover the genome of A. nosocomialis in the metagenomic sample. Together with publicly available genomes of A. nosocomialis, the features of population genetics and molecular epidemiology were deeply analyzed. A draft genome was reconstructed for the metagenomic strain WHM01, derived from the ST410 A. nosocomialis dominating the microbial community, thereby prompting its highly pathogenic risk, which is associated with infection and persistence. The structure of the bacterial pangenome was characterized, including the 1862 core and 11,815 accessory genes present in the 157 strains. The genetic diversity of the genes coding for the 128 virulence factors assigned to 14 functional categories was uncovered in this nosocomial pathogen, such as the lipooligosaccharide, capsule, type IV pilus, and outer membrane proteins. Our work revealed genomic properties of ST410 A. nosocomialis, which is prevalent in China, and further highlighted that metagenomic surveillance may be a prospective application for evaluating the pathogenic characteristics of the nosocomial opportunistic pathogens.\n\nMetagenomic Insights into Pathogenic Characterization of ST410 Acinetobacter nosocomialis Prevalent in China.", "token_count": 430, "char_count": 1703, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [ "ST410", "WHM01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:29.898149", "source": { "split": "train_shard_00001", "doc_id": 1363 }, "chunk_id": "train_shard_00001_1363_0", "global_id": 7575 }, { "text": "Reported cases of listeriosis from food of non-animal origin (FNAO) are increasing. In order to assess the risk of exposure to Listeria monocytogenes from FNAO, the genetic characterization of the pathogen in FNAO products and in primary production and processing plants needs to be investigated. For this, 123 samples of fresh and frozen soft fruit and 407 samples of 39 plants in Bavaria, Germany that produce and process FNAO were investigated for Listeria contamination. As a result, 64 Listeria spp. isolates were detected using ISO 11290-1:2017. Environmental swabs and water and food samples were investigated. L. seeligeri (36/64, 56.25%) was the most frequently identified species, followed by L. monocytogenes (8/64, 12.50%), L. innocua (8/64, 12.50%), L. ivanovii (6/64, 9.38%), L. newyorkensis (5/64, 7.81%), and L. grayi (1/64, 1.56%). Those isolates were subsequently sequenced by whole-genome sequencing and subjected to pangenome analysis to retrieve data on the genotype, serotype, antimicrobial resistance (AMR), and virulence markers. Eight out of sixty-four Listeria spp. isolates were identified as L. monocytogenes. The serogroup analysis detected that 62.5% of the L. monocytogenes isolates belonged to serogroup IIa (1/2a and 3a) and 37.5% to serogroup IVb (4b, 4d, and 4e). Furthermore, the MLST (multilocus sequence typing) analysis of the eight detected L", "token_count": 520, "char_count": 1469, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:09:30.585073", "source": { "split": "train_shard_00001", "doc_id": 1364 }, "chunk_id": "train_shard_00001_1364_0", "global_id": 7576 }, { "text": "monocytogenes isolates identified seven different sequence types (STs) and clonal complexes (CCs), i.e., ST1/CC1, ST2/CC2, ST6/CC6, ST7/CC7, ST21/CC21, ST504/CC475, and ST1413/CC739. The core genome MLST analysis also showed high allelic differences and suggests plant-specific isolates. Regarding the AMR, we detected phenotypic resistance against benzylpenicillin, fosfomycin, and moxifloxacin in all eight L. monocytogenes isolates. Moreover, virulence factors, such as prfA, hly, plcA, plcB, hpt, actA, inlA, inlB, and mpl, were identified in pathogenic and nonpathogenic Listeria species. The significance of L. monocytogenes in FNAO is growing and should receive increasing levels of attention.\n\nGenetic Characterization of Listeria from Food of Non-Animal Origin Products and from Producing and Processing Companies in Bavaria, Germany.", "token_count": 341, "char_count": 938, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7928, "quality_score": 0.8964, "entities": { "genes": [ "CC739", "ST2", "ST6", "CC475", "ST21", "CC21", "ST1413", "ST7", "CC7", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:31.185094", "source": { "split": "train_shard_00001", "doc_id": 1364 }, "chunk_id": "train_shard_00001_1364_1", "global_id": 7577 }, { "text": "

Background

Antimicrobial and antifungal species are essential members of the healthy human microbiota. Several different species of lactobacilli that naturally inhabit the human body have been explored for their probiotic capabilities including strains of the species Lactobacillus gasseri. However, L. gasseri (identified by 16S rRNA gene sequencing) has been associated with urogenital symptoms. Recently a new sister taxon of L. gasseri was described: L. paragasseri. L. paragasseri is also posited to have probiotic qualities.

Methods

Here, we present a genomic investigation of all (n = 79) publicly available genome assemblies for both species. These strains include isolates from the vaginal tract, gastrointestinal tract, urinary tract, oral cavity, wounds, and lungs.

Results

The two species cannot be distinguished from short-read sequencing of the 16S rRNA as the full-length gene sequences differ only by two nucleotides. Based upon average nucleotide identity (ANI), we identified 20 strains deposited as L. gasseri that are in fact representatives of L. paragasseri. Investigation of the genic content of the strains of these two species suggests recent divergence and/or frequent gene exchange between the two species. The genomes frequently harbored intact prophage sequences, including prophages identified in strains of both species. To further explore the antimicrobial potential associated with both species, genome assemblies were examined for biosynthetic gene clusters. Gassericin T and S were identified in 46 of the genome assemblies, with all L. paragasseri strains including one or both bacteriocins. This suggests that the properties once ascribed to L. gasseri may better represent the L. paragasseri species.", "token_count": 513, "char_count": 1837, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6016, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:09:31.881596", "source": { "split": "train_shard_00001", "doc_id": 1365 }, "chunk_id": "train_shard_00001_1365_0", "global_id": 7578 }, { "text": "Genomic insights into Lactobacillus gasseri and Lactobacillus paragasseri.", "token_count": 37, "char_count": 88, "word_count": 8, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:32.275202", "source": { "split": "train_shard_00001", "doc_id": 1365 }, "chunk_id": "train_shard_00001_1365_1", "global_id": 7579 }, { "text": "A novel strain identified as Comamonas sp. was isolated from the soil of the Brazilian savanna-like Cerrado biome, a global hotspot for biodiversity. Phylogenetic analysis based on 16 S rRNA gene sequences showed that this strain is classified as Betaproteobacteria from the family Comamonadaceae. The digital DNA-DNA hybridization (dDDH) and Average Nucleotide Identity (ANI) results, of respectively 48.6% and < 93%, indicated that Comamonas sp. consists in a new species with Comamonas testosteroni as its closest strain. Comamonas sp. is a Gram-negative, rod-shaped, and non-spore-forming bacterium. Its colonies typically exhibit a round, convex, and irregular shape with a clear color and spotted edges. It is characterized as non-fermenting, aerobic, and motile, presenting both oxidase and catalase activities. The optimal growth parameters for this bacterial strain are 30 °C, a pH range of 5-8, and 0% NaCl. In addition, its fatty acid profile included palmitic acid (C16:0) at 26.94%, 13-Methyltetradecanoic Acid (iso-C15:0) at 10.94%, myristic acid (C14:0) at 8.94%, and a summed feature comprising 16:1 ω7c, 16:1 ω6c, or 16:1 at 15.8%. Genomic analysis of Comamonas sp. revealed a GC content of 62.1% across its 5.6 Mb genome. Phylogenomic and pangenome analyses, along with in silico phenotypic characterization indicate that this strain represents a novel species within the Comamonas genus, which we propose to name Comamonas brasiliensis nov.\n\nGenomic and taxonomic characterization of the Comamonas sp. nov., a bacterium isolated from Brazilian Cerrado soil.", "token_count": 501, "char_count": 1609, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:32.930145", "source": { "split": "train_shard_00001", "doc_id": 1366 }, "chunk_id": "train_shard_00001_1366_0", "global_id": 7580 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) causes foodborne outbreaks that can lead to complications such as hemolytic uremic syndrome. Their main reservoir is cattle, and ground beef has been frequently associated with disease and outbreaks. In this study, we attempted to understand the genetic relationship among STEC isolated in Chile from different sources, their relationship to STEC from the rest of the world, and to identify molecular markers of Chilean STEC. We sequenced 62 STEC isolated in Chile using MiSeq Illumina. In silico typing was determined using tools of the Center Genomic Epidemiology, Denmark University (CGE/DTU). Genomes of our local STEC collection were compared with 113 STEC isolated worldwide through a core genome MLST (cgMLST) approach, and we also searched for distinct genes to be used as molecular markers of Chilean isolates. Genomes in our local collection were grouped based on serogroup and sequence type, and clusters were formed within local STEC. In the worldwide STEC analysis, Chilean STEC did not cluster with genomes of the rest of the world suggesting that they are not phylogenetically related to previously described STEC. The pangenome of our STEC collection was 11,650 genes, but we did not identify distinct molecular markers of local STEC. Our results showed that there may be local emerging STEC with unique features, nevertheless, no molecular markers were detected. Therefore, there might be elements such as a syntenic organization that might explain differential clustering detected between local and worldwide STEC.\n\nWhole-Genome Phylogenetic Analysis Reveals a Wide Diversity of Non-O157 STEC Isolated From Ground Beef and Cattle Feces.", "token_count": 414, "char_count": 1714, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5875, "quality_score": 0.7938, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:33.554109", "source": { "split": "train_shard_00001", "doc_id": 1367 }, "chunk_id": "train_shard_00001_1367_0", "global_id": 7581 }, { "text": "

Background

Lactobacillus plantarum is widely used in the manufacture of dairy products, fermented foods, and bacteriocins. The genomes of the strains contain multiple genes which may have been acquired by horizontal gene transfer. Many of these genes are important for the regulation, metabolism, and transport of various sugars; however, other genes may carry and spread virulence and antibiotic resistance determinants. In this way, monitoring these genomes is essential to the manufacture of food. In this study, we aim to provide an overview of the genomic properties of L. plantarum based on approaches of comparative genomics.

Results

The finding of the current study indicates that the core genome of L. plantarum presents 1425 protein-coding genes and is mostly related to the metabolic process. The accessory genome has on average 1320 genes that encodes protein involved in processes as the formation of bacteriocins, degradation of halogen, arsenic detoxification, and nisin resistance. Most of the strains show an ancestral synteny, similar to the one described in the genomes of L. pentosus KCA1 and L. plantarum WCFS1. The lifestyle island analyses did not show a pattern of arrangement or gene content according to habitat.

Conclusions

Our results suggest that there is a high rate of transfer of genetic material between the strains. We did not identify any virulence factors and antibiotic resistance genes on the genomes. Thus, the strains may be useful for the biotechnology, bioremediation, and production of bacteriocins. The potential applications are, however, restricted to particular strains.\n\nComparative Genomic Analysis of Lactobacillus plantarum: An Overview.", "token_count": 448, "char_count": 1752, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [ "WCFS1", "KCA1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:34.191297", "source": { "split": "train_shard_00001", "doc_id": 1368 }, "chunk_id": "train_shard_00001_1368_0", "global_id": 7582 }, { "text": "

Background

Genome-wide association studies (GWAS) are rapidly advancing due to the improved resolution and completeness provided by Telomere-to-Telomere (T2T) and pangenome assemblies. While recent advancements in GWAS methods have primarily focused on identifying genetic variants associated with discrete phenotypes, approaches for quantitative traits (QTs) remain underdeveloped. This has often led to significant variants being overlooked due to biases from genotype multicollinearity and strict p-value thresholds.

Results

We propose an enhanced ensemble learning approach for QT analysis that integrates regularized variant selection with machine learning-based association methods, validated through comprehensive biological enrichment analysis. We benchmarked four widely recognized single nucleotide polymorphism (SNP) feature selection methods-least absolute shrinkage and selection operator, ridge regression, elastic-net, and mutual information-alongside four association methods: linear regression, random forest, support vector regression (SVR), and XGBoost. Our approach is evaluated on simulated datasets and validated using a subset of the PennCATH real dataset, including imputed versions, focusing on low-density lipoprotein (LDL)-cholesterol levels as a QT. The combination of elastic-net with SVR outperformed other methods across all datasets. Functional annotation of top 100 SNPs identified through this superior ensemble method revealed their expression in tissues involved in LDL cholesterol regulation. We also confirmed the involvement of six known genes (APOB, TRAPPC9, RAB2A, CCL24, FCHO2, and EEPD1) in cholesterol-related pathways and identified potential drug targets, including APOB, PTK2B, and PTPN12.

Conclusions

In conclusion, our ensemble learning approach effectively identifies variants associated with QTs, and we expect its performance to improve further with the integration of T2T and pangenome references in future GWAS.\n\nImproving genetic variant identification for quantitative traits using ensemble learning-based approaches.", "token_count": 496, "char_count": 2095, "word_count": 258, "semantic_coherence": 1, "information_density": 0.7403, "quality_score": 0.8702, "entities": { "genes": [ "RAB2A", "TRAPPC9", "PTK2B", "FCHO2", "PTPN12", "CCL24", "EEPD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:34.844100", "source": { "split": "train_shard_00001", "doc_id": 1369 }, "chunk_id": "train_shard_00001_1369_0", "global_id": 7583 }, { "text": "With the increasing availability of high-quality genome assemblies, pangenome graph is emerging as a new paradigm in the genomics field for identifying, encoding, and interpreting genomic variation landscape at both population and species levels. However, it remains a major challenge in understanding and interpretating pangenome graph via biologically informative visualization. To facilitate a better examination of pangenome graph towards novel biological insights, here we present VRPG, a web-based interactive visualization framework of pangenome graph. VRPG provides dynamic and efficient supports for exploring and annotating pangenome graphs along a reference-based coordinate system. Moreover, VRPG shines with its unique features in highlighting the directed path of any graph-constitutive assembly as well as in denoting copy number variation of genomic segments represented by graph-constitutive nodes, which are highly valuable in genome comparison and variant analysis. Additionally, VRPG enables side-by-side visualization between pangenome graph and reference-based annotation features, bridging the graph and linear genome context. To further demonstrate its features and scalability, we applied VRPG to the cutting-edge yeast and human reference pangenome graphs derived from hundreds of high-quality genome assemblies via a dedicated website ( https://www.evomicslab.org/app/vrpg/ ). Contact: yuejiaxing@gmail.com

Key points

Developed an intuitive visualization framework for pangenome graph. Empowered graph-based feature highlighting and variant visualization. Enabled connecting reference-based annotation features in the context of pangenome graph.\n\nVRPG: an interactive visualization framework for reference-projected pangenome graph", "token_count": 382, "char_count": 1767, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:35.435152", "source": { "split": "train_shard_00001", "doc_id": 1370 }, "chunk_id": "train_shard_00001_1370_0", "global_id": 7584 }, { "text": "Bacterial genetic discontinuity, representing abrupt breaks in genomic identity among species, is crucial for grasping microbial diversity and evolution. Advances in genomic sequencing have enhanced our ability to track and characterize genetic discontinuity in bacterial populations. However, exploring systematically the degree to which bacterial diversity exists as a continuum or is sorted into discrete and readily defined species remains a challenge in microbial ecology. Here, we aimed to quantify the genetic discontinuity ( δ ) and investigate how this metric is related to ecology. We harnessed a dataset comprising 210,129 genomes to systematically explore genetic discontinuity patterns across several distantly related species, finding clear breakpoints which varied depending on the taxa in question. By delving into pangenome characteristics, we uncovered a significant association between pangenome saturation and genetic discontinuity. Closed pangenomes were associated with more pronounced breaks, exemplified by Mycobacterium tuberculosis . Additionally, through a machine learning approach, we detected key features that impact genetic discontinuity prediction. Our study enhances the understanding of bacterial genetic patterns and their ecological implications, offering insights into species boundaries for prokaryotes.\n\nRelating Ecological Diversity to Genetic Discontinuity across Bacterial Species", "token_count": 287, "char_count": 1423, "word_count": 186, "semantic_coherence": 1, "information_density": 0.672, "quality_score": 0.836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:35.990254", "source": { "split": "train_shard_00001", "doc_id": 1371 }, "chunk_id": "train_shard_00001_1371_0", "global_id": 7585 }, { "text": "Considering the increase in the consumption of yeasts as human probiotics, the aim of this study was to broadly investigate the beneficial properties of the lactic yeast Kluyveromyces marxianus (formerly Kluyveromyces fragilis) B0399. Several potential probiotic traits of K. marxianus B0399 were investigated by using in vitro assays, including adhesion and immune modulation, and the effect of the administration of 10(7) CFU/day of K. marxianus B0399 on the composition and metabolic activity of the human intestinal microbiota was investigated in a 3-stage continuous-culture system simulating the human colon. We demonstrated that this strain was highly adhesive to human enterocyte-like Caco-2 cells and modulated the immune response, inducing proinflammatory cytokines in peripheral blood mononuclear cells (PBMCs). In the presence of inflammatory stimulation with lipopolysaccharide (LPS), K. marxianus B0399 provoked decreases in the levels of production of proinflammatory cytokines in PBMCs and Caco-2 cells, thus ameliorating the inflammatory response. Furthermore, K. marxianus B0399 impacted the colonic microbiota, increasing the bifidobacterial concentration in the stages of the colonic model system simulating the proximal and transverse colon. The amounts of the short-chain fatty acids acetate and propionate also increased following yeast supplementation. Finally, K. marxianus B0399 was found to induce a decrease of the cytotoxic potential of the culture supernatant from the first stage of the colonic model system. The effects of K. marxianus B0399 on adhesion, immune function, and colonic microbiota demonstrate that this strain possesses a number of beneficial and strain-specific properties desirable for a microorganism considered for application as a probiotic.", "token_count": 472, "char_count": 1792, "word_count": 250, "semantic_coherence": 1, "information_density": 0.548, "quality_score": 0.774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:36.635410", "source": { "split": "train_shard_00001", "doc_id": 1372 }, "chunk_id": "train_shard_00001_1372_0", "global_id": 7586 }, { "text": "Potential probiotic Kluyveromyces marxianus B0399 modulates the immune response in Caco-2 cells and peripheral blood mononuclear cells and impacts the human gut microbiota in an in vitro colonic model system.", "token_count": 57, "char_count": 208, "word_count": 30, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:36.995237", "source": { "split": "train_shard_00001", "doc_id": 1372 }, "chunk_id": "train_shard_00001_1372_1", "global_id": 7587 }, { "text": "

Motivation

A pangenome represents many diverse genome sequences of the same species. In order to cope with small variations as well as structural variations, recent research focused on the development of graph-based models of pangenomes. Mapping is the process of finding the original location of a DNA read in a reference sequence, typically a genome. Using a pangenome instead of a (linear) reference genome can, e.g. reduce mapping bias, the tendency to incorrectly map sequences that differ from the reference genome. Mapping reads to a graph, however, is more complex and needs more resources than mapping to a reference genome. Reducing the complexity of the graph by encoding simple variations like SNPs in a simple way can accelerate read mapping and reduce the memory requirements at the same time.

Results

We introduce graphs based on elastic-degenerate strings (ED strings, EDS) and the linearized form of these EDS graphs as a new representation for pangenomes. In this representation, small variations are encoded directly in the sequence. Structural variations are encoded in a graph structure. This reduces the size of the representation in comparison to sequence graphs. In the linearized form, mapping techniques that are known from ordinary strings can be applied with appropriate adjustments. Since most variations are expressed directly in the sequence, the mapping process rarely has to take edges of the EDS graph into account. We developed a prototypical software tool GED-MAP that uses this representation together with a minimizer index to map short reads to the pangenome. Our experiments show that the new method works on a whole human genome scale, taking structural variants properly into account. The advantage of GED-MAP, compared with other pangenomic short read mappers, is that the new representation allows for a simple indexing method. This makes GED-MAP fast and memory efficient.

Availability and implementation

Sources are available at: https://github.com/thomas-buechler-ulm/gedmap.\n\nEfficient short read mapping to a pangenome that is represented by a graph of ED strings.", "token_count": 465, "char_count": 2135, "word_count": 317, "semantic_coherence": 1, "information_density": 0.5268, "quality_score": 0.7634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:37.637212", "source": { "split": "train_shard_00001", "doc_id": 1373 }, "chunk_id": "train_shard_00001_1373_0", "global_id": 7588 }, { "text": "A. baumannii has become one of the most important multidrug resistant nosocomial pathogens all over the world. Nonetheless, very little is known about the diversity of A. baumannii lineages co-existing in hospital settings. Here, using whole-genome sequencing, epidemiological data and antimicrobial susceptibility tests, we uncover the transmission dynamics of extensive and multidrug resistant A. baumannii in a tertiary hospital for a decade. Our core genome phylogeny of almost 300 genomes suggests that there were several introductions of lineages from international clone 2 into the hospital. The molecular dating analysis shows that these introductions happened between 2004 and 2015. Furthermore, using the accessory genome, we show that these lineages were extensively disseminated across many wards in the hospital. Our results demonstrate that accessory genome variation can be a very powerful tool for conducting genomic epidemiology. We anticipate future studies employing the accessory genome as a phylogenomic marker over very short microevolutionary scales.\n\nAccessory genomic epidemiology of co-circulating Acinetobacter baumannii clones", "token_count": 280, "char_count": 1161, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6855, "quality_score": 0.8428, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:38.190311", "source": { "split": "train_shard_00001", "doc_id": 1374 }, "chunk_id": "train_shard_00001_1374_0", "global_id": 7589 }, { "text": "Two strains of filamentous, colorless sulfur bacteria were isolated from bacterial fouling in the outflow of hydrogen sulfide-containing waters from a coal mine (Thiothrix sp. Ku-5) and on the seashore of the White Sea (Thiothrix sp. AS). Metagenome-assembled genome (MAG) A52 was obtained from a sulfidic spring in the Volgograd region, Russia. Phylogenetic analysis based on the 16S rRNA gene sequences showed that all genomes represented the genus Thiothrix. Based on their average nucleotide identity and digital DNA-DNA hybridization data these new isolates and the MAG represent three species within the genus Thiothrix with the proposed names Thiothrix subterranea sp. nov. Ku-5T, Thiothrix litoralis sp. nov. AST, and \"Candidatus Thiothrix anitrata\" sp. nov. A52. The complete genome sequences of Thiothrix fructosivorans QT and Thiothrix unzii A1T were determined. Complete genomes of seven Thiothrix isolates, as well as two MAGs, were used for pangenome analysis. The Thiothrix core genome consisted of 1,355 genes, including ones for the glycolysis, the tricarboxylic acid cycle, the aerobic respiratory chain, and the Calvin cycle of carbon fixation", "token_count": 425, "char_count": 1283, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:38.819823", "source": { "split": "train_shard_00001", "doc_id": 1375 }, "chunk_id": "train_shard_00001_1375_0", "global_id": 7590 }, { "text": "Genes for dissimilatory oxidation of reduced sulfur compounds, namely the branched SOX system (SoxAXBYZ), direct (soeABC) and indirect (aprAB, sat) pathways of sulfite oxidation, sulfur oxidation complex Dsr (dsrABEFHCEMKLJONR), sulfide oxidation systems SQR (sqrA, sqrF), and FCSD (fccAB) were found in the core genome. Genomes differ in the set of genes for dissimilatory reduction of nitrogen compounds, nitrogen fixation, and the presence of various types of RuBisCO.\n\nComparative Genome Analysis of the Genus Thiothrix Involving Three Novel Species, Thiothrix subterranea sp. nov. Ku-5, Thiothrix litoralis sp. nov. AS and \"Candidatus Thiothrix anitrata\" sp. nov. A52, Revealed the Conservation of the Pathways of Dissimilatory Sulfur Metabolism and Variations in the Genetic Inventory for Nitrogen Metabolism and Autotrophic Carbon Fixation.", "token_count": 340, "char_count": 931, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:39.383104", "source": { "split": "train_shard_00001", "doc_id": 1375 }, "chunk_id": "train_shard_00001_1375_1", "global_id": 7591 }, { "text": "

ABSTRACT

The design of highly specific primers and guide RNAs (gRNA) for CRISPR-based diagnostics is often a laborious process. Several tools exist for gRNA design, but most are tailored for genome editing applications. Here, we present PathoGD, an end-to-end bioinformatic pipeline comprising pangenome and k -mer modules for rapid and high-throughput design of primers and gRNAs for CRISPR-Cas12a-based pathogen detection. We validated and demonstrated high specificity of a subset of PathoGD-designed primers and gRNAs for the detection of Neisseria gonorrhoeae and Streptococcus pyogenes. PathoGD will serve as an important resource for designing CRISPR-based diagnostic assays for current and emerging pathogens.\n\nPathoGD: an integrative genomics approach for CRISPR-based target design of rapid pathogen diagnostics", "token_count": 226, "char_count": 830, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8451, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:39.865853", "source": { "split": "train_shard_00001", "doc_id": 1376 }, "chunk_id": "train_shard_00001_1376_0", "global_id": 7592 }, { "text": "Genome-wide association studies (GWAS) are surging again owing to newer high-quality T2T-CHM13 and human pangenome references. Conventional GWAS methods have several limitations, including high false negatives. Non-conventional machine learning-based methods are warranted for analyzing newly sequenced, albeit complex, genomic regions. We present a robust machine learning-based framework for feature selection and association analysis, incorporating functional enrichment analysis to avoid false negatives. We benchmarked four popular single nucleotide polymorphism (SNP) feature selection methods: least absolute shrinkage and selection operator, ridge regression, elastic-net, and mutual information. Furthermore, we evaluated four association methods: linear regression, random forest, support vector regression (SVR), and XGBoost. We assessed proposed framework on diverse datasets, including subsets of publicly available PennCATH datasets as well as imputed, rare-variants, and simulated datasets. Low-density lipoprotein (LDL) cholesterol level was used as a phenotype for illustration. Our analysis revealed elastic-net combined with SVR consistently outperformed other methods across various datasets. Functional annotation of top 100 SNPs from PennCATH-real dataset revealed their expression in LDL cholesterol-related tissues. Our analysis validated three previously known genes (APOB, TRAPPC9, and EEPD1) implicated in cholesterol-regulated pathways. Also, rare-variant dataset analysis confirmed 37 known genes associated with LDL cholesterol. We identified several important genes, including APOB (familial-hypercholesterolemia), PTK2B (Alzheimer’s disease), and PTPN12 (myocardial ischemia/reperfusion injuries) as potential drug targets for cholesterol-related diseases. Our comprehensive analyses highlight elastic-net combined with SVR for association analysis could overcome limitations of conventional GWAS approaches. Our framework effectively detects common and rare variants associated with complex traits, enhancing the understanding of complex diseases.\n\nEnhancing genotype-phenotype association with optimized machine learning and biological enrichment methods", "token_count": 500, "char_count": 2188, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6973, "quality_score": 0.8487, "entities": { "genes": [ "EEPD1", "CHM13", "TRAPPC9", "PTPN12", "PTK2B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:40.518082", "source": { "split": "train_shard_00001", "doc_id": 1377 }, "chunk_id": "train_shard_00001_1377_0", "global_id": 7593 }, { "text": "

ABSTRACT

Introduction

Phytobacter diazotrophicus is an emerging opportunistic pathogen associated with hospital outbreaks and a reservoir of antimicrobial resistance genes; however, its clonal epidemiology remains poorly understood. Accurate identification and rapid clonal typing are crucial for infection control. Core genome MLST (cgMLST) is the genomic gold standard; however, it is both costly and time-consuming. Fourier-transform infrared (FT-IR) spectroscopy using the IR Biotyper ® emerges as a rapid and accessible typing alternative.

Objective

This study evaluated the performance of the IR Biotyper ® in discriminating P. diazotrophicu s outbreak isolates, compared to cgMLST.

Methodology

Eight epidemiologically relevant isolates, including two from a total parenteral nutrition (TPN) outbreak and four from a hemodialysis clinic, along with two outliers, were analyzed. Its identification was confirmed by API20E, MALDI-TOF MS, nif L gene qPCR, and WGS. Both cgMLST, based on 7,755 conserved genes, and the Fourier Transform Infrared (FT-IR) Spectroscopy by IR Biotyper ® were used for clonal typing, with the spectral cutoff empirically determined based on known clonal isolates.

Results

Both methodologies demonstrated remarkable agreement in detecting clonal clusters. The two TPN outbreak isolates showed 23 allele differences (ADs) by cgMLST and consistently clustered according to the IR Biotyper. Similarly, the four isolates from the outbreak at hemodialysis clinic formed homogeneous clusters by both methods (5-27 ADs by cgMLST). The outlier isolates were consistently discriminated.

Conclusion

FT-IR spectroscopy (IR Biotyper ® ) proved promising and complementary to cgMLST for typing P. diazotrophicus in outbreak scenarios, offering a rapid and cost-effective alternative for detecting clonal events", "token_count": 522, "char_count": 1887, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [ "API20E" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:09:41.175398", "source": { "split": "train_shard_00001", "doc_id": 1378 }, "chunk_id": "train_shard_00001_1378_0", "global_id": 7594 }, { "text": "Its applicability in routine epidemiological surveillance is significant.

Statement of Importance

Phytobacter diazotrophicus is an emerging opportunistic pathogen of increasing concern in clinical environments, associated with hospital outbreaks and carrying antimicrobial resistance genes. Rapid detection and precise clonal characterization are essential for infection control and epidemiological surveillance. However, these are challenging for less-understood species. Genomic methods, such as cgMLST, are the gold standard, but their cost and time limitations hinder routine application in outbreak response. This study evaluated the IR Biotyper system, a rapid and accessible phenotypic tool that uses Fourier Transform Infrared Spectroscopy, compared to cgMLST for clonal typing of P. diazotrophicus . Our findings demonstrate a remarkable agreement between the two methods in identifying clonal clusters. This validation suggests the potential of the IR Biotyper as an effective tool for real-time screening and active surveillance of P. diazotrophicus in clinical settings. This enables a more agile response to outbreaks and aids in managing antimicrobial resistance, reserving high-resolution genomic analyses for more in-depth investigations.\n\nOutbreak Investigation of Phytobacter diazotrophicus Using Fourier Transform Infrared Spectroscopy compared to cgMLST", "token_count": 316, "char_count": 1390, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6742, "quality_score": 0.8371, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:41.735292", "source": { "split": "train_shard_00001", "doc_id": 1378 }, "chunk_id": "train_shard_00001_1378_1", "global_id": 7595 }, { "text": "The production of prebiotic galacto-oligosaccharides (GOS) considers the enzymatic synthesis by lactose transgalactosylation and the purification from the reacted mixture (raw GOS). Simultaneous synthesis and purification of GOS (SSP) was conducted in a one-pot operation using β-galactosidase from Aspergillus oryzae and Saccharomyces cerevisiae or Kluyveromyces marxianus cells, allowing the selective removal of unwanted carbohydrates (monosaccharides and lactose). The reaction was carried out in a stirred reactor at 40 °C, pH 4.5 and 200 rpm, using lactose without additional supplements, evaluating the effect of yeast genus (S. cerevisiae or K. marxianus), enzyme-substrate ratio (20–400 IUH/g lactose), initial lactose concentration (20–50% w/w) and substrate mass-biomass ratio (0.05–0.4). The best GOS yield was obtained with S. cerevisiae at 50 IUH/g lactose and 0.25 g cell biomass/g carbohydrates. These conditions were used for scaling-up into a bioreactor (1000 g of 40% w/w lactose) operated under temperature and pH control at an aeration rate of 5 vvm, obtaining a GOS yield of 40% at 24 h of reaction, which is significantly higher than obtained in the conventional system of GOS synthesis. SSP may represent a technological advantage in terms of productivity and yield of GOS production.\n\nSimultaneous synthesis and purification (SSP) of galacto-oligosaccharides in batch operation", "token_count": 440, "char_count": 1402, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8284, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:42.382031", "source": { "split": "train_shard_00001", "doc_id": 1379 }, "chunk_id": "train_shard_00001_1379_0", "global_id": 7596 }, { "text": "Pangenomes exhibit remarkable variability in many prokaryotic species. This variation is maintained through the processes of horizontal gene transfer and gene loss. Repeated acquisitions of near-identical homologs can easily be observed across pangenomes, leading to the question of whether these parallel events potentiate similar evolutionary trajectories, or whether the remarkably different genetic background of the recipients mean that post-acquisition evolutionary trajectories end up being quite different. In this study, we present a machine learning method that predicts the presence or absence of genes in the Escherichia coli pangenome based on the presence of other accessory genes within the genome. We are, in effect, asking whether gene acquisitions potentiate similar evolutionary trajectories or not. Our analysis leverages the repeated transfer of genes through the E. coli pangenome to observe patterns of repeated evolution following similar events. The presence or absence of a substantial set of genes is highly predictable, from other genes alone, indicating that selection potentiates and maintains gene-gene co-occurrence and avoidance relationships deterministically over long-term bacterial evolution despite differences in host evolutionary history. We propose that the pangenome can be understood as a set of genes with relationships that govern their likely cohabitants, analogous to an ecosystem’s set of interacting organisms. Our findings highlight intra-genomic gene fitness effects as key drivers of prokaryotic evolution, with ensuing pangenome-wide emergence of repeated patterns of community structure.\n\nContingency, Repeatability and Predictability in the Evolution of a Prokaryotic Pangenome", "token_count": 357, "char_count": 1732, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:43.002652", "source": { "split": "train_shard_00001", "doc_id": 1380 }, "chunk_id": "train_shard_00001_1380_0", "global_id": 7597 }, { "text": "Whole genome sequencing has increasingly become the essential method for studying the genetic mechanisms of antimicrobial resistance and for surveillance of drug-resistant bacterial pathogens. The majority of bacterial genomes sequenced to date have been sequenced with Illumina sequencing technology, owing to its high-throughput, excellent sequence accuracy, and low cost. However, because of the short-read nature of the technology, these assemblies are fragmented into large numbers of contigs, hindering the obtaining of full information of the genome. We develop Pasa, a graph-based algorithm that utilizes the pangenome graph and the assembly graph information to improve scaffolding quality. By leveraging the population information of the bacteria species, Pasa is able to utilize the linkage information of the gene families of the species to resolve the contig graph of the assembly. We show that our method outperforms the current state of the art in terms of accuracy, and at the same time, is computationally efficient to be applied to a large number of existing draft assemblies.\n\nPasa: Leverage population pangenome graph to scaffold prokaryote genome assemblies", "token_count": 253, "char_count": 1178, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:43.504947", "source": { "split": "train_shard_00001", "doc_id": 1381 }, "chunk_id": "train_shard_00001_1381_0", "global_id": 7598 }, { "text": "Intestinal bowel disease (IBD) is a chronic, early-onset, recurrent gastrointestinal immune-related disease that has become globalized. Although the combination of genetic, environmental, and immunological factors leads to intestinal inflammation and barrier damage, the etiology of IBD is not clearly defined. In recent years, diet-microbiota interactions have been widely studied for their potential in pathogenesis and treatment for IBD. Meanwhile, the significant efficacy of exclusive enteral nutrition (EEN) has been observed in clinical practice with modulation in gut microbiota, but the specific mechanisms and optimization measures remain challenging. Therefore, we first describe the development of existing microbial research techniques and the perspectives that can be broadened. We then synthesize findings on how dietary components impact IBD progression and treatment through microbiota. Finally, based on correlating clinical and basic experiments, we summarize the current status and potential mechanisms of EEN for treating IBD, especially the contradictory points encountered in its application.\n\nExploring diet-microbiota interactions and therapeutic nutrition management in inflammatory bowel disease.", "token_count": 255, "char_count": 1223, "word_count": 160, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:44.029997", "source": { "split": "train_shard_00001", "doc_id": 1382 }, "chunk_id": "train_shard_00001_1382_0", "global_id": 7599 }, { "text": "High-throughput massive parallel sequencing has significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with the complete genome reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing with Oxford Nanopore Technologies (ONT) presents an alternative that offers benefits including real-time sequencing and cost efficiency, particularly useful in resource-limited settings. However, the historically higher error rates of ONT data have so far limited its application in high-precision genomic typing. The recent release of ONT's R10.4.1 chemistry, with significantly improved raw read accuracy (Q20+), offers a potential solution to this problem. The aim of this study is to evaluate the performance of ONT's latest chemistry for bacterial genomic typing against the gold-standard Illumina technology, focusing on three respiratory pathogens of public health importance, Klebsiella pneumoniae, Bordetella pertussis, and Corynebacterium diphtheriae, and their related species. Using the Rapid Barcoding Kit V14, we generate and analyze genome assemblies with different basecalling models, at different simulated depths of coverage. ONT assemblies are compared to the Illumina reference for completeness and core genome multilocus sequence typing (cgMLST) accuracy (number of allelic mismatches). Our results show that genomes obtained from raw ONT data basecalled with Dorado SUP v0.9.0, assembled with Flye, and with a minimum coverage depth of 35×, optimized accuracy for all bacterial species tested. Error rates are consistently <0.5% for each cgMLST scheme, indicating that ONT R10.4.1 data are suitable for high-resolution genomic typing applied to outbreak investigations and public health surveillance.\n\nAccurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing.", "token_count": 476, "char_count": 1961, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:45.397175", "source": { "split": "train_shard_00001", "doc_id": 1383 }, "chunk_id": "train_shard_00001_1383_0", "global_id": 7600 }, { "text": "We investigated the intra-hospital distribution of C. difficile strains by whole-genome sequencing (WGS) of isolates collected in 2022 at the University Hospital Centre (UHC) Zagreb. In total, 103 patients with first-episode CDI in 2022 at UHC Zagreb were included, based on the screening stool antigen test for GDH (RidaQuick CD GDH; R-Biopharm AG, Germany), confirmed by Eazyplex C. difficile assays (Eazyplex CD assay; AmplexDiagnostics GmbH, Germany) specific for A, B, and binary toxins. Demographic and clinical data were retrospectively analyzed from electronic medical records. All samples were subjected to WGS analysis. Genetic clusters were formed from isolates with no more than six allelic differences according to core genome MLST. We identified six clusters containing 2-59 isolates with 15 singletons and 30 instances of possible intra-hospital transmission, mostly in the COVID-19 ward. WGS analysis proved useful in identifying clusters of isolates connecting various patient wards with possible transmission routes in the hospital setting. It could be used to support local and national surveillance of CDI infections and their transmission pathways.\n\nWhole-Genome Sequencing-Based Characterization of Clostridioides difficile Infection Cases at the University Hospital Centre Zagreb.", "token_count": 340, "char_count": 1324, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:45.973438", "source": { "split": "train_shard_00001", "doc_id": 1384 }, "chunk_id": "train_shard_00001_1384_0", "global_id": 7601 }, { "text": "

Aims

Clostridium tertium, increasingly recognized as the emerging human pathogen frequently isolated from environmental and clinical specimens, remains genetically underexplored despite its clinical relevance. This study aims to explore the genetic characteristics of C. tertium by genomic analysis.

Methods and results

This study presented a comprehensive genomic investigation of 45 C. tertium strains from the GenBank database. Genome sizes (3.27-4.55 Mbp) and coding gene counts varied markedly across strains. Phylogenetic analyses based on 16S rRNA gene and core genome uncovered distinct intra-species lineages, including evolutionarily divergent clusters likely shaped by niche specialization. Pan-genomic analysis confirmed an open genome, with accessory and strain-specific genes enriched in functions related to environmental adaptation and regulation. Functional annotation further identified diverse virulence factor genes (e.g. clpP, nagK) and antibiotic resistance genes [e.g. vatB, tetA(P)] co-occurring with mobile genetic elements (MGEs), suggesting that horizontal gene transfer (HGT) may be a key driver of genome plasticity in C. tertium. Notably, one-third of the strains carried CRISPR-Cas systems, indicating the defense potential against exogenous genetic elements.

Conclusions

Clostridium tertium exhibited extensive genetic diversity and genome plasticity, probably driven by MGE-mediated HGT, defense mechanisms of CRISPR-Cas systems, and functional adaptation related to virulence and resistance. These traits may underlie its ability to colonize diverse environments and acquire pathogenicity and resistance.\n\nComparative genomics reveals the genetic diversity and plasticity of Clostridium tertium.", "token_count": 427, "char_count": 1751, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7018, "quality_score": 0.8509, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:46.595684", "source": { "split": "train_shard_00001", "doc_id": 1385 }, "chunk_id": "train_shard_00001_1385_0", "global_id": 7602 }, { "text": "

Background

Antifungal resistance is an expanding and increasingly significant issue representing a global threat for public health. In the last few years, different cases of dermatophytosis infections due to terbinafine-resistant Trichophyton mentagrophytes have been reported worldwide. In particular, T. mentagrophytes genotype VIII, proposed as T. indotineae, represents an emerging pathogen showing increasing spread worldwide that exhibits reduced susceptibility to different antifungal agents.

Objectives

Here, we characterise the genome of a T. indotineae clinical strain (named PG11NEG-TBRES) resistant to terbinafine and fluconazole isolated in the northern part of Italy.

Methods

Whole genome sequencing was performed with the Illumina MiSeq and Oxford Nanopore MinION systems, and hybrid genome assembly was executed with Unicycler. Phylogenomic and copy number analyses were performed by core genome SNPs analysis and coverage depth of mapping reads.

Results

PG11NEG-TBRES belonged to the T. mentagrophytes genotype VIII (known as T. indotineae) and analysis of SQLE gene showed that the PG11NEG-TBRES strain harboured Leu393Ser. Phylogenomic analysis revealed that PG11NEG-TBRES was clonally related to fluconazole-resistant strains; deep genomic analysis showed the presence of different mutations within ERG4, MDR1 and MFS genes involved in ergosterol biosynthesis and the presence of five copies of tinCYP51b in comparison to susceptible isolates.

Conclusions

Our work highlights the importance of genomic characterisation to define the mechanism related to antifungal resistance and to monitor the spread of emerging dermatophytosis infections.\n\nClinical Characteristics and Genomic Analysis of a Trichophyton indotineae Strain Resistant to Terbinafine and Fluconazole Isolated in Italy.", "token_count": 504, "char_count": 1851, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6034, "quality_score": 0.8017, "entities": { "genes": [ "MDR1", "ERG4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:47.251795", "source": { "split": "train_shard_00001", "doc_id": 1386 }, "chunk_id": "train_shard_00001_1386_0", "global_id": 7603 }, { "text": "

Background

The use of thermotolerant yeast strains can improve the efficiency of ethanol fermentation, allowing fermentation to occur at temperatures higher than 40 °C. This characteristic could benefit traditional bio-ethanol production and allow simultaneous saccharification and fermentation (SSF) of starch or lignocellulosic biomass.

Results

We identified and characterized the physiology of a new thermotolerant strain (LBGA-01) able to ferment at 40 °C, which is more resistant to stressors as sucrose, furfural and ethanol than CAT-1 industrial strain. Furthermore, this strain showed similar CAT-1 resistance to acetic acid and lactic acid, and it was also able to change the pattern of genes involved in sucrose assimilation (SUC2 and AGT1). Genes related to the production of proteins involved in secondary products of fermentation were also differentially regulated at 40 °C, with reduced expression of genes involved in the formation of glycerol (GPD2), acetate (ALD6 and ALD4), and acetyl-coenzyme A synthetase 2 (ACS2). Fermentation tests using chemostats showed that LBGA-01 had an excellent performance in ethanol production in high temperature.

Conclusion

The thermotolerant LBGA-01 strain modulates the production of key genes, changing metabolic pathways during high-temperature fermentation, and increasing its resistance to high concentration of ethanol, sugar, lactic acid, acetic acid, and furfural. Results indicate that this strain can be used to improve first- and second-generation ethanol production in Brazil.\n\nPhysiological characterization of a new thermotolerant yeast strain isolated during Brazilian ethanol production, and its application in high-temperature fermentation.", "token_count": 486, "char_count": 1772, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [ "AGT1", "ACS2", "SUC2", "ALD4", "GPD2", "ALD6" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:47.901961", "source": { "split": "train_shard_00001", "doc_id": 1387 }, "chunk_id": "train_shard_00001_1387_0", "global_id": 7604 }, { "text": "Diversity within lower taxonomic units in microbial communities is a key trait, giving rise to important ecological functions. In the rhizosphere, these functions include disease suppression and pathogen inhibition. However, limited effort has been given to exploring intragenus microdiversity in an increasingly homogenous agricultural system. Through an integrative approach combining culture-dependent and -independent methods, we explore the rhizosphere Pseudomonas pangenome and demonstrate cultivar-dependent taxonomic and functional microdiversity between two closely related modern winter wheat cultivars. A Fusarium- resistant cultivar demonstrated increased Pseudomonas taxonomic diversity but not biosynthetic diversity when compared to the susceptible cultivar, coinciding with a thinner root diameter of the resistant cultivar. We found enrichment of Pseudomonas isolates capable of antagonizing Fusarium as well as chitinase-encoding genes and pyoverdine gene clusters in the resistant cultivar. Across closely related Pseudomonas isolates from the two cultures, there were differences in genomic content and biosynthetic gene clusters. Ultimately, we highlight the need for fine-scale analysis to uncover the hidden microdiversity within rhizosphere Pseudomonas .\n\nPseudomonastaxonomic and functional microdiversity in the wheat rhizosphere is cultivar- dependent and links to disease resistance profile and root diameter", "token_count": 329, "char_count": 1443, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6612, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:48.467487", "source": { "split": "train_shard_00001", "doc_id": 1388 }, "chunk_id": "train_shard_00001_1388_0", "global_id": 7605 }, { "text": "

Background

Aldo-keto reductases-catalyzed transformations of ketones to chiral alcohols have become an established biocatalytic process step in the pharmaceutical industry. Previously, we have discovered an aldo-keto reductase (AKR) from Kluyveromyces marxianus that is active to the aliphatic tert-butyl 6-substituted (5R/S)-hydroxy-3-oxohexanoates, but it is inactive to aromatic ketones. In order to acquire an excellent KmAKRmutant for ensuring the simultaneous improvement of activity-thermostability toward tert-butyl 6-cyano-(5R)-hydroxy-3-oxohexanoate ((5R)-1) and broadening the universal application prospects toward more substrates covering both aliphatic and aromatic ketones, a fluorescence-based high-throughput (HT) screening technique was established.

Main methods and major results

The directed evolution of KmAKR variant M5 (KmAKR-W297H/Y296W/K29H/Y28A/T63M) produced the \"best\" variant M5-Q213A/T23V. It exhibited enhanced activity-thermostability toward (5R)-1, improved activity toward all 18 test substrates and strict R-stereoselectivity toward 10 substrates in comparison to M5. The enhancement of enzymatic activity and the extension of substrate scope covering aromatic ketones are proposed to be largely attributed to pushing the binding pocket of M5-Q213A/T23V to the enzyme surface, decreasing the steric hindrance at the entrance and enhancing the flexibility of loops surrounding the active center", "token_count": 425, "char_count": 1443, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6954, "quality_score": 0.8477, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:49.093695", "source": { "split": "train_shard_00001", "doc_id": 1389 }, "chunk_id": "train_shard_00001_1389_0", "global_id": 7606 }, { "text": "In addition, combined with 0.94 g dry cell weight (DCW) L-1 glucose dehydrogenase from Exiguobacterium sibiricum (EsGDH) for NADPH regeneration, 2.81 g DCW L-1 M5-Q213A/T23V completely converted (5R)-1 of up to 450 g L-1 at 120 g g-1 substrates/catalysts (S/C), yielding the corresponding optically pure tert-butyl 6-cyano-(3R,5R)-dihydroxyhexanoate ((3R,5R)-2, > 99.5% d.e.p ) with a space-time yield (STY) of 1.08 kg L-1 day-1 .

Conclusions

A fluorescence-based HT screening system was developed to tailor KmAKR's activity, thermostability and substrate scope. The \"best\" variant M5-Q213A/T23V holds great potential application for the synthesis of aliphatic/aromatic R-configuration alcohols.\n\nFluorescence-based screening for engineered aldo-keto reductase KmAKR with improved catalytic performance and extended substrate scope.", "token_count": 357, "char_count": 916, "word_count": 107, "semantic_coherence": 1, "information_density": 0.8037, "quality_score": 0.9019, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:49.662939", "source": { "split": "train_shard_00001", "doc_id": 1389 }, "chunk_id": "train_shard_00001_1389_1", "global_id": 7607 }, { "text": "

Background

The yeast Kluyveromyces marxianus features specific traits that render it attractive for industrial applications. These include production of ethanol which, together with thermotolerance and the ability to grow with a high specific growth rate on a wide range of substrates, could make it an alternative to Saccharomyces cerevisiae as an ethanol producer. However, its ability to co-ferment C5 and C6 sugars under oxygen-limited conditions is far from being fully characterized.

Results

In the present study, K. marxianus CBS712 strain was cultivated in defined medium with glucose and xylose as carbon source. Ethanol fermentation and sugar consumption of CBS712 were investigated under different oxygen supplies (1.75%, 11.00% and 20.95% of O2) and different temperatures (30°C and 41°C). By decreasing oxygen supply, independently from the temperature, both biomass production as well as sugar utilization rate were progressively reduced. In all the tested conditions xylose consumption followed glucose exhaustion. Therefore, xylose metabolism was mainly affected by oxygen depletion. Loss in cell viability cannot explain the decrease in sugar consumption rates, as demonstrated by single cell analyses, while cofactor imbalance is commonly considered as the main cause of impairment of the xylose reductase (KmXR) - xylitol dehydrogenase (KmXDH) pathway. Remarkably, when these enzyme activities were assayed in vitro, a significant decrease was observed together with oxygen depletion, not ascribed to reduced transcription of the corresponding genes.

Conclusions

In the present study both oxygen supply and temperature were shown to be key parameters affecting the fermentation capability of sugars in the K. marxianus CBS712 strain. In particular, a direct correlation was observed between the decreased efficiency to consume xylose with the reduced specific activity of the two main enzymes (KmXR and KmXDH) involved in its catabolism", "token_count": 483, "char_count": 1977, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8105, "entities": { "genes": [ "CBS712" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:50.312185", "source": { "split": "train_shard_00001", "doc_id": 1390 }, "chunk_id": "train_shard_00001_1390_0", "global_id": 7608 }, { "text": "These data suggest that, in addition to the impairment of the oxidoreductive pathway being determined by the cofactor imbalance, post-transcriptional and/or post-translational regulation of the pathway enzymes contributes to the efficiency of xylose catabolism in micro-aerobic conditions. Overall, the presented work provides novel information on the fermentation capability of the CBS712 strain that is currently considered as the reference strain of the genus K. marxianus.\n\nEffect of oxygenation and temperature on glucose-xylose fermentation in Kluyveromyces marxianus CBS712 strain.", "token_count": 145, "char_count": 588, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7179, "quality_score": 0.859, "entities": { "genes": [ "CBS712" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:50.740847", "source": { "split": "train_shard_00001", "doc_id": 1390 }, "chunk_id": "train_shard_00001_1390_1", "global_id": 7609 }, { "text": "Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli are resistant to the critically important third- and fourth-generation cephalosporin antibiotics and present a risk to animal and human health. In Zimbabwe, there is an evidence gap concerning the prevalence and diversity of ESBL-producing E. coli in poultry. In this study, we screened for ESBL-E. coli at farms (n=50) and markets (n=10) using MacConkey agar supplemented with 4 µg ml-1 ceftriaxone. ESBL-E. coli were detected at every market and at 21 farms, giving a farm-level prevalence of 42%. Seventy isolates were obtained and tested for antimicrobial susceptibility, whilst 69 of these were further analysed by whole-genome sequencing. A total of eight distinct bla CTX-M variants were identified, and 69 out of 70 isolates were multidrug-resistant. Genomic analysis revealed evidence for clonal expansion of an ESBL-producing clone and horizontal gene transfer via plasmids being responsible for the dissemination of ESBL-E. coli. Geographic Information System mapping was used to visualize the distribution of the ESBL-producing clones. For example, ST1141 isolates were clonal, having a highly conserved core genome, and harboured bla CTX-M-15 and 11 additional antimicrobial resistance genes on a ~338 kbp IncHI2 plasmid which was not present in other isolates. This clone was present at nine farms. In contrast, a conserved ~93 kbp IncFII plasmid harbouring bla CTX-M-55 was present in isolates from three different multilocus sequence types obtained from six farms", "token_count": 512, "char_count": 1660, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6637, "quality_score": 0.8319, "entities": { "genes": [ "ST1141" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:51.374760", "source": { "split": "train_shard_00001", "doc_id": 1391 }, "chunk_id": "train_shard_00001_1391_0", "global_id": 7610 }, { "text": "This study provides insight into the burden and distribution of ESBL-E. coli at poultry farms in Zimbabwe and provides molecular genetic evidence for clonal expansion and plasmid transfer as being important mechanisms for the dissemination of ESBL-E. coli in this setting. This study underscores the importance of adopting measures, such as prudent antimicrobial use and farm biosecurity, that can limit the development and dissemination of ESBL-producing E. coli.\n\nDissemination of extended-spectrum beta-lactamase-producing <i>Escherichia coli</i> in poultry in Zimbabwe.", "token_count": 180, "char_count": 606, "word_count": 78, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:51.819252", "source": { "split": "train_shard_00001", "doc_id": 1391 }, "chunk_id": "train_shard_00001_1391_1", "global_id": 7611 }, { "text": "

Background

The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures.

Results

Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ∼60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable elements content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species.

Conclusions

Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.\n\nA 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici", "token_count": 458, "char_count": 1985, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:52.451832", "source": { "split": "train_shard_00001", "doc_id": 1392 }, "chunk_id": "train_shard_00001_1392_0", "global_id": 7612 }, { "text": "

Background

Non-O1 and non-O139 Vibrio cholerae (NOVC) that cause bacteraemia have attracted the attention of the public health community around the world, mainly due to the prospect of outbreaks and the way to treat such infections.

Objectives

To identify V. cholerae lineages and their antibiotic resistance and virulence factors associated with bacteraemia.

Methods

Vibrio cholerae genomes associated with strains isolated from blood were retrieved and subjected to core genome-based phylogenomic analysis with Roary. The virulome and resistome were searched with abricate using the VFDB and CARD databases.

Findings

Analysis showed that, in addition to V. cholerae, Vibrio paracholerae also causes bacteraemia. The NOVC group was highly diverse, although genomes from different countries were related. Most bacteraemic Vibrios came from countries not affected by epidemic/endemic cholera. The NOVCs virulome presented factors, such as type III and VI secretion systems, HapA, HlyA, RTX, and TLH. Importantly, no resistance to third-generation cephalosporin has been identified in the resistome of NOVCs.

Main conclusions

The presence of multiple NOVC lineages that cause bacteraemia in different parts of the world shows that there is no geographic and socioeconomic restriction for these cases. Therefore, healthcare systems need to be aware of this uncommon but deadly Vibrio infection.\n\nVibrio cholerae and Vibrio paracholerae bacteraemia strains encompass lineages that share resistome and virulome profiles.", "token_count": 423, "char_count": 1551, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:53.079982", "source": { "split": "train_shard_00001", "doc_id": 1393 }, "chunk_id": "train_shard_00001_1393_0", "global_id": 7613 }, { "text": "We propose a polynomial algorithm computing a minimum plain-text representation of k-mer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a minor runtime increase, we shrink the representation by up to 59% over unitigs and 26% over previous work. Additionally, the number of strings is decreased by up to 97% over unitigs and 90% over previous work. Finally, a small representation has advantages in downstream applications, as it speeds up SSHash-Lite queries by up to 4.26× over unitigs and 2.10× over previous work.\n\nMatchtigs: minimum plain text representation of k-mer sets.", "token_count": 171, "char_count": 678, "word_count": 105, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:53.522055", "source": { "split": "train_shard_00001", "doc_id": 1394 }, "chunk_id": "train_shard_00001_1394_0", "global_id": 7614 }, { "text": "Three actinobacterial strains, designated as KSW-48, KSWW-56 and SSW1-59 T, were isolated from seawater, rock-attached living and dried seaweeds collected at Gwakji Beach in Jeju, Republic of Korea. All the isolates showed growth at 15-42 °C and pH 5-10, and tolerated NaCl for growth up to 10%. The 16S rRNA gene-based phylogeny showed that the novel strains were closely related with the type strains of Microbacterium aquimaris and Microbacterium luteum, with the 16S rRNA gene sequence similarity of 99.93-100% (0-1 nt differences) with one another and of 99.86-99.93% (1-2 nt differences) with Microbacterium aquimaris KCTC 19124 T, followed by (98.98-99.04%; 14-15 nt differences) with Microbacterium luteum A18JL200T. The core genome-based phylogenomic tree reflected the tree topologies of the 16S rRNA gene-based phylogeny. The chemotaxonomic features were in agreement with the classification in the genus Microbacterium as follow. The cell wall diamino acid and the whole-cell sugars were ornithine. The muramic acid of the cell-wall peptidoglycan was of the N-glycolyl form. The predominant menaquinones were MK-10, MK-11 and MK-12. The polar lipids in common consisted of phosphatidylglycerol and an unidentified glycolipid. The presence of diphosphatidylglycerol and an additional unidentified glycolipid were variable depending on isolated strains", "token_count": 470, "char_count": 1395, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6205, "quality_score": 0.8103, "entities": { "genes": [ "SSW1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:54.164777", "source": { "split": "train_shard_00001", "doc_id": 1395 }, "chunk_id": "train_shard_00001_1395_0", "global_id": 7615 }, { "text": "The major fatty acids were anteiso-C15:0, anteiso-C17:0 and iso-C16:0. Average nucleotide identity and digital DNA-DNA hybridisation values showed that strain KSW-48 and SSW1-59 T represented a new species of the genus Microbacterium, while KSWW-56 was a strain of Microbacterium aquimaris. Based on the results obtained here, Microbacterium xanthum sp. nov. (type strain, SSW1-59 T = KCTC 49622 T = KACC 23361 T = DSM 116382 T = MCCC 1K08947T) are proposed. Also, it is proposed that Microbacterium ihumii Yacouba et al. 2023 be reclassified as a later heterotypic synonym of Microbacterium tenebrionis Lee and Kim 2023 by high genomic similarity.\n\nMicrobacterium xanthum sp. nov. Isolated from Seaweed, with the Reclassification of Microbacterium ihumii Yacouba et al. 2023 as a Later Heterotypic Synonym of Microbacterium tenebrionis Lee and Kim 2023.", "token_count": 392, "char_count": 953, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [ "SSW1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:54.798476", "source": { "split": "train_shard_00001", "doc_id": 1395 }, "chunk_id": "train_shard_00001_1395_1", "global_id": 7616 }, { "text": "Genome sequence study of an industrially-important strain, Bacillus subtilis M9, a mutant version of wild strain Bacillus subtilis MZK05 was conducted to uncover genetic factors responsible for enhanced serine proteases expression in addition to its other industrial enzymes, metabolites and bacteriocins producing efficacy. The wild type and the mutant genome contained a size of 4,145,727 and 4,045,950 bp, with 4,352 and 4,383 genes; and 477 and 478 subsystems respectively. Genomic comparison with 31 B. subtilis sourced from different countries showed both wild and mutant shared same type of genome structure with 20 others. Moreover, 6,000 kb pangenome showed that they share 3082, 1449, and 25757 core, unique and accessory genes respectively. A sum of 32,559 mutations were found with three major genomic structural changes in the upstream and downstream of an extracellular alkaline serine protease, AprX and a periplasmic serine protease, HtrC in M9 genome when compared to the wild type. Furthermore, 11 different serine protease genes and 4 different signal peptidases were found with several mutational changes in M9. In addition, mutations found in core genome of BsM9 in phage-like element, major capsid protein, and phage portal protein are the likely reasons of high-level serine protease activity.\n\nComparative Genomics of Bacillus Subtilis MZK05 and Its Mutant Strain Revealed Genetic Factors Responsible for Enhanced Serine Protease Expression", "token_count": 422, "char_count": 1464, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6037, "quality_score": 0.8018, "entities": { "genes": [ "MZK05" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:55.442401", "source": { "split": "train_shard_00001", "doc_id": 1396 }, "chunk_id": "train_shard_00001_1396_0", "global_id": 7617 }, { "text": "

Background

Spathaspora passalidarum is a yeast with the highly effective capability of fermenting several monosaccharides in lignocellulosic hydrolysates, especially xylose. However, this yeast was shown to be sensitive to furfural released during pretreatment and hydrolysis processes of lignocellulose biomass. We aimed to improve furfural tolerance in a previously isolated S. passalidarum CMUWF1-2, which presented thermotolerance and no detectable glucose repression, via adaptive laboratory evolution (ALE).

Results

An adapted strain, AF2.5, was obtained from 17 sequential transfers of CMUWF1-2 in YPD broth with gradually increasing furfural concentration. Strain AF2.5 could tolerate higher concentrations of furfural, ethanol and 5-hydroxymethyl furfuraldehyde (HMF) compared with CMUWF1-2 while maintaining the ability to utilize glucose and other sugars simultaneously. Notably, the lag phase of AF2.5 was 2 times shorter than that of CMUWF1-2 in the presence of 2.0 g/l furfural, which allowed the highest ethanol titers to be reached in a shorter period. To investigate more in-depth effects of furfural, intracellular reactive oxygen species (ROS) accumulation was observed and, in the presence of 2.0 g/l furfural, AF2.5 exhibited 3.41 times less ROS accumulation than CMUWF1-2 consistent with the result from nuclear chromatins diffusion, which the cells number of AF2.5 with diffuse chromatins was also 1.41 and 1.24 times less than CMUWF1-2 at 24 and 36 h, respectively.

Conclusions

An enhanced furfural tolerant strain of S. passalidarum was achieved via ALE techniques, which shows faster and higher ethanol productivity than that of the wild type. Not only furfural tolerance but also ethanol and HMF tolerances were improved.", "token_count": 508, "char_count": 1770, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [ "AF2", "CMUWF1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:56.149171", "source": { "split": "train_shard_00001", "doc_id": 1397 }, "chunk_id": "train_shard_00001_1397_0", "global_id": 7618 }, { "text": "Improving furfural tolerance in a xylose-fermenting yeast Spathaspora passalidarum CMUWF1-2 via adaptive laboratory evolution.", "token_count": 39, "char_count": 126, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "CMUWF1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:56.519584", "source": { "split": "train_shard_00001", "doc_id": 1397 }, "chunk_id": "train_shard_00001_1397_1", "global_id": 7619 }, { "text": "Streptococcus agalactiae (group B Streptococcus [GBS]) causes disease in a wide range of animals. The serotype Ib lineage is highly adapted to aquatic hosts, exhibiting substantial genome reduction compared with terrestrial conspecifics. Here, we sequence genomes from 40 GBS isolates, including 25 isolates from wild fish and captive stingrays in Australia, six local veterinary or human clinical isolates, and nine isolates from farmed tilapia in Honduras, and compared them with 42 genomes from public databases. Phylogenetic analysis based on nonrecombinant core-genome single nucleotide polymorphisms (SNPs) indicated that aquatic serotype Ib isolates from Queensland were distantly related to local veterinary and human clinical isolates. In contrast, Australian aquatic isolates are most closely related to a tilapia isolate from Israel, differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on core-genome SNPs indicates the dissemination of sequence type 261 (ST-261) from an ancestral tilapia strain, which is congruent with several introductions of tilapia into Australia from Israel during the 1970s and 1980s. Pangenome analysis identified 1,440 genes as core, with the majority being dispensable or strain specific, with non-protein-coding intergenic regions (IGRs) divided among core and strain-specific genes. Aquatic serotype Ib strains have lost many virulence factors during adaptation, but six adhesins were well conserved across the aquatic isolates and might be critical for virulence in fish and for targets in vaccine development", "token_count": 416, "char_count": 1592, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:57.142937", "source": { "split": "train_shard_00001", "doc_id": 1398 }, "chunk_id": "train_shard_00001_1398_0", "global_id": 7620 }, { "text": "The close relationship among recent ST-261 isolates from Ghana, the United States, and China with the Israeli tilapia isolate from 1988 implicates the global trade in tilapia seed for aquaculture in the widespread dissemination of serotype Ib fish-adapted GBS.IMPORTANCEStreptococcus agalactiae (GBS) is a significant pathogen of humans and animals. Some lineages have become adapted to particular hosts, and serotype Ib is highly specialized to fish. Here, we show that this lineage is likely to have been distributed widely by the global trade in tilapia for aquaculture, with probable introduction into Australia in the 1970s and subsequent dissemination in wild fish populations. We report here the variability in the polysaccharide capsule among this lineage but identify a cohort of common surface proteins that may be a focus of future vaccine development to reduce the biosecurity risk in international fish trade.\n\nMicroevolution of Streptococcus agalactiae ST-261 from Australia Indicates Dissemination via Imported Tilapia and Ongoing Adaptation to Marine Hosts or Environment.", "token_count": 282, "char_count": 1102, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:57.692376", "source": { "split": "train_shard_00001", "doc_id": 1398 }, "chunk_id": "train_shard_00001_1398_1", "global_id": 7621 }, { "text": "Limosilactobacillus fermentum CRL2085, isolated from feedlot cattle rations, displayed high efficiency as a probiotic when administered to animals. A comprehensive genomic analysis was performed to elucidate the genetic basis underlying its probiotic potential. Fifteen genomic islands and CRISPR-Cas elements were identified in its genome. Pan-genomic analysis highlighted the dynamic evolution of this species, and clustering based on the nucleotide genomic similarity only partially correlated with the source of isolation or the geographic origin of the strains. Several genes known to confer probiotic properties were identified, including those related to adhesion, resistance to acidic pH and bile salts, tolerance to oxidative stress, metabolism/transport of sugars and other compounds, and genes for exopolysaccharide biosynthesis. In silico analysis of antimicrobial resistance genes and virulence determinants confirmed the safety of this strain. Moreover, genes related to B-group vitamins biosynthesis and feruloyl esterase hydrolase were also found, showing the nutritional contribution of the strain, which also showed moderate adhesion capability, exopolysaccharide production when grown with sucrose, and the capacity to metabolise 42 out of 95 carbon substrates tested. This data provides the genetic basis for deciphering the mechanisms beyond the benefits demonstrated by its use during cattle intensive raising and confirms its promising role as a probiotic.\n\nGenomic Characterisation of Limosilactobacillus fermentum CRL2085 Unveiling Probiotic Traits for Application in Cattle Feed.", "token_count": 380, "char_count": 1605, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "CRL2085" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:58.269847", "source": { "split": "train_shard_00001", "doc_id": 1399 }, "chunk_id": "train_shard_00001_1399_0", "global_id": 7622 }, { "text": "1 Long-read sequencing (LRS) enables variant calling of high-quality structural variants (SVs). Genotypers of SVs utilize these precise call sets to increase the recall and precision of genotyping in short-read sequencing (SRS) samples. With the extensive growth in availabilty of SRS datasets in recent years, we should be able to calculate accurate population allele frequencies of SV. However, reprocessing hundreds of terabytes of raw SRS data to genotype new variants is impractical for population-scale studies, a computational challenge known as the N+1 problem. Solving this computational bottleneck is necessary to analyze new SVs from the growing number of pangenomes in many species, public genomic databases, and pathogenic variant discovery studies. To address the N+1 problem, we propose The Great Genotyper, a population genotyping workflow. Applied to a human dataset, the workflow begins by preprocessing 4.2K short-read samples of a total of 183TB raw data to create an 867GB Counting Colored De Bruijn Graph (CCDG). The Great Genotyper uses this CCDG to genotype a list of phased or unphased variants, leveraging the CCDG population information to increase both precision and recall. The Great Genotyper offers the same accuracy as the state-of-the-art genotypers with the addition of unprecedented performance. It took 100 hours to genotype 4.5M variants in the 4.2K samples using one server with 32 cores and 145GB of memory. A similar task would take months or even years using single-sample genotypers. The Great Genotyper opens the door to new ways to study SVs. We demonstrate its application in finding pathogenic variants by calculating accurate allele frequency for novel SVs. Also, a premade index is used to create a 4K reference panel by genotyping variants from the Human Pangenome Reference Consortium (HPRC). The new reference panel allows for SV imputation from genotyping microarrays. Moreover, we genotype the GWAS catalog and merge its variants with the 4K reference panel", "token_count": 509, "char_count": 2010, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:58.935759", "source": { "split": "train_shard_00001", "doc_id": 1400 }, "chunk_id": "train_shard_00001_1400_0", "global_id": 7623 }, { "text": "We show 6.2K events of high linkage between the HPRC’s SVs and nearby GWAS SNPs, which can help in interpreting the effect of these SVs on gene functions. This analysis uncovers the detailed haplotype structure of the human fibrinogen locus and revives the pathogenic association of a 28 bp insertion in the FGA gene with thromboembolic disorders.\n\nThe Great Genotyper: A Graph-Based Method for Population Genotyping of Small and Structural Variants", "token_count": 126, "char_count": 449, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7746, "quality_score": 0.8873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:09:59.327094", "source": { "split": "train_shard_00001", "doc_id": 1400 }, "chunk_id": "train_shard_00001_1400_1", "global_id": 7624 }, { "text": "The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by horizontal gene transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes potentially relevant for environmental interactions and adaptation to extremophilic conditions. Altogether, our results support scenarios that conciliate \"Neutral\" and \"Constant Diversity\" models of bacterial evolution.\n\nGenome Variation in the Model Halophilic Bacterium Salinibacter ruber.", "token_count": 359, "char_count": 1595, "word_count": 218, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:00.264315", "source": { "split": "train_shard_00001", "doc_id": 1401 }, "chunk_id": "train_shard_00001_1401_0", "global_id": 7625 }, { "text": "Agave tequilana fructans (ATF) constitute a substrate for bioethanol and tequila industries. As Kluyveromyces marxianus produces specific fructanases for ATF hydrolysis, as well as ethanol, it can perform simultaneous saccharification and fermentation. In this work, fifteen K. marxianus yeasts were evaluated to develop inoculums with fructanase activity on ATF. These inoculums were added to an ATF medium for simultaneous saccharification and fermentation. All the yeasts, showed exo-fructanhydrolase activity with different substrate specificities. The yeast with highest fructanase activity in the inoculums showed the lowest ethanol production level (20 g/l). Five K. marxianus strains were the most suitable for the simultaneous saccharification and fermentation of ATF. The volatile compounds composition was evaluated at the end of fermentation, and a high diversity was observed between yeasts, nevertheless all of them produced high levels of isobutyl alcohol. The simultaneous saccharification and fermentation of ATF with K. marxianus strains has potential for industrial application.\n\nSimultaneous saccharification and fermentation of Agave tequilana fructans by Kluyveromyces marxianus yeasts for bioethanol and tequila production.", "token_count": 321, "char_count": 1246, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5509, "quality_score": 0.7754, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:00.829107", "source": { "split": "train_shard_00001", "doc_id": 1402 }, "chunk_id": "train_shard_00001_1402_0", "global_id": 7626 }, { "text": "The emergence of Clostridium difficile as a significant human diarrheal pathogen is associated with the production of highly transmissible spores and the acquisition of antimicrobial resistance genes (ARGs) and virulence factors. Unlike the hospital-associated C. difficile RT027 lineage, the community-associated C. difficile RT078 lineage is isolated from both humans and farm animals; however, the geographical population structure and transmission networks remain unknown. Here, we applied whole-genome phylogenetic analysis of 248 C. difficile RT078 strains from 22 countries. Our results demonstrate limited geographical clustering for C. difficile RT078 and extensive coclustering of human and animal strains, thereby revealing a highly linked intercontinental transmission network between humans and animals. Comparative whole-genome analysis reveals indistinguishable accessory genomes between human and animal strains and a variety of antimicrobial resistance genes in the pangenome of C. difficile RT078. Thus, bidirectional spread of C. difficile RT078 between farm animals and humans may represent an unappreciated route disseminating antimicrobial resistance genes between humans and animals. These results highlight the importance of the \"One Health\" concept to monitor infectious disease emergence and the dissemination of antimicrobial resistance genes.\n\nZoonotic Transfer of Clostridium difficile Harboring Antimicrobial Resistance between Farm Animals and Humans.", "token_count": 393, "char_count": 1531, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5803, "quality_score": 0.7902, "entities": { "genes": [ "RT078", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:01.448897", "source": { "split": "train_shard_00001", "doc_id": 1403 }, "chunk_id": "train_shard_00001_1403_0", "global_id": 7627 }, { "text": "The gene Bcin04g03490 has been shown to control development and pathogenicity in the plant necrotroph Botrytis cinerea. We have identified the orthologous gene in two formae speciales of the Fusarium oxysporum species complex; it maps to chromosome 7 in the core genome of the lycopersici forma specialis. It encodes a protein with two distinct domains, a GAL4-like Zn(II)2Cys6 binuclear cluster DNA-binding domain and an acetyltransferase domain, as previously shown in B. cinerea. Null mutants were generated in both formae speciales (phaseoli and lycopersici), and the phenotypes exhibited during in culture growth and plant colonization were analyzed. The results obtained demonstrate that this virulence factor is required for complete colonization of the plant host stem vascular tissue and full virulence in F. oxysporum but not for the initial stages of root colonization. In addition, null mutants showed a severe alteration in the formation of aerial mycelia and a drastic reduction of sporulation. These observations are consistent with a master role of FoG4MAT in the gene regulation of different processes crucial for normal development and full disease induction in the plant host.\n\nFoG4MAT Is a New Virulence Factor in <i>Fusarium oxysporum</i> also Involved in Growth, Differentiation, and Sporulation.", "token_count": 398, "char_count": 1400, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": { "genes": [ "GAL4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:02.073557", "source": { "split": "train_shard_00001", "doc_id": 1404 }, "chunk_id": "train_shard_00001_1404_0", "global_id": 7628 }, { "text": "Essential genes in bacterial pathogens are potential drug targets and vaccine candidates because disrupting their function is lethal. The development of new antibiotics, in addition to effective prevention measures such as vaccination, contributes to addressing the global problem of bacterial antibiotic resistance. The aim of this present study was to determine the essential genes of Vibrio anguillarum, a bacterial pathogen of aquatic animals, as a means to identify putative targets for novel drugs and to assist the prioritisation of potential vaccine candidates. Essential genes were characterised by a Tn-seq approach using the TnSC189 mariner transposon to construct a library of 52,662 insertion mutants. In total, 329 essential genes were identified, with 34.7% found within the core genome of this species; each of these genes represents a strong potential drug target. Seven essential gene products were predicted to reside in the cell membrane or be released extracellularly, thus serving as putative vaccine candidates. Comparison to essential gene data from five other studies of Vibrio species revealed 13 proteins to be conserved across the studies, while 25 genes were specific to V. anguillarum and not found to be essential in the other Vibrio spp. This study provides new information on the essential genes of Vibrio species and the methodology may be applied to other pathogens to guide the development of new drugs and vaccines, which will assist efforts to counter antibiotic resistance.\n\nEssential Genes of Vibrio anguillarum and Other Vibrio spp. Guide the Development of New Drugs and Vaccines.", "token_count": 412, "char_count": 1671, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5425, "quality_score": 0.7713, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:02.698561", "source": { "split": "train_shard_00001", "doc_id": 1405 }, "chunk_id": "train_shard_00001_1405_0", "global_id": 7629 }, { "text": "The pentose phosphate pathway (PPP) is essential for human health and provides, amongst others, the reduction power to cope with oxidative stress. In contrast to the model baker's yeast, the PPP also contributes to a large extent to glucose metabolism in the milk yeast Kluyveromyces lactis. Yet, the physiological consequences of mutations in genes encoding PPP enzymes in K. lactis have been addressed for only a few. We here embarked on a systematic study of such mutants, deleting ZWF1, SOL4, GND1, RKI1, RPE1, TKL1, TAL1, and SHB17. Interestingly, GND1, RKI1, and TKL1 were found to be essential under standard growth conditions. Epistasis analyses revealed that a lack of Zwf1 rescued the lethality of the gnd1 deletion, indicating that it is caused by the accumulation of 6-phosphogluconate. Moreover, the slow growth of a tal1 null mutant, which lacks fructose-1,6-bisphosphate aldolase, was aggravated by deleting the SHB17 gene encoding sedoheptulose-1,7-bisphosphatase. A mitotically stable tetOFF system was established for conditional expression of TAL1 and TKL1, encoding transaldolase and transketolase in the non-oxidative part of the PPP, and employed in a global proteome analysis upon depletion of the enzymes. Results indicate that fatty acid degradation is upregulated, providing an alternative energy source", "token_count": 486, "char_count": 1462, "word_count": 198, "semantic_coherence": 1, "information_density": 0.702, "quality_score": 0.851, "entities": { "genes": [ "TKL1", "GND1", "RPE1", "ZWF1", "RKI1", "TAL1", "SOL4", "SHB17" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:03.349215", "source": { "split": "train_shard_00001", "doc_id": 1406 }, "chunk_id": "train_shard_00001_1406_0", "global_id": 7630 }, { "text": "In addition, tal1 and tkl1 null mutants were complemented by heterologous expression of the respective genes from baker's yeast and humans. These data demonstrate the importance of the PPP for basic sugar metabolism and oxidative stress response in K. lactis and the potential of this yeast as a model for the study of PPP enzymes from heterologous sources, including human patients.\n\nGenetic and Physiological Characterization of the Pentose Phosphate Pathway in the Yeast <i>Kluyveromyces lactis</i>.", "token_count": 155, "char_count": 535, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:03.787099", "source": { "split": "train_shard_00001", "doc_id": 1406 }, "chunk_id": "train_shard_00001_1406_1", "global_id": 7631 }, { "text": "Recent studies have shown that Escherichia coli can survive in different environments, including soils, and they can maintain populations in sterile soil for a long period of time. This indicates that growth-supporting nutrients are available; however, when grown in non-sterile soils, populations decline, suggesting that other biological factors play a role in controlling E. coli populations in soil. Free-living protozoa can affect the bacterial population by grazing. We hypothesized that E. coli strains capable of surviving in non-sterile soil possess mechanisms to protect themselves from amoeba predation. We determined the grazing rate of E. coli pasture isolates by using Dictyostelium discoideum. Bacterial suspensions applied to lactose agar as lines were allowed to grow for 24 h, when 4 μL of D. discoideum culture was inoculated in the center of each bacterial line. Grazing distances were measured after 4 days. The genomes of five grazing-susceptible and five grazing-resistant isolates were sequenced and compared. Grazing distance varied among isolates, which indicated that some E. coli are more susceptible to grazing by protozoa than others. When presented with a choice between grazing-susceptible and grazing-resistant isolates, D. discoideum grazed only on the susceptible strain. Grazing susceptibility phenotype did not align with the phylogroup, with both B1 and E strains found in both grazing groups. They also did not align by core genome phylogeny. Whole genome comparisons revealed that the five most highly grazed strains had 389 shared genes not found in the five least grazed strains. Conversely, the five least grazed strains shared 130 unique genes. The results indicate that long-term persistence of E. coli in soil is due at least in part to resistance to grazing by soil amoeba.", "token_count": 500, "char_count": 1883, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:04.438637", "source": { "split": "train_shard_00001", "doc_id": 1407 }, "chunk_id": "train_shard_00001_1407_0", "global_id": 7632 }, { "text": "Escherichia coli Strains Display Varying Susceptibility to Grazing by the Soil Amoeba Dictyostelium discoideum.", "token_count": 48, "char_count": 125, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:04.802853", "source": { "split": "train_shard_00001", "doc_id": 1407 }, "chunk_id": "train_shard_00001_1407_1", "global_id": 7633 }, { "text": "

Background

The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures.

Results

Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species.

Conclusions

Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.\n\nA 19-isolate reference-quality global pangenome for the fungal wheat pathogen Zymoseptoria tritici.", "token_count": 453, "char_count": 1974, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6389, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:05.440271", "source": { "split": "train_shard_00001", "doc_id": 1408 }, "chunk_id": "train_shard_00001_1408_0", "global_id": 7634 }, { "text": "Improved understanding of the genetic basis of Campylobacter spp. colonization of poultry at specific growth stage is the key to developing a farm-based strategy to prevent flock colonization. In this study, 39 Campylobacter spp. strains (chicken isolates, n = 29; environmental isolates, n = 10) were collected from six marked chickens at the growth stage from week 7 to week 13. Then, we use comparative genomics techniques to analyze the temporal genomic characteristics of Campylobacter spp. in individual chickens across a production cycle. Genotype, average nucleotide identity (ANI), and phylogenetic trees all indicated the evolutionary relationships between the strains from different sampling weeks. The clustering of isolates was not dependent on sampling time and sample source, indicating that strains could persist over several weeks in a flock. Notably, 10 antimicrobial resistance (AMR) genes were identified in the genome of Campylobacter coli isolates, and the genomes of isolates sampled at week 11 harbored fewer AMR genes and insertion sequences (IS) than the isolates from other weeks. Consistent with this, pangenome-wide association analysis demonstrated that gene acquisition and loss could happen at week 11 and week 13. These genes were mainly associated with cell membrane biogenesis, ion metabolism, and DNA replication, suggesting that genomic change may be related to Campylobacter adaptive response. This is a novel study focused on the genetic changes occurring in Campylobacter spp. isolates in a particular space and time; it highlights that accessory genes and AMR genes were overall stable at chicken farm, which will help us understand the survival and the transmission route of Campylobacter spp. better, and have the potential to inform the strategy on the safety control of market-ready chickens.", "token_count": 489, "char_count": 1900, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:06.088950", "source": { "split": "train_shard_00001", "doc_id": 1409 }, "chunk_id": "train_shard_00001_1409_0", "global_id": 7635 }, { "text": "Genomic Insights into Pangenome and Antimicrobial Resistance in Campylobacter spp. Isolated from Chickens at Specific Growth Stages.", "token_count": 44, "char_count": 139, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:06.469055", "source": { "split": "train_shard_00001", "doc_id": 1409 }, "chunk_id": "train_shard_00001_1409_1", "global_id": 7636 }, { "text": "

Background

The development of clean or novel alternative energy has become a global trend that will shape the future of energy. In the present study, 3 microbial strains with different oxygen requirements, including Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, were used to construct a hydrogen production system that was composed of a mixed aerobic-facultative anaerobic-anaerobic consortium. The effects of metal ions, organic acids and carbohydrate substrates on this system were analyzed and compared using electrochemical and kinetic assays. It was then tested using small-scale experiments to evaluate its ability to convert starch in 5 L of organic wastewater into hydrogen. For the one-step biohydrogen production experiment, H1 medium (nutrient broth and potato dextrose broth) was mixed directly with GAM broth to generate H2 medium (H1 medium and GAM broth). Finally, Clostridium acetobutylicum ATCC 824, Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D of three species microbial co-culture to produce hydrogen under anaerobic conditions. For the two-step biohydrogen production experiment, the H1 medium, after cultured the microbial strains Enterobacter cloacae ATCC 13047 and Kluyveromyces marxianus 15D, was centrifuged to remove the microbial cells and then mixed with GAM broth (H2 medium)", "token_count": 397, "char_count": 1387, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:07.107578", "source": { "split": "train_shard_00001", "doc_id": 1410 }, "chunk_id": "train_shard_00001_1410_0", "global_id": 7637 }, { "text": "Afterward, the bacterial strain Clostridium acetobutylicum ATCC 824 was inoculated into the H2 medium to produce hydrogen by anaerobic fermentation.

Results

The experimental results demonstrated that the optimum conditions for the small-scale fermentative hydrogen production system were at pH 7.0, 35°C, a mixed medium, including H1 medium and H2 medium with 0.50 mol/L ferrous chloride, 0.50 mol/L magnesium sulfate, 0.50 mol/L potassium chloride, 1% w/v citric acid, 5% w/v fructose and 5% w/v glucose. The overall hydrogen production efficiency in the shake flask fermentation group was 33.7 mL/h(-1).L(-1), and those the two-step and the one-step processes of the small-scale fermentative hydrogen production system were 41.2 mL/h(-1).L(-1) and 35.1 mL/h(-1).L(-1), respectively.

Conclusion

Therefore, the results indicate that the hydrogen production efficiency of the two-step process is higher than that of the one-step process.\n\nFeasibility of biohydrogen production from industrial wastes using defined microbial co-culture.", "token_count": 341, "char_count": 1048, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:07.708775", "source": { "split": "train_shard_00001", "doc_id": 1410 }, "chunk_id": "train_shard_00001_1410_1", "global_id": 7638 }, { "text": "The Klebsiella pneumoniae species complex (KpSC) is a major source of nosocomial infections globally with high rates of resistance to antimicrobials. Consequently, there is growing interest in understanding virulence factors and their association with cellular metabolic processes for developing novel anti-KpSC therapeutics. Phenotypic assays have revealed metabolic diversity within the KpSC, but metabolism research has been neglected due to experiments being difficult and cost-intensive. Genome-scale metabolic models (GSMMs) represent a rapid and scalable in silico approach for exploring metabolic diversity, which compile genomic and biochemical data to reconstruct the metabolic network of an organism. Here we use a diverse collection of 507 KpSC isolates, including representatives of globally distributed clinically relevant lineages, to construct the most comprehensive KpSC pan-metabolic model to date, KpSC pan v2. Candidate metabolic reactions were identified using gene orthology to known metabolic genes, prior to manual curation via extensive literature and database searches. The final model comprised a total of 3550 reactions, 2403 genes and can simulate growth on 360 unique substrates. We used KpSC pan v2 as a reference to derive strain-specific GSMMs for all 507 KpSC isolates, and compared these to GSMMs generated using a prior KpSC pan-reference (KpSC pan v1) and two single-strain references. We show that KpSC pan v2 includes a greater proportion of accessory reactions (8.8 %) than KpSC pan v1 (2.5 %). GSMMs derived from KpSC pan v2 also generate more accurate growth predictions, with high median accuracies of 95.4 % (aerobic, n=37 isolates) and 78.8 % (anaerobic, n=36 isolates) for 124 matched carbon substrates", "token_count": 487, "char_count": 1776, "word_count": 255, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:08.388028", "source": { "split": "train_shard_00001", "doc_id": 1411 }, "chunk_id": "train_shard_00001_1411_0", "global_id": 7639 }, { "text": "KpSC pan v2 is freely available at https://github.com/kelwyres/KpSC-pan-metabolic-model, representing a valuable resource for the scientific community, both as a source of curated metabolic information and as a reference to derive accurate strain-specific GSMMs. The latter can be used to investigate the relationship between KpSC metabolism and traits of interest, such as reservoirs, epidemiology, drug resistance or virulence, and ultimately to inform novel KpSC control strategies.\n\nA validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex.", "token_count": 149, "char_count": 584, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7763, "quality_score": 0.8882, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:08.826066", "source": { "split": "train_shard_00001", "doc_id": 1411 }, "chunk_id": "train_shard_00001_1411_1", "global_id": 7640 }, { "text": "Ethyl acetate can be synthesized from acetyl-CoA and ethanol via a reaction by alcohol acetyltransferases (AATase) in yeast. In order to increase the yield of acetyl-CoA, different terminators were used to optimize the expressions of acetyl-CoA synthetase (ACS1/2) and aldehyde dehydrogenase (ALD6) to increase the contents of acetyl-CoA in Saccharomyces cerevisiae. ATF1 coding AATase was coexpressed in expression cassettes of ACS1/ACS2 and ALD6 to promote the carbon flux toward ethyl acetate from acetyl-CoA. Further to improve ethyl acetate production, four heterologous AATase including HuvEAT1 (Hanseniaspora uvarum), KamEAT1 (Kluyveromyces marxianus), VAAT (wild strawberry), and AeAT9 (kiwifruit) were introduced. Subsequently mitochondrial transport and utilization of pyruvate and acetyl-CoA were impeded to increase the ethyl acetate accumulation in cytoplasm. Under the optimal fermentation conditions, the engineered strain of PGAeΔPOR2 produced 1.69 g/L ethyl acetate, which was the highest value reported to date by metabolic engineering methods.\n\nMetabolic Engineering of Saccharomyces cerevisiae for Ethyl Acetate Biosynthesis.", "token_count": 391, "char_count": 1187, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6645, "quality_score": 0.8322, "entities": { "genes": [ "ACS1", "ALD6", "ACS2", "ATF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:09.440803", "source": { "split": "train_shard_00001", "doc_id": 1412 }, "chunk_id": "train_shard_00001_1412_0", "global_id": 7641 }, { "text": "Genomic surveillance of pathogens is essential to trace infections and analyze resistance markers. Core genome multilocus sequence typing (cgMLST) facilitates genomic surveillance by simplified analysis and standardization. However, its application is limited by the poor cost-efficiency of short-read (SR) sequencing. Oxford Nanopore long-read sequencing (ONT-LR), which allows fast on-site analysis with comparatively low costs, could provide an alternative. Despite ONT-LR raw read accuracy improvement, evidence for methylation-based errors accumulates. PCR-based library preparation, suggested as a solution, presumably poses difficulties for GC-rich bacteria. We challenged ONT-LR-based cgMLST using the highly GC-rich pathogen Burkholderia pseudomallei to develop a clinically applicable workflow. Our B. pseudomallei cgMLST scheme was applied to ONT-LR data, and the results were validated against SR data. Native, rapid, and PCR-based library preparation was performed and combined with different basecalling models (SUP@bacterial-methylation, SUP@v4.2, SUP@v4.3, and SUP@v5.0) and polishing strategies (medaka_consensus, medaka_variant, r103_min_high_g360). To ensure reliability across genotypes, we included 14 sequence types and 27 genotypes. The recommended ONT-LR workflow at study initiation (SUP@v4.2, medaka_consensus) showed nearly 200 allele differences compared with the reference for specific strains. PCR-based library preparation resulted in missing targets and typing errors of up to 21 alleles. Native barcoding with SUP@v5.0 basecalling and r103_min_high_g360 polishing outperformed the PCR-based approach in all parameters reducing the error rate to a maximum of two allele differences. The optimized ONT-LR-based cgMLST workflow for B. pseudomallei integrates high resolution and ease of implementation with enhanced cost-efficiency for rapid diagnostics", "token_count": 512, "char_count": 1904, "word_count": 238, "semantic_coherence": 1, "information_density": 0.7185, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:10.093407", "source": { "split": "train_shard_00001", "doc_id": 1413 }, "chunk_id": "train_shard_00001_1413_0", "global_id": 7642 }, { "text": "The developed protocol might serve as a guideline for other GC-rich pathogens.

Importance

This study highlights a significant advancement in genomic surveillance of bacterial pathogens, specifically addressing the challenges posed by the GC-rich species Burkholderia pseudomallei. Core genome multilocus sequence typing (cgMLST) is widely used for bacterial typing as it combines high resolution with simple implementation and standardization. To improve cost efficiency and thus accessibility, we changed the sequencing approach from Illumina short-read (SR) to Oxford Nanopore long-read sequencing (ONT-LR). ONT-LR-based cgMLST showed a very high error rate compared with SR-based cgMLST, most likely due to methylation-associated errors. PCR-based library preparation, which is proposed to correct these errors, did not achieve the required accuracy. In contrast, native barcoding with advanced basecalling and polishing strategies massively reduces allelic differences. This optimized ONT-LR cgMLST workflow provides a transformative solution for cost-efficient, high-resolution typing of B. pseudomallei. Furthermore, this study can serve as a guide for similarly challenging bacteria.\n\nImproving Nanopore sequencing-based core genome MLST for global infection control: a strategy for GC-rich pathogens like <i>Burkholderia pseudomallei</i>.", "token_count": 344, "char_count": 1379, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7616, "quality_score": 0.8808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:10.659449", "source": { "split": "train_shard_00001", "doc_id": 1413 }, "chunk_id": "train_shard_00001_1413_1", "global_id": 7643 }, { "text": "

Summary

Metagenome Assembled Genomes (MAGs) are often incomplete, with sequences missing due to errors in assembly or low coverage. Incomplete MAGs present a particular challenge for identification of shared genes within a microbial population, known as core genes, as a core gene missing in only a few assemblies will result in it being mischaracterized at a lower frequency. Here, we present CELEBRIMBOR, a snakemake pangenome analysis pipeline which uses a measure of genome completeness to automatically adjust the frequency threshold at which core genes are identified, enabling accurate core gene identification in MAGs.

Availability and implementation

CELEBRIMBOR is published under open source Apache 2.0 licence at https://github.com/bacpop/CELEBRIMBOR and is available as a Docker container. Supplementary material is available in the online version of the article.\n\nCELEBRIMBOR: Pangenomes from metagenomes", "token_count": 227, "char_count": 935, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7364, "quality_score": 0.8682, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:11.127827", "source": { "split": "train_shard_00001", "doc_id": 1414 }, "chunk_id": "train_shard_00001_1414_0", "global_id": 7644 }, { "text": "

Background and aim

Campylobacter fetus is one of the most important pathogens that severely affects livestock industry worldwide. C. fetus mediated bovine genital campylobacteriosis infection in cattle has been associated with significant economic losses in livestock production in the Pampas region, the most productive area of Argentina. The present study aimed to establish the genomic relationships between C. fetus strains, isolated from the Pampas region, at local and global levels. The study also explored the utility of multi-locus sequence typing (MLST) as a typing technique for C. fetus.

Materials and methods

For pangenome and phylogenetic analysis, whole genome sequences for 34 C. fetus strains, isolated from cattle in Argentina were downloaded from GenBank. A local maximum likelihood (ML) tree was constructed and linked to a Microreact project. In silico analysis based on MLST was used to obtain information regarding sequence type (ST) for each strain. For global phylogenetic analysis, a core genome ML-tree was constructed using genomic dataset for 265 C. fetus strains, isolated from various sources obtained from 20 countries.

Results

The local core genome phylogenetic tree analysis described the presence of two major clusters (A and B) and one minor cluster (C). The occurrence of 82% of the strains in these three clusters suggested a clonal population structure for C. fetus. The MLST analysis for the local strains revealed that 31 strains were ST4 type and one strain was ST5 type. In addition, a new variant was identified that was assigned a novel ST, ST70. In the present case, ST4 was homogenously distributed across all the regions and clusters. The global analysis showed that most of the local strains clustered in the phylogenetic groups that comprised exclusively of the strains isolated from Argentina. Interestingly, three strains showed a close genetic relationship with bovine strains obtained from Uruguay and Brazil", "token_count": 514, "char_count": 2040, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5473, "quality_score": 0.7736, "entities": { "genes": [ "ST5", "ST70", "ST4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:11.787940", "source": { "split": "train_shard_00001", "doc_id": 1415 }, "chunk_id": "train_shard_00001_1415_0", "global_id": 7645 }, { "text": "The ST5 strain grouped in a distant cluster, with strains obtained from different sources from various geographic locations worldwide. Two local strains clustered in a phylogenetic group comprising intercontinental Campylobacter fetus venerealis strains.

Conclusion

The results of the study suggested active movement of animals, probably due to economic trade between different regions of the country as well as with neighboring countries. MLST results were partially concordant with phylogenetic analysis. Thus, this method did not qualify as a reliable subtyping method to assess C. fetus diversity in Argentina. The present study provided a basic platform to conduct future research on C. fetus, both at local and international levels.\n\nPhylogenomic analysis for Campylobacter fetus ocurring in Argentina.", "token_count": 206, "char_count": 843, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7434, "quality_score": 0.8717, "entities": { "genes": [ "ST5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:12.250547", "source": { "split": "train_shard_00001", "doc_id": 1415 }, "chunk_id": "train_shard_00001_1415_1", "global_id": 7646 }, { "text": "While Kluyveromyces marxianus is a promising yeast strain for biotechnological applications, genetic engineering of this strain is still challenging, especially when multiple genes are to be transformed. Sequential gene integration, which takes advantage of repetitive insertion/excision of the URA3 gene as a marker, has been the best option until now, because the URA3-deletion mutant is the only precondition for this method. However, we found that the introduced gene is co-excised during the URA3 excision step for next gene introduction, resulting in a very low cumulative probability (<1.57×10⁻⁶ % for 4 genes) of integrating all genes of interest. To overcome this extremely low probability, and to reduce labor and time, all 4 genes were simultaneously transformed. Surprisingly, the infamously high 'non-homologous end joining' activity of K. marxianus enabled simultaneous integration of all 4 genes in a single step, with a probability of 7.9%. Various K. marxianus strains could also be similarly transformed. Our finding not only reduces the labor and time required for such procedures, but also removes a number of preconditions, such as pre-made vectors, selection markers and knockout mutants, which are needed to introduce many genes into K. marxianus.\n\nSimultaneous integration of multiple genes into the Kluyveromyces marxianus chromosome.", "token_count": 325, "char_count": 1359, "word_count": 200, "semantic_coherence": 1, "information_density": 0.63, "quality_score": 0.815, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:12.825940", "source": { "split": "train_shard_00001", "doc_id": 1416 }, "chunk_id": "train_shard_00001_1416_0", "global_id": 7647 }, { "text": "

Background

Bacterial plant pathogens of the Pectobacterium genus are responsible for a wide spectrum of diseases in plants, including important crops such as potato, tomato, lettuce, and banana. Investigation of the genetic diversity underlying virulence and host specificity can be performed at genome level by using a comprehensive comparative approach called pangenomics. A pangenomic approach, using newly developed functionalities in PanTools, was applied to analyze the complex phylogeny of the Pectobacterium genus. We specifically used the pangenome to investigate genetic differences between virulent and avirulent strains of P. brasiliense, a potato blackleg causing species dominantly present in Western Europe.

Results

Here we generated a multilevel pangenome for Pectobacterium, comprising 197 strains across 19 species, including type strains, with a focus on P. brasiliense. The extensive phylogenetic analysis of the Pectobacterium genus showed robust distinct clades, with most detail provided by 452,388 parsimony-informative single-nucleotide polymorphisms identified in single-copy orthologs. The average Pectobacterium genome consists of 47% core genes, 1% unique genes, and 52% accessory genes. Using the pangenome, we zoomed in on differences between virulent and avirulent P. brasiliense strains and identified 86 genes associated to virulent strains. We found that the organization of genes is highly structured and linked with gene conservation, function, and transcriptional orientation.

Conclusion

The pangenome analysis demonstrates that evolution in Pectobacteria is a highly dynamic process, including gene acquisitions partly in clusters, genome rearrangements, and loss of genes. Pectobacterium species are typically not characterized by a set of species-specific genes, but instead present themselves using new gene combinations from the shared gene pool. A multilevel pangenomic approach, fusing DNA, protein, biological function, taxonomic group, and phenotypes, facilitates studies in a flexible taxonomic context.", "token_count": 497, "char_count": 2073, "word_count": 272, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:13.476879", "source": { "split": "train_shard_00001", "doc_id": 1417 }, "chunk_id": "train_shard_00001_1417_0", "global_id": 7648 }, { "text": "The Pectobacterium pangenome, with a focus on Pectobacterium brasiliense, shows a robust core and extensive exchange of genes from a shared gene pool.", "token_count": 38, "char_count": 150, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:13.841837", "source": { "split": "train_shard_00001", "doc_id": 1417 }, "chunk_id": "train_shard_00001_1417_1", "global_id": 7649 }, { "text": "Three β-lactam resistant bacterial strains isolated from gut samples of wild Atlantic mackerel (Scomber scombrus) collected from the northern North Sea were characterized by polyphasic analyses. The strains were determined to belong to the genus Pseudomonas but could not be assigned to a known species. The nearly-complete 16S rRNA gene sequence showed the highest similarity (99.9%) to four different species, although partial rpoD sequence exhibited relatively low similarities to Pseudomonas proteolytica (93.4%) and other Pseudomonas spp. Genome sequencing and subsequent digital DNA-DNA hybridization (dDDH), average nucleotide identity (ANI) analysis and core genome analysis confirmed that these strains represent a novel species within the genus Pseudomonas. The three strains demonstrated ANIb values >99.5% with each other, confirming that all three strains (CCUG 74779T = CECT 30571T, CCUG 74780 and CCUG 74781) belong to the same genomospecies. Phylogenomic analysis confirmed that the strains form a distinct genomic clade, representing a novel taxonomic species, for which the name Pseudomonas imrae sp. nov., is proposed, with strain CCUG 74779T (=CECT 30571T) designated as the type strain. We report the complete genome sequence of the type strain of P. imrae sp. nov. and show that it carries a gene encoding a novel variant of a chromosomally-encoded class C β-lactamase, which has been designated as PFL-7.", "token_count": 468, "char_count": 1527, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6762, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:14.489208", "source": { "split": "train_shard_00001", "doc_id": 1418 }, "chunk_id": "train_shard_00001_1418_0", "global_id": 7650 }, { "text": "Description of <i>Pseudomonas imrae</i> sp. nov., carrying a novel class C β-lactamase gene variant, isolated from gut samples of Atlantic mackerel (<i>Scomber scombrus</i>).", "token_count": 73, "char_count": 198, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:14.855702", "source": { "split": "train_shard_00001", "doc_id": 1418 }, "chunk_id": "train_shard_00001_1418_1", "global_id": 7651 }, { "text": "Pangenome graphs can represent all variation between multiple reference genomes, but current approaches to build them exclude complex sequences or are based upon a single reference. In response, we developed the PanGenome Graph Builder (PGGB), a pipeline for constructing pangenome graphs without bias or exclusion. PGGB uses all-to-all alignments to build a variation graph in which we can identify variation, measure conservation, detect recombination events, and infer phylogenetic relationships.\n\nBuilding pangenome graphs", "token_count": 109, "char_count": 526, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:15.239739", "source": { "split": "train_shard_00001", "doc_id": 1419 }, "chunk_id": "train_shard_00001_1419_0", "global_id": 7652 }, { "text": "Considering the increasing interest in understanding the biotic component of methane removal from our atmosphere, it becomes essential to study the physiological characteristics and genomic potential of methanotroph isolates, especially their traits allowing them to adapt to elevated growth temperatures. The genetic signatures of Methylocaldum species have been detected in many terrestrial and aquatic ecosystems. A small set of representatives of this genus has been isolated and maintained in culture. The genus is commonly described as moderately thermophilic, with the growth optimum reaching 50 °C for some strains. Here, we present a comparative analysis of genomes of three Methylocaldum strains-two terrestrial M. szegediense strains (O-12 and Norfolk) and one marine strain, Methylocaldum marinum (S8). The examination of the core genome inventory of this genus uncovers significant redundancy in primary metabolic pathways, including the machinery for methane oxidation (numerous copies of pmo genes) and methanol oxidation (duplications of mxaF, xoxF1-5 genes), three pathways for one-carbon (C1) assimilation, and two methods of carbon storage (glycogen and polyhydroxyalkanoates). We also investigate the genetics of melanin production pathways as a key feature of the genus.\n\nGenomic Insights into Moderately Thermophilic Methanotrophs of the Genus Methylocaldum.", "token_count": 390, "char_count": 1436, "word_count": 191, "semantic_coherence": 1, "information_density": 0.7016, "quality_score": 0.8508, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:15.860253", "source": { "split": "train_shard_00001", "doc_id": 1420 }, "chunk_id": "train_shard_00001_1420_0", "global_id": 7653 }, { "text": "Fungal infections are difficult to prevent and treat in large part due to strain heterogeneity which confounds diagnostic predictability. Yet the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined the extent to which Starships —giant transposons capable of mobilizing numerous fungal genes—generate genetic and phenotypic variability in the opportunistic human pathogen Aspergillus fumigatus . We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology and multiple isolates of the same reference strain, to reveal 20 distinct Starships that are generating genomic heterogeneity over timescales relevant for experimental reproducibility. Starship -mobilized genes encode diverse functions, including known biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal evolution wherein Starships help generate variation in genome structure, gene content and expression among fungal strains. Together, our results demonstrate that Starships are a previously hidden mechanism generating genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen.

Importance

No “one size fits all” option exists for treating fungal infections in large part due to genetic and phenotypic variability among strains. Accounting for strain heterogeneity is thus fundamental for developing efficacious treatments and strategies for safeguarding human health. Here, we report significant progress towards achieving this goal by uncovering a previously hidden mechanism generating heterogeneity in the human fungal pathogen Aspergillus fumigatus giant transposons called Starships that span dozens of kilobases and mobilize fungal genes as cargo. By conducting a systematic investigation of these unusual transposons in a single fungal species, we demonstrate their contributions to population-level variation at the genome, pangenome and transcriptome levels. The Starship compendium we develop will not only help predict variation introduced by these elements in laboratory experiments but will serve as a foundational resource for determining how Starships impact clinically-relevant phenotypes, such as antifungal resistance and pathogenicity.", "token_count": 500, "char_count": 2388, "word_count": 315, "semantic_coherence": 1, "information_density": 0.6254, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:16.511379", "source": { "split": "train_shard_00001", "doc_id": 1421 }, "chunk_id": "train_shard_00001_1421_0", "global_id": 7654 }, { "text": "Giant transposons promote strain heterogeneity in a major fungal pathogen", "token_count": 17, "char_count": 73, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:16.862484", "source": { "split": "train_shard_00001", "doc_id": 1421 }, "chunk_id": "train_shard_00001_1421_1", "global_id": 7655 }, { "text": "

Background

Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk of patient DNA leakage. To mitigate this risk, we need near-comprehensive removal of human DNA sequence at the point of sequencing, typically involving use of resource-constrained devices. Existing benchmarks have largely focused on use of standardised databases and largely ignored the computational requirements of depletion pipelines as well as the impact of human genome diversity.

Results

We benchmarked host removal pipelines on simulated Illumina and Nanopore metagenomic samples. We found that construction of a custom kraken database containing diverse human genomes results in the best balance of accuracy and computational resource usage. In addition, we benchmarked pipelines using kraken and minimap2 for taxonomic classification of Mycobacterium reads using standard and custom databases. With a database representative of the Mycobacterium genus, both tools obtained near-perfect precision and recall for classification of Mycobacterium tuberculosis . Computational efficiency of these custom databases was again superior to most standard approaches, allowing them to be executed on a laptop device.

Conclusions

Nanopore sequencing and a custom kraken human database with a diversity of genomes leads to superior host read removal from simulated metagenomic samples while being executable on a laptop. In addition, constructing a taxon-specific database provides excellent taxonomic read assignment while keeping runtime and memory low. We make all customised databases and pipelines freely available.\n\nPangenome databases provide superior host removal and mycobacteria classification from clinical metagenomic data", "token_count": 398, "char_count": 1856, "word_count": 247, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:17.478766", "source": { "split": "train_shard_00001", "doc_id": 1422 }, "chunk_id": "train_shard_00001_1422_0", "global_id": 7656 }, { "text": "Ralstonia solanacearum species complex (RSSC) strains are bacteria that colonize plant xylem and cause vascular wilt diseases. However, individual strains vary in host range, optimal disease temperatures, and physiological traits. To increase our understanding of the evolution, diversity, and biology of the RSSC, we performed a meta-analysis of 100 representative RSSC genomes. These 100 RSSC genomes contain 4,940 genes on average, and a pangenome analysis found that there are 3,262 genes in the core genome (∼60% of the mean RSSC genome) with 13,128 genes in the extensive flexible genome. Although a core genome phylogenetic tree and a genome similarity matrix aligned with the previously named species ( R. solanacearum, R. pseudosolanacearum, R. syzygii ) and phylotypes (I-IV), these analyses also highlighted an unrecognized sub-clade of phylotype II. Additionally, we identified differences between phylotypes with respect to gene content and recombination rate, and we delineated population clusters based on the extent of horizontal gene transfer. Multiple analyses indicate that phylotype II is the most diverse phylotype, and it may thus represent the ancestral group of the RSSC. Additionally, we also used our genome-based framework to test whether the RSSC sequence variant (sequevar) taxonomy is a robust method to define within-species relationships of strains. The sequevar taxonomy is based on alignments of a single conserved gene ( egl ). Although sequevars in phylotype II describe monophyletic groups, the sequevar system breaks down in the highly recombinogenic phylotype I, which highlights the need for an improved cost-effective method for genotyping strains in phylotype I. Finally, we enabled quick and precise genome-based identification of newly sequenced Ralstonia strains by assigning Life Identification Numbers (LINs) to the 100 strains and by circumscribing the RSSC and its sub-groups in the LINbase Web service", "token_count": 500, "char_count": 1951, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6237, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:18.137797", "source": { "split": "train_shard_00001", "doc_id": 1423 }, "chunk_id": "train_shard_00001_1423_0", "global_id": 7657 }, { "text": "

IMPACT STATEMENT

The Ralstonia solanacearum species complex (RSSC) includes dozens of economically important pathogens of many cultivated and wild plants. The extensive genetic and phenotypic diversity that exists within the RSSC has made it challenging to subdivide this group into meaningful subgroups with relevance to plant disease control and plant biosecurity. This study provides a solid genome-based framework for improved classification and identification of the RSSC by analyzing one hundred representative RSSC genome sequences with a suite of comparative evolutionary genomic tools. The results also lay the foundation for additional in-depth studies to gain further insights into evolution and biology of this heterogeneous complex of destructive plant pathogens.

DATA SUMMARY

The authors confirm that all raw data and code and protocols have been provided within the manuscript. All publicly available sequencing data used for analysis have been supplemented with accession numbers to access the data. The assembled genome of strain 19-3PR_UW348 was submitted to NCBI under Bioproject PRJNA775652 Biosample SAMN22612291. This Whole Genome Shotgun project has been deposited at GenBank under the accession JAJMMU000000000. The version described in this paper is version JAJMMU010000000.\n\nMeta Analysis of the Ralstonia solanacearum species complex (RSSC) based on comparative evolutionary genomics and reverse ecology", "token_count": 372, "char_count": 1455, "word_count": 200, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [ "JAJMMU000000000", "JAJMMU010000000", "PRJNA775652", "SAMN22612291" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:18.749803", "source": { "split": "train_shard_00001", "doc_id": 1423 }, "chunk_id": "train_shard_00001_1423_1", "global_id": 7658 }, { "text": "Salmonella enterica subsp. enterica serovar Infantis is the most prevalent serovar found in broilers and broiler meat and is among the top five serovars responsible for human infections in Europe. In 2008, a multidrug-resistant S. Infantis isolate emerged in Israel with a mosaic megaplasmid named pESI, associated with increased virulence, biofilm formation, and multidrug resistance. Since then, S. Infantis clones with pESI-like plasmids have been reported worldwide, replacing pESI-free clones. Here, we typed 161 S. Infantis isolates of poultry (n = 133) and human clinical (n = 28) origin using whole-genome sequencing. The isolates were collected between 2007 and 2021. In addition, we performed PacBio/Illumina sequencing for two representative pESI-like plasmids and compared them with publicly available sequences. All isolates belonged to sequence type 32 (ST32), except for one isolate that represented a novel single-locus variant of ST32. Core genome MLST (cgMLST) analysis revealed 14 clusters of genetically closely related isolates, of which four suggested broiler-to-human transmission of S. Infantis. pESI-like plasmids were present in 148/161 (91.9%) isolates; all were highly similar to the publicly available pESI-like sequences but lacked extended-spectrum beta-lactamase (ESBL) genes. PacBio/Illumina hybrid assembly allowed the reconstruction of two novel complete pESI variants. The present study revealed that the multidrug-resistant, pESI-positive S. Infantis clone became the predominant S. Infantis clone in Slovenian broilers and humans during the last decade. Continued surveillance of resistant S", "token_count": 512, "char_count": 1699, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6916, "quality_score": 0.8458, "entities": { "genes": [ "ST32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:19.424054", "source": { "split": "train_shard_00001", "doc_id": 1424 }, "chunk_id": "train_shard_00001_1424_0", "global_id": 7659 }, { "text": "Infantis clones along the food chain is needed to guide public health efforts. IMPORTANCE Salmonella Infantis clones with pESI-like plasmids harboring several virulence and resistance genes have been reported worldwide. In the present study, we compared the population structure of 161 Salmonella Infantis isolates obtained from humans and broilers in Slovenia from 2007 to 2021. Whole-genome sequencing showed that most human isolates clustered apart from broiler isolates, suggesting an alternative source of infection. Most isolates were multidrug resistant due to the presence of pESI-like plasmids, of which two variants (pS89 and pS19) were fully reconstructed using long-read sequencing. Both exhibited high similarity with the original Israeli pESI plasmid and German p2747 plasmid. The prototype plasmid pS89 harbored the typical pESI-associated resistance genes aadA1, qacEΔ1, sul1, and tet(A), which were absent in the truncated plasmid pS19.\n\nClonal Spread of pESI-Positive Multidrug-Resistant ST32 Salmonella enterica Serovar Infantis Isolates among Broilers and Humans in Slovenia.", "token_count": 342, "char_count": 1137, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [ "ST32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:20.027113", "source": { "split": "train_shard_00001", "doc_id": 1424 }, "chunk_id": "train_shard_00001_1424_1", "global_id": 7660 }, { "text": "The present study introduces a procedure for designing a sourdough with a desirable aroma to promote the acceptability of sourdough bread’s flavor. Different combinations of the most common flours and microbial species in sourdough fermentation were designed using the D‐optimal algorithm and evaluated by panelists. We selected a combination of rye, barley, and oat (1:1:1) fermented by co‐culture of Leuconostoc mesenteroides and Kluyveromyces marxianus. Also, we presented a novel method for choosing the most effective factors on the aroma intensity using an electronic nose (e‐nose) system via singular value decomposition method. The effect of fermentation conditions (i.e., time, temperature, and dough yield), amino acids (phenylalanine, leucine, and asparagine), sugars (fructose, glucose, sucrose, and sorbitol), and enrichment by other parts of the grain (starch, embryo, and bran) were examined. Reducing temperature and increasing DY and time lead to producing stronger aroma in selected sourdough. Overall, fructose, phenylalanine, and bran among studied ingredients showed the highest impact on the intensity of aroma. PRACTICAL APPLICATIONS: Improving the flavor is among the most challenging issues facing food manufacturers. The use of sourdough in the bread industry is a traditional method and has recently gained popularity among producers and consumers as it can improve texture, shelf life, and nutritional value. However, the fermentation process does not always lead to the desired flavor. Therefore, to solve this problem, an extensive study in flours and microbial strains widely used in sourdough production was conducted and the best combination was proposed. This product is a suitable alternative to chemical flavors. For future studies, the strategy proposed for detecting the most effective factors in aroma generation using an e‐nose can be used for flavor improvement in other food products.\n\nInvestigating effective variables to produce desirable aroma in sourdough using e‐nose and sensory panel", "token_count": 474, "char_count": 2032, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6156, "quality_score": 0.8078, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:20.672605", "source": { "split": "train_shard_00001", "doc_id": 1425 }, "chunk_id": "train_shard_00001_1425_0", "global_id": 7661 }, { "text": "Sierra Mixe maize is a landrace variety from Oaxaca, Mexico, that utilizes nitrogen derived from the atmosphere via an undefined nitrogen fixation mechanism. The diazotrophic microbiota associated with the plant's mucilaginous aerial root exudate composed of complex carbohydrates was previously identified and characterized by our group where we found 23 lactococci capable of biological nitrogen fixation (BNF) without containing any of the proposed essential genes for this trait (nifHDKENB). To determine the genes in Lactococcus associated with this phenotype, we selected 70 lactococci from the dairy industry that are not known to be diazotrophic to conduct a comparative population genomic analysis. This showed that the diazotrophic lactococcal genomes were distinctly different from the dairy isolates. Examining the pangenome followed by genome-wide association study and machine learning identified genes with the functions needed for BNF in the maize isolates that were absent from the dairy isolates. Many of the putative genes received an 'unknown' annotation, which led to the domain analysis of the 135 homologs. This revealed genes with molecular functions needed for BNF, including mucilage carbohydrate catabolism, glycan-mediated host adhesion, iron/siderophore utilization, and oxidation/reduction control. This is the first report of this pathway in this organism to underpin BNF. Consequently, we proposed a model needed for BNF in lactococci that plausibly accounts for BNF in the absence of the nif operon in this organism.\n\nIdentification of Nitrogen Fixation Genes in Lactococcus Isolated from Maize Using Population Genomics and Machine Learning.", "token_count": 444, "char_count": 1703, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:21.313827", "source": { "split": "train_shard_00001", "doc_id": 1426 }, "chunk_id": "train_shard_00001_1426_0", "global_id": 7662 }, { "text": "Urinary tract infection (UTI) develops after a pathogen adheres to the inner lining of the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and account for high morbidity in the clinical and community settings. Of greater concern are the strains carrying antimicrobial resistance (AMR)-conferring genes. The gravity of a UTI is also determined by a spectrum of other virulence factors. This study represents a pilot project to investigate the burden of AMR among uropathogens in East Africa. We examined bacterial samples isolated in 2017-2018 from in- and out-patients in Kenya (KY) and Uganda (UG) that presented with clinical symptoms of UTI. We reconstructed the evolutionary history of the strains, investigated their population structure, and performed comparative analysis their pangenome contents. We found 55 Escherichia coli and 19 Klebsiella pneumoniae strains confirmed uropathogenic following screening for the prevalence of UTI virulence genes including fimH, iutA, feoA/B/C, mrkD, and foc. We identified 18 different sequence types in E. coli population while all K. pneumoniae strains belong to ST11. The most prevalent E. coli sequence types were ST131 (26%), ST335/1193 (10%), and ST10 (6%). Diverse plasmid types were observed in both collections such as Incompatibility (IncF/IncH/IncQ1/IncX4) and Col groups. Pangenome analysis of each set revealed a total of 2862 and 3464 genes comprised the core genome of E. coli and K. pneumoniae population, respectively", "token_count": 503, "char_count": 1617, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6844, "quality_score": 0.8422, "entities": { "genes": [ "ST131", "ST335", "ST10", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:21.968616", "source": { "split": "train_shard_00001", "doc_id": 1427 }, "chunk_id": "train_shard_00001_1427_0", "global_id": 7663 }, { "text": "Among these are acquired AMR determinants including fluoroquinolone resistance-conferring genes aac(3)-Ib-cr and other significant genes: aad, tet, sul1, sul2, and cat, which are associated with aminoglycoside, tetracycline, sulfonamide, and chloramphenicol resistance, respectively. Accessory genomes of both species collections were detected several β-lactamase genes, blaCTX-M, blaTEM and blaOXA, or blaNDM. Overall, 93% are multi-drug resistant in the E. coli collection while 100% of the K. pneumoniae strains contained genes that are associated with resistance to three or more antibiotic classes. Our findings illustrate the abundant acquired resistome and virulome repertoire in uropathogenic E. coli and K. pneumoniae, which are mainly disseminated via clonal and horizontal transfer, circulating in the East African region. We further demonstrate here that routine genomic surveillance is necessary for high-resolution bacterial epidemiology of these important AMR pathogens.\n\nPan-Resistome Characterization of Uropathogenic <i>Escherichia coli</i> and <i>Klebsiella pneumoniae</i> Strains Circulating in Uganda and Kenya, Isolated from 2017-2018.", "token_count": 449, "char_count": 1323, "word_count": 148, "semantic_coherence": 1, "information_density": 0.7568, "quality_score": 0.8784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:22.599338", "source": { "split": "train_shard_00001", "doc_id": 1427 }, "chunk_id": "train_shard_00001_1427_1", "global_id": 7664 }, { "text": "Rare DNA alterations that cause heritable diseases are only partially resolvable by clinical next-generation sequencing due to the difficulty of detecting structural variation (SV) in all genomic contexts. Long-read, high fidelity genome sequencing (HiFi-GS) detects SVs against reference genomes with increased sensitivity and also enables the assembly of personal and graph genomes. We leveraged standard reference genomes, publicly available human haploid assemblies (n=94), together with a large collection of HiFi-GS data from a rare disease program (Genomic Answers for Kids, GA4K, n=574 assemblies). These data allowed us to build a deep population graph genome distinguishing very rare SVs from recurrent polymorphisms. Using graphs to discover SVs, we obtained a higher level of reproducibility than that obtained by the standard reference approach. We observed over 200,000 SV alleles unique to the rare disease GA4K cohort, including nearly 1,000 rare variants that impact coding sequence. With improved specificity for rare SVs, we isolate 30 candidate SVs in phenotypically prioritized genes, including known disease SVs. We isolate novel diagnostic SV in KMT2E in a patient demonstrating use of personal assemblies coupled with pangenome graphs as a new handle for rare disease genomics.\n\nPangenome graphs improve the analysis of rare genetic diseases", "token_count": 325, "char_count": 1365, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6768, "quality_score": 0.8384, "entities": { "genes": [ "GA4K", "KMT2E" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:23.174399", "source": { "split": "train_shard_00001", "doc_id": 1428 }, "chunk_id": "train_shard_00001_1428_0", "global_id": 7665 }, { "text": "In the presented work, we have developed edible kefiran films containing Lactobacillus plantarum CIDCA 8327 and Kluyveromyces marxianus CIDCA 8154. Thickness, moisture content and optical properties of films were not altered by the incorporation of microorganisms. During the film obtaining, lactobacillus concentration decreased one logarithmic cycle and no loss on yeast viability was detected. Both microorganisms included in glycerol plasticized kefiran films successfully maintained their viability during storage. After 35days at 20°°C L. plantarum viability decreased less than 1.3 logarithmic cycles and K. marxianus 0.7 logarithmic cycles.The high susceptibility of free cells of lactobacilli to acid was slightly diminished by the inclusion in the kefiran matrix. Inclusion of K. marxianus CIDCA 8154 significantly improved their survival to the sequential acid–bile treatment (36.3%) compared with the corresponding free cells (8.7%). The obtained edible kefiran films have great potential as an alternative way for probiotic delivery.The edible kefiran films containing probiotics presented in this manuscript are interesting matrices for probiotic administration since the neutral polysaccharide kefiran, produced by lactic acid bacteria, has health-promoting properties itself. Films can be obtained simply and inexpensively. They are transparent, thin and have good mechanical properties among those constituted by biomacromolecules. Likewise, kefiran films can preserve the viability of probiotics in non-refrigerated conditions.\n\nEdible kefiran films as vehicle for probiotic microorganisms", "token_count": 407, "char_count": 1607, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:23.794920", "source": { "split": "train_shard_00001", "doc_id": 1429 }, "chunk_id": "train_shard_00001_1429_0", "global_id": 7666 }, { "text": "Improvements in nanopore sequencing necessitate efficient classification methods, including pre-filtering and adaptive sampling algorithms that enrich for reads of interest. Signal-based approaches circumvent the computational bottleneck of basecalling. But past methods for signal-based classification do not scale efficiently to large, repetitive references like pangenomes, limiting their utility to partial references or individual genomes. We introduce Sigmoni: a rapid, multiclass classification method based on the r -index that scales to references of hundreds of Gbps. Sigmoni quantizes nanopore signal into a discrete alphabet of picoamp ranges. It performs rapid, approximate matching using matching statistics, classifying reads based on distributions of picoamp matching statistics and co-linearity statistics. Sigmoni is 10-100 × faster than previous methods for adaptive sampling in host depletion experiments with improved accuracy, and can query reads against large microbial or human pangenomes.\n\nSigmoni: classification of nanopore signal with a compressed pangenome index", "token_count": 229, "char_count": 1091, "word_count": 143, "semantic_coherence": 1, "information_density": 0.7133, "quality_score": 0.8566, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:24.269552", "source": { "split": "train_shard_00001", "doc_id": 1430 }, "chunk_id": "train_shard_00001_1430_0", "global_id": 7667 }, { "text": "

Background

Natural products constitute more than half of all biomolecules lately being used in clinical settings. Mannoprotein derived from the yeast cell wall has found full biotechnological applications.

Objective

This study was intended to investigate the antioxidant, anticancer, and toxicological properties of Kluyveromyces marxianus mannoprotein (KM).

Methods

The KM extract was obtained through a sequence of operations, including centrifugation for cell isolation, precipitation with potassium citrate/sodium metabisulfite, and recovery and purification. Its antioxidant, growth inhibition, macrophage mitogenic, and toxic activities were evaluated for its future use in the biomedical field.

Results

Significant inhibitory effects of KM were obtained on reactive species. It showed antiproliferative activity against HeLa (human cervical adenocarcinoma) and MCF-7 (human breast cancer) cell lines with no toxic effects on HUVECs (human umbilical vein endothelial cells). The in vitro model of CHO-K1 (Chinese hamster ovary) cell lines did not show the cytotoxic and genotoxic of KM. Moreover, it enhanced macrophage activity in terms of nitric oxide (NO) production and viability. No sign of acute toxicity was found in BALB/c mice, and body weight remained unchanged in guinea pigs over three months.

Conclusion

Comprehensive biological evaluations in this study are expected to expand the potential of KM as a natural material.\n\nBiological Properties of Yeast-based Mannoprotein for Prospective Biomedical Applications.", "token_count": 422, "char_count": 1567, "word_count": 202, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:24.892490", "source": { "split": "train_shard_00001", "doc_id": 1431 }, "chunk_id": "train_shard_00001_1431_0", "global_id": 7668 }, { "text": "In industrial settings and processes, yeasts may face multiple adverse environmental conditions. These include exposure to non-optimal temperatures or pH, osmotic stress, and deleterious concentrations of diverse inhibitory compounds. These toxic chemicals may result from the desired accumulation of added-value bio-products, yeast metabolism, or be present or derive from the pre-treatment of feedstocks, as in lignocellulosic biomass hydrolysates. Adaptation and tolerance to industrially relevant stress factors involve highly complex and coordinated molecular mechanisms occurring in the yeast cell with repercussions on the performance and economy of bioprocesses, or on the microbiological stability and conservation of foods, beverages, and other goods. To sense, survive, and adapt to different stresses, yeasts rely on a network of signaling pathways to modulate the global transcriptional response and elicit coordinated changes in the cell. These pathways cooperate and tightly regulate the composition, organization and biophysical properties of the cell wall. The intricacy of the underlying regulatory networks reflects the major role of the cell wall as the first line of defense against a wide range of environmental stresses. However, the involvement of cell wall in the adaptation and tolerance of yeasts to multiple stresses of biotechnological relevance has not received the deserved attention. This article provides an overview of the molecular mechanisms involved in fine-tuning cell wall physicochemical properties during the stress response of Saccharomyces cerevisiae and their implication in stress tolerance. The available information for non-conventional yeast species is also included. These non-Saccharomyces species have recently been on the focus of very active research to better explore or control their biotechnological potential envisaging the transition to a sustainable circular bioeconomy.\n\nThe cell wall and the response and tolerance to stresses of biotechnological relevance in yeasts.", "token_count": 439, "char_count": 2042, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5872, "quality_score": 0.7936, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:25.525632", "source": { "split": "train_shard_00001", "doc_id": 1432 }, "chunk_id": "train_shard_00001_1432_0", "global_id": 7669 }, { "text": "A new thermostable Cu/Zn SOD from a thermotolerant yeast strain Kluyveromyces marxianus NBIMCC 1984 has been purified and characterized. The purification procedure comprises thermal treatment and dialysis, ion-exchange chromatography and chromatofocusing. The methodology is a rapid, efficient and highly specific, generating pure preparation (specific activity 996 U mg of protein(-1)) with a yield of 53%. The purified enzyme is a homodimer with Mw of 34,034 Da and has high N-terminal homology with other yeasts' Cu/Zn SOD enzymes. The protein is characterized with some unique features such as-thermostability (t(1/2) at 70 degrees C=30 min), pH stability in the alkaline range (7.5-8.5) and resistance to inhibitors and variety of chemicals. These characteristics reveal possibilities for wide practical application of K. marxianus Cu/Zn SOD enzyme.\n\nPurification and partial characterization of Cu/Zn superoxide dismutase from Kluyveromyces marxianus yeast.", "token_count": 273, "char_count": 963, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7239, "quality_score": 0.8619, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:26.076101", "source": { "split": "train_shard_00001", "doc_id": 1433 }, "chunk_id": "train_shard_00001_1433_0", "global_id": 7670 }, { "text": "Most crop plants, including sugar beet ( Beta vulgaris subsp. vulgaris ), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wild relatives (CWRs) harbour useful traits relevant for crop improvement, including enhanced adaptation to biotic and abiotic stresses. Especially polyploids are interesting from an evolutionary perspective as genes undergo reorganisation after the polyploidisation event. Through neo-and subfunctionalisation, novel functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. Particularly in the face of climate change, specific stress and pathogen resistances or tolerances gain importance. To introduce such traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. The identification of genes underlying traits of interest is crucial for crop improvement. For beets, the section Corollinae contains the tetraploid species Beta corolliflora (2n=4x=36) that harbours salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits of B. corolliflora is increased compared to those of the known diploids in this section (all 2n=2x=18). Nevertheless, neither the parental relationships of B. corolliflora have been resolved, nor are genomic resources available to steer sustainable, genomics-informed breeding. To benefit from the resources offered by polyploid beet wild relatives, we generated a comprehensive pangenome dataset including B. corolliflora , Beta lomatogona , and Beta macrorhiza , as well as a more distant wild beet Patellifolia procumbens (2n=2x=18). Joined analyses with publicly available genome sequences of two additional wild beets allowed the identification of genomic regions absent from cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours. In addition, we present strong evidence for the parental relationship of the B. corolliflora wild beet as an autotetraploid emerging from B. macrorhiza .\n\nPangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet", "token_count": 513, "char_count": 2221, "word_count": 309, "semantic_coherence": 1, "information_density": 0.6117, "quality_score": 0.8058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:26.730290", "source": { "split": "train_shard_00001", "doc_id": 1434 }, "chunk_id": "train_shard_00001_1434_0", "global_id": 7671 }, { "text": "

Background

Listeria (L.) monocytogenes is primarily transmitted via contaminated food and can cause listeriosis, an infection often associated with sepsis and meningitis in at-risk individuals. Accurate outbreak detection relies on whole genome sequencing (WGS) and core genome multilocus sequence typing (cgMLST), which use allele thresholds to identify related strains.

Methods

This study investigated mutation rates in L. monocytogenes, focusing on isolates with DNA repair deficiencies. Serial subcultivations were performed, comparing a repair-deficient isolate with a wild-type control. Genetic variability was assessed using WGS and cgMLST.

Results

Mutation rates were significantly higher in repair-deficient isolates, exceeding typical cgMLST thresholds currently used in Listeria outbreak investigations, leading to a misclassification of related isolates as unrelated. An additional analysis of the Austrian Listeria database revealed that such deficiencies are rare among isolates.

Conclusions

The standard 7-allele cgMLST threshold effectively identifies related strains in most cases, but may require adjustments for hypermutator strains. Incorporating DNA repair data could improve the accuracy of outbreak investigations, ensuring reliable public health responses.\n\nAssessing mutation accumulation in DNA repair-deficient <i>Listeria monocytogenes</i>: implications for cgMLST cluster thresholds in outbreak analysis.", "token_count": 393, "char_count": 1502, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7644, "quality_score": 0.8822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:27.349326", "source": { "split": "train_shard_00001", "doc_id": 1435 }, "chunk_id": "train_shard_00001_1435_0", "global_id": 7672 }, { "text": "

Summary

Gene expression is an essential step in the translation of genotypes into phenotypes. However, little is known about the transcriptome architecture and the underlying genetic effects at a species-level. Here, we generated and analyzed the pan-transcriptome of ∼1,000 yeast natural isolates across 4,977 core and 1,468 accessory genes. We found that the accessory genome is an underappreciated driver of the transcriptome divergence. Global gene expression patterns combined with population structure show that the heritable expression variation mainly lies within subpopulation-specific signatures, for which the accessory genes are overrepresented. Genome-wide association analyses consistently highlight that the accessory genes are associated with proportionally more variants with larger effect sizes, illustrating the critical role of the accessory genome on the transcriptional landscape within and between populations.\n\nPan-transcriptome reveals a large accessory genome contribution to gene expression variation in yeast", "token_count": 225, "char_count": 1045, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6642, "quality_score": 0.8321, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:27.822902", "source": { "split": "train_shard_00001", "doc_id": 1436 }, "chunk_id": "train_shard_00001_1436_0", "global_id": 7673 }, { "text": "To the best of our knowledge, only six B. glycinifermentans sp. genome sequences are available in the public database. Here, we performed genome sequencing and comparative genomics analysis of B. glycinifermentans strain JRCGR-1. Cluster analysis of strain JRCGR-1 genes showed that 92.6% of genes were present in the orthogroups and 7.4% genes were not assigned to any group. The pangenome size was calculated at 8329 genes and presented an open genome characteristic. Phylogeny based on the pan and core genome demonstrated that all the B. glycinifermentans strains belong to the same clade. The strain JRCGR-1, ANI, TETRA and DDH values were in the range of 96.1-99.04%, 0.996-997, 73.5–84.7%, respectively. The strain JRCGR genome exhibits a high level of synteny with multiple locations in B . sonorensis sp. and B. licheniformis sp. The finding of the current study provides knowledge that facilitates a better understanding of this at the genomic level.\n\nGenomic Features and Comparative Genomic Analysis of novel Bacillus glycinifermentans strain JRCGR-1", "token_count": 303, "char_count": 1062, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8086, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:28.384733", "source": { "split": "train_shard_00001", "doc_id": 1437 }, "chunk_id": "train_shard_00001_1437_0", "global_id": 7674 }, { "text": "In the present study, a thermophilic strain designated CamBx3 was isolated from the Campanario hot spring, Chile. Based on 16S rRNA gene sequence, phylogenomic, and average nucleotide identity analysis the strain CamBx3 was identified as Bacillus paralicheniformis. Genome analysis of B. paralicheniformis CamBx3 revealed the presence of genes related to heat tolerance, exopolysaccharides (EPS), dissimilatory nitrate reduction, and assimilatory sulfate reduction. The pangenome analysis of strain CamBx3 with eight Bacillus spp. resulted in 26,562 gene clusters, 7,002 shell genes, and 19,484 cloud genes. The EPS produced by B. paralicheniformis CamBx3 was extracted, partially purified, and evaluated for its functional activities. B. paralicheniformis CamBx3 EPS with concentration 5 mg mL-1 showed an optimum 92 mM ferrous equivalent FRAP activity, while the same concentration showed a maximum 91% of Fe2+ chelating activity. B. paralicheniformis CamBx3 EPS (0.2 mg mL-1) demonstrated β-glucosidase inhibition. The EPS formed a viscoelastic gel at 45°C with a maximum instantaneous viscosity of 315 Pa.s at acidic pH 5. The present study suggests that B. paralicheniformis CamBx3 could be a valuable resource for biopolymers and bioactive molecules for industrial applications.\n\nGenome-based approach to evaluate the metabolic potentials and exopolysaccharides production of Bacillus paralicheniformis CamBx3 isolated from a Chilean hot spring.", "token_count": 507, "char_count": 1547, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:29.051308", "source": { "split": "train_shard_00001", "doc_id": 1438 }, "chunk_id": "train_shard_00001_1438_0", "global_id": 7675 }, { "text": "Staphylococcus argenteus (SARG) was discovered in 2009 as part of the Staphylococcus aureus (SAUR) complex and has been documented from various locations worldwide. In this article we describe the genomic features of five strains of SARG found in Christchurch, New Zealand. Isolates were first detected in 2019 using MALDI-ToF identification, and their identities confirmed using whole genome sequencing (WGS). Genomic features, including antimicrobial resistance markers and virulence factors were compared to other SARG sequences in NCBI GenBank and well-characterised features in SAUR. Four isolates belonged to ST2250 and one isolate to ST2793. Phylogenetic analysis based on core genome analysis revealed that all 5 isolates were phylogenetically distinct with four isolates clustering in the ST2250 clade. Three isolates contained staphylococcal cassette chromosome mec (SCCmec) type IV 2Bc, harbouring the mecA gene conferring resistance to beta-lactam antibiotics. All five strains shared many of the virulence genes found in the global SARG and SAUR isolates;however, no TSST-1 or PVL pathogenic genes were detected. This publication contributes additional data on global occurrences and genomic features of SARG.\n\nCharacterisation of Staphylococcus argenteus in Christchurch, New Zealand, and comparison to global strains.", "token_count": 357, "char_count": 1332, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6613, "quality_score": 0.8306, "entities": { "genes": [ "ST2793", "ST2250" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:29.637658", "source": { "split": "train_shard_00001", "doc_id": 1439 }, "chunk_id": "train_shard_00001_1439_0", "global_id": 7676 }, { "text": "The Lactobacillaceae family’s significance in food and health, combined with available strain-specific genomes, enables genome assessment through pangenome analysis. The ‘Alleleome’ of the core pangenomes of the Lactobacillaceae family, which identifies natural sequence variations, was reconstructed from the amino acid and nucleotide sequences of the core genes across 2,447 strains of 26 species. It comprised 3.71 million amino acid variants in 29,448 core genes across the family. The alleleome analysis of the Lactobacillaceae family revealed key findings: 1) In the core pangenome, amino acid substitutions prevailed over rare insertions and deletions, 2) Purifying negative selection primarily influenced core gene variations in the family, with diversifying selection noted in L. helveticus . L. plantarum ’s core alleleome was investigated due to its industrial importance. In L. plantarum , the defining characteristics of its core alleleome included: 1) It is highly conserved; 2) Among 235 isolation sources, the primary categories displaying variant prevalence were fermented food, feces, and unidentified sources; 3) It is predominantly characterized by ‘conservative’ and ‘moderately conservative’ mutations; and 4) Phylogroup-specific core variant gene analysis identified unique variants (DltX, FabZ1, Pts23B, CspP) in phylogroups ‘I’ and ‘B’ which could be used as identifier or validation markers of strain or phylogroup.\n\nGenomic insights intoLactobacillaceae: Analyzing the “Alleleome” of core pangenomes for enhanced understanding of strain diversity and revealing Phylogroup-specific unique variants", "token_count": 419, "char_count": 1630, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:30.261555", "source": { "split": "train_shard_00001", "doc_id": 1440 }, "chunk_id": "train_shard_00001_1440_0", "global_id": 7677 }, { "text": "Serotype surveillance of Streptococcus pneumoniae (the pneumococcus) is critical for understanding the effectiveness of current vaccination strategies. However, existing methods for serotyping are limited in their ability to identify co-carriage of multiple pneumococci and detect novel serotypes. To develop a scalable and portable serotyping method that overcomes these challenges, we employed nanopore adaptive sampling (NAS), an on-sequencer enrichment method that selects for target DNA in real-time, for direct detection of S. pneumoniae in complex samples. Whereas NAS targeting the whole S. pneumoniae genome was ineffective in the presence of nonpathogenic streptococci, the method was both specific and sensitive when targeting the capsular biosynthetic locus (CBL), the operon that determines S. pneumoniae serotype. NAS significantly improved coverage and yield of the CBL relative to sequencing without NAS and accurately quantified the relative prevalence of serotypes in samples representing co-carriage. To maximize the sensitivity of NAS to detect novel serotypes, we developed and benchmarked a new pangenome-graph algorithm, named GNASTy. We show that GNASTy outperforms the current NAS implementation, which is based on linear genome alignment, when a sample contains a serotype absent from the database of targeted sequences. The methods developed in this work provide an improved approach for novel serotype discovery and routine S. pneumoniae surveillance that is fast, accurate, and feasible in low-resource settings. Although NAS facilitates whole-genome enrichment under ideal circumstances, GNASTy enables targeted enrichment to optimize serotype surveillance in complex samples.\n\nOptimizing nanopore adaptive sampling for pneumococcal serotype surveillance in complex samples using the graph-based GNASTy algorithm.", "token_count": 450, "char_count": 1878, "word_count": 250, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:30.924958", "source": { "split": "train_shard_00001", "doc_id": 1441 }, "chunk_id": "train_shard_00001_1441_0", "global_id": 7678 }, { "text": "Antimicrobial resistance (AMR) gene cassettes comprise an AMR gene flanked by short recombination sites ( attI × attC or attC × attC ). Integrons are genetic elements able to capture, excise, and shuffle these cassettes, providing ‘adaptation on demand’, and can be found on both chromosomes and plasmids. Understanding the patterns of integron diversity may help to understand the epidemiology of AMR genes. As a case study, we examined the clinical resistance gene bla GES-5 , an integron-associated class A carbapenemase first reported in Greece in 2004 and since observed worldwide, which to our knowledge has not been the subject of a previous global analysis. Using a dataset comprising all NCBI contigs containing bla GES-5 ( n = 431), we developed a pangenome graph-based workflow to characterise and cluster the diversity of bla GES-5 -associated integrons. We demonstrate that bla GES-5 -associated integrons on plasmids are different to those on chromosomes. Chromosomal integrons were almost all identified in P. aeruginosa ST235, with a consistent gene cassette content and order. We observed instances where insertion sequence IS 110 disrupted attC sites, which might immobilise the gene cassettes and explain the conserved integron structure despite the presence of intI1 integrase promoters, which would typically facilitate capture or excision and rearrangement. The plasmid-associated integrons were more diverse in their gene cassette content and order, which could be an indication of greater integrase activity and ‘shuffling’ of integrons on plasmids.\n\nGlobal genomic epidemiology ofblaGES-5carbapenemase-associated integrons", "token_count": 426, "char_count": 1665, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:31.570640", "source": { "split": "train_shard_00001", "doc_id": 1442 }, "chunk_id": "train_shard_00001_1442_0", "global_id": 7679 }, { "text": "Cheese whey is a by-product of cheese-manufacturing industries, and the utilization of whey is a challenging problem either to use it or dispose it, because only few microorganisms can metabolize the whey lactose. Enzymatic hydrolysis of whey lactose to glucose and galactose by β-galactosidase is the approach for biotechnological application. Kluyveromyces marxianus cells were permeabilized with non-toxic, biodegradable, anionic detergent N-lauroyl sarcosine (N-LS) for the enzyme activity. The permeabilization process parameters (N-LS concentration, solvent volume, temperature and incubation time) were optimized. The maximum β-galactosidase activity of 1,220 IU/g dry weight was obtained using permeabilized cells under optimized conditions. Moreover, viability of the permeabilized cells was also evaluated, which showed that cells were alive; however, viability was reduced by two log cycles. The permeabilized cells were evaluated for whey lactose hydrolysis. The maximum lactose hydrolysis of 91% was observed with 600 mg (dry cell weight/100 mL) in whey powder (5% w/v) solution at 180-min incubation, pH 6.5 and 30 °C. Further, the hydrolyzed whey was evaluated for amelioration of growth of non-lactose-consuming yeast Saccharomyces cerevisiae. S. cerevisiae was able to grow in hydrolyzed whey simultaneously with K. marxianus. The study confirmed that N-LS could be used to permeabilize K. marxianus cells to make available the enzyme activity.\n\nPermeabilization of Kluyveromyces marxianus with mild detergent for whey lactose hydrolysis and augmentation of mixed culture.", "token_count": 459, "char_count": 1589, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:32.250515", "source": { "split": "train_shard_00001", "doc_id": 1443 }, "chunk_id": "train_shard_00001_1443_0", "global_id": 7680 }, { "text": "Mycoplasma mycoides subsp. mycoides (Mmm) is the causative agent of contagious bovine pleuropneumonia (CBPP), a severe respiratory disease affecting cattle mostly in sub-Saharan African countries. CBPP can cause significant economic losses, and there is a need for efficacious vaccines to help bring the disease under control. To that end, all publicly available non-redundant whole genome sequences of Mmm strains isolated from cattle (n = 15) were used to identify a 93% core genome of 806 genes, which included 86 of 208 genes encoding outer membrane and extracellular proteins identified from the literature. Many of them and their encoded protein products were found to be highly conserved at the sequence level, including at the sites of predicted epitope binding with bovine major histocompatibility complex (MHC) Class I and II molecules. Despite the high sequence conservation, multiple proteins had large differences in the numbers of MHC Class I and II epitopes and their predicted binding strengths. These results highlight several promising targets supporting the development of new recombinant protein vaccines for CBPP.\n\nDiversity and T-cell antigenic potentials of <i>Mycoplasma mycoides</i> subsp. <i>mycoides</i> vaccine candidates.", "token_count": 356, "char_count": 1309, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7418, "quality_score": 0.8709, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:32.842378", "source": { "split": "train_shard_00001", "doc_id": 1444 }, "chunk_id": "train_shard_00001_1444_0", "global_id": 7681 }, { "text": "The Lacticaseibacillus paracasei species is comprised by nomadic bacteria inhabiting a wide variety of ecological niches, from fermented foodstuffs to host-associated microenvironments. Lc. paracasei SP5 is a novel strain, originally isolated from kefir grains that presents desirable probiotic and biotechnological attributes. In this study, we applied genomic tools to further characterize the probiotic and biotechnological potential of the strain. Firstly, whole genome sequencing and assembly, were performed to construct the chromosome map of the strain and determine its genomic stability. Lc. paracasei SP5 carriers several insertion sequences, however, no plasmids or mobile elements were detected. Furthermore, phylogenomic and comparative genomic analyses were utilized to study the nomadic attributes of the strain, and more specifically, its metabolic capacity and ability to withstand environmental stresses imposed during food processing and passage through the gastrointestinal (GI) tract. More specifically, Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-active enzyme (CAZymes) analyses provided evidence for the ability of the stain to utilize an array of carbohydrates as growth substrates. Consequently, genes for heat, cold, osmotic shock, acidic pH, and bile salt tolerance were annotated. Importantly bioinformatic analysis showed that the novel strain does not harbor acquired antimicrobial resistance genes nor virulence factors, in agreement with previous experimental data. Putative bacteriocin biosynthesis clusters were identified using BAGEL4, suggesting its potential antimicrobial activity. Concerning microbe-host interactions, adhesins, moonlighting proteins, exopolysaccharide (EPS) biosynthesis genes and pilins mediating the adhesive phenotype were, also, pinpointed in the genome of Lc. paracasei SP5. Validation of this phenotype was performed by employing a microbiological method and confocal microscopy. Conclusively, Lc", "token_count": 513, "char_count": 2011, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6911, "quality_score": 0.8456, "entities": { "genes": [ "BAGEL4", "SP5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:33.499268", "source": { "split": "train_shard_00001", "doc_id": 1445 }, "chunk_id": "train_shard_00001_1445_0", "global_id": 7682 }, { "text": "paracasei SP5 harbors genes necessary for the manifestation of the probiotic character and application in the food industry. Upcoming studies will focus on the mechanisms of action of the novel strain at multiple levels.\n\nGenomic Insight Into Lacticaseibacillus paracasei SP5, Reveals Genes and Gene Clusters of Probiotic Interest and Biotechnological Potential.", "token_count": 98, "char_count": 373, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [ "SP5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:33.883749", "source": { "split": "train_shard_00001", "doc_id": 1445 }, "chunk_id": "train_shard_00001_1445_1", "global_id": 7683 }, { "text": "The Gram positive bacterium Streptococcus pneumoniae (pneumococcus) is a major human pathogen. It is a common colonizer of the human host, and in the nasopharynx, sinus, and middle ear it survives as a biofilm. This mode of growth is optimal for multi-strain colonization and genetic exchange. Over the last decades, the far-reaching use of antibiotics and the widespread implementation of pneumococcal multivalent conjugate vaccines have posed considerable selective pressure on pneumococci. This scenario provides an exceptional opportunity to study the evolution of the pangenome of a clinically important bacterium, and has the potential to serve as a case study for other species. The goal of this review is to highlight key findings in the studies of pneumococcal genomic diversity and plasticity.\n\nPuzzling Over the Pneumococcal Pangenome.", "token_count": 210, "char_count": 853, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:34.352307", "source": { "split": "train_shard_00001", "doc_id": 1446 }, "chunk_id": "train_shard_00001_1446_0", "global_id": 7684 }, { "text": "Carbapenem-resistant Enterobacteriaceae (CRE) are a global threat to human health and are increasingly being isolated from nonclinical settings. OXA-48-producing Escherichia coli sequence type 38 (ST38) is the most frequently reported CRE type in wild birds and has been detected in gulls or storks in North America, Europe, Asia, and Africa. The epidemiology and evolution of CRE in wildlife and human niches, however, remains unclear. We compared wild bird origin E. coli ST38 genome sequences generated by our research group and publicly available genomic data derived from other hosts and environments to (i) understand the frequency of intercontinental dispersal of E. coli ST38 clones isolated from wild birds, (ii) more thoroughly measure the genomic relatedness of carbapenem-resistant isolates from gulls sampled in Turkey and Alaska, USA, using long-read whole-genome sequencing and assess the spatial dissemination of this clone among different hosts, and (iii) determine whether ST38 isolates from humans, environmental water, and wild birds have different core or accessory genomes (e.g., antimicrobial resistance genes, virulence genes, plasmids) which might elucidate bacterial or gene exchange among niches. Our results suggest that E. coli ST38 strains, including those resistant to carbapenems, are exchanged between humans and wild birds, rather than separately maintained populations within each niche. Furthermore, despite close genetic similarity among OXA-48-producing E. coli ST38 clones from gulls in Alaska and Turkey, intercontinental dispersal of ST38 clones among wild birds is uncommon. Interventions to mitigate the dissemination of antimicrobial resistance throughout the environment (e.g., as exemplified by the acquisition of carbapenem resistance by birds) may be warranted. IMPORTANCE Carbapenem-resistant bacteria are a threat to public health globally and have been found in the environment as well as the clinic", "token_count": 483, "char_count": 1964, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8087, "entities": { "genes": [ "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:35.012017", "source": { "split": "train_shard_00001", "doc_id": 1447 }, "chunk_id": "train_shard_00001_1447_0", "global_id": 7685 }, { "text": "Some bacterial clones are associated with carbapenem resistance genes, such as Escherichia coli sequence type 38 (ST38) and the carbapenemase gene blaOXA-48. This is the most frequently reported carbapenem-resistant clone in wild birds, though it was unclear if it circulated within wild bird populations or was exchanged among other niches. The results from this study suggest that E. coli ST38 strains, including those resistant to carbapenems, are frequently exchanged among wild birds, humans, and the environment. Carbapenem-resistant E. coli ST38 clones in wild birds are likely acquired from the local environment and do not constitute an independent dissemination pathway within wild bird populations. Management actions aimed at preventing the environmental dissemination and acquisition of antimicrobial resistance by wild birds may be warranted.\n\nExchange of Carbapenem-Resistant Escherichia coli Sequence Type 38 Intercontinentally and among Wild Bird, Human, and Environmental Niches.", "token_count": 255, "char_count": 1015, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6547, "quality_score": 0.8273, "entities": { "genes": [ "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:35.493305", "source": { "split": "train_shard_00001", "doc_id": 1447 }, "chunk_id": "train_shard_00001_1447_1", "global_id": 7686 }, { "text": "Wild Malus species harbor untapped genetic diversity to advance apple breeding, particularly for disease resistance and stress tolerance. However, existing marker panels, developed mainly using Malus domestica accessions, introduce ascertainment bias and limit detecting rare variants in wild species. We developed and validated a medium-density and cost-effective pan-generic 3K apple DArTag panel optimized to capture genome-wide variation across the Malus genus. The panel was constructed using conserved, syntenic, and collinear genomic blocks identified within the core genome of 13 Malus accessions for cross-species transferability. The panel was validated across three bi-parental mapping populations totaling 593 progeny. Across these populations, 2,461–3,234 SNP markers were polymorphic and 1,482–2,620 were informative. Each population contained over 900 multiallelic micro-haplotype loci, with several hundred loci exhibiting three or four distinct haplotypes. Markers were uniformly distributed across all 17 chromosomes, each containing between 60–230 informative SNPs. The panel was further evaluated on 174 diverse germplasm accessions from 20 Malus species. It exhibited strong cross-species transferability, exceptionally low rates of missing data (<0.5%), and clear genetic differentiation between wild and domesticated accessions. Genome-wide association studies (GWAS) identified a major locus on chromosome 4 significantly linked to fruit length, weight, and width in addition to trait-specific associations on chromosomes 1, 6, 9, and 11. The cost-effectiveness of genotyping per sample (<$15), combined with these results, underscore the panel′s broad utility for quantitative trait locus (QTL) mapping in bi-parental and diverse populations, marker-assisted selection in the breeding programs, and genetic diversity analysis across the Malus genus.\n\nA pan-generic marker panel for apples to enable genetic research and breeding across Malus species", "token_count": 490, "char_count": 1981, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6756, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:36.144434", "source": { "split": "train_shard_00001", "doc_id": 1448 }, "chunk_id": "train_shard_00001_1448_0", "global_id": 7687 }, { "text": "A strictly aerobic, Gram-stain-negative, rod-shaped and motile bacterium, designated strain KMM 296, isolated from the coelomic fluid of mussel Crenomytilus grayanus , was investigated in details due to its ability to produce a highly active alkaline phosphatase of the structural family PhoA. A previous taxonomic study placed the strain to the species Cobetia marina , a member of the family Halomonadaceae of the class Gammaproteobacteria . However, the comprehensive phylogenetic analysis based on 16S rRNA gene sequencing revealed that the strain KMM 296 is most closely related to Cobetia amphilecti NRIC 815 T with the 16S rRNA gene sequence similarity of 100%. The mussel isolate grew with 0.5-19% NaCl and at 4 - 42°C and hydrolysed Tweens 20 and 40, and L-tyrosine. The DNA G+C content was 62.5 mol%. The prevalent fatty acids were C 18:1 ω7 c , C 12:0 3-OH, C 18:1 ω7 c , C 12:0 and C 17:0 cyclo. The polar lipid profile was characterized by the presence of phosphatidylethanolamine, phosphatidylglycerol, phosphatidic acid, and unidentified aminolipid, phospholipid, and lipids. The major respiratory quinone was Q-8. According to phylogenetic evidence and similarity in the chemotaxonomic and genotypic properties of the mussel isolate and its nearest neighbors, the strain KMM 296 represents a member of the species C. amphilecti . A comparative analysis of the type strains genomes of the species C. amphilecti and C. litoralis showed that they belong to a single species. In addition, a high similarity of the genome sequences of C. pacifica NRIC 813 T and C", "token_count": 500, "char_count": 1574, "word_count": 253, "semantic_coherence": 1, "information_density": 0.581, "quality_score": 0.7905, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:36.793422", "source": { "split": "train_shard_00001", "doc_id": 1449 }, "chunk_id": "train_shard_00001_1449_0", "global_id": 7688 }, { "text": "marina LMG 2217 T also allows suggesting the affiliation of these two species to one species. Based on the rules of priority, C. litoralis should be reclassified as a later heterotypic synonym of C. amphilecti , and C. pacifica is a later heterotypic synonym of C. marina . The emended descriptions of the species C. amphilecti and C. marina are also proposed.\n\nPangenome- and genome-based taxonomic classification inference for the marine bacterial strain KMM 296 producing a highly active PhoA alkaline phosphatase and closely relatedCobetiaspecies", "token_count": 160, "char_count": 557, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6941, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:37.232063", "source": { "split": "train_shard_00001", "doc_id": 1449 }, "chunk_id": "train_shard_00001_1449_1", "global_id": 7689 }, { "text": "The potential impact of aromatic and pectinolytic yeasts on cocoa flavour was investigated using two defined mixed starter cultures encompassing strains of Pichia kluyveri and Kluyveromyces marxianus for inoculating cocoa beans in small scale tray fermentations. Samples for microbial and metabolite analysis were collected at 12-24 hour intervals during 120 h of fermentation. Yeast isolates were grouped by (GTG)5-based rep-PCR fingerprinting and identified by sequencing of the D1/D2 region of the 26S rRNA gene and the actin gene. Pulsed Field Gel Electrophoresis (PFGE) was conducted on isolates belonging to the species P. kluyveri and K. marxianus to verify strain level identity with the inoculated strains. Furthermore, Denaturing Gradient Gel Electrophoresis (DGGE) was performed to follow yeast and bacterial dynamics over time including the presence of the bacterial inoculum consisting of Lactobacillus fermentum and Acetobacter pasteurianus. Yeast cell counts peaked after 12 h of fermentation with the predominant species being identified as Hanseniaspora opuntiae and Hanseniaspora thailandica. P. kluyveri and K. marxianus were found to compose 9.3% and 13.5% of the yeast population, respectively, after 12 h of fermentation whilst PFGE showed that ~88% of all P. kluyveri isolates and 100% of all K. marxianus isolates were identical to the inoculated strains. Despite never being the dominant yeast species at any stage of fermentation, the un-conched chocolates produced from the two inoculated fermentations were judged by sensory analysis to differ in flavour profile compared to the spontaneously fermented control. This could indicate that yeasts have a greater impact on the sensory qualities of cocoa than previously assumed.", "token_count": 479, "char_count": 1752, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6016, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:37.879624", "source": { "split": "train_shard_00001", "doc_id": 1450 }, "chunk_id": "train_shard_00001_1450_0", "global_id": 7690 }, { "text": "Influencing cocoa flavour using Pichia kluyveri and Kluyveromyces marxianus in a defined mixed starter culture for cocoa fermentation.", "token_count": 41, "char_count": 134, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:38.241418", "source": { "split": "train_shard_00001", "doc_id": 1450 }, "chunk_id": "train_shard_00001_1450_1", "global_id": 7691 }, { "text": "Among coagulase-negative staphylococci, Staphylococcus haemolyticus is a primary cause of bloodstream infections in preterm infants, with gut colonisation being recognised as a risk factor for subsequent infection. Through a re-analysis of a 16S rRNA gene sequencing dataset (n=497 preterm infants), we found that S. haemolyticus was abundant and prevalent in the gut in the first month of life. To better understand the diversity of S. haemolyticus among preterm infants, we generated genome sequences of S. haemolyticus strains (n=140), which were isolated from 44 stool samples of 22 preterm infants from four different hospitals in the United Kingdom. Core genome phylogenetic analyses, incorporating 126 publicly available S. haemolyticus genome sequences, showed that 85/140 (60.1%) of the isolates, from three different hospitals, formed a clonal group with 79/85 (92.9%) strains being assigned to Multi-Locus Sequence Type (ST) 49. Antibiotic resistance genes were highly prevalent in the genome sequences. Using logistic regression, we found a strong association between the presence of the gene mecA and phenotypic resistance to oxacillin (odds ratio [OR]: 158.00, p<0.0001), and the aacA-aphD gene and phenotypic resistance to gentamicin aacA-aphD (OR: 162.00, p<0.001). None of the strains from the preterm infant cohort had a complete Staphylococcal Cassette Chromosome mec (SCC mec ) element. The aacA-aphD gene was associated with the transposon Tn 4001. Using hybrid genome assemblies, we found it to be present on the chromosome (54.5% of strains) or on diverse plasmids (27.3%). Four strains (18.2%) had Tn 4001 copies on both plasmid and chromosome", "token_count": 514, "char_count": 1667, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6194, "quality_score": 0.8097, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:39.253056", "source": { "split": "train_shard_00001", "doc_id": 1451 }, "chunk_id": "train_shard_00001_1451_0", "global_id": 7692 }, { "text": "Our data suggest the existence of a distinct sub-population of S. haemolyticus that has adapted to colonise the gut of preterm infants. Prevalent resistance to antibiotics is of clinical concern and the diversity of genetic contexts of mecA and Tn 4001 suggests widespread horizontal gene transfer and recombination in this species.\n\nStaphylococcus haemolyticus is a reservoir of antibiotic resistance genes in the preterm infant gut", "token_count": 113, "char_count": 440, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7231, "quality_score": 0.8615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:39.630296", "source": { "split": "train_shard_00001", "doc_id": 1451 }, "chunk_id": "train_shard_00001_1451_1", "global_id": 7693 }, { "text": "Long non-coding RNAs (lncRNAs) are regulatory molecules interacting in a wide array of biological processes. LncRNAs in fungal pathogens can be responsive to stress and play roles in regulating growth and nutrient acquisition. Recent evidence suggests that lncRNAs may also play roles in virulence, such as regulating pathogenicity-associated enzymes and on-host reproductive cycles. Despite the importance of lncRNAs, only few model fungi have well-documented inventories of lncRNA. In this study, we apply a machine-learning based pipeline to predict high-confidence lncRNA candidates in Zymoseptoria tritici, an important global pathogen of wheat impacting global food production. We analyzed genomic features of lncRNAs and the most likely associated processes through analyses of expression over a host infection cycle. We find that lncRNAs are frequently expressed during early infection, before the switch to necrotrophic growth. They are mostly located in facultative heterochromatic regions, which are known to contain many genes associated with pathogenicity. Furthermore, we find that lncRNAs are frequently co-expressed with genes that may be involved in responding to host signals, such as those responses to oxidative stress. Finally, we assess pangenome features of lncRNAs using four additional reference-quality genomes. We find evidence that the repertoire of expressed lncRNAs varies substantially between individuals, even though lncRNA loci tend to be shared at the genomic level. Overall, this study provides a repertoire and putative functions of lncRNAs in Z. tritici enabling molecular genetics and functional analyses in an important pathogen.

Impact statement

Long non-coding RNAs (lncRNAs) serve distinct roles from messenger RNA. Despite not encoding proteins, lncRNAs can control important cellular processes such as growth and response to stress. In fungal pathogens, lncRNAs are particularly interesting because they can influence how pathogens infect and harm their hosts. Yet, only very few fungal pathogens have high-quality repertoires of lncRNA established", "token_count": 506, "char_count": 2102, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:40.269620", "source": { "split": "train_shard_00001", "doc_id": 1452 }, "chunk_id": "train_shard_00001_1452_0", "global_id": 7694 }, { "text": "Here, we used machine learning to identify lncRNA in the major wheat pathogen Zymoseptoria tritici. We found that lncRNAs are highly active during the early stages of infection, before the pathogen switches to necrotrophic growth. These lncRNAs are mainly located in regions of the genome associated with pathogenicity. The repertoire of expressed lncRNAs varies substantially among individuals highlighting the potential for pathogen adaptation based on variation in lncRNAs. By expanding our knowledge of lncRNAs in important pathogen models, we enable research to comprehensively investigating their roles across fungi.\n\nThe expression landscape and pangenome of long non-coding RNA in the fungal wheat pathogenZymoseptoria tritici", "token_count": 183, "char_count": 741, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7379, "quality_score": 0.8689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:40.717724", "source": { "split": "train_shard_00001", "doc_id": 1452 }, "chunk_id": "train_shard_00001_1452_1", "global_id": 7695 }, { "text": "Escherichia coli and other Enterobacteriaceae are diverse species with \"open\" pangenomes, where genes move intra- and interspecies via horizontal gene transfer. However, most analyses focus on clinical isolates. The pangenome dynamics of natural populations remain understudied, despite their suggested role as reservoirs for antimicrobial resistance (AMR) genes. Here, we analyze near-complete genomes for 827 Enterobacteriaceae (553 Escherichia and 274 non-Escherichia spp.) with 2292 circularized plasmids in total, collected from 19 locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30-km radius at three time points over a year. We find different dynamics for chromosomal and plasmid-borne genes. Plasmids have a higher burden of AMR genes and insertion sequences, and AMR-gene-carrying plasmids show evidence of being under stronger selective pressure. Environmental niche and local geography both play a role in shaping plasmid dynamics. Our results highlight the importance of local strategies for controlling the spread of AMR.\n\nNiche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae.", "token_count": 316, "char_count": 1204, "word_count": 162, "semantic_coherence": 1, "information_density": 0.7531, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:41.280540", "source": { "split": "train_shard_00001", "doc_id": 1453 }, "chunk_id": "train_shard_00001_1453_0", "global_id": 7696 }, { "text": "Two recent articles describe a pangenome of potato and a graph-based pangenome for tomato, respectively. The latter improves our understanding of the tomato genomics architecture even further and the use of this graph-based pangenome versus a single reference dramatically improves heritability in tomato.\n\nSolanaceae pangenomes are coming of graphical age to bring heritability back.", "token_count": 92, "char_count": 391, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:41.657007", "source": { "split": "train_shard_00001", "doc_id": 1454 }, "chunk_id": "train_shard_00001_1454_0", "global_id": 7697 }, { "text": "In many bioinformatics applications the task is to identify biologically significant locations in an individual genome. In our work, we are interested in finding high-density clusters of such biologically meaningful locations in a graph representation of a pangenome, which is a collection of related genomes. Different formulations of finding such clusters were previously studied for sequences. In this work, we study an extension of this problem for graphs, which we formalize as finding a set of vertex-disjoint paths with a maximum score in a weighted directed graph. We provide a linear-time algorithm for a special class of graphs corresponding to elastic-degenerate strings, one of pangenome representations. We also provide a fixed-parameter tractable algorithm for directed acyclic graphs with a special path decomposition of a limited width.\n\nIdentifying Clusters in Graph Representations of Genomes", "token_count": 180, "char_count": 910, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:42.116190", "source": { "split": "train_shard_00001", "doc_id": 1455 }, "chunk_id": "train_shard_00001_1455_0", "global_id": 7698 }, { "text": "Furunculosis, caused by Aeromonas salmonicida, poses a significant threat to both salmonid and non-salmonid fish in diverse aquatic environments. This study explores the genomic intricacies of re-emergent A. salmonicida outbreaks in Atlantic salmon (Salmo salar). Previous clinical cases have exhibited pathological characteristics, such as periorbital hemorrhages and gastrointestinal abnormalities. Genomic sequencing of three Chilean isolates (ASA04, ASA05, and CIBA_5017) and 25 previously described genomes determined the pan-genome, phylogenomics, insertion sequences, and restriction-modification systems. Unique gene families have contributed to an improved understanding of the psychrophilic and mesophilic clades, while phylogenomic analysis has been used to identify mesophilic and psychrophilic strains, thereby further differentiating between typical and atypical psychrophilic isolates. Diverse insertion sequences and restriction-modification patterns have highlighted genomic structural differences, and virulence factor predictions can emphasize exotoxin disparities, especially between psychrophilic and mesophilic strains. Thus, a novel plasmid was characterized which emphasized the role of plasmids in virulence and antibiotic resistance. The analysis of antibiotic resistance factors revealed resistance against various drug classes in Chilean strains. Overall, this study elucidates the genomic dynamics of re-emergent A. salmonicida and provides novel insights into their virulence, antibiotic resistance, and population structure.\n\nGenomics of Re-Emergent Aeromonas salmonicida in Atlantic Salmon Outbreaks.", "token_count": 433, "char_count": 1667, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [ "ASA05", "ASA04" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:42.795959", "source": { "split": "train_shard_00001", "doc_id": 1456 }, "chunk_id": "train_shard_00001_1456_0", "global_id": 7699 }, { "text": "

Background

Pseudomonas aeruginosa is a ubiquitous environmental microorganism and also a common cause of infection. Its ability to survive in many different environments and persistently colonize humans is linked to its presence in biofilms formed on indwelling device surfaces. Biofilm promotes adhesion to, and survival on surfaces, protects from desiccation and the actions of antibiotics and disinfectants.

Results

We examined the genetic basis for biofilm production on polystyrene at room (22 °C) and body temperature (37 °C) within 280 P. aeruginosa. 193 isolates (69 %) produced more biofilm at 22 °C than at 37 °C. Using GWAS and pan-GWAS, we found a number of accessory genes significantly associated with greater biofilm production at 22 °C. Many of these are present on a 165 kb region containing genes for heavy metal resistance (arsenic, copper, mercury and cadmium), transcriptional regulators and methytransferases. We also discovered multiple core genome SNPs in the A-type flagellin gene and Type II secretion system gene xpsD. Analysis of biofilm production of isolates of the MDR ST111 and ST235 lineages on stainless-steel revealed several accessory genes associated with enhanced biofilm production. These include a putative translocase with homology to a Helicobacter pylori type IV secretion system protein, a TA system II toxin gene and the alginate biosynthesis gene algA, several transcriptional regulators and methytransferases as well as core SNPs in genes involved in quorum sensing and protein translocation.

Conclusions

Using genetic association approaches we discovered a number of accessory genes and core-genome SNPs that were associated with enhanced early biofilm formation at 22 °C compared to 37 °C. These included a 165 kb genomic island containing multiple heavy metal resistance genes, transcriptional regulators and methyltransferases", "token_count": 496, "char_count": 1899, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5846, "quality_score": 0.7923, "entities": { "genes": [ "ST111", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:44.196333", "source": { "split": "train_shard_00001", "doc_id": 1457 }, "chunk_id": "train_shard_00001_1457_0", "global_id": 7700 }, { "text": "We hypothesize that this genomic island may be associated with overall genotypes that are environmentally adapted to survive at lower temperatures. Further work to examine their importance in, for example gene-knockout studies, are required to confirm their relevance. GWAS and pan-GWAS approaches have great potential as a first step in examining the genetic basis of novel bacterial phenotypes.\n\nBiofilm associated genotypes of multiple antibiotic resistant Pseudomonas aeruginosa.", "token_count": 109, "char_count": 483, "word_count": 67, "semantic_coherence": 1, "information_density": 0.8806, "quality_score": 0.9403, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:44.582335", "source": { "split": "train_shard_00001", "doc_id": 1457 }, "chunk_id": "train_shard_00001_1457_1", "global_id": 7701 }, { "text": "

Objectives

Development of a system for direct lactose to ethanol fermentation provides a market for the massive amounts of underutilized whey permeate made by the dairy industry. For this system, glucose and galactose metabolism were uncoupled in Saccharomyces cerevisiae by deleting two negative regulatory genes, GAL80 and MIG1, and introducing the essential lactose hydrolase LAC4 and lactose transporter LAC12, from the native but inefficient lactose fermenting yeast Kluyveromyces marxianus.

Results

Previously, integration of the LAC4 and LAC12 genes into the MIG1 and NTH1 loci was achieved to construct strain AY-51024M. Low rates of lactose conversion led us to generate the Δmig1Δgal80 diploid mutant strain AY-GM from AY-5, which exhibited loss of diauxic growth and glucose repression, subsequently taking up galactose for consumption at a significantly higher rate and yielding higher ethanol concentrations than strain AY-51024M. Similarly, in cheese whey permeate powder solution (CWPS) during three, repeated, batch processes in a 5L bioreactor containing either 100 g/L or 150 g/L lactose, the lactose uptake and ethanol productivity rates were both significantly greater than that of AY-51024M, while the overall fermentation times were considerably lower.

Conclusions

Using the Cre-loxp system for deletion of the MIG1 and GAL80 genes to relieve glucose repression, and LAC4 and LAC12 overexpression to increase lactose uptake and conversion provides an efficient basis for yeast fermentation of whey permeate by-product into ethanol.\n\nUncoupling glucose sensing from GAL metabolism for heterologous lactose fermentation in Saccharomyces cerevisiae.", "token_count": 496, "char_count": 1690, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5991, "quality_score": 0.7996, "entities": { "genes": [ "NTH1", "LAC12", "LAC4", "MIG1", "GAL80" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:45.236428", "source": { "split": "train_shard_00001", "doc_id": 1458 }, "chunk_id": "train_shard_00001_1458_0", "global_id": 7702 }, { "text": "The draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia) is presented. The complete genome assembly was of 2 713 207 bp with predicted completeness of 99.38%. Genome structural annotation revealed 2674 protein-coding genes, 127 pseudogenes and 77 RNA genes. Pangenome analysis of 7 currently available high quality Caldanaerobacter spp. genomes including 1523vc revealed 4673 gene clusters. Of them, 1130 clusters formed a core genome of genus Caldanaerobacter. Of the rest 3543 Caldanaerobacter pangenome genes, 385 were exclusively represented in 1523vc genome. 101 of 2801 Caldanaerobacter CDS were found to be encoding carbohydrate-active enzymes (CAZymes). The majority of CAZymes were predicted to be involved in degradation of beta-linked polysaccharides as chitin, cellulose and hemicelluloses, reflecting the metabolism of strain 1523vc, isolated on cellulose. 5 of 101 CAZyme genes were found to be unique for the strain 1523vc and belonged to GH23, GT56, GH15 and two CE9 family proteins. The draft genome of strain 1523vc was deposited at DBJ/EMBL/GenBank under the accessions JABEQB000000000, PRJNA629090 and SAMN14766777 for Genome, Bioproject and Biosample, respectively.", "token_count": 470, "char_count": 1319, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.8361, "entities": { "genes": [ "GH15", "SAMN14766777", "GH23", "CE9", "JABEQB000000000", "GT56", "PRJNA629090" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:45.876893", "source": { "split": "train_shard_00001", "doc_id": 1459 }, "chunk_id": "train_shard_00001_1459_0", "global_id": 7703 }, { "text": "Data on draft genome sequence of Caldanaerobacter sp. strain 1523vc, a thermophilic bacterium, isolated from a hot spring of Uzon Caldera, (Kamchatka, Russia).", "token_count": 57, "char_count": 166, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:46.242852", "source": { "split": "train_shard_00001", "doc_id": 1459 }, "chunk_id": "train_shard_00001_1459_1", "global_id": 7704 }, { "text": "The pathogenic bacterium Clostridioides difficile is a worldwide health burden with increasing morbidity, mortality and antibiotic resistances. Therefore, extensive research efforts are made to unravel its virulence and dissemination. One crucial aspect for C. difficile is its mobilome, which for instance allows the spread of antibiotic resistance genes (ARG) or influence strain virulence. As a nosocomial pathogen, the majority of strains analyzed originated from clinical environments and infected individuals. Nevertheless, C. difficile can also be present in human intestines without disease development or occur in diverse environmental habitats such as puddle water and soil, from which several strains could already be isolated. We therefore performed comprehensive genome comparisons of closely related clinical and non-clinical strains to identify the effects of the clinical background. Analyses included the prediction of virulence factors, ARGs, mobile genetic elements (MGEs), and detailed examinations of the pan genome. Clinical-related trends were thereby observed. While no significant differences were identified in fundamental C. difficile virulence factors, the clinical strains carried more ARGs and MGEs, and possessed a larger accessory genome. Detailed inspection of accessory genes revealed higher abundance of genes with unknown function, transcription-associated, or recombination-related activity. Accessory genes of these functions were already highlighted in other studies in association with higher strain virulence. This specific trend might allow the strains to react more efficiently on changing environmental conditions in the human host such as emerging stress factors, and potentially increase strain survival, colonization, and strain virulence. These findings indicated an adaptation of the strains to the clinical environment. Further, implementation of the analysis results in pairwise genome comparisons revealed that the majority of these accessory genes were encoded on predicted MGEs, shedding further light on the mobile genome of C. difficile. We therefore encourage the inclusion of non-clinical strains in comparative analyses.\n\nComparative genome analyses of clinical and non-clinical Clostridioides difficile strains.", "token_count": 506, "char_count": 2313, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5817, "quality_score": 0.7908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:46.868158", "source": { "split": "train_shard_00001", "doc_id": 1460 }, "chunk_id": "train_shard_00001_1460_0", "global_id": 7705 }, { "text": "The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and guide public health actions, the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks were examined. A total of 48 isolates from human cases and cooling towers were sequenced and compared using single-nucleotide polymorphism (SNP)-based core-genome multilocus sequencing typing (MLST) and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (CBD) in March and May and those in suburb 1. These isolates were designated the \"main cluster\" and consisted of isolates from two patients from the CBD March outbreak, one patient and one tower isolate from suburb 1, and isolates from two cooling towers and three patients from the CBD May outbreak. All main cluster isolates were sequence type 211 (ST211), which previously has only been reported in Canada. Significantly, pangenome analysis identified mobile genetic elements containing a unique type IV A F-type secretion system (T4ASS), which was specific to the main cluster, and cocirculating clinical strains, suggesting a potential mechanism for increased fitness and persistence of the outbreak clone. Genome sequencing enabled linking of the geographically dispersed environmental sources of infection among the spatially and temporally coinciding cases of legionellosis in a highly populated urban setting. The discovery of a unique T4ASS emphasizes the role of genome recombination in the emergence of successful Lp1 clones.IMPORTANCE A new emerging clone has been responsible for a prolonged legionellosis outbreak in Sydney, Australia. The use of whole-genome sequencing linked two outbreaks thought to be unrelated and confirmed the outliers. These findings led to the resampling and subsequent identification of the source, guiding public health actions and bringing the outbreak to a close. Significantly, the outbreak clone was identified as sequence type 211 (ST211). Our study reports this ST in the Southern Hemisphere and presents a description of ST211 genomes from both clinical and environmental isolates", "token_count": 519, "char_count": 2261, "word_count": 327, "semantic_coherence": 1, "information_density": 0.578, "quality_score": 0.789, "entities": { "genes": [ "ST211" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:47.503783", "source": { "split": "train_shard_00001", "doc_id": 1461 }, "chunk_id": "train_shard_00001_1461_0", "global_id": 7706 }, { "text": "A unique mobile genetic element containing a type IV secretion system was identified in Lp1 ST211 isolates linked to the main cluster and Lp1 ST42 isolates that were cocirculating at the time of the outbreak.\n\nGenome Sequencing Links Persistent Outbreak of Legionellosis in Sydney (New South Wales, Australia) to an Emerging Clone of Legionella pneumophila Sequence Type 211.", "token_count": 99, "char_count": 375, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8276, "quality_score": 0.9138, "entities": { "genes": [ "ST211", "ST42" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:47.882106", "source": { "split": "train_shard_00001", "doc_id": 1461 }, "chunk_id": "train_shard_00001_1461_1", "global_id": 7707 }, { "text": "Streptococcus equi subsp. equi (SEE) is a host-restricted equine pathogen considered to have evolved from Streptococcus equi subsp. zooepidemicus (SEZ). SEZ is promiscuous in host range and is commonly recovered from horses as a commensal. Comparison of a single strain each of SEE and SEZ using whole-genome sequencing, supplemented by PCR of selected genes in additional SEE and SEZ strains, was used to characterize the evolution of SEE. But the known genetic variability of SEZ warrants comparison of the whole genomes of multiple SEE and SEZ strains. To fill this knowledge gap, we utilized whole-genome sequencing to characterize the accessory genome elements (AGEs; i.e., elements present in some SEE strains but absent in SEZ or vice versa) and methylomes of 50 SEE and 50 SEZ isolates from Texas. Consistent with previous findings, AGEs consistently found in all SEE isolates were primarily from mobile genetic elements that might contribute to host restriction or pathogenesis of SEE. Fewer AGEs were identified in SEZ because of the greater genomic variability among these isolates. The global methylation patterns of SEE isolates were more consistent than those of the SEZ isolates. Among homologous genes of SEE and SEZ, differential methylation was identified only in genes of SEE encoding proteins with functions of quorum sensing, exopeptidase activity, and transitional metal ion binding. Our results indicate that effects of genetic mobile elements in SEE and differential methylation of genes shared by SEE and SEZ might contribute to the host specificity of SEE. IMPORTANCE Strangles, caused by the host-specific bacterium Streptococcus equi subsp. equi (SEE), is the most commonly diagnosed infectious disease of horses worldwide. Its ancestor, Streptococcus equi subsp. zooepidemicus (SEZ), is frequently isolated from a wide array of hosts, including horses and humans", "token_count": 499, "char_count": 1926, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5366, "quality_score": 0.7683, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:48.536154", "source": { "split": "train_shard_00001", "doc_id": 1462 }, "chunk_id": "train_shard_00001_1462_0", "global_id": 7708 }, { "text": "A comparison of the genomes of a single strain of SEE and SEZ has been reported, but sequencing of further isolates has revealed variability among SEZ strains. Thus, the importance of this study is that it characterizes genomic and methylomic differences of multiple SEE and SEZ isolates from a common geographic region (viz., Texas). Our results affirm many of the previously described differences between the genomes of SEE and SEZ, including the role of mobile genetic elements in contributing to host restriction. We also provide the first characterization of the global methylome of Streptococcus equi and evidence that differential methylation might contribute to the host restriction of SEE.\n\nDifferences in the Accessory Genomes and Methylomes of Strains of Streptococcus equi subsp. equi and of Streptococcus equi subsp. zooepidemicus Obtained from the Respiratory Tract of Horses from Texas.", "token_count": 233, "char_count": 922, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:49.006760", "source": { "split": "train_shard_00001", "doc_id": 1462 }, "chunk_id": "train_shard_00001_1462_1", "global_id": 7709 }, { "text": "UCYN-A (Cand. Atelocyanobacterium thalassa) has recently been recognized as a globally-distributed, early stage, nitrogen-fixing organelle (the 'nitroplast') of cyanobacterial origin present in select species of haptophyte algae (e.g., Braarudosphaera bigelowii). Although the nitroplast was recognized as the UCYN-A2 sublineage, it is yet to be confirmed in other sublineages of the algal/UCYN-A complex. We used water samples collected from Halifax Harbour (Bedford Basin, Nova Scotia, Canada) and the offshore Scotian Shelf to further our understanding of B. bigelowii and UCYN-A in the coastal Northwest Atlantic. Sequencing data revealed UCYN-A-associated haptophyte signatures and yielded near-complete metagenome-assembled genomes (MAGs) for UCYN-A1, UCYN-A4, and the plastid of the A4-associated haptophyte. Comparative genomics provided new insights into the pangenome of UCYN-A. The UCYN-A4 MAG is the first genome sequenced from this sublineage and shares ~85% identity with the UCYN-A2 nitroplast. Genes missing in the reduced genome of the nitroplast were also missing in the A4 MAG supporting its likely classification as a nitroplast as well. The UCYN-A1 MAG was found to be nearly 100% identical to the reference genome despite coming from different ocean basins. Time-series data paired with the recurrence of specific microbes in enrichment cultures gave insight into the microbes that frequently co-occur with the algal/UCYN-A complex (e.g., Pelagibacter ubique). Overall, our study expands knowledge of UCYN-A and its host across major ocean basins and investigates their co-occurring microbes in the coastal Northwest Atlantic (NWA), thereby facilitating future studies on the underpinnings of haptophyte-associated diazotrophy in the sea.", "token_count": 507, "char_count": 1760, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6735, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:49.650394", "source": { "split": "train_shard_00001", "doc_id": 1463 }, "chunk_id": "train_shard_00001_1463_0", "global_id": 7710 }, { "text": "Targeted metagenomics reveals pangenomic diversity of the nitroplast (UCYN-A) and its algal host plastid", "token_count": 31, "char_count": 104, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:50.005560", "source": { "split": "train_shard_00001", "doc_id": 1463 }, "chunk_id": "train_shard_00001_1463_1", "global_id": 7711 }, { "text": "Abstract

Horizontal gene transfer (HGT) is a major driver of bacterial evolution, but its role in shaping the human gut microbiome over time remains poorly understood. Here, we present a longitudinal metagenomic analysis of 676 fecal samples from 338 individuals collected ~4 years apart, using a newly developed workflow to detect recent HGT events from metagenome-assembled genomes. We identified 5,644 high-confidence HGT events occurring within the past ~10,000 years across 116 gut bacterial species. We find that species pairs with a HGT relationship were significantly more likely to maintain stable ecological relationships over the 4-year period, suggesting that gene exchange contributes to ecological stability. Notably, HGT and strain replacement act together to disseminate mobile genes in the population. Furthermore, our observation that an individual's mobile gene pool remains highly personalized and stable over time indicates that host lifestyles drive specific gene transfer. For example, proton pump inhibitor usage was linked to increased transfer of multidrug transporter genes. Our findings demonstrate, at individual gut microbiome level, that HGT is both an integral and stabilizing force in the human gut ecosystem and an important mechanism for disseminating adaptive functions, underscoring their potential for tracking host lifestyle.

\n\nLongitudinal Gut Microbiota Tracking Reveals the Persistent Spread of Mobile Genes and HGT-Driven Community Stabilization", "token_count": 333, "char_count": 1510, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6986, "quality_score": 0.8493, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:50.574100", "source": { "split": "train_shard_00001", "doc_id": 1464 }, "chunk_id": "train_shard_00001_1464_0", "global_id": 7712 }, { "text": "

Key message

Genome adaptation, driven by mutations, transposable elements, and structural variations, relies on plasticity and instability. This allows populations to evolve, enhance fitness, and adapt to challenges like climate change. Genomes adapt via mutations, transposable elements, DNA structural changes, and epigenetics. Genome plasticity enhances fitness by providing the genetic variation necessary for organisms to adapt their traits and survive, which is especially critical during rapid climate shifts. This plasticity often stems from genome instability, which facilitates significant genomic alterations like duplications or deletions. While potentially harmful initially, these changes increase genetic diversity, aiding adaptation. Major genome reorganizations arise from polyploidization and horizontal gene transfer, both linked to instability. Plasticity and restructuring can modify Quantitative Trait Loci (QTLs), contributing to adaptation. Tools like landscape genomics identify climate-selected regions, resurrection ecology reveals past adaptive responses, and pangenome analysis examines a species' complete gene set. Signatures of past selection include reduced diversity and allele frequency shifts. Gene expression plasticity allows environmental adaptation without genetic change through mechanisms like alternative splicing, tailoring protein function. Co-opted transposable elements also generate genetic and regulatory diversity, contributing to genome evolution. This review consolidates these findings, repositioning genome instability not as a mere source of random error but as a fundamental evolutionary engine that provides the rapid adaptive potential required for plant survival in the face of accelerating climate change.\n\nClimate change and plant genomic plasticity.", "token_count": 352, "char_count": 1819, "word_count": 228, "semantic_coherence": 1, "information_density": 0.7018, "quality_score": 0.8509, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:51.148205", "source": { "split": "train_shard_00001", "doc_id": 1465 }, "chunk_id": "train_shard_00001_1465_0", "global_id": 7713 }, { "text": "Genomic characterization of Cannabis sativa has accelerated rapidly in the last decade as sequencing costs have decreased and public and private interest in the species has increased. Here, we present seven new chromosome-level haplotype-phased genomes of C. sativa. All of these genotypes were alive at the time of publication, and several have numerous years of associated phenotype data. We performed a k-mer-based pangenome analysis to contextualize these assemblies within over 200 existing assemblies. This allowed us to identify unique haplotypes and genomic diversity among Cannabis sativa genotypes. We leveraged linkage maps constructed from F2 progeny of two of the assembled genotypes to characterize the recombination rate across the genome showing strong periphery-biased recombination. Lastly, we re-aligned a bulk segregant analysis dataset for the major-effect flowering locus Early1 to several of the new assemblies to evaluate the impact of reference bias on the mapping results and narrow the locus to a smaller region of the chromosome. These new assemblies, combined with the continued propagation of the genotypes, will contribute to the growing body of genomic resources for C. sativa to accelerate future research efforts.\n\nComparison of Recombination Rate, Reference Bias, and Unique Pangenomic Haplotypes in <i>Cannabis sativa</i> Using Seven De Novo Genome Assemblies.", "token_count": 384, "char_count": 1461, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:51.762468", "source": { "split": "train_shard_00001", "doc_id": 1466 }, "chunk_id": "train_shard_00001_1466_0", "global_id": 7714 }, { "text": "

Introduction

The antibiotic crisis is a major human health problem. Bioprospecting screenings suggest that proteobacteria and other extremophile microorganisms have biosynthetic potential for the production novel antimicrobial compounds. An Antarctic Sphingomonas strain (So64.6b) previously showed interesting antibiotic activity and elicitation response, then a relationship between environmental adaptations and its biosynthetic potential was hypothesized. We aimed to determine the genomic characteristics in So64.6b strain related to evolutive traits for the adaptation to the Antarctic environment that could lead to its diversity of potentially novel antibiotic metabolites.

Methods

The complete genome sequence of the Antarctic strain was obtained and mined for Biosynthetic Gene Clusters (BGCs) and other unique genes related to adaptation to extreme environments. Comparative genome analysis based on multi-locus phylogenomics, BGC phylogeny, and pangenomics were conducted within the closest genus, aiming to determine the taxonomic affiliation and differential characteristics of the Antarctic strain.

Results and discussion

The Antarctic strain So64.6b showed a closest identity with Sphingomonas alpina, however containing a significant genomic difference of ortholog cluster related to degradation multiple pollutants. Strain So64.6b had a total of six BGC, which were predicted with low to no similarity with other reported clusters; three were associated with potential novel antibiotic compounds using ARTS tool. Phylogenetic and synteny analysis of a common BGC showed great diversity between Sphingomonas genus but grouping in clades according to similar isolation environments, suggesting an evolution of BGCs that could be linked to the specific ecosystems. Comparative genomic analysis also showed that Sphingomonas species isolated from extreme environments had the greatest number of predicted BGCs and a higher percentage of genetic content devoted to BGCs than the isolates from mesophilic environments. In addition, some extreme-exclusive clusters were found related to oxidative and thermal stress adaptations, while pangenome analysis showed unique resistance genes on the Antarctic strain included in genetic islands", "token_count": 515, "char_count": 2276, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:52.418626", "source": { "split": "train_shard_00001", "doc_id": 1467 }, "chunk_id": "train_shard_00001_1467_0", "global_id": 7715 }, { "text": "Altogether, our results showed the unique genetic content on Antarctic strain Sphingomonas sp. So64.6, -a probable new species of this genetically divergent genus-, which could have potentially novel antibiotic compounds acquired to cope with Antarctic poly-extreme conditions.\n\nAntarctic Sphingomonas sp. So64.6b showed evolutive divergence within its genus, including new biosynthetic gene clusters.", "token_count": 109, "char_count": 408, "word_count": 52, "semantic_coherence": 1, "information_density": 0.9038, "quality_score": 0.9519, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:52.797801", "source": { "split": "train_shard_00001", "doc_id": 1467 }, "chunk_id": "train_shard_00001_1467_1", "global_id": 7716 }, { "text": "Rice seed microbiota play a vital role throughout their growth and developmental stages. Xanthomonas sontii is known as an abundant, core-vertically transmitted rice seed endophyte with probiotic properties. Studies reveal a less explored world of non-pathogenic Xanthomonas (NPX) species like X. sontii and X. indica that are associated with healthy rice seeds. The present study reports the isolation, biochemical characterization, and in-depth taxonogenomic evidence for a third NPX species, X. protegens , from rice seeds, a taxonomic outlier of X. sontii . It also highlights the importance of using multiple taxonogenomic indices to identify taxonomic outlier species. Similar to the other two NPX species, the new member species is also non-pathogenic and provides in vivo protection to rice plants from Xanthomonas oryzae pv. oryzae upon leaf clip inoculation. The pangenome investigation suggested a set of unique genes to the novel species that might be important in adaptation to rice plants and differentiate it from other NPX species. The study will allow the design of markers for the identification of these NPX members, targeted culturomics of a particular NPX species and in the discovery of other novel NPX species from healthy rice seed microbiome for further exploitation in rice health.\n\nXanthomonas protegenssp. nov., a rice seed-associated probiotic and taxonomic outlier species ofXanthomonas sontii", "token_count": 356, "char_count": 1437, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:53.376479", "source": { "split": "train_shard_00001", "doc_id": 1468 }, "chunk_id": "train_shard_00001_1468_0", "global_id": 7717 }, { "text": "To improve the xylose fermentation ability of Kluyveromyces marxianus, a xylose assimilation pathway through xylose isomerase was constructed. The genes encoding xylose reductase (KmXyl1) and xylitol dehydrogenase (KmXyl2) were disrupted in K. marxianus YHJ010 and the resultant strain was named YRL002. A codon-optimized xylose isomerase gene from Orpinomyces was transformed into K. marxianus YRL002 and expressed under GAPDH promoter. The transformant was adapted in the SD medium containing 1 % casamino acid with 2 % xylose as sole carbon source. After 32 times of trans-inoculation, a strain named YRL005, which can grow at a specific growth rate of 0.137/h with xylose as carbon source, was obtained. K. marxianus YRL005 could ferment 30.15 g/l of xylose and produce 11.52 g/l ethanol with a yield of 0.38 g/g, production rate of 0.069 g/l/h at 42 °C, and also could ferment 16.60 g/l xylose to produce 5.21 g/l ethanol with a yield of 0.31 g/g, and production rate of 0.054 g/l h at 45 °C. Co-fermentation with 2 % glucose could not improve the amount and yield of ethanol fermented from xylose obviously, but it could improve the production rate. Furthermore, K. marxianus YRL005 can ferment with the corn cob hydrolysate, which contained 20.04 g/l xylose to produce 8.25 g/l ethanol. It is a good platform to construct thermo-tolerant xylose fermentation yeast.\n\nImproved xylose fermentation of Kluyveromyces marxianus at elevated temperature through construction of a xylose isomerase pathway.", "token_count": 513, "char_count": 1504, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5404, "quality_score": 0.7702, "entities": { "genes": [ "YRL005", "YHJ010", "YRL002" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:54.029797", "source": { "split": "train_shard_00001", "doc_id": 1469 }, "chunk_id": "train_shard_00001_1469_0", "global_id": 7718 }, { "text": "Intergeneric fusants were obtained by protoplast fusion between the thermotolerant yeast, Kluyveromyces marxianus, and the starch-assimilating yeast, Schwanniomyces occidentalis. Two thermotolerant fusants growing at 40 degrees C were screened on the medium containing soluble starch. These fusants showed weak growth in a soluble starch medium and the production of a little amylase. The carbon source assimilation and the chromosome composition of the fusants were similar to those of the K. marxianus parent. However, a chromosomal difference from K. marxianus was recognized in the fusants. These results show the possibility that the fusants are amylase-producing strains rearranged from K. marxianus.\n\nGrowth characteristics of fusants by protoplast fusion between the thermotolerant yeast, Kluyveromyces marxianus, and the starch-assimilating yeast, Schwanniomyces occidentalis.", "token_count": 233, "char_count": 885, "word_count": 118, "semantic_coherence": 1, "information_density": 0.5763, "quality_score": 0.7881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:54.546617", "source": { "split": "train_shard_00001", "doc_id": 1470 }, "chunk_id": "train_shard_00001_1470_0", "global_id": 7719 }, { "text": "Bacillus anthracis causes anthrax through virulence factors encoded on two plasmids. However, non-B. anthracis organisms within the closely related, environmentally ubiquitous Bacillus cereus group (BCG) may cause an anthrax-like disease in humans through the partial adoption of anthrax-associated virulence genes, challenging the definition of anthrax disease. To elucidate these phenomena and their evolutionary past, we performed whole-genome sequencing on non-anthracis BCG isolates, including 93 archival (1967-2003) and 5 contemporary isolates (2019-2023). We produced annotated genomic assemblies and performed a pan-genome analysis to identify evidence of virulence gene homology and virulence gene acquisition by linear inheritance or horizontal gene transfer. At least one anthrax-associated virulence gene was annotated in ten isolates. Most homologous sequences in archival isolates showed evidence of pseudogenization and subsequent gene loss. The presence or absence of accessory genes, including anthrax-associated virulence genes, aligned with the phylogenetic structure of the BCG core genome. These findings support the hypothesis that anthrax-associated virulence genes were inherited from a common ancestor in the BCG and were retained or lost across different lineages, and contribute to a growing body of work informing public health strategies related to anthrax surveillance and identification.\n\nInvestigating Anthrax-Associated Virulence Genes among Archival and Contemporary <i>Bacillus cereus</i> Group Genomes.", "token_count": 413, "char_count": 1579, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8284, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:55.185869", "source": { "split": "train_shard_00001", "doc_id": 1471 }, "chunk_id": "train_shard_00001_1471_0", "global_id": 7720 }, { "text": "Pangenomes are collections of annotated genome sequences of multiple individuals of a species. The structural variants uncovered by these datasets are a major asset to genetic analysis in crop plants. Here, we report a pangenome of barley comprising long-read sequence assemblies of 76 wild and domesticated genomes and short-read sequence data of 1,315 genotypes. An expanded catalogue of sequence variation in the crop includes structurally complex loci that have become hot spots of gene copy number variation in evolutionarily recent times. To demonstrate the utility of the pangenome, we focus on four loci involved in disease resistance, plant architecture, nutrient release, and trichome development. Novel allelic variation at a powdery mildew resistance locus and population-specific copy number gains in a regulator of vegetative branching were found. Expansion of a family of starch-cleaving enzymes in elite malting barleys was linked to shifts in enzymatic activity in micro-malting trials. Deletion of an enhancer motif is likely to change the developmental trajectory of the hairy appendages on barley grains. Our findings indicate that rapid evolution at structurally complex loci may have helped crop plants adapt to new selective regimes in agricultural ecosystems.\n\nAdaptive diversification through structural variation in barley", "token_count": 298, "char_count": 1348, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:55.791392", "source": { "split": "train_shard_00001", "doc_id": 1472 }, "chunk_id": "train_shard_00001_1472_0", "global_id": 7721 }, { "text": "

Motivation

Pangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments. Existing related approaches depend on a single reference, a specific ordering of genomes or a de Bruijn model based on a fixed k-mer length. A scalable, self-contained method to build pangenome graphs without such limitations would be a key step in pangenome construction and manipulation pipelines.

Results

We design the seqwish algorithm, which builds a variation graph from a set of sequences and alignments between them. We first transform the alignment set into an implicit interval tree. To build up the variation graph, we query this tree-based representation of the alignments to reduce transitive matches into single DNA segments in a sequence graph. By recording the mapping from input sequence to output graph, we can trace the original paths through this graph, yielding a pangenome variation graph. We present an implementation that operates in external memory, using disk-backed data structures and lock-free parallel methods to drive the core graph induction step. We demonstrate that our method scales to very large graph induction problems by applying it to build pangenome graphs for several species.

Availability and implementation

seqwish is published as free software under the MIT open source license. Source code and documentation are available at https://github.com/ekg/seqwish. seqwish can be installed via Bioconda https://bioconda.github.io/recipes/seqwish/README.html or GNU Guix https://github.com/ekg/guix-genomics/blob/master/seqwish.scm.\n\nUnbiased pangenome graphs.", "token_count": 403, "char_count": 1755, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8174, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:56.427789", "source": { "split": "train_shard_00001", "doc_id": 1473 }, "chunk_id": "train_shard_00001_1473_0", "global_id": 7722 }, { "text": "

Summary

Pangenomes are replacing single reference genomes as the definitive representation of DNA sequence within a species or clade. Pangenome analysis predominantly leverages graph-based methods that require computationally intensive multiple genome alignments, do not scale to highly complex eukaryotic genomes, limit their scope to identifying structural variants (SVs), or incur bias by relying on a reference genome. Here, we present PanKmer, a toolkit designed for reference-free analysis of pangenome datasets consisting of dozens to thou-sands of individual genomes. PanKmer decomposes a set of input genomes into a table of observed k -mers and their presence-absence values in each genome. These are stored in an efficient k -mer index data format that encodes SNPs, INDELs, and SVs. It also includes functions for downstream analysis of the k -mer index, such as calculating sequence similarity statistics between individuals at whole-genome or local scales. For example, k -mers can be “anchored” in any individual genome to quantify sequence variability or conservation at a specific locus. This facilitates workflows with various biological applications, e.g. identifying cases of hybridization between plant species. PanKmer provides researchers with a valuable and convenient means to explore the full scope of genetic variation in a population, without reference bias.

Availability and implementation

PanKmer is implemented as a Python package with components written in Rust, released under a BSD license. The source code is available from the Python Package Index (PyPI) at https://pypi.org/project/pankmer/ as well as Gitlab at https://gitlab.com/salk-tm/pankmer . Full documentation is available at https://salk-tm.gitlab.io/pankmer/ .

Supplementary information

Supplementary data are available online\n\nPanKmer:k-mer based and reference-free pangenome analysis", "token_count": 455, "char_count": 1916, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6692, "quality_score": 0.8346, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:57.063026", "source": { "split": "train_shard_00001", "doc_id": 1474 }, "chunk_id": "train_shard_00001_1474_0", "global_id": 7723 }, { "text": "

Motivation

Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space are still challenging due to this high diversity. In contrast, amino acid sequences have higher similarity due to evolutionary constraints, whereby a single amino acid may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, panproteomes present an attractive alternative leveraging the higher sequence similarity while not losing much of the genome in non-coding regions.

Results

We present PanPA, a method that takes a set of multiple sequence alignments of protein sequences, indexes them, and builds a graph for each multiple sequence alignment. In the querying step, it can align DNA or amino acid sequences back to these graphs. We first showcase that PanPA generates correct alignments on a panproteome from 1350 Escherichia coli. To demonstrate that panproteomes allow comparisons at longer phylogenetic distances, we compare DNA and protein alignments from 1073 Salmonella enterica assemblies against E.coli reference genome, pangenome, and panproteome using BWA, GraphAligner, and PanPA, respectively; with PanPA aligning around 22% more sequences. We also aligned a DNA short-reads whole genome sequencing (WGS) sample from S.enterica against the E.coli reference with BWA and the panproteome with PanPA, where PanPA was able to find alignment for 68% of the reads compared to 5% with BWA.

Availalability and implementation

PanPA is available at https://github.com/fawaz-dabbaghieh/PanPA.\n\nPanPA: generation and alignment of panproteome graphs.", "token_count": 492, "char_count": 1921, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:57.712688", "source": { "split": "train_shard_00001", "doc_id": 1475 }, "chunk_id": "train_shard_00001_1475_0", "global_id": 7724 }, { "text": "

Background

Targeting of cellular proteins to the extracellular environment is directed by a secretory signal sequence located at the N-terminus of a secretory protein. These signal sequences usually contain an N-terminal basic amino acid followed by a stretch containing hydrophobic residues, although no consensus signal sequence has been identified. In this study, simple modeling of signal sequences was attempted using Gaussia princeps secretory luciferase (GLuc) in the yeast Kluyveromyces marxianus, which allowed comprehensive recombinant gene construction to substitute synthetic signal sequences.

Results

Mutational analysis of the GLuc signal sequence revealed that the GLuc hydrophobic peptide length was lower limit for effective secretion and that the N-terminal basic residue was indispensable. Deletion of the 16th Glu caused enhanced levels of secreted protein, suggesting that this hydrophilic residue defined the boundary of a hydrophobic peptide stretch. Consequently, we redesigned this domain as a repeat of a single hydrophobic amino acid between the N-terminal Lys and C-terminal Glu. Stretches consisting of Phe, Leu, Ile, or Met were effective for secretion but the number of residues affected secretory activity. A stretch containing sixteen consecutive methionine residues (M16) showed the highest activity; the M16 sequence was therefore utilized for the secretory production of human leukemia inhibitory factor protein in yeast, resulting in enhanced secreted protein yield.

Conclusions

We present a new concept for the provision of secretory signal sequence ability in the yeast K. marxianus, determined by the number of residues of a single hydrophobic residue located between N-terminal basic and C-terminal acidic amino acid boundaries.\n\nSynthetic signal sequences that enable efficient secretory protein production in the yeast Kluyveromyces marxianus.", "token_count": 451, "char_count": 1908, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:58.345761", "source": { "split": "train_shard_00001", "doc_id": 1476 }, "chunk_id": "train_shard_00001_1476_0", "global_id": 7725 }, { "text": "The phosphoethanolamine modified exopolysaccharide cellulose is a major extracellular matrix component of Escherichia coli and Salmonella typhimurium . Upon enhanced acute virulence, however, cellulose production can be diminished or entirely abolished. Here, we report that homologs of the bcsABC core genes of the core genome bcs cellulose biosynthesis operon and even entire bcs operons can be mobilized on plasmids and are occasionally manifested on E. coli chromosomes at alternative locations. While BcsA2 and BcsA3 cellulose synthases are restricted to the genus Escherichia , the BcsA4 cellulose synthase and the entire associated bcs gene cluster are highly similar to one of the two chromosomal bcs gene clusters harboured by Klebsiella pneumoniae . Cyclic di-GMP turnover proteins known to post-translationally regulate cellulose biosynthesis are frequently localized on bcs operon bearing plasmids. In thermotolerant meat derived E. coli 740v1 harbouring a type 4 bcs operon on a plasmid, chemical and genetic evidence indicates that cellulose is produced in M9 minimal medium and upon activation by the second messenger cyclic di-GMP, an allosteric activator of the cellulose synthase, respectively. With gene duplication and horizontal gene transfer to contribute to the multiplication of bcs operons in a number of different bacterial species, the ecological role(s) of multiplication, transfer and replacement of cellulose biosynthesis operons also in species other than E. coli still need to be unraveled.\n\nDiverse horizontally transferred cellulose biosynthesis gene clusters in Escherichia coli strains", "token_count": 435, "char_count": 1628, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:10:58.974678", "source": { "split": "train_shard_00001", "doc_id": 1477 }, "chunk_id": "train_shard_00001_1477_0", "global_id": 7726 }, { "text": ": Among more than twenty species belonging to the class Mollecutes, Mycoplasma bovis is the most common cause of bovine mycoplasmosis in North America and Europe. Bovine mycoplasmosis causes significant economic loss in the cattle industry. The number of M. bovis positive herds recently has increased in North America and Europe. Since antibiotic treatment is ineffective and no efficient vaccine is available, M. bovis induced mycoplasmosis is primarily controlled by herd management measures such as the restriction of moving infected animals out of the herds and culling of infected or shedders of M. bovis. To better understand the population structure and genomic factors that may contribute to its transmission, we sequenced 147 M. bovis strains isolated from four different countries viz. USA (n = 121), Canada (n = 22), Israel (n = 3) and Lithuania (n = 1). All except two of the isolates (KRB1 and KRB8) were isolated from two host types i.e., bovine (n = 75) and bison (n = 70). We performed a large-scale comparative analysis of M. bovis genomes by integrating 103 publicly available genomes and our dataset (250 total genomes). Whole genome single nucleotide polymorphism (SNP) based phylogeny using M. agalactiae as an outgroup revealed that M. bovis population structure is composed of five different clades. USA isolates showed a high degree of genomic divergence in comparison to the Australian isolates. Based on host of origin, all the isolates in clade IV was of bovine origin, whereas majority of the isolates in clades III and V was of bison origin. Our comparative genome analysis also revealed that M", "token_count": 517, "char_count": 1739, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6084, "quality_score": 0.8042, "entities": { "genes": [ "KRB1", "KRB8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:10:59.634322", "source": { "split": "train_shard_00001", "doc_id": 1478 }, "chunk_id": "train_shard_00001_1478_0", "global_id": 7727 }, { "text": "bovis has an open pangenome with a large breadth of unexplored diversity of genes. The function based analysis of autogenous vaccine candidates (n = 10) included in this study revealed that their functional diversity does not span the genomic diversity observed in all five clades identified in this study. Our study also found that M. bovis genome harbors a large number of IS elements and their number increases significantly (p = 7.8x10-6) as the genome size increases. Collectively, the genome data and the whole genome-based population analysis in this study may help to develop better understanding of M. bovis induced mycoplasmosis in cattle.\n\nPopulation Genomic Analysis of Mycoplasma bovis Elucidates Geographical Variations and Genes associated with Host-Types.", "token_count": 223, "char_count": 821, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:00.097964", "source": { "split": "train_shard_00001", "doc_id": 1478 }, "chunk_id": "train_shard_00001_1478_1", "global_id": 7728 }, { "text": "

Background

Non-coding RNAs (ncRNAs), which perform diverse regulatory roles, have been found in organisms from all superkingdoms of life. However, there have been limited numbers of studies on the functions of ncRNAs, especially in nonmodel organisms such as Kluyveromyces marxianus that is widely used in the field of industrial biotechnology.

Results

In this study, we measured changes in transcriptome at three time points during the exponential growth phase of K. marxianus by using strand-specific RNA-seq. We found that approximately 60% of the transcriptome consists of ncRNAs transcribed from antisense and intergenic regions of the genome that were transcribed at lower levels than mRNA. In the transcriptome, a substantial number of long antisense ncRNAs (lancRNAs) are differentially expressed and enriched in carbohydrate and energy metabolism pathways. Furthermore, this enrichment is evolutionarily conserved, at least in yeast. Particularly, the mode of regulation of mRNA/lancRNA pairs is associated with mRNA transcription levels; the correlation between the pairs is positive at high mRNA transcriptional levels and negative at low levels. In addition, significant induction of mRNA and coverage of more than half of the mRNA sequence by a lancRNA strengthens the positive correlation between mRNA/lancRNA pairs.

Conclusions

Transcriptome sequencing of K. marxianus in the exponential growth phase reveals pervasive transcription of ncRNAs with evolutionarily conserved functions. Studies of the mode of regulation of mRNA/lancRNA pairs suggest that induction of lancRNA may be associated with switch-like behavior of mRNA/lancRNA pairs and efficient regulation of the carbohydrate and energy metabolism pathways in the exponential growth phase of K. marxianus being used in industrial applications.\n\nFunctional elucidation of the non-coding RNAs of Kluyveromyces marxianus in the exponential growth phase.", "token_count": 507, "char_count": 1946, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5243, "quality_score": 0.7622, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:00.754222", "source": { "split": "train_shard_00001", "doc_id": 1479 }, "chunk_id": "train_shard_00001_1479_0", "global_id": 7729 }, { "text": "The transmission of foodborne pathogens via contact with contaminated surfaces in meat processing is a significant public health concern. This study characterizes Escherichia coli (n = 50) obtained before and after disinfection in slaughterhouses in Edo State, Nigeria, focusing on biocide and antimicrobial susceptibility, biofilm formation, and curli fimbriae and cellulose production. Whole genome sequencing (WGS) was employed to assess the genetic diversity, resistome, and virulome of the isolates. Biocide susceptibility testing did not suggest resistance, with minimum inhibitory and minimum bactericidal concentrations significantly lower than in-use concentrations. Isolates obtained after disinfection of slaughterhouse surfaces formed stronger biofilms on average, independent of curli fimbriae and cellulose production. Phylogenetic analysis revealed a broad variety of genotypes, including atypical enteropathogenic E. coli and extraintestinal pathogenic lineages such as the global lineage ST10. Notably, two E. coli harbouring blaCTX₋M₋₁₅ were identified. Core genome MLST verified clonal spread within slaughterhouses as well as recurring isolation of clones over time. Venn analysis indicated that carrying virulence genes encoding effector delivery systems favoured strong biofilm formation. Our findings suggest that meat-processing environments can serve as reservoirs for E. coli carrying blaCTX₋M₋₁₅E. coli, contributing to the dissemination of pathogenic strains that pose significant environmental and public health risks.\n\nGenetic diversity, biocide susceptibility and biofilm forming ability of Escherichia coli isolates from slaughterhouse environments in Nigeria", "token_count": 401, "char_count": 1691, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8463, "entities": { "genes": [ "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:01.375643", "source": { "split": "train_shard_00001", "doc_id": 1480 }, "chunk_id": "train_shard_00001_1480_0", "global_id": 7730 }, { "text": "The yeast Kluyveromyces marxianus is considered as a potential alternative to Saccharomyces cerevisiae in producing ethanol as a biofuel. In this study, we investigated the ethanol fermentation properties of novel K. marxianus strain DMB1, isolated from bagasse hydrolysates. This strain utilized sorbitol as well as various pentoses and hexoses as single carbon sources under aerobic conditions and produced ethanol from glucose in hydrolysates of the Japanese cedar at 42 °C. Reference strains K. marxianus NBRC1777 and S. cerevisiae BY4743 did not assimilate sorbitol or ferment lignocellulosic hydrolysates to ethanol at this temperature. Thus strain DMB1 appears to be optimal for producing bioethanol at high temperatures, and might provide a valuable means of increasing the efficiency of ethanol fermentation.\n\nBioethanol production from Lignocellulosic biomass by a novel Kluyveromyces marxianus strain.", "token_count": 251, "char_count": 912, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6589, "quality_score": 0.8295, "entities": { "genes": [ "DMB1", "BY4743", "NBRC1777" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:01.874298", "source": { "split": "train_shard_00001", "doc_id": 1481 }, "chunk_id": "train_shard_00001_1481_0", "global_id": 7731 }, { "text": "Erratum: Development and implementation of a Core Genome Multilocus Sequence Typing (cgMLST) scheme for <i>Haemophilus influenzae</i>.", "token_count": 49, "char_count": 146, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:02.235291", "source": { "split": "train_shard_00001", "doc_id": 1482 }, "chunk_id": "train_shard_00001_1482_0", "global_id": 7732 }, { "text": "The wisent ( Bison bonasus ) is Europe’s largest land mammal. We produced a HiFi read-based wisent assembly with a contig N50 value of 91 Mb containing 99.7% of BUSCO genes which improves contiguity a thousand-fold over an existing assembly. Extended runs of homozygosity in the wisent genome compromised the separation of the HiFi reads into parental-specific read sets, which resulted in inferior haplotype assemblies. A bovine super-pangenome built with assemblies from wisent, bison, gaur, yak, taurine and indicine cattle identified a 1,580 bp deletion removing the protein-coding sequence of THRSP encoding thyroid hormone-responsive protein from the wisent and bison genomes. Analysis of 725 sequenced samples across the Bovinae subfamily showed that the deletion is fixed in both Bison species but absent in Bos and Bubalus . The THRSP transcript is abundant in adipose, fat, liver, muscle, and mammary gland tissue of Bos and Bubalus , but absent in bison indicating that the deletion inactivates THRSP possibly contributing to low bison milk and meat fat content. We show that super-pangenomes can reveal potentially trait-associated variation across phylogenies, but also demonstrate that haplotype assemblies from species that went through population bottlenecks warrant scrutiny, as they may have accumulated long runs of homozygosity that complicate phasing.\n\nWisent genome assembly uncovers extended runs of homozygosity and a large deletion that inactivates the thyroid hormone responsive gene", "token_count": 396, "char_count": 1509, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:02.857367", "source": { "split": "train_shard_00001", "doc_id": 1483 }, "chunk_id": "train_shard_00001_1483_0", "global_id": 7733 }, { "text": "Candidatus Accumulibacter is a unique and pivotal genus of polyphosphate-accumulating organisms (PAOs) prevalent in wastewater treatment plants, and plays mainstay roles in the global phosphorus cycle. Whereas, the efforts toward a complete understanding of their genetic and metabolic characteristics are largely hindered by major limitations in existing sequence-based annotation methods, leaving more than half of their protein-encoding genes unannotated. To address the challenge, we developed a comprehensive approach integrating pangenome analysis, gene-based protein structure and function prediction, and metatranscriptomic analysis, extending beyond the constraints of sequence-centric methodologies. The application to Ca . Accumulibacter allowed the establishment of the pan- Ca . Accumulibacter proteome structure database, providing references for >200,000 proteins. Benchmarking on 28 Ca . Accumulibacter genomes showed major increases in the average annotation coverage from 51% to 83%. Genetic and metabolic characteristics that had eluded exploration via conventional methods were unraveled. For instance, the identification of a previously unknown phosphofructokinase gene suggests that all Ca. Accumulibacter encoded a complete Embden-Meyerhof-Parnas pathway. A previously defined homolog of phosphate-specific transport system accessory protein (PhoU) was actually an inorganic phosphate transport (Pit) accessory protein, regulating Pit instead of the high-affinity phosphate transport (Pst), a key to the emergence of the polyphosphate-accumulating trait of Ca. Accumulibacter. Additional lineage members were found encoding complete denitrification pathways. This study offers a readily usable and transferable tool for the establishment of high-coverage annotation reference databases for diverse cultured and uncultured bacteria, facilitating the exploration and understanding of genomic dark matter in the bacterial domain.

Synopsis

A integrated and advanced approach unraveling key genomic dark matter in Ca . Accumulibacter and readily applicable to diverse bacteria for customerized high-coverage annotation reference database establishment", "token_count": 490, "char_count": 2178, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:03.505789", "source": { "split": "train_shard_00001", "doc_id": 1484 }, "chunk_id": "train_shard_00001_1484_0", "global_id": 7734 }, { "text": "From gene to structure: Unraveling genomic dark matter inCa. Accumulibacter", "token_count": 27, "char_count": 82, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:03.866720", "source": { "split": "train_shard_00001", "doc_id": 1484 }, "chunk_id": "train_shard_00001_1484_1", "global_id": 7735 }, { "text": "The Klebsiella pneumoniae Species Complex (KpSC) is a major source of nosocomial infections globally with high rates of resistance to antimicrobials. Consequently, there is growing interest in understanding virulence factors and their association with cellular metabolic processes for developing novel anti-KpSC therapeutics. Phenotypic assays have revealed metabolic diversity within the KpSC, but metabolism research has been neglected due to experiments being difficult and cost-intensive. Genome-scale metabolic models (GSMMs) represent a rapid and scalable in silico approach for exploring metabolic diversity, which compiles genomic and biochemical data to reconstruct the metabolic network of an organism. Here we use a diverse collection of 507 KpSC isolates, including representatives of globally distributed clinically-relevant lineages, to construct the most comprehensive KpSC pan-metabolic model to-date, KpSC pan v2. Candidate metabolic reactions were identified using gene orthology to known metabolic genes, prior to manual curation via extensive literature and database searches. The final model comprised a total of 3,550 reactions, 2,403 genes and can simulate growth on 360 unique substrates. We used KpSC pan v2 as a reference to derive strain-specific GSMMs for all 507 KpSC isolates, and compared these to GSMMs generated using a prior KpSC pan-reference (KpSC pan v1) and two single-strain references. We show that KpSC pan v2 includes a greater proportion of accessory reactions (8.8%) than KpSC pan v1 (2.5%). GSMMs derived from KpSC pan v2 also result in more accuracy growth predictions than those derived from other references in both aerobic (median accuracy = 95.4%) and anaerobic (median accuracy = 78.8%). KpSC pan v2 also generates more accurate growth predictions, with high median accuracies of 95.4% (aerobic, n=37 isolates) and 78.8% (anaerobic, n=36 isolates) for 124 matched carbon substrates", "token_count": 520, "char_count": 1932, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:04.511508", "source": { "split": "train_shard_00001", "doc_id": 1485 }, "chunk_id": "train_shard_00001_1485_0", "global_id": 7736 }, { "text": "KpSC pan v2 is freely available at https://github.com/kelwyres/KpSC-pan-metabolic-model , representing a valuable resource for the scientific community, both as a source of curated metabolic information and as a reference to derive accurate strain-specific GSMMs. The latter can be used to investigate the relationship between KpSC metabolism and traits of interest, such as reservoirs, epidemiology, drug resistance or virulence, and ultimately to inform novel KpSC control strategies.

Significance as a BioResource to the community

Klebsiella pneumoniae and its close relatives in the K. pneumoniae Species Complex (KpSC) are priority antimicrobial resistant pathogens that exhibit extensive genomic diversity. There is growing interest in understanding KpSC metabolism, and genome scale metabolic models (GSMMs) provide a rapid, scalable option for exploration of whole cell metabolism plus phenotype prediction. Here we present a KpSC pan-metabolic model representing the cellular metabolism of 507 diverse KpSC isolates. Our model is the largest and most comprehensive of its kind, comprising >2,400 genes associated with >3,500 metabolic reactions, plus manually curated evidence annotations. These data alone represent a key knowledge resource for the Klebsiella research community; however, our model’s greatest impact lies in its potential for use as a reference from which highly accurate strain-specific GSMMs can be derived to inform in depth strain-specific and/or large-scale comparative analyses.

Data summary

Klebsiella pneumoniae species complex (KpSC) pan v2 metabolic model available at https://github.com/kelwyres/KpSC-pan-metabolic-model . All KpSC isolate whole genome sequences used in this work were reported previously and are available under Bioprojects PRJEB6891, PRJNA351909, PRJNA493667, PRJNA768294, PRJNA253462, PRJNA292902 and PRJNA391323", "token_count": 515, "char_count": 1888, "word_count": 250, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [ "PRJNA493667", "PRJNA351909", "PRJNA292902", "PRJNA768294", "PRJNA391323", "PRJEB6891", "PRJNA253462" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:05.153741", "source": { "split": "train_shard_00001", "doc_id": 1485 }, "chunk_id": "train_shard_00001_1485_1", "global_id": 7737 }, { "text": "Individual accessions listed in Table S1. Strain-specific GSMMs used for comparative analyses (deposited in Figshare - 10.6084/m9.figshare.24871914), plus their associated MEMOTE reports (indicates completeness and annotation quality), reaction and gene presence-absence matrices across all isolates. Growth phenotype predictions derived from strain-specific GSMMs are available in Table S4. Binarised Biolog growth phenotype data for n=37 isolates (plates PM1 and PM2, aerobic and anaerobic conditions) are available in Tables S6 & S7. Additional growth assay data for six substrates not included on Biolog plates PM1 and PM2 (deposited in Figshare - 10.6084/m9.figshare.24871914).\n\nA validated pangenome-scale metabolic model for theKlebsiella pneumoniaespecies complex", "token_count": 240, "char_count": 778, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7475, "quality_score": 0.8737, "entities": { "genes": [ "PM1", "PM2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:05.630929", "source": { "split": "train_shard_00001", "doc_id": 1485 }, "chunk_id": "train_shard_00001_1485_2", "global_id": 7738 }, { "text": "Methicillin-resistant Staphylococcus aureus bloodstream infections (MRSA-BSI) are a significant cause of mortality. We analysed the evolution of the molecular and clinical epidemiology of MRSA-BSI (n = 784) in adult patients (Barcelona, 1990−2019). Isolates were tested for antimicrobial susceptibility and genotyped (PFGE), and a selection was sequenced (WGS) to characterise the pangenome and mechanisms underlying antimicrobial resistance. Increases in patient age (60 to 71 years), comorbidities (Charlson’s index > 2, 10% to 94%), community-onset healthcare-associated acquisition (9% to 60%), and 30-day mortality (28% to 36%) were observed during the 1990−1995 and 2014−2019 periods. The proportion of catheter-related BSIs fell from 57% to 20%. Current MRSA-BSIs are caused by CC5-IV and an upward trend of CC8-IV and CC22-IV clones. CC5 and CC8 had the lowest core genome proportions. Antimicrobial resistance rates fell, and only ciprofloxacin, tobramycin, and erythromycin remained high (>50%) due to GyrA/GrlA changes, the presence of aminoglycoside-modifying enzymes (AAC(6′)-Ie-APH(2″)-Ia and ANT(4′)-Ia), and mph(C)/msr(A) or erm (C) genes. Two CC22-IV strains showed daptomycin resistance (MprF substitutions). MRSA-BSI has become healthcare-associated, affecting elderly patients with comorbidities and causing high mortality rates. Clonal replacement with CC5-IV and CC8-IV clones resulted in lower antimicrobial resistance rates. The increased frequency of the successful CC22-IV, associated with daptomycin resistance, should be monitored.", "token_count": 511, "char_count": 1559, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7282, "quality_score": 0.8641, "entities": { "genes": [ "CC5", "CC22", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:06.292364", "source": { "split": "train_shard_00001", "doc_id": 1486 }, "chunk_id": "train_shard_00001_1486_0", "global_id": 7739 }, { "text": "Molecular Epidemiology, Antimicrobial Susceptibility, and Clinical Features of Methicillin-Resistant Staphylococcus aureus Bloodstream Infections over 30 Years in Barcelona, Spain (1990-2019).", "token_count": 69, "char_count": 199, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:06.691286", "source": { "split": "train_shard_00001", "doc_id": 1486 }, "chunk_id": "train_shard_00001_1486_1", "global_id": 7740 }, { "text": "Accurate, quantitative phenotyping aids in the discovery of quantitative trait loci, particularly those with minor effects. Previously, we optimized replicated precision phenotyping of mapping families after inoculation of leaf discs with the grapevine powdery mildew pathogen (Erysiphe necator). Pathogen colonies were stained, and hyphal density was estimated using hyphal transects. This approach outperformed field evaluations and other controlled phenotyping methods but required one or two person-months of microscopy per experiment to evaluate resistance across 300 host genotypes. More recently, we combined advanced macrophotography, robotic sample positioning, and convolutional neural networks to produce a high-throughput phenotyping device, which was modified and commercialized as \"Blackbird.\" Here, that device was tested for nondestructive image collection and computer vision quantification of foliar grapevine powdery mildew. Blackbird outpaced manual microscopy up to 60-fold and nondestructively generated time-series segregating phenotypes from 2 to 9 days postinoculation (dpi). Paired analysis of these phenotypes with RNase H2-amplicon sequencing haplotype markers targeting the Vitis core genome detected REN13 on chromosome 8. Genetic analysis of Blackbird convolutional neural network data explained a greater proportion of the phenotypic variance via hyphae at 4 dpi (24.5%) and conidia at 9 dpi (24.0%) than manual microscopy at 8 dpi (15.8%). As a moderate-effect resistance locus in the widely planted resistant variety 'Norton', which already produces commercial wine quality, REN13 could significantly delay epidemics and could be useful in grape breeding programs to increase the durability of stronger resistance loci (e.g., RUN1, REN4, or REN12) in resistance gene stacks while maintaining fruit quality.", "token_count": 506, "char_count": 1889, "word_count": 249, "semantic_coherence": 1, "information_density": 0.747, "quality_score": 0.8735, "entities": { "genes": [ "REN4", "REN13", "RUN1", "REN12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:07.351774", "source": { "split": "train_shard_00001", "doc_id": 1487 }, "chunk_id": "train_shard_00001_1487_0", "global_id": 7741 }, { "text": "A Device for Computer Vision Analysis of Fungal Features Outperforms Quantitative Manual Microscopy by Experts in Discerning a Host Resistance Locus.", "token_count": 35, "char_count": 149, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:07.733099", "source": { "split": "train_shard_00001", "doc_id": 1487 }, "chunk_id": "train_shard_00001_1487_1", "global_id": 7742 }, { "text": "Actinobacillus pleuropneumoniae (APP) is the causative agent of pleuropneumonia in pigs, one of the most relevant bacterial respiratory diseases in the swine industry. To date, 19 serotypes have been described based on capsular polysaccharide typing with significant virulence dissimilarities. In this study, 16 APP isolates from Spanish origin were selected to perform antimicrobial susceptibility tests and comparative genomic analysis using whole genome sequencing (WGS). To obtain a more comprehensive worldwide molecular epidemiologic analyses, all APP whole genome assemblies available at the National Center for Biotechnology Information (NCBI) at the time of the study were also included. An in-house in silico PCR approach enabled the correct serotyping of unserotyped or incorrectly serotyped isolates and allowed for the discrimination between serotypes 9 and 11. A pangenome analysis identified the presence or absence of gene clusters to be serotype specific, as well as virulence profile analyses targeting the apx operons. Antimicrobial resistance genes were correlated to the presence of specific plasmids. Altogether, this study provides new insights into the genetic variability within APP serotypes, correlates phenotypic tests with bioinformatic analyses and manifests the benefits of populated databases for a better assessment of diversity and variability of relatively unknown pathogens. Overall, genomic comparative analysis enhances the understanding of transmission and epidemiological patterns of this species and suggests vertical transmission of the pathogen, including the resistance genes, within the Spanish integrated systems. IMPORTANCE Pleuropneumonia is one of the most relevant respiratory infections in the swine industry. Despite Actinobacillus pleuropneumoniae (APP) being one of the most important pathogens in the pig production, this is the first comparative study including all available whole genome sequencing data from NCBI. Moreover, this study also includes 16 APP isolates of Spanish origin with known epidemiological relationships through vertical integrated systems. Genomic comparisons provided a deeper understanding of molecular and epidemiological knowledge between different APP serotypes", "token_count": 510, "char_count": 2266, "word_count": 305, "semantic_coherence": 1, "information_density": 0.577, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:08.398644", "source": { "split": "train_shard_00001", "doc_id": 1488 }, "chunk_id": "train_shard_00001_1488_0", "global_id": 7743 }, { "text": "Furthermore, determination of resistance and toxin profiles allowed correlation with the presence of mobile genetic elements and specific serotype, respectively.\n\nRevealing Genomic Insights of the Unexplored Porcine Pathogen Actinobacillus pleuropneumoniae Using Whole Genome Sequencing.", "token_count": 65, "char_count": 287, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:08.770926", "source": { "split": "train_shard_00001", "doc_id": 1488 }, "chunk_id": "train_shard_00001_1488_1", "global_id": 7744 }, { "text": "A novel mangrove soil-derived actinomycete, strain S2-29T, was found to be most closely related to Saccharopolyspora karakumensis 5K548T based on 16 S rRNA sequence (99.24% similarity) and genomic phylogenetic analyses. However, significant divergence in digital DNA-DNA hybridization, average nucleotide identity, and unique biosynthetic gene cluster possession distinguished S2-29T as a distinct Saccharopolyspora species. Pan genome evaluation revealed exceptional genomic flexibility in genus Saccharopolyspora, with > 95% accessory genome content. Strain S2-29T harbored 718 unique genes, largely implicated in energetic metabolisms, indicating different metabolic capacities from its close relatives. Several uncharacterized biosynthetic gene clusters in strain S2-29T highlighted the strain's untapped capacity to produce novel functional compounds with potential biotechnological applications. Designation as novel species Saccharopolyspora mangrovi sp. nov. (type strain S2-29T = JCM 34,548T = CGMCC 4.7716T) was warranted, expanding the known Saccharopolyspora diversity and ecology. The discovery of this mangrove-adapted strain advances understanding of the genus while highlighting an untapped source of chemical diversity.\n\nSaccharopolyspora mangrovi sp. nov., a novel mangrove soil actinobacterium with distinct metabolic potential revealed by comparative genomic analysis.", "token_count": 442, "char_count": 1476, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7225, "quality_score": 0.8613, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:09.403098", "source": { "split": "train_shard_00001", "doc_id": 1489 }, "chunk_id": "train_shard_00001_1489_0", "global_id": 7745 }, { "text": "

Background

The non-conserved accessory genome of bacteria can be associated with important adaptive characteristics that can contribute to niche specificity or pathogenicity of strains. High degrees of structural and compositional diversity in genomic islands and other elements of the accessory genome can complicate characterization of accessory genome contents among populations of strains. Methods for easily and effectively defining the distributions of discrete elements of the accessory genome among bacterial strains in a population are needed to explore the relationships between the flexible genome and bacterial adaptive traits.

Results

We have developed the open-source software package ClustAGE. This program, written in Perl, uses BLAST to cluster nucleotide accessory genomic elements from the genomes of multiple bacterial strains and to identify their distribution within the study population. The program output can be used in combination with strain phenotype data or other characteristics to detect associations. Optional graphical output is available for visualizing accessory genome gene content and distribution patterns. The capabilities of the software are demonstrated on a collection of 14 Pseudomonas aeruginosa genome sequences.

Conclusions

The ClustAGE software and utilities are effective for identifying characteristics and distributions of accessory genomic elements among groups of bacterial genomes. The ability to easily and effectively characterize the accessory genome of a sequence collection may provide a better understanding of the accessory genome's contribution to a species' adaptation and pathogenesis. The ClustAGE source code can be downloaded from https://clustage.sourceforge.io and a limited web-based implementation is available at http://vfsmspineagent.fsm.northwestern.edu/cgi-bin/clustage.cgi .\n\nClustAGE: a tool for clustering and distribution analysis of bacterial accessory genomic elements.", "token_count": 420, "char_count": 1971, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5437, "quality_score": 0.7718, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:10.029692", "source": { "split": "train_shard_00001", "doc_id": 1490 }, "chunk_id": "train_shard_00001_1490_0", "global_id": 7746 }, { "text": "The yeast Kluyveromyces marxianus has been pointed out as a promising microorganism for a variety of industrial bioprocesses. Although genetic tools have been developed for this yeast and different potential applications have been investigated, quantitative physiological studies have rarely been reported. Here, we report and discuss the growth, substrate consumption, metabolite formation, and respiratory parameters of K. marxianus CBS 6556 during aerobic batch bioreactor cultivations, using a defined medium with different sugars as sole carbon and energy source, at 30 and 37 °C. Cultivations were carried out both on single sugars and on binary sugar mixtures. Carbon balances closed within 95 to 101 % in all experiments. Biomass and CO2 were the main products of cell metabolism, whereas by-products were always present in very low proportion (<3 % of the carbon consumed), as long as full aerobiosis was guaranteed. On all sugars tested as sole carbon and energy source (glucose, fructose, sucrose, lactose, and galactose), the maximum specific growth rate remained between 0.39 and 0.49 h(-1), except for galactose at 37 °C, which only supported growth at 0.31 h(-1). Different growth behaviors were observed on the binary sugar mixtures investigated (glucose and lactose, glucose and galactose, lactose and galactose, glucose and fructose, galactose and fructose, fructose and lactose), and the observations were in agreement with previously published data on the sugar transport systems in K. marxianus. We conclude that K. marxianus CBS 6556 does not present any special nutritional requirements; grows well in the range of 30 to 37 °C on different sugars; is capable of growing on sugar mixtures in a shorter period of time than Saccharomyces cerevisiae, which is interesting from an industrial point of view; and deviates tiny amounts of carbon towards metabolite formation, as long as full aerobiosis is maintained.", "token_count": 488, "char_count": 1932, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6054, "quality_score": 0.8027, "entities": { "genes": [ "CO2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:10.679523", "source": { "split": "train_shard_00001", "doc_id": 1491 }, "chunk_id": "train_shard_00001_1491_0", "global_id": 7747 }, { "text": "Growth of the yeast Kluyveromyces marxianus CBS 6556 on different sugar combinations as sole carbon and energy source.", "token_count": 32, "char_count": 118, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:11.033287", "source": { "split": "train_shard_00001", "doc_id": 1491 }, "chunk_id": "train_shard_00001_1491_1", "global_id": 7748 }, { "text": "We evaluated the effects of probiotic compounds on the composition of the gut microbiota. Forty newborn calves were random allocated to the lactic acid bacteria + yeast group (LS group), lactic acid bacteria group (L group), yeast group (S group), and control group (D group). Probiotics containing Lactococcus lactis subsp. lactis, Pediococcus pentosaceus, Lactobacillus plantarum, Saccharomyces cerevisiae, and Kluyveromyces marxianus were fed to calves in the three treatment groups for 15 days. The feeding process lasted 15 days. Fecal samples were collected from all calves at the end of the trial and analyzed using high-throughput 16S rRNA sequencing. Totals of 1,029,260 high-quality reads and 420,010,128 bp of sequences were obtained. Among the four groups, the alpha diversity of gut microbes was significantly higher in newborn cattle in the LS group than in those in the L, S, and D groups. Overall, the dominant phyla were Firmicutes, Actinobacteria, and Bacteroidetes, whereas Bifidobacterium was the most abundant phylum in the gut of cattle in the LS group. Newborn calves from the compound probiotic groups had closely clustered gut bacterial communities and had lower rates of diarrhea. Overall, compound probiotics regulated the intestinal microbiota community structure of newborn calves and improved intestinal health. New information relevant to the prevention of diarrhea is provided by our research in newborn calves.\n\nCompound Probiotics Improve the Diarrhea Rate and Intestinal Microbiota of Newborn Calves.", "token_count": 473, "char_count": 1605, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:11.672387", "source": { "split": "train_shard_00001", "doc_id": 1492 }, "chunk_id": "train_shard_00001_1492_0", "global_id": 7749 }, { "text": "

Background

Methicillin-resistant Staphylococcus aureus (MRSA), a leading cause of chronic infections, forms prolific biofilms which afford an escape route from antibiotic treatment and host immunity. However, MRSA clones are genetically diverse, and mechanisms underlying biofilm formation remain under-studied. Such studies form the basis for developing targeted therapeutics. Here, we studied the temporal changes in the biofilm transcriptome of three pandemic MRSA clones: USA300, HEMRSA-15, and ST239.

Methods

Biofilm formation was assessed using a static model with one representative strain per clone. Total RNA was extracted from biofilm and planktonic cultures after 24, 48, and 72 h of growth, followed by rRNA depletion and sequencing (Illumina Inc., San Diego, CA, United States, NextSeq500, v2, 1 × 75 bp). Differentially expressed gene (DEG) analysis between phenotypes and among early (24 h), intermediate (48 h), and late (72 h) stages of biofilms was performed together with in silico co-expression network construction and compared between clones. To understand the influence of SCCmec and ACME on biofilm formation, isogenic mutants containing deletions of the entire elements or of single genes therein were constructed in USA300.

Results

Genes involved in primarily core genome-encoded KEGG pathways (transporters and others) were upregulated in 24-h biofilm culture compared to 24-h planktonic culture. However, the number of affected pathways in the ST239 24 h biofilm (n = 11) was remarkably lower than that in USA300/EMRSA-15 biofilms (USA300: n = 27, HEMRSA-15: n = 58)", "token_count": 503, "char_count": 1658, "word_count": 229, "semantic_coherence": 1, "information_density": 0.7555, "quality_score": 0.8777, "entities": { "genes": [ "USA300", "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:12.329455", "source": { "split": "train_shard_00001", "doc_id": 1493 }, "chunk_id": "train_shard_00001_1493_0", "global_id": 7750 }, { "text": "The clfA gene, which encodes clumping factor A, was the single common DEG identified across the three clones in 24-h biofilm culture (2.2- to 2.66-fold). In intermediate (48 h) and late (72 h) stages of biofilms, decreased expression of central metabolic and fermentative pathways (glycolysis/gluconeogenesis, fatty acid biosynthesis), indicating a shift to anaerobic conditions, was already evident in USA300 and HEMRSA-15 in 48-h biofilm cultures; ST239 showed a similar profile at 72 h. Last, SCCmec+ACME deletion and opp3D disruption negatively affected USA300 biofilm formation.

Conclusion

Our data show striking differences in gene expression during biofilm formation by three of the most important pandemic MRSA clones, USA300, HEMRSA-15, and ST239. The clfA gene was the only significantly upregulated gene across all three strains in 24-h biofilm cultures and exemplifies an important target to disrupt early biofilms. Furthermore, our data indicate a critical role for arginine catabolism pathways in early biofilm formation.\n\nThe dynamic transcriptome during maturation of biofilms formed by methicillin-resistant Staphylococcus aureus.", "token_count": 361, "char_count": 1189, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7063, "quality_score": 0.8531, "entities": { "genes": [ "USA300", "ST239" ], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:12.898730", "source": { "split": "train_shard_00001", "doc_id": 1493 }, "chunk_id": "train_shard_00001_1493_1", "global_id": 7751 }, { "text": "As the structural characteristics of peptides affect their functional properties, they are an important factor for peptide stability. The stability characteristic was investigated in two groups of synthetic peptides, analogues of VLSTSFPPK (VL-9). The latter was previously purified from Kluyveromyces marxianus protein hydrolysate. In the first group, the replacement impact of Pro in antepenultimate position with Tyr, Cys and His on antioxidant stability against heat, NaCl, and pH and in the second group, the replacement effect of Lys in C-terminal with Trp, Tyr, and Phe on the stability of antihypertensive activity under gastrointestinal digestion were studied. Pro containing peptide (VL-9) showed the highest antioxidant stability against heat and salt. Despite the positive effect of Cys in antioxidant activity of peptides (VCK-9), it decreased the heat and salt stability. Tyr increased the ABTS cation radical scavenging activity and resulting peptide had the same thermal stability as the primary peptide and higher sensitivity to salt. Despite not significant effect of His on the antioxidant activity, it caused a slight instability against heat and salt. The antioxidant peptides studied showed the highest stability at neutral pH. The higher hydrophilicity of Lys in the peptide sequence caused higher ACE-inhibitory stability in simulated GI digestion.\n\nThe stability of antioxidant and ACE-inhibitory peptides as influenced by peptide sequences", "token_count": 359, "char_count": 1465, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5425, "quality_score": 0.7712, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:13.486238", "source": { "split": "train_shard_00001", "doc_id": 1494 }, "chunk_id": "train_shard_00001_1494_0", "global_id": 7752 }, { "text": "

Objectives

Pseudomonas aeruginosa (P. aeruginosa) stands out as a key culprit in the colonization of burn wounds, instigating grave infections of heightened severity. In this study, we have performed comparative whole genome analysis of a difficult to treat extensively drug resistant P. aeruginosa isolated from a burn patient in order to elucidate genomic diversity, molecular patterns, mechanisms and genes responsible for conferring antimicrobial resistance and virulence.

Method

P. aeruginosa SHNIBPS206 was isolated from an infected burn wound of a critically injured burn patient. Whole genome sequencing was carried out and annotated with Prokka. Sequence type, serotype, antimicrobial resistance genes and mechanisms, virulence genes, metal resistance genes and CRISPR/Cas systems were investigated. Later, pangenome analysis was carried out to find out genomic diversity.

Result

P. aeruginosa SHNIBPS206 (MLST 357, Serotype O11) was resistant to 14 antibiotics including carbapenems and harboured all four classes of beta lactamase producing genes: Class A (blaPME-1, blaVEB-9), Class B (blaNDM-1), Class C (blaPDC-11) and Class D (blaOXA-846). Mutational analysis of Porin D gave valuable insights. Several efflux pump, virulence and metal resistance genes were also detected. Pangenome analysis revealed high genomic diversity among different strains of P. aeruginosa.

Conclusion

To our knowledge, this is the first report of an extensively drug resistant ST 357 P. aeruginosa from Bangladesh, which is an epidemic high-risk P. aeruginosa clone. Further research and in-depth comprehensive studies are required to investigate the prevalence of such high-risk clone of P. aeruginosa in Bangladesh.", "token_count": 501, "char_count": 1792, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [ "SHNIBPS206" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:14.134864", "source": { "split": "train_shard_00001", "doc_id": 1495 }, "chunk_id": "train_shard_00001_1495_0", "global_id": 7753 }, { "text": "Unveiling a high-risk epidemic clone (ST 357) of 'Difficult to Treat Extensively Drug-Resistant' (DT-XDR) Pseudomonas aeruginosa from a burn patient in Bangladesh: A resilient beast revealing coexistence of four classes of beta lactamases.", "token_count": 73, "char_count": 239, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8788, "quality_score": 0.9394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:14.501866", "source": { "split": "train_shard_00001", "doc_id": 1495 }, "chunk_id": "train_shard_00001_1495_1", "global_id": 7754 }, { "text": "We present the genome of Listeria monocytogenes BDSA isolated from ready-to-eat (RTE) meat collected in Dhaka, Bangladesh. The genome displays the Listeria pathogenicity island 1 and virulence, stress response, and antimicrobial resistance genes. It was phylogenetically classified as ST7, and clustered with serotype 1/2a belonging to lineage II.\n\nDraft genome sequence of Listeria monocytogenes BDSA strain isolated from ready-to-eat chicken product in Dhaka, Bangladesh.", "token_count": 151, "char_count": 487, "word_count": 64, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "ST7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:14.938014", "source": { "split": "train_shard_00001", "doc_id": 1496 }, "chunk_id": "train_shard_00001_1496_0", "global_id": 7755 }, { "text": "Kluyveromyces marxianus possesses a useful potential to assimilate a wide variety of substrates at a high temperature, but the negative effect by coexisting glucose is critical for utilization of biomass containing various sugars. Such a negative effect on the activity of inulinase, which is the sole enzyme to hydrolyze sucrose, raffinose and inulin, has been demonstrated in K. marxianus without analysis at the gene level. To clarify the utilization capability of sucrose, raffinose and inulin and the glucose effect on inulinase in K. marxianus DMKU 3-1042, its growth and metabolite profiles on these sugars were examined with or without glucose under a static condition, in which glucose repression evidently occurs. Consumption of sucrose was not influenced by glucose or 2-deoxyglucose. On the other hand, raffinose and inulin consumption was hampered by glucose at 30°C but hardly hampered at 45°C. Unlike Saccharomyces cerevisiae, increase in glucose concentration had no effect on sucrose utilization. These sugar-specific glucose effects were consistent with the level of inulinase activity but not with that of the KmINU1 transcript, which was repressed in the presence of glucose via KmMig1p. This inconsistency may be due to sufficient activity of inulinase even when glucose is present. Our results encourage us to apply K. marxianus DMKU 3-1042 to high-temperature ethanol fermentation with biomass containing these sugars with glucose.\n\nUtilization capability of sucrose, raffinose and inulin and its less-sensitiveness to glucose repression in thermotolerant yeast Kluyveromyces marxianus DMKU 3-1042.", "token_count": 448, "char_count": 1621, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5336, "quality_score": 0.7668, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:15.573864", "source": { "split": "train_shard_00001", "doc_id": 1497 }, "chunk_id": "train_shard_00001_1497_0", "global_id": 7756 }, { "text": "In this work, laccase enzymes were evaluated to detoxify the whole slurry from steam-exploded wheat straw. For it, two different strategies, laccase treatment before or after enzymatic hydrolysis, were employed. The detoxification efficiency was analyzed on enzymatic hydrolysis and fermentation levels by the thermotolerant yeast Kluyveromyces marxianus. Laccases reduced phenolic compounds without affecting weak acids and furan derivates. A lower glucose recovery was observed when laccase treatments were carried out before enzymatic hydrolysis, phenomenon that was not showed after enzymatic hydrolysis. In contrast, both laccase treatment strategies enhanced ethanol concentrations, reducing significantly the lag phase of the yeast and allowing substrate loading increments of saccharification and fermentation broths.\n\nDifferent laccase detoxification strategies for ethanol production from lignocellulosic biomass by the thermotolerant yeast Kluyveromyces marxianus CECT 10875.", "token_count": 237, "char_count": 986, "word_count": 126, "semantic_coherence": 1, "information_density": 0.7063, "quality_score": 0.8532, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:16.045395", "source": { "split": "train_shard_00001", "doc_id": 1498 }, "chunk_id": "train_shard_00001_1498_0", "global_id": 7757 }, { "text": "Ethanol fermentation was carried out with Kluyveromyces marxianus cells at various temperatures (30, 35, 40, and 45 °C). Fermentation performance of the immobilized yeast on banana leaf sheath pieces and the free yeast were evaluated and compared. Generally, ethanol production of the immobilized and free yeast was stable in a temperature range of 30-40 °C. Temperature of 45 °C restricted yeast growth and lengthened the fermentation. The immobilized yeast demonstrated faster sugar assimilation and higher ethanol level in the fermentation broth in comparison with the free yeast at all fermentation temperatures. Change in fatty acid level in cellular membrane was determined to clarify the response of the free and immobilized yeast to thermal stress. The free cells of K. marxianus responded to temperature increase by increasing saturated fatty acid (C16:0 and C18:0) level and by decreasing unsaturated fatty acid (C18:1 and C18:2) level in cellular membrane. For fermentation at 40 °C with immobilized cells of K. marxianus, however, the changes were not observed in both saturated fatty acid (C16:0) and unsaturated fatty acid (C18:1 and C18:2) level.\n\nImpact of high temperature on ethanol fermentation by Kluyveromyces marxianus immobilized on banana leaf sheath pieces.", "token_count": 363, "char_count": 1282, "word_count": 193, "semantic_coherence": 1, "information_density": 0.4819, "quality_score": 0.7409, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:16.623258", "source": { "split": "train_shard_00001", "doc_id": 1499 }, "chunk_id": "train_shard_00001_1499_0", "global_id": 7758 }, { "text": "Recent advances in pangenomics have led to the rapid development of graph-based pangenomes that code genetic variant as nodes and edges preserve the contiguity of the sequence and structural variation between individuals. Data visualization is an essential component of genomic data analysis. However, the further application of the graph-based pangenome is still suffered from lacking bioinformatics tools to visualize graph format pangenomes and understand the reads alignment on graph pangenomes. In this research, we developed a novel bioinformatics platform, VAG (Visualizing read alignments in graph genomes), to overcome these challenges. VAG includes multifunctional modules integrated into a single command line and an online visualization platform supported through a web server. This tool can extract specific sequence regions from a graph pangenome and display read alignments on different paths of a graph pangenome. In addition, VAG provides population-level presence/absence variations frequency analysis and sequence path navigation to identify the population differentiation regions. To demonstrate the usage, we investigated genetic variations using a rice graph pangenome with population-level sequencing data to identify important genes and gene clusters underlying the indica–japonica differentiation with VAG. After investigating read alignments on the graph pangenome, we identified many false-positive alignments due to TE insertions. To reduce the impact of these misleading alignments, we developed a navigation module to determine and filter those false-positive alignments based on the pair-end alignment information. The utilization of mate-pair information in VAG provides a reliable reference for variation identification. Additionally, we developed a VAG web server to provide a user-friendly and interactive platform to visualize the read alignment data. VAG was also applied to SV discovery in the cucumber and soybean graph-based pangenome and details of VAG can be accessed by the following website ( https://ricegenomichjx.xiaomy.net/VAG/sequenceextraction.php ).\n\nVisualization and review of reads alignment on the graphical pan-genome with VAG", "token_count": 444, "char_count": 2182, "word_count": 298, "semantic_coherence": 1, "information_density": 0.5738, "quality_score": 0.7869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:17.258560", "source": { "split": "train_shard_00001", "doc_id": 1500 }, "chunk_id": "train_shard_00001_1500_0", "global_id": 7759 }, { "text": "Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.\n\nEcology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota.", "token_count": 502, "char_count": 1934, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5508, "quality_score": 0.7754, "entities": { "genes": [ "PRL2023" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:18.268055", "source": { "split": "train_shard_00001", "doc_id": 1501 }, "chunk_id": "train_shard_00001_1501_0", "global_id": 7760 }, { "text": "Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, Vibrio and Pseudoalteromonas, both which belong to the Enterobacterales order of Gammaproteobacteria, and compared the genomic openness with that of monopartite genomes in the same order. We applied pangenome analysis, codon usage analysis and the HGTector software to detect horizontally transferred genes. Our findings suggest that the chromids of Vibrio and Pseudoalteromonas originated from two separate plasmid acquisition events. Bipartite genomes were found to be more open compared to monopartite. We found that the shell and cloud pangene categories drive the openness of bipartite genomes in Vibrio and Pseudoalteromonas. Based on this and our two recent studies, we propose a hypothesis that explains how chromids and the chromosome terminus region contribute to the genomic plasticity of bipartite genomes.\n\nBipartite Genomes in Enterobacterales: Independent Origins of Chromids, Elevated Openness and Donors of Horizontally Transferred Genes.", "token_count": 368, "char_count": 1421, "word_count": 196, "semantic_coherence": 1, "information_density": 0.5816, "quality_score": 0.7908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:18.870727", "source": { "split": "train_shard_00001", "doc_id": 1502 }, "chunk_id": "train_shard_00001_1502_0", "global_id": 7761 }, { "text": "

Background

High-risk Escherichia coli clones, such as sequence type (ST)131 and ST1193, along with multidrug-resistant (MDR) Klebsiella pneumoniae, are globally recognized for their significant role in urinary tract infections (UTIs). This study aimed to provide an overview of the virulence factors, clonal diversity, and antibiotic resistance profiles of extended-spectrum cephalosporin (ESC)-E. coli and K. pneumoniae causing UTIs in humans in the Tebessa region of Algeria.

Methods

Forty E. coli and 17 K. pneumoniae isolates exhibiting ESC-resistance were recovered (July 2022-January 2024) from urine samples of patients at three healthcare facilities to be phenotypically and genotypically characterized. Whole genome sequencing (WGS) was performed on the ST1193 clone.

Results

Among K. pneumoniae isolates, all except one harbored CTX-M-15, with a single isolate carrying blaCTX-M-194. Additionally, two K. pneumoniae isolates co-harboring blaCTX-M-15 and blaNDM exhibited phenotypic and genotypic hypervirulence traits. Fluoroquinolone resistance (FQR) was detected in 94.1% of K. pneumoniae isolates. The E", "token_count": 460, "char_count": 1258, "word_count": 145, "semantic_coherence": 1, "information_density": 0.7862, "quality_score": 0.8931, "entities": { "genes": [ "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:19.540383", "source": { "split": "train_shard_00001", "doc_id": 1503 }, "chunk_id": "train_shard_00001_1503_0", "global_id": 7762 }, { "text": "coli isolates carried diverse ESC-resistance genes, including CTX-M-15 (87.5%), CTX-M-27 (5%), CTX-M-1, CMY-59, and CMY-166 (2.5% each). Co-carriage of blaESC and blaOXA-48 was identified in three E. coli isolates, while 62.5% exhibited FQR. Phylogenetic analysis revealed that 52.5% of E. coli belonged to phylogroup B2, including the high-risk clonal complex (CC)131 CH40-30 (17 isolates) and ST1193 (one isolate). In silico analysis of the ST1193 genome determined O75:H5-B2 (CH14-64), and the carriage of IncI1-I(Alpha) and IncF [F-:A1:B10] plasmids. Notably, core genome single-nucleotide polymorphism (SNP) analysis demonstrated high similarity between the Algerian ST1193 isolate and a previously annotated genome from a hospital in Northwest Spain.

Conclusions

This study highlights the spread and genetic diversity of E. coli CC131 CH40-30 and hypervirulent K. pneumoniae clones in Algeria. It represents the first report of a CTX-M-15-carrying E. coli ST1193 in the region. The findings emphasize the urgent need for antibiotic optimization programs and enhanced surveillance to curb the dissemination of high-risk clones that pose an increasing public health threat in Algeria. A simplified method based on virulence traits for E. coli and K. pneumoniae is proposed here for antimicrobial resistance (AMR) monitoring.", "token_count": 516, "char_count": 1424, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [ "CH14", "CC131", "CH40", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:20.232821", "source": { "split": "train_shard_00001", "doc_id": 1503 }, "chunk_id": "train_shard_00001_1503_1", "global_id": 7763 }, { "text": "Phenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing <i>Klebsiella pneumoniae</i> and High-Risk <i>Escherichia coli</i> CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Human Patients in Algeria.", "token_count": 116, "char_count": 295, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [ "CC131", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:20.626908", "source": { "split": "train_shard_00001", "doc_id": 1503 }, "chunk_id": "train_shard_00001_1503_2", "global_id": 7764 }, { "text": "Early embryonic exogenous feeding of bioactive substances is a topic of interest in poultry production, potentially improving gastrointestinal tract (GIT) development, stimulating immunization, and maximizing the protection capability of newly hatched chicks. However, the biophysiological actions and effects of in ovo administered bioactive substances are inconsistent or not fully understood. Thus, this paper summarizes the functional effects of bioactive substances and their interaction merits to augment GIT development, the immune system, and microbial homeostasis in newly hatched chicks. Prebiotics, probiotics, and synbiotics are potential bioactive substances that have been administered in embryonic eggs. Their biological effects are enhanced by a variety of mechanisms, including the production of antimicrobial peptides and antibiotic responses, regulation of T lymphocyte numbers and immune-related genes in either up- or downregulation fashion, and enhancement of macrophage phagocytic capacity. These actions occur directly through the interaction with immune cell receptors, stimulation of endocytosis, and phagocytosis. The underlying mechanisms of bioactive substance activity are multifaceted, enhancing GIT development, and improving both the innate and adaptive immune systems. Thus summarizing these modes of action of prebiotics, probiotics and synbiotics can result in more informed decisions and also provides baseline for further research.\n\nBiophysiology of in ovo administered bioactive substances to improve gastrointestinal tract development, mucosal immunity, and microbiota in broiler chicks.", "token_count": 366, "char_count": 1627, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:21.202720", "source": { "split": "train_shard_00001", "doc_id": 1504 }, "chunk_id": "train_shard_00001_1504_0", "global_id": 7765 }, { "text": "CRISPR-Cas adaptive immunity systems provide defense against mobile genetic elements and are often countered by diverse anti-CRISPR (Acr) proteins. The Type IE CRISPR-Cas of Escherichia coli K12 has been a model for structural and functional studies and is a part of the species’ core genome. However, this system is transcriptionally silent, which has fueled questions about its true biological function. To clarify the role of this system in defense, we carried out a census of Acr proteins found in Enterobacterales and identified AcrIE9 as a potent inhibitor of the E. coli K12 Type IE CRISPR-Cas system. While sharing little sequence identity, AcrIE9 proteins from Pseudomonas and Escherichia both interact with the Cas7 subunit of the Cascade complex, thus preventing its binding to DNA. We further show that AcrIE9 is genetically linked to AcrIE10, forming the most widespread anti-CRISPR cluster in Enterobacterales , and this module often co-occurs with a novel HTH-like protein with unusual architecture.\n\nA census of anti-CRISPR proteins reveals AcrIE9 as an inhibitor of Escherichia coli K12 Type IE CRISPR-Cas system", "token_count": 304, "char_count": 1136, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6474, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:21.772796", "source": { "split": "train_shard_00001", "doc_id": 1505 }, "chunk_id": "train_shard_00001_1505_0", "global_id": 7766 }, { "text": "Acinetobacter baumannii is widely recognized as a multidrug-resistant pathogen, but with most public genome datasets biased toward hospital-derived isolates. Little is thus known about A. baumannii isolates from healthy individuals from the community. This study analysed genome sequences from nine A. baumannii isolates obtained from the upper respiratory tract of healthy individuals of the indigenous Orang Asli community in their rural settlements located in the east coast of Peninsular Malaysia. Genomic analysis revealed all nine A. baumannii isolates to be genetically distinct and included three new sequence types (STs) under the Pasteur scheme and six novel STs under the Oxford scheme. Notably, one isolate, A. baumannii 19064, belonged to Global Clone 8 (GC8), a lineage associated with clinical infections. Core genome phylogeny indicated that the Orang Asli community isolates were interleaved with several non-GC clinical isolates from the tertiary hospital within the same state. This is suggestive of the potential of these community isolates to cause infections under conducive conditions. This is also attested by the identification of several virulence factors in their genomes. All nine isolates carried various intrinsic bla OXA-51-like class D β-lactamase genes and class C Acinetobacter -derived cephalosporinase (ADC) bla ADC genes but remained susceptible to meropenem. Two isolates, A. baumannii 19053 and 19062, were tetracycline resistant but minocycline susceptible and harboured the tet(39)-tetR gene pair within mobile p dif modules located on distinct Rep_3 family plasmids. Only one isolate, A. baumannii 19055, is plasmid-free; the rest mainly harboured cryptic Rep_3-type plasmids, often containing identifiable p dif modules. These findings highlight the clinical relevance of A. baumannii strains residing in healthy individuals, particularly in isolated communities that are seldom accessible to public health. Despite their remote location, the Orang Asli A", "token_count": 509, "char_count": 1998, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "GC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:22.426349", "source": { "split": "train_shard_00001", "doc_id": 1506 }, "chunk_id": "train_shard_00001_1506_0", "global_id": 7767 }, { "text": "baumannii isolates possess virulence factors and antibiotic resistance genes similar to those found in hospital settings. This underscores the importance of genomic surveillance of commensal pathogens, and taking this road which is less travelled can help inform broader epidemiological insights and guide future public health strategies.\n\nThe road less travelled: Exploring the genomic characteristics and antimicrobial resistance potential of Acinetobacter baumannii from the indigenous Orang Asli community in Peninsular Malaysia", "token_count": 118, "char_count": 539, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:22.807028", "source": { "split": "train_shard_00001", "doc_id": 1506 }, "chunk_id": "train_shard_00001_1506_1", "global_id": 7768 }, { "text": "Abstract

Background In microbial diagnostics, whole-genome sequencing (WGS) is used to address key questions such as species identification, presence of antimicrobial resistance genes (ARGs), virulence genes, and outbreak detection. The choice of sequencing technology is crucial to ensure high-quality data, cost-effectiveness, and efficient reporting times. We aimed to compare Illumina (short-read) and ONT (long-read) sequencing methods for WGS on different bacterial species for base accuracy and reliable taxonomic and ARG identification. Materials and Methods We used clinical isolates of ESKAPE pathogens (n = 12) and ATCC strains (n = 8) of varying %G + C. Illumina sequencing was performed on MiSeq (PE150) and ONT sequencing using GridION with R9.4.1 and R10.4.1 flowcells. Base-calling was performed using Guppy, Dorado, and Rerio software. We used de novo assembly with Unicycler for Illumina and Flye for ONT, and two types of hybrid assemblies, Unicycler and Polypolish. We annotated genomes with Bakta and assessed the quality (QUAST, GTDB-Tk). We identified ARGs (AMRFinderPlus) and plasmids (MOB-suite). We mapped reads and called SNPs using Minimap2, Pilon, vcftools, and Snippy (Illumina). Core genome MLST analysis was conducted with Ridom Seqsphere+. Results We observed that Illumina sequencing provided consistently high-quality reads (median Q-score 35), whereas for ONT R10.4.1, SUP mode showed higher median quality (median Q-score 15.3) compared to R9.4.1 (median Q-score 13.9, SUP mode)", "token_count": 473, "char_count": 1551, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "PE150" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:23.455420", "source": { "split": "train_shard_00001", "doc_id": 1507 }, "chunk_id": "train_shard_00001_1507_0", "global_id": 7769 }, { "text": "We observed that Illumina-based assemblies generated fewer genes annotated as disrupted; for ONT assemblies, the base-caller affects assembly annotation accuracy, with High accuracy (HAC) and Super accuracy (SUP) base-calling modes perform better than FAST mode. ONT assemblies resolved rRNA operons better than Illumina assemblies. Sequencing errors were determined by SNP calling, and varied widely by species, with ONT often generating more sequencing errors compared to Illumina. Hybrid assemblies combine accuracy and completeness effectively. Taxonomic identification and ARG detection were reliable across all methods. Conclusion Combining Illumina and ONT technologies yielded optimal bacterial genome sequencing results, leveraging the high accuracy of short reads and improved contiguity of ONT long reads. The HAC and SUP ONT models with Dorado notably enhance genome assembly annotation and resolution of complex regions, although species-specific issues, likely due to repeat regions and base modifications, remain challenging even in SUP mode with Dorado. Hybrid approaches currently offer the most comprehensive and accurate genome assemblies for clinical microbiology. For reliable cgMLST even using the most recent ONT methods, resolution must be assessed on a species-by-species basis.

\n\nBenchmarking Illumina and Oxford Nanopore Technologies (ONT) sequencing platforms for whole genome sequencing of bacterial genomes and use in clinical microbiology", "token_count": 327, "char_count": 1472, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6784, "quality_score": 0.8392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:24.017345", "source": { "split": "train_shard_00001", "doc_id": 1507 }, "chunk_id": "train_shard_00001_1507_1", "global_id": 7770 }, { "text": "Since its emergence in the beginning of the 90's, multidrug-resistant (MDR) Salmonella enterica subsp. enterica serovar Kentucky has become a significant public health problem, especially in East Africa. This study aimed to investigate the antimicrobial resistance profile and the genotypic relatedness of Salmonella Kentucky isolated from animal sources in Ethiopia and Kenya (n=19). We also investigated population evolutionary dynamics through phylogenetic and pangenome analyses with additional publicly available Salmonella Kentucky ST198 genomes (n=229). All the 19 sequenced Salmonella Kentucky isolates were identified as ST198. Among these isolates, the predominant genotypic antimicrobial resistance profile observed in ten (59.7%) isolates included the aac(3)-Id, aadA7, strA-strB, blaTEM-1B, sul1, and tet(A) genes, which mediated resistance to gentamicin, streptomycin/spectinomycin, streptomycin, ampicillin, sulfamethoxazole and tetracycline, respectively; and gyrA and parC mutations associated to ciprofloxacin resistance. Four isolates harbored plasmid types Incl1 and/or Col8282; two of them carried both plasmids. Salmonella Pathogenicity islands (SPI-1 to SPI-5) were highly conserved in the 19 sequenced Salmonella Kentucky isolates. Moreover, at least one Pathogenicity Island (SPI 1-4, SPI 9 or C63PI) was identified among the 229 public Salmonella Kentucky genomes", "token_count": 495, "char_count": 1519, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7278, "quality_score": 0.8639, "entities": { "genes": [ "ST198" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:24.668837", "source": { "split": "train_shard_00001", "doc_id": 1508 }, "chunk_id": "train_shard_00001_1508_0", "global_id": 7771 }, { "text": "The phylogenetic analysis revealed that almost all Salmonella Kentucky ST198 isolates (17/19) stemmed from a single strain that has accumulated ciprofloxacin resistance-mediating mutations. A total of 8,104 different genes were identified in a heterogenic and still open Salmonella Kentucky ST198 pangenome. Considering the virulence factors and antimicrobial resistance genes detected in Salmonella Kentucky, the implications of this pathogen to public health and the epidemiological drivers for its dissemination must be investigated.\n\nGenomic and Evolutionary Analysis of Salmonella enterica Serovar Kentucky Sequence Type 198 Isolated From Livestock In East Africa.", "token_count": 193, "char_count": 697, "word_count": 89, "semantic_coherence": 1, "information_density": 0.764, "quality_score": 0.882, "entities": { "genes": [ "ST198" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:25.116241", "source": { "split": "train_shard_00001", "doc_id": 1508 }, "chunk_id": "train_shard_00001_1508_1", "global_id": 7772 }, { "text": "We demonstrate herein the ability of Kluyveromyces marxianus to be an efficient ethanol producer and host for expressing heterologous proteins as an alternative to Saccharomyces cerevisiae. Growth and ethanol production by strains of K. marxianus and S. cerevisiae were compared under the same conditions. K. marxianus DMKU3-1042 was found to be the most suitable strain for high-temperature growth and ethanol production at 45 degrees C. This strain, but not S. cerevisiae, utilized cellobiose, xylose, xylitol, arabinose, glycerol, and lactose. To develop a K. marxianus DMKU3-1042 derivative strain suitable for genetic engineering, a uracil auxotroph was isolated and transformed with a linear DNA of the S. cerevisiae ScURA3 gene. Surprisingly, Ura(+) transformants were easily obtained. By Southern blot hybridization, the linear ScURA3 DNA was found to have inserted randomly into the K. marxianus genome. Sequencing of one Lys(-) transformant confirmed the disruption of the KmLYS1 gene by the ScURA3 insertion. A PCR-amplified linear DNA lacking K. marxianus sequences but containing an Aspergillus alpha-amylase gene under the control of the ScTDH3 promoter together with an ScURA3 marker was subsequently used to transform K. marxianus DMKU3-1042 in order to obtain transformants expressing Aspergillus alpha-amylase. Our results demonstrate that K. marxianus DMKU3-1042 can be an alternative cost-effective bioethanol producer and a host for transformation with linear DNA by use of S. cerevisiae-based molecular genetic tools.\n\nHigh-temperature ethanol fermentation and transformation with linear DNA in the thermotolerant yeast Kluyveromyces marxianus DMKU3-1042.", "token_count": 479, "char_count": 1677, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5424, "quality_score": 0.7712, "entities": { "genes": [ "DMKU3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:25.761553", "source": { "split": "train_shard_00001", "doc_id": 1509 }, "chunk_id": "train_shard_00001_1509_0", "global_id": 7773 }, { "text": "Gardnerella is the primary pathogenic bacterial genus present in the polymicrobial condition known as bacterial vaginosis (BV). Despite BV's high prevalence and associated chronic and acute women's health impacts, the Gardnerella pangenome is largely uncharacterized at both the genetic and functional metabolic levels. Here, we used genome-scale metabolic models to characterize in silico the Gardnerella pangenome metabolic content. We also assessed the metabolic functional capacity in a BV-positive cervicovaginal fluid context. The metabolic capacity varied widely across the pangenome, with 38.15% of all reactions being core to the genus, compared to 49.60% of reactions identified as being unique to a smaller subset of species. We identified 57 essential genes across the pangenome via in silico gene essentiality screens within two simulated vaginal metabolic environments. Four genes, gpsA, fas, suhB, and psd, were identified as core essential genes critical for the metabolic function of all analyzed bacterial species of the Gardnerella genus. Further understanding these core essential metabolic functions could inform novel therapeutic strategies to treat BV. Machine learning applied to simulated metabolic network flux distributions showed limited clustering based on the sample isolation source, which further supports the presence of extensive core metabolic functionality across this genus. These data represent the first metabolic modeling of the Gardnerella pangenome and illustrate strain-specific interactions with the vaginal metabolic environment across the pangenome. IMPORTANCE Bacterial vaginosis (BV) is the most common vaginal infection among reproductive-age women. Despite its prevalence and associated chronic and acute women's health impacts, the diverse bacteria involved in BV infection remain poorly characterized. Gardnerella is the genus of bacteria most commonly and most abundantly represented during BV", "token_count": 509, "char_count": 2037, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5858, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:26.416362", "source": { "split": "train_shard_00001", "doc_id": 1510 }, "chunk_id": "train_shard_00001_1510_0", "global_id": 7774 }, { "text": "In this paper, we use metabolic models, which are a computational representation of the possible functional metabolism of an organism, to investigate metabolic conservation, gene essentiality, and pathway utilization across 110 Gardnerella strains. These models allow us to investigate in silico how strains may differ with respect to their metabolic interactions with the vaginal-host environment.\n\nMetabolic Network Models of the Gardnerella Pangenome Identify Key Interactions with the Vaginal Environment.", "token_count": 134, "char_count": 530, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7536, "quality_score": 0.8768, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:26.841938", "source": { "split": "train_shard_00001", "doc_id": 1510 }, "chunk_id": "train_shard_00001_1510_1", "global_id": 7775 }, { "text": "

SUMMARY

Bacteroides fragilis is a prominent member of the human gut microbiota, playing crucial roles in maintaining gut homeostasis and host health. Although it primarily functions as a beneficial commensal, B. fragilis can become pathogenic. To determine the genetic basis of its duality, we conducted a comparative genomic analysis of 813 B. fragilis strains, representing both commensal and pathogenic origins. Our findings reveal that pathogenic strains emerge across diverse phylogenetic lineages, due in part to rapid gene exchange and the adaptability of the accessory genome. We identified 16 phylogenetic groups, differentiated by genes associated with capsule composition, interspecies competition, and host interactions. A microbial genome-wide association study identified 44 genes linked to extra-intestinal survival and pathogenicity. These findings reveal how genomic diversity within commensal species can lead to the emergence of pathogenic traits, broadening our understanding of microbial evolution in the gut.\n\nPathogenicBacteroides fragilisstrains can emerge from gut-resident commensals", "token_count": 268, "char_count": 1125, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7181, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:27.394000", "source": { "split": "train_shard_00001", "doc_id": 1511 }, "chunk_id": "train_shard_00001_1511_0", "global_id": 7776 }, { "text": "Expression and splicing quantitative trait loci (e/sQTL) are large contributors to phenotypic variability. Achieving sufficient statistical power for e/sQTL mapping requires large cohorts with both genotypes and molecular phenotypes, and so the genomic variation is often called from short read alignments which are unable to comprehensively resolve structural variation. Here we build a pangenome from 16 HiFi haplotype-resolved assemblies to identify small and structural variation and genotype them with PanGenie in 307 short read samples. We find high (>90%) concordance of PanGenie-genotyped and DeepVariant-called small variation, and confidently genotype close to 21M small and 43k structural variants in the larger population. We validate 85% of these structural variants (with MAF>0.1) directly with a subset of 25 short read samples that also have medium coverage HiFi reads. We then conduct e/sQTL mapping with this comprehensive variant set in a subset of 117 cattle that have testis transcriptome data and find 92 structural variants as causal candidates for eQTL and 73 for sQTL. We find that roughly half of top associated structural variants affecting expression or splicing are transposable elements, such as SV-eQTLs for STN1 and MYH7 and SV-sQTLs for CEP89 and ASAH2 . Extensive linkage disequilibrium between small and structural variation results in only 28 additional eQTL and 17 sQTL discovered when including SVs, although many top associated SVs are compelling candidates.\n\nPangenome genotyped structural variation improves molecular phenotype mapping in cattle", "token_count": 396, "char_count": 1586, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "STN1", "CEP89", "ASAH2", "MYH7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:28.011372", "source": { "split": "train_shard_00001", "doc_id": 1512 }, "chunk_id": "train_shard_00001_1512_0", "global_id": 7777 }, { "text": "Yeasts are known to have versatile metabolic traits, while how these metabolic traits have evolved has not been elucidated systematically. We performed integrative evolution analysis to investigate how genomic evolution determines trait generation by reconstructing genome-scale metabolic models (GEMs) for 332 yeasts. These GEMs could comprehensively characterize trait diversity and predict enzyme functionality, thereby signifying that sequence-level evolution has shaped reaction networks towards new metabolic functions. Strikingly, using GEMs, we can mechanistically map different evolutionary events, e.g. horizontal gene transfer and gene duplication, onto relevant subpathways to explain metabolic plasticity. This demonstrates that gene family expansion and enzyme promiscuity are prominent mechanisms for metabolic trait gains, while GEM simulations reveal that additional factors, such as gene loss from distant pathways, contribute to trait losses. Furthermore, our analysis could pinpoint to specific genes and pathways that have been under positive selection and relevant for the formulation of complex metabolic traits, i.e. thermotolerance and the Crabtree effect. Our findings illustrate how multidimensional evolution in both metabolic network structure and individual enzymes drives phenotypic variations.\n\nYeast metabolic innovations emerged via expanded metabolic network and gene positive selection.", "token_count": 297, "char_count": 1422, "word_count": 184, "semantic_coherence": 1, "information_density": 0.7065, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:28.572685", "source": { "split": "train_shard_00001", "doc_id": 1513 }, "chunk_id": "train_shard_00001_1513_0", "global_id": 7778 }, { "text": "Bacteria belonging to the genera Dickeya and Pectobacterium are responsible for significant economic losses in a wide variety of crops and ornamentals. During last years, increasing losses in potato production have been attributed to the appearance of Dickeya solani. The D. solani strains investigated so far share genetic homogeneity, although different virulence levels were observed among strains of various origins. The purpose of this study was to investigate the genetic traits possibly related to the diverse virulence levels by means of comparative genomics. First, we developed a new genome assembly pipeline which allowed us to complete the D. solani genomes. Four de novo sequenced and ten publicly available genomes were used to identify the structure of the D. solani pangenome, in which 74.8 and 25.2% of genes were grouped into the core and dispensable genome, respectively. For D. solani panregulon analysis, we performed a binding site prediction for four transcription factors, namely CRP, KdgR, PecS and Fur, to detect the regulons of these virulence regulators. Most of the D. solani potential virulence factors were predicted to belong to the accessory regulons of CRP, KdgR, and PecS. Thus, some differences in gene expression could exist between D. solani strains. The comparison between a highly and a low virulent strain, IFB0099 and IFB0223, respectively, disclosed only small differences between their genomes but significant differences in the production of virulence factors like pectinases, cellulases and proteases, and in their mobility. The D. solani strains also diverge in the number and size of prophages present in their genomes. Another relevant difference is the disruption of the adhesin gene fhaB2 in the highly virulent strain. Strain IFB0223, which has a complete adhesin gene, is less mobile and less aggressive than IFB0099", "token_count": 521, "char_count": 1953, "word_count": 286, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [ "IFB0099", "IFB0223" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:29.232326", "source": { "split": "train_shard_00001", "doc_id": 1514 }, "chunk_id": "train_shard_00001_1514_0", "global_id": 7779 }, { "text": "This suggests that in this case, mobility rather than adherence is needed in order to trigger disease symptoms. This study highlights the utility of comparative genomics in predicting D. solani traits involved in the aggressiveness of this emerging plant pathogen.\n\nComparison of Highly and Weakly Virulent Dickeya solani Strains, With a View on the Pangenome and Panregulon of This Species.", "token_count": 103, "char_count": 405, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7667, "quality_score": 0.8833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:29.622077", "source": { "split": "train_shard_00001", "doc_id": 1514 }, "chunk_id": "train_shard_00001_1514_1", "global_id": 7780 }, { "text": "Members of the genus Flavobacterium are widely distributed and produce various polysaccharide-degrading enzymes. Many species in the genus have been isolated and characterized. However, few studies have focused on marine isolates or fish pathogens, and in-depth genomic analyses, particularly comparative analyses of isolates from different habitat types, are lacking. Here, we isolated 20 strains of the genus from various environments in South Korea and sequenced their full-length genomes. Combined with published sequence data, we examined genomic traits, evolution, environmental adaptation, and putative metabolic functions in total 187 genomes of isolated species in Flavobacterium categorized as marine, host-associated, and terrestrial including freshwater. A pangenome analysis revealed a correlation between genome size and coding or noncoding density. Flavobacterium spp. had high levels of diversity, allowing for novel gene repertories via recombination events. Defense-related genes only accounted for approximately 3% of predicted genes in all Flavobacterium genomes. While genes involved in metabolic pathways did not differ with respect to isolation source, there was substantial variation in genomic traits; in particular, the abundances of tRNAs and rRNAs were higher in the host-associdated group than in other groups. One genome in the host-associated group contained a Microviridae prophage closely related to an enterobacteria phage. The proteorhodopsin gene was only identified in four terrestrial strains isolated for this study. Furthermore, recombination events clearly influenced genomic diversity and may contribute to the response to environmental stress. These findings shed light on the high genetic variation in Flavobacterium and functional roles in diverse ecosystems as a result of their metabolic versatility. IMPORTANCE The genus Flavobacterium is a diverse group of bacteria that are found in a variety of environments. While most species of this genus are harmless and utilize organic substrates such as proteins and polysaccharides, some members may play a significant role in the cycling for organic substances within their environments", "token_count": 517, "char_count": 2228, "word_count": 304, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:30.256583", "source": { "split": "train_shard_00001", "doc_id": 1515 }, "chunk_id": "train_shard_00001_1515_0", "global_id": 7781 }, { "text": "Nevertheless, little is known about the genomic dynamics and/or metabolic capacity of Flavobacterium. Here, we found that Flavobacterium species may have an open pangenome, containing a variety of diverse and novel gene repertoires. Intriguingly, we discovered that one genome (classified into host-associated group) contained a Microviridae prophage closely related to that of enterobacteria. Proteorhodopsin may be expressed under conditions of light or oxygen pressure in some strains isolated for this study. Our findings significantly contribute to the understanding of the members of the genus Flavobacterium diversity exploration and will provide a framework for the way for future ecological characterizations.\n\nPangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium.", "token_count": 215, "char_count": 885, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7565, "quality_score": 0.8783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:30.766393", "source": { "split": "train_shard_00001", "doc_id": 1515 }, "chunk_id": "train_shard_00001_1515_1", "global_id": 7782 }, { "text": "Fermented foods are defined as foods or beverages produced through controlled microbial growth, and the conversion of food components through enzymatic action. In recent years, fermented foods have undergone a surge in popularity, mainly due to their proposed health benefits. The aim of this review is to define and characterise common fermented foods (kefir, kombucha, sauerkraut, tempeh, natto, miso, kimchi, sourdough bread), their mechanisms of action (including impact on the microbiota), and the evidence for effects on gastrointestinal health and disease in humans. Putative mechanisms for the impact of fermented foods on health include the potential probiotic effect of their constituent microorganisms, the fermentation-derived production of bioactive peptides, biogenic amines, and conversion of phenolic compounds to biologically active compounds, as well as the reduction of anti-nutrients. Fermented foods that have been tested in at least one randomised controlled trial (RCT) for their gastrointestinal effects were kefir, sauerkraut, natto, and sourdough bread. Despite extensive in vitro studies, there are no RCTs investigating the impact of kombucha, miso, kimchi or tempeh in gastrointestinal health. The most widely investigated fermented food is kefir, with evidence from at least one RCT suggesting beneficial effects in both lactose malabsorption and Helicobacter pylori eradication. In summary, there is very limited clinical evidence for the effectiveness of most fermented foods in gastrointestinal health and disease. Given the convincing in vitro findings, clinical high-quality trials investigating the health benefits of fermented foods are warranted.\n\nFermented Foods: Definitions and Characteristics, Impact on the Gut Microbiota and Effects on Gastrointestinal Health and Disease.", "token_count": 444, "char_count": 1823, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5494, "quality_score": 0.7747, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:31.433720", "source": { "split": "train_shard_00001", "doc_id": 1516 }, "chunk_id": "train_shard_00001_1516_0", "global_id": 7783 }, { "text": "Streptococcus agalactiae (group B streptococcus; GBS) is a colonizer of the gastrointestinal and urogenital tracts, and an opportunistic pathogen of infants and adults. The worldwide population of GBS is characterized by clonal complexes (CCs) with different invasive potentials. CC17, for example, is a hypervirulent lineage commonly associated with neonatal sepsis and meningitis, while CC1 is less invasive in neonates and more commonly causes invasive disease in adults with comorbidities. The genetic basis of GBS virulence and the extent to which different CCs have adapted to different host environments remain uncertain. We have therefore applied a pan-genome-wide association study (GWAS) approach to 1,988 GBS strains isolated from different hosts and countries. Our analysis identified 279 CC-specific genes associated with virulence, disease, metabolism, and regulation of cellular mechanisms that may explain the differential virulence potential of particular CCs. In CC17 and CC23, for example, we have identified genes encoding pilus, quorum-sensing proteins, and proteins for the uptake of ions and micronutrients which are absent in less invasive lineages. Moreover, in CC17, carriage and disease strains were distinguished by the allelic variants of 21 of these CC-specific genes. Together our data highlight the lineage-specific basis of GBS niche adaptation and virulence.IMPORTANCE GBS is a leading cause of mortality in newborn babies in high- and low-income countries worldwide. Different strains of GBS are characterized by different degrees of virulence, where some are harmlessly carried by humans or animals and others are much more likely to cause disease.The genome sequences of almost 2,000 GBS samples isolated from both animals and humans in high- and low- income countries were analyzed using a pan-genome-wide association study approach. This allowed us to identify 279 genes which are associated with different lineages of GBS, characterized by a different virulence and preferred host", "token_count": 491, "char_count": 2034, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5666, "quality_score": 0.7833, "entities": { "genes": [ "CC1", "CC23", "CC17" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:32.132640", "source": { "split": "train_shard_00001", "doc_id": 1517 }, "chunk_id": "train_shard_00001_1517_0", "global_id": 7784 }, { "text": "Additionally, we propose that the GBS now carried in humans may have first evolved in animals before expanding clonally once adapted to the human host.These findings are essential to help understand what is causing GBS disease and how the bacteria have evolved and are transmitted.\n\nPan-GWAS of Streptococcus agalactiae Highlights Lineage-Specific Genes Associated with Virulence and Niche Adaptation.", "token_count": 94, "char_count": 401, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8276, "quality_score": 0.9138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:32.546180", "source": { "split": "train_shard_00001", "doc_id": 1517 }, "chunk_id": "train_shard_00001_1517_1", "global_id": 7785 }, { "text": "Klebsiella pneumoniae is considered an opportunistic pathogen frequently involved with healthcare-associated infections. The genome of K. pneumoniae is versatile, harbors diverse virulence factors and easily acquires and exchanges resistance plasmids, facilitating the emergence of new threatening clones. In the last years, ST16 has been described as an emergent, clinically relevant strain, increasingly associated with outbreaks, and carrying virulence factors (such as ICEKp, iuc, rmpADC/2) and a diversity of resistance genes. However, a far-reaching phylogenetic study of ST16, including geographically, clinically and temporally distributed isolates is not available. In this work, we analyzed all publicly available ST16 K. pneumoniae genomes in terms of virulence factors, including capsular lipopolysaccharide and polysaccharide diversity, plasmids and antimicrobial resistance genes. A core genome SNP analysis shows that less than 1% of studied sites were variant sites, with a median pairwise single nucleotide polymorphism difference of 87 SNPs. The number and diversity of antimicrobial resistance genes, but not of virulence-related genes, increased consistently in ST16 strains during the studied period. A genomic comparison between ST16 and the high-risk clone ST11 K. pneumoniae, showed great similarities in their capacity to acquire resistance and virulence markers, differing mostly in the great diversity of capsular lipopolysaccharide and polysaccharide types in ST11, in comparison with ST16. While virulence and antimicrobial resistance scores indicated that ST11 might still constitute a more difficult-to-manage strain, results presented here demonstrate the great potential of the ST16 clone becoming critical in public health.", "token_count": 463, "char_count": 1806, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8151, "entities": { "genes": [ "ST16", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:33.193912", "source": { "split": "train_shard_00001", "doc_id": 1518 }, "chunk_id": "train_shard_00001_1518_0", "global_id": 7786 }, { "text": "A Comprehensive Genomic Analysis of the Emergent Klebsiella pneumoniae ST16 Lineage: Virulence, Antimicrobial Resistance and a Comparison with the Clinically Relevant ST11 Strain.", "token_count": 60, "char_count": 186, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [ "ST16", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:33.558490", "source": { "split": "train_shard_00001", "doc_id": 1518 }, "chunk_id": "train_shard_00001_1518_1", "global_id": 7787 }, { "text": "Repeats are the most diverse and dynamic, but also the least well understood component of microbial genomes. For all we know, repeat-associated mutations such as duplications, deletions, inversions, and gene conversion might be as common as point mutations, but because of short-read myopia and methodological bias they have received much less attention. Long-read sequencing opens the perspective of resolving repeats and systematically investigating the mutations they induce. For this study, we assembled the genomes of 16 closely related strains of the bacterial pathogen Mycobacterium tuberculosis from PacBio HiFi reads, with the aim of characterizing the full spectrum of DNA polymorphisms. We find that complete and accurate genomes can be assembled from HiFi reads, with read size being the main limitation in the presence of duplications. By combining a reference-free pangenome graph with extensive repeat annotation, we identified 110 variants, 58 of which can be assigned to repeat-associated mutational mechanisms such as strand slippage and homologous recombination. While recombination events are less frequent than point mutations, they can affect large regions and introduce multiple variants at once, as shown by three gene conversion events and a duplication of 7.3 kb that involve ppe18 and ppe57, two genes possibly involved in immune subversion. Our study shows that the contribution of repeat-associated mechanisms of mutation can be similar to that of point mutations at the microevolutionary scale of an outbreak. A large reservoir of unstudied genetic variation in this \"monomorphic\" bacterial pathogen awaits investigation.\n\nLarge contribution of repeats to genetic variation in a transmission cluster of Mycobacterium tuberculosis", "token_count": 392, "char_count": 1759, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:34.184176", "source": { "split": "train_shard_00001", "doc_id": 1519 }, "chunk_id": "train_shard_00001_1519_0", "global_id": 7788 }, { "text": "Structural variants (SVs) contribute significantly to human genetic diversity and disease 1–4 . Previously, SVs have remained incompletely resolved by population genomics, with short-read sequencing facing limitations in capturing the whole spectrum of SVs at nucleotide resolution 5–7 . Here we leveraged nanopore sequencing 8 to construct an intermediate coverage resource of 1,019 long-read genomes sampled within 26 human populations from the 1000 Genomes Project. By integrating linear and graph-based approaches for SV analysis via pangenome graph-augmentation, we uncover 167,291 sequence-resolved SVs in these samples, considerably advancing SV characterization compared to population-wide short-read sequencing studies 3,4 . Our analysis details diverse SV classes—deletions, duplications, insertions, and inversions—at population-scale. LINE-1 and SVA retrotransposition activities frequently mediate transductions 9,10 of unique sequences, with both mobile element classes transducing sequences at either the 3′- or 5′-end, depending on the source element locus. Furthermore, analyses of SV breakpoint junctions suggest a continuum of homology-mediated rearrangement processes are integral to SV formation, and highlight evidence for SV recurrence involving repeat sequences. Our open-access dataset underscores the transformative impact of long-read sequencing in advancing the characterisation of polymorphic genomic architectures, and provides a resource for guiding variant prioritisation in future long-read sequencing-based disease studies.\n\nLong-read sequencing and structural variant characterization in 1,019 samples from the 1000 Genomes Project", "token_count": 389, "char_count": 1666, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6981, "quality_score": 0.8491, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:34.804292", "source": { "split": "train_shard_00001", "doc_id": 1520 }, "chunk_id": "train_shard_00001_1520_0", "global_id": 7789 }, { "text": "Pangenomics is the study of related genomes collectively, usually from the same species or closely related taxa. Originally, pangenomes were defined for bacterial species. After the concept was extended to eukaryotic genomes, two definitions of pangenome evolved in parallel: the gene-based approach, which defines the pangenome as the union of all genes, and the sequence-based approach, which defines the pangenome as the set of all nonredundant genomic sequences. Estimating the total size of the pangenome for a given species has been subject of study since the very first mention of pangenomes. Traditionally, this is performed predicting the ratio at which new genes are discovered, referred to as the openness of the species. Here, we abstract each genome as a set of items, which is entirely agnostic of the two approaches (gene-based, sequence-based). Genes are a viable option for items, but also other possibilities are feasible, e.g., genome sequence substrings of fixed length k (k-mers). In the present study, we investigate the use of k-mers to estimate the openness as an alternative to genes, and compare the results. An efficient implementation is also provided.\n\nRevisiting pangenome openness with k-mers", "token_count": 281, "char_count": 1223, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6064, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:35.369212", "source": { "split": "train_shard_00001", "doc_id": 1521 }, "chunk_id": "train_shard_00001_1521_0", "global_id": 7790 }, { "text": "Thermo-tolerant yeast Kluyveromyces marxianus is able to utilize a wide range of substrates, including xylose; however, the xylose fermentation ability is weak because of the redox imbalance under oxygen-limited conditions. Alleviating the intracellular redox imbalance through engineering the coenzyme specificity of NADPH-preferring xylose reductase (XR) and improving the expression of XR should promote xylose consumption and fermentation. In this study, the native xylose reductase gene (Kmxyl1) of the K. marxianus strain was substituted with XR or its mutant genes from Pichia stipitis (Scheffersomyces stipitis). The ability of the resultant recombinant strains to assimilate xylose to produce xylitol and ethanol at elevated temperature was greatly improved. The strain YZB014 expressing mutant PsXR N272D, which has a higher activity with both NADPH and NADH as the coenzyme, achieved the best results, and produced 3.55 g l(-1) ethanol and 11.32 g l(-1) xylitol-an increase of 12.24- and 2.70-fold in product at 42 °C, respectively. A 3.94-fold increase of xylose consumption was observed compared with the K. marxianus YHJ010 harboring KmXyl1. However, the strain YZB015 expressing a mutant PsXR K21A/N272D, with which co-enzyme preference was completely reversed from NADPH to NADH, failed to ferment due to the low expression. So in order to improve xylose consumption and fermentation in K. marxianus, both higher activity and co-enzyme specificity change are necessary.\n\nImproving ethanol and xylitol fermentation at elevated temperature through substitution of xylose reductase in Kluyveromyces marxianus.", "token_count": 491, "char_count": 1622, "word_count": 232, "semantic_coherence": 1, "information_density": 0.569, "quality_score": 0.7845, "entities": { "genes": [ "YZB015", "YHJ010", "YZB014" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:36.018449", "source": { "split": "train_shard_00001", "doc_id": 1522 }, "chunk_id": "train_shard_00001_1522_0", "global_id": 7791 }, { "text": "

Background

Fervidobacterium is a genus of thermophilic anaerobic Gram-negative rod-shaped bacteria belonging to the phylum Thermotogota. They can grow through fermentation on a wide range of sugars and protein-rich substrates. Some can also break down feather keratin, which has significant biotechnological potential. Fervidobacteria genomes have undergone several horizontal gene transfer events, sharing DNA with unrelated microbial taxa. Despite increasing biotechnological and evolutionary interest in this genus, only seven species have been described to date. Here, we present and describe six new and complete Fervidobacterium genomes, including the type strains Fervidobacterium gondwanense CBS-1 T, F. islandicum H-21 T and F. thailandense FC2004T, one novel isolate from Georgia (strain GSH) and two strains (DSM 21710 and DSM 13770) that have not been previously described along with an evolutionary and phylogenomic analysis of the genus.

Results

The complete genomes were around 2 Mb with approximately 2,000 CDS identified and annotated in each of them and a G + C content ranging from 38.9 mol% to 45.8 mol%. Phylogenomic comparisons of all currently available Fervidobacterium genomes, including OrthoANI and TYGS analyses, as well as a phylogenetic analysis based on the 16S rRNA gene, identified six species and nine subspecies clusters across the genus, with a consistent topology and a distant and separately branching species, Fervidobacterium thailandense. F. thailandense harbored the highest number of transposases, CRISPR clusters, pseudo genes and horizontally transferred regions The pan genome of the genus showed that 44% of the genes belong to the cloud pangenome, with most of the singletons found also in F", "token_count": 502, "char_count": 1787, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6932, "quality_score": 0.8466, "entities": { "genes": [ "FC2004" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:36.675462", "source": { "split": "train_shard_00001", "doc_id": 1523 }, "chunk_id": "train_shard_00001_1523_0", "global_id": 7792 }, { "text": "thailandense.

Conclusions

The additional genome sequences described in this work and the comparison with all available Fervidobacterium genome sequences provided new insights into the evolutionary history of this genus and supported a phylogenetic reclassification. The phylogenomic results from OrthoANI and TYGS analyses revealed that F. riparium and F. gondwanense belong to the same genome species, and includes Fervidobacterium sp. 13770, while \"F. pennivorans\" strain DYC belongs to a separate genome species, whereas Fervidobacterium sp. 21710 and Fervidobacterium sp. GSH within the Fervidobacterium pennivorans clade represent two subspecies. F. changbaicum is reclassified as F. islandicum.\n\nComparative genomics of Fervidobacterium: a new phylogenomic landscape of these wide-spread thermophilic anaerobes.", "token_count": 242, "char_count": 824, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7048, "quality_score": 0.8524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:37.158604", "source": { "split": "train_shard_00001", "doc_id": 1523 }, "chunk_id": "train_shard_00001_1523_1", "global_id": 7793 }, { "text": "The genus Geomonas comprises Gram-stain-negative, diazotrophic bacteria associated with soil and plant environments, whose taxonomic classification has not yet been thoroughly investigated. Although 16S rRNA gene-based phylogeny remains a useful preliminary tool, it often lacks the resolution needed for accurate species delineation. In this study, we conducted a comprehensive comparative genomic analysis encompassing all validly published Geomonas species, integrating whole-genome phylogenomics, average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH) and other genome-based metrics to refine their classification. Phylogenetic trees constructed from 16S rRNA gene sequences and core genome alignments consistently demonstrated close genomic clustering between Geomonas diazotrophica Red69ᵀ and Geomonas nitrogeniifigens RF4ᵀ, as well as between Geomonas fuzhouensis RG17ᵀ and Geomonas subterranea RG2ᵀ. ANI and dDDH values for these strain pairs exceeded species delineation thresholds (>96% ANI and >70 % dDDH), strongly supporting their taxonomic unification. Despite minor phenotypic variations, genomic coherence suggests that Geomonas nitrogeniifigens Liu et al. 2022 should be reclassified as Geomonas diazotrophica Xu et al. 2022, and Geomonas fuzhouensis Yang et al. 2023 should be recognized as a later heterotypic synonym of Geomonas subterranea Liu et al. 2022. These findings underscore the necessity of integrating whole-genome analyses into microbial taxonomy to ensure species classifications reflect true genomic relationships.", "token_count": 518, "char_count": 1663, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7426, "quality_score": 0.8713, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:37.817080", "source": { "split": "train_shard_00001", "doc_id": 1524 }, "chunk_id": "train_shard_00001_1524_0", "global_id": 7794 }, { "text": "Genome-based reclassification within <i>Geomonas</i>: <i>Geomonas nitrogeniifigens</i> Liu <i>et al.</i> 2022 as a heterotypic synonym of <i>Geomonas diazotrophica</i> Xu <i>et al.</i> 2022 and <i>Geomonas fuzhouensis</i> Yang <i>et al.</i> 2023 as a later heterotypic synonym of <i>Geomonas subterranea</i> Liu <i>et al.</i> 2022.", "token_count": 231, "char_count": 439, "word_count": 40, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:38.290833", "source": { "split": "train_shard_00001", "doc_id": 1524 }, "chunk_id": "train_shard_00001_1524_1", "global_id": 7795 }, { "text": "Objective: To analyze the genomic characteristics and antibiotic resistance of Listeria monocytogenes isolated from food sources in Beijing City in 2022. Methods: A total of 83 strains of Listeria monocytogenes were isolated from three major categories of food, namely raw poultry, raw livestock meat and ready-to-eat foods, in Beijing's food safety risk monitoring in 2022. Whole-genome sequencing (WGS) was performed to determine serogroups, multilocus sequence typing (ST) and core genome multilocus sequence typing (cgMLST). Virulence genes and antibiotic resistance genes were identified using the VFDB and ResFinder 3.0 databases. Antimicrobial susceptibility to eight antibiotics was tested via the broth microdilution method. Results: The predominant serogroup was 1/2a, 3a (61.2%). All the isolates were divided into 14 STs, with ST121 (21.7%), ST8 (20.5%), ST9 (13.3%), and ST87 (13.3%) as the dominant types. All 83 isolates were classified into 75 cgMLST types, with six clusters showing identical profiles, indicating potential clonal transmission. Comparative genomic analysis revealed that strains of the same ST clustered together regardless of geographic origin, and some Beijing isolates differed by fewer than 10 alleles from strains isolated in other countries. All the isolates in the study carried virulence islands 1(LIPI-1) and LIPI-2. LIPI-3 was detected in ST1, ST11 and ST3 isolates, while LIPI-4 was found in ST87 isolates. About 42 isolates (50.6%, including ST1, ST11, ST5, ST307, ST8, ST9, ST155, and ST3) harbored SSI-1, and 18 ST121 isolates carried SSI-2", "token_count": 508, "char_count": 1623, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6853, "quality_score": 0.8427, "entities": { "genes": [ "ST3", "ST307", "ST5", "ST155", "ST8", "ST1", "ST11", "ST87", "ST121", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:38.949717", "source": { "split": "train_shard_00001", "doc_id": 1525 }, "chunk_id": "train_shard_00001_1525_0", "global_id": 7796 }, { "text": "Only 3.61% (three strains) and 4.82% (four strains) of isolates exhibited resistance to tetracycline and erythromycin, respectively. No resistance to other tested antibiotics was observed. Conclusion: Foodborne Listeria monocytogenes in Beijing exhibits high genomic diversity but is dominated by specific STs, some of which are associated with hypervirulence. Some Beijing isolates have homology with food-derived isolates from other countries.\n\n[Genomic characteristics and antimicrobial resistance of <i>Listeria monocytogenes</i> isolated from food in Beijing, City 2022].", "token_count": 175, "char_count": 602, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7838, "quality_score": 0.8919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:39.404995", "source": { "split": "train_shard_00001", "doc_id": 1525 }, "chunk_id": "train_shard_00001_1525_1", "global_id": 7797 }, { "text": "Photobacterium (P.) is a genus widely studied in regards to its association with and ubiquitous presence in marine environments. However, certain species (P. phosphoreum, P. carnosum, P. iliopiscarium) have been recently described to colonize and spoil raw meats without a marine link. We have studied 27 strains from meat as well as 26 strains from marine environments in order to probe for intraspecies marine/terrestrial subpopulations and identify distinct genomic features acquired by environmental adaptation. We have conducted phylogenetic analysis (MLSA, ANI, fur, codon usage), search of plasmids (plasmidSPADES), phages (PHASTER), CRISPR-cas operons (CRISPR-finder) and secondary metabolites gene clusters (antiSMASH, BAGEL), in addition to a targeted gene search for specific pathways (e.g. TCA cycle, pentose phosphate, respiratory chain) and elements relevant for growth, adaptation and competition (substrate utilization, motility, bioluminescence, sodium and iron transport). P. carnosum appears as a conserved single clade, with one isolate from MAP fish clustering apart that doesn't, however, show distinct features that could indicate different adaptation. The species harbors genes for a wide carbon source utilization (glycogen/starch, maltose, pullulan, fucose) for colonization of diverse niches in its genome. P. phosphoreum is represented by two different clades on the phylogenetic analyses not correlating to their origin or distribution of other features analyzed that can be divided into two novel subspecies based on genome-wide values", "token_count": 428, "char_count": 1607, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:40.036931", "source": { "split": "train_shard_00001", "doc_id": 1526 }, "chunk_id": "train_shard_00001_1526_0", "global_id": 7798 }, { "text": "A more diverse antimicrobial activity (sactipeptides, microcins), production of secondary metabolites (siderophores and arylpolyenes), stress response and adaptation (bioluminescence, sodium transporters, catalase, high affinity for oxygen cytochrome cbb3 oxidase, DMSO reductase and proton translocating NADH dehydrogenase) is predicted compared to the other species. P. iliopiscarium was divided into two clades based on source of isolation correlating with phylogeny and distribution of several traits. The species shows traits common to the other two species, similar carbon utilization/transport gene conservation as P. carnosum for the meat-isolated strains, and predicted utilization of marine-common DMSO and flagellar cluster for the sea-isolated strains. Results additionally suggest that photobacteria are highly prone to horizontal acquisition/loss of genetic material and genetic transduction, and that it might be a strategy for increasing the frequency of strain- or species-specific features that offers a growth/competition advantage.\n\nComparative genomics of Photobacterium species from terrestrial and marine habitats.", "token_count": 288, "char_count": 1158, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7603, "quality_score": 0.8801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:40.599129", "source": { "split": "train_shard_00001", "doc_id": 1526 }, "chunk_id": "train_shard_00001_1526_1", "global_id": 7799 }, { "text": "Shigellosis is a diarrheal disease caused mainly by Shigella flexneri and Shigella sonnei Infection is thought to be largely self-limiting, with short- to medium-term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM)-associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 and 1,862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM-associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart to shed light on the adaptation of these important pathogens during infection. We find that pairs likely associated with persistent infection/carriage and with a smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection, and with a greater SNP distance. We observed antimicrobial resistance acquisition during Shigella carriage, including the gain of an extended-spectrum beta-lactamase gene during carriage. Finally, we explored large chromosomal structural variations and rearrangements in seven (five chronic and two reinfection associated) pairs of S. flexneri 3a isolates from an MSM-associated epidemic sublineage, which revealed variations at several common regions across isolate pairs, mediated by insertion sequence elements and comprising a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection/carriage. In addition, we have also created a complete reference genome and biobanked isolate of the globally important pathogen, S. flexneri 3a.IMPORTANCEShigella spp", "token_count": 487, "char_count": 1969, "word_count": 257, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:41.964801", "source": { "split": "train_shard_00001", "doc_id": 1527 }, "chunk_id": "train_shard_00001_1527_0", "global_id": 7800 }, { "text": "are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrheal illness among children under the age of five in low-income countries. In high-income countries, shigellosis is also a sexually transmissible disease among men who have sex with men. Within the latter setting, we have captured prolonged and/or recurrent infection with shigellae of the same serotype, challenging the belief that Shigella infection is short lived and providing an early opportunity to study the evolution of the pathogen over the course of infection. Using this recently emerged transmission scenario, we comprehensively characterize the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genomic regions, findings that have relevance for other Enterobacteriaceae.\n\nAccessory Genome Dynamics and Structural Variation of <i>Shigella</i> from Persistent Infections.", "token_count": 236, "char_count": 1011, "word_count": 138, "semantic_coherence": 1, "information_density": 0.7174, "quality_score": 0.8587, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:42.439987", "source": { "split": "train_shard_00001", "doc_id": 1527 }, "chunk_id": "train_shard_00001_1527_1", "global_id": 7801 }, { "text": "Emergence and spread of the hypervirulent pathotype of Klebsiella pneumoniae have significantly increased infection rates in community as well as healthcare settings. There is an increasing interest to identify discriminating features between classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) to facilitate our understanding of the rapid emergence and dissemination of the hypervirulent pathotype. Here, we sought to identify unique epigenetic signatures of hvKp pathotype that differ from its classical counterpart using single-base resolution methylome analysis of native DNA sequencing on the Oxford Nanopore Technologies platform. The overall global adenine methylation in GATC motifs (i.e., Dam methylation motif) and cytosine methylation in CCWGG motifs (i.e., Dcm methylation motif) were significantly higher in hvKp isolates compared to that in cKp isolates, irrespective of their position in chromosomes or putative extra-chromosomal genetic elements. Notably, we observed significant enrichment of hypermethylated GATC and CCWGG motifs in the virulome of hvKp compared to hvKp genes not directly associated with virulence. We also observed increased methylation of GATC and CCWGG motifs in the capsule synthesis locus of hvKp isolates compared to cKp isolates. Furthermore, we identified several differentially methylated genes (DMGs) between the two pathotypes; interestingly, these DMGs include metal ion transporters, multidrug efflux pumps, transcriptional regulators of stress response, and genes associated with biofilm formation. Our results highlight hypermethylation of GATC and CCWGG motifs as unique epigenetic signatures of hvKp isolates.IMPORTANCEHypervirulent Klebsiella pneumoniae (hvKp) is a more virulent and rapidly evolving hypermucoviscous pathotype of classical K. pneumoniae (cKp)", "token_count": 508, "char_count": 1866, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:43.127184", "source": { "split": "train_shard_00001", "doc_id": 1528 }, "chunk_id": "train_shard_00001_1528_0", "global_id": 7802 }, { "text": "The hypervirulent pathotype is a major public health concern and is associated with high infection rates in community as well as hospital settings. With the recent emergence of multidrug-resistant hvKp, it has become imperative to investigate non-classical mechanisms such as epigenetics in addition to canonical biochemical and genetic mechanisms that delineate and differentiate the hypervirulent pathotype from its classical counterpart. Here, we identify genome-wide differences in adenine and cytosine methylation marks at well-characterized motifs between the two pathotypes. Overall, significantly higher levels of methylation were observed across chromosomal DNA and extrachromosomal elements in hvKp compared to cKp. Among hvKp isolates, the genes associated with virulence are particularly enriched for methylation marks. Our findings shed light on how epigenetic signatures may help distinguish the pathogenic potential of bacteria.\n\nDistinct epigenetic signatures of classical and hypervirulent Klebsiella pneumoniae.", "token_count": 241, "char_count": 1036, "word_count": 136, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:43.645361", "source": { "split": "train_shard_00001", "doc_id": 1528 }, "chunk_id": "train_shard_00001_1528_1", "global_id": 7803 }, { "text": "

SUMMARY

Through vaginal colonization, GBS causes severe outcomes including neonatal sepsis and meningitis. Although intrapartum antibiotic prophylaxis (IAP) has reduced neonatal disease rates, persistent GBS colonization has been observed in patients following prophylaxis. To determine whether IAP selects for genomic signatures that enhance GBS survival and persistence, a pangenome analysis was performed on 97 isolates from 58 participants before (prenatal) and after (postpartum) IAP/childbirth. Thirty-one of the 34 paired strains from participants with persistent colonization clustered together in the core gene phylogeny, suggesting that the strains recovered at the postpartum sampling were highly similar to those recovered at the prenatal visit. A core-gene mutation analysis identified mutations in 74% (n=23) of the 31 postpartum genomes when compared to the prenatal strains of the same multilocus sequence type recovered from the same individuals. Several strains had acquired mutations in the same colonization-associated genes, though two postpartum strains accounted for most of the mutations. These two outliers were classified as mutators based on high mutation rates and mutations within DNA repair system genes. Increased biofilm production was observed in half of the postpartum strains relative to the prenatal strains, which is supported by the presence of point mutations in genes associated with adherence. Together, these findings suggest that antibiotics may impose a selective pressure on GBS that selects for mutations and phenotypes that promote adaptation and survival in vivo . Enhanced survival in the genitourinary tract can lead to persistent colonization, increasing the likelihood of invasive disease in subsequent pregnancies and in newborns following IAP.\n\nGenomic adaptation in group B Streptococcus following intrapartum antibiotic prophylaxis and childbirth", "token_count": 460, "char_count": 1919, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6151, "quality_score": 0.8075, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:44.334308", "source": { "split": "train_shard_00001", "doc_id": 1529 }, "chunk_id": "train_shard_00001_1529_0", "global_id": 7804 }, { "text": "

Background

Tanzania is one of seven countries with the highest disease burden caused by cholera in Africa. We studied the evolution of Vibrio cholerae O1 isolated in Tanzania during the past three decades.

Methodology/principal findings

Genome-wide analysis was performed to characterize V. cholerae O1 responsible for the Tanzanian 2015-2017 outbreak along with strains causing outbreaks in the country for the past three decades. The genomes were further analyzed in a global context of 590 strains of the seventh cholera pandemic (7PET), as well as environmental isolates from Lake Victoria. All Tanzanian cholera outbreaks were caused by the 7PET lineage. The T5 sub-lineage (ctxB3) dominated outbreaks until 1997, followed by the T10 atypical El Tor (ctxB1) up to 2015, which were replaced by the T13 atypical El Tor of the current third wave (ctxB7) causing most cholera outbreaks until 2017 with T13 being phylogenetically related to strains from East African countries, Yemen and Lake Victoria. The strains were less drug resistant with approximate 10-kb deletions found in the SXT element, which encodes resistance to sulfamethoxazole and trimethoprim. Nucleotide deletions were observed in the CTX prophage of some strains, which warrants further virulence studies. Outbreak strains share 90% of core genes with V. cholerae O1 from Lake Victoria with as low as three SNPs difference and a significantly similar accessory genome, composed of genomic islands namely the CTX prophage, Vibrio Pathogenicity Islands; toxin co-regulated pilus biosynthesis proteins and the SXT-ICE element.

Conclusion/significance

Characterization of V. cholerae O1 from Tanzania reveals genetic diversity of the 7PET lineage composed of T5, T10 and T13 sub-lineages with introductions of new sequence types from neighboring countries", "token_count": 513, "char_count": 1843, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5925, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:45.009037", "source": { "split": "train_shard_00001", "doc_id": 1530 }, "chunk_id": "train_shard_00001_1530_0", "global_id": 7805 }, { "text": "The presence of these sub-lineages in environmental isolates suggests that the African Great Lakes may serve as aquatic reservoirs for survival of V. cholerae O1 favoring continuous human exposure.\n\nGenomic insights into Vibrio cholerae O1 responsible for cholera epidemics in Tanzania between 1993 and 2017.", "token_count": 83, "char_count": 308, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:45.378935", "source": { "split": "train_shard_00001", "doc_id": 1530 }, "chunk_id": "train_shard_00001_1530_1", "global_id": 7806 }, { "text": "

Background

Flood-related waterborne diseases are an acute consequence of natural disasters, primarily due to contamination of drinking water supplies. With climate change driving an increase in extreme weather events, such as floods, the risk of waterborne disease outbreak is expected to rise. This report summarizes an outbreak investigation of Shiga toxin-producing Escherichia coli (STEC) O26:H11 in the Belgian-Luxembourg following the mid-July 2021 floods.

Methods

In summer 2021, STEC O26 isolates referred to the Belgian National Reference Centre (NRC) were first characterized with IS621-typing, followed by whole genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST). As an outbreak was suspected, a national-level investigation was initiated. A retrospective analysis compared STEC incidence between flooded and non-flooded municipalities in Wallonia.

Results

The NRC identified a cluster of ten cases infected with STEC O26:H11 (stx2a+ and eae+), with identical IS621-profile. Six were confirmed by WGS; all six isolates of sequence type (ST) 21 were closely related. All six cases developed haemolytic uraemic syndrome (HUS) and resided in the Belgian-Luxembourg, heavily impacted by the mid-July 2021 floods. Retrospective analysis showed an increase in STEC cases in flooded areas of Wallonia. Surveillance questionnaires linked the illness to contaminated tap water that was consumed by all cases. Phylogenetic analysis revealed cross-border spread in the neighbouring Grand Duchy (GD) of Luxembourg", "token_count": 435, "char_count": 1594, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [ "IS621" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:46.020850", "source": { "split": "train_shard_00001", "doc_id": 1531 }, "chunk_id": "train_shard_00001_1531_0", "global_id": 7807 }, { "text": "Five Luxembourgish cases, including two STEC-HUS cases, were epidemiologically linked to a same daycare centre.

Conclusions

This report describes an HUS cluster of STEC O26:H11 (ST21, stx2a+, eae+) in Belgium following severe mid-July 2021 floods. Contaminated tap water was identified as the probable source of infection of the Belgian-Luxembourg cases, with possible secondary person-to-person transmission to children in a GD Luxembourgish daycare centre. This outbreak highlights the importance of sharing molecular typing data between countries and the need for rapid public health interventions following climate-driven disasters.\n\nShiga toxin-producing Escherichia coli O26:H11 associated with a cluster of haemolytic uraemic syndrome cases following the mid-July 2021 floods in Belgium.", "token_count": 228, "char_count": 834, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7714, "quality_score": 0.8857, "entities": { "genes": [ "ST21" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:46.493450", "source": { "split": "train_shard_00001", "doc_id": 1531 }, "chunk_id": "train_shard_00001_1531_1", "global_id": 7808 }, { "text": "

ABSTRACT

Clostridioides difficile PCR ribotype (RT) 002 is the second most prevalent RT in the Netherlands. In 2019, an increase in C. difficile infections (CDI) due to a clonal RT002 strains was reported in Ireland. In retrospect, a significant increase in the proportion of CDI due to RT002 was detected in the Netherlands between May 2017-May 2018 (11.9% of 683 cases vs 6.5% of 865 in the previous year). Our aim was to analyze and characterize CDI due to RT002 over time and to assess whether RT002 isolates in the Netherlands were related to the Irish RT002 isolates. Over the period May 2009-April 2021, Dutch patients with CDI due to RT002 showed less severe CDI (22%) in comparison with hypervirulent RTs (RT027; 29% and RT078; 25%), similar to grouped data from other non-hypervirulent ribotypes (21%). However, RT002-associated CDI prior to the increased proportion (2009-2017) showed CDI severity similar to CDI associated with hypervirulent types, whereas this was no longer the case after the increase (2017-2021). Using core genome MLST, Dutch isolates were found not to be related to the Irish outbreak strain. Several Dutch strains clustered together without an evident epidemiological link, suggesting recent emergence.

Importance

Clostridioides difficile is a significant cause of hospital-associated infections, making it relevant to understand the emergence and spread of different ribotypes. This study highlights a rise in cases of PCR ribotype 002 (RT002) in the Netherlands, suggesting changes in its prevalence. Despite the increase in RT002 infections, the severity of disease appears to have decreased and is lower compared to more virulent ribotypes. Further research is needed to understand the factors driving this change", "token_count": 505, "char_count": 1770, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5815, "quality_score": 0.7907, "entities": { "genes": [ "RT078", "RT002", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:47.148455", "source": { "split": "train_shard_00001", "doc_id": 1532 }, "chunk_id": "train_shard_00001_1532_0", "global_id": 7809 }, { "text": "Additionally, this study underscores some limitations of core genome multi-locus sequence typing (cgMLST). cgMLST is valuable for identifying genetic relationships, however it cannot always distinguish between widespread recently emerged strains and local transmission chains, making it challenging to determine the exact sources of infection. Continued surveillance and genetic characterization of C. difficile are essential to better understand these trends and improve control measures.\n\nIncrease ofClostridioides difficilePCR ribotype 002 infection coincides with decreased disease severity in hospitalized patients in the Netherlands", "token_count": 131, "char_count": 645, "word_count": 80, "semantic_coherence": 1, "information_density": 0.8875, "quality_score": 0.9437, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:47.570624", "source": { "split": "train_shard_00001", "doc_id": 1532 }, "chunk_id": "train_shard_00001_1532_1", "global_id": 7810 }, { "text": "Abstract

Background Identification of Human leukocyte antigen (HLA) types from DNA-sequenced human samples is important in organ transplantation and cancer immunotherapy and remains a challenging task considering sequence homology and extreme polymorphism of HLA genes. Results We present Orthanq, a novel statistical model and corresponding application for transparent and uncertainty-aware quantification of haplotypes. We utilize our approach to perform HLA typing while, for the first time, reporting uncertainty of predictions and transparently observing mutations beyond reported HLA types. Using 99 gold standard samples from 1000 Genomes, Illumina Platinum Genomes and Genome In a Bottle projects, we show that Orthanq can provide superior accuracy and shorter runtimes than state-of-the-art HLA typers. Conclusions Orthanq is is the first approach that allows to directly utilize existing pangenome alignments and type all HLA loci. Moreover, it can be generalized for usages beyond HLA typing, e.g. for virus lineage quantification. Orthanq is available under https://orthanq.github.io.

\n\nOrthanq: transparent and uncertainty-aware haplotype quantification with application in HLA-typing", "token_count": 286, "char_count": 1219, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7125, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:48.133813", "source": { "split": "train_shard_00001", "doc_id": 1533 }, "chunk_id": "train_shard_00001_1533_0", "global_id": 7811 }, { "text": "In Algeria, Smen is a fermented butter produced in households using empirical methods. Smen fermentation is driven by autochthonous microorganisms; it improves butter shelf-life and yields highly fragrant products used as ingredients in traditional dishes as well as in traditional medicine. The present study is aimed at investigating microbial diversity and dynamics during Algerian Smen fermentation using both culture-dependent and culture-independent approaches, as well as by monitoring volatile organic compound production. To reach this goal, fifteen Smen samples (final products) produced in households from different regions in Algeria were collected and analyzed. In addition, microbial and volatile compound dynamics at the different stages of Smen manufacturing were investigated for one Smen preparation. The results showed that Smen is a microbiologically safe product, as all hygiene and safety criteria were respected. The dominant microorganisms identified by both techniques were LAB and yeasts. Lactococcus spp. and Streptococcus thermophilus were the main bacterial species involved in spontaneous raw milk fermentation preceding butter-making, while lactobacilli and enterococci were the only bacteria found to be viable during Smen maturation. Regarding fungal diversity, yeast species were only recovered from two mature Smen samples by culturing, while different species (e.g., Geotrichum candidum, Moniliella sp.) were identified in all samples by the culture-independent approach. Using microbial analysis of a single batch, many of these were found viable during manufacturing. Concerning the volatile profiles, they were highly diverse and characterized by a high prevalence of short chain fatty acids, methylketones, and esters. Correlation analysis between microbial diversity and volatile profiles showed that several yeast (Moniliella sp., K", "token_count": 492, "char_count": 1982, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:48.790054", "source": { "split": "train_shard_00001", "doc_id": 1534 }, "chunk_id": "train_shard_00001_1534_0", "global_id": 7812 }, { "text": "marxianus) and LAB (e.g., Lactococcus spp., S. thermophilus) species were strongly correlated with one or more volatile organic compound families, including several ethyl esters and methyl ketones that can be linked to pleasant, sweetly floral, fruity, buttery, and creamy odors. This study clearly identified key microorganisms involved in Smen fermentation and maturation that could be used in the future for better fermentation control and improvement of quality attributes.\n\nDeciphering the Microbiota and Volatile Profiles of Algerian Smen, a Traditional Fermented Butter.", "token_count": 168, "char_count": 609, "word_count": 81, "semantic_coherence": 1, "information_density": 0.8519, "quality_score": 0.9259, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:49.231417", "source": { "split": "train_shard_00001", "doc_id": 1534 }, "chunk_id": "train_shard_00001_1534_1", "global_id": 7813 }, { "text": "The use of the yeasts Candida utilis, Kluyveromyces marxianus and Saccharomyces cerevisiae as protein sources in diets for Atlantic salmon (Salmo salar) pre-smolts was investigated. An 89day study was conducted using triplicate groups of Atlantic salmon with 28g initial weight kept in fresh water. The dietary treatments consisted of a control diet based on high-quality fish meal (FM diet) and three experimental diets with C. utilis (CU diet), K. marxianus (KM diet) or S. cerevisiae (SC diet) yeast, substituting 40% of the crude protein (CP) from FM. There was no difference in final weight or specific growth rate (SGR) of fish fed the CU diet and the FM diet. The SC diet resulted in lower final weight and SGR, and higher average daily feed intake (ADFI) and feed conversion ratio (FCR) than the FM diet, and higher ADFI and FCR than the KM and CU diets. Fish fed the SC diet had decreased retention of nitrogen and energy, while fish fed the CU diet had increased nitrogen retention compared with those fed the FM diet. In general, feeding the SC diets gave lower digestibility of CP, amino acids, and energy compared with the FM, KM and CU diets, whereas there was no difference in nutrient or amino acid digestibility between the KM and CU diet and the FM diet. Feeding KM and SC gave higher total gut weight and higher distal intestinal weight compared with the FM diet. Plasma cholesterol level was lower for the KM and SC diets while plasma glutathione peroxidase levels were higher for the KM diet compared with the FM diet. In conclusion, feeding moderate levels of S. cerevisiae reduced growth performance and nutrient utilization, while C. utilis and K. marxianus were shown to be promising protein sources in diets for Atlantic salmon, capable of replacing 40% of the protein from high-quality fishmeal without adversely affecting growth performance, digestibility or nutrient retention.", "token_count": 481, "char_count": 1906, "word_count": 316, "semantic_coherence": 1, "information_density": 0.481, "quality_score": 0.7405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:49.879722", "source": { "split": "train_shard_00001", "doc_id": 1535 }, "chunk_id": "train_shard_00001_1535_0", "global_id": 7814 }, { "text": "Evaluation of Candida utilis, Kluyveromyces marxianus and Saccharomyces cerevisiae yeasts as protein sources in diets for Atlantic salmon (Salmo salar)", "token_count": 43, "char_count": 151, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:50.242194", "source": { "split": "train_shard_00001", "doc_id": 1535 }, "chunk_id": "train_shard_00001_1535_1", "global_id": 7815 }, { "text": "Members of the Mesorhizobium genus are soil bacteria that often form nitrogen-fixing symbioses with legumes. Most characterised Mesorhizobium spp. genomes are ~8 Mb in size and harbour extensive pangenomes including large integrative and conjugative elements (ICEs) carrying genes required for symbiosis (ICESyms). Here, we document and compare the conjugative mobilome of 41 complete Mesorhizobium genomes. We delineated 56 ICEs and 24 integrative and mobilizable elements (IMEs) collectively occupying 16 distinct integration sites, along with 24 plasmids. We also demonstrated horizontal transfer of the largest (853,775 bp) documented ICE, the tripartite ICEMspSymAA22. The conjugation systems of all identified ICEs and several plasmids were related to those of the paradigm ICESym ICEMlSymR7A, with each carrying conserved genes for conjugative pilus formation (trb), excision (rdfS), DNA transfer (rlxS) and regulation (fseA). ICESyms have likely evolved from a common ancestor, despite occupying a variety of distinct integration sites and specifying symbiosis with diverse legumes. We found extensive evidence for recombination between ICEs and particularly ICESyms, which all uniquely lack the conjugation entry-exclusion factor gene trbK. Frequent duplication, replacement and pseudogenization of genes for quorum-sensing-mediated activation and antiactivation of ICE transfer suggests ICE transfer regulation is constantly evolving. Pangenome-wide association analysis of the ICE identified genes potentially involved in symbiosis, rhizosphere colonisation and/or adaptation to distinct legume hosts", "token_count": 491, "char_count": 1703, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [ "AA22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:50.895003", "source": { "split": "train_shard_00001", "doc_id": 1536 }, "chunk_id": "train_shard_00001_1536_0", "global_id": 7816 }, { "text": "In summary, the Mesorhizobium genus has accumulated a large and dynamic pangenome that evolves through ongoing horizontal gene transfer of large conjugative elements related to ICEMlSymR7A.\n\nComparative analysis of integrative and conjugative mobile genetic elements in the genus Mesorhizobium.", "token_count": 95, "char_count": 326, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7949, "quality_score": 0.8974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:51.268253", "source": { "split": "train_shard_00001", "doc_id": 1536 }, "chunk_id": "train_shard_00001_1536_1", "global_id": 7817 }, { "text": "Horizontal gene transfer (HGT) is a fundamental process in the evolution of prokaryotes, making major contributions to diversification and adaptation. Typically, HGT is facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages that generally impose fitness costs on their hosts. However, a substantial fraction of bacterial genes is involved in defense mechanisms that limit the propagation of MGEs, raising the possibility that they can actively restrict HGT. Here we examine whether defense systems curb HGT by exploring the connections between HGT rate and the presence of 73 defense systems in 12 bacterial species. We found that only 6 defense systems, 3 of which are different CRISPR-Cas subtypes, are associated with the reduced gene gain rate on the scale of species evolution. The hosts of such defense systems tend to have a smaller pangenome size and harbor fewer phage-related genes compared to genomes lacking these systems, suggesting that these defense mechanisms inhibit HGT by limiting the integration of prophages. We hypothesize that restriction of HGT by defense systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and fitness effect of HGT in bacterial populations.\n\nDefense systems and horizontal gene transfer in bacteria", "token_count": 282, "char_count": 1333, "word_count": 201, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:51.828497", "source": { "split": "train_shard_00001", "doc_id": 1537 }, "chunk_id": "train_shard_00001_1537_0", "global_id": 7818 }, { "text": "The bacterial genus Rhizobium comprises diverse symbiotic nitrogen-fixing species associated with the roots of plants in the Leguminosae family. Multiple genomic clusters defined by whole genome comparisons occur within Rhizobium, but their equivalence to species is controversial. In this study we investigated such genomic clusters to ascertain their significance in a species phylogeny context. Phylogenomic inferences based on complete sets of ribosomal proteins and stringent core genome markers revealed the main lineages of Rhizobium. The clades corresponding to R. etli and R. leguminosarum species show several genomic clusters with average genomic nucleotide identities (ANI > 95%), and a continuum of divergent strains, respectively. They were found to be inversely correlated with the genetic distance estimated from concatenated ribosomal proteins. We uncovered evidence of a Rhizobium pangenome that was greatly expanded, both in its chromosomes and plasmids. Despite the variability of extra-chromosomal elements, our genomic comparisons revealed only a few chromid and plasmid families. The presence/absence profile of genes in the complete Rhizobium genomes agreed with the phylogenomic pattern of species divergence. Symbiotic genes were distributed according to the principal phylogenomic Rhizobium clades but did not resolve genome clusters within the clades. We distinguished some types of symbiotic plasmids within Rhizobium that displayed different rates of synonymous nucleotide substitutions in comparison to chromosomal genes. Symbiotic plasmids may have been repeatedly transferred horizontally between strains and species, in the process displacing and substituting pre-existing symbiotic plasmids. In summary, the results indicate that Rhizobium genomic clusters, as defined by whole genomic identities, might be part of a continuous process of evolutionary divergence that includes the core and the extrachromosomal elements leading to species formation.", "token_count": 522, "char_count": 2054, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8044, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:52.484768", "source": { "split": "train_shard_00001", "doc_id": 1538 }, "chunk_id": "train_shard_00001_1538_0", "global_id": 7819 }, { "text": "Phylogenomic Rhizobium Species Are Structured by a Continuum of Diversity and Genomic Clusters.", "token_count": 35, "char_count": 102, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:52.846536", "source": { "split": "train_shard_00001", "doc_id": 1538 }, "chunk_id": "train_shard_00001_1538_1", "global_id": 7820 }, { "text": "Biotechnology requires efficient microbial cell factories. The budding yeast Saccharomyces cerevisiae is an important cell factory but for a sustainable use of natural resources more diverse cellular attributes are essential. Here, we benchmarked non-conventional yeasts Kluyveromyces marxianus (KM) and Rhodotorula toruloides (RT) against the extensively characterized strains of S. cerevisiae , CEN.PK and W303. We developed a computational method for the characterization of cell/vacuole volumes and observed an inverse relationship between the maximal growth rate and the median cell volume that was responsive to monovalent cations. We found that the supplementation of certain K + concentrations to CEN.PK cultures containing 1.0 M Na + increased the specific growth rate by four-fold with a parabolic shift in the median cell/vacuole volumes. The impairment of ethanol and acetate utilization in CEN.PK, acetate in W303, at the higher K + /Na + concentrations implied an interference in the metabolic pathways required for their consumption. In RT cultures, the supplementation of K + /Na + induced a trade-off in glucose utilization but alleviated cellular aggregates formation where specified cationic concentrations increased the beta-carotene yield by 60% compared with the reference. Our comparative analysis of cell/vacuole volumes using exponential phase cultures showed that the median volumes decreased the most for KM and the least for RT in response to studied cations. Noteworthy for the implication in aging research using yeasts, the vacuole to cell volume ratio increased with the increase in cell volume for W303 and KM, but not for CEN.PK and RT.

Importance

For designing efficient bioprocesses characterization of microbial cell factories in the relevant culture environment is important. The control of cell volume in response to salt stress is crucial for the productivity of microbial cell factories. We developed an open source computational method for the analysis of optical microscopy images that allowed us to quantify changes in cell/vacuole volumes in response to common salts in yeasts", "token_count": 507, "char_count": 2130, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5446, "quality_score": 0.7723, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:53.483768", "source": { "split": "train_shard_00001", "doc_id": 1539 }, "chunk_id": "train_shard_00001_1539_0", "global_id": 7821 }, { "text": "Our study provides a framework for appreciating the role of cellular/organellar volumes in response to changing physiological environment. Our analysis showed that K + /Na + interactions could be used for improving the cellular fitness of CEN.PK and increasing the productivity of beta-carotene in R. toruloides , which is a commercially important antioxidant and a valuable additive in foods.\n\nCharacterization of potassium, sodium and their interactions effects in yeasts", "token_count": 107, "char_count": 473, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7681, "quality_score": 0.8841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:53.873274", "source": { "split": "train_shard_00001", "doc_id": 1539 }, "chunk_id": "train_shard_00001_1539_1", "global_id": 7822 }, { "text": "

Background

Phylogenetic analyses of the bacterial genomes based on the simple classification in core- genes and accessory genes pools could offer an incomplete view of the evolutionary processes, of which some are still unresolved. A combined strategy based on stratified phylogeny and ancient molecular polymorphisms is proposed to infer detailed evolutionary reconstructions by using a large number of whole genomes. This strategy, based on the highest number of genomes available in public databases, was evaluated for improving knowledge of the ancient diversification of E. coli. This staggered evolutionary scenario was also used to investigate whether the diversification of the ancient E. coli lineages could be associated with particular lifestyles and adaptive strategies.

Results

Phylogenetic reconstructions, exploiting 6220 available genomes in Genbank, established the E. coli core genome in 1023 genes, representing about 20% of the complete genome. The combined strategy using stratified phylogeny plus molecular polymorphisms inferred three ancient lineages (D, EB1A and FGB2). Lineage D was the closest to E. coli root. A staggered diversification could also be proposed in EB1A and FGB2 lineages and the phylogroups into these lineages. Several molecular markers suggest that each lineage had different adaptive trajectories. The analysis of gained and lost genes in the main lineages showed that functions of carbohydrates utilization (uptake of and metabolism) were gained principally in EB1A lineage, whereas loss of environmental-adaptive functions in FGB2 lineage were observed, but this lineage showed higher accumulated mutations and ancient recombination events. The population structure of E. coli was re-evaluated including up to 7561 new sequenced genomes, showing a more complex population structure of E. coli, as a new phylogroup, phylogroup I, was proposed.

Conclusions

A staggered reconstruction of E. coli phylogeny is proposed, indicating evolution from three ancestral lineages to reach all main known phylogroups. New phylogroups were confirmed, suggesting an increasingly complex population structure of E. coli", "token_count": 517, "char_count": 2173, "word_count": 302, "semantic_coherence": 1, "information_density": 0.5563, "quality_score": 0.7781, "entities": { "genes": [ "FGB2", "EB1A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:54.508255", "source": { "split": "train_shard_00001", "doc_id": 1540 }, "chunk_id": "train_shard_00001_1540_0", "global_id": 7823 }, { "text": "However these new phylogroups represent < 1% of the global E. coli population. A few key evolutionary forces have driven the diversification of the two main E. coli lineages, metabolic flexibility in one of them and colonization-virulence in the other.\n\nStratified reconstruction of ancestral Escherichia coli diversification.", "token_count": 83, "char_count": 326, "word_count": 47, "semantic_coherence": 1, "information_density": 0.7872, "quality_score": 0.8936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:54.910594", "source": { "split": "train_shard_00001", "doc_id": 1540 }, "chunk_id": "train_shard_00001_1540_1", "global_id": 7824 }, { "text": "Helcococcus ovis ( H. ovis ) is an opportunistic bacterial pathogen of a wide range of animal hosts including domestic ruminants, swine, avians, and humans. In this study, we sequenced the genomes of 35 Helcococcus sp. clinical isolates from the uterus of dairy cows and explored their antimicrobial resistance and biochemical phenotypes. Phylogenetic and average nucleotide identity analyses placed four Helcococcus isolates within a cryptic clade-representing an undescribed species, for which we propose the name Helcococcus bovis sp. nov. We applied whole genome comparative analyses to explore the pangenome, resistome, virulome, and taxonomic diversity of the remaining 31 H. ovis isolates . H. ovis was more often isolated from cows with metritis, however, there was no associations between H. ovis gene clusters and uterine infection. The phylogenetic distribution of high-virulence determinants of H. ovis is consistent with convergent gene loss in the species. The majority of H. ovis strains (30/31) contain mobile tetracycline resistance genes, leading to higher minimum inhibitory concentrations of tetracyclines in vitro. In summary, this study showed that the presence of H. ovis is associated with uterine infection in dairy cows, that mobile genetic element-mediated tetracycline resistance is widespread in H. ovis , and that there is evidence of co-occurring virulence factors across clades suggesting convergent gene loss in the species. Finally, we introduced a novel Helcococcus species closely related to H. ovis , called H. bovis sp. nov.

Highlights

The presence of Helcococcus ovis is associated with uterine infection in dairy cows Mobile genetic element-mediated tetracycline resistance is widespread in H. ovis Co-occurring virulence factors across clades suggest convergent gene loss in the species Helcococcus bovis is a novel species closely related to Helcococcus ovis", "token_count": 500, "char_count": 1909, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5018, "quality_score": 0.7509, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:55.585722", "source": { "split": "train_shard_00001", "doc_id": 1541 }, "chunk_id": "train_shard_00001_1541_0", "global_id": 7825 }, { "text": "Pangenomic analysis ofHelcococcus ovisreveals widespread tetracycline resistance and a novel bacterial species,Helcococcus bovis", "token_count": 49, "char_count": 142, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:55.952700", "source": { "split": "train_shard_00001", "doc_id": 1541 }, "chunk_id": "train_shard_00001_1541_1", "global_id": 7826 }, { "text": "Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na+/H+ antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes", "token_count": 505, "char_count": 1776, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6638, "quality_score": 0.8319, "entities": { "genes": [ "SG8" ], "proteins": [], "pathways": [ "glycolysis", "respiration" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:56.653555", "source": { "split": "train_shard_00001", "doc_id": 1542 }, "chunk_id": "train_shard_00001_1542_0", "global_id": 7827 }, { "text": "IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.\n\n(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota.", "token_count": 247, "char_count": 972, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7373, "quality_score": 0.8686, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:57.138659", "source": { "split": "train_shard_00001", "doc_id": 1542 }, "chunk_id": "train_shard_00001_1542_1", "global_id": 7828 }, { "text": "Listeria monocytogenes poses significant public health and food safety risks due to its environmental resilience and pathogenicity. In this study, we utilized whole-genome sequencing to characterize 15 L. monocytogenes strains isolated from Nantong, China (2020-2023), recovered from food and clinical samples. Antimicrobial susceptibility testing revealed that the Nantong isolates exhibited high resistance rates to ciprofloxacin (93.3%) and oxacillin (66.6%). Of particular concern, isolate NTLM03 exhibited the most extensive resistance profile, demonstrating resistance to six antimicrobials, including clindamycin, trimethoprim/sulfamethoxazole, erythromycin, chloramphenicol, ciprofloxacin, and tetracycline. Seven distinct multilocus sequence types were identified, with ST9 being the most prevalent. Virulence analysis revealed premature stop codons in the inlA gene of all ST9 isolates, a marker indicative of reduced virulence. In contrast, ST87 isolates carried the full-length inlA gene and the complete Listeria Pathogenicity Island-4 (LM9005581_70009 to LM9005581_70014), associated with high virulence. Core genome single nucleotide polymorphism (cgSNP) analysis demonstrated close relatedness (SNPs <20) among isolates from the same batch of meat products (NTLM03, NTLM04, NTLM05), suggesting a potential common contamination source. Furthermore, we examined the genetic relatedness of Nantong isolates with domestic and international L. monocytogenes strains. Two characteristic L. monocytogenes plasmids were assembled: the multidrug-resistant (MDR) plasmid pNTLM03 and the cadmium-resistant plasmid pNTLM08", "token_count": 522, "char_count": 1689, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7214, "quality_score": 0.8607, "entities": { "genes": [ "NTLM04", "NTLM03", "ST87", "NTLM05", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:11:57.795827", "source": { "split": "train_shard_00001", "doc_id": 1543 }, "chunk_id": "train_shard_00001_1543_0", "global_id": 7829 }, { "text": "Surprisingly, pNTLM03 shared a highly similar MDR region with Listeria innocua plasmids pLI42 and pLI203 from Chinese food sources. The transfer of antimicrobial resistance genes between Listeria species and other genera through various genetic mechanisms may increase the potential for the evolution of resistant L. monocytogenes strains, thereby increasing the difficulty of clinical treatment.\n\nGenetic Diversity, Antimicrobial Resistance, and Virulence Profiles of <i>Listeria monocytogenes</i> Isolates from Nantong, China (2020-2023).", "token_count": 175, "char_count": 573, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8406, "quality_score": 0.9203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:58.248093", "source": { "split": "train_shard_00001", "doc_id": 1543 }, "chunk_id": "train_shard_00001_1543_1", "global_id": 7830 }, { "text": "Vibriosis caused by Vibrio vulnificus is a major problem in aquatic animals, particularly brown marble groupers (Epinephelus fuscoguttatus). V. vulnificus biotype I has recently been isolated and classified into subgroups SUKU_G1, SUKU_G2, and SUKU_G3 according to the different types of virulence genes. In a previous study, we have shown that biotype I V. vulnificus strains were classified into three subgroups according to the different types of virulence genes, which exhibited different phenotypes in terms of growth rate and virulence. To gain insight into the different genetic features revealed by the potential virulence mechanisms of V. vulnificus in relation to a spectrum of pathogenesis, comparative genomic analyses of three biotype I V. vulnificus strains belonging to different subgroups (SUKU_G1, SUKU_G2, and SUKU_G3) were performed. The V. vulnificus genome is composed of two circular chromosomes with average sizes of 3 Mbp and 1.7 Mbp that are evolutionarily related based on the analysis of orthologous genes. A comparative genome analysis of V. vulnificus revealed 5200 coding sequences, of which 3887 represented the core genome and the remaining 1313 constituted the dispensable genome. The most virulent isolate (SUKU_G1) carries unique enzymes that are important for lipopolysaccharide (LPS) and capsular polysaccharide (CPS) synthesis, as well as flagellar glycosylation, and harbors another type of repeat in toxin (RTX) and bacterial defense mechanisms", "token_count": 454, "char_count": 1540, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6019, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:58.891715", "source": { "split": "train_shard_00001", "doc_id": 1544 }, "chunk_id": "train_shard_00001_1544_0", "global_id": 7831 }, { "text": "The less virulent isolate (SUKU_G2) shares enzymes related to CPS biosynthesis or flagellar glycosylation, while the avirulent isolate (SUKU_G3) and a less virulent isolate (SUKU_G2) share enzymes related to the production of rare sugars. Interestingly, the isolates from the three subgroups containing specific CMP-N-acetylneuraminate-producing enzymes that are correlated with their growth abilities. Collectively, these observations provide an understanding of the molecular mechanisms underlying disease pathogenesis and support the development of strategies for bacterial disease prevention and control.\n\nComparative Genome Analysis of Piscine Vibrio vulnificus: Virulence-Associated Metabolic Pathways.", "token_count": 186, "char_count": 715, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:59.341025", "source": { "split": "train_shard_00001", "doc_id": 1544 }, "chunk_id": "train_shard_00001_1544_1", "global_id": 7832 }, { "text": "Reference genomes provide mapping targets and coordinate systems but introduce biases when samples under study diverge sufficiently from them. Pangenome references seek to address this by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers can be used to construct pangenome graphs, but thanks to advances in long-read sequencing, high-quality phased assemblies are becoming widely available. Constructing a pangenome graph directly from assemblies, as opposed to variant calls, leverages the graph’s ability to consistently represent variation at different scales and reduces biases introduced by reference-based variant calls. Pangenome construction in this way is equivalent to multiple genome alignment. Here we present the Minigraph-Cactus pangenome pipeline, a method to create pangenomes directly from whole-genome alignments, and demonstrate its ability to scale to 90 human haplotypes from the Human Pangenome Reference Consortium (HPRC). This tool was designed to build graphs containing all forms of genetic variation while still being practical for use with current mapping and genotyping tools. We show that this graph is useful both for studying variation within the input haplotypes, but also as a basis for achieving state of the art performance in short and long read mapping, small variant calling and structural variant genotyping. We further measure the effect of the quality and completeness of reference genomes used for analysis within the pangenomes, and show that using the CHM13 reference from the Telomere-to-Telomere Consortium improves the accuracy of our methods, even after projecting back to GRCh38. We also demonstrate that our method can apply to nonhuman data by showing improved mapping and variant detection sensitivity with a Drosophila melanogaster pangenome.\n\nPangenome Graph Construction from Genome Alignment with Minigraph-Cactus", "token_count": 417, "char_count": 1960, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6228, "quality_score": 0.8114, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:11:59.979948", "source": { "split": "train_shard_00001", "doc_id": 1545 }, "chunk_id": "train_shard_00001_1545_0", "global_id": 7833 }, { "text": "Karnal bunt of wheat, caused by the fungus Tilletia indica, is a major quarantine disease that not only affects global wheat trade but also leads to yield loss and reduced grain quality. With global climate change, the disease has spread to new areas across continents, increasing vulnerabilities and creating a worrisome scenario, as once established, it is extremely difficult to eradicate. Host resistance remains the most effective strategy to combat Karnal bunt. However, only a few resistant sources have been identified so far and are being deployed in breeding programs. Various omics approaches including genomics, transcriptomics, proteomics and metabolomics have gained considerable attention for their role in enhancing disease resistance and improving agronomic yield in wheat. Notably, the integration of multiple omics and epiomics strategies has led to substantial advancements in identifying candidate genes, analyzing pathways, and understanding key elements of stress responses, thereby improving yields. Renowned for its data-mining capabilities, Machine Learning offers an opportunity to enhance the precision of current trait association methods. Nonetheless, its application in predicting disease resistance is still not widespread. In this review, we explore various omics technologies and platforms employed in wheat research to deepen the understanding of the molecular mechanisms involved in host-pathogen interactions, thereby advancing resistance to Karnal bunt of wheat. Furthermore, we emphasize the potential of Machine Learning as a significant tool for pinpointing genetic loci that contribute to host resistance.\n\nHarnessing multi-omics approaches to combat Karnal bunt of wheat: a review of advances and future prospects.", "token_count": 353, "char_count": 1764, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:00.557066", "source": { "split": "train_shard_00001", "doc_id": 1546 }, "chunk_id": "train_shard_00001_1546_0", "global_id": 7834 }, { "text": "Four genes encoding alcohol dehydrogenase (Adh) isozymes in the thermotolerant yeast Kluyveromyces marxianus, a potent candidate for ethanol production at high temperatures, were investigated. Of these, KmADH3 and KmADH4 were cloned and sequenced, and their deduced amino acid sequences were compared with those of KmAdh1 and KmAdh2 and other Adhs of Kluyveromyces lactis and Saccharomyces cerevisiae. The four KmAdhs had high sequence similarity, though KmAdh3 and KmAdh4 possessed an amino-terminal extension as a mitochondrial targeting sequence, and appear to belong to the zinc-containing Adh family. These results and the results of Southern blot experiments suggest that there are at least four Adh isozymes in K. marxianus, two cytoplasmic enzymes and two mitochondrial enzymes. The expression profile revealed that KmADH genes are differently expressed depending on growth phase and carbon source, suggesting that these highly homologous Adhs play distinctive roles in cells.\n\nComparison of the gene expression patterns of alcohol dehydrogenase isozymes in the thermotolerant yeast Kluyveromyces marxianus and their physiological functions.", "token_count": 305, "char_count": 1149, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:01.121857", "source": { "split": "train_shard_00001", "doc_id": 1547 }, "chunk_id": "train_shard_00001_1547_0", "global_id": 7835 }, { "text": "We conducted a global-scale study to identify H. pylori antimicrobial-resistant genes (ARG), address their global distribution, and understand their effect on the antimicrobial resistance (AMR) phenotypes of the clinical isolates. We identified ARG using several well-known tools against extensive bacterial ARG databases, then analyzed their correlation with clinical antibiogram data from dozens of patients across countries. This revealed that combining multiple tools and databases, followed by manual selection of ARG from the annotation results, produces more conclusive results than using a single tool or database alone. After curation, the results showed that H. pylori has 42 ARG against 11 different antibiotic classes (16 genes related to single antibiotic class resistance and 26 genes related to multidrug resistance). Further analysis revealed that H. pylori naturally harbors ARG in the core genome, called the 'Set of ARG commonly found in the Core Genome of H. pylori (ARG-CORE)', while ARG-ACC-the ARG in the accessory genome-are exclusive to particular strains. In addition, we detected 29 genes of potential efflux pump-related AMR that were mostly categorized as ARG-CORE. The ARG distribution appears to be almost similar either by geographical or H. pylori populations perspective; however, some ARG had a unique distribution since they tend to be found only in a particular region or population. Finally, we demonstrated that the presence of ARG may not directly correlate with the sensitive/resistance phenotype of clinical patient isolates but may influence the minimum inhibitory concentration phenotype.\n\nGlobal Antimicrobial Resistance Gene Study of Helicobacter pylori: Comparison of Detection Tools, ARG and Efflux Pump Gene Analysis, Worldwide Epidemiological Distribution, and Information Related to the Antimicrobial-Resistant Phenotype.", "token_count": 463, "char_count": 1914, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6189, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:01.762772", "source": { "split": "train_shard_00001", "doc_id": 1548 }, "chunk_id": "train_shard_00001_1548_0", "global_id": 7836 }, { "text": "

Background

Single amplified genomes (SAGs) and metagenome-assembled genomes (MAGs) are the predominant sources of information about the coding potential of uncultured microbial lineages, but their strengths and limitations remain poorly understood. Here, we performed a direct comparison of two previously published collections of thousands of SAGs and MAGs obtained from the same, global environment.

Results

We found that SAGs were less prone to chimerism and more accurately reflected the relative abundance and the pangenome content of microbial lineages inhabiting the epipelagic of the tropical and subtropical ocean, as compared to MAGs. SAGs were also better suited to link genome information with taxa discovered through 16S rRNA amplicon analyses. Meanwhile, MAGs had the advantage of more readily recovering genomes of rare lineages.

Conclusions

Our analyses revealed the relative strengths and weaknesses of the two most commonly used genome recovery approaches in environmental microbiology. These considerations, as well as the need for better tools for genome quality assessment, should be taken into account when designing studies and interpreting data that involve SAGs or MAGs. Video Abstract.\n\nGenomic representativeness and chimerism in large collections of SAGs and MAGs of marine prokaryoplankton.", "token_count": 319, "char_count": 1341, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6831, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:02.338310", "source": { "split": "train_shard_00001", "doc_id": 1549 }, "chunk_id": "train_shard_00001_1549_0", "global_id": 7837 }, { "text": "Porphyromonas gingivalis is an oral human pathogen associated with the onset and progression of periodontitis, a chronic immune-inflammatory disease characterized by the destruction of the teeth-supporting tissue. P. gingivalis belongs to the genus Porphyromonas, which is characterized by being composed of Gram-negative, asaccharolytic, non-spore-forming, non-motile, obligatory anaerobic species, inhabiting niches such as the oral cavity, urogenital tract, gastrointestinal tract and infected wound from different mammals including humans. Among the Porphyromonas genus, P. gingivalis stands out for its specificity in colonizing the human oral cavity and its keystone pathogen role in periodontitis pathogenesis. To understand the evolutionary process behind P. gingivalis in the context of the Pophyoromonas genus, in this study, we performed a comparative genomics study with publicly available Porphyromonas genomes, focused on four main objectives: (A) to confirm the phylogenetic position of P. gingivalis in the Porphyromonas genus by phylogenomic analysis; (B) the definition and comparison of the pangenomes of P. gingivalis and its relative P. gulae; and (C) the evaluation of the gene family gain/loss events during the divergence of P. gingivalis and P. gulae; (D) the evaluation of the evolutionary pressure (represented by the calculation of Tajima-D values and dN/dS ratios) comparing gene families of P. gingivalis and P. gulae. Our analysis found 84 high-quality assemblies representing P. gingivalis and 14 P", "token_count": 503, "char_count": 1652, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:02.996539", "source": { "split": "train_shard_00001", "doc_id": 1550 }, "chunk_id": "train_shard_00001_1550_0", "global_id": 7838 }, { "text": "gulae strains (from a total of 233 Porphyromonas genomes). Phylogenomic analysis confirmed that P. gingivalis and P. gulae are highly related lineages, close to P. loveana. Both organisms harbored open pangenomes, with a strong core-to-accessory ratio for housekeeping genes and a negative ratio for unknown function genes. Our analyses also characterized the gene set differentiating P. gulae from P. gingivalis, mainly associated with unknown functions. Relevant virulence factors, such as the FimA, Mfa1, and the hemagglutinins, are conserved in P. gulae, P. gingivalis, and P. loveana, suggesting that the origin of those factors occurred previous to the P. gulae - P. gingivalis divergence. These results suggest an unexpected evolutionary relationship between the P. gulae - P. gingivalis duo and P. loveana, showing more clues about the origin of the role of those organisms in periodontitis.\n\nPhylogenomic analysis of the Porphyromonas gingivalis - Porphyromonas gulae duo: approaches to the origin of periodontitis.", "token_count": 358, "char_count": 1119, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6291, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:03.571036", "source": { "split": "train_shard_00001", "doc_id": 1550 }, "chunk_id": "train_shard_00001_1550_1", "global_id": 7839 }, { "text": "Clostridium difficile is toxin-producing antimicrobial resistant (AMR) enteropathogen historically associated with diarrhea and pseudomembranous colitis in hospitalized patients. In recent years, there have been dramatic increases in the incidence and severity of C. difficile infection (CDI), and associated morbidity and mortality, in both healthcare and community settings. C. difficile is an ancient and diverse species that displays a sympatric lifestyle, establishing itself in a range of ecological niches external to the healthcare system. These sources/reservoirs include food, water, soil, and over a dozen animal species, in particular, livestock such as pigs and cattle. In a manner analogous to human infection, excessive antimicrobial exposure, particularly to cephalosporins, is driving the expansion of C. difficile in livestock populations worldwide. Subsequent spore contamination of meat, vegetables grown in soil containing animal feces, agricultural by-products such as compost and manure, and the environment in general (households, lawns, and public spaces) is contributing to a persistent community source/reservoir of C. difficile and the insidious rise of CDI in the community. The whole-genome sequencing era continues to redefine our view of this complex pathogen. The application of high-resolution microbial genomics in a One Health framework (encompassing clinical, veterinary, and environment derived datasets) is the optimal paradigm for advancing our understanding of CDI in humans and animals. This approach has begun to yield critical insights into the genetic diversity, evolution, AMR, and zoonotic potential of C. difficile. In Europe, North America, and Australia, microevolutionary analysis of the C. difficile core genome shows strains common to humans and animals (livestock or companion animals) do not form distinct populations but share a recent evolutionary history. Moreover, for C", "token_count": 482, "char_count": 1981, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:04.574413", "source": { "split": "train_shard_00001", "doc_id": 1551 }, "chunk_id": "train_shard_00001_1551_0", "global_id": 7840 }, { "text": "difficile sequence type 11 and PCR ribotypes 078 and 014, major lineages of One Health importance, this approach has substantiated inter-species clonal transmission between animals and humans. These findings indicate either a zoonosis or anthroponosis. Moreover, they challenge the existing paradigm and the long-held misconception that CDI is primarily a healthcare-associated infection. In this article, evolutionary, and zoonotic aspects of CDI are discussed, including the anthropomorphic factors that contribute to the spread of C. difficile from the farm to the community.\n\nGenomic Delineation of Zoonotic Origins of Clostridium difficile.", "token_count": 171, "char_count": 663, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7753, "quality_score": 0.8876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:05.016484", "source": { "split": "train_shard_00001", "doc_id": 1551 }, "chunk_id": "train_shard_00001_1551_1", "global_id": 7841 }, { "text": "Abstract

The pangenome of Pediococcus sp. was constructed with five bacterial strains isolated from oat silage produced by smallholder farmers from a region in the highlands of the Colombian Andes. The goal of this work was to use genome mining to elucidate some potential mechanisms of action associated with plant growth promotion and biocontrol in lactic acid bacteria (LAB). Multiple genes were uncovered, including those associated with antibiosis and antimicrobial compound production, genes that induce plant defense and phytohormone activation. Additionally, genome sequencing suggested mechanisms for LAB to protect against abiotic and biotic stress. Furthermore, genes that may improve phosphorus availability and those that might stimulate root growth were present. We then tested some of these findings in vitro. For instance, the biocontrol activity of these strains was evaluated against the fungal pathogens Fusarium oxsyporum f. sp. cubense (Foc R1 and Foc TR4) and the bacterial pathogen Ralstonia solanacearum (Rs). All tested strains showed the ability to significantly inhibit pathogen growth in vitro. The capability of LAB to grow at high concentrations of fusaric acid was demonstrated, suggesting that LAB might have detoxification mechanisms to compete with other microorganisms. Also, the ability of LAB to solubilize phosphate and produce IAA was demonstrated. These two properties might be involved in the plant-growth promotion. Here we show that genomic sequencing can be an efficient tool to identify putative biocontrol or plant-growth promoting related sequences for genome mining.

\n\nGenome mining to elucidate antimicrobial and plant growth promoting potentials in Lactic acid bacteria", "token_count": 404, "char_count": 1741, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6064, "quality_score": 0.8032, "entities": { "genes": [ "TR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:05.636124", "source": { "split": "train_shard_00001", "doc_id": 1552 }, "chunk_id": "train_shard_00001_1552_0", "global_id": 7842 }, { "text": "Macrorhabdus ornithogaster (MO) is an infectious fungus that causes gastric damage in birds. In this study, we established nested and seminested polymerase chain reaction (PCR) methods that specifically amplify the domain D1/D2 region (D1/D2) of 26S ribosomal DNA (rDNA), internal transcribed spacer (ITS) of rDNA, and intergenic spacer (IGS) 1 region from avian feces. Phylogenetic analysis of MO collected from Japanese pet birds showed little genetic variation; analysis based on these regions did not distinguish between host species order, differences in MO shape, or host gastrointestinal symptoms. These regions were found to be unsuitable for molecular epidemiological studies of MO and further investigation into other genetic regions is required.\n\nValidation of the usefulness of 26S rDNA D1/D2, internal transcribed spacer, and intergenic spacer 1 for molecular epidemiological analysis of Macrorhabdus ornithogaster.", "token_count": 241, "char_count": 928, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7252, "quality_score": 0.8626, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:06.118401", "source": { "split": "train_shard_00001", "doc_id": 1553 }, "chunk_id": "train_shard_00001_1553_0", "global_id": 7843 }, { "text": "This study was carried out to characterize and recover residual soluble proteins after cultivation of mono- (Kluyveromyces marxianus) and mixed culture (K. marxianus and Saccharomyces cerevisiae) on whey, to serve as food-grade single-cell protein (SCP). Batch fermentation was carried out at 35°C and pH 5.5 for mono-culture and 30°C and pH 6.5 for mixed culture. The yeasts biomass was separated from the fermented broth by centrifugation leaving residual soluble proteins in the fermented whey supernatant (FWS). The yeasts biomass was treated in two-step with a novel combination of chemicals (N-lauroyl sarcosine and NH4OH), which reduced the nucleic acid content in the biomass to the desired level (below 2%w/w) for food-grade SCP. The characteristics of the proteins were evaluated by electrophoresis. During fermentation, a fraction of the whey proteins was consumed. The electrophoresis results revealed that the fermented proteins were different from the native whey proteins and that they were partially hydrolyzed. The ultrafiltration operational parameters were optimized (in series) using 10kDa and 1kDa membranes. A permeate flux of 413LMH and transmembrane pressure-TMP of 80kPa resulted in the highest recovery with the 10kDa membrane followed by a permeate flux of 2760LMH and a TMP of 210kPa were determined for the 1kDa membrane. Recovery of the total proteins under these optimized conditions was 84% and 92% from mono- and mixed culture FWS, respectively.\n\nFood-grade single-cell protein production, characterization and ultrafiltration recovery of residual fermented whey proteins from whey", "token_count": 464, "char_count": 1614, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5508, "quality_score": 0.7754, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:06.756277", "source": { "split": "train_shard_00001", "doc_id": 1554 }, "chunk_id": "train_shard_00001_1554_0", "global_id": 7844 }, { "text": "

ABSTRACT

Genome mining is revolutionizing natural products discovery efforts. The rapid increase in available genomes demands comprehensive computational platforms to effectively extract biosynthetic knowledge encoded across bacterial pangenomes. Here, we present BGCFlow, a novel systematic workflow integrating analytics for large-scale genome mining of bacterial pangenomes. BGCFlow incorporates several genome analytics and mining tools grouped into five common stages of analysis such as; i) data selection, ii) functional annotation, iii) phylogenetic analysis, iv) genome mining, and v) comparative analysis. Furthermore, BGCFlow provides easy configuration of different projects, parallel distribution, scheduled job monitoring, an interactive database to visualize tables, exploratory Jupyter notebooks, and customized reports. Here, we demonstrate the application of BGCFlow by investigating the phylogenetic distribution of various biosynthetic gene clusters detected across 42 genomes of the Saccharopolyspora genus, known to produce industrially important secondary/specialized metabolites. The BGCFlow-guided analysis predicted more accurate dereplication of BGCs and guided the targeted comparative analysis of selected RiPPs. The scalable, interoperable, adaptable, re-entrant, and reproducible nature of the BGCFlow will provide an effective novel way to extract the biosynthetic knowledge in the ever-growing genomic datasets of biotechnologically relevant bacterial species. BGCFlow is available for downloading at https://github.com/NBChub/bgcflow .\n\nBGCFlow: Systematic pangenome workflow for the analysis of biosynthetic gene clusters across large genomic datasets", "token_count": 386, "char_count": 1695, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:07.390368", "source": { "split": "train_shard_00001", "doc_id": 1555 }, "chunk_id": "train_shard_00001_1555_0", "global_id": 7845 }, { "text": "Chinese indicine cattle harbor a much higher genetic diversity compared with other domestic cattle, but their genome architecture remains uninvestigated. Using PacBio HiFi sequencing data from 10 Chinese indicine cattle across southern China, we assembled 20 high-quality partially phased genomes and integrated them into a multiassembly graph containing 148.5 Mb (5.6%) of novel sequence. We identified 156,009 high-confidence nonredundant structural variants (SVs) and 206 SV hotspots spanning ∼195 Mb of gene-rich sequence. We detected 34,249 archaic introgressed fragments in Chinese indicine cattle covering 1.93 Gb (73.3%) of the genome. We inferred an average of 3.8%, 3.2%, 1.4%, and 0.5% of introgressed sequence originating, respectively, from banteng-like, kouprey-like, gayal-like, and gaur-like Bos species, as well as 0.6% of unknown origin. Introgression from multiple donors might have contributed to the genetic diversity of Chinese indicine cattle. Altogether, this study highlights the contribution of interspecies introgression to the genomic architecture of an important livestock population and shows how exotic genomic elements can contribute to the genetic variation available for selection.\n\nA Chinese indicine pangenome reveals a wealth of novel structural variants introgressed from other Bos species.", "token_count": 359, "char_count": 1342, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:07.979582", "source": { "split": "train_shard_00001", "doc_id": 1556 }, "chunk_id": "train_shard_00001_1556_0", "global_id": 7846 }, { "text": "Genome reduction and associated metabolic deficiencies have been described in various lineages of parasitic and symbiotic microorganisms that obtain essential nutrients from their partners, and in some free-living microorganisms that inhabit stable environments. The animal gut is a relatively stable ecosystem, characterized by an abundance of organic substances and a high concentration of microorganisms, which provides favorable conditions for the survival of microorganisms with reduced genomes. Metagenomic analysis of 49 samples of feces of farm animals (cows, sheep, yaks, and horses) revealed uncultured lineages of bacteria with reduced genomes (<1 Mbp): family UBA1242 (Christensenellales, Firmicutes), order Rs-D84 (Alphaproteobacteria), and family UBA9783 (Opitutales, Verrucomicrobiota), defined in genome-taxonomy database. Analysis of the genomes showed that these bacteria lacked pathways for the biosynthesis of amino acids, nucleotides, lipids, and many other essential metabolites. The UBA9783 genomes encoded a near-complete Embden-Meyerhof glycolytic pathway and the non-oxidative phase of the pentose phosphate pathway, while in UBA1242 and Rs-D84, these pathways are incomplete. All bacteria are limited to fermentative metabolism and lack aerobic and anaerobic respiratory pathways. All UBA9783 and some Rs-D84 genomes encoded F0F1-type ATP synthase and pyrophosphate-energized proton pump; they also can import and utilize peptides and some amino acids", "token_count": 438, "char_count": 1535, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6735, "quality_score": 0.8367, "entities": { "genes": [ "UBA9783", "UBA1242" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:08.664113", "source": { "split": "train_shard_00001", "doc_id": 1557 }, "chunk_id": "train_shard_00001_1557_0", "global_id": 7847 }, { "text": "While UBA9783 bacteria could thrive as specialized free-living organisms in the organic-rich gut environment, the UBA1242 and Rs-D84 lineages appear to have adopted the lifestyle of an obligate symbiont/parasite, obtaining metabolites from other cells.IMPORTANCEThe microbiota of the animal gastrointestinal tracts is a complex community of microorganisms which interact in a synergistic or antagonistic relationship and play key nutritional and metabolic roles. However, despite its importance, the gut microbiota of farm animals, especially its uncultured majority, remains largely unexplored. We performed a metagenomic analysis of the gut microbiome of farm animals and characterized three uncultured lineages of bacteria with reduced genomes (<1 Mbp) from the phyla Firmicutes, Proteobacteria, and Verrucomicrobiota. These bacteria were predicted to possess key metabolic deficiencies such as the inability to synthesize essential cell metabolites, suggesting their adaptation to the lifestyle of a symbiont/parasite, or a scavenger obtaining nutrients from the organic-rich gut environment. This study shows that genome reduction with metabolic specialization and adaptation to a partner-dependent lifestyle occurred through convergent evolution in several phylogenetically distant lineages of gut microbiota.\n\nNovel lineages of bacteria with reduced genomes from the gut of farm animals.", "token_count": 345, "char_count": 1415, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6237, "quality_score": 0.8118, "entities": { "genes": [ "UBA9783", "UBA1242" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:09.230543", "source": { "split": "train_shard_00001", "doc_id": 1557 }, "chunk_id": "train_shard_00001_1557_1", "global_id": 7848 }, { "text": "Structural variation is known to play an important and often overlooked role in regulating disease and traits, but accurately detecting structural variants from sequencing data has traditionally been difficult. However, recent improvements in high-quality genome assembly along with methodological advancements in pangenome creation have opened up the landscape for methods that use such pangenomes for structural variant calling and genotyping. We here present KAGE2, which accurately and efficiently genotypes structural variation by exploiting the availability of pangenomes that represent known variation in a population. Through comprehensive benchmarking, we highlight limitations of existing methodology and show that KAGE2 is more accurate and considerably faster than existing methods.\n\nKAGE 2: Fast and accurate genotyping of structural variation using pangenomes", "token_count": 166, "char_count": 873, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [ "KAGE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:09.674885", "source": { "split": "train_shard_00001", "doc_id": 1558 }, "chunk_id": "train_shard_00001_1558_0", "global_id": 7849 }, { "text": "During the mezcal fermentation process, yeasts are affected by several stresses that can affect their fermentation capability. These stresses, such as thermal shock, ethanol, osmotic and growth inhibitors are common during fermentation. Cells have improved metabolic systems and they express stress response genes in order to decrease the damage caused during the stress, but to the best of our knowledge, there are no published works exploring the effect of oxidants and prooxidants, such as H2O2 and menadione, during growth. In this article, we describe the behavior of Kluyveromyces marxianus isolated from spontaneous mezcal fermentation during oxidative stress, and compared it with that of Saccharomyces cerevisiae strains that were also obtained from mezcal, using the W303-1A strain as a reference. S. cerevisiae strains showed greater viability after oxidative stress compared with K. marxianus strains. However, when the yeast strains were grown in the presence of oxidants in the media, K. marxianus exhibited a greater ability to grow in menadione than it did in H2O2. Moreover, when K. marxianus SLP1 was grown in a minibioreactor, its behavior when exposed to menadione was different from its behavior with H2O2. The yeast maintained the ability to consume dissolved oxygen during the 4 h subsequent to the addition of menadione, and then stopped respiration. When exposed to H2O2, the yeast stopped consuming oxygen for the following 8 h, but began to consume oxygen when stressors were no longer applied. In conclusion, yeast isolated from spontaneous mezcal fermentation was able to resist oxidative stress for a long period of time.\n\nRespiratory capacity of the Kluyveromyces marxianus yeast isolated from the mezcal process during oxidative stress.", "token_count": 436, "char_count": 1768, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5428, "quality_score": 0.7714, "entities": { "genes": [ "SLP1" ], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:10.304818", "source": { "split": "train_shard_00001", "doc_id": 1559 }, "chunk_id": "train_shard_00001_1559_0", "global_id": 7850 }, { "text": "Urinary tract infections (UTIs) are one of the most common human bacterial infections. While UTIs are commonly associated with colonization by Escherichia coli, members of this species also have been found within the bladder of individuals with no lower urinary tract symptoms (no LUTS), also known as asymptomatic bacteriuria. Prior studies have found that both uropathogenic E. coli (UPEC) strains and E. coli isolates that are not associated with UTIs encode for virulence factors. Thus, the reason(s) why E. coli sometimes causes UTI-like symptoms remain(s) elusive. In this study, the genomes of 66 E. coli isolates from adult female bladders were sequenced. These isolates were collected from four cohorts, including women: (1) without lower urinary tract symptoms, (2) overactive bladder symptoms, (3) urgency urinary incontinence, and (4) a clinical diagnosis of UTI. Comparative genomic analyses were conducted, including core and accessory genome analyses, virulence and motility gene analyses, and antibiotic resistance prediction and testing. We found that the genomic content of these 66 E. coli isolates does not correspond with the participant's symptom status. We thus looked beyond the E. coli genomes to the composition of the entire urobiome and found that the presence of E. coli alone was not sufficient to distinguish between the urobiomes of individuals with UTI and those with no LUTS. Because E. coli presence, abundance, and genomic content appear to be weak predictors of UTI status, we hypothesize that UTI symptoms associated with detection of E. coli are more likely the result of urobiome composition.\n\nGenomic Survey of E. coli From the Bladders of Women With and Without Lower Urinary Tract Symptoms.", "token_count": 501, "char_count": 1810, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5693, "quality_score": 0.7846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:10.957950", "source": { "split": "train_shard_00001", "doc_id": 1560 }, "chunk_id": "train_shard_00001_1560_0", "global_id": 7851 }, { "text": "

Objective

This study aimed to investigate the identification of blaCARBA-positive multidrug-resistant Mixta calida isolates from human hosts and to elucidate their genomic determinants in a species-wide context.

Methods

Two carbapenemase-producing M. calida isolates were received by the Galway Reference Laboratory Service in Ireland between June and July 2024. One isolate originated from a sputum sample, while the other was recovered from a routine screening rectal swab. Initial identification was performed using MALDI-ToF mass spectrometry, with genomic confirmation via 16S rRNA sequencing, digital DNA-DNA hybridization, and Average Nucleotide Identity analysis. Antimicrobial susceptibility testing was conducted using a MicroScan panel, following EUCAST and CLSI guidelines. Whole-genome sequencing, plasmid replicon typing, and antibiotic-resistance-gene and virulence-factor profiling were employed. Comparative analysis included all additional canonical M. calida genomes from NCBI database.

Results

Both Irish isolates were taxonomically placed as M. calida and exhibited multidrug resistance against penicillins, cephalosporins, monobactams and ertapenem. The acquired genes blaKPC-3, blaOXA-9, and blaTEM-122 were detected on plasmid-borne contigs, indicating horizontal acquisition. Seven plasmid replicon types were shared between the two isolates. Both plasmid replicons and acquired antimicrobial-resistance-genes (ARGs) were seldomly identified across the species. Phylogenetic inference based on core genome analysis identified a monophyletic cluster, suggesting a single introductory event.

Conclusion

This study documents a dual occurrence of blaCARBA-positive M. calida in human colonisation and infection", "token_count": 497, "char_count": 1815, "word_count": 210, "semantic_coherence": 1, "information_density": 0.719, "quality_score": 0.8595, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:11.612057", "source": { "split": "train_shard_00001", "doc_id": 1561 }, "chunk_id": "train_shard_00001_1561_0", "global_id": 7852 }, { "text": "The findings highlight the potential for horizontal-gene-transfer to drive the emergence of multidrug-resistant profiles in the species, underscoring the need for enhanced surveillance, diagnostic precision, and targeted infection control strategies to mitigate public health risks.

Impact statement

This study reports blaESBL and blaCARBA-positive multi-drug resistant Mixta calida isolates from distinct human hosts. Genomic analysis revealed the co-occurrence of plasmid-borne resistance genes blaKPC-3, blaOXA-9, and blaTEM-122. Species-wide phylogenetic analysis grouped the two isolates into a monophyletic cluster, suggesting a single introductory event.\n\nIdentification of bla<sub>ESBL</sub>- and bla<sub>CARBA</sub>- Positive Multi-Drug Resistant Mixta calida Isolates from Distinct Human Hosts.", "token_count": 268, "char_count": 890, "word_count": 94, "semantic_coherence": 1, "information_density": 0.734, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:12.160463", "source": { "split": "train_shard_00001", "doc_id": 1561 }, "chunk_id": "train_shard_00001_1561_1", "global_id": 7853 }, { "text": "Abstract

Background- Kefir is a complex microbial community that plays a critical role in the fermentation and production of bioactive peptides, and has health-improving properties. In this study, we employed shotgun metagenomics and peptidomics approaches to further characterize Brazilian kefir. Results- We successfully assembled the novel genome of Lactobacillus kefiranofaciens (LkefirU) and conducted a comprehensive pangenome analysis to compare it with other strains. Furthermore, we performed a peptidome analysis, revealing the presence of bioactive peptides encrypted by L. kefiranofaciens in the Brazilian kefir sample, and utilized in silicoprospecting and molecular docking techniques to identify potential anti-Alzheimer peptides, targeting β-amyloid (fibril and plaque), BACE, and acetylcholinesterase. Through this analysis, we identified two peptides that show promise as compounds with anti-Alzheimer properties. Conclusions -These findings not only provide insights into the genome of L. kefiranofaciens but also serve as a promising prototype for the development of novel anti-Alzheimer compounds derived from Brazilian kefir.

\n\nUnveiling the Brazilian Kefir Microbiome: Discovery of a novel Lactobacillus kefiranofaciens (LkefirU) genome and in silico prospection of bioactive peptides with potential anti-Alzheimer properties", "token_count": 409, "char_count": 1477, "word_count": 175, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:12.787651", "source": { "split": "train_shard_00001", "doc_id": 1562 }, "chunk_id": "train_shard_00001_1562_0", "global_id": 7854 }, { "text": "Yersinia enterocolitica is a common cause of food-borne gastroenteritis worldwide. Recent work defining the phylogeny of the genus Yersinia subdivided Y. enterocolitica into six distinct phylogroups. Here, we provide detailed analyses of the evolutionary processes leading to the emergence of these phylogroups. The dominant phylogroups isolated from human infections, PG3-5, show very little diversity at the sequence level, but do present marked patterns of gain and loss of functions, including those involved in pathogenicity and metabolism, including the acquisition of phylogroup-specific O-antigen loci. We tracked gene flow across the species in the core and accessory genome, and show that the non-pathogenic PG1 strains act as a reservoir for diversity, frequently acting as donors in recombination events. Analysis of the core and accessory genome also suggested that the different Y. enterocolitica phylogroups may be ecologically separated, in contrast to the long-held belief of common shared ecological niches across the Y. enterocolitica species.\n\nDirectional gene flow and ecological separation in Yersinia enterocolitica.", "token_count": 304, "char_count": 1181, "word_count": 160, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [ "PG1", "PG3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:13.358704", "source": { "split": "train_shard_00001", "doc_id": 1563 }, "chunk_id": "train_shard_00001_1563_0", "global_id": 7855 }, { "text": "DNA damage activates a robust transcriptional stress response, but much less is known about how DNA damage impacts translation. The advent of genome editing with Cas9 has intensified interest in understanding cellular responses to DNA damage. Here, we find that DNA double-strand breaks (DSBs), including those induced by Cas9, trigger the loss of ribosomal protein RPS27A from ribosomes via p53-independent proteasomal degradation. Comparisons of Cas9 and dCas9 ribosome profiling and mRNA-seq experiments reveal a global translational response to DSBs that precedes changes in transcript abundance. Our results demonstrate that even a single DSB can lead to altered translational output and ribosome remodeling, suggesting caution in interpreting cellular phenotypes measured immediately after genome editing.\n\nDouble stranded DNA breaks and genome editing trigger loss of ribosomal protein RPS27A.", "token_count": 210, "char_count": 900, "word_count": 126, "semantic_coherence": 1, "information_density": 0.746, "quality_score": 0.873, "entities": { "genes": [ "RPS27A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:13.827554", "source": { "split": "train_shard_00001", "doc_id": 1564 }, "chunk_id": "train_shard_00001_1564_0", "global_id": 7856 }, { "text": "

Objective

VanD-type vancomycin resistance is rarely reported in Enterococcus faecalis. This study aimed to characterise five VanD-type vancomycin-resistant E. faecalis strains isolated over 8 years from three hospitals in a local city in Japan, with a focus on resistance mechanisms, genetic background, and phylogenetic classification.

Methods

Five E. faecalis strains (SVR2085, SVR2281, SVR2330, SVR2331, and SVR2332) were analysed using antimicrobial susceptibility testing, plasmid profiling, and whole-genome sequencing. Genomic islands (GIs) containing vanD gene clusters were characterised. Core GI gene and core genome phylogenies were compared, and vanD homologues were classified using public database sequences.

Results

All strains exhibited high-level resistance to vancomycin (MIC >1024-64 mg/L), multiple drug resistance, and carried pheromone-responsive plasmids encoding bacteriocin 41 as a colonisation factor. Four strains shared nearly identical GIs (126-185 kbp), while SVR2330 had a structurally distinct GI. Phylogenetic analysis showed that the four similar strains formed a single cluster, suggesting a common ancestor, whereas SVR2330 was divergent. Comparative analysis of 37 vanD homologues revealed high genetic diversity, allowing classification into three subgroups - vanD(I), vanD(II), and vanD(III). The vanD of SVR2330 was assigned as vanD(III)-4, and the others as vanD(II)-6, -11, -15, and -17.

Conclusions

This study proposes a new classification scheme for diverse vanD genes and provides the first evidence of the regional spread and long-term persistence of VanD-type vancomycin-resistant E. faecalis in Japan.", "token_count": 494, "char_count": 1678, "word_count": 215, "semantic_coherence": 1, "information_density": 0.707, "quality_score": 0.8535, "entities": { "genes": [ "SVR2330", "SVR2332", "SVR2281", "SVR2331", "SVR2085" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:14.482802", "source": { "split": "train_shard_00001", "doc_id": 1565 }, "chunk_id": "train_shard_00001_1565_0", "global_id": 7857 }, { "text": "First report of regional spreading and long-term inhabitation of VanD-type vancomycin-resistant Enterococcus faecalis clinical strains: A proposal of new classification of vanD gene subtypes.", "token_count": 46, "char_count": 191, "word_count": 24, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:14.845108", "source": { "split": "train_shard_00001", "doc_id": 1565 }, "chunk_id": "train_shard_00001_1565_1", "global_id": 7858 }, { "text": "

Objectives

Stenotrophomonas maltophilia (Sm) is responsible for infections in immunocompromised and hospitalized patients. Its genomic diversity has led to the description of a large complex including numerous genogroups. Regarding acquired resistances, cefiderocol (CeFiDeroCol, CFDC) is a promising therapeutic option. We aimed to evaluate the CFDC susceptibility of a large panel of Sm strains and explored the genetic support and background of resistance.

Methods

We prospectively collected 154 non-duplicated clinical and environmental strains from five university hospitals between January 2023 and April 2024. All the strains were whole-genome sequenced and their genetic background studied using multi-locus sequence typing , core genome multi-locus sequence typing, and genogroup determination. CFDC susceptibility was tested using a two-step approach with a marketed product (screening step) and the broth microdilution method (confirmation step). Strains exhibiting an MIC >1 mg/L were considered as non-susceptible (ns). We used a national 2013 strain collection to confirm the resistance in a particular genogroup. The genetic support of CFDC non-susceptibility was studied according to a collection of previously selected CFDC mutants.

Results

Six of 154 Sm strains (4%) were non-susceptible to CFDC, including one environmental strain and five clinical strains. None of the patients was exposed to CFDC. The strains belonged to four different sequence type (ST) (ST87, n = 2; ST39, n = 2; ST18, n = 1; and unknown, n = 1) but to the same genogroup (genogroup 4). All seven 2013 genogroup 4 strains were also non-susceptible to CFDC", "token_count": 446, "char_count": 1668, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6186, "quality_score": 0.8093, "entities": { "genes": [ "ST39", "ST18", "ST87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:15.480502", "source": { "split": "train_shard_00001", "doc_id": 1566 }, "chunk_id": "train_shard_00001_1566_0", "global_id": 7859 }, { "text": "None of the previously published mutations/deletions were identified, but common non-synonymous mutations were found in tonB and tolQ; a common polymorphism was identified in the promoter region of smet.

Discussion

The natural intrinsic non-susceptibility of the genogroup 4 could hamper the contribution of CFDC for the empiric treatment of Sm infections.\n\nUnexpected natural cefiderocol resistance in Stenotrophomonas maltophilia associated to the genogroup 4 genetic background.", "token_count": 126, "char_count": 488, "word_count": 63, "semantic_coherence": 1, "information_density": 0.746, "quality_score": 0.873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:15.866328", "source": { "split": "train_shard_00001", "doc_id": 1566 }, "chunk_id": "train_shard_00001_1566_1", "global_id": 7860 }, { "text": "The short arms of the human acrocentric chromosomes 13, 14, 15, 21 and 22 (SAACs) share large homologous regions, including ribosomal DNA repeats and extended segmental duplications1,2. Although the resolution of these regions in the first complete assembly of a human genome-the Telomere-to-Telomere Consortium's CHM13 assembly (T2T-CHM13)-provided a model of their homology3, it remained unclear whether these patterns were ancestral or maintained by ongoing recombination exchange. Here we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologous sequences. Utilizing an all-to-all comparison of the human pangenome from the Human Pangenome Reference Consortium4 (HPRC), we find that contigs from all of the SAACs form a community. A variation graph5 constructed from centromere-spanning acrocentric contigs indicates the presence of regions in which most contigs appear nearly identical between heterologous acrocentric chromosomes in T2T-CHM13. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the pseudo-homologous regions than in the corresponding short and long arms, indicating higher rates of recombination6,7. The pseudo-homologous regions include sequences that have previously been shown to lie at the breakpoint of Robertsonian translocations8, and their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14 and 21. The ubiquity of signals of recombination between heterologous acrocentric chromosomes seen in the HPRC draft pangenome suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed from cytogenetic studies 50 years ago9.\n\nRecombination between heterologous human acrocentric chromosomes.", "token_count": 512, "char_count": 1943, "word_count": 246, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:16.494397", "source": { "split": "train_shard_00001", "doc_id": 1567 }, "chunk_id": "train_shard_00001_1567_0", "global_id": 7861 }, { "text": "

Background

Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains.

Results

The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15 % of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates.

Conclusions

We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.\n\nPangenome-wide and molecular evolution analyses of the Pseudomonas aeruginosa species.", "token_count": 513, "char_count": 2318, "word_count": 315, "semantic_coherence": 1, "information_density": 0.5905, "quality_score": 0.7952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:12:17.137023", "source": { "split": "train_shard_00001", "doc_id": 1568 }, "chunk_id": "train_shard_00001_1568_0", "global_id": 7862 }, { "text": "Platelets play an important role in defense against pathogens; however, the interaction between Escherichia coli and platelets has not been well described and detailed. Our goal was to study the interaction between platelets and selected strains of E. coli in order to evaluate the antibacterial effect of platelets and to assess bacterial effects on platelet activation. Washed platelets and supernatants of pre-activated platelets were incubated with five clinical colistin-resistant and five laboratory colistin-sensitive strains of E. coli in order to study bacterial growth. Platelet activation was measured with flow cytometry by evaluating CD62P expression. To identify the difference in strain behavior toward platelets, a pangenome analysis using Roary and O-antigen serotyping was carried out. Both whole platelets and the supernatant of activated platelets inhibited growth of three laboratory colistin-sensitive strains. In contrast, platelets promoted growth of the other strains. There was a negative correlation between platelet activation and bacterial growth. The Roary results showed no logical clustering to explain the mechanism of platelet resistance. The diversity of the responses might be due to strains of different types of O-antigen. Our results show a bidirectional interaction between platelets and E. coli whose expression is dependent on the bacterial strain involved.\n\nThe Antibacterial Effect of Platelets on Escherichia coli Strains.", "token_count": 357, "char_count": 1502, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5433, "quality_score": 0.7716, "entities": { "genes": [ "CD62P" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:17.719984", "source": { "split": "train_shard_00001", "doc_id": 1569 }, "chunk_id": "train_shard_00001_1569_0", "global_id": 7863 }, { "text": "Tenacibaculum maritimum is a ubiquitous marine bacterium with a remarkable ability to adhere to and form biofilm structures on abiotic and biotic surfaces including the skin and mucus of various marine fish species. Excessive colonisation of the fish epidermal surface is often associated with tenacibaculosis, a life-threatening skin infection that can progress to ulcerative lesions. Tenacibaculosis causes ongoing losses to finfish aquaculture worldwide, including the Atlantic salmon (Salmo salar) industry in Tasmania, Australia, and the King (Chinook) salmon (Oncorhynchus tshawytscha) industry in New Zealand, with no effective vaccine available. In this study we provide an evidence base for vaccine development by linking genomic analysis with antibody-based serotyping. We assembled and curated thirty-six complete genomes and thirty-six contig-level genomes of isolates from Tasmania and New Zealand, as well as three genomes of the overseas strains – Baxa lyl-1 (contig-level), NCIMB 2158 (complete), and NCIMB 2154ᵀ type strain (complete). Core genome phylogenetic analysis indicated a high degree of geographic endemism and largely independent evolution of T. maritimum in Australia and New Zealand. Two main O-antigen gene cluster (O-AGC) types were identified in each location: type 3–2 was predominant in Tasmania, type 3–0 was predominant in New Zealand, while type 2–1 was the second most abundant type in both Tasmania and New Zealand. O-AGC type 3–2 appears to be endemic to Oceania, and one of the distinct phylogenetic lineages harbouring this O-antigen type (clade C1) appears to be endemic to Tasmania. Somewhat surprisingly, O-AGC types were highly conserved within phylogenetic clades and/or sub-clades. In the case of Tasmania, there was a partial concordance between O-AGC typing and antibody-based serotyping", "token_count": 493, "char_count": 1838, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6353, "quality_score": 0.8177, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:18.372752", "source": { "split": "train_shard_00001", "doc_id": 1570 }, "chunk_id": "train_shard_00001_1570_0", "global_id": 7864 }, { "text": "Importantly, variation in serotyping results within O-AGC type 3–2 isolates was clearly linked to phylogenetic clustering. In the case of New Zealand, antibody serotyping did not distinguish between O-AGC types. We hypothesise this may be due to high amount of a colanic acid (CA) capsule or similar exopolysaccharide and its binding to the LPS core. Stress-inducible CA capsule is critical for biofilm formation in other bacterial species, and here we report for the first time the putative CA exopolysaccharide cluster (K-AGC) in T. maritimum which may aid more rigorous typing and vaccine development.\n\nGenomics and serotyping of Tenacibaculum maritimum outbreak isolates from Australia and New Zealand for guided vaccine development and stewardship", "token_count": 194, "char_count": 752, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7411, "quality_score": 0.8705, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:18.816597", "source": { "split": "train_shard_00001", "doc_id": 1570 }, "chunk_id": "train_shard_00001_1570_1", "global_id": 7865 }, { "text": "This study characterizes 81 S. rostri isolates from bovine mastitis (of which 80 were subclinical). The isolates were first identified as S. microti by MALDI-TOF MS, but later whole genome sequencing analysis allowed reclassification as S. rostri. The isolates were derived from 52 cows and nine dairy herds in Denmark. To describe the pathogenicity of S. rostri, we used whole genome sequencing to infer the distribution of genes associated with virulence, antibiotic resistance, and mobile genetic elements. Also, we performed a core-genome phylogeny analysis to study the genetic relatedness among the isolates. All 81 isolates expressed the same virulence profile comprising two putative virulence genes, clpP and clpC. Three isolates carried a resistance gene encoding streptomycin (str) or lincomycin (lnuA) resistance. The distribution of plasmids suggested the detected antibiotic resistance genes to be plasmid-mediated. Phages were abundant among the isolates, and the single isolate from clinical mastitis acquired a phage disparate from the rest, which potentially could be involved with virulence in S. rostri. The core genome phylogeny revealed a strong genetic intra-herd conservation, which indicates the source of introduction being herd-specific and might further imply the ability of S. rostri to adapt to the bovine niche and spread from cow-to-cow in a contagious manner. With this study, we aim to acquaint clinicians and professionals with the existence of S. rostri which might have been overlooked so far.\n\nComparative Genomics of Staphylococcus rostri, an Undescribed Bacterium Isolated from Dairy Mastitis.", "token_count": 474, "char_count": 1717, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6125, "quality_score": 0.8063, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:19.471981", "source": { "split": "train_shard_00001", "doc_id": 1571 }, "chunk_id": "train_shard_00001_1571_0", "global_id": 7866 }, { "text": "The cloning of DNA fragments into vectors or host genomes has traditionally been performed using Escherichia coli with restriction enzymes and DNA ligase or homologous recombination-based reactions. We report here a novel DNA cloning method that does not require DNA end processing or homologous recombination, but that ensures highly accurate cloning. The method exploits the efficient non-homologous end-joining (NHEJ) activity of the yeast Kluyveromyces marxianus and consists of a novel functional marker selection system. First, to demonstrate the applicability of NHEJ to DNA cloning, a C-terminal-truncated non-functional ura3 selection marker and the truncated region were PCR-amplified separately, mixed and directly used for the transformation. URA3(+) transformants appeared on the selection plates, indicating that the two DNA fragments were correctly joined by NHEJ to generate a functional URA3 gene that had inserted into the yeast chromosome. To develop the cloning system, the shortest URA3 C-terminal encoding sequence that could restore the function of a truncated non-functional ura3 was determined by deletion analysis, and was included in the primers to amplify target DNAs for cloning. Transformation with PCR-amplified target DNAs and C-terminal truncated ura3 produced numerous transformant colonies, in which a functional URA3 gene was generated and was integrated into the chromosome with the target DNAs. Several K. marxianus circular plasmids with different selection markers were also developed for NHEJ-based cloning and recombinant DNA construction. The one-step DNA cloning method developed here is a relatively simple and reliable procedure among the DNA cloning systems developed to date.\n\nNon-homologous end joining-mediated functional marker selection for DNA cloning in the yeast Kluyveromyces marxianus.", "token_count": 433, "char_count": 1842, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5483, "quality_score": 0.7741, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:20.130048", "source": { "split": "train_shard_00001", "doc_id": 1572 }, "chunk_id": "train_shard_00001_1572_0", "global_id": 7867 }, { "text": "Intestinal microbiota and the host's immune system form a symbiotic alliance that sustains normal development and function in the human gut. Changes such as dietary habits among societies in developed countries have led to the development of unbalanced microbial populations in the gut, likely contributing to the dramatic increase in inflammatory diseases in the last few decades. Recent advances in DNA sequencing technologies have tremendously helped to characterize the microbiome associated with disease, both in identifying global alterations and discovering specific biomarkers that potentially contribute to disease pathogenesis, as evidenced by animal studies. Beyond bacterial alterations, non-bacterial components such as fungi, viruses, and microbial metabolites have been implicated in these diseases, influencing immune responses and gut homeostasis. Multi-omics approaches integrating metagenomics, metabolomics, and transcriptomics offer a more comprehensive understanding of the microbiome's role in disease pathogenesis, paving the way for innovative diagnostic and therapeutic strategies. Unraveling the metagenomic profiles associated with disease may facilitate earlier diagnosis and intervention, as well as the development of more personalized and effective therapeutic strategies. This review synthesizes recent and relevant microbiome research studies aimed at characterizing the microbial signatures associated with inflammatory bowel disease, colorectal cancer, and celiac disease.\n\nMicrobiome Markers in Gastrointestinal Disorders: Inflammatory Bowel Disease, Colorectal Cancer, and Celiac Disease.", "token_count": 347, "char_count": 1626, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:20.738912", "source": { "split": "train_shard_00001", "doc_id": 1573 }, "chunk_id": "train_shard_00001_1573_0", "global_id": 7868 }, { "text": "Enterohemorrhagic Escherichia coli continues to be a significant public health risk. With the onset of next generation sequencing, whole genome sequences require a new paradigm of analysis relevant for epidemiology and drug discovery. A large-scale bacterial population genomic analysis was applied to 702 isolates of serotypes associated with EHEC resulting in five pangenome clusters. Serotype incongruence with pangenome types suggests recombination clusters. Core genome analysis was performed to determine the population wide distribution of sdiA as potential drug target. Protein modelling revealed nonsynonymous variants are notably absent in the ligand binding site for quorum sensing, indicating that population wide conservation of the sdiA ligand site can be targeted for potential prophylactic purposes. Applying pathotype-wide pangenomics as a guide for determining evolution of pharmacophore sites is a potential approach in drug discovery.\n\nLarge scale enterohemorrhagic E coli population genomic analysis using whole genome typing reveals recombination clusters and potential drug target", "token_count": 238, "char_count": 1103, "word_count": 150, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:21.219261", "source": { "split": "train_shard_00001", "doc_id": 1574 }, "chunk_id": "train_shard_00001_1574_0", "global_id": 7869 }, { "text": "Accurate genotyping of Killer cell Immunoglobulin-like Receptor (KIR) genes plays a pivotal role in enhancing our understanding of innate immune responses, disease correlations, and the advancement of personalized medicine. However, due to the high variability of the KIR region and high level of sequence similarity among different KIR genes, the currently available genotyping methods are unable to accurately infer copy numbers, genotypes and haplotypes of individual KIR genes from next-generation sequencing data. Here we introduce Geny, a new computational tool for precise genotyping of KIR genes. Geny utilizes available KIR haplotype databases and proposes a novel combination of expectation-maximization filtering schemes and integer linear programming-based combinatorial optimization models to resolve ambiguous reads, provide accurate copy number estimation and estimate the haplotype of each copy for the genes within the KIR region. We evaluated Geny on a large set of simulated short-read datasets covering the known validated KIR region assemblies and a set of Illumina short-read samples sequenced from 25 validated samples from the Human Pangenome Reference Consortium collection and showed that it outperforms the existing genotyping tools in terms of accuracy, precision and recall. We envision Geny becoming a valuable resource for understanding immune system response and consequently advancing the field of patient-centric medicine.\n\nGeny: A Genotyping Tool for Allelic Decomposition of Killer Cell Immunoglobulin-Like Receptor Genes", "token_count": 353, "char_count": 1557, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:21.798222", "source": { "split": "train_shard_00001", "doc_id": 1575 }, "chunk_id": "train_shard_00001_1575_0", "global_id": 7870 }, { "text": "A thermotolerant yeast strain named Kluyveromyces marxianus IMB4 was used in a simultaneous saccharification and fermentation (SSF) process using Kanlow switchgrass as a feedstock. Switchgrass was pretreated using hydrothermolysis at 200 degrees C for 10 min. After pretreatment, insoluble solids were separated from the liquid prehydrolyzate by filtration and washed with deionized water to remove soluble sugars and inhibitors. Insoluble solids were then hydrolyzed using a commercial cellulase preparation and the released glucose was fermented to ethanol by K. marxianus IMB4 in an SSF process. SSF temperature was 37, 41, or 45 degrees C and pH was 4.8 or 5.5. SSF was conducted for 7 days. Results were compared with a control of Saccharomyces cerevisiae D(5)A at 37 degrees C and pH 4.8. Fermentation by IMB4 at 45 and 41 degrees C ceased after 3 and 4 days, respectively, when a pH 4.8 citrate buffer was used. Fermentation continued for all 7 days using IMB4 at 37 degrees C and the control. When pH 5.5 citrate buffer was used, fermentation ceased after 96 h using IMB4 at 45 degrees C, and ethanol yield was greater than when pH 4.8 citrate buffer was used (78% theoretical). Ethanol yield using IMB4 at 45 degrees C, pH 5.5 was greater than the control after 48, 72, and 96 h (P < 0.05).\n\nSimultaneous saccharification and fermentation of Kanlow switchgrass pretreated by hydrothermolysis using Kluyveromyces marxianus IMB4.", "token_count": 459, "char_count": 1436, "word_count": 233, "semantic_coherence": 1, "information_density": 0.4936, "quality_score": 0.7468, "entities": { "genes": [ "IMB4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:22.437341", "source": { "split": "train_shard_00001", "doc_id": 1576 }, "chunk_id": "train_shard_00001_1576_0", "global_id": 7871 }, { "text": "The spread of the novel coronavirus (SARS-CoV-2) has triggered a global emergency, that demands urgent solutions for detection and therapy to prevent escalating health, social and economic impacts. The spike protein (S) of this virus enables binding to the human receptor ACE2, and hence presents a prime target for vaccines preventing viral entry into host cells 1 . The S proteins from SARS-CoV-1 and SARS-CoV-2 are similar 2 , but structural differences in the receptor binding domain (RBD) preclude the use of SARS-CoV-1–specific neutralizing antibodies to inhibit SARS-CoV-2 3 . Here we used comparative pangenomic analysis of all sequenced Betacoronaviruses to reveal that, among all core gene clusters present in these viruses, the envelope protein E shows a variant shared by SARS and SARS-Cov2 with two completely-conserved key functional features, an ion-channel and a PDZ-binding Motif (PBM). These features trigger a cytokine storm that activates the inflammasome, leading to increased edema in lungs causing the acute respiratory distress syndrome (ARDS) 4-6 , the leading cause of death in SARS-CoV-1 and SARS-CoV-2 infection 7,8 . However, three drugs approved for human use may inhibit SARS-CoV-1 and SARS-CoV-2 Protein E, either acting upon the ion channel (Amantadine and Hexamethylene amiloride 9,10 ) or the PBM (SB203580 5 ), thereby potentially increasing the survival of the host, as already demonstrated for SARS-CoV-1in animal models. Hence, blocking the SARS protein E inhibits development of ARDS in vivo ", "token_count": 428, "char_count": 1532, "word_count": 233, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8584, "entities": { "genes": [ "ACE2", "SB203580" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:23.068605", "source": { "split": "train_shard_00001", "doc_id": 1577 }, "chunk_id": "train_shard_00001_1577_0", "global_id": 7872 }, { "text": "Given that our results demonstrate that the protein E subcluster for the SARS clade is quasi -identical for the key functional regions of SARS-CoV-1 and SARS-CoV-2, we conclude that use of approved drugs shown to act as SARS E protein inhibitors can help prevent further casualties from COVID-2019 while vaccines and other preventive measures are being developed.\n\nFunctional pangenome analysis suggests inhibition of the protein E as a readily available therapy for COVID-2019", "token_count": 117, "char_count": 477, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7534, "quality_score": 0.8767, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:23.450601", "source": { "split": "train_shard_00001", "doc_id": 1577 }, "chunk_id": "train_shard_00001_1577_1", "global_id": 7873 }, { "text": "Novel antihypertensive peptides released by Kluyveromyces marxianus from bovine lactoferrin (LF) have been identified. K. marxianus LF permeate was fractionated by semipreparative high performance liquid chromatography and 35 peptides contained in the angiotensin I-converting enzyme (ACE)-inhibitory fractions were identified by using an ion trap mass spectrometer. On the basis of peptide abundance and common structural features, six peptides were chemically synthesized. Four of them (DPYKLRP, PYKLRP, YKLRP, and GILRP) exerted in vitro inhibitory effects on ACE activity and effectively decreased systolic blood pressure after oral administration to spontaneously hypertensive rats (SHRs). Stability against gastrointestinal enzymes suggested that the sequence LRP could contribute to the in vivo effects of parental peptides. Finally, there were reductions in circulating ACE activity and angiotensin II level in SHRs after either DPYKLRP or LRP intake, thus confirming ACE inhibition as the in vivo mechanism for their antihypertensive effect.\n\nNovel antihypertensive lactoferrin-derived peptides produced by Kluyveromyces marxianus: gastrointestinal stability profile and in vivo angiotensin I-converting enzyme (ACE) inhibition.", "token_count": 346, "char_count": 1237, "word_count": 162, "semantic_coherence": 1, "information_density": 0.716, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:24.029196", "source": { "split": "train_shard_00001", "doc_id": 1578 }, "chunk_id": "train_shard_00001_1578_0", "global_id": 7874 }, { "text": "Staphylococcus aureus (SA) is an opportunistic pathogen and human commensal that is frequently present in the upper respiratory tract, gastrointestinal tract and skin. While SA can cause diseases ranging from minor skin infections to life-threatening bacteraemia, it can also be carried asymptomatically. Indigenous individuals in the Southwest USA experience high rates of invasive SA disease. As carriage is the most significant risk factor for disease, understanding the dynamics of SA carriage, and in particular co-carriage of multiple strains, is important to develop strategies to prevent transmission in vulnerable communities. Here, we investigated SA co-carriage and intrahost evolution by sampling several colonies from multiple anatomical sites and whole-genome sequencing (WGS) on 310 SA isolates collected from 60 Indigenous adults participating in a cross-sectional carriage study. We assessed the richness and diversity of SA isolates via differences in multilocus sequence type, core-genome SNPs and genome content. Using WGS data, we identified 95 distinct SA intra-subject lineages (ISLs) among 60 participants; co-carriage was detected in 42% (25/60). Notably, two participants each carried four distinct SA ISLs. Variation in antibiotic resistance determinants among carried strains was identified among 42% (25/60) of participants. Lastly, we found unequal distribution of clonal complex by body site, suggesting that certain lineages may be adapted to specific anatomical sites. Together, these findings suggest that co-carriage may occur more frequently than previously appreciated and further our understanding of SA intrahost diversity during carriage, which has implications for surveillance activities and epidemiological investigations.\n\nMulti-strain carriage and intrahost diversity of <i>Staphylococcus aureus</i> among Indigenous adults in the USA.", "token_count": 450, "char_count": 1906, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6719, "quality_score": 0.8359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:24.667863", "source": { "split": "train_shard_00001", "doc_id": 1579 }, "chunk_id": "train_shard_00001_1579_0", "global_id": 7875 }, { "text": "Numerous traditionally aged cheeses are surface ripened and develop a biofilm, known as the cheese rind, on their surfaces. The rind of such cheeses comprises a complex community of bacterial and fungal species that are jointly responsible for the typical characteristics of the various cheese varieties. Surface ripening starts directly after brining with the rapid colonization of the cheese surface by yeasts. The initially dominant yeasts are acid and salt-tolerant and are capable of metabolizing the lactate produced by the starter lactic acid bacteria and of producing NH3 from amino acids. Both processes cause the pH of the cheese surface to rise dramatically. This so-called deacidification process enables the establishment of a salt-tolerant, Gram-positive bacterial community that is less acid-tolerant. Over the past decade, knowledge of yeast diversity in cheeses has increased considerably. The yeast species with the highest prevalence on surface-ripened cheeses are Debaryomyces hansenii and Geotrichum candidum, but up to 30 species can be found. In the cheese core, only lactose-fermenting yeasts, such as Kluyveromyces marxianus, are expected to grow. Yeasts are recognized as having an indispensable impact on the development of cheese flavour and texture because of their deacidifying, proteolytic, and/or lipolytic activity. Yeasts are used not only in the production of surface-ripened cheeses but also as adjunct cultures in the vat milk in order to modify ripening behaviour and flavour of the cheese. However, yeasts may also be responsible for spoilage of cheese, causing early blowing, off-flavour, brown discolouration, and other visible alterations of cheese.\n\nCheese yeasts.", "token_count": 416, "char_count": 1718, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6016, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:25.300234", "source": { "split": "train_shard_00001", "doc_id": 1580 }, "chunk_id": "train_shard_00001_1580_0", "global_id": 7876 }, { "text": "The availability of bacterial pangenome data grows exponentially, requiring efficient new methods of analysis. Currently popular approaches for the fast comparison of genomes have the drawback of not being based on explicit evolutionary models of diversification. Making sense of bacterial genome evolution, and notably in the accessory genome, requires however to take into account the complex processes by which the genomes evolve. Here we present the Pantagruel bioinformatic software pipeline, which enables the construction of a complete bacterial pangenome database geared towards the inference of gene evolution scenarios using gene tree/species tree reconciliation. Pantagruel is a modular pipeline that combines state-of-the-art external software with unique new methods. It can be executed with no supervision to perform a standard pangenome analysis, or be configured by advanced users to integrate methods of choice. A relational database underlies its data structure, allowing efficient retrieval of the large-scale data generated by integrative analyses of pangenome evolutionary history. From the reconstructed gene evolution scenarios, two main outputs are derived: firstly the gene tree-aware assignation of orthology, allowing the fine analysis of gene gain and loss history over the species phylogeny, and secondly a network of gene-to-gene association based on correlated events in scenarios of gene evolution, leading to the definition of co-evolved gene modules. Pantagruel is available as an open source software package at https://github.com/flass/pantagruel .\n\nAutomated reconstruction of all gene histories in large bacterial pangenome datasets and search for co-evolved gene modules with Pantagruel", "token_count": 366, "char_count": 1725, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:25.881614", "source": { "split": "train_shard_00001", "doc_id": 1581 }, "chunk_id": "train_shard_00001_1581_0", "global_id": 7877 }, { "text": "Agave juice is fermented and distilled twice in order to obtain mezcal, a traditional spirit beverage. The goal of this study was to select yeast or yeast mixtures that could be used in industrial production of high-quality mezcal. Yeasts isolated during fermentation of Agave duranguensis were tested to identify the best strains with respect to the chemical and organoleptic characteristics of the produced mezcal. Three individual yeast strains were selected for further study: Torulaspora delbrueckii strain ITD-00014a, Saccharomyces cerevisiae strain ITD-00185, and Kluyveromyces marxianus strain ITD-00147. Analysis of the response surfaces permitted identification of three inoculants: one mixture (75% S. cerevisiae ITD-00185 and 25% T. delbrueckii ITD-00014a) and two pure strains (100% K. marxianus ITD-00147 and 100% S. cerevisiae ITD-00185). Mezcal made by using the inoculant constituted by 75% S. cerevisiae ITD-00185 and 25% T. delbrueckii ITD-00014a (named mezcal 75Sc/25Td) was the best in terms of yield, richness of volatile compounds, and acceptability in sensory tests. We propose using this mixture of yeasts to develop a product that can be used as an inoculant in industrial production of mezcal and others spirits from different agave species.\n\nPerformance of mixtures of Saccharomyces and non-Saccharomyces native yeasts during alcoholic fermentation of Agave duranguensis juice", "token_count": 438, "char_count": 1404, "word_count": 202, "semantic_coherence": 1, "information_density": 0.599, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:26.512933", "source": { "split": "train_shard_00001", "doc_id": 1582 }, "chunk_id": "train_shard_00001_1582_0", "global_id": 7878 }, { "text": "Campylobacter species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the Campylobacter genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the Campylobacter genus core genome (500 loci) using publicly available Campylobacter complete genomes (n = 498) and constructed a core genome phylogeny using 2,193 publicly available Campylobacter genomes to examine inter-species diversity and species boundaries. Utilizing 8,440 Campylobacter genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated Campylobacter species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had in silico DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool Campylobacter Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%", "token_count": 424, "char_count": 1545, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:27.140649", "source": { "split": "train_shard_00001", "doc_id": 1583 }, "chunk_id": "train_shard_00001_1583_0", "global_id": 7879 }, { "text": "The ANI genomic species definitions proposed here allow consistent species definition in the Campylobacter genus and will facilitate the detection of novel species in the future.IMPORTANCEIn recent years, Campylobacter has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the Campylobacter genus in public databases. Currently, a standardized Campylobacter species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the Campylobacter genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the Campylobacter species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed Campylobacter Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to Campylobacter genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus Campylobacter.\n\nUncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses.", "token_count": 377, "char_count": 1508, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5699, "quality_score": 0.785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:27.718852", "source": { "split": "train_shard_00001", "doc_id": 1583 }, "chunk_id": "train_shard_00001_1583_1", "global_id": 7880 }, { "text": "The emergence of mobilized colistin resistance genes (mcr) has become a serious concern in clinical practice, compromising treatment options for life-threatening infections. In this study, colistin-resistant Klebsiella pneumoniae harboring mcr-8.1 was recovered from infected patients in the largest public hospital of Bangladesh, with a prevalence of 0.3% (3/1,097). We found mcr-8.1 in an identical highly stable multidrug-resistant IncFIB(pQil) plasmid of ∼113 kb, which belonged to an epidemiologically successful K. pneumoniae clone, ST15. The resistance mechanism was proven to be horizontally transferable, which incurred a fitness cost to the host. The core genome phylogeny suggested the clonal spread of mcr-8.1 in a Bangladeshi hospital. Core genome single-nucleotide polymorphisms among the mcr-8.1-positive K. pneumoniae isolates ranged from 23 to 110", "token_count": 301, "char_count": 920, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7288, "quality_score": 0.8644, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:28.279322", "source": { "split": "train_shard_00001", "doc_id": 1584 }, "chunk_id": "train_shard_00001_1584_0", "global_id": 7881 }, { "text": "It has been hypothesized that mcr-8.1 was inserted into IncFIB(pQil) with preexisting resistance loci, blaTEM-1b and blaCTX-M-15, by IS903B Coincidentally, all resistance determinants in the plasmid [mcr-8.1, ampC, sul2, 1d-APH(6), APH(3'')-Ib, blaTEM-1b, blaCTX-M-15] were bracketed by IS903B, demonstrating the possibility of intra- and interspecies and intra- and intergenus transposition of entire resistance loci. This is the first report of an mcr-like mechanism from human infections in Bangladesh. However, given the acquisition of mcr-8.1 by a sable conjugative plasmid in a successful high-risk clone of K. pneumoniae ST15, there is a serious risk of dissemination of mcr-8.1 in Bangladesh from 2017 onwards.IMPORTANCE There is a marked paucity in our understanding of the epidemiology of colistin-resistant bacterial pathogens in South Asia. A report by Davies and Walsh (Lancet Infect Dis 18:256-257, https://doi.org/10.1016/S1473-3099(18)30072-0, 2018) suggests the export of colistin from China to India, Vietnam, and South Korea in 2016 was approximately 1,000 tons and mainly used as a poultry feed additive", "token_count": 506, "char_count": 1286, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6962, "quality_score": 0.8481, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:28.921772", "source": { "split": "train_shard_00001", "doc_id": 1584 }, "chunk_id": "train_shard_00001_1584_1", "global_id": 7882 }, { "text": "A few reports forecast that the prevalence of mcr in humans and livestock will increase in South Asia. Given the high prevalence of blaCTX-M-15 and blaNDM in India, Bangladesh, and Pakistan, colistin has become the invariable option for the management of serious infections, leading to the emergence of mcr-like mechanisms in South Asia. Systematic scrutiny of the prevalence and transmission of mcr variants in South Asia is vital to understanding the drivers of mcr genes and to initiate interventions to overcome colistin resistance.\n\nEmergence of Mobile Colistin Resistance (<i>mcr-8</i>) in a Highly Successful Klebsiella pneumoniae Sequence Type 15 Clone from Clinical Infections in Bangladesh.", "token_count": 232, "char_count": 776, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:29.390361", "source": { "split": "train_shard_00001", "doc_id": 1584 }, "chunk_id": "train_shard_00001_1584_2", "global_id": 7883 }, { "text": "Abstract

Levilactobacillus brevis is a significant member of lactobacilli due to its remarkable industrial and probiotic features. In this study, the L. brevis DY55bre strain was isolated from a lactic acid-fermented beverage known as \"shalgam\". Its genome size was 2.485.670bp, with a GC content of 45.72%. It is predicted to possess 2699 coding sequences, including 82 tRNA, 7 rRNA, 3 ncRNA, 42 CRISPR spacers, and 155 pseudogenes. Unlike previous research, the DY55bre genome only has one CAS system, Type-1E. The clusters of orthologous groups (COGs) comparison and pangenome analysis were performed using other genomes of L.brevis. Like other obligate heterofermentative lactobacilli, DY55bre has araBAD operon but no 1-phosphofructokinase(pfk) enzyme. Further, it can produce lactic acid, acetic acid, ethanol, 1-propanol, propanal, butane-2,3-diol, acetaldehyde, acetoin, and diacetyl as an outcome of carbohydrate metabolism. On the other side, DY55bre has the ability to produce the amino acids L-asparagine, L-aspartate, L-glutamine, L-glutamate, S-Adenosyl-L-methionine, citrulline, arginine, serine, glycine, and GABA. These amino acid and carbohydrate metabolism products are valuable due to their economic value and health benefits to humans and animals. Finally, probiogenomic assessment results demonstrated that L. brevis DY55bre has gut adaption features that allow it to withstand a wide range of stressors.

", "token_count": 520, "char_count": 1551, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7437, "quality_score": 0.8719, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:12:30.050424", "source": { "split": "train_shard_00001", "doc_id": 1585 }, "chunk_id": "train_shard_00001_1585_0", "global_id": 7884 }, { "text": "Functional genomics evaluation of Levilactobacillus brevis strain DY55bre acquired from a lactic acid fermented beverage to further understand its biotechnological and probiotic potential", "token_count": 45, "char_count": 187, "word_count": 23, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:30.421749", "source": { "split": "train_shard_00001", "doc_id": 1585 }, "chunk_id": "train_shard_00001_1585_1", "global_id": 7885 }, { "text": "

Introduction

Colistin has emerged as the last resort for treating multidrug-resistant Enterobacter cloacae complex (ECC) infections. The primary purposes of this study were to demonstrate the presence of colistin heteroresistance in ECC and to further investigate their clinical characteristics, molecular epidemiology and mechanisms.

Methods

Population analysis profiles (PAP) were performed to confirm the heteroresistance phenotype. Average nucleotide identity (ANI) was determined to classify ECC species. Phylogenetic analysis based on core genome single nucleotide polymorphisms (cg-SNPs), multilocus sequence typing (MLST) and core genome MLST (cg-MLST). Risk factors and clinical outcomes of infections were analyzed through a retrospective case-control study. Potential mechanisms of colistin heteroresistance were evaluated using polymerase chain reaction (PCR), efflux pump inhibition assays and reverse transcription quantitative PCR (RT-qPCR).

Results

A high proportion (24.4%) of the non-resistant strains were colistin-heteroresistant isolates. Among the several ECC species, Enterobacter kobei had the largest percentage (29.4%) of colistin-heteroresistant isolates, followed by Enterobacter hormaechei (20.5%) and Enterobacter bugandensis (20.0%). Notably, only one strain (0.8%; 1/132) of Enterobacter hormaechei was fully resistant to colistin. Different ECC species showed varying heteroresistance levels: Enterobacter roggenkampii, Enterobacter kobei, Enterobacter asburiae and Enterobacter bugandensis displayed high heteroresistance levels  (MIC ≥ 128 mg/L). 75% of all ST116 and ST56 strains were heteroresistant to colistin", "token_count": 510, "char_count": 1733, "word_count": 200, "semantic_coherence": 1, "information_density": 0.71, "quality_score": 0.855, "entities": { "genes": [ "ST56", "ST116" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:31.088419", "source": { "split": "train_shard_00001", "doc_id": 1586 }, "chunk_id": "train_shard_00001_1586_0", "global_id": 7886 }, { "text": "The infection of ST116 and ST56 strains as well as exposure to cephalosporin antibiotics were independent risk factors for colistin-heteroresistant ECC infections. Mechanistic analysis revealed that heteroresistance strongly correlated with the overexpression of arnA, regulated by the PhoPQ two-component system (TCS). Notably, mgrB had minimal impact. AcrAB-TolC efflux pump genes showed unsynchronized expression; High acrB expression was strongly associated with colistin heteroresistance, while acrA and tolC were not.

Discussion

Colistin heteroresistance showed species-dependent variations in levels and prevalence rates. The colistin-heteroresistant mechanisms were complex, involving coordinated regulation of multiple genes. These results highlighted the need for tailored antimicrobial stewardship. In addition, the development of direct, reliable and rapid clinical methods for detecting heteroresistance is essential for improving infection management and prevention.\n\nClinical characteristics, molecular epidemiology and mechanisms of colistin heteroresistance in <i>Enterobacter cloacae</i> complex.", "token_count": 298, "char_count": 1168, "word_count": 132, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "ST56", "ST116" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:31.685330", "source": { "split": "train_shard_00001", "doc_id": 1586 }, "chunk_id": "train_shard_00001_1586_1", "global_id": 7887 }, { "text": "Abstract

Human genomics is witnessing an ongoing paradigm shift from a single reference sequence to a pangenome form but populations of Asian ancestry are underrepresented. Here, we present the first effort (Phase I) of the Chinese Pangenome Consortium (CPC) with a collection of 116 high-quality and haplotype-phased de novo assemblies based on 58 core samples representing 36 minority Chinese ethnic groups. With > 30.65× High-Fidelity long-reads sequence coverage, an average contiguity N50 > 35.63 Mb, and an average total size of 3.01 Gb, the CPC core assemblies cover ~96.54% and ~93.59% of the latest reference sequence GRCh38 and a Telomere-to-Telomere haploid assembly T2T-CHM13, respectively. Moreover, the CPC Phase I data add 189 million base pairs of euchromatic polymorphic sequence and 1,367 protein-coding gene duplications to GRCh38. We also identify from the CPC pangenome ~15.9 million small variants and ~78 thousand structural variants (SVs), of which ~6.1 million (38.0%) small variants and ~25 thousand (32.4%) SVs are not reported in a recently released pangenome reference by the Human Pangenome Reference Consortium (HPRC)1. The CPC data demonstrate a remarkable increase in discovering novel or missing sequences when individuals are included from underrepresented minority ethnic groups, suggesting the necessity of a more comprehensive sampling effort for both CPC and HPRC.

\n\nA Pangenome Reference of 36 Chinese populations", "token_count": 429, "char_count": 1497, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6495, "quality_score": 0.8248, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:32.343493", "source": { "split": "train_shard_00001", "doc_id": 1587 }, "chunk_id": "train_shard_00001_1587_0", "global_id": 7888 }, { "text": "

Background

Multicellular animals and bacteria frequently engage in predator-prey and host-pathogen interactions, such as the well-studied relationship between Pseudomonas aeruginosa and the nematode Caenorhabditis elegans. This study investigates the genomic and genetic basis of bacterial-driven variability in P. aeruginosa virulence towards C. elegans to provide evolutionary insights into host-pathogen relationships.

Results

Natural isolates of P. aeruginosa that exhibit diverse genomes display a broad range of virulence towards C. elegans. Using gene association and genetic analysis, we identify accessory genome elements that correlate with virulence, including both known and novel virulence determinants. Among the novel genes, we find a viral-like mobile element, the teg block, that impairs virulence and whose acquisition is restricted by CRISPR-Cas systems. Further genetic and genomic evidence suggests that spacer-targeted elements preferentially associate with lower virulence while the presence of CRISPR-Cas associates with higher virulence.

Conclusions

Our analysis demonstrates substantial strain variation in P. aeruginosa virulence, mediated by specific accessory genome elements that promote increased or decreased virulence. We exemplify that viral-like accessory genome elements that decrease virulence can be restricted by bacterial CRISPR-Cas immune defense systems, and suggest a positive, albeit indirect, role for host CRISPR-Cas systems in virulence maintenance.\n\nThe Pseudomonas aeruginosa accessory genome elements influence virulence towards Caenorhabditis elegans.", "token_count": 391, "char_count": 1624, "word_count": 200, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:32.991111", "source": { "split": "train_shard_00001", "doc_id": 1588 }, "chunk_id": "train_shard_00001_1588_0", "global_id": 7889 }, { "text": "Abstract

Background Non-O1, non-O139 Vibrio cholerae is an uncommon cause of pneumonia, particularly following freshwater exposure. Non-O1, non-O139 Vibrio cholerae was identified from bronchoalveolar lavage through culture and quantitative polymerase chain reaction (qPCR) in Hungary. Epidemiological investigation traced the source of infection in a designated bathing site in a lake in Central Hungary, where non-O1,non-O139 Vibrio cholerae was isolated from surface water. Methods We conducted whole-genome sequencing and comparative genomic analysis on a clinical isolate (N=1) and three phenotypically distinct environmental isolates (N=3). In addition, we reviewed the available literature on pulmonary infections associated with Vibrio cholerae. Results Core genome multilocus sequence typing (cgMLST) revealed that the clinical and environmental isolates clustered together with zero allelic differences. Multilocus sequence typing (MLST) identified a new sequence type (ST1605), representing a novel combination of known allele variants. In silico analysis of antibiotic resistance genes identified the presence of blaCARB-7. Both the clinical and environmental isolates exhibited identical virulence gene profiles, reinforcing the hypothesis that the infection was acquired from the local water source. Conclusions This study represents the first investigation of a primary pulmonary Vibrio cholerae infection in Europe following a near-drowning event. While Vibrio vulnificus and Vibrio metschnikovii have been implicated in similar pneumonia cases, the precise virulence mechanisms of these species remain poorly understood", "token_count": 484, "char_count": 1843, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [ "ST1605" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:33.641171", "source": { "split": "train_shard_00001", "doc_id": 1589 }, "chunk_id": "train_shard_00001_1589_0", "global_id": 7890 }, { "text": "Although non-O1, non-O139 Vibrio cholerae infections linked to recreational water exposure are rare in Hungary (1-2 cases annually), this study underscores the importance of ongoing surveillance to detect potential outbreaks and inform public health responses.

\n\nGenomic characterization of non-O1, non-O139 Vibrio cholerae causing rare clinical manifestation", "token_count": 101, "char_count": 379, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8913, "quality_score": 0.9457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:34.013908", "source": { "split": "train_shard_00001", "doc_id": 1589 }, "chunk_id": "train_shard_00001_1589_1", "global_id": 7891 }, { "text": "

Background

Efficient bioconversion of lignocellulosic biomass to bioethanol is one of key challenges in the situation of increasing bioethanol demand. The ethanologenic microbes for such conversion are required to possess abilities of utilization of various sugars including xylose and arabinose in lignocellulosic biomass. As required additional characteristics, there are a weak or no glucose repression that allows cells to simultaneously utilize various sugars together with glucose and thermotolerance for fermentation at high temperatures, which has several advantages including reduction of cooling cost. Spathaspora passalidarum ATCC MYA-4345, a type strains, isolated previously have mainly of these abilities or characteristics but its thermotolerance is not so strong and its glucose repression on xylose utilization is revealed.

Results

Newly isolated S. passalidarum CMUWF1-2 was found to have a high ability to produce ethanol from various sugars included in lignocellulosic biomass at high temperatures. The strain achieved ethanol yields of 0.43 g, 0.40 g and 0.20 g ethanol/g xylose at 30 °C, 37 °C and 40 °C, respectively. Interestingly, no significant glucose repression was observed in experiments with mixed sugars, being consistent with the strong resistance to 2-deoxyglucose, and antimycin A showed no effect on its growth in xylose medium. Moreover, the strain was tolerant to glucose and ethanol at concentrations up to 35.0% (w/v) and 8.0% (v/v), respectively.

Conclusions

S. passalidarum CMUWF1-2 was shown to achieve efficient production of ethanol from various sugars and a high ethanol yield from xylose with little accumulation of xylitol. The strain also exhibited stress-resistance including thermotolerance and no detectable glucose repression as beneficial characteristics. Therefore, S", "token_count": 504, "char_count": 1844, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5748, "quality_score": 0.7874, "entities": { "genes": [ "CMUWF1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:34.666185", "source": { "split": "train_shard_00001", "doc_id": 1590 }, "chunk_id": "train_shard_00001_1590_0", "global_id": 7892 }, { "text": "passalidarum CMUWF1-2 has remarkable potential for conversion of lignocellulosic biomass to bioethanol.\n\nHighly efficient conversion of xylose to ethanol without glucose repression by newly isolated thermotolerant Spathaspora passalidarum CMUWF1-2.", "token_count": 76, "char_count": 248, "word_count": 29, "semantic_coherence": 1, "information_density": 0.8621, "quality_score": 0.931, "entities": { "genes": [ "CMUWF1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:35.038299", "source": { "split": "train_shard_00001", "doc_id": 1590 }, "chunk_id": "train_shard_00001_1590_1", "global_id": 7893 }, { "text": "

Background

Data regarding yeast microbiota in goat milk is scarce.

Aims

To isolate and identify species of the genus Candida in milk samples from clinically healthy goats, and evaluate their enzymatic activity and biofilm formation.

Methods

1092 milk samples from clinically healthy goats were collected and processed. The yeast isolates were identified by phenotypic, methods and their enzymatic activity (phospholipase, hemolysin and protease) and biofilm formation evaluated.

Results

We obtained 221 Candida isolates belonging to six species: Candida kefyr (35.7%), Candida guilliermondii (33%), Candida famata (23.5%), Candida glabrata (5.9%), Candida albicans (1.35%) and Candida parapsilosissensu lato (0.45%). Protease activity was detected in all Candida species while hemolysin activity was only present in C. kefyr, C. guilliermondii, C. famata and C. albicans. Only C. albicans showed phospholipase activity. With the exception of C. parapsilosis sensu lato, all Candida species formed biofilm, with 60.19% of the isolates being poor producers, 9.93% moderate producers, and 1.35% strong producers.

Conclusions

The milk of clinically healthy goats contains several species of the genus Candida that could play a role as opportunistic pathogens in mastitis.\n\nCharacterization, enzymatic activity and biofilm formation of Candida species isolated from goat milk.", "token_count": 413, "char_count": 1407, "word_count": 183, "semantic_coherence": 1, "information_density": 0.5738, "quality_score": 0.7869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:35.658052", "source": { "split": "train_shard_00001", "doc_id": 1591 }, "chunk_id": "train_shard_00001_1591_0", "global_id": 7894 }, { "text": "

Background

Candida species are a group of coexistent microorganisms in the oral cavity that opportunistically cause disease in vulnerable people, including addicts. This study is aimed at identifying and determining the frequency of Candida species in the oral cavity of the addicts to inform the epidemiological panel and to warn to prevent the resistance of the species.

Materials and methods

In this study, sampling was done from the oral cavity of 83 addicts who referred to Addiction Treatment Centers in Isfahan, Iran, using moist sterile swab. The presence of yeast on the direct microscope slides of 58 samples was confirmed. To carry out culture and the primary identification, Sabouraud dextrose agar medium with chloramphenicol as well as HiCrome Candida agar medium was used. Isolates were identified by polymerase chain reaction (PCR) restriction fragment length polymorphism (using specific primers ITS1-ITS4 and MSP I enzyme) and Duplex PCR test (using specific primers CDU1-CDU2/CAL1-CAL2).

Results

Out of 93 Candida isolates which had been isolated from 58 culture-positive samples of the oral cavity, Candida albicans (41.93%) were the most prevalent species, followed by Candida dubliniensis (24.73%), Candida glabrata (21.50%), Candida kefyr (8.60%), Candida tropicalis (2.15%), and Candida parapsilosis (1.07%), respectively", "token_count": 450, "char_count": 1437, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6754, "quality_score": 0.8377, "entities": { "genes": [ "CAL1", "ITS1", "CDU1", "ITS4", "CAL2", "CDU2" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:36.305915", "source": { "split": "train_shard_00001", "doc_id": 1592 }, "chunk_id": "train_shard_00001_1592_0", "global_id": 7895 }, { "text": "In 33 cases (56.90%), the presence of more than one Candida species was observed.

Conclusion

Compared to the studies conducted on the oral cavity of healthy controls, smoking certain drugs can have a significant effect on the presence and frequency of Candida species, particularly C. dubliniensis and C. glabrata.\n\nFrequency of Candida Species in the Oral Cavity of Narcotics and Stimulants Smokers in Isfahan, Using Polymerase Chain Reaction-Restriction Fragment Length Polymorphism Method.", "token_count": 160, "char_count": 527, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:36.746196", "source": { "split": "train_shard_00001", "doc_id": 1592 }, "chunk_id": "train_shard_00001_1592_1", "global_id": 7896 }, { "text": "Carbapenem resistance and other antibiotic resistance genes (ARGs) can be found in plasmids in Acinetobacter , but many plasmid types in this genus have not been well-characterised. Here we describe the distribution, diversity and evolutionary capacity of rep group 13 (GR13) plasmids that are found in Acinetobacter species from diverse environments. Our investigation was prompted by the discovery of two GR13 plasmids in A. baumannii isolated in an intensive care unit (ICU). The plasmids harbour distinct accessory genes: pDETAB5 contains bla NDM-1 and genes that confer resistance to four further antibiotic classes, while pDETAB13 carries putative alcohol tolerance determinants. Both plasmids contain multiple dif modules, which are flanked by p dif sites recognised by XerC/XerD tyrosine recombinases. The ARG-containing dif modules in pDETAB5 are almost identical to those found in pDETAB2, a GR34 plasmid from an unrelated A. baumannii isolated in the same ICU a month prior. Examination of a further 41 complete, publicly available plasmid sequences revealed that the GR13 pangenome consists of just four core but 1086 accessory genes, 123 in the shell and 1063 in the cloud, reflecting substantial capacity for diversification. The GR13 core genome includes genes for replication and partitioning, and for a putative tyrosine recombinase. Accessory segments encode proteins with diverse putative functions, including for metabolism, antibiotic/heavy metal/alcohol tolerance, restriction-modification, an anti-phage system and multiple toxin-antitoxin systems. The movement of dif modules and actions of insertion sequences play an important role in generating diversity in GR13 plasmids. Discrete GR13 plasmid lineages are internationally disseminated and found in multiple Acinetobacter species, which suggests they are important platforms for the accumulation, horizontal transmission and persistence of accessory genes in this genus", "token_count": 480, "char_count": 1947, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [ "GR13", "GR34" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:37.399297", "source": { "split": "train_shard_00001", "doc_id": 1593 }, "chunk_id": "train_shard_00001_1593_0", "global_id": 7897 }, { "text": "

Impact statement

Acinetobacter species are particularly well-adapted for persistence in hospital environments where they pose a life-threatening infection risk to the most clinically-vulnerable patients. Plasmids with the potential to transfer multiple antibiotic resistance determinants between Acinetobacter species are therefore concerning, but most are not well-characterised. This work sheds further light on the poorly-understood mobile gene pool associated with Acinetobacter . We show here that GR13 plasmids carry a small set of core genes but have access to a highly diverse set of accessory segments that might provide fitness advantages under certain conditions. The complex evolutionary dynamics of GR13 plasmids appear to be driven by the exchange of dif modules and by the actions of a diverse population of insertion sequences. The novel dif modules characterised here emphasise the broader importance of these elements to the dissemination of accessory genes in Acinetobacter . This study has improved our understanding of the diversity and distribution of dif modules, plasmids that carry them, and how both disseminate in the continuum of Acinetobacter populations that link hospitals and the wider environment.\n\nGR13-type plasmids in Acinetobacter potentiate the accumulation and horizontal transfer of diverse accessory genes", "token_count": 292, "char_count": 1362, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6283, "quality_score": 0.8141, "entities": { "genes": [ "GR13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:37.964983", "source": { "split": "train_shard_00001", "doc_id": 1593 }, "chunk_id": "train_shard_00001_1593_1", "global_id": 7898 }, { "text": "The Arcobacteraceae family groups Gram-negative bacterial species previously included in the family Campylobacteraceae. These species of which some are considered foodborne pathogens, have been isolated from different environmental niches and hosts. They have been isolated from various types of foods, though predominantly from food of animal origin, as well as from stool of humans with enteritis. Their different abilities to survive in different hosts and environments suggest an evolutionary pressure with consequent variation in their genome content. Moreover, their different physiological and genomic characteristics led to the recent proposal to create new genera within this family, which is however criticized due to the lack of discriminatory features and biological and clinical relevance. Aims of the present study were to assess the Arcobacteraceae pangenome, and to characterize existing similarities and differences in 20 validly described species. For this, analysis has been conducted on the genomes of the corresponding type strains obtained by Illumina sequencing, applying several bioinformatic tools. Results of the present study do not support the proposed division into different genera and revealed the presence of pangenome partitions with numbers comparable to other Gram-negative bacteria genera, such as Campylobacter. Different gene class compositions in animal and human-associated species are present, including a higher percentage of virulence-related gene classes such as cell motility genes. The adaptation to environmental and/or host conditions of some species was identified by the presence of specific genes. Furthermore, a division into pathogenic and non-pathogenic species is suggested, which can support future research on food safety and public health.\n\nArcobacteraceae comparative genome analysis demonstrates genome heterogeneity and reduction in species isolated from animals and associated with human illness", "token_count": 379, "char_count": 1957, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6236, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:38.536808", "source": { "split": "train_shard_00001", "doc_id": 1594 }, "chunk_id": "train_shard_00001_1594_0", "global_id": 7899 }, { "text": "There is an evolving interest in the adoption and incorporation of plant proteins in Western diets as sustainable alternatives to meat consumption. This is typically motivated by the environmental and public health concerns posed by animal-based diets. However, plant proteins have been demonstrated to exhibit reduced bioavailability as a consequence of high concentrations of anti-nutritional factors (ANFs) and complex protein structures, leading to incompletely digested protein reaching the colon. This undigested protein undergoes microbial putrefaction, generating metabolites like ammonia, phenols, and hydrogen sulfide that are potentially associated with inflammation, gut barrier dysfunction, and chronic diseases. Literature searches utilizing tools such as Google Scholar and PubMed were performed with identifying relevant work in both putrefaction and fermentation, to highlight gaps for future research. There is evidence that including a microbial fermentation step in the processing of plant proteins can degrade ANFs, hydrolyze protein structure, and increase free amino acids, thereby improving upper gastrointestinal digestibility. The application of fermentation strategies can address both nutritional and safety challenges by pre-digesting proteins and enriching functional metabolites such as SCFAs and polyphenols. However, gaps persist in understanding many elements of fermentation of plant proteins including microbial consortia optimization, in vivo impacts, and long-term health outcomes. This review examines protein putrefaction in the gut and its association with adverse health impacts, and furthermore, fermentation is evaluated as a potential processing aid for plant proteins to enhance digestibility and mitigate putrefaction risks.\n\nApplication and utilization of fermentation as a processing tool to mitigate protein putrefaction in plant-based diets.", "token_count": 403, "char_count": 1899, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:40.271131", "source": { "split": "train_shard_00001", "doc_id": 1595 }, "chunk_id": "train_shard_00001_1595_0", "global_id": 7900 }, { "text": "High-fidelity (HiFi) sequencing has facilitated the assembly and analysis of the most repetitive region of the genome, the centromere. Nevertheless, our current understanding of human centromeres draws from a relatively small number of telomere-to-telomere assemblies, and so has not yet captured its full diversity. In this study, we investigated the genomic diversity of human centromere higher order repeats (HORs) using both HiFi reads and haplotype-resolved assemblies from hundreds of samples drawn from ongoing pangenome-sequencing projects and reprocessed using a novel HOR annotation pipeline, HiCAT-human. We use this wealth of data to provide a global survey of the centromeric HOR landscape, in particular finding that 23 HORs exhibited significant copy number variability between populations. We detected three centromere genotypes with imbalance population frequencies on each of chromosome 5, 8 and 17. An inter-assembly comparison of HOR loci further revealed that while HOR array structures are diverse, they nevertheless tend to form a number of specific landscapes, each exhibiting different levels of HOR subunit expansion and possibly reflecting a cyclical evolutionary transition from homogeneous to nested structures and back.\n\nCentromere landscapes resolved from hundreds of human genomes", "token_count": 295, "char_count": 1312, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7135, "quality_score": 0.8568, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:40.830727", "source": { "split": "train_shard_00001", "doc_id": 1596 }, "chunk_id": "train_shard_00001_1596_0", "global_id": 7901 }, { "text": "

Background

The foodborne bacterium Listeria monocytogenes (Lm) causes a range of diseases, from mild gastroenteritis to invasive infections that have high fatality rate in vulnerable individuals. Understanding the population genomic structure of invasive Lm is critical to informing public health interventions and infection control policies that will be most effective especially in local and regional communities.

Methods

We sequenced the whole draft genomes of 936 Lm isolates from human clinical samples obtained in a two-decade active surveillance program across 58 counties in New York State, USA. Samples came mostly from blood and cerebrospinal fluid. We characterized the phylogenetic relationships, population structure, antimicrobial resistance genes, virulence genes, and mobile genetic elements.

Results

The population is genetically heterogenous, consisting of lineages I-IV, 89 clonal complexes, 200 sequence types, and six known serogroups. In addition to intrinsic antimicrobial resistance genes (fosX, lin, norB, and sul), other resistance genes tetM, tetS, ermG, msrD, and mefA were sparsely distributed in the population. Within each lineage, we identified clusters of isolates with ≤ 20 single nucleotide polymorphisms in the core genome alignment. These clusters may represent isolates that share a most recent common ancestor, e.g., they are derived from the same contamination source or demonstrate evidence of transmission or outbreak. We identified 38 epidemiologically linked clusters of isolates, confirming eight previously reported disease outbreaks and the discovery of cryptic outbreaks and undetected chains of transmission, even in the rarely reported Lm lineage III (ST3171). The presence of animal-associated lineages III and IV may suggest a possible spillover of animal-restricted strains to humans", "token_count": 448, "char_count": 1858, "word_count": 251, "semantic_coherence": 1, "information_density": 0.7171, "quality_score": 0.8586, "entities": { "genes": [ "ST3171" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:41.471285", "source": { "split": "train_shard_00001", "doc_id": 1597 }, "chunk_id": "train_shard_00001_1597_0", "global_id": 7902 }, { "text": "Many transmissible clones persisted over several years and traversed distant sites across the state.

Conclusions

Our findings revealed the bacterial determinants of invasive listeriosis, driven mainly by the diversity of locally circulating lineages, intrinsic and mobile antimicrobial resistance and virulence genes, and persistence across geographical and temporal scales. Our findings will inform public health efforts to reduce the burden of invasive listeriosis, including the design of food safety measures, source traceback, and outbreak detection.\n\nLong-term persistence of diverse clones shapes the transmission landscape of invasive Listeria monocytogenes.", "token_count": 146, "char_count": 673, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7412, "quality_score": 0.8706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:41.904763", "source": { "split": "train_shard_00001", "doc_id": 1597 }, "chunk_id": "train_shard_00001_1597_1", "global_id": 7903 }, { "text": "Campylobacter ureolyticus is a Gram-negative, anaerobic, non-spore-forming bacteria that causes gastrointestinal infections. Being the most prevalent cause of bacterial enteritis globally, infection by this bacterium is linked with significant morbidity and mortality in children and immunocompromised patients. No information on pan-therapeutic drug targets for this species is available yet. In the current study, a pan-genome analysis was performed on 13 strains of C. ureolyticus to prioritize potent drug targets from the identified core genome. In total, 26 druggable proteins were identified using subtractive genomics. To the best of the authors' knowledge, this is the first report on the mining of drug targets in C. ureolyticus. UDP-3-O-acyl-N-acetylglucosamine deacetylase (LpxC) was selected as a promiscuous pharmacological target for virtual screening of two bacterial-derived natural product libraries, i.e., postbiotics (n = 78) and streptomycin (n = 737) compounds. LpxC inhibitors from the ZINC database (n = 142 compounds) were also studied with reference to LpxC of C. ureolyticus. The top three docked compounds from each library (including ZINC26844580, ZINC13474902, ZINC13474878, Notoginsenoside St-4, Asiaticoside F, Paraherquamide E, Phytoene, Lycopene, and Sparsomycin) were selected based on their binding energies and validated using molecular dynamics simulations. To help identify potential risks associated with the selected compounds, ADMET profiling was also performed and most of the compounds were considered safe. Our findings may serve as baseline information for laboratory studies leading to the discovery of drugs for use against C. ureolyticus infections.", "token_count": 516, "char_count": 1754, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.834, "entities": { "genes": [ "ZINC13474878", "ZINC26844580", "ZINC13474902" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:12:42.534349", "source": { "split": "train_shard_00001", "doc_id": 1598 }, "chunk_id": "train_shard_00001_1598_0", "global_id": 7904 }, { "text": "Identification of Therapeutic Targets in an Emerging Gastrointestinal Pathogen Campylobacter ureolyticus and Possible Intervention through Natural Products.", "token_count": 43, "char_count": 163, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:42.899737", "source": { "split": "train_shard_00001", "doc_id": 1598 }, "chunk_id": "train_shard_00001_1598_1", "global_id": 7905 }, { "text": "Nicotinamide adenine dinucleotide (NAD+) has emerged as a key component in prokaryotic and eukaryotic immune systems. The recent discovery that Toll/interleukin-1 receptor (TIR) proteins function as NAD+ hydrolases (NADase) links NAD+-derived small molecules with immune signaling. We investigated pathogen manipulation of host NAD+ metabolism as a virulence strategy. Using the pangenome of the model bacterial pathogen Pseudomonas syringae, we conducted a structure-based similarity search from 35,000 orthogroups for type III effectors (T3Es) with potential NADase activity. Thirteen T3Es, including five newly identified candidates, were identified that possess domain(s) characteristic of seven NAD+-hydrolyzing enzyme families. Most Pseudomonas syringae strains that depend on the type III secretion system to cause disease, encode at least one NAD+-manipulating T3E, and many have several. We experimentally confirmed the type III-dependent secretion of a novel T3E, named HopBY, which shows structural similarity to both TIR and adenosine diphosphate ribose (ADPR) cyclase. Homologs of HopBY were predicted to be type VI effectors in diverse bacterial species, indicating potential recruitment of this activity by microbial proteins secreted during various interspecies interactions. HopBY efficiently hydrolyzes NAD+ and specifically produces 2'cADPR, which can also be produced by TIR immune receptors of plants and by other bacteria. Intriguingly, this effector promoted bacterial virulence, indicating that 2'cADPR may not be the signaling molecule that directly initiates immunity. This study highlights a host-pathogen battleground centered around NAD+ metabolism and provides insight into the NAD+-derived molecules involved in plant immunity.", "token_count": 512, "char_count": 1871, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7076, "quality_score": 0.8538, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:43.543399", "source": { "split": "train_shard_00001", "doc_id": 1599 }, "chunk_id": "train_shard_00001_1599_0", "global_id": 7906 }, { "text": "Pangenomic analysis reveals plant NAD+ manipulation as an important virulence activity of bacterial pathogen effectors.", "token_count": 32, "char_count": 130, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:43.917285", "source": { "split": "train_shard_00001", "doc_id": 1599 }, "chunk_id": "train_shard_00001_1599_1", "global_id": 7907 }, { "text": "The effect of the addition of enzymatic extract of Kluyveromyces marxianus NRRL-Y-7571 during the maceration and fermentation steps of Cabernet Sauvignon wine production was evaluated. The results obtained in the analytical determinations of the wines showed levels within the limits established by legislation and similar to values found in other studies. The results show that by adding the enzyme to the red wines these showed color characteristics considered to be superior to those of the control wine and accelerated the extraction of phenolic compounds and anthocyanins. It was observed that by using the commercial enzyme preparation there was an increase of 15 % in polyphenol content compared to the control wine and an increase of 28 % when the crude enzyme extract was used. Anthocyanin content in the wine increased after treatment with the commercial enzyme preparation (10 %) and with the use of the crude enzymatic extract (22 %). Considering all comparison criteria, the K. marxianus enzymatic extract showed results statistically similar or superior to those obtained with the commercial enzyme preparation.\n\nVariation in phenolic compounds, anthocyanins, and color in red wine treated with enzymatic extract of Kluyveromyces marxianus.", "token_count": 295, "char_count": 1254, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5105, "quality_score": 0.7553, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:44.523673", "source": { "split": "train_shard_00001", "doc_id": 1600 }, "chunk_id": "train_shard_00001_1600_0", "global_id": 7908 }, { "text": "

ABSTRACT

Variation in the genome of Pseudomonas aeruginosa , an important pathogen, can have dramatic impacts on the bacterium’s ability to cause disease. We therefore asked whether it was possible to predict the virulence of P. aeruginosa isolates based upon their genomic content. We applied a machine learning approach to a genetically and phenotypically diverse collection of 115 clinical P. aeruginosa isolates using genomic information and corresponding virulence phenotypes in a mouse model of bacteremia. We defined the accessory genome of these isolates through the presence or absence of accessory genomic elements (AGEs), sequences present in some strains but not others. Machine learning models trained using AGEs were predictive of virulence, with a mean nested cross-validation accuracy of 75% using the random forest algorithm. However, individual AGEs did not have a large influence on the algorithm’s performance, suggesting instead that the virulence prediction derives from a diffuse genomic signature. These results were validated with an independent test set of 25 P. aeruginosa isolates whose virulence was predicted with 72% accuracy. Machine learning models trained using core genome single nucleotide variants and whole genome k-mers also predicted virulence. Our findings are a proof of concept for the use of bacterial genomes to predict pathogenicity in P. aeruginosa and highlight the potential of this approach for predicting patient outcomes.

IMPORTANCE

Pseudomonas aeruginosa is a clinically important gram-negative opportunistic pathogen. As a species, P. aeruginosa has a large degree of heterogeneity both through variation in sequences found throughout the species (core genome) and the presence or absence of sequences in different isolates (accessory genome). P. aeruginosa isolates also differ markedly in their ability to cause disease. In this study, we used machine learning to predict the virulence level of P. aeruginosa isolates in a mouse bacteremia model based on genomic content. We show that both the accessory and core genome are predictive of virulence. This study provides a machine learning framework to investigate relationships between bacterial genomes and complex phenotypes such as virulence.", "token_count": 513, "char_count": 2268, "word_count": 330, "semantic_coherence": 1, "information_density": 0.5212, "quality_score": 0.7606, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:12:45.620602", "source": { "split": "train_shard_00001", "doc_id": 1601 }, "chunk_id": "train_shard_00001_1601_0", "global_id": 7909 }, { "text": "A Genome-based Model to Predict the Virulence ofPseudomonas aeruginosaIsolates", "token_count": 30, "char_count": 85, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:45.970532", "source": { "split": "train_shard_00001", "doc_id": 1601 }, "chunk_id": "train_shard_00001_1601_1", "global_id": 7910 }, { "text": "

Background

Kluyveromyces marxianus combines the ease of genetic manipulation and fermentation with the ability to efficiently secrete high molecular weight proteins, performing eukaryotic post-translational modifications. It is able to grow efficiently in a wide range of temperatures. The secretion performances were analyzed in the host K. marxianus L3 in the range between 5°C and 40°C by means of 3 different reporter proteins, since temperature appears a key parameter for production and secretion of recombinant proteins.

Results

The recombinant strains were able to grow up to 40°C and, along the tested temperature interval (5-40°C), the specific growth rates (μ) were generally lower as compared to those of the untransformed strain. Biomass yields were slightly affected by temperature, with the highest values reached at 15°C and 30°C. The secretion of the endogenous β-fructofuranosidase, used as an internal control, was efficient in the range of the tested temperature, as evaluated by assaying the enzyme activity in the culture supernatants. The endogenous β-fructofuranosidase production was temperature dependent, with the highest yield at 30°C. The heterologous proteins HSA, GAA and Sod1p were all successfully produced and secreted between 5°C and 40°C, albeit each one presented a different optimal production temperature (15, 40, 5-30°C for HSA, GAA and Sod1p, respectively).

Conclusions

K. marxianus L3 has been identified as a promising and flexible cell factory. In a sole host, the optimization of growth temperatures for the efficient secretion of each individual protein can be carried out over a wide range of temperatures.\n\nThermal adaptability of Kluyveromyces marxianus in recombinant protein production.", "token_count": 460, "char_count": 1759, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5783, "quality_score": 0.7892, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:46.606087", "source": { "split": "train_shard_00001", "doc_id": 1602 }, "chunk_id": "train_shard_00001_1602_0", "global_id": 7911 }, { "text": "Eggerthella lenta is an anaerobic, high GC, Gram-positive bacillus commonly found in the human digestive tract that belongs to the class Coriobacteriia of the phylum Actinobacteria. This species has been of increasing interest as an important player in the metabolism of xenobiotics and dietary compounds. However, little is known regarding its susceptibility to bacteriophage predation and how this may influence its fitness. Here, we report the isolation of seven novel E. lenta strains using cefotaxime and ceftriaxone as selective agents. We conducted comparative and pangenome analyses of these strains and those publicly available to investigate the diversity of prophages associated with this species. Prophage gene products represent a minimum of 5.8% of the E. lenta pangenome, comprising at least ten distantly related prophage clades that display limited homology to currently known bacteriophages. All clades possess genes implicated in virion structure, lysis, lysogeny and, to a limited extent, DNA replication. Some prophages utilise tyrosine recombinases and diversity generating retroelements to generate phase variation among targeted genes. The prophages have differing levels of sensitivity to the CRISPR/cas systems of their hosts, with spacers from 44 E. lenta isolates found to target only five out of the ten identified prophage clades. Furthermore, using a PCR-based approach targeting the prophage attP site, we were able to determine that several of these elements can excise from the host chromosome, thus supporting the notion that these are active prophages. The findings of this study provide further insights into the diversity of prophages infecting species of the phylum Actinobacteria.\n\nSelective Isolation of Eggerthella lenta from Human Faeces and Characterisation of the Species Prophage Diversity.", "token_count": 478, "char_count": 1878, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:47.254074", "source": { "split": "train_shard_00001", "doc_id": 1603 }, "chunk_id": "train_shard_00001_1603_0", "global_id": 7912 }, { "text": "Domestication of cranberry and blueberry began in the United States in the early 1800s and 1900s, respectively, and in part owing to their flavors and health-promoting benefits are now cultivated and consumed worldwide. The industry continues to face a wide variety of production challenges (e.g. disease pressures) as well as a demand for higher-yielding cultivars with improved fruit quality characteristics. Unfortunately, molecular tools to help guide breeding efforts for these species have been relatively limited compared with those for other high-value crops. Here, we describe the construction and analysis of the first pangenome for both blueberry and cranberry. Our analysis of these pangenomes revealed both crops exhibit great genetic diversity, including the presence-absence variation of 48.4% genes in highbush blueberry and 47.0% genes in cranberry. Auxiliary genes, those not shared by all cultivars, are significantly enriched with molecular functions associated with disease resistance and the biosynthesis of specialized metabolites, including compounds previously associated with improving fruit quality traits. The discovery of thousands of genes, not present in the previous reference genomes for blueberry and cranberry, will serve as the basis of future research and as potential targets for future breeding efforts. The pangenome, as a multiple-sequence alignment, as well as individual annotated genomes, are publicly available for analysis on the Genome Database for Vaccinium - a curated and integrated web-based relational database. Lastly, the core-gene predictions from the pangenomes will serve useful to develop a community genotyping platform to guide future molecular breeding efforts across the family.\n\nBlueberry and cranberry pangenomes as a resource for future genetic studies and breeding efforts", "token_count": 394, "char_count": 1838, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:47.870350", "source": { "split": "train_shard_00001", "doc_id": 1604 }, "chunk_id": "train_shard_00001_1604_0", "global_id": 7913 }, { "text": "In 2011, a novel methicillin resistance gene, mecC, was described in human and bovine Staphylococcus aureus isolates. mecC-positive S. aureus is most commonly associated with livestock and wildlife populations across Europe and is particularly prevalent in hedgehogs, but only occasionally causes human infections. In this study, we characterize and investigate the origin of two human S. aureus isolates containing mecC genes from New Zealand. The two isolates were identified from patients with severe invasion infections as part of an S. aureus bacteraemia study. Whole-genome sequencing was used to characterize staphylococcal cassette chromosome mec (SCCmec) elements and perform phylogenetic comparisons with publicly available strains from mecC-associated clonal complexes, including isolates from hedgehogs from New Zealand and Europe/United Kingdom (UK), and livestock, wildlife and human isolates from Europe/UK. The two isolates from our study have almost identical SCCmec type XI elements containing a mecC gene. However, this gene contains a premature stop codon, consistent with the methicillin-susceptible phenotype observed for these isolates. Core genome SNP analyses showed that the two isolates are 234 SNPs apart and are most closely related to an isolate obtained from a New Zealand hedgehog. However, there are considerable differences in the mecC mobile element between the human and hedgehog isolates, indicating the presence of an as-yet-unknown reservoir of mecC S. aureus in the New Zealand environment.\n\nGenomic epidemiology of mecC-carrying Staphylococcus aureus isolates from human clinical cases in New Zealand.", "token_count": 502, "char_count": 1740, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6352, "quality_score": 0.8176, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:48.520271", "source": { "split": "train_shard_00001", "doc_id": 1605 }, "chunk_id": "train_shard_00001_1605_0", "global_id": 7914 }, { "text": "

Background

Bacterial infections pose a global health threat across clinical and community settings. Over the past decade, the alarming expansion of antimicrobial resistance (AMR) has progressively narrowed therapeutic options, particularly for healthcare-associated infections. This critical situation has been formally recognized by the World Health Organization as a major public health concern. Epidemiological studies have demonstrated that the dissemination of AMR is frequently mediated by specific high-risk bacterial lineages, often designated as \"global clones\" or \"clonal complexes.\" Consequently, surveillance of these epidemic clones and elucidation of their pathogenic mechanisms and AMR acquisition pathways have become essential research priorities. The advent of whole genome sequencing has revolutionized these investigations, enabling comprehensive epidemiological tracking and detailed analysis of mobile genetic elements responsible for resistance gene transfer. However, despite the exponential increase in available bacterial genome sequences, significant challenges persist. Current genomic datasets often suffer from uneven representation of clinically relevant strains and inconsistent availability of accompanying metadata. These limitations create substantial obstacles for large-scale comparative studies and hinder effective surveillance efforts.

Description

This database represents a comprehensive genomic analysis of 98,950 Staphylococcus aureus isolates, a high-priority bacterial pathogen of global clinical significance. We provide detailed isolate characterization through several established typing schemes including multilocus sequence typing (MLST), clonal complex (CC) assignments, spa typing results, and core genome MLST (cgMLST) profiles. The dataset also documents the presence of CRISPR-Cas systems in these isolates. Beyond fundamental typing data, our resource incorporates the distribution of antimicrobial resistance determinants, virulence factors, and plasmid replicons. These systematically curated genomic features offer researchers valuable insights into isolate epidemiology, resistance mechanisms, and horizontal gene transfer patterns in this highly concerning pathogen.

Conclusion

This database is freely available under CC BY-NC-SA at https://doi.org/10.5281/zenodo.14833440 . The data provided enables researchers to identify optimal reference isolates for various genomic studies, supporting critical investigations into S", "token_count": 522, "char_count": 2505, "word_count": 297, "semantic_coherence": 1, "information_density": 0.7306, "quality_score": 0.8653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:12:49.178628", "source": { "split": "train_shard_00001", "doc_id": 1606 }, "chunk_id": "train_shard_00001_1606_0", "global_id": 7915 }, { "text": "aureus epidemiology and antimicrobial resistance evolution. This resource will ultimately inform the development of more effective prevention and control measures against this high-priority pathogen.\n\nGenomic typing, antimicrobial resistance gene, virulence factor and plasmid replicon database for the important pathogenic bacteria Staphylococcus aureus.", "token_count": 82, "char_count": 355, "word_count": 42, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:49.546032", "source": { "split": "train_shard_00001", "doc_id": 1606 }, "chunk_id": "train_shard_00001_1606_1", "global_id": 7916 }, { "text": "

Background

Citrobacter species are Gram-negative opportunistic pathogens commonly reported in nosocomial-acquired infections. This study characterised four Citrobacter species that were isolated from surface water in the North West Province, South Africa.

Results

Phenotypic antimicrobial susceptibility profiles of the isolates demonstrated their ability to produce the extended-spectrum β-lactamase (ESBL). Whole genomes were sequenced to profile antibiotic resistance and virulence genes, as well as mobile genetic elements. In silico taxonomic identification was conducted by using multi-locus sequence typing and average nucleotide identity. A pangenome was used to determine the phylogenomic landscape of the Citrobacter species by using 109 publicly available genomes. The strains S21 and S23 were identified as C. braakii, while strains S24 and S25 were C. murliniae and C. portucalensis, respectively. Comparative genomics and sequenced genomes of the ESBL-producing isolates consisted of n = 91; 83% Citrobacter species in which bla-CMY-101 (n = 19; 32,2%) and bla-CMY-59 (n = 12; 38,7%) were prevalent in C. braakii, and C. portucalensis strains, respectively. Macrolide (acrAB-TolC, and mdtG) and aminoglycoside (acrD) efflux pumps genes were identified in the four sequenced Citrobacter spp. isolates. The quinolone resistance gene, qnrB13, was exclusive to the C. portucalensis S25 strain. In silico analysis detected plasmid replicon types IncHI1A, IncP, and Col(VCM04) in C. murliniae S24 and C. portucalensis S25, respectively. These potentially facilitate the T4SS secretion system in Citrobacter species. In this study, the C. braakii genomes could be distinguished from C", "token_count": 529, "char_count": 1728, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8147, "entities": { "genes": [ "VCM04" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:12:50.172911", "source": { "split": "train_shard_00001", "doc_id": 1607 }, "chunk_id": "train_shard_00001_1607_0", "global_id": 7917 }, { "text": "murliniae and C. portucalensis on the basis of gene encoding for cell surface localisation of the CPS (vexC) and identification of genes involved in capsule polymer synthesis (tviB and tviE). A cluster for the salmochelin siderophore system (iro-BCDEN) was found in C. murliniae S24. This is important when it comes to the pathogenicity pathway that confers an advantage in colonisation.

Conclusions

The emerging and genomic landscapes of these ESBL-producing Citrobacter species are of significant concern due to their dissemination potential in freshwater systems. The presence of these ESBL and multidrug-resistant (MDR) pathogens in aquatic environments is of One Health importance, since they potentially impact the clinical domain, that is, in terms of human health and the agricultural domain, that is, in terms of animal health and food production as well as the environmental domain.\n\nThe phylogenomic landscape of extended-spectrum β-lactamase producing Citrobacter species isolated from surface water.", "token_count": 252, "char_count": 1019, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:50.656922", "source": { "split": "train_shard_00001", "doc_id": 1607 }, "chunk_id": "train_shard_00001_1607_1", "global_id": 7918 }, { "text": "Morganella morganii is a Gram-negative, opportunistic pathogen that is often associated with nosocomial infections. Here, the genomic characteristics and antimicrobial resistance (AMR) of Morganella clinical isolates between 2016 and 2023 were determined. A total of 218 clinical isolates were mainly identified from urinary tract (48.2%) and respiratory tract (16.5%), with 105 isolates randomly selected for whole genome sequencing. The highest rates of antibiotic resistance were observed with SAM (68.3%), followed by CIP (39.9%), and SXT (37.2%). Distance analysis suggested that the 105 newly sequenced isolates could be divided into two groups: M. morganii subsp. morganii and M. morganii subsp. sibonii. While, the average nucleotide identity between these groups showed only 91.5-92.2% similarity, raising the possibility that they may be distinct species. Phylogenomic analysis revealed that the 102 M. morganii isolates fell into six clades, with clades 4-6 making up the majority. Core genome multi-locus sequence type analysis indicted high genomic diversity among different hosts and relatively stability (< 10 SNPs accumulated over three years) within the same host. Together with epidemiological data, isolates of four genetic clusters could be possible nosocomial transmissions. The identified 80 AMR genes belonged to 15 drug-related classes, with tet(B) gene being the most prevalent, followed by sul1, catA2, and sul2 genes. This study provided comprehensive genomic insights and AMR patterns of Morganella isolates in China, highlighting the necessity for continuous monitoring through whole genome sequencing.", "token_count": 491, "char_count": 1715, "word_count": 230, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:51.313253", "source": { "split": "train_shard_00001", "doc_id": 1608 }, "chunk_id": "train_shard_00001_1608_0", "global_id": 7919 }, { "text": "Genomic epidemiology and antimicrobial resistance of <i>Morganella</i> clinical isolates between 2016 and 2023.", "token_count": 46, "char_count": 123, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:51.670943", "source": { "split": "train_shard_00001", "doc_id": 1608 }, "chunk_id": "train_shard_00001_1608_1", "global_id": 7920 }, { "text": "Pseudomonas aeruginosa, a harmful nosocomial pathogen associated with cystic fibrosis and burn wounds, encodes for a large number of LysR-type transcriptional regulator proteins. To understand how and why LTTR proteins evolved with such frequency and to establish whether any relationships exist within the distribution we set out to identify the patterns underpinning LTTR distribution in P. aeruginosa and to uncover cluster-based relationships within the pangenome. Comparative genomic studies revealed that in the JGI IMG database alone ~86 000 LTTRs are present across the sequenced genomes (n=699). They are widely distributed across the species, with core LTTRs present in >93 % of the genomes and accessory LTTRs present in <7 %. Analysis showed that subsets of core LTTRs can be classified as either variable (typically specific to P. aeruginosa) or conserved (and found to be distributed in other Pseudomonas species). Extending the analysis to the more extensive Pseudomonas database, PA14 rooted analysis confirmed the diversification patterns and revealed PqsR, the receptor for the Pseudomonas quinolone signal (PQS) and 2-heptyl-4-quinolone (HHQ) quorum-sensing signals, to be amongst the most variable in the dataset. Successful complementation of the PAO1 pqsR - mutant using representative variant pqsR sequences suggests a degree of structural promiscuity within the most variable of LTTRs, several of which play a prominent role in signalling and communication. These findings provide a new insight into the diversification of LTTR proteins within the P. aeruginosa species and suggests a functional significance to the cluster, conservation and distribution patterns identified.\n\nComparative genomics reveals distinct diversification patterns among LysR-type transcriptional regulators in the ESKAPE pathogen Pseudomonas aeruginosa.", "token_count": 502, "char_count": 1927, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [ "PA14", "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:52.321476", "source": { "split": "train_shard_00001", "doc_id": 1609 }, "chunk_id": "train_shard_00001_1609_0", "global_id": 7921 }, { "text": "

ABSTRACT

Fungal pathogens exhibit extensive strain heterogeneity, including variation in virulence. Whether closely related non-pathogenic species also exhibit strain heterogeneity remains unknown. Here, we comprehensively characterized the pathogenic potentials (i.e., the ability to cause morbidity and mortality) of 16 diverse strains of Aspergillus fischeri , a non-pathogenic close relative of the major pathogen Aspergillus fumigatus . In vitro immune response assays and in vivo virulence assays using a mouse model of pulmonary aspergillosis showed that A. fischeri strains varied widely in their pathogenic potential. Furthermore, pangenome analyses suggest that A. fischeri genomic and phenotypic diversity is even greater. Genomic, transcriptomic, and metabolomic profiling identified several pathways and secondary metabolites associated with variation in virulence. Notably, strain virulence was associated with the simultaneous presence of the secondary metabolites hexadehydroastechrome and gliotoxin. We submit that examining the pathogenic potentials of non-pathogenic close relatives is key for understanding the origins of fungal pathogenicity.\n\nStrain heterogeneity in a non-pathogenic fungus highlights factors contributing to virulence", "token_count": 308, "char_count": 1266, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:52.894811", "source": { "split": "train_shard_00001", "doc_id": 1610 }, "chunk_id": "train_shard_00001_1610_0", "global_id": 7922 }, { "text": "

Background

Porphyromonas gingivalis (hereafter \"Pg\") is an oral pathogen that has been hypothesized to act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg. Insights into the factors shaping the striking strain-level variation in Pg, and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. One of the key forces often shaping strain-level diversity in microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg.

Results

Here we systematically addressed the question of whether Pg are infected by phages-and we found that they are. We found that prophages are common in Pg, they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg, and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain-level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures.

Conclusion

This work definitively establishes that phages are a major unrecognized force shaping the ecology and intra-species strain-level diversity of the well-studied oral pathogen Pg", "token_count": 461, "char_count": 1973, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5643, "quality_score": 0.7821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:53.539004", "source": { "split": "train_shard_00001", "doc_id": 1611 }, "chunk_id": "train_shard_00001_1611_0", "global_id": 7923 }, { "text": "The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg, and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly. Video Abstract.\n\nPhages are unrecognized players in the ecology of the oral pathogen Porphyromonas gingivalis.", "token_count": 92, "char_count": 412, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:53.907074", "source": { "split": "train_shard_00001", "doc_id": 1611 }, "chunk_id": "train_shard_00001_1611_1", "global_id": 7924 }, { "text": "This study aimed to select thermotolerant yeast for bioethanol production from cellulose-rich corncob (CRC) residue. An effective yeast strain was identified as Saccharomyces cerevisiae TC-5. Bioethanol production from CRC residue via separate hydrolysis and fermentation (SHF), simultaneous saccharification and fermentation (SSF), and prehydrolysis-SSF (pre-SSF) using this strain were examined at 35-42 °C compared with the use of commercial S. cerevisiae. Temperatures up to 40 °C did not affect ethanol production by TC-5. The ethanol concentration obtained via the commercial S. cerevisiae decreased with increasing temperatures. The highest bioethanol concentrations obtained via SHF, SSF, and pre-SSF at 35-40 °C of strain TC-5 were not significantly different (20.13-21.64 g/L). The SSF process, with the highest ethanol productivity (0.291 g/L/h), was chosen to study the effect of solid loading at 40 °C. A CRC level of 12.5% (w/v) via fed-batch SSF resulted in the highest ethanol concentrations of 38.23 g/L. Thereafter, bioethanol production via fed-batch SSF with 12.5% (w/v) CRC was performed in 5-L bioreactor. The maximum ethanol concentration and ethanol productivity values were 31.96 g/L and 0.222 g/L/h, respectively. The thermotolerant S. cerevisiae TC-5 is promising yeast for bioethanol production under elevated temperatures via SSF and the use of second-generation substrates.", "token_count": 474, "char_count": 1459, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5578, "quality_score": 0.7789, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:54.555413", "source": { "split": "train_shard_00001", "doc_id": 1612 }, "chunk_id": "train_shard_00001_1612_0", "global_id": 7925 }, { "text": "Bioethanol Production from Cellulose-Rich Corncob Residue by the Thermotolerant Saccharomyces cerevisiae TC-5.", "token_count": 44, "char_count": 117, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:54.917521", "source": { "split": "train_shard_00001", "doc_id": 1612 }, "chunk_id": "train_shard_00001_1612_1", "global_id": 7926 }, { "text": "Biofilm formation has been shown to be critical to the success of uropathogens. Although Staphylococcus saprophyticus is a common cause of urinary tract infections, its biofilm production capacity, composition, genetic basis, and origin are poorly understood. We investigated biofilm formation in a large and diverse collection of S. saprophyticus (n = 422). Biofilm matrix composition was assessed in representative strains (n = 63) belonging to two main S. saprophyticus lineages (G and S) recovered from human infection, colonization, and food-related environment using biofilm detachment approach. To identify factors that could be associated with biofilm formation and structure variation, we used a pangenome-wide association study approach. Almost all the isolates (91%; n = 384/422) produced biofilm. Among the 63 representative strains, we identified eight biofilm matrix phenotypes, but the most common were composed of protein or protein-extracellular DNA (eDNA)-polysaccharides (38%, 24/63 each). Biofilms containing protein-eDNA-polysaccharides were linked to lineage G and environmental isolates, whereas protein-based biofilms were produced by lineage S and infection isolates (p < 0.05). Putative biofilm-associated genes, namely, aas, atl, ebpS, uafA, sasF, sasD, sdrH, splE, sdrE, sdrC, sraP, and ica genes, were found with different frequencies (3-100%), but there was no correlation between their presence and biofilm production or matrix types", "token_count": 489, "char_count": 1597, "word_count": 204, "semantic_coherence": 1, "information_density": 0.7206, "quality_score": 0.8603, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:55.592817", "source": { "split": "train_shard_00001", "doc_id": 1613 }, "chunk_id": "train_shard_00001_1613_0", "global_id": 7927 }, { "text": "Notably, icaC_1 was ubiquitous in the collection, while icaR was lineage G-associated, and only four strains carried a complete ica gene cluster (icaADBCR) except one that was without icaR. We provided evidence, using a comparative genomic approach, that the complete icaADBCR cluster was acquired multiple times by S. saprophyticus and originated from other coagulase-negative staphylococci. Overall, the composition of S. saprophyticus biofilms was distinct in environmental and clinical isolates, suggesting that modulation of biofilm structure could be a key step in the pathogenicity of these bacteria. Moreover, biofilm production in S. saprophyticus is ica-independent, and the complete icaADBCR was acquired from other staphylococci.\n\nStaphylococcus saprophyticus From Clinical and Environmental Origins Have Distinct Biofilm Composition.", "token_count": 284, "char_count": 930, "word_count": 114, "semantic_coherence": 1, "information_density": 0.6404, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:56.159486", "source": { "split": "train_shard_00001", "doc_id": 1613 }, "chunk_id": "train_shard_00001_1613_1", "global_id": 7928 }, { "text": "Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low- and middle-income countries. Some children nevertheless remain never or rarely colonized during early life. Understanding how this protection is conferred could be helpful for designing future interventions to protect children's health. Here, we investigated whether differences in gut microbiome development could underlie differential susceptibility to ESBL-E gut colonization over time among children in peri-urban Lima. Weekly stool and daily surveys were collected from 345 children < 3 years old during a 2016-19 study of enteric infections. A subset of children (n = 12) was rarely gut-colonized with ESBL-E from 1-16 months of age. We performed short-read metagenomic sequencing of stool collected at 3, 6, 7, 9, 12, and 16 months from these children and a random subset of 42 frequently colonized children, and characterized differences in their exposures and gut microbiomes. No differences in gut taxa or functional pathways were identified over time, though children harbored differentially abundant taxa, more unique E. coli strains, and a higher abundance of blaCTX-M gene copies at ESBL-E-positive versus negative timepoints. Differing patterns of ESBL-E colonization over time among children in peri-urban Lima do not appear to be related to differences in gut microbiome development.\n\nRole of the gut microbiome in frequent gut colonization with extended-spectrum β lactamase-producing Enterobacterales among Peruvian children.", "token_count": 433, "char_count": 1613, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:56.844461", "source": { "split": "train_shard_00001", "doc_id": 1614 }, "chunk_id": "train_shard_00001_1614_0", "global_id": 7929 }, { "text": "Colonic spirochetosis, diagnosed based on the striking appearance in histological sections, still has an obscure clinical relevance, and only a few bacterial isolates from this condition have been characterized to date. In a randomized, population-based study in Stockholm, Sweden, 745 healthy individuals underwent colonoscopy with biopsy sampling. Of these individuals, 17 (2.3%) had colonic spirochetosis, which was associated with eosinophilic infiltration and a 3-fold-increased risk for irritable bowel syndrome (IBS). We aimed to culture the bacteria and perform whole-genome sequencing of the isolates from this unique representative population sample. From 14 out of 17 individuals with spirochetosis we successfully isolated, cultured, and performed whole-genome sequencing of in total 17 isolates, including the Brachyspira aalborgi type strain, 513A. Also, 16S analysis of the mucosa-associated microbiota was performed in the cases and nonspirochetosis controls. We found one isolate to be of the species Brachyspira pilosicoli; all remaining isolates were of the species Brachyspira aalborgi Besides displaying extensive genetic heterogeneity, the isolates harbored several mucin-degrading enzymes and other virulence-associated genes that could confer a pathogenic potential in the human colon. We also showed that 16S amplicon sequencing using standard primers for human microbiota studies failed to detect Brachyspira due to primer incompatibility.IMPORTANCE This is the first report of whole-genome analysis of clinical isolates from individuals with colonic spirochetosis. This characterization provides new opportunities in understanding the physiology and potentials of these bacteria that densely colonize the gut in the individuals infected", "token_count": 453, "char_count": 1798, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:57.490584", "source": { "split": "train_shard_00001", "doc_id": 1615 }, "chunk_id": "train_shard_00001_1615_0", "global_id": 7930 }, { "text": "The observation that standard 16S amplicon primers fail to detect colonic spirochetosis may have major implications for studies searching for associations between members of the microbiota and clinical conditions such as irritable bowel syndrome (IBS) and should be taken into consideration in project design and interpretation of gastrointestinal tract microbiota in population-based and clinical settings.\n\nIsolates from Colonic Spirochetosis in Humans Show High Genomic Divergence and Potential Pathogenic Features but Are Not Detected Using Standard Primers for the Human Microbiota.", "token_count": 126, "char_count": 587, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7875, "quality_score": 0.8938, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:57.873855", "source": { "split": "train_shard_00001", "doc_id": 1615 }, "chunk_id": "train_shard_00001_1615_1", "global_id": 7931 }, { "text": "The yeast Kluyveromyces marxianus is a potential microbial catalyst for fuel ethanol production from a wide range of biomass substrates. To improve its growth and ethanol yield at elevated temperature under microaerophilic conditions, K. marxianus NRRL Y-1109 was irradiated with UV-C using automated protocols on a robotic platform for picking and spreading irradiated cultures and for processing the resulting plates. The plates were incubated under anaerobic conditions on xylose or glucose for 5 mo at 46 °C. Two K. marxianus mutant strains (designated 7-1 and 8-1) survived and were isolated from the glucose plates. Both mutant strains, but not wild type, grew aerobically on glucose at 47 °C. All strains grew anaerobically at 46 °C on glucose, galactose, galacturonic acid, and pectin; however, only 7-1 grew anaerobically on xylose at 46 °C. Saccharomyces cerevisiae NRRL Y-2403 did not grow at 46 °C on any of these substrates. With glucose as a carbon source, ethanol yield after 3 d at 46 °C was higher for 8-1 than for wild type (0.51 and 0.43 g ethanol/g glucose, respectively). With galacturonic acid as a carbon source, the ethanol yield after 7 d at 46 °C was higher for 7-1 than for wild type (0.48 and 0.34 g ethanol/g galacturonic acid, respectively). These mutant strains have potential application in fuel ethanol production at elevated temperature from sugar constituents of starch, sucrose, pectin, and cellulosic biomass.\n\nAutomated UV-C mutagenesis of Kluyveromyces marxianus NRRL Y-1109 and selection for microaerophilic growth and ethanol production at elevated temperature on biomass sugars.", "token_count": 506, "char_count": 1620, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5059, "quality_score": 0.753, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:58.503338", "source": { "split": "train_shard_00001", "doc_id": 1616 }, "chunk_id": "train_shard_00001_1616_0", "global_id": 7932 }, { "text": "Comparative genomic analysis of Vibrio cholerae El Tor associated with endemic cholera in Asia revealed two distinct lineages, one dominant in Bangladesh and the other in India. An in depth whole genome study of V. cholerae El Tor clinical strains isolated during endemic cholera in Bangladesh (1991 – 2017) included reference genome sequence data obtained online. Core genome phylogeny established using single nucleotide polymorphisms (SNPs) showed V. cholerae El Tor strains comprised two lineages, BD-1 and BD-2, which, according to Bayesian phylodynamic analysis, originated from paraphyletic group BD-0 around 1981. BD-1 and BD-2 lineages overlapped temporally but were negatively associated as causative agents of cholera 2004-2017. Genome wide association study (GWAS) revealed 140 SNPs and 31 indels, resulting in gene alleles unique to BD-1 and BD-2. Regression analysis of root to tip distance and year of isolation indicated early BD-0 strains at the base, whereas BD-1 and BD-2 subsequently emerged and progressed by accumulating SNPs. Pangenome analysis provided evidence of gene acquisition by both BD-1 and BD-2, of which six crucial proteins of known function were predominant in BD-2. BD-1 and BD-2 diverged and have distinctively different genomic traits, namely heterogeneity in VSP-2, VPI-1, mobile elements, toxin encoding elements, and total gene abundance. In addition, the observed phage-inducible chromosomal island-like element (PLE1), and SXT ICE elements (ICE TET ) in BD-2 presumably provided a fitness advantage for the lineage to outcompete BD-1 as the etiological agent of the endemic cholera in Bangladesh, with implications for global cholera epidemiology", "token_count": 468, "char_count": 1690, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [ "PLE1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:59.155015", "source": { "split": "train_shard_00001", "doc_id": 1617 }, "chunk_id": "train_shard_00001_1617_0", "global_id": 7933 }, { "text": "

Importance

Cholera is a global disease with specific reference to the Bay of Bengal Ganges Delta where Vibrio cholerae O1 El Tor, causative agent of the disease showed two circulating lineages, one dominant in Bangladesh and the other in India. Results of in-depth genomic study of V. cholerae associated with endemic cholera during the past 27 years (1991 – 2017) indicate emergence and succession of the two lineages, BD-1 and BD-2, arising from a common ancestral paraphylatic group, BD-0, comprising the early strains and short-term evolution of the bacterium in Bangladesh. Among the two V. cholerae lineages, BD-2 supersedes BD-1 and is predominant in the most recent endemic cholera in Bangladesh. The BD-2 lineage contained significantly more SNPs and indels, and showed richness in gene abundance, including antimicrobial resistance genes, gene cassettes, and PLE to fight against bacteriophage infection, acquired over time. These findings have important epidemic implications at a global scale.\n\nGenomic characteristics of recently recognized Vibrio cholerae El Tor lineages associated with cholera in Bangladesh, 1991-2017", "token_count": 315, "char_count": 1150, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6726, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:12:59.711568", "source": { "split": "train_shard_00001", "doc_id": 1617 }, "chunk_id": "train_shard_00001_1617_1", "global_id": 7934 }, { "text": "Salmonella Dublin (S. Dublin) and Salmonella Typhimurium (S. Typhimurium) are commonly linked to bovine salmonellosis. S. Dublin is, however, considered a bovine-adapted serovar for primarily infecting and thriving in cattle. Using S. Typhimurium (a generalist serovar) as a benchmark, this study investigates genomic factors contributing to S. Dublin's adaptation to cattle hosts in the U.S. A total of 1337 S. Dublin and 787 S. Typhimurium whole-genome sequences from bovine sources were analyzed with CARD (version 4.0.0), ARG-NOTT (version 6), and AMRfinderPlus (version 4.0.3) for antimicrobial resistance (AMR) genes; VFDB and AMRfinderPlus for virulence genes; AMRFinderPlus for stress genes; and Plasmidfinder for plasmids. Existing clonal groups among isolates of the two serovars were also investigated using the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) model. The results revealed minimal genomic variation among S. Dublin isolates. Comparatively, the IncX1 plasmid was somewhat exclusively identified in S. Dublin isolates and each carried an average of four plasmids (p-value < 0.05). Furthermore, S. Dublin isolates exhibited a higher prevalence of AMR genes against key antimicrobials, including aminoglycosides, beta-lactams, tetracyclines, and sulfonamides, commonly used in U.S. cattle production", "token_count": 460, "char_count": 1447, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6865, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:00.356135", "source": { "split": "train_shard_00001", "doc_id": 1618 }, "chunk_id": "train_shard_00001_1618_0", "global_id": 7935 }, { "text": "Additionally, Type VI secretion system genes tssJKLM and hcp2/tssD2, essential for colonization, were found exclusively in S. Dublin isolates with over 50% of these isolates possessing genes that confer resistance to heavy metal stressors, like mercury. These findings suggest that S. Dublin's adaptation to bovine hosts in the U.S. is supported by a conserved genetic makeup enriched with AMR genes, virulence factors, and stress-related genes, enabling it to colonize and persist in the bovine gut.\n\nComparative Genomic Profiles of <i>Salmonella</i> Typhimurium and <i>Salmonella</i> Dublin Bovine Isolates from the U.S. Indicate Possible Factors Associated with the Host Adaptation of <i>Salmonella</i> Dublin in the Region.", "token_count": 252, "char_count": 798, "word_count": 103, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:00.847114", "source": { "split": "train_shard_00001", "doc_id": 1618 }, "chunk_id": "train_shard_00001_1618_1", "global_id": 7936 }, { "text": "Pest control in agriculture employs diverse strategies, among which the use of predatory insects has steadily increased. The use of several species within the genus Orius in pest control is widely spread, particularly in Mediterranean Europe. Commercial mass rearing of predatory insects is costly, and research efforts have concentrated on diet manipulation and selective breeding to reduce costs and improve efficacy. The characterisation and contribution of microbial symbionts to Orius sp. fitness, behaviour, and potential impact on human health has been neglected. This paper provides the first genome sequence level description of the predominant culturable facultative bacterial symbionts associated with five Orius species (O. laevigatus, O. niger, O. pallidicornis, O. majusculus, and O. albidipennis) from several geographical locations. Two types of symbionts were broadly classified as members of the genera Serratia and Leucobacter, while a third constitutes a new genus within the Erwiniaceae. These symbionts were found to colonise all the insect specimens tested, which evidenced an ancestral symbiotic association between these bacteria and the genus Orius. Pangenome analyses of the Serratia sp. isolates offered clues linking Type VI secretion system effector-immunity proteins from the Tai4 sub-family to the symbiotic lifestyle.\n\nComparative Genomics of Facultative Bacterial Symbionts Isolated from European <i>Orius</i> Species Reveals an Ancestral Symbiotic Association.", "token_count": 427, "char_count": 1570, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:01.473551", "source": { "split": "train_shard_00001", "doc_id": 1619 }, "chunk_id": "train_shard_00001_1619_0", "global_id": 7937 }, { "text": "

Objectives

We investigated the epidemiological patterns of carbapenem-resistant, bla KPC-2 harbouring Klebsiella pneumoniae (K. pneumoniae) ST 307 isolates in a tertiary hospital in South Korea between 2019 and 2021 and compared them to isolates collected from 25 hospitals through a nationwide survey, using whole genome sequencing and phylogenetic analysis.

Methods

Whole genome sequences of 25 isolates from hospital GB2 and 45 isolates from 25 other hospitals were analysed for antibiotic resistance gene profiles, virulence gene profiles, plasmid replicons, and phylogenetic relationships.

Results

Core genome single nucleotide polymorphism (cgSNP)-based phylogenetic analysis categorized the 70 isolates into three distinct groups and 13 subgroups, supported by high bootstrap values and low SNP differences. Subgroup 1 comprised the 18 isolates from GB2 collected over 3 years, suggesting long-term persistence and repeated outbreaks within GB2. Region-specific dissemination was indicated by several subgroups containing isolates from different hospitals within the same province. Subgroup 7 comprised isolates from multiple provinces and years, suggesting potential long-distance transmission via patient transfers or community reservoirs. All isolates carried multiple β-lactam resistance genes; bla CTX-M-15 was observed in 67 isolates (89.3%) and the OXA variants in 70 isolates (93.3%)", "token_count": 420, "char_count": 1470, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6885, "quality_score": 0.8443, "entities": { "genes": [ "GB2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:02.098977", "source": { "split": "train_shard_00001", "doc_id": 1620 }, "chunk_id": "train_shard_00001_1620_0", "global_id": 7938 }, { "text": "None of the isolates carried the rmpA/rmpA2 or magA genes, while 58 of the 70 (82.9%) harboured yersiniabactin-encoding genes.

Conclusions

Our findings reveal both clonal persistence within a tertiary hospital and region-specific dissemination of bla KPC-2 producing K. pneumoniae ST307 across South Korea. These results highlight the importance of continuous nationwide surveillance and genomic analysis to implement effective infection control measures to mitigate further dissemination.\n\nClonal dissemination and persistence of Carbapenem-resistant <i>bla</i> <sub>KPC-2</sub> harbouring <i>Klebsiella pneumoniae</i> ST307 in a Tertiary Hospital in the Republic of Korea.", "token_count": 256, "char_count": 756, "word_count": 84, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:02.639639", "source": { "split": "train_shard_00001", "doc_id": 1620 }, "chunk_id": "train_shard_00001_1620_1", "global_id": 7939 }, { "text": "Enterococcus faecium is a frequent causative agent of nosocomial infection mainly acquired from outgoing hospital patients (Hospital Acquired Infection-HAIs). They are largely involved in the outbreaks of bacteremia, UTI, and endocarditis with a high transmissibility rate. The recent emergence of VRE strain (i.e. vancomycin resistant enterococcus) turned it into high priority pathogen for which new drug research is of dire need. Therefore, in current study, pangenome and resistome analyses were performed for available antibiotic-resistant genomes (n = 216) of E. faecium. It resulted in the prediction of around 5,059 genes as an accessory gene, 1,076 genes as core and 1,558 genes made up a unique genome fraction. Core genes common to all strains were further used for the identification of potent drug targets by applying subtractive genomics approach. Moreover, the COG functional analysis showed that these genomes are highly enriched in metabolic pathways such as in translational, ribosomal, proteins, carbohydrates and nucleotide transport metabolism. Through subtractive genomics it was observed that 431 proteins were non-homologous to the human proteome, 166 identified as essential for pathogen survival while 26 as potential and unique therapeutic targets. Finally, 3-dehydroquinate dehydrogenase was proposed as a potent drug target for further therapeutic candidate identification. Moreover, the molecular docking and dynamic simulation technique were applied to performed a virtual screening of natural product libraries (i.e., TCM and Ayurvedic compounds) along with 3-amino-4,5-dihydroxy-cyclohex-1-enecarboxylate (DHS) as a standard compound to validate the study", "token_count": 453, "char_count": 1709, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7021, "quality_score": 0.8511, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:03.278246", "source": { "split": "train_shard_00001", "doc_id": 1621 }, "chunk_id": "train_shard_00001_1621_0", "global_id": 7940 }, { "text": "Consequently, Argeloside I, Apigenin-7-O-gentiobioside (from Ayurvedic library), ZINC85571062, and ZINC85570908 (TCM library) compounds were identified as potential inhibitors of 3-dehydroquinate dehydrogenase. The study proposed new compounds as novel therapeutics, however, further experimental validation is needed as a follow-up.Communicated by Ramaswamy H. Sarma.\n\nPangenome profiling of novel drug target against vancomycin-resistant <i>Enterococcus faecium</i>.", "token_count": 167, "char_count": 487, "word_count": 52, "semantic_coherence": 1, "information_density": 0.9038, "quality_score": 0.9519, "entities": { "genes": [ "ZINC85571062", "ZINC85570908" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:03.715604", "source": { "split": "train_shard_00001", "doc_id": 1621 }, "chunk_id": "train_shard_00001_1621_1", "global_id": 7941 }, { "text": "Probiotics have been widely tested for their effect on mental well-being, albeit with heterogeneous outcomes. Direct and indirect effects through the gut microbiome might lie at the basis of these observations. Here, in a post-hoc analysis, we assessed the effect of 4-week consumption of a probiotic candidate strain on the gut microbiome in students exposed to academic stress. Healthy students were randomized to consume a fermented milk product with Lacticaseibacillus rhamnosus CNCM I-3690 (N = 39) or an acidified non-fermented milk product (N = 40) twice daily for 4 weeks before academic exams. The gut microbiome was analysed by Quantitative Microbiome Profiling based on 16S rRNA gene amplicon and shotgun metagenomic sequencing. Stress and anxiety were assessed using both objective and self-reported markers. Changes of alpha-diversity markers and community shifts from baseline (beta diversity) were lower in L. rhamnosus treated individuals over controls, suggesting lower overall changes of gut microbiota during psychological stress in the Probiotic group. The intake of L. rhamnosus CNCM I-3690 induced differential abundance of some species, such as the maintenance of the quantitative abundance of Ruminococcus bicirculans, and co-varied with species, which differed according to visits (i.e., stress level), suggesting a potential beneficial effect of the strain before the highest increase of stress level. The higher quantitative abundance of F. prausnitzii induced by the probiotic intake was associated with lowered self-reported anxiety levels before the exam. Functional analysis revealed minor changes upon intake of the probiotic strain. Taken together, using a quantitative framework, we found that L. rhamnosus CNCM I-3690 has a potential effect on gut microbiome response to stress, although further studies are needed to better understand the precise interaction.\n\nProbiotic-mediated modulation of gut microbiome in students exposed to academic stress: a randomized controlled trial.", "token_count": 490, "char_count": 2015, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7948, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:04.364834", "source": { "split": "train_shard_00001", "doc_id": 1622 }, "chunk_id": "train_shard_00001_1622_0", "global_id": 7942 }, { "text": "Various carbon sources were evaluated for production of inulinase by yeast, Kluyveromyces marxianus MTCC 3995. Highest inulinase activity was observed with Dahlia extract (25.3 nkat mL(-1)) as carbon source. The enzyme activity was 1.4 folds higher than that observed in media containing pure chicory inulin (17.8 nkat mL(-1)). The yeast showed good growth on a simple medium containing dahlia extract (20% w/v) and yeast extract (2%w/v) as carbon and nitrogen source respectively, in 96 h. at 28°C and 120 rpm. Lowest inulinase yield (4.8 nkat mL(-1)) was seen in the medium containing glucose as C-source. Although varied inulinase levels were noticed on different C- sources, Inulinase: Sucrase (I/S) ratios were noticed to be similar. Among various protein sources tested, yeast extract was found to be the best source followed by beef extract (17.9 nkat mL(-1)) and peptone (13.8 nkat mL(-1)). The enzyme was optimally active at pH (4.0) and 50°C. TLC analysis of end product revealed that inulinase hydrolyzed inulin exclusively into fructose. Results suggest that the dahlia extract induced exoinulinase synthesis in Kluyveromyces marxianus and can be utilized as a potential substrate for inulinase production.\n\nProduction of inulinase from Kluyveromyces marxianus using dahlia tuber extract.", "token_count": 385, "char_count": 1300, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:04.986738", "source": { "split": "train_shard_00001", "doc_id": 1623 }, "chunk_id": "train_shard_00001_1623_0", "global_id": 7943 }, { "text": "The emergence of multidrug-resistant bacteria in agro-environments poses serious risks to public health and ecological balance. In this study, Exiguobacterium sp. E21L, an endophytic strain, was isolated from carrot leaves cultivated in soil amended with sewage treatment plant-derived sludge. The strain exhibited resistance to clinically relevant antibiotics, including beta-lactams, fluoroquinolones, aminoglycosides, and macrolides, with a high Multi-Antibiotic Resistance Index of 0.88. Whole-genome sequencing revealed a genome of 3.06 Mb, encoding 3894 protein-coding genes, including antimicrobial resistance genes (ARGs) such as blaNDM, ermF, tetW, and sul1, along with heavy metal resistance genes (HMRGs) like czcD, copB, and nikA. Genomic islands carrying ARGs and stress-related genes suggested potential horizontal gene transfer. The strain demonstrated robust biofilm formation, high cell hydrophobicity (> 80%), and significant auto-aggregation (90% at 48 h), correlating with genes associated with motility, quorum sensing, and stress adaptation. Notably, phenotypic assays confirmed survival under simulated gastrointestinal conditions, emphasizing its resilience in host-associated environments. Comparative genomics positioned Exiguobacterium sp. E21L near Exiguobacterium chiriqhucha RW-2, with a core genome of 2716 conserved genes. Functional annotations revealed genes involved in xenobiotic degradation, multidrug efflux pumps, and ABC-type transporters, indicating versatile resistance mechanisms and metabolic capabilities. The presence of ARGs, HMRGs, and MGEs (mobile genetic elements) highlights the potential role of Exiguobacterium sp. E21L as a reservoir for resistance determinants in agricultural ecosystems. These findings emphasized the need for stringent regulations on sludge-based fertilizers and advanced sludge treatment strategies to mitigate AMR risks in agro-environments.", "token_count": 511, "char_count": 1917, "word_count": 241, "semantic_coherence": 1, "information_density": 0.7469, "quality_score": 0.8734, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:05.638343", "source": { "split": "train_shard_00001", "doc_id": 1624 }, "chunk_id": "train_shard_00001_1624_0", "global_id": 7944 }, { "text": "Sludge amended soil induced multidrug and heavy metal resistance in endophytic Exiguobacterium sp. E21L: genomics evidences", "token_count": 35, "char_count": 123, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:05.999804", "source": { "split": "train_shard_00001", "doc_id": 1624 }, "chunk_id": "train_shard_00001_1624_1", "global_id": 7945 }, { "text": "Ravenia spectabilis Engl. belongs to the family Rutaceae is known to possess several biologically active phytomolecules. This study was planned to investigate the chemical composition and antimicrobial activity of the leaf essential oil of R. spectabilis. The hydrodistillation of fresh leaves of R. spectabilis gave 0.19 ± 0.02% essential oil. The resulting essential oil was analysed by gas chromatography-flame ionization detector (GC-FID) and gas chromatography-mass spectrometry (GC-MS). Altogether, thirty-one constituents forming 97.6 ± 1.72% of the total oil composition were identified. Major components of the oil were sabinene (60.8 ± 0.36%), α-pinene (5.4 ± 0.30%), myrcene (4.8 ± 0.25%), δ-3-carene (4.7 ± 0.62%) and β-pinene (4.3 ± 0.17%). The in-vitro antimicrobial potential of the oil was examined against eight human pathogenic bacterial and fungal strains. The essential oil showed significant activity against Staphylococcus aureus, Staphylococcus epidermidis, methicillin-resistant Staphylococcus aureus, methicillin-resistant Staphylococcus epidermidis, Candida albicans, and Candida kefyr. This is the first report on R. spectabilis leaf essential oil composition and its antimicrobial activity. The essential oil could be a promising natural source of sabinene and antimicrobial for developing new phytotherapeutics.", "token_count": 517, "char_count": 1438, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:06.629465", "source": { "split": "train_shard_00001", "doc_id": 1625 }, "chunk_id": "train_shard_00001_1625_0", "global_id": 7946 }, { "text": "Chemical composition and antimicrobial activity of the leaf essential oil of Ravenia spectabilis Engl. (Rutaceae).", "token_count": 36, "char_count": 121, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:07.010410", "source": { "split": "train_shard_00001", "doc_id": 1625 }, "chunk_id": "train_shard_00001_1625_1", "global_id": 7947 }, { "text": "Introduction. Commensal Neisseria spp. are highly prevalent in the oropharynx as part of the healthy microbiome. N. meningitidis can colonise the oropharynx too from where it can cause invasive meningococcal disease. To identify N. meningitidis, clinical microbiology laboratories often rely on Matrix Assisted Laser Desorption/Ionisation Time of Flight Mass Spectrometry (MALDI-TOF MS).Hypothesis/Gap statement. N. meningitidis may be misidentified by MALDI-TOF MS.Aim. To conduct genomic surveillance of oropharyngeal Neisseria spp. in order to: (i) verify MALDI-TOF MS species identification, and (ii) characterize commensal Neisseria spp. genomes.Methodology. We analysed whole genome sequence (WGS) data from 119 Neisseria spp. isolates from a surveillance programme for oropharyngeal Neisseria spp. in Belgium. Different species identification methods were compared: (i) MALDI-TOF MS, (ii) Ribosomal Multilocus Sequence Typing (rMLST) and (iii) rplF gene species identification. WGS data were used to further characterize Neisseria species found with supplementary analyses of Neisseria cinerea genomes.Results. Based on genomic species identification, isolates from the oropharyngeal Neisseria surveilence study were composed of the following species: N. meningitidis (n=23), N. subflava (n=61), N. mucosa (n=15), N", "token_count": 526, "char_count": 1486, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:07.652207", "source": { "split": "train_shard_00001", "doc_id": 1626 }, "chunk_id": "train_shard_00001_1626_0", "global_id": 7948 }, { "text": "oralis (n=8), N. cinerea (n=5), N. elongata (n=3), N. lactamica (n=2), N. bacilliformis (n=1) and N. polysaccharea (n=1). Of these 119 isolates, four isolates identified as N. meningitidis (n=3) and N. subflava (n=1) by MALDI-TOF MS, were determined to be N. polysaccharea (n=1), N. cinerea (n=2) and N. mucosa (n=1) by rMLST. Phylogenetic analyses revealed that N. cinerea isolates from the general population (n=3, cluster one) were distinct from those obtained from men who have sex with men (MSM, n=2, cluster two). The latter contained genomes misidentified as N. meningitidis using MALDI-TOF MS. These two N. cinerea clusters persisted after the inclusion of published N. cinerea WGS (n=42). Both N. cinerea clusters were further defined through pangenome and Average Nucleotide Identity (ANI) analyses.Conclusion. This study provides insights into the importance of genomic genus-wide Neisseria surveillance studies to improve the characterization and identification of the Neisseria genus.", "token_count": 504, "char_count": 1232, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6712, "quality_score": 0.8356, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:08.335622", "source": { "split": "train_shard_00001", "doc_id": 1626 }, "chunk_id": "train_shard_00001_1626_1", "global_id": 7949 }, { "text": "Genomic oropharyngeal Neisseria surveillance detects MALDI-TOF MS species misidentifications and reveals a novel Neisseria cinerea clade.", "token_count": 52, "char_count": 151, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:08.728441", "source": { "split": "train_shard_00001", "doc_id": 1626 }, "chunk_id": "train_shard_00001_1626_2", "global_id": 7950 }, { "text": "Thermotolerant inulin-utilizing yeast strains are desirable for ethanol production from Jerusalem artichoke tubers by consolidated bioprocessing (CBP). To obtain such strains, 21 naturally occurring yeast strains isolated by using an enrichment method and 65 previously isolated Saccharomyces cerevisiae strains were investigated in inulin utilization, extracellular inulinase activity, and ethanol fermentation from inulin and Jerusalem artichoke tuber flour at 40 °C. The strains Kluyveromyces marxianus PT-1 (CGMCC AS2.4515) and S. cerevisiae JZ1C (CGMCC AS2.3878) presented the highest extracellular inulinase activity and ethanol yield in this study. The highest ethanol concentration in Jerusalem artichoke tuber flour fermentation (200 g L(-1)) at 40 °C achieved by K. marxianus PT-1 and S. cerevisiae JZ1C was 73.6 and 65.2 g L(-1), which corresponded to the theoretical ethanol yield of 90.0 and 79.7 %, respectively. In the range of 30 to 40 °C, temperature did not have a significant effect on ethanol production for both strains. This study displayed the distinctive superiority of K. marxianus PT-1 and S. cerevisiae JZ1C in the thermotolerance and utilization of inulin-type oligosaccharides reserved in Jerusalem artichoke tubers. It is proposed that both K. marxianus and S. cerevisiae have considerable potential in ethanol production from Jerusalem artichoke tubers by a high temperature CBP.\n\nThermotolerant Kluyveromyces marxianus and Saccharomyces cerevisiae strains representing potentials for bioethanol production from Jerusalem artichoke by consolidated bioprocessing.", "token_count": 478, "char_count": 1593, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5318, "quality_score": 0.7659, "entities": { "genes": [ "AS2", "JZ1C" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:09.382002", "source": { "split": "train_shard_00001", "doc_id": 1627 }, "chunk_id": "train_shard_00001_1627_0", "global_id": 7951 }, { "text": "

Background

Listeria monocytogenes is a foodborne pathogen that can lead to severe pregnancy outcomes. This study reports the clinical and genomic characteristics of a Listeria-mediated stillbirth identified in January 2022 through the Child Health and Mortality Prevention Surveillance (CHAMPS) project in Bangladesh. The Lm-BD-CHAMPS-01 isolate was recovered from the blood and cerebrospinal fluid (CSF) of a male stillborn. Maternal history, clinical, and demographic data were collected by the CHAMPS surveillance platform. An expert panel evaluated all reports to determine the role of L. monocytogenes infection in the causal chain of stillbirth. Genomic characterization included multilocus sequence typing (MLST), core genome MLST (cgMLST), serotyping, and the presence or absence of virulence genes. Genetic divergence and phylogenetic analyses were conducted to determine the relationship with other reported isolates globally.

Results

The isolate Lm-BD-CHAMPS-01 was identified as a novel cgMLST CT11424. It belonged to ST 308, Serotype 4b, Clonal Complex 1, and Phylogenetic Lineage 1. Key L. monocytogenes virulence genes facilitating the crossing of the placental barrier, including full-length inlA, LIPI-1, and LIPI-3, were detected. The isolate was closely related to clinical L. monocytogenes isolates, as determined by GrapeTree based on cgMLST. SNP-based phylogenetic analysis found Lm-BD-CHAMPS-01 to be the most distant from other CC1 isolates in the database. Possible sources of infection included the consumption of contaminated raw vegetables or exposure to pigeons.

Conclusions

This is the first genome sequence of clinical L. monocytogenes from Bangladesh, which also caused stillbirth. Rural healthcare professionals should be aware of L. monocytogenes infection risks during pregnancy", "token_count": 494, "char_count": 1835, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6504, "quality_score": 0.8252, "entities": { "genes": [ "CT11424", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:10.036503", "source": { "split": "train_shard_00001", "doc_id": 1628 }, "chunk_id": "train_shard_00001_1628_0", "global_id": 7952 }, { "text": "Pregnant women should be counseled on the dangers of exposure to animals or birds and consumption of potentially contaminated raw food to prevent adverse pregnancy outcomes due to L. monocytogenes infection.\n\nA novel virulent core genome multilocus sequence type CT 11424 of Listeria monocytogenes isolate causing stillbirth in Bangladesh.", "token_count": 84, "char_count": 339, "word_count": 49, "semantic_coherence": 1, "information_density": 0.898, "quality_score": 0.949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:10.408004", "source": { "split": "train_shard_00001", "doc_id": 1628 }, "chunk_id": "train_shard_00001_1628_1", "global_id": 7953 }, { "text": "Bacteriocins are antimicrobial peptides produced by different species of bacteria, especially the Gram-positive lactic acid bacteria (LAB). Pediococcus pentosaceus is widely applied in the industry and stands out as Bacteriocin-Like Inhibitory Substances (BLIS) producer known to inhibit pathogens commonly considered a concern in the food industries. This study aimed to perform in silico comparisons of P. pentosaceus genomes available in the public GenBank database focusing on their pediocin-like bacteriocins repertoire. The pan-genome analysis evidenced a temporal signal in the pattern of gene gain and loss, supporting the hypothesis that the complete genetic repertoire of this group of bacteria is still uncovered. Thirteen bacteriocin genes from Class II and III were predicted in the accessory genome. Four pediocin-like bacteriocins (54% of the detected bacteriocin repertoire) and their accompanying immunity genes are highlighted; penocin A, coagulin A, pediocin PA-1, and plantaricin 423. Additionally, in silico, modeling of the pediocin-like bacteriocins revealed different configurations of the helix motif compared to other physically determined pediocin-like structures. Comparative and phylogenomic analyses support the hypothesis that a dynamic mechanism of bacteriocin acquisition and purging is not dependent on the bacterial isolation source origin. Synteny analysis revealed that while coagulin A, pediocin PA-1, and Plantaricin 423 loci are associated with insertion sequences mainly from the IS30 family and are likely of plasmid origin, penocin A lies in a conserved chromosomal locus. The results presented here provide insights into the unique pediocin-like bacteriocin peptide fold, genomic diversity, and the evolution of the bacteriocin genetic repertoire of P. pentosaceus, shedding new insights into the role of these biomolecules for application in inhibiting bacterial pathogens, and suggesting that prospecting and sequencing new strains is still an alternative to mining for new probiotic compounds.", "token_count": 519, "char_count": 2082, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6325, "quality_score": 0.8163, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:11.037429", "source": { "split": "train_shard_00001", "doc_id": 1629 }, "chunk_id": "train_shard_00001_1629_0", "global_id": 7954 }, { "text": "Pan-genomic and comparative analysis of Pediococcus pentosaceus focused on the in silico assessment of pediocin-like bacteriocins.", "token_count": 47, "char_count": 144, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:11.409583", "source": { "split": "train_shard_00001", "doc_id": 1629 }, "chunk_id": "train_shard_00001_1629_1", "global_id": 7955 }, { "text": "Conversion of lactose into ethyl acetate by Kluyveromyces marxianus allows economic reuse of whey-borne sugar. The high volatility of ethyl acetate enables its process-integrated recovery by stripping. This stripping is governed by both the aeration rate and the partition coefficient, K EA,L/G. Cultivation at elevated temperatures should decrease the K EA,L/G value and thus favor stripping. K. marxianus DSM 5422 as a potent producer of ethyl acetate was cultivated aerobically in whey-borne media for studying temperature-dependent growth and ester formation. Shake flask cultivation proved thermal tolerance of this yeast growing from 7 to 47 °C with a maximum rate of 0.75 h(-1) at 40 °C. The biomass yield was 0.41 g/g at moderate temperatures while low and high temperatures caused distinct drops. The observed μ-T and Y X/S-T dependencies were described by mathematical models. Further cultivations were done in an 1-L stirred reactor for exploring the effect of temperature on ester synthesis. Cultivation at 32 °C caused significant ester formation (Y EA/S = 0.197 g/g) while cultivation at 42 °C suppressed ester synthesis (Y EA/S = 0.002 g/g). The high temperature affected metal dissolution from the bioreactor delivering iron for yeast growth and preventing ester synthesis. Cultivation at 32 °C with a switch to 42 °C at the onset of ester synthesis allowed quick and efficient ester production (Y EA/S = 0.289 g/g). The high temperature lowered the K EA,L/G value from 78 to 44 L/L which heightened the gas-phase ester concentration (favoring ester recovery) without increasing the liquid-phase concentration (avoiding product inhibition).\n\nGrowth of Kluyveromyces marxianus and formation of ethyl acetate depending on temperature.", "token_count": 493, "char_count": 1748, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7943, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:12.055079", "source": { "split": "train_shard_00001", "doc_id": 1630 }, "chunk_id": "train_shard_00001_1630_0", "global_id": 7956 }, { "text": "Clostridioides difficile PCR ribotype (RT) 002 is the second most prevalent RT in the Netherlands. In 2019, an increase in Clostridioides difficile infections (CDIs) due to clonal RT002 strains was reported in Ireland. In retrospect, a significant increase in the proportion of CDI due to RT002 was detected in the Netherlands between May 2017 and May 2018 (11.9% of 683 cases vs 6.5% of 865 in the previous year). Our aim was to analyze and characterize CDI due to RT002 over time and to assess whether RT002 isolates in the Netherlands were related to the Irish RT002 isolates.During the period from May 2009 to April 2021, Dutch patients with CDI due to RT002 showed less severe CDI (22%) in comparison with hypervirulent RTs (RT027, 29%, and RT078, 25%), similar to grouped data from other non-hypervirulent ribotypes (21%). However, RT002-associated CDI prior to the increased proportion (2009-2017) showed CDI severity similar to CDI associated with hypervirulent types, whereas this was no longer the case after the increase (2017-2021). Using core genome multi-locus sequence typing (cgMLST), Dutch isolates were found not to be related to the Irish outbreak strain. Several Dutch strains clustered together without an evident epidemiological link, suggesting recent emergence. We conclude that the increase of RT002 in Ireland and the Netherlands does not represent clonal spread but is more likely associated with clinical, epidemiological, or treatment changes.IMPORTANCEClostridioides difficile is a significant cause of hospital-associated infections, making it relevant to understand the emergence and spread of different ribotypes. This study highlights a rise in cases of PCR RT002 in the Netherlands, suggesting changes in its prevalence", "token_count": 499, "char_count": 1775, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5865, "quality_score": 0.7932, "entities": { "genes": [ "RT078", "RT002", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:12.711183", "source": { "split": "train_shard_00001", "doc_id": 1631 }, "chunk_id": "train_shard_00001_1631_0", "global_id": 7957 }, { "text": "Despite the increase in RT002 infections, the severity of disease appears to have decreased and is lower compared to more virulent ribotypes. Further research is needed to understand the factors driving this change. Additionally, this study underscores some limitations of cgMLST. cgMLST is valuable for identifying genetic relationships. However, it cannot always distinguish between widespread, recently emerged strains and local transmission chains, making it challenging to determine the exact sources of infection. Continued surveillance and genetic characterization of C. difficile are essential to better understand these trends and improve control measures.\n\nIncrease of <i>Clostridioides difficile</i> PCR ribotype 002 infection with decreased disease severity in hospitalized patients in the Netherlands.", "token_count": 182, "char_count": 833, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7523, "quality_score": 0.8761, "entities": { "genes": [ "RT002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:13.147435", "source": { "split": "train_shard_00001", "doc_id": 1631 }, "chunk_id": "train_shard_00001_1631_1", "global_id": 7958 }, { "text": "Staphylococcus pseudintermedius is a major bacterial colonizer and opportunistic pathogen in dogs. Methicillin-resistant S. pseudintermedius (MRSP) continues to emerge as a significant challenge to maintaining canine health. We sought to determine the phylogenetic relationships of S. pseudintermedius across five states in the New England region of the United States and place them in a global context. The New England dataset consisted of 125 previously published S. pseudintermedius genomes supplemented with 45 newly sequenced isolates. The core genome phylogenetic tree revealed many deep branching lineages consisting of 142 multi-locus sequence types (STs). In silico detection of the mecA gene revealed 40 MRSP and 130 methicillin-susceptible S. pseudintermedius (MSSP) isolates. MRSP were derived from five structural types of SCCmec, the mobile genetic element that carries the mecA gene conferring methicillin resistance. Although many genomes were MSSP, they nevertheless harbored genes conferring resistance to many other antibiotic classes, including aminoglycosides, macrolides, tetracyclines and penams. We compared the New England genomes to 297 previously published genomes sampled from five other states in the United States and 13 other countries. Despite the prevalence of the clonally expanding ST71 found worldwide and in other parts of the United States, we did not detect it in New England. We next sought to interrogate the combined New England and global datasets for the presence of coincident gene pairs linked to antibiotic resistance. Analysis revealed a large co-circulating accessory gene cluster, which included mecA as well as eight other resistance genes [aac (6')-Ie-aph (2″)-Ia, aad (6), aph (3')-IIIa, sat4, ermB, cat, blaZ, and tetM]", "token_count": 524, "char_count": 1857, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6078, "quality_score": 0.8039, "entities": { "genes": [ "ST71" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:13.774950", "source": { "split": "train_shard_00001", "doc_id": 1632 }, "chunk_id": "train_shard_00001_1632_0", "global_id": 7959 }, { "text": "Furthermore, MRSP isolates carried significantly more accessory genes than their MSSP counterparts. Our results provide important insights to the evolution and geographic spread of high-risk clones that can threaten the health of our canine companions.\n\nAccessory Genome Dynamics of Local and Global Staphylococcus pseudintermedius Populations.", "token_count": 82, "char_count": 351, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:14.148546", "source": { "split": "train_shard_00001", "doc_id": 1632 }, "chunk_id": "train_shard_00001_1632_1", "global_id": 7960 }, { "text": "Pseudomonas syringae pv. actinidiae (Psa) is the causal agent of the bacterial canker of kiwifruit, affecting the kiwifruit cultivation worldwide. Due to its large spread and detrimental effects on kiwi production, this pathogen has been extensively studied and it is currently divided into five different biovars. Taking advantages of the recent possibility to compare whole genome sequences instead of few targeted genetic markers, here we provide the first comparative genome analysis of 153 Psa genome sequences available in the NBCI public database. The results of this pangenome analysis, beside supporting previous phylogenetic characterisations, provides new details about the pathogenicity features of the different biovars.\n\nA Genome-wide comparative analysis to characterise the phylogenetic relationship and the pathogenicity of Pseudomonas syringae pv. actinidiae strains", "token_count": 211, "char_count": 884, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7049, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:14.612057", "source": { "split": "train_shard_00001", "doc_id": 1633 }, "chunk_id": "train_shard_00001_1633_0", "global_id": 7961 }, { "text": "Suspended and immobilized cocultures of the thermotolerant yeast, Kluyveromyces marxianus DMKU 3-1042 and the mesophilic flocculent yeast, Saccharomyces cerevisiae M30 were studied for their abilities to improve production and stability of ethanol fermentation. Sugarcane juice and blackstrap molasses, at initial sugar concentrations of 220 g/L, were used as carbon sources. The results indicated that the coculture system could improve ethanol production from both sugarcane juice and blackstrap molasses when the operating temperature ranged between 33 °C and 45 °C. High temperature tolerances were achieved when the coculture was immobilized. The immobilized coculture was more effective in high-temperature ethanol fermentation than the suspended cultures. The coculture immobilized on thin-shell silk cocoon and fermented at 37 °C and 40 °C generated maximal ethanol concentrations of 81.4 and 77.3 g/L, respectively, which were 5.9-8.7% and 16.8-39.0% higher than those of the suspended cultures, respectively.\n\nHigh-temperature ethanol fermentation by immobilized coculture of Kluyveromyces marxianus and Saccharomyces cerevisiae.", "token_count": 322, "char_count": 1139, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6078, "quality_score": 0.8039, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:15.179136", "source": { "split": "train_shard_00001", "doc_id": 1634 }, "chunk_id": "train_shard_00001_1634_0", "global_id": 7962 }, { "text": "

Background

Pseudomonas aeruginosa is an important opportunistic pathogen responsible for many infections in hospitalized and immunocompromised patients. Previous reports estimated that approximately 10% of its 6.6 Mbp genome varies from strain to strain and is therefore referred to as \"accessory genome\". Elements within the accessory genome of P. aeruginosa have been associated with differences in virulence and antibiotic resistance. As whole genome sequencing of bacterial strains becomes more widespread and cost-effective, methods to quickly and reliably identify accessory genomic elements in newly sequenced P. aeruginosa genomes will be needed.

Results

We developed a bioinformatic method for identifying the accessory genome of P. aeruginosa. First, the core genome was determined based on sequence conserved among the completed genomes of twelve reference strains using Spine, a software program developed for this purpose. The core genome was 5.84 Mbp in size and contained 5,316 coding sequences. We then developed an in silico genome subtraction program named AGEnt to filter out core genomic sequences from P. aeruginosa whole genomes to identify accessory genomic sequences of these reference strains. This analysis determined that the accessory genome of P. aeruginosa ranged from 6.9-18.0% of the total genome, was enriched for genes associated with mobile elements, and was comprised of a majority of genes with unknown or unclear function. Using these genomes, we showed that AGEnt performed well compared to other publically available programs designed to detect accessory genomic elements. We then demonstrated the utility of the AGEnt program by applying it to the draft genomes of two previously unsequenced P. aeruginosa strains, PA99 and PA103.

Conclusions

The P. aeruginosa genome is rich in accessory genetic material. The AGEnt program accurately identified the accessory genomes of newly sequenced P. aeruginosa strains, even when draft genomes were used. As P. aeruginosa genomes become available at an increasingly rapid pace, this program will be useful in cataloging the expanding accessory genome of this bacterium and in discerning correlations between phenotype and accessory genome makeup", "token_count": 523, "char_count": 2249, "word_count": 320, "semantic_coherence": 1, "information_density": 0.5344, "quality_score": 0.7672, "entities": { "genes": [ "PA103", "PA99" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:15.835305", "source": { "split": "train_shard_00001", "doc_id": 1635 }, "chunk_id": "train_shard_00001_1635_0", "global_id": 7963 }, { "text": "The combination of Spine and AGEnt should be useful in defining the accessory genomes of other bacterial species as well.\n\nCharacterization of the core and accessory genomes of Pseudomonas aeruginosa using bioinformatic tools Spine and AGEnt.", "token_count": 59, "char_count": 242, "word_count": 36, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:16.196230", "source": { "split": "train_shard_00001", "doc_id": 1635 }, "chunk_id": "train_shard_00001_1635_1", "global_id": 7964 }, { "text": "

Motivation

Pangenomics alignment has emerged as an opportunity to reduce bias in biomedical research. Traditionally, short read aligners—such as Bowtie and BWA—were used to index a single reference genome, which was then used to find approximate alignments of reads to that genome. Unfortunately, these methods can only index a small number of genomes due to the linear-memory requirement of the algorithms used to construct the index. Although there are a couple of emerging pangenome aligners that can index a larger number of genomes more algorithmic progress is needed to build an index for all available data.

Results

Emerging pangenomic methods include VG, Giraffe, and Moni, where the first two methods build an index a variation graph from the multiple alignment of the sequences, and Moni simply indexes all the sequences in a manner that takes the repetition of the sequences into account. Moni uses a preprocessing technique called prefix-free parsing to build a dictionary and parse from the input—these, in turn, are used to build the main run-length encoded BWT, and suffix array of the input. This is accomplished in linear space in the size of the dictionary and parse. Therein lies the open problem that we tackle in this paper. Although the dictionary scales nicely (sub-linear) with the size of the input, the parse becomes orders of magnitude larger than the dictionary. To scale the construction of Moni, we need to remove the parse from the construction of the RLBWT and suffix array. We accomplish this, in this paper by applying prefix-free parsing recursively on the parse. Although conceptually simple, this leads to an algorithmic challenge of constructing the RLBWT and suffix array without access to the parse. We solve this problem, implement it, and demonstrate that this improves the construction time by a factor of 8.9 the running time and by a factor of 2.7 the memory required.

Availability

Our implementation is open source and available at https://github.com/marco-oliva/r-pfbwt .

Contact

Marco Oliva at marco.oliva@ufl.edu\n\nBuilding a Pangenome Alignment Index via Recursive Prefix-Free Parsing", "token_count": 509, "char_count": 2169, "word_count": 335, "semantic_coherence": 1, "information_density": 0.5373, "quality_score": 0.7687, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:16.829425", "source": { "split": "train_shard_00001", "doc_id": 1636 }, "chunk_id": "train_shard_00001_1636_0", "global_id": 7965 }, { "text": "

Background

Clinically important lineages in Klebsiella , especially those expressing multi-drug resistance (MDR), pose severe threats to public health worldwide. They arose from the co-evolution of the vertically inherited core genome and horizontal gene transfers by plasmids, which has not been systematically explored.

Results

We designed KleTy, which consists of dedicated typing schemes for both the core genome and plasmids in Klebsiella . We demonstrated the superior performance of KleTy over many state-of-the-art pipelines using both simulated and real data. We used both schemes to genotype 33,272 Klebsiella genomes, categorising them into 1,773 distinct populations and predicting the presence of 87,410 plasmids from 837 clusters (PCs). Notably, Klebsiella is the center of the plasmid-exchange network within Enterobacteriaceae. Our results associated the international emergence of prevalent Klebsiella populations with only four carbapenem-resistance (CR) PCs, two hypervirulent PCs, and two hvCR-PCs encoding both carbapenemase and hypervirulence. Furthermore, we observed the ongoing international emergence of bla NDM , accompanied by the replacement of the previously dominant population, bla KPC -encoding HC1360_8 (CC258), during 2003-2018, with the emerging bla NDM -encoding HC1360_3 (CC147) thereafter. Additionally, expansions of carbapenem-resistant Klebsiella pneumoniae (hvCRKP) were evidenced in both populations, driven by plasmids of MDR-hypervirulence convergences.

Conclusions

The study illuminates how the global genetic landscape of Klebsiella has been shaped by the co-evolution of both the core genome and the plasmids, underscoring the importance of surveillance and control of the dissemination of plasmids for curtailing the emergence of hvCRKPs.", "token_count": 497, "char_count": 1815, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8174, "entities": { "genes": [ "CC258", "CC147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:17.497132", "source": { "split": "train_shard_00001", "doc_id": 1637 }, "chunk_id": "train_shard_00001_1637_0", "global_id": 7966 }, { "text": "KleTy: integrated typing scheme for core genome and plasmids reveals repeated emergence of multi-drug resistant epidemic lineages in Klebsiella worldwide", "token_count": 35, "char_count": 153, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:17.853842", "source": { "split": "train_shard_00001", "doc_id": 1637 }, "chunk_id": "train_shard_00001_1637_1", "global_id": 7967 }, { "text": "Kluyveromyces marxianus NBRC1777 was identified as a thermotolerant yeast and was developed as a host for the expression of thermostable cellulase genes. The previously isolated genes for thermostable endo-beta-1,4-glucanase, cellobiohydrolase, and beta-glucosidase were introduced into the chromosome of K. marxianus and successfully expressed under the control of high-expression promoters. The recombinant K. marxianus expressing cellulase genes became able to grow in synthetic medium containing cellobiose or carboxymethyl-cellulose as the single carbon source. Moreover, the recombinant strain produced 43.4 g/L ethanol from 10% cellobiose. These results suggest that K. marxianus may afford a useful host system, which may be applicable to the simultaneous saccharification and fermentation and the foundation of cellulose consolidated bioprocessing.\n\nConstruction of thermotolerant yeast expressing thermostable cellulase genes.", "token_count": 250, "char_count": 936, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "NBRC1777" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:18.342193", "source": { "split": "train_shard_00001", "doc_id": 1638 }, "chunk_id": "train_shard_00001_1638_0", "global_id": 7968 }, { "text": "The availability and cost of fishmeal constitute a bottleneck in Atlantic salmon production expansion. Fishmeal is produced from wild fish species and constitutes the major feed ingredient in carnivorous species such as the Atlantic salmon. These natural stocks are at risk of depletion and it is therefore of major importance to find alternative protein sources that meet the nutritional requirements of the Atlantic salmon, without compromising the animals' health. Terrestrial animal by-products have been used in aquaculture feed, but their use is limited by the lack of several essential amino acids and consumer acceptance. In the case of plant ingredients, it is necessary to take into account both their concentration and the extraction methodologies, since, if not dosed correctly, they can cause macro- and microscopic alterations of the structure of the gastrointestinal tract and can also negatively modulate the microbiota composition. These alterations may compromise the digestive functions, growth of the animal, and, ultimately, its well-being. An updated revision of alternative protein sources is provided, with the respective impact on the intestine health in terms of both morphology and microbiota composition. Such information may constitute the premise for the choice and development of Atlantic salmon feeds that guarantee fish health and growth performance without having a significant impact on the surrounding environment, both in terms of depletion of the fish's natural stocks and in terms of pressure on the terrestrial agriculture. The sustainability of aquaculture should be a priority when choosing next-generation ingredients.\n\nHow Do Alternative Protein Resources Affect the Intestine Morphology and Microbiota of Atlantic Salmon?", "token_count": 358, "char_count": 1766, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:18.926944", "source": { "split": "train_shard_00001", "doc_id": 1639 }, "chunk_id": "train_shard_00001_1639_0", "global_id": 7969 }, { "text": "Nematodes of the genus Steinernema and their Xenorhabdus bacterial symbionts are lethal entomopathogens that are useful in the biocontrol of insect pests, as sources of diverse natural products, and as research models for mutualism and parasitism. Xenorhabdus play a central role in all aspects of the Steinernema lifecycle, and a deeper understanding of their genomes therefore has the potential to spur advances in each of these applications. Here, we report a comparative genomics analysis of Xenorhabdus griffiniae , including the symbiont of Steinernema hermaphroditum nematodes, for which genetic and genomic tools are being developed. We sequenced and assembled circularized genomes for three Xenorhabdus strains: HGB2511, ID10 and TH1. We then determined their relationships to other Xenorhabdus and delineated their species via phylogenomic analyses, concluding that HGB2511 and ID10 are Xenorhabdus griffiniae while TH1 is a novel species. These additions to the existing X. griffiniae landscape further allowed for the identification of two subspecies within the clade. Consistent with other Xenorhabdus , the analysed X. griffiniae genomes each encode a wide array of antimicrobials and virulence-related proteins. Comparative genomic analyses, including the creation of a pangenome, revealed that a large amount of the intraspecies variation in X. griffiniae is contained within the mobilome and attributable to prophage loci. In addition, CRISPR arrays, secondary metabolite potential and toxin genes all varied among strains within the X. griffiniae species. Our findings suggest that phage-related genes drive the genomic diversity in closely related Xenorhabdus symbionts, and that these may underlie some of the traits most associated with the lifestyle and survival of entomopathogenic nematodes and their bacteria: virulence and competition. This study establishes a broad knowledge base for further exploration of not only the relationships between X. griffiniae species and their nematode hosts but also the molecular mechanisms that underlie their entomopathogenic lifestyle.", "token_count": 526, "char_count": 2098, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5686, "quality_score": 0.7843, "entities": { "genes": [ "HGB2511", "TH1", "ID10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:19.608995", "source": { "split": "train_shard_00001", "doc_id": 1640 }, "chunk_id": "train_shard_00001_1640_0", "global_id": 7970 }, { "text": "Analyses ofXenorhabdus griffiniaegenomes reveal two distinct sub-species that display intra-species variation due to prophages", "token_count": 43, "char_count": 133, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:19.974055", "source": { "split": "train_shard_00001", "doc_id": 1640 }, "chunk_id": "train_shard_00001_1640_1", "global_id": 7971 }, { "text": "

Background

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), poses a threat to global wheat production. Deployment of widely effective resistance genes underpins management of this ongoing threat. This study focused on the mapping of stripe rust resistance gene YR63 from a Portuguese hexaploid wheat landrace AUS27955 of the Watkins Collection.

Results

YR63 exhibits resistance to a broad spectrum of Pst races from Australia, Africa, Asia, Europe, Middle East and South America. It was mapped to the short arm of chromosome 7B, between two single nucleotide polymorphic (SNP) markers sunCS_YR63 and sunCS_67, positioned at 0.8 and 3.7 Mb, respectively, in the Chinese Spring genome assembly v2.1. We characterised YR63 locus using an integrated approach engaging targeted genotyping-by-sequencing (tGBS), mutagenesis, resistance gene enrichment and sequencing (MutRenSeq), RNA sequencing (RNASeq) and comparative genomic analysis with tetraploid (Zavitan and Svevo) and hexaploid (Chinese Spring) wheat genome references and 10+ hexaploid wheat genomes. YR63 is positioned at a hot spot enriched with multiple nucleotide-binding and leucine rich repeat (NLR) and kinase domain encoding genes, known widely for defence against pests and diseases in plants and animals. Detection of YR63 within these gene clusters is not possible through short-read sequencing due to high homology between members. However, using the sequence of a NLR member we were successful in detecting a closely linked SNP marker for YR63 and validated on a panel of Australian bread wheat, durum and triticale cultivars.

Conclusions

This study highlights YR63 as a valuable source for resistance against Pst in Australia and elsewhere. The closely linked SNP marker will facilitate rapid introgression of YR63 into elite cultivars through marker-assisted selection", "token_count": 511, "char_count": 1876, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6906, "quality_score": 0.8453, "entities": { "genes": [ "YR63", "AUS27955" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:20.648757", "source": { "split": "train_shard_00001", "doc_id": 1641 }, "chunk_id": "train_shard_00001_1641_0", "global_id": 7972 }, { "text": "The bottleneck of this study reinforces the necessity for a long-read sequencing such as PacBio or Oxford Nanopore based techniques for accurate detection of the underlying resistance gene when it is part of a large gene cluster.\n\nWheat stripe rust resistance locus YR63 is a hot spot for evolution of defence genes - a pangenome discovery.", "token_count": 81, "char_count": 340, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [ "YR63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:21.043285", "source": { "split": "train_shard_00001", "doc_id": 1641 }, "chunk_id": "train_shard_00001_1641_1", "global_id": 7973 }, { "text": "

Summary

The ever-increasing number of sequenced genomes necessitates the development of pangenomic approaches for comparative genomics. Introduced in 2016, PanTools is a platform that allows pangenome construction, homology grouping and pangenomic read mapping. The use of graph database technology makes PanTools versatile, applicable from small viral genomes like SARS-CoV-2 up to large plant or animal genomes like tomato or human. Here, we present our third major update to PanTools that enables the integration of functional annotations and provides both gene-level analyses and phylogenetics.

Availability and implementation

PanTools is implemented in Java 8 and released under the GNU GPLv3 license. Software and documentation are available at https://git.wur.nl/bioinformatics/pantools.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nPanTools v3: functional annotation, classification and phylogenomics.", "token_count": 244, "char_count": 972, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7607, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:21.525948", "source": { "split": "train_shard_00001", "doc_id": 1642 }, "chunk_id": "train_shard_00001_1642_0", "global_id": 7974 }, { "text": "In this work a neuro-fuzzy based model of a whey batch fermentation process by a strain Kluyveromyces marxianus var. lactis MC5 is presented. A three-layered neuro-fuzzy network is realized. The simulation results are compared with conventional models (based on mass balance and differential equations). The neuro-fuzzy model provides a better fitness and allows inclusion of linguistic variables (such as colour, smell, taste, morphophysiology, etc.). The accuracy is approximately equal to this achieved by a conventional neural network. The proposed approach is flexible (with regard to the process model) and quite robust (with regard to the possible uncertainties and to the optimization surface). Future work will focus on applying this approach for modelling of different biotechnological processes.\n\nNeuro-fuzzy based model of batch fermentation of Kluyveromyces marxianus var. lactis MC5.", "token_count": 232, "char_count": 925, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [ "MC5" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:21.993832", "source": { "split": "train_shard_00001", "doc_id": 1643 }, "chunk_id": "train_shard_00001_1643_0", "global_id": 7975 }, { "text": "

Background

Campylobacteriosis represents a global public health threat with various socio-economic impacts. Among different Campylobacter species, Campylobacter jejuni (C. jejuni) is considered to be the foremost Campylobacter species responsible for most of gastrointestinal-related infections. Although these species are reported to primarily inhabit birds, its high genetic and phenotypic diversity allowed their adaptation to other animal reservoirs and to the environment that may impact on human infection.

Main body

A stringent and consistent surveillance program based on high resolution subtyping is crucial. Recently, different epidemiological investigations have implemented high-throughput sequencing technologies and analytical pipelines for higher resolution subtyping, accurate source attribution, and detection of antimicrobial resistance determinants among these species. In this review, we aim to present a comprehensive overview on the epidemiology, clinical presentation, antibiotic resistance, and transmission dynamics of Campylobacter, with specific focus on C. jejuni. This review also summarizes recent attempts of applying whole-genome sequencing (WGS) coupled with bioinformatic algorithms to identify and provide deeper insights into evolutionary and epidemiological dynamics of C. jejuni precisely along the farm-to-fork continuum.

Conclusion

WGS is a valuable addition to traditional surveillance methods for Campylobacter. It enables accurate typing of this pathogen and allows tracking of its transmission sources. It is also advantageous for in silico characterization of antibiotic resistance and virulence determinants, and hence implementation of control measures for containment of infection.\n\nGenomic insights into zoonotic transmission and antimicrobial resistance in Campylobacter jejuni from farm to fork: a one health perspective.", "token_count": 399, "char_count": 1894, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:22.607262", "source": { "split": "train_shard_00001", "doc_id": 1644 }, "chunk_id": "train_shard_00001_1644_0", "global_id": 7976 }, { "text": "Salmonella enterica subsp. enterica serovar Typhimurium DT104, a multidrug-resistant phage type, has emerged globally as a major cause of foodborne outbreaks particularly associated with contaminated beef products. In this study, we sequenced three S. Typhimurium DT104 strains associated with a 2009 outbreak caused by ground beef, including the outbreak source strain and two clinical strains. The goal of the study was to gain a stronger understanding of the genomics and genomic epidemiology of highly clonal S. typhimurium DT104 strains associated with bovine sources. Our study found no single nucleotide polymorphisms (SNPs) between the ground beef source strain and the clinical isolates from the 2009 outbreak. SNP analysis including twelve other S. typhimurium strains from bovine and clinical sources, including both DT104 and non-DT104, determined DT104 strains averaged 55.0 SNPs between strains compared to 474.5 SNPs among non-DT104 strains. Phylogenetic analysis separated the DT104 strains from the non-DT104 strains, but strains did not cluster together based on source of isolation even within the DT104 phage type. Pangenome analysis of the strains confirmed previous studies showing that DT104 strains are missing the genes for the allantoin utilization pathway, but this study confirmed that the genes were part of a deletion event and not substituted or disrupted by the insertion of another genomic element. Additionally, cgMLST analysis revealed that DT104 strains with cattle as the source of isolation were quite diverse as a group and did not cluster together, even among strains from the same country. Expansion of the analysis to 775 S. typhimurium ST19 strains associated with cattle from North America revealed diversity between strains, not limited to just among DT104 strains, which suggests that the cattle environment is favorable for a diverse group of S", "token_count": 513, "char_count": 1936, "word_count": 284, "semantic_coherence": 1, "information_density": 0.5352, "quality_score": 0.7676, "entities": { "genes": [ "DT104", "ST19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:23.266706", "source": { "split": "train_shard_00001", "doc_id": 1645 }, "chunk_id": "train_shard_00001_1645_0", "global_id": 7977 }, { "text": "typhimurium strains and not just DT104 strains.\n\nGenomic Characterization of Salmonella typhimurium DT104 Strains Associated with Cattle and Beef Products.", "token_count": 57, "char_count": 166, "word_count": 20, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [ "DT104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:23.626351", "source": { "split": "train_shard_00001", "doc_id": 1645 }, "chunk_id": "train_shard_00001_1645_1", "global_id": 7978 }, { "text": "Abstract

Background Listeria monocytogenes (Lm) is a foodborne pathogen that can lead to severe pregnancy outcomes. This study reports the clinical and genomic characteristics of a Listeria-mediated stillbirth identified through the Child Health and Mortality Prevention Surveillance (CHAMPS) project in Bangladesh. The Lm-BD-CHAMPS-01 isolate was recovered from the blood and cerebrospinal fluid (CSF) of a male stillborn baby. Maternal history, clinical, and demographic data were collected by the CHAMPS surveillance platform. An expert panel evaluated all reports to determine the role of Lm infection in the causal chain of stillbirth. Genomic characterization included multilocus sequence typing (MLST), core genome MLST (cgMLST), serotyping, and the presence or absence of virulence and stress adaptation genes. Genetic divergence and phylogenetic analyses were conducted to determine the relationship with other reported isolates globally. Results The isolate Lm-BD-CHAMPS-01 was identified as a novel cgMLST CT11424. It belonged to ST 308, Serotype 4b, Clonal Complex 1, and Phylogenetic Lineage 1. Key Lm virulence genes facilitating the crossing of the placental barrier, including full-length inlA, LIPI-1, and LIPI-3, were detected. The isolate was closely related to clinical Lm isolates, as determined by Grapetree based on cgMLST. SNP-based phylogenetic analysis found Lm-BD-CHAMPS-01 to be the most distant from other CC1 isolates in the database. Possible sources of infection included the consumption of contaminated raw vegetables or exposure to pigeons", "token_count": 499, "char_count": 1764, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "CT11424", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:24.277562", "source": { "split": "train_shard_00001", "doc_id": 1646 }, "chunk_id": "train_shard_00001_1646_0", "global_id": 7979 }, { "text": "Conclusions The virulence profile of the first genome sequence of clinical Lm from Bangladesh, which also caused stillbirth, underscores the understudied nature of this pathogen in the region. Rural healthcare professionals should be aware of Lm infection risks during pregnancy. Pregnant women should be counseled on the dangers of consuming potentially contaminated raw food and exposure to animals or birds to prevent adverse pregnancy outcomes due to Lm infection.

\n\nHyper virulent Core Genome Multilocus Sequence Type CT 11424 of Listeria monocytogenes isolate causing stillbirth in Bangladesh", "token_count": 166, "char_count": 653, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7907, "quality_score": 0.8953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:24.715831", "source": { "split": "train_shard_00001", "doc_id": 1646 }, "chunk_id": "train_shard_00001_1646_1", "global_id": 7980 }, { "text": "In this study, yeasts were isolated and characterized from twelve traditional sourdough samples which belongs to Black Sea and Aegean regions of Turkey. Twenty six yeast species were isolated and identified by both 26S rDNA sequencing and FTIR spectroscopy. Saccharomyces cerevisiae (50%), Torulaspora delbrueckii (40%) and Kluyveromyces marxianus (10%) were found in 12 Turkish traditional sourdough samples. S. cerevisiae was found to be the most dominant species in Aegean region while T. delbrueckii was the most frequently isolated species in Black Sea region. Some technological properties of isolated yeast species such as acidity development, resistance to NaCI and potassium sorbate, and yeast effect on bread quality were investigated. Breads were prepared by S. cerevisiae TGM38 strain demonstrated the highest bread volume compared the other yeasts used in the study. This study showed the yeast diversity and technological properties of traditional Turkish sourdough breads fermented by chosen yeast species.\n\nBiodiversity and technological properties of yeasts from Turkish sourdough.", "token_count": 303, "char_count": 1140, "word_count": 157, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [ "TGM38" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:25.279888", "source": { "split": "train_shard_00001", "doc_id": 1647 }, "chunk_id": "train_shard_00001_1647_0", "global_id": 7981 }, { "text": "

ABSTRACT

Facioscapulohumeral muscular dystrophy (FSHD) is the only human disease associated with epigenetic changes at a macrosatellite array. Almost 95% of FSHD cases carry a reduced number (≤10) of tandem 3.3 kilobase repeats, termed D4Z4, on chromosome 4q35; remaining cases bear variants in chromatin remodeling factors, such as SMCHD1, DNMT3B, LRIF1. Reduced CpG methylation is used for the molecular diagnosis of FSHD, but D4Z4-like sequences dispersed in the genome can generate ambiguous results. By analyzing complete haplotype level assemblies from the T2T-CHM13 human genome and 86 haploid genomes from the human pangenome project, we uncovered the extensive number of D4Z4-like elements and their widespread inter- and intra-individual variability. An original analytical approach was developed to elucidate this previously unaccounted wealth of D4Z4-like elements and to analyze CpG methylation at D4Z4 in bisulfite-treated DNA from 29 FSHD index cases and 15 relatives. Integrated analysis of clinical phenotype, D4Z4 CpG methylation level and gene variants showed that low D4Z4 methylation was associated with variants in the SMCHD1 gene, but not with the patients’ clinical phenotypes. This is the first study showing the relevance of the pangenome and T2T-CHM13 assemblies for investigating the genotype-phenotype correlation in genetic diseases. The extension and the variability of D4Z4-like elements scattered throughout the human genome and the inconsistent association of phenotypes with methylation profiles advocate for a critical revision of FSHD diagnostic tests based on D4Z4 CpG methylation assays and indicate that molecular investigations must be complemented by family studies for the proper interpretation of results.\n\nA human pan-genomic analysis reconfigures the genetic and epigenetic make up of facioscapulohumeral muscular dystrophy", "token_count": 514, "char_count": 1878, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5947, "quality_score": 0.7973, "entities": { "genes": [ "DNMT3B", "SMCHD1", "CHM13", "LRIF1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:25.935944", "source": { "split": "train_shard_00001", "doc_id": 1648 }, "chunk_id": "train_shard_00001_1648_0", "global_id": 7982 }, { "text": "Corynebacterium amycolatum is a nonlipophilic coryneform which is increasingly being recognized as a relevant human and animal pathogen showing multidrug resistance to commonly used antibiotics. However, little is known about the molecular mechanisms involved in transition from colonization to the MDR invasive phenotype in clinical isolates. In this study, we performed a comprehensive pan-genomic analysis of C. amycolatum, including 26 isolates from different countries. We obtained the novel genome sequences of 8 of them, which are multidrug resistant clinical isolates from Spain and Tunisia. They were analyzed together with other 18 complete or draft C. amycolatum genomes retrieved from GenBank. The species C. amycolatum presented an open pan-genome (α = 0.854905), with 3,280 gene families, being 1,690 (51.52%) in the core genome, 1,121 related to accessory genes (34.17%), and 469 related to unique genes (14.29%). Although some classic corynebacterial virulence factors are absent in the species C. amycolatum, we did identify genes associated with immune evasion, toxin, and antiphagocytosis among the predicted putative virulence factors. Additionally, we found genomic evidence for extensive acquisition of antimicrobial resistance genes through genomic islands.\n\nPan-genomic analysis of Corynebacterium amycolatum gives insights into molecular mechanisms underpinning the transition to a pathogenic phenotype.", "token_count": 422, "char_count": 1477, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6853, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:26.561655", "source": { "split": "train_shard_00001", "doc_id": 1649 }, "chunk_id": "train_shard_00001_1649_0", "global_id": 7983 }, { "text": "

Background

Clostridioides difficile infections (CDI) present significant health risks and are among the most important nosocomial infections. Ribotype (RT) 027 poses a particular risk due to its proposed \"hypervirulence\". Traditionally, C. difficile isolates are characterized using PCR-ribotyping. More recently, whole genome sequence (WGS) analysis is increasingly used, which may provide a higher discriminatory power. This study aimed to assess the distribution of different C. difficile RTs in hospitals in the Berlin-Brandenburg area, and to analyse the heterogeneity within isolates of different ribotypes using WGS.

Methods

Between February 2020 and November 2021, stool samples from patients with laboratory-confirmed CDI were collected from 22 hospitals (approximately 13,900 beds) in Berlin and Brandenburg. Toxigenic isolates (n = 476) were further characterized by ribotyping, antibiotic susceptibility testing, toxinotyping, and core genome multilocus sequence typing (cgMLST).

Results

Sixty-five different RTs were detected, with RT014 (16.1%), RT027 (12.8%), and RT001 (7.6%) being the most prevalent. RT027 isolates exhibited resistance to several antibiotics. Further, cgMLST analysis revealed very close genetic relatedness between RT027 isolates despite being epidemiologically unrelated. Similar findings of a monomorphic population were observed for RT078 isolates. In contrast, other RTs showed a heterogenic population structure.

Conclusions

This study provides first insights into the distribution of C. difficile genotypes, corresponding antimicrobial resistance, and clonal relatedness using cgMLST, highlighting RT027 as the second most common genotype for the studied area. For the monomorphic RT027 and RT078 populations, new definitions of clonal relatedness might be necessary.", "token_count": 500, "char_count": 1838, "word_count": 232, "semantic_coherence": 1, "information_density": 0.694, "quality_score": 0.847, "entities": { "genes": [ "RT078", "RT014", "RT001", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:27.212093", "source": { "split": "train_shard_00001", "doc_id": 1650 }, "chunk_id": "train_shard_00001_1650_0", "global_id": 7984 }, { "text": "Whole genome sequence analysis reveals limited diversity among Clostridioides difficile ribotype 027 and 078 isolates collected in 22 hospitals in Berlin and Brandenburg, Germany.", "token_count": 45, "char_count": 179, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:27.569250", "source": { "split": "train_shard_00001", "doc_id": 1650 }, "chunk_id": "train_shard_00001_1650_1", "global_id": 7985 }, { "text": "

Summary

Natural killer (NK) cells are essential components of the innate immune system, with their activity significantly regulated by Killer cell Immunoglobulin-like Receptors (KIRs). The diversity and structural complexity of KIR genes present significant challenges for accurate genotyping, essential for understanding NK cell functions and their implications in health and disease. Traditional genotyping methods struggle with the variable nature of KIR genes, leading to inaccuracies that can impede immunogenetic research. These challenges extend to high-quality phased assemblies, which have been recently popularized by the Human Pangenome Consortium. This article introduces BAKIR (Biologically informed Annotator for KIR locus), a tailored computational tool designed to overcome the challenges of KIR genotyping and annotation on high-quality, phased genome assemblies. BAKIR aims to enhance the accuracy of KIR gene annotations by structuring its annotation pipeline around identifying key functional mutations, thereby improving the identification and subsequent relevance of gene and allele calls. It uses a multi-stage mapping, alignment, and variant calling process to ensure high-precision gene and allele identification, while also maintaining high recall for sequences that are significantly mutated or truncated relative to the known allele database. BAKIR has been evaluated on a subset of the HPRC assemblies, where BAKIR was able to improve many of the associated annotations and call novel variants. BAKIR is freely available on GitHub, offering ease of access and use through multiple installation methods, including pip, conda, and singularity container, and is equipped with a user-friendly command-line interface, thereby promoting its adoption in the scientific community.

Availability and implementation

BAKIR is available at github.com/algo-cancer/bakir.\n\nBiologically-informed killer cell immunoglobulin-like receptor gene annotation tool.", "token_count": 443, "char_count": 1986, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8352, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:28.559357", "source": { "split": "train_shard_00001", "doc_id": 1651 }, "chunk_id": "train_shard_00001_1651_0", "global_id": 7986 }, { "text": "

Background

Leuconostoc lactis forms a crucial member of the genus Leuconostoc and has been widely used in the fermentation industry to convert raw material into acidified and flavored products in dairy and plant-based food systems. Since the ecological niches that strains of Ln. lactis being isolated from were truly diverse such as the human gut, dairy, and plant environments, comparative genome analysis studies are needed to better understand the strain differences from a metabolic adaptation point of view across diverse sources of origin. We compared eight Ln. lactis strains of 1.2.28, aa_0143, BIOML-A1, CBA3625, LN19, LN24, WIKIM21, and WiKim40 using bioinformatics to elucidate genomic level characteristics of each strain for better utilization of this species in a broad range of applications in food industry.

Results

Phylogenomic analysis of twenty-nine Ln. lactis strains resulted in nine clades. Whole-genome sequence analysis was performed on eight Ln. lactis strains representing human gastrointestinal tract and fermented foods microbiomes. The findings of the present study are based on comparative genome analysis against the reference Ln. lactis CBA3625 genome. Overall, a ~ 41% of all CDS were conserved between all strains. When the coding sequences were assigned to a function, mobile genetic elements, mainly insertion sequences were carried by all eight strains. All strains except LN24 and WiKim40 harbor at least one intact putative prophage region, and two of the strains contained CRISPR-Cas system. All strains encoded Lactococcin 972 bacteriocin biosynthesis gene clusters except for CBA3625.

Conclusions

The findings in the present study put forth new perspectives on genomics of Ln. lactis via complete genome sequence based comparative analysis and further determination of genomic characteristics. The outcomes of this work could potentially pave the way for developing elements for future strain engineering applications.", "token_count": 519, "char_count": 1983, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6312, "quality_score": 0.8156, "entities": { "genes": [ "WIKIM21", "LN24", "CBA3625", "LN19" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:29.216436", "source": { "split": "train_shard_00001", "doc_id": 1652 }, "chunk_id": "train_shard_00001_1652_0", "global_id": 7987 }, { "text": "Comparative genomics of Leuconostoc lactis strains isolated from human gastrointestinal system and fermented foods microbiomes.", "token_count": 33, "char_count": 127, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:29.571736", "source": { "split": "train_shard_00001", "doc_id": 1652 }, "chunk_id": "train_shard_00001_1652_1", "global_id": 7988 }, { "text": "Three novel, Gram-stain-negative, non-motile, rod-shaped bacterial strains, designated Du54ᵀ, Du274ᵀ and P351ᵀ, were isolated from contaminated environments in Anseong, South Korea. Strains Du54ᵀ and Du274ᵀ originated from landfill soil, whilst P351ᵀ was obtained from parking lot soil. These sites are frequently exposed to pollutants such as petroleum hydrocarbons, heavy metals and industrial runoff, which exert selective pressures on microbial communities. The taxonomic positions of the strains were determined using a polyphasic approach, including 16S rRNA gene sequencing, draft genome analysis and whole-genome-based phylogenetic reconstruction. Phylogenetic trees based on both 16S rRNA genes and core genome sequences (Type Genome Server and AutoMLST) showed that the three isolates belong to the genus Pedobacter. Du54ᵀ exhibited the highest 16S rRNA gene sequence similarity to Pedobacter insulae KCTC 12820ᵀ (98.40%), Du274ᵀ to Pedobacter bambusae KACC 17544ᵀ (98.31%) and P351ᵀ to Pedobacter mongoliensis KCTC 52859ᵀ (97.65%). The draft genomes of Du54ᵀ, Du274ᵀ and P351ᵀ were 4.43, 4.51 and 4.63 Mb in size, with G+C contents of 37.7, 40.6 and 39.2 %, respectively", "token_count": 454, "char_count": 1209, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7186, "quality_score": 0.8593, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:30.210887", "source": { "split": "train_shard_00001", "doc_id": 1653 }, "chunk_id": "train_shard_00001_1653_0", "global_id": 7989 }, { "text": "Average nucleotide identity and digital DNA-DNA hybridization values between the novel strains and their closest relatives ranged from 73.76 to 76.36% and 18.8 to 22.6%, respectively, supporting their delineation as novel species. Genomic annotation revealed 294, 302 and 238 genes in Du54ᵀ, Du274ᵀ and P351ᵀ, respectively, associated with metal resistance, efflux transporters and stress response. All strains lacked flexirubin-type pigments, contained menaquinone-7 as the major respiratory quinone and possessed phosphatidylethanolamine as the dominant polar lipid. The predominant fatty acids included iso-C16:0 and summed feature 3 (C16:1  ω7c and/or C16 : 1  ω6c). Based on these results, the names Pedobacter anseongensis sp. nov., Pedobacter immunditicola sp. nov. and Pedobacter superstes sp. nov. are proposed for strains Du54ᵀ (=KACC 23093ᵀ=LMG 32954ᵀ), Du274ᵀ (=KACC 23094ᵀ=LMG 32955ᵀ) and P351ᵀ (=KACC 23095ᵀ=LMG 32956ᵀ), respectively.", "token_count": 424, "char_count": 1016, "word_count": 131, "semantic_coherence": 1, "information_density": 0.771, "quality_score": 0.8855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:30.850207", "source": { "split": "train_shard_00001", "doc_id": 1653 }, "chunk_id": "train_shard_00001_1653_1", "global_id": 7990 }, { "text": "<i>Pedobacter anseongensis</i> sp. nov., <i>Pedobacter immunditicola</i> sp. nov. and <i>Pedobacter superstes</i> sp. nov., three novel species isolated from hydrocarbon- and heavy metal-contaminated soils.", "token_count": 98, "char_count": 242, "word_count": 23, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:31.266861", "source": { "split": "train_shard_00001", "doc_id": 1653 }, "chunk_id": "train_shard_00001_1653_2", "global_id": 7991 }, { "text": "Maximal exact matches (MEMs) are widely used in bioinformatics, originally for genome-to-genome comparison but especially for DNA alignment ever since Li (2013) presented BWA-MEM. Building on work by Bannai, Gagie and I (2018) and again targeting alignment, Rossi et al. (2022) recently built an index called MONI that is based on the run-length compressed Burrows-Wheeler Transform and can find MEMs efficiently with respect to pangenomes. In this paper we define k -MEMs to be maximal substrings of a pattern that each occur exactly at least k times in a text (so a MEM is a 1-MEM) and briefly explain why computing k -MEMs could be useful for pangenome-to-pangenome comparison. We then show that, when k is given at construction time, MONI can easily be extended to find k -MEMs efficiently as well.\n\nMONI-k: An index for efficient pangenome-to-pangenome comparison", "token_count": 240, "char_count": 875, "word_count": 139, "semantic_coherence": 1, "information_density": 0.741, "quality_score": 0.8705, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:31.765937", "source": { "split": "train_shard_00001", "doc_id": 1654 }, "chunk_id": "train_shard_00001_1654_0", "global_id": 7992 }, { "text": "

Purpose:

Curtobacterium flaccumfaciens is a Gram-positive bacterium which has been isolated from different plants and abiotic environment. Curtobacterium. flaccumfaciens pv. flaccumfaciens (Cff) is a pathogenic bacterium that infects legume, which is causing great economic losses. At the genomic level, the metabolic and phylogenetic characteristics, and differences in pathogenicity between pathogenic and nonpathogenic C. flaccumfaciens strains have not been analyzed in detail. Methods Therefore, in order to discuss the differences in genome, phylogeny, gene function and mobile genetic elements between pathogenic and nonpathogenic strains, pangenomics and comparative genomics were used in this study to analyze 12 C. flaccumfaciens strains. Result The pangenome of C. flaccumfaciens is open. Phylogenetic analysis showed that there was no correlation between the phylogeny and pathogenicity of C. flaccumfaciens . KAAS annotation of the core genome shows that the citrate cycle was incomplete. In addition, gene islands analysis of the three pathogenicity-related genes encoding for pectate lyase, serine protease and cellulases showed that they only existed in the Cffs and LMG3645 strains. LMG3645 might be a pathogenic strain. Conclusion This study clearly and reliably revealed the differences between the pathogenic and nonpathogenic strains of C. flaccumfaciens at the genomic level, and paves the way for further research on its pathogenicity.\n\nGenomic Analysis of Curtobacterium Flaccumfaciens Reveals the Differences Between Pathogenic and Nonpathogenic Strains", "token_count": 421, "char_count": 1591, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5622, "quality_score": 0.7811, "entities": { "genes": [ "LMG3645" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:32.415052", "source": { "split": "train_shard_00001", "doc_id": 1655 }, "chunk_id": "train_shard_00001_1655_0", "global_id": 7993 }, { "text": "This study focused on L. paracasei strains isolated from fermented palm sap in southern Thailand that exhibit potential probiotic characteristics, including antibiotic susceptibility, resistance to gastrointestinal stresses, and antimicrobial activity against various pathogens. However, a thorough investigation of the whole genome sequences of L. paracasei isolates is required to ensure their safety and probiotic properties for human applications. This study aimed to sequence the genome of L. paracasei isolated from fermented palm sap, to assess its safety profile, and to conduct a comprehensive comparative genomic analysis with other Lacticaseibacillus species. The genome sizes of the seven L. paracasei strains ranged from 3,070,747 bp to 3,131,129 bp, with a GC content between 46.11% and 46.17% supporting their classification as nomadic lactobacilli. In addition, the minimal presence of cloud genes and a significant number of core genes suggest a high degree of relatedness among the strains. Meanwhile, phylogenetic analysis of core genes revealed that the strains possessed distinct genes and were grouped into two distinct clades. Genomic analysis revealed key genes associated with probiotic functions, such as those involved in gastrointestinal, oxidative stress resistance, vitamin synthesis, and biofilm disruption. This study is consistent with previous studies that used whole-genome sequencing and bioinformatics to assess the safety and potential benefits of probiotics in various food fermentation processes. Our findings provide valuable insights into the potential use of seven L. paracasei strains isolated from fermented palm sap as probiotic and postbiotic candidates in functional foods and pharmaceuticals.\n\nProbiotic Insights from the Genomic Exploration of Lacticaseibacillus paracasei Strains Isolated from Fermented Palm Sap.", "token_count": 483, "char_count": 1913, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5736, "quality_score": 0.7868, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:33.086722", "source": { "split": "train_shard_00001", "doc_id": 1656 }, "chunk_id": "train_shard_00001_1656_0", "global_id": 7994 }, { "text": "Objective: To investigate the drug resistance gene characteristics, plasmid characteristics and genome tracing of Shigella sonnei causing a bacillary dysentery outbreak in Shandong Province. Methods: Sixty-five Shigella sonnei strains isolated from a 2021 outbreak in a county of Shandong Province were analyzed using antimicrobial susceptibility testing, whole genome sequencing (WGS), characterization of resistance and virulence genes, plasmid profiling, core genome multilocus sequence typing (cgMLST), and single nucleotide polymorphism (SNP) analysis. Results: All isolates had the same resistance phenotype and genotypes and were multidrug-resistant ESBL-producing Shigella sonnei, carrying important virulence genes. Plasmid analysis revealed a conserved genetic arrangement, pil(M/N/O2/P)-tra(F/H/J/K/N/O/P/Q)-ISEcp1-blaCTX-M-14-Tn903-yub(J/I/F/G/E/D), and shared across strains from diverse regions and bacterial species. The cgMLST and SNP analyses demonstrated concordant clustering, with all 65 outbreak-related strains forming a single cluster alongside human-derived strains from Guangxi", "token_count": 471, "char_count": 1316, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7231, "quality_score": 0.8615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:33.730063", "source": { "split": "train_shard_00001", "doc_id": 1657 }, "chunk_id": "train_shard_00001_1657_0", "global_id": 7995 }, { "text": "Conclusion: The ESBL-producing Shigella sonnei responsible for the outbreak shares a homologous relationship with Guangxi human-derived strains, and the detected resistance plasmids and virulence genes underscore the need to strengthen drug resistance surveillance and genome tracing.\n\n[Plasmid characteristics and genome tracing analysis of a bacterial dysentery outbreak in Shandong Province, originating from <i>Shigella sonnei</i> producing extended spectrum β-lactamase].", "token_count": 133, "char_count": 502, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8276, "quality_score": 0.9138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:34.156821", "source": { "split": "train_shard_00001", "doc_id": 1657 }, "chunk_id": "train_shard_00001_1657_1", "global_id": 7996 }, { "text": "Staphylococcus schleiferi and Staphylococcus coagulans, closely related bacterial species within the Staphylococcus genus, present a challenge in classification and diagnosis due to their close genetic proximity and overlapping phenotypic features. Moreover, our understanding of the virulence mechanisms in staphylococcal species, beyond the extensively studied Staphylococcus aureus, remains limited, underscoring the importance of using comparative data to enhance our insights into virulence within these bacterial species. This study employed a comprehensive approach, utilizing comparative genomics, to identify genomic distinctions between S. schleiferi and S. coagulans, aiming to address the challenges in the accurate classification and diagnosis of these organisms and identify unique features. Whole genome sequencing was performed on six clinical isolates, and their genomes were compared to identify variations in gene content and virulence factors. De novo assembly and annotation revealed two samples as S. coagulans and four samples as S. schleiferi. Analysis of the core genomes revealed conserved regions crucial for defining species identity, while accessory genomic elements contained unique genes, possibly impacting the pathogenicity of the species.\n\nWhole Genome Sequencing and Comparative Genomics of Six Staphylococcus schleiferi and Staphylococcus coagulans Isolates.", "token_count": 371, "char_count": 1464, "word_count": 183, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:34.735959", "source": { "split": "train_shard_00001", "doc_id": 1658 }, "chunk_id": "train_shard_00001_1658_0", "global_id": 7997 }, { "text": "

ABSTRACT

As adoption of nanopore sequencing technology continues to advance, the need to maintain large volumes of raw current signal data for reanalysis with updated algorithms is a growing challenge. Here we introduce slow5curl , a software package designed to streamline nanopore data sharing, accessibility and reanalysis. Slow5curl allows a user to fetch a specified read or group of reads from a raw nanopore dataset stored on a remote server, such as a public data repository, without downloading the entire file. Slow5curl uses an index to quickly fetch specific reads from a large dataset in SLOW5/BLOW5 format and highly parallelised data access requests to maximise download speeds. Using all public nanopore data from the Human Pangenome Reference Consortium (>22 TB), we demonstrate how slow5curl can be used to quickly fetch and reanalyse signal reads corresponding to a set of target genes from each individual in large cohort dataset ( n = 91), minimising the time, egress costs, and local storage requirements for their reanalysis. We provide slow5curl as a free, open-source package that will reduce frictions in data sharing for the nanopore community: https://github.com/BonsonW/slow5curl\n\nStreamlining remote nanopore data access withslow5curl", "token_count": 306, "char_count": 1280, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6421, "quality_score": 0.8211, "entities": { "genes": [ "SLOW5", "BLOW5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:35.312786", "source": { "split": "train_shard_00001", "doc_id": 1659 }, "chunk_id": "train_shard_00001_1659_0", "global_id": 7998 }, { "text": "Biocontrol efficacy of an antagonistic yeast Kluyveromyces marxianus was evaluated individually or in combination with sodium bicarbonate (SBC) against green mold of citrus fruit caused by Penicillium digitatum. Their effects on postharvest quality of citrus fruit were also investigated. The results indicated that the antagonistic activity of K. marxianus at 1×10⁸ CFU/mL on green mold of citrus fruit was enhanced by 2% SBC treatment. In artificial inoculation trials, disease control after 3 and 6 days, respectively, with the mixture of K. marxianus and 2% SBC (18.33%, 58.33%) was significantly improved over that obtained with K. marxianus (41.67%, 70.00%) or SBC (43.33%, 81.67%) alone. The combination of K. marxianus with SBC was as effective as the imazalil treatment in natural infection trials, which gave about 90% control of green mold. Addition of 2% SBC significantly stimulated the growth of K. marxianus in citrus fruit wounds after 72 h. Moreover, K. marxianus, SBC and their combination did not impair quality parameters including weight loss, fruit firmness, total soluble solids, titratable acidity and ascorbic acid at 4 °C for 30 days followed by 20 °C for 15 days. These results suggested that the use of SBC is a useful approach to improve the efficacy of K. marxianus for the postharvest green mold of citrus fruit.\n\nCombination of Kluyveromyces marxianus and sodium bicarbonate for controlling green mold of citrus fruit.", "token_count": 423, "char_count": 1450, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5531, "quality_score": 0.7765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:35.935151", "source": { "split": "train_shard_00001", "doc_id": 1660 }, "chunk_id": "train_shard_00001_1660_0", "global_id": 7999 }, { "text": "Acinetobacter baumannii (AB) infections have become a global public health concern due to the continued increase in the incidence of infection and the rate of resistance to carbapenems. This study aimed to investigate the genomic features of AB strains recovered from a tertiary hospital and assess the clinical implications of the findings. A total of 217 AB strains were collected between 2016 and 2018 at a tertiary hospital in Guangzhou, with 183 (84.33%) being carbapenem-resistant AB (CRAB), with the main mechanism being the carriage of the blaOXA-23 gene. The overall mortality rate of patients caused by such strains was 15.21% (n = 33). Artificial lung ventilation and the use of meropenem were mortality risk factors in AB-infected patients, while KL2 AB infection was negatively associated. Core genome multilocus sequence typing and clustering analysis were performed on the integrated AB genome collection from the NCBI database and this study to illustrate the population structure among China. The results revealed diverse core genome profiles (n = 17) among AB strains from China, and strains from this single hospital exhibited most of the core genome profiles (n = 13), suggesting genetic variability within the hospital and transmission across the country. These findings show that the high transmission potential of the CRAB strains and meropenem usage that confers a selective advantage of CRAB clinically are two major factors that pose significant challenges to the effective clinical management of AB infections. Understanding the genetic features and transmission patterns of clinical AB strains is crucial for the effective control of infections caused by this pathogen.\n\nCharacterization of Acinetobacter baumannii at a tertiary hospital in Guangzhou: a genomic and clinical study.", "token_count": 433, "char_count": 1820, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5474, "quality_score": 0.7737, "entities": { "genes": [ "KL2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:37.206908", "source": { "split": "train_shard_00001", "doc_id": 1661 }, "chunk_id": "train_shard_00001_1661_0", "global_id": 8000 }, { "text": "The adoption of agriculture, first documented ∼12,000 years ago in the Fertile Crescent, triggered a rapid shift toward starch-rich diets in human populations. Amylase genes facilitate starch digestion and increased salivary amylase copy number has been observed in some modern human populations with high starch intake, though evidence of recent selection is lacking. Here, using 52 long-read diploid assemblies and short read data from ∼5,600 contemporary and ancient humans, we resolve the diversity, evolutionary history, and selective impact of structural variation at the amylase locus. We find that amylase genes have higher copy numbers in populations with agricultural subsistence compared to fishing, hunting, and pastoral groups. We identify 28 distinct amylase structural architectures and demonstrate that nearly identical structures have arisen recurrently on different haplotype backgrounds throughout recent human history. AMY1 and AMY2A genes each exhibit multiple duplications/deletions with mutation rates >10,000-fold the SNP mutation rate, whereas AMY2B gene duplications share a single origin. Using a pangenome graph-based approach to infer structural haplotypes across thousands of humans, we identify extensively duplicated haplotypes present at higher frequencies in modern day populations with traditionally agricultural diets. Leveraging 533 ancient human genomes we find that duplication-containing haplotypes (i.e. haplotypes with more amylase gene copies than the ancestral haplotype) have increased in frequency more than seven-fold over the last 12,000 years providing evidence for recent selection in West Eurasians. Together, our study highlights the potential impacts of the agricultural revolution on human genomes and the importance of long-read sequencing in identifying signatures of selection at structurally complex loci.\n\nGlobal diversity, recurrent evolution, and recent selection on amylase structural haplotypes in humans", "token_count": 442, "char_count": 1967, "word_count": 267, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [ "AMY2A", "AMY1", "AMY2B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:37.836961", "source": { "split": "train_shard_00001", "doc_id": 1662 }, "chunk_id": "train_shard_00001_1662_0", "global_id": 8001 }, { "text": "Abstract

Background Ethyl acetate is a widely used industrial solvent that is currently produced by chemical conversions from fossil resources. Several yeast species are able to convert sugars to ethyl acetate under aerobic conditions. However, performing ethyl acetate synthesis anaerobically may result in enhanced production efficiency, making the process economically more viable. Results We engineered an E. coli strain that is able to convert glucose to ethyl acetate as the main fermentation product under anaerobic conditions. The key enzyme of the pathway is an alcohol acetyltransferase (AAT) that catalyses the formation of ethyl acetate from acetyl-CoA and ethanol. To select a suitable AAT, the ethyl acetate-forming capacities of Atf1 from Saccharomyces cerevisiae, Eat1 from Kluyveromyces marxianus and Eat1 from Wickerhamomyces anomalus were compared. Heterologous expression of the AAT-encoding genes under control of the inducible LacI/ T7 and XylS/ Pm promoters allowed optimisation of their expression levels. Conclusion Engineering efforts on protein and fermentation level resulted in an E. coli strain that anaerobically produced ethyl acetate from glucose at an unprecedented level, i.e. 0.48 C-mol/C-mol or 72% of the maximum pathway yield.

\n\nMultilevel optimisation of anaerobic ethyl acetate production in engineered Escherichia coli", "token_count": 377, "char_count": 1382, "word_count": 192, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:38.420579", "source": { "split": "train_shard_00001", "doc_id": 1663 }, "chunk_id": "train_shard_00001_1663_0", "global_id": 8002 }, { "text": "Background. National epidemiological investigations of microbial infections greatly benefit from the increased information gained by whole-genome sequencing (WGS) in combination with standardized approaches for data sharing and analysis.Aim. To evaluate the quality and accuracy of WGS data generated by different laboratories but analysed by joint pipelines to reach a national surveillance approach.Methods. A national methicillin-resistant Staphylococcus aureus (MRSA) collection of 20 strains was distributed to nine participating laboratories that performed in-house procedures for WGS. Raw data were shared and analysed by three pipelines: 1928 Diagnostics, JASEN (GMS pipeline) and CLC-Genomics Workbench. The outcomes were compared according to quality, correct strain identification and genetic distances.Results. One isolate contained intraspecies contamination and was excluded from further analysis. The mean sequencing depth varied between sites and technologies. However, all analysis methods identified 12 strains that belonged to one of five outbreak clusters. The cut-off definition was set to <10 allele differences for core genome multilocus sequence typing (cgMLST) and <20 genetic differences for SNP analysis in a pairwise comparison.Conclusions. MRSA isolates, which are whole genome sequenced by different laboratories and analysed using the same bioinformatic pipelines, yielded comparable results for outbreak clustering for both cgMLST and SNP, using the 1928 analysis pipeline. In this study, JASEN was best suited to analyse Illumina data and CLC to analyse within respective technology. In the future, real-time sharing of data and harmonized analysis within the Genomic Medicine Sweden consortium will further facilitate investigations of outbreaks and transmission routes.\n\nEvaluation of nationwide analysis surveillance for methicillin-resistant <i>Staphylococcus aureus</i> within Genomic Medicine Sweden.", "token_count": 471, "char_count": 1993, "word_count": 255, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:39.064788", "source": { "split": "train_shard_00001", "doc_id": 1664 }, "chunk_id": "train_shard_00001_1664_0", "global_id": 8003 }, { "text": "

ABSTRACT

The Human Pangenome is a new reference build that addresses many of the limitations of the current reference. The first release is based on 94 high-quality haploid assemblies from individuals with diverse backgrounds. To facilitate the Pangenomes adoption in the wider research community, we conducted a multiple genome comparative analysis against the current GRCh38 reference. We applied a k-mer indexing strategy to identify highly conserved sequences that are omnipresent across all Pangenome assemblies, the reference and CHM13, a reference assembly with telomere-to-telomere chromosomes. Pan-conserved tag segments provided an informative set of universally conserved sequences. Examining the intervals between pairs of these segments defined highly conserved segments of the genome versus ones that have structurally related polymorphisms. We identified a Pangenome landscape of 60,764 polymorphic intervals with unique and geo-ethnic features. Overall, this study of the Pangenome revealed the conserved versus divergent features including the landscape of polymorphic structural variants.\n\nThe Human Pangenome’s sequence conservation reveals a landscape of polymorphic structural variations", "token_count": 276, "char_count": 1217, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:39.613663", "source": { "split": "train_shard_00001", "doc_id": 1665 }, "chunk_id": "train_shard_00001_1665_0", "global_id": 8004 }, { "text": "The existing de novo methods of complete genome assembly are not able to generate large-scale pangenomes with complete assemblies due to the shortcomings such as requiring multiple types of sequencing data of high price, requiring large amount of manual curation, and not being able to achieve haplotype-resolved complete assembly of long tandem repeats in most situations. To solve this problem, in this study, we propose a new genome assembly mode called reference-guided assembly which relies on the reference information to recall the reads for complex genomic regions of interest and assembles them in de novo -like way. As a proof-of-concept, we developed an algorithm TRFill which can reassemble or fill the gaps of tandem repeats in chromosome-level assembly in either haploid or diploid way using only HiFi and Hi-C data. The experimental results on human centromeres and tomato subtelomeres show that TRFill successfully improved the completeness and correctness of about two thirds of the tested tandem repeat sequences. Furthermore, TRFill improved the completeness of subtelomeric tandem repeats by 50% in a recently published tomato pangenome, enabling a population-level analysis of the subtelomeric tandem repeats, which found the ‘local law of sequence similarity of tandem repeats’ providing theoretical basis for reference-guided assembly in turn.\n\nReference-guided automatic assembly of genomic tandem repeats with only HiFi and Hi-C data enables population-level analysis", "token_count": 338, "char_count": 1492, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:40.185242", "source": { "split": "train_shard_00001", "doc_id": 1666 }, "chunk_id": "train_shard_00001_1666_0", "global_id": 8005 }, { "text": "Microbial adaptation is driven by the circulation of mobile genetic elements (MGEs) among bacteria. On the one hand, MGEs can be viewed as selfish genes that spread like infectious diseases in a host population. On the other hand, the horizontal transfer and the loss of these MGEs are often viewed as a form of sexual reproduction that reshuffles genetic diversity in a way that may sometimes be adaptive for bacteria cells. Here, we show how these 2 perspectives can be reconciled using a single unified framework capturing the dynamics of multiple, interacting MGEs. We apply this framework to study how interactions between MGEs affecting rates of horizontal gene transfer and segregation loss shape the short- and long-term evolutionary dynamics of MGEs and the bacteria population. We show that these interactions produce nonrandom MGE associations that can speed up or slow down microbial adaptation depending on the evolutionary conflicts between MGEs as well as between MGEs and their bacterial hosts. Moreover, we show how these interactions affect the evolutionary potential of the bacteria population. We discuss the implications of these predictions for the community response to environmental stressors such as antibiotic treatment or vaccination campaigns as well as the evolution of accessory genomes.\n\nHorizontal gene transfer, segregation loss, and the speed of microbial adaptation.", "token_count": 284, "char_count": 1401, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5587, "quality_score": 0.7793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:40.745767", "source": { "split": "train_shard_00001", "doc_id": 1667 }, "chunk_id": "train_shard_00001_1667_0", "global_id": 8006 }, { "text": "Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.\n\nRecent advances in the genomic resources for sheep.", "token_count": 206, "char_count": 1053, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6792, "quality_score": 0.8396, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:41.210122", "source": { "split": "train_shard_00001", "doc_id": 1668 }, "chunk_id": "train_shard_00001_1668_0", "global_id": 8007 }, { "text": "

Background

Campylobacter jejuni and C. coli are the most common causes of bacterial enteritis worldwide whereas symptomatic and asymptomatic infections are associated with stunting in children in low- and middle-income countries. Little is known about their sources and transmission pathways in low- and middle-income countries, and particularly for infants and young children. We assessed the genomic diversity of C. jejuni in Eastern Ethiopia to determine the attribution of infections in infants under 1 year of age to livestock (chickens, cattle, goats and sheep) and other humans (siblings, mothers).

Results

Among 287 C. jejuni isolates, 48 seven-gene sequence types (STs), including 11 previously unreported STs were identified. Within an ST, the core genome STs of multiple isolates differed in fewer than five alleles. Many of these isolates do not belong to the most common STs reported in high-resource settings, and of the six most common global STs, only ST50 was found in our study area. Isolates from the same infant sample were closely related, while those from consecutive infant samples often displayed different STs, suggesting rapid clearance and new infection. Four different attribution models using different genomic profiling methods, assumptions and estimation methods predicted that chickens are the primary reservoir for infant infections. Infections from chickens are transmitted with or without other humans (mothers, siblings) as intermediate sources. Model predictions differed in terms of the relative importance of cattle versus small ruminants as additional sources.

Conclusions

The transmission pathways of C. jejuni in our study area are highly complex and interdependent. While chickens are the most important reservoir of C. jejuni, ruminant reservoirs also contribute to the infections. The currently nonculturable species Candidatus C. infans is also highly prevalent in infants and is likely anthroponotic. Efforts to reduce the colonization of infants with Campylobacter and ultimately stunting in low-resource settings are best aimed at protecting proximate sources such as caretakers' hands, food and indoor soil through tight integration of the currently siloed domains of nutrition, food safety and water, sanitation and hygiene.", "token_count": 525, "char_count": 2297, "word_count": 326, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8113, "entities": { "genes": [ "ST50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:41.865984", "source": { "split": "train_shard_00001", "doc_id": 1669 }, "chunk_id": "train_shard_00001_1669_0", "global_id": 8008 }, { "text": "Transmission pathways of Campylobacter jejuni between humans and livestock in rural Ethiopia are highly complex and interdependent.", "token_count": 29, "char_count": 131, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:42.221629", "source": { "split": "train_shard_00001", "doc_id": 1669 }, "chunk_id": "train_shard_00001_1669_1", "global_id": 8009 }, { "text": "The aim of this work was to obtain insights about the factors that determine the lactose fermentative metabolism of Kluyveromyces marxianus UFV-3. K. marxianus UFV-3 and Kluyveromyces lactis JA6 were cultured in a minimal medium containing different lactose concentrations (ranging from 0.25 to 64 mmol l(-1)) under aerobic and hypoxic conditions to evaluate their growth kinetics, gene expression and enzymatic activity. The increase in lactose concentration and the decrease in oxygen level favoured ethanol yield for both yeasts but in K. marxianus UFV-3 the effect was more pronounced. Under hypoxic conditions, the activities of β-galactosidase and pyruvate decarboxylase from K. marxianus UFV-3 were significantly higher than those in K. lactis JA6. The expression of the LAC4 (β-galactosidase), RAG6 (pyruvate decarboxylase), GAL7 (galactose-1-phosphate uridylyltransferase) and GAL10 (epimerase) genes in K. marxianus UFV-3 was higher under hypoxic conditions than under aerobic conditions. The high expression of genes of the Leloir pathway, LAC4 and RAG6, associated with the high activity of β-galactosidase and pyruvate decarboxylase contribute to the high fermentative flux in K. marxianus UFV-3. These data on the fermentative metabolism of K. marxianus UFV-3 will be useful for optimising the conversion of cheese whey lactose to ethanol.\n\nThe high fermentative metabolism of Kluyveromyces marxianus UFV-3 relies on the increased expression of key lactose metabolic enzymes.", "token_count": 457, "char_count": 1489, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5305, "quality_score": 0.7653, "entities": { "genes": [ "GAL10", "JA6", "LAC4", "GAL7", "RAG6" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:42.858957", "source": { "split": "train_shard_00001", "doc_id": 1670 }, "chunk_id": "train_shard_00001_1670_0", "global_id": 8010 }, { "text": "Bacteria harness an impressive repertoire of resistance mechanisms to evade the inhibitory action of antibiotics. One such mechanism involves efflux pump-mediated extrusion of drugs from the bacterial cell, which significantly contributes to multidrug resistance. Intriguingly, most drug efflux pumps are chromosomally encoded components of the intrinsic antibiotic resistome. In addition, in terms of xenobiotic detoxification, bacterial efflux systems often exhibit significant levels of functional redundancy. Efflux pumps are also considered to be highly conserved; however, the extent of conservation in many bacterial species has not been reported and the majority of genes that encode efflux pumps appear to be dispensable for growth. These observations, in combination with an increasing body of experimental evidence, imply alternative roles in bacterial physiology. Indeed, the ability of efflux pumps to facilitate antibiotic resistance could be a fortuitous by-product of ancient physiological functions. Using Escherichia coli as a model organism, we here evaluated the evolutionary conservation of drug efflux pumps and we provide phylogenetic analysis of the major efflux families. We show the E. coli drug efflux system has remained relatively stable and the majority (∼80%) of pumps are encoded in the core genome. This analysis further supports the importance of drug efflux pumps in E. coli physiology. In this review, we also provide an update on the roles of drug efflux pumps in the detoxification of endogenously synthesized substrates and pH homeostasis. Overall, gaining insight into drug efflux pump conservation, common evolutionary ancestors, and physiological functions could enable strategies to combat these intrinsic and ancient elements.\n\nThe Evolutionary Conservation of Escherichia coli Drug Efflux Pumps Supports Physiological Functions.", "token_count": 444, "char_count": 1894, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5682, "quality_score": 0.7841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:43.529780", "source": { "split": "train_shard_00001", "doc_id": 1671 }, "chunk_id": "train_shard_00001_1671_0", "global_id": 8011 }, { "text": "Lacticaseibacillus casei, Lacticaseibacillus chiayiensis, and Lacticaseibacillus zeae are very closely related Lacticaseibacillus species. L. casei has long been proposed as a probiotic, whereas studies on functional characterization for L. chiayiensis and L. zeae are some compared to L. casei. In this study, L. casei FBL6, L. chiayiensis FBL7, and L. zeae FBL8 were isolated from raw milk, and their probiotic properties were investigated. Genomic analysis demonstrated the role of L. chiayiensis and L. zeae as probiotic candidates. The three strains were tolerant to acid and bile salt, with inhibitory action against pathogenic bacterial strains and capacity of antioxidants. Complete genome sequences of the three strains were analyzed to highlight the probiotic properties at the genetic level, which results in the discovery of genes corresponding to phenotypic characterization. Moreover, genes known to confer probiotic characteristics were identified, including genes related to biosynthesis, defense machinery, adhesion, and stress adaptation. The comparative genomic analysis with other available genomes revealed 256, 214, and 32 unique genes for FBL6, FBL7, and FBL8, respectively. These genomes contained individual genes encoding proteins that are putatively involved in carbohydrate transport and metabolism, prokaryotic immune system for antiviral defense, and physiological control processes. In particular, L. casei FBL6 had a bacteriocin gene cluster that was not present in other genomes of L. casei, resulting in this strain may exhibit a wide range of antimicrobial activity compared to other L. casei strains", "token_count": 520, "char_count": 1775, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [ "FBL6", "FBL7", "FBL8" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:44.192301", "source": { "split": "train_shard_00001", "doc_id": 1672 }, "chunk_id": "train_shard_00001_1672_0", "global_id": 8012 }, { "text": "Our data can help us understand the probiotic functionalities of the three strains and suggest that L. chiayiensis and L. zeae species, which are closely related to L. casei, can also be considered as novel potential probiotic candidate strains.\n\nComplete Genome Sequencing and Comparative Genomics of Three Potential Probiotic Strains, Lacticaseibacillus casei FBL6, Lacticaseibacillus chiayiensis FBL7, and Lacticaseibacillus zeae FBL8.", "token_count": 157, "char_count": 480, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [ "FBL6", "FBL7", "FBL8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:44.669701", "source": { "split": "train_shard_00001", "doc_id": 1672 }, "chunk_id": "train_shard_00001_1672_1", "global_id": 8013 }, { "text": "Traditionally, industrial tequila production has used spontaneous fermentation or Saccharomyces cerevisiae yeast strains. Despite the potential of non-Saccharomyces strains for alcoholic fermentation, few studies have been performed at industrial level with these yeasts. Therefore, in this work, Agave tequilana juice was fermented at an industrial level using two non-Saccharomyces yeasts (Pichia kluyveri and Kluyveromyces marxianus) with fermentation efficiency higher than 85 %. Pichia kluyveri (GRO3) was more efficient for alcohol and ethyl lactate production than S. cerevisiae (AR5), while Kluyveromyces marxianus (GRO6) produced more isobutanol and ethyl-acetate than S. cerevisiae (AR5). The level of volatile compounds at the end of fermentation was compared with the tequila standard regulation. All volatile compounds were within the allowed range except for methanol, which was higher for S. cerevisiae (AR5) and K. marxianus (GRO6). The variations in methanol may have been caused by the Agave tequilana used for the tests, since this compound is not synthesized by these yeasts.\n\nPerformance evaluation of Pichia kluyveri, Kluyveromyces marxianus and Saccharomyces cerevisiae in industrial tequila fermentation.", "token_count": 337, "char_count": 1228, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6095, "quality_score": 0.8047, "entities": { "genes": [ "GRO6", "GRO3", "AR5" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:45.256736", "source": { "split": "train_shard_00001", "doc_id": 1673 }, "chunk_id": "train_shard_00001_1673_0", "global_id": 8014 }, { "text": "Nontypeable Haemophilus influenzae (NTHi) colonizes human upper respiratory airways and plays a key role in the course and pathogenesis of acute exacerbations of chronic obstructive pulmonary disease (COPD). Currently, it is not possible to distinguish COPD isolates of NTHi from other clinical isolates of NTHi using conventional genotyping methods. Here, we analysed the core and accessory genome of 568 NTHi isolates, including 40 newly sequenced isolates, to look for genetic distinctions between NTHi isolates from COPD with respect to other illnesses, including otitis media, meningitis and pneumonia. Phylogenies based on polymorphic sites in the core-genome did not show discrimination between NTHi strains collected from different clinical phenotypes. However, pan-genome-wide association studies identified 79 unique NTHi accessory genes that were significantly associated with COPD. Furthermore, many of the COPD-related NTHi genes have known or predicted roles in virulence, transmembrane transport of metal ions and nutrients, cellular respiration and maintenance of redox homeostasis. This indicates that specific genes may be required by NTHi for its survival or virulence in the COPD lung. These results advance our understanding of the pathogenesis of NTHi infection in COPD lungs.\n\nWhole-genome analyses reveal gene content differences between nontypeable Haemophilus influenzae isolates from chronic obstructive pulmonary disease compared to other clinical phenotypes.", "token_count": 377, "char_count": 1501, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:45.838557", "source": { "split": "train_shard_00001", "doc_id": 1674 }, "chunk_id": "train_shard_00001_1674_0", "global_id": 8015 }, { "text": "

Background

The thermotolerant yeast is beneficial in terms of efficiency improvement of processes and reduction of costs, while Saccharomyces cerevisiae does not efficiently grow and ferment at high-temperature conditions. The sterol composition alteration from ergosterol to fecosterol in the cell membrane of S. cerevisiae affects the thermotolerant capability.

Results

In this study, S. cerevisiae ERG5, ERG4, and ERG3 were knocked out using the CRISPR-Cas9 approach to impact the gene expression involved in ergosterol synthesis. The highest thermotolerant strain was S. cerevisiae ERG5ΔERG4ΔERG3Δ, which produced 22.1 g/L ethanol at 37 °C using the initial glucose concentration of 50 g/L with an increase by 9.4% compared with the wild type (20.2 g/L). The ethanol concentration of 9.4 g/L was produced at 42 ℃, which was 2.85-fold of the wild-type strain (3.3 g/L). The molecular mechanism of engineered S. cerevisiae at the RNA level was analyzed using the transcriptomics method. The simultaneous deletion of S. cerevisiae ERG5, ERG4, and ERG3 caused 278 up-regulated genes and 1892 down-regulated genes in comparison with the wild-type strain. KEGG pathway analysis indicated that the up-regulated genes relevant to ergosterol metabolism were ERG1, ERG11, and ERG5, while the down-regulated genes were ERG9 and ERG26. S. cerevisiae ERG5ΔERG4ΔERG3Δ produced 41.6 g/L of ethanol at 37 °C with 107.7 g/L of corn liquefied glucose as carbon source.

Conclusion

Simultaneous deletion of ERG5, ERG4, and ERG3 resulted in the thermotolerance improvement of S", "token_count": 515, "char_count": 1582, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5507, "quality_score": 0.7753, "entities": { "genes": [ "ERG1", "ERG3", "ERG5", "ERG9", "ERG26", "ERG11", "ERG4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:46.491077", "source": { "split": "train_shard_00001", "doc_id": 1675 }, "chunk_id": "train_shard_00001_1675_0", "global_id": 8016 }, { "text": "cerevisiae ERG5ΔERG4ΔERG3Δ with cell viability improvement by 1.19-fold at 42 °C via modification of steroid metabolic pathway. S. cerevisiae ERG5ΔERG4ΔERG3Δ could effectively produce ethanol at 37 °C using corn liquefied glucose as carbon source. Therefore, S. cerevisiae ERG5ΔERG4ΔERG3Δ had potential in ethanol production at a large scale under supra-optimal temperature.\n\nThermotolerance improvement of engineered Saccharomyces cerevisiae ERG5 Delta ERG4 Delta ERG3 Delta, molecular mechanism, and its application in corn ethanol production.", "token_count": 174, "char_count": 545, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7746, "quality_score": 0.8873, "entities": { "genes": [ "ERG4", "ERG3", "ERG5" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:46.931225", "source": { "split": "train_shard_00001", "doc_id": 1675 }, "chunk_id": "train_shard_00001_1675_1", "global_id": 8017 }, { "text": "Kluyveromyces marxianus is now considered one of the best choices of option for industrial applications of yeast because the strain is able to grow at high temperature, utilizes various carbon sources, and grows fast. However, the use of K. marxianus as a host for industrial applications is still limited. This limitation is largely due to a lack of knowledge on the characteristics of the promoters since the time and amount of protein expression is strongly dependent on the promoter employed. In this study, four well-known constitutive promoters (P(CYC), P(TEF), P(GPD), and P(ADH)) of Saccharomyces cerevisiae were characterized in K. marxianus in terms of protein expression level and their stochastic behavior. After constructing five URA3-auxotrophic K. marxianus strains and a plasmid vector, four cassettes each comprising one of the promoters--the gene for the green fluorescence protein (GFP)--CYC1 terminator (T(CYC)) were inserted into the vector. GFP expression under the control of each one of the promoters was analyzed by reverse transcription PCR, fluorescence microscopy, and flow cytometer. Using these combined methods, the promoter strength was determined to be in the order of P(GPD) > P(ADH) ∼ P(TEF) >> P(CYC). All promoters except for the P(CYC) exhibited three distinctive populations, including non-expressing cells, weakly expressing cells, and strongly expressing cells. The relative ratios between populations were strongly dependent on the promoter and culture time. Forward scattering was independent of GFP fluorescence intensity, indicating that the different fluorescence intensities were not just due to different cell sizes derived from budding. It also excluded the possibility that the non-expressing cells resulted from plasmid loss because plasmid stability was maintained at almost 100 % over the culture time. The same cassettes, cloned into a single copy plasmid pRS416 and transformed into S. cerevisiae, showed only one population. When the cassettes were integrated into the chromosome, the stochastic behavior was markedly reduced", "token_count": 498, "char_count": 2081, "word_count": 305, "semantic_coherence": 1, "information_density": 0.6098, "quality_score": 0.8049, "entities": { "genes": [ "CYC1", "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:47.584682", "source": { "split": "train_shard_00001", "doc_id": 1676 }, "chunk_id": "train_shard_00001_1676_0", "global_id": 8018 }, { "text": "These combined results imply that the gene expression stochasticity should be overcome in order to use this strain for delicate metabolic engineering, which would require the co-expression of several genes.\n\nCharacterization of Saccharomyces cerevisiae promoters for heterologous gene expression in Kluyveromyces marxianus.", "token_count": 71, "char_count": 323, "word_count": 42, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:47.945761", "source": { "split": "train_shard_00001", "doc_id": 1676 }, "chunk_id": "train_shard_00001_1676_1", "global_id": 8019 }, { "text": "Alterations caused by Trypanosoma cruzi in the composition of gut microbiome may play a vital role in the host-parasite interactions that shapes physiology and immune responses against infection. Thus, a better understanding of this parasite-host-microbiome interaction may yield relevant information in the comprehension of the pathophysiology of the disease and the development of new prophylactic and therapeutic alternatives. Therefore, we implemented a murine model with two mice strains (BALB/c and C57BL/6) to evaluate the impact of Trypanosoma cruzi (Tulahuen strain) infection on the gut microbiome utilizing cytokine profiling and shotgun metagenomics. Higher parasite burdens were observed in cardiac and intestinal tissues, including changes in anti-inflammatory (interleukin-4 [IL-4] and IL-10) and proinflammatory (gamma interferon, tumor necrosis factor alpha, and IL-6) cytokines. Bacterial species such as Bacteroides thetaiotaomicron, Faecalibaculum rodentium, and Lactobacillus johnsonii showed a decrease in relative abundance, while Akkermansia muciniphila and Staphylococcus xylosus increased. Likewise, as infection progressed, there was a decrease in gene abundances related to metabolic processes such as lipid synthesis (including short-chain fatty acids) and amino acid synthesis (including branched-chain amino acids). High-quality metagenomic assembled genomes of L. johnsonii and A. muciniphila among other species were reconstructed, confirming, functional changes associated with metabolic pathways that are directly affected by the loss of abundance of specific bacterial taxa. IMPORTANCE Chagas disease (CD) is caused by the protozoan Trypanosoma cruzi, presenting acute and chronic phases where cardiomyopathy, megaesophagus, and/or megacolon stand out. During the course of its life cycle, the parasite has an important gastrointestinal tract transit that leads to severe forms of CD", "token_count": 510, "char_count": 1926, "word_count": 255, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:48.581585", "source": { "split": "train_shard_00001", "doc_id": 1677 }, "chunk_id": "train_shard_00001_1677_0", "global_id": 8020 }, { "text": "The intestinal microbiome plays an essential role in the immunological, physiological, and metabolic homeostasis of the host. Therefore, parasite-host-intestinal microbiome interactions may provide information on certain biological and pathophysiological aspects related to CD. The present study proposes a comprehensive evaluation of the potential effects of this interaction based on metagenomic and immunological data from two mice models with different genetic, immunological, and microbiome backgrounds. Our findings suggest that there are alterations in the immune and microbiome profiles that affect several metabolic pathways that can potentially promote the infection's establishment, progression, and persistence. In addition, this information may prove essential in the research of new prophylactic and therapeutic alternatives for CD.\n\nMicrobiome Alterations Driven by Trypanosoma cruzi Infection in Two Disjunctive Murine Models.", "token_count": 211, "char_count": 949, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7049, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:49.045929", "source": { "split": "train_shard_00001", "doc_id": 1677 }, "chunk_id": "train_shard_00001_1677_1", "global_id": 8021 }, { "text": "The occurrence and effects of the dry and rainy seasons on yeast populations in traditional Serro Minas cheese, one of the most popular cheeses produced from raw milk in Brazil, were studied over the course of 60days of ripening. Enzymatic activity exhibited by these yeast isolates was also studied. A total of 19 yeast species were identified via sequence analysis of the D1/D2 domains of the large subunit of the rRNA gene. Fourteen yeast species were obtained from cheese produced during the dry season, and fifteen species were obtained from cheese produced during the rainy season. High diversity indices for the yeast species were determined for cheese manufactured during both seasons (average H′D=1.7 and H′R=1.5, respectively). The predominant species in Serro Minas cheese included Debaryomyces hansenii, Kodamaea ohmeri and Kluyveromyces marxianus. D. hansenii 28.12 showed low lipolytic and high proteolytic activity. K. marxianus 83F and 60P demonstrated lipolytic and β-galactosidase activity, respectively. K. ohmeri 88A displayed low lipolytic and β-galactosidase activity. Maximal lipase, β-galactosidase and protease activity was observed at 20°C and pH6.0, 30°C and pH7.0 and 50°C and pH6.0, respectively. Considering that D. hansenii 28.12, K. ohmeri 88A and K. marxianus 60P together showed protease, lipase and β-galactosidase activity in this study, further research on the possibility of including these yeasts as part of a starter culture and research on their effects on the sensory properties of Serro Minas cheese merit more study.\n\nThe influence of seasons and ripening time on yeast communities of a traditional Brazilian cheese", "token_count": 464, "char_count": 1659, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5462, "quality_score": 0.7731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:49.682696", "source": { "split": "train_shard_00001", "doc_id": 1678 }, "chunk_id": "train_shard_00001_1678_0", "global_id": 8022 }, { "text": "The feasibility of using a single vector to clone a cytochrome P450 monooxygenase (P450) in different yeasts and then compare whole-cell hydroxylase activity was investigated. A broad-range yeast expression vector using the ylTEFp to drive expression of the cloned gene and the scTEFp to drive the hygromycin resistance marker gene was used to clone the genes encoding two self-sufficient P450s, CYP102A1 and CYP505A1. Both genes were cloned into Saccharomyces cerevisiae, Kluyveromyces marxianus, Yarrowia lipolytica (two strains) and Arxula adeninivorans. 4-Hexylbenzoic acid (HBA), which is subterminally hydroxylated by both CYP102A1 and CYP505A1, was used to compare whole-cell hydroxylase activity of transformants. Kluyveromyces marxianus and A. adeninivorans exhibited activity with both CYP102A1 and CYP505A1, while S. cerevisiae only displayed CYP102A1 activity and Y. lipolytica only CYP505A1 activity. The highest CYP102A1 activity (0.8 mM HBA converted in 24 h) was observed with concentrated resting-cell suspensions of S. cerevisiae. The CYP505A1 activity observed with growing cultures of A. adeninivorans was however at least 12 times higher than the CYP102A1 activity of S. cerevisiae with up to 2 mM HBA converted within 6 h. The use of K. marxianus and A. adeninivorans for P450 expression has not previously been reported.\n\nA broad-range yeast expression system reveals Arxula adeninivorans expressing a fungal self-sufficient cytochrome P450 monooxygenase as an excellent whole-cell biocatalyst.", "token_count": 498, "char_count": 1517, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5628, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:50.335595", "source": { "split": "train_shard_00001", "doc_id": 1679 }, "chunk_id": "train_shard_00001_1679_0", "global_id": 8023 }, { "text": "

Background:

Koumiss is a naturally fermented mare’s milk. Over recent decades, numerous studies have revealed the diversity of lactic acid bacteria in koumiss. However, there is limited information available regarding its secondary major component yeast profile. Results A total of 119 bacterial and 36 yeast species were identified among the 14 koumiss samples. The dominant bacterial species in koumiss were Lactobacillus helveticus , Lactobacillus kefiranofaciens , Lactococcus lactis , Lactococcus raffinolactis , and Citrobacter freundii. The main yeast species were Dekkera anomala , Kazachstania unispora , Meyerozyma caribbica , Pichia sp.BZ159 , Kluyveromyces marxianus , and uncultured Guehomyces . The bacterial and yeast Shannon diversity of the Xilinhaote-urban group were higher than those of the Xilingol-rural group. The most dominant organic acids were lactic, acetic, tartaric, and malic acids. Lactic acid bacteria species were mostly responsible for the accumulation of those organic acids, although Kazachstania unispora , Dekkera anomala , and Meyerozyma caribbica may also have contributed. Redundancy analysis suggested that both bacteria and yeast respond to koumiss flavor, such as Lactobacillus helveticus and Dekkera anomala are associated with sourness, astringency, bitterness, and aftertaste, whereas Lactococcus lactis and Kazachstania unispora are associated with umami. Conclusions Our results suggest that differences were observed in koumiss microbiota of Xilinhaote-urban and Xilingol-rural samples. The biodiversity of the former was higher than the latter group. Positive or negative correlations between bacteria and yeast microbiota and taste also were found.\n\nProfiling of Koumiss Microbiota and Organic Acids and their Effects on Koumiss Taste", "token_count": 500, "char_count": 1800, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5502, "quality_score": 0.7751, "entities": { "genes": [ "BZ159" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:50.991004", "source": { "split": "train_shard_00001", "doc_id": 1680 }, "chunk_id": "train_shard_00001_1680_0", "global_id": 8024 }, { "text": "

Background

A pangenome aims to capture the complete genetic diversity within a species and reduce bias in genetic analysis inherent in using a single reference genome. However, the current linear format of most plant pangenomes limits the presentation of position information for novel sequences. Graph pangenomes have been developed to overcome this limitation. However, there is a lack of bioinformatics analysis tools for graph format genomes.

Results

To overcome this problem, we have developed a novel pangenome construction strategy and a downstream pangenome analysis pipeline that captures position information while maintaining a linearized layout. We applied this strategy to construct a high-quality rice pangenome using 12 representative rice genomes and analyze an international rice panel with 413 diverse accessions using the pangenome reference. Our results provide insights into rice population structure and genomic diversity. Applying the pangenome for PAV-based GWAS analysis can identify causal structural variations for rice grain weight and plant height, while SNP-based GWAS can only identify approximate genomic locations. Additionally, a new locus (qPH8-1) was found to be associated with plant height on chromosome 8 that could not be detected using the SNP-based GWAS.

Conclusions

Our results demonstrate that the pangenome constructed by our pipeline combined with PAV-based GWAS can provide additional power for genomic and genetic analysis. The pangenome constructed in this study and associated genome sequence data provide valuable genomic resources for future rice crop improvement.\n\nA pangenome analysis pipeline (PSVCP) provides insights into rice functional gene identification", "token_count": 368, "char_count": 1741, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:51.563067", "source": { "split": "train_shard_00001", "doc_id": 1681 }, "chunk_id": "train_shard_00001_1681_0", "global_id": 8025 }, { "text": "

Background

Gene duplication is a prevalent phenomenon and a major driving force underlying genome evolution. The process leading to the fixation of gene duplicates following duplication is critical to understand how genome evolves but remains fragmentally understood. Most previous studies on gene retention are based on gene duplicate analyses in single reference genome. No population-based comparative gene retention analysis has been performed to date.

Results

Taking advantage of recently published genomic data in Triticeae, we dissected a divergent homogentisate phytyltransferase (HPT2) lineage caught in the middle stage of gene fixation following duplication. The presence/absence of HPT2 in barley (diploid), wild emmer (tetraploid), and bread wheat (hexaploid) pangenome lines appears to be associated with gene dosage constraint and environmental adaption. Based on these observations, we adopted a phylogeny-based orthology inference approach and performed comparative gene retention analyses across barley, wild emmer, and bread wheat. This led to the identification of 326 HPT2-pattern-like genes at whole genome scale, representing a pool of gene duplicates in the middle stage of gene fixation. Majority of these HPT2-pattern-like genes were identified as small-scale duplicates, such as dispersed, tandem, and proximal duplications. Natural selection analyses showed that HPT2-pattern-like genes have experienced relaxed selection pressure, which is generally accompanied with partial positive selection and transcriptional divergence. Functional enrichment analyses showed that HPT2-pattern-like genes are over-represented with molecular-binding and defense response functions, supporting the potential role of environmental adaption during gene retention. We also observed that gene duplicates from larger gene family are more likely to be lost, implying a gene dosage constraint effect. Further comparative gene retention analysis in barley and bread wheat pangenome lines revealed combined effects of species-specific selection and gene dosage constraint.

Conclusions

Comparative gene retention analyses at the population level support gene dosage constraint, environmental adaption, and species-specific selection as three factors that may affect gene retention following gene duplication", "token_count": 514, "char_count": 2334, "word_count": 302, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7897, "entities": { "genes": [ "HPT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:52.214876", "source": { "split": "train_shard_00001", "doc_id": 1682 }, "chunk_id": "train_shard_00001_1682_0", "global_id": 8026 }, { "text": "Our findings shed light on the evolutionary process leading to the retention of newly formed gene duplicates and will greatly improve our understanding on genome evolution via duplication.\n\nComparative gene retention analysis in barley, wild emmer, and bread wheat pangenome lines reveals factors affecting gene retention following gene duplication.", "token_count": 69, "char_count": 349, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:52.582382", "source": { "split": "train_shard_00001", "doc_id": 1682 }, "chunk_id": "train_shard_00001_1682_1", "global_id": 8027 }, { "text": "Gardnerella is the primary pathogenic bacterial genus present in the polymicrobial infection known as bacterial vaginosis (BV). Despite BV’s high prevalence and associated chronic and acute women’s health impacts, the Gardnerella pangenome is largely uncharacterized at both the genetic and functional metabolic level. Here, we used genome scale metabolic models to characterize in silico the Gardnerella pangenome metabolic content and assessed metabolic functional capacity within a BV positive cervicovaginal fluid context. Metabolic capacity varied widely across the pangenome, with 38.15% of all reactions as core to the genus, compared to 49.6% of reactions identified as unique to a smaller subset of species. Four genes – gpsA, fas, suhB, psd – were identified as core essential genes, critical for in silico metabolic function of all analyzed bacterial species in the Gardnerella genus. Further understanding of these core essential metabolic functions could inform novel therapeutic strategies to treat BV. These data represent the first metabolic modelling of the Gardnerella pangenome and illustrate strain-specific interactions with the vaginal metabolic environment across the pangenome.\n\nMetabolic network models ofGardnerellapangenome identify interactions in the vaginal environment", "token_count": 309, "char_count": 1306, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:53.153101", "source": { "split": "train_shard_00001", "doc_id": 1683 }, "chunk_id": "train_shard_00001_1683_0", "global_id": 8028 }, { "text": "Thermophilic cyanobacteria have been extensively studied in Yellowstone National Park (YNP) hot springs, particularly during decades of work on the thick laminated mats of Octopus and Mushroom springs. However, focused studies of cyanobacteria outside these two hot springs have been lacking, especially regarding how physical and chemical parameters along with community morphology influence the genomic makeup of these organisms. Here, we used a metagenomic approach to examine cyanobacteria existing at the upper temperature limit of photosynthesis. We examined 15 alkaline hot spring samples across six geographic areas of YNP, all with various physical and chemical parameters and community morphology. We recovered 22 metagenome-assembled genomes (MAGs) belonging to thermophilic cyanobacteria, notably an uncultured Synechococcus-like taxon recovered from a setting at the upper temperature limit of photosynthesis, 73°C, in addition to thermophilic Gloeomargarita. Furthermore, we found that three distinct groups of Synechococcus-like MAGs recovered from different temperature ranges vary in their genomic makeup. MAGs from the uncultured very-high-temperature (up to 73°C) Synechococcus-like taxon lack key nitrogen metabolism genes and have genes implicated in cellular stress responses that diverge from other Synechococcus-like MAGs. Across all parameters measured, temperature was the primary determinant of taxonomic makeup of recovered cyanobacterial MAGs. However, total Fe, community morphology, and biogeography played an additional role in the distribution and abundance of upper-temperature-limit-adapted Synechococcus-like MAGs. These findings expand our understanding of cyanobacterial diversity in YNP and provide a basis for interrogation of understudied thermophilic cyanobacteria", "token_count": 476, "char_count": 1848, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6271, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:53.795727", "source": { "split": "train_shard_00001", "doc_id": 1684 }, "chunk_id": "train_shard_00001_1684_0", "global_id": 8029 }, { "text": "IMPORTANCE Oxygenic photosynthesis arose early in microbial evolution-approximately 2.5 to 3.5 billion years ago-and entirely reshaped the biological makeup of Earth. However, despite the span of time in which photosynthesis has been refined, it is strictly limited to temperatures below 73°C, a barrier that many other biological processes have been able to overcome. Furthermore, photosynthesis at temperatures above 56°C is limited to circumneutral and alkaline pH. Hot springs in Yellowstone National Park (YNP), which have a large diversity in temperatures, pH, and geochemistry, provide a natural laboratory to study thermophilic microbial mats and the cyanobacteria within. While cyanobacteria in YNP microbial mats have been studied for decades, a vast majority of the work has focused on two springs within the same geyser basin, both containing similar community morphologies. Thus, the drivers of cyanobacterial adaptations to the upper limits of photosynthesis across a variety of environmental parameters have been understudied. Our findings provide new insights into the influence of these parameters on both taxonomic diversity and genomic content of cyanobacteria across a range of hot spring samples.\n\nDistribution and Genomic Variation of Thermophilic Cyanobacteria in Diverse Microbial Mats at the Upper Temperature Limits of Photosynthesis.", "token_count": 334, "char_count": 1367, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6237, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:54.362649", "source": { "split": "train_shard_00001", "doc_id": 1684 }, "chunk_id": "train_shard_00001_1684_1", "global_id": 8030 }, { "text": "Genetic variations in protein expression are implicated in a broad spectrum of common diseases and complex traits. However, the fundamental genetic architecture and variation of protein expression have received comparatively less attention than either mRNA or classical phenotypes. In this study, we systematically quantified proteins in the brains of a large family of rats using tandem mass tag (TMT)-based quantitative mass-spectrometry (MS) technology. We identified and quantified a comprehensive proteome of 8,119 proteins from Spontaneously Hypertensive (SHR/Olalpcv), Brown Norway with polydactyly-luxate (BN-Lx/Cub), and 29 of their fully inbred HXB/BXH progeny. Differential expression (DE) analysis identified 597 proteins with significant differences in expression between the parental strains (fold change > 2 and FDR < 0.01). We characterized 95 variant peptides by proteogenomics approach and discovered 464 proteins linked to strong cis -acting quantitative trait loci (pQTLs, FDR < 0.05). We also explored the linkage of pQTLs with behavioral phenotypes in rats and examined the sex-specific pQTLs to reveal both distinct and shared cis -pQTLs between sexes. Furthermore, by creating a novel view of the rat pangenome, we improved the ability to pinpoint candidate genes underlying pQTL. Finally, we explored the connection between the pQTLs in rat and human disorders, underscoring the translational potential of our findings. Collectively, this work demonstrates the value of large and systematic proteo-genetic datasets in understanding protein modulation in the brain and its functional linkage to complex central nervous system (CNS) traits.\n\nGenetic Modulation of Protein Expression in Rat Brain", "token_count": 423, "char_count": 1718, "word_count": 243, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:54.988187", "source": { "split": "train_shard_00001", "doc_id": 1685 }, "chunk_id": "train_shard_00001_1685_0", "global_id": 8031 }, { "text": "

Motivation

Pangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions. Nevertheless, analyzing hundreds of gigabase-scale genomes using pangenome graphs is difficult as it is not well-supported by existing tools. Hence, fast and versatile software is required to ask advanced questions to such data in an efficient way.

Results

We wrote Optimized Dynamic Genome/Graph Implementation (ODGI), a novel suite of tools that implements scalable algorithms and has an efficient in-memory representation of DNA pangenome graphs in the form of variation graphs. ODGI supports pre-built graphs in the Graphical Fragment Assembly format. ODGI includes tools for detecting complex regions, extracting pangenomic loci, removing artifacts, exploratory analysis, manipulation, validation and visualization. Its fast parallel execution facilitates routine pangenomic tasks, as well as pipelines that can quickly answer complex biological questions of gigabase-scale pangenome graphs.

Availability and implementation

ODGI is published as free software under the MIT open source license. Source code can be downloaded from https://github.com/pangenome/odgi and documentation is available at https://odgi.readthedocs.io. ODGI can be installed via Bioconda https://bioconda.github.io/recipes/odgi/README.html or GNU Guix https://github.com/pangenome/odgi/blob/master/guix.scm.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nODGI: understanding pangenome graphs.", "token_count": 401, "char_count": 1681, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7085, "quality_score": 0.8543, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:55.629069", "source": { "split": "train_shard_00001", "doc_id": 1686 }, "chunk_id": "train_shard_00001_1686_0", "global_id": 8032 }, { "text": "Pantoea stewartii subsp. indologenes (Psi) is a causative agent of leafspot of foxtail millet and pearl millet; however, novel strains were recently identified that are pathogenic on onion. Our recent host range evaluation study identified two pathovars; P. stewartii subsp. indologenes pv. cepacicola pv. nov. and P. stewartii subsp. indologenes pv. setariae pv. nov. that are pathogenic on onion and millets or on millets only, respectively. In the current study we developed a pan-genome using the whole genome sequencing of newly identified/classified Psi strains from both pathovars [pv. cepacicola (n= 4) and pv. setariae (n=13)]. The full spectrum of the pan-genome contained 7,030 genes. Among these, 3,546 (present in genomes of all 17 strains) were the core genes that were a subset of 3,682 soft-core genes (present in ≥16 strains). The accessory genome included 1,308 shell genes and 2,040 cloud genes (present in ≤ 2 strains). The pan-genome showed a clear liner progression with >6,000 genes, suggesting the pan-genome of Psi is open. Comparative phylogenetic analysis showed differences in phylogenetic clustering of Pantoea spp. using PAVs/wgMLST approach in comparison to core genome SNP-based phylogeny. Further, we conducted a horizontal gene transfer (HGT) study including four other Pantoea species namely, P. stewartii subsp. stewartii LMG 2715T, P. ananatis LMG 2665T, P. agglomerans LMG L15, and P. allii LMG 24248T. A total of 317 HGT events among four Pantoea species were identified with most gene transfers observed between Psi pv. cepacicola and Psi pv. setariae", "token_count": 517, "char_count": 1600, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:56.318319", "source": { "split": "train_shard_00001", "doc_id": 1687 }, "chunk_id": "train_shard_00001_1687_0", "global_id": 8033 }, { "text": "Pan-GWAS analysis predicted a total of 154 genes including seven cluster of genes associated with the pathogenicity phenotype on onion. One of the clusters contain 11 genes with known functions and are found to be chromosomally located.\n\nPan-genome of Novel Pantoea stewartii subsp. indologenes Reveal Genes Involved in Onion Pathogenicity and Evidence of Lateral Gene Transfer", "token_count": 112, "char_count": 395, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8036, "quality_score": 0.9018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:56.731468", "source": { "split": "train_shard_00001", "doc_id": 1687 }, "chunk_id": "train_shard_00001_1687_1", "global_id": 8034 }, { "text": "Plasmids play important roles in bacterial genome diversification. In the Serratia marcescens complex (SMC), a notable contribution of plasmids to genome diversification was also suggested by our recent analysis of >600 draft genomes. As accurate analyses of plasmids in draft genomes are difficult, in this study we analysed 142 closed genomes covering the entire complex, 67 of which were obtained in this study, and identified 132 plasmids (1.9-244.4 kb in length) in 77 strains. While the average numbers of plasmids in clinical and non-clinical strains showed no significant difference, strains belonging to clade 2 (one of the two hospital-adapted lineages) contained more plasmids than the others. Pangenome analysis revealed that of the 28 954 genes identified, 12.8 % were plasmid-specific, and 1.4 % were present in plasmids or chromosomes depending on the strain. In the latter group, while transposon-related genes were most prevalent (31.4 % of the function-predicted genes), genes related to antimicrobial resistance and heavy metal resistance accounted for a notable proportion (22.7 %). Mash distance-based clustering separated the 132 plasmids into 23 clusters and 50 singletons. Most clusters/singletons showed notably different GC contents compared to those of host chromosomes, suggesting their recent or relatively recent appearance in the SMC. Among the 23 clusters, 17 were found in only clinical or only non-clinical strains, suggesting the possible preference of their distribution on the environmental niches of host strains. Regarding the host strain phylogeny, 16 clusters were distributed in two or more clades, suggesting their interclade transmission. Moreover, for many plasmids, highly homologous plasmids were found in other species, indicating the broadness of their potential host ranges, beyond the genus, family, order, class or even phylum level", "token_count": 485, "char_count": 1891, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6282, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:57.387744", "source": { "split": "train_shard_00001", "doc_id": 1688 }, "chunk_id": "train_shard_00001_1688_0", "global_id": 8035 }, { "text": "Importantly, highly homologous plasmids were most frequently found in Klebsiella pneumoniae and other species in the family Enterobacteriaceae, suggesting that this family, particularly K. pneumoniae, is the main source for plasmid exchanges with the SMC. These results highlight the power of closed genome-based analysis in the investigation of plasmids and provide important insights into the nature of plasmids distributed in the SMC.\n\nSystematic analysis of plasmids of the Serratia marcescens complex using 142 closed genomes.", "token_count": 151, "char_count": 559, "word_count": 75, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:57.818396", "source": { "split": "train_shard_00001", "doc_id": 1688 }, "chunk_id": "train_shard_00001_1688_1", "global_id": 8036 }, { "text": "The microbes present in the human gastrointestinal tract are regularly linked to human health and disease outcomes. Thanks to technological and methodological advances in recent years, metagenomic sequencing data, and computational methods designed to analyze metagenomic data, have contributed to improved understanding of the link between the human gut microbiome and disease. However, while numerous methods have been recently developed to extract quantitative and qualitative results from host-associated microbiome data, improved computational tools are still needed to track microbiome dynamics with short-read sequencing data. Previously we have proposed KOMB as a de novo tool for identifying copy number variations in metagenomes for characterizing microbial genome dynamics in response to perturbations. In this work, we present KombOver (KO), which includes four key contributions with respect to our previous work: (i) it scales to large microbiome study cohorts, (ii) it includes both k-core and K-truss based analysis, (iii) we provide the foundation of a theoretical understanding of the relation between various graph-based metagenome representations, and (iv) we provide an improved user experience with easier-to-run code and more descriptive outputs/results. To highlight the aforementioned benefits, we applied KO to nearly 1000 human microbiome samples, requiring less than 10 minutes and 10 GB RAM per sample to process these data. Furthermore, we highlight how graph-based approaches such as k-core and K-truss can be informative for pinpointing microbial community dynamics within a myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) cohort. KO is open source and available for download/use at: https://github.com/treangenlab/komb.\n\nKombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome.", "token_count": 426, "char_count": 1877, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6537, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:58.440717", "source": { "split": "train_shard_00001", "doc_id": 1689 }, "chunk_id": "train_shard_00001_1689_0", "global_id": 8037 }, { "text": "

Background

Winkia neuii, previously known as Actinomyces neuii, is increasingly recognized as a causative agent of various human infections, while its taxonomy and genomic insights are still understudied.

Methods

A Winkia strain NY0527 was isolated from the hip abscess of a patient, and its antibiotic susceptibility was assessed. The genome was hybrid assembled from long-reads and short-reads sequencing. Whole-genome-based analyses on taxa assignment, strain diversity, and pathogenesis were conducted.

Results

The strain was found to be highly susceptible to beta-lactam antibiotics, but resistant to erythromycin, clindamycin, and amikacin. The complete genome sequences of this strain were assembled and found to consist of a circular chromosome and a circular plasmid. Sequence alignment to the NCBI-nt database revealed that the plasmid had high sequence identity (>90%) to four Corynebacterium plasmids, with 40-50% query sequence coverage. Furthermore, the plasmid was discovered to possibly originate from the sequence recombination events of two Corynebacterium plasmid families. Phylogenomic tree and genomic average nucleotide identity analyses indicated that many Winkia sp. strains were still erroneously assigned as Actinomyces sp. strains, and the documented subspecies within W. neuii should be reclassified as two separate species (i.e., W. neuii and W. anitratus). The core genome of each species carried a chromosome-coded beta-lactamase expression repressor gene, which may account for their broadly observed susceptibility to beta-lactam antibiotics in clinical settings. Additionally, an ermX gene that expresses fluoroquinolone resistance was shared by some W. neuii and W", "token_count": 524, "char_count": 1808, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6537, "quality_score": 0.8268, "entities": { "genes": [ "NY0527" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:13:59.102826", "source": { "split": "train_shard_00001", "doc_id": 1690 }, "chunk_id": "train_shard_00001_1690_0", "global_id": 8038 }, { "text": "anitratus strains, possibly acquired by IS6 transposase-directed gene transfer events. In contrast, tetracycline resistance genes were exclusively carried by W. neuii strains. In particular, W. neuii was found to be more pathogenic than W. anitratus by encoding more virulence factors (i.e., 35-38 in W. neuii vs 27-31 in W. anitratus). Moreover, both species encoded two core pathogenic virulence factors, namely hemolysin and sialidase, which may facilitate their infections by expressing poreformation, adhesion, and immunoglobulin deglycosylation activities.

Conclusion

This study highlights the underappreciated taxonomic diversity of Winkia spp. and provides populational genomic insights into their antibiotic susceptibility and pathogenesis for the first time, which could be helpful in the clinical diagnosis and treatment of Winkia spp. infections.\n\nComparative genomic analyses of the clinically-derived Winkia strain NY0527: the reassignment of W. neuii subsp. neuii and W. neuii subsp. antitratus into two separate species and insights into their virulence characteristics.", "token_count": 371, "char_count": 1181, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.831, "entities": { "genes": [ "IS6", "NY0527" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:13:59.681719", "source": { "split": "train_shard_00001", "doc_id": 1690 }, "chunk_id": "train_shard_00001_1690_1", "global_id": 8039 }, { "text": "

Introduction

Neisseria gonorrhoeae (Ng) has successively developed resistance to all previously recommended antimicrobial therapies, with ceftriaxone being the last option for monotherapy of gonorrhea. Global emergence and international spread of the FC428 clone derived mosaic penA-60 allele, associated with highlevel ceftriaxone minimum inhibitory concentrations (MICs) in non FC428 clone Ng lineages, has become an increasing concern. The penA-60 allele carrying Ng was first identified in the U.S. in Las Vegas, Nevada (2019; GCWGS-102723), with a multi-locus sequence type (MLST)-1901 strain, in a non FC428 clone Ng lineage, which is associated with a historically ceftriaxone susceptible core genogroup. Later in 2022, an allele genetically similar to penA-60, mosaic penA-237, was identified in the UK (H22-722) and France (F92) with high-level ceftriaxone MICs and both belonged to MLST-1901.

Methods

In this study, we assessed phylogenomic relatedness and antimicrobial resistance (AMR) determinant profiles of these three isolates with high-level ceftriaxone MICs among a global collection of 2,104 genomes belonging to the MLST-1901 core genome cluster group 31, which includes strains separated by a locus threshold of 200 or fewer differences (Ng_cgc_200). Recombination events in and around the penA coding region were catalogued and potential sources of inter species recombinant DNA were also inferred.

Results

The global population structure of MLST-1901 core genogroup falls into 4 major lineages", "token_count": 497, "char_count": 1580, "word_count": 209, "semantic_coherence": 1, "information_density": 0.689, "quality_score": 0.8445, "entities": { "genes": [ "FC428" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:00.340826", "source": { "split": "train_shard_00001", "doc_id": 1691 }, "chunk_id": "train_shard_00001_1691_0", "global_id": 8040 }, { "text": "Isolates GCWGS-10723, F92, and H22-722 clustered within Lineage 1, which was dominated by non-mosaic penA-5 alleles. These three isolates formed a clade within Lineage 1 that consisted of isolates from North America and southeast Asia. Neisseria subflava and Neisseria sicca were identified as likely progenitors of two independent recombination events that may have led to the generation of mosaic penA-60 and penA-237, within a possible non-mosaic penA-5 background.

Discussions

Our study suggests that there are multiple evolutionary pathways that could generate concerning mosaic penA alleles via homologous recombination of historically susceptible Ng lineages with Neisseria commensals. Enhanced surveillance of gonococcal strains and Neisseria commensals is crucial for understanding of the evolution of AMR, particularly in less-studied regions (e.g., Asia), where high-level ceftriaxone MICs and multi-drug resistance are more prevalent.\n\nEmergence and evolution of mosaic penA-60 and penA-237 alleles in a Neisseria gonorrhoeae core genogroup that was historically susceptible to extended spectrum cephalosporins.", "token_count": 389, "char_count": 1207, "word_count": 150, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:00.970826", "source": { "split": "train_shard_00001", "doc_id": 1691 }, "chunk_id": "train_shard_00001_1691_1", "global_id": 8041 }, { "text": "Tools that classify sequencing reads against a database of reference sequences require efficient index data-structures. The r-index is a compressed full-text index that answers substring presence/absence, count, and locate queries in space proportional to the amount of distinct sequence in the database: [Formula: see text] space, where r is the number of Burrows-Wheeler runs. To date, the r-index has lacked the ability to quickly classify matches according to which reference sequences (or sequence groupings, i.e., taxa) a match overlaps. We present new algorithms and methods for solving this problem. Specifically, given a collection D of d documents, [Formula: see text] over an alphabet of size σ, we extend the r-index with [Formula: see text] additional words to support document listing queries for a pattern [Formula: see text] that occurs in [Formula: see text] documents in D in [Formula: see text] time and [Formula: see text] space, where w is the machine word size. Applied in a bacterial mock community experiment, our method is up to three times faster than a comparable method that uses the standard r-index locate queries. We show that our method classifies both simulated and real nanopore reads at the strain level with higher accuracy compared with other approaches. Finally, we present strategies for compacting this structure in applications in which read lengths or match lengths can be bounded.\n\nEfficient taxa identification using a pangenome index.", "token_count": 372, "char_count": 1528, "word_count": 229, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:01.551174", "source": { "split": "train_shard_00001", "doc_id": 1692 }, "chunk_id": "train_shard_00001_1692_0", "global_id": 8042 }, { "text": "

Unlabelled

The symbiotic relationship between vestimentiferan tubeworms and their intracellular chemosynthetic bacteria is one of the more noteworthy examples of adaptation to deep-sea hydrothermal vent environments. The tubeworm symbionts have never been cultured in the laboratory. Nucleotide sequences from the small subunit rRNA gene suggest that the intracellular symbionts of the eastern Pacific vent tubeworms Oasisia alvinae, Riftia pachyptila, Tevnia jerichonana, and Ridgeia piscesae belong to the same phylotype of gammaproteobacteria, \"Candidatus Endoriftia persephone.\" Comparisons of symbiont genomes between the East Pacific Rise tubeworms R. pachyptila and T. jerichonana confirmed that these two hosts share the same symbionts. Two Ridgeia symbiont genomes were assembled from trophosome metagenomes from worms collected from the Juan de Fuca Ridge (one and five individuals, respectively). We compared these assemblies to those of the sequenced Riftia and Tevnia symbionts. Pangenome composition, genome-wide comparisons of the nucleotide sequences, and pairwise comparisons of 2,313 orthologous genes indicated that \"Ca Endoriftia persephone\" symbionts are structured on large geographical scales but also on smaller scales and possibly through host specificity.

Importance

Remarkably, the intracellular symbionts of four to six species of eastern Pacific vent tubeworms all belong to the same phylotype of gammaproteobacteria, \"Candidatus Endoriftia persephone.\" Understanding the structure, dynamism, and interconnectivity of \"Ca Endoriftia persephone\" populations is important to advancing our knowledge of the ecology and evolution of their host worms, which are often keystone species in vent communities. In this paper, we present the first genomes for symbionts associated with the species R. piscesae, from the Juan de Fuca Ridge", "token_count": 501, "char_count": 1871, "word_count": 250, "semantic_coherence": 1, "information_density": 0.576, "quality_score": 0.788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:02.214920", "source": { "split": "train_shard_00001", "doc_id": 1693 }, "chunk_id": "train_shard_00001_1693_0", "global_id": 8043 }, { "text": "We then combine these genomes with published symbiont genomes from the East Pacific Rise tubeworms R. pachyptila and T. jerichonana to develop a portrait of the \"Ca Endoriftia persephone\" pangenome and an initial outline of symbiont population structure in the different host species. Our study is the first to apply genome-wide comparisons of \"Ca Endoriftia persephone\" assemblies in the context of population genetics and molecular evolution.\n\nInsights into Symbiont Population Structure among Three Vestimentiferan Tubeworm Host Species at Eastern Pacific Spreading Centers.", "token_count": 150, "char_count": 577, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:02.649692", "source": { "split": "train_shard_00001", "doc_id": 1693 }, "chunk_id": "train_shard_00001_1693_1", "global_id": 8044 }, { "text": "The creation and comparison of minimal genomes will help better define the most fundamental mechanisms supporting life. Mesoplasma florum is a near-minimal, fast-growing, nonpathogenic bacterium potentially amenable to genome reduction efforts. In a comparative genomic study of 13 M. florum strains, including 11 newly sequenced genomes, we have identified the core genome and open pangenome of this species. Our results show that all of the strains have approximately 80% of their gene content in common. Of the remaining 20%, 17% of the genes were found in multiple strains and 3% were unique to any given strain. On the basis of random transposon mutagenesis, we also estimated that ~290 out of 720 genes are essential for M. florum L1 in rich medium. We next evaluated different genome reduction scenarios for M. florum L1 by using gene conservation and essentiality data, as well as comparisons with the first working approximation of a minimal organism, Mycoplasma mycoides JCVI-syn3.0. Our results suggest that 409 of the 473 M. mycoides JCVI-syn3.0 genes have orthologs in M. florum L1. Conversely, 57 putatively essential M. florum L1 genes have no homolog in M. mycoides JCVI-syn3.0. This suggests differences in minimal genome compositions, even for these evolutionarily closely related bacteria. IMPORTANCE The last years have witnessed the development of whole-genome cloning and transplantation methods and the complete synthesis of entire chromosomes. Recently, the first minimal cell, Mycoplasma mycoides JCVI-syn3.0, was created. Despite these milestone achievements, several questions remain to be answered. For example, is the composition of minimal genomes virtually identical in phylogenetically related species. On the basis of comparative genomics and transposon mutagenesis, we investigated this question by using an alternative model, Mesoplasma florum, that is also amenable to genome reduction efforts. Our results suggest that the creation of additional minimal genomes could help reveal different gene compositions and strategies that can support life, even within closely related species.", "token_count": 518, "char_count": 2126, "word_count": 312, "semantic_coherence": 1, "information_density": 0.5673, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:03.288088", "source": { "split": "train_shard_00001", "doc_id": 1694 }, "chunk_id": "train_shard_00001_1694_0", "global_id": 8045 }, { "text": "Inferring the Minimal Genome of <i>Mesoplasma florum</i> by Comparative Genomics and Transposon Mutagenesis.", "token_count": 44, "char_count": 120, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:03.654485", "source": { "split": "train_shard_00001", "doc_id": 1694 }, "chunk_id": "train_shard_00001_1694_1", "global_id": 8046 }, { "text": "Genomics analyses often use a large sequence collection as a reference, like a pangenome or taxonomic database. We previously described SPUMONI, which performs binary classification of nanopore reads using pangenomic matching statistics. Here we describe SPUMONI 2, an improved version that is faster, more memory efficient, works effectively for both short and long reads, and can solve multi-class classification problems with the aid of a novel sampled document array structure. By incorporating minimizers, SPUMONI 2 reduces index size by a factor of 2 compared to SPUMONI, yielding an index more than 65 times smaller than minimap2’s for a mock community pangenome. SPUMONI 2 also achieves a speed improvement of 3-fold compared to SPUMONI and 15-fold compared to minimap2. We show SPUMONI 2 achieves an advantageous mix of accuracy and efficiency for short and long reads, including in an adaptive sampling scenario. We further demonstrate that SPUMONI 2 can detect contaminated contigs in genome assemblies, and can perform multi-class metagenomic read classification.\n\nSPUMONI 2: Improved pangenome classification using a compressed index of minimizer digests", "token_count": 281, "char_count": 1167, "word_count": 173, "semantic_coherence": 1, "information_density": 0.659, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:04.210440", "source": { "split": "train_shard_00001", "doc_id": 1695 }, "chunk_id": "train_shard_00001_1695_0", "global_id": 8047 }, { "text": "

Background

Kluyveromyces marxianus has recently become a species of interest for ethanol production since it can produce ethanol at high temperature and on a wide variety of substrates. However, the reason why this yeast can produce ethanol at high temperature is largely unknown.

Results

The ethanol fermentation capability of K. marxianus GX-UN120 at 40°С was found to be the same as that of Saccharomyces cerevisiae at 34°С. Zymogram analysis showed that alcohol dehydrogenase 1 (KmAdh1) was largely induced during ethanol production, KmAdh4 was constitutively expressed at a lower level and KmAdh2 and KmAdh3 were almost undetectable. The genes encoding the four alcohol dehydrogenases (ADHs) were cloned from strain GX-UN120. Each KmADH was expressed in Escherichia coli and each recombinant protein was digested with enterokinase to remove the fusion protein. The optimum pH of the purified recombinant KmAdh1 was 8.0 and that of KmAdh2, KmAdh3 and KmAdh4 was 7.0. The optimum temperatures of KmAdh1, KmAdh2, KmAdh3 and KmAdh4 were 50, 45, 55 and 45°C, respectively. The K(m) values of the recombinant KmAdh1 and KmAdh2 were 4.0 and 1.2 mM for acetaldehyde and 39.7 and 49.5 mM for ethanol, respectively. The V(max) values of the recombinant KmAdh1 and KmAdh2 were 114.9 and 21.6 μmol min⁻¹ mg⁻¹ for acetaldehyde and 57.5 and 1.8 μmol min⁻¹ mg⁻¹ for ethanol, respectively", "token_count": 507, "char_count": 1392, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5728, "quality_score": 0.7864, "entities": { "genes": [ "UN120" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:04.864629", "source": { "split": "train_shard_00001", "doc_id": 1696 }, "chunk_id": "train_shard_00001_1696_0", "global_id": 8048 }, { "text": "KmAdh3 and KmAdh4 catalyze the oxidation reaction of ethanol to acetaldehyde but not the reduction reaction of acetaldehyde to ethanol, and the K(m) values of the recombinant KmAdh3 and KmAdh4 were 26.0 and 17.0 mM for ethanol, respectively. The V(max) values of the recombinant KmAdh3 and KmAdh4 were 12.8 and 56.2 μmol min⁻¹ mg⁻¹ for ethanol, respectively.

Conclusion

These data in this study collectively indicate that KmAdh1 is the primary ADH responsible for the production of ethanol from the reduction of acetaldehyde in K. marxianus. The relatively high optimum temperature of KmAdh1 may partially explain the ability of K. marxianus to produce ethanol at high temperature. Understanding the biochemical characteristics of KmAdhs will enhance our fundamental knowledge of the metabolism of ethanol fermentation in K. marxianus.\n\nAlcohol dehydrogenases from Kluyveromyces marxianus: heterologous expression in Escherichia coli and biochemical characterization.", "token_count": 313, "char_count": 974, "word_count": 137, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:05.428622", "source": { "split": "train_shard_00001", "doc_id": 1696 }, "chunk_id": "train_shard_00001_1696_1", "global_id": 8049 }, { "text": "Understanding the ecology of pathogens is important for disease management. Recently, a devastating canker disease was found on red alder (Alnus rubra) planted as landscape trees. Bacteria were isolated from two groups of symptomatic trees located approximately 1 km apart, and one strain from each group was used to complete Koch's postulates. The results showed that these bacteria can cause disease not only on red alder but also on two other alder species. Unexpectedly, analyses of genome sequences of bacterial strains identified them as Lonsdalea quercina, a pathogenic species previously known to cause dieback of oak species, but not alder. Additionally, a core genome phylogeny clustered bacterial strains isolated from red alder within a subclade of L. quercina strains isolated from symptomatic oak trees. Consistent with the close phylogenetic relationship, there was no obvious evidence for divergence in genome composition of strains isolated from red alder and oak. Altogether, the findings indicate that L. quercina is a potential threat to Alnus species.\n\nCanker and Dieback of Alnus rubra Is Caused by Lonsdalea quercina", "token_count": 274, "char_count": 1139, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:05.974352", "source": { "split": "train_shard_00001", "doc_id": 1697 }, "chunk_id": "train_shard_00001_1697_0", "global_id": 8050 }, { "text": "

Background

The emergence of extensively drug-resistant (XDR) Salmonella in humans poses a significant public health and therapeutic challenge. However, limited data are available on XDR Salmonella isolates from Guizhou province, China. This study aimed to investigate the molecular epidemiology and resistance patterns of XDR Salmonella isolates from clinical samples in this region.

Methods

A total of 931 Salmonella isolates were screened for XDR isolates through antimicrobial susceptibility testing. These XDR isolates were subjected to whole-genome sequencing (WGS) and bioinformatic analysis to further systematically investigating the molecular epidemiology and resistance patterns of XDR Salmonella isolates.

Results

Between 2019 and 2023, 931 Salmonella isolates were collected from clinical samples in Guizhou. Of these isolates, 51 (5.5%) were identified as XDR and classified into 16 serovars. Among the serovars, 15 corresponded to a specific sequence type, except for S. Typhimurium serovars. The predominant serovars, S. 1,4,[5],12:i:-, S. Enteritidis, and S. Kentucky, were divided into ST34, ST11, and ST198, respectively. Genomic analysis showed that all XDR isolates harbored at least eight antimicrobial resistance genes (ARGs) and multidrug efflux pumps. Highly prevalent point mutations in gyrA (D87 and S83) and parC (S80I) were detected, along with eight plasmid-mediated quinolone resistance (PMQR) genes", "token_count": 492, "char_count": 1542, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [ "ST34", "ST198", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:06.628335", "source": { "split": "train_shard_00001", "doc_id": 1698 }, "chunk_id": "train_shard_00001_1698_0", "global_id": 8051 }, { "text": "The qnrS1 gene was the most common (43.1%), followed by oqxA, aac-(6')-lb-cr variant, qnrB4, qnrS2, qnrA1, qepA2, and oqxB. The predominant β-lactamase gene was blaTEM-1 (54.9%), and blaCTX-M-55 (35.3%) was the most prevalent extended-spectrum β-lactamase subtype. Notably, blaNDM-1 gene was identified for the first time in Salmonella from Guizhou, and one S. 1,4,[5],12:i:- isolate contained the mcr-1.1 gene. ARGs profiles varied by serovars, with S. 1,4,[5],12:i:- isolates carrying the highest number. Ten plasmid types were identified, predominantly IncHI2/IncHI2A (47.5%). Key resistance genes such as tetA, PMQR, blaCTX-M , mcr-1.1, and blaNDM-1 were located on IncHI2/IncHI2A plasmids. Notably, 75.0% of the conjugative plasmids belonged to IncHI2/IncHI2A, indicating that horizontal gene transfer through conjugation facilitates ARGs dissemination", "token_count": 471, "char_count": 1066, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7739, "quality_score": 0.887, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:07.301156", "source": { "split": "train_shard_00001", "doc_id": 1698 }, "chunk_id": "train_shard_00001_1698_1", "global_id": 8052 }, { "text": "Core genome multilocus sequence typing (cgMLST) analysis revealed significant genetic diversity, with 39 core genome sequence types (cgSTs) identified and no evidence of outbreaks.

Conclusion

The rising prevalence of XDR Salmonella in Guizhou province is concerning. Initial whole-genome sequencing (WGS) data provide critical insights for understanding and controlling XDR Salmonella infections, aiding public health officials in identifying emerging threats and trends.\n\nGenomic analyses reveal presence of extensively drug-resistant <i>Salmonella enterica</i> serovars isolated from clinical samples in Guizhou province, China, 2019-2023.", "token_count": 179, "char_count": 674, "word_count": 78, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:07.751916", "source": { "split": "train_shard_00001", "doc_id": 1698 }, "chunk_id": "train_shard_00001_1698_2", "global_id": 8053 }, { "text": "

Background

Carbon sources for biofuel production are wide-ranging and their availability depends on the climate and soil conditions of the land where the production chain is located. Henequen (Agave fourcroydes Lem.) is cultivated in Yucatán, Mexico to produce natural fibers from the leaves, and a juice containing fructans is produced during this process. Fructans can be hydrolyzed to fructose and glucose and metabolized into ethanol by appropriate yeasts. In Mexico, different Agave species provide the carbon source for (distilled and non-distilled) alcoholic beverage production using the stem of the plant, whilst the leaves are discarded. In this work, we investigated the effect of thermal acid and enzymatic hydrolysis of the juice on the amount of reducing sugars released. Growth curves were generated with the yeasts Saccharomyces cerevisiae and Kluyveromyces marxianus and fermentations were then carried out with Kluyveromyces marxianus to determine alcohol yields.

Results

With thermal acid hydrolysis, the greatest increase in reducing sugars (82.6%) was obtained using 5% H2SO4 at 100°C with a 30 min reaction time. Statistically similar results can be obtained using the same acid concentration at a lower temperature and with a shorter reaction time (60°C, 15 min), or by using 1% H2SO4 at 100°C with a 30 min reaction time. In the case of enzymatic hydrolysis, the use of 5.75, 11.47 and 22.82 U of enzyme did not produce significant differences in the increase in reducing sugars. Although both hydrolysis processes obtained similar results, the difference was observed after fermentation. Ethanol yields were 50.3 ± 4 and 80.04 ± 5.29% of the theoretical yield respectively.

Conclusions

Final reducing sugars concentrations obtained with both thermal acid and enzymatic hydrolysis were similar. Saccharomyces cerevisiae, a good ethanol producer, did not grow in the hydrolysates", "token_count": 520, "char_count": 1924, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5851, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:08.416484", "source": { "split": "train_shard_00001", "doc_id": 1699 }, "chunk_id": "train_shard_00001_1699_0", "global_id": 8054 }, { "text": "Only Kluyveromyces marxianus was able to grow in them, giving a higher ethanol yield with the enzymatic hydrolysate. The leaves account for a non-negligible weight of the total agave plant biomass, so this work complements the knowledge already developed on agave fermentations by making it possible to produce ethanol from almost the entire plant (stem and leaves).\n\nHydrolysis of Agave fourcroydes Lemaire (henequen) leaf juice and fermentation with Kluyveromyces marxianus for ethanol production.", "token_count": 133, "char_count": 499, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7671, "quality_score": 0.8836, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:08.877572", "source": { "split": "train_shard_00001", "doc_id": 1699 }, "chunk_id": "train_shard_00001_1699_1", "global_id": 8055 }, { "text": "

Objective

Whole genome sequencing (WGS) can help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time intensive. Given recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource approach providing accurate WGS-pathogen comparison within a time frame allowing for infection prevention and control (IPC) interventions.

Methods

WGS was prospectively performed on pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecaller. Potential transmission was assessed via Ridom SeqSphere+ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cutoff values. The accuracy of our ONT pipeline was determined relative to Illumina.

Results

Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold standard, our ONT pipeline achieved a mean identity score of Q60 for assembled genomes, even with a coverage rate as low as 40×. The mean time from initiating DNA extraction to complete analysis was 2 days (IQR 2-3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of sequenced strains). Integrating ONT with epidemiological data, >70% (15/21) of putative transmission cluster isolates originated from patients with potential healthcare transmission links.

Conclusions

Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in IPC efforts.\n\nRapid whole genome characterization of antimicrobial-resistant pathogens using long-read sequencing to identify potential healthcare transmission.", "token_count": 494, "char_count": 2013, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:09.535960", "source": { "split": "train_shard_00001", "doc_id": 1700 }, "chunk_id": "train_shard_00001_1700_0", "global_id": 8056 }, { "text": "

Background

Candida species are harmless commensals of hosts, including humans, but they can cause infection when the immune system is compromised. Infections with non-albicans species can occur, ranging from urinary tract infections to sepsis, especially among patients in intensive care units.

Case

The patient, a 37-year-old woman, presented with severe abdominal pain, fever, and vomiting. The patient's symptoms and fever continued in spite of treatment with antibiotics, and she underwent exploratory laparotomy. Cyst content culture results showed that Candida kefyr was present in the cyst.

Conclusion

To the best of our knowledge, this is the first case report of a tubo-ovarian abscess caused by C. kefyr. Rare pathogens can be found in patients with a tubo-ovarian abscess, so culture of the abscess material is important for determining subsequent treatment, particularly in women who require an operation for tubo-ovarian abscess.\n\nCase Report of a Tubo-ovarian Abscess Caused by Candida kefyr.", "token_count": 273, "char_count": 1028, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:10.450682", "source": { "split": "train_shard_00001", "doc_id": 1701 }, "chunk_id": "train_shard_00001_1701_0", "global_id": 8057 }, { "text": "Xylitol dehydrogenase (XDH) (EC 1.1.1.9) is one of the key enzymes in the xylose fermentation pathway in yeast and fungi. A xylitol dehydrogenase gene (XYL2) encoding a XDH was cloned from Kluyveromyces marxianus NBRC 1777, and the in vivo function was validated by disruption and complementation analysis. The highest activity of KmXDH could be observed at pH 9.5 during 55°C. The values of k(cat)/K(m) indicate that KmXDH prefers NAD(+) to NADP(+) (k(cat)/K(m NAD)(+) 3681/min mM and k(cat)/K(m NADP)(+) 1361/min mM). The different coenzyme preference between KmXR and KmXDH caused an accumulation of NADH in the xylose utilization pathway. The redox imbalance may be one of the reasons to cause the poor xylose fermentation under oxygen-limited conditions in K. marxianus NBRC1777.\n\nIdentification of a xylitol dehydrogenase gene from Kluyveromyces marxianus NBRC1777.", "token_count": 320, "char_count": 871, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6692, "quality_score": 0.8346, "entities": { "genes": [ "XYL2", "NBRC1777" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:11.013621", "source": { "split": "train_shard_00001", "doc_id": 1702 }, "chunk_id": "train_shard_00001_1702_0", "global_id": 8058 }, { "text": "Vibrio harveyi is a significant pathogen in marine aquaculture, causing vibriosis in various marine species. This study presents a comparative genomic analysis of two V. harveyi strains, N8T11 and 45T2, which exhibit differing virulence profiles. Virulence assays revealed that N8T11 caused 92% mortality in infected fish, while 45T2 resulted in 0% mortality. Whole-genome sequencing revealed that strain N8T11 harbors five plasmids (pN8T11a, pN8T11b, pN8T11c, pN8T11d and pN8T11e) absent in 45T2, encoding genes potentially linked to virulence, such as siderophore-mediated iron acquisition and stress response mechanisms. Pan-genome analysis highlighted substantial genomic plasticity within V. harveyi, with mobile genetic elements, including plasmids and prophages, contributing to horizontal gene transfer. Conjugation experiments demonstrated that all five N8T11 plasmids can transfer to 45T2 with efficiencies up to 87%, with pN8T11b remaining stable across multiple subcultures, enabling the dissemination of virulence-associated genes. These findings suggest that plasmid-mediated gene transfer plays a role in the virulence variability observed between V. harveyi strains. This study contributes to understanding the genomic factors underlying pathogenicity in V. harveyi and provides insights for future research aimed at controlling vibriosis in aquaculture.\n\nComparative Genomic Analysis of Two <i>Vibrio harveyi</i> Strains from <i>Larimichthys crocea</i> with Divergent Virulence Profiles.", "token_count": 468, "char_count": 1563, "word_count": 196, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:11.662929", "source": { "split": "train_shard_00001", "doc_id": 1703 }, "chunk_id": "train_shard_00001_1703_0", "global_id": 8059 }, { "text": "The study of livestock microbiota has immediate benefits for animal health as well as mitigating food contamination and emerging pathogens. While prior research has indicated the gastrointestinal tract of cattle as the source for many zoonoses, including Shiga-toxin producing Escherichia coli and antibiotic resistant bacteria, the bovine urinary tract microbiota has yet to be thoroughly investigated. Here, we describe 5 E. coli and 4 Pseudomonas aeruginosa strains isolated from urine of dairy Gyr cattle. While both species are typically associated with urinary tract infections and mastitis, all of the animals sampled were healthy. The bovine urinary strains were compared to E. coli and P. aeruginosa isolates from other bovine samples as well as human urinary samples. While the bovine urinary E. coli isolates had genomic similarity to isolates from the gastrointestinal tract of cattle and other agricultural animals, the bovine urinary P. aeruginosa strains were most similar to human isolates suggesting niche adaptation rather than host adaptation. Examination of prophages harbored by these bovine isolates revealed similarity with prophages within distantly related E. coli and P. aeruginosa isolates from the human urinary tract. This suggests that related urinary phages may persist and/or be shared between mammals. Future studies of the bovine urinary microbiota are needed to ascertain if E. coli and P. aeruginosa are resident members of this niche and/or possible sources for emerging pathogens in humans.\n\nEscherichia coli and Pseudomonas aeruginosa Isolated From Urine of Healthy Bovine Have Potential as Emerging Human and Bovine Pathogens.", "token_count": 489, "char_count": 1757, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5203, "quality_score": 0.7602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:12.308765", "source": { "split": "train_shard_00001", "doc_id": 1704 }, "chunk_id": "train_shard_00001_1704_0", "global_id": 8060 }, { "text": "Abstract

The emergence and spread of antibiotic resistance (AMR) in clinically important bacterial pathogens severely compromised the effectiveness of commonly used antibiotics in healthcare. Acquisition and transmission of AMR genes (ARGs) are often facilitated by sublethal concentrations of antibiotics in a microbially dense environments. In this study, we used sewage samples (n=371) from six Indian cities between June and December 2023 to assess the concentration of eleven antibiotics, microbial diversity, and ARG richness. Our findings revealed the presence of antibiotics from seven drug classes and over 2000 bacterial ASVs. Metagenomic (n=220) and isolated genome sequences (n=305) of aerobic and anaerobic bacterial species identified 82 ARGs associated with 80 mobile genetic elements (MGEs). These MGEs were predominantly found in multidrug-resistant bacterial pathogens. Comparative core genome analysis of multi drug-resistant (MDR) bacterial isolates (n=7166) showed a strong genetic similarity between sewage-derived strains and clinical pathogens. Our results highlight sewage as a significant reservoir for ARGs, where genetic exchanges occur, facilitating the evolution and spread of AMR pathogens within both community and healthcare settings. Additionally, the dipstick-based assay developed for detection of ARGs in the present study could be employed for sewage surveillance in low resource settings for better understanding of resistance prevalence.

\n\nAntibiotic Contamination and AMR Dynamics in the Urban Sewage Microbiome: Insights from a Longitudinal surveillance", "token_count": 399, "char_count": 1617, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6977, "quality_score": 0.8488, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:12.928967", "source": { "split": "train_shard_00001", "doc_id": 1705 }, "chunk_id": "train_shard_00001_1705_0", "global_id": 8061 }, { "text": "

Objectives

High-quality species-specific transposable element (TE) libraries are required for studies to elucidate the evolutionary dynamics of TEs and gain an understanding of their impacts on host genomes. Such high-quality TE resources are severely lacking for species in the fungal kingdom. To facilitate future studies on the putative role of TEs in rapid adaptation observed in the fungal wheat pathogen Zymoseptoria tritici, we produced a manually curated TE library. This was generated by detecting TEs in 19 reference genome assemblies representing the global diversity of the species supplemented by multiple sister species genomes. Improvements over previous TE libraries have been made on TE boundary resolution, detection of ORFs, TE domains, terminal inverted repeats, and class-specific motifs.

Data description

A TE consensus library for Z. tritici formatted for use with RepeatMasker. This data is relevant to other researchers investigating TE-host evolutionary dynamics in Z. tritici or who are interested in comparative studies of the fungal kingdom. Further, this TE library can be used to improve gene annotation. Finally, this TE library increases the number of manually curated TE datasets, providing resources to further our understanding of TE diversity.\n\nA pangenome-guided manually curated library of transposable elements for Zymoseptoria tritici.", "token_count": 312, "char_count": 1391, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:13.487356", "source": { "split": "train_shard_00001", "doc_id": 1706 }, "chunk_id": "train_shard_00001_1706_0", "global_id": 8062 }, { "text": "This paper presents a new data structure, GIN-TONIC, designed to index arbitrary string-labelled directed graphs representing, for instance, pangenomes or transcriptomes. GIN-TONIC provides several capabilities not offered by other graph-indexing methods based on the FM-index. It is non-hierarchical, handling a graph as a single monolithic object; it indexes at nucleotide resolution all possible walks in the graph without the need to explicitly store them; it supports exact substring queries in polynomial time and space for all possible walk roots in the graph, even if there are exponentially many walks corresponding to such roots. Specific ad-hoc optimisations, such as a precomputed cache, allow GIN-TONIC to achieve excellent performance for input graphs of various topologies and sizes. Robust scalability capabilities and a querying performance close to that of a linear FM-Index are demonstrated for two real-world applications, a human pangenome and transcriptome. Source code and associated benchmarks are available on GitHub.

Availability and implementation

GIN-TONIC and all related programs are available at https://github.com/uensalo/gin .\n\nGIN-TONIC: Non-hierarchical full-text indexing for graph-genomes", "token_count": 283, "char_count": 1234, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7262, "quality_score": 0.8631, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:14.040621", "source": { "split": "train_shard_00001", "doc_id": 1707 }, "chunk_id": "train_shard_00001_1707_0", "global_id": 8063 }, { "text": "The remarkable pace of genomic data generation is rapidly transforming our understanding of life at the micron scale. Yet this data stream also creates challenges for team science. A single microbe can have multiple versions of genome architecture, functional gene annotations, and gene identifiers; additionally, the lack of mechanisms for collating and preserving advances in this knowledge raises barriers to community coalescence around shared datasets. \"Digital Microbes\" are frameworks for interoperable and reproducible collaborative science through open source, community-curated data packages built on a (pan)genomic foundation. Housed within an integrative software environment, Digital Microbes ensure real-time alignment of research efforts for collaborative teams and facilitate novel scientific insights as new layers of data are added. Here we describe two Digital Microbes: 1) the heterotrophic marine bacterium Ruegeria pomeroyi DSS-3 with >100 transcriptomic datasets from lab and field studies, and 2) the pangenome of the cosmopolitan marine heterotroph Alteromonas containing 339 genomes. Examples demonstrate how an integrated framework collating public (pan)genome-informed data can generate novel and reproducible findings.\n\nDigital Microbe: A Genome-Informed Data Integration Framework for Collaborative Research on Emerging Model Organisms", "token_count": 297, "char_count": 1365, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7569, "quality_score": 0.8785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:14.601821", "source": { "split": "train_shard_00001", "doc_id": 1708 }, "chunk_id": "train_shard_00001_1708_0", "global_id": 8064 }, { "text": "Acinetobacter is ubiquitous, and it has a high species diversity and a complex evolutionary pattern. To elucidate the mechanism of its high ability to adapt to various environment, 312 genomes of Acinetobacter strains were analyzed using the phylogenomic and comparative genomics methods. It was revealed that the Acinetobacter genus has an open pan-genome and strong genome plasticity. The pan-genome consists of 47,500 genes, with 818 shared by all the genomes of Acinetobacter, while 22,291 are unique genes. Although Acinetobacter strains do not have a complete glycolytic pathway to directly utilize glucose as carbon source, most of them harbored the n-alkane-degrading genes alkB/alkM (97.1% of tested strains) and almA (96.7% of tested strains), which were responsible for medium-and long-chain n-alkane terminal oxidation reaction, respectively. Most Acinetobacter strains also have catA (93.3% of tested strains) and benAB (92.0% of tested strains) genes that can degrade the aromatic compounds catechol and benzoic acid, respectively. These abilities enable the Acinetobacter strains to easily obtain carbon and energy sources from their environment for survival. The Acinetobacter strains can manage osmotic pressure by accumulating potassium and compatible solutes, including betaine, mannitol, trehalose, glutamic acid, and proline. They respond to oxidative stress by synthesizing superoxide dismutase, catalase, disulfide isomerase, and methionine sulfoxide reductase that repair the damage caused by reactive oxygen species", "token_count": 500, "char_count": 1645, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6791, "quality_score": 0.8395, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:15.253505", "source": { "split": "train_shard_00001", "doc_id": 1709 }, "chunk_id": "train_shard_00001_1709_0", "global_id": 8065 }, { "text": "In addition, most Acinetobacter strains contain many efflux pump genes and resistance genes to manage antibiotic stress and can synthesize a variety of secondary metabolites, including arylpolyene, β-lactone and siderophores among others, to adapt to their environment. These genes enable Acinetobacter strains to survive extreme stresses. The genome of each Acinetobacter strain contained different numbers of prophages (0-12) and genomic islands (GIs) (6-70), and genes related to antibiotic resistance were found in the GIs. The phylogenetic analysis revealed that the alkM and almA genes have a similar evolutionary position with the core genome, indicating that they may have been acquired by vertical gene transfer from their ancestor, while catA, benA, benB and the antibiotic resistance genes could have been acquired by horizontal gene transfer from the other organisms.\n\nA comprehensive genomic analysis provides insights on the high environmental adaptability of Acinetobacter strains.", "token_count": 283, "char_count": 1059, "word_count": 142, "semantic_coherence": 1, "information_density": 0.662, "quality_score": 0.831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:15.803917", "source": { "split": "train_shard_00001", "doc_id": 1709 }, "chunk_id": "train_shard_00001_1709_1", "global_id": 8066 }, { "text": "Haloarchaea are salt-loving archaea and potential source of industrially relevant halotolerant enzymes. In the present study, three reddish-pink, extremely halophilic archaeal strains, namely wsp1 (wsp-water sample Pondicherry), wsp3, and wsp4, were isolated from the Indian Solar saltern. The phylogenetic analysis based on 16S rRNA gene sequences suggests that both wsp3 and wsp4 strains belong to Halogeometricum borinquense while wsp1 is closely related to Haloferax volcanii species. The comparative genomics revealed an open pangenome for both genera investigated here. Whole-genome sequence analysis revealed that these isolates have multiple copies of industrially/biotechnologically important unique genes and enzymes. Among these unique enzymes, for recombinant expression and purification, we selected four putative α-amylases identified in these three isolates. We successfully purified functional halotolerant recombinant Amy2, from wsp1 using pelB signal sequence-based secretion strategy using Escherichia coli as an expression host. This method may prove useful to produce functional haloarchaeal secretory recombinant proteins suitable for commercial or research applications. Biochemical analysis of Amy2 suggests the halotolerant nature of the enzyme having maximum enzymatic activity observed at 1 M NaCl. We also report the isolation and characterization of carotenoids purified from these isolates. This study highlights the presence of several industrially important enzymes in the haloarchaeal strains which may potentially have improved features like stability and salt tolerance suitable for industrial applications.\n\nBiochemical and Taxonomic Characterization of Novel Haloarchaeal Strains and Purification of the Recombinant Halotolerant α-Amylase Discovered in the Isolate.", "token_count": 449, "char_count": 1823, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6766, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:16.442042", "source": { "split": "train_shard_00001", "doc_id": 1710 }, "chunk_id": "train_shard_00001_1710_0", "global_id": 8067 }, { "text": "Clostridioides difficile (CD) is a major planetary health burden. A Gram-positive opportunistic pathogen, CD, colonizes the large intestine and is implicated in sepsis, pseudomembranous colitis, and colorectal cancer. C. difficile infection typically following antibiotic exposure results in dysbiosis of the gut microbiome, and is one of the leading causes of diarrhea in the elderly population. While several studies have focused on the toxigenic strains of CD, gut commensals such as Clostridium butyricum (CB) and Clostridium tertium (CT) could harbor toxin/virulence genes, and thus pose a threat to human health. In this study, we sequenced and characterized three isolates, namely, CT (MALS001), CB (MALS002), and CD (MALS003) for their antimicrobial, cytotoxic, antiproliferative, genomic, and proteomic profiles. Although in vitro cytotoxic and antiproliferative potential were observed predominantly in CD MALS003, genome analysis revealed pathogenic potential of CB MALS002 and CT MALS001. Pangenome analysis revealed the presence of several accessory genes typically involved in fitness, virulence, and resistance characteristics in the core genomes of sequenced strains. The presence of an array of virulence and antimicrobial resistance genes in CB MALS002 and CT MALS001 suggests their potential role as emerging pathogens with significant impact on planetary health.\n\nEmerging Pathogens in Planetary Health and Lessons from Comparative Genome Analyses of Three Clostridia Species.", "token_count": 446, "char_count": 1538, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [ "MALS002", "MALS001", "MALS003" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:17.077156", "source": { "split": "train_shard_00001", "doc_id": 1711 }, "chunk_id": "train_shard_00001_1711_0", "global_id": 8068 }, { "text": "Abstract

Background Genetic engineering of microorganisms has become a common practice to establish microbial cell factories for a wide range of compounds. Ethyl acetate is an industrial solvent that is used in several applications, mainly as a biodegradable organic solvent with low toxicity. While ethyl acetate is produced by several natural yeast species, the main mechanism of production has remained elusive until the discovery of Eat1 in Wickerhamomyces anomalus . Unlike other yeast alcohol acetyl transferases (AATs), Eat1 is located in the yeast mitochondria, suggesting that the coding sequence contains a mitochondrial pre-sequence. For expression in prokaryotic hosts such as E. coli , expression of heterologous proteins with eukaryotic signal sequences may not be optimal. Results Unprocessed and synthetically truncated eat1 variants of Kluyveromyces marxianus and Wickerhamomyces anomalus have been compared in vitro regarding enzyme activity and stability. While the specific activity remained unaffected, half-life improved for several truncated variants. The same variants showed better performance regarding ethyl acetate production when expressed in E. coli. Conclusion By analysing and predicting the N-terminal pre-sequences of different Eat1 proteins and systematically trimming them, the stability of the enzymes in-vitro could be improved, leading to an overall improvement of in-vivo ethyl acetate production in E. coli . Truncated variants of eat1 could therefore benefit future engineering approaches towards efficient ethyl acetate production.

\n\nFrom Eat to trEat: Engineering the mitochondrial Eat1 enzyme for enhanced ethyl acetate production in Escherichia coli", "token_count": 412, "char_count": 1717, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:17.697062", "source": { "split": "train_shard_00001", "doc_id": 1712 }, "chunk_id": "train_shard_00001_1712_0", "global_id": 8069 }, { "text": "Several models and algorithms have been proposed to build pangenomes from multiple input assemblies, but their impact on variant representation, and consequently downstream analyses, is largely unknown. We create multi-species “super-pangenomes” using pggb, cactus, and minigraph with the Bos taurus taurus reference sequence and eleven haplotype-resolved assemblies from taurine and indicine cattle, bison, yak, and gaur. We recover 221k nonredundant structural variations (SVs) from the pangenomes, of which 135k (61%) are common to all three. SVs derived from assembly-based calling show high agreement with the consensus calls from the pangenomes (96%), but validate only a small proportion of variations private to each graph. Pggb and cactus, which also incorporate base-level variation, have approximately 95% exact matches with assembly-derived small variant calls, which significantly improves the edit rate when realigning assemblies compared to minigraph. We use the three pangenomes to investigate 9,566 variable number tandem repeats (VNTRs), finding 63% have identical predicted repeat counts in the three graphs, while minigraph can over or underestimate the count given its approximate coordinate system. We examine a highly variable VNTR locus and show that repeat unit copy number impacts expression of proximal genes and non-coding RNA. Our findings indicate good consensus between the three pangenome methods but also show their individual strengths and weaknesses that need to be considered when analysing different types of variants from multiple input assemblies.\n\nGraph construction method impacts variation representation and analyses in a bovine super-pangenome", "token_count": 388, "char_count": 1687, "word_count": 237, "semantic_coherence": 1, "information_density": 0.7089, "quality_score": 0.8544, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:18.317892", "source": { "split": "train_shard_00001", "doc_id": 1713 }, "chunk_id": "train_shard_00001_1713_0", "global_id": 8070 }, { "text": "Colorectal cancer (CRC) ranks third among all cancers in terms of prevalence. There is growing evidence that gut microbiota has a role in the development of colorectal cancer. Fusobacterium nucleatum is overrepresented in the gastrointestinal tract and tumor microenvironment of patients with CRC. This suggests the role of F. nucleatum as a potential risk factor in the development of CRC. Hence, we aimed to explore whole genomes of F. nucleatum strains related to CRC to predict potential therapeutic markers through a pan-genome integrated subtractive genomics approach. In the current study, we identified 538 proteins as essential for F. nucleatum survival, 209 non-homologous to a human host, and 12 as drug targets. Eventually, riboflavin synthase (RiS) was selected as a therapeutic target for further processing. Three different inhibitor libraries of lead-like natural products, i.e., cyanobactins (n = 237), streptomycins (n = 607), and marine bacterial secondary metabolites (n = 1226) were screened against it. After the structure-based study, three compounds, i.e., CMNPD3609 (−7.63) > Malyngamide V (−7.03) > ZINC06804365 (−7.01) were prioritized as potential inhibitors of F. nucleatum. Additionally, the stability and flexibility of these compounds bound to RiS were determined via a molecular dynamics simulation of 50 ns. Results revealed the stability of these compounds within the binding pocket, after 5 ns. ADMET profiling showed compounds as drug-like, non-permeable to the blood brain barrier, non-toxic, and HIA permeable. Pan-genomics mediated drug target identification and the virtual screening of inhibitors is the preliminary step towards inhibition of this pathogenic oncobacterium and we suggest mouse model experiments to validate our findings.", "token_count": 478, "char_count": 1779, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.832, "entities": { "genes": [ "ZINC06804365", "CMNPD3609" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:18.964140", "source": { "split": "train_shard_00001", "doc_id": 1714 }, "chunk_id": "train_shard_00001_1714_0", "global_id": 8071 }, { "text": "Therapeutic Target Identification and Inhibitor Screening against Riboflavin Synthase of Colorectal Cancer Associated Fusobacterium nucleatum.", "token_count": 43, "char_count": 149, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:19.364135", "source": { "split": "train_shard_00001", "doc_id": 1714 }, "chunk_id": "train_shard_00001_1714_1", "global_id": 8072 }, { "text": "The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small \"hard\" core genome consisting of 381 orthologous groups (OGs), while a \"soft\" core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the \"open\" pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.\n\nComparative Genomics of the Rhodococcus Genus Shows Wide Distribution of Biodegradation Traits.", "token_count": 493, "char_count": 1715, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5726, "quality_score": 0.7863, "entities": { "genes": [ "WAY2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:20.027942", "source": { "split": "train_shard_00001", "doc_id": 1715 }, "chunk_id": "train_shard_00001_1715_0", "global_id": 8073 }, { "text": "Alternaria linariae is an economically important foliar pathogen that causes early blight disease in tomatoes. Understanding genetic diversity, population genetic structure, and evolutionary potential is crucial to contemplating effective disease management strategies. We leveraged genotyping-by-sequencing (GBS) technology to compare genome-wide variation in 124 isolates of Alternaria spp. (A. alternata, A. linariae, and A. solani) for comparative genome analysis and to test the hypotheses of genetic differentiation and linkage disequilibrium (LD) in A. linariae collected from tomatoes in western North Carolina. We performed a pangenome-aware variant calling and filtering with GBSapp and identified 53,238 variants conserved across the reference genomes of three Alternaria spp. The highest marker density was observed on chromosome 1 (7 Mb). Both discriminant analysis of principal components and Bayesian model-based STRUCTURE analysis of A. linariae isolates revealed three subpopulations with minimal admixture. The genetic differentiation coefficients (FST) within A. linariae subpopulations were similar and high (0.86), indicating that alleles in the subpopulations are fixed and the genetic structure is likely due to restricted recombination. Analysis of molecular variance indicated higher variation among populations (89%) than within the population (11%). We found long-range LD between pairs of loci in A. linariae, supporting the hypothesis of low recombination expected for a fungal pathogen with limited sexual reproduction. Our findings provide evidence of a high level of population genetic differentiation in A. linariae, which reinforces the importance of developing tomato varieties with broad-spectrum resistance to various isolates of A. linariae.", "token_count": 477, "char_count": 1874, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:20.714354", "source": { "split": "train_shard_00001", "doc_id": 1716 }, "chunk_id": "train_shard_00001_1716_0", "global_id": 8074 }, { "text": "Genotyping-by-Sequencing Reveals Population Differentiation and Linkage Disequilibrium in Alternaria linariae from Tomato.", "token_count": 39, "char_count": 129, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:21.106511", "source": { "split": "train_shard_00001", "doc_id": 1716 }, "chunk_id": "train_shard_00001_1716_1", "global_id": 8075 }, { "text": "

Background

Oral candidiasis is a common disease in cancer patients subject to chemotherapy. The aim of this study was to evaluate the risk factors of rising oral candidiasis incidence and to identify the Candida species isolated from oral lesions of cancer patients and their antifungal sensitivity.

Materials and methods

A total of 645 patients with cancer were examined. Several Candida species were isolated from specimens and identified by morphological and molecular methods. The susceptibility of isolates to amphotericin B, fluconazole, and nystatin was also investigated.

Results

A total of 74 isolates of Candida were recovered from oral cavity of 61 cancer patients with oral candidiasis. The isolates included Candida albicans (n = 56; 75.5%), Candida glabrata (n = 4; 5.4%), Candida krusei (n = 5; 7%), Candida tropical (n = 7; 9.4%), and Candida kefyr (n = 2; 2.7%)", "token_count": 343, "char_count": 984, "word_count": 134, "semantic_coherence": 1, "information_density": 0.597, "quality_score": 0.7985, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:21.673806", "source": { "split": "train_shard_00001", "doc_id": 1717 }, "chunk_id": "train_shard_00001_1717_0", "global_id": 8076 }, { "text": "A total (n = 72; 98.65%) of isolates were susceptible to nystatin, (n = 58; 78.4%) of them were susceptible to fluconazole, and (n = 8; 10.8%) of susceptible dose-dependent isolates were specified, (n = 46; 62.16%) of isolates were susceptible to amphotericin B.

Conclusion

Finally, in addition to emphasis on topical nystatin application in the first stage of oral candidiasis in these patients, using alternative systemic drugs such as fluconazole and amphotericin B can be considered for the resistant candida isolates to nystatin.\n\nIdentification of Candida Species and Antifungal Susceptibility in Cancer Patients with Oral Lesions in Ahvaz, Southern West of Iran.", "token_count": 233, "char_count": 704, "word_count": 101, "semantic_coherence": 1, "information_density": 0.6535, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:22.137391", "source": { "split": "train_shard_00001", "doc_id": 1717 }, "chunk_id": "train_shard_00001_1717_1", "global_id": 8077 }, { "text": "The advancements in sequencing technologies and assembly methods enable the regular production of high-quality genome assemblies characterizing complex regions. However, challenges remain in efficiently interpreting variations at various scales, from smaller tandem repeats to megabase re-arrangements, across many human genomes. We present a pangenome research toolkit enabling analyses of complex pangenome variations at multiple scales. A graph decomposition method is developed for interpreting such variations. Surveying a set of 395 challenging and medically important genes in pangenome provides quantitative insights into repetitiveness and diversity that could impact the accuracy of variant calls. We apply the graph decomposition methods to the Y-chromosome gene, DAZ1/DAZ2/DAZ3/DAZ4, of which structural variants have been linked to male infertility, and X-chromosome genes OPN1LW and OPN1MW linked to eye disorders, highlighting the power of PGR-TK and pangenomics to resolve complex variation in regions of the genome that were previously too complex to analyze across many haplotypes.\n\nMultiscale Analysis of Pangenome Enables Improved Representation of Genomic Diversity For Repetitive And Clinically Relevant Genes", "token_count": 279, "char_count": 1231, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6848, "quality_score": 0.8424, "entities": { "genes": [ "DAZ4", "DAZ3", "DAZ2", "DAZ1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:22.691366", "source": { "split": "train_shard_00001", "doc_id": 1718 }, "chunk_id": "train_shard_00001_1718_0", "global_id": 8078 }, { "text": "Hospital bloodstream infection (BSI) caused by methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of morbidity and mortality and is frequently related to invasive procedures and medically complex patients. An important feature of MRSA is the clonal structure of its population. Specific MRSA clones may differ in their pathogenic, epidemiological, and antimicrobial resistance profiles. Whole-genome sequencing is currently the most robust and discriminatory technique for tracking hypervirulent/well-adapted MRSA clones. However, it remains an expensive and time-consuming technique that requires specialized personnel. In this work, we describe a pangenome protocol, based on binary matrix (1,0) of open reading frames (ORFs), that can be used to quickly find diagnostic, apomorphic sequence mutations that can serve as biomarkers. We use this technique to create a diagnostic screen for MRSA isolates circulating in the Rio de Janeiro metropolitan area, the RdJ clone, which is prevalent in BSI. The method described here has 100% specificity and sensitivity, eliminating the need to use genomic sequencing for clonal identification. The protocol used is relatively simple and all the steps, formulas and commands used are described in this work, such that this strategy can also be used to identify other MRSA clones and even clones from other bacterial species.\n\nRdJ detection tests to identify a unique MRSA clone of ST105-SCCmecII lineage and its variants disseminated in the metropolitan region of Rio de Janeiro.", "token_count": 373, "char_count": 1552, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8267, "entities": { "genes": [ "ST105" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:23.278389", "source": { "split": "train_shard_00001", "doc_id": 1719 }, "chunk_id": "train_shard_00001_1719_0", "global_id": 8079 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) is a foodborne pathogen, and serotype O157:H7 is typically associated with severe disease. Australian STEC epidemiology differs from many other countries, as severe outbreaks and HUS cases appear to be more often associated with non-O157 serogroups. It is not known why Australian strains of O157 STEC might differ in virulence to international strains. Here we investigate the reduced virulence of Australian strains. Multiple genetic analyses were performed, including SNP-typing, to compare the core genomes of the Australian to the international isolates, and accessory genome analysis to determine any significant differences in gene presence/absence that could be associated with their phenotypic differences in virulence. The most distinct difference between the isolates was the absence of the stx2a gene in all Australian isolates, with few other notable differences observed in the core and accessory genomes of the O157 STEC isolates analyzed in this study. The presence of stx1a in most Australian isolates was another notable observation. Acquisition of stx2a seems to coincide with the emergence of highly pathogenic STEC. Due to the lack of other notable genotypic differences observed between Australian and international isolates characterized as highly pathogenic, this may be further evidence that the absence of stx2a in Australian O157 STEC could be a significant characteristic defining its mild virulence. Further work investigating the driving force(s) behind Stx prophage loss and acquisition is needed to determine if this potential exists in Australian O157 isolates.\n\nCore and Accessory Genome Comparison of Australian and International Strains of O157 Shiga Toxin-Producing Escherichia coli.", "token_count": 444, "char_count": 1808, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5197, "quality_score": 0.7598, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:23.908923", "source": { "split": "train_shard_00001", "doc_id": 1720 }, "chunk_id": "train_shard_00001_1720_0", "global_id": 8080 }, { "text": "

Background

Species of the genus Monascus are economically important and widely used in the production of food colorants and monacolin K. However, they have also been known to produce the mycotoxin citrinin. Currently, taxonomic knowledge of this species at the genome level is insufficient.

Methods

This study presents genomic similarity analyses through the analysis of the average nucleic acid identity of the genomic sequence and the whole genome alignment. Subsequently, the study constructed a pangenome of Monascus by reannotating all the genomes and identifying a total of 9,539 orthologous gene families. Two phylogenetic trees were constructed based on 4,589 single copy orthologous protein sequences and all the 5,565 orthologous proteins, respectively. In addition, carbohydrate active enzymes, secretome, allergic proteins, as well as secondary metabolite gene clusters were compared among the included 15 Monascus strains.

Results

The results clearly revealed a high homology between M. pilosus and M. ruber, and their distant relationship with M. purpureus. Accordingly, all the included 15 Monascus strains should be classified into two distinctly evolutionary clades, namely the M. purpureus clade and the M. pilosus-M. ruber clade. Moreover, gene ontology enrichment showed that the M. pilosus-M. ruber clade had more orthologous genes involved with environmental adaptation than the M. purpureus clade. Compared to Aspergillus oryzae, all the Monascus species had a substantial gene loss of carbohydrate active enzymes. Potential allergenic and fungal virulence factor proteins were also found in the secretome of Monascus", "token_count": 525, "char_count": 1774, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6422, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:24.562570", "source": { "split": "train_shard_00001", "doc_id": 1721 }, "chunk_id": "train_shard_00001_1721_0", "global_id": 8081 }, { "text": "Furthermore, this study identified the pigment synthesis gene clusters present in all included genomes, but with multiple nonessential genes inserted in the gene cluster of M. pilosus and M. ruber compared to M. purpureus. The citrinin gene cluster was found to be intact and highly conserved only among M. purpureus genomes. The monacolin K gene cluster was found only in the genomes of M. pilosus and M. ruber, but the sequence was more conserved in M. ruber.

Conclusion

This study provides a paradigm for phylogenetic analysis of the genus Monascus, and it is believed that this report will lead to a better understanding of these food microorganisms in terms of classification, metabolic differentiation, and safety.\n\nInsight into the phylogeny and metabolic divergence of Monascus species (M. pilosus, M. ruber, and M. purpureus) at the genome level.", "token_count": 291, "char_count": 946, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6269, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:25.120142", "source": { "split": "train_shard_00001", "doc_id": 1721 }, "chunk_id": "train_shard_00001_1721_1", "global_id": 8082 }, { "text": "Klebsiella pneumoniae is a Gram-negative pathogen that has a large accessory genome of plasmids and chromosomal gene loci. This accessory genome divides K. pneumoniae strains into opportunistic, hypervirulent, and multidrug-resistant groups and separates K. pneumoniae from two closely related species, Klebsiella variicola and Klebsiella quasipneumoniae. Some strains of K. pneumoniae act as opportunistic pathogens, infecting critically ill and immunocompromised patients. These K. pneumoniae are a common cause of health-care associated infections including pneumonia, urinary tract infections (UTIs), and bloodstream infections. K. variicola and K. quasipneumoniae are often clinically indistinguishable from opportunistic K. pneumoniae. Other strains of K. pneumoniae are hypervirulent, infecting healthy people in community settings and causing severe infections including pyogenic liver abscess, endophthalmitis, and meningitis. A third group of K. pneumoniae encode carbapenemases, making them highly antibiotic-resistant. These strains act as opportunists but are exceedingly difficult to treat. All of these groups of K. pneumoniae and related species can colonize the gastrointestinal tract, and the accessory genome may determine if a colonizing strain remains asymptomatic or progresses to cause disease. This review will explore the associations between colonization and infection with opportunistic, antibiotic-resistant, and hypervirulent K. pneumoniae strains and the role of the accessory genome in distinguishing these groups and related species. As K", "token_count": 483, "char_count": 1671, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5874, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:25.768123", "source": { "split": "train_shard_00001", "doc_id": 1722 }, "chunk_id": "train_shard_00001_1722_0", "global_id": 8083 }, { "text": "pneumoniae infections become progressively more difficult to treat in the face of antibiotic resistance and hypervirulent strains, an increased understanding of the epidemiology and pathogenesis of these bacteria is vital.\n\nColonization, Infection, and the Accessory Genome of Klebsiella pneumoniae.", "token_count": 80, "char_count": 310, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8205, "quality_score": 0.9103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:26.136167", "source": { "split": "train_shard_00001", "doc_id": 1722 }, "chunk_id": "train_shard_00001_1722_1", "global_id": 8084 }, { "text": "

Purpose

Brucellosis is a bacterial zoonotic disease caused by genus Brucella. The disease is often transmitted to humans by direct or indirect contact with infected livestock or from laboratory exposure. In this study two clinical isolates of Brucella melitensis were subjected to whole genome sequencing (WGS) using Ion Torrent PGM and Oxford Nanopore MinIon platform.

Methods

The two hybrid complete genomes were subjected to core gene SNP analysis to identify the relative evolutionary position. To distinguish between the various lineages of B. melitensis, Pangenome analysis was carried out.

Results

Phylogenetic analysis revealed that both the study isolates (ST8) clustered along the other Asian isolates that formed genotype II. Genome wide analyses of 326 B melitensis isolates suggests 2171 gene clusters were shared across all the genomes while 3552 gene clusters were considered as accessory genes.

Conclusion

Here we attempted to provide the gain and loss of six unique genes that defined the phylogenetic lineages and complex evolutionary process. As the severity and prevalence of human brucellosis is increasing a better understanding of Brucella genomics and transmission dynamics is needed.\n\nGenomic analysis of Brucella melitensis reveals new insights into phylogeny and evolutionary divergence.", "token_count": 331, "char_count": 1343, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6865, "quality_score": 0.8432, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:26.705288", "source": { "split": "train_shard_00001", "doc_id": 1723 }, "chunk_id": "train_shard_00001_1723_0", "global_id": 8085 }, { "text": "Decades of antimicrobial overuse to treat respiratory disease in foals have promoted the emergence and spread of zoonotic multidrug-resistant (MDR) Rhodococcus equi worldwide. Three main R. equi MDR clonal populations-2287, G2106, and G2017-have been identified so far. However, only clones 2287 and G2016 have been isolated from sick animals, with clone 2287 being the main MDR R. equi recovered. The genetic mechanisms that make this MDR clone superior to the others at infecting foals are still unknown. Here, we performed a deep genetic characterization of the accessory genomes of 207 R. equi isolates, and we describe IME2287, a novel genetic element in the accessory genome of clone 2287, potentially involved in the maintenance and spread of this MDR population over time. IME2287 is a putative self-replicative integrative mobilizable element (IME) carrying a DNA replication and partitioning operon and genes encoding its excision and integration from the R. equi genome via a serine recombinase. Additionally, IME2287 encodes a protein containing a Toll/interleukin-1 receptor (TIR) domain that may inhibit TLR-mediated NF-kB signaling in the host and a toxin-antitoxin (TA) system, whose orthologs have been associated with antibiotic resistance/tolerance, virulence, pathogenicity islands, bacterial persistence, and pathogen trafficking. This new set of genes may explain the success of clone 2287 over the other MDR R. equi clones.\n\nExploring the Accessory Genome of Multidrug-Resistant Rhodococcus equi Clone 2287.", "token_count": 481, "char_count": 1579, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [ "IME2287" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:27.358668", "source": { "split": "train_shard_00001", "doc_id": 1724 }, "chunk_id": "train_shard_00001_1724_0", "global_id": 8086 }, { "text": "The recovery and characterization of a multidrug-resistant, KPC-3-producing Klebsiella michiganensis that was obtained from Venus clam samples is reported in this study. A whole-genome sequencing (WGS) analysis using Illumina and Nanopore technologies of the K. michiganensis 23999A2 isolate revealed that the strain belonged to the new sequence type 382 (ST382) and carried seven plasmid replicon sequences, including four IncF type plasmids (FII, FIIY, FIIk, and FIB), one IncHI1 plasmid, and two Col plasmids. The FIB and FIIk plasmids showed high homology to each other and to multireplicon pKpQIL-like plasmids that are found in epidemic KPC-K. pneumoniae clones worldwide. The strain carried multiple β-lactamase genes on the IncF plasmids: blaOXA-9 and blaTEM-1A on FIB, blaKPC-3 inserted in a Tn4401a on FIIK, and blaSHV-12 on FIIY. The IncHI1-ST11 harbored no resistance gene. The curing of the strain caused the loss of all of the bla genes and a rearrangement of the IncF plasmids. Conjugal transfer of the blaOXA-9, blaTEM-1A and blaKPC-3 genes occurred at a frequency of 5 × 10-7, using K", "token_count": 493, "char_count": 1295, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8324, "entities": { "genes": [ "ST11", "ST382" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:28.012359", "source": { "split": "train_shard_00001", "doc_id": 1725 }, "chunk_id": "train_shard_00001_1725_0", "global_id": 8087 }, { "text": "quasipneumoniae as a recipient, and all of the bla genes were transferred through a pKpQIL that originated from the recombination of the FIB and FIIk plasmids of the donor. A comparison with 31 K. michiganensis genomes that are available in the NCBI database showed that the closest phylogenetic relatives of K. michiganensis 23999A2 are an environmental isolate from soil in South Korea and a clinical isolate from human sputum in Japan. Finally, a pan-genome analysis showed a large accessory genome of the strain as well as the great genomic plasticity of the K. michiganensis species. IMPORTANCE Klebsiella michiganensis is an emerging nosocomial pathogen, and, so far, few studies describe isolates of clinical origin in the environment. This study contributes to the understanding of how the dissemination of carbapenem-resistance outside the hospital setting may be related to the circulation of pKpQIL-like plasmids that are derived from epidemic Klebsiella pneumoniae strains. The recovery of a carbapenem-resistant isolate in clams is of great concern, as bivalves could represent vehicles of transmission of pathogens and resistance genes to humans via the food chain. The study demonstrates the plasticity of K. michiganensis genome, which is probably useful to multiple environment adaptation and to the evolution of the species.\n\nThe Emerging Nosocomial Pathogen Klebsiella michiganensis: Genetic Analysis of a KPC-3 Producing Strain Isolated from Venus Clam.", "token_count": 415, "char_count": 1526, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5818, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:28.633633", "source": { "split": "train_shard_00001", "doc_id": 1725 }, "chunk_id": "train_shard_00001_1725_1", "global_id": 8088 }, { "text": "

Introduction

A clonal shift from staphylococcal cassette chromosome mec (SCCmec) type II/ST5 methicillin-resistant Staphylococcus aureus (MRSA) to SCCmec type IV/clonal complex (CC)1 MRSA has occurred rapidly in Japan. Our previous research in a geriatric hospital found SCCmec type IV/CC1 MRSA prevalence in long-term care wards. Due to intensive personal care requirements, frequent contact with healthcare providers can potentially cause unintentional nosocomial MRSA transmission. We performed polymerase chain reaction-based open reading frame typing (POT) and core genome multilocus sequence typing (cgMLST) to investigate the occurrence of nosocomial transmission and to compare the results of these methods.

Methods

POT and whole genome sequencing were performed in 83 MRSA isolates. Commercial automated software (Ridom SeqSphere+) was used to perform cgMLST. MRSA isolates with 0-8 allelic differences were considered related, and medical records were consulted in these cases.

Results

SCCmec type IV/CC1 MRSA was the most frequently detected clone (n = 56, 67.5 %), which was divided into 14 POT types, followed by SCCmec type I/ST8 (n = 9) and SCCmec type IV/ST8 (n = 8). Identical POT types were found across 7 of 11 wards. However, cgMLST analysis identified only three cases (six strains) of high genetic similarity, indicating nosocomial transmission; only one involved SCCmec type IV/CC1 (two strains). The mean allelic difference in the core genomes between strains with identical POT types in the same ward was 55.3 ± 22.0.

Conclusions

The cgMLST method proved more effective for identifying nosocomial transmissions compared to POT, highlighting its utility in tracking MRSA spread in healthcare settings.", "token_count": 493, "char_count": 1754, "word_count": 245, "semantic_coherence": 1, "information_density": 0.698, "quality_score": 0.849, "entities": { "genes": [ "ST5", "CC1", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:29.280342", "source": { "split": "train_shard_00001", "doc_id": 1726 }, "chunk_id": "train_shard_00001_1726_0", "global_id": 8089 }, { "text": "Comparison of the effectiveness of core genome multilocus sequence typing and polymerase chain reaction-based open reading frame typing in tracing nosocomial methicillin-resistant Staphylococcus aureus transmission.", "token_count": 49, "char_count": 215, "word_count": 25, "semantic_coherence": 1, "information_density": 0.92, "quality_score": 0.96, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:29.632968", "source": { "split": "train_shard_00001", "doc_id": 1726 }, "chunk_id": "train_shard_00001_1726_1", "global_id": 8090 }, { "text": "The 10q11.22 chromosomal region is a duplication-rich interval of the human genome and one of the last to be fully assembled. It carries copy number-variable genes associated with intellectual disability, bipolar disorder, and obesity. In this study, we characterized the structural diversity at this locus by analyzing 64 haploid assemblies produced by the Human Pangenome Reference Consortium. We identified 11 alternative haplotypes that differ in the copy number and/or orientation of large genomic segments, ranging from hundreds of kilobase pairs (kbp) to over one megabase pair (Mbp). We uncovered a 2.4 Mbp size difference between the shortest and longest haplotypes. Breakpoint analysis revealed that genomic instability results from nonallelic homologous recombination between segmental duplication (SD) pairs with varying similarity (94.4%-99.6%). Nonetheless, these pairs generally recombine at positions where their identity is higher (>99.6%). Recurrent inversions occur with different breakpoints within the same inverted SD pair. Inversion polymorphisms shuffle the entire SD arrangement, creating new predispositions to copy-number variations. The SD architecture is associated with a catarrhine-specific subgroup of the AGAP gene family, which likely triggered the accumulation of SDs at this locus over the past 25 million years of human evolution. Our results reveal extensive structural diversity and genomic instability at the 10q11.22 locus, and expand the general understanding of the mutational mechanisms behind SD-mediated rearrangements.\n\n<i>AGAP</i> duplicons associate with structural diversity at Chromosome 10q11.22.", "token_count": 419, "char_count": 1667, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6933, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:30.254925", "source": { "split": "train_shard_00001", "doc_id": 1727 }, "chunk_id": "train_shard_00001_1727_0", "global_id": 8091 }, { "text": "The mobilome, defined as the collection of mobile genetic elements within a bacterial genome, plays a critical role in the adaptation of bacteria to abiotic and biotic drivers. In particular, prophages have been reported to contribute to bacterial resistance to virulent bacteriophages, the competitive interaction of bacterial hosts within microbial communities, and in pathogenicity and virulence. It is therefore critical to better understand the role of prophages in distributing genes and functions within and among bacterial species to predict how bacteria adapt to their biotic environment. Pseudomonas syringae offers an ideal study system to ask these questions both because of its broad range of lifestyles (spanning from environmental growth to plant pathogens) and its high intraspecies diversity. To examine the role of the mobilome in this species complex, we compared 590 genomes available from public databases and annotated the defense mechanisms, effectors, and prophages in the genomes. We found that this species complex has an elaborate phage pandefensome consisting of 139 defense mechanisms. Host-associated P. syringae isolates were found to have both elaborate phage defensomes and effectoromes. Assessing taxonomical signatures of the observed prophages uncovered broad differences in the types and numbers of genes encoded by different phage families, emphasizing how the evolutionary advantages conferred to hosts will depend on the prophage composition and offering insight to how these genes might disperse within a community. Our study highlights the intimate association of phage families with their hosts and uncovers their key role in shaping ecology for this widespread species complex.

Significance statement

The bacterial accessory genome, including the mobilome and prophages, plays a critical role in shaping bacterial adaptation to abiotic and biotic drivers. These prophages are widespread across bacterial taxa and likely maintained because of their evolutionary advantage. Our ability to predict how a bacterial population will evolve over time requires a better understanding of where key functional traits arrive. To address this question, we assessed prophage-encoded phage defenses and effector across Pseudomonas syringae . We show that prophages carrying these genes belong to specific phage taxa with differences in the types of genes encoded", "token_count": 508, "char_count": 2401, "word_count": 346, "semantic_coherence": 1, "information_density": 0.5318, "quality_score": 0.7659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:30.911505", "source": { "split": "train_shard_00001", "doc_id": 1728 }, "chunk_id": "train_shard_00001_1728_0", "global_id": 8092 }, { "text": "This emphasizes the evolutionary advantage of these prophages, offering a framework to uncover how these genes disperse within microbial communities and their role in pathogen evolution.\n\nEvidence for the key roles of thePseudomonas syringaemobilome in shaping biotic interactions", "token_count": 70, "char_count": 287, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:31.315836", "source": { "split": "train_shard_00001", "doc_id": 1728 }, "chunk_id": "train_shard_00001_1728_1", "global_id": 8093 }, { "text": "Phage therapy has been proposed as a possible alternative treatment for infections caused by the ubiquitous bacterial pathogen Staphylococcus aureus. However, successful phage therapy requires knowing both host and phage genetic factors influencing host range for rational cocktail formulation. To further our understanding of host range, we searched 40,000+ public S. aureus genome sequences for previously identified phage resistance genes. We found that phage adsorption targets and genes that block phage assembly were significantly more conserved than genes targeting phage biosynthesis. Core phage resistance genes had similar nucleotide diversity, ratio of non-synonymous to synonymous substitutions, and functionality (measured by delta-bitscore) to other core genes in a set of 380 non-redundant S. aureus genomes (each from a different MLST sequence type). Non-core phage resistance genes were significantly less consistent with the core genome phylogeny than all non-core genes in this set. Only superinfection immunity genes correlated with empirically determined temperate phage resistance, accessory genome content, and numbers of accessory antibiotic resistance or virulence genes encoded per strain. Taken together, these results suggested that, while phage adsorption genes are heavily conserved in the S. aureus species, they are not undergoing positive selection, arms race dynamics. They also suggested genes classified as involved in assembly are least phylogenetically constrained and superinfection immunity genes best predict both empirical phage resistance and levels of phage-mediated HGT.

Importance

Staphylococcus aureus is a widespread, hospital- and community-acquired pathogen that is commonly antibiotic resistant. It causes diverse diseases affecting both the skin and internal organs. Its ubiquity, antibiotic resistance, and disease burden make new therapies urgent, such as phage therapy, in which viruses specific to infecting bacteria clear infection. S. aureus phage host range not only determines whether phage therapy will be successful by killing bacteria but also horizontal gene transfer through transduction of host genetic material by phages. In this work, we comprehensively reviewed existing literature to build a list of S. aureus phage resistance genes and searched our database of almost 43,000 S", "token_count": 529, "char_count": 2356, "word_count": 327, "semantic_coherence": 1, "information_density": 0.6147, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:31.964564", "source": { "split": "train_shard_00001", "doc_id": 1729 }, "chunk_id": "train_shard_00001_1729_0", "global_id": 8094 }, { "text": "aureus genomes for these genes to understand their patterns of evolution, finding that prophages’ superinfection immunity correlates best with phage resistance and HGT. These findings improved our understanding of the relationship between known phage resistance genes and phage host range in the species.\n\nSpecies-scale genomic analysis of S. aureus genes influencing phage host range and their relationships to virulence and antibiotic resistance genes", "token_count": 101, "char_count": 460, "word_count": 63, "semantic_coherence": 1, "information_density": 0.6984, "quality_score": 0.8492, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:32.361489", "source": { "split": "train_shard_00001", "doc_id": 1729 }, "chunk_id": "train_shard_00001_1729_1", "global_id": 8095 }, { "text": "

Motivation

Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space efficiently.

Results

We propose the GBZ file format based on data structures used in the Giraffe short-read aligner. The format provides good compression, and the files can be efficiently loaded into in-memory data structures. We provide compression and decompression tools and libraries for using GBZ graphs, and we show that they can be efficiently used on a variety of systems.

Availability and implementation

C++ and Rust implementations are available at https://github.com/jltsiren/gbwtgraph and https://github.com/jltsiren/gbwt-rs, respectively.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nGBZ file format for pangenome graphs.", "token_count": 238, "char_count": 959, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6612, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:32.879524", "source": { "split": "train_shard_00001", "doc_id": 1730 }, "chunk_id": "train_shard_00001_1730_0", "global_id": 8096 }, { "text": "Yersinia pseudotuberculosis is a Gram-negative intestinal pathogen of humans and has been responsible for several nationwide gastrointestinal outbreaks. Large-scale population genomic studies have been performed on the other human pathogenic species of the genus Yersinia, Yersinia pestis and Yersinia enterocolitica allowing a high-resolution understanding of the ecology, evolution and dissemination of these pathogens. However, to date no purpose-designed large-scale global population genomic analysis of Y. pseudotuberculosis has been performed. Here we present analyses of the genomes of 134 strains of Y. pseudotuberculosis isolated from around the world, from multiple ecosystems since the 1960s. Our data display a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages into Europe and the rest of the world. These lineages can be differentiated by CRISPR cluster arrays, and we show that the lineages are limited with respect to inter-lineage genetic exchange. This restriction of genetic exchange maintains the discrete lineage structure in the population despite co-existence of lineages for thousands of years in multiple countries. Our data highlights how CRISPR can be informative of the evolutionary trajectory of bacterial lineages, and merits further study across bacteria.\n\nPhylogeographic separation and formation of sexually discrete lineages in a global population of Yersinia pseudotuberculosis.", "token_count": 373, "char_count": 1528, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6422, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:33.469102", "source": { "split": "train_shard_00001", "doc_id": 1731 }, "chunk_id": "train_shard_00001_1731_0", "global_id": 8097 }, { "text": "

Objectives

Staphylococcus aureus is an important zoonotic pathogen that has often been seen in animals through the prism of the MRSA clonal complex (CC) 398 in pigs and in-contact humans. The goal of this study was first to assess the prevalence of MRSA, and second to look for MSSA CC398 in cats, dogs and horses in France.

Methods

Clinical S. aureus isolates (n = 479) were collected from 186 cats, 143 dogs and 150 horses during 2022-2023 all over the French territory. Antibiograms were performed on all isolates. MRSA and MSSA CC398 isolates were subject to WGS. Core genome (cg) MLST-based and SNP-based phylogenetic analyses were performed using published methodologies, and characterization of the isolates was performed using publicly available tools.

Results

Sixty-six MRSA isolates were identified in 14 cats (7.5%), 9 dogs (6.3%) and 43 horses (28.7%). The epidemiology of MRSA in cats and dogs remained stable since a previous study in 2015, with the presence of both CC398 and human-associated clones. In horses, in contrast, an important increase in MRSA (from 10% to 28.7%) was observed, potentially attributable to the emergence of the ST612 clones. In parallel, CC398 MSSA, a clone usually described as animal-independent, was found in 24.2% of the cat isolates.

Conclusions

Our study, which is leading the way to a genomic surveillance of S. aureus in France, revealed the emergence of both MRSA ST612 in horses and MSSA CC398 in cats. These clones should be closely monitored to avoid their zoonotic spread and to understand their dynamics of transmission between humans and animals.", "token_count": 491, "char_count": 1632, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [ "ST612", "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:34.118019", "source": { "split": "train_shard_00001", "doc_id": 1732 }, "chunk_id": "train_shard_00001_1732_0", "global_id": 8098 }, { "text": "Emergence of MRSA ST612 in horses and of MSSA CC398 in cats in France.", "token_count": 25, "char_count": 70, "word_count": 14, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [ "ST612", "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:34.478189", "source": { "split": "train_shard_00001", "doc_id": 1732 }, "chunk_id": "train_shard_00001_1732_1", "global_id": 8099 }, { "text": "

Background

Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae, we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.

Results

High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani, comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.

Conclusions

The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D. solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.", "token_count": 529, "char_count": 2274, "word_count": 325, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:35.936759", "source": { "split": "train_shard_00001", "doc_id": 1733 }, "chunk_id": "train_shard_00001_1733_0", "global_id": 8100 }, { "text": "Comparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani.", "token_count": 37, "char_count": 152, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:36.303024", "source": { "split": "train_shard_00001", "doc_id": 1733 }, "chunk_id": "train_shard_00001_1733_1", "global_id": 8101 }, { "text": "Longitudinal studies of extraintestinal pathogenic Escherichia coli (ExPEC) and epidemic clones of E. coli in association with New Delhi metallo-β-lactamase (blaNDM) in septicaemic neonates are rare. This study captured the diversity of 80 E. coli isolates collected from septicaemic neonates in terms of antibiotic susceptibility, resistome, phylogroups, sequence types (ST), virulome, plasmids, and integron types over a decade (2009 to 2019). Most of the isolates were multidrug-resistant and, 44% of them were carbapenem-resistant, primarily due to blaNDM. NDM-1 was the sole NDM-variant present in conjugative IncFIA/FIB/FII replicons until 2013, and it was subsequently replaced by other variants, such as NDM-5/-7 found in IncX3/FII. A core genome analysis for blaNDM+ve isolates showed the heterogeneity of the isolates. Fifty percent of the infections were caused by isolates of phylogroups B2 (34%), D (11.25%), and F (4%), whereas the other half were caused by phylogroups A (25%), B1 (11.25%), and C (14%). The isolates were further distributed in approximately 20 clonal complexes (STC), including five epidemic clones (ST131, ST167, ST410, ST648, and ST405). ST167 and ST131 (subclade H30Rx) were dominant, with most of the ST167 being blaNDM+ve and blaCTX-M-15+ve", "token_count": 518, "char_count": 1433, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "ST131", "ST410", "ST167", "ST405", "ST648" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:36.934869", "source": { "split": "train_shard_00001", "doc_id": 1734 }, "chunk_id": "train_shard_00001_1734_0", "global_id": 8102 }, { "text": "In contrast, the majority of ST131 isolates were blaNDM-ve but blaCTX-M-15+ve, and they possessed more virulence determinants than did ST167. A single nucleotide polymorphism (SNP)-based comparative genome analysis of epidemic clones ST167 and ST131 in a global context revealed that the study isolates were present in close proximity but were distant from global isolates. The presence of antibiotic-resistant epidemic clones causing sepsis calls for a modification of the recommended antibiotics with which to treat neonatal sepsis. IMPORTANCE Multidrug-resistant and virulent ExPEC causing sepsis in neonates is a challenge to neonatal health. The presence of enzymes, such as carbapenemases (blaNDM) that hydrolyze most β-lactam antibiotic compounds, result in difficulties when treating neonates. The characterization of ExPECs collected over 10 years showed that 44% of ExPECs were carbapenem-resistant, possessing transmissible blaNDM genes. The isolates belonged to different phylogroups that are considered to be either commensals or virulent. The isolates were distributed in around 20 clonal complexes (STC), including two predominant epidemic clones (ST131 and ST167). ST167 possessed few virulence determinants but was blaNDM+ve. In contrast, ST131 harbored several virulence determinants but was blaNDM-ve. A comparison of the genomes of these epidemic clones in a global context revealed that the study isolates were present in close proximity but were distant from global isolates", "token_count": 518, "char_count": 1694, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7929, "entities": { "genes": [ "ST131", "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:37.566576", "source": { "split": "train_shard_00001", "doc_id": 1734 }, "chunk_id": "train_shard_00001_1734_1", "global_id": 8103 }, { "text": "The presence of epidemic clones in a vulnerable population with contrasting characteristics and the presence of resistance genes call for strict vigilance.\n\nA Decade-Long Evaluation of Neonatal Septicaemic Escherichia coli: Clonal Lineages, Genomes, and New Delhi Metallo-Beta-Lactamase Variants.", "token_count": 76, "char_count": 296, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:37.935700", "source": { "split": "train_shard_00001", "doc_id": 1734 }, "chunk_id": "train_shard_00001_1734_2", "global_id": 8104 }, { "text": "Genotyping of 2,882 Pseudomonas aeruginosa isolates that had been collected during the last 40 years identified the ExoU-positive lineages PA14 (ST253) and ST235 as the second and third most frequent clones in the P. aeruginosa population. Both clones were approximately 2-fold more frequently detected in animate habitats than in soil or aquatic habitats. While ST253 clone isolates were causing mainly acute and chronic infections in humans, ST235 isolates had been preferentially collected from hospitalized patients with severe acute infections, particularly, keratitis, urinary tract infections, burn wounds, and ventilator-associated pneumonia. The two major exoU clones differed substantially in the composition and flexibility of the accessory genome and by more than 8,000 amino acid sequences. Pronounced sequence variation between orthologs was noted in genes encoding elements of secretion systems and secreted effector molecules, including the type III secretion system, indicating the modes of action of the different clones. When comparing representatives of the two clones in batch culture, the PA14 strain orchestrated the quorum sensing circuitry for the expression of pathogenic traits and stopped growing in batch culture when it entered the stationary phase, but the quorum sensing-deficient ST235 strain expressed high type III secretion activity and continued to grow and to divide. In summary, unrestricted growth, high constitutive type III secretion activity, and facilitated uptake of foreign DNA could be major features that have made ST235 a global high-risk clone associated with poor outcomes of acute nosocomial infections.IMPORTANCE The ubiquitous and metabolically versatile environmental bacterium Pseudomonas aeruginosa can cause infections in a wide variety of hosts, including insects, plants, animals, and humans. P", "token_count": 465, "char_count": 1892, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.8321, "entities": { "genes": [ "PA14", "ST253", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:38.577223", "source": { "split": "train_shard_00001", "doc_id": 1735 }, "chunk_id": "train_shard_00001_1735_0", "global_id": 8105 }, { "text": "aeruginosa is one of the ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens that are the major cause of nosocomial infections in the United States and are a threat all over the world because of their capacity to become increasingly resistant to all available antibiotics. Most experimental work on P. aeruginosa has been performed with reference strains PAO1 and PA14, providing deep insight into key metabolic and regulatory pathways thought to be applicable to all P. aeruginosa strains. However, this comparative study on the two most common exoU-positive clones taught us that there are major lineages in the population such as the global high-risk clone ST235 that exhibit uncommon traits of lifestyle, genome mobility, and pathogenicity distinct from those in our knowledge gained from the studies with the reference strains.\n\nPhenotypic and Genomic Comparison of the Two Most Common ExoU-Positive Pseudomonas aeruginosa Clones, PA14 and ST235.", "token_count": 325, "char_count": 1127, "word_count": 153, "semantic_coherence": 1, "information_density": 0.719, "quality_score": 0.8595, "entities": { "genes": [ "PA14", "PAO1", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:39.139664", "source": { "split": "train_shard_00001", "doc_id": 1735 }, "chunk_id": "train_shard_00001_1735_1", "global_id": 8106 }, { "text": "Mycoplasma pneumoniae (M. pneumoniae), a slow-growing, fastidious Gram-negative bacterium and a leading cause of community-acquired pneumonia globally, remains understudied and underreported across numerous geographical areas in China despite its worldwide significance. This study employed probe capture sequencing for targeted enrichment and direct sequencing of M. pneumoniae from clinical samples, combined with comparative genomic analyses of contemporary and historical global genomes. Core genome and pan-genome revealed that the M. pneumoniae genomes were classified into two distinct clades, P1-I and P1-II, each associated with a specific sequence type (ST). Most of the genomes sequenced in this study were identified as P1-I (86.96%, 20/23), contrasting with the previously reported predominance of P1-II in the area. A limited number of single-nucleotide variations were identified in the virulence-associated genes between P1-I and P1-II, leading to amino acid substitutions. The A2063G point mutation in the 23S rRNA gene was detected in all sequenced genomes (23/23), demonstrating a 100% mutation rate. This study provides the first reported application of probe capture methodology for M. pneumoniae, highlighting the critical importance of sustained surveillance efforts to monitor the evolution and epidemiology of this pathogen.\n\nWhole-genome probe capture sequencing reveals genomic diversity and characteristics of <i>Mycoplasma pneumoniae</i> in Nanjing, China.", "token_count": 412, "char_count": 1532, "word_count": 200, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:39.765903", "source": { "split": "train_shard_00001", "doc_id": 1736 }, "chunk_id": "train_shard_00001_1736_0", "global_id": 8107 }, { "text": "Aim: Akkermansia are common members of the human gastrointestinal microbiota. The prevalence of these mucophilic bacteria, especially Akkermansia muciniphila (A. muciniphila), correlates with immunological and metabolic health. The genus Akkermansia in humans includes species with significantly larger genomes than A. muciniphila, leading us to postulate that this added genetic content may influence how they impact human metabolic and immunological health. Methods: We conducted a pangenomic analysis of 234 Akkermansia complete or near-complete genomes. We also used high-resolution species and subspecies assignments to reanalyze publicly available metagenomic datasets to determine if there are relationships between Akkermansia species and A. muciniphila clades with various disease outcomes. Results: Analysis of genome-wide average nucleotide identity, 16S rRNA gene identity, conservation of core Akkermansia genes, and analysis of the fatty acid composition of representative isolates support the partitioning of the genus Akkermansia into several species. In addition, A. muciniphila sensu stricto, the most prevalent Akkermansia species in humans, should be subdivided into two subspecies. For a pediatric cohort, we observed species-specific correlations between Akkermansia abundance with baseline obesity or after various interventions. For inflammatory bowel disease cohorts, we identified a decreased abundance of Akkermansia in patients with ulcerative colitis or Crohn's disease, which was species and subspecies-dependent. In patients undergoing immune checkpoint inhibitor therapies for non-small cell lung carcinoma, we observed a significant association between one A. muciniphila subspecies and survival outcomes", "token_count": 524, "char_count": 1863, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:40.421790", "source": { "split": "train_shard_00001", "doc_id": 1737 }, "chunk_id": "train_shard_00001_1737_0", "global_id": 8108 }, { "text": "Conclusion: Our findings suggest that the prevalence of specific Akkermansia species and/or subspecies can be crucial in evaluating their association with human health, particularly in different disease contexts, and is an important consideration for their use as probiotics.\n\nPangenomic analysis identifies correlations between Akkermansia species and subspecies and human health outcomes.", "token_count": 99, "char_count": 411, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8431, "quality_score": 0.9216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:40.802509", "source": { "split": "train_shard_00001", "doc_id": 1737 }, "chunk_id": "train_shard_00001_1737_1", "global_id": 8109 }, { "text": "

Objective

Routine use of whole genome sequencing (WGS) has been shown to help identify transmission of pathogens causing healthcare-associated infections (HAIs). However, the current gold standard of short-read, Illumina-based WGS is labor and time-intensive. In light of recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing, we sought to establish a low resource utilization approach capable of providing accurate WGS-based comparisons of HAI pathogens within a time frame allowing for infection prevention and control (IPC) interventions.

Methods

WGS was prospectively performed on antimicrobial-resistant pathogens at increased risk of potential healthcare transmission using the ONT MinION sequencer with R10.4.1 flow cells and Dorado basecalling algorithm. Potential transmission was assessed via Ridom SeqSphere+ for core genome multilocus sequence typing and MINTyper for reference-based core genome single nucleotide polymorphisms using previously published cut-off values. The accuracy of our ONT pipeline was determined relative to Illumina-based WGS data generated from the same genomic DNA sample.

Results

Over a six-month period, 242 bacterial isolates from 216 patients were sequenced by a single operator. Compared to the Illumina gold-standard data, our ONT pipeline achieved a Q score of 60 for assembled genomes, even with a coverage rate of as low as 40X. The mean time from initiating DNA extraction to complete genetic analysis was 2 days (IQR 2-3.25 days). We identified five potential transmission clusters comprising 21 isolates (8.7% of all sequenced strains). Combining ONT WGS data with epidemiological data, >70% (15/21) of the isolates originated from patients with potential healthcare transmission links.

Conclusions

Via a stand-alone ONT pipeline, we detected potentially transmitted HAI pathogens rapidly and accurately, aligning closely with epidemiological data. Our low-resource method has the potential to assist in the efficient detection and deployment of preventative measures against HAI transmission.", "token_count": 519, "char_count": 2104, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6655, "quality_score": 0.8328, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:41.438727", "source": { "split": "train_shard_00001", "doc_id": 1738 }, "chunk_id": "train_shard_00001_1738_0", "global_id": 8110 }, { "text": "Rapid Whole Genome Characterization of High-Risk Pathogens Using Long-Read Sequencing to Identify Potential Healthcare Transmission", "token_count": 31, "char_count": 131, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:41.798805", "source": { "split": "train_shard_00001", "doc_id": 1738 }, "chunk_id": "train_shard_00001_1738_1", "global_id": 8111 }, { "text": "Streptococcus mutans is considered a primary etiologic agent of dental caries, which is the most common chronic infectious disease worldwide. S. mutans B04Sm5 was recently shown to produce reutericyclins and mutanocyclin through the muc biosynthetic gene cluster and to utilize reutericyclins to inhibit the growth of neighboring commensal streptococci. In this study, examination of S. mutans and muc phylogeny suggested evolution of an ancestral S. mutans muc into three lineages within one S. mutans clade and then horizontal transfer of muc to other S. mutans clades. The roles of the mucG and mucH transcriptional regulators and the mucI transporter were also examined. mucH was demonstrated to encode a transcriptional activator of muc. mucH deletion reduced production of mutanocyclin and reutericyclins and eliminated the impaired growth and inhibition of neighboring streptococci phenotypes, which are associated with reutericyclin production. ΔmucG had increased mutanocyclin and reutericyclin production, which impaired growth and increased the ability to inhibit neighboring streptococci. However, deletion of mucG also caused reduced expression of mucD, mucE, and mucI. Deletion of mucI reduced mutanocyclin and reutericylin production but enhanced growth, suggesting that mucI may not transport reutericyclin as its homolog does in Limosilactobacillus reuteri. Further research is needed to determine the roles of mucG and mucI and to identify any cofactors affecting the activity of the mucG and mucH regulators", "token_count": 505, "char_count": 1652, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5708, "quality_score": 0.7854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:42.448763", "source": { "split": "train_shard_00001", "doc_id": 1739 }, "chunk_id": "train_shard_00001_1739_0", "global_id": 8112 }, { "text": "Overall, this study provided pangenome and phylogenetic analyses that serve as a resource for S. mutans research and began elucidation of the regulation of reutericyclins and mutanocyclin production in S. mutans. IMPORTANCE S. mutans must be able to outcompete neighboring organisms in its ecological niche in order to cause dental caries. S. mutans B04Sm5 inhibited the growth of neighboring commensal streptococci through production of reutericyclins via the muc biosynthetic gene cluster. In this study, an S. mutans pangenome database and updated phylogenetic tree were generated that will serve as valuable resources for the S. mutans research community and that provide insights into the carriage and evolution of S. mutans muc. The MucG and MucH regulators, and the MucI transporter, were shown to modulate production of reutericyclins and mutanocyclin. These genes also affected the ability of S. mutans to inhibit neighboring commensals, suggesting that they may play a role in S. mutans virulence.\n\nmucG, mucH, and mucI Modulate Production of Mutanocyclin and Reutericyclins in Streptococcus mutans B04Sm5.", "token_count": 330, "char_count": 1151, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5783, "quality_score": 0.7892, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:43.018432", "source": { "split": "train_shard_00001", "doc_id": 1739 }, "chunk_id": "train_shard_00001_1739_1", "global_id": 8113 }, { "text": "The European Commission (EC) proposal for New Genomic Techniques (NGTs) of July 2023 specifies that Category 1 NGT (NGT1) plants, which are considered equivalent to conventional plants, that is those obtainable by conventional plant breeding or mutagenesis, may differ from the recipient or parental plant by no more than 20 insertions, which cannot be longer than 20 bp; deletions can be no more than 20 but of any size. Here, we examine the proposed 20/20 NGT1 limit against the background of the theoretical considerations and older data used to frame it and in light of recent data from highly contiguous long-read assemblies for reference genomes and pangenomes. We find that current genomic data indicate that natural variation in germplasm used by breeders is much greater than earlier understood and that both conventional breeding and mutagenesis can introduce genomic changes that are both more extensive in size and more frequent than the NGT Category 1 '20 insertions of maximum 20 bp' limit would allow. Furthermore, natural variation also scales with genome size and complexity, a factor not considered in the EC proposal. We conclude that the proposed cut-offs under which an NGT plant is considered equivalent to conventional plants do not align with what is observed in nature, conventional breeding and mutagenesis. Updating the 20/20 rule to broader limits would facilitate breeding for climate resilience, farming sustainability and nutritional security, while ensuring that NGT1 plants are equivalent to conventional ones.\n\nProposed EU NGT legislation in light of plant genetic variation.", "token_count": 361, "char_count": 1609, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5783, "quality_score": 0.7892, "entities": { "genes": [ "NGT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:43.630393", "source": { "split": "train_shard_00001", "doc_id": 1740 }, "chunk_id": "train_shard_00001_1740_0", "global_id": 8114 }, { "text": "The growth and survival of an organism in a particular environment is highly depends on the certain indispensable genes, termed as essential genes. Sulfate-reducing bacteria (SRB) are obligate anaerobes which thrives on sulfate reduction for its energy requirements. The present study used Oleidesulfovibrio alaskensis G20 (OA G20) as a model SRB to categorize the essential genes based on their key metabolic pathways. Herein, we reported a feedback loop framework for gene of interest discovery, from bio-problem to gene set of interest, leveraging expert annotation with computational prediction. Defined bio-problem was applied to retrieve the genes of SRB from literature databases (PubMed, and PubMed Central) and annotated them to the genome of OA G20. Retrieved gene list was further used to enrich protein-protein interaction and was corroborated to the pangenome analysis, to categorize the enriched gene sets and the respective pathways under essential and non-essential. Interestingly, the sat gene (dde_2265) from the sulfur metabolism was the bridging gene between all the enriched pathways. Gene clusters involved in essential pathways were linked with the genes from seleno-compound metabolism, amino acid metabolism, secondary metabolite synthesis, and cofactor biosynthesis. Furthermore, pangenome analysis demonstrated the gene distribution, where 69.83% of the 116 enriched genes were mapped under \"persistent,\" inferring the essentiality of these genes. Likewise, 21.55% of the enriched genes, which involves specially the formate dehydrogenases and metallic hydrogenases, appeared under \"shell.\" Our methodology suggested that semi-automated text mining and network analysis may play a crucial role in deciphering the previously unexplored genes and key mechanisms which can help to generate a baseline prior to perform any experimental studies.\n\nIntegration of text mining and biological network analysis: Identification of essential genes in sulfate-reducing bacteria.", "token_count": 492, "char_count": 2006, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6272, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:44.294173", "source": { "split": "train_shard_00001", "doc_id": 1741 }, "chunk_id": "train_shard_00001_1741_0", "global_id": 8115 }, { "text": "

Background

Verona integron-encoded metallo-β-lactamase-producing Pseudomonas aeruginosa (VIM-PA) outbreaks are frequently linked to contaminated sink-drains in the intensive care unit (ICU). This study aims to investigate a VIM-PA outbreak occurring at 4 ICUs in a Belgian university center.

Methods

Between 01/01/2019 and 30/07/2023, data were retrospectively retrieved. Whole-genome sequencing of VIM-PA was carried out for available isolates and the core genome multilocus sequencing typing (cgMLST) was used to confirm clonality. New case incidence was estimated by analyzing the weekly data of at-risk and VIM-PA-colonized patients, fitting a regression model.

Results

Fifty-one patients were colonized, among them, 32 (63%) were infected by VIM-PA, which contributed to 7 deaths. The outbreak investigation showed that 19 (47%) of the examined sink-drains grew at least once a VIM-PA. Two major clusters were observed by cgMLST: ST111 (59 clones with 40 clinical isolates), and ST17 (8 clones with 6 clinical isolates). The estimated incidence rate of new cases was significantly higher in one unit.

Conclusions

A 5-year prolonged outbreak at the UZ Brussel ICUs was caused by only 2 VIM-PA clones, both linked to sink-drains, with minimal mutations occurring throughout the years. Statistical modeling found different incidence rates between units. Tailored interventions were hence prioritized.\n\nFive-year VIM-producing Pseudomonas aeruginosa outbreak in four Belgian ICUs, an investigation report (2019-2023).", "token_count": 460, "char_count": 1547, "word_count": 205, "semantic_coherence": 1, "information_density": 0.7122, "quality_score": 0.8561, "entities": { "genes": [ "ST17", "ST111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:44.986621", "source": { "split": "train_shard_00001", "doc_id": 1742 }, "chunk_id": "train_shard_00001_1742_0", "global_id": 8116 }, { "text": "In December 2023, the World Health Organization reported an Australian nosocomial Ralstonia pickettii outbreak caused by contaminated saline solutions, causing bloodstream infections. The Antibiotic Resistance Surveillance, a Germany-wide laboratory network, has identified five R. pickettii-bacteraemia cases since August 2023 (0-1 annually 2019-2022), prompting an outbreak investigation to identify the source. We defined a case as a person with R. pickettii in any material (possible) or in blood culture (probable), confirmed if in the genetic outbreak cluster. We implemented nationwide R. pickettii surveillance, subjected isolates to core genome multilocus sequence typing, and compared cases by exposure, including medical products. From August 2023 to June 2024, we detected 25 cases. For eighteen cases, isolates were available, and sequences from six cases clustered within 6 allelic differences but showed >43 allelic differences from Australian outbreak-associated sequences. These confirmed cases occurred in three hospitals across three federal states between October 2023 and March 2024, linked only by saline solution exposure. Four products and 11 lots matched across two of three hospitals. Retain sample testing remained negative. The R. pickettii outbreak in Germany was likely linked to saline solutions, although no product/lot was confirmed. Tracing products/lots was particularly challenging. Patient-level documentation of medical products/lots and official mandates for the testing of retained samples could improve product traceback in future outbreaks.\n\nNosocomial Outbreak of <i>Ralstonia pickettii</i> Infections Likely Linked to Saline Solutions in Germany from August 2023 to March 2024-Challenges in Medical Product-Related Outbreaks.", "token_count": 460, "char_count": 1816, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6597, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:45.632244", "source": { "split": "train_shard_00001", "doc_id": 1743 }, "chunk_id": "train_shard_00001_1743_0", "global_id": 8117 }, { "text": "Campylobacter is a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies on Campylobacter generally focus on specific pathogenic species such as C. coli and C. jejuni . Currently, there are thousands of publicly available Campylobacter genomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all available Campylobacter genomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III of C. coli is in fact a novel species (referred here as Campylobacter spp12 ). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinct Campylobacter species. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics of Campylobacter species with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that the Campylobacter genus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.\n\nComparative genomics and phylogenomics ofCampylobacterunveil potential novel species and provide insights into niche segregation", "token_count": 303, "char_count": 1406, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:46.208567", "source": { "split": "train_shard_00001", "doc_id": 1744 }, "chunk_id": "train_shard_00001_1744_0", "global_id": 8118 }, { "text": "Foodborne diseases (FBDs) are infections of the gastrointestinal tract caused by foodborne pathogens (FBPs) such as bacteria [Salmonella, Listeria monocytogenes and Shiga toxin-producing E. coli (STEC)] and several viruses, but also parasites and some fungi. Artificial intelligence (AI) and its sub-discipline machine learning (ML) are re-emerging and gaining an ever increasing popularity in the scientific community and industry, and could lead to actionable knowledge in diverse ranges of sectors including epidemiological investigations of FBD outbreaks and antimicrobial resistance (AMR). As genotyping using whole-genome sequencing (WGS) is becoming more accessible and affordable, it is increasingly used as a routine tool for the detection of pathogens, and has the potential to differentiate between outbreak strains that are closely related, identify virulence/resistance genes and provide improved understanding of transmission events within hours to days. In most cases, the computational pipeline of WGS data analysis can be divided into four (though, not necessarily consecutive) major steps: de novo genome assembly, genome characterization, comparative genomics, and inference of phylogeny or phylogenomics. In each step, ML could be used to increase the speed and potentially the accuracy (provided increasing amounts of high-quality input data) of identification of the source of ongoing outbreaks, leading to more efficient treatment and prevention of additional cases. In this review, we explore whether ML or any other form of AI algorithms have already been proposed for the respective tasks and compare those with mechanistic model-based approaches.\n\nMachine Learning Approaches for Epidemiological Investigations of Food-Borne Disease Outbreaks.", "token_count": 411, "char_count": 1791, "word_count": 245, "semantic_coherence": 1, "information_density": 0.7429, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:46.824482", "source": { "split": "train_shard_00001", "doc_id": 1745 }, "chunk_id": "train_shard_00001_1745_0", "global_id": 8119 }, { "text": "

Background:

High-risk Escherichia coli clones, such as Sequence Type (ST)131 and ST1193, along with multidrug-resistant (MDR) Klebsiella pneumoniae, are globally recognized for their significant role in urinary tract infections (UTIs). This study investigates the characteristics of these pathogens in the Tebessa re-gion of Algeria.

Methods:

Forty E. coli and 17 K. pneumoniae isolates exhibiting extended-spectrum cephalosporin (ESC)-resistance were phenotypically and genotypically characterized. Whole genome sequencing (WGS) was performed on the ST1193 clone.

Results:

Among K. pneumoniae isolates, all except one har-bored CTX-M-15, with a single isolate carrying blaCTX-M-194. Additionally, two K. pneumoniae isolates co-harboring blaCTX-M-15 and blaNDM exhibited both phenotypic and genotypic hypervirulence traits. Fluoroquinolone resistance (FQR) was de-tected in 94.1% of K. pneumoniae isolates. The E. coli isolates carried diverse ESC-resistance genes, including CTX-M-15 (87.5%), CTX-M-27 (5%), CTX-M-1, CMY-59, and CMY-166 (2.5% each). Co-carriage of blaESC and blaOXA-48 was identi-fied in three E. coli isolates, while 62.5% exhibited FQR. Phylogenetic analysis revealed that 52.5% of E. coli belonged to phylogroup B2, including the high-risk clonal complex (CC)131 CH40-30 (17 isolates) and ST1193 (one isolate). The vir-ulence profile indicated that 72.5% of isolates met the criteria for extraintestinal pathogenic E", "token_count": 525, "char_count": 1465, "word_count": 191, "semantic_coherence": 1, "information_density": 0.7539, "quality_score": 0.877, "entities": { "genes": [ "CH40", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:14:47.484051", "source": { "split": "train_shard_00001", "doc_id": 1746 }, "chunk_id": "train_shard_00001_1746_0", "global_id": 8120 }, { "text": "coli (ExPEC), while 47.5% were classified as uropathogenic E. coli (UPEC). Characterization of CC131 clone showed that virotypes F and E ac-counted for 59% of isolates. In silico analysis of the ST1193 genome determined O75:H5-B2 (CH14-64), and the carriage of IncI1-I(Alpha) and IncF [F-:A1:B10] plasmids. Notably, core genome single-nucleotide polymorphism (SNP) analy-sis demonstrated high similarity between the Algerian ST1193 isolate and a previously annotated genome from a hospital in Northwest Spain.

Conclusions:

This study highlights the spread and genetic diversity of E. coli CC131 CH40-30 and hypervirulent K. pneumoniae clones in Algeria. Additionally, it represents the first report of a CTX-M-15-carrying E. coli ST1193 in the country. These findings emphasize the urgent need for surveillance programs and optimized antibiotic stewardship to curb the dissemination of high-risk clones that pose an increas-ing public health threat in Algeria.\n\nPhenotypic and Genotypic Characterization of ESBL-, AmpC-, and Carbapenemase-Producing Klebsiella pneumoniae and High-Risk Escherichia coli CC131, with the First Report of ST1193 as a Causative Agent of Urinary Tract Infections in Algeria", "token_count": 392, "char_count": 1209, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "CH14", "CH40", "CC131", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:48.097288", "source": { "split": "train_shard_00001", "doc_id": 1746 }, "chunk_id": "train_shard_00001_1746_1", "global_id": 8121 }, { "text": "

Objectives

Collectively, the Hajj and Umrah pilgrimages draw >30 million pilgrims to the Kingdom of Saudi Arabia (KSA) each year. Before Hajj 2024 (14 to 19 June), the meningococcal serogroup W ST-11 complex (W:cc11) Hajj-strain sublineage caused multiple international cases of invasive meningococcal disease (IMD) associated with travel to the Middle East and Asia. Here we identify and characterise the strains responsible.

Methods

All Hajj strain sublineage genomes on PubMLST.org underwent core genome MLST comparisons (PubMLST.org).

Results

Isolates from 30 cases, across seven countries, formed five phylogenetic clusters within two distinct strains. Travel histories included KSA, other Middle Eastern countries, India, Mauritius, Kenya via Turkey, and no known associated travel. The prevalent strain, representing four clusters, had no African, and limited Middle Eastern, representation. The geo-temporal distribution of available genomes indicated Eastern Europe as a possible source.

Conclusions

The rapid expansion of Umrah/travel-related W:cc11 IMD cases in early 2024 was due to multiple strains/sublineages. Despite the involvement of non-KSA travel-destinations, the coincidence of cases with the busy month of Ramadan, and the abrupt cessation during Hajj (when vaccine compliance is maximal), suggest that Umrah was a key driver and highlight the need to reinforce mandatory vaccination whilst maintaining global vigilance.\n\nUmrah- and travel-associated meningococcal disease due to multiple serogroup W ST-11 sub-strains pre-Hajj 2024.", "token_count": 434, "char_count": 1585, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:48.728612", "source": { "split": "train_shard_00001", "doc_id": 1747 }, "chunk_id": "train_shard_00001_1747_0", "global_id": 8122 }, { "text": "Ribonucleotides have shown many promising applications in food and pharmaceutical industries. The aim of the present study was to produce ribonucleotides (RNA) by Kluyveromyces marxianus ATCC 8,554 utilizing cheese whey, a dairy industry waste, as a main substrate under batch fermentation conditions. The effects of temperature, pH, aeration rate, agitation and initial cellular concentration were studied simultaneously through factorial design for RNA, biomass production and lactose consumption. The maximum RNA production (28.66 mg/g of dry biomass) was observed at temperature 30°C, pH 5.0 and 1 g/l of initial cellular concentration after 2 h of fermentation. Agitation and aeration rate did not influence on RNA concentration (p > 0.05). Maximum lactose consumption (98.7%) and biomass production (6.0 g/l) was observed after 12 h of incubation. This study proves that cheese whey can be used as an adequate medium for RNA production by K. marxianus under the optimized conditions at industrial scale.\n\nFermentative production of ribonucleotides from whey by Kluyveromyces marxianus: effect of temperature and pH.", "token_count": 314, "char_count": 1121, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:49.290637", "source": { "split": "train_shard_00001", "doc_id": 1748 }, "chunk_id": "train_shard_00001_1748_0", "global_id": 8123 }, { "text": "Protein sequences can be transformed into vectors composed of counts for each amino acid (vector of Residue Counts; vRC) that are mathematically tractable and retain information about homology. We use vRCs to perform alignment-free, residue-based, pangenome analysis (ARPA; https://github.com/Arnavlal/ARPA ). ARPA is 70-90 times faster at identifying homologous gene clusters compared to standard techniques, and offers rapid calculation, visualization, and novel phylogenetic approaches for pangenomes.\n\nEfficient Pangenome Construction through Alignment-Free Residue Pangenome Analysis (ARPA)", "token_count": 149, "char_count": 595, "word_count": 74, "semantic_coherence": 1, "information_density": 0.8784, "quality_score": 0.9392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:49.729024", "source": { "split": "train_shard_00001", "doc_id": 1749 }, "chunk_id": "train_shard_00001_1749_0", "global_id": 8124 }, { "text": "Pressmud, a by-product from the sugarcane industry, was used as a carbon source for the production of inulinase in solid-state fermentation (SSF). Statistical experimental designs were employed to screen the nutrients and optimize the media composition for the production of inulinase by Kluyveromyces marxianus var. marxianus. Eighteen various nutrients were selected for preliminary screening of production medium component by Plackett-Burman design (PBD) technique. Five nutrients were found to be significant for inulinase production and they were optimized by central composite design (CCD). The optimal media components for solid-state fermentation of inulinase using pressmud were (g/gds): corn steep liquor, 0.06072; urea, 0.01916; beef extract, 0.00957; FeSO4 · 7H2O, 0.00013; K2HPO4, 0.00441. The effect of moisture content and substrate concentration was also studied. From the results it was found that a maximum inulinase activity of 288 U/gds occurs at the moisture content of 65% and substrate concentration of 10 g. The constants in the Michaelis-Menten equation were evaluated and a high R (2) value implied the fitness of the model. Artificial neural network (ANN) modeling was also employed to predict the inulinase production.\n\nOptimization, kinetics, and modeling of inulinase production by K. marxianus var. marxianus.", "token_count": 372, "char_count": 1340, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:50.321360", "source": { "split": "train_shard_00001", "doc_id": 1750 }, "chunk_id": "train_shard_00001_1750_0", "global_id": 8125 }, { "text": "Degenerative Cervical Myelopathy (DCM) is the most common cause of spinal cord impairment in elderly populations. It describes a spectrum of disorders that cause progressive spinal cord compression, neurological impairment, loss of bladder and bowel functions, and gastrointestinal dysfunction. The gut microbiota has been recognized as an environmental factor that can modulate both the function of the central nervous system and the immune response through the microbiota-gut-brain axis. Changes in gut microbiota composition or microbiota-producing factors have been linked to the progression and development of several pathologies. However, little is known about the potential role of the gut microbiota in the pathobiology of DCM. Here, DCM was induced in C57BL/6 mice by implanting an aromatic polyether material underneath the C5-6 laminae. The extent of DCM-induced changes in microbiota composition was assessed by 16S rRNA sequencing of the fecal samples. The immune cell composition was assessed using flow cytometry. To date, several bacterial members have been identified using BLAST against the largest collection of metagenome-derived genomes from the mouse gut. In both, female and males DCM caused gut dysbiosis compared to the sham group. However, dysbiosis was more pronounced in males than in females, and several bacterial members of the families Lachnospiraceae and Muribaculaceae were significantly altered in the DCM group. These changes were also associated with altered microbe-derived metabolic changes in propionate-, butyrate-, and lactate-producing bacterial members. Our results demonstrate that DCM causes dynamic changes over time in the gut microbiota, reducing the abundance of butyrate-producing bacteria, and lactate-producing bacteria to a lesser extent. Genome-scale metabolic modeling using gapseq successfully identified pyruvate-to-butanoate and pyruvate-to-propionate reactions involving genes such as Buk and ACH1, respectively. These results provide a better understanding of the sex-specific molecular effects of changes in the gut microbiota on DCM pathobiology.", "token_count": 497, "char_count": 2109, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6041, "quality_score": 0.802, "entities": { "genes": [ "ACH1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:51.331441", "source": { "split": "train_shard_00001", "doc_id": 1751 }, "chunk_id": "train_shard_00001_1751_0", "global_id": 8126 }, { "text": "Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice.", "token_count": 23, "char_count": 72, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:51.682149", "source": { "split": "train_shard_00001", "doc_id": 1751 }, "chunk_id": "train_shard_00001_1751_1", "global_id": 8127 }, { "text": "Lactococcus lactis strains are important components in industrial starter cultures for cheese manufacturing. They have many strain-dependent properties, which affect the final product. Here, we explored the use of machine learning to create systematic, high-throughput screening methods for these properties. Fast acidification of milk is such a strain-dependent property. To predict the maximum hourly acidification rate (Vmax), we trained Random Forest (RF) models on four different genomic representations: Presence/absence of gene families, counts of Pfam domains, the 8 nucleotide long subsequences of their DNA (8-mers), and the 9 nucleotide long subsequences of their DNA (9-mers). Vmax was measured at different temperatures, volumes, and in the presence or absence of yeast extract. These conditions were added as features in each RF model. The four models were trained on 257 strains, and the correlation between the measured Vmax and the predicted Vmax was evaluated with Pearson Correlation Coefficients (PC) on a separate dataset of 85 strains. The models all had high PC scores: 0.83 (gene presence/absence model), 0.84 (Pfam domain model), 0.76 (8-mer model), and 0.85 (9-mer model). The models all based their predictions on relevant genetic features and showed consensus on systems for lactose metabolism, degradation of casein, and pH stress response. Each model also predicted a set of features not found by the other models.\n\nMachine learning predicts and provides insights into milk acidification rates of Lactococcus lactis.", "token_count": 364, "char_count": 1546, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8355, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:52.260839", "source": { "split": "train_shard_00001", "doc_id": 1752 }, "chunk_id": "train_shard_00001_1752_0", "global_id": 8128 }, { "text": "Sulfur-oxidizing and sulfate-reducing bacteria in salt marsh sediments are major controllers of ecosystem-scale carbon cycling. Cross-site comparisons of S-cycling communities are difficult given the rampant uncultured microbial diversity in sediment, yet comparisons are essential for revealing biogeographic, phylogenetic and functionally significant variation. Here, we use deep shotgun metagenomic sequencing data to construct and compare metagenome-assembled genomes (MAGs) of sulfur-cycling bacteria from Massachusetts and Alabama salt marshes that contrast in seasonality and sediment organic matter content. Samples were collected from sediments under Sporobolus alterniflorus and Sporobolus pumilus in separate MA vegetation zones, and under Sporobolus alterniflorus and Juncus roemerianus co-rooted in AL marsh. We grouped metagenomic data by plant species and site and identified 38 MAGs that included pathways for dissimilatory sulfate reduction or sulfide oxidation. Phylogenetic analyses indicated that 30 of the 38 were affiliated with uncultivated lineages. Read-mapping to MAGs showed significant differentiation of AL and MA samples, differentiation of samples taken in S. alterniflorus and S. pumilus vegetation zones in MA, but no differentiation of samples taken under S. alterniflorus and J. roemerianus that were rooted together in AL marsh. Pangenomic analyses of eight ubiquitous MAGs also detected site- and vegetation-specific genomic features, including varied sulfur-cycling operons, carbon fixation pathways, fixed single nucleotide variants, and active diversity-generating retroelements. This genetic diversity, detected at multiple scales even within uncultured groups, suggests evolutionary relationships affected by distance and local environment, and demonstrates differential microbial capacities for sulfur and carbon cycling in salt marsh sediments.

Importance

Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems", "token_count": 495, "char_count": 2075, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6208, "quality_score": 0.8104, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:52.917872", "source": { "split": "train_shard_00001", "doc_id": 1753 }, "chunk_id": "train_shard_00001_1753_0", "global_id": 8129 }, { "text": "Sulfate reducers are the major decomposers in salt marsh systems, and sulfur-oxidizing bacteria remove sulfide, a toxic byproduct of sulfate reduction, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here we use comparative genomics to overcome these challenges and provide an in-depth characterization of microbial diversity in salt marshes. We characterize sulfur-cycling communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with sulfur-cycling uncultivated lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.\n\nDiversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes", "token_count": 234, "char_count": 1054, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:53.388274", "source": { "split": "train_shard_00001", "doc_id": 1753 }, "chunk_id": "train_shard_00001_1753_1", "global_id": 8130 }, { "text": "Bacterial vaginosis (BV) is a common vaginal infection and has been associated with increased risk for a wide array of health issues. BV is linked with a variety of heterogeneous pathogenic anaerobic bacteria, among which Mobiluncus is strongly associated with BV diagnosis. However, their genetic features, pathogenicity, interspecific diversity, and evolutionary characters have not been illustrated at genomic level. The current study performed phylogenomic and comparative genomic analyses of Mobiluncus. Phylogenomic analyses revealed remarkable phylogenetic distinctions among different species. Compared with M. curtisii, M. mulieris had a larger genome and pangenome size with more insertion sequences but less CRISPR-Cas systems. In addition, these two species were diverse in profile of virulence factors, but harbored similar antibiotic resistance genes. Statistically different functional genome profiles between strains from the two species were determined, as well as correlations of some functional genes/pathways with putative pathogenicity. We also showed that high levels of horizontal gene transfer might be an important strategy for species diversification and pathogenicity. Collectively, this study provides the first genome sequence level description of Mobiluncus, and may shed light on its virulence/pathogenicity, functional diversification, and evolutionary dynamics. Our study could facilitate the further investigations of this important pathogen, and might improve the future treatment of BV.\n\nGenomic Insights Into the Interspecific Diversity and Evolution of Mobiluncus, a Pathogen Associated With Bacterial Vaginosis.", "token_count": 392, "char_count": 1685, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:54.002624", "source": { "split": "train_shard_00001", "doc_id": 1754 }, "chunk_id": "train_shard_00001_1754_0", "global_id": 8131 }, { "text": "N. gonorrhoeae and N. meningitidis, the only two human pathogens of Neisseria, are closely related species. But the niches they survived in and their pathogenic characteristics are distinctly different. However, the genetic basis of these differences has not yet been fully elucidated. In this study, comparative genomics analysis was performed based on 15 N. gonorrhoeae, 75 N. meningitidis, and 7 nonpathogenic Neisseria genomes. Core-pangenome analysis found 1111 conserved gene families among them, and each of these species groups had opening pangenome. We found that 452, 78, and 319 gene families were unique in N. gonorrhoeae, N. meningitidis, and both of them, respectively. Those unique gene families were regarded as candidates that related to their pathogenicity and niche adaptation. The relationships among them have been partly verified by functional annotation analysis. But at least one-third genes for each gene set have not found the certain functional information. Simple sequence repeat (SSR), the basis of gene phase variation, was found abundant in the membrane or related genes of each unique gene set, which may facilitate their adaptation to variable host environments. Protein-protein interaction (PPI) analysis found at least five distinct PPI clusters in N. gonorrhoeae and four in N. meningitides, and 167 and 52 proteins with unknown function were contained within them, respectively.\n\nGenus-Wide Comparative Genomics Analysis of Neisseria to Identify New Genes Associated with Pathogenicity and Niche Adaptation of Neisseria Pathogens.", "token_count": 461, "char_count": 1651, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6043, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:54.641422", "source": { "split": "train_shard_00001", "doc_id": 1755 }, "chunk_id": "train_shard_00001_1755_0", "global_id": 8132 }, { "text": "

Background

Ogataea (Hansenula) polymorpha is one of the most thermotolerant xylose-fermenting yeast species reported to date. Several metabolic engineering approaches have been successfully demonstrated to improve high-temperature alcoholic fermentation by O. polymorpha. Further improvement of ethanol production from xylose in O. polymorpha depends on the identification of bottlenecks in the xylose conversion pathway to ethanol.

Results

Involvement of peroxisomal enzymes in xylose metabolism has not been described to date. Here, we found that peroxisomal transketolase (known also as dihydroxyacetone synthase) and peroxisomal transaldolase (enzyme with unknown function) in the thermotolerant methylotrophic yeast, Ogataea (Hansenula) polymorpha, are required for xylose alcoholic fermentation, but not for growth on this pentose sugar. Mutants with knockout of DAS1 and TAL2 coding for peroxisomal transketolase and peroxisomal transaldolase, respectively, normally grow on xylose. However, these mutants were found to be unable to support ethanol production. The O. polymorpha mutant with the TAL1 knockout (coding for cytosolic transaldolase) normally grew on glucose and did not grow on xylose; this defect was rescued by overexpression of TAL2. The conditional mutant, pYNR1-TKL1, that expresses the cytosolic transketolase gene under control of the ammonium repressible nitrate reductase promoter did not grow on xylose and grew poorly on glucose media supplemented with ammonium", "token_count": 492, "char_count": 1584, "word_count": 200, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "TKL1", "TAL2", "DAS1", "TAL1" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:55.305891", "source": { "split": "train_shard_00001", "doc_id": 1756 }, "chunk_id": "train_shard_00001_1756_0", "global_id": 8133 }, { "text": "Overexpression of DAS1 only partially restored the defects displayed by the pYNR1-TKL1 mutant. The mutants defective in peroxisome biogenesis, pex3Δ and pex6Δ, showed normal growth on xylose, but were unable to ferment this sugar. Moreover, the pex3Δ mutant of the non-methylotrophic yeast, Scheffersomyces (Pichia) stipitis, normally grows on and ferments xylose. Separate overexpression or co-overexpression of DAS1 and TAL2 in the wild-type strain increased ethanol synthesis from xylose 2 to 4 times with no effect on the alcoholic fermentation of glucose. Overexpression of TKL1 and TAL1 also elevated ethanol production from xylose. Finally, co-overexpression of DAS1 and TAL2 in the best previously isolated O. polymorpha xylose to ethanol producer led to increase in ethanol accumulation up to 16.5 g/L at 45 °C; or 30-40 times more ethanol than is produced by the wild-type strain.

Conclusions

Our results indicate the importance of the peroxisomal enzymes, transketolase (dihydroxyacetone synthase, Das1), and transaldolase (Tal2), in the xylose alcoholic fermentation of O. polymorpha.\n\nPeroxisomes and peroxisomal transketolase and transaldolase enzymes are essential for xylose alcoholic fermentation by the methylotrophic thermotolerant yeast, Ogataea (Hansenula) polymorpha.", "token_count": 509, "char_count": 1408, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6236, "quality_score": 0.8118, "entities": { "genes": [ "TKL1", "TAL2", "DAS1", "TAL1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:55.980924", "source": { "split": "train_shard_00001", "doc_id": 1756 }, "chunk_id": "train_shard_00001_1756_1", "global_id": 8134 }, { "text": "Various consortia of yeasts and bacteria involved in the natural fermentation process of tequila have been identified, particularly non-Saccharomyces yeasts. This study evaluates the fermentative capacity of two non-Saccharomyces yeasts (isolated from traditional mezcal fermentation): Kluyveromyces marxianus (DU3) and Pichia kluyveri (GRO3), and assesses their production of volatile compounds. The values found are compared with those of the same attributes of a Saccharomyces cerevisiae (AR5) isolated from tequila fermentation. The fermentations were performed in two different media, agave juice (JA) and a semi-synthetic medium (M11). The study also compared free and immobilized yeast fermentations in the JA medium in order to evaluate the potential benefits of immobilization on the yeast behaviour. This study demonstrated the potential of non-Saccharomyces yeasts, which fermented the agave juice in the same manner as S. cerevisiae but with higher ester production. Furthermore, K. marxianus produced more higher alcohols than S. cerevisiae. This could lead to tequila with different aroma profiles. Results were different in the synthetic medium, thus showing sensitivity to the composition of the medium. No significant differences between yeast fermentations with free and immobilized cells were detected, except for ethanol yield.\n\nFermentative capacity of Saccharomyces and non-Saccharomyces in agave juice and semi-synthetic medium", "token_count": 362, "char_count": 1450, "word_count": 200, "semantic_coherence": 1, "information_density": 0.595, "quality_score": 0.7975, "entities": { "genes": [ "GRO3", "DU3", "AR5" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:56.591694", "source": { "split": "train_shard_00001", "doc_id": 1757 }, "chunk_id": "train_shard_00001_1757_0", "global_id": 8135 }, { "text": "Kefir grains are a microbial consortium of different genera of bacteria and yeasts. In this study, the performance of Tunisian Kefir grains during the biological treatment of a mixture of Gouda cheese whey and white wastewaters (GCW) in ratio 1:1 with very high organic matter concentration is investigated. The biological process was evaluated and optimized through the response surface methodology. Under the optimum conditions, Kefir grains concentration of 1.02%, temperature at 36.68 °C, and incubation time of 5.14 days, the removal efficiencies of COD, PO43-, and NO3- were 87, 37.48, and 39.5%, respectively. Interestingly, the reusability tests of the grains proved not only their high resistance to harsh environmental conditions but also their great potential for more practical applications. Particularly, different strains were isolated from the grains and identified as Kluyveromyces marxianus, Lactoccocus lactis, Lactobacillus kefiri, and Bacillus spp. using 16S rDNA sequence analysis and rep-PCR fingerprinting. At the biological level, the raw GCW (RGCW) has a negative impact on the Hordeum vulgare both on seed germination, and on the growth parameters of seedlings. Interestingly, after Kefir grains treatment, the treated GCW (TGCW) allow a seedlings growth and germination rate similar to those soaked in water.\n\nA new practical approach for the biological treatment of a mixture of cheese whey and white wastewaters using Kefir grains.", "token_count": 406, "char_count": 1504, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:57.253142", "source": { "split": "train_shard_00001", "doc_id": 1758 }, "chunk_id": "train_shard_00001_1758_0", "global_id": 8136 }, { "text": "The microbiota hosted in the pig gastrointestinal tract are important to health of this biomedical model. However, the individual species and functional repertoires that make up the pig gut microbiome remain largely undefined. Here we comprehensively investigated the genomes and functions of the piglet gut microbiome using culture-based and metagenomics approaches. A collection included 266 cultured genomes and 482 metagenome-assembled genomes (MAGs) that were clustered to 428 species across 10 phyla was established. Among these clustered species, 333 genomes represent potential new species. Less matches between cultured genomes and MAGs revealed a substantial bias for the acquisition of reference genomes by the two strategies. Glycoside hydrolases was the dominant category of carbohydrate-active enzymes. Four-hundred forty-five secondary metabolite biosynthetic genes were predicted from 292 genomes with bacteriocin being the most. Pan genome analysis of Limosilactobacillus reuteri uncover the biosynthesis of reuterin was strain-specific and the production was experimentally determined. This study provides a comprehensive view of the microbiome composition and the function landscape of the gut of weanling piglets and a valuable bacterial resource for further experimentations. IMPORTANCE The microorganism communities resided in mammalian gastrointestinal tract impacted the health and disease of the host. Our study complements metagenomic analysis with culture-based approach to establish a bacteria and genome collection and comprehensively investigate the microbiome composition and function of the gut of weanling piglets. We provide a valuable resource for further study of gut microbiota of weanling piglet and development of probiotics for prevention of disease.\n\nA Bacterial Genome and Culture Collection of Gut Microbial in Weanling Piglet.", "token_count": 443, "char_count": 1884, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5703, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:57.885556", "source": { "split": "train_shard_00001", "doc_id": 1759 }, "chunk_id": "train_shard_00001_1759_0", "global_id": 8137 }, { "text": "Abstract

BackgroundButyrivibrio and Pseudobutyrivibrio dominate in anaerobic gastrointestinal microbiomes, particularly the rumen, where they play a key role in harvesting energy from the diet. Within these genera, 5 rumen species have been classified (B. fibrisolvens, B. hungatei, B. proteoclasticus, P. ruminis and P. xylanivorans); nonetheless, the phylogeny and evolution of these genera is still unclear. Given the recent increase in available genomes, a re-investigation of the phylogenetic systematics and evolution of Butyrivibrio and Pseudobutyrivibrio is timely.ResultsWe show, using both a 16S rDNA and 40 gene marker phylogenetic tree, that 6 species, namely 1. P. ruminis, 2. P. xylanivorans, 3. B. fibrisolvens, 4. Butyrivibrio sp., 5. B. hungatei, and 6. B. proteclasticus likely exist. Pangenome analysis at 100% core definition showed a high abundance of accessory genes (91.50 to 99.34%) compared with core genes (0.66 to 8.50%), illustrating possession of very open genomes. Across the 71 genomes, 870 COGs (clusters of orthologous genes) were shared by all taxa, suggesting evolution through speciation from a common ancestor", "token_count": 494, "char_count": 1446, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7697, "quality_score": 0.8848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:58.536902", "source": { "split": "train_shard_00001", "doc_id": 1760 }, "chunk_id": "train_shard_00001_1760_0", "global_id": 8138 }, { "text": "Further analysis of Carbohydrate-Active Enzymes (CAZymes) genes show that most are within the accessory genome and orthologous in descent with numerous within-family CAZyme isoforms apparent, CAZyme family tree lineages show that these isoforms largely group according to the 6 species, suggesting extensive horizontal gene transfer within these families.ConclusionsWe show the extensive genomic variation found within Butyrivibrio, and to a lesser extent, Pseudobutyrivibrio. and demonstrate the existence of a new Butyrivibrio species. The Butyrivibrio and Pseudobutyrivibrio genomes are very open with very low % core genomes and high % accessory genomes., and possess a number of GH isoforms that we hypothesise facilitate metabolic plasticity and resilience under dietary perturbations. This study utilizes all currently available genomes and consequently provides a major advancement in our understanding of these important anaerobic bacteria.

\n\nPhylogenetic systematics of Butyrivibrio and Pseudobutyrivibrio genomes illustrate possession of open genomes rich in orthologous accessory genes with an abundance of carbohydrate-active enzyme isoforms", "token_count": 325, "char_count": 1255, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6601, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:59.099396", "source": { "split": "train_shard_00001", "doc_id": 1760 }, "chunk_id": "train_shard_00001_1760_1", "global_id": 8139 }, { "text": "

Motivation

Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet.

Results

We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.

Availability and implementation

Source code and test data are available from https://gitlab.ub.uni-bielefeld.de/gi/plast.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nDetecting high-scoring local alignments in pangenome graphs.", "token_count": 354, "char_count": 1586, "word_count": 211, "semantic_coherence": 1, "information_density": 0.654, "quality_score": 0.827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:14:59.675146", "source": { "split": "train_shard_00001", "doc_id": 1761 }, "chunk_id": "train_shard_00001_1761_0", "global_id": 8140 }, { "text": "Mobile genetic elements (MGEs) are relevant agents in bacterial adaptation and evolutionary diversification. Stable appropriation of these DNA elements depends on host factors, among which are the nucleoid-associated proteins (NAPs). NAPs are highly abundant proteins that bind and bend DNA, altering its topology and folding, thus affecting all known cellular DNA processes from replication to expression. Even though NAP coding genes are found in most prokaryotic genomes, their functions in host chromosome biology and xenogeneic silencing are only known for a few NAP families. Less is known about the occurrence, abundance, and roles of MGE-encoded NAPs in foreign elements establishment and mobility. In this study, we used a combination of comparative genomics and phylogenetic strategies to gain insights into the diversity, distribution, and functional roles of NAPs within the class Acidithiobacillia with a special focus on their role in MGE biology. Acidithiobacillia class members are aerobic, chemolithoautotrophic, acidophilic sulfur-oxidizers, encompassing substantial genotypic diversity attributable to MGEs. Our search for NAP protein families (PFs) in more than 90 genomes of the different species that conform the class, revealed the presence of 1,197 proteins pertaining to 12 different NAP families, with differential occurrence and conservation across species. Pangenome-level analysis revealed 6 core NAP PFs that were highly conserved across the class, some of which also existed as variant forms of scattered occurrence, in addition to NAPs of taxa-restricted distribution. Core NAPs identified are reckoned as essential based on the conservation of genomic context and phylogenetic signals. In turn, various highly diversified NAPs pertaining to the flexible gene complement of the class, were found to be encoded in known plasmids or, larger integrated MGEs or, present in genomic loci associated with MGE-hallmark genes, pointing to their role in the stabilization/maintenance of these elements in strains and species with larger genomes", "token_count": 498, "char_count": 2081, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:00.329431", "source": { "split": "train_shard_00001", "doc_id": 1762 }, "chunk_id": "train_shard_00001_1762_0", "global_id": 8141 }, { "text": "Both core and flexible NAPs identified proved valuable as markers, the former accurately recapitulating the phylogeny of the class, and the later, as seed in the bioinformatic identification of novel episomal and integrated mobile elements.\n\nPangenome-level analysis of nucleoid-associated proteins in the Acidithiobacillia class: insights into their functional roles in mobile genetic elements biology.", "token_count": 99, "char_count": 410, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7593, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:00.710921", "source": { "split": "train_shard_00001", "doc_id": 1762 }, "chunk_id": "train_shard_00001_1762_1", "global_id": 8142 }, { "text": "Vibrio vulnificus is a well-known opportunistic pathogen causing food-borne illnesses by ingestion of contaminated seafood. A new strain of V. vulnificus FORC_016 was isolated from a patient's blood sample in South Korea. The genome consists of two circular DNA chromosomes: chromosome I (3,234,424 bp with a G + C contents of 46.60% containing 2,889 ORFs, 106 tRNA genes, and 31 rRNA genes) and chromosome II (1,837,945 bp with a GC content of 47.00% containing 1,572 ORFs, 13 tRNA genes, and 3 rRNA genes). In addition, chromosome I has a super integron (SI) containing 209 ORFs, which is probably associated with various additional functions including antibiotic resistance and pathogenicity. Pan-genome analysis with other V. vulnificus genomes revealed that core genome regions contain most of the important virulence factors. However, accessory genome regions are located in the SI region and contain unique genes regarding cell wall biosynthesis and generation of host cell protecting capsule, suggesting possible resistance ability against environmental stresses. Comparative RNA-Seq analysis of samples between contact and no contact to the crab conditions showed that expressions of amino acid/peptide and carbohydrate transport and utilization genes were down-regulated, but expressions of cell division and growth-related genes were up-regulated, suggesting that the crab may be a nutrition reservoir for rapid propagation of V. vulnificus. Therefore, consumption of the contaminated fresh crab would provide a large number of V. vulnificus to humans, which may be more dangerous. Consequently, biocontrol of V. vulnificus may be critical to ensure the safety in seafood consumption.", "token_count": 484, "char_count": 1737, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6506, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:01.358187", "source": { "split": "train_shard_00001", "doc_id": 1763 }, "chunk_id": "train_shard_00001_1763_0", "global_id": 8143 }, { "text": "Fresh Crab Plays an Important Role as a Nutrient Reservoir for the Rapid Propagation of Vibrio vulnificus.", "token_count": 36, "char_count": 113, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:01.750069", "source": { "split": "train_shard_00001", "doc_id": 1763 }, "chunk_id": "train_shard_00001_1763_1", "global_id": 8144 }, { "text": "

Background

Development of new pan-genome analysis tools is important, as the pangenome of a microbial species has become an important method to define the diversity of a selected taxon, most commonly a species, in the last years. This enables comparison of strains from different ecological niches and can be used to define the functional potential in a bacterial population. It gives us a much better view of microbial genomics than can be gained from singular genomes which after all are just single representatives of a much more varied population.

Results

We present Panakeia, a tool which strives to be easy to use and providing a detailed view of the pangenome structure which can efficiently be utilised for discovery, or further in-depth analysis, of features of interest. It analyses synteny and multiple structural patterns of the pangenome, giving insights into the biological diversity and evolution of the studied taxon. Panakeia hence provides both broad and detailed information on the structure of a pangenome, for diverse and highly clonal populations of bacteria.

Conclusions

Previously published pangenome tools often reduce the information to a presence/absence matrix of unconnected genes or generate massive hard to interpret output graphs. However, Panakeia includes synteny and structural information and presents it in a way that can readily be used for further analysis. Panakeia can be downloaded at https://github.com/BioSina/Panakeia together with a detailed User Guide.\n\nPanakeia - a universal tool for bacterial pangenome analysis.", "token_count": 350, "char_count": 1584, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:02.323979", "source": { "split": "train_shard_00001", "doc_id": 1764 }, "chunk_id": "train_shard_00001_1764_0", "global_id": 8145 }, { "text": "

Background

It has been shown that the microflora of the gastrointestinal tract undergoes changes in obese individuals. The present study aimed to investigate the effect of kefir fortified with two strains, Lactobacillus helveticus and Bifidobacterium longum, on depression, appetite, oxidative stress, and inflammatory parameters in overweight and obese elderly individuals.

Methods

This study was a double-blind, randomized, and placebo-controlled clinical trial conducted on 67 elderly men aged over 65, who were randomly divided into two groups. One group (n = 35) received one bottle (240 cc) of regular kefir as a placebo, while the intervention group (n = 32) received one bottle of probiotic-fortified kefir for eight weeks. Depression and appetite were evaluated using the Geriatric Depression Scale-15 (GDS-15) and a validated Visual Analogue Scale (VAS), respectively. Oxidative stress parameters were assessed using the standard calorimetric method, and inflammatory parameters were measured via the enzyme-linked immunosorbent assay method (ELISA). The differences between the two groups were compared using the independent samples T-test.

Results

The median age of participant in both groups was 65 years. A significant difference in depression scores and the mean change between the two groups was observed after eight weeks (p = 0.001 and p = 0.042, respectively). Within-group comparison revealed a significant increase in appetite scores in both groups (p < 0.05 for both). Moreover, a significant difference in the changes in total antioxidant capacity (TAC) was noted (p = 0.009)", "token_count": 454, "char_count": 1620, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:02.962660", "source": { "split": "train_shard_00001", "doc_id": 1765 }, "chunk_id": "train_shard_00001_1765_0", "global_id": 8146 }, { "text": "However, no significant differences were observed in other oxidative and inflammatory parameters between the two groups (p˃0.05 for all).

Conclusions

The results demonstrated the positive impact of two specific strains of Bifidobacterium and Lactobacillus on improving depression in the elderly. However, when comparing the two groups, no significant effects were observed on appetite, inflammation, and oxidative stress parameters, except for TAC.\n\nThe effect of probiotic-fortified kefir on depression, appetite, oxidative stress, and inflammatory parameters in Iranian overweight and obese elderly: a randomized, double-blind, placebo-controlled clinical trial.", "token_count": 165, "char_count": 671, "word_count": 84, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:03.398319", "source": { "split": "train_shard_00001", "doc_id": 1765 }, "chunk_id": "train_shard_00001_1765_1", "global_id": 8147 }, { "text": "Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central for defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/Bacteroides xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multilocus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens, which harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors. IMPORTANCE Nonharmful bacteria are the primary microbial symbionts that inhabit the human gastrointestinal tract. These bacteria play many beneficial roles and in some cases can modify disease states, making it important to understand which nutrients sustain specific lineages. This knowledge will in turn lead to strategies to intentionally manipulate the gut microbial ecosystem", "token_count": 508, "char_count": 2242, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6271, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:04.031993", "source": { "split": "train_shard_00001", "doc_id": 1766 }, "chunk_id": "train_shard_00001_1766_0", "global_id": 8148 }, { "text": "We designed a scalable, high-throughput platform for measuring the ability of gut bacteria to utilize polysaccharides, of which many are derived from dietary fiber sources that can be manipulated easily. Our results provide paths to expand phenotypic surveys of more diverse gut bacteria to understand their functions and also to leverage dietary fibers to alter the physiology of the gut microbial community.\n\nPhenotypic and Genomic Diversification in Complex Carbohydrate-Degrading Human Gut Bacteria.", "token_count": 118, "char_count": 503, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:04.423303", "source": { "split": "train_shard_00001", "doc_id": 1766 }, "chunk_id": "train_shard_00001_1766_1", "global_id": 8149 }, { "text": "Understanding the ecology of pathogens is important for disease management. Recently, a devastating canker disease was found on red alder (Alnus rubra) planted as landscape trees. Bacteria were isolated from two groups of symptomatic trees located approximately 1 km apart, and one strain from each group was used to complete Koch's postulates. The results showed that these bacteria can cause disease not only on red alder but also on two other alder species. Unexpectedly, analyses of genome sequences of bacterial strains identified them as Lonsdalea quercina, a pathogenic species previously known to cause dieback of oak species, but not alder. Additionally, a core genome phylogeny clustered bacterial strains isolated from red alder within a subclade of L. quercina strains isolated from symptomatic oak trees. Consistent with the close phylogenetic relationship, there was no obvious evidence for divergence in genome composition of strains isolated from red alder and oak. Altogether, the findings indicate that L. quercina is a potential threat to Alnus species.\n\nCanker and Dieback of <i>Alnus rubra</i> Is Caused by <i>Lonsdalea quercina</i>.", "token_count": 341, "char_count": 1227, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6416, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:05.004478", "source": { "split": "train_shard_00001", "doc_id": 1767 }, "chunk_id": "train_shard_00001_1767_0", "global_id": 8150 }, { "text": "Introduction. Antimicrobial resistance (AMR) is a growing global concern. Clonal lineages of CTX-M β-lactamase-producing Escherichia coli (CTXE) and quinolone-resistant E. coli (QREC) were disseminated among the deer population in a famous tourist destination (Nara Park; NP) in Japan. Hypothesis/gap statement. The molecular characteristics of CTXE or QREC isolates, which could pose a threat to public health, have not been elucidated. Aim. This study aimed to characterize the genetic traits of CTXE and QREC isolates derived from NP deer and compare them with lineages prevalent worldwide. Methodology. Sixteen CTXE and three QREC isolates recovered from NP deer faeces between 2018 and 2020 were analysed using whole-genome sequencing (WGS). For endemic lineages, phylogenetic trees were constructed against the isolates registered in the EnteroBase database using the core genome SNP scheme. Results. The most prevalent lineage in NP deer was ST3580. Several pandemic lineages, such as sequence type (ST) 38, ST58 and ST117, were included. The QREC lineages prevalent among deer were designated as extra-intestinal pathogenic E. coli or uropathogenic E. coli (UPEC). Thirteen of the 24 antimicrobial resistance genes (ARGs) were considered high-risk ARG families. Chromosomal integration of bla CTX-M-15 was observed in all plasmid-negative isolates. Phylogenetic analysis suggested relationships between NP isolates and isolates sourced from the environment or poultry. Conclusion. ST3580 has a high potential for clonal dissemination", "token_count": 496, "char_count": 1629, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6697, "quality_score": 0.8349, "entities": { "genes": [ "ST58", "ST117", "ST3580" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:05.658933", "source": { "split": "train_shard_00001", "doc_id": 1768 }, "chunk_id": "train_shard_00001_1768_0", "global_id": 8151 }, { "text": "Furthermore, multiple clinically relevant lineages of CTXE and QREC are endemic in NP deer; however, they could be less virulent than isolates belonging to the same lineages, which could cause severe infectious diseases. Further studies are required to investigate the relationship between chromosomal integration of plasmid-encoded genes and the stable propagation of AMR bacteria in wildlife and the environment.\n\nMolecular characteristics of CTX-M β-lactamase-producing and quinolone-resistant Escherichia coli among deer in a popular tourist spot in Japan.", "token_count": 131, "char_count": 560, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8052, "quality_score": 0.9026, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:06.081698", "source": { "split": "train_shard_00001", "doc_id": 1768 }, "chunk_id": "train_shard_00001_1768_1", "global_id": 8152 }, { "text": "

Background

Pullorum disease is a serious problem in many countries. Caused by Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum), it creates huge economic losses in the poultry industry. Although pullorum disease has been well-controlled in many developed countries, it is still a critical problem in developing countries. However, there is still a lack of information on S. Pullorum strains isolated from different regions and sources in China. The objective of this study was to supply the antimicrobial resistance patterns and clonal relationships of S. Pullorum from breeder chicken farms.

Methods

In this study, a total of 114 S. Pullorum strains recovered from 11 provinces and municipalities in China between 2020 and 2021 were selected. These 114 S. Pullorum strains were analyzed using whole genome sequencing (WGS). Antimicrobial resistance (AMR) was tested both by genotypic prediction using the WGS method and using disc diffusion to assess phenotypic AMR.

Results

These 114 sequenced S. Pullorum strains were divided into three sequence types (STs), the dominant STs was ST92 (104/114). Further core genome multi-locus sequence typing analysis indicated that 114 S. Pullorum strains may have a close relationship, which could be clonally transmitted among different provinces and municipalities. Our results showed a close relationship between the S. Pullorum strains found in different regions, indicating these strains may have been transmitted in China a long time ago. Nearly all S. Pullorum strains 94.74% (n = 108) were resistant to at least one antimicrobial class, and 35.96% of the examined Salmonella strains were considered multiple drug resistant.

Conclusion

Overall, this study showed that S. Pullorum strains in China have a close genetic relationship in terms of antimicrobial resistance, suggesting widespread clonal transmission.", "token_count": 491, "char_count": 1906, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7934, "entities": { "genes": [ "ST92" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:06.732804", "source": { "split": "train_shard_00001", "doc_id": 1769 }, "chunk_id": "train_shard_00001_1769_0", "global_id": 8153 }, { "text": "Antimicrobial resistance and clonal relationships of Salmonella enterica Serovar Gallinarum biovar pullorum strains isolated in China based on whole genome sequencing.", "token_count": 40, "char_count": 167, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:07.096942", "source": { "split": "train_shard_00001", "doc_id": 1769 }, "chunk_id": "train_shard_00001_1769_1", "global_id": 8154 }, { "text": "

Introduction

The global increase of multidrug-resistant organisms (MDROs) is one of the most urgent public health threats affecting both humans and animals. The One Health concept emphasizes the interconnectedness of human, animal and environmental health and highlights the need for integrated approaches to combat antimicrobial resistance (AMR). Although the sharing of environments and antimicrobial agents between companion animals and humans poses a risk for MDRO transmission, companion animals have been studied to a lesser extent than livestock animals. This study therefore used core genome multilocus sequence typing (cgMLST) to investigate the genetic relationships and putative transmission of MDROs between humans and pets.

Methods

This descriptive integrated typing study included 252 human isolates, 53 dog isolates and 10 cat isolates collected from 2019 to 2022 at the Charité University Hospital in Berlin, Germany. CgMLST was performed to characterize methicillin-resistant Staphylococcus aureus, vancomycin-resistant enterococci and multidrug-resistant gram-negative bacteria. The genetic diversity of the MDROs of the different host populations was determined and compared based on sequence type and core genome complex type.

Results

Within this study the majority of samples from pets and humans was genetically distinct. However, for some isolates, the number of allelic differences identified by cgMLST was low. Two cases of putative household transmission or shared source of VR E. faecium and MDR E. coli between humans and pets were documented.

Conclusions

The interaction between humans and their pets appears to play a minor role in the spread of the MDROs studied. However, further research is needed. This study emphasizes the importance of comprehensive molecular surveillance and a multidisciplinary One Health approach to understand and contain the spread of MDROs in human and animal populations.

Trial registration

The study is registered with the German Clinical Trials Register (DRKS00030009).\n\nThe genetic relationship between human and pet isolates: a core genome multilocus sequence analysis of multidrug-resistant bacteria.", "token_count": 511, "char_count": 2201, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5825, "quality_score": 0.7912, "entities": { "genes": [ "DRKS00030009" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:07.752153", "source": { "split": "train_shard_00001", "doc_id": 1770 }, "chunk_id": "train_shard_00001_1770_0", "global_id": 8155 }, { "text": "This study provides an emended description of Acinetobacter faecalis, a species previously described based on a single isolate (YIM 103518T) from elephant feces in China. Our emended description is based on 15 novel isolates conspecific with the A. faecalis type strain, obtained from eight cattle farms in the Czech Republic. The A. faecalis strains have relatively small genomes (≈2.5-2.7 Mbp), with a GC content of 36.3-36.7 mol%. Core genome-based phylogenetic analysis showed that the 15 strains, together with the type strain of A. faecalis, form a distinct and internally coherent phylogroup within the genus. Pairwise genomic ANIb values for the 16 A. faecalis strains were 97.32-99.04 %, while ANIb values between the genomes of the 16 strains and those of the other Acinetobacter spp. were ≤ 86.2 %. Analysis of whole-cell MALDI-TOF mass spectra supported the distinctness and cohesiveness of the taxon. The A. faecalis strains could be differentiated from the other validly named Acinetobacter spp. by the absence of hemolytic activity along with their ability to grow at 37 °C and on L-aspartate, ethanol, and L-glutamate but not at 41 °C or on adipate or 2,3-butanediol. Reduced susceptibility to sulfamethoxazole, trimethoprim and/or streptomycin was shown in eight strains, along with the presence of corresponding antibiotic resistance genes. In conclusion, this study provides a comprehensive description of A. faecalis and demonstrates its occurrence in cattle feces. Though the ecological role of A. faecalis remains unknown, our results show its ability to acquire antibiotic resistance genes, likely as an adaptation to antibiotic selection pressure in livestock farms.\n\nEvidence for the occurrence of Acinetobacter faecalis in cattle feces and its emended description.", "token_count": 508, "char_count": 1801, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5852, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:08.409888", "source": { "split": "train_shard_00001", "doc_id": 1771 }, "chunk_id": "train_shard_00001_1771_0", "global_id": 8156 }, { "text": "

Background

The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are currently circulating worldwide due to the fastidious nature of the bacteria and the difficulty to isolate cultures. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Our understanding of the genetic diversity of strains during human infection is therefore limited.

Methods

Here, we carried out hybridization capture followed by Illumina sequencing of the core genome directly from 20 clinical samples that were PCR positive for pathogenic Leptospira to elucidate the genetic diversity of currently circulating Leptospira strains in mainland France.

Results

Capture with RNA probes covering the L. interrogans core genome resulted in a 72 to 13,000-fold increase in pathogen reads relative to standard sequencing without capture. Variant analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genomes was then carried out to determine the genotype of the infecting strain. For samples with sufficient coverage (19/20 samples with coverage > 8×), we could unambiguously identify L. interrogans serovars Icterohaemorrhagiae and Copenhageni (14 samples), L. kirschneri serovar Grippotyphosa (4 samples), and L. interrogans serovar Pyrogenes (1 sample) as the infecting strains.

Conclusions

We obtained high-quality genomic data with suitable coverage for confident core genome genotyping of the agent of leptospirosis for most of our clinical samples. The recovery of the genome of the serovars Icterohaemorrhagiae and Copenhageni directly from multiple clinical samples revealed low adaptive diversification of the core genes during human infection", "token_count": 492, "char_count": 1950, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5526, "quality_score": 0.7763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:09.132377", "source": { "split": "train_shard_00001", "doc_id": 1772 }, "chunk_id": "train_shard_00001_1772_0", "global_id": 8157 }, { "text": "The ability to generate culture-free genomic data opens new opportunities for better understanding of the epidemiology of this fastidious pathogen and pathogenesis of this neglected disease.\n\nCore genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing.", "token_count": 66, "char_count": 305, "word_count": 41, "semantic_coherence": 1, "information_density": 0.8537, "quality_score": 0.9268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:09.515079", "source": { "split": "train_shard_00001", "doc_id": 1772 }, "chunk_id": "train_shard_00001_1772_1", "global_id": 8158 }, { "text": "Here, we report the characterization of two Cupriavidus strains, NOV2-1 and OV2-1, isolated from an iron-oxide deposit in an underground tunnel of the Naica mine in Mexico. This unique biotope, characterized by its high temperature (≈50 °C) and the presence of heavy metals, is no longer available for sampling at this time. The genomes of NOV2-1 and OV2-1 comprised two replicons: a chromosome of 3.58 and 3.53 Mb, respectively, and a chromid of 2.1 Mb in both strains. No plasmids were found. The average nucleotide identity and the core genome phylogeny showed that NOV2-1 and OV2-1 belonged to the Cupriavidus gilardii species. NOV2-1 and OV2-1 grew up to 48 °C, with an optimal temperature of 42 °C. Discrete differences were observed between C. gilardii CCUG38401T, NOV2-1, and OV2-1 in the biochemical tests. NOV2-1 and OV2-1 presented resistance to zinc, lead, copper, cadmium, nickel, and cobalt. Several complete and incomplete gene clusters related to the resistance to these heavy metals (ars, czc, cop 1, sil-cop 2, cup, mmf, and mer) were detected in the genome of these strains. Although further studies are needed to determine the origin and role of the detected gene clusters, it is suggested that the czc system may have been mobilized by horizontal gene transfer. This study expands the extreme biotopes where Cupriavidus strains can be retrieved.", "token_count": 484, "char_count": 1468, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [ "NOV2", "OV2", "CCUG38401" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:10.166266", "source": { "split": "train_shard_00001", "doc_id": 1773 }, "chunk_id": "train_shard_00001_1773_0", "global_id": 8159 }, { "text": "Physiology, Heavy Metal Resistance, and Genome Analysis of Two <i>Cupriavidus gilardii</i> Strains Isolated from the Naica Mine (Mexico).", "token_count": 53, "char_count": 149, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:10.522840", "source": { "split": "train_shard_00001", "doc_id": 1773 }, "chunk_id": "train_shard_00001_1773_1", "global_id": 8160 }, { "text": "Enterobacter xiangfangensis is a novel, multidrug-resistant pathogen belonging to the Enterobacter genus and has the ability to acquire resistance to multiple antibiotic classes. However, there is currently no registered E. xiangfangensis drug on the market that has been shown to be effective. Hence, there is an urgent need to identify novel therapeutic targets and effective treatments for E. xiangfangensis. In the current study, a bacterial pan genome analysis and subtractive proteomics approach was employed to the core proteomes of six strains of E. xiangfangensis using several bioinformatic tools, software, and servers. However, 2611 nonredundant proteins were predicted from the 21,720 core proteins of core proteome. Out of 2611 nonredundant proteins, 372 were obtained from Geptop2.0 as essential proteins. After the subtractive proteomics and subcellular localization analysis, only 133 proteins were found in cytoplasm. All cytoplasmic proteins were examined using BLASTp against the virulence factor database, which classifies 20 therapeutic targets as virulent. Out of these 20, 3 cytoplasmic proteins: ferric iron uptake transcriptional regulator (FUR), UDP-2,3diacylglucosamine diphosphatase (UDP), and lipid-A-disaccharide synthase (lpxB) were chosen as potential drug targets. These drug targets are important for bacterial survival, virulence, and growth and could be used as therapeutic targets. More than 2500 plant chemicals were used to molecularly dock these proteins. Furthermore, the lowest-binding energetic docked compounds were found. The top five hit compounds, Adenine, Mollugin, Xanthohumol C, Sakuranetin, and Toosendanin demonstrated optimum binding against all three target proteins", "token_count": 511, "char_count": 1784, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6737, "quality_score": 0.8369, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:11.154303", "source": { "split": "train_shard_00001", "doc_id": 1774 }, "chunk_id": "train_shard_00001_1774_0", "global_id": 8161 }, { "text": "Furthermore, molecular dynamics simulations and MM/GBSA analyses validated the stability of ligand-protein complexes and revealed that these compounds could serve as potential E. xiangfangensis replication inhibitors. Consequently, this study marks a significant step forward in the creation of new and powerful drugs against E. xiangfangensis. Future studies should validate these targets experimentally to prove their function in E. xiangfangensis survival and virulence.\n\nIntegrated Pangenome Analysis and Pharmacophore Modeling Revealed Potential Novel Inhibitors against Enterobacter xiangfangensis.", "token_count": 158, "char_count": 632, "word_count": 75, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:11.592542", "source": { "split": "train_shard_00001", "doc_id": 1774 }, "chunk_id": "train_shard_00001_1774_1", "global_id": 8162 }, { "text": "Pantoea ananatis is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally), for a phosphonate secondary metabolite, and the onion-virulence regions, OVR (localized on a megaplasmid), for onion pathogenicity and virulence, respectively. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains ( n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic ( n = 51)- vs. non-pathogenic ( n = 30)-strains phenotypically. Pan-GWAS revealed a large core genome of 3,153 genes and a flexible accessory genome of ≤5,065 genes. Phylogenomic analysis using pan-GWAS and presence and absence variants (PAVs) distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis . The pan-GWAS also predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, TraR/DksA family transcriptional regulator, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. This is the first report of using pan-GWAS on P. ananatis for the prediction of novel genes contributing to pathogenicity in onion, which will be utilized for further functional analyses", "token_count": 524, "char_count": 1855, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:12.231033", "source": { "split": "train_shard_00001", "doc_id": 1775 }, "chunk_id": "train_shard_00001_1775_0", "global_id": 8163 }, { "text": "Pan-genomic differences (using PAVs) differentiated onion pathogenic from non-pathogenic strains of P. ananatis , which has been difficult to achieve using single or multiple gene-based phylogenetic analyses. The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the ‘ alt ’ cluster that aid in P. ananatis colonization in onion bulbs. We concluded that HiVir/PASVIL genes are associated with pathogenic P. ananatis strains and the alt gene cluster alone is not responsible for pathogenicity on onion. The pan-genome also provides clear evidence of constantly evolving accessory genes in P. ananatis that may contribute to host-range expansion and niche-adaptation.

Author summary

Pantoea ananatis is a major bacterial pathogen that causes center rot of onion and diseases of a number of other plant species. In order to understand the genome architecture and identify genes responsible for pathogenicity in onion, a pan-genome analysis was performed. We used 81 strains of P. ananatis collected over 20 years from different regions of the state of Georgia, USA. The pan-genome study identified a core genome with a conserved set of genes and an accessory genome that displayed variation among strains. We conducted pan-GWAS (pan-genome-wide association study) using presence and absence variants (PAVs) in the genomes and associated onion-pathogenic phenotypes based on a red-onion scale necrosis assay. The study resulted in identification of genes, including a cluster of chromosomal HiVir/PASVIL genes, that are significantly associated with the onion pathogenic phenotype. In addition, we identified 28 novel genes, a majority of which ( n = 20) have hypothetical functions. We concluded and further substantiated earlier findings that a cluster of genes is responsible for pathogenicity on onion", "token_count": 478, "char_count": 1904, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5658, "quality_score": 0.7829, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:12.880373", "source": { "split": "train_shard_00001", "doc_id": 1775 }, "chunk_id": "train_shard_00001_1775_1", "global_id": 8164 }, { "text": "The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the ‘ alt ’ cluster that aid in bacterial colonization of onion bulbs by P. ananatis strains. We concluded that HiVir/PASVIL genes are associated with onion-pathogenic strains, and the alt gene cluster alone is not responsible for pathogenicity on onion. This study also provides potential evidence of constantly evolving accessory genes in P. ananatis which may help in host range expansion and adaptation to diverse niches.\n\nPan-genome-wide analysis ofPantoea ananatisidentified genes linked to pathogenicity in onion", "token_count": 177, "char_count": 674, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7245, "quality_score": 0.8622, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:13.330344", "source": { "split": "train_shard_00001", "doc_id": 1775 }, "chunk_id": "train_shard_00001_1775_2", "global_id": 8165 }, { "text": "Whey arising in huge amounts during milk processing is a valuable renewable resource in the field of White Biotechnology. Kluyveromyces marxianus is able to convert whey-borne lactose into ethyl acetate, an environmentally friendly solvent. Formation of ethyl acetate as a bulk product is triggered by iron (Fe). K. marxianus DSM 5422 was cultivated aerobically in whey-borne medium originally containing 40 μg/L Fe, supplemented with 1, 3 or 10 mg/L Fe in the pre-culture, using an 1 L or 70 L stirred reactor. The highest Fe content in the pre-culture promoted yeast growth in the main culture causing a high sugar consumption for growth and dissatisfactory formation of ethyl acetate, while the lowest Fe content limited yeast growth and promoted ester synthesis but slowed down the process. An intermediate Fe dose (ca. 0.5 μg Fe/g sugar) lastly represented a compromise between some yeast growth, a quite high yield of ethyl acetate and an acceptable duration of the process. The mass of ethyl acetate related to the sugar consumed amounted to 0.113, 0.265 and 0.239 g/g in the three processes corresponding to 21.9%, 51.4% and 46.3% of the theoretically maximum yield. The performance on a pilot scale was somewhat higher than on lab scale.\n\nFormation of ethyl acetate from whey by Kluyveromyces marxianus on a pilot scale.", "token_count": 373, "char_count": 1329, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6326, "quality_score": 0.8163, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:13.910214", "source": { "split": "train_shard_00001", "doc_id": 1776 }, "chunk_id": "train_shard_00001_1776_0", "global_id": 8166 }, { "text": "Echinocandin drugs are widely used for the treatment of candidemia. Resistance is considered rare, and only a few cases of breakthrough candidiasis in patients receiving echinocandin have been reported worldwide. We report here for the first time a Candida kefyr isolate that acquired echinocandin resistance very rapidly after the initiation of caspofungin treatment for candidemia. We characterized the FKS gene mutation responsible for the resistance via the comparison of isolates sampled before and during treatment.\n\nRapid emergence of echinocandin resistance during Candida kefyr fungemia treatment with caspofungin.", "token_count": 148, "char_count": 623, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:14.352588", "source": { "split": "train_shard_00001", "doc_id": 1777 }, "chunk_id": "train_shard_00001_1777_0", "global_id": 8167 }, { "text": "Kluyveromyces marxianus is homothallic hemiascomycete yeast frequently isolated from dairy environments. It possesses phenotypic traits such as enhanced thermotolerance, inulinase production, and rapid growth rate that distinguish it from its closest relative Kluyveromyces lactis. Certain of these traits, notably fermentation of lactose and inulin to ethanol, make this yeast attractive for industrial production of ethanol from inexpensive substrates. There is relatively little known, however, about the diversity in this species, at the genetic, metabolic or physiological levels. This study compared phenotypic traits of 13 K. marxianus strains sourced from two European Culture Collections. A wide variety of responses to thermo, osmotic, and cell wall stress were observed, with some strains showing multi-stress resistance. These traits generally appeared unlinked indicating that, as with other yeasts, multiple resistance/adaptation pathways are present in K. marxianus. The data indicate that it should be possible to identify the molecular basis of traits to facilitate selection or engineering of strains adapted for industrial environments. The loci responsible for mating were also identified by genome sequencing and PCR analysis. It was found that K. marxianus can exist as stable haploid or diploid cells, opening up additional prospects for future strain engineering.\n\nPhysiological and metabolic diversity in the yeast Kluyveromyces marxianus.", "token_count": 334, "char_count": 1464, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8498, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:14.921165", "source": { "split": "train_shard_00001", "doc_id": 1778 }, "chunk_id": "train_shard_00001_1778_0", "global_id": 8168 }, { "text": "Biochemical and molecular analysis was used for identification of different kefir yeasts species from Brazil, Canada and the United States of America. The sugar/ethanol-resistant activity of the yeasts was evaluated. Saccharomyces cerevisiae and Kluyveromyces marxianus had the highest growth rates, suggesting biotechnological applications possible for these strains.\n\nIdentification and assessment of kefir yeast potential for sugar/ethanol-resistance.", "token_count": 106, "char_count": 454, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7321, "quality_score": 0.8661, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:15.307581", "source": { "split": "train_shard_00001", "doc_id": 1779 }, "chunk_id": "train_shard_00001_1779_0", "global_id": 8169 }, { "text": "Transposable Elements are ubiquitous mobile DNA sequences evolving among their hosts’ genomes, generating insertion polymorphisms that contribute to genomic diversity. We present GraffiTE, a flexible pipeline to analyze polymorphic mobile elements. By integrating state-of-the-art structural variant detection algorithms and graph genomes, GraffiTE identifies polymorphic mobile elements from genomic assemblies and/or long-read sequencing data, and genotypes these variants using short or long read sets. Benchmarking on simulated and real datasets reports high precision and recall rates. GraffiTE is designed to allow non-expert users to perform comprehensive analyses, including in models with limited transposable element knowledge and is compatible with various sequencing technologies. GraffiTE is freely available at https://github.com/cgroza/GraffiTE . Here, we demonstrate the versatility of GraffiTE by analyzing human, Drosophila melanogaster, maize, and Cannabis sativa pangenome data. These analyses reveal the landscapes of polymorphic mobile elements and their frequency variations across individuals, strains, and cultivars.\n\nA Unified Framework to Analyze Transposable Element Insertion Polymorphisms using Graph Genomes", "token_count": 289, "char_count": 1238, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7308, "quality_score": 0.8654, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:15.873695", "source": { "split": "train_shard_00001", "doc_id": 1780 }, "chunk_id": "train_shard_00001_1780_0", "global_id": 8170 }, { "text": "

Background

Multi system symptoms such as gastrointestinal tract and respiratory tract exist in coronavirus disease 2019 (COVID-19) patients. There is a lack of reliable evidence to prove that probiotics are effective in improving these symptoms. In this study, we aimed to evaluate the efficacy of probiotics in meta-analysis.

Methods

We systematically searched PubMed, Embase, Web of Science, and Cochrane Library up to February 15, 2023. Randomized controlled trials or high quality retrospective studies comparing the efficacy of probiotics as supplementation with non-probiotics in improving symptoms for patients with COVID-19 were included. This meta-analysis assessed endpoints using Review Manager 5.3.

Result

Ten citations comprising 1198 patients with COVID-19 were included. The results showed that probiotics could increase the number of people with overall symptom improvement (RR = 1.62, 95% CI [1.10, 2.38], P = 0.01) and shorten the duration (days) of overall symptoms (MD = -1.26, 95% CI [-2.36, -0.16], P = 0.02). For the duration (days) of specific symptoms, probiotics could improve diarrhea (MD = -2.12, 95% CI [-2.41, -1.83], P < 0.00001), cough (MD = -2.21, 95% CI [-4.56, 0.13], P = 0.06) and shortness of breath (MD = -1.37, 95% CI [-2.22, -0.53], P = 0.001). Probiotics had no obvious effect on fever, headache and weakness", "token_count": 483, "char_count": 1399, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6601, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:16.526457", "source": { "split": "train_shard_00001", "doc_id": 1781 }, "chunk_id": "train_shard_00001_1781_0", "global_id": 8171 }, { "text": "For inflammation, probiotics could effectively reduce C-reactive Protein (CRP) serum level (mg/L) (MD = -4.03, 95% CI [-5.12, -2.93], P < 0.00001). Regarding hospital stay (days), probiotics group was shorter than non-probiotics group (MD = -0.98, 95% CI [-1.95, -0.01], P = 0.05).

Conclusion

To some extent probiotics could improve the overall symptoms, inflammatory reaction and shorten hospital stay of patients with COVID-19. Probiotics may improve gastrointestinal symptoms (such as improving intestinal flora and reducing the duration of diarrhea) and further improve respiratory symptoms through the gut-lung axis.

Systematic review registration

https://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=398309, identifier: CRD42023398309.\n\nProbiotics improve symptoms of patients with COVID-19 through gut-lung axis: a systematic review and meta-analysis.", "token_count": 310, "char_count": 897, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7048, "quality_score": 0.8524, "entities": { "genes": [ "CRD42023398309" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:17.085442", "source": { "split": "train_shard_00001", "doc_id": 1781 }, "chunk_id": "train_shard_00001_1781_1", "global_id": 8172 }, { "text": "Durian (Durio zibethinus), which yields the fruit known as the \"King of Fruits,\" is an important economic crop in Southeast Asia. Several durian cultivars have been developed in this region. In this study, we resequenced the genomes of three popular durian cultivars in Thailand, including Kradumthong (KD), Monthong (MT), and Puangmanee (PM) to investigate genetic diversities of cultivated durians. KD, MT, and PM genome assemblies were 832.7, 762.6, and 821.6 Mb, and their annotations covered 95.7, 92.4, and 92.7% of the embryophyta core proteins, respectively. We constructed the draft durian pangenome and analyzed comparative genomes with related species in Malvales. Long terminal repeat (LTR) sequences and protein families in durian genomes had slower evolution rates than that in cotton genomes. However, protein families with transcriptional regulation function and protein phosphorylation function involved in abiotic and biotic stress responses appeared to evolve faster in durians. The analyses of phylogenetic relationships, copy number variations (CNVs), and presence/absence variations (PAVs) suggested that the genome evolution of Thai durians was different from that of the Malaysian durian, Musang King (MK). Among the three newly sequenced genomes, the PAV and CNV profiles of disease resistance genes and the expressions of methylesterase inhibitor domain containing genes involved in flowering and fruit maturation in MT were different from those in KD and PM. These genome assemblies and their analyses provide valuable resources to gain a better understanding of the genetic diversity of cultivated durians, which may be useful for the future development of new durian cultivars.\n\nResequencing of durian genomes reveals large genetic variations among different cultivars.", "token_count": 442, "char_count": 1805, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:17.714274", "source": { "split": "train_shard_00001", "doc_id": 1782 }, "chunk_id": "train_shard_00001_1782_0", "global_id": 8173 }, { "text": "Background: The World Health Organization defines probiotics as \"live microorganisms, which when administered in adequate amounts confer a health benefit on the host\". In this framework, probiotic strains should be regarded as safe for human and animal consumption, i.e., they should possess the GRAS (generally recognized as safe) status, notified by the local authorities. Consistently, strains of selected Bifidobacterium species are extensively used as probiotic agents to prevent and ameliorate a broad spectrum of human and/or animal gastrointestinal disorders. Even though probiotic properties are often genus- or species-associated, strain-level differences in the genetic features conferring individual probiotic properties to commercialized bifidobacterial strains have not been investigated in detail. Methods: In this study, we built a genomic database named Integrated Probiotic DataBase (IPDB), whose first iteration consists of common bifidobacterial strains used in probiotic products for which public genome sequences were available, such as members of B. longum subsp. longum, B. longum subsp. infantis, B. bifidum, B. breve, and B. animalis subsp. lactis taxa. Furthermore, the IPDB was exploited to perform comparative genome analyses focused on genetic factors conferring structural, functional, and chemical features predicted to be involved in microbe-host and microbe-microbe interactions. Results and conclusion: Our analyses revealed strain-level genetic differences, underlining the importance of inspecting the strain-specific and outcome-specific efficacy of probiotics. In this context, IPDB represents a valuable resource for obtaining genetic information of well-established bifidobacterial probiotic strains.\n\nThe Integrated Probiotic Database: a genomic compendium of bifidobacterial health-promoting strains.", "token_count": 490, "char_count": 1927, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:18.369251", "source": { "split": "train_shard_00001", "doc_id": 1783 }, "chunk_id": "train_shard_00001_1783_0", "global_id": 8174 }, { "text": "The Kluyveromyces marxianus strains CBS 6556, CBS 397 and CBS 712(T) were cultivated on a defined medium with either glucose, lactose or sucrose as the sole carbon source, at 30 and 37°C. The aim of this work was to evaluate the diversity within this species, in terms of the macroscopic physiology. The main properties evaluated were: intensity of the Crabtree effect, specific growth rate, biomass yield on substrate, metabolite excretion and protein secretion capacity, inferred by measuring extracellular inulinase activity. The strain Kluyveromyces lactis CBS 2359 was evaluated in parallel, since it is the best described Kluyveromyces yeast and thus can be used as a control for the experimental setup. K. marxianus CBS 6556 presented the highest specific growth rate (0.70 h(-1)) and the highest specific inulinase activity (1.65 U mg(-1) dry cell weight) among all strains investigated, when grown at 37°C with sucrose as the sole carbon source. The lowest metabolite formation and highest biomass yield on substrate (0.59 g dry cell weight g sucrose(-1)) was achieved by K. marxianus CBS 712(T) at 37°C. Taken together, the results show a systematic comparison of carbon and energy metabolism among three of the best known K. marxianus strains, in parallel to K. lactis CBS 2359.\n\nPhysiological diversity within the Kluyveromyces marxianus species [corrected].", "token_count": 391, "char_count": 1370, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:18.987034", "source": { "split": "train_shard_00001", "doc_id": 1784 }, "chunk_id": "train_shard_00001_1784_0", "global_id": 8175 }, { "text": "Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits1,2. The solution to this problem is to identify all causal genetic variants and to measure their individual contributions3,4. Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largely due to resolving incomplete linkage disequilibrium through the inclusion of additional causal structural variants identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, structural variants improve the power to identify genetic factors underlying agronomically important traits leading to, for example, the identification of two new genes potentially contributing to soluble solid content. The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.\n\nGraph pangenome captures missing heritability and empowers tomato breeding.", "token_count": 348, "char_count": 1573, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6124, "quality_score": 0.8062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:19.601471", "source": { "split": "train_shard_00001", "doc_id": 1785 }, "chunk_id": "train_shard_00001_1785_0", "global_id": 8176 }, { "text": "

Purpose

Staphylococcus warneri is an opportunistic pathogen responsible for hospital-acquired infections (HAIs). The aim of this study was to describe an outbreak caused by S. warneri infection in a neonatal intensive care unit (NICU) and provide investigation, prevention and control strategies for this outbreak.

Methods

We conducted an epidemiological investigation of the NICU S. warneri outbreak, involving seven neonates, staff, and environmental screening, to identify the source of infection. WGS analyses were performed on S. warneri isolates, including species identification, core genome single-nucleotide polymorphism (cgSNP) analysis, pan-genome analysis, and genetic characterization assessment of the prevalence of specific antibiotic resistance and virulence genes.

Results

Eight S. warneri strains were isolated from this outbreak, with seven from neonates and one from environment. Six clinical cases within three days in 2021 were linked to one strain isolated from environmental samples; isolates varied by 0-69 SNPs and were confirmed to be from an outbreak through WGS. Multiple infection prevention measures were implemented, including comprehensive environmental disinfection and stringent protocols, and all affected neonates were transferred to the isolation wards. Following these interventions, no further cases of S. warneri infections were observed. Furthermore, pan-genome analysis results suggested that in human S. warneri may exhibit host specificity.

Conclusion

The investigation has revealed that the outbreak was linked to the milk preparation workbench by the WGS. It is recommended that there be a stronger focus on environmental disinfection management in order to raise awareness, improve identification, and prevention of healthcare-associated infections that are associated with the hospital environment.\n\nWGS Analysis of Staphylococcus warneri Outbreak in a Neonatal Intensive Care Unit.", "token_count": 495, "char_count": 2016, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5898, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:20.269658", "source": { "split": "train_shard_00001", "doc_id": 1786 }, "chunk_id": "train_shard_00001_1786_0", "global_id": 8177 }, { "text": "Antibiotic resistant Staphylococcus infections are a global concern, with increasing cases of resistant Staphylococcus aureus and Staphylococcus haemolyticus found circulating in the Middle East. While extensive surveys have described the prevalence of resistant infections in Europe, Asia, and North America, the population structure of resistant staphylococcal Middle Eastern clinical isolates is poorly characterized. We performed whole genome sequencing of 56 S. aureus and 10 S. haemolyticus isolates from Alexandria Main University Hospital. Supplemented with additional publicly available genomes from the region (34 S. aureus and 6 S. haemolyticus ), we present the largest genomic study of staphylococcal Middle Eastern isolates. These genomes include 20 S. aureus multilocus sequence typing (MLST) types and 9 S. haemolyticus MLSTs, including 3 and 1 new MLSTs, respectively. Phylogenomic analyses of each species core genome largely mirrored MLSTs, irrespective of geographical origin. The hospital-acquired spa t037/SCC mec III/MLST CC8 clone represented the largest clade, comprising 22% of S. aureus isolates. Similar to other regional genome surveys of S. aureus , the Middle Eastern isolates have an open pangenome, a strong indicator of gene exchange of virulence factors and antibiotic resistance genes with other reservoirs. We recommend stricter implementation of antibiotic stewardship and infection control plans in the region.

Impact Statement

Staphylococci are under-studied despite their prevalence within the Middle East. Methicillin-resistant Staphylococcus aureus (MRSA) is endemic to hospitals in this region, as are other antibiotic-resistant strains of S. aureus and S. haemolyticus . To provide insight into the strains currently in circulation within Egypt, we performed whole genome sequencing of 56 S. aureus and 10 S. haemolyticus isolates from Alexandria Main University Hospital (AMUH)", "token_count": 515, "char_count": 1932, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5688, "quality_score": 0.7844, "entities": { "genes": [ "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:20.955356", "source": { "split": "train_shard_00001", "doc_id": 1787 }, "chunk_id": "train_shard_00001_1787_0", "global_id": 8178 }, { "text": "Through analysis of these genomes, as well as other genomes of isolates from the Middle East, we were able to produce a more complete picture of the current diversity than traditional molecular typing strategies. Furthermore, the S. haemolyticus genome analyses provide the first insight into strains found in Egypt. Our analysis of resistance and virulence mechanisms carried by these strains provides invaluable insight into future plans of antibiotic stewardship and infection control within the region.

Data Summary

Raw sequencing reads and assembled genomes can be found at BioProject Accession number PRJNA648411 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA648411 ).\n\nPhylogenomic study ofStaphylococcus aureusandStaphylococcus haemolyticusclinical isolates from Egypt", "token_count": 217, "char_count": 800, "word_count": 102, "semantic_coherence": 1, "information_density": 0.8039, "quality_score": 0.902, "entities": { "genes": [ "PRJNA648411" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:21.444450", "source": { "split": "train_shard_00001", "doc_id": 1787 }, "chunk_id": "train_shard_00001_1787_1", "global_id": 8179 }, { "text": "

ABSTRACT

High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates ( n =59 clinical, n =49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several putative homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.\n\nExtended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes", "token_count": 475, "char_count": 1632, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:22.084159", "source": { "split": "train_shard_00001", "doc_id": 1788 }, "chunk_id": "train_shard_00001_1788_0", "global_id": 8180 }, { "text": "In tequila production, fermentation is an important step. Fermentation determines the ethanol productivity and organoleptic properties of the beverage. In this study, a yeast isolated from native residual agave must was identified as Kluyveromyces marxianus UMPe-1 by 26S rRNA sequencing. This yeast was compared with the baker's yeast Saccharomyces cerevisiae Pan1. Our findings demonstrate that the UMPe-1 yeast was able to support the sugar content of agave must and glucose up to 22% (w/v) and tolerated 10% (v/v) ethanol concentration in the medium with 50% cells survival. Pilot and industrial fermentation of agave must tests showed that the K. marxianus UMPe-1 yeast produced ethanol with yields of 94% and 96% with respect to fermentable sugar content (glucose and fructose, constituting 98%). The S. cerevisiae Pan1 baker's yeast, however, which is commonly used in some tequila factories, showed 76% and 70% yield. At the industrial level, UMPe-1 yeast shows a maximum velocity of fermentable sugar consumption of 2.27g·L(-1)·h(-1) and ethanol production of 1.38g·L(-1)·h(-1), providing 58.78g ethanol·L(-1) at 72h fermentation, which corresponds to 96% yield. In addition, the major and minor volatile compounds in the tequila beverage obtained from UMPe-1 yeast were increased. Importantly, 29 volatile compounds were identified, while the beverage obtained from Pan1-yeast contained fewer compounds and in lower concentrations. The results suggest that the K. marxianus UMPe-1 is a suitable yeast for agave must fermentation, showing high ethanol productivity and increased volatile compound content comparing with a S. cerevisiae baker's yeast used in tequila production.", "token_count": 495, "char_count": 1686, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5447, "quality_score": 0.7724, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:22.742143", "source": { "split": "train_shard_00001", "doc_id": 1789 }, "chunk_id": "train_shard_00001_1789_0", "global_id": 8181 }, { "text": "Ethanol yield and volatile compound content in fermentation of agave must by Kluyveromyces marxianus UMPe-1 comparing with Saccharomyces cerevisiae baker's yeast used in tequila production.", "token_count": 54, "char_count": 189, "word_count": 25, "semantic_coherence": 1, "information_density": 0.96, "quality_score": 0.98, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:23.104664", "source": { "split": "train_shard_00001", "doc_id": 1789 }, "chunk_id": "train_shard_00001_1789_1", "global_id": 8182 }, { "text": "Chronic airway infections with Pseudomonas aeruginosa are the major co-morbidity in most people with cystic fibrosis (CF) sustained by neutrophils as the major drivers of lung inflammation, damage, and remodeling. Phagocytosis assays were performed with clonal consortia of longitudinal P. aeruginosa airway isolates collected from people with CF since the onset of lung colonization until patient's death or replacement by another clone. The extra- and intracellular abundance of individual strains was assessed by deep amplicon sequencing of strain-specific single nucleotide variants in the bacterial genome. The varied microevolution of the accessory genome of the P. aeruginosa clones during mild and severe courses of infection corresponded with a differential persistence of clonal progeny in the neutrophil phagosome. By simultaneously exposing the ancestor and its progeny to the same habitat, the study recapitulated the time lapse of the temporal change of the fitness of the clone to survive in neutrophils.\n\nCompetitive survival of clonal serial Pseudomonas aeruginosa isolates from cystic fibrosis airways in human neutrophils.", "token_count": 308, "char_count": 1169, "word_count": 163, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:23.679087", "source": { "split": "train_shard_00001", "doc_id": 1790 }, "chunk_id": "train_shard_00001_1790_0", "global_id": 8183 }, { "text": "

Motivation

Alignment of reads to a reference genome sequence is one of the key steps in the analysis of human whole-genome sequencing data obtained through Next-generation sequencing (NGS) technologies. The quality of the subsequent steps of the analysis, such as the results of clinical interpretation of genetic variants or the results of a genome-wide association study, depends on the correct identification of the position of the read as a result of its alignment. The amount of human NGS whole-genome sequencing data is constantly growing. There are a number of human genome sequencing projects worldwide that have resulted in the creation of large-scale databases of genetic variants of sequenced human genomes. Such information about known genetic variants can be used to improve the quality of alignment at the read alignment stage when analysing sequencing data obtained for a new individual, for example, by creating a genomic graph. While existing methods for aligning reads to a linear reference genome have high alignment speed, methods for aligning reads to a genomic graph have greater accuracy in variable regions of the genome. The development of a read alignment method that takes into account known genetic variants in the linear reference sequence index allows combining the advantages of both sets of methods.

Results

In this paper, we present the minimap2_index_modifier tool, which enables the construction of a modified index of a reference genome using known single nucleotide variants and insertions/deletions (indels) specific to a given human population. The use of the modified minimap2 index improves variant calling quality without modifying the bioinformatics pipeline and without significant additional computational overhead. Using the PrecisionFDA Truth Challenge V2 benchmark data (for HG002 short-read data aligned to the GRCh38 linear reference (GCA_000001405.15) with parameters k = 27 and w = 14) it was demonstrated that the number of false negative genetic variants decreased by more than 9500, and the number of false positives decreased by more than 7000 when modifying the index with genetic variants from the Human Pangenome Reference Consortium.", "token_count": 498, "char_count": 2208, "word_count": 329, "semantic_coherence": 1, "information_density": 0.5258, "quality_score": 0.7629, "entities": { "genes": [ "HG002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:24.330702", "source": { "split": "train_shard_00001", "doc_id": 1791 }, "chunk_id": "train_shard_00001_1791_0", "global_id": 8184 }, { "text": "Enhancing SNV identification in whole-genome sequencing data through the incorporation of known genetic variants into the minimap2 index.", "token_count": 30, "char_count": 137, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:24.686432", "source": { "split": "train_shard_00001", "doc_id": 1791 }, "chunk_id": "train_shard_00001_1791_1", "global_id": 8185 }, { "text": "The Human Pangenome Reference Consortium (HPRC) presents a first draft human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals. These assemblies cover more than 99% of the expected sequence and are more than 99% accurate at the structural and base-pair levels. Based on alignments of the assemblies, we generated a draft pangenome that captures known variants and haplotypes, reveals novel alleles at structurally complex loci, and adds 119 million base pairs of euchromatic polymorphic sequence and 1,529 gene duplications relative to the existing reference, GRCh38. Roughly 90 million of the additional base pairs derive from structural variation. Using our draft pangenome to analyze short-read data reduces errors when discovering small variants by 34% and boosts the detected structural variants per haplotype by 104% compared to GRCh38-based workflows, and by 34% compared to using previous diversity sets of genome assemblies.\n\nA Draft Human Pangenome Reference", "token_count": 269, "char_count": 1041, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6447, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:25.236471", "source": { "split": "train_shard_00001", "doc_id": 1792 }, "chunk_id": "train_shard_00001_1792_0", "global_id": 8186 }, { "text": "Probiotics are known for their health-promoting resources and are considered as beneficial microorganisms. The current study focuses on the isolation, and on a complete in vitro and in vivo characterization, of yeast and lactic acid bacteria acquired from traditional homemade kefir in order to assess their potentiality as probiotic candidates. In particular, the isolates Pichia kudriavzevii Y1, Lactococcus lactis subsp. hordniae LAB1 and Lactococcus lactis subsp. lactis LAB2 were subjected to in vitro characterization to evaluate their suitability as probiotics. Resistance to acid and bile salts, auto-aggregation, co-aggregation, hydrophobicity, and biofilm production capability were examined, as well as their antioxidant activity. A safety assessment was also conducted to confirm the non-pathogenic nature of the isolates, with hemolysis assay and antibiotic resistance assessment. Moreover, mortality in the invertebrate model Galleria mellonella was evaluated. Current findings showed that P. kudriavzevii exhibited estimable probiotic properties, placing them as promising candidates for functional foods. Both lactic acid bacteria isolated in this work could be classified as potential probiotics with advantageous traits, including antimicrobial activity against enteric pathogens and good adhesion ability on intestinal cells. This study revealed that homemade kefir could be a beneficial origin of different probiotic microorganisms that may enhance health and wellness.\n\nEvaluation of Potential Probiotic Properties and In Vivo Safety of Lactic Acid Bacteria and Yeast Strains Isolated from Traditional Home-Made Kefir.", "token_count": 439, "char_count": 1688, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.8131, "entities": { "genes": [ "LAB1", "LAB2" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:25.869565", "source": { "split": "train_shard_00001", "doc_id": 1793 }, "chunk_id": "train_shard_00001_1793_0", "global_id": 8187 }, { "text": "Fostering a \"balanced\" gut microbiome through the administration of beneficial microbes that can competitively exclude pathogens has gained a lot of attention and use in human and animal medicine. However, little is known about how microbes affect the horizontal gene transfer of antimicrobial resistance (AMR). To shed more light on this question, we challenged neonatal broiler chicks raised on reused broiler chicken litter-a complex environment made up of decomposing pine shavings, feces, uric acid, feathers, and feed-with Salmonella enterica serovar Heidelberg (S. Heidelberg), a model pathogen. Neonatal chicks challenged with S. Heidelberg and raised on reused litter were more resistant to S. Heidelberg cecal colonization than chicks grown on fresh litter. Furthermore, chicks grown on reused litter were at a lower risk of colonization with S. Heidelberg strains that encoded AMR on IncI1 plasmids. We used 16S rRNA gene sequencing and shotgun metagenomics to show that the major difference between chicks grown on fresh litter and those grown on reused litter was the microbiome harbored in the litter and ceca. The microbiome of reused litter samples was more uniform and enriched in functional pathways related to the biosynthesis of organic and antimicrobial molecules than that in fresh litter samples. We found that Escherichia coli was the main reservoir of plasmids encoding AMR and that the IncI1 plasmid was maintained at a significantly lower copy per cell in reused litter compared to fresh litter. These findings support the notion that commensal bacteria play an integral role in the horizontal transfer of plasmids encoding AMR to pathogens like Salmonella. IMPORTANCE Antimicrobial resistance spread is a worldwide health challenge, stemming in large part from the ability of microorganisms to share their genetic material through horizontal gene transfer. To address this issue, many countries and international organizations have adopted a One Health approach to curtail the proliferation of antimicrobial-resistant bacteria", "token_count": 499, "char_count": 2089, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5686, "quality_score": 0.7843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:26.517883", "source": { "split": "train_shard_00001", "doc_id": 1794 }, "chunk_id": "train_shard_00001_1794_0", "global_id": 8188 }, { "text": "This includes the removal and reduction of antibiotics used in food animal production and the development of alternatives to antibiotics. However, there is still a significant knowledge gap in our understanding of how resistance spreads in the absence of antibiotic selection and the role commensal bacteria play in reducing antibiotic resistance transfer. In this study, we show that commensal bacteria play a key role in reducing the horizontal gene transfer of antibiotic resistance to Salmonella, provide the identity of the bacterial species that potentially perform this function in broiler chickens, and also postulate the mechanism involved.\n\nLitter Commensal Bacteria Can Limit the Horizontal Gene Transfer of Antimicrobial Resistance to Salmonella in Chickens.", "token_count": 159, "char_count": 770, "word_count": 112, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:26.961527", "source": { "split": "train_shard_00001", "doc_id": 1794 }, "chunk_id": "train_shard_00001_1794_1", "global_id": 8189 }, { "text": "Crop pangenomes made from individual cultivar assemblies promise easy access to conserved genes, but genome content variability and inconsistent identifiers hamper their exploration. To address this, we define pangenes, which summarize a species coding potential and link back to original annotations. The protocol get_pangenes performs whole genome alignments (WGA) to call syntenic gene models based on coordinate overlaps. A benchmark with small and large plant genomes shows that pangenes recapitulate phylogeny-based orthologies and produce complete soft-core gene sets. Moreover, WGAs support lift-over and help confirm gene presence-absence variation. Source code and documentation: https://github.com/Ensembl/plant-scripts .\n\nGET_PANGENES: calling pangenes from plant genome alignments confirms presence-absence variation.", "token_count": 193, "char_count": 830, "word_count": 104, "semantic_coherence": 1, "information_density": 0.8173, "quality_score": 0.9087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:27.411368", "source": { "split": "train_shard_00001", "doc_id": 1795 }, "chunk_id": "train_shard_00001_1795_0", "global_id": 8190 }, { "text": "

Motivation

High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. Several ongoing pangenome projects are producing collections of high-quality assemblies of various species. Each project has already generated assemblies of hundreds of gigabytes on disk, greatly impeding the distribution of and access to such rich datasets.

Results

Here, we show how to reduce the size of the sequenced genomes by 2-3 orders of magnitude. Our tool compresses the genomes significantly better than the existing programs and is much faster. Moreover, its unique feature is the ability to access any contig (or its part) in a fraction of a second and easily append new samples to the compressed collections. Thanks to this, AGC could be useful not only for backup or transfer purposes but also for routine analysis of pangenome sequences in common pipelines. With the rapidly reduced cost and improved accuracy of sequencing technologies, we anticipate more comprehensive pangenome projects with much larger sample sizes. AGC is likely to become a foundation tool to store, distribute and access pangenome data.

Availability and implementation

The source code of AGC is available at https://github.com/refresh-bio/agc. The package can be installed via Bioconda at https://anaconda.org/bioconda/agc.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nAGC: compact representation of assembled genomes with fast queries and updates.", "token_count": 342, "char_count": 1531, "word_count": 209, "semantic_coherence": 1, "information_density": 0.689, "quality_score": 0.8445, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:27.985735", "source": { "split": "train_shard_00001", "doc_id": 1796 }, "chunk_id": "train_shard_00001_1796_0", "global_id": 8191 }, { "text": "Kenya is the seventh most prominent producer of common beans globally and the second leading producer in East Africa. However, the annual national productivity is low due to insufficient quantities of vital nutrients and nitrogen in the soils. Rhizobia are symbiotic bacteria that fix nitrogen through their interaction with leguminous plants. Nevertheless, inoculating beans with commercial rhizobia inoculants results in sparse nodulation and low nitrogen supply to the host plants because these strains are poorly adapted to the local soils. Several studies describe native rhizobia with much better symbiotic capabilities than commercial strains, but only a few have conducted field studies. This study aimed to test the competence of new rhizobia strains that we isolated from Western Kenya soils and for which the symbiotic efficiency was successfully determined in greenhouse experiments. Furthermore, we present and analyze the whole-genome sequence for a promising candidate for agricultural application, which has high nitrogen fixation features and promotes common bean yields in field studies. Plants inoculated with the rhizobial isolate S3 or with a consortium of local isolates (COMB), including S3, produced a significantly higher number of seeds and seed dry weight when compared to uninoculated control plants at two study sites. The performance of plants inoculated with commercial isolate CIAT899 was not significantly different from uninoculated plants (p > 0.05), indicating tight competition from native rhizobia for nodule occupancy. Pangenome analysis and the overall genome-related indices showed that S3 is a member of R. phaseoli. However, synteny analysis revealed significant differences in the gene order, orientation, and copy numbers between S3 and the reference R. phaseoli. Isolate S3 is phylogenomically similar to R. phaseoli. However, it has undergone significant genome rearrangements (global mutagenesis) to adapt to harsh conditions in Kenyan soils. Its high nitrogen fixation ability shows optimal adaptation to Kenyan soils, and the strain can potentially replace nitrogenous fertilizer application. We recommend that extensive fieldwork in other parts of the country over a period of five years be performed on S3 to check on how the yield changes with varying whether conditions.", "token_count": 518, "char_count": 2352, "word_count": 340, "semantic_coherence": 1, "information_density": 0.6265, "quality_score": 0.8132, "entities": { "genes": [ "CIAT899" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:28.644618", "source": { "split": "train_shard_00001", "doc_id": 1797 }, "chunk_id": "train_shard_00001_1797_0", "global_id": 8192 }, { "text": "Molecular Characterization of Indigenous Rhizobia from Kenyan Soils Nodulating with Common Beans.", "token_count": 25, "char_count": 97, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:28.999957", "source": { "split": "train_shard_00001", "doc_id": 1797 }, "chunk_id": "train_shard_00001_1797_1", "global_id": 8193 }, { "text": "A low FODMAP (fermentable oligosaccharides, disaccharides, monosaccharides, and polyols) diet allows most irritable bowel syndrome (IBS) patients to manage their gastrointestinal symptoms by avoiding FODMAP-containing foods, such as onions, pulses, and products made from wheat or rye. The downside of a low FODMAP diet is the reduced intake of dietary fiber. Applying sourdoughs—with specific FODMAP-targeting metabolic properties—to wholegrain bread making can help to remarkably reduce the content of FODMAPs in bread without affecting the content of the slowly fermented and well-tolerated dietary fiber. In this review, we outline the metabolism of FODMAPs in conventional sourdoughs and outline concepts related to fructan and mannitol metabolism that allow development of low FODMAP sourdough bread. We also summarize clinical studies where low FODMAP but high fiber, rye sourdough bread was tested for its effects on gut fermentation and gastrointestinal symptoms with very promising results. The sourdough bread-making process offers a means to develop natural and fiber-rich low FODMAP bakery products for IBS patients and thereby help them to increase their dietary fiber intake.\n\nUse of Sourdough in Low FODMAP Baking.", "token_count": 318, "char_count": 1242, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:29.556239", "source": { "split": "train_shard_00001", "doc_id": 1798 }, "chunk_id": "train_shard_00001_1798_0", "global_id": 8194 }, { "text": "In this study, a total of ten strains of kefir grains were isolated. Lactic acid bacteria and yeast were the research subjects. The final compound fermentation starter was produced using Leu. Mesenteroides, Lactobacillus kefir, Lactobacillus casei, and K. marxianus. The fermented milk of the compound fermentation starter and kefir grains were compared in curding time, acidity, water holding capacity (WHC), ethanol content, the viability of strains, and sensory score. The results showed that the quality of the fermented milk was similar, but the kinds of volatile aroma components in the kefir produced by the compound strain starter were significantly more than those of the kefir grains. The result of this study will help simplify and stabilize the industrial production of kefir, and provide a reference for the development of different flavored yogurt products. NOVELTY IMPACT STATEMENT: The dominant kefir grain strains were divided to create the strain compound starter, which can be used in place of kefir grains. It can ferment and produce a milk drink with similar characteristics to traditional kefir grains. The dairy industry can develop using strain starters to overcome the limitations of kefir grains and produce kefir products with consistently high quality.\n\nIsolation and screening of high‐quality lactic acid bacteria and yeast strains in kefir grains and preparation of kefir compound fermentation starter", "token_count": 342, "char_count": 1431, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5484, "quality_score": 0.7742, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:30.126215", "source": { "split": "train_shard_00001", "doc_id": 1799 }, "chunk_id": "train_shard_00001_1799_0", "global_id": 8195 }, { "text": "A novel technology development based on the production of a low-cost starter culture for ripening of cheeses and baking is reported in the present study. The starter culture comprises thermally dried cells of Kluyveromyces marxianus encapsulated in micro- and nano-tubular cellulose. For production of a low-cost and effective biocatalyst, whey was used as raw material for biomass production and thermal drying methods (convective, conventional, and vacuum) were applied and evaluated at drying temperatures ranging from 35 to 60 °C. The effect of drying temperature of biocatalysts on fermentability of lactose and whey was evaluated. Storage stability and suitability of biocatalysts as a commercial starter cultures was also assessed and evaluated. All thermally dried biocatalysts were found to be active in lactose and whey fermentation. In all cases, there was sugar conversion ranging from 92 to 100 %, ethanol concentration of up to 1.47 % (v/v), and lactic acid concentrations ranged from 4.1 to 5.5 g/l. However, convective drying of the encapsulated cells of K. marxianus in micro- and nano-tubular cellulose was faster and a more effective drying method while drying at 42 °C appear to be the best drying temperature in terms of cell activity, ethanol, and lactic acid formation. Storage of the biocatalysts for 3 months at 4 °C proved maintenance of its activity even though fermentation times increased by 50-100 % compared with the fresh dried ones.\n\nNovel technology development through thermal drying of encapsulated Kluyveromyces marxianus in micro- and nano-tubular cellulose in lactose fermentation and its evaluation for food production.", "token_count": 446, "char_count": 1659, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5336, "quality_score": 0.7668, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:30.757531", "source": { "split": "train_shard_00001", "doc_id": 1800 }, "chunk_id": "train_shard_00001_1800_0", "global_id": 8196 }, { "text": "In this study, the production and optimization of extracellular lipase from Kluyveromyces marxianus IFO 0288 was investigated by using optimized nutritional and cultural conditions in a yeast medium containing glucose as the carbon source in fully aerobic batch fermentation (150 rpm). The influence of four fermentation parameters (type of lipidic source, initial culture pH, temperature, and length of fermentation) on growth and lipase production was investigated and evaluated using the conventional \"one variable at a time\" approach and response surface methodology. An 18-fold increase in lipase production during 65 h of fermentation was obtained with optimized nutritional (0.5 % olive oil) and cultivation (pH 6.5, 35 °C) conditions by employing the conventional optimization method. By applying the response surface methodology technique the initial pH value of 6.4 and temperature of 32.5 °C were identified as optimal and led to further improvements (up to 18-fold) of extracellular lipase production. The results provide, for the first time, evidence that K. marxianus has the potential to be used as an efficient producer of extracellular lipase with prospective application in a variety of industrial and biotechnological areas.\n\nExperimental investigation and optimization of process variables affecting the production of extracellular lipase by Kluyveromyces marxianus IFO 0288.", "token_count": 335, "char_count": 1395, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6219, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:31.725035", "source": { "split": "train_shard_00001", "doc_id": 1801 }, "chunk_id": "train_shard_00001_1801_0", "global_id": 8197 }, { "text": "

Background

Avian mycoplasmas are small bacteria associated with several pathogenic conditions in many wild and poultry bird species. Extensive genomic data are available for many avian mycoplasmas, yet no comparative studies focusing on this group of mycoplasmas have been undertaken so far.

Results

Here, based on the comparison of forty avian mycoplasma genomes belonging to ten different species, we provide insightful information on the phylogeny, pan/core genome, energetic metabolism, and virulence of these avian pathogens. Analyses disclosed considerable inter- and intra-species genomic variabilities, with genome sizes that can vary by twice as much. Phylogenetic analysis based on concatenated orthologous genes revealed that avian mycoplasmas fell into either Hominis or Pneumoniae groups within the Mollicutes and could split into various clusters. No host co-evolution of avian mycoplasmas can be inferred from the proposed phylogenetic scheme. With 3,237 different gene clusters, the avian mycoplasma group under study proved diverse enough to have an open pan genome. However, a set of 150 gene clusters was found to be shared between all avian mycoplasmas, which is likely encoding essential functions. Comparison of energy metabolism pathways showed that avian mycoplasmas rely on various sources of energy. Superposition between phylogenetic and energy metabolism groups revealed that the glycolytic mycoplasmas belong to two distinct phylogenetic groups (Hominis and Pneumoniae), while all the arginine-utilizing mycoplasmas belong only to Hominis group. This can stand for different evolutionary strategies followed by avian mycoplasmas and further emphasizes the diversity within this group. Virulence determinants survey showed that the involved gene arsenals vary significantly within and between species, and could even be found in species often reported apathogenic. Immunoglobulin-blocking proteins were detected in almost all avian mycoplasmas", "token_count": 479, "char_count": 1986, "word_count": 272, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:32.402317", "source": { "split": "train_shard_00001", "doc_id": 1802 }, "chunk_id": "train_shard_00001_1802_0", "global_id": 8198 }, { "text": "Although these systems are not exclusive to this group, they seem to present some particular features making them unique among mycoplasmas.

Conclusion

This comparative genomic study uncovered the significant variable nature of avian mycoplasmas, furthering our knowledge on their biological attributes and evoking new hallmarks.\n\nA sweeping view of avian mycoplasmas biology drawn from comparative genomic analyses.", "token_count": 94, "char_count": 422, "word_count": 55, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:32.790845", "source": { "split": "train_shard_00001", "doc_id": 1802 }, "chunk_id": "train_shard_00001_1802_1", "global_id": 8199 }, { "text": "

Motivation

Compared to eukaryotes, prokaryote genomes are more diverse through different mechanisms, including a higher mutation rate and horizontal gene transfer. Therefore, using a linear representative reference can cause a reference bias. Graph-based pangenome methods have been developed to tackle this problem. However, comparisons in DNA space is still challenging due to this high diversity. In contrast, amino acids have higher similarity due to evolutionary constraints, resulting in conserved amino acids that, however, may be encoded by several synonymous codons. Coding regions cover the majority of the genome in prokaryotes. Thus, building panproteomes leverages the high sequence similarity while not losing much of the genome in non-coding regions.

Results

We present PanPA , a method that takes a set of multiple sequence alignments (MSAs) of proteins or protein clusters, indexes them, and builds a graph for each MSA. In the querying step, it can align DNA or amino acid sequences back to these graphs. We first showcase that PanPA generates correct alignments on a panproteome from 1,350 E. coli . To demonstrate that panproteomes allow longer phylogenetic distance comparison, we compare DNA and protein alignments from 1,073 S. enterica assemblies against E. coli reference genome, pangenome, and panproteome using BWA , GraphAligner , and PanPA respectively, where PanPA was able to produce around 22% more alignments. We also aligned DNA short-reads WGS sample from S. enterica against the E. coli reference with BWA and the panproteome with PanPA , where PanPA was able to find alignment for 69% of the reads compared to 5% with BWA

Availability

PanPA is available at https://github.com/fawaz-dabbaghieh/PanPA

Contact

fawaz@hhu.de , olga.kalinina@helmholtz-hzi.de

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nPanPA: generation and alignment of panproteome graphs", "token_count": 514, "char_count": 1974, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6312, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:33.897898", "source": { "split": "train_shard_00001", "doc_id": 1803 }, "chunk_id": "train_shard_00001_1803_0", "global_id": 8200 }, { "text": "Epiphytic yeasts represent an important source for the development of novel strategies aiming to combat food microbial contamination. The present study deals with the characterization of nine yeast strains belonging to Starmerella, Candida, Metschinikowia, Lachancea, Kodamaea and Pichia genera, isolated from the surface of plants from the Botanical Garden \"Dimitrie Brandza\" (Bucharest, Romania) for use as antimicrobial and probiotic agents. The tests involved the determination of the safe status, cell growth under stress conditions, and activity against pathogenic Candida and bacteria strains, respectively, as well as phytopathogenic filamentous fungi and lipolytic activity. None of the nine strains showed all the characteristics for virulence and pathogenicity, with the rare positive results being explained rather by their adaptability to the habitats of origin. The strains Lachancea thermotolerans CMGB-ST12 and Kodamaea ohmeri CMGB-ST19 grew at 37 °C; Metschnikowia reukaufii CMGB-ST21.2, M. reukaufii CMGB-ST.8.1 and M. reukaufii CMGB ST10 grew in the presence of 10% NaCl, while L. thermotolerans CMGB-ST12 and K. ohmeri CMGB-ST19 tolerated both acidic and alkaline pH values well (3.0 to 12.0). The studied yeast strains showed good antimicrobial activity against Candida krusei, Candida albicans and Gram-negative bacterial strains, with K", "token_count": 486, "char_count": 1474, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [ "ST12", "ST21", "ST19", "ST10" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:34.552054", "source": { "split": "train_shard_00001", "doc_id": 1804 }, "chunk_id": "train_shard_00001_1804_0", "global_id": 8201 }, { "text": "ohmeri CMGB-ST19 and Pichia membranaefaciens CMGB-ST53 inhibiting up to 100% the development of filamentous fungi. All the strains produced lipases for tributyrin hydrolysis, the best producer being Starmerella bombi CMGB-ST1, and only Candida magnoliae CMGB-ST8.2 tested positive against other probiotic yeasts. Overall, our nine yeast strains show high potential for industrial applications, for obtaining probiotic products and for preventing the development of a wide range of microbial food contaminants.\n\nEpiphytic Yeasts from South Romania for Preventing Food Microbial Contamination.", "token_count": 182, "char_count": 616, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7848, "quality_score": 0.8924, "entities": { "genes": [ "ST8", "ST1", "ST19", "ST53" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:34.992776", "source": { "split": "train_shard_00001", "doc_id": 1804 }, "chunk_id": "train_shard_00001_1804_1", "global_id": 8202 }, { "text": "Switchgrass (Panicum virgatum) was subjected to hydrothermolysis pretreatment and then used to study the effect of enzyme loading and temperature in a simultaneous saccharification and fermentation (SSF) with the thermotolerant yeast strain Kluyveromyces marxianus IMB3 at 8% solid loading. Various loadings of Accellerase 1500 between 0.1 and 1.1 mL g(-1) glucan were tested in SSF at 45 °C (activity of enzyme was 82.2 FPU mL(-1)). The optimum enzyme loading was 0.7 mL g(-1) glucan based on the six different enzyme loadings tested. SSFs were performed at 37, 41 and 45 °C with an enzyme loading of 0.7 mL g(-1) glucan. The highest ethanol concentration of 22.5 g L(-1) was obtained after 168 h with SSF at 45 °C, which was equivalent to 86% yield. Four different batch and fed-batch strategies were evaluated using a total solid loading of 12% (dry basis). About 32 g L(-1) ethanol was produced with the four strategies, which was equivalent to 82% yield.\n\nSimultaneous saccharification and fermentation of Kanlow switchgrass by thermotolerant Kluyveromyces marxianus IMB3: the effect of enzyme loading, temperature and higher solid loadings.", "token_count": 366, "char_count": 1146, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5722, "quality_score": 0.7861, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:35.572091", "source": { "split": "train_shard_00001", "doc_id": 1805 }, "chunk_id": "train_shard_00001_1805_0", "global_id": 8203 }, { "text": "The evolutionary fate of multi-strain pathogens is shaped by host-pathogen ecological interactions. In bacterial pathogens of plants, enhanced strain characterization and advances in our understanding of molecular mechanisms underlying defense pathways open the door for revisiting the role of negative frequency-dependent selection (NFDS) in strain structure, including its interplay with genetic exchange. NFDS arising from specific defense is one potential mechanism for generating, maintaining, and structuring pathogen diversity. In plants, specific protection against microbial pathogens involves Resistance proteins (R-proteins) that recognize virulence factors (effectors) secreted by pathogens, typically to subvert the initial line of host defense. Here we formulate a stochastic computational co-evolution model that explicitly incorporates variable length R-gene and effector repertoires, and migration from their regional pools. We use this model to understand potential mechanisms shaping effector repertoire structure and associated strain coexistence in the generalist plant pathogen P. syringae . The demonstration of a modular structure in our numerical simulations motivates the analysis of genome sequences from 76 strains collected in the Midwestern US and 1104 strains from global sources. We find that effector repertories both locally and globally exhibit a modular structure, with higher similarity within than between clusters. The observed modules are consistent with the core genome phylogeny and are unexplained by plant host species, location of isolation, and genetic linkage between effectors. An extension of the model is needed to take into account the evidence for genetic exchange and the phylogenetic congruence of effector modules. We initialize the system with a phylogenetically congruent modular structure and include recombination rates decreasing as a function of phylogenetic distance. We show that NFDS can counter-balance the effects of mixing due to recombination and in so doing, contributes to the maintenance of strain structure. These findings indicate that the observed similarity clusters may constitute, in part, emergent niches arising from eco-evolutionary dynamics that contribute to strain coexistence.\n\nNegative frequency-dependent selection contributes to modular structure of effector repertoires in Pseudomonas syringae", "token_count": 513, "char_count": 2388, "word_count": 322, "semantic_coherence": 1, "information_density": 0.6118, "quality_score": 0.8059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:36.224440", "source": { "split": "train_shard_00001", "doc_id": 1806 }, "chunk_id": "train_shard_00001_1806_0", "global_id": 8204 }, { "text": "Native American individuals in the Southwestern USA experience a higher burden of invasive Staphylococcus aureus disease than the general population. However, little is known about S. aureus carriage in these communities. A cross-sectional study was conducted to determine the carriage prevalence, risk factors and genomic epidemiology of S. aureus among Native American children (<5 years, n=121) and adults (≥18 years, n=167) in the Southwestern USA. Short- and long-read sequencing data were generated using Illumina and Oxford Nanopore Technology platforms to produce high-quality hybrid assemblies, and antibiotic-resistance, virulence and pangenome analyses were performed. S. aureus carriage prevalence was 20.7 % among children, 30.2 % among adults 18-64 years and 16.7 % among adults ≥65 years. Risk factors among adults included recent surgery, prior S. aureus infection among household members, and recent use of gyms or locker rooms by household members. No risk factors were identified among children. The bacterial population structure was dominated by clonal complex 1 (CC1) (21.1 %), CC5 (22.2 %) and CC8 (22.2 %). Isolates from children and adults were intermixed throughout the phylogeny. While the S. aureus population was diverse, the carriage prevalence was comparable to that in the general USA population. Genomic and risk-factor data suggest household, community and healthcare transmission are important components of the local epidemiology.\n\nCarriage prevalence and genomic epidemiology of Staphylococcus aureus among Native American children and adults in the Southwestern USA.", "token_count": 470, "char_count": 1667, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5739, "quality_score": 0.787, "entities": { "genes": [ "CC5", "CC1", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:36.869264", "source": { "split": "train_shard_00001", "doc_id": 1807 }, "chunk_id": "train_shard_00001_1807_0", "global_id": 8205 }, { "text": "Listeria monocytogenes contamination in ready-to-eat chilled pot skewer products represent a significant public health concern in China. This study assessed the prevalence, molecular characteristics, and potential transmission risks of L. monocytogenes in 340 commercially available chilled pot skewer samples collected in 2019 and 2021. Bacterial isolation revealed an overall contamination rate of 20.6% (70/340), with no significant differences among meat-based (15.5%), vegetarian (19.5%), or mixed meat-vegetable (26.5%) products. Serogroups 1/2b, 3b, 7 (47.4%) and 1/2a, 3 (35.5%) predominated. Multilocus sequence typing (MLST) identified high-risk clones ST87 (27.6%) and ST121 (22.4%)-both associated with listeriosis outbreaks-along with rare lineages such as ST378 (1.3%). Core genome MLST (cgMLST) analysis of 76 isolates revealed extensive genetic diversity (59 cgMLST types), suggesting multiple contamination sources within production facilities. However, persistence of specific strains (≤ 2 allelic differences) across time points (2019-2021) was observed in certain manufacturers. Comparative genomics with clinical isolates from Beijing (2013-2022) revealed shared sequence types (e.g., ST87/CC87). These findings underscore the urgent need for enhanced surveillance in food processing environments. Future investigations should adopt a One Health framework to trace contamination routes and evaluate intervention control measures for this emerging food safety challenge.\n\nPrevalence and characteristics of <i>Listeria monocytogenes</i> in ready-to-eat chilled pot skewer products.", "token_count": 463, "char_count": 1626, "word_count": 203, "semantic_coherence": 1, "information_density": 0.798, "quality_score": 0.899, "entities": { "genes": [ "CC87", "ST378", "ST87", "ST121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:37.508852", "source": { "split": "train_shard_00001", "doc_id": 1808 }, "chunk_id": "train_shard_00001_1808_0", "global_id": 8206 }, { "text": "The fermentation of both glucose and xylose is important to maximize ethanol yield from renewable biomass feedstocks. In this article, we analyze growth, sugar consumption, and ethanol formation by the yeast Kluyveromyces marxianus UFV-3 using various glucose and xylose concentrations and also under conditions of reduced respiratory activity. In almost all the conditions analyzed, glucose repressed xylose assimilation and xylose consumption began after glucose had been exhausted. A remarkable difference was observed when mixtures of 5 g L(-1) glucose/20 g L(-1) xylose and 20 g L(-1) glucose/20 g L(-1) xylose were used. In the former, the xylose consumption began immediately after the glucose depletion. Indeed, there was no striking diauxic phase, as observed in the latter condition, in which there was an interval of 30 h between glucose depletion and the beginning of xylose consumption. Ethanol production was always higher in a mixture of glucose and xylose than in glucose alone. The highest ethanol concentration (8.65 g L(-1)) and cell mass concentration (4.42 g L(-1)) were achieved after 8 and 74 h, respectively, in a mixture of 20 g L(-1) glucose/20 g L(-1) xylose. When inhibitors of respiration were added to the medium, glucose repression of xylose consumption was alleviated completely and K. marxianus was able to consume xylose and glucose simultaneously.\n\nKinetics of growth and ethanol formation from a mix of glucose/xylose substrate by Kluyveromyces marxianus UFV-3.", "token_count": 440, "char_count": 1497, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5351, "quality_score": 0.7675, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:38.134009", "source": { "split": "train_shard_00001", "doc_id": 1809 }, "chunk_id": "train_shard_00001_1809_0", "global_id": 8207 }, { "text": "Introduction. One third of people with CF in the UK are co-infected by both Staphylococcus aureus and Pseudomonas aeruginosa. Chronic bacterial infection in CF contributes to the gradual destruction of lung tissue, and eventually respiratory failure in this group.Gap Statement. The contribution of S. aureus to cystic fibrosis (CF) lung decline in the presence or absence of P. aeruginosa is unclear. Defining the molecular and phenotypic characteristics of a range of S. aureus clinical isolates will help further understand its pathogenic capabilities.Aim. Our objective was to use molecular and phenotypic tools to characterise twenty-five clinical S. aureus isolates collected from mono- and coinfection with P. aeruginosa from people with CF at the Royal Victoria Infirmary, Newcastle upon Tyne.Methodology. Genomic DNA was extracted and sequenced. Multilocus sequence typing was used to construct phylogeny from the seven housekeeping genes. A pangenome was calculated using Roary, and cluster of Orthologous groups were assigned using eggNOG-mapper which were used to determine differences within core, accessory, and unique genomes. Characterisation of sequence type, clonal complex, agr and spa types was carried out using PubMLST, eBURST, AgrVATE and spaTyper, respectively. Antibiotic resistance was determined using Kirby-Bauer disc diffusion tests. Phenotypic testing of haemolysis was carried out using ovine red blood cell agar plates and mucoid phenotypes visualised using Congo red agar.Results. Clinical strains clustered closely based on agr type, sequence type and clonal complex. COG analysis revealed statistically significant enrichment of COG families between core, accessory and unique pangenome groups. The unique genome was significantly enriched for replication, recombination and repair, and defence mechanisms", "token_count": 516, "char_count": 1945, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6628, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:38.797235", "source": { "split": "train_shard_00001", "doc_id": 1810 }, "chunk_id": "train_shard_00001_1810_0", "global_id": 8208 }, { "text": "The presence of known virulence genes and toxins were high within this group, and unique genes were identified in 11 strains. Strains which were isolated from the same patient all surpassed average nucleotide identity thresholds, however, differed in phenotypic traits. Antimicrobial resistance to macrolides was significantly higher in the coinfection group.Conclusion. There is huge variation in genetic and phenotypic capabilities of S. aureus strains. Further studies on how these may differ in relation to other species in the CF lung may give insight into inter-species interactions.\n\nCharacterisation of key genotypic and phenotypic traits of clinical cystic fibrosis Staphylococcus aureus isolates.", "token_count": 184, "char_count": 727, "word_count": 100, "semantic_coherence": 1, "information_density": 0.77, "quality_score": 0.885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:39.244348", "source": { "split": "train_shard_00001", "doc_id": 1810 }, "chunk_id": "train_shard_00001_1810_1", "global_id": 8209 }, { "text": "Microbial production of chemicals and proteins from biomass-derived and waste sugar streams is a rapidly growing area of research and development. While the model yeast Saccharomyces cerevisiae is an excellent host for the conversion of glucose to ethanol, production of other chemicals from alternative substrates often requires extensive strain engineering. To avoid complex and intensive engineering of S. cerevisiae, other yeasts are often selected as hosts for bioprocessing based on their natural capacity to produce a desired product: for example, the efficient production and secretion of proteins, lipids, and primary metabolites that have value as commodity chemicals. Even when using yeasts with beneficial native phenotypes, metabolic engineering to increase yield, titer, and production rate is essential. The non-conventional yeasts Kluyveromyces lactis, K. marxianus, Scheffersomyces stipitis, Yarrowia lipolytica, Hansenula polymorpha and Pichia pastoris have been developed as eukaryotic hosts because of their desirable phenotypes, including thermotolerance, assimilation of diverse carbon sources, and high protein secretion. However, advanced metabolic engineering in these yeasts has been limited. This review outlines the challenges of using non-conventional yeasts for strain and pathway engineering, and discusses the developed solutions to these problems and the resulting applications in industrial biotechnology.\n\nGenome and metabolic engineering in non-conventional yeasts: Current advances and applications.", "token_count": 366, "char_count": 1557, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:39.820769", "source": { "split": "train_shard_00001", "doc_id": 1811 }, "chunk_id": "train_shard_00001_1811_0", "global_id": 8210 }, { "text": "

ABSTRACT

Vibrio cholerae O1 causes the diarrheal disease cholera, and the small intestine is the site of active infection. During cholera, cholera toxin is secreted from V. cholerae and induces a massive fluid influx into the small intestine, which causes vomiting and diarrhea. Typically, V. cholerae genomes are sequenced from bacteria passed in stool, but rarely from vomit, a fluid that may more closely represents the site of active infection. We hypothesized that the V. cholerae O1 population bottlenecks along the gastrointestinal tract would result in reduced genetic variation in stool compared to vomit. To test this, we sequenced V. cholerae genomes from ten cholera patients with paired vomit and stool samples. Genetic diversity was low in both vomit and stool, consistent with a single infecting population rather than co-infection with divergent V. cholerae O1 lineages. The number of single nucleotide variants decreased between vomit and stool in four patients, increased in two, and remained unchanged in four. The number of genes encoded in the V. cholerae genome decreased between vomit and stool in eight patients and increased in two. Pangenome analysis of assembled short-read sequencing demonstrated that the toxin-coregulated pilus operon more frequently contained deletions in genomes from vomit compared to stool. However, these deletions were not detected by PCR or long-read sequencing, indicating that interpreting gene presence or absence patterns from short-read data alone may be incomplete. Overall, we found that V. cholerae O1 isolated from stool is genetically similar to V. cholerae recovered from the upper intestinal tract.

IMPORTANCE

Vibrio cholerae O1, the bacterium that causes cholera, is ingested in contaminated food or water and then colonizes the upper small intestine and is excreted in stool. Shed V. cholerae genomes are usually studied, but V. cholerae isolated from vomit may be more representative of where V. cholerae colonizes in the upper intestinal epithelium. V", "token_count": 531, "char_count": 2039, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5244, "quality_score": 0.7622, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:40.478415", "source": { "split": "train_shard_00001", "doc_id": 1812 }, "chunk_id": "train_shard_00001_1812_0", "global_id": 8211 }, { "text": "cholerae may experience bottlenecks, or large reductions in bacterial population sizes or genetic diversity, as it passes through the gut. Passage through the gut may select for distinct V. cholerae mutants that are adapted for survival and gut colonization. We did not find strong evidence for such adaptive mutations, and instead observed that passage through the gut results in modest reductions in V. cholerae genetic diversity, and only in some patients. These results fill a gap in our understanding of the V. cholerae life cycle, transmission, and evolution.\n\nDiversity ofVibrio choleraeO1 through the human gastrointestinal tract during cholera", "token_count": 157, "char_count": 659, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:40.917492", "source": { "split": "train_shard_00001", "doc_id": 1812 }, "chunk_id": "train_shard_00001_1812_1", "global_id": 8212 }, { "text": "The present study evaluated the co-production of β-galactosidase and ethanol by Kluyveromyces marxianus ATCC 36907 and Kluyveromyces lactis NRRL Y-8279 using as carbon source the lactose found on \"coalho\" cheese whey. Cheese whey was subjected to partial deproteinization, and physicochemical parameters were assessed. Cultivations were carried out in an shaker to evaluate two carbon/nitrogen (C:N) ratios. The best C:N ratio (1.5:1) was carried to 1.5-L bioreactor cultivation in order to increase co-production yields. The stability of β-galactosidase was assessed against different temperatures and pH, and in the presence of metal ions. Concerning the co-production of β-galactosidase and ethanol, K. lactis proved to be more efficient in both the C:N ratios, reaching 21.09 U·mL-1 of activity and 7.10 g·L-1 of ethanol in 16 h. This study describes the development of a viable and value-adding biotechnological process using a regional cheese by-product from Northeast Brazil for co-production of biomolecules of industrial interest.\n\nPotential of \"coalho\" cheese whey as lactose source for β-galactosidase and ethanol co-production by Kluyveromyces spp. yeasts.", "token_count": 405, "char_count": 1218, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:41.537164", "source": { "split": "train_shard_00001", "doc_id": 1813 }, "chunk_id": "train_shard_00001_1813_0", "global_id": 8213 }, { "text": "This work is focused on the synthesis of the fructooligosaccharides (FOS) from sucrose and inulin, using free, immobilized and pre-treated immobilized inulinase from Kluyveromyces marxianus NRRL Y 7571 and Aspergillus niger in an aqueous-organic system. Initially, the influence of pre-treatment using four different gases, propane, n-butane, CO(2) and liquefied petroleum gas (LPG), was investigated towards FOS production and best results were found when both enzymes were previously treated with LPG. The best reaction yields were obtained when the immobilized enzymes were treated with LPG. Considering FOS synthesis using the enzyme from A. niger, yields of 26.62% of GF2 (kestose), 30.62% of GF3 (nystose) and 8.47% of GF4 (fructosyl nystose) were achieved using sucrose as substrate. Using inulinases from K. marxianus NRRL Y 7571, 11.89% of GF2 and 20.83% of GF3 were obtained, using inulin as substrate. However, promising results were achieved using the free form of inulinase from A. niger (77.19% of GF2; 14.03% of GF3 and 0.07% of GF4) using inulin as substrate.\n\nEnzymatic synthesis of fructooligosaccharides by inulinases from Aspergillus niger and Kluyveromyces marxianus NRRL Y-7571 in aqueous-organic medium.", "token_count": 408, "char_count": 1226, "word_count": 181, "semantic_coherence": 1, "information_density": 0.547, "quality_score": 0.7735, "entities": { "genes": [ "GF3", "GF4", "GF2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:42.155635", "source": { "split": "train_shard_00001", "doc_id": 1814 }, "chunk_id": "train_shard_00001_1814_0", "global_id": 8214 }, { "text": "Thousands of DNA sequences in global populations are not present in the human reference genome, named nonreference sequence (NRS). Long-read sequencing (LRS) technologies enable better discovery of NRS with large length, particularly in repetitive regions. Here, we de novo assembled 539 genomes in five genetically divergent human populations sequenced by LRS technology and identified 5.1 million NRSs. These NRSs were merged into 45,284 nonredundant NRSs, of which 66.2% were novel. 78.5% of NRSs were repeat sequences, such as VNTR and STR. 38.7% of NRSs were common in the five populations, 35.6% were population specific, while 21.3% were ancestral and present in nonhuman primates. 144 NRS hotspots spanned 141 Mb of the human genome and many NRSs contained known functional domains or intersected with coding genes. Based on graph-based pangenome, we detected 565 transcript expression quantitative trait loci on NRSs, of which 467 were novel. We also detected 39 NRS candidates for adaptive selection within the human population related to the language system and diabetes. GWAS revealed 14 NRSs significantly associated with eight phenotypes, such as anaemia. Furthermore, we identified 154 NRSs in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the landscape of human NRS and provides novel insights into functions of NRS to facilitate evolutionary and biomedical research.\n\nGraph pangenome reveals functional, evolutionary, and phenotypic significance of human nonreference sequences", "token_count": 408, "char_count": 1553, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:42.776468", "source": { "split": "train_shard_00001", "doc_id": 1815 }, "chunk_id": "train_shard_00001_1815_0", "global_id": 8215 }, { "text": "A feeding trial was conducted to investigate the effects of differently processed yeast products (hydrolyzed or non-hydrolyzed) derived from Kluyveromyces fragilis on immunological parameters of piglets in an early phase post weaning (d 1–14). A total of 48 male and female piglets (6.17 ± 0.32 kg BW, weaned at d 25) were allocated to three dietary groups (n = 8 replicates with two piglets each) receiving a control diet (CON) or diets with 1% non-hydrolyzed yeast (Diet NHY) or 1% hydrolyzed yeast (Diet HY). The piglets were fed isoenergetic and isonitrogenous diets and had ad-libitum access to feed (mash form) and drinking water. Blood samples were taken at d 1 and d 14 for differential blood count and phenotyping of lymphocytes and at d 1, d 3 and d 14 for analysis of phagocytic activity of leukocytes. Eight animals per treatment were sacrificed 2 weeks after weaning for jejunal and colonal tissue sampling for mRNA extraction and gene expression analysis of cytokines (TNFα, IL-6, IL-10, IL-12) and of tight junction proteins. Different treatments had no effect on piglet growth rate. Fecal scores were improved at d 8 after weaning in the yeast supplemented Groups HY and NHY (P < 0.05). Differential blood count, phenotyping of lymphocytes, and mRNA expression of cytokines and tight junction proteins were not affected by dietary treatment. Significant time-dependent effects on the blood concentrations (G/L) of leucocytes, lymphocytes, monocytes, and on phenotypes of peripheral lymphocytes (%) such as B-cells (P < 0.001), cytotoxic T-cells and monocytes (P < 0.01) have been observed", "token_count": 512, "char_count": 1604, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:43.451413", "source": { "split": "train_shard_00001", "doc_id": 1816 }, "chunk_id": "train_shard_00001_1816_0", "global_id": 8216 }, { "text": "The difference between lymphocyte counts on d 1 and d 14 was highest in Group HY (P < 0.001). Compared with Group CON, the phagocytic activity of monocytes at d 3 after weaning was higher in Groups HY and NHY (P < 0.05). In conclusion, both yeast products (HY and NHY) had minor effects on adaptive immune parameters, but increased innate immune response such as phagocytosis activity at d 3. Changes in adaptive immune response were more time-dependent than diet-dependent.\n\nEffect of time and dietary supplementation with processed yeasts (Kluyveromyces fragilis) on immunological parameters in weaned piglets", "token_count": 171, "char_count": 611, "word_count": 97, "semantic_coherence": 1, "information_density": 0.732, "quality_score": 0.866, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:43.920845", "source": { "split": "train_shard_00001", "doc_id": 1816 }, "chunk_id": "train_shard_00001_1816_1", "global_id": 8217 }, { "text": "Five Gram-stain-positive, aerobic, non-motile actinobacterial strains designated as CPCC 205763T, CPCC 203386T, CPCC 205716T, CPCC 203406T, and CPCC 203407 were obtained from different ecosystems associated with four kinds of Chinese traditional medicinal plants. The 16S rRNA gene sequences of these five strains showed closely related to members of the genus Herbiconiux of the family Microbacteriaceae, with the highest similarities of 97.4-99.7% to the four validly named species of Herbiconiux. In the phylogenetic trees based on 16S rRNA gene sequences and the core genome, these isolates clustered into the clade of the genus Herbiconiux within the lineage of the family Microbacteriaceae. The overall genome relatedness indexes (values of ANI and dDDH) and the phenotypic properties (morphological, physiological and chemotaxonomic characteristics) of these isolates, readily supported to affiliate them to the genus Herbiconiux, representing four novel species, with the isolates CPCC 203406T and CPCC 203407 being classified in the same species. For which the names Herbiconiux aconitum sp. nov. (type strain CPCC 205763T = I19A-01430T = CGMCC 1.60067T), Herbiconiux daphne sp. nov", "token_count": 486, "char_count": 1335, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6353, "quality_score": 0.8176, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:44.605052", "source": { "split": "train_shard_00001", "doc_id": 1817 }, "chunk_id": "train_shard_00001_1817_0", "global_id": 8218 }, { "text": "(type strain CPCC 203386T = I10A-01569T = DSM 24546T = KCTC 19839T), Herbiconiux gentiana sp. nov. (type strain CPCC 205716T = I21A-01427T = CGMCC 1.60064T), and Herbiconiux oxytropis sp. nov. (type strain CPCC 203406T = I10A-02268T = DSM 24549T = KCTC 19840T) were proposed, respectively. In the genomes of these five strains, the putative encoding genes for amidase, endoglucanase, phosphatase, and superoxidative dismutase were retrieved, which were classified as biosynthetic genes/gene-clusters regarding plant growth-promotion (PGP) functions. The positive results from IAA-producing, cellulose-degrading and anti-oxidation experiments further approved their potential PGP bio-functions. Pangenome analysis of the genus Herbiconiux supported the polyphasic taxonomy results and confirmed their bio-function potential.\n\nPangenome analysis of the genus Herbiconiux and proposal of four new species associated with Chinese medicinal plants.", "token_count": 461, "char_count": 1092, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:45.279505", "source": { "split": "train_shard_00001", "doc_id": 1817 }, "chunk_id": "train_shard_00001_1817_1", "global_id": 8219 }, { "text": "The Cacao tree ( Theobroma cacao L.) is a major cash crop and an important source of income for millions of farmers across Africa, Asia and Latin America. However, cacao farmers and producing countries are facing multiple challenges including pest and disease management, sustainable production under threat of climate changes and diversification of cocoa flavor profiles. Addressing these challenging requires a deeper understanding of the existing genetic diversity of the species. Yet, very little is known about the intraspecific gene content variation. In this study, we used the genome of 216 accessions of T. cacao (including 185 newly re-sequenced) covering a broad genetic diversity of the species to construct the first pan-genome of the cacao tree. As a result, we predicted a total of 30,489 pan-genes, enriching the reference Criollo genome with 1,407 new genes. Our analysis revealed that only a small fraction of these genes (9.2%) is dispensable, being absent in some individuals. However, these genes could represent a valuable resource for breeding efforts aimed at improving disease resistance in the species. We used this new pangenome resource to gain insights into how diversification and domestication processes have influenced genomic variability within the species. Notably, we observed a significant loss of genes within the domesticated Criollo genetic group. Furthermore, we found evidences suggesting that domestication processes have had an impact on the vigor and disease tolerance of Criollo accessions. In summary, our research has contributed to a better understanding of the cacao tree’s genome diversity. These findings offer new avenues for biological discovery and breeding, ultimately addressing the challenges faced by cacao farmers and producing countries.\n\nPangenomic exploration ofTheobroma cacao: New Insights into Gene Content Diversity and Selection During Domestication", "token_count": 426, "char_count": 1923, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:45.908918", "source": { "split": "train_shard_00001", "doc_id": 1818 }, "chunk_id": "train_shard_00001_1818_0", "global_id": 8220 }, { "text": "Marinobacter spp. are cosmopolitan in saline environments, displaying a diverse set of metabolisms that allow them to competitively occupy these environments, some of which can be extreme in both salinity and temperature. Here, we introduce a distinct cluster of Marinobacter genomes, composed of novel isolates and in silico assembled genomes obtained from subzero, hypersaline cryopeg brines, relic seawater-derived liquid habitats within permafrost sampled near Utqiaġvik, Alaska. Using these new genomes and 45 representative publicly available genomes of Marinobacter spp. from other settings, we assembled a pangenome to examine how the new extremophile members fit evolutionarily and ecologically, based on genetic potential and environmental source. This first genus-wide genomic analysis revealed that Marinobacter spp. in general encode metabolic pathways that are thermodynamically favored at low temperature, cover a broad range of organic compounds, and optimize protein usage, e.g., the Entner-Doudoroff pathway, the glyoxylate shunt, and amino acid metabolism. The new isolates contributed to a distinct clade of subzero brine-dwelling Marinobacter spp. that diverged genotypically and phylogenetically from all other Marinobacter members. The subzero brine clade displays genomic characteristics that may explain competitive adaptations to the extreme environments they inhabit, including more abundant membrane transport systems (e.g., for organic substrates, compatible solutes, and ions) and stress-induced transcriptional regulatory mechanisms (e.g., for cold and salt stress) than in the other Marinobacter clades. We also identified more abundant signatures of potential horizontal transfer of genes involved in transcription, the mobilome, and a variety of metabolite exchange systems, which led to considering the importance of this evolutionary mechanism in an extreme environment where adaptation via vertical evolution is physiologically rate limited", "token_count": 503, "char_count": 2040, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6805, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:46.564270", "source": { "split": "train_shard_00001", "doc_id": 1819 }, "chunk_id": "train_shard_00001_1819_0", "global_id": 8221 }, { "text": "Assessing these new extremophile genomes in a pangenomic context has provided a unique view into the ecological and evolutionary history of the genus Marinobacter, particularly with regard to its remarkable diversity and its opportunism in extremely cold and saline environments.\n\nEvolutionary Divergence of Marinobacter Strains in Cryopeg Brines as Revealed by Pangenomics.", "token_count": 98, "char_count": 388, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8269, "quality_score": 0.9135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:46.939731", "source": { "split": "train_shard_00001", "doc_id": 1819 }, "chunk_id": "train_shard_00001_1819_1", "global_id": 8222 }, { "text": "Pyrenophora tritici-repentis (tan spot) is a destructive foliar pathogen of wheat with global impact. This ascomycete fungus possesses a highly plastic open pangenome shaped by the gain and loss of effector genes. This study investigated the allelic variations in the chlorosis-encoding gene ToxB across 422 isolates representing all identified pathotypes and worldwide origins. To gain better insights into ToxB evolution, we examined its presence and variability in other Pyrenophora spp. A ToxB haplotype network was constructed, revealing the evolutionary relationships of this gene (20 haplotypes) across four Pyrenophora species. Notably, toxb, the homolog of ToxB, was detected for the first time in the barley pathogen Pyrenophora teres. The ToxB/toxb genes display evidence of selection that is characterized by loss of function, duplication, and diverse mutations. Within the ToxB/toxb open reading frame, 72 mutations were identified, including 14 synonymous, 55 nonsynonymous, and 3 indel mutations. Remarkably, a, ∼5.6-kb Copia-like retrotransposon, named Copia-1_Ptr, was found inserted in the toxb gene of a race 3 isolate. This insert disrupted the ToxB gene's function, a first case of effector gene disruption by a transposable element in P. tritici-repentis. Additionally, a microsatellite with 25 nucleotide repeats (0 to 10) in the upstream region of ToxB suggested a potential mechanism influencing ToxB expression and regulation", "token_count": 489, "char_count": 1577, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.8349, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:47.591743", "source": { "split": "train_shard_00001", "doc_id": 1820 }, "chunk_id": "train_shard_00001_1820_0", "global_id": 8223 }, { "text": "Exploring ToxB-like protein distribution in other ascomycetes revealed the presence of ToxB-like proteins in 19 additional species, including the Leotiomycetes class for the first time. The presence/absence pattern of ToxB-like proteins defied species relatedness compared with a phylogenetic tree, suggesting a past horizontal gene transfer event during the evolution of the ToxB gene. [Formula: see text] Copyright © 2024 His Majesty the King in Right of Canada, as represented by the Minister of Agriculture and Agri-Food. This is an open access article distributed under the CC BY-NC-ND 4.0 International license.\n\nEvolution of the <i>Toxb</i> Gene in <i>Pyrenophora tritici-repentis</i> and Related Species.", "token_count": 214, "char_count": 743, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7624, "quality_score": 0.8812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:48.049690", "source": { "split": "train_shard_00001", "doc_id": 1820 }, "chunk_id": "train_shard_00001_1820_1", "global_id": 8224 }, { "text": "A novel extracellular hydrolase of ∼45kDa molecular mass was purified from Kluyveromyces marxianus IFO 0288 cultures and characterized as serine protease. The K(m)-value of protease (designated protease-KM-IFO-0288-A), which was found active in media containing elevated [NaCl] but lacking EDTAK(2), decreased with increasing [Ca(2+)]. The protease maintained considerable activity at the range of 10-60°C and pH 6.00-10.25, with optimum k(cat)/K(m)-value at 35.5°C and pH 7.75. It was strongly affected by specific irreversible inhibitors of serine proteases while was unaffected by inhibitors of cysteine proteases. Significant rate constants, activation energies, and proton inventories were estimated from the profiles of Michaelis-Menten parameters, versus pH, temperature and deuterium atom fraction, in the hydrolysis of Suc-AAPF-pNA showing that protease-KM-IFO-0288-A performs catalysis via a charge-relay system. The properties of protease-KM-IFO-0288-A suggest that K. marxianus represents a valuable source of extracellular protease of biotechnological interest which, given its GRAS status, could find several important applications.\n\nPurification, kinetic characterization and properties of a novel thermo-tolerant extracellular protease from Kluyveromyces marxianus IFO 0288 with potential biotechnological interest.", "token_count": 395, "char_count": 1331, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6964, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:48.667405", "source": { "split": "train_shard_00001", "doc_id": 1821 }, "chunk_id": "train_shard_00001_1821_0", "global_id": 8225 }, { "text": "

Introduction

Klebsiella variicola is an emerging bacterial pathogen commonly associated with opportunistic human infections.

Methods

In this study, we characterized and analyzed the core genome of a β-lactam-resistant K. variicola subsp. variicola isolate from a human in Kunming, Yunnan, China.

Results

The human-derived β-lactam-resistant K. variicola genome was assembled into 37 contigs, with a total genome size of 5,667,700 bp. K. variicola comprises multiple antimicrobial resistance (AMR) genes, including blaLEN-22, fosA, OqxA, and OqxB, as well as the virulence-associated factors fimH, nlpI, and iutA. The β-lactam-resistant K. variicola genome comprised K and O (KL30 and O3/O3a) serotypes. We also identified 29 SNPs from three different snpEff categories: 18 low, five moderate, and six modifiers. Subsequently, we identified five assembled replicons, including three plasmids. Plasmid pKp5-1, plasmid p15WZ-82_res, and plasmid pKP91, and two phage regions: phage region-1, which resembled Entero-phage-HK446, and phage region-2, which was questionable with phage-Erwini-vB-EhrS-59. Furthermore, secondary metabolites, such as redox-cofactor, butyrolactone, azole-containing-RiPP, terpene-precursors (two distinct clusters), NRP-metallophores, and RiPP-like gene clusters were also identified in the K", "token_count": 515, "char_count": 1410, "word_count": 165, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [ "KL30", "HK446" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:49.324411", "source": { "split": "train_shard_00001", "doc_id": 1822 }, "chunk_id": "train_shard_00001_1822_0", "global_id": 8226 }, { "text": "variicola genome.

Discussion

Identifying key antibiotic resistance determinants, virulence factors, capsule serotypes, secondary metabolites, plasmids, and phage replicons emphasizes the zoonotic potential of this pathogen. Given the potential zoonotic implications, a multidisciplinary approach should be used to prevent the spread of β-lactam-resistant K. variicola.\n\nComprehensive Genome Analysis of a Human-Derived β-Lactam-Resistant <i>Klebsiella variicola</i> Isolate from China.", "token_count": 160, "char_count": 515, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8519, "quality_score": 0.9259, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:49.764450", "source": { "split": "train_shard_00001", "doc_id": 1822 }, "chunk_id": "train_shard_00001_1822_1", "global_id": 8227 }, { "text": "Shewanella algae is widely distributed in marine and freshwater habitats, and has been proved to be an emerging marine zoonotic and human pathogen. However, the genomic characteristics and pathogenicity of Shewanella algae are unclear. Here, the whole-genome features of 55 S. algae strains isolated from different sources were described. Pan-genome analysis yielded 2863 (19.4 %) genes shared among all strains. Functional annotation of the core genome showed that the main functions are focused on basic lifestyle such as metabolism and energy production. Meanwhile, the phylogenetic tree of the single nucleotide polymorphisms (SNPs) of core genome divided the 55 strains into three clades, with the majority of strains from China falling into the first two clades. As for the accessory genome, 167 genomic islands (GIs) and 65 phage-related elements were detected. The CRISPR-Cas system with a high degree of confidence was predicted in 23 strains. The GIs carried a suite of virulence genes and mobile genetic elements, while prophages contained several transposases and integrases. Horizontal genes transfer based on homology analysis indicated that these GIs and prophages were parts of major drivers for the evolution and the environmental adaptation of S. algae. In addition, a rich putative virulence-associated gene pool was found. Eight classes of antibiotic-associated resistance genes were detected, and the carriage rate of β-lactam resistance genes was 100 %. In conclusion, S. algae exhibits a high intra-species diversity in the aspects of population structure, virulence-associated genes and potential drug resistance, which is helpful for its evolution in pathogenesis and environmental adaptability.\n\nGenomic analysis reveals high intra-species diversity of Shewanella algae.", "token_count": 477, "char_count": 1845, "word_count": 261, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:50.406367", "source": { "split": "train_shard_00001", "doc_id": 1823 }, "chunk_id": "train_shard_00001_1823_0", "global_id": 8228 }, { "text": "Abstract

Background The use of thermotolerant yeast strains can improve the efficiency of ethanol fermentation, allowing fermentation to occur at temperatures higher than 40 °C. This increment in temperature could benefit traditional bio-ethanol production and allow simultaneous saccharification and fermentation (SSF) of starch or lignocellulosic biomass. Results We identified and characterized the physiology of a new thermotolerant strain able to fermentate at 40 °C while producing high yields of ethanol. Our results showed that, in comparison to the industrial yeast CAT-1, our strain was more resistant to various stressors generated during the production of first- and second-generation ethanol, and it also was able to change the pattern of genes involved in sucrose assimilation (SUC2 and AGT1). The formation of secondary products of fermentation was different at 40ºC, with reduced expression of genes involved in the formation of glycerol (GPD2), acetate (ALD6 and ALD4), and acetyl-CoA (ACS2). Conclusion The LBGA-01 strain is a thermotolerant strain that modulates the production of key genes, changing metabolic pathways during high-temperature fermentation, and increasing its tolerance to the high concentration of ethanol, sugar, acetic lactic, acetic acid, furfural and HMF. This indicates that this strain can be used to improve first- and second-generation ethanol production in Brazil.

\n\nPhysiological characterization of a new thermotolerant yeast strain isolated during Brazilian ethanol production and its application in high temperature fermentation", "token_count": 428, "char_count": 1671, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [ "AGT1", "ACS2", "SUC2", "ALD4", "GPD2", "ALD6" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:51.036851", "source": { "split": "train_shard_00001", "doc_id": 1824 }, "chunk_id": "train_shard_00001_1824_0", "global_id": 8229 }, { "text": "Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.\n\nRoving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group.", "token_count": 379, "char_count": 1590, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:51.626596", "source": { "split": "train_shard_00001", "doc_id": 1825 }, "chunk_id": "train_shard_00001_1825_0", "global_id": 8230 }, { "text": "Probiotics refer to living microorganisms that exert a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic-resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis and some relevant biochemical tests to uncover the probiotic potentials of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. The strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1,916,674 bp) contained 1911 CDS, and no gene was identified for either antibiotic resistance or toxic metabolites. It carried genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance, and acidic pH tolerance. Genes were annotated for inhibiting pathogenic bacteria by inhibitory substances [bacteriocin: Helveticin-J (331 bp) and Enterolysin-A (275 bp), hydrogen peroxide, and acid]; blockage of adhesion sites; and competition for nutrients. The genes involved in its metabolic pathway were detected as suitable for digesting indigestible nutrients in the human gut. The TY-11 genome possessed an additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subsp. bulgaricus", "token_count": 474, "char_count": 1695, "word_count": 232, "semantic_coherence": 1, "information_density": 0.7069, "quality_score": 0.8534, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:52.271181", "source": { "split": "train_shard_00001", "doc_id": 1826 }, "chunk_id": "train_shard_00001_1826_0", "global_id": 8231 }, { "text": "During the phenotypic testing, the isolate TY-11 demonstrated high antagonistic activity (inhibition zone of 21.33 ± 1.53 mm) against Escherichia coli ATCC 8739 and was not sensitive to any of the 10 tested antibiotics. This study was the first study to explore the molecular insights into probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus.

Importance

This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed transmission electron microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. In our current investigation, we revealed a number of common and unique excellences of the probiotic Lactobacillus delbrueckii subsp. indicus TY-11 that are likely to be important to illustrate its intestinal residence and probiotic roles. This is the first study to explore the molecular insights into intestinal residence and probiotic roles, including antimicrobial activities and antibiotic sensitivity, of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus.\n\nFunctional genomic analysis of the isolated potential probiotic Lactobacillus delbrueckii subsp. indicus TY-11 and its comparison with other Lactobacillus delbrueckii strains.", "token_count": 481, "char_count": 1574, "word_count": 200, "semantic_coherence": 1, "information_density": 0.55, "quality_score": 0.775, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:52.919287", "source": { "split": "train_shard_00001", "doc_id": 1826 }, "chunk_id": "train_shard_00001_1826_1", "global_id": 8232 }, { "text": "Enterococcus belongs to a group of microorganisms known as lactic acid bacteria (LAB), which constitute a broad heterogeneous group of generally food-grade microorganisms historically used in food preservation. Enterococci live as commensals of the gastrointestinal tract of warm-blooded animals, although they also are present in food of animal origin (milk, cheese, fermented sausages), vegetables, and plant materials because of their ability to survive heat treatments and adverse environmental conditions. The biotechnological traits of enterococci can be applied in the food industry; however, the emergence of enterococci as a cause of nosocomial infections makes their food status uncertain. Recent advances in high-throughput sequencing allow the subtyping of bacterial pathogens, but it cannot reflect the temporal dynamics and functional activities of microbiomes or bacterial isolates. Moreover, genetic analysis is based on sequence homologies, inferring functions from databases. Here, we used an end-to-end proteomic workflow to rapidly characterize two bacteriocin-producing Enterococcus faecium (Efm) strains. The proteome analysis was performed with liquid chromatography coupled to a trapped ion mobility spectrometry-time-of-flight mass spectrometry instrument (TimsTOF) for high-throughput and high-resolution characterization of bacterial proteins. Thus, we identified almost half of the proteins predicted in the bacterial genomes (>1100 unique proteins per isolate), including quantifying proteins conferring resistance to antibiotics, heavy metals, virulence factors, and bacteriocins. The obtained proteomes were annotated according to function, resulting in 22 complete KEGG metabolic pathway modules for both strains. The workflow used here successfully characterized these bacterial isolates and showed great promise for determining and optimizing the bioengineering and biotechnology properties of other LAB strains in the food industry.\n\nRapid Proteomic Characterization of Bacteriocin-Producing Enterococcus faecium Strains from Foodstuffs.", "token_count": 477, "char_count": 2079, "word_count": 268, "semantic_coherence": 1, "information_density": 0.7052, "quality_score": 0.8526, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:53.563581", "source": { "split": "train_shard_00001", "doc_id": 1827 }, "chunk_id": "train_shard_00001_1827_0", "global_id": 8233 }, { "text": "Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialog between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon, a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids, and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains' pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.\n\nRoot Exudates Alter the Expression of Diverse Metabolic, Transport, Regulatory, and Stress Response Genes in Rhizosphere Pseudomonas.", "token_count": 481, "char_count": 2027, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:54.213561", "source": { "split": "train_shard_00001", "doc_id": 1828 }, "chunk_id": "train_shard_00001_1828_0", "global_id": 8234 }, { "text": "A simultaneous saccharification fermentation (SSF) system was studied for ethanol production in flour industrial sweetpotato (ISP) feedstocks (lines: white DM02-180 and purple NC-413) as an integrated cost saving process, and to examine the feasibility of extracting anthocyanins from flour purple ISPs under a simultaneous extraction and fermentation (SEF) system. Furthermore, a separate hydrolysis fermentation (SHF) configuration was carried out to establish a baseline in sugar consumption and ethanol production from the ISP lines. The thermotolerant ethanol producing yeast strain Kluyveromyces marxianus NCYC 851 and the mesophilic Saccharomyces cerevisiae Ethanol Red were evaluated, using commercial alpha amylases for hydrolysis of available ISP starch to sugars. Fermentation by S. cerevisiae during SHF had an ethanol yield of 0.32g/g dry ISP, a 1.1-fold increase above that produced by K. marxianus. Subsequent studies showed that ethanol yield could be increased in a SSF system with a maximum ethanol yield of 0.39g/g dry ISP achieved, a 15% increase compared with using a SHF system when S. cerevisiae was used. Simultaneous extraction and fermentation of flour purple-fleshed NC-413 ISPs was studied to evaluate the effect of pH on extraction of total monomeric anthocyanins (TMA) and ethanol production. On average, maximum ethanol yield ranged from 0.31 to 0.34g/g dry ISP and TMA concentration ranged from 45 to 64mg cyanidin-3-glu/100g dry powder (10–22mg/100g fresh weight) with the greatest ethanol production coming from non-adjusted pH fermentations. The highest anthocyanin recovery, 64mg cyanidin-3-glu/100g dry powder was obtained at 35°C and pH 4.5 using S. cerevisiae Ethanol Red", "token_count": 513, "char_count": 1710, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5709, "quality_score": 0.7854, "entities": { "genes": [ "DM02" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:15:54.880669", "source": { "split": "train_shard_00001", "doc_id": 1829 }, "chunk_id": "train_shard_00001_1829_0", "global_id": 8235 }, { "text": "This study showed the feasibility of extracting anthocyanins and producing ethanol simultaneously in one unit operation without the need of purified solvents.\n\nSimultaneous saccharification and fermentation of industrial sweetpotatoes for ethanol production and anthocyanins extraction", "token_count": 62, "char_count": 285, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:55.254315", "source": { "split": "train_shard_00001", "doc_id": 1829 }, "chunk_id": "train_shard_00001_1829_1", "global_id": 8236 }, { "text": "

Objective

Outbreaks of Pseudomonas aeruginosa infections have been linked to water-related sources. We describe the investigation of a suspected outbreak of five P. aeruginosa infections in pediatric oncology patients in 2021 that triggered a retrospective review and prospective monitoring of additional cases, environmental sampling, and bacterial genomic analysis.

Setting and patients

Pediatric oncology center.

Methods

Medical records of patients with P. aeruginosa were reviewed and staff were interviewed to identify common exposures. Environmental samples were cultured for P. aeruginosa. Patient and environmental isolates underwent whole genome sequencing and core genome multi-locus sequence typing (cgMLST) and sequences were added to a previously existing library of P. aeruginosa clinical isolates collected in 2017 and onwards to determine strain relatedness.

Findings

During 2019-2022, 82 patients with 110 episodes of P. aeruginosa infections were identified and 132 isolates of P. aeruginosa were sequenced. Twenty-three environmental samples were collected, of which two grew P. aeruginosa in culture. CgMLST demonstrated four multi-patient isolate clusters but no genetic relatedness among the isolates from the patients in the suspected outbreak. Two sink-derived isolates from 2021 were genetically related to patient-derived isolates from 2018 and 2017.

Conclusions

Sequencing revealed there is no common source or linkage between the isolates of the suspected P. aeruginosa outbreak in 2021. However, it revealed genetic relatedness of previous patient strains to later strains collected from hospital sinks, suggesting persistent colonization of a reservoir with P. aeruginosa.", "token_count": 495, "char_count": 1808, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:55.935896", "source": { "split": "train_shard_00001", "doc_id": 1830 }, "chunk_id": "train_shard_00001_1830_0", "global_id": 8237 }, { "text": "A persistent sink reservoir as a potential source of <i>Pseudomonas aeruginosa</i> infections in pediatric oncology patients.", "token_count": 42, "char_count": 137, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:56.314735", "source": { "split": "train_shard_00001", "doc_id": 1830 }, "chunk_id": "train_shard_00001_1830_1", "global_id": 8238 }, { "text": "

Aims

Developing an innovative process for ethanol fermentation from Jerusalem artichoke tubers under very high gravity (VHG) conditions.

Methods and results

A consolidated bioprocessing (CBP) strategy that integrated inulinase production, saccharification of inulin contained in Jerusalem artichoke tubers and ethanol production from sugars released from inulin by the enzyme was developed with the inulinase-producing yeast Kluyveromyces marxianus Y179 and fed-batch operation. The impact of inoculum age, aeration, the supplementation of pectinase and nutrients on the ethanol fermentation performance of the CBP system was studied. Although inulinase activities increased with the extension of the seed incubation time, its contribution to ethanol production was negligible because vigorously growing yeast cells harvested earlier carried out ethanol fermentation more efficiently. Thus, the overnight incubation that has been practised in ethanol production from starch-based feedstocks is recommended. Aeration facilitated the fermentation process, but compromised ethanol yield because of the negative Crabtree effect of the species, and increases the risk of contamination under industrial conditions. Therefore, nonaeration conditions are preferred for the CBP system. Pectinase supplementation reduced viscosity of the fermentation broth and improved ethanol production performance, particularly under high gravity conditions, but the enzyme cost should be carefully balanced. Medium optimization was performed, and ethanol concentration as high as 94·2 g l(-1) was achieved when 0·15 g l(-1) K(2) HPO(4) was supplemented, which presents a significant progress in ethanol production from Jerusalem artichoke tubers.

Conclusions

A CBP system using K. marxianus is suitable for efficient ethanol production from Jerusalem artichoke tubers under VHG conditions.

Significance and impact of the study

Jerusalem artichoke tubers are an alternative to grain-based feedstocks for ethanol production. The high ethanol concentration achieved using K", "token_count": 506, "char_count": 2077, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5768, "quality_score": 0.7884, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:56.990140", "source": { "split": "train_shard_00001", "doc_id": 1831 }, "chunk_id": "train_shard_00001_1831_0", "global_id": 8239 }, { "text": "marxianus with the CBP system not only saves energy consumption for ethanol distillation, but also significantly reduces the amount of waste distillage discharged from the distillation system.\n\nConsolidated bioprocessing strategy for ethanol production from Jerusalem artichoke tubers by Kluyveromyces marxianus under high gravity conditions.", "token_count": 81, "char_count": 342, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:57.409906", "source": { "split": "train_shard_00001", "doc_id": 1831 }, "chunk_id": "train_shard_00001_1831_1", "global_id": 8240 }, { "text": "Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1T as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1TS), 'Igneacidithiobacillus siniensis' (S30A2T), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 TS), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 TS)", "token_count": 458, "char_count": 1407, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7485, "quality_score": 0.8742, "entities": { "genes": [ "VAN18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:58.057637", "source": { "split": "train_shard_00001", "doc_id": 1832 }, "chunk_id": "train_shard_00001_1832_0", "global_id": 8241 }, { "text": "Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.\n\nAcidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'.", "token_count": 211, "char_count": 894, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:58.517144", "source": { "split": "train_shard_00001", "doc_id": 1832 }, "chunk_id": "train_shard_00001_1832_1", "global_id": 8242 }, { "text": "

Introduction

Sweet sorghum genotypes are distinguished from non-sweet types by their ability to accumulate high concentrations of sugar in their stems, which makes them valuable for both bioenergy production and as an alternative source of sugar. Previous work has reported numerous gene copy number differences in metal metabolism and iron transport genes between the sweet and non-sweet genotypes. The objective of this study was to investigate which genes are differentially expressed by the sweet and non-sweet genotypes under varying iron conditions.

Methods

Three sweet and three non-sweet sorghum genotypes were grown hydroponically under two conditions (control and low iron), and root tissue from the plants was harvested for RNA extraction and sequencing after 9 days. To obtain a more complete picture of diverse iron-response mechanisms in sorghum, we constructed a pan-transcriptome from 10 founder parents of the Carbon-Partitioning Nested Association Mapping population.

Results

Differential expression analysis using the pan-transcriptome revealed 209 genes that responded differently to iron stress in the sweet and non-sweet types, which was more than twice as many genes found using only a single reference genome. Enrichment analysis based on age of duplication event showed that duplicate gene copies that are differentially expressed due to genotype effect appear to be specific to sorghum while most duplicate gene copies that are differentially expressed due to iron treatment appear to be more evolutionary conserved across plants.

Discussion

This study highlights the importance of the non-core genome and the utility of the pan-transcriptome in sorghum. It also revealed that different sorghum genotypes respond to iron stress differently.\n\nUtilizing a pan-transcriptome reveals genotype-specific responses to iron deficiency in Sorghum bicolor", "token_count": 429, "char_count": 1914, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6022, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:59.146602", "source": { "split": "train_shard_00001", "doc_id": 1833 }, "chunk_id": "train_shard_00001_1833_0", "global_id": 8243 }, { "text": "The present paper explores the diversity of mycobiota inhabiting raw milk sampled at different altitudes (1400 m, 1800 m, 2200 m) from cows grazing Alpine pastures of Valle d'Aosta (North-Western Italian Alps). To this aim, multilocus sequencing was performed at barcodes commonly used for fungal identification (ITS1, D1/D2 domains of the 26S rRNA gene, and part of the β-tubulin gene). A total of 31 species were detected, most of them yeasts, followed by moulds and by 2 sequences of macroscopic fungi. Several yeasts and moulds were well-characterized inhabitants of the dairy environment, known to positively contribute to cheesemaking. Among these, Candida was the most represented genus with a tendency to cluster at the highest altitudes (6 over 8 observations at ≥ 1800 m), and Kluyveromyces marxianus the most abundant single species, retrieved at all altitudes. The environmental ascomycetous Atrotorquata lineata, never put in relation with food nor described outside North-America, was another species among those most frequently retrieved and was detected in 6 milks at 1400 and 1800 m. The remaining fungi, in general never reported in milk, were mostly environmental. Many of them resulted associated with plants as pathogens or symbionts. Finally, the highest sampled altitude yielded a significant fungal diversity (17 species). This work enlarges the knowledge of fungal consortia inhabiting raw milk and introduces microbial ecology among the altitude-dependent factors, in the composition of Alpine pastures, with the potential of shaping the properties of milks and cheeses, together with the already described physical, chemical and botanical variables.\n\nDiversity of fungal flora in raw milk from the Italian Alps in relation to pasture altitude.", "token_count": 457, "char_count": 1770, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:15:59.779739", "source": { "split": "train_shard_00001", "doc_id": 1834 }, "chunk_id": "train_shard_00001_1834_0", "global_id": 8244 }, { "text": "

Objective

Multidrug-resistant (MDR) Acinetobacter baumannii is a major issue within healthcare facilities in Bangladesh due to its frequent association with hospital-acquired infections. In this study we report on a carbapenem-resistant draft genome sequence of an A. baumannii BD20 sample isolated from an infected wound in Bangladesh.

Methods

A. baumannii BD20 was isolated from an infected burn wound. Whole-genome sequencing was carried out and annotated using PGAP and Prokka. Sequence type, antimicrobial resistance genes, virulence factor genes, and metal resistance genes were investigated. Core genome multilocus sequence typing-based phylogenomic analysis between A. baumannii BD20 and 213 A. baumannii strains retrieved from the NCBI GenBank database was performed using the BacWGSTdb 2.0 server.

Results

A. baumannii BD20 (MLST 491) was resistant to all the antibiotics tested, except for colistin and polymyxin B. Along with many other antibiotic resistance genes, the isolate harbored three classes of beta lactamase-producing genes: blaGES-11 (class A), blaOXA-69 (class D), blaADC-10 (class C), and blaADC-11 (class C). Additionally, the strain carried several virulence genes and metal resistance determinants, which may contribute to its increased virulence. Core genome MLST-based phylogenomic analysis revealed that A. baumannii BD20 was closely related to another ST491 strain isolated from Singapore.

Conclusions

The findings of this study underscore the growing challenge of MDR A. baumannii, emphasizing the need for vigilant surveillance and infection-control measures in healthcare settings in order to address these emerging threats effectively.", "token_count": 498, "char_count": 1745, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6518, "quality_score": 0.8259, "entities": { "genes": [ "BD20", "ST491" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:00.431331", "source": { "split": "train_shard_00001", "doc_id": 1835 }, "chunk_id": "train_shard_00001_1835_0", "global_id": 8245 }, { "text": "Epidemiological pattern and genomic insights into multidrug-resistant ST491 Acinetobacter baumannii BD20 isolated from an infected wound in Bangladesh: Concerning co-occurrence of three classes of beta lactamase genes.", "token_count": 60, "char_count": 218, "word_count": 27, "semantic_coherence": 1, "information_density": 0.963, "quality_score": 0.9815, "entities": { "genes": [ "BD20", "ST491" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:00.789506", "source": { "split": "train_shard_00001", "doc_id": 1835 }, "chunk_id": "train_shard_00001_1835_1", "global_id": 8246 }, { "text": "Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions", "token_count": 521, "char_count": 1624, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6483, "quality_score": 0.8242, "entities": { "genes": [ "GR8", "TUAT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:01.430155", "source": { "split": "train_shard_00001", "doc_id": 1836 }, "chunk_id": "train_shard_00001_1836_0", "global_id": 8247 }, { "text": "Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.\n\nComparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7.", "token_count": 154, "char_count": 684, "word_count": 90, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:01.863566", "source": { "split": "train_shard_00001", "doc_id": 1836 }, "chunk_id": "train_shard_00001_1836_1", "global_id": 8248 }, { "text": "The availability of multiple sequenced genomes from a single species made it possible to explore intra- and inter-specific genomic comparisons at higher resolution and build clade-specific pangenomes of several crops. The pan-genomes of crops constructed from various cultivars/accessions, landraces, and wild ancestral species represent a compendium of genes and structural variations and allow researchers to search for the novel genes and alleles that were inadvertently lost in domesticated crops during the historical process of crop domestication or in the process of extensive plant breeding. Fortunately, many valuable genes and alleles associated with desirable traits like disease resistance, abiotic stress tolerance, plant architecture, and nutrition qualities exist in landraces, ancestral species, and crop wild relatives. The novels genes from the wild ancestors and landraces can be introduced back to high-yielding varieties of modern crops by implementing classical plant breeding, genomic selection, and transgenic/gene editing approaches. Thus, pan-genomic represents a great leap in plant research and offers new avenues for targeted breeding for mitigating the impact of global climate change. Here we summarize the tools used for pangenome assembly and annotations, web-portals hosting plant pangenomes. Furthermore, we highlight a few discoveries made in crops using the pan-genomic approach and its future potential.\n\nExploring Pan-Genomes of Crops: Genomic Resources and Tools for Unraveling Gene Evolution, Function, and Adaptation", "token_count": 328, "char_count": 1558, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:02.439959", "source": { "split": "train_shard_00001", "doc_id": 1837 }, "chunk_id": "train_shard_00001_1837_0", "global_id": 8249 }, { "text": "

Motivation

Pangenome graphs representing aligned genome assemblies are being shared in the text-based Graphical Fragment Assembly format. As the number of assemblies grows, there is a need for a file format that can store the highly repetitive data space-efficiently.

Results

We propose the GBZ file format based on data structures used in the Giraffe short read aligner. The format provides good compression, and the files can be efficiently loaded into in-memory data structures. We provide compression and decompression tools and libraries for using GBZ graphs, and we show that they can be efficiently used on a variety of systems.

Availability

C++ and Rust implementations are available at https://github.com/jltsiren/gbwtgraph and https://github.com/jltsiren/gbwt-rs , respectively.

Contact

jouni.siren@iki.fi

Supplementary information

Supplementary data are available online.\n\nGBZ File Format for Pangenome Graphs", "token_count": 255, "char_count": 965, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6693, "quality_score": 0.8346, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:02.933398", "source": { "split": "train_shard_00001", "doc_id": 1838 }, "chunk_id": "train_shard_00001_1838_0", "global_id": 8250 }, { "text": "

Background

In 2004-2005, an outbreak of impetigo occurred at a correctional facility during a sentinel outbreak of methicillin- resistant Staphylococcus aureus (MRSA) in Alberta, Canada. Next-generation sequencing (NGS) was used to characterize the group A Streptococcus (GAS) isolates and evaluate whether genomic biomarkers could distinguish between those recovered alone and those co-isolated with S. aureus.

Methods

Superficial wound swabs collected from all adults with impetigo during this outbreak were cultured using standard methods. NGS was used to characterize and compare all of the GAS and S. aureus genomes.

Results

Fifty-three adults were culture positive for GAS, with a subset of specimens also positive for MRSA (n = 5) or methicillin-sensitive S. aureus (n = 3). Seventeen additional MRSA isolates from this facility from the same time frame (no GAS co-isolates) were also included. All 78 bacterial genomes were analyzed for the presence of known virulence factors, plasmids, and antimicrobial resistance (AMR) genes. Among the GAS isolates were 12 emm types, the most common being 41.2 (n = 27; 51%). GAS genomes were phylogenetically compared with local and public datasets of invasive and non-invasive isolates. GAS genomes had diverse profiles for virulence factors, plasmids, and AMR genes. Pangenome analysis did not identify horizontally transferred genes in the co-infection versus single infections.

Conclusions

GAS recovered from invasive and non-invasive sources were not genetically distinguishable", "token_count": 498, "char_count": 1622, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6326, "quality_score": 0.8163, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:03.585427", "source": { "split": "train_shard_00001", "doc_id": 1839 }, "chunk_id": "train_shard_00001_1839_0", "global_id": 8251 }, { "text": "Virulence factors, plasmids, and AMR profiles grouped by emm type, and no genetic changes were identified that predict co-infection or horizontal gene transfer between GAS and S. aureus.\n\nGenomic analysis of group A Streptococcus isolated during a correctional facility outbreak of MRSA in 2004.", "token_count": 94, "char_count": 316, "word_count": 44, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:03.959445", "source": { "split": "train_shard_00001", "doc_id": 1839 }, "chunk_id": "train_shard_00001_1839_1", "global_id": 8252 }, { "text": "Kluyveromyces marxianus is able to transform lactose into ethyl acetate as a bulk product which offers a chance for an economical reuse of whey-borne sugar. Ethyl acetate is highly volatile and allows its process-integrated recovery by stripping from the aerated bioreactor. Extensive formation of ethyl acetate by K. marxianus DSM 5422 required restriction of yeast growth by a lack of trace elements. Several aerobic batch processes were done in a 1-L stirred reactor using whey-borne culture medium supplemented with an individual trace element solution excluding Mn, Mo, Fe, Cu, or Zn for identifying the trace element(s) crucial for the observed ester synthesis. Only a lack of Fe, Cu, or Zn restricted yeast growth while exclusion of Mn and Mo did not exhibit any effect due to a higher amount of the latter in the used whey. Limitation of growth by Fe or Cu caused significant production of ethyl acetate while limitation by Zn resulted in formation of ethanol. A lack of Fe or Cu obviously makes the respiratory chain inefficient resulting in an increased mitochondrial NADH level followed by a reduced metabolic flux of acetyl-SCoA into the citrate cycle. Synthesis of ethyl acetate from acetyl-SCoA and ethanol by alcoholysis is thus interpreted as an overflow metabolism.\n\nFormation of ethyl acetate by Kluyveromyces marxianus on whey during aerobic batch cultivation at specific trace element limitation.", "token_count": 361, "char_count": 1416, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:04.544177", "source": { "split": "train_shard_00001", "doc_id": 1840 }, "chunk_id": "train_shard_00001_1840_0", "global_id": 8253 }, { "text": "A significant amount of literature is available on biocorrosion, which makes manual extraction of crucial information such as genes and proteins a laborious task. Despite the fast growth of biology related corrosion studies, there is a limited number of gene collections relating to the corrosion process (biocorrosion). Text mining offers a potential solution by automatically extracting the essential information from unstructured text. We present a text mining workflow that extracts biocorrosion associated genes/proteins in sulfate-reducing bacteria (SRB) from literature databases (e.g., PubMed and PMC). This semi-automatic workflow is built with the Named Entity Recognition (NER) method and Convolutional Neural Network (CNN) model. With PubMed and PMCID as inputs, the workflow identified 227 genes belonging to several Desulfovibrio species. To validate their functions, Gene Ontology (GO) enrichment and biological network analysis was performed using UniprotKB and STRING-DB, respectively. The GO analysis showed that metal ion binding, sulfur binding, and electron transport were among the principal molecular functions. Furthermore, the biological network analysis generated three interlinked clusters containing genes involved in metal ion binding, cellular respiration, and electron transfer, which suggests the involvement of the extracted gene set in biocorrosion. Finally, the dataset was validated through manual curation, yielding a similar set of genes as our workflow; among these, hysB and hydA, and sat and dsrB were identified as the metal ion binding and sulfur metabolism genes, respectively. The identified genes were mapped with the pangenome of 63 SRB genomes that yielded the distribution of these genes across 63 SRB based on the amino acid sequence similarity and were further categorized as core and accessory gene families. SRB's role in biocorrosion involves the transfer of electrons from the metal surface via a hydrogen medium to the sulfate reduction pathway. Therefore, genes encoding hydrogenases and cytochromes might be participating in removing hydrogen from the metals through electron transfer", "token_count": 502, "char_count": 2177, "word_count": 305, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "respiration" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:05.202281", "source": { "split": "train_shard_00001", "doc_id": 1841 }, "chunk_id": "train_shard_00001_1841_0", "global_id": 8254 }, { "text": "Moreover, the production of corrosive sulfide from the sulfur metabolism indirectly contributes to the localized pitting of the metals. After the corroboration of text mining results with SRB biocorrosion mechanisms, we suggest that the text mining framework could be utilized for genes/proteins extraction and significantly reduce the manual curation time.\n\nText-Mining to Identify Gene Sets Involved in Biocorrosion by Sulfate-Reducing Bacteria: A Semi-Automated Workflow.", "token_count": 120, "char_count": 474, "word_count": 64, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:05.593833", "source": { "split": "train_shard_00001", "doc_id": 1841 }, "chunk_id": "train_shard_00001_1841_1", "global_id": 8255 }, { "text": "The contribution of Debaryomyces hansenii, Kluyveromyces lactis and Kluyveromyces marxianus strains to the typical flavour of traditional ewes' and goats' cheeses was assessed. Fourteen yeast strains were grown in liquid medium mimicking cheese composition and volatile compounds were identified by gas chromatography-mass spectrometry. Yeasts were able to produce key volatile compounds characteristic of the cheeses from which they were isolated. Inter-species and inter-strain variations were observed. Under the conditions tested, D. hansenii produced the lowest levels of volatile compounds, with large intra-strain variations. Kluyveromyces strains primarily produced esters and alcohols. K. marxianus strains were associated with the production of acids, ethyl decanoate, 1-propanol and benzaldehyde, whereas K. lactis was correlated with the presence of ketones, ethyl acetate and secondary alcohols. In conclusion, this study shows the heterogeneous potential of dairy yeasts to contribute to final cheese flavour.\n\nPotential impact of dairy yeasts on the typical flavour of traditional ewes' and goats' cheeses", "token_count": 283, "char_count": 1120, "word_count": 152, "semantic_coherence": 1, "information_density": 0.5987, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:06.159689", "source": { "split": "train_shard_00001", "doc_id": 1842 }, "chunk_id": "train_shard_00001_1842_0", "global_id": 8256 }, { "text": "Probiotics, like lactic acid bacteria, are non-pathogenic microbes that exert health benefits to the host when administered in adequate quantity. Currently, research is being conducted on the molecular events and applications of probiotics. The suggested mechanisms by which probiotics exert their action include; competitive exclusion of pathogens for adhesion sites, improvement of the intestinal mucosal barrier, gut immunomodulation, and neurotransmitter synthesis. This review emphasizes the recent advances in the health benefits of probiotics and the emerging applications of probiotics in the food industry. Due to their capability to modulate gut microbiota and attenuate the immune system, probiotics could be used as an adjuvant in hypertension, hypercholesterolemia, cancer, and gastrointestinal diseases. Considering the functional properties, probiotics are being used in the dairy, beverage, and baking industries. After developing the latest techniques by researchers, probiotics can now survive within harsh processing conditions and withstand GI stresses quite effectively. Thus, the potential of probiotics can efficiently be utilized on a commercial scale in food processing industries.\n\nProbiotics: mechanism of action, health benefits and their application in food industries.", "token_count": 279, "char_count": 1298, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:06.720318", "source": { "split": "train_shard_00001", "doc_id": 1843 }, "chunk_id": "train_shard_00001_1843_0", "global_id": 8257 }, { "text": "

ABSTRACT

Through horizontal gene transfer, closely related bacterial strains have assimilated distinct sets of genes, resulting in significantly varied lifestyles. However, it is not clear how strains are able to properly regulate horizontally transferred virulence genes. We hypothesized that strains may use components of the core genome to regulate diverse horizontally acquired genes. To investigate how closely related bacteria assimilate and activate horizontally acquired DNA, we used a model of Pseudomonas fluorescens subspecies brassicacearum strains, N2E2 and N2C3, which exhibit contrasting lifestyles on the model plant Arabidopsis. P. brassicacearum strain N2E2 is a plant commensal and contains the genes that encode biosynthetic enzymes for the anti-fungal compound 2,4-Diacetylphloroglucinol (DAPG). In contrast, N2C3 lacks DAPG biosynthesis and has gained a pathogenic island encoding syringomycin (SYR)-and syringopeptin (SYP)-like toxins from the plant pathogen P. syringae. This causes a transition in lifestyle from plant-protective N2E2 to plant pathogenic N2C3. We found that N2E2 and N2C3 share a highly conserved two-component system GacA/S, a known regulator of DAPG and SYR/SYP. Using knockout mutations, we found that a ΔgacA mutation resulted in loss of expression of SYR/SYP virulence genes and returned pathogenic N2C3 to a plant commensal lifestyle. Our study further explored the conservation of regulatory control across strains by demonstrating that GacA genes from both distant and closely related Pseudomonas strains could functionally complement one another across the genus.

IMPORTANCE

Emerging pathogens represent a significant threat to humans, agriculture, and natural ecosystems. Bacterial horizontal gene transfer aids in the acquisition of novel genes that facilitate bacterial adaptation to new environments. Our work shows a novel role for GacA in orchestrating the regulatory changes necessary for virulence and lifestyle transitions facilitated by HGT", "token_count": 515, "char_count": 2019, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6223, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:07.377775", "source": { "split": "train_shard_00001", "doc_id": 1844 }, "chunk_id": "train_shard_00001_1844_0", "global_id": 8258 }, { "text": "These findings suggest that the GacA/S system plays a key role in mediating transitions across diverse Pseudomonas symbiotic lifestyles. It provides insights into the mechanisms that drive the emergence of pathogenic strains and highlights potential targets for managing bacterial threats to plant health.\n\nGacA regulates symbiosis and mediates lifestyle transitions in Pseudomonas", "token_count": 90, "char_count": 388, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:07.792950", "source": { "split": "train_shard_00001", "doc_id": 1844 }, "chunk_id": "train_shard_00001_1844_1", "global_id": 8259 }, { "text": "Tripeptide glutathione, which plays important roles in many cellular mechanisms, is also a biotechnology-oriented molecule with applications in medicine, food and cosmetic. Here, the engineering of the yeast Yarrowia lipolytica for the production of this metabolite at high titer values from various agro-industrial by-products is reported. The constitutive overexpression of the glutathione biosynthetic genes GSH1 and GSH2 encoding respectively γ-glutamylcysteine synthetase and glutathione synthetase, together with the INU1 gene from Kluyveromyces marxianus encoding inulinase yielded a glutathione titer value and a productivity of 644 nmol/mg protein and 510 µmol/gDCW, respectively. These values were obtained during bioreactor batch cultures in a medium exclusively comprising an extract of Jerusalem artichoke tuber, used as a source of inulin, and ammonium sulfate, used as a nitrogen source.\n\nEngineering Yarrowia lipolytica for the Synthesis of Glutathione from Organic By-Products.", "token_count": 312, "char_count": 1047, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7015, "quality_score": 0.8507, "entities": { "genes": [ "GSH1", "INU1", "GSH2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:08.376655", "source": { "split": "train_shard_00001", "doc_id": 1845 }, "chunk_id": "train_shard_00001_1845_0", "global_id": 8260 }, { "text": "In this work, an alternative matrix for probiotics delivery constituted by whey proteins and polysaccharide kefiran was investigated. Edible transparent and homogeneous films containing the microorganisms Lactobacillus paracasei CIDCA 8339 and Kluyveromyces marxianus CIDCA 8154 with probiotic characteristics have been developed. Inclusion of microorganisms did not modify thickness, color or mechanical characteristics of films. This matrix showed good capability protecting the included probiotics from stress during film obtaining process and through gastrointestinal passage simulation. At the end of the applied gastrointestinal tract model, 7.1.105 CFU/cm2K. marxianus CIDCA 8154 and 1.65.107 CFU/cm2L. paracasei CIDCA 8339 remain viable, having decreased less than 0.6 logarithm cycle with respect to those originally included, even after 57 days of films storage.\n\nWhey protein-kefiran films as driver of probiotics to the gut", "token_count": 263, "char_count": 935, "word_count": 126, "semantic_coherence": 1, "information_density": 0.754, "quality_score": 0.877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:08.955001", "source": { "split": "train_shard_00001", "doc_id": 1846 }, "chunk_id": "train_shard_00001_1846_0", "global_id": 8261 }, { "text": "Xylulokinase is one of the key enzymes in xylose metabolism and fermentation, and fine-tuned expression of xylulokinase can improve xylose fermentation in yeast. To improve the efficiency of xylose fermentation in Kluyveromyces marxianus, the gene KmXYL3, which encodes a D: -xylulokinase (E.C. 2.7.1.17), was isolated from K. marxianus NBRC1777. KmXYL3 was expressed in Escherichia coli BL21 (DE3) cells, and the specific activity of the resulting recombinant purified xylulokinase was 23.5 mU/mg. Disruption of KmXYL3 resulted in both loss of xylitol utilization and marked decrease in xylose utilization, proving that KmXYL3 encodes a xylulokinase that catalyzes the reaction from xylulose to xylulose 5-phosphate in the xylose metabolic pathway. The slow assimilation of xylose observed in the KmXYL3-disrupted strain indicates that KmXYL3 is critical for xylose and xylitol utilization; however, K. marxianus utilizes a bypass pathway for xylose assimilation, and this pathway does not involve xylitol or xylulose.\n\nIdentification of a xylulokinase catalyzing xylulose phosphorylation in the xylose metabolic pathway of Kluyveromyces marxianus NBRC1777.", "token_count": 393, "char_count": 1158, "word_count": 162, "semantic_coherence": 1, "information_density": 0.5617, "quality_score": 0.7809, "entities": { "genes": [ "BL21", "DE3", "NBRC1777" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:09.594343", "source": { "split": "train_shard_00001", "doc_id": 1847 }, "chunk_id": "train_shard_00001_1847_0", "global_id": 8262 }, { "text": "Cheese whey fermentation with Kluyveromyces marxianus was carried out at 40 °C and pH 3.5 to examine simultaneous single-cell protein production and chemical oxygen demand (COD) removal, determine the fate of soluble whey protein and characterize intermediate metabolites. After 36 h of batch fermentation, the biomass concentration increased from 2.0 to 6.0 g/L with 55 % COD reduction (including protein), whereas soluble whey protein concentration decreased from 5.6 to 4.1 g/L. It was confirmed through electrophoresis (SDS-PAGE) that the fermented whey protein was different from native whey protein. HPLC and GC-MS analysis revealed a change in composition of organic compounds post-fermentation. High inoculum concentration in batch fermentation resulted in an increase in biomass concentration from 10.3 to 15.9 g/L with 80 % COD reduction (including protein) within 36 h with residual protein concentration of 4.5 g/L. In third batch fermentation, the biomass concentration increased from 7.3 to 12.4 g/L with 71 % of COD removal and residual protein concentration of 4.3 g/L after 22 h. After 22 h, the batch process was shifted to a continuous process with cell recycle, and the steady state was achieved after another 60 h with biomass yield of 0.19 g biomass/g lactose and productivity of 0.26 g/L h. COD removal efficiency was 78-79 % with residual protein concentration of 3.8-4.2 g/L. The aerobic continuous fermentation process with cell recycle could be applied to single-cell protein production with substantial COD removal at low pH and high temperature from cheese whey.\n\nSimultaneous single-cell protein production and COD removal with characterization of residual protein and intermediate metabolites during whey fermentation by K. marxianus.", "token_count": 483, "char_count": 1765, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5038, "quality_score": 0.7519, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:10.246413", "source": { "split": "train_shard_00001", "doc_id": 1848 }, "chunk_id": "train_shard_00001_1848_0", "global_id": 8263 }, { "text": "The ability of Leptospirae to persist in environments and animal hosts but to cause clinically highly variable disease in humans has made leptospirosis the most common zoonotic disease. Considering the paucity of data on variation in complete genomes of human pathogenic Leptospirae, we have used a combination of Single Molecule Real-Time (SMRT) and Illumina sequencing to obtain complete genome sequences of six human clinical L. interrogans isolates from Malaysia. All six contained the larger (4.28-4.56 Mb) and smaller (0.34-0.395 Mb) chromosome typical of human pathogenic Leptospirae and 0-7 plasmids. Only 24% of the plasmid sequences could be matched to databases. We identified a chromosomal core genome of 3318 coding sequences and strain-specific accessory genomes of 49-179 coding sequences. These sequences enabled detailed genomic strain typing (Genome BLAST Distance Phylogeny, DNA-DNA hybridization, and multi locus sequence typing) and phylogenetic classification (whole-genome SNP genotyping). Even though there was some shared synteny and collinearity across the six genomes, there was evidence of major genome rearrangement, likely driven by horizontal gene transfer and homologous recombination. Mobile genetic elements were identified in all strains in highly varying numbers, including in the rfb locus, which defines serogroups and contributes to immune escape and pathogenesis. On the other hand, there was high conservation of virulence-associated genes including those relating to sialic acid, alginate, and lipid A biosynthesis. These findings suggest (i) that the antigenic variation, adaption to various host environments, and broad spectrum of virulence of L. interrogans are in part due to a high degree of genomic plasticity and (ii) that human pathogenic strains maintain a core set of genes required for virulence.", "token_count": 482, "char_count": 1871, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6704, "quality_score": 0.8352, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:10.896814", "source": { "split": "train_shard_00001", "doc_id": 1849 }, "chunk_id": "train_shard_00001_1849_0", "global_id": 8264 }, { "text": "Complete Genome Sequencing of Leptospira interrogans Isolates from Malaysia Reveals Massive Genome Rearrangement but High Conservation of Virulence-Associated Genes.", "token_count": 49, "char_count": 172, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:11.254665", "source": { "split": "train_shard_00001", "doc_id": 1849 }, "chunk_id": "train_shard_00001_1849_1", "global_id": 8265 }, { "text": "

Motivation

Pangenome variation graphs model the mutual alignment of collections of DNA sequences. A set of pairwise alignments implies a variation graph, but there are no scalable methods to generate such a graph from these alignments. Existing related approaches depend on a single reference, a specific ordering of genomes, or a de Bruijn model based on a fixed k -mer length. A scalable, self-contained method to build pangenome graphs without such limitations would be a key step in pangenome construction and manipulation pipelines.

Results

We design the seqwish algorithm, which builds a variation graph from a set of sequences and alignments between them. We first transform the alignment set into an implicit interval tree. To build up the variation graph, we query this tree-based representation of the alignments to reduce transitive matches into single DNA segments in a sequence graph. By recording the mapping from input sequence to output graph, we can trace the original paths through this graph, yielding a pangenome variation graph. We present an implementation that operates in external memory, using disk-backed data structures and lock-free parallel methods to drive the core graph induction step. We demonstrate that our method scales to very large graph induction problems by applying it to build pangenome graphs for several species.

Availability

seqwish is published as free software under the MIT open source license. Source code and documentation are available at https://github.com/ekg/seqwish . seqwish can be installed via Bioconda https://bioconda.github.io/recipes/seqwish/README.html or GNU Guix https://github.com/ekg/guix-genomics/blob/master/seqwish.scm .

Contact

egarris5@uthsc.edu\n\nUnbiased pangenome graphs", "token_count": 421, "char_count": 1780, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6305, "quality_score": 0.8153, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:11.881316", "source": { "split": "train_shard_00001", "doc_id": 1850 }, "chunk_id": "train_shard_00001_1850_0", "global_id": 8266 }, { "text": "Species belonging to the Mycobacterium kansasii complex (MKC) are frequently isolated from humans and the environment and can cause serious diseases. The most common MKC infections are caused by the species M. kansasii (stricto sensu), leading to tuberculosis-like disease. However, a broad spectrum of virulence, antimicrobial resistance and pathogenicity of these non-tuberculous mycobacteria (NTM) are observed across the MKC. Many genomic aspects of the MKC that relate to these broad phenotypes are not well elucidated. Here, we performed genomic analyses from a collection of 665 MKC strains, isolated from environmental, animal and human sources. We inferred the MKC pangenome, mobilome, resistome, virulome and defense systems and show that the MKC species harbors unique and shared genomic signatures. High frequency of presence of prophages and different types of defense systems was observed. We found that the M. kansasii species splits into four lineages, of which three are lowly represented and mainly in Brazil, while one lineage is dominant and globally spread. Moreover, we show that four sub-lineages of this most distributed M. kansasii lineage emerged during the 20th century. Further analysis of the M. kansasii genomes revealed almost 300 regions of difference contributing to genomic diversity, as well as fixed mutations that may explain the M. kansasii's increased virulence and drug resistance.\n\nPhylogenomic and genomic analysis reveals unique and shared genetic signatures of Mycobacterium kansasii complex species", "token_count": 378, "char_count": 1543, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:12.827279", "source": { "split": "train_shard_00001", "doc_id": 1851 }, "chunk_id": "train_shard_00001_1851_0", "global_id": 8267 }, { "text": "

Background

As complete and accurate genome sequences are becoming easier to obtain, more researchers wish to get one or more of them to support their research endeavors. Reliable and well-documented sequence assembly workflows find use in reference or pangenome projects.

Results

We describe modifications to the TRITEX genome assembly workflow motivated by the rise of fast and easy long-read contig assembly of inbred plant genomes and the routine deployment of the toolchains in pangenome projects. New features include the use as surrogates of or complements to dense genetic maps and the introduction of user-editable tables to make the curation of contig placements easier and more intuitive.

Conclusion

Even maximally contiguous sequence assemblies of the telomere-to-telomere sort, and to a yet greater extent, the fragmented kind require validation, correction, and comparison to reference standards. As pangenomics is burgeoning, these tasks are bound to become more widespread and TRITEX is one tool to get them done. This technical guide is supported by a step-by-step computational tutorial accessible under https://tritexassembly.bitbucket.io/ . The TRITEX source code is hosted under this URL: https://bitbucket.org/tritexassembly .\n\nA technical guide to TRITEX, a computational pipeline for chromosome-scale sequence assembly of plant genomes.", "token_count": 327, "char_count": 1381, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6138, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:13.396837", "source": { "split": "train_shard_00001", "doc_id": 1852 }, "chunk_id": "train_shard_00001_1852_0", "global_id": 8268 }, { "text": "The genus Geobacillus is abundant in ecological diversity and is also well-known as an authoritative source for producing various thermostable enzymes. Although it is clear now that Geobacillus evolved from Bacillus, relatively little knowledge has been obtained regarding its evolutionary mechanism, which might also contribute to its ecological diversity and biotechnology potential. Here, a statistical comparison of thirty-two Geobacillus genomes was performed with a specific focus on pan- and core genomes. The pan-genome of this set of Geobacillus strains contained 14,913 genes, and the core genome contained 940 genes. The Clusters of Orthologous Groups (COG) and Carbohydrate-Active Enzymes (CAZymes) analysis revealed that the Geobacillus strains had huge potential industrial application in composting for agricultural waste management. Detailed comparative analyses showed that basic functional classes and housekeeping genes were conserved in the core genome, while genes associated with environmental interaction or energy metabolism were more enriched in the pan-genome. Therefore, the evolution of Geobacillus seems to be guided by environmental parameters. In addition, horizontal gene transfer (HGT) events among different Geobacillus species were detected. Altogether, pan-genome analysis was a useful method for detecting the evolutionary mechanism, and Geobacillus' evolution was directed by the environment and HGT events.\n\nPan-Genome Analyses of Geobacillus spp. Reveal Genetic Characteristics and Composting Potential.", "token_count": 420, "char_count": 1613, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:14.022694", "source": { "split": "train_shard_00001", "doc_id": 1853 }, "chunk_id": "train_shard_00001_1853_0", "global_id": 8269 }, { "text": "Carbapenem and colistin-resistant Klebsiella pneumoniae pose a significant threat to public health, particularly in intensive care units, due to high morbidity and mortality rates. This study aimed to analyze five NDM carbapenemase-producing multidrug-resistant K. pneumoniae isolates from different hospitals. Antimicrobial susceptibility testing, hypermucoviscosity analysis, biofilm production assessment, MLST, PCR, and whole-genome sequencing were conducted. All isolates harbored NDM-5 metallo-β-lactamase, belonging to MLST 307, were biofilm producers and exhibited a stop codon (Q30) along MgrB. Genomic analysis revealed multiple-replicon plasmids carrying resistance genes, notably blaNDM-5, blaCTX-M-15, rmtB, and qnrB1, with complex genetic structures encoding several mobile genetic elements, including the Tn3 family and IS26. All isolates harbored wzi173 (capsule-locus KL102), iutA (a siderophore-associated gene), and the type 3 fimbriae mrkABCDFHIJ operon. The core genome single nucleotide polymorphisms (SNPs) analysis suggests the circulation of two strains of ST307 clone (SNPs range differences 4-77). These findings highlight the potential plasticity of the high-risk ST307 clone and the urgent need for surveillance and intervention strategies to combat antimicrobial resistance. To our knowledge, this is the first report of K. pneumoniae ST307 carrying blaNDM-5 and the first description of ST307 in Uruguay", "token_count": 484, "char_count": 1544, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7487, "quality_score": 0.8743, "entities": { "genes": [ "IS26", "ST307", "KL102" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:14.673655", "source": { "split": "train_shard_00001", "doc_id": 1854 }, "chunk_id": "train_shard_00001_1854_0", "global_id": 8270 }, { "text": "The presence of blaNDM-5 and pan-aminoglycoside resistance rmtB genes are identified for the first time in Uruguay.\n\nEmergence of Multidrug-Resistant NDM-5-Producing ST307 <i>Klebsiella pneumoniae</i> in Uruguay, 2023.", "token_count": 107, "char_count": 255, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [ "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:15.048888", "source": { "split": "train_shard_00001", "doc_id": 1854 }, "chunk_id": "train_shard_00001_1854_1", "global_id": 8271 }, { "text": "Pseudomonas aeruginosa is a leading cause of infections in immunocompromised individuals and in healthcare settings. This study aims to understand the relationships between phenotypic diversity and the functional metabolic landscape of P. aeruginosa clinical isolates. To better understand the metabolic repertoire of P. aeruginosa in infection, we deeply profiled a representative set from a library of 971 clinical P. aeruginosa isolates with corresponding patient metadata and bacterial phenotypes. The genotypic clustering based on whole-genome sequencing of the isolates, multi-locus sequence types, and the phenotypic clustering generated from a multi-parametric analysis were compared to each other to assess the genotype-phenotype correlation. Genome-scale metabolic network reconstructions were developed for each isolate through amendments to an existing PA14 network reconstruction. These network reconstructions show diverse metabolic functionalities and enhance the collective P. aeruginosa pangenome metabolic repertoire. Characterizing this rich set of clinical P. aeruginosa isolates allows for a deeper understanding of the genotypic and metabolic diversity of the pathogen in a clinical setting and lays a foundation for further investigation of the metabolic landscape of this pathogen and host-associated metabolic differences during infection.

Impact statement

Pseudomonas aeruginosa is a leading cause of infections in immunocompromised individuals and in healthcare settings. The treatment of these infections is complicated by the presence of a variety of virulence mechanisms and metabolic uniqueness among clinically relevant strains. This study is an attempt to understand the relationships between isolate phenotypic diversity and the functional metabolic landscape within a representative group of P. aeruginosa clinical isolates. Characterizing this rich set of clinical P. aeruginosa isolates allows for a deeper understanding of genotypic and metabolic diversity of the pathogen in a clinical setting and lays a foundation for further investigation of the metabolic landscape of this pathogen and host-associated metabolic differences in infection.\n\nModel-driven characterization of functional diversity ofPseudomonas aeruginosaclinical isolates with broadly representative phenotypes", "token_count": 511, "char_count": 2332, "word_count": 305, "semantic_coherence": 1, "information_density": 0.4131, "quality_score": 0.7066, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:15.679508", "source": { "split": "train_shard_00001", "doc_id": 1855 }, "chunk_id": "train_shard_00001_1855_0", "global_id": 8272 }, { "text": "

Purpose

This study aimed to investigate the distribution and characteristics of high-risk, difficult-to-treat resistant Pseudomonas aeruginosa (DTR-PA) sequence type (ST) 463 in intensive care units (ICUs) in East China.

Patients and methods

This 11-month study investigated Carbapenem-resistant Pseudomonas aeruginosa (CRPA) in patients and environments across four ICUs in a large teaching hospital in East China. It involved whole-genome sequencing, antibiotic susceptibility testing, and biofilm-forming ability testing of all the isolates. Molecular epidemiology and phylogenetic relationships were assessed using multi-locus sequence typing (MLST) and core genome multi-locus sequence typing (cgMLST). Bacterial virulence was evaluated using Galleria mellonella infection model.

Results

A total of 54 CRPA were isolated from the environment and inpatients in ICUs and classified into 25 STs, with ST463 identified as the predominant ST (13/54, 24.07%). All 13 ST463 PA isolates belonged to DTR-PA, including 4 from patients and 9 from environments primarily from wastewater dumping pools. All ST463-DTR-PA isolates carried bla KPC-2 and exhibited exoU+/exoS+ virulence genotype. There were 3 KPC-ST463-DTR-PA additionally carried bla AFM-1, resulting in resistance to last-resort antibiotics. ST463-DTR-PA had higher biofilm-forming ability and mortality in infected larvae than non-ST463-DTR-PA. Both clinical and environmental strains showed high virulence", "token_count": 484, "char_count": 1550, "word_count": 188, "semantic_coherence": 1, "information_density": 0.7181, "quality_score": 0.859, "entities": { "genes": [ "ST463" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:16.337186", "source": { "split": "train_shard_00001", "doc_id": 1856 }, "chunk_id": "train_shard_00001_1856_0", "global_id": 8273 }, { "text": "CgMLST results revealed that several ST463-DTR-PA isolated from different ICUs were genetically related.

Conclusion

KPC-ST463-DTR-PA can widely colonize in ICU environment. Contamination and incomplete disinfection in humid environments may provide evolutionary opportunities for ST463-DTR-PA. Hence, it's worth our vigilance about the growing prevalence of ST463-DTR-PA in East China's ICUs. Meanwhile, it is important to strengthen the management of the ICU environment, especially water reservoirs, and even to promote the management of patients without water.\n\nEnvironmental Persistence of High-Risk KPC-Producing ST463 <i>Pseudomonas aeruginosa</i> in Intensive Care Units in East China.", "token_count": 201, "char_count": 711, "word_count": 87, "semantic_coherence": 1, "information_density": 0.8161, "quality_score": 0.908, "entities": { "genes": [ "ST463" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:16.798025", "source": { "split": "train_shard_00001", "doc_id": 1856 }, "chunk_id": "train_shard_00001_1856_1", "global_id": 8274 }, { "text": "

Summary

A Wheeler graph represents a collection of strings in a way that is particularly easy to index and query. Such a graph is a practical choice for representing a graph-shaped pangenome, and it is the foundation for current graph-based pangenome indexes. However, there are no practical tools to visualize or to check graphs that may have the Wheeler properties. Here we present Wheelie , an algorithm that combines a renaming heuristic with a permutation solver ( Wheelie-PR ) or a Satisfiability Modulo Theory (SMT) solver ( Wheelie-SMT ) to check whether a given graph has the Wheeler properties, a problem that is NP complete in general. Wheelie can check a variety of random and real-world graphs in far less time than any algorithm proposed to date. It can check a graph with 1,000s of nodes in seconds. We implement these algorithms together with complementary visualization tools in the WGT toolkit, available as open source software at https://github.com/Kuanhao-Chao/Wheeler_Graph_Toolkit .\n\nWGT: Tools and algorithms for recognizing, visualizing and generating Wheeler graphs", "token_count": 270, "char_count": 1100, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6294, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:17.360160", "source": { "split": "train_shard_00001", "doc_id": 1857 }, "chunk_id": "train_shard_00001_1857_0", "global_id": 8275 }, { "text": "Bacteria of the genus Brucella are facultative intracellular parasites that cause brucellosis, a severe animal and human disease. Recently, a group of taxonomists merged the brucellae with the primarily free-living, phylogenetically related Ochrobactrum spp. in the genus Brucella. This change, founded only on global genomic analysis and the fortuitous isolation of some opportunistic Ochrobactrum spp. from medically compromised patients, has been automatically included in culture collections and databases. We argue that clinical and environmental microbiologists should not accept this nomenclature, and we advise against its use because (i) it was presented without in-depth phylogenetic analyses and did not consider alternative taxonomic solutions; (ii) it was launched without the input of experts in brucellosis or Ochrobactrum; (iii) it applies a non-consensus genus concept that disregards taxonomically relevant differences in structure, physiology, population structure, core-pangenome assemblies, genome structure, genomic traits, clinical features, treatment, prevention, diagnosis, genus description rules, and, above all, pathogenicity; and (iv) placing these two bacterial groups in the same genus creates risks for veterinarians, medical doctors, clinical laboratories, health authorities, and legislators who deal with brucellosis, a disease that is particularly relevant in low- and middle-income countries. Based on all this information, we urge microbiologists, bacterial collections, genomic databases, journals, and public health boards to keep the Brucella and Ochrobactrum genera separate to avoid further bewilderment and harm.\n\nIf You're Not Confused, You're Not Paying Attention: <i>Ochrobactrum</i> Is Not Brucella.", "token_count": 444, "char_count": 1787, "word_count": 231, "semantic_coherence": 1, "information_density": 0.7056, "quality_score": 0.8528, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:17.999211", "source": { "split": "train_shard_00001", "doc_id": 1858 }, "chunk_id": "train_shard_00001_1858_0", "global_id": 8276 }, { "text": "

Background

Healthcare-associated wastewater and asymptomatic patient reservoirs colonized by carbapenemase-producing Enterobacterales (CPE) contribute to nosocomial CPE dissemination, but the characteristics and dynamics of this remain unclear.

Methods

We systematically sampled wastewater sites (n = 4488 samples; 349 sites) and patients (n = 1247) across six wards over 6-12 months to understand blaKPC-associated CPE (KPC-E) diversity within these reservoirs and transmission in a healthcare setting. Up to five KPC-E-positive isolates per sample were sequenced (Illumina). Recombination-adjusted phylogenies were used to define genetically related strains; assembly and mapping-based approaches were used to characterize antimicrobial resistance genes, insertion sequences (ISs) and Tn4401 types/target site sequences. The accessory genome was evaluated in some of the largest clusters, and those crossing reservoirs.

Results

Wastewater site KPC-E-positivity was substantial [101/349 sites (28.9%); 228/5601 (4.1%) patients cultured]. Thirteen KPC-E species and 109 strains were identified using genomics, and 24% of wastewater and 26% of patient KPC-E-positive samples harboured one or more strains. Most diversity was explained by the individual niche, suggesting localized factors are important in selection and spread. Tn4401 + flanking target site sequence diversity was greater in wastewater sites (P < 0.001), which might favour Tn4401-associated transposition/evolution", "token_count": 474, "char_count": 1556, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7433, "quality_score": 0.8717, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:18.646010", "source": { "split": "train_shard_00001", "doc_id": 1859 }, "chunk_id": "train_shard_00001_1859_0", "global_id": 8277 }, { "text": "Shower/bath- and sluice/mop-associated sites were more likely to be KPC-E-positive (adjusted OR = 2.69; 95% CI: 1.44-5.01; P = 0.0019; and adjusted OR = 2.60; 95% CI: 1.04-6.52; P = 0.0410, respectively). Different strains had different blaKPC dissemination dynamics.

Conclusions

We identified substantial and diverse KPC-E colonization of wastewater sites and patients in this hospital setting. Reservoir and niche-specific factors (e.g. microbial interactions, selection pressures), and different strains and mobile genetic elements likely affect transmission dynamics. This should be considered in surveillance and control strategies.\n\nGenomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of bla KPC-carbapenemase-producing Enterobacterales in a hospital setting.", "token_count": 282, "char_count": 903, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:19.194935", "source": { "split": "train_shard_00001", "doc_id": 1859 }, "chunk_id": "train_shard_00001_1859_1", "global_id": 8278 }, { "text": "The ubiquitous inflammophilic pathobiont Fusobacterium nucleatum is widely recognized for its strong association with a variety of human dysbiotic diseases such as periodontitis and oral/extraoral abscesses, as well as multiple types of cancer . F. nucleatum is currently subdivided into four subspecies: F. nucleatum subspecies nucleatum ( Fn. nucleatum ) , animalis ( Fn. animalis), polymorphum ( Fn. polymorphum ), and vincentii/fusiforme ( Fn. vincentii ). Although these subspecies have been historically considered as functionally interchangeable in the oral cavity, direct clinical evidence is largely lacking for this assertion. Consequently, we assembled a collection of oral clinical specimens to determine whether F. nucleatum subspecies prevalence in the oral cavity stratifies by local oral health status. Patient-matched clinical specimens of both disease-free dental plaque and odontogenic abscess were analyzed with newly developed culture-dependent and culture-independent approaches using 44 and 60 oral biofilm/tooth abscess paired specimens, respectively. Most oral cavities were found to simultaneously harbor multiple F. nucleatum subspecies, with a greater diversity present within dental plaque compared to abscesses. In dental plaque, Fn. polymorphum is clearly the dominant organism, but this changes dramatically within odontogenic abscesses where Fn. animalis is heavily favored over all other fusobacteria. Surprisingly, the most commonly studied F. nucleatum subspecies, Fn. nucleatum, is only a minor constituent in the oral cavity. To gain further insights into the genetic basis for these phenotypes, we subsequently performed pangenome, phylogenetic, and functional enrichment analyses of oral fusobacterial genomes using the Anvi’o platform, which revealed significant genotypic distinctions among F. nucleatum subspecies. Accordingly, our results strongly support a taxonomic reassignment of each F. nucleatum subspecies into distinct Fusobacterium species. Of these, Fn. animalis should be considered as the most clinically relevant at sites of active inflammation, despite being among the least characterized oral fusobacteria.", "token_count": 533, "char_count": 2165, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:19.883791", "source": { "split": "train_shard_00001", "doc_id": 1860 }, "chunk_id": "train_shard_00001_1860_0", "global_id": 8279 }, { "text": "The prevalence ofFusobacterium nucleatumsubspecies in the oral cavity stratifies by local health status", "token_count": 32, "char_count": 110, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:20.276063", "source": { "split": "train_shard_00001", "doc_id": 1860 }, "chunk_id": "train_shard_00001_1860_1", "global_id": 8280 }, { "text": "

Background

The prevention of vancomycin-resistant Enterococcus faecium (VREfm) infections and transmissions poses a major challenge to hospitals. Vancomycin resistance can be plasmid encoded; however, as the analysis of plasmids is challenging, so far only a few reports have provided a detailed characterization of plasmids in nosocomial VREfm transmission. Here we describe a nosocomial VREfm outbreak caused by a vanA positive ST80 isolate. vanA plasmid sequence data was used to distinguish outbreak-associated isolates from sporadic VREfm cases and to investigate the spread of this plasmid within the local VREfm population.

Methods

446 VREfm isolates were collected from routine surveillance between 01/2022 and 02/2024 and analyzed using long-read whole genome sequencing (lrWGS). Genetic relatedness of isolates was evaluated based on core genome multilocus sequence typing (cgMLST). Genetically similar vanA plasmids were identified using a Mash based approach.

Results

30 genetically similar VREfm isolates were identified in patients' screening and environmental samples. Infection control evaluation confirmed transmission through shared hospital rooms. All outbreak-related VREfm isolates, including environmental samples, carried a highly similar vanA plasmid (Mash distance of < 0.001) with an identical replicon type. After enhanced infection control measures were established, no new transmissions were detected. Comparison with additional VREfm isolates from the respective department showed no evidence for further plasmid transmission.

Conclusions

Our study illustrates how vanA plasmid analysis can support the evaluation of VREfm transmission in hospitals. The outbreak-associated vanA plasmids were genetically highly similar, but could be clearly distinguished from other vanA plasmids in the local hospital population. Taken together, detailed analysis of hospital-associated vanA plasmids can improve our understanding of VREfm transmission and epidemiology.", "token_count": 482, "char_count": 2014, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8081, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:20.947070", "source": { "split": "train_shard_00001", "doc_id": 1861 }, "chunk_id": "train_shard_00001_1861_0", "global_id": 8281 }, { "text": "Characterization of vanA-harboring plasmids supports differentiation of outbreak-related and sporadic vancomycin-resistant Enterococcus faecium isolates in a tertiary care hospital.", "token_count": 49, "char_count": 181, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:21.361390", "source": { "split": "train_shard_00001", "doc_id": 1861 }, "chunk_id": "train_shard_00001_1861_1", "global_id": 8282 }, { "text": "Rodents and bats are the most diverse mammal group that host Bartonella species. In the Americas, they were described as harboring Bartonella species; however, they were mostly characterized to the genotypic level. We describe here Bartonella isolates obtained from blood samples of one rodent (Peromyscus yucatanicus from San José Pibtuch, Yucatan) and two bat species (Desmodus rotundus from Progreso, and Pteronotus parnellii from Chamela-Cuitzmala) from Mexico. We sequenced and described the genomic features of three Bartonella strains and performed phylogenomic and pangenome analyses to decipher their phylogenetic relationships. The mouse-associated genome was closely related to Bartonella vinsonii. The two bat-associated genomes clustered into a single distinct clade in between lineages 3 and 4, suggesting to be an ancestor of the rodent-associated Bartonella clade (lineage 4). These three genomes showed <95% OrthoANI values compared to any other Bartonella genome, and therefore should be considered as novel species. In addition, our analyses suggest that the B. vinsonii complex should be revised, and all B. vinsonii subspecies need to be renamed and considered as full species. The phylogenomic clustering of the bat-associated Bartonella strains and their virulence factor profile (lack of the Vbh/TraG conjugation system remains of the T4SS) suggest that it should be considered as a new lineage clade (L5) within the Bartonella genus.\n\nGenomic Characterization of Three Novel Bartonella Strains in a Rodent and Two Bat Species from Mexico.", "token_count": 505, "char_count": 1668, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5921, "quality_score": 0.7961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:22.017458", "source": { "split": "train_shard_00001", "doc_id": 1862 }, "chunk_id": "train_shard_00001_1862_0", "global_id": 8283 }, { "text": "

Background

Aliarcobacter butzleri is a Gram-negative, curved or spiral-shaped, microaerophilic bacterium and causes human infections, specifically diarrhea, fever, and sepsis. The research objective of this study was to employ computer-aided drug design techniques to identify potential natural product inhibitors of a vital enzyme in this bacterium. The pyrimidine biosynthesis pathway in its core genome fraction is crucial for its survival and presents a potential target for novel therapeutics. Hence, novel small molecule inhibitors were identified (from traditional Chinese medicinal (TCM) compound library) against it, which may be used for possible curbing of infection by A. butzleri. Methods. A comprehensive subtractive genomics approach was utilized to identify a key enzyme (orotidine-5'-phosphate decarboxylase) cluster conserved in the core genome fraction of A. butzleri. It was selected for inhibitor screening due to its vital role in pyrimidine biosynthesis. TCM library (n > 36,000 compounds) was screened against it using pharmacophore model based on orotidylic acid (control), and the obtained lead-like molecules were subjected to structural docking using AutoDock Vina. The top-scoring compounds, ZINC70454134, ZINC85632684, and ZINC85632721, underwent further scrutiny via a combination of physiological-based pharmacokinetics, toxicity assessment, and atomic-scale dynamics simulations (100 ns).

Results

Among the screened compounds, ZINC70454134 displayed the most favorable characteristics in terms of binding, stability, absorption, and safety parameters", "token_count": 461, "char_count": 1626, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [ "ZINC85632684", "ZINC70454134", "ZINC85632721" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:22.657086", "source": { "split": "train_shard_00001", "doc_id": 1863 }, "chunk_id": "train_shard_00001_1863_0", "global_id": 8284 }, { "text": "Overall, traditional Chinese medicine (TCM) compounds exhibited high bioavailability, but in diseased states (cirrhosis, renal impairment, and steatosis), there was a significant decrease in absorption, Cmax, and AUC of the compounds compared to the healthy state. Furthermore, MD simulation demonstrated that the ODCase-ZINC70454134 complex had a superior overall binding affinity, supported by PCA proportion of variance and eigenvalue rank analysis. These favorable characteristics underscore its potential as a promising drug candidate.

Conclusion

The computer-aided drug design approach employed for this study helped expedite the discovery of antibacterial compounds against A. butzleri, offering a cost-effective and efficient approach to address infection by it. It is recommended that ZINC70454134 should be considered for further experimental analysis due to its indication as a potential therapeutic agent for combating A. butzleri infections. This study provides valuable insights into the molecular basis of biophysical inhibition of A. butzleri through TCM compounds.\n\nExploring Lead-Like Molecules of Traditional Chinese Medicine for Treatment Quest against Aliarcobacter butzleri: In Silico Toxicity Assessment, Dynamics Simulation, and Pharmacokinetic Profiling.", "token_count": 332, "char_count": 1321, "word_count": 166, "semantic_coherence": 1, "information_density": 0.753, "quality_score": 0.8765, "entities": { "genes": [ "ZINC70454134" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:23.220320", "source": { "split": "train_shard_00001", "doc_id": 1863 }, "chunk_id": "train_shard_00001_1863_1", "global_id": 8285 }, { "text": "

Introduction

Porcine brucellosis, caused by Brucella suis biovar 2, is currently the only type of brucellosis officially reported in farm animals in Germany, with outbreaks confirmed through direct pathogen detection. In most European countries, this bacterial pathogen is also found in wild animals, which are considered reservoirs for the disease. Since 2003, 22 outbreaks of porcine brucellosis have been reported in Germany.

Methods

A comprehensive study was conducted on German B. suis biovar 2 isolates obtained from routine diagnostic investigations of domestic pigs and wildlife. The dataset included isolates from 18 reported outbreaks. The aim was to assess epidemiological links and the genomic diversity of the bacterium. B. suis biovar 2 isolates were subjected to whole-genome sequencing (WGS) and analyzed using multilocus sequence typing (MLST), core genome MLST, and single-nucleotide polymorphism (SNP) analysis.

Results

Three different MLST sequence types were identified and further subdivided into eight clusters. This approach conclusively confirmed officially reported primary and secondary outbreaks caused by the sale of infected animals. In individual cases, remarkable similarities were found between domestic and wild animal isolates, that is, differing by only 2-4 nucleotides. This similarity suggests brucellosis transmission events. Both wild boars and hares can be considered reservoirs of Brucella spp. infections, including brucellosis. In Northern Germany, persistent B. suis biovar 2 foci were detected, as well as transmission across Germany and potentially to other European countries. Notably, hare isolates varied significantly from the majority of German wild boar and domestic pig isolates.

Discussion

As most brucellosis outbreaks occurred in outdoor holdings, reliable monitoring of these herds is recommended, although the exposure of these animals to external factors (e.g., vectors) poses a challenge. However, it is imperative in light of the increase in organic free-range and pasture farming, which promotes direct or indirect contact with wild animals.", "token_count": 526, "char_count": 2168, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6495, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:23.876280", "source": { "split": "train_shard_00001", "doc_id": 1864 }, "chunk_id": "train_shard_00001_1864_0", "global_id": 8286 }, { "text": "Genomic epidemiology of <i>Brucella suis</i> biovar 2 in German swine and wildlife, 2003-2023.", "token_count": 49, "char_count": 106, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:24.238198", "source": { "split": "train_shard_00001", "doc_id": 1864 }, "chunk_id": "train_shard_00001_1864_1", "global_id": 8287 }, { "text": "Recurrent respiratory infections (RRI) are an intriguing challenge for both otolaryngologists and paediatricians. Therefore, to prevent RRI is an ambitious target in clinical practice. In this regard, modulation of the immune system may have a critical role. Sinerga, a dietary supplement (containing: palmitoylethanolamide (PEA), Kluyveromyces marxianus B0399, bovine colostrum, and phenylalanine), was supplemented in 20 allergic children with RRI (20/30 days per 3 months) and treated with standard therapy (antihistamine plus intranasal corticosteroid). Other 20 allergic children with RRI were treated only with standard therapy. Sinerga significantly reduced the number of RI and the size of both inferior and middle turbinate consistently with the postulated mechanisms of action. In conclusion, the current study demonstrated that Sinerga supplementation in allergic children with RRI may significantly prevent RI and reduce events depending on allergic inflammation.\n\nSinerga may prevent recurrent respiratory infections in allergic children.", "token_count": 266, "char_count": 1058, "word_count": 142, "semantic_coherence": 1, "information_density": 0.662, "quality_score": 0.831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:24.790067", "source": { "split": "train_shard_00001", "doc_id": 1865 }, "chunk_id": "train_shard_00001_1865_0", "global_id": 8288 }, { "text": "During host colonization, plant pathogenic fungi secrete proteins, called effectors, to facilitate infection. Collectively, effectors may defeat the plant immune system, but usually not all effectors are equally important for infecting a particular host plant. In Fusarium oxysporum f.sp. lycopersici , all known effector genes – also called SIX genes – are located on a single accessory chromosome which is required for pathogenicity and can also be horizontally transferred to another strain. To narrow down the minimal region required for virulence, we selected partial pathogenicity chromosome deletion strains by fluorescence-assisted cell sorting of a strain in which the two arms of the pathogenicity chromosome were labelled with GFP and RFP , respectively. By testing the virulence of these deletion mutants, we show that the complete long arm and part of the short arm of the pathogenicity chromosome are not required for virulence. In addition, we demonstrate that smaller versions of the pathogenicity chromosome can also be transferred to a non-pathogenic strain and they are sufficient to turn the non-pathogen into a pathogen. Surprisingly, originally non-pathogenic strains that had received a smaller version of the pathogenicity chromosome were much more aggressive than recipients with a complete pathogenicity chromosome. Whole genome sequencing analysis revealed that partial deletions of the pathogenicity chromosome occurred mainly close to repeats, and that spontaneous duplication of sequences in accessory regions is frequent both in chromosome deletion strains and in horizontal transfer (recipient) strains.

Author Summary

Fungal genomes can often be divided into a core genome, which is essential for growth, and an accessory genome which is dispensable. The accessory genome in fungi can be beneficial under some conditions. For example, in some plant-pathogenic fungi, virulence genes are present in the accessory genome, which enable these fungi to cause disease on certain hosts. In Fusarium oxysporum f.sp. lycopersici , which infects tomato, all host-specific virulence genes are located on a single accessory chromosome. This ‘pathogenicity chromosome’ can be horizontally transferred between strains", "token_count": 522, "char_count": 2245, "word_count": 324, "semantic_coherence": 1, "information_density": 0.5247, "quality_score": 0.7623, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:25.448538", "source": { "split": "train_shard_00001", "doc_id": 1866 }, "chunk_id": "train_shard_00001_1866_0", "global_id": 8289 }, { "text": "Here, we found that many suspected virulence genes are in fact not required for virulence because strains without a large part of the pathogenicity chromosome, including these genes, showed no reduced virulence. In addition, we demonstrate that partial pathogenicity chromosomes can be horizontally transferred to a non-pathogen. Surprisingly, originally non-pathogenic strains that had received a partial pathogenicity chromosome were more virulent than strains that had received the complete pathogenicity chromosome.\n\nA partial pathogenicity chromosome inFusarium oxysporumis sufficient to cause disease and can be horizontally transferred", "token_count": 152, "char_count": 649, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6941, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:25.882861", "source": { "split": "train_shard_00001", "doc_id": 1866 }, "chunk_id": "train_shard_00001_1866_1", "global_id": 8290 }, { "text": "Guayule rubber production leaves >80% biomass as ground bagasse, which can be hydrolyzed to release sugars but also fermentation inhibitors. Here inhibitor generation and sugar conversion by the CO2-H2O pretreatment and enzyme hydrolysis were studied. Different pretreatment conditions: 550-4900 psi, 160-195 °C, 10-60 min and fixed 66.7% water, generated widely varying amounts of inhibitors (per dry-bagasse mass): 0.014-0.252% hydroxymethylfurfural, 0.012-0.794% furfural and 0.17-8.02% acetic acid. The condition (195 °C/3400 psi/30 min) giving highest reducing sugar (86.9 ± 1.5%) and cellulose (99.2 ± 1.3%) conversions generated more inhibitors. Kluyveromyces marxianus fermentation showed complete growth and ethanol production inhibition at ≥14 g/L combined inhibitors. Considering both sugars and inhibitors, the optimum condition was 180 °C, 1800 psi and 30 min, enabling 82.8 ± 2.8% reducing sugar, 74.8 ± 4.8% cellulose and 88.5 ± 6.9% hemicellulose conversions with low levels of hydroxymethylfurfural (0.07%), furfural (0.25%) and acetic acid (3.0%). The optimized CO2-H2O pretreatment gave much lower inhibitor formation and higher sugar conversion than other pretreatment methods.", "token_count": 495, "char_count": 1241, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7607, "quality_score": 0.8804, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:26.529104", "source": { "split": "train_shard_00001", "doc_id": 1867 }, "chunk_id": "train_shard_00001_1867_0", "global_id": 8291 }, { "text": "Minimization of fermentation inhibitor generation by carbon dioxide-water based pretreatment and enzyme hydrolysis of guayule biomass.", "token_count": 36, "char_count": 134, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:26.880774", "source": { "split": "train_shard_00001", "doc_id": 1867 }, "chunk_id": "train_shard_00001_1867_1", "global_id": 8292 }, { "text": "The ability of Kluyveromyces marxianus to convert lactose into ethyl acetate offers a chance for an economic reuse of whey. Former experiments with K. marxianus DSM 5422 proved limitation of growth by iron (Fe) or copper as a precondition for significant ester synthesis. Several aerobic batch and chemostat cultivations were done with whey-borne media of a variable Fe content for exploring the effect of Fe on growth, the Fe content of biomass, and metabolite synthesis. At low Fe doses, Fe was the growth-limiting factor, the available Fe was completely absorbed by the yeasts, and the biomass formation linearly depended on the Fe dose governed by a minimum Fe content in the yeasts, x (Fe,min). At batch conditions, x (Fe,min) was 8.8 μg/g, while during chemostat cultivation at D = 0.15 h(-1), it was 23 μg/g. At high Fe doses, sugar was the growth-limiting factor, Fe was more or less absorbed, and the formed biomass became constant. Significant amounts of ethyl acetate were only formed at Fe limitation while high Fe doses suppressed ester formation. Analysis of formed metabolites such as glycerol, pyruvate, acetate, ethanol, ethyl acetate, isocitrate, 2-oxoglutarate, succinate, and malate during chemostat cultivation allowed some interpretation of the Fe-dependent mechanism of ester synthesis; formation of ethyl acetate from acetyl-SCoA and ethanol is obviously initiated by a diminished metabolic flux of acetyl-SCoA into the citrate cycle and by a limited oxidation of NADH in the respiratory chain since Fe is required for the function of aconitase, succinate dehydrogenase, and the electron-transferring proteins.\n\nFormation of ethyl acetate by Kluyveromyces marxianus on whey during aerobic batch and chemostat cultivation at iron limitation.", "token_count": 497, "char_count": 1796, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5444, "quality_score": 0.7722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:27.530982", "source": { "split": "train_shard_00001", "doc_id": 1868 }, "chunk_id": "train_shard_00001_1868_0", "global_id": 8293 }, { "text": "Whole genome sequencing (WGS) and data concerning identity and safety for Saccharomyces cerevisiae CBS 493.94 are reported. This strain was isolated from a British brewery in 1958 and deposited at the CBS culture collection Westerdijk Fungal Biodiversity Institute under the accession number CBS 493.94. The long-reads sequencing data, obtained via PacBio Sequel, and short-reads data, via Illumina NovaSeq 6000, were deposited at NCBI under accession number PRJNA1044661. The hybrid assembly was made publicly available via Zenodo and NCBI. For strain identification, data from 18S rRNA, ANI dendrogram and Core Genome single nucleotide polymorphism (SNP) Tree showed that the present isolate belongs to the genus Saccharomyces, species cerevisiae. The potential genes of concern, e.g. antimycotic resestance genes, were not detected. This strain is commonly used as a feed additive for animal health improvement and the present data summarise the unambiguous identity and strain's FKS1 gene does not code for any amino acid variants of concern.\n\nGenome sequence data of Saccharomyces cerevisiae CBS 493.94.", "token_count": 333, "char_count": 1136, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6914, "quality_score": 0.8457, "entities": { "genes": [ "FKS1", "PRJNA1044661" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:28.107617", "source": { "split": "train_shard_00001", "doc_id": 1869 }, "chunk_id": "train_shard_00001_1869_0", "global_id": 8294 }, { "text": "The major histocompatibility complex (MHC) is a region of the human genome that is key to immune system function but sometimes refractory to genomic analyses due to extreme polymorphism and structural variation. We performed targeted long-read sequencing and de novo assembly of MHC to create 246 highly accurate, fully contiguous, and phased full-length sequences, mostly from data provided by the Human Pangenome Reference Consortium (HPRC). We identified alleles at high resolution across 39 loci including the class I and II HLA (human leukocyte antigen) genes, discovering 1,246 putative novel allele sequences. We identified copy number variation in the C4A and C4B genes and found significant linkage disequilibrium between C4A∼C4B haplotypes and 14 MHC loci. We build our sequences into a novel “pan-MHC” reference graph, and we demonstrate that this improves the accuracy of short-read variant calling. Our haplotypes and graph contain significantly more population diversity than preexisting MHC sequences, thus improving the prospects for global health equity in this clinically important genomic region.\n\nA pan-MHC reference graph with 246 fully contiguous phased sequences", "token_count": 286, "char_count": 1185, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7399, "quality_score": 0.8699, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:28.662609", "source": { "split": "train_shard_00001", "doc_id": 1870 }, "chunk_id": "train_shard_00001_1870_0", "global_id": 8295 }, { "text": "High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.", "token_count": 497, "char_count": 1631, "word_count": 226, "semantic_coherence": 1, "information_density": 0.646, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:29.309164", "source": { "split": "train_shard_00001", "doc_id": 1871 }, "chunk_id": "train_shard_00001_1871_0", "global_id": 8296 }, { "text": "Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes.", "token_count": 47, "char_count": 137, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:29.664757", "source": { "split": "train_shard_00001", "doc_id": 1871 }, "chunk_id": "train_shard_00001_1871_1", "global_id": 8297 }, { "text": "Industrial microbes have become the core of biological manufacturing, which utilized as the cell factory for production of plenty of chemicals, fuels and medicine. However, the challenge that the extreme stress conditions exist in production is unavoidable for cell factory. Consequently, to enhance robustness of the chassis cell lays the foundation for development of bio-manufacturing. Currently, the researches on cell tolerance covered various aspects, involving reshaping regulatory network, cell membrane modification and other stress response. In fact, the strategies employed to improve cell robustness could be summarized into two directions, irrational engineering and rational engineering. In this review, the metabolic engineering technologies on enhancement of microbe tolerance to industrial conditions are summarized. Meanwhile, the novel thoughts emerged with the development of biological instruments and synthetic biology are discussed.\n\nAdvance of tolerance engineering on microbes for industrial production.", "token_count": 188, "char_count": 1028, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:30.114932", "source": { "split": "train_shard_00001", "doc_id": 1872 }, "chunk_id": "train_shard_00001_1872_0", "global_id": 8298 }, { "text": "Acanthamoeba triangularis strain SH 621 is a free-living amoeba belonging to Acanthamoeba ribo-genotype T4. This ubiquitous protist is among the free-living amoebas responsible for Acanthamoeba keratitis, a severe infection of human cornea. Genome sequencing and genomic comparison were carried out to explore the biological functions and to better understand the virulence mechanism related to the pathogenicity of Acanthamoeba keratitis. The genome assembly harbored a length of 66.43 Mb encompassing 13,849 scaffolds. The analysis of predicted proteins reported the presence of 37,062 ORFs. A complete annotation revealed 33,168 and 16,605 genes that matched with NCBI non-redundant protein sequence (nr) and Cluster of Orthologous Group of proteins (COG) databases, respectively. The Kyoto Encyclopedia of Genes and Genomes Pathway (KEGG) annotation reported a great number of genes related to carbohydrate, amino acid and lipid metabolic pathways. The pangenome performed with 8 available amoeba genomes belonging to genus Acanthamoeba revealed a core genome containing 843 clusters of orthologous genes with a ratio core genome/pangenome of less than 0.02. We detected 48 genes related to virulent factors of Acanthamoeba keratitis. Best hit analyses in nr database identified 99 homologous genes shared with amoeba-resisting microorganisms. This study allows the deciphering the genome of a free-living amoeba with medical interest and provides genomic data to better understand virulence-related Acanthamoeba keratitis.\n\nDescription of Virulent Factors and Horizontal Gene Transfers of Keratitis-Associated Amoeba Acanthamoeba Triangularis by Genome Analysis.", "token_count": 514, "char_count": 1716, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:30.742043", "source": { "split": "train_shard_00001", "doc_id": 1873 }, "chunk_id": "train_shard_00001_1873_0", "global_id": 8299 }, { "text": "The bacterial pan-genome consists of core genes shared by all members of a taxonomy and accessory genes found in only a subset. The correlation among genes within the pan-genome could advance our understanding of evolution and tackle medical challenges. Here, we discovered a strong intra-genomic correlation among bacterial pan-genes within each of Escherichia coli , Listeria monocytogenes , Staphylococcus aureus , and Campylobacter jejuni . With a convolutional neural network assisted core genome knock-out simulation, we found that different combinations of fewer than 20 highly variable core genes could recover the sub-species type classified by complete core genome with accuracy >95%. This observation led us to test the genes-to-genes predictability: with more than 52,000 assemblies from each species, combinations of highly variable core genes could predict the sequence variants of other core genes (average accuracy >94%) within the same genome and could also predict sequence variants (average accuracy >91%) as well as the presence (average AUROC >0.91) of some accessory genes. Furthermore, combinations of highly variable core genes could also predict multiple antibiotic resistances (AUROC >0.80) in large published datasets of E. coli , S. aureus , and Mycobacterium tuberculosis . Collectively, we propose that genes within the same genome can strongly correlate with each other. Therefore, the strain phylogeny and the status of other genes could be uniformly represented by combinations of highly variable core genes, which could further represent certain phenotypes including in vitro resistance.\n\nIntra-genomic genes-to-genes correlation enables bacterial genome representation", "token_count": 394, "char_count": 1703, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5574, "quality_score": 0.7787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:31.939050", "source": { "split": "train_shard_00001", "doc_id": 1874 }, "chunk_id": "train_shard_00001_1874_0", "global_id": 8300 }, { "text": "Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from metagenomic (i.e., multispecies) samples, including those from the human microbiome. In this study, methods are presented to obtain complete bacterial genomes from human saliva using complementary Oxford Nanopore (ONT) and Illumina sequencing. Applied to 3 human saliva samples, these methods resulted in 11 complete bacterial genomes: 3 Saccharibacteria clade G6 (also known as Ca. Nanogingivalaceae HMT-870), 1 Saccharibacteria clade G1 HMT-348, 2 Rothia mucilaginosa, 2 Actinomyces graevenitzii, 1 Mogibacterium diversum, 1 Lachnospiraceae HMT-096, and 1 Lancefieldella parvula; and one circular chromosome of Ruminococcaceae HMT-075 (which likely has at least 2 chromosomes). The 4 Saccharibacteria genomes, as well as the Actinomyces graeventizii genomes, represented the first complete genomes from their respective bacterial taxa. Aside from the complete genomes, the assemblies contained 147 contigs of over 500,000 bp each and thousands of smaller contigs, together representing a myriad of additional draft genomes including many which are likely nearly complete. The complete genomes enabled highly accurate pangenome analysis, which identified unique and missing features of each genome compared to its closest relatives with complete genomes available in public repositories. These features provide clues as to the lifestyle and ecological role of these bacteria within the human oral microbiota, which will be particularly useful in designing future studies of the taxa that have never been isolated or cultivated", "token_count": 498, "char_count": 1823, "word_count": 250, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:32.625333", "source": { "split": "train_shard_00001", "doc_id": 1875 }, "chunk_id": "train_shard_00001_1875_0", "global_id": 8301 }, { "text": "IMPORTANCE Obtaining complete and accurate genomes is crucial to the study of any organism. Previously, obtaining complete genomes of bacteria, including those of the human microbiome, frequently required isolation of the organism, as well as low-throughput, manual sequencing methods to resolve repeat regions. Advancements in long-read sequencing technologies, including Oxford Nanopore (ONT), have made it possible to obtain complete, closed bacterial genomes from metagenomic samples. This study reports methods to obtain complete genomes from the human oral microbiome using complementary ONT and Illumina sequencing of saliva samples. Eleven complete genomes were obtained from 3 human saliva samples, with genomes of Saccharibacteria HMT-870, Saccharibacteria HMT-348, and Actinomyces graeventzii being the first complete genomes from their respective taxa. Obtaining complete bacterial genomes in a high-throughput manner will help illuminate the metabolic and ecological roles of important members of the human microbiota, particularly those that have remained recalcitrant to isolation and cultivation.\n\nUsing Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples.", "token_count": 301, "char_count": 1225, "word_count": 160, "semantic_coherence": 1, "information_density": 0.5813, "quality_score": 0.7906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:33.219435", "source": { "split": "train_shard_00001", "doc_id": 1875 }, "chunk_id": "train_shard_00001_1875_1", "global_id": 8302 }, { "text": "

Background

Drug treatments and vaccine designs against the opportunistic human pathogen Pseudomonas aeruginosa have multiple issues, all associated with the diverse genetic traits present in this pathogen, ranging from multi-drug resistant genes to the molecular machinery for the biosynthesis of biofilms. Several candidate vaccines against P. aeruginosa have been developed, which target the outer membrane proteins; however, major issues arise when attempting to establish complete protection against this pathogen due to its presumably genotypic variation at the strain level. To shed light on this concern, we proposed this study to assess the P. aeruginosa pangenome and its molecular evolution across multiple strains.

Results

The P. aeruginosa pangenome was estimated to contain more than 16,000 non-redundant genes, and approximately 15% of these constituted the core genome. Functional analyses of the accessory genome indicated a wide presence of genetic elements directly associated with pathogenicity. An in-depth molecular evolution analysis revealed the full landscape of selection forces acting on the P. aeruginosa pangenome, in which purifying selection drives evolution in the genome of this human pathogen. We also detected distinctive positive selection in a wide variety of outer membrane proteins, with the data supporting the concept of substantial genetic variation in proteins probably recognized as antigens. Approaching the evolutionary information of genes under extremely positive selection, we designed a new Multi-Locus Sequencing Typing assay for an informative, rapid, and cost-effective genotyping of P. aeruginosa clinical isolates.

Conclusions

We report the unprecedented pangenome characterization of P. aeruginosa on a large scale, which included almost 200 bacterial genomes from one single species and a molecular evolutionary analysis at the pangenome scale. Evolutionary information presented here provides a clear explanation of the issues associated with the use of protein conjugates from pili, flagella, or secretion systems as antigens for vaccine design, which exhibit high genetic variation in terms of non-synonymous substitutions in P. aeruginosa strains.", "token_count": 489, "char_count": 2234, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5987, "quality_score": 0.7994, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:33.883473", "source": { "split": "train_shard_00001", "doc_id": 1876 }, "chunk_id": "train_shard_00001_1876_0", "global_id": 8303 }, { "text": "Pangenome-wide and molecular evolution analyses of thePseudomonas aeruginosa species", "token_count": 26, "char_count": 91, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:34.238584", "source": { "split": "train_shard_00001", "doc_id": 1876 }, "chunk_id": "train_shard_00001_1876_1", "global_id": 8304 }, { "text": "To improve inulin utilization and ethanol fermentation, exoinulinase genes from the yeast Kluyveromyces marxianus and the recently identified yeast, Candida kutaonensis, were expressed in Saccharomyces cerevisiae. S. cerevisiae harboring the exoinulinase gene from C. kutaonensis gave higher ethanol yield and productivity from both inulin (0.38 vs. 0.34 g/g and 1.35 vs. 1.22 g l⁻¹ h⁻¹) and Jerusalem artichoke tuber flour (0.47 vs. 0.46 g/g and 1.62 vs. 1.54 g l⁻¹ h⁻¹) compared with the strain expressing the exoinulinase gene from K. marxianus. Thus, the exoinulinase gene from C. kutaonensis is advantageous for engineering S. cerevisiae to improve ethanol fermentation from inulin sources.\n\nExpression of exoinulinase genes in Saccharomyces cerevisiae to improve ethanol production from inulin sources", "token_count": 275, "char_count": 807, "word_count": 116, "semantic_coherence": 1, "information_density": 0.5948, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:34.798204", "source": { "split": "train_shard_00001", "doc_id": 1877 }, "chunk_id": "train_shard_00001_1877_0", "global_id": 8305 }, { "text": "Metabiotics are the structural components of probiotic bacteria, functional metabolites, and/or signaling molecules with numerous beneficial properties. A novel Lactococcus lactis strain, UTNCys6-1, was isolated from wild Amazonian camu-camu fruits (Myrciaria dubia), and various functional metabolites with antibacterial capacity were found. The genome size is 2,226,248 base pairs, and it contains 2248 genes, 2191 protein-coding genes (CDSs), 50 tRNAs, 6 rRNAs, 1 16S rRNA, 1 23S rRNA, and 1 tmRNA. The average GC content is 34.88%. In total, 2148 proteins have been mapped to the EggNOG database. The specific annotation consisted of four incomplete prophage regions, one CRISPR-Cas array, six genomic islands (GIs), four insertion sequences (ISs), and four regions of interest (AOI regions) spanning three classes of bacteriocins (enterolysin_A, nisin_Z, and sactipeptides). Based on pangenome analysis, there were 6932 gene clusters, of which 751 (core genes) were commonly observed within the 11 lactococcal strains. Among them, 3883 were sample-specific genes (cloud genes) and 2298 were shell genes, indicating high genetic diversity. A sucrose transporter of the SemiSWEET family (PTS system: phosphoenolpyruvate-dependent transport system) was detected in the genome of UTNCys6-1 but not the other 11 lactococcal strains. In addition, the metabolic profile, antimicrobial susceptibility, and inhibitory activity of both protein-peptide extract (PPE) and exopolysaccharides (EPSs) against several foodborne pathogens were assessed in vitro", "token_count": 487, "char_count": 1563, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7757, "quality_score": 0.8879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:35.442932", "source": { "split": "train_shard_00001", "doc_id": 1878 }, "chunk_id": "train_shard_00001_1878_0", "global_id": 8306 }, { "text": "Furthermore, UTNCys6-1 was predicted to be a non-human pathogen that was unable to tolerate all tested antibiotics except gentamicin; metabolized several substrates; and lacks virulence factors (VFs), genes related to the production of biogenic amines, and acquired antibiotic resistance genes (ARGs). Overall, this study highlighted the potential of this strain for producing bioactive metabolites (PPE and EPSs) for agri-food and pharmaceutical industry use.\n\nMetabiotics Signature through Genome Sequencing and In Vitro Inhibitory Assessment of a Novel Lactococcus lactis Strain UTNCys6-1 Isolated from Amazonian Camu-Camu Fruits.", "token_count": 177, "char_count": 640, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8118, "quality_score": 0.9059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:35.880300", "source": { "split": "train_shard_00001", "doc_id": 1878 }, "chunk_id": "train_shard_00001_1878_1", "global_id": 8307 }, { "text": "

ABSTRACT

Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62-1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62-1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12 and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain “polysaccharide niches”. Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans . Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization. Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.", "token_count": 512, "char_count": 1952, "word_count": 242, "semantic_coherence": 1, "information_density": 0.7107, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:36.515039", "source": { "split": "train_shard_00001", "doc_id": 1879 }, "chunk_id": "train_shard_00001_1879_0", "global_id": 8308 }, { "text": "CAZymes inMaribacter dokdonensis62-1 from the Patagonian shelf: Genomics and physiology compared to related flavobacteria and a co-occurringAlteromonasstrain", "token_count": 61, "char_count": 171, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:36.889714", "source": { "split": "train_shard_00001", "doc_id": 1879 }, "chunk_id": "train_shard_00001_1879_1", "global_id": 8309 }, { "text": "Ustilago maydis is an important plant pathogen that causes corn smut disease and serves as an effective biotechnological production host. The lack of a comprehensive metabolic overview hinders a full understanding of the organism's environmental adaptation and a full use of its metabolic potential. Here, we report the first genome-scale metabolic model (GSMM) of Ustilago maydis (iUma22) for the simulation of metabolic activities. iUma22 was reconstructed from sequencing and annotation using PathwayTools, and the biomass equation was derived from literature values and from the codon composition. The final model contains over 25% annotated genes (6909) in the sequenced genome. Substrate utilization was corrected by BIOLOG phenotype arrays, and exponential batch cultivations were used to test growth predictions. The growth data revealed a decrease in glucose uptake rate with rising glucose concentration. A pangenome of four different U. maydis strains highlighted missing metabolic pathways in iUma22. The new model allows for studies of metabolic adaptations to different environmental niches as well as for biotechnological applications.\n\nUstilago maydis Metabolic Characterization and Growth Quantification with a Genome-Scale Metabolic Model.", "token_count": 324, "char_count": 1285, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6534, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:37.461357", "source": { "split": "train_shard_00001", "doc_id": 1880 }, "chunk_id": "train_shard_00001_1880_0", "global_id": 8310 }, { "text": "Mycobacterium abscessus is a multidrug resistant bacterium that causes pulmonary and extrapulmonary disease. The reported prevalence of pulmonary M. abscessus infections appears to be increasing in the United States (US) and around the world. In the last five years, multiple studies have utilized whole genome sequencing to investigate the genetic epidemiology of two clinically relevant subspecies, M. abscessus subsp. abscessus (MAB) and M. abscessus subsp. massiliense (MMAS). Phylogenomic comparisons of clinical isolates revealed that substantial proportions of patients have MAB and MMAS isolates that belong to genetically similar clusters also known as 'dominant clones'. Unlike the genetic lineages of Mycobacterium tuberculosis that tend to be geographically clustered, the MAB and MMAS clones have been found in clinical populations from the US, Europe, Australia and South America. Moreover, the clones have been associated with worse clinical outcomes and show increased pathogenicity in macrophage and mouse models. While some have suggested that they may have spread locally and then globally through 'indirect transmission' within cystic fibrosis (CF) clinics, isolates of these clones have also been associated with sporadic pulmonary infections in non-CF patients and unrelated hospital-acquired soft tissue infections. M. abscessus has long been thought to be acquired from the environment, but the prevalence, exposure risk and environmental reservoirs of the dominant clones are currently not known. This review summarizes the genomic studies of M. abscessus and synthesizes the current knowledge surrounding the geographically diverse dominant clones identified from patient samples. Furthermore, it discusses the limitations of core genome comparisons for studying these genetically similar isolates and explores the breadth of accessory genome variation that has been observed to date", "token_count": 490, "char_count": 1972, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:38.111554", "source": { "split": "train_shard_00001", "doc_id": 1881 }, "chunk_id": "train_shard_00001_1881_0", "global_id": 8311 }, { "text": "The combination of both core and accessory genome variation among these isolates may be the key to elucidating the origin, spread and evolution of these frequent genotypes.\n\nA Closer Look at the Genomic Variation of Geographically Diverse Mycobacterium abscessus Clones That Cause Human Infection and Disease.", "token_count": 82, "char_count": 316, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8043, "quality_score": 0.9022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:38.480985", "source": { "split": "train_shard_00001", "doc_id": 1881 }, "chunk_id": "train_shard_00001_1881_1", "global_id": 8312 }, { "text": "

Objectives

Prevotella copri is considered to be a contributing factor in rheumatoid arthritis (RA). However, in some non-Westernised countries, healthy individuals also harbour an abundance of P. copri in the intestine. This study investigated the pathogenicity of RA patient-derived P. copri (P. copri RA) compared with healthy control-derived P. copri (P. copri HC).

Methods

We obtained 13 P. copri strains from the faeces of patients with RA and healthy controls. Following whole genome sequencing, the sequences of P. copri RA and P. copri HC were compared. To analyse the arthritis-inducing ability of P. copri, we examined two arthritis models (1) a collagen-induced arthritis model harbouring P. copri under specific-pathogen-free conditions and (2) an SKG mouse arthritis model under P. copri-monocolonised conditions. Finally, to evaluate the ability of P. copri to activate innate immune cells, we performed in vitro stimulation of bone marrow-derived dendritic cells (BMDCs) by P. copri RA and P. copri HC.

Results

Comparative genomic analysis revealed no apparent differences in the core gene contents between P. copri RA and P. copri HC, but pangenome analysis revealed the high genome plasticity of P. copri. We identified a P", "token_count": 518, "char_count": 1486, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:39.110870", "source": { "split": "train_shard_00001", "doc_id": 1882 }, "chunk_id": "train_shard_00001_1882_0", "global_id": 8313 }, { "text": "copri RA-specific genomic region as a conjugative transposon. In both arthritis models, P. copri RA-induced more severe arthritis than P. copri HC. In vitro BMDC stimulation experiments revealed the upregulation of IL-17 and Th17-related cytokines (IL-6, IL-23) by P. copri RA.

Conclusion

Our findings reveal the genetic diversity of P. copri, and the genomic signatures associated with strong arthritis-inducing ability of P. copri RA. Our study contributes towards elucidation of the complex pathogenesis of RA.\n\nGenomic repertoires linked with pathogenic potency of arthritogenic Prevotella copri isolated from the gut of patients with rheumatoid arthritis.", "token_count": 266, "char_count": 768, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7174, "quality_score": 0.8587, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:39.659304", "source": { "split": "train_shard_00001", "doc_id": 1882 }, "chunk_id": "train_shard_00001_1882_1", "global_id": 8314 }, { "text": "Leuconostoc is a genus of saccharolytic heterofermentative lactic acid bacteria that inhabit plant-derived matrices and a variety of fermented foods (dairy products, dough, milk, vegetables, and meats), contributing to desired fermentation processes or playing a role in food spoilage. At present, the genus encompasses 17 recognized species. In total, 216 deposited genome sequences of Leuconostoc were analyzed, to check the delineation of species and to infer their evolutive genealogy utilizing a minimum evolution tree of Average Nucleotide Identity (ANI) and the core genome alignment. Phylogenomic relationships were compared to those obtained from the analysis of 16S rRNA, pheS, and rpoA genes. All the phylograms were subjected to split decomposition analysis and their topologies were compared to check the ambiguities in the inferred phylogenesis. The minimum evolution ANI tree exhibited the most similar topology with the core genome tree, while single gene trees were less adherent and provided a weaker phylogenetic signal. In particular, the 16S rRNA gene failed to resolve several bifurcations and Leuconostoc species. Based on an ANI threshold of 95%, the organization of the genus Leuconostoc could be amended, redefining the boundaries of the species L. inhae, L. falkenbergense, L. gelidum, L. lactis, L. mesenteroides, and L. pseudomesenteroides. Two strains currently recognized as L. mesenteroides were split into a separate lineage representing a putative species (G16), phylogenetically related to both L. mesenteroides (G18) and L. suionicum (G17). Differences among the four subspecies of L. mesenteroides were not pinpointed by ANI or by the conserved genes. The strains of L", "token_count": 530, "char_count": 1792, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6175, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:40.323083", "source": { "split": "train_shard_00001", "doc_id": 1883 }, "chunk_id": "train_shard_00001_1883_0", "global_id": 8315 }, { "text": "pseudomesenteroides were ascribed to two putative species, G13 and G14, the former including also all the strains presently belonging to L. falkenbergense. L. lactis was split into two phylogenetically related lineages, G9 and G10, putatively corresponding to separate species and both including subgroups that may correspond to subspecies. The species L. gelidum and L. gasicomitatum were closely related but separated into different species, the latter including also L. inhae strains. These results, integrating information of ANI, core genome, and housekeeping genes, complemented the taxonomic delineation with solid information on the phylogenetic lineages evolved within the genus Leuconostoc.\n\nPhylogenomic analysis of the genus Leuconostoc.", "token_count": 227, "char_count": 795, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8544, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:40.792026", "source": { "split": "train_shard_00001", "doc_id": 1883 }, "chunk_id": "train_shard_00001_1883_1", "global_id": 8316 }, { "text": "Region-specific Helicobacter pylori subpopulations have been identified. It is proposed that the hspAmerind subpopulation is being displaced from the Americans by an hpEurope population following the conquest. Our study aimed to describe the genomes and methylomes of H. pylori isolates from distinct Peruvian communities: 23 strains collected from three groups of Native Americans (Asháninkas [ASHA, n = 9], Shimaas [SHIM, n = 5] from Amazonas, and Punos from the Andean highlands [PUNO, n = 9]) and 9 modern mestizos from Lima (LIM). Closed genomes and DNA modification calls were obtained using SMRT/PacBio sequencing. We performed evolutionary analyses and evaluated genomic/epigenomic differences among strain groups. We also evaluated human genome-wide data from 74 individuals from the selected Native communities (including the 23 H. pylori strains donors) to compare host and bacterial backgrounds. There were varying degrees of hspAmerind ancestry in all strains, ranging from 7% in LIM to 99% in SHIM. We identified three H. pylori subpopulations corresponding to each of the Native groups and a novel hspEuropePeru which evolved in the modern mestizos. The divergence of the indigenous H. pylori strains recapitulated the genetic structure of Native Americans. Phylogenetic profiling showed that Orthogroups in the indigenous strains seem to have evolved differentially toward epigenomic regulation and chromosome maintenance, whereas OGs in the modern mestizo (LIM) seem to have evolved toward virulence and adherence", "token_count": 439, "char_count": 1586, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:41.423466", "source": { "split": "train_shard_00001", "doc_id": 1884 }, "chunk_id": "train_shard_00001_1884_0", "global_id": 8317 }, { "text": "The prevalence of cagA +/vacA s1i1m1 genotype was similar across populations (p = 0.32): 89% in ASHA, 67% in PUNO, 56% in LIM and 40% in SHIM. Both cagA and vacA sequences showed that LIM strains were genetically differentiated (p < 0.001) as compared to indigenous strains. We identified 642 R-M systems with 39% of the associated genes located in the core genome. We found 692 methylation motifs, including 254 population-specific sequences not previously described. In Peru, hspAmerind is not extinct, with traces found even in a heavily admixed mestizo population. Notably, our study identified three new hspAmerind subpopulations, one per Native group; and a new subpopulation among mestizos that we named hspEuropePeru. This subpopulation seems to have more virulence-related elements than hspAmerind. Purifying selection driven by variable host immune response may have shaped the evolution of Peruvian subpopulations, potentially impacting disease outcomes.\n\nIdentification of New Helicobacter pylori Subpopulations in Native Americans and Mestizos From Peru.", "token_count": 345, "char_count": 1127, "word_count": 156, "semantic_coherence": 1, "information_density": 0.7628, "quality_score": 0.8814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:41.994736", "source": { "split": "train_shard_00001", "doc_id": 1884 }, "chunk_id": "train_shard_00001_1884_1", "global_id": 8318 }, { "text": "

ABSTRACT

At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence of this, any individual genome or clonal population will contain merely a fraction of the total genetic diversity of any operationally defined “species”, with the collective from that group presenting the broader genomic diversity known as the pangenome. Pangenomes are valuable concepts for studying evolution and adaptation in microorganisms, as they partition genomes into core regions (present in all the genomes, and responsible for housekeeping and species-level niche adaptation) and accessory regions (present only in some genomes, and responsible for ecotype divergence). Here we present SuperPang , an algorithm capable of producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes or MAGs. SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate our approach by analyzing the intra-species diversity of Polynucleobacter , a clade of ubiquitous freshwater microorganisms characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.\n\nExploring intra-species diversity through non-redundant pangenome assemblies", "token_count": 402, "char_count": 1869, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:42.613288", "source": { "split": "train_shard_00001", "doc_id": 1885 }, "chunk_id": "train_shard_00001_1885_0", "global_id": 8319 }, { "text": "

Research highlights

Type O8 is the most prevalent serotype of APEC isolated from Wenchang chicken embryos (Hainan, China).The isolates were more than 90% resistant to erythromycin, amoxicillin, ampicillin, and tetracycline.19.2% of the isolates were multi-resistant to more than 14 antibiotics.APEC of the same serotype isolated from Hainan Wenchang embryos have close relationships in the evolutionary tree of the core genome.\n\nEpidemiological investigation and drug resistance analysis of avian pathogenic <i>Escherichia coli</i> (APEC) of Wenchang chickens in Hainan, China.", "token_count": 195, "char_count": 597, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:43.061205", "source": { "split": "train_shard_00001", "doc_id": 1886 }, "chunk_id": "train_shard_00001_1886_0", "global_id": 8320 }, { "text": "

Background

The goal of the current study was to elucidate the genomic background of biofilm formation in Klebsiella pneumoniae.

Methods

Clinical isolates were screened for biofilm formation using the crystal violet assay. Antimicrobial resistance (AMR) profiles were assessed by disk diffusion and broth microdilution tests. Biofilm formation was correlated to virulence and resistance genes screened by PCR. Draft genomes of three isolates that form strong biofilm were generated by Illumina sequencing.

Results

Only the siderophore-coding gene iutA was significantly associated with more pronounced biofilm formation. ST1399-KL43-O1/O2v1 and ST11-KL15-O4 were assigned to the multidrug-resistant strain K21 and the extensively drug-resistant strain K237, respectively. ST1999-KL38-O12 was assigned to K57. Correlated with CRISPR/Cas distribution, more plasmid replicons and prophage sequences were identified in K21 and K237 compared to K57. The acquired AMR genes (blaOXA-48, rmtF, aac(6')-Ib and qnrB) and (blaNDM-1, blaCTX-M, aph(3')-VI, qnrS, and aac(6')-Ib-cr) were found in K237 and K21, respectively", "token_count": 443, "char_count": 1240, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [ "ST1399", "KL43", "ST1999", "KL38", "ST11", "KL15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:43.690402", "source": { "split": "train_shard_00001", "doc_id": 1887 }, "chunk_id": "train_shard_00001_1887_0", "global_id": 8321 }, { "text": "The latter showed a novel ISEcp1-mediated chromosomal integration of replicon type IncM1 plasmid-like structure harboring blaCTX-M-14 and aph(3')-VI that uniquely interrupted rcsC. The plasmid-mediated heavy metal resistance genes merACDEPRT and arsABCDR were spotted in K21, which also exclusively carried the acquired virulence genes mrkABCDF and the hypervirulence-associated genes iucABCD-iutA, and rmpA/A2. Pangenome analysis revealed NTUH-K2044 accessory genes most frequently shared with K21.

Conclusions

While less virulent to Galleria mellonella than ST1999 (K57), the strong biofilm former, multidrug-resistant, NDM-producer K. pneumoniae K21 (ST1399-KL43-O1/O2v1) carries a novel chromosomally integrated plasmid-like structure and hypervirulence-associated genes and represents a serious threat to countries in the area.\n\nComparative genomic analysis of strong biofilm-forming Klebsiella pneumoniae isolates uncovers novel ISEcp1-mediated chromosomal integration of a full plasmid-like sequence.", "token_count": 401, "char_count": 1123, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7311, "quality_score": 0.8655, "entities": { "genes": [ "ST1399", "KL43", "ST1999" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:44.329759", "source": { "split": "train_shard_00001", "doc_id": 1887 }, "chunk_id": "train_shard_00001_1887_1", "global_id": 8322 }, { "text": "Polyploidy, the result of whole-genome duplication (WGD), is a major driver of eukaryote evolution. All angiosperms have undergone ancient WGDs, and today stable polyploids account for a substantial portion of both wild and domesticated plant species. Despite its centrality in evolution, WGD is a hugely disruptive mutation, and we still lack a clear understanding of its fitness consequences. Here, we study whether WGD results in greater diversity of genomic structural variants (SVs) and how this influences evolutionary dynamics in nature. Using a set of long-read sequenced samples from the plant genus Cochlearia (Brassicaceae), which contains diploids and a recent ploidy series up to octoploid, we show that masking of recessive mutations due to WGD has led to a substantial and progressive accumulation of genic SVs across four ploidy levels. Such SVs likely constitute a genetic load and thus reduce the adaptive potential of polyploid populations. However, this SV accumulation also provides a rich pool of standing genetic variation upon which selection may act in novel environments. By constructing a graph-based pangenome for Cochlearia , we identify SVs in hundreds of samples and study the genomic basis of environmental adaptation. We find putatively beneficial SVs involved in pathogen resistance, root development, and salt tolerance, many of which are unique to polyploids. Finally, we explore the adaptive landscapes of SVs and SNPs, identify geographical regions where SVs make novel contributions to adaptive variation, and predict that the role of SVs in environmental adaptation increases due to rapid climate change.\n\nImpact of whole-genome duplications on structural variant evolution in the plant genusCochlearia", "token_count": 392, "char_count": 1749, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:44.973544", "source": { "split": "train_shard_00001", "doc_id": 1888 }, "chunk_id": "train_shard_00001_1888_0", "global_id": 8323 }, { "text": "Whole genome sequencing is replacing traditional laboratory surveillance methods as the primary tool to track and characterize clusters and outbreaks of the foodborne and zoonotic pathogen Salmonella enterica (S. enterica). In this study, 438 S. enterica isolates representing 35 serovars and 13 broad vehicle categories from one hundred epidemiologically confirmed outbreaks were evaluated for genetic variation to develop epidemiologically relevant interpretation guidelines for Salmonella disease cluster detection. The Illumina sequences were analyzed by core genome multi-locus sequence typing (cgMLST) and screened for antimicrobial resistance (AR) determinants and plasmids. Ninety-three of the one hundred outbreaks exhibited a close allele range (less than 10 allele differences with a subset closer than 5). The remaining seven outbreaks showed increased variation, of which three were considered polyclonal. A total of 16 and 28 outbreaks, respectively, showed variations in the AR and plasmid profiles. The serovars Newport and I 4,[5],12:i:-, as well as the zoonotic and poultry product vehicles, were overrepresented among the outbreaks, showing increased variation. A close allele range in cgMLST profiles can be considered a reliable proxy for epidemiological relatedness for the vast majority of S. enterica outbreak investigations. Variations associated with mobile elements happen relatively frequently during outbreaks and could be reflective of changing selective pressures.\n\nGenetic Diversity in Salmonella enterica in Outbreaks of Foodborne and Zoonotic Origin in the USA in 2006-2017.", "token_count": 408, "char_count": 1650, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:45.629455", "source": { "split": "train_shard_00001", "doc_id": 1889 }, "chunk_id": "train_shard_00001_1889_0", "global_id": 8324 }, { "text": "Escherichia coli is the leading cause of urinary tract infections (UTIs) in children and adults. The gastrointestinal tract is the primary reservoir of uropathogenic E. coli, which can be acquired from a variety of environmental exposures, including retail meat. In the current study, we used a novel statistical-genomic approach to estimate the proportion of pediatric UTIs caused by foodborne zoonotic E. coli strains. E. coli urine isolates were collected from DC residents aged 2 months to 17 years from the Children's National Medical Center Laboratory, 2013-2014. During the same period, E. coli isolates were collected from retail poultry products purchased from 15 sites throughout DC. A total of 52 urine and 56 poultry isolates underwent whole-genome sequencing, core genome phylogenetic analysis, and host-origin prediction by a Bayesian latent class model that incorporated data on the presence of mobile genetic elements (MGEs) among E. coli isolates from multiple vertebrate hosts. A total of 56 multilocus sequence types were identified among the isolates. Five sequence types-ST10, ST38, ST69, ST117, and ST131-were observed among both urine and poultry isolates. Using the Bayesian latent class model, we estimated that 19% (10/52) of the clinical E. coli isolates in our population were foodborne zoonotic strains. These data suggest that a substantial portion of pediatric UTIs in the Washington DC region may be caused by E. coli strains originating in food animals and likely transmitted via contaminated poultry meat.IMPORTANCEEscherichia coli UTIs are a heavy public health burden and can have long-term negative health consequences for pediatric patients. E. coli has an extremely broad host range, including humans, chickens, turkeys, pigs, and cattle. E", "token_count": 527, "char_count": 1852, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6217, "quality_score": 0.8109, "entities": { "genes": [ "ST131", "ST10", "ST117", "ST69", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:46.297536", "source": { "split": "train_shard_00001", "doc_id": 1890 }, "chunk_id": "train_shard_00001_1890_0", "global_id": 8325 }, { "text": "coli derived from food animals is a frequent contaminant of retail meat products, but little is known about the risk these strains pose to pediatric populations. Quantifying the proportion of pediatric UTIs caused by food-animal-derived E. coli, characterizing the highest-risk strains, and identifying their primary reservoir species could inform novel intervention strategies to reduce UTI burden in this vulnerable population. Our results suggest that retail poultry meat may be an important vehicle for pediatric exposure to zoonotic E. coli strains capable of causing UTIs. Vaccinating poultry against the highest-risk strains could potentially reduce poultry colonization, poultry meat contamination, and downstream pediatric infections.\n\nPediatric urinary tract infections caused by poultry-associated Escherichia coli.", "token_count": 212, "char_count": 851, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7477, "quality_score": 0.8739, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:46.761223", "source": { "split": "train_shard_00001", "doc_id": 1890 }, "chunk_id": "train_shard_00001_1890_1", "global_id": 8326 }, { "text": "

Objectives

The incidence of Legionnaires' disease steadily increases worldwide. Although Legionella pneumophila is known as pathogenic, systematic investigations into antibiotic resistance are scarce, and reports of resistance in isolates are recently emerging.

Methods

Clinical cases and metadata reported to the Belgian National Reference Centre between 2011 and 2022 were retrospectively analyzed. A total of 283 clinical isolates were typed by core genome multi-locus sequence typing (cgMLST). Acquired genes or mutations triggering resistance were extracted from all of them.

Results

The number of Legionnaires' disease cases has increased in Belgium. Urinary antigen testing remains the main used test, but polymerase chain reaction and serology allow the diagnostic in 14.8% and 2.4% of cases, respectively. cgMLST showed a good discrimination between sequence typing (ST) and minimal variation for ST47 isolates, whereas ST1s were more diverse. Genotypic screening identified a 23S ribosomal RNA mutation linked to a high-level macrolide resistance in one isolate of ST188, which is genetically closed to resistant isolates from France.

Conclusion

The increase in incidence is of concern and likely an under-estimate due to the reliance on urine antigen testing. Routine typing by cgMLST allows good discrimination and the first clinical isolate reported as resistant for macrolides was cultured, underscoring the need to define resistance breakpoints and incorporate antimicrobial susceptibility testing as routine clinical investigation practice.\n\nOccurrence of macrolides resistance in Legionella pneumophila ST188: Results of the Belgian epidemiology and resistome investigation of clinical isolates.", "token_count": 428, "char_count": 1741, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8253, "entities": { "genes": [ "ST47", "ST188" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:47.387744", "source": { "split": "train_shard_00001", "doc_id": 1891 }, "chunk_id": "train_shard_00001_1891_0", "global_id": 8327 }, { "text": "Species-specific genes, also known as orphans, are ubiquitous across life’s domains. In prokaryotes, species-specific orphan genes (SSOGs) are mostly thought to originate in external elements such as viruses, followed by horizontal gene transfer, while the scenario of native origination, through rapid divergence or de novo, is mostly dismissed. However, quantitative evidence supporting either scenario is lacking. Here, we systematically analyzed genomes from 4,644 human gut microbiome species and identified over 600,000 unique SSOGs, representing an average of 2.6% of a given species’ pangenome. These sequences are mostly rare within each species yet show signs of purifying selection. Overall, SSOGs use optimal codons less frequently, and their proteins are more disordered than those of conserved genes (i.e., non-SSOGs). Importantly, across species, the GC content of SSOGs closely matches that of conserved ones. In contrast, the ∼5% of SSOGs that share similarity to known viral sequences have distinct characteristics, including lower GC content. Thus, SSOGs with similarity to viruses differ from the remaining SSOGs, contrasting an external origination scenario for most SSOGs. By examining the orthologous genomic region in closely related species, we show that a small subset of SSOGs likely evolved natively de novo and find that these genes also differ in their properties from the remaining SSOGs. Our results challenge the notion that external elements are the dominant source of prokaryotic genetic novelty and will enable future studies into the biological role and relevance of species-specific genes in the human gut.\n\nLarge-scale investigation of species-specific orphan genes in the human gut microbiome elucidates their evolutionary origins", "token_count": 412, "char_count": 1770, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:48.010400", "source": { "split": "train_shard_00001", "doc_id": 1892 }, "chunk_id": "train_shard_00001_1892_0", "global_id": 8328 }, { "text": "Correct identifications of isolates and strains of the Mitis-Group of the genus Streptococcus are particularly difficult, due to high genetic similarity, resulting from horizontal gene transfer and homologous recombination, and unreliable phenotypic and genotypic biomarkers for differentiating the species. Streptococcus pneumoniae and Streptococcus pseudopneumoniae are the most closely related species of the clade. In this study, publicly-available genome sequences for Streptococcus pneumoniae and S. pseudopneumoniae were analyzed, using a pangenomic approach, to find candidates for species-unique gene markers; ten species-unique genes for S. pneumoniae and nine for S. pseudopneumoniae were identified. These species-unique gene marker candidates were verified by PCR assays for identifying S. pneumoniae and S. pseudopneumoniae strains isolated from clinical samples. All determined species-level unique gene markers for S. pneumoniae were detected in all S. pneumoniae clinical isolates, whereas fewer of the unique S. pseudopneumoniae gene markers were present in more than 95% of the clinical isolates. In parallel, taxonomic identifications of the clinical isolates were confirmed, using conventional optochin sensitivity testing, targeted PCR-detection for the \"Xisco\" gene, as well as genomic ANIb similarity analyses for the genome sequences of selected strains. Using mass spectrometry-proteomics, species-specific peptide matches were observed for four of the S. pneumoniae gene markers and for three of the S. pseudopneumoniae gene markers. Application of multiple species-level unique biomarkers of S. pneumoniae and S", "token_count": 499, "char_count": 1747, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5273, "quality_score": 0.7636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:48.660587", "source": { "split": "train_shard_00001", "doc_id": 1893 }, "chunk_id": "train_shard_00001_1893_0", "global_id": 8329 }, { "text": "pseudopneumoniae, is proposed as a protocol for the routine clinical laboratory for improved, reliable differentiation, and identification of these pathogenic and commensal species.\n\nA Pangenome Approach for Discerning Species-Unique Gene Markers for Identifications of Streptococcus pneumoniae and Streptococcus pseudopneumoniae.", "token_count": 95, "char_count": 348, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7949, "quality_score": 0.8974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:49.036165", "source": { "split": "train_shard_00001", "doc_id": 1893 }, "chunk_id": "train_shard_00001_1893_1", "global_id": 8330 }, { "text": "Aeromonas spp. are commonly found in the aquatic environment and have been responsible for motile Aeromonas septicemia (MAS) in striped catfish, resulting in significant economic loss. These organisms also cause a range of opportunistic infections in humans with compromised immune systems. Here, we conducted a genomic investigation of 87 Aeromonas isolates derived from diseased catfish, healthy catfish and environmental water in catfish farms affected by MAS outbreaks in eight provinces in Mekong Delta (years: 2012-2022), together with 25 isolates from humans with bloodstream infections (years: 2010-2020). Genomics-based typing method precisely delineated Aeromonas species while traditional methods such as aerA PCR and MALDI-TOF were unable identify A. dhakensis. A. dhakensis was found to be more prevalent than A. hydrophila in both diseased catfish and human infections. A. dhakensis sequence type (ST) 656 followed by A. hydrophila ST251 were the predominant virulent species-lineages in diseased catfish (43.7 and 20.7 %, respectively), while diverse STs were found in humans with bloodstream infections. There was evidence of widespread transmission of ST656 and ST251 on striped catfish in the Mekong Delta region. ST656 and ST251 isolates carried a significantly higher number of acquired antimicrobial resistance (AMR) genes and virulence factors in comparison to other STs. They, however, exhibited several distinctions in key virulence factors (i.e. lack of type IV pili and enterotoxin ast in A. dhakensis), AMR genes (i.e. presence of imiH carbapenemase in A. dhakensis), and accessory gene content", "token_count": 522, "char_count": 1712, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6511, "quality_score": 0.8255, "entities": { "genes": [ "ST251", "ST656" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:49.668676", "source": { "split": "train_shard_00001", "doc_id": 1894 }, "chunk_id": "train_shard_00001_1894_0", "global_id": 8331 }, { "text": "To uncover potential conserved proteins of Aeromonas spp. for vaccine development, pangenome analysis has unveiled 2202 core genes between ST656 and ST251, of which 78 proteins were in either outer membrane or extracellular proteins. Our study represents one of the first genomic investigations of the species distribution, genetic landscape, and epidemiology of Aeromonas in diseased catfish and human infections in Vietnam. The emergence of antimicrobial resistant and virulent A. dhakensis strains underscores the needs of enhanced genomic surveillance and strengthening vaccine research and development in preventing Aeromonas diseases in catfish and humans, and the search for potential vaccine candidates could focus on Aeromonas core genes encoded for membrane and secreted proteins.\n\nGenomic characterization of Aeromonas spp. isolates from striped catfish with motile Aeromonas septicemia and human bloodstream infections in Vietnam.", "token_count": 268, "char_count": 991, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [ "ST251", "ST656" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:50.236053", "source": { "split": "train_shard_00001", "doc_id": 1894 }, "chunk_id": "train_shard_00001_1894_1", "global_id": 8332 }, { "text": "

Background

Faecalibacterium prausnitzii is a ubiquitous member of the human gut microbiome, constituting up to 15% of the total bacteria in the human gut. Substantial evidence connects decreased levels of F. prausnitzii with the onset and progression of certain forms of inflammatory bowel disease, which has been attributed to its anti-inflammatory potential. Two phylogroups of F. prausnitzii have been identified, with a decrease in phylogroup I being a more sensitive marker of intestinal inflammation. Much of the genomic and physiological data available to date was collected using phylogroup II strains. Little analysis of F. prausnitzii genomes has been performed so far and genetic differences between phylogroups I and II are poorly understood.

Results

In this study we sequenced 11 additional F. prausnitzii genomes and performed comparative genomics to investigate intraspecies diversity, functional gene complement and the mobilome of 31 high-quality draft and complete genomes. We reveal a very low level of average nucleotide identity among F. prausnitzii genomes and a high level of genome plasticity. Two genomogroups can be separated based on differences in functional gene complement, albeit that this division does not fully agree with separation based on conserved gene phylogeny, highlighting the importance of horizontal gene transfer in shaping F. prausnitzii genomes. The difference between the two genomogroups is mainly in the complement of genes associated with catabolism of carbohydrates (such as a predicted sialidase gene in genomogroup I) and amino acids, as well as defense mechanisms.

Conclusions

Based on the combination of ANI of genomic sequences, phylogenetic analysis of core proteomes and functional differences we propose to separate the species F. prausnitzii into two new species level taxa: F", "token_count": 461, "char_count": 1859, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:50.877623", "source": { "split": "train_shard_00001", "doc_id": 1895 }, "chunk_id": "train_shard_00001_1895_0", "global_id": 8333 }, { "text": "prausnitzii sensu stricto (neotype strain A2-165T = DSM 17677T = JCM 31915T) and F. moorei sp. nov. (type strain ATCC 27768T = NCIMB 13872T).\n\nComparative analysis of Faecalibacterium prausnitzii genomes shows a high level of genome plasticity and warrants separation into new species-level taxa.", "token_count": 164, "char_count": 351, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:51.321690", "source": { "split": "train_shard_00001", "doc_id": 1895 }, "chunk_id": "train_shard_00001_1895_1", "global_id": 8334 }, { "text": "

Objectives

Staphylococcus aureus is a leading cause of hospital-acquired infections worldwide. Over recent decades, methicillin-resistant Staphylococcus aureus (MRSA), which is resistant to multiple antimicrobials, has emerged as a significant pathogenic strain in both hospital and community settings. The rapid emergence and dissemination of MRSA clones are driven by a dynamic and evolving population, spreading swiftly across regions on epidemiological time scales. Despite the vast geographical expanse and diverse demographics of the Kingdom of Saudi Arabia and the broader West Asia region, the population diversity of MRSA in hospitals in these areas remains underexplored.

Methods

We conducted a large-scale genomic analysis of a systematic Staphylococcus aureus collection obtained from 34 hospitals across all provinces of KSA, from diverse body sites between 2022 and 2024. The dataset comprised 581 MRSA and 31 methicillin-susceptible Staphylococcus aureus (MSSA) isolates, all subjected to whole-genome sequencing. A combination of phylogenetic and population genomics approaches was utilized to analyze the genomic data. Hybrid sequencing approach was employed to retrieve the complete plasmid content.

Results

The population displayed remarkable diversity, comprising 48 distinct sequence types (STs), with the majority harboring community-associated SCCmec loci (types IVa, V/VII, and VI). Virulence factors associated with community-acquired MRSA (CA-MRSA), including Panton-Valentine Leukocidin (PVL) genes, were identified in 12 distinct STs. Dominant clones, including ST8-t008 (USA300), ST88-t690, ST672-t3841, ST6-t304, and ST5-t311, were associated with infections at various body sites and were widely disseminated across the country", "token_count": 518, "char_count": 1815, "word_count": 228, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [ "ST6", "ST88", "ST672", "ST5", "ST8", "USA300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:51.951901", "source": { "split": "train_shard_00001", "doc_id": 1896 }, "chunk_id": "train_shard_00001_1896_0", "global_id": 8335 }, { "text": "Linezolid and vancomycin resistance were mediated by cfr-carrying plasmids and mutations in the vraR gene (involved in cell-wall stress response) and the murF gene (involved in peptidoglycan biosynthesis) in five isolates, respectively. Phylodynamic analysis revealed rapid expansion of the dominant clones, with their emergence estimated to have occurred 10-20 years ago. Plasmidome analysis uncovered a diverse repertoire of blaZ-containing plasmids and the sharing of erm(C)-encoding plasmids among major clades. The acquisition of plasmids coincided with clonal expansion.

Conclusions

Our results highlight the recent concurrent expansion and geographical dissemination of CA-MRSA clones across hospitals. These findings also underscore the interplay between clonal spread and horizontal gene transfer in shaping the resistance landscape of MRSA.\n\nMethicillin-resistant <i>Staphylococcus aureus</i> in Saudi Arabia: genomic evidence of recent clonal expansion and plasmid-driven resistance dissemination.", "token_count": 300, "char_count": 1062, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6929, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:52.517293", "source": { "split": "train_shard_00001", "doc_id": 1896 }, "chunk_id": "train_shard_00001_1896_1", "global_id": 8336 }, { "text": "Pangenomes are replacing single reference genomes to capture all variants within a species or clade, but their analysis predominantly leverages graph-based methods that require multiple high-quality genomes and computationally intensive multiple-genome alignments. K-mer decomposition is an alternative to graph-based pangenomes. However, how to directly use k-mers for the population genetic analyses is unknown. Here, we developed a novel strategy that uses the variants of k-mer count in the genome for population analyses. To test the effectivity of this method, we compared it directly to the SNP-based method on the analysis of population structure and genetic diversity of 267 Saccharomyces cerevisiae strains within two simulated datasets and a real sequence dataset. The population structure identified with k-mers recapitulates that obtained using SNPs, indicating the effectiveness of k-mer-based approach, and higher genetic diversity within real dataset supported k-mers contained more genetic variants. Based on k-mer frequency, we found not only SNP but also some insertion/deletion and horizontal gene transfer (HGT) fragments related to the adaptive evolution of S. cerevisiae. Our study creates a framework for the alignment- and reference-free (ARF) method in population genetic analyses, which will be more pronounced in the species with no complete genome or highly diverged species.\n\nAn alignment- and reference-free strategy using <i>k</i>-mer present pattern for population genomic analyses.", "token_count": 391, "char_count": 1590, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:53.134501", "source": { "split": "train_shard_00001", "doc_id": 1897 }, "chunk_id": "train_shard_00001_1897_0", "global_id": 8337 }, { "text": "Brochothrix thermosphacta is a dominant but poorly studied meat spoilage organism. It is a close relative of the foodborne pathogen Listeria monocytogenes, and Brochothrix constitutes the second genus in the Listeriaceae family. Here, the genomes of 12 B. thermosphacta strains were sequenced, assembled into draft genomes, characterized, and compared with the genomes of Brochothrix campestris and L. monocytogenes Phenotypic properties including biogenic amine production and antibiotic and heavy metal susceptibilities were tested. Comparative genomic analyses revealed a high degree of similarity among the B. thermosphacta strains, with bacteriophage genes constituting a significant proportion of the accessory genome. Genes for the production of the malodorous compounds acetate, acetoin, butanediol, and fatty acids were found, as were stress response regulatory genes, which likely play important roles in the spoilage process. Amino acid decarboxylases were not identified in the genomes, and phenotypic testing confirmed their absence. Orthologs of Listeria virulence proteins involved in virulence regulation, intracellular survival, and surface protein anchoring were found; however, key virulence genes were absent. Analysis of antibiotic susceptibility showed that strains were sensitive to the four tested antibiotics, except for one tetracycline-resistant isolate with plasmid-mediated tetracycline resistance genes. Strains tolerated higher levels of copper and cobalt than of cadmium although not at concentrations high enough to categorize the strains as being resistant", "token_count": 436, "char_count": 1653, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6869, "quality_score": 0.8435, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:53.766029", "source": { "split": "train_shard_00001", "doc_id": 1898 }, "chunk_id": "train_shard_00001_1898_0", "global_id": 8338 }, { "text": "This study provides insight into the Brochothrix genome, links previous phenotypic data and data provided here to the gene inventory, and identifies genes that may contribute to the persistence of this organism in the food chain.IMPORTANCE Despite increasing knowledge and advances in food preservation techniques, microbial spoilage of foods causes substantial losses, with negative social and economic consequences. To better control the contamination and microbial spoilage of foods, fundamental knowledge of the biology of key spoilage bacteria is crucial. As a common meat spoilage organism, B. thermosphacta contributes substantially to spoilage-associated losses. Nonetheless, this organism and particularly its genome remain largely unstudied. This study contributes to improving our knowledge of the Brochothrix genus. Spoilage-relevant pathways and genes that may play a role in the survival of this organism in a food processing environment were identified, linking previous phenotypic data and data provided here to the gene inventory of Brochothrix and establishing parallels to and differences from the closely related foodborne pathogen L. monocytogenes.\n\nInsight into the Genome of Brochothrix thermosphacta, a Problematic Meat Spoilage Bacterium.", "token_count": 315, "char_count": 1305, "word_count": 175, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7914, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:54.316791", "source": { "split": "train_shard_00001", "doc_id": 1898 }, "chunk_id": "train_shard_00001_1898_1", "global_id": 8339 }, { "text": "Some marine microbes are seemingly \"ubiquitous,\" thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal (\"Candidatus Nitrosopelagicus brevis\") populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in \"Ca. N. brevis\" at HOT, driven by a higher rate of homologous recombination. In contrast, \"Ca. N. brevis\" at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of \"Ca. N. brevis.\" IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats", "token_count": 521, "char_count": 2317, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7978, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:54.976314", "source": { "split": "train_shard_00001", "doc_id": 1899 }, "chunk_id": "train_shard_00001_1899_0", "global_id": 8340 }, { "text": "We show that the marine AOA \"Candidatus Nitrosopelagicus brevis\" in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to \"Ca. N. brevis\" have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.\n\nDifferentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations.", "token_count": 135, "char_count": 593, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8082, "quality_score": 0.9041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:55.405553", "source": { "split": "train_shard_00001", "doc_id": 1899 }, "chunk_id": "train_shard_00001_1899_1", "global_id": 8341 }, { "text": "

Introduction

Enterococcus faecium is a widespread acid-lactic bacterium found in the environment, humans, and animal microbiota, and it also plays a role in the production of traditional food. However, the worldwide emergence of multidrug-resistant E. faecium strains represents a major public health threat and is the primary reason that the genus Enterococcus is not recommended for the Qualified Presumption of Safety (QPS) list of the European Food Safety Authority (EFSA), raising concerns about its presence in food products.

Methods

In this study, 39 E. faecium and 5 E. lactis isolates were obtained from artisanal brine cheeses and dry sausages, sourced from 21 different Montenegrin producers. The isolates were collected following the ISO 15214:1998 international method and processed for whole-genome sequencing (WGS).

Results

Genome analysis based on core genome multilocus sequence type (cgMLST) revealed a high diversity among isolates. Furthermore, the isolates carried antimicrobial resistance genes; the virulence genes acm, sgrA, and ecbA; the bacteriocin genes Enterolysin A, Enterocin A, Enterocin P, Duracin Q, Enterocin B, Bacteriocin 31, Enterocin EJ97, Sactipeptides, and Enterocin SEK4; the secondary metabolite genes T3PKS, cyclic lactone autoinducer, RiPP-like, and NRPS and a maximum of eight plasmids.

Conclusion

This study highlights the need for careful monitoring of E. faecium and E. lactis strains in food to ensure they do not pose any potential risks to consumer safety.", "token_count": 513, "char_count": 1641, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7042, "quality_score": 0.8521, "entities": { "genes": [ "EJ97", "SEK4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:16:56.078117", "source": { "split": "train_shard_00001", "doc_id": 1900 }, "chunk_id": "train_shard_00001_1900_0", "global_id": 8342 }, { "text": "Genetic diversity and distinction of Enterococcus faecium and Enterococcus lactis in traditional Montenegrin brine cheeses and salamis.", "token_count": 49, "char_count": 149, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:56.461904", "source": { "split": "train_shard_00001", "doc_id": 1900 }, "chunk_id": "train_shard_00001_1900_1", "global_id": 8343 }, { "text": "The gut microbiome has been implicated in the pathogenesis of inflammatory bowel disease (IBD). Studies suggest that the IBD gut microbiome is less diverse than that of the unaffected population, a phenomenon often referred to as dysbiosis. However, these studies have heavily focused on bacteria, while other intestinal microorganisms-fungi, protozoa, and bacteriophages-have been neglected. Of the nonbacterial microbes that have been studied in relation to IBD, most are thought to be pathogens, although there is evidence that some of these species may instead be harmless commensals. In this review, we discuss the nonbacterial gut microbiome of IBD, highlighting the current biases, limitations, and outstanding questions that can be addressed with high-throughput DNA sequencing methods. Further, we highlight the importance of studying nonbacterial microorganisms alongside bacteria for a comprehensive view of the whole IBD biome and to provide a more precise definition of dysbiosis in patients. With the rise in popularity of microbiome-altering therapies for the treatment of IBD, such as fecal microbiota transplantation, it is important that we address these knowledge gaps to ensure safe and effective treatment of patients.\n\nThe Neglected Gut Microbiome: Fungi, Protozoa, and Bacteriophages in Inflammatory Bowel Disease.", "token_count": 317, "char_count": 1337, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6302, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:57.497151", "source": { "split": "train_shard_00001", "doc_id": 1901 }, "chunk_id": "train_shard_00001_1901_0", "global_id": 8344 }, { "text": "

Background

Carbapenem-resistant Enterobacterales (CRE) infections pose a significant global public health threat, with colistin as the last line of defense. Increasing colistin resistance presents a formidable clinical challenge. This study aimed to elucidate the molecular characteristics and resistance mechanisms of clinical colistin-resistant (ColR) CRE strains in Xuzhou, China.

Methods

The broth microdilution method and PCR were performed to detect antibiotic resistance phenotype and resistance genotype. Pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST) were used to determine genetic relatedness. Whole-genome sequencing (WGS) was carried out to characterize plasmids carrying resistance genes. Phylogenetic analysis was conducted by constructing phylogenetic tree based on single nucleotide polymorphism (SNP) and core genome multilocus sequence typing (cgMLST).

Results

In 14 ColR-carbapenem-resistant Klebsiella pneumoniae (ColR-CRKP) strains, the inactivation of the mgrB gene leads to colistin resistance. The mcr-1 gene, carried by a plasmid, mediated colistin resistance in 4 ColR-carbapenem-resistant Escherichia coli (ColR-CREC) strains. PFGE revealed potential cloning epidemics in both ColR-CRKP and ColR-CREC. WGS of E. coli 104 demonstrated the distribution of multiple crucial resistance genes on four plasmids. Notably, mcr-1 was located on the IncI2 plasmid while bla NDM-5 was located on the IncFII plasmid", "token_count": 474, "char_count": 1543, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7258, "quality_score": 0.8629, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:58.150353", "source": { "split": "train_shard_00001", "doc_id": 1902 }, "chunk_id": "train_shard_00001_1902_0", "global_id": 8345 }, { "text": "Phylogenetic trees, based on SNP and cgMLST, illustrate that the clonal epidemic strains, as exemplified by E. coli 104, have the potential to spread across regions and species.

Conclusion

This study underscores that mutations in the mgrB gene and the presence of mcr-1 contribute to the development of colistin resistance in CRE. Additionally, it enriches local epidemiological knowledge, facilitating a better understanding and control of the spread of mcr-1.\n\nEmergence, Molecular Characteristics and Resistance Mechanisms of Colistin-Resistant <i>Enterobacterales</i> in Xuzhou, China.", "token_count": 198, "char_count": 643, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7595, "quality_score": 0.8797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:58.597222", "source": { "split": "train_shard_00001", "doc_id": 1902 }, "chunk_id": "train_shard_00001_1902_1", "global_id": 8346 }, { "text": "

Objectives

Burkholderia dolosa is a clinically important opportunistic pathogen in inpatients. Here we characterised an extensively drug-resistant and hypervirulent B. dolosa isolate from a patient hospitalised for stroke.

Methods

Resistance to 41 antibiotics was tested with the agar disc diffusion, minimum inhibitory concentration, or broth microdilution method. The complete genome was assembled using short-reads and long-reads and the hybrid de novo assembly method. Allelic profiles obtained by multilocus sequence typing were analysed using the PubMLST database. Antibiotic-resistance and virulence genes were predicted in silico using public databases and the 'baargin' workflow. B. dolosa N149 phylogenetic relationships with all available B. dolosa strains and Burkholderia cepacia complex strains were analysed using the pangenome obtained with Roary.

Results

B. dolosa N149 displayed extensive resistance to 31 antibiotics and intermediate resistance to 4 antibiotics. The complete genome included three circular chromosomes (6 338 630 bp in total) and one plasmid (167 591 bp). Genotypic analysis revealed various gene clusters (acr, amr, amp, emr, ade, bla and tet) associated with resistance to 35 antibiotic classes. The major intrinsic resistance mechanisms were multidrug efflux pump alterations, inactivation and reduced permeability of targeted antibiotics. Moreover, 91 virulence genes (encoding proteins involved in adherence, formation of capsule, biofilm and colony, motility, phagocytosis inhibition, secretion systems, protease secretion, transmission and quorum sensing) were identified. B. dolosa N149 was assigned to a novel sequence type (ST2237) and formed a mono-phylogenetic clade separated from other B. dolosa strains.

Conclusions

This study provided insights into the antimicrobial resistance and virulence mechanisms of B. dolosa.", "token_count": 509, "char_count": 1897, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6911, "quality_score": 0.8455, "entities": { "genes": [ "ST2237" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:59.259208", "source": { "split": "train_shard_00001", "doc_id": 1903 }, "chunk_id": "train_shard_00001_1903_0", "global_id": 8347 }, { "text": "Genomic insights into an extensively drug-resistant and hypervirulent Burkholderia dolosa N149 isolate of a novel sequence type (ST2237) from a Vietnamese patient hospitalised for stroke.", "token_count": 50, "char_count": 187, "word_count": 25, "semantic_coherence": 1, "information_density": 0.96, "quality_score": 0.98, "entities": { "genes": [ "ST2237" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:16:59.615657", "source": { "split": "train_shard_00001", "doc_id": 1903 }, "chunk_id": "train_shard_00001_1903_1", "global_id": 8348 }, { "text": "

Background

Vibrio cholerae, the causative agent of cholera, is a well-studied species, whereas Vibrio metoecus is a recently described close relative that is also associated with human infections. The availability of V. metoecus genomes provides further insight into its genetic differences from V. cholerae. Additionally, both species have been co-isolated from a cholera-free brackish coastal pond and have been suggested to interact with each other by horizontal gene transfer (HGT).

Results

The genomes of 17 strains from each species were sequenced. All strains share a large core genome (2675 gene families) and very few genes are unique to each species (< 3% of the pan-genome of both species). This led to the identification of potential molecular markers-for nitrite reduction, as well as peptidase and rhodanese activities-to further distinguish V. metoecus from V. cholerae. Interspecies HGT events were inferred in 21% of the core genes and 45% of the accessory genes. A directional bias in gene transfer events was found in the core genome, where V. metoecus was a recipient of three times (75%) more genes from V. cholerae than it was a donor (25%).

Conclusion

V. metoecus was misclassified as an atypical variant of V. cholerae due to their resemblance in a majority of biochemical characteristics. More distinguishing phenotypic assays can be developed based on the discovery of potential gene markers to avoid any future misclassifications. Furthermore, differences in relative abundance or seasonality were observed between the species and could contribute to the bias in directionality of HGT.\n\nGenomes of Vibrio metoecus co-isolated with Vibrio cholerae extend our understanding of differences between these closely related species.", "token_count": 463, "char_count": 1774, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:00.258957", "source": { "split": "train_shard_00001", "doc_id": 1904 }, "chunk_id": "train_shard_00001_1904_0", "global_id": 8349 }, { "text": "

ABSTRACT

The recent global outbreak of Monkeypox, caused by the Monkeypox virus (MPVX) emerged in Europe in 2022 and rapidly spread to over 40 countries. The Americas are currently facing the highest impact, reporting over 50,000 cases by early 2023. Here, we analyze 880 MPXV isolates worldwide to gain insights into the evolutionary patterns and initial introduction events of the virus in Mexico. We found that MPXV entered Mexico on multiple occasions, from the United Kingdom, Portugal, and Canada, and subsequently spread locally in different regions of Mexico. Additionally, we show that MPXV has an open pangenome, highlighting the role of gene turnover in shaping its genomic diversity, rather than SNPs variations, which do not contribute significantly to genome diversity. Although the genome presents multiple SNP sites in coding regions, these remain under purifying selection, suggesting their evolutionary conservation. One notable exception is the amino acid site 63 of the protein encoded by the Cop-A4L gene, intricately related to viral maturity, for which we picked up a strong signal of positive selection. Ancestral state reconstruction deduced that the ancestral state at site 63 corresponds to the amino acid valine, present only in isolates of clade I. However, the isolates of the current outbreak evolved for threonine at site 63. Finally, our findings contribute to the knowledge of the evolutionary processes of the Monkeypox virus.\n\nGenetic Insights into the Microevolutionary Dynamics and Early Introductions of Human Monkeypox Virus in Mexico", "token_count": 372, "char_count": 1583, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6527, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:00.844288", "source": { "split": "train_shard_00001", "doc_id": 1905 }, "chunk_id": "train_shard_00001_1905_0", "global_id": 8350 }, { "text": "Mycoplasmopsis bovis is a worldwide economically important pathogen of cattle that can cause or indirectly contribute to bovine respiratory disease. M. bovis is also a primary etiological agent of respiratory disease in bison with high mortality rates. A major challenge in the development of an efficacious M. bovis vaccine is the design of antigens that contain both MHC-1 and MHC-2 T-cell epitopes, and that account for population level diversity within the species. Publicly available genomes and sequence read archive libraries of 381 M. bovis strains isolated from cattle (n = 202) and bison (n = 179) in North America were used to identify a core genome of 575 genes, including 38 that encode either known or predicted secreted or outer membrane proteins. The antigenic potentials of the proteins were characterized by the presence and strength of their T-cell epitopes, and their protein variant diversity at the population-level. The proteins had surprisingly low diversity and varying predictive levels of T-cell antigenicity. These results provide a reference for the selection or design of antigens for vaccine testing against strains infecting North American cattle and bison.\n\nDiversity and antigenic potentials of Mycoplasmopsis bovis secreted and outer membrane proteins within a core genome of strains isolated from North American bison and cattle.", "token_count": 372, "char_count": 1414, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.7861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:01.432843", "source": { "split": "train_shard_00001", "doc_id": 1906 }, "chunk_id": "train_shard_00001_1906_0", "global_id": 8351 }, { "text": "

Background:

Multi-drug-resistant Gram negative bacteria producing metallo-β-lactamase are an increasing concern. Here we describe three cases of infection due to difficult to treat resistant P. aeruginosa producing metallo-β-lactamases, successfully treated with antibiotic combination of cefiderocol plus imipenem-relebactam and report on the molecular and epidemiological features of the isolates and the in vitro synergistic effects of different antibiotic combinations to guide the antibiotic treatment.Patients and methods: Three P. aeruginosa strains were isolated from respiratory or blood cultures of three different patients. Minimum inhibitory concentrations breackpoints were interpreted according to EUCAST recommendations. Next Generation Sequencing data were used for in silico identifying resistance genes, sequence types and for core genome multi-locus sequence typing analysis. The fractional inhibitory concentration index was performed as a measure of synergy of cefiderocol plus imipenem and imipenem-relebactam.

Results:

The three isolates exhibited different multi-drug resistant and molecular profiles, carrying blaIMP-13 (isolates named Pse-1 and Pse-3) and blaVIM-2 carbapenemases (isolate Pse-2). Typing showed that the isolates did not cluster and belonged to different sequence types. The E-test method showed the presence of synergy of cefiderocol in combination with imipenem-relebactam in the two P. aeruginosa isolates producing IMP-13 (Pse-1 and Pse-3). No synergy was observed in the isolate producing VIM-2 (Pse-2).

Conclusion:

Cefiderocol in association with imipenem-relebactam exhibited a synergistic effect against IMP-producing P. aeruginosa isolates. Further studies with a range of drugs and an expanded number of isolates are required to ascertain potential novel synergistic associations and the clinical utility of the fractional inhibitory concentration index.", "token_count": 482, "char_count": 1934, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6024, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:02.085335", "source": { "split": "train_shard_00001", "doc_id": 1907 }, "chunk_id": "train_shard_00001_1907_0", "global_id": 8352 }, { "text": "Combating Metallo-β-Lactamase-Producing Pseudomonas aeruginosa: The Fractional Inhibitory Concentration Index as a Tool to Evaluate Antibiotic Synergy", "token_count": 48, "char_count": 150, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:02.445330", "source": { "split": "train_shard_00001", "doc_id": 1907 }, "chunk_id": "train_shard_00001_1907_1", "global_id": 8353 }, { "text": "End 2023, the UK Health Security Agency sent an alert about a new hypervirulent Clostridioides difficile PCR ribotype, ribotype 955 (RT955), causing slowly progressing infection clusters in hospitals in the Midlands. Between March 2018 and February 2022, surveillance of Clostridioides difficile infections (CDI) was performed in southern Serbia with centres providing medical services for approximately 750,000 inhabitants. Using the ECDC recommended protocol, clinical, epidemiological and microbiological data were collected. C. difficile RT955 was identified in 27 (7%) of 383 surveyed patients with CDI. Of 27 patients, 16 (59%) was older than 60 years and 19 (70%) were male. CDI was always associated with previous antibiotic therapy and had a hospital onset in 23 (85%) patients. The clinical presentation was milder than reported in UK. All sequenced strains belonged to multilocus sequence type (ST) 1 and were highly similar, with 0-1 alleles differences in a core genome multilocus sequence typing analysis. The strains differed clearly from the UK RT955 outbreak strain by whole genome sequencing and phenotypic susceptibility to metronidazole, lincosamides and rifampicin. Interestingly, a high-level erythromycin resistance was observed associated with the presence of the mrmA gene. Both the UK and Serbian RT955 strains contained gyrA_p.T82I associated with resistance to fluoroquinolone antimicrobials and carried the PnimBG promoter mutation, suggestive for haem-dependent metronidazole resistance. We conclude that C. difficile RT955 is present in southern Serbia since 2018. The Serbian RT955 strains differed clearly from a representative UK cluster strain.", "token_count": 491, "char_count": 1721, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6807, "quality_score": 0.8403, "entities": { "genes": [ "RT955" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:03.090881", "source": { "split": "train_shard_00001", "doc_id": 1908 }, "chunk_id": "train_shard_00001_1908_0", "global_id": 8354 }, { "text": "Emerging <i>Clostridioides difficile</i> strains belonging to PCR ribotype 955 in Serbia are distinct from metronidazole-resistant RT955 outbreak isolates from the UK.", "token_count": 61, "char_count": 179, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [ "RT955" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:03.454623", "source": { "split": "train_shard_00001", "doc_id": 1908 }, "chunk_id": "train_shard_00001_1908_1", "global_id": 8355 }, { "text": "Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of Vibrio parahaemolyticus, a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups (IGs) involving 1,560 coding genes. 82 IGs are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. One strategy involves a divergent profile in multiple genome regions, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.\n\nThe landscape of coadaptation in <i>Vibrio parahaemolyticus</i>.", "token_count": 272, "char_count": 1122, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7484, "quality_score": 0.8742, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:04.016082", "source": { "split": "train_shard_00001", "doc_id": 1909 }, "chunk_id": "train_shard_00001_1909_0", "global_id": 8356 }, { "text": "A nationwide study on the occurrence of extended-spectrum β-lactamase (ESBL)/AmpC in nonhospitalized horses in the Netherlands was performed. Molecular characterization was done, and questionnaires were analyzed to identify factors associated with carriage. In total, 796 horse owners were approached; 281 of these submitted a fecal sample from their horse(s), resulting in 362 samples. All samples were cultured qualitatively in Luria-Bertani (LB) broth and subsequently on MacConkey agar, both supplemented with 1 mg/liter cefotaxime (LB+ and MC+). Positive samples were subsequently cultured quantitatively on MC+. Initial extended-spectrum-β-lactamase (ESBL)/AmpC screening was performed by PCR, followed by whole-genome sequencing on selected strains. Associations between ESBL/AmpC carriage and questionnaire items were analyzed using a univariate generalized estimating equation (GEE) regression analysis, followed by a multiple GEE model for relevant factors. In total, 39 of 362 samples (11%) were determined to be positive for ESBL/AmpC. blaCTX-M-1-carrying isolates were obtained from 77% of positive samples (n = 30)", "token_count": 332, "char_count": 1153, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:04.594956", "source": { "split": "train_shard_00001", "doc_id": 1910 }, "chunk_id": "train_shard_00001_1910_0", "global_id": 8357 }, { "text": "Other ESBL/AmpC genes observed included blaCTX-M-2, blaCTX-M-14, blaCTX-M-15, blaCTX-M-32, blaSHV-12, blaCMY-2, and blaACT-10 A high association between the presence of blaCTX-M-1 and IncHI1 plasmids was observed (46% of samples; n = 18). Based on core genome analysis (n = 48 isolates), six Escherichia coli clusters were identified, three of which represented 80% of the isolates. A negative association between ESBL/AmpC carriage and horses being in contact with other horses at a different site was observed. The presence of a dog on the premises and housing in a more densely human-populated region were positively associated.IMPORTANCE Extended-spectrum β-lactamases (ESBLs) are widespread in human and animal populations and in the environment. Many different ESBL variants exist. The dissemination of ESBLs within and between populations and the environment is also largely influenced by genetic mobile elements (e.g., plasmids) that facilitate spread of these ESBLs. In order to identify potential attributable ESBL sources for, e.g., the human population, it is important to identify the different ESBL variants, the bacteria carrying them, and the potential risk factors for ESBL carriage from other potential sources. This nationwide study focuses on ESBL carriage in the open horse population and investigated the molecular characteristics, geographical distribution throughout the Netherlands, and potential risk factors for fecal ESBL carriage in horses. These data can be used for future attribution studies in order to reduce potential transmission of ESBL-producing bacteria between sources.", "token_count": 507, "char_count": 1781, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6348, "quality_score": 0.8174, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:05.243488", "source": { "split": "train_shard_00001", "doc_id": 1910 }, "chunk_id": "train_shard_00001_1910_1", "global_id": 8358 }, { "text": "Fecal Carriage of Extended-Spectrum-β-Lactamase/AmpC-Producing Escherichia coli in Horses.", "token_count": 44, "char_count": 97, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:05.602740", "source": { "split": "train_shard_00001", "doc_id": 1910 }, "chunk_id": "train_shard_00001_1910_2", "global_id": 8359 }, { "text": "This study was intended to investigate the microbes involved in preparation Takrarishta. ‘Takrarishta’ is an ayurvedic fermented medicinal product used against inflammatory bowel disease (IBD). Total 13 cultures including 11 bacteria and 2 yeasts were isolated from actively fermenting Takrarishta. The isolates were characterized morphologically, biochemically and were further identified by 16S rRNA/18S rRNA ITS gene sequencing. Among the isolates, 8 isolates obeyed the probiotic characteristics while the principal component analysis (PCA) revealed that Lactobacillus plantarum TP5 and Kluyveromyces marxianus TP6 and TM1 were the most potent probiotics. The Takrarishta preparation is based upon strong scientific temperaments like modern concept of fermenting prebiotic, using probiotic microbes to get postbiotics for better efficacy. This outcome provides a strong evidence in support of Takrarishta being a fermented product for the treatment of IBD.\n\nFinding out potent probiotic cultures from ayurvedic formulation Takrarishta through in-vitro probiotic characterization and principal component analysis", "token_count": 289, "char_count": 1115, "word_count": 148, "semantic_coherence": 1, "information_density": 0.7162, "quality_score": 0.8581, "entities": { "genes": [ "TP5", "TM1", "TP6" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:06.161818", "source": { "split": "train_shard_00001", "doc_id": 1911 }, "chunk_id": "train_shard_00001_1911_0", "global_id": 8360 }, { "text": "

Introduction

Type F Clostridium perfringens (C. perfringens) represents a significant pathogen in human gastrointestinal diseases, primarily through its cpe gene encoding C. perfringens enterotoxin (CPE). This investigation examined the prevalence, antimicrobial resistance patterns, and genetic characteristics of Type F C. perfringens within the Chinese population.

Methods

The study analyzed 2,068 stool samples collected from 11 provincial hospitals in 2024. Antimicrobial susceptibility testing was conducted following Clinical & Laboratory Standards Institute (CLSI) guidelines, while whole-genome sequencing provided detailed genetic profiles. Evolutionary relationships and clonal transmission patterns were investigated through phylogenetic and genetic environment analyses.

Results

The prevalence of Type F C. perfringens was 2.38%, with isolates predominantly identified in human clinical samples and higher detection rates in gastroenterology departments. Notably, 47.1% of isolates demonstrated high resistance to metronidazole, while all exhibited intermediate resistance to erythromycin. Phylogenetic analysis revealed high similarity among isolates from patients within the same province (single-nucleotide polymorphism (SNPs)<100), and genetic environment analysis indicated potential horizontal gene transfer between animal and human strains.

Conclusions

This investigation predominantly identified Type F C. perfringens in human clinical cases, with sporadic detection in pets and food products. These findings highlight the emergence of Type F C. perfringens outbreaks among diarrheal patients, emphasizing the necessity for targeted interventions as virulence factors increase.\n\nMolecular Epidemiology of Type F Clostridium perfringens Among Diarrheal Patients and Virulence-Resistance Dynamics - 11 Provinces, China, 2024.", "token_count": 504, "char_count": 1936, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:06.812576", "source": { "split": "train_shard_00001", "doc_id": 1912 }, "chunk_id": "train_shard_00001_1912_0", "global_id": 8361 }, { "text": "

Objectives

Staphylococcus pseudintermedius is the primary pathogen that causes pyoderma in companion animals. The increasing number of multidrug-resistant strains, including methicillin-resistant S. pseudintermedius (MRSP), has become a major concern, highlighting the need for comprehensive data on antimicrobial susceptibility. Furthermore, with advancements in the accurate identification of S. pseudintermedius in human clinical patients, it is imperative to elucidate its definitive zoonotic potential.

Methods

We analyzed 111 strains of S. pseudintermedius derived from companion animals and 21 strains of S. pseudintermedius from human clinical patients to clarify antimicrobial susceptibility and correlation between strains derived from companion animals and humans.

Results

Approximately half of the animal-derived S. pseudintermedius isolates were MRSP. The isolates, particularly MRSP, exhibited high resistance to multiple antimicrobials used to treat pyoderma. Although florfenicol and fusidic acid are not approved for the treatment of pyoderma in companion animals in Japan, their efficacy has been demonstrated. Genetic analysis revealed that ST121, ST45, and ST71 were the most common ST types in animals. Additionally, ten novel STs were identified. ST45 and ST71 have frequently been identified in companion animals abroad, suggesting potential international transmission. However, ST121 has rarely been reported outside Japan, indicating its unique evolutionary trajectory within the country. Furthermore, these sequence types were identified in strains isolated from humans. Core genome analysis revealed nearly identical genotypes, suggesting transmission from companion animals to humans.

Conclusion

A limited number of approved antimicrobials are effective against S. pseudintermedius (particularly MRSP), which is being transmitted as a zoonotic infection from companion animals to humans.\n\nAntimicrobial susceptibility and genetic diversity of staphylococcus pseudintermedius isolated from companion animals and human clinical patients in Japan: Potential zoonotic implications.", "token_count": 488, "char_count": 2134, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7898, "entities": { "genes": [ "ST71", "ST45", "ST121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:07.460461", "source": { "split": "train_shard_00001", "doc_id": 1913 }, "chunk_id": "train_shard_00001_1913_0", "global_id": 8362 }, { "text": "The production of mead holds great value for the Polish liquor industry, which is why the bacterium that spoils mead has become an object of concern and scientific interest. This article describes, for the first time, Lactobacillus hilgardii FLUB newly isolated from mead, as a mead spoilage bacteria. Whole genome sequencing of L. hilgardii FLUB revealed a 3 Mbp chromosome and five plasmids, which is the largest reported genome of this species. An extensive phylogenetic analysis and digital DNA-DNA hybridization confirmed the membership of the strain in the L. hilgardii species. The genome of L. hilgardii FLUB encodes 3043 genes, 2871 of which are protein coding sequences, 79 code for RNA, and 93 are pseudogenes. L. hilgardii FLUB possesses three clustered regularly interspaced short palindromic repeats (CRISPR), eight genomic islands (44,155 bp to 6345 bp), and three (two intact and one incomplete) prophage regions. For the first time, the characteristics of the genome of this species were described and a pangenomic analysis was performed. The concept of the pangenome was used not only to establish the genetic repertoire of this species, but primarily to highlight the unique characteristics of L. hilgardii FLUB. The core of the genome of L. hilgardii is centered around genes related to the storage and processing of genetic information, as well as to carbohydrate and amino acid metabolism. Strains with such a genetic constitution can effectively adapt to environmental changes. L. hilgardii FLUB is distinguished by an extensive cluster of metabolic genes, arsenic detoxification genes, and unique surface layer proteins", "token_count": 474, "char_count": 1699, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:08.142828", "source": { "split": "train_shard_00001", "doc_id": 1914 }, "chunk_id": "train_shard_00001_1914_0", "global_id": 8363 }, { "text": "Variants of MRS broth with ethanol (10-20%), glucose (2-25%), and fructose (2-24%) were prepared to test the strain's growth preferences using Bioscreen C and the PYTHON script. L. hilgardii FLUB was found to be more resistant than a reference strain to high concentrations of alcohol (18%) and sugars (25%). It exhibited greater preference for fructose than glucose, which suggests it has a fructophilic nature. Comparative genomic analysis supported by experimental research imitating the conditions of alcoholic beverages confirmed the niche specialization of L. hilgardii FLUB to the mead environment.\n\nGenome and Pangenome Analysis of Lactobacillus hilgardii FLUB-A New Strain Isolated from Mead.", "token_count": 220, "char_count": 722, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:08.618329", "source": { "split": "train_shard_00001", "doc_id": 1914 }, "chunk_id": "train_shard_00001_1914_1", "global_id": 8364 }, { "text": "Macrococci are usually found as commensals on the skin and mucosa of animals and have been isolated from mammal-derived fermented foods; however, they can also act as opportunistic pathogens. Here, we used whole-genome sequencing, comparative genomics, extensive biotyping, MALDI-TOF mass spectrometry, and chemotaxonomy to characterize Macrococcus sp. strains isolated from livestock and human-related specimens. Based on the results of polyphasic taxonomy, we propose the species Macrococcus psychrotolerans sp. nov. (type strain NRL/St 95/376T = CCM 8659T = DSM 111350T) belonging to the Macrococcus caseolyticus phylogenetic clade. It grows at 4°C, and the core genome of the isolates contains suspected genes contributing to low-temperature tolerance. Variable genetic elements include prophages, chromosomal islands, a composite staphylococcal cassette chromosome island, and many plasmids that affect the overall genome expansion and adaptation to specific ecological settings of the studied isolates. Large plasmids carrying the methicillin resistance gene mecB were identified in M. psychrotolerans sp. nov. strains and confirmed as self-transmissible to Staphylococcus aureus in vitro. In addition to plasmids with circular topology, a 150-kb-long linear plasmid with 14.1-kb-long inverted terminal repeats, harboring many IS elements and putative genes for a type IV secretion system was revealed. The described strains were isolated from human clinical material, food-producing animals, meat, and a wooden cheese board and have the potential to proliferate at refrigerator temperatures", "token_count": 476, "char_count": 1672, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7248, "quality_score": 0.8624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:09.318569", "source": { "split": "train_shard_00001", "doc_id": 1915 }, "chunk_id": "train_shard_00001_1915_0", "global_id": 8365 }, { "text": "Their presence in the food chain and human infections indicates that attention needs to be paid to this potential novel opportunistic pathogen.IMPORTANCEThe study offers insights into the phenotypic and genomic features of a novel species of the genus Macrococcus that occurs in livestock, food, and humans. The large number of diverse mobile genetic elements contributes to the adaptation of macrococci to various environments. The ability of the described microorganisms to grow at refrigerator temperatures, enabled by genes that are predicted to contribute to low-temperature tolerance, raises food safety concerns. Confirmed in vitro conjugative transfer of plasmid-borne mecB gene to S. aureus poses a significant risk of spread of broad β-lactam resistance. In addition, the intergeneric plasmid transfer to S. aureus is indicative of horizontal gene transfer events that may be more frequent than generally accepted. Determining a complete sequence and gene content of linear megaplasmid with exceptional topology for the Staphylococcaceae family suggests its possible role in shuttling adaptive traits through an exchange of genetic information.\n\nEvidence of <i>in vitro mecB</i>-mediated β-lactam antibiotic resistance transfer to <i>Staphylococcus aureus</i> from <i>Macrococcus psychrotolerans</i> sp. nov., a psychrophilic bacterium from food-producing animals and human clinical specimens.", "token_count": 391, "char_count": 1481, "word_count": 193, "semantic_coherence": 1, "information_density": 0.715, "quality_score": 0.8575, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:09.941873", "source": { "split": "train_shard_00001", "doc_id": 1915 }, "chunk_id": "train_shard_00001_1915_1", "global_id": 8366 }, { "text": "Pantoea ananatis, a gram negative and facultative anaerobic bacterium is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally comprised of 14 genes), for a phosphonate secondary metabolite, and the 'alt' gene cluster (located in plasmid and comprised of 11 genes) that aids in bacterial colonization in onion bulbs by imparting tolerance to thiosulfinates. We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51)- vs. non-pathogenic (n = 30)-strains phenotypically. Pan-genome analysis revealed a large core genome of 3,153 genes and a flexible accessory genome. Pan-GWAS using the presence and absence variants (PAVs) predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion. Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, conjugal transfer, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Further, a core-genome SNPs-based phylogeny and horizontal gene transfer (HGT) studies were also conducted to assess the extent of lateral gene transfer among diverse P", "token_count": 519, "char_count": 1793, "word_count": 250, "semantic_coherence": 1, "information_density": 0.696, "quality_score": 0.848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:10.601310", "source": { "split": "train_shard_00001", "doc_id": 1916 }, "chunk_id": "train_shard_00001_1916_0", "global_id": 8367 }, { "text": "ananatis strains. Phylogenetic analysis based on PAVs and whole genome multi locus sequence typing (wgMLST) rather than core-genome SNPs distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. A total of 1182 HGT events including the HiVir/PASVIL and alt cluster genes were identified. These events could be regarded as a major contributing factor to the diversification, niche-adaptation and potential acquisition of pathogenicity/virulence genes in P. ananatis.\n\nPan-Genome-Wide Analysis of Pantoea ananatis Identified Genes Linked to Pathogenicity in Onion.", "token_count": 207, "char_count": 673, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7738, "quality_score": 0.8869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:11.059194", "source": { "split": "train_shard_00001", "doc_id": 1916 }, "chunk_id": "train_shard_00001_1916_1", "global_id": 8368 }, { "text": "Bifidobacteria are members of the gut microbiota of animals, including mammals, birds, and social insects. In this study, we analyzed and determined the pangenome of Bifidobacterium animalis species, encompassing B. animalis subsp. animalis and the B. animalis subsp. lactis taxon, which is one of the most intensely exploited probiotic bifidobacterial species. In order to reveal differences within the B. animalis species, detailed comparative genomics and phylogenomics analyses were performed, indicating that these two subspecies recently arose through divergent evolutionary events. A subspecies-specific core genome was identified for both B. animalis subspecies, revealing the existence of subspecies-defining genes involved in carbohydrate metabolism. Notably, these in silico analyses coupled with carbohydrate profiling assays suggest genetic adaptations toward a distinct glycan milieu for each member of the B. animalis subspecies, resulting in a divergent evolutionary development of the two subspecies.IMPORTANCE The majority of characterized B. animalis strains have been isolated from human fecal samples. In order to explore genome variability within this species, we isolated 15 novel strains from the gastrointestinal tracts of different animals, including mammals and birds. The present study allowed us to reconstruct the pangenome of this taxon, including the genome contents of 56 B. animalis strains. Through careful assessment of subspecies-specific core genes of the B. animalis subsp. animalis/lactis taxon, we identified genes encoding enzymes involved in carbohydrate transport and metabolism, while unveiling specific gene acquisition and loss events that caused the evolutionary emergence of these two subspecies.", "token_count": 505, "char_count": 1850, "word_count": 239, "semantic_coherence": 1, "information_density": 0.59, "quality_score": 0.795, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:11.704350", "source": { "split": "train_shard_00001", "doc_id": 1917 }, "chunk_id": "train_shard_00001_1917_0", "global_id": 8369 }, { "text": "Dissecting the Evolutionary Development of the Species Bifidobacterium animalis through Comparative Genomics Analyses.", "token_count": 36, "char_count": 125, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:12.065346", "source": { "split": "train_shard_00001", "doc_id": 1917 }, "chunk_id": "train_shard_00001_1917_1", "global_id": 8370 }, { "text": "Francisella tularensis is one of several biothreat agents for which a licensed vaccine is needed to protect against this pathogen. To aid in the development of a vaccine protective against pneumonic tularemia, we generated and characterized a panel of F. tularensis isolates that can be used as challenge strains to assess vaccine efficacy. Our panel consists of both historical and contemporary isolates derived from clinical and environmental sources, including human, tick, and rabbit isolates. Whole genome sequencing was performed to assess the genetic diversity in comparison to the reference genome F. tularensis Schu S4. Average nucleotide identity analysis showed >99% genomic similarity across the strains in our panel, and pan-genome analysis revealed a core genome of 1,707 genes, and an accessory genome of 233 genes. Three of the strains in our panel, FRAN254 (tick-derived), FRAN255 (a type B strain), and FRAN256 (a human isolate) exhibited variation from the other strains. Moreover, we identified several unique mutations within the Francisella Pathogenicity Island across multiple strains in our panel, revealing unexpected diversity in this region. Notably, FRAN031 (Scherm) completely lacked the second pathogenicity island but retained virulence in mice. In contrast, FRAN037 (Coll) was attenuated in a murine pneumonic tularemia model and had mutations in pdpB and iglA which likely led to attenuation. All of the strains, except FRAN037, retained full virulence, indicating their effectiveness as challenge strains for future vaccine testing. Overall, we provide a well-characterized panel of virulent F. tularensis strains that can be utilized in ongoing efforts to develop an effective vaccine against pneumonic tularemia to ensure protection is achieved across a range F. tularensis strains.", "token_count": 500, "char_count": 1874, "word_count": 267, "semantic_coherence": 1, "information_density": 0.603, "quality_score": 0.8015, "entities": { "genes": [ "FRAN037", "FRAN255", "FRAN031", "FRAN254", "FRAN256" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:12.713394", "source": { "split": "train_shard_00001", "doc_id": 1918 }, "chunk_id": "train_shard_00001_1918_0", "global_id": 8371 }, { "text": "Development, Phenotypic Characterization and Genomic Analysis of a Francisella tularensis Panel for Tularemia Vaccine Testing.", "token_count": 43, "char_count": 133, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:13.070958", "source": { "split": "train_shard_00001", "doc_id": 1918 }, "chunk_id": "train_shard_00001_1918_1", "global_id": 8372 }, { "text": "Streptococcus agalactiae evasion from the human defense mechanisms has been linked to the production of DNases. These were proposed to contribute to the hypervirulence of S. agalactiae ST17/capsular-type III strains, mostly associated with neonatal meningitis. We performed a comparative genomic analysis between ST17 and ST19 human strains with different cell tropism and distinct DNase production phenotypes. All S. agalactiae ST17 strains, with the exception of 2211-04, were found to display DNase activity, while the opposite scenario was observed for ST19, where 1203-05 was the only DNase(+) strain. The analysis of the genetic variability of the seven genes putatively encoding secreted DNases in S. agalactiae revealed an exclusive amino acid change in the predicted signal peptide of GBS0661 (NucA) of the ST17 DNase(-), and an exclusive amino acid change alteration in GBS0609 of the ST19 DNase(+) strain. Further core-genome analysis identified some specificities (SNVs or indels) differentiating the DNase(-) ST17 2211-04 and the DNase(+) ST19 1203-05 from the remaining strains of each ST. The pan-genomic analysis evidenced an intact phage without homology in S. agalactiae and a transposon homologous to TnGBS2.3 in ST17 DNase(-) 2211-04; the transposon was also found in one ST17 DNase(+) strain, yet with a different site of insertion. A group of nine accessory genes were identified among all ST17 DNase(+) strains, including the Eco47II family restriction endonuclease and the C-5 cytosine-specific DNA methylase. None of these loci was found in any DNase(-) strain, which may suggest that these proteins might contribute to the lack of DNase activity", "token_count": 500, "char_count": 1671, "word_count": 250, "semantic_coherence": 1, "information_density": 0.564, "quality_score": 0.782, "entities": { "genes": [ "ST17", "ST19", "GBS0661", "GBS0609" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:13.720634", "source": { "split": "train_shard_00001", "doc_id": 1919 }, "chunk_id": "train_shard_00001_1919_0", "global_id": 8373 }, { "text": "In summary, we provide novel insights on the genetic diversity between DNase(+) and DNase(-) strains, and identified genetic traits, namely specific mutations affecting predicted DNases (NucA and GBS0609) and differences in the accessory genome, that need further investigation as they may justify distinct DNase-related virulence phenotypes in S. agalactiae .\n\nGenomic insights on DNase production inStreptococcus agalactiaeST17 and ST19 strains", "token_count": 128, "char_count": 453, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [ "ST17", "ST19", "GBS0609" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:14.145656", "source": { "split": "train_shard_00001", "doc_id": 1919 }, "chunk_id": "train_shard_00001_1919_1", "global_id": 8374 }, { "text": "With increasing urbanization and industrialization, the prevalence of inflammatory bowel diseases (IBDs) has steadily been rising over the past two decades. IBD involves flares of gastrointestinal (GI) inflammation accompanied by microbiota perturbations. However, microbial mechanisms that trigger such flares remain elusive. Here, we analyzed the association of the emerging pathogen atypical enteropathogenic E. coli (aEPEC) with IBD disease activity. The presence of diarrheagenic E. coli was assessed in stool samples from 630 IBD patients and 234 age- and sex-matched controls without GI symptoms. Microbiota was analyzed with 16S ribosomal RNA gene amplicon sequencing, and 57 clinical aEPEC isolates were subjected to whole-genome sequencing and in vitro pathogenicity experiments including biofilm formation, epithelial barrier function and the ability to induce pro-inflammatory signaling. The presence of aEPEC correlated with laboratory, clinical and endoscopic disease activity in ulcerative colitis (UC), as well as microbiota dysbiosis. In vitro, aEPEC strains induce epithelial p21-activated kinases, disrupt the epithelial barrier and display potent biofilm formation. The effector proteins espV and espG2 distinguish aEPEC cultured from UC and Crohn's disease patients, respectively. EspV-positive aEPEC harbor more virulence factors and have a higher pro-inflammatory potential, which is counteracted by 5-ASA. aEPEC may tip a fragile immune-microbiota homeostasis and thereby contribute to flares in UC. aEPEC isolates from UC patients display properties to disrupt the epithelial barrier and to induce pro-inflammatory signaling in vitro.\n\nAtypical enteropathogenic E. coli are associated with disease activity in ulcerative colitis.", "token_count": 501, "char_count": 1789, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:14.796393", "source": { "split": "train_shard_00001", "doc_id": 1920 }, "chunk_id": "train_shard_00001_1920_0", "global_id": 8375 }, { "text": "

Background

Bacterial genomes follow a U-shaped frequency distribution whereby most genomic loci are either rare (accessory) or common (core); the union of these is the pan-genome. The alignable fraction of two genomes from a single species can be low (e.g. 50-70%), such that no single reference genome can access all single nucleotide polymorphisms (SNPs). The pragmatic solution is to choose a close reference, and analyse SNPs only in the core genome. Given much bacterial adaptability hinges on the accessory genome, this is an unsatisfactory limitation.

Results

We present a novel pan-genome graph structure and algorithms implemented in the software pandora , which approximates a sequenced genome as a recombinant of reference genomes, detects novel variation and then pan-genotypes multiple samples. The method takes fastq as input and outputs a multi-sample VCF with respect to an inferred data-dependent reference genome, and is available at https://github.com/rmcolq/pandora . Constructing a reference graph from 578 E. coli genomes, we analyse a diverse set of 20 E. coli isolates. We show pandora recovers at least 13k more rare SNPs than single-reference based tools, achieves equal or better error rates with Nanopore as with Illumina data, 6-24x lower Nanopore error rates than other tools, and provides a stable framework for analysing diverse samples without reference bias. We also show that our inferred recombinant VCF reference genome is significantly better than simply picking the closest RefSeq reference.

Conclusions

This is a step towards comprehensive cohort analysis of bacterial pan-genomic variation, with potential impacts on genotype/phenotype and epidemiological studies.\n\nNucleotide-resolution bacterial pan-genomics with reference graphs", "token_count": 458, "char_count": 1800, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6576, "quality_score": 0.8288, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:15.444287", "source": { "split": "train_shard_00001", "doc_id": 1921 }, "chunk_id": "train_shard_00001_1921_0", "global_id": 8376 }, { "text": "Candidatus Accumulibacter plays a major role in enhanced biological phosphorus removal (EBPR), but the key genomic elements in metagenome assembled genomes enabling their phosphorus cycling ability remain unclear. Pangenome analyses were performed to systematically compare the genomic makeup of Ca. Accumulibacter and non- Ca . Accumulibacter members within the Rhodocyclaceae family. Metatranscriptomic analyses of an enrichment culture of Ca. Accumulibacter clade IIC strain SCUT-2 were performed to investigate gene transcription characteristics in a typical anaerobic-aerobic cycle. Two hundred ninety-eight core genes were shown to be obtained by Ca. Accumulibacter at their least common ancestor. One hundred twenty-four of them were acquired via horizontal gene transfer (HGT) based on best-match analysis against the NCBI database. Fourty-four laterally derived genes were actively transcribed in a typical EBPR cycle, including the polyphosphate kinase 2 (PPK2) gene. Genes in the phosphate regulon (Pho) were poorly transcribed. Via a systematical analysis of the occurrences of these genes in closely related Dechloromonas -polyphosphate accumulating organisms (PAOs) and Propionivibrio -non-PAOs, a Pho dysregulation hypothesis is proposed to explain the mechanism of EBPR. It states that the PhoU acquired by HGT fails in regulating the high-affinity phosphate transport (Pst) system. To avoid phosphate poisoning, the laterally acquired PPK2 is employed to condense excess phosphate into polyphosphate. Alternatively, genes encoding PhoU and PPK2 are obtained from different donor bacteria, leading to unmatched phosphate concentration thresholds for their activation/inactivation. PPK2 tends to reduce the intracellular phosphate to concentration levels perceived by PhoU as low-phosphate states. PhoU is not activated to turn off the Pst system, resulting in continuous phosphate uptake. In conclusion, based on integrated genomic analyses, the HGT of pho U and ppk 2 and the resultant Pho dysregulation may have triggered the development and evolution of the P cycling trait in Ca. Accumulibacter.", "token_count": 529, "char_count": 2115, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6373, "quality_score": 0.8186, "entities": { "genes": [ "PPK2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:16.103938", "source": { "split": "train_shard_00001", "doc_id": 1922 }, "chunk_id": "train_shard_00001_1922_0", "global_id": 8377 }, { "text": "Integrated genomics provides insights for the evolution of the polyphosphate accumulation trait ofCa.Accumulibacter", "token_count": 32, "char_count": 122, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:16.468222", "source": { "split": "train_shard_00001", "doc_id": 1922 }, "chunk_id": "train_shard_00001_1922_1", "global_id": 8378 }, { "text": "

Background

Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.

Results

We developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium. Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 min on a conventional computer. Moreover, the interaction networks that our software creates reflect correct evolutionary relationships between species, which we confirmed with average nucleotide identity analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user's choice regarding which set of genomes they are going to study.

Conclusions

GENPPI can help fill the gap concerning the considerable number of novel genomes assembled monthly and our ability to process interaction networks considering the noncore genes for all completed genome versions. With GENPPI, a user dictates how many and how evolutionarily correlated the genomes answer a scientific query.\n\nGENPPI: standalone software for creating protein interaction networks from genomes.", "token_count": 501, "char_count": 2330, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5963, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:17.117784", "source": { "split": "train_shard_00001", "doc_id": 1923 }, "chunk_id": "train_shard_00001_1923_0", "global_id": 8379 }, { "text": "Emerging and re-emerging plant diseases continue to present multifarious threats to global food security. Considerable recent efforts are therefore being channeled towards understanding the nature of pathogen emergence, their spread and evolution. Xanthomonas euvesicatoria pv. perforans (Xep ), one of the causal agents of bacterial spot of tomato, rapidly emerged and displaced other bacterial spot xanthomonads in tomato production regions around the world. In less than three decades, it has become a dominant xanthomonad pathogen in tomato production systems across the world and presents a model for understanding diversification of recently emerged bacterial plant pathogens. Although Xep has been continuously monitored in Florida since its discovery, the global population structure and evolution at the genome-scale is yet to be fully explored. The objectives of this work were to determine genetic diversity globally to ascertain if different tomato production regions contain genetically distinct Xep populations, to examine genetic relatedness of strains collected in tomato seed production areas in East Asia and other production regions, and to evaluate variation in type III effectors, which are critical pathogenicity and virulence factors, in relationship to population structure. We used genome data from 270 strains from 13 countries for phylogenetic analysis and characterization of Xop effector gene diversity among strains. Our results showed notable genetic diversity in the pathogen. We found genetically similar strains in distant tomato production regions, including seed production regions, and diversification over the past 100 years, which is consistent with intercontinental dissemination of the pathogen in hybrid tomato production chains. Evolution of the Xep pangenome, including the acquisition and loss of type III secreted effectors, is apparent within and among phylogenetic lineages. The apparent long-distance movement of the pathogen, together with variants that may not yet be widely distributed, poses risks of emergence of new variants in tomato production.\n\nDiversification of an emerging bacterial plant pathogen; insights from the global spread ofXanthomonas euvesicatoriapv.perforans", "token_count": 479, "char_count": 2245, "word_count": 312, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:17.765848", "source": { "split": "train_shard_00001", "doc_id": 1924 }, "chunk_id": "train_shard_00001_1924_0", "global_id": 8380 }, { "text": "

Motivation

Aligning reads to a variation graph is a standard task in pangenomics, with downstream applications such as improving variant calling. While the vg toolkit [Garrison et al. (Variation graph toolkit improves read mapping by representing genetic variation in the reference. Nat Biotechnol 2018;36:875-9)] is a popular aligner of short reads, GraphAligner [Rautiainen and Marschall (GraphAligner: rapid and versatile sequence-to-graph alignment. Genome Biol 2020;21:253-28)] is the state-of-the-art aligner of erroneous long reads. GraphAligner works by finding candidate read occurrences based on individually extending the best seeds of the read in the variation graph. However, a more principled approach recognized in the community is to co-linearly chain multiple seeds.

Results

We present a new algorithm to co-linearly chain a set of seeds in a string labeled acyclic graph, together with the first efficient implementation of such a co-linear chaining algorithm into a new aligner of erroneous long reads to acyclic variation graphs, GraphChainer. We run experiments aligning real and simulated PacBio CLR reads with average error rates 15% and 5%. Compared to GraphAligner, GraphChainer aligns 12-17% more reads, and 21-28% more total read length, on real PacBio CLR reads from human chromosomes 1, 22, and the whole human pangenome. On both simulated and real data, GraphChainer aligns between 95% and 99% of all reads, and of total read length. We also show that minigraph [Li et al. (The design and construction of reference pangenome graphs with minigraph. Genome Biol 2020;21:265-19.)] and minichain [Chandra and Jain (Sequence to graph alignment using gap-sensitive co-linear chaining. In: Proceedings of the 27th Annual International Conference on Research in Computational Molecular Biology (RECOMB 2023)", "token_count": 515, "char_count": 1844, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6189, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:18.427092", "source": { "split": "train_shard_00001", "doc_id": 1925 }, "chunk_id": "train_shard_00001_1925_0", "global_id": 8381 }, { "text": "Springer, 2023, 58-73.)] obtain an accuracy of <60% on this setting.

Availability and implementation

GraphChainer is freely available at https://github.com/algbio/GraphChainer. The datasets and evaluation pipeline can be reached from the previous address.\n\nChaining for accurate alignment of erroneous long reads to acyclic variation graphs.", "token_count": 93, "char_count": 348, "word_count": 42, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:18.798406", "source": { "split": "train_shard_00001", "doc_id": 1925 }, "chunk_id": "train_shard_00001_1925_1", "global_id": 8382 }, { "text": "The effects of adding trace acids in ethanol based organosolv treatment were investigated to increase the enzymatic digestibility of Japanese cypress. A high glucose yield (60%) in the enzymatic hydrolysis was obtained by treating the sample at 170 °C for 45 min in 50% ethanol liquor containing 0.4% hydrochloric acid. Moreover, the enzymatic digestibility of the treated sample was improved to ∼70% by changing the enzyme from acremonium cellulase to Accellerase1500. Field emission scanning electron microscopy revealed the presence of lignin droplets and partial cellulose nanofibers on the surface of the treated sample. Simultaneous saccharification and fermentation of the treated samples using thermotolerant yeast (Kluyveromyces marxianus NBRC1777) was tested. A high ethanol concentration (22.1 g/L) was achieved using the EtOH50/W50/HCl0.4-treated sample compared with samples from other treatments.\n\nEthanol-based organosolv treatment with trace hydrochloric acid improves the enzymatic digestibility of Japanese cypress (Chamaecyparis obtusa) by exposing nanofibers on the surface.", "token_count": 306, "char_count": 1094, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8221, "entities": { "genes": [ "NBRC1777" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:19.369461", "source": { "split": "train_shard_00001", "doc_id": 1926 }, "chunk_id": "train_shard_00001_1926_0", "global_id": 8383 }, { "text": "

Objectives

To analyse characteristics of Clostridioides difficile PCR ribotype 176 clinical isolates from Poland, the Czech Republic and Slovakia with regard to the differences in its epidemiology.

Methods

Antimicrobial susceptibility testing and whole genome sequencing were performed on a selected group of 22 clonally related isolates as determined by multilocus variable-number tandem repeat analysis (n = 509). Heterologous expression and functional analysis of the newly identified methyltransferase were performed.

Results

Core genome multilocus sequence typing found 10-37 allele differences. All isolates were resistant to fluoroquinolones (gyrA_p. T82I), aminoglycosides with aac(6')-Ie-aph(2'')-Ia in six isolates. Erythromycin resistance was detected in 21/22 isolates and 15 were also resistant to clindamycin with ermB gene. Fourteen isolates were resistant to rifampicin with rpoB_p. R505K or p. R505K/H502N, and five to imipenem with pbp1_p. P491L and pbp3_p. N537K. PnimBG together with nimB_p. L155I were detected in all isolates but only five were resistant to metronidazole on chocolate agar. The cfrE, vanZ1 and cat-like genes were not associated with linezolid, teicoplanin and chloramphenicol resistance, respectively. The genome comparison identified six transposons carrying antimicrobial resistance genes", "token_count": 505, "char_count": 1461, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:20.058132", "source": { "split": "train_shard_00001", "doc_id": 1927 }, "chunk_id": "train_shard_00001_1927_0", "global_id": 8384 }, { "text": "The ermB gene was carried by new Tn7808, Tn6189 and Tn6218-like. The aac(6')-Ie-aph(2'')-Ia were carried by Tn6218-like and new Tn7806 together with cfrE gene. New Tn7807 carried a cat-like gene. Tn6110 and new Tn7806 contained an RlmN-type 23S rRNA methyltransferase, designated MrmA, associated with high-level macrolide resistance in isolates without ermB gene.

Conclusions

Multidrug-resistant C. difficile PCR ribotype 176 isolates carry already described and unique transposons. A novel mechanism for erythromycin resistance in C. difficile was identified.\n\nGenomic islands and molecular mechanisms relating to drug-resistance in <i>Clostridioides</i> (<i>Clostridium</i>) <i>difficile</i> PCR ribotype 176.", "token_count": 382, "char_count": 874, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:20.664614", "source": { "split": "train_shard_00001", "doc_id": 1927 }, "chunk_id": "train_shard_00001_1927_1", "global_id": 8385 }, { "text": "

Background

Clinically important lineages in Klebsiella, especially those expressing multi-drug resistance (MDR), pose severe threats to public health worldwide. They arose from the co-evolution of the vertically inherited core genome and horizontal gene transfers by plasmids, which has not been systematically explored.

Methods

We designed KleTy, which consists of dedicated typing schemes for both the core genome and plasmids in Klebsiella. We compared the performance of KleTy with many state-of-the-art pipelines using both simulated and real data.

Results

Employing KleTy, we genotyped 33,272 Klebsiella genomes, categorizing them into 1773 distinct populations and predicting the presence of 87,410 plasmids from 837 clusters (PCs). Notably, Klebsiella is the center of the plasmid-exchange network within Enterobacteriaceae. Our results associated the international emergence of prevalent Klebsiella populations with only four carbapenem-resistance (CR) PCs, two hypervirulent PCs, and two hvCR-PCs encoding both carbapenemase and hypervirulence. Furthermore, we observed the ongoing international emergence of blaNDM, accompanied by the replacement of the previously dominant population, blaKPC-encoding HC1360_8 (CC258), during 2003-2018, with the emerging blaNDM-encoding HC1360_3 (CC147) thereafter", "token_count": 392, "char_count": 1365, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [ "CC258", "CC147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:21.316545", "source": { "split": "train_shard_00001", "doc_id": 1928 }, "chunk_id": "train_shard_00001_1928_0", "global_id": 8386 }, { "text": "Additionally, expansions of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hvCRKP) were evidenced in both populations, driven by plasmids of MDR-hypervirulence convergences.

Conclusions

The study illuminates how the global genetic landscape of Klebsiella has been shaped by the co-evolution of both the core genome and the plasmids, underscoring the importance of surveillance and control of the dissemination of plasmids for curtailing the emergence of hvCRKPs.\n\nKleTy: integrated typing scheme for core genome and plasmids reveals repeated emergence of multi-drug resistant epidemic lineages in Klebsiella worldwide.", "token_count": 172, "char_count": 636, "word_count": 80, "semantic_coherence": 1, "information_density": 0.6625, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:21.807388", "source": { "split": "train_shard_00001", "doc_id": 1928 }, "chunk_id": "train_shard_00001_1928_1", "global_id": 8387 }, { "text": "

Background

Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage.

Methods

We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features.

Results

Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of \"hybrid\" resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype.

Conclusions

To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.", "token_count": 501, "char_count": 1866, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6624, "quality_score": 0.8312, "entities": { "genes": [ "ST395" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:22.459063", "source": { "split": "train_shard_00001", "doc_id": 1929 }, "chunk_id": "train_shard_00001_1929_0", "global_id": 8388 }, { "text": "Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395.", "token_count": 29, "char_count": 103, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:22.823023", "source": { "split": "train_shard_00001", "doc_id": 1929 }, "chunk_id": "train_shard_00001_1929_1", "global_id": 8389 }, { "text": "Ethanol production by K. marxianus in whey from organic cheese production was examined in batch and continuous mode. The results showed that no pasteurization or freezing of the whey was necessary and that K. marxianus was able to compete with the lactic acid bacteria added during cheese production. The results also showed that, even though some lactic acid fermentation had taken place prior to ethanol fermentation, K. marxianus was able to take over and produce ethanol from the remaining lactose, since a significant amount of lactic acid was not produced (1-2 g/l). Batch fermentations showed high ethanol yield (~0.50 g ethanol/g lactose) at both 30°C and 40°C using low pH (4.5) or no pH control. Continuous fermentation of nonsterilized whey was performed using Ca-alginate-immobilized K. marxianus. High ethanol productivity (2.5-4.5 g/l/h) was achieved at dilution rate of 0.2/h, and it was concluded that K. marxianus is very suitable for industrial ethanol production from whey.\n\nProduction of bioethanol from organic whey using Kluyveromyces marxianus.", "token_count": 309, "char_count": 1067, "word_count": 163, "semantic_coherence": 1, "information_density": 0.5951, "quality_score": 0.7975, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:23.397691", "source": { "split": "train_shard_00001", "doc_id": 1930 }, "chunk_id": "train_shard_00001_1930_0", "global_id": 8390 }, { "text": "Soil-borne Ralstonia solanacearum species complex (RSSC) bacteria disrupt rhizosphere and endophytic microbial communities as they invade roots and fatally wilt plants. RSSC pathogens secrete antimicrobial toxins using a type VI secretion system (T6SS). To investigate how evolution and ecology have shaped pathogen T6SS biology, we analyzed the T6SS gene content and architecture across the RSSC pangenome and their evolutionarily relatives. Our analysis reveals that two ecologically similar Burkholderiaceae taxa, xylem pathogenic RSSC bacteria and Acidovorax , have convergently evolved to wield large arsenals of T6SS toxins. To understand the mechanisms underlying genomic enrichment of T6SS toxins, we compiled an atlas of 1,069 auxiliary (“ aux ”) T6SS toxin clusters across 99 high-quality RSSC genomes. We classified 25 types of aux clusters with toxins that predominantly target lipids, nucleic acids, or unknown cellular substrates. The aux clusters were in diverse genetic neighborhoods and had complex phylogenetic distributions, suggesting frequent horizontal gene flow. Phages and other mobile genetic elements account for most of the aux cluster acquisition on the chromosome but very little on the megaplasmid. Nevertheless, RSSC genomes were more enriched in aux clusters on the megaplasmid. Secondary replicons like megaplasmids often evolve more rapidly than the more evolutionarily stable chromosome. Although the single ancestral T6SS was broadly conserved in the RSSC, the T6SS was convergently lost in atypical lineages with vectored transmission. Overall, our data suggest dynamic interplay between the lifestyle of soil-transmitted RSSC lineages and the evolution of T6SSs with robust arsenals of toxins. This pangenomic atlas poises the RSSC as an emerging, tractable model to understand the role of the T6SS in shaping pathogen populations.\n\nA pangenomic atlas reveals that eco-evolutionary dynamics shape plant pathogen type VI secretion systems", "token_count": 502, "char_count": 1975, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6477, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:24.049000", "source": { "split": "train_shard_00001", "doc_id": 1931 }, "chunk_id": "train_shard_00001_1931_0", "global_id": 8391 }, { "text": "

Motivation

Pangenome graphs provide a complete representation of the mutual alignment of collections of genomes. These models offer the opportunity to study the entire genomic diversity of a population, including structurally complex regions. Nevertheless, analyzing hundreds of gigabase-scale genomes using pangenome graphs is difficult as it is not well-supported by existing tools. Hence, fast and versatile software is required to ask advanced questions to such data in an efficient way.

Results

We wrote ODGI, a novel suite of tools that implements scalable algorithms and has an efficient in-memory representation of DNA pangenome graphs in the form of variation graphs. ODGI supports pre-built graphs in the Graphical Fragment Assembly format. ODGI includes tools for detecting complex regions, extracting pangenomic loci, removing artifacts, exploratory analysis, manipulation, validation, and visualization. Its fast parallel execution facilitates routine pangenomic tasks, as well as pipelines that can quickly answer complex biological questions of gigabase-scale pangenome graphs.

Availability

ODGI is published as free software under the MIT open source license. Source code can be downloaded from https://github.com/pangenome/odgi and documentation is available at https://odgi.readthedocs.io . ODGI can be installed via Bioconda https://bioconda.github.io/recipes/odgi/README.html or GNU Guix https://github.com/pangenome/odgi/blob/master/guix.scm .

Contact

egarris5@uthsc.edu\n\nODGI: understanding pangenome graphs", "token_count": 386, "char_count": 1565, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7026, "quality_score": 0.8513, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:24.664555", "source": { "split": "train_shard_00001", "doc_id": 1932 }, "chunk_id": "train_shard_00001_1932_0", "global_id": 8392 }, { "text": "A thermotolerant Kluyveromyces marxianus mutant was developed by exposing yeast cultures repeatedly to 48°C incubation temperature, and the strain was characterized with a significantly increased trehalose content. Unexpectedly, the strain was sensitive to alcohol, osmotic and oxidative stress, which correlated with the increases in the trehalose concentrations. Intracellular glutathione levels declined in both wild-type and mutant cells when exposed to elevating incubation temperatures. Finally, we reached the surprising conclusion that neither trehalose nor glutathione metabolisms should be aimed at in future strain development programs with K. marxianus.\n\nTrehalose overproduction affects the stress tolerance of Kluyveromyces marxianus ambiguously.", "token_count": 177, "char_count": 760, "word_count": 97, "semantic_coherence": 1, "information_density": 0.732, "quality_score": 0.866, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:25.113031", "source": { "split": "train_shard_00001", "doc_id": 1933 }, "chunk_id": "train_shard_00001_1933_0", "global_id": 8393 }, { "text": "Co-linear chaining is a widely used technique in sequence alignment tools that follow seed-filter-extend methodology. It is a mathematically rigorous approach to combine short exact matches. For colinear chaining between two sequences, efficient subquadratic-time chaining algorithms are well-known for linear, concave and convex gap cost functions [Eppstein et al . JACM’92]. However, developing extensions of chaining algorithms for directed acyclic graphs (DAGs) has been challenging. Recently, a new sparse dynamic programming framework was introduced that exploits small path cover of pangenome reference DAGs, and enables efficient chaining [Makinen et al . TALG’19, RECOMB’18]. However, the underlying problem formulation did not consider gap cost which makes chaining less effective in practice. To address this, we develop novel problem formulations and optimal chaining algorithms that support a variety of gap cost functions. We demonstrate empirically the ability of our provably-good chaining implementation to align long reads more precisely in comparison to existing aligners. For mapping simulated long reads from human genome to a pangenome DAG of 95 human haplotypes, we achieve 98.7% precision while leaving < 2% reads unmapped.

Implementation

https://github.com/at-cg/minichain\n\nSequence to graph alignment using gap-sensitive co-linear chaining", "token_count": 319, "char_count": 1374, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7112, "quality_score": 0.8556, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:25.663050", "source": { "split": "train_shard_00001", "doc_id": 1934 }, "chunk_id": "train_shard_00001_1934_0", "global_id": 8394 }, { "text": "Due to the undesirable consequences associated with antibiotics use, researchers and food producers have studied alternative feeding, for the control of fish diseases and animal welfare improvement. However, the beneficial properties of RNA yeasts extract in aquaculture have been barely considered. The present study investigated the beneficial properties of RNA yeast extract from Kluyveromyces fragilis on survival rate, weight and length as well as on molecular pathways involved in growth, immuno‐system and oxidative stress using zebrafish (Danio rerio) as an experimental model. The yeast extract has been administrated to zebrafish at three different concentrations (60–180–300 ppm) via zooplankton (Artemia salina) for 21 days. Results highlighted yeast extract RNA capability to enhance growth and to improve larvae survival rate in a dose‐dependent manner. In fact, gene expression data showed the ability of the RNA yeast extract to up‐regulate genes involved in growth and to restore stress‐related condition due to the early larval development coupled with the RNA yeast extract administration. In addition, gene expression showed that RNA yeast extract acts as inflammatory‐reducer, but did not enhance the immune response. Histological analysis showed that all three treated groups displayed a thicker gut epithelium, higher intestinal crypts coupled with higher enterocytes lengths compared to control group. In conclusion, these findings provide a large gene network through which yeast RNA extract acts and, by inducing transcriptional changes, modulate the physiological control of growth and inflammatory response coupled with the increase in length and dry weight, together with a higher survival ratio and an intestinal architecture amelioration.\n\nKluyveromyces fragilis RNA extract supplementation promotes growth, modulates stress and inflammatory response in zebrafish", "token_count": 420, "char_count": 1894, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:26.285910", "source": { "split": "train_shard_00001", "doc_id": 1935 }, "chunk_id": "train_shard_00001_1935_0", "global_id": 8395 }, { "text": "Enterococcus is a genus of Gram-positive bacteria that are commensal to the gastrointestinal tracts of humans but some species have been increasingly implicated as agents of nosocomial infections. The increase in infections and the spread of antibiotic-resistant strains have contributed to renewed interest in the discovery of Enterococcus phages. The aims of this study were (1) the isolation, characterization, and genome sequencing of a phage capable of infecting an antibiotic-resistant E. faecalis strain, and (2) the comparative genomic analysis of publicly-available Enterococcus phages. For this purpose, multiple phages were isolated from wastewater treatment plant (WWTP) influent using a high-level aminoglycoside-resistant (HLAR) E. faecalis strain as the host. One phage, phiNASRA1, demonstrated a high lytic efficiency (∼97.52%). Transmission electron microscopy (TEM) and whole-genome sequencing (WGS) showed that phiNASRA1 belongs to the Siphoviridae family of double-stranded DNA viruses. The phage was approximately 250 nm in length and its complete genome (40,139 bp, 34.7% GC) contained 62 open reading frames (ORFs). Phylogenetic comparisons of phiNASRA1 and 31 publicly-available Enterococcus phages, based on the large subunit terminase and portal proteins, grouped phage by provenance, size, and GC content. In particular, both phylogenies grouped phages larger than 100 kbp into distinct clades. A phylogeny based on a pangenome analysis of the same 32 phages also grouped phages by provenance, size, and GC content although agreement between the two single-locus phylogenies was higher", "token_count": 480, "char_count": 1654, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6784, "quality_score": 0.8392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:26.935792", "source": { "split": "train_shard_00001", "doc_id": 1936 }, "chunk_id": "train_shard_00001_1936_0", "global_id": 8396 }, { "text": "Per the pangenome phylogeny, phiNASRA1 was most closely related to phage LY0322 that was similar in size, GC content, and number of ORFs (40,139 and 40,934 bp, 34.77 and 34.80%, and 60 and 64 ORFs, respectively). The pangenome analysis did illustrate the high degree of sequence diversity and genome plasticity as no coding sequence was homologous across all 32 phages, and even 'conserved' structural proteins (e.g., the large subunit terminase and portal proteins) were homologous in no more than half of the 32 phage genomes. These findings contribute to a growing body of literature devoted to understanding phage biology and diversity. We propose that this high degree of diversity limited the value of the single-locus and pangenome phylogenies. By contrast, the high degree of homology between phages larger than 100 kbp suggests that pangenome analyses of more similar phages is a viable method for assessing subclade diversity. Future work is focused on validating phiNASRA1 as a potential therapeutic agent to eradicate antibiotic-resistant E. faecalis infections in an animal model.\n\nIsolation, characterization, and comparative genomic analysis of a phage infecting high-level aminoglycoside-resistant (HLAR) Enterococcus faecalis.", "token_count": 357, "char_count": 1257, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8342, "entities": { "genes": [ "LY0322" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:27.512288", "source": { "split": "train_shard_00001", "doc_id": 1936 }, "chunk_id": "train_shard_00001_1936_1", "global_id": 8397 }, { "text": "Plant microbiota is believed to be an accessory genome extending plant functions, forming holobiont together with the host plant. Plant disease resistance, therefore, is inextricably linked with plant microbiota, which play important roles in plant growth and health. In order to explore the relationship between plant microbiota and disease resistance, we investigated the tobacco microbiome of two varieties with contrasting disease resistance levels to bacterial wilt and black shank. Comparative microbiome analysis indicated that the resistant variety assembled a distinct microbiota with higher network complexity and diversity. While Pseudomonas and Ensifer , that contain biocontrol and beneficial members, were enriched in the rhizosphere of the resistant variety, Ralstonia , a genus including the known causative pathogen, was enriched in the susceptible variety. Metagenome sequencing revealed that biocontrol functions were more abundant in the resistant variety, such as hydrogen cyanide synthase, pyochelin biosynthesis, and arthrofactin-type cyclic lipopeptide synthetase. Further analysis indicated that contigs encoding the corresponding genes were mostly assigned to Pseudomonas . Among all the metagenome-assembled-genomes, positive selection was suggested in the genome assigned to Pseudomonas only in the rhizosphere of the resistant variety. The search of biosynthetic gene clusters in the Pseudomonas genome revealed a non-ribosomal peptide synthetase, the compound of which was brabantamide A, with known antimicrobial activity. Collectively, our study suggests that the plant microbiota might be involved in the microbe-mediated disease resistance. Particularly, our results highlight Pseudomonas in the rhizosphere of the disease-resistant variety as the promising biocontrol candidate. Our study may facilitate further screening of bacterial isolates and the targeted design of microbial communities.\n\nDistinct microbiota assembly and functional patterns revealed by comparative analysis of disease resistant and susceptible tobacco (Nicotiana tabacum) varieties", "token_count": 474, "char_count": 2090, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5612, "quality_score": 0.7806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:28.149499", "source": { "split": "train_shard_00001", "doc_id": 1937 }, "chunk_id": "train_shard_00001_1937_0", "global_id": 8398 }, { "text": "Flocculation is a very useful phenotype for industrial yeast strains, since it facilitates cell harvest and represents an easy way of cell immobilization in continuous fermentation processes. The present work represents the first time that an inducible flocculation phenotype has been generated in a non flocculent strain of Kluyveromyces marxianus. This was accomplished by expressing Saccharomyces cerevisiae FLO5 gene in K. marxianus CECT 11769 strain. The FLO 5 gene was placed under the control of an EPG promoter, not repressed by glucose and induced by anoxia. Our experimental approach successfully generated two novel K. marxianus flocculent phenotypes: one inducible and one constitutive. The constitutive phenotype originated from deletions in the FLO5 promoter region, indicating the existence of putative upstream repressor site involved in oxygen regulation of the EPG1 promoter. The novel strains here generated had a unique set of characteristics that provided an advantage, over the wild-type strain, for the industrial co-production of ethanol and polygalacturonase.\n\nA novel Kluyveromyces marxianus strain with an inducible flocculation phenotype.", "token_count": 291, "char_count": 1166, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6566, "quality_score": 0.8283, "entities": { "genes": [ "FLO5", "EPG1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:28.708217", "source": { "split": "train_shard_00001", "doc_id": 1938 }, "chunk_id": "train_shard_00001_1938_0", "global_id": 8399 }, { "text": "In recent years, Salmonella infection is a major global public health concern, particularly in food safety. This study analyzed the genomes of 102 Salmonella strains isolated between 2016 and 2023 from food, foodborne disease patients, and food poisoning incidents, focusing on their molecular characteristics, antibiotic resistance genes (ARGs), and virulence genes. S. enterica serovar Enteritidis (37.3%) and S. enterica serovar Typhimurium (21.6%, including its monophasic variant 1,4,[5],12:i:-) were the main strains among 22 serotypes. Multilocus sequence typing revealed 23 sequence types (STs), with ST11, ST19, and ST34 as the most prevalent. All strains carried at least 24 ARGs. Detection rates for aac(6')-Iy, blaTEM-1, and sul2 ranged from 44.1% to 63.7%, mainly in S. Enteritidis and S. Typhimurium. Rates for qnrS1, sul1, and aadA were 12.8% to 16.7%, while mcr-1 appeared in one ST34 S. Typhimurium strain. All strains contained at least 98 virulence genes. The genes pefABCD, mig-5, and spvBCD were in 48.0% of strains, while rck was found in 36.3%, mainly linked to S. Enteritidis and S. Typhimurium", "token_count": 495, "char_count": 1269, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6982, "quality_score": 0.8491, "entities": { "genes": [ "ST34", "ST19", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:30.012809", "source": { "split": "train_shard_00001", "doc_id": 1939 }, "chunk_id": "train_shard_00001_1939_0", "global_id": 8400 }, { "text": "The tssM gene was found in 37.3% of the strains, exclusively in S. Enteritidis. Core genome single nucleotide polymorphisms (cgSNPs) analysis grouped the strains into nine clusters, with 75.5% belonging to three major groups. Food poisoning event 1 was correlated with cluster 3, while events 2 and 3 were linked to cluster 1. Across events, SNP differences among strains were ≤6. Strains with SNP differences ≤10 were also found in other clusters. This method is promising for tracking sporadic cases and identifying potential foodborne safety incidents. Salmonella strains in the region exhibit substantial genetic diversity, demonstrating the efficacy of cgSNPs analysis for source tracking. Ongoing surveillance is essential given the prevalence of ARGs and virulence genes. This study provides a data foundation for local Salmonella epidemiology.\n\nMolecular Characterization of Whole Genome Sequencing of <i>Salmonella</i> spp. in Shapingba District, Chongqing, China, 2016-2023.", "token_count": 293, "char_count": 1024, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7518, "quality_score": 0.8759, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:30.571695", "source": { "split": "train_shard_00001", "doc_id": 1939 }, "chunk_id": "train_shard_00001_1939_1", "global_id": 8401 }, { "text": "

Objectives

Sheep farming represents an important economic sector in Algeria, and the potential dissemination of methicillin-resistant Staphylococcaceae (MRS) is a critical veterinary and public health concern. This study aimed to determine the prevalence and types of MRS in ovine in Algeria and characterize them using whole-genome sequencing (WGS) analysis.

Methods

Two hundred sheep from 20 different Algerian farms across 3 regions were screened for nasal colonization with MRS. The isolates were identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), their minimal inhibitory concentration (MIC) was determined by broth microdilution, and the presence of the mec gene was confirmed with polymerase chain reaction (PCR). The mec-positive isolates were sequenced using Illumina technology to build species specific core genome multilocus sequence typing (cgMLST)- and single nucleotide polymorphisms (SNPs)-based phylogenies and perform an in silico screening for antimicrobial resistance genes.

Results

The prevalence of MRS-positive farms was 85% (95% confidence interval [CI] = 69.34%-100%) across the sampled farms. Ten distinct Staphylococcaceae species were identified, with Staphylococcus saprophyticus (S. saprophyticus; n = 29), Mammaliicoccus lentus (M. lentus; n = 24), and Staphylococcus haemolyticus (S. haemolyticus; n = 19) being the predominant species. WGS-based phylogeny and SNP analysis (0 to 126 SNPs) revealed that isolates of these three species were highly related, indicating clonal dissemination within and between farms", "token_count": 459, "char_count": 1623, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7418, "quality_score": 0.8709, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:31.210429", "source": { "split": "train_shard_00001", "doc_id": 1940 }, "chunk_id": "train_shard_00001_1940_0", "global_id": 8402 }, { "text": "MRS exhibited a multi-drug resistance pattern, with detection of resistance genes for β-lactams, tetracyclines, fusidic acid, trimethoprim, aminoglycosides, tiamulin, and macrolides.

Conclusions

Specific clonal lineages of methicillin-resistant S. saprophyticus, S. haemolyticus, and M. lentus are widespread in Algerian sheep farms. Enhancing hygiene practices on farms is recommended to prevent further dissemination of these resistant strains to animals and humans. © 2025 The Author(s). Published by Elsevier Ltd on behalf of International Society for Antimicrobial Chemotherapy.\n\nClonal dissemination of methicillin-resistant Staphylococcaceae between Algerian sheep farms.", "token_count": 200, "char_count": 685, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7927, "quality_score": 0.8963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:31.655726", "source": { "split": "train_shard_00001", "doc_id": 1940 }, "chunk_id": "train_shard_00001_1940_1", "global_id": 8403 }, { "text": "Escherichia coli is a major causative agent of environmental bovine mastitis, and this disease causes significant economic losses for the dairy industry. There is still debate in the literature as to whether mammary pathogenic E. coli (MPEC) is indeed a unique E. coli pathotype or if this infection is merely an opportunistic infection caused by any E. coli isolate being displaced from the bovine gastrointestinal tract to the environment and then into the udder. In this study, we conducted a thorough genomic analysis of 113 MPEC isolates from clinical mastitis cases and 100 environmental E. coli isolates from the environment of dairy farms around the world. A phylogenomic analysis indicated that MPEC and the environmental E. coli isolates formed clades based on common sequence types and O antigens but did not cluster based on mammary pathogenicity. The comparison of core and soft-core genes of each set of isolates identified the three genes of the ferric dicitrate uptake system (Fec), fecI, fecR and fecA, as soft-core genes of MPEC (n=110). These genes were also present in 27 E. coli isolates from environmental sources. Rather than being a virulence gene cluster, it is likely that the Fec system provides a competitive advantage to E. coli in the mammary gland - an iron-poor environment. Using this cluster as a marker for MPEC may offer an opportunity to develop novel treatments for E. coli mastitis, based on its presence.\n\nComparative genomic analysis of <i>Escherichia coli</i> isolated from cases of bovine clinical mastitis and the dairy farm environment.", "token_count": 484, "char_count": 1684, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5613, "quality_score": 0.7806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:32.327873", "source": { "split": "train_shard_00001", "doc_id": 1941 }, "chunk_id": "train_shard_00001_1941_0", "global_id": 8404 }, { "text": "Candida glabrata is a fungal microbe associated with multiple vertebrate microbiomes and their terrestrial environments. In humans, the species has emerged as an opportunistic pathogen that now ranks as the second-leading cause of candidiasis in Europe and North America (Beardsley et al. Med Mycol 2024, 62). People at highest risk of infection include the elderly, immunocompromised individuals and/or long-term residents of hospital and assisted-living facilities. C. glabrata is intrinsically drug-resistant, metabolically versatile and able to avoid detection by the immune system. Analyses of its 12.3 Mb genome indicate a stable pangenome Marcet-Houben et al. (BMC Biol 2022, 20) and phylogenetic affinity with Saccharomyces cerevisiae. Recent phylogenetic analyses suggest reclassifying C. glabrata as Nakaseomyces glabratus Lakashima and Sugita (Med Mycol J 2022, 63: 119-132).\n\nMicrobe Profile: <i>Candida glabrata</i> - a master of deception.", "token_count": 362, "char_count": 1035, "word_count": 132, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:32.946328", "source": { "split": "train_shard_00001", "doc_id": 1942 }, "chunk_id": "train_shard_00001_1942_0", "global_id": 8405 }, { "text": "Agaricus bisporus is an extensively cultivated edible mushroom. Demand for cultivation is continuously growing and difficulties associated with breeding programs now means strains are effectively considered monoculture. While commercial growing practices are highly efficient and tightly controlled, the over-use of a single strain has led to a variety of disease outbreaks from a range of pathogens including bacteria, fungi and viruses. To address this, the Agaricus Resource Program (ARP) was set up to collect wild isolates from diverse geographical locations through a bounty-driven scheme to create a repository of wild Agaricus germplasm. One of the strains collected, Agaricus bisporus var. bisporus ARP23, has been crossed extensively with white commercial varieties leading to the generation of a novel hybrid with a dark brown pileus commonly referred to as 'Heirloom'. Heirloom has been successfully implemented into commercial mushroom cultivation. In this study the whole genome of Agaricus bisporus var. bisporus ARP23 was sequenced and assembled with Illumina and PacBio sequencing technology. The final genome was found to be 33.49 Mb in length and have significant levels of synteny to other sequenced Agaricus bisporus strains. Overall, 13,030 putative protein coding genes were located and annotated. Relative to the other A. bisporus genomes that are currently available, Agaricus bisporus var. bisporus ARP23 is the largest A. bisporus strain in terms of gene number and genetic content sequenced to date. Comparative genomic analysis shows that the A. bisporus mating loci in unifactorial and unsurprisingly highly conserved between strains. The lignocellulolytic gene content of all A. bisporus strains compared is also very similar. Our results show that the pangenome structure of A", "token_count": 512, "char_count": 1902, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "ARP23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:33.636848", "source": { "split": "train_shard_00001", "doc_id": 1943 }, "chunk_id": "train_shard_00001_1943_0", "global_id": 8406 }, { "text": "bisporus is quite diverse with between 60-70% of the total protein coding genes per strain considered as being orthologous and syntenically conserved. These analyses and the genome sequence described herein are the starting point for more detailed molecular analyses into the growth and phenotypical responses of Agaricus bisporus var. bisporus ARP23 when challenged with economically important mycoviruses.\n\nWhole Genome Sequence of the Commercially Relevant Mushroom Strain Agaricus bisporus var. bisporus ARP23.", "token_count": 157, "char_count": 546, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7465, "quality_score": 0.8732, "entities": { "genes": [ "ARP23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:34.099667", "source": { "split": "train_shard_00001", "doc_id": 1943 }, "chunk_id": "train_shard_00001_1943_1", "global_id": 8407 }, { "text": "Structural variation (SV), refers to insertions, deletions, inversions, and duplications in human genomes. With advances in whole genome sequencing (WGS) technologies, a plethora of SV detection methods have been developed. However, dissecting SVs from WGS data remains a challenge, with the majority of SV detection methods prone to a high false-positive rate, and no existing method able to precisely detect a full range of SV’s present in a sample. Previous studies have shown that none of the existing SV callers can maintain high accuracy across various SV lengths and genomic coverages. Here, we report an integrated structural variant calling framework, VISTA (Variant Identification and Structural Variant Analysis) that leverages the results of individual callers using a novel and robust filtering and merging algorithm. In contrast to existing consensus-based tools which ignore the length and coverage, VISTA overcomes this limitation by executing various combinations of top-performing callers based on variant length and genomic coverage to generate SV events with high accuracy. We evaluated the performance of VISTA on using comprehensive gold-standard datasets across varying organisms and coverage. We benchmarked VISTA using the Genome-in-a-Bottle (GIAB) gold standard SV set, haplotype-resolved de novo assemblies from The Human Pangenome Reference Consortium (HPRC) 1,2 , along with an in-house PCR-validated mouse gold standard set. VISTA maintained the highest F1 score among top consensus-based tools measured using a comprehensive gold standard across both mouse and human genomes. VISTA also has an optimized mode, where the calls can be optimized for precision or recall. VISTA-optimized is able to attain 100% precision and the highest sensitivity among other variant callers. In conclusion, VISTA represents a significant advancement in structural variant calling, offering a robust and accurate framework that outperforms existing consensus-based tools and sets a new standard for SV detection in genomic research.\n\nVISTA: An integrated framework for structural variant discovery", "token_count": 460, "char_count": 2109, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5875, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:34.741414", "source": { "split": "train_shard_00001", "doc_id": 1944 }, "chunk_id": "train_shard_00001_1944_0", "global_id": 8408 }, { "text": "The objective of the present laboratory scale experiment was to compare ethanol production by Kluyveromyces marxianus strain ATCC8554 and Candida kefyr ATCC 14245 from unconcentrated and concentrated cheese whey permeate. The results indicated that ethanol production was greater when using concentrated whey permeate (9.8% lactose) compared to unconcentrated whey permeate (4.9% lactose) by both the yeasts, especially in presence of growth supplements. The rate and extent of ethanol formation increased noticeably and partly linearly for both the yeasts with sharp and partly linear decrease in both lactose and Chemical Oxygen Demand (COD), especially after the first 10 h of fermentation; total time of fermentation was 60 h. The optimum pH and temperature conditions for ethanol production were 4.8 and 30º C respectively. Klu. marxianus strain had greater ethanol producing ability from cheese permeate whey than Can. kefyr.\n\nComparison of ethanol production from cheese whey permeate by two yeast strains.", "token_count": 266, "char_count": 1013, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6309, "quality_score": 0.8154, "entities": { "genes": [ "ATCC8554" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:35.297224", "source": { "split": "train_shard_00001", "doc_id": 1945 }, "chunk_id": "train_shard_00001_1945_0", "global_id": 8409 }, { "text": "Furcraea necrotic streak virus (FNSV) is the causative agent of necrotic streak disease, also known as macana in fique crops (Furcraea spp.) resulting in damage to leaf fibres and economic losses. The rhizospheric fungus Olpidium spp. is present in the roots of affected plants and may play a role in the disease transmission. FNSV infection and the role of fungi were examined in macanavirus‐diseased plants in Colombia. Spherical, and icosahedral (24.7 ± 1.98 nm), non‐enveloped virions with a granular surface were isolated from field fique plants showing signs of macana disease, and the viral genome was completely sequenced. Taxonomic status was assigned through sequence analysis (Macanavirus genus in Tombusviridae family). The variability of the virus pangenome was evaluated in diseased fique plants from ecologically different Andean regions that showed low gene flow. Olpidium virulentus zoospores, identified by internal transcribed spacer (ITS) sequencing and microscopic analysis, were associated with viral particles and resting spores in diseased fique roots. An in vitro virion–zoospore binding assay showed that FNSV and O. virulentus zoospores interacted. Transmission assays in lettuce (Lactuca sativa), a model plant used to study this virus, showed 100% infection when a preincubated mixture of zoospores and FNSV was added to roots, whereas only 33% infection occurred when FNSV was added alone. This demonstrated the ability of O. virulentus to act as a vector for FNSV, potentially enhancing viral transmissibility in field fique crops. This is the first report of FNSV being transmitted by O. virulentus, a rhizosphere fungus.\n\nTransmission of Furcraea necrotic streak virus (FNSV) by Olpidium virulentus", "token_count": 466, "char_count": 1731, "word_count": 257, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:35.938957", "source": { "split": "train_shard_00001", "doc_id": 1946 }, "chunk_id": "train_shard_00001_1946_0", "global_id": 8410 }, { "text": "

Background

Hot spring biofilms provide a window into the survival strategies of microbial communities in extreme environments and offer potential for biotechnological applications. This study focused on green and brown biofilms thriving on submerged plant litter within the Sungai Klah hot spring in Malaysia, characterised by temperatures of 58-74 °C. Using Illumina shotgun metagenomics and Nanopore ligation sequencing, we investigated the microbial diversity and functional potential of metagenome-assembled genomes (MAGs) with specific focus on biofilm formation, heat stress response, and carbohydrate catabolism.

Results

Leveraging the power of both Illumina short-reads and Nanopore long-reads, we employed an Illumina-Nanopore hybrid assembly approach to construct MAGs with enhanced quality. The dereplication process, facilitated by the dRep tool, validated the efficiency of the hybrid assembly, yielding MAGs that reflected the intricate microbial diversity of these extreme ecosystems. The comprehensive analysis of these MAGs uncovered intriguing insights into the survival strategies of thermophilic taxa in the hot spring biofilms. Moreover, we examined the plant litter degradation potential within the biofilms, shedding light on the participation of diverse microbial taxa in the breakdown of starch, cellulose, and hemicellulose. We highlight that Chloroflexota and Armatimonadota MAGs exhibited a wide array of glycosyl hydrolases targeting various carbohydrate substrates, underscoring their metabolic versatility in utilisation of carbohydrates at elevated temperatures.

Conclusions

This study advances understanding of microbial ecology on plant litter under elevated temperature by revealing the functional adaptation of MAGs from hot spring biofilms. In addition, our findings highlight potential for biotechnology application through identification of thermophilic lignocellulose-degrading enzymes. By demonstrating the efficiency of hybrid assembly utilising Illumina-Nanopore reads, we highlight the value of combining multiple sequencing methods for a more thorough exploration of complex microbial communities.", "token_count": 513, "char_count": 2164, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6022, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:36.591607", "source": { "split": "train_shard_00001", "doc_id": 1947 }, "chunk_id": "train_shard_00001_1947_0", "global_id": 8411 }, { "text": "Integrating multi-platform assembly to recover MAGs from hot spring biofilms: insights into microbial diversity, biofilm formation, and carbohydrate degradation.", "token_count": 39, "char_count": 161, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:36.950455", "source": { "split": "train_shard_00001", "doc_id": 1947 }, "chunk_id": "train_shard_00001_1947_1", "global_id": 8412 }, { "text": "ABSTRACTBetween 2018 and 2024, we conducted systematic whole-genome sequencing and phylogenomic analysis on 263 V. cholerae O1 isolates from cholera patients across four provinces in the Democratic Republic of Congo (North-Kivu, South-Kivu, Tanganyika, and Kasai Oriental). These isolates were classified into the AFR10d and AFR10e sublineages of AFR10 lineage, originating from the third wave of the seventh El Tor cholera pandemic (7PET). Compared to the strains analysed between 2014 and 2017, both sublineages had few genetic changes in the core genome but recent isolates (2022-2024) had significant CTX prophage rearrangement. AFR10e spread across all four provinces, while AFR10d appeared to be extinct by the end of 2020. Since 2022, most V. cholerae O1 isolates exhibited significant CTX prophage rearrangements, including a tandem repeat of an environmental satellite phage RS1 downstream the ctxB toxin gene of the CTX-Φ-3 prophage on the large chromosome, as well as two or more arrayed copies of an environmental pre-CTX-Φ prophage precursor on the small chromosome. We used Illumina data for mapping and coverage estimation to identify isolates with unique CTX-Φ genomic features. Gene localization was then determined on MinION-derived assemblies, revealing an organization similar to that of non-O1 V. cholerae isolates found in Asia (O139 VC1374, and environmental O4 VCE232), but never described in V. cholerae O1 El Tor from the third wave", "token_count": 475, "char_count": 1500, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6697, "quality_score": 0.8349, "entities": { "genes": [ "AFR10", "VCE232", "VC1374", "RS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:37.592176", "source": { "split": "train_shard_00001", "doc_id": 1948 }, "chunk_id": "train_shard_00001_1948_0", "global_id": 8413 }, { "text": "In conclusion, while the core genome of AFR10d and AFR10e showed minimal changes, significant alterations in the CTX-Φ and pre-CTX-Φ prophage content and organization were identified in AFR10e from 2022 onwards.\n\nGenomic evolution and rearrangement of CTX-Φ prophage elements in Vibrio cholerae during the 2018-2024 cholera outbreaks in eastern Democratic Republic of the Congo.", "token_count": 121, "char_count": 385, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:37.971513", "source": { "split": "train_shard_00001", "doc_id": 1948 }, "chunk_id": "train_shard_00001_1948_1", "global_id": 8414 }, { "text": "Comamonas is often reported to be one of the major members of microbial communities in various natural and engineered environments. Versatile catabolic capabilities of Comamonas have been studied extensively in the last decade. In contrast, little is known about the ecological roles and adaptation of Comamonas to different environments as well as the virulence of potentially pathogenic Comamonas strains. In this study, we provide genomic insights into the potential ecological roles and virulence of Comamonas by analysing the entire gene set (pangenome) and the genes present in all genomes (core genome) using 34 genomes of 11 different Comamonas species. The analyses revealed that the metabolic pathways enabling Comamonas to acquire energy from various nutrient sources are well conserved. Genes for denitrification and ammonification are abundant in Comamonas, suggesting that Comamonas plays an important role in the nitrogen biogeochemical cycle. They also encode sophisticated redox sensory systems and diverse c-di-GMP controlling systems, allowing them to be able to effectively adjust their biofilm lifestyle to changing environments. The virulence factors in Comamonas were found to be highly species-specific. The conserved strategies used by potentially pathogenic Comamonas for surface adherence, motility control, nutrient acquisition and stress tolerance were also revealed.\n\nThe Core- and Pan-Genomic Analyses of the Genus Comamonas: From Environmental Adaptation to Potential Virulence.", "token_count": 404, "char_count": 1594, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:38.591233", "source": { "split": "train_shard_00001", "doc_id": 1949 }, "chunk_id": "train_shard_00001_1949_0", "global_id": 8415 }, { "text": "Upon infection, transcriptional shifts in both a host bacterium and its invading phage determine host and viral fitness. The xenobiotic response element (XRE) family of transcription factors (TFs), which are commonly encoded by bacteria and phages, regulate diverse features of bacterial cell physiology and impact phage infection dynamics. Through a pangenome analysis of Caulobacter species isolated from soil and aquatic ecosystems, we uncovered an apparent radiation of a paralogous XRE TF gene cluster, several of which have established functions in the regulation of holdfast adhesin development and biofilm formation in C. crescentus . We further discovered related XRE TFs across the class Alphaproteobacteria and its phages, including the φCbK Caulophage, suggesting that members of this gene cluster impact host-phage interactions. Here we show that that a closely related group of XRE proteins, encoded by both C. crescentus and φCbK, can form heteromeric associations and control the transcription of a common gene set, influencing processes including holdfast development and the production of φCbK virions. The φCbK XRE paralog, tgrL , is highly expressed at the earliest stages of infection and can directly repress transcription of hfiA , a potent holdfast inhibitor, and gafYZ , a transcriptional activator of prophage-like gene transfer agents (GTAs) encoded on the C. crescentus chromosome. XRE proteins encoded from the C. crescentus chromosome also directly repress gafYZ transcription, revealing a functionally redundant set of host regulators that may protect against spurious production of GTA particles and inadvertent cell lysis. Deleting host XRE transcription factors reduced φCbK burst size, while overexpressing these genes or φCbK tgrL rescued this burst defect. We conclude that an XRE TF gene cluster, shared by C. crescentus and φCbK, plays an important role in adhesion regulation under phage-free conditions, and influences host-phage dynamics during infection.", "token_count": 489, "char_count": 1997, "word_count": 292, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:39.239718", "source": { "split": "train_shard_00001", "doc_id": 1950 }, "chunk_id": "train_shard_00001_1950_0", "global_id": 8416 }, { "text": "XRE Transcription Factors Conserved inCaulobacterand φCbK Modulate Adhesin Development and Phage Production", "token_count": 36, "char_count": 114, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:39.593981", "source": { "split": "train_shard_00001", "doc_id": 1950 }, "chunk_id": "train_shard_00001_1950_1", "global_id": 8417 }, { "text": "

Aim

The aim of this study was to find suitable yeast isolates as potential microbial feed additives for ruminants.

Methods and results

Yeast isolates from traditional fermented food (tapai) and home-made wine were selected based on their tolerance to volatile fatty acids (VFA) mixture of acetic, propionic and butyric acids and to pH and temperature according to the rumen condition. The ability to grow in and produce ethanol was determined in yeast extract peptone glucose broth supplemented with a VFA mixture (VFA-YEPG medium). Fifty-five isolates showed OD(660 nm) values between 0.35-0.6, and 27 isolates showed ethanol production in the range of 0.17-0.30% (v/v). All selected isolates were identified as Kluyveromyces marxianus base on biochemical tests (BioLog kit; Biolog Inc., Hayward, CA) and molecular techniques. The best isolate in terms of ethanol production (K. marxianus WJ1) significantly (P < 0.01) improved in vitro apparent dry matter (DM) digestibility of alfalfa (Medicago sativa), guinea grass (Panicum maximum) and timothy (Phleum pretense) hay by rumen microbes.

Conclusion

Yeast isolates from tapai and wine were able to grow in VFA-YEPG medium, and K. marxianus WJ1 improved in vitro DM digestibility of plant substrates.

Significance and impact of the study

This study indicated the possibility of using K. marxianus as a microbial feed additive.\n\nCharacterization of Kluyveromyces marxianus as a potential feed additive for ruminants.", "token_count": 447, "char_count": 1495, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [ "WJ1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:40.582462", "source": { "split": "train_shard_00001", "doc_id": 1951 }, "chunk_id": "train_shard_00001_1951_0", "global_id": 8418 }, { "text": "Hausa koko is an indigenous porridge processed from millet in Ghana. The process involves fermentation stages, giving the characteristic organoleptic properties of the product that is produced largely at a small-scale household level and sold as a street food. Like many other indigenous foods, quality control is problematic and depends on the skills of the processor. In order to improve the quality of the product and standardize the process for large-scale production, we need a deeper understanding of the microbial processes. The aim of this study is to investigate the microbial community involved in the production of this traditional millet porridge and the metabolites produced during processing. High-throughput amplicon sequencing was used to identify the bacterial (16S rRNA V4 hypervariable region) and fungal [Intergenic Transcribed Spacer (ITS)] communities associated with the fermentation, while nuclear magnetic resonance (NMR) was used for metabolite profiling. The bacterial community diversity was reduced during the fermentation processes with an increase and predominance of lactobacilli. Other dominant bacteria in the fermentation included Pediococcus, Weissella, Lactococcus, Streptococcus, Leuconostoc, and Acetobacter. The species Limosilactobacillus fermentum and Ligilactobacillus salivarius accounted for some of the diversities within and between fermentation time points and processors. The fungal community was dominated by the genus Saccharomyces. Other genera such as Pichia, Candida, Kluyveromyces, Nakaseomyces, Torulaspora, and Cyberlindnera were also classified", "token_count": 468, "char_count": 1714, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:41.226810", "source": { "split": "train_shard_00001", "doc_id": 1952 }, "chunk_id": "train_shard_00001_1952_0", "global_id": 8419 }, { "text": "The species Saccharomyces cerevisiae, Stachybotrys sansevieriae, Malassezia restricta, Cyberlindnera fabianii, and Kluyveromyces marxianus accounted for some of the diversities within some fermentation time points. The species S. sansevieria and M. restricta may have been reported for the first time in cereal fermentation. This is the most diverse microbial community reported in Hausa koko. In this study, we could identify and quantify 33 key different metabolites produced by the interactions of the microbial communities with the millet, composed of organic compounds, sugars, amino acids and intermediary compounds, and other key fermentation compounds. An increase in the concentration of organic acids in parallel with the reduction of sugars occurred during the fermentation process while an initial increase of amino acids followed by a decrease in later fermentation steps was observed.\n\nMicrobial Diversity and Metabolite Profile of Fermenting Millet in the Production of <i>Hausa koko</i>, a Ghanaian Fermented Cereal Porridge.", "token_count": 321, "char_count": 1109, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6463, "quality_score": 0.8231, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:41.791286", "source": { "split": "train_shard_00001", "doc_id": 1952 }, "chunk_id": "train_shard_00001_1952_1", "global_id": 8420 }, { "text": "Bread wheat is one of humanity’s most important staple crops, characterized by a large and complex genome with a high level of gene presence/absence variation between cultivars, hampering genomic approaches for crop improvement. With the growing global population and the increasing impact of climate change on crop yield, there is an urgent need to apply genomic approaches to accelerate wheat breeding. With recent advances in DNA sequencing technology, a growing number of high-quality reference genomes are becoming available, reflecting the genetic content of a diverse range of cultivars. However, information on the presence or absence of genomic regions has been hard to visualize and interrogate due to the size of these genomes and the lack of suitable bioinformatics tools. To address this limitation, we have produced a wheat pangenome graph maintained within an online database to facilitate interrogation and comparison of wheat cultivar genomes. The database allows users to visualize regions of the pangenome to assess presence/absence variation between bread wheat genomes. Database URL: http://www.appliedbioinformatics.com.au/wheat_panache\n\nWheat Panache - a pangenome graph database representing presence/absence variation across 16 bread wheat genomes", "token_count": 267, "char_count": 1272, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:42.341988", "source": { "split": "train_shard_00001", "doc_id": 1953 }, "chunk_id": "train_shard_00001_1953_0", "global_id": 8421 }, { "text": "Streptococcus pneumoniae causes over one million deaths from lower respiratory infections per annum worldwide. Although mortality is very high in Southeast Asian countries, molecular epidemiological information remains unavailable for some countries. In this study, we report, for the first time, the whole-genome sequences and genetic profiles of pneumococcal strains isolated in Myanmar. We isolated 60 streptococcal strains from 300 children with acute respiratory infection at Yangon Children's Hospital in Myanmar. We obtained whole-genome sequences and identified the species, serotypes, sequence types, antimicrobial resistance (AMR) profiles, virulence factor profiles and pangenome structure using sequencing-based analysis. Average nucleotide identity analysis indicated that 58 strains were S. pneumoniae and the other 2 strains were Streptococcus mitis. The major serotype was 19F (11 strains), followed by 6E (6B genetic variant; 7 strains) and 15 other serotypes; 5 untypable strains were also detected. Multilocus sequence typing analysis revealed 39 different sequence types, including 11 novel ones. In addition, genetic profiling indicated that AMR genes and mutations spread among pneumococcal strains in Myanmar. A minimum inhibitory concentration assay indicated that several pneumococcal strains had acquired azithromycin and tetracycline resistance, whereas no strains were found to be resistant against levofloxacin and high-dose penicillin G. Phylogenetic and pangenome analysis showed various pneumococcal lineages and that the pneumococcal strains contain a rich and mobile gene pool, providing them with the ability to adapt to selective pressures. This molecular epidemiological information can help in tracking global infection and supporting AMR control in addition to public health interventions in Myanmar.\n\nEpidemiological analysis of pneumococcal strains isolated at Yangon Children's Hospital in Myanmar via whole-genome sequencing-based methods.", "token_count": 502, "char_count": 2003, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:42.993782", "source": { "split": "train_shard_00001", "doc_id": 1954 }, "chunk_id": "train_shard_00001_1954_0", "global_id": 8422 }, { "text": "

Background

Urinary tract infection (UTI) develops after a pathogen adhered to the inner lining of the urinary tract. Cases of UTIs are predominantly caused by several Gram-negative bacteria and account for high morbidity in the clinical and community settings. Of greater concern are the strains carrying antimicrobial resistance (AMR)-conferring genes. The gravity of UTI is also determined by a spectrum of other virulence factors. This study represents a pilot project to investigate the burden of AMR among uropathogens in East Africa.

Methods

We examined bacterial samples isolated in 2017-2018 from in- and out-patients in Kenya (KY) and Uganda (UG) that presented with clinical symptoms of UTI. We reconstructed the evolutionary history of the strains, investigated their population structure and performed comparitive analysis their pangenome contents.

Results

We found 55 Escherichia coli and 19 Klebsiella pneumoniae strains confirmed uropathogenic following screening for the prevalence of UTI virulence genes including fimH, iutA, feoA / B / C, mrkD and foc . We identified 18 different sequence types in E. coli population while all K. pneumoniae strains belong to ST11. The most prevalent E. coli sequence types were ST131 (26%), ST335/1193 (10%) and ST10 (6%). Diverse plasmid types were observed in both collections such as Incompatibility (IncF/IncH/IncQ1/IncX4) and Col groups. Pangenome analysis of each set revealed a total of 2,862 and 3,464 genes comprised the core genome of E. coli and K. pneumoniae population, respectively. Among these are AMR determinants including fluoroquinolone resistance-conferring genes aac (3 )-Ib-cr and other significant genes: aad, tet, sul1, sul2 , and cat , which are associated with aminoglycoside, tetracycline, sulfonamide and chloramphenicol resistance", "token_count": 528, "char_count": 1839, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [ "ST131", "ST335", "ST10", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:43.653822", "source": { "split": "train_shard_00001", "doc_id": 1955 }, "chunk_id": "train_shard_00001_1955_0", "global_id": 8423 }, { "text": "Accessory genomes of both species collection were detected several β-lactamase genes, bla CTX-M , bla TEM and bla OXA or bla NDM . Overall, 93% are multi-drug resistant in the E. coli collection while 100% of the K. pneumoniae strains contained genes that are associated with resistance to 3 or more antibiotic classes.

Conclusions

Our findings illustrate the abundant resistome and virulome repertoire in uropathogenic E. coli and K. pneumoniae , which are mainly disseminated via clonal and horizontal transfer, circulating in the East African region. We further demonstrate here that routine genomic surveillance is necessary for high-resolution bacterial epidemiology of these important AMR pathogens.\n\nPan-resistome characterization of uropathogenic Escherichia coli and Klebsiella pneumoniae strains circulating in Uganda and Kenya isolated from 2017-2018", "token_count": 258, "char_count": 884, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7561, "quality_score": 0.878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:44.207280", "source": { "split": "train_shard_00001", "doc_id": 1955 }, "chunk_id": "train_shard_00001_1955_1", "global_id": 8424 }, { "text": "Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4000 Klebsiella pneumoniae genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that K. pneumoniae has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available on multiple public platforms.\n\nIntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.", "token_count": 385, "char_count": 1740, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:44.839741", "source": { "split": "train_shard_00001", "doc_id": 1956 }, "chunk_id": "train_shard_00001_1956_0", "global_id": 8425 }, { "text": "Soybean (Glycine max) is a legume species of significant economic and nutritional value. The yield of soybean continues to increase with the breeding of improved varieties, and this is likely to continue with the application of advanced genetic and genomic approaches for breeding. Genome technologies continue to advance rapidly, with an increasing number of high-quality genome assemblies becoming available. With accumulating data from marker arrays and whole-genome resequencing, studying variations between individuals and populations is becoming increasingly accessible. Furthermore, the recent development of soybean pangenomes has highlighted the significant structural variation between individuals, together with knowledge of what has been selected for or lost during domestication and breeding, information that can be applied for the breeding of improved cultivars. Because of this, resources such as genome assemblies, SNP datasets, pangenomes and associated databases are becoming increasingly important for research underlying soybean crop improvement.\n\nGenetic and Genomic Resources for Soybean Breeding Research.", "token_count": 225, "char_count": 1136, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:45.339876", "source": { "split": "train_shard_00001", "doc_id": 1957 }, "chunk_id": "train_shard_00001_1957_0", "global_id": 8426 }, { "text": "Between 2018 and 2022, we conducted whole-genome sequencing and phylogenomic analysis on 173 Vibrio cholerae bacteria (172 V. cholerae O1 and 1 V. cholerae non-O1/non-O139 isolates) from cholera patients across four provinces in the Democratic Republic of Congo (North-Kivu, South-Kivu, Tanganyika, and Kasai Oriental). All V. cholerae O1 isolates were classified into the AFR10d and AFR10e sublineages of AFR10 lineage, originating from the third wave of the seventh El Tor cholera pandemic (7PET). Compared to the strains analysed between 2014 and 2017, we observed only limited genetic changes in the core genome of both sublineages. However, AFR10e expanded across the four provinces, whereas AFR10d appeared to become extinct by the end of 2020. The V. cholerae isolates from 2022 exhibited significant rearrangement in the CTX prophage and associated phage satellites. Notably, this included the tandem repeat of a novel environmental satellite phage RS1 downstream the ctxB t oxin gene of the CTX-Φ-3 prophage on the large chromosome, and two tandemly arrayed copies of the pre-CTX-Φ prophage precursor on the small chromosome. In conclusion, while the core genome of V. cholerae O1 AFR10d and AFR10e sublineages showed minimal changes, significant alterations in the content and organisation of elements associated with the CTX-Φ and pre-CTX prophages were identified in AFR10e V. cholerae O1 isolated in 2022.\n\nGenomic evolution and rearrangement of CTX-Φ prophage elements in Vibrio cholerae during the 2018-2022 cholera outbreaks in The Democratic Republic of Congo", "token_count": 490, "char_count": 1576, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5805, "quality_score": 0.7903, "entities": { "genes": [ "AFR10", "RS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:46.020077", "source": { "split": "train_shard_00001", "doc_id": 1958 }, "chunk_id": "train_shard_00001_1958_0", "global_id": 8427 }, { "text": "

Background

Systemic Candidia infections are of major concern in neonates, especially in those with risk factors such as longer use of broad spectrum antibiotics. Recent studies showed that also term babies with underlying gastrointestinal or urinary tract abnormalities are much more prone to systemic Candida infection. We report a very rare case of candidiasis caused by Candida kefyr in a term neonate.

Case presentation

Renal agenesis on the left side was diagnosed antenatally and anal atresia postnatally. Moreover, a vesico-ureteral-reflux (VUR) grade V was detected by cystography. The first surgical procedure, creating a protective colostoma, was uneventful. Afterwards our patient developed urosepsis caused by Enterococcus faecalis and was treated with piperacillin. The child improved initially, but deteriorated again. A further urine analysis revealed Candida kefyr in a significant number. As antibiotic resistance data about this non-albicans Candida species are limited, we started liposomal amphotericin B (AMB), but later changed to fluconazole after receiving the antibiogram. Candiduria persisted and abdominal imaging showed a Candida pyelonephritis. Since high grade reflux was prevalent we instilled AMB into the child's bladder as a therapeutic approach. While undergoing surgery (creating a neo-rectum) a recto-vesical fistula could be shown and subsequently was resected. The child recovered completely under systemic fluconazole therapy over 3 months.

Conclusions

Candidiasis is still of major concern in neonates with accompanying risk factors. As clinicians are confronted with an increasing number of non-albicans Candida species, knowledge about these pathogens and their sensitivities is of major importance.\n\nCandidiasis caused by Candida kefyr in a neonate: case report.", "token_count": 470, "char_count": 1828, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6948, "quality_score": 0.8474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:46.675059", "source": { "split": "train_shard_00001", "doc_id": 1959 }, "chunk_id": "train_shard_00001_1959_0", "global_id": 8428 }, { "text": "Bacillus pumilus 64-1, a bacterial strain isolated from the marine sponge Plakina cyanorosea, which exhibits antimicrobial activity against both pathogenic and drug-resistant Gram-positive and Gram-negative bacteria. This study aimed to conduct an in-depth genomic analysis of this bioactive sponge-derived strain. The nearly complete genome of strain 64-1 consists of 3.6 Mbp (41.5% GC), which includes 3,705 coding sequences (CDS). An open pangenome was observed when limiting to the type strains of the B. pumilus group and aquatic-derived B. pumilus representatives. The genome appears to encode for at least 12 potential biosynthetic gene clusters (BGCs), including both types I and III polyketide synthases (PKS), non-ribosomal peptide synthetases (NRPS), and one NRPS-T1PKS hybrid, among others. In particular, bacilysin and other bacteriocin-coding genes were found and may be associated with the detected antimicrobial activity. Strain 64-1 also appears to possess a broad repertoire of genes encoding for plant cell wall-degrading carbohydrate-active enzymes (CAZymes). A myriad of genes which may be involved in various process required by the strain in its marine habitat, such as those encoding for osmoprotectory transport systems and the biosynthesis of compatible solutes were also present. Several heavy metal tolerance genes are also present, together with various mobile elements including a region encoding for a type III-B Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) region, four prophage segments and transposase elements. This is the first report on the genomic characterization of a cultivable bacterial member of the Plakina cyanorosea holobiont.", "token_count": 485, "char_count": 1729, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6958, "quality_score": 0.8479, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:47.326715", "source": { "split": "train_shard_00001", "doc_id": 1960 }, "chunk_id": "train_shard_00001_1960_0", "global_id": 8429 }, { "text": "Peeling the Layers Away: The Genomic Characterization of Bacillus pumilus 64-1, an Isolate With Antimicrobial Activity From the Marine Sponge Plakina cyanorosea (Porifera, Homoscleromorpha).", "token_count": 78, "char_count": 204, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:47.691939", "source": { "split": "train_shard_00001", "doc_id": 1960 }, "chunk_id": "train_shard_00001_1960_1", "global_id": 8430 }, { "text": "Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus paired isolates (34 pairs) were sourced from 34 CRS patients at least 6 months apart. Isolates were grown into 48 h biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41 % (14/34 pairs) of S. aureus isolates were persistent, while 59 % (20/34 pairs) were non-persistent. Persistent isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. Furthermore, a significant increase in the copy number of conserved plasmids of persistent strains was observed. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics, which was linked to a significant increase in biofilm biomass over time, indicating a potential biofilm pathoadaptive process in persistent isolates. In conclusion, our study provides important insights into the mutational changes during S. aureus persistence in CRS patients highlighting potential pathoadaptive mechanisms in S. aureus persistent isolates culminating in increased biofilm biomass.", "token_count": 511, "char_count": 1977, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8007, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:48.329022", "source": { "split": "train_shard_00001", "doc_id": 1961 }, "chunk_id": "train_shard_00001_1961_0", "global_id": 8431 }, { "text": "The intra-host evolutionary landscape and pathoadaptation of persistent Staphylococcus aureus in chronic rhinosinusitis.", "token_count": 37, "char_count": 127, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:48.699008", "source": { "split": "train_shard_00001", "doc_id": 1961 }, "chunk_id": "train_shard_00001_1961_1", "global_id": 8432 }, { "text": "

Purpose of review

Recent advances in genetics are pushing the frontiers of health research in Africa. Notable developments include the release of the draft human pangenome reference, regulatory approval of gene editing therapies for sickle cell disease, and the announcements of major initiatives such as the Ghana Genome Project, the Personalized Medicine in North Africa Initiative, Nigeria's 100K Genome Project and South Africa's 110K Human Genomes Project. Additionally, gene-based therapies for HIV are on the horizon, with clinical trials planned in some African countries. Despite this progress, a pressing challenge remains: ensuring equitable access and delivery of genomics medicine worldwide, particularly in Africa and other low and middle income regions.

Summary and a call to action

Science diplomacy and academic-industry partnerships are key to achieving \"Genomics for All.\" This requires collaboration between African governments, academic institutions, funding agencies, commercial biotechnology companies, civil society, and international health organizations. Together, these stakeholders must define and establish a sustainable framework to support genetic research in Africa, increase the availability of genetic data from African populations, and set-up translational genomics medicine initiatives tailored to the continent's unique healthcare needs. Science advocacy and diplomacy is also needed to establish mechanisms that prevent the hoarding of genetic resources, including genetic data and novel interventions, and guarantee equitable access to the scientific, medical and economic benefits of genomics for all nations. Achieving this vision may necessitate international treaties to promote equitable access to genomic innovations, responsible and ethical cross-border data sharing, and long-term strategies to address funding gaps in genomic research and its application in medicine and healthcare in Africa.\n\nScience and Society: Pathways to Equitable Access and Delivery of Genomics Medicine in Africa.", "token_count": 407, "char_count": 2051, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6204, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:49.320464", "source": { "split": "train_shard_00001", "doc_id": 1962 }, "chunk_id": "train_shard_00001_1962_0", "global_id": 8433 }, { "text": "Oenococcus oeni, the only species of lactic acid bacteria capable of fully completing malolactic fermentation under challenging wine conditions, continues to intrigue researchers owing to its remarkable adaptability, particularly in combating acid stress. However, the mechanism underlying its superior adaptation to wine stresses still remains elusive due to the lack of viable genetic manipulation tools for this species. In this study, we conducted genomic sequencing and acid resistance phenotype analysis of 255 O. oeni isolates derived from diverse wine regions across China, aiming to elucidate their strain diversity and genotype-phenotype associations of acid resistance through comparative genomics. A significant correlation between phenotypes and evolutionary relationships was observed. Notably, phylogroup B predominantly consisted of acid-resistant isolates, primarily originating from Shandong and Shaanxi wine regions. Furthermore, we uncovered a noteworthy linkage between prophage genomic islands and acid resistance phenotype. Using genome-wide association studies, we identified key genes correlated with acid resistance, primarily involved in carbohydrates and amino acid metabolism processes. This study offers profound insights into the genetic diversity and genetic basis underlying adaptation mechanisms to acid stress in O. oeni.IMPORTANCEThis study provides valuable insights into the genetic basis of acid resistance in Oenococcus oeni, a key lactic acid bacterium in winemaking. By analyzing 255 isolates from diverse wine regions in China, we identified significant correlations between strain diversity, genomic islands, and acid resistance phenotypes. Our findings reveal that certain prophage-related genomic islands and specific genes are closely linked to acid resistance, offering a deeper understanding of how O. oeni adapts to acidic environments. These discoveries not only advance our knowledge of microbial stress responses but also pave the way for selecting and engineering acid-resistant strains, enhancing malolactic fermentation efficiency and wine quality. This research underscores the importance of genomics in improving winemaking practices and addressing challenges posed by high-acidity wines.", "token_count": 487, "char_count": 2281, "word_count": 299, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:49.969456", "source": { "split": "train_shard_00001", "doc_id": 1963 }, "chunk_id": "train_shard_00001_1963_0", "global_id": 8434 }, { "text": "Comparative genomic analysis of 255 <i>Oenococcus oeni</i> isolates from China: unveiling strain diversity and genotype-phenotype associations of acid resistance.", "token_count": 53, "char_count": 174, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:50.331313", "source": { "split": "train_shard_00001", "doc_id": 1963 }, "chunk_id": "train_shard_00001_1963_1", "global_id": 8435 }, { "text": "The genus Aeromonas is a common gastrointestinal pathogen associated with human and animal infections. Due to the high level of cross-species similarity, their evolutionary dynamics and genetic diversity are still fragmented. Hereby, we investigated the pan-genomes of 29 Aeromonas species, as well as Aeromonas species in microbial communities, to clarify their evolutionary dynamics and genetic diversity, with special focus on virulence factors and horizontal gene transfer events. Our study revealed an open pan-genome of Aeromonas containing 10,144 gene families. These Aeromonas species exhibited different functional constraints, with the single-copy core genes and most accessory genes experiencing purifying selection. The significant congruence between core genome and pan-genome trees revealed that core genes mainly affected evolutionary divergences of Aeromonas species. Gene gains and losses revealed a high level of genome plasticity, exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. The selective constraints shaped virulence gene pools of these Aeromonas strains, where genes encoding hemolysin were ubiquitous. Of these strains, Aeromonas aquatica MX16A seemed to be more resistant, as it harbored most resistance genes. Finally, the virulence factors of Aeromonas in microbial communities were quite dynamic in response to environment changes. For example, the virulence diversity of Aeromonas in microbial communities could reach levels that match some of the most virulent Aeromonas species (such as A. hydrophila) in penetrated-air and modified-air packaging", "token_count": 448, "char_count": 1735, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [ "MX16A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:50.974388", "source": { "split": "train_shard_00001", "doc_id": 1964 }, "chunk_id": "train_shard_00001_1964_0", "global_id": 8436 }, { "text": "Our work shed some light onto genetic diversity, evolutionary history, and functional features of Aeromonas, which could facilitate the detection and prevention of infections.IMPORTANCE Aeromonas has long been known as a gastrointestinal pathogen, yet it has many species whose evolutionary dynamics and genetic diversity had been unclear until now. We have conducted pan-genome analysis for 29 Aeromonas species and revealed a high level of genome plasticity exhibited by hundreds of gene expansions and contractions, horizontally transferred genes, and mobile genetic elements. These species also contained many virulence factors both identified from single isolated species and microbial community. This pan-genome study could elevate the level for detection and prevention of Aeromonas infections.\n\nComprehensive Analysis Reveals the Evolution and Pathogenicity of Aeromonas, Viewed from Both Single Isolated Species and Microbial Communities.", "token_count": 239, "char_count": 989, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:51.438954", "source": { "split": "train_shard_00001", "doc_id": 1964 }, "chunk_id": "train_shard_00001_1964_1", "global_id": 8437 }, { "text": "To improve inulin utilization and ethanol fermentation, exoinulinase genes from the yeast Kluyveromyces marxianus and the recently identified yeast, Candida kutaonensis, were expressed in Saccharomyces cerevisiae. S. cerevisiae harboring the exoinulinase gene from C. kutaonensis gave higher ethanol yield and productivity from both inulin (0.38 vs. 0.34 g/g and 1.35 vs. 1.22 g l(-1) h(-1)) and Jerusalem artichoke tuber flour (0.47 vs. 0.46 g/g and 1.62 vs. 1.54 g l(-1) h(-1)) compared with the strain expressing the exoinulinase gene from K. marxianus. Thus, the exoinulinase gene from C. kutaonensis is advantageous for engineering S. cerevisiae to improve ethanol fermentation from inulin sources.\n\nExpression of exoinulinase genes in Saccharomyces cerevisiae to improve ethanol production from inulin sources.", "token_count": 262, "char_count": 816, "word_count": 116, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:51.991250", "source": { "split": "train_shard_00001", "doc_id": 1965 }, "chunk_id": "train_shard_00001_1965_0", "global_id": 8438 }, { "text": "Objective: To investigate the drug-resistant gene characteristics and core genome characteristics of carbapenem-resistant Enterobacter cloacae (CR-ECL) in rural residents of Weifang City, Shandong Province. Methods: Fecal samples were collected from rural community residents in Weifang City, Shandong Province in 2017. Drug-resistant strains were screened using a carbapenem-resistant enterobacter chromogenic medium. CR-ECL positive strains were acquired via Matrix Assisted Laser Desorption Ionization Time of Flight Mass Spectrometry(MALDI-TOFMS) analysis. The antibiotic resistance phenotype of CR-ECL was determined using a microbroth dilution assay. Whole genome sequencing (WGS) and analysis were conducted, along with an examination of the immediate vicinity of the blaNDM gene and phylogenetic analysis of the strains. Results: A total of 628 fecal samples were collected and tested, of which 6 were CR-ECL positive (detection rate 0.96%), all exhibiting multiple drug resistance (MDR) phenotypes. Six CR-ECL strains had four MLST genotypes (ST), all of which carried multiple drug resistance genes (blaNDM-1, blaNDM-5, etc.) and virulence genes (acrA, acrB, entB, fepC, etc.). There were mobile genetic elements ISAba125, TN3-IS3000, TN3 and IS5 in the genetic environment surrounding the blaNDM gene. The phylogenetic tree showed that the multi-locus sequence typing of the core genome (cgMLST) was consistent with the single nucleotide polymorphism (SNPs) results", "token_count": 517, "char_count": 1632, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [ "IS5", "IS3000", "TN3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:52.647758", "source": { "split": "train_shard_00001", "doc_id": 1966 }, "chunk_id": "train_shard_00001_1966_0", "global_id": 8439 }, { "text": "The cgMLST results showed that the allele differences between strains 2BC0101B and 2BC0251B, 2BG0561B and 2BI0221B were 2 and 1, respectively. The SNPs results showed that the above two pairs of bacteria also clustered together. It was found that the strains of chicken fecal samples in the National Center for Biotechnology Information (NCBI) database were located in the center of the evolutionary tree, and the local sequences could be traced back to American human sequences. Conclusion: Multidrug-resistant CR-ECL is detected in rural community residents in Weifang City, Shandong Province.\n\n[Analysis of gene characteristics and core genome characteristics of carbapenem-resistant Enterobacter cloacae in rural residents of Weifang City, Shandong Province].", "token_count": 204, "char_count": 770, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6881, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:53.109524", "source": { "split": "train_shard_00001", "doc_id": 1966 }, "chunk_id": "train_shard_00001_1966_1", "global_id": 8440 }, { "text": "

Background

Bacteriophages that infect the opportunistic pathogen Pseudomonas aeruginosa have been classified into several groups. One of them, which includes temperate phage particles with icosahedral heads and long flexible tails, bears genomes whose architecture and replication mechanism, but not their nucleotide sequences, are like those of coliphage Mu. By comparing the genomic sequences of this group of P. aeruginosa phages one could draw conclusions about their ontogeny and evolution.

Results

Two newly isolated Mu-like phages of P. aeruginosa are described and their genomes sequenced and compared with those available in the public data banks. The genome sequences of the two phages are similar to each other and to those of a group of P. aeruginosa transposable phages. Comparing twelve of these genomes revealed a common genomic architecture in the group. Each phage genome had numerous genes with homologues in all the other genomes and a set of variable genes specific for each genome. The first group, which comprised most of the genes with assigned functions, was named \"core genome\", and the second group, containing mostly short ORFs without assigned functions was called \"accessory genome\". Like in other phage groups, variable genes are confined to specific regions in the genome.

Conclusion

Based on the known and inferred functions for some of the variable genes of the phages analyzed here, they appear to confer selective advantages for the phage survival under particular host conditions. We speculate that phages have developed a mechanism for horizontally acquiring genes to incorporate them at specific loci in the genome that help phage adaptation to the selective pressures imposed by the host.\n\nCore and accessory genome architecture in a group of Pseudomonas aeruginosa Mu-like phages.", "token_count": 416, "char_count": 1842, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5531, "quality_score": 0.7766, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:53.727227", "source": { "split": "train_shard_00001", "doc_id": 1967 }, "chunk_id": "train_shard_00001_1967_0", "global_id": 8441 }, { "text": "Helicobacter pylori infection has been linked to gastrointestinal diseases including gastric cancer. High rates of H. pylori infection and gastric cancer have been reported in indigenous populations within the United States. We report whole-genome sequencing of three H. pylori isolates originating from Native American patients presenting with gastric disease.\n\nWhole-genome sequencing of Helicobacter pylori isolates from Native American gastric biopsy specimens.", "token_count": 141, "char_count": 500, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7377, "quality_score": 0.8689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:54.158303", "source": { "split": "train_shard_00001", "doc_id": 1968 }, "chunk_id": "train_shard_00001_1968_0", "global_id": 8442 }, { "text": "There are few naturally occurring environments where both acid and salinity stress exist together, consequently, there has been little evolutionary pressure for microorganisms to develop systems that enable them to deal with both stresses simultaneously. Members of the genus Acidihalobacter are iron- and sulfur-oxidizing, halotolerant acidophiles that have developed the ability to tolerate acid and saline stress and, therefore, have the potential to bioleach ores with brackish or saline process waters under acidic conditions. The genus consists of four members, A. prosperus DSM 5130T, A. prosperus DSM 14174, A. prosperus F5 and \"A. ferrooxidans\" DSM 14175. An in depth genome comparison was undertaken in order to provide a more comprehensive description of the mechanisms of halotolerance used by the different members of this genus. Pangenome analysis identified 29, 3 and 9 protein families related to halotolerance in the core, dispensable and unique genomes, respectively. The genes for halotolerance showed Ka/Ks ratios between 0 and 0.2, confirming that they are conserved and stabilized. All the Acidihalobacter genomes contained similar genes for the synthesis and transport of ectoine, which was recently found to be the dominant osmoprotectant in A. prosperus DSM 14174 and A. prosperus DSM 5130T. Similarities also existed in genes encoding low affinity potassium pumps, however, A. prosperus DSM 14174 was also found to contain genes encoding high affinity potassium pumps. Furthermore, only A. prosperus DSM 5130T and \"A. ferrooxidans\" DSM 14175 contained genes allowing the uptake of taurine as an osmoprotectant", "token_count": 527, "char_count": 1767, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6198, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:54.791247", "source": { "split": "train_shard_00001", "doc_id": 1969 }, "chunk_id": "train_shard_00001_1969_0", "global_id": 8443 }, { "text": "Variations were also seen in genes encoding proteins involved in the synthesis and/or transport of periplasmic glucans, sucrose, proline, and glycine betaine. This suggests that versatility exists in the Acidihalobacter genus in terms of the mechanisms they can use for halotolerance. This information is useful for developing hypotheses for the search for life on exoplanets and moons.\n\nUncovering the Mechanisms of Halotolerance in the Extremely Acidophilic Members of the Acidihalobacter Genus Through Comparative Genome Analysis.", "token_count": 148, "char_count": 547, "word_count": 75, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:55.236386", "source": { "split": "train_shard_00001", "doc_id": 1969 }, "chunk_id": "train_shard_00001_1969_1", "global_id": 8444 }, { "text": "Escherichia coli comprises diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond, as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity/virulence genes (stxI, stxII, eaeA, hlyA, ST, and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azithromycin. Our results showed that isolates from water, sediment, and water plants were similar by phylogroup distribution, virulence gene distribution, and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail, and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem.\n\nNiche Preference of Escherichia coli in a Peri-Urban Pond Ecosystem.", "token_count": 475, "char_count": 1804, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:55.869389", "source": { "split": "train_shard_00001", "doc_id": 1970 }, "chunk_id": "train_shard_00001_1970_0", "global_id": 8445 }, { "text": "As prokaryotes diverge by evolution, essential 'core' genes required for conserved phenotypes are preferentially retained, while inessential 'accessory' genes are lost or diversify. We used the recently expanded number of myxobacterial genome sequences to investigate the conservation of their signalling proteins, focusing on two sister genera (Myxococcus and Corallococcus), and on a species within each genus (Myxococcus xanthus and Corallococcus exiguus). Four new C. exiguus genome sequences are also described here. Despite accessory genes accounting for substantial proportions of each myxobacterial genome, signalling proteins were found to be enriched in the core genome, with two-component system genes almost exclusively so. We also investigated the conservation of signalling proteins in three myxobacterial behaviours. The linear carotenogenesis pathway was entirely conserved, with no gene gain/loss observed. However, the modular fruiting body formation network was found to be evolutionarily plastic, with dispensable components in all modules (including components required for fruiting in the model myxobacterium M. xanthus DK1622). Quorum signalling (QS) is thought to be absent from most myxobacteria, however, they generally appear to be able to produce CAI-I (cholerae autoinducer-1), to sense other QS molecules, and to disrupt the QS of other organisms, potentially important abilities during predation of other prokaryotes.\n\nA Genomic Survey of Signalling in the Myxococcaceae.", "token_count": 399, "char_count": 1544, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6812, "quality_score": 0.8406, "entities": { "genes": [ "DK1622" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:56.536614", "source": { "split": "train_shard_00001", "doc_id": 1971 }, "chunk_id": "train_shard_00001_1971_0", "global_id": 8446 }, { "text": "

ABSTRACT

Intracellular gene transfers (IGTs) between the nucleus and organelles, including plastids and mitochondria, constantly reshapes the nuclear genome during evolution. Despite the substantial contribution of IGTs to genome variation, the dynamic trajectories of IGTs at the pangenomic level remain elusive. Here, we propose a novel approach, IGTminer, to map the evolutionary trajectories of IGTs by collinearity and gene reannotation across multiple genome assemblies. IGTminer was applied to create a nuclear organelle gene (NOG) map across 67 genomes covering 15 Poaceae species, including important crops, revealing the polymorphisms and trajectory dynamics of NOGs. The NOGs produced were verified by experimental evidence and resequencing datasets. We found that most of the NOGs were recently transferred and lineage specific, and that Triticeae species tended to have more NOGs than other Poaceae species. Wheat had a higher retention rate of NOGs than maize and rice, and the retained NOGs were likely involved in the photosynthesis and translation pathways. Large numbers of NOG clusters were aggregated in hexaploid wheat during two rounds of polyploidization and contributed to the genetic diversities among modern wheat varieties. Finally, we proposed a radiocarbon-like model illustrating the transfer and elimination dynamics of NOGs, highlighting the unceasing integration and selective retention of NOGs over evolutionary time. In addition, we implemented an interactive webserver for NOG exploration in Poaceae. In summary, this study provides new resources and clues for the roles of IGTs in shaping inter- and intraspecies genome variation and driving plant genome evolution.\n\nPangenome-based dynamic trajectories of intracellular gene transfers in Poaceae unveil a high rate of unceasing integration and selective retention in Triticeae", "token_count": 445, "char_count": 1873, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:57.203120", "source": { "split": "train_shard_00001", "doc_id": 1972 }, "chunk_id": "train_shard_00001_1972_0", "global_id": 8447 }, { "text": "Bartonella henselae, a Gram-negative facultative intracellular bacterium, is the etiological agent of cat-scratch disease and also causes bacillary angiomatosis in immunocompromised individuals. Although the ability to promote vascular endothelial cell proliferation differs among Bartonella species, variations among strains within B. henselae remain unclear. Bartonella angiogenic factor A (BafA) and Bartonella adhesin A (BadA) have been identified as autotransporters of B. henselae that are involved in endothelial cell proliferation. Although strain-specific differences in the expression of BadA and the VirB/D4 type IV secretion system have been reported, BafA expression among B. henselae strains has yet to be examined. Therefore, the present study investigated the proliferation-promoting ability of 13 B. henselae strains from several sources in human umbilical vein endothelial cells (HUVECs). We identified BafA variants 1 and 2 based on the deduced amino acid sequences of its passenger domain. The recombinant proteins of both variants exhibited similar proliferation activity against HUVECs. However, BafA variant 2 strains showed cytotoxicity at a high bacterial inoculum in a direct coculture with HUVECs, which was attenuated in an indirect coculture. These strains, in contrast to BafA variant 1 strains, highly expressed BadA and exhibited bacterial aggregation. Based on a core genome SNP analysis of 50 B. henselae strains, the BafA variant types corresponded to clades 1-4. These results indicate that vasoproliferative traits differ among B. henselae clades based on the variant types. Therefore, this study provides a new conceptual framework in which the clades of B", "token_count": 508, "char_count": 1767, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6224, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:57.899808", "source": { "split": "train_shard_00001", "doc_id": 1973 }, "chunk_id": "train_shard_00001_1973_0", "global_id": 8448 }, { "text": "henselae may predict their pathogenicity in humans.IMPORTANCEBartonella species including Bartonella henselae, Bartonella quintana, and Bartonella bacilliformis cause vasoproliferative lesions. Their proliferation-promoting ability in vascular endothelial cells differs among Bartonella species; however, it is unclear whether these differences exist among B. henselae strains. We herein showed that B. henselae strains exhibited variable proliferation-promoting ability and cytotoxicity in vascular endothelial cells, which corresponded to the bafA gene variants possessed by the strains. The expression levels of Bartonella angiogenic factor A (BafA) and Bartonella adhesin A, as well as the degree of proliferation-promoting ability and cytotoxicity in endothelial cells, varied among the strains. A core genome SNP analysis of strains using whole genome sequencing data divided B. henselae strains into four clades, with each clade corresponding to BafA variants 1-4. These results suggest the differential vasoproliferative potency of B. henselae, with potential implications in clinical management, including risk stratification and predictions of the clinical course.\n\nDifferential vasoproliferative traits of Bartonella henselae strains associated with autotransporter BafA variants.", "token_count": 407, "char_count": 1386, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:58.529646", "source": { "split": "train_shard_00001", "doc_id": 1973 }, "chunk_id": "train_shard_00001_1973_1", "global_id": 8449 }, { "text": "Vibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States. The draft genomes of 132 North American clinical and oyster V. parahaemolyticus isolates were sequenced to investigate their phylogenetic and biogeographic relationships. The majority of oyster isolate sequence types (STs) were from a single harvest location; however, four were identified from multiple locations. There was population structure along the Gulf and Atlantic Coasts of North America, with what seemed to be a hub of genetic variability along the Gulf Coast, with some of the same STs occurring along the Atlantic Coast and one shared between the coastal waters of the Gulf and those of Washington State. Phylogenetic analyses found nine well-supported clades. Two clades were composed of isolates from both clinical and oyster sources. Four were composed of isolates entirely from clinical sources, and three were entirely from oyster sources. Each single-source clade consisted of one ST. Some human isolates lack tdh, trh, and some type III secretion system (T3SS) genes, which are established virulence genes of V. parahaemolyticus Thus, these genes are not essential for pathogenicity. However, isolates in the monophyletic groups from clinical sources were enriched in several categories of genes compared to those from monophyletic groups of oyster isolates. These functional categories include cell signaling, transport, and metabolism. The identification of genes in these functional categories provides a basis for future in-depth pathogenicity investigations of V. parahaemolyticusIMPORTANCEVibrio parahaemolyticus is the most common cause of seafood-borne illness reported in the United States and is frequently associated with shellfish consumption. This study contributes to our knowledge of the biogeography and functional genomics of this species around North America. STs shared between the Gulf Coast and the Atlantic seaboard as well as Pacific waters suggest possible transport via oceanic currents or large shipping vessels. STs frequently isolated from humans but rarely, if ever, isolated from the environment are likely more competitive in the human gut than other STs", "token_count": 518, "char_count": 2267, "word_count": 323, "semantic_coherence": 1, "information_density": 0.5573, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:17:59.188129", "source": { "split": "train_shard_00001", "doc_id": 1974 }, "chunk_id": "train_shard_00001_1974_0", "global_id": 8450 }, { "text": "This could be due to additional functional capabilities in areas such as cell signaling, transport, and metabolism, which may give these isolates an advantage in novel nutrient-replete environments such as the human gut.\n\nPhylogenetic and Biogeographic Patterns of Vibrio parahaemolyticus Strains from North America Inferred from Whole-Genome Sequence Data.", "token_count": 85, "char_count": 357, "word_count": 49, "semantic_coherence": 1, "information_density": 0.898, "quality_score": 0.949, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:17:59.560689", "source": { "split": "train_shard_00001", "doc_id": 1974 }, "chunk_id": "train_shard_00001_1974_1", "global_id": 8451 }, { "text": "The frequency and variety of infections caused by fungi are increasing. However, changes and intercenter and regional differences are observed in the distribution of fungal species over the years. It is important to update the epidemiological data in order to enable early and appropriate treatment. In this retrospective study, the number of fungi isolated from clinical samples, their distribution at the genus/ species level and the variations over the years in Hacettepe University hospital which is a regional center for patients at risk of fungal infection were investigated. For this purpose, laboratory records from 2008- 2019 were examined and 21813 fungal strains isolated from 19636 clinical samples were detected. When the first (2008-2013) and second (2014-2019) six-year periods were compared, a 2.5 fold increase was observed in the number of specimens yielding fungal growth (first period; n= 5620, second period; n= 14016). Fungi were most frequently isolated from urine (45.0%), lower respiratory tract (30.7%) and blood (6.8%) samples. Mould isolation rate in all samples increased significantly in the second six-year period (from 8.3% to 10.6%, p≤ 0.001). As expected, the most frequent yeast was Candida albicans (57.0%) and mould was Aspergillus fumigatus complex (50.4%). In the second six-year period, isolation of C.albicans (59.3% to 56.0%, p≤ 0.001) among yeasts and A.fumigatus complex (58.1% to 48.0%, p≤ 0.001) among moulds decreased significantly. In urine specimens, most common fungi were C.albicans (49.8%), Candida glabrata complex (15.6%), Candida tropicalis (8.9%) and Candida kefyr (7.5%)", "token_count": 485, "char_count": 1627, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:00.210417", "source": { "split": "train_shard_00001", "doc_id": 1975 }, "chunk_id": "train_shard_00001_1975_0", "global_id": 8452 }, { "text": "In lower respiratory tract specimens, the most common mould was A.fumigatus complex (51.2%), which has decreased from 63.7% in the first six years to 47.1% in the second period (p≤ 0.001). Over the same period, other Aspergillus species (from 25.5% to 34.1%, p= 0.002) and non-Aspergillus moulds (from 36.3% to 52.9%, p≤ 0.001) were increased. In blood samples, C.albicans (44.4%), Candida parapsilosis complex (21.5%) and C.glabrata complex (13.0%) were the most frequent species. In the second six-year period, the frequency of C.albicans decreased from 47.3% to 42.2% (p= 0.059) and the frequency of C.glabrata complex increased from 9.5% to 15.5% (p≤ 0.001) when compared to the first period. For the sterile specimens other than blood, the most common species were C.albicans (37.8%), C.glabrata complex (9.1%) and C.parapsilosis complex (4.7%). However, the number of fungal isolates and the distribution of the species showed great variation over the years. In our center, a substantial increase in the number of fungal strains isolated from the clinical specimens were observed over a 12-years period. In addition and similar to previously published reports, the increase of strains belonging to species with decreased antifungal susceptibility and/or species with unknown susceptibility were detected. The use of local data is required in order to implement early and appropriate antifungal treatment because of inter-center and regional differences observed in epidemiological trends regarding the distributions of fungal genera and species. Surveillance studies to be conducted with the participation of large and sufficient numbers of centers in our country, as we have done for our center, will also contribute to approaches regarding the management of fungal infections by revealing the epidemiological data in a comprehensive manner.", "token_count": 519, "char_count": 1848, "word_count": 275, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:00.860871", "source": { "split": "train_shard_00001", "doc_id": 1975 }, "chunk_id": "train_shard_00001_1975_1", "global_id": 8453 }, { "text": "[Changing Trends in Isolation Frequencies and Species of Clinical Fungal Strains: What Do the 12-years (2008-2019) Mycology Laboratory Data Tell About?]", "token_count": 54, "char_count": 152, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:01.219091", "source": { "split": "train_shard_00001", "doc_id": 1975 }, "chunk_id": "train_shard_00001_1975_2", "global_id": 8454 }, { "text": "

Introduction

The emergence and spread of new strains of zoonotic bacteria, such as multidrug resistant (MDR) Salmonella Infantis, represent a growing health risk for humans in and outside Europe due to foodborne infections of poultry meat origin.

Objectives

In order to understand genome relations of S. Infantis strains from Hungary and from different geographic regions, we performed a comprehensive genome analysis of nine Hungarian and 67 globally selected strains of S. Infantis and 26 Salmonella strains representing 13 non-Infantis serovars.

Results

Analyses of whole-, and accessory genomes, showed that almost all S. Infantis strains were separated from the non-Infantis serovars. S. Infantis strains from Hungary formed subclusters based on their time of isolation. In whole genome sequence analysis, the Swiss strains of S. Infantis were closely related to each other and clustered together with subclusters of strains from Hungary, Japan, Italy, United States, and Israel. The accessory genome analysis revealed that the Swiss strains were distinct from most of the strains investigated, including the Hungarian ones. Analysis of the cloud genes offered the most detailed insight into the genetic distance and relationship of S. Infantis strains confirming that the Swiss and Hungarian strains belonged to different lineages. As expected, core genome analysis provided the least discriminatory power for analysis of S. Infantis. Genomic sequences of nine strains from Brazil, Israel, Mexico, Nigeria, and Senegal (deposited as S. Infantis) proved to be outliers from the S. Infantis clade", "token_count": 456, "char_count": 1699, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5647, "quality_score": 0.7823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:01.859394", "source": { "split": "train_shard_00001", "doc_id": 1976 }, "chunk_id": "train_shard_00001_1976_0", "global_id": 8455 }, { "text": "They were predicted to be Salmonella Rissen, Salmonella Ouakarm, Salmonella Kentucky, Salmonella Thompson, and Salmonella enterica subsp. diarizonae.

Conclusion

Accessory genome of S. Infantis showed the highest diversity suggesting a faster evolution than that of the whole genomes contributing to the emergence of multiple genetic variants of S. Infantis worldwide. Accordingly, in spite of the comprehensive analysis of several genomic characteristics, no epidemiologic links between these S. Infantis strains from different countries could be established. It is also concluded that several strains originally designated as S. Infantis need in databanks reclassification.\n\nComparative Genome Analysis of Hungarian and Global Strains of Salmonella Infantis.", "token_count": 242, "char_count": 843, "word_count": 100, "semantic_coherence": 1, "information_density": 0.69, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:02.349289", "source": { "split": "train_shard_00001", "doc_id": 1976 }, "chunk_id": "train_shard_00001_1976_1", "global_id": 8456 }, { "text": "The aim of the present study was to evaluate the use of thermally-dried Kluyveromyces marxianus as baker's yeast. Bread samples produced by thermally-dried K. marxianus were compared with samples produced by wet K. marxianus culture and by commercial baker's yeast. The type of the culture had no effect on loaf weight, loaf volume, specific loaf volume, density or moisture loss, in contrast to pH, total titrable acidity (TTA), and moisture content. The use of thermally-dried K. marxianus resulted in lower pH values and higher TTA, while the bread samples showed higher resistance to spoilage as counts of moulds and yeasts were significantly lower during preservation. The SPME GC/MS analysis of volatiles and the preliminary sensory evaluation showed no significant differences in the profile of aroma-related compounds or overall quality of the tested samples.\n\nEvaluation of thermally-dried Kluyveromyces marxianus as baker's yeast", "token_count": 239, "char_count": 939, "word_count": 141, "semantic_coherence": 1, "information_density": 0.5745, "quality_score": 0.7872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:02.822336", "source": { "split": "train_shard_00001", "doc_id": 1977 }, "chunk_id": "train_shard_00001_1977_0", "global_id": 8457 }, { "text": "Milk is a source of many valuable nutrients, including minerals, vitamins and proteins, with an important role in adult health. Milk and dairy products naturally containing or with added probiotics have healthy functional food properties. Indeed, probiotic microorganisms, which beneficially affect the host by improving the intestinal microbial balance, are recognized to affect the immune response and other important biological functions. In addition to macronutrients and micronutrients, biologically active peptides (BPAs) have been identified within the amino acid sequences of native milk proteins; hydrolytic reactions, such as those catalyzed by digestive enzymes, result in their release. BPAs directly influence numerous biological pathways evoking behavioral, gastrointestinal, hormonal, immunological, neurological, and nutritional responses. The addition of BPAs to food products or application in drug development could improve consumer health and provide therapeutic strategies for the treatment or prevention of diseases. Herein, we review the scientific literature on probiotics, BPAs in milk and dairy products, with special attention to milk from minor species (buffalo, sheep, camel, yak, donkey, etc.); safety assessment will be also taken into consideration. Finally, recent advances in foodomics to unveil the probiotic role in human health and discover novel active peptide sequences will also be provided.\n\nMilk and Its Derivatives as Sources of Components and Microorganisms with Health-Promoting Properties: Probiotics and Bioactive Peptides.", "token_count": 352, "char_count": 1570, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7103, "quality_score": 0.8551, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:03.406736", "source": { "split": "train_shard_00001", "doc_id": 1978 }, "chunk_id": "train_shard_00001_1978_0", "global_id": 8458 }, { "text": "

Aims

The focus of the research was to identify yeasts from barley kernels in order to study their folate production capability while maintaining high viscosity caused by soluble fibres in oat bran fermentation.

Methods and results

The 65 isolated yeasts were characterized by API carbohydrate utilization tests, and assays for extracellular enzyme activities were the following: amylase, beta-glucanase, cellulase or CMCase, lipase, protease and xylanase. Yeasts were identified by partial DNA sequencing of the 25S D1/D2 and ITS1-5.8S-ITS2 regions. They belonged to the genera Aureobasidium, Cryptococcus, Pseudozyma and Rhodotorula. Folate production was determined from supernatant and cells grown in a rich laboratory medium or directly from oat bran solution inoculated with the appropriate yeast. Food yeasts, Saccharomyces cerevisiae, Candida milleri, Kluyveromyces marxianus and Galactomyces geotrichum, were used for comparison. Most of the yeasts isolated from barley destroyed the solid, viscous structure of the oat bran solution, indicating that they degraded the viscosity-generating soluble fibres, considered to be nutritionally advantageous. The best folate producers were S. cerevisiae, followed by Pseudozyma sp., Rhodotorula glutinis and K. marxianus. The yeasts maintaining high viscosity were used together with lactic acid bacteria (LAB) Streptococcus thermophilus or Lactobacillus rhamnosus to ferment oat bran solution. None of the yeasts isolated from barley, contrary to S. cerevisiae and C", "token_count": 428, "char_count": 1532, "word_count": 208, "semantic_coherence": 1, "information_density": 0.649, "quality_score": 0.8245, "entities": { "genes": [ "ITS2", "ITS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:04.033573", "source": { "split": "train_shard_00001", "doc_id": 1979 }, "chunk_id": "train_shard_00001_1979_0", "global_id": 8459 }, { "text": "milleri, produced together with LAB significant amounts of folate.

Conclusions

Fermentative yeasts together with LAB are potential for use in developing novel high folate content healthy foods and snacks from oat bran.

Significance and impact of the study

High soluble fibre content and high natural folate content but low energy content food and snack products with pleasant fermentation aroma provide possibilities for new developments in the food industry.\n\nProduction of folate in oat bran fermentation by yeasts isolated from barley and diverse foods.", "token_count": 136, "char_count": 570, "word_count": 79, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:04.466009", "source": { "split": "train_shard_00001", "doc_id": 1979 }, "chunk_id": "train_shard_00001_1979_1", "global_id": 8460 }, { "text": "

ABSTRACT

An abundance of microbial genomes have been sequenced in the past two decades. For fundamental comparative genomic investigations, where the goal is to determine the major gain and loss events shaping the pangenome of a species, it is often unnecessary and computationally onerous to include all available genomes in studies. In addition, over-representation of specific lineages due to sampling and sequencing bias can have undesired effects on evolutionary analyses. To assist users with genomic dereplication , selecting a subset of representative genomes, for downstream comparative genomic investigations, we developed skDER & CiDDER ( https://github.com/raufs/skDER ). skDER combines recent advances to efficiently estimate average nucleotide identity (ANI) between thousands of microbial genomes with two efficient algorithms for genomic dereplication. Further, CiDDER implements an approach whereby protein clusters are determined across all genomes and genomes are iteratively selected as representatives until a user-defined saturation of the total protein space is achieved. To support ease of use, several auxiliary functionalities are implemented within the two programs, including arguments to: (i) test the number of representative genomes resulting from a variety of clustering parameters, (ii) automate downloading of genomes belonging to a bacterial species or genus by name, (iii) cluster non-representative genomes to their closest representative genomes, and (iv) automatically filter predicted plasmids and phages prior to dereplication. We further assess the effects of filtering mobile genetic elements (MGEs) on ANI and alignment fraction (AF) estimates between pairs of genomes and find that MGEs tend to slightly deflate both metrics in one species.

DATA SUMMARY

skDER and CiDDER are provided as open-source software implemented in Python and C++ on Github: https://github.com/raufs/skDER ; with version updates tracked on Zenodo: https://zenodo.org/records/13887710 1 . Installation of the software is supported via both Bioconda 2 and Docker. Additional code and data for analyses presented in this manuscript can be found on Zenodo at: https://zenodo.org/records/13891800 3 ", "token_count": 518, "char_count": 2231, "word_count": 308, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:05.095262", "source": { "split": "train_shard_00001", "doc_id": 1980 }, "chunk_id": "train_shard_00001_1980_0", "global_id": 8461 }, { "text": "Pre-computed representative genomes selected by skDER (v1.0.7) for 18 common bacterial taxonomic groups, referencing classifications from GTDB release 214 4 , are also provided on Zenodo at: https://zenodo.org/records/10041203 5 .

IMPACT STATEMENT

Due to the increased availability of genomes for certain microbial species, performing fundamental comparative genomic investigations has become restricted to those with access to more advanced computational infrastructure. Genomic dereplication, the process of selecting distinct representative genomes to capture the breadth of a taxonomic group, thus presents a valuable solution to overcome this embarrassment of riches. Specifically, genomic dereplication allows simplifying the scale of comparative investigations while minimizing the risk of biasing analyses to specific lineages, which might be overrepresented in genomic databases. We present here two programs for genomic dereplication, one based on ANI-inference, skDER, and the other based on assessing the saturation of total coding-genes sampled, CIDDER. These tools are implemented with a variety of auxiliary options and designed for ease of use.\n\nskDER & CiDDER: two scalable approaches for microbial genome dereplication", "token_count": 293, "char_count": 1245, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7246, "quality_score": 0.8623, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:05.660323", "source": { "split": "train_shard_00001", "doc_id": 1980 }, "chunk_id": "train_shard_00001_1980_1", "global_id": 8462 }, { "text": "

Objectives

The emergence of carbapenem-resistant Klebsiella pneumoniae presents significant health challenges. Here, we present the structural genome sequence of an NDM-5-producing K. pneumoniae (HZKP2) in China.

Methods

Antimicrobial susceptibility tests were conducted via broth microdilution. Whole-genome sequencing was performed for genomic analysis. Wzi and capsular polysaccharide (KL) were analysed using Kaptive. Resistance genes, virulence factors, and comparative genomics analyses were also conducted. Multilocus sequence typing (MLST), replicons type, and core genome MLST analysis were further conducted using BacWGSTdb server.

Results

HZKP2 was resistant to cefepime, ceftazidime, ciprofloxacin, ciprofloxacin, meropenem, and ertapenem. It harboured fosA, blaSHV-187, oqxA, oqxB, sul1, dfrA1, tet(A), floR, aph(6)-Id, aph(3'')-Ib, sul2, blaCTX-M-55, and blaNDM-5. Based on the RAST results, 5563 genes that belonged to 398 subsystems were annotated. The complete genome sequence of HZKP2 was characterized as ST1, wzi 19, and KL19, 5 five contigs totalling 5 654 446 bp, including one chromosome and four plasmids. Further analysis found that blaNDM-5 was located in a 46 161 bp IncX3 plasmid (pHZKP2-3)", "token_count": 465, "char_count": 1284, "word_count": 159, "semantic_coherence": 1, "information_density": 0.7987, "quality_score": 0.8994, "entities": { "genes": [ "HZKP2", "KL19", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:06.299345", "source": { "split": "train_shard_00001", "doc_id": 1981 }, "chunk_id": "train_shard_00001_1981_0", "global_id": 8463 }, { "text": "The genetic structure of blaNDM-5 gene was ISKox3-IS26-bleMBL-blaNDM-5-IS5-ISAb125-IS3000. Further analysis revealed that insertion sequences mediated the dissemination of blaNDM-5 from other species of Enterobacterales. Phylogenetic analysis showed that the closest relative was from a human stool specimen in China, which differed by 53 core genome MLST alleles.

Conclusions

Our study provides the first structural perspective of the ST1 K. pneumoniae isolate producing NDM-5 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant K. pneumoniae in clinical settings.\n\nGenome sequence of a sequence type 1 NDM-5-producing carbapenem-resistant Klebsiella pneumoniae in China.", "token_count": 250, "char_count": 848, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [ "IS26", "ST1", "IS5", "IS3000" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:06.786939", "source": { "split": "train_shard_00001", "doc_id": 1981 }, "chunk_id": "train_shard_00001_1981_1", "global_id": 8464 }, { "text": "Multiple sclerosis (MS) is defined as an inflammatory disorder that chronically affects the central nervous system of young people mostly and is distributed globally. It is associated with degeneration and demyelination of the myelin sheath around the nerves, resulting in multiple neurological disability symptoms ranging from mild to severe cases that end with paralysis sometimes. MS is one of the rising diseases globally that is unfortunately associated with reduced quality of life and adding national economic burdens. The definite MS mechanism is not clearly defined; however, all the previous researches confirm the role of the immune system as the master contributor in the pathogenesis. Innate and adaptive immune cells are activated peripherally then attracted toward the central nervous system (CNS) due to the breakdown of the blood-brain barrier. Recently, the gut-brain axis was shown to depend on gut metabolites that are produced by different microorganisms in the colon. The difference in microbiota composition between individuals is responsible for diversity in secreted metabolites that affect immune responses locally in the gut or systemically when reach blood circulation to the brain. It may enhance or suppress immune responses in the central nervous system (CNS) (repeated short forms); consequently, it may exacerbate or ameliorate MS symptoms. Recent data showed that some metabolites can be used as adjuvant therapy in MS and other inflammatory diseases. This review sheds light on the nature of MS and the possible interaction between gut microbiota and immune system regulation through the gut-brain axis, hence contributing to MS pathogenesis.\n\nMultiple Sclerosis: A Story of the Interaction Between Gut Microbiome and Components of the Immune System.", "token_count": 384, "char_count": 1785, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:07.401924", "source": { "split": "train_shard_00001", "doc_id": 1982 }, "chunk_id": "train_shard_00001_1982_0", "global_id": 8465 }, { "text": "High-throughput massive parallel sequencing has significantly improved bacterial pathogen genomics, diagnostics, and epidemiology. Despite its high accuracy, short-read sequencing struggles with complete genome reconstruction and assembly of extrachromosomal elements such as plasmids. Long-read sequencing with Oxford Nanopore Technologies (ONT) presents an alternative that offers benefits like real-time sequencing and cost-efficiency, particularly useful in resource-limited settings. However, the higher error rates of ONT have so far limited its application in high-precision genomic typing. The recent release of ONT’s R10.4.1 chemistry, with significantly improved raw read accuracy (Q20+), offers a potential solution to this problem. The aim of this study was to evaluate the performance of ONT’s latest chemistry for bacterial genomic typing against the gold standard Illumina technology, focusing on three respiratory pathogens of public health importance, Klebsiella pneumoniae, Bordetella pertussis , and Corynebacterium diphtheriae , and their related species. Using the Rapid Barcoding Kit V14, we generated and analyzed genome assemblies with different basecalling tools and models, at different simulated depths of coverage. ONT assemblies were compared to the Illumina reference for completeness and core genome multilocus sequence typing (cgMLST) accuracy (number of allelic mismatches). Our results show that genomes obtained from raw data basecalled with Dorado (with both simplex and duplex reads) SUP v0.7.1, assembled with Flye, and with a minimum coverage depth of 30×, optimized the accuracy for all bacterial species tested. The error rates were consistently below 1% of each cgMLST scheme, indicating that ONT R10.4.1 data is suitable for high-resolution genomic typing applied to outbreak investigations and public health surveillance.\n\nAccurate genotyping of three major respiratory bacterial pathogens with ONT R10.4.1 long-read sequencing", "token_count": 467, "char_count": 1971, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6779, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:08.043250", "source": { "split": "train_shard_00001", "doc_id": 1983 }, "chunk_id": "train_shard_00001_1983_0", "global_id": 8466 }, { "text": "Nitrogen has a significant effect on the fermentation rate and the chemical composition of alcoholic beverages. Nitrogen deficiency during fermentation of Agave juice for mescal production can lead to slow fermentations and end-products with low aromatic compound variety. In this study, the effects of NH4Cl supplementation on volatile compound formation in Agave duranguensis juice fermented at 28 °C with the native yeast strains Saccharomyces cerevisiae ITD00185, Hanseniaspora uvarum ITD00108, Torulaspora delbrueckii ITD00110 and Kluyveromyces marxianus ITD00211 were analysed. Nitrogen content in the Agave juice unsupplemented with NH4Cl was low. In the control treatments, the four yeasts consumed nitrogen at approximately the same rate, almost completely finishing by 24 h. Nitrogen supplementation increased biomass production with S. cerevisie, H. uvarum and T. delbrueckii but not with K. marxianus. K. marxianus consumed the total assimilable nitrogen more slowly than the other strains in the supplemented fermentations. In addition, the volatile compound profile differed between the studied yeasts. Volatile compound production by S. cerevisiae, H. uvarum and K. marxianus was higher in the supplemented fermentations, compared to the unsupplemented ones. In T. delbrueckii, the initial volatile compound concentrations remained unchanged, or decreased for some compounds, with nitrogen supplementation. The initial acetic acid and vanillin concentrations decreased with all strains tested and nitrogen supplementation. Furthermore, the concentration of higher alcohols increased with S. cerevisiae and H. uvarum in the NH4Cl-supplemented fermentations, but they decreased with T. delbrueckii and K. marxianus. In conclusion, the addition of an inorganic nitrogen source promotes microorganism metabolism, increases biomass formation and benefits the fermentation process.", "token_count": 493, "char_count": 1890, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5469, "quality_score": 0.7734, "entities": { "genes": [ "ITD00108", "ITD00211", "ITD00110", "ITD00185" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:08.750552", "source": { "split": "train_shard_00001", "doc_id": 1984 }, "chunk_id": "train_shard_00001_1984_0", "global_id": 8467 }, { "text": "Volatile compound production in Agave duranguensis juice fermentations using four native yeasts and NH4Cl supplementation", "token_count": 26, "char_count": 121, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:09.120620", "source": { "split": "train_shard_00001", "doc_id": 1984 }, "chunk_id": "train_shard_00001_1984_1", "global_id": 8468 }, { "text": "Global dissemination of K. pneumoniae clones poses health hazards to the public. Genomic epidemiology studies with comprehensive data set further revealed clone divergence, showing a high complexity in evolution. Moreover, clones carrying both acquired virulent and antimicrobial-resistant genes emerged and might replace the carbapenem-resistant clones. Co-occurrence of virulence and resistance is emerging. An unbiased collection of 3,061 clinical K. pneumoniae isolates (January 5, 2013 to July 24, 2018) underwent whole-genome sequencing. Pairwise core-genome single-nucleotide polymorphism (cgSNP) distances identified clone divergence and transmission events. A sum of 2,193 nonduplicated genomes clustered into four phenotypically indistinguishable species complexes. 93% (n = 2,035) were KpI with its largest clonal group (CG) being CG11 (n = 406). Three hundred ninety-three were ST11 and three hundred seventy-four carried blaKPC-2. Noticeably, CG11 is divided into two main subclones based on the capsule synthesis K loci (KL). CG11-KL64 showed a clear hypervirulent plus antimicrobial-resistant (hv+AMR) characteristic. Besides, the phylogenetic structure revealed the clone divergence of CG25, and this is the first report with sufficient CG25 genomes to identify the divergence. The outcomes of the hv+AMR CG25 cluster 1 affected patients were poorer (P < 0.05). Moreover, two episodes of strain transmissions were associated with CG25 cluster 1. Other transmissions were associated with ST20 and ST307. Genomic epidemiology identified clone divergence of CG11 and CG25. The hv+AMR subclones pose greater threats on a global scale", "token_count": 513, "char_count": 1684, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6916, "quality_score": 0.8458, "entities": { "genes": [ "CG25", "ST20", "KL64", "ST307", "ST11", "CG11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:09.798295", "source": { "split": "train_shard_00001", "doc_id": 1985 }, "chunk_id": "train_shard_00001_1985_0", "global_id": 8469 }, { "text": "Nosocomial transmissions of the high-risk clones raised our concerns about the evolution and transmission of emerging clones among newborns and critically ill patients. IMPORTANCE The convergence of AMR and acquired virulence posing higher risks to the public is a focusing point. With sufficient genomes and genotypes, we successfully identify the convergence in two subclones, the previously reported CG11-KL64, and the newly reported CG25 cluster 1. The novel finding of the CG25 divergence was not only revealed by the phylogenetic tree but also confirmed by the clinical outcome data and the accessory genome patterns. Moreover, the transmission subclones circulated in two clinically important wards highlights the deficiency of infection control program using conventional methods. Without the assistance of whole-genome sequencing, the transmissions of high-risk clones could not be identified.\n\nLarge-Scale Genomic Epidemiology of Klebsiella pneumoniae Identified Clone Divergence with Hypervirulent Plus Antimicrobial-Resistant Characteristics Causing Within-Ward Strain Transmissions.", "token_count": 260, "char_count": 1102, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7192, "quality_score": 0.8596, "entities": { "genes": [ "KL64", "CG11", "CG25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:10.385855", "source": { "split": "train_shard_00001", "doc_id": 1985 }, "chunk_id": "train_shard_00001_1985_1", "global_id": 8470 }, { "text": "Pseudomonas aeruginosa ST308 clone has been reported to carry carbapenemase genes such as blaIMP and blaVIM but has been rarely associated with blaNDM-1. A total of 199 P. aeruginosa ST308 clinical and environmental isolates obtained between April 2019 and November 2020 from a tertiary-care hospital in Singapore were characterized using whole-genome sequencing. In addition, 71 blaNDM-1-positive ST308 whole-genome sequences from two other local tertiary-care hospitals in Singapore and 83 global blaNDM-1-negative ST308 whole-genome sequences in public databases were included to assess phylogenetic relationships and perform genome analyses. Phylogenetic analysis and divergent time estimation revealed that blaNDM-1-positive P. aeruginosa ST308 was introduced into Singapore in 2005 (95 % highest posterior density: 2001 to 2008). Core genome, resistome, and analyses of all local blaNDM-1-positive ST308 isolates showed chromosomal integration of multiple antibiotic resistance genes (ARGs) [aac(3)-Id, aac(6')-Il, aadA6, aadA11, dfrB5, msr(E), floR, sul2, and qnrVC1], which was absent in global blaNDM-1-negative ST308 sequences", "token_count": 499, "char_count": 1350, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6954, "quality_score": 0.8477, "entities": { "genes": [ "ST308" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:11.045049", "source": { "split": "train_shard_00001", "doc_id": 1986 }, "chunk_id": "train_shard_00001_1986_0", "global_id": 8471 }, { "text": "Most ARGs and virulence genes were conserved across isolates originating from the three different local hospitals. Close genetic relatedness of the blaNDM-1-positive ST308 clinical and environmental isolates suggests cocirculation between the hospital environment and human hosts with the hospital environment as a potential reservoir. Core genome single nucleotide polymorphism analyses revealed possible clonal transmission of blaNDM-1-positive ST308 isolates between the three hospitals over 7 years. Bloodstream isolates accounted for six of 95 (6.3%) clinical isolates. This study reports the introduction of a pathogenic blaNDM-1-positive P. aeruginosa ST308 more than a decade ago in Singapore and warrants surveillance for wider dissemination. IMPORTANCE P. aeruginosa is a Gram-negative opportunistic pathogen ubiquitously found in the environment and a major cause of nosocomial infections. While the P. aeruginosa ST308 clone has been known to bear blaIMP and blaVIM among global isolates, reports of blaNDM-1-positive P. aeruginosa ST308 are rare. The local blaNDM-1-positive P. aeruginosa ST308 isolates detected in this study appear to be unique to this region, with evidence of chromosomal acquisition of multiple ARGs compared to global blaNDM-1-negative P. aeruginosa ST308 isolates. Surveillance in Singapore and beyond for dissemination is essential to determine whether existing measures are sufficient to control the spread of this ST308 clone.\n\nDissemination of Pseudomonas aeruginosa blaNDM-1-Positive ST308 Clone in Singapore.", "token_count": 511, "char_count": 1719, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": { "genes": [ "ST308" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:11.696521", "source": { "split": "train_shard_00001", "doc_id": 1986 }, "chunk_id": "train_shard_00001_1986_1", "global_id": 8472 }, { "text": "The sensory quality of chocolate is widely determined by the qualitative and quantitative composition of volatile compounds resulting from microbial metabolism during fermentation, and Maillard reactions taking place during drying, roasting and conching. The influence of applying mixed starter cultures on the formation of flavour precursors, composition of volatile aroma compounds and sensory profile was investigated in cocoa inoculated with cultures encompassing a highly aromatic strain of Pichia kluyveri or a pectinolytic strain of Kluyveromyces marxianus, and compared to commercially fermented heap and tray cocoa. Although only minor differences in the concentration of free amino acids and reducing sugars was measured, identification and quantification by dynamic headspace gas chromatography–mass spectrometry (HS/GC–MS) revealed pronounced differences in the composition of volatiles in roasted cocoa liquors and finished chocolates. 19 of the 56 volatile compounds identified in the chocolates were found in significantly higher amounts in the tray fermented sample, whilst significantly higher amounts of 2-methoxyphenol was measured in the two inoculated chocolates. The P. kluyveri inoculated chocolate was characterized by a significantly higher concentration of phenylacetaldehyde and the K. marxianus inoculated chocolate by significantly higher amounts of benzyl alcohol, phenethyl alcohol, benzyl acetate and phenethyl acetate compared to a spontaneously fermented control. Sensory profiling described the heap and tray fermented chocolates as sweet with cocoa and caramel flavours, whilst the inoculated chocolates were characterized as fruity, acid and bitter with berry, yoghurt and balsamic flavours. The choice of fermentation technique had the greatest overall impact on the volatile aroma and sensory profile, but whilst the application of starter cultures did affect the volatile aroma profile, differences were too small to significantly change consumer perception of the chocolates as compared to a spontaneously fermented control.\n\nImpact of starter cultures and fermentation techniques on the volatile aroma and sensory profile of chocolate", "token_count": 495, "char_count": 2176, "word_count": 298, "semantic_coherence": 1, "information_density": 0.4866, "quality_score": 0.7433, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:12.349327", "source": { "split": "train_shard_00001", "doc_id": 1987 }, "chunk_id": "train_shard_00001_1987_0", "global_id": 8473 }, { "text": "Clostridioides difficile is one of the leading causes of antibiotic-associated diarrhea. In this study, we characterized 76C. difficile isolates, obtained from three Mediterranean mussel (Mytilus galloprovincialis) farms in Slovenia from November 2014 to October 2015 (sampling period 1) and from January to December 2021 (sampling period 2). The overall isolation rate of C. difficile from all the examined mussels was 59.8 %. A statistically significant trend of seasonal variation was observed, with a higher isolation rate in the colder months of the year (87.9 %; sea temperature ≤ 15 °C) compared with the warmer months (31.8 %; sea temperature > 15 °C). Whole-genome sequencing (WGS) revealed that the isolates belonged to 31 different sequence types (STs), which were associated with three clades (1, 4, and 5) and two cryptic clades (C-II and C-III). Five isolates, which belonged to ST11 (clade 5), harbored all the main toxin genes (A+B+CDT+) and chromosomal mutations conferring fluoroquinolone resistance. Core genome multilocus sequence typing (cgMLST) revealed four clusters of 2-3 isolates, three of which included isolates from different farms, suggesting that clonal C. difficile strains are circulating among the Slovenian mussel farms. The results highlight the presence of hypervirulent strains in mussels; therefore, at-risk population groups should be alerted to the risks associated with consuming shellfish.\n\nGenomic analysis reveals the presence of hypervirulent and fluoroquinolone-resistant Clostridioides difficile in farmed mussels (Mytilus galloprovincialis) in Slovenia.", "token_count": 469, "char_count": 1635, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8253, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:13.001359", "source": { "split": "train_shard_00001", "doc_id": 1988 }, "chunk_id": "train_shard_00001_1988_0", "global_id": 8474 }, { "text": "Salmonella is a major threat to both human and animal health. However, the diversity and antibiotic resistance of animal-derived Salmonella and their association with human infections remain largely unexplored. In this study, Salmonella strains were isolated, identified, and sequenced from dead embryos and cloacal swab samples obtained from 278 large-scale duck farms in 11 cities in Shandong Province. The results show that a total of 57 Salmonella strains were isolated, with the dominant sequence types (ST) being ST17 (15/57) and ST19 (9/57), while the dominant serotypes were S. Indiana (15/57) and S. Typhimurium (11/57). Furthermore, genomic analysis has revealed the presence of prevalent antibiotic resistance genes (ARGs), which are often associated with co-transfer mechanisms. Over 52.63% of the strains were observed to carry two or more ARGs, especially one Salmonella strain that carried twenty-eight distinct ARGs. Furthermore, core genome multilocus sequence typing analysis (cgMLST) indicated that the 57 Salmonella strains may have a close relationship, which could be clonally transmitted among different cities. The results demonstrated a close relationship between the Salmonella strains identified in diverse geographical regions, suggesting that these strains may have been widely disseminated through clonal transmission. The mutation analysis reveals significant mutations at parC (T57S), gyrA (S83F), parC (S80R), gyrA (D87N), and gyrA (S83Y). These findings emphasize the necessity for monitoring and controlling Salmonella infections in animals, as they may serve as a reservoir for ARGs with the potential to affect human health or even be the source of pathogens that infect humans.", "token_count": 520, "char_count": 1820, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6559, "quality_score": 0.8279, "entities": { "genes": [ "ST17", "ST19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:13.657789", "source": { "split": "train_shard_00001", "doc_id": 1989 }, "chunk_id": "train_shard_00001_1989_0", "global_id": 8475 }, { "text": "Antimicrobial Resistance Genes and Clonal Relationships of Duck-Derived Salmonella in Shandong Province, China in 2023.", "token_count": 44, "char_count": 126, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:14.014320", "source": { "split": "train_shard_00001", "doc_id": 1989 }, "chunk_id": "train_shard_00001_1989_1", "global_id": 8476 }, { "text": "Abstract

Background Campylobacter jejuni and C. coli are the most common causes of bacterial enteritis worldwide whereas symptomatic and asymptomatic infections are associated with stunting in children in low- and middle-income countries. Little is known about their sources and transmission pathways in low- and middle-income countries, and particularly for infants and young children. We assessed the genomic diversity of C. jejuni in Eastern Ethiopia to determine the attribution of infections in infants under 1 year of age to livestock (chickens, cattle, goats and sheep) and other humans (siblings, mothers). Results Among 287 C. jejuni isolates, 48 seven-gene sequence types (STs), including 11 previously unreported STs were identified. Within an ST, the core genome STs of multiple isolates differed in fewer than five alleles. Many of these isolates do not belong to the most common STs reported in high-resource settings, and of the six most common global STs, only ST50 was found in our study area. Isolates from the same infant sample were closely related, while those from consecutive infant samples often displayed different STs, suggesting rapid clearance and new infection. Four different attribution models using different genomic profiling methods, assumptions and estimation methods predicted that chickens are the primary reservoir for infant infections. Infections from chickens are transmitted with or without other humans (mothers, siblings) as intermediate sources Model predictions differed in terms of the relative importance of cattle vs. small ruminants as additional sources. Conclusions The transmission pathways of C. jejuni in our study area are highly complex and interdependent. While chickens are the most important reservoir of C. jejuni, ruminant reservoirs also contribute to the infections. The currently nonculturable species Candidatus C. infans is also highly prevalent in infants and is likely anthroponotic", "token_count": 498, "char_count": 2092, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "ST50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:14.661875", "source": { "split": "train_shard_00001", "doc_id": 1990 }, "chunk_id": "train_shard_00001_1990_0", "global_id": 8477 }, { "text": "Efforts to reduce the colonization of infants with Campylobacter and ultimately stunting in low-resource settings are best aimed at protecting proximate sources such as caretakers’ hands, food and indoor soil through tight integration of the currently siloed domains of nutrition, food safety and water, sanitation and hygiene.

\n\nTransmission pathways of Campylobacter jejuni between humans and livestock in rural Ethiopia are highly complex and interdependent", "token_count": 110, "char_count": 480, "word_count": 64, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:15.045148", "source": { "split": "train_shard_00001", "doc_id": 1990 }, "chunk_id": "train_shard_00001_1990_1", "global_id": 8478 }, { "text": "The genus Ligilactobacillus encompasses species adapted to vertebrate hosts and fermented food. Their genomes encode adaptations to the host lifestyle. Reports of gut microbiota from chicken and turkey gastrointestinal tract have shown a high persistence of Ligilactobacillus aviarius along the digestive system compared to other species found in the same host. However, its adaptations to poultry as a host has not yet been described. In this work, the pan-genome of Ligilactobacillus aviarius was explored to describe the functional adaptability to the gastrointestinal environment. The core genome is composed of 1179 gene clusters that are present at least in one copy that codifies to structural, ribosomal and biogenesis proteins. The rest of the identified regions were classified into three different functional clusters of orthologous groups (clusters) that codify carbohydrate metabolism, envelope biogenesis, viral defence mechanisms, and mobilome inclusions. The pan-genome of Ligilactobacillus aviarius is a closed pan-genome, frequently found in poultry and highly prevalent across chicken faecal samples. The genome of L. aviarius codifies different clusters of glycoside hydrolases and glycosyltransferases that mediate interactions with the host cells. Accessory features, such as antiviral mechanisms and prophage inclusions, variate amongst strains from different GIT sections. This information provides hints about the interaction of this species with viral particles and other bacterial species. This work highlights functional adaptability traits present in L. aviarius that make it a dominant key member of the poultry gut microbiota and enlightens the convergent ecological relation of this species to the poultry gut environment.\n\nHost specific adaptations of Ligilactobacillus aviarius to poultry.", "token_count": 478, "char_count": 1872, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6024, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:15.689792", "source": { "split": "train_shard_00001", "doc_id": 1991 }, "chunk_id": "train_shard_00001_1991_0", "global_id": 8479 }, { "text": "Hypervirulent Klebsiella pneumoniae (hvKP) can cause severe infections even in healthy individuals. Currently, no data are available on the frequency of hvKP-induced bloodstream infections (BSI) in Hungary. Our investigation revealed that of the 157 K. pneumoniae isolated from BSI in 2020-2022 at a university hospital in Hungary, three (2%) carried the hypervirulence-associated rmpA and iutAiucABCD genes. The complete genomes of these three hvKP isolates were sequenced. They were unrelated and belonged to ST5, ST86, and ST6771, a single-locus variant of ST893, i.e., to internationally known hvKP clones. In the K. pneumoniae ST86 and ST6771 isolates, the rmpA/A2, aerobactin, and salmochelin siderophore genes were located on virulence plasmids highly similar to those of K. pneumoniae ST23 and ST86 isolated in Asia, while the K. pneumoniae ST5 isolate harboured rmpA, iroBCDN, and yersiniabactin locus on a chromosomally integrated ICEKp1 element. Comparison of the core genome MLST of the three Hungarian hvKP isolates to genomes belonging to the same ST/CC deposited in the Bigsdb database of the Pasteur Institute revealed that, although no direct epidemiological link could be established, KP48326 K. pneumoniae ST86, isolated in Pécs, clustered with a Greek isolate (ID-48733). The emergence of K", "token_count": 487, "char_count": 1404, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [ "ST23", "ST5", "ST893", "KP48326", "ST86", "ST6771" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:16.340137", "source": { "split": "train_shard_00001", "doc_id": 1992 }, "chunk_id": "train_shard_00001_1992_0", "global_id": 8480 }, { "text": "pneumoniae belonging to known hypervirulent clones in Hungary, albeit sporadic, is alarming and underscores the importance of continued whole-genome-based epidemiological surveillance.IMPORTANCEThis study represents the first investigation of the prevalence of hypervirulent K. pneumoniae (hvKP) in bloodstream infections in Hungary, conducted at the University Hospital of Pécs. Our findings emphasize the need to accurately identify hvKP strains, integrating both phenotypic and genotypic screening. Whole genome sequencing revealed genetic diversity among the Hungarian hvKP isolates, confirming the emergence of globally disseminating hvKP clones-ST86, CC893, and ST5-in Hungary. The localization of hypervirulence-related genes on mobile genetic elements, e.g., on virulence plasmids or on ICEKp1 similar to those found in hvKP isolates from different continents, underscores the significant role of horizontal gene transfer in the spread of hvKP. Overall, the study enhances our understanding of hvKP epidemiology and underscores the importance of continued molecular surveillance and control measures to mitigate the threat of hvKP infections in Hungary.\n\nHypervirulent <i>Klebsiella pneumoniae</i> causing bloodstream infections in Hungary.", "token_count": 343, "char_count": 1278, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [ "ST5", "ST86", "CC893" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:16.909445", "source": { "split": "train_shard_00001", "doc_id": 1992 }, "chunk_id": "train_shard_00001_1992_1", "global_id": 8481 }, { "text": "

ABSTRACT

We sequenced the genome of a global collection (40 isolates) of the fungus Pyrenophora tritici-repentis (Ptr), a major foliar pathogen of wheat and model for the evolution of necrotrophic pathogens. Ptr exhibited an open-pangenome, with 43% of genes in the core set and 57% defined as accessory (present in only a subset of isolates), of which 56% were singleton genes (present in only one isolate). A clear distinction between pathogenic and non-pathogenic genomes was observed in size, gene content, and phylogenetic relatedness. Chromosomal rearrangements and structural organization, specifically around the effector coding genes, were explored further using the annotated genomes of two isolates sequenced by PacBio RS II and Illumina HiSeq. The Ptr genome exhibited major chromosomal rearrangements, including chromosomal fusion, translocation, and segment duplications. An intraspecies translocation of ToxA , the necrosis-inducing effector-coding gene, was facilitated within Ptr via a 143 kb ‘ Starship’ transposon (dubbed ‘Horizon’). Additionally, ToxB , the gene encoding the chlorosis-inducing effector, was clustered as three copies on a 294 kb transposable element in a ToxB-producing isolate. ToxB and its carrying transposon were missing from the ToxB non-coding reference isolate, but the homolog toxb and the transposon were both present in another non-coding isolate. The Ptr genome also appears to exhibit a ‘one-compartment’ organization, but may still possess a ‘two-speed genome’ that is facilitated by copy-number variation as reported in other fungal pathosystems.

IMPORTANCE

Ptr is one of the most destructive wheat pathogens worldwide. Its genome is a mosaic of present and absent effectors, and serves as a model for examining the evolutionary processes behind the acquisition of virulence in necrotrophs and disease emergence", "token_count": 520, "char_count": 1881, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:17.564588", "source": { "split": "train_shard_00001", "doc_id": 1993 }, "chunk_id": "train_shard_00001_1993_0", "global_id": 8482 }, { "text": "In this work, we took advantage of a diverse collection of pathogenic Ptr isolates with different global origins and applied short- and long-read sequencing technologies to dissect the Ptr genome. This study provides comprehensive insights into the Ptr genome and highlights its structural organization as an open pangenome with ‘one-compartment’. In addition, we identified the potential involvement of transposable elements in genome expansion and the movement of virulence factors. The ability of effector-coding genes to shuffle across chromosomes on large transposons was illustrated by the intraspecies translocation of ToxA and the multi-copy ToxB . In terms of gene contents, the Ptr genome exhibits a large percentage of orphan genes, particularly in non-pathogenic or weakly-virulent isolates.\n\nDissecting thePyrenophora tritici-repentis(tan spot of wheat) pangenome", "token_count": 211, "char_count": 883, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7131, "quality_score": 0.8566, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:18.027421", "source": { "split": "train_shard_00001", "doc_id": 1993 }, "chunk_id": "train_shard_00001_1993_1", "global_id": 8483 }, { "text": "Each case of melioidosis results from a single event when a human is infected by the environmental bacterium Burkholderia pseudomallei. Darwin, in tropical northern Australia, has the highest incidences of melioidosis globally, and the Darwin Prospective Melioidosis Study (DPMS) commenced in 1989, documenting all culture-confirmed melioidosis cases. From 2000 to 2019, we sampled DPMS patients' environments for B. pseudomallei when a specific location was considered to be where infection occurred, with the aim of using genomic epidemiology to understand B. pseudomallei transmission and infecting scenarios. Environmental sampling was performed at 98 DPMS patient sites, where we collected 975 environmental samples (742 soil and 233 water). Genotyping matched the clinical and epidemiologically linked environmental B. pseudomallei for 19 patients (19%), with the environmental isolates cultured from soil (n = 11) and water (n = 8) sources. B. pseudomallei isolates from patients and their local environments that matched on genotyping were subjected to whole-genome sequencing (WGS). Of the 19 patients with a clinical-environmental genotype match, 17 pairs clustered on a Darwin core genome single-nucleotide polymorphism (SNP) phylogeny, later confirmed by single sequence typing (ST) phylogenies and pairwise comparative genomics. When related back to patient clinical scenarios, the matched clinical and environmental B. pseudomallei pairs informed likely modes of infection: percutaneous inoculation, inhalation, and ingestion. Targeted environmental sampling for B. pseudomallei can inform infecting scenarios for melioidosis and dangerous occupational and recreational activities and identify hot spots of B. pseudomallei presence. However, WGS and careful genomics are required to avoid overcalling the relatedness between clinical and environmental isolates of B. pseudomallei.", "token_count": 489, "char_count": 1908, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:18.673769", "source": { "split": "train_shard_00001", "doc_id": 1994 }, "chunk_id": "train_shard_00001_1994_0", "global_id": 8484 }, { "text": "Genomic Epidemiology Links Burkholderia pseudomallei from Individual Human Cases to B. pseudomallei from Targeted Environmental Sampling in Northern Australia.", "token_count": 38, "char_count": 159, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:19.033606", "source": { "split": "train_shard_00001", "doc_id": 1994 }, "chunk_id": "train_shard_00001_1994_1", "global_id": 8485 }, { "text": "After introducing pneumococcal conjugate vaccines (PCVs), serotype replacement occurred in Streptococcus pneumoniae. Predicting which pneumococcal strains will become common in carriage after vaccination can enhance vaccine design, public health interventions, and understanding of pneumococcal evolution. Invasive pneumococcal isolates were collected during 1998-2018 by the Active Bacterial Core surveillance (ABCs). Carriage data from Massachusetts (MA) and Southwest United States were used to calculate weights. Using pre-vaccine data, serotype-specific inverse-invasiveness weights were defined as the ratio of the proportion of the serotype in carriage to the proportion in invasive data. Genomic data were processed under bioinformatic pipelines to define genetically similar sequence clusters (i.e., strains), and accessory genes (COGs) present in 5-95% of isolates. Weights were applied to adjust observed strain proportions and COG frequencies. The negative frequency-dependent selection (NFDS) model predicted strain proportions by calculating the post-vaccine strain composition in the weighted invasive disease population that would best match pre-vaccine COG frequencies. Inverse-invasiveness weighting increased the correlation of COG frequencies between invasive and carriage data in linear or logit scale for pre-vaccine, post-PCV7, and post-PCV13; and between different epochs in the invasive data. Weighting the invasive data significantly improved the NFDS model's accuracy in predicting strain proportions in the carriage population in the post-PCV13 epoch, with the adjusted R2 increasing from 0.254 before weighting to 0.545 after weighting. The weighting system adjusted invasive disease data to better represent the pneumococcal carriage population, allowing the NFDS mechanism to predict strain proportions in carriage in the post-PCV13 epoch", "token_count": 459, "char_count": 1894, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5918, "quality_score": 0.7959, "entities": { "genes": [ "PCV13", "PCV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:19.675007", "source": { "split": "train_shard_00001", "doc_id": 1995 }, "chunk_id": "train_shard_00001_1995_0", "global_id": 8486 }, { "text": "Our methods enrich the value of genomic sequences from invasive disease surveillance.IMPORTANCEStreptococcus pneumoniae, a common colonizer in the human nasopharynx, can cause invasive diseases including pneumonia, bacteremia, and meningitis mostly in children under 5 years or older adults. The PCV7 was introduced in 2000 in the United States within the pediatric population to prevent disease and reduce deaths, followed by PCV13 in 2010, PCV15 in 2022, and PCV20 in 2023. After the removal of vaccine serotypes, the prevalence of carriage remained stable as the vacated pediatric ecological niche was filled with certain non-vaccine serotypes. Predicting which pneumococcal clones, and which serotypes, will be most successful in colonization after vaccination can enhance vaccine design and public health interventions, while also improving our understanding of pneumococcal evolution. While carriage data, which are collected from the pneumococcal population that is competing to colonize and transmit, are most directly relevant to evolutionary studies, invasive disease data are often more plentiful. Previously, evolutionary models based on negative frequency-dependent selection (NFDS) on the accessory genome were shown to predict which non-vaccine strains and serotypes were most successful in colonization following the introduction of PCV7. Here, we show that an inverse-invasiveness weighting system applied to invasive disease surveillance data allows the NFDS model to predict strain proportions in the projected carriage population in the post-PCV13/pre-PCV15 and pre-PCV20 epoch. The significance of our research lies in using a sample of invasive disease surveillance data to extend the use of NFDS as an evolutionary mechanism to predict post-PCV13 population dynamics. This has shown that we can correct for biased sampling that arises from differences in virulence and can enrich the value of genomic data from disease surveillance and advance our understanding of how NFDS impacts carriage population dynamics after both PCV7 and PCV13 vaccination.\n\nPrediction of post-PCV13 pneumococcal evolution using invasive disease data enhanced by inverse-invasiveness weighting.", "token_count": 520, "char_count": 2200, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5649, "quality_score": 0.7825, "entities": { "genes": [ "PCV20", "PCV13", "PCV15", "PCV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:20.332513", "source": { "split": "train_shard_00001", "doc_id": 1995 }, "chunk_id": "train_shard_00001_1995_1", "global_id": 8487 }, { "text": "Flocculating yeasts are highly useful in fermentation processes because these cells can be separated easily from the fermentation mash. However, native yeasts are usually non-flocculating, including Kluyveromyces marxianus, which exhibits a potent high-temperature ethanol fermentation ability. We describe here the construction of flocculent K. marxianus strains via the introduction of the FLO1, FLO5, FLO9, and FLO10 genes from Saccharomyces cerevisiae. The S. cerevisiae FLO genes were overexpressed by upstream insertion of the constitutive TDH3 promoter, resulting in flocculent S. cerevisiae strains. These TDH3p-FLO sequences were then amplified by PCR and introduced directly into a K. marxianus strain. These K. marxianus strains showed a flocculation phenotype, indicating that the introduced S. cerevisiae TDH3 promoter and all FLO genes were functional in this strain. Moreover, a flocculating K. marxianus strain showed the same ethanol production profile as that of its wild-type parent. The K. marxianus flocculating strains we generated should be useful in the future development of cost-effective fed-batch and continuous fermentation systems at high temperatures.\n\nConstruction of flocculent Kluyveromyces marxianus strains suitable for high-temperature ethanol fermentation.", "token_count": 343, "char_count": 1294, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "TDH3", "FLO5", "FLO9", "FLO1", "FLO10" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:20.935819", "source": { "split": "train_shard_00001", "doc_id": 1996 }, "chunk_id": "train_shard_00001_1996_0", "global_id": 8488 }, { "text": "Secondary metabolites (SMs) produced by bacteria from unusual environments can contribute to mitigate some of the health and environmental challenges we face. The knowledge of the diversity and applicability of SMs produced by environmental Gram-negatives is lagging behind that of Gram-positives. Examples include some members of genus Pedobacter that produce nonribosomal peptides active against bacteria listed by the WHO as a priority for R&D of new drugs. Herein, a total of 233 biosynthetic gene clusters (BGCs) were identified in the Pedobacter´s pangenome, which encode the biosynthesis of RiPPs (27%), terpenes (22%), hybrid SMs (17%), PKs (12%), NRPs (9%) and siderophores (6%). Most of BGCs did not have significant hits with MIBiG database, which highlights the novelty of their products. From all species, P. cryoconitis and P. lusitanus encode the highest number and diversity of BGCs. Giving their applicability and ecological roles, the BGCs for the production of siderophores and terpenoids were analysed in detail. It was concluded that some species can be a source of squalene and novel siderophores and carotenoids, which deserve further characterization. This study highlights the genus Pedobacter as a prolific source of SMs, probably with a wide range of biological activities and applications hitherto unknown.\n\nThe pangenome of environmental Gram-negative bacteria and its hidden, but promising, biotechnological potential", "token_count": 366, "char_count": 1447, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:21.530245", "source": { "split": "train_shard_00001", "doc_id": 1997 }, "chunk_id": "train_shard_00001_1997_0", "global_id": 8489 }, { "text": "Escherichia coli is present in multiple hosts and environmental compartments as a normal inhabitant, temporary or persistent colonizer, and as a pathogen. Transmission of E. coli between hosts and with the environment is considered to occur more often in areas with poor sanitation. We performed whole-genome comparative analyses on 60 E. coli isolates from soils and fecal sources (cattle, chickens, and humans) in households in rural Bangladesh. Isolates from household soils were in multiple branches of the reconstructed phylogeny, intermixed with isolates from fecal sources. Pairwise differences between all strain pairs were large (minimum, 189 single nucleotide polymorphisms [SNPs]), suggesting high diversity and heterogeneous origins of the isolates. The presence of multiple virulence and antibiotic resistance genes is indicative of the risk that E. coli from soil and feces represent for the transmission of variants that pose potential harm to people. Analysis of the accessory genomes of the Bangladeshi E. coli relative to E. coli genomes available in NCBI identified a common pool of accessory genes shared among E. coli isolates in this geographic area. Together, these findings indicate that in rural Bangladesh, a high level of E. coli in soil is likely driven by contributions from multiple and diverse E. coli sources (human and animal) that share an accessory gene pool relatively unique to previously published E. coli genomes. Thus, interventions to reduce environmental pathogen or antimicrobial resistance transmission should adopt integrated One Health approaches that consider heterogeneous origins and high diversity to improve effectiveness and reduce prevalence and transmission.IMPORTANCEEscherichia coli is reported in high levels in household soil in low-income settings. When E. coli reaches a soil environment, different mechanisms, including survival, clonal expansion, and genetic exchange, have the potential to either maintain or generate E. coli variants with capabilities of causing harm to people", "token_count": 523, "char_count": 2139, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5657, "quality_score": 0.7828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:22.244501", "source": { "split": "train_shard_00001", "doc_id": 1998 }, "chunk_id": "train_shard_00001_1998_0", "global_id": 8490 }, { "text": "In this study, we used whole-genome sequencing to identify that E. coli isolates collected from rural Bangladeshi household soils, including pathogenic and antibiotic-resistant variants, are diverse and likely originated from multiple diverse sources. In addition, we observed specialization of the accessory genome of this Bangladeshi E. coli compared to E. coli genomes available in current sequence databases. Thus, to address the high level of pathogenic and antibiotic-resistant E. coli transmission in low-income settings, interventions should focus on addressing the heterogeneous origins and high diversity.\n\nHigh Genomic Diversity and Heterogenous Origins of Pathogenic and Antibiotic-Resistant Escherichia coli in Household Settings Represent a Challenge to Reducing Transmission in Low-Income Settings.", "token_count": 216, "char_count": 841, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6389, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:22.711245", "source": { "split": "train_shard_00001", "doc_id": 1998 }, "chunk_id": "train_shard_00001_1998_1", "global_id": 8491 }, { "text": "Vibrio vulnificus, an opportunistic pathogen, is the causative agent of a life-threatening septicemia and a rising problem for aquaculture worldwide. The genetic factors that differentiate its clinical and environmental strains remain enigmatic. Furthermore, clinical strains have emerged from every clade of V. vulnificus In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species from an evolutionary and ecological point of view. Genome comparisons and bioinformatic analyses of 113 V. vulnificus isolates indicate that the population of V. vulnificus is made up of four different clusters. We found evidence that recombination and gene flow between the two largest clusters (cluster 1 [C1] and C2) have drastically decreased to the point where they are diverging independently. Pangenome and phenotypic analyses showed two markedly different lifestyles for these two clusters, indicating commensal (C2) and bloomer (C1) ecotypes, with differences in carbohydrate utilization, defense systems, and chemotaxis, among other characteristics. Nonetheless, we identified frequent intra- and interspecies exchange of mobile genetic elements (e.g., antibiotic resistance plasmids, novel \"chromids,\" or two different and concurrent type VI secretion systems) that provide high levels of genetic diversity in the population. Surprisingly, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together. We propose an evolutionary model of V. vulnificus that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections and emergence.IMPORTANCEVibrio vulnificus is an emergent marine pathogen and is the cause of a deadly septicemia. However, the genetic factors that differentiate its clinical and environmental strains and its several biotypes remain mostly enigmatic", "token_count": 507, "char_count": 2055, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:23.373262", "source": { "split": "train_shard_00001", "doc_id": 1999 }, "chunk_id": "train_shard_00001_1999_0", "global_id": 8492 }, { "text": "In this work, we investigated the underlying genomic properties and population dynamics of the V. vulnificus species to elucidate the traits that make these strains emerge as a human pathogen. The acquisition of different ecological determinants could have allowed the development of highly divergent clusters with different lifestyles within the same environment. However, we identified strains from both clusters in the mucosa of aquaculture species, indicating that manmade niches are bringing strains from the two clusters together, posing a potential risk of recombination and of emergence of novel variants. We propose a new evolutionary model that provides a perspective that could be broadly applicable to other pathogenic vibrios and facultative bacterial pathogens to pursue strategies to prevent their infections.\n\nEvolutionary Model of Cluster Divergence of the Emergent Marine Pathogen Vibrio vulnificus: From Genotype to Ecotype.", "token_count": 212, "char_count": 957, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6963, "quality_score": 0.8481, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:23.830117", "source": { "split": "train_shard_00001", "doc_id": 1999 }, "chunk_id": "train_shard_00001_1999_1", "global_id": 8493 }, { "text": "Bacteria of the Vibrio genus are the most predominant infectious agents threatening marine wildlife and aquaculture. Due to the large genetic diversity of these pathogens, the molecular determinants of Vibrio virulence are only poorly understood. Furthermore, studies tend to ignore co-evolutionary interactions between different host populations and their locally encountered Vibrio communities. Here, we explore the molecular targets of such co-evolutionary interactions by analyzing the genomes of nine Vibrio strains from the Splendidus-clade showing opposite virulence patterns towards two populations of Pacific oysters introduced into European Wadden Sea. By contrasting Vibrio phylogeny to their host specific virulence patterns, we could identify two core genome genes (OG1907 and OG 3159) that determine the genotype by genotype (G × G) interactions between oyster larvae and their sympatric Vibrio communities. Both genes show positive selection between locations targeting only few amino acid positions. Deletion of each gene led to a loss of the host specific virulence patterns while complementation with OG3159 alleles from both locations could recreate the wild type phenotypes matching the origin of the allele. This indicates that both genes can act as a genetic switch for Vibrio-oyster coevolution demonstrating that local adaptation in distinct Vibrio lineages can rely on only few genes independent of larger pathogenicity islands or plasmids.\n\nMolecular Targets for Coevolutionary Interactions Between Pacific Oyster Larvae and Their Sympatric Vibrios.", "token_count": 417, "char_count": 1645, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6306, "quality_score": 0.8153, "entities": { "genes": [ "OG1907", "OG3159" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:24.459317", "source": { "split": "train_shard_00001", "doc_id": 2000 }, "chunk_id": "train_shard_00001_2000_0", "global_id": 8494 }, { "text": "Ethanol production at high temperatures has garnered much interest in recent years and a key factor is the availability of thermotolerant yeasts. During an investigation on the diversity of thermotolerant yeasts from different habitats, a novel yeast species from the spent wash of a distillery unit associated with a sugar factory was isolated. Phylogenetic analysis of D1/D2 large subunit and ITS rRNA genes placed this species in the ascomycetous genus Wickerhamiella. The novel species can be distinguished from the closely related species Wickerhamiella pararugosa using these rRNA gene regions. The cells of the new species are ovoid to ellipsoid with a diameter of 3.5-6.0×2.4-3.10 µm, while W. pararugosa cells are cylindrical with a cell diameter of 1.5-3.0×6-23 µm. This novel species represents, together with Wickerhamiella cacticola, one of the two most thermotolerant yeast species in the genus Wickerhamiella, able to grow at 42 °C. Wickerhamiella shivajii sp. nov. is proposed during this study.\n\nWickerhamiella shivajii sp. nov., a thermotolerant yeast isolated from distillery effluent.", "token_count": 352, "char_count": 1153, "word_count": 164, "semantic_coherence": 1, "information_density": 0.628, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:25.389111", "source": { "split": "train_shard_00001", "doc_id": 2001 }, "chunk_id": "train_shard_00001_2001_0", "global_id": 8495 }, { "text": "The human gut microbiome composition has been linked to Parkinson's disease (PD). However, knowledge of the gut microbiota on the genome level is still limited. Here we performed deep metagenomic sequencing and binning to build metagenome-assembled genomes (MAGs) from 136 human fecal microbiomes (68 PD samples and 68 control samples). We constructed 952 non-redundant high-quality MAGs and compared them between PD and control groups. Among these MAGs, there were 22 different genomes of Collinsella and Prevotella, indicating high variability of those genera in the human gut environment. Microdiversity analysis indicated that Ruminococcus bromii was statistically significantly (p < 0.002) more diverse on the strain level in the control samples compared to the PD samples. In addition, by clustering all genes and performing presence-absence analysis between groups, we identified several control-specific (p < 0.05) related genes, such as speF and Fe-S oxidoreductase. We also report detailed annotation of MAGs, including Clusters of Orthologous Genes (COG), Cas operon type, antiviral gene, prophage, and secondary metabolites biosynthetic gene clusters, which can be useful for providing a reference for future studies.\n\nMetagenome-assembled microbial genomes from Parkinson's disease fecal samples.", "token_count": 341, "char_count": 1309, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7243, "quality_score": 0.8622, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:25.956324", "source": { "split": "train_shard_00001", "doc_id": 2002 }, "chunk_id": "train_shard_00001_2002_0", "global_id": 8496 }, { "text": "Ceftazidime-avibactam (CZA) is a recently approved combination synthetic β-lactamase inhibitor used in human clinical medicine. Cases of CZA resistance in humans have already been reported, but limited research has investigated CZA resistance in pets. This study explored the prevalence and transmission of CZA-resistant Escherichia coli (CZAREC) among pets, their owners, veterinarians, and the environment in animal hospitals. A total of 5,419 clinical samples were collected from dogs and cats, along with samples from the environment (n = 5,843), veterinarians (n = 557), and pet owners (n = 368) in animal hospitals. From these samples, 760 Escherichia coli (E. coli) isolates were obtained, out of which 60 were identified as CZAREC. These included 34 isolates from the environment (9.14 %, n = 372), three from veterinarians (8.11 %, n = 37), and 23 from animals (6.82 %, n = 337). No CZAREC isolates were found in pet owners. The predominant sequence types of CZARECs were ST156 (n = 20), ST410 (n = 19) and ST101 (n = 7). Bayesian analysis revealed six clusters comprising 47 isolates from the hospital environment, pets, and veterinaries, displaying genetic relatedness of less than 100 core genome single nucleotide polymorphisms (cgSNPs) between any two isolates in each cluster. Some CZAREC isolates with high genetic similarity persisted in the same animal hospital for four to six months. Moreover, discriminant analysis of principal components indicated that most isolates from different hosts shared a genetic source in the human/dog/cat merged cluster. Overall, evidence of CZARECs transmission was found among pets, the environment, and veterinarians in animal hospitals", "token_count": 496, "char_count": 1710, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [ "ST410", "ST156", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:26.611662", "source": { "split": "train_shard_00001", "doc_id": 2003 }, "chunk_id": "train_shard_00001_2003_0", "global_id": 8497 }, { "text": "The findings emphasize the importance of monitoring CZARECs in the veterinary clinical setting to ensure the health of both pets and humans.\n\nTransmission of ceftazidime-avibactam-resistant <i>Escherichia coli</i> among pets, veterinarians and animal hospital environment.", "token_count": 79, "char_count": 284, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:26.978350", "source": { "split": "train_shard_00001", "doc_id": 2003 }, "chunk_id": "train_shard_00001_2003_1", "global_id": 8498 }, { "text": "Growth of selected microorganisms of industrial interest (Saccharomyces cerevisiae, Kluyveromyces marxianus and kefir) by solid state fermentation (SSF) of various food industry waste mixtures was studied. The fermented products were analysed for protein, and nutrient minerals content, as well as for aroma volatile compounds by GC/MS. The substrate fermented by K. marxianus contained the highest sum of fat and protein concentration (59.2% w/w dm) and therefore it could be considered for utilisation of its fat content and for livestock feed enrichment. Regarding volatiles, the formation of high amounts of ε-pinene was observed only in the SSF product of kefir at a yield estimated to be 4 kg/tn of SSF product. A preliminary design of a biorefinery-type process flow sheet and its economic analysis, indicated potential production of products (enriched livestock feed, fat and ε-pinene) of significant added value.\n\nSolid state fermentation of food waste mixtures for single cell protein, aroma volatiles and fat production.", "token_count": 263, "char_count": 1031, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6688, "quality_score": 0.8344, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:27.533990", "source": { "split": "train_shard_00001", "doc_id": 2004 }, "chunk_id": "train_shard_00001_2004_0", "global_id": 8499 }, { "text": "The function of mitochondrial Adh3 in the thermotolerant yeast Kluyveromyces marxianus was investigated. An ADH3-disrupted mutant exhibited growth retardation on non-fermentable carbon sources, except for ethanol, and this was suppressed by supplementation with antioxidants. Detailed analysis of the phenotype revealed that the mutant showed an increase in the activity of NADH dehydrogenase, sensitivity to H(2)O(2), and accumulation of reactive oxygen species (ROS), and that these carbon sources increased the activity of succinate dehydrogenase. The increase in both activities may reflect enhanced expression of both dehydrogenases by elevation of their substrate levels. The ROS level became low when antioxidants were added. These findings suggest that the ADH3 mutation and such carbon sources cause an elevation of the substrate level of the respiratory chain and eventually of the ROS level via increased expression of primary dehydrogenases, which in turn causes cell growth retardation. Adh3 might thus play a crucial role in the control of the NADH/NAD(+) balance in mitochondria.\n\nThe crucial role of alcohol dehydrogenase Adh3 in Kluyveromyces marxianus mitochondrial metabolism.", "token_count": 302, "char_count": 1195, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6095, "quality_score": 0.8047, "entities": { "genes": [ "ADH3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:28.793219", "source": { "split": "train_shard_00001", "doc_id": 2005 }, "chunk_id": "train_shard_00001_2005_0", "global_id": 8500 }, { "text": "In vitro interactions of broad-spectrum azole isavuconazole with flavonoid isoquercitrin were evaluated by a broth microdilution checkerboard technique based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) reference methodology for antifungal susceptibility testing against 60 Candida strains belonging to the species Candida albicans (n = 10), Candida glabrata (n = 30), Candida kefyr (n = 6), Candida krusei (n = 5), Candida parapsilosis (n = 4), and Candida tropicalis (n = 5). The results were analyzed with the fractional inhibitory concentration index and by response surface analysis based on the Bliss model. Synergy was found for all C. glabrata strains, when the results were interpreted by the fractional inhibitory concentration index, and for 60% of the strains when response surface analysis was used. Interaction for all other species was indifferent for all strains tested, whatever interpretation model used. Importantly, antagonistic interaction was never observed.\n\nSynergistic In Vitro Interaction of Isavuconazole and Isoquercitrin against Candida glabrata.", "token_count": 388, "char_count": 1210, "word_count": 156, "semantic_coherence": 1, "information_density": 0.5705, "quality_score": 0.7853, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:29.405136", "source": { "split": "train_shard_00001", "doc_id": 2006 }, "chunk_id": "train_shard_00001_2006_0", "global_id": 8501 }, { "text": "

Background

Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species characterized by specific repeat-rich genome compartments with exceptionally high sequence variability. Dynamic genome structure may enable fast adaptation to host genetics. The wheat pathogen Zymoseptoria tritici with its highly variable genome, has emerged as a model organism to study genome evolution of plant pathogens. Here, we compared genomes of Z. tritici isolates and of sister species infecting wild grasses to address the evolution of genome composition and structure.

Results

Using long-read technology, we sequenced and assembled genomes of Z. ardabiliae, Z. brevis, Z. pseudotritici and Z. passerinii, together with two isolates of Z. tritici. We report a high extent of genome collinearity among Zymoseptoria species and high conservation of genomic, transcriptomic and epigenomic signatures of compartmentalization. We identify high gene content variability both within and between species. In addition, such variability is mainly limited to the accessory chromosomes and accessory compartments. Despite strong host specificity and non-overlapping host-range between species, predicted effectors are mainly shared among Zymoseptoria species, yet exhibiting a high level of presence-absence polymorphism within Z. tritici. Using in planta transcriptomic data from Z. tritici, we suggest different roles for the shared orthologs and for the accessory genes during infection of their hosts.

Conclusion

Despite previous reports of high genomic plasticity in Z. tritici, we describe here a high level of conservation in genomic, epigenomic and transcriptomic composition and structure across the genus Zymoseptoria. The compartmentalized genome allows the maintenance of a functional core genome co-occurring with a highly variable accessory genome.\n\nGenome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria.", "token_count": 495, "char_count": 2097, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5668, "quality_score": 0.7834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:30.053358", "source": { "split": "train_shard_00001", "doc_id": 2007 }, "chunk_id": "train_shard_00001_2007_0", "global_id": 8502 }, { "text": "The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, consisting of core and accessory genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for Pyrenophora tritici-repentis (Ptr), the causal agent of tan (or yellow) spot disease in wheat. In this study, 15 new Ptr genomes were sequenced, assembled and annotated, including isolates from three races not previously sequenced. Together with 11 previously published Ptr genomes, a pangenome for 26 Ptr isolates from Australia, Europe, North Africa and America, representing nearly all known races, revealed a conserved core-gene content of 57 % and presents a new Ptr resource for searching natural homologues (orthologues not acquired by horizontal transfer from another species) using remote protein structural homology. Here, we identify for the first time a non-synonymous mutation in the Ptr necrotrophic effector gene ToxB, multiple copies of the inactive toxb within an isolate, a distant natural Pyrenophora homologue of a known Parastagonopora nodorum necrotrophic effector (SnTox3), and clear genomic break points for the ToxA effector horizontal transfer region. This comprehensive genomic analysis of Ptr races includes nine isolates sequenced via long read technologies. Accordingly, these resources provide a more complete representation of the species, and serve as a resource to monitor variations potentially involved in pathogenicity.\n\nA global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology.", "token_count": 438, "char_count": 1756, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6449, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:30.688040", "source": { "split": "train_shard_00001", "doc_id": 2008 }, "chunk_id": "train_shard_00001_2008_0", "global_id": 8503 }, { "text": "Abstract

The keeping of livestock has been posited as a risk factor for the emergence of zoonoses and the spread of antimicrobial resistance. However, quantitative evidence regarding the major sources of pathogenic and drug-resistant bacteria and transmission routes between hosts remains lacking. In the largest epidemiological study of this nature to date, we sampled Escherichia coli from humans, livestock, food, wildlife and the environment of 99 households across Nairobi, Kenya to gain a deeper understanding of sharing of bacteria among hosts and potential reservoirs. By analysing whole genome sequencing data from 1,338 E. coli isolates, we reconstruct sharing patterns for the sampled E. coli and its antimicrobial resistance determinants. We find that the diversity and sharing patterns of E. coli is heavily structured by household, which is the primary epidemiological interface for bacterial strain sharing. Strain sharing within households was strongly shaped by host type. We also find evidence for inter-household and inter-host sharing, and importantly, between humans and animals, although this occurs much less frequently. We find similar strain sharing patterns for the E. coli accessory genome, suggesting that it is shaped by recent evolutionary history and is strongly associated with the core genome. Resistome similarity, however, were quite differently distributed across host and household, consistent with their being driven by shared exposure to antimicrobials. Our results indicate that there is potential for the exchange of bacteria between humans, livestock and wildlife in the same household in a tropical urban setting, with wider mixing occurring over a period of months or years, but this does not drive the distribution of antimicrobial resistance.

\n\nLandscape genomics of Escherichia coli in livestock-keeping households across a rapidly developing urban city", "token_count": 451, "char_count": 2007, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:31.326340", "source": { "split": "train_shard_00001", "doc_id": 2009 }, "chunk_id": "train_shard_00001_2009_0", "global_id": 8504 }, { "text": "Pediococcus pentosaceus, which often occurs in fermented foods, is characterized by numerous positive effects on the human health, such as the presence of possible probiotic abilities, the reduction of cholesterol levels, satisfactory antimicrobial activity, and certain therapeutic functions. This study was conducted with the goal of describing the genomic content of Pediococcus pentosaceus ENM104, a strain known for its inhibitory effects against pathogenic bacteria and its remarkable probiotic potential, including the induction of significant reductions in cholesterol levels and the production of γ-aminobutyric acid (GABA). The P. pentosaceus ENM104 chromosome is circular. The chromosome is 1,734,928 bp with a GC content of 37.2%. P. pentosaceus also harbors a circular plasmid, pENM104, that is 71,811 bp with a GC content of 38.1%. Functional annotations identified numerous genes associated with probiotic traits, including those involved in stress adaptation (e.g., heat stress: htpX, dnaK, and dnaJ), bile tolerance (e.g., ppaC), vitamin biosynthesis (e.g., ribU, ribZ, ribF, and btuD), immunomodulation (e.g., dltA, dltC, and dltD), and bacteriocin production (e.g., pedA). Notably, genes responsible for lowering cholesterol levels (bile salt hydrolase, bsh) and GABA synthesis (glutamate/GABA antiporter, gadC) were also identified", "token_count": 501, "char_count": 1477, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [ "ENM104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:31.979511", "source": { "split": "train_shard_00001", "doc_id": 2010 }, "chunk_id": "train_shard_00001_2010_0", "global_id": 8505 }, { "text": "The in vitro assay results using cell-free supernatants of P. pentosaceus ENM104 revealed antibacterial activity against carbapenem-resistant bacteria, such as Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii, and the inhibition zone diameter increased progressively over time. This comprehensive study provides valuable insights into the molecular characteristics of P. pentosaceus ENM104, emphasizing its potential as a probiotic. Its notable cholesterol-lowering, GABA-producing, and antimicrobial capabilities suggest promising applications in the pharmaceutical and food industries. Future research should focus on further exploring these functional properties and assessing the strain's efficacy in clinical settings.\n\nGenomic Insights into Pediococcus pentosaceus ENM104: A Probiotic with Potential Antimicrobial and Cholesterol-Reducing Properties.", "token_count": 254, "char_count": 924, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7885, "quality_score": 0.8942, "entities": { "genes": [ "ENM104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:32.465531", "source": { "split": "train_shard_00001", "doc_id": 2010 }, "chunk_id": "train_shard_00001_2010_1", "global_id": 8506 }, { "text": "Streptococcus gordonii is a gram-positive, mutualistic bacterium found in the human body. It is found in the oral cavity, upper respiratory tract, and intestines, and presents a serious clinical problem because it can lead to opportunistic infections in individuals with weakened immune systems. Streptococci are the most prevalent inhabitants of oral microbial communities, and are typical oral commensals found in the human oral cavity. These streptococci, along with many other oral microbes, produce multispecies biofilms that can attach to salivary pellicle components and other oral bacteria via adhesin proteins expressed on the cell surface. Antibiotics are effective against this bacterium, but resistance against antibodies is increasing. Therefore, a more effective treatment is needed. Vaccines offer a promising method for preventing this issue. This study generated a multi-epitope vaccine against Streptococcus gordonii by targeting the completely sequenced proteomes of five strains. The vaccine targets are identified using a pangenome and subtractive proteomic approach. In the present study, 13 complete strains out of 91 strains of S. gordonii are selected. The pangenomics results revealed that out of 2835 pan genes, 1225 are core genes. Out of these 1225 core genes, 643 identified as non-homologous proteins by subtractive proteomics. A total of 20 essential proteins are predicted from non-homologous proteins. Among these 20 essential proteins, only five are identified as surface proteins. The vaccine construct is designed based on selected B- and T-cell epitopes of the antigenic proteins with the help of linkers and adjuvants. The designed vaccine is docked against TLR2. The expression of the protein is determined using in silico gene cloning. Findings concluded that Vaccine I with adjuvant shows higher interactions with TLR2, suggesting that the vaccine has the ability to induce a humoral and cell-mediated response to treat and prevent infection; this makes it promising as a vaccine against infectious diseases caused by S", "token_count": 510, "char_count": 2085, "word_count": 305, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [ "TLR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:33.141404", "source": { "split": "train_shard_00001", "doc_id": 2011 }, "chunk_id": "train_shard_00001_2011_0", "global_id": 8507 }, { "text": "gordonii. Furthermore, validation of the vaccine construct is required by in vitro and in vivo trials to check its actual potency and safety for use to prevent infectious diseases caused by S. gordonii.\n\nReverse Vaccinology Approach to Identify Novel and Immunogenic Targets against Streptococcus gordonii.", "token_count": 91, "char_count": 324, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8444, "quality_score": 0.9222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:33.546819", "source": { "split": "train_shard_00001", "doc_id": 2011 }, "chunk_id": "train_shard_00001_2011_1", "global_id": 8508 }, { "text": "Brucellosis represents a significant global health concern that is endemic in many regions of the world. It is most prevalent in the Mediterranean region, especially in Maghreb (Tunisia, Morocco and Algeria). In Tunisia the diagnosis of human brucellosis is primarily based on serological tests and cultivation of the causative pathogen, without the knowledge of the underlying Brucella species or biovar. In addition, the scarcity of laboratories with adequate biosecurity measures to handle suspected specimen constitutes a significant challenge. Furthermore, the absence of full genome data limits our understanding of the genetic diversity of Brucella in Tunisia in comparison to the strains circulating in the North African region and the world. In the present study, a total of 36 bacterial isolates derived from human patients diagnosed with brucellosis in Tunisia were subjected to examination. Real-time PCR confirmed all isolates as B. melitensis. In subsequent core genome-based MLST analysis (cgMLST) based on 2706 target genes, the isolates formed two separate but closely related clusters with a distance of 140 alleles. Intra-cluster diversity was 1 to 6 alleles. In the larger geographical context and in comparison to almost 1000 other Brucella genomes, the isolates showed the highest genetic relationship to B. melitensis isolates from Italy and Egypt with distances of 130 and 150 alleles, respectively. All isolates were most similar to biovar 3 genotype. Markedly, strains from a reported brucellosis outbreak in Austria were grouped closely (26 and 27 alleles respectively) together with strains from Tunisia, suggesting that this country may represent their geographical origin. This research represents a significant advancement in our understanding of B. melitensis strains circulating in the Maghreb region, as it is the first study to elucidate the molecular characterization of strains isolated from humans in Tunisia. The cgMLST analysis of the strains provided information on the regional distribution of the strains and the association with neighboring countries and significant outbreaks in the region. The data will form the basis of a future reference framework for strains circulating in the Mediterranean region.", "token_count": 503, "char_count": 2249, "word_count": 333, "semantic_coherence": 1, "information_density": 0.5526, "quality_score": 0.7763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:34.231286", "source": { "split": "train_shard_00001", "doc_id": 2012 }, "chunk_id": "train_shard_00001_2012_0", "global_id": 8509 }, { "text": "Genomic Characterization of Clinical Brucella melitensis Isolates from Tunisia: Integration into the Global Population Structure", "token_count": 30, "char_count": 128, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:34.627275", "source": { "split": "train_shard_00001", "doc_id": 2012 }, "chunk_id": "train_shard_00001_2012_1", "global_id": 8510 }, { "text": "Vascular wilt disease incited by Fusarium oxysporum f. sp. carthami (Foc) in Safflower poses a significant threat to its production in India. A comprehensive understanding of the molecular underpinning of compatible and incompatible interaction is of extreme economic importance. In the present study, the genome of a virulent (IARI-5175) and a avirulent (F-00845) Foc strain were sequenced and assembled using data generated from Illumina in combination with Nanopore technologies and HiC. Foc genomes were assembled into 88 and 23 scaffolds with an estimated total size of 46 Mb and 42 Mb respectively for IARI-5175 and F-00845 strains. Reference based mapping of Foc genome with F. oxysporum f. sp. lycopersici (Fol) resulted in chromosomal level ordering of genome and simultaneous identification of accessory genome. Additionally, two lineage specific chromosomes were also identified for virulent Foc strain IARI-5175. Genomic comparisons were made on the basis of effectors, CAZymes, secondary metabolites and mycotoxins to understand the global view pathogenicity in Foc. Moreover, the transcriptome of Foc during compatible and incompatible interaction was sequenced and analyzed leading to the identification of differentially regulated genes. Taken together our study laid a solid foundation to explore novel effector genes that play a crucial role in the establishment of disease and can further be used as targets to devise new strategies to curb wilt disease in safflower.\n\nComparative Genomic and Transcriptomic Analysis of Avirulent and Virulent Strains ofFusarium oxysporumf. sp.carthami: Insights into Pathogenesis and Virulence Determinants in Safflower Infections", "token_count": 440, "char_count": 1697, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6529, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:35.253866", "source": { "split": "train_shard_00001", "doc_id": 2013 }, "chunk_id": "train_shard_00001_2013_0", "global_id": 8511 }, { "text": "Aeromonas caviae is an emerging human enteric pathogen. However, the genomic features and virulence genes of A. caviae strains from human gastroenteritis and other sources have not been fully elucidated. Here, we conducted a genomic analysis of 565 global A. caviae strains isolated from different sources, including 261 strains isolated from faecal samples of gastroenteritis patients, of which 18 genomes were sequenced in this study. The presence of bacterial virulence genes and secretion systems in A. caviae strains from different sources was compared, and the phylogenetic relationship of A. caviae strains was assessed based on the core genome. The complete genome of A. caviae strain A20-9 isolated from a gastroenteritis patient was obtained in this study, from which 300 putative virulence factors and a T4SS-encoding plasmid, pAC, were identified. Genes encoding T4SS were also identified in a novel genomic island, ACI-1, from other T4SS-positive strains. The prevalence of T4SS was significantly lower in A. caviae strains from gastroenteritis patients than in environmental strains (3 %, P<0.0001 vs 14 %, P<0.01). Conversely, the prevalence of T6SS was significantly higher in A. caviae strains isolated from gastroenteritis patients than in environmental strains (25 %, P<0.05 vs 13  %, P<0.01). Four phylogenetic clusters were formed based on the core genome of 565 A. caviae strains, and strains carrying T6SS often showed close phylogenetic relationships", "token_count": 499, "char_count": 1572, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5204, "quality_score": 0.7602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:35.916787", "source": { "split": "train_shard_00001", "doc_id": 2014 }, "chunk_id": "train_shard_00001_2014_0", "global_id": 8512 }, { "text": "T3SS, aerolysin and thermostable cytotonic enterotoxin were absent in all 565 A. caviae strains. Our findings provide novel information on the genomic features of A. caviae and suggest that T6SS may play a role in A. caviae-induced human gastroenteritis.\n\nAnalysis of global Aeromonas caviae genomes revealed that strains carrying T6SS are more common in human gastroenteritis than in environmental sources and are often phylogenetically related.", "token_count": 151, "char_count": 481, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8154, "quality_score": 0.9077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:36.355499", "source": { "split": "train_shard_00001", "doc_id": 2014 }, "chunk_id": "train_shard_00001_2014_1", "global_id": 8513 }, { "text": "Background: Multi-drug-resistant Gram-negative bacteria producing metallo-β-lactamase are an increasing concern. Here, we described three cases of infection due to difficult-to-treat and drug-resistant P. aeruginosa producing metallo-β-lactamases, which were successfully treated with antibiotic combination of cefiderocol plus imipenem-relebactam, and reported on the molecular and epidemiological features of the isolates and the in vitro synergistic effects of different antibiotic combinations guiding antibiotic treatment. Patients and methods: Three P. aeruginosa strains were isolated from respiratory or blood cultures of three different patients. Minimum inhibitory concentrations breakpoints were interpreted according to EUCAST recommendations. Next-generation sequencing data were used for in silico identification of resistance genes and sequence types and for core genome multi-locus sequence typing analysis. The fractional inhibitory concentration index was performed as a measure of synergy of cefiderocol plus imipenem and imipenem-relebactam. Results: The three isolates exhibited different multi-drug-resistant and molecular profiles carrying blaIMP-13 (imipenemase metallo-β-lactamase-13) (isolates named Pse-1 and Pse-3) and blaVIM-2 (Verona integron-encoded metallo-β-lactamase-2) (isolate Pse-2). Typing showed that the isolates did not cluster and belonged to different sequence types. The E-test method showed the presence of synergy of cefiderocol in combination with imipenem-relebactam in the two P. aeruginosa isolates producing IMP-13 (Pse-1 and Pse-3). No synergy was observed in the isolate producing VIM-2 (Pse-2). Conclusions: Cefiderocol in association with imipenem-relebactam exhibited a synergistic effect against IMP-producing P. aeruginosa isolates", "token_count": 511, "char_count": 1845, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:36.997030", "source": { "split": "train_shard_00001", "doc_id": 2015 }, "chunk_id": "train_shard_00001_2015_0", "global_id": 8514 }, { "text": "Further studies with a range of drugs and an expanded number of isolates are required to ascertain potential novel synergistic associations and the clinical utility of the fractional inhibitory concentration index.\n\nCombating Metallo-β-Lactamase-Producing Pseudomonas aeruginosa: The Fractional Inhibitory Concentration Index as a Tool to Evaluate Antibiotic Synergy.", "token_count": 93, "char_count": 374, "word_count": 47, "semantic_coherence": 1, "information_density": 0.7872, "quality_score": 0.8936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:37.382113", "source": { "split": "train_shard_00001", "doc_id": 2015 }, "chunk_id": "train_shard_00001_2015_1", "global_id": 8515 }, { "text": "The exploitation of various agro-industrial wastes for microbial cell mass production of Kluyveromyces marxianus, kefir, and Saccharomyces cerevisiae is reported in the present investigation. Specifically, the promotional effect of whole orange pulp on cell growth in mixtures consisting of cheese whey, molasses, and potato pulp in submerged fermentation processes was examined. A 2- to 3-fold increase of cell mass was observed in the presence of orange pulp. Likewise, the promotional effect of brewer's spent grains on cell growth in solid state fermentation of mixtures of whey, molasses, potato pulp, malt spent rootlets, and orange pulp was examined. The cell mass was increased by 3-fold for K. marxianus and 2-fold for S. cerevisiae in the presence of these substrates, proving their suitability for single-cell protein production without the need for extra nutrients. Cell growth kinetics were also studied by measurements of cell counts at various time intervals at different concentrations of added orange pulp. The protein content of the fermented substrates was increased substantially, indicating potential use of mixed agro-industrial wastes of negligible cost, as protein-enriched livestock feed, achieving at the same time creation of added value and waste minimization.\n\nDiscarded oranges and brewer's spent grains as promoting ingredients for microbial growth by submerged and solid state fermentation of agro-industrial waste mixtures.", "token_count": 354, "char_count": 1456, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5308, "quality_score": 0.7654, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:37.970560", "source": { "split": "train_shard_00001", "doc_id": 2016 }, "chunk_id": "train_shard_00001_2016_0", "global_id": 8516 }, { "text": "Outbreaks caused by vancomycin-resistant enterococci that transcend jurisdictional boundaries are occurring worldwide. This study focused on a vancomycin-resistant enterococcus outbreak that occurred between 2018 and 2021 across two cities in Hiroshima, Japan. The study involved genetic and phylogenetic analyses using whole-genome sequencing of 103 isolates of vancomycin-resistant enterococci to identify the source and transmission routes of the outbreak. Phylogenetic analysis was performed using core genome multilocus sequence typing and core single-nucleotide polymorphisms; infection routes between hospitals were inferred using BadTrIP. The outbreak was caused by Enterococcus faecium sequence type (ST) 80 carrying the vanA plasmid, which was derived from strain A10290 isolated in India. Of the 103 isolates, 93 were E. faecium ST80 transmitted across hospitals. The circular vanA plasmid of the Hiroshima isolates was similar to the vanA plasmid of strain A10290 and transferred from E. faecium ST80 to other STs of E. faecium and other Enterococcus species by conjugation. The inferred transmission routes across hospitals suggest the existence of a central hospital serving as a hub, propagating vancomycin-resistant enterococci to multiple hospitals. Our study highlights the importance of early intervention at the key central hospital to prevent the spread of the infection to small medical facilities, such as nursing homes, with limited medical resources and a high number of vulnerable individuals.\n\nGenomic analysis of inter-hospital transmission of vancomycin-resistant <i>Enterococcus faecium</i> sequence type 80 isolated during an outbreak in Hiroshima, Japan.", "token_count": 478, "char_count": 1754, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5603, "quality_score": 0.7802, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:38.612363", "source": { "split": "train_shard_00001", "doc_id": 2017 }, "chunk_id": "train_shard_00001_2017_0", "global_id": 8517 }, { "text": "This study explores the genomic basis of heavy metal resistance in Staphylococcus warneri strain TWSL_1, isolated from industrial textile effluent. The strain exhibited strong resistance to Cd²+, Pb²+ and Cu²+, with MICs of 50, 1,200 and 75 mg l-1, respectively. Whole-genome sequencing revealed a 2.66 Mb genome with 2,567 CDSs and a 99.81% average nucleotide identity to S. warneri WS479. Comparative genomic analysis at the genus level revealed that S. warneri strain TWSL_1 possesses a unique and expanded repertoire of heavy metal resistance genes, including the cadmium efflux system accessory protein and cadmium resistance protein, which are absent in pathogenic Staphylococcus sp. used for the comparison. Phylogenetic analysis confirmed its classification within S. warneri, with strong bootstrap support (100). Functional annotation highlighted metabolic versatility and stress response capabilities, supporting its adaptation to metal-rich environments. S. warneri TWSL_1 demonstrated high Pb²+ removal efficiency, reducing concentrations by over 70%. These findings highlight S. warneri TWSL_1 as a promising candidate for heavy metal bioremediation with potential applications in environmental detoxification and monitoring strategies.\n\nMulti-metal-resistant Staphylococcus warneri strain TWSL_1: revealing heavy metal-resistant genomic features by whole-genome sequencing and analysis.", "token_count": 451, "char_count": 1504, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6973, "quality_score": 0.8486, "entities": { "genes": [ "WS479" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:39.249021", "source": { "split": "train_shard_00001", "doc_id": 2018 }, "chunk_id": "train_shard_00001_2018_0", "global_id": 8518 }, { "text": "1 Since the emergence of SARS-CoV-2 in Wuhan in 2019 its host reservoir has not been established. Phylogenetic analysis was performed on whole genome sequences (WGS) of 71 coronaviruses and a Breda virus. A subset comprising two SARS-CoV-2 Wuhan viruses and 8 of the most closely related coronavirus sequences were used for host reservoir analysis using Bayesian Evolutionary Analysis Sampling Trees (BEAST). Within these genomes, 20 core genome fragments were combined into 2 groups each with similar clock rates (5.9×10 −3 and 1.1×10 −3 subs/site/year). Pooling the results from these fragment groups yielded a most recent common ancestor (MRCA) shared between SARS-COV-2 and the bat isolate RaTG13 around 2007 (95% HPD: 2003, 2011). Further, the host of the MRCA was most likely a bat (probability 0.64 - 0.87). Hence, the spillover into humans must have occurred at some point between 2007 and 2019 and bats may have been the most likely host reservoir.\n\nIdentification of the host reservoir of SARS-CoV-2 and determining when it spilled over into humans", "token_count": 322, "char_count": 1058, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6726, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:39.812459", "source": { "split": "train_shard_00001", "doc_id": 2019 }, "chunk_id": "train_shard_00001_2019_0", "global_id": 8519 }, { "text": "Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. We report the genome of a non-clinical E. bugandensis strain, which was integrated with publicly available genomes to study the pangenome and general population structure of E. bugandensis. Core- and whole-genome multilocus sequence typing allowed the detection of five E. bugandensis phylogroups (PG-A to E), which contain important antimicrobial resistance and virulence determinants. We uncovered several extended-spectrum β-lactamases, including blaCTX-M-55 and blaNDM-5, present in an IncX replicon type plasmid, described here for the first time in E. bugandensis. Genetic context analysis of blaNDM-5 revealed the resemblance of this plasmid with other IncX plasmids from other bacteria from the same country. Three distinctive siderophore producing operons were found in E. bugandensis: enterobactin (ent), aerobactin (iuc/iut), and salmochelin (iro). Our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis.\n\nPopulation structure and pangenome analysis of Enterobacter bugandensis uncover the presence of blaCTX-M-55, blaNDM-5 and blaIMI-1, along with sophisticated iron acquisition strategies.", "token_count": 371, "char_count": 1353, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:40.387901", "source": { "split": "train_shard_00001", "doc_id": 2020 }, "chunk_id": "train_shard_00001_2020_0", "global_id": 8520 }, { "text": "Gastrointestinal colonization by the nosocomial pathogen vancomycin-resistant Enterococcus faecium (VREfm) can lead to bloodstream infections with high mortality rates. Shifts in VREfm lineages found within healthcare settings occur, but reasons underlying these changes are not understood. Here we sequenced 710 VREfm clinical isolates collected between 2017 and 2022 from a large tertiary care centre. Genomic analyses revealed a polyclonal VREfm population, although 46% of isolates formed genetically related clusters, suggesting a high transmission rate. Comparing these data to a global collection of 15,631 publicly available VREfm genomes collected between 2002 and 2022 identified replacement of the sequence type (ST) 17 VREfm lineage by emergent ST80 and ST117 lineages at the local and global level. Comparative genomic and functional analyses revealed that emergent lineages encoded bacteriocin T8, which conferred a competitive advantage over bacteriocin T8-negative strains in vitro and upon colonization of the mouse gut. Bacteriocin T8 carriage was also strongly associated with strain emergence in the global genome collection. These data suggest that bacteriocin T8-mediated competition may have contributed to VREfm lineage replacement.\n\nBacteriocin production facilitates nosocomial emergence of vancomycin-resistant Enterococcus faecium.", "token_count": 340, "char_count": 1359, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6978, "quality_score": 0.8489, "entities": { "genes": [ "ST80", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:40.968477", "source": { "split": "train_shard_00001", "doc_id": 2021 }, "chunk_id": "train_shard_00001_2021_0", "global_id": 8521 }, { "text": "

Background

Previous studies reported the prevalence of mcr-1 among clinical infected Salmonella isolates in China. However, the transmission dynamics of mcr-1 in different ecological niches were not well investigated. Our objective is to exhibit the transmission dynamics of mcr-1 in Salmonella.

Methods

598 Salmonella isolates were recovered from ten hospitals; besides 936 pig faces and 167 pork samples were collected from January 2015 to December 2017 in Guangzhou, China. PCR and sequencing were used to identify mcr-1-positive Salmonella. Antimicrobial susceptibility testing was performed with 16 antimicrobials. Conjugation, S1-PFGE, and Southern blot were used to determine the transferability and location of mcr-1. Whole-genome sequencing was used to investigate pangenome, phylogeny, plasmid, and transposon.

Results

Eleven mcr-1-positive Salmonella isolates were identified from patients with infectious diarrhea. Five pig fecal samples and three pork samples contained mcr-1-positive Salmonella isolates. All isolates were multi-drug resistant. The mcr-1 genes were located on ∼210-250 kb IncHI2-pST3 plasmids, and 12 mcr-1 genes were transferable. All isolates were assigned to ST34 or its genetically closed STs. The distribution of the core-genome network was significantly correlated with source distributions. The accessory genes-based network demonstrated that the diverse clonal complexes could share highly similar accessory genomes.

Conclusions

The prevalence of mcr-1-positive Salmonella among different sources was low. Clonal transmission could not be the main reason for the expansion of mcr-1-positive Salmonella, but be attributed to the horizontal transfer of IncHI2-pST3 plasmid. Continuous surveillance on Salmonella should be performed to investigate the response of colistin banning in food-producing animals by mcr-1-positive Salmonella populations.", "token_count": 515, "char_count": 1913, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.798, "entities": { "genes": [ "ST34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:41.625235", "source": { "split": "train_shard_00001", "doc_id": 2022 }, "chunk_id": "train_shard_00001_2022_0", "global_id": 8522 }, { "text": "Prevalence, genomic characteristics, and transmission dynamics of mcr-1-positive Salmonella enterica Typhimurium from patients with infectious diarrhea.", "token_count": 39, "char_count": 152, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:41.985440", "source": { "split": "train_shard_00001", "doc_id": 2022 }, "chunk_id": "train_shard_00001_2022_1", "global_id": 8523 }, { "text": "

Background

Despite the applications of Bacillus subtilis group species in various sectors, limited information is available regarding their phages. Here, 61 B. subtilis group species-infecting phages (BSPs) were studied for their taxonomic classification considering the genome-size, genomic diversity, and the host, followed by the identification of orthologs taxonomic signature genes.

Results

BSPs have widely ranging genome sizes that can be bunched into groups to demonstrate correlations to family and subfamily classifications. Comparative analysis re-confirmed the existing, BSPs-containing 14 genera and 21 species and displayed inter-genera similarities within existing subfamilies. Importantly, it also revealed the need for the creation of new taxonomic classifications, including 28 species, nine genera, and two subfamilies (New subfamily1 and New subfamily2) to accommodate inter-genera relatedness. Following pangenome analysis, no ortholog shared by all BSPs was identified, while orthologs, namely, the tail fibers/spike proteins and poly-gamma-glutamate hydrolase, that are shared by more than two-thirds of the BSPs were identified. More importantly, major capsid protein (MCP) type I, MCP type II, MCP type III and peptidoglycan binding proteins that are distinctive orthologs for Herelleviridae, Salasmaviridae, New subfamily1, and New subfamily2, respectively, were identified and analyzed which could serve as signatures to distinguish BSP members of the respective taxon.

Conclusions

In this study, we show the genomic diversity and propose a comprehensive classification of 61 BSPs, including the proposition for the creation of two new subfamilies, followed by the identification of orthologs taxonomic signature genes, potentially contributing to phage taxonomy.\n\nGenomic diversity and comprehensive taxonomical classification of 61 Bacillus subtilis group member infecting bacteriophages, and the identification of ortholog taxonomic signature genes.", "token_count": 491, "char_count": 2001, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8198, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:42.633668", "source": { "split": "train_shard_00001", "doc_id": 2023 }, "chunk_id": "train_shard_00001_2023_0", "global_id": 8524 }, { "text": "

Background

Microbial strains of variable functional capacities co-exist in microbiomes. Current bioinformatics methods of strain analysis cannot provide the direct linkage between strain composition and their gene contents from metagenomic data.

Methods

Here we present StrainPanDA ( Strain -level Pan genome D ecomposition A nalysis), a novel method that uses the pangenome coverage profile of multiple metagenomic samples to simultaneously reconstruct the composition and gene content variation of co-existing strains in microbial communities.

Results

We systematically validate the accuracy and robustness of StrainPanDA using synthetic datasets. To demonstrate the power of gene-centric strain profiling, we then apply StrainPanDA to analyze the gut microbiome samples of infants, as well as patients treated with fecal microbiota transplantation. We show that the linked reconstruction of strain composition and gene content profiles is critical for understanding the relationship between microbial adaptation and strain-specific functions ( e.g., nutrient utilization, pathogenicity).

Conclusions

StrainPanDA can be applied to metagenomic datasets to detect association between molecular functions and microbial/host phenotypes to formulate testable hypotheses and gain novel biological insights at the strain or subspecies level.\n\nStrainPanDA: linked reconstruction of strain composition and gene content profiles via pangenome-based decomposition of metagenomic data", "token_count": 331, "char_count": 1510, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6477, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:43.205272", "source": { "split": "train_shard_00001", "doc_id": 2024 }, "chunk_id": "train_shard_00001_2024_0", "global_id": 8525 }, { "text": "This study examined the diversity and persistence of Salmonella in the surface waters of agricultural regions of Brazil, Chile, and Mexico. Research groups (three in 2019-2020 and five in 2021-2022) conducted a long-term survey of surface water across 5-8 months annually (n = 30 monthly). On-site, each team filtered 10-L water samples with modified Moore Swabs to capture Salmonella, which were then isolated and identified using conventional microbiological techniques. Salmonella isolates were sequenced on Illumina platforms. Salmonella was present in 1,493/3,291 water samples (45.8%), with varying isolation rates across countries and years. Newport, Infantis, and Typhimurium were the most frequent among the 128 different serovars. Notably, 22 serovars were found in all three countries, representing almost half of the 1,911 different isolates collected. The resistome comprised 72 antimicrobial resistance (AMR) genes and six point mutations in three genes. At least one AMR determinant was observed in 33.8% (646/1,911) of the isolates, of which 47.4% (306/646) were potentially multidrug resistant. Phylogeny based on core genome multilocus sequence typing (cgMLST) showed that most isolates clustered according to sequence type and country of origin. Only 14 cgMLST multi-country clusters were detected among the 275 clusters. However, further analysis confirmed that close genetic relatedness occurred mostly among isolates from the same country, with three exceptions. Interestingly, isolates closely related phylogenetically were recovered over multiple years within the same country, indicating the persistence of certain Salmonella in those areas", "token_count": 466, "char_count": 1707, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7137, "quality_score": 0.8568, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:43.851780", "source": { "split": "train_shard_00001", "doc_id": 2025 }, "chunk_id": "train_shard_00001_2025_0", "global_id": 8526 }, { "text": "In conclusion, surface waters in these regions are consistently contaminated with diverse Salmonella, including strains that persist over time.IMPORTANCESalmonella is a leading foodborne pathogen responsible for millions of illnesses, hospitalizations, and deaths annually. Although Salmonella-contaminated water has now been recognized as an important contamination source in the agrifood chain, there is a lack of knowledge on the global occurrence and diversity of Salmonella in surface water. Moreover, there has been insufficient research on Salmonella in surface waters from Latin American countries that are major producers and exporters of agricultural products. Incorporating genetic profiling of Salmonella isolates from underrepresented regions, such as Latin America, enhances our understanding of the pathogen's ecology, evolution, antimicrobial resistance, and pathogenicity. Moreover, leveraging genomic data derived from pathogens isolated from diverse geographical areas is critical for assessing the potential public health risk posed by the pathogen and expediting investigations of foodborne outbreaks. Ultimately, global efforts contribute significantly to reducing the incidence of foodborne infections.\n\nA multicenter genomic epidemiological investigation in Brazil, Chile, and Mexico reveals the diversity and persistence of <i>Salmonella</i> populations in surface waters.", "token_count": 330, "char_count": 1451, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:44.425646", "source": { "split": "train_shard_00001", "doc_id": 2025 }, "chunk_id": "train_shard_00001_2025_1", "global_id": 8527 }, { "text": "This study investigated antimicrobial resistance (AMR) phenotypes and genotypes exhibited by Neisseria gonorrhoeae from Yaoundé, Cameroon. AMR to tetracycline, penicillin and ciprofloxacin was observed although none of the isolates had reduced susceptibility to azithromycin, cefixime or ceftriaxone. Whole genome sequence (WGS) data were obtained and, using a threshold of 300 or fewer locus differences in the N. gonorrhoeae core gene multilocus sequence typing (cgMLST) scheme, four distinct core genome lineages were identified. Publicly available WGS data from 1355 gonococci belonging to these four lineages were retrieved from the PubMLST database, allowing the Cameroonian isolates to be examined in the context of existing data and compared with related gonococci. Examination of AMR genotypes in this dataset found an association between the core genome and AMR with, for example, isolates belonging to the core genome group, Ng_cgc_300 : 21, possessing GyrA and ParC alleles with amino acid substitutions conferring high-level resistance to ciprofloxacin while lineages Ng_cgc_300 : 41 and Ng_cgc_300 : 243 were predicted to be susceptible to several antimicrobials. A core genome lineage, Ng_cgc_300 : 498, was observed which largely consisted of gonococci originating from Africa. Analyses from this study demonstrate the advantages of using the N. gonorrhoeae cgMLST scheme to find related gonococci to carry out genomic analyses that enhance our understanding of the population biology of this important pathogen.\n\nPhenotypic and genotypic characterization of Neisseria gonorrhoeae isolates from Yaoundé, Cameroon, 2019 to 2020.", "token_count": 508, "char_count": 1671, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6026, "quality_score": 0.8013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:45.108305", "source": { "split": "train_shard_00001", "doc_id": 2026 }, "chunk_id": "train_shard_00001_2026_0", "global_id": 8528 }, { "text": "

Background

Brassica napus is an important agricultural species, improving stress resistance was one of the main breeding goals at present. Non-specific lipid transfer proteins (nsLTPs) are small, basic proteins which are involved in some biotic or abiotic stress responses. B. napus is susceptible to a variety of fungal diseases, so identify the BnLTPs and their expression in disease responses is very important. The common reference genome of B. napus does not contain all B. napus genes because of gene presence/absence variations between individuals. Therefore, it was necessary to search for candidate BnLTP genes in the B. napus pangenome.

Results

In the present study, the BnLTP genes were identified throughout the pangenome, and different BnLTP genes were presented among varieties. Totally, 246 BnLTP genes were identified and could be divided into five types (1, 2, C, D, and G). The classification, phylogenetic reconstruction, chromosome distribution, functional annotation, and gene expression were analyzed. We also identified potential cis-elements that respond to biotic and abiotic stresses in the 2 kb upstream regions of all BnLTP genes. RNA sequencing analysis showed that the BnLTP genes were involved in the response to Sclerotinia sclerotiorum infection. We identified 32 BnLTPs linked to blackleg resistance quantitative trait locus (QTL).

Conclusion

The identification and analysis of LTP genes in the B. napus pangenome could help to elucidate the function of BnLTP family members and provide new information for future molecular breeding in B. napus.\n\nCharacterization of non-specific lipid transfer protein (nsLtp) gene families in the Brassica napus pangenome reveals abundance variation.", "token_count": 439, "char_count": 1741, "word_count": 248, "semantic_coherence": 1, "information_density": 0.621, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:45.753128", "source": { "split": "train_shard_00001", "doc_id": 2027 }, "chunk_id": "train_shard_00001_2027_0", "global_id": 8529 }, { "text": "The most common approach to sampling the bacterial populations within an infected or colonised host is to sequence genomes from a single colony obtained from a culture plate. However, it is recognized that this method does not capture the genetic diversity in the population. An alternative is to sequence a mixture containing multiple colonies (“pool-seq”), but this has the disadvantage that it is a non-homogeneous sample, making it difficult to perform specific experiments. We compared differences in measures of genetic diversity between eight single-colony isolates (singles) and pool-seq on a set of 2286 S. aureus culture samples. The samples were obtained by swabbing three body sites on 85 human participants quarterly for a year, who initially presented with a methicillin-resistant S. aureus skin and soft-tissue infection (SSTI). We compared parameters such as sequence quality, contamination, allele frequency, nucleotide diversity and pangenome diversity in each pool to the corresponding singles. Comparing singles from the same culture plate, we found that 18% of sample collections contained mixtures of multiple Multilocus sequence types (MLSTs or STs). We showed that pool-seq data alone could predict the presence of multi-ST populations with 95% accuracy. We also showed that pool-seq could be used to estimate the number of polymorphic sites in the population. Additionally, we found that the pool may contain clinically relevant genes such as antimicrobial resistance markers that may be missed when only examining singles. These results highlight the potential advantage of analysing genome sequences of total populations obtained from clinical cultures rather than single colonies.

Graphical Abstract

\n\nComparison of genomic diversity between single and pooledStaphylococcus aureuscolonies isolated from human colonisation cultures", "token_count": 405, "char_count": 1873, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:46.431417", "source": { "split": "train_shard_00001", "doc_id": 2028 }, "chunk_id": "train_shard_00001_2028_0", "global_id": 8530 }, { "text": "

Introduction:

Antimicrobial resistance (AMR) is a growing global concern. Clonal lineages of CTX-M β-lactamase-producing Escherichia coli (CTXE) and quinolone-resistant E. coli (QREC) were disseminated among deer population in a famous tourist destination (Nara Park; NP) in Japan. Hypothesis or gap statement: The molecular characteristics of CTXE or QREC isolates which could pose a threat to public health has not been elucidated.

Aim:

This study aimed to characterize the genetic traits of CTXE and QREC isolates derived from NP deer and compare them with lineages prevalent worldwide. Methodology: Sixteen CTXE and three QREC isolates recovered from NP deer feces between 2018 and 2020 were analyzed using whole-genome sequencing. For endemic lineages, phylogenetic trees were constructed against the isolates registered in EnteroBase database using the core genome single nucleotide polymorphism scheme.

Results:

The most prevalent lineage in NP deer was ST3580. Several pandemic lineages, such as sequence type (ST) 38, ST58, and ST117, were included. The QREC lineages prevalent among deer were designated as extra-intestinal pathogenic E. coli or uropathogenic E. coli. Thirteen of the 24 antimicrobial resistance genes (ARGs) were considered high-risk ARG families. Chromosomal integration of blaCTX-M-15 was observed in all plasmid-negative isolates. Phylogenetic analysis suggested relationships between NP isolates and isolates sourced from environment or poultry.

Conclusion:

ST3580 has high potential to disseminate clonally. Furthermore, multiple clinically relevant lineages of CTXE and QREC are endemic in NP deer; however, they could be less virulent than isolates belonging to the same lineages which could cause severe infectious diseases", "token_count": 499, "char_count": 1796, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [ "ST58", "ST117", "ST3580" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:47.096079", "source": { "split": "train_shard_00001", "doc_id": 2029 }, "chunk_id": "train_shard_00001_2029_0", "global_id": 8531 }, { "text": "Further studies are required to investigate the relationship between chromosomal integration of plasmid-encoded genes and the stable propagation of AMR bacteria in wildlife and the environment.\n\nMolecular characteristics of CTX-M β-lactamase-producing and quinolone-resistant Escherichia coli among deer in a popular tourist spot in Japan", "token_count": 81, "char_count": 338, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:47.472153", "source": { "split": "train_shard_00001", "doc_id": 2029 }, "chunk_id": "train_shard_00001_2029_1", "global_id": 8532 }, { "text": "The wide adoption of bacterial genome sequencing and encoding both core and accessory genome variation using k-mers has allowed bacterial genome wide association studies (GWAS) to identify genetic variants associated with relevant phenotypes such as those linked to infection. Significant limitations still remain as far as the interpretation of association results is concerned, which affects the wider adoption of GWAS methods on microbial data sets. We have developed a simple computational method (panfeed) that explicitly links each k-mer to their gene cluster at base resolution level, which allows us to avoid biases introduced by a global de Bruijn graph as well as more easily map and annotate associated variants. We tested panfeed on two independent data sets, correctly identifying previously characterized causal variants, which demonstrates the precision of the method, as well as its scalable performance. panfeed is a command line tool written in the python programming language and available at https://github.com/microbial-pangenomes-lab/panfeed .\n\nImproved interpretability of bacterial genome-wide associations using gene cluster centric k-mers", "token_count": 242, "char_count": 1164, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:47.956489", "source": { "split": "train_shard_00001", "doc_id": 2030 }, "chunk_id": "train_shard_00001_2030_0", "global_id": 8533 }, { "text": "Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, encompassing both pandemic and non-pandemic, toxigenic, and environmental variants, to explore the diversity of mobile genetic elements (MGEs) and bacterial defense systems. Our findings include both conserved and novel MGEs across the strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiviral mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and/or bacteriophages and suggests that non-pandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and invading MGEs. Overall, this research offers foundational insights into V. cholerae's genetic complexity and adaptive strategies, with implications for understanding the differences between environmental strains and their pandemic relatives, and the potential evolutionary paths that led to the emergence of pandemic strains.\n\nExploring Mobile Genetic Elements in Vibrio cholerae", "token_count": 379, "char_count": 1711, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:48.539479", "source": { "split": "train_shard_00001", "doc_id": 2031 }, "chunk_id": "train_shard_00001_2031_0", "global_id": 8534 }, { "text": "As decreasing DNA sequencing costs leads to a steadily increasing rate of generated data, the development of efficient algorithms for processing of the sequence data is increasingly important to reduce costs and energy consumption. Recent work have shown that genotyping can be done efficiently and accurately using alignment-free methods that are based on analyzing kmers from sequenced reads. In particular, we have recently presented the KAGE genotyper, which uses an efficient pangenome representation of known individuals in a population to further increase accuracy and efficiency. While existing genotypers like KAGE use the Central Processing Unit (CPU) to count and analyze kmers, the Graphical Processing Unit (GPU) has shown promising for reducing runtime for similar problems. We here present GKAGE, a new and improved version of KAGE that utilizes the GPU to further increase the computational efficiency. This is done by counting and analyzing large amounts of kmers in the many parallel cores of a GPU. We show that GKAGE is, on hardware of comparable cost, able to genotype an individual up to an order of magnitude faster than KAGE while producing the same output, which makes it by far the fastest genotyper available today. GKAGE can run on consumer-grade GPUs, and enables genotyping of a human sample in only a matter of minutes without the need for expensive high-performance computers. GKAGE is open source and available at https://github.com/kage-genotyper/kage .\n\nUltra-fast genotyping of SNPs and short indels using GPU acceleration", "token_count": 340, "char_count": 1558, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:49.112029", "source": { "split": "train_shard_00001", "doc_id": 2032 }, "chunk_id": "train_shard_00001_2032_0", "global_id": 8535 }, { "text": "

Motivation

Pangenomes provide novel insights for population and quantitative genetics, genomics and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.

Results

The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin or R) and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1× coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity.

Availability and implementation

All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/. The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/. The PHG database of NAM parent haplotypes is in the CyVerse data store (https://de.cyverse.org/de/) and named/iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db.

Supplementary information

Supplementary data are available at Bioinformatics online.", "token_count": 498, "char_count": 1896, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:49.762460", "source": { "split": "train_shard_00001", "doc_id": 2033 }, "chunk_id": "train_shard_00001_2033_0", "global_id": 8536 }, { "text": "The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation.", "token_count": 24, "char_count": 90, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:50.114791", "source": { "split": "train_shard_00001", "doc_id": 2033 }, "chunk_id": "train_shard_00001_2033_1", "global_id": 8537 }, { "text": "Source attribution has traditionally involved combining epidemiological data with different pathogen characterisation methods, including 7-gene multi locus sequence typing (MLST) or serotyping, however, these approaches have limited resolution. In contrast, whole genome sequencing data provide an overview of the whole genome that can be used by attribution algorithms. Here, we applied a random forest (RF) algorithm to predict the primary sources of human clinical Salmonella Typhimurium (S. Typhimurium) and monophasic variants (monophasic S. Typhimurium) isolates. To this end, we utilised single nucleotide polymorphism diversity in the core genome MLST alleles obtained from 1,061 laboratory-confirmed human and animal S. Typhimurium and monophasic S. Typhimurium isolates as inputs into a RF model. The algorithm was used for supervised learning to classify 399 animal S. Typhimurium and monophasic S. Typhimurium isolates into one of eight distinct primary source classes comprising common livestock and pet animal species: cattle, pigs, sheep, other mammals (pets: mostly dogs and horses), broilers, layers, turkeys, and game birds (pheasants, quail, and pigeons). When applied to the training set animal isolates, model accuracy was 0.929 and kappa 0.905, whereas for the test set animal isolates, for which the primary source class information was withheld from the model, the accuracy was 0.779 and kappa 0.700. Subsequently, the model was applied to assign 662 human clinical cases to the eight primary source classes. In the dataset, 60/399 (15.0%) of the animal and 141/662 (21.3%) of the human isolates were associated with a known outbreak of S. Typhimurium definitive type (DT) 104", "token_count": 501, "char_count": 1756, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6305, "quality_score": 0.8153, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:50.764086", "source": { "split": "train_shard_00001", "doc_id": 2034 }, "chunk_id": "train_shard_00001_2034_0", "global_id": 8538 }, { "text": "All but two of the 141 DT104 outbreak linked human isolates were correctly attributed by the model to the primary source classes identified as the origin of the DT104 outbreak. A model that was run without the clonal DT104 animal isolates produced largely congruent outputs (training set accuracy 0.989 and kappa 0.985; test set accuracy 0.781 and kappa 0.663). Overall, our results show that RF offers considerable promise as a suitable methodology for epidemiological tracking and source attribution for foodborne pathogens.\n\nDevelopment and validation of a random forest algorithm for source attribution of animal and human Salmonella Typhimurium and monophasic variants of S. Typhimurium isolates in England and Wales utilising whole genome sequencing data.", "token_count": 203, "char_count": 775, "word_count": 114, "semantic_coherence": 1, "information_density": 0.693, "quality_score": 0.8465, "entities": { "genes": [ "DT104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:51.221730", "source": { "split": "train_shard_00001", "doc_id": 2034 }, "chunk_id": "train_shard_00001_2034_1", "global_id": 8539 }, { "text": "The Atg12-Atg5 conjugate, which is formed by an ubiquitin-like conjugation system, is essential to autophagosome formation, a central event in autophagy. Despite its importance, the molecular mechanism of the Atg12-Atg5 conjugate formation has not been elucidated. Here, we report the solution and crystal structures of Atg10 and Atg5 homologs from Kluyveromyces marxianus (Km), a thermotolerant yeast. KmAtg10 comprises an E2-core fold with characteristic accessories, including two β strands, whereas KmAtg5 has two ubiquitin-like domains and a helical domain. The nuclear magnetic resonance experiments, mutational analyses, and crosslinking experiments showed that KmAtg10 directly recognizes KmAtg5, especially its C-terminal ubiquitin-like domain, by its characteristic two β strands. Kinetic analysis suggests that Tyr56 and Asn114 of KmAtg10 may place the side chain of KmAtg5 Lys145 into the optimal orientation for its conjugation reaction with Atg12. These structural features enable Atg10 to mediate the formation of the Atg12-Atg5 conjugate without a specific E3 enzyme.\n\nStructural insights into Atg10-mediated formation of the autophagy-essential Atg12-Atg5 conjugate.", "token_count": 347, "char_count": 1183, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:51.792145", "source": { "split": "train_shard_00001", "doc_id": 2035 }, "chunk_id": "train_shard_00001_2035_0", "global_id": 8540 }, { "text": "

Introduction

Non-baumannii Acinetobacter species are increasingly isolated in the clinical setting and the environment. The aim of the present study was to analyze a genome database of 837 Acinetobacter spp. isolates, which included 798 non-baumannii Acinetobacter genomes, in order to define the concordance of classification and discriminatory power of 7-gene MLST, 53-gene MLST, and single-nucleotide polymorphism (SNPs) phylogenies.

Methods

Phylogenies were performed on Pasteur Multilocus Sequence Typing (MLST) or ribosomal Multilocus Sequence Typing (rMLST) concatenated alleles, or SNPs extracted from core genome alignment.

Results

The Pasteur MLST scheme was able to identify and genotype 72 species in the Acinetobacter genus, with classification results concordant with the ribosomal MLST scheme. The discriminatory power and genotyping reliability of the Pasteur MLST scheme were assessed in comparison to genome-wide SNP phylogeny on 535 non-baumannii Acinetobacter genomes assigned to Acinetobacter pittii, Acinetobacter nosocomialis, Acinetobacter seifertii, and Acinetobacter lactucae (heterotypic synonym of Acinetobacter dijkshoorniae), which were the most clinically relevant non-baumannii species of the A. baumannii group. The Pasteur MLST and SNP phylogenies were congruent at Robinson-Fould and Matching cluster tests and grouped genomes into four and three clusters in A. pittii, respectively, and one each in A. seifertii", "token_count": 517, "char_count": 1567, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:18:52.447706", "source": { "split": "train_shard_00001", "doc_id": 2036 }, "chunk_id": "train_shard_00001_2036_0", "global_id": 8541 }, { "text": "Furthermore, A. lactucae genomes were grouped into one cluster within A. pittii genomes. The SNP phylogeny of A. nosocomialis genomes showed a heterogeneous population and did not correspond to the Pasteur MLST phylogeny, which identified two recombinant clusters. The antimicrobial resistance genes belonging to at least three different antimicrobial classes were identified in 91 isolates assigned to 17 distinct species in the Acinetobacter genus. Moreover, the presence of a class D oxacillinase, which is a naturally occurring enzyme in several Acinetobacter species, was found in 503 isolates assigned to 35 Acinetobacter species.

Conclusion

In conclusion, Pasteur MLST phylogeny of non-baumannii Acinetobacter isolates coupled with in silico detection of antimicrobial resistance makes it important to study the population structure and epidemiology of Acinetobacter spp. isolates.\n\nPhylogenomics of Acinetobacter species and analysis of antimicrobial resistance genes.", "token_count": 318, "char_count": 1053, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:53.007431", "source": { "split": "train_shard_00001", "doc_id": 2036 }, "chunk_id": "train_shard_00001_2036_1", "global_id": 8542 }, { "text": "

Purpose

To evaluate the performance of core genome multilocus sequence typing (cgMLST) for genotyping Mycobacterium tuberculosis (M.tuberculosis) Strains in regions where the lineage 2 strains predominate.

Methods

We compared clustering by whole-genome SNP typing with cgMLST clustering in the analysis of WGS data of 6240 strains from five regions of China. Using both the receiver operating characteristic (ROC) curve and epidemiological investigation to determine the optimal threshold for defining genomic clustering by cgMLST. The performance of cgMLST was evaluated by quantifying the sensitivity, specificity and concordance of clustering between two methods. Logistic regression was used to gauge the impact of strain genetic diversity and lineage on cgMLST clustering.

Results

The optimal threshold for cgMLST to define genomic clustering was determined to be ≤ 10 allelic differences between strains. The overall sensitivity and specificity of cgMLST averaged 99.6% and 96.3%, respectively; the concordance of clustering between two methods averaged 97.1%. Concordance was significantly correlated with strain genetic diversity and was 3.99 times (95% CI, 2.94-5.42) higher in regions with high genetic diversity (π > 1.55 × 10-4) compared to regions with low genetic diversity. The difference missed statistical significance, while concordance for lineage 2 strains (96.8%) was less than that for lineage 4 strains (98.3%). CONCLUSION : cgMLST showed a discriminatory power comparable to whole-genome SNP typing and could be used to genotype clinical M.tuberculosis strains in different regions of China. The discriminative power of cgMLST was significantly correlated with strain genetic diversity and was slightly lower with strains from regions with low genetic diversity.", "token_count": 504, "char_count": 1819, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5261, "quality_score": 0.7631, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:53.656847", "source": { "split": "train_shard_00001", "doc_id": 2037 }, "chunk_id": "train_shard_00001_2037_0", "global_id": 8543 }, { "text": "Performance evaluation of core genome multilocus sequence typing for genotyping of Mycobacterium tuberculosis strains in China: based on multicenter, population-based collection.", "token_count": 42, "char_count": 178, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:54.014415", "source": { "split": "train_shard_00001", "doc_id": 2037 }, "chunk_id": "train_shard_00001_2037_1", "global_id": 8544 }, { "text": "The short arms of the human acrocentric chromosomes 13, 14, 15, 21, and 22 share large homologous regions, including the ribosomal DNA repeats and extended segmental duplications (Floutsakou et al. 2013; van Sluis et al. 2019). While the complete assembly of these regions in the Telomere-to-Telomere consortium’s CHM13 provided a model of their homology (Nurk et al. 2022), it remained unclear if these patterns were ancestral or maintained by ongoing recombination exchange. Here, we show that acrocentric chromosomes contain pseudo-homologous regions (PHRs) indicative of recombination between non-homologs. Considering an all-to-all comparison of the high-quality human pangenome from the Human Pangenome Reference Consortium (HPRC) (Liao et al. 2022), we find that contigs from all of the acrocentric short arms form a community similar to those formed by single chromosomes or the sex chromosome pair. A variation graph (Garrison et al. 2018) constructed from centromere-spanning acrocentric contigs indicates the presence of regions where most contigs appear nearly identical between heterologous CHM13 acrocentrics. Except on chromosome 15, we observe faster decay of linkage disequilibrium in the PHRs than in the corresponding short and long arms, indicating higher rates of recombination (N. Li and Stephens 2003; Huttley et al. 1999). The PHRs include sequences previously shown to lie at the breakpoint of Robertsonian translocations (Jarmuz-Szymczak et al. 2014), and we show that their arrangement is compatible with crossover in inverted duplications on chromosomes 13, 14, and 21", "token_count": 458, "char_count": 1596, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6352, "quality_score": 0.8176, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:54.662799", "source": { "split": "train_shard_00001", "doc_id": 2038 }, "chunk_id": "train_shard_00001_2038_0", "global_id": 8545 }, { "text": "The ubiquity of signals of recombination between heterologous chromosomes seen in the HPRC draft pangenome’s acrocentric assemblies suggests that these shared sequences form the basis for recurrent Robertsonian translocations, providing sequence and population-based confirmation of hypotheses first developed cytogenetically fifty years ago (Hamerton et al. 1975).\n\nRecombination between heterologous human acrocentric chromosomes", "token_count": 105, "char_count": 431, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8269, "quality_score": 0.9135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:55.038054", "source": { "split": "train_shard_00001", "doc_id": 2038 }, "chunk_id": "train_shard_00001_2038_1", "global_id": 8546 }, { "text": "The Fe3O4 nanoparticle synthesized by Acidithiobacillus ferrooxidans have a broad practical value, while the low yield limits their commercial application. Herein, we employed a 12C6+ heavy-ion beam to induce mutagenesis of A. ferrooxidans BYM and successfully screened a mutant BYMT-200 with a 1.36 mg/L Fe3O4 nanoparticle yield, which could stably inherit over many generations based on assessing cell magnetism and Fe3O4 nanoparticle synthesis. Comparative genome analysis detected 14 mutation sites, causing six synonymous mutations, one missense mutation, and one nonsense mutation. We further annotated the genes involved in the mutation, such as hcp, hsdM, yghU, K7B00_11365, and K7B00_11355, which are responsible for the substantial changes in the Fe3O4 nanoparticle yield of A. ferrooxidans. Additionally, we performed a pan-genome analysis to understand how these genes regulate Fe3O4 nanoparticle synthesis. The core genome of 2376 orthologous clusters was identified and visualized by progressive Mauve alignment and OrthoVenn. A total of 109 regulatory genes related to iron metabolism were identified, mainly involved in electron transport, iron acquisition, iron storage, and oxidative stress. The mutant genes are closely related to iron-sulfur clusters and oxidative stress. Accordingly, we proposed a hypothetical mechanism for increasing Fe3O4 nanoparticle production in A. ferrooxidans BYMT-200 to withstand high oxidative stress caused by heavy ion radiation", "token_count": 486, "char_count": 1634, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:55.692389", "source": { "split": "train_shard_00001", "doc_id": 2039 }, "chunk_id": "train_shard_00001_2039_0", "global_id": 8547 }, { "text": "Our study offers significant theoretical guidance for further acquiring the high-yield Fe3O4 nanoparticle-producing bacteria and studying the mechanism of its synthesis.\n\nComparative genomics analysis of the reason for <sup>12</sup>C<sup>6+</sup> heavy-ion irradiation in improving Fe<sub>3</sub>O<sub>4</sub> nanoparticle yield of Acidithiobacillus ferrooxidans.", "token_count": 150, "char_count": 433, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8718, "quality_score": 0.9359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:56.123833", "source": { "split": "train_shard_00001", "doc_id": 2039 }, "chunk_id": "train_shard_00001_2039_1", "global_id": 8548 }, { "text": "Prokaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration, such as gene amelioration and compensatory evolution. Within bacterial species, the extent and relative importance of these different mechanisms has never been considered altogether. In this study, a phylogeny-based method was used to investigate the occurrence of these different evolutionary responses in Pseudomonas aeruginosa. Selection on codon usage of genes acquired through HGT was observed over evolutionary time, with the overall codon usage converging towards that of the core genome. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. This pattern therefore seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes.\n\nEvolutionary responses to codon usage of horizontally transferred genes in <i>Pseudomonas aeruginosa</i>: gene retention, amelioration and compensatory evolution.", "token_count": 381, "char_count": 1846, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:56.720096", "source": { "split": "train_shard_00001", "doc_id": 2040 }, "chunk_id": "train_shard_00001_2040_0", "global_id": 8549 }, { "text": "Haemophilus influenzae is a major cause of community-acquired pneumonia. While studied extensively in various laboratory models, less is known about the cell function while inside the human lung. We present the first analysis of the global gene expression of H. influenzae while the bacteria are in the lung during pneumonia (in vivo conditions) and contrast it with bacterial isolates that have been cultured under standard laboratory conditions (in vitro conditions). Patients with pneumonia were recruited from emergency departments and intensive care units during 2018-2020 (n = 102). Lower respiratory samples were collected for bacterial culture and RNA extraction. Patient samples with H. influenzae (n = 8) and colonies from bacterial cultures (n = 6) underwent RNA sequencing. The reads were then pseudo-aligned to core and pan genomes created from 15 reference strains. While bacteria cultured in vitro clustered tightly by principal component analysis of core genome (n = 1067) gene expression, bacteria in the patient samples had more diverse transcriptomic signatures and did not group with their lab-cultured counterparts. In total, 328 core genes were significantly differentially expressed between in vitro and in vivo conditions. The most highly upregulated genes in vivo included tbpA and fbpA, which are involved in the acquisition of iron from transferrin, and the stress response gene msrAB. The biosynthesis of nucleotides/purines and molybdopterin-scavenging processes were also significantly enriched in vivo. In contrast, major metabolic pathways and iron-sequestering genes were downregulated under this condition", "token_count": 490, "char_count": 1758, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6345, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:57.395110", "source": { "split": "train_shard_00001", "doc_id": 2041 }, "chunk_id": "train_shard_00001_2041_0", "global_id": 8550 }, { "text": "In conclusion, extensive transcriptomic differences were found between bacteria while in the human lung and bacteria that were cultured in vitro. IMPORTANCE The human-specific pathogen Haemophilus influenzae is generally not well suited for studying in animal models, and most laboratory models are unlikely to approximate the diverse environments encountered by bacteria in the human airways accurately. Thus, we have examined the global gene expression of H. influenzae during pneumonia. Extensive differences in the global gene expression profiles were found in H. influenzae while in the human lung compared to bacteria that were grown in the laboratory. In contrast, the gene expression profiles of isolates collected from different patients were found to cluster together when grown under the same laboratory conditions. Interesting observations were made of how H. influenzae acquires and uses iron and molybdate, endures oxidative stress, and regulates central metabolism while in the lung. Our results indicate important processes during infection and can guide future research on genes and pathways that are relevant in the pathogenesis of H. influenzae pneumonia.\n\nIn vivo gene expression profile of Haemophilus influenzae during human pneumonia.", "token_count": 302, "char_count": 1313, "word_count": 182, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:57.976913", "source": { "split": "train_shard_00001", "doc_id": 2041 }, "chunk_id": "train_shard_00001_2041_1", "global_id": 8551 }, { "text": "

Background

Salmonella enterica encompasses over 2,600 serovars, including several commonly associated with severe infection in humans. Salmonella is a major cause of sepsis in Africa; however, diagnosis requires clinical microbiology facilities. Environmental surveillance has the potential to play a role in Salmonella surveillance.

Methods

We undertook water-based environmental surveillance in Blantyre, Malawi, from 2018-2020, taking samples from rivers (87.9%), a sewage plant (8.85%) and other water sources (3.24%), isolating and storing 1,042 non-typhoidal Salmonella (NTS) isolates in this period. Of these, 341 NTS isolates were whole genome sequenced, genome quality was checked, duplicate genomes from any given sample were removed and core genome phylogeny was reconstructed. AMRFinder, PathogenWatch and SISTR were used to further investigate serovar, sequence type and antimicrobial resistance determinants.

Results

After quality checks, and removal of duplicate genomes, 270 NTS genomes remained for further analysis. Multiple Salmonella serovars associated with human infection were detected, of which S. Typhimurium (55/270 isolates) was the most common, including 44 of Sequence Type (ST) 313, a serovar commonly associated with severe invasive disease (iNTS). Six lineage 2 ST313 genomes possessed AMR genes predicting multidrug resistance (MDR), while 29 lineage 3 isolates contained no AMR predictive genes. PCR based detection of staG has been proposed as a diagnostic marker of S. Typhi; however, all eight genomes that contained staG identified as Salmonella enterica serovar Orion, raising concerns about the specificity of this marker as a monoplex for environmental surveillance of S", "token_count": 463, "char_count": 1733, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [ "ST313" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:58.658886", "source": { "split": "train_shard_00001", "doc_id": 2042 }, "chunk_id": "train_shard_00001_2042_0", "global_id": 8552 }, { "text": "Typhi.

Discussion

The study identified diverse Salmonella serovars in the environment, including those reported to cause invasive disease, emphasizing the complex but potentially valuable contribution of implementing environmental surveillance for Salmonella in high burden areas lacking diagnostic microbiology capacity.\n\nDiversity of Salmonella enterica isolates from urban river and sewage water in Blantyre, Malawi.", "token_count": 92, "char_count": 426, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:59.033442", "source": { "split": "train_shard_00001", "doc_id": 2042 }, "chunk_id": "train_shard_00001_2042_1", "global_id": 8553 }, { "text": "

ABSTRACT

Despite the notable clinical impact, recent molecular epidemiology regarding third-generation cephalosporin-resistant Klebsiella pneumoniae (3GC-R Kp ) in the United States remains limited. We performed whole genome sequencing of 3GC-R Kp bacteremia isolates collected from March 2016 to May 2022 at a tertiary care cancer center in Houston, TX using Illumina and Oxford Nanopore Technologies platforms. A comprehensive comparative genomic analysis was performed to dissect population structure, transmission dynamics, and pan-genomic signatures of our 3GC-R Kp population. Of the 194 3GC-R Kp bacteremias that occurred during our study timeframe, we were able to analyze 153 (79%) bacteremia isolates, 126 initial and 27 recurrent isolates respectively. While isolates belonging to the widely prevalent clonal group (CG) 258 were rarely observed, the predominant clonal group, CG307, accounted for 37 (29%) index isolates and displayed a significant correlation (Pearson correlation test P -value = 0.03) with the annual frequency of 3GC-R Kp bacteremia. Within our CG307 cohort, 89% (33/37) of our isolates belong to the global rather than previously described Texas-specific clade. Strikingly, we identified a new CG307 sub-clade ( i.e., cluster 1 isolates) comprised of 18 isolates characterized by the chromosomally-encoded bla SHV-205 and unique accessory genome content. This CG307 sub-clade was detected in various United States regions, with genome sequences from 24 additional strains becoming recently available in the NCBI SRA database. Collectively, this study underscores the emergence and dissemination of a distinct CG307 sub-clade that is a prevalent cause of 3GC-R Kp bacteremia among cancer patients seen in Houston, TX and has recently been isolated throughout the United States", "token_count": 503, "char_count": 1816, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8398, "entities": { "genes": [ "CG307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:18:59.696783", "source": { "split": "train_shard_00001", "doc_id": 2043 }, "chunk_id": "train_shard_00001_2043_0", "global_id": 8554 }, { "text": "

DATA SUMMARY

WGS data sequenced during this study period was submitted to NCBI and can be accessed within BioProject PRJNA648389. WGS data from previous study of carbapenem non-susceptible Enterobacterales can be accessed from BioProject PRJNA836696. Assembly information and BioAccession numbers are provided in Table S1.

IMPACT STATEMENT

Infections due to 3 rd generation cephalosporin resistant Klebsiella pneumoniae (3GC-R Kp ) are considered among the most urgent public health threats. However, molecular epidemiology studies on 3GC-R Kp in the United States are limited. Our analysis indicates a preponderance of genetically diverse 3GC-R Kp isolates harboring the key antimicrobial resistance determinant bla CTX-M-15 at our institution. Importantly, however, we detected evidence of long duration transmission of highly genetically related CG307 and CG29 specific clusters at our institution. Interestingly, we rarely detected the pandemic CG258 lineage in our cohort and did not detect more than two genetically related CG258 isolates from this lineage. We found that 90% of our isolates from the most prevalent clonal group, CG307, belonged to a novel, nested-population of a “global” CG307 clade in contrast to the more commonly detected “Texas-specific” clade that has circulated in our region. We searched the NCBI SRA database using genomic markers of the novel CG307 clade and found evidence of this clade causing recent invasive infections in other locations across the United States. Our study highlights the shifting population dynamics of K. pneumoniae causing invasive infections and the necessity to continue AMR surveillance in order to identify emerging high-risk populations.\n\nIdentification of A Novel CG307 Sub-clade in Third Generation Cephalosporin ResistantKlebsiella pneumoniaeCausing Invasive Infections in the United States", "token_count": 505, "char_count": 1881, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8038, "entities": { "genes": [ "CG29", "CG258", "CG307", "PRJNA836696", "PRJNA648389" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:00.350510", "source": { "split": "train_shard_00001", "doc_id": 2043 }, "chunk_id": "train_shard_00001_2043_1", "global_id": 8555 }, { "text": "Since 2014, the long-term decreasing trend in human salmonellosis, caused mainly by the consumption of Salmonella-contaminated poultry products, has stagnated in the European Union (EU). As Poland has been the leading poultry meat producer in the EU since 2014, we analysed whole genome sequences of 275 Salmonella (S.) Enteritidis strains from the poultry food production chain (n = 216) and humans (n = 59) (2008-2019) to shed light on the genetic content and relatedness of the S. Enteritidis population in Poland. Most (99.3%) of the strains belonged to ST11. Overall, 5.8% of strains possessed at least one antimicrobial resistance gene (ARG), the most common being qnrB19 (n = 9). Mutations in quinolone resistance-determining regions (QRDRs) were observed in 46.9% of strains, and the most common mutation was gyrA (S83Y; n = 95). In 95.6% of strains, at least one plasmid replicon was detected, with the highest prevalence of IncFII(S)_1 (n = 263) and IncFIB(S)_1 (n = 262). The composition of Salmonella pathogenicity islands (SPIs) was uniform among 96.7% of strains carrying CS54, SPI-1-SPI-3, SPI-5, SPI-6, SPI-9, SPI-12 and SPI-14", "token_count": 491, "char_count": 1234, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6648, "quality_score": 0.8324, "entities": { "genes": [ "CS54", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:01.003573", "source": { "split": "train_shard_00001", "doc_id": 2044 }, "chunk_id": "train_shard_00001_2044_0", "global_id": 8556 }, { "text": "Core genome multilocus sequence typing (cgMLST) analysis revealed no apparent clustering based on source or year of isolation. None of the genetic determinants studied here seemed to trigger changes in Salmonella epidemiology. However, other factors, such as improvements in reporting and control, could influence infection trends and are, therefore, worth further elucidation.\n\nMolecular Characteristics of Epidemiologically Successful <i>Salmonella</i> Enteritidis in Poland.", "token_count": 121, "char_count": 496, "word_count": 61, "semantic_coherence": 1, "information_density": 0.918, "quality_score": 0.959, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:01.387854", "source": { "split": "train_shard_00001", "doc_id": 2044 }, "chunk_id": "train_shard_00001_2044_1", "global_id": 8557 }, { "text": "The Pacific oyster (PO), Crassostrea gigas, is an important commercial marine species but periodically experiences large stock losses due to disease events known as summer mortality. Summer mortality has been linked to environmental perturbations and numerous viral and bacterial agents, indicating this disease is multifactorial in nature. In 2013 and 2014, several summer mortality events occurred within the Port Stephens estuary (NSW, Australia). Extensive culture and molecular-based investigations were undertaken and several potentially pathogenic Vibrio species were identified. To improve species identification and genomically characterise isolates obtained from this outbreak, whole-genome sequencing (WGS) and subsequent genomic analyses were performed on 48 bacterial isolates, as well as a further nine isolates from other summer mortality studies using the same batch of juveniles. Average nucleotide identity (ANI) identified most isolates to the species level and included members of the Photobacterium, Pseudoalteromonas, Shewanella and Vibrio genera, with Vibrio species making up more than two-thirds of all species identified. Construction of a phylogenomic tree, ANI analysis, and pan-genome analysis of the 57 isolates represents the most comprehensive culture-based phylogenomic survey of Vibrios during a PO summer mortality event in Australian waters and revealed large genomic diversity in many of the identified species. Our analysis revealed limited and inconsistent associations between isolate species and their geographical origins, or host health status. Together with ANI and pan-genome results, these inconsistencies suggest that to determine the role that microbes may have in Pacific oyster summer mortality events, isolate identification must be at the taxonomic level of strain. Our WGS data (specifically, the accessory genomes) differentiated bacterial strains, and coupled with associated metadata, highlight the possibility of predicting a strain's environmental niche and level of pathogenicity.", "token_count": 483, "char_count": 2095, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:02.046021", "source": { "split": "train_shard_00001", "doc_id": 2045 }, "chunk_id": "train_shard_00001_2045_0", "global_id": 8558 }, { "text": "Phylogenomic diversity of Vibrio species and other Gammaproteobacteria isolated from Pacific oysters (Crassostrea gigas) during a summer mortality outbreak.", "token_count": 51, "char_count": 170, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:02.404490", "source": { "split": "train_shard_00001", "doc_id": 2045 }, "chunk_id": "train_shard_00001_2045_1", "global_id": 8559 }, { "text": "Autophagy is an intracellular degradation system by which cytoplasmic materials are enclosed by an autophagosome and delivered to a lysosome/vacuole. Atg18 plays a critical role in autophagosome formation as a complex with Atg2 and phosphatidylinositol 3-phosphate (PtdIns(3)P). However, little is known about the structure of Atg18 and its recognition mode of Atg2 or PtdIns(3)P. Here, we report the crystal structure of Kluyveromyces marxianus Hsv2, an Atg18 paralog, at 2.6 Å resolution. The structure reveals a seven-bladed β-propeller without circular permutation. Mutational analyses of Atg18 based on the K. marxianus Hsv2 structure suggested that Atg18 has two phosphoinositide-binding sites at blades 5 and 6, whereas the Atg2-binding region is located at blade 2. Point mutations in the loops of blade 2 specifically abrogated autophagy without affecting another Atg18 function, the regulation of vacuolar morphology at the vacuolar membrane. This architecture enables Atg18 to form a complex with Atg2 and PtdIns(3)P in parallel, thereby functioning in the formation of autophagosomes at autophagic membranes.\n\nStructure-based analyses reveal distinct binding sites for Atg2 and phosphoinositides in Atg18.", "token_count": 355, "char_count": 1217, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:02.982173", "source": { "split": "train_shard_00001", "doc_id": 2046 }, "chunk_id": "train_shard_00001_2046_0", "global_id": 8560 }, { "text": "Eubacterium species are a group of obligated anaerobic gram-positive bacilli that are recognized as commensals of the gastrointestinal tract flora. Cases of bacteremia mediated by Eubacterium are rare. This report describes a case of bacteremia caused by Eubacterium callanderi in an 82-year-old female with a history of a cecal perforation secondary to an obstructing sigmoid stricture. The results showed the utility of using whole genome sequencing to identify the causative agent and underlined the significance to identify anaerobic organisms in diagnostic microbiology practice and to perform antimicrobial susceptibility testing to guide therapy and enhance patient outcomes.\n\nEubacterium callanderi bacteremia: A case report.", "token_count": 207, "char_count": 761, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6961, "quality_score": 0.848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:03.443476", "source": { "split": "train_shard_00001", "doc_id": 2047 }, "chunk_id": "train_shard_00001_2047_0", "global_id": 8561 }, { "text": "Computational pangenomics is an emerging research field that is changing the way computer scientists are facing challenges in biological sequence analysis. In past decades, contributions from combinatorics, stringology, graph theory and data structures were essential in the development of a plethora of software tools for the analysis of the human genome. These tools allowed computational biologists to approach ambitious projects at population scale, such as the 1000 Genomes Project. A major contribution of the 1000 Genomes Project is the characterization of a broad spectrum of genetic variations in the human genome, including the discovery of novel variations in the South Asian, African and European populations-thus enhancing the catalogue of variability within the reference genome. Currently, the need to take into account the high variability in population genomes as well as the specificity of an individual genome in a personalized approach to medicine is rapidly pushing the abandonment of the traditional paradigm of using a single reference genome. A graph-based representation of multiple genomes, or a graph pangenome, is replacing the linear reference genome. This means completely rethinking well-established procedures to analyze, store, and access information from genome representations. Properly addressing these challenges is crucial to face the computational tasks of ambitious healthcare projects aiming to characterize human diversity by sequencing 1M individuals (Stark et al. 2019). This tutorial aims to introduce readers to the most recent advances in the theory of data structures for the representation of graph pangenomes. We discuss efficient representations of haplotypes and the variability of genotypes in graph pangenomes, and highlight applications in solving computational problems in human and microbial (viral) pangenomes.\n\nComputational graph pangenomics: a tutorial on data structures and their applications.", "token_count": 410, "char_count": 1977, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5812, "quality_score": 0.7906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:04.067659", "source": { "split": "train_shard_00001", "doc_id": 2048 }, "chunk_id": "train_shard_00001_2048_0", "global_id": 8562 }, { "text": "Carbohydrate-active enzymes (CAZymes) are an important feature of bacteria in productive marine systems such as continental shelves, where phytoplankton and macroalgae produce diverse polysaccharides. We herein describe Maribacter dokdonensis 62-1, a novel strain of this flavobacterial species, isolated from alginate-supplemented seawater collected at the Patagonian continental shelf. M. dokdonensis 62-1 harbors a diverse array of CAZymes in multiple polysaccharide utilization loci (PUL). Two PUL encoding polysaccharide lyases from families 6, 7, 12, and 17 allow substantial growth with alginate as sole carbon source, with simultaneous utilization of mannuronate and guluronate as demonstrated by HPLC. Furthermore, strain 62-1 harbors a mixed-feature PUL encoding both ulvan- and fucoidan-targeting CAZymes. Core-genome phylogeny and pangenome analysis revealed variable occurrence of these PUL in related Maribacter and Zobellia strains, indicating specialization to certain \"polysaccharide niches.\" Furthermore, lineage- and strain-specific genomic signatures for exopolysaccharide synthesis possibly mediate distinct strategies for surface attachment and host interaction. The wide detection of CAZyme homologs in algae-derived metagenomes suggests global occurrence in algal holobionts, supported by sharing multiple adaptive features with the hydrolytic model flavobacterium Zobellia galactanivorans. Comparison with Alteromonas sp. 76-1 isolated from the same seawater sample revealed that these co-occurring strains target similar polysaccharides but with different genomic repertoires, coincident with differing growth behavior on alginate that might mediate ecological specialization", "token_count": 479, "char_count": 1743, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7371, "quality_score": 0.8685, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:04.713287", "source": { "split": "train_shard_00001", "doc_id": 2049 }, "chunk_id": "train_shard_00001_2049_0", "global_id": 8563 }, { "text": "Altogether, our study contributes to the perception of Maribacter as versatile flavobacterial polysaccharide degrader, with implications for biogeochemical cycles, niche specialization and bacteria-algae interactions in the oceans.\n\nCAZymes in Maribacter dokdonensis 62-1 From the Patagonian Shelf: Genomics and Physiology Compared to Related Flavobacteria and a Co-occurring Alteromonas Strain.", "token_count": 131, "char_count": 416, "word_count": 48, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:05.143486", "source": { "split": "train_shard_00001", "doc_id": 2049 }, "chunk_id": "train_shard_00001_2049_1", "global_id": 8564 }, { "text": "Avian-pathogenic Escherichia coli (APEC) is a subgroup of extraintestinal pathogenic E.coli (ExPEC) presumed to be zoonotic and to represent an external reservoir for extraintestinal infections in humans, including uropathogenic E. coli (UPEC) causing urinary tract infections. Comparative genomics has previously been applied to investigate whether APEC and human ExPEC are distinct entities. Even so, whole-genome-based studies are limited, and large-scale comparisons focused on single sequence types (STs) are not available yet. In this study, comparative genomic analysis was performed on 323 APEC and human ExPEC genomes belonging to sequence type 95 (ST95) to investigate whether APEC and human ExPEC are distinct entities. Our study showed that APEC of ST95 did not constitute a unique ExPEC branch and was genetically diverse. A large genetic overlap between APEC and certain human ExPEC was observed, with APEC located on multiple branches together with closely related human ExPEC, including nearly identical APEC and human ExPEC. These results illustrate that certain ExPEC clones may indeed have the potential to cause infection in both poultry and humans. Previously described ExPEC-associated genes were found to be encoded on ColV plasmids. These virulence-associated plasmids seem to be crucial for ExPEC strains to cause avian colibacillosis and are strongly associated with strains of the mixed APEC/human ExPEC clusters. The phylogenetic analysis revealed two distinct branches consisting of exclusively closely related human ExPEC which did not carry the virulence-associated plasmids, emphasizing a lower avian virulence potential of human ExPEC in relation to an avian host.IMPORTANCE APEC causes a range of infections in poultry, collectively called colibacillosis, and is the leading cause of mortality and is associated with major economic significance in the poultry industry", "token_count": 497, "char_count": 1937, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5912, "quality_score": 0.7956, "entities": { "genes": [ "ST95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:05.799789", "source": { "split": "train_shard_00001", "doc_id": 2050 }, "chunk_id": "train_shard_00001_2050_0", "global_id": 8565 }, { "text": "A growing number of studies have suggested APEC as an external reservoir of human ExPEC, including UPEC, which is a reservoir. ExPEC belonging to ST95 is considered one of the most important pathogens in both poultry and humans. This study is the first in-depth whole-genome-based comparison of ST95 E. coli which investigates both the core genomes as well as the accessory genomes of avian and human ExPEC. We demonstrated that multiple lineages of ExPEC belonging to ST95 exist, of which the majority may cause infection in humans, while only part of the ST95 cluster seem to be avian pathogenic. These findings further support the idea that urinary tract infections may be a zoonotic infection.\n\nDiversity and Population Overlap between Avian and Human Escherichia coli Belonging to Sequence Type 95.", "token_count": 210, "char_count": 810, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "ST95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:06.263318", "source": { "split": "train_shard_00001", "doc_id": 2050 }, "chunk_id": "train_shard_00001_2050_1", "global_id": 8566 }, { "text": "The genus Pseudooceanicola from the alphaproteobacterial Roseobacter group currently includes ten validated species. We herein describe strain Lw-13eT, the first Pseudooceanicola species from marine macroalgae, isolated from the brown alga Fucus spiralis abundant at European and North American coasts. Physiological and pangenome analyses of Lw-13eT showed corresponding adaptive features. Adaptations to the tidal environment include a broad salinity tolerance, degradation of macroalgae-derived substrates (mannitol, mannose, proline), and resistance to several antibiotics and heavy metals. Notably, Lw-13eT can degrade oligomeric alginate via PL15 alginate lyase encoded in a polysaccharide utilization locus (PUL), rarely described for roseobacters to date. Plasmid localization of the PUL strengthens the importance of mobile genetic elements for evolutionary adaptations within the Roseobacter group. PL15 homologs were primarily detected in marine plant-associated metagenomes from coastal environments but not in the open ocean, corroborating its adaptive role in algae-rich habitats. Exceptional is the tolerance of Lw-13eT against the broad-spectrum antibiotic tropodithietic acid, produced by Phaeobacter spp. co-occurring in coastal habitats. Furthermore, Lw-13eT exhibits features resembling terrestrial plant-bacteria associations, i.e. biosynthesis of siderophores, terpenes and volatiles, which may contribute to mutual bacteria-algae interactions. Closest described relative of Lw-13eT is Pseudopuniceibacterium sediminis CY03T with 98.4% 16S rRNA gene sequence similarity", "token_count": 480, "char_count": 1668, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7638, "quality_score": 0.8819, "entities": { "genes": [ "CY03", "PL15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:07.267728", "source": { "split": "train_shard_00001", "doc_id": 2051 }, "chunk_id": "train_shard_00001_2051_0", "global_id": 8567 }, { "text": "However, protein sequence-based core genome phylogeny and average nucleotide identity indicate affiliation of Lw-13eT with the genus Pseudooceanicola. Based on phylogenetic, physiological and (chemo)taxonomic distinctions, we propose strain Lw-13eT (=DSM 29013T=LMG 30557T) as a novel species with the name Pseudooceanicola algae.\n\nPseudooceanicola algae sp. nov., isolated from the marine macroalga Fucus spiralis, shows genomic and physiological adaptations for an algae-associated lifestyle.", "token_count": 184, "char_count": 538, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8689, "quality_score": 0.9344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:07.713695", "source": { "split": "train_shard_00001", "doc_id": 2051 }, "chunk_id": "train_shard_00001_2051_1", "global_id": 8568 }, { "text": "Linezolid-resistant Enterococcus faecalis (LREfs) carrying optrA are increasingly reported globally from multiple sources, but we lack a comprehensive analysis of human and animal optrA-LREfs strains. To assess if optrA is dispersed in isolates with varied genetic backgrounds or with common genetic features, we investigated the phylogenetic structure, genetic content [antimicrobial resistance (AMR), virulence, prophages, plasmidome] and optrA-containing platforms of 27 publicly available optrA-positive E. faecalis genomes from different hosts in seven countries. At the genome-level analysis, an in-house database with 64 virulence genes was tested for the first time. Our analysis showed a diversity of clones and adaptive gene sequences related to a wide range of genera from Firmicutes. Phylogenies of core and accessory genomes were not congruent, and at least PAI-associated and prophage genes contribute to such differences. Epidemiologically unrelated clones (ST21, ST476-like and ST489) obtained from human clinical and animal hosts in different continents over eight years (2010-2017) could be phylogenetically related (3-126 SNPs difference). optrA was located on the chromosome within a Tn6674-like element (n=10) or on medium-size plasmids (30-60 kb; n=14) belonging to main plasmid families (RepA_N/Inc18/Rep_3). In most cases, the immediate gene vicinity of optrA was generally identical in chromosomal (Tn6674) or plasmid (impB-fexA-optrA) backbones", "token_count": 514, "char_count": 1575, "word_count": 200, "semantic_coherence": 1, "information_density": 0.725, "quality_score": 0.8625, "entities": { "genes": [ "ST21", "ST476", "ST489" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:19:08.348761", "source": { "split": "train_shard_00001", "doc_id": 2052 }, "chunk_id": "train_shard_00001_2052_0", "global_id": 8569 }, { "text": "Tn6674 was always inserted into the same ∆radC integration site and embedded in a 32 kb chromosomal platform common to strains from different origins (patients, healthy humans, and animals) in Europe, Africa, and Asia during 2012-2017. This platform is conserved among hundreds of E. faecalis genomes and proposed as a chromosomal hotspot for optrA integration. The finding of optrA in strains sharing common adaptive features and genetic backgrounds across different hosts and countries suggests the occurrence of common and independent genetic events occurring in distant regions and might explain the easy de novo generation of optrA-positive strains. It also anticipates a dramatic increase of optrA carriage and spread with a serious impact on the efficacy of linezolid for the treatment of Gram-positive infections.\n\nComparative genomics of global optrA-carrying Enterococcus faecalis uncovers a common chromosomal hotspot for optrA acquisition within a diversity of core and accessory genomes.", "token_count": 309, "char_count": 1077, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6849, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:08.956840", "source": { "split": "train_shard_00001", "doc_id": 2052 }, "chunk_id": "train_shard_00001_2052_1", "global_id": 8570 }, { "text": "Ethanol productions from cheese whey powder (CWP) solution were investigated by using free or immobilized cells of Kluyveromyces marxianus in monocultures or mixed cultures with free or immobilized cells of K. marxianus and Saccharomyces cerevisiae. K. marxianus free cells produced 3.8% v/v ethanol in monocultures, while S. cerevisiae immobilized cells produced 5.3% v/v ethanol in mixed cultures. The percentage of theoretical yield was found to be higher in mixed cultures than that in monocultures. The maximum ethanol fermentation efficiency was achieved (79.9% of the theoretical value) using mixed cultures of immobilized cells of K. marxianus and S. cerevisiae. The beads were relatively stable without significant reduction in activity for about eight batches of fermentation.\n\nImproved ethanol production by mixed immobilized cells of Kluyveromyces marxianus and Saccharomyces cerevisiae from cheese whey powder solution fermentation.", "token_count": 251, "char_count": 945, "word_count": 133, "semantic_coherence": 1, "information_density": 0.5188, "quality_score": 0.7594, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:09.469820", "source": { "split": "train_shard_00001", "doc_id": 2053 }, "chunk_id": "train_shard_00001_2053_0", "global_id": 8571 }, { "text": "Genome assembly databases are growing rapidly. The sequence content in each new assembly can be largely redundant with previous ones, but this is neither conceptually nor algorithmically easy to measure. We propose new methods and a new tool called DandD that addresses the question of how much new sequence is gained when a sequence collection grows. DandD can describe how much human structural variation is being discovered in each new human genome assembly and when discoveries will level off in the future. DandD uses a measure called δ (“delta”), developed initially for data compression. Computing δ directly requires counting k-mers, but DandD can rapidly estimate it using genomic sketches. We also propose δ as an alternative to k-mer-specific cardinalities when computing the Jaccard coefficient, avoiding the pitfalls of a poor choice of k. We demonstrate the utility of DandD’s functions for estimating δ, characterizing the rate of pangenome growth, and computing allpairs similarities using k-independent Jaccard. DandD is open source software available at: https://github.com/jessicabonnie/dandd .\n\nDandD: efficient measurement of sequence growth and similarity", "token_count": 264, "char_count": 1177, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:10.041403", "source": { "split": "train_shard_00001", "doc_id": 2054 }, "chunk_id": "train_shard_00001_2054_0", "global_id": 8572 }, { "text": "Fura is a spontaneously fermented pearl millet product consumed in West Africa. The yeast species involved in the fermentation were identified by pheno- and genotypic methods to be Candida krusei, Kluyveromyces marxianus, Candida tropicalis, Candida rugosa, Candida fabianii, Candida norvegensis and Trichosporon asahii. C. krusei and K. marxianus were found to be the dominant species. Survival in pH 2.5 or in the presence of bile salts (0.3% (w/v) oxgall) and growth at 37°C were independently determined as indicators of the survival potential of the isolates during passage through the human gastrointestinal tract. Selected yeast species isolates were assessed for their probiotic potential. All of the examined yeast isolates survived and grew at human gastrointestinal conditions in pH 2.5, 0.3% (w/v) oxgall at 37°C. The effect on the transepithelial electrical resistance (TEER) across polarized monolayers of intestinal epithelial cells of human (Caco-2) and porcine (IPEC-J2) origin, were determined. The Caco-2 cells and IPEC-J2 cells displayed clearly different relative TEER results. The strains of C. krusei, K. marxianus, C. rugosa and T. asahii were able to increase the relative TEER of Caco-2 monolayers after 48h. In comparison, the relative TEER of IPEC-J2 monolayers decreased when exposed to the same yeasts, even though T. asahii did not differ significantly from Saccharomyces cerevisiae var. boulardii which is used as a human probiotic. C. tropicalis resulted in the largest relative TEER decrease for both the human and the porcine cell model assays. Hyphal growth was observed for C. albicans and C. tropicalis after 48h of incubation with polarized Caco-2 monolayers, whereas this was not the case for the remaining yeast species", "token_count": 514, "char_count": 1760, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:19:10.754281", "source": { "split": "train_shard_00001", "doc_id": 2055 }, "chunk_id": "train_shard_00001_2055_0", "global_id": 8573 }, { "text": "In the present study new yeast strains with potential probiotic properties have been isolated to be used potentially as starter cultures for fura production.\n\nBiodiversity and probiotic potential of yeasts isolated from Fura, a West African spontaneously fermented cereal.", "token_count": 62, "char_count": 272, "word_count": 39, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:11.119023", "source": { "split": "train_shard_00001", "doc_id": 2055 }, "chunk_id": "train_shard_00001_2055_1", "global_id": 8574 }, { "text": "The intracellular beta-glucosidase from Kluyveromyces marxianus NBRC1777 (KmBglI) belongs to glycoside hydrolase family 3 and has a unique domain architecture. Selenomethionine-labelled KmBglI was purified and crystallized by the hanging-drop vapour-diffusion method using the purified enzyme at 30 mg ml(-1), 0.04 M potassium dihydrogen phosphate pH 5.1, 16%(w/v) PEG 8000 and 20%(v/v) glycerol. The crystal belonged to space group C2, with unitcell parameters a = 245.8, b = 148.7, c = 119.9 angstrom, beta = 112.9 degrees. Multiple-wavelength anomalous dispersion data were collected at 2.4 and 2.5 angstrom resolution. A tetramer was assumed to be present in the asymmetric unit, which gave a Matthews coefficient of 2.6 angstrom(3) Da(-1).\n\nPurification, crystallization and preliminary X-ray analysis of beta-glucosidase from Kluyveromyces marxianus NBRC1777.", "token_count": 318, "char_count": 865, "word_count": 120, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [ "NBRC1777" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:11.681478", "source": { "split": "train_shard_00001", "doc_id": 2056 }, "chunk_id": "train_shard_00001_2056_0", "global_id": 8575 }, { "text": "

Methods:

that use a linear genome reference for genome sequencing data analysis are reference biased. In the field of clinical genetics for rare diseases, a resulting reduction in genotyping accuracy in some regions has likely prevented the resolution of some cases. Pangenome graphs embed population variation into a reference structure. While pangenome graphs have helped to reduce reference mapping bias, further performance improvements are possible. We introduce VG-Pedigree, a pedigree-aware workflow based on the pangenome-mapping tool of Giraffe (Sirén et al. 2021) and the variant-calling tool DeepTrio (Kolesnikov et al. 2021) using a specially-trained model for Giraffe-based alignments. We demonstrate mapping and variant calling improvements in both single-nucleotide variants (SNVs) and insertion and deletion (INDEL) variants over those produced by alignments created using BWA-MEM to a linear-reference and Giraffe mapping to a pangenome graph containing data from the 1000 Genomes Project. We have also adapted and upgraded the deleterious-variant (DV) detecting methods and programs of Gu et al. into a streamlined workflow (Gu et al. 2019). We used these workflows in combination to detect small lists of candidate DVs among 15 family quartets and quintets of the Undiagnosed Diseases Program (UDP). All candidate DVs that were previously diagnosed using the mendelian models covered by the previously published Gu et al. methods were recapitulated by these workflows. The results of these experiments indicate a slightly greater absolute count of DVs are detected in the proband population than in their matched unaffected siblings.\n\nA Complete Pedigree-Based Graph Workflow for Rare Candidate Variant Analysis", "token_count": 422, "char_count": 1740, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:12.312350", "source": { "split": "train_shard_00001", "doc_id": 2057 }, "chunk_id": "train_shard_00001_2057_0", "global_id": 8576 }, { "text": "Previously, we demonstrated that the majority of vancomycin-resistant Enterococcus faecium (VREfm) strains from in-patients of the University Hospital Erlangen, Germany, belonged to only three clonal lineages, namely ST117/CT71 vanB and two novel ST1299 vanA lineages classified as CT3109 and CT1903. The goal of the current study was (i) to investigate whether VREfm is also detectable in wastewater of the city of Erlangen, (ii) to identify their molecular features, and (iii) to clarify whether VREfm could arise from the community of the city of Erlangen or can be (directly) connected to nosocomial infections in the hospital setting. From April to May 2023, a total of 244 VREfm strains from raw wastewater of the city of Erlangen were analyzed by core genome multilocus sequence typing (cgMLST). Moreover, 20 of them were further investigated for single nucleotide polymorphisms (SNPs). The molecular characterization of the wastewater VREfm strains revealed a high prevalence (27.9%) of the recently identified clonal lineage ST1299/CT3109 vanA, which is mainly characterized by the presence of the tetracycline-resistance determinant tet(M) and the virulence genes pilA and prpA. The SNPs analysis revealed the presence of two major clusters, namely cluster I (≤65 SNPs), which included well-known hospital-adapted vanB clonal lineages such as ST117/CT71 and ST80/CT1065 and cluster II (≤70 SNPs), which were mainly characterized by the lineage ST1299/CT3109 vanA", "token_count": 470, "char_count": 1535, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6083, "quality_score": 0.8041, "entities": { "genes": [ "ST1299", "CT1903", "CT1065", "CT3109", "CT71", "ST117", "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:12.955929", "source": { "split": "train_shard_00001", "doc_id": 2058 }, "chunk_id": "train_shard_00001_2058_0", "global_id": 8577 }, { "text": "Based on the concomitant resistance to vancomycin and tetracycline, we propose that ST1299/CT3109 vanA primarily originated and spread outside of hospital settings.IMPORTANCEThis study provides a detailed genomic analysis of vancomycin-resistant Enterococcus faecium (VREfm) strains isolated from municipal wastewater with a particular focus on clonal lineages, antimicrobial resistance, and the presence of virulence genes. The high wastewater prevalence of the recently identified clonal lineage ST1299/CT3109 vanA, which has been previously detected in hospitals, suggests an enormous potential for future spread in Germany.\n\nHigh prevalence of the recently identified clonal lineage ST1299/CT3109 vanA among vancomycin-resistant Enterococcus faecium strains isolated from municipal wastewater.", "token_count": 233, "char_count": 832, "word_count": 100, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [ "ST1299", "CT3109" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:13.432049", "source": { "split": "train_shard_00001", "doc_id": 2058 }, "chunk_id": "train_shard_00001_2058_1", "global_id": 8578 }, { "text": "We identified Streptomyces globisporus bja209 through a targeted screen of actinomycetes from natural habitats using an E. coli JW5503 ΔtolC DualRep2(c) reporter strain. This strain produced antibacterial compounds whose action depended on the growth medium. HPLC-MS and genomic analysis revealed two metabolites: albomycin δ2 (a translation inhibitor) and desferrioxamine E. The latter induced the SOS response. Desferrioxamine E exhibited a narrow spectrum of antagonistic activity against carbapenem-resistant A. baumannii and C. michiganensis, and its production was critically regulated by iron concentration. Notably, the structurally similar desferrioxamine B was inactive. Contrary to previous reports, pangenome analysis of published GenBank genomes revealed that albomycin BGC is restricted to specific S. globisporus strains and not present in other Streptomycetes phylogenetic clades. The C-1027 BGC was found in a large linear plasmid (165.5 kb) of the S. globisporus bja209 strain and also found exclusively on linear plasmids in some of the published S. globisporus genomes.\n\nThe Regulation of the Albomycin and Desferrioxamine E Biosynthesis in <i>Streptomyces globisporus</i> bja209.", "token_count": 397, "char_count": 1261, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7134, "quality_score": 0.8567, "entities": { "genes": [ "JW5503" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:14.041008", "source": { "split": "train_shard_00001", "doc_id": 2059 }, "chunk_id": "train_shard_00001_2059_0", "global_id": 8579 }, { "text": "A new allele, the EPG1-2 gene, which codes for an endopolygalacturonase in Kluyveromyces marxianus CECT1043, has been cloned. The gene has 1086 bp and the protein 362 amino acids, one more than the previously described Epg1p. Epg1-2p shows a high degree of similarity with the polygalacturonases of fungi and yeasts. The sequences common to all of the polygalacturonases of prokaryotes, fungi, and higher plants are also conserved in Epg1-2p. The EPG1-2 gene has been expressed in Pichia pastoris , and, when fused with the signal peptide of the alpha-factor of Saccharomyces cerevisiae , the protein is properly secreted into the media. The recombinant enzyme does not appear to be fully glycosylated by P. pastoris or not glycosylated in the same manner as in K. marxianus, but it maintains the same optimum temperature (55 degrees C) and pH (4.5) and the same stability at different temperatures and pH values as the native enzyme, also showing the same hydrolytic behavior. The recombinant strain produces 200-fold more enzyme than the wild-type strain of K. marxianus, making it a yeast of potential industrial interest for the production of endopolygalacturonase for the food industry.\n\nCloning, characterization, and functional analysis of the EPG1-2 gene: a new allele coding for an endopolygalacturonase in Kluyveromyces marxianus.", "token_count": 398, "char_count": 1340, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [ "CECT1043", "EPG1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:14.658125", "source": { "split": "train_shard_00001", "doc_id": 2060 }, "chunk_id": "train_shard_00001_2060_0", "global_id": 8580 }, { "text": "Six Gram-reaction-positive, strictly aerobic, mycelium-forming actinobacteria were isolated from soils collected from a natural cave in Jeju, Republic of Korea. The isolates produced well-developed, branched, substrate mycelia and white aerial mycelia that differentiated into straight or flexuous chains of smooth-surfaced spores. Cells showed growth at 15-30 °C, pH 3.5-8.0 and 0-1% (w/v) NaCl. Most of the isolates also grew at pH 10.0. The cell-wall peptidoglycan in common contained ll-diaminopimelic acid, galactose, glucose, mannose and rhamnose. The major menaquinone was MK-9(H6) and MK-9(H8). The polar lipids in common contained phosphatidylglycerol, phosphatidylinositol and an unidentified phospholipid, with the presence of diphosphatidylglycerol and phosphatidylethanolamine in some strains. The predominant fatty acids in common were anteiso-C15 : 0, iso-C16 : 0 and C16 : 0. Strains N1-1T, N1-3 and N1-12 contained genomes of 8.44-8.77 Mbp, and strains N1-5 and N1-10T consisted of genomes of 9.00-9.17 Mbp, while strain N8-3T contained the smallest genome (7.33 Mbp) among the isolates. The genomic DNA G+C contents of the isolates were 71.5-72.2%. Three representatives of the isolates encompassed 16-29 biosynthetic gene clusters predicted to encode for secondary metabolites", "token_count": 497, "char_count": 1383, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:15.313727", "source": { "split": "train_shard_00001", "doc_id": 2061 }, "chunk_id": "train_shard_00001_2061_0", "global_id": 8581 }, { "text": "The core genome-based phylogenomic tree showed that they formed three distinct clusters within the genus Streptacidiphilus, with the closest relative, the type strain of Streptacidiphilus carbonis, which was also supported by 16S rRNA gene phylogeny. The orthologous average nucleotide identity (≤88.2%) and digital DNA-DNA hybridization (≤30.3%) between three representatives of the isolates and members of the genus Streptacidiphilus and among them supported that the isolates represent three new species of the genus Streptacidiphilus, for which the names Streptacidiphilus alkalitolerans [type strain, N1-1T (=KCTC 19224T=DSM 45080T)], Streptacidiphilus cavernicola [type strain, N8-3T (=KCTC 29470T=DSM 117389T)] and Streptacidiphilus jeojiensis sp. nov. [type strain, N1-10T (=KCTC 19257T=DSM 117391T=NRRL B-24556T)] are proposed.", "token_count": 410, "char_count": 1002, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6916, "quality_score": 0.8458, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:15.929634", "source": { "split": "train_shard_00001", "doc_id": 2061 }, "chunk_id": "train_shard_00001_2061_1", "global_id": 8582 }, { "text": "<i>Streptacidiphilus alkalitolerans</i> sp. nov., <i>Streptacidiphilus cavernicola</i> sp. nov. and <i>Streptacidiphilus jeojiensis</i> sp. nov. isolated from a cave, and an emended description of the genus <i>Streptacidiphilus</i>.", "token_count": 127, "char_count": 280, "word_count": 25, "semantic_coherence": 1, "information_density": 0.76, "quality_score": 0.88, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:16.314023", "source": { "split": "train_shard_00001", "doc_id": 2061 }, "chunk_id": "train_shard_00001_2061_2", "global_id": 8583 }, { "text": "Simultaneous Saccharification and Fermentation (SSF) is effective for minimizing sugar inhibition during high solids fermentation of biomass solids to ethanol. However, fungal enzymes used during SSF are optimal between 50–60°C, whereas most fermentative yeast, such as Saccharomyces cerevisiae , do not tolerate temperatures above 37°C. Kluveromyces marxianus variant CBS 6556 is a thermotolerant eukaryote that thrives at 43°C, thus potentially serving as a promising new host for SSF operation in biorefineries. Here, we demonstrate the application of CBS 6556 in SSF configuration to understand its capabilities and limitations as compared to a proven SSF strain, S. cerevisiae D5A. For this study, we first pretreated hardwood poplar chips using Co-Solvent Enhanced Lignocellulosic Fractionation (CELF) to remove lignin and hemicellulose and to produce cellulose-enriched pretreated solids for SSF. Our results demonstrate that although CBS 6556 could not directly outperform D5A, it demonstrated superior growth rates at higher temperatures and higher early stage ethanol productivity. We discovered that CBS 6556’s membrane was particularly sensitive to higher ethanol concentrations causing it to suffer earlier fermentation arrest than D5A. Cross-examination of metabolite data between CBS 6556 and D5A and cell surface imaging suggests that the combined stresses of high ethanol concentrations and temperature to CBS 6556’s cell membrane was a primary factor limiting its ethanol productivity. Hence, we believe K. marxianus to be an excellent host for future genetic engineering efforts to improve membrane robustness in order to achieve higher ethanol productivity and titers, serving as a viable alternative to D5A.\n\nProspects of thermotolerant Kluveromyces marxianus for high solids ethanol fermentation of lignocellulosic biomass", "token_count": 483, "char_count": 1844, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:16.961908", "source": { "split": "train_shard_00001", "doc_id": 2062 }, "chunk_id": "train_shard_00001_2062_0", "global_id": 8584 }, { "text": "Host genetics, sex, and other within-source factors have been associated with characteristic effects on the fecal microbiome in mice, however, the commercial source of mice remains the dominant factor. Increasing evidence indicates that supplier-specific microbiomes in particular confer differences in disease susceptibility in models of inflammatory conditions, as well as baseline behavior and body morphology. However, current knowledge regarding the compositional differences between suppliers is based on 16S rRNA amplicon sequencing data, and functional differences between these communities remain poorly defined. Here, we applied a meta-omic (metagenomic and metatranscriptomic) approach to biomolecules (DNA/RNA) extracted from murine fecal samples representative of two large U.S. suppliers of research mice, which differ in composition, and influence baseline physiology and behavior as well as disease severity in mouse models of intestinal disease. We reconstructed high-quality metagenome-assembled genomes (MAGs), frequently containing genomic content unique to each supplier. These differences were observed both within pangenomes of dominant taxa as well as the epibiont Saccharimonadaceae . Additionally, transcriptional activity and pathway analyses revealed key functional differences between the metagenomes associated with each supplier, including differences in carbohydrate enzyme activity and dissimilatory sulfate reduction by sulfate-reducing bacteria (SRB). These data provide a detailed characterization of the baseline differences in the fecal metagenome of laboratory mice from two U.S. commercial suppliers suggesting that these functional differences are influenced by differences in the initial inoculum of colony founders, as well as additional taxa gained during growth of the production colony.\n\nMulti-omics analysis of mouse fecal microbiome reveals supplier-dependent functional differences and novel metagenome-assembled genomes", "token_count": 408, "char_count": 1969, "word_count": 254, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:17.586629", "source": { "split": "train_shard_00001", "doc_id": 2063 }, "chunk_id": "train_shard_00001_2063_0", "global_id": 8585 }, { "text": "

Background

The surveillance of antimicrobial resistance genes (ARGs) and bacteria is one critical approach to prevent and control antimicrobial resistance (AMR). Next-generation sequencing (NGS) is a powerful tool in monitoring the emergence and spread of ARGs and resistant bacteria. The horizontal transfer of ARGs across host bacteria mediated by plasmids is a challenge in NGS surveillance for resistance because short-read sequencing can hardly generate the complete plasmid genome sequence, and the correlation between ARGs and plasmids are difficult to determine.

Methods

The complete genome sequences of 455 mcr-carrying plasmids (pMCRs), and the data of their host bacteria and isolation regions were collected from the NCBI database. Genes of Inc types and ARGs were searched for each plasmid. The genome similarity of these plasmids was analyzed by pangenome clustering and genome alignment.

Results

A total of 52 Inc types, including a variety of fusion plasmids containing 2 or more Inc types were identified in these pMCRs and carried by complex host bacteria. The cooccurrence of ARGs in pMCRs was generally observed, with an average of 3.9 ARGs per plasmid. Twenty-two clusters with consistent or highly similar sequences and gene compositions were identified by the pangenome clustering, which were characterized with distributions in different countries/regions, years or host bacteria in each cluster.

Discussion

Based on the complete plasmid sequences, distribution of mcr genes in different Inc type plasmids, their co-existence with other AMRs, and transmission of one pMCR across regions and host bacteria can be revealed definitively. Complete plasmid genomes and comparisons in the laboratory network are necessary for spread tracing of ARG-carrying plasmids and risk assessment in AMR surveillance.\n\nTrans-Regional and Cross-Host Spread of mcr-Carrying Plasmids Revealed by Complete Plasmid Sequences - 44 Countries, 1998-2020.", "token_count": 511, "char_count": 2003, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5343, "quality_score": 0.7671, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:18.249228", "source": { "split": "train_shard_00001", "doc_id": 2064 }, "chunk_id": "train_shard_00001_2064_0", "global_id": 8586 }, { "text": "Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, kerato conjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017, mostly in Europe. The average chromosome size of the M. feriruminatoris strains was 1,040±0,024 kbp, with 24 % G+C and 852±31 CDS. The core genome and pan-genome of the M. feriruminatoris species contained 628 and 1312 protein families, respectively. The M. feriruminatoris strains displayed a relatively closed pan-genome, with many features and putative virulence factors shared with species from the M. mycoides cluster, including the MIB-MIP Ig cleavage system, a repertoire of DUF285 surface proteins and a complete biosynthetic pathway for galactan. M. feriruminatoris genomes were found to be mostly syntenic, although repertoires of mobile genetic elements, including Mycoplasma Integrative and Conjugative Elements, insertion sequences, and a single plasmid varied. Phylogenetic- and gene content analyses confirmed that M. feriruminatoris was closer to the M. mycoides cluster than to the ruminant species M. yeatsii and M. putrefaciens. Ancestral genome reconstruction showed that the emergence of the M", "token_count": 513, "char_count": 1565, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [ "DUF285" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:19:18.904671", "source": { "split": "train_shard_00001", "doc_id": 2065 }, "chunk_id": "train_shard_00001_2065_0", "global_id": 8587 }, { "text": "feriruminatoris species was associated with the gain of 17 gene families, some of which encode defence enzymes and surface proteins, and the loss of 25 others, some of which are involved in sugar transport and metabolism. This comparative study suggests that the M. mycoides cluster could be extended to include M. feriruminatoris. We also find evidence that the specific organization and structure of the DnaA boxes around the oriC of M. feriruminatoris may contribute to drive the remarkable fast growth of this minimal bacterium.\n\nComparative genomics of Mycoplasma feriruminatoris, a fast-growing pathogen of wild Caprinae.", "token_count": 189, "char_count": 673, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7263, "quality_score": 0.8632, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:19.354214", "source": { "split": "train_shard_00001", "doc_id": 2065 }, "chunk_id": "train_shard_00001_2065_1", "global_id": 8588 }, { "text": "Waste streams from the wood processing industry can serve as feedstream for ethanol production from biomass residues. Hardboard manufacturing process wastewater (HPW) was evaluated on the basis of monomeric sugar recovery and fermentability as a novel feedstream for ethanol production. Dilute acid hydrolysis, coupled with concentration of the wastewater resulted in a hydrolysate with 66 g/l total fermentable sugars. As xylose accounted for 53 % of the total sugars, native xylose-fermenting yeasts were evaluated for their ability to produce ethanol from the hydrolysate. The strains selected were, in decreasing order by ethanol yields from xylose (Y p/s, based on consumed sugars), Scheffersomyces stipitis ATCC 58785 (CBS 6054), Pachysolen tannophilus ATCC 60393, and Kluyveromyces marxianus ATCC 46537. The yeasts were compared on the basis of substrate utilization and ethanol yield during fermentations of the hydrolysate, measured using an HPLC. S. stipitis, P. tannophilus, and K. marxianus produced 0.34, 0.31, and 0.36 g/g, respectively. The yeasts were able to utilize between 58 and 75 % of the available substrate. S. stipitis outperformed the other yeast during the fermentation of the hydrolysate; consuming the highest concentration of available substrate and producing the highest ethanol concentration in 72 h. Due to its high sugar content and low inhibitor levels after hydrolysis, it was concluded that HPW is a suitable feedstream for ethanol production by S. stipitis.\n\nEvaluation of hardboard manufacturing process wastewater as a feedstream for ethanol production.", "token_count": 450, "char_count": 1593, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6026, "quality_score": 0.8013, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:19.987640", "source": { "split": "train_shard_00001", "doc_id": 2066 }, "chunk_id": "train_shard_00001_2066_0", "global_id": 8589 }, { "text": "

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a great public health problem and is associated with many disease outbreaks and high mortality rates. Alarmingly, K. pneumoniae has been isolated from food in several recent studies. This study aimed to investigate the prevalence and characteristics of CRKP in food samples from Egypt.

Methods

A total of 311 food samples (including 116 minced meat, 92 chicken meat, 75 diced meat, and 28 mutton) were collected from local markets in Egypt and were screened for CRKP with the determination of their antimicrobial resistance profiles. The whole genome sequence was done for 23 CRKP isolates to clarify the relationship between CRKP from food and human cases in Egypt using the SNP core genome. The conjugation probability of the blaNDM-5 harboring plasmid was identified using oriTfinder RESULTS: CRKP was isolated from 11% (35/311) of the samples, with 45.71% (16/35) of them showing resistance to colistin, one of the last-resort options for treating CRKP-mediated infections. In addition to the carbapenem and colistin resistance, the CRKP isolates frequently exhibited resistance to multiple antimicrobials including β-lactams, fluoroquinolones, aminoglycosides, tetracyclines, and chloramphenicol. In addition, most of the CRKP were potentially hypervirulent K. pneumoniae (HvKP) identified as phylogroup Kp1 and of high-risk groups as detected in STs reported in many human outbreaks globally, such as ST383 and ST147. The core-genome phylogeny showed similarities between the isolates from this study and those previously isolated from clinical human samples in Egypt", "token_count": 468, "char_count": 1663, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6043, "quality_score": 0.8021, "entities": { "genes": [ "ST147", "ST383" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:20.636946", "source": { "split": "train_shard_00001", "doc_id": 2067 }, "chunk_id": "train_shard_00001_2067_0", "global_id": 8590 }, { "text": "In addition, analysis of the plasmid on which blaNDM is encoded revealed that several antimicrobial resistance genes such as blaOXA-9, blaCTX-M-15, aac(6')-Ib, qnrS1, and several virulence genes are encoded on the same plasmid.

Conclusions

This study is significant for food safety and public health and is important to further identify the change in the epidemiology of CRKP infections, especially the consumption of contaminated food products.\n\nCarbapenem and colistin-resistant hypervirulent Klebsiella pneumoniae: An emerging threat transcending the egyptian food chain.", "token_count": 179, "char_count": 614, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7532, "quality_score": 0.8766, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:21.111682", "source": { "split": "train_shard_00001", "doc_id": 2067 }, "chunk_id": "train_shard_00001_2067_1", "global_id": 8591 }, { "text": "The potential of 20 dairy yeast strains belonging to Debaryomyces hansenii, Kluyveromyces lactis and Kluyveromyces marxianus species was examined for the production of milk protein-derived antihypertensive hydrolysates. For this purpose yeast strains were grown in microbiological medium with casein or lactoferrin as sole nitrogen source, and the inhibitory effects of casein and lactoferrin hydrolysates (CSHs and LFHs) on angiotensin I-converting enzyme (ACE) activity were determined. Based on the ACE-inhibitory activity, four CSHs and five LFHs were selected, and permeate fractions with molecular masses lower than 3kDa (pCSHs and pLFHs) were obtained. In vitro ACE-inhibitory potencies (IC50) of permeates varied from 18.8 to 87.6μg/ml (pCSHs) and from 50.2 to 500μg/ml (pLFHs). K. marxianus Km2 strain grown on either casein or lactoferrin produced the most potent permeates. pCSHs and pLFHs were orally administered to spontaneously hypertensive rats (SHRs) and exerted in vivo antihypertensive effect. In conclusion, the present study contributes to a better insight into bioactive compounds produced by dairy yeasts and shows the feasibility of selected yeasts to produce orally effective antihypertensive milk protein-derived hydrolysates.\n\nDairy yeasts produce milk protein-derived antihypertensive hydrolysates", "token_count": 405, "char_count": 1325, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6464, "quality_score": 0.8232, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:21.774778", "source": { "split": "train_shard_00001", "doc_id": 2068 }, "chunk_id": "train_shard_00001_2068_0", "global_id": 8592 }, { "text": "Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared to core genes, accessory genes are enriched in functions involved in genome integrity. We found no evidence for recent horizontal gene transfer between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent than that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that environmentally transmitted symbionts that associate with individual hosts over their lifetime show features of narrow symbioses, where the frequency of HGT is constrained.\n\nPangenome evolution in environmentally transmitted symbionts of deep-sea mussels is governed by vertical inheritance", "token_count": 427, "char_count": 1891, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:22.429734", "source": { "split": "train_shard_00001", "doc_id": 2069 }, "chunk_id": "train_shard_00001_2069_0", "global_id": 8593 }, { "text": "This study aimed to characterize carbapenem-resistant Acinetobacter baumannii (CRAB) isolates from Jiangxi patients using whole-genome sequencing (WGS). We subjected 100 clinical CRAB strains isolated from the three local largest teaching hospitals to WGS and antimicrobial susceptibility testing. Molecular epidemiology was investigated using multilocus sequence typing, core genome multilocus typing, core genome single-nucleotide polymorphism phylogeny, and pulsed-field gel electrophoresis. The most prevalent acquired carbapenemase was blaOXA-23, predominant in all isolates (100%). Isolates belonging to the dominating international clone IC2 accounted for 92% of all isolates. International IC11 (ST164Pas/ST1418Ox) clone was found in an additional 8% (eight isolates), with seven isolates (87.5%) carrying an acquired additional blaNDM-1 carbapenemase. The oxa23-associated Tn2009, either alone or in a tandem repeat structure containing four copies of blaOXA-23, was discovered in 62% (57 isolates) of IC2. The oxa23-associated Tn2006 was identified in 38% (35 isolates) of IC2 and all IC11 isolates. A putative conjugative RP-T1 (formerly RepAci6) plasmid with blaOXA-23 in Tn2006 within AbaR4, designated pSRM1.1, was found in IC2 A. baumannii strain SRM1", "token_count": 497, "char_count": 1409, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7024, "quality_score": 0.8512, "entities": { "genes": [ "ST164", "IC11", "IC2", "SRM1", "ST1418" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:23.104274", "source": { "split": "train_shard_00001", "doc_id": 2070 }, "chunk_id": "train_shard_00001_2070_0", "global_id": 8594 }, { "text": "The blaNDM-1 gene found in seven IC11 isolates was located on a novel Tn6924-like transposon, a first-time report in IC11. These findings underscore the significant importance of real-time surveillance to prevent the further spread of CRAB.

Importance

Carbapenem-resistant Acinetobacter baumannii (CRAB) is notorious for causing difficult-to-treat infections. To elucidate the molecular and clinical epidemiology of CRAB in Jiangxi, clinical CRAB isolates were collected and underwent whole-genome sequencing and antibiotic susceptibility phenotyping. Key findings included the predominance of OXA-23-producing IC2 A. baumannii, marked by the emergence of OXA-23 and NDM-1-producing IC11 strains.\n\nMulticenter retrospective genomic characterization of carbapenemase-producing Acinetobacter baumannii isolates from Jiangxi patients 2021-2022: identification of a novel international clone, IC11.", "token_count": 298, "char_count": 947, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7339, "quality_score": 0.867, "entities": { "genes": [ "IC11", "IC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:23.660960", "source": { "split": "train_shard_00001", "doc_id": 2070 }, "chunk_id": "train_shard_00001_2070_1", "global_id": 8595 }, { "text": "

Summary

The ancient, ongoing coevolutionary battle between bacteria and their viral predators, bacteriophages, has given rise to sophisticated immune systems including restriction-modification and CRISPR-Cas. Dozens of additional anti-phage systems have been identified based on their co-location within so-called defense islands, but whether these computational screens are exhaustive is unclear. Here, we developed an experimental selection scheme agnostic to genomic context to identify defense systems encoded in 71 diverse E. coli strains. Our results unveil 21 new and conserved defense systems, none of which were previously detected as enriched in defense islands. Additionally, our work indicates that intact prophages and mobile genetic elements are primary reservoirs and distributors of defense systems in E. coli , with defense systems typically carried in specific locations, or hotspots. These hotspots in homologous prophages and mobile genetic elements encode dozens of additional, as-yet uncharacterized defense system candidates. Collectively, our findings reveal an extended landscape of antiviral immunity in E. coli and provide a generalizable approach for mapping defense systems in other species.\n\nMapping the landscape of anti-phage defense mechanisms in the E. coli pangenome", "token_count": 287, "char_count": 1317, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7039, "quality_score": 0.852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:24.215912", "source": { "split": "train_shard_00001", "doc_id": 2071 }, "chunk_id": "train_shard_00001_2071_0", "global_id": 8596 }, { "text": "Bacillus anthracis, the causative agent of anthrax disease, is a worldwide threat to livestock, wildlife and public health. It is also considered one of the most important pathogens of bioterrorism. Rapid and reliable diagnosis and administration of antimicrobials are essential for effective anthrax treatment. In this study, we determined the in vitro susceptibilities of 40 isolates of B. anthracis isolated in Croatia over the recent two decades to 18 antimicrobials. Whole-genome sequencing was performed, and bioinformatics tools were used to determine virulence factors and antimicrobial resistance genes. Core genome-based multilocus sequence typing was used for isolate comparison and phylogenetic analysis. All isolates were susceptible to all antimicrobials recommended for post-exposure prophylaxis or anthrax therapy. Susceptibility was found to all other tested antimicrobials that are an alternative for primary therapy. We found two beta-lactamase genes, but their expression is not sufficient to confer resistance. In all isolates used in this study, we found 21 virulence genes, 8 of which are responsible for toxin and capsule production. As far as phylogenetic analysis is concerned, the B. anthracis isolates from Croatia are categorised into two clades. The first is clade A, subclade Trans Eurasia, and the other is clade B, subclade B2.\n\nAntimicrobial Resistance Profile, Whole-Genome Sequencing and Core Genome Multilocus Sequence Typing of B. anthracis Isolates in Croatia from 2001 to 2022.", "token_count": 419, "char_count": 1545, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5864, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:24.840049", "source": { "split": "train_shard_00001", "doc_id": 2072 }, "chunk_id": "train_shard_00001_2072_0", "global_id": 8597 }, { "text": "Advantages of pangenomes over linear reference assemblies for genome research have recently been established. However, potential effects of sequence platform and assembly approach, or of combining assemblies created by different approaches, on pangenome construction have not been investigated. We generated haplotype-resolved assemblies from the offspring of three bovine trios representing increasing levels of heterozygosity that each demonstrate a substantial improvement in contiguity, completeness, and accuracy over the current Bos taurus reference genome. Diploid coverage as low as 20x for HiFi or 60x for ONT was sufficient to produce two haplotype-resolved assemblies meeting the standards set by the Vertebrate Genome Project. Structural variant-based pangenomes created from the haplotype-resolved assemblies demonstrated significant consensus regardless of sequence platform, assembler algorithm, or coverage. Inspecting pangenome topologies identified 90 thousand structural variants including 931 overlapping with coding sequences; this approach revealed variants affecting QRICH2, PRDM9, HSPA1A, TAS2R46 , and GC that have potential to affect phenotype.\n\nStructural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies", "token_count": 293, "char_count": 1294, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7012, "quality_score": 0.8506, "entities": { "genes": [ "QRICH2", "PRDM9", "HSPA1A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:25.406858", "source": { "split": "train_shard_00001", "doc_id": 2073 }, "chunk_id": "train_shard_00001_2073_0", "global_id": 8598 }, { "text": "Barley genomic resources are increasing rapidly, with the publication of a barley pangenome as one of the latest developments. Two-row spring barley cultivars are intensely studied as they are the source of high-quality grain for malting and distilling. Here we provide data from a European two-row spring barley population containing 209 different genotypes registered for the UK market between 1830 to 2014. The dataset encompasses RNA-sequencing data from six different tissues across a range of barley developmental stages, phenotypic datasets from two consecutive years of field-grown trials in the United Kingdom, Germany and the USA; and whole genome shotgun sequencing from all cultivars, which was used to complement the RNA-sequencing data for variant calling. The outcomes are a filtered SNP marker file, a phenotypic database and a large gene expression dataset providing a comprehensive resource which allows for downstream analyses like genome wide association studies or expression associations.\n\nGenomic resources for a historical collection of cultivated two-row European spring barley genotypes", "token_count": 241, "char_count": 1112, "word_count": 161, "semantic_coherence": 1, "information_density": 0.646, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:25.892480", "source": { "split": "train_shard_00001", "doc_id": 2074 }, "chunk_id": "train_shard_00001_2074_0", "global_id": 8599 }, { "text": "Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition", "token_count": 496, "char_count": 1823, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:27.348775", "source": { "split": "train_shard_00001", "doc_id": 2075 }, "chunk_id": "train_shard_00001_2075_0", "global_id": 8600 }, { "text": "Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.\n\nPopulation genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer.", "token_count": 211, "char_count": 813, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7717, "quality_score": 0.8859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:27.807349", "source": { "split": "train_shard_00001", "doc_id": 2075 }, "chunk_id": "train_shard_00001_2075_1", "global_id": 8601 }, { "text": "The combined effect of simultaneous saccharification and fermentation and separate hydrolysis and fermentation (SHF) for ethanol production by Kluyveromyces marxianus 6556 was studied using two lignocellulosic feedstocks viz., corncob and soybean cake. The ethanologenic efficiency of K. marxianus 6556 was observed as 28% (theoretical yield) in a fermentation medium containing glucose, but, there was no ethanol production by cells grown on xylose. A maximum sugar release of 888 mg/g corncob and 552 mg/g soybean cake was achieved through acid hydrolysis pretreatment. Furthermore, corncob and soybean cake treated with commercial cellulase (100 IU for 48 h) from Trichoderma reesei yielded reducing sugars of 205 and 100 mg/g, respectively. Simultaneous saccharification and fermentation resulted in highest ethanol production of 5.68 g/l on corncob and 2.14 g/l on soybean cake after 48 h of incubation. On the contrary, the presence of inhibitors decreased the overall ethanol yield in the hydrolysates obtained through SHF of corncob and soybean cake.\n\nImproved bioethanol production through simultaneous saccharification and fermentation of lignocellulosic agricultural wastes by Kluyveromyces marxianus 6556", "token_count": 362, "char_count": 1216, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:28.381217", "source": { "split": "train_shard_00001", "doc_id": 2076 }, "chunk_id": "train_shard_00001_2076_0", "global_id": 8602 }, { "text": "Fungi produce a wealth of pharmacologically bioactive secondary metabolites (SMs) from biosynthetic gene clusters (BGCs). It is common practice for drug discovery efforts to treat species' secondary metabolomes as being well represented by a single or a small number of representative genomes. However, this approach misses the possibility that intraspecific population dynamics, such as adaptation to environmental conditions or local microbiomes, may harbor novel BGCs that contribute to the overall niche breadth of species. Using 94 isolates of Aspergillus flavus, a cosmopolitan model fungus, sampled from seven states in the United States, we dereplicate 7,821 BGCs into 92 unique BGCs. We find that more than 25% of pangenomic BGCs show population-specific patterns of presence/absence or protein divergence. Population-specific BGCs make up most of the accessory-genome BGCs, suggesting that different ecological forces that maintain accessory genomes may be partially mediated by population-specific differences in secondary metabolism. We use ultra-high-performance high-resolution mass spectrometry to confirm that these genetic differences in BGCs also result in chemotypic differences in SM production in different populations, which could mediate ecological interactions and be acted on by selection. Thus, our results suggest a paradigm shift that previously unrealized population-level reservoirs of SM diversity may be of significant evolutionary, ecological, and pharmacological importance. Last, we find that several population-specific BGCs from A. flavus are present in Aspergillus parasiticus and Aspergillus minisclerotigenes and discuss how the microevolutionary patterns we uncover inform macroevolutionary inferences and help to align fungal secondary metabolism with existing evolutionary theory.\n\nMicroevolution in the pansecondary metabolome of Aspergillus flavus and its potential macroevolutionary implications for filamentous fungi.", "token_count": 482, "char_count": 1999, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:29.028278", "source": { "split": "train_shard_00001", "doc_id": 2077 }, "chunk_id": "train_shard_00001_2077_0", "global_id": 8603 }, { "text": "

Background

Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering.

Results

This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM (P. vivax Peruvian AMazon). The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions.

Conclusions

Our findings show that the PvPAM reference genome more accurately represents South American P", "token_count": 508, "char_count": 1950, "word_count": 286, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:29.682168", "source": { "split": "train_shard_00001", "doc_id": 2078 }, "chunk_id": "train_shard_00001_2078_0", "global_id": 8604 }, { "text": "vivax isolates in comparison to PvP01 and PvW1. In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.\n\nA new Plasmodium vivax reference genome for South American isolates.", "token_count": 107, "char_count": 383, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7258, "quality_score": 0.8629, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:30.060402", "source": { "split": "train_shard_00001", "doc_id": 2078 }, "chunk_id": "train_shard_00001_2078_1", "global_id": 8605 }, { "text": "

Objectives

We describe the clonal spread of New Delhi metallo-β-lactamase (NDM) 1-producing Pseudomonas aeruginosa isolates belonging to the ST773 clone in Spain and the Netherlands, associated with the transfer of Ukrainian patients during the war.

Methods

Between March and December 2022, nine NDM-1-producing P. aeruginosa ST773 isolates were recovered from nine Ukrainian patients evacuated to two Spanish (n = 3) and five Dutch (n = 6) hospitals. Antimicrobial susceptibility testing was studied (Sensititre, Microscan, EUCAST-2023). Whole genome sequencing (Illumina, Oxford-Nanopore) was used to analyze the genetic relatedness, the resistome, and the prophage content.

Results

All NDM-1-producing P. aeruginosa ST773 isolates exhibited resistance to all tested antimicrobials except colistin, aztreonam, and cefiderocol. Genomic analysis revealed that all isolates had an identical resistome and a chromosomally encoded integrative conjugative element carrying the bla NDM-1 gene. The core genome multilocus sequence typing and core genome single nucleotide polymorphisms analysis showed highly related isolates, irrespective of country of isolation, distant from other NDM-1-ST773 P. aeruginosa not collected in Ukraine. Both analysis revealed two closely related clusters, spanning the Spanish and Dutch isolates. In addition, a high content of prophages was identified in all strains, most of them in more than one isolate simultaneously, regardless of their origin country. Moreover, an identical phage tail-like bacteriocin cluster was identified in all NDM-1-ST773 P. aeruginosa.

Conclusions

We report a clonal dissemination of NDM-producing P", "token_count": 519, "char_count": 1756, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [ "ST773" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:19:30.690982", "source": { "split": "train_shard_00001", "doc_id": 2079 }, "chunk_id": "train_shard_00001_2079_0", "global_id": 8606 }, { "text": "aeruginosa ST773 to the Netherlands and Spain associated with patients from Ukraine. Our work highlights the importance of genomic surveillance and to understand the dynamics of resistance in multidrug-resistant bacteria after the transfer of patients from conflict zones. International collaboration is crucial to address global antimicrobial resistance.\n\nSimultaneous clonal spread of NDM-1-producing Pseudomonas aeruginosa ST773 from Ukrainian patients in the Netherlands and Spain.", "token_count": 111, "char_count": 496, "word_count": 63, "semantic_coherence": 1, "information_density": 0.6984, "quality_score": 0.8492, "entities": { "genes": [ "ST773" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:31.075252", "source": { "split": "train_shard_00001", "doc_id": 2079 }, "chunk_id": "train_shard_00001_2079_1", "global_id": 8607 }, { "text": "Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.\n\nFunctional host-specific adaptation of the intestinal microbiome in hominids.", "token_count": 334, "char_count": 1579, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:31.642650", "source": { "split": "train_shard_00001", "doc_id": 2080 }, "chunk_id": "train_shard_00001_2080_0", "global_id": 8608 }, { "text": "Abstract

Background: Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species characterized by specific repeat-rich genome compartments with exceptionally high sequence variability. Dynamic genome structure may enable fast adaptation to host genetics. The wheat pathogen Zymoseptoria tritici with its highly variable genome, has emerged as a model organism to study genome evolution of plant pathogens. Here, we compared genomes of Z. tritici isolates and of sister species infecting wild grasses to address the evolution of genome composition and structure. Results: Using long-read technology, we sequenced and assembled genomes of Z. ardabiliae, Z. brevis, Z. pseudotritici and Z. passerinii, together with two isolates of Z. tritici. We report a high extent of genome collinearity among Zymoseptoria species and high conservation of genomic, transcriptomic and epigenomic signatures of compartmentalization. We identify high gene content variability both within and between species. In addition, such variability is mainly limited to the accessory chromosomes and accessory compartments. Despite strong host specificity and non-overlapping host-range between species, predicted effectors are mainly shared among Zymoseptoria species, yet exhibiting a high level of presence-absence polymorphism within Z. tritici. Using in planta transcriptomic data from Z. tritici, we suggest different roles for the shared orthologs and for the accessory genes during infection of their hosts. Conclusion: Despite previous reports of high genomic plasticity in Z", "token_count": 504, "char_count": 1969, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:32.300088", "source": { "split": "train_shard_00001", "doc_id": 2081 }, "chunk_id": "train_shard_00001_2081_0", "global_id": 8609 }, { "text": "tritici, we describe here a high level of conservation in genomic, epigenomic and transcriptomic composition and structure across the genus Zymoseptoria. The compartmentalized genome allows the maintenance of a functional core genome co-occurring with a highly variable accessory genome.

\n\nGenome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria", "token_count": 101, "char_count": 415, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:32.678140", "source": { "split": "train_shard_00001", "doc_id": 2081 }, "chunk_id": "train_shard_00001_2081_1", "global_id": 8610 }, { "text": "Investigating plant genomes offers crucial foundational resources for exploring various aspects of plant biology and applications, such as functional genomics and breeding practices. With the development in sequencing and assembly technology, several Nicotiana tabacum genomes have been published. In this paper, we reviewed the progress on N. tabacum genome assembly and quality, from the initial draft genomes to the recent high-quality chromosome-level assemblies. The application of long-read sequencing, optical mapping, and Hi-C technologies has significantly improved the contiguity and completeness of N. tabacum genome assemblies, with the latest assemblies having a contig N50 size over 50 Mb. Despite these advancements, further improvements are still required and possible, particularly on the development of pan-genome and telomere-to-telomere (T2T) genomes. These new genomes will capture the genomic diversity and variations among different N. tabacum cultivars and species, and provide a comprehensive view of the N. tabacum genome structure and gene content, so to deepen our understanding of the N. tabacum genome and facilitate precise breeding and functional genomics.\n\nRetrospect and prospect of Nicotiana tabacum genome sequencing.", "token_count": 328, "char_count": 1302, "word_count": 173, "semantic_coherence": 1, "information_density": 0.659, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:33.297217", "source": { "split": "train_shard_00001", "doc_id": 2082 }, "chunk_id": "train_shard_00001_2082_0", "global_id": 8611 }, { "text": "Corynebacterium ulcerans is an emerging zoonotic pathogen that belongs to the Corynebacterium diphtheriae (Cd) species complex (CdSC), and that causes diphtheria-like infections in humans. Our understanding of the transmission, phylogeography and evolution of C. ulcerans remains limited, in part due to the lack of a standardized genomic epidemiology toolkit. The aim of this work was to develop a core genome multi-locus sequence typing (cgMLST) scheme for high-resolution genotyping and classification of C. ulcerans strains, and to explore transmission, spatial spread and genomic evolution among 582 C. ulcerans isolates from sporadic clinical cases and reported case clusters. The cgMLST scheme combines 1,628 loci with highly reproducible allele calls and shows high strain subtyping resolution. We demonstrate its utility for capturing population structure by defining sublineages (SL, maximum 940 allele differences) and clonal groups (CG, 194 allele differences, AD) and for epidemiological surveillance by defining genetic clusters, i.e., previously undetected chains of transmission (25 AD). Genetic clusters correspond to cryptic and case clusters that were associated with specific geographical regions within France. Major C. ulcerans sublineages (SL325, SL331, SL339) and clonal groups (CG325, CG331, CG583) showed strong associations with diphtheria toxin variants and tox-carrying prophages or other genetic elements. The evolutionary dynamics of tox gene presence or absence varied sharply among clonal groups. The cgMLST scheme is publicly available ( https://bigsdb.pasteur.fr/diphtheria ) and provides a common framework for investigating the ecology, evolution and variations in virulence among C. ulcerans strains. The implementation of a standardized high-resolution genotyping method will also facilitate the tracing of C. ulcerans transmission and spread across hosts and from local to global spatial scales.", "token_count": 488, "char_count": 1935, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [ "SL325", "SL331", "SL339", "CG331", "CG583", "CG325" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:33.972646", "source": { "split": "train_shard_00001", "doc_id": 2083 }, "chunk_id": "train_shard_00001_2083_0", "global_id": 8612 }, { "text": "Genomic Epidemiology and Microevolution of the Zoonotic PathogenCorynebacterium ulcerans", "token_count": 32, "char_count": 95, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:34.352468", "source": { "split": "train_shard_00001", "doc_id": 2083 }, "chunk_id": "train_shard_00001_2083_1", "global_id": 8613 }, { "text": "In 2020, I wrote an mSphere of Influence commentary on two studies that shaped my research perspective on the human gut microbiome (McNulty et al., Sci Transl Med 3:106ra106, 2011, https://doi.org/10.1126/scitranslmed.3002701; Hamilton et al., Gut Microbes 4:125, 2013, https://doi.org/10.4161/gmic.23571). The microbiome field has continued to progress since the publication of these studies over 10 years ago, emerging as a considerable factor in almost all areas focused on disease development. My previous commentary highlighted two areas that piqued my interest early on in my career: (i) that the extant microbial community should be considered when proposing to manipulate the microbiota, such as via probiotics or fecal microbiota transplantation, and (ii) that realized (i.e., transcribed) functional changes of the microbiota may occur independent of changes in its composition. Since writing that commentary, two microbiota-based therapeutics for the treatment of Clostridioides difficile infection have been approved, highlighting the potential success of using the microbiota to treat or prevent disease. Despite these wins and ever-growing evidence of the importance of the microbiome in managing our health, translating mechanistic studies into therapeutic value has been slower. In this minireview, I expand upon two large questions that would increase our ability to translate the microbiome into therapies, highlighting both historical and recent progress.\n\nStraining to define a healthy microbiome.", "token_count": 400, "char_count": 1524, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:34.998195", "source": { "split": "train_shard_00001", "doc_id": 2084 }, "chunk_id": "train_shard_00001_2084_0", "global_id": 8614 }, { "text": "Abstract

Background: Pantoea ananatis is a member of a Pantoea spp. complex that causes center rot of onion, which significantly affects onion yield and quality. This pathogen does not have typical virulence factors like type II or type III secretion systems but appears to require a biosynthetic gene-cluster, HiVir/PASVIL (located chromosomally), for a phosphonate secondary metabolite, and the onion-virulence regions, OVR (localized on a megaplasmid), for onion pathogenicity and virulence, respectively. Results: We conducted a deep pan-genome-wide association study (pan-GWAS) to predict additional genes associated with pathogenicity in P. ananatis using a panel of diverse strains (n = 81). We utilized a red-onion scale necrosis assay as an indicator of pathogenicity. Based on this assay, we differentiated pathogenic (n = 51) - vs. non-pathogenic (n = 30)-strains phenotypically. Pan-GWAS revealed a large core genome of 3,153 genes and a flexible accessory genome of ≤5,065 genes. Phylogenomic analysis using pan-GWAS and presence and absence variants (PAVs) distinguished red-scale necrosis inducing (pathogenic) strains from non-scale necrosis inducing (non-pathogenic) strains of P. ananatis. The pan-GWAS also predicted 42 genes, including 14 from the previously identified HiVir/PASVIL cluster associated with pathogenicity, and 28 novel genes that were not previously associated with pathogenicity in onion", "token_count": 479, "char_count": 1588, "word_count": 200, "semantic_coherence": 1, "information_density": 0.715, "quality_score": 0.8575, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:35.653845", "source": { "split": "train_shard_00001", "doc_id": 2085 }, "chunk_id": "train_shard_00001_2085_0", "global_id": 8615 }, { "text": "Of the 28 novel genes identified, eight have annotated functions of site-specific tyrosine kinase, N-acetylmuramoyl-L-alanine amidase, TraR/DksA family transcriptional regulator, and HTH-type transcriptional regulator. The remaining 20 genes are currently hypothetical. Conclusions: This is the first report of using pan-GWAS on P. ananatis for the prediction of novel genes contributing to pathogenicity in onion, which will be utilized for further functional analyses. Pan-genomic differences (using PAVs) differentiated onion pathogenic from non-pathogenic strains of P. ananatis, which has been difficult to achieve using single or multiple gene-based phylogenetic analyses. The pan-genome analysis also allowed us to evaluate the presence and absence of HiVir/PASVIL genes and 11 megaplasmid-borne OVR-A genes regarded as the ‘alt’ cluster that aid in P. ananatis colonization in onion bulbs. We concluded that HiVir/PASVIL genes are associated with pathogenic P. ananatis strains and the alt gene cluster alone is not responsible for pathogenicity on onion. The pan-genome also provides clear evidence of constantly evolving accessory genes in P. ananatis that may contribute to host-range expansion and niche-adaptation.

\n\nPan-Genome-Wide Analysis of Pantoea Ananatis Identified Genes Linked to Pathogenicity in Onion", "token_count": 418, "char_count": 1459, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6464, "quality_score": 0.8232, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:36.279779", "source": { "split": "train_shard_00001", "doc_id": 2085 }, "chunk_id": "train_shard_00001_2085_1", "global_id": 8616 }, { "text": "Staphylococcus saprophyticus is a common pathogen of the urinary tract, a heavy metal-rich environment, but information regarding its heavy metal resistance is unknown. We investigated 422 S. saprophyticus isolates from human infection and colonization/contamination, animals, and environmental sources for resistance to copper, zinc, arsenic, and cadmium using the agar dilution method. To identify the genes associated with metal resistance and assess possible links to pathogenicity, we accessed the whole-genome sequence of all isolates and used in silico and pangenome-wide association approaches. The MIC values for copper and zinc were uniformly high (1,600 mg/liter). Genes encoding copper efflux pumps (copA, copB, copZ, mco, and csoR) and zinc transporters (zinT, czrAB, znuBC, and zur) were abundant in the population (20 to 100%). Arsenic and cadmium showed various susceptibility levels. Genes encoding the ars operon (arsRDABC), an ABC transporter and a two-component permease, were linked to resistance to arsenic (MICs ≥ 1,600 mg/liter; 14% [58/422]; P < 0.05). At least three cad genes (cadA or cadC and cadD-cadX or czrC) and genes encoding multidrug efflux pumps and hyperosmoregulation in acidified conditions were associated with resistance to cadmium (MICs ≥ 200 mg/liter; 20% [85/422]; P < 0.05). These resistance genes were frequently carried by mobile genetic elements", "token_count": 515, "char_count": 1491, "word_count": 203, "semantic_coherence": 1, "information_density": 0.67, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:19:36.937260", "source": { "split": "train_shard_00001", "doc_id": 2086 }, "chunk_id": "train_shard_00001_2086_0", "global_id": 8617 }, { "text": "Resistance to arsenic and cadmium were linked to human infection and a clonal lineage originating in animals (P < 0.05). Altogether, S. saprophyticus was highly resistant to heavy metals and accumulated multiple metal resistance determinants. The highest arsenic and cadmium resistance levels were associated with infection, suggesting resistance to these metals is relevant for S. saprophyticus pathogenicity.\n\nStaphylococcus saprophyticus Causing Infections in Humans Is Associated with High Resistance to Heavy Metals.", "token_count": 141, "char_count": 528, "word_count": 71, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:37.367269", "source": { "split": "train_shard_00001", "doc_id": 2086 }, "chunk_id": "train_shard_00001_2086_1", "global_id": 8618 }, { "text": "

Background

Efficient xylose alcoholic fermentation is one of the key to a successful lignocellulosic ethanol production. However, regulation of this process in the native xylose-fermenting yeasts is poorly understood. In this work, we paid attention to the transcriptional factor Cat8 and its possible role in xylose alcoholic fermentation in Ogataea (Hansenula) polymorpha. In Saccharomyces cerevisiae, organism, which does not metabolize xylose, gene CAT8 encodes a Zn-cluster transcriptional activator necessary for expression of genes involved in gluconeogenesis, respiration, glyoxylic cycle and ethanol utilization. Xylose is a carbon source that could be fermented to ethanol and simultaneously could be used in gluconeogenesis for hexose synthesis. This potentially suggests involvement of CAT8 in xylose metabolism.

Results

Here, the role of CAT8 homolog in the natural xylose-fermenting thermotolerant yeast O. polymorpha was characterized. The CAT8 ortholog was identified in O. polymorpha genome and deleted both in the wild-type strain and in advanced ethanol producer from xylose. Constructed cat8Δ strain isolated from wild strain showed diminished growth on glycerol, ethanol and xylose as well as diminished respiration on the last substrate. At the same time, cat8Δ mutant isolated from the best available O. polymorpha ethanol producer showed only visible defect in growth on ethanol. CAT8 deletant was characterized by activated transcription of genes XYL3, DAS1 and RPE1 and slight increase in the activity of several enzymes involved in xylose metabolism and alcoholic fermentation. Ethanol production from xylose in cat8Δ mutants in the background of wild-type strain and the best available ethanol producer from xylose increased for 50 and 30%, respectively. The maximal titer of ethanol during xylose fermentation was 12.5 g ethanol/L at 45 °C", "token_count": 511, "char_count": 1883, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5581, "quality_score": 0.779, "entities": { "genes": [ "CAT8", "DAS1", "XYL3", "RPE1" ], "proteins": [], "pathways": [ "metabolism", "fermentation", "respiration" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:37.997299", "source": { "split": "train_shard_00001", "doc_id": 2087 }, "chunk_id": "train_shard_00001_2087_0", "global_id": 8619 }, { "text": "Deletion of CAT8 did not change ethanol production from glucose. Gene CAT8 was also overexpressed under control of the strong constitutive promoter GAP of glyceraldehyde-3-phosphate dehydrogenase. Corresponding strains showed drop in ethanol production in xylose medium whereas glucose alcoholic fermentation remained unchanged. Available data suggest on specific role of Cat8 in xylose alcoholic fermentation.

Conclusions

The CAT8 gene is one of the first identified genes specifically involved in regulation of xylose alcoholic fermentation in the natural xylose-fermenting yeast O. polymorpha.\n\nTranscriptional activator Cat8 is involved in regulation of xylose alcoholic fermentation in the thermotolerant yeast Ogataea (Hansenula) polymorpha.", "token_count": 207, "char_count": 754, "word_count": 96, "semantic_coherence": 1, "information_density": 0.6354, "quality_score": 0.8177, "entities": { "genes": [ "CAT8" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:38.463687", "source": { "split": "train_shard_00001", "doc_id": 2087 }, "chunk_id": "train_shard_00001_2087_1", "global_id": 8620 }, { "text": "

Background

Structural variants (SVs) play important roles in adaptation evolution and species diversification. Especially, in plants, many phenotypes of response to the environment were found to be associated with SVs. Despite the prevalence and significance of SVs, long insertions remain poorly detected and studied in all but model species.

Results

We used whole-genome resequencing of paired reads from 80 Asian butternuts to detect long insertions and further analyse their characteristics and potential functional effects. By combining of mapping-based and de novo assembly-based methods, we obtained a multiple related species pangenome representing higher taxonomic groups. We obtained 89,312 distinct contigs totaling 147,773,999 base pair (bp) of new sequences, of which 347 were putative long insertions placed in the reference genome. Most of the putative long insertions appeared in multiple species; in contrast, only 62 putative long insertions appeared in one species, which may be involved in the response to the environment. 65 putative long insertions fell into 61 distinct protein-coding genes involved in plant development, and 105 putative long insertions fell into upstream of 106 distinct protein-coding genes involved in cellular respiration. 3,367 genes were annotated in 2,606 contigs. We propose PLAINS ( https://github.com/CMB-BNU/PLAINS.git ), a streamlined, comprehensive pipeline for the prediction and analysis of long insertions using whole-genome resequencing.

Conclusions

Our study lays down an important foundation for further whole-genome long insertion studies, allowing the investigation of their effects by experiments.\n\nCharacteristics and potential functional effects of long insertions in Asian butternuts.", "token_count": 427, "char_count": 1772, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6076, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:39.085597", "source": { "split": "train_shard_00001", "doc_id": 2088 }, "chunk_id": "train_shard_00001_2088_0", "global_id": 8621 }, { "text": "Four Gram-stain-negative bacterial strains, CS20T, AUT15.5T, XENO-11T, and CCN3.3T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel species within the genus Xenorhabdus (Gammaproteobacteria, Morganellaceae). In this study, we described these new species using whole-genome phylogenomic reconstructions, sequence identity values from core genome sequences, and phenotypic characterization. Phylogenetic reconstructions based on 16S rRNA gene sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T, (ii) strain AUT15.5T is closely related to X. budapestensis DSM 16342T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The 16S rRNA gene sequence similarity value between strain CS20T and X. stockiae DSM 17904T is 97.8%, between strain AUT15.5T and X. budapestensis DSM 16342T is 98.1%, between strain XENO-11T and X. khoisanae DSM 25463T is 97.8%, and between strain CCN3.3T and X. griffiniae DSM 17911T is 98.6%", "token_count": 510, "char_count": 1290, "word_count": 151, "semantic_coherence": 1, "information_density": 0.5762, "quality_score": 0.7881, "entities": { "genes": [ "AUT15", "CS20", "CCN3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:39.734224", "source": { "split": "train_shard_00001", "doc_id": 2089 }, "chunk_id": "train_shard_00001_2089_0", "global_id": 8622 }, { "text": "Phylogenomic reconstructions using whole-genome sequences showed that: (i) strain CS20T is closely related to X. stockiae DSM 17904T and X. innexi DSM 16336T, (ii) strain AUT15.5T is closely related to X. indica DSM 17382T, (iii) strain XENO-11T is closely related to X. khoisanae DSM 25463T, and (iv) strain CCN3.3T is closely related to X. griffiniae DSM 17911T. The digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values between strains CS20T, AUT15.5T, XENO-11T, and CCN3.3T and the type strains of their more closely related species are below the 70% and the 95-96% divergence thresholds, respectively, used for prokaryotic species delineation. Hence, we propose the following four new species: Xenorhabdus bharatensis sp. nov. (the type strain is CS20T=CCM 9320T=CCOS 2070T), X. entomophaga sp. nov. (the type strain is XENO-11T=CCM 9389T=CCOS 2111T), X. siamensis sp. nov. (the type strain is AUT15.5T=CCM 9405T=CCOS 2116T), and X. thailandensis sp. nov", "token_count": 511, "char_count": 1229, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [ "AUT15", "CS20", "CCN3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:40.388818", "source": { "split": "train_shard_00001", "doc_id": 2089 }, "chunk_id": "train_shard_00001_2089_1", "global_id": 8623 }, { "text": "(the type strain is CCN3.3T=CCM 9406T=CCOS 2115T). The following biochemical tests may be useful for differentiating the novel species from their more closely related taxa: acetoin production, arginine dihydrolase, citrate utilization, gelatinase, glucose oxidation, indole production, and tryptophan deaminase. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.\n\nXenorhabdus bharatensis sp. nov., Xenorhabdus entomophaga sp. nov., Xenorhabdus siamensis sp. nov., and Xenorhabdus thailandensis sp. nov. Isolated from Steinernema Entomopathogenic Nematodes.", "token_count": 226, "char_count": 710, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7927, "quality_score": 0.8963, "entities": { "genes": [ "CCN3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:40.853529", "source": { "split": "train_shard_00001", "doc_id": 2089 }, "chunk_id": "train_shard_00001_2089_2", "global_id": 8624 }, { "text": "RESEARCH HIGHLIGHTSPan-RV analysis was used for the first time in the discovery of APEC-protective proteins.A total of 53 potential protective proteins were screened out.Four proteins were verified as potential vaccine candidates using western blotting.\n\nCombining pangenome analysis to identify potential cross-protective antigens against avian pathogenic Escherichia coli.", "token_count": 101, "char_count": 381, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:41.234175", "source": { "split": "train_shard_00001", "doc_id": 2090 }, "chunk_id": "train_shard_00001_2090_0", "global_id": 8625 }, { "text": "Clostridium botulinum Group I and Clostridium sporogenes are closely related bacteria responsible for foodborne, infant and wound botulism. A comparative genomic study with 556 highly diverse strains of C. botulinum Group I and C. sporogenes (including 417 newly sequenced strains) has been carried out to characterise the genetic diversity and spread of these bacteria and their neurotoxin genes. Core genome single-nucleotide polymorphism (SNP) analysis revealed two major lineages; C. botulinum Group I (most strains possessed botulinum neurotoxin gene(s) of types A, B and/or F) and C. sporogenes (some strains possessed a type B botulinum neurotoxin gene). Both lineages contained strains responsible for foodborne, infant and wound botulism. A new C. sporogenes cluster was identified that included five strains with a gene encoding botulinum neurotoxin sub-type B1. There was significant evidence of horizontal transfer of botulinum neurotoxin genes between distantly related bacteria. Population structure/diversity have been characterised, and novel associations discovered between whole genome lineage, botulinum neurotoxin sub-type variant, epidemiological links to foodborne, infant and wound botulism, and geographic origin. The impact of genomic and physiological variability on the botulism risk has been assessed. The genome sequences are a valuable resource for future research (e.g., pathogen biology, evolution of C. botulinum and its neurotoxin genes, improved pathogen detection and discrimination), and support enhanced risk assessments and the prevention of botulism.", "token_count": 436, "char_count": 1646, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:41.867001", "source": { "split": "train_shard_00001", "doc_id": 2091 }, "chunk_id": "train_shard_00001_2091_0", "global_id": 8626 }, { "text": "Diversity of the Genomes and Neurotoxins of Strains of <i>Clostridium botulinum</i> Group I and <i>Clostridium sporogenes</i> Associated with Foodborne, Infant and Wound Botulism.", "token_count": 78, "char_count": 203, "word_count": 23, "semantic_coherence": 1, "information_density": 0.7826, "quality_score": 0.8913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:42.235929", "source": { "split": "train_shard_00001", "doc_id": 2091 }, "chunk_id": "train_shard_00001_2091_1", "global_id": 8627 }, { "text": "Bacterial genomes exhibit widespread horizontal gene transfer, resulting in highly variable genome content that complicates the inference of genetic interactions. In this study, we develop a method for detecting coevolving genes from large datasets of bacterial genomes that we call a “coevolution score”. The method is based on pairwise comparisons of closely related individuals, analogous to a pedigree study in eukaryotic populations. This approach avoids the need for an accurate phylogenetic tree and allows very large datasets to be analyzed for signatures of recent coevolution. We apply our method to all of the more than 3 million pairs of genes from the entire annotated Staphylococcus aureus accessory genome of 2,756 annotated genes using a database of over 40,000 whole genomes. We find many pairs of genes that that appear to be gained or lost in a coordinated manner, as well as pairs where the gain of one gene is associated with the loss of the other. These pairs form networks of dozens of rapidly coevolving genes, primarily consisting of genes involved in metal resistance, virulence, mechanisms of horizontal gene transfer, and antibiotic resistance, particularly the SCC mec complex. Our results reflect the fact that the evolution of many bacterial pathogens since the middle of the twentieth century has largely been driven by antibiotic resistance gene gain, and in the case of S. aureus the SCC mec complex is the most prominent of these elements driving the evolution of resistance. The frequent coincidence of these gene gain or loss events suggests that S. aureus switch between antibiotic-resistant niches and antibiotic-susceptible ones. While we focus on gene gain and loss, our method can also detect genes which tend to acquire substitutions in tandem or, in datasets that include phenotypic information, genotype-phenotype or phenotype-phenotype coevolution.\n\nDetecting patterns of accessory genome coevolution in bacterial species using data from thousands of bacterial genomes", "token_count": 452, "char_count": 2014, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:42.874962", "source": { "split": "train_shard_00001", "doc_id": 2092 }, "chunk_id": "train_shard_00001_2092_0", "global_id": 8628 }, { "text": "

Background

The hospital-adapted A1 group of Enterococcus faecium remains an organism of significant concern in the context of drug-resistant hospital-associated infections. How this pathogen evolves and disseminates remains poorly understood.

Methods

A large, globally representative collection of short-read genomic data from the hospital-associated A1 group of Enterococcus faecium was assembled (n = 973). We analysed, using a novel analysis approach, global diversity in terms of both the dynamics of the accessory genome and homologous recombination among conserved genes.

Results

Two main modes of genomic evolution continue to shape E. faecium: the acquisition and loss of genes, including antimicrobial resistance genes, through mobile genetic elements including plasmids, and homologous recombination of the core genome. These events lead to new clones emerging at the local level, followed by the erosion of signals of clonality through recombination, and in some identifiable cases producing new clonal clusters. These patterns lead to new, emerging lineages which are able to spread globally over relatively short timeframes.

Conclusions

The ability of A1 E. faecium to continually present new combinations of genes for potential selection suggests that controlling this pathogen will remain challenging but establishing a framework for understanding genomic evolution is likely to aid in tracking the threats posed by newly emerging lineages.\n\nThe global dissemination of hospital clones of Enterococcus faecium.", "token_count": 360, "char_count": 1554, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:43.449340", "source": { "split": "train_shard_00001", "doc_id": 2093 }, "chunk_id": "train_shard_00001_2093_0", "global_id": 8629 }, { "text": "This comprehensive review explores the potential of using lactobacilli as a probiotic in the management of COVID-19. Our findings suggest that lactobacilli show promise in reducing the risk of death, gastrointestinal and overall symptoms, and respiratory failure, as well as in lowering cytokines and inflammatory markers associated with the disease. The molecular mechanisms by which lactobacilli protect against COVID-19 and other viral infections may be related to the reduction in inflammation, modulation of the immune response, and direct interaction with viruses to produce antiviral substances. However, the selected studies demonstrate the presence of mixed findings for various clinical, biochemical, hematological, and immunological parameters, which may be attributed to methodological differences among studies. We highlight the importance of clearly describing randomization processes to minimize bias and caution against small sample sizes and inappropriate statistical tests that could lead to errors. This review offers valuable insights into the therapeutic potential of lactobacilli in the context of COVID-19 and identifies avenues for further research and applications. These findings hold promise for the development of novel approaches to managing COVID-19 and warrant further investigation into the potential benefits of lactobacilli in combating the disease.\n\nThe Influence of Probiotic Lactobacilli on COVID-19 and the Microbiota.", "token_count": 314, "char_count": 1456, "word_count": 200, "semantic_coherence": 1, "information_density": 0.62, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:44.006394", "source": { "split": "train_shard_00001", "doc_id": 2094 }, "chunk_id": "train_shard_00001_2094_0", "global_id": 8630 }, { "text": "

Motivation

With the fast development of sequencing technology, accurate de novo genome assembly is now possible even for larger genomes. Graph-based representations of genomes arise both as part of the assembly process, but also in the context of pangenomes representing a population. In both cases, polymorphic loci lead to bubble structures in such graphs. Detecting bubbles is hence an important task when working with genomic variants in the context of genome graphs.

Results

Here, we present a fast general-purpose tool, called BubbleGun, for detecting bubbles and superbubbles in genome graphs. Furthermore, BubbleGun detects and outputs runs of linearly connected bubbles and superbubbles, which we call bubble chains. We showcase its utility on de Bruijn graphs and compare our results to vg's snarl detection. We show that BubbleGun is considerably faster than vg especially in bigger graphs, where it reports all bubbles in less than 30 min on a human sample de Bruijn graph of around 2 million nodes.

Availability and implementation

BubbleGun is available and documented as a Python3 package at https://github.com/fawaz-dabbaghieh/bubble_gun under MIT license.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nBubbleGun: enumerating bubbles and superbubbles in genome graphs.", "token_count": 344, "char_count": 1352, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6865, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:44.575325", "source": { "split": "train_shard_00001", "doc_id": 2095 }, "chunk_id": "train_shard_00001_2095_0", "global_id": 8631 }, { "text": "The recent years have seen the rise of pangenomes as comparative genomic tools to better understand the evolution of gene content among microbial genomes in close phylogenetic groups such as species. While the core or persistent genome is often well-known as it includes essential or ubiquitous genes, the variable genome is usually less characterized and includes many genes with unknown functions even among the most studied organisms. It gathers important genes for strain adaptation that are acquired by horizontal gene transfer. Here, we introduce panModule, an original method to identify conserved modules in pangenome graphs built from thousands of microbial genomes. These modules correspond to synteny blocks composed of consecutive genes that are conserved in a subset of the compared strains. Identifying conserved modules can provide insights on genes involved in the same functional processes, and as such is a very helpful tool to facilitate the understanding of genomic regions with complex evolutionary histories. The panModule method was benchmarked on a curated dataset of conserved modules in Escherichia coli genomes. Its use was illustrated through a study of a high pathogenicity island in Klebsiella pneumoniae that allowed a better understanding of this region. panModule is freely available and accessible through the PPanGGOLiN software suite ( https://github.com/labgem/PPanGGOLiN ).\n\npanModule: detecting conserved modules in the variable regions of a pangenome graph", "token_count": 313, "char_count": 1496, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:45.139883", "source": { "split": "train_shard_00001", "doc_id": 2096 }, "chunk_id": "train_shard_00001_2096_0", "global_id": 8632 }, { "text": "

Unlabelled

Four samples of Tibetan kefir grains (TK-ZJUJ 01-04) from Tibet and surrounding areas were investigated via phenotypic and genotypic methods to compare and analyze the diversity of culturable microflora among different origins. As a result, 4 genera of microorganisms from TK-ZJUJ01: Bacillus subtilis (2.9 × 10(7) cfu/mL), Lactococcus lactis (8.2 × 10(7) cfu/mL), Kluyveromyces marxianus (3.0 × 10(6) cfu/mL), Saccharomyces cerevisiae (9.0 × 10(6) cfu/mL); 4 genera from TK-ZJUJ02: Lactobacillus kefiri (1.0 × 10(8) cfu/mL), Pichia kudriavzevii (5.0 × 10(6) cfu/mL), K. marxianus (1.9 × 10(7) cfu/mL), Kazachstania unispora (6.2 × 10(7) cfu/mL); 6 genera from TK-ZJUJ03: Leuconostoc lactis (4.6 × 10(7) cfu/mL), L. lactis (3.0 × 10(7) cfu/mL), Lactobacillus plantarum (3.0 × 10(7) cfu/mL), K. unispora (3.0 × 10(6) cfu/mL), K. marxianus (2.0 × 10(6) cfu/mL), (1.7 × 10(7) cfu/mL); and 4 genera from TK-ZJUJ04: L", "token_count": 478, "char_count": 931, "word_count": 137, "semantic_coherence": 1, "information_density": 0.5547, "quality_score": 0.7774, "entities": { "genes": [ "ZJUJ02", "ZJUJ04", "ZJUJ01", "ZJUJ03" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:45.813231", "source": { "split": "train_shard_00001", "doc_id": 2097 }, "chunk_id": "train_shard_00001_2097_0", "global_id": 8633 }, { "text": "plantarum (1.8 × 10(7) cfu/mL), Acetobacter fabarum (5.0 × 10(6) cfu/mL), K. unispora (6.2 × 10(7) cfu/mL), Pichia guilliermondii (6.2 × 10(7) cfu/mL) were identified. Yeasts like P. kudriavzevii and P. guilliermondii isolated in this study were the first time reported in Tibetan kefir grains. For TK-ZJUJ 01-03, lactic acid bacteria were the major microorganisms, which accounted for more than 50% of all the microbial population, while for TK-ZJUJ04, the largest microbial group was yeasts which accounted for more than 50%. In a word, study of diversity and composition of microflora provided us theoretical foundation for further investigation and application of Tibetan kefir grains.

Practical application

This is the basic research in order to develop and industrialize a new kind of yogurt starter which is naturally formed microbiota with both lactic acid bacteria and yeasts in it.\n\nInvestigation on culturable microflora in Tibetan kefir grains from different areas of China.", "token_count": 315, "char_count": 993, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8176, "entities": { "genes": [ "ZJUJ04" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:46.387658", "source": { "split": "train_shard_00001", "doc_id": 2097 }, "chunk_id": "train_shard_00001_2097_1", "global_id": 8634 }, { "text": "Abstract

Background Species of the genus Vibrio, one of the most diverse bacteria genera, have undergone niche adaptation followed by clonal expansion. Niche adaptation and ultimately the formation of ecotypes and speciation in this genus has been suggested to be mainly driven by horizontal gene transfer (HGT) through mobile genetic elements (MGEs). Our knowledge about the diversity and distribution of Vibrio MGEs is heavily biased towards human pathogens and our understanding of the distribution of core genomic signatures and accessory genes encoded on MGEs within specific Vibrio clades is still incomplete. We used nine different strains of the marine bacterium Vibrio alginolyticus isolated from pipefish in the Kiel-Fjord to perform a multiscale-comparative genomic approach that allowed us to investigate (1) those genomic signatures that characterize a habitat-specific ecotype and (2) the source of genomic variation within this ecotype.Results We found that the nine isolates from the Kiel-Fjord have a closed-pangenome and did not differ based on core-genomic signatures. Unique genomic regions and a unique repertoire of MGEs within the Kiel-Fjord isolates suggest that the acquisition of gene-blocks by HGT played an important role in the evolution of this ecotype. Additionally, we found that ~90% of the genomic variation among the nine isolates is encoded on MGEs, which supports ongoing theory that accessory genes are predominately located on MGEs and shared by HGT. Lastly, we could show that these nine isolates share a unique virulence and resistance profile which clearly separates them from all other investigated V. alginolyticus strains and suggests that these are habitat-specific genes, required for a successful colonization of the pipefish, the niche of this ecotype. Conclusion We conclude that all nine V", "token_count": 486, "char_count": 1991, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5818, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:47.079546", "source": { "split": "train_shard_00001", "doc_id": 2098 }, "chunk_id": "train_shard_00001_2098_0", "global_id": 8635 }, { "text": "alginolyticus strains from the Kiel-Fjord belong to a unique ecotype, which we named the Kiel-alginolyticus ecotype. The low sequence variation of the core-genome in combination with the presence of MGE encoded relevant traits, as well as the presence of a suitable niche (here the pipefish), suggest, that this ecotype might have evolved from a clonal expansion following HGT driven niche-adaptation.

\n\nGenomic variation among closely related Vibrio alginolyticus strains is located on mobile genetic elements", "token_count": 140, "char_count": 539, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7973, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:47.505944", "source": { "split": "train_shard_00001", "doc_id": 2098 }, "chunk_id": "train_shard_00001_2098_1", "global_id": 8636 }, { "text": "Multipartite bacteria have one chromosome and one or more chromid. Chromids are believed to have properties that enhance genomic flexibility, making them a favored integration site for new genes. However, the mechanism by which chromosomes and chromids jointly contribute to this flexibility is not clear. To shed light on this, we analyzed the openness of chromosomes and chromids of the two bacteria, Vibrio and Pseudoalteromonas, both in the Enterobacterales order of gamma-proteobacteria, and compared it with monopartite genomes in the same order. We applied pangenome analysis, codon usage analysis and the HGTector software to detect horizontally transferred genes. Our findings suggest that the chromids of Vibrio and Pseudoalteromonas likely originated from two separate plasmid acquisition events. Bipartite genomes were found to be more open compared to monopartite. We found that the shell and cloud pangene categories drive the openness of bipartite genomes in Vibrio and Pseudoalteromonas. Based on this and our two recent studies, we propose a hypothesis that explains how chromids and the chromosome terminus region contribute to the genomic plasticity of bipartite genomes.\n\nBipartite Genomes in Enterobacterales: Independent Origins of Chromids, Elevated Openness and Donors of Horizontally Transferred Genes", "token_count": 313, "char_count": 1326, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6073, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:48.063225", "source": { "split": "train_shard_00001", "doc_id": 2099 }, "chunk_id": "train_shard_00001_2099_0", "global_id": 8637 }, { "text": "

Background

Most of the extraintestinal human infections worldwide are caused by specific extraintestinal pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, a high-risk globally disseminated ExPEC. To get insights on the aspects of the global ST38 epidemiology and evolution as a multidrug-resistant and pathogenic lineage concerning the three axes of the One Health concept (humans, animals, and natural environments), this study performed a global phylogenomic analysis on ST38 genomes.

Methods

A phylogenetic reconstruction based on 376 ST38 genomes recovered from environments, humans, livestock, and wild and domestic animals in all continents throughout three decades was performed. The global information concerning the ST38 resistome and virulome was also approached by in silico analyses.

Results

In general, the phylogenomic analyses corroborated the zoonotic character of the ExPEC ST38, since clonal strains were recovered from both animal and human sources distributed worldwide. Moreover, our findings revealed that, independent of host sources and geographic origin, the genomes were distributed in two major clades (Clades 1 and 2). However, the ST38 accessory genome was not strictly associated with clades and sub-clades, as found for the type 2 T3SS ETT2 that was evenly distributed throughout Clades 1 and 2. Of note was the presence of the Yersinia pestis-like high-pathogenicity island (HPI) exclusively in the major Clade 2, in which prevails most of the genomes from human origin recovered worldwide (2000 to 2020).

Conclusions

This evidence corroborates the HPI association with successful E. coli ST38 establishment in human infections.", "token_count": 477, "char_count": 1786, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [ "ETT2", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:48.708066", "source": { "split": "train_shard_00001", "doc_id": 2100 }, "chunk_id": "train_shard_00001_2100_0", "global_id": 8638 }, { "text": "Global Genomic Epidemiology of Escherichia coli (ExPEC) ST38 Lineage Revealed a Virulome Associated with Human Infections.", "token_count": 45, "char_count": 129, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:49.072322", "source": { "split": "train_shard_00001", "doc_id": 2100 }, "chunk_id": "train_shard_00001_2100_1", "global_id": 8639 }, { "text": "

Objectives

Enterococcus faecium is a common cause of hospital-acquired infections and is associated with vancomycin resistance. The hospital environment is often a reservoir for E. faecium due to its ability to survive on surfaces. In 2019 we noted increasing prevalence of vanA E. faecium causing bloodstream infections. We aimed to assess the hospital environment as a reservoir of vanA E. faecium .

Methods

We conducted a point prevalence survey of the environment at the Alfred Hospital, Melbourne, Australia. We sampled all wards (n=12), 10 surface types and 357 surfaces. Resulting E. faecium isolates underwent short-read whole genome sequencing and were compared to invasive infection (bloodstream) isolates. The van operon, multi-locus sequence type (MLST) and core genome MLST (cgMLST) were determined.

Results

Twenty percent (73/357) of surfaces isolated E. faecium with a median of 20% positivity per ward (IQR 11.6-30.6%). vanA and vanB were detected in 12/73 (16%) and 58/73 (79%) environmental genomes, respectively. In contrast, a higher proportion of bloodstream isolates carried vanA (32/72 [44%], P <0.001). Environmental genomes belonged to 10 MLSTs and 10 cgMLSTs, with ST796/ST78 accounting for 54/73 (74%) genomes. Clinical STs and cgMLSTs overlapped with environmental but were more diverse. We noted 13 putative genomic transmission clusters. One cluster contained 25/44 (57%) vanA genomes, with the majority being clinical (22/26 genomes, 85%). Environmental-clinical links were observed in 292/895 (33%) putative genomic transmission links. In completed assemblies, the vanA and vanB operons were located on pRE25-like plasmids and the chromosome, respectively", "token_count": 520, "char_count": 1714, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [ "ST78", "ST796" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:19:50.088562", "source": { "split": "train_shard_00001", "doc_id": 2101 }, "chunk_id": "train_shard_00001_2101_0", "global_id": 8640 }, { "text": "

Conclusion

We noted a 20% prevalence of E. faecium environmental colonisation but the vanA operon was detected in only 12/73 genomes. We identified distinct environmental and patient reservoirs, with most environmental genomes carrying the vanB operon and having distinct STs/cgMLST clusters. Environment-clinical reservoir spillover was detected but accounted for a minority of putative transmission links.\n\nHospitalEnterococcus faeciumdemonstrates distinct environmental and patient reservoirs: a genomic point prevalence survey", "token_count": 137, "char_count": 546, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:50.512059", "source": { "split": "train_shard_00001", "doc_id": 2101 }, "chunk_id": "train_shard_00001_2101_1", "global_id": 8641 }, { "text": "

Aims

To study fuel ethanol fermentation with Kluyveromyces marxianus ATCC8554 from Jerusalem artichoke (Helianthus tuberosus) grown in salina and irrigated with a mixture of seawater and freshwater.

Methods and results

The growth and ethanol fermentation of K. marxianus ATCC8554 were studied using inulin as substrate. The activity of inulinase, which attributes to the hydrolysis of inulin, the main carbohydrate in Jerusalem artichoke, was monitored. The optimum temperatures were 38 degrees C for growth and inulinase production, and 35 degrees C for ethanol fermentation. Aeration was not necessary for ethanol fermentation with the K. marxianus from inulin. Then, the fresh Jerusalem artichoke tubers grown in salina and irrigated with 25% and 50% seawater were further examined for ethanol fermentation with the K. marxianus, and a higher ethanol yield was achieved for the Jerusalem artichoke tuber irrigated with 25% seawater. Furthermore, the dry meal of the Jerusalem artichoke tubers irrigated with 25% seawater was examined for ethanol fermentation at three solid concentrations of 200, 225 and 250 g l(-1), and the highest ethanol yield of 0.467, or 91.5% of the theoretical value of 0.511, was achieved for the slurry with a solid concentration of 200 g l(-1).

Conclusions

Halophilic Jerusalem artichoke can be used for fuel ethanol production.

Significance and impact of the study

Halophilic Jerusalem artichoke, not competing with grain crops for arable land, is a sustainable feedstock for fuel ethanol production.\n\nEthanol fermentation with Kluyveromyces marxianus from Jerusalem artichoke grown in salina and irrigated with a mixture of seawater and freshwater.", "token_count": 511, "char_count": 1710, "word_count": 244, "semantic_coherence": 1, "information_density": 0.459, "quality_score": 0.7295, "entities": { "genes": [ "ATCC8554" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:51.149782", "source": { "split": "train_shard_00001", "doc_id": 2102 }, "chunk_id": "train_shard_00001_2102_0", "global_id": 8642 }, { "text": "In some parts of the world, Corynebacterium diphtheriae has reemerged as a pathogen, especially as a cause of infections among impoverished and marginalized populations. We performed whole-genome sequencing (WGS) on all cutaneous C. diphtheriae isolates (n = 56) from Vancouver's inner-city population over a 3-year time period (2015 to 2018). All isolates with complete genome assembly were toxin negative, contained a common set of 22 virulence factors, and shared a highly conserved accessory genome. One of our isolates harbored a novel plasmid conferring macrolide and lincosamide resistance. Fifty-two out of 56 isolates were multilocus sequence type 76, and single nucleotide variants (SNV) and core-genome multilocus sequence typing (cgMLST) analysis demonstrated tight clustering of our isolates relative to all publicly available C. diphtheriae genomes. All sequence type 76 (ST76) study isolates were within a median of 22 SNVs and 13 cgMLST alleles of each other, while NCBI genomes were within a median of 17,436 SNVs and 1,552 cgMLST alleles of each other (both P < 2.2 × 10-16). A single strain of C. diphtheriae appears to be causing cutaneous infections in the low-income population of Vancouver. Further research is needed to elucidate transmission networks in our study population and standardize C. diphtheriae epidemiological typing when whole genomes are sequenced.\n\nWhole-Genome Sequencing of Corynebacterium diphtheriae Isolates Recovered from an Inner-City Population Demonstrates the Predominance of a Single Molecular Strain.", "token_count": 512, "char_count": 1612, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6344, "quality_score": 0.8172, "entities": { "genes": [ "ST76" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:51.786784", "source": { "split": "train_shard_00001", "doc_id": 2103 }, "chunk_id": "train_shard_00001_2103_0", "global_id": 8643 }, { "text": "

Background

Chickens and ducks are vital sources of animal protein for humans. Recent pangenome studies suggest that a single genome is insufficient to represent the genetic information of a species, highlighting the need for more comprehensive genomes. The bird genome has more than tens of microchromosomes, but comparative genomics, annotations, and the discovery of variations are hindered by inadequate telomere-to-telomere level assemblies. We aim to complete the chicken and duck genomes, recover missing genes, and reveal common and unique chromosomal features between birds.

Results

The near telomere-to-telomere genomes of Silkie Gallus gallus and Mallard Anas platyrhynchos were successfully assembled via multiple high-coverage complementary technologies, with quality values of 36.65 and 44.17 for Silkie and Mallard, respectively; and BUSCO scores of 96.55% and 96.97% for Silkie and Mallard, respectively; the mapping rates reached over 99.52% for both assembled genomes, these evaluation results ensured high completeness and accuracy. We successfully annotated 20,253 and 19,621 protein-coding genes for Silkie and Mallard, respectively, and assembled gap-free sex chromosomes in Mallard for the first time. Comparative analysis revealed that microchromosomes differ from macrochromosomes in terms of GC content, repetitive sequence abundance, gene density, and levels of 5mC methylation. Different types of arrangements of centromeric repeat sequence centromeres exist in both Silkie and the Mallard genomes, with Mallard centromeres being invaded by CR1. The highly heterochromatic W chromosome, which serves as a refuge for ERVs, contains disproportionately long ERVs. Both Silkie and the Mallard genomes presented relatively high 5mC methylation levels on sex chromosomes and microchromosomes, and the telomeres and centromeres presented significantly higher 5mC methylation levels than the whole genome", "token_count": 494, "char_count": 1938, "word_count": 262, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [ "CR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:52.444411", "source": { "split": "train_shard_00001", "doc_id": 2104 }, "chunk_id": "train_shard_00001_2104_0", "global_id": 8644 }, { "text": "Finally, we recovered 325 missing genes via our new genomes and annotated TNFA in Mallard for the first time, revealing conserved protein structures and tissue-specific expression.

Conclusions

The near telomere-to-telomere assemblies in Mallard and Silkie, with the first gap-free sex chromosomes in ducks, significantly enhanced our understanding of genetic structures in birds, specifically highlighting the distinctive chromosome features between the chicken and duck genomes. This foundational work also provides a series of newly identified missing genes for further investigation.\n\nNear telomere-to-telomere genome assemblies of Silkie Gallus gallus and Mallard Anas platyrhynchos restored the structure of chromosomes and \"missing\" genes in birds.", "token_count": 182, "char_count": 761, "word_count": 99, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:52.886045", "source": { "split": "train_shard_00001", "doc_id": 2104 }, "chunk_id": "train_shard_00001_2104_1", "global_id": 8645 }, { "text": "The potential of cashew apple bagasse as a source of sugars for ethanol production by Kluyveromyces marxianus CE025 was evaluated in this work. This strain was preliminarily cultivated in a synthetic medium containing glucose and xylose and was able to produce ethanol and xylitol at pH 4.5. Next, cashew apple bagasse hydrolysate (CABH) was prepared by a diluted sulfuric acid pretreatment and used as fermentation media. This hydrolysate is rich in glucose, xylose, and arabinose and contains traces of formic acid and acetic acid. In batch fermentations of CABH at pH 4.5, the strain produced only ethanol. The effects of temperature on the kinetic parameters of ethanol fermentation by K. marxianus CE025 using CABH were also evaluated. Maximum specific growth rate (μ(max)), overall yields of ethanol based on glucose consumption [Formula: see text] and based on glucose + xylose consumption (Y ( P/S )), overall yield of ethanol based on biomass (Y ( P/X )), and ethanol productivity (P (E)) were determined as a function of temperature. Best results of ethanol production were achieved at 30°C, which is also quite close to the optimum temperature for the formation of biomass. The process yielded 12.36 ± 0.06 g l(-1) of ethanol with a volumetric production rate of 0.257 ± 0.002 g l(-1) h(-1) and an ethanol yield of 0.417 ± 0.003 g g(-1) glucose.\n\nCashew apple bagasse as a source of sugars for ethanol production by Kluyveromyces marxianus CE025.", "token_count": 449, "char_count": 1457, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5462, "quality_score": 0.7731, "entities": { "genes": [ "CE025" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:53.525962", "source": { "split": "train_shard_00001", "doc_id": 2105 }, "chunk_id": "train_shard_00001_2105_0", "global_id": 8646 }, { "text": "

Objectives

The Indian isolate of Cryptococcus neoformans underwent complete genome sequencing to elucidate its genomic architecture and functional characteristics. Furthermore, this study aimed to comprehensively characterize the virulence factors (virulome), antibiotic resistance genes (resistome), and the pan-genome of C. neoformans spp. through a comparative genomic analysis, providing insights into the genetic diversity and evolutionary relationships among strains.

Methods

The genomic data of a clinical strain of C. neoformans was assembled and annotated by MaSuRCA5 and Braker tool. Along with this, the assembled genomic data of the 11 strains were retrieved from NCBI datasets. The comparative virulome, resistome, phylogeny and of the 12 C. neoformans genomes were analyzed using DFVF, AFRbase, BLAST, CLUSTAL Omega, MEGAX, and Orthovenn3, respectively.

Results

The sequenced isolate was identified as a member of the Cryptococcus neoformans var. grubii subspecies. Notably, virulence-related genes comprise approximately 4.8% of the total genome. A comparative genomic analysis of 12 study genomes revealed variations in virulence patterns, including differences in melanization, immune evasion, blood-brain barrier evasion, transcriptional regulation, and oxidative stress response. The phylogenetic study using MLST and orthologous clusters categorized the subspecies grubii and neoformans in different clades. Pan-genome analysis showed that 73.6% of orthologous gene clusters and 77.72% of orthologous proteins were conserved across all 12 study genomes, indicating a shared core genome. Furthermore, the evolutionary relatedness study of the pan-genome revealed gene expansion and contraction events among the study strains.

Conclusion

This pioneering study presents the first comprehensive genomic and comparative genomic analysis of Cryptococcus sp., incorporating data on virulence genes, antibiotic resistance, and pan-genome dynamics", "token_count": 519, "char_count": 1994, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5891, "quality_score": 0.7946, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:19:54.185454", "source": { "split": "train_shard_00001", "doc_id": 2106 }, "chunk_id": "train_shard_00001_2106_0", "global_id": 8647 }, { "text": "Key findings reveal that strains Cn, H99, and JEC21 harbor crucial virulence genes associated with infection severity. While all study strains possess genes promoting antifungal resistance (AFR), most lack specific single nucleotide polymorphisms defining AFR. Consistent with pan-genome analysis, our results show significant gene expansion and contraction events in these strains. This study underscores the importance of bioinformatic tools for efficient whole-genome analysis and large-scale comparative genomics research.\n\nHybrid Genome Sequence ofCryptococcus neoformansof Indian origin and Comparative Genome Analysis", "token_count": 150, "char_count": 631, "word_count": 79, "semantic_coherence": 1, "information_density": 0.8734, "quality_score": 0.9367, "entities": { "genes": [ "JEC21" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:54.619181", "source": { "split": "train_shard_00001", "doc_id": 2106 }, "chunk_id": "train_shard_00001_2106_1", "global_id": 8648 }, { "text": "

Background

As adoption of nanopore sequencing technology continues to advance, the need to maintain large volumes of raw current signal data for reanalysis with updated algorithms is a growing challenge. Here we introduce slow5curl, a software package designed to streamline nanopore data sharing, accessibility, and reanalysis.

Results

Slow5curl allows a user to fetch a specified read or group of reads from a raw nanopore dataset stored on a remote server, such as a public data repository, without downloading the entire file. Slow5curl uses an index to quickly fetch specific reads from a large dataset in SLOW5/BLOW5 format and highly parallelized data access requests to maximize download speeds. Using all public nanopore data from the Human Pangenome Reference Consortium (>22 TB), we demonstrate how slow5curl can be used to quickly fetch and reanalyze raw signal reads corresponding to a set of target genes from each individual in large cohort dataset (n = 91), minimizing the time, egress costs, and local storage requirements for their reanalysis.

Conclusions

We provide slow5curl as a free, open-source package that will reduce frictions in data sharing for the nanopore community: https://github.com/BonsonW/slow5curl.\n\nStreamlining remote nanopore data access with slow5curl.", "token_count": 320, "char_count": 1314, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [ "SLOW5", "BLOW5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:55.190901", "source": { "split": "train_shard_00001", "doc_id": 2107 }, "chunk_id": "train_shard_00001_2107_0", "global_id": 8649 }, { "text": "We used whole genome sequencing (WGS) as an epidemiologic surveillance tool to elucidate the transmission dynamics of Shiga toxin-producing Escherichia coli (STEC) strains along the beef production chain in South Africa. Isolates were obtained from a cattle farm, abattoirs and retail outlets. Isolates were analysed using WGS on a MiSeq platform (Illumina, San Diego, CA, USA) and phylogenetic analysis was carried out. Of the 85 isolates, 39% (33) carried the stx gene and 61% (52) had lost the stx gene. The prevalence of stx subtypes was as follows; stx1a 55% (18/33), stx1b 52% (17/33), stx2a 55% (18/33), stx2b 27% (9/33), stx2dB 30% (10/33) and stx2d1A 15% (5/33). Thirty-five different serogenotypes were detected, of which 65% (56) were flagellar H-antigens and 34% (29) were both O-antigens and flagellar H-antigens. We identified 50 different sequence types (STs), and only nine of the isolates were assigned to three different clonal complexes. Core genome phylogenetic analysis revealed genetic relatedness, and isolates clustered mainly according to their STs and serogenotypes regardless of stx subtypes", "token_count": 509, "char_count": 1310, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7219, "quality_score": 0.8609, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:55.840392", "source": { "split": "train_shard_00001", "doc_id": 2108 }, "chunk_id": "train_shard_00001_2108_0", "global_id": 8650 }, { "text": "This study provides evidence of horizontal transmission and recirculation of STEC strains in Gauteng province and demonstrates that every stage of the beef production chain plays a significant role in STEC entry into the food chain.\n\nEvidence for Horizontal Transmission and Recirculation of Shiga Toxin-Producing <i>Escherichia coli</i> in the Beef Production Chain in South Africa Using Whole Genome Sequencing.", "token_count": 107, "char_count": 425, "word_count": 59, "semantic_coherence": 1, "information_density": 0.6949, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:56.224012", "source": { "split": "train_shard_00001", "doc_id": 2108 }, "chunk_id": "train_shard_00001_2108_1", "global_id": 8651 }, { "text": "The microbial stability of kefir grains and kefir beverage during 10‐week propagation in two different laboratories was investigated. Plate counts and denaturing gel gradient electrophoresis (DGGE) fingerprints of lactobacilli and yeasts from kefir grains were comparable between the two laboratories, with Lactobacillus kefiranofaciens subsp. kefirgranum, Lb. kefiri, Lb. parakefiri, Kluyveromyces marxianus and Kazachstania exigua being the prevalent microorganisms. The counts and composition of lactobacilli and yeasts in the kefir beverage in all serial sampling in both laboratories were also very stable and similar to those obtained with kefir grains. Our findings demonstrate that a stable microbiota of kefir grains ensures consistent and constant product quality that is of crucial importance for dairy industry.\n\nStability of prevailing lactobacilli and yeasts in kefir grains and kefir beverages during ten weeks of propagation", "token_count": 258, "char_count": 940, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6231, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:56.774387", "source": { "split": "train_shard_00001", "doc_id": 2109 }, "chunk_id": "train_shard_00001_2109_0", "global_id": 8652 }, { "text": "The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis . We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis . Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling identification of targets for metabolic engineering of bioproduction hosts.\n\nPopulation genomics-guided engineering of phenazine biosynthesis inPseudomonas chlororaphis", "token_count": 458, "char_count": 1924, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8228, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:57.452385", "source": { "split": "train_shard_00001", "doc_id": 2110 }, "chunk_id": "train_shard_00001_2110_0", "global_id": 8653 }, { "text": "L-Lactate is an indicator of food quality, so its monitoring is essential. Enzymes of L-Lactate metabolism are promising tools for this aim. We describe here some highly sensitive biosensors for L-Lactate determination which were developed using flavocytochrome b2 (Fcb2) as a bio-recognition element, and electroactive nanoparticles (NPs) for enzyme immobilization. The enzyme was isolated from cells of the thermotolerant yeast Ogataea polymorpha. The possibility of direct electron transfer from the reduced form of Fcb2 to graphite electrodes has been confirmed, and the amplification of the electrochemical communication between the immobilized Fcb2 and the electrode surface was demonstrated to be achieved using redox nanomediators, both bound and freely diffusing. The fabricated biosensors exhibited high sensitivity (up to 1436 A·M-1·m-2), fast responses, and low limits of detection. One of the most effective biosensors, which contained co-immobilized Fcb2 and the hexacyanoferrate of gold, having a sensitivity of 253 A·M-1·m-2 without freely diffusing redox mediators, was used for L-Lactate analysis in samples of yogurts. A high correlation was observed between the values of analyte content determined using the biosensor and referenced enzymatic-chemical photometric methods. The developed biosensors based on Fcb2-mediated electroactive nanoparticles can be promising for applications in laboratories of food control.\n\nFlavocytochrome b2-Mediated Electroactive Nanoparticles for Developing Amperometric L-Lactate Biosensors.", "token_count": 499, "char_count": 1713, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:58.121786", "source": { "split": "train_shard_00001", "doc_id": 2111 }, "chunk_id": "train_shard_00001_2111_0", "global_id": 8654 }, { "text": "Despite contributing to the large disease burden in West Africa, little is known about the genomic epidemiology of Streptococcus pneumoniae which cause meningitis among children under 5 years old in the region. We analysed whole-genome sequencing data from 185 S. pneumoniae isolates recovered from suspected paediatric meningitis cases as part of the World Health Organization (WHO) invasive bacterial diseases surveillance from 2010 to 2016. The phylogeny was reconstructed, accessory genome similarity was computed and antimicrobial-resistance patterns were inferred from the genome data and compared to phenotypic resistance from disc diffusion. We studied the changes in the distribution of serotypes pre- and post-pneumococcal conjugate vaccine (PCV) introduction in the Central and Western sub-regions separately. The overall distribution of non-vaccine, PCV7 (4, 6B, 9V, 14, 18C, 19F and 23F) and additional PCV13 serotypes (1, 3, 5, 6A, 19A and 7F) did not change significantly before and after PCV introduction in the Central region (Fisher's test P value 0.27) despite an increase in the proportion of non-vaccine serotypes to 40 % (n=6) in the post-PCV introduction period compared to 21.9 % (n=14). In the Western sub-region, PCV13 serotypes were more dominant among isolates from The Gambia following the introduction of PCV7, 81 % (n=17), compared to the pre-PCV period in neighbouring Senegal, 51 % (n=27)", "token_count": 472, "char_count": 1477, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8325, "entities": { "genes": [ "PCV13", "PCV7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:58.806481", "source": { "split": "train_shard_00001", "doc_id": 2112 }, "chunk_id": "train_shard_00001_2112_0", "global_id": 8655 }, { "text": "The phylogeny illustrated the diversity of strains associated with paediatric meningitis in West Africa and highlighted the existence of phylogeographical clustering, with isolates from the same sub-region clustering and sharing similar accessory genome content. Antibiotic-resistance genotypes known to confer resistance to penicillin, chloramphenicol, co-trimoxazole and tetracycline were detected across all sub-regions. However, there was no discernible trend linking the presence of resistance genotypes with the vaccine introduction period or whether the strain was a vaccine or non-vaccine serotype. Resistance genotypes appeared to be conserved within selected sub-clades of the phylogenetic tree, suggesting clonal inheritance. Our data underscore the need for continued surveillance on the emergence of non-vaccine serotypes as well as chloramphenicol and penicillin resistance, as these antibiotics are likely still being used for empirical treatment in low-resource settings. This article contains data hosted by Microreact.\n\nPhylogeography and resistome of pneumococcal meningitis in West Africa before and after vaccine introduction.", "token_count": 269, "char_count": 1147, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7267, "quality_score": 0.8633, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:19:59.367027", "source": { "split": "train_shard_00001", "doc_id": 2112 }, "chunk_id": "train_shard_00001_2112_1", "global_id": 8656 }, { "text": "Small mammals are known to carry Campylobacter spp.; however, little is known about the genotypes and their role in human infections. We studied intestinal content from small wild mammals collected in their natural habitats in Finland in 2010-2017, and in close proximity to 40 pig or cattle farms in 2017. The animals were trapped using traditional Finnish metal snap traps. Campylobacter spp. were isolated from the intestinal content using direct plating on mCCDA. A total of 19% of the captured wild animals (n = 577) and 41% of the pooled farm samples (n = 227) were positive for C. jejuni, which was the only Campylobacter species identified. The highest prevalence occurred in yellow-necked mice (Apodemus flavicollis) and bank voles (Myodes glareolus) which carried Campylobacter spp. in 66.3 and 63.9% of the farm samples and 41.5 and 24.4% of individual animals trapped from natural habitats, respectively. Interestingly, all house mouse (Mus musculus) and shrew (Sorex spp.) samples were negative for Campylobacter spp. C. jejuni isolates (n = 145) were further characterized by whole-genome sequencing. Core genome multilocus sequence typing (cgMLST) clustering showed that mouse and vole strains were separated from the rest of the C. jejuni population (636 and 671 allelic differences, 94 and 99% of core loci, respectively). Very little or no alleles were shared with C. jejuni genomes described earlier from livestock or human isolates. FastANI results further indicated that C", "token_count": 514, "char_count": 1608, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6422, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:20:00.029937", "source": { "split": "train_shard_00001", "doc_id": 2113 }, "chunk_id": "train_shard_00001_2113_0", "global_id": 8657 }, { "text": "jejuni strains from voles are likely to represent a new previously undescribed species or subspecies of Campylobacter. Core-genome phylogeny showed that there was no difference between isolates originating from the farm and wild captured animals. Instead, the phylogeny followed the host species-association. There was some evidence (one strain each) of livestock-associated C. jejuni occurring in a farm-caught A. flavicollis and a brown rat (Rattus norvegicus), indicating that although small mammals may not be the original reservoir of Campylobacter colonizing livestock, they may sporadically carry C. jejuni strains occurring mainly in livestock and be associated with disease in humans.\n\nHost-Dependent Clustering of <i>Campylobacter</i> Strains From Small Mammals in Finland.", "token_count": 243, "char_count": 841, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7315, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:00.513244", "source": { "split": "train_shard_00001", "doc_id": 2113 }, "chunk_id": "train_shard_00001_2113_1", "global_id": 8658 }, { "text": "Whole‐genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.\n\nNGSEP 4: Efficient and accurate identification of orthogroups and whole‐genome alignment", "token_count": 259, "char_count": 1285, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6045, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:01.056311", "source": { "split": "train_shard_00001", "doc_id": 2114 }, "chunk_id": "train_shard_00001_2114_0", "global_id": 8659 }, { "text": "Giardia duodenalis (syn. G. intestinalis, G. lamblia) is a widespread gastrointestinal protozoan parasite with debated taxonomic status. Currently, eight distinct genetic sub-groups, termed assemblages A-H, are defined based on a few genetic markers. Assemblages A and B may represent distinct species and are both of human public health relevance. Genomic studies are scarce and the few reference genomes available, in particular for assemblage B, are insufficient for adequate comparative genomics. Here, by combining long- and short-read sequences generated by PacBio and Illumina sequencing technologies, we provide nine annotated genome sequences for reference from new clinical isolates (four assemblage A and five assemblage B parasite isolates). Isolates chosen represent the currently accepted classification of sub-assemblages AI, AII, BIII and BIV. Synteny over the whole genome was generally high, but we report chromosome-level translocations as a feature that distinguishes assemblage A from B parasites. Orthologue gene group analysis was used to define gene content differences between assemblage A and B and to contribute a gene-set-based operational definition of respective taxonomic units. Giardia is tetraploid, and high allelic sequence heterogeneity (ASH) for assemblage B vs. assemblage A has been observed so far. Noteworthy, here we report an extremely low ASH (0.002%) for one of the assemblage B isolates (a value even lower than the reference assemblage A isolate WB-C6). This challenges the view of low ASH being a notable feature that distinguishes assemblage A from B parasites, and low ASH allowed assembly of the most contiguous assemblage B genome currently available for reference. In conclusion, the description of nine highly contiguous genome assemblies of new isolates of G. duodenalis assemblage A and B adds to our understanding of the genomics and species population structure of this widespread zoonotic parasite.", "token_count": 496, "char_count": 1985, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:01.706270", "source": { "split": "train_shard_00001", "doc_id": 2115 }, "chunk_id": "train_shard_00001_2115_0", "global_id": 8660 }, { "text": "Highly contiguous genomes of human clinical isolates of Giardia duodenalis reveal assemblage- and sub-assemblage-specific presence-absence variation in protein-coding genes.", "token_count": 51, "char_count": 180, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:02.061996", "source": { "split": "train_shard_00001", "doc_id": 2115 }, "chunk_id": "train_shard_00001_2115_1", "global_id": 8661 }, { "text": "Most studies on bacterial virulence focus on the pathogen itself. However, it is important to recall that the in-host behavior and the virulence of bacterial pathogens constitute a complex situation that depends on both the microorganisms and the infected host. While healthy people (the community) is infected by classical pathogenic microorganisms, able to cope with the anti-infection defenses of the host, in the case of people with basal diseases, debilitated or immunodepressed, the range of pathogens able to cause infection is wider and includes the so-named opportunistic pathogens, which lack the inherent ability to cause disease in healthy hosts and rarely produce infections in the community. Some of the most relevant opportunistic pathogens, as Stenotrophomonas maltophilia, have an environmental origin and, in occasions, present interesting biotechnological properties. Consequently, it is important knowing whether S. maltophilia isolates recovered from infections constitute a specific phylogenetic branch that has evolved toward acquiring a virulent phenotype as it happens in the case of classical pathogens or rather, any member of this bacterial species is capable of producing infection and its pathogenic behavior is mainly a consequence of the host situation. To address this question, we analyzed a set of environmental and clinical S. maltophilia strains. Our results indicate that this opportunistic pathogen presents a large core genome and that the distribution of genes in general, and of known virulence determinants in particular, is similar among environmental and clinical isolates. The majority of genes not belonging to the S. maltophilia core genome are present in just one or two of the analyzed strains. This indicates that, more than speciation into different lineages (virulent and environmental), the evolution of S. maltophilia is based in the strain-specific acquisition of genes, likely involved in the adaptation of this bacterial species to different microniches. In addition, both environmental and clinical isolates present low susceptibility to several antimicrobials. Altogether our results support that S", "token_count": 487, "char_count": 2196, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5478, "quality_score": 0.7739, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:02.715647", "source": { "split": "train_shard_00001", "doc_id": 2116 }, "chunk_id": "train_shard_00001_2116_0", "global_id": 8662 }, { "text": "maltophilia does not present a specific evolutionary branch toward virulence and most likely infection is mainly the consequence of the impaired anti-infective response of the infected patients.\n\nDouble-Face Meets the Bacterial World: The Opportunistic Pathogen Stenotrophomonas maltophilia.", "token_count": 78, "char_count": 302, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:03.081527", "source": { "split": "train_shard_00001", "doc_id": 2116 }, "chunk_id": "train_shard_00001_2116_1", "global_id": 8663 }, { "text": "Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLSB agents in vitro, but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, n=36) to 115.6 (RT002, ST8, n=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, n=169)", "token_count": 467, "char_count": 1310, "word_count": 181, "semantic_coherence": 1, "information_density": 0.779, "quality_score": 0.8895, "entities": { "genes": [ "RT056", "RT014", "RT002", "ST8", "ST34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:03.724847", "source": { "split": "train_shard_00001", "doc_id": 2117 }, "chunk_id": "train_shard_00001_2117_0", "global_id": 8664 }, { "text": "Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, n=14; RT002, n=3; RT056, n=2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse C. difficile strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.\n\nDefining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia.", "token_count": 295, "char_count": 1110, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7355, "quality_score": 0.8677, "entities": { "genes": [ "RT056", "RT014", "RT002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:04.293558", "source": { "split": "train_shard_00001", "doc_id": 2117 }, "chunk_id": "train_shard_00001_2117_1", "global_id": 8665 }, { "text": "High genomic plasticity within Escherichia coli enables it to acquire and accumulate genetic material through horizontal gene transfer. In this study, we sought to investigate the virulence genes, phylogroups, antibiotic resistance genes, plasmid replicons, multilocus sequence types (MLST), and core genome MLST of multidrug-resistant E. coli recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement in Nairobi, Kenya. A total of 39 multidrug-resistant (MDR) strains had their DNA extracted, and whole-genome sequencing was done using the Illumina HiSeq 2000 platform. Twenty-six E. coli assemblies were analyzed using web-based bioinformatics tools available at the Centre for Genomic Epidemiology and EnteroBase. The isolates were categorized into four main phylogroups, where 10/26 (38.5%) belonged to the B2 phylogroup, 4/26 (15.4%) belonged to D, 3/26 (11.5%) belonged to A, 1/26 (3.8%) belonged to B1, while 8/26 (30.8%) were not determined. FimH30 was predominantly found in the most frequent phylogroup B2 and sequence type (ST) 131. The most common beta-lactam resistance genes were bla TEM-1B and blaCTXM 15, followed by three fluoroquinolone resistance genes [qnrS1 6/26 (23.1%), qnrB4 2/26 (7.7%), and aac(6')-Ib-cr, 8/26 (30.8%)]", "token_count": 475, "char_count": 1348, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7624, "quality_score": 0.8812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:04.940269", "source": { "split": "train_shard_00001", "doc_id": 2118 }, "chunk_id": "train_shard_00001_2118_0", "global_id": 8666 }, { "text": "Of 26 isolates, 15 had at least one amino acid substitution in the housekeeping genes gyrA (p.S83L), gyrA (p.D87N), parC (p.S80I), parC (p.E84V), parC (p.S57T), and parE (p.I529L), associated with resistance to fluoroquinolones. A total of 40 diverse virulence genes were detected among the isolates. Thirteen different STs were isolated from the E. coli genomes, which included ST 131, ST 3036, ST 38, ST 10, ST 12569, ST 15271, ST 2076, ST 311, ST 3572, ST 394, ST 453, ST 46, and ST 1722. Only two isolates (2/26, 7.7%) from the Municipal City Council clinic were genetically related. Additionally, the most abundant plasmid replicon identified belonged to the IncF family, IncFII(pRSB107), in particular, followed by the Col family. The study highlighted the first E. coli ST46 to harbor the bla NDM5 gene encoded in Col(BS512), IncFII(pRSB107), and IncFIB(AP001918) plasmid replicons in Kenya. We further demonstrated the diversity of MDR E", "token_count": 457, "char_count": 1064, "word_count": 150, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [ "ST46", "BS512", "AP001918", "NDM5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:05.571962", "source": { "split": "train_shard_00001", "doc_id": 2118 }, "chunk_id": "train_shard_00001_2118_1", "global_id": 8667 }, { "text": "coli associated with diarrhea in an endemic setting in Kenya.

Importance

This study investigated the molecular characterization of multidrug-resistant Escherichia coli isolated from diarrheagenic children under 5 years of age in Mukuru Informal Settlement in Nairobi, Kenya. This is an important addition to the genomic analysis data of multi-drug resistant diarrheal Escherichia coli in Kenya. The use of whole-genome sequencing to identify and characterize these isolates is valuable and provides valuable insights into the molecular epidemiology of E. coli in the region.\n\nMolecular characterization of multidrug-resistant <i>E. coli</i> recovered from diarrheagenic children under 5 years from Mukuru Informal Settlement, Nairobi, Kenya, based on whole-genome sequencing analysis.", "token_count": 239, "char_count": 828, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:06.039658", "source": { "split": "train_shard_00001", "doc_id": 2118 }, "chunk_id": "train_shard_00001_2118_2", "global_id": 8668 }, { "text": "The health-promoting effects of probiotics are species-specific, and hence it is important to declare the correct information in products. However, some studies have identified issues related to the accuracy of labeling commercial probiotic products. In this study, we developed a high-resolution real-time PCR method based on pangenome analysis for a more affordable, rapid, and accurate identification of commercial probiotic products than sequencing methods. We selected 25 species or subspecies primarily used for probiotic strains and are closely related to them as targets. To extract molecular markers, 354 whole-genome sequences present in the target genomes but not in the pangenome of other genomes were compared, which resulted in the identification of molecular marker genes. The marker genes exhibited 100% specificity for 100 strains as assessed by the real-time PCR method. Fifty probiotic and dairy products were investigated to verify the information claimed on the label. Real-time PCR results showed that most products reflected the bacterial species declared in the label claim, whereas 12 products showed the presence of undeclared species or missing species. Our method for accurately verifying the labeling of probiotic products would be useful for quality control and safety.\n\nValidation of probiotic species or subspecies identity in commercial probiotic products using high-resolution PCR method based on large-scale genomic analysis", "token_count": 312, "char_count": 1459, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5952, "quality_score": 0.7976, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:06.592299", "source": { "split": "train_shard_00001", "doc_id": 2119 }, "chunk_id": "train_shard_00001_2119_0", "global_id": 8669 }, { "text": "Acetobacter pasteurianus is an industrial strain used for the vinegar production. Many A. pasteurianus strains with different phenotypic characteristics have been isolated so far. To understand the genetic background underpinning these phenotypes, a comparative genomic analysis of A. pasteurianus strains was conducted. Based on bioinformatics and experimental results, we report the following. (i) The gene repertoire related to the respiratory chains showed that several horizontal gene transfer events occurred after the divergence of these strains, indicating that the respiratory chain in A. pasteurianus has the diversity to adapt to its environment. (ii) There is a clear difference in thermotolerance even between 12 closely related strains. NBRC 3279, NBRC 3284, and NBRC 3283, in particular, which have only 55 mutations in total, showed differences in thermotolerance. The Na+/H+ antiporter gene nhaK2 was mutated in the thermosensitive NBRC 3279 and NBRC 3284 strains and not in the thermotolerant NBRC 3283 strain. The Na+/H+ antiporter activity of the three strains and expression of nhaK2 gene from NBRC 3283 in the two thermosensitive strains showed that these mutations are critical for thermotolerance. These results suggested that horizontal gene transfer events and several mutations have affected the phenotypes of these closely related strains.IMPORTANCEAcetobacter pasteurianus, an industrial vinegar-producing strain, exhibits diverse phenotypic differences such as respiratory activity related to acetic acid production, acetic acid resistance, or thermotolerance. In this study, we investigated the correlations between genome sequences and phenotypes among closely related A. pasteurianus strains", "token_count": 505, "char_count": 1831, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5607, "quality_score": 0.7803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:07.252508", "source": { "split": "train_shard_00001", "doc_id": 2120 }, "chunk_id": "train_shard_00001_2120_0", "global_id": 8670 }, { "text": "The gene repertoire related to the respiratory chains showed that the respiratory components of A. pasteurianus has a diversity caused by several horizontal gene transfers and mutations. In three closely related strains with clear differences in their thermotolerances, we found that the insertion or deletion that occurred in the Na+/H+ antiporter gene nhaK2 is directly related to their thermotolerance. Our study suggests that a relatively quick mutation has occurred in the closely related A. pasteurianus due to its genetic instability and that this has largely affected its phenotype.\n\nComparative Genomic Analysis of Closely Related Acetobacter pasteurianus Strains Provides Evidence of Horizontal Gene Transfer and Reveals Factors Necessary for Thermotolerance.", "token_count": 213, "char_count": 819, "word_count": 109, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:07.716269", "source": { "split": "train_shard_00001", "doc_id": 2120 }, "chunk_id": "train_shard_00001_2120_1", "global_id": 8671 }, { "text": "Ornithobacterium rhinotracheale is a causative agent of respiratory tract infections in avian hosts worldwide but is a particular problem for commercial turkey production. Little is known about the ecologic and evolutionary dynamics of O. rhinotracheale, which makes prevention and control of this pathogen a challenge. The purpose of this study was to gain insight into the genetic relationships between O. rhinotracheale populations through comparative genomics of clinical isolates from different U.S. turkey producers. O. rhinotracheale clinical isolates were collected from four major U.S. turkey producers and several independent turkey growers from the upper Midwest and Southeast, and whole-genome sequencing was performed. Genomes were compared phylogenetically using single nucleotide polymorphism (SNP)-based analysis, and then assembly and annotations were performed to identify genes encoding putative virulence factors and antimicrobial resistance determinants. A pangenome approach was also used to establish a core set of genes consistently present in O. rhinotracheale and to highlight differences in gene content between phylogenetic clades. A total of 1,457 nonrecombinant SNPs were identified from 157 O. rhinotracheale genomes, and four distinct phylogenetic clades were identified. Isolates clustered by company on the phylogenetic tree, however, and each company had isolates in multiple clades with similar collection dates, indicating that there are multiple O. rhinotracheale strains circulating within each of the companies examined", "token_count": 406, "char_count": 1608, "word_count": 213, "semantic_coherence": 1, "information_density": 0.662, "quality_score": 0.831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:08.332844", "source": { "split": "train_shard_00001", "doc_id": 2121 }, "chunk_id": "train_shard_00001_2121_0", "global_id": 8672 }, { "text": "Additionally, several antimicrobial resistance proteins, putative virulence factors, and the pOR1 plasmid were associated with particular clades and multilocus sequence types, which may explain why the same strains seem to have persisted in the same turkey operations for decades.IMPORTANCE The whole-genome approach enhances our understanding of evolutionary relationships between clinical Ornithobacterium rhinotracheale isolates from different commercial turkey producers and allows for identification of genes associated with virulence, antimicrobial resistance, or mobile genetic elements that are often excluded using traditional typing methods. Additionally, differentiating O. rhinotracheale isolates at the whole-genome level may provide insight into selection of the most appropriate autogenous vaccine strain, or groups of strains, for a given population of clinical isolates.\n\nGenomic Landscape of Ornithobacterium rhinotracheale in Commercial Turkey Production in the United States.", "token_count": 229, "char_count": 1016, "word_count": 126, "semantic_coherence": 1, "information_density": 0.754, "quality_score": 0.877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:08.802755", "source": { "split": "train_shard_00001", "doc_id": 2121 }, "chunk_id": "train_shard_00001_2121_1", "global_id": 8673 }, { "text": "

Purpose of review

Colorectal cancer is the second deadliest cancer in the world, and its prevalence has been increasing alarmingly in recent years. After researchers discovered the existence of dysbiosis in colorectal cancer, they considered the use of probiotics in the treatment of colorectal cancer. However, for various reasons, including the low safety profile of probiotics in susceptible and immunocompromised patient5s, and the risk of developing antibiotic resistance, researchers have shifted their focus to non-living cells, their components, and metabolites. This review aims to comprehensively evaluate the literature on the effects of diet, microbiota, and postbiotics on colorectal cancer and the future of postbiotics.

Recent findings

The link between diet, gut microbiota, and colorectal cancer has been established primarily as a relationship rather than a cause-effect relationship. The gut microbiota can convert gastrointestinal tract and dietary factors into either onco-metabolites or tumor suppressor metabolites. There is serious dysbiosis in the microbiota in colorectal cancer. Postbiotics appear to be promising agents in the prevention and treatment of colorectal cancer. It has been shown that various postbiotics can selectively induce apoptosis in CRC, inhibit cell proliferation, growth, invasion, and migration, modulate the immune system, suppress carcinogenic signaling pathways, maintain intestinal epithelial integrity, and have a synergistic effect with chemotherapy drugs. However, it is also reported that some postbiotics are ineffective and may be risky in terms of safety profile in some patients. Many issues need to be researched about postbiotics. Large-scale, randomized, double-blind clinical studies are needed.\n\nThe Crucial Roles of Diet, Microbiota, and Postbiotics in Colorectal Cancer.", "token_count": 447, "char_count": 1854, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:09.468401", "source": { "split": "train_shard_00001", "doc_id": 2122 }, "chunk_id": "train_shard_00001_2122_0", "global_id": 8674 }, { "text": "In this study, we aimed to elucidate a prolonged outbreak of extensively drug-resistant (XDR) Pseudomonas aeruginosa, at two adjacent hospitals over a time course of 4 years. Since all strains exhibited a similar antibiotic susceptibility pattern and carried the carbapenemase gene blaVIM, a monoclonal outbreak was assumed. To shed light on the intra-hospital evolution of these strains over time, whole genome sequence (WGS) analysis of 100 clinical and environmental outbreak strains was employed. Phylogenetic analysis of the core genome revealed the outbreak to be polyclonal, rather than monoclonal as initially suggested. The vast majority of strains fell into one of two major clusters, composed of 27 and 59 strains, and their accessory genome each revealed over 400 and 600 accessory genes, respectively, thus indicating an unexpectedly high structural diversity among phylogenetically clustered strains. Further analyses focused on the cluster with 59 strains, representing the hospital from which both clinical and environmental strains were available. Our investigation clearly shows both accumulation and loss of genes occur very frequently over time, as reflected by analysis of protein enrichment as well as functional enrichment. In addition, we investigated adaptation through single nucleotide polymorphisms (SNPs). Among the genes affected by SNPs, there are a multidrug efflux pump (mexZ) and a mercury detoxification operon (merR) with deleterious mutations, potentially leading to loss of repression with resistance against antibiotics and disinfectants. Our results not only confirm WGS to be a powerful tool for epidemiologic analyses, but also provide insights into molecular evolution during an XDR P. aeruginosa hospital outbreak. Genome mutation unveiled a striking genetic plasticity on an unexpectedly high level, mostly driven by horizontal gene transfer. Our study adds valuable information to the molecular understanding of \"real-world\" Intra-hospital P. aeruginosa evolution and is a step forward toward more personalized medicine in infection control.", "token_count": 507, "char_count": 2133, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8356, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:10.140198", "source": { "split": "train_shard_00001", "doc_id": 2123 }, "chunk_id": "train_shard_00001_2123_0", "global_id": 8675 }, { "text": "Molecular Evolution of Extensively Drug-Resistant (XDR) Pseudomonas aeruginosa Strains From Patients and Hospital Environment in a Prolonged Outbreak.", "token_count": 46, "char_count": 157, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:10.520155", "source": { "split": "train_shard_00001", "doc_id": 2123 }, "chunk_id": "train_shard_00001_2123_1", "global_id": 8676 }, { "text": "Six strains, WILCCON 0050, WILCCON 0051, WILCCON 0052, WILCCON 0053, WILCCON 0054, WILCCON 0055T, were isolated from four different faecal samples of wild boars on Pulau Ubin, Singapore, Singapore. Based on core genome phylogenetic analysis, the six strains formed a distinct clade within the genus Limosilactobacillus (Lm.), with the most closely related type strain being Lm. mucosae DSM 13345T. The minimum ANI, dDDH, and AAI values within these six strains were 97.8%, 78.8%, and 98.6%, respectively. In contrast, the ANI, dDDH, and AAI values with Lm. mucosae DSM 13345T were lower, ranging between 94.8-95.1%, 57.1-59.0%, and 95.9-97.0%, respectively. While ANI and AAI were close to the thresholds of 95% and 97% for bacterial species delineation, respectively, dDDH was significantly lower than the threshold value of 70%. Based on our phylogenomic, phenotypic and chemotaxonomic analyses, we propose a novel species with the name Limosilactobacillus allomucosae sp. nov., with WILCCON 0055T (DSM 117632T = LMG 33563T) as the designated type strain. In vitro investigations revealed the strains' ability to break down raffinose-family oligosaccharides, and to utilize prebiotics such as xylo-oligosaccharides and galacturonic acid, thereby enhancing fibre digestion and nutrient absorption", "token_count": 494, "char_count": 1363, "word_count": 188, "semantic_coherence": 1, "information_density": 0.7021, "quality_score": 0.8511, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:11.204207", "source": { "split": "train_shard_00001", "doc_id": 2124 }, "chunk_id": "train_shard_00001_2124_0", "global_id": 8677 }, { "text": "Moreover, strong auto-aggregation properties, as well as resistance to low pH and porcine bile were observed, suggesting their potential survival and persistence during passage through the gut. The high bile tolerance of these strains appears to be attributed to their ability to deconjugate a wide range of conjugated bile compounds. In silico analysis indicated a strong potential for mucin-binding activity, which aids their colonization in the gut. These characteristics indicate the potential suitability of strains of Lm. allomucosae as probiotics for domestic pigs.\n\nLimosilactobacillus allomucosae sp. nov., a novel species isolated from wild boar faecal samples as a potential probiotic for domestic pigs.", "token_count": 169, "char_count": 714, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6796, "quality_score": 0.8398, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:11.650289", "source": { "split": "train_shard_00001", "doc_id": 2124 }, "chunk_id": "train_shard_00001_2124_1", "global_id": 8678 }, { "text": "

Background

Lacticaseibacillus (formerly Lactobacillus) rhamnosus is widely used in probiotics or food supplements to promote microbiome health and may also be part of the normal microbiota of the human gastrointestinal tract. However, it rarely also causes invasive or severe infections in patients. It has been postulated that these infections may originate from probiotics or from endogenous commensal reservoirs. In this report, we examine the population structure of Lacticaseibacillus rhamnosus and investigate the utility of using bacterial genomics to identify the source of invasive Lacticaseibacillus infections.

Methods

Core genome phylogenetic analysis was performed on 602 L. rhamnosus genome sequences from the National Center for Biotechnology public database. This information was then used along with newly generated sequences of L. rhamnosus isolates from yogurt to investigate a fatal case of L. rhamnosus endocarditis.

Results

Phylogenetic analysis demonstrated substantial genetic overlap of L. rhamnosus isolates cultured from food, probiotics, infected patients, and colonized individuals. This was applied to a patient who had both consumed yogurt and developed L. rhamnosus endocarditis to attempt to identify the source of his infection. The sequence of the isolate from the patient's bloodstream differed at only one nucleotide position from one of the yogurt isolates. Both isolates belonged to a clade, identified here as clade YC, composed of mostly gastrointestinal isolates from healthy individuals, some of which also differed by only a single nucleotide change from the patient's isolate.

Conclusions

As illustrated by this case, whole genome sequencing may be insufficient to reliably determine the source of invasive infections caused by L. rhamnosus.\n\nThe global population stru cture of Lacticaseibacillus rhamnosus and its application to an investigation of a rare case of infective endocarditis.", "token_count": 491, "char_count": 1963, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5836, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:12.300292", "source": { "split": "train_shard_00001", "doc_id": 2125 }, "chunk_id": "train_shard_00001_2125_0", "global_id": 8679 }, { "text": "The genus Brevundimonas consists of Gram-negative bacteria widely distributed in environment and can cause human infections. However, the genomic characteristics and pathogenicity of Brevundimonas remain poorly studied. Here, the whole-genome features of 24 Brevundimonas type strains were described. Brevundimonas spp. had relatively small genomes (3.13 ± 0.29 Mb) within the family Caulobacteraceae but high G+C contents (67.01 ± 2.19 mol%). Two-dimensional hierarchical clustering divided those genomes into 5 major clades, in which clades II and V contained nine and five species, respectively. Interestingly, phylogenetic analysis showed a one-to-one match between core and accessory genomes, which suggested coevolution of species within the genus Brevundimonas. The unique genes were annotated to biological functions like catalytic activity, signaling and cellular processes, multisubstance metabolism, etc. The majority of Brevundimonas spp. harbored virulence-associated genes icl, tufA, kdsA, htpB, and acpXL, which encoded isocitrate lyase, elongation factor, 2-dehydro-3-deoxyphosphooctonate aldolase, heat shock protein, and acyl carrier protein, respectively. In addition, genomic islands (GIs) and phages/prophages were identified within the Brevundimonas genus", "token_count": 444, "char_count": 1368, "word_count": 164, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:12.938280", "source": { "split": "train_shard_00001", "doc_id": 2126 }, "chunk_id": "train_shard_00001_2126_0", "global_id": 8680 }, { "text": "Importantly, a novel Brevundimonas species was identified from the feces of a patient (suffering from diarrhea) by the analyses of biochemical characteristics, phylogenetic tree of 16S rRNA gene, multilocus sequence analysis (MLSA) sequences, and genomic data. The name Brevundimonas pishanensis sp. nov. was proposed, with type strain CHPC 1.3453 (= GDMCC 1.2503T = KCTC 82824T). Brevundimonas spp. also showed obvious slow growth compared with that of Escherichia coli. Our study reveals insights into genomic characteristics and potential virulence-associated genes of Brevundimonas spp., and provides a basis for further intensive study of the pathogenicity of Brevundimonas. IMPORTANCEBrevundimonas spp., a group of bacteria from the family Caulobacteraceae, is associated with nosocomial infections, deserve widespread attention. Our study elucidated genes potentially associated with the pathogenicity of the Brevundimonas genus. We also described some new characteristics of Brevundimonas spp., such as small chromosome size, high G+C content, and slow-growth phenotypes, which made the Brevundimonas genus a good model organism for in-depth studies of growth rate traits. Apart from the comparative analysis of the genomic features of the Brevundimonas genus, we also reported a novel Brevundimonas species, Brevundimonas pishanensis, from the feces of a patient with diarrhea. Our study promotes the understanding of the pathogenicity characteristics of Brevundimonas species bacteria.", "token_count": 511, "char_count": 1615, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6146, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:13.585269", "source": { "split": "train_shard_00001", "doc_id": 2126 }, "chunk_id": "train_shard_00001_2126_1", "global_id": 8681 }, { "text": "Comparative Genomic Analysis Reveals Potential Pathogenicity and Slow-Growth Characteristics of Genus Brevundimonas and Description of Brevundimonas pishanensis sp. nov.", "token_count": 59, "char_count": 183, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:13.939571", "source": { "split": "train_shard_00001", "doc_id": 2126 }, "chunk_id": "train_shard_00001_2126_2", "global_id": 8682 }, { "text": "Invasive non-typhoidal Salmonella disease (iNTS) is caused by certain variants of Salmonella enterica serovar Typhimurium, and is a particular clinical problem in sub-Saharan Africa. A novel sequence type of S. Typhimurium, ST313, is responsible for about two thirds of human bloodstream infections. Previously, RNA-seq based comparative transcriptomic analysis of ST313 and the well-studied ST19 sequence type identified genes and sRNAs that were differentially expressed in 16 infection-relevant growth conditions, but many of these genes remain to be studied at a functional level. This thesis is focused on the investigation of the links between the accessory genome and differentially-expressed genes of S. Typhimurium ST313 and ST19. Several ST313 isolates from the UK were recently discovered that are closely related to ST313 lineages from Africa, and cause gastroenteritis but not bloodstream infection. The genome-based analysis of the UK ST313 isolates revealed several homologs of novel prophages BTP1 and BTP5 in African ST313. An experimental approach showed that these homologs of BTP1 have a similar host range to the African ST313-derived BTP1 phage, and a range of different levels of spontaneous induction. ... (continues)\n\nImpact of the accessory genome upon the biology of African Salmonella enterica serovar Typhimurium ST313", "token_count": 354, "char_count": 1347, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [ "BTP1", "ST19", "ST313", "BTP5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:14.510569", "source": { "split": "train_shard_00001", "doc_id": 2127 }, "chunk_id": "train_shard_00001_2127_0", "global_id": 8683 }, { "text": "Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through variable pangenomic genes: genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, owing to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo genome assemblies of 16 diverse yeast isolates. With these assemblies, we resolved QTLs for growth on maltose, sucrose, raffinose, and oxidative stress to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also duplicate onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings show the need for highly complete genome assemblies to identify the genetic basis of trait variation.\n\nHighly complete long-read genomes reveal pangenomic variation underlying yeast phenotypic diversity.", "token_count": 371, "char_count": 1662, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:15.094331", "source": { "split": "train_shard_00001", "doc_id": 2128 }, "chunk_id": "train_shard_00001_2128_0", "global_id": 8684 }, { "text": "Mawè and tchoukoutou are two traditional fermented foods largely consumed in Benin, West Africa. Their preparations remain as a house art and they are the result of spontaneous fermentation processes. In this study, dynamics of the yeast populations occurring during spontaneous fermentations of mawè and tchoukoutou were investigated using both culture-dependent and -independent approaches. For each product, two productions were followed. Samples were taken at different fermentation times and yeasts were isolated, resulting in the collection of 177 isolates. They were identified by the PCR-DGGE technique followed by the sequencing of the D1/D2 domain of the 26S rRNA gene. The predominant yeast species identified were typed by rep-PCR. Candida krusei was the predominant yeast species in mawè fermentation followed by Candida glabrata and Kluyveromyces marxianus. Other yeast species were detected in lower numbers. The yeast successions that took place during mawè fermentation lead to a final population comprising Saccharomyces cerevisiae, C. krusei and K. marxianus. The yeast populations dominating the fermentation of tchoukoutou were found to consist of S. cerevisiae, almost exclusively. Other yeast species were detected in the early stages of fermentation. For the predominant species a succession of biotypes was demonstrated by rep-PCR for the fermentation of both products. The direct analysis at DNA and RNA levels in the case of mawè did not reveal any other species except those already identified by culture-based analysis. On the other hand, for tchoukoutou, four species were identified that were not detected by the culture-based approach. The spontaneous fermentation of mawè and tchoukoutou in the end were dominated by a few autochthonous species.\n\nYeast dynamics during spontaneous fermentation of mawè and tchoukoutou, two traditional products from Benin.", "token_count": 467, "char_count": 1888, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5036, "quality_score": 0.7518, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:15.736814", "source": { "split": "train_shard_00001", "doc_id": 2129 }, "chunk_id": "train_shard_00001_2129_0", "global_id": 8685 }, { "text": "Multidrug-resistant Acinetobacter baumannii is a major concern in healthcare institutions worldwide. Several reports described the dissemination of A. baumannii high-risk clones that are responsible for a high number of difficult-to-treat infections. In our study, 19 multidrug-resistant A. baumannii strains from Budapest, Hungary, were investigated based on whole-genome sequencing (WGS). The obtained results were analysed together with data from 433 strains of A. baumannii from the Pathogenwatch database. WGS analysis of 19 A. baumannii strains detected that 12 belonged to ST2 and seven belonged to ST636. Among ST2 strains, 11 out of 12 carried either blaOXA-23 or blaOXA-58 genes; however, all strains of ST636 uniformly carried blaOXA-72 gene. All strains of ST2 and ST636 carried blaOXA-66 and blaADC-25 genes. Based on core genome multilocus sequence typing (cgMLST), 10 strains of ST2 belonged to cgMLST906, one strain to cgMLST458, and one strain to cgMLST1320; by contrast, all strains of ST636 belonged to cgMLST1178. Certain virulence determinants were present in all strains of both ST2 and ST636, namely, Ata, Bap, BfmRS, T2SS and PNAG. Interestingly, OmpA was present in all strains of ST2, but it was absent in all strains of ST636", "token_count": 486, "char_count": 1377, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": { "genes": [ "ST2", "ST636" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:16.392222", "source": { "split": "train_shard_00001", "doc_id": 2130 }, "chunk_id": "train_shard_00001_2130_0", "global_id": 8686 }, { "text": "Comparative analysis of 19 strains of this study and the collection of 433 isolates from Pathogenwatch database, proved a diverse clonal distribution of high-risk A. baumannii clones in Europe. The major clone in Europe is ST2, which is present all over the continent. However, ST636 has been mainly reported in Eastern Europe. Interestingly, cgMLSTs of ST2 correspond to the production of different beta-lactamases, namely, OXA-82 in cgMLST116, OXA-72 in cgMLST506, and cgMLST556, PER-1 in cgMLST456 and cgMLST1041. Our study demonstrates that the ST2 high-risk clone of A. baumannii is the most widespread in Europe; however, based on cgMLST analysis, a detailed detection of beta-lactamase production can be determined.\n\nGenomic Investigation and Comparative Analysis of European High-Risk Clone of Acinetobacter baumannii ST2.", "token_count": 267, "char_count": 851, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [ "ST2", "ST636" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:16.931403", "source": { "split": "train_shard_00001", "doc_id": 2130 }, "chunk_id": "train_shard_00001_2130_1", "global_id": 8687 }, { "text": "Acinetobacter baumannii (A. baumannii) challenges clinical infection treatment due to its resistance to various antibiotics. Multiple resistance genes in the core genome or mobile elements contribute to multidrug resistance in A. baumannii. Macrolide phosphotransferase gene mphE has been identified in A. baumannii, which is particularly relevant to macrolide antibiotics. Here, we determined the structure of MphE protein in three states: the apo state, the complex state with erythromycin and guanosine triphosphate (GTP), and the complex state with azithromycin and guanosine. Interestingly, GTP and two magnesium ions were observed in the erythromycin-bound MphE complex. This structure captured the active state of MphE, in which the magnesium ions stabilized the active site and assisted the transfer of phosphoryl groups. Based on these structures, we verified that the conserved residues Asp29, Asp194, His199, and Asp213 play an important role in the catalytic phosphorylation of MphE leading to drug resistance. Our work helps to understand the molecular basis of drug resistance and provides reference targets for optimizing macrolide antibiotics.\n\nCrystal Structures of the Acinetobacter baumannii Macrolide Phosphotransferase E.", "token_count": 359, "char_count": 1284, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:17.502067", "source": { "split": "train_shard_00001", "doc_id": 2131 }, "chunk_id": "train_shard_00001_2131_0", "global_id": 8688 }, { "text": "In many dairy products, Leuconostoc spp. is a natural part of non-starter lactic acid bacteria (NSLAB) accounting for flavor development. However, data on the genomic diversity of Leuconostoc spp. isolates obtained from cheese are still scarce. The focus of this study was the genomic characterization of Leuconostoc spp. obtained from different traditional Montenegrin brine cheeses with the aim to explore their diversity and provide genetic information as a basis for the selection of strains for future cheese production. In 2019, sixteen Leuconostoc spp. isolates were obtained from white brine cheeses from nine different producers located in three municipalities in the northern region of Montenegro. All isolates were identified as Ln. mesenteroides. Classical multilocus sequence tying (MLST) and core genome (cg) MLST revealed a high diversity of the Montenegrin Ln. mesenteroides cheese isolates. All isolates carried genes of the bacteriocin biosynthetic gene clusters, eight out of 16 strains carried the citCDEFG operon, 14 carried butA, and all 16 isolates carried alsS and ilv, genes involved in forming important aromas and flavor compounds. Safety evaluation indicated that isolates carried no pathogenic factors and no virulence factors. In conclusion, Ln. mesenteroides isolates from Montenegrin traditional cheeses displayed a high genetic diversity and were unrelated to strains deposited in GenBank.\n\nGenetic Diversity of Leuconostoc mesenteroides Isolates from Traditional Montenegrin Brine Cheese.", "token_count": 459, "char_count": 1618, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5694, "quality_score": 0.7847, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:18.134603", "source": { "split": "train_shard_00001", "doc_id": 2132 }, "chunk_id": "train_shard_00001_2132_0", "global_id": 8689 }, { "text": "

Background

Infection in the oviduct (salpingitis) is the most common bacterial infection in egg laying hens and is mainly caused by Escherichia coli. The disease is responsible for decreased animal welfare, considerable economic loss as well as a risk of horizontal and vertical transmission of pathogenic E. coli. The outcome of salpingitis may be either acute or chronic. It has not yet been clarified whether the pathological manifestation is a result of the characteristics of the E. coli or whether the manifestation is associated with host factors such as host immunity.

Results

From the core- and accessory genome analysis and comparison of 62 E. coli no genetic markers were found to be associated to either acute or chronic infection. Twenty of the 62 genomes harboured at least one antimicrobial resistance gene with resistance against sulfonamides being the most common. The increased serum survival and iron chelating genes iss and iroN were highly prevalent in genomes from both acute and chronic salpingitis.

Conclusion

Our analysis revealed that no genetic markers could differentiate the E. coli isolated from acute versus chronic salpingitis in egg laying hens. The difference in pathological outcome may be related to other factors such as immunological status, genetics and health of the host. These data indicate that salpingitis is another manifestation of colibacillosis.\n\nWhole genome sequence comparison of avian pathogenic Escherichia coli from acute and chronic salpingitis of egg laying hens.", "token_count": 364, "char_count": 1541, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5526, "quality_score": 0.7763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:18.718717", "source": { "split": "train_shard_00001", "doc_id": 2133 }, "chunk_id": "train_shard_00001_2133_0", "global_id": 8690 }, { "text": "Dairy industries have a high environmental impact, with very high energy and water consumption and polluting effluents. To increase the sustainability of these industries it is urgent to implement technologies for wastewater treatment allowing water recycling and energy savings. In this study, dairy wastewater was processed by ultrafiltration and nanofiltration or ultrafiltration and reverse osmosis (UF/RO) and retentates from the second membrane separation processes were assessed for bioenergy production. Lactose-fermenting yeasts were tested in direct conversion of the retentates (lactose-rich streams) into bioethanol. Two Kluyveromyces strains efficiently fermented all the lactose, with ethanol yields higher than 90% (>0.47 g/g yield). Under severe oxygen-limiting conditions, the K. marxianus PYCC 3286 strain reached 70 g/L of ethanol, which is compatible with energy-efficient distillation processes. In turn, the RO permeate is suitable for recycling into the cleaning process. The proposed integrated process, using UF/RO membrane technology, could allow water recycling (RO permeate) and bioenergy production (from RO retentate) for a more sustainable dairy industry.\n\nIntegrated Process for Bioenergy Production and Water Recycling in the Dairy Industry: Selection of Kluyveromyces Strains for Direct Conversion of Concentrated Lactose-Rich Streams into Bioethanol.", "token_count": 359, "char_count": 1406, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:19.297345", "source": { "split": "train_shard_00001", "doc_id": 2134 }, "chunk_id": "train_shard_00001_2134_0", "global_id": 8691 }, { "text": "Numerous different species of LAB are used in different fields due to their unique characteristics. However, Lacticaseibacillus chiayiensis, a newly established species in 2018, has limited microorganism resources, and lacks comprehensive evaluations of its properties. In this study, L. chiayiensis AACE3, isolated from fermented blueberry, was evaluated by genomic analysis and in vitro assays of the properties. The genome identified genes associated with biofilm formation (luxS, ccpA, brpA), resistance to oxidative stress (tpx, trxA, trxB, hslO), tolerance to acidic conditions (dltA, dltC), resistance to unfavorable osmotic pressure (opuBB, gbuA, gbuB, gbuC), and adhesion (luxS, dltA, dltC). The AACE3 showed 112 unique genes, relative to the other three L. chiayiensis strains. Among them, the presence of genes such as clpP, pepO, and feoA suggests a possible advantage of AACE3 over other L. chiayiensis in terms of environmental adaptation", "token_count": 397, "char_count": 1120, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7591, "quality_score": 0.8796, "entities": { "genes": [ "AACE3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:19.913165", "source": { "split": "train_shard_00001", "doc_id": 2135 }, "chunk_id": "train_shard_00001_2135_0", "global_id": 8692 }, { "text": "In vitro evaluation of the properties revealed that AACE3 had robust antibacterial activity against eight common pathogens: Streptococcus agalactiae, Staphylococcus aureus, Escherichia coli, Salmonella enteritidis, Salmonella choleraesuis, Shigella flexneri, Pseudomonas aeruginosa, and Klebsiella pneumoniae. In addition, AACE3 showed more than 80% survival rate in all tests simulating gastrointestinal fluid, and it exhibited high antioxidant capacity. Interestingly, the cell culture supernatant was superior to intact organisms and ultrasonically crushed bacterial extracts in all tests of antioxidant capacity. These results suggested that the antioxidant capacity may originate from certain metabolites and extracellular enzymes produced by AACE3. Moreover, AACE3 was a moderate biofilm producer due to the self-agglomeration effect. Taken together, L. chiayiensis AACE3 appears to be a candidate strain for combating the growing incidence of pathogen infections and antioxidant production.\n\nGenomic and in-vitro characteristics of a novel strain Lacticaseibacillus chiayiensis AACE3 isolated from fermented blueberry.", "token_count": 368, "char_count": 1209, "word_count": 143, "semantic_coherence": 1, "information_density": 0.7622, "quality_score": 0.8811, "entities": { "genes": [ "AACE3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:20.485305", "source": { "split": "train_shard_00001", "doc_id": 2135 }, "chunk_id": "train_shard_00001_2135_1", "global_id": 8693 }, { "text": "Bifidobacteria colonize the human gastrointestinal tract, vagina, oral cavity and breast milk. They influence human physiology and nutrition through health-promoting effects, play an important role as primary colonizers of the newborn gut, and contribute to vaginal microbiome homeostasis by producing lactic acid. Nevertheless, the mechanisms by which bifidobacteria are transmitted from mother to infant remains in discussion. Moreover, studies have suggested that Bifidobacterium spp. have specializations for gut colonization, but comparisons of strains of the same bifidobacteria species from different body sites are lacking. Here, our objective was to compare the genomes of Bifidobacterium breve (n = 17) and Bifidobacterium longum (n = 26) to assess whether gut and vaginal isolates of either species were distinguishable based on genome content. Comparison of the general genome features showed that vaginal and gut isolates did not differ in size, GC content, number of genes and CRISPR, either for B. breve or B. longum. Average nucleotide identity and whole genome phylogeny analysis revealed that vaginal and gut isolates did not cluster separately. Vaginal and gut isolates also had a similar COG (Cluster of Orthologous Group) category distribution. Differences in the accessory genomes between vaginal and gut strains were observed, but were not sufficient to distinguish isolates based on their origin. The results of this study support the hypothesis that the vaginal and gut microbiomes are colonized by a shared community of Bifidobacterium, and further emphasize the potential importance of the maternal vaginal microbiome as a source of infant gut microbiota.\n\nBifidobacteria isolated from vaginal and gut microbiomes are indistinguishable by comparative genomics.", "token_count": 420, "char_count": 1787, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:21.108877", "source": { "split": "train_shard_00001", "doc_id": 2136 }, "chunk_id": "train_shard_00001_2136_0", "global_id": 8694 }, { "text": "In this study, we conducted a whole-genome analysis of the Lacticaseibacillus paracasei subsp. paracasei 2LB isolated from Kazakh traditional fermented milk (koumiss) to identify genes associated with the safety and probiotic potential of the strain. A comparative genomic analysis of the core and pan-genome of L. paracasei 2LB was performed. Functional annotation revealed the presence of genes putatively involved in metabolism, genetic information processing, and cellular processes. In terms of safety parameters, the stability of its genetic material, the absence of the ability to synthesize virulence factors, and genes responsible for antibiotic resistance were characterized. Also, in vitro studies of the L. paracasei 2LB strain showed resistance to stress factors and antimicrobial activity, and the presence of coding sequences encoding adhesion factors, bacteriocins, bile salts, pH, cold and heat shock, and osmotic stress was observed through genomic analysis. These results indicate that the L. paracasei 2LB strain is a potential probiotic candidate and demonstrate that whole-genome analysis is a useful method for assessing the quality and safety of probiotics.\n\n<i>Lacticaseibacillus paracasei</i> subsp. <i>paracasei</i> 2LB: Identification of Genes to Assess the Safety and Probiotic Potential of the Strain.", "token_count": 382, "char_count": 1390, "word_count": 187, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7914, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:21.716757", "source": { "split": "train_shard_00001", "doc_id": 2137 }, "chunk_id": "train_shard_00001_2137_0", "global_id": 8695 }, { "text": "There is a critical gap in knowledge about how Gram-negative bacterial pathogens, using survival strategies developed for other niches, cause lethal bacteremia. Facultative anaerobic species of the Enterobacterales order are the most common cause of Gram-negative bacteremia, including Escherichia coli , Klebsiella pneumoniae , Serratia marcescens, Citrobacter freundii, and Enterobacter hormaechei . Bacteremia often leads to sepsis, a life-threatening organ dysfunction resulting from an unregulated immune response to infection. Despite a lack of specialization for this host environment, Gram-negative pathogens cause nearly half of bacteremia cases annually. Based on our existing Tn-Seq fitness factor data from a murine model of bacteremia combined with comparative genomics of the five Enterobacterales species above, we prioritized 18 conserved fitness genes or operons for further characterization. Each mutant in each species was used to cochallenge C57BL/6 mice via tail vein injection along with the respective wild-type strain to determine competitive indices for each fitness gene or operon. Among the five species, we found three fitness factor genes, that when mutated, attenuated the mutant for all species in the spleen and liver ( tatC, ruvA, gmhB ). Nine additional fitness factor genes or operons were validated as outcompeted by wild-type in three or four bacterial species in the spleen ( xerC , wzxE , arcA , prc , apaGH , atpG , lpdA , ubiH , aroC ). Overall, 17 of 18 fitness factor mutants were attenuated in at least one species in the spleen or liver. Together, these findings allow for the development of a model of bacteremia pathogenesis that may include future targets of therapy against bloodstream infections.

>Author Summary

Frequent cases of bacteremia plague our ICUs, bone marrow transplant units, and inpatient facilities. Nearly half of these infections are caused by Gram-negative bacteria. The Enterobacterales order including E. coli , K. pneumoniae, S. marcescens, C. freundii , and E", "token_count": 523, "char_count": 2040, "word_count": 307, "semantic_coherence": 1, "information_density": 0.6319, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:20:22.398372", "source": { "split": "train_shard_00001", "doc_id": 2138 }, "chunk_id": "train_shard_00001_2138_0", "global_id": 8696 }, { "text": "hormaechei are leading causes of bacteremia. An alarming proportion of these are due to antibiotic-resistant isolates, which are four times more likely to kill than antibiotic-susceptible isolates. Clearly, we need new therapeutic targets to treat cases of bacteremia and sepsis. Previously, it has been unclear what genes contribute to their ability to survive in this hostile host environment. We have previously undertaken unbiased genetic screens to identify 18 genes shared by all five bacterial genera that are required for survival in blood and blood-filtering organs. These include genes that encode proteins that maintain proton motive force, resist antimicrobial peptides and complement, mediate genome maintenance, transport key metabolites and proteins, avoid oxidative stress, acquire iron, and regulate key pathways. Mutants, constructed in these shared genes in the five species, were validated for a high proportion of genes as critical for infection in the mouse model of bacteremia.\n\nFitness Factor Genes Conserved within the Multi-species Core Genome of Gram-negative Enterobacterales Species Contribute to Bacteremia Pathogenesis", "token_count": 264, "char_count": 1149, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7301, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:22.988703", "source": { "split": "train_shard_00001", "doc_id": 2138 }, "chunk_id": "train_shard_00001_2138_1", "global_id": 8697 }, { "text": "

Background

Tigecycline remains a last-resort antibiotic for treating multidrug-resistant (MDR) Gram-negative pathogens. The emergence of tet(X4)-mediated high-level tigecycline resistance in Escherichia coli has raised global concern, yet its prevalence in healthy human populations remains limited.

Methods

We conducted a community-based surveillance study involving 245 fecal samples from healthy individuals in three urban communities in Shenzhen, China. Tigecycine-resistant strains were isolated using MacConkey agar supplemented with 2 mg/L tigecycline and confirmed by PCR detection of tet(X). Antimicrobial susceptibility testing, whole-genome sequencing (WGS), and phylogenetic analysis were performed.

Results

Tigecycline-resistant E. coli were detected in 1.6% (4/245) of samples. All isolates carried tet(X4) and exhibited an MDR phenotype. WGS revealed that tet(X4) was located on IncY (n=1) and IncFIA8-IncHI1/ST17 plasmids (n=3), which closely resembled previously described plasmids and co-harbored additional resistance genes. The core tet(X4)-carrying region in all four plasmids, associated with ISCR2, was highly similar to that of p47EC-the first tet(X4)-bearing plasmid identified in porcine E. coli in China", "token_count": 427, "char_count": 1322, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7974, "quality_score": 0.8987, "entities": { "genes": [ "ST17", "CR2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:23.634881", "source": { "split": "train_shard_00001", "doc_id": 2139 }, "chunk_id": "train_shard_00001_2139_0", "global_id": 8698 }, { "text": "Notably, the three IncFIA-IncHI1/ST17 plasmids shared an identical 12,536-bp region structured as IS1-catD-tet(X4)-ISCR2-ΔISCR2-floR-ΔISCR2. Virulence-associated genes involved in adhesion, iron acquisition, biofilm formation, and secretion systems were also identified in four tet(X4)-positive isolates. The four isolates belonged to globally distributed sequence types ST10, ST201, ST877, and ST1308. Phylogenomic analysis demonstrated close genetic relatedness between these community isolates and strains from diverse geographical regions and hosts.

Conclusions

This study reveals silent intestinal colonization by tet(X4)-positive MDR E. coli among healthy urban residents, highlighting the role of community reservoirs in the dissemination of last-resort antibiotic resistance. These findings underscore the urgent need for One Health-oriented antimicrobial resistance surveillance and intervention strategies that extend beyond clinical settings.\n\nCommunity gut colonization by <i>tet</i>(X4)-positive multidrug-resistant <i>Escherichia coli</i> in healthy individuals from urban residents in Shenzhen, China.", "token_count": 381, "char_count": 1217, "word_count": 128, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [ "ST877", "ST17", "ST201", "CR2", "ST10", "ST1308" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:24.211086", "source": { "split": "train_shard_00001", "doc_id": 2139 }, "chunk_id": "train_shard_00001_2139_1", "global_id": 8699 }, { "text": "Whole-genome sequencing (WGS) for public health surveillance and epidemiological investigation of foodborne pathogens predominantly relies on sequencing platforms that generate short reads. Continuous improvement of long-read nanopore sequencing, such as Oxford nanopore technologies (ONT), presents a potential for leveraging multiple advantages of the technology in public health and food industry settings, including rapid turnaround and onsite applicability in addition to superior read length. Using an established cohort of Salmonella Enteritidis isolates for subtyping evaluation, we assessed the technical readiness of nanopore long read sequencing for single nucleotide polymorphism (SNP) analysis and core-genome multilocus sequence typing (cgMLST) of a major foodborne pathogen. By multiplexing three isolates per flow cell, we generated sufficient sequencing depths in <7 h of sequencing for robust subtyping. SNP calls by ONT and Illumina reads were highly concordant despite homopolymer errors in ONT reads (R9.4.1 chemistry). In silico correction of such errors allowed accurate allelic calling for cgMLST and allelic difference measurements to facilitate heuristic detection of outbreak isolates. IMPORTANCE Evaluation, standardization, and implementation of the ONT approach to WGS-based, strain-level subtyping is challenging, in part due to its relatively high base-calling error rates and frequent iterations of sequencing chemistry and bioinformatic analytics. Our study established a baseline for the continuously evolving nanopore technology as a viable solution to high-quality subtyping of Salmonella, delivering comparable subtyping performance when used standalone or together with short-read platforms. This study paves the way for evaluating and optimizing the logistics of implementing the ONT approach for foodborne pathogen surveillance in specific settings.\n\nSubtyping Evaluation of Salmonella Enteritidis Using Single Nucleotide Polymorphism and Core Genome Multilocus Sequence Typing with Nanopore Reads.", "token_count": 470, "char_count": 2060, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6506, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:25.740302", "source": { "split": "train_shard_00001", "doc_id": 2140 }, "chunk_id": "train_shard_00001_2140_0", "global_id": 8700 }, { "text": "Salmonella is a foodborne pathogen that poses a severe public health threat. Salmonella enterica serovar Derby (S. Derby) is one of the top five serovars isolated from humans and animals, and it carries the potential risk of transmission to humans through consumption of pork and related products. This study isolated 98 S. Derby, mainly from pork, and clinical samples in Guangdong to investigate and compare their molecular characteristics, phylogenetic relationships, transmission routes, antimicrobial resistance phenotypes, genotypes, and virulence profiles. Whole-genome sequencing (WGS) revealed that all S. Derby isolates belonged to ST40 and displayed a relatively large core genome. Phylogenomic analysis indicated the possibility of clonal transmission of S. Derby not only between pork and humans but also across geographic areas in Guangdong over an extended period of time. Discriminant analysis of principal components (DAPC) model showed that a significant proportion of S. Derby isolates retrieved from multiple hosts originated from pork. Furthermore, similar antimicrobial resistance phenotypes and genotypes were found in S. Derby strains recovered from animal products and humans. All S. Derby isolates were found to contain numerous virulence genes, primarily related to fimbrial adherence determinants and secretion system components. This study offers valuable insights into the transmission routes of S. Derby between pork and humans and provides essential data for public health management.\n\nPopulation genomics of emerging multidrug-resistant Salmonella derby from pork and human in Guangdong, China", "token_count": 369, "char_count": 1626, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6332, "quality_score": 0.8166, "entities": { "genes": [ "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:26.330662", "source": { "split": "train_shard_00001", "doc_id": 2141 }, "chunk_id": "train_shard_00001_2141_0", "global_id": 8701 }, { "text": "Compared to short-read sequencing data, long-read sequencing facilitates single contiguous de novo assemblies and characterization of the prophage region of the genome. Here, we describe our methodological approach to using Oxford Nanopore Technology (ONT) sequencing data to quantify genetic relatedness and to look for microevolutionary events in the core and accessory genomes to assess the within-outbreak variation of four genetically and epidemiologically linked isolates. Analysis of both Illumina and ONT sequencing data detected one SNP between the four sequences of the outbreak isolates. The variant calling procedure highlighted the importance of masking homologous sequences in the reference genome regardless of the sequencing technology used. Variant calling also highlighted the systemic errors in ONT base-calling and ambiguous mapping of Illumina reads that results in variations in the genetic distance when comparing one technology to the other. The prophage component of the outbreak strain was analysed, and nine of the 16 prophages showed some similarity to the prophage in the Sakai reference genome, including the stx2a-encoding phage. Prophage comparison between the outbreak isolates identified minor genome rearrangements in one of the isolates, including an inversion and a deletion event. The ability to characterize the accessory genome in this way is the first step to understanding the significance of these microevolutionary events and their impact on the evolutionary history, virulence and potentially the likely source and transmission of this zoonotic, foodborne pathogen.\n\nAnalysis of a small outbreak of Shiga toxin-producing Escherichia coli O157:H7 using long-read sequencing.", "token_count": 400, "char_count": 1739, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:26.948330", "source": { "split": "train_shard_00001", "doc_id": 2142 }, "chunk_id": "train_shard_00001_2142_0", "global_id": 8702 }, { "text": "

Background

The BOP (Bambusoideae, Oryzoideae, and Pooideae) clade of the Poaceae has a common ancestor, with similarities to the genomes of rice, Oryza sativa (2n = 24; genome size 389 Mb) and Brachypodium, Brachypodium distachyon (2n = 10; 271 Mb). We exploit chromosome-scale genome assemblies to show the nature of genomic expansion, structural variation, and chromosomal rearrangements from rice and Brachypodium, to diploids in the tribe Aveneae (e.g., Avena longiglumis, 2n = 2x = 14; 3,961 Mb assembled to 3,850 Mb in chromosomes).

Results

Most of the Avena chromosome arms show relatively uniform expansion over the 10-fold to 15-fold genome-size increase. Apart from non-coding sequence diversification and accumulation around the centromeres, blocks of genes are not interspersed with blocks of repeats, even in subterminal regions. As in the tribe Triticeae, blocks of conserved synteny are seen between the analyzed species with chromosome fusion, fission, and nesting (insertion) events showing deep evolutionary conservation of chromosome structure during genomic expansion. Unexpectedly, the terminal gene-rich chromosomal segments (representing about 50 Mb) show translocations between chromosomes during speciation, with homogenization of genome-specific repetitive elements within the tribe Aveneae. Newly-formed intergenomic translocations of similar extent are found in the hexaploid A", "token_count": 449, "char_count": 1420, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6788, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:27.589758", "source": { "split": "train_shard_00001", "doc_id": 2143 }, "chunk_id": "train_shard_00001_2143_0", "global_id": 8703 }, { "text": "sativa.

Conclusions

The study provides insight into evolutionary mechanisms and speciation in the BOP clade, which is valuable for measurement of biodiversity, development of a clade-wide pangenome, and exploitation of genomic diversity through breeding programs in Poaceae.\n\nGenome-wide expansion and reorganization during grass evolution: from 30 Mb chromosomes in rice and Brachypodium to 550 Mb in Avena.", "token_count": 114, "char_count": 415, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8364, "quality_score": 0.9182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:27.970539", "source": { "split": "train_shard_00001", "doc_id": 2143 }, "chunk_id": "train_shard_00001_2143_1", "global_id": 8704 }, { "text": "

Background

In Italy the introduction of meningococcal C conjugate vaccine in 2005 has led to a significant reduction of invasive meningococcal disease (IMD) caused by Neisseria meningitidis of serogroup C (MenC). However, this serogroup is still responsible of sporadic cases, clusters and local outbreaks. The study aims to investigate the genotype and antimicrobial susceptibility profile of MenC isolates collected in Italy from 2000 to 2020.

Methods

Bacterial isolates and biological samples (blood or cerebrospinal fluid) from invasive meningococcal cases are collected and characterized at the National Reference Laboratory for IMD of Istituto Superiore di Sanità. Antimicrobial susceptibility was determined by MIC Test Strip Method and interpreted according to the EUCAST breakpoints guideline. Genotypic characteristics, including multi locus sequence typing (MLST), finetype, and antimicrobial resistance target genes were performed and analyzed using the PubMLST database. Genomic comparison of core genome MLST (cgMLST) of MenC genomes was also carried out.

Results

From 2000 to 2020, a total of 665 MenC isolates were investigated for antimicrobial susceptibility and 301 for genotyping. Over two decades, almost all MenC isolates resulted susceptible to antimicrobials with few isolates resulting resistant to ciprofloxacin (N = 2), penicillin G (N = 13), and rifampicin (N = 9), respectively. Molecular typing of MenC obtained from isolates or clinical specimens identified mostly the genotype C:P1.5-1,10-8:F3-6:ST-11(cc11)", "token_count": 471, "char_count": 1589, "word_count": 210, "semantic_coherence": 1, "information_density": 0.681, "quality_score": 0.8405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:28.620651", "source": { "split": "train_shard_00001", "doc_id": 2144 }, "chunk_id": "train_shard_00001_2144_0", "global_id": 8705 }, { "text": "However, phylogenetic analysis, performed on genomes from MenC isolates, identified two sub lineages, 11.1 and 11.2, among cc11, of which the sub lineage 11.2 was the predominant.

Conclusion

Wider application of the genomic analysis and monitoring of antimicrobial susceptibility represent key aspects of IMD surveillance and to monitor the continued evolution of these hyperinvasive strains.\n\nAntimicrobial susceptibility profiles and genotyping of Neisseria meningitidis of serogroup C, Italy, 2000-2020.", "token_count": 157, "char_count": 520, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:29.059796", "source": { "split": "train_shard_00001", "doc_id": 2144 }, "chunk_id": "train_shard_00001_2144_1", "global_id": 8706 }, { "text": "The taxonomic relationships of 10 strains isolated from seaweeds collected from two beaches in Republic of Korea were studied by sequencing and analyses of 16S rRNA genes and whole genomes. For the construction of a more reliable and robust 16S rRNA gene phylogeny, the authentic and nearly complete 16S rRNA gene sequences of all the Microbacterium type strains were selected through pairwise comparison of the sequences contained in several public databases including the List of Prokaryotic names with Standing in Nomenclature (LPSN). The clustering of the ten study strains into five distinct groups was apparent in this single gene-based phylogenetic tree. In addition, the 16S rRNA gene sequences of a few type strains were shown to be incorrectly listed in LPSN. An overall phylogenomic clustering of the genus Microbacterium was performed with a total of 113 genomes by core genome analysis. As a result, nine major (≥ three type strains) and eight minor (two type strains) clusters were defined mostly at gene support index of 92 and mean intra-cluster OrthoANIu of >80.00%. All of the study strains were assigned to a Microbacterium liquefaciens clade and distributed further into four subclusters in the core genome-based phylogenetic tree. In vitro phenotypic assays for physiological, biochemical, and chemotaxonomic characteristics were also carried out with the ten study strains and seven closely related type strains. Comparison of the overall genomic relatedness indices (OGRI) including OrthoANIu and digital DNA-DNA hybridization supported that the study strains constituted four new species of the genus Microbacterium. In addition, some Microbacterium type strains were reclassified as members of preexisting species", "token_count": 475, "char_count": 1780, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5824, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:29.708829", "source": { "split": "train_shard_00001", "doc_id": 2145 }, "chunk_id": "train_shard_00001_2145_0", "global_id": 8707 }, { "text": "Moreover, some of them were embedded in a new genus of the family Microbacteriaceae based on their distinct separation in the core genome-based phylogenetic tree and amino acid identity matrices. Based on the results here, four new species, namely, Microbacterium aurugineum sp. nov., Microbacterium croceum sp. nov., Microbacterium galbinum sp. nov., and Microbacterium sufflavum sp. nov., are described, along with the proposal of Paramicrobacterium gen. nov. containing five reclassified Microbacterium species from the \"Microbacterium agarici clade\", with Paramicrobacterium agarici gen. nov., comb. nov. as the type species.\n\nFour new Microbacterium species isolated from seaweeds and reclassification of five Microbacterium species with a proposal of Paramicrobacterium gen. nov. under a genome-based framework of the genus Microbacterium.", "token_count": 304, "char_count": 936, "word_count": 115, "semantic_coherence": 1, "information_density": 0.5826, "quality_score": 0.7913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:30.272509", "source": { "split": "train_shard_00001", "doc_id": 2145 }, "chunk_id": "train_shard_00001_2145_1", "global_id": 8708 }, { "text": "Abstract

Background In the context of pathogen surveillance, it is crucial to ensure interoperability and harmonized data. Several surveillance systems are designed to compare bacteria and identify outbreak clusters based on core genome MultiLocus Sequence Typing (cgMLST). Among the different approaches available to generate bacterial cgMLST, our research used an assembly-based approach (chewBBACA tool). Methods Simulations of short-read sequencing were conducted for 5 genomes of 27 pathogens of interest in animal, plant, and human health to evaluate the repeatability and reproducibility of cgMLST. Various quality parameters, such as read quality and depth of sequencing were applied, and several read simulations and genome assemblies were repeated using three tools: SPAdes, Unicycler and Shovill. In vitro sequencing were also used to evaluate assembly impact on cgMLST results, for 6 bacterial species: Bacillus thuringiensis, Listeria monocytogenes, Salmonella enterica, Staphylococcus aureus, and Vibrio parahaemolyticus. Results The results highlighted variability in cgMLST, which appears unrelated to the assembly tools, but rather induced by the intrinsic composition of the genomes themselves. This variability observed in simulated sequencing was further validated with real data for five of the bacterial pathogens studied. Conclusion This highlights that the intrinsic genome composition affects assembly and resulting cgMLST profiles, that variability in bioinformatics tools can induce a bias in cgMLST profiles. In conclusion, we propose that the completeness of cgMLST schemes should be considered when clustering strains.

\n\nUnraveling the Impact of Genome Assembly on Bacterial Typing: A One Health Perspective", "token_count": 446, "char_count": 1831, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:30.913237", "source": { "split": "train_shard_00001", "doc_id": 2146 }, "chunk_id": "train_shard_00001_2146_0", "global_id": 8709 }, { "text": "Faecalibacterium prausnitzii is a commensal bacterium, ubiquitous in the gastrointestinal tracts of animals and humans. This species is a functionally important member of the microbiota and studies suggest it has an impact on the physiology and health of the host. F. prausnitzii is the only identified species in the genus Faecalibacterium, but a recent study clustered strains of this species in two different phylogroups. Here, we propose the existence of distinct species in this genus through the use of comparative genomics. Briefly, we performed analyses of 16S rRNA gene phylogeny, phylogenomics, whole genome Multi-Locus Sequence Typing (wgMLST), Average Nucleotide Identity (ANI), gene synteny, and pangenome to better elucidate the phylogenetic relationships among strains of Faecalibacterium. For this, we used 12 newly sequenced, assembled, and curated genomes of F. prausnitzii, which were isolated from feces of healthy volunteers from France and Australia, and combined these with published data from 5 strains downloaded from public databases. The phylogenetic analysis of the 16S rRNA sequences, together with the wgMLST profiles and a phylogenomic tree based on comparisons of genome similarity, all supported the clustering of Faecalibacterium strains in different genospecies. Additionally, the global analysis of gene synteny among all strains showed a highly fragmented profile, whereas the intra-cluster analyses revealed larger and more conserved collinear blocks. Finally, ANI analysis substantiated the presence of three distinct clusters-A, B, and C-composed of five, four, and four strains, respectively. The pangenome analysis of each cluster corroborated the classification of these clusters into three distinct species, each containing less variability than that found within the global pangenome of all strains", "token_count": 497, "char_count": 1885, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6274, "quality_score": 0.8137, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:31.567123", "source": { "split": "train_shard_00001", "doc_id": 2147 }, "chunk_id": "train_shard_00001_2147_0", "global_id": 8710 }, { "text": "Here, we propose that comparison of pangenome subsets and their associated α values may be used as an alternative approach, together with ANI, in the in silico classification of new species. Altogether, our results provide evidence not only for the reconsideration of the phylogenetic and genomic relatedness among strains currently assigned to F. prausnitzii, but also the need for lineage (strain-based) differentiation of this taxon to better define how specific members might be associated with positive or negative host interactions.\n\nNew Insights into the Diversity of the Genus Faecalibacterium.", "token_count": 155, "char_count": 623, "word_count": 89, "semantic_coherence": 1, "information_density": 0.8202, "quality_score": 0.9101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:32.002325", "source": { "split": "train_shard_00001", "doc_id": 2147 }, "chunk_id": "train_shard_00001_2147_1", "global_id": 8711 }, { "text": "

Purpose

The purpose of this study was to evaluate the in vitro antifungal effects of n-butyl-2-cyanoacrylate (nB2CA; Histoacryl Blue; B. Braun, Melsungen, Germany) against a variety of different fungal species.

Methods

Inocula taken from suspensions prepared with Aspergillus flavus, Aspergillus fumigatus, Aspergillus niger, Aspergillus ochraceus, Aspergillus oryzae, Fusarium solanii, Fusarium oxysporum, Trichoderma spp., Rhizomucor spp., Scedosporium apiospermum, Penicillium commune, Phoma glomerata, and Chrysosporium spp. molds and Candida albicans, Candida glabrata, Candida parapsilosis, Candida kruzei, Candida dubliniensis, Candida tropicalis, Candida kefyr, and Trichosporon asahii yeasts were spread on the surface of RPMI1640 agar media. Then, 50 μL of nB2CA was dropped on the surface of these media and they were incubated at 35°C. Observation of a clear zone of inhibition around the nB2CA was regarded as an indicator of the susceptibility of the fungi to nB2CA, and the absence of this zone was interpreted as an indicator of nonsusceptibility. The inhibition zone diameter was measured across the largest clear zone.

Results

A zone of inhibition was observed around nB2CA for all of the yeast and mold species except A. flavus, A. oryzae, and Chrysosporium spp. Among molds, the largest zone of inhibition was observed with P. glomerata (25.7 ± 0.6 mm), whereas among yeasts, the largest zone of inhibition was observed with C. kruzei (19.3 ± 1.5 mm).

Conclusions

nB2CA has shown antifungal activity against 18 different mold and yeast species, but not against A", "token_count": 522, "char_count": 1611, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.793, "entities": { "genes": [ "RPMI1640" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:20:32.632394", "source": { "split": "train_shard_00001", "doc_id": 2148 }, "chunk_id": "train_shard_00001_2148_0", "global_id": 8712 }, { "text": "flavus, A. oryzae, and Chrysosporium spp. molds.\n\nIn Vitro Antifungal Effect of Acrylic Corneal Glue (N-Butyl-2-Cyanoacrylate).", "token_count": 56, "char_count": 127, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:33.008747", "source": { "split": "train_shard_00001", "doc_id": 2148 }, "chunk_id": "train_shard_00001_2148_1", "global_id": 8713 }, { "text": "Latilactobacillus sakei , a lactic acid bacterium in diverse environments such as fermented foods, meat, and the human gastrointestinal tract, exhibits significant genetic diversity and niche-specific adaptations. This study conducts a comprehensive comparative genomic analysis of 30 complete L. sakei genomes to uncover the genetic mechanisms underlying these adaptations. Phylogenetic analysis divided the species into three distinct clades that did not correlate with the source of isolation and did not suggest any niche-specific evolutionary direction. The pan-genome analysis revealed a substantial core genome alongside a diverse genetic repertoire, indicating both high genetic conservation and adaptability. Predicted growth rates based on codon use bias analysis suggest that L. sakei strains have an overall faster growth rate and may be able to efficiently dominant in competitive environments. Plasmid analysis revealed a variety of plasmids carrying genes essential for carbohydrate metabolism, enhancing L. sakei’ s ability to thrive in various fermentation substrates. It was also found that the number of genes belonging to the GH1 family among sugar metabolism-related genes present on chromosomes and plasmids varies between strains, and that AA1, which is involved in alcohol oxidation, has been acquired from plasmids. BLAST analysis revealed that some strains have environmental adaptation gene clusters of cell surface polysaccharides that may mediate attachment to food and mucosa. These findings not only underscore the genetic and functional diversity of L. sakei but also highlight its potential as a potent starter culture in fermentation and as a probiotic. The knowledge gleaned from this study lays a solid foundation for future research aimed at harnessing the genetic traits of L. sakei strains for industrial and health-related applications.\n\nComparative genomic analysis ofLatilactobacillus sakeistrains provides new insights into their association with different niche adaptations", "token_count": 438, "char_count": 2024, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8292, "entities": { "genes": [ "AA1", "GH1" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:33.670246", "source": { "split": "train_shard_00001", "doc_id": 2149 }, "chunk_id": "train_shard_00001_2149_0", "global_id": 8714 }, { "text": "Yersinia enterocolitica (Y. enterocolitica) is the most frequent etiological agent of yersiniosis and has been responsible for several national outbreaks in Norway and elsewhere. A standardized high-resolution method, such as core genome Multilocus Sequence Typing (cgMLST), is needed for pathogen traceability at the national and international levels. In this study, we developed and implemented a cgMLST scheme for Y. enterocolitica. We designed a cgMLST scheme in SeqSphere + using high-quality genomes from different Y. enterocolitica biotype sublineages. The scheme was validated if more than 95% of targets were found across all tested Y. enterocolitica: 563 Norwegian genomes collected between 2012 and 2022 and 327 genomes from public data sets. We applied the scheme to known outbreaks to establish a threshold for identifying major complex types (CTs) based on the number of allelic differences. The final cgMLST scheme included 2,582 genes with a median of 97.9% (interquartile range 97.6%-98.8%) targets found across all tested genomes. Analysis of outbreaks identified all outbreak strains using single linkage clustering at four allelic differences. This threshold identified 311 unique CTs in Norway, of which CT18, CT12, and CT5 were identified as the most frequently associated with outbreaks. The cgMLST scheme showed a very good performance in typing Y. enterocolitica using diverse data sources and was able to identify outbreak clusters. We recommend the implementation of this scheme nationally and internationally to facilitate Y. enterocolitica surveillance and improve outbreak response in national and cross-border outbreaks.\n\nDevelopment and implementation of a core genome multilocus sequence typing scheme for Yersinia enterocolitica: a tool for surveillance and outbreak detection.", "token_count": 485, "char_count": 1867, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5769, "quality_score": 0.7885, "entities": { "genes": [ "CT5", "CT12", "CT18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:34.332375", "source": { "split": "train_shard_00001", "doc_id": 2150 }, "chunk_id": "train_shard_00001_2150_0", "global_id": 8715 }, { "text": "Campylobacter is a leading cause of human gastroenteritis worldwide and is commonly identified in poultry products. Current knowledge of its dissemination patterns in poultry production largely relies on the less sensitive traditional genotyping methods. In this study, whole-genome sequencing was applied to 324 Campylobacter isolates sampled from a chicken abattoir in the Greater Vancouver area throughout 2020. Core genome multi-locus sequence typing analysis revealed a highly diverse and dynamic Campylobacter population containing 27 distinct lineages. A wide range of plasmids was characterized, and a high prevalence of antibiotic resistance was observed among these isolates. Distinct subpopulations were identified in 10 lineages, suggesting that some Campylobacter populations may have diversified within the local agricultural environment. Some lineages were frequently reintroduced to the abattoir, suggesting the potential presence of hidden Campylobacter reservoirs upstream of slaughter. Comparisons between biological and environmental samples suggest a high probability of between-batch cross-contamination. Locally sourced public Campylobacter isolates showed strong genomic correlations with the lineages identified in this study. Notably, lineages 1629a and 1629b were identified to have persisted within the local poultry production ecosystem for several years, explaining their recurrent detection. In conclusion, this study enhances our understanding of Campylobacter population dynamics in the chicken abattoir environment, providing insights for controlling this foodborne pathogen in poultry production systems.IMPORTANCEUsing whole-genome sequencing, this study revealed a highly diverse and dynamic Campylobacter population within the chicken abattoir. The high prevalence of antibiotic resistance marked the critical need for surveillance in this region. The findings highlighted the likely existence of a hidden common source of Campylobacter upstream in the poultry production chain, which significantly contributes to the repeated introduction of the same lineages into the abattoir", "token_count": 491, "char_count": 2179, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5942, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:35.470874", "source": { "split": "train_shard_00001", "doc_id": 2151 }, "chunk_id": "train_shard_00001_2151_0", "global_id": 8716 }, { "text": "Given the frequent reintroductions, the current understanding of Campylobacter persistence in the abattoir environment (up to 21 days) may require revision. Additionally, batch-to-batch dissemination of Campylobacter strains during processing is highly possible. A robust geographic association was also observed between the Campylobacter population in the abattoir and the local community. In sum, this study provides insights into the dynamics of Campylobacter contamination in the poultry production chain, offering guidance for improving prevention and control strategies.\n\nLongitudinal and cross-sectional sampling and whole genome sequencing of <i>Campylobacter</i> in a chicken abattoir reveal highly dynamic population structure.", "token_count": 190, "char_count": 777, "word_count": 94, "semantic_coherence": 1, "information_density": 0.734, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:35.920133", "source": { "split": "train_shard_00001", "doc_id": 2151 }, "chunk_id": "train_shard_00001_2151_1", "global_id": 8717 }, { "text": "

Objectives

Candida species are among the most important causes of hospital acquired blood borne infections, and with high rates of mortality and morbidity, these infections are still a major problem today. History of gastrointestinal surgery, administration of total parenteral nutrition and/or wide spectrum antibiotics and immune suppression following organ transplantations are considered serious risk factors for these infections. This study aimed to evaluate the patients from our general surgery department with diagnosed candidemia; by means of strain, treatment and prognosis.

Material and methods

Patients with positive blood cultures for Candida species who were treated in the wards and Ege University Faculty of Medicine general surgery department of surgical intensive care units of our between 2012 and 2017 were retrospectively analyzed by means of strain, treatment and prognosis.

Results

A total of 50 patients were enrolled in the study. Mean age was 58.96 years and 54% of the patients were female. There were nine patients with organ transplantation (four liver and five kidney transplantations), six with intestinal perforation and three with anastomotic leakage. Isolated strains were Candida albicans (36%; 18/50), Candida tropicalis (14%; 7/50), Candida glabrata (12%; 6/50), Candida parapsilosis (8%; 4/50), Candida kefyr (6%; 3/50), Candida krusei (4%; 2/50), Candida pulcherrima (2%; 1/50), Cryptococcus neoformans (2%, 1/50), Geotrichum capitatum (2%, 1/50), Candida spp. (unidentified, 14%; 7/50) with decreasing frequency. The highest antifungal sensitivity rates (> 90%) were measured for amphotericin B, voriconazole and echinocandins among all isolates. One-month mortality rate was 43.4% (20/46)", "token_count": 511, "char_count": 1751, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8445, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:36.555502", "source": { "split": "train_shard_00001", "doc_id": 2152 }, "chunk_id": "train_shard_00001_2152_0", "global_id": 8718 }, { "text": "Documented eradication was achieved among 24 of the 33 patients who had control blood culture samples (72.7%), and mean eradication time was 7.6 days. Echocardiography was performed in 14% (7/50) and ophthalmic examination in 8% (4/50).

Conclusion

Although C. albicans appears to be the dominant strain in patients with candidemia, frequencies of other strains are increasing. Early diagnosis and treatment of patients with candidemia is of vital importance due to high mortality and morbidity rates.\n\nRetrospective evaluation of candidemic patients among general surgery department in a tertiary care university hospital.", "token_count": 164, "char_count": 629, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:37.011645", "source": { "split": "train_shard_00001", "doc_id": 2152 }, "chunk_id": "train_shard_00001_2152_1", "global_id": 8719 }, { "text": "Pyrus (pear) is among the most nutritious fruits and contains fibers that have great health benefits to humans. It is mostly cultivated in temperate regions globally and is highly subjected to biotic and abiotic stresses which affect its yield. Pheophorbide a oxygenase (PAO) is an essential component of the chlorophyll degradation system and contributes to the senescence of leaves. It is responsible for opening the pheophorbide a porphyrin macrocycle and forming the main fluorescent chlorophyll catabolite However, this gene family and its members have not been explored in Pyrus genomes. Here we report a pangenome-wide investigation has been conducted on eight Pyrus genomes: Cuiguan, Shanxi Duli, Zhongai 1, Nijisseiki, Yunhong No.1, d'Anjou, Bartlett v2.0, and Dangshansuli v.1.1. The phylogenetic history, their gene structure, conservation patterns of motifs, their distribution on chromosomes, and gene duplication are studied in detail which shows the intraspecific structural conservation as well as evolutionary patterns of Pyrus PAOs. Cis-elements, protein-protein interactions (PPI), and the Gene Ontology (GO) enrichment analyses show their potential biological functions. Furthermore, their expression in various tissues, fruit hardening conditions, and drought stress conditions is also studied. Based on phylogenetics, the identified PAOs were divided into four groups. The expansion of this gene family in Pyrus is caused by both tandem and segmental duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process. The Pyrus PAO genes were enriched in hormones-related, light, development, and stress-related elements. RNA-seq data analysis showed that PAOs have varied levels of expression under diseased and abiotic stress conditions. The 3D structures of PAOs are also predicted to get more insights into functional conservation. Our research can be used further to get a deeper knowledge of the PAO gene family in Pyrus and to guide future research on improving the genetic composition of Pyrus to enhance stress tolerance.", "token_count": 519, "char_count": 2119, "word_count": 302, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8311, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:20:37.646960", "source": { "split": "train_shard_00001", "doc_id": 2153 }, "chunk_id": "train_shard_00001_2153_0", "global_id": 8720 }, { "text": "Comparative genomics analysis of pheophorbide a oxygenase (PAO) genes in eight pyrus genomes and their regulatory role in multiple stress responses in Chinese pear (Pyrus bretschneideri).", "token_count": 66, "char_count": 208, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:38.020834", "source": { "split": "train_shard_00001", "doc_id": 2153 }, "chunk_id": "train_shard_00001_2153_1", "global_id": 8721 }, { "text": "BackgroundBrucellosis is a bacterial zoonosis causing severe illness in humans and animals and leading to economic losses in the livestock production in Türkiye and other endemic countries.AimWe aimed at investigating genomic differences of Brucella isolates from animals and humans in Türkiye.MethodsWe used whole genome sequencing (WGS) to assess the genetic diversity of Brucella isolates from 41 provinces in Türkiye and compared with isolates from other countries. We applied allele-based typing and core genome single nucleotide polymorphism (cgSNP) determination.ResultsOf the 106 Turkish Brucella isolates included, 57 were B. abortus and 49 were B. melitensis. One B. melitensis and two B. abortus isolates were identified as vaccine strains. Most (n = 55) B. abortus isolates clustered in three major branches, with no spatial discernible pattern. Of the B. melitensis isolates, 48 were assigned to the Eastern Mediterranean lineage with no discernible patterns between host species, location and sampling date. The Turkish isolates clustered with isolates from neighbouring countries such as Greece and Syria, but some also with isolates from human patients in European countries, like Germany, Norway and Sweden, suggesting that the source may be travel-related.ConclusionSeveral B. melitensis and B. abortus lineages are circulating in Türkiye. To decrease the prevalence and prevent brucellosis in animals and humans, stricter control measures are needed, particularly in areas where humans and animals have close contact. Furthermore, illegal transportation of animals across borders should be more closely controlled and regulated.\n\nGenomic analysis of Brucella isolates from animals and humans, Türkiye, 2010 to 2020.", "token_count": 502, "char_count": 1825, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:38.677171", "source": { "split": "train_shard_00001", "doc_id": 2154 }, "chunk_id": "train_shard_00001_2154_0", "global_id": 8722 }, { "text": "Cancer is among the deadliest diseases with few truly curative therapies. Recent studies have shown that the human intestinal microbiota contains bacteria that exhibit potent suppressive effects on cancer or coordinate anticancer functions with the immune system. However, whether the peculiar anticancer trait was acquired stochastically by a strain of a non-anticancer bacterial species or an intrinsic property of a phylogenetic lineage of bacteria remained unclear. In this study, we compared a human gut isolate Streptomyces sp. BI87, which had highly effective anticancer activities, with the type strain of Streptomyces albidoflavus, DSM 40455T, which was most closely related to BI87 among 30 type strains of the genus Streptomyces but did not show any detectable anticancer activities. We found that, although BI87 and DSM 40455T had >99% 16S rDNA sequence similarity, they are phylogenetically separated by a genetic boundary into distinct natural species as evaluated by the 3Cs definition of bacterial species based on the ratio of common genes with zero sequence degeneracy. In addition to the anticancer activities, BI87 encodes several biological characteristics different from DSM 40455T, including those of antibacterial and antiviral spectra, secondary metabolites, structural composition in the cell wall, and major cellular fatty acids. Based on the genomic and phenotypic distinctions of BI87 from closely related Streptomyces strains, we propose that the anticancer bacterial strain BI87 represents a new lineage at the natural species level within the genus Streptomyces.IMPORTANCEThe characterization of the anticancer bacterial strain, Streptomyces sp", "token_count": 464, "char_count": 1751, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6375, "quality_score": 0.8187, "entities": { "genes": [ "BI87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:39.327343", "source": { "split": "train_shard_00001", "doc_id": 2155 }, "chunk_id": "train_shard_00001_2155_0", "global_id": 8723 }, { "text": "BI87, isolated from a healthy human, suggests the prevalent existence of anticancer microbes in the gut microbiome of humans, which may be nurtured and harnessed for cancer prevention or treatment without the need for the introduction of engineered and non-indigenous microbes to a person or the use of radio- or chemo-therapies. Also important is the finding that a close relative of BI87, Streptomyces albidoflavus DSM40455T, does not express appreciable anticancer properties in the same in vitro and in vivo experiments, demonstrating that Streptomyces sp. BI87 represents a novel bacterial lineage with selective suppressive activities on cancer, at the phylogenetic level of natural species. Genomic comparisons between BI87 and DSM40455T demonstrate that phylogenetic delineation of closely related bacteria needs to be conducted at the level of natural species rather than OTUs, as an OTU may contain phenotypically or even phylogenetically radically distinct bacteria.\n\n<i>Streptomyces</i> sp. BI87 from human gut: potent anticancer activities and divergence from known <i>Streptomyces</i> lineages.", "token_count": 347, "char_count": 1182, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6943, "quality_score": 0.8471, "entities": { "genes": [ "BI87", "DSM40455" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:39.892313", "source": { "split": "train_shard_00001", "doc_id": 2155 }, "chunk_id": "train_shard_00001_2155_1", "global_id": 8724 }, { "text": "

ABSTRACT

Consistent gene annotation in crops is becoming harder as genomes for new cultivars are frequently published. Gene sets from recently sequenced accessions have different gene identifiers to those on the reference accession, and might be of higher quality due to technical advances. For these reasons there is a need to define pangenes, which represent all known syntenic orthologues for a gene model and can be linked back to the original annotation sources. A pangene set effectively summarizes our current understanding of the coding potential of a crop and can be used to inform gene model annotation in new cultivars. Here we present an approach (get_pangenes) to identify and analyze pangenes that is not biased towards the reference annotation. The method involves computing Whole Genome Alignments (WGA), which are used to estimate gene model overlaps. After a benchmark on Arabidopsis , rice, wheat and barley datasets, we find that minimap2 performs better than the GSAlign WGA algorithm. Our results show that pangenes recapitulate known phylogeny-based orthologies while adding extra core gene models in rice. More importantly, get_pangenes can also produce clusters of genome segments (gDNA) that overlap with gene models annotated in other cultivars. By lifting-over CDS sequences, gDNA clusters can help refine gene models across individuals and confirm or reject observed gene Presence-Absence Variation. A collection of flowering-related genes from the barley pangenome are discussed in detail. Documentation and source code are available at https://github.com/Ensembl/plant-scripts .\n\nCalling pangenes from plant genome alignments confirms presence-absence variation", "token_count": 384, "char_count": 1701, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6748, "quality_score": 0.8374, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:40.504527", "source": { "split": "train_shard_00001", "doc_id": 2156 }, "chunk_id": "train_shard_00001_2156_0", "global_id": 8725 }, { "text": "

ABSTRACT

By decomposing genome sequences into k -mers, it is possible to estimate genome differences without alignment. Techniques such as k- mer minimisers (MinHash), have been developed and are often accurate approximations of distances based on full k -mer sets. These and other alignment-free methods avoid the large temporal and computational expense of alignment or mapping. However, these k -mer set comparisons are not entirely accurate within-species and can be completely inaccurate within-lineage. This is due, in part, to their inability to distinguish core polymorphism from accessory differences. Here we present a new approach, KmerAperture , which uses information on the k -mer relative genomic positions to determine the type of polymorphism causing differences in k -mer presence and absence between pairs of genomes. Single SNPs are expected to result in contiguous series of relative unique k -mers of length L = k . On the other hand, series of length L > k may be caused by accessory differences of length L - k +1; when the start and end of the sequence are contiguous with homologous sequence. Alternatively, they may be caused by multiple SNPs within k bp from each other and KmerAperture can determine whether that is the case. To demonstrate use cases KmerAperture was benchmarked using datasets including a very low diversity simulated population with accessory content independent from the number of SNPs, a simulated population were SNPs are spatially dense, a moderately diverse real cluster of genomes ( Escherichia coli ST1193) with a large accessory genome and a low diversity real genome cluster ( Salmonella Typhimurium ST34). We show that KmerAperture can accurately distinguish both core and accessory sequence diversity without alignment, outperforming other k -mer based tools.\n\nKmerAperture: Retainingk-mer synteny for alignment-free extraction of core and accessory differences between bacterial genomes", "token_count": 459, "char_count": 1969, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.7929, "entities": { "genes": [ "ST34", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:41.142443", "source": { "split": "train_shard_00001", "doc_id": 2157 }, "chunk_id": "train_shard_00001_2157_0", "global_id": 8726 }, { "text": "

Background

Most DNA methylation studies have used a single reference genome with little attention paid to the bias introduced due to the reference chosen. Reference genome artifacts and genetic variation, including single nucleotide polymorphisms (SNPs) and structural variants (SVs), can lead to differences in methylation sites (CpGs) between individuals of the same species. We analyzed whole-genome bisulfite sequencing data from the fetal liver of Angus (Bos taurus taurus), Brahman (Bos taurus indicus), and reciprocally crossed samples. Using reference genomes for each breed from the Bovine Pangenome Consortium, we investigated the influence of reference genome choice on the breed and parent-of-origin effects in methylome analyses.

Results

Our findings revealed that ∼75% of CpG sites were shared between Angus and Brahman, ∼5% were breed specific, and ∼20% were unresolved. We demonstrated up to ∼2% quantification bias in global methylation when an incorrect reference genome was used. Furthermore, we found that SNPs impacted CpGs 13 times more than other autosomal sites (P < $5 \\times {10}^{ - 324}$) and SVs contained 1.18 times (P < $5 \\times {10}^{ - 324}$) more CpGs than non-SVs. We found a poor overlap between differentially methylated regions (DMRs) and differentially expressed genes (DEGs) and suggest that DMRs may be impacting enhancers that target these DEGs. DMRs overlapped with imprinted genes, of which 1, DGAT1, which is important for fat metabolism and weight gain, was found in the breed-specific and sire-of-origin comparisons.

Conclusions

This work demonstrates the need to consider reference genome effects to explore genetic and epigenetic differences accurately and identify DMRs involved in controlling certain genes.\n\nDNA methylation analysis to differentiate reference, breed, and parent-of-origin effects in the bovine pangenome era.", "token_count": 504, "char_count": 1900, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [ "DGAT1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:41.800163", "source": { "split": "train_shard_00001", "doc_id": 2158 }, "chunk_id": "train_shard_00001_2158_0", "global_id": 8727 }, { "text": "

Background

The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis.

Results

One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with aminoglycoside, beta-lactam, bacitracin, cationic antimicrobial peptide, fluoroquinolone, and rifampin", "token_count": 480, "char_count": 1936, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.832, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:42.454107", "source": { "split": "train_shard_00001", "doc_id": 2159 }, "chunk_id": "train_shard_00001_2159_0", "global_id": 8728 }, { "text": "These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei.

Conclusions

Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.\n\nComparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity.", "token_count": 184, "char_count": 836, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6449, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:42.899609", "source": { "split": "train_shard_00001", "doc_id": 2159 }, "chunk_id": "train_shard_00001_2159_1", "global_id": 8729 }, { "text": "The Brown Ring Disease (BRD) caused high mortality rates since 1986 in the Manila clam Venerupis philippinarum introduced and cultured in Western Europe from the 1970s. The causative agent of BRD is a Gram-Negative bacterium, Vibrio tapetis, which is also pathogenic to fish. Here we report the first assembly of the complete genome of V. tapetis CECT4600T, together with the genome sequences of 16 additional strains isolated across a broad host and geographic range. Our extensive genome dataset allowed us to describe the pathogen pan- and core genomes and to identify putative virulence factors. The V. tapetis core genome consists of 3,352 genes, including multiple potential virulence factors represented by haemolysins, transcriptional regulators, Type I restriction modification system, GGDEF domain proteins, several conjugative plasmids, and a Type IV secretion system. Future research on the coevolutionary arms race between V. tapetis virulence factors and host resistance mechanisms will improve our understanding of how pathogenicity develops in this emerging pathogen.\n\nVibrio tapetis Displays an Original Type IV Secretion System in Strains Pathogenic for Bivalve Molluscs.", "token_count": 342, "char_count": 1242, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7225, "quality_score": 0.8613, "entities": { "genes": [ "CECT4600" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:43.477609", "source": { "split": "train_shard_00001", "doc_id": 2160 }, "chunk_id": "train_shard_00001_2160_0", "global_id": 8730 }, { "text": "

Objectives

This study describes the detection and tracking of emergency neurosurgical cross-transmission infections with carbapenem-resistant Klebsiella oxytoca (CRKO).

Methods

We conducted an epidemiological investigation and a rapid screening of 66 surveillance samples using the chromogenic selective medium. Two CRKO isolates from infected patients and three from the preoperative shaving razors had similar resistance profiles identified by the clinical laboratory.

Results

The whole genome sequencing (WGS) results identified all isolates as Klebsiella michiganensis (a species in the K. oxytoca complex) with sequence type 29 (ST29) and carrying resistance genes bla KPC-2 and bla OXY-5, as well as IncF plasmids. The pairwise average nucleotide identity values of 5 isolates ranged from 99.993% to 99.999%. Moreover, these isolates displayed a maximum genetic difference of 3 among 5,229 targets in the core genome multilocus sequence typing scheme, and the razors were confirmed as the contamination source. After the implementation of controls and standardized shaving procedures, no new CRKO infections occurred.

Conclusion

Contaminated razors can be sources of neurosurgical site infections with CRKO, and standard shaving procedures need to be established. Chromogenic selective medium can help rapidly identify targeted pathogens, and WGS technologies are effective mean in tracking the transmission source in an epidemic or outbreak investigation. Our findings increase the understanding of microbial transmission in surgery to improve patient care quality.\n\nCarbapenem-resistant Klebsiella oxytoca transmission linked to preoperative shaving in emergency neurosurgery, tracked by rapid detection via chromogenic medium and whole genome sequencing.", "token_count": 491, "char_count": 1856, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8254, "entities": { "genes": [ "ST29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:44.124284", "source": { "split": "train_shard_00001", "doc_id": 2161 }, "chunk_id": "train_shard_00001_2161_0", "global_id": 8731 }, { "text": "We used whole genome sequencing (WGS) analysis to investigate the population structure of 877 Streptococcus pneumoniae isolates from five carriage studies from 2002 (N = 346), 2010 (N = 127), 2013 (N = 153), 2016 (N = 187) and 2018 (N = 64) in UK households which covers the period pre-PCV7 to post-PCV13 implementation. The genomic lineages seen in the population were determined using multi-locus sequence typing (MLST) and PopPUNK (Population Partitioning Using Nucleotide K-mers) which was used for local and global comparisons. A Roary core genome alignment of all the carriage genomes was used to investigate phylogenetic relationships between the lineages. The results showed an influx of previously undetected sequence types after vaccination associated with non-vaccine serotypes. A small number of lineages persisted throughout, associated with both non-vaccine and vaccine types (such as ST199), or that could be an example of serotype switching from vaccine to non-vaccine types (ST177). Serotype 3 persisted throughout the study years, represented by ST180 and Global Pneumococcal Sequencing Cluster (GPSC) 12; the local PopPUNK analysis and core genome maximum likelihood phylogeny separated them into two clades, one of which is only seen in later study years. The genomic data showed that serotype replacement in the carriage studies was mostly due to a change in genotype as well as serotype, but that some important genetic lineages, previously associated with vaccine types, persisted.\n\nThe Genomics of Streptococcus Pneumoniae Carriage Isolates from UK Children and Their Household Contacts, Pre-PCV7 to Post-PCV13.", "token_count": 489, "char_count": 1684, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [ "PCV13", "PCV7", "ST177", "ST180", "ST199" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:44.773238", "source": { "split": "train_shard_00001", "doc_id": 2162 }, "chunk_id": "train_shard_00001_2162_0", "global_id": 8732 }, { "text": "Artisanal Minas cheese (QMA) is traditionally elaborate using raw milk and endogenous ferment (pingo - whey or rala - grated ripened cheese). In the present study, 91 yeast strains were isolated and identified from pingo and rala. Eight yeast species were identified by the MALDI-TOF mass spectrometry and confirmed by sequencing of the ITS region. The yeasts' protease and lipase activities were evaluated in addition to probiotic properties such as tolerance to low pH and bile salts, hydrophobicity, autoaggregation, co-aggregation with pathogens, and antimicrobial susceptibility. The rala ferment showed a greater variety of species. Yarrowia lipolytica was the dominant specie (52.7% of isolates), followed by the Kluyveromyces lactis and Kodamaea ohmeri (9.9 and 6.6%, respectively). From the total yeasts evaluated, 74 strains showed positive enzymatic activity: 52 strains showed lipolytic (51 Y. lipolytica and one Trichosporon japonicum) and 44 proteolytic activities (18 Y. lipolytica, 13 K. ohmeri, 11 K. lactis, and 2 Wickerhamiella sp.). All evaluated isolates demonstrated tolerance to pH 2.0, and 69 isolates supported the presence of bile salts. From them, 12 isolates showed the capacity of autoaggregation (> 30%) and hydrophobicity (> 90.0%) and were then selected for co-aggregation and antibiotic resistance assays. All selected isolates showed co-aggregation with Salmonella Enteritidis, Escherichia coli, and Listeria monocytogenes greater than 30%. None of the yeast showed sensibility to the evaluated antibiotics and antagonistic activity against the evaluated pathogens. The results demonstrated that pingo and rala have different yeast composition with different enzymatic activity, which may affect the characteristics of the cheese. Furthermore, some yeast strains: Y. lipolytica (9 strains isolated from rala) and K", "token_count": 513, "char_count": 1848, "word_count": 265, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:20:45.447309", "source": { "split": "train_shard_00001", "doc_id": 2163 }, "chunk_id": "train_shard_00001_2163_0", "global_id": 8733 }, { "text": "ohmeri (3 strains isolated from pingo) demonstrated attractive probiotic potential.\n\nNovel yeasts with potential probiotic characteristics isolated from the endogenous ferment of artisanal Minas cheese.", "token_count": 48, "char_count": 202, "word_count": 25, "semantic_coherence": 1, "information_density": 0.88, "quality_score": 0.94, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:45.837176", "source": { "split": "train_shard_00001", "doc_id": 2163 }, "chunk_id": "train_shard_00001_2163_1", "global_id": 8734 }, { "text": "Abstract

Valuable genetic variation lies unused in gene banks due to the difficulty of exploiting heterogeneous germplasm accessions. Advances in molecular breeding, including transgenics and genome editing, present the opportunity to exploit hidden sequence variation directly. Here we describe the pangenome data structure induced by wholegenome sequencing of pooled individuals from wild populations of Patellifolia spp., a source of disease resistance genes for the related crop species sugar beet (Beta vulgaris). We represent the pangenome of a heterogeneous population sample as a set of phased reads mapped to a reference genome assembly derived from the sequence pool or other sources. We show that this basic data structure can be queried by homology to identify short haplotypic variants present in the wild relative, at genes of agronomic interest in the crop. Further we demonstrate the possibility of cataloging short haplotypic variation in all Patellifolia genomic regions that have corresponding single copy orthologous regions in sugar beet. The data structure, termed a \"phased read archive\", can be produced, altered, and queried using standard tools to facilitate discovery of agronomicallyimportant sequence variation in heterogeneous germplasm.

\n\nA Pan-Genome Data Structure Induced by Pooled Sequencing Facilitates Variant Mining in Heterogeneous Germplasm", "token_count": 329, "char_count": 1453, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:46.418528", "source": { "split": "train_shard_00001", "doc_id": 2164 }, "chunk_id": "train_shard_00001_2164_0", "global_id": 8735 }, { "text": "Outer membrane proteins (OMPs) of Aeromonas hydrophila have a variety of functional roles in virulence and pathogenesis and represent promising targets for vaccine development. The main objective of this study was to develop an in-silico model of beta-barrel OMP present among the valid A. hydrophila pangenomes (n = 22). With a program named the β-barrel Outer Membrane Protein Predictor (BOMP), total beta-barrel OMPs (n = 3127) were predicted across 22 genomes with the estimated median number of 64 per genome. In pangenome analysis, only 32 OMPs were found to be conserved. These beta-barrel OMPs also showed variations among source of isolation, COG and KEGG classes. Among 32 conserved OMPs, a highly antigenic protein was identified by utilizing Vaxijen. With B cell epitope predictions, two fragments of amino acid sequences i.e. GLTLGAQFTGNNDPQNADRSN (21 mer) and FKPSLAYLRTDVKDNARGI DDTATEY (26 mer) bearing B-cell binding sites were selected. Further, an epitope (12 amino acids: GLTLGAQFTGNN) that complexes to maximum MHC alleles with a higher antigenicity was determined. The analysis of evolutionary forces on the identified OMP sequence and epitope indicated that none of basic amino acid sites has shown significantly different substitution ratios. This conserved protein and epitope will be helpful in developing a vaccine that may be effective against all the A. hydrophila strains. Also, this study provides a theoretical basis for vaccine design against other pathogenic bacteria.

Supplementary information

The online version contains supplementary material available at 10.1007/s10989-021-10259-z.", "token_count": 479, "char_count": 1648, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6838, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:47.104688", "source": { "split": "train_shard_00001", "doc_id": 2165 }, "chunk_id": "train_shard_00001_2165_0", "global_id": 8736 }, { "text": "In Silico Analysis of Potential Outer Membrane Beta-Barrel Proteins in Aeromonas hydrophila Pangenome.", "token_count": 37, "char_count": 109, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:47.510061", "source": { "split": "train_shard_00001", "doc_id": 2165 }, "chunk_id": "train_shard_00001_2165_1", "global_id": 8737 }, { "text": "Background/Objectives: Carbapenem resistance poses a significant health threat. This study reports the first detection and characterization of a novel variant of New Delhi metallo-β-lactamase (blaNDM-60) in Escherichia coli from the United Arab Emirates (UAE), including its genetic context and relationship to global strains. Methods: NDM-60-producing E. coli was isolated from a rectal swab during routine screening. Characterization involved whole-genome sequencing, antimicrobial susceptibility testing, and comparative genomic analysis with 66 known NDM variants. Core genome analysis was performed against 42 global E. coli strains, including the single other reported NDM-60-positive isolate. Results: The strain demonstrated extensive drug resistance, including resistance to novel β-lactam/β-lactamase inhibitor combinations, notably taniborbactam. NDM-60 differs from the closely related NDM-5 by a single amino acid substitution (Asp202Asn) and two amino acid substitutions (Val88Leu and Met154Leu) compared to NDM-1. NDM-60 is located on a nonconjugative IncX3 plasmid. The strain belongs to sequence type 940 (ST940). Phylogenetic analysis revealed high diversity among the global ST940 strains, which carry a plethora of resistance genes and originated from humans, animals, and the environment from diverse geographic locations. Conclusions: NDM-60 emergence in the UAE represents a significant evolution in carbapenemase diversity. Its presence on a nonconjugative plasmid may limit spread; however, its extensive resistance profile is concerning. Further studies are needed to determine the prevalence, dissemination, and clinical impact of NDM-60. NDM evolution underscores the ongoing challenge in managing antimicrobial resistance and the critical importance of vigilant molecular surveillance. It also highlights the pressing demand to discover new antibiotics to fight resistant bacteria.", "token_count": 526, "char_count": 1977, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [ "ST940" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:20:48.151087", "source": { "split": "train_shard_00001", "doc_id": 2166 }, "chunk_id": "train_shard_00001_2166_0", "global_id": 8738 }, { "text": "Novel Variant of New Delhi Metallo-Beta-Lactamase (blaNDM-60) Discovered in a Clinical Strain of Escherichia coli from the United Arab Emirates: An Emerging Challenge in Antimicrobial Resistance.", "token_count": 79, "char_count": 220, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:48.524130", "source": { "split": "train_shard_00001", "doc_id": 2166 }, "chunk_id": "train_shard_00001_2166_1", "global_id": 8739 }, { "text": "The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.\n\nPhylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents.", "token_count": 368, "char_count": 1504, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:49.117311", "source": { "split": "train_shard_00001", "doc_id": 2167 }, "chunk_id": "train_shard_00001_2167_0", "global_id": 8740 }, { "text": "In this work we analysed the whole genome extended multilocus sequence typing (wgMLST) of four Pseudomonas aeruginosa strains that are characterized by being virulent despite having a defective Las quorum-sensing (QS) system, and compare them with the wgMLST of the PAO1 and PA14 type strains. This comparison was done to determine whether there was a genomic characteristic that was common to the strains with an atypical QS response. The analysed strains include two environmental isolates (ID 4365 isolated from the Indian Ocean, and M66 isolated from the Churince water system in Cuatro Ciénegas Coahuila, México), one veterinary isolate (strain 148 isolated from the stomach of a dolphin) and a clinical strain (INP43 that is a cystic fibrosis pediatric isolate). We determine that the six analysed strains have a core genome of 4689 loci that was used to construct a wgMLST-phylogeny tree. Using the cano-wgMLST_BacCompare software we found that there was no common genomic characteristic to the strains with an atypical QS-response and we identify ten loci that are highly discriminatory of the six strains' phylogeny so that their MLST can reconstruct the wgMLST-phylogeny tree of these strains. We discuss here the nature of these ten highly discriminatory genes in the context of P. aeruginosa virulence and evolution.\n\nTracking the genome of four Pseudomonas aeruginosa isolates that have a defective Las quorum-sensing system, but are still virulent.", "token_count": 405, "char_count": 1483, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5664, "quality_score": 0.7832, "entities": { "genes": [ "PA14", "INP43", "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:49.740700", "source": { "split": "train_shard_00001", "doc_id": 2168 }, "chunk_id": "train_shard_00001_2168_0", "global_id": 8741 }, { "text": "Investigating the genomic epidemiology of major bacterial pathogens is integral to understanding transmission, evolution, colonisation, disease, antimicrobial resistance, and vaccine impact. Furthermore, the recent accumulation of large numbers of whole genome sequences for many bacterial species enhances the development of robust genome-wide typing schemes to define the overall bacterial population structure and lineages within it. Using previously published data, we developed the Pneumococcal Genome Library (PGL), a curated dataset of 30,976 genomes and contextual data for carriage and disease pneumococci recovered between 1916-2018 in 82 countries. We leveraged the size and diversity of the PGL to develop a core genome multilocus sequence typing (cgMLST) scheme comprised of 1,222 loci. Finally, using multilevel single-linkage clustering, we stratified pneumococci into hierarchical clusters based on allelic similarity thresholds, and defined these with a taxonomic life identification number (LIN) barcoding system. The PGL, cgMLST scheme, and LIN barcodes represent a high-quality genomic resource and fine-scale clustering approaches for the analysis of pneumococcal populations, which support the genomic epidemiology and surveillance of this leading global pathogen.

Impact statement

Many thousands of pneumococcal genomes are available in the public domain, and this creates opportunities for the scientific community to re-use existing data; however, these data are most useful when the contextual data (provenance and phenotype) are also linked to the genomes. Therefore, we created a curated, open-access database in PubMLST that contained nearly 31,000 published pneumococcal genomes and the corresponding contextual data for each genome. This large and diverse pneumococcal database was used to create a novel cgMLST scheme and multilevel clustering method to define genetic lineages with high resolution and a standardised nomenclature. These are open-access resources for all to use and provide a unified framework for the characterisation of global pneumococcal populations.", "token_count": 496, "char_count": 2112, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6285, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:50.390276", "source": { "split": "train_shard_00001", "doc_id": 2169 }, "chunk_id": "train_shard_00001_2169_0", "global_id": 8742 }, { "text": "Development of the Pneumococcal Genome Library, a core genome multilocus sequence typing scheme, and a taxonomic life identification number barcoding system to investigate and define pneumococcal population structure", "token_count": 46, "char_count": 216, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:50.754150", "source": { "split": "train_shard_00001", "doc_id": 2169 }, "chunk_id": "train_shard_00001_2169_1", "global_id": 8743 }, { "text": "1. Ancient environmental DNA (eDNA) is a crucial source of in-formation for past environmental reconstruction. However, the com-putational analysis of ancient eDNA involves not only the inherited challenges of ancient DNA (aDNA) but also the typical difficulties of eDNA samples, such as taxonomic identification and abundance esti-mation of identified taxonomic groups. Current methods for ancient eDNA fall into those that only perform mapping followed by taxo-nomic identification and those that purport to do abundance estima-tion. The former leaves abundance estimates to users, while methods for the latter are not designed for large metagenomic datasets and are often imprecise and challenging to use. 2. Here, we introduce euka, a tool designed for rapid and accurate characterisation of ancient eDNA samples. We use a taxonomy-based pangenome graph of reference genomes for robustly assigning DNA sequences and use a maximum-likelihood framework for abundance estimation. At the present time, our database is restricted to mito-chondrial genomes of tetrapods and arthropods but can be expanded in future versions. 3. We find euka to outperform current taxonomic profiling tools as well as their abundance estimates. Crucially, we show that regardless of the filtering threshold set by existing methods, euka demonstrates higher accuracy. Furthermore, our approach is robust to sparse data, which is idiosyncratic of ancient eDNA, detecting a taxon with an average of fifty reads aligning. We also show that euka is consistent with competing tools on empirical samples and about ten times faster than current quantification tools. 4. euka’s features are fine-tuned to deal with the challenges of ancient eDNA, making it a simple-to-use, all-in-one tool. It is available on GitHub: https://github.com/grenaud/vgan . euka enables re-searchers to quickly assess and characterise their sample, thus allowing it to be used as a routine screening tool for ancient eDNA.\n\neuka: Robust detection of eukaryotic taxa from modern and ancient environmental DNA using pangenomic reference graphs", "token_count": 483, "char_count": 2090, "word_count": 308, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:51.398567", "source": { "split": "train_shard_00001", "doc_id": 2170 }, "chunk_id": "train_shard_00001_2170_0", "global_id": 8744 }, { "text": "

Background

Brucellosis, developing complications including arthritis, spondylitis, sacroiliitis, and osteomyelitis, is one of the most common zoonotic diseases in the current world which causes economic losses to the livestock industry and is a great public health concern. Brucella melitensis are the main pathogen of brucellosis epidemics in China, most of which are located in northern China. However, there is limited knowledge about the epidemiology of osteoarthritis-associated brucellosis. This study was aimed to reveal the prevalence of osteoarthritis-associated brucellosis in Inner Mongolia and also to investigate the molecular characteristics of B. melitensis isolates.

Methods and results

In 2018, the osteoarthritis symptoms of brucellosis in the Brucellosis department of a hospital in Inner Mongolia were investigated. Twenty osteoarthritis-associated B. melitensis strains, isolated from the inpatients in Inner Mongolia during 2013-2017, were subjected to whole genome sequencing. The multilocus sequence type (MLST) and core genome SNP (cgSNP) analysis were conducted to detect molecular epidemiological characteristics. The incidence of brucellosis osteoarthritis symptoms in males (85/120, 70.8%) was significantly higher than that in females (35/120, 29.2%), and the age of patients was concentrated between 41 and 60 years old. In silico analyses indicated ST8 was the prevalent sequence type and the transmission of osteoarthritis-associated B. melitensis among different geographical areas. All strains carry virulence genes, including cgs, lpsA, manCoAg, pgm, pmm, virB4, wbdA and wboA.

Conclusion

Our study showed the close epidemiologically connection of osteoarthritis-associated B. melitensis strains in northern China. And ST8 was the prevalent sequence type which need our attention.", "token_count": 501, "char_count": 1838, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:52.046800", "source": { "split": "train_shard_00001", "doc_id": 2171 }, "chunk_id": "train_shard_00001_2171_0", "global_id": 8745 }, { "text": "Molecular epidemiological characteristics of osteoarthritis-associated Brucella melitensis in China: evidence from whole-genome sequencing-based analysis.", "token_count": 38, "char_count": 154, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:52.400824", "source": { "split": "train_shard_00001", "doc_id": 2171 }, "chunk_id": "train_shard_00001_2171_1", "global_id": 8746 }, { "text": "Background/Objectives: Infections in dogs caused by methicillin-resistant staphylococci (MRS) present limited treatment options. This study's objective was to investigate the molecular epidemiology of Staphylococcus spp. cultured exclusively from clinical canine skin and ear samples in Queensland, Australia, using whole-genome sequencing (WGS). Methods: Forty-two Staphylococcus spp. isolated from clinical canine skin and ear samples, from an unknown number of dogs, were sourced from two veterinary diagnostic laboratories between January 2022 and May 2023. These isolates underwent matrix-assisted laser desorption ionisation- time of flight bacterial identification, minimum inhibitory concentration testing using SensititreTM plates and WGS. Phylogenetic trees and core genome multilocus sequence typing (cgMLST) minimum spanning trees (MSTs) were constructed. Results: The isolates included methicillin-resistant and -sensitive S. pseudintermedius (MRSP: 57.1%, 24/42; and MSSP: 19.1%, 8/42), methicillin-resistant and -sensitive S. coagulans (MRSC: 14.3%, 6/42; and MSSC: 2.4%, 1/42) and methicillin-resistant coagulase-negative staphylococci (MR-CoNS: 7.1%, 3/42). Thirty-nine isolates were included after WGS, where all MRS harboured the mecA gene. Eighteen sequence types (STs) were identified, including three novel MRSP and six novel MSSP STs. MRSP ST496-V-VII (23%; 9/39) and MRSP ST749-IV-(IVg) (12.8%; 5/39) were commonly isolated", "token_count": 508, "char_count": 1514, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7486, "quality_score": 0.8743, "entities": { "genes": [ "ST749", "ST496" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:53.035333", "source": { "split": "train_shard_00001", "doc_id": 2172 }, "chunk_id": "train_shard_00001_2172_0", "global_id": 8747 }, { "text": "Phylogenetic analysis of single nucleotide polymorphisms showed that MRSP, MRSC and MSSC were similar to globally isolated staphylococci from canine skin and ear infections. Using cgMLST MSTs, MRSP isolates were not closely related to global strains. Conclusions: Our findings revealed a genotypically diverse geographical distribution and phylogenetic relatedness of staphylococci cultured from clinical canine skin and ear samples across Queensland. This highlights the importance of ongoing surveillance to aid in evidence-based treatment decisions and antimicrobial stewardship.\n\nMolecular Epidemiological Characteristics of Staphylococcus pseudintermedius, Staphylococcus coagulans, and Coagulase-Negative Staphylococci Cultured from Clinical Canine Skin and Ear Samples in Queensland.", "token_count": 220, "char_count": 811, "word_count": 97, "semantic_coherence": 1, "information_density": 0.701, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:53.501931", "source": { "split": "train_shard_00001", "doc_id": 2172 }, "chunk_id": "train_shard_00001_2172_1", "global_id": 8748 }, { "text": "Fructanase and fructosyltransferase are interesting for the tequila process and prebiotics production (functional food industry). In this study, one hundred thirty non-Saccharomyces yeasts isolated from \"Mezcal de Oaxaca\" were screened for fructanase and fructosyltransferase activity. On solid medium, fifty isolates grew on Agave tequilana fructans (ATF), inulin or levan. In liquid media, inulin and ATF induced fructanase activities of between 0.02 and 0.27U/ml depending of yeast isolate. High fructanase activity on sucrose was observed for Kluyveromyces marxianus and Torulaspora delbrueckii, while the highest fructanase activity on inulin and ATF was observed for Issatchenkia orientalis, Cryptococcus albidus, and Candida apicola. Zygosaccharomyces bisporus and Candida boidinii had a high hydrolytic activity on levan. Sixteen yeasts belonging to K. marxianus, T. delbrueckii and C. apicola species were positive for fructosyltransferase activity. Mezcal microbiota proved to showed to be a source for new fructanase and fructosyltransferases with potential application in the tequila and food industry.\n\nFructanase and fructosyltransferase activity of non-Saccharomyces yeasts isolated from fermenting musts of Mezcal.", "token_count": 355, "char_count": 1230, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:54.072534", "source": { "split": "train_shard_00001", "doc_id": 2173 }, "chunk_id": "train_shard_00001_2173_0", "global_id": 8749 }, { "text": "

Background

A zoonotic association has been suggested for several PCR ribotypes (RTs) of Clostridioides difficile. In central parts of Sweden, RT046 was found dominant in neonatal pigs at the same time as a RT046 hospital C. difficile infection (CDI) outbreak occurred in the southern parts of the country.

Objective

To detect possible transmission of RT046 between pig farms and human CDI cases in Sweden and investigate the diversity of RT046 in the pig population using whole genome sequencing (WGS).

Methods

WGS was performed on 47 C. difficile isolates from pigs (n = 22), the farm environment (n = 7) and human cases of CDI (n = 18). Two different core genome multilocus sequencing typing (cgMLST) schemes were used together with a single nucleotide polymorphisms (SNP) analysis and the results were related to time and location of isolation of the isolates.

Results

The pig isolates were closely related (≤6 cgMLST alleles differing in both cgMLST schemes) and conserved over time and were clearly separated from isolates from the human hospital outbreak (≥76 and ≥90 cgMLST alleles differing in the two cgMLST schemes). However, two human isolates were closely related to the pig isolates, suggesting possible transmission. The SNP analysis was not more discriminate than cgMLST.

Conclusion

No general pattern suggesting zoonotic transmission was apparent between pigs and humans, although contrasting results from two isolates still make transmission possible. Our results support the need for high resolution WGS typing when investigating hospital and environmental transmission of C. difficile.\n\nWhole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans.", "token_count": 453, "char_count": 1757, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5476, "quality_score": 0.7738, "entities": { "genes": [ "RT046" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:54.710470", "source": { "split": "train_shard_00001", "doc_id": 2174 }, "chunk_id": "train_shard_00001_2174_0", "global_id": 8750 }, { "text": "The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.\n\nThe banana genome hub: a community database for genomics in the Musaceae.", "token_count": 352, "char_count": 1606, "word_count": 219, "semantic_coherence": 1, "information_density": 0.653, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:55.289038", "source": { "split": "train_shard_00001", "doc_id": 2175 }, "chunk_id": "train_shard_00001_2175_0", "global_id": 8751 }, { "text": "Taxonomic classification is an essential step in the analysis of microbiome data that depends on a reference database of whole genome sequences. Taxonomic classifiers are built on established reference species, such as the Human Microbiome Project database, that is growing rapidly. While constructing a population wide pangenome of the bacterium Hungatella , we discovered that the Human Microbiome Project reference species Hungatella hathewayi (WAL 18680) was significantly different to other members of this genus. Specifically, the reference lacked the core genome as compared to the other members. Further analysis, using average nucleotide identity (ANI) and 16s rRNA comparisons, indicated that WAL18680 was misclassified as Hungatella . The error in classification is being amplified in the taxonomic classifiers and will have a compounding effect as microbiome analyses are done, resulting in inaccurate assignment of community members and will lead to fallacious conclusions and possibly treatment. As automated genome homology assessment expands for microbiome analysis, outbreak detection, and public health reliance on whole genomes increases this issue will likely occur at an increasing rate. These observations highlight the need for developing reference free methods for epidemiological investigation using whole genome sequences and the criticality of accurate reference databases.\n\nMisclassification of a whole genome sequence reference defined by the Human Microbiome Project: a detrimental carryover effect to microbiome studies", "token_count": 323, "char_count": 1550, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [ "WAL18680" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:55.863263", "source": { "split": "train_shard_00001", "doc_id": 2176 }, "chunk_id": "train_shard_00001_2176_0", "global_id": 8752 }, { "text": "

Background

Vagococcus fluvialis is a species of lactic acid bacteria found both free-living in river and seawater and associated to hosts, such as marine sponges. This species has been greatly understudied, with no complete genome assembly available to date, which is essential for the characterisation of the mobilome.

Results

We sequenced and assembled de novo the complete genome sequences of five V. fluvialis isolates recovered from marine sponges. Pangenome analysis of the V. fluvialis species (total of 17 genomes) showed a high intraspecific diversity, with 45.5% of orthologous genes found to be strain specific. Despite this diversity, analyses of gene functions clustered all V. fluvialis species together and separated them from other sequenced Vagococcus species. V. fluvialis strains from different habitats were highly similar in terms of functional diversity but the sponge-isolated strains were enriched in several functions related to the marine environment. Furthermore, sponge-isolated strains carried a significantly higher number of mobile genetic elements (MGEs) compared to previously sequenced V. fluvialis strains from other environments. Sponge-isolated strains carried up to 4 circular plasmids each, including a 48-kb conjugative plasmid. Three of the five strains carried an additional circular extrachromosomal sequence, assumed to be an excised prophage as it contained mainly viral genes and lacked plasmid replication genes. Insertion sequences (ISs) were up to five times more abundant in the genomes of sponge-isolated strains compared to the others, including several IS families found exclusively in these genomes.

Conclusions

Our findings highlight the dynamics and plasticity of the V. fluvialis genome. The abundance of mobile genetic elements in the genomes of sponge-isolated V. fluvialis strains suggests that the mobilome might be key to understanding the genomic signatures of symbiosis in bacteria.", "token_count": 482, "char_count": 1968, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5709, "quality_score": 0.7855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:56.508198", "source": { "split": "train_shard_00001", "doc_id": 2177 }, "chunk_id": "train_shard_00001_2177_0", "global_id": 8753 }, { "text": "Comparative genome analysis of Vagococcus fluvialis reveals abundance of mobile genetic elements in sponge-isolated strains.", "token_count": 31, "char_count": 124, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:56.865452", "source": { "split": "train_shard_00001", "doc_id": 2177 }, "chunk_id": "train_shard_00001_2177_1", "global_id": 8754 }, { "text": "The genomic repertoire of vibrios has been extensively studied, particularly regarding their metabolic plasticity, symbiotic interactions, and resistance mechanisms to environmental stressors. However, little is known about the genomic diversity and adaptations of vibrios inhabiting deep-sea marine sediments. In this study, we investigated the genomic diversity of vibrios isolated from deep-sea core sediments collected using a manned submersible off Japan. A total of 50 vibrio isolates were obtained and characterized phenotypically, and by genome sequencing. From this total, we disclosed 22 novel species examining genome-to-genome distance, average amino acid identity, and phenotypes (Alivibrio: 1; Enterovibrio: 1; Photobacterium: 8; Vibrio: 12). The novel species have fallen within known clades (e.g., Fisheri, Enterovibrio, Profundum, and Splendidus) and novel clades (JAMM0721, JAMM0388, JAMM0395). The 28 remainder isolates were identified as known species: Aliivibrio sifiae (2), A. salmonicida (1), Enterovibrio baiacu (1), E. norvegicus (1), Photobacterium profundum (3), P. angustum (1), P. chitiniliticum (1), P. frigidiphilum (1), Photobacterium indicum (1), P. sanguinicancri (1). P. swingsii (2), Vibrio alginolyticus (3), V. anguillarum (1), V. campbellii (1), V. fluvialis (1), V. gigantis (1), V. lentus (1), V. splendidus (4), and V. tasmaniensis (1)", "token_count": 447, "char_count": 1377, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6898, "quality_score": 0.8449, "entities": { "genes": [ "JAMM0388", "JAMM0721", "JAMM0395" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:57.498743", "source": { "split": "train_shard_00001", "doc_id": 2178 }, "chunk_id": "train_shard_00001_2178_0", "global_id": 8755 }, { "text": "Genomic analyses revealed that all 50 vibrios harbored genes associated with high-pressure adaptation, including sensor kinases, chaperones, autoinducer-2 (AI-2) signaling, oxidative damage repair, polyunsaturated fatty acid biosynthesis, and stress response mechanisms related to periplasmic and outer membrane protein misfolding under heat shock and osmotic stress. Additionally, alternative sigma factors, trimethylamine oxide (TMAO) respiration, and osmoprotectant acquisition pathways were identified, further supporting their ability to thrive in deep-sea environments. Notably, the genomes exhibited a high prevalence of antibiotic resistance genes, with antibiotic efflux pumps being the most abundant group. The ugd gene expanded in number in some novel species (Photobacterium satsumensis sp. nov. JAMM1754: 4 copies; Vibrio makurazakiensis sp. nov. JAMM1826: 3 copies). This gene may confer antibiotic (polymyxin) resistance to these vibrios.\n\nGenomic Repertoire of Twenty-Two Novel Vibrionaceae Species Isolated from Marine Sediments.", "token_count": 287, "char_count": 1046, "word_count": 133, "semantic_coherence": 1, "information_density": 0.8496, "quality_score": 0.9248, "entities": { "genes": [ "JAMM1754", "JAMM1826" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:58.086213", "source": { "split": "train_shard_00001", "doc_id": 2178 }, "chunk_id": "train_shard_00001_2178_1", "global_id": 8756 }, { "text": "

Background

Haemorrhagic septicaemia (HS) is a highly fatal and predominant disease in livestock, particularly cattle and buffalo in the tropical regions of the world. Pasteurella multocida (P. multocida), serotypes B:2 and E:2, are reported to be the main causes of HS wherein serotype B:2 is more common in Asian countries including Pakistan and costs heavy financial losses every year. As yet, very little molecular and genomic information related to the HS-associated serotypes of P. multocida isolated from Pakistan is available. Therefore, this study aimed to explore the characteristics of novel bovine isolates of P. multocida serotype B:2 at the genomic level and perform comparative genomic analysis of various P. multocida strains from Pakistan to better understand the genetic basis of pathogenesis and virulence.

Results

To understand the genomic variability and pathogenomics, we characterized three HS-associated P. multocida serotype B:2 strains isolated from the Faisalabad (PM1), Peshawar (PM2) and Okara (PM3) districts of Punjab, Pakistan. Together with the other nine publicly available Pakistani-origin P. multocida strains and a reference strain Pm70, a comparative genomic analysis was performed. The sequenced strains were characterized as serotype B and belong to ST-122. The strains contain no plasmids; however, each strain contains at least two complete prophages. The pan-genome analysis revealed a higher number of core genes indicating a close resemblance to the studied genomes and very few genes (1%) of the core genome serve as a part of virulence, disease, and defense mechanisms. We further identified that studied P. multocida B:2 strains harbor common antibiotic resistance genes, specifically PBP3 and EF-Tu. Remarkably, the distribution of virulence factors revealed that OmpH and plpE were not present in any P. multocida B:2 strains while the presence of these antigens was reported uniformly in all serotypes of P", "token_count": 497, "char_count": 1971, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5903, "quality_score": 0.7951, "entities": { "genes": [ "PBP3", "PM1", "PM2", "PM3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:58.750488", "source": { "split": "train_shard_00001", "doc_id": 2179 }, "chunk_id": "train_shard_00001_2179_0", "global_id": 8757 }, { "text": "multocida.

Conclusion

This study's findings indicate the absence of OmpH and PlpE in the analyzed P. multocida B:2 strains, which are known surface antigens and provide protective immunity against P. multocida infection. The availability of additional genomic data on P. multocida B:2 strains from Pakistan will facilitate the development of localized therapeutic agents and rapid diagnostic tools specifically targeting HS-associated P. multocida B:2 strains.\n\nGenomic characterization and comparative genomic analysis of HS-associated Pasteurella multocida serotype B:2 strains from Pakistan.", "token_count": 152, "char_count": 601, "word_count": 77, "semantic_coherence": 1, "information_density": 0.6883, "quality_score": 0.8442, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:20:59.238413", "source": { "split": "train_shard_00001", "doc_id": 2179 }, "chunk_id": "train_shard_00001_2179_1", "global_id": 8758 }, { "text": "Escherichia coli is a common bacterial species in the gastrointestinal tracts of warm-blooded animals and humans. Pathogenicity and antimicrobial resistance in E. coli may emerge via host switching from animal reservoirs. Despite its potential clinical importance, knowledge of the population structure of commensal E. coli within wild hosts and the epidemiological links between E. coli in nonhuman hosts and E. coli in humans is still scarce. In this study, we analyzed the whole-genome sequencing data of a collection of 119 commensal E. coli strains recovered from the guts of 55 mammal and bird species in Mexico and Venezuela in the 1990s. We observed low concordance between the population structures of E. coli isolates colonizing wild animals and the phylogeny, taxonomy, and ecological and physiological attributes of the host species, with distantly related E. coli strains often colonizing the same or similar host species and distantly related host species often hosting closely related E. coli strains. We found no evidence for recent transmission of E. coli genomes from wild animals to either domesticated animals or humans. However, multiple livestock- and human-related virulence factor genes were present in E. coli of wild animals, including virulence factors characteristic of Shiga toxin-producing E. coli (STEC) and atypical enteropathogenic E. coli (aEPEC), where several isolates from wild hosts harbored the locus of enterocyte effacement (LEE) pathogenicity island. Moreover, E. coli isolates from wild animal hosts often harbored known antibiotic resistance determinants, including those against ciprofloxacin, aminoglycosides, tetracyclines, and beta-lactams, with some determinants present in multiple, distantly related E", "token_count": 520, "char_count": 1853, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:20:59.880876", "source": { "split": "train_shard_00001", "doc_id": 2180 }, "chunk_id": "train_shard_00001_2180_0", "global_id": 8759 }, { "text": "coli lineages colonizing very different host animals. We conclude that genome pools of E. coli colonizing the guts of wild animals and humans share virulence and antibiotic resistance genes, underscoring the idea that wild animals could serve as reservoirs for E. coli pathogenicity in human and livestock infections.IMPORTANCEEscherichia coli is a clinically important bacterial species implicated in human- and livestock-associated infections worldwide. The bacterium is known to reside in the guts of humans, livestock, and wild animals. Although wild animals are recognized as potential reservoirs for pathogenic E. coli strains, the knowledge of the population structure of E. coli in wild hosts is still scarce. In this study, we used fine resolution of whole-genome sequencing to provide novel insights into the evolution of E. coli genomes from a small yet diverse collection of strains recovered within a broad range of wild animal species (including mammals and birds), the coevolution of E. coli strains with their hosts, and the genetics of pathogenicity of E. coli strains in wild hosts in Mexico. Our results provide evidence for the clinical importance of wild animals as reservoirs for pathogenic strains and highlight the need to include nonhuman hosts in the surveillance programs for E. coli infections.\n\nGenomic Epidemiology and Evolution of <i>Escherichia coli</i> in Wild Animals in Mexico.", "token_count": 401, "char_count": 1498, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5374, "quality_score": 0.7687, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:00.502228", "source": { "split": "train_shard_00001", "doc_id": 2180 }, "chunk_id": "train_shard_00001_2180_1", "global_id": 8760 }, { "text": "Several marine Debaryomyces hansenii strains have shown probiotic effects on aquatic animals, and D. hansenii-derived β-glucans have recently provided immunostimulant effects on goat leukocytes. This study assessed the probiotic effects of live yeast D. hansenii CBS 8339 on newborn goats administered orally, and subsequently challenged in vitro with Escherichia coli. D. hansenii CBS 8339 demonstrated the capacity to survive gastrointestinal tract conditions (bile salts and acid pH tolerance) and adhere to goat intestine. Twelve Saanen × Nubian crossbred newborn goats (2.9 ± 0.47 kg) were fed with a controlled diet or D. hansenii (0.7 g/kg body weight per day)-supplemented milk for 30 days. Blood samples of newborn goats were taken at days 15 and 30, and peripheral blood leukocytes were isolated for bacterial challenge, and immunological and antioxidant analyses. Despite cell viability was higher in leukocytes of goat kids fed with the yeast supplement, protection against E. coli challenge was not significantly affected. On the other hand, at day 15, oral administration of D. hansenii enhanced respiratory burst and catalase activity and increased superoxide dismutase activity after challenge. In contrast, at day 30, administration of the yeast supplement increased peroxidase activity and enhanced nitric oxide production and catalase activity after challenge. Finally, the yeast-supplemented diet upregulated the expression of the receptor genes TLR (2, 4, 6), modulator genes Raf.1, Syk, and Myd88, transcription factor gene AP-1, and cytokine genes IL-1β and TNF-α only at day 15 in leukocytes from unchallenged goat kids. These results demonstrated that a short time (15 days) of orally administering the probiotic D. hansenii CBS 8339 to newborn goats stimulated innate immune and antioxidant parameters and the expression of immune-related gene signaling pathways.", "token_count": 528, "char_count": 1889, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8123, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:21:01.162347", "source": { "split": "train_shard_00001", "doc_id": 2181 }, "chunk_id": "train_shard_00001_2181_0", "global_id": 8761 }, { "text": "Probiotic effects of marine Debaryomyces hansenii CBS 8339 on innate immune and antioxidant parameters in newborn goats.", "token_count": 36, "char_count": 120, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:01.520347", "source": { "split": "train_shard_00001", "doc_id": 2181 }, "chunk_id": "train_shard_00001_2181_1", "global_id": 8762 }, { "text": "Kluyveromyces marxianus var. marxianus, a causal agent of onion (Allium cepa L.) soft rot, was originally isolated from Walla Walla sweet onion bulbs grown in Oregon and subsequently isolated from onion throughout the southeast Washington onion-growing area, but was not found to be infecting dry bulb storage onions grown in central Washington (1). During September of 2001, a yeast was isolated from dry storage onion bulbs (cv. Teton) grown under sprinkler irrigation in central Washington, exhibiting soft rot symptoms and identified to be K. marxianus var. marxianus (2). Koch's postulate was completed using cv. Teton bulbs surface disinfested with 0.5% NaOCl for 2 min. This isolate and four isolates of Kluyveromyces marxianus var. marxianus (1) were cultured on potato dextrose agar and resuspended to an OD600 = 0.3 (approximately 105 CFU/ml). One-half of a milliliter of each isolate was inoculated to onion using the cut bulb method with three replicates and incubated in a moist chamber at 25°C for 7 days. Onion slices inoculated with the new isolate exhibited soft rot symptoms similar to those caused by the known isolates while no symptoms were observed for the water control. The yeast reisolated from symptomatic tissue was confirmed to be K. marxianus var. marxianus (2). The identification of K. marxianus var. marxianus infecting dry bulb storage onions grown in the Columbia Basin is of interest because the disease can be confused with bacterial soft rot and could become a serious problem in this important storage onion-growing region. References: (1) D. A. Johnson et al. Plant Dis. 72:359, 1988. (2) N. J. W. Kreger-van Rig, ed. The Yeasts: A Taxonomic Study. Elsevier, Amsterdam, 1984.", "token_count": 509, "char_count": 1736, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:02.152446", "source": { "split": "train_shard_00001", "doc_id": 2182 }, "chunk_id": "train_shard_00001_2182_0", "global_id": 8763 }, { "text": "Occurrence of Kluyveromyces marxianus var. marxianus Causing Onion Soft Rot in the Columbia Basin of Washington State.", "token_count": 35, "char_count": 118, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:02.519571", "source": { "split": "train_shard_00001", "doc_id": 2182 }, "chunk_id": "train_shard_00001_2182_1", "global_id": 8764 }, { "text": "Raoultella planticola harboring genes that confer resistance to antimicrobials, such as carbapenems, have been associated with severe infections in immunocompromised patients. In this study, we reported the first whole genome sequence of a Brazilian isolate of R. planticola and the genomic context of antibiotic resistance markers. By whole-genome sequencing (WGS) of a carbapenem-resistant R. planticola isolate, RpHUM1, we found 23 resistance-encoding genes belonging to 9 classes of antibiotics (aminoglycosides, β-lactams, fluoroquinolones, fosfomycin, macrolides, phenicols, sulfonamides, tetracycline, and diaminopyrimidine derivatives) and 3 plasmids (RpHUM1pEaer-4382s, RpHUM1_pFDAARGOS_440, and RpHUM1pRSF1010). This isolate coharbored the genes blaKPC-2, which is carried by the plasmid RpHUM1pEaer-4382s, and blaNDM-1 and blaCTX-M-15 all located in the accessory genome. In addition, these genes were associated with, at least, one mobile genetic element. This comprehensive knowledge is of great importance for implementation of control measures to prevent the rapid dissemination of this neglected microorganism and their genetic resistance background.\n\nWhole Genome Sequencing of an Extensively Drug-Resistant Raoultella planticola Isolate Containing blaKPC-2, blaNDM-1, and blaCTX-M-15.", "token_count": 493, "char_count": 1438, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6933, "quality_score": 0.8466, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:03.168260", "source": { "split": "train_shard_00001", "doc_id": 2183 }, "chunk_id": "train_shard_00001_2183_0", "global_id": 8765 }, { "text": "

Background

Small-quantity lipid-based nutrient supplements (SQ-LNS), which has been widely tested to reduce child stunting, has largely modest effects to date, but the mechanisms underlying these modest effects are unclear. Child stunting is a longstanding indicator of chronic undernutrition and it remains a prevalent public health problem. The infant gut microbiome may be a key contributor to stunting; and mother and infant fucosyltransferase (FUT) phenotypes are important determinants of infant microbiome composition.

Methods

We investigated whether mother-infant FUT status (n = 792) and infant gut microbiome composition (n = 354 fecal specimens from 172 infants) modified the impact of an infant and young child feeding (IYCF) intervention, that included SQ-LNS, on stunting at age 18 months in secondary analysis of a randomized trial in rural Zimbabwe.

Findings

We found that the impact of the IYCF intervention on stunting was modified by: (i) mother-infant FUT2+/FUT3- phenotype (difference-in-differences -32.6% [95% CI: -55.3%, -9.9%]); (ii) changes in species composition that reflected microbiome maturation (difference-in-differences -68.1% [95% CI: -99.0%, -28.5%); and (iii) greater relative abundance of B. longum (differences-in-differences 49.1% [95% CI: 26.6%, 73.6%]). The dominant strains of B", "token_count": 415, "char_count": 1343, "word_count": 180, "semantic_coherence": 1, "information_density": 0.7056, "quality_score": 0.8528, "entities": { "genes": [ "FUT2", "FUT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:03.796696", "source": { "split": "train_shard_00001", "doc_id": 2184 }, "chunk_id": "train_shard_00001_2184_0", "global_id": 8766 }, { "text": "longum when the intervention started were most similar to the proficient milk oligosaccharide utilizer subspecies infantis, which decreased with infant age and differed by mother-infant FUT2+/FUT3- phenotypes.

Interpretation

These findings indicate that a persistently \"younger\" microbiome at initiation of the intervention reduced its benefits on stunting in areas with a high prevalence of growth restriction.

Funding

Bill and Melinda Gates Foundation, UK DFID/Aid, Wellcome Trust, Swiss Agency for Development and Cooperation, US National Institutes of Health, UNICEF, and Nutricia Research Foundation.\n\nBifidobacterium longum and microbiome maturation modify a nutrient intervention for stunting in Zimbabwean infants.", "token_count": 193, "char_count": 736, "word_count": 91, "semantic_coherence": 1, "information_density": 0.8022, "quality_score": 0.9011, "entities": { "genes": [ "FUT2", "FUT3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:04.248519", "source": { "split": "train_shard_00001", "doc_id": 2184 }, "chunk_id": "train_shard_00001_2184_1", "global_id": 8767 }, { "text": "

Background

Our understanding of the factors influencing the emergence, dissemination and global distribution of epidemic clones of bacteria is limited. ST59 is a major epidemic clone of community-associated MRSA in East Asia, responsible for extensive morbidity and mortality, but has a much lower prevalence in other parts of the world. The geographic origin of ST59 and its international routes of dissemination are unclear and disputed in the literature.

Results

To investigate the origin and spread of the ST59 clone, we obtained whole genome sequences of isolates from four continents, sampled over more than a decade, and carried out a time-scaled phylogeographic analysis. We discover that two distinct ST59 clades emerged concurrently, in East Asia and the USA, but underwent clonal expansion at different times. The East Asia clade was strongly enriched for gene determinants associated with antibiotic resistance, consistent with regional differences in antibiotic usage. Both clones spread independently to Australia and Europe, and we found evidence of the persistence of multi-drug resistance following export from East Asia. Direct transfer of strains between Taiwan and the USA was not observed in either direction, consistent with geographic niche exclusion.

Conclusions

Our results resolve a longstanding controversy regarding the origin of the ST59 clone, revealing the major global source and sink populations and routes for the spread of multi-drug resistant clones. Additionally, our findings indicate that diversification of the accessory genome of epidemic clones partly reflects region-specific patterns of antibiotic usage, which may influence bacterial fitness after transmission to different geographic locations.\n\nIdentification of source and sink populations for the emergence and global spread of the East-Asia clone of community-associated MRSA.", "token_count": 410, "char_count": 1898, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5947, "quality_score": 0.7973, "entities": { "genes": [ "ST59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:04.880842", "source": { "split": "train_shard_00001", "doc_id": 2185 }, "chunk_id": "train_shard_00001_2185_0", "global_id": 8768 }, { "text": "

Aims

To obtain yeast and bacteria from ruminal fluids that possess aflatoxin B1 (AFB1 ) detoxifying ability for use in animal feed.

Methods and results

Sources of isolation were ruminal fluids of three nonfistulated dairy cows, fed diets containing cassava pulp, rice straw or distillery yeast sludge. The isolation was carried out to screen for the isolates that were active in both anaerobic and aerobic conditions. Three yeast and three bacteria isolates were selected. Up to 85% of AFB1 was detoxified by yeast isolates and up to 60% AFB1 reduction was evident by bacteria isolates. Two yeast isolates were identified as Kluyveromyces marxianus and one isolate as Pichia kudriavzevii. The three bacteria isolates were identified as Enterococcus faecium, Corynebacterium phoceense and C. vitaeruminis. All strains showed high biomass production when cultivated in medium with 80 g l-1 glucose.

Conclusions

The isolated yeast and bacteria with AFB1 detoxifying ability showed a good potential to be applied as an aflatoxin-detoxifying agent to ingredients used to feed dairy cattle.

Significance and impact of the study

The abilities of isolates to survive and be active in anaerobic and aerobic conditions rendered them to be active in cattle's rumen. Their biomass could be produced in bulk and used as feed supplement for aflatoxin detoxification in dairy cattle.\n\nIsolation and screening of aflatoxin-detoxifying yeast and bacteria from ruminal fluids to reduce aflatoxin B<sub>1</sub> contamination in dairy cattle feed.", "token_count": 479, "char_count": 1634, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:05.528918", "source": { "split": "train_shard_00001", "doc_id": 2186 }, "chunk_id": "train_shard_00001_2186_0", "global_id": 8769 }, { "text": "Cryptic fungal pathogens pose significant identification and disease management challenges due to their morphological resemblance to known pathogenic species while harboring genetic and (often) infection-relevant trait differences. The cryptic fungal pathogen Aspergillus latus , an allodiploid hybrid originating from Aspergillus spinulosporus and an unknown close relative of Aspergillus quadrilineatus within section Nidulantes , remains poorly understood. The absence of accurate diagnostics for A. latus has led to misidentifications, hindering epidemiological studies and the design of effective treatment plans. We conducted an in-depth investigation of the genomes and phenotypes of 44 globally distributed isolates (41 clinical isolates and three type strains) from Aspergillus section Nidulantes . We found that 21 clinical isolates were A. latus ; notably, standard methods of pathogen identification misidentified all A. latus isolates. The remaining isolates were identified as A. spinulosporus (8), A. quadrilineatus (1), or A. nidulans (11). Phylogenomic analyses shed light on the origin of A. latus , indicating one or two hybridization events gave rise to the species during the Miocene, approximately 15.4 to 8.8 million years ago. Characterizing the A. latus pangenome uncovered substantial genetic diversity within gene families and biosynthetic gene clusters. Transcriptomic analysis revealed that both parental genomes are actively expressed in nearly equal proportions and respond to environmental stimuli. Further investigation into infection-relevant chemical and physiological traits, including drug resistance profiles, growth under oxidative stress conditions, and secondary metabolite biosynthesis, highlight distinct phenotypic profiles of the hybrid A. latus compared to its parental and closely related species. Leveraging our comprehensive genomic and phenotypic analyses, we propose five genomic and phenotypic markers as diagnostics for A. latus species identification. These findings provide valuable insights into the evolutionary origin, genomic outcome, and phenotypic implications of hybridization in a cryptic fungal pathogen, thus enhancing our understanding of the underlying processes contributing to fungal pathogenesis", "token_count": 508, "char_count": 2265, "word_count": 301, "semantic_coherence": 1, "information_density": 0.6478, "quality_score": 0.8239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:06.188735", "source": { "split": "train_shard_00001", "doc_id": 2187 }, "chunk_id": "train_shard_00001_2187_0", "global_id": 8770 }, { "text": "Furthermore, our study underscores the effectiveness of extensive genomic and phenotypic analyses as a promising approach for developing diagnostics applicable to future investigations of cryptic and emerging pathogens.\n\nEvolutionary origin, population diversity, and diagnostics for a cryptic hybrid pathogen", "token_count": 62, "char_count": 309, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8205, "quality_score": 0.9103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:06.553328", "source": { "split": "train_shard_00001", "doc_id": 2187 }, "chunk_id": "train_shard_00001_2187_1", "global_id": 8771 }, { "text": "A single strain of Candida anglica, isolated from cider, is available in international yeast collections. We present here seven new strains isolated from French PDO cheeses. For one of the cheese strains, we achieved a high-quality genome assembly of 13.7 Mb with eight near-complete telomere-to-telomere chromosomes. The genomes of two additional cheese strains and of the cider strain were also assembled and annotated, resulting in a core genome of 5966 coding sequences. Phylogenetic analysis showed that the seven cheese strains clustered together, away from the cider strain. Mating-type locus analysis revealed the presence of a MATa locus in the cider strain but a MATalpha locus in all cheese strains. The presence of LINE retrotransposons at identical genome position in the cheese strains, and two different karyotypic profiles resulting from chromosomal rearrangements were observed. Together, these findings are consistent with clonal propagation of the cheese strains. Phenotypic trait variations were observed within the cheese population under stress conditions whereas the cider strain was found to have a much greater capacity for growth in all conditions tested.\n\nDifferential adaptation of the yeast Candida anglica to fermented food", "token_count": 295, "char_count": 1253, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6054, "quality_score": 0.8027, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:07.115635", "source": { "split": "train_shard_00001", "doc_id": 2188 }, "chunk_id": "train_shard_00001_2188_0", "global_id": 8772 }, { "text": "The purpose of this study was to isolate, identify, and characterize the thermotolerant yeasts for use in high-temperature ethanol fermentation. Thermotolerant yeasts were isolated and screened from soil samples collected from the Mekong Delta, Vietnam, using the enrichment method. Classification and identification of the selected thermotolerant yeasts were performed using matrix-assisted laser desorption ionization/time-of-fight mass spectrometry (MALDI-TOF/MS) and nucleotide sequencing of the D1/D2 domain of the 26S rDNA and the internal transcribed spacer (ITS) 1 and 2 regions. The ethanol production by the selected thermotolerant yeast was carried out using pineapple waste hydrolysate (PWH) as feedstock. A total of 174 yeast isolates were obtained from 80 soil samples collected from 13 provinces in the Mekong Delta, Vietnam. Using MALDI-TOF/MS and nucleotide sequencing of the D1/D2 domain and the ITS 1 and 2 regions, six different yeast species were identified, including Meyerozyma caribbica, Saccharomyces cerevisiae, Candida tropicalis, Torulaspora globosa, Pichia manshurica, and Pichia kudriavzevii. Among the isolated thermotolerant yeasts, P. kudriavzevii CM4.2 displayed great potential for high-temperature ethanol fermentation. The maximum ethanol concentration (36.91 g/L) and volumetric ethanol productivity (4.10 g/L h) produced at 45 °C by P. kudriavzevii CM4.2 were achieved using PWH containing 103.08 g/L of total sugars as a feedstock. These findings clearly demonstrate that the newly isolated thermotolerant yeast P. kudriavzevii CM4.2 has a high potential for second-generation bioethanol production at high temperature.\n\nIsolation and characterization of thermotolerant yeasts for the production of second-generation bioethanol", "token_count": 511, "char_count": 1767, "word_count": 238, "semantic_coherence": 1, "information_density": 0.563, "quality_score": 0.7815, "entities": { "genes": [ "CM4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:07.767147", "source": { "split": "train_shard_00001", "doc_id": 2189 }, "chunk_id": "train_shard_00001_2189_0", "global_id": 8773 }, { "text": "Candidatus Altiarchaea are widespread across aquatic subsurface ecosystems and possess a highly conserved core genome, yet adaptations of this core genome to different biotic and abiotic factors based on gene expression remain unknown. Here, we investigated the metatranscriptome of two Ca . Altiarchaeum populations that thrive in two substantially different subsurface ecosystems. In Crystal Geyser, a high-CO 2 groundwater system in the USA, Ca . Altiarchaeum crystalense co-occurs with the symbiont Ca . Huberiarchaeum crystalense, while in the Muehlbacher sulfidic spring in Germany, an artesian spring high in sulfide concentration, Ca . A. hamiconexum is heavily infected with viruses. We here mapped metatranscriptome reads against their genomes to analyze the in situ expression profile of their core genomes. Out of 537 shared gene clusters, 331 were functionally annotated and 130 differed significantly in expression between the two sites. Main differences were related to genes involved in cell defense like CRISPR-Cas, virus defense, replication, and transcription as well as energy and carbon metabolism. Our results demonstrate that altiarchaeal populations in the subsurface are likely adapted to their environment while influenced by other biological entities that tamper with their core metabolism. We consequently posit that viruses and symbiotic interactions can be major energy sinks for organisms in the deep biosphere.

(Originality-Significance Statement

Organisms of the uncultivated phylum Ca . Altiarchaeota are globally widespread and fulfill essential roles in carbon cycling, e . g ., carbon fixation in the continental subsurface. Here, we show that the transcriptional activity of organisms in the continental subsurface differ significantly depending on the geological and microbial setting of the ecosystem explaining many of the previously observed physiological traits of this organism group.)\n\nDifferential expression of core metabolic functions inCandidatusAltiarchaeum inhabiting distinct subsurface ecosystems", "token_count": 483, "char_count": 2065, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:08.415204", "source": { "split": "train_shard_00001", "doc_id": 2190 }, "chunk_id": "train_shard_00001_2190_0", "global_id": 8774 }, { "text": "

Background

Shigella sonnei , a leading cause of shigellosis, is a global health concern, particularly affecting children under five. The emergence of multidrug-resistant (MDR) strains, including resistance to key antibiotics like ciprofloxacin and third-generation cephalosporins, exacerbates treatment challenges. This study investigates the genetic and antimicrobial resistance profiles of S. sonnei isolates from Tunisia, focusing on an outbreak of extended-spectrum beta-lactamase (ESBL)-producing strains.

Methods

We analysed nine S. sonnei isolates collected between September 2022 and January 2023 from Tunisian hospitals, using whole genome sequencing (WGS). Standard bacterial identification and serotyping methods were employed alongside antimicrobial susceptibility testing. We examined the genetic relatedness of the isolates, identified resistance genes, and characterised virulence factors.

Results

All the isolates were confirmed as S. sonnei H6, biotype a, and belonged to lineage 3, clade 6 and sub-lineage 3. All harboured bla CTX-M-15 , conferring resistance to third-generation cephalosporins. These were chromosomally integrated, suggesting stable resistance. Five isolates exhibited fluoroquinolone resistance associated with the qn rS1 gene, and all isolates had a single quinolone resistance-determining region mutation (GyrA-D87Y). Additionally, the plasmid-borne mph A gene, conferring resistance to macrolides, was prevalent. Single-linkage hierarchical clustering analysis indicated close genetic relationships with S. sonnei strains from Europe, particularly France and the UK (0 to 31 core genome MLST allele differences), indicating recent international dissemination.

Conclusion

This study provides the first comprehensive molecular characterisation of MDR S. sonnei in Tunisia, highlighting a significant public health threat. The findings underscore the importance of continuous genomic surveillance to track the spread of resistant strains and inform public health interventions.", "token_count": 520, "char_count": 2050, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6965, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:21:09.071839", "source": { "split": "train_shard_00001", "doc_id": 2191 }, "chunk_id": "train_shard_00001_2191_0", "global_id": 8775 }, { "text": "Whole Genome Sequencing Analysis of a Recent Multi-Drug ResistantShigella sonneiOutbreak Among Tunisian Children", "token_count": 35, "char_count": 119, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:09.435573", "source": { "split": "train_shard_00001", "doc_id": 2191 }, "chunk_id": "train_shard_00001_2191_1", "global_id": 8776 }, { "text": "

Background

Colistin is commonly used as a last-resort antibiotic for multidrug resistance (MDR) bacterial infections. The emergence of colistin-resistant (CL-R) Salmonella has become a significant public health concern. However, the prevalence of CL-R Salmonella in Guizhou province remains unknown. Therefore, it is necessary to monitor CL-R Salmonella in Guizhou and systematically elucidate their characteristics-related resistance, virulence, and molecular epidemiology to develop effective public health strategies against resistant pathogens.

Methods

The CL-R Salmonella isolates were identified from 933 Salmonella isolates by antimicrobial resistance testing. To further evaluate the molecular epidemiology, the CL-R Salmonella isolates underwent whole-genome sequencing (WGS) analysis followed by bioinformatic analysis.

Results

A total of 43 CL-R isolates (4.6%) were identified from 933 Salmonella isolates, of which 39 isolates being MDR (resistance to three or more classes of antimicrobials). WGS analysis revealed 34 antibiotic resistance genes (ARGs), and point mutations in the gyrA gene (D87Y and D87G) were identified in all 43 CL-R isolates. Only one isolate carried the mcr-1.1 gene, a known colistin resistance. All CL-R isolates were found to carry multidrug efflux pumps. Furthermore, the most common resistance gene was aac(6')-ly (40 out of 43), followed by blaTEM-1 (39 out of 43). The majority of CL-R isolates contained the virulence factor spvB and a notable diversity in other virulence factors with varied functions", "token_count": 508, "char_count": 1657, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:10.094682", "source": { "split": "train_shard_00001", "doc_id": 2192 }, "chunk_id": "train_shard_00001_2192_0", "global_id": 8777 }, { "text": "Core genome multilocus sequence typing (cgMLST) revealed that 43 CL-R Salmonella isolates were divided into 19 cgSTs, with cgST179151 (10 out of 43) being the most prevalent. Additionally, the CL-R Salmonella isolates exhibited genetic similarities with human Salmonella isolates from Poland, Canada, and Zhejiang province. Among the 42 CL-R isolates lacking markers for CL-R, 12 single-nucleotide variations (SNVs) were observed in 24 isolates using genome-wide association study (GWAS) analysis, which was possibly associated with colistin resistance.

Conclusion

This study revealed that the majority of CL-R Salmonella isolates in Guizhou province exhibited MDR, with complex resistance mechanisms, representing a significant public health challenge. The genetic similarities between isolates from Guizhou and other regions suggested the possibility of international transmission or shared reservoirs of resistance. These results highlighted the urgent need for enhanced surveillance and effective public health strategies to address the risks posed by these pathogens in Guizhou.\n\nGenome analysis of colistin-resistant Salmonella isolates from human sources in Guizhou of southwestern China, 2019-2023.", "token_count": 336, "char_count": 1248, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:10.702333", "source": { "split": "train_shard_00001", "doc_id": 2192 }, "chunk_id": "train_shard_00001_2192_1", "global_id": 8778 }, { "text": "While the role of flies as potential vectors for bacterial transmission is well recognized, the epidemiological features and genomic characteristics of associated antimicrobial-resistant strains remain underexplored. This study conducted a nationwide surveillance including 3689 flies and 838 isolates from sixteen human communities (HCs) and eight animal farms (AFs) across 21 provinces in China. Our findings revealed high carriage rates of carbapenem-resistant Enterobacteriaceae (CRE) in flies, with 27.0 % in AFs and 15.3 % in HCs. Among the 705 CRE strains identified, Providencia spp. (n = 356) and Escherichia coli (n = 231) were predominant, with 90.6 % attributed to the dissemination of the blaNDM gene. Phylogenetic tree analysis highlighted frequent clonal transmission events, with over 18 and 13 clonal evolutionary clades in Providencia spp. and E. coli, respectively. Notably, spearman analysis linked the increase of CRE prevalence in AFs flies to environmental factors like precipitation (p < 0.028) and temperature (p < 0.037), while in HCs, it positively corelated with the total meat production (p < 0.027) in each province except for Hainan. Despite significant differences in ciprofloxacin resistance (p ≤ 0.001) among E. coli strains from HCs and AFs, core genome cluster analysis and Uniform Manifold Approximation and Projection (UMAP) approach indicated these strains exhibiting close relatedness to clinical strains. This comprehensive study underscores the critical role of flies in the escalation of CRE spread within the ecosystem in China. Flies found in both HCs and AFs contribute to the dissemination of CRE, highlighting the need for urgent interventions to address this pressing issue.", "token_count": 480, "char_count": 1734, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:11.393522", "source": { "split": "train_shard_00001", "doc_id": 2193 }, "chunk_id": "train_shard_00001_2193_0", "global_id": 8779 }, { "text": "Epidemiological and genomic analysis revealed the significant role of flies in dissemination of carbapenem-resistant Enterobacteriaceae (CRE) in China.", "token_count": 37, "char_count": 151, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:11.778274", "source": { "split": "train_shard_00001", "doc_id": 2193 }, "chunk_id": "train_shard_00001_2193_1", "global_id": 8780 }, { "text": "The ability of Kluyveromyces marxianus IMB3 to decolorize Remazol Black-B dye was investigated. The effect of environmental conditions, such as pH and temperature were examined. No noticeable effects on decolorization were observed when pH varied from 3.0-5.5. Maximum colour removal, 98%, was achieved at 37 degrees C. Little or no colour removal was detected when K. marxianus IMB3 was incubated under anaerobic conditions. Further investigation, in which decolorization was monitored under extreme temperatures and low pH (to inhibit growth) and using ten fold dense inoculum, revealed that decolorization was due to biosorption to the yeast cells and not due to a metabolic reaction.\n\nDecolorization of Remazol Black-B using a thermotolerant yeast, Kluyveromyces marxianus IMB3.", "token_count": 216, "char_count": 782, "word_count": 114, "semantic_coherence": 1, "information_density": 0.7018, "quality_score": 0.8509, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:12.248065", "source": { "split": "train_shard_00001", "doc_id": 2194 }, "chunk_id": "train_shard_00001_2194_0", "global_id": 8781 }, { "text": "

Introduction

Pseudomonas aeruginosa (P.aeruginosa) is an important opportunistic pathogen with broad environmental adaptability and complex drug resistance. Single-molecule real-time (SMRT) sequencing technique has longer read-length sequences, more accuracy, and the ability to identify epigenetic DNA alterations.

Methods

This study applied SMRT technology to sequence a clinical strain P. aeruginosa PA3 to obtain its genome sequence and methylation modification information. Genomic, comparative, pan-genomic, and epigenetic analyses of PA3 were conducted.

Results

General genome annotations of PA3 were discovered, as well as information about virulence factors, regulatory proteins (RPs), secreted proteins, type II toxin-antitoxin (TA) pairs, and genomic islands. A genome-wide comparison revealed that PA3 was comparable to other P. aeruginosa strains in terms of identity, but varied in areas of horizontal gene transfer (HGT). Phylogenetic analysis showed that PA3 was closely related to P. aeruginosa 60503 and P. aeruginosa 8380. P. aeruginosa's pan-genome consists of a core genome of roughly 4,300 genes and an accessory genome of at least 5,500 genes. The results of the epigenetic analysis identified one main methylation sites, N6-methyladenosine (m6A) and 1 motif (CATNNNNNNNTCCT/AGGANNNNNNNATG). 16 meaningful methylated sites were picked", "token_count": 422, "char_count": 1428, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7247, "quality_score": 0.8624, "entities": { "genes": [ "PA3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:12.878404", "source": { "split": "train_shard_00001", "doc_id": 2195 }, "chunk_id": "train_shard_00001_2195_0", "global_id": 8782 }, { "text": "Among these, purH, phaZ, and lexA are of great significance playing an important role in the drug resistance and biological environment adaptability of PA3, and the targeting of these genes may benefit further antibacterial studies.

Disucssion

This study provided a detailed visualization and DNA methylation information of the PA3 genome and set a foundation for subsequent research into the molecular mechanism of DNA methyltransferase-controlled P. aeruginosa pathogenicity.\n\nComparative genomics and DNA methylation analysis of Pseudomonas aeruginosa clinical isolate PA3 by single-molecule real-time sequencing reveals new targets for antimicrobials.", "token_count": 181, "char_count": 697, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7674, "quality_score": 0.8837, "entities": { "genes": [ "PA3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:13.322231", "source": { "split": "train_shard_00001", "doc_id": 2195 }, "chunk_id": "train_shard_00001_2195_1", "global_id": 8783 }, { "text": "Disease resistance improvement remains a major focus in breeding programs as diseases continue to devastate Brassica production systems due to intensive cultivation and climate change. Genomics has paved the way to understand the complex genomes of Brassicas, which has been pivotal in the dissection of the genetic underpinnings of agronomic traits driving the development of superior cultivars. The new era of genomics-assisted disease resistance breeding has been marked by the development of high-quality genome references, accelerating the identification of disease resistance genes controlling both qualitative (major) gene and quantitative resistance. This facilitates the development of molecular markers for marker assisted selection and enables genome editing approaches for targeted gene manipulation to enhance the genetic value of disease resistance traits. This review summarizes the key advances in the development of genomic resources for Brassica species, focusing on improved genome references, based on long-read sequencing technologies and pangenome assemblies. This is further supported by the advances in pathogen genomics, which have resulted in the discovery of pathogenicity factors, complementing the mining of disease resistance genes in the host. Recognizing the co-evolutionary arms race between the host and pathogen, it is critical to identify novel resistance genes using crop wild relatives and synthetic cultivars or through genetic manipulation via genome-editing to sustain the development of superior cultivars. Integrating these key advances with new breeding techniques and improved phenotyping using advanced data analysis platforms will make disease resistance improvement in Brassica species more efficient and responsive to current and future demands.\n\nKey Advances in the New Era of Genomics-Assisted Disease Resistance Improvement of Brassica Species.", "token_count": 399, "char_count": 1931, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5747, "quality_score": 0.7874, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:13.942178", "source": { "split": "train_shard_00001", "doc_id": 2196 }, "chunk_id": "train_shard_00001_2196_0", "global_id": 8784 }, { "text": "Superoxide dismutase (SOD) activity is one major defense line against oxidative stress for all of the aerobic organisms, and industrial production of this enzyme is highly demanded. The Cu/Zn superoxide dismutase gene (KmSOD1) of Kluyveromyces marxianus L3 was cloned and characterized. The deduced KmSod1p protein shares 86% and 71% of identity with Kluyveromyces lactis and Saccharomyces cerevisiae Sod1p, respectively. The characteristic motifs and the amino acid residues involved in coordinating copper and zinc and in enzymatic function were conserved. To the aim of developing a microbial production of Cu/Zn superoxide dismutase, we engineered the K. marxianus L3 strain with the multicopy plasmid YG-KmSOD1 harboring the KmSOD1 gene. The production of KmSOD1p in K. marxianus L3 and K. marxianus L3 (pYG-KmSOD1) in response to different compositions of the culture medium was evaluated. The highest specific activity (472 U(SOD) mg(prot) (-1)) and the highest volumetric yield (8.8 x 10(5) U(SOD) l(-1)) were obtained by the recombinant strain overexpressing KmSOD1 in the presence of Cu(2+) and Zn(2+) supplements to the culture media. The best performing culture conditions were positively applied to a laboratory scale fed-batch process reaching a volumetric yield of 1.4 x 10(6) U(SOD) l(-1).\n\nCharacterization of the superoxide dismutase SOD1 gene of Kluyveromyces marxianus L3 and improved production of SOD activity.", "token_count": 436, "char_count": 1432, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7929, "entities": { "genes": [ "SOD1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:14.571223", "source": { "split": "train_shard_00001", "doc_id": 2197 }, "chunk_id": "train_shard_00001_2197_0", "global_id": 8785 }, { "text": "Two mixed starter cultures were used for sourdough bread making to evaluate their ability to improve quality and increase bread shelf-life: Lactobacillus delbrueckii ssp. bulgaricus or Lactobacillus helveticus mixed with the lactose fermenting yeast Kluyveromyces marxianus as alternative baker's yeast. Control sourdough breads (K. marxianus) without the addition of bacteria, were also prepared. The changes on the headspace aroma volatiles during storage were assessed using solid-phase microextraction (SPME) GC-MS analysis. The effect of these changes on bread flavour was evaluated by consumer preference evaluations and the results were co-evaluated with those from the GC-MS analysis. The obtained results showed differences in the volatile composition of the different types of breads examined, as well as dramatic decreases of the number and the amount of volatiles after five days of storage. The sourdough breads made with K. marxianus and L. bulgaricus, had a more complex aroma profile, longer shelf-life and achieved the highest scores in the sensory tests.\n\nEvolution of aroma volatiles during storage of sourdough breads made by mixed cultures of Kluyveromyces marxianus and Lactobacillus delbrueckii ssp. bulgaricus or Lactobacillus helveticus", "token_count": 316, "char_count": 1261, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:15.129878", "source": { "split": "train_shard_00001", "doc_id": 2198 }, "chunk_id": "train_shard_00001_2198_0", "global_id": 8786 }, { "text": "

Background

People with cystic fibrosis (CF) may not expectorate sputum at young ages or after they receive CFTR modulators. While oropharyngeal swabs are commonly used to test for lower airway pathogens, it is unknown whether Staphylococcus aureus from the oropharynx matches the strain(s) infecting the lungs. Our goal was to determine whether oropharyngeal and sputum isolates of S. aureus are genetically distinct in a cohort of patients with CF.

Methods

We obtained historical S. aureus isolates from patients who intermittently expectorated sputum in 2018, and we prospectively cultured S. aureus from oropharyngeal swabs and sputum from subjects with CF between August 2020 and February 2022. We performed short-read whole genome sequencing, determined sequence type, and performed phylogenetic analysis using S. aureus core genome single nucleotide polymorphisms (SNPs). We assigned isolates from a patient to the same strain if they had the same sequence type and differed by ≤ 60 SNPs or the isolates were not disturbed by clade breaker analysis.

Results

36 subjects had S. aureus in ≥ 1 oropharyngeal swab and ≥ 1 sputum in 2018. In the prospective collection, 31 subjects had synchronous oropharyngeal swab and sputum collections. Although polyclonal infections were detected, sputum and oropharyngeal isolates of S. aureus typically matched the same strain within study subjects, both over the span of 2018 (31/36 patients) and when collected simultaneously from 2020 to 2022 (29/31 patients).

Conclusions

In patients with CF who intermittently produce sputum, oropharyngeal swabs identify S. aureus with genetic and phenotypic similarity to those cultured from sputum.", "token_count": 512, "char_count": 1710, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5918, "quality_score": 0.7959, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:15.785420", "source": { "split": "train_shard_00001", "doc_id": 2199 }, "chunk_id": "train_shard_00001_2199_0", "global_id": 8787 }, { "text": "Genetic Concordance of Staphylococcus aureus From Oropharyngeal and Sputum Cultures in People With Cystic Fibrosis.", "token_count": 41, "char_count": 115, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:16.138478", "source": { "split": "train_shard_00001", "doc_id": 2199 }, "chunk_id": "train_shard_00001_2199_1", "global_id": 8788 }, { "text": "Vibrio parahaemolyticus biofilms on the seafood processing plant surfaces are a potential source of seafood contamination and subsequent food poisoning. Strains differ in their ability to form biofilm, but little is known about the genetic characteristics responsible for biofilm development. In this study, pangenome and comparative genome analysis of V. parahaemolyticus strains reveals genetic attributes and gene repertoire that contribute to robust biofilm formation. The study identified 136 accessory genes that were exclusively present in strong biofilm forming strains and these were functionally assigned to the Gene Ontology (GO) pathways of cellulose biosynthesis, rhamnose metabolic and catabolic processes, UDP-glucose processes and O antigen biosynthesis (p < 0.05). Strategies of CRISPR-Cas defence and MSHA pilus-led attachment were implicated via Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation. Higher levels of horizontal gene transfer (HGT) were inferred to confer more putatively novel properties on biofilm-forming V. parahaemolyticus. Furthermore, cellulose biosynthesis, a neglected potential virulence factor, was identified as being acquired from within the order Vibrionales. The cellulose synthase operons in V. parahaemolyticus were examined for their prevalence (22/138, 15.94 %) and were found to consist of the genes bcsG, bcsE, bcsQ, bcsA, bcsB, bcsZ, bcsC. This study provides insights into robust biofilm formation of V. parahaemolyticus at the genomic level and facilitates: identification of key attributes for robust biofilm formation, elucidation of biofilm formation mechanisms and development of potential targets for novel control strategies of persistent V. parahaemolyticus.\n\nComparative genome identification of accessory genes associated with strong biofilm formation in Vibrio parahaemolyticus", "token_count": 465, "char_count": 1851, "word_count": 250, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:16.775994", "source": { "split": "train_shard_00001", "doc_id": 2200 }, "chunk_id": "train_shard_00001_2200_0", "global_id": 8789 }, { "text": "

Background

Members of the F. oxysporium species complex (FOSC) in the f. sp. apii (Foa) are pathogenic on celery and those in f. sp. coriandrii (Foci) are pathogenic on coriander (=cilantro). Foci was first reported in California in 2005; a new and highly aggressive race 4 of Foa was observed in 2013 in California. Preliminary evidence indicated that Foa can also cause disease on coriander, albeit are less virulent than Foci. Comparative genomics was used to investigate the evolutionary relationships between Foa race 4, Foa race 3, and the Foci, which are all in FOSC Clade 2, and Foa race 2, which is in FOSC Clade 3.

Results

A phylogenetic analysis of 2718 single-copy conserved genes and mitochondrial DNA sequence indicated that Foa races 3 and 4 and the Foci are monophyletic within FOSC Clade 2; these strains also are in a single somatic compatibility group. However, in the accessory genomes, the Foci versus Foa races 3 and 4 differ in multiple contigs. Based on significantly increased expression of Foa race 4 genes in planta vs. in vitro, we identified 23 putative effectors and 13 possible pathogenicity factors. PCR primers for diagnosis of either Foa race 2 or 4 and the Foci were identified. Finally, mixtures of conidia that were pre-stained with different fluorochromes indicated that Foa race 4 formed conidial anastomosis tubes (CATs) with Foci. Foa race 4 and Foa race 2, which are in different somatic compatibility groups, did not form CATs with each other.

Conclusions

There was no evidence that Foa race 2 was involved in the recent evolution of Foa race 4; Foa race 2 and 4 are CAT-incompatible", "token_count": 483, "char_count": 1648, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5485, "quality_score": 0.7743, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:17.784772", "source": { "split": "train_shard_00001", "doc_id": 2201 }, "chunk_id": "train_shard_00001_2201_0", "global_id": 8790 }, { "text": "Although Foa races 3 and 4 and the Foci are closely related, there is no evidence that either Foci contributed to the evolution of Foa race 4, or that Foa race 4 was the recent recipient of a multi-gene chromosomal segment from another strain. However, horizontal chromosome transfer could account for the major difference in the accessory genomes of Foa race 4 and the Foci and for their differences in host range.\n\nGenomic differences between the new Fusarium oxysporum f. sp. apii (Foa) race 4 on celery, the less virulent Foa races 2 and 3, and the avirulent on celery f. sp. coriandrii.", "token_count": 162, "char_count": 591, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:18.222373", "source": { "split": "train_shard_00001", "doc_id": 2201 }, "chunk_id": "train_shard_00001_2201_1", "global_id": 8791 }, { "text": "

A bstract

We present Panakeia, a tool which strives to be easy to use and providing a detailed view of the pangenome structure which can efficiently be utilised for discovery, or further in-depth analysis, of features of interest. It analyses synteny and multiple structural patterns of the pangenome, giving insights into the biological diversity and evolution of the studied taxon. Panakeia hence provides both broad and detailed information on the structure of a pangenome, for diverse and highly clonal populations of bacteria. Development of new pan-genome analysis tools is important, as the pangenome of a microbial species has become an important method to define the diversity of a selected taxon, most commonly a species, in the last years. This enables comparison of strains from different ecological niches and can be used to define the functional potential in a bacterial population. It gives us a much better view of microbial genomics than can be gained from singular genomes which after all are just single representatives of a much more varied population. Previously published pangenome tools often reduce the information to a presence/absence matrix of unconnected genes or generate massive hard to interpret output graphs. However, Panakeia includes synteny and structural information and presents it in a way that can readily be used for further analysis. Panakeia can be downloaded at https://github.com/BioSina/Panakeia .\n\nPanakeia - A universal tool for bacterial pangenome analysis", "token_count": 324, "char_count": 1515, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:18.792504", "source": { "split": "train_shard_00001", "doc_id": 2202 }, "chunk_id": "train_shard_00001_2202_0", "global_id": 8792 }, { "text": "The E. coli strain harboring the polyketide synthase ( Pks) island encodes the genotoxin colibactin, a secondary metabolite reported to have severe implications for human health and for the progression of colorectal cancer. The present study involved whole-genome-wide comparison and phylogenetic analysis of pks harboring E. coli isolates to gain insight into the distribution and evolution of these organism. Fifteen E. coli strains isolated from patients with ulcerative colitis were sequenced, 13 of which harbored pks islands. In addition, 2,654 genomes from the public database were also screened for pks harboring E. coli genomes, 158 of which were pks -positive isolates. Whole-genome-wide comparison and phylogenetic analysis revealed that 171 (158+13) pks -positive isolates belonged to phylogroup B2, and most of the isolates associated to sequence types ST73 and ST95. One isolate from an ulcerative colitis (UC) patient was of the sequence type ST8303. The maximum likelihood tree based on the core genome of pks -positive isolates revealed horizontal gene transfer across sequence types and serotypes. Virulome and resistome analyses revealed the preponderance of virulence genes and a reduced number of antimicrobial genes in Pks -positive isolates. This study strongly contributes to understanding the evolution of pks islands in E. coli .\n\nGenomic characterization ofEscherichia coliharbor a polyketide synthase (pks) island associated with colorectal cancer (CRC) development", "token_count": 408, "char_count": 1507, "word_count": 216, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [ "ST95", "ST8303", "ST73" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:19.409904", "source": { "split": "train_shard_00001", "doc_id": 2203 }, "chunk_id": "train_shard_00001_2203_0", "global_id": 8793 }, { "text": "The inulinase gene (INU1) from Kluyveromyces marxianus NCYC2887 strain was overexpressed by using GAL10 promotor in a △gal80 strain of Saccharomyces cerevisiae. The inulinase gene lacking the original signal sequence was fused in-frame to mating factor alpha signal sequence for secretory expression. Use of the △gal80 strain allowed the galactose-free induction of inulinase expression using a glucose-only medium. Shake flask cultivation in YPD medium produced 34.6 U/ml of the recombinant inulinase, which was approximately 13-fold higher than that produced by K. marxianus NCYC2887. It was found that the use of the △gal80 strain improved the expression of inulinase in the recombinant S. cerevisiae in both the aerobic and the anaerobic condition by about 2.9- and 1.7-fold, respectively. 5 L fed-batch fermentation using YPD medium was performed under aerobic condition with glucose feeding, which resulted in the inulinase production of 31.7 U/ml at OD600 of 67. Ethanol fermentation of dried powder of Jerusalem artichoke, an inulin-rich biomass, was also performed using the recombinant S. cerevisiae expressing INU1 and K. marxianus NCYC2887. Fermentation in a 5L scale fermentor was carried out at an aeration rate of 0.2 vvm, an agitation rate of 300 rpm, and the pH was controlled at 5.0. The temperature was maintained at 30degrees C and 37degrees C, respectively, for the recombinant S. cerevisiae and K. marxianus. The maximum productivities of ethanol were 59.0 and 53.5 g/L, respectively.\n\nRecombinant Production of an Inulinase in a Saccharomyces cerevisiae gal80 Strain.", "token_count": 505, "char_count": 1590, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5417, "quality_score": 0.7708, "entities": { "genes": [ "GAL10", "NCYC2887", "INU1", "OD600" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:20.065430", "source": { "split": "train_shard_00001", "doc_id": 2204 }, "chunk_id": "train_shard_00001_2204_0", "global_id": 8794 }, { "text": "Saccharibacteria (formerly TM7) have reduced genomes and a small cell size and appear to have a parasitic lifestyle dependent on a bacterial host. Although there are at least 6 major clades of Saccharibacteria inhabiting the human oral cavity, complete genomes of oral Saccharibacteria were previously limited to the G1 clade. In this study, nanopore sequencing was used to obtain three complete genome sequences from clade G6. Phylogenetic analysis suggested the presence of at least 3 to 5 distinct species within G6, with two discrete taxa represented by the 3 complete genomes. G6 Saccharibacteria were highly divergent from the more-well-studied clade G1 and had the smallest genomes and lowest GC content of all Saccharibacteria. Pangenome analysis showed that although 97% of shared pan-Saccharibacteria core genes and 89% of G1-specific core genes had putative functions, only 50% of the 244 G6-specific core genes had putative functions, highlighting the novelty of this group. Compared to G1, G6 harbored divergent metabolic pathways. G6 genomes lacked an F1Fo ATPase, the pentose phosphate pathway, and several genes involved in nucleotide metabolism, which were all core genes for G1. G6 genomes were also unique compared to that of G1 in that they encoded d-lactate dehydrogenase, adenylate cyclase, limited glycerolipid metabolism, a homolog to a lipoarabinomannan biosynthesis enzyme, and the means to degrade starch. These differences at key metabolic steps suggest a distinct lifestyle and ecological niche for clade G6, possibly with alternative hosts and/or host dependencies, which would have significant ecological, evolutionary, and likely pathogenic implications", "token_count": 496, "char_count": 1749, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8112, "entities": { "genes": [ "TM7" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:20.718219", "source": { "split": "train_shard_00001", "doc_id": 2205 }, "chunk_id": "train_shard_00001_2205_0", "global_id": 8795 }, { "text": "IMPORTANCESaccharibacteria are ultrasmall parasitic bacteria that are common members of the oral microbiota and have been increasingly linked to disease and inflammation. However, the lifestyle and impact on human health of Saccharibacteria remain poorly understood, especially for the clades with no complete genomes (G2 to G6) or cultured isolates (G2 and G4 to G6). Obtaining complete genomes is of particular importance for Saccharibacteria, because they lack many of the \"essential\" core genes used for determining draft genome completeness, and few references exist outside clade G1. In this study, complete genomes of 3 G6 strains, representing two candidate species, were obtained and analyzed. The G6 genomes were highly divergent from that of G1 and enigmatic, with 50% of the G6 core genes having no putative functions. The significant difference in encoded functional pathways is suggestive of a distinct lifestyle and ecological niche, probably with alternative hosts and/or host dependencies, which would have major implications in ecology, evolution, and pathogenesis.\n\nComplete Genomes of Clade G6 Saccharibacteria Suggest a Divergent Ecological Niche and Lifestyle.", "token_count": 307, "char_count": 1217, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6725, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:21.289060", "source": { "split": "train_shard_00001", "doc_id": 2205 }, "chunk_id": "train_shard_00001_2205_1", "global_id": 8796 }, { "text": "

ABSTRACT

Corynebact e rium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum , C. pseudodiphtheriticum, C. accolens , and C. tuberculostearicum . To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the USA. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution spanning Africa and North America. All species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent versus accessory genome of each species indicating limited strain-level variability in metabolic capacity. Based on prevalence data, at least two Corynebacterium species likely coexist in the nasal microbiota of 82% of adults. So, it was surprising that core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the USA clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in most of the strains in the Botswana clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.

IMPORTANCE

Pangenomic analysis with estimation of functional capabilities facilitates our understanding of the full biologic diversity of bacterial species", "token_count": 483, "char_count": 2021, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5971, "quality_score": 0.7985, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:21.967877", "source": { "split": "train_shard_00001", "doc_id": 2206 }, "chunk_id": "train_shard_00001_2206_0", "global_id": 8797 }, { "text": "We performed systematic genomic, phylogenomic, and pangenomic analyses with qualitative estimation of the metabolic capabilities of four common human nasal Corynebacterium species, along with focused experimental validations, generating a foundational resource. The prevalence of each species in human nasal microbiota is consistent with the common coexistence of at least two species. We identified a notably high level of metabolic conservation within and among species indicating limited options for species to occupy distinct metabolic niches, highlighting the importance of investigating interactions among nasal Corynebacterium species. Comparing strains from two continents, C. pseudodiphtheriticum had restricted geographic strain distribution characterized by an evolutionarily recent loss of assimilatory sulfate reduction in USA strains. Our findings contribute to understanding the functions of Corynebacterium within human nasal microbiota and to evaluating their potential for future use as biotherapeutics.\n\nMetabolic capabilities are highly conserved among human nasal-associatedCorynebacteriumspecies in pangenomic analyses", "token_count": 248, "char_count": 1147, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6853, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:22.477584", "source": { "split": "train_shard_00001", "doc_id": 2206 }, "chunk_id": "train_shard_00001_2206_1", "global_id": 8798 }, { "text": "Citrus bacterial canker (CBC) is an important disease of citrus cultivars worldwide that causes blister-like lesions on host plants and leads to more severe symptoms such as plant defoliation and premature fruit drop. The causative agent, Xanthomonas citri pv. citri, exists as three pathotypes-A, A*, and Aw-which differ in their host range and elicited host response. To date, comparative analyses have been hampered by the lack of closed genomes for the A* pathotype. In this study, we sequenced and assembled six CBC isolates of pathotype A* using second- and third-generation sequencing technologies to produce complete, closed assemblies. Analysis of these genomes and reference A, A*, and Aw sequences revealed genetic groups within the A* pathotype. Investigation of accessory genomes revealed virulence factors, including type IV secretion systems and heavy metal resistance genes, differentiating the genetic groups. Genomic comparisons of closed genome assemblies also provided plasmid distribution information for the three genetic groups of A*. The genomes presented here complement existing closed genomes of A and Aw pathotypes that are publicly available and open opportunities to investigate the evolution of X. citri pv. citri and the virulence factors that contribute to this serious pathogen.\n\nComparative Genomics of Xanthomonas citri pv. citri A* Pathotype Reveals Three Distinct Clades with Varying Plasmid Distribution.", "token_count": 388, "char_count": 1518, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:23.122330", "source": { "split": "train_shard_00001", "doc_id": 2207 }, "chunk_id": "train_shard_00001_2207_0", "global_id": 8799 }, { "text": "Abstract

Klebsiella pneumoniae is the causative agent of numerous types of infections in humans, includes urinary tract infections (UTIs), respiratory tract infections, and bloodstream infections. The hypervirulent Klebsiella pneumoniae associated with severe community-acquired infections. Hypervirulent Klebsiella pneumoniae(hvKP) is more virulent than classical Klebsiella pneumoniae (cKP) and it is an evolving pathotype due to the acquisition of genetic determinants which is responsible for its open genome. In the present study, we have performed the pan-genome analysis of Klebsiella pneumoniae for the determination of virulence proteins and genomic variation among its strains using a tool pangenome analysis pipeline (PGAP-1.2.1). The whole genome sequences of fifty-one Klebsiella pneumoniae strains was downloaded from NCBI using Refseq database. These sequences were converted into PGAP required extension files. Thirty-nine proteins and their corresponding protein sequences involved in the pathogenesis of the organism were downloaded from UniprotKB for BLAST analysis. After blast analysis, twenty-five strains were selected out of fifty-one strains based on 90-100% homology. A wide variety of selected pathogenic proteins were present in core and shared genome which includes siderophores specifically (salmochelin), adhesion proteins, extracellular toxins, and complement resistant proteins. The presence of carbapenem resistance and hypermucoviscosity proteins in unique genome indicated that Klebsiella pneumoniaeis continuously evolving through horizontal gene transfer (HGT)", "token_count": 465, "char_count": 1736, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:24.523302", "source": { "split": "train_shard_00001", "doc_id": 2208 }, "chunk_id": "train_shard_00001_2208_0", "global_id": 8800 }, { "text": "Additionally, the presence of siderophores like salmochelin and aerobactin indicates the presence of hypervirulent Klebsiella pneumoniae. Phylogenetic tree shows that strain GCF_000009885 (NTUH-K2044) was distant from all the other strains.

\n\nPan-genome analysis of Hypervirulent Klebsiella pneumoniae to evaluate genomic diversity and pathogenic potential among strains", "token_count": 120, "char_count": 390, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8444, "quality_score": 0.9222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:24.905783", "source": { "split": "train_shard_00001", "doc_id": 2208 }, "chunk_id": "train_shard_00001_2208_1", "global_id": 8801 }, { "text": "Many bacterial species, such as the alphaproteobacterium Sinorhizobium meliloti, are characterized by open pangenomes and contain multipartite genomes consisting of a chromosome and other large-sized replicons, such as chromids, megaplasmids, and plasmids. The evolutionary forces in both functional and structural aspects that shape the pangenome of species with multipartite genomes are still poorly understood. Therefore, we sequenced the genomes of 10 new S. meliloti strains, analyzed with four publicly available additional genomic sequences. Results indicated that the three main replicons present in these strains (a chromosome, a chromid, and a megaplasmid) partly show replicon-specific behaviors related to strain differentiation. In particular, the pSymB chromid was shown to be a hot spot for positively selected genes, and, unexpectedly, genes resident in the pSymB chromid were also found to be more widespread in distant taxa than those located in the other replicons. Moreover, through the exploitation of a DNA proximity network, a series of conserved \"DNA backbones\" were found to shape the evolution of the genome structure, with the rest of the genome experiencing rearrangements. The presented data allow depicting a scenario where the pSymB chromid has a distinctive role in intraspecies differentiation and in evolution through positive selection, whereas the pSymA megaplasmid mostly contributes to structural fluidity and to the emergence of new functions, indicating a specific evolutionary role for each replicon in the pangenome evolution.\n\nReplicon-dependent bacterial genome evolution: the case of Sinorhizobium meliloti.", "token_count": 387, "char_count": 1652, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:25.521065", "source": { "split": "train_shard_00001", "doc_id": 2209 }, "chunk_id": "train_shard_00001_2209_0", "global_id": 8802 }, { "text": "

Motivation

Pangenomes provide novel insights for population and quantitative genetics, genomics, and breeding not available from studying a single reference genome. Instead, a species is better represented by a pangenome or collection of genomes. Unfortunately, managing and using pangenomes for genomically diverse species is computationally and practically challenging. We developed a trellis graph representation anchored to the reference genome that represents most pangenomes well and can be used to impute complete genomes from low density sequence or variant data.

Results

The Practical Haplotype Graph (PHG) is a pangenome pipeline, database (PostGRES & SQLite), data model (Java, Kotlin, or R), and Breeding API (BrAPI) web service. The PHG has already been able to accurately represent diversity in four major crops including maize, one of the most genomically diverse species, with up to 1000-fold data compression. Using simulated data, we show that, at even 0.1X coverage, with appropriate reads and sequence alignment, imputation results in extremely accurate haplotype reconstruction. The PHG is a platform and environment for the understanding and application of genomic diversity.

Availability

All resources listed here are freely available. The PHG Docker used to generate the simulation results is https://hub.docker.com/ as maizegenetics/phg:0.0.27. PHG source code is at https://bitbucket.org/bucklerlab/practicalhaplotypegraph/src/master/ . The code used for the analysis of simulated data is at https://bitbucket.org/bucklerlab/phg-manuscript/src/master/ . The PHG database of NAM parent haplotypes is in the CyVerse data store ( https://de.cyverse.org/de/ ) and named /iplant/home/shared/panzea/panGenome/PHG_db_maize/phg_v5Assemblies_20200608.db.

Contact

pjb39@cornell.edu", "token_count": 499, "char_count": 1833, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6624, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:26.174687", "source": { "split": "train_shard_00001", "doc_id": 2210 }, "chunk_id": "train_shard_00001_2210_0", "global_id": 8803 }, { "text": "The Practical Haplotype Graph, a platform for storing and using pangenomes for imputation", "token_count": 23, "char_count": 89, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:26.527085", "source": { "split": "train_shard_00001", "doc_id": 2210 }, "chunk_id": "train_shard_00001_2210_1", "global_id": 8804 }, { "text": "The beneficial effects attributed to Bifidobacterium are largely attributed to their immunomodulatory capabilities, which are likely to be species- and even strain-specific. However, their strain-specificity in direct and indirect immune modulation remain largely uncharacterized. We have shown that B. pseudolongum UMB-MBP-01, a murine isolate strain, is capable of suppressing inflammation and reducing fibrosis in vivo. To ascertain the mechanism driving this activity and to determine if it is specific to UMB-MBP-01, we compared it to a porcine tropic strain B. pseudolongum ATCC25526 using a combination of cell culture and in vivo experimentation and comparative genomics approaches. Despite many shared features, we demonstrate that these two strains possess distinct genetic repertoires in carbohydrate assimilation, differential activation signatures and cytokine responses signatures in innate immune cells, and differential effects on lymph node morphology with unique local and systemic leukocyte distribution. Importantly, the administration of each B. pseudolongum strain resulted in major divergence in the structure, composition, and function of gut microbiota. This was accompanied by markedly different changes in intestinal transcriptional activities, suggesting strain-specific modulation of the endogenous gut microbiota as a key to immune modulatory host responses. Our study demonstrated a single probiotic strain can influence local, regional, and systemic immunity through both innate and adaptive pathways in a strain-specific manner. It highlights the importance to investigate both the endogenous gut microbiome and the intestinal responses in response to probiotic supplementation, which underpins the mechanisms through which the probiotic strains drive the strain-specific effect to impact health outcomes.\n\nStrain-specific alterations in gut microbiome and host immune responses elicited by tolerogenic Bifidobacterium pseudolongum.", "token_count": 439, "char_count": 1965, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8084, "entities": { "genes": [ "ATCC25526" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:27.150968", "source": { "split": "train_shard_00001", "doc_id": 2211 }, "chunk_id": "train_shard_00001_2211_0", "global_id": 8805 }, { "text": "The future sustainability of viticulture depends on the development of grapevine cultivars with genetic resistance to diseases such as powdery mildew, downy mildew, and Pierce's disease. Recent advances in grape and pathogen genomics have dramatically improved our approach to durable disease resistance. The availability of diploid genome references for wild species, combined with the ability to phase resistance haplotypes and conduct genome-wide association and expression analyses, has greatly enhanced our ability to dissect genetic resistance loci. This progress is yielding candidate genes that will form the foundation for precise breeding, gene stacking, and genome editing in grape improvement programs. As resistance genes are deployed in vineyards, pathogen populations evolve to adapt and evade these defenses, posing ongoing challenges. Understanding the adaptive mechanisms of grapevine pathogens in response to resistant cultivars is crucial. Grape pathogenomics is advancing rapidly, marked by the sequencing of many pathogen genomes, the discovery of effectors, including the first ones responsible for disease resistance breakdown, and the development of graph-based pangenomes. These advancements offer valuable insights into pathogen evolution and inform strategies for sustainable disease management. Together, these genomic tools and insights are paving the way for developing resilient grapevine varieties, ensuring the long-term sustainability of viticulture.\n\nAdvances in grape and pathogen genomics toward durable grapevine disease resistance.", "token_count": 320, "char_count": 1571, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:27.714626", "source": { "split": "train_shard_00001", "doc_id": 2212 }, "chunk_id": "train_shard_00001_2212_0", "global_id": 8806 }, { "text": "

Background

Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as 'core' or 'dispensable' is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to 'conditionally dispensable', this concept still requires the assignment of genes to distinct groups.

Results

Here, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores.

Conclusions

Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.\n\nReference-based QUantification Of gene Dispensability (QUOD).", "token_count": 467, "char_count": 1991, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:28.360656", "source": { "split": "train_shard_00001", "doc_id": 2213 }, "chunk_id": "train_shard_00001_2213_0", "global_id": 8807 }, { "text": "Mining novel specific molecular targets and establishing efficient identification methods are significant for detecting Pseudomonas aeruginosa, which can enable P. aeruginosa tracing in food and water. Pangenome analysis was used to analyze the whole genomic sequences of 2017 strains (including 1,000 P. aeruginosa strains and 1,017 other common foodborne pathogen strains) downloaded from gene databases to obtain novel species-specific genes, yielding a total of 11 such genes. Four novel target genes, UCBPP-PA14_00095, UCBPP-PA14_03237, UCBPP-PA14_04976, and UCBPP-PA14_03627, were selected for use, which had 100% coverage in the target strain and were not present in nontarget bacteria. PCR primers (PA1, PA2, PA3, and PA4) and qPCR primers (PA12, PA13, PA14, and PA15) were designed based on these target genes to establish detection methods. For the PCR primer set, the minimum detection limit for DNA was 65.4 fg/μl, which was observed for primer set PA2 of the UCBPP-PA14_03237 gene. The detection limit in pure culture without pre-enrichment was 105 colony-forming units (CFU)/ml for primer set PA1, 103 CFU/ml for primer set PA2, and 104 CFU/ml for primer set PA3 and primer set PA4. Then, qPCR standard curves were established based on the novel species-specific targets", "token_count": 460, "char_count": 1373, "word_count": 192, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [ "PA13", "PA14", "PA3", "PA12", "PA4", "PA15", "PA1", "PA2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:28.997362", "source": { "split": "train_shard_00001", "doc_id": 2214 }, "chunk_id": "train_shard_00001_2214_0", "global_id": 8808 }, { "text": "The standard curves showed perfect linear correlations, with R 2 values of 0.9901 for primer set PA12, 0.9915 for primer set PA13, 0.9924 for primer set PA14, and 0.9935 for primer set PA15. The minimum detection limit of the real-time PCR (qPCR) assay was 102 CFU/ml for pure cultures of P. aeruginosa. Compared with the endpoint PCR and traditional culture methods, the qPCR assay was more sensitive by one or two orders of magnitude. The feasibility of these methods was satisfactory in terms of sensitivity, specificity, and efficiency after evaluating 29 ready-to-eat vegetable samples and was almost consistent with that of the national standard detection method. The developed assays can be applied for rapid screening and detection of pathogenic P. aeruginosa, providing accurate results to inform effective monitoring measures in order to improve microbiological safety.\n\n<i>Pseudomonas aeruginosa</i> Detection Using Conventional PCR and Quantitative Real-Time PCR Based on Species-Specific Novel Gene Targets Identified by Pangenome Analysis.", "token_count": 313, "char_count": 1108, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8452, "entities": { "genes": [ "PA14", "PA13", "PA12", "PA15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:29.553983", "source": { "split": "train_shard_00001", "doc_id": 2214 }, "chunk_id": "train_shard_00001_2214_1", "global_id": 8809 }, { "text": "The adaptive potential of plant fungal pathogens is largely governed by the gene content of a species, comprised of core and ancillary genes across the pathogen isolate repertoire. To approximate the complete gene repertoire of a globally significant crop fungal pathogen, a pan genomic analysis was undertaken for Pyrenophora tritici-repentis (Ptr), the causal agent of tan (or yellow) spot disease in wheat. In this study, fifteen new Ptr genomes were sequenced, assembled and annotated, including isolates from three races not previously sequenced. Together with eleven previously published Ptr genomes, a pangenome for twenty-six Ptr isolates from Australia, Europe, North Africa and America, representing nearly all known races, revealed a conserved core-gene content of 57% and presents a new Ptr resource for searching natural homologues using remote protein structural homology. Here, we identify for the first time a nonsynonymous mutation in the Ptr effector gene ToxB , multiple copies of toxb , a distant natural Pyrenophora homologue of a known Parastagonopora nodorum effector, and clear genomic break points for the ToxA effector horizontal transfer region. This comprehensive genomic analysis of Ptr races includes nine isolates sequenced via long read technologies. Accordingly, these resources provide a more complete representation of the species, and serve as a resource to monitor variations potentially involved in pathogenicity.

Author Notes

All supporting data, code and protocols have been provided within the article or through supplementary data files. Five supplementary data files and fifteen supplementary figures are available with the online version of this article.

Impact Statement

Our Pyrenophora tritici-repentis (Ptr) pangenome study provides resources and analyses for the identification of pathogen virulence factors, of high importance to microbial research. Key findings include: 1) Analysis of eleven new sequenced (with three new races not previously available) and previously published isolates, 26 genomes in total, representing the near complete Ptr race set for known effector production collected from Australia, Europe, North Africa and the Americas. 2) We show that although Ptr has low core gene conservation, the whole genome divergence of other wheat pathogens was greater", "token_count": 518, "char_count": 2343, "word_count": 338, "semantic_coherence": 1, "information_density": 0.6213, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:21:30.210357", "source": { "split": "train_shard_00001", "doc_id": 2215 }, "chunk_id": "train_shard_00001_2215_0", "global_id": 8810 }, { "text": "3) The new PacBio sequenced genomes provide unambiguous genomic break points for the large ToxA effector horizontal transfer region, which is only present in ToxA producing races. 4) A new web-based Ptr resource for searching in silico remote protein structural homology is presented, and a distant natural Pyrenophora protein homologue of a known effector from another wheat pathogen is identified for the first time.

Data Summary

The sources and genomic sequences used throughout this study have been deposited in the National Centre for Biotechnology Information (NCBI), under the assembly accession numbers provided in Tables 1 and 2 (available in the online version of this article). The new M4 resource for protein structural homology is freely available through the BackPhyre web-portal URL, http://www.sbg.bio.ic.ac.uk/phyre2/ .\n\nA global pangenome for the wheat fungal pathogen Pyrenophora tritici-repentis and prediction of effector protein structural homology", "token_count": 243, "char_count": 986, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6714, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:30.689806", "source": { "split": "train_shard_00001", "doc_id": 2215 }, "chunk_id": "train_shard_00001_2215_1", "global_id": 8811 }, { "text": "Salmonella enterica serovar Agona is commonly detected in raw animal feed components during routine microbial monitoring of Australian commercial animal feed mills. We hypothesized that Salmonella-contaminated raw feed components originate at the rendering or oil seed crushing plant and are distributed to mills in different locations. Our objective was to investigate the source of Salmonella Agona contaminated raw feed components. Whole genome sequences of 37 Salmonella Agona isolates, 36 from raw feed components and 1 from finished feed, collected from 10 Australian feed mills located in 4 Australian states, were compared using core genome phylogenetic analysis. After DNA extraction and de novo draft assembly of the paired reads, the draft genomes were aligned using conserved signature indel phylogeny against a reference genome for Salmonella Agona, to identify single nucleotide polymorphisms in the core genome. Five distinct clades corresponding to the five different suppliers of Salmonella Agona-contaminated raw feed components were identified in the resulting phylogenetic tree. The results also provided evidence of cross-transference of Salmonella Agona between canola meal, meat meal, and finished feed within a mill. Core genome phylogenetic analysis facilitated tracing the source of Salmonella contamination in feed mills.\n\nInvestigating the Source of Salmonella Agona Contamination in Australian Feed Mills Using Core Genome Phylogenetic Analysis.", "token_count": 390, "char_count": 1544, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5749, "quality_score": 0.7874, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:31.310804", "source": { "split": "train_shard_00001", "doc_id": 2216 }, "chunk_id": "train_shard_00001_2216_0", "global_id": 8812 }, { "text": "The present work is initiated to investigate whether a defined culture comprising a mixture of three yeast species, Kluyveromyces marxianus, Saccharomyces cerevisiae, and Pichia stipitis can ferment a mixture of sugars to produce bioethanol at rates higher than those achieved by pure cultures of the same. For this purpose, we develop models of single species based on the hybrid cybernetic model framework, and simulate fermentations in the mixed culture by combining individual models. An underlying assumption is that the behavior of each species is determined only by the common environment independently of the presence and metabolism of other species. Model performance is thoroughly assessed using the experimental data available in the literature. The dynamic behavior of mixed cultures in mixed culture experiments are accurately predicted by the model reflecting faithfully the simultaneous/sequential uptake patterns of mixed substrates. This model is then used to investigate performance of various possible reactor configurations. With the foregoing species of organisms, mixed culture itself does not lead to a significant increase of bioethanol productivity. Rather, the model shows that substantial improvement is acquired by sequential use of different, properly chosen organisms during fermentation. Thus, the successive use of K. marxianus and P. stipitis is shown to increase bioethanol productivity up to about 58% in comparison to fermentation by single species alone.\n\nOn enhancing productivity of bioethanol with multiple species.", "token_count": 315, "char_count": 1555, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6161, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:31.870684", "source": { "split": "train_shard_00001", "doc_id": 2217 }, "chunk_id": "train_shard_00001_2217_0", "global_id": 8813 }, { "text": "The β-galactosidase activity of 15 Kluyveromyces strains isolated from cheese belonging to Kluyveromyces lactis and Kluyveromyces marxianus species was tested for the production of oligosaccharides derived from lactose (GOS) and lactulose (OsLu). All Kluyveromyces crude cell extracts (CEEs) produced GOS, such as 6-galactobiose and 3'-, 4'-, and 6'-galactosyl-lactose. At 4 h of reaction, the main trisaccharide formed was 6'-galactosyl-lactose (20 g/100 g of total carbohydrates). The formation of OsLu was also observed by all CEEs tested, with 6-galactobiose, 6'-galactosyl-lactulose, and 1-galactosyl-lactulose being found in all of the reaction mixtures. The synthesis of trisaccharides predominated over other oligosaccharides. K. marxianus strain O3 produced the highest yields of GOS and OsLu after 4 h of reaction, reaching 42 g/100 g of total carbohydrates (corresponding to 80% lactose hydrolysis) and 45 g/100 g of total carbohydrates (corresponding to 87% lactulose hydrolysis), respectively. Therefore, the present study contributes to a better insight into dairy Kluyveromyces β-galactosidases and shows the feasibility of these enzymes to transglycosylate lactose and lactulose, producing high yields of prebiotic oligosaccharides.\n\nEvaluation of oligosaccharide synthesis from lactose and lactulose using β-galactosidases from Kluyveromyces isolated from artisanal cheeses.", "token_count": 471, "char_count": 1403, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6183, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:32.517049", "source": { "split": "train_shard_00001", "doc_id": 2218 }, "chunk_id": "train_shard_00001_2218_0", "global_id": 8814 }, { "text": "The ultraviolet-C (UV-C) decimal reduction energy (DUV-C) values of 17 spoilage yeasts and their composited inoculum were determined in coconut liquid endosperm (pH 5.26, 5.8 °Brix, 0.04% malic acid, 0.17% w/v insoluble solids). Growth kinetic parameters of all the test yeast strains were first established to standardize the growth stage of the cells prior to inactivation studies. Approximately 4.0 to 5.0 log CFU/mL cells in the mid-stationary growth phase (30.3 to 39.9 h, 25 °C) were suspended in 4 mL turbulent flowing juice and subjected to UV-C irradiation at a surface irradiance range of 3.42 to 4.99 mW/cm2. Survivor populations after exposure to predetermined UV-C energy were enumerated, and were used to derive the DUV-C values using the linear regression and Baranyi and Roberts (1994) model fitting. Results show that the yeast strains exhibited either log-linear or biphasic inactivation behavior with inactivation lag. The most UV-C resistant spoilage yeast was found to be Cryptococcus albidus (LJY1) with DUV-C values of 122.72 and 214.89 mJ/cm2 determined from linear regression and model-fitting, respectively. The least UV-C resistant was Torulaspora delbrueckii (LYJ5) with a DUV-C of 17.34 (linear regression) and 17.35 mJ/cm2 (model-fitting)", "token_count": 492, "char_count": 1345, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8395, "entities": { "genes": [ "LJY1", "LYJ5" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:33.169977", "source": { "split": "train_shard_00001", "doc_id": 2219 }, "chunk_id": "train_shard_00001_2219_0", "global_id": 8815 }, { "text": "The DUV-C values determined from the model fitting were generally greater than those calculated from linear regression, although only those determined for C. albidus were significantly different. To the investigators' knowledge, this is the first report of the UV-C inactivation kinetic parameters of Kluyveromyces marxianus, Trichosporon cutaneum, Pichia anomala, and Meyerozyma guilliermondii and C. albidus in coconut liquid endosperm. The results of this study can be used in the establishment and validation of UV-C process schedules for coconut liquid endosperm and other similar commodities.\n\nDecimal reduction energies of UV-C-irradiated spoilage yeasts in coconut liquid endosperm.", "token_count": 178, "char_count": 701, "word_count": 95, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:33.621546", "source": { "split": "train_shard_00001", "doc_id": 2219 }, "chunk_id": "train_shard_00001_2219_1", "global_id": 8816 }, { "text": "

Background

Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes.

Methods

We accessed 451 historic (1965-1987) MRSA isolates stored in the Culture Collection of Switzerland, mostly collected from the Zurich region. We determined phenotypic antimicrobial resistance (AMR) and performed whole genome sequencing (WGS) using Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international assemblies from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCCmec cassette types, AMR, and virulence genes.

Results

Among the 451 historic Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-III", "token_count": 506, "char_count": 1644, "word_count": 225, "semantic_coherence": 1, "information_density": 0.7111, "quality_score": 0.8556, "entities": { "genes": [ "ST7839", "ST7842", "ST239", "ST7837", "ST7843", "ST7844", "ST247" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:34.278752", "source": { "split": "train_shard_00001", "doc_id": 2220 }, "chunk_id": "train_shard_00001_2220_0", "global_id": 8817 }, { "text": "Early MRSA were predominantly from clonal complex (CC)8. From 1980 to the end of the twentieth century, we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally.

Conclusions

The combined analysis of 1761 historic and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss-German and international MRSA across time.\n\nHistoric methicillin-resistant Staphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection.", "token_count": 149, "char_count": 597, "word_count": 82, "semantic_coherence": 1, "information_density": 0.8049, "quality_score": 0.9024, "entities": { "genes": [ "CC8", "CC5", "CC22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:34.737491", "source": { "split": "train_shard_00001", "doc_id": 2220 }, "chunk_id": "train_shard_00001_2220_1", "global_id": 8818 }, { "text": "Verotoxigenic Escherichia coli (VTEC) are food- and water-borne pathogens associated with both sporadic illness and outbreaks of enteric disease. While it is known that cattle are reservoirs of VTEC, little is known about the genomic variation of VTEC in cattle, and whether the variation in genomes reported for human outbreak strains is consistent with individual animal or group/herd sources of infection. A previous study of VTEC prevalence identified serotypes carried persistently by three consecutive cohorts of heifers within a closed herd of cattle. This present study aimed to: (i) determine whether the genomic relatedness of bovine isolates is similar to that reported for human strains associated with single source outbreaks, (ii) estimate the rates of genome change among dominant serotypes over time within a cattle herd, and (iii) identify genomic features of serotypes associated with persistence in cattle. Illumina MiSeq genome sequencing and genotyping based on allelic and single nucleotide variations were completed, while genome change over time was measured using Bayesian evolutionary analysis sampling trees. The accessory genome, including the non-protein-encoding intergenic regions (IGRs), virulence factors, antimicrobial-resistance genes and plasmid gene content of representative persistent and sporadic cattle strains were compared using Fisher's exact test corrected for multiple comparisons. Herd strains from serotypes O6:H34 (n=22), O22:H8 (n=30), O108:H8 (n=39), O139:H19 (n=44) and O157:H7 (n=106) were readily distinguishable from epidemiologically unrelated strains of the same serotype using a similarity threshold of 10 or fewer allele differences between adjacent nodes. Temporal-cohort clustering within each serotype was supported by date randomization analysis. Substitutions per site per year were consistent with previously reported values for E", "token_count": 507, "char_count": 1940, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6654, "quality_score": 0.8327, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:35.409581", "source": { "split": "train_shard_00001", "doc_id": 2221 }, "chunk_id": "train_shard_00001_2221_0", "global_id": 8819 }, { "text": "coli; however, there was low branch support for these values. Acquisition of the phage-encoded Shiga toxin 2 gene in serotype O22:H8 was observed. Pan-genome analyses identified accessory regions that were more prevalent in persistent serotypes (P≤0.05) than in sporadic serotypes. These results suggest that VTEC serotypes from a specific cattle population are highly clonal with a similar level of relatedness as human single-source outbreak-associated strains, but changes in the genome occur gradually over time. Additionally, elements in the accessory genomes may provide a selective advantage for persistence of VTEC within cattle herds.\n\nAssessing the genomic relatedness and evolutionary rates of persistent verotoxigenic Escherichia coli serotypes within a closed beef herd in Canada.", "token_count": 211, "char_count": 811, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:35.881576", "source": { "split": "train_shard_00001", "doc_id": 2221 }, "chunk_id": "train_shard_00001_2221_1", "global_id": 8820 }, { "text": "

Background

Carbapenem-resistant Acinetobacter baumannii (CRAB) poses a critical global threat, especially in ICUs. Yet, reports on ST164 CRAB harboring blaNDM-1 remain scarce. This study investigates two clinical CRAB isolates, L4773hy and L4796hy, derived from intestinal colonization in Hangzhou, China, focusing on their phenotypic and genomic characteristics as well as the broader transmission of ST164 A. baumannii.

Methods

Bacterial identification was performed using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) mass spectrometry. Antimicrobial susceptibility was assessed via agar and broth microdilution. Whole-genome sequencing employed Illumina NovaSeq 6000 and Oxford Nanopore platforms. Resistance genes, insertion elements, transposons, and integrons were detected using ResFinder, PlasmidFinder, VFDB, ISFinder, pdifFinder, and IntegronFinder. Strains were typed by MLST, and a phylogenetic tree was constructed with kSNP3.0. Genetic environment diagrams were generated using Easyfig 2.2.5.

Results

Two blaNDM-1-carrying A. baumannii isolates exhibiting extensive resistance to carbapenems, cephalosporins, and fluoroquinolones. Whole-genome sequencing and genetic environment analysis revealed the presence of a conserved structural sequence (ISAba14-ISAba14-aphA-ISAba125-blaNDM-1-bleMBL) on their chromosomes. Phylogenetic and clonal dissemination analysis showed that ST164 CRAB is primarily distributed in China and exhibits clonal spread", "token_count": 478, "char_count": 1569, "word_count": 173, "semantic_coherence": 1, "information_density": 0.763, "quality_score": 0.8815, "entities": { "genes": [ "ST164" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:36.525317", "source": { "split": "train_shard_00001", "doc_id": 2222 }, "chunk_id": "train_shard_00001_2222_0", "global_id": 8821 }, { "text": "Pathogenicity studies indicated that blaNDM-1-positive ST164 strains have enhanced survival under immune pressure but do not display increased virulence in infection models.

Conclusion

This study provides the genomic and phenotypic characterization of intestinally colonized ST164 blaNDM-1 positive CRAB in Hangzhou, China. The elucidation of the genetic environment of blaNDM-1 further confirms the clonal dissemination of ST164 isolates, highlighting the importance of enhanced surveillance and infection control measures to mitigate the spread of these multidrug-resistant pathogens.\n\nGenomic and phenotypic insights into ST164 bla<sub>NDM-1</sub>-positive Acinetobacter baumannii from intestinal colonization in China.", "token_count": 224, "char_count": 774, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7356, "quality_score": 0.8678, "entities": { "genes": [ "ST164" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:36.990444", "source": { "split": "train_shard_00001", "doc_id": 2222 }, "chunk_id": "train_shard_00001_2222_1", "global_id": 8822 }, { "text": "Mucins are large glycoproteins whose degradation requires the expression of several glycosil hydrolases to catalyze the cleavage of the oligosaccharide chains and release monosaccharides that can be assimilated. In this study, we present a characterization on the strains Clostridium celatum WC0700, Clostridium tertium WC0709, and Paraclostridium bifermentans WC0705. These three strains were previously isolated from enrichment cultures on mucin of fecal samples from healthy subjects and can use mucin as sole carbon and nitrogen source. Genome analysis and in vitro functional analysis of these strains elucidated their physiological and biochemical features. C. celatum WC0700 harbored the highest number of glycosyl hydrolases specific for mucin degradation, while P. bifermentans WC0705 had the least. These predicted differences were confirmed growing the strains on 5 mucin-decorating monosaccharides (L-fucose, N-Acetylneuraminic acid, galactose, N-acetylgalactosamine, and N-acetylglucosamine) as only source of carbon. Fermenting mucin, they all produced formic, acetic, propionic, butyric, isovaleric, and lactic acids, and ethanol; acetic acid was the main primary metabolite. Further catabolic capabilities were investigated, as well as antibiotic susceptibility, biofilm formation, tolerance to oxygen and temperature. The potential pathogenicity of the strains was evaluated through in silico research of virulence factors. The merge between comparative and functional genomics and biochemical/physiological characterization provided a comprehensive view of these mucin degraders, reassuring on the safety of these species and leaving ample scope for deeper investigations on the relationship with the host and for assessing if some relevant health-promoting effect could be ascribed to these SCFA producing species.", "token_count": 518, "char_count": 1882, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6967, "quality_score": 0.8484, "entities": { "genes": [ "WC0700", "WC0705", "WC0709" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:21:37.652588", "source": { "split": "train_shard_00001", "doc_id": 2223 }, "chunk_id": "train_shard_00001_2223_0", "global_id": 8823 }, { "text": "Genomic and functional analysis of the mucinolytic species Clostridium celatum, Clostridium tertium, and Paraclostridium bifermentans.", "token_count": 56, "char_count": 155, "word_count": 15, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:38.016307", "source": { "split": "train_shard_00001", "doc_id": 2223 }, "chunk_id": "train_shard_00001_2223_1", "global_id": 8824 }, { "text": "Cutibacterium acnes is a common cause of prosthetic joint infections (PJIs). The C. acnes population can be divided into six main phylotypes (IA1, IA2, IB, IC, II and III) that are associated with different clinical conditions and normal skin. A single-locus sequence typing (SLST) scheme can distinguish ten main SLST types: A-E (all IA1), F (IA2), G (IC), H (IB), K (II), L (III). We genome-sequenced and compared 16 strains of C. acnes isolated from healthy skin (n = 4) and PJIs (n = 12), including six PJI cases with a good outcome (four shoulder PJIs, one hip PJI, one knee PJI) and six with infection relapse (three shoulder PJIs, three hip PJIs). The sequenced strains belonged to four different phylotypes (IA1, IA2, IB and II) and seven different SLST types. All five type IB strains (all SLST type H1) were PJI isolates (three hip PJIs, two shoulder PJIs), and four of these caused infection relapse (three hip PJIs, one shoulder PJI). Isolates from PJI cases with a good outcome belonged to three different phylotypes (IA, IB, II). Interestingly, four strains (three strains from PJI cases with good outcome and one strain from healthy skin) contained a linear plasmid; these strains belonged to different SLST types (A1, C1, F4, H1) and were isolated in three different hospitals. This study suggests that type IB strains have the potential to cause infection relapse, in particular regarding hip PJIs. Moreover, our study revealed that strains belonging to the same SLST type can differ in their accessory genome in different geographic locations, indicative of microevolution.", "token_count": 504, "char_count": 1692, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5594, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:38.671269", "source": { "split": "train_shard_00001", "doc_id": 2224 }, "chunk_id": "train_shard_00001_2224_0", "global_id": 8825 }, { "text": "Genomic Analysis of Cutibacterium acnes Strains Isolated from Prosthetic Joint Infections.", "token_count": 30, "char_count": 97, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:39.032264", "source": { "split": "train_shard_00001", "doc_id": 2224 }, "chunk_id": "train_shard_00001_2224_1", "global_id": 8826 }, { "text": "Escherichia coli is an indicator microorganism in One Health antibiotic resistance surveillance programmes. The purpose of the study was to describe and compare E. coli isolates obtained from pigs and human contacts from a commercial farm in South Africa using conventional methods and whole genome sequencing (WGS). Porcine E. coli isolates were proportionally more resistant phenotypically and harboured a richer diversity of antibiotic resistance genes, as compared to human E. coli isolates. Different pathovars, namely ExPEC (12.43%, 21/169), ETEC (4.14%; 7/169), EPEC (2.96%, 5/169), EAEC (2.96%, 5/169) and STEC (1.18%, 2/169) were detected at low frequencies. Sequence type complex (STc) 10 were the most prevalent (85.51%, 59/169) among human and porcine isolates. Six STcs (STc10, STc86, STc168, STc206, STc278 and STc469) were shared at the human-livestock interface according to multilocus sequence typing (MLST). Core genome MLST and hierarchical clustering (HC) showed that human and porcine isolates were overall genetically diverse, but some clustering at HC2 to HC200 were observed. In conclusion, even though the isolates shared a spatio-temporal relationship, there were still differences in the virulence potential, antibiotic resistance profiles, and cgMLST and HC according to the source of isolation.\n\nWhole Genome Sequencing of Human and Porcine Escherichia coli Isolates on a Commercial Pig Farm in South Africa", "token_count": 443, "char_count": 1445, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [ "HC2", "HC200" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:39.660417", "source": { "split": "train_shard_00001", "doc_id": 2225 }, "chunk_id": "train_shard_00001_2225_0", "global_id": 8827 }, { "text": "Strains belonging to the yeast species Kluyveromyces marxianus have been isolated from a great variety of habitats, which results in a high metabolic diversity and a substantial degree of intraspecific polymorphism. As a consequence, several different biotechnological applications have been investigated with this yeast: production of enzymes (beta-galactosidase, beta-glucosidase, inulinase, and polygalacturonases, among others), of single-cell protein, of aroma compounds, and of ethanol (including high-temperature and simultaneous saccharification-fermentation processes); reduction of lactose content in food products; production of bioingredients from cheese-whey; bioremediation; as an anticholesterolemic agent; and as a host for heterologous protein production. Compared to its congener and model organism, Kluyveromyces lactis, the accumulated knowledge on K. marxianus is much smaller and spread over a number of different strains. Although there is no publicly available genome sequence for this species, 20% of the CBS 712 strain genome was randomly sequenced (Llorente et al. in FEBS Lett 487:71-75, 2000). In spite of these facts, K. marxianus can envisage a great biotechnological future because of some of its qualities, such as a broad substrate spectrum, thermotolerance, high growth rates, and less tendency to ferment when exposed to sugar excess, when compared to K. lactis. To increase our knowledge on the biology of this species and to enable the potential applications to be converted into industrial practice, a more systematic approach, including the careful choice of (a) reference strain(s) by the scientific community, would certainly be of great value.\n\nThe yeast Kluyveromyces marxianus and its biotechnological potential.", "token_count": 439, "char_count": 1757, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:40.294328", "source": { "split": "train_shard_00001", "doc_id": 2226 }, "chunk_id": "train_shard_00001_2226_0", "global_id": 8828 }, { "text": "Fermentation of Theobroma cacao (cacao) seeds is an absolute requirement for the full development of chocolate flavor precursors. An adequate aeration of the fermenting cacao seed mass is a fundamental prerequisite for a satisfactory fermentation. Here, we evaluated whether a controlled inoculation of cacao seed fermentation using a Kluyveromyces marxianus hybrid yeast strain, with an increased pectinolytic activity, would improve an earlier liquid drainage ('sweatings') from the fermentation mass, developing a superior final product quality. Inoculation with K. marxianus increased by one third the volume of drained liquid and affected the microorganism population structure during fermentation, which was detectable up to the end of the process. Introduction of the hybrid yeast affected the profile of total seed protein degradation evaluated by polyacrylamide gel electrophoresis, with improved seed protein degradation, and reduction of titrable acidity. Sensorial evaluation of the chocolate obtained from beans fermented with the K. marxianus inoculation was more accepted by analysts in comparison with the one from cocoa obtained through natural fermentation. The increase in mass aeration during the first 24 h seemed to be fundamental for the improvement of fermentation quality, demonstrating the potential application of this improved hybrid yeast strain with superior exogenous pectinolytic activity.\n\nFermentation of cacao (Theobroma cacao L.) seeds with a hybrid Kluyveromyces marxianus strain improved product quality attributes.", "token_count": 360, "char_count": 1553, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:40.883717", "source": { "split": "train_shard_00001", "doc_id": 2227 }, "chunk_id": "train_shard_00001_2227_0", "global_id": 8829 }, { "text": "

Background

Antagonistic co-evolution can drive rapid adaptation in pathogens and shape genome architecture. Comparative genome analyses of several fungal pathogens revealed highly variable genomes, for many species characterized by specific repeat-rich genome compartments with exceptionally high sequence variability. Dynamic genome architecture may enable fast adaptation to host genetics. The wheat pathogen Zymoseptoria tritici with its highly variable genome and has emerged as a model organism to study the genomic evolution of plant pathogens. Here, we compared genomes of Z. tritici isolates and genomes of sister species infecting wild grasses to address the evolution of genome composition and structure.

Results

Using long-read technology, we sequenced and assembled genomes of Z. ardabiliae , Z. brevis , Z. pseudotritici and Z. passerinii , together with two isolates of Z. tritici . We report a high extent of genome collinearity among Zymoseptoria species and high conservation of genomic, transcriptomic and epigenomic signatures of compartmentalization. We identify high gene content variability both within and between species. In addition, such variability is mainly limited to the accessory chromosomes and accessory compartments. Despite strong host specificity and non-overlapping host-range between species, effectors are mainly shared among Zymoseptoria species, yet exhibiting a high level of presence-absence polymorphism within Z. tritici . Using in planta transcriptomic data from Z. tritici , we suggest different roles for the shared orthologs and for the accessory genes during infection of their hosts.

Conclusion

Despite previous reports of high genomic plasticity in Z. tritici , we describe here a high level of conservation in genomic, epigenomic and transcriptomic signatures of genome architecture and compartmentalization across the genus Zymoseptoria . The compartmentalized genome may reflect purifying selection to retain a functional core genome and relaxed selection on the accessory genome allowing a higher extent of polymorphism.", "token_count": 489, "char_count": 2103, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5479, "quality_score": 0.774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:41.534549", "source": { "split": "train_shard_00001", "doc_id": 2228 }, "chunk_id": "train_shard_00001_2228_0", "global_id": 8830 }, { "text": "Genome compartmentalization predates species divergence in the plant pathogen genus Zymoseptoria", "token_count": 28, "char_count": 103, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:41.900357", "source": { "split": "train_shard_00001", "doc_id": 2228 }, "chunk_id": "train_shard_00001_2228_1", "global_id": 8831 }, { "text": "

Background

Cronobacter sakazakii is an emerging opportunistic bacterial pathogen known to cause neonatal and pediatric infections, including meningitis, necrotizing enterocolitis, and bacteremia. Multiple disease outbreaks of C. sakazakii have been documented in the past few decades, yet little is known of its genomic diversity, adaptation, and evolution. Here, we analyzed the pan-genome characteristics and phylogenetic relationships of 237 genomes of C. sakazakii and 48 genomes of related Cronobacter species isolated from diverse sources.

Results

The C. sakazakii pan-genome contains 17,158 orthologous gene clusters, and approximately 19.5% of these constitute the core genome. Phylogenetic analyses reveal the presence of at least ten deep branching monophyletic lineages indicative of ancestral diversification. We detected enrichment of functions involved in proton transport and rotational mechanism in accessory genes exclusively found in human-derived strains. In environment-exclusive accessory genes, we detected enrichment for those involved in tryptophan biosynthesis and indole metabolism. However, we did not find significantly enriched gene functions for those genes exclusively found in food strains. The most frequently detected virulence genes are those that encode proteins associated with chemotaxis, enterobactin synthesis, ferrienterobactin transporter, type VI secretion system, galactose metabolism, and mannose metabolism. The genes fos which encodes resistance against fosfomycin, a broad-spectrum cell wall synthesis inhibitor, and mdf(A) which encodes a multidrug efflux transporter were found in nearly all genomes. We found that a total of 2991 genes in the pan-genome have had a history of recombination", "token_count": 448, "char_count": 1755, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:42.536952", "source": { "split": "train_shard_00001", "doc_id": 2229 }, "chunk_id": "train_shard_00001_2229_0", "global_id": 8832 }, { "text": "Many of the most frequently recombined genes are associated with nutrient acquisition, metabolism and toxin production.

Conclusions

Overall, our results indicate that the presence of a large accessory gene pool, ability to switch between ecological niches, a diverse suite of antibiotic resistance, virulence and niche-specific genes, and frequent recombination partly explain the remarkable adaptability of C. sakazakii within and outside the human host. These findings provide critical insights that can help define the development of effective disease surveillance and control strategies for Cronobacter-related diseases.\n\nPan-genome diversification and recombination in Cronobacter sakazakii, an opportunistic pathogen in neonates, and insights to its xerotolerant lifestyle.", "token_count": 177, "char_count": 786, "word_count": 100, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:42.979549", "source": { "split": "train_shard_00001", "doc_id": 2229 }, "chunk_id": "train_shard_00001_2229_1", "global_id": 8833 }, { "text": "Antibiotics have, indeed, altered the course of human history as is evidenced by the increase in human life expectancy since the 1940s. Many of these natural compounds are produced by bacteria that, by necessity, must have efficient self-resistance mechanisms. The methymycin/pikromycin producing species Streptomyces venezuelae, for example, utilizes β-glucosylation of its macrolide products to neutralize their effects within the confines of the cell. Once released into the environment, these compounds are activated by the removal of the glucose moiety. In S. venezuelae, the enzyme responsible for removal of the sugar from the parent compound is encoded by the desR gene and referred to as DesR. It is a secreted enzyme containing 828 amino acid residues, and it is known to be a retaining glycosidase. Here, we describe the structure of the DesR/D-glucose complex determined to 1.4-Å resolution. The overall architecture of the enzyme can be envisioned in terms of three regions: a catalytic core and two auxiliary domains. The catalytic core harbors the binding platform for the glucose ligand. The first auxiliary domain adopts a \"PA14 fold,\" whereas the second auxiliary domain contains an immunoglobulin-like fold. Asp 273 and Glu 578 are in the proper orientation to function as the catalytic base and proton donor, respectively, required for catalysis. The overall fold of the core region places DesR into the GH3 glycoside hydrolase family of enzymes. Comparison of the DesR structure with the β-glucosidase from Kluyveromyces marxianus shows that their PA14 domains assume remarkably different orientations.\n\nThe structure of DesR from Streptomyces venezuelae, a β-glucosidase involved in macrolide activation.", "token_count": 455, "char_count": 1726, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [ "PA14", "GH3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:43.613283", "source": { "split": "train_shard_00001", "doc_id": 2230 }, "chunk_id": "train_shard_00001_2230_0", "global_id": 8834 }, { "text": "Introduction:Pseudomonas otitidis, known for carrying the blaPOM-1 gene and linked to various diseases, is widely distributed. However, its prevalence in Ghana is unknown, mainly due to misidentification or inadequate research. In this study, for the first time, we characterized P. otitidis from Densu river water in Ghana. Methods: The antimicrobial susceptibility and whole genome characteristics of two strains (Tg_9B and BC12) were determined. The resistance and virulence features were determined using ResFinder and the VFDB database, respectively. Maximum-likelihood phylogeny was conducted based on amino acid sequences of blaPOM-1 and P. otitidis core genomes. Results: The strains carried blaPOM-1 on the chromosome, with only Tg_9B showing intermediate resistance to meropenem. Tg_9B had a unique genetic make-up downstream of blaPOM-1, compared with BC12 and other reference strains. Both strains harbored virulence factors able to induce pathogenicity through immune evasion. The efflux pump genes (adeF, rsmA, and qacG) were present in the genomes of all the strains used in this study. The amino acid sequences of POM-1 in the strains shared a sequence homology with seven other sequences from different countries. Conclusions: This study highlights the emergence of blaPOM-1 harboring P. otitidis in Ghana and affirms the conservation of blaPOM-1 and adeF, rsmA, and qacG in the species.", "token_count": 523, "char_count": 1617, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [ "BC12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:21:44.271409", "source": { "split": "train_shard_00001", "doc_id": 2231 }, "chunk_id": "train_shard_00001_2231_0", "global_id": 8835 }, { "text": "Emergence of Carbapenem-Resistant blaPOM-1 Harboring Pseudomonas otitidis Isolated from River Water in Ghana.", "token_count": 54, "char_count": 134, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:44.629638", "source": { "split": "train_shard_00001", "doc_id": 2231 }, "chunk_id": "train_shard_00001_2231_1", "global_id": 8836 }, { "text": "Whole-genome sequencing (WGS) of Staphylococcus aureus is increasingly used as part of infection prevention practices. In this study, we established a long-read technology-based WGS screening program of all first-episode methicillin-resistant Staphylococcus aureus (MRSA) blood infections at a major urban hospital. A survey of 132 MRSA genomes assembled from long reads enabled detailed characterization of an outbreak lasting several months of a CC5/ST105/USA100 clone among 18 infants in a neonatal intensive care unit (NICU). Available hospital-wide genome surveillance data traced the origins of the outbreak to three patients admitted to adult wards during a 4-month period preceding the NICU outbreak. The pattern of changes among complete outbreak genomes provided full spatiotemporal resolution of its progression, which was characterized by multiple subtransmissions and likely precipitated by equipment sharing between adults and infants. Compared to other hospital strains, the outbreak strain carried distinct mutations and accessory genetic elements that impacted genes with roles in metabolism, resistance, and persistence. This included a DNA recognition domain recombination in the hsdS gene of a type I restriction modification system that altered DNA methylation. Transcriptome sequencing (RNA-Seq) profiling showed that the (epi)genetic changes in the outbreak clone attenuated agr gene expression and upregulated genes involved in stress response and biofilm formation. Overall, our findings demonstrate the utility of long-read sequencing for hospital surveillance and for characterizing accessory genomic elements that may impact MRSA virulence and persistence.\n\nA Complete Genome Screening Program of Clinical Methicillin-Resistant Staphylococcus aureus Isolates Identifies the Origin and Progression of a Neonatal Intensive Care Unit Outbreak.", "token_count": 451, "char_count": 1896, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [ "ST105", "CC5", "USA100" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:45.266015", "source": { "split": "train_shard_00001", "doc_id": 2232 }, "chunk_id": "train_shard_00001_2232_0", "global_id": 8837 }, { "text": "

ABSTRACT

As nucleus-forming phages become better characterized, understanding their unifying similarities and unique differences will help us understand how they occupy varied niches and infect diverse hosts. All identified nucleus-forming phages fall within the proposed Chimalliviridae family and share a core genome of 68 unique genes including chimallin, the major nuclear shell protein. A well-studied but non-essential protein encoded by many nucleus-forming phages is PhuZ, a tubulin homolog which aids in capsid migration, nucleus rotation, and nucleus positioning. One clade that represents 24% of all currently known chimalliviruses lacks a PhuZ homolog. Here we show that Erwinia phage Asesino, one member of this PhuZ-less clade, shares a common overall replication mechanism with other characterized nucleus-forming phages despite lacking PhuZ. We show that Asesino replicates via a phage nucleus that encloses phage DNA and partitions proteins in the nuclear compartment and cytoplasm in a manner similar to previously characterized nucleus-forming phages. Consistent with a lack of PhuZ, however, we did not observe active positioning or rotation of the phage nucleus within infected cells. These data show that some nucleus-forming phages have evolved to replicate efficiently without PhuZ, providing an example of a unique variation in the nucleus-based replication pathway.\n\nAsesino: a nucleus-forming phage that lacks PhuZ", "token_count": 352, "char_count": 1450, "word_count": 205, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:45.863783", "source": { "split": "train_shard_00001", "doc_id": 2233 }, "chunk_id": "train_shard_00001_2233_0", "global_id": 8838 }, { "text": "Hypervirulent Klebsiella pneumoniae (hvKP) has raised grave concerns in recent years and can cause severe infections with diverse anatomic locations including liver abscess, meningitis, and endophthalmitis. However, there is limited data about neck abscess caused by hvKP. A K. pneumoniae strain Kp_whw was isolated from neck abscess. We characterized the genetic background, virulence determinates of the strain by genomic analysis and dertermined the virulence level by serum resistance assay. Kp_whw belonged to sequence type (ST) 1049 K locus (KL) 5. Kp_whw showed hypermucoviscosity phenotype and was resistant to ampicillin but susceptible to the majority of the other antimicrobial agents. A pLVPK-like virulence plasmid and a chromosomal ICEKp5-like mobile genetic element were carried by Kp_whw, resulting in the risk of dissemination of hypervirulence. The strain exhibited relative higher level of core genome allelic diversity than accessory genome profile, in comparison to hvKP of K1/K2 serotype. Kp_whw was finally demonstrated as virulent as the ST23 K1 serotype hvKP strain NTUH-K2044 in vitro. In conclusion, this work elaborates the genetic background of a clinical hvKP strain with an uncommon ST, reinforcing our understanding of virulence mechanisms of hvKP.\n\nGenome-Based Analysis of a Sequence Type 1049 Hypervirulent Klebsiella pneumoniae Causing Bacteremic Neck Abscess.", "token_count": 426, "char_count": 1424, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8342, "entities": { "genes": [ "ST23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:46.510953", "source": { "split": "train_shard_00001", "doc_id": 2234 }, "chunk_id": "train_shard_00001_2234_0", "global_id": 8839 }, { "text": "

Aims

Characterize global genomic features of 86 genomes of Salmonella Gallinarum (SG) and Pullorum (SP), which are important pathogens causing systemic infections in poultry.

Methods and results

All genomes harbored efflux pump encoding gene mdsA and gold tolerance genes golS and golT. Aminoglycoside (aac(6')-Ib, aadA5, aph(6)-Id, aph(3'')-Ib, ant(2'')-Ia), beta-lactam (blaTEM-1, blaTEM-135), efflux pump (mdsB), fosfomycin (fosA3), sulfonamide (sul1, sul2), tetracycline [tet(A)], trimethoprim (dfrA17), acid (asr), and disinfectant (qacEdelta1) resistance genes, gyrA, gyrB, and parC quinolone resistance point mutations, and mercury tolerance genes (mer) were found in different frequencies. Additionally, 310 virulence genes, pathogenicity islands (including SPI-1, 2, 3, 4, 5, 6, 9, 10, 12, 13, and 14), plasmids [IncFII(S), ColpVC, IncX1, IncN, IncX2, and IncC], and prophages (Fels-2, ST104, 500465-1, pro483, Gifsy-2, 103 203_sal5, Fels-1, RE-2010, vB_SenS-Ent2, and L-413C) were detected. MLST showed biovar-specific sequence types, and core genome MLST showed country-specific and global-related clusters.

Conclusion

SG and SP global strains carry many virulence factors and important antimicrobial resistance genes. The diverse plasmids and prophages suggest genetic variability", "token_count": 504, "char_count": 1314, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8988, "entities": { "genes": [ "ST104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:47.211939", "source": { "split": "train_shard_00001", "doc_id": 2235 }, "chunk_id": "train_shard_00001_2235_0", "global_id": 8840 }, { "text": "MLST and cgMLST differentiated biovars and showed profiles occurring locally or worldwide.\n\nInsights into the global genomic features of Salmonella enterica serovar Gallinarum biovars Gallinarum and Pullorum.", "token_count": 52, "char_count": 208, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8519, "quality_score": 0.9259, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:47.608830", "source": { "split": "train_shard_00001", "doc_id": 2235 }, "chunk_id": "train_shard_00001_2235_1", "global_id": 8841 }, { "text": "The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has greatly benefited society 1, 2 . However, it still has many gaps and errors, and does not represent a biological human genome since it is a blend of multiple individuals 3, 4 . Recently, a high-quality telomere-to-telomere reference genome, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a duplicate genome, and is thus nearly homozygous 5 . To address these limitations, the Human Pangenome Reference Consortium (HPRC) recently formed with the goal of creating a collection of high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity 6 . Here, in our first scientific report, we determined which combination of current genome sequencing and automated assembly approaches yields the most complete, accurate, and cost-effective diploid genome assemblies with minimal manual curation. Approaches that used highly accurate long reads and parent-child data to sort haplotypes during assembly outperformed those that did not. Developing a combination of all the top performing methods, we generated our first high- quality diploid reference assembly, containing only ∼4 gaps (range 0-12) per chromosome, most within + 1% of CHM13’s length. Nearly 1/4th of protein coding genes have synonymous amino acid changes between haplotypes, and centromeric regions showed the highest density of variation. Our findings serve as a foundation for assembling near-complete diploid human genomes at the scale required for constructing a human pangenome reference that captures all genetic variation from single nucleotides to large structural rearrangements.\n\nAutomated assembly of high-quality diploid human reference genomes", "token_count": 436, "char_count": 1872, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6397, "quality_score": 0.8199, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:48.250965", "source": { "split": "train_shard_00001", "doc_id": 2236 }, "chunk_id": "train_shard_00001_2236_0", "global_id": 8842 }, { "text": "Escherichia coli is both a highly prevalent commensal and a major opportunistic pathogen causing bloodstream infections (BSI). A systematic analysis characterizing the genomic determinants of extra-intestinal pathogenic vs. commensal isolates in human populations, which could inform mechanisms of pathogenesis, diagnostics, prevention and treatment is still lacking. We used a collection of 1282 BSI and commensal E. coli isolates collected in France over a 17-year period (2000-2017) and we compared their pangenomes, genetic backgrounds (phylogroups, STs, O groups), presence of virulence-associated genes (VAGs) and antimicrobial resistance genes, finding significant differences in all comparisons between commensal and BSI isolates. A machine learning linear model trained on all the genetic variants derived from the pangenome and controlling for population structure reveals similar differences in VAGs, discovers new variants associated with pathogenicity (capacity to cause BSI), and accurately classifies BSI vs. commensal strains. Pathogenicity is a highly heritable trait, with up to 69% of the variance explained by bacterial genetic variants. Lastly, complementing our commensal collection with an older collection from 1980, we predict that pathogenicity increased steadily from 23% in 1980 to 46% in 2010. Together our findings imply that E. coli exhibit substantial genetic variation contributing to the transition between commensalism and pathogenicity and that this species evolved towards higher pathogenicity.\n\nThe bacterial genetic determinants ofEscherichia colicapacity to cause bloodstream infections in humans", "token_count": 398, "char_count": 1643, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:48.865319", "source": { "split": "train_shard_00001", "doc_id": 2237 }, "chunk_id": "train_shard_00001_2237_0", "global_id": 8843 }, { "text": "A total of 114 Actinobacillus pleuropneumoniae isolates from porcine hemorrhagic necrotic pleuropneumonia were characterized by the examination of biotype, serovar, antibiotic resistance genes, and genes of toxin production. Pulsed-field gel electrophoresis was used to analyze their genetic relationship, which identified 16 clusters. Serovar 2 (50 isolates), serovar 13 (25 isolates), serovar 9 (11 isolates), and serovar 16 (7 isolates) were the most frequent serovars. Serovar 2 formed nine distinguishable clusters; serovar 13 and serovar 16 were less diverse, exhibiting two potentially related subclusters; serovar 9 was represented by a single cluster. Remarkably small differences were seen in the core genome when nine representative isolates of serovar 13 were subjected to whole-genome sequencing. Tetracycline resistance was relatively frequent in the two clusters of serovar 13; one of them was also frequently resistant against beta-lactams. Resistance in other serovars was sporadic. All isolates carried the apxIV gene. The toxin profiles of serovar 2 were characterized by the production of ApxII and ApxIII toxins, except for a small cluster of three isolates: serovar 9 and serovar 16 isolates produced ApxI and ApxII toxins. Serovar 13 carried apxII and apxIBD genes, indicating the production of the ApxII toxin, but not of ApxI or ApxIII. The unusually high frequency and low diversity of serovar 13 are not explained by its virulence properties, but the high frequency of resistance to beta-lactams and tetracyclines may have played a role in its spread. The emergence of serovar 16 may be facilitated by its high virulence, also explaining its high clonality.", "token_count": 495, "char_count": 1712, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5595, "quality_score": 0.7798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:49.513211", "source": { "split": "train_shard_00001", "doc_id": 2238 }, "chunk_id": "train_shard_00001_2238_0", "global_id": 8844 }, { "text": "Genetic Diversity of Actinobacillus pleuropneumoniae Serovars in Hungary.", "token_count": 30, "char_count": 80, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:49.863152", "source": { "split": "train_shard_00001", "doc_id": 2238 }, "chunk_id": "train_shard_00001_2238_1", "global_id": 8845 }, { "text": "To contend with environmental challenges, bacteria have evolved numerous stress response pathways. A notable example is the adoption of a dormant state called persistence, whereby cells reversibly restrict their growth and await favorable conditions. The genetics of persistence remain poorly understood, and genes called toxin-antitoxin (TA) systems have controversially been implicated in this phenotype. To examine their role in persistence, we construct a pan-TA deletion strain of the bacterial pathogen Legionella pneumophila and test its capacity to survive diverse stresses. We identify a single predicted TA system, GndRX, that under genotoxic stress conditions leads to cell death rather than promoting survival, whereas ∆gndRX cells adopt a viable but nonculturable state. Strikingly, this enhanced survival is conferred to wild-type cells in a contact-dependent manner during co-culture. Despite having homology to other TA systems, GndRX displays non-canonical activity, and we hypothesize that it has undergone functional domestication by the cell. Overall, our work reveals both a new physiological function for TA systems in bacteria as well as a heretofore undescribed phenomenon of contact-dependent survival within persister cells.\n\nA bacterial toxin-antitoxin system involved in an unusual response to genotoxic stress.", "token_count": 299, "char_count": 1339, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7326, "quality_score": 0.8663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:50.425367", "source": { "split": "train_shard_00001", "doc_id": 2239 }, "chunk_id": "train_shard_00001_2239_0", "global_id": 8846 }, { "text": "Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca2+ concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H+ antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches", "token_count": 491, "char_count": 1826, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:51.075220", "source": { "split": "train_shard_00001", "doc_id": 2240 }, "chunk_id": "train_shard_00001_2240_0", "global_id": 8847 }, { "text": "This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.\n\nDistinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering.", "token_count": 82, "char_count": 421, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:51.445758", "source": { "split": "train_shard_00001", "doc_id": 2240 }, "chunk_id": "train_shard_00001_2240_1", "global_id": 8848 }, { "text": "PURPOSE: This study is to determine the dynamics in the microflora of cornelian cherry tarhana (CCT), a traditional food of Turkey, by MALDI-TOF/TOF MS. METHODS: Non-fermented and fermented CCT productions were performed by using flours of bread wheat, wholegrain hull-less barley, buckwheat, and clear flour. Identification of the isolates obtained from raw materials and various production steps of the CCT was performed by MALDI-TOF/TOF MS. Dendograms were prepared by cluster analysis and the distances between the strains isolated during production stages and from cornelian cherry puree were determined. RESULTS: Totally, 231 isolates were obtained and 45.5% of them were identified at species level, 30.3% at genus level while 24.2% of the isolates could not be identified. It was found that microflora of cornelian cherry tarhana is mainly composed of yeasts. Thirty-two percent of the identified yeast isolates were Hanseniaspora uvarum and the others were Saccharomycescerevisiae (19.6%), Torulaspora delbrueckii (18.6%), Candida krusei (11.3%), Candida lusitaniae (9.3%), Metschnikowia pulcherrima (3.1%), Wickerhamomyces anomalus (2.1%), Candida kefyr (2.1%), Cyberlindnera fabianii (1%), and Candida parapsilosis (1%). Only two lactic acid bacteria could be isolated, which were Lactobacillus reuteri and Enterococcus spp., originating from buckwheat flour and clear flour, respectively. Dendograms revealed that some of the yeast strains isolated during production were originating from cornelian cherry. CONCLUSIONS: Microflora of CCT was investigated for the first time. This is one of the few studies using MALDI-TOF/TOF MS for identification of food originated yeasts. Novel species–identified, endogenic yeasts which could have potential technological characteristics were introduced.", "token_count": 518, "char_count": 1803, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:21:52.079516", "source": { "split": "train_shard_00001", "doc_id": 2241 }, "chunk_id": "train_shard_00001_2241_0", "global_id": 8849 }, { "text": "MALDI-TOF/TOF mass spectrometry for determination of yeast diversity in traditional cornelian cherry tarhana produced with different cereal/pseudocereal flours", "token_count": 42, "char_count": 159, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:52.448888", "source": { "split": "train_shard_00001", "doc_id": 2241 }, "chunk_id": "train_shard_00001_2241_1", "global_id": 8850 }, { "text": "

Background

To contain intra-hospital transmission of third-generation cephalosporin-resistant Enterobacterales (3GCR-E), contact isolation precautions are recommended.

Aim

To quantify transmissions of 3GCR Escherichia coli and 3GCR Klebsiella pneumoniae within a hospital.

Methods

An automated outbreak detection system (AODS) was used to identify clusters (N≥2) of 3GCR Enterobacterales for the years 2016, 2018 and 2020. Clusters were defined by phenotypic agreement of microbiological results and spatial and temporal relationship. Core genome multi-locus sequence typing (cgMLST) was used to confirm whether the cluster isolates were transmitted between patients.

Findings

A total of 4343 3GCR E. coli and 1377 K. pneumoniae isolates were analysed. Among the 3GCR E. coli isolates, the AODS identified 304 isolates as cluster isolates, the median cluster size was two (range: 2-5). The cgMLST analysis revealed that a total of 23 (7.5%) 3GCR E. coli cluster isolates were transmission-associated, of which 20 isolates (87%) were detected in intensive care patients. Among the 3GCR K. pneumoniae isolates, the AODS identified 73 isolates as cluster isolates, the median cluster size was two (range: 2-4). CgMLST revealed that 35 (48%) 3GCR K. pneumoniae cluster isolates were transmission associated, of which 27 isolates (77%) were detected in intensive care patients.

Conclusion

For 3GCR K. pneumoniae, cgMLST confirmed the AODS results more frequently than for 3GCR E. coli. Therefore, contact isolation precautions for 3GCR K", "token_count": 492, "char_count": 1568, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5355, "quality_score": 0.7678, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:53.099348", "source": { "split": "train_shard_00001", "doc_id": 2242 }, "chunk_id": "train_shard_00001_2242_0", "global_id": 8851 }, { "text": "pneumoniae may be appropriate on intensive care units, but only in certain circumstances, such as outbreaks, for Enterobacterales with lower transmissibility, such as E. coli.\n\nAnalysis of transmission-related third-generation cephalosporin-resistant Enterobacterales by electronic data mining and core genome multi-locus sequence typing.", "token_count": 81, "char_count": 338, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9268, "quality_score": 0.9634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:53.472127", "source": { "split": "train_shard_00001", "doc_id": 2242 }, "chunk_id": "train_shard_00001_2242_1", "global_id": 8852 }, { "text": "The extreme conditions of the Antarctic environment have driven the evolution of highly specialized microbial communities with unique adaptations. In this study, we characterized five Pseudomonas isolates from James Ross Island, which displayed notable taxonomic and metabolite features. Phylogenomic analysis revealed that strain P2663T occupies a distinct phylogenetic position within the Pseudomonas genus, related to species Pseudomonas svalbardensis, Pseudomonas silesiensis, Pseudomonas mucoides, Pseudomonas prosekii, and Pseudomonas gregormendelii. The novelty of five Antarctic isolates was further confirmed through analyses of housekeeping genes, ribotyping, and REP-PCR profiling. MALDI-TOF MS analysis identified 11 unique mass spectrometry signals shared by the Antarctic isolates, which were not detected in other related species. Additionally, chemotaxonomic characterization, including fatty acid composition, demonstrated similarities with related Pseudomonas species. Phenotypic assessments revealed distinctive biochemical and physiological traits. In-depth genomic analysis of strain P2663T uncovered numerous genes which could be involved in survival in extreme Antarctic conditions, including those encoding cold-shock and heat-shock proteins, oxidative and osmotic stress response proteins, and carotenoid-like pigments. Genome mining further revealed several biosynthetic gene clusters, some of which are associated with antimicrobial activity. Functional assays supported the antimicrobial capabilities of this novel species, showing antagonistic effects against clinical isolates of Pseudomonas aeruginosa, possibly mediated by tailocins (phage tail-like particles). This comprehensive polyphasic study characterized a new cold-adapted species, for which we propose the name Pseudomonas rossensis sp. nov.", "token_count": 488, "char_count": 1903, "word_count": 224, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:54.117026", "source": { "split": "train_shard_00001", "doc_id": 2243 }, "chunk_id": "train_shard_00001_2243_0", "global_id": 8853 }, { "text": "Pseudomonas rossensis sp. nov., a novel psychrotolerant species produces antimicrobial agents targeting resistant clinical isolates of Pseudomonas aeruginosa.", "token_count": 52, "char_count": 172, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:54.483774", "source": { "split": "train_shard_00001", "doc_id": 2243 }, "chunk_id": "train_shard_00001_2243_1", "global_id": 8854 }, { "text": "

Background

Multi-drug resistant (MDR) Klebsiella pneumoniae is a public health concern due to its presence in Bangladeshi poultry products and its ability to spread resistance genes. This study genetically characterizes a distinct MDR K. pneumoniae isolate from the gut of poultry in Noakhali, Bangladesh, offering insights into its resistance mechanisms and public health impact.

Methods

Klebsiella pneumoniae isolates from broiler and layer poultry were identified using biochemical and molecular analyses. Eleven isolates were tested for antibiotic sensitivity and categorized by their Multiple Antibiotic Resistance Index (MARI) profiles. The isolate with the highest MARI was selected for whole-genome sequencing using Illumina technology. The sequencing data were analyzed for genome annotation, pan-genome analysis, genome similarities, sequence type identification, and the identification of genetic determinants of resistance and virulence genes.

Result

We identified 10 MARI profiles among 11 K. pneumoniae isolates, with values ranging from 0.64 to 0.94. The highest MARI of 0.94 was found in an isolate from a layer poultry. This isolate's genome, 5401,789 base pairs long with 89.6 % coverage, showed potential inter-species dissemination, as indicated by core genome phylogenetic analysis. It possessed genes conferring resistance to fluoroquinolones, aminoglycosides, β-lactams, folate pathway antagonists, fosfomycin, macrolides, quinolones, rifamycin, tetracyclines, and polymyxins, including colistin.

Conclusion

Poultry serve as reservoirs for MDR K. pneumoniae, which can spread to other species and pose significant health risks. Rigorous monitoring of antibiotic use and genetic characterization of MDR bacterial isolates are essential to mitigate this threat.", "token_count": 499, "char_count": 1811, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:55.133381", "source": { "split": "train_shard_00001", "doc_id": 2244 }, "chunk_id": "train_shard_00001_2244_0", "global_id": 8855 }, { "text": "Whole genome sequencing of multidrug-resistant Klebsiella pneumoniae from poultry in Noakhali, Bangladesh: Assessing risk of transmission to humans in a pilot study.", "token_count": 46, "char_count": 165, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:55.499579", "source": { "split": "train_shard_00001", "doc_id": 2244 }, "chunk_id": "train_shard_00001_2244_1", "global_id": 8856 }, { "text": "The gut microbiota composition can affect the tumor microenvironment and its interaction with the immune system, thereby having implications for treatment predictions. This article reviews the studies available to better understand how the gut microbiome helps the immune system fight cancer. To describe this fact, different mechanisms and approaches utilizing probiotics to improve advancements in cancer treatment will be discussed. Moreover, not only calorie intake but also the variety and quality of diet can influence cancer patients' immunotherapy treatment because dietary patterns can impair immunological activities either by stimulating or suppressing innate and adaptive immunity. Therefore, it is interesting and critical to understand gut microbiome composition as a biomarker to predict cancer immunotherapy outcomes and responses. Here, more emphasis will be given to the recent development in immunotherapies utilizing microbiota to improve cancer therapies, which is beneficial for cancer patients.\n\nThe Microbiome Modulates the Immune System to Influence Cancer Therapy.", "token_count": 209, "char_count": 1090, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:55.963908", "source": { "split": "train_shard_00001", "doc_id": 2245 }, "chunk_id": "train_shard_00001_2245_0", "global_id": 8857 }, { "text": "This paper evaluates the fermentative potential of Kluyveromyces marxianus grown in sugarcane bagasse cellulosic and hemicellulosic hydrolysates obtained by acid hydrolysis. Ethanol was obtained from a single glucose fermentation product, whereas xylose assimilation resulted in xylitol as the main product and ethanol as a by-product derived from the metabolism of this pentose. Fermentation performed in a simulated hydrolysate medium with a glucose concentration similar to that of the hydrolysate resulted in ethanol productivity (Qp = 0.86 g L⁻¹ h⁻¹) that was tenfold higher than the one observed in the cellulosic hydrolysate. However, the use of hemicellulosic hydrolysate favored xylose assimilation in comparison with simulated medium with xylose and glucose concentrations similar to those found in this hydrolysate, without toxic compounds such as acetic acid and phenols. Under this condition, xylitol yield was 53.8 % higher in relation to simulated medium. Thus, the total removal of toxic compounds from the hydrolysate is not necessary to obtain bioproducts from lignocellulosic hydrolysates.\n\nEvaluation of fermentative potential of Kluyveromyces marxianus ATCC 36907 in cellulosic and hemicellulosic sugarcane bagasse hydrolysates on xylitol and ethanol production", "token_count": 358, "char_count": 1282, "word_count": 180, "semantic_coherence": 1, "information_density": 0.55, "quality_score": 0.775, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:56.545047", "source": { "split": "train_shard_00001", "doc_id": 2246 }, "chunk_id": "train_shard_00001_2246_0", "global_id": 8858 }, { "text": "The lactobacilli associated with a fermented goat milk product from Tajikistan were isolated to characterize their technological properties and antibiotic resistances in order to assess their suitability for development as starter cultures. In this study, twenty three strains were identified by 16S rRNA sequencing as typical dairy-associated lactic acid bacterial strains, i.e. L. plantarum, L. pentosus, L. delbrueckii, L. helveticus and L. paracasei. These strains were generally susceptible to most antibiotics tested in this study and this allowed a selection of strains as safe starters. The draft genomes of four representative strains were sequenced and the number of contigs of the four assembled genomes ranged from 51 to 245 and the genome sizes ranged from 1.75 to 3.24 Mbp. These representative strains showed differences in their growth behavior and pH-reducing abilities in in vitro studies. The co-inoculation of these Lactobacillus spp. strains together with a yeast Kluyveromyces marxianus MBT-5698, or together with the yeast and an additional Streptococcus thermophilus MBT-2, led to a pH reduction to 3.4 after 48 h. Only in the case of fermentation inoculated with the co-culture, the viscosity of the milk increased noticeably. In contrast, fermentations with single strains did not lead to gelation of the milk or to a decrease in the pH after 24h. The results of this study provide a comprehensive understanding of the predominant lactobacilli related to Tajikistani fermented milk products.\n\nIsolation and Characterization of Lactic Acid Bacteria from Fermented Goat Milk in Tajikistan.", "token_count": 492, "char_count": 1683, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5785, "quality_score": 0.7893, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:57.194180", "source": { "split": "train_shard_00001", "doc_id": 2247 }, "chunk_id": "train_shard_00001_2247_0", "global_id": 8859 }, { "text": "

Background

The auxin response factor (ARF) is a key regulator involved in plant growth, development, and stress response. In this study, we systematically identified the ARF gene family using a pan-genomic approach based on 47 high-quality potato genomes.

Results

Among the 28 members of the potato ARF pan-gene family, no core or private genes were identified. Only one gene was classified as near-core, while the remaining genes were considered non-essential. Ka/Ks analysis indicated that a single gene was under positive selection, whereas the rest of the family members were subject to purifying selection. Structural variations across the 21 potato genomes did not significantly alter the expression of ARF pan-gene family members, and no notable expression differences were detected. However, these structural variations did lead to changes in conserved domains in certain strains. RNA-seq analysis revealed differential expression of ARF family members under drought stress compared to control conditions, with variation in expression levels among different genes. Further investigation suggested that transcription factors are involved in regulating the expression of ARF gene family members.

Conclusions

Our findings revealed the function of the auxin response-factor family members in biological processes in potato, and provide a new theoretical reference for drought resistance-breeding in this important crop species.\n\nPan-genome identification and expression analysis of the ARF gene family in potato.", "token_count": 328, "char_count": 1538, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:57.765871", "source": { "split": "train_shard_00001", "doc_id": 2248 }, "chunk_id": "train_shard_00001_2248_0", "global_id": 8860 }, { "text": "The effects of yeasts on the survival of probiotic and non-probiotic lactic acid bacteria (LAB) were studied in fermented milk under non-refrigerated conditions (30 degrees C) with a view to develop ambient-stable fermented milk with live LAB. Five yeasts tested (Saccharomyces bayanus, Williopsis saturnus var. saturnus, Yarrowia lipolytica, Candida kefyr and Kluyveromyces marxianus) enhanced the survival of Lactobacillus bulgaricus (but not Streptococcus thermophilus) in a mixed yoghurt culture in yoghurt by approximately 10(2) to 10(5)-fold. Seven yeasts examined (Candida krusei, Geotrichum candidum, Pichia subpelliculosa, Kloeckera apiculata, Pichia membranifaciens, Schizosaccharomyces pombe and Y. lipolytica) improved the survival of Lactobacillus rhamnosus in fermented milk by approximately10(3) to 10(6)-fold. W. saturnus var. saturnus enhanced the survival of Lactobacillus acidophilus, L. rhamnosus (probiotic) and Lactobacillus reuteri by up to 10(6)-fold, but the same yeast failed to improve the survival of Lactobacillus johnsonii (probiotic), S. thermophilus and L. bulgaricus in fermented milk. These results provide definitive evidence that yeasts possess stability-enhancing effects on LAB and that the specific effects of yeasts on LAB stability vary with yeasts as well as with LAB. However, the molecular mechanism of such interaction of yeasts with LAB remains to be found.\n\nEnhancement of survival of probiotic and non-probiotic lactic acid bacteria by yeasts in fermented milk under non-refrigerated conditions.", "token_count": 470, "char_count": 1543, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:58.437395", "source": { "split": "train_shard_00001", "doc_id": 2249 }, "chunk_id": "train_shard_00001_2249_0", "global_id": 8861 }, { "text": "

Background

The emergence of the ST11-CRKP (ST11-CRKP) strain is expected to become a serious public health problem in China. As one of the most serious complications in patients with acute myeloid lymphoma, infections can cause systemic infection and life-threatening sepsis, seriously affecting the morbidity, mortality, and quality of life of patients. Thus, ST11-CRKP infections in patients with acute myeloid lymphoma are worthy of our attention.

Aim

To investigate the occurrence and genetic characteristics of the ST11-CRKP from a patient with acute myeloid lymphoma.

Methods

Species identification was determined by MALDI-TOF MS. Antimicrobial susceptibility testing (AST) was conducted by VITEK 2 system with AST-N335 panel. Whole-genome sequencing was performed on the Illumina NovaSeq 6000 platform. Phylogenetic analyses were performed using Snippy based on the core-genome SNPs.

Findings

S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), Southern blot and Whole-genome analysis indicated blaKPC-2 genes were located on plasmids with a conserved genetic environment. Moreover, the eight ST11-CRKP strains carry a variety of antimicrobial resistance genes (ARGs) and virulence factors. The ability of biofilm formation of eight strains was verified by a crystal violet assay. Core genome single-nucleotide polymorphism (cgSNP) analysis suggesting a possible bacterial translocation event.

Conclusion

We performed a comprehensive analysis of ST11-CRKP strains from a patient with acute myelocytic leukemia. Our study emphasized the need for continuous surveillance of ST11-CRKP in the clinic especially in the immunocompromised population.", "token_count": 489, "char_count": 1708, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:59.115299", "source": { "split": "train_shard_00001", "doc_id": 2250 }, "chunk_id": "train_shard_00001_2250_0", "global_id": 8862 }, { "text": "ST11 KPC-2-Producing Klebsiella pneumoniae Isolated from Patient with Acute Myelocytic Leukemia.", "token_count": 44, "char_count": 103, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:21:59.511308", "source": { "split": "train_shard_00001", "doc_id": 2250 }, "chunk_id": "train_shard_00001_2250_1", "global_id": 8863 }, { "text": "Hungatella hathewayi has been observed to be a member of the gut microbiome. Unfortunately, little is known about this organism in spite of being associated with human fatalities; it is important to understand virulence mechanisms and epidemiological prospective to cause disease. In this study, a patient with chronic neurologic symptoms presented to the clinic with subsequent isolation of a strain with phenotypic characteristics suggestive of Clostridium difficile. However, whole-genome sequence found the organism to be H. hathewayi. Analysis including publicly available Hungatella genomes found substantial genomic differences as compared to the type strain, indicating this isolate was not C. difficile. We examined the whole-genome of Hungatella species and related genera, using comparative genomics to fully examine species identification and toxin production. Orthogonal phylogenetic using the 16S rRNA gene and entire genome analyses that included genome distance analyses using Genome-to-Genome Distance (GGDC), Average Nucleotide Identity (ANI), and a pan-genome analysis with inclusion of available public genomes determined the speciation to be Hungatella. Two clearly differentiated groups were identified, one including a reference H. hathewayi genome (strain DSM-13,479) and a second group that was determined to be H. effluvii, which included our clinical isolate. Also, some genomes reported as H. hathewayi were found to belong to other genera, including Clostridium and Faecalicatena. We show that the Hungatella species have an open pan-genome reflecting high genomic diversity. This study highlights the importance of correctly assigning taxonomic identification, particularly in disease-associated strains, to better understand virulence and therapeutic options.", "token_count": 490, "char_count": 1881, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:00.602944", "source": { "split": "train_shard_00001", "doc_id": 2251 }, "chunk_id": "train_shard_00001_2251_0", "global_id": 8864 }, { "text": "Analyses of publicly available Hungatella hathewayi genomes revealed genetic distances indicating they belong to more than one species.", "token_count": 34, "char_count": 142, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:00.957825", "source": { "split": "train_shard_00001", "doc_id": 2251 }, "chunk_id": "train_shard_00001_2251_1", "global_id": 8865 }, { "text": "Phenolic contents were determined in S. kali leaves, stems, and roots at the beginning, the mid and the end of the vegetative period, as well as the floral bud and open flower at the reproductive stage. Antioxidant and antimicrobial activities were also assessed. Moreover, the major metabolites were identified by HPLC. Results showed a maximum of total phenol contents in the photosynthetic organs, followed by stems and roots. A similar tendency was found for the flavonoids and condensed tannins. Concerning antioxidant analysis, antiradical and Fe-reduced activities were higher in leaves and stems whereas Fe-chelating activity was higher in leaves and roots. Independently of the plant organ, total phenol and flavonoid contents were maximal at the end of the vegetative period whereas tannin content was maximal at the reproductive one. Phenolic contents were related to the organ, the development stage, and their interaction. Concerning the antimicrobial activity, stem extracts were the most efficient against human pathogen strains (Bacteria: Staphylococcus epidermidis, Staphylococcus aureus, Micrococcus luteus, Escherichia coli and Pseudomonas aeruginosa. Fungi: Candida kefyr, C. holmii, C. albicans, C. sake and C. glabrata). Moreover, nine natural products were identified in leaf and stem extracts of S. kali known for their biological activities. As a whole, biological activities of S. kali seem to be strongly related to organs and to the development stage. The phytochemical tests by HPLC demonstrated the presence of nine compounds among them two alkaloids: salsoline and fraxidin. Some molecules are presented in both organs (salsoline, resorcinol, luteolin 7-o-glucoside; and hyperoside). Therefore, endogenous factors greatly account for the biological potential of this medicinal halophyte.\n\nBiological activities and phytochemical analysis of phenolic extracts from Salsola kali L.. Role of endogenous factors in the selection of the best plant extracts", "token_count": 509, "char_count": 1982, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5505, "quality_score": 0.7753, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:01.590381", "source": { "split": "train_shard_00001", "doc_id": 2252 }, "chunk_id": "train_shard_00001_2252_0", "global_id": 8866 }, { "text": "Understanding the genetic causes of trait variation is a primary goal of genetic research. One way that individuals can vary genetically is through the existence of variable pangenomic genes – genes that are only present in some individuals in a population. The presence or absence of entire genes could have large effects on trait variation. However, variable pangenomic genes can be missed in standard genotyping workflows, due to reliance on aligning short-read sequencing to reference genomes. A popular method for studying the genetic basis of trait variation is linkage mapping, which identifies quantitative trait loci (QTLs), regions of the genome that harbor causative genetic variants. Large-scale linkage mapping in the budding yeast Saccharomyces cerevisiae has found thousands of QTLs affecting myriad yeast phenotypes. To enable the resolution of QTLs caused by variable pangenomic genes, we used long-read sequencing to generate highly complete de novo assemblies of 16 diverse yeast isolates. With these assemblies we resolved growth QTLs to specific genes that are absent from the reference genome but present in the broader yeast population at appreciable frequency. Copies of genes also recombine onto chromosomes where they are absent in the reference genome, and we found that these copies generate additional QTLs whose resolution requires pangenome characterization. Our findings demonstrate the power of long-read sequencing to identify the genetic basis of trait variation.\n\nLong-read genomes reveal pangenomic variation underlying yeast phenotypic diversity", "token_count": 340, "char_count": 1583, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6017, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:02.169578", "source": { "split": "train_shard_00001", "doc_id": 2253 }, "chunk_id": "train_shard_00001_2253_0", "global_id": 8867 }, { "text": "In the genomics of plants and the phytoecosystem, Pyrus (pear) is among the most nutritious fruits and contains fiber that has great health benefits to humans. It is mostly cultivated in temperate regions and is one of the most cultivated pome fruits globally. Pears are highly subjected to biotic and abiotic stresses that affect their yield. TIR1/AFB proteins act as auxin co-receptors during the signaling of nuclear auxins and play a primary role in development-related regulatory processes and responses to biotic and abiotic stresses. However, this gene family and its members have not been explored in Pyrus genomes, and understanding these genes will help obtain useful insights into stress tolerance and ultimately help maintain a high yield of pears. This study reports a pangenome-wide investigation of TIR1/AFB genes from eight Pyrus genomes: Cuiguan (Pyrus pyrifolia), Shanxi Duli (P. betulifolia), Zhongai 1 [(P. ussuriensis × communis) × spp.], Nijisseiki (P. pyrifolia), Yunhong No.1 (P. pyrifolia), d'Anjou (P. communis), Bartlett v2.0 (P. communis), and Dangshansuli v.1.1 (P. bretschneideri). These genes were randomly distributed on 17 chromosomes in each genome. Based on phylogenetics, the identified TIR1/AFB genes were divided into six groups. Their gene structure and motif pattern showed the intraspecific structural conservation as well as evolutionary patterns of Pyrus TIR1/AFBs. The expansion of this gene family in Pyrus is mainly caused by segmental duplication; however, a few genes showed tandem duplication. Moreover, positive and negative selection pressure equally directed the gene's duplication process", "token_count": 516, "char_count": 1739, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [ "TIR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:22:02.830718", "source": { "split": "train_shard_00001", "doc_id": 2254 }, "chunk_id": "train_shard_00001_2254_0", "global_id": 8868 }, { "text": "The GO and PPI analysis showed that Pyrus TIR1/AFB genes are associated with abiotic stress- and development-related signaling pathways. The promoter regions of Pyrus TIR1/AFB genes were enriched in hormone-, light-, development-, and stress-related cis elements. Furthermore, publicly available RNA-seq data analysis showed that DaTIR1/AFBs have varied levels of expression in various tissues and developmental stages, fruit hardening disease conditions, and drought stress conditions. This indicated that DaTIR1/AFB genes might play critical roles in response to biotic and abiotic stresses. The DaTIR1/AFBs have similar protein structures, which show that they are involved in the same function. Hence, this study will broaden our knowledge of the TIR1/AFB gene family in Pyrus, elucidating their contribution to conferring resistance against various environmental stresses, and will also provide valuable insights for future researchers.\n\nComparative genomic profiling of transport inhibitor Response1/Auxin signaling F-box (TIR1/AFB) genes in eight Pyrus genomes revealed the intraspecies diversity and stress responsiveness patterns.", "token_count": 311, "char_count": 1188, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7434, "quality_score": 0.8717, "entities": { "genes": [ "TIR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:03.400796", "source": { "split": "train_shard_00001", "doc_id": 2254 }, "chunk_id": "train_shard_00001_2254_1", "global_id": 8869 }, { "text": "Oomycete and fungal pathogens, mainly Phytophthora and Fusarium species, are notorious causal agents of huge economic losses and environmental damages. For instance, Phytophthora ramorum, Phytophthora cryptogea, Phytophthora plurivora and Fusarium solani cause significant losses in nurseries and in forest ecosystems. Chemical treatments, while harmful to the environment and human health, have been proved to have little or no impact on these species. Recently, biocontrol bacterial species were used to cope with these pathogens and have shown promising prospects towards sustainable and eco-friendly agricultural practices. Olive trees prone to Phytophthora and Fusarium disease outbreaks are suitable for habitat-adapted symbiotic strategies, to recover oomycetes and fungal pathogen biocontrol agents. Using this strategy, we showed that olive trees-associated microbiome represents a valuable source for microorganisms, promoting plant growth and healthy benefits in addition to being biocontrol agents against oomycete and fungal diseases. Isolation, characterization and screening of root microbiome of olive trees against numerous Phytophthora and other fungal pathogens have led to the identification of the Bacillus velezensis OEE1, with plant growth promotion (PGP) abilities and strong activity against major oomycete and fungal pathogens. Phylogenomic analysis of the strain OEE1 showed that B. velezensis suffers taxonomic imprecision that blurs species delimitation, impacting their biofertilizers' practical use. Genome mining of several B. velezensis strains available in the GenBank have highlighted a wide array of plant growth promoting rhizobacteria (PGPR) features, metals and antibiotics resistance and the degradation ability of phytotoxic aromatic compounds. Strain OEE1 harbours a large repertoire of secreted and volatile secondary metabolites", "token_count": 511, "char_count": 1956, "word_count": 250, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [ "OEE1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:04.058853", "source": { "split": "train_shard_00001", "doc_id": 2255 }, "chunk_id": "train_shard_00001_2255_0", "global_id": 8870 }, { "text": "Rarefaction analysis of secondary metabolites richness in the B. velezenis genomes, unambiguously documented new secondary metabolites from ongoing genome sequencing efforts that warrants more efforts in order to assess the huge diversity in the species. Comparative genomics indicated that B. velezensis harbours a core genome endowed with PGP features and accessory genome encoding diverse secondary metabolites. Gas Chromatography-Mass Spectrometry (GC-MS) analysis of OEE1 Volatile Organic Compounds (VOCs) and Liquid Chromatography High Resolution Mas Spectrometry (LC-HRMS) analysis of secondary metabolites identified numerous molecules with PGP abilities that are known to interfere with pathogen development. Moreover, B. velezensis OEE1 proved effective in protecting olive trees against F. solani in greenhouse experiments and are able to inhabit olive tree roots. Our strategy provides an effective means for isolation of biocontrol agents against recalcitrant pathogens. Their genomic analysis provides necessary clues towards their efficient implementation as biofertilizers.\n\nOlea europaea L. Root Endophyte Bacillus velezensis OEE1 Counteracts Oomycete and Fungal Harmful Pathogens and Harbours a Large Repertoire of Secreted and Volatile Metabolites and Beneficial Functional Genes.", "token_count": 348, "char_count": 1341, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7018, "quality_score": 0.8509, "entities": { "genes": [ "OEE1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:04.630312", "source": { "split": "train_shard_00001", "doc_id": 2255 }, "chunk_id": "train_shard_00001_2255_1", "global_id": 8871 }, { "text": "

Background

Oat ( Avena sativa , 2 n =6 x =42) is an important crop, and with its wild relatives including A. longiglumis (ALO, 2 n =6 x =14), has advantageous agronomic and nutritional traits. A de-novo chromosome-level ALO genome assembly was made to investigate diversity and structural genome variation between Avena species and other Poaceae in an evolutionary context, and develop genomic resources to identify the pangenome and economic traits within Pooideae.

Results

The 3.85 gigabase ALO genome (seven pseudo-chromosomes), contained 40,845 protein-coding genes and 87% repetitive sequences (84.21% transposable elements). An LTR retrotransposon family was abundant at all chromosome centromeres, and genes were distributed without major terminal clusters. Comparisons of synteny with A. eriantha and A. strigosa showed evolutionary translocations of terminal segments including many genes. Comparison with rice ( x =12) and the ancestral grass karyotype showed synteny and features of chromosome evolution including fusions, translocations and insertions of syntenic blocks across Pooideae species. With a genome size 10 times larger than rice, ALO showed relatively uniform expansion along the chromosome arms, with few gene-poor regions along arms, and no major duplications nor deletions. Linked gene networks were identified (mixed-linkage glucans and cellulose synthase genes), and CYP450 genes may be related to salt-tolerance.

Conclusions

The high-continuity genome assembly shows gene, chromosomal structural and copy number variation, providing a reference for the Avena pangenome, defining the full spectrum of diversity. Chromosomal rearrangements and genome expansion demonstrate features of evolution across the genus and grass BOP-clade, contributing to exploitation of gene and genome diversity through precision breeding.", "token_count": 483, "char_count": 1873, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6628, "quality_score": 0.8314, "entities": { "genes": [ "CYP450" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:05.295455", "source": { "split": "train_shard_00001", "doc_id": 2256 }, "chunk_id": "train_shard_00001_2256_0", "global_id": 8872 }, { "text": "Chromosome-scale genome assembly of the diploid oat Avena longiglumis reveals the landscape of repetitive sequences, genes and chromosome evolution in grasses", "token_count": 47, "char_count": 165, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:05.654686", "source": { "split": "train_shard_00001", "doc_id": 2256 }, "chunk_id": "train_shard_00001_2256_1", "global_id": 8873 }, { "text": "We adopted a bioinformatics-based technique to identify strain-specific markers, which were then used to quantify the abundances of three distinct B. longum sup. longum strains in fecal samples of humans and mice. A pangenome analysis of 205 B. longum sup. longum genomes revealed the accumulation of considerable strain-specific genes within this species; specifically, 28.7% of the total identified genes were strain-specific. We identified 32, 14, and 49 genes specific to B. longum sup. longum RG4-1, B. longum sup. longum M1-20-R01-3, and B. longum sup. longum FGSZY6M4, respectively. After performing an in silico validation of these strain-specific markers using a nucleotide BLAST against both the B. longum sup. longum genome database and an NR/NT database, RG4-1_01874 (1331 bp), M1-20-R01-3_00324 (1745 bp), and FGSZY6M4_01477 (1691 bp) were chosen as target genes for strain-specific quantification. The specificities of the qPCR primers were validated against 47 non-target microorganisms and fecal baseline microbiota to ensure that they produced no PCR amplification products. The performance of the qPCR primer-based analysis was further assessed using fecal samples. After oral administration, the target B. longum strains appeared to efficiently colonize both the human and mouse guts, with average population levels of >108 CFU/g feces. The bioinformatics pipeline proposed here can be applied to the quantification of various bacterial species.", "token_count": 502, "char_count": 1566, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [ "RG4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:06.309895", "source": { "split": "train_shard_00001", "doc_id": 2257 }, "chunk_id": "train_shard_00001_2257_0", "global_id": 8874 }, { "text": "Quantitative Detection of Bifidobacterium longum Strains in Feces Using Strain-Specific Primers.", "token_count": 34, "char_count": 103, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:06.662023", "source": { "split": "train_shard_00001", "doc_id": 2257 }, "chunk_id": "train_shard_00001_2257_1", "global_id": 8875 }, { "text": "Dysbiosis of the neonatal gut microbiome during early life has been suggested as the missing link that may explain higher rates of certain diseases in caesarean section-delivered infants. Many studies report delivery mode-related dysbiosis in infants due to a lack of maternal vaginal microbiome exposure, prompting interventions to correct the neonatal gut microbiome by transferring these missing microbes after caesarean delivery. The maternal vaginal microbiome is among the first microbial exposures that many infants experience, yet little is known about the extent of direct transmission of maternal vaginal microbes. As part of the Maternal Microbiome Legacy Project, we aimed to determine if maternal vaginal bacteria are vertically transmitted to infants. We employed cpn60 microbiome profiling, culture-based screening, molecular strain typing, and whole-genome sequencing to determine whether identical maternal vaginal strains were present in infant stool microbiomes. We identified identical cpn60 sequence variants in both halves of maternal-infant dyads in 204 of 585 Canadian women and their newborn infants (38.9%). The same species of Bifidobacterium and Enterococcus were cultured from maternal and corresponding infant samples in 33 and 13 of these mother-infant dyads, respectively. Pulsed-field gel electrophoresis and whole-genome sequencing determined that near-identical strains were detected in these dyads irrespective of delivery mode, indicating an alternative source in cases of caesarean delivery. Overall, we demonstrated that vertical transmission of maternal vaginal microbiota is likely limited and that transmission from other maternal body sites, such as the gut and breast milk, may compensate for the lack of maternal vaginal microbiome exposure during caesarean delivery. IMPORTANCE The importance of the gut microbiome in human health and disease is widely recognized, and there has been a growing appreciation that alterations in gut microbiome composition during a \"critical window\" of development may impact health in later life", "token_count": 503, "char_count": 2108, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5616, "quality_score": 0.7808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:07.314422", "source": { "split": "train_shard_00001", "doc_id": 2258 }, "chunk_id": "train_shard_00001_2258_0", "global_id": 8876 }, { "text": "Attempts to correct gut microbiome dysbiosis related to birth mode are underpinned by the assumption that the lack of exposure to maternal vaginal microbes during caesarean delivery is responsible for dysbiosis. Here, we demonstrate that there is limited transmission of the maternal vaginal microbiome to the neonatal gut, even in cases of vaginal delivery. Furthermore, the presence of identical strains shared between mothers and infants in early life, even in cases of caesarean delivery, highlights compensatory microbial exposures and sources for the neonatal stool microbiome other than the maternal vagina.\n\nBirth Mode Does Not Determine the Presence of Shared Bacterial Strains between the Maternal Vaginal Microbiome and the Infant Stool Microbiome.", "token_count": 180, "char_count": 759, "word_count": 111, "semantic_coherence": 1, "information_density": 0.6036, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:07.750790", "source": { "split": "train_shard_00001", "doc_id": 2258 }, "chunk_id": "train_shard_00001_2258_1", "global_id": 8877 }, { "text": "Enterococcus faecalis is an opportunistic pathogen that causes infective endocarditis. Despite in vitro synergy of the recommended combination ampicillin and ceftriaxone (AC), E. faecalis infective endocarditis (EFIE) mortality remains high. We characterized 119 isolates from EFIE patients in our health system from 2018 to 2023 genomically and phenotypically. Three genetic lineages (ST6, ST40, and ST179) accounted for 41% of all infections. ST6 isolates were less susceptible to ceftriaxone and AC in dual-antibiotic checkerboard assays, but also exhibited decreased survival in dual-antibiotic killing assays using humanized AC exposures. ST6 isolates encoded a known genetic disruption affecting pbp4 as well as mutation of a putative hydrolase called phnP. Functional studies confirmed that both alterations contributed to altered AC susceptibility. Finally, we found that ampicillin plus daptomycin showed robust growth inhibition and killing against EFIE isolates with decreased AC susceptibility. These findings enhance our understanding of EFIE and may guide better therapeutic strategies.\n\nFunctional genomics of antibiotic susceptibility in Enterococcus faecalis from infective endocarditis.", "token_count": 313, "char_count": 1204, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "ST6", "ST179", "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:08.305863", "source": { "split": "train_shard_00001", "doc_id": 2259 }, "chunk_id": "train_shard_00001_2259_0", "global_id": 8878 }, { "text": "The neurotoxin formed by Clostridium botulinum Group II is a major cause of foodborne botulism, a deadly intoxication. This study aims to understand the genetic diversity and spread of C. botulinum Group II strains and their neurotoxin genes. A comparative genomic study has been conducted with 208 highly diverse C. botulinum Group II strains (180 newly sequenced strains isolated from 16 countries over 80 years, 28 sequences from Genbank). Strains possessed a single type B, E, or F neurotoxin gene or were closely related strains with no neurotoxin gene. Botulinum neurotoxin subtype variants (including novel variants) with a unique amino acid sequence were identified. Core genome single-nucleotide polymorphism (SNP) analysis identified two major lineages-one with type E strains, and the second dominated by subtype B4 strains with subtype F6 strains. This study revealed novel details of population structure/diversity and established relationships between whole-genome lineage, botulinum neurotoxin subtype variant, association with foodborne botulism, epidemiology, and geographical source. Additionally, the genome sequences represent a valuable resource for the research community (e.g., understanding evolution of C. botulinum and its neurotoxin genes, dissecting key aspects of C. botulinum Group II biology). This may contribute to improved risk assessments and the prevention of foodborne botulism.\n\nPan-Genomic Analysis of <i>Clostridium botulinum</i> Group II (Non-Proteolytic <i>C. botulinum</i>) Associated with Foodborne Botulism and Isolated from the Environment.", "token_count": 448, "char_count": 1645, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:08.945494", "source": { "split": "train_shard_00001", "doc_id": 2260 }, "chunk_id": "train_shard_00001_2260_0", "global_id": 8879 }, { "text": "Gut colonization with multidrug-resistant Enterobacterales (MDR-Ent) has reached worrisome levels worldwide. In this context, Escherichia ruysiae is a recently described species mostly found in animals. However, its spread and impact on humans is poorly understood. A stool sample from a healthy individual living in India was screened for the presence of MDR-Ent using culture-based methods. Colonies were routinely identified using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) and phenotypically characterized by broth microdilution. Illumina and Nanopore whole-genome sequencing (WGS) platforms were implemented to generate a complete assembly. E. ruysiae genomes deposited in international databases were used for a core genome phylogenetic analysis. An extended-spectrum β-lactamase (ESBL)-producing E. coli strain (S1-IND-07-A) was isolated from the stool. WGS confirmed that S1-IND-07-A was indeed E. ruysiae, belonged to sequence type 5792 (ST5792), core genome (cg) ST89059, serotype O13/O129-:H56-like, clade IV phylogroup, and possessed five virulence factors. A copy of blaCTX-M-15 and five other antimicrobial resistance genes (ARGs) were detected in a conjugative IncB/O/K/Z plasmid. A database search identified 70 further E. ruysiae strains from 16 countries (44, 15, and 11 strains isolated from animals, the environment, and humans, respectively). The core genome phylogeny revealed five major STs: ST6467, ST8084, ST2371, ST9287, and ST5792", "token_count": 503, "char_count": 1566, "word_count": 203, "semantic_coherence": 1, "information_density": 0.7685, "quality_score": 0.8842, "entities": { "genes": [ "ST9287", "ST8084", "ST2371", "ST6467", "ST89059", "ST5792" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:09.592349", "source": { "split": "train_shard_00001", "doc_id": 2261 }, "chunk_id": "train_shard_00001_2261_0", "global_id": 8880 }, { "text": "Three out of the seventy strains possessed important ARGs: OTP1704 (blaCTX-M-14; ST6467), SN1013-18 (blaCTX-M-15; ST5792), and CE1758 (blaCMY-2; ST7531). These strains were of human, environmental, and wild animal origin, respectively. E. ruysiae may acquire clinically important ARGs and transmit them to other species. Due to its zoonotic potential, further efforts are needed to improve routine detection and surveillance across One Health settings. IMPORTANCE Escherichia ruysiae is a recently described species of the cryptic clades III and IV of the genus Escherichia and is commonly found in animals and the environment. This work highlights the zoonotic potential of E. ruysiae, as it has been shown to colonize the human intestinal tract. Importantly, E. ruysiae may be associated with conjugative plasmids carrying clinically relevant antibiotic resistance genes. Therefore, it is important to closely monitor this species. Overall, this study highlights the need for improved identification of Escherichia species and continued surveillance of zoonotic pathogens in One Health settings.\n\nEscherichia ruysiae May Serve as a Reservoir of Antibiotic Resistance Genes across Multiple Settings and Regions.", "token_count": 374, "char_count": 1294, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6628, "quality_score": 0.8314, "entities": { "genes": [ "CE1758", "SN1013", "OTP1704", "ST7531", "ST6467", "ST5792" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:10.211969", "source": { "split": "train_shard_00001", "doc_id": 2261 }, "chunk_id": "train_shard_00001_2261_1", "global_id": 8881 }, { "text": "Antimicrobial resistance (AMR) is a growing threat in healthcare systems, particularly in the management of infections in critically ill patients. This study highlights how to identify clusters and putative sharing of mobile genetic elements, such as transposons, in the hospital setting using long-read whole genome sequencing (lrWGS). The approach described here can be employed to investigate the transmission dynamics of KPC-3-positive Klebsiella pneumoniae at multiple levels, from the entire isolate down to individual plasmids and transposons. Here, a bla KPC-3 harboring transposon cluster was identified by using a Mash-based distance calculation for plasmids. This approach was used to investigate a local accumulation of KPC-3-positive Klebsiella pneumoniae on surgical and infectious disease wards of a tertiary care center in Germany over a time of six months. In total, seven patients were affected. Core genome multi-locus sequence typing analysis (cgMLST) identified two distinct genetic clusters: a sequence type (ST) 307 cluster (n = 5) and a ST101 cluster (n = 2). All isolates carried a bla KPC-3 carbapenemase. Further Mash distance-based plasmid analysis was not consistent with plasmid transfer due to genetic heterogeneity, but identified a transposon cluster across all isolates. Infection control evaluation of patient movements within their hospital admission supports a possible clonal transmission. Subsequent infection control measures, including point prevalence screening and enhanced contact precautions, successfully contained further transmissions. The study illustrates the value of in-depth plasmid analysis in understanding the transmission dynamics and epidemiology of AMR, particularly in hospital environments.\n\nIn-depth characterization of <i>Klebsiella pneumoniae</i> carbapenemase (KPC)-encoding plasmids points at transposon-related transmission of resistance genes.", "token_count": 485, "char_count": 1973, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6693, "quality_score": 0.8346, "entities": { "genes": [ "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:10.876361", "source": { "split": "train_shard_00001", "doc_id": 2262 }, "chunk_id": "train_shard_00001_2262_0", "global_id": 8882 }, { "text": "Staphylococcus capitis is a frequent cause of late-onset sepsis in neonates admitted to Neonatal Intensive Care Units (NICU). One clone of S. capitis, NRCS-A has been isolated from NICUs globally although the reasons for the global success of this clone are not well understood.We analysed a collection of S. capitis colonising babies admitted to two NICUs, one in the UK and one in Germany as well as corresponding pathological clinical isolates. Genome analysis identified a population structure of three groups; non-NRCS-A isolates, NRCS-A isolates, and a group of 'proto NRCS-A' - isolates closely related to NRCS-A but not associated with neonatal infection. All bloodstream isolates belonged to the NRCS-A group and were indistinguishable from strains carried on the skin or in the gut. NRCS-A isolates showed increased tolerance to chlorhexidine and antibiotics relative to the other S. capitis as well as enhanced ability to grow at higher pH values. Analysis of the pangenome of 138 isolates identified characteristic nsr and tarJ genes in both the NRCS-A and proto groups. A CRISPR-cas system was only seen in NRCS-A isolates which also showed enrichment of genes for metal acquisition and transport.We found evidence for transmission of S. capitis NRCS-A within NICU, with related isolates shared between babies and multiple acquisitions by some babies. Our data show NRCS-A strains commonly colonise uninfected babies in NICU representing a potential reservoir for potential infection. This work provides more evidence that adaptation to survive in the gut and on skin facilitates spread of NRCS-A, and that metal acquisition and tolerance may be important to the biology of NRCS-A. Understanding how NRCS-A survives in NICUs can help develop infection control procedures against this clone.", "token_count": 490, "char_count": 1852, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:11.567216", "source": { "split": "train_shard_00001", "doc_id": 2263 }, "chunk_id": "train_shard_00001_2263_0", "global_id": 8883 }, { "text": "Characterisation of neonatal Staphylococcus capitis NRCS-A isolates compared with non NRCS-A Staphylococcus capitis from neonates and adults.", "token_count": 56, "char_count": 155, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:11.957139", "source": { "split": "train_shard_00001", "doc_id": 2263 }, "chunk_id": "train_shard_00001_2263_1", "global_id": 8884 }, { "text": "

Background

A revolutionary diversion from classical vaccinology to reverse vaccinology approach has been observed in the last decade. The ever-increasing genomic and proteomic data has greatly facilitated the vaccine designing and development process. Reverse vaccinology is considered as a cost-effective and proficient approach to screen the entire pathogen genome. To look for broad-spectrum immunogenic targets and analysis of closely-related bacterial species, the assimilation of pangenome concept into reverse vaccinology approach is essential. The categories of species pangenome such as core, accessory, and unique genes sets can be analyzed for the identification of vaccine candidates through reverse vaccinology.

Results

We have designed an integrative computational pipeline term as \"PanRV\" that employs both the pangenome and reverse vaccinology approaches. PanRV comprises of four functional modules including i) Pangenome Estimation Module (PGM) ii) Reverse Vaccinology Module (RVM) iii) Functional Annotation Module (FAM) and iv) Antibiotic Resistance Association Module (ARM). The pipeline is tested by using genomic data from 301 genomes of Staphylococcus aureus and the results are verified by experimentally known antigenic data.

Conclusion

The proposed pipeline has proved to be the first comprehensive automated pipeline that can precisely identify putative vaccine candidates exploiting the microbial pangenome. PanRV is a Linux based package developed in JAVA language. An executable installer is provided for ease of installation along with a user manual at https://sourceforge.net/projects/panrv2/ .\n\nPanRV: Pangenome-reverse vaccinology approach for identifications of potential vaccine candidates in microbial pangenome.", "token_count": 406, "char_count": 1771, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:12.577349", "source": { "split": "train_shard_00001", "doc_id": 2264 }, "chunk_id": "train_shard_00001_2264_0", "global_id": 8885 }, { "text": "Bacillus species isolated from Polish bee pollen (BP) and bee bread (BB) were characterized for in silico probiotic and safety attributes. A probiogenomics approach was used, and in-depth genomic analysis was performed using a wide array of bioinformatics tools to investigate the presence of virulence and antibiotic resistance properties, mobile genetic elements, and secondary metabolites. Functional annotation and Carbohydrate-Active enZYmes (CAZYme) profiling revealed the presence of genes and a repertoire of probiotics properties promoting enzymes. The isolates BB10.1, BP20.15 (isolated from bee bread), and PY2.3 (isolated from bee pollen) genome mining revealed the presence of several genes encoding acid, heat, cold, and other stress tolerance mechanisms, adhesion proteins required to survive and colonize harsh gastrointestinal environments, enzymes involved in the metabolism of dietary molecules, antioxidant activity, and genes associated with the synthesis of vitamins. In addition, genes responsible for the production of biogenic amines (BAs) and D-/L-lactate, hemolytic activity, and other toxic compounds were also analyzed. Pan-genome analyses were performed with 180 Bacillus subtilis and 204 Bacillus velezensis genomes to mine for any novel genes present in the genomes of our isolates. Moreover, all three isolates also consisted of gene clusters encoding secondary metabolites.\n\nIn Silico Safety Assessment of Bacillus Isolated from Polish Bee Pollen and Bee Bread as Novel Probiotic Candidates.", "token_count": 421, "char_count": 1553, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.809, "entities": { "genes": [ "BB10", "BP20", "PY2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:13.208766", "source": { "split": "train_shard_00001", "doc_id": 2265 }, "chunk_id": "train_shard_00001_2265_0", "global_id": 8886 }, { "text": "Mawè is a West African spontaneous fermented cereal-based dough. Different types of mawè exist varying in type of cereal and/or production condition, with fermentations lasting 24-48 h. With the aim of obtaining a comprehensive understanding of the microbial ecology of mawè processing, a microbiological characterisation was performed for four mawè types, produced at eight sites in Benin. At the onset of the fermentations lactic acid bacteria (LAB) and yeast counts were on average 7.5 ± 1.03 and 4.8 ± 0.79 Log10 cfu/g, which increased to 9.2 ± 0.38 and 7.4 ± 0.42 Log10 cfu/g, respectively, at the end of the fermentations. LAB (n = 321) and yeasts (n = 298), isolated during the fermentations, were identified. The predominant LAB and yeast species were Lactobacillus fermentum and Pichia kudriavzevii, respectively, followed by Kluyveromyces marxianus, all present throughout the mawè fermentations. Further, microbial successions took place with Weissella confusa occurring mostly at the onset, while Pediococcus acidilactici and Saccharomyces cerevisiae were mainly associated with the end of the fermentations. Species diversity was influenced both by type of cereal and production condition. The dominating strain clusters of L. fermentum and P. kudriavzevii were ubiquitous and strain diversities were influenced by type of cereal and production site.\n\nOccurrence of lactic acid bacteria and yeasts at species and strain level during spontaneous fermentation of mawè, a cereal dough produced in West Africa.", "token_count": 473, "char_count": 1541, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5771, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:13.847560", "source": { "split": "train_shard_00001", "doc_id": 2266 }, "chunk_id": "train_shard_00001_2266_0", "global_id": 8887 }, { "text": "In 2011 a novel methicillin resistance gene, mecC, was described in human and bovine Staphylococcus aureus isolates. mecC-positive S. aureus is most commonly associated with livestock and wildlife populations across Europe and is particularly prevalent in hedgehogs, but only occasionally causes human infections. In this study we characterize and investigate the origin of two human S. aureus isolates containing mecC genes from New Zealand. The two isolates were identified from patients with severe invasion infection as part of a S. aureus bacteraemia study. Whole genome sequencing (WGS) was used to characterize staphylococcal cassette chromosome mec (SCCmec) elements and perform phylogenetic comparisons with publicly available strains from mecC-associated clonal complexes, including isolates from hedgehogs from New Zealand and Europe/UK, and livestock, wildlife and human isolates from Europe/UK. The two isolates from our study have almost identical SCCmec type XI elements containing a mecC gene. However this gene contains a premature stop codon, consistent with the methicillin susceptible phenotype observed for these isolates. Core genome SNP analyses showed that the two isolates are 234 SNPs apart and are most closely related to an isolate obtained from a New Zealand hedgehog. However, there are considerable differences in the mecC mobile element between the human and hedgehog isolates, indicating the presence of an as yet unknown reservoir of mecC S. aureus in the New Zealand environment.\n\nGenomic epidemiology of mecC-carrying Staphylococcus aureus isolates from human clinical cases in New Zealand.", "token_count": 406, "char_count": 1626, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:14.465958", "source": { "split": "train_shard_00001", "doc_id": 2267 }, "chunk_id": "train_shard_00001_2267_0", "global_id": 8888 }, { "text": "

Background

The methylotrophic yeast, Hansenula polymorpha is an industrially important microorganism, and belongs to the best studied yeast species with well-developed tools for molecular research. The complete genome sequence of the strain NCYC495 of H. polymorpha is publicly available. Some of the well-studied strains of H. polymorpha are known to ferment glucose, cellobiose and xylose to ethanol at elevated temperature (45 - 50°C) with ethanol yield from xylose significantly lower than that from glucose and cellobiose. Increased yield of ethanol from xylose was demonstrated following directed metabolic changes but, still the final ethanol concentration achieved is well below what is considered feasible for economic recovery by distillation.

Results

In this work, we describe the construction of strains of H. polymorpha with increased ethanol production from xylose using an ethanol-non-utilizing strain (2EthOH-) as the host. The transformants derived from 2EthOH- overexpressing modified xylose reductase (XYL1m) and native xylitol dehydrogenase (XYL2) were isolated. These transformants produced 1.5-fold more ethanol from xylose than the original host strain. The additional overexpression of XYL3 gene coding for xylulokinase, resulted in further 2.3-fold improvement in ethanol production with no measurable xylitol formed during xylose fermentation. The best ethanol producing strain obtained by metabolic engineering approaches was subjected to selection for resistance to the known inhibitor of glycolysis, the anticancer drug 3-bromopyruvate. The best mutant selected had an ethanol yield of 0.3 g/g xylose and produced up to 9.8 g of ethanol/l during xylose alcoholic fermentation at 45°C without correction for ethanol evaporation.

Conclusions

Our results indicate that xylose conversion to ethanol at elevated temperature can be significantly improved in H", "token_count": 518, "char_count": 1904, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.8069, "entities": { "genes": [ "NCYC495", "XYL2", "XYL3" ], "proteins": [], "pathways": [ "glycolysis", "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:22:15.123633", "source": { "split": "train_shard_00001", "doc_id": 2268 }, "chunk_id": "train_shard_00001_2268_0", "global_id": 8889 }, { "text": "polymorpha by combining methods of metabolic engineering and classical selection.\n\nMetabolic engineering and classical selection of the methylotrophic thermotolerant yeast Hansenula polymorpha for improvement of high-temperature xylose alcoholic fermentation.", "token_count": 62, "char_count": 259, "word_count": 29, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:15.487725", "source": { "split": "train_shard_00001", "doc_id": 2268 }, "chunk_id": "train_shard_00001_2268_1", "global_id": 8890 }, { "text": "Extraintestinal pathogenic Escherichia coli (ExPEC) are responsible for a variety of human infections (urinary tract infections, septicemia, meningitis) and can be routinely isolated from treated sewage. However, the phenotypic properties mediating treatment resistance in ExPEC remain elusive. Herein, we examined heat-resistance in presumptive wastewater ExPEC (W-ExPEC) surviving sewage chlorination or full-scale wastewater treatment. Interestingly, heat-resistance in W-ExPEC was triggered by exposure to hypo-osmotic conditions (i.e., sterile distilled water), resulting in a 10- to 1,000-fold increase in heat-resistance compared to cells exposed to iso-osmotic conditions (i.e., phosphate buffered saline). Remarkably, hypo-osmotic induction of heat resistance occurred extremely fast, in as little as 30 s, and was reversible, demonstrating the phenotypic plasticity of this stress response. Hypo-osmotic stressed W-ExPEC strains survived 58 °C temperatures for up to 20 min - this compared to the clinical reference ExPEC strain, CTF073, which became non-culturable after only 5 min of exposure at this temperature (>8 log10 decline in culturability). The upper thermotolerance level of W-ExPEC (defined as the temperature where culturability was lost after 5 min of exposure) was 62 °C, compared to 58 °C for CFT073. The finding that osmotic stress acts as an anticipatory inducer of heat resistance in W-ExPEC is novel, providing some insights into the possible mechanisms triggering a treatment resistant phenotype in W-ExPEC. The evolution of treatment resistance is worrying prospect for public health, given that waste treatment is a hallmark of infectious disease control in modern society.", "token_count": 478, "char_count": 1714, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.834, "entities": { "genes": [ "CTF073", "CFT073" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:16.132065", "source": { "split": "train_shard_00001", "doc_id": 2269 }, "chunk_id": "train_shard_00001_2269_0", "global_id": 8891 }, { "text": "Hypo-osmotic stress is an anticipatory trigger of heat-resistance in presumptive extraintestinal pathogenic <i>Escherichia coli</i> isolated from treated sewage.", "token_count": 57, "char_count": 173, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:16.490465", "source": { "split": "train_shard_00001", "doc_id": 2269 }, "chunk_id": "train_shard_00001_2269_1", "global_id": 8892 }, { "text": "The transition towards graph pangenomes is posing several new challenging questions, most notably how to extend the classical notion of read alignment from a sequence-to-sequence to a sequence-to-graph setting. Especially on variation graphs, where paths corresponding to individual genomes are labeled, notions of alignments that are strongly inspired by the classical ones are usually able to capture only variations that can be expressed by mismatches or gaps, such as SNPs or short insertions and deletions. On the other hand the recent investigation of pangenomes at bacterial scale (Colquhoun et al, 2021) shows that most tools are tailored for human pangenomes and are not suited to bacteria which exhibit, among other characteristics, a larger variability. Such variability leads to the need for incorporating a greater flexibility when computing an alignment. In this paper, we extend the usual notion of sequence-to-graph alignment by including recombinations among the variations that explicitly represented and evaluated in an alignment. From a computational modeling point of view, a recombination corresponds to identifying a new path of the variation graph which is a mosaic of two different paths, possibly joined by a new arc. We provide a dynamic programming algorithm for computing an optimal alignment that allows recombinations with an affine penalty. We have implemented our approach with the tool RecGraph and we have analyzed its accuracy over some over some bacterial pangenome graphs.\n\nRecGraph: adding recombinations to sequence-to-graph alignments", "token_count": 320, "char_count": 1575, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:17.052843", "source": { "split": "train_shard_00001", "doc_id": 2270 }, "chunk_id": "train_shard_00001_2270_0", "global_id": 8893 }, { "text": "

Significance Statement

Genetic exchange among bacteria shapes the microbial world. From the acquisition of antimicrobial resistance genes to fundamental questions about the nature of bacterial species, this powerful evolutionary force has preoccupied scientists for decades. However, the mixing of genes between species rests on a paradox. On one hand, promoting adaptation by conferring novel functionality, on the other potentially introducing disharmonious gene combinations (negative epistasis) that will be selected against. Taking an interdisciplinary approach to analyse natural populations of the enteric bacteria Campylobacter , an ideal example of long-range admixture, we demonstrate that genes can independently transfer across species boundaries and rejoin in epistasis in a recipient genome. This challenges conventional ideas and highlights the possibility of single step evolution by saltation. Recombination of short DNA fragments via horizontal gene transfer (HGT) can both introduce beneficial alleles and create genomic disharmony through negative epistasis. For non-core (accessory) genes, the negative epistatic cost is likely to be minimal because the incoming genes have not co-evolved with the recipient genome. By contrast, for the core genome, interspecific recombination is expected to be rare because disruptive allelic replacement is likely to introduce negative epistasis. Why then is homologous recombination common in the core of bacterial genomes? To understand this enigma we take advantage of an exceptional model system, the common enteric pathogens Campylobacter jejuni and Campylobacter coli , that are known for very high magnitude interspecies gene flow in the core genome. As expected, HGT does indeed disrupt co-adapted allele pairings (negative epistasis). However, multiple HGT events enable recovery of the genome’s co-adaption between introgressing alleles, even in core metabolism genes (e.g., formate dehydrogenase). These findings demonstrate that, even for complex traits, genetic coalitions can be decoupled, transferred and independently reinstated in a new genetic background – facilitating transition between fitness peaks. In this example, the two-step recombinational process is associated with C. coli that are adapted to the agricultural niche.", "token_count": 493, "char_count": 2312, "word_count": 318, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:17.700463", "source": { "split": "train_shard_00001", "doc_id": 2271 }, "chunk_id": "train_shard_00001_2271_0", "global_id": 8894 }, { "text": "A two-hit epistasis model prevents core genome disharmony in recombining bacteria", "token_count": 20, "char_count": 81, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:18.051993", "source": { "split": "train_shard_00001", "doc_id": 2271 }, "chunk_id": "train_shard_00001_2271_1", "global_id": 8895 }, { "text": "Streptococcus mutans is considered a primary etiologic agent of dental caries, which is the most common chronic infectious disease worldwide. S. mutans B04Sm5 was recently shown to produce reutericyclins and mutanocyclin through the muc biosynthetic gene cluster, and to utilize reutericyclins to inhibit the growth of neighboring commensal Streptococci. In this study, examination of S. mutans and muc phylogeny suggested evolution of an ancestral S. mutans muc into three lineages within one S. mutans clade, and then horizontal transfer of muc to other S. mutans clades. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. mucH was demonstrated to encode a transcriptional activator of muc. mucH deletion reduced production of mutanocyclin and reutericyclins, and eliminated the impaired growth and inhibition of neighboring Streptococci phenotypes which are associated with reutericyclin production. Δ mucG had increased mutanocyclin and reutericyclin production, which impaired growth and increased the ability to inhibit neighboring Streptococci. However, deletion of mucG also caused reduced expression of mucD, mucE , and mucI . Deletion of mucI reduced mutanocyclin and reutericylin production, but enhanced growth, suggesting that mucI may not transport reutericyclin as its homolog does in Limosilactobacillus reuteri . Further research is needed to determine the roles of mucG and mucI , and to identify any co-factors affecting the activity of the mucG and mucH regulators. Overall, this study provided pangenome and phylogenetic analysis that serves as a resource for S. mutans research, and began elucidation of the regulation of reutericyclins and mutanocyclin production in S. mutans .

Importance

S. mutans must be able to outcompete neighboring organisms in its ecological niche in order to cause dental caries. S", "token_count": 504, "char_count": 1893, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5415, "quality_score": 0.7708, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:18.705238", "source": { "split": "train_shard_00001", "doc_id": 2272 }, "chunk_id": "train_shard_00001_2272_0", "global_id": 8896 }, { "text": "mutans B04Sm5 inhibited the growth of neighboring commensal Streptococci through production of reutericyclins via the muc biosynthetic gene cluster. In this study, carriage of muc was examined across S. mutans , which showed that 35 of 244 RefSeq S. mutans genomes encoded muc and provided a valuable update to the S. mutans pangenome and phylogeny. The roles of the mucG and mucH transcriptional regulators, and the mucI transporter, were also examined. All 3 genes impacted production of mutanocyclin and reutericyclins, which affected the growth rates, transcriptomes, and the ability of the S. mutans strains to inhibit the growth of neighboring commensals.\n\nmucG, mucH, and mucI modulate production of mutanocyclin and reutericyclins in Streptococcus mutans B04Sm5", "token_count": 242, "char_count": 790, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:19.186305", "source": { "split": "train_shard_00001", "doc_id": 2272 }, "chunk_id": "train_shard_00001_2272_1", "global_id": 8897 }, { "text": "Abstract

Background The Klebsiella pneumoniae (KP) species complex comprises KP as the predominant species, and four others including Klebsiella variicola (KV) and Klebsiella quasipneumoniae (KQ), all capable of causing clinical infections and often challenging to differentiate. The emergence of multidrug-resistant and hypervirulent KP strains has led to severe infections with limited treatment options, underscoring the need to understand the factors contributing to KP's prevalence. Methods This study compared globally disseminated KP lineages with less abundant KV and KQ strains across multiple omics levels to identify characteristics potentially explaining KP's success over closely related species. Results We identified 107 genes of the core genome in eight clinical KP strains from four different sequence types (STs). Transcriptome and proteome analyses in human urine-like medium revealed different regulatory patterns between KP and KV strains, with metabolic responses playing a pivotal role. A total of 193 genes specific to the investigated KP STs were identified, exhibiting differential expression at the transcriptomic and/or proteomic levels. Comparison of these regulated genes to over 6,000 publicly available Klebsiella genomes highlighted genes adaptively regulated or uniquely present in KP genomes. For example, a gene cluster for the cellobiose phosphotransferase system, previously linked to bacterial virulence and biofilm formation, was found exclusively in KP. Conclusion Our study underscores the metabolic flexibility of KP strains in response to specific environmental conditions, potentially crucial for their success as opportunistic pathogens. We identified markers enriched in KP STs, providing a foundation for future investigations and potential utilization in alternative treatment strategies to conventional antibiotics.

\n\nMulti-omics investigation reveals unique markers underpinning the success of Klebsiella pneumoniae over closely related species", "token_count": 488, "char_count": 2072, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6742, "quality_score": 0.8371, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:19.834725", "source": { "split": "train_shard_00001", "doc_id": 2273 }, "chunk_id": "train_shard_00001_2273_0", "global_id": 8898 }, { "text": "Serratia marcescens is an opportunistic pathogen with a propensity to cause nosocomial outbreaks, particularly in neonatal intensive care units (NICUs). We present a sustained outbreak spanning over 18 months (1 January 2022-29 August 2023) in a NICU in Antwerp, Belgium, affecting 61 neonates, identified through samples taken for diagnostic purposes and by rectal screening. Ten neonates were infected: five with lower respiratory tract infection, four with conjunctivitis and one fatal case with sepsis. In a logistic regression analysis, nursing in an incubator was significantly associated with acquisition of S. marcescens (odds ratio (OR): 2.99; 95% confidence interval (CI): 1.14-8.25; p < 0.05). Whole genome sequencing-based multilocus sequence typing (wgMLST) and core genome single nucleotide polymorphism (cgSNP) analysis of isolates from clinical (n = 4), screening (n = 52) and environmental samples (n = 8), identified eight clusters and five singletons not associated with the clusters. Although outbreak measures were successful in containing further spread within the ward during sudden surges when > 4 cases per week were identified (peak events), several peaks with different clonal clusters occurred. The emergence of similar outbreaks in Belgian hospitals underscores the need of continuous surveillance and NICU-specific infection prevention and control (IPC) measures.\n\nGenomic epidemiological analysis of a single-centre polyclonal outbreak of Serratia marcescens, Belgium, 2022 to 2023.", "token_count": 438, "char_count": 1534, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7617, "quality_score": 0.8808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:20.471998", "source": { "split": "train_shard_00001", "doc_id": 2274 }, "chunk_id": "train_shard_00001_2274_0", "global_id": 8899 }, { "text": "Non-typhoidal Salmonella is a common cause of gastroenteritis worldwide, but current non-typhoidal Salmonella surveillance is suboptimal. Here we evaluated the utility of wastewater monitoring to enhance surveillance for this foodborne pathogen. In June 2022, we tested composite raw sewage collected twice a week from two treatment plants in central Pennsylvania for non-typhoidal Salmonella and characterized isolates using whole genome sequencing. We recovered 43 Salmonella isolates from wastewater samples, differentiated by genomic analysis into seven serovars: 16 Panama (37.2%), 9 Senftenberg (20.9%), and 8 Baildon (18.6%), 3 or fewer for four other serovars. We assessed genetic relatedness and epidemiologic links between non-typhoidal Salmonella serovars from wastewater and isolates from patients with salmonellosis. All S. Baildon serovars from wastewater were genetically and epidemiologically associated with a known salmonellosis outbreak. S. Baildon from wastewater and 42 outbreak-related isolates in the national outbreak detection database had the same core genome multilocus sequence typing and code differed by no or one single polynucleotide polymorphisms. One of the 42 outbreak-related isolates was obtained from a patient residing in the wastewater sample collection catchment area, which serves approximately 17000 people. S. Baildon is a rare serovar (reported in <1% cases nationally over five years). Our study underscores the value of monitoring sewage from a defined population to supplement traditional surveillance methods for evidence of Salmonella infections and to determine the extent of outbreaks.

Importance statement

During the COVID-19 pandemic, surveillance for SARS-CoV-2 in wastewater was a powerful tool for assessing community burden days ahead of traditional reporting. Here, we show that domestic sewage monitoring is useful for surveillance for a foodborne pathogen. Salmonella enterica was detected in samples from two wastewater treatment plants in central Pennsylvania during June 2022. Using whole genome sequencing, we demonstrated that isolates of variant S ", "token_count": 513, "char_count": 2124, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:22:21.799449", "source": { "split": "train_shard_00001", "doc_id": 2275 }, "chunk_id": "train_shard_00001_2275_0", "global_id": 8900 }, { "text": "Baildon clustered with those from an outbreak that occurred in a similar time frame. Case reports were primarily from Pennsylvania, and one individual lived within the treatment center catchment area. This study provides support for the utility of domestic sewage surveillance in assisting public health agencies identify communities impacted by infectious diseases.\n\nOutbreak-associatedSalmonellaBaildon found in wastewater demonstrates how sewage monitoring can supplement traditional disease surveillance", "token_count": 101, "char_count": 514, "word_count": 65, "semantic_coherence": 1, "information_density": 0.9077, "quality_score": 0.9538, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:22.209670", "source": { "split": "train_shard_00001", "doc_id": 2275 }, "chunk_id": "train_shard_00001_2275_1", "global_id": 8901 }, { "text": "Human health and disease have increasingly been shown to be impacted by the gut microbiota, and mouse models are essential for investigating these effects. However, the compositions of human and mouse gut microbiotas are distinct, limiting translation of microbiota research between these hosts. To address this, we constructed the Mouse Gastrointestinal Bacteria Catalogue (MGBC), a repository of 26,640 high-quality mouse microbiota-derived bacterial genomes. This catalog enables species-level analyses for mapping functions of interest and identifying functionally equivalent taxa between the microbiotas of humans and mice. We have complemented this with a publicly deposited collection of 223 bacterial isolates, including 62 previously uncultured species, to facilitate experimental investigation of individual commensal bacteria functions in vitro and in vivo. Together, these resources provide the ability to identify and test functionally equivalent members of the host-specific gut microbiotas of humans and mice and support the informed use of mouse models in human microbiota research.\n\nThe Mouse Gastrointestinal Bacteria Catalogue enables translation between the mouse and human gut microbiotas via functional mapping.", "token_count": 263, "char_count": 1233, "word_count": 168, "semantic_coherence": 1, "information_density": 0.5893, "quality_score": 0.7946, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:22.788733", "source": { "split": "train_shard_00001", "doc_id": 2276 }, "chunk_id": "train_shard_00001_2276_0", "global_id": 8902 }, { "text": "

Introduction

Escherichia fergusonii is regarded as an emerging pathogen with zoonotic potential. In the current study, we undertook source-wise comparative genomic analyses (resistome, virulome, mobilome and pangenome) to understand the antimicrobial resistance, virulence, mobile genetic elements and phylogenetic diversity of E. fergusonii.

Methods

Six E. fergusonii strains (5 multidrug resistant strains and 1 biofilm former) were isolated from poultry (duck faeces and retail chicken samples). Following confirmation by phenotypic and molecular methods, the isolates were further characterized and their genomes were sequenced. Comparative resisto-virulo-mobilome analyses and pangenomics were performed for E. fergusonii genomes, while including 125 other E. fergusonii genomes available from NCBI database.

Results and discussion

Avian and porcine strains of E. fergusonii were found to carry significantly higher number of antimicrobial resistance genes (p < 0.05) and mobile genetic elements (plasmids, transposons and integrons) (p < 0.05), while the pathogenic potential of bovine strains was significantly higher compared to other strains (p < 0.05). Pan-genome development trends indicated open pan-genome for all strains (0 < γ < 1). Genomic diversity of avian strains was found to be greater than that from other sources. Phylogenetic analysis revealed close clustering among isolates of similar isolation source and geographical location. Indian isolates of E. fergusonii clustered closely with those from Chinese and a singleton Australian isolate. Overall, being the first pangenomic study on E", "token_count": 500, "char_count": 1707, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6514, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:23.476029", "source": { "split": "train_shard_00001", "doc_id": 2277 }, "chunk_id": "train_shard_00001_2277_0", "global_id": 8903 }, { "text": "fergusonii, our analysis provided important cues on genomic features of the emerging pathogen E. fergusonii while highlighting the potential role of avian strains in dissemination of AMR.\n\nAvian strains of emerging pathogen Escherichia fergusonii are phylogenetically diverse and harbor the greatest AMR dissemination potential among different sources: Comparative genomic evidence.", "token_count": 110, "char_count": 400, "word_count": 50, "semantic_coherence": 1, "information_density": 0.74, "quality_score": 0.87, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:23.894227", "source": { "split": "train_shard_00001", "doc_id": 2277 }, "chunk_id": "train_shard_00001_2277_1", "global_id": 8904 }, { "text": "

Background

In Santiago, Chile, where typhoid had been hyperendemic (1977-1991), we investigated whether residual chronic carriers could be detected among household contacts of non-travel-related typhoid cases occurring during 2017-2019.

Methods

Culture-confirmed cases were classified as autochthonous (domestically acquired) versus travel/immigration related. Household contacts of cases had stool cultures and serum Vi antibody measurements to detect chronic Salmonella Typhi carriers. Whole genome sequences of acute cases and their epidemiologically linked chronic carrier isolates were compared.

Results

Five of 16 autochthonous typhoid cases (31.3%) were linked to 4 chronic carriers in case households; 2 cases (onsets 23 months apart) were linked to the same carrier. Carriers were women aged 69-79 years with gallbladder dysfunction and Typhi fecal excretion; 3 had highly elevated serum anti-Vi titers. Genomic analyses revealed close identity (≤11 core genome single-nucleotide polymorphism [SNP] differences) between case and epidemiologically linked carrier isolates; all were genotypes prevalent in 1980s Santiago. A cluster of 4 additional autochthonous cases unlinked to a carrier was identified based on genomic identity (0-1 SNPs). Travel/immigration isolate genotypes were typical for the countries of travel/immigration.

Conclusions

Although autochthonous typhoid cases in Santiago are currently rare, 5 of 16 such cases (31.3%) were linked to elderly chronic carriers identified among household contacts of cases.\n\nDetecting Residual Chronic Salmonella Typhi Carriers on the Road to Typhoid Elimination in Santiago, Chile, 2017-2019.", "token_count": 460, "char_count": 1683, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:24.533980", "source": { "split": "train_shard_00001", "doc_id": 2278 }, "chunk_id": "train_shard_00001_2278_0", "global_id": 8905 }, { "text": "

Background

Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crops. We examine the evolutionary relationships of 391 agricultural and environmental strains using whole-genome sequencing and evolutionary genomic analyses.

Results

We describe the phylogenetic distribution of all 77,728 orthologous gene families in the pan-genome, reconstruct the core genome phylogeny using the 2410 core genes, hierarchically cluster the accessory genome, identify the diversity and distribution of type III secretion systems and their effectors, predict ecologically and evolutionary relevant loci, and establish the molecular evolutionary processes operating on gene families. Phylogenetic and recombination analyses reveals that the species complex is subdivided into primary and secondary phylogroups, with the former primarily comprised of agricultural isolates, including all of the well-studied P. syringae strains. In contrast, the secondary phylogroups include numerous environmental isolates. These phylogroups also have levels of genetic diversity typically found among distinct species. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also find that \"ecologically significant\" virulence-associated loci and \"evolutionarily significant\" loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange.

Conclusions

While inter-phylogroup recombination occurs relatively rarely, it is an important force maintaining the genetic cohesion of the species complex, particularly among primary phylogroup strains. This level of genetic cohesion, and the shared plant-associated niche, argues for considering the primary phylogroups as a single biological species.\n\nRecombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex.", "token_count": 471, "char_count": 2100, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:25.177612", "source": { "split": "train_shard_00001", "doc_id": 2279 }, "chunk_id": "train_shard_00001_2279_0", "global_id": 8906 }, { "text": "

ABSTRACT

Staphylococcus aureus (SA) is an opportunistic pathogen and human commensal that is frequently present in the upper respiratory tract, gastrointestinal tract, and on the skin. While SA can cause disease ranging from minor skin infections to life-threatening bacteremia, it can also be carried asymptomatically. Indigenous individuals in the Southwest United States experience high rates of invasive SA disease. As carriage is the most significant risk factor for disease, understanding the dynamics of SA carriage, and in particular co-carriage of multiple strains, is important to develop strategies to prevent transmission in vulnerable communities. Here we investigated SA co-carriage and intrahost evolution by performing high density sampling from multiple anatomical sites and whole-genome sequencing (WGS) on 310 SA isolates collected from 60 Indigenous adults participating in a cross-sectional carriage study. We assessed the richness and diversity of SA isolates via differences in multi-locus sequence type (MLST), core-genome single-nucleotide-polymorphisms (SNPs), and genome content. Using WGS data, we identified 95 distinct SA populations among 60 participants; co-carriage was detected in 42% (25/60). Notably, two participants each carried four distinct SA strains. Variation in antibiotic resistance determinants among carried strains was identified among 42% (25/60) of participants. Lastly, we found unequal distribution of clonal complex by body site, suggesting that certain lineages may be adapted to specific anatomical sites. Together, these findings suggest that co-carriage may occur more frequently than previously appreciated and further our understanding of SA intrahost diversity during carriage, which has implications for surveillance activities and epidemiological investigations.\n\nMulti-strain carriage and intrahost diversity ofStaphylococcus aureusamong Indigenous adults in the US", "token_count": 449, "char_count": 1944, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:25.817117", "source": { "split": "train_shard_00001", "doc_id": 2280 }, "chunk_id": "train_shard_00001_2280_0", "global_id": 8907 }, { "text": "

Background

Pathogens with a global distribution face diverse biotic and abiotic conditions across populations. Moreover, the ecological and evolutionary history of each population is unique. Xylella fastidiosa is a xylem-dwelling bacterium infecting multiple plant hosts, often with detrimental effects. As a group, X. fastidiosa is divided into distinct subspecies with allopatric historical distributions and patterns of multiple introductions from numerous source populations. The capacity of X. fastidiosa to successfully colonize and cause disease in naïve plant hosts varies among subspecies, and potentially, among populations. Within Central America (i.e. Costa Rica) two X. fastidiosa subspecies coexist: the native subsp. fastidiosa and the introduced subsp. pauca. Using whole genome sequences, the patterns of gene gain/loss, genomic introgression, and genetic diversity were characterized within Costa Rica and contrasted to other X. fastidiosa populations.

Results

Within Costa Rica, accessory and core genome analyses showed a highly malleable genome with numerous intra- and inter-subspecific gain/loss events. Likewise, variable levels of inter-subspecific introgression were found within and between both coexisting subspecies; nonetheless, the direction of donor/recipient subspecies to the recombinant segments varied. Some strains appeared to recombine more frequently than others; however, no group of genes or gene functions were overrepresented within recombinant segments. Finally, the patterns of genetic diversity of subsp. fastidiosa in Costa Rica were consistent with those of other native populations (i.e. subsp. pauca in Brazil).

Conclusions

Overall, this study shows the importance of characterizing local evolutionary and ecological history in the context of world-wide pathogen distribution.\n\nImpacts of local population history and ecology on the evolution of a globally dispersed pathogen.", "token_count": 459, "char_count": 1948, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:26.457419", "source": { "split": "train_shard_00001", "doc_id": 2281 }, "chunk_id": "train_shard_00001_2281_0", "global_id": 8908 }, { "text": "

Objectives

To investigate the tet(X) gene, a determinant of tigecycline resistance, in the emerging pathogen Elizabethkingia meningoseptica and its association with an integrative and conjugative element (ICE).

Methods

All E. meningoseptica genomes from the National Center for Biotechnology Information (n = 87) were retrieved and annotated for resistome searches using the CARD database. A phylogenic analysis was performed based on the E. meningoseptica core genome. The ICE was identified through comparative genomics with other ICEs occurring in Elizabethkingia spp.

Results

Phylogenetic analysis revealed E. meningoseptica genomes from six countries distributed across different lineages, some of which persisted for years. The common resistome of these genomes included blaBlaB, blaCME, blaGOB, ranA/B, aadS, and catB (genes associated with resistance to β-lactams, aminoglycosides, and chloramphenicol). Some genomes also presented additional resistance genes (dfrA, ereD, blaVEB, aadS, and tet(X)). Interestingly, tet(X) and aadS were located in an ICE of 49 769 bp (ICEEmSQ101), which was fully obtained from the E. meningoseptica SQ101 genome. We also showed evidence that the other 27 genomes harboured this ICE. The distribution of ICEEmSQ101, carrying tet(X), was restricted to a single Chinese lineage.

Conclusions

The tet(X) gene is not prevalent in the species E. meningoseptica, as previously stated for the genus Elizabethkingia, since it is present only in a single Chinese lineage. We identified that several E", "token_count": 479, "char_count": 1604, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [ "SQ101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:27.101750", "source": { "split": "train_shard_00001", "doc_id": 2282 }, "chunk_id": "train_shard_00001_2282_0", "global_id": 8909 }, { "text": "meningoseptica genomes harboured an ICE that mobilized the Elizabethkingia tet(X) gene and exhibited characteristics similar to the ICEs of other Flavobacteria, which would favour their transmission in this bacterial family.\n\nPrevalence and characterization of an integrative and conjugative element carrying tet(X) gene in Elizabethkingia meningoseptica.", "token_count": 89, "char_count": 355, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:27.476188", "source": { "split": "train_shard_00001", "doc_id": 2282 }, "chunk_id": "train_shard_00001_2282_1", "global_id": 8910 }, { "text": "GABA (γ-aminobutyric acid) is a non-protein amino acid that occurs naturally in the human brain, animals, plants and microorganisms. It is primarily produced by the irreversible action of glutamic acid decarboxylase (GAD) on the α-decarboxylation of L-glutamic acid. As a major neurotransmitter in the brain, GABA plays a crucial role in behavior, cognition, and the body's stress response. GABA is mainly synthesized through the GABA shunt and the polyamine degradation pathways. It works through three receptors (GABAA, GABAB, and GABAC), each exhibiting different pharmacological and physiological characteristics. GABA has a variety of physiological roles and applications. In plants, it regulates growth, development and stress responses. In mammals, it influences physiological functions such as nervous system regulation, blood pressure equilibrium, liver and kidneys enhancement, hormone secretion regulation, immunity enhancement, cancer prevention, as well as anti-aging effects. As a biologically active ingredient, GABA possesses unique physiological effects and medicinal value, leading to its widespread application and substantially increased market demand in the food and pharmaceutical industries. GABA is primarily produced through chemical synthesis, plant enrichment and microbial fermentation. In this review, we first make an overview of GABA, focusing on its synthesis, metabolism, GABA receptors and physiological functions. Next, we describe the industrial production methods of GABA. Finally, we discuss the development of ligands for the GABA receptor binding site, the prospects of GABA production and application, as well as its clinical trials in potential drugs or compounds targeting GABA for the treatment of epilepsy. The purpose of this review is to attract researchers from various fields to focus on GABA research, promote multidisciplinary communications and collaborations, break down disciplinary barriers, stimulate innovative research ideas and methods, and advance the development and application of GABA in medicine, agriculture, food and other fields.", "token_count": 497, "char_count": 2129, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6241, "quality_score": 0.8121, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:28.131067", "source": { "split": "train_shard_00001", "doc_id": 2283 }, "chunk_id": "train_shard_00001_2283_0", "global_id": 8911 }, { "text": "Insights and progress on the biosynthesis, metabolism, and physiological functions of gamma-aminobutyric acid (GABA): a review.", "token_count": 38, "char_count": 127, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:28.493171", "source": { "split": "train_shard_00001", "doc_id": 2283 }, "chunk_id": "train_shard_00001_2283_1", "global_id": 8912 }, { "text": "Lateral gene transfer (LGT) has been reported in multiple eukaryotes. This process seems particularly widespread in the grass family, although we know very little about the underlying dynamics and how it impacts gene content variation within a species. Alloteropsis semialata is a tropical grass, and multiple LGT were detected in a reference genome assembled from an Australian individual. As part of this study we assemble three additional de novo genomes for A. semialata and one for its sister species Alloteropsis angusta . In total we detect 168 LGT across the five reference genomes. Using whole-genome resequencing data for a further 40 individuals we establish the distribution of these transfers and map their origin along the species phylogeny. This shows that many LGTs were acquired relatively recently, with numerous secondary losses. Exponential decay models indicate that the rate of LGT acquisitions varied significantly among lineages [6-28 per Ma], with a high rate of subsequent LGT losses [11-24% per Ma] that largely exceeds that of native loci [0.02-0.8% per Ma]. This high turnover creates large intraspecific structural variants, with a preponderance of LGT occurring as accessory genes in the Alloteropsis pangenome. The acquired genes represent unparalleled genetic novelties, having independently evolved for tens of millions of years before they were transferred. Ultimately, the rapid LGT turnover generates standing variation that can fuel local adaptation.\n\nVariation in the rate lateral gene transfers accumulate in a grass lineage", "token_count": 347, "char_count": 1564, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6795, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:29.070589", "source": { "split": "train_shard_00001", "doc_id": 2284 }, "chunk_id": "train_shard_00001_2284_0", "global_id": 8913 }, { "text": "Shigellosis is a serious public health issue in many developing countries. The emergence of multidrug-resistant (MDR) Shigella isolates has deepened the treatment difficulty and health burden of shigellosis. China is the largest developing country in the world, but so far, the genome of MDR Shigella isolates has not been well characterized. In this study, 60 clinical isolates of Shigella spp. in Fujian Province, southeast China, from 2005 to 2019 were characterized for drug resistance phenotype, whole-genome sequencing and bioinformatics analysis. The results showed that the MDR rate of Shigella isolates was 100%, among which the resistance rates of cefotaxime, ciprofloxacin and azithromycin were 36.67, 21.67 and 10.00 %, respectively. The positive rate of extended-spectrum beta-lactamase (ESBL)-producing strains was 23.33%. The resistance profiles of Shigella flexneri and Shigella sonnei to some antimicrobials differed. The MDR isolates carried multiple antimicrobial resistance genes, among which blaCTX-M-14 and blaCTX-M-15 mediated ESBL resistance. 'ISEcp1 -blaCTX-M -IS903' (type I) and 'ISEcp1 -blaCTX-M' (type II) were the most common genetic environments around the blaCTX-M genes, and plasmids containing these structures included IncFII, IncI1, IncI2 and IncN. The double gene mutation pattern of gyrA and parC resulted in a significant decrease in the sensitivity of S. flexneri to ciprofloxacin", "token_count": 505, "char_count": 1525, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8308, "entities": { "genes": [ "IS903" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:29.719494", "source": { "split": "train_shard_00001", "doc_id": 2285 }, "chunk_id": "train_shard_00001_2285_0", "global_id": 8914 }, { "text": "The overall resistance phenotype and genotype concordance rate was 88.50%, and the sensitivity and specificity of the genotype antimicrobial susceptibility test (AST) were 93.35 and 82.53 %, respectively. However, inconsistency occurred between phenotypic and genotype profiles for a few antibiotics. Phylogenomic investigation with core genome multi-locus sequence typing (cgMLST) and SNPs were used to characterize the endemic transmission of these infections in Fujian and their evolutionary origin within the global context. For S. flexneri, Fujian isolates were all limited to PG3 and could be divided into three phylogenetic clusters. The ciprofloxacin-resistant strains were mainly F2a and FXv and assigned to the three clusters with different quinolone resistance-determining region mutation patterns. For S. sonnei, most Fujian strains belonged to Lineage III with genotype 3.7.6, except three isolates of Lineage I with genotype 1.3. The strains carrying the blaCTX-M genes were dispersed, indicating different origins of gene acquisition. Most of the circulating isolates in Fujian Province were not related to major international outbreak lineages and were only endemic to the country. In conclusion, multi-drug resistance of Shigella isolates in Fujian Province was serious, and genome-based laboratory surveillance will be crucial to the clinical treatment and public health measures for shigellosis.\n\nGenome and antibiotic resistance characteristics of <i>Shigella</i> clinical isolates in Fujian Province, Southeast China, 2005-2019.", "token_count": 424, "char_count": 1589, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [ "PG3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:30.346865", "source": { "split": "train_shard_00001", "doc_id": 2285 }, "chunk_id": "train_shard_00001_2285_1", "global_id": 8915 }, { "text": "Campylobacter showae a bacterium historically linked to gingivitis and periodontitis, has recently been associated with inflammatory bowel disease and colorectal cancer. Our aim was to generate genome sequences for new clinical C. showae strains and identify functional properties explaining their pathogenic potential. Eight C. showae genomes were assessed, four strains isolated from inflamed gut tissues from paediatric Crohn's disease patients, three strains from colonic adenomas, and one from a gastroenteritis patient stool. Genome assemblies were analyzed alongside the only 3 deposited C. showae genomes. The pangenome from these 11 strains consisted of 4686 unique protein families, and the core genome size was estimated at 1050 ± 15 genes with each new genome contributing an additional 206 ± 16 genes. Functional assays indicated that colonic strains segregated into 2 groups: adherent/invasive vs. non-adherent/non-invasive strains. The former possessed Type IV secretion machinery and S-layer proteins, while the latter contained Cas genes and other CRISPR associated proteins. Comparison of gene profiles with strains in Human Microbiome Project metagenomes showed that gut-derived isolates share genes specific to tongue dorsum and supragingival plaque counterparts. Our findings indicate that C. showae strains are phenotypically and genetically diverse and suggest that secretion systems may play an important role in virulence potential.\n\nComparative genomics and genome biology of Campylobacter showae.", "token_count": 416, "char_count": 1565, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7123, "quality_score": 0.8561, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:30.972872", "source": { "split": "train_shard_00001", "doc_id": 2286 }, "chunk_id": "train_shard_00001_2286_0", "global_id": 8916 }, { "text": "This study was aimed to study the effect of commercial cellulases (Celluclast 1.5 LFG) on Kluyveromyces marxianus CECT 10875 growth and ethanol production in SSF processes. Preliminary tests carried out in glucose (50 g/L) fermentation medium showed that high enzyme amounts (2.5-3.5 FPU/mL) could cause a negative effect on K. marxianus growth rate and viable cells number. However, the maximum ethanol production was not affected and about 86% of the theoretical (22 g/L) was reached in all cases independently of the enzyme dosage. In SSF experiments, cell viability was always affected by enzyme loading. Nevertheless, slight differences observed on cell viability during glucose fermentation processes with the detected concentrations of the additives did not justify the negative effect observed in SSF experiments.\n\nEffect of different cellulase dosages on cell viability and ethanol production by Kluyveromyces marxianus in SSF processes.", "token_count": 246, "char_count": 946, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6115, "quality_score": 0.8058, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:31.459591", "source": { "split": "train_shard_00001", "doc_id": 2287 }, "chunk_id": "train_shard_00001_2287_0", "global_id": 8917 }, { "text": "Campylobacter is the most common cause of bacterial gastroenteritis worldwide and diarrheal disease is a major cause of child morbidity, growth faltering and mortality in low- and middle-income countries (LMICs). Despite evidence of high incidence and differences in disease epidemiology, there is limited genomic data from studies in developing countries. In this study, we characterised the genetic diversity and accessory genome content of a collection of Campylobacter isolates from Cairo, Egypt. In total, 112 Campylobacter isolates were collected from broiler carcasses (n=31), milk and dairy products (n=24) and patients (n=57) suffering from gastroenteritis. Among the most common sequence types (STs) we identified were the globally disseminated, host generalist ST-21 clonal complex (CC21) and the poultry specialist CC206, CC464 and CC48. Notably, CC45 and the cattle-specialist CC42 were under-represented with a total absence of CC61. Comparative genomics were used to quantify core and accessory genome sharing among isolates from the same country compared to sharing between countries. Lineage-specific accessory genome sharing was significantly higher among isolates from the same country, particularly CC21 which demonstrated greater local geographical clustering. In contrast, no geographic clustering was noted in either the core or accessory genomes of the CC828, suggesting a highly admixed population. A greater proportion of C. coli isolates were multidrug resistant (MDR) compared to C. jejuni . This is a significant public health concern as MDR food chain pathogens are difficult to treat and often pose increased mortality risk demanding enhanced prevention strategies in the Egyptian market to combat such a threat.

Impact statement

Campylobacter is the leading bacterial cause of gastroenteritis worldwide and despite high incidence in low- and middle-income countries, where infection can be fatal, culture-based isolation is rare and the genotypes responsible for disease are seldom identified. Here, we sequenced the genomes of a collection of isolates from clinical cases and potential infection reservoirs from Cairo in Egypt and characterised their genetic diversity", "token_count": 515, "char_count": 2210, "word_count": 314, "semantic_coherence": 1, "information_density": 0.6051, "quality_score": 0.8025, "entities": { "genes": [ "CC45", "CC828", "CC61", "CC464", "CC48", "CC21", "CC206", "CC42" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:22:32.121332", "source": { "split": "train_shard_00001", "doc_id": 2288 }, "chunk_id": "train_shard_00001_2288_0", "global_id": 8918 }, { "text": "Among the most common genotypes we identified were globally disseminated lineages implicated in human disease worldwide, including the host generalist ST-21 clonal complex (CC21) and the poultry specialist genotypes CC206, CC464 and CC48. Notably however, some other globally common genotypes were under-represented or entirely absent from our collection, including those from cattle-specialist lineages, CC42 and CC61. By focussing on specific lineages, we demonstrate that there is increased accessory genome sharing in specific clonal complexes. This increased local sharing of genes may have contributed to a greater proportion of C. coli isolates possessing antimicrobial resistance determinants that suggest they could be multidrug resistant (MDR). This is a significant public health concern as MDR food chain pathogens are difficult to treat and often pose increased mortality risk demanding enhanced prevention strategies.

Data summary

Short read data are available on the NCBI Sequence Read Archive, associated with BioProject PRJNA576513 ( https://www.ncbi.nlm.nih.gov/bioproject/PRJNA576513 ). Assembled genomes, supplementary material and additional analysis files are available from FigShare: https://doi.org/10.6084/m9.figshare.9956597 . Phylogenetic trees can be visualised and manipulated on Microreact for C. jejuni ( https://next.microreact.org/project/Cjejuni_Egypt ) and C. coli ( https://next.microreact.org/project/Ccoli_Egypt ) separately, or combined Cairo and Oxford data with additional PopPunk network clustering ( https://microreact.org/project/Campy-Egypt ).\n\nLocal accessory gene sharing drives lineage-specific acquisition of antimicrobial resistance in Egyptian Campylobacter spp.", "token_count": 465, "char_count": 1729, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7277, "quality_score": 0.8638, "entities": { "genes": [ "CC61", "CC464", "CC48", "CC21", "CC206", "CC42", "PRJNA576513" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:32.755925", "source": { "split": "train_shard_00001", "doc_id": 2288 }, "chunk_id": "train_shard_00001_2288_1", "global_id": 8919 }, { "text": "

ABSTRACT

Plant pathogens secrete proteins called effectors that target host cellular processes to promote disease. Recently, structural genomics has identified several families of fungal effectors that share a similar three-dimensional structure despite remarkably variable amino-acid sequences and surface properties. To explore the selective forces that underlie the sequence variability of structurally-analogous effectors, we focused on MAX effectors, a structural family of effectors that are major determinants of virulence in the rice blast fungus Pyricularia oryzae . Using structure-informed gene annotation, we identified 58 to 78 MAX effector genes per genome in a set of 120 isolates representing seven host-associated lineages. The expression of MAX effector genes was primarily restricted to the early biotrophic phase of infection and strongly influenced by the host plant. Pangenome analyses of MAX effectors demonstrated extensive presence/absence polymorphism and identified gene loss events possibly involved in host range adaptation. However, gene knock-in experiments did not reveal a strong effect on virulence phenotypes suggesting that other evolutionary mechanisms are the main drivers of MAX effector losses. MAX effectors displayed high levels of standing variation and high rates of non-synonymous substitutions, pointing to widespread positive selection shaping the molecular diversity of MAX effectors. The combination of these analyses with structural data revealed that positive selection acts mostly on residues located in particular structural elements and at specific positions. By providing a comprehensive catalog of amino acid polymorphism, and by identifying the structural determinants of the sequence diversity, our work will inform future studies aimed at elucidating the function and mode of action of MAX effectors.

AUTHOR SUMMARY

Fungal plant pathogens use small secreted proteins, called effectors, to manipulate to their own advantage their host’s physiology and immunity. The evolution of these effectors, whether spontaneously or in response to human actions, can lead to epidemics or the emergence of new diseases. It is therefore crucial to understand the mechanisms underlying this evolution", "token_count": 476, "char_count": 2261, "word_count": 313, "semantic_coherence": 1, "information_density": 0.6422, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:33.405155", "source": { "split": "train_shard_00001", "doc_id": 2289 }, "chunk_id": "train_shard_00001_2289_0", "global_id": 8920 }, { "text": "In this article, we report on the evolution of effectors in one of the prime experimental model systems of plant pathology, Pyricularia oryzae , the fungus causing blast diseases in rice, wheat, and other cereals or grasses. We further characterize in this fungus a particular class of effectors, called MAX effectors, using structural models based on experimental protein structures of effectors. We show that this class of effector is produced by the pathogen during the early stages of infection, when plant cells are still alive. By comparing the gene content of isolates infecting different plant species, we show that the MAX effector arsenal is highly variable from one isolate to another. Finally, using the inferential framework of population genetics, we demonstrate that MAX effectors exhibit very high genetic variability and that this results from the action of natural selection.\n\nAdaptive evolution in virulence effectors of the rice blast fungusPyricularia oryzae", "token_count": 216, "char_count": 986, "word_count": 150, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:33.860981", "source": { "split": "train_shard_00001", "doc_id": 2289 }, "chunk_id": "train_shard_00001_2289_1", "global_id": 8921 }, { "text": "The molecular basis of how temperature affects cell metabolism has been a long-standing question in biology, where the main obstacles are the lack of high-quality data and methods to associate temperature effects on the function of individual proteins as well as to combine them at a systems level. Here we develop and apply a Bayesian modeling approach to resolve the temperature effects in genome scale metabolic models (GEM). The approach minimizes uncertainties in enzymatic thermal parameters and greatly improves the predictive strength of the GEMs. The resulting temperature constrained yeast GEM uncovered enzymes that limit growth at superoptimal temperatures, and squalene epoxidase (ERG1) was predicted to be the most rate limiting. By replacing this single key enzyme with an ortholog from a thermotolerant yeast strain, we obtained a thermotolerant strain that outgrew the wild type, demonstrating the critical role of sterol metabolism in yeast thermosensitivity. Therefore, apart from identifying thermal determinants of cell metabolism and enabling the design of thermotolerant strains, our Bayesian GEM approach facilitates modelling of complex biological systems in the absence of high-quality data and therefore shows promise for becoming a standard tool for genome scale modeling.\n\nBayesian genome scale modelling identifies thermal determinants of yeast metabolism", "token_count": 299, "char_count": 1385, "word_count": 200, "semantic_coherence": 1, "information_density": 0.63, "quality_score": 0.815, "entities": { "genes": [ "ERG1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:34.470539", "source": { "split": "train_shard_00001", "doc_id": 2290 }, "chunk_id": "train_shard_00001_2290_0", "global_id": 8922 }, { "text": "Fusobacterium is a bacterium associated with colorectal cancer (CRC) tumorigenesis, progression, and metastasis. Fap2 is a fusobacteria-specific outer membrane galactose-binding lectin that mediates Fusobacterium adherence to and invasion of CRC tumors. Advances in omics analyses provide an opportunity to profile and identify microbial genomic features that correlate with the cancer-associated bacterial virulence factor Fap2. Here, we analyze genomes of Fusobacterium colon tumor isolates and find that a family of post-translational modification enzymes containing Fic domains is associated with Fap2 positivity in these strains. We demonstrate that Fic family genes expand with the presence of Fap2 in the fusobacterial pangenome. Through comparative genomic analysis, we find that Fap2+ Fusobacteriota are highly enriched with Fic gene families compared to other cancer-associated and human gut microbiome bacterial taxa. Using a global data set of CRC shotgun metagenomes, we show that fusobacterial Fic and Fap2 genes frequently co-occur in the fecal microbiomes of individuals with late-stage CRC. We further characterize specific Fic gene families harbored by Fap2+ Fusobacterium animalis genomes and detect recombination events and elements of horizontal gene transfer via synteny analysis of Fic gene loci. Exposure of a F. animalis strain to a colon adenocarcinoma cell line increases gene expression of fusobacterial Fic and virulence-associated adhesins. Finally, we demonstrate that Fic proteins are synthesized by F. animalis as Fic peptides are detectable in F. animalis monoculture supernatants", "token_count": 463, "char_count": 1685, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:35.128831", "source": { "split": "train_shard_00001", "doc_id": 2291 }, "chunk_id": "train_shard_00001_2291_0", "global_id": 8923 }, { "text": "Taken together, our study uncovers Fic genes as potential virulence factors in Fap2+ fusobacterial genomes.IMPORTANCEAccumulating data support that bacterial members of the intra-tumoral microbiota critically influence colorectal cancer progression. Yet, relatively little is known about non-adhesin fusobacterial virulence factors that may influence carcinogenesis. Our genomic analysis and expression assays in fusobacteria identify Fic domain-containing genes, well-studied virulence factors in pathogenic bacteria, as potential fusobacterial virulence features. The Fic family proteins that we find are encoded by fusobacteria and expressed by Fusobacterium animalis merit future investigation to assess their roles in colorectal cancer development and progression.\n\nVirulence factor discovery identifies associations between the Fic gene family and Fap2<sup>+</sup> fusobacteria in colorectal cancer microbiomes.", "token_count": 245, "char_count": 947, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:35.639628", "source": { "split": "train_shard_00001", "doc_id": 2291 }, "chunk_id": "train_shard_00001_2291_1", "global_id": 8924 }, { "text": "Orientia tsutsugamushi is an obligate intracellular bacterium associated with trombiculid mites and is the causative agent of scrub typhus, a life-threatening febrile disease. Strain typing of O. tsutsugamushi is based on its immunodominant surface antigen, 56-kDa type-specific antigen (TSA56). However, TSA56 gene sequence-based phylogenetic analysis is only partially congruent with core genome-based phylogenetic analysis. Thus, this study investigated whether concatenated surface antigen sequences, including surface cell antigen (Sca) proteins, can reflect the genome-scale phylogeny of O. tsutsugamushi. Complete genomes were obtained for two common O. tsutsugamushi strains in Taiwan, TW-1 and TW-22, and the core genome/proteome was identified for 11 O. tsutsugamushi strains. Phylogenetic analysis was performed using maximum likelihood (ML) and neighbor-joining (NJ) methods, and the congruence between trees was assessed using a quartet similarity measure. Phylogenetic analysis based on 691 concatenated core protein sequences produced identical tree topologies with ML and NJ methods. Among TSA56 and core Sca proteins (ScaA, ScaC, ScaD, and ScaE), TSA56 trees were most similar to the core protein tree, and ScaA trees were the least similar. However, concatenated ScaA and TSA56 sequences produced trees that were highly similar to the core protein tree, the NJ tree being more similar. Strain-level characterization of O. tsutsugamushi may be improved by coanalyzing ScaA and TSA56 sequences, which are also important targets for their combined immunogenicity.", "token_count": 472, "char_count": 1620, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [ "TSA56" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:36.310075", "source": { "split": "train_shard_00001", "doc_id": 2292 }, "chunk_id": "train_shard_00001_2292_0", "global_id": 8925 }, { "text": "Concatenated ScaA and TSA56 Surface Antigen Sequences Reflect Genome-Scale Phylogeny of <i>Orientia tsutsugamushi</i>: An Analysis Including Two Genomes from Taiwan.", "token_count": 62, "char_count": 177, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "TSA56" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:36.670151", "source": { "split": "train_shard_00001", "doc_id": 2292 }, "chunk_id": "train_shard_00001_2292_1", "global_id": 8926 }, { "text": "

Objective

To analyse the pan-genome of three black-pigmented periodontal pathogens: Porphyromonas gingivalis, Prevotella intermedia and Prevotella nigrescens.

Methods

Pan-genome analyses of 66, 33 and 5 publicly available whole-genome sequences of P. gingivalis, P. intermedia and P. nigrescens, respectively, were performed using Pan-genome Analysis Pipeline software (version 1.2.1; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, PR China). Phylogenetic trees were constructed based on the entire pan-genome and single nucleotide polymorphisms within the core genome. The distribution and abundance of virulence genes in the core and dispensable genomes were also compared in the three species.

Results

All three species possess an open pan-genome. The core genome of P. gingivalis, P. intermedia and P. nigrescens included 1001, 1514 and 1745 orthologous groups, respectively, which were mainly related to basic cellular functions such as metabolism. The dispensable genome of P. gingivalis, P. intermedia and P. nigrescens was composed of 2814, 2689 and 906 orthologous groups, respectively, and it was enriched in genes involved in pathogenicity or with unknown functions. Phylogenetic trees presented a clear separation of P. gingivalis, P. intermedia and P. nigrescens, verifying the reclassification of the black-pigmented species. Furthermore, the three species shared almost the same virulence factors involved in adhesion, proteolysis and evasion of host defences. Some of these virulence genes were conserved across species whereas others belonged to the dispensable genome, which might be acquired through horizontal gene transfer.

Conclusion

This study highlighted the usefulness of pan-genome analysis to infer evolutionary cues for black-pigmented species, indicating their homology and phylogenomic diversity.", "token_count": 510, "char_count": 1877, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5935, "quality_score": 0.7967, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:37.319750", "source": { "split": "train_shard_00001", "doc_id": 2293 }, "chunk_id": "train_shard_00001_2293_0", "global_id": 8927 }, { "text": "Evolutionary and Pan-genome Analysis of Three Important Black-pigmented Periodontal Pathogens.", "token_count": 26, "char_count": 94, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:37.685353", "source": { "split": "train_shard_00001", "doc_id": 2293 }, "chunk_id": "train_shard_00001_2293_1", "global_id": 8928 }, { "text": "The liver is extremely vulnerable to damage because of its role in metabolism. Toxin, metabolic syndrome, alcohol, microorganisms, and autoimmune diseases can be the cause of liver damage. While different etiologies can cause liver disease, pathophysiologically, there are similarities in the role of free radicals, inflammatory mediators, and gut microbiome during the disease development. Therefore, ingredients with antioxidant, antiinflammatory, and antidysbiotic properties have the potential to act as hepatoprotectors; and water kefir is one of them. Water kefir is a traditional fermented drink made from water kefir grains, sugar, and dried fruit. Water kefir is dominated by lactic acid bacteria and yeast as a fermented beverage, and several species of this group of microorganisms have been shown as probiotics. According to researches, water kefir has strong antioxidant, antiinflammatory, and hepatoprotective effects. Even so, there are still few researches reported about water kefir as a hepatoprotective agent. Several studies, on the other hand, showed promising results. This review discusses the relationship between the pathophysiology of liver disease and the pharmacological activity of water kefir and other probiotics in general, which leads to the potential prospect of water kefir research as a hepatoprotective agent.\n\nHepatoprotective Properties of Water Kefir: A Traditional Fermented Drink and Its Potential Role.", "token_count": 360, "char_count": 1445, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5805, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:38.258365", "source": { "split": "train_shard_00001", "doc_id": 2294 }, "chunk_id": "train_shard_00001_2294_0", "global_id": 8929 }, { "text": "Depending on the scale of observation, bacterial genomes are both organized and fluid. While individual bacterial genomes show signatures of organization (e.g., operons), pan-genomes reveal genome fluidity, both in terms of gene content and order (synteny). Here we ask how mutational forces (including recombination and horizontal gene transfer) combine with selection and gene interactions to shape genome organization and variation both within and across strains. We first build an evolutionary simulation model to assess the impact of gene interactions on pan-genome structure. A neutral evolutionary model can produce transient co-segregation of initially linked genes but is vulnerable on longer time-scales to perturbing mutational events. In contrast, incorporation of modular gene fitness interactions can produce sustainable clusters of linked and co-segregating genes, with the network of co-segregation recapitulating the defined simulation ‘ground-truth’ network of gene interactions. To test our model predictions, we exploit the increasing number of closed genomes in model species to define gene co-segregation networks in the pan-genomes of Escherichia coli and Pseudomonas aeruginosa . Using these highly curated pan-genomes, we identify modular clusters of physically linked and co-segregating genes and show that the resulting co-segregation networks map onto underlying gene-regulatory and metabolic gene interaction networks. The results imply that co-segregation networks can contribute to accessory genome annotation, and more generally that gene interactions are the primary force shaping genome structure and operon evolution.\n\nModular gene interactions drive modular pan-genome evolution in bacteria", "token_count": 360, "char_count": 1726, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5812, "quality_score": 0.7906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:38.841330", "source": { "split": "train_shard_00001", "doc_id": 2295 }, "chunk_id": "train_shard_00001_2295_0", "global_id": 8930 }, { "text": "Corynebacterium pseudotuberculosis is a pathogen of veterinary relevance diseases, being divided into two biovars: equi and ovis; causing ulcerative lymphangitis and caseous lymphadenitis, respectively. The isolation and sequencing of C. pseudotuberculosis biovar ovis strains in the Northern and Northeastern regions of Brazil exhibited the emergence of this pathogen, which causes economic losses to small ruminant producers, and condemnation of carcasses and skins of animals. Through the pan-genomic approach, it is possible to determine and analyze genes that are shared by all strains of a species-the core genome. However, many of these genes do not have any predicted function, being characterized as hypothetical proteins (HP). In this study, we considered 32 C. pseudotuberculosis biovar ovis genomes for the pan-genomic analysis, where were identified 172 HP present in a core genome composed by 1255 genes. We are able to functionally annotate 80 sequences previously characterized as HP through the identification of structural features as conserved domains and families. Furthermore, we analyzed the physicochemical properties, subcellular localization and molecular function. Additionally, through RNA-seq data, we investigated the differential gene expression of the annotated HP. Genes inserted in pathogenicity islands had their virulence potential evaluated. Also, we have analyzed the existence of functional associations for their products based on protein-protein interaction networks, and perform the structural prediction of three targets. Due to the integration of different strategies, this study can underlie deeper in vitro researches in the characterization of these HP and the search for new solutions for combat this pathogen.\n\nIn silico functional prediction of hypothetical proteins from the core genome of Corynebacterium pseudotuberculosis biovar ovis.", "token_count": 482, "char_count": 1950, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6388, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:39.488644", "source": { "split": "train_shard_00001", "doc_id": 2296 }, "chunk_id": "train_shard_00001_2296_0", "global_id": 8931 }, { "text": "

Aims

Indri indri is a lemur of Madagascar which is critically endangered. The analysis of the microbial ecology of the intestine offers tools to improve conservation efforts. This study aimed to achieve a functional genomic analysis of three Lactiplantibacillus plantarum isolates from indris.

Methods and results

Samples were obtained from 18 indri; 3 isolates of Lp. plantarum were obtained from two individuals. The three isolates were closely related to each other, with <10 single nucleotide polymorphisms, suggesting that the two individuals shared diet-associated microbes. The genomes of the three isolates were compared to 96 reference strains of Lp. plantarum. The three isolates of Lp. plantarum were not phenotypically resistant to antibiotics but shared all 17 genes related to antimicrobial resistance that are part of the core genome of Lp. plantarum. The genomes of the three indri isolates of Lp. plantarum also encoded for the 6 core genome genes coding for enzymes related to metabolism of hydroxybenzoic and hydroxycinnamic acids. The phenotype for metabolism of hydroxycinnamic acids by indri isolates of Lp. plantarum matched the genotype.

Conclusions

Multiple antimicrobial resistance genes and gene coding for metabolism of phenolic compounds were identified in the genomes of the indri isolates, suggesting that Lp. plantarum maintains antimicrobial resistance in defense of antimicrobial plant secondary pathogens and that their metabolism by intestinal bacteria aids digestion of plant material by primate hosts.\n\nPhysiological and genomic characterization of Lactiplantibacillus plantarum isolated from Indri indri in Madagascar.", "token_count": 449, "char_count": 1679, "word_count": 234, "semantic_coherence": 1, "information_density": 0.4957, "quality_score": 0.7479, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:40.122988", "source": { "split": "train_shard_00001", "doc_id": 2297 }, "chunk_id": "train_shard_00001_2297_0", "global_id": 8932 }, { "text": "

Background

The V. parahaemolyticus pandemic clone, results in the development of gastrointestinal illness in humans. Toxigenic strains of this species are frequently isolated from aquatic habitats and organisms such as mollusks and crustaceans. Reports on the isolation of the pandemic clone started in 1996, when a new O3:K6 clone was identified in Asia, that rapidly spread worldwide, becoming the predominant clone isolated from clinical cases. In this study whole genome sequencing was accomplished with an Illumina MiniSeq platform, upon six novel V. parahaemolyticus strains, that have been isolated in Mexico since 1998 and three representative genomes of strains that were isolated from reported outbreaks in other American countries, and were deposited in the GenBank. These nine genomes were compared against the reference sequence of the O3:K6 pandemic strain (RIMD 2210633), which was isolated in 1996, to determine sequence differences within American isolates and between years of isolation.

Results

The results indicated that strains that were isolated at different times and from different countries, were highly genetically similar, among them as well as to the reference strain RIMD 2210633, indicating a high level of genetic stability among the strains from American countries between 1996 to 2012, without significant genetic changes relative to the reference strain RIMD 2210633, which was isolated in 1996 and was considered to be representative of a novel O3:K6 pandemic strain.

Conclusions

The genomes of V. parahaemolyticus strains isolated from clinical and environmental sources in Mexico and other American countries, presented common characteristics that have been reported for RIMD 2210633 O3:K6 pandemic strain. The major variations that were registered in this study corresponded to genes non associated to virulence factors, which could be the result of adaptations to different environmental conditions. Nevertheless, results do not show a clear pattern with the year or locality where the strains were isolated, which is an indication of a genomic stability of the studied strains.", "token_count": 505, "char_count": 2139, "word_count": 308, "semantic_coherence": 1, "information_density": 0.526, "quality_score": 0.763, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:40.776464", "source": { "split": "train_shard_00001", "doc_id": 2298 }, "chunk_id": "train_shard_00001_2298_0", "global_id": 8933 }, { "text": "Genomic stability among O3:K6 V. parahaemolyticus pandemic strains isolated between 1996 to 2012 in American countries.", "token_count": 40, "char_count": 119, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:41.130787", "source": { "split": "train_shard_00001", "doc_id": 2298 }, "chunk_id": "train_shard_00001_2298_1", "global_id": 8934 }, { "text": "

Background

In spite of its advantageous physiological properties for bioprocess applications, the use of the yeast Kluyveromyces marxianus as a host for heterologous protein production has been very limited, in constrast to its close relative Kluyveromyces lactis. In the present work, the model protein glucose oxidase (GOX) from Aspergillus niger was cloned into K. marxianus CBS 6556 and into K. lactis CBS 2359 using three different expression systems. We aimed at verifying how each expression system would affect protein expression, secretion/localization, post-translational modification, and biochemical properties.

Results

The highest GOX expression levels (1552 units of secreted protein per gram dry cell weight) were achieved using an episomal system, in which the INU1 promoter and terminator were used to drive heterologous gene expression, together with the INU1 prepro sequence, which was employed to drive secretion of the enzyme. In all cases, GOX was mainly secreted, remaining either in the periplasmic space or in the culture supernatant. Whereas the use of genetic elements from Saccharomyces cerevisiae to drive heterologous protein expression led to higher expression levels in K. lactis than in K. marxianus, the use of INU1 genetic elements clearly led to the opposite result. The biochemical characterization of GOX confirmed the correct expression of the protein and showed that K. marxianus has a tendency to hyperglycosylate the protein, in a similar way as already observed for other yeasts, although this tendency seems to be smaller than the one of e.g. K. lactis and S. cerevisiae. Hyperglycosylation of GOX does not seem to affect its affinity for the substrate, nor its activity.

Conclusions

Taken together, our results indicate that K. marxianus is indeed a good host for the expression of heterologous proteins, not only for its physiological properties, but also because it correctly secretes and folds these proteins.", "token_count": 501, "char_count": 1979, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5911, "quality_score": 0.7955, "entities": { "genes": [ "INU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:41.781421", "source": { "split": "train_shard_00001", "doc_id": 2299 }, "chunk_id": "train_shard_00001_2299_0", "global_id": 8935 }, { "text": "Heterologous expression of glucose oxidase in the yeast Kluyveromyces marxianus.", "token_count": 26, "char_count": 80, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:42.134551", "source": { "split": "train_shard_00001", "doc_id": 2299 }, "chunk_id": "train_shard_00001_2299_1", "global_id": 8936 }, { "text": "Abstract

Polyploidy and life strategy transitions between annuality and perenniality often occur in flowering plants. However, the evolutionary propensities of polyploids and genetic bases of such transitions remain elusive. We assembled plantum genomes of representative perennial species across the genus Glycine including five diploids and a young allopolyploid, and constructed a Glycine super-pangenome framework by integrating 26 annual soybean genomes. The perennials exhibited greater genome stability than the annuals, with few centromere repeats abundant in the latter. Biased subgenome fractionation has occurred in the allopolyploid, primarily by accumulation of small deletions in gene clusters through illegitimate recombination, which was associated with preexisting local genomic differentiation. A gene annotated to modulate vegetative to reproductive phase transition was identified to have undergone adaptive evolution underlying the perenniality-annuality transition. Our study provides mechanistic insights into polyploid genome evolution and lays a foundation for unleashing genetic potential from the perennial gene pool for soybean improvement.

\n\nA super-pangenome framework of the genus Glycine unveils polyploid evolution and life-strategy transition", "token_count": 296, "char_count": 1298, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:42.687241", "source": { "split": "train_shard_00001", "doc_id": 2300 }, "chunk_id": "train_shard_00001_2300_0", "global_id": 8937 }, { "text": "Today, the increasing rate of cancer-related mortality, has rendered cancer a major global challenge, and the second leading cause of death worldwide. Conventional approaches in the treatment of cancer mainly include chemotherapy, surgery, immunotherapy, and radiotherapy. However, these approaches still come with certain disadvantages, including drug resistance, and different side effects such as gastrointestinal (GI) irritation (e.g., diarrhea, mucositis). This has encouraged scientists to look for alternative therapeutic methods and adjuvant therapies for a more proper treatment of malignancies. Application of probiotics as an adjuvant therapy in the clinical management of cancer appears to be a promising strategy, with several notable advantages, e.g., increased safety, higher tolerance, and negligible GI side effects. Both in vivo and in vitro analyses have indicated the active role of yeast probiotics in mitigating the rate of cancer cell proliferation, and the induction of apoptosis through regulating the expression of cancer-related genes and cellular pathways. Strain-specific anti-cancer activities of yeast probiotics strongly suggest that their administration along with the current cancer therapies may be an efficient method to reduce the side effects of these approaches. The main purpose of this article is to evaluate the efficacy of yeast probiotics in alleviating the adverse effects associated with cancer therapies.\n\nRecent advances in the application of probiotic yeasts, particularly Saccharomyces, as an adjuvant therapy in the management of cancer with focus on colorectal cancer.", "token_count": 349, "char_count": 1620, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6211, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:43.615911", "source": { "split": "train_shard_00001", "doc_id": 2301 }, "chunk_id": "train_shard_00001_2301_0", "global_id": 8938 }, { "text": "As a proven source of potent and selective antimicrobials, Xenorhabdus bacteria are important to an age plagued with difficult-to-treat microbial infections. Yet, only twenty-seven species have been described to date. In this study, a new Xenorhabdus species was discovered through genomic studies on three isolates from Kenyan soils. Soils in Western Kenya were surveyed for steinernematids and Steinernema isolates VH1 and BG5 were recovered from red volcanic loam soils from cultivated land in Vihiga and clay soils from riverine land in Bungoma respectively. From the two nematode isolates, Xenorhabdus sp. BG5 and Xenorhabdus sp. VH1 were isolated. The genomes of these two, plus that of X. griffiniae XN45 —this was previously isolated from Steinernema sp. scarpo that also originated from Kenyan soils— were sequenced and assembled. Nascent genome assemblies of the three isolates were of good quality with over 70% of their proteome having known functions. These three isolates formed the X. griffiniae clade in a phylogenomic reconstruction of the genus. Their species were delineated using three overall genome relatedness indices: an unnamed species of the genus, Xenorhabdus sp. BG5, X. griffiniae VH1, and X. griffiniae XN45. A pangenome analysis of this clade revealed that over 70% of species-specific genes encoded unknown functions.  Transposases were linked to genomic islands in Xenorhabdus sp. BG5. Thus, overall genome-related indices sufficiently delineated species of two new Xenorhabdus isolates from Kenya, both of which were closely related to X. griffiniae. The functions encoded by most species specific genes in the X. griffiniae clade remain unknown.\n\nDraft genomes, phylogenomic reconstruction and comparative genome analysis of three Xenorhabdus strains isolated from soil dwelling nematodes in Kenya", "token_count": 498, "char_count": 1832, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5519, "quality_score": 0.7759, "entities": { "genes": [ "VH1", "XN45", "BG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:44.264996", "source": { "split": "train_shard_00001", "doc_id": 2302 }, "chunk_id": "train_shard_00001_2302_0", "global_id": 8939 }, { "text": "Even across genomes of the same species, prokaryotes exhibit remarkable flexibility in gene content. We do not know whether this flexible or \"accessory\" content is mostly neutral or adaptive, largely due to the lack of explicit analyses of accessory gene function. Here, across 96 diverse prokaryotic species, I show that a considerable fraction (~40%) of accessory genomes harbours beneficial metabolic functions. These functions take two forms: (1) they significantly expand the biosynthetic potential of individual strains, and (2) they help reduce strain-specific metabolic auxotrophies via intra-species metabolic exchanges. I find that the potential of both these functions increases with increasing genome flexibility. Together, these results are consistent with a significant adaptive role for prokaryotic pangenomes.\n\nMetabolic adaptations underlying genome flexibility in prokaryotes.", "token_count": 201, "char_count": 894, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7541, "quality_score": 0.877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:44.728700", "source": { "split": "train_shard_00001", "doc_id": 2303 }, "chunk_id": "train_shard_00001_2303_0", "global_id": 8940 }, { "text": "Acinetobacter bereziniae has emerged as a significant human pathogen, acquiring multiple antibiotic resistance genes, including carbapenemases. This study focuses on characterizing the plasmids harboring the blaNDM-1 and tet(Y) genes in two carbapenem-resistant A. bereziniae isolates (UCO-553 and UCO-554) obtained in Chile during the COVID-19 pandemic. Methods: Antibiotic susceptibility testing was conducted on UCO-553 and UCO-554. Both isolates underwent whole-genome sequencing to ascertain their sequence type (ST), core genome multilocus sequence-typing (cgMLST) profile, antibiotic resistance genes, plasmids, and mobile genetic elements. Conjugation experiments were performed for both isolates. Results: Both isolates exhibited broad resistance, including resistance to carbapenems, third-generation cephalosporins, fluoroquinolones, tetracycline, cotrimoxazole, and aminoglycosides. Both isolates belong to sequence type STPAS1761, with a difference of 17 out of 2984 alleles. Each isolate carried a 47,274 bp plasmid with blaNDM-1 and aph(3')-VI genes and two highly similar plasmids: a 35,184 bp plasmid with tet(Y), sul2, aph(6)-Id, and aph(3″)-Ib genes, and a 6078 bp plasmid containing the ant(2″)-Ia gene. Quinolone-resistance mutations were identified in the gyrA and parC genes of both isolates", "token_count": 507, "char_count": 1452, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:45.383828", "source": { "split": "train_shard_00001", "doc_id": 2304 }, "chunk_id": "train_shard_00001_2304_0", "global_id": 8941 }, { "text": "Importantly, blaNDM-1 was located within a Tn125 transposon, and tet(Y) was embedded in a Tn5393 transposon. Conjugation experiments successfully transferred blaNDM-1 and tet(Y) into the A. baumannii ATCC 19606 strain, indicating the potential for horizontal gene transfer. Conclusions: This study highlights the critical role of plasmids in disseminating resistance genes in A. bereziniae and underscores the need for the continued genomic surveillance of this emerging pathogen. The findings emphasize the importance of monitoring A. bereziniae for its potential to cause difficult-to-treat infections and its capacity to spread resistance determinants against clinically significant antibiotics.\n\nCo-Occurrence of Two Plasmids Encoding Transferable blaNDM-1 and tet(Y) Genes in Carbapenem-Resistant Acinetobacter bereziniae.", "token_count": 311, "char_count": 951, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:45.944422", "source": { "split": "train_shard_00001", "doc_id": 2304 }, "chunk_id": "train_shard_00001_2304_1", "global_id": 8942 }, { "text": "Myxobacteria are fascinating and complex microbes. They prey upon other members of the soil microbiome by secreting antimicrobial proteins and metabolites, and will undergo multicellular development if starved. The genome sequence of the model myxobacterium Myxococcus xanthus DK1622 was published in 2006 and 15 years later, 163 myxobacterial genome sequences have now been made public. This explosion in genomic data has enabled comparative genomics analyses to be performed across the taxon, providing important insights into myxobacterial gene conservation and evolution. The availability of myxobacterial genome sequences has allowed system-wide functional genomic investigations into entire classes of genes. It has also enabled post-genomic technologies to be applied to myxobacteria, including transcriptome analyses (microarrays and RNA-seq), proteome studies (gel-based and gel-free), investigations into protein-DNA interactions (ChIP-seq) and metabolism. Here, we review myxobacterial genome sequencing, and summarise the insights into myxobacterial biology that have emerged as a result. We also outline the application of functional genomics and post-genomic approaches in myxobacterial research, highlighting important findings to emerge from seminal studies. The review also provides a comprehensive guide to the genomic datasets available in mid-2021 for myxobacteria (including 24 genomes that we have sequenced and which are described here for the first time).\n\nMyxobacterial Genomics and Post-Genomics: A Review of Genome Biology, Genome Sequences and Related 'Omics Studies.", "token_count": 398, "char_count": 1602, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8178, "entities": { "genes": [ "DK1622" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:46.601038", "source": { "split": "train_shard_00001", "doc_id": 2305 }, "chunk_id": "train_shard_00001_2305_0", "global_id": 8943 }, { "text": "The selected thermotolerant, lactose-utilizing yeast strain Kluyveromyces marxianus NBIMCC 8362 possesses high specific d-amino acid oxidase activity (60Ug(-1)), which was increased nine-fold (545Ug(-1)) by design of the growth medium and conditions for d-amino oxidase induction. Applying an optimized simple and rapid procedure for chemical permeabilization of K. marxianus cells with the cationic detergent cetyltrimethylammonium bromide, the enzyme activities (d-amino acid oxidase and catalase) of the cells have been further increased for up to 43- and 58-fold, respectively. However, the enzyme activities of the permeabilized cells decreased rapidly due to the leakage of the enzymes. Treating the permeabilized cells with 0.1% glutaraldehyde at 4°C for 10min stabilized the enzyme in the cells and prevented their outflow. The process is stable for 10 cycles and the productivity measured was 16.6mmmoll(-1)h(-1). The d-alanine transformation efficiency of K. marxianus permeabilized and GA entrapted cells was 98%.\n\nOver-expression of DAAO and catalase in Kluyveromyces marxianus through media optimization, permeabilization and GA stabilization techniques.", "token_count": 341, "char_count": 1167, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:47.195270", "source": { "split": "train_shard_00001", "doc_id": 2306 }, "chunk_id": "train_shard_00001_2306_0", "global_id": 8944 }, { "text": "The increasing prevalence of noncommunicable diseases in the aging population has been correlated with a decline in innate and adaptive immune responses; hence, it is imperative to identify approaches to improve immune function, prevent related disorders, and reduce or treat age-associated health complications. Prebiotic supplementation is a promising approach to modulate the gut microbiome and immune system, offering a potential strategy to maintain the integrity of immune function in older individuals. This review summarizes the current research on prebiotic galacto-oligosaccharide (GOS) immunomodulatory mechanisms mediated by bacterial-derived metabolites, including short-chain fatty acids and secondary bile acids, to maintain immune homeostasis. The potential applications of GOS as immunotherapy for age-related disease prevention in older individuals are also highlighted. This aligns with the global shift toward proactive healthcare and emphasizes the significance of early intervention in directing an individual's health trajectory.\n\nGalacto-Oligosaccharides and the Elderly Gut: Implications for Immune Restoration and Health.", "token_count": 245, "char_count": 1147, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7248, "quality_score": 0.8624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:47.711207", "source": { "split": "train_shard_00001", "doc_id": 2307 }, "chunk_id": "train_shard_00001_2307_0", "global_id": 8945 }, { "text": "

Background

In South Africa, the annual incidence of enteric fever averaged 0.1 per 100 000 persons between 2003 and 2018. During 2021 an increase in the number of enteric fever cases was observed. An outbreak investigation was conducted to determine the magnitude and source of the outbreak.

Methods

We performed a cross-sectional descriptive study. Data were collected through telephonic or face-to-face interviews with cases or proxies via a standardized case investigation form. Whole genome sequencing was performed on all Salmonella Typhi isolates. Drinking water samples were collected, tested, and analyzed. Descriptive analysis was performed with Microsoft Excel.

Results

Between January 2020 and September 2022, a cluster of 53 genetically highly related Salmonella Typhi isolates was identified from 5 provinces in South Africa. Isolates associated with the cluster showed ≤5 allelic differences, as determined following core genome multilocus sequence typing analysis. Most cases (60%, 32/53) were in the North West province. Males represented 68% (36/53). Of these, 72% (26/36) were aged 15 to 49 years, with a median age of 31 years. Where occupation was known within this age group, 78% (14/18) were illegal gold miners. Illegal miners reported illness onset while working underground. Five municipal tap water samples were tested and showed no evidence of fecal contamination.

Conclusions

This outbreak predominantly affected illegal gold miners, likely due to the consumption of contaminated groundwater while working in a gold mine shaft. In addition, this investigation highlights the value of whole genome sequencing to detect clusters and support epidemiologic investigation of enteric fever outbreaks.\n\nA Prolonged Outbreak of Enteric Fever Associated With Illegal Miners in the City of Matlosana, South Africa, November 2020-September 2022.", "token_count": 504, "char_count": 1905, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:48.390585", "source": { "split": "train_shard_00001", "doc_id": 2308 }, "chunk_id": "train_shard_00001_2308_0", "global_id": 8946 }, { "text": "Multidrug resistance (MDR) represents a global threat to health. Although plasmids can play an important role in the dissemination of MDR, they have not been commonly linked to the emergence of antimicrobial resistance in the pathogen Pseudomonas aeruginosa . We used whole genome sequencing to characterize a collection of P. aeruginosa clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicated that 1) these large plasmids comprise a family present in different members of the Pseudomonas genus and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the pangenome of the megaplasmid family is highly flexible and diverse, comprising a substantial core genome (average of 48% of plasmid genes), but with individual members carrying large numbers of unique genes. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s.

Funding

This work was supported by the International Pseudomonas Genomics Consortium, funded by Cystic Fibrosis Canada [RCL]; and the Secretaría de Educación, Ciencia, Tecnología e Innovación (SECTEI), Mexico [AC].\n\nA megaplasmid family responsible for dissemination of multidrug resistance inPseudomonas", "token_count": 423, "char_count": 1742, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6792, "quality_score": 0.8396, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:49.018496", "source": { "split": "train_shard_00001", "doc_id": 2309 }, "chunk_id": "train_shard_00001_2309_0", "global_id": 8947 }, { "text": "Given the lack of genetic characterization data for multidrug-resistant (MDR) Salmonella in South Korean poultry, we analyzed 53 MDR Salmonella strains from 1232 poultry meat samples (723 chicken, 509 duck) using whole-genome sequencing. Five serotypes were identified: S. Infantis (30/53, 56.6%), S. Enteritidis (11/53, 20.8%), S. Virchow (9/53, 17.0%), S. Agona (2/53, 3.8%), and S. Indiana (1/53, 1.9%). Sequence types (STs) included ST32, ST11, ST16, ST13, and ST17, with three major clusters, each having two subclusters. Eight core genome sequence types (cgSTs) were identified: 225993, 2268, 58360, 150996, 232041, 96964, 117577, and 267045. Salmonella Infantis and S. Enteritidis had two (117577, 267045) and three (225993, 2268, 58360) cgSTs, respectively, whereas S. Virchow showed allelic differences in identical cgSTs. The S. Enteritidis subcluster was classified as chicken or duck. Twenty-eight antimicrobial resistance genes (ARGs), 10 plasmid replicons, 11 Salmonella pathogenicity islands (SPIs), and 230 virulence genes were identified, showing distinct profiles by cluster and subcluster", "token_count": 500, "char_count": 1191, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7922, "quality_score": 0.8961, "entities": { "genes": [ "ST13", "ST17", "ST32", "ST16", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:49.670840", "source": { "split": "train_shard_00001", "doc_id": 2310 }, "chunk_id": "train_shard_00001_2310_0", "global_id": 8948 }, { "text": "Salmonella Infantis, the primary MDR Salmonella, carried the IncFIB (pN55391) plasmid, 10-11 ARGs, nine SPIs, and approximately 163 virulence genes. Three major MDR Salmonella serotypes (S. Infantis, S. Enteritidis, and S. Virchow) had specific genetic profiles that can inform epidemiological surveillance.\n\nGenetic Characteristics of Multidrug-Resistant Salmonella Isolated from Poultry Meat in South Korea.", "token_count": 168, "char_count": 458, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8491, "quality_score": 0.9245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:50.104986", "source": { "split": "train_shard_00001", "doc_id": 2310 }, "chunk_id": "train_shard_00001_2310_1", "global_id": 8949 }, { "text": "

Background

To carry out a whole genome sequencing (WGS)-based investigation on the emergence and spread of the largest multidrug-resistant tuberculosis (MDR TB) outbreak that has been thriving among HIV-negative patients, Tunisia, since the early 2000s.

Methods

We performed phylogeographic analyses and molecular dating based on a WGS dataset representing 68 unique Mycobacterium tuberculosis isolates, covering almost the entire MDR TB outbreak for the time period 2001-2016.

Results

The data indicate that the ancestor of the MDR TB outbreak emerged in the region of Bizerte, as early as 1974 (95% CI 1951-1985), from where it spread to other regions by 1992 (95% CI 1980-1996). Analysis of a minimum spanning tree based on core genome Multilocus Sequence Typing (cgMLST) uncovered the early spill-over of the fitness-compensated MDR TB strain from the prison into the general population. Indeed, cases with history of incarceration were found to be directly or indirectly linked to up to 22 new outbreak cases (32.35%) among the non-imprisoned population. By around 2008, the MDR TB outbreak strain had acquired additional resistance, leading to an XDR phenotype.

Conclusions

WGS allowed refining our understanding of the emergence and evolution of the largest MDR TB outbreak in Tunisia, whose causative strain has been circulating silently for almost 26 years before. Our study lends further support to the critical role of prisons-related cases in the early spread of the outbreak among the general population. The shift to an XDR phenotype of such an epidemic clone prompts an urgent need to undertake drastic control measures.\n\nOn the onset and dispersal of a major MDR TB clone among HIV-negative patients, Tunisia.", "token_count": 489, "char_count": 1754, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5946, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:50.754110", "source": { "split": "train_shard_00001", "doc_id": 2311 }, "chunk_id": "train_shard_00001_2311_0", "global_id": 8950 }, { "text": "In the present work, a thermophilic esterase from Thermus thermophilus HB27 was cloned into Kluyveromyces marxianus and into Kluyveromyces lactis using two different expression systems, yielding four recombinant strains. K. lactis showed the highest esterase expression levels (294 units per gram dry cell weight, with 65% of cell-bound enzyme) using an episomal system with the PGK promoter and terminator from Saccharomyces cerevisiae combined with the K. lactis k1 secretion signal. K. marxianus showed higher secretion efficiency of the heterologous esterase (56.9 units per gram dry cell weight, with 34% of cell-bound enzyme) than K. lactis. Hydrolytic activities for the heterologous esterases were maximum at pH values between 8.0 and 9.0 for both yeast species and at temperatures of 50 °C and 45 °C for K. marxianus and K. lactis, respectively. When compared to previously published data on this same esterase produced in the original host or in S. cerevisiae, our results indicate that Kluyveromyces yeasts can be considered good hosts for the heterologous secretion of thermophilic esterases, which have a potential application in biodiesel production or in resolving racemates.\n\nHeterologous expression of a thermophilic esterase in Kluyveromyces yeasts.", "token_count": 360, "char_count": 1267, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6277, "quality_score": 0.8138, "entities": { "genes": [ "HB27" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:51.337513", "source": { "split": "train_shard_00001", "doc_id": 2312 }, "chunk_id": "train_shard_00001_2312_0", "global_id": 8951 }, { "text": "Clostridium difficile is a spore-forming anaerobic bacterium that causes colitis in patients with disrupted colonic microbiota. While some individuals are asymptomatic C. difficile carriers, symptomatic disease ranges from mild diarrhea to potentially lethal toxic megacolon. The wide disease spectrum has been attributed to the infected host's age, underlying diseases, immune status, and microbiome composition. However, strain-specific differences in C. difficile virulence have also been implicated in determining colitis severity. Because patients infected with C. difficile are unique in terms of medical history, microbiome composition, and immune competence, determining the relative contribution of C. difficile virulence to disease severity has been challenging, and conclusions regarding the virulence of specific strains have been inconsistent. To address this, we used a mouse model to test 33 clinical C. difficile strains isolated from patients with disease severities ranging from asymptomatic carriage to severe colitis, and we determined their relative in vivo virulence in genetically identical, antibiotic-pretreated mice. We found that murine infections with C. difficile clade 2 strains (including multilocus sequence type 1/ribotype 027) were associated with higher lethality and that C. difficile strains associated with greater human disease severity caused more severe disease in mice. While toxin production was not strongly correlated with in vivo colonic pathology, the ability of C. difficile strains to grow in the presence of secondary bile acids was associated with greater disease severity. Whole-genome sequencing and identification of core and accessory genes identified a subset of accessory genes that distinguish high-virulence from lower-virulence C", "token_count": 475, "char_count": 1869, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5813, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:51.980140", "source": { "split": "train_shard_00001", "doc_id": 2313 }, "chunk_id": "train_shard_00001_2313_0", "global_id": 8952 }, { "text": "difficile strains.IMPORTANCEClostridium difficile is an important cause of hospital-associated intestinal infections, and recent years have seen an increase in the number and severity of cases in the United States. A patient's antibiotic history, immune status, and medical comorbidities determine, in part, the severity of C. difficile infection. The relative virulence of different clinical C. difficile strains, although postulated to determine disease severity in patients, has been more difficult to consistently associate with mild versus severe colitis. We tested 33 distinct clinical C. difficile isolates for their ability to cause disease in genetically identical mice and found that C. difficile strains belonging to clade 2 were associated with higher mortality. Differences in survival were not attributed to differences in toxin production but likely resulted from the distinct gene content in the various clinical isolates.\n\nPathogenicity Locus, Core Genome, and Accessory Gene Contributions to Clostridium difficile Virulence.", "token_count": 278, "char_count": 1095, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:52.527608", "source": { "split": "train_shard_00001", "doc_id": 2313 }, "chunk_id": "train_shard_00001_2313_1", "global_id": 8953 }, { "text": "The yeast Kluyveromyces marxianus presents several interesting features that make this species a promising industrial yeast for the production of several compounds. In order to take full advantage of this yeast and its particular properties, proper tools for gene disruption and metabolic engineering are needed. The Cre-loxP system is a very versatile tool that allows for gene marker rescue, resulting in mutant strains free of exogenous selective markers, which is a very important aspect for industrial application. As the Cre-loxP system works in some non-conventional yeasts, namely Kluyveromyces lactis, we wished to know whether it also works in K. marxianus. Here, we report the validation of this system in K. marxianus CBS 6556, by disrupting two copies of the LAC4 gene, which encodes a beta-galactosidase activity.\n\nApplication of the Cre-loxP system for multiple gene disruption in the yeast Kluyveromyces marxianus.", "token_count": 231, "char_count": 930, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [ "LAC4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:52.994406", "source": { "split": "train_shard_00001", "doc_id": 2314 }, "chunk_id": "train_shard_00001_2314_0", "global_id": 8954 }, { "text": "Species belonging to the genus Novosphingobium are found in many different habitats and have been identified as metabolically versatile. Through comparative genomic analysis, we identified habitat-specific genes and regulatory hubs that could determine habitat selection for Novosphingobium spp. Genomes from 27 Novosphingobium strains isolated from diverse habitats such as rhizosphere soil, plant surfaces, heavily contaminated soils, and marine and freshwater environments were analyzed. Genome size and coding potential were widely variable, differing significantly between habitats. Phylogenetic relationships between strains were less likely to describe functional genotype similarity than the habitat from which they were isolated. In this study, strains (19 out of 27) with a recorded habitat of isolation, and at least 3 representative strains per habitat, comprised four ecological groups-rhizosphere, contaminated soil, marine, and freshwater. Sulfur acquisition and metabolism were the only core genomic traits to differ significantly in proportion between these ecological groups; for example, alkane sulfonate (ssuABCD) assimilation was found exclusively in all of the rhizospheric isolates. When we examined osmolytic regulation in Novosphingobium spp. through ectoine biosynthesis, which was assumed to be marine habitat specific, we found that it was also present in isolates from contaminated soil, suggesting its relevance beyond the marine system. Novosphingobium strains were also found to harbor a wide variety of mono- and dioxygenases, responsible for the metabolism of several aromatic compounds, suggesting their potential to act as degraders of a variety of xenobiotic compounds. Protein-protein interaction analysis revealed β-barrel outer membrane proteins as habitat-specific hubs in each of the four habitats-freshwater (Saro_1868), marine water (PP1Y_AT17644), rhizosphere (PMI02_00367), and soil (V474_17210)", "token_count": 512, "char_count": 1983, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6409, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:53.650939", "source": { "split": "train_shard_00001", "doc_id": 2315 }, "chunk_id": "train_shard_00001_2315_0", "global_id": 8955 }, { "text": "These outer membrane proteins could play a key role in habitat demarcation and extend our understanding of the metabolic versatility of the Novosphingobium species. IMPORTANCE This study highlights the significant role of a microorganism's genetic repertoire in structuring the similarity between Novosphingobium strains. The results suggest that the phylogenetic relationships were mostly influenced by metabolic trait enrichment, which is possibly governed by the microenvironment of each microbe's respective niche. Using core genome analysis, the enrichment of a certain set of genes specific to a particular habitat was determined, which provided insights on the influence of habitat on the distribution of metabolic traits in Novosphingobium strains. We also identified habitat-specific protein hubs, which suggested delineation of Novosphingobium strains based on their habitat. Examining the available genomes of ecologically diverse bacterial species and analyzing the habitat-specific genes are useful for understanding the distribution and evolution of functional and phylogenetic diversity in the genus Novosphingobium.\n\nComparative Genomic Analysis Reveals Habitat-Specific Genes and Regulatory Hubs within the Genus Novosphingobium.", "token_count": 316, "char_count": 1295, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:54.202850", "source": { "split": "train_shard_00001", "doc_id": 2315 }, "chunk_id": "train_shard_00001_2315_1", "global_id": 8956 }, { "text": "

Key message

We found that the flowering time order of accessions in a genetic population considerably varied across environments, and homolog copies of essential flowering time genes played different roles in different locations. Flowering time plays a critical role in determining the life cycle length, yield, and quality of a crop. However, the allelic polymorphism of flowering time-related genes (FTRGs) in Brassica napus, an important oil crop, remains unclear. Here, we provide high-resolution graphics of FTRGs in B. napus on a pangenome-wide scale based on single nucleotide polymorphism (SNP) and structural variation (SV) analyses. A total of 1337 FTRGs in B. napus were identified by aligning their coding sequences with Arabidopsis orthologs. Overall, 46.07% of FTRGs were core genes and 53.93% were variable genes. Moreover, 1.94%, 0.74%, and 4.49% FTRGs had significant presence-frequency differences (PFDs) between the spring and semi-winter, spring and winter, and winter and semi-winter ecotypes, respectively. SNPs and SVs across 1626 accessions of 39 FTRGs underlying numerous published qualitative trait loci were analyzed. Additionally, to identify FTRGs specific to an eco-condition, genome-wide association studies (GWASs) based on SNP, presence/absence variation (PAV), and SV were performed after growing and observing the flowering time order (FTO) of plants in a collection of 292 accessions at three locations in two successive years. It was discovered that the FTO of plants in a genetic population changed a lot across various environments, and homolog copies of some key FTRGs played different roles in different locations. This study revealed the molecular basis of the genotype-by-environment (G × E) effect on flowering and recommended a pool of candidate genes specific to locations for breeding selection.\n\nStructural variations and environmental specificities of flowering time-related genes in Brassica napus.", "token_count": 500, "char_count": 1956, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6064, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:54.852309", "source": { "split": "train_shard_00001", "doc_id": 2316 }, "chunk_id": "train_shard_00001_2316_0", "global_id": 8957 }, { "text": "The definition of bacterial essential genes has been widely pursued using different approaches. Their study has impacted several fields of research such as synthetic biology, the construction of bacteria with minimal chromosomes, the search for new antibiotic targets, or the design of strains with biotechnological applications. Bacterial genomes are mosaics that only share a small subset of gene-sequences (core genome) even among members of the same species. It has been reported that the presence of essential genes is highly variable between closely related bacteria and even among members of the same species, due to the phenomenon known as \"non-orthologous gene displacement\" that refers to the coding for an essential function by genes with no sequence homology due to horizontal gene transfer (HGT). The existence of dormant forms among bacteria and the high incidence of HGT have been proposed to be driving forces of bacterial evolution, and they might have a role in the low level of conservation of essential genes among related bacteria by non-orthologous gene displacement, but this correlation has not been recognized. The aim of this mini-review is to give a brief overview of the approaches that have been taken to define and study essential genes, and the implications of non-orthologous gene displacement in bacterial evolution, focusing mainly in the case of Escherichia coli. To this end, we reviewed the available literature, and we searched for the presence of the essential genes defined by mutagenesis in the genomes of the 63 best-sequenced E. coli genomes that are available in NCBI database. We could not document specific cases of non-orthologous gene displacement among the E. coli strains analyzed, but we found that the quality of the genome-sequences in the database is not enough to make accurate predictions about the conservation of essential-genes among members of this bacterial species.\n\nVariability of Bacterial Essential Genes Among Closely Related Bacteria: The Case of Escherichia coli.", "token_count": 455, "char_count": 2059, "word_count": 313, "semantic_coherence": 1, "information_density": 0.5016, "quality_score": 0.7508, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:55.492581", "source": { "split": "train_shard_00001", "doc_id": 2317 }, "chunk_id": "train_shard_00001_2317_0", "global_id": 8958 }, { "text": "Rationale: Pneumococcal pneumonia remains a global health problem. Pneumococcal colonization increases local and systemic protective immunity, suggesting that nasal administration of live attenuated Streptococcus pneumoniae (Spn) strains could help prevent infections. Objectives: We used a controlled human infection model to investigate whether nasopharyngeal colonization with attenuated S. pneumoniae strains protected against recolonization with wild-type (WT) Spn (SpnWT). Methods: Healthy adults aged 18-50 years were randomized (1:1:1:1) for nasal administration twice (at a 2-wk interval) with saline solution, WT Spn6B (BHN418), or one of two genetically modified Spn6B strains, SpnA1 (Δfhs/piaA) or SpnA3 (ΔproABC/piaA) (Stage I). After 6 months, participants were challenged with SpnWT to assess protection against the homologous serotype (Stage II). Measurements and Main Results: 125 participants completed both study stages per intention to treat. No serious adverse events were reported. In Stage I, colonization rates were similar among groups: SpnWT, 58.1% (18 of 31); SpnA1, 60% (18 of 30); and SpnA3, 59.4% (19 of 32). Anti-Spn nasal IgG levels after colonization were similar in all groups, whereas serum IgG responses were higher in the SpnWT and SpnA1 groups than in the SpnA3 group. In colonized individuals, increases in IgG responses were identified against 197 Spn protein antigens and serotype 6 capsular polysaccharide using a pangenome array", "token_count": 485, "char_count": 1527, "word_count": 208, "semantic_coherence": 1, "information_density": 0.7212, "quality_score": 0.8606, "entities": { "genes": [ "BHN418" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:56.138036", "source": { "split": "train_shard_00001", "doc_id": 2318 }, "chunk_id": "train_shard_00001_2318_0", "global_id": 8959 }, { "text": "Participants given SpnWT or SpnA1 in Stage I were partially protected against homologous challenge with SpnWT (29% and 30% recolonization rates, respectively) at stage II, whereas those exposed to SpnA3 achieved a recolonization rate similar to that in the control group (50% vs. 47%, respectively). Conclusions: Nasal colonization with genetically modified live attenuated Spn was safe and induced protection against recolonization, suggesting that nasal administration of live attenuated Spn could be an effective strategy for preventing pneumococcal infections. Clinical trial registered with the ISRCTN registry (ISRCTN22467293).\n\nA Randomized Controlled Clinical Trial of Nasal Immunization with Live Virulence Attenuated <i>Streptococcus pneumoniae</i> Strains Using Human Infection Challenge.", "token_count": 225, "char_count": 818, "word_count": 105, "semantic_coherence": 1, "information_density": 0.781, "quality_score": 0.8905, "entities": { "genes": [ "ISRCTN22467293" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:56.598299", "source": { "split": "train_shard_00001", "doc_id": 2318 }, "chunk_id": "train_shard_00001_2318_1", "global_id": 8960 }, { "text": "Vaginal infections affect millions of women annually worldwide. Therapeutic options are limited, moreover drug-resistance increases the need to find novel antimicrobials for health promotion. Recently phytochemicals were re-discovered for medical treatment. Myrtle (Myrtus communis L.) plant extracts showed in vitro antioxidant, antiseptic and anti-inflammatory properties thanks to their bioactive compounds. The aim of the present study was to create novel nanodevices to deliver three natural extracts from leaves, seeds and fruit of myrtle, in vaginal milieu. We explored their effect on human cells (HeLa, Human Foreskin Fibroblast-1 line, and stem cells isolated from skin), resident microflora (Lactobacillus acidophilus) and on several vaginal pathogens (Trichomonas vaginalis, Escherichia coli, Staphylococcus aureus, Candida albicans, Candida kefyr, Candida glabrata, Candida parapsilosis, Candida krusei). Polycaprolactone-Gelatin nanofibers encapsulated with leaves extract and soaked with seed extracts exhibited a different capability in regard to counteracting microbial proliferation. Moreover, these nanodevices do not affect human cells and resident microflora viability. Results reveal that some of the tested nanofibers are interesting candidates for future vaginal infection treatments.\n\nMyrtle-Functionalized Nanofibers Modulate Vaginal Cell Population Behavior While Counteracting Microbial Proliferation.", "token_count": 433, "char_count": 1506, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7318, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:57.226617", "source": { "split": "train_shard_00001", "doc_id": 2319 }, "chunk_id": "train_shard_00001_2319_0", "global_id": 8961 }, { "text": "

Objectives

Shiga toxin-producing Escherichia coli (STEC) are globally significant foodborne pathogens. Dairy calves are a known reservoir of both O157 and non-O157 STEC. The objective of this study was to comprehensively evaluate the genomic attributes, diversity, virulence factors, and antimicrobial resistance gene (ARG) profiles of the STEC from preweaned and postweaned dairy calves in commercial dairy herds.

Methods

In total, 31 non-O157 STEC were identified as part of a larger study focused on the pangenome of >1000 E. coli isolates from the faeces of preweaned and postweaned dairy calves on commercial dairy farms. These 31 genomes were sequenced on an Illumina NextSeq500 platform.

Results

Based on the phylogenetic analyses, the STEC isolates were determined to be polyphyletic, with at least three phylogroups: A (32%), B1 (58%), and G (3%). These phylogroups represented at least 16 sequence types and 11 serogroups, including two of the 'big six' serogroups, O103 and O111. Several Shiga toxin gene subtypes were identified in the genomes, including stx1a, stx2a, stx2c, stx2d, and stx2g. Using the ResFinder database, the majority of the isolates (>50%) were determined to be multidrug-resistant strains because they harboured genes conferring resistance to three or more classes of antimicrobials, including some of human health significance (e.g., β-lactams, macrolides, and fosfomycin)", "token_count": 463, "char_count": 1483, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6436, "quality_score": 0.8218, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:57.865476", "source": { "split": "train_shard_00001", "doc_id": 2320 }, "chunk_id": "train_shard_00001_2320_0", "global_id": 8962 }, { "text": "Additionally, non-O157 STEC strain persistence and transmission within a farm was observed.

Conclusion

Dairy calves are a reservoir of phylogenomically diverse multidrug-resistant non-O157 STEC. Information from this study may inform assessments of public health risk and guide preharvest prevention strategies focusing on STEC reservoirs.\n\nGenomic diversity of antimicrobial-resistant and Shiga toxin gene-harboring non-O157 Escherichia coli from dairy calves.", "token_count": 131, "char_count": 468, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8393, "quality_score": 0.9196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:58.288213", "source": { "split": "train_shard_00001", "doc_id": 2320 }, "chunk_id": "train_shard_00001_2320_1", "global_id": 8963 }, { "text": "Pangenome theory implies that individuals from a given group/species share only a given part of their genome (core-genome), the remaining part being the dispensable one. Domestication process implies a small number of founder individuals, and thus a large core-genome compared to dispensable at the first steps of domestication. We sequenced at high depth 120 cultivated African rice Oryza glaberrima and of 74 wild relatives O. barthii , and mapped them on the external reference from Asian rice O. sativa . We then use a novel DepthOfCoverage approach to identif missing genes. After comparing the two species, we shown that the cultivated species has a smaller core-genome than the wild one, as well as an expected smaller dispensable one. This unexpected output however replaces in perspective the inadequacy of cultivated crops to wilderness.\n\nComparison of two African rice species through a new pan-genomic approach on massive data", "token_count": 216, "char_count": 938, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6781, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:58.777307", "source": { "split": "train_shard_00001", "doc_id": 2321 }, "chunk_id": "train_shard_00001_2321_0", "global_id": 8964 }, { "text": "The foodborne pathogen, Listeria monocytogenes, (Lm), frequently undergoes selection pressure associated with the extensive use of disinfectants, such as quaternary ammonium compounds, which are widely used in food processing plants. The repeated exposure to sub-inhibitory biocide concentrations can induce increased tolerance to these compounds, but can also trigger the development of antibiotic resistance, and both increase the risk of food contamination and persistence in food production environments. Although the acquisition of genes can explain biocide tolerance, the genetic mechanisms underlying the adaptive cross-resistance to antibiotics remain unclear. We previously showed that repeated exposure to benzalkonium chloride (BC) and didecyldimethyl ammonium chloride (DDAC) led to reduced susceptibility to ciprofloxacin in Lm strains from diverse sources. Here, we compared the genomes of 16 biocide-adapted and 10 parental strains to identify the molecular mechanisms of fluoroquinolone cross-resistance. A core genome SNP analysis identified various mutations in the transcriptional regulator fepR (lmo2088) for 94% of the adapted strains and mutations in other effectors at a lower frequency. FepR is a local repressor of the MATE fluoroquinolone efflux pump FepA. The impact of the mutations on the structure and function of the protein was assessed by performing in silico prediction and protein homology modeling. Our results show that 75% of the missense mutations observed in fepR are located in the HTH domain of the protein, within the DNA interaction site. These mutations are predicted to reduce the activity of the regulator, leading to the overexpression of the efflux pump responsible for the ciprofloxacin-enhanced resistance.", "token_count": 459, "char_count": 1799, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6466, "quality_score": 0.8233, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:59.435095", "source": { "split": "train_shard_00001", "doc_id": 2322 }, "chunk_id": "train_shard_00001_2322_0", "global_id": 8965 }, { "text": "FepR as a Central Genetic Target in the Adaptation to Quaternary Ammonium Compounds and Cross-Resistance to Ciprofloxacin in Listeria monocytogenes.", "token_count": 58, "char_count": 162, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:22:59.836013", "source": { "split": "train_shard_00001", "doc_id": 2322 }, "chunk_id": "train_shard_00001_2322_1", "global_id": 8966 }, { "text": "Bacterial defense barriers, such as DNA methylation-associated restriction-modification (R-M) and the CRISPR-Cas system, play an important role in bacterial antimicrobial resistance (AMR). Recently, a novel R-M system based on DNA phosphorothioate (PT) modification has been shown to be widespread in the kingdom of Bacteria as well as Archaea. However, the potential role of the PT R-M system in bacterial AMR remains unclear. In this study, we explored the role of PT R-Ms in AMR with a series of common clinical pathogenic bacteria. By analyzing the distribution of AMR genes related to mobile genetic elements (MGEs), it was shown that the presence of PT R-M effectively reduced the distribution of horizontal gene transfer (HGT)-derived AMR genes in the genome, even in the bacteria that did not tend to acquire AMR genes by HGT. In addition, unique gene variation analysis based on pangenome analysis and MGE prediction revealed that the presence of PT R-M could suppress HGT frequency. Thus, this is the first report showing that the PT R-M system has the potential to repress HGT-derived AMR gene acquisition by reducing the HGT frequency. IMPORTANCE In this study, we demonstrated the effect of DNA PT modification-based R-M systems on horizontal gene transfer of AMR genes in pathogenic bacteria. We show that there is no apparent association between the genetic background of the strains harboring PT R-Ms and the number of AMR genes or the kinds of gene families. The strains equipped with PT R-M harbor fewer plasmid-derived, prophage-derived, or integrating mobile genetic element (iMGE)-related AMR genes and have a lower HGT frequency, but the degree of inhibition varies among different bacteria. In addition, compared with Salmonella enterica and Escherichia coli, Klebsiella pneumoniae prefers to acquire MGE-derived AMR genes, and there is no coevolution between PT R-M clusters and bacterial core genes.", "token_count": 485, "char_count": 1945, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5217, "quality_score": 0.7609, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:00.516042", "source": { "split": "train_shard_00001", "doc_id": 2323 }, "chunk_id": "train_shard_00001_2323_0", "global_id": 8967 }, { "text": "The DNA Phosphorothioation Restriction-Modification System Influences the Antimicrobial Resistance of Pathogenic Bacteria.", "token_count": 34, "char_count": 122, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:00.871370", "source": { "split": "train_shard_00001", "doc_id": 2323 }, "chunk_id": "train_shard_00001_2323_1", "global_id": 8968 }, { "text": "

Background

We analyzed an outbreak of Bacillus cereus group (Bcg) at a single-center neonatal intensive care unit level IV by conducting comprehensive sampling of both patients and the environment.

Methods

Between 06/2020 and 10/2021, all Bcg isolates identified by both regular colonization screening and additional sampling of the environment were subjected to whole-genome sequencing, followed by in vitro extraction of MLST ST, resistance genes and virulence factors. Using publicly available genome sequences, we defined an ad hoc core genome multilocus sequence typing (cgMLST) scheme comprising 2759 target genes for Bcg typing, which we applied to the detected isolates. We have compared the results with a stable cgMLST that was published in the meantime and completed the investigation with a SNP analysis.

Results

We analyzed 28 Bcg isolates from patient and environmental samples using MLST and cgMLST. This revealed multiple sequence types, with ST127 being the most common (n = 13). Both cgMLST schemes grouped ten of the 13 ST127 isolates into a cluster, including two invasive isolates from two different patients and several environmental samples. SNP analysis postulated a screen from a ventilation machine as a possible reservoir.

Conclusion

In sensitive settings such as neonatal intensive care units, considering the environment in outbreak analyses is crucial, especially when investigating potential transmission routes through shared devices. When dealing with widespread bacteria such as Bcg, high-resolution typing techniques are necessary. In this study, we successfully resolved an outbreak of Bcg infections using a custom cgMLST scheme combined with a SNP analysis.\n\nInvestigating environmental transmission to resolve a Bacillus cereus group outbreak in a neonatal intensive care unit using core genome multilocus sequence typing.", "token_count": 449, "char_count": 1890, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [ "ST127" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:01.507013", "source": { "split": "train_shard_00001", "doc_id": 2324 }, "chunk_id": "train_shard_00001_2324_0", "global_id": 8969 }, { "text": "

Background

Salmonella enterica is a leading cause of foodborne illness worldwide resulting in considerable public health and economic costs. Testing for the presence of this pathogen in food is often hampered by the presence of background microflora that may present as Salmonella (false positives). False positive isolates belonging to the genus Citrobacter can be difficult to distinguish from Salmonella due to similarities in their genetics, cell surface antigens, and other phenotypes. In order to understand the genetic basis of these similarities, a comparative genomic approach was used to define the pan-, core, accessory, and unique coding sequences of a representative population of Salmonella and Citrobacter strains.

Results

Analysis of the genomic content of 58 S. enterica strains and 37 Citrobacter strains revealed the presence of 31,130 and 1540 coding sequences within the pan- and core genome of this population. Amino acid sequences unique to either Salmonella (n = 1112) or Citrobacter (n = 195) were identified and revealed potential niche-specific adaptations. Phylogenetic network analysis of the protein families encoded by the pan-genome indicated that genetic exchange between Salmonella and Citrobacter may have led to the acquisition of similar traits and also diversification within the genera.

Conclusions

Core genome analysis suggests that the Salmonella enterica and Citrobacter populations investigated here share a common evolutionary history. Comparative analysis of the core and pan-genomes was able to define the genetic features that distinguish Salmonella from Citrobacter and highlight niche specific adaptations.\n\nSimilar yet different: phylogenomic analysis to delineate Salmonella and Citrobacter species boundaries.", "token_count": 425, "char_count": 1783, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:02.139595", "source": { "split": "train_shard_00001", "doc_id": 2325 }, "chunk_id": "train_shard_00001_2325_0", "global_id": 8970 }, { "text": "The mutualistic interactions between Riftia pachyptila and its endosymbiont Candidatus Endoriftia persephone (short Endoriftia) have been extensively researched. However, the closed Endoriftia genome is still lacking. Here, by employing single‐molecule real‐time sequencing we present the closed chromosomal sequence of Endoriftia. In contrast to theoretical predictions of enlarged and mobile genetic element‐rich genomes related to facultative endosymbionts, the closed Endoriftia genome is streamlined with fewer than expected coding sequence regions, insertion‐, prophage‐sequences and transposase‐coding sequences. Automated and manually curated functional analyses indicated that Endoriftia is more versatile regarding sulphur metabolism than previously reported. We identified the presence of two identical rRNA operons and two long CRISPR regions in the closed genome. Additionally, pangenome analyses revealed the presence of three types of secretion systems (II, IV and VI) in the different Endoriftia populations indicating lineage‐specific adaptations. The in depth mobilome characterization identified the presence of shared genomic islands in the different Endoriftia drafts and in the closed genome, suggesting that the acquisition of foreign DNA predates the geographical dispersal of the different endosymbiont populations. Finally, we found no evidence of epigenetic regulation in Endoriftia, as revealed by gene screenings and absence of methylated modified base motifs in the genome. As a matter of fact, the restriction‐modification system seems to be dysfunctional in Endoriftia, pointing to a higher importance of molecular memory‐based immunity against phages via spacer incorporation into CRISPR system. The Endoriftia genome is the first closed tubeworm endosymbiont to date and will be valuable for future gene oriented and evolutionary comparative studies.\n\nThe complete and closed genome of the facultative generalist Candidatus Endoriftia persephone from deep‐sea hydrothermal vents", "token_count": 469, "char_count": 2012, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6292, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:02.784449", "source": { "split": "train_shard_00001", "doc_id": 2326 }, "chunk_id": "train_shard_00001_2326_0", "global_id": 8971 }, { "text": "The attributes of the yeast Kluyveromyces marxianus (rapid growth rate at high temperature, utilization of a wide range of inexpensive carbon sources) make it a promising industrial host for the synthesis of protein and non-protein products. However, no stable multicopy plasmids are currently available for long-term culture of K. marxianus. To allow the stable genetic/metabolic engineering of K. marxianus, a method for integrating precise numbers of the same or different genes was developed for this yeast. A K. marxianus URA3 deletion mutant was constructed and the URA3 blaster (UB) reusable selection cassette from Saccharomyces cerevisiae was used to select sequential, untargeted chromosomal insertions of the Bacillus megaterium lactate dehydrogenase (LDH) gene. Following excision of the UB cassette from the chromosomes, the integrating vector was retransformed into the strain and a second copy of LDH was inserted, demonstrating the success of this method for sequential gene integrations in K. marxianus. LDH activity and lactic acid concentration increased with each gene insertion, further illustrating the success of this method.\n\nSequential gene integration for the engineering of Kluyveromyces marxianus.", "token_count": 305, "char_count": 1225, "word_count": 176, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:03.360238", "source": { "split": "train_shard_00001", "doc_id": 2327 }, "chunk_id": "train_shard_00001_2327_0", "global_id": 8972 }, { "text": "The family Rhizobiaceae includes many genera of soil bacteria, often isolated for their association with plants. Herein, we investigate the genomic diversity of a group of Rhizobium species and unclassified strains isolated from atypical environments, including seawater, rock matrix or polluted soil. Based on whole-genome similarity and core genome phylogeny, we show that this group corresponds to the genus Pseudorhizobium. We thus reclassify Rhizobium halotolerans, R. marinum, R. flavum and R. endolithicum as P. halotolerans comb. nov., P. marinum comb. nov. , P. flavum comb. nov. and R. endolithicum comb. nov., respectively, and show that P. pelagicum is a synonym of P. marinum . We also delineate a new chemolithoautotroph species, P. banfieldiae sp. nov., whose type strain is NT-26 T (= DSM 106348 T = CFBP 8663 T ). This genome-based classification was supported by a chemotaxonomic comparison, with gradual taxonomic resolution provided by fatty acid, protein and metabolic profiles. In addition, we used a phylogenetic approach to infer scenarios of duplication, horizontal transfer and loss for all genes in the Pseudorhizobium pangenome. We thus identify the key functions associated with the diversification of each species and higher clades, shedding light on the mechanisms of adaptation to their respective ecological niches. Respiratory proteins acquired at the origin of Pseudorhizobium are combined with clade-specific genes to encode different strategies for detoxification and nutrition in harsh, nutrient-poor environments. Finally, we predict diagnostic phenotypes for the distinction of P. banfieldiae from other Pseudorhizobium species, including autotrophy and sensitivity to the azo dye Congo Red, which we experimentally validated.\n\nPhylogenomic analysis reveals the basis of adaptation of Pseudorhizobium species to extreme environments", "token_count": 499, "char_count": 1879, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6506, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:04.012385", "source": { "split": "train_shard_00001", "doc_id": 2328 }, "chunk_id": "train_shard_00001_2328_0", "global_id": 8973 }, { "text": "

ABSTRACT

The fungal plant pathogen Neonectria neomacrospora (C. Booth & Samuels) Mantiri & Samuels (Ascomycota, Hypocreales) is a bark parasite causing twig blight, canker, and in severe cases, dieback in fir ( Abies spp.). Although often described as a mild pathogen, foresty and phytosanitary agencies have expressed their concern for potential economic impact. Two epidemics caused by this species are known: one from eastern Canada and one current within Northern Europe. We present key genome features of N. neomacrospora , to facilitate the research into the biology of this pathogen. We present the first genome assembly of N. neomacrospora as well as the first pangenome within this genus. The reference genome for N. neomacrospora is a long-read sequenced Danish isolate, while the pangenome is pieced together using additional 60 short-read sequenced strains covering the known geographical distribution of the species, including Europe, North America, and China. The gapless reference genome consist of twelve chromosomes sequenced telomere to telomere to a total length of 37.1 Mb. The mitochondrial genome was assembled and circularised with a length of 22 Kb. The gapless nuclear genome contains a total of 11,291 annotated genes, where 642 only have a hypothetical function, and a 4.3 % repeat content. Two minor chromosomes are enriched in transposable elements, AT content, and effector candidates. Chromosome 12 segregates within the population, indicating an accessory nature. The pangenome compile 15,101 genes, 34% more genes than present in the single isolate reference genome of N. neomacrospora . These genes organise into 13,069 homologous clusters, of which 8,316 clusters are present in all analysed strains, 985 are private to single strains. The British Columbian population branched out before the other populations and are characterized by comparatively larger genomes. The increased genome size can be explained by an expansion of repetitive elements", "token_count": 525, "char_count": 1991, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6577, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:04.668783", "source": { "split": "train_shard_00001", "doc_id": 2329 }, "chunk_id": "train_shard_00001_2329_0", "global_id": 8974 }, { "text": "The comparative analysis finds a higher number of genes with a signal peptide within N. neomacrospora and species within the genus compared to the closely related genera. A species-specific pattern is observed in the carbohydrate-active enzyme repertoire, with a reduced number of polysaccharide lyases, compared to other species within the genus. The CAZymes battery responsible for plant cell wall degradation is similar to that observed in necrotrophic and hemibiotrophic plant pathogenic fungi. The genome size of N. neomacrospora is close to the median size for Ascomycota but is the smallest genome within the Neonectria genus. Comparative analysis revealed significant intraspecies genome size differences between populations explained by a difference in repeat content. Isolates with the smallest genomes formed a monophyletic group consisting of all strains from Europe and Quebec. Based on the field observations, we assume that N. neomacrospora is a hemibiotroph. Our analysis revealed a secretome consistent with a hemibiotrophic lifestyle.\n\nThe pangenome of the fungal pathogenNeonectria neomacrospora", "token_count": 279, "char_count": 1121, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:05.226338", "source": { "split": "train_shard_00001", "doc_id": 2329 }, "chunk_id": "train_shard_00001_2329_1", "global_id": 8975 }, { "text": "Ruminococcus gnavus is prevalent in the intestines of humans and animals, and ambiguities have been reported regarding its relations with the development of diseases and host well-being. We postulate the ambiguities of its function in different cases may be attributed to strain-level variability of genomic features of R. gnavus. We performed comparative genomic and pathogenicity prediction analysis on 152 filtered high-quality genomes, including 4 genomes of strains isolated from healthy adults in this study. The mean G+C content of genomes of R. gnavus was 42.73±0.33 mol%, and the mean genome size was 3.46±0.34 Mbp. Genome-wide evolutionary analysis revealed R. gnavus genomes were divided into three major phylogenetic clusters. Pan-core genome analysis revealed that there was a total of 28 072 predicted genes, and the core genes, soft-core genes, shell genes and cloud genes accounted for 3.74 % (1051/28 072), 1.75 % (491/28 072), 9.88 % (2774/28 072) and 84.63 % (23 756/28 072) of the total genes, respectively. The small proportion of core genes reflected the wide divergence among R. gnavus strains. We found certain coding sequences with determined health benefits (such as vitamin production and arsenic detoxification), whilst some had an implication of health adversity (such as sulfide dehydrogenase subunits). The functions of the majority of core genes were unknown", "token_count": 447, "char_count": 1425, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:05.871603", "source": { "split": "train_shard_00001", "doc_id": 2330 }, "chunk_id": "train_shard_00001_2330_0", "global_id": 8976 }, { "text": "The most widespread genes functioning in antibiotic resistance and virulence are tetO (tetracycline-resistance gene, present in 75 strains) and cps4J (capsular polysaccharide biosynthesis protein Cps4J encoding gene, detected in 3 genomes), respectively. Our results revealed genomic divergence and the existence of certain safety-relevant factors of R. gnavus. This study provides new insights for understanding the genomic features and health relevance of R. gnavus, and raises concerns regarding predicted prevalent pathogenicity and antibiotic resistance among most of the strains.\n\nComparative genomics reveals extensive intra-species genetic divergence of the prevalent gut commensal Ruminococcus gnavus.", "token_count": 200, "char_count": 745, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:06.320655", "source": { "split": "train_shard_00001", "doc_id": 2330 }, "chunk_id": "train_shard_00001_2330_1", "global_id": 8977 }, { "text": "Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C", "token_count": 518, "char_count": 2048, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:06.975526", "source": { "split": "train_shard_00001", "doc_id": 2331 }, "chunk_id": "train_shard_00001_2331_0", "global_id": 8978 }, { "text": "difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.\n\nA local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment.", "token_count": 232, "char_count": 989, "word_count": 126, "semantic_coherence": 1, "information_density": 0.754, "quality_score": 0.877, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:07.451609", "source": { "split": "train_shard_00001", "doc_id": 2331 }, "chunk_id": "train_shard_00001_2331_1", "global_id": 8979 }, { "text": "

Introduction

Gonorrhoea is a major public health concern. With the global emergence and spread of resistance to last-line antibiotic treatment options, gonorrhoea threatens to be untreatable in the future. Therefore, this study performed whole genome characterization of Neisseria gonorrhoeae collected in Ghana to identify lineages of circulating strains as well as their phenotypic and genotypic antimicrobial resistance (AMR) profiles.

Methods

Whole genome sequencing (WGS) was performed on 56 isolates using both the Oxford Nanopore MinION and Illumina MiSeq sequencing platforms. The Comprehensive Antimicrobial Resistance Database (CARD) and PUBMLST.org/neisseria databases were used to catalogue chromosomal and plasmid genes implicated in AMR. The core genome multi-locus sequence typing (cgMLST) approach was used for comparative genomics analysis.

Results and discussion

In vitro resistance measured by the E-test method revealed 100%, 91.0% and 85.7% resistance to tetracycline, penicillin and ciprofloxacin, respectively. A total of 22 sequence types (STs) were identified by multilocus sequence typing (MLST), with ST-14422 (n = 10), ST-1927 (n = 8) and ST-11210 (n = 7) being the most prevalent. Six novel STs were also identified (ST-15634, 15636-15639 and 15641). All isolates harboured chromosomal AMR determinants that confer resistance to beta-lactam antimicrobials and tetracycline. A single cefixime-resistant strain, that belongs to N", "token_count": 490, "char_count": 1516, "word_count": 196, "semantic_coherence": 1, "information_density": 0.7092, "quality_score": 0.8546, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:08.101779", "source": { "split": "train_shard_00001", "doc_id": 2332 }, "chunk_id": "train_shard_00001_2332_0", "global_id": 8980 }, { "text": "gonorrhoeae multiantigen sequence type (NG-MAST) ST1407, a type associated with widespread cephalosporin resistance was identified. Neisseria gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR), identified 29 unique sequence types, with ST-464 (n = 8) and the novel ST-3366 (n = 8) being the most prevalent. Notably, 20 of the 29 STs were novel, indicative of the unique nature of molecular AMR determinants in the Ghanaian strains. Plasmids were highly prevalent: pTetM and pblaTEM were found in 96% and 92% of isolates, respectively. The TEM-135 allele, which is an amino acid change away from producing a stable extended-spectrum β-lactamase that could result in complete cephalosporin resistance, was identified in 28.5% of the isolates. Using WGS, we characterized N. gonorrhoeae strains from Ghana, giving a snapshot of the current state of gonococcal AMR in the country and highlighting the need for constant genomic surveillance.\n\nWhole genome analysis and antimicrobial resistance of Neisseria gonorrhoeae isolates from Ghana.", "token_count": 358, "char_count": 1096, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "ST1407" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:08.673810", "source": { "split": "train_shard_00001", "doc_id": 2332 }, "chunk_id": "train_shard_00001_2332_1", "global_id": 8981 }, { "text": "The present study aimed to comprehensively dissect the petroleum hydrocarbon degradation mechanism of Acinetobacter vivianii KJ-1. The isolated and identified strain was able to proliferate using diesel as the sole carbonaceous substrate. Via comparative genomics, an in-depth analysis was performed to elucidate the genome similarities and disparities between this strain and related strains, thereby uncovering a core genome as well as genes with uncharacterized functions. Transcriptome analysis, carried out under different substrate conditions (C16, diesel, sodium acetate) manifested distinct gene expression modalities. A multitude of genes associated with alkane metabolism were differentially expressed, among which alkB1_1 and alkB1_2 was conspicuously upregulated. Prokaryotic expression of alkB1_1 was implemented, and the enzyme activity of the recombinant protein peaked at a pH level of approximately 7.0 and within a temperature range of 30 to 40 °C. The recombinant strain was shown to possess the ability to degrade n-hexadecane. Collectively, this research not only augments the understanding of the degradation mechanism of A. vivianii KJ-1 but also provides a fundamental basis for developing bioremediation strategies targeting petroleum hydrocarbon-contaminated environments.\n\nComparative Genomics, Transcriptome, and Prokaryotic Expression Analysis of <i>alk</i>B1_1 in <i>Acinetobacter vivianii</i> KJ-1: Revealing the Mechanism of Petroleum Hydrocarbon Degradation.", "token_count": 430, "char_count": 1550, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:09.299238", "source": { "split": "train_shard_00001", "doc_id": 2333 }, "chunk_id": "train_shard_00001_2333_0", "global_id": 8982 }, { "text": "Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were challenging with previous reference-based methods. In this work, we extend these methods into transcriptomics to analyze sequencing data using the pantranscriptome: a population-level transcriptomic reference. Our novel toolchain can construct spliced pangenome graphs, map RNA-seq data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. This workflow improves accuracy over state-of-the-art RNA-seq mapping methods, and it can efficiently quantify haplotype-specific transcript expression without needing to characterize a sample’s haplotypes beforehand.\n\nHaplotype-aware pantranscriptome analyses using spliced pangenome graphs", "token_count": 211, "char_count": 932, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7611, "quality_score": 0.8805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:09.760870", "source": { "split": "train_shard_00001", "doc_id": 2334 }, "chunk_id": "train_shard_00001_2334_0", "global_id": 8983 }, { "text": "The iron-oxidizing Gallionellaceae drive a wide variety of biogeochemical cycles through their metabolisms and biominerals. To better understand the environmental impacts of Gallionellaceae, we need to improve our knowledge of their diversity and metabolisms, especially any novel iron oxidation mechanisms. Here, we used a pangenomic analysis of 103 genomes to resolve Gallionellaceae phylogeny and explore the range of genomic potential. Using a concatenated ribosomal protein tree and key gene patterns, we determined Gallionellaceae has four genera, divided into two groups–iron-oxidizing bacteria (FeOB) Gallionella , Sideroxydans , and Ferriphaselus with known iron oxidases (Cyc2, MtoA) and nitrite-oxidizing bacteria (NOB) Candidatus Nitrotoga with nitrite oxidase (Nxr). The FeOB and NOB have similar electron transport chains, including genes for reverse electron transport and carbon fixation. Auxiliary energy metabolisms including S oxidation, denitrification, and organotrophy were scattered throughout the Gallionellaceae FeOB. Within FeOB, we found genes that may represent adaptations for iron oxidation, including a variety of extracellular electron uptake (EEU) mechanisms. FeOB genomes encoded more predicted c -type cytochromes overall, notably more multiheme c -type cytochromes (MHCs) with >10 CXXCH motifs. These include homologs of several predicted outer membrane porin-MHC complexes, including MtoAB and Uet. MHCs are known to efficiently conduct electrons across longer distances and function across a wide range of redox potentials that overlap with mineral redox potentials, which can help expand the range of usable iron substrates. Overall, the results of pangenome analyses suggest that the Gallionellaceae genera Gallionella , Sideroxydans , and Ferriphaselus are primarily iron oxidizers, capable of oxidizing dissolved Fe 2+ as well as a range of solid iron or other mineral substrates", "token_count": 481, "char_count": 1921, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:10.413274", "source": { "split": "train_shard_00001", "doc_id": 2335 }, "chunk_id": "train_shard_00001_2335_0", "global_id": 8984 }, { "text": "

Importance

Neutrophilic iron-oxidizing bacteria (FeOB) produce copious iron (oxyhydr)oxides that can profoundly influence biogeochemical cycles, notably the fate of carbon and many metals. To fully understand environmental microbial iron oxidation, we need a thorough accounting of iron oxidation mechanisms. In this study we show the Gallionellaceae FeOB have both known iron oxidases as well as uncharacterized multiheme cytochromes (MHCs). MHCs are predicted to transfer electrons from extracellular substrates and likely confer metabolic capabilities that help Gallionellaceae occupy a range of different iron- and mineral-rich niches. Gallionellaceae appear to specialize in iron oxidation, so it makes sense that they would have multiple mechanisms to oxidize various forms of iron, given the many iron minerals on Earth, as well as the physiological and kinetic challenges faced by FeOB. The multiple iron/mineral oxidation mechanisms may help drive the widespread ecological success of Gallionellaceae.\n\nGallionellaceae pangenomic analysis reveals insight into phylogeny, metabolic flexibility, and iron oxidation mechanisms", "token_count": 278, "char_count": 1141, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7124, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:10.989773", "source": { "split": "train_shard_00001", "doc_id": 2335 }, "chunk_id": "train_shard_00001_2335_1", "global_id": 8985 }, { "text": "Prophages can have major clinical implications through their ability to change pathogenic bacterial traits. There is limited understanding of the prophage role in ecological, evolutionary, adaptive processes and pathogenicity of Helicobacter pylori, a widespread bacterium causally associated with gastric cancer. Inferring the exact prophage genomic location and completeness requires complete genomes. The international Helicobacter pylori Genome Project (HpGP) dataset comprises 1011 H. pylori complete clinical genomes enriched with epigenetic data. We thoroughly evaluated the H. pylori prophage genomic content in the HpGP dataset. We investigated population evolutionary dynamics through phylogenetic and pangenome analyses. Additionally, we identified genome rearrangements and assessed the impact of prophage presence on bacterial gene disruption and methylome. We found that 29.5% (298) of the HpGP genomes contain prophages, of which only 32.2% (96) were complete, minimizing the burden of prophage carriage. The prevalence of H. pylori prophage sequences was variable by geography and ancestry, but not by disease status of the human host. Prophage insertion occasionally results in gene disruption that can change the global bacterial epigenome. Gene function prediction allowed the development of the first model for lysogenic-lytic cycle regulation in H. pylori. We have disclosed new prophage inactivation mechanisms that appear to occur by genome rearrangement, merger with other mobile elements, and pseudogene accumulation. Our analysis provides a comprehensive framework for H. pylori prophage biological and genomics, offering insights into lysogeny regulation and bacterial adaptation to prophages.", "token_count": 466, "char_count": 1790, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:11.671520", "source": { "split": "train_shard_00001", "doc_id": 2336 }, "chunk_id": "train_shard_00001_2336_0", "global_id": 8986 }, { "text": "Gene content, phage cycle regulation model and prophage inactivation disclosed by prophage genomics in the <i>Helicobacter pylori</i> Genome Project.", "token_count": 50, "char_count": 161, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:12.053184", "source": { "split": "train_shard_00001", "doc_id": 2336 }, "chunk_id": "train_shard_00001_2336_1", "global_id": 8987 }, { "text": "

Background

Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a pathogen known to reside in cattle feedlots. This retrospective study examined 181 STEC O157:H7 strains collected over 23 years from a closed-system feedlot. All strains were subjected to short-read sequencing, with a subset of 36 also subjected to long-read sequencing.

Results

Over 96% of the strains fell into four phylogenetically distinct clades. Clade membership was associated with multiple factors including stx composition and the alleles of a well-characterized polymorphism (tir 255 T > A). Small plasmids (2.7 to 40 kb) were found to be primarily clade specific. Within each clade, chromosomal rearrangements were observed along with a core phageome and clade specific phages. Across both core and mobile elements of the genome, multiple SNP alleles were in complete linkage disequilibrium across all strains within specific clades. Clade evolutionary rates varied between 0.9 and 2.8 SNP/genome/year with two tir A allele clades having the lowest evolutionary rates. Investigation into possible causes of the differing rates was not conclusive but revealed a synonymous based mutation in the DNA polymerase III of the fastest evolving clade. Phylogenetic trees generated through our bioinformatic pipeline versus the NCBI's pathogen detection project were similar, with the two tir A allele clades matching individual NCBI SNP clusters, and the two tir T allele clades assigned to multiple closely-related SNP clusters.

Conclusions

In one ecological niche, a diverse STEC O157:H7 population exhibited different rates of evolution that associated with SNP alleles in linkage disequilibrium in the core genome and mobile elements, including tir 255 T > A.", "token_count": 497, "char_count": 1758, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8123, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:12.738112", "source": { "split": "train_shard_00001", "doc_id": 2337 }, "chunk_id": "train_shard_00001_2337_0", "global_id": 8988 }, { "text": "Rates of evolutionary change of resident Escherichia coli O157:H7 differ within the same ecological niche.", "token_count": 31, "char_count": 106, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:13.093553", "source": { "split": "train_shard_00001", "doc_id": 2337 }, "chunk_id": "train_shard_00001_2337_1", "global_id": 8989 }, { "text": "Bacteria use diverse strategies and molecular machinery to maintain copper homeostasis and to cope with its toxic effects. Some genetic elements providing copper resistance are acquired by horizontal gene transfer; however, little is known about how they are controlled and integrated into the central regulatory network. Here, we studied two copper-responsive systems in a clinical isolate of Pseudomonas paraeruginosa and deciphered the regulatory and cross-regulation mechanisms. To do so, we combined mutagenesis, transcriptional fusion analyses and copper sensitivity phenotypes. Our results showed that the accessory CusRS two-component system (TCS) responds to copper and activates both its own expression and that of the adjacent nine-gene operon to provide resistance to elevated levels of extracellular copper. The same locus was also found to be regulated by two core-genome-encoded TCSs - the copper-responsive CopRS and the zinc-responsive CzcRS. Although the target palindromic sequence – ATTCATnnATGTAAT – is the same for the three response regulators, transcriptional outcomes differ. Thus, depending on the operon/regulator pair, binding can result in different activation levels (from none to high), with the systems demonstrating considerable plasticity. Unexpectedly, although the classical CusRS and the noncanonical CopRS TCSs rely on distinct signaling mechanisms (kinase-based vs . phosphatase-based), we discovered cross-talk in the absence of the cognate sensory kinases. This cross-talk occurred between the proteins of these two otherwise independent systems. The entire locus is part of an Integrative and Conjugative Element, and was found in other Pseudomonas strains where its expression could provide copper resistance under appropriate conditions. The results presented here illustrate how acquired genetic elements can become part of endogenous regulatory networks, providing a physiological advantage. They also highlight the potential for broader effects of accessory regulatory proteins through interference with core regulatory proteins.

Author Summary

Two-component regulatory systems play a key role in bacterial life by detecting and integrating a wide range of signals, allowing bacteria to continuously monitor and adapt to a changing environment. They weave a complex network with a few highly interconnected phosphorelays and numerous cross-regulations", "token_count": 510, "char_count": 2407, "word_count": 331, "semantic_coherence": 1, "information_density": 0.6344, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:13.731857", "source": { "split": "train_shard_00001", "doc_id": 2338 }, "chunk_id": "train_shard_00001_2338_0", "global_id": 8990 }, { "text": "Our study reveals connections between zinc and copper homeostasis in a pathogenic bacterium, with cross-regulation observed for three independent, closely related transcriptional regulators, CzcR, CopR and CusR. Zinc and copper play a major role in host-pathogen interactions, and bacteria that synergize their responses to the two elements can harness a growth advantage and enhanced fitness in specific conditions. We also observed unexpected cross-talk between the core genome-encoded CopRS system and the horizontally acquired CusRS system, although the molecular control exerted by a histidine kinase on its cognate regulator differs. This plasticity observed within the two signaling systems ensures a normal regulatory response to the copper signal required to maintain copper homeostasis.\n\nCross-regulation and cross-talk of conserved and accessory two-component regulatory systems orchestratePseudomonascopper resistance", "token_count": 204, "char_count": 936, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7398, "quality_score": 0.8699, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:14.195541", "source": { "split": "train_shard_00001", "doc_id": 2338 }, "chunk_id": "train_shard_00001_2338_1", "global_id": 8991 }, { "text": "

Background

Porphyromonas gingivalis (hereafter “ Pg ”) is an oral pathogen that can act as a keystone driver of inflammation and periodontal disease. Although Pg is most readily recovered from individuals with actively progressing periodontal disease, healthy individuals and those with stable non-progressing disease are also colonized by Pg . Insights into the factors shaping the striking strain-level variation in Pg , and its variable associations with disease, are needed to achieve a more mechanistic understanding of periodontal disease and its progression. A key force shaping strain level diversity in all microbial communities is infection of bacteria by their viral (phage) predators and symbionts. Surprisingly, although Pg has been the subject of study for over 40 years, essentially nothing is known of its phages, and the prevailing paradigm is that phages are not important in the ecology of Pg .

Results

Here we systematically addressed the question of whether Pg are infected by phages - and we found that they are. We found that prophages are common in Pg , they are genomically diverse, and they encode genes that have the potential to alter Pg physiology and interactions. We found that phages represent unrecognized targets of the prevalent CRISPR-Cas defense systems in Pg , and that Pg strains encode numerous additional mechanistically diverse candidate anti-phage defense systems. We also found that phages and candidate anti-phage defense system elements together are major contributors to strain level diversity and the species pangenome of this oral pathogen. Finally, we demonstrate that prophages harbored by a model Pg strain are active in culture, producing extracellular viral particles in broth cultures.

Discussion

This work definitively establishes that phages are a major unrecognized force shaping the ecology and intraspecies strain-level diversity of the well-studied oral pathogen Pg . The foundational phage sequence datasets and model systems that we establish here add to the rich context of all that is already known about Pg , and point to numerous avenues of future inquiry that promise to shed new light on fundamental features of phage impacts on human health and disease broadly.", "token_count": 515, "char_count": 2258, "word_count": 344, "semantic_coherence": 1, "information_density": 0.5407, "quality_score": 0.7703, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:14.855689", "source": { "split": "train_shard_00001", "doc_id": 2339 }, "chunk_id": "train_shard_00001_2339_0", "global_id": 8992 }, { "text": "Phages are important unrecognized players in the ecology of the oral pathogenPorphyromonas gingivalis", "token_count": 32, "char_count": 108, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:15.211826", "source": { "split": "train_shard_00001", "doc_id": 2339 }, "chunk_id": "train_shard_00001_2339_1", "global_id": 8993 }, { "text": "

Background/objectives

Limosilactobacillus (Lm.) reuteri is a widely utilized probiotic, recognized for its significant role in alleviating symptoms associated with gastrointestinal and psychiatric disorders. However, the effectiveness of Lm. reuteri is strain-specific, and its genetic diversity leads to significant differences in phenotypes among different strains. This study aims to identify potential probiotic strains by comparing the strain-specific characteristics of Lm. reuteri to better understand their efficacy and mechanisms in alleviating stress-induced anxiety-like behaviors and gastrointestinal symptoms.

Methods

We cultivated 11 strains of Lm. reuteri from healthy human samples and conducted phenotypic and genomic characterizations. Two strains, WLR01 (=GOLDGUT-LR99) and WLR06, were screened as potential probiotics and were tested for their efficacy in alleviating anxiety-like behavior and intestinal symptoms in mouse models subjected to sleep deprivation (SD) and water avoidance stress (WAS).

Results

The results showed that the selected strains effectively improved mouse behaviors, including cognitive impairment and inflammatory response, as well as improving anxiety and regulating gut microbiota composition. The improvements with WLR01 were associated with the regulation of the NLRP3 inflammasome pathway in the SD model mice and were associated with visceral hypersensitivity and intestinal integrity in the WAS model mice.

Conclusions

In summary, this study identified the Lm. reuteri strain WLR01 as having the potential to alleviate anxiety-like behavior and intestinal symptoms through the analysis of Lm. reuteri genotypes and phenotypes, as well as validation in mouse models, thereby laying the foundation for future clinical applications.", "token_count": 483, "char_count": 1852, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "WLR01", "NLRP3", "LR99", "WLR06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:15.865421", "source": { "split": "train_shard_00001", "doc_id": 2340 }, "chunk_id": "train_shard_00001_2340_0", "global_id": 8994 }, { "text": "Limosilactobacillus reuteri Alleviates Anxiety-like Behavior and Intestinal Symptoms in Two Stressed Mouse Models.", "token_count": 43, "char_count": 121, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:16.223763", "source": { "split": "train_shard_00001", "doc_id": 2340 }, "chunk_id": "train_shard_00001_2340_1", "global_id": 8995 }, { "text": "Streptococcus pneumoniae can be divided into many strains, each a distinct set of isolates sharing similar core and accessory genomes, which co-circulate within the same hosts. Previous analyses suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), which maintains accessory loci at equilibrium frequencies. Long-term simulations demonstrated NFDS stabilised clonally-evolving multi-strain populations through preventing the loss of variation through drift, based on polymorphism frequencies, pairwise genetic distances and phylogenies. However, allowing symmetrical recombination between isolates evolving under multi-locus NFDS generated unstructured populations of diverse genotypes. Replication of the observed data improved when multi-locus NFDS was combined with recombination that was instead asymmetrical, favouring deletion of accessory loci over insertion. This combination separated populations into strains through outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. Although simplistic modelling of recombination likely limited these simulations' ability to maintain some properties of genomic data as accurately as those lacking recombination, the combination of asymmetrical recombination and multi-locus NFDS could restore multi-strain population structures from randomised initial populations. As many bacteria inhibit insertions into their chromosomes, this combination may commonly underlie the co-existence of strains within a niche.\n\nNegative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures.", "token_count": 375, "char_count": 1771, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6934, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:16.812397", "source": { "split": "train_shard_00001", "doc_id": 2341 }, "chunk_id": "train_shard_00001_2341_0", "global_id": 8996 }, { "text": "

Background

Invasive Haemophilus influenzae serotype a (Hia) disease is rare, with most cases reported among Indigenous populations in North America. In England, national surveillance was enhanced following an increase in laboratory-confirmed invasive Hia disease since the 2016-17 epidemiological year. This study aimed to describe the epidemiological trends, clinical characteristics of cases, and assess potential genomic drivers.

Methods

Hospital laboratories in England routinely submit invasive H influenzae isolates to the UK Health Security Agency for confirmation and serotyping. In this prospective national surveillance study we contacted the general practitioners and clinicians of all patients with laboratory-confirmed invasive Hia from the 2008-09 to the 2021-22 epidemiological year to complete a clinical questionnaire on demographics, underlying conditions, clinical presentation, complications, outcomes, and travel history of the patient. All Hia invasive isolates from residents in England were included in the study; non-invasive isolates were excluded. Multilocus sequence typing (MLST), whole genome single-nucleotide polymorphism, and k-mer-based analysis of bacterial isolates were performed following Illumina whole-genome sequencing (WGS). Outcomes included epidemiological trends, clinical characteristics of confirmed Hia cases, and genomic analyses.

Findings

From the 2008-09 to the 2021-22 epidemiological years, there were 52 cases of invasive infection with H influenzae serotype a in England (25 [48%] in female patients and 27 [52%] in male patients)", "token_count": 401, "char_count": 1607, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:17.430701", "source": { "split": "train_shard_00001", "doc_id": 2342 }, "chunk_id": "train_shard_00001_2342_0", "global_id": 8997 }, { "text": "There were zero to two annual Hia cases (accounting for <0·5% of serotyped H influenzae isolates) until 2015-16, after which cases increased across England to 19 cases in 2021-22 (incidence 0·03 cases per 100 000), when Hia accounted for 19 (4%) of 484 serotyped H influenzae isolates, 19 (19%) of 100 capsulated cases, and 37% (19 of 52) of all H influenzae cases between 2008-09 and 2021-22. Most of the recent increase in cases occurred among individuals aged 65 years and older (17 [33%] of 52), who typically presented with bacteraemic pneumonia (13 [76%] of 17), and infants younger than 1 year, who had the highest incidence and were more likely to present with meningitis (five [50%] of ten). Overall case fatality rate was 7·7% (95% CI 2·1-19·7; four of 52 patients). WGS found that closely related MLST sequence types ST1511 (20 [39%] of 51), ST23 (13 [25%] of 51), and ST56 (seven [14%] of 51) accounted for most cases, with no evidence of serotype b strains switching capsule to Hia. Duplication of the capsule operon, associated with more severe disease, was present in 32 (80%) of 40 of these sequence types. Analysis of the core and accessory genome content grouped most isolates into a single strain.

Interpretation

The persistent increase in invasive Hia cases across England and across all age groups suggests widespread transmission, consistent with reports from other European countries, and will require close monitoring.

Funding

UK Health Security Agency.", "token_count": 482, "char_count": 1491, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8445, "entities": { "genes": [ "ST23", "ST1511", "ST56" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:18.071432", "source": { "split": "train_shard_00001", "doc_id": 2342 }, "chunk_id": "train_shard_00001_2342_1", "global_id": 8998 }, { "text": "Trends in invasive Haemophilus influenzae serotype a disease in England from 2008-09 to 2021-22: a prospective national surveillance study.", "token_count": 46, "char_count": 139, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:18.432852", "source": { "split": "train_shard_00001", "doc_id": 2342 }, "chunk_id": "train_shard_00001_2342_2", "global_id": 8999 }, { "text": "

ABSTRACT

Klebsiella aerogenes is an important pathogen in healthcare-associated infections. Nevertheless, in comparison to other clinically important pathogens, K. aerogenes population structure, genetic diversity, and pathogenicity remain poorly understood. Here, we elucidate K. aerogenes clonal complexes (CCs) and genomic features associated with resistance and virulence. We present a detailed description of the population structure of K. aerogenes based on 97 publicly available genomes by using both, multilocus sequence typing and single nucleotide polymorphisms extracted from core genome. We also assessed virulence and resistance profiles using VFDB and CARD, respectively. We show that K. aerogenes has an open pangenome and a large effective population size, which account for its high genomic diversity and support that negative selection prevents fixation of most deleterious alleles. The population is structured in at least ten CCs, including two novel ones identified here, CC9 and CC10. The repertoires of resistance genes comprise a high number of antibiotic efflux proteins as well as narrow and extended spectrum β-lactamases. Regarding the population structure, we identified two clusters based on virulence profile due to the presence of the toxin-encoding clb operon and the siderophore production genes, irp and ybt. Notably, CC3 comprises the majority of K. aerogenes isolates associated with hospital outbreaks, emphasizing the importance of its constant monitoring. Collectively, our results can be useful in the development of new therapeutic and surveillance strategies worldwide.\n\nGenomic analysis unveils important aspects of population structure, virulence, and antimicrobial resistance inKlebsiella aerogenes", "token_count": 410, "char_count": 1760, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [ "CC9", "CC3", "CC10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:19.677261", "source": { "split": "train_shard_00001", "doc_id": 2343 }, "chunk_id": "train_shard_00001_2343_0", "global_id": 9000 }, { "text": "The genome sequence assembly of the diploid and highly homozygous V. vinifera genotype PN40024 serves as the reference for many grapevine studies. Despite several improvements of the PN40024 genome assembly, its current version PN12X.v2 is quite fragmented and only represents the haploid state of the genome with mixed haplotypes. In fact, despite the PN40024 genome is nearly homozygous, it still contains various heterozygous regions. Taking the opportunity of the improvements that long-read sequencing technologies offer to fully discriminate haplotype sequences and considering that several Vitis sp. genomes have recently been assembled with these approaches, an improved version of the reference, called PN40024.v4, was generated. Through incorporating long genomic sequencing reads to the assembly, the continuity of the 12X.v2 scaffolds was highly increased. The number of scaffolds decreased from 2,059 to 640 and the number of N bases was reduced by 88%. Additionally, the full alternative haplotype sequence was built for the first time, the chromosome anchoring was improved and the amount of unplaced scaffolds were reduced by half. To obtain a high-quality gene annotation that outperforms previous versions, a liftover approach was complemented with an optimized annotation workflow for Vitis . Integration of the gene reference catalogue and its manual curation have also assisted in improving the annotation, while defining the most reliable estimation to date of 35,230 genes. Finally, we demonstrate that PN40024 resulted from selfings of cv. ‘Helfensteiner’ (cross of cv. ‘Pinot noir’ and ‘Schiava grossa’) instead of a single ‘Pinot noir’. These advances will help maintaining the PN40024 genome as a gold-standard reference also contributing in the eventual elaboration of the grapevine pangenome.\n\nAn improved reference of the grapevine genome supports reasserting the origin of the PN40024 highly-homozygous genotype", "token_count": 501, "char_count": 1942, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7943, "entities": { "genes": [ "PN40024", "PN12X" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:20.336491", "source": { "split": "train_shard_00001", "doc_id": 2344 }, "chunk_id": "train_shard_00001_2344_0", "global_id": 9001 }, { "text": "An isolate of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from soil when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain was closely related to Lysinibacillus fusiformis NRRL NRS-350T (99.7%) and Lysinibacillus sphaericus NRRL B-23268T (99.2%). In phenotypic characterization, the novel strain was found to grow between 10 and 45 °C and tolerate up to 8% (w/v) NaCl. Furthermore, the strain grew in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C15: 0 (52.3%), anteiso-C15: 0 (14.8%), C16:1ω7C alcohol (11.2%), and C16: 0 (9.5%). The cell-wall peptidoglycan contained lysine-aspartic acid, the same as congeners. A draft genome was assembled and the DNA G+C content was determined to be 37.1% (mol content). A phylogenomic analysis on the core genome of the new strain and 5 closest type strains of Lysinibacillus revealed this strain formed a distinct monophyletic clade with the nearest neighbor being Lysinibacillus fusiformis. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations (DDH) showed this species was below the species threshold of 70%. Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus pinottii sp. nov", "token_count": 513, "char_count": 1561, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6787, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:20.997267", "source": { "split": "train_shard_00001", "doc_id": 2345 }, "chunk_id": "train_shard_00001_2345_0", "global_id": 9002 }, { "text": "is proposed, with type strain PB211T (= NRRL B-65672T, = CCUG 77181T).\n\nLysinibacillus pinottii sp. nov., a novel species with anti-mosquito and anti-mollusk activity.", "token_count": 95, "char_count": 200, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9583, "quality_score": 0.9792, "entities": { "genes": [ "PB211" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:21.384874", "source": { "split": "train_shard_00001", "doc_id": 2345 }, "chunk_id": "train_shard_00001_2345_1", "global_id": 9003 }, { "text": "Salmonella Cerro has become one of the most prevalent Salmonella serotypes isolated from dairy cattle in several U.S. states, including New York where it represented 36% of all Salmonella isolates of bovine origin in 2015. This serotype is commonly isolated from dairy cattle with clinical signs of salmonellosis, including diarrhea and fever, although it has also been identified in herds without evidence of clinical disease or decreased production. To better understand the transmission patterns and drivers of its geographic spread, we have studied the genomic similarity and microevolution of S. Cerro isolates from the northeast U.S. and Texas. Eighty-three out of 86 isolates were confirmed as multilocus sequence type 367. We identified core genome SNPs in 57 upstate New York (NY), 2 Pennsylvania (PA), and 27 Texas S. Cerro isolates from dairy cattle, farm environments, raw milk, and one human clinical case and used them to construct a tip-dated phylogeny. S. Cerro isolates clustered in three distinct clades, including (i) clade I (n = 3; 2013) comprising isolates from northwest Texas (NTX), (ii) clade II (n = 14; 2009-2011, 2014) comprising isolates from NY, and (iii) clade III comprising isolates from NY, PA, and central Texas (CTX) in subclade IIIa (n = 45; 2008-2014), and only CTX isolates in subclade IIIb (n = 24; 2013). Temporal phylogenetic analysis estimated the divergence of these three clades from the most recent common ancestor in approximately 1980. The CTX clade IIIb was estimated to have evolved and diverged from the NY ancestor around 2004", "token_count": 510, "char_count": 1648, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:22.021518", "source": { "split": "train_shard_00001", "doc_id": 2346 }, "chunk_id": "train_shard_00001_2346_0", "global_id": 9004 }, { "text": "Furthermore, gradual temporal loss of genes encoding a D-alanine transporter, involved in virulence, was observed. These genes were present in the isolates endemic to NTX clade I and were gradually lost in clades II and III. The virulence gene orgA, which is part of the Salmonella Pathogenicity Island 1, was lost in a subgroup of Texas isolates in clades I and IIIb. All S. Cerro isolates had an additional cytosine inserted in a cytosine-rich region of the virulence gene sopA, resulting in premature termination of translation likely responsible for loss of pathogenic capacity in humans. A group of closely related NY isolates was characterized by the loss of hydrogen sulfide production due to the truncation or complete loss of phsA. Our data suggest the ability of Salmonella to rapidly diverge and adapt to specific niches (e.g., bovine niche), and to modify virulence-related characteristics such as the ability to utilize tetrathionate as an alternative electron acceptor, which is commonly used to detect Salmonella. Overall, our results show that clinical outcome data and genetic data for S. Cerro isolates, such as truncations in virulence genes leading to novel pheno- and pathotypes, should be correlated to allow for accurate risk assessment.\n\nTemporal Genomic Phylogeny Reconstruction Indicates a Geospatial Transmission Path of Salmonella Cerro in the United States and a Clade-Specific Loss of Hydrogen Sulfide Production.", "token_count": 398, "char_count": 1506, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6126, "quality_score": 0.8063, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:22.644226", "source": { "split": "train_shard_00001", "doc_id": 2346 }, "chunk_id": "train_shard_00001_2346_1", "global_id": 9005 }, { "text": "Infection caused by KPC and NDM carbapenemases co-producing Klebsiella pneumoniae (KPC_NDM_CRKP) poses serious public health concerns. Here, we elucidate the prevalence of a hypertransmissible lncM1 plasmid, pKPC_NDM, co-carrying blaKPC-2 and blaNDM-1 genes in sequence type 1049 K_locus 5 (ST1049-KL5) KPC_NDM_CRKP isolates. Genetic and clonal relatedness analyses using pulsed-field gel electrophoresis, single nucleotide polymorphism analysis and core genome multilocus sequence typing suggested clonal dissemination of ST1049-KL5 KPC_NDM_CRKP strains in our hospital. Whole genome sequencing identified an identical 76,517 bp- blaKPC-2 and blaNDM-1 genes co-carrying IncM1 plasmid pKPC_NDM and a pLVPK-like hypervirulent plasmid in all ST1049-KL5 KPC_NDM_CRKP isolates. pKPC_NDM shared 100% identity with a previously sequenced plasmid CRKP35_unnamed4, demonstrating high transferability in conjugation assay, with conjugation frequencies reaching 10-4 and 10-5 in Escherichia coli and K. pneumoniae recipients, respectively. It also maintained favorable stability and flexible compatibility, with retention rates exceeding 80% after 10 days of continuous passage, and could be compatible with pre-existing blaKPC- or blaNDM-carrying plasmids in recipient strains. This study summarizes the characteristics of KPC_NDM_CRKP outbreaks and highlights the importance of ongoing surveillance and infection control strategies to address the challenges posed by ST1049 K", "token_count": 513, "char_count": 1555, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7473, "quality_score": 0.8737, "entities": { "genes": [ "KL5", "ST1049" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:23.321031", "source": { "split": "train_shard_00001", "doc_id": 2347 }, "chunk_id": "train_shard_00001_2347_0", "global_id": 9006 }, { "text": "pneumoniae strains.\n\nPrevalence of ST1049-KL5 carbapenem-resistant Klebsiella pneumoniae with a blaKPC-2 and blaNDM-1 co-carrying hypertransmissible IncM1 plasmid.", "token_count": 79, "char_count": 185, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [ "KL5", "ST1049" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:23.696720", "source": { "split": "train_shard_00001", "doc_id": 2347 }, "chunk_id": "train_shard_00001_2347_1", "global_id": 9007 }, { "text": "Arachis hypogaea (peanut) is a leading oil and protein-providing crop with a major food source in many countries. It is mostly grown in tropical regions and is largely affected by abiotic and biotic stresses. Cysteine-rich receptor-like kinases (CRKs) is a family of transmembrane proteins that play important roles in regulating stress-signaling and defense mechanisms, enabling plants to tolerate stress conditions. However, almost no information is available regarding this gene family in Arachis hypogaea and its progenitors. This study conducts a pangenome-wide investigation of A. hypogaea and its two progenitors, A. duranensis and A. ipaensis CRK genes (AhCRKs, AdCRKs, and AiCRKs). The gene structure, conserved motif patterns, phylogenetic history, chromosomal distribution, and duplication were studied in detail, showing the intraspecies structural conservation and evolutionary patterns. Promoter cis-elements, protein-protein interactions, GO enrichment, and miRNA targets were also predicted, showing their potential functional conservation. Their expression in salt and drought stresses was also comprehensively studied. The CRKs identified were divided into three groups, phylogenetically. The expansion of this gene family in peanuts was caused by both types of duplication: tandem and segmental. Furthermore, positive as well as negative selection pressure directed the duplication process. The peanut CRK genes were also enriched in hormones, light, development, and stress-related elements. MicroRNA (miRNA) also targeted the AhCRK genes, which suggests the regulatory association of miRNAs in the expression of these genes. Transcriptome datasets showed that AhCRKs have varying expression levels under different abiotic stress conditions. Furthermore, the multi-stress responsiveness of the AhCRK genes was evaluated using a machine learning-based method, Random Forest (RF) classifier", "token_count": 523, "char_count": 1999, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6899, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:24.381137", "source": { "split": "train_shard_00001", "doc_id": 2348 }, "chunk_id": "train_shard_00001_2348_0", "global_id": 9008 }, { "text": "The 3D structures of AhCRKs were also predicted. Our study can be utilized in developing a detailed understanding of the stress regulatory mechanisms of the CRK gene family in peanuts and its further studies to improve the genetic makeup of peanuts to thrive better under stress conditions.\n\nIntegrated omics and machine learning-assisted profiling of cysteine-rich-receptor-like kinases from three peanut spp. revealed their role in multiple stresses.", "token_count": 121, "char_count": 473, "word_count": 66, "semantic_coherence": 1, "information_density": 0.803, "quality_score": 0.9015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:24.784783", "source": { "split": "train_shard_00001", "doc_id": 2348 }, "chunk_id": "train_shard_00001_2348_1", "global_id": 9009 }, { "text": "This study aimed to understand the epidemiological characteristics of Salmonella in Tibetan pigs. We isolated, identified, and examined via antimicrobial susceptibility testing on Salmonella from Tibetan pigs breeder farms and slaughterhouses in Tibet, China. A genetic evolutionary tree was constructed on the basis of whole genome sequencing (WGS). A total of 81 Salmonella isolates were isolated from 987 samples. The main serovars were Salmonella Typhimurium and Salmonella London in Tibetan pigs. The isolated Salmonella Typhimurium isolates subjected to antimicrobial susceptibility testing showed varying degrees of resistance to β-lactams, aminoglycosides, fluoroquinolones, sulfonamides, tetracyclines, and amphenicols. WGS analysis was performed on 20 Salmonella Typhimurium isolates in Tibet (n = 10), Jiangsu (n = 10), and 205 genome sequences downloaded from the Enterobase database to reveal their epidemiological and genetic characteristics. They were divided into two clusters based on core genome single-nucleotide polymorphisms: Cluster A with 112 isolates from Tibet and other regions in China and Cluster B with 113 isolates from Jiangsu and other regions. The isolates in Cluster A were further divided into two subclusters: A-1 with 40 isolates including Tibet and A-2 with 72 isolates from other regions. Virulence factors analysis revealed that all isolates from Tibet carried adeG, but this observation was not as common in Salmonella isolates from Jiangsu and other regions of China", "token_count": 456, "char_count": 1585, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5417, "quality_score": 0.7708, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:25.431244", "source": { "split": "train_shard_00001", "doc_id": 2349 }, "chunk_id": "train_shard_00001_2349_0", "global_id": 9010 }, { "text": "Antibiotic resistance genes (ARGs) analysis showed that all isolates from Tibet carried blaTEM-55 and rmtB, which were absent in Salmonella isolates from Jiangsu and other regions of China. Genetic characteristic analysis and biofilm determination indicated that the biofilm formation capabilities of the isolates from Tibet were stronger than those of the isolates from Jiangsu and other regions of China. Our research revealed the epidemic patterns and genomic characteristics of Salmonella in Tibetan pigs and provided theoretical guidance for the prevention and control of local salmonellosis.\n\nPrevalence and Characteristics of Salmonella from Tibetan Pigs in Tibet, China.", "token_count": 181, "char_count": 724, "word_count": 96, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:25.873056", "source": { "split": "train_shard_00001", "doc_id": 2349 }, "chunk_id": "train_shard_00001_2349_1", "global_id": 9011 }, { "text": "

Background

Oenococcus oeni is a lactic acid bacteria species adapted to the low pH, ethanol-rich environments of wine and cider fermentation, where it performs the crucial role of malolactic fermentation. It has a small genome and has lost the mutS-mutL DNA mismatch repair genes, making it a hypermutable and highly specialized species. Two main lineages of strains, named groups A and B, have been described to date, as well as other subgroups correlated to different types of wines or regions. A third group \"C\" has also been hypothesized based on sequence analysis, but it remains controversial. In this study we have elucidated the species population structure by sequencing 14 genomes of new strains isolated from cider and kombucha and performing comparative genomics analyses.

Results

Sequence-based phylogenetic trees confirmed a population structure of 4 clades: The previously identified A and B, a third group \"C\" consisting of the new cider strains and a small subgroup of wine strains previously attributed to group B, and a fourth group \"D\" exclusively represented by kombucha strains. A pair of complete genomes from group C and D were compared to the circularized O. oeni PSU-1 strain reference genome and no genomic rearrangements were found. Phylogenetic trees, K-means clustering and pangenome gene clusters evidenced the existence of smaller, specialized subgroups of strains. Using the pangenome, genomic differences in stress resistance and biosynthetic pathways were found to uniquely distinguish the C and D clades.

Conclusions

The obtained results, including the additional cider and kombucha strains, firmly established the O. oeni population structure. Group C does not appear as fully domesticated as group A to wine, but showed several unique patterns which may be due to ongoing specialization to the cider environment. Group D was shown to be the most divergent member of O. oeni to date, appearing as the closest to a pre-domestication state of the species.", "token_count": 486, "char_count": 2012, "word_count": 305, "semantic_coherence": 1, "information_density": 0.5803, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:26.513707", "source": { "split": "train_shard_00001", "doc_id": 2350 }, "chunk_id": "train_shard_00001_2350_0", "global_id": 9012 }, { "text": "Expanding the biodiversity of Oenococcus oeni through comparative genomics of apple cider and kombucha strains.", "token_count": 33, "char_count": 111, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:26.868817", "source": { "split": "train_shard_00001", "doc_id": 2350 }, "chunk_id": "train_shard_00001_2350_1", "global_id": 9013 }, { "text": "To evaluate the effects of temperature and relative humidity (RH) on microbial and biochemical ripening kinetics, Camembert-type cheeses were prepared from pasteurized milk seeded with Kluyveromyces marxianus, Geotrichum candidum, Penicillium camemberti, and Brevibacterium aurantiacum. Microorganism growth and biochemical changes were studied under different ripening temperatures (8, 12, and 16°C) and RH (88, 92, and 98%). The central point runs (12°C, 92% RH) were both reproducible and repeatable, and for each microbial and biochemical parameter, 2 kinetic descriptors were defined. Temperature had significant effects on the growth of both K. marxianus and G. candidum, whereas RH did not affect it. Regardless of the temperature, at 98% RH the specific growth rate of P. camemberti spores was significantly higher [between 2 (8°C) and 106 times (16°C) higher]. However, at 16°C, the appearance of the rind was no longer suitable because mycelia were damaged. Brevibacterium aurantiacum growth depended on both temperature and RH. At 8°C under 88% RH, its growth was restricted (1.3 × 10(7) cfu/g), whereas at 16°C and 98% RH, its growth was favored, reaching 7.9 × 10(9) cfu/g, but the rind had a dark brown color after d 20. Temperature had a significant effect on carbon substrate consumption rates in the core as well as in the rind. In the rind, when temperature was 16°C rather than 8°C, the lactate consumption rate was approximately 2.9 times higher under 88% RH. Whatever the RH, temperature significantly affected the increase in rind pH (from 4.6 to 7.7 ± 0.2)", "token_count": 494, "char_count": 1579, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6194, "quality_score": 0.8097, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:27.880627", "source": { "split": "train_shard_00001", "doc_id": 2351 }, "chunk_id": "train_shard_00001_2351_0", "global_id": 9014 }, { "text": "At 8°C, an increase in rind pH was observed between d 6 and 9, whereas at 16°C, it was between d 2 and 3. Temperature and RH affected the increasing rate of the underrind thickness: at 16°C, half of the cheese thickness appeared ripened on d 14 (wrapping day). However, at 98% RH, the underrind was runny. In conclusion, some descriptors, such as yeast growth and the pH in the rind, depended solely on temperature. However, our findings highlight the fact that the interactions between temperature and RH played a role in P. camemberti sporulation, B. aurantiacum growth, carbon substrate consumption rates, and the thickening of the cheese underrind. Moreover, the best ripening conditions to achieve an optimum between microorganism growth and biochemical kinetics were 13°C and 94% RH.\n\nTemperature and relative humidity influence the microbial and physicochemical characteristics of Camembert-type cheese ripening.", "token_count": 252, "char_count": 919, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6643, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:28.369279", "source": { "split": "train_shard_00001", "doc_id": 2351 }, "chunk_id": "train_shard_00001_2351_1", "global_id": 9015 }, { "text": "Metagenomic surveys have revealed that natural microbial communities are predominantly composed of sequence-discrete, species-like populations but the genetic and/or ecological mechanisms that maintain such populations remain speculative, limiting our understanding of population speciation and adaptation to environmental perturbations. To address this knowledge gap, we sequenced 112 Salinibacter ruber isolates and 12 companion metagenomes recovered from four adjacent saltern ponds in Mallorca, Spain that were experimentally manipulated to dramatically alter salinity and light intensity, the two major drivers of these ecosystems. Our analyses showed that the pangenome of the local Sal. ruber population is open and similar in size (∼15,000 genes) to that of randomly sampled Escherichia coli genomes. While most of the accessory (non-core) genes showed low in situ coverage based on the metagenomes compared to the core genes, indicating that they were functionally unimportant and/or ephemeral, 3.49% of them became abundant when salinity (but not light intensity) conditions changed and encoded for functions related to osmoregulation. Nonetheless, the ecological advantage of these genes, while significant, was apparently not strong enough to purge diversity within the population. Collectively, our results revealed a possible mechanism for how this immense gene diversity is maintained, which has implications for the prokaryotic species concept.

Significance Statement

The pangenomes of bacterial species, i.e., the number of non-redundant genes carried by members of the species, can be enormous based on the genome sequencing of isolates from various sites around the globe and different years. However, to what extent this pattern of gene diversity applies to natural bacterial populations, i.e., strains co-occurring in the same site, and the value of this diversity for population adaptation during environmental transition remains unclear. This study showed that while the pangenome of a natural population can be similarly large, only a small fraction of the pangenome appears to be functionally important when conditions change. Taken together, these results provided quantitative insights into the extent and functional significance of the accessory pangenome of a natural, species-like population.\n\nToward quantifying the adaptive role of bacterial pangenomes during environmental perturbations", "token_count": 512, "char_count": 2428, "word_count": 336, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:29.025759", "source": { "split": "train_shard_00001", "doc_id": 2352 }, "chunk_id": "train_shard_00001_2352_0", "global_id": 9016 }, { "text": "Phages and plasmids play important roles in bacterial evolution and diversification. Although many draft genomes have been generated, phage and plasmid genomes are usually fragmented, limiting our understanding of their dynamics. Here, we performed a systematic analysis of 239 draft genomes and 7 complete genomes of Shiga toxin (Stx)-producing Escherichia coli O145:H28, the major virulence factors of which are encoded by prophages (PPs) or plasmids. The results indicated that PPs are more stably maintained than plasmids. A set of ancestrally acquired PPs was well conserved, while various PPs, including Stx phages, were acquired by multiple sublineages. In contrast, gains and losses of a wide range of plasmids have frequently occurred across the O145:H28 lineage, and only the virulence plasmid was well conserved. The different dynamics of PPs and plasmids have differentially impacted the pangenome of O145:H28, with high proportions of PP- and plasmid-associated genes in the variably present and rare gene fractions, respectively. The dynamics of PPs and plasmids have also strongly impacted virulence gene repertoires, such as the highly variable distribution of stx genes and the high conservation of a set of type III secretion effectors, which probably represents the core effectors of O145:H28 and the genes on the virulence plasmid in the entire O145:H28 population. These results provide detailed insights into the dynamics of PPs and plasmids, and show the application of genomic analyses using a large set of draft genomes and appropriately selected complete genomes.\n\nDifferential dynamics and impacts of prophages and plasmids on the pangenome and virulence factor repertoires of Shiga toxin-producing Escherichia coli O145:H28.", "token_count": 470, "char_count": 1773, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:29.670102", "source": { "split": "train_shard_00001", "doc_id": 2353 }, "chunk_id": "train_shard_00001_2353_0", "global_id": 9017 }, { "text": "Yersinia enterocolitica is a significant foodborne pathogen causing gastrointestinal illnesses worldwide. This study investigates the prevalence and genomic characteristics of Y. enterocolitica to assess potential health risks in southeastern China, a region lacking mandatory yersiniosis monitoring. From 2939 samples collected between 2008 and 2022, 105 isolates were recovered. The highest prevalence was found in rodents (8.1%), followed by retail meats (7.1%), other foods (3.7%), and human clinical cases (0.8%). In addition to meats and rodents, ready-to-eat salads, seafood, and frozen food products were identified as potential transmission vehicles. Various bioserotypes and sequence types (STs) was identified, including twelve previously unreported STs. Biotype 1A, exhibiting greater genetic diversity than more pathogenic biotypes (3 and 4), was frequently found in human clinical cases. Phylogenetic analysis revealed two main lineages, with isolates primarily clustered by biotype and pathogenic traits. Antimicrobial susceptibility testing revealed 46.7% (49/105) of isolates were multidrug resistant (MDR), with frequent resistance to polymyxin B (100%), azithromycin (50.5%), and sulfanilamide isoxazole (31.4%). These findings highlight the ecological complexity and diversity of Y. enterocolitica, especially non-pathogenic biotype 1A strains, and underscore the need for enhanced food safety and antimicrobial stewardship to mitigate the public health impact of Y. enterocolitica infections. KEY POINTS: Biotype 1 A strains exhibited greater genetic diversity than pathogenic biotypes. Pathogenic strains were mainly associated with lineage HC1490_2, not HC1490_10. Higher MDR levels were observed in biotype 3 and 4 strains.", "token_count": 482, "char_count": 1747, "word_count": 232, "semantic_coherence": 1, "information_density": 0.7155, "quality_score": 0.8578, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:30.319695", "source": { "split": "train_shard_00001", "doc_id": 2354 }, "chunk_id": "train_shard_00001_2354_0", "global_id": 9018 }, { "text": "Prevalence and genomic insights into Yersinia enterocolitica in Southeastern China (2008-2022).", "token_count": 32, "char_count": 95, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:30.674037", "source": { "split": "train_shard_00001", "doc_id": 2354 }, "chunk_id": "train_shard_00001_2354_1", "global_id": 9019 }, { "text": "

Background

Non-hypermucoviscous carbapenem-resistant Klebsiella pneumoniae with enhanced virulence lacking hvKP-specific virulence factors is uncommon, and the virulence mechanisms of this organism are not understood.

Methods

Following a retrospective study of carbapenem-resistant K. pneumoniae based on core genome multilocus sequence typing (cgMLST), isolates that caused high mortality were investigated with a genome-wide association study (GWAS), proteome analysis and an animal model.

Results

The subclone of sequence type 11 (ST11) K. pneumoniae, which belongs to complex type 3176 (CT3176) and K-locus 47 (KL47), was highlighted due to the high mortality of infected patients. GWAS analysis showed that transcriptional regulatory gene ampR was associated with the CT3176 isolates. In a mouse model, the mortality, bacterial load and pathological changes of mice infected with ampR-carrying isolates were distinct from those infected with ampR-null isolates. The ampR gene that enhances the virulence of the non-hypermucoviscous KL47 strain was unable to enhance the virulence of hypermucoviscous KL1 strain. Proteome analysis showed that the expression of WcaJ in the ampR + isolates was significantly higher than that in the ampR - isolates. Quantification of capsular polysaccharide confirmed that more capsule polysaccharide was produced by ampR+ and ampR-complementary strains compared to ampR- strains", "token_count": 491, "char_count": 1565, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6263, "quality_score": 0.8132, "entities": { "genes": [ "KL1", "CT3176", "KL47", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:31.322310", "source": { "split": "train_shard_00001", "doc_id": 2355 }, "chunk_id": "train_shard_00001_2355_0", "global_id": 9020 }, { "text": "It is suggested that the enhancement of the initial stage of capsule synthesis may be the cause of the enhanced virulence of these non-hypermucoviscous ST11 carbapenem-resistant K. pneumoniae isolates.

Conclusion

Non-hypermucoviscous ST11 carbapenem-resistant K. pneumoniae with enhanced virulence warrants continued surveillance and investigation.\n\nAmpR Increases the Virulence of Carbapenem-Resistant Klebsiella pneumoniae by Regulating the Initial Step of Capsule Synthesis.", "token_count": 161, "char_count": 505, "word_count": 57, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:31.757763", "source": { "split": "train_shard_00001", "doc_id": 2355 }, "chunk_id": "train_shard_00001_2355_1", "global_id": 9021 }, { "text": "High-quality sequence assembly is the ultimate representation of complete genetic information of an individual. Several ongoing pangenome projects are producing collections of high-quality assemblies of various species. Here, we show how to represent the sequenced genomes in 2–3 orders of magnitude smaller space, allowing easy and fast extraction of any contig or its part.\n\nAGC: Compact representation of assembled genomes", "token_count": 86, "char_count": 425, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:32.131103", "source": { "split": "train_shard_00001", "doc_id": 2356 }, "chunk_id": "train_shard_00001_2356_0", "global_id": 9022 }, { "text": "In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.\n\nA strategy for building and using a human reference pangenome", "token_count": 200, "char_count": 1012, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6779, "quality_score": 0.8389, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:32.601956", "source": { "split": "train_shard_00001", "doc_id": 2357 }, "chunk_id": "train_shard_00001_2357_0", "global_id": 9023 }, { "text": "

Background

Glässer's disease, caused by Haemophilus parasuis (HPS), is responsible for economic losses in the pig industry worldwide. However, the existing commercial vaccines offer poor protection and there are significant barriers to the development of effective vaccines.

Methods

In the current study, we aimed to identify potential vaccine candidates and design a multi-epitope vaccine against HPS by performing pan-genomic analysis of 121 strains and using a reverse vaccinology approach.

Results

The designed vaccine constructs consist of predicted epitopes of B and T cells derived from the outer membrane proteins of the HPS core genome. The vaccine was found to be highly immunogenic, non-toxic, and non-allergenic as well as have stable physicochemical properties. It has a high binding affinity to Toll-like receptor 2. In addition, in silico immune simulation results showed that the vaccine elicited an effective immune response. Moreover, the mouse polyclonal antibody obtained by immunizing the vaccine protein can be combined with different serotypes and non-typable Haemophilus parasuis in vitro.

Conclusion

The overall results of the study suggest that the designed multi-epitope vaccine is a promising candidate for pan-prophylaxis against different strains of HPS.\n\nDesign of a multi-epitope vaccine against Haemophilus parasuis based on pan-genome and immunoinformatics approaches.", "token_count": 373, "char_count": 1459, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6771, "quality_score": 0.8385, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:33.179389", "source": { "split": "train_shard_00001", "doc_id": 2358 }, "chunk_id": "train_shard_00001_2358_0", "global_id": 9024 }, { "text": "Erythrobacter species are extensively studied marine bacteria that produce various carotenoids. Due to their photoheterotrophic ability, it has been suggested that they play a crucial role in marine ecosystems. It is essential to identify the genome sequence and the genes of the species to predict their role in the marine ecosystem. In this study, we report the complete genome sequence of the marine bacterium Erythrobacter sp. 3-20A1M. The genome size was 3.1 Mbp and its GC content was 64.8%. In total, 2998 genetic features were annotated, of which 2882 were annotated as functional coding genes. Using the genetic information of Erythrobacter sp. 3-20A1M, we performed pangenome analysis with other Erythrobacter species. This revealed highly conserved secondary metabolite biosynthesis-related COG functions across Erythrobacter species. Through subsequent secondary metabolite biosynthetic gene cluster prediction and KEGG analysis, the carotenoid biosynthetic pathway was proven conserved in all Erythrobacter species, except for the spheroidene and spirilloxanthin pathways, which are only found in photosynthetic Erythrobacter species. The presence of virulence genes, especially the plant-algae cell wall degrading genes, revealed that Erythrobacter sp. 3-20A1M is a potential marine plant-algae scavenger.\n\nAssessment of Erythrobacter Species Diversity through Pan-Genome Analysis with Newly Isolated Erythrobacter sp. 3-20A1M.", "token_count": 450, "char_count": 1511, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6193, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:33.815506", "source": { "split": "train_shard_00001", "doc_id": 2359 }, "chunk_id": "train_shard_00001_2359_0", "global_id": 9025 }, { "text": "

ABSTRACT

Genetic variation is the driving force of plant-pathogen co-evolution. Large-scale genetic variations such as structural variations (SVs) often alter genome stability and organismal fitness. However, the pangenomic landscape and functional implications of SVs remain largely unexplored in plant pathogens. Here, we characterized the pangenomic and SV landscape in wheat head blight fungus Fusarium graminearum by producing and comparing chromosome-level (average contig N50 of 8.9 Mb) genome assemblies of 98 accessions using a reference-guided approach. Accounting for 29.05% and 19.01% of F. graminearum pangenome, respectively, accessory and private genomes are enriched with functions related to membrane trafficking, metabolism of fatty acids and tryptophans, with the private also enriched with putative effectors. Furthermore, using chromosome-level assemblies, we detected 52,420 SVs, 69.51% of which are inaccessible using read-mapping based approach. Over a half (55.65%) of 52,645 merged SVs affected 1,660 protein-coding genes, the most variable of which are involved in fungal virulence, cellular contact and communications. Interestingly, highly variable effectors and secondary metabolic enzymes are co-localized with SVs at subtelomeric and centromeric regions. Collectively, this landmark study shows the prevalence and functional relevance of SVs in F. graminearum , providing a valuable resource for future pangenomic studies in this cosmopolitan pathogen of cereal crops.\n\nStructural variants contribute to pangenome evolution of a plant pathogenic fungus", "token_count": 427, "char_count": 1593, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:34.448118", "source": { "split": "train_shard_00001", "doc_id": 2360 }, "chunk_id": "train_shard_00001_2360_0", "global_id": 9026 }, { "text": "We present a new method and software tool called rowbowt that applies a pangenome index to the problem of inferring genotypes from short-read sequencing data. The method uses a novel indexing structure called the marker array. Using the marker array, we can genotype variants with respect from large panels like the 1000 Genomes Project while avoiding the reference bias that results when aligning to a single linear reference. rowbowt can infer accurate genotypes in less time and memory compared to existing graph-based methods. The method is implemented in the open source software tool rowbowt available at https://github.com/alshai/rowbowt .\n\nPangenomic genotyping with the marker array", "token_count": 155, "char_count": 691, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7115, "quality_score": 0.8558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:34.918187", "source": { "split": "train_shard_00001", "doc_id": 2361 }, "chunk_id": "train_shard_00001_2361_0", "global_id": 9027 }, { "text": "

Background

The 2022 outbreak of mpox (formerly known as monkeypox) led to the spread of monkeypox virus (MPXV) in over 110 countries, demanding effective disease management and surveillance. As current diagnostics rely largely on centralised laboratory testing, our objective was to develop a simple rapid point-of-care assay to detect MPXV in clinical samples using isothermal amplification coupled with CRISPR and CRISPR-associated protein (Cas) technology.

Methods

In this proof-of-concept study, we developed a portable isothermal amplification CRISPR-Cas12a-based assay for the detection of MPXV. We designed a panel of 22 primer-guide RNA sets using pangenome and gene-agnostic approaches, and subsequently shortlisted the three sets producing the strongest signals for evaluation of analytical sensitivity and specificity using a fluorescence-based readout. The set displaying 100% specificity and the lowest limit of detection (LOD) was selected for further assay validation using both a fluorescence-based and lateral-flow readout. Assay specificity was confirmed using a panel of viral and bacterial pathogens. Finally, we did a blind concordance study on genomic DNA extracted from 185 clinical samples, comparing assay results with a gold-standard quantitative PCR (qPCR) assay. We identified the optimal time to detection and analysed the performance of the assay relative to qPCR using receiver operating characteristic (ROC) curves. We also assessed the compatibility with lateral-flow strips, both visually and computationally, where strips were interpreted blinded to the fluorescence results on the basis of the presence or absence of test bands.

Findings

With an optimal run duration of approximately 45 min from isothermal amplification to CRISPR-assay readout, the MPXV recombinase polymerase amplification CRISPR-Cas12a-based assay with the selected primer-guide set had an LOD of 1 copy per μL and 100% specificity against tested viral pathogens", "token_count": 506, "char_count": 1990, "word_count": 272, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:35.590480", "source": { "split": "train_shard_00001", "doc_id": 2362 }, "chunk_id": "train_shard_00001_2362_0", "global_id": 9028 }, { "text": "Blinded concordance testing of 185 clinical samples resulted in 100% sensitivity (95% CI 89·3-100) and 99·3% specificity (95% CI 95·7-100) using the fluorescence readout. For optimal time to detection by fluorescence readout, we estimated the areas under the ROC curve to be 0·98 at 2 min and 0·99 at 4 min. Lateral-flow strips had 100% sensitivity (89·3-100) and 98·6% specificity (94·7-100) with both visual and computational assessment. Overall, lateral-flow results were highly concordant with fluorescence-based readouts (179 of 185 tests, 96·8% concordant), with discrepancies associated with low viral load samples.

Interpretation

Our assay for the diagnosis of mpox displayed good performance characteristics compared with qPCR. Although optimisation of the assay will be required before deployment, its usability and versatility present a potential solution to MPXV detection in low-resource and remote settings, as well as a means of community-based, on-site testing.

Funding

Victorian Medical Research Accelerator Fund and the Australian Government Department of Health.\n\nRapid detection of monkeypox virus using a CRISPR-Cas12a mediated assay: a laboratory validation and evaluation study.", "token_count": 364, "char_count": 1215, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:36.234844", "source": { "split": "train_shard_00001", "doc_id": 2362 }, "chunk_id": "train_shard_00001_2362_1", "global_id": 9029 }, { "text": "

Background

Klebsiella pneumoniae ST101 is an emerging high-risk clone which exhibits extensive drug resistance. Bacterial strains residing in multiple hosts show unique signatures related to host adaptation. In this study, we assess the genetic relationship of K. pneumoniae ST101 isolated from hospital samples, the environment, community, and livestock using whole genome sequencing (WGS).

Materials and methods

We selected ten K. pneumoniae ST101 strains from hospitalized patients in Italy (n = 3) (2014) and Spain (n = 5) (2015-2016) as well as Belgian livestock animals (n = 2) (2017-2018). WGS was performed with 2 × 250 bp paired-end sequencing (Nextera XT) sample preparation kit and MiSeq (Illumina Inc.). Long-read sequencing (Pacbio Sequel I) was used to sequence the two livestock strains and three Italian hospital-associated strains. Furthermore, a public ST101 sequence collection of 586 strains (566 hospital-associated strains, 12 environmental strains, six strains from healthy individuals, one food-associated strain and one pig strain) was obtained. BacPipe and Kleborate were used to conduct genome analysis. ISFinder was used to find IS elements, and PHASTER was utilized to identify prophages. A phylogenetic tree was constructed to illustrate genetic relatedness.

Results

Hospital-associated K. pneumoniae ST101 showed higher resistance scores than non-clinical isolates from healthy individuals, the environment, food and livestock (1.85 ± 0.72 in hospital-associated isolates vs. 1.14 ± 1.13 in non-clinical isolates, p < 0.01)", "token_count": 514, "char_count": 1632, "word_count": 217, "semantic_coherence": 1, "information_density": 0.682, "quality_score": 0.841, "entities": { "genes": [ "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:36.931182", "source": { "split": "train_shard_00001", "doc_id": 2363 }, "chunk_id": "train_shard_00001_2363_0", "global_id": 9030 }, { "text": "Importantly, the lack of integrative conjugative elements ICEKp bearing iron-scavenging yersiniabactin siderophores (ybt) in livestock-associated strains suggests a lower pathogenicity potential than hospital-associated strains. Mobile genetic elements (MGE) appear to be an important source of diversity in K. pneumoniae ST101 strains from different origins, with a highly stable genome and few recombination events outside the prophage-containing regions. Core genome MLST based analysis revealed a distinct genetic clustering between human and livestock-associated isolates.

Conclusion

The study of K. pneumoniae ST101 hospital-associated and strains from healthy individuals and animals revealed a genetic diversity between these two groups, allowing us to identify the presence of yersiniabactin siderophores in hospital-associated isolates. Resistance and virulence levels in livestock-associated strains were considerably lower than hospital-associated strains, implying that the public health risk remains low. The introduction of an ICEKp into animal strains, on the other hand, might pose a public threat over time.\n\nDiversity in the Characteristics of Klebsiella pneumoniae ST101 of Human, Environmental, and Animal Origin.", "token_count": 341, "char_count": 1283, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [ "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:37.497513", "source": { "split": "train_shard_00001", "doc_id": 2363 }, "chunk_id": "train_shard_00001_2363_1", "global_id": 9031 }, { "text": "

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. The study aimed to identify the antimicrobial resistance and accessory genes, the clonal relatedness, and the evolutionary dynamics of selected CRKP isolates recovered in an adult and pediatric intensive care unit of a tertiary hospital in Greece.

Methods

Twenty-four CRKP isolates recovered during 2018-2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST, and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed using various bioinformatics software.

Results

The isolates belonged to eight sequence types: 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM, and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16, and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323, and ST39 were classified into distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs.

Conclusions

The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates.", "token_count": 513, "char_count": 1683, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [ "ST15", "ST39", "ST323", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:38.146125", "source": { "split": "train_shard_00001", "doc_id": 2364 }, "chunk_id": "train_shard_00001_2364_0", "global_id": 9032 }, { "text": "Genetic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates in a Tertiary Hospital in Greece, 2018-2022.", "token_count": 54, "char_count": 140, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:38.502033", "source": { "split": "train_shard_00001", "doc_id": 2364 }, "chunk_id": "train_shard_00001_2364_1", "global_id": 9033 }, { "text": "The Pseudomonas aeruginosa genome (G + C content 65-67%, size 5.5-7 Mbp) is made up of a single circular chromosome and a variable number of plasmids. Sequencing of complete genomes or blocks of the accessory genome has revealed that the genome encodes a large repertoire of transporters, transcriptional regulators, and two-component regulatory systems which reflects its metabolic diversity to utilize a broad range of nutrients. The conserved core component of the genome is largely collinear among P. aeruginosa strains and exhibits an interclonal sequence diversity of 0.5-0.7%. Only a few loci of the core genome are subject to diversifying selection. Genome diversity is mainly caused by accessory DNA elements located in 79 regions of genome plasticity that are scattered around the genome and show an anomalous usage of mono- to tetradecanucleotides. Genomic islands of the pKLC102/PAGI-2 family that integrate into tRNA(Lys) or tRNA(Gly) genes represent hotspots of inter- and intraclonal genomic diversity. The individual islands differ in their repertoire of metabolic genes that make a large contribution to the pangenome. In order to unravel intraclonal diversity of P. aeruginosa, the genomes of two members of the PA14 clonal complex from diverse habitats and geographic origin were compared. The genome sequences differed by less than 0.01% from each other. One hundred ninety-eight of the 231 single nucleotide substitutions (SNPs) were non-randomly distributed in the genome. Non-synonymous SNPs were mainly found in an integrated Pf1-like phage and in genes involved in transcriptional regulation, membrane and extracellular constituents, transport, and secretion. In summary, P. aeruginosa is endowed with a highly conserved core genome of low sequence diversity and a highly variable accessory genome that communicates with other pseudomonads and genera via horizontal gene transfer.\n\nPseudomonas aeruginosa Genomic Structure and Diversity.", "token_count": 511, "char_count": 1962, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5854, "quality_score": 0.7927, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:39.125207", "source": { "split": "train_shard_00001", "doc_id": 2365 }, "chunk_id": "train_shard_00001_2365_0", "global_id": 9034 }, { "text": "

ABSTRACT

Implementation of identical biodesign strategies into different species often results in different performance, a process called the “chassis effect”. Our current understanding of how cellular host context underpins its ability to be engineered is lacking and closing this knowledge gap will greatly improve the rational design of microorganisms. Here, we combined global differential gene expression analysis and pangenomics to uncover how genome structure and function relates to the observed chassis effect of an engineered genetic inverter device operating in six closely related Stutzerimonas hosts. The differential expression of the core genome, gene clusters shared between all hosts, was found to be the main source of significant concordance to the observed device performance, whereas specialty genes from respective accessory genomes were not significant. A data-driven investigation revealed that genes related to denitrification and efflux pumps were among the most differentially expressed gene clusters in response to the engineered device. This study establishes that the effectiveness of synthetic gene circuits can be traced along differences in closely related microbial hosts that each represent unique hardware options for biodesign.\n\nPangenomic landscapes shape the genetic circuit performance in aStutzerimonasbiodesign toolkit", "token_count": 282, "char_count": 1376, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7112, "quality_score": 0.8556, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:39.690675", "source": { "split": "train_shard_00001", "doc_id": 2366 }, "chunk_id": "train_shard_00001_2366_0", "global_id": 9035 }, { "text": "

SUMMARY

As population genomics is transitioning from single reference genomes to pangenomes, major improvements in terms of genome contiguity, phylogenetic sampling, haplotype phasing and structural variant (SV) calling are required. Here, we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising 142 reference-quality genomes from strains of various geographic and ecological origins that faithfully represent the genomic diversity and complexity of the species. The ca. 4,800 non-redundant SVs we identified impact the expression of genes near the breakpoints and contribute to gene repertoire evolution through disruptions, duplications, fusions and horizontal transfers. We discovered frequent cases of complex aneuploidies, preferentially involving large chromosomes that underwent large SVs. We also characterized the evolutionary dynamics of complex genomic regions that classically remain unassembled in short read-based projects, including the 5 Ty families and the 32 individual telomeres. Overall, the ScRAP represents a crucial step towards establishing a high-quality, unified and complete S. cerevisiae pangenome.\n\n142 telomere-to-telomere assemblies reveal the genome structural landscape inSaccharomyces cerevisiae", "token_count": 310, "char_count": 1275, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7578, "quality_score": 0.8789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:40.261251", "source": { "split": "train_shard_00001", "doc_id": 2367 }, "chunk_id": "train_shard_00001_2367_0", "global_id": 9036 }, { "text": "

Background

Probiotics have been used to regulate the gut microbiota and physiology in various contexts, but their precise mechanisms of action remain unclear.

Results

By population genomic analysis of 418 Bifidobacterium longum strains, including 143 newly sequenced in this study, three geographically distinct gene pools/populations, BLAsia1, BLAsia2, and BLothers, were identified. Genes involved in cell wall biosynthesis, particularly peptidoglycan biosynthesis, varied considerably among the core genomes of the different populations, but accessory genes that contributed to the carbohydrate metabolism were significantly distinct. Although active transmission was observed inter-host, inter-country, inter-city, intra-community, and intra-family, a single B. longum clone seemed to reside within each individual. A significant negative association was observed between host age and relative abundance of B. longum, while there was a strong positive association between host age and strain genotype [e.g., single nucleotide polymorphisms in the arginine biosynthesis pathway]. Further animal experiments performed with the B. longum isolates via using a D-galactose-induced aging mouse model supported these associations, in which B. longum strains with different genotypes in arginine biosynthesis pathway showed divergent abilities on protecting against host aging possibly via their different abilities to modify the metabolism of gut microbes.

Conclusions

This is the first known example of research on the evolutionary history and transmission of this probiotic species. Our results propose a new mechanistic insight for promoting host longevity via the informed use of specific probiotics or molecules. Video abstract.\n\nHuman gut-derived B. longum subsp. longum strains protect against aging in a D-galactose-induced aging mouse model.", "token_count": 450, "char_count": 1869, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6762, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:40.898948", "source": { "split": "train_shard_00001", "doc_id": 2368 }, "chunk_id": "train_shard_00001_2368_0", "global_id": 9037 }, { "text": "

ABSTRACT

Fundamental to effective Legionnaires’ disease outbreak control is the ability to rapidly identify the environmental source(s) of the causative agent, Legionella pneumophila . Genomics has revolutionised pathogen surveillance but L. pneumophila has a complex ecology and population structure that can limit source inference based on standard core genome phylogenetics. Here we present a powerful machine learning approach that assigns the geographical source of Legionnaires’ disease outbreaks more accurately than current core genome comparisons. Models were developed upon 534 L. pneumophila genome sequences, including 149 genomes linked to 20 previously reported Legionnaires’ disease outbreaks through detailed case investigations. Our classification models were developed in a cross-validation framework using only environmental L. pneumophila genomes. Assignments of clinical isolate geographic origins demonstrated high predictive sensitivity and specificity of the models, with no false positives or false negatives for 13 out of 20 outbreak groups, despite the presence of within-outbreak polyclonal population structure. Analysis of the same 534-genome panel with a conventional phylogenomic tree and a core genome multi-locus sequence type allelic distance-based classification approach revealed that our machine learning method had the highest overall classification performance – agreement with epidemiological information. Our multivariate statistical learning approach maximises use of genomic variation data and is thus well-suited for supporting Legionnaires’ disease outbreak investigations.\n\nHigh performanceLegionella pneumophilasource attribution using genomics-based machine learning classification", "token_count": 375, "char_count": 1746, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6712, "quality_score": 0.8356, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:41.481644", "source": { "split": "train_shard_00001", "doc_id": 2369 }, "chunk_id": "train_shard_00001_2369_0", "global_id": 9038 }, { "text": "The application of Kluyveromyces marxianus (IFO 288), Lactobacillus delbrueckii ssp. bulgaricus (ATCC 11842) and Lactobacillus helveticus (ATCC 15009) as starter cultures for sourdough bread making was examined. Production of lactic and acetic acids, bread rising, volatile composition, shelf-life and organoleptic quality of the sourdough breads were evaluated. The amount of starter culture added to the flour, the dough fermentation temperature and the amount of sourdough used were examined in order to optimise the bread making process. The use of mixed cultures led to higher total titratable acidities and lactic acid concentrations compared to traditionally made breads. Highest acidity (3.41 g lactic acid/kg of bread) and highest resistance to mould spoilage were observed when bread was made using 50% sourdough containing 1% K. marxianus and 4% L. delbrueckii ssp. bulgaricus. The use of these cultures also improved the aroma of sourdough breads, as shown by sensory evaluations and as revealed by GC-MS analysis.\n\nApplication of Kluyveromyces marxianus, Lactobacillus delbrueckii ssp. bulgaricus and L. helveticus for sourdough bread making", "token_count": 324, "char_count": 1154, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5808, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:42.048947", "source": { "split": "train_shard_00001", "doc_id": 2370 }, "chunk_id": "train_shard_00001_2370_0", "global_id": 9039 }, { "text": "A study was carried out to select the conditions for cultivation of Kluyveromyces marxianus CDBBL 278 in solid-state culture (SSC) using polyurethane foam (PUF) as an inert support. PUF was impregnated with culture media containing lactose (50 g/L) as the carbon and energy source. Evaluation of culture parameters during different growth phases was carried out by respirometry. The effect of inoculum level, buffer capacity of the medium, and nitrogen source upon the yield of biomass on lactose (Yx/s) and production of lactase and inulinase was investigated. The highest lactase titre was achieved with an inoculum level of 1 x 10(7) cells per gram of wet matter (gwm) and 20% of the total nitrogen source provided as urea. The best biomass yield (0.37) was obtained when less than 40% of the total nitrogen was provided as urea. Using potassium phosphate allowed 90% substrate consumption in 30 h. In the best conditions, intracellular lactase and extracellular inulinase activities of 1147.7 IU/gX and 241.6 IU/gX were obtained, respectively, with a lag phase of 13.8 h and a rate of respiratory activity (microCO2) of 0.23 +/- 0.01 h(-1). To our knowledge, this is the first report on lactase production by K. marxianus CDBBL 278 in SSC. This study gives basic information about biomass yield and enzyme production using lactose as the sole carbon source in SSC on an inert support.\n\nLactase production by solid-state cultivation of Kluyveromyces marxianus CDBBL 278 on an inert support: effect of inoculum, buffer, and nitrogen source.", "token_count": 458, "char_count": 1542, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5547, "quality_score": 0.7773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:42.686075", "source": { "split": "train_shard_00001", "doc_id": 2371 }, "chunk_id": "train_shard_00001_2371_0", "global_id": 9040 }, { "text": "Cyclic nucleotide-gated channels (CNGC) gene family has been found to be involved in physiological processes including signaling pathways, environmental stresses, plant growth, and development. This gene family of non-selective cation channels is known to regulate the uptake of calcium and is reported in several plant species. The pangenome-wide studies enable researchers to understand the genetic diversity comprehensively; as a comparative analysis of multiple plant species or member of a species at once helps to better understand the evolutionary relationships and diversity present among them. In the current study, pangenome-wide analysis of the CNGC gene family has been performed on five Citrus species. As a result, a total of 32 genes in Citrus sinensis, 27 genes in Citrus recticulata, 30 genes in Citrus grandis, 31 genes in Atalantia buxfolia, and 30 genes in Poncirus trifoliata were identified. In addition, two unique genes CNGC13 and CNGC14 were identified, which may have potential roles. All the identified CNGC genes were unevenly distributed on 9 chromosomes except P. trifoliata had genes distributed on 7 chromosomes and were classified into four major groups and two sub-groups namely I, II, III, IV-A, and IV-B. Cyclic nucleotide binding (CNB) motif, calmodulin-binding motif (CaMB), and motif for IQ-domain were conserved in Citrus Spp. Intron exon structures of citrus species were not exactly as same as the gene structures of Arabidopsis. The majority of cis-regulatory elements (CREs) were light responsive and others include growth, development, and stress-related indicating potential roles of the CNGC gene family in these functions", "token_count": 475, "char_count": 1746, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [ "CNGC13", "CNGC14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:43.333632", "source": { "split": "train_shard_00001", "doc_id": 2372 }, "chunk_id": "train_shard_00001_2372_0", "global_id": 9041 }, { "text": "Both segmental and tandem duplication were involved in the expansion of the CNGC gene family in Citrus Spp. The miRNAs are involved in the response of CsCNGC genes towards drought stress along with having regulatory association in the expression of these genes. Protein- Protein interaction (PPI) analysis also showed the interaction of CNGC proteins with other CNGCs which suggested their potential role in pathways regulating different biological processes. GO enrichment revealed that CNGC genes were involved in the transport of ions across membranes. Furthermore, tissue-specific expression patterns of leaves sample of C. sinensis were studied under drought stress. Out of 32 genes of C. sinensis 3 genes i.e., CsCNGC1.4, CsCNGC2.1, and CsCNGC4.2 were highly up-regulated, and only CsCNGC4.6 was highly down-regulated. The qRT-PCR analysis also showed that CNGC genes were highly expressed after treatment with drought stress, while gene expression was lower under controlled conditions. This work includes findings based on multiple genomes instead of one, therefore, this will provide more genomic information rather than single genome-based studies. These findings will serve as a basis for further functional insights into the CNGC gene family.\n\nPangenome-wide analysis of cyclic nucleotide-gated channel (CNGC) gene family in citrus Spp. Revealed their intraspecies diversity and potential roles in abiotic stress tolerance.", "token_count": 385, "char_count": 1491, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:43.953355", "source": { "split": "train_shard_00001", "doc_id": 2372 }, "chunk_id": "train_shard_00001_2372_1", "global_id": 9042 }, { "text": "Sulfidogenic bacteria cause numerous issues in the oil industry since they produce sulfide, corroding steel equipment, reducing oil quality, and worsening the environmental conditions in oil fields. The purpose of this work was to isolate and taxonomically identify the sulfidogenic bacteria responsible for the corrosion of steel equipment at the Karazhanbas oil field (Kazakhstan). In this study, we characterized five sulfidogenic strains of the genera Pseudodesulfovibrio, Oleidesulfovibrio, and Acetobacterium isolated from the formation water of the Karazhanbas oil field (Kazakhstan). Sulfate-reducing strain 9FUST revealed 98.9% similarity of the 16S rRNA gene sequence with the closely related strain 'Pseudodesulfovibrio methanolicus' 5S69T and was studied in detail to enhance the taxonomic resolution. Strain 9FUST grew optimally at 23-28 °C, pH 6.5, and 0-2% (w/v) NaCl. The strain used lactate, pyruvate, methanol, ethanol, fructose, ribose, and H2/CO2 (in the presence of acetate) as carbon and energy sources for sulfate reduction. Iso-C17:1 ω11, C15:0, iso-C15:0, and C16:0 were the predominant fatty acids. The genome is 4.20 Mbp with a G + C content of 64.0%. The average nucleotide identity and digital DNA-DNA hybridization values with Pseudodesulfovibrio spp", "token_count": 497, "char_count": 1442, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:44.607067", "source": { "split": "train_shard_00001", "doc_id": 2373 }, "chunk_id": "train_shard_00001_2373_0", "global_id": 9043 }, { "text": "genomes were 72.5-91.6% (<95%) and 18.5-45.0% (<70%), respectively, and supported our conclusion that 9FUST (=VKM B-3654T = KCTC 25498T) belonged to a novel Pseudodesulfovibrio species, for which the name Pseudodesulfovibrio karagichevae sp. nov. is proposed. Pangenome analysis of sixteen Pseudodesulfovibrio species and functional annotation analysis of identified genes revealed complete modules of enzymes of the main metabolic pathways, characteristic of bacteria of this genus, and unique genes highlighting the adaptations of strain 9FUST in carbohydrate metabolism, nutrient uptake, and environmental stress response. Isolation of these strains expands our understanding of the diversity of sulfidogens in oil reservoirs and can be used to test the effectiveness of biocides used in an oil field.\n\nSulfate-Reducing Bacteria Isolated from an Oil Field in Kazakhstan and a Description of Pseudodesulfovibrio karagichevae sp. nov.", "token_count": 321, "char_count": 1007, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6899, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:45.167224", "source": { "split": "train_shard_00001", "doc_id": 2373 }, "chunk_id": "train_shard_00001_2373_1", "global_id": 9044 }, { "text": "With the advent of relatively low cost whole genome sequencing (WGS), it is now possible to obtain sequences from large numbers of bacterial strains and interrogate their core and accessory genomes in relation to associated metadata. While there are some bacterial species with preferred hosts, especially in terms of disease, there has been no real systematic genomic investigation of host and niche specificity of 'generalist' bacteria, i.e., those that can be isolated from multiple hosts and environments. The main aim of this research was to determine if host and/or niche-specific proteins can be identified for 'multi-host adapted' bacteria such as E. coli and Salmonella Typhimurium (STm) in order to predict the 'origin' of a strain and its zoonotic potential from its sequence. Two datasets of 'multi-host' bacteria were analysed: 1,203 STm isolates from 4 hosts (avian, bovine, human and swine) and E. coli from 6 hosts (avian, bovine, canine, environmental, human and swine). Based on classical core genome analysis such as core phylogeny, multilocus sequence typing and phylo-grouping, no strong correlations with host were identified. The accessory genome was also investigated for host-based associations, and ... (continues)\n\nBacterial host attribution and bioinformatic characterisation of enteric bacteria Salmonella enterica and Escherichia coli from different hosts and environments", "token_count": 335, "char_count": 1402, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:45.743908", "source": { "split": "train_shard_00001", "doc_id": 2374 }, "chunk_id": "train_shard_00001_2374_0", "global_id": 9045 }, { "text": "

Background

Long-read sequencing in metagenomics facilitates the assembly of complete genomes out of complex microbial communities. These genomes include essential biologic information such as the ribosomal genes or the mobile genetic elements, which are usually missed with short-reads. We applied long-read metagenomics with Nanopore sequencing to retrieve high-quality metagenome-assembled genomes (HQ MAGs) from a dog fecal sample.

Results

We used nanopore long-read metagenomics and frameshift aware correction on a canine fecal sample and retrieved eight single-contig HQ MAGs, which were > 90% complete with < 5% contamination, and contained most ribosomal genes and tRNAs. At the technical level, we demonstrated that a high-molecular-weight DNA extraction improved the metagenomics assembly contiguity, the recovery of the rRNA operons, and the retrieval of longer and circular contigs that are potential HQ MAGs. These HQ MAGs corresponded to Succinivibrio, Sutterella, Prevotellamassilia, Phascolarctobacterium, Catenibacterium, Blautia, and Enterococcus genera. Linking our results to previous gastrointestinal microbiome reports (metagenome or 16S rRNA-based), we found that some bacterial species on the gastrointestinal tract seem to be more canid-specific -Succinivibrio, Prevotellamassilia, Phascolarctobacterium, Blautia_A sp900541345-, whereas others are more broadly distributed among animal and human microbiomes -Sutterella, Catenibacterium, Enterococcus, and Blautia sp003287895. Sutterella HQ MAG is potentially the first reported genome assembly for Sutterella stercoricanis, as assigned by 16S rRNA gene similarity", "token_count": 487, "char_count": 1654, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6986, "quality_score": 0.8493, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:46.393038", "source": { "split": "train_shard_00001", "doc_id": 2375 }, "chunk_id": "train_shard_00001_2375_0", "global_id": 9046 }, { "text": "Moreover, we show that long reads are essential to detect mobilome functions, usually missed in short-read MAGs.

Conclusions

We recovered eight single-contig HQ MAGs from canine feces of a healthy dog with nanopore long-reads. We also retrieved relevant biological insights from these specific bacterial species previously missed in public databases, such as complete ribosomal operons and mobilome functions. The high-molecular-weight DNA extraction improved the assembly's contiguity, whereas the high-accuracy basecalling, the raw read error correction, the assembly polishing, and the frameshift correction reduced the insertion and deletion errors. Both experimental and analytical steps ensured the retrieval of complete bacterial genomes.\n\nLong-read metagenomics retrieves complete single-contig bacterial genomes from canine feces.", "token_count": 201, "char_count": 846, "word_count": 108, "semantic_coherence": 1, "information_density": 0.787, "quality_score": 0.8935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:46.850393", "source": { "split": "train_shard_00001", "doc_id": 2375 }, "chunk_id": "train_shard_00001_2375_1", "global_id": 9047 }, { "text": "The Kluyveromyces lactis Cu/Zn SOD gene (SOD1) was fused with the toxin K1 signal sequence to obtain extracellular production of superoxide dismutase. Kluyveromyces marxianus L3 and K. lactis MW98-8C strains were transformed and compared as hosts for the secretion. The effects of the media composition were evaluated: In K. lactis, the highest volumetric activity was obtained in YKK synthetic medium in the presence of Cu(2+)/Zn(2+) cofactors (9.6 kU l(-1)). In K. marxianus, active SOD was produced only in YPD medium supplemented with Cu(2+) and Zn(2+) (8.8 kU l(-1)). In order to improve the production of secreted active SOD in K. lactis, the SOD1 copper carrier (CCS1) was overexpressed and targeted to the secretory apparatus. A positive effect was observed only when K. lactis was grown in a medium without Cu(2+)/Zn(2+) supplement. The best performing culture conditions for K. lactis and K. marxianus recombinant strains were successfully applied to two laboratory-scale fed-batch processes, and volumetric SOD activities increased up to 19.4 and 24.1 kU l(-1), respectively.\n\nSecretion of Kluyveromyces lactis Cu/Zn SOD: strategies for enhanced production.", "token_count": 350, "char_count": 1168, "word_count": 175, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7971, "entities": { "genes": [ "SOD1", "CCS1", "MW98" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:47.445996", "source": { "split": "train_shard_00001", "doc_id": 2376 }, "chunk_id": "train_shard_00001_2376_0", "global_id": 9048 }, { "text": "Human listeriosis is a foodborne disease caused by Listeria monocytogenes contamination. Most cases occur due to consumption of ready-to-eat (RTE) foods. Stewed meat in seasoning, a type of pre-packaged ready-to-eat (RTE) food, is a popular traditional product in China. We used whole genome sequencing to analyze core genome multilocus sequence typing (cgMLST), serogroups and multilocus typing sequence typing (ST) of 67 L. monocytogenes isolates. The L. monocytogenes serogroup IIb-ST5 was predominantly isolated from different sources and linked to stewed meat in seasoning of Brand A, B, and C with <7 allelic differences by cgMLST, suggesting that this kind of food may be a high-risk food causing sporadic cases of listeriosis. Furthermore, L. monocytogenes isolates from different batches of stewed meat in seasoning products processed in the same processing plant had <5 five allelic differences, confirming that contamination occurred during manufacture. Additionally, 16 L. monocytogenes isolates from Plant A were the same clone (0 allelic difference), which confirmed the strong ability of L. monocytogenes to survive in the processing environment. Thus, increased and frequent monitoring, as well as constant technical support for the control of L. monocytogenes in food processing plants is necessary.\n\nSurveillance of stewed meat products in Shanghai, China: Importance of controlling processing environment contamination for Listeria monocytogenes", "token_count": 363, "char_count": 1464, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6124, "quality_score": 0.8062, "entities": { "genes": [ "ST5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:48.038044", "source": { "split": "train_shard_00001", "doc_id": 2377 }, "chunk_id": "train_shard_00001_2377_0", "global_id": 9049 }, { "text": "The yeast populations of natural whey starter (NWS) samples from dairies of PDO Parmigiano Reggiano cheese production area were enumerated and characterised. Yeasts were detected with an average value higher than 3 log cfu mL−1 and in a case study we highlighted the correlation between the yeast growth and incorrect management of NWS fermentation. Isolated strains showed the typical Kluyveromyces marxianus PCR-RFLP pattern and D1/D2 sequences obtained displayed similarity values ranging from 99% to 100% for the same species. RAPD-PCR fingerprinting revealed 14 biotypes. The ability of several strains to grow at 52 °C demonstrates that the yeasts may be perfectly integrated into the ecosystem of NWS. This work confirms that yeasts are part of the NWS secondary microbiota, composed by wild strains with relevant biotechnological interest.\n\nDetection and identification of yeasts in natural whey starter for Parmigiano Reggiano cheese-making", "token_count": 244, "char_count": 949, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7357, "quality_score": 0.8679, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:48.557492", "source": { "split": "train_shard_00001", "doc_id": 2378 }, "chunk_id": "train_shard_00001_2378_0", "global_id": 9050 }, { "text": "Staphylococcus pseudintermedius is the foremost cause of opportunistic canine skin and mucosal infections worldwide. Multidrug resistant (MDR) and methicillin-resistant S. pseudintermedius (MRSP) lineages have disseminated globally in the last decade and present significant treatment challenges. However, little is known regarding the factors that contribute to the success of MDR lineages. In this study, we compared the genome sequence of 110 UK isolates of S. pseudintermedius to 2,166 genomes of S. pseudintermedius populations from different continents. A novel core genome multi-locus typing scheme was generated to allow large scale, rapid and detailed analysis of S. pseudintermedius phylogenies, and was used to show that the S. pseudintermedius population structure is broadly segregated into an MDR population and a non-MDR population. MRSP lineages are predicted to either encode certain resistance genes chromosomally, or on plasmids, and this is associated with their MLST sequence type. Comparison of lineages most frequently implicated in disease, ST-45 and ST-71, with the phylogenetically related ST-496 lineage that has a comparatively low disease rate, revealed that ST-45 and ST-71 genomes encode distinct combinations of phage-defence systems and concurrently encode a high number of intact prophages. In contrast, ST-496 genomes encode a wider array of phage defence systems and lack intact, complete prophages. Additionally, we show that distinct prophages are widespread in S. pseudintermedius and appear to account for the vast majority of genomic diversity. These findings indicate that MRSP lineages have significant structural genomic differences, and that prophage integration, and differential antiviral systems correlate with the emergence of successful genotypes.

Impact Statement

Staphylococcus pseudintermedius is a major cause of soft tissue infections in dogs but may occasionally infect other companion animals and humans, most often veterinary professionals in primary care. Methicillin-resistant Staphylococcus pseudintermedius (MRSP) have emerged worldwide and are often linked to resistance to multiple antimicrobials, resulting in a significant health burden", "token_count": 523, "char_count": 2211, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6073, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:49.233480", "source": { "split": "train_shard_00001", "doc_id": 2379 }, "chunk_id": "train_shard_00001_2379_0", "global_id": 9051 }, { "text": "Here, we analysed a large collection of S. pseudintermedius genome sequences, which has allowed a detailed characterisation of the molecular epidemiology and diversity of the species using a novel typing scheme. Here we show that closely related MRSP lineages differ in whether specific antibiotic resistance genes are encoded on potentially mobilisable plasmids, or more stably on the chromosome, indicating differing evolutionary trajectories of MRSP lineages. Comparison of the S. pseudintermedius types most frequently implicated in clinical cases to those associated with commensal carriage, showed that known genes thought to contribute to disease are universal, and therefore, not associated with the high incidence rates of disease of particular lineages. We demonstrate that MRSP sequence types linked to high disease rates lack specific phage-defence systems and are associated with a high burden of prophages.

Data statement

All supporting data, code and protocols have been provided either within the article, through supplementary data files, or via Figshare and Zenodo. Six supplementary figures and one supplementary file are available with the online version of this article.

Data summary

All genome sequencing data (sequencing reads and genome assemblies) are available at the Sequence Read Archive (SRA) and Genomes repositories at NCBI, in Bioproject number PRJNA1153484. The information for the individual S. pseudintermedius genomes has been included in Supplementary File 1. Genome assemblies used in this study are available from https://zenodo.org/records/13692319 , DOI 10.5281/zenodo.13692318 . The S. pseudintermedius cgMLST scheme developed for this study has been made available via Zenodo ( https://zenodo.org/records/13633136 , DOI: 10.5281/zenodo.13633135) and Figshare ( https://doi.org/10.6084/m9.figshare.26911654.v1 , DOI: 10.6084/m9.figshare.26911654).", "token_count": 518, "char_count": 1907, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8066, "entities": { "genes": [ "PRJNA1153484" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:23:49.883327", "source": { "split": "train_shard_00001", "doc_id": 2379 }, "chunk_id": "train_shard_00001_2379_1", "global_id": 9052 }, { "text": "Global phylogenomic analysis ofStaphylococcus pseudintermediusreveals genomic and prophage diversity in multi-drug resistant lineages", "token_count": 43, "char_count": 140, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:50.241942", "source": { "split": "train_shard_00001", "doc_id": 2379 }, "chunk_id": "train_shard_00001_2379_2", "global_id": 9053 }, { "text": "The aims of this work were to characterize the fermentation process of mezcal from San Luis Potosi, México and identify the yeasts present in the fermentation using molecular culture-dependent methods (RFLP of the 5.8S-ITS and sequencing of the D1/D2 domain) and also by using a culture-independent method (DGGE). The alcoholic fermentations of two separate musts obtained from Agave salmiana were analyzed. Sugar, ethanol and major volatile compounds concentrations were higher in the first fermentation, which shows the importance of having a quality standard for raw materials, particularly in the concentration of fructans, in order to produce fermented Agave salmiana must with similar characteristics. One hundred ninety-two (192) different yeast colonies were identified, from those present on WL agar plates, by RFLP analysis of the ITS1-5.8S- ITS2 from the rRNA gene, with restriction endonucleases, HhaI, HaeIII and HinfI. The identified yeasts were: Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia kluyveri, Zygosaccharomyces bailii, Clavispora lusitaniae, Torulaspora delbrueckii, Candida ethanolica and Saccharomyces exiguus. These identifications were confirmed by sequencing the D1-D2 region of the 26S rRNA gene. With the PCR-DGGE method, bands corresponding to S. cerevisiae, K. marxianus and T. delbrueckii were clearly detected, confirming the results obtained with classic techniques.\n\nYeast communities associated with artisanal mezcal fermentations from Agave salmiana.", "token_count": 412, "char_count": 1501, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6796, "quality_score": 0.8398, "entities": { "genes": [ "ITS2", "ITS1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:50.865602", "source": { "split": "train_shard_00001", "doc_id": 2380 }, "chunk_id": "train_shard_00001_2380_0", "global_id": 9054 }, { "text": "Extensive microdiversity within Prochlorococcus, the most abundant marine cyanobacterium, occurs at scales from a single droplet of seawater to ocean basins. To interpret the structuring role of variations in genetic potential, as well as metabolic and physiological acclimation, we developed a mechanistic constraint-based modeling framework that incorporates the full suite of genes, proteins, metabolic reactions, pigments, and biochemical compositions of 69 sequenced isolates spanning the Prochlorococcus pangenome. Optimizing each strain to the local, observed physical and chemical environment along an Atlantic Ocean transect, we predicted variations in strain-specific patterns of growth rate, metabolic configuration, and physiological state, defining subtle niche subspaces directly attributable to differences in their encoded metabolic potential. Predicted growth rates covaried with observed ecotype abundances, affirming their significance as a measure of fitness and inferring a nonlinear density dependence of mortality. Our study demonstrates the potential to interpret global-scale ecosystem organization in terms of cellular-scale processes.\n\nBasin-scale biogeography of marine phytoplankton reflects cellular-scale optimization of metabolism and physiology.", "token_count": 290, "char_count": 1292, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7205, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:51.439868", "source": { "split": "train_shard_00001", "doc_id": 2381 }, "chunk_id": "train_shard_00001_2381_0", "global_id": 9055 }, { "text": "\"Candidatus Actinomarinales\" was defined as a subclass of exclusively marine Actinobacteria with small cells and genomes. We have collected all the available genomes in databases to assess the diversity included in this group and analyzed it by comparative genomics. We have found the equivalent of five genera and 18 genomospecies. They have genome reduction parameters equal to those of freshwater actinobacterial \"Candidatus Nanopelagicales\" or marine alphaproteobacterial Pelagibacterales Genome recruitment shows that they are found only in the photic zone and mainly in surface waters, with only one genus that is found preferentially at or below the deep chlorophyll maximum. \"Ca Actinomarinales\" show a highly conserved core genome (80% of the gene families conserved for the whole order) with a saturation of genomic diversity of the flexible genome at the genomospecies level. We found only a flexible genomic island preserved throughout the order; it is related to the sugar decoration of the envelope and uses several tRNAs as hot spots to increase its genomic diversity. Populations had a discrete level of sequence diversity similar to other marine microbes but drastically different from the much higher levels found for Pelagibacterales Genomic analysis suggests that they are all aerobic photoheterotrophs with one type 1 rhodopsin and a heliorhodopsin. Like other actinobacteria, they possess the F420 coenzyme biosynthesis pathway, and its lower reduction potential could provide access to an increased range of redox chemical transformations. Last, sequence analysis revealed the first \"Ca Actinomarinales\" phages, including a prophage, with metaviromic islands related to sialic acid cleavage.IMPORTANCE Microbiology is in a new age in which sequence databases are primary sources of information about many microbes. However, in-depth analysis of environmental genomes thus retrieved is essential to substantiate the new knowledge", "token_count": 503, "char_count": 2007, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:52.092865", "source": { "split": "train_shard_00001", "doc_id": 2382 }, "chunk_id": "train_shard_00001_2382_0", "global_id": 9056 }, { "text": "Here, we study 182 genomes belonging to the only known exclusively marine pelagic group of the phylum Actinobacteria The aquatic branch of this phylum is largely known from environmental sequencing studies (single-amplified genomes [SAGs] and metagenome-assembled genomes [MAGs]), and we have collected and analyzed the available information present in databases about the \"Ca. Actinomarinales.\" They are among the most streamlined microbes to live in the epipelagic zone of the ocean, and their study is critical to obtain a proper view of the diversity of Actinobacteria and their role in aquatic ecosystems.\n\nGenomes of the \"Candidatus Actinomarinales\" Order: Highly Streamlined Marine Epipelagic Actinobacteria.", "token_count": 207, "char_count": 743, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:52.557247", "source": { "split": "train_shard_00001", "doc_id": 2382 }, "chunk_id": "train_shard_00001_2382_1", "global_id": 9057 }, { "text": "Bacillus endophthalmitis is a devastating eye infection that causes rapid blindness through extracellular tissue-destructive exotoxins. Despite its importance, knowledge of the phylogenetic relationships and population structure of intraocular Bacillus spp. is lacking. In this study, we sequenced the whole genomes of eight Bacillus intraocular pathogens independently isolated from 8/52 patients with posttraumatic Bacillus endophthalmitis infections in the Eye Hospital of Wenzhou Medical University between January 2010 and December 2018. Phylogenetic analysis revealed that the pathogenic intraocular isolates belonged to Bacillus cereus, Bacillus thuringiensis and Bacillus toyonensis To determine the virulence of the ocular isolates, three representative strains were injected into mouse models, and severe endophthalmitis leading to blindness was observed. Through incorporating publicly available genomes for Bacillus spp., we found that the intraocular pathogens could be isolated independently but displayed a similar genetic context. In addition, our data provide genome-wide support for intraocular and gastrointestinal sources of Bacillus spp. belonging to different lineages. Importantly, we identified five molecular signatures of virulence and motility genes associated with intraocular infection, namely, plcA-2, InhA-3, InhA-4, hblA-5, and fliD using pangenome-wide association studies", "token_count": 432, "char_count": 1496, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:53.184588", "source": { "split": "train_shard_00001", "doc_id": 2383 }, "chunk_id": "train_shard_00001_2383_0", "global_id": 9058 }, { "text": "The characterization of overrepresented genes in the intraocular isolates holds value to predict bacterial evolution and for the design of future intervention strategies in patients with endophthalmitis.IMPORTANCE In this study, we provided a detailed and comprehensive clinicopathological and pathogenic report of Bacillus endophthalmitis over the 8 years of the study period. We first reported the whole-genome sequence of Bacillus spp. causing devastating endophthalmitis and found that Bacillus toyonensis is able to cause endophthalmitis. Finally, we revealed significant endophthalmitis-associated virulence genes involved in hemolysis, immunity inhibition, and pathogenesis. Overall, as more sequencing data sets become available, these data will facilitate comparative research and will reveal the emergence of pathogenic \"ocular bacteria.\"\n\nMolecular Signatures Related to the Virulence of Bacillus cereus Sensu Lato, a Leading Cause of Devastating Endophthalmitis.", "token_count": 256, "char_count": 1002, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8543, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:53.728924", "source": { "split": "train_shard_00001", "doc_id": 2383 }, "chunk_id": "train_shard_00001_2383_1", "global_id": 9059 }, { "text": "Deciphering the genomic variation that represents microevolutionary processes toward species divergence is key to understanding microbial speciation, which has long been under debate. Streptomycetes are filamentous bacteria that are ubiquitous in nature and the richest source of antibiotics; however, their speciation processes remain unknown. To tackle this issue, we performed a comprehensive population genomics analysis on Streptomyces albidoflavus residing in different habitats and with a worldwide distribution and identified and characterized the foundational changes within the species. We detected three well-defined phylogenomic clades, of which clades I and III mainly contained free-living (soil/marine) and insect-associated strains, respectively, and clade II had a mixed origin. By performing genome-wide association studies (GWAS), we identified a number of genetic variants associated with free-living or entomic (denoting or relating to insects) habitats in both the accessory and core genomes. These variants contributed collectively to the population structure and had annotated or confirmed functions that likely facilitate differential adaptation of the species. In addition, we detected higher levels of homologous recombination within each clade and in the free-living group than within the whole species and in the entomic group. A subset of the insect-associated strains (clade III) showed a relatively independent evolutionary trajectory with more symbiosis-favorable genes but little genetic interchange with the other lineages. Our results demonstrate that ecological adaptation promotes genetic differentiation in S. albidoflavus, suggesting a model of ecological speciation with gene flow in streptomycetes.IMPORTANCE Species are the fundamental units of ecology and evolution, and speciation leads to the astounding diversity of life on Earth. Studying speciation is thus of great significance to understand, protect, and exploit biodiversity, but it is a challenge in the microbial world. In this study, using population genomics, we placed Streptomyces albidoflavus strains in a spectrum of speciation and showed that the genetic differences between phylogenomic clusters evolved mainly by environmental selection and gene-specific sweeps", "token_count": 511, "char_count": 2302, "word_count": 308, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:54.387465", "source": { "split": "train_shard_00001", "doc_id": 2384 }, "chunk_id": "train_shard_00001_2384_0", "global_id": 9060 }, { "text": "These findings highlight the role of ecology in structuring recombining bacterial species, making a step toward a deeper understanding of microbial speciation. Our results also raise concerns of an underrated microbial diversity at the intraspecies level, which can be utilized for mining of ecologically relevant natural products.\n\nPopulation Genomics Insights into Adaptive Evolution and Ecological Differentiation in Streptomycetes.", "token_count": 94, "char_count": 435, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8793, "quality_score": 0.9397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:54.760871", "source": { "split": "train_shard_00001", "doc_id": 2384 }, "chunk_id": "train_shard_00001_2384_1", "global_id": 9061 }, { "text": "

Background

Coronavirus disease 2019 is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) leads to respiratory failure and obstructive alveolar damage, which may be fatal in immunocompromised individuals. COVID-19 pandemic has severe global implications badly, and the situation in the world is depreciating with the emergence of novel variants. The aim of our study is to explore the genome of SARS-CoV2 followed by in silico reverse vaccinology analysis. This will help to identify the most putative vaccine candidate against the virus in a robust manner and enables cost-effective development of vaccines compared with traditional strategies.

Methods

The genomic sequencing data is retrieved from NCBI (Reference Sequence Number NC_045512.2). The sequences are explored through comparative genomics approaches by GENOMICS to find out the core genome. The comprehensive set of proteins obtained was employed in computational vaccinology approaches for the prediction of the best possible B and T cell epitopes through ABCpred and IEDB Analysis Resource, respectively. The multi-epitopes were further tested against human toll-like receptor and cloned in E. coli plasmid vector.

Findings

The designed Multiepitope Subunit Vaccine was non-allergenic, antigenic (0.6543), & non-toxic, with significant connections with the human leukocyte antigen (HLA) binding alleles, and collective global population coverage of 84.38%. It has 276 amino acids, consisting of an adjuvant with the aid of EAAAK linker, AAY linkers used to join the 4 CTL epitopes, GPGPG linkers used to join the 3 HTL epitopes and KK linkers used to join the 7 B-cell epitopes. MESV docking with human pathogenic toll-like receptors-3 (TLR3) exhibited a stable & high binding affinity. An in-silico codon optimization approach was used in the codon system of E", "token_count": 497, "char_count": 1872, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8407, "entities": { "genes": [ "TLR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:55.410506", "source": { "split": "train_shard_00001", "doc_id": 2385 }, "chunk_id": "train_shard_00001_2385_0", "global_id": 9062 }, { "text": "coli (strain K12) to obtain the GC-Content of Escherichia coli (strain K12): 50.7340272413779 and CAI-Value of the improved sequence: 0.9542834278823386. The multi-epitope vaccine’s optimized gene sequence was cloned in-silico in E. coli plasmid vector pET-30a (+), BamHI and HindIII restriction sites were added to the N and C-terminals of the sequence, respectively.

Conclusion

There is a pressing need to combat COVID-19 and we need quick and reliable approaches against Covid-19. By using In-silico approaches, we acquire an effective vaccine that could trigger adequate immune responses at the cellular and humoral level. The suggested sequences can be further validated through in vivo and in vitro experimentation.

Statement of Significance

Current developments in the immunological bioinformatics areas has resulted in different servers and tools that are cost and time efficient for the traditional vaccine development. Though for designing a multiple epitope vaccine the antigenic epitopes prediction of a relevant protein by immunoinformatic methods are very helpful.\n\nPangenome analysis of SARS-CoV2 strains to Identify Potential vaccine targets by Reverse Vaccinology", "token_count": 325, "char_count": 1198, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7305, "quality_score": 0.8653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:55.972424", "source": { "split": "train_shard_00001", "doc_id": 2385 }, "chunk_id": "train_shard_00001_2385_1", "global_id": 9063 }, { "text": "Leptospirosis is one of the most common zoonotic infections and a major problem in terms of both veterinary medicine and public health. However, the disease is under-recognised and under-diagnosed worldwide, particularly in horses. Clinical leptospirosis in horses is mainly associated with recurrent uveitis (ERU), which has recently been studied more intensively, and reproductive disorders, the epidemiology of which is still relatively poorly understood. To enhance our comprehension of abortions caused by leptospirosis in horses and to identify the causative strains, a serological study was carried out with subsequent molecular characterisation of the isolate obtained. Using the microscopic agglutination test (MAT), serum samples from mares that aborted and foetal fluids (when available) were tested for antibodies against Leptospira spp. Furthermore, bacteria isolation from kidney cultures was conducted. Of 97 mare serum samples, 21 (21.64%) tested positive, with Grippotyphosa and Pomona being the most frequently detected serogroups. A significantly higher seroprevalence was found in aborting mares compared to the healthy horse population from the same geographical area, as well as a pronounced seasonal variation. Leptospiral antibodies were not detected in any of the foetal fluids, but isolation was successful in 1 case out of 39 (2.56%). Genotyping by multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) identified the obtained isolate as Leptospira kirschneri, serogroup Pomona, serovar Mozdok. Further surveillance and molecular typing of Leptospira strains causing abortion in horses would be invaluable in understanding the prevalence and impact of leptospirosis on equine reproductive health in Europe.\n\nAssociation between Exposure to Leptospira spp. and Abortion in Mares in Croatia.", "token_count": 476, "char_count": 1876, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:56.618025", "source": { "split": "train_shard_00001", "doc_id": 2386 }, "chunk_id": "train_shard_00001_2386_0", "global_id": 9064 }, { "text": "The possible biotechnological application of a recombinant endopolygalacturonase of Kluyveromyces marxianus (KMPG) for the aroma enhancement of Albariño wine was studied. The addition of this enzyme to the must gives rise to a significant increase of the total compounds responsible for the aroma as opposed to the effect when using a commercial pectic enzyme. This increase also results in a significant rise of the odoriferous aglycones which are direct determinants of the aroma. Wines made by using the KMPG enzyme are characterised by a greater richness and diversity with regard to the number of aromatic compounds present, clearly differing from those obtained with a commercial pectic preparation. Based on compounds with odour activity values (OAV)>1, the wines obtained with the enzyme KMPG are richer in citric, balsamic, spicy and above all floral (violet and rose) aromas than untreated wines or wines supplemented with a commercial enzyme.\n\nAlbariño wine aroma enhancement through the use of a recombinant polygalacturonase from Kluyveromyces marxianus.", "token_count": 274, "char_count": 1067, "word_count": 160, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:57.167545", "source": { "split": "train_shard_00001", "doc_id": 2387 }, "chunk_id": "train_shard_00001_2387_0", "global_id": 9065 }, { "text": "Objective: To understand the etiological characteristics of 2 serotypes of Salmonella strains isolated from a foodborne disease outbreak. Methods: A total of 11 anal swabs of the cases, 13 suspected contaminated food and 10 environmental samples were collected from a foodborne disease outbreak occurred on September 8, 2022 in a school. The anal swabs were enriched with selenite brilliant green enrichment broth (SBG) and brain heart infusion broth (BHI) respectively. PCR detection and culture of common intestinal pathogens were carried out. The suspected food samples were tested according to national standards for food safety. Multiple suspected Salmonella colonies were obtained and selected for serotype determination and whole genome sequencing. Serotypes were determined based on the whole-genome sequence, and clustering analysis was performed based on core genome single nucleotide polymorphism (SNP). Results: The positive rates of Salmonella in anal swabs and suspected food samples were 9/11 and 5/13 respectively. Both Salmonella Uganda and Salmonella Idikan were isolated from 4 anal swabs and 4 suspected food samples. For the remaining samples, only Salmonella Uganda or Salmonella Idikan was isolated in each sample. The positive rate of Salmonella in 11 anal swabs of the cases after BHI enrichment for 12 h and 24 h were all 9/11 in real-time PCR, same to the culture results. Salmonella Uganda and Salmonella Idikan formed two independent and genetically distant lineages in the clustering tree based on core genome SNP, and 0-14 and 0-23 SNP were observed in Salmonella Uganda and Salmonella Idikan respectively", "token_count": 499, "char_count": 1741, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5304, "quality_score": 0.7652, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:57.817213", "source": { "split": "train_shard_00001", "doc_id": 2388 }, "chunk_id": "train_shard_00001_2388_0", "global_id": 9066 }, { "text": "Conclusions: This foodborne disease outbreak was probably caused by Salmonella Uganda and Salmonella Idikan, which both exhibited strong genetic diversity. The PCR based pathogen screening strategy plus pathogen enrichment for cases' annal swabs can be used in the routine outbreak investigation.\n\n[Etiological analysis on a foodborne disease outbreak caused by two serotypes of Salmonella].", "token_count": 111, "char_count": 419, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:58.191895", "source": { "split": "train_shard_00001", "doc_id": 2388 }, "chunk_id": "train_shard_00001_2388_1", "global_id": 9067 }, { "text": "Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individual-specific binding events. GRAFIMO is available as an open-source tool, under the MIT license, at https://github.com/pinellolab/GRAFIMO and https://github.com/InfOmics/GRAFIMO .

Author summary

Transcription factors (TFs) are key regulatory proteins and mutations occurring in their binding sites can alter the normal transcriptional landscape of a cell and lead to disease states. Pangenome variation graphs (VGs) efficiently encode genomes from a population of individuals and their genetic variations. GRAFIMO is an open-source tool that extends the traditional PWM scanning procedure to VGs. By scanning for potential TBFS in VGs, GRAFIMO can simultaneously search thousands of genomes while accounting for SNPs, indels, and structural variants. GRAFIMO reports motif occurrences, their statistical significance, frequency, and location within the reference or alternative haplotypes in a given VG", "token_count": 503, "char_count": 2168, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5584, "quality_score": 0.7792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:58.844916", "source": { "split": "train_shard_00001", "doc_id": 2389 }, "chunk_id": "train_shard_00001_2389_0", "global_id": 9068 }, { "text": "GRAFIMO makes it possible to study how genetic variation affects the binding landscape of known TFs within a population of individuals.\n\nGRAFIMO: variant and haplotype aware motif scanning on pangenome graphs", "token_count": 49, "char_count": 208, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9677, "quality_score": 0.9839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:59.238511", "source": { "split": "train_shard_00001", "doc_id": 2389 }, "chunk_id": "train_shard_00001_2389_1", "global_id": 9069 }, { "text": "In this work, we present an optimized nanopore long-read only sequencing workflow for epidemiologic analysis of clonal outbreaks built with open-source tools. A set of unrelated clinical Pseudomonas aeruginosa isolates (n = 10) was chosen for workflow optimization, and sequencing libraries were prepared using a modified rapid barcoding strategy that incorporates temperature ramps to improve performance for high-GC content genomes. Sequencing data were used to benchmark the performance of the dorado suite (v0.9.1), including its basecaller, pre-assembly read error correction, and post-assembly polishing algorithms. All long-read assemblies and core genome multilocus sequence typing (cgMLST) were performed with Flye and pyMLST, respectively. Results were compared with a standard reference Illumina short-read approach, and discordant positions were determined at the core and whole-genome levels. Optimal performance was found with dorado sup@v5.0.0 basecalling with the inclusion of dorado error correction and dorado polish with its bacterial model. This workflow was then validated with four retrospective hospital outbreak isolate sets, including Klebsiella pneumoniae (n = 12), P. aeruginosa (n = 11), Enterococcus faecium (n = 10), and Staphylococcus aureus (n = 10). The nanopore-only assemblies obtained from the optimized pipeline demonstrated fully concordant cgMLST-based minimum spanning trees compared to the Illumina short-read reference. At the whole-genome level, high concordance was also observed, with as few as two discordant positions per genome compared to short-read assemblies", "token_count": 464, "char_count": 1679, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:23:59.918994", "source": { "split": "train_shard_00001", "doc_id": 2390 }, "chunk_id": "train_shard_00001_2390_0", "global_id": 9070 }, { "text": "This optimized library preparation and open-source computational workflow enables nanopore-only clonality and outbreak analysis with performance comparable to that of Illumina short-read sequencing and will contribute critically to hospital infection control.

Importance

For the past decade, bacterial whole-genome sequencing has been performed using high-accuracy short-read sequencing. More recently, long-read sequencing with Oxford Nanopore Technologies (ONT) instruments has emerged as a potential alternative based on multiple advantages, including lower costs, portability, and speed. However, this platform has suffered from basecall error rates that were too high for many applications in clinical microbiology, including outbreak tracing. With the release of new flow cell chemistries and basecall algorithms, the accuracy has improved dramatically, making this approach feasible for outbreak investigations. In this work, we optimize a streamlined nanopore-only workflow for epidemiologic analysis of bacterial pathogens. The workflow was validated with isolates from four previously identified clinical outbreaks with varying GC content and demonstrated fully concordant cgMLST clustering as compared to short-read references. This workflow will facilitate the broader implementation of ONT-only genomes and cgMLST analysis to assist in hospital outbreaks worldwide.\n\nAn open-source nanopore-only sequencing workflow for analysis of clonal outbreaks delivers short-read level accuracy.", "token_count": 315, "char_count": 1504, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:00.508858", "source": { "split": "train_shard_00001", "doc_id": 2390 }, "chunk_id": "train_shard_00001_2390_1", "global_id": 9071 }, { "text": "

Importance

Salt marshes are known for their significant carbon storage capacity, and sulfur cycling is closely linked with the ecosystem-scale carbon cycling in these ecosystems. Sulfate reducers are key for the decomposition of organic matter, and sulfur oxidizers remove toxic sulfide, supporting the productivity of marsh plants. To date, the complexity of coastal environments, heterogeneity of the rhizosphere, high microbial diversity, and uncultured majority hindered our understanding of the genomic diversity of sulfur-cycling microbes in salt marshes. Here, we use comparative genomics to overcome these challenges and provide an in-depth characterization of sulfur-cycling microbial diversity in salt marshes. We characterize communities across distinct sites and plant species and uncover extensive genomic diversity at the taxon level and specific genomic features present in MAGs affiliated with uncultivated sulfur-cycling lineages. Our work provides insights into the partnerships in salt marshes and a roadmap for multiscale analyses of diversity in complex biological systems.\n\nDiversity at single nucleotide to pangenome scales among sulfur cycling bacteria in salt marshes.", "token_count": 267, "char_count": 1201, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6503, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:01.070005", "source": { "split": "train_shard_00001", "doc_id": 2391 }, "chunk_id": "train_shard_00001_2391_0", "global_id": 9072 }, { "text": "

Background

Burkholderia pseudomallei is a soil-dwelling bacterium and the causative agent of melioidosis. The global burden and distribution of melioidosis is poorly understood, including in the Caribbean. B. pseudomallei was previously isolated from humans and soil in eastern Puerto Rico but the abundance and distribution of B. pseudomallei in Puerto Rico as a whole has not been thoroughly investigated.

Methodology/principal findings

We collected 600 environmental samples (500 soil and 100 water) from 60 sites around Puerto Rico. We identified B. pseudomallei by isolating it via culturing and/or using PCR to detect its DNA within complex DNA extracts. Only three adjacent soil samples from one site were positive for B. pseudomallei with PCR; we obtained 55 isolates from two of these samples. The 55 B. pseudomallei isolates exhibited fine-scale variation in the core genome and contained four novel genomic islands. Phylogenetic analyses grouped Puerto Rico B. pseudomallei isolates into a monophyletic clade containing other Caribbean isolates, which was nested inside a larger clade containing all isolates from Central/South America. Other Burkholderia species were commonly observed in Puerto Rico; we cultured 129 isolates from multiple soil and water samples collected at numerous sites around Puerto Rico, including representatives of B. anthina, B. cenocepacia, B. cepacia, B. contaminans, B. glumae, B. seminalis, B. stagnalis, B. ubonensis, and several unidentified novel Burkholderia spp.

Conclusions/significance

B. pseudomallei was only detected in three soil samples collected at one site in north central Puerto Rico with only two of those samples yielding isolates. All previous human and environmental B. pseudomallei isolates were obtained from eastern Puerto Rico. These findings suggest B. pseudomallei is ecologically established and widely dispersed in the environment in Puerto Rico but rare. Phylogeographic patterns suggest the source of B. pseudomallei populations in Puerto Rico and elsewhere in the Caribbean may have been Central or South America.", "token_count": 513, "char_count": 2109, "word_count": 298, "semantic_coherence": 1, "information_density": 0.5403, "quality_score": 0.7701, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:24:01.741673", "source": { "split": "train_shard_00001", "doc_id": 2392 }, "chunk_id": "train_shard_00001_2392_0", "global_id": 9073 }, { "text": "Burkholderia pseudomallei, the causative agent of melioidosis, is rare but ecologically established and widely dispersed in the environment in Puerto Rico.", "token_count": 36, "char_count": 155, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:02.092810", "source": { "split": "train_shard_00001", "doc_id": 2392 }, "chunk_id": "train_shard_00001_2392_1", "global_id": 9074 }, { "text": "

Background

Pseudomonas aeruginosa is an important opportunistic pathogen especially in nosocomial infections due to its easy adaptation to different environments; this characteristic is due to the great genetic diversity that presents its genome. In addition, it is considered a pathogen of critical priority due to the high antimicrobial resistance.

Objectives

The aim of this study was to characterize the mobile genetic elements present in the chromosome of six Mexican P. aeruginosa strains isolated from adults with pneumonia and children with bacteremia.

Methods

The genomic DNA of six P. aeruginosa strains were isolated and sequenced using PacBio RS-II platform. They were annotated using Prokaryotic Genome Annotation Pipeline and manually curated and analyzed for the presence of mobile genetic elements, antibiotic resistances genes, efflux pumps and virulence factors using several bioinformatics programs and databases.

Results

The global analysis of the strains chromosomes showed a novel chromosomal rearrangement in two strains, possibly mediated by subsequent recombination and inversion events. They have a high content of mobile genetic elements: 21 genomic islands, four new islets, four different integrative conjugative elements, 28 different prophages, one CRISPR-Cas arrangements, and one class 1 integron. The acquisition of antimicrobials resistance genes into these elements are in concordance with their phenotype of multi-drug resistance.

Conclusion

The accessory genome increased the ability of the strains to adapt or survive to the hospital environment, promote genomic plasticity and chromosomal rearrangements, which may affect the expression or functionality of the gene and might influence the clinical outcome, having an impact on the treatment.\n\nDiversity in the composition of the accessory genome of Mexican Pseudomonas aeruginosa strains.", "token_count": 451, "char_count": 1915, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6353, "quality_score": 0.8176, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:02.731319", "source": { "split": "train_shard_00001", "doc_id": 2393 }, "chunk_id": "train_shard_00001_2393_0", "global_id": 9075 }, { "text": "Acinetobacter haemolyticus is a Gammaproteobacterium that has been involved in serious diseases frequently linked to the nosocomial environment. Most of the strains causing such infections are sensitive to a wide variety of antibiotics, but recent reports indicate that this pathogen is acquiring very efficiently carbapenem-resistance determinants like the blaNDM-1 gene, all over the world. With this work we contribute with a collection set of 31 newly sequenced nosocomial A. haemolyticus isolates. Genome analysis of these sequences and others collected from RefSeq indicates that their chromosomes are organized in 12 syntenic blocks that contain most of the core genome genes. These blocks are separated by hypervariable regions that are rich in unique gene families, but also have signals of horizontal gene transfer. Genes involved in virulence or encoding different secretion systems are located inside syntenic regions and have recombination signals. The relative order of the synthetic blocks along the A. haemolyticus chromosome can change, indicating that they have been subject to several kinds of inversions. Genomes of this microorganism show large differences in gene content even if they are in the same clade. Here we also show that A. haemolyticus has an open pan-genome.\n\nChromosome Architecture and Gene Content of the Emergent Pathogen Acinetobacter haemolyticus.", "token_count": 349, "char_count": 1429, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6373, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:03.313322", "source": { "split": "train_shard_00001", "doc_id": 2394 }, "chunk_id": "train_shard_00001_2394_0", "global_id": 9076 }, { "text": "Recombination is a major driver of evolution in bacterial populations, because it can spread and combine independently evolved beneficial mutations. Recombinant lineages of bacterial pathogens of plants are typically associated with the colonization of novel hosts and the emergence of new diseases. Here we show that recombination between evolutionarily and phenotypically distinct plant-pathogenic lineages generated recombinant lineages with unique combinations of pathogenicity and virulence factors. Xanthomonas euvesicatoria and Xanthomonas perforans are two closely related lineages causing bacterial spot disease on tomato and pepper worldwide. We sequenced the genomes of atypical strains collected from tomato in Nigeria and observed recombination in the type III secretion system and effector genes, which showed alleles from both X. euvesicatoria and X. perforans Wider horizontal gene transfer was indicated by the fact that the lipopolysaccharide cluster of one strain was most similar to that of a distantly related Xanthomonas pathogen of barley. This strain and others have experienced extensive genomewide homologous recombination, and both species exhibited dynamic open pangenomes. Variation in effector gene repertoires within and between species must be taken into consideration when one is breeding tomatoes for disease resistance. Resistance breeding strategies that target specific effectors must consider possibly dramatic variation in bacterial spot populations across global production regions, as illustrated by the recombinant strains observed here.IMPORTANCE The pathogens that cause bacterial spot of tomato and pepper are extensively studied models of plant-microbe interactions and cause problematic disease worldwide. Atypical bacterial spot strains collected from tomato in Nigeria, and other strains from Italy, India, and Florida, showed evidence of genomewide recombination that generated genetically distinct pathogenic lineages. The strains from Nigeria and Italy were found to have a mix of type III secretion system genes from X. perforans and X", "token_count": 481, "char_count": 2140, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5749, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:03.964482", "source": { "split": "train_shard_00001", "doc_id": 2395 }, "chunk_id": "train_shard_00001_2395_0", "global_id": 9077 }, { "text": "euvesicatoria, as well as effectors from Xanthomonas gardneri These genes and effectors are important in the establishment of disease, and effectors are common targets of resistance breeding. Our findings point to global diversity in the genomes of bacterial spot pathogens, which is likely to affect the host-pathogen interaction and influence management decisions.\n\nGenomic Inference of Recombination-Mediated Evolution in Xanthomonas euvesicatoria and X. perforans.", "token_count": 116, "char_count": 479, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:04.346050", "source": { "split": "train_shard_00001", "doc_id": 2395 }, "chunk_id": "train_shard_00001_2395_1", "global_id": 9078 }, { "text": "Salmonella is responsible for many nontyphoidal foodborne infections and enteric (typhoid) fever in humans. Of the two Salmonella species, Salmonella enterica is highly diverse and includes 10 known subspecies and approximately 2,600 serotypes. Understanding the evolutionary processes that generate the tremendous diversity in Salmonella is important in reducing and controlling the incidence of disease outbreaks and the emergence of virulent strains. In this study, we aim to elucidate the impact of homologous recombination in the diversification of S. enterica subspecies. Using a data set of previously published 926 Salmonella genomes representing the 10 S. enterica subspecies and Salmonella bongori, we calculated a genus-wide pan-genome composed of 84,041 genes and the S. enterica pan-genome of 81,371 genes. The size of the accessory genomes varies between 12,429 genes in S. enterica subsp. arizonae (subsp. IIIa) to 33,257 genes in S. enterica subsp. enterica (subsp. I). A total of 12,136 genes in the Salmonella pan-genome show evidence of recombination, representing 14.44% of the pan-genome. We identified genomic hot spots of recombination that include genes associated with flagellin and the synthesis of methionine and thiamine pyrophosphate, which are known to influence host adaptation and virulence. Last, we uncovered within-species heterogeneity in rates of recombination and preferential genetic exchange between certain donor and recipient strains. Frequent but biased recombination within a bacterial species may suggest that lineages vary in their response to environmental selection pressure", "token_count": 507, "char_count": 1720, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:04.984575", "source": { "split": "train_shard_00001", "doc_id": 2396 }, "chunk_id": "train_shard_00001_2396_0", "global_id": 9079 }, { "text": "Certain lineages, such as the more uncommon non-enterica subspecies (non-S. enterica subsp. enterica), may also act as a major reservoir of genetic diversity for the wider population.IMPORTANCE S. enterica is a major foodborne pathogen, which can be transmitted via several distinct routes from animals and environmental sources to human hosts. Multiple subspecies and serotypes of S. enterica exhibit considerable differences in virulence, host specificity, and colonization. This study provides detailed insights into the dynamics of recombination and its contributions to S. enterica subspecies evolution. Widespread recombination within the species means that new adaptations arising in one lineage can be rapidly transferred to another lineage. We therefore predict that recombination has been an important factor in the emergence of several major disease-causing strains from diverse genomic backgrounds and their ability to adapt to disparate environments.\n\nDistinct but Intertwined Evolutionary Histories of Multiple Salmonella enterica Subspecies.", "token_count": 270, "char_count": 1105, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7361, "quality_score": 0.8681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:05.549145", "source": { "split": "train_shard_00001", "doc_id": 2396 }, "chunk_id": "train_shard_00001_2396_1", "global_id": 9080 }, { "text": "

Unlabelled

Pseudomonas aeruginosa is an antibiotic-refractory pathogen with a large genome and extensive genotypic diversity. Historically, P. aeruginosa has been a major model system for understanding the molecular mechanisms underlying type I clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated protein (CRISPR-Cas)-based bacterial immune system function. However, little information on the phylogenetic distribution and potential role of these CRISPR-Cas systems in molding the P. aeruginosa accessory genome and antibiotic resistance elements is known. Computational approaches were used to identify and characterize CRISPR-Cas systems within 672 genomes, and in the process, we identified a previously unreported and putatively mobile type I-C P. aeruginosa CRISPR-Cas system. Furthermore, genomes harboring noninhibited type I-F and I-E CRISPR-Cas systems were on average ~300 kb smaller than those without a CRISPR-Cas system. In silico analysis demonstrated that the accessory genome (n = 22,036 genes) harbored the majority of identified CRISPR-Cas targets. We also assembled a global spacer library that aided the identification of difficult-to-characterize mobile genetic elements within next-generation sequencing (NGS) data and allowed CRISPR typing of a majority of P. aeruginosa strains. In summary, our analysis demonstrated that CRISPR-Cas systems play an important role in shaping the accessory genomes of globally distributed P. aeruginosa isolates.

Importance

P. aeruginosa is both an antibiotic-refractory pathogen and an important model system for type I CRISPR-Cas bacterial immune systems. By combining the genome sequences of 672 newly and previously sequenced genomes, we were able to provide a global view of the phylogenetic distribution, conservation, and potential targets of these systems. This analysis identified a new and putatively mobile P", "token_count": 486, "char_count": 1926, "word_count": 258, "semantic_coherence": 1, "information_density": 0.562, "quality_score": 0.781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:06.195950", "source": { "split": "train_shard_00001", "doc_id": 2397 }, "chunk_id": "train_shard_00001_2397_0", "global_id": 9081 }, { "text": "aeruginosa CRISPR-Cas subtype, characterized the diverse distribution of known CRISPR-inhibiting genes, and provided a potential new use for CRISPR spacer libraries in accessory genome analysis. Our data demonstrated the importance of CRISPR-Cas systems in modulating the accessory genomes of globally distributed strains while also providing substantial data for subsequent genomic and experimental studies in multiple fields. Understanding why certain genotypes of P. aeruginosa are clinically prevalent and adept at horizontally acquiring virulence and antibiotic resistance elements is of major clinical and economic importance.\n\nPhylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa.", "token_count": 169, "char_count": 729, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:06.635204", "source": { "split": "train_shard_00001", "doc_id": 2397 }, "chunk_id": "train_shard_00001_2397_1", "global_id": 9082 }, { "text": "Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, multi-locus sequence typing (MLST), Neisseria gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains compared to previous molecular typing schemes. However, WGS remains unavailable or not affordable in many laboratories, and thus bioinformatic tools that allow the integration of data among laboratories with and without access to WGS are imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for fast, simultaneous and accurate sequence typing of N. gonorrhoeae from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes, NG-MAST genogroups and penA mosaicism, facilitating multiple sequence typing from large WGS assembly collections. Exact and closest matches for existing alleles and sequence types are reported. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 min. The mapping of typing results on a core genome tree of 2375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance as a driver of gonococcal evolution. This article contains data hosted by Microreact.", "token_count": 478, "char_count": 1879, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6576, "quality_score": 0.8288, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:07.276683", "source": { "split": "train_shard_00001", "doc_id": 2398 }, "chunk_id": "train_shard_00001_2398_0", "global_id": 9083 }, { "text": "pyngoST: fast, simultaneous and accurate multiple sequence typing of Neisseria gonorrhoeae genome collections.", "token_count": 35, "char_count": 117, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:07.651870", "source": { "split": "train_shard_00001", "doc_id": 2398 }, "chunk_id": "train_shard_00001_2398_1", "global_id": 9084 }, { "text": "Grain legumes are a rich source of dietary protein for millions of people globally and thus a key driver for securing global food security. Legume plant-based 'dietary protein' biofortification is an economic strategy for alleviating the menace of rising malnutrition-related problems and hidden hunger. Malnutrition from protein deficiency is predominant in human populations with an insufficient daily intake of animal protein/dietary protein due to economic limitations, especially in developing countries. Therefore, enhancing grain legume protein content will help eradicate protein-related malnutrition problems in low-income and underprivileged countries. Here, we review the exploitable genetic variability for grain protein content in various major grain legumes for improving the protein content of high-yielding, low-protein genotypes. We highlight classical genetics-based inheritance of protein content in various legumes and discuss advances in molecular marker technology that have enabled us to underpin various quantitative trait loci controlling seed protein content (SPC) in biparental-based mapping populations and genome-wide association studies. We also review the progress of functional genomics in deciphering the underlying candidate gene(s) controlling SPC in various grain legumes and the role of proteomics and metabolomics in shedding light on the accumulation of various novel proteins and metabolites in high-protein legume genotypes. Lastly, we detail the scope of genomic selection, high-throughput phenotyping, emerging genome editing tools, and speed breeding protocols for enhancing SPC in grain legumes to achieve legume-based dietary protein security and thus reduce the global hunger risk.\n\nEnsuring Global Food Security by Improving Protein Content in Major Grain Legumes Using Breeding and 'Omics' Tools.", "token_count": 400, "char_count": 1845, "word_count": 250, "semantic_coherence": 1, "information_density": 0.592, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:08.273613", "source": { "split": "train_shard_00001", "doc_id": 2399 }, "chunk_id": "train_shard_00001_2399_0", "global_id": 9085 }, { "text": "Haemophilus influenzae is a major cause of community and hospital acquired pneumonia. While extensively studied in various laboratory models, less is known about how this species persists and causes infection inside the human lung. We present the first study on the H. influenzae in vivo transcriptome during pneumonia, and contrast this with isolates cultured in vitro under standard laboratory conditions. Patients with pneumonia were recruited from emergency departments and intensive care units in a Swedish referral hospital during 2018-2020 (n=102). Duplicates of lower respiratory samples were collected for bacterial culture and RNA-extraction. Patient samples with H. influenzae (n=18) from which bacterial mRNA of adequate quantity and quality could be extracted (n=8) underwent RNA-sequencing, along with duplicates of lab-cultured counterparts (n=7). The transcripts were aligned to core and pan genomes created from 15 reference strains. While in vitro bacteria clustered tightly in principal component analyses of core genome (n=1067) expression, the in vivo samples displayed diverse transcriptomic signatures and did not group with their lab-grown counterparts. In total, 328 core genes were significantly differentially expressed between in vitro and in vivo conditions. The most upregulated genes in vivo included the transferrin-acquisition genes tbp1 and fbpA and the reductase gene msrAB involved in stress response pathways. Biosynthesis of nucleotides/purines, response-to-heat systems, and molybdopterin-scavenging processes were also significantly upregulated in vivo. Major metabolic pathways and iron-sequestering processes were downregulated in vivo. In conclusion, extensive transcriptomic differences were found between bacteria collected in the human lung during pneumonia and isogenic bacteria cultured in vitro.\n\nTheHaemophilus influenzaein vivo gene expression reveals major clues about bacterial central metabolism, acquisition of trace elements, and other essential pathways during infection of the human lung", "token_count": 496, "char_count": 2052, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:08.926389", "source": { "split": "train_shard_00001", "doc_id": 2400 }, "chunk_id": "train_shard_00001_2400_0", "global_id": 9086 }, { "text": "

Background

Since 2019, the incidence of anthrax in the Ningxia Hui Autonomous Region has increased significantly compared with previous years, so in this situation the anthrax in the Ningxia region not only had a detrimental impact on public health, but also inflicted significant economic repercussions. Therefore, we conducted a molecular epidemiological study of 20 strains from 2019-2023 isolates. This study investigated the origin of Bacillus anthracis and its genetic diversity.

Methods

We conducted canonical single-nucleotide polymorphisms (CanSNPs) typing and whole genome sequencing based on the extracted nucleic acid of Bacillus anthracis. Based on the whole genome drafts, we studied the genomic characteristics of 20 isolates. Meanwhile, we performed phylogenetic studies based on genome-wide core single-nucleotide polymorphisms (SNPs) using MEGA's Maximum Likelihood (ML) method and core-genome-based multilocus sequence typing (cgMLST) of the core genomes of these strains using BioNumerics' minimum spanning tree (MST) model.

Results

The 20 isolates were categorized into sub-lineages A.Br.001/002, and comparative genomic analyses of these strains with other isolates from other parts of the world showed that the strains from Ningxia were correlated with isolates from Europe, Indonesia, Georgia (USA), and Beijing (China). For the 20 isolates in Ningxia, the genetic relationship of the isolates isolated from the same year or region was relatively close.

Conclusion

The A.Br.001/002 subgroup was the dominant endemic strain in Ningxia. The genetic relationship and phylogenesis between isolates from Ningxia and strains from Europe and Indonesia suggest that anthrax spread around the globe through ancient trade routes.", "token_count": 491, "char_count": 1786, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:09.930161", "source": { "split": "train_shard_00001", "doc_id": 2401 }, "chunk_id": "train_shard_00001_2401_0", "global_id": 9087 }, { "text": "Whole Genome-Sequencing and Phylogenetic Analysis of Bacillus anthracis from 2019-2023 in Ningxia Hui Autonomous Region, China.", "token_count": 53, "char_count": 134, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:10.292731", "source": { "split": "train_shard_00001", "doc_id": 2401 }, "chunk_id": "train_shard_00001_2401_1", "global_id": 9088 }, { "text": "

Background

In 2015, Staphylococcus argenteus was reported for the first time as a novel species of the Staphylococcus aureus complex. While S. argenteus has been found in many countries, its presence in Indonesia has not been reported yet. Our aim is to confirm S. argenteus presence in Indonesia, describe its characteristics and analyze its genomic diversity.

Methods

The S. aureus isolates used in this study were collected from patients with skin and soft tissue infections in Indonesia, between July 2009 to February 2010. Randomly selected isolates were recultured from -80 C° stocks and analyzed using matrix-assisted laser desorption/ionization - time of flight (MALDI-TOF). Isolates identified as S. argenteus, S. roterodami, or S. schweitzeri and S. aureus with a low score in the MALDI-TOF analysis were analyzed by a real-time PCR targeting the nucA gene able to identify true S. argenteus. Isolates identified as S. argenteus were further characterized by whole genome sequencing. Vitek®2 (bioMérieux) was used for antimicrobial susceptibility testing.

Results

Fifteen isolates were identified as S. argenteus, with the majority belonging to ST2250. Two pairs of isolates proved to be identical by core genome multilocus sequence typing analysis. Most isolates were susceptible to all antibiotics tested, except for seven isolates (46.7 %) that were resistant to benzylpenicillin, and one isolate was resistant to tetracycline (6.7 %). The presence of resistance genes blaZ and tet(45) correlated with these findings. Notably, the sey enterotoxin gene was prevalent in 80 % of the isolates. Other virulence factor genes were less prevalent. Plasmid replicon types in S. argenteus were also known to S. aureus.

Conclusion

Our study reveals the occurrence of S. argenteus in Indonesia. The diversity within Indonesian S. argenteus matches the global diversity of S", "token_count": 538, "char_count": 1904, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [ "ST2250" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:24:10.923248", "source": { "split": "train_shard_00001", "doc_id": 2402 }, "chunk_id": "train_shard_00001_2402_0", "global_id": 9089 }, { "text": "argenteus. Identical isolates between patients indicate potential transmission events. A lower prevalence of a broad panel of virulence factors suggests that S. argenteus is less virulent than S. aureus.\n\nIdentification and characterization of Staphylococcus argenteus from Indonesia.", "token_count": 66, "char_count": 284, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:11.339492", "source": { "split": "train_shard_00001", "doc_id": 2402 }, "chunk_id": "train_shard_00001_2402_1", "global_id": 9090 }, { "text": "

Objectives

Pseudomonas aeruginosa (P. aeruginosa) are ubiquitous opportunistic pathogens that combine intrinsic and acquired multidrug resistance phenotypes. Due to different types of acquired genes, carbapenem resistance has been expanding in this species. This study hypothesised that the spread of carbapenem resistance among P. aeruginosa is influenced by phylogenomic features, being distinct for different genes.

Methods

To test this hypothesis, the genomes of P. aeruginosa harbouring blaVIM-2 or blaNDM-1 genes were compared. The blaVIM-2 gene was selected because, although frequent, it is almost restricted to this species and blaNDM-1 gene due to its wide interspecies distribution. A group of genomes harbouring the genes blaVIM-2 (n = 116) or blaNDM-1 (n = 27), available in GenBank, was characterised based on core phylogenomic analysis, functional categories in the accessory genome and mobile genetic elements flanking the selected genes.

Results

Most blaVIM-2 gene hosts belonged to multilocus sequence types (ST) ST111 (n = 32 of 116) and ST233 (n = 27 of 116) and were reported in Europe (n = 75 of 116). The blaNDM-1 gene hosts were distributed by different STs (ST38, ST773, ST235, ST357 and ST654), frequently from Asia (n = 11 of 27). Significant differences in the prevalence of functional protein/enzyme annotations per number of accessory genomes were observed between blaVIM-2+ and blaNDM-1+", "token_count": 497, "char_count": 1550, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [ "ST773", "ST233", "ST357", "ST235", "ST111", "ST38", "ST654" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:12.008937", "source": { "split": "train_shard_00001", "doc_id": 2403 }, "chunk_id": "train_shard_00001_2403_0", "global_id": 9091 }, { "text": "The blaVIM-2 gene was frequently inserted in the Tn402-like and Tn21 transposons family and rarely in IS6100, while blaNDM-1 gene was preferentially flanked by ISAba125 and bleMBL genes or associated with IS91 insertion sequence.

Conclusion

The hypothesis that carbapenem resistance gene acquisition is not random among phylogenomic lineages was confirmed, suggesting the importance of phylogeny in the dissemination of antibiotic resistance genes.\n\nInsight into phylogenomic bias of bla<sub>VIM-2</sub> or bla<sub>NDM-1</sub> dissemination amongst carbapenem-resistant Pseudomonas aeruginosa.", "token_count": 217, "char_count": 657, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7671, "quality_score": 0.8836, "entities": { "genes": [ "IS6100", "IS91" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:12.503642", "source": { "split": "train_shard_00001", "doc_id": 2403 }, "chunk_id": "train_shard_00001_2403_1", "global_id": 9092 }, { "text": "Arcobacter butzleri is a food and waterborne bacteria and an emerging human pathogen, frequently displaying a multidrug resistant character. Still, no comprehensive genome-scale comparative analysis has been performed so far, which has limited our knowledge on A. butzleri diversification and pathogenicity. Here, we performed a deep genome analysis of A. butzleri focused on decoding its core- and pan-genome diversity and specific genetic traits underlying its pathogenic potential and diverse ecology. In total, 49 A. butzleri strains (collected from human, animal, food and environmental sources) were screened. A. butzleri (genome size 2.07-2.58 Mbp) revealed a large open pan-genome with 7474 genes (about 50% being singletons) and a small core-genome with 1165 genes. The core-genome is highly diverse (≥55% of the core genes presenting at least 40/49 alleles), being enriched with genes associated with housekeeping functions. In contrast, the accessory genome presented a high proportion of loci with an unknown function, also being particularly overrepresented by genes associated with defence mechanisms. A. butzleri revealed a plastic virulome (including newly identified determinants), marked by the differential presence of multiple adaptation-related virulence factors, such as the urease cluster ureD(AB)CEFG (phenotypically confirmed), the hypervariable hemagglutinin-encoding hecA , a putative type I secretion system (T1SS) harboring another agglutinin potentially related to adherence and a novel VirB/D4 T4SS likely linked to interbacterial competition and cytotoxicity. In addition, A. butzleri harbors a large repertoire of efflux pumps (EPs) (ten “core” and nine differentially present) and other antibiotic resistant determinants. We provide the first description of a genetic determinant of macrolides resistance in A. butzleri , by associating the inactivation of a TetR repressor (likely regulating an EP) with erythromycin resistance", "token_count": 509, "char_count": 1962, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6801, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:13.181699", "source": { "split": "train_shard_00001", "doc_id": 2404 }, "chunk_id": "train_shard_00001_2404_0", "global_id": 9093 }, { "text": "Fluoroquinolones resistance correlated with the Thr-85-Ile substitution in GyrA and ampicillin resistance was linked to an OXA-15-like β-lactamase. Remarkably, by decoding the polymorphism pattern of the porin- and adhesin-encoding main antigen PorA, this study strongly supports that this pathogen is able to exchange porA as a whole and/or hypervariable epitope-encoding regions separately, leading to a multitude of chimeric PorA presentations that can impact pathogen-host interaction during infection. Ultimately, our unprecedented screening of short sequence repeats detected potential phase-variable genes related to adaptation and host/environment interaction, such as lipopolysaccharide modification and motility/chemotaxis, suggesting that phase variation likely modulate A. butzleri key adaptive functions. In summary, this study constitutes a turning point on A. butzleri comparative genomics revealing that this human gastrointestinal pathogen is equipped with vast virulence and antibiotic resistance arsenals, which, coupled with its remarkable core- and pan-genome diversity, opens a multitude of phenotypic fingerprints for environmental/host adaptation and pathogenicity.

IMPACT STATEMENT

Diarrhoeal diseases are the most common cause of human illness caused by foodborne hazards, but the surveillance of diarrhoeal diseases is biased towards the most commonly searched infectious agents (namely Campylobacter jejuni and C. coli ). In fact, other less studied pathogens are frequently found as the etiological agent when refined non-selective culture conditions are applied. A hallmark example is the diarrhoeal-causing Arcobacter butzleri which, despite being also associated with extra-intestinal diseases, such as bacteremia in humans and mastitis in animals, and displaying high rates of antibiotic resistance, has not yet been profoundly investigated regarding its epidemiology, diversity and pathogenicity. To overcome the general lack of knowledge on A. butzleri comparative genomics, we provide the first comprehensive genome-scale analysis of A", "token_count": 492, "char_count": 2080, "word_count": 273, "semantic_coherence": 1, "information_density": 0.7033, "quality_score": 0.8516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:13.828150", "source": { "split": "train_shard_00001", "doc_id": 2404 }, "chunk_id": "train_shard_00001_2404_1", "global_id": 9094 }, { "text": "butzleri focused on exploring the intraspecies virulome content and diversity, resistance determinants, as well as how this pathogen shapes its genome towards ecological adaptation and host invasion. The unveiled scenario of A. butzleri rampant diversity and plasticity reinforces the pathogenic potential of this food and waterborne hazard, while opening multiple research lines that will certainly contribute to the future development of more robust species-oriented diagnostics and molecular surveillance of A. butzleri .

DATA SUMMARY

A. butzleri raw sequence reads generated in the present study were deposited in the European Nucleotide Archive (ENA) (BioProject PRJEB34441). The assembled contigs (.fasta and .gbk files), the nucleotide sequences of the predicted transcripts (CDS, rRNA, tRNA, tmRNA, misc_RNA) (.ffn files) and the respective amino acid sequences of the translated CDS sequences (.faa files) are available at http://doi.org/10.5281/zenodo.3434222 . Detailed ENA accession numbers, as well as the draft genome statistics are described in Table S1.\n\nVirulence and antibiotic resistance plasticity ofArcobacter butzleri: insights on the genomic diversity of an emerging human pathogen", "token_count": 329, "char_count": 1220, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7048, "quality_score": 0.8524, "entities": { "genes": [ "PRJEB34441" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:14.395330", "source": { "split": "train_shard_00001", "doc_id": 2404 }, "chunk_id": "train_shard_00001_2404_2", "global_id": 9095 }, { "text": "In 1989, Bouvet and Jeanjean delineated five proteolytic genomic species (GS) of Acinetobacter, each with two to four human isolates. Three were later validly named, whereas the remaining two (GS15 and GS16) have been awaiting nomenclatural clarification. Here we present the results of the genus-wide taxonomic study of 13 human strains classified as GS16 (n=10) or GS15 (n=3). Based on core genome phylogenetic analysis, the strains formed two respective but closely related phylogroups within the Acinetobacter haemolytic clade. The intraspecies genomic average nucleotide identity based on blast (ANIb) values for GS16 and GS15 reached ≥94.9 % and ≥98.7, respectively, whereas ANIb values between them were 92.5-93.5% and those between them and the known species were ≤91.5 %. GS16 and GS15 could be differentiated from the other Acinetobacter species by their ability to lyse gelatin and sheep blood and to assimilate d,l-lactate, along with their inability to acidify d-glucose and assimilate glutarate. In contrast, GS16 and GS15 were indistinguishable from one another by metabolic/physiological features or whole-cell MALDI-TOF mass spectra. All the GS15/GS16 genomes contained genes encoding a class D β-lactamase, Acinetobacter-derived cephalosporinase and aminoglycoside 6'-N-acetyltransferase. Searching NCBI databases revealed genome sequences of three additional isolates of GS16, but none of GS15", "token_count": 482, "char_count": 1461, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6965, "quality_score": 0.8483, "entities": { "genes": [ "GS16", "GS15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:15.036937", "source": { "split": "train_shard_00001", "doc_id": 2405 }, "chunk_id": "train_shard_00001_2405_0", "global_id": 9096 }, { "text": "We conclude that our data support GS16 as representing a novel species, but leave the question of the taxonomic status of GS15 open, given its close relatedness to GS16 and the small number of available strains. We propose the name Acinetobacter higginsii sp. nov. for GS16, with the type strain NIPH 1872T (CCM 9243T=CIP 70.18T=ATCC 17988T).\n\nProposal for Acinetobacter higginsii sp. nov. to accommodate organisms of human clinical origin previously classified as Acinetobacter genomic species 16.", "token_count": 196, "char_count": 563, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [ "GS16", "GS15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:15.487580", "source": { "split": "train_shard_00001", "doc_id": 2405 }, "chunk_id": "train_shard_00001_2405_1", "global_id": 9097 }, { "text": "The Gram-negative non-motile Klebsiella pneuomoniae is currently a major cause of hospital-acquired (HA) and community-acquired (CA) infections, leading to great public health concern globally, while rapid identification and accurate tracing of the pathogenic bacterium is essential in facilitating monitoring and controlling of K. pneumoniae outbreak and dissemination. Multi-locus sequence typing (MLST) is a commonly used typing approach with low cost that is able to distinguish bacterial isolates based on the allelic profiles of several housekeeping genes, despite low resolution and labor intensity of the method. Core-genome MLST scheme (cgMLST) is recently proposed to sub-type and monitor outbreaks of bacterial strains with high resolution and reliability, which uses hundreds or thousands of genes conserved in all or most members of the species. However, the method is complex and requires whole genome sequencing of bacterial strains with high costs. Therefore, it is urgently needed to develop novel methods with high resolution and low cost for bacterial typing. Surface enhanced Raman spectroscopy (SERS) is a rapid, sensitive and cheap method for bacterial identification. Previous studies confirmed that classification and prediction of bacterial strains via SERS spectral analysis correlated well with MLST typing results. However, there is currently no similar comparative analysis in K. pneumoniae strains. In this pilot study, 16 K. pneumoniae strains with different sequencing typings (STs) were selected and a phylogenetic tree was constructed based on core genome analysis. SERS spectra (N = 45/each strain) were generated for all the K. pneumoniae strains, which were then comparatively classified and predicted via six representative machine learning (ML) algorithms. According to the results, SERS technique coupled with the ML algorithm support vector machine (SVM) could achieve the highest accuracy (5-Fold Cross Validation = 100%) in terms of differentiating and predicting all the K. pneumoniae strains that were consistent to corresponding MLSTs", "token_count": 512, "char_count": 2136, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6309, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:16.149934", "source": { "split": "train_shard_00001", "doc_id": 2406 }, "chunk_id": "train_shard_00001_2406_0", "global_id": 9098 }, { "text": "In sum, we show in this pilot study that the SERS-SVM based method is able to accurately predict K. pneumoniae MLST types, which has the application potential in clinical settings for tracing dissemination and controlling outbreak of K. pneumoniae in hospitals and communities with low costs and high rapidity.\n\nClassification and prediction of Klebsiella pneumoniae strains with different MLST allelic profiles via SERS spectral analysis.", "token_count": 123, "char_count": 467, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:16.538917", "source": { "split": "train_shard_00001", "doc_id": 2406 }, "chunk_id": "train_shard_00001_2406_1", "global_id": 9099 }, { "text": "Chloroviruses (family Phycodnaviridae) are large double-stranded DNA (dsDNA) viruses that infect unicellular green algae present in inland waters. These viruses have been isolated using three main chlorella-like green algal host cells, traditionally called NC64A, SAG, and Pbi, revealing extensive genetic diversity. In this study, we performed a functional genomic analysis on 36 chloroviruses that infected the three different hosts. Phylogenetic reconstruction based on the DNA polymerase B family gene clustered the chloroviruses into three distinct clades. The viral pan-genome consists of 1,345 clusters of orthologous groups of genes (COGs), with 126 COGs conserved in all viruses. Totals of 368, 268, and 265 COGs are found exclusively in viruses that infect NC64A, SAG, and Pbi algal hosts, respectively. Two-thirds of the COGs have no known function, constituting the \"dark pan-genome\" of chloroviruses, and further studies focusing on these genes may identify important novelties. The proportions of functionally characterized COGs composing the pan-genome and the core-genome are similar, but those related to transcription and RNA processing, protein metabolism, and virion morphogenesis are at least 4-fold more represented in the core genome. Bipartite network construction evidencing the COG sharing among host-specific viruses identified 270 COGs shared by at least one virus from each of the different host groups. Finally, our results reveal an open pan-genome for chloroviruses and a well-established core genome, indicating that the isolation of new chloroviruses can be a valuable source of genetic discovery. IMPORTANCE Chloroviruses are large dsDNA viruses that infect unicellular green algae distributed worldwide in freshwater environments. They comprise a genetically diverse group of viruses; however, a comprehensive investigation of the genomic evolution of these viruses is still missing", "token_count": 501, "char_count": 1932, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6654, "quality_score": 0.8327, "entities": { "genes": [ "NC64A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:17.974314", "source": { "split": "train_shard_00001", "doc_id": 2407 }, "chunk_id": "train_shard_00001_2407_0", "global_id": 9100 }, { "text": "Here, we performed a functional pan-genome analysis comprising 36 chloroviruses associated with three different algal hosts in the family Chlorellaceae, referred to as zoochlorellae because of their endosymbiotic lifestyle. We identified a set of 126 highly conserved genes, most of which are related to essential functions in the viral replicative cycle. Several genes are unique to distinct isolates, resulting in an open pan-genome for chloroviruses. This profile is associated with generalist organisms, and new insights into the evolution and ecology of chloroviruses are presented. Ultimately, our results highlight the potential for genetic diversity in new isolates.\n\nFunctional Genomic Analyses Reveal an Open Pan-genome for the Chloroviruses and a Potential for Genetic Innovation in New Isolates.", "token_count": 201, "char_count": 814, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6783, "quality_score": 0.8391, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:18.433702", "source": { "split": "train_shard_00001", "doc_id": 2407 }, "chunk_id": "train_shard_00001_2407_1", "global_id": 9101 }, { "text": "In the simultaneous saccharification and fermentation to ethanol of 100 g l(-1) microcrystalline cellulose, the cellobiose-fermenting recombinant Klebsiella oxytoca P2 outperformed a range of cellobiose-fermenting yeasts used in earlier work, despite producing less ethanol than reported earlier for this organism under similar conditions. The time taken by K. oxytoca P2 to produce up to about 33 g l(-1) ethanol was much less than for any other organism investigated, including ethanol-tolerant strains of Saccharomyces pastorianus, Kluyveromyces marxianus and Zymomonas mobilis. Ultimately, it produced slightly less ethanol (maximum 36 g l(-1)) than these organisms, reflecting its lower ethanol tolerance. Significant advantages were obtained by co-culturing K. oxytoca P2 with S. pastorianus, K. marxianus or Z. mobilis, either isothermally, or in conjunction with temperature-profiling to raise the cellulase activity. Co-cultures produced significantly more ethanol, more rapidly, than either of the constituent strains in pure culture at the same inoculum density. K. oxytoca P2 dominated the early stages of the co-cultures, with ethanol production in the later stages due principally to the more ethanol tolerant strain. The usefulness of K. oxytoca P2 in cellulose simultaneous saccharification and fermentation should be improved by mutation of the strain to increase its ethanol tolerance.\n\nEvaluation of a recombinant Klebsiella oxytoca strain for ethanol production from cellulose by simultaneous saccharification and fermentation: comparison with native cellobiose-utilising yeast strains and performance in co-culture with thermotolerant yeast and Zymomonas mobilis.", "token_count": 461, "char_count": 1684, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5609, "quality_score": 0.7804, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:19.068228", "source": { "split": "train_shard_00001", "doc_id": 2408 }, "chunk_id": "train_shard_00001_2408_0", "global_id": 9102 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is a leading cause of severe and often fatal infections. MRSA epidemics have occurred in waves, whereby a previously successful lineage has been replaced by a more fit and better adapted lineage. Selection pressures in both hospital and community settings are not uniform across the globe, which has resulted in geographically distinct epidemiology. This review focuses on the mechanisms that trigger the establishment and maintenance of current, dominant MRSA lineages across the globe. While the important role of antibiotic resistance will be mentioned throughout, factors which influence the capacity of S. aureus to colonize and cause disease within a host will be the primary focus of this review. We show that while MRSA possesses a diverse arsenal of toxins including alpha-toxin, the success of a lineage involves more than just producing toxins that damage the host. Success is often attributed to the acquisition or loss of genetic elements involved in colonization and niche adaptation such as the arginine catabolic mobile element, as well as the activity of regulatory systems, and shift metabolism accordingly (e.g., the accessory genome regulator, agr). Understanding exactly how specific MRSA clones cause prolonged epidemics may reveal targets for therapies, whereby both core (e.g., the alpha toxin) and acquired virulence factors (e.g., the Panton-Valentine leukocidin) may be nullified using anti-virulence strategies.\n\nVirulence attributes of successful methicillin-resistant Staphylococcus aureus lineages.", "token_count": 387, "char_count": 1608, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:19.691790", "source": { "split": "train_shard_00001", "doc_id": 2409 }, "chunk_id": "train_shard_00001_2409_0", "global_id": 9103 }, { "text": "

Introduction

The auxanographic carbohydrate assimilation had been an important method for differentiation of yeasts. Prevailing methods described in the literature for carbohydrate assimilation has limited scope for use in large scale yeast identification.

Aim

To optimize the large scale auxanographic carbohydrate assimilation method for yeast identification.

Materials and methods

A modified auxanographic carbohydrate assimilation method was developed and a total of 35 isolates of Candida species comprising of four ATCC (American Type Culture Collection) Candida strains (Candida albicans ATCC 90028, Candida tropicalis ATCC 90018, Candida parapsilosis ATCC 750, Candida krusei ATCC 6258) and 31 clinical isolates of Candida tropicalis (n=13), Candida krusei (n=7), Candida glabrata (n=3), Candida kefyr (n=3), Candida albicans (n=5) were validated. The carbohydrates tested were Glucose, Sucrose, Maltose, Lactose, Cellubiose, Raffinose, Trehalose, Xylose, Galactose and Dulcitol.

Results

A total of 35 Candida species were tested for their carbohydrate assimilative property and the results were consistent with the existing standard protocols. A well circumscribed opaque yeast growth indicated assimilation of the test carbohydrate and translucent to opalescent growth with the outline of initial inoculum alone indicated lack of assimilation", "token_count": 491, "char_count": 1465, "word_count": 174, "semantic_coherence": 1, "information_density": 0.592, "quality_score": 0.796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:20.341342", "source": { "split": "train_shard_00001", "doc_id": 2410 }, "chunk_id": "train_shard_00001_2410_0", "global_id": 9104 }, { "text": "The control plate indicated no growth of the Candida species.

Conclusion

The carbohydrate assimilation tests finds utility for yeast diversity studies exploring novel ecological niches. The technique described here facilitates testing of an extended range of carbohydrates and yeasts in a cost effective manner.\n\nAuxanographic Carbohydrate Assimilation Method for Large Scale Yeast Identification.", "token_count": 104, "char_count": 411, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8431, "quality_score": 0.9216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:20.722460", "source": { "split": "train_shard_00001", "doc_id": 2410 }, "chunk_id": "train_shard_00001_2410_1", "global_id": 9105 }, { "text": "Inflammatory bowel disease (IBD) is an incurable, chronic disorder of the gastrointestinal tract whose incidence increases every year. Scientific research constantly delivers new information about the disease and its multivariate, complex etiology. Nevertheless, full discovery and understanding of the complete mechanism of IBD pathogenesis still pose a significant challenge to today's science. Recent studies have unanimously confirmed the association of gut microbial dysbiosis with IBD and its contribution to the regulation of the inflammatory process. It transpires that the altered composition of pathogenic and commensal bacteria is not only characteristic of disturbed intestinal homeostasis in IBD, but also of viruses, parasites, and fungi, which are active in the intestine. The crucial function of the microbial metabolome in the human body is altered, which causes a wide range of effects on the host, thus providing a basis for the disease. On the other hand, human genomic and functional research has revealed more loci that play an essential role in gut homeostasis regulation, the immune response, and intestinal epithelial function. This review aims to organize and summarize the currently available knowledge concerning the role and interaction of crucial factors associated with IBD pathogenesis, notably, host genetic composition, intestinal microbiota and metabolome, and immune regulation.\n\nThe Role of Host Genetics and Intestinal Microbiota and Metabolome as a New Insight into IBD Pathogenesis.", "token_count": 334, "char_count": 1522, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:21.298275", "source": { "split": "train_shard_00001", "doc_id": 2411 }, "chunk_id": "train_shard_00001_2411_0", "global_id": 9106 }, { "text": "

Importance

The International Space Station (ISS) is a unique, hermetically sealed environment, subject to environmental pressures not encountered on Earth, including microgravity and radiation (cosmic ionising/UV). While bacteria's adaptability during spaceflight remains elusive, recent research suggests that it may be species and even clone-specific. Considering the documented spaceflight-induced suppression of the human immune system, a deper understanding of the genomics of potential human pathogens in space could shed light on species and lineages of medical astromicrobiological significance. In this study, we used hybrid assembly methods and comparative genomics to deliver a comprehensive genomic characterization of 10 Klebsiella isolates retrieved from the ISS. Our analysis unveiled that Klebsiella quasipneumoniae ST138 demonstrates both spatial and temporal persistence aboard the ISS, showing evidence of genomic divergence from its Earth-based ST138 lineage. Moreover, we characterized plasmids from Klebsiella species of ISS origin, which harbored genes for disinfectant resistance and enhanced thermotolerance, suggestin possible adaptive advantages. Furthermore, we identified a mobile genetic element containing a hypervirulence-associated locus belonging to a Klebsiella pneumoniae isolate of the \"high-risk\" ST101 clone. Our work provides insights into the adaptability and persistence of Klebsiella species during spaceflight, highlighting the importance of understanding the dynamics of potential pathogenic bacteria in such environments.\n\nGenomic analysis reveals the presence of emerging pathogenic Klebsiella lineages aboard the International Space Station.", "token_count": 418, "char_count": 1739, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6884, "quality_score": 0.8442, "entities": { "genes": [ "ST138", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:21.913905", "source": { "split": "train_shard_00001", "doc_id": 2412 }, "chunk_id": "train_shard_00001_2412_0", "global_id": 9107 }, { "text": "The yeast Torulaspora delbrueckii is gaining importance for biotechnology due to its ability to increase wine sensorial complexity and for enhancing pre-frozen bread dough leavening. However, little is known about its population structure, variation in gene content, or possible domestication routes. Here, we address these issues and update the delimitation of T. delbrueckii along five major clades. Among the three European clades, a basal lineage is associated with the wild arboreal niche, while the two other lineages are linked with anthropic environments, one to wine fermentations and the other to diverse sources including dairy products and bread dough (Mix- Anthropic clade). Using 62 genomes we identified 5629 genes in the pangenome of T. delbrueckii and 270 genes in the cloud genome. A pangenome tree analysis showed that wine strains have a genome composition more similar to European wild arboreal strains than to those of the Mix Anthropic clade, in contradiction with the phylogenetic analysis. An association of gene content and ecology gave further support to the hypothesis that the Mix - Anthropic clade has the most specialized genome content and indicated that some of the exclusive genes were implicated in galactose and maltose utilization. More detailed analyses traced the acquisition of a cluster of GAL genes in strains associated with dairy products and the expansion and functional diversification of MAL genes in strains isolated from bread dough. Contrary to S. cerevisiae, domestication in T. delbrueckii is not primed by alcoholic fermentation and appears to be a recent event.\n\nA glimpse at an early stage of microbe domestication revealed in the variable genome of Torulaspora delbrueckii, an emergent industrial yeast", "token_count": 416, "char_count": 1758, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6022, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:22.537635", "source": { "split": "train_shard_00001", "doc_id": 2413 }, "chunk_id": "train_shard_00001_2413_0", "global_id": 9108 }, { "text": "Streptococcus pneumoniae adapts within hosts through genetic variation and genome plasticity, facilitating persistence under antibiotic and immune pressures. Here, we investigated a prolonged pneumococcal carriage episode (>337 days) in a healthy, HIV-uninfected adult in Malawi. Whole-genome sequencing of single-colony isolates and plate sweep samples confirmed persistent colonisation by a multidrug-resistant serotype 3 strain with a distinct sequence type (GPSC10-ST18362), which maintained stable predominance despite transient acquisition of other serotypes. The sequentially sampled isolates showed 2 to 11 single-nucleotide polymorphism differences, no evidence of recombination, and modest gene loss involving mobile genetic elements. The total genome size decreased from 2.06 Mb to 2.03 Mb across isolates. Intrahost single-nucleotide variants were identified in genes related to metabolism, stress response, and DNA repair, but showed no consistent signatures of positive selection. Capsular locus analysis revealed deletions consistent with GPSC10-related vaccine-escape profiles. These findings highlight the capacity of GPSC10-ST18362 to persist asymptomatically for months with limited within-host genomic diversity.\n\nWithin-host genetic diversity of pneumococcal serotype 3 during one-year prolonged carriage in a healthy adult.", "token_count": 342, "char_count": 1345, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7765, "quality_score": 0.8882, "entities": { "genes": [ "GPSC10", "ST18362" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:23.117819", "source": { "split": "train_shard_00001", "doc_id": 2414 }, "chunk_id": "train_shard_00001_2414_0", "global_id": 9109 }, { "text": "The role of indigenous fungi in the appropriate development of sensory properties and the safety of dry-fermented sausages has been widely established. Nonetheless, their applications as probiotic agents have not been elucidated in such products yet, despite their promising functional features. Thus, it should be interesting to evaluate the probiotic potential of native Debaryomyces hansenii isolates from dry-fermented sausages and their application in the meat industry, because it is the most frequently isolated yeast species from these foodstuffs and its probiotic effects for animals as well as its possible probiotic activity for human beings have been demonstrated. Within the functional ability of foodborne yeasts, anti-inflammatory, antioxidant, antimicrobial, antigenotoxic, and immunomodulatory properties have been reported. Similarly, the use of dry-fermented sausages as vehicles for probiotic moulds remains a challenge because the survival and development of moulds in the gastrointestinal tract are still unknown. Nevertheless, some moulds have been isolated from faeces possibly from their spores as a form of resistance. Additionally, their beneficial effects on animals and humans, such as the decrease in lipid content and the anti-inflammatory activity, have been reported, although they seem to be more related to their postbiotic capacity due to the generated bioactive compounds with profunctional attributes than to their role as probiotics. Therefore, further studies providing knowledge useful for generating dry-fermented sausages with improved functionality are fully necessary.\n\nPerspectives on the Probiotic Potential of Indigenous Moulds and Yeasts in Dry-Fermented Sausages.", "token_count": 386, "char_count": 1720, "word_count": 236, "semantic_coherence": 1, "information_density": 0.589, "quality_score": 0.7945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:23.772200", "source": { "split": "train_shard_00001", "doc_id": 2415 }, "chunk_id": "train_shard_00001_2415_0", "global_id": 9110 }, { "text": "When testing conditions that prevail in fruit juice industry it was found that Listeria monocytogenes ATCC 7644 and a wild strain of Listeria innocua were highly hydrophobic, expressed swimming and twitching, co‐aggregated with yeast cells and produced exopolysaccharide, all characteristics that would favor the adhesive process. In mono‐species biofilms, L. innocua adhered on stainless steel at significantly higher counts than L. monocytogenes achieving values of 6.64 ± 0.01 and 5.80 ± 0.21 log CFU/cm². In dual species biofilms with resident yeasts, L. innocua cells counts increase significantly in the presence of Candida tropicalis and Candida krusei and decrease significantly in the presence of Rhodotorula mucilaginosa and Candida kefyr. When cocultured with Candida tropicalis, the cell numbers of L. monocytogenes had a significant increase. These results revealed synergic and antagonistic interactions among species. PRACTICAL APPLICATIONS: The study supports the plausibility that interactions between L. monocytogenes and members of resident microbiota, such as C. tropicalis, C. krusei, C. kefyr, and R. mucilaginosa, might play an important role for the survival and dissemination of L. monocytogenes. Apple juice processing conditions was used as simulation of the real condition in fruit juice processing environment and these results will alert to fruit juice industry to adopt the best cleaning and disinfecting practices against Listeria.\n\nMultispecies biofilms between Listeria monocytogenes and Listeria innocua with resident microbiota isolated from apple juice processing equipment", "token_count": 417, "char_count": 1610, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:24.420765", "source": { "split": "train_shard_00001", "doc_id": 2416 }, "chunk_id": "train_shard_00001_2416_0", "global_id": 9111 }, { "text": "In response to the massive use of biocides for controlling Listeria monocytogenes (hereafter Lm) contaminations along the food chain, strains showing biocide tolerance emerged. Here, accessory genomic elements were associated with biocide tolerance through pangenome-wide associations performed on 197 Lm strains from different lineages, ecological, geographical and temporal origins. Mobile elements, including prophage-related loci, the Tn6188_qacH transposon and pLMST6_emrC plasmid, were widespread across lineage I and II food strains and associated with tolerance to benzalkonium-chloride (BC), a quaternary ammonium compound (QAC) widely used in food processing. The pLMST6_emrC was also associated with tolerance to another QAC, the didecyldimethylammonium-chloride, displaying a pleiotropic effect. While no associations were detected for chemically reactive biocides (alcohols and chlorines), genes encoding for cell-surface proteins were associated with BC or polymeric biguanide tolerance. The latter was restricted to lineage I strains from animal and the environment. In conclusion, different genetic markers, with polygenic nature or not, appear to have driven the Lm adaptation to biocide, especially in food strains but also from animal and the environment. These markers could aid to monitor and predict the spread of biocide tolerant Lm genotypes across different ecological niches, finally reducing the risk of such strains in food industrial settings.\n\nGenomic elements located in the accessory repertoire drive the adaptation to biocides in Listeria monocytogenes strains from different ecological niches", "token_count": 396, "char_count": 1626, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7977, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:25.066691", "source": { "split": "train_shard_00001", "doc_id": 2417 }, "chunk_id": "train_shard_00001_2417_0", "global_id": 9112 }, { "text": "Lactobacillus reuteri YSJL-12 was isolated from healthy sow fresh feces and used as probiotics additives previously. To investigate the genetic basis on probiotic potential and identify the genes in the strain, the complete genome of YSJL-12 was sequenced. Then comparative genome analysis on 9 strains of Lactobacillus reuteri was performed. The genome of YSJL-12 consisted of a circular 2,084,748 bp chromosome and 2 circular plasmids (51,906 and 15,134 bp). From among the 2065 protein-coding sequences (CDSs), the genes resistant to the environmental stress were identified. The function of COG (Clusters of Orthologous Group) protein genes was predicted, and the KEGG (Kyoto Encyclopedia of Genes and Genomes) pathways were analyzed. The comparative genome analysis indicated that the pan-genome contained a core genome of 1257 orthologous gene clusters, an accessory genome of 1064 orthologous gene clusters, and 1148 strain-specific genes, and the antibacterial mechanism among Lactobacillus reuteri strains might be different. The phylogenetic analysis and genomic collinearity revealed that the phylogenetic relationship among 9 strains of Lactobacillus reuteri was connected with host species and showed host specificity. The research could help us to better predict genes function and understand genetic basis on adapting to host gut in Lactobacillus reuteri YSJL-12.\n\nComplete Genome and Comparative Genome Analysis of Lactobacillus reuteri YSJL-12, a Potential Probiotics Strain Isolated From Healthy Sow Fresh Feces.", "token_count": 479, "char_count": 1572, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5275, "quality_score": 0.7638, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:25.710160", "source": { "split": "train_shard_00001", "doc_id": 2418 }, "chunk_id": "train_shard_00001_2418_0", "global_id": 9113 }, { "text": "Horizontal gene transfer (HGT) is a ubiquitous force in microbial evolution. Previous work has shown that the human gut is a hotspot for gene transfer between species, but the more subtle exchange of variation within species-also known as recombination-remains poorly characterized in this ecosystem. Here, we show that the genetic structure of the human gut microbiome provides an opportunity to measure recent recombination events from sequenced fecal samples, enabling quantitative comparisons across diverse commensal species that inhabit a common environment. By analyzing recent recombination events in the core genomes of 29 human gut bacteria, we observed widespread heterogeneities in the rates and lengths of transferred fragments, which are difficult to explain by existing models of ecological isolation or homology-dependent recombination rates. We also show that natural selection helps facilitate the spread of genetic variants across strain backgrounds, both within individual hosts and across the broader population. These results shed light on the dynamics of in situ recombination, which can strongly constrain the adaptability of gut microbial communities.\n\nDynamics of bacterial recombination in the human gut microbiome.", "token_count": 248, "char_count": 1242, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:26.202753", "source": { "split": "train_shard_00001", "doc_id": 2419 }, "chunk_id": "train_shard_00001_2419_0", "global_id": 9114 }, { "text": "

Objectives

Non-albicans Candida (NAC) species are increasingly identified as pathogens causing oral candidiasis. Incidence rates for azole resistance among NAC species have been continuously reported. This study aimed to evaluate the azole susceptibility profiles and to characterise the azole resistance mechanisms of oral clinical NAC isolates.

Methods

In vitro susceptibility patterns of 85 NAC species isolates were determined by the broth microdilution method. Azole resistance-related genes (ERG3, ERG11 and PDR1) of Candida glabrata isolates were sequenced to determine the presence of nucleotide substitutions. Expression levels of various resistance-related genes were also evaluated by RT-qPCR in azole-susceptible, susceptible dose-dependent (SDD) and resistant Candida isolates.

Results

Two C. glabrata isolates (2.4% of all NAC isolates) were resistant to all three azoles tested (fluconazole, itraconazole and ketoconazole). All clinical isolates of Candida tropicalis and Candida kefyr were susceptible to azoles. Silent mutations were found in the CgERG11 and CgERG3 genes of clinical C. glabrata isolates. Interestingly, two missense mutations in CgPDR1 (N768D and E818K) were identified only in resistant C. glabrata isolates. The presence of a CgPDR1 missense mutation in resistant isolates is associated with overexpression of its own product as well as multidrug transporters including ABC and MFS transporters.

Conclusion

A gain-of-function (GOF) mutation in CgPDR1 is associated with upregulation of various drug transporters, which appears to serve as a primary mechanism for azole resistance in the detected C. glabrata isolates. Therefore, analysis of GOF mutations in the PDR1 regulator provides a better understanding of the development of antifungal resistance.", "token_count": 491, "char_count": 1819, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [ "ERG11", "PDR1", "ERG3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:26.868044", "source": { "split": "train_shard_00001", "doc_id": 2420 }, "chunk_id": "train_shard_00001_2420_0", "global_id": 9115 }, { "text": "Missense mutation in CgPDR1 regulator associated with azole-resistant Candida glabrata recovered from Thai oral candidiasis patients.", "token_count": 35, "char_count": 133, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:27.225969", "source": { "split": "train_shard_00001", "doc_id": 2420 }, "chunk_id": "train_shard_00001_2420_1", "global_id": 9116 }, { "text": "Lactic acid production using Kluyveromyces marxianus (IFO 288), Lactobacillus delbrueckii ssp. bulgaricus (ATCC 11842) and Lactobacillus helveticus (ATCC 15009) individually or as mixed culture on cheese whey in stirred or static fermentation conditions was evaluated. Lactic acid production, residual sugar and cell biomass were the main features examined. Increased lactic acid production was observed, when mixed cultures were used in comparison to individual ones. The highest lactic acid concentrations were achieved when K. marxianus yeast was combined with L. delbrueckii ssp. bulgaricus, and when all the strains were used revealing possible synergistic effects between the yeast and the two lactic acid bacteria. The same synergistic effects were further observed and verified when the mixed cultures were applied in sourdough fermentations, proving that the above microbiological system could be applied in the food fermentations where high lactic acid production is sought.\n\nLactic acid production by mixed cultures of Kluyveromyces marxianus, Lactobacillus delbrueckii ssp. bulgaricus and Lactobacillus helveticus.", "token_count": 290, "char_count": 1126, "word_count": 156, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:27.785283", "source": { "split": "train_shard_00001", "doc_id": 2421 }, "chunk_id": "train_shard_00001_2421_0", "global_id": 9117 }, { "text": "

Introduction

Microorganisms can have major impacts on the success of NASA's missions, including the integrity of materials, the protection of extraterrestrial environments, the reliability of scientific results, and maintenance of crew health. Robust cleaning and sterilization protocols for spacecraft and associated environments are currently in place in NASA facilities, but microbial contamination should be further controlled and its impact on NASA's missions and science must be minimized. To address this, air and surfaces across cleanrooms and uncontrolled spaces at the Marshall Space Flight Center were sampled and microbial burden and diversity were analyzed.

Methods

A library of 82 microbial strains was isolated, curated, characterized, and a subset (n = 24) was subjected to simulated space environmental stressors, including desiccation, vacuum, proton radiation, and ultraviolet radiation. Out of these, four non-spore-former species (Arthrobacter koreensis PPS68, Paenarthrobacter sp. PPS72, Mycetocola sp. PPS117, and Erwinia sp. PPS120) exhibiting the highest resistance to tested stressors were selected for whole genome sequencing and comparative genomic, pan-resistomics and functional analyses.

Results

The analysis revealed genomic features among these four species, encompassing genes critical for amino acid biosynthesis, carbohydrate metabolism, and stress response mechanisms. Erwinia sp. PPS120 had genomic features indicative of metabolic flexibility and stress response capabilities, particularly under oxidative stress conditions. Notably, strain A. koreensis PPS68 had unique genomic features predictive of resilience to desiccation and ionizing radiation, supported by genes for oxidative stress resistance, membrane stability, and nutrient acquisition. A", "token_count": 484, "char_count": 1864, "word_count": 231, "semantic_coherence": 1, "information_density": 0.7186, "quality_score": 0.8593, "entities": { "genes": [ "PPS68", "PPS120", "PPS117", "PPS72" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:28.435948", "source": { "split": "train_shard_00001", "doc_id": 2422 }, "chunk_id": "train_shard_00001_2422_0", "global_id": 9118 }, { "text": "koreensis contains several genes which are also reported in established radioresistant strains, for predicted functions related to DNA-repair, osmoprotection, and efflux.

Discussion

NASA cleanrooms harbor hardy non-spore-forming bacteria capable of surviving vacuum, ionizing radiation, and UV. Their adaptations to space stressors suggest limitations of today's spore-centric bioburden assays to explore expanded planetary-protection standards. The modular exposure assay and reference genomes are important resources for microbial risk assessment, decontamination design, and safeguarding both robotic missions and closed human habitats in space and earth where microbial presence and colonization could compromise life-support systems and crew health.\n\nEffects of simulated space environmental conditions on cleanroom microbes.", "token_count": 188, "char_count": 841, "word_count": 101, "semantic_coherence": 1, "information_density": 0.8317, "quality_score": 0.9158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:28.883625", "source": { "split": "train_shard_00001", "doc_id": 2422 }, "chunk_id": "train_shard_00001_2422_1", "global_id": 9119 }, { "text": "Two ethanologenic yeasts, Saccharomyces cerevisiae and Kluyveromyces marxianus, were used to ferment sugar solutions modeling hydrolyzed Valencia orange peel waste at 37°C. Orange stripper oil produced from orange peel was added in various amounts to determine its effect on ethanol production. The minimum peel oil concentration that inhibited ethanol production was determined after 24, 48 and 72 h and the two yeasts were compared to one another in terms of ethanol yield. Minimum inhibitory peel oil concentrations for ethanol production were 0.05% at 24 h, 0.10% at 48 h, and 0.15% at 72 h for both yeasts. S. cerevisiae produced more ethanol than K. marxianus at each time point.\n\nEthanol production by Saccharomyces cerevisiae and Kluyveromyces marxianus in the presence of orange-peel oil", "token_count": 235, "char_count": 796, "word_count": 123, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:29.356799", "source": { "split": "train_shard_00001", "doc_id": 2423 }, "chunk_id": "train_shard_00001_2423_0", "global_id": 9120 }, { "text": "The genus Shewanella encompasses a diverse group of Gram negative, primarily aquatic bacteria with a remarkable ecological relevance, an outstanding set of metabolic features and an emergent clinical importance. The rapid expansion of the genus over the 2000 s has prompted questions on the real taxonomic position of some isolates and species. Recent work by us and others identified inconsistencies in the existing species classification. In this study we aimed to clarify such issues across the entire genus, making use of the genomic information publicly available worldwide. Phylogenomic analyses, including comparisons based on genome-wide identity indexes (digital DNA-DNA hybridization and Average Nucleotide Identity) combined with core and accessory genome content evaluation suggested that the taxonomic position of 64 of the 131 analyzed strains should be revisited. Based on the genomic information currently available, emended descriptions for some Shewanella species are proposed. Our study establishes for the first time a whole-genome based phylogeny for Shewanella spp. including a classification at the subspecific level.\n\nWhole-Genome Sequencing Redefines Shewanella Taxonomy.", "token_count": 288, "char_count": 1224, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7186, "quality_score": 0.8593, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:29.917251", "source": { "split": "train_shard_00001", "doc_id": 2424 }, "chunk_id": "train_shard_00001_2424_0", "global_id": 9121 }, { "text": "

Background

The burden of Clostridioides difficile as a nosocomial- and community-acquired pathogen has been increasing over the recent decades, including reports of severe outbreaks. Molecular and virulence genotyping are central for the epidemiological surveillance of this pathogen, but need to balance accuracy and rapid turnaround time of the results. While Illumina short-read sequencing has been adopted as the gold standard to investigate C. difficile virulence and transmission routes, little is known about the potential of Nanopore long-read sequencing in this field. The goal of our study was to compare sequencing and assembly quality of 37 C. difficile isolates using Illumina (SPAdes assembled) and Nanopore (Flye and Unicycler assembled) data alone, along with hybrid assemblies obtained with short-read polishing of long reads.

Results

Illumina sequencing produced reads with an average quality of 99.68% (Q25), while Nanopore sequencing produced reads reaching an average quality of 96.84% (Q15), showing a tenfold difference in quality. Sequence type (ST) designation from Nanopore assemblies failed to detect ST5, ST7, ST8, ST13 and ST49, while ST designation based on unpolished Nanopore reads using Krocus was successful for all STs. Nanopore sequences exhibited an average of 640 base errors per genome (~ 0.015% substitution rate), which was reflected by the incorrect assignment of over 180 alleles in core genome multilocus sequence typing (cgMLST) analysis. As a result, Nanopore-derived phylogenies were not as accurate as the Illumina reference, and therefore inadequate for precise investigation of transmission events. Both sequencing platforms provided comparable, satisfactory results for the detection of virulence genes tcdA, tcdB, cdtAB and in-frame deletions in tcdC.

Conclusion

Compared to Illumina, Nanopore has higher error rate, which limits its application for high-resolution epidemiological surveillance", "token_count": 516, "char_count": 1968, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [ "ST13", "ST5", "ST7", "ST8", "ST49" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:24:30.571327", "source": { "split": "train_shard_00001", "doc_id": 2425 }, "chunk_id": "train_shard_00001_2425_0", "global_id": 9122 }, { "text": "However, the short analysis time, lower cost and more simple procedure combined with correctly identified STs and virulence genes, makes it an alternative when fast and less detailed analyses are preferred.\n\nComparison of Illumina and Oxford Nanopore sequencing data quality for Clostridioides difficile genome analysis and their application for epidemiological surveillance.", "token_count": 77, "char_count": 375, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:30.940508", "source": { "split": "train_shard_00001", "doc_id": 2425 }, "chunk_id": "train_shard_00001_2425_1", "global_id": 9123 }, { "text": "

Background

Climate change will result in more frequent droughts that impact soil-inhabiting microbiomes in the agriculturally vital North American perennial grasslands. In this study, we used the combination of culturomics and high-resolution genomic sequencing of microbial consortia isolated from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii . We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions.

Results

Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified the bacterial population of interest – MAG- Pseudomonas . Further metabolic pathway and pangenome analyses detected genes and pathways related to nitrogen transformation and stress responses in MAG- Pseudomonas .

Conclusions

Our data indicate that the metagenome-assembled MAG- Pseudomonas has the functional potential to contribute to the plant host’s growth during stressful conditions. This study provided insights into optimizing plant productivity under drought conditions.\n\nCulturomics of Andropogon gerardii rhizobiome revealed nitrogen transforming capabilities of stress-tolerant Pseudomonas under drought conditions", "token_count": 348, "char_count": 1367, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6726, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:31.513464", "source": { "split": "train_shard_00001", "doc_id": 2426 }, "chunk_id": "train_shard_00001_2426_0", "global_id": 9124 }, { "text": "Considering the increasing interest in understanding the biotic component of methane removal from our atmosphere, it becomes essential to study the physiological characteristics and genomic potential of methanotroph isolates, especially their traits allowing them to adapt to elevated growth temperatures. The genetic signatures of Methylocaldum species have been detected in many terrestrial and aquatic ecosystems. A small set of representatives of this genus has been isolated and maintained in culture. The genus is commonly described as moderately thermophilic, with the growth optimum reaching 50oC for some strains. Here, we present a comparative analysis of genomes of three Methylocaldum strains—two terrestrial M. szegediense strains (O-12 and Norfolk) and one marine strain Methylocaldum marinum (S8). The examination of the core genome inventory of this genus uncovers significant redundancy in primary metabolic pathways, including the machinery for methane oxidation (numerous copies of pmo genes) and methanol oxidation (duplications of mxaF, xoxF1-5 genes), three pathways for one-carbon (C1) assimilation, and two methods of carbon storage (glycogen and polyhydroxyalkanoates). We also investigate the genetics of melanin production pathways, as a key feature of the genus.\n\nGenomic Insights into Moderately Thermophilic Methanotrophs of the Genus Methylocaldum", "token_count": 348, "char_count": 1387, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:32.084501", "source": { "split": "train_shard_00001", "doc_id": 2427 }, "chunk_id": "train_shard_00001_2427_0", "global_id": 9125 }, { "text": "

ABSTRACT

We recently discovered that some bacteriophages establish a nucleus-like replication compartment (phage nucleus), but the core genes that define nucleus-based phage replication and their phylogenetic distribution were unknown. By studying phages that encode the major phage nucleus protein chimallin, including previously sequenced yet uncharacterized phages, we discovered that chimallin-encoding phages share a set of 72 highly conserved genes encoded within seven distinct gene blocks. Of these, 21 core genes are unique to this group, and all but one of these unique genes encode proteins of unknown function. We propose that phages with this core genome comprise a novel viral family we term Chimalliviridae. Fluorescence microscopy and cryo-electron tomography studies of Erwinia phage vB_EamM_RAY confirm that many of the key steps of nucleus-based replication encoded in the core genome are conserved among diverse chimalliviruses, and reveal that non-core components can confer intriguing variations on this replication mechanism. For instance, unlike previously studied nucleus-forming phages, RAY doesn’t degrade the host genome, and its PhuZ homolog appears to form a five-stranded filament with a lumen. This work expands our understanding of phage nucleus and PhuZ spindle diversity and function, providing a roadmap for identifying key mechanisms underlying nucleus-based phage replication.\n\nIdentifying the core genome of the nucleus-forming bacteriophage family and characterization ofErwiniaphage RAY", "token_count": 376, "char_count": 1543, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:32.668087", "source": { "split": "train_shard_00001", "doc_id": 2428 }, "chunk_id": "train_shard_00001_2428_0", "global_id": 9126 }, { "text": "We propose a polynomial algorithm computing a minimum plain-text representation of kmer sets, as well as an efficient near-minimum greedy heuristic. When compressing read sets of large model organisms or bacterial pangenomes, with only a minor runtime increase, we shrink the representation by up to 60% over unitigs and 27% over previous work. Additionally, the number of strings is decreased by up to 97% over unitigs and 91% over previous work. Finally, a small representation has advantages in downstream applications, as it speeds up SSHash-Lite queries by up to 4.26× over unitigs and 2.10× over previous work.

Availability

matchtigs: https://github.com/algbio/matchtigs SSHash-Lite: https://github.com/jermp/sshash-lite\n\nMatchtigs: minimum plain text representation of kmer sets", "token_count": 215, "char_count": 794, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:33.144313", "source": { "split": "train_shard_00001", "doc_id": 2429 }, "chunk_id": "train_shard_00001_2429_0", "global_id": 9127 }, { "text": "Pangenomes – the cumulative set of genes encoded by a species – arise from evolutionary forces including horizontal gene transfer (HGT), drift, and selection. The relative importance of drift and selection in shaping pangenome structure has been recently debated, and the role of sequence evolution (point mutations) within mobile genes has been largely ignored, with studies focusing mainly on patterns of gene presence or absence. The effects of drift, selection, and HGT on pangenome evolution likely depends on the time scale being studied, ranging from ancient ( e.g. , between distantly related species) to recent ( e.g. , within a single animal host), and the unit of selection being considered ( e.g. , the gene, whole genome, microbial species, or human host). To shed light on pangenome evolution within microbiomes on relatively recent time scales, we investigate the selective pressures acting on mobile genes using a dataset that previously identified such genes in the gut metagenomes of 176 Fiji islanders. We mapped the metagenomic reads to mobile genes to call single nucleotide variants (SNVs) and calculate population genetic metrics that allowed us to infer deviations from a neutral evolutionary model. We found that mobile gene sequence evolution varied more by gene family than by human social attributes, such as household or village membership, suggesting that selection at the level of gene function is most relevant on these short time scales. Patterns of mobile gene sequence evolution could be qualitatively recapitulated with a simple evolutionary simulation, without the need to invoke an adaptive advantage of mobile genes to their bacterial host genome. This suggests that, at least on short time scales, a majority of the pangenome need not be adaptive. On the other hand, a subset of gene functions including defense mechanisms and secondary metabolism showed an aberrant pattern of molecular evolution, consistent with species-specific selective pressures or negative frequency-dependent selection not seen in prophages, transposons, or other gene categories. That mobile genes of different functions behave so differently suggests stronger selection at the gene level, rather than at the genome level. While pangenomes may be largely adaptive to their bacterial hosts on longer evolution time scales, here we show that, on shorter “human” time scales, drift and gene-specific selection predominate.", "token_count": 499, "char_count": 2435, "word_count": 370, "semantic_coherence": 1, "information_density": 0.5595, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:33.796759", "source": { "split": "train_shard_00001", "doc_id": 2430 }, "chunk_id": "train_shard_00001_2430_0", "global_id": 9128 }, { "text": "Pangenome sequence evolution within human gut microbiomes is explained by gene-specific rather than host-specific selective pressures", "token_count": 26, "char_count": 133, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:34.158655", "source": { "split": "train_shard_00001", "doc_id": 2430 }, "chunk_id": "train_shard_00001_2430_1", "global_id": 9129 }, { "text": "We previously reported that Kluyveromyces marxianus YIT 8292 exhibited more potent hypocholesterolemic activity than other yeasts containing Saccharomyces cerevisiae . To clarify the reason for the higher hypocholesterolemic activity, we examined the side-chain structure of cell surface polysaccharide, mannan, of K. marxianus YIT 8292. The result shows that K. marxianus YIT 8292 had shorter alpha-(1,2)-linked oligomannosyl side chains and lower phosphate content in mannan than S. cerevisiae. The association between its structural features and hypocholesterolemic activity was investigated by comparing the hypocholesterolemic activities of S. cerevisiae mannan mutants in rats fed a high-cholesterol diet. S. cerevisiae mnn5 mutant with deficiencies in the phosphorylation and elongation of mannan side chains showed higher hypocholesterolemic activity than the wild-type strain. These results show that the side-chain length and phosphate contents of mannan affect hypocholesterolemic activity.\n\nSide-chain structure of cell surface polysaccharide, mannan, affects hypocholesterolemic activity of yeast.", "token_count": 299, "char_count": 1110, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:34.723736", "source": { "split": "train_shard_00001", "doc_id": 2431 }, "chunk_id": "train_shard_00001_2431_0", "global_id": 9130 }, { "text": "Campylobacteriosis is the most common cause of acute gastrointestinal bacterial infection in Europe, with most infections linked to the consumption of contaminated food. While previous studies found an increasing rate of antimicrobial resistance (AMR) in Campylobacter spp. over the past decades, the investigation of additional clinical isolates is likely to provide novel insights into the population structure and mechanisms of virulence and drug resistance of this important human pathogen. Therefore, we combined whole-genome sequencing and antimicrobial-susceptibility testing of 340 randomly selected Campylobacter jejuni isolates from humans with gastroenteritis, collected in Switzerland over an 18 year period. In our collection, the most common multilocus sequence types (STs) were ST-257 (n=44), ST-21 (n=36) and ST-50 (n=35); the most common clonal complexes (CCs) were CC-21 (n=102), CC-257 (n=49) and CC-48 (n=33). High heterogeneity was observed among STs, with the most abundant STs recurring over the entire study period, while others were observed only sporadically. Source attribution based on ST assigned more than half of the strains to the 'generalist' category (n=188), 25  % as 'poultry specialist' (n=83), and only a few to 'ruminant specialist' (n=11) or 'wild bird' origin (n=9). The isolates displayed an increased frequency of AMR from 2003 to 2020, with the highest rates of resistance observed for ciprofloxacin and nalidixic acid (49.8 %), followed by tetracycline (36.9 %)", "token_count": 497, "char_count": 1590, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7248, "quality_score": 0.8624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:35.421795", "source": { "split": "train_shard_00001", "doc_id": 2432 }, "chunk_id": "train_shard_00001_2432_0", "global_id": 9131 }, { "text": "Quinolone-resistant isolates carried chromosomal gyrA mutations T86I (99.4 %) and T86A (0.6 %), whereas tetracycline-resistant isolates carried tet(O) (79.8 %) or mosaic tetO/32/O (20.2 %) genes. A novel chromosomal cassette carrying several resistance genes, including aph(3')-III, satA and aad(6), and flanked by insertion sequence elements was detected in one isolate. Collectively, our data revealed an increasing prevalence of resistance to quinolones and tetracycline in C. jejuni isolates from Swiss patients over time, linked to clonal expansion of gyrA mutants and acquisition of the tet(O) gene. Investigation of source attribution suggests that infections are most likely related to isolates from poultry or generalist backgrounds. These findings are relevant to guide future infection prevention and control strategies.\n\nWhole-genome-based characterization of Campylobacter jejuni from human patients with gastroenteritis collected over an 18 year period reveals increasing prevalence of antimicrobial resistance.", "token_count": 332, "char_count": 1095, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7518, "quality_score": 0.8759, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:36.010455", "source": { "split": "train_shard_00001", "doc_id": 2432 }, "chunk_id": "train_shard_00001_2432_1", "global_id": 9132 }, { "text": "

Objective

A core genome multilocus sequence typing (cgMLST) scheme to genotype and identify potential risk clonal groups (CGs) in Proteus mirabilis.

Methods

In this work, we propose a publicly available cgMLST scheme for P. mirabilis using chewBBACA. In total 72 complete P. mirabilis genomes, representing the diversity of this species, were used to set up a cgMLST scheme targeting 1,842 genes, 635 unfinished (contig, chromosome, and scaffold) genomes were used for its validation.

Results

We identified a total of 205 CGs from 695 P. mirabilis strains with regional distribution characteristics. Of these, 159 unique CGs were distributed in 16 countries. CG20 and CG3 carried large numbers of shared and unique antibiotic resistance genes. Nine virulence genes ( papC, papD, papE, papF, papG, papH, papI, papJ, and papK) related to the P fimbrial operon that cause severe urinary tract infections were only found in CG20. These CGs require attention due to potential risks.

Conclusion

This research innovatively performs high-resolution molecular typing of P. mirabilis using whole-genome sequencing technology combined with a bioinformatics pipeline (chewBBACA). We found that the CGs of P. mirabilis showed regional distribution differences. We expect that our research will contribute to the establishment of cgMLST for P. mirabilis.\n\nA Core Genome Multilocus Sequence Typing Scheme for Proteus mirabilis.", "token_count": 510, "char_count": 1560, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [ "CG3", "CG20" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:36.691976", "source": { "split": "train_shard_00001", "doc_id": 2433 }, "chunk_id": "train_shard_00001_2433_0", "global_id": 9133 }, { "text": "Giant viruses have been isolated and characterized in different environments, expanding our knowledge about the biology of these unique microorganisms. In the last 2 years, a new group was discovered, the cedratviruses, currently composed of only two isolates and members of a putative new family, \"Pithoviridae,\" along with previously known pithoviruses. Here we report the isolation and biological and genomic characterization of two novel cedratviruses isolated from samples collected in France and Brazil. Both viruses were isolated using Acanthamoeba castellanii as a host cell and exhibit ovoid particles with corks at either extremity of the particle. Curiously, the Brazilian cedratvirus is ∼20% smaller and presents a shorter genome of 460,038 bp, coding for fewer proteins than other cedratviruses. In addition, it has a completely asyntenic genome and presents a lower amino acid identity of orthologous genes (∼73%). Pangenome analysis comprising the four cedratviruses revealed an increase in the pangenome concomitant with a decrease in the core genome with the addition of the two novel viruses. Finally, phylogenetic analyses clustered the Brazilian virus in a separate branch within the group of cedratviruses, while the French isolate is closer to the previously reported Cedratvirus lausannensis Taking all together, we propose the existence of a second lineage of this emerging viral genus and provide new insights into the biodiversity and ubiquity of these giant viruses.IMPORTANCE Various giant viruses have been described in recent years, revealing a unique part of the virosphere. A new group among the giant viruses has recently been described, the cedratviruses, which is currently composed of only two isolates. In this paper, we describe two novel cedratviruses isolated from French and Brazilian samples. Biological and genomic analyses showed viruses with different particle sizes, genome lengths, and architecture, revealing the existence of a second lineage of this new group of giant viruses", "token_count": 488, "char_count": 2046, "word_count": 301, "semantic_coherence": 1, "information_density": 0.5548, "quality_score": 0.7774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:37.371033", "source": { "split": "train_shard_00001", "doc_id": 2434 }, "chunk_id": "train_shard_00001_2434_0", "global_id": 9134 }, { "text": "Our results provide new insights into the biodiversity of cedratviruses and highlight the importance of ongoing efforts to prospect for and characterize new giant viruses.\n\nMorphologic and Genomic Analyses of New Isolates Reveal a Second Lineage of Cedratviruses.", "token_count": 66, "char_count": 263, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:37.735948", "source": { "split": "train_shard_00001", "doc_id": 2434 }, "chunk_id": "train_shard_00001_2434_1", "global_id": 9135 }, { "text": "Enterococcus spp. are commensals of the gastrointestinal tracts of humans and animals and colonize a variety of niches such as water, soil, and food. Over the last three decades, enterococci have evolved as opportunistic pathogens, being considered ESKAPE pathogens responsible for hospital-associated infections. Enterococci's ubiquitous nature, excellent adaptative capacity, and ability to acquire virulence and resistance genes make them excellent sentinel proxies for assessing the presence/spread of pathogenic and virulent clones and hazardous determinants across settings of the human-animal-environment triad, allowing for a more comprehensive analysis of the One Health continuum. This review provides an overview of enterococcal fitness and pathogenic traits; the most common clonal complexes identified in clinical, veterinary, food, and environmental sources; as well as the dissemination of pathogenic genomic traits (virulome, resistome, and mobilome) found in high-risk clones worldwide, across the One Health continuum.\n\nDissemination of Enterococcal Genetic Lineages: A One Health Perspective.", "token_count": 271, "char_count": 1118, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7007, "quality_score": 0.8503, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:38.296604", "source": { "split": "train_shard_00001", "doc_id": 2435 }, "chunk_id": "train_shard_00001_2435_0", "global_id": 9136 }, { "text": "K. marxianus was cultivated under conditions of PEF (pulse electric field) action and a selenium source. The culture duration after which cells were treated with PEF, the field exposure time and the selenium concentration in the medium were all optimized. Optimization of culture duration caused a 33% increase in selenium accumulation in cells as compared to the control with no PEF treatment. The highest selenium accumulation--about 167 microg/g dry mass (DM)--was recorded after 3-minute PEF treatment of 16-hour culture. A roughly two-fold increase in selenium content was achieved after optimization of culture duration and PEF treatment time. Finding the optimum selenium concentration in the medium brought about a 13-fold increase of selenium accumulation in the cells of K. marxianus.\n\nThe influence of a pulsating electric field on selenium accumulation in Kluyveromyces marxianus cells.", "token_count": 219, "char_count": 898, "word_count": 133, "semantic_coherence": 1, "information_density": 0.5489, "quality_score": 0.7744, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:38.770000", "source": { "split": "train_shard_00001", "doc_id": 2436 }, "chunk_id": "train_shard_00001_2436_0", "global_id": 9137 }, { "text": "Sorghum (Sorghum bicolor L.) is a staple food crops in the arid and rainfed production ecologies. Sorghum plays a critical role in resilient farming and is projected as a smart crop to overcome the food and nutritional insecurity in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought adaptation traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.\n\nSorghum Pan-Genome Explores the Functional Utility for Genomic-Assisted Breeding to Accelerate the Genetic Gain.", "token_count": 409, "char_count": 1714, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:39.388038", "source": { "split": "train_shard_00001", "doc_id": 2437 }, "chunk_id": "train_shard_00001_2437_0", "global_id": 9138 }, { "text": "Aim: Clostridia are relevant commensals of the human gut due to their major presence and correlations to the host. In this study, we investigated intestinal Clostridia of 51 healthy subjects and reconstructed their taxonomy and phylogeny. The relatively small number of intestinal Clostridia allowed a systematic whole genome approach based on average amino acid identity (AAI) and core genome with the aim of revising the current classification into genera and determining evolutionary relationships. Methods: 51 healthy subjects' metagenomes were retrieved from public databases. After the dataset's validation through comparison with Human Microbiome Project (HMP) samples, the metagenomes were profiled using MetaPhlAn3 to identify the population ascribed to the class Clostridia. Intestinal Clostridia genomes were retrieved and subjected to AAI analysis and core genome identification. Phylogeny investigation was conducted with RAxML and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithms, and SplitsTree for split decomposition. Results: 225 out of 406 bacterial taxonomic units were ascribed to Bacillota [Firmicutes], among which 124 were assigned to the class Clostridia. 77 out of the 124 taxonomic units were referred to a species, altogether covering 87.7% of Clostridia abundance. According to the lowest AAI genus boundary set at 55%, 15 putative genera encompassing more than one species (G1 to G15) were identified, while 19 species did not cluster with any other one and each appeared to belong to a diverse genus. Phylogenetic investigations highlighted that most of the species clustered into three main evolutive clades", "token_count": 479, "char_count": 1743, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6722, "quality_score": 0.8361, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:40.033313", "source": { "split": "train_shard_00001", "doc_id": 2438 }, "chunk_id": "train_shard_00001_2438_0", "global_id": 9139 }, { "text": "Conclusion: This study shed light on the species of Clostridia colonizing the gut of healthy adults and pinpointed several gaps in knowledge regarding the taxonomy and the phylogeny of Clostridia.\n\nProfiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis.", "token_count": 91, "char_count": 314, "word_count": 41, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:40.412891", "source": { "split": "train_shard_00001", "doc_id": 2438 }, "chunk_id": "train_shard_00001_2438_1", "global_id": 9140 }, { "text": "The Telomere-to-Telomere consortium recently assembled the first truly complete sequence of a human genome. To resolve the most complex repeats, this project relied on manual integration of ultra-long Oxford Nanopore sequencing reads with a high-resolution assembly graph built from long, accurate PacBio HiFi reads. We have improved and automated this strategy in Verkko, an iterative, graph-based pipeline for assembling complete, diploid genomes. Verkko begins with a multiplex de Bruijn graph built from long, accurate reads and progressively simplifies this graph via the integration of ultra-long reads and haplotype-specific markers. The result is a phased, diploid assembly of both haplotypes, with many chromosomes automatically assembled from telomere to telomere. Running Verkko on the HG002 human genome resulted in 20 of 46 diploid chromosomes assembled without gaps at 99.9997% accuracy. The complete assembly of diploid genomes is a critical step towards the construction of comprehensive pangenome databases and chromosome-scale comparative genomics.\n\nVerkko: telomere-to-telomere assembly of diploid chromosomes", "token_count": 285, "char_count": 1128, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [ "HG002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:40.973115", "source": { "split": "train_shard_00001", "doc_id": 2439 }, "chunk_id": "train_shard_00001_2439_0", "global_id": 9141 }, { "text": "

ABSTRACT

We present here FrangiPANe, a pipeline developed to build panreference using short reads through a map-then-assemble strategy. Applying it to 248 African rice genomes using an improved CG14 reference genome, we identified an average of 8 Mb of new sequences and 5,290 new contigs per individual. In total, 1.4 G of new sequences, consisting of 1,306,676 contigs, were assembled. We validated 97.7% of the contigs of the TOG5681 cultivar individual assembly from short reads on a newly long reads genome assembly of the same TOG5681 cultivar. FrangiPANe also allowed the anchoring of 31.5% of the new contigs within the CG14 reference genome, with a 92.5% accuracy at 2kb span. We annotated in addition 3,252 new genes absent from the reference. FrangiPANe was developed as a modular and interactive application to simplify the construction of a panreference using the map-then-assemble approach. It is available as a Docker image containing (i) a Jupyter notebook centralizing codes, documentation and interactive visualization of results, (ii) python scripts and (iii) all the software and libraries requested for each step of the analysis. We foreseen our approach will help leverage large-scale illumina dataset for pangenome studies in GWAS or detection of selection.\n\nFrangiPANe, a tool for creating a panreference using left behind reads", "token_count": 369, "char_count": 1361, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [ "TOG5681", "CG14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:41.560550", "source": { "split": "train_shard_00001", "doc_id": 2440 }, "chunk_id": "train_shard_00001_2440_0", "global_id": 9142 }, { "text": "As many bacteria detected in Antarctic environments are neither true psychrophiles nor endemic species, their proliferation in spite of environmental extremes gives rise to genome adaptations. Janthinobacterium sp. CG23_2 is a bacterial isolate from the Cotton Glacier stream, Antarctica. To understand how Janthinobacterium sp. CG23_2 has adapted to its environment, we investigated its genomic traits in comparison to genomes of 35 published Janthinobacterium species. While we hypothesized that genome shrinkage and specialization to narrow ecological niches would be energetically favorable for dwelling in an ephemeral Antarctic stream, the genome of Janthinobacterium sp. CG23_2 was on average 1.7 ± 0.6 Mb larger and predicted 1411 ± 499 more coding sequences compared to the other Janthinobacterium spp. Putatively identified horizontal gene transfer events contributed 0.92 Mb to the genome size expansion of Janthinobacterium sp. CG23_2. Genes with high copy numbers in the species-specific accessory genome of Janthinobacterium sp. CG23_2 were associated with environmental sensing, locomotion, response and transcriptional regulation, stress response, and mobile elements-functional categories which also showed molecular adaptation to cold. Our data suggest that genome plasticity and the abundant complementary genes for sensing and responding to the extracellular environment supported the adaptation of Janthinobacterium sp. CG23_2 to this extreme environment.\n\nJanthinobacterium CG23_2: Comparative Genome Analysis Reveals Enhanced Environmental Sensing and Transcriptional Regulation for Adaptation to Life in an Antarctic Supraglacial Stream.", "token_count": 480, "char_count": 1724, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:42.204632", "source": { "split": "train_shard_00001", "doc_id": 2441 }, "chunk_id": "train_shard_00001_2441_0", "global_id": 9143 }, { "text": "The global expansion in aquaculture production implies an emerging need of suitable and sustainable protein sources. Currently, the fish feed industry is dependent on high‐quality protein sources of marine and plant origin. Yeast derived from processing of low‐value and non‐food lignocellulosic biomass is a potential sustainable source of protein in fish diets. Following enzymatic hydrolysis, the hexose and pentose sugars of lignocellulosic substrates and supplementary nutrients can be converted into protein‐rich yeast biomass by fermentation. Studies have shown that yeasts such as Saccharomyces cerevisiae, Candida utilis and Kluyveromyces marxianus have favourable amino acid composition and excellent properties as protein sources in diets for fish, including carnivorous species such as Atlantic salmon and rainbow trout. Suitable downstream processing of the biomass to disrupt cell walls is required to secure high nutrient digestibility. A number of studies have shown various immunological and health benefits from feeding fish low levels of yeast and yeast‐derived cell wall fractions. This review summarises current literature on the potential of yeast from lignocellulosic biomass as an alternative protein source for the aquaculture industry. It is concluded that further research and development within yeast production can be important to secure the future sustainability and economic viability of intensive aquaculture. © 2016 Society of Chemical Industry\n\nYeast derived from lignocellulosic biomass as a sustainable feed resource for use in aquaculture", "token_count": 346, "char_count": 1575, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7986, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:42.780446", "source": { "split": "train_shard_00001", "doc_id": 2442 }, "chunk_id": "train_shard_00001_2442_0", "global_id": 9144 }, { "text": "

Background

Colistin (CST) is a last-line drug for multidrug-resistant Gram-negative bacterial infections. CST-heteroresistant Enterobacter cloacae complex (ECC) has been isolated. However, integrated analysis of epidemiology and resistance mechanisms based on the complete ECC species identification has not been performed.

Methods

Clinical isolates identified as \"E. cloacae complex\" by MALDI-TOF MS Biotyper Compass in a university hospital in Japan were analyzed. Minimum inhibitory concentrations of CST were determined by the broth microdilution method. The population analysis profiling (PAP) was performed for detecting the heteroresistant phenotype. The heat shock protein 60 (hsp60) cluster was determined from its partial nucleotide sequence. From the data of whole-genome sequencing, average nucleotide identity (ANI) for determining ECC species, multilocus sequence type, core genome single-nucleotide-polymorphism-based phylogenetic analysis were performed. phoPQ-, eptA-, and arnT-deleted mutants were established to evaluate the mechanism underlying colistin heteroresistance. The arnT mRNA expression levels were determined by reverse transcription quantitative PCR.

Results

Thirty-eight CST-resistant isolates, all of which exhibited the heteroresistant phenotype by PAP, were found from 138 ECC clinical isolates (27.5%). The prevalence of CST-resistant isolates did not significantly differ among the origin of specimens (29.0%, 27.8%, and 20.2% for respiratory, urine, and blood specimens, respectively). hsp60 clusters, core genome phylogeny, and ANI revealed that the CST-heteroresistant isolates were found in all or most of Enterobacter roggenkampii (hsp60 cluster IV), Enterobacter kobei (cluster II), Enterobacter chuandaensis (clusters III and IX), and Enterobacter cloacae subspecies (clusters XI and XII)", "token_count": 508, "char_count": 1855, "word_count": 231, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:43.437057", "source": { "split": "train_shard_00001", "doc_id": 2443 }, "chunk_id": "train_shard_00001_2443_0", "global_id": 9145 }, { "text": "No heteroresistant isolates were found in Enterobacter hormaechei subspecies (clusters VIII, VI, and III) and Enterobacter ludwigii (cluster V). CST-induced mRNA upregulation of arnT, which encodes 4-amino-4-deoxy-L-arabinose transferase, was observed in the CST-heteroresistant isolates, and it is mediated by phoPQ pathway. Isolates possessing mcr-9 and mcr-10 (3.6% and 5.6% of total ECC isolates, respectively) exhibited similar CST susceptibility and PAP compared with mcr-negative isolates.

Conclusions

Significant prevalence (approximately 28%) of CST heteroresistance is observed in ECC clinical isolates, and they are accumulated in specific species and lineages. Heteroresistance is occurred by upregulation of arnT mRNA induced by CST. Acquisition of mcr genes contributes less to CST resistance in ECC.\n\nHigh prevalence of colistin heteroresistance in specific species and lineages of Enterobacter cloacae complex derived from human clinical specimens.", "token_count": 285, "char_count": 971, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:43.993535", "source": { "split": "train_shard_00001", "doc_id": 2443 }, "chunk_id": "train_shard_00001_2443_1", "global_id": 9146 }, { "text": "Sulfur-oxidizing Thioglobaceae , often referred to as SUP05 and Arctic96BD clades, are widespread and common to hydrothermal vents and oxygen minimum zones. They impact global biogeochemical cycles and exhibit a variety of host-associated and free-living lifestyles. The evolutionary driving forces that led to the versatility, adoption of multiple lifestyles and global success of this family are largely unknown. Here, we perform an in-depth comparative genomic analysis using all available and newly generated Thioglobaceae genomes. Gene content variation was common, throughout taxonomic ranks and lifestyles. We uncovered a pool of variable genes within most Thioglobaceae populations in single environmental samples and we referred to this as the ‘hidden pangenome’. The ‘hidden pangenome’ is often overlooked in comparative genomic studies and our results indicate a much higher intra-specific diversity within environmental bacterial populations than previously thought. Our results show that core-community functions are different from species core genomes suggesting that core functions across populations are divided among the intra-specific members within a population. Defense mechanisms against foreign DNA and phages were enriched in symbiotic lineages, indicating an increased exchange of genetic material in symbioses. Our study suggests that genomic plasticity and frequent exchange of genetic material drives the global success of this family by increasing its evolvability in a heterogeneous environment.\n\nThe hidden pangenome: comparative genomics reveals pervasive diversity in symbiotic and free-living sulfur-oxidizing bacteria", "token_count": 351, "char_count": 1651, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6413, "quality_score": 0.8206, "entities": { "genes": [ "SUP05" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:44.576934", "source": { "split": "train_shard_00001", "doc_id": 2444 }, "chunk_id": "train_shard_00001_2444_0", "global_id": 9147 }, { "text": "

Background

Men who have sex with men (MSM) are more vulnerable to acquiring sexually transmitted infections (STIs). In 2019, for instance, 74% of European Neisseria gonorrhoeae (Ng) cases among males affected MSM. A recent report by the World Health Organization showed that most of the 2020' interim targets to end STIs by 2030 had not been met. A broadened understanding of STI transmission networks could guide future elimination strategies and reduce the STI burden. Therefore, we used whole-genome sequencing (WGS) to determine Ng-clusters and assess sexual mixing.

Methods

WGS was performed on Ng-isolates collected at the Medical University of Vienna, Austria and was used for core genome multi-locus sequencing typing cluster analysis. Epidemiologic and infection-specific details were extracted from medical records.

Results

Genomic analysis and demographic data were available for 415 isolates, and 43.9% (182/415) were allocated to 31 Ng-clusters. Nine clusters comprised samples from heterosexual individuals only (women N = 4, human immunodeficiency virus (HIV)-negative men N = 49, HIV-positive man N = 1), nine clusters included MSM only (HIV-negative N = 22, HIV-positive N = 13) and 13 clusters included both heterosexuals and MSM (HIV-negative N = 75, HIV-positive N = 18). Current use of HIV pre-exposure prophylaxis (PrEP) was reported by 22.8% of MSM", "token_count": 464, "char_count": 1449, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7277, "quality_score": 0.8639, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:45.222789", "source": { "split": "train_shard_00001", "doc_id": 2445 }, "chunk_id": "train_shard_00001_2445_0", "global_id": 9148 }, { "text": "In multivariate analysis, only 'MSM' predicted clustering with isolates from HIV-positive individuals (adjusted odds ratio 10.24 (95% CI 5.02-20.90)).

Conclusions

Sexual mixing of HIV-positive, HIV-negative MSM and non-MSM was frequently observed. Furthermore, HIV-serodiscordant clustering highlights the importance of PrEP rollout to avert HIV transmission. Our findings can inform future STI prevention strategies and continuous surveillance efforts are required to keep up with transmission dynamics.\n\nGenotypic cluster analysis of Neisseria gonorrhoeae reveals a spectrum of sexual mixing including among HIV-serodiscordant men who have sex with men.", "token_count": 182, "char_count": 669, "word_count": 83, "semantic_coherence": 1, "information_density": 0.8795, "quality_score": 0.9398, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:45.662224", "source": { "split": "train_shard_00001", "doc_id": 2445 }, "chunk_id": "train_shard_00001_2445_1", "global_id": 9149 }, { "text": "The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.\n\nExtension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.", "token_count": 277, "char_count": 1245, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6928, "quality_score": 0.8464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:46.216615", "source": { "split": "train_shard_00001", "doc_id": 2446 }, "chunk_id": "train_shard_00001_2446_0", "global_id": 9150 }, { "text": "

Motivation

Increasing amounts of individual genomes sequenced per species motivate the usage of pangenomic approaches. Pangenomes may be represented as graphical structures, e.g. compacted colored de Bruijn graphs, which offer a low memory usage and facilitate reference-free sequence comparisons. While sequence-to-graph mapping to graphical pangenomes has been studied for some time, no local alignment search tool in the vein of BLAST has been proposed yet.

Results

We present a new heuristic method to find maximum scoring local alignments of a DNA query sequence to a pangenome represented as a compacted colored de Bruijn graph. Our approach additionally allows a comparison of similarity among sequences within the pangenome. We show that local alignment scores follow an exponential-tail distribution similar to BLAST scores, and we discuss how to estimate its parameters to separate local alignments representing sequence homology from spurious findings. An implementation of our method is presented, and its performance and usability are shown. Our approach scales sublinearly in running time and memory usage with respect to the number of genomes under consideration. This is an advantage over classical methods that do not make use of sequence similarity within the pangenome.\n\nDetecting High Scoring Local Alignments in Pangenome Graphs", "token_count": 291, "char_count": 1367, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:46.781831", "source": { "split": "train_shard_00001", "doc_id": 2447 }, "chunk_id": "train_shard_00001_2447_0", "global_id": 9151 }, { "text": "

Background

The opportunistic pathogen Staphylococcus aureus is an asymptomatically carried member of the microbiome of about one third of the human population at any given point in time. Body sites known to harbor S. aureus are the skin, nasopharynx, and gut. In particular, the mechanisms allowing S. aureus to pass the gut epithelial barrier and to invade the bloodstream were so far poorly understood. Therefore, the objective of our present study was to investigate the extent to which genetic differences between enteric S. aureus isolates and isolates that caused serious bloodstream infections contribute to the likelihood of invasive disease.

Results

Here, we present genome-wide association studies (GWAS) that compare the genome sequences of 69 S. aureus isolates from enteric carriage by healthy volunteers and 95 isolates from bloodstream infections. We complement our GWAS results with a detailed characterization of the cellular and extracellular proteomes of the representative gut and bloodstream isolates, and by assaying the virulence of these isolates with infection models based on human gut epithelial cells, human blood cells, and a small animal infection model. Intriguingly, our results show that enteric and bloodstream isolates with the same sequence type (ST1 or ST5) are very similar to each other at the genomic and proteomic levels. Nonetheless, bloodstream isolates are not necessarily associated with an invasive profile. Furthermore, we show that the main decisive factor preventing infection of gut epithelial cells in vitro is the presence of a tight barrier.

Conclusions

Our data show that virulence is a highly variable trait, even within a single clone. Importantly, however, there is no evidence that blood stream isolates possess a higher virulence potential than those from the enteric carriage. In fact, some gut isolates from healthy carriers were more virulent than bloodstream isolates. Based on our present observations, we propose that the integrity of the gut epithelial layer, rather than the pathogenic potential of the investigated enteric S. aureus isolates, determines whether staphylococci from the gut microbiome will become invasive pathogens. Video Abstract.", "token_count": 515, "char_count": 2237, "word_count": 326, "semantic_coherence": 1, "information_density": 0.5583, "quality_score": 0.7791, "entities": { "genes": [ "ST5", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:24:47.465692", "source": { "split": "train_shard_00001", "doc_id": 2448 }, "chunk_id": "train_shard_00001_2448_0", "global_id": 9152 }, { "text": "Staphylococcus aureus populations from the gut and the blood are not distinguished by virulence traits-a critical role of host barrier integrity.", "token_count": 33, "char_count": 145, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:47.846062", "source": { "split": "train_shard_00001", "doc_id": 2448 }, "chunk_id": "train_shard_00001_2448_1", "global_id": 9153 }, { "text": "

Background

Lactiplantibacillus plantarum is a species found in a wide range of ecological niches, including vegetables and dairy products, and it may occur naturally in the human gastrointestinal tract. The precise mechanisms underlying the beneficial properties of these microbes to their host remain obscure. Although Lactic acid bacteria are generally regarded as safe, there are rare cases of the emergence of infections and antibiotic resistance by certain probiotics.

Objective

An in silico whole genome sequence analysis of putative probiotic bacteria was set up to identify strains, predict desirable functional properties, and identify potentially detrimental antibiotic resistance and virulence genes.

Methods

We characterized the genomes of three L. plantarum strains (54B, 54C, and 55A) isolated from Ethiopian traditional cottage cheese. Whole-genome sequencing was performed using Illumina MiSeq sequencing. The completeness and quality of the genome of L. plantarum strains were assessed through CheckM.

Results

Analyses results showed that L. plantarum 54B and 54C are closely related but different strains. The genomes studied did not harbor resistance and virulence factors. They had five classes of carbohydrate-active enzymes with several important functions. Cyclic lactone autoinducer, terpenes, Type III polyketide synthases, ribosomally synthesized and post-translationally modified peptides-like gene clusters, sactipeptides, and all genes required for riboflavin biosynthesis were identified, evidencing their promising probiotic properties. Six bacteriocin-like structures encoding genes were found in the genome of L. plantarum 55A.

Conclusions

The lack of resistome and virulome and their previous functional capabilities suggest the potential applicability of these strains in food industries as bio-preservatives and in the prevention and/or treatment of infectious diseases", "token_count": 508, "char_count": 1976, "word_count": 248, "semantic_coherence": 1, "information_density": 0.7056, "quality_score": 0.8528, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:48.498207", "source": { "split": "train_shard_00001", "doc_id": 2449 }, "chunk_id": "train_shard_00001_2449_0", "global_id": 9154 }, { "text": "The results also provide insights into the probiotic potential and safety of these three strains and indicate avenues for further mechanistic studies using these isolates.\n\nGenomic Characterization of Lactiplantibacillus plantarum Strains: Potential Probiotics from Ethiopian Traditional Fermented Cottage Cheese.", "token_count": 80, "char_count": 320, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8718, "quality_score": 0.9359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:48.928321", "source": { "split": "train_shard_00001", "doc_id": 2449 }, "chunk_id": "train_shard_00001_2449_1", "global_id": 9155 }, { "text": "Purpose: The present study was conducted to assess the ability of probiotic bacteria and yeasts strains to reduce aflatoxin B1 (AFB1) in gastrointestinal simulated conditions. Aflatoxins are potent carcinogenic and immunosuppressive agents. Acute exposure to a high level of aflatoxins leads to aflatoxicosis, which cause rapid death due to liver failure. It is anticipated that consumption of probiotic microorganisms capable of binding aflatoxins can reduce the risk of AFB1 on human health to a certain extent. Methods: For this purpose, the bacteria (1 × 1010 cfu/mL) and yeasts count (2 × 108 cells/mL) and AFB1 concentration (10 ppb) were adjusted. Then, the samples were incubated in the simulated medium, human gastric secretions and small intestine. The concentration of residual AFB1 was determined using enzyme-linked immunosorbent assay (ELISA). The results were statistically analyzed by SPSS 16 software. Results: The native isolated bacteria and yeasts in the simulated gastrointestinal tract condition showed a significant effect on AFB1 reduction (P <0.05). The AFB1 reduction ability of native probiotic microorganisms was strain dependent. The highest binding ability in bacteria belonged to Lactobacillus rhamnosus (31.14%) and at yeasts belonged to Saccharomyces cerevisiae (30.46%). Conclusion: The use of probiotic strains is the appropriate biological method to reduce AFB1 in the human gastrointestinal tract. Probiotic bacteria could help to decrease the harmful effects of AFB1 in humans through enhancing the food safety.\n\nDetoxification of Aflatoxin B1 by Probiotic Yeasts and Bacteria Isolated From Dairy Products of Iran.", "token_count": 499, "char_count": 1744, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5875, "quality_score": 0.7937, "entities": { "genes": [ "AFB1" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:49.582710", "source": { "split": "train_shard_00001", "doc_id": 2450 }, "chunk_id": "train_shard_00001_2450_0", "global_id": 9156 }, { "text": "Synbiotics are food supplements that combine probiotics and prebiotics to synergistically elicit a health effect in humans. Lactobacillus plantarum exhibits remarkable genetic and phenotypic diversity, in particular in strain-specific carbohydrate utilization capacities, and several strains are marketed as probiotics. We have screened 77 L. plantarum strains for their abilities to utilize specific prebiotic fibers, revealing variable and strain-specific growth efficiencies on isomalto- and galactooligosaccharides. We identified a single strain within the screening panel that was able to effectively utilize inulin and fructooligosaccharides (FOS), which did not support efficient growth of the rest of the strains. In the panel we tested, we did not find strains that could utilize arabinoxylooligosaccharides or sulfated fucoidan. The strain-specific growth phenotype on isomaltooligosaccharides was further analyzed using high-performance anion-exchange chromatography, which revealed distinct substrate utilization phenotypes within the strain panel. The strain-specific phenotypes could be linked to the strains' genotypes by identifying gene clusters coding for carbohydrate membrane transport systems that are predicted to be involved in the utilization of isomaltose and other (unidentified) oligosaccharides in the isomaltooligosaccharide substrate.IMPORTANCE Synbiotics combine prebiotics and probiotics to synergistically enhance the health benefits associated with these ingredients. Lactobacillus plantarum is encountered as a natural inhabitant of the gastrointestinal tract, and specific strains are marketed as probiotics based on their strain-specific health-promoting activities. Strain-specific stimulation of growth through prebiotic substrates could enhance the persistence and/or activity of L", "token_count": 456, "char_count": 1852, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:50.581438", "source": { "split": "train_shard_00001", "doc_id": 2451 }, "chunk_id": "train_shard_00001_2451_0", "global_id": 9157 }, { "text": "plantarumin situ Our study establishes a high-throughput screening model for prebiotic substrate utilization by individual strains of bacteria, which can be readily employed for synbiotic matchmaking approaches that aim to enhance the intestinal delivery of probiotics through strain-specific, selective growth stimulation.\n\nSynbiotic Matchmaking in Lactobacillus plantarum: Substrate Screening and Gene-Trait Matching To Characterize Strain-Specific Carbohydrate Utilization.", "token_count": 124, "char_count": 487, "word_count": 56, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:50.968229", "source": { "split": "train_shard_00001", "doc_id": 2451 }, "chunk_id": "train_shard_00001_2451_1", "global_id": 9158 }, { "text": "Growth, substrate consumption, metabolite formation, biomass composition and respiratory parameters of Kluyveromyces marxianus ATCC 26548 were determined during aerobic batch and chemostat cultivations, using mineral medium with glucose as the sole carbon source, at 30 degrees C and pH 5.0. Carbon balances closed within 95-101% in all experiments. A maximum specific growth rate of 0.56 h(-1), a biomass yield on glucose of 0.51 g g(-1), and a maximum specific consumption of oxygen of 11.1 mmol g(-1) h(-1) were obtained during batch cultures. The concentration of excreted metabolites was very low at the culture conditions applied, representing 6% of the consumed carbon at most. Acetate and pyruvate were excreted to a larger extent than ethanol under the batch conditions, and the protein content accounted for 54.6% of the biomass dry weight. Steady states were obtained during chemostats at dilution rates of 0.1, 0.25 and 0.5 h(-1). At the two former dilution rates, cells grew at carbon limitation and the biomass yield on glucose was similar to that obtained under the batch conditions. Metabolite formation was rather low, accounting for a total of 0.005 C-mol C-mol(-1) substrate. At 0.5 h(-1), although the biomass yield on glucose was similar to the value obtained under the above-mentioned conditions, the cultivation was not under carbon limitation. Under this condition, 2-oxoglutarate, acetate, pyruvate and ethanol were the prevalent metabolites excreted. Total metabolite formation only accounted to 0.056 C-mol C-mol(-1) of substrate. A very high protein and a low carbohydrate content (71.9% and 9.6% of biomass dry weight, respectively) were measured in cells under this condition. It is concluded that K. marxianus aligns with the so-called aerobic-respiring or Crabtree-negative yeasts", "token_count": 518, "char_count": 1812, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5604, "quality_score": 0.7802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:24:51.600779", "source": { "split": "train_shard_00001", "doc_id": 2452 }, "chunk_id": "train_shard_00001_2452_0", "global_id": 9159 }, { "text": "Furthermore, it has one of the highest growth rates among yeasts, and a high capacity of converting sugar into biomass, even when carbon is not the limiting nutrient. These results provide useful data regarding the future application of K. marxianus in processes aimed at the production of biomass-linked compounds, with high yields and productivities.\n\nPhysiology of the yeast Kluyveromyces marxianus during batch and chemostat cultures with glucose as the sole carbon source.", "token_count": 111, "char_count": 477, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:51.989701", "source": { "split": "train_shard_00001", "doc_id": 2452 }, "chunk_id": "train_shard_00001_2452_1", "global_id": 9160 }, { "text": "The purpose of this study was to evaluate the use of single cell proteins (Kluyveromyces marxianus) as fishmeal substitutes for Oreochromis niloticus during long‐term feeding under natural climatic conditions. Juveniles (150) were divided into two groups: the control group, fed with conventional fish diet (T1); and the experimental group, fed with the alternative diet (T2). T1 animals had a higher final weight and per cent weight gain than T2 animals, which we mainly observed in winter and autumn. The lipid content ranged from 1.9% to 3.8% in liver and from 0.2% to 1% in white muscle for both groups. T2 animals had a higher protein concentration in the fillet and the lipid content in this tissue was not altered by diet. Liver and plasma protein content in both groups and the muscle content in T1 decreased during growth. Specific fatty acids (FAs) were selectively retained in fillet phospholipids (PLs), primarily as C22:6n3, which was found at high levels in the PLs of both groups during all seasons. Despite the differences observed, the percentage of polyunsaturated FAs in the fillet was similar throughout the experiment for both diets, reaching approximately 50% of the total FA in the PLs.\n\nThe use of Kluyveromyces marxianus in the diet of Red‐Stirling tilapia (Oreochromis niloticus, Linnaeus) exposed to natural climatic variation: effects on growth performance, fatty acids, and protein deposition", "token_count": 361, "char_count": 1421, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:52.568319", "source": { "split": "train_shard_00001", "doc_id": 2453 }, "chunk_id": "train_shard_00001_2453_0", "global_id": 9161 }, { "text": "Several recombinant Kluyveromyces marxianus strains were constructed through overexpressing the Neurospora crassa xylose reductase genes. YZJ015, which maintained the original xylitol dehydrogenase gene, produced xylitol with the highest productivity (1.49 g L(-1) h(-1)) from 100 g L(-1) xylose at 42 °C. Even at 45 °C, YZJ015 was still able to produce 60.03 g L(-1) xylitol from 100 g L(-1) xylose with a productivity of 1.25 g L(-1)h(-1). In addition, for 20 rounds of cell recycling at 42 °C, YZJ015 produced 71.35 g L(-1) xylitol from 100 g L(-1) xylose with a productivity of 4.43 g L(-1) h(-1) per cycle. YZJ017, in which the xylitol dehydrogenase gene was disrupted, produced 100.02 g L(-1) xylitol at a yield of 1.01 g g(-1) from 100 g L(-1) xylose with 40 g L(-1) glycerol as co-substrate at 42 °C. These engineered strains provide an excellent foundation for xylitol production at elevated temperatures.\n\nXylitol production at high temperature by engineered Kluyveromyces marxianus.", "token_count": 371, "char_count": 993, "word_count": 157, "semantic_coherence": 1, "information_density": 0.5414, "quality_score": 0.7707, "entities": { "genes": [ "YZJ015", "YZJ017" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:53.144395", "source": { "split": "train_shard_00001", "doc_id": 2454 }, "chunk_id": "train_shard_00001_2454_0", "global_id": 9162 }, { "text": "

Background

Community-associated Clostridioides difficile infection is a major public health hazard to adults and older children. Infants frequently excrete toxigenic C difficile asymptomatically in their stool, but their importance as a community reservoir of C difficile is uncertain.

Methods

Families of healthy infants were recruited at the baby's 4-month well child visit and were followed longitudinally until the baby was approximately 9 months old. Babies and mothers submitted stool or rectal swabs every 2 weeks that were cultivated for C difficile; fathers' participation was encouraged but not required. Clostridioides difficile isolates were strain-typed by fluorescent polymerase chain reaction ribotyping and by core genome multilocus sequence typing, and the number of families in whom the same strain was cultivated from >1 family member (\"strain sharing\") was assessed.

Results

Thirty families were enrolled, including 33 infants (3 sets of twins) and 30 mothers; 19 fathers also participated. Clostridioides difficile was identified in 28 of these 30 families over the course of the study, and strain sharing was identified in 17 of these 28. In 3 families, 2 separate strains were shared. The infant was involved in 17 of 20 instances of strain sharing, and in 13 of these, the baby was identified first, with or without a concomitantly excreting adult. Excretion of shared strains usually was persistent.

Conclusions

Clostridioides difficile strain sharing was frequent in healthy families caring for an infant, increasing the likelihood that asymptomatically excreting babies and their families represent a reservoir of the organism in the community.\n\nMolecular Epidemiology of Clostridioides difficile Colonization in Families With Infants.", "token_count": 503, "char_count": 1847, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5976, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:53.792627", "source": { "split": "train_shard_00001", "doc_id": 2455 }, "chunk_id": "train_shard_00001_2455_0", "global_id": 9163 }, { "text": "Typhoid fever is endemic in many parts of the world and remains a major public health concern in tropical and sub-tropical developing nations, including Fiji. To address high rates of typhoid fever, the Northern Division of Fiji implemented a mass vaccination with typhoid conjugate vaccine (Vi-polysaccharide conjugated to tetanus toxoid) as a public health control measure in 2023. In this study we define the genomic epidemiology of Salmonella Typhi in the Northern Division prior to island-wide vaccination, sequencing 85% (n=419) of the total cases from the Northern and Central Divisions of Fiji that occurred in the period 2017-2019. We found elevated rates of nucleotide polymorphisms in the tviD and tviE genes (responsible for Vi-polysaccharide synthesis) relative to core genome levels within the Fiji endemic S. Typhi genotype 4.2. Expansion of these findings within a globally representative database of 12 382 S. Typhi (86 genotyphi clusters) showed evidence of convergent evolution of the same tviE mutations across the S. Typhi population, indicating that tvi selection has occurred both independently and globally. The functional impact of tvi mutations on the Vi-capsular structure and other phenotypic characteristics are not fully elucidated, yet commonly occurring tviE polymorphisms localize adjacent to predicted active site residues when overlayed against the predicted TviE protein structure. Given the central role of the Vi-polysaccharide in S. Typhi biology and vaccination, further integrated epidemiological, genomic and phenotypic surveillance is required to determine the spread and functional implications of these mutations.", "token_count": 477, "char_count": 1742, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:54.434946", "source": { "split": "train_shard_00001", "doc_id": 2456 }, "chunk_id": "train_shard_00001_2456_0", "global_id": 9164 }, { "text": "Genetic heterogeneity in the <i>Salmonella</i> Typhi Vi capsule locus: a population genomic study from Fiji.", "token_count": 41, "char_count": 120, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:54.790609", "source": { "split": "train_shard_00001", "doc_id": 2456 }, "chunk_id": "train_shard_00001_2456_1", "global_id": 9165 }, { "text": "The gut microbiota is composed of several microbial strains with diverse and variable compositions in both healthy and sick people. An undisturbed gut microbiota needs to be sustained in order to perform all physiological, metabolic, and immune functions in a normal way to prevent the development of diseases. This article has reviewed the published information on the issue of disruption of the balance of the gut microbiota. This disruption could be for many reasons, such as microbial infection in the gastrointestinal tract, food poisoning, diarrhoea, chemotherapy, malnutrition, lifestyle, and ageing. If this disruption is not restored to normal, it might cause dysbiosis. Eventually, a gut microbiota interrupted by dysbiosis might initiate several health issues, such as inflammation of the gastrointestinal tract, the induction of cancer, and the progression of a variety of diseases such as irritable bowel syndrome and inflammatory bowel disease. This review concluded that biotherapy is a natural way of using probiotic products, whether in form of food, beverages, or supplements, to restore the gut microbiota disrupted by dysbiosis. Metabolites secreted by the ingested probiotics help to relieve gastrointestinal tract inflammation and can avoid the induction of cancer.\n\nBiotherapy Using Probiotics as Therapeutic Agents to Restore the Gut Microbiota to Relieve Gastrointestinal Tract Inflammation, IBD, IBS and Prevent Induction of Cancer.", "token_count": 350, "char_count": 1458, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5728, "quality_score": 0.7864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:55.360054", "source": { "split": "train_shard_00001", "doc_id": 2457 }, "chunk_id": "train_shard_00001_2457_0", "global_id": 9166 }, { "text": "Xanthomonas citri subspecies citri (XCC) is the cause of bacterial citrus canker, responsible for major economic losses to the citrus industry that includes sweet orange, lime and grapefruit production in regions including South America, United States, China and Japan. Other X. citri subsp. and pathovars are responsible for diseases in crops such as soy bean, common bean, mango, pomegranate and cashew. Tracing the spread of X. citri disease has been performed using several different typing methods over the years but recent studies using genomic sequencing have been key to understanding evolutionary relationships within the species including fundamental differences between XCC pathotypes. In this study we developed a core genome multilocus typing scheme (cgMLST) for X. citri based upon 250 genomes comprising multiple examples of X. citri subsp. citri pathotypes A, A* and A w , X. citri subsp. malvacearum and X. citri pathovars aurantifolii, fuscans, glycines, malvacearum, mangiferaeindicae, viticola, vignicola and single isolates of X. citri pathovars dieffenbachiae and punicae . This dataset included genomic sequencing of 100 novel XCC isolates. The cgMLST scheme, based upon 1618 core genes across 250 genomes, has been implemented at PubMLST ( https://pubmlst.org/organisms/xanthomonas-citri/ ). Grapetree minimum-spanning, and iTOL Neighbour-joining phylogenies generated from cgMLST data resolved almost identical groupings of isolates to a core genome SNP - based neighbour joining phylogeny taking 4 min, 15 min and 36 h respectively. These resolved identical groupings of XCC pathotypes and X. citri subsp. and pathovars. X. citri cgMLST should prove to be an increasingly valuable resource for the study of this key species of plant pathogenic bacteria. Users can submit genomic and associated metadata to compare with previously characterised isolates at PubMLST.org to allow rapid characterization of local, national and global epidemiology of these pathogens and examine evolutionary relationships.", "token_count": 528, "char_count": 2027, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8236, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:24:56.011342", "source": { "split": "train_shard_00001", "doc_id": 2458 }, "chunk_id": "train_shard_00001_2458_0", "global_id": 9167 }, { "text": "Core genome MLST for epidemiological and evolutionary analyses of phytopathogenicXanthomonas citri", "token_count": 33, "char_count": 105, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:56.368021", "source": { "split": "train_shard_00001", "doc_id": 2458 }, "chunk_id": "train_shard_00001_2458_1", "global_id": 9168 }, { "text": "

Background

Salmonella Infantis (S. Infantis) is one of the most frequent Salmonella serovars isolated from human cases of salmonellosis and the most detected serovar from animal and food sources in Europe. The serovar is commonly associated with poultry and there is increasing concern over multidrug resistant clones spreading worldwide, as the dominating clones are characterized by presence of large plasmids carrying multiple resistance genes. Increasing the knowledge of the S. Infantis population and evolution is important for understanding and preventing further spread. In this study, we analysed a collection of strains representing different decades, sources and geographic locations. We analysed the population structure and the accessory genome, in particular we identified prophages with a view to understand the role of prophages in relation to the evolution of this serovar.

Results

We sequenced a global collection of 100 S. Infantis strains. A core-genome SNP analysis separated five strains in e-Burst Group (eBG) 297 with a long branch. The remaining strains, all in eBG31, were divided into three lineages that were estimated to have separated approximately 150 years ago. One lineage contained the vast majority of strains. In five of six clusters, no obvious correlation with source or geographical locations was seen. However, one cluster contained mostly strains from human and avian sources, indicating a clone with preference for these sources. The majority of strains within this cluster harboured a pESI-like plasmid with multiple resistance genes. Another lineage contained three genetic clusters with more rarely isolated strains of mainly animal origin, possibly less sampled or less infectious clones. Conserved prophages were identified in all strains, likely representing bacteriophages which integrated into the chromosome of a common ancestor to S. Infantis. We also saw that some prophages were specific to clusters and were probably introduced when the clusters were formed.

Conclusions

This study analysed a global S. Infantis population and described its genetic structure. We hypothesize that the population has evolved in three separate lineages, with one more successfully emerging lineage", "token_count": 505, "char_count": 2255, "word_count": 323, "semantic_coherence": 1, "information_density": 0.5697, "quality_score": 0.7848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:57.022762", "source": { "split": "train_shard_00001", "doc_id": 2459 }, "chunk_id": "train_shard_00001_2459_0", "global_id": 9169 }, { "text": "We furthermore detected conserved prophages present in the entire population and cluster specific prophages, which probably shaped the population structure.\n\nWGS based study of the population structure of Salmonella enterica serovar Infantis.", "token_count": 51, "char_count": 242, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8438, "quality_score": 0.9219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:57.381635", "source": { "split": "train_shard_00001", "doc_id": 2459 }, "chunk_id": "train_shard_00001_2459_1", "global_id": 9170 }, { "text": "Breast milk contains human milk oligosaccharides (HMOs) that cannot be digested by infants, yet nourish their developing gut microbiome. While Bifidobacterium are the best-known utilizers of individual HMOs, a longitudinal study examining the evolving microbial community at high-resolution coupled with mothers' milk HMO composition is lacking. Here, we developed a high-throughput method to quantify Bifidobacterium longum subsp. infantis (BL. infantis), a proficient HMO-utilizer, and applied it to a longitudinal cohort consisting of 21 mother-infant dyads. We observed substantial changes in the infant gut microbiome over the course of several months, while the HMO composition in mothers' milk remained relatively stable. Although Bifidobacterium species significantly influenced sample variation, no specific HMOs correlated with Bifidobacterium species abundance. Surprisingly, we found that BL. infantis colonization began late in the breastfeeding period both in our cohort and in other geographic locations, highlighting the importance of focusing on BL. infantis dynamics in the infant gut.\n\nLongitudinal quantification of Bifidobacterium longum subsp. infantis reveals late colonization in the infant gut independent of maternal milk HMO composition.", "token_count": 300, "char_count": 1264, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:57.941210", "source": { "split": "train_shard_00001", "doc_id": 2460 }, "chunk_id": "train_shard_00001_2460_0", "global_id": 9171 }, { "text": "An estimated 2 billion species of microbes exist on Earth with orders of magnitude more strains. Microbial pangenomes are created by aggregating all genomes of a single clade and reflect the metabolic diversity of groups of organisms. As de novo metagenome analysis techniques have matured and reference genome databases have expanded, metapangenome analysis has risen in popularity as a tool to organize the functional potential of organisms in relation to the environment from which those organisms were sampled. However, the reliance on assembly and binning or on reference databases often leaves substantial portions of metagenomes unanalyzed, thereby underestimating the functional potential of a community. To address this challenge, we present a method for metapangenomics that relies on amino acid k-mers (k aa -mers) and metagenome assembly graph queries. To enable this method, we first show that k aa -mers estimate pangenome characteristics and that open reading frames can be accurately predicted from short shotgun sequencing reads using the previously developed tool orpheum. These techniques enable pangenomics to be performed directly on short sequencing reads. To enable metapangenome analysis, we combine these approaches with compact de Bruijn assembly graph queries to directly generate sets of sequencing reads for a specific species from a metagenome. When applied to stool metagenomes from an individual receiving antibiotics over time, we show that these approaches identify strain fluctuations that coincide with antibiotic exposure.\n\nProtein k-mers enable assembly-free microbial metapangenomics", "token_count": 341, "char_count": 1622, "word_count": 234, "semantic_coherence": 1, "information_density": 0.641, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:58.508298", "source": { "split": "train_shard_00001", "doc_id": 2461 }, "chunk_id": "train_shard_00001_2461_0", "global_id": 9172 }, { "text": "

Aims

Cells limit the cell number of dense biofilms by releasing self-inhibitory molecules. Here, we aim to assess the effectiveness of yeast quorum sensing (QS) molecules and the antifungal agent natamycin against yeast biofilms of strains commonly isolated from fruit juice ultrafiltration membranes.

Methods and results

Yeast QS molecules, such as tyrosol, 2-phenylethanol and farnesol, were detected by solvent extraction and HS-SPME GC-MS in Candida tropicalis cultures. The effect of QS molecules on mono- and multispecies biofilms formed by Rhodotorula mucilaginosa, C. tropicalis, Candida krusei and Candida kefyr was evaluated by plate count and epifluorescence microscopy. Farnesol caused a decrease in cell number and disrupted mono- and multispecies yeast biofilms during adhesion (0·6 mmol l-1 ). 2-phenyl ethanol 1·2 mmol l-1 stimulated biofilm density and increased cell number in both mono- and multispecies biofilms, while tyrosol did not show effects when tested against C. tropicalis biofilms (0·05-1·2 mmol l-1 ). Natamycin caused a strong decrease in cell number and disruption of biofilm structure in C. tropicalis biofilms at high concentrations (0·3-1·2 mmol l-1 ). The combination of farnesol 0·6 mmol l-1 and natamycin at 0·01 mmol l-1 , the maximum concentration of natamycin accepted for direct addition into fruit juices, effectively reduced cell counts and disrupted the structure of C", "token_count": 472, "char_count": 1495, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5942, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:59.148429", "source": { "split": "train_shard_00001", "doc_id": 2462 }, "chunk_id": "train_shard_00001_2462_0", "global_id": 9173 }, { "text": "tropicalis biofilms.

Conclusion

Farnesol 0·6 mmol l-1 significantly increased the inhibition exerted by natamycin 0·01 mmol l-1 (~5 ppm) reducing biofilm development from juice on stainless steel surfaces.

Significance and impact of the study

These results support the use of QS molecules as biofilm inhibitors in beverages and would certainly inspire the design of novel preservative and cleaning products for the food industry based on combinatory approaches.\n\nEffect of quorum sensing molecules and natamycin on biofilms of Candida tropicalis and other yeasts isolated from industrial juice filtration membranes.", "token_count": 180, "char_count": 651, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7381, "quality_score": 0.869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:24:59.651776", "source": { "split": "train_shard_00001", "doc_id": 2462 }, "chunk_id": "train_shard_00001_2462_1", "global_id": 9174 }, { "text": "The wheat pathogen Parastagonospora nodorum has emerged as a model necrotrophic fungal species with growing genomic resources. Recent population-level pan-genome studies were leveraged to provide novel insights into pathogen evolution and effector-like gene contents relevant to local crop disease outbreaks. In this study, we examined 156 isolates representing a regional population from the Western Australian (WA) wheat-belt region, and 17 internationally sourced isolates. We observed a highly diverse local population, within which were numerous small and highly similar clusters of isolates from hotter and drier regions. Pan-genome assembly and orthologous gene datasets resulted in 3579 predicted effector candidates, 2291 of which exhibited presence-absence variation (PAV) across the population, and 1362 were specific to WA isolates. There was an abundance of mutations (including repeat-induced point mutation (RIP)), distributed in ‘hot-spots’ within the pan-genomic landscape that were rich in effector candidates. Three characterised effector loci ( ToxA , Tox1 and Tox3 ) were located within sub- telomeric regions of lower diversity, but were nestled within larger high-diversity regions. RIP was widespread across the genome, but non-synonymous RIP-like mutations were strongly selected against. These improved bioinformatic resources for P. nodorum , represent progressive advancements in fungal pan-genomics, with a view towards supporting region- specific surveillance of host-pathogen interactions.\n\nPathogenicity effector candidates and accessory genome revealed by pan-genomic analysis of Parastagonospora nodorum", "token_count": 383, "char_count": 1644, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7294, "quality_score": 0.8647, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:00.263612", "source": { "split": "train_shard_00001", "doc_id": 2463 }, "chunk_id": "train_shard_00001_2463_0", "global_id": 9175 }, { "text": "With the recent technological advancement in cultivation-independent high-throughput sequencing, metagenomes have tremendously improved our ability to characterize the genomic contents of the whole microbial communities. In this chapter, we argue the notion of pangenome can be applied beyond the available genome sequences by leveraging metagenome-assembled genomes, to form a comprehensive representation of the genetic content of a taxonomic group in a particular environment. We present the concept of the meta-pangenome, a representation of the totality of genes belonging to a species identified in multiple metagenomic samplings of a particular habitat. As an essential component in genome-centric pangenome analyses, we emphasize the importance to perform stringent quality assessment and validation to ensure the high quality of metagenomic deconvoluted genomes. This expansion from the traditional pangenome concept to the meta-pangenome overcomes many of the biases associated with whole-genome sequencing, and addresses the in vivo ecological context to further develop a systems-level understanding of microbial ecosystems.\n\nMeta-Pangenome: At the Crossroad of Pangenomics and Metagenomics", "token_count": 257, "char_count": 1202, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:00.844916", "source": { "split": "train_shard_00001", "doc_id": 2464 }, "chunk_id": "train_shard_00001_2464_0", "global_id": 9176 }, { "text": "Denmark is a low prevalence country with regard to methicillin resistant Staphylococcus aureus (MRSA). In 2008 and 2014, two neonatal wards in the Copenhagen area experienced outbreaks with a typical community acquired MRSA belonging to the same spa type and sequence type (t015:ST45) and both were PVL and ACME negative. In outbreak 1, the isolates harbored SCCmec IVa and in outbreak 2 SCCmec V. The clinical presentation differed between the two outbreaks, as none of five MRSA positive mothers in outbreak 1 had mastitis vs. five of six MRSA positive mothers in outbreak 2 (p < 0.02). To investigate if whole-genome sequencing could identify virulence genes associated with mastitis, t015:ST45 isolates from Denmark (N = 101) were whole-genome sequenced. Sequence analysis confirmed two separate outbreaks with no sign of sustained spread into the community. Analysis of the accessory genome between isolates from the two outbreaks revealed a S. aureus pathogenicity island containing enterotoxin C and enterotoxin-like L only in isolates from outbreak 2. Enterotoxin C and enterotoxin-like L carrying S. aureus are associated with bovine mastitis and our findings indicate that these may also be important virulence factors for human mastitis.\n\nStaphylococcal aureus Enterotoxin C and Enterotoxin-Like L Associated with Post-partum Mastitis.", "token_count": 421, "char_count": 1409, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.8069, "entities": { "genes": [ "ST45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:01.503860", "source": { "split": "train_shard_00001", "doc_id": 2465 }, "chunk_id": "train_shard_00001_2465_0", "global_id": 9177 }, { "text": "The molecular characterization of 14 strains of Kluyveromyces marxianus isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico, was performed by AP-PCR analysis, PCR-RFLP of 5.8S-ITS, and complete NTS regions. A sequence analysis of the D1/D2 domain of the 26S rDNA was also carried out in six selected strains. The AP-PCR approach had the highest discrimination power for the molecular characterization of new henequen K. marxianus strains. PCR-RFLP of 5.8S-ITS regions did not reveal polymorphisms in this group of strains. The restriction enzyme digestion analysis of NTS region enables the separation among strains which coincides with ascospore shape groups. The molecular tools used in this article may be useful to confirm a preliminary screen of yeasts isolated from henequen without the use of growth characteristics or morpho-physiological tests.\n\nMolecular characterization of Kluyveromyces marxianus strains isolated from Agave fourcroydes (Lem.) in Yucatan, Mexico.", "token_count": 265, "char_count": 981, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6312, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:02.054431", "source": { "split": "train_shard_00001", "doc_id": 2466 }, "chunk_id": "train_shard_00001_2466_0", "global_id": 9178 }, { "text": "

Objectives

To determine the Etest-based epidemiological cut-off values (ECVs) for antifungal agents against the most frequent yeast and Aspergillus fumigatus species isolated in 12 French hospitals.

Methods

For each antifungal agent, the Etest MICs in yeast and A. fumigatus isolates from 12 French laboratories were retrospectively collected from 2004 to 2018. The ECVs were then calculated using the iterative statistical method with a 97.5% cut-off.

Results

Forty-eight Etest ECVs were determined for amphotericin B, caspofungin, micafungin, anidulafungin, fluconazole, voriconazole, posaconazole and itraconazole, after pooling and analysing the MICs of 9654 Candida albicans, 2939 Candida glabrata SC, 1458 Candida parapsilosis SC, 1148 Candida tropicalis, 575 Candida krusei, 518 Candida kefyr, 241 Candida lusitaniae, 131 Candida guilliermondii and 1526 Aspergillus fumigatus species complex isolates. These ECVs were 100% concordant (identical or within one two-fold dilution) with the previously reported Etest-based ECVs (when available), and they were concordant in 76.1% of cases with the Clinical and Laboratory Standards Institute ECVs and in 81.6% of cases with the European Committee on Antimicrobial Susceptibility Testing ECVs.

Conclusions

On the basis of these and other previous results, we recommend the determination of method-dependent ECVs", "token_count": 464, "char_count": 1392, "word_count": 181, "semantic_coherence": 1, "information_density": 0.663, "quality_score": 0.8315, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:02.692918", "source": { "split": "train_shard_00001", "doc_id": 2467 }, "chunk_id": "train_shard_00001_2467_0", "global_id": 9179 }, { "text": "Etest ECVs should not be used instead of breakpoints, but may be useful to identify non-wild-type isolates with potential resistance to antifungal agents, and to indicate that an isolate may not respond as expected to the standard treatment.\n\nMulticentre study to determine the Etest epidemiological cut-off values of antifungal drugs in Candida spp. and Aspergillus fumigatus species complex.", "token_count": 98, "char_count": 393, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7931, "quality_score": 0.8966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:03.066240", "source": { "split": "train_shard_00001", "doc_id": 2467 }, "chunk_id": "train_shard_00001_2467_1", "global_id": 9180 }, { "text": "

Purpose

Clinical and in vitro studies showed selected oral microorganisms to be related to delayed wound healing and ulcerative oral mucositis. However, it is not known whether this effect is due to reduced metabolism and/or the reduced reproductive capacity of epithelial cells. Therefore, we studied the influence of the oral microorganisms Porphyromonas gingivalis, Candida glabrata, and Candida kefyr on cell metabolism and reproductive capacity of oral epithelial cells, aimed to further unravel the pathogenesis of oral mucositis.

Methods

Oral epithelial cells were exposed to different concentrations of P. gingivalis, C. glabrata, and C. kefyr as mono-infections or mixed together. An MTT assay was performed to determine the effect on cell metabolism. A clonogenic assay was used to study the effect on the reproductive capacity of oral epithelial cells.

Results

The metabolism of oral epithelial cells was reduced when the microorganisms were present in high concentrations: P. gingivalis at a multiplicity of infection (MOI) of 1000 and the Candida spp. at MOI 100. No statistical difference was observed in the ability of a single epithelial cell to grow into a colony of cells between control and P. gingivalis, C. glabrata, and C. kefyr, independent of the concentrations and combinations used.

Conclusion

P. gingivalis, C. glabrata, and C. kefyr lowered the metabolic activity of oral epithelial cells in high concentrations, yet they did not influence the reproductive capacity of epithelial cells. Their impact on ulcerative oral mucositis is likely due to an effect on the migration, proliferation, and metabolism of epithelial cells.\n\nExploring the role of oral microorganisms in the pathogenesis of mucositis by assessing their impact on metabolic activity and reproductive capacity of epithelial cells in vitro.", "token_count": 509, "char_count": 1861, "word_count": 269, "semantic_coherence": 1, "information_density": 0.4535, "quality_score": 0.7268, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:03.694046", "source": { "split": "train_shard_00001", "doc_id": 2468 }, "chunk_id": "train_shard_00001_2468_0", "global_id": 9181 }, { "text": "Since 2016, devastating bacterial blotch affecting the fruiting bodies of Agaricus bisporus, Cordyceps militaris, Flammulina filiformis, and Pleurotus ostreatus in China has caused severe economic losses. We isolated 102 bacterial strains and characterized them polyphasically. We identified the causal agent as Pseudomonas tolaasii and confirmed the pathogenicity of the strains. A host range test further confirmed the pathogen's ability to infect multiple hosts. This is the first report in China of bacterial blotch in C. militaris caused by P. tolaasii. Whole-genome sequences were generated for three strains: Pt11 (6.48 Mb), Pt51 (6.63 Mb), and Pt53 (6.80 Mb), and pangenome analysis was performed with 13 other publicly accessible P. tolaasii genomes to determine their genetic diversity, virulence, antibiotic resistance, and mobile genetic elements. The pangenome of P. tolaasii is open, and many more gene families are likely to emerge with further genome sequencing. Multilocus sequence analysis using the sequences of four common housekeeping genes (glns, gyrB, rpoB, and rpoD) showed high genetic variability among the P. tolaasii strains, with 115 strains clustered into a monophyletic group. The P. tolaasii strains possess various genes for secretion systems, virulence factors, carbohydrate-active enzymes, toxins, secondary metabolites, and antimicrobial resistance genes that are associated with pathogenesis and adapted to different environments", "token_count": 510, "char_count": 1613, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8544, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:04.332959", "source": { "split": "train_shard_00001", "doc_id": 2469 }, "chunk_id": "train_shard_00001_2469_0", "global_id": 9182 }, { "text": "The myriad of insertion sequences, integrons, prophages, and genome islands encoded in the strains may contribute to genome plasticity, virulence, and antibiotic resistance. These findings advance understanding of the determinants of virulence, which can be targeted for the effective control of bacterial blotch disease.\n\nCharacterization, Pathogenicity, Phylogeny, and Comparative Genomic Analysis of Pseudomonas tolaasii Strains Isolated from Various Mushrooms in China.", "token_count": 121, "char_count": 480, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7869, "quality_score": 0.8934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:04.718659", "source": { "split": "train_shard_00001", "doc_id": 2469 }, "chunk_id": "train_shard_00001_2469_1", "global_id": 9183 }, { "text": "Auto-brewery syndrome (ABS), also known as gut fermentation syndrome, is a very rare disorder. It is characterized by the endogenous production of alcohol. It typically presents with the signs of alcohol intoxication, such as staggering gait, slurred speech, gastrointestinal distress, and state of confusion. Due to the nonspecific symptoms, it is necessary to rule out other etiologies before reaching a diagnosis of ABS. The confirmatory test for this syndrome is the raised levels of blood or breath ethanol after a glucose challenge test. The management includes the use of antifungal drugs and avoidance of a carbohydrate-rich diet. In this review, we summarize the etiology, clinical presentation, diagnostic tests, management, and medicolegal aspects of ABS.\n\nAuto-Brewery Syndrome: A Clinical Dilemma.", "token_count": 196, "char_count": 810, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7311, "quality_score": 0.8655, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:05.177255", "source": { "split": "train_shard_00001", "doc_id": 2470 }, "chunk_id": "train_shard_00001_2470_0", "global_id": 9184 }, { "text": "Kluyveromyces marxianus DMKU 3-1042, isolated by an enrichment technique in a sugar cane juice medium supplemented with 4% (w/v) ethanol at 35 degrees C, produced high concentrations of ethanol at both 40 and 45 degrees C. Ethanol production by this strain in shaking flask cultivation in sugar cane juice media at 37 degrees C was highest in a medium containing 22% total sugars, 0.05% (NH(4))(2)SO(4), 0.05% KH(2)PO(4), and 0.15% MgSO(4).7H(2)O and having a pH of 5.0; the ethanol concentration reached 8.7% (w/v), productivity 1.45 g/l/h and yield 77.5% of theoretical yield. At 40 degrees C, a maximal ethanol concentration of 6.78% (w/v), a productivity of 1.13 and a yield 60.4% of theoretical yield were obtained from the same medium, except that the pH was adjusted to 5.5. In a study on ethanol production in a 5l jar fermenter with an agitation speed of 300 rpm and an aeration rate of 0.2 vvm throughout the fermentation, K. marxianus DMKU 3-1042 yielded a final ethanol concentration of 6.43% (w/v), a productivity of 1.3g/l/h and a yield of 57.1% of theoretical yield.\n\nProduction of fuel ethanol at high temperature from sugar cane juice by a newly isolated Kluyveromyces marxianus.", "token_count": 422, "char_count": 1196, "word_count": 196, "semantic_coherence": 1, "information_density": 0.551, "quality_score": 0.7755, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:05.800535", "source": { "split": "train_shard_00001", "doc_id": 2471 }, "chunk_id": "train_shard_00001_2471_0", "global_id": 9185 }, { "text": "Identification of plasmids from sequencing data is an important and challenging problem related to antimicrobial resistance spread and other One-Health issues. In our work, we provide a new architecture for identifying plasmid contigs in fragmented genome assemblies built from short-read data. Unlike previous machine-learning approaches for this problem, which classify individual contigs separately, we employ graph neural networks (GNNs) to include information from the assembly graph. Propagation of information from nearby nodes in the graph allows accurate classification of even short contigs that are difficult to classify based on sequence features or database searches alone. Our new species-agnostic software tool plASgraph outperforms recently developed PlasForest, which uses database searches to supplement sequence-based features. Since our tool does not rely on existing plasmid databases, it is more suitable for classification of contigs in novel species and discovery of previously unknown plasmid sequences. Our tool can also be trained on a specific species, and in that scenario it outperforms mlplasmids trained on the same species. On one hand, our work provides a new, accurate, and easy to use tool for plasmid classification; on the other hand, it serves as a motivation for more widespread use of GNNs in bioinformatics, such as in pangenome sequence analysis, where sequence graphs serve as a fundamental data structure.

Availability

https://github.com/cchauve/plASgraph\n\nplASgraph - using graph neural networks to detect plasmid contigs from an assembly graph", "token_count": 341, "char_count": 1599, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6228, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:06.375902", "source": { "split": "train_shard_00001", "doc_id": 2472 }, "chunk_id": "train_shard_00001_2472_0", "global_id": 9186 }, { "text": "Listeria monocytogenes is a foodborne pathogen. In 2022, we collected 15 strains of L. monocytogenes isolated from patients in some foodborne disease sentinel monitoring hospitals in Sichuan Province. Through whole genome sequencing (WGS), we obtained the virulence genes carried by the strains, multi-locus sequence typing (MLST), core genome MLST (cgMLST), clonal complex (CC), and serum groups and constructed a phylogenetic tree and minimum spanning tree with nonhuman strains. An analysis shows that all 15 strains of L. monocytogenes carry virulence genes LIPI-1 and LIPI-2, whereas the carrying rates of LIPI-3 and LIPI-4 virulence genes are relatively low. The MLST typing results showed a total of 10 sequence types (ST), including 10 CCs, with ST7 being the dominant type. The cgMLST clearly distinguishes strains of different lineages and CC types. The serum group is divided into three types: IIa, IIb, and IVb, with IIa being the dominant serum group. An analysis of antibiotic genes showed that all 15 strains carried FosX, lin, mprF, and norB with high carrying rates. The minimum inhibitory concentration results indicated that all were susceptible to eight antibiotics (ampicillin, penicillin, tetracycline, meropenem, erythromycin, vancomycin, ciprofloxacin, and trimethoprim-sulfamethoxazole). The analysis of strains isolated from different sources of Listeria revealed varying degrees of diversity, and the contamination of meat and environment within the province is closely related to clinical cases. L. monocytogenes isolated from clinical cases in Sichuan Province carry multiple virulence and antibiotic genes, with high potential pathogenicity", "token_count": 519, "char_count": 1761, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [ "ST7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:25:07.030371", "source": { "split": "train_shard_00001", "doc_id": 2473 }, "chunk_id": "train_shard_00001_2473_0", "global_id": 9187 }, { "text": "It is necessary to further strengthen the monitoring and control of food and environment by L. monocytogenes within Sichuan Province.\n\nCharacteristics of Clinical Isolates of Listeria monocytogenes in Sichuan, China, in 2022 Based on Whole Genome Sequencing Analysis.", "token_count": 82, "char_count": 281, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8684, "quality_score": 0.9342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:07.400896", "source": { "split": "train_shard_00001", "doc_id": 2473 }, "chunk_id": "train_shard_00001_2473_1", "global_id": 9188 }, { "text": "A series of 3-benzoyl imidazo[1,2-a]pyrimidines, obtained from N-heteroarylformamidines in good yields, was tested in silico and in vitro for binding and inhibition of seven Candida species (Candida albicans (ATCC 10231), Candida dubliniensis (CD36), Candida glabrata (CBS138), Candida guilliermondii (ATCC 6260), Candida kefyr, Candida krusei (ATCC 6358) and Candida tropicalis (MYA-3404)). To predict binding mode and energy, each compound was docked in the active site of the lanosterol 14α-demethylase enzyme (CYP51), essential for fungal growth of Candida species. Antimycotic activity was evaluated as the 50% minimum inhibitory concentration (MIC50) for the test compounds and two reference drugs, ketoconazole and fluconazole. All test compounds had a better binding energy (range: -6.11 to -9.43 kcal/mol) than that found for the reference drugs (range: 48.93 to -6.16 kcal/mol). In general, the test compounds showed greater inhibitory activity of yeast growth than the reference drugs. Compounds 4j and 4f were the most active, indicating an important role in biological activity for the benzene ring with electron-withdrawing substituents. These compounds show the best MIC50 against C. guilliermondii and C. glabrata, respectively", "token_count": 484, "char_count": 1348, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6743, "quality_score": 0.8371, "entities": { "genes": [ "MIC50", "CD36", "CYP51", "CBS138" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:08.050055", "source": { "split": "train_shard_00001", "doc_id": 2474 }, "chunk_id": "train_shard_00001_2474_0", "global_id": 9189 }, { "text": "The current findings suggest that the 3-benzoyl imidazo[1,2-a]pyrimidine derivatives, herein synthesized by an accessible methodology, are potential antifungal drugs.\n\nSynthesis, Molecular Docking, and Antimycotic Evaluation of Some 3-Acyl Imidazo[1,2-a]pyrimidines.", "token_count": 100, "char_count": 273, "word_count": 29, "semantic_coherence": 1, "information_density": 0.9655, "quality_score": 0.9828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:08.427863", "source": { "split": "train_shard_00001", "doc_id": 2474 }, "chunk_id": "train_shard_00001_2474_1", "global_id": 9190 }, { "text": "

Rationale

Pneumococcal pneumonia remains a global health problem. Pneumococcal colonisation increases local and systemic protective immunity, suggesting nasal administration of live attenuated S. pneumoniae strains could help prevent infections.

Objectives

We used a controlled human infection model to investigate whether nasopharyngeal colonisation with attenuated S. pneumoniae strains protected against re-colonisation with wild-type (WT) S. pneumoniae (Spn).

Methods

Healthy adults aged 18-50 years were randomised (1:1:1:1) for nasal administration twice (two weeks interval) with saline, WT Spn6B (BHN418) or one of two genetically modified Spn6B strains - SpnA1 (Δ fhs/piaA ) or SpnA3 (Δ proABC/piaA ) (Stage I). After 6 months, participants were challenged with SpnWT to assess protection against re-colonisation (Stage II).

Measurements and Main Results

125 participants completed both study stages as per intention to treat. No Serious Adverse Events were reported. In Stage I, colonisation rates were similar amongst groups: SpnWT 58.1% (18/31), SpnA1 60% (18/30) and SpnA3 59.4% (19/32). Anti-Spn nasal IgG levels post-colonisation were similar in all groups whilst serum IgG responses were higher in the SpnWT and SpnA1 groups than the SpnA3 group. In colonised individuals, increases in IgG responses were identified against 197 Spn protein antigens and serotype 6 capsular polysaccharide using a pangenome array. Participants given SpnWT or SpnA1 but not SpnA3 in phase 1 were partially protected against re-colonisation with SpnWT (recolonisation rates of 29% versus 30% respectively)", "token_count": 495, "char_count": 1637, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6814, "quality_score": 0.8407, "entities": { "genes": [ "BHN418" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:09.084092", "source": { "split": "train_shard_00001", "doc_id": 2475 }, "chunk_id": "train_shard_00001_2475_0", "global_id": 9191 }, { "text": "

Conclusion

Nasal colonisation with genetically modified live attenuated Spn was safe and induced protection against recolonisation, suggesting nasal adminstration of live attenuated Spn could be an effective stategy for preventing pneumococcal infections.\n\nA Randomised Controlled Trial of Nasal Immunisation with Live Virulence AttenuatedStreptococcus pneumoniaeStrains using Human Infection Challenge", "token_count": 111, "char_count": 418, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:09.468905", "source": { "split": "train_shard_00001", "doc_id": 2475 }, "chunk_id": "train_shard_00001_2475_1", "global_id": 9192 }, { "text": "Gut bacteria from the Enterobacteriaceae family are a major cause of opportunistic infections worldwide. Given their prevalence among healthy human gut microbiomes, interspecies interactions may play a role in modulating infection resistance. Here we uncover global ecological patterns linked to Enterobacteriaceae colonization and abundance by leveraging a large-scale dataset of 12,238 public human gut metagenomes spanning 45 countries. Machine learning analyses identified a robust gut microbiome signature associated with Enterobacteriaceae colonization status, consistent across health states and geographic locations. We classified 172 gut microbial species as co-colonizers and 135 as co-excluders, revealing a genus-wide signal of colonization resistance within Faecalibacterium and strain-specific co-colonization patterns of the underexplored Faecalimonas phoceensis. Co-exclusion is linked to functions involved in short-chain fatty acid production, iron metabolism and quorum sensing, while co-colonization is linked to greater functional diversity and metabolic resemblance to Enterobacteriaceae. Our work underscores the critical role of the intestinal environment in the colonization success of gut-associated opportunistic pathogens with implications for developing non-antibiotic therapeutic strategies.\n\nEcological dynamics of Enterobacteriaceae in the human gut microbiome across global populations.", "token_count": 321, "char_count": 1419, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6971, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:10.038562", "source": { "split": "train_shard_00001", "doc_id": 2476 }, "chunk_id": "train_shard_00001_2476_0", "global_id": 9193 }, { "text": "

Objectives

Isavuconazole is a recent extended-spectrum triazole with activity against yeasts. However, few data are available about the in vitro activity of rare yeast species. We report the MIC distribution of isavuconazole compared with fluconazole for a large collection of common or rare yeasts.

Methods

Isavuconazole and fluconazole MICs were determined using the EUCAST method for 1457 clinical isolates, mainly recovered from invasive infections, belonging to 29 species. They were sent to the National Reference Centre for Invasive Mycoses & Antifungals between January 2015 and October 2017 and species identification was performed using a polyphasic approach (matrix-assisted laser desorption/ionization time of flight analysis and a molecular method).

Results

Isavuconazole had effective in vitro activity against Cryptococcus neoformans (MIC90 < 0.25 mg/L), the five most common Candida spp. (MIC90 ≤ 0.5 mg/L for Candida albicans, Candida glabrata, Candida tropicalis, Candida parapsilosis, and Candida krusei) and also against the majority of rare species, including Candida kefyr and Candida lusitaniae. A few isolates of C. albicans (0.7%, 3/404), C. glabrata (2.7%, 5/184), C. tropicalis (1.0%, 1/96) and C. parapsilosis (0.8%, 1/127) exhibited MIC ≥4 mg/L. All were also resistant to fluconazole according to the EUCAST breakpoints. Some isolates with isavuconazole MIC ≥4 mg/L were also observed among rarer species: Meyerozyma guilliermondii (8.7%, 2/23), Wickerhamomyces anomalus (10.0%, 1/10)", "token_count": 502, "char_count": 1536, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [ "MIC90" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:10.692485", "source": { "split": "train_shard_00001", "doc_id": 2477 }, "chunk_id": "train_shard_00001_2477_0", "global_id": 9194 }, { "text": "Other rare species Saprochaete clavata, Magnusiomyces capitatus, and Rhodotorula mucilaginosa had high MIC50 (≥1 mg/L) and MIC90 (≥4 mg/L) and could be considered as resistant to isavuconazole.

Conclusions

We confirmed the good in vitro activity of isavuconazole against common Candida, Cryptococcus species and the majority of the rare yeast species studied.\n\nIsavuconazole MIC distribution of 29 yeast species responsible for invasive infections (2015-2017).", "token_count": 155, "char_count": 467, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7705, "quality_score": 0.8852, "entities": { "genes": [ "MIC90", "MIC50" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:11.127162", "source": { "split": "train_shard_00001", "doc_id": 2477 }, "chunk_id": "train_shard_00001_2477_1", "global_id": 9195 }, { "text": "Over the last few years, pangenome analyses have been applied to eukaryotes, especially to important crops. A handful of eukaryotic pangenome studies have demonstrated widespread variation in gene presence/absence among plant species and its implications on agronomically important traits. In this chapter, we focus on the methodology of pangenome analysis, which can generally be classified into two different types of approaches, a homolog-based strategy and a “map-to-pan” strategy. In a homolog-based strategy, the genomes of individuals are independently assembled, and the presence/absence of a gene family is determined by clustering protein sequences into homologs. Alternatively, in a “map-to-pan” strategy, pangenome sequences are constructed by combining a well-annotated reference genome with newly identified non-reference representative sequences, from which the presence/absence of a gene is then determined based on read coverage after individual reads are mapped to the pangenome. We highlight the advantages and limitations of the homolog-based strategy and several variant approaches to the “map-to-pan” strategy. We conclude that the “map-to-pan” strategy is highly recommended for eukaryotic pangenome analysis. However, programs and parameters for pangenome analysis need to be carefully selected for eukaryotes with different genome sizes.\n\nComputational Strategies for Eukaryotic Pangenome Analyses", "token_count": 308, "char_count": 1422, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5938, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:11.745023", "source": { "split": "train_shard_00001", "doc_id": 2478 }, "chunk_id": "train_shard_00001_2478_0", "global_id": 9196 }, { "text": "Brenneria species are bacterial plant pathogens mainly affecting woody plants. Association of all members with devastating disorders (e.g., acute oak decline in Iran and United Kingdom) are due to adaptation and pathogenic behavior in response to host and environmental factors. Some species, including B. goodwinii, B. salicis, and B. nigrifluens, also show endophytic residence. Here we show that all species including novel Brenneria sp. are closely related. Gene-based and genome/pangenome-based phylogeny divide the genus into two distinct lineages, Brenneria clades A and B. The two clades were functionally distinct and were consistent with their common and special potential activities as determined via annotation of functional domains. Pangenome analysis demonstrated that the core pathogenicity factors were highly conserved, an hrp gene cluster encoding a type III secretion system was found in all species except B. corticis. An extensive repertoire of candidate virulence factors was identified. Comparative genomics indicated a repertoire of plant cell wall degrading enzymes, metabolites/antibiotics, and numerous prophages providing new insights into Brenneria-host interactions and appropriate targets for further characterization. This work not only documented the genetic differentiation of Brenneria species but also delineates a more functionally driven understanding of Brenneria by comparison with relevant Pectobacteriaceae thereby substantially enriching the extent of information available for functional genomic investigations.\n\nComparative Genomics, Pangenome, and Phylogenomic Analyses of Brenneria spp., and Delineation of Brenneria izadpanahii sp. nov.", "token_count": 486, "char_count": 1810, "word_count": 225, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:12.423553", "source": { "split": "train_shard_00001", "doc_id": 2479 }, "chunk_id": "train_shard_00001_2479_0", "global_id": 9197 }, { "text": "Abstract

Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a targeted cultivation method enriching methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modelling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyses include co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which were absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.

\n\nExpanding the cultivated human archaeome by targeted isolation of novel Methanobrevibacter strains from fecal samples", "token_count": 355, "char_count": 1474, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7588, "quality_score": 0.8794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:13.048763", "source": { "split": "train_shard_00001", "doc_id": 2480 }, "chunk_id": "train_shard_00001_2480_0", "global_id": 9198 }, { "text": "Staphylococcus aureus is not only part of normal flora but also an opportunistic pathogen relevant to microbial genomics, public health, and veterinary medicine. In addition to being a well-known human pathogen, S. aureus causes various infections in economically important livestock animals such as cows, sheep, goats, and pigs. There are very few studies that have examined the pan-genome of S. aureus or the host-specific strains' pan-genomes. We report on livestock-associated S. aureus' (LA-SA) pan-genome and suggest that virulence is not the primary interest in evolution of its genome. LA-SA' complete genomes were retrieved from the NCBI and pan-genome was constructed by high-speed Roary pipeline. The pan-genome size was 4637 clusters, whereas 42.46% of the pan-genome was associated with the core genome. We found 1268 genes were associated with the strain-unique genome, and the remaining 1432 cluster with the accessory genome. COG (clusters of orthologous group of proteins) analysis of the core genes revealed 34% of clusters related to metabolism responsible for amino acid and inorganic ion transport (COG categories E and P), followed by carbohydrate metabolism (category G). Virulent gene analysis revealed the core genes responsible for antiphagocytosis and iron uptake. The fluidity of pan-genome was calculated as 0.082 ± 0.025. Importantly, the positive selection analysis suggested a slower rate of evolution among the LA-SA genomes. We call for comparative microbial and pan-genome research between human and LA-SA that can help further understand the evolution of virulence and thus inform future microbial diagnostics and drug discovery.", "token_count": 483, "char_count": 1721, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:13.707017", "source": { "split": "train_shard_00001", "doc_id": 2481 }, "chunk_id": "train_shard_00001_2481_0", "global_id": 9199 }, { "text": "Analyses of Livestock-Associated Staphylococcus aureus Pan-Genomes Suggest Virulence Is Not Primary Interest in Evolution of Its Genome.", "token_count": 46, "char_count": 143, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:14.067146", "source": { "split": "train_shard_00001", "doc_id": 2481 }, "chunk_id": "train_shard_00001_2481_1", "global_id": 9200 }, { "text": "

Background

The core genome consists of genes shared by the vast majority of a species and is therefore assumed to have been subjected to substantially stronger purifying selection than the more mobile elements of the genome, also known as the accessory genome. Here we examine intragenic base composition differences in core genomes and corresponding accessory genomes in 36 species, represented by the genomes of 731 bacterial strains, to assess the impact of selective forces on base composition in microbes. We also explore, in turn, how these results compare with findings for whole genome intragenic regions.

Results

We found that GC content in coding regions is significantly higher in core genomes than accessory genomes and whole genomes. Likewise, GC content variation within coding regions was significantly lower in core genomes than in accessory genomes and whole genomes. Relative entropy in coding regions, measured as the difference between observed and expected trinucleotide frequencies estimated from mononucleotide frequencies, was significantly higher in the core genomes than in accessory and whole genomes. Relative entropy was positively associated with coding region GC content within the accessory genomes, but not within the corresponding coding regions of core or whole genomes.

Conclusion

The higher intragenic GC content and relative entropy, as well as the lower GC content variation, observed in the core genomes is most likely associated with selective constraints. It is unclear whether the positive association between GC content and relative entropy in the more mobile accessory genomes constitutes signatures of selection or selective neutral processes.\n\nThe nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes.", "token_count": 382, "char_count": 1836, "word_count": 261, "semantic_coherence": 1, "information_density": 0.4751, "quality_score": 0.7375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:14.650302", "source": { "split": "train_shard_00001", "doc_id": 2482 }, "chunk_id": "train_shard_00001_2482_0", "global_id": 9201 }, { "text": "Throughout history, spices have been employed for their pharmaceutical attributes and as a culinary enhancement. The food industry widely employs artificial preservatives to retard the deterioration induced by microbial proliferation, enzymatic processes, and oxidative reactions. Nevertheless, the utilization of these synthetic preservatives in food products has given rise to significant apprehension among consumers, primarily stemming from the potential health risks that they pose. These risks encompass a spectrum of adverse effects, including but not limited to gastrointestinal disorders, the disruption of gut microbiota, allergic reactions, respiratory complications, and concerns regarding their carcinogenic properties. Consequently, consumers are displaying an increasing reluctance to purchase preserved food items that contain such additives. Spices, known for their antimicrobial value, are investigated for their potential as food preservatives. The review assesses 25 spice types for their inherent antimicrobial properties and their applicability in inhibiting various foodborne microorganisms and suggests further future investigations regarding their use as possible natural food preservatives that could offer safer, more sustainable methods for extending shelf life. Future research should delve deeper into the use of natural antimicrobials, such as spices, to not only replace synthetic preservatives but also optimize their application in food safety and shelf-life extension. Moreover, there is a need for continuous innovation in encapsulation technologies for antimicrobial agents. Developing cost-effective and efficient methods, along with scaling up production processes, will be crucial to competing with traditional antimicrobial options in terms of both efficacy and affordability.\n\nSpices as Sustainable Food Preservatives: A Comprehensive Review of Their Antimicrobial Potential.", "token_count": 389, "char_count": 1917, "word_count": 250, "semantic_coherence": 1, "information_density": 0.676, "quality_score": 0.838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:15.271031", "source": { "split": "train_shard_00001", "doc_id": 2483 }, "chunk_id": "train_shard_00001_2483_0", "global_id": 9202 }, { "text": "The comparison of multiple genome sequences sampled from a bacterial population reveals considerable diversity in both the core and the accessory parts of the pangenome. This diversity can be analysed in terms of microevolutionary events that took place since the genomes shared a common ancestor, especially deletion, duplication, and recombination. We review the basic modelling ingredients used implicitly or explicitly when performing such a pangenome analysis. In particular, we describe a basic neutral phylogenetic framework of bacterial pangenome microevolution, which is not incompatible with evaluating the role of natural selection. We survey the different ways in which pangenome data is summarised in order to be included in microevolutionary models, as well as the main methodological approaches that have been proposed to reconstruct pangenome microevolutionary history.\n\nBacterial Microevolution and the Pangenome", "token_count": 193, "char_count": 929, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:15.721554", "source": { "split": "train_shard_00001", "doc_id": 2484 }, "chunk_id": "train_shard_00001_2484_0", "global_id": 9203 }, { "text": "Introduction. Enterococcus faecium has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland has a recalcitrant vancomycin-resistant bloodstream infection rate compared to other developed countries.Hypothesis/Gap statement. Vancomycin resistance rates persist amongst E. faecium isolates from Irish hospitals. The evolutionary genomics governing these trends have not been fully elucidated.Methodology. A set of 28 vancomycin-resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in silico methodologies (comparative genomics, pangenomics, phylogenetics, genotypics and comparative functional analyses) to uncover distinct evolutionary, coevolutionary and clinically relevant population trends.Results. These results suggest that a stable (in terms of genome size, GC% and number of genes), yet genetically diverse population (in terms of gene content) of E. faecium persists in Ireland with acquired resistance arising via plasmid acquisition (vanA) or, to a lesser extent, chromosomal recombination (vanB). Population analysis revealed five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation-mediated resistance and chromosomally harboured arsenals of virulence factors. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates.Conclusions. These results highlight the evolutionary history of Irish E", "token_count": 517, "char_count": 2068, "word_count": 243, "semantic_coherence": 1, "information_density": 0.7202, "quality_score": 0.8601, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:25:16.361124", "source": { "split": "train_shard_00001", "doc_id": 2485 }, "chunk_id": "train_shard_00001_2485_0", "global_id": 9204 }, { "text": "faecium isolates and may provide insight into underlying infection dynamics in a clinical setting. Due to the apparent ease of vancomycin resistance acquisition over time, susceptible E. faecium should be concurrently reduced in Irish hospitals to mitigate potential resistant infections.\n\nComparative genomics and pangenomics of vancomycin-resistant and susceptible Enterococcus faecium from Irish hospitals.", "token_count": 106, "char_count": 427, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8302, "quality_score": 0.9151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:16.746380", "source": { "split": "train_shard_00001", "doc_id": 2485 }, "chunk_id": "train_shard_00001_2485_1", "global_id": 9205 }, { "text": "The emergence of antimicrobial-resistant and mastitis-associated Staphylococcus aureus is of great concern due to the huge economic losses worldwide. Here, we report draft genome sequences of two Staphylococcus aureus strains which were isolated from raw milk samples obtained from mastitis-infected cows in Bangladesh. The strains were isolated and identified using conventional microbiological and molecular polymerase chain reaction (PCR) methods. Antibiotic susceptibility testing was performed. Genomic DNA of the two strains was extracted and the strains were sequenced using the Illumina NextSeq 550 platform. The assembled contigs were analyzed for virulence determinants, antimicrobial resistance genes, extra-chromosomal plasmids, and multi-locus sequence type (MLST). The genomes of the two strains were compared with other publicly available genome sequences of Staphylococcus aureus strains. The raw read sequences were downloaded and all sequence files were analyzed identically to generate core genome phylogenetic trees. The genome of BR-MHR281strain did not harbour any antibiotic resistance determinants, however BR-MHR220 strain harbored mecA and blaZ genes. Analysis of BR-MHR220 strain revealed that it was assigned to sequence type (ST-6), clonal complex (CC) 5 and spa type t304, while BR-MHR281 strain belonged to ST-2454, CC8, and harbored the spa type t7867. The findings of the present study and the genome sequences of BR-MHR220 and BR-MHR281 strains will provide data on the detection and genomic analysis and characterization of mastitis-associated Staphylococcus aureus in Bangladesh", "token_count": 475, "char_count": 1670, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5874, "quality_score": 0.7937, "entities": { "genes": [ "MHR220", "MHR281", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:17.386342", "source": { "split": "train_shard_00001", "doc_id": 2486 }, "chunk_id": "train_shard_00001_2486_0", "global_id": 9206 }, { "text": "In addition, the findings of the present study will serve as reference genomes for future molecular epidemiological studies and will provide significant data which help understand the prevalence, pathogenesis and antimicrobial resistance of mastitis-associated Staphylococcus aureus.\n\nMolecular identification and whole genome sequence analyses of methicillin-resistant and mastitis-associated Staphylococcus aureus sequence types 6 and 2454 isolated from dairy cows.", "token_count": 124, "char_count": 481, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7759, "quality_score": 0.8879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:17.769780", "source": { "split": "train_shard_00001", "doc_id": 2486 }, "chunk_id": "train_shard_00001_2486_1", "global_id": 9207 }, { "text": "OBJECTIVES: To investigate gene expression profiles of the thermotolerant yeast Saccharomyces cerevisiae strain KKU-VN8, a potential high-ethanol producer, in response to various stresses during high-temperature ethanol fermentation using sweet sorghum juice (SSJ) under optimal conditions. RESULTS: The maximal ethanol concentration obtained by S. cerevisiae KKU-VN8 using SSJ at 40 °C was 66.6 g/l, with a productivity of 1.39 g/l/h and a theoretical ethanol yield of 81%. Quantitative RT-PCR assays were performed to investigate the gene expression profiles of S. cerevisiae KKU-VN8. Differential expression of genes encoding heat-shock proteins (HSP82, HSP104, SSA4), genes involved in trehalose metabolism (TPS1, TPS2, NTH1) and genes involved the glycolytic pathway (ADH1, ADH2, CDC19) at various time points during fermentation was observed. The expression levels of HSP82, HSP104, SSA4, ADH1 and CDC19 were significantly higher than those of the controls (10.2-, 4-, 8-, 8.9- and 5.9-fold higher, respectively). In contrast, the expression levels of TPS1, TPS2, NTH1 and ADH2 were approx. 2-fold less than those of the controls. CONCLUSIONS: The highly expressed genes encoding heat-shock proteins, HSP82 and SSA4, potentially play an important role in helping S. cerevisiae KKU-VN8 cope with various stresses that occur during high-temperature fermentation, leading to higher ethanol production efficiency.\n\nGene expression profiles of the thermotolerant yeast Saccharomyces cerevisiae strain KKU-VN8 during high-temperature ethanol fermentation using sweet sorghum juice", "token_count": 484, "char_count": 1580, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5853, "quality_score": 0.7926, "entities": { "genes": [ "SSA4", "VN8", "HSP82", "NTH1", "ADH1", "CDC19", "TPS2", "TPS1", "HSP104", "ADH2" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:18.416867", "source": { "split": "train_shard_00001", "doc_id": 2487 }, "chunk_id": "train_shard_00001_2487_0", "global_id": 9208 }, { "text": "Citrobacter species are opportunistic bacterial pathogens that have been implicated in both nosocomial and community-acquired infections. Among the genus Citrobacter, Citrobacter koseri is often isolated from clinical material, and has been known to cause meningitis and brain abscess in neonates and immunocompromised individuals. The virulence determinants of Citrobacter, however, remain largely unknown. Based on traditional methods, the genus Citrobacter has been divided into 11 species, but this has been problematic. Here, we determined an improved, detailed, and more accurate phylogeny of the genus Citrobacter based on whole genome sequence (WGS) data from 129 Citrobacter genomes, 31 of which were sequenced in this study. A maximum likelihood (ML) phylogeny constructed with core genome single-nucleotide polymorphisms (SNPs) classified all Citrobacter isolates into 11 distinct groups, with all C. koseri strains clustering into a single group. For comprehensive and systematic comparative genomic analyses, we investigated the distribution of virulence factors, resistance genes, and macromolecular secretion systems among the Citrobacter genus. Moreover, combined with group-specific genes analysis, we identified a key gene cluster for iron transport, which is present in the C. koseri group, but absent in other the groups, suggesting that the high-pathogenicity island (HPI) cluster may be important for the pathogenicity of C. koseri. Animal experiments showed that loss of the HPI cluster significantly decreased C. koseri virulence in mice and rat. Further, we provide evidence to explain why Citrobacter freundii is less susceptible than C. koseri to several antibiotics in silico", "token_count": 506, "char_count": 1815, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6583, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:19.073932", "source": { "split": "train_shard_00001", "doc_id": 2488 }, "chunk_id": "train_shard_00001_2488_0", "global_id": 9209 }, { "text": "Overall, our data reveal novel virulence clusters specific to the predominantly pathogenic C. koseri strains, which form the basis for elucidating the virulence mechanisms underlying these important pathogens.\n\nComparative Genomic Analysis of Citrobacter and Key Genes Essential for the Pathogenicity of Citrobacter koseri.", "token_count": 96, "char_count": 344, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8605, "quality_score": 0.9302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:19.451424", "source": { "split": "train_shard_00001", "doc_id": 2488 }, "chunk_id": "train_shard_00001_2488_1", "global_id": 9210 }, { "text": "The enzymatic defence system in the 2 yeasts Kluyveromyces marxianus and Rhodotorula glutinis, differing in their mode of oxygen uptake and energy generation, was characterized and compared with the well-studied facultatively fermentative Crabtree-positive Saccharomyces cerevisiae strain. Twofold higher superoxide dismutase (SOD) and catalase activities were detected in K. marxianus and R. glutinis when cells were cultured on glucose. Further increases of 10%-15% in SOD activity and 30%-50% in catalase were measured in all studied yeasts strains after transfer to media containing ethanol. An evaluation of the ratio of Cu/Zn SOD / Mn SOD was performed as a measure of the oxidative metabolism. A 20% decrease was observed when the respiratory source of energy was ethanol, with the lowest ratio being observed for the oxidative type of K. marxianus yeasts. Electrophoretic analysis revealed that all tested strains possess active Cu/Zn and Mn SODs. A reverse electrophoretic mobility pattern of K. marxianus and R. glutinis SOD enzymes was observed in comparison with the same couple in S. cerevisiae. The investigation of electrophoretic profile of catalase enzymes showed that alongside their different taxonomic status and fermentative capacity, all tested strains possess 2 separate catalases. The role of antioxidant enzymes in preventing oxidant-induced cytotoxicity (treatment with hydrogen peroxide, paraquat, and menadione) was shown.\n\nComparison of enzymatic antioxidant defence systems in different metabolic types of yeasts.", "token_count": 414, "char_count": 1543, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5792, "quality_score": 0.7896, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:20.075307", "source": { "split": "train_shard_00001", "doc_id": 2489 }, "chunk_id": "train_shard_00001_2489_0", "global_id": 9211 }, { "text": "Sulfurospirillum species strains are frequently detected in various pristine and contaminated environments and participate in carbon, sulfur, nitrogen, and halogen elements cycling. Recently we obtained the complete genome sequences of two newly isolated Sulfurospirillum strains, ACSDCE and ACSTCE, capable of dechlorinating tetrachloroethene to cis-1,2-dichloroethene and trichloroethene under low-pH conditions, but a detailed analysis of these two genomes in reference to other Sulfurospirillum genomes for an improved understanding of Sulfurospirillum evolution and ecophysiology has not been accomplished. Here, we performed phylogenetic and pangenome analyses with 12 completed Sulfurospirillum genomes, including those of strain ACSTCE and strain ACSDCE, to unravel the evolutionary and metabolic potentials in the genus Sulfurospirillum. Based on 16S rRNA gene and whole-genome phylogenies, strains ACSTCE, ACSDCE, and JPD-1 could be clustered into a single species, proposed as \"Candidatus Sulfurospirillum acididehalogenans.\" TimeTree analysis suggested that the organohalide-respiring (OHR) Sulfurospirillum might acquire the ability to use chlorinated electron acceptors later than other energy conservation processes. Nevertheless, the ambiguity of the phylogenetic relations among Sulfurospirillum strains complicated the interpretation of acquisition and loss of metabolic traits", "token_count": 455, "char_count": 1531, "word_count": 175, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:20.711947", "source": { "split": "train_shard_00001", "doc_id": 2490 }, "chunk_id": "train_shard_00001_2490_0", "global_id": 9212 }, { "text": "Interestingly, all OHR Sulfurospirillum genomes except the ones of Sulfurospirillum multivorans strains harbor a well-aligned and conserved region comprising the genetic components required for the organohalide respiration chain. Pangenome results further revealed that a total of 34,620 gene products, annotated from the 12 Sulfurospirillum genomes, can be classified into 4,118 homolog families and 2,075 singleton families. Various Sulfurospirillum species strains have conserved metabolisms as well as individual enzymes and biosynthesis capabilities. For instance, only the OHR Sulfurospirillum species strains possess the quinone-dependent pyruvate dehydrogenase (PoxB) gene, and only \"Ca. Sulfurospirillum acididehalogenans\" strains harbor urea transporter and urease genes. The plasmids found in strain ACSTCE and strain ACSDCE feature genes coding for type II toxin-antitoxin systems and transposases and are promising tools for the development of robust gene editing tools for Sulfurospirillum. IMPORTANCE Organohalide-respiring bacteria (OHRB) play critical roles in the detoxification of chlorinated pollutants and bioremediation of subsurface environments (e.g., groundwater and sediment) impacted by anthropogenic chlorinated solvents. The majority of known OHRB cannot perform reductive dechlorination below neutral pH, hampering the applications of OHRB for remediating acidified groundwater due to fermentation and reductive dechlorination", "token_count": 442, "char_count": 1527, "word_count": 185, "semantic_coherence": 1, "information_density": 0.7081, "quality_score": 0.8541, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation", "respiration" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:21.351005", "source": { "split": "train_shard_00001", "doc_id": 2490 }, "chunk_id": "train_shard_00001_2490_1", "global_id": 9213 }, { "text": "Previously we isolated two Sulfurospirillum strains, ACSTCE and ACSDCE, capable of dechlorinating tetrachloroethene under acidic conditions (e.g., pH 5.5), and obtained the complete genomes of both strains. Notably, two plasmid sequences were identified in the genomes of strain ACSTCE and strain ACSDCE that may be conducive to unraveling the genetic modification mechanisms in the genus Sulfurospirillum. Our findings improve the current understanding of Sulfurospirillum species strains regarding their biogeographic evolution, genome dynamics, and functional diversity. This study has applied values for the bioremediation of toxic and persistent organohalide pollutants in low-pH environments.\n\nComparative Genomic Analysis Reveals Preserved Features in Organohalide-Respiring Sulfurospirillum Strains.", "token_count": 252, "char_count": 879, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7745, "quality_score": 0.8873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:21.837302", "source": { "split": "train_shard_00001", "doc_id": 2490 }, "chunk_id": "train_shard_00001_2490_2", "global_id": 9214 }, { "text": "Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungus that damages economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host range. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and selected subgroups (AG1-IA, AG1-IB, AG1-IC, AG2-2IIIB, AG3-PT (isolates Rhs 1AP and the hypovirulent Rhs1A1), AG3-TB, AG4-HG-I (isolates Rs23 and R118-11), AG5, AG6, and AG8), in which six genomes are reported for the first time, wherein we discovered unique and shared secretomes, CAZymes, and effectors across the AGs. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other basidiomycetes, we also elucidated the molecular factors potentially involved in determining the AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms, to assist mycologists in formulating new hypotheses.\n\nPangenome analysis of the soil-borne fungal phytopathogenRhizoctonia solaniand development of a comprehensive web resource: RsolaniDB", "token_count": 433, "char_count": 1619, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [ "AG3", "AG4", "AG6", "AG1", "AG8", "AG2", "AG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:22.464869", "source": { "split": "train_shard_00001", "doc_id": 2491 }, "chunk_id": "train_shard_00001_2491_0", "global_id": 9215 }, { "text": "

Background

The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO 2 levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study is Enterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections.

Results

Distinct from their Earth counterparts, ISS E. bugandensis strains have exhibited resistance mechanisms that categorise them within the ESKAPE pathogen group, a collection of pathogens recognised for their formidable resistance to antimicrobial treatments. During the 2-year Microbial Tracking 1 mission, 13 strains of multidrug-resistant E. bugandensis were isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derived E. bugandensis in comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution of E. bugandensis across the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonisation of E. bugandensis in space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongside E. bugandensis in the ISS across multiple missions and spatial locations", "token_count": 467, "char_count": 2116, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6537, "quality_score": 0.8269, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:23.108052", "source": { "split": "train_shard_00001", "doc_id": 2492 }, "chunk_id": "train_shard_00001_2492_0", "global_id": 9216 }, { "text": "This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS.

Conclusions

Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession of E. bugandensis within the ISS environment. The implications of these findings are twofold. Firstly, they shed light on microbial behaviour, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats. Video Abstract.\n\nGenomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station.", "token_count": 193, "char_count": 913, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7739, "quality_score": 0.887, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:23.556829", "source": { "split": "train_shard_00001", "doc_id": 2492 }, "chunk_id": "train_shard_00001_2492_1", "global_id": 9217 }, { "text": "Abstract

Background: Dickeya solani is an important plant pathogenic bacterium causing severe losses in European potato production. This species draws a lot of attention due to its remarkable virulence, great devastating potential and easier spread in contrast to other Dickeya spp. In view of a high need for extensive studies on economically important soft rot Pectobacteriaceae , we performed a comparative genomics analysis on D. solani strains to search for genetic foundations that would explain the differences in the observed virulence levels within the D. solani population.

Results:

High quality assemblies of 8 de novo sequenced D. solani genomes have been obtained. Whole-sequence comparison, ANIb, ANIm, Tetra and pangenome-oriented analyses performed on these genomes and the sequences of 14 additional strains revealed an exceptionally high level of homogeneity among the studied genetic material of D. solani strains. With the use of 22 genomes, the pangenome of D. solani , comprising 84.7% core, 7.2% accessory and 8.1% unique genes, has been almost completely determined, suggesting the presence of a nearly closed pangenome structure. Attribution of the genes included in the D. solani pangenome fractions to functional COG categories showed that higher percentages of accessory and unique pangenome parts in contrast to the core section are encountered in phage/mobile elements- and transcription- associated groups with the genome of RNS 05.1.2A strain having the most significant impact. Also, the first D. solani large-scale genome-wide phylogeny computed on concatenated core gene alignments is herein reported.

Conclusions:

The almost closed status of D. solani pangenome achieved in this work points to the fact that the unique gene pool of this species should no longer expand. Such a feature is characteristic of taxa whose representatives either occupy isolated ecological niches or lack efficient mechanisms for gene exchange and recombination, which seems rational concerning a strictly pathogenic species with clonal population structure. Finally, no obvious correlations between the geographical origin of D", "token_count": 507, "char_count": 2178, "word_count": 315, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:24.217420", "source": { "split": "train_shard_00001", "doc_id": 2493 }, "chunk_id": "train_shard_00001_2493_0", "global_id": 9218 }, { "text": "solani strains and their phylogeny were found, which might reflect the specificity of the international seed potato market.

\n\nComparative genomics and pangenome-oriented studies reveal high homogeneity of the agronomically relevant enterobacterial plant pathogen Dickeya solani", "token_count": 67, "char_count": 280, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:24.594316", "source": { "split": "train_shard_00001", "doc_id": 2493 }, "chunk_id": "train_shard_00001_2493_1", "global_id": 9219 }, { "text": "A mild alkaline pretreatment (deacetylation) prior to the dilute acid pretreatment was evaluated as a strategy to improve the sugars recovery and ethanol production from both hemicellulose and cellulose fractions of rice straw. This pretreatment was carried out using different conditions of temperature (50–70°C) and NaOH loading (20–80mg NaOH/g biomass), which were combined according to a 22 central composite design. In this step the removal of acetyl groups as well as the impact of this step on biomass composition were evaluated. In order to assess the impact of the deacetylation on hemicellulosic hydrolysate composition, the influence of the reaction time (30–90min) and sulfuric acid concentration (0.5–1.5% w/v) was also studied, using the alkaline-pretreated solid (deacetylated) and rice straw in natura. The best sequential pretreatment conditions were scaled-up to 50-L reactor, being obtained a cellulose-rich pretreated solid (cellulignin) and a hemicellulosic hydrolysate, which was concentrated to 70g/L xylose to be used as fermentation medium. A significant improvement on ethanol production from xylose by Scheffersomyces stipitis NRRL Y-7124 was observed when the biomass was submitted to deacetylation (about 4-fold). The enzymatic conversion of cellulose was also improved (from 73 to 89%) when the deacetylated cellulignin was used, resulting in an enhancement of the ethanol production (from 12.7 to 20.4g/L) during the simultaneous saccharification and fermentation with Kluyveromyces marxianus NRRL Y-6860. In brief, biomass deacetylation prior to dilute acid pretreatment was an efficient strategy for rice straw processing, substantially improving the ethanol production from both pentose and hexose sugars.", "token_count": 485, "char_count": 1739, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5732, "quality_score": 0.7866, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:25.296208", "source": { "split": "train_shard_00001", "doc_id": 2494 }, "chunk_id": "train_shard_00001_2494_0", "global_id": 9220 }, { "text": "Alkaline deacetylation as a strategy to improve sugars recovery and ethanol production from rice straw hemicellulose and cellulose", "token_count": 32, "char_count": 130, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:25.678783", "source": { "split": "train_shard_00001", "doc_id": 2494 }, "chunk_id": "train_shard_00001_2494_1", "global_id": 9221 }, { "text": "Mouse gut microbiome research is pivotal for understanding the human gut microbiome, providing insights into disease modeling, host-microbe interactions, and the dietary influence on the gut microbiome. To enhance the translational value of mouse gut microbiome studies, we need detailed and high-quality catalogs of mouse gut microbial genomes. We introduce the Mouse Reference Gut Microbiome (MRGM), a comprehensive catalog with 42,245 non-redundant mouse gut bacterial genomes across 1,524 species. MRGM marks a 40% increase in the known taxonomic diversity of mouse gut microbes, capturing previously underrepresented lineages through refined genome quality assessment techniques. MRGM not only broadens the taxonomic landscape but also enriches the functional landscape of the mouse gut microbiome. Using deep learning, we have elevated the Gene Ontology annotation rate for mouse gut microbial proteins from 3.2% with orthology to 60%, marking an over 18-fold increase. MRGM supports both DNA- and marker-based taxonomic profiling by providing custom databases, surpassing previous catalogs in performance. Finally, taxonomic and functional comparisons between human and mouse gut microbiota reveal diet-driven divergences in their taxonomic composition and functional enrichment. Overall, our study highlights the value of high-quality microbial genome catalogs in advancing our understanding of the co-evolution between gut microbes and their host.\n\nMRGM: an enhanced catalog of mouse gut microbial genomes substantially broadening taxonomic and functional landscapes.", "token_count": 367, "char_count": 1576, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:26.260961", "source": { "split": "train_shard_00001", "doc_id": 2495 }, "chunk_id": "train_shard_00001_2495_0", "global_id": 9222 }, { "text": "

Objectives

To answer to the following questions: is there any relationship between oral hygiene and the growth of yeast in patients without mucosal inflammation; and is there a need for mycological examination patients without mucosal inflammation?

Background

Patients with candidiasis may report varied symptoms, but such infections are most often asymptomatic. In addition to its high incidence in denture users (60%-100%), there is a concern that Candida species from the oral cavity may colonize the upper gastrointestinal tract and lead to septicemia, which has a 40%-79% mortality rate and can require a prolonged hospital stay. It is thus important for all physicians to be aware of the risk factors, diagnosis, and treatment of oral candidiasis in older patients.

Methods

A retrospective study was carried out on a group of patients who had undergone mycological examination and assessment of the intensity of yeast growth, and oral hygiene.

Results

Ninety-one denture wearers who lacked signs of clinical inflammation were included in the study. The growth of Candida albicans was as follows: 14 patients had up to 20 colonies; 19 patients had over 20 colonies. Ten percent of patients with good oral hygiene proved to have more than 20 yeast colonies. 5% of patients with bad oral hygiene had more than 20 colonies.

Conclusions

There was no relationship found between hygiene and the growth rate of fungal microorganisms. In patients without clinical symptoms of stomatitis, mycological examination should be considered.\n\nRelationship between oral hygiene and fungal growth in patients: users of an acrylic denture without signs of inflammatory process.", "token_count": 452, "char_count": 1713, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5628, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:26.892303", "source": { "split": "train_shard_00001", "doc_id": 2496 }, "chunk_id": "train_shard_00001_2496_0", "global_id": 9223 }, { "text": "Emerging evidence suggests the Pseudomonas aeruginosa accessory genome is enriched with uncharacterized virulence genes. Identification and characterization of such genes may reveal novel pathogenic mechanisms used by particularly virulent isolates. Here, we utilized a mouse bacteremia model to quantify the virulence of 100 individual P. aeruginosa bloodstream isolates and performed whole-genome sequencing to identify accessory genomic elements correlated with increased bacterial virulence. From this work, we identified a specific contact-dependent growth inhibition (CDI) system enriched among highly virulent P. aeruginosa isolates. CDI systems contain a large exoprotein (CdiA) with a C-terminal toxin (CT) domain that can vary between different isolates within a species. Prior work has revealed that delivery of a CdiA-CT domain upon direct cell-to-cell contact can inhibit replication of a susceptible target bacterium. Aside from mediating interbacterial competition, we observed our virulence-associated CdiA-CT domain to promote toxicity against mammalian cells in culture and lethality during mouse bacteremia. Structural and functional studies revealed this CdiA-CT domain to have in vitro tRNase activity, and mutations that abrogated this tRNAse activity in vitro also attenuated virulence. Furthermore, CdiA contributed to virulence in mice even in the absence of contact-dependent signaling. Overall, our findings indicate that this P. aeruginosa CDI system functions as both an interbacterial inhibition system and a bacterial virulence factor against a mammalian host. These findings provide an impetus for continued studies into the complex role of CDI systems in P. aeruginosa pathogenesis.\n\nA comparative genomics approach identifies contact-dependent growth inhibition as a virulence determinant.", "token_count": 459, "char_count": 1858, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:27.533243", "source": { "split": "train_shard_00001", "doc_id": 2497 }, "chunk_id": "train_shard_00001_2497_0", "global_id": 9224 }, { "text": "

ABSTRACT

Livestock have been proposed as a reservoir for drug-resistant Escherichia coli that infect humans. We isolated and sequenced 431 E. coli (including 155 ESBL-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1517 E. coli associated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, indicating that E. coli causing serious human infection do not directly originate from livestock. By contrast, we observed highly related isolates from the same animal species on different farms. Analysis of accessory (variable) genomes identified a virulence cassette associated previously with cystitis and neonatal meningitis that was only present in isolates from humans. Screening all 1948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions of humans and livestock isolates. We identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that in this setting, there was limited evidence to support the suggestion that antimicrobial resistant pathogens that cause serious infection in humans originate from livestock.

Importance

The increasing prevalence of E. coli bloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources of E. coli associated with serious human disease. E. coli from 1517 patients with bloodstream infection were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was little overlap in the mobile elements carrying these genes. In addition, a virulence cassette found in humans isolates was not identified in any livestock-associated isolate. Our findings do not support the idea that E", "token_count": 524, "char_count": 2271, "word_count": 322, "semantic_coherence": 1, "information_density": 0.5093, "quality_score": 0.7547, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:25:28.187912", "source": { "split": "train_shard_00001", "doc_id": 2498 }, "chunk_id": "train_shard_00001_2498_0", "global_id": 9225 }, { "text": "coli causing invasive disease or their resistance genes are commonly acquired from livestock.\n\nOne Health genomic surveillance ofEscherichia colidemonstrates distinct lineages and mobile genetic elements in isolates from humans versus livestock", "token_count": 59, "char_count": 251, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9677, "quality_score": 0.9839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:28.549580", "source": { "split": "train_shard_00001", "doc_id": 2498 }, "chunk_id": "train_shard_00001_2498_1", "global_id": 9226 }, { "text": "

Background

Lignin is an intricate phenolic polymer found in plant cell walls that has tremendous potential for being converted into value-added products with the possibility of significantly increasing the economics of bio-refineries. Although lignin in nature is bio-degradable, its biocatalytic conversion is challenging due to its stable complex structure and recalcitrance. In this context, an understanding of strain's genomics, enzymes, and degradation pathways can provide a solution for breaking down lignin to unlock the full potential of lignin as a dominant valuable bioresource. A gammaproteobacterial strain AORB19 has been isolated previously from decomposed wood based on its high laccase production. This work then focused on the detailed genomic and functional characterization of this strain based on whole genome sequencing, the identification of lignin degradation products, and the strain's laccase production capabilities on various agro-industrial residues.

Results

Lignin degrading bacterial strain AORB19 was identified as Serratia quinivorans based on whole genome sequencing and core genome phylogeny. The strain comprised a total of 123 annotated CAZyme genes, including ten cellulases, four hemicellulases, five predicted carbohydrate esterase genes, and eight lignin-degrading enzyme genes. Strain AORB19 was also found to possess genes associated with metabolic pathways such as the β-ketoadipate, gentisate, anthranilate, homogentisic, and phenylacetate CoA pathways. LC-UV analysis demonstrated the presence of p-hydroxybenzaldehyde and vanillin in the culture media which constitutes potent biosignatures indicating the strain's capability to degrade lignin", "token_count": 433, "char_count": 1706, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6741, "quality_score": 0.8371, "entities": { "genes": [ "AORB19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:29.178607", "source": { "split": "train_shard_00001", "doc_id": 2499 }, "chunk_id": "train_shard_00001_2499_0", "global_id": 9227 }, { "text": "Finally, the study evaluated the laccase production of Serratia AORB19 grown with various industrial raw materials, with the highest activity detected on flax seed meal (257.71 U/L), followed by pea hull (230.11 U/L), canola meal (209.56 U/L), okara (187.67 U/L), and barley malt sprouts (169.27 U/L).

Conclusions

The whole genome analysis of Serratia quinivorans AORB19, elucidated a repertoire of genes, pathways and enzymes vital for lignin degradation that widens the understanding of ligninolytic metabolism among bacterial lignin degraders. The LC-UV analysis of the lignin degradation products coupled with the ability of S. quinivorans AORB19 to produce laccase on diverse agro-industrial residues underscores its versatility and its potential to contribute to the economic viability of bio-refineries.\n\nUncovering the lignin-degrading potential of Serratia quinivorans AORB19: insights from genomic analyses and alkaline lignin degradation.", "token_count": 307, "char_count": 956, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6899, "quality_score": 0.845, "entities": { "genes": [ "AORB19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:29.743658", "source": { "split": "train_shard_00001", "doc_id": 2499 }, "chunk_id": "train_shard_00001_2499_1", "global_id": 9228 }, { "text": "With the advance of sequencing technologies, the landscape of genomic analysis has been transformed, by moving from single strain to species (or even higher taxa)-wide genomic resolution, toward the direction of capturing the “totality” of life diversity; from this scientific advance and curiosity, the concept of “pangenome” was born. Herein we will review, from practical and technical implementation, existing projects of pangenome analysis, with the aim of providing the reader with a snapshot of useful tools should they need to embark on such a pangenomic journey.\n\nA Review of Pangenome Tools and Recent Studies", "token_count": 129, "char_count": 619, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7128, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:30.164014", "source": { "split": "train_shard_00001", "doc_id": 2500 }, "chunk_id": "train_shard_00001_2500_0", "global_id": 9229 }, { "text": "Escherichia coli is a ubiquitous component of the human gut microbiome, but is also a common pathogen, causing around 40, 000 bloodstream infections (BSI) in the United Kingdom (UK) annually. The number of E. coli BSI has increased over the last decade in the UK, and emerging antimicrobial resistance (AMR) profiles threaten treatment options. Here, we combined clinical, epidemiological, and whole genome sequencing data with high content imaging to characterise over 300 E. coli isolates associated with BSI in a large teaching hospital in the East of England. Overall, only a limited number of sequence types (ST) were responsible for the majority of organisms causing invasive disease. The most abundant (20 % of all isolates) was ST131, of which around 90 % comprised the pandemic O25b:H4 group. ST131-O25b:H4 isolates were frequently multi-drug resistant (MDR), with a high prevalence of extended spectrum β-lactamases (ESBL) and fluoroquinolone resistance. There was no association between AMR phenotypes and the source of E. coli bacteraemia or whether the infection was healthcare-associated. Several clusters of ST131 were genetically similar, potentially suggesting a shared transmission network. However, there was no clear epidemiological associations between these cases, and they included organisms from both healthcare-associated and non-healthcare-associated origins. The majority of ST131 isolates exhibited strong binding with an anti-O25b antibody, raising the possibility of developing rapid diagnostics targeting this pathogen. In summary, our data suggest that a restricted set of MDR E. coli populations can be maintained and spread across both community and healthcare settings in this location, contributing disproportionately to invasive disease and AMR.\n\nThe clinical, genomic, and microbiological profile of invasive multi-drug resistant Escherichia coli in a major teaching hospital in the United Kingdom.", "token_count": 512, "char_count": 1978, "word_count": 277, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:31.171142", "source": { "split": "train_shard_00001", "doc_id": 2501 }, "chunk_id": "train_shard_00001_2501_0", "global_id": 9230 }, { "text": "Flavobacterium columnare is the causative agent of columnaris disease in freshwater fish. Columnaris disease can cause heavy economic losses in aquaculture. In this study, whole-genome sequencing was used to characterize this pathogen. F. columnare isolate AH-01 had a circular chromosome and plasmid that encoded a total of 3,022 genes. Isolate GX-01 only had a circular chromosome and encoded 2,965 genes. Genomic islands, prophage regions, and CRISPR/Cas systems were identified in both genomes. Both genomes presented evidence of gene variation and horizontal transfer, both of which are the essential components of genetic diversity, genome plasticity, and functional evolution. Single-gene phylogeny and comparative genome analyses were performed to investigate the variation and evolution of this pathogen. Genetic analysis of 16S rRNA and housekeeping gene sequences significantly clustered 55 F. columnare isolates into four clades. The intragroup identity of the 16S rRNA gene exceeded 99%, while the intergroup identity was below the species delineation threshold. We discovered significant translocation, inversion, and rearrangement events that influenced local synteny within each group. Notably, the observed alignments varied considerably among all the studied groups. The core genomes of all strains with available sequences comprised 747 genes, corresponding to approximately 25% of the genome. Core genome multilocus sequence typing, genome-wide orthology and phylogenetic analyses, and average nucleotide identity suggested that the currently existing F. columnare was an assemblage of several distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. The present investigation provided genomic evidence of gene variation and horizontal transfer, which were the basis of genetic diversity, genome plasticity, and functional evolution. The findings supported a proposed new taxonomic perspective on F. columnare.\n\nGenomic evidence of genetic diversity and functional evolution in Flavobacterium columnare.", "token_count": 500, "char_count": 2119, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:31.829694", "source": { "split": "train_shard_00001", "doc_id": 2502 }, "chunk_id": "train_shard_00001_2502_0", "global_id": 9231 }, { "text": "Archaea are integral components of the human microbiome but persist as understudied entities within the gastrointestinal tract (GIT), primarily due to the lack of cultured representatives for comprehensive mechanistic investigations. With only four Methanobrevibacter smithii isolates from humans available according to the Global Catalogue of Microorganisms (GCM), the existing cultures fail to adequately represent the observed diversity, as underscored by recent findings. This study introduces a targeted cultivation method for enriching methanogenic archaea from human fecal samples. Applied to 16 stool samples from healthy and diseased donors, the method aimed to genomically characterize the archaeal cultures and establish correlations with gastrointestinal disorders. The procedure combines methane breath testing, in silico metabolic modelling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyses include co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which were absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from diverse participant cohorts revealed features potentially associated with gastrointestinal diseases. This work substantially broadens the scope of available archaeal representatives for functional and mechanistic studies in the human GIT. The established protocol facilitates the cultivation of methanogenic archaea from nearly every human fecal sample, offering insights into the adaptability of Candidatus Methanobrevibacter intestini genomes in critical microbiome situations.\n\nExpanding the cultivated human archaeome by targeted isolation of novelMethanobrevibacterstrains from fecal samples", "token_count": 457, "char_count": 2084, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:32.468098", "source": { "split": "train_shard_00001", "doc_id": 2503 }, "chunk_id": "train_shard_00001_2503_0", "global_id": 9232 }, { "text": "The intestine is the largest organ in terms of surface area in the human body. It is responsible not only for absorbing nutrients but also for protection against the external world. The gut microbiota is essential in maintaining a properly functioning intestinal barrier, primarily through producing its metabolites: short-chain fatty acids, bile acids, and tryptophan derivatives. Ethanol overconsumption poses a significant threat to intestinal health. Not only does it damage the intestinal epithelium, but, maybe foremostly, it changes the gut microbiome. Those ethanol-driven changes shift its metabolome, depriving the host of the protective effect the physiological gut microbiota has. This literature review discusses the impact of ethanol consumption on the gut, the gut microbiota, and its metabolome, providing a comprehensive overview of the mechanisms through which ethanol disrupts intestinal homeostasis and discussing potential avenues for new therapeutic intervention.\n\nEthanol-induced changes to the gut microbiome compromise the intestinal homeostasis: a review.", "token_count": 250, "char_count": 1081, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:32.956959", "source": { "split": "train_shard_00001", "doc_id": 2504 }, "chunk_id": "train_shard_00001_2504_0", "global_id": 9233 }, { "text": "Sphingopyxis inhabit diverse environmental niches, including marine, freshwater, oceans, soil and anthropogenic sites. The genus includes 20 phylogenetically distinct, valid species, but only a few with a sequenced genome. In this work, we analyzed the nearly complete genome of the newly described species, Sphingopyxislindanitolerans, and compared it to the other available Sphingopyxis genomes. The genome included 4.3 Mbp in total and consists of a circular chromosome, and two putative plasmids. Among the identified set of lin genes responsible for γ-hexachlorocyclohexane pesticide degradation, we discovered a gene coding for a new isoform of the LinA protein. The significant potential of this species in the remediation of contaminated soil is also correlated with the fact that its genome encodes a higher number of enzymes potentially involved in aromatic compound degradation than for most other Sphingopyxis strains. Additional analysis of 44 Sphingopyxis representatives provides insights into the pangenome of Sphingopyxis and revealed a core of 734 protein clusters and between four and 1667 unique proteins per genome.\n\nGenomic Analysis of γ-Hexachlorocyclohexane-Degrading Sphingopyxis lindanitolerans WS5A3p Strain in the Context of the Pangenome of Sphingopyxis.", "token_count": 406, "char_count": 1367, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:33.580658", "source": { "split": "train_shard_00001", "doc_id": 2505 }, "chunk_id": "train_shard_00001_2505_0", "global_id": 9234 }, { "text": "

Introduction

Whole genome sequencing (WGS) is increasingly used for characterizing foodborne pathogens and it has become a standard typing technique for surveillance and research purposes. WGS data can help assessing microbial risks and defining risk mitigating strategies for foodborne pathogens, including Salmonella enterica.

Methods

To test the hypothesis that (combinations of) different genes can predict the probability of infection [P(inf)] given exposure to a certain pathogen strain, we determined P(inf) based on invasion potential of 87 S. enterica strains belonging to 15 serovars isolated from animals, foodstuffs and human patients, in an in vitro gastrointestinal tract (GIT) model system. These genomes were sequenced with WGS and screened for genes potentially involved in virulence. A random forest (RF) model was applied to assess whether P(inf) of a strain could be predicted based on the presence/absence of those genes. Moreover, the association between P(inf) and biofilm formation in different experimental conditions was assessed.

Results and discussion

P(inf) values ranged from 6.7E-05 to 5.2E-01, showing variability both among and within serovars. P(inf) values also varied between isolation sources, but no unambiguous pattern was observed in the tested serovars. Interestingly, serovars causing the highest number of human infections did not show better ability to invade cells in the GIT model system, with strains belonging to other serovars displaying even higher infectivity. The RF model did not identify any virulence factor as significant P(inf) predictors. Significant associations of P(inf) with biofilm formation were found in all the different conditions for a limited number of serovars, indicating that the two phenotypes are governed by different mechanisms and that the ability to form biofilm does not correlate with the ability to invade epithelial cells", "token_count": 470, "char_count": 1946, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6618, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:34.225871", "source": { "split": "train_shard_00001", "doc_id": 2506 }, "chunk_id": "train_shard_00001_2506_0", "global_id": 9235 }, { "text": "Other omics techniques therefore seem more promising as alternatives to identify genes associated with P(inf), and different hypotheses, such as gene expression rather than presence/absence, could be tested to explain phenotypic virulence [P(inf)].\n\nAssessing phenotypic virulence of Salmonella enterica across serovars and sources.", "token_count": 84, "char_count": 339, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8837, "quality_score": 0.9419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:34.596463", "source": { "split": "train_shard_00001", "doc_id": 2506 }, "chunk_id": "train_shard_00001_2506_1", "global_id": 9236 }, { "text": "A gene in a given taxonomic group is either present in every individual (core), or absent in at least a single individual (dispensable). Previous pangenomic studies have identified certain functional differences between core and dispensable genes. However, identifying if a gene belongs to the core or dispensable portion of the genome requires the construction of a pangenome, which involves sequencing the genomes of many individuals. Here we aim to leverage the previously characterized core and dispensable gene content for two grass species ( Brachypodium distachyon and Oryza sativa ) to construct a machine learning model capable of accurately classifying genes as core or dispensable using only a single annotated reference genome. Such a model may mitigate the need for pangenome construction, an expensive hurdle especially in orphan crops which often lack the adequate genomic resources.\n\nMachine learning approaches to identify core and dispensable genes in pangenomes", "token_count": 204, "char_count": 980, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6849, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:35.062735", "source": { "split": "train_shard_00001", "doc_id": 2507 }, "chunk_id": "train_shard_00001_2507_0", "global_id": 9237 }, { "text": "Scientists agree that the increased human impact on the environment since the 19th century has positioned our planet in a period of rapid and intense change, particularly to our natural ecosystems [...].\n\nEditorial: Functional Genomics in Plant Breeding 2.0.", "token_count": 59, "char_count": 258, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8974, "quality_score": 0.9487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:35.424826", "source": { "split": "train_shard_00001", "doc_id": 2508 }, "chunk_id": "train_shard_00001_2508_0", "global_id": 9238 }, { "text": "Background and Objective: Enterococci are typically found in a healthy human gastrointestinal tract but can cause severe infections in immunocompromised patients. Such infections are treated with antibiotics. This study addresses the rising concern of antimicrobial resistance (AMR) in Enterococci, focusing on the prevalence of vancomycin-resistant enterococcus (VRE) strains. Materials and Methods: The pilot study involved 140 Enterococci isolates collected between 2021 and 2022 from two multidisciplinary hospitals (with and without local therapeutic drug monitoring protocol of vancomycin) in Latvia. Microbiological assays and whole genome sequencing were used. AMR gene prevalence with resistance profiles were determined and the genetic relationship and outbreak evaluation were made by applying core genome multi-locus sequence typing (cgMLST). Results: The acquired genes and mutations were responsible for resistance against 10 antimicrobial classes, including 25.0% of isolates expressing resistance to vancomycin, predominantly of the vanB type. Genetic diversity among E. faecalis and E. faecium isolates was observed and seven potential outbreak clusters were identified, three of them containing sequence types ST6, ST78 and ST80. The prevalence of vancomycin resistance was highest in the hospital without a therapeutic drug-monitoring protocol and in E. faecium. Notably, a case of linezolid resistance due to a mutation was documented. Conclusions: The study illustrates the concerning prevalence of multidrug-resistant Enterococci in Latvian hospitals, showcasing the rather widespread occurrence of vancomycin-resistant strains. This highlights the urgency of implementing efficient infection control mechanisms and the need for continuous VRE surveillance in Latvia to define the scope and pattern of the problem, influencing clinical decision making and planning further preventative measures.", "token_count": 483, "char_count": 1973, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [ "ST6", "ST80", "ST78" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:36.096501", "source": { "split": "train_shard_00001", "doc_id": 2509 }, "chunk_id": "train_shard_00001_2509_0", "global_id": 9239 }, { "text": "Evaluation of Antimicrobial Resistancein Clinical Isolates of Enterococcus spp. Obtained from Hospital Patients in Latvia.", "token_count": 41, "char_count": 129, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:36.480340", "source": { "split": "train_shard_00001", "doc_id": 2509 }, "chunk_id": "train_shard_00001_2509_1", "global_id": 9240 }, { "text": "Cherries are one of the economically important fruit crops in the Rosaceae family, Prunus genus. As the first fruits of the spring season in the northern hemisphere, their attractive appearance, intensely desirable tastes, high nutrients content, and consumer-friendly size captivate consumers worldwide. In the past 30 years, although cherry geneticists and breeders have greatly progressed in understanding the genetic and molecular basis underlying fruit quality, adaptation to climate change, and biotic and abiotic stress resistance, the utilization of cherry genomic data in genetics and molecular breeding has remained limited to date. Here, we thoroughly investigated recent discoveries in constructing genetic linkage maps, identifying quantitative trait loci (QTLs), genome-wide association studies (GWAS), and validating functional genes of edible cherries based on available de novo genomes and genome resequencing data of edible cherries. We further comprehensively demonstrated the genetic architecture of the main agronomic traits of edible cherries by methodically integrating QTLs, GWAS loci, and functional genes into the identical reference genome with improved annotations. These collective endeavors will offer new perspectives on the availability of sequence data and the construction of an interspecific pangenome of edible cherries, ultimately guiding cherry breeding strategies and genetic improvement programs, and facilitating the exploration of similar traits and breeding innovations across Prunus species.\n\nGenomes and integrative genomic insights into the genetic architecture of main agronomic traits in the edible cherries.", "token_count": 361, "char_count": 1677, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6489, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:37.097446", "source": { "split": "train_shard_00001", "doc_id": 2510 }, "chunk_id": "train_shard_00001_2510_0", "global_id": 9241 }, { "text": "

Background

Akkermansia muciniphila is one of the most dominant bacteria that resides on the mucus layer of intestinal tract and plays key role in human health, however, little is known about its genomic content.

Results

Herein, we for the first time characterized the genomic architecture of A. muciniphila based on whole-genome sequencing, assembling, and annotating of 39 isolates derived from human and mouse feces. We revealed a flexible open pangenome of A. muciniphila currently consisting of 5644 unique proteins. Phylogenetic analysis identified three species-level A. muciniphila phylogroups exhibiting distinct metabolic and functional features. Based on the comprehensive genome catalogue, we reconstructed 106 newly A. muciniphila metagenome assembled genomes (MAGs) from available metagenomic datasets of human, mouse and pig gut microbiomes, revealing a transcontinental distribution of A. muciniphila phylogroups across mammalian gut microbiotas. Accurate quantitative analysis of A. muciniphila phylogroups in human subjects further demonstrated its strong correlation with body mass index and anti-diabetic drug usage. Furthermore, we found that, during their mammalian gut evolution history, A. muciniphila acquired extra genes, especially antibiotic resistance genes, from symbiotic microbes via recent lateral gene transfer.

Conclusions

The genome repertoire of A. muciniphila provided insights into population structure, evolutionary and functional specificity of this significant bacterium.\n\nGenome sequencing of 39 Akkermansia muciniphila isolates reveals its population structure, genomic and functional diverisity, and global distribution in mammalian gut microbiotas.", "token_count": 434, "char_count": 1715, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:37.768372", "source": { "split": "train_shard_00001", "doc_id": 2511 }, "chunk_id": "train_shard_00001_2511_0", "global_id": 9242 }, { "text": "* Author for correspondence and reprint requests Z. Naturforsch. 65c, 141-147 (2010); received June 17/July 21, 2009 The superoxide radical (O2-), hydrogen peroxide (H2O2) and nitric oxide (NO) are pleiotropic inflammatory mediators which play an important role in inflammatory joint diseases. They are overproduced during rheumatoid arthritis and its experimental model - adjuvant-induced arthritis in rodents--and may be detected both systemically and intra-articularly. Their secretion is up-regulated by proinflammatory cytokines such as IFN-gamma, IL-12, IL-6 and TNF-alpha, and they are responsible for the destruction of joint tissue. In this work, the effect of superoxide dismutase (SOD) from a thermotolerant yeast strain, Kluyveromyces marxianus, on the production of proinflammatory cytokines, reactive oxygen and nitrogen species was studied. Mice received three intraperitoneal injections of yeast SOD at a dose of 10 mg/ kg body weight (30,000 U/kg) on consecutive days starting on the day after arthritic induction. On days 3, 8 and 14 post induction peritoneal macrophages were isolated and both spontaneous and stimulated production of reactive oxygen and nitrogen metabolites were measured. Early in arthritic development yeast SOD treatment did not influence the O2- production, but on day 14 both spontaneous and PMA-induced secretion were dramatically reduced. Spontaneous H2O2 release was inhibited on day 14, while PMA-stimulated production was decreased from the beginning of the arthritic development. Yeast SOD treatment effectively suppressed the spontaneous and recombinant mouse IFN-gamma + LPS induced release of NO as well. Serum levels of proinflammatory cytokines, IL-12, IFN-gamma, IL-6 and TNF-alpha, were also significantly reduced", "token_count": 509, "char_count": 1768, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6586, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:38.427240", "source": { "split": "train_shard_00001", "doc_id": 2512 }, "chunk_id": "train_shard_00001_2512_0", "global_id": 9243 }, { "text": "The obtained results show some of the mechanisms of action of SOD in reducing the severity of arthritic inflammation. Besides direct inhibition of joint tissue destruction exogenous SOD substantially limits the existing positive feedback between secretion of reactive oxygen species and inflammatory cytokine production.\n\nEffect of yeast superoxide dismutase treatment on some mediators of inflammation during adjuvant-induced arthritis in mice.", "token_count": 102, "char_count": 445, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7833, "quality_score": 0.8917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:38.803273", "source": { "split": "train_shard_00001", "doc_id": 2512 }, "chunk_id": "train_shard_00001_2512_1", "global_id": 9244 }, { "text": "The in vitro interaction of amphotericin B in combination with colistin was evaluated against a total of 86 strains comprising of 47 Candida species (10 Candida albicans, 15 Candida auris, five Candida glabrata, three Candida kefyr, five Candida krusei, four Candida parapsilosis and five Candida tropicalis), 29 Aspergillus species (five Aspergillus flavus, 10 Aspergillus fumigatus, four Aspergillus nidulans, five Aspergillus niger, and five Aspergillus terreus), and 10 Rhizopus species (seven Rhizopus arrhizus, one Rhizopus delemar and two Rhizopus microsporus) strains. For the determination of the interaction, a microdilution checkerboard technique based on the European Committee on Antimicrobial Susceptibility Testing (EUCAST) reference method for antifungal susceptibility testing was used. Results of the checkerboard technique were evaluated by the fractional inhibitory concentration index (FICI) based on the Loewe additivity model for all isolates. Different inhibition endpoints were used to capture both the interaction at MIC and sub-MIC levels. Additionally, checkerboard technique results for Candida species were evaluated by response surface analysis based on the Bliss independence model. Against common Candida species, the combination was synergistic for 75% of the strains by FICI and for 66% of the strains by response surface analysis. For C", "token_count": 497, "char_count": 1515, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5781, "quality_score": 0.7891, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:39.453925", "source": { "split": "train_shard_00001", "doc_id": 2513 }, "chunk_id": "train_shard_00001_2513_0", "global_id": 9245 }, { "text": "tropicalis, the interaction was antagonistic for three isolates by FICI, but antagonism was not confirmed by response surface analysis. Interestingly, synergistic and antagonistic FICIs were simultaneously present on checkboard microplates of all three strains. Against C. auris the combination was synergistic for 73% of the strains by response surface analysis and for 33% of the strains by FICI. This discrepancy could be related to the insensitivity of the FICI to detect weak interactions. Interaction for all other strains was indifferent. For Aspergillus and Rhizopus species combination exhibited only indifferent interactions against all tested strains.\n\nIn Vitro Activity of Amphotericin B in Combination with Colistin against Fungi Responsible for Invasive Infections.", "token_count": 211, "char_count": 804, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:39.918481", "source": { "split": "train_shard_00001", "doc_id": 2513 }, "chunk_id": "train_shard_00001_2513_1", "global_id": 9246 }, { "text": "Proteins secreted to the extracellular environment or to the periphery of the cell envelope, the secretome, play essential roles in foraging, antagonistic and mutualistic interactions. We hypothesize that arms races, genetic conflicts and varying selective pressures should lead to the rapid change of sequences and gene repertoires of the secretome. The analysis of 42 bacterial pan-genomes shows that secreted, and especially extracellular proteins, are predominantly encoded in the accessory genome, i.e. among genes not ubiquitous within the clade. Genes encoding outer membrane proteins might engage more frequently in intra-chromosomal gene conversion because they are more often in multi-genic families. The gene sequences encoding the secretome evolve faster than the rest of the genome and in particular at non-synonymous positions. Cell wall proteins in Firmicutes evolve particularly fast when compared with outer membrane proteins of Proteobacteria. Virulence factors are over-represented in the secretome, notably in outer membrane proteins, but cell localization explains more of the variance in substitution rates and gene repertoires than sequence homology to known virulence factors. Accordingly, the repertoires and sequences of the genes encoding the secretome change fast in the clades of obligatory and facultative pathogens and also in the clades of mutualists and free-living bacteria. Our study shows that cell localization shapes genome evolution. In agreement with our hypothesis, the repertoires and the sequences of genes encoding secreted proteins evolve fast. The particularly rapid change of extracellular proteins suggests that these public goods are key players in bacterial adaptation.\n\nRapid evolution of the sequences and gene repertoires of secreted proteins in bacteria.", "token_count": 403, "char_count": 1808, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5039, "quality_score": 0.752, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:40.536681", "source": { "split": "train_shard_00001", "doc_id": 2514 }, "chunk_id": "train_shard_00001_2514_0", "global_id": 9247 }, { "text": "

Background

Pseudoalteromonas is a genus of ubiquitous marine bacteria used as model organisms to study the biological mechanisms involved in the adaptation to cold conditions. A remarkable feature shared by these bacteria is their ability to produce secondary metabolites with a strong antimicrobial and antitumor activity. Despite their biotechnological relevance, representatives of this genus are still lacking (with few exceptions) an extensive genomic characterization, including features involved in the evolution of secondary metabolites production. Indeed, biotechnological applications would greatly benefit from such analysis.

Results

Here, we analyzed the genomes of 38 strains belonging to different Pseudoalteromonas species and isolated from diverse ecological niches, including extreme ones (i.e. Antarctica). These sequences were used to reconstruct the largest Pseudoalteromonas pangenome computed so far, including also the two main groups of Pseudoalteromonas strains (pigmented and not pigmented strains). The downstream analyses were conducted to describe the genomic diversity, both at genus and group levels. This allowed highlighting a remarkable genomic heterogeneity, even for closely related strains. We drafted all the main evolutionary steps that led to the current structure and gene content of Pseudoalteromonas representatives. These, most likely, included an extensive genome reduction and a strong contribution of Horizontal Gene Transfer (HGT), which affected biotechnologically relevant gene sets and occurred in a strain-specific fashion. Furthermore, this study also identified the genomic determinants related to some of the most interesting features of the Pseudoalteromonas representatives, such as the production of secondary metabolites, the adaptation to cold temperatures and the resistance to abiotic compounds.

Conclusions

This study poses the bases for a comprehensive understanding of the evolutionary trajectories followed in time by this peculiar bacterial genus and for a focused exploitation of their biotechnological potential.\n\nThe pangenome of (Antarctic) Pseudoalteromonas bacteria: evolutionary and functional insights.", "token_count": 469, "char_count": 2199, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6035, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:41.184466", "source": { "split": "train_shard_00001", "doc_id": 2515 }, "chunk_id": "train_shard_00001_2515_0", "global_id": 9248 }, { "text": "

Objectives

The emergence of antimicrobial-resistant and mastitis-associated Enterococcus faecalis and Enterococcus faecium is of great concern due to the huge economic losses associated with enterococcal infections. Here we report the draft genome sequences of E. faecalis and E. faecium strains that were isolated from raw milk samples obtained from mastitis-infected cows in Bangladesh.

Methods

The two strains were isolated, identified, and genomic DNA was sequenced using the Illumina NextSeq 550 platform. The assembled contigs were analysed for virulence, antimicrobial resistance genes, and multilocus sequence type. The genomes were compared to previously reported E. faecalis and E. faecium genomes to generate core genome phylogenetic trees.

Results

E. faecalis strain BR-MHR218Efa and E. faecium strain BR-MHR268Efe belonged to multilocus sequence types ST-190 and ST-22, respectively, both of which appear to represent relatively rare sequence types. BR-MHR268Efe harboured only one antibiotic resistance gene encoding resistance towards macrolides (lsa(A)), while BR-MHR218Efa harboured ten different antibiotic resistance genes encoding resistance to aminoglycosides (ant[6]-Ia, aph(3')-III), sulphonamides (aac(6')-II), lincosamides (lnu(B)), macrolides (erm(B)), MLSB antibiotics (msr(C)), tetracyclines (tet(M), tet(L)), trimethoprim (dfrG), and pleuromutilin-lincosamide-streptogramin A (lsa(E)). Virulence gene composition was different between the two isolates. BR-MHR218Efa harboured only two virulence genes involved in adherence (acm and scm)", "token_count": 486, "char_count": 1587, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:41.837204", "source": { "split": "train_shard_00001", "doc_id": 2516 }, "chunk_id": "train_shard_00001_2516_0", "global_id": 9249 }, { "text": "BR-MHR268Efe harboured eight complete virulence operons including three operons involved in adherence (Ace, Ebp pili, and EfaA), two operons involved in biofilm formation (BopD and Fsr), and three exoenzymes (gelatinase, hyaluronidase, SprE).

Conclusions

The genome sequences of the strains BR-MHR268Efe and BR-MHR218Efa will serve as a reference point for molecular epidemiological studies of mastitis-associated E. faecalis and E. faecium. Additionally, the findings will help understand the complex antimicrobial-resistance in livestock-assoiated Enterococci.\n\nDraft genome sequences of clinical mastitis-associated Enterococcus faecalis and Enterococcus faecium carrying multiple antimicrobial resistance genes isolated from dairy cows.", "token_count": 223, "char_count": 747, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7416, "quality_score": 0.8708, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:42.304960", "source": { "split": "train_shard_00001", "doc_id": 2516 }, "chunk_id": "train_shard_00001_2516_1", "global_id": 9250 }, { "text": "

Summary

Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from metagenomic (i.e. multispecies) samples, including those from the human microbiome. In this study, methods are presented to obtain complete bacterial genomes from human saliva using complementary Oxford Nanopore (ONT) and Illumina sequencing. Applied to 3 human saliva samples, these methods resulted in 11 complete bacterial genomes: 3 Saccharibacteria clade G6 (aka Ca. Nanogingivalaceae HMT-870), 1 Saccharibacteria clade G1 HMT-348, 2 Rothia mucilaginosa , 2 Actinomyces graevenitzii , 1 Mogibacterium diversum , 1 Lachnospiraceae HMT-096, 1 Lancefieldella parvula , and one circular chromosome of Ruminococcaceae HMT-075 (which likely has at least 2 chromosomes). The 4 Saccharibacteria genomes, as well as the Actinomyces graeventizii genomes, represented the first complete genomes from their respective bacterial taxa. Aside from the complete genomes, the assemblies contained 147 contigs of over 500,000 bp each and thousands of smaller contigs, together representing many additional draft genomes including many which are likely near-complete. The complete genomes enabled highly accurate pangenome analysis, which identified unique and missing features of each genome compared to its closest relatives with complete genomes available in public repositories. These features provide clues as to the lifestyle and ecological role of these bacteria within the human oral microbiota, which will be particularly useful in designing future studies of the specific taxa that have never been isolated or cultivated.\n\nUsing nanopore sequencing to obtain complete genomes from saliva samples", "token_count": 474, "char_count": 1855, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6269, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:42.943275", "source": { "split": "train_shard_00001", "doc_id": 2517 }, "chunk_id": "train_shard_00001_2517_0", "global_id": 9251 }, { "text": "Kinetic parameters for production of beta-xylosidase by Kluyveromyces marxianus were determined in growth media containing glucose, xylose, cellobiose, sucrose and lactose as carbon sources. K. marxianus achieved maximum beta-xylosidase specific product yield (Y(P/X)) when grown on xylose. Basal level of activity was achieved in cultures grown on glucose. Kinetic parameters of enzyme production and cell mass formation were correlated. Enzyme synthesis was regulated by an induction mechanism and growth-dependent repression mechanism. Thermodynamic analysis revealed that the cell system exerted protection against thermal inactivation. A partially purified enzyme showed good stability when incubated at 60 degrees C and was quite stable at a pH of 5.0-7.0 and may be exploited for commercial applications.\n\nKinetic parameters and thermodynamic values of beta-xylosidase production by Kluyveromyces marxianus.", "token_count": 234, "char_count": 914, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:43.415721", "source": { "split": "train_shard_00001", "doc_id": 2518 }, "chunk_id": "train_shard_00001_2518_0", "global_id": 9252 }, { "text": "Background: Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made. Methods: We simulated data from a defined \"true tree\" using a realistic evolutionary model. We built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree. Results: We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other. Conclusions: We recommend three approaches, depending on requirements for accuracy and computational time. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology. We have publicly released our simulated data and code to enable further comparisons.\n\nEvaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study.", "token_count": 436, "char_count": 2021, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6098, "quality_score": 0.8049, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:44.046556", "source": { "split": "train_shard_00001", "doc_id": 2519 }, "chunk_id": "train_shard_00001_2519_0", "global_id": 9253 }, { "text": "The proliferation of opportunistic pathogens Vibrio parahaemolyticus, Vibrio alginolyticus, and Vibrio owensii have impeded the rapid development of aquaculture farming. The study aimed to analyze the whole genome of pathogenic Vibrio strains associated with hepatopancreatic necrosis in Penaeus vannamei. The analysis included genomic characterization, virulence genes profiling, antibiotic resistance genes (ARGs) identification, antimicrobial resistance phenotypes, clustered regularly interspaced short palindromic repeats (CRISPR) and prophage prediction, multi-locus sequence typing, and pan-genome analysis of Vibrio isolates from Guangdong and Jiangsu provinces, China. Sequence analysis of the specimens revealed 29 V. parahaemolyticus isolates, three V. alginolyticus isolates, and one V. owensii isolate. Their genomes are 4.9–5.9 Mbp in size, with a GC content of 44.4–45.4%. Each Vibrio isolate harbored >120 virulence genes. Out of the 33 isolates, 13 (39%) demonstrated multidrug-resistant (MDR). Notably, at least 14 isolates exhibited heightened resistance to sulfamethoxazole, erythromycin, and amoxicillin, with a cumulative detection of 20 ARGs. Nevertheless, no significant correlation was found between the composition of ARGs and the observed antimicrobial resistance phenotypes. All Vibrio isolates differed in the presence of prophage and CRISPR sequences; and two of these prophages harbored virulence genes but not ARGs. The study identified 17 distinct sequence types (STs) in V. parahaemolyticus isolates, primarily ST415 (n = 5), while two Vibrio isolates were classified as ST3. Using the 117 V", "token_count": 484, "char_count": 1625, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6743, "quality_score": 0.8372, "entities": { "genes": [ "ST3", "ST415" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:44.691713", "source": { "split": "train_shard_00001", "doc_id": 2520 }, "chunk_id": "train_shard_00001_2520_0", "global_id": 9254 }, { "text": "parahaemolyticus strains available in the National Center for Biotechnology Information database as a reference, pan-genomic analysis and phylogenetic analysis of the core genome revealed that clinical isolates of the same STs clustered into the same clade, irrespective of isolation date and geographic origins. In summary, these data enhance our understanding of the molecular characteristics and epidemiological risk of Vibrio strains in southern China, especially regarding shrimp aquaculture.\n\nGenomic characterization and comparative genomic analysis of pathogenic Vibrio isolated from aquaculture-grown white-leg shrimp (Penaeus vannamei) in Guangdong and Jiangsu, China", "token_count": 161, "char_count": 677, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7386, "quality_score": 0.8693, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:45.130604", "source": { "split": "train_shard_00001", "doc_id": 2520 }, "chunk_id": "train_shard_00001_2520_1", "global_id": 9255 }, { "text": "Ab-AMR is a comprehensive repository of drug resistance mechanisms in Acinetobacter baumannii . The current version of Ab-AMR provides a drug resistance profile of 788 genomes. In order to ensure that the datasets in Ab-AMR have relevance both to the research and clinical community, standards of defining MIC breakpoints, whole genome sequence quality metrics as defined by EUCAST/CLSI and classification of isolates into susceptible, MDR, XDR and PDR as defined by CDC/ECDC are implemented. As of now, 364 DR determinants associated with antibiotic inactivation (β-lactamases, aminoglycoside modification, chloramphenicol acetyltransferase), efflux, protein modulating permeability and alteration of target site are comprehensively annotated. In addition, data from pangenome analysis across 788 genomes is also provided for identification of core and accessory DR determinants. AB ATCC 17978 (Accession- CP000521.1 ), the reference strain, was annotated on January 1, 2014 but subsequently the same strain was re-annotated on March 21, 2017 (NZ_CP018664.1) due to incorrect assembly. Therefore, the genome comparison of both, 2014 and 2017 versions were performed for maintaining the correct annotations as most of the literature data referred to the earlier version of the reference genome. In Ab-AMR, the reference coordinates of the revised reference genome are used to represent manually curated and comprehensively annotated data on 614 essential genes, 1334 genes mapped to pathways, 221 PDB structures, 81 reported drug targets, 364 genes with reported resistance mechanism, 118 transcription factors, 4 sigma factors and 14 two component systems. Ab-AMR is made using the standard php-mysql framework and offers various search tools including a query builder that facilitates query on over 60 different features for addressing complex questions like core genes which are also essential and have a role to play in drug resistance with no known human homolog, etc", "token_count": 501, "char_count": 1972, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [ "CP000521" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:45.781784", "source": { "split": "train_shard_00001", "doc_id": 2521 }, "chunk_id": "train_shard_00001_2521_0", "global_id": 9256 }, { "text": "Ab-AMR offers a centralized data resource for systematic mapping of DR determinants, both plasmid and chromosomal mediated, along with deep annotation of clinical isolates. Database URL: https://datascience.imtech.res.in/anshu/ab-amr/\n\nAb-AMR: A Comprehensive Repository of Acinetobacter baumannii to Understand the Molecular Landscape of Antimicrobial Resistance", "token_count": 110, "char_count": 370, "word_count": 42, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:46.162607", "source": { "split": "train_shard_00001", "doc_id": 2521 }, "chunk_id": "train_shard_00001_2521_1", "global_id": 9257 }, { "text": "

ABSTRACT

The N2-fixing symbiosis between rhizobia and legumes is negatively impacted by numerous stresses, including low temperatures. To identify genomic features and biochemical pathways of rhizobia that could foster improved symbiotic function under low temperatures, we isolated and characterized three Mesorhizobium strains from legume nodules collected at two distant northern Canadian sites. Whereas the classical determinants of nodulation and nitrogen fixation are located on the chromosome of most mesorhizobia, whole genome sequencing revealed that these genes are on a large symbiotic megaplasmid in all three of the newly isolated strains. A pangenome-wide association study identified 25 genes putatively associated with mesorhizobia isolated from arctic or subarctic environments, with the genomic location of many of these genes implying a relationship with legume symbiosis. Phylogenetic and sequence analyses of the common nodulation genes revealed alleles that are highly conserved amongst mesorhizobia isolated from northern climates but uncommon in mesorhizobia isolated from similar plant hosts in other climatic regions, suggesting potential functional adaptive differences and the horizontal transfer of these alleles between northern rhizobia. We speculate that nod sequence divergence was driven by climatic factors, and that the encoded proteins may be particularly stable and/or active at low temperatures.\n\nWhole genome sequencing of three mesorhizobia isolated from northern Canada to identify genomic adaptations promoting nodulation in cold climates", "token_count": 357, "char_count": 1590, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:46.739393", "source": { "split": "train_shard_00001", "doc_id": 2522 }, "chunk_id": "train_shard_00001_2522_0", "global_id": 9258 }, { "text": "Comprehending bacterial genomic variation linked to distinct environments can yield novel insights into mechanisms underlying differential adaptation and transmission of microbes across environments. Gaining such insights is particularly crucial for pathogens as it benefits public health surveillance. However, the understanding of bacterial genomic variation is limited by a scarcity of investigations in genomic variation coupled with different ecological contexts. To address this limitation, we focused on Listeria, an important bacterial genus for food safety that includes the human pathogen L. monocytogenes, and analyzed a large-scale genomic dataset collected by us from natural and food-associated environments across the United States. Through comparative genomics analyses on 449 isolates from the soil and 390 isolates from agricultural water and produce processing facilities representing L. monocytogenes, L. seeligeri, L. innocua, and L. welshimeri, we find that the genomic profiles strongly differ by environments within each species. This is supported by the environment-associated subclades and differential presence of plasmids, stress islands, and accessory genes involved in cell envelope biogenesis and carbohydrate transport and metabolism. Core genomes of Listeria species are also strongly associated with environments and can accurately predict isolation sources at the lineage level in L. monocytogenes using machine learning. We find that the large environment-associated genomic variation in Listeria appears to be jointly driven by soil property, climate, land use, and accompanying bacterial species, chiefly representing Actinobacteria and Proteobacteria. Collectively, our data suggest that populations of Listeria species have genetically adapted to different environments, which may limit their transmission from natural to food-associated environments.\n\nComparative genomics unveils extensive genomic variation between populations of Listeria species in natural and food-associated environments.", "token_count": 419, "char_count": 2034, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6217, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:47.375048", "source": { "split": "train_shard_00001", "doc_id": 2523 }, "chunk_id": "train_shard_00001_2523_0", "global_id": 9259 }, { "text": "Acinetobacter baumannii is a nosocomial pathogen that frequently causes healthcare-acquired infections. The global spread of multidrug-resistant (MDR) strains with its ability to survive in the environment for extended periods imposes a pressing public health threat. Two MDR A. baumannii outbreaks occurred in 2012 and 2014 in a companion animal intensive care unit (caICU) in the Netherlands. Whole-genome sequencing (WGS) was performed on dog clinical isolates (n = 6), environmental isolates (n = 5), and human reference strains (n = 3) to investigate if the isolates of the two outbreaks were related. All clinical isolates shared identical resistance phenotypes displaying multidrug resistance. Multi-locus Sequence Typing (MLST) revealed that all clinical isolates belonged to sequence type ST2. The core genome MLST (cgMLST) results confirmed that the isolates of the two outbreaks were not related. Comparative genome analysis showed that the outbreak isolates contained different gene contents, including mobile genetic elements associated with antimicrobial resistance genes (ARGs). The time-measured phylogenetic reconstruction revealed that the outbreak isolates diverged approximately 30 years before 2014. Our study shows the importance of WGS analyses combined with molecular clock investigations to reduce transmission of MDR A. baumannii infections in companion animal clinics.\n\nGenomic Investigation of Two Acinetobacter baumannii Outbreaks in a Veterinary Intensive Care Unit in The Netherlands.", "token_count": 402, "char_count": 1564, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.819, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:48.028102", "source": { "split": "train_shard_00001", "doc_id": 2524 }, "chunk_id": "train_shard_00001_2524_0", "global_id": 9260 }, { "text": "The Gram positive, non-pathogenic endospore-forming soil inhabiting prokaryote Bacillus amyloliquefaciens is a plant growth-promoting rhizobacterium. Bacillus amyloliquefaciens processes wide biocontrol abilities and numerous strains have been reported to suppress diverse bacterial, fungal and fungal-like pathogens. Knowledge about strain level biocontrol abilities is warranted to translate this knowledge into developing more efficient biocontrol agents and bio-fertilizers. Ever-expanding genome studies of B. amyloliquefaciens are showing tremendous increase in strain-specific new secondary metabolite clusters which play key roles in the suppression of pathogens and plant growth promotion. In this report, we have used genome mining of all sequenced B. amyloliquefaciens genomes to highlight species boundaries, the diverse strategies used by different strains to promote plant growth and the diversity of their secondary metabolites. Genome composition of the targeted strains suggest regions of genomic plasticity that shape the structure and function of these genomes and govern strain adaptation to different niches. Our results indicated that B. amyloliquefaciens: (i) suffer taxonomic imprecision that blurs the debate over inter-strain genome diversity and dynamics, (ii) have diverse strategies to promote plant growth and development, (iii) have an unlocked, yet to be delimited impressive arsenal of secondary metabolites and products, (iv) have large number of so-called orphan gene clusters, i.e., biosynthetic clusters for which the corresponding metabolites are yet unknown, and (v) have a dynamic pan genome with a secondary metabolite rich accessory genome.\n\nComparative Genomics of Bacillus amyloliquefaciens Strains Reveals a Core Genome with Traits for Habitat Adaptation and a Secondary Metabolites Rich Accessory Genome.", "token_count": 475, "char_count": 1892, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:48.686494", "source": { "split": "train_shard_00001", "doc_id": 2525 }, "chunk_id": "train_shard_00001_2525_0", "global_id": 9261 }, { "text": "A variety of methods exists for typing bacteria. However, guidelines for the application and interpretation of typing tools in epidemiologic investigations of Staphylococcus aureus are lacking. This study aimed to identify appropriate typing methods for S. aureus population studies and outbreak investigation. We compared pulsed-field gel electrophoresis (PFGE), seven loci multi-locus sequence typing (MLST), core genome MLST (cgMLST), core single nucleotide polymorphism (cSNP), and enterotoxin (se/SE) profiles on 351 S. aureus isolates. The discriminatory power, concordance, and congruence of typing results were assessed. cgMLST, cSNP, and PFGE yielded the highest discrimination value, followed by se/SE typing and MLST. The best concordance of results was found between cgMLST and cSNP, while the best congruence was observed for cgMLST and cSNP with all methods, followed by PFGE with MLST. The strengths and weaknesses of each method are highlighted. For population structure, cgMLST and cSNP performed better than PFGE and MLST in terms of resolution of clusters and in phylogenetic inference. Enterotoxin profiles matched with MLST groups, suggesting the use of se/SE typing to predict MLST results. For the retrospective analysis of 31 outbreaks, all methods performed almost equally to discriminate epidemiologically related strains and can be used to unambiguously distinguish outbreak strains.\n\nEpidemiology of Staphylococcus aureus food isolates: Comparison of conventional methods with whole genome sequencing typing methods", "token_count": 383, "char_count": 1543, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6065, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:49.307324", "source": { "split": "train_shard_00001", "doc_id": 2526 }, "chunk_id": "train_shard_00001_2526_0", "global_id": 9262 }, { "text": "

ABSTRACT

Large regions of prokaryotic genomes are currently without any annotation, in part due to well-established limitations of annotation tools. For example, it is routine for annotation tools to misreport or completely omit genes using alternative start codons. Therefore, we present StORF-Reporter, a tool that takes an annotated genome and returns missing CDS genes from unannotated regions. StORF-Reporter consists of two parts. The first begins with the extraction of unannotated regions from an annotated genome. Next, Stop-ORFs (StORFs) are identified in these unannotated regions. StORFs are open reading frames that are delimited by stop codons and thus can capture those genes most often missing in genome annotations. We show that this methodology recovers genes missing from canonical genome annotations. We inspected the results of the genomes of model organisms, the pangenome of Escherichia coli, and a further 6,223 prokaryotic genomes of 179 genera from the Ensembl Bacteria database. StORF-Reporter was able to extend the core, soft-core and accessory gene-collections, identify novel gene families and extend families into additional genera. The high levels of sequence conservation observed between genera suggest that many of these StORF sequences are likely to be functional genes that must now be added to the canonical annotations.\n\nStORF-Reporter: Finding Genes between Genes", "token_count": 348, "char_count": 1413, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:49.904467", "source": { "split": "train_shard_00001", "doc_id": 2527 }, "chunk_id": "train_shard_00001_2527_0", "global_id": 9263 }, { "text": "Kluyveromyces marxianus IMB3 yeast cells were immobilized on delignified cellulosic material, apple, and quince separately. Both immobilized and free cells were used in high-temperature wine making, and their fermented grape must contained 3 to 4% alcohol. Semisweet wines were produced by the addition of potable alcohol to the fermented must. Preliminary sensory evaluation of the produced semisweet wines showed good flavor and aroma. The final product contained extremely low levels of higher and amyl alcohols while ethyl acetate was at levels usually present in wines. The ferment produced may be blended with other products to improve their quality.\n\nHigh-temperature wine making using the thermotolerant yeast strain Kluyveromyces marxianus IMB3.", "token_count": 185, "char_count": 754, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7156, "quality_score": 0.8578, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:50.361292", "source": { "split": "train_shard_00001", "doc_id": 2528 }, "chunk_id": "train_shard_00001_2528_0", "global_id": 9264 }, { "text": "Vine tea (Ampelopsis grossedentata) is a plant resource with good nutritional and medicinal, and is widely consumed in China. This study aimed to develop a functional vine tea fermentation broth using microbial fermentation and cellulase degradation. First, the most suitable probiotics for vine tea fermentation were screened, and the fermentation conditions were optimized. Then, a new cellulase (Cel 906, MW076177) was added to evaluate the changes in the contents of effective substances and to study its efficacy. The results show that saccharomyces cerevisiae Y-401 was identified as the best strain, the optimal fermentation conditions were a time of 94.60 h, feeding concentration of 115.21 g/L, and temperature of about 34.97°C. The vine tea fermentation broth has a strong inhibitory ability on 2,2'-azinobis3-ethylbenzothiazoline-6-sulfonic acid (ABTS) (99.73%), peroxyl (53.15%), superoxide anion radicals (84.13%), and 1,1-Diphenyl-2-trinitrophenylhydrazine (DPPH) (92.48%). It has a decent inhibitory impact on the cell viability, tyrosinase activity (32.25%), and melanin synthesis (63.52%) of B16-F10 melanoma cells induced by α-MSH. Inflammatory cell recruitment was reduced in a zebrafish inflammation model. Therefore, this vine tea fermented broth has strong antioxidant, anti-melanoma, and anti-inflammatory effects, and has healthcare potential as a probiotic tea.\n\nEffects of novel cellulase (Cel 906) and probiotic yeast fermentation on antioxidant and anti-inflammatory activities of vine tea (Ampelopsis grossedentata).", "token_count": 513, "char_count": 1566, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [ "MW076177" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:25:50.989349", "source": { "split": "train_shard_00001", "doc_id": 2529 }, "chunk_id": "train_shard_00001_2529_0", "global_id": 9265 }, { "text": "

Background

The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Viral quasispecies emerge from de novo mutations that occur in individual patients. In combination, these sets of viral mutations provide distinct genetic fingerprints that reveal the patterns of transmission and have utility in contact tracing.

Methods

Leveraging thousands of sequenced SARS-CoV-2 genomes, we performed a viral pangenome analysis to identify conserved genomic sequences. We used a rapid and highly efficient computational approach that relies on k-mers, short tracts of sequence, instead of conventional sequence alignment. Using this method, we annotated viral mutation signatures that were associated with specific strains. Based on these highly conserved viral sequences, we developed a rapid and highly scalable targeted sequencing assay to identify mutations, detect quasispecies variants, and identify mutation signatures from patients. These results were compared to the pangenome genetic fingerprints.

Results

We built a k-mer index for thousands of SARS-CoV-2 genomes and identified conserved genomics regions and landscape of mutations across thousands of virus genomes. We delineated mutation profiles spanning common genetic fingerprints (the combination of mutations in a viral assembly) and a combination of mutations that appear in only a small number of patients. We developed a targeted sequencing assay by selecting primers from the conserved viral genome regions to flank frequent mutations. Using a cohort of 100 SARS-CoV-2 clinical samples, we identified genetic fingerprints consisting of strain-specific mutations seen across populations and de novo quasispecies mutations localized to individual infections. We compared the mutation profiles of viral samples undergoing analysis with the features of the pangenome.

Conclusions

We conducted an analysis for viral mutation profiles that provide the basis of genetic fingerprints. Our study linked pangenome analysis with targeted deep sequenced SARS-CoV-2 clinical samples", "token_count": 511, "char_count": 2208, "word_count": 297, "semantic_coherence": 1, "information_density": 0.5051, "quality_score": 0.7525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:51.636565", "source": { "split": "train_shard_00001", "doc_id": 2530 }, "chunk_id": "train_shard_00001_2530_0", "global_id": 9266 }, { "text": "We identified quasispecies mutations occurring within individual patients and determined their general prevalence when compared to over 70,000 other strains. Analysis of these genetic fingerprints may provide a way of conducting molecular contact tracing.\n\nProfiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies.", "token_count": 83, "char_count": 373, "word_count": 48, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:52.010775", "source": { "split": "train_shard_00001", "doc_id": 2530 }, "chunk_id": "train_shard_00001_2530_1", "global_id": 9267 }, { "text": "The Brassica genus contains abundant economically important vegetable and oilseed crops, which are under threat of diseases caused by fungal, bacterial and viral pathogens. Resistance gene analogues (RGAs) are associated with quantitative and qualitative disease resistance and the identification of candidate RGAs associated with disease resistance is crucial for understanding the mechanism and management of diseases through breeding. The availability of Brassica genome assemblies has greatly facilitated reference-based quantitative trait loci (QTL) mapping for disease resistance. In addition, pangenomes, which characterise both core and variable genes, have been constructed for B. rapa, B. oleracea and B. napus. Genome-wide characterisation of RGAs using conserved domains and motifs in reference genomes and pangenomes reveals their clustered arrangements and presence of structural variations. Here, we comprehensively review RGA identification in important Brassica genome and pangenome assemblies. Comparison of the RGAs in QTL between resistant and susceptible individuals allows for efficient identification of candidate disease resistance genes. However, the reference-based QTL mapping and RGA candidate identification approach is restricted by the under-represented RGA diversity characterised in the limited number of Brassica assemblies. The species-wide repertoire of RGAs make up the pan-resistance gene analogue genome (pan-RGAome). Building a pan-RGAome, through either whole genome resequencing or resistance gene enrichment sequencing, would effectively capture RGA diversity, greatly expanding breeding resources that can be utilised for crop improvement.\n\nFrontiers in Dissecting and Managing Brassica Diseases: From Reference-Based RGA Candidate Identification to Building Pan-RGAomes.", "token_count": 437, "char_count": 1871, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6213, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:52.647648", "source": { "split": "train_shard_00001", "doc_id": 2531 }, "chunk_id": "train_shard_00001_2531_0", "global_id": 9268 }, { "text": "

Introduction

Urinary tract infections (UTIs) are one of the leading causes of multidrug-resistance (MDR) spread and infection-related deaths. Escherichia coli is by far the main causative agent. We conducted a prospective study on complicated urinary tract infections (cUTIs) i) to monitor the high-risk clones that could be compromising the therapeutic management and ii) to compare the cUTI etiology with uncomplicated infections (uUTIs) occurring in the same period and health area.

Methods

154 non-duplicated E. coli recovered from cUTIs in 2020 at the Hospital Universitario Central de Asturias (Spain) constituted the study collection.

Results

Most cUTI isolates belonged to phylogroup B2 (72.1%) and met the uropathogenic (UPEC) status (69.5%) (≥3 of chuA, fyuA, vat, and yfcV genes). MDR was exhibited by 35.7% of the isolates, similarly to data observed in the uUTI collection. A significant difference observed in cUTI was the higher level of fluoroquinolone resistance (FQR) (47.4%), where the pandemic clonal groups B2-CC131 and B2-ST1193 (CH14-64) comprised 28% of the 154 E. coli, representing 52.1% of the FQR isolates. Other prevalent FQR clones were D-ST69 (CH35-27), D-ST405 (CH37-27), and B2-ST429 (CH40-20) (three isolates each). We uncovered an increased genetic and genomic diversity of the CC131: 10 different virotypes, 8 clonotypes (CH), and 2 STs", "token_count": 506, "char_count": 1443, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7387, "quality_score": 0.8693, "entities": { "genes": [ "CH14", "CH35", "ST405", "CH37", "ST69", "ST1193", "ST429", "CC131", "CH40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:53.308112", "source": { "split": "train_shard_00001", "doc_id": 2532 }, "chunk_id": "train_shard_00001_2532_0", "global_id": 9269 }, { "text": "The presence of bla CTX-M-15 was determined in 12 (7.8%) isolates (all CC131), which showed 10 different core genome (cg)STs and 2 fimH types (fimH30 and fimH602) but the same set of chromosomal mutations conferring FQR (gyrA p.S83L, gyrA p.D87N, parC p.S80I, parC p.E84V, and parE p.I529L). In addition, the plasmidome analysis revealed 10 different IncF formulae in CC131 genomes.

Conclusion

We proved here that non-lactose fermenting screening, together with the detection of O25b (rfbO25b), H4 (fliCH4), and H5 (fliCH5) genes, and phylogroup and clonotyping assignation, is a reasonable approach that can be easily implemented for the surveillance of emerging high-risk clones associated with FQR spread in cUTIs, such as the uncommonly reported O25b:H4-B2-ST9126-CC131 (CH1267-30). Since E. coli CC131 and ST1193 are also involved in the community uUTIs of this health area, interventions to eradicate these MDR clones, along with surveillance for other emerging ones, are essential for antibiotic use optimization programs.\n\nFluoroquinolone resistance in complicated urinary tract infections: association with the increased occurrence and diversity of Escherichia coli of clonal complex 131, together with ST1193.", "token_count": 510, "char_count": 1357, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [ "ST9126", "CC131", "CH1267", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:53.957619", "source": { "split": "train_shard_00001", "doc_id": 2532 }, "chunk_id": "train_shard_00001_2532_1", "global_id": 9270 }, { "text": "The rapidly expanding number of sequenced bacterial strains and species, and the ongoing curation of bacterial pangenomes has uncovered unexpected complexities in understanding and addressing antibiotic resistance in the context of the pangenome. It is becoming apparent that differences in the genetic background can cause species and strain-specific responses to the same antibiotic, triggering differential selective pressures and thereby strain or species-specific adaptive outcomes. In this chapter, we consider how the pangenome, on a between and within species level, can affect the response to antibiotics and the development of resistance as well as the role selective pressures such as antibiotics play in shaping and maintaining the pangenome. We review the tools that are used to study antibiotic resistance within a pangenomic context, highlight recent findings, discuss strategies for predicting the emergence of resistance and consider how effective therapies can be developed in the context of the pangenome.\n\nA Pangenomic Perspective on the Emergence, Maintenance, and Predictability of Antibiotic Resistance", "token_count": 228, "char_count": 1125, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5975, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:54.433564", "source": { "split": "train_shard_00001", "doc_id": 2533 }, "chunk_id": "train_shard_00001_2533_0", "global_id": 9271 }, { "text": "In Australia, gonococcal isolates are monitored for antimicrobial susceptibilities. In Western Australia (WA), gonorrhoea notification rates increased by 63 % between 2013 and 2016, with the steepest increase occurring between 2015 and 2016, before stabilizing at this higher baseline between 2017 and 2020. This increased prevalence was associated with antimicrobial-susceptible (AMS) lineages. To understand the provenance of these isolates causing gonorrhoea in WA, whether they were introduced or expanded from endogenous lineages, 741 isolates were collected in 2017 and characterized by both iPLEX typing and whole genome sequencing (WGS). Antibiograms and genocoding of the isolates revealed that AMS isolates were most prevalent in the remote regions, while the urban/rural regions were characterized by antimicrobial-resistant (AMR) isolates. iPLEX typing identified 78 iPLEX genotypes (WA-1 to WA-78) of which 20 accounted for over 88 % of isolates. WA-10 was the most frequently identified genotype in the urban/rural regions whilst WA-29 was the most frequently identified genotype in the remote regions. Genotypes WA-38, WA-52 and WA-13 accounted for 81 % (n=36/44) of the azithromycin-resistant N. gonorrhoeae (AziR) isolates. A representative isolate of each iPLEX genotype and AMR biotype was whole genome sequenced and analysed using MLST, NG-MAST and NG-STAR, and the novel core genome clustering Ng_cgc_400 typing scheme. Five predominant Bayesian population groups (termed BPG-1 to 5) were identified in the study collection. BPG-1 and BPG-2 were associated with AMS isolates from the remote regions", "token_count": 493, "char_count": 1633, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5905, "quality_score": 0.7953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:55.092753", "source": { "split": "train_shard_00001", "doc_id": 2534 }, "chunk_id": "train_shard_00001_2534_0", "global_id": 9272 }, { "text": "BPG-1 and BPG-2 were shown to be unique to the remote regions based on a minimum spanning tree against 4000 international isolates. AMS isolates in urban/rural regions were dominated by international lineages. AziR and Cef DS (decreased susceptibility to ceftriaxone) was concentrated in three urban/rural genomic groups (BPG-3, 4 and 5). Azithromycin minimum inhibitory concentrations (0.5-16 mg l-1) correlated with the accumulation of mtrR mutations or/and the fraction of 23S rRNA C2611T mutated copies. The majority of isolates in BPG-3, 4 and 5 could be correlated with known AMR lineages circulating globally and nationally. In conclusion, the surge in AMS isolates in WA in 2017 was due to importation of international AMS lineages into urban/rural regions, whilst the local AMS lineages persisted largely in the remote regions. Bridging between the urban/rural and remote regions was relatively rare, but continued surveillance is required to prevent ingress of AMR strains/lineages into the remote regions of WA.\n\nTravel-associated lineages and unique endemic antimicrobial-susceptible lineages of Neisseria gonorrhoeae predominate in Western Australia.", "token_count": 343, "char_count": 1188, "word_count": 168, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:55.671526", "source": { "split": "train_shard_00001", "doc_id": 2534 }, "chunk_id": "train_shard_00001_2534_1", "global_id": 9273 }, { "text": "Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. Recently, the ninth allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, was reported. However, its clinical and public health significance remains unclear. We queried genomes of carbapenem-resistant Enterobacterales (CRE) for mcr-9 from a convenience sample of clinical isolates collected between 2012 and 2017 through the Georgia Emerging Infections Program, a population- and laboratory-based surveillance program. Isolates underwent phenotypic characterization and whole-genome sequencing. Phenotypic characteristics, genomic features, and clinical outcomes of mcr-9-positive and -negative CRE cases were then compared. Among 235 sequenced CRE genomes, 13 (6%) were found to harbor mcr-9, all of which were Enterobacter cloacae complex. The median MIC and rates of heteroresistance and inducible resistance to colistin were similar between mcr-9-positive and -negative isolates. However, rates of resistance were higher among mcr-9-positive isolates across most antibiotic classes. All cases had significant health care exposures. The 90-day mortality was similarly high in both mcr-9-positive (31%) and -negative (7%) CRE cases. Nucleotide identity and phylogenetic analysis did not reveal geotemporal clustering. mcr-9-positive isolates had a significantly higher number of median [range] antimicrobial resistance (AMR) genes (16 [4 to 22] versus 6 [2 to 15]; P < 0.001) than did mcr-9-negative isolates. Pangenome tests confirmed a significant association of mcr-9 detection with mobile genetic element and heavy metal resistance genes", "token_count": 519, "char_count": 1745, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6697, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:25:56.328240", "source": { "split": "train_shard_00001", "doc_id": 2535 }, "chunk_id": "train_shard_00001_2535_0", "global_id": 9274 }, { "text": "Overall, the presence of mcr-9 was not associated with significant changes in colistin resistance or clinical outcomes, but continued genomic surveillance to monitor for emergence of AMR genes is warranted. IMPORTANCE Colistin is a last-resort antibiotic for multidrug-resistant Gram-negative infections. A recently described allele of the mobile colistin resistance (mcr) gene family, designated mcr-9, has been widely reported among Enterobacterales species. However, its clinical and public health significance remains unclear. We compared characteristics and outcomes of mcr-9-positive and -negative CRE cases. All cases were acquired in the health care setting and associated with a high rate of mortality. The presence of mcr-9 was not associated with significant changes in colistin resistance, heteroresistance, or inducible resistance but was associated with resistance to other antimicrobials and antimicrobial resistance (AMR), virulence, and heavy metal resistance (HMR) genes. Overall, the presence of mcr-9 was not associated with significant phenotypic changes or clinical outcomes. However, given the increase in AMR and HMR gene content and potential clinical impact, continued genomic surveillance of multidrug-resistant organisms to monitor for emergence of AMR genes is warranted.\n\nClinical and Genomic Epidemiology of mcr-9-Carrying Carbapenem-Resistant Enterobacterales Isolates in Metropolitan Atlanta, 2012 to 2017.", "token_count": 399, "char_count": 1509, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5492, "quality_score": 0.7746, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:56.939115", "source": { "split": "train_shard_00001", "doc_id": 2535 }, "chunk_id": "train_shard_00001_2535_1", "global_id": 9275 }, { "text": "Untreated wastewater is a reservoir for multidrug-resistant bacteria, but its role in the spread of antibiotic resistance in the human population remains poorly investigated. In this study, we isolated a KPC-2-producing ST2787 Klebsiella quasipneumoniae subsp. quasipneumoniae (WW14A), recovered from raw sewage at a wastewater treatment plant in Argentina in 2018 and determined its complete genome sequence. Strain WW14A was resistant to all β-lactams, ciprofloxacin and amikacin. A core genome phylogenetic analysis indicated that WW14A was closely related to a GES-5-producing Taiwanese strain isolated from hospital wastewater in 2015 and it was clearly distinct from strains isolated recently in Argentina and Brazil. Interestingly, blaKPC-2 was harbored by a recently described IncP-6 broad-spectrum plasmid which was sporadically reported worldwide and had never been reported before in Argentina. We investigated the presence of the IncP-6 replicon in isolates obtained from the same sampling and found a novel non-typable/IncP-6 hybrid plasmid in a newly assigned ST1407 Enterobacter asburiae (WW19C) also harboring blaKPC-2. Nanopore sequencing and hybrid assembly of strains WW14A and WW19C revealed that both IncP-6 plasmids shared 72% of coverage (~20 kb), with 99.99% of sequence similarity and each one also presented uniquely combined regions that were derived from other plasmids recently reported in different countries of South America, Asia, and Europe", "token_count": 446, "char_count": 1530, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [ "WW14A", "ST2787", "ST1407", "WW19C" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:57.571238", "source": { "split": "train_shard_00001", "doc_id": 2536 }, "chunk_id": "train_shard_00001_2536_0", "global_id": 9276 }, { "text": "The region harboring the carbapenem resistance gene (~11 kb) in both plasmids contained a Tn3 transposon disrupted by a Tn3-ISApu-flanked element and the core sequence was composed by ΔISKpn6/blaKPC-2/ΔblaTEM-1/ISKpn27. Both strains also carried genes conferring resistance to heavy metals (e.g., arsenic, mercury, lead, cadmium, copper), pesticides (e.g., glyphosate), disinfectants, and several virulence-related genes, posing a potential pathogenic risk in the case of infections. This is the first study documenting blaKPC-2 associated with IncP-6 plasmids in K. quasipneumoniae and Enterobacter cloacae complex from wastewater in Argentina and highlights the circulation of IncP-6 plasmids as potential reservoirs of blaKPC-2 in the environment.\n\nCharacterization of Emerging Pathogens Carrying blaKPC-2 Gene in IncP-6 Plasmids Isolated From Urban Sewage in Argentina.", "token_count": 359, "char_count": 1012, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7069, "quality_score": 0.8534, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:58.140568", "source": { "split": "train_shard_00001", "doc_id": 2536 }, "chunk_id": "train_shard_00001_2536_1", "global_id": 9277 }, { "text": "

Background

The population structure and the correlation between antimicrobial resistance (AMR) phenotypes and genotypes in Aeromonas species isolated from patients with gastroenteritis are not well understood. The aims of the study were to: (1) investigate the antimicrobial susceptibility profiles of Aeromonas species isolated from patients with gastroenteritis; (2) explore the relationship between AMR genes and resistance phenotypes; and (3) describe the population structure of these isolates and provide evidence of transmission events among them.

Methods

This microbiological survey was performed at the Microbiology Laboratory of the Emek Medical Center in Afula, Israel. Cultivation of Aeromonas was attempted from stool samples that tested positive by PCR. Antimicrobial susceptibility testing (AST) was performed using the Sensititre GN3F microdilution panel. Whole genome sequencing (WGS) was done using the Illumina NextSeq500/550 system. Phylogenetic studies involved multi-locus sequence typing (MLST) and core genome (cg) MLST. Resistance mechanisms were identified using the Comprehensive Antibiotic Resistance Database and compared with the AST results.

Results

The study included 67 patient-unique isolates. The species that were identified included A. caviae (n = 58), A. dhakensis (n = 3), A. media (n = 2), A. veronii (n = 2) and A. hydrophila (n = 2). Isolates were almost uniformly susceptible to amikacin, gentamicin, aztreonam, cefepime, ceftazidime, ciprofloxacin and meropenem. All isolates with the exception of 1-2 isolates were resistant to ampicillin, cefazolin and ampicillin-sulbactam which was compatible with the presence of the blaOXA genes", "token_count": 506, "char_count": 1711, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [ "GN3F" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:58.796525", "source": { "split": "train_shard_00001", "doc_id": 2537 }, "chunk_id": "train_shard_00001_2537_0", "global_id": 9278 }, { "text": "Variable resistance rates were observed to cefuroxime, cefoxitin, ceftriaxone, piperacillin-tazobactam that were not correlated with the presence of other β-lactamase genes. Resistance to tetracycline and trimethoprim-sulfamethoxazole correlated with the presence of tetA and sul1, respectively. The population structure of A. caviae was highly diverse with the minority of the isolates (16/57) clustering into six defined sequence types. A cgMLST-based distance of four genes was found in one pair of isolates, suggesting common source transmission.

Conclusions

A. caviae is the dominant species related to gastroenteritis and is characterized by a diverse population structure, with almost no evidence for common-source transmission. Resistance rates to most antimicrobial agents were low and partially matched with the presence of resistance genes.\n\nPhenotypic and genotypic analysis of antimicrobial resistance and population structure of gastroenteritis-related Aeromonas isolates.", "token_count": 255, "char_count": 993, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:59.278612", "source": { "split": "train_shard_00001", "doc_id": 2537 }, "chunk_id": "train_shard_00001_2537_1", "global_id": 9279 }, { "text": "

Motivation

Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of genome plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to genomic islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date, no methods are available to identify GIs using hundreds of genomes to explore their diversity.

Results

We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on metagenome assembled genomes by redefining the borders of the leuX tRNA hotspot, a well-studied spot of insertion in Escherichia coli. panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies.

Availability and implementation

The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN. Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata.\n\npanRGP: a pangenome-based method to predict genomic islands and explore their diversity.", "token_count": 375, "char_count": 1539, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:25:59.885827", "source": { "split": "train_shard_00001", "doc_id": 2538 }, "chunk_id": "train_shard_00001_2538_0", "global_id": 9280 }, { "text": "Background: Staphylococcus epidermidis is a common skin commensal that has emerged as a pathogen in hospitals, mainly related to medical devices-associated infections. Noteworthy, infection rates by S. epidermidis have the tendency to rise steeply in next decades together with medical devices use and immunocompromized population growth. Staphylococcus epidermidis population structure includes two major clonal lineages (A/C and B) that present contrasting pathogenic potentials. To address this distinction and explore the basis of increased pathogenicity of A/C lineage, we performed a detailed comparative analysis using phylogenetic and integrated pangenome-wide-association study (panGWAS) approaches and compared the lineages's phenotypes in in vitro conditions mimicking carriage and infection. Results: Each S. epidermidis lineage had distinct phenotypic signatures in skin and infection conditions and differed in genomic content. Combination of phenotypic and genotypic data revealed that both lineages were well adapted to skin environmental cues. However, they appear to occupy different skin niches, perform distinct biological functions in the skin and use different mechanisms to complete the same function: lineage B strains showed evidence of specialization to survival in microaerobic and lipid rich environment, characteristic of hair follicle and sebaceous glands; lineage A/C strains showed evidence for adaption to diverse osmotic and pH conditions, potentially allowing them to occupy a broader and more superficial skin niche. In infection conditions, A/C strains had an advantage, having the potential to bind blood-associated host matrix proteins, form biofilms at blood pH, resist antibiotics and macrophage acidity and to produce proteases. These features were observed to be rare in the lineage B strains. PanGWAS analysis produced a catalog of putative S. epidermidis virulence factors and identified an epidemiological molecular marker for the more pathogenic lineage", "token_count": 501, "char_count": 2056, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6558, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:00.565143", "source": { "split": "train_shard_00001", "doc_id": 2539 }, "chunk_id": "train_shard_00001_2539_0", "global_id": 9281 }, { "text": "Conclusion: The prevalence of A/C lineage in infection is probably related to a higher metabolic and genomic versatility that allows rapid adaptation during transition from a commensal to a pathogenic lifestyle. The putative virulence and phenotypic factors associated to A/C lineage constitute a reliable framework for future studies on S. epidermidis pathogenesis and the finding of an epidemiological marker for the more pathogenic lineage is an asset for the management of S. epidermidis infections.\n\nDistinct Phenotypic and Genomic Signatures Underlie Contrasting Pathogenic Potential of <i>Staphylococcus epidermidis</i> Clonal Lineages.", "token_count": 188, "char_count": 676, "word_count": 88, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:01.014780", "source": { "split": "train_shard_00001", "doc_id": 2539 }, "chunk_id": "train_shard_00001_2539_1", "global_id": 9282 }, { "text": "In this study, our aim was to elucidate the relationship between Anoxybacillus rupiensis DSM 17127T and Anoxybacillus geothermalis GSsed3T through whole-genome phylogenetic analysis. The obtained 16S rRNA gene sequence from the genome of A. rupiensis DSM 17127T exhibited a 99.8% similarity with A. geothermalis GSsed3T. In the phylogenetic trees constructed using whole-genome sequences and 16S rRNA gene sequences, A. rupiensis DSM 17127T and A. geothermalis GSsed3T were observed to form a clade, indicating a close relationship between them. Moreover, the average amino acid identity, average nucleotide identity, and digital DNA-DNA hybridization values calculated between A. rupiensis DSM 17127T and A. geothermalis GSsed3T exceeded the threshold values typically used for species demarcation. Furthermore, the phylogenomic analysis based on the core genome of the strains in question provided additional support for the formation of a monophyletic clade by A. rupiensis DSM 17127T and A. geothermalis GSsed3T. Most phenotypic and chemotaxonomic features between both strains were almost identical except for a few exceptions. These findings suggest that both strains should be classified as belonging to the same species, and we propose that A. geothermalis GSsed3T is a later heterotypic synonym of A. rupiensis DSM 17127T.", "token_count": 468, "char_count": 1463, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:01.699688", "source": { "split": "train_shard_00001", "doc_id": 2540 }, "chunk_id": "train_shard_00001_2540_0", "global_id": 9283 }, { "text": "Genome-Based Reclassification of Anoxybacillus geothermalis Filippidou et al. 2016 as a Later Heterotypic Synonym of Anoxybacillus rupiensis Derekova et al. 2007.", "token_count": 62, "char_count": 162, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:02.076132", "source": { "split": "train_shard_00001", "doc_id": 2540 }, "chunk_id": "train_shard_00001_2540_1", "global_id": 9284 }, { "text": "The bacterial genus Sodalis is represented by insect endosymbionts as well as free-living species. While the former have been studied frequently, the distribution of the latter is not yet clear. Here, we present a description of a free-living strain, Sodalis ligni sp. nov., originating from decomposing deadwood. The favored occurrence of S. ligni in deadwood is confirmed by both 16S rRNA gene distribution and metagenome data. Pangenome analysis of available Sodalis genomes shows at least three groups within the Sodalis genus: deadwood-associated strains, tsetse fly endosymbionts and endosymbionts of other insects. This differentiation is consistent in terms of the gene frequency level, genome similarity and carbohydrate-active enzyme composition of the genomes. Deadwood-associated strains contain genes for active decomposition of biopolymers of plant and fungal origin and can utilize more diverse carbon sources than their symbiotic relatives. Deadwood-associated strains, but not other Sodalis strains, have the genetic potential to fix N2, and the corresponding genes are expressed in deadwood. Nitrogenase genes are located within the genomes of Sodalis, including S. ligni, at multiple loci represented by more gene variants. We show decomposing wood to be a previously undescribed habitat of the genus Sodalis that appears to show striking ecological divergence.\n\nEcological Divergence Within the Enterobacterial Genus Sodalis: From Insect Symbionts to Inhabitants of Decomposing Deadwood.", "token_count": 433, "char_count": 1588, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6262, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:02.702924", "source": { "split": "train_shard_00001", "doc_id": 2541 }, "chunk_id": "train_shard_00001_2541_0", "global_id": 9285 }, { "text": "

Summary

Streptococcus suis is a leading cause of bacterial meningitis in SE Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis . The source-sink dynamics between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome comparisons with a selection of invasive serotype 2 isolates identified increased genetic diversity and more frequent AMR carriage in isolates from healthy pigs. Multiple antimicrobial resistance genes were identified conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptinle to three or more different antimicrobial classes, and 75% of non-serotype 2 isolates were non-susceptible to 6 or more classes (compared to 37.5% of serotype 2 isolates). Antimicrobial resistance genes were found on integrative and conjugative elements (ICE) previously observed in other species, suggesting mobile gene pool which can be accessed by invasive disease isolates.

Significance statement

The zoonotic pathogen Streptococcus suis causes respiratory disease in pigs and is among the most common causative agents of human clinical bacterial meningitis in SE Asia. We collected isolates from farmed healthy pigs in Northern Thailand, representing a source population from which invasive isolates have recently emerged – linked to the pork production industry. Pangenome characterisation of the isolates revealed a reservoir of genetic diversity and antimicrobial resistance suggesting that One Health approaches may be beneficial in tackling the increase in antimicrobial resistance.\n\nNon-serotype 2 isolates from healthy pigs are a potential zoonotic reservoir ofStreptococcus suisgenetic diversity and antimicrobial resistance", "token_count": 514, "char_count": 2199, "word_count": 302, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:03.361387", "source": { "split": "train_shard_00001", "doc_id": 2542 }, "chunk_id": "train_shard_00001_2542_0", "global_id": 9286 }, { "text": "Studies of the pangenome have been empowered by an exponentially increasing amount of strain-specific genome sequencing data. With this data deluge comes a need for new tools to contextualize, analyze, and interpret such a vast amount of information. Network reconstructions, genome-scale metabolic models (GEMs), and the corresponding computational analysis frameworks such as flux balance analysis (FBA) have been proven useful toward this end. Network reconstructions can be used to interpret genomic variation not just from a single strain but for an entire species. By applying these approaches at the pangenome scale, it becomes possible to systematically evaluate phenotypic properties for an entire species thus enabling the study of a panphenome directly from a pangenome. Applying insights gained from analysis of the panphenome has diverse implications with applications ranging from human health to metabolic engineering. The future of pangenomics will include panphenomic analyses, thus supplementing traditional pangenomic analyses and helping to address the Big-data-to-knowledge grand challenge of analyzing thousands of genomic sequences.\n\nPangenome Flux Balance Analysis Toward Panphenomes", "token_count": 255, "char_count": 1207, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6826, "quality_score": 0.8413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:03.858151", "source": { "split": "train_shard_00001", "doc_id": 2543 }, "chunk_id": "train_shard_00001_2543_0", "global_id": 9287 }, { "text": "Plasmids and temperate phages are key contributors to bacterial evolution. They are usually regarded as very distinct. However, some elements, termed phage-plasmids, are known to be both plasmids and phages, e.g. P1, N15 or SSU5. The number, distribution, relatedness and characteristics of these phage-plasmids are poorly known. Here, we screened for these elements among ca. 2500 phages and 12000 plasmids and identified 780 phage-plasmids across very diverse bacterial phyla. We grouped 92% of them by similarity of gene repertoires to eight defined groups and 18 other broader communities of elements. The existence of these large groups suggests that phage-plasmids are ancient. Their gene repertoires are large, the average element is larger than an average phage or plasmid, and they include slightly more homologs to phages than to plasmids. We analyzed the pangenomes and the genetic organization of each group of phage-plasmids and found the key phage genes to be conserved and co-localized within distinct groups, whereas genes with homologs in plasmids are much more variable and include most accessory genes. Phage-plasmids are a sizeable fraction of the sequenced plasmids (∼7%) and phages (∼5%), and could have key roles in bridging the genetic divide between phages and other mobile genetic elements.\n\nBacteria have numerous distinctive groups of phage-plasmids with conserved phage and variable plasmid gene repertoires.", "token_count": 369, "char_count": 1437, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5953, "quality_score": 0.7977, "entities": { "genes": [ "SSU5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:04.440995", "source": { "split": "train_shard_00001", "doc_id": 2544 }, "chunk_id": "train_shard_00001_2544_0", "global_id": 9288 }, { "text": "

A bstract

Typical analysis workflows map reads to a reference genome in order to detect genetic variants. Generating such alignments introduces references biases, in particular against insertion alleles absent in the reference and comes with substantial computational burden. In contrast, recent k-mer-based genotyping methods are fast, but struggle in repetitive or duplicated regions of the genome. We propose a novel algorithm, called PanGenie, that leverages a pangenome reference built from haplotype-resolved genome assemblies in conjunction with k-mer count information from raw, short-read sequencing data to genotype a wide spectrum of genetic variation. The given haplotypes enable our method to take advantage of linkage information to aid genotyping in regions poorly covered by unique k-mers and provides access to regions otherwise inaccessible by short reads. Compared to classic mapping-based approaches, our approach is more than 4× faster at 30× coverage and at the same time, reached significantly better genotype concordances for almost all variant types and coverages tested. Improvements are especially pronounced for large insertions (> 50bp), where we are able to genotype > 99.9% of all tested variants with over 90% accuracy at 30× short-read coverage, where the best competing tools either typed less than 60% of variants or reached accuracies below 70%. PanGenie now enables the inclusion of this commonly neglected variant type in downstream analyses.\n\nPangenome-based genome inference", "token_count": 354, "char_count": 1524, "word_count": 221, "semantic_coherence": 1, "information_density": 0.724, "quality_score": 0.862, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:05.024130", "source": { "split": "train_shard_00001", "doc_id": 2545 }, "chunk_id": "train_shard_00001_2545_0", "global_id": 9289 }, { "text": "Recent work provides the first method to measure the relative fitness of genomic variants within a population that scales to large numbers of genomes. A key component of the computation involves finding conserved haplotype blocks, which can be done in linear time. Here, we extend the notion of conserved haplotype blocks to pangenomes, which can store more complex variation than a single reference genome. We define a maximal perfect pangenome haplotype block and give a linear-time, suffix tree based approach to find all such blocks from a set of pangenome haplotypes. We demonstrate the method by applying it to a pangenome built from yeast strains.\n\nExtending Maximal Perfect Haplotype Blocks to the Realm of Pangenomics", "token_count": 166, "char_count": 726, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6783, "quality_score": 0.8391, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:05.468400", "source": { "split": "train_shard_00001", "doc_id": 2546 }, "chunk_id": "train_shard_00001_2546_0", "global_id": 9290 }, { "text": "

Aims of the study

Listeriosis is a notifiable disease in Switzerland. In summer 2022, the Swiss Federal Office of Public Health noticed an increase in reports of listeriosis cases, indicating a possible ongoing outbreak. Here we present the approaches applied for rapidly confirming the outbreak, detecting the underlying source of infection and the measures put in place to eliminate it and contain the outbreak.

Methods

For close surveillance and early detection of outbreak situations with their possible sources, listeriosis patients in Switzerland are systematically interviewed about risk behaviours and foods consumed prior to the infection. Listeria monocytogenes isolates derived from patients in medical laboratories are sent to the National Reference Laboratory for Enteropathogenic Bacteria and Listeria, where they routinely undergo whole-genome sequencing. Interview and whole-genome sequencing data are continuously linked for comparison and analysis.

Results

In summer 2022, 20 patient-derived L. monocytogenes serotype 4b sequence type 388 strains were found to belong to an outbreak cluster (≤10 different alleles between neighbouring isolates) based on core genome multilocus sequence typing analysis. Geographically, 18 of 20 outbreak cases occurred in northeastern Switzerland. The median age of patients was 77.4 years (range: 58.1-89.7), with both sexes equally affected. Rolling analysis of the interview data revealed smoked trout from a local producer as a suspected infection source, triggering an on-site investigation of the production facility and sampling of the suspected products by the responsible cantonal food inspection team on 15 July 2022. Seven of ten samples tested positive for L. monocytogenes and the respective cantonal authority ordered a ban on production and distribution as well as a product recall. The Federal Food Safety and Veterinary Office released a nationwide public alert covering the smoked fish products concerned. Whole-genome sequencing analysis confirmed the interrelatedness of the L. monocytogenes smoked trout product isolates and the patient-derived isolates", "token_count": 495, "char_count": 2147, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8176, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:06.129003", "source": { "split": "train_shard_00001", "doc_id": 2547 }, "chunk_id": "train_shard_00001_2547_0", "global_id": 9291 }, { "text": "Following the ban on production and distribution and the product recall, reporting of new outbreak-related cases rapidly dropped to zero.

Conclusions

This listeriosis outbreak could be contained within a relatively short time thanks to identification of the source of contamination through the established combined approach of timely interviewing of every listeriosis patient or a representative and continuous molecular analysis of the patient- and food-derived L. monocytogenes isolates. These findings highlight the effectiveness of this well-established, joint approach involving the federal and cantonal authorities and the research institutions mandated to contain listeriosis outbreaks in Switzerland.\n\nRapid detection of the source of a Listeria monocytogenes outbreak in Switzerland through routine interviewing of patients and whole-genome sequencing.", "token_count": 178, "char_count": 868, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:06.573100", "source": { "split": "train_shard_00001", "doc_id": 2547 }, "chunk_id": "train_shard_00001_2547_1", "global_id": 9292 }, { "text": "The population structure of human isolates of Listeria monocytogenes in Emilia-Romagna, Italy, from 2012 to 2018 was investigated with the aim of evaluating the presence of genomic clusters indicative of possible outbreaks, the proportion of cluster-associated vs. sporadic isolates and different methods and metrics of genomic analysis for use in routine surveillance. In the 2012-2018 period the notification rate of confirmed invasive cases in Emilia-Romagna was 0.91 per 100,000 population per year, more than twice the average rate of EU countries. Out of the total 283 cases, 268 (about 95%) isolates were typed through whole genome sequencing (WGS) for cluster detection with methods based on core-genome multi-locus sequence typing and single nucleotide polymorphisms. Between 66 and 72% of listeriosis cases belonged to genomic clusters which included up to 27 cases and lasted up to 5 years. This proportion of cluster-associated cases is higher than previously estimated in other European studies. Rarefaction analysis, performed by reducing both the number of consecutive years of surveillance considered and the proportion of isolates included in the analysis, suggested that the observed high proportion of cluster-associated cases can be ascribed to the long surveillance duration (7 years) and the high notification and typing rates of this study. Our findings show that a long temporal perspective and high surveillance intensity, intended as both exhaustiveness of the system to report cases and high WGS-typing rate, are critical for sensitive detection of possible outbreaks within a WGS-based surveillance of listeriosis. Furthermore, the power and complexity of WGS interpretation emerged from the integration of genomic and epidemiological information in the investigation of few past outbreaks within the study, indicating that the use of multiple approaches, including the analysis of the accessory genome, is needed to accurately elucidate the population dynamics of Listeria monocytogenes.\n\nPopulation Structure of Listeria monocytogenes in Emilia-Romagna (Italy) and Implications on Whole Genome Sequencing Surveillance of Listeriosis.", "token_count": 513, "char_count": 2184, "word_count": 311, "semantic_coherence": 1, "information_density": 0.5563, "quality_score": 0.7781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:07.207532", "source": { "split": "train_shard_00001", "doc_id": 2548 }, "chunk_id": "train_shard_00001_2548_0", "global_id": 9293 }, { "text": "Backgrunod/Objectives: Routine identification of common bacterial pathogens is typically efficient, utilizing standardized, cost-effective methods. However, the diagnostic process becomes significantly more complex when dealing with rare or unexpected microorganisms, especially as they can be considered colonizers in many cases. Methods: This study presents diagnostic details of an uncommon pathogen, Vibrio alginolyticus, isolated from auricular discharge in a patient with non-Hodgkin lymphoma diagnosed with persistent otitis externa and explores its identification through both conventional and modern laboratory approaches. Sequential ear discharge cultures resulted in phenotypically similar but genomically different Vibrio alginolyticus isolates. We complemented classical methods like conventional culture (on Columbia agar and CLED agar), Vitek2 Compact identification, and EUCAST disk diffusion antimicrobial susceptibility testing (following the EUCAST version 12.0 guidelines) with MALDI-TOF mass spectrometry and Illumina/Nanopore whole genome sequencing. Comparative analysis of the genomes was performed with the PeGAS pipeline, Unicycler, and 1928Diagnostics SNP analysis. Results: The Vitek2 analysis identified both isolates as V. alginolyticus with 99% confidence, and this was supported by the MALDI-TOF MS results. The first isolate (A) was fully susceptible to the antibiotics tested, while the second (B) showed resistance to ciprofloxacin. Whole genome sequencing revealed 99.23% and 98.60% nucleotide identity to the V. alginolyticus reference genome for isolates A and B, respectively, with a 99.8% match between them. Isolate B acquired a gyrA (c.1870C>T) mutation that correlates with the ciprofloxacin resistance (MIC > 0.5 mg/L)", "token_count": 493, "char_count": 1818, "word_count": 230, "semantic_coherence": 1, "information_density": 0.7522, "quality_score": 0.8761, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:07.881465", "source": { "split": "train_shard_00001", "doc_id": 2549 }, "chunk_id": "train_shard_00001_2549_0", "global_id": 9294 }, { "text": "Both genomes carry hlyA (hemolysin), toxR (cholera toxin regulator), genes involved in biofilm formation (rpoN, relA, spoT, opp), luxS (motility), proA, vacB (virulence factors), and tet(34) (oxytetracycline resistance). A core genome SNP distance of <100 indicates clonal relatedness. Our integrated (phenotypic and genomic) diagnostic approach confirmed V. alginolyticus and documented host resistance evolution, with a virulence repertoire that could explain the clinical evolution. Conclusions: This case highlights the utility of molecular methods in confirming species identity, detecting resistance markers, characterizing virulence determinants, and differentiating a pathogen from a colonizer, supporting targeted clinical management.\n\nUncommon Pathogens in Common Presentations: Genetic Profiling and Virulence Determinants of <i>Vibrio alginolyticus</i> Isolated from a Case of External Otitis.", "token_count": 317, "char_count": 1001, "word_count": 113, "semantic_coherence": 1, "information_density": 0.823, "quality_score": 0.9115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:08.443501", "source": { "split": "train_shard_00001", "doc_id": 2549 }, "chunk_id": "train_shard_00001_2549_1", "global_id": 9295 }, { "text": "Hypervirulent Aeromonas hydrophila (vAh) has emerged as the etiologic agent of epidemic outbreaks of motile Aeromonas septicemia (MAS) in high-density aquaculture of farmed carp in China and catfish in the United States, which has caused millions of tons of lost fish. We conducted a global survey to better understand the evolution, geographical distribution, and phylogeny of vAh. Aeromonas isolates were isolated from fish that showed clinical symptoms of MAS, and pure cultures were screened for the ability to utilize myo-inositol as the sole carbon source. A total of 113 myo-inositol-utilizing bacterial strains were included in this study, including additional strains obtained from previously published culture collections. Based on a gyrB phylogeny, this collection included 66 A. hydrophila isolates, 48 of which were vAh. This collection also included five new vAh isolates from diseased Pangas catfish (Pangasius pangasius) and striped catfish (Pangasianodon hypophthalmus) obtained in Cambodia and Vietnam, respectively. Genome sequences were generated from representative vAh and non-vAh isolates to evaluate the potential for lateral genetic transfer of the myo-inositol catabolism pathway. Phylogenetic analyses of each of the nine genes required for myo-inositol utilization revealed the close affiliation of vAh strains regardless of geographic origin and suggested lateral genetic transfer of this catabolic pathway from an Enterobacter species. Prediction of virulence factors was conducted to determine differences between vAh and non-vAh strains in terms of virulence and secretion systems. Core genome phylogenetic analyses on vAh isolates and Aeromonas spp. disease isolates (55 in total) were conducted to evaluate the evolutionary relationships among vAh and other Aeromonas sp. isolates, which supported the clonal nature of vAh isolates", "token_count": 512, "char_count": 1928, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:09.105699", "source": { "split": "train_shard_00001", "doc_id": 2550 }, "chunk_id": "train_shard_00001_2550_0", "global_id": 9296 }, { "text": "IMPORTANCE This global survey of vAh brought together scientists that study fish disease to evaluate the evolution, geographical distribution, phylogeny, and hosts of vAh and other Aeromonas sp. isolates. In addition to vAh isolates from China and the United States, four new vAh isolates were isolated from the lower Mekong River basin in Cambodia and Vietnam, indicating the significant threat of vAh to modern aquaculture and the need for improved biosecurity to prevent vAh spread.\n\nA Global Survey of Hypervirulent Aeromonas hydrophila (vAh) Identified vAh Strains in the Lower Mekong River Basin and Diverse Opportunistic Pathogens from Farmed Fish and Other Environmental Sources.", "token_count": 176, "char_count": 701, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:09.543219", "source": { "split": "train_shard_00001", "doc_id": 2550 }, "chunk_id": "train_shard_00001_2550_1", "global_id": 9297 }, { "text": "

ABSTRACT

Background

White lupin is an old crop with renewed interest due to its seed high protein content and high nutritional value. Despite a long domestication history in the Mediterranean basin, modern breeding efforts have been fairly scarce. Recent sequencing of its genome has provided tools for further description of genetic resources but detailed characterization is still missing.

Results

Here, we report the genome sequencing of several accessions that were used to establish a white lupin pangenome. We defined core genes that are present in all individuals and variable genes that are absent in some and may represent a gene pool for stress adaptation. We believe that the identification of novel genes, together with a more comprehensive reference sequence, represents a significant improvement of the white lupin genetic resources. As an example, we used this pangenome to identify selection footprints and to provide a candidate gene for one of the main QTLs associated with late flowering in Ethiopian lupin types. A 686 nucleotide deletion was identified in exon 3 of the LaFTa1 ( Lupinus albus Flowering Time a1 ) gene that suggests a molecular origin for this trait of importance, defining the need for vernalization in some lupins.

Conclusions

The white lupin pangenome provides a novel genetic resource to better understand how domestication has shaped the genomic variability amongst this crop. It will be of major importance for breeders to select new breeding traits and incorporate them into new, more efficient and robust cultivars in order to face a growing demand for plant protein sources, notably in Europe.\n\nPangenome of white lupin provides insights into the diversity of the species", "token_count": 394, "char_count": 1753, "word_count": 270, "semantic_coherence": 1, "information_density": 0.637, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:10.505893", "source": { "split": "train_shard_00001", "doc_id": 2551 }, "chunk_id": "train_shard_00001_2551_0", "global_id": 9298 }, { "text": "Streptococcus pneumoniae (pneumococcus) is a Gram-positive coccus causing both non-invasive and invasive infectious diseases. Pneumococcal diseases are vaccine preventable. Invasive pneumococcal diseases (IPD) meeting the international case definition are reported nationally and internationally and are subject to surveillance programmes in many countries, including the Czech Republic. An important part of IPD surveillance is the monitoring of causative serotypes and their frequency over time and in relation to ongoing vaccination programmes. In the world and in the Czech Republic, whole genome sequencing (WGS) is increasingly used for pneumococci, which allows for serotyping from sequencing data, precise analysis of their genetic relationships, and the study of genes present in their genome. Whole-genome sequencing enables the generation of reliable and internationally comparable data that can be easily shared. Sequencing data are analysed using bioinformatics tools that require knowledge in the field of natural sciences with an emphasis on genetics and expertise in bioinformatics. This publication presents some options for pneumococcal analysis, i.e., serotyping, multilocus sequence typing (MLST), ribosomal MLST (rMLST), core genome MLST (cgMLST), whole genome MLST (wgMLST), single nucleotide polymorphism (SNP) analysis, assignment to Global Pneumococcal Sequence Cluster (GPSC), and identification of virulence genes and antibiotic resistance genes. The WGS strategies and applications for Europe and WGS implementation in practice are presented. WGS analysis of pneumococci allows for improved IPD surveillance, thanks to molecular serotyping, more detailed typing, generation of internationally comparable data, and improved evaluation of the effectiveness of vaccination programmes.\n\nPosibilities for use of whole genome sequencing (WGS) for the analysis of Streptococcus pneumoniae isolates.", "token_count": 441, "char_count": 1919, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:11.136712", "source": { "split": "train_shard_00001", "doc_id": 2552 }, "chunk_id": "train_shard_00001_2552_0", "global_id": 9299 }, { "text": "In has increasingly been observed that viral and bacterial coinfection frequently occurs among cultured shrimp and this coinfection could exacerbate the disease phenotype. Here, we describe a newly discovered bacterial strain, Vibrio harveyi PH1009 collected from Masbate Island, Philippines that was found to be co-infecting with the White Spot Syndrome virus in a sample of black tiger prawn, Penaeus monodon. The genome of V. harveyi PH1009 was sequenced, assembled, and annotated. Average Nucleotide identity calculation with Vibrio harveyi strains confirmed its taxonomic identity. It is a potential multi-drug and multi-heavy metal resistant strain based on the multiple antibiotic and heavy metal resistance determinants annotated on its genome. Two prophage regions were identified in its genome. One contained genes for Zona occludens toxin (Zot) and Accessory cholera toxin (Ace), essential toxins of toxigenic V. cholerae strains apart from CTX toxins. Pan-genome analysis of V. harveyi strains, including PH1009, revealed an \"open\" pan-genome for V. harveyi and a core genome mainly composed of genes necessary for growth and metabolism. Phylogenetic tree based on the core genome alignment revealed that PH1009 was closest to strains QT520, CAIM 1754, and 823tez1. Published virulence factors present on the strain QT520 suggest similar pathogenicity with PH1009. However, PH1009 Zot was not found on related strains but was present in strains HENC-01 and CAIM 148. Most unique genes found in the PH1009 strain were identified as hypothetical proteins", "token_count": 479, "char_count": 1613, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [ "QT520", "PH1009" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:12.535787", "source": { "split": "train_shard_00001", "doc_id": 2553 }, "chunk_id": "train_shard_00001_2553_0", "global_id": 9300 }, { "text": "Further annotation showed that several of these hypothetical proteins were phage transposases, integrases, and transcription regulators, implying the role of bacteriophages in the distinct genomic features of the PH1009 genome. The PH1009 genome will serve as a valuable genomic resource for comparative genomic studies and in understanding the disease mechanism of the Vibrio harveyi species.\n\nGenomic analysis of Vibrio harveyi strain PH1009, a potential multi-drug resistant pathogen due to acquisition of toxin genes.", "token_count": 143, "char_count": 535, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7397, "quality_score": 0.8699, "entities": { "genes": [ "PH1009" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:12.974767", "source": { "split": "train_shard_00001", "doc_id": 2553 }, "chunk_id": "train_shard_00001_2553_1", "global_id": 9301 }, { "text": "

Background

Clostridium perfringens causes a range of diseases in animals and humans including necrotic enteritis in chickens and food poisoning and gas gangrene in humans. Necrotic enteritis is of concern in commercial chicken production due to the cost of the implementation of infection control measures and to productivity losses. This study has focused on the genomic analysis of a range of chicken-derived C. perfringens isolates, from around the world and from different years. The genomes were sequenced and compared with 20 genomes available from public databases, which were from a diverse collection of isolates from chickens, other animals, and humans. We used a distance based phylogeny that was constructed based on gene content rather than sequence identity. Similarity between strains was defined as the number of genes that they have in common divided by their total number of genes. In this type of phylogenetic analysis, evolutionary distance can be interpreted in terms of evolutionary events such as acquisition and loss of genes, whereas the underlying properties (the gene content) can be interpreted in terms of function. We also compared these methods to the sequence-based phylogeny of the core genome.

Results

Distinct pathogenic clades of necrotic enteritis-causing C. perfringens were identified. They were characterised by variable regions encoded on the chromosome, with predicted roles in capsule production, adhesion, inhibition of related strains, phage integration, and metabolism. Some strains have almost identical genomes, even though they were isolated from different geographic regions at various times, while other highly distant genomes appear to result in similar outcomes with regard to virulence and pathogenesis.

Conclusions

The high level of diversity in chicken isolates suggests there is no reliable factor that defines a chicken strain of C. perfringens, however, disease-causing strains can be defined by the presence of netB-encoding plasmids. This study reveals that horizontal gene transfer appears to play a significant role in genetic variation of the C. perfringens chromosome as well as the plasmid content within strains.", "token_count": 484, "char_count": 2201, "word_count": 319, "semantic_coherence": 1, "information_density": 0.5987, "quality_score": 0.7994, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:13.671950", "source": { "split": "train_shard_00001", "doc_id": 2554 }, "chunk_id": "train_shard_00001_2554_0", "global_id": 9302 }, { "text": "Whole genome analysis reveals the diversity and evolutionary relationships between necrotic enteritis-causing strains of Clostridium perfringens.", "token_count": 34, "char_count": 145, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:14.038871", "source": { "split": "train_shard_00001", "doc_id": 2554 }, "chunk_id": "train_shard_00001_2554_1", "global_id": 9303 }, { "text": "This comprehensive review explores the evolving role of probiotic-based foods and beverages, highlighting their potential as functional and \"future foods\" that could significantly enhance nutrition, health, and overall well-being. These products are gaining prominence for their benefits in gut health, immune support, and holistic wellness. However, their future success depends on addressing critical safety concerns and navigating administrative complexities. Ensuring that these products \"do more good than harm\" involves rigorous evaluations of probiotic strains, particularly those sourced from the human gastrointestinal tract. Lactic acid bacteria (LABs) serve as versatile and effective functional starter cultures for the development of probiotic foods and beverages. The review emphasizes the role of LABs as functional starter cultures and the development of precision probiotics in advancing these products. Establishing standardized guidelines and transparent practices is essential, requiring collaboration among regulatory bodies, industry stakeholders, and the scientific community. The review underscores the importance of innovation in developing \"friendly bacteria,\" \"super probiotics,\" precision fermentation, and effective safety assessments. The prospects of functional probiotic-based foods and beverages rely on refining these elements and adapting to emerging scientific advancements. Ultimately, empowering consumers with accurate information, fostering innovation, and maintaining stringent safety standards will shape the future of these products as trusted and beneficial components of a health-conscious society. Probiotic-based foods and beverages, often infused with LABs, a \"friendly bacteria,\" are emerging as \"super probiotics\" and \"future foods\" designed to \"do more good than harm\" for overall health.\n\nProgress in Probiotic Science: Prospects of Functional Probiotic-Based Foods and Beverages.", "token_count": 426, "char_count": 1988, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:14.660842", "source": { "split": "train_shard_00001", "doc_id": 2555 }, "chunk_id": "train_shard_00001_2555_0", "global_id": 9304 }, { "text": "Understanding the impact of DNA variation on human traits is a fundamental question in human genetics. Variable number tandem repeats (VNTRs) make up roughly 3% of the human genome but are often excluded from association analysis due to poor read mappability or divergent repeat content. While methods exist to estimate VNTR length from short-read data, it is known that VNTRs vary in both length and repeat (motif) composition. Here, we use a repeat-pangenome graph (RPGG) constructed on 35 haplotype-resolved assemblies to detect variation in both VNTR length and repeat composition. We align population scale data from the Genotype-Tissue Expression (GTEx) Consortium to examine how variations in sequence composition may be linked to expression, including cases independent of overall VNTR length. We find that 9,422 out of 39,125 VNTRs are associated with nearby gene expression through motif variations, of which only 23.4% associations are accessible from length. Fine-mapping identifies 174 genes to be likely driven by variation in certain VNTR motifs and not overall length. We highlight two genes, CACNA1C and RNF213 that have expression associated with motif variation, demonstrating the utility of RPGG analysis as a new approach for trait association in multiallelic and highly variable loci.\n\nThe motif composition of variable-number tandem repeats impacts gene expression", "token_count": 329, "char_count": 1387, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6618, "quality_score": 0.8309, "entities": { "genes": [ "CACNA1C", "RNF213" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:15.228613", "source": { "split": "train_shard_00001", "doc_id": 2556 }, "chunk_id": "train_shard_00001_2556_0", "global_id": 9305 }, { "text": "Background: The genus Enterococcus includes a diverse group of bacteria that are commonly found in the gastrointestinal tracts of humans and animals, as well as in various environmental habitats. Methods: In this study, Enterococcus lactis RB10, isolated from goat feces, was subjected to comprehensive genomic and functional analysis to assess its safety and potential as a probiotic strain. Results: The genome of E. lactis RB10, with a size of 2,713,772 bp and a GC content of 38.3%, was assembled using Oxford Nanopore Technologies (ONT). Genome annotation revealed 3375 coding sequences (CDSs) and highlighted key metabolic pathways involved in carbohydrate, protein, and amino acid metabolism. The strain was susceptible to important antibiotics, including ampicillin, chloramphenicol, tetracycline, and vancomycin, but exhibited resistance to aminoglycosides, a common trait in Enterococcus species with non-hemolytic activity. Genomic analysis further identified two intrinsic antimicrobial resistance genes (ARGs). The strain also demonstrated antimicrobial activity against Bacillus cereus DMST 11098 and Salmonella Typhi DMST 22842, indicating pathogen-specific effects. Key genes for adhesion, biofilm formation, and stress tolerance were also identified, suggesting that RB10 could potentially colonize the gut and compete with pathogens. Moreover, the presence of bacteriocin and secondary metabolite biosynthetic gene clusters suggests its potential for further evaluation as a biocontrol agent and gut health promoter. Conclusions: However, it is important to note that E. lactis RB10 was isolated from goat feces, a source that may harbor both commensal and opportunistic bacteria, and therefore additional safety assessments are necessary. While further validation is needed, E", "token_count": 520, "char_count": 1875, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6815, "quality_score": 0.8407, "entities": { "genes": [ "RB10" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:15.882865", "source": { "split": "train_shard_00001", "doc_id": 2557 }, "chunk_id": "train_shard_00001_2557_0", "global_id": 9306 }, { "text": "lactis RB10 exhibits promising probiotic properties with low pathogenic risk, supporting its potential use in food and health applications.\n\nGenomic Characterization and Safety Evaluation of <i>Enterococcus lactis</i> RB10 Isolated from Goat Feces.", "token_count": 80, "char_count": 264, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [ "RB10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:16.252562", "source": { "split": "train_shard_00001", "doc_id": 2557 }, "chunk_id": "train_shard_00001_2557_1", "global_id": 9307 }, { "text": "Nisin A, the prototypical lantibiotic, is an antimicrobial peptide currently utilised as a food preservative, with potential for therapeutic applications. Here, we describe nisin E, a novel nisin variant produced by two Streptococcus equinus strains, APC4007 and APC4008, isolated from sheep milk. Shotgun whole genome sequencing and analysis revealed biosynthetic gene clusters similar to nisin U, with a unique rearrangement of the core peptide encoding gene within the cluster. The 3100.8 Da peptide by MALDI-TOF mass spectrometry, is 75% identical to nisin A, with 10 differences, including 2 deletions: Ser29 and Ile30, and 8 substitutions: Ile4Lys, Gly18Thr, Asn20Pro, Met21Ile, His27Gly, Val32Phe, Ser33Gly, and Lys34Asn. Nisin E producing strains inhibited species of Lactobacillus, Bacillus, and Clostridiodes and were immune to nisin U. Sequence alignment identified putative promoter sequences across the nisin producer genera, allowing for the prediction of genes in Streptococcus to be potentially regulated by nisin. S. equinus pangenome BLAST analyses detected 6 nisin E operons across 44 publicly available genomes. An additional 20 genomes contained a subset of nisin E transport/immunity and regulatory genes (nseFEGRK), without adjacent peptide production genes. These genes suggest that nisin E response mechanisms, distinct from the canonical nisin immunity and resistance operons, are widespread across the S. equinus species. The discovery of this new nisin variant and its immunity determinants in S. equinus suggests a central role for nisin in the competitive nature of the species.", "token_count": 518, "char_count": 1671, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6767, "quality_score": 0.8384, "entities": { "genes": [ "APC4008", "APC4007" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:16.883392", "source": { "split": "train_shard_00001", "doc_id": 2558 }, "chunk_id": "train_shard_00001_2558_0", "global_id": 9308 }, { "text": "Nisin E Is a Novel Nisin Variant Produced by Multiple Streptococcus equinus Strains.", "token_count": 35, "char_count": 91, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:17.244956", "source": { "split": "train_shard_00001", "doc_id": 2558 }, "chunk_id": "train_shard_00001_2558_1", "global_id": 9309 }, { "text": "Water-buffalo Mozzarella (WBM) cheese is one of the several 'pasta filata' or stretched curd cheeses that originated in southern Italy, traditionally manufactured from raw milk employing natural whey starter cultures. Lactose- and galactose-fermenting yeasts isolated from WBM were studied to evaluate their role in the ripening of this cheese. The kinetic parameters of the growth of the yeasts as well as their principal metabolic end-products showed a great variability depending on the species. Moreover, the genetic polymorphism of the yeasts was studied for their differentiation at species level by means of the polymerase chain reaction (PCR) fingerprinting and mitochondrial DNA (mtDNA) restriction analysis. While the differentiation based on metabolic traits was not able to discriminate Kluyveromyces marxianus, Candida kefyr and C. sphaerica, the PCR analysis with primers M13 and RF2 resulted in a reliable and rapid method for differentiating at species level Saccharomyces cerevisiae, K. marxianus, K. lactis and their anamorphic species. Furthermore, mtDNA analysis proved to be more discriminating at strain level.\n\nPhenotypic and genotypic diversity of yeasts isolated from water-buffalo Mozzarella cheese.", "token_count": 309, "char_count": 1225, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [ "RF2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:17.813774", "source": { "split": "train_shard_00001", "doc_id": 2559 }, "chunk_id": "train_shard_00001_2559_0", "global_id": 9310 }, { "text": "

Background

Sinorhizobium meliloti is a model system for the studies of symbiotic nitrogen fixation. An extensive polymorphism at the genetic and phenotypic level is present in natural populations of this species, especially in relation with symbiotic promotion of plant growth. AK83 and BL225C are two nodule-isolated strains with diverse symbiotic phenotypes; BL225C is more efficient in promoting growth of the Medicago sativa plants than strain AK83. In order to investigate the genetic determinants of the phenotypic diversification of S. meliloti strains AK83 and BL225C, we sequenced the complete genomes for these two strains.

Results

With sizes of 7.14 Mbp and 6.97 Mbp, respectively, the genomes of AK83 and BL225C are larger than the laboratory strain Rm1021. The core genome of Rm1021, AK83, BL225C strains included 5124 orthologous groups, while the accessory genome was composed by 2700 orthologous groups. While Rm1021 and BL225C have only three replicons (Chromosome, pSymA and pSymB), AK83 has also two plasmids, 260 and 70 Kbp long. We found 65 interesting orthologous groups of genes that were present only in the accessory genome, consequently responsible for phenotypic diversity and putatively involved in plant-bacterium interaction. Notably, the symbiosis inefficient AK83 lacked several genes required for microaerophilic growth inside nodules, while several genes for accessory functions related to competition, plant invasion and bacteroid tropism were identified only in AK83 and BL225C strains. Presence and extent of polymorphism in regulons of transcription factors involved in symbiotic interaction were also analyzed", "token_count": 474, "char_count": 1663, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [ "BL225C", "AK83" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:18.460028", "source": { "split": "train_shard_00001", "doc_id": 2560 }, "chunk_id": "train_shard_00001_2560_0", "global_id": 9311 }, { "text": "Our results indicate that regulons are flexible, with a large number of accessory genes, suggesting that regulons polymorphism could also be a key determinant in the variability of symbiotic performances among the analyzed strains.

Conclusions

In conclusions, the extended comparative genomics approach revealed a variable subset of genes and regulons that may contribute to the symbiotic diversity.\n\nExploring the symbiotic pangenome of the nitrogen-fixing bacterium Sinorhizobium meliloti.", "token_count": 118, "char_count": 498, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7538, "quality_score": 0.8769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:18.838518", "source": { "split": "train_shard_00001", "doc_id": 2560 }, "chunk_id": "train_shard_00001_2560_1", "global_id": 9312 }, { "text": "

Background

Acinetobacter baumannii, a Gram-negative bacterium, is a public health threat due to its role in nosocomial infections and increasing antibiotic resistance. In Nigeria, data on the molecular epidemiology of A. baumannii is scarce. This study investigates the genetic diversity and the presence of antimicrobial resistance determinants and virulence-related genes in whole-genome sequencing data of 189 Nigerian A. baumannii isolates deposited in public repositories. Genotypes were determined in-silico by multilocus sequence typing (MLST) and core genome MLST (cgMLST). Further, antimicrobial resistance (AMR) and virulence-related genes were analyzed.

Results

Most isolates (57.67%) originated from South-west Nigeria. Isolates of human origin accounted for 33.86%, while environmental sources comprised 6.87%, and 59.27% lacked information on the source of isolation. The cgMLST analysis revealed a multitude of genomic lineages circulating in Nigeria. The MLST Oxford scheme identified 44 sequence types (STs) in 62.96% of strains, with ST1089 being the most prevalent. The MLST Pasteur could assign 95.77% of strains to 49 STs, with ST2(IC2) and ST85(IC9) being the most dominant. Antimicrobial resistance analysis detected 168 genes encoding resistance to 12 antibiotic classes, with cephalosporin, carbapenem, and aminoglycoside resistance genes being the most prevalent. Notably, blaADC-79 (23.81%), blaOXA-23 (30.69%), and aph(3″)-Ib (30%) were frequent variants encountered. Seventeen multi-efflux system genes conferring resistance to multiple antibiotic classes were identified", "token_count": 488, "char_count": 1637, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [ "ST2", "ST1089", "IC2", "ST85", "IC9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:19.494602", "source": { "split": "train_shard_00001", "doc_id": 2561 }, "chunk_id": "train_shard_00001_2561_0", "global_id": 9313 }, { "text": "Virulence gene analysis revealed 137 genes encoding six mechanisms, with genes for nutritional factors, effector delivery systems, and biofilm production being the most prevalent.

Conclusion

This study highlights the diversity in AMR and virulence genes of A. baumannii in Nigeria, emphasizing the need for ongoing genomic surveillance to inform infection control and develop antibiotic resistance management strategies.\n\nComprehensive molecular epidemiology of Acinetobacter baumannii from diverse sources in Nigeria.", "token_count": 117, "char_count": 525, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:19.874224", "source": { "split": "train_shard_00001", "doc_id": 2561 }, "chunk_id": "train_shard_00001_2561_1", "global_id": 9314 }, { "text": "The Escherichia coli sequence type (ST) 131 C2/H30Rx clade with the blaCTX-M-15 gene had been most responsible for the global dissemination of extended-spectrum β-lactamase (ESBL)-producing E. coli. ST131 C1/H30R with blaCTX-M-27 emerged among ESBL-producing E. coli in Japan during the late 2000s. To investigate the possible expansion of a single clade, we performed whole-genome sequencing for 43 Japan and 10 global ST131 isolates with blaCTX-M-27 (n = 16), blaCTX-M-14 (n = 16), blaCTX-M-15 (n = 13), and others (n = 8). We also included 8 ST131 genomes available in public databases. Core genome-based analysis of 61 isolates showed that ST131 with blaCTX-M-27 from 5 countries formed a distinct cluster within the C1/H30R clade, named C1-M27 clade. Accessory genome analysis identified a unique prophage-like region, supporting C1-M27 as a distinct clade. Our findings indicate that the increase of ESBL-producing E. coli in Japan is due mainly to emergence of the C1-M27 clade.\n\nGlobal Escherichia coli Sequence Type 131 Clade with blaCTX-M-27 Gene.", "token_count": 416, "char_count": 1145, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6149, "quality_score": 0.8075, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:20.495343", "source": { "split": "train_shard_00001", "doc_id": 2562 }, "chunk_id": "train_shard_00001_2562_0", "global_id": 9315 }, { "text": "The city of Sydney, Australia, experienced a persistent outbreak of Legionella pneumophila serogroup 1 (Lp1) pneumonia in 2016. To elucidate the source and bring the outbreak to a close we examined the genomes of clinical and environmental Lp1 isolates recovered over 7 weeks. A total of 48 isolates from patients and cooling towers were sequenced and compared using SNP-based, core-genome MLST and pangenome approaches. All three methods confirmed phylogenetic relatedness between isolates associated with outbreaks in the Central Business District (March and May) and Suburb 1. These isolates were designated “Main cluster” and consisted of isolates from two patients from the CBD March outbreak, one patient and one tower isolate from Suburb 1 and isolates from two cooling towers and three patients from the CDB May outbreak. All main cluster isolates were sequence type ST211 which has only ever been reported in Canada. Significantly, pangenome analysis identified mobile genetic elements containing a unique T4ASS that was specific to the main cluster and co-circulating clinical strains, suggesting a potential mechanism for increased fitness and persistence of the outbreak clone. Genome sequencing was key in deciphering the environmental sources of infection among the spatially and temporally coinciding cases of legionellosis in this highly populated urban setting. Further, the discovery of a unique T4ASS emphasises the potential contribution of genome recombination in the emergence of successful Lp1 clones.\n\nGenome sequencing links persistent outbreak of legionellosis in Sydney to an emerging clone ofLegionella pneumophilaST211", "token_count": 378, "char_count": 1654, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [ "ST211" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:21.076644", "source": { "split": "train_shard_00001", "doc_id": 2563 }, "chunk_id": "train_shard_00001_2563_0", "global_id": 9316 }, { "text": "Exo-inulinases are members of the glycoside hydrolase family 32 and function by hydrolyzing inulin into fructose with yields up to 90-95%. The N-terminal tail contributes to enzyme thermotolerance, which plays an important role in enzyme applications. However, the role of N-terminal amino acid residues in the thermal performance and structural properties of exo-inulinases remains to be elucidated. In this study, three and six residues of the N-terminus starting from Gln23 of the exo-inulinase InuAGN25 were deleted and expressed in Escherichia coli. After digestion with human rhinovirus 3 C protease to remove the N-terminal amino acid fusion sequence that may affect the thermolability of enzymes, wild-type RfsMInuAGN25 and its mutants RfsMutNGln23Δ3 and RfsMutNGln23Δ6 were produced. Compared with RfsMInuAGN25, thermostability of RfsMutNGln23Δ3 was enhanced while that of RfsMutNGln23Δ6 was slightly reduced. Compared with the N-terminal structures of RfsMInuAGN25 and RfsMutNGln23Δ6, RfsMutNGln23Δ3 had a higher content of (1) the helix structure, (2) salt bridges (three of which were organized in a network), (3) cation-π interactions (one of which anchored the N-terminal tail). These structural properties may account for the improved thermostability of RfsMutNGln23Δ3. The study provides a better understanding of the N-terminus-function relationships that are useful for rational design of thermostability of exo-inulinases.\n\nRemoval of N-terminal tail changes the thermostability of the low-temperature-active exo-inulinase InuAGN25.", "token_count": 462, "char_count": 1558, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:21.715320", "source": { "split": "train_shard_00001", "doc_id": 2564 }, "chunk_id": "train_shard_00001_2564_0", "global_id": 9317 }, { "text": "Vibrio anguillarum is a marine bacterium that can cause vibriosis in many fish and shellfish species, leading to high mortalities and economic losses in aquaculture. Although putative virulence factors have been identified, the mechanism of pathogenesis of V. anguillarum is not fully understood. Here, we analyzed whole-genome sequences of a collection of V. anguillarum strains and compared them to virulence of the strains as determined in larval challenge assays. Previously identified virulence factors were globally distributed among the strains, with some genetic diversity. However, the pan-genome revealed that six out of nine high-virulence strains possessed a unique accessory genome that was attributed to pathogenic genomic islands, prophage-like elements, virulence factors, and a new set of gene clusters involved in biosynthesis, modification, and transport of polysaccharides. In contrast, V. anguillarum strains that were medium to nonvirulent had a high degree of genomic homogeneity. Finally, we found that a phylogeny based on the core genomes clustered the strains with moderate to no virulence, while six out of nine high-virulence strains represented phylogenetically separate clusters. Hence, we suggest a link between genotype and virulence characteristics of Vibrio anguillarum, which can be used to unravel the molecular evolution of V. anguillarum and can also be important from survey and diagnostic perspectives. IMPORTANCE Comparative genome analysis of strains of a pathogenic bacterial species can be a powerful tool to discover acquisition of mobile genetic elements related to virulence. Here, we compared 28 V. anguillarum strains that differed in virulence in fish larval models. By pan-genome analyses, we found that six of nine highly virulent strains had a unique core and accessory genome. In contrast, V. anguillarum strains that were medium to nonvirulent had low genomic diversity", "token_count": 521, "char_count": 1988, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5516, "quality_score": 0.7758, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:22.372470", "source": { "split": "train_shard_00001", "doc_id": 2565 }, "chunk_id": "train_shard_00001_2565_0", "global_id": 9318 }, { "text": "Integration of genomic and phenotypic features provides insights into the evolution of V. anguillarum and can also be important for survey and diagnostic purposes.\n\nComparative Genome Analyses of Vibrio anguillarum Strains Reveal a Link with Pathogenicity Traits.", "token_count": 79, "char_count": 277, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:22.746993", "source": { "split": "train_shard_00001", "doc_id": 2565 }, "chunk_id": "train_shard_00001_2565_1", "global_id": 9319 }, { "text": "Plant growth-promoting rhizobacteria (PGPR) can produce hormone-like substances, promote plant nutrient uptake, enhance plant resistance, inhibit the growth of pathogenic bacteria, and induce plant resistance to biotic and abiotic stresses. Bacillus is one of the most studied genera that promote plant root development. Since its discovery in 2009, B. aryabhattai has shown promising properties such as promoting plant growth and improving crop yield. However, the mechanisms of B. aryabhattai promoting plant growth remain to be investigated. In this study, the chromosome of B. aryabhattai strain LAD and five plasmids within the cell were sequenced and annotated. The genome, with a length of 5,194,589 bp and 38.12% GC content, contains 5,288 putative protein-coding genes, 39 rRNA, and 112 tRNA. The length of the five plasmids ranged from 116,519 to 212,484 bp, and a total of 810 putative protein-coding genes, 4 rRNA, and 32 tRNA were predicted in the plasmids. Functional annotation of the predicted genes revealed numerous genes associated with indole-3 acetic acid (IAA) and exopolysaccharides (EPSs) biosynthesis, membrane transport, nitrogen cycle metabolism, signal transduction, cell mobility, stress response, and antibiotic resistance on the genome which benefits the plants. Genes of carbohydrate-active enzymes were detected in both the genome and plasmids suggesting that LAD has the capacity of synthesizing saccharides and utilizing organic materials like root exudates. LAD can utilize different carbon sources of varied carbon chain length, i.e., methanol, acetate, glycerol, glucose, sucrose, and starch for growth and temperature adaptation suggesting a high versatility of LAD for thriving in fluctuating environments", "token_count": 513, "char_count": 1773, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:23.375955", "source": { "split": "train_shard_00001", "doc_id": 2566 }, "chunk_id": "train_shard_00001_2566_0", "global_id": 9320 }, { "text": "LAD produced the most EPSs with sucrose as sole carbon source, and high concentration of IAA was produced when the maize plant was cultivated with LAD, which may enhance plant growth. LAD significantly stimulated the development of the maize root. The genome-based information and experimental evidence demonstrated that LAD with diverse metabolic capabilities and positive interactions with plants has tremendous potential for adaptation to the dynamic soil environments and promoting plant growth.\n\nMolecular mechanisms of plant growth promotion for methylotrophic Bacillus aryabhattai LAD.", "token_count": 130, "char_count": 599, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7229, "quality_score": 0.8614, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:23.808528", "source": { "split": "train_shard_00001", "doc_id": 2566 }, "chunk_id": "train_shard_00001_2566_1", "global_id": 9321 }, { "text": "Shigellosis is a diarrhoeal disease caused mainly by Shigella flexneri and Shigella sonnei . Infection from Shigella is thought to be largely self-limiting, with short- to medium- term and serotype-specific immunity provided following clearance. However, cases of men who have sex with men (MSM) associated shigellosis have been reported where Shigella of the same serotype were serially sampled from individuals between 1 to 1862 days apart, possibly due to persistent carriage or reinfection with the same serotype. Here, we investigate the accessory genome dynamics of MSM associated S. flexneri and S. sonnei isolates serially sampled from individual patients at various days apart. We find that pairs likely associated with persistent carriage infection and with smaller single nucleotide polymorphism (SNP) distance, demonstrated significantly less variation in accessory genome content than pairs likely associated with reinfection and with greater SNP-distance. We also observed evidence of antimicrobial resistance (AMR) acquisition during persistent Shigella infection, specifically the gain of extended spectrum beta-lactamase genes in two pairs associated with persistent carriage. Finally, we explored chromosomal structural variations and rearrangements in seven (5 chronic and 2 reinfection associated) pairs of S. flexneri 3a isolates from a MSM-associated epidemic sublineage, which revealed variations at several common regions across pairs. These variations were mediated by insertion sequence (IS) elements which facilitated plasticity of genetic material with a distinct predicted functional profile. This study provides insight on the variation of accessory genome dynamics and large structural genomic changes in Shigella during persistent infection.

Importance

Shigella spp are Gram-negative bacteria that are the etiological agent of shigellosis, the second most common cause of diarrhoeal illness globally, particularly among children under the age of 5 in low-income countries. In high-income countries, an alternative transmission pathway of sexually transmissible disease among men who have sex with men (MSM) is emerging as the dominant presentation of the disease", "token_count": 481, "char_count": 2203, "word_count": 305, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:24.465228", "source": { "split": "train_shard_00001", "doc_id": 2567 }, "chunk_id": "train_shard_00001_2567_0", "global_id": 9322 }, { "text": "Within MSM we have captured prolonged infection and/or recurrent infection with shigellae of the same serotype, challenging the belief that Shigella infection is short-lived, and confers homologous serotypic immunity. Using this recently-emerged transmission scenario we comprehensively characterise the genomic changes that occur over the course of individual infection with Shigella and uncover a distinct functional profile of variable genome regions in these globally important pathogens.\n\nAccessory genome dynamics and structural variation ofShigellafrom persistent infections", "token_count": 128, "char_count": 588, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7973, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:24.919354", "source": { "split": "train_shard_00001", "doc_id": 2567 }, "chunk_id": "train_shard_00001_2567_1", "global_id": 9323 }, { "text": "

Objectives

Klebsiella pneumoniae is a major opportunistic pathogen that is a member of the Enterobacteriaceae. Klebsiella pneumoniae causes pneumonia in mink and has become the primary infectious disease that limits mink farming. In this study, we report the draft genome sequence of a multidrug-resistant (MDR) strain of K. pneumoniae that harbours the mcr-1 gene isolated from a mink in China.

Methods

The agar microdilution method was used to determine the minimum inhibitory concentration of the strain. The entire genomic DNA was sequenced using an Illumina MiSeq platform. A multilocus sequence type (MLST) and a core genome SNP phylogenetic tree analysis with a heatmap of the resistance genes and virulence genes were performed.

Results

The size of the genome was 5451.826 kb, and it included one chromosome and one plasmid. The draft genome of K. pneumoniae indicated that the isolate was a member of MLST 661. Four types of virulence genes were detected. The results of antimicrobial susceptibility testing showed multiple drug resistance, and 17 resistance genes were identified.

Conclusion

The genome sequence reported in this study will help to reveal the key role of antibiotic resistance and pathogenic mechanisms. It will provide useful information for the role of mobile genetic elements in the adaptive translocation and spread of antimicrobial resistance.\n\nDraft genome sequence analysis of a mcr-1-producing Klebsiella pneumoniae ST661 isolated from a mink in China.", "token_count": 404, "char_count": 1515, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5753, "quality_score": 0.7877, "entities": { "genes": [ "ST661" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:25.570880", "source": { "split": "train_shard_00001", "doc_id": 2568 }, "chunk_id": "train_shard_00001_2568_0", "global_id": 9324 }, { "text": "Archaea are vital components of the human microbiome, yet their study within the gastrointestinal tract (GIT) is limited by the scarcity of cultured representatives. Our study presents a method for the targeted enrichment and isolation of methanogenic archaea from human fecal samples. The procedure combines methane breath testing, in silico metabolic modeling, media optimization, FACS, dilution series, and genomic sequencing through Nanopore technology. Additional analyzes include the co-cultured bacteriome, comparative genomics of archaeal genomes, functional comparisons, and structure-based protein function prediction of unknown differential traits. Successful establishment of stable archaeal cultures from 14 out of 16 fecal samples yielded nine previously uncultivated strains, eight of which are absent from a recent archaeome genome catalog. Comparative genomic and functional assessments of Methanobrevibacter smithii and Candidatus Methanobrevibacter intestini strains from individual donors revealed features potentially associated with gastrointestinal diseases. Our work broadens available archaeal representatives for GIT studies, and offers insights into Candidatus Methanobrevibacter intestini genomes' adaptability in critical microbiome contexts.\n\nTargeted isolation of Methanobrevibacter strains from fecal samples expands the cultivated human archaeome.", "token_count": 313, "char_count": 1380, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7093, "quality_score": 0.8547, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:26.135112", "source": { "split": "train_shard_00001", "doc_id": 2569 }, "chunk_id": "train_shard_00001_2569_0", "global_id": 9325 }, { "text": "

Background

Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called \"alphabet-plasmas\", and collectively dubbed \"E-plasma\", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.

Results

Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the \"E-plasma\" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of \"E-plasma\", which is much more developed than other representatives of the order Thermoplasmatales", "token_count": 442, "char_count": 1875, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [ "PM4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:26.771269", "source": { "split": "train_shard_00001", "doc_id": 2570 }, "chunk_id": "train_shard_00001_2570_0", "global_id": 9326 }, { "text": "In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.

Conclusions

This study has analysed the metagenome-assembled genome of \"E-plasma\", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.\n\nEvolutionary patterns of archaea predominant in acidic environment.", "token_count": 155, "char_count": 683, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7262, "quality_score": 0.8631, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:27.208047", "source": { "split": "train_shard_00001", "doc_id": 2570 }, "chunk_id": "train_shard_00001_2570_1", "global_id": 9327 }, { "text": "This work investigated the influence of compressed CO2 treatment on the enzymatic activity of immobilized inulinases, and the production of fructooligosacharides in aqueous medium using these enzymes. The effects of system pressure, exposure time and depressurization rate on the enzymatic activity were evaluated through central composite designs (CCD) 23. Inulinase from Kluyveromyces marxianus NRRL Y-7571 presented an increase of 104% in the residual activity using CO2 at 275bar submitted to 6h treatment, at a depressurization rate of 10kgm−3min−1. For Aspergillus niger commercial inulinase, a decrease in enzyme activity was observed (residual activity of 39%) using CO2 treatment at 75bar for 6h exposure at the highest depressurization rate (200kgm−3min−1). Enzymatic activities changed significantly depending on the enzyme source and the experimental treatment conditions investigated. The values of FOS obtained using inulinases from A. niger were 30.64% of GF2; 13.90% of GF3 and 2.88% of GF4 in the medium containing inulin as substrate. Results demonstrate that the use of compressed CO2 might be of technological importance as a preceding, preparation step, to improve enzyme activity, hence helping the development of new biotransformation processes.\n\nFructooligosacharides production in aqueous medium with inulinase from Aspergillus niger and Kluyveromyces marxianus NRRL Y-7571 immobilized and treated in pressurized CO2", "token_count": 392, "char_count": 1441, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5743, "quality_score": 0.7871, "entities": { "genes": [ "GF3", "CO2", "GF4", "GF2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:27.825003", "source": { "split": "train_shard_00001", "doc_id": 2571 }, "chunk_id": "train_shard_00001_2571_0", "global_id": 9328 }, { "text": "All land plants seal their above ground body parts with a lipid-rich hydrophobic barrier called the cuticle that protects tissues from dehydration and other terrestrial threats. Mutational studies in several model species, including barley, have resolved multiple loci regulating cuticular metabolism and development. Of particular importance are the eceriferum ( cer ) mutants characterized by visual alterations in cuticular wax. In barley, some cer mutants, such as cer-x lines, show defects in the distinctive β-diketone-enriched wax bloom on reproductive stage leaf sheaths, stems and spikes. In our study we exploited extensive allelic populations, near-isogenic lines and powerful genotyping platforms to identify variation in the HvWAX INDUCER1 ( HvWIN1 ) gene as causal for cer-x mutants. We show that HvWIN1 function reduces cuticular permeability, promotes the accumulation of β-diketones, and regulates cuticular metabolic gene expression. Analyses across the barley pangenome and hundreds of exome-capture datasets revealed high sequence conservation of HvWIN1 but also two non-synonymous variants exclusive to cultivated germplasm. Taken together, we suggest that variation in HvWIN1 controls multiple cuticular features in barley by controlling the expression of genes involved in cuticle development.\n\nA WAX INDUCER1/SHINE transcription factor controls cuticular wax in barley", "token_count": 339, "char_count": 1392, "word_count": 193, "semantic_coherence": 1, "information_density": 0.7098, "quality_score": 0.8549, "entities": { "genes": [ "INDUCER1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:28.399920", "source": { "split": "train_shard_00001", "doc_id": 2572 }, "chunk_id": "train_shard_00001_2572_0", "global_id": 9329 }, { "text": "

Purpose

Traditional epidemiological investigations of healthcare-associated Clostridioides difficile infection (HA-CDI) are often insufficient. This study aimed to evaluate a procedure that includes secondary isolation and genomic typing of single toxigenic colonies using core genome multilocus sequence typing (cgMLST) for the investigation of C. difficile transmission.

Methods

We analyzed retrospectively all toxigenic C. difficile-positive stool samples stored at the Lausanne University Hospital over 6 consecutive months. All isolates were initially typed and classified using a modified double-locus sequence typing (DLST) method. Genome comparison of isolates with the same DLST and clustering were subsequently performed using cgMLST. The electronic administrative records of patients with CDI were investigated for spatiotemporal epidemiological links supporting hospital transmission. A comparative descriptive analysis between genomic and epidemiological data was then performed.

Results

From January to June 2021, 86 C. difficile isolates were recovered from thawed samples of 71 patients. Thirteen different DLST types were shared by > 1 patient, and 13 were observed in single patients. A genomic cluster was defined as a set of isolates from different patients with ≤ 3 locus differences, determined by cgMLST. Seven genomic clusters were identified, among which plausible epidemiological links were identified in only 4/7 clusters.

Conclusion

Among clusters determined by cgMLST analysis, roughly 40% included unexplained HA-CDI acquisitions, which may be explained by unidentified epidemiological links, asymptomatic colonization, and/or shared common community reservoirs. The use of DLST, followed by whole genome sequencing analysis, is a promising and cost-effective stepwise approach for the investigation of CDI transmission in the hospital setting.\n\nCore genome multilocus sequence typing of Clostridioides difficile to investigate transmission in the hospital setting.", "token_count": 487, "char_count": 2024, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:29.055051", "source": { "split": "train_shard_00001", "doc_id": 2573 }, "chunk_id": "train_shard_00001_2573_0", "global_id": 9330 }, { "text": "Global use of single-use non-biodegradable plastics, like bottles made of polyethylene tereph-thalate (PET), have contributed to catastrophic levels of plastic pollution. Fortunately, microbi-al communities are adapting to assimilate plastic waste. Previously, our work showed a full consortium of five bacteria capable of synergistically degrading PET. Using omics approaches we identified key genes implicated in PET degradation within the consortium’s pangenome and transcriptome. This analysis led to the discovery of a novel PETase, EstB, discovered to hydrolyze oligomer BHET, and polymer PET. Besides genes implicated in PET degradation, many other biodegradation genes were discovered. Over 200 plastic and plasticizer degrada-tion related genes were discovered through the Plastic Microbial Biodegradation Database (PMBD). Diverse carbon source utilization was observed by a microbial community-based as-say, which paired with an abundant number of plastic and plasticizer degrading enzymes in-dicates a promising possibility for mixed plastic degradation. Using RNAseq differential analysis, several genes were predicted to be involved in PET degradation including aldehyde dehydrogenases and several classes of hydrolases. Active transcription of PET monomer me-tabolism was also observed, including the generation of polyhydroxyalkanoate (PHA) bi-opolymers. These results present an exciting opportunity for the bio-recycling of mixed plastic waste with upcycling potential.\n\nMicrobial Consortia and Mixed Plastic Waste: Pangenomic Analysis Reveals Potential for Degradation of Multiple Plastic Types via Previously Identified PET Degrading Bacteria", "token_count": 416, "char_count": 1667, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6728, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:29.676217", "source": { "split": "train_shard_00001", "doc_id": 2574 }, "chunk_id": "train_shard_00001_2574_0", "global_id": 9331 }, { "text": "Variable number tandem repeat sequences (VNTR) are composed of consecutive repeats of short segments of DNA with hypervariable repeat count and composition. They include protein coding sequences and associations with clinical disorders. It has been difficult to incorporate VNTR analysis in disease studies that use short-read sequencing because the traditional approach of mapping to the human reference is less effective for repetitive and divergent sequences. We solve VNTR mapping for short reads with a repeat-pangenome graph (RPGG), a data structure that encodes both the population diversity and repeat structure of VNTR loci from multiple haplotype-resolved assemblies. We developed software to build a RPGG, and use the RPGG to estimate VNTR composition with short reads. We used this to discover VNTRs with length stratified by continental population, and novel expression quantitative trait loci, indicating that RPGG analysis of VNTRs will be critical for future studies of diversity and disease.\n\nProfiling variable-number tandem repeat variation across populations using repeat-pangenome graphs", "token_count": 232, "char_count": 1108, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:30.153278", "source": { "split": "train_shard_00001", "doc_id": 2575 }, "chunk_id": "train_shard_00001_2575_0", "global_id": 9332 }, { "text": "In the fermentation process of henequen (Agave fourcroydes Lem.) leaf juice, complemented with industrial molasses, the use of an inoculum comprising two yeasts: Kluyveromyces marxianus (isolated from the henequen plant) and Saccharomyces cerevisiae (commercial strain) was studied. An ethanol production of 5.22+/-1.087% v/v was obtained. Contrary to expected, a decrease on ethanol production was observed with the use of the K. marxianus strain. The best results were obtained when a mixture of 25% K. marxianus and 75% S. cerevisiae or S. cerevisiae alone were used with an initial inoculum concentration of 3x10(7)cellmL(-1). Furthermore, it was possible to detect a final concentration of approximately 2-4gL(-1) of reducing sugars that are not metabolized by the yeasts for the ethanol production. These results show that although the use of a mixture of yeasts can be of interest for the production of alcoholic beverages, it can be the opposite in the case of ethanol production for industrial purposes where manipulation of two strains can raise the production costs.\n\nEthanol production from henequen (Agave fourcroydes Lem.) juice and molasses by a mixture of two yeasts.", "token_count": 329, "char_count": 1183, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5444, "quality_score": 0.7722, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:30.714392", "source": { "split": "train_shard_00001", "doc_id": 2576 }, "chunk_id": "train_shard_00001_2576_0", "global_id": 9333 }, { "text": "Horizontal gene transfer (HGT) is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer and about its effects on the recipient organism's physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ∼12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative, positive, and epistatic selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.\n\nAdaptive evolution of hybrid bacteria by horizontal gene transfer.", "token_count": 320, "char_count": 1479, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:31.286565", "source": { "split": "train_shard_00001", "doc_id": 2577 }, "chunk_id": "train_shard_00001_2577_0", "global_id": 9334 }, { "text": "

Background

Whole genome sequence (WGS)-based strain typing finds increasing use in the epidemiologic analysis of bacterial pathogens in both public health as well as more localized infection control settings.

Aims

This minireview describes methodologic approaches that have been explored for WGS-based epidemiologic analysis and considers the challenges and pitfalls of data interpretation.

Sources

Personal collection of relevant publications.

Content

When applying WGS to study the molecular epidemiology of bacterial pathogens, genomic variability between strains is translated into measures of distance by determining single nucleotide polymorphisms in core genome alignments or by indexing allelic variation in hundreds to thousands of core genes, assigning types to unique allelic profiles. Interpreting isolate relatedness from these distances is highly organism specific, and attempts to establish species-specific cutoffs are unlikely to be generally applicable. In cases where single nucleotide polymorphism or core gene typing do not provide the resolution necessary for accurate assessment of the epidemiology of bacterial pathogens, inclusion of accessory gene or plasmid sequences may provide the additional required discrimination.

Implications

As with all epidemiologic analysis, realizing the full potential of the revolutionary advances in WGS-based approaches requires understanding and dealing with issues related to the fundamental steps of data generation and interpretation.\n\nWhole genome sequencing options for bacterial strain typing and epidemiologic analysis based on single nucleotide polymorphism versus gene-by-gene-based approaches.", "token_count": 363, "char_count": 1699, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6714, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:31.864654", "source": { "split": "train_shard_00001", "doc_id": 2578 }, "chunk_id": "train_shard_00001_2578_0", "global_id": 9335 }, { "text": "Clostridium perfringens, a spore-forming bacterium that produces >20 toxins, is known to cause both human and animal intestinal diseases including; foodborne diarrhoea, preterm necrotising enterocolitis (NEC) and necrotic enteritis (NE) in chickens. Currently, there is very limited information on genomic virulence determinants, and the phylogenic and epidemiology landscape of this enteric pathogen, thus in this thesis I sought to comprehensively explore intestinal-associated C. perfringens strains using both genomic and phenotypic methodologies. Whole Genome Sequencing (WGS) and bioinformatic approaches was used to examine a novel collection of C. perfringens isolates and publically available genomes (n=552, including 109 public genomes) from a diverse range of hosts and disease states including; NEC-associated preterm infants, foodborne diarrhoea patients, NEassociated broilers, and healthy humans and animals. These genomes were analysed in combination or as discreet disease subsets to determine infection-linked virulence features, genomic epidemiology and hyper-virulent genotypes, and indicated a highly diverse pangenome (7.4% core genome), toxin-specific and novel virulence factors, widespread distribution ... (continues)\n\nThe role of Clostridium perfringens in intestinal diseases", "token_count": 328, "char_count": 1304, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7262, "quality_score": 0.8631, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:32.427965", "source": { "split": "train_shard_00001", "doc_id": 2579 }, "chunk_id": "train_shard_00001_2579_0", "global_id": 9336 }, { "text": "The filtrate from steam-pretreated poplar was analyzed to identify degradation compounds. The effect of selected compounds on growth and ethanolic fermentation of the thermotolerant yeast strain Kluyveromyces marxianus CECT 10875 was tested. Several fermentations on glucose medium, containing individual inhibitory compounds found in the hydrolysate, were carried out. The degree of inhibition on yeast strain growth and ethanolic fermentation was determined. At concentrations found in the prehy-drolysate, none of the individual compounds significantly affected the fermentation. For all tested compounds, growth was inhibited to a lesser extent than ethanol production. Lower concentrations of catechol (0.96 g/L) and 4-hydroxybenzaldehyde (1.02 g/L) were required to produce the 50% reduction in cell mass in comparison to other tested compounds.\n\nEffect of lignocellulosic degradation compounds from steam explosion pretreatment on ethanol fermentation by thermotolerant yeast Kluyveromyces marxianus.", "token_count": 265, "char_count": 1007, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6165, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:32.975613", "source": { "split": "train_shard_00001", "doc_id": 2580 }, "chunk_id": "train_shard_00001_2580_0", "global_id": 9337 }, { "text": "The nature of the toxic compounds produced by Saccharomyces cerevisiae CCMI 885 that induce the early death of Hanseniaspora guilliermondii during mixed fermentations, as well as their ability to inhibit the growth of other non-Saccharomyces wine-related strains, was investigated. The killing effect of mixed supernatants towards H. guilliermondii was inactivated by protease treatments, thus revealing the proteinaceous nature of the toxic compounds. Analysis of the protein pattern of mixed supernatants on Tricine SDS-PAGE showed that this S. cerevisiae strain secretes peptides (<10 kDa), which were detected only when death of H. guilliermondii was already established. Death-inducing supernatants were ultrafiltrated by 10 and 2 kDa membranes, respectively, and the inhibitory effect of those permeates were tested in H. guilliermondii cultures. Results indicated that the (2-10) kDa protein fraction of those supernatants seemed to contain antimicrobial peptides active against H. guilliermondii. Thus, the (2-10) kDa protein fraction was concentrated and its inhibitory effect tested against strains of Kluyveromyces marxianus, Kluyveromyces thermotolerans, Torulaspora delbrueckii and H. guilliermondii. Under the growth conditions used for these tests, the (2-10) kDa protein fraction of S. cerevisiae CCMI 885 supernatants exhibited a fungistatic effect against all the strains and a fungicidal effect against K. marxianus.\n\nSaccharomyces cerevisiae CCMI 885 secretes peptides that inhibit the growth of some non-Saccharomyces wine-related strains.", "token_count": 428, "char_count": 1560, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5352, "quality_score": 0.7676, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:33.599745", "source": { "split": "train_shard_00001", "doc_id": 2581 }, "chunk_id": "train_shard_00001_2581_0", "global_id": 9338 }, { "text": "Ustilago maydis is an important plant pathogen causing corn-smut disease and an effective biotechnological production host. The lack of a comprehensive metabolic overview hinders a full understanding of environmental adaptation and a full use of the organism’s metabolic potential. Here, we report the first genome scale metabolic model (GSMM) of Ustilago maydis (iUma22) for the simulation of metabolic activities. iUma22 was reconstructed from sequencing and annotation using PathwayTools, the biomass equation was derived from literature values and from the codon composition. The final model contains over 25% of annotated genes in the sequenced genome. Substrate utilization was corrected by Biolog-Phenotype arrays and exponential batch cultivations were used to test growth predictions. A pan-genome of four different U. maydis strains revealed missing metabolic pathways in iUma22. The majority of metabolic differences between iUma22 and the pangenome occurs in the inositol, purine and starch metabolic pathways. The new model allows studies of metabolic adaptations to different environmental niches as well as for biotechnological applications.\n\nA Genome-Scale Metabolic Model for the Smut-FungusUstilago maydis", "token_count": 307, "char_count": 1230, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:34.175796", "source": { "split": "train_shard_00001", "doc_id": 2582 }, "chunk_id": "train_shard_00001_2582_0", "global_id": 9339 }, { "text": "BackgroundVancomycin-resistant enterococci (VRE) are increasing in Denmark and Europe. Linezolid and vancomycin-resistant enterococci (LVRE) are of concern, as treatment options are limited. Vancomycin-variable enterococci (VVE) harbour the vanA gene complex but are phenotypically vancomycin-susceptible.AimThe aim was to describe clonal shifts for VRE and VVE in Denmark between 2015 and 2022 and to investigate genotypic linezolid resistance among the VRE and VVE.MethodsFrom 2015 to 2022, 4,090 Danish clinical VRE and VVE isolates were whole genome sequenced. We extracted vancomycin resistance genes and sequence types (STs) from the sequencing data and performed core genome multilocus sequence typing (cgMLST) analysis for Enterococcus faecium. All isolates were tested for the presence of mutations or genes encoding linezolid resistance.ResultsIn total 99% of the VRE and VVE isolates were E. faecium. From 2015 through 2019, 91.1% of the VRE and VVE were vanA E. faecium. During 2020, to the number of vanB E. faecium increased to 254 of 509 VRE and VVE isolates. Between 2015 and 2022, seven E", "token_count": 381, "char_count": 1143, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:34.761491", "source": { "split": "train_shard_00001", "doc_id": 2583 }, "chunk_id": "train_shard_00001_2583_0", "global_id": 9340 }, { "text": "faecium clusters dominated: ST80-CT14 vanA, ST117-CT24 vanA, ST203-CT859 vanA, ST1421-CT1134 vanA (VVE cluster), ST80-CT1064 vanA/vanB, ST117-CT36 vanB and ST80-CT2406 vanB. We detected 35 linezolid vancomycin-resistant E. faecium and eight linezolid-resistant VVEfm.ConclusionFrom 2015 to 2022, the numbers of VRE and VVE increased. The spread of the VVE cluster ST1421-CT1134 vanA E. faecium in Denmark is a concern, especially since VVE diagnostics are challenging. The finding of LVRE, although in small numbers, ia also a concern, as treatment options are limited.\n\nSurveillance of vancomycin-resistant enterococci reveals shift in dominating clusters from vanA to vanB Enterococcus faecium clusters, Denmark, 2015 to 2022.", "token_count": 339, "char_count": 816, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7374, "quality_score": 0.8687, "entities": { "genes": [ "CT14", "CT1064", "CT859", "CT2406", "CT1134", "ST1421", "ST117", "CT24", "CT36", "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:35.334784", "source": { "split": "train_shard_00001", "doc_id": 2583 }, "chunk_id": "train_shard_00001_2583_1", "global_id": 9341 }, { "text": "An extracellular β-glucanase secreted by Kluyveromyces marxianus was identified for the first time. The optimal conditions for the production of this enzyme were evaluated by response surface methodology. The optimal conditions to produce β-glucanase were a glucose concentration of 4% (w/v), a pH of 5.5, and an incubation temperature of 35 °C. Response surface methodology was also used to determine the pH and temperature required for the optimal enzymatic activity. The highest enzyme activity was obtained at a pH of 5.5 and a temperature of 55 °C. Furthermore, the enzyme was partially purified and sequenced, and its specificity for different substrates was evaluated. The results suggest that the enzyme is an endo-β-1,3(4)-glucanase. After optimizing the conditions for β-glucanase production, the culture supernatant was found to be effective in digesting the cell wall of the yeast Saccharomyces cerevisiae, showing the great potential of β-glucanase in the biotechnological production of soluble β-glucan.\n\nProduction and characterization of β-glucanase secreted by the yeast Kluyveromyces marxianus.", "token_count": 305, "char_count": 1112, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5466, "quality_score": 0.7733, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:35.903627", "source": { "split": "train_shard_00001", "doc_id": 2584 }, "chunk_id": "train_shard_00001_2584_0", "global_id": 9342 }, { "text": "Long-term care facilities (LTCFs) for older people play an important and unique role in multidrug-resistant organism transmission. Herein, we investigated the genetic characteristics of mobile colistin resistance gene (mcr-1)-carrying Escherichia coli strains isolated from wastewater of LTCFs in Shanghai. Antimicrobial susceptibility test was carried out by agar dilution methods. Whole-genome sequencing and plasmid sequencing were conducted, and resistance genes and sequence types of colistin in E. coli isolates were analyzed. Core genome multilocus sequence typing (cgMLST) analysis was performed by the Ridom SeqSphere+ software. Phylogenetic tree through the maximum likelihood method was constructed by MEGA X. Out of 306 isolates, only 1 E. coli named ECSJ33 was found, and the plasmid pECSJ33 from ECSJ33 harbored the mcr-1 gene that was located with 59,080 bp belonging to IncI2 type. The plasmid pECSJ33 was capable of conjugation with an efficiency of 2.9 × 10-2. Bioinformatic analysis indicated pECSJ33 shared backbone with the previously reported mcr-1-harboring pHNGDF93 isolated from fish source. Moreover, the cgMLST analysis revealed that ECSJ33 belongs to different lineages from those reported from previous E. coli strains but shared high similarity to NCTC11129 in cluster 11. The phylogenetic tree revealed MCR-1 of ECSJ33 in this study was mostly of animal food origin and that they were closely related. Our study firstly reports detection of genome sequence of a multidrug-resistant mcr-1-harboring E. coli ST155 from wastewater of LTCF source in China", "token_count": 502, "char_count": 1656, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [ "ST155", "ECSJ33", "NCTC11129" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:36.568223", "source": { "split": "train_shard_00001", "doc_id": 2585 }, "chunk_id": "train_shard_00001_2585_0", "global_id": 9343 }, { "text": "The data may prove that the plasmid pECSJ33 belongs to food origin and help to understand the antimicrobial resistance mechanisms and genomic features of colistin resistance under One Health approach.IMPORTANCEOne Escherichia coli named ECSJ33 was found from wastewater of a long-term care facility (LTCF) and the plasmid pECSJ33 from ECSJ33 harbored the mobile colistin resistance gene (mcr-1) that was located with 59,080 bp belonging to IncI2 type, which was capable of conjugation with an efficiency of 2.9 × 10-2. This paper firstly reports an mcr-1-carrying E. coli strain ST155 isolated from LTCF in China. Comparative genomics analysis indicated pECSJ33 shared backbone with the previously reported mcr-1-harboring pHNGDF93 isolated from fish source. The phylogenetic tree revealed MCR-1 protein of ECSJ33 in this study was mostly of animal food origin and that they were closely related. Therefore, the pECSJ33 could be considered as food-origin transmission mcr-1-harboring plasmid.\n\nGenetic epidemiology and plasmid-mediated transmission of mcr-1 by Escherichia coli ST155 from wastewater of long-term care facilities.", "token_count": 378, "char_count": 1196, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [ "ST155", "ECSJ33" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:37.160093", "source": { "split": "train_shard_00001", "doc_id": 2585 }, "chunk_id": "train_shard_00001_2585_1", "global_id": 9344 }, { "text": "Inflammatory bowel disease and food allergies are a growing topic in the field of nutrition science. Polyphenols, which are the most important secondary metabolites of plants, demonstrated to modulate the expression and/or production of numerous proteins, but also to regulate the intestinal ecosystem. In this context, our aim was the investigation of protective effects against the gastrointestinal mucosa of fortified milk kefir obtained by adding seeds extract from Sangiovese cv. Pomace. Methods: An ultrasound-assisted method was used to obtain the extracts. All the extracts were assayed for the antioxidant activity. The best extract was used as an additive of fermented milk kefir to obtain a fortified final product. Kefir samples were analyzed by NMR spectroscopy. The efficiency of the barrier functions was evaluated by measuring trans-epithelial electric resistance (TEER) using a voltmeter. Results: the enriched kefir (Ksgn) possesses higher antioxidant performances compared to the unfortified sample (Kwht). Kwht and Ksgn did not alter Caco-2 TEER in basal condition.\n\nSangiovese cv Pomace Seeds Extract-Fortified Kefir Exerts Anti-Inflammatory Activity in an In Vitro Model of Intestinal Epithelium Using Caco-2 Cells.", "token_count": 339, "char_count": 1258, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6966, "quality_score": 0.8483, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:37.772221", "source": { "split": "train_shard_00001", "doc_id": 2586 }, "chunk_id": "train_shard_00001_2586_0", "global_id": 9345 }, { "text": "Leptospirosis is a globally distributed zoonotic disease. The standard serological test, known as Microscopic Agglutination Test (MAT), requires the use of live Leptospira strains. To enhance its sensitivity and specificity, the usage of locally circulating strains is recommended. However, to date, no local strain is available from Austria. This study aimed to isolate circulating Leptospira strains from cattle in Austria to enhance the performances of the routine serological test for both humans and animals. We used a statistical approach combined with a comprehensive literature search to profile cattle with greater risk of leptospirosis infection and implemented a targeted sampling between November 2021 and October 2022. Urine and/or kidney tissue were sampled from 410 cattle considered at higher risk of infection. Samples were inoculated into EMJH-STAFF culture media within 2-6 hours and a PCR assay was used to confirm the presence/absence of pathogenic Leptospira in each sample. Isolates were further characterised by core genome multilocus sequence typing (cgMLST). Nine out of 429 samples tested positive by PCR, from which three isolates were successfully cultured and identified as Leptospira borgpetersenii serogroup Sejroe serovar Hardjobovis, cgMLST cluster 40. This is the first report on the isolation and genotyping of local zoonotic Leptospira in Austria, which holds the potential for a significant improvement in diagnostic performance in the country. Although the local strain was identified as a cattle-adapted serovar, it possesses significant zoonotic implications. Furthermore, this study contributes to a better understanding of the epidemiology of leptospirosis in Europe.\n\nFirst isolation and genotyping of pathogenic Leptospira spp. from Austria", "token_count": 426, "char_count": 1785, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:38.402749", "source": { "split": "train_shard_00001", "doc_id": 2587 }, "chunk_id": "train_shard_00001_2587_0", "global_id": 9346 }, { "text": "Professor Pangloss and the Pangenome: Does <i>Staphylococcus aureus</i> Have the Best of All Possible Worlds?", "token_count": 44, "char_count": 121, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:38.765815", "source": { "split": "train_shard_00001", "doc_id": 2588 }, "chunk_id": "train_shard_00001_2588_0", "global_id": 9347 }, { "text": "The fluoroquinolone-resistant sequence type 1193 (ST1193) of Escherichia coli, from the ST14 clonal complex (STc14) within phylogenetic group B2, has appeared recently as an important cause of extraintestinal disease in humans. Although this emerging lineage has been characterized to some extent using conventional methods, it has not been studied extensively at the genomic level. Here, we used whole-genome sequence analysis to compare 355 ST1193 isolates with 72 isolates from other STs within STc14. Using core genome phylogeny, the ST1193 isolates formed a tightly clustered clade with many genotypic similarities, unlike ST14 isolates. All ST1193 isolates possessed the same set of three chromosomal mutations conferring fluoroquinolone resistance, carried the fimH64 allele, and were lactose non-fermenting. Analysis revealed an evolutionary progression from K1 to K5 capsular types and acquisition of an F-type virulence plasmid, followed by changes in plasmid structure congruent with genome phylogeny. In contrast, the numerous identified antimicrobial resistance genes were distributed incongruently with the underlying phylogeny, suggesting frequent gain or loss of the corresponding resistance gene cassettes despite retention of the presumed carrier plasmids. Pangenome analysis revealed gains and losses of genetic loci occurring during the transition from ST14 to ST1193 and from the K1 to K5 capsular types. Using time-scaled phylogenetic analysis, we estimated that current ST1193 clades first emerged approximately 25 years ago. Overall, ST1193 appears to be a recently emerged clone in which both stepwise and mosaic evolution have contributed to epidemiologic success.\n\nPhylogenomic Analysis of Extraintestinal Pathogenic Escherichia coli Sequence Type 1193, an Emerging Multidrug-Resistant Clonal Group.", "token_count": 499, "char_count": 1847, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8413, "entities": { "genes": [ "ST1193", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:39.420564", "source": { "split": "train_shard_00001", "doc_id": 2589 }, "chunk_id": "train_shard_00001_2589_0", "global_id": 9348 }, { "text": "Shigellosis is a gastrointestinal infection caused by species of Shigella. A large outbreak of Shigella flexneri serotype 2a occurred in Albuquerque, New Mexico between May 2021 and November 2023 that involved humans and non-human primates (NHP) from a local zoo. We analyzed the genomes of 202 New Mexican isolates as well as 15 closely related isolates from other states, and four from NHP. The outbreak was initially detected within men who have sex with men but then predominantly affected people experiencing homelessness. Nearly 70% of cases were hospitalized and there was one human death. The outbreak extended into Albuquerque's BioPark Zoo, causing high morbidity and six deaths in NHPs. All isolates were multidrug-resistant, including towards fluoroquinolones, a first line treatment option which led to treatment failures in human and NHP populations. We show the circulation of the same S. flexneri strain in humans and NHPs, causing fatalities in both populations. This study demonstrates the threat of antimicrobial resistant organisms to vulnerable human and NHP populations and emphasizes the value of genomic surveillance within a One Health framework.\n\nMultidrug-resistant Shigella flexneri outbreak affecting humans and non-human primates in New Mexico, USA.", "token_count": 310, "char_count": 1279, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:39.992106", "source": { "split": "train_shard_00001", "doc_id": 2590 }, "chunk_id": "train_shard_00001_2590_0", "global_id": 9349 }, { "text": "Streptomyces rimosus is best known as the primary source of the tetracycline class of antibiotics, most notably oxytetracycline, which have been widely used against many gram-positive and gram-negative pathogens and protozoan parasites. However, despite the medical and agricultural importance of S. rimosus, little is known of its evolutionary history and genome dynamics. In this study, we aim to elucidate the pan-genome characteristics and phylogenetic relationships of 32 S. rimosus genomes. The S. rimosus pan-genome contains more than 22,000 orthologous gene clusters, and approximately 8.8% of these genes constitutes the core genome. A large part of the accessory genome is composed of 9,646 strain-specific genes. S. rimosus exhibits an open pan-genome (decay parameter α = 0.83) and high gene diversity between strains (genomic fluidity φ = 0.12). We also observed strain-level variation in the distribution and abundance of biosynthetic gene clusters (BGCs) and that each individual S. rimosus genome has a unique repertoire of BGCs. Lastly, we observed variation in recombination, with some strains donating or receiving DNA more often than others, strains that tend to frequently recombine with specific partners, genes that often experience recombination more than others, and variable sizes of recombined DNA sequences. We conclude that the high levels of inter-strain genomic variation in S. rimosus is partly explained by differences in recombination among strains. These results have important implications on current efforts for natural drug discovery, the ecological role of strain-level variation in microbial populations, and addressing the fundamental question of why microbes have pan-genomes.\n\nWithin-Species Genomic Variation and Variable Patterns of Recombination in the Tetracycline Producer Streptomyces rimosus.", "token_count": 506, "char_count": 1898, "word_count": 262, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:40.650060", "source": { "split": "train_shard_00001", "doc_id": 2591 }, "chunk_id": "train_shard_00001_2591_0", "global_id": 9350 }, { "text": "Even closely related prokaryotes often show an astounding diversity in their ability to grow in different nutritional environments. It has been hypothesized that complex metabolic adaptations-those requiring the independent acquisition of multiple new genes-can evolve via selectively neutral intermediates. However, it is unclear whether this neutral exploration of phenotype space occurs in nature, or what fraction of metabolic adaptations is indeed complex. Here, we reconstruct metabolic models for the ancestors of a phylogeny of 53 Escherichia coli strains, linking genotypes to phenotypes on a genome-wide, macroevolutionary scale. Based on the ancestral and extant metabolic models, we identify 3,323 phenotypic innovations in the history of the E. coli clade that arose through changes in accessory genome content. Of these innovations, 1,998 allow growth in previously inaccessible environments, while 1,325 increase biomass yield. Strikingly, every observed innovation arose through the horizontal acquisition of a single DNA segment less than 30 kb long. Although we found no evidence for the contribution of selectively neutral processes, 10.6% of metabolic innovations were facilitated by horizontal gene transfers on earlier phylogenetic branches, consistent with a stepwise adaptation to successive environments. Ninety-eight percent of metabolic phenotypes accessible to the combined E. coli pangenome can be bestowed on any individual strain by transferring a single DNA segment from one of the extant strains. These results demonstrate an amazing ability of the E. coli lineage to adapt to novel environments through single horizontal gene transfers (followed by regulatory adaptations), an ability likely mirrored in other clades of generalist bacteria.\n\nEach of 3,323 metabolic innovations in the evolution of E. coli arose through the horizontal transfer of a single DNA segment.", "token_count": 470, "char_count": 1937, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6347, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:41.298990", "source": { "split": "train_shard_00001", "doc_id": 2592 }, "chunk_id": "train_shard_00001_2592_0", "global_id": 9351 }, { "text": "New Zealand is a remote country in the South Pacific Ocean. The isolation and relatively late arrival of humans into New Zealand has meant there is a recorded history of the introduction of domestic species. Honey bees (Apis mellifera) were introduced to New Zealand in 1839, and the disease American foulbrood was subsequently found in the 1870s. Paenibacillus larvae, the causative agent of American foulbrood, has been genome sequenced in other countries. We sequenced the genomes of P. larvae obtained from 164 New Zealand apiaries where American foulbrood was identified in symptomatic hives during visual inspection. Multi-locus sequencing typing (MLST) revealed the dominant sequence type to be ST18, with this clonal cluster accounting for 90.2% of isolates. Only two other sequence types (with variants) were identified, ST5 and ST23. ST23 was only observed in the Otago area, whereas ST5 was limited to two geographically non-contiguous areas. The sequence types are all from the enterobacterial repetitive intergenic consensus I (ERIC I) genogroup. The ST18 and ST5 from New Zealand and international P. larvae all clustered by sequence type. Based on core genome MLST and SNP analysis, localized regional clusters were observed within New Zealand, but some closely related genomes were also geographically dispersed, presumably due to hive movements by beekeepers.\n\nGenomic analysis of the population structure of Paenibacillus larvae in New Zealand.", "token_count": 395, "char_count": 1497, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6516, "quality_score": 0.8258, "entities": { "genes": [ "ST5", "ST18", "ST23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:41.916206", "source": { "split": "train_shard_00001", "doc_id": 2593 }, "chunk_id": "train_shard_00001_2593_0", "global_id": 9352 }, { "text": "An early example of Big data in biology: how a mathematical model, developed to address a practical question in vaccinology, transformed established concepts, opening biology to the “unbounded.”\n\nThe Pangenome: A Data-Driven Discovery in Biology", "token_count": 57, "char_count": 245, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:42.281351", "source": { "split": "train_shard_00001", "doc_id": 2594 }, "chunk_id": "train_shard_00001_2594_0", "global_id": 9353 }, { "text": "Error correction is the canonical first step in long-read sequencing data analysis. The current standard is to make use of a consensus sequence as a template. However, in mixed samples, such as metagenomes or organisms of higher ploidy, consensus induced biases can mask true variants affecting haplotypes of lower frequencies, because they are mistaken as errors. The novelty presented here is to use graph based, instead of sequence based consensus as a template for identifying errors. The advantage is that graph based reference systems also capture variants of lower frequencies, so do not mistakenly mask them as errors. We present VeChat, as a novel approach to implement this idea: VeChat distinguishes errors from haplotype-specific true variants based on variation graphs, which reflect a popular type of data structure for pangenome reference systems. Upon initial construction of an ad-hoc variation graph from the raw input reads, nodes and edges that are due to errors are pruned from that graph by way of an iterative procedure that is based on principles from frequent itemset mining. Upon termination, the graph exclusively contains nodes and edges reflecting true sequential phenomena. Final re-alignments of the raw reads indicate where and how reads need to be corrected. Extensive benchmarking experiments demonstrate that PacBio and ONT reads corrected by VeChat contain 4 to 15, or, respectively, 2 to 10 times less errors than when corrected state of the art approaches. VeChat is implemented in an easy-to-use open-source tool and publicly available at https://github.com/HaploKit/vechat .\n\nVeChat: Correcting errors in long reads using variation graphs", "token_count": 360, "char_count": 1678, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6328, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:42.863838", "source": { "split": "train_shard_00001", "doc_id": 2595 }, "chunk_id": "train_shard_00001_2595_0", "global_id": 9354 }, { "text": "

ABSTRACT

Most of the extraintestinal human infections worldwide are determined by some specific Extraintestinal Pathogenic Escherichia coli (ExPEC) lineages, which also present a zoonotic character. One of these lineages belongs to ST38, which is considered a uropathogenic/enteroaggregative E. coli hybrid and a high-risk globally disseminated ExPEC. To get insights on the aspects of ST38 epidemiology and evolution as a multidrug resistant and pathogenic lineage, this study performed a global comparative genomic analysis on ST38 genomes. A total of 376 genomes recovered from environments, humans, livestock, wild and domestic animals in all continents throughout three decades were analyzed considering the ST38 phylogenomics, resistome, plasmidome, and virulome. In general, our analyses revealed that, independently of host sources and geographic origin, these genomes were distributed in two clusters comprising clonal and non-clonal genomes. Moreover, the ST38 accessory genome was not strictly associated with clusters and sub-clusters. Interestingly, the High Pathogenicity Island (HPI) prevailed in the major cluster (cluster 2), which comprised most of the genomes from human origin recovered worldwide (2000 to 2020). In addition, the ExPEC ST38 harbors a huge and diverse plasmidome that might contribute to the evolution of this lineage, reflecting in ST38 ability to live in a diversity of niches as a commensal or pathogenic organism.\n\nGlobal genomic epidemiology, resistome, virulome and plasmidome of the Extraintestinal Pathogenic Escherichia coli (ExPEC) ST38 lineage", "token_count": 427, "char_count": 1606, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [ "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:43.494658", "source": { "split": "train_shard_00001", "doc_id": 2596 }, "chunk_id": "train_shard_00001_2596_0", "global_id": 9355 }, { "text": "Age-related neurodegenerative diseases involving amyloid aggregation remain one of the biggest challenges of modern medicine. Alterations in the gastrointestinal microbiome play an active role in the aetiology of neurological disorders. Here, we dissect the amyloidogenic properties of biofilm-associated proteins (BAPs) of the gut microbiota and their implications for synucleinopathies. We demonstrate that BAPs are naturally assembled as amyloid-like fibrils in insoluble fractions isolated from the human gut microbiota. We show that BAP genes are part of the accessory genomes, revealing microbiome variability. Remarkably, the abundance of certain BAP genes in the gut microbiome is correlated with Parkinson's disease (PD) incidence. Using cultured dopaminergic neurons and Caenorhabditis elegans models, we report that BAP-derived amyloids induce α-synuclein aggregation. Our results show that the chaperone-mediated autophagy is compromised by BAP amyloids. Indeed, inoculation of BAP fibrils into the brains of wild-type mice promote key pathological features of PD. Therefore, our findings establish the use of BAP amyloids as potential targets and biomarkers of α-synucleinopathies.\n\nGut microbiota produces biofilm-associated amyloids with potential for neurodegeneration.", "token_count": 341, "char_count": 1285, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:44.060349", "source": { "split": "train_shard_00001", "doc_id": 2597 }, "chunk_id": "train_shard_00001_2597_0", "global_id": 9356 }, { "text": "

Background

Candiduria is a common infection among hospitalised patients. Although the clinical relevance of yeasts in urine is not clearly defined, fungal urinary tract infections have increased significantly in the last decades, becoming a growing public health problem. Candida albicans is the most commonly reported species in urinary infections, although other species of the genus are becoming particularly important, because some of them are linked with resistance to antifungal drugs.

Aims

This study aimed to evaluate the frequency of Candida species causing candiduria in a hospital in Honduras.

Methods

A simple and cost-effective PCR-RFLP approach was used, by amplifying a partial sequence of the ribosomal ITS1-ITS2 region and a subsequent digestion with the enzyme MspI.

Results

During 2016, an analysis was performed on 73 urine samples from patients of different ages. Seven species were found. Candida albicans/dubliniensis was the most frequent species (30%); Candida glabrata (28.8%) was the most isolated among the rest of the species. Candida kefyr was the least frequent species found (2.5%).

Conclusions

This study shows, for the first time in Honduras, the frequency of the Candida species isolated from urine using PCR-RFLP for their identification. This approach could be applied in future epidemiological studies at local and national level.\n\nMolecular identification of Candida species from urinary infections in Honduras.", "token_count": 374, "char_count": 1486, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8137, "entities": { "genes": [ "ITS2", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:44.640673", "source": { "split": "train_shard_00001", "doc_id": 2598 }, "chunk_id": "train_shard_00001_2598_0", "global_id": 9357 }, { "text": "Stenotrophomonas maltophilia is a Gram-negative opportunistic pathogen that can infect the lungs of people with cystic fibrosis (CF). The highly viscous mucus in the CF lung, expectorated as sputum, serves as the primary nutrient source for microbes colonizing this site and induces virulence-associated phenotypes and gene expression in several CF pathogens. Here, we characterized the transcriptional responses of three S. maltophilia strains during exposure to synthetic CF sputum medium (SCFM2) to gain insight into how this organism interacts with the host in the CF lung. These efforts led to the identification of 881 transcripts differentially expressed by all three strains, many of which reflect the metabolic pathways used by S. maltophilia in sputum, as well as altered stress responses. The latter correlated with increased resistance to peroxide exposure after pregrowth in SCFM2 for two of the strains. We also compared the SCFM2 transcriptomes of two S. maltophilia CF isolates to that of the acute infection strain, S. maltophilia K279a, allowing us to identify CF isolate-specific signatures in differential gene expression. The expression of genes from the accessory genomes was also differentially altered in response to SCFM2. Finally, a number of biofilm-associated genes were differentially induced in SCFM2, particularly in K279a, which corresponded to increased aggregation and biofilm formation in this strain relative to both CF strains. Collectively, this work details the response of S. maltophilia to an environment that mimics important aspects of the CF lung, identifying potential survival strategies and metabolic pathways used by S. maltophilia during infections.IMPORTANCEStenotrophomonas maltophilia is an important infecting bacterium in the airways of people with cystic fibrosis (CF). However, compared to the other CF pathogens, S. maltophilia has been relatively understudied", "token_count": 525, "char_count": 1987, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5668, "quality_score": 0.7834, "entities": { "genes": [ "SCFM2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:45.297288", "source": { "split": "train_shard_00001", "doc_id": 2599 }, "chunk_id": "train_shard_00001_2599_0", "global_id": 9358 }, { "text": "The significance of our research is to provide insight into the global transcriptomic changes of S. maltophilia in response to a medium that was designed to mimic important aspects of the CF lung. This study elucidates the overall metabolic changes that occur when S. maltophilia encounters the CF lung and generates a road map of candidate genes to test using in vitro and in vivo models of CF.\n\nStenotrophomonas maltophilia Differential Gene Expression in Synthetic Cystic Fibrosis Sputum Reveals Shared and Cystic Fibrosis Strain-Specific Responses to the Sputum Environment.", "token_count": 179, "char_count": 613, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6966, "quality_score": 0.8483, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:45.745688", "source": { "split": "train_shard_00001", "doc_id": 2599 }, "chunk_id": "train_shard_00001_2599_1", "global_id": 9359 }, { "text": "Maize was cofermented with pigeon pea for ogi production and evaluated for microbiological qualities. White maize and pigeon pea were mixed at ratios of 90:10, 80:20, 70:30, 60:40, and 50:50, respectively, with 100:0 serving as the control. Mixtures were cofermented for 96 h at 27 ± 2°C, and microbiological and sensory qualities analyzed were carried out using analysis of variance. Values were significant at p ≤ .05. Results showed that there was a gradual decrease in the pH and increase in total titratable acidity (TTA), respectively, during fermentation in all the samples. At the end of fermentation, pH ranged from 3.47 to 4.27 and TTA ranged from 0.47% to 0.54%, respectively. Total heterotrophic count (THPC) ranged from 5.76 to 5.90 log cfu/g; lactic acid bacteria (LAB) from 6.15 to 5.98 log cfu/g; and yeasts from 5.51 to 5.79 log cfu/g. Microorganisms isolated were lactic acid bacteria (Lactobacillus buchneri, L. casei, L. pentosus, Pediococcus pentosaceus), yeasts (Saccharomyces cerevisiae, Candida kefyr, C. krusei, C. tropicalis), molds (Aspergillus niger, A. flavus, Penicillium oxalicum, Mucor racemosus and Rhizopus stolonifer) and other aerobic bacteria (Klebsiella oxytoca, Enterobacter amnigenus, Staphylococcus xylosus, Bacillus subtilis, B", "token_count": 511, "char_count": 1321, "word_count": 188, "semantic_coherence": 1, "information_density": 0.7128, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:46.379696", "source": { "split": "train_shard_00001", "doc_id": 2600 }, "chunk_id": "train_shard_00001_2600_0", "global_id": 9360 }, { "text": "firmus, Corynebacterium kutscheri, C. striatum, and C. afermentans). In conclusion, the total heterotrophic plate count (THPC) in fortified maize: pigeon pea products was very high. This could constitute health hazards to infants as weaning foods. However, the microbial loads could be reduced through heat treatment as ogi is usually boiled or treated with boiled water before consumption and it can therefore be concluded that the fortified maize: pigeon pea products could be used as weaning foods.\n\nMicrobiological assessment of maize ogi cofermented with pigeon pea.", "token_count": 160, "char_count": 582, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7529, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:46.829358", "source": { "split": "train_shard_00001", "doc_id": 2600 }, "chunk_id": "train_shard_00001_2600_1", "global_id": 9361 }, { "text": "

Background

Hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) has been spreading rapidly worldwide. Here, we investigated the genomic characteristics of ST11 K. pneumoniae isolate SM117 with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 and multiple plasmid-borne virulence genes from a county level hospital in China.

Methods

Antimicrobial susceptibility of K. pneumoniae SM117 was evaluated. The Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms were applied to sequence the genome and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, antibiotic resistance genes, plasmid replicon types and virulence genes. The phylogenetic analysis was performed based on the core genome single nucleotide polymorphisms (cgSNPs) using CSI Phylogeny 1.4, and further visualized by Interactive Tree of Life (iTOL) V5 web server.

Results

The whole-genome sequence of K. pneumoniae SM117 is made up of eight contigs totaling 6,104,486 bp, contain a 5,612,620 bp single chromosome and seven plasmids. The isolate was assigned to ST11 with capsular serotype KL25, co-carrying including bla NDM-5, bla KPC-2 and multiple plasmid-borne virulence genes including rmpA2 and aerobactin genes iucABCD-iutA", "token_count": 519, "char_count": 1501, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6559, "quality_score": 0.828, "entities": { "genes": [ "SM117", "KL25", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:47.843105", "source": { "split": "train_shard_00001", "doc_id": 2601 }, "chunk_id": "train_shard_00001_2601_0", "global_id": 9362 }, { "text": "The coexistence of bla KPC and bla NDM in K. pneumoniae strains exhibit a high degree of resistance to β-lactam antibiotics. The strain SM117 also carries multiple antibiotic resistance genes, making it resistant to all antibiotics except polymyxin. The closest relative of K. pneumoniae C793 was identified in 2023 from a hospital surface sample in Zhejiang, China, with just 52 SNPs difference.

Conclusion

This study reported the genomic characteristics of a multidrug-resistant ST11 K. pneumoniae with capsular serotype KL25, co-carrying bla NDM-5, two copies of bla KPC-2 genes and multiple plasmid-borne virulence genes in China. These findings will provide important knowledge of the antibiotic resistance mechanisms, genomic epidemiological characteristics and transmission dynamics of multidrug-resistant K. pneumoniae.\n\nGenomic Characteristics of a Carbapenem-Resistant Klebsiella pneumoniae Co-Carrying bla NDM-5 and bla KPC-2 Capsular Type KL25 Recovered from a County Level Hospital in China.", "token_count": 391, "char_count": 1154, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [ "SM117", "KL25", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:48.480688", "source": { "split": "train_shard_00001", "doc_id": 2601 }, "chunk_id": "train_shard_00001_2601_1", "global_id": 9363 }, { "text": "A total of 16 different strains of Microbacterium spp. were isolated from contaminated soil and enriched on the carcinogen, hexavalent chromium [Cr(VI)]. The majority of the isolates (11 of the 16) were able to tolerate concentrations (0.1 mM) of cobalt, cadmium, and nickel, in addition to Cr(VI) (0.5-20 mM). Interestingly, these bacteria were also able to tolerate three different antibiotics (ranges: ampicillin 0-16 μg ml-1, chloramphenicol 0-24 μg ml-1, and vancomycin 0-24 μg ml-1). To gain genetic insight into these tolerance pathways, the genomes of these isolates were assembled and annotated. The genomes of these isolates not only have some shared genes (core genome) but also have a large amount of variability. The genomes also contained an annotated Cr(VI) reductase (chrR) that could be related to Cr(VI) reduction. Further, various heavy metal tolerance (e.g., Co/Zn/Cd efflux system) and antibiotic resistance genes were identified, which provide insight into the isolates' ability to tolerate metals and antibiotics. Overall, these isolates showed a wide range of tolerances to heavy metals and antibiotics and genetic diversity, which was likely required of this population to thrive in a contaminated environment.\n\nComparative genomics of 16 Microbacterium spp. that tolerate multiple heavy metals and antibiotics.", "token_count": 413, "char_count": 1390, "word_count": 198, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:49.117295", "source": { "split": "train_shard_00001", "doc_id": 2602 }, "chunk_id": "train_shard_00001_2602_0", "global_id": 9364 }, { "text": "Acinetobacter baumannii is a significant nosocomial bacterial pathogen that poses a substantial infection risk due to its high resistance to antibiotics and ability to survive in hospital environments. In this study, we performed comprehensive in silico and in vitro analyses on 79 A. baumannii clinical isolates from different geographical locations to uncover their genomic and epidemiological characteristics as well as their antibiotic and phage susceptibilities. Our findings revealed considerable genomic diversity among the isolates, as shown by average nucleotide identity (ANI) heat maps, multilocus sequence typing (MLST), and core genome MLST (cgMLST). We identified several international clones known for their high antibiotic resistance and global prevalence. Surprisingly, we also observed that the number of antimicrobial resistance genes (ARGs) was higher in isolates containing CRISPR-Cas systems. Plaque assays with 13 phages indicated that Acinetobacter phages have a narrow host range, with capsule loci (KL) serving as a good indicator of phage-bacteria interactions. The presence of CRISPR-Cas systems and other antiviral defense mechanisms in A. baumannii genomes also appears to play a key role in providing phage resistance, regardless of the phage receptors. We also found that spacers associated with subtypes I-F1 and I-F2 CRISPR-Cas systems predominantly target prophages, suggesting a role in maintaining genomic stability and contributing to phage-bacteria co-evolution. Overall, this study provides a set of highly characterized A. baumannii clinical isolates for future studies on antibiotic-phage-bacteria interactions.IMPORTANCEAcinetobacter baumannii poses a significant challenge to the healthcare system due to its antibiotic resistance and strong survival mechanisms. This study examines a diverse collection of 79 clinical isolates to deepen our understanding of A. baumannii's genetic characteristics and its defense mechanisms against both antibiotics and phages", "token_count": 514, "char_count": 2067, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:49.823168", "source": { "split": "train_shard_00001", "doc_id": 2603 }, "chunk_id": "train_shard_00001_2603_0", "global_id": 9365 }, { "text": "Genomic analysis revealed globally prevalent, highly resistant clones and uncovered a complex role for CRISPR-Cas systems. Although CRISPR-Cas systems were not widespread among these isolates, they primarily targeted prophages. Additionally, the study emphasizes the importance of capsule types as indicators of phage susceptibility. Together, these findings provide insights into the pathogen's resilience and evolutionary adaptations, potentially guiding future research on infection control strategies and new therapeutic approaches to combat A. baumannii infections.\n\n<i>In silico</i> and <i>in vitro</i> comparative analysis of 79 <i>Acinetobacter baumannii</i> clinical isolates.", "token_count": 196, "char_count": 728, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8706, "quality_score": 0.9353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:50.273624", "source": { "split": "train_shard_00001", "doc_id": 2603 }, "chunk_id": "train_shard_00001_2603_1", "global_id": 9366 }, { "text": "The stunning ability of bacteria to evolve and adapt has contributed to the success of these single cells, which have inhabited the Earth for billions of years and play vital roles in the environment and in human health. The goal of this chapter is to present and discuss the population-level organizational scheme of bacterial pangenomes, wherein genes are distributed among the strains of a species, such that each individual strain encodes only a subset of the genes available at the population level. Genes from the accessory/distributed genome (those present only in a subset of strains within a species) impart diverse functions or variations on a conserved function to strains. Moreover, horizontal gene transfer generates novel gene combinations. The maintenance and spread of any given gene arrangement are influenced by fitness. Further, the extent of genomic plasticity is regulated by restriction modification systems, phage-defense systems, and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)—associated proteins (CRISPR-Cas). The combination of a pangenome structure and genomic plasticity reveals a successful strategy for bacterial adaptation to ever-changing environments. From a clinical perspective, pangenome analyses inform the selection of therapeutic targets, designed to focus either on an entire species or on virulence features within a species. Further, they provide a framework for modeling the efficacy of drugs and vaccines. In summary, following the explosion in sequencing technology, pangenome studies have revealed remarkable genomic organizations at the levels of species, with important implications to our understanding of evolution, and our ability to design therapeutics and predict their long-term outcomes.\n\nThe Bacterial Guide to Designing a Diversified Gene Portfolio", "token_count": 373, "char_count": 1829, "word_count": 261, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:50.865755", "source": { "split": "train_shard_00001", "doc_id": 2604 }, "chunk_id": "train_shard_00001_2604_0", "global_id": 9367 }, { "text": "

Background

Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently been described, yet their clinical impact and antibiotic resistance profiles are largely unknown. We aimed to explore Klebsiella group- and species-specific clinical impact, antimicrobial resistance (AMR) and virulence.

Methods

We analysed whole-genome sequence data of a diverse selection of Klebsiella spp. isolates and identified resistance and virulence factors. Using the genomes of 3594 Klebsiella isolates, we predicted the masses of 56 ribosomal subunit proteins and identified species-specific marker masses. We then re-analysed over 22,000 Matrix-Assisted Laser Desorption Ionization - Time Of Flight (MALDI-TOF) mass spectra routinely acquired at eight healthcare institutions in four countries looking for these species-specific markers. Analyses of clinical and microbiological endpoints from a subset of 957 patients with infections from Klebsiella species were performed using generalized linear mixed-effects models.

Results

Our comparative genomic analysis shows group- and species-specific trends in accessory genome composition. With the identified species-specific marker masses, eight Klebsiella species can be distinguished using MALDI-TOF MS. We identified K. pneumoniae (71.2%; n = 12,523), K. quasipneumoniae (3.3%; n = 575), K. variicola (9.8%; n = 1717), \"K. quasivariicola\" (0.3%; n = 52), K. oxytoca (8.2%; n = 1445), K. michiganensis (4.8%; n = 836), K. grimontii (2.4%; n = 425) and K. huaxensis (0.1%; n = 12). Isolates belonging to the K. oxytoca group, which includes the species K. oxytoca, K", "token_count": 530, "char_count": 1772, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:51.517807", "source": { "split": "train_shard_00001", "doc_id": 2605 }, "chunk_id": "train_shard_00001_2605_0", "global_id": 9368 }, { "text": "michiganensis and K. grimontii, were less often resistant to 4th-generation cephalosporins than isolates of the K. pneumoniae group, which includes the species K. pneumoniae, K. quasipneumoniae, K. variicola and \"K. quasivariicola\" (odds ratio = 0.17, p < 0.001, 95% confidence interval [0.09,0.28]). Within the K. pneumoniae group, isolates identified as K. pneumoniae were more often resistant to 4th-generation cephalosporins than K. variicola isolates (odds ratio = 2.61, p = 0.003, 95% confidence interval [1.38,5.06]). K. oxytoca group isolates were found to be more likely associated with invasive infection to primary sterile sites than K. pneumoniae group isolates (odds ratio = 2.39, p = 0.0044, 95% confidence interval [1.05,5.53]).

Conclusions

Currently misdiagnosed Klebsiella spp. can be distinguished using a ribosomal marker-based approach for MALDI-TOF MS. Klebsiella groups and species differed in AMR profiles, and in their association with invasive infection, highlighting the importance for species identification to enable effective treatment options.\n\nWhole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study.", "token_count": 398, "char_count": 1239, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5723, "quality_score": 0.7861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:52.137700", "source": { "split": "train_shard_00001", "doc_id": 2605 }, "chunk_id": "train_shard_00001_2605_1", "global_id": 9369 }, { "text": "As a result of millions of years of transposon activity, multiple rounds of ancient polyploidization, and large populations that preserve diversity, maize has an extremely structurally diverse genome, evidenced by high-quality genome assemblies that capture substantial levels of both tropical and temperate diversity. We generated a pangenome representation (the Practical Haplotype Graph, PHG) of these assemblies in a database, representing the pangenome haplotype diversity and providing an initial estimate of structural diversity. We leveraged the pangenome to accurately impute haplotypes and genotypes of taxa using various kinds of sequence data, ranging from WGS to extremely-low coverage GBS. We imputed the genotypes of the recombinant inbred lines of the NAM population with over 99% mean accuracy, while unrelated germplasm attained a mean imputation accuracy of 92 or 95% when using GBS or WGS data, respectively. Most of the imputation errors occur in haplotypes within European or tropical germplasm, which have yet to be represented in the maize PHG database. Also, the PHG stores the imputation data in a 30,000-fold more space-efficient manner than a standard genotype file, which is a key improvement when dealing with large scale data.\n\nA Maize Practical Haplotype Graph Leverages Diverse NAM Assemblies", "token_count": 323, "char_count": 1325, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:52.699548", "source": { "split": "train_shard_00001", "doc_id": 2606 }, "chunk_id": "train_shard_00001_2606_0", "global_id": 9370 }, { "text": "

Background:

Colistin (CST) is a last-line drug for multidrug-resistant Gram-negative bacterial infections. CST-heteroresistant Enterobacter cloacae complex (ECC) has been isolated. However, integrated analysis of epidemiology and resistance mechanisms based on the complete ECC species identification has not been performed.

Methods:

Clinical isolates identified as “ E. cloacae complex” by MALDI-TOF MS Biotyper Compass in a university hospital in Japan were analyzed. Minimum inhibitory concentrations of CST were determined by the broth microdilution method. The population analysis profiling (PAP) was performed for detecting the heteroresistant phenotype. The heat shock protein 60 ( hsp60 ) cluster was determined from its partial nucleotide sequence. From the data of whole-genome sequencing, average nucleotide identity (ANI) for determining ECC species, multilocus sequence type, core genome SNPs-based phylogenetic analysis were performed. phoPQ- , eptA-, and arnT -deleted mutants were established to evaluate the mechanism underlying colistin heteroresistance. The arnT mRNA expression levels were determined by reverse transcription quantitative PCR.

Results:

Thirty-eight CST-resistant isolates, all of which exhibited the heteroresistant phenotype by PAP, were found from 138 ECC clinical isolates (27.5%). The prevalence of CST-resistant isolates did not significantly differ among the origin of specimens (29.0%, 27.8%, and 20.2% for respiratory, urine, and blood specimens, respectively). hsp60 clusters, core genome phylogeny, and ANI revealed that the CST-heteroresistant isolates were found in all or most of Enterobacter roggenkampii ( hsp60 cluster IV), Enterobacter kobei (cluster II), Enterobacter chuandaensis (clusters III and IX), and Enterobacter cloacae subspecies (cluster XI and XII) ", "token_count": 503, "char_count": 1846, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:53.355187", "source": { "split": "train_shard_00001", "doc_id": 2607 }, "chunk_id": "train_shard_00001_2607_0", "global_id": 9371 }, { "text": "No heteroresistant isolates were found in Enterobacter hormaechei subspecies (cluster VIII, VI, and III) and Enterobacter ludwigii (cluster V). Upregulation of arnT , which encodes 4-amino-4-deoxy-L-arabinose transferase, mRNA induced by CST was observed in the CST-heteroresistant isolates, and it is mediated by phoPQ pathway. Isolates possessing mcr-9- and mcr-10 (3.6% and 5.6% of total ECC isolates, respectively) exhibited similar CST susceptibility and PAP compared with mcr -negative isolates.

Conclusions:

Significant prevalence (approximately 28%) of CST heteroresistance is observed in ECC clinical isolates, and theyare accumulated in specific species and lineages. Heteroresistance is occurred by upregulation of arnT mRNA induced by CST. Acquisition of mcr genes contributes less to CST resistance in ECC.\n\nHigh prevalence of colistin heteroresistance in specific species and lineages of Enterobacter cloacae complex derived from human clinical specimens", "token_count": 285, "char_count": 978, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:53.910614", "source": { "split": "train_shard_00001", "doc_id": 2607 }, "chunk_id": "train_shard_00001_2607_1", "global_id": 9372 }, { "text": "

Unlabelled

We isolated, identified and characterized yeast strains from grapes, and their fermented musts, sampled in the small island of Linosa, where there are no wineries and therefore the possibility of territory contamination by industrial strains is minimal. By traditional culture-dependent methods, we isolated 3805 colonies, distinguished by molecular methods in 17 different species. Five hundred and forty-four isolates were analysed for the main oenological characteristics such as fermentative vigour with and without sulphites, sugar consumption and production of alcohol, volatile acidity, hydrogen sulphide, glycerol and β-glucosidase. This analysis identified Kluyveromyces marxianus (seldomly used in winemaking) as the most interesting candidate yeast for the production of innovative wines.

Significance and impact of the study

In recent years, interest is growing for wine production by non-Saccharomyces yeasts, both in research and in the industry. This study describes the yeast population of the grapes in a small-secluded island in the Mediterranean Sea, useful site for the search of new strains. Evaluation of fundamental oenological characters identifies potential best yeasts to assay in experimental vinifications. We also describe, for the first time, 14 new colony morphologies on WL Nutrient Agar, culture medium used to monitor the yeast population dynamics.\n\nIsolation, identification and oenological characterization of non-Saccharomyces yeasts in a Mediterranean island.", "token_count": 353, "char_count": 1523, "word_count": 205, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:54.493527", "source": { "split": "train_shard_00001", "doc_id": 2608 }, "chunk_id": "train_shard_00001_2608_0", "global_id": 9373 }, { "text": "Bacterial resistance to β-lactams is mainly attributed to CTX-M-type extended-spectrum β-lactamases (ESBLs). However, the predominant sequence type (ST) of blaCTX-M-carrying Escherichia coli (blaCTX-M-Ec) in chickens, an important food animal, in China and its contribution to human β-lactam resistance are not investigated. In this study, approximately 1808 chicken-derived strains collected from 10 provinces from 2012 to 2020 were screened for blaCTX-M-Ec, and 222 blaCTX-M-Ec were identified. Antimicrobial susceptibility tests, whole genome sequencing and conjugation experiment were performed. All quality-controlled 136 chicken-derived blaCTX-M-Ec and 1193 human-derived blaCTX-M-Ec genomes were downloaded from NCBI and EnteroBase to comprehensively analyze the prevalence of blaCTX-M-Ec in China. blaCTX-M-55 (153/358, 42.7% in chicken isolates; 312/1193, 26.2% in human isolates) and blaCTX-M-14 (92/358, 25.7% in chicken isolates; 450/1193, 37.7% in human isolates) were dominant in blaCTX-M-Ec. The STs of blaCTX-M-Ec were diverse and scattered, with ST155 (n = 21) and ST152 (n = 120) being the most abundant in chicken- and human-derived isolates, respectively", "token_count": 491, "char_count": 1295, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6987, "quality_score": 0.8494, "entities": { "genes": [ "ST155", "ST152" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:55.146498", "source": { "split": "train_shard_00001", "doc_id": 2609 }, "chunk_id": "train_shard_00001_2609_0", "global_id": 9374 }, { "text": "Few examples indicated that chicken- and human-derived blaCTX-M-Ec have 10 or less core genome single nucleotide polymorphisms (cgSNPs). Genetic environment analysis indicated that ISEcp1, IS26 and IS903B were closely associated with blaCTX-M transfer. The almost identical pc61-55 and pM-64-1161 indicated the possibility of plasmid-mediated transmission of blaCTX-M between humans and chickens. Although the genomes of most blaCTX-M-Ec isolated from chickens and humans were quite different, the prevalence and genetic environment of blaCTX-M variants in both hosts were convergent. CTX-M-mediated resistance is more likely to spread through horizontal gene transmission than bacterial clones.\n\nEpidemiological characteristics of human- and chicken-derived CTX-M-type extended-spectrum β-lactamase-producing Escherichia coli from China.", "token_count": 259, "char_count": 893, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7524, "quality_score": 0.8762, "entities": { "genes": [ "IS26", "IS903B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:55.689014", "source": { "split": "train_shard_00001", "doc_id": 2609 }, "chunk_id": "train_shard_00001_2609_1", "global_id": 9375 }, { "text": "Escherichia coli and other Enterobacteriaceae are highly diverse species with ‘open’ pangenomes 1,2 , where genes move intra- and inter-species via horizontal gene transfer 3 . These species can cause clinical infections 4,5 as well as persist environmentally 6,7 . Environmental populations have been suggested as important reservoirs of antimicrobial resistance (AMR) genes. However, as most analyses focus on clinical isolates 8,9 , the pangenome dynamics of natural populations remain understudied, particularly the role of plasmids. Here, we reconstructed near-complete genomes for 828 Enterobacteriaceae , including 553 Escherichia spp. and 275 non- Escherichia species with 2,293 circularised plasmids in total, collected from nineteen locations (livestock farms and wastewater treatment works in the United Kingdom) within a 30km radius at three timepoints over the course of a year. We find different dynamics for the chromosomal and plasmid-borne components of the pangenome, showing that plasmids have a higher burden of both AMR genes and insertion sequences, and AMR plasmids show evidence of being under stronger selective pressure. Focusing on E. coli , we observe that plasmid dynamics are more strongly dominated by niche and local geography, rather than phylogeny or season. Our results highlight the diversity of the AMR reservoir in these species and niches, and the importance of local strategies for controlling the emergence and spread of AMR.\n\nNiche and local geography shape the pangenome of wastewater- and livestock-associatedEnterobacteriaceae", "token_count": 395, "char_count": 1578, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6798, "quality_score": 0.8399, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:56.305709", "source": { "split": "train_shard_00001", "doc_id": 2610 }, "chunk_id": "train_shard_00001_2610_0", "global_id": 9376 }, { "text": "Nicotinamide adenine dinucleotide (NAD + ) has emerged as a key component in prokaryotic and eukaryotic immune systems and the recent discovery that Toll/interleukin-1 receptor (TIR) proteins function as NAD + hydrolases (NADase) link NAD + -derived small molecules with immune signalling. We investigated pathogen manipulation of host NAD + metabolism as a virulence strategy. Using the pangenome of the model bacterial pathogen Pseudomonas syringae, we conducted a structure-based similarity search from 35,000 orthogroups for type III effectors (T3Es) with potential NADase activity. Thirteen T3Es, including five newly identified candidates, were identified that possess domain(s) characteristic of seven NAD + -hydrolyzing enzyme families. Most P. syringae strains that depend on the Type III secretion system to cause disease, encode at least one NAD + -manipulating T3E, and many have several. We experimentally confirmed the type III-dependent secretion of a novel T3E, named HopBY, which shows structural similarity to both TIR and adenosine diphosphate ribose (ADPR) cyclase. Homologs of HopBY were predicted to be type VI effectors in diverse bacterial species, indicating potential recruitment of this activity by microbial proteins secreted during various interspecies interactions. HopBY efficiently hydrolyzes NAD + and specifically produces 2’cADPR, which can also be produced by TIR immune receptors of plants and other bacteria. Intriguingly, this effector promoted bacterial virulence, indicating that 2’cADPR may not be the signalling molecule that directly initiates immunity. This study highlights a host-pathogen battle ground centred around NAD + metabolism and provides insight into the NAD + -derived molecules involved in plant immunity.

Significance statement

NAD + metabolism plays a crucial role in plant and bacterial immunity. However, the diversity and scope of NAD + processing steps in immune signalling remain unclear. Furthermore, whether pathogens can manipulate NAD + metabolism to promote virulence is unknown", "token_count": 518, "char_count": 2058, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:26:56.963564", "source": { "split": "train_shard_00001", "doc_id": 2611 }, "chunk_id": "train_shard_00001_2611_0", "global_id": 9377 }, { "text": "By conducting a pangenomic screen of the plant pathogen P. syringae, we found 13 type III effectors that potentially possess NADase activities, indicating that NAD + manipulation is an important virulence mechanism. Further characterization of a newly identified effector HopBY showed that it produces a cyclic ADP-ribose isomer (2’cADPR) and promotes bacterial infection and symptom development. This study clarifies the role of 2’cADPR in immune signalling and provides an example of effectors as useful molecular probes to understand immunity.\n\nPangenomic analysis reveals plant NAD+manipulation as an important virulence activity of bacterial pathogen effectors", "token_count": 161, "char_count": 676, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7634, "quality_score": 0.8817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:57.402738", "source": { "split": "train_shard_00001", "doc_id": 2611 }, "chunk_id": "train_shard_00001_2611_1", "global_id": 9378 }, { "text": "

Introduction

Shewanella is an important opportunistic pathogen distributed in marine environments that has caused an increasing number of clinical infections. However, there are few reports on the distribution and characteristics of Shewanella in the diarrheal pathogen spectrum. In this study, we have systematically described the prevalence of Shewanella infections in diarrhea patients in Beijing, China 2017-2019, and genome characteristics and antimicrobial susceptibility of Shewanella isolates.

Methods

Stool samples were collected from diarrhea patients in a surveillance project from 2017 to 2019. Shewanella strains were isolated, and identified using VITEKR 2 COMPACT and MALDI-TOF MS. Average nucleotide identity (ANI) analysis, multi-locus sequence typing (MLST), phylogenetic analysis, virulence-associated genes and antimicrobial resistance genes analysis were used for genome characteristics description. The antibiotic susceptibility test was performed with microbroth dilution method.

Results

1104 fecal samples were collected, and the Shewanella detection rate was 2.36% (26/1104). The main manifestations of infection caused by Shewanella spp. were diarrhea (100%, 26/26), abdominal pain (65.38%, 17/26), and vomiting (38.46%, 10/26). The 26 isolates were classified into 3 species (S. algae (n = 18), S. indica (n = 5), and S. chilikensis (n = 3)) and 22 sequence types", "token_count": 503, "char_count": 1503, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6989, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:58.048985", "source": { "split": "train_shard_00001", "doc_id": 2612 }, "chunk_id": "train_shard_00001_2612_0", "global_id": 9379 }, { "text": "Core genome single nucleotide polymorphism-based evolutionary tree identified three clone groups corresponding to three infection events in the same months in 2017 and 2019. The putative virulence-associated gene pool consisted of 56 potential virulence genes, including 19 virulence gene factors. The resistance rates of the 26 isolates to 17 antibiotics from high to low were as follows: polymyxin E (76.92%), cefotaxime (57.69%), ampicillin (50%), ampicillin-sulbactam (34.62%), nalidixic acid (15.38%), ciprofloxacin (11.54%), selectrin (3.846%,1/26), and tetracycline (3.846%, 1/26). The rate of multidrug resistance was 38.46% (10/26).

Discussion

Monitoring for Shewanella spp. should be added to the routine surveillance of infectious diarrhea during the epidemic season.\n\nPrevalence and molecular characteristics of Shewanella infection in diarrhea patients in Beijing, China 2017-2019.", "token_count": 323, "char_count": 915, "word_count": 116, "semantic_coherence": 1, "information_density": 0.7845, "quality_score": 0.8922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:58.609339", "source": { "split": "train_shard_00001", "doc_id": 2612 }, "chunk_id": "train_shard_00001_2612_1", "global_id": 9380 }, { "text": "The metagenome-assembled genome (MAG) sequence of Stenotrophomonas maltophilia strain UJ_SKK_5.5 was obtained from the gut microbiome of Macrotermes bellicosus (termite) from hot, arid Nigeria. The assembled genome (4,313,335 bp) contains 157 contigs, the N50 is 41,072 bp, the GC content is 66.57%, and there are 3,925 protein coding sequences, 3,886 proteins with functional assignments, 39 pseudogenes, and 67 RNA genes.\n\nMetagenome-Assembled Genome Sequence of Stenotrophomonas maltophilia Strain UJ_SKK_5.5, Obtained from the Gut Microbiome of a Macrotermes bellicosus Termite Collected from Hot, Arid Nigeria.", "token_count": 230, "char_count": 633, "word_count": 83, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:59.076716", "source": { "split": "train_shard_00001", "doc_id": 2613 }, "chunk_id": "train_shard_00001_2613_0", "global_id": 9381 }, { "text": "Pasteurella multocida is a multi-host pathogen that infects a wide spectrum of domestic and wild animals including humans. Despite its impact on health and economics, P. multocida is considered an enigmatic pathogen and the genetic basis of its pathogenicity and host adaptation still remains unclear. Here we present a detailed genomic framework based on 336 whole-genome sequences of P. multocida isolates from different animal species and countries. Our data provide genomic support of the existence of two very divergent phylogroups (PmI and PmII), which present a barrier to homologous recombination suggesting genetic isolation. Additionally, a torCAD operon, which reduces TMAO (trimethylamine N -oxide) to produce energy during bacterial anaerobic respiration, is present only in PmI and can act as a hypothetical driver of niche segregation between phylogroups. The PmI phylogroup harbors strains that infect a wider range of hosts than PmII, and shows a highly diverse phylogeny and accessory genome. We identified nine clonal lineages for PmI, seven of which are associated with specific hosts or diseases and contain distinct accessory gene pools that can confer ecologically relevant phenotypes. We found differential presence of a trehalose metabolism operon in the bovine lineage associated with pneumonic pasteurellosis; while, citrate, L-arabinose, L-fucose, and D-allose operons are only present in avian lineages. These findings suggest that alternative metabolic pathways may facilitate the establishment of P. multocida during host colonization in the early stages of infection promoting the adaptation of P. multocida lineages to certain hosts.\n\nGenomic diversity, population structure and accessory genome analysis ofPasteurella multocida: New Insights into host adaptation and disease specialization", "token_count": 436, "char_count": 1830, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:26:59.710222", "source": { "split": "train_shard_00001", "doc_id": 2614 }, "chunk_id": "train_shard_00001_2614_0", "global_id": 9382 }, { "text": "

Background

The genus Geobacillus comprises bacteria that are Gram positive, thermophilic spore-formers, which are found in a variety of environments from hot-springs, cool soils, to food manufacturing plants, including dairy manufacturing plants. Despite considerable interest in the use of Geobacillus spp. for biotechnological applications, the taxonomy of this genus is unclear, in part because of differences in DNA-DNA hybridization (DDH) similarity values between studies. In addition, it is also difficult to use phenotypic characteristics to define a bacterial species. For example, G. stearothermophilus was traditionally defined as a species that does not utilise lactose, but the ability of dairy strains of G. stearothermophilus to use lactose has now been well established.

Results

This study compared the genome sequences of 63 Geobacillus isolates and showed that based on two different genomic approaches (core genome comparisons and average nucleotide identity) the Geobacillus genus could be divided into sixteen taxa for those Geobacillus strains that have genome sequences available thus far. In addition, using Geobacillus stearothermophilus as an example, we show that inclusion of the accessory genome, as well as phenotypic characteristics, is not suitable for defining this species. For example, this is the first study to provide evidence of dairy adaptation in G. stearothermophilus - a phenotypic feature not typically considered standard in this species - by identifying the presence of a putative lac operon in four dairy strains.

Conclusions

The traditional polyphasic approach of combining both genotypic and phenotypic characteristics to define a bacterial species could not be used for G. stearothermophilus where many phenotypic characteristics vary within this taxon. Further evidence of this discordant use of phenotypic traits was provided by analysis of the accessory genome, where the dairy strains contained a putative lac operon. Based on the findings from this study, we recommend that novel bacterial species should be defined using a core genome approach.", "token_count": 508, "char_count": 2122, "word_count": 301, "semantic_coherence": 1, "information_density": 0.5482, "quality_score": 0.7741, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:00.416852", "source": { "split": "train_shard_00001", "doc_id": 2615 }, "chunk_id": "train_shard_00001_2615_0", "global_id": 9383 }, { "text": "Insights into the Geobacillus stearothermophilus species based on phylogenomic principles.", "token_count": 26, "char_count": 90, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:00.799997", "source": { "split": "train_shard_00001", "doc_id": 2615 }, "chunk_id": "train_shard_00001_2615_1", "global_id": 9384 }, { "text": "As a biocontrol bacteria, Brevibacillus has been the subject of extensive research for agricultural applications. Antibacterial peptides (AMPs) are the main antibacterial products of Brevibacillus. This study isolated a strain of Br. brevis HNCS-1 from tea garden soil, and the strain has an antagonistic effect against five types of pathogens of tea diseases, namely Gloeosporium theae-sinensis, Elsinoe leucospira, Phyllosticta theaefolia, Fusarium sp., and Cercospora theae. To determine the genetic characteristics implicated in the biocontrol mechanism, the genome sequence of the HNCS-1 strain was obtained and analyzed further, and the data are deposited in the GenBank repository (No. CP128411). Comparative genomics analyses revealed that the HNCS-1 strain and 17 public Br. brevis share a core genome composed of 3,742 genes. Interestingly, only one non-ribosomal peptide synthetase (NRPS) gene cluster annotated as edeine is present in the core genome. And UHPLC-MS/MS detection results showd that edeine B and edeine A were the principal antibacterial peptides in the HNCS-1 strain. This study proves that edeine is the main antibacterial peptide of Br. brevis, and provides a new strategy for the identification of antibacterial products from other biocontrol bacteria.\n\nBrevibacillus brevis HNCS-1: a biocontrol bacterium against tea plant diseases.", "token_count": 424, "char_count": 1419, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8051, "entities": { "genes": [ "CP128411" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:01.456087", "source": { "split": "train_shard_00001", "doc_id": 2616 }, "chunk_id": "train_shard_00001_2616_0", "global_id": 9385 }, { "text": "Staphylococcal food poisoning (SFP) is one of the most common foodborne diseases in the world. This study aimed to investigate the molecular epidemiological characteristics of Staphylococcus aureus isolated from SFP. A total of 103 S. aureus isolates were obtained during 2011-2022 in Sichuan, southwest China. All isolates were tested for the genomic characteristics and phylogenetic analysis by performing whole-genome sequencing. Multilocus sequence typing analysis showed 17 multilocus sequence types (STs), ST7 (23.30%), ST5 (22.33%), and ST6 (16.50%) being the most common. A total of 45 virulence genes were detected, 22 of which were staphylococcal enterotoxin (SE) genes. Among the identified SE genes, selX exhibited the highest prevalence (86.4%). All isolates carried at least one SE gene. The results of the antimicrobial resistance (AMR) gene detection revealed 41 AMR genes of 12 classes. β-lactam resistance genes (blal, blaR1, blaZ) and tetracycline resistance gene (tet(38)) exhibited a higher prevalence rate. Core genome single nucleotide polymorphism showed phylogenetic clustering of the isolates with the same region, year, and ST. The results indicated that the SFP isolates in southwest of China harbored multiple toxin and resistance genes, with a high prevalence of new SEs. Therefore, it is important to monitor the antimicrobial susceptibility and SE of S. aureus to reduce the potential risks to public health.\n\nMolecular Characteristics of Staphylococcus aureus Isolates form Food-Poisoning Outbreaks (2011-2022) in Sichuan, China.", "token_count": 504, "char_count": 1625, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6267, "quality_score": 0.8133, "entities": { "genes": [ "ST5", "ST7", "ST6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:02.143217", "source": { "split": "train_shard_00001", "doc_id": 2617 }, "chunk_id": "train_shard_00001_2617_0", "global_id": 9386 }, { "text": "

Background

Rezafungin is a novel echinocandin with excellent activity against common Candida species; however, limited data are available regarding rare Candida species.

Methods

We determined the in vitro susceptibility of 689 clinical isolates of 5 common and 19 rare Candida species, as well as Saccharomyces cerevisiae. The activity of rezafungin was compared with that of anidulafungin, caspofungin, micafungin, amphotericin B and fluconazole, using CLSI broth microdilution methodology (Fourth Edition: M27).

Results

Rezafungin MIC90 values were 0.06 mg/L for Candida albicans (n=125), Candida tropicalis (n=51), Candida dubliniensis (n=22), Candida inconspicua (n=41), Candida sojae (n=10), Candida lipolytica (n=10) and Candida pulcherrima (n=10), 0.12 mg/L for Candida glabrata (n=81), Candida krusei (n=53), Candida kefyr (n=52) and Candida fabianii (n=15), 0.25 mg/L for Candida lusitaniae (n=46) and Candida auris (n=19), 0.5 mg/L for Candida metapsilosis (n=15) and S. cerevisiae (n=21), 1 mg/L for Candida orthopsilosis (n=15) and Candida guilliermondii (n=27) and 2 mg/L for Candida parapsilosis sensu stricto (n=59)", "token_count": 465, "char_count": 1152, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8433, "entities": { "genes": [ "MIC90" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:02.783804", "source": { "split": "train_shard_00001", "doc_id": 2618 }, "chunk_id": "train_shard_00001_2618_0", "global_id": 9387 }, { "text": "Caspofungin MIC90 values were 0.25-2 mg/L for all species, while micafungin and anidulafungin MIC90 values were similar to those of rezafungin. Fluconazole resistance was found in C. albicans (5.6%) and C. glabrata (4.9%); rezafungin was effective against these isolates as well. Amphotericin B MIC values did not exceed 2 mg/L.

Conclusions

Rezafungin showed excellent in vitro activity against both WT and azole-resistant Candida species, as well as against S. cerevisiae. Rezafungin had similar activity to other echinocandins (excluding caspofungin) against common Candida species and, notably, against clinically relevant uncommon Candida species.\n\nIn vitro activity of rezafungin against common and rare Candida species and Saccharomyces cerevisiae.", "token_count": 244, "char_count": 761, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.835, "entities": { "genes": [ "MIC90" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:03.265294", "source": { "split": "train_shard_00001", "doc_id": 2618 }, "chunk_id": "train_shard_00001_2618_1", "global_id": 9388 }, { "text": "Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and is difficult to treat, causing increased morbidity and mortality rates in critically ill patients. We conducted a multicenter cross-sectional study of intensive care unit (ICU) inpatients in 78 hospitals to investigate the prevalence and molecular characteristics of CRKP in Henan Province, China, a hyperepidemic region. A total of 327 isolates were collected and downsampled to 189 for whole-genome sequencing. Molecular typing revealed that sequence type 11 (ST11) of clonal group 258 (CG258) was predominant (88.9%, n = 168), followed by ST2237 (5.8%, n = 11) and ST15 (2.6%, n = 5). We used core genome multilocus sequence typing (cgMLST) to further classified the population into 13 subtypes. Capsule polysaccharide (K-antigen) and lipopolysaccharide (LPS; O-antigen) typing revealed that K64 (48.1%, n = 91) and O2a (49.2%, n = 93) were the most common. We studied isolates collected from both the airway and the gut of the same patients and showed that intestinal carriage was associated with respiratory colonization (odds ratio = 10.80, P < 0.0001)", "token_count": 429, "char_count": 1180, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7326, "quality_score": 0.8663, "entities": { "genes": [ "CG258", "ST15", "ST2237", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:03.895981", "source": { "split": "train_shard_00001", "doc_id": 2619 }, "chunk_id": "train_shard_00001_2619_0", "global_id": 9389 }, { "text": "Most isolates (95.2%, n = 180) showed multiple drug resistance (MDR), while 59.8% (n = 113) exhibited extensive drug resistance (XDR), and all isolates harbored either blaKPC-2 (98.9%, n = 187) or blaCTX-M and blaSHV extended-spectrum beta-lactamases (ESBLs) (75.7%, n = 143). However, most were susceptible to ceftazidime-avibactam (CZA) (94.7%, n = 179) and colistin (97.9%, n = 185). We found mgrB truncations in isolates conferring resistance to colistin and mutations in blaSHV and OmpK35 and OmpK36 osmoporins in CZA-resistant isolates. Using a regularized regression model, we found that the aerobactin sequence type and the salmochelin sequence type, among others, were predictors of the hypermucoviscosity phenotype. IMPORTANCE In this study, we address the ongoing epidemic of carbapenem-resistant Klebsiella pneumoniae, a critical threat to public health. The alarming genotypic and phenotypic convergence of multidrug resistance and virulence highlights the increasingly aggravated threat posed by K. pneumoniae. This calls for a combined effort of physicians and scientists to study the potential mechanisms and establish guidelines for antimicrobial therapies and interventions", "token_count": 489, "char_count": 1319, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:04.544309", "source": { "split": "train_shard_00001", "doc_id": 2619 }, "chunk_id": "train_shard_00001_2619_1", "global_id": 9390 }, { "text": "To this end, we have conducted a genomic epidemiology and characterization study using isolates collected in a coordinated effort of multiple hospitals. Innovative biological discoveries of clinical importance are made and brought to the attention of clinical researchers and practitioners. This study presents an important advance in the application of genomics and statistics to recognize, understand, and control an infectious disease of concern.\n\nGenomic Epidemiology and Characterization of Carbapenem-Resistant Klebsiella pneumoniae in ICU Inpatients in Henan Province, China: a Multicenter Cross-Sectional Study.", "token_count": 131, "char_count": 619, "word_count": 82, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:04.969510", "source": { "split": "train_shard_00001", "doc_id": 2619 }, "chunk_id": "train_shard_00001_2619_2", "global_id": 9391 }, { "text": "

Objectives

To utilize long-read nanopore sequencing (R10.4.1 flowcells) for WGS of a cluster of MDR Shigella sonnei, specifically characterizing genetic predictors of antimicrobial resistance (AMR).

Methods

WGS was performed on S. sonnei isolates identified from stool and blood between September 2021 and October 2022. Bacterial DNA from clinical isolates was extracted on the MagNA Pure 24 and sequenced on the GridION utilizing R10.4.1 flowcells. Phenotypic antimicrobial susceptibility testing was interpreted based on CLSI breakpoints. Sequencing data were processed with BugSeq, and AMR was assessed with BugSplit and ResFinder.

Results

Fifty-six isolates were sequenced, including 53 related to the cluster of cases. All cluster isolates were identified as S. sonnei by sequencing, with global genotype 3.6.1.1.2 (CipR.MSM5), MLST 152 and PopPUNK cluster 3. Core genome MLST (cgMLST, examining 2513 loci) and reference-based MLST (refMLST, examining 4091 loci) both confirmed the clonality of the isolates. Cluster isolates were resistant to ampicillin (blaTEM-1), trimethoprim/sulfamethoxazole (dfA1, dfrA17; sul1, sul2), azithromycin (ermB, mphA) and ciprofloxacin (gyrA S83L, gyrA D87G, parC S80I). No genomic predictors of resistance to carbapenems were identified.

Conclusions

WGS with R10.4.1 enabled rapid sequencing and identification of an MDR S. sonnei community cluster. Genetic predictors of AMR were concordant with phenotypic antimicrobial susceptibility testing.", "token_count": 496, "char_count": 1513, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6564, "quality_score": 0.8282, "entities": { "genes": [ "MSM5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:05.623290", "source": { "split": "train_shard_00001", "doc_id": 2620 }, "chunk_id": "train_shard_00001_2620_0", "global_id": 9392 }, { "text": "WGS of a cluster of MDR Shigella sonnei utilizing Oxford Nanopore R10.4.1 long-read sequencing.", "token_count": 33, "char_count": 95, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:05.974186", "source": { "split": "train_shard_00001", "doc_id": 2620 }, "chunk_id": "train_shard_00001_2620_1", "global_id": 9393 }, { "text": "

Objectives

To investigate gene expression profiles of the thermotolerant yeast Saccharomyces cerevisiae strain KKU-VN8, a potential high-ethanol producer, in response to various stresses during high-temperature ethanol fermentation using sweet sorghum juice (SSJ) under optimal conditions.

Results

The maximal ethanol concentration obtained by S. cerevisiae KKU-VN8 using SSJ at 40 °C was 66.6 g/l, with a productivity of 1.39 g/l/h and a theoretical ethanol yield of 81%. Quantitative RT-PCR assays were performed to investigate the gene expression profiles of S. cerevisiae KKU-VN8. Differential expression of genes encoding heat-shock proteins (HSP82, HSP104, SSA4), genes involved in trehalose metabolism (TPS1, TPS2, NTH1) and genes involved the glycolytic pathway (ADH1, ADH2, CDC19) at various time points during fermentation was observed. The expression levels of HSP82, HSP104, SSA4, ADH1 and CDC19 were significantly higher than those of the controls (10.2-, 4-, 8-, 8.9- and 5.9-fold higher, respectively). In contrast, the expression levels of TPS1, TPS2, NTH1 and ADH2 were approx. 2-fold less than those of the controls.

Conclusions

The highly expressed genes encoding heat-shock proteins, HSP82 and SSA4, potentially play an important role in helping S. cerevisiae KKU-VN8 cope with various stresses that occur during high-temperature fermentation, leading to higher ethanol production efficiency.\n\nGene expression profiles of the thermotolerant yeast Saccharomyces cerevisiae strain KKU-VN8 during high-temperature ethanol fermentation using sweet sorghum juice.", "token_count": 498, "char_count": 1600, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": { "genes": [ "SSA4", "VN8", "HSP82", "NTH1", "ADH1", "CDC19", "TPS2", "TPS1", "HSP104", "ADH2" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:06.622101", "source": { "split": "train_shard_00001", "doc_id": 2621 }, "chunk_id": "train_shard_00001_2621_0", "global_id": 9394 }, { "text": "Integrons are mobile genetic elements that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4 thousand Klebsiella pneumoniae genomes for the presence of integrons and antibiotic resistance genes within them. Our data shows that K. pneumoniae has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available at https://github.com/gem-pasteur/Integron_Finder .\n\nIntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella", "token_count": 375, "char_count": 1734, "word_count": 250, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:07.215293", "source": { "split": "train_shard_00001", "doc_id": 2622 }, "chunk_id": "train_shard_00001_2622_0", "global_id": 9395 }, { "text": "Isolation and functional characterization of microorganisms are relevant steps for generating starter cultures with functional properties, and more recently, those related to improving mental health. Milk kefir grains have been recently investigated as a source of health-related strains. This study focused on the evaluation of microorganisms from artisanal Mexican milk kefir grains regarding probiotic properties, in vitro fermentability with commercial prebiotics (lactulose, inulin, and citrus pectin), and γ-aminobutyric acid (GABA)-producing capacity. Microorganisms were identified belonging to genera Lactococcus, Lactobacillus, Leuconostoc, and Kluyveromyces. The probiotic properties were assessed by aggregation abilities, antimicrobial activity, antibiotic susceptibility, and resistance to in vitro gastrointestinal digestion, showing a good performance compared with commercial probiotics. Most of isolates maintained a concentration above 6 log colony forming units/mL after the intestinal phase. Specific isolates of Kluyveromyces (BIOTEC009 and BIOTEC010), Leuconostoc (BIOTEC011 and BIOTEC012), and Lactobacillus (BIOTEC014 and BIOTEC15) showed a high fermentability in media supplemented with commercial prebiotics. The capacity to produce GABA was classified as medium for L. lactis BIOTEC006, BIOTEC007, and BIOTEC008; K. lactis BIOTEC009; L. pseudomesenteroides BIOTEC012; and L. kefiri BIOTEC014, and comparable to that obtained for commercial probiotics. Finally, a multivariate approach was performed, allowing the grouping of 2-5 clusters of microorganisms that could be further considered new promising cultures for functional dairy food applications.", "token_count": 521, "char_count": 1756, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7028, "quality_score": 0.8514, "entities": { "genes": [ "BIOTEC012", "BIOTEC010", "BIOTEC007", "BIOTEC006", "BIOTEC009", "BIOTEC008", "BIOTEC15", "BIOTEC014", "BIOTEC011" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:07.872596", "source": { "split": "train_shard_00001", "doc_id": 2623 }, "chunk_id": "train_shard_00001_2623_0", "global_id": 9396 }, { "text": "Probiotic Properties, Prebiotic Fermentability, and GABA-Producing Capacity of Microorganisms Isolated from Mexican Milk Kefir Grains: A Clustering Evaluation for Functional Dairy Food Applications.", "token_count": 53, "char_count": 198, "word_count": 23, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:08.236667", "source": { "split": "train_shard_00001", "doc_id": 2623 }, "chunk_id": "train_shard_00001_2623_1", "global_id": 9397 }, { "text": "Chlamydomonas reinhardtii is an important eukaryotic alga that has been studied as a model organism for decades. Despite extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of C. reinhardtii field isolates, and in six we discovered sequences belonging to endogenous giant viruses that reach up to several hundred kilobases in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta , the closest sequenced phylogenetic relatives of C. reinhardtii . Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and inter-strain genomic variability of C. reinhardtii . Our findings suggest that the endogenization of giant viruses can have important implications for structuring the population dynamics and ecology of protists in the environment.\n\nEndogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii", "token_count": 278, "char_count": 1183, "word_count": 169, "semantic_coherence": 1, "information_density": 0.5976, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:08.793612", "source": { "split": "train_shard_00001", "doc_id": 2624 }, "chunk_id": "train_shard_00001_2624_0", "global_id": 9398 }, { "text": "One approach towards maintaining healthy microbiota in the human gastrointestinal tract is through the consumption of probiotics. Until now, the majority of probiotic research has focused on probiotic bacteria, but over the last few years more and more studies have demonstrated the probiotic properties of yeast, and also of species besides the well-studied Saccharomyces cerevisiae var. boulardii. Probiotic strains have to present the ability to survive in harsh conditions of the host body, like the digestive tract. Must fermentation might be an example of a similar harsh environment. In the presented study, we examined the probiotic potential of 44 yeast strains isolated from Polish wines. The tested isolates belonged to six species: Hanseniaspora uvarum, Pichia kluyveri, Metschnikowia pulcherrima, Metschnikowia ziziphicola, Saccharomyces cerevisiae and Starmerella bacillaris. The tested strains were subjected to an assessment of probiotic properties, their safety and their other properties, such as enzymatic activity or antioxidant properties, in order to assess their potential usefulness as probiotic yeast candidates. Within the most promising strains were representatives of three species: H. uvarum, M. pulcherrima and S. cerevisiae. H. uvarum strains 15 and 16, as well as S. cerevisiae strain 37, showed, among other features, survivability in gastrointestinal tract conditions exceeding 100%, high hydrophobicity and autoaggregation, had no hemolytic activity and did not produce biogenic amines. The obtained results show that Polish wines might be a source of potential probiotic yeast candidates with perspectives for further research.\n\nProbiotic Yeasts and How to Find Them-Polish Wines of Spontaneous Fermentation as Source for Potentially Probiotic Yeasts.", "token_count": 501, "char_count": 1850, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:09.442711", "source": { "split": "train_shard_00001", "doc_id": 2625 }, "chunk_id": "train_shard_00001_2625_0", "global_id": 9399 }, { "text": "The Escherichia coli lineage known as clonal complex 95 (CC95) is a cosmopolitan human-associated lineage responsible for a significant fraction of extraintestinal infections of humans. Whole-genome sequence data of 200 CC95 strains from various origins enabled determination of the CC95 pangenome. The pangenome analysis revealed that strains of the complex could be assigned to one of five subgroups that vary in their serotype, extraintestinal virulence, virulence gene content, and antibiotic resistance gene profile. A total of 511 CC95 strains isolated from humans living in France, Australia, and the United States were screened for their subgroup membership using a PCR-based method. The CC95 subgroups are nonrandomly distributed with respect to their geographic origin. The relative frequency of the subgroups was shown to change through time, although the nature of the changes varies with continent. Strains of the subgroups are also nonrandomly distributed with respect to source of isolation (blood, urine, or feces) and host sex. Collectively, the evidence indicates that although strains belonging to CC95 may be cosmopolitan, human movement patterns have been insufficient to homogenize the distribution of the CC95 subgroups. Rather, the manner in which CC95 strains evolve appears to vary both spatially and temporally. Although CC95 strains appeared globally as pandemic, fine-scale structure analysis shows epidemic patterns of the CC95 subgroups. Furthermore, the observation that the relative frequency of CC95 subgroups at a single locality has changed over time indicates that the relative fitness of the subgroups has changed. IMPORTANCEEscherichia coli clonal complex 95 represents a cosmopolitan, genetically diverse lineage, and the extensive substructure observed in this lineage is epidemiologically and clinically relevant. The frequency with which CC95 strains are responsible for extraintestinal infection appears to have been stable over the past 15 years. However, the different subgroups identified within this lineage have an epidemic structure depending on the host, sample, continent, and time", "token_count": 499, "char_count": 2154, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5523, "quality_score": 0.7761, "entities": { "genes": [ "CC95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:10.846287", "source": { "split": "train_shard_00001", "doc_id": 2626 }, "chunk_id": "train_shard_00001_2626_0", "global_id": 9400 }, { "text": "Thus, the evolution and spread of strains belonging to CC95 are very different from those of another cosmopolitan human-associated clonal complex, CC131, which has increased significantly in frequency as a cause of extraintestinal infection over the past 15 years due to the evolution and spread of two very closely related, nearly monomorphic lineages.\n\nFine-Scale Structure Analysis Shows Epidemic Patterns of Clonal Complex 95, a Cosmopolitan Escherichia coli Lineage Responsible for Extraintestinal Infection.", "token_count": 132, "char_count": 520, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [ "CC131", "CC95" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:11.270014", "source": { "split": "train_shard_00001", "doc_id": 2626 }, "chunk_id": "train_shard_00001_2626_1", "global_id": 9401 }, { "text": "Shiga-toxin-producing Escherichia coli (STEC) is associated with diarrhea and hemolytic uremic syndrome (HUS). STEC infections in Costa Rica are rarely reported in children. We gathered all the records of STEC infections in children documented at the National Children's Hospital, a tertiary referral hospital, from 2015 to 2020. Clinical, microbiological, and genomic information were analyzed and summarized. A total of 3,768 diarrheal episodes were reviewed. Among them, 31 STEC were characterized (29 fecal, 1 urine, and 1 bloodstream infection). The prevalence of diarrheal disease due to STEC was estimated at 0.8% (n = 29/3,768), and HUS development was 6.4% (n = 2/31). The stx1 gene was found in 77% (n = 24/31) of STEC strains. In silico genomic predictions revealed a predominant prevalence of serotype O118/O152:H2, accompanied by a cluster exhibiting allele differences ranging from 33 to 8, using a core-genome multilocus sequence typing (cgMLST) approach. This is the first study using a genomic approach for STEC infections in Costa Rica.IMPORTANCEThis study provides a comprehensive description of clinical, microbiological, genomic, and demographic data from patients who attended the only pediatric hospital in Costa Rica with Shiga-toxin-producing Escherichia coli (STEC) infections. Despite the low prevalence of STEC infections, we found a predominant serotype O118/O152:H2, highlighting the pivotal role of genomics in understanding the epidemiology of public health threats such as STEC", "token_count": 481, "char_count": 1559, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:11.914244", "source": { "split": "train_shard_00001", "doc_id": 2627 }, "chunk_id": "train_shard_00001_2627_0", "global_id": 9402 }, { "text": "Employing a genomic approach for this pathogen for the first time in Costa Rica, we identified a higher prevalence of STEC in children under 2 years old, especially those with gastrointestinal comorbidities, residing in densely populated regions. Limitations such as potential geographic bias and lack of strains due to direct molecular diagnostics are acknowledged, emphasizing the need for continued surveillance to uncover the true extent of circulating serotypes and potential outbreaks in Costa Rica.\n\nA 6-year retrospective study of clinical features, microbiology, and genomics of Shiga toxin-producing Escherichia coli in children who presented to a tertiary referral hospital in Costa Rica.", "token_count": 172, "char_count": 706, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7525, "quality_score": 0.8762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:12.389075", "source": { "split": "train_shard_00001", "doc_id": 2627 }, "chunk_id": "train_shard_00001_2627_1", "global_id": 9403 }, { "text": "In our previous microbiome profiling analysis, Lactobacillus (L.) johnsonii was suggested to contribute to resistance against chronic heat stress-induced diarrhea in weaned piglets. Forty-nine L. johnsonii strains were isolated from these heat stress-resistant piglets, and their probiotic properties were assessed. Strains N5 and N7 exhibited a high survival rate in acidic and bile environments, along with an antagonistic effect against Salmonella. To identify genes potentially involved in these observed probiotic properties, the complete genome sequences of N5 and N7 were determined using a combination of Illumina and nanopore sequencing. The genomes of strains N5 and N7 were found to be highly conserved, with two N5-specific and four N7-specific genes identified. Multiple genes involved in gastrointestinal environment adaptation and probiotic properties, including acidic and bile stress tolerance, anti-inflammation, CAZymes, and utilization and biosynthesis of carbohydrate compounds, were identified in both genomes. Comparative genome analysis of the two genomes and 17 available complete L. johnsonii genomes revealed 101 genes specifically harbored by strains N5 and N7, several of which were implicated in potential probiotic properties. Overall, this study provides novel insights into the genetic basis of niche adaptation and probiotic properties, as well as the genome diversity of L. johnsonii.\n\nCharacterization of Probiotic Properties and Whole-Genome Analysis of Lactobacillus johnsonii N5 and N7 Isolated from Swine.", "token_count": 427, "char_count": 1601, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5981, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:13.037878", "source": { "split": "train_shard_00001", "doc_id": 2628 }, "chunk_id": "train_shard_00001_2628_0", "global_id": 9404 }, { "text": "

Introduction

In this work, 170 strains covering 13 species from the Lactobacillaceae family were analyzed to determine minimal inhibitory concentration (MIC) distributions to nine antimicrobial agents, and genes potentially conferring resistance. This allows a proposal of tentative Epidemiological Cut-Offs (ECOFFs) that follows the phylogeny for interpretation of resistance in the 13 species.

Methods

The 170 strains originated from different sources, geographical areas, and time periods. MICs for nine antibiotics were determined according to the ISO 10932 standard for lactobacillia and by a modified CLSI-method for Leuconostoc and Pediococcus which ensured sufficient growth. The strains were whole genome sequenced, subtyped by core genome analysis, and assessed for the presence of antibiotic resistance genes using the ResFinder and NCBI AMRFinder databases.

Results and discussion

The data provide evidence that antimicrobial susceptibility follows phylogeny instead of fermentation pattern and accordingly, tentative ECOFFs were defined. For some species the tentative ECOFFs for specific antibiotics are above the cut-off values set by the European Food Safety Authority (EFSA) which are primarily defined according to fermentation pattern or at genus level. The increased tolerance for specific antibiotics observed for some species was evaluated to be innate, as only for one strain phenotypic resistance was found to be related to an acquired resistance gene. In general, more data are needed to define ECOFFs and since the number of isolates available for industrial relevant bacterial species are often limited compared to clinically relevant species, it is important; 1) that strains are unambiguously defined at species level and subtyped through core genome analysis, 2) MIC determination are performed by use of a standardized method to define species-specific MIC distributions and 3) that known antimicrobial resistance genes are determined in whole genome sequences to support the MIC determinations.", "token_count": 495, "char_count": 2069, "word_count": 283, "semantic_coherence": 1, "information_density": 0.583, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:13.738079", "source": { "split": "train_shard_00001", "doc_id": 2629 }, "chunk_id": "train_shard_00001_2629_0", "global_id": 9405 }, { "text": "Antimicrobial susceptibility testing and tentative epidemiological cut-off values for Lactobacillaceae family species intended for ingestion.", "token_count": 39, "char_count": 148, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:14.142297", "source": { "split": "train_shard_00001", "doc_id": 2629 }, "chunk_id": "train_shard_00001_2629_1", "global_id": 9406 }, { "text": "

Purpose

Comparative genomic analysis of strains may help us to better understand the wide diversity of their genetic profiles. The aim of this study was to analyse the genomic features of the resistome and virulome of Brazilian first methicillin-resistant Staphylococcus aureus (MRSA) isolates and their relationship to other Brazilian and international MRSA strains.

Methodology

The whole genomes of three MRSA strains previously isolated in Vitória da Conquista were sequenced, assembled, annotated and compared with other MRSA genomes. A phylogenetic tree was constructed and the pan-genome and accessory and core genomes were constructed. The resistomes and virulomes of all strains were identified.Results/Key findings. Phylogenetic analysis of all 49 strains indicated different clones showing high similarity. The pan-genome of the analysed strains consisted of 4484 genes, with 31 % comprising the gene portion of the core genome, 47 % comprising the accessory genome and 22 % being singletons. Most strains showed at least one gene related to virulence factors associated with immune system evasion, followed by enterotoxins. The strains showed multiresistance, with the most recurrent genes conferring resistance to beta-lactams, fluoroquinolones, aminoglycosides and macrolides.

Conclusions

Our comparative genomic analysis showed that there is no pattern of virulence gene distribution among the clones analysed in the different regions. The Brazilian strains showed similarity with clones from several continents.\n\nGenomic profile of Brazilian methicillin-resistant Staphylococcus aureus resembles clones dispersed worldwide.", "token_count": 420, "char_count": 1660, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:14.774086", "source": { "split": "train_shard_00001", "doc_id": 2630 }, "chunk_id": "train_shard_00001_2630_0", "global_id": 9407 }, { "text": "An alcoholic beverage (35.4%v/v ethanol) was produced by distillation of the fermented broth obtained by continuous whey fermentation with a lactose-fermenting yeast Kluyveromyces marxianus. Forty volatile compounds were identified in this drink by gas chromatography. Higher alcohols were the most abundant group of volatile compounds present, with isoamyl, isobutyl, 1-propanol, and isopentyl alcohols being found in highest quantities (887, 542, 266, and 176mg/l, respectively). Ethyl acetate had the highest concentration (138mg/l) among the esters. Besides higher alcohols and esters, other components, including aldehydes, acids and terpenes were also identified in the whey spirit. Considering that the quality of an alcoholic beverage can be evaluated by the relation between isoamyl alcohol/2-methyl-1-propanol and 2-methyl-1-propanol/1-propanol, which have to be higher than unity, it was concluded that a novel spirit of acceptable organoleptic characteristics can be produced by cheese whey continuous fermentation with K. marxianus.\n\nCharacterisation of volatile compounds in an alcoholic beverage produced by whey fermentation", "token_count": 318, "char_count": 1140, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8137, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:15.342411", "source": { "split": "train_shard_00001", "doc_id": 2631 }, "chunk_id": "train_shard_00001_2631_0", "global_id": 9408 }, { "text": "

Objectives

Since its discovery, blaNDM-5 has spread widely amongst Escherichia coli strains in clinical patients, causing carbapenem resistance. Here we report the complete genome sequence of an NDM-5-producing E. coli strain isolated from the faecal sample of a healthy individual in Hangzhou, China.

Methods

The whole-genome sequence of E. coli CREC8 was obtained utilising both the Nanopore sequencer and the Illumina NovaSeq 6000 platform. Antimicrobial resistance genes, multilocus sequence typing, and plasmid replicons were identified using the BacWGSTdb server. The phylogenetic relationship between CREC8 and other E. coli strains was investigated using the core genome multilocus sequence typing (cgMLST) strategy.

Results

The complete genome sequence of E. coli CREC8 consists of one chromosome and 7 plasmids. CREC8 belongs to ST167 according to the MLST scheme. Seven ARGs were identified, including carbapenem resistance gene blaNDM-5 which was located in an IncFIA/IncFII type plasmid. A total of 164 E. coli ST167 strains related to 25 countries across four continents can be retrieved from the NCBI database, 95 of them carrying the blaNDM gene with blaNDM-5 the most (N = 79). Phylogenetic analysis revealed a worldwide distribution of E. coli ST167 strains, with China having the highest prevalence (37%, 61/165).

Conclusion

In summary, we reported a blaNDM-5-carrying E. coli ST167 strain isolated from a healthy individual in China. Such strains are more commonly isolated from hospitalised patients but are rarely isolated from healthy individuals. This indicates a further epidemic of carbapenem-resistant E. coli strains in the healthy population which needs our attention.", "token_count": 518, "char_count": 1781, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6116, "quality_score": 0.8058, "entities": { "genes": [ "ST167", "CREC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:16.010739", "source": { "split": "train_shard_00001", "doc_id": 2632 }, "chunk_id": "train_shard_00001_2632_0", "global_id": 9409 }, { "text": "Genomic insights into a blaNDM-5-carrying Escherichia coli ST167 isolate recovered from faecal sample of a healthy individual in China.", "token_count": 46, "char_count": 146, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [ "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:16.372236", "source": { "split": "train_shard_00001", "doc_id": 2632 }, "chunk_id": "train_shard_00001_2632_1", "global_id": 9410 }, { "text": "Population studies provide insights into the interplay between the gut microbiome and geographical, lifestyle, genetic and environmental factors. However, low- and middle-income countries, in which approximately 84% of the world's population lives1, are not equitably represented in large-scale gut microbiome research2-4. Here we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,801 women from Burkina Faso, Ghana, Kenya and South Africa. By engaging with communities that range from rural and horticultural to post-industrial and urban informal settlements, we capture a far greater breadth of the world's population diversity. Using shotgun metagenomic sequencing, we identify taxa with geographic and lifestyle associations, including Treponema and Cryptobacteroides species loss and Bifidobacterium species gain in urban populations. We uncover 1,005 bacterial metagenome-assembled genomes, and we identify antibiotic susceptibility as a factor that might drive Treponema succinifaciens absence in urban populations. Finally, we find an HIV infection signature defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals so far, and paired with extensive clinical biomarkers and demographic data, provides extensive opportunity for microbiome-related discovery.\n\nExpanding the human gut microbiome atlas of Africa.", "token_count": 367, "char_count": 1549, "word_count": 200, "semantic_coherence": 1, "information_density": 0.695, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:16.957389", "source": { "split": "train_shard_00001", "doc_id": 2633 }, "chunk_id": "train_shard_00001_2633_0", "global_id": 9411 }, { "text": "Treating Helicobacter pylori (H. pylori) infection requires large quantities of antibiotics, thus dramatically promoting the enrichment and dissemination of antimicrobial resistance (AMR) in feces. However, the influence of H. pylori eradication on the AMR mobility and the gut microbiota evolution has yet to be thoroughly investigated. Here, a study involving 12 H. pylori-positive participants was conducted, and the pre- and post- eradication fecal samples were sequenced. Metagenomic analysis revealed that the eradication treatment drastically altered the gut microbiome, with the Escherichia and Klebsiella genera emerging as the predominant bacteria. Interestingly, the eradication treatment significantly increased the relative abundance and diversity of resistome and mobilome in gut microbiota. Eradication of H. pylori also enriched AMR genes (ARGs) conferring resistance to antibiotics not administered because of the co-location with other ARGs or mobile genetic elements (MGEs). Additionally, the Escherichia and Klebsiella genera were identified as the primary bacterial hosts of these highly transferable ARGs. Furthermore, the genomic variations associated with ARGs in Escherichia coli (E. coli) caused by the eradication treatment were profiled, including the parC, parE, and gyrA genes. These findings revealed that H. pylori eradication promoted the enrichment of ARGs and MGEs in the Escherichia and Klebsiella genera, and further facilitated bacterial evolution through the horizontal transfer of ARGs and genomic variations.\n\nEradication of Helicobacter pylori reshapes gut microbiota and facilitates the evolution of antimicrobial resistance through gene transfer and genomic mutations in the gut.", "token_count": 425, "char_count": 1723, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5745, "quality_score": 0.7872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:17.582001", "source": { "split": "train_shard_00001", "doc_id": 2634 }, "chunk_id": "train_shard_00001_2634_0", "global_id": 9412 }, { "text": "A Gram-stain-positive aerobic, rod-shaped, spore-producing bacterium forming colonies with convex elevation and a smooth, intact margin was isolated from a freshwater sample collected from a well situated in an agricultural field. The 16S rRNA gene sequence of the isolated strain BA0131T showed the highest sequence similarity to Lysinibacillus yapensis ylb-03T (99.25%) followed by Ureibacillus chungkukjangi 2RL3-2T (98.91%) and U. sinduriensis BLB-1T (98.65%). The strain BA0131T was oxidase and catalase positive and urease negative. It also tested positive for esculin hydrolysis and reduction of potassium nitrate, unlike its phylogenetically closest relatives. The predominant fatty acids in strain BA0131T included were anteiso-C15:0, iso-C16:0, iso-C15:0, iso-C14:0 and the major polar lipids comprised were phosphatidylglycerol, diphosphatidylglycerol and phosphatidylethanolamine. The respiratory quinones identified in strain BA0131T were MK8 (H2) (major) and MK8 (minor). The strain BA0131T shared the lowest dDDH values with L. yapensis ylb-03T (21%) followed by U. chungkukjangi 2RL3-2T (24.2%) and U. sinduriensis BLB-1T (26.4%) suggesting a closer genetic relationship U. sinduriensis BLB-1T. The ANI percentage supported the close relatedness with U", "token_count": 518, "char_count": 1444, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [ "MK8", "BA0131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:18.239868", "source": { "split": "train_shard_00001", "doc_id": 2635 }, "chunk_id": "train_shard_00001_2635_0", "global_id": 9413 }, { "text": "sinduriensis BLB-1T (83.61%) followed by U. chungkukjangi 2RL3-2T (82.03%) and U. yapensis ylb-03T (79.57%). The core genome-based phylogeny constructed using over 13,704 amino acid positions and 92 core genes revealed the distinct phylogenetic position of strain BA0131T among the genus Ureibacillus. The distinct physiological, biochemical characteristics and genotypic relatedness data indicate the strain BA0131T represents a novel species of the genus Ureibacillus for which the name Ureibacillus aquaedulcis sp. nov. (Type strain, BA0131T = MCC 5284 = JCM 36475) is proposed. Additionally, based on extensive genomic and phylogenetic analyses, we propose reclassification of two species, L. yapensis and L. antri, as U. yapensis comb. nov. (Type strain, ylb-03T = JCM 32871T = MCCC 1A12698T) and U. antri (Type strain, SYSU K30002T = CGMCC 1.13504T = KCTC 33955T).\n\nUreibacillus aquaedulcis sp. nov., isolated from freshwater well and reclassification of Lysinibacillus yapensis and Lysinibacillus antri as Ureibacillus yapensis comb. nov. and Ureibacillus antri comb. Nov.", "token_count": 508, "char_count": 1211, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6144, "quality_score": 0.8072, "entities": { "genes": [ "BA0131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:18.887424", "source": { "split": "train_shard_00001", "doc_id": 2635 }, "chunk_id": "train_shard_00001_2635_1", "global_id": 9414 }, { "text": "Abstract

Fusarium is an Ascomycota with several relevant pathogenic species of plants and animals. Some phytopathogenic species have received special attention due to their negative economic impact on the agricultural industry around the world. Traditionally, identification and taxonomic analysis of Fusarium have relied on morphological and phenotypic features, including the hosts of the fungus, leading to taxonomic conflicts that have been solved using molecular systematic technologies. In this work, we applied a phylogenomic approach that allowed us to resolve the evolutionary history of the species complexes of the genus and present evidence that supports the F. ventricosum species complex as the most basal lineage of the genus. Additionally, we present evidence that proposes modifications to the previous hypothesis of the evolutionary history of the F. staphyleae, F. newnesense, F. nisikadoi, F. oxysporum, and F. fujikuroi species complexes. Evolutionary analysis showed that the genome GC content have a tendency to be lower in more modern lineages, below 49.3%, while genome size gain and losses are present during the evolution of the genus. Interestingly core genome duplication events have a positive correlation with the genome size. Evolutionary and genome conservation analysis supports the F3 hypothesis of Fusarium as a more compact and conserved group in terms of genome conservation. By contrast the most basal clades, outside the F3 hypothesis only share 8.8% of its genomic sequences with the F3 clade.

\n\nAn evolutionary view of the Fusarium genome", "token_count": 434, "char_count": 1755, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5787, "quality_score": 0.7894, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:19.516374", "source": { "split": "train_shard_00001", "doc_id": 2636 }, "chunk_id": "train_shard_00001_2636_0", "global_id": 9415 }, { "text": "Abstract

Background: N4-like viruses, with specific genomic features and propagation signatures, comprise a unique viral clade within the Podoviridae family. N4-like viruses are commonly characterized by the N4-like major capsid protein (MCP) and a giant virion-encapsulated RNA polymerase (N4-like RNAP) with a size of approximately 3,500-aa, which is the largest viral protein so far described. To date, our understanding of N4-like viruses is largely derived from 80 viral isolates that infect bacteria. Thus, it is necessary to expand the diversity of N4-like viruses in culturing-independent methods.

Methods:

A Hidden-Markov-Module based method was designed based on two characterized N4-specific marker genes, major capsid protein and N4-like virion-encapsulated RNA polymerase. Viral sub-clades were classified based on the monophyly presented in phylogenic tree and the results of pangenome analysis. Further analysis assessed different distribution patterns, genomic properties, hosts’ metabolism reprogramming potentialities, significance of viral tRNA and horizontal gene transfer landscape.

Results:

We identified 1,000 N4-like virus sequences from genomes and metagenomes representing diverse habitats from around the world. N4-like viruses have been classified into 27 sub-clades and detected in almost all habitats from pole to pole, including some novel habitats, such as oral mucosa and Antarctica. Virulent factors might be crucial for some human-associated N4-like viruses to reprogram the metabolism of host cells and mediate their pathogenic ability through horizontal gene transfer. From the pangenome analysis, the protein diversity was expended over 7-fold and 17 conserved house-keeping genes were identified. Transcriptional compensation of tRNA indicates that producing progeny virion might be the main significance of viral tRNAs", "token_count": 476, "char_count": 1895, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6614, "quality_score": 0.8307, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:20.168135", "source": { "split": "train_shard_00001", "doc_id": 2637 }, "chunk_id": "train_shard_00001_2637_0", "global_id": 9416 }, { "text": "From the horizontal gene transfer network, some N4-like viral sub-clades were observed that potentially infect some important human pathogens, such as Campylobacteria and Veillonella , which have not been considered as potential hosts of N4-like virus or even any virus.

Conclusion:

This study expands the knowledge of N4-like viruses via global metagenomic datasets, reveals the novel ecological and genomic signatures of these viruses and will provide the backbone for further N4-like virus studies.

\n\nIdentification of hidden N4-like viruses and their interactions with hosts in global metagenomes", "token_count": 144, "char_count": 612, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7674, "quality_score": 0.8837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:20.595233", "source": { "split": "train_shard_00001", "doc_id": 2637 }, "chunk_id": "train_shard_00001_2637_1", "global_id": 9417 }, { "text": "Campylobacter jejuni and Salmonella enterica co-infections in gastroenteritis cases are underexplored, particularly in relation to microbiome dysbiosis. This study uses metagenomic and culture-based approaches to investigate pathogen genotypes and stool microbiome composition. Stool samples from three patients were analysed using culture, qPCR and whole genome sequencing (WGS) of genomes and metagenomes. Strain typing and antimicrobial resistance (AMR) profiling were conducted for both pathogens. The stool microbiome structure was compared between the three patients and across three time points in one patient. C. jejuni and Salmonella enterica were of different strains and different proportions in the cases. C. jejuni sequence types were identified as ST-794, ST-50 and ST-10025, while S. enterica serovars Enteritidis ST-183 and S. Derby ST-39 were identified. C. jejuni AMR genotypes included bla OXA-447 , gyr A (T86I), and tet (O). S. Enteritidis contained AMR gene mdsa A-B, and S. Derby contained mdsa A-B and fos A7 genes. Despite similarities in Bristol scales for stool composition, the three cases exhibited distinct microbiome population structures, suggesting there is no one signature microbial profile of microbiomes with a Campylobacter - Salmonella co-infection. A temporal trend towards microbial diversity was observed within a patient, shifting from Proteobacteria dominance (93.3%) during acute infection towards Bacteroidetes (89.5%) abundance post-infection, suggesting that moving towards diverse communities may play a key role in patient recovery. These findings reveal a case study of microbiome disruption for patients infected with C. jejuni and S. enterica and highlight the value of direct stool sequencing in understanding pathogen abundance in stool and microbiome dysbiosis.", "token_count": 465, "char_count": 1817, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:21.236711", "source": { "split": "train_shard_00001", "doc_id": 2638 }, "chunk_id": "train_shard_00001_2638_0", "global_id": 9418 }, { "text": "Case study: Genomic characteristics of the gut microbiome, Campylobacter and Salmonella genotypes in three cases of gastroenteritis co-infections", "token_count": 48, "char_count": 159, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:21.591854", "source": { "split": "train_shard_00001", "doc_id": 2638 }, "chunk_id": "train_shard_00001_2638_1", "global_id": 9419 }, { "text": "

Background

Providencia rettgeri is a nosocomial pathogen associated with urinary tract infections and related to Healthcare-Associated Infection (HAI). In recent years isolates producing New Delhi Metallo-β-lactamase (NDM) and other β-lactamases have been reported that reduce the efficiency of clinical antimicrobial treatments. In this study, we analyzed antibiotic resistance, the presence of resistance genes and the clonal relationship of two P. rettgeri isolates obtained from male patients admitted to the same hospital in Bogotá - Colombia, 2015.

Results

Antibiotic susceptibility profile evaluated by the Kirby-Bauer method revealed that both isolates were resistant to third-generation carbapenems and cephalosporins. Whole-genome sequencing (Illumina HiSeq) followed by SPAdes assembling, Prokka annotation in combination with an in-house Python program and resistance gene detection by ResFinder identified the same six β-lactamase genes in both isolates: blaNDM-1, blaVIM-2, blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1. Additionally, various resistance genes associated with antibiotic target alteration (arnA, PmrE, PmrF, LpxA, LpxC, gyrB, folP, murA, rpoB, rpsL, tet34) were found and four efflux pumps (RosAB, EmrD, mdtH and cmlA). The additional resistance to gentamicin in one of the two isolates could be explained by a detected SNP in CpxA (Cys191Arg) which is involved in the stress response of the bacterial envelope. Genome BLAST comparison using CGView, the ANI value (99.99%) and the pangenome (using Roary) phylogenetic tree (same clade, small distance) showed high similarity between the isolates", "token_count": 512, "char_count": 1706, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7376, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:22.237418", "source": { "split": "train_shard_00001", "doc_id": 2639 }, "chunk_id": "train_shard_00001_2639_0", "global_id": 9420 }, { "text": "The rMLST analysis indicated that both isolates were typed as rST-61,696, same as the RB151 isolate previously isolated in Bucaramanga, Colombia, 2013, and the FDAARGOS_330 isolate isolated in the USA, 2015.

Conclusions

We report the coexistence of the carbapenemase genes blaNDM-1, and blaVIM-2, together with the β-lactamase genes blaCTX-M-15, blaOXA-10, blaCMY-2 and blaTEM-1, in P. rettgeri isolates from two patients in Colombia. Whole-genome sequence analysis indicated a circulation of P. rettgeri rST-61,696 strains in America that needs to be investigated further.\n\nGenome-based characterization of two Colombian clinical Providencia rettgeri isolates co-harboring NDM-1, VIM-2, and other β-lactamases.", "token_count": 283, "char_count": 784, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7021, "quality_score": 0.8511, "entities": { "genes": [ "RB151" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:22.800190", "source": { "split": "train_shard_00001", "doc_id": 2639 }, "chunk_id": "train_shard_00001_2639_1", "global_id": 9421 }, { "text": "Three Gram-reaction-positive bacterial strains, designated KSW-18T, KSW2-22, and KSW4-11T, were isolated from seawater, and two dried seaweed samples collected at Gwakji Beach in Jeju, Republic of Korea, respectively, and their taxonomic positions were examined by a polyphasic approach. The 16S rRNA gene phylogeny showed that strain KSW4-11T was tightly associated with Microbacterium oleivorans NBRC 103075T, while strains KSW-18T and KSW2-22 formed a distinctive subline at the base of a clade including the above two strains. The three isolates showed high sequence similarity with one another (99.7-99.9%; 1-4 nt differences) and Microbacterium oleivorans (99.8-99.9%; 1-3 nt differences). The chemotaxonomic features were typical for the genus Microbacterium; Lysine as the diagnostic diamino acid and N-glycolylated muramic acid of the peptidoglycans, the predominant menaquinones of MK-11, MK-10 and MK-12, the major fatty acids of anteiso-C15:0 and anteiso-C17:0, and the major polar lipids including diphosphatidylglycerol, phosphatidylglycerol, and two or three unidentified glycolipids. In core genome-based phylogenetic tree, strains KSW-18T and KSW2-22 were closely associated with Microbacterium oleivorans NBRC 103075T, while strain KSW4-11T formed a distinctive subline at the base of a clade including the above three strains, in contrast to the 16S rRNA gene tree", "token_count": 511, "char_count": 1493, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6073, "quality_score": 0.8037, "entities": { "genes": [ "KSW4", "KSW2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:23.456063", "source": { "split": "train_shard_00001", "doc_id": 2640 }, "chunk_id": "train_shard_00001_2640_0", "global_id": 9422 }, { "text": "Strains KSW-18T and KSW2-22 shared an OrthoANIu of 98.6% and a digital DNA-DNA hybridization of 87.6% with each other, representing that they were strains of a species, while the OrthoANIu and digital DNA-DNA hybridization values between strains KSW-18T and KSW4-11T, and between both of these isolates and all members of the genus Microbacterium were ≤86.5% and ≤30.7%, respectively. The analyses of overall genomic relatedness indices and phenotypic distinctness support that the three isolates represent two new species of the genus Microbacterium. Based on the results obtained here, Microbacterium aquilitoris sp. nov. (type strain KSW-18T = KCTC 49623T = NBRC 115222T) and Microbacterium gwkjiense sp. nov. (type strain KSW4-11T = KACC 23321T = DSM 116380T) are proposed.\n\nMicrobacterium aquilitoris sp. nov. and Microbacterium gwkjiense sp. nov., isolated from beach.", "token_count": 372, "char_count": 973, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6094, "quality_score": 0.8047, "entities": { "genes": [ "KSW4", "KSW2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:24.029276", "source": { "split": "train_shard_00001", "doc_id": 2640 }, "chunk_id": "train_shard_00001_2640_1", "global_id": 9423 }, { "text": "To identify genome-based features characteristic of the avian and human pathogen Chlamydia(C.) psittaci and related chlamydiae, we analyzed whole-genome sequences of 33 strains belonging to 12 species. Using a novel genome analysis tool termed Roary ILP Bacterial Annotation Pipeline (RIBAP), this panel of strains was shown to share a large core genome comprising 784 genes and representing approximately 80% of individual genomes. Analyzing the most variable genomic sites, we identified a set of features of C. psittaci that in its entirety is characteristic of this species: (i) a relatively short plasticity zone of less than 30,000 nt without a tryptophan operon (also in C. abortus, C. avium, C. gallinacea, C. pneumoniae), (ii) a characteristic set of of Inc proteins comprising IncA, B, C, V, X, Y (with homologs in C. abortus, C. caviae and C. felis as closest relatives), (iii) a 502-aa SinC protein, the largest among Chlamydia spp., and (iv) an elevated number of Pmp proteins of subtype G (14 in C. psittaci, 14 in Cand. C. ibidis). In combination with future functional studies, the common and distinctive criteria revealed in this study provide important clues for understanding the complexity of host-specific behavior of individual Chlamydia spp.\n\nComparative Genome Analysis of 33 Chlamydia Strains Reveals Characteristic Features of Chlamydia Psittaci and Closely Related Species.", "token_count": 462, "char_count": 1484, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:24.691170", "source": { "split": "train_shard_00001", "doc_id": 2641 }, "chunk_id": "train_shard_00001_2641_0", "global_id": 9424 }, { "text": "Genome sequencing of Klebsiella pneumoniae PVN-1, isolated from effluent treatment plant (ETP), generates a 5.064 Mb draft genome with 57.6% GC content. The draft genome assembled into 19 contigs comprises 4783 proteins, 3 rRNA, 44 tRNA, 8 other RNA, 4911 genes, and 73 pseudogenes. Genome information revealed the presence of phosphate metabolism/solubilizing, potassium solubilizing, auxin production, and other plant benefiting attributes like enterobactin and pyrroloquinoline quinone biosynthesis genes. Presence of gcd and pqq genes in K. pneumoniae PVN-1 genome validates the inorganic phosphate solubilizing potential (528.5 mg/L). Pangenome analysis identified a unique 5'-Nucleotidase that further assists in enhanced phosphate acquisition. Additionally, the genetic potential for complete benzoate, catechol, and phenylacetate degradation with stress response and heavy metal (Cu, Zn, Ni, Co) resistance was identified in K. pneumoniae PVN-1. Functioning of annotated plant benefiting genes validates by the metabolic activity of auxin production (7.40 µg/mL), nitrogen fixation, catalase activity, potassium solubilization (solubilization index-3.47), and protease activity (proteolytic index-2.27). In conclusion, the K. pneumoniae PVN-1 genome has numerous beneficial qualities that can be employed to enhance plant growth as well as for phytoremediation.

Supplementary information

The online version contains supplementary material available at 10.1007/s13205-021-03020-2.", "token_count": 504, "char_count": 1536, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:25.365353", "source": { "split": "train_shard_00001", "doc_id": 2642 }, "chunk_id": "train_shard_00001_2642_0", "global_id": 9425 }, { "text": "Revealing the potential of Klebsiella pneumoniae PVN-1 for plant beneficial attributes by genome sequencing and analysis.", "token_count": 38, "char_count": 128, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:25.748087", "source": { "split": "train_shard_00001", "doc_id": 2642 }, "chunk_id": "train_shard_00001_2642_1", "global_id": 9426 }, { "text": "The cultivated strawberry, Fragaria ×ananassa, is a recently domesticated fruit species of economic interest worldwide. As such, there is significant interest in continuous varietal improvement. Genomics-assisted improvement, including the use of DNA markers and genomic selection have facilitated significant improvements of numerous key traits during strawberry breeding. CRISPR/Cas-mediated genome editing allows targeted mutations and precision nucleotide substitutions in the target genome, revolutionizing functional genomics and crop improvement. Genome editing is beginning to gain traction in the more challenging polyploid crops, including allo-octoploid strawberry. The release of high-quality reference genomes and comprehensive subgenome-specific genotyping and gene expression profiling data in octoploid strawberry will lead to a surge in trait discovery and modification by using CRISPR/Cas. Genome editing has already been successfully applied for modification of several strawberry genes, including anthocyanin content, fruit firmness and tolerance to post-harvest disease. However, reports on many other important breeding characteristics associated with fruit quality and production are still lacking, indicating a need for streamlined genome editing approaches and tools in Fragaria ×ananassa. In this review, we present an overview of the latest advancements in knowledge and breeding efforts involving CRISPR/Cas genome editing for the enhancement of strawberry varieties. Furthermore, we explore potential applications of this technology for improving other Rosaceous plant species.\n\nAdvances in genomics and genome editing for improving strawberry (Fragaria ×ananassa).", "token_count": 369, "char_count": 1715, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:26.361786", "source": { "split": "train_shard_00001", "doc_id": 2643 }, "chunk_id": "train_shard_00001_2643_0", "global_id": 9427 }, { "text": "In many regions of the world, including the United States, human and animal fecal genetic markers have been found in flood waters. In this study, we use high-resolution whole genomic sequencing to examine the origin and distribution of Salmonella enterica after the 2018 Hurricane Florence flooding. We specifically asked whether S. enterica isolated from water samples collected near swine farms in North Carolina shortly after Hurricane Florence had evidence of swine origin. To investigate this, we isolated and fully sequenced 18 independent S. enterica strains from 10 locations (five flooded and five unflooded). We found that all strains have extremely similar chromosomes with only five single nucleotide polymorphisms (SNPs) and possessed two plasmids assigned bioinformatically to the incompatibility groups IncFIB and IncFII. The chromosomal core genome and the IncFIB plasmid are most closely related to environmental Salmonella strains isolated previously from the southeastern US. In contrast, the IncFII plasmid was found in environmental S. enterica strains whose genomes were more divergent, suggesting the IncFII plasmid is more promiscuous than the IncFIB type. We identified 65 antibiotic resistance genes (ARGs) in each of our 18 S. enterica isolates. All ARGs were located on the Salmonella chromosome, similar to other previously characterized environmental isolates. All isolates with different SNPs were resistant to a panel of commonly used antibiotics. These results highlight the importance of environmental sources of antibiotic-resistant S. enterica after extreme flood events.\n\nLocal and Environmental Reservoirs of Salmonella enterica After Hurricane Florence Flooding.", "token_count": 442, "char_count": 1764, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8086, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:26.993935", "source": { "split": "train_shard_00001", "doc_id": 2644 }, "chunk_id": "train_shard_00001_2644_0", "global_id": 9428 }, { "text": "In recent times K. pneumoniae , a common nosocomial pathogen, tends to evolve more virulent and multidrug-resistant. Urinary tract infections by antibiotic resistant and virulent K. pneumoniae are a growing concern due to the challenging treatment strategies. Hence understanding the genome and validating the genomic profile along with pan-genome analysis will facilitate surveillance of high risk-clones of K. pneumoniae to underpin management strategies toward early detection. Thus, the present study aimed to correlate genotypic and phenotypic antimicrobial resistance and pathogenicity associated with sequence types and virulence factors in Klebsiella spp. The complete genome profile of 3 K. pneumoniae and a K. variicola were analysed in the study which was assigned to ST200, ST45, ST147 and ST of K. variicola are not known. The accessory genome comprised 66% of genes consisting of shell and cloud genes in K. pneumoniae . The phenotypic antimicrobial resistance identified kp3 to have maximum resistance and the susceptibility of environment isolate K. variicola was less resistant to the tested antibiotics. The in vitro and genomic antimicrobial resistance profiling showed concordance with all the tested antibiotics against the 4 study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA , rmpA2 and magA . Though the genes encoding for major virulence factors; hypermucoviscosity, yersiniabactin and allantoin metabolism were absent, significant pathogenicity and mortality were observed for kp3 isolate in the Zebrafish infection model. In contrast, the isolates predicted with the aerobactin gene were observed with least mortality rate. In the present study virulome and in vivo study illustrate the discrepancies in the virulence. To the best of our knowledge, this is the first report on the presence of ste, stf , stc and sti major fimbrial operons of Salmonella enteric serotype Typhimurium in K. pneumoniae genome, that might contribute to the virulence of kp3", "token_count": 527, "char_count": 2078, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5599, "quality_score": 0.7799, "entities": { "genes": [ "ST45", "ST147", "ST200" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:27.649266", "source": { "split": "train_shard_00001", "doc_id": 2645 }, "chunk_id": "train_shard_00001_2645_0", "global_id": 9429 }, { "text": "Our study highlights the further necessity of genomic and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high risk K. pneumoniae clones.\n\nComparative Analysis of Complete Genome Sequences and Phenotypic Correlation of Klebsiella spp.", "token_count": 68, "char_count": 282, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7949, "quality_score": 0.8974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:28.014655", "source": { "split": "train_shard_00001", "doc_id": 2645 }, "chunk_id": "train_shard_00001_2645_1", "global_id": 9430 }, { "text": "Gardnerella vaginalis has long been associated with bacterial vaginosis, a condition that increases the risk of women to preterm birth, sexually transmitted infections, and other adverse sequelae. However, G. vaginalis is also commonly found in healthy asymptomatic women of all ages. This raises the question if genetic differences among strains might distinguish potentially pathogenic from commensal strains. To disentangle the diversity of G. vaginalis, we invoked the concept of ecotypes-lineages of genetically and ecologically distinct strains within a named species-to better understand their evolutionary history and identify functional characteristics. We compared the genomes of G. vaginalis to six species in the closely related Bifidobacterium genus and found that G. vaginalis has a large accessory genome relative to Bifidobacterium, including many unique genes possibly involved in metabolism, drug resistance, and virulence. We then performed a comparative genomic analysis of 35 strains of G. vaginalis to infer a phylogeny based on the combined analysis of the core genome, using nucleotide substitution models, and the accessory genome, using gene gain/loss models. With the inferred tree topology, we performed comparisons of functional gene content among lineages that diverged at varying depths in the phylogeny and found significant differences in the representation of genes putatively involved in pathogenicity. Our functional enrichment analysis suggests that some lineages of G. vaginalis may possess enhanced pathogenic capabilities, including genes involved in mucus degradation like sialidases, while others may be commensal strains, lacking many of these pathogenic capabilities. The combined phylogenetic evidence and functional enrichment analysis allowed us to identify distinct ecotypes that have evolved in G. vaginalis as the result of the differential gene gain/loss for specific functions, including the capability to cause disease. We finally discuss how this analysis framework could be used to gain insight into the etiology of bacterial vaginosis and improve diagnosis.", "token_count": 527, "char_count": 2183, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8003, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:28.659148", "source": { "split": "train_shard_00001", "doc_id": 2646 }, "chunk_id": "train_shard_00001_2646_0", "global_id": 9431 }, { "text": "Focusing the diversity of Gardnerella vaginalis through the lens of ecotypes.", "token_count": 26, "char_count": 84, "word_count": 11, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:29.022089", "source": { "split": "train_shard_00001", "doc_id": 2646 }, "chunk_id": "train_shard_00001_2646_1", "global_id": 9432 }, { "text": "The inhibitory effects of various lignocellulose degradation products on glucose fermentation by the thermotolerant yeast Kluyveromyces marxianus were studied in batch cultures. The toxicity of the aromatic alcohol catechol and two aromatic aldehydes (4-hydroxybenzaldehyde and vanillin) was investigated in binary combinations. The aldehyde furfural that usually is present in relatively high concentration in hydrolyzates from pentose degradation was also tested. Experiments were conducted by combining agents at concentrations that individually caused 25% inhibition of growth. Compared to the relative toxicity of the individual compounds, combinations of furfural with catechol and 4-hydroxybenzaldehyde were additive (50% inhibition of growth). The other binary combinations assayed (catechol with 4-hydroxybenzaldehyde, and vanillin with catechol, furfural, or 4-hydroxybenzaldehyde) showed synergistic effect on toxicity and caused a 60-90% decrease in cell mass production. The presence of aldehydes in the fermentation medium strongly inhibited cell growth and ethanol production. Kluyveromyces marxianus reduces aldehydes to their corresponding alcohols to mitigate the toxicity of these compounds. The total reduction of aldehydes was needed to start ethanol production. Vanillin, in binary combination, was dramatically toxic and was the only compound for which inhibition could not be overcome by yeast strain assimilation, causing a 90% reduction in both cell growth and fermentation.\n\nEffect of binary combinations of selected toxic compounds on growth and fermentation of Kluyveromyces marxianus.", "token_count": 415, "char_count": 1614, "word_count": 215, "semantic_coherence": 1, "information_density": 0.586, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:29.644804", "source": { "split": "train_shard_00001", "doc_id": 2647 }, "chunk_id": "train_shard_00001_2647_0", "global_id": 9433 }, { "text": "

Background

Tannerella forsythia is a bacterial pathogen implicated in periodontal disease. Numerous virulence-associated T. forsythia genes have been described, however, it is necessary to expand the knowledge on T. forsythia's genome structure and genetic repertoire to further elucidate its role within pathogenesis. Tannerella sp. BU063, a putative periodontal health-associated sister taxon and closest known relative to T. forsythia is available for comparative analyses. In the past, strain confusion involving the T. forsythia reference type strain ATCC 43037 led to discrepancies between results obtained from in silico analyses and wet-lab experimentation.

Results

We generated a substantially improved genome assembly of T. forsythia ATCC 43037 covering 99% of the genome in three sequences. Using annotated genomes of ten Tannerella strains we established a soft core genome encompassing 2108 genes, based on orthologs present in > = 80% of the strains analysed. We used a set of known and hypothetical virulence factors for comparisons in pathogenic strains and the putative periodontal health-associated isolate Tannerella sp. BU063 to identify candidate genes promoting T. forsythia's pathogenesis. Searching for pathogenicity islands we detected 38 candidate regions in the T. forsythia genome. Only four of these regions corresponded to previously described pathogenicity islands. While the general protein O-glycosylation gene cluster of T. forsythia ATCC 43037 has been described previously, genes required for the initiation of glycan synthesis are yet to be discovered. We found six putative glycosylation loci which were only partially conserved in other bacteria. Lastly, we performed a comparative analysis of translational bias in T. forsythia and Tannerella sp. BU063 and detected highly biased genes.

Conclusions

We provide resources and important information on the genomes of Tannerella strains. Comparative analyses enabled us to assess the suitability of T", "token_count": 529, "char_count": 2008, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [ "BU063" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:30.305340", "source": { "split": "train_shard_00001", "doc_id": 2648 }, "chunk_id": "train_shard_00001_2648_0", "global_id": 9434 }, { "text": "forsythia virulence factors as therapeutic targets and to suggest novel putative virulence factors. Further, we report on gene loci that should be addressed in the context of elucidating T. forsythia's protein O-glycosylation pathway. In summary, our work paves the way for further molecular dissection of T. forsythia biology in general and virulence of this species in particular.\n\nComparative genome characterization of the periodontal pathogen Tannerella forsythia.", "token_count": 120, "char_count": 469, "word_count": 66, "semantic_coherence": 1, "information_density": 0.803, "quality_score": 0.9015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:30.685373", "source": { "split": "train_shard_00001", "doc_id": 2648 }, "chunk_id": "train_shard_00001_2648_1", "global_id": 9435 }, { "text": "

Introduction

To understand the prevalence of avian methicillin-resistant Staphylococcus aureus (MRSA) and the current status of drug resistance in Qingdao, a comprehensive molecular epidemiological investigation and analysis of evolutionary relationships of MRSA isolates from broiler and layer chickens and waterfowl was conducted.

Material and methods

One hundred and two avian MRSA strains were identified by multi-locus sequence typing, staphylococcal protein A (spa) and staphylococcal cassette chromosome mec (SCCmec) typing, and whole-genome sequencing.

Results

The sequence type (ST) 9-t899-SCCmec IVb type represented the highest proportion of avian-derived MRSA strains (71.57%), with ST398 type strains occasionally observed in broilers and waterfowl. The poultry-derived MRSA strains were all resistant to eight or more antimicrobials. Avian-derived MRSA strains carried 20 resistance genes, 109 virulence genes and 10 plasmids. Strains carrying the cfr oxazolidinone resistance gene were occasionally seen in broiler- and layer-derived MRSA. Single nucleotide polymorphism (SNP) core genome evolution and locus difference analysis showed that the closest strains were all of ST9-t899 type (to which also affiliated the highest number of strains) and this type occurred on all three kinds of poultry farm, but the SNP difference loci between strains of the same type ranged from 0 to 1472.

Conclusion

The dominant type of MRSA from different poultry sources in Qingdao is ST9-t899-SCCmec IVb, which is commonly resistant to a variety of antimicrobial drugs and carries a variety of resistance genes and a large number of virulence genes", "token_count": 508, "char_count": 1719, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [ "ST398", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:31.317830", "source": { "split": "train_shard_00001", "doc_id": 2649 }, "chunk_id": "train_shard_00001_2649_0", "global_id": 9436 }, { "text": "Sequence type 9-t899 type is widely spread among the three kinds of poultry investigated, but there are differences in affiliations.\n\nMolecular epidemiological characteristics and genetic evolutionary relationships of methicillin-resistant Staphylococcus aureus of different avian origins in Qingdao, China, using whole-genome sequencing.", "token_count": 89, "char_count": 345, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9024, "quality_score": 0.9512, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:31.695132", "source": { "split": "train_shard_00001", "doc_id": 2649 }, "chunk_id": "train_shard_00001_2649_1", "global_id": 9437 }, { "text": "

Background:

The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are circulating worldwide due to the fastidious nature of the bacteria and its difficulty to be culture isolated. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Methods Here, to elucidate the genomic diversity of Leptospira circulating strains, hybridization capture followed by Illumina sequencing of the core genome was performed directly from 20 clinicall samples that were PCR positive for pathogenic Leptospira . Results A set of samples subjected to capture with RNA probes covering the L. interrogans core genome resulted in 72 to 13,000-fold increase in pathogen reads when compared to standard sequencing without capture. A SNP analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genome was then performed in order to determine the genotype of the infecting strain. For samples with sufficent coverage (19/20 samples with coverage > 8X), we could unambigously identify L. interrogans sv Icterohaemorrhagiae (14 samples), L. kirschneri sv Grippotyphosa (4 samples) and L. interrogans sv Pyrogenes (1 sample) as the infecting strain. Conclusions We obtained for most of our clinicall samples high quality genomic data at suitable coverage for confident core genome genotyping of the agent of leptospirosis. The ability to generate culture-free genomic data opens new opportunities to better understand the epidemiology and evolution of this fastidious pathogen.\n\nCore genome sequencing and genotyping of Leptospira interrogans in clinical samples by target capture sequencing", "token_count": 466, "char_count": 1873, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5699, "quality_score": 0.7849, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:32.340600", "source": { "split": "train_shard_00001", "doc_id": 2650 }, "chunk_id": "train_shard_00001_2650_0", "global_id": 9438 }, { "text": "The genus Helicobacter is a group of Gram-negative, helical-shaped pathogens consisting of at least 36 bacterial species. Helicobacter pylori (H. pylori), infecting more than 50% of the human population, is considered as the major cause of gastritis, peptic ulcer, and gastric cancer. However, the genetic underpinnings of H. pylori that are responsible for its large scale epidemic and gastrointestinal environment adaption within human beings remain unclear. Core-pan genome analysis was performed among 75 representative H. pylori and 24 non-pylori Helicobacter genomes. There were 1173 conserved protein families of H. pylori and 673 of all 99 Helicobacter genus strains. We found 79 genome unique regions, a total of 202,359bp, shared by at least 80% of the H. pylori but lacked in non-pylori Helicobacter species. The operons, genes, and sRNAs within the H. pylori unique regions were considered as potential ones associated with its pathogenicity and adaptability, and the relativity among them has been partially confirmed by functional annotation analysis. However, functions of at least 54 genes and 10 sRNAs were still unclear. Our analysis of protein-protein interaction showed that 30 genes within them may have the cooperation relationship.\n\nComparative Genomics of H. pylori and Non-Pylori Helicobacter Species to Identify New Regions Associated with Its Pathogenicity and Adaptability.", "token_count": 458, "char_count": 1492, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:33.344948", "source": { "split": "train_shard_00001", "doc_id": 2651 }, "chunk_id": "train_shard_00001_2651_0", "global_id": 9439 }, { "text": "Metabolic syndrome (MS) comprises a vast range of metabolic dysfunctions, which can be associated to cardiovascular disease risk factors. MS is reaching pandemic levels worldwide and it currently affects around 25% in the adult population of developed countries. The definition states for the diagnosis of MS may be clear, but it is also relevant to interpret the patient data and realize whether similar criteria were used by different clinicians. The different criteria explain, at least in part, the controversies on the theme. Several studies are presently focusing on the microbiota changes according to the components of MS. It is widely accepted that the gut microbiota is a regulator of metabolic homeostasis, being the gut microbiome in MS described as dysbiotic and certain taxonomic groups associated to metabolic changes. Probiotics, and more recently synbiotics, arise as promising therapeutic alternatives that can mitigate some metabolic disturbances, namely by correcting the microbiome and bringing homeostasis to the gut. The most recent studies were revised and the promising results and perspectives revealed in this review.\n\nMicrobiota Modulation in Patients with Metabolic Syndrome.", "token_count": 258, "char_count": 1204, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:33.893368", "source": { "split": "train_shard_00001", "doc_id": 2652 }, "chunk_id": "train_shard_00001_2652_0", "global_id": 9440 }, { "text": "The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.\n\nSemi-automated assembly of high-quality diploid human reference genomes.", "token_count": 423, "char_count": 1803, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6405, "quality_score": 0.8202, "entities": { "genes": [ "CHM13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:34.514269", "source": { "split": "train_shard_00001", "doc_id": 2653 }, "chunk_id": "train_shard_00001_2653_0", "global_id": 9441 }, { "text": "

ABSTRACT

Background

The genome of SARS-CoV-2 is susceptible to mutations during viral replication due to the errors generated by RNA-dependent RNA polymerases. These mutations enable the SARS-CoV-2 to evolve into new strains. Viral quasispecies emerge from de novo mutations that occur in individual patients. In combination, these sets of viral mutations provide distinct genetic fingerprints that reveal the patterns of transmission and have utility in contract tracing.

Methods

Leveraging thousands of sequenced SARS-CoV-2 genomes, we performed a viral pangenome analysis to identify conserved genomic sequences. We used a rapid and highly efficient computational approach that relies on k-mers, short tracts of sequence, instead of conventional sequence alignment. Using this method, we annotated viral mutation signatures that were associated with specific strains. Based on these highly conserved viral sequences, we developed a rapid and highly scalable targeted sequencing assay to identify mutations, detect quasispecies and identify mutation signatures from patients. These results were compared to the pangenome genetic fingerprints.

Results

We built a k-mer index for thousands of SARS-CoV-2 genomes and identified conserved genomics regions and landscape of mutations across thousands of virus genomes. We delineated mutation profiles spanning common genetic fingerprints (the combination of mutations in a viral assembly) and rare ones that occur in only small fraction of patients. We developed a targeted sequencing assay by selecting primers from the conserved viral genome regions to flank frequent mutations. Using a cohort of SARS-CoV-2 clinical samples, we identified genetic fingerprints consisting of strain-specific mutations seen across populations and de novo quasispecies mutations localized to individual infections. We compared the mutation profiles of viral samples undergoing analysis with the features of the pangenome.

Conclusions

We conducted an analysis for viral mutation profiles that provide the basis of genetic fingerprints. Our study linked pangenome analysis with targeted deep sequenced SARS-CoV-2 clinical samples", "token_count": 514, "char_count": 2202, "word_count": 300, "semantic_coherence": 1, "information_density": 0.51, "quality_score": 0.755, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:35.175773", "source": { "split": "train_shard_00001", "doc_id": 2654 }, "chunk_id": "train_shard_00001_2654_0", "global_id": 9442 }, { "text": "We identified quasispecies mutations occurring within individual patients, mutations demarcating dominant species and the prevalence of mutation signatures, of which a significant number were relatively unique. Analysis of these genetic fingerprints may provide a way of conducting molecular contact tracing.\n\nProfiling SARS-CoV-2 mutation fingerprints that range from the viral pangenome to individual infection quasispecies", "token_count": 88, "char_count": 425, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:35.545668", "source": { "split": "train_shard_00001", "doc_id": 2654 }, "chunk_id": "train_shard_00001_2654_1", "global_id": 9443 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) belonging to the O26 serogroup represent an important cause of Hemolitic Uremic Syndrome (HUS) in children worldwide. The localization of STEC virulence genes on mobile genetic elements allowed the emergence of clones showing different assets of this accessory genomic fraction. A novel O26 STEC clone belonging to Sequence Type (ST) 29 and harboring stx2a, ehxA and etpD plasmid-borne genes has emerged and spread in Europe since the mid-1990s, while another ST29 clone positive for stx2d and lacking plasmid-borne virulence genes was recently described as emerging in France. In Italy, O26 has been the most frequently detected STEC serogroup from HUS cases since the late 1990s. In this study we describe the genomic characterization and population structure of 144 O26 STEC strains isolated from human sources in Italy in the period 1989-2020. A total of 89 strains belonged to ST21, 52 to ST29, two to ST396 and one to ST4944. ST29 strains started to be isolated from 1999. 24 strains were shown to harbour stx1a, alone (n=20) or in combination with stx2a (n=4). The majority of the strains (n=118) harbored stx2a genes only and the two ST396 strains harbored stx2d. A Hierarchical Clustering on Principal Components (HCPC) analysis, based on the detection of accessory virulence genes, antimicrobial resistance (AMR) genes and plasmid replicons, classified the strains in seven clusters identified with numbers from 1 to 7, containing two, 13, 39, 63, 16, 10 and one strain, respectively", "token_count": 518, "char_count": 1602, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8237, "entities": { "genes": [ "ST21", "ST4944", "ST396", "ST29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:36.179167", "source": { "split": "train_shard_00001", "doc_id": 2655 }, "chunk_id": "train_shard_00001_2655_0", "global_id": 9444 }, { "text": "The majority of the genetic features defining the clusters corresponded to plasmid-borne virulence genes, AMR genes and plasmid replicons, highlighting specific assets of plasmid-borne features associated with different clusters. Core genome Multi Locus Sequence Typing grouped ST21 and ST29 strains in three clades each, with each ST29 clade exactly corresponding to one HCPC cluster. Our results showed high conservation of either the core or the accessory genomic fraction in populations of ST29 O26 STEC, differently from what observed in ST21 strains, suggesting that a different selective pressure could drive the evolution of different populations of these pathogens possibly involving different ecological niches.\n\nPopulation Analysis of O26 Shiga Toxin-Producing Escherichia coli Causing Hemolytic Uremic Syndrome in Italy, 1989-2020, Through Whole Genome Sequencing.", "token_count": 223, "char_count": 883, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7603, "quality_score": 0.8802, "entities": { "genes": [ "ST21", "ST29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:36.699858", "source": { "split": "train_shard_00001", "doc_id": 2655 }, "chunk_id": "train_shard_00001_2655_1", "global_id": 9445 }, { "text": "Globally, the anaerobic bacterium Clostridium perfringens causes severe disease in a wide array of hosts; however, C. perfringens strains are also carried asymptomatically. Accessory genes are responsible for much of the observed phenotypic variation and virulence within this species, with toxins frequently encoded on conjugative plasmids and many isolates carrying up to 10 plasmids. Despite this unusual biology, current genomic analyses have largely excluded isolates from healthy hosts or environmental sources. Accessory genomes, including plasmids, also have often been excluded from broader scale phylogenetic investigations. Here we interrogate a comprehensive collection of 464 C. perfringens genomes and identify the first putative non-conjugative enterotoxin (CPE)-encoding plasmids and a putative novel conjugative locus (Bcp) with sequence similarity to a locus reported from Clostridium botulinum. We sequenced and archived 102 new C. perfringens genomes, including those from rarely sequenced toxinotype B, C, D and E isolates. Long-read sequencing of 11 C. perfringens strains representing all toxinotypes (A-G) identified 55 plasmids from nine distinct plasmid groups. Interrogation of the 464 genomes in this collection identified 1045 plasmid-like contigs from the nine plasmid families, with a wide distribution across the C. perfringens isolates. Plasmids and plasmid diversity play an essential role in C. perfringens pathogenicity and broader biology. We have expanded the C. perfringens genome collection to include temporal, spatial and phenotypically diverse isolates including those carried asymptomatically in the gastrointestinal microbiome. This analysis has resulted in the identification of novel C. perfringens plasmids whilst providing a comprehensive understanding of species diversity.", "token_count": 514, "char_count": 1907, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6194, "quality_score": 0.8097, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:37.376402", "source": { "split": "train_shard_00001", "doc_id": 2656 }, "chunk_id": "train_shard_00001_2656_0", "global_id": 9446 }, { "text": "Extensive genome analysis identifies novel plasmid families in Clostridium perfringens.", "token_count": 26, "char_count": 94, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:37.760767", "source": { "split": "train_shard_00001", "doc_id": 2656 }, "chunk_id": "train_shard_00001_2656_1", "global_id": 9447 }, { "text": "Aligning reads to a variation graph is a standard task in pangenomics, with downstream applications such as improving variant calling. While the vg toolkit (Garrison et al., Nature Biotechnology , 2018) is a popular aligner of short reads, GraphAligner (Rautiainen and Marschall, Genome Biology , 2020) is the state-of-the-art aligner of erroneous long reads. GraphAligner works by finding candidate read occurrences based on individually extending the best seeds of the read in the variation graph. However, a more principled approach recognized in the community is to co-linearly chain multiple seeds. We present a new algorithm to co-linearly chain a set of seeds in a string labeled acyclic graph, together with the first efficient implementation of such a co-linear chaining algorithm into a new aligner of erroneous long reads to acyclic variation graphs, GraphChainer . Compared to GraphAligner , GraphChainer aligns 12% to 17% more reads, and 21% to 28% more total read length, on real PacBio reads from human chromosomes 1, 22 and the whole human pangenome. On both simulated and real data, GraphChainer aligns between 95% and 99% of all reads, and of total read length. We also show that minigraph (Li et al., Genome Biology , 2020) and minichain (Chandra and Jain, RECOMB , 2023) obtain an accuracy of less than 60% on this setting. GraphChainer is freely available at https://github.com/algbio/GraphChainer . The datasets and evaluation pipeline can be reached from the previous address.\n\nChaining for Accurate Alignment of Erroneous Long Reads to Acyclic Variation Graphs*", "token_count": 434, "char_count": 1596, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5927, "quality_score": 0.7964, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:38.427749", "source": { "split": "train_shard_00001", "doc_id": 2657 }, "chunk_id": "train_shard_00001_2657_0", "global_id": 9448 }, { "text": "

Aims

To test the suitability of cheese whey powder (CWP) solution for ethanol fermentation and to compare performances of different Kluyveromyces marxianus strains for ethanol fermentation from CWP solution.

Methods and results

Batch ethanol fermentation of cheese whey (CW), CWP and lactose solutions with the same initial sugar contents were compared by using two different K. marxianus strains and the CWP solution was found to be the most suitable substrate. CWP solution was fermented to ethanol using three different yeast strains and DSMZ-7239 was found to be the most suitable one yielding the highest rate and extent (3.3%, v/v) of ethanol formation.

Conclusions

CWP solution and K. marxianus strain of DSMZ-7239 were found to be more suitable for ethanol fermentation with the highest ethanol yield when compared with the other substrates and the yeast strains tested.

Significance and impact of the study

CWP can be used as a concentrated form of CW for ethanol fermentations with considerable advantages.\n\nComparison of yeast strains for batch ethanol fermentation of cheese-whey powder (CWP) solution.", "token_count": 316, "char_count": 1143, "word_count": 164, "semantic_coherence": 1, "information_density": 0.4878, "quality_score": 0.7439, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:38.990191", "source": { "split": "train_shard_00001", "doc_id": 2658 }, "chunk_id": "train_shard_00001_2658_0", "global_id": 9449 }, { "text": "The availability of increasing quantities of crop pangenome data permits the detailed association of gene content with agronomic traits. Here, we investigate disease resistance gene content of diverse soybean cultivars and report a significant negative correlation between the number of NLR resistance ( R ) genes and yield. We find no association between R- genes with seed weight, oil or protein content, and we find no correlation between yield and the number of RLK, RLP genes, or the total number of genes. These results suggest that recent yield improvement in soybean may be partially associated with the selective loss of NLR genes. Three quarters of soybean NLR genes do not show presence/absence variation, limiting the ability to select for their absence, and so the deletion or disabling of select NLR genes may support future yield improvement.\n\nYield is negatively correlated with nucleotide-binding leucine-rich repeat gene content in soybean", "token_count": 201, "char_count": 957, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:39.465169", "source": { "split": "train_shard_00001", "doc_id": 2659 }, "chunk_id": "train_shard_00001_2659_0", "global_id": 9450 }, { "text": "We report the complete genome sequencing of novel Pseudomonas stutzeri strain MP4687 isolated from cattle rumen. Various strains of P. stutzeri have been reported from different environmental samples including oil-contaminated sites, crop roots, air, and human clinical samples, but not from rumen samples, which is being reported here for the first time. The genome of P. stutzeri MP4687 has a single replicon, 4.75 Mb chromosome and a G + C content of 63.45%. The genome encodes for 4,790 protein coding genes including 164 CAZymes and 345 carbohydrate processing genes. The isolate MP4687 harbors LCB hydrolyzing potential through endoglucanase (4.5 U/mL), xylanase (3.1 U/mL), β-glucosidase (3.3 U/mL) and β-xylosidase (1.9 U/mL) activities. The pangenome analysis further revealed that MP4687 has a very high number of unique genes (>2100) compared to other P. stutzeri genomes, which might have an important role in rumen functioning.\n\nComplete genome sequencing and comparative genome characterization of the lignocellulosic biomass degrading bacterium Pseudomonas stutzeri MP4687 from cattle rumen.", "token_count": 377, "char_count": 1134, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.8509, "entities": { "genes": [ "MP4687" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:40.046195", "source": { "split": "train_shard_00001", "doc_id": 2660 }, "chunk_id": "train_shard_00001_2660_0", "global_id": 9451 }, { "text": "Pseudomonas fluorescens UM270 is a rhizosphere-colonizing bacterium that produces multiple diffusible and volatile compounds involved in plant growth-promoting activities. Strain UM270 exhibits excellent biocontrol capacities against diverse fungal pathogens . In a previous study, the general UM270 genome characteristics were published. Here, we report a deeper analysis of its gene content and compare it to other P. fluorescens strains to unveil the genetic elements that might explain UM270's great colonizing and plant growth-promoting capabilities. Our analyses found high variation in genome size and gene content among the eight Pseudomonas genomes analyzed (strains UM270, Pf0-1, A506, F113, SBW25, PICF-7, UK4 and UW4). A core genome of 3,039 coding DNA sequences (CDSs) was determined, with 599 CDSs present only in the UM270 genome. From these unique UM270 genes, a set of 192 CDSs was found to be involved in signaling, rhizosphere colonization and competence, highlighted as important traits to achieve an effective biocontrol and plant growth promotion.\n\nGenome Comparison of Pseudomonas fluorescens UM270 with Related Fluorescent Strains Unveils Genes Involved in Rhizosphere Competence and Colonization.", "token_count": 381, "char_count": 1263, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7052, "quality_score": 0.8526, "entities": { "genes": [ "SBW25", "UW4", "UM270", "UK4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:40.625249", "source": { "split": "train_shard_00001", "doc_id": 2661 }, "chunk_id": "train_shard_00001_2661_0", "global_id": 9452 }, { "text": "Editorial: Evolution of abiotic stress responses in land plants.", "token_count": 15, "char_count": 64, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:40.977073", "source": { "split": "train_shard_00001", "doc_id": 2662 }, "chunk_id": "train_shard_00001_2662_0", "global_id": 9453 }, { "text": "Jerusalem artichoke is a low-requirement sugar crop containing cellulose and hemicellulose in the stalk and a high content of inulin in the tuber. However, the lignocellulosic component in Jerusalem artichoke stalk reduces the fermentability of the whole plant for efficient bioethanol production. In this study, Jerusalem artichoke stalk was pretreated sequentially with dilute acid and alkali, and then hydrolyzed enzymatically. During enzymatic hydrolysis, approximately 88 % of the glucan and xylan were converted to glucose and xylose, respectively. Batch and fed-batch simultaneous saccharification and fermentation of both pretreated stalk and tuber by Kluyveromyces marxianus CBS1555 were effectively performed, yielding 29.1 and 70.2 g/L ethanol, respectively. In fed-batch fermentation, ethanol productivity was 0.255 g ethanol per gram of dry Jerusalem artichoke biomass, or 0.361 g ethanol per gram of glucose, with a 0.924 g/L/h ethanol productivity. These results show that combining the tuber and the stalk hydrolysate is a useful strategy for whole biomass utilization in effective bioethanol fermentation from Jerusalem artichoke.\n\nEthanol production using whole plant biomass of Jerusalem artichoke by Kluyveromyces marxianus CBS1555.", "token_count": 347, "char_count": 1252, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6034, "quality_score": 0.8017, "entities": { "genes": [ "CBS1555" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:41.541501", "source": { "split": "train_shard_00001", "doc_id": 2663 }, "chunk_id": "train_shard_00001_2663_0", "global_id": 9454 }, { "text": "Metagenomic data from Obsidian Pool (Yellowstone National Park, USA) and 13 genome sequences were used to reassess genus-wide biodiversity for the extremely thermophilic Caldicellulosiruptor The updated core genome contains 1,401 ortholog groups (average genome size for 13 species = 2,516 genes). The pangenome, which remains open with a revised total of 3,493 ortholog groups, encodes a variety of multidomain glycoside hydrolases (GHs). These include three cellulases with GH48 domains that are colocated in the glucan degradation locus (GDL) and are specific determinants for microcrystalline cellulose utilization. Three recently sequenced species, Caldicellulosiruptor sp. strain Rt8.B8 (renamed here Caldicellulosiruptor morganii), Thermoanaerobacter cellulolyticus strain NA10 (renamed here Caldicellulosiruptor naganoensis), and Caldicellulosiruptor sp. strain Wai35.B1 (renamed here Caldicellulosiruptor danielii), degraded Avicel and lignocellulose (switchgrass). C. morganii was more efficient than Caldicellulosiruptor bescii in this regard and differed from the other 12 species examined, both based on genome content and organization and in the specific domain features of conserved GHs. Metagenomic analysis of lignocellulose-enriched samples from Obsidian Pool revealed limited new information on genus biodiversity", "token_count": 447, "char_count": 1395, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7176, "quality_score": 0.8588, "entities": { "genes": [ "GH48", "NA10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:42.176955", "source": { "split": "train_shard_00001", "doc_id": 2664 }, "chunk_id": "train_shard_00001_2664_0", "global_id": 9455 }, { "text": "Enrichments yielded genomic signatures closely related to that of Caldicellulosiruptor obsidiansis, but there was also evidence for other thermophilic fermentative anaerobes (Caldanaerobacter, Fervidobacterium, Caloramator, and Clostridium). One enrichment, containing 89.8% Caldicellulosiruptor and 9.7% Caloramator, had a capacity for switchgrass solubilization comparable to that of C. bescii These results refine the known biodiversity of Caldicellulosiruptor and indicate that microcrystalline cellulose degradation at temperatures above 70°C, based on current information, is limited to certain members of this genus that produce GH48 domain-containing enzymes.IMPORTANCE The genus Caldicellulosiruptor contains the most thermophilic bacteria capable of lignocellulose deconstruction, which are promising candidates for consolidated bioprocessing for the production of biofuels and bio-based chemicals. The focus here is on the extant capability of this genus for plant biomass degradation and the extent to which this can be inferred from the core and pangenomes, based on analysis of 13 species and metagenomic sequence information from environmental samples. Key to microcrystalline hydrolysis is the content of the glucan degradation locus (GDL), a set of genes encoding glycoside hydrolases (GHs), several of which have GH48 and family 3 carbohydrate binding module domains, that function as primary cellulases. Resolving the relationship between the GDL and lignocellulose degradation will inform efforts to identify more prolific members of the genus and to develop metabolic engineering strategies to improve this characteristic.", "token_count": 483, "char_count": 1720, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [ "GH48" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:42.819806", "source": { "split": "train_shard_00001", "doc_id": 2664 }, "chunk_id": "train_shard_00001_2664_1", "global_id": 9456 }, { "text": "Genus-Wide Assessment of Lignocellulose Utilization in the Extremely Thermophilic Genus Caldicellulosiruptor by Genomic, Pangenomic, and Metagenomic Analyses.", "token_count": 52, "char_count": 158, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:43.180209", "source": { "split": "train_shard_00001", "doc_id": 2664 }, "chunk_id": "train_shard_00001_2664_2", "global_id": 9457 }, { "text": "

Introduction

Koumiss is a low-alcohol product made from fermented mare's milk, which is popular in Kazakhstan, Russia, and other countries of Central Asia, China, and Mongolia. Natural mare's milk is fermented in symbiosis of two types of microorganisms (lactobacteria and yeast). Koumiss's microbial composition varies depending on the geographical, climatic, and cultural conditions. Based on a phenotypic characteristic from samples, Wu, R. and colleagues identified the following bacteria isolated in inner Mongolia, an autonomous region of China: L.casei, L.helveticus, L.plantarum, L.coryniformis subsp. coryniformis, L.paracasei, L.kefiranofaciens, L.curvatus, L.fermentum, and W.kandleri. Studies of the yeast composition in koumiss also showed significant variations. Thus, there were Saccharomyces unisporus related 48.3% of isolates, to Kluyveromyces marxianus (27.6%), Pichia membranaefaciens (15.0%), and Saccharomyces cerevisiae (9.2%) from 87 isolated yeast cultures. The purpose of this study was to examine the bacterial composition in koumiss.

Methods

To extract DNA, 1.8 ml of fermented milk was centrifuged to generate a pellet, which was suspended in 450 μl of lysis buffer P1 from the Powerfood Microbial DNA Isolation kit (MoBio Laboratories Inc, USA). Amplification of the microflora was used to determine the composition of a fragment of the gene 16S rRNA and ITS1. Plasmid library with target insertion was obtained on the basis of height copy plasmid vectors producing high pGem-T. The definition of direct nucleotide sequencing was performed by the method of Sanger using a set of \"BigDye Terminanor v 3.1 Cycle sequencing Kit with automatic genetic analyzer ABI 3730xl (Applied Biosystems, USA)", "token_count": 514, "char_count": 1738, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6983, "quality_score": 0.8492, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:43.811120", "source": { "split": "train_shard_00001", "doc_id": 2665 }, "chunk_id": "train_shard_00001_2665_0", "global_id": 9458 }, { "text": "Informax Vector NTI Suite 9, Sequence Scanner v 1.0 software package used for the analysis.

Results

Our studies showed that in the most samples of koumiss isolated from Akmola region (Central Kazakhstan) prevailed the following bacteria species: Lactobacillus diolivorans, Lactobacillus acidophilus, L. casei, L. curvatus yeast genus Torula (62.4%) and Saccharomyces cerevisiae (37.6%).

Conclusion

Thus, the first metagenomic research of koumiss, which was conducted in Kazakhstan, showed significant variations in microbial composition.\n\nMetagenomic Analysis of Koumiss in Kazakhstan.", "token_count": 181, "char_count": 599, "word_count": 74, "semantic_coherence": 1, "information_density": 0.8243, "quality_score": 0.9122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:44.267396", "source": { "split": "train_shard_00001", "doc_id": 2665 }, "chunk_id": "train_shard_00001_2665_1", "global_id": 9459 }, { "text": "Fuels and polymer precursors are widely used in daily life and in many industrial processes. Although these compounds are mainly derived from petrol, bacteria and yeast can produce them in an environment-friendly way. However, these molecules exhibit toxic solvent properties and reduce cell viability of the microbial producer which inevitably impedes high product titers. Hence, studying how product accumulation affects microbes and understanding how microbial adaptive responses counteract these harmful defects helps to maximize yields. Here, we specifically focus on the mode of toxicity of industry-relevant alcohols, terpenoids and aromatics and the associated stress-response mechanisms, encountered in several relevant bacterial and yeast producers. In practice, integrating heterologous defense mechanisms, overexpressing native stress responses or triggering multiple protection pathways by modifying the transcription machinery or small RNAs (sRNAs) are suitable strategies to improve solvent tolerance. Therefore, tolerance engineering, in combination with metabolic pathway optimization, shows high potential in developing superior microbial producers.\n\nIncreasing Solvent Tolerance to Improve Microbial Production of Alcohols, Terpenoids and Aromatics.", "token_count": 260, "char_count": 1268, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7362, "quality_score": 0.8681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:44.816040", "source": { "split": "train_shard_00001", "doc_id": 2666 }, "chunk_id": "train_shard_00001_2666_0", "global_id": 9460 }, { "text": "Among the five Kluyveromyces marxianus strains tested for β-galactosidase production, K. marxianus NCIM 3465 showed maximum enzyme activity of 1.62 IU mg⁻¹ dry weight. Different levels (5-25%, w/v) of dried cauliflower waste were incorporated into whey to evaluate the effect of its supplementation on enzyme production. Although a marginal increase in enzyme production was seen by incorporating 5% and 10% cauliflower waste in whey, nearly 15% increase in β-galactosidase production was observed when cauliflower waste level was increased to 20% compared with whey alone. Supplementing whey with 20% cauliflower waste also decreased the production time. Lactose concentration in whey, mainly responsible for increasing the biological oxygen demand load of the effluent water, decreased from 4.2% to nearly 0% at 24 h. Thus, this study demonstrated that both these by-products/residues could be effectively used for β-galactosidase production at commercial scale.\n\nEnhanced β-galactosidase production by supplementing whey with cauliflower waste", "token_count": 291, "char_count": 1046, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6824, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:45.374802", "source": { "split": "train_shard_00001", "doc_id": 2667 }, "chunk_id": "train_shard_00001_2667_0", "global_id": 9461 }, { "text": "

Purpose

Carbapenemase-producing Enterobacterales (CPE) pose a serious threat for healthcare facilities worldwide, yet the mode of transmission is often unclear. Recently, we recorded an increase of blaOXA-48-harboring isolates at our hospital associated with patients with previous medical treatment in the Ukraine. We used long-read whole genome sequencing (lrWGS) to characterize these isolates including their plasmids.

Methods

Samples were collected as part of clinical routine diagnostic or screening of multi-drug resistance bacteria (MDRB). Antimicrobial susceptibility testing was performed and all MDRB (n = 10) were sequenced by lrWGS for genotyping, identification of antimicrobial resistance (AMR) genes, and characterization of plasmids.

Results

While routine analysis of core genome multilocus sequence typing (cgMLST) did not show any genetic similarities between isolates, we found an unexpected high similarity in the plasmid diversity of different Enterobacterales in patients with previous medical treatment in the Ukraine. This included an IncL/M plasmid carrying blaOXA-48 and additional small non-AMR-coding plasmids.

Conclusion

Our results show that lrWGS can be used in the routine setting to uncover similarities in plasmids and may give further information about potential epidemiologic associations. In the future, analysis of both AMR and non-AMR plasmids may provide an additional layer of information for molecular surveillance of CPE.\n\nCharacterization of blaOXA-48-carrying plasmids and small non-AMR-coding plasmids collected from Ukrainian patients.", "token_count": 434, "char_count": 1645, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6796, "quality_score": 0.8398, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:46.010030", "source": { "split": "train_shard_00001", "doc_id": 2668 }, "chunk_id": "train_shard_00001_2668_0", "global_id": 9462 }, { "text": "

Objectives

Here we report a complete genome sequence of a multidrug-resistant Salmonella Rissen, carrying blaCTX-M-55 and Tn6777, isolated from a Chinese paediatric patient.

Methods

Whole genome of S. Rissen S1905 was sequenced using the Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. Unicycler was used to perform a de novo assembly of Illumina and Nanopore reads. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. In silico multilocus sequence typing, plasmid replicons, antimicrobial resistance genes and virulence factors were identified from the genome sequence by multiple bioinformatics tools. Core genome multilocus sequence typing analysis between S. Rissen S1905 and all retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server.

Results

Six contigs totaling 5 056 896 bp make up the complete genome sequence of S. Rissen S1905, which includes 1 chromosome and 5 plasmids. The blaCTX-M-55 was embedded in the ISEcp1-blaCTX-M-55-wbuC transposition unit located in an 85 991-bp IncI1 plasmid. However, the pco-sil operon and other eight antimicrobial resistance genes were carried by Tn6777 in the chromosome. There are 162 virulence genes in S1905. S. Rissen S1905 belongs to ST469; the closest relative was another isolate originating from a human faecal specimen in Shanghai, China, which differed by 60 core genome multilocus sequence type alleles.

Conclusion

These data on the multidrug-resistant S", "token_count": 496, "char_count": 1549, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8104, "entities": { "genes": [ "ST469" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:46.665094", "source": { "split": "train_shard_00001", "doc_id": 2669 }, "chunk_id": "train_shard_00001_2669_0", "global_id": 9463 }, { "text": "Rissen carrying blaCTX-M-55 and Tn6777 can provide a foundation for further studies on the molecular epidemiological characteristics, pathogenicity, antimicrobial resistance mechanisms, and dissemination mechanism of Salmonella.\n\nGenomic characterization of a multidrug-resistant Salmonella Rissen ST469 carrying bla<sub>CTX-M-55</sub> gene and Tn6777 isolated from a paediatric patient in China.", "token_count": 126, "char_count": 419, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [ "ST469" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:47.052128", "source": { "split": "train_shard_00001", "doc_id": 2669 }, "chunk_id": "train_shard_00001_2669_1", "global_id": 9464 }, { "text": "

Background

Candida species can become opportunistic pathogens causing local or systemic invasive infections. Gastroesophageal candidiasis may depend on the Candida colonization and local damage of the mucosal barrier. Risk factors are gastric acid suppression, diabetes mellitus, chronic debilitating states such as carcinomas, and the use of systemic antibiotics and corticosteroids. The aim of this study is collection and molecular identification of Candida species from gastroesophageal lesions among pediatrics in Isfahan, and determination of minimum inhibitory concentration (MIC) ranges for clinical isolates.

Materials and methods

A total of 200 patients underwent endoscopy (130 specimens from gastritis and 70 samples from esophagitis) were included in this study between April 2015 and November 2015. All specimens were subcultured on sabouraud dextrose agar, and genomic DNA of all strains was extracted using boiling method. Polymerase chain reaction and DNA sequencing of the ITS1-5.8SrDNA-ITS2 region were used for the identification of all Candida strains. MIC ranges were determined for itraconazole (ITC), amphotericin B (AmB), and fluconazole (FLU) by E-test.

Results

Twenty of 200 suspected patients (10%) were positive by direct microscopy and culture. Candida albicans was the most common species (60%) followed by Candida glabrata (30%), Candida parapsilosis (5%), and Candida kefyr (5%)", "token_count": 459, "char_count": 1489, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8446, "entities": { "genes": [ "ITS2", "ITS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:47.692527", "source": { "split": "train_shard_00001", "doc_id": 2670 }, "chunk_id": "train_shard_00001_2670_0", "global_id": 9465 }, { "text": "MIC ranges were determined for FLU (0.125-8 μg/mL), ITC (0.008-0.75 μg/mL), and AmB (0.008-0.75 μg/mL), respectively.

Conclusion

Every colonization of Candida species should be considered as a potentially factor of mucocutaneous candidiasis and should be treated with antifungal drugs.\n\nIsolation of Candida Species from Gastroesophageal Lesions among Pediatrics in Isfahan, Iran: Identification and Antifungal Susceptibility Testing of Clinical Isolates by E-test.", "token_count": 175, "char_count": 486, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7797, "quality_score": 0.8898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:48.140807", "source": { "split": "train_shard_00001", "doc_id": 2670 }, "chunk_id": "train_shard_00001_2670_1", "global_id": 9466 }, { "text": "The human gut microbiome matures towards the adult composition during the first years of life and is implicated in early immune development. Here, we investigate the effects of microbial genomic diversity on gut microbiome development using integrated early childhood data sets collected in the DIABIMMUNE study in Finland, Estonia and Russian Karelia. We show that gut microbial diversity is associated with household location and linear growth of children. Single nucleotide polymorphism- and metagenomic assembly-based strain tracking revealed large and highly dynamic microbial pangenomes, especially in the genus Bacteroides, in which we identified evidence of variability deriving from Bacteroides-targeting bacteriophages. Our analyses revealed functional consequences of strain diversity; only 10% of Finnish infants harboured Bifidobacterium longum subsp. infantis, a subspecies specialized in human milk metabolism, whereas Russian infants commonly maintained a probiotic Bifidobacterium bifidum strain in infancy. Groups of bacteria contributing to diverse, characterized metabolic pathways converged to highly subject-specific configurations over the first two years of life. This longitudinal study extends the current view of early gut microbial community assembly based on strain-level genomic variation.\n\nGenomic variation and strain-specific functional adaptation in the human gut microbiome during early life.", "token_count": 305, "char_count": 1427, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6614, "quality_score": 0.8307, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:48.734241", "source": { "split": "train_shard_00001", "doc_id": 2671 }, "chunk_id": "train_shard_00001_2671_0", "global_id": 9467 }, { "text": "Yersiniosis is a common zoonotic enteric disease among humans, which has been linked to pigs and contaminated food, especially pork. The epidemiology of yersiniosis is still obscure, and studies on yersiniosis in pets are very scarce. In this study, we performed pheno- and genotypic characterisation of 50 Yersinia strains isolated from pets in Finland between 2012 and 2023. Y. enterocolitica 4/O:3/ST135, the most common type in human yersiniosis, was also the most common type (68%) found in clinical faecal samples in our study. Also, human pathogenic Y. enterocolitica 2/O:9/ST139 and Y. pseudotuberculosis O:1/ST9 and O:1/ST42 strains carrying all essential pathogenic genes were identified. Three Y. enterocolitica 4/O:3/ST9 strains were multi-drug-resistant and two of them were highly related, showing one allelic difference (AD) with core genome multi-locus sequence typing. Non-pathogenic, genotypically highly diverse Y. enterocolitica 1A strains, showing more than 1000 ADs and missing the essential virulence genes, were also recognised in dogs and cats. Our study demonstrates that pets can excrete human pathogenic Yersinia in their faeces and may serve as an infection source for human yersiniosis, especially in families with small children in close contact with their pets.\n\nEnteropathogenic <i>Yersinia</i> with Public Health Relevance Found in Dogs and Cats in Finland.", "token_count": 452, "char_count": 1452, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6733, "quality_score": 0.8366, "entities": { "genes": [ "ST135", "ST139", "ST42", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:49.397941", "source": { "split": "train_shard_00001", "doc_id": 2672 }, "chunk_id": "train_shard_00001_2672_0", "global_id": 9468 }, { "text": "Typhoid fever is endemic in many parts of the world and remains a major public health concern in tropical and sub-tropical developing nations, including Fiji. To address high rates of typhoid fever, the Northern Division of Fiji is implementing a mass vaccination with typhoid conjugate vaccine (Vi-polysaccharide conjugated to tetanus toxoid) as a public health control measure in 2023. In this study we define the genomic epidemiology of S . Typhi in the Northern Division prior to island-wide vaccination, sequencing 85% (n=419) of the total cases from the Northern Division and Central Divisions of Fiji that occurred in the period 2017-2019. We found elevated rates of nucleotide polymorphisms in tviD and tviE genes (responsible for Vi-polysaccharide synthesis) relative to core genome levels within the Fiji endemic S . Typhi genotype 4.2. Expansion of these findings within a globally representative database of 12,382 S . Typhi (86 genotyphi clusters) showed evidence of convergent evolution of the same tviE mutations across the S . Typhi population, indicating that tvi selection has occurred both independently and globally. The functional impact of tvi mutations on the Vi-capsular structure and other phenotypic characteristics are presently unknown, yet commonly occurring tviE polymorphisms localise adjacent to predicted active site residues when overlayed against the predicted TviE protein structure. Given the central role of the Vi-polysaccharide in S . Typhi biology and vaccination, further integrated epidemiological, genomic, and phenotypic surveillance is required to determine the spread and functional implications of these mutations.\n\nGenetic heterogeneity in theSalmonellaTyphi Vi capsule locus: A population genomic study from Fiji", "token_count": 442, "char_count": 1769, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:50.077524", "source": { "split": "train_shard_00001", "doc_id": 2673 }, "chunk_id": "train_shard_00001_2673_0", "global_id": 9469 }, { "text": "The hypocholesterolemic activities of 81 yeast strains were examined in rats fed a high cholesterol diet (HCD). Male Wistar rats were fed an HCD or an HCD supplemented with 10% yeast for 7 d. It was found that the hypocholesterolemic activities of the yeasts varied remarkably between strains. Kluyveromyces marxianus YIT 8292 exhibited the most potent hypocholesterolemic activity among the yeasts that were tested. K. marxianus YIT 8292 significantly decreased not only plasma total cholesterol but also liver total cholesterol when administered as a dietary admixture at a concentration of 3%. In contrast, brewer's yeast and baker's yeast, which have been predominantly used for food, did not exhibit hypocholesterolemic activity even when administered at a concentration of 10%. These results suggest that K. marxianus YIT 8292 may be utilized as a novel food material with the ability to contribute to the prevention of hypercholesterolemia.\n\nPotent hypocholesterolemic activity of the yeast Kluyveromyces marxianus YIT 8292 in rats fed a high cholesterol diet.", "token_count": 305, "char_count": 1067, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5901, "quality_score": 0.795, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:50.659636", "source": { "split": "train_shard_00001", "doc_id": 2674 }, "chunk_id": "train_shard_00001_2674_0", "global_id": 9470 }, { "text": "The taxonomic status of strain P5891T, isolated from an Adélie penguin beak swab, was investigated. Based on the 16S rRNA gene sequence, the strain was identified as a potentially novel Corynebacterium species, with the highest sequence similarities to Corynebacterium rouxii FRC0190T (96.7 %) and Corynebacterium epidermidicanis DSM 45586T (96.6 %). The average nucleotide identity values between strain P5891T and C. rouxii FRC0190T and C. epidermidicanis DSM 45586T were 68.2 and 69.2 %, respectively. The digital DNA-DNA hybridization values between strain P5891T and C. rouxii FRC0190T and C. epidermidicanis DSM 45586T were 23.7 and 21.4 %, respectively. Phylogenetic trees based on the 16S rRNA sequence placed strain P5891T in a separate branch with Corynebacterium canis 1170T and Corynebacterium freiburgense 1045T, while a phylogenomic tree based on the Corynebacterium species core genome placed the strain next to Corynebacterium choanae 200CHT", "token_count": 488, "char_count": 1177, "word_count": 138, "semantic_coherence": 1, "information_density": 0.5797, "quality_score": 0.7899, "entities": { "genes": [ "FRC0190" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:51.314652", "source": { "split": "train_shard_00001", "doc_id": 2675 }, "chunk_id": "train_shard_00001_2675_0", "global_id": 9471 }, { "text": "Extensive phenotyping and genomic analyses clearly confirmed that strain P5891T represents a novel species of the genus Corynebacterium, for which the name Corynebacterium mendelii sp. nov. is proposed, with the type strain P5891T (=CCM 8862T=LMG 31627T).\n\nCorynebacterium mendelii sp. nov., a novel bacterium isolated from Adélie penguin oral cavity.", "token_count": 159, "char_count": 416, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8163, "quality_score": 0.9082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:51.751321", "source": { "split": "train_shard_00001", "doc_id": 2675 }, "chunk_id": "train_shard_00001_2675_1", "global_id": 9472 }, { "text": "Human gut microbiomes (microbiotas) are highly individualistic in taxonomic composition but nevertheless are functionally similar. Thus, collectively, they comprise a \"metacommunity.\" In ecological terminology, the assembly of human gut microbiomes is influenced by four processes: selection, speciation, drift, and dispersal. As a result of fortuitous events associated with these processes, individual microbiomes are taxonomically \"tailor-made\" for each host. However, functionally they are \"off-the-shelf\" because of similar functional outputs resulting from metabolic redundancy developed in host-microbe symbiosis. Because of this, future microbiological and molecular studies of microbiomes should emphasize the metabolic interplay that drives the human gut metacommunity and that results in these similar functional outputs. This knowledge will support the development of remedies for specific functional dysbioses and hence provide practical examples of precision medicine.\n\nThe human gut metacommunity as a conceptual aid in the development of precision medicine.", "token_count": 234, "char_count": 1073, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6547, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:52.222114", "source": { "split": "train_shard_00001", "doc_id": 2676 }, "chunk_id": "train_shard_00001_2676_0", "global_id": 9473 }, { "text": "

Introduction

Kefir beverage has beneficial microorganisms that have health-giving properties; therefore, they have a good potential to be probiotic. This study evaluated the probiotic potential, technological, and safety characteristics of Enterococcus faecalis, Lactococcus lactis, and Pichia fermentans isolated from traditional kefir beverages.

Method

First, isolates were evaluated in terms of resistance to acid, alkali, bile salts, trypsin, and pepsin of the gastrointestinal tract. The auto-aggregation and co-aggregation ability of isolates were measured using spectrophotometry. Antimicrobial activities were assayed against important food-borne pathogens using the agar well diffusion method. Moreover, gamma-aminobutyric acid (GABA) production was investigated by thin-layer chromatography (TLC).

Result

Among the isolates, P. fermentans had an 85% total survival rate, but its amount reached below 6 log CFU/ml which is considered non-resistant, and it showed the highest auto-aggregation (74.67%). Moreover, only L. lactis showed antimicrobial activity and had the highest co-aggregation with E. coli PTCC 1338 (54.33%) and L. monocytogenes ATCC 7644 (78%). Finally, an evaluation of the technological and safety characteristics of the strains showed that the strains produced GABA and were safe.

Discussion

Although the isolates were not resistant to the gastrointestinal tract, their supernatant contained valuable natural compounds, including antioxidants, GABA, and antimicrobials, which can be used to produce functional foods and medicines", "token_count": 476, "char_count": 1636, "word_count": 200, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:52.866690", "source": { "split": "train_shard_00001", "doc_id": 2677 }, "chunk_id": "train_shard_00001_2677_0", "global_id": 9474 }, { "text": "In addition, other approaches, such as increasing the initial number of strains, using foods as carriers of isolates, and encapsulating the isolates, can effectively increase the survivability of isolates in the gastrointestinal tract.\n\nEvaluation of the probiotic, technological, safety attributes, and GABA-producing capacity of microorganisms isolated from Iranian milk kefir beverages.", "token_count": 90, "char_count": 389, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:53.241736", "source": { "split": "train_shard_00001", "doc_id": 2677 }, "chunk_id": "train_shard_00001_2677_1", "global_id": 9475 }, { "text": "The potential probiotic function of Latilactobacills curvatus has attracted the attention of researchers. To explore the differences in the genomes of L. curvatus, nine strains were isolated from various sources, including feces and fermented vegetables and compared with 25 strains from the NCBI database. The findings indicated that the average genome size, GC content, and CDS of L. curvatus were 1.94 MB, 41.9%, and 1825, respectively. Its core genome is associated with transcription, translation, carbohydrate transport and metabolism, and defense functions. The pan-genome of L. curvatus was in a closed state. The genetic diversity of L. curatus is mainly manifested in its ability to use carbohydrates, antibiotic resistance, bacteriocin operon, and polymeric regularly interspaced short palindromic repeats (CRISPR)-Cas for bacterial immunity. The CRISPR system of 34 strains of L. curvatus was predominantly found to be of the IIA type with a few IIC and IE types. These findings will contribute to a better understanding of this species.\n\nPhenotype-genotype analysis of Latilactobacills curvatus from different niches: Carbohydrate metabolism, antibiotic resistance, bacteriocin, phage fragments and linkages with CRISPR-Cas systems", "token_count": 321, "char_count": 1244, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6554, "quality_score": 0.8277, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:53.805538", "source": { "split": "train_shard_00001", "doc_id": 2678 }, "chunk_id": "train_shard_00001_2678_0", "global_id": 9476 }, { "text": "

Background

Typhoid fever, caused by Salmonella Typhi, follows a fecal-oral transmission route and is a major global public health concern, especially in developing countries like Bangladesh. Increasing emergence of antimicrobial resistance (AMR) is a serious issue; the list of treatments for typhoid fever is ever-decreasing. In addition to IncHI1-type plasmids, Salmonella genomic island (SGI) 11 has been reported to carry AMR genes. Although reports suggest a recent reduction in multidrug resistance (MDR) in the Indian subcontinent, the corresponding genomic changes in the background are unknown.

Results

Here, we assembled and annotated complete closed chromosomes and plasmids for 73 S. Typhi isolates using short-length Illumina reads. S. Typhi had an open pan-genome, and the core genome was smaller than previously reported. Considering AMR genes, we identified five variants of SGI11, including the previously reported reference sequence. Five plasmids were identified, including the new plasmids pK91 and pK43; pK43and pHCM2 were not related to AMR. The pHCM1, pPRJEB21992 and pK91 plasmids carried AMR genes and, along with the SGI11 variants, were responsible for resistance phenotypes. pK91 also contained qnr genes, conferred high ciprofloxacin resistance and was related to the H58-sublineage Bdq, which shows the same phenotype. The presence of plasmids (pHCM1 and pK91) and SGI11 were linked to two H58-lineages, Ia and Bd. Loss of plasmids and integration of resistance genes in genomic islands could contribute to the fitness advantage of lineage Ia isolates.

Conclusions

Such events may explain why lineage Ia is globally widespread, while the Bd lineage is locally restricted. Further studies are required to understand how these S. Typhi AMR elements spread and generate new variants. Preventive measures such as vaccination programs should also be considered in endemic countries; such initiatives could potentially reduce the spread of AMR.", "token_count": 527, "char_count": 1990, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8275, "entities": { "genes": [ "SGI11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:27:54.466777", "source": { "split": "train_shard_00001", "doc_id": 2679 }, "chunk_id": "train_shard_00001_2679_0", "global_id": 9477 }, { "text": "Analysis of isolates from Bangladesh highlights multiple ways to carry resistance genes in Salmonella Typhi.", "token_count": 21, "char_count": 108, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:54.816060", "source": { "split": "train_shard_00001", "doc_id": 2679 }, "chunk_id": "train_shard_00001_2679_1", "global_id": 9478 }, { "text": "Pangenome analysis is fundamental to explore evolutionary processes occurring in bacterial populations. However, the lack of standardized methods for handling diverse pangenomic datasets and complex metadata hinders more straightforward and reproducible downstream analyses. To fill this gap, we introduce Pagoo, a new framework that integrates pangenome data, analytical methods and visualization tools in a single object that can be easily stored, shared and responsively queried for improved biological interpretation of bacterial evolution.\n\nStraightforward and reproducible analysis of bacterial pangenomes using Pagoo", "token_count": 125, "char_count": 623, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:55.202669", "source": { "split": "train_shard_00001", "doc_id": 2680 }, "chunk_id": "train_shard_00001_2680_0", "global_id": 9479 }, { "text": "

Context

The role of hypericin-mediated photodynamic antimicrobial properties on pathogenic fungi and photodynamic therapy for human cancer cells is known. Antifungal properties of Hypericum perforatum L. (Hypericaceae) and Fagopyrum esculentum Moench. (Polygonaceae) extracts were also studied. The different polarities of solvents can cause complication in the identification of antifungal effects of separate biologically active compounds. In recent experimental work, we compared antifungal properties of purified hypericin, hypericin tetrasulphonic acid (hypericin + S) and fagopyrin, which is analogue of hypericin.

Objective

The antifungal properties of aromatic polyketide derivatives such as hypericin, hypericin + S and fagopyrin on the selected pathogenic fungi and spoilage yeasts have been studied.

Materials and methods

The antifungal properties of hypericin, hypericin + S and fagopyrin were determined using the broth microdilution method against a set of pathogenic fungi and spoilage yeasts including: Microsporum canis, Trichophyton rubrum, Fusarium oxysporum, Exophiala dermatitidis, Candida albicans, Kluyveromyces marxianus, Pichia fermentans and Saccharomyces cerevisiae. The tested concentrations of hypericin, hypericin + S and fagopyrin ranged from 750 to 0.011 μg/mL and MIC values were evaluated after 48 h incubation at 30 °C.

Results

The results confirm different antifungal properties of hypericin, hypericin + S and fagopyrin on the selected pathogenic fungi and spoilage yeasts", "token_count": 497, "char_count": 1538, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6173, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:55.862994", "source": { "split": "train_shard_00001", "doc_id": 2681 }, "chunk_id": "train_shard_00001_2681_0", "global_id": 9480 }, { "text": "For pathogenic fungi, the minimum inhibitory concentrations of hypericin ranged 0.18-46.9 μg/mL, hypericin + S 0.18-750 μg/mL and fagopyrin 11.7-46.9 μg/mL. For spoilage yeasts, the MICs of hypericin and hypericin + S ranged 0.18-46.9 and 0.011-0.73 μg/mL, respectively.

Discussion and conclusion

The results obtained herein indicate that various chemical structures of hypericin, hypericin + S and fagopyrin can develop different antifungal properties.\n\nAntifungal properties of hypericin, hypericin tetrasulphonic acid and fagopyrin on pathogenic fungi and spoilage yeasts.", "token_count": 243, "char_count": 582, "word_count": 75, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:56.348906", "source": { "split": "train_shard_00001", "doc_id": 2681 }, "chunk_id": "train_shard_00001_2681_1", "global_id": 9481 }, { "text": "

Aims

Lactobacillus acidophilus has been extensively applied in plentiful probiotic products. Although several studies have been performed to investigate the beneficial characteristics and genome function of L. acidophilus, comparative genomic analysis remains scarce. In this study, we collected 74 L. acidophilus genomes from our gut bacterial genome collection and the public database and conducted a comprehensive comparative genomic analysis.

Methods and results

This study revealed the potential correlation of the genomic diversity and niche adaptation of L. acidophilus from different perspectives. The pan-genome of L. acidophilus was found to be open, with metabolism, information storage, and processing genes mainly distributed in the core genome. Phage- and peptidase-associated genes were found in the genome of the specificity of animal-derived strains, which were related to the adaptation of the animal gut. SNP analysis showed the differences of the utilization of vitamin B12 in cellular of L. acidophilus strains from animal gut and others.

Conclusions

This work provides new insights for the genomic diversity analysis of L. acidophilus and uncovers the ecological adaptation of the specific strains.\n\nComparative genomic analysis reveals niche adaption of Lactobacillus acidophilus.", "token_count": 321, "char_count": 1325, "word_count": 178, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:56.906853", "source": { "split": "train_shard_00001", "doc_id": 2682 }, "chunk_id": "train_shard_00001_2682_0", "global_id": 9482 }, { "text": "Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.\n\nggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks.", "token_count": 474, "char_count": 2103, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6175, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:57.551636", "source": { "split": "train_shard_00001", "doc_id": 2683 }, "chunk_id": "train_shard_00001_2683_0", "global_id": 9483 }, { "text": "

Background

Little is known about susceptibility of Staphylococcus lugdunensis to antiseptics. The objective of this study was to evaluate, at the molecular and phenotypic level, the susceptibility of 49 clinical S. lugdunensis strains (belonging to the seven clonal complexes [CCs] defined by multilocus sequence typing) to two antiseptics frequently used in healthcare settings (chlorhexidine digluconate [CHX] and chloride benzalkonium [BAC]).

Results

The minimum inhibitory concentrations (MICs), by broth microdilution method, varied for BAC from 0.25 mg/L to 8 mg/L (MIC50 = 1 mg/L, MIC90 = 2 mg/L) and for CHX from 0.5 mg/L to 2 mg/L (MIC50 = 1 mg/L, MIC90 = 2 mg/L). The BAC and CHX minimum bactericidal concentrations (MBCs) varied from 2 mg/L to 8 mg/L (MBC50 = 4 mg/L, MBC90 = 8 mg/L) and from 2 mg/L to 4 mg/L (MBC50 and MBC90 = 4 mg/L), respectively. A reduced susceptibility to CHX (MIC = 2 mg/L) was observed for 12.2% of the strains and that to BAC (MIC ≥ 4 mg/L) for 4.1%", "token_count": 487, "char_count": 1090, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5305, "quality_score": 0.7652, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:58.199076", "source": { "split": "train_shard_00001", "doc_id": 2684 }, "chunk_id": "train_shard_00001_2684_0", "global_id": 9484 }, { "text": "The norA resistance gene was detected in all the 49 isolates, whereas the qacA gene was rarely encountered (two strains; 4.1%). The qacC, qacG, qacH, and qacJ genes were not detected. The two strains harboring the qacA gene had reduced susceptibility to both antiseptics and belonged to CC3.

Conclusion

The norA gene was detected in all the strains, suggesting that it could belong to the core genome of S. lugdunensis. S. lugdunensis is highly susceptible to both antiseptics tested. Reduced susceptibility to BAC and CHX was a rare phenomenon. Of note, a tendency to higher MICs of BAC was detected for CC3 isolates. These results should be confirmed on a larger collection of strains.\n\nImpact of clonal lineages on susceptibility of Staphylococcus lugdunensis to chlorhexidine digluconate and chloride benzalkonium.", "token_count": 235, "char_count": 825, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8228, "entities": { "genes": [ "CC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:58.671094", "source": { "split": "train_shard_00001", "doc_id": 2684 }, "chunk_id": "train_shard_00001_2684_1", "global_id": 9485 }, { "text": "In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov", "token_count": 462, "char_count": 1634, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6727, "quality_score": 0.8364, "entities": { "genes": [ "RM3662" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:59.311101", "source": { "split": "train_shard_00001", "doc_id": 2685 }, "chunk_id": "train_shard_00001_2685_0", "global_id": 9486 }, { "text": "(type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.\n\n<i>Campylobacter devanensis</i> sp. nov., <i>Campylobacter porcelli</i> sp. nov., and <i>Campylobacter vicugnae</i> sp. nov., three novel <i>Campylobacter lanienae</i>-like species recovered from swine, small ruminants, and camelids.", "token_count": 267, "char_count": 542, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [ "RM12175", "RM6137" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:27:59.864014", "source": { "split": "train_shard_00001", "doc_id": 2685 }, "chunk_id": "train_shard_00001_2685_1", "global_id": 9487 }, { "text": "Klebsiella michiganensis is an emerging hospital-acquired bacterial pathogen, particularly strains harboring plasmid-mediated carbapenemase genes. Here, we recovered and characterized a multidrug-resistant strain, bla KPC-2-producing Klebsiella michiganensis LS81, which was isolated from the abdominal drainage fluid of a clinical patient in China, and further characterized the co-harboring plasmid. K. michiganensis LS81 tested positive for the bla KPC-2 genes by PCR sequencing, with bla KPC-2 located on a plasmid as confirmed by S1 nuclease pulsed-field gel electrophoresis combined with Southern blotting. In the transconjugants, the bla KPC-2 genes were successfully transferred to the recipient strain E. coli EC600. Whole-genome sequencing and bioinformatics analysis confirmed that this strain belongs to sequence type 196 (ST196), with a complete genome comprising a 5,926,662bp circular chromosome and an 81,451bp IncM2 plasmid encoding bla KPC-2 (designated pLS81-KPC). The IncM2 plasmid carried multiple β-lactamase genes such as bla TEM-1B, bla CTX-M-3, and bla KPC-2 inserted in truncated Tn6296 with the distinctive core structure ISKpn27-bla KPC-2-ISKpn6", "token_count": 515, "char_count": 1384, "word_count": 157, "semantic_coherence": 1, "information_density": 0.707, "quality_score": 0.8535, "entities": { "genes": [ "ST196", "EC600", "LS81" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:28:00.522337", "source": { "split": "train_shard_00001", "doc_id": 2686 }, "chunk_id": "train_shard_00001_2686_0", "global_id": 9488 }, { "text": "A comparison with 46 K. michiganensis genomes available in the NCBI database revealed that the closest phylogenetic relative of K. michiganensis LS81 is a clinical isolate from a wound swab in the United Kingdom. Ultimately, the pan-genomic analysis unveiled a substantial accessory genome within the strain, alongside significant genomic plasticity within the K. michiganensis species, emphasizing the necessity for continuous surveillance of this pathogen in clinical environments.\n\nGenomic characterization of a bla KPC-2-producing IncM2 plasmid harboring transposon ΔTn6296 in Klebsiella michiganensis.", "token_count": 198, "char_count": 659, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7284, "quality_score": 0.8642, "entities": { "genes": [ "LS81" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:01.018621", "source": { "split": "train_shard_00001", "doc_id": 2686 }, "chunk_id": "train_shard_00001_2686_1", "global_id": 9489 }, { "text": "

ABSTRACT

Whole-genome alignment allows researchers to understand the genomic structure and variations among the genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment, and visualization. Our results showed that the NGSEP algorithm for ortholog identification has competitive accuracy and better efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. Finally, our software includes a new graphical user interface. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.\n\nNGSEP 4: Efficient and Accurate Identification of Orthogroups and Whole-Genome Alignment", "token_count": 271, "char_count": 1309, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:01.595729", "source": { "split": "train_shard_00001", "doc_id": 2687 }, "chunk_id": "train_shard_00001_2687_0", "global_id": 9490 }, { "text": "The uptake and recovery of Pb (II) ions were investigated by using sodium alginate beads. Biosorption experiments are carried out in batch mode. The experimental results showed that the beads were effective in removing Pb (II) ions from solution. Biosorption equilibrium was approached within 16hrs. Pseudo first order was applicable to all the sorption data over the entire time range. The sorption data conformed well for the Langmuir isotherm model. The maximum adsorption capacity (qmax) onto alginate beads was 62.5 mg g-1 for Pb (II) ions. The maximum uptake of metal ions was obtained at pH 7. At temperature 35 degreeC, the biosorption of metal ions was found to be highest, with increase or decrease in temperature resulted in a decrease in the metal ions uptake capacity. The maximum removal efficiency of 94.02% was obtained at 100 mg I' of metal concentration with 200 numbers of immobilized beads. The results suggested that alginate beads can be used as a biosorbent for an efficient removal of Pb (II) ions from aqueous solution.\n\nBiosorption of lead by Kluyveromyces marxianus immobilized in alginate beads.", "token_count": 303, "char_count": 1123, "word_count": 181, "semantic_coherence": 1, "information_density": 0.5635, "quality_score": 0.7818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:02.193071", "source": { "split": "train_shard_00001", "doc_id": 2688 }, "chunk_id": "train_shard_00001_2688_0", "global_id": 9491 }, { "text": "

Purpose of review

To describe the epidemiology, strategies for early detection, and clinical management of infections caused by the most commonly found multidrug-resistant (MDR) Candida spp.

Recent findings

Increasing numbers of reports describing invasive infections by MDR Candida auris and Candida glabrata has been reported in medical centers worldwide.

Summary

We checked all papers published along the last 10 years describing epidemiological, diagnostic, and clinical aspects of infections by MDR Candida spp., with emphasis on C. auris and C. glabrata spp. C. auris has been reported in 15 countries and multidrug resistance rates is usually above 30%. Horizontal transmission is a great concern regarding C. auris. C. glabrata ranks the second most reported Candida spp. in deep-seated infections from United States and some European Centers, although multidrug resistance rates above 10% are restricted to some US centers. Candida haemulonii complex isolates with poor susceptibility to azoles and amphotericin B have been isolated in superficial and deep-seated infections, whereas Candida guilliiermondii complex isolates with poor susceptibility to azoles and echinocandins have been recovered from catheter-related bloodstream infections. Other potential MDR Candida species are Candida krusei, Candida lusitaniae, Candida kefyr, Yarrowia (Candida) lypolitica, and Candida rugosa.\n\nEmerging multidrug-resistant Candida species.", "token_count": 384, "char_count": 1463, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:02.838151", "source": { "split": "train_shard_00001", "doc_id": 2689 }, "chunk_id": "train_shard_00001_2689_0", "global_id": 9492 }, { "text": "Some species of the genus Alicyclobacillus cause spoilage in juices and other beverages due to the production of guaiacol, a phenolic compound, and off-aroma. However, little is known about the genomic determinants of guaiacol production across the genus. In this study, we found that several of the genes significantly enriched in guaiacol-producing Alicyclobacillus spp. are associated with oxidative stress response, including vdcC, a phenolic acid decarboxylase putatively responsible for guaiacol synthesis. The food industry recognizes Alicyclobacillus acidoterrestris as the primary guaiacol-producing species found in beverages, though that species was recently split into two closely related yet genetically distinct species, Alicyclobacillus suci and A. acidoterrestris. We found that strains of A. suci (63.0 ± 14.2 ppm) produced significantly (P < 0.01) more guaiacol on average in media than did strains of A. acidoterrestris (25.2 ± 7.0 ppm). Additionally, A. suci and Alicyclobacillus fastidiosus genomes each had duplicate copies of vdcC, while only a single copy of vdcC was found in the genomes of A. acidoterrestris, Alicyclobacillus acidiphilus, and Alicyclobacillus herbarius. Although the food industry has not historically differentiated between A. suci and A. acidoterrestris, it may be increasingly important to target the species with greater spoilage potential", "token_count": 485, "char_count": 1506, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:03.493670", "source": { "split": "train_shard_00001", "doc_id": 2690 }, "chunk_id": "train_shard_00001_2690_0", "global_id": 9493 }, { "text": "Therefore, we also demonstrated that sequencing a single locus, such as the full-length 16S region or rpoB, is sufficient to differentiate between A. acidoterrestris and A. suci.

Importance

Microbial spoilage increases food waste. To address that challenge, it is critical to recognize and control those microbial groups with the greatest spoilage potential. Non-specific targeting of broad microbial groups (e.g., the genus of Alicyclobacillus) in which only some members cause food spoilage results in untenable, overly broad interventions. Much of the food industry does not differentiate between guaiacol-producing and non-guaiacol-producing Alicyclobacillus species. This is overly broad because Alicyclobacillus spp. which cannot produce guaiacol can be present in beverages without causing spoilage. Furthermore, no distinction is made between Alicyclobacillus suci and Alicyclobacillus acidoterrestris because A. suci is newly split from A. acidoterrestris and most of the food industry still considers them to be the same. However, these findings indicate that A. suci may have greater spoilage potential than A. acidoterrestris due to differences in their genomic determinants for guaiacol production.\n\n<i>Alicyclobacillus suci</i> produces more guaiacol in media and has duplicate copies of <i>vdcC</i> compared to closely related <i>Alicyclobacillus acidoterrestris</i>.", "token_count": 470, "char_count": 1509, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6649, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:04.135472", "source": { "split": "train_shard_00001", "doc_id": 2690 }, "chunk_id": "train_shard_00001_2690_1", "global_id": 9494 }, { "text": "Whey and scotta are effluents coming from cheese and ricotta processing respectively. Whey contains minerals, lipids, lactose and proteins; scotta contains mainly lactose. Whey can be reused in several ways, such as protein extraction or animal feeding, while nowadays scotta is just considered as a waste; moreover, due to very high volumes of whey produced in the world, it poses serious environmental and disposal problems. Alternative destinations of these effluents, such as biotechnological transformations, can be a way to reach both goals of improving the added value of the agroindustrial processes and reducing their environmental impact. In this work we investigated the way to produce bioethanol from lactose of whey and scotta and to optimize the fermentation yields. Kluyveromyces marxianus var. marxianus was chosen as lactose-fermenting yeast. Batch, aerobic and anaerobic, fermentations and semicontinuous fermentations in dispersed phase and in packed bed reactor were carried out of row whey, scotta and mix 1:1 whey:scotta at a laboratory scale. Different temperatures (28-40°C) were also tested to check whether the thermotolerance of the chosen yeast could be useful to improve the ethanol yield. The best performances were reached at low temperatures (28°C); high temperatures are also compatible with good ethanol yields in whey fermentations, but not in scotta fermentations. Semicontinuous fermentations in dispersed phase gave the best fermentation performances, particularly with scotta. Then both effluents can be considered suitable for ethanol production. The good yields obtained from scotta allow us to transform this waste in a source.\n\nProduction of bioethanol from effluents of the dairy industry by Kluyveromyces marxianus.", "token_count": 431, "char_count": 1760, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6031, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:04.764557", "source": { "split": "train_shard_00001", "doc_id": 2691 }, "chunk_id": "train_shard_00001_2691_0", "global_id": 9495 }, { "text": "Legume crops, belonging to the Fabaceae family, are of immense importance for sustaining global food security. Many legumes are profitable crops for smallholder farmers due to their unique ability to fix atmospheric nitrogen and their intrinsic ability to thrive on marginal land with minimum inputs and low cultivation costs. Recent progress in genomics shows promise for future genetic gains in major grain legumes. Still it remains limited in minor legumes/underutilized legumes, including adzuki bean, cluster bean, horse gram, lathyrus, red clover, urd bean, and winged bean. In the last decade, unprecedented progress in completing genome assemblies of various legume crops and resequencing efforts of large germplasm collections has helped to identify the underlying gene(s) for various traits of breeding importance for enhancing genetic gain and contributing to developing climate-resilient cultivars. This review discusses the progress of genomic resource development, including genome-wide molecular markers, key breakthroughs in genome sequencing, genetic linkage maps, and trait mapping for facilitating yield improvement in underutilized legumes. We focus on 1) the progress in genomic-assisted breeding, 2) the role of whole-genome resequencing, pangenomes for underpinning the novel genomic variants underlying trait gene(s), 3) how adaptive traits of wild underutilized legumes could be harnessed to develop climate-resilient cultivars, 4) the progress and status of functional genomics resources, deciphering the underlying trait candidate genes with putative function in underutilized legumes 5) and prospects of novel breeding technologies, such as speed breeding, genomic selection, and genome editing. We conclude the review by discussing the scope for genomic resources developed in underutilized legumes to enhance their production and play a critical role in achieving the \"zero hunger\" sustainable development goal by 2030 set by the United Nations.\n\nProgress of Genomics-Driven Approaches for Sustaining Underutilized Legume Crops in the Post-Genomic Era.", "token_count": 460, "char_count": 2082, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:05.403424", "source": { "split": "train_shard_00001", "doc_id": 2692 }, "chunk_id": "train_shard_00001_2692_0", "global_id": 9496 }, { "text": "Listeria monocytogenes causes foodborne outbreaks with high mortality. For improvement of outbreak cluster detection, the German consiliary laboratory for listeriosis implemented whole-genome sequencing (WGS) in 2015. A total of 424 human L. monocytogenes isolates collected in 2007 to 2017 were subjected to WGS and core-genome multilocus sequence typing (cgMLST). cgMLST grouped the isolates into 38 complexes, reflecting 4 known and 34 unknown disease clusters. Most of these complexes were confirmed by single nucleotide polymorphism (SNP) calling, but some were further differentiated. Interestingly, several cgMLST cluster types were further subtyped by pulsed-field gel electrophoresis, partly due to phage insertions in the accessory genome. Our results highlight the usefulness of cgMLST for routine cluster detection but also show that cgMLST complexes require validation by methods providing higher typing resolution. Twelve cgMLST clusters included recent cases, suggesting activity of the source. Therefore, the cgMLST nomenclature data presented here may support future public health actions.\n\nWhole-Genome Sequencing of Recent Listeria monocytogenes Isolates from Germany Reveals Population Structure and Disease Clusters.", "token_count": 323, "char_count": 1251, "word_count": 166, "semantic_coherence": 1, "information_density": 0.747, "quality_score": 0.8735, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:05.983175", "source": { "split": "train_shard_00001", "doc_id": 2693 }, "chunk_id": "train_shard_00001_2693_0", "global_id": 9497 }, { "text": "

Background

Klebsiella pneumoniae (KP), often multidrug-resistant (MDR), is a significant public health concern and frequently associated with various diseases including urinary-tract infection. In addition, in recent years, an increasing number of studies reports on the emergence of convergent KP that combine MDR with hypervirulence leading to severely limited treatment options and thus calling for alternative approaches.

Methods

In this study, we compared high-risk clonal KP lineages with less pathogenic Klebsiella variicola (KV) and Klebsiella quasipneumoniae (KQ) strains on multiple-omics levels and performed integrative data analysis to identify unique markers that could be subsequently leveraged as novel targets in alternative treatment strategies.

Results

Our initial genomic analysis revealed 107 genes as part of the patho-core genome in eight clinical KP that were associated with different metabolic pathways. Subsequent transcriptome and proteome analyses in infection-mimicking media demonstrated similar regulatory patterns among KP vs. other Klebsiella strains, again with metabolic responses playing a pivotal role. In total, we identified 193 KP-specific, differentially expressed genes on transcriptomic and/or proteomic levels. When then comparing these regulated genes to over 6,000 publicly available Klebsiella genomes, we identified unique markers either in KP genomes or adaptively regulated on transcriptomics and/or proteomics levels. An example for the latter was a gene cluster for the cellobiose phosphotransferase system that has been previously described in the context of bacterial virulence and biofilm formation.

Conclusion

In conclusion, our study not only highlights that KP strains demonstrate metabolic flexibility in response to particular environmental conditions, which is potentially important for their success as opportunistic pathogens, but identified unique KP-markers. Subsequent studies are needed to explore whether these markers might be prospectively used as novel anti-virulence targets, providing alternatives to traditional antibiotics.", "token_count": 493, "char_count": 2135, "word_count": 279, "semantic_coherence": 1, "information_density": 0.7025, "quality_score": 0.8513, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:06.635068", "source": { "split": "train_shard_00001", "doc_id": 2694 }, "chunk_id": "train_shard_00001_2694_0", "global_id": 9498 }, { "text": "Multi-omics investigations uncover unique pathogenic markers in clinicalKlebsiella pneumoniaethat could be leveraged as novel antimicrobial targets", "token_count": 44, "char_count": 154, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:07.000770", "source": { "split": "train_shard_00001", "doc_id": 2694 }, "chunk_id": "train_shard_00001_2694_1", "global_id": 9499 }, { "text": "A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E", "token_count": 506, "char_count": 2080, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5399, "quality_score": 0.7699, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:08.281599", "source": { "split": "train_shard_00001", "doc_id": 2695 }, "chunk_id": "train_shard_00001_2695_0", "global_id": 9500 }, { "text": "coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.\n\nWhy are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador.", "token_count": 89, "char_count": 328, "word_count": 47, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:08.664550", "source": { "split": "train_shard_00001", "doc_id": 2695 }, "chunk_id": "train_shard_00001_2695_1", "global_id": 9501 }, { "text": "Advances in the treatment of cancer have significantly improved mortality rates; however, this has come at a cost, with many treatments still limited by their toxic side effects. Mucositis in both the mouth and gastrointestinal tract is common following many anti-cancer agents, manifesting as ulcerative lesions and associated symptoms throughout the alimentary tract. The pathogenesis of mucositis was first defined in 2004 by Sonis, and almost 20 years on, the model continues to be updated reflecting ongoing research initiatives and more sophisticated analytical techniques. The most recent update, published by the Multinational Association for Supportive Care in Cancer and the International Society for Oral Oncology (MASCC/ISOO), highlights the numerous co-occurring events that underpin mucositis development. Most notably, a role for the ecosystem of microorganisms that reside throughout the alimentary tract (the oral and gut microbiota) was explored, building on initial concepts proposed by Sonis. However, many questions remain regarding the true causal contribution of the microbiota and associated metabolome. This review aims to provide an overview of this rapidly evolving area, synthesizing current evidence on the microbiota's contribution to mucositis development and progression, highlighting (i) components of the 5-phase model where the microbiome may be involved, (ii) methodological challenges that have hindered advances in this area, and (iii) opportunities for intervention.\n\nUpdated perspectives on the contribution of the microbiome to the pathogenesis of mucositis using the MASCC/ISOO framework.", "token_count": 358, "char_count": 1630, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:09.248799", "source": { "split": "train_shard_00001", "doc_id": 2696 }, "chunk_id": "train_shard_00001_2696_0", "global_id": 9502 }, { "text": "Polyploidization or whole-genome duplication (WGD) is a well-known speciation and adaptation mechanism in angiosperms, while subgenome dominance is a crucial phenomenon in allopolyploids, established following polyploidization. The dominant subgenomes contribute more to genome evolution and homoeolog expression bias, both of which confer advantages for short-term phenotypic adaptation and long-term domestication. In this review, we firstly summarize the probable mechanistic basis for subgenome dominance, including the effects of genetic [transposon, genetic incompatibility, and homoeologous exchange (HE)], epigenetic (DNA methylation and histone modification), and developmental and environmental factors on this evolutionary process. We then move to Brassica rapa, a typical allopolyploid with subgenome dominance. Polyploidization provides the B. rapa genome not only with the genomic plasticity for adapting to changeable environments, but also an abundant genetic basis for morphological variation, making it a representative species for subgenome dominance studies. According to the 'two-step theory', B. rapa experienced genome fractionation twice during WGD, in which most of the genes responding to the environmental cues and phytohormones were over-retained, enhancing subgenome dominance and consequent adaption. More than this, the pangenome of 18 B. rapa accessions with different morphotypes recently constructed provides further evidence to reveal the impacts of polyploidization and subgenome dominance on intraspecific diversification in B. rapa. Above and beyond the fundamental understanding of WGD and subgenome dominance in B. rapa and other plants, however, it remains elusive why subgenome dominance has tissue- and spatiotemporal-specific features and could shuffle between homoeologous regions of different subgenomes by environments in allopolyploids", "token_count": 467, "char_count": 1925, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:09.889353", "source": { "split": "train_shard_00001", "doc_id": 2697 }, "chunk_id": "train_shard_00001_2697_0", "global_id": 9503 }, { "text": "We lastly propose acceleration of the combined application of resynthesized allopolyploids, omics technology, and genome editing tools to deepen mechanistic investigations of subgenome dominance, both genetic and epigenetic, in a variety of species and environments. We believe that the implications of genomic and genetic basis of a variety of ecologically, evolutionarily, and agriculturally interesting traits coupled with subgenome dominance will be uncovered and aid in making new discoveries and crop breeding.\n\nSubgenome dominance and its evolutionary implications in crop domestication and breeding.", "token_count": 131, "char_count": 607, "word_count": 82, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:10.316697", "source": { "split": "train_shard_00001", "doc_id": 2697 }, "chunk_id": "train_shard_00001_2697_1", "global_id": 9504 }, { "text": "Defining investigation-worthy genomic clusters among strains of Salmonella Enteritidis is challenging because of their highly clonal nature. We investigated a cluster identified by core genome multilocus sequence typing (cgMLST) consisting of 265 isolates with isolation dates spanning two and a half years. This cluster experienced chaining, growing to a range of 14 alleles. The volume of isolates and broad allele range of this cluster made it difficult to ascertain whether it represented a common-source outbreak. We explored laboratory-based methods to subdivide and refine this cluster. These methods included using cgMLST with a narrower allele range, whole genome multilocus sequence typing (wgMLST) and high-quality single-nucleotide polymorphism (hqSNP) analysis. At each analysis level, epidemiologists retroactively reviewed exposures, geography, and temporality for potential commonalities. Lowering the threshold to 0 alleles using cgMLST proved an effective method to refine this analysis, resulting in this large cluster being subdivided into 34 smaller clusters. Additional analysis by wgMLST and hqSNP provided enhanced cluster resolution, with the majority of clusters being further refined. These analysis methods combined with more stringent allele thresholds and layering of epidemiologic data proved useful in helping to subdivide this large cluster into actionable subclusters.\n\nChallenges Associated with Investigating <i>Salmonella</i> Enteritidis with Low Genomic Diversity in New York State: The Impact of Adjusting Analytical Methods and Correlation with Epidemiological Data.", "token_count": 387, "char_count": 1625, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:10.937708", "source": { "split": "train_shard_00001", "doc_id": 2698 }, "chunk_id": "train_shard_00001_2698_0", "global_id": 9505 }, { "text": "The life-threatening pathogen Leptospira interrogans is the most common agent of leptospirosis, an emerging zoonotic disease. However, little is known about the strains that are circulating worldwide due to the fastidious nature of the bacteria and its difficulty to be culture isolated. In addition, the paucity of bacteria in blood and other clinical samples has proven to be a considerable challenge for directly genotyping the agent of leptospirosis directly from patient material. Here, to elucidate the genomic diversity of Leptospira circulating strains, hybridization capture followed by Illumina sequencing of the core genome was performed directly from 20 biological samples that were PCR positive for pathogenic Leptospira . A set of samples subjected to capture with RNA probes covering the L. interrogans core genome resulted in 72 to 13,000-fold increase in pathogen reads when compared to standard sequencing without capture. A SNP analysis of the genomes sequenced from the biological samples using 273 Leptospira reference genome was then performed in order to determine the genotype of the infecting strain. For samples with sufficent coverage (19/20 samples with coverage >8X), we could unambigously identify L. interrogans sv Icterohaemorrhagiae (14 samples), L. kirschneri sv Grippotyphosa (4 samples) and L. interrogans sv Pyrogenes (1 sample) as the infecting strain. In conclusion, we obtained for most of our biological samples high quality genomic data at suitable coverage for confident core genome genotyping of the agent of leptospirosis. The ability to generate culture-free genomic data opens new opportunities to better understand the epidemiology and evolution of this fastidious pathogen.\n\nCore genome sequencing and genotyping ofLeptospira interrogansin clinical samples by target capture sequencing", "token_count": 448, "char_count": 1841, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5677, "quality_score": 0.7838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:11.581365", "source": { "split": "train_shard_00001", "doc_id": 2699 }, "chunk_id": "train_shard_00001_2699_0", "global_id": 9506 }, { "text": "

Background

Invasive fungal infections are increasing, and Candida yeasts are the main cause. Species other than Candida albicans are becoming more frequent, and some of them may have variable patterns of susceptibility to antifungal agents, making it important to identify them correctly. Conventional identification methods used by most laboratories may present with drawbacks. Mass spectrometry (MALDI-TOF MS) has emerged as an alternative method.

Aims

The aim of this study was to evaluate the concordance of the identification, at species level, by conventional methods (API) and MALDI-TOF MS.

Methods

The following species and number of isolates were studied: Candida parapsilosis (28), Candida glabrata (34), Candida krusei (24), Candida tropicalis (45), Candida guilliermondii (30), C. albicans (28), Candida dubliniensis (6), Candida kefyr (1), and Candida lipolytica (1) from the strain collection of Autonomous City of Buenos Aires Mycology Network (RMCABA). The strains C. parapsilosis 22019, C. glabrata 90030, C. krusei 6258 and C. albicans 68548 from the American Type Culture Collection (ATCC) were also included. Discrepancies were resolved by genotyping.

Results and conclusions

The direct concordance between the conventional identification method and MALDI-TOF MS was 92.5% (186/201).\n\n[Identification of Candida yeasts: Conventional methods and MALDI-TOF MS].", "token_count": 422, "char_count": 1408, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:12.206521", "source": { "split": "train_shard_00001", "doc_id": 2700 }, "chunk_id": "train_shard_00001_2700_0", "global_id": 9507 }, { "text": "Non-typhoidal Salmonella is a common cause of gastroenteritis worldwide, but current non-typhoidal Salmonella surveillance is suboptimal. Here, we evaluated the utility of wastewater monitoring to enhance traditional surveillance for this foodborne pathogen. In June 2022, we tested raw sewage collected twice a week from two treatment plants in central Pennsylvania for non-typhoidal Salmonella and characterized isolates using whole-genome sequencing. We recovered 43 Salmonella isolates from wastewater samples, differentiated by genomic analysis into seven serovars: 16 Panama (37.2%), 9 Senftenberg (20.9%), 8 Baildon (18.6%), and 3 or fewer of four other serovars. We assessed genetic relatedness and epidemiologic links between these wastewater isolates with those from patients with salmonellosis. All S. Baildon isolates from wastewater were genetically similar to those associated with a known contemporaneous salmonellosis outbreak. S. Baildon from wastewater and 42 outbreak-related isolates in the national outbreak detection database had the same core genome multilocus sequence typing, and outbreak code differed by zero or one single polynucleotide polymorphism. One of the 42 outbreak-related isolates was obtained from a patient residing in the wastewater sample collection catchment area, which serves approximately 17000 people. S. Baildon is a rare serovar (reported in <1% cases nationally, over five years). Our study underscores the value of monitoring sewage from a defined population to supplement traditional surveillance methods for the evidence of Salmonella infections and to determine the extent of outbreaks.IMPORTANCEDuring the COVID-19 pandemic, monitoring for SARS-CoV-2 in wastewater was highly effective in identifying the variants of concern earlier than clinical surveillance methods. Here, we show that monitoring domestic sewage can also augment traditional reporting of foodborne illnesses to public health authorities", "token_count": 508, "char_count": 2016, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:13.257723", "source": { "split": "train_shard_00001", "doc_id": 2701 }, "chunk_id": "train_shard_00001_2701_0", "global_id": 9508 }, { "text": "Our study detected multiple Salmonella enterica serovars in samples from two wastewater treatment plants in central Pennsylvania. Using whole-genome sequencing, we demonstrated that the isolates of variant S. Baildon clustered with those from a foodborne salmonellosis outbreak that occurred in a similar time frame. Cases were primarily from Pennsylvania, and one individual lived within the wastewater treatment catchment area. This study highlights the effectiveness of domestic sewage testing as a proactive public health strategy to track and respond to infectious disease outbreaks.\n\nOutbreak-associated Salmonella Baildon found in wastewater demonstrates how sewage monitoring can supplement traditional disease surveillance.", "token_count": 163, "char_count": 753, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7938, "quality_score": 0.8969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:13.709117", "source": { "split": "train_shard_00001", "doc_id": 2701 }, "chunk_id": "train_shard_00001_2701_1", "global_id": 9509 }, { "text": "The identification of bacterial effectors is essential to understand how obligatory intracellular bacteria such as Ehrlichia spp. manipulate the host cell for survival and replication. Infection of mammals – including humans – by the intracellular pathogenic bacteria Ehrlichia spp. depends largely on the injection of virulence proteins that hijack host cell processes. Several hypothetical virulence proteins have been identified in Ehrlichia spp., but one so far has been experimentally shown to translocate into host cells via the type IV secretion system. However, the current challenge is to identify most of the type IV effectors (T4Es) to fully understand their role in Ehrlichia spp. virulence and host adaptation. Here, we predict the T4E repertoires of four sequenced Ehrlichia spp. and four other Anaplasmataceae as comparative models (pathogenic Anaplasma spp. and Wolbachia endosymbiont) using previously developed S4TE 2.0 software. This analysis identified 579 predicted T4Es (228 pT4Es for Ehrlichia spp. only). The effector repertoires of Ehrlichia spp. overlapped, thereby defining a conserved core effectome of 92 effectors shared by all strains. In addition, 69 species-specific T4Es were predicted with non-canonical GC% mostly in gene sparse regions of the genomes and we observed a bias in pT4Es according to host-specificity. We also identified new protein domain combinations, suggesting novel effector functions. This work presenting the predicted effector collection of Ehrlichia spp. can serve as a guide for future functional characterisation of effectors and design of alternative control strategies against these bacteria.\n\nThe super repertoire of type IV effectors in the pangenome ofEhrlichiaspp. provides insights into host-specificity and pathogenesis", "token_count": 447, "char_count": 1794, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:14.408170", "source": { "split": "train_shard_00001", "doc_id": 2702 }, "chunk_id": "train_shard_00001_2702_0", "global_id": 9510 }, { "text": "Prevotella copri is an abundant member of the human gastrointestinal microbiome, whose relative abundance has curiously been associated with positive and negative impacts on diseases, such as Parkinson's disease and rheumatoid arthritis. Yet, the verdict is still out on the definitive role of P. copri in human health, and on the effect of different diets on its relative abundance in the gut microbiome. The puzzling discrepancies among P. copri studies have only recently been attributed to the diversity of its strains, which substantially differ in their encoded metabolic patterns from the commonly used reference strain. However, such strain differences cannot be resolved by common 16S rRNA amplicon profiling methods. Here, we scrutinize P. copri, its versatile metabolic potential, and the hypotheses behind the conflicting observations on its association with diet and human health. We also provide suggestions for designing studies and bioinformatics pipelines to better research P. copri.\n\nThe curious case of Prevotella copri.", "token_count": 268, "char_count": 1082, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6948, "quality_score": 0.8474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:14.972977", "source": { "split": "train_shard_00001", "doc_id": 2703 }, "chunk_id": "train_shard_00001_2703_0", "global_id": 9511 }, { "text": "Rhizoctonia solani is a collective group of genetically and pathologically diverse basidiomycetous fungi that damage economically important crops. Its isolates are classified into 13 Anastomosis Groups (AGs) and subgroups having distinctive morphology and host ranges. The genetic factors driving the unique features of R. solani pathology are not well characterized due to the limited availability of its annotated genomes. Therefore, we performed genome sequencing, assembly, annotation and functional analysis of 12 R. solani isolates covering 7 AGs and select subgroups (AG1-IA; AG1-IB; AG1-IC; AG2-2IIIB; AG3-PT, isolates Rhs 1AP and the hypovirulent Rhs1A1; AG3-TB; AG4-HG-I, isolates Rs23 and R118-11; AG5; AG6; and AG8), in which six genomes are reported for the first time. Using a pangenome comparative analysis of 12 R. solani isolates and 15 other Basidiomycetes, we defined the unique and shared secretomes, CAZymes, and effectors across the AGs. We have also elucidated the R. solani-derived factors potentially involved in determining AG-specific host preference, and the attributes distinguishing them from other Basidiomycetes. Finally, we present the largest repertoire of R. solani genomes and their annotated components as a comprehensive database, viz. RsolaniDB, with tools for large-scale data mining, functional enrichment and sequence analysis not available with other state-of-the-art platforms.\n\nPangenome Analysis of the Soilborne Fungal Phytopathogen Rhizoctonia solani and Development of a Comprehensive Web Resource: RsolaniDB.", "token_count": 459, "char_count": 1600, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6713, "quality_score": 0.8356, "entities": { "genes": [ "AG3", "AG4", "AG6", "AG1", "AG8", "AG2", "AG5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:15.617881", "source": { "split": "train_shard_00001", "doc_id": 2704 }, "chunk_id": "train_shard_00001_2704_0", "global_id": 9512 }, { "text": "Antibiotic resistance (AR) is the result of microbes' natural evolution to withstand the action of antibiotics used against them. AR is rising to a high level across the globe, and novel resistant strains are emerging and spreading very fast. Acinetobacter baumannii is a multidrug resistant Gram-negative bacteria, responsible for causing severe nosocomial infections that are treated with several broad spectrum antibiotics: carbapenems, β-lactam, aminoglycosides, tetracycline, gentamicin, impanel, piperacillin, and amikacin. The A. baumannii genome is superplastic to acquire new resistant mechanisms and, as there is no vaccine in the development process for this pathogen, the situation is more worrisome. This study was conducted to identify protective antigens from the core genome of the pathogen. Genomic data of fully sequenced strains of A. baumannii were retrieved from the national center for biotechnological information (NCBI) database and subjected to various genomics, immunoinformatics, proteomics, and biophysical analyses to identify potential vaccine antigens against A. baumannii. By doing so, four outer membrane proteins were prioritized: TonB-dependent siderphore receptor, OmpA family protein, type IV pilus biogenesis stability protein, and OprD family outer membrane porin. Immuoinformatics predicted B-cell and T-cell epitopes from all four proteins. The antigenic epitopes were linked to design a multi-epitopes vaccine construct using GPGPG linkers and adjuvant cholera toxin B subunit to boost the immune responses. A 3D model of the vaccine construct was built, loop refined, and considered for extensive error examination. Disulfide engineering was performed for the stability of the vaccine construct. Blind docking of the vaccine was conducted with host MHC-I, MHC-II, and toll-like receptors 4 (TLR-4) molecules", "token_count": 492, "char_count": 1878, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:16.267448", "source": { "split": "train_shard_00001", "doc_id": 2705 }, "chunk_id": "train_shard_00001_2705_0", "global_id": 9513 }, { "text": "Molecular dynamic simulation was carried out to understand the vaccine-receptors dynamics and binding stability, as well as to evaluate the presentation of epitopes to the host immune system. Binding energies estimation was achieved to understand intermolecular interaction energies and validate docking and simulation studies. The results suggested that the designed vaccine construct has high potential to induce protective host immune responses and can be a good vaccine candidate for experimental in vivo and in vitro studies.\n\nVaccinomics to Design a Multi-Epitopes Vaccine for Acinetobacter baumannii.", "token_count": 129, "char_count": 614, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6824, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:16.687184", "source": { "split": "train_shard_00001", "doc_id": 2705 }, "chunk_id": "train_shard_00001_2705_1", "global_id": 9514 }, { "text": "Species constitute the fundamental units of taxonomy and an ideal species definition would embody groups of genetically cohesive organisms reflecting their shared history, traits, and ecology. In contrast to animals and plants, where genetic cohesion can essentially be characterized by sexual compatibility and population structure, building a biologically relevant species definition remains a challenging endeavor in prokaryotes. Indeed, the structure, ecology, and dynamics of microbial populations are still largely enigmatic, and many aspects of prokaryotic genomics deviate from sexual organisms. In this chapter, I present the main concepts and operational definitions commonly used to designate microbial species. I further emphasize how these different concepts accommodate the idiosyncrasies of prokaryotic genomics, in particular, the existence of a core- and a pangenome. Although prokaryote genomics is undoubtedly different from animals and plants, there is growing evidence that gene flow—similar to sexual reproduction—plays a significant role in shaping the genomic cohesiveness of microbial populations, suggesting that, to some extent, a species definition based on the Biological Species Concept is applicable to prokaryotes. Building a satisfying species definition remains to be accomplished, but the integration of genomic data, ecology, and bioinformatics tools has expanded our comprehension of prokaryotic populations and their dynamics.\n\nThe Prokaryotic Species Concept and Challenges", "token_count": 315, "char_count": 1512, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:17.246131", "source": { "split": "train_shard_00001", "doc_id": 2706 }, "chunk_id": "train_shard_00001_2706_0", "global_id": 9515 }, { "text": "Pangenomes offer detailed characterizations of core and accessory genes found in a set of closely related microbial genomes, generally by clustering genes based on sequence homology. In comparison, metagenomes facilitate highly resolved investigations of the relative distribution of microbial genomes and individual genes across environments through read recruitment analyses. Combining these complementary approaches can yield unique insights into the functional basis of microbial niche partitioning and fitness, however, advanced software solutions are lacking. Here we present an integrated analysis and visualization strategy that provides an interactive and reproducible framework to generate pangenomes and to study them in conjunction with metagenomes. To investigate its utility, we applied this strategy to a Prochlorococcus pangenome in the context of a large-scale marine metagenomic survey. The resulting Prochlorococcus metapangenome revealed remarkable differential abundance patterns between very closely related isolates that belonged to the same phylogenetic cluster and that differed by only a small number of gene clusters in the pangenome. While the relationships between these genomes based on gene clusters correlated with their environmental distribution patterns, phylogenetic analyses using marker genes or concatenated single-copy core genes did not recapitulate these patterns. The metapangenome also revealed a small set of core genes that mostly occurred in hypervariable genomic islands of the Prochlorococcus populations, which systematically lacked read recruitment from surface ocean metagenomes. Notably, these core gene clusters were all linked to sugar metabolism, suggesting potential benefits to Prochlorococcus from a high sequence diversity of sugar metabolism genes. The rapidly growing number of microbial genomes and increasing availability of environmental metagenomes provide new opportunities to investigate the functioning and the ecology of microbial populations, and metapangenomes can provide unique insights for any taxon and biome for which genomic and sufficiently deep metagenomic data are available.\n\nLinking pangenomes and metagenomes: the Prochlorococcus metapangenome.", "token_count": 478, "char_count": 2263, "word_count": 296, "semantic_coherence": 1, "information_density": 0.598, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:17.889843", "source": { "split": "train_shard_00001", "doc_id": 2707 }, "chunk_id": "train_shard_00001_2707_0", "global_id": 9516 }, { "text": "Since 2010, outbreaks of haemorrhagic septicaemia (HS) caused by Pasteurella (P.) multocida capsular type B (PmB) emerged in Germany. In 2017, we noticed a close spatiotemporal relationship between HS outbreak sites and wolf (Canis lupus) territories. Thus, the main objectives of our study were to investigate the molecular epidemiology of German PmB-HS-isolates and to assess the role of wolves as putative vectors of this pathogen. We collected 83 PmB isolates from HS outbreaks that occurred between 2010 and 2019 and sampled 150 wolves, which were found dead in the years 2017 to 2019, revealing another three PmB isolates. A maximum-likelihood-based phylogeny of the core genomes of 65 PmB-HS-isolates and the three PmB-wolf-isolates showed high relatedness. Furthermore, all belonged to capsular:LPS:MLST genotype B:L2:ST122RIRDC and showed highly similar virulence gene profiles, but clustered separately from 35 global ST122RIRDC strains. Our data revealed that German HS outbreaks were caused by a distinct genomic lineage of PmB-ST122 strains, hinting towards an independent, ongoing epidemiologic event. We demonstrated for the first time, that carnivores, i.e., wolves, might harbour PmB as a part of their oropharyngeal microbiota. Furthermore, the results of our study imply that wolves can carry the pathogen over long distances, indicating a major role of that animal species in the ongoing epidemiological event of HS in Germany.", "token_count": 505, "char_count": 1553, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [ "ST122" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:18.540747", "source": { "split": "train_shard_00001", "doc_id": 2708 }, "chunk_id": "train_shard_00001_2708_0", "global_id": 9517 }, { "text": "Re-Emergence and Spread of Haemorrhagic Septicaemia in Germany: The Wolf as a Vector?", "token_count": 28, "char_count": 85, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:18.895066", "source": { "split": "train_shard_00001", "doc_id": 2708 }, "chunk_id": "train_shard_00001_2708_1", "global_id": 9518 }, { "text": "

Motivation

Antimicrobial resistance (AMR) is becoming a huge problem in both developed and developing countries, and identifying strains resistant or susceptible to certain antibiotics is essential in fighting against antibiotic-resistant pathogens. Whole-genome sequences have been collected for different microbial strains in order to identify crucial characteristics that allow certain strains to become resistant to antibiotics; however, a global inspection of the gene content responsible for AMR activities remains to be done.

Results

We propose a pan-genome-based approach to characterize antibiotic-resistant microbial strains and test this approach on the bacterial model organism Escherichia coli. By identifying core and accessory gene clusters and predicting AMR genes for the E. coli pan-genome, we not only showed that certain classes of genes are unevenly distributed between the core and accessory parts of the pan-genome but also demonstrated that only a portion of the identified AMR genes belong to the accessory genome. Application of machine learning algorithms to predict whether specific strains were resistant to antibiotic drugs yielded the best prediction accuracy for the set of AMR genes within the accessory part of the pan-genome, suggesting that these gene clusters were most crucial to AMR activities in E. coli. Selecting subsets of AMR genes for different antibiotic drugs based on a genetic algorithm (GA) achieved better prediction performances than the gene sets established in the literature, hinting that the gene sets selected by the GA may warrant further analysis in investigating more details about how E. coli fight against antibiotics.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nA pan-genome-based machine learning approach for predicting antimicrobial resistance activities of the Escherichia coli strains.", "token_count": 428, "char_count": 1917, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5682, "quality_score": 0.7841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:19.520883", "source": { "split": "train_shard_00001", "doc_id": 2709 }, "chunk_id": "train_shard_00001_2709_0", "global_id": 9519 }, { "text": "A strain of Kluyveromyces marxianus was grown in batch culture in lactose-based media at varying initial lactose concentrations (10-60 g L(-1)) at 30 degrees C, pH 5.0, dissolved oxygen concentrations greater than 20%. Increasing the concentration of mineral salts three-fold at 40 g L(-1) and 60 g L(-1) initial lactose concentration showed only a small increase in the yield of biomass, from 0.38 g g(-1) to 0.41 g g(-1), indicating that the initial batch cultures were not significantly nutrient- (mineral salts)-limited. A relatively high biomass concentration (105 g L(-1)) was obtained in fed-batch culture following extended lactose feeding. An average specific growth rate (0.27 h(-1)), biomass yield (0.38 g g(-1)) and overall productivity (2.9 g L(-1) h(-1)) were obtained for these fed-batch conditions. This fed-batch protocol provides a strategy for achieving relatively high concentrations and productivities of K. marxianus on other lactose-based substrate streams (e.g., whey) from the dairy industry.\n\nFed-batch fermentation for production of Kluyveromyces marxianus FII 510700 cultivated on a lactose-based medium.", "token_count": 330, "char_count": 1132, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6524, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:20.089277", "source": { "split": "train_shard_00001", "doc_id": 2710 }, "chunk_id": "train_shard_00001_2710_0", "global_id": 9520 }, { "text": "Clostridioides difficile (Clostridium difficile) sequence type 11 (ST11) is well established in production animal populations worldwide and contributes considerably to the global burden of C. difficile infection (CDI) in humans. Increasing evidence of shared ancestry and genetic overlap of PCR ribotype 078 (RT078), the most common ST11 sublineage, between human and animal populations suggests that CDI may be a zoonosis. We performed whole-genome sequencing (WGS) on a collection of 207 ST11 and closely related ST258 isolates of human and veterinary/environmental origin, comprising 16 RTs collected from Australia, Asia, Europe, and North America. Core genome single nucleotide variant (SNV) analysis identified multiple intraspecies and interspecies clonal groups (isolates separated by ≤2 core genome SNVs) in all the major RT sublineages: 078, 126, 127, 033, and 288. Clonal groups comprised isolates spread across different states, countries, and continents, indicative of reciprocal long-range dissemination and possible zoonotic/anthroponotic transmission. Antimicrobial resistance genotypes and phenotypes varied across host species, geographic regions, and RTs and included macrolide/lincosamide resistance (Tn6194 [ermB]), tetracycline resistance (Tn6190 [tetM] and Tn6164 [tet44]), and fluoroquinolone resistance (gyrA/B mutations), as well as numerous aminoglycoside resistance cassettes", "token_count": 461, "char_count": 1480, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7705, "quality_score": 0.8852, "entities": { "genes": [ "RT078", "ST11", "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:20.737626", "source": { "split": "train_shard_00001", "doc_id": 2711 }, "chunk_id": "train_shard_00001_2711_0", "global_id": 9521 }, { "text": "The population was defined by a large \"open\" pan-genome (10,378 genes), a remarkably small core genome of 2,058 genes (only 19.8% of the gene pool), and an accessory genome containing a large and diverse collection of important prophages of the Siphoviridae and Myoviridae This study provides novel insights into strain relatedness and genetic variability of C. difficile ST11, a lineage of global One Health importance.IMPORTANCE Historically, Clostridioides difficile (Clostridium difficile) has been associated with life-threatening diarrhea in hospitalized patients. Increasing rates of C. difficile infection (CDI) in the community suggest exposure to C. difficile reservoirs outside the hospital, including animals, the environment, or food. C. difficile sequence type 11 (ST11) is known to infect/colonize livestock worldwide and comprises multiple ribotypes, many of which cause disease in humans, suggesting CDI may be a zoonosis. Using high-resolution genomics, we investigated the evolution and zoonotic potential of ST11 and a new closely related ST258 lineage sourced from diverse origins. We found multiple intra- and interspecies clonal transmission events in all ribotype sublineages. Clones were spread across multiple continents, often without any health care association, indicative of zoonotic/anthroponotic long-range dissemination in the community. ST11 possesses a massive pan-genome and numerous clinically important antimicrobial resistance elements and prophages, which likely contribute to the success of this globally disseminated lineage of One Health importance.\n\nEvolutionary and Genomic Insights into Clostridioides difficile Sequence Type 11: a Diverse Zoonotic and Antimicrobial-Resistant Lineage of Global One Health Importance.", "token_count": 497, "char_count": 1833, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6653, "quality_score": 0.8326, "entities": { "genes": [ "ST11", "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:21.389138", "source": { "split": "train_shard_00001", "doc_id": 2711 }, "chunk_id": "train_shard_00001_2711_1", "global_id": 9522 }, { "text": "The aroma of a deacidified cheese medium is the result of the overall perception of a large number of molecules belonging to different classes. The volatile compound composition of (60%) cheese medium (pH 5.8) deacidified by Debaryomyces hansenii (DCM(Dh)) was compared with the one deacidified by Kluyveromyces marxianus (DCM(Km)). It was determined by dynamic headspace extraction, followed by gas chromatography separation and quantification as well as by mass spectrometry identification. Whatever the media tested, a first class of volatile compounds can be represented by the ones not produced by any of the yeasts, but some of them are affected by K. marxianus or by D. hansenii. A second class of volatile compounds can be represented by the ones produced by K. marxianus, which were essentially esters. Their concentrations were generally higher than their thresholds, explaining the DCM(Km) global fruity odor. A third class can be represented by the ones generated by D. hansenii, which were essentially methyl ketones with fruity, floral (rose), moldy, cheesy, or wine odor plus 2-phenylethanol with a faded-rose odor. The impact of methyl ketones on the DCMDh global flavor was lower than the impact of 2-phenylethanol and even negligible. Therefore, the global faded-rose odor of D. hansenii DCM can be explained by a high concentration of 2-phenylethanol.\n\nComparison of volatile compounds produced in model cheese medium deacidified by Debaryomyces hansenii or Kluyveromyces marxianus.", "token_count": 391, "char_count": 1501, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5419, "quality_score": 0.7709, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:22.010922", "source": { "split": "train_shard_00001", "doc_id": 2712 }, "chunk_id": "train_shard_00001_2712_0", "global_id": 9523 }, { "text": "A Burkholderia gladioli strain, named BBB-01, was isolated from rice shoots based on the confrontation plate assay activity against several plant pathogenic fungi. The genome of this bacterial strain consists of two circular chromosomes and one plasmid with 8,201,484 base pairs in total. Pangenome analysis of 23 B. gladioli strains suggests that B. gladioli BBB-01 has the closest evolutionary relationship to B. gladioli pv. gladioli and B. gladioli pv. agaricicola. B. gladioli BBB-01 emitted dimethyl disulfide and 2,5-dimethylfuran when it was cultivated in lysogeny broth and potato dextrose broth, respectively. Dimethyl disulfide is a well-known pesticide, while the bioactivity of 2,5-dimethylfuran has not been reported. In this study, the inhibition activity of the vapor of these two compounds was examined against phytopathogenic fungi, including Magnaporthe oryzae, Gibberella fujikuroi, Sarocladium oryzae, Phellinus noxius and Colletotrichumfructicola, and human pathogen Candida albicans. In general, 2,5-dimethylfuran is more potent than dimethyl disulfide in suppressing the growth of the tested fungi, suggesting that 2,5-dimethylfuran is a potential fumigant to control plant fungal disease.\n\nFungicidal Activity of Volatile Organic Compounds Emitted by Burkholderia gladioli Strain BBB-01.", "token_count": 496, "char_count": 1424, "word_count": 180, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:22.660763", "source": { "split": "train_shard_00001", "doc_id": 2713 }, "chunk_id": "train_shard_00001_2713_0", "global_id": 9524 }, { "text": "Infections caused by fungal pathogens such as Candida and Cryptococcus are associated with high mortality rates, partly due to limitations in the current antifungal arsenal. This highlights the need for antifungal drug targets with novel mechanisms of action. The trehalose biosynthesis pathway is a promising antifungal drug target because trehalose biosynthesis is essential for virulence in Cryptococcus neoformans and Candida albicans and is also a mediator of fungal stress responses, such as thermotolerance. To exploit its untapped antifungal potentials, we screened the St. Jude 3-point pharmacophore library to identify small molecule inhibitors of the first enzyme in the trehalose biosynthesis pathway, trehalose-6-phosphate synthase (Tps1). Structure-guided optimization of a potent hit, SJ6675, yielded a water-soluble inhibitor named 4456dh. Employing biochemical, structural, and cell-based assays, we demonstrate that 4456dh inhibits Tps1 enzymatic activity, suppresses trehalose synthesis, and exerts a fungicidal effect. Notably, the structure of Tps1 in complex with 4456 reveals that 4456 occupies the substrate binding pocket. Importantly, 4456dh renders normally thermotolerant fungal pathogens unable to survive at elevated temperatures, which is critical as we investigate the emergence of fungi from the environment due to a warming climate. Overall, this work develops the water-soluble 4456dh as an early-stage antifungal drug that has a distinct mechanism of action compared to existing clinical antifungals.IMPORTANCEThe rise of fungal infections in recent years is alarming due to an increase in the vulnerable immunocompromised population, global temperature increase, and limited antifungal treatment options", "token_count": 486, "char_count": 1768, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [ "SJ6675" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:23.317991", "source": { "split": "train_shard_00001", "doc_id": 2714 }, "chunk_id": "train_shard_00001_2714_0", "global_id": 9525 }, { "text": "One of the major hurdles in developing new drugs is the identification of fungal-specific antifungal drug targets due to highly conserved cellular machinery between fungi and humans. Here, we describe a small molecule inhibitor, 4456dh, of the trehalose biosynthesis pathway. This pathway is present in fungi but not in humans. Trehalose plays a critical role in stress responses such as thermotolerance in fungal pathogens and is essential for their virulence. We show that treatment with 4456dh blocks the production of trehalose and renders fungal cells inviable. Thus far, 4456dh is active against two fungal pathogens of critical importance, suggesting broad-spectrum activity.\n\nInhibitors of trehalose-6-phosphate synthase activity in fungal pathogens compromise thermal tolerance pathways.", "token_count": 201, "char_count": 796, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7257, "quality_score": 0.8628, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:23.781579", "source": { "split": "train_shard_00001", "doc_id": 2714 }, "chunk_id": "train_shard_00001_2714_1", "global_id": 9526 }, { "text": "Enterococcus faecium, a common resident of the human gastrointestinal tract, is also a major pathogen. Prompt initiation of appropriate treatment is essential to improve patient outcome in disseminated E. faecium infections. However, ampicillin resistance is frequent in this species, rendering treatment difficult. We used a comprehensive approach, including clinical data review, whole-genome sequencing, and mass spectrometry, to characterize ampicillin-susceptible (EFM-S) and ampicillin-resistant (EFM-R) isolates. We included all patients with culture-confirmed E. faecium infection attending our hospital over a 16-month period. A comparison of 32 patients infected with EFM-S strains and 251 patients infected with EFM-R strains revealed that EFM-R isolates were strongly associated with a longer hospital stay, history of prior hospitalization, and the carriage of multidrug-resistant organisms. An analysis of the genomes of 26 EFM-S and 26 EFM-R isolates from paired patients revealed a population structure almost perfectly matching ampicillin susceptibility, with resistant isolates in clade A1, and susceptible isolates in clades A2 and B. The clade B and A2 isolates mostly came from digestive or biliary tract samples, whereas clade A1 isolates were mostly obtained from urine and blood. Finally, we built a custom database for matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), which differentiated between clade B and clade A1/A2 strains with high-positive and high-negative predictive values (95.6% and 100%, respectively). This study provides important new insight into the clinical features and clades associated with EFM-S and EFM-R isolates. In combination with MALDI-TOF MS, these data could facilitate the rapid initiation of the most appropriate treatment.IMPORTANCEEnterococcus faecium is an important human pathogen in which the prevalence of ampicillin resistance is high", "token_count": 508, "char_count": 1970, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6113, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:24.436325", "source": { "split": "train_shard_00001", "doc_id": 2715 }, "chunk_id": "train_shard_00001_2715_0", "global_id": 9527 }, { "text": "However, little is known about the clinical characteristics of patients infected with ampicillin-resistant and ampicillin-susceptible strains. Indeed, current knowledge is based on genus-wide studies of Enterococcus or studies of very small numbers of susceptible isolates, precluding robust conclusions. Our data highlight specific clinical features related to the epidemiology of EFM-S and EFM-R strains, such as length of hospital stay, history of prior hospitalization, carriage of multidrug-resistant organisms, and type of sample from which the isolate was obtained. The use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry with a custom-built database may make it possible to distinguish clade B isolates, which are typically susceptible to ampicillin, from clade A1/A2 isolates (A1 being typically resistant), thereby facilitating the management of these infections.\n\nAmpicillin-susceptible Enterococcus faecium infections: clinical features, causal clades, and contribution of MALDI-TOF to early detection.", "token_count": 264, "char_count": 1060, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7556, "quality_score": 0.8778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:25.012458", "source": { "split": "train_shard_00001", "doc_id": 2715 }, "chunk_id": "train_shard_00001_2715_1", "global_id": 9528 }, { "text": "The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa , a comprehensive genome annotation including gene structure, alternative splicing events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the UTR regions of 20,340 annotated genes and corrected 886 wrongly-spliced genes. We also identified 28,564 alternative splicing (AS) events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.\n\nImproved reference genome annotation of Brassica rapa by PacBio RNA sequencing", "token_count": 389, "char_count": 1392, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:25.644100", "source": { "split": "train_shard_00001", "doc_id": 2716 }, "chunk_id": "train_shard_00001_2716_0", "global_id": 9529 }, { "text": "

Background

Coevolution between modern aphids and their primary obligate, bacterial endosymbiont, Buchnera aphidicola, has been previously reported at different classification levels based on molecular phylogenetic analyses. However, the Buchnera genome remains poorly understood within the Rhus gall aphids.

Results

We assembled the complete genome of the endosymbiont Buchnera in 16 aphid samples, representing 13 species in all six genera of Rhus gall aphids by shotgun genome skimming method. We compared the newly assembled genomes with those from GenBank to comprehensively investigate patterns of coevolution between the bacteria Buchnera and their aphid hosts. Buchnera genomes were mostly collinear, and the pan-genome contained 684 genes, in which the core genome contained 256 genes with some lineages having large numbers of tandem gene duplications. There has been substantial gene-loss in each Buchnera lineage. We also reconstructed the phylogeny for Buchnera and their host aphids, respectively, using 72 complete genomes of Buchnera, along with the complete mitochondrial genomes and three nuclear genes of 31 corresponding host aphid accessions. The cophylogenetic test demonstrated significant coevolution between these two partner groups at individual, species, generic, and tribal levels.

Conclusions

Buchnera exhibits very high levels of genomic sequence divergence but relative stability in gene order. The relationship between the symbionts Buchnera and its aphid hosts shows a significant coevolutionary pattern and supports complexity of the obligate symbiotic relationship.\n\nComparative genomics of the primary endosymbiont Buchnera aphidicola in aphid hosts and their coevolutionary relationships.", "token_count": 436, "char_count": 1746, "word_count": 231, "semantic_coherence": 1, "information_density": 0.645, "quality_score": 0.8225, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:26.304684", "source": { "split": "train_shard_00001", "doc_id": 2717 }, "chunk_id": "train_shard_00001_2717_0", "global_id": 9530 }, { "text": "

Background and purpose

By using advanced detection/identification methods, the list of emerging uncommon opportunistic yeast infections is rapidly expanding worldwide. Our aim in the present study was sequence-based species delineation of previously unidentified yeasts obtained from a clinically yeast collection.

Materials and methods

A total of twenty three out of the 855 (5.7%) yeast isolates which formerly remained unidentified by PCR-RFLP method, were subjected to sequence analysis of the entire internal transcribed spacers (ITS) regions of rDNA. The precise species recognition was performed by the comparison of the sequences with the reliable GenBank database.

Results

Sequencing analysis of the ITS region of the strains revealed several uncommon yeasts that were not reported previously in Iran. The species include Hanseniaspora uvarum, Saccharomyces cerevisiae, Sporidiobolus salmonicolor, Pichia fabianii, Pichia fermentans, Candida famata, Candida inconspicua, Candida maqnoliae, Candida guilliermondii, Candida kefyr, Candida rugosa, Candida lusitaniae, Candida orthopsilosis, and Candida viswanathii.

Conclusion

We identified several rare clinical isolates selected from a big collection at the species level by ITS-sequencing. As the list of yeast species as opportunistic human fungal infections is increasing dramatically, and many isolates remain unidentified using conventional methods, more sensitive and specific advanced approaches help us to clarify the aspects of microbial epidemiology of the yeast infections.\n\nMolecular identification of uncommon clinical yeast species in Iran.", "token_count": 430, "char_count": 1669, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:26.957621", "source": { "split": "train_shard_00001", "doc_id": 2718 }, "chunk_id": "train_shard_00001_2718_0", "global_id": 9531 }, { "text": "Inflammatory bowel diseases (IBD) include a spectrum of chronic inflammatory disorders of the gastrointestinal tract whose pathogenesis is yet to be elucidated. The intestinal microbiome has been studied as a causal component, with certain microbiotic alterations having been observed in subtypes of IBD. Physical exercise is a modulator of the intestinal microbiome, causing shifts in its composition that are partially corrective of those observed in IBD; furthermore, physical exercise may be beneficial in patients with certain IBD subtypes. This review studies the effects of physical exercise on the human gut microbiome while investigating pathophysiologic mechanisms that could explain physical activity's clinical effects on patients with IBD.\n\nRole of exercise in preventing and restoring gut dysbiosis in patients with inflammatory bowel diseases: A review.", "token_count": 194, "char_count": 868, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:27.415775", "source": { "split": "train_shard_00001", "doc_id": 2719 }, "chunk_id": "train_shard_00001_2719_0", "global_id": 9532 }, { "text": "Microorganisms play a role in oral mucositis after cancer therapy. The current study explored the hypothesis that Candida spp. alone and together with Porphyromonas gingivalis cause delayed healing of oral ulcerations due to the inhibition of wound closure. An in vitro scratch assay model was used to study the influence of viable and heat-killed Candida glabrata, Candida kefyr, and Candida albicans on cell migration of oral epithelial cells. Separately, the effect of conditioned medium of Candida spp. and the effect of a mixed infection of Candida spp. with P. gingivalis on wound closure was studied. In the presence of 10 viable C. glabrata or C. kefyr versus one epithelial cell, with a multiplicity of infection (MOI) of 10, the relative closure of the scratch was 26% and 17%, respectively. At a MOI of 1, this was 60% for C. glabrata and 78% for C. kefyr. The inhibition of oral epithelial cell migration challenged with either C. glabrata or C. kefyr together with P. gingivalis was stronger than the inhibition caused by one of both organisms separately. Candida spp. inhibit cell migration in vitro. A combination of Candida spp. and P. gingivalis inhibited cell migration more than either microorganism separately.\n\nCandida and Porphyromonas gingivalis: the effect on wound closure in vitro.", "token_count": 490, "char_count": 1461, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:28.066430", "source": { "split": "train_shard_00001", "doc_id": 2720 }, "chunk_id": "train_shard_00001_2720_0", "global_id": 9533 }, { "text": "

Background

Enterococcus faecium is a commensal of the gastrointestinal tract of animals and humans but also a causative agent of hospital-acquired infections. Resistance against glycopeptides and to vancomycin has motivated the inclusion of E. faecium in the WHO global priority list. Vancomycin resistance can be conferred by the vanA gene cluster on the transposon Tn1546, which is frequently present in plasmids. The vanA gene cluster can be disseminated clonally but also horizontally either by plasmid dissemination or by Tn1546 transposition between different genomic locations.

Methods

We performed a retrospective study of the genomic epidemiology of 309 vancomycin-resistant E. faecium (VRE) isolates across 32 Dutch hospitals (2012-2015). Genomic information regarding clonality and Tn1546 characterization was extracted using hierBAPS sequence clusters (SC) and TETyper, respectively. Plasmids were predicted using gplas in combination with a network approach based on shared k-mer content. Next, we conducted a pairwise comparison between isolates sharing a potential epidemiological link to elucidate whether clonal, plasmid, or Tn1546 spread accounted for vanA-type resistance dissemination.

Results

On average, we estimated that 59% of VRE cases with a potential epidemiological link were unrelated which was defined as VRE pairs with a distinct Tn1546 variant. Clonal dissemination accounted for 32% cases in which the same SC and Tn1546 variants were identified. Horizontal plasmid dissemination accounted for 7% of VRE cases, in which we observed VRE pairs belonging to a distinct SC but carrying an identical plasmid and Tn1546 variant", "token_count": 456, "char_count": 1676, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:28.703207", "source": { "split": "train_shard_00001", "doc_id": 2721 }, "chunk_id": "train_shard_00001_2721_0", "global_id": 9534 }, { "text": "In 2% of cases, we observed the same Tn1546 variant in distinct SC and plasmid types which could be explained by mixed and consecutive events of clonal and plasmid dissemination.

Conclusions

In related VRE cases, the dissemination of the vanA gene cluster in Dutch hospitals between 2012 and 2015 was dominated by clonal spread. However, we also identified outbreak settings with high frequencies of plasmid dissemination in which the spread of resistance was mainly driven by horizontal gene transfer (HGT). This study demonstrates the feasibility of distinguishing between modes of dissemination with short-read data and provides a novel assessment to estimate the relative contribution of nested genomic elements in the dissemination of vanA-type resistance.\n\nMode and dynamics of vanA-type vancomycin resistance dissemination in Dutch hospitals.", "token_count": 198, "char_count": 856, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:29.149489", "source": { "split": "train_shard_00001", "doc_id": 2721 }, "chunk_id": "train_shard_00001_2721_1", "global_id": 9535 }, { "text": "Enterococcus faecium has emerged as an important nosocomial pathogen, which is increasingly difficult to treat due to the genetic acquisition of vancomycin resistance. Ireland exhibits a recalcitrant vancomycin resistant bloodstream infection rate compared to other developed countries. A set of 28 vancomycin resistant isolates was sequenced to construct a dataset alongside 61 other publicly available Irish genomes. This dataset was extensively analysed using in-silico methodologies and uncovered distinct evolutionary, coevolutionary, and clinically relevant population trends. These results suggest that a stable (in terms of genome size, GC%, and number of genes), yet genetically diverse population (in terms of gene content) of Enterococcus faecium persist in Ireland with acquired resistance arising via plasmid acquisition ( vanA ) or to a lesser extent, chromosomal recombination ( vanB ). Population analysis described five clusters with one cluster partitioned into four clades which transcend isolation dates. Pangenomic and recombination analyses revealed an open (whole genome and chromosomal specific) pangenome illustrating a rampant evolutionary pattern. Comparative resistomics and virulomics uncovered distinct chromosomal and mobilomal propensity for multidrug resistance, widespread chromosomal point-mutation mediated resistance, and chromosomal harboured arsenals of virulence factors. Comparative phagomics revealed a core prophagome of three prophages throughout the dataset. Interestingly, a potential difference in biofilm formation strategies was highlighted by coevolutionary analysis, suggesting differential biofilm genotypes between vanA and vanB isolates. These results highlight the evolutionary history of Irish Enterococcus faecium isolates and may provide an insight into underlying infection dynamics in a clinical setting.\n\n“Comparative genomics and pangenomics of vancomycin resistant and susceptibleEnterococcus faeciumfrom Irish hospitals across 20 years”", "token_count": 452, "char_count": 2007, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:29.783505", "source": { "split": "train_shard_00001", "doc_id": 2722 }, "chunk_id": "train_shard_00001_2722_0", "global_id": 9536 }, { "text": "In this study, various yeasts (Kluyveromyces marxianus, Saccharomyces turicensis, Pichia fermentans) and lactic acid bacteria (Lactobacillus kefiranofaciens, Lactobacillus kefiri, Leuconostoc mesenteroides) were entrapped in 2 different microspheres using an entrapment ratio for the strains that was based on the distribution ratio of these organisms in kefir grains. The purpose of this study was to develop a new technique to produce kefir using immobilized starter cultures isolated from kefir grains. An increase in cell counts with fermentation cycles was observed for both the lactic acid bacteria (LAB) and yeasts, whereas the cell counts of kefir grains were very stable during cultivation. Scanning electron microscopy showed that the short-chain lactobacilli and lactococci occupied the surface of the LAB microspheres, whereas the long-chain lactobacilli were inside the microspheres. When the yeasts were analyzed, cells at a high density were entrapped in cracks on the surface and within the microspheres, where they were surrounded by the short-chain lactobacilli. The distribution of the LAB and yeast species in kefir produced from grains and microspheres showed that there was no significant difference between the kefirs produced by the 2 methods; moreover, Leu. mesenteroides and K. marxianus were the predominating microflora in both types of kefir. There was no significant difference in the ethanol and exopolysaccharide contents between the 2 kefirs, although the acidity was different.\n\nMicrobiological and chemical properties of kefir manufactured by entrapped microorganisms isolated from kefir grains.", "token_count": 423, "char_count": 1630, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5579, "quality_score": 0.779, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:30.409206", "source": { "split": "train_shard_00001", "doc_id": 2723 }, "chunk_id": "train_shard_00001_2723_0", "global_id": 9537 }, { "text": "Soybeans possess unexpected flavors and are difficult to be absorbed by the gastrointestinal tract. Kefir grain fermentation provides diverse strains and bioactive compounds, which may enhance flavor and bioaccessibility. Third-generation sequencing was applied to analyze the microbial diversity in milk and soybean kefir grains in this study. In both types of kefir grains, the most common bacterial genus was Lactobacillus, and their fungal communities were dominated by Kazachstania. Lactobacillus kefiranofaciens was the most abundant species in kefir grains, while Lactobacillus kefiri showed a higher proportion in soybean kefir grains. In addition, the quantification of free amino acids and volatile flavor compounds in soybean solution and soybean kefir have shown the increased content of glutamic acid and a decreased amount of unpleasant beany flavor compounds, demonstrating that the nutritive value and sensory properties of soybean can be improved by kefir grain fermentation. Finally, the bioconversion of isoflavones during fermentation and in vitro digestion was evaluated, suggesting that fermentation is beneficial for aglycone formation and absorption. To conclude, kefir fermentation is proposed to change the microbial structure of kefir grains, promote the nutritional value of soybean-based fermented products, and provide possible solutions for the development of soybean products.\n\nMicrobial Community Variations and Bioconversion Improvements during Soybean-Based Fermentation by Kefir Grains.", "token_count": 396, "char_count": 1550, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:31.025171", "source": { "split": "train_shard_00001", "doc_id": 2724 }, "chunk_id": "train_shard_00001_2724_0", "global_id": 9538 }, { "text": "

ABSTRACT

Microorganisms contribute to the biology and physiology of eukaryotic hosts and affect other organisms through natural products. Xenorhabdus and Photorhabdus ( XP ) living in mutualistic symbiosis with entomopathogenic nematodes produce a myriad of natural products to mediate bacteria–nematode–insect interactions. However, a lack of systematic analysis of the biosynthetic gene clusters (BGCs) has limited the understanding of how natural products justify the bacterial niche specificity. Here we combine pangenome and sequence similarity networks to analyze BGCs from 45 XP species. The identified 1,000 BGCs belong to 176 families, over half of which are unknown. Eleven BGCs represent the most conserved families. We then homologously express the ubiquitous and unique BGCs and identify compounds featuring unusual architectures. The bioactivity evaluation demonstrates that the prevalent compounds are eukaryotic proteasome inhibitors, insect virulence factors, or insect immune suppressors. These findings account for the functional basis of bacterial natural products in this tripartite relationship.\n\nGlobal analysis of biosynthetic gene clusters reveals conserved and unique natural products in entomopathogenic nematode-symbiotic bacteria", "token_count": 304, "char_count": 1267, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6886, "quality_score": 0.8443, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:31.590302", "source": { "split": "train_shard_00001", "doc_id": 2725 }, "chunk_id": "train_shard_00001_2725_0", "global_id": 9539 }, { "text": "

Background

The European Community has adopted very restrictive policies regarding the dissemination and use of genetically modified organisms (GMOs). In fact, a maximum threshold of 0.9% of contaminating GMOs is tolerated for a \"GMO-free\" label. In recent years, imports of undescribed GMOs have been detected. Their sequences are not described and therefore not detectable by conventional approaches, such as PCR.

Results

We developed DUGMO, a bioinformatics pipeline for the detection of genetically modified (GM) bacteria, including unknown GM bacteria, based on Illumina paired-end sequencing data. The method is currently focused on the detection of GM bacteria with - possibly partial - transgenes in pure bacterial samples. In the preliminary steps, coding sequences (CDSs) are aligned through two successive BLASTN against the host pangenome with relevant tuned parameters to discriminate CDSs belonging to the wild type genome (wgCDS) from potential GM coding sequences (pgmCDSs). Then, Bray-Curtis distances are calculated between the wgCDS and each pgmCDS, based on the difference of genomic vocabulary. Finally, two machine learning methods, namely the Random Forest and Generalized Linear Model, are carried out to target true GM CDS(s), based on six variables including Bray-Curtis distances and GC content. Tests carried out on a GM Bacillus subtilis showed 25 positive CDSs corresponding to the chloramphenicol resistance gene and CDSs of the inserted plasmids. On a wild type B. subtilis, no false positive sequences were detected.

Conclusion

DUGMO detects exogenous CDS, truncated, fused or highly mutated wild CDSs in high-throughput sequencing data, and was shown to be efficient at detecting GM sequences, but it might also be employed for the identification of recent horizontal gene transfers.\n\nDUGMO: tool for the detection of unknown genetically modified organisms with high-throughput sequencing data for pure bacterial samples.", "token_count": 485, "char_count": 1976, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6441, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:32.244400", "source": { "split": "train_shard_00001", "doc_id": 2726 }, "chunk_id": "train_shard_00001_2726_0", "global_id": 9540 }, { "text": "Two Gram-stain-positive, aerobic, non-spore-forming, non-motile, irregular rod-shaped actinobacteria, designated as D2-41T and D3-21, were isolated from soil samples collected in a natural cave in Jeju, Republic of Korea. Both of the isolates were shown to share 100 % 16S rRNA sequence identity. The cell wall contained meso-diaminopimelic acid, arabinose and galactose. The predominant menaquinone was MK-8(H2). The polar lipids contained phosphatidylethanolamine, phosphatidylglycerol, phosphatidylinositol, phosphatidylinositol mannoside, an unidentified aminolipid, an unidentified aminoglycolipid, an unidentified phospholipid and two unidentified lipids. The predominant fatty acids were C16 : 0 and summed feature 3 (C16 : 1  ω7c and/or iso-C15 : 0 2-OH). Mycolic acids of C30-C38 were present. The 16S rRNA gene trees showed that the organisms occupied a distinct position remotely located from recognized genera within the order Mycobacteriales, albeit with the 16S rRNA gene similarities of 97.0-97.1 % with Rhodococcus olei, Rhodococcus rhodnii and Rhodococcus triatomae. The genome sizes and DNA G+C contents of strains D2-41T and D3-21 were 4.77-4.88 Mbp and 69.8 mol%, respectively", "token_count": 517, "char_count": 1333, "word_count": 165, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:28:32.893555", "source": { "split": "train_shard_00001", "doc_id": 2727 }, "chunk_id": "train_shard_00001_2727_0", "global_id": 9541 }, { "text": "Both of the isolates shared an average nucleotide identity of 99.4 % and digital DNA-DNA hybridization of 95.2 % to each other, revealing that strains D2-41T and D3-21 belonged to the same species. In the core genome-based phylogenomic tree, both of the isolates were found to be closely associated with members of the genus Tomitella. However, strains D2-41T and D3-21 revealed the highest amino acid identity values (mean 66.5 %, range 66.2-67.0 % with the genus Prescottella of the family Nocardiaceae, followed by the genus Tomitella (mean 64.1 %, range 63.6-64.7 %) of the family Tomitellaceae. Based on the combined data obtained here, the novel isolates belong to a new genus of the new family for which the name Speluncibacter jeojiensis gen. nov. sp. nov. is proposed, with Speluncibacteraceae fam. nov. The type strain is strain D2-41T (=KACC 17930T=DSM 101875T).\n\nSpeluncibacter jeojiensis gen. nov. sp. nov., a novel bacterium of the order Mycobacteriales isolated from a cave and a proposal of Speluncibacteraceae fam. nov.", "token_count": 417, "char_count": 1161, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5976, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:33.515089", "source": { "split": "train_shard_00001", "doc_id": 2727 }, "chunk_id": "train_shard_00001_2727_1", "global_id": 9542 }, { "text": "The family Peptostreptococcaceae, which contains 15 genera including Clostridioides, presently lacks proper circumscription. Using 52 available genomes for Peptostreptococcaceae species, we report comprehensive phylogenomic and comparative analyses to reliably discern their evolutionary relationships. In phylogenetic trees based on core genome proteins and 16S rRNA gene sequences, the examined species formed a strongly supported clade designated as Peptostreptococcaceae sensu stricto. This clade encompassed the genera Peptostreptococcus (type genus), Asaccharospora, Clostridioides, Intestinibacter, Paeniclostridium, Paraclostridium, Peptacetobacter, Romboutsia and Terrisporobacter, and two misclassified species (viz. Eubacterium tenue and 'Clostridium dakarense'). The distinctness of this clade is strongly supported by eight identified conserved signature indels (CSIs), which are specific for the species from this clade. Based on the robust evidence provided by presented studies, we are proposing the emendment of family Peptostreptococcaceae to only the genera within the Peptostreptococcaceae sensu stricto clade. We also report 67 other novel CSIs, which reliably demarcate different Peptostreptococcaceae species clades and clarify the classification of some misclassified species", "token_count": 449, "char_count": 1432, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6981, "quality_score": 0.8491, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:34.158267", "source": { "split": "train_shard_00001", "doc_id": 2728 }, "chunk_id": "train_shard_00001_2728_0", "global_id": 9543 }, { "text": "Based on the consistent evidence obtained from different presented studies, we are making the following proposals to clarify the classification of Peptostreptococcaceae species: (i) transfer of Eubacterium tenue, Paeniclostridium ghonii and Paeniclostridium sordellii as comb. nov. into the genus Paraclostridium; (ii) transfer of Clostridioides mangenotii as a comb. nov. into Metaclostridioides gen. nov.; (iii) classification of 'Clostridium dakarense' as a novel species Faecalimicrobium dakarense gen. nov., sp. nov. (type strain FF1T; genome and 16S rRNA accession numbers GCA_000499525.1 and KC517358, respectively); (iv) transfer of two misclassified species, Clostridium paradoxum and Clostridium thermoalcaliphilum, into Alkalithermobacter gen. nov.; and (v) proposals for two novel families, Peptoclostridiaceae fam. nov. and Tepidibacteraceae fam. nov., to accommodate remaining unclassified Peptostreptococcaceae genera. The described CSIs specific for different families and genera provide novel and reliable means for the identification, diagnostics and biochemical studies on these bacteria.\n\nRobust demarcation of the family Peptostreptococcaceae and its main genera based on phylogenomic studies and taxon-specific molecular markers.", "token_count": 459, "char_count": 1374, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6519, "quality_score": 0.8259, "entities": { "genes": [ "FF1", "KC517358" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:34.799940", "source": { "split": "train_shard_00001", "doc_id": 2728 }, "chunk_id": "train_shard_00001_2728_1", "global_id": 9544 }, { "text": "Microbial lipids, used as taxonomic markers and physiological indicators, have mainly been studied through cultivation. However, this approach is limited due to the scarcity of cultures of environmental microbes, thereby restricting insights into the diversity of lipids and their ecological roles. Addressing this limitation, here we apply metalipidomics combined with metagenomics in the Black Sea, classifying and tentatively identifying 1623 lipid-like species across 18 lipid classes. We discovered over 200 novel, abundant, and structurally diverse sphingolipids in euxinic waters, including unique 1-deoxysphingolipids with long-chain fatty acids and sulfur-containing groups. Sphingolipids were thought to be rare in bacteria and their molecular and ecological functions in bacterial membranes remain elusive. However, genomic analysis focused on sphingolipid biosynthesis genes revealed that members of 38 bacterial phyla in the Black Sea can synthesize sphingolipids, representing a 4-fold increase from previously known capabilities and accounting for up to 25% of the microbial community. These sphingolipids appear to be involved in oxidative stress response, cell wall remodeling, and are associated with the metabolism of nitrogen-containing molecules. Our findings underscore the effectiveness of multi-omics approaches in exploring microbial chemical ecology.\n\nProduction of structurally diverse sphingolipids by anaerobic marine bacteria in the euxinic Black Sea water column.", "token_count": 362, "char_count": 1494, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7337, "quality_score": 0.8668, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:35.387611", "source": { "split": "train_shard_00001", "doc_id": 2729 }, "chunk_id": "train_shard_00001_2729_0", "global_id": 9545 }, { "text": "Enterococci are commensal bacteria of the gastrointestinal tract of humans, animals, and insects. They are also found in soil, water, and plant ecosystems. The presence of enterococci in human, animal, and environmental settings makes these bacteria ideal candidates to study antimicrobial resistance in the One-Health continuum. This study focused on Enterococcus hirae isolates (n = 4,601) predominantly isolated from beef production systems including bovine feces (n = 4,117, 89.5%), catch-basin water (n = 306, 66.5%), stockpiled bovine manure (n = 24, 0.5%), and natural water sources near feedlots (n = 145, 32%), and a few isolates from urban wastewater (n = 9, 0.2%) denoted as human-associated environmental samples. Antimicrobial susceptibility profiling of a subset (n = 1,319) of E. hirae isolates originating from beef production systems (n = 1,308) showed high resistance to tetracycline (65%) and erythromycin (57%) with 50.4% isolates harboring multi-drug resistance, whereas urban wastewater isolates (n = 9) were resistant to nitrofurantoin (44.5%) and tigecycline (44.5%) followed by linezolid (33.3%). Genes for tetracycline (tetL, M, S/M, and O/32/O) and macrolide resistance erm(B) were frequently found in beef production isolates. Antimicrobial resistance profiles of E", "token_count": 516, "char_count": 1394, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6417, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:28:36.040271", "source": { "split": "train_shard_00001", "doc_id": 2730 }, "chunk_id": "train_shard_00001_2730_0", "global_id": 9546 }, { "text": "hirae isolates recovered from different environmental settings appeared to reflect the kind of antimicrobial usage in beef and human sectors. Comparative genomic analysis of E. hirae isolates showed an open pan-genome that consisted of 1,427 core genes, 358 soft core genes, 1701 shell genes, and 7,969 cloud genes. Across species comparative genomic analysis conducted on E. hirae, Enterococcus faecalis and Enterococcus faecium genomes revealed that E. hirae had unique genes associated with vitamin production, cellulose, and pectin degradation, traits which may support its adaptation to the bovine digestive tract. E. faecium and E. faecalis more frequently harbored virulence genes associated with biofilm formation, iron transport, and cell adhesion, suggesting niche specificity within these species.\n\nGenomic Characterization of Enterococcus hirae From Beef Cattle Feedlots and Associated Environmental Continuum.", "token_count": 286, "char_count": 982, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:36.597934", "source": { "split": "train_shard_00001", "doc_id": 2730 }, "chunk_id": "train_shard_00001_2730_1", "global_id": 9547 }, { "text": "Aluminum (Al) toxicity poses a significant challenge for the yield improvement of chickpea, which is an economically important legume crop with high nutritional value in human diets. The genetic basis of Al-tolerance in chickpea remains unclear. Here, we assessed the Al-tolerance of 8 wild Cicer and one cultivated chickpea (PBA Pistol) accessions by measuring the root elongation in solution culture under control (0 μM Al3+) and Al treatments (15, 30 μM Al3+). Compared to PBA Pistol, the wild Cicer accessions displayed both tolerant and sensitive phenotypes, supporting wild Cicer as a potential genetic pool for Al-tolerance improvement. To identify potential genes related to Al-tolerance in chickpea, genome-wide screening of multidrug and toxic compound extrusion (MATE) encoding genes was performed. Fifty-six MATE genes were identified in total, which can be divided into 4 major phylogenetic groups. Four chickpea MATE genes (CaMATE1-4) were clustered with the previously characterized citrate transporters MtMATE66 and MtMATE69 in Medicago truncatula. Transcriptome data showed that CaMATE1-4 have diverse expression profiles, with CaMATE2 being root-specific. qRT-PCR analyses confirmed that CaMATE2 and CaMATE4 were highly expressed in root tips and were up-regulated upon Al treatment in all chickpea lines. Further measurement of carboxylic acids showed that malonic acid, instead of malate or citrate, is the major extruded acid by Cicer spp. root", "token_count": 488, "char_count": 1585, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8498, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:37.283426", "source": { "split": "train_shard_00001", "doc_id": 2731 }, "chunk_id": "train_shard_00001_2731_0", "global_id": 9548 }, { "text": "Protein structural modeling analyses revealed that CaMATE2 has a divergent substrate-binding cavity from Arabidopsis AtFRD3, which may explain the different acid-secretion profile for chickpea. Pangenome survey showed that CaMATE1-4 have much higher genetic diversity in wild Cicer than that in cultivated chickpea. This first identification of CaMATE2 and CaMATE4 responsive to Al3+ treatment in Cicer paves the way for future functional characterization of MATE genes in Cicer spp., and to facilitate future design of gene-specific markers for Al-tolerant line selection in chickpea breeding programs.\n\nIdentification of two chickpea multidrug and toxic compound extrusion transporter genes transcriptionally upregulated upon aluminum treatment in root tips.", "token_count": 231, "char_count": 820, "word_count": 103, "semantic_coherence": 1, "information_density": 0.767, "quality_score": 0.8835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:37.764001", "source": { "split": "train_shard_00001", "doc_id": 2731 }, "chunk_id": "train_shard_00001_2731_1", "global_id": 9549 }, { "text": "The mouse reference is one of the most widely used and accurately assembled mammalian genomes, and is the foundation for a wide range of bioinformatics and genetics tools. However, it represents the genomic organization of a single inbred mouse strain. Recently, inexpensive and fast genome sequencing has enabled the assembly of other common mouse strains at a quality approaching that of the reference. However, using these alternative assemblies in standard genomics analysis pipelines presents significant challenges. It has been suggested that a pangenome reference assembly, which incorporates multiple genomes into a single representation, are the path forward, but there are few standards for, or instances of practical pangenome representations suitable for large eukaryotic genomes. We present a pragmatic graph-based pangenome representation as a genomic resource for the widely-used recombinant-inbred mouse genetic reference population known as the Collaborative Cross (CC) and its eight founder genomes. Our pangenome representation leverages existing standards for genomic sequence representations with backward-compatible extensions to describe graph topology and genome-specific annotations along paths. It packs 83 mouse genomes (8 founders + 75 CC strains) into a single graph representation that captures important notions relating genomes such as identity-by-descent and highly variable genomic regions. The introduction of special anchor nodes with sequence content provides a valid coordinate framework that divides large eukaryotic genomes into homologous segments and addresses most of the graph-based position reference issues. Parallel edges between anchors place variants within a context that facilitates orthogonal genome comparison and visualization. Furthermore, our graph structure allows annotations to be placed in multiple genomic contexts and simplifies their maintenance as the assembly improves. The CC reference pangenome provides an open framework for new tool chain development and analysis.\n\nThe Collaborative Cross Graphical Genome", "token_count": 416, "char_count": 2075, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:38.430287", "source": { "split": "train_shard_00001", "doc_id": 2732 }, "chunk_id": "train_shard_00001_2732_0", "global_id": 9550 }, { "text": "A Gram-staining-negative, aerobic bacterium, designated strain PT3T was isolated from laboratory-reared larvae of the Japanese sea cucumber Apostichopus japonicus. Phylogenetic analysis based on the 16S rRNA gene nucleotide sequences revealed that PT3T was closely related to Amphritea ceti RA1T (= KCTC 42154T = NBRC 110551T) and Amphritea spongicola MEBiC05461T (= KCCM 42943T = JCM 16668T) both with 98.3% sequence similarity, however, average nucleotide identity (ANI) and in silico DNA-DNA hybridization (in silico DDH) values among these three strains were below 95% and 70%, respectively, confirming the novelty of PT3T. Furthermore, the average amino acid identity (AAI) values of PT3T against other Amphritea species were on the reported genus delineation boundary (64-67%). Multilocus sequence analysis using four protein-coding genes (recA, mreB, rpoA, and topA) further demonstrated that PT3T, Amphritea ceti and Amphritea spongicola formed a monophyletic clade clearly separate from other members of the genus Amphritea. Three strains (PT3T, A. ceti　KCTC 42154T and A. spongicola JCM 16668T) also showed higher similarities in their core genomes compared to those of the other Amphritea spp. Based on the genome-based taxonomic approach, Aliamphritea gen. nov. was proposed together with the reclassification of the genus Amphritea and Aliamphritea ceti comb. nov. (type strain RA1T = KCTC 42154T = NBRC 110551T), Aliamphritea spongicola comb. nov", "token_count": 489, "char_count": 1460, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [ "RA1T", "PT3T" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:39.124742", "source": { "split": "train_shard_00001", "doc_id": 2733 }, "chunk_id": "train_shard_00001_2733_0", "global_id": 9551 }, { "text": "(type strain MEBiC05461T = KCCM 42943T = JCM 16668T), and Aliamphritea hakodatensis sp. nov. (type strain PT3T = JCM 34607T = KCTC 82591T) were suggested.\n\nTaxonomic revision of the genus Amphritea supported by genomic and in silico chemotaxonomic analyses, and the proposal of Aliamphritea gen. nov.", "token_count": 122, "char_count": 300, "word_count": 46, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [ "PT3T" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:39.509408", "source": { "split": "train_shard_00001", "doc_id": 2733 }, "chunk_id": "train_shard_00001_2733_1", "global_id": 9552 }, { "text": "Candida auris is a World Health Organization critical-priority fungal pathogen that has variable resistance to antifungal treatments. Multiple clades have been identified through genomic analysis and have appeared in different geographic locations simultaneously. Due to a combination of factors including antifungal resistance, ability to colonize and persist in the environment, and thermotolerance, it can thrive. Infected patients are associated with a high mortality rate, especially those with multiple health risk factors like those associated with other Candida species. This review highlights the current situation of this pathogen to help provide guidance for future work.\n\n<i>Candida auris</i>: A Continuing Threat.", "token_count": 172, "char_count": 752, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:39.959377", "source": { "split": "train_shard_00001", "doc_id": 2734 }, "chunk_id": "train_shard_00001_2734_0", "global_id": 9553 }, { "text": "

Objectives

Antimicrobial resistance (AMR) including multidrug-resistant (MDR) and extensively drug-resistant (XDR) Pseudomonas aeruginosa has emerged as one of the serious public health threats across the globe. Southeast Asia is a 'hot spot' of antimicrobial-resistant bacteria, including MDR P. aeruginosa. Despite Myanmar being located in Southeast Asia and suffering from a high infectious disease burden, data on MDR and XDR P. aeruginosa from Myanmar are limited. In this communication, we report the draft genome of an XDR P. aeruginosa isolate, MMXDRPA001, that was identified during a routine diagnosis in Myanmar.

Methods

An MMXDRPA001 isolate colonising a hospitalised patient was characterised by antibiotic resistance profiling following standard methods and whole-genome sequencing using an Illumina MiSeq platform. The generated reads were de novo assembled using SPAdes (v.3.9.1). Annotation was performed by Prokka (v.1.14.0). Sequence type, antimicrobial resistance and virulence-related genes were predicted from the sequence. The phylogenetic relationships of all P. aeruginosa isolates were determined using core genome single-nucleotide polymorphisms (SNPs) analysis utilising Snippy (v.4.6.0) and Gubbins (v.2.3.4).

Results

P. aeruginosa MMXDRPA001 was resistant to most antipseudomonal β-lactams, aminoglycosides and quinolones. The assembly comprised 145 contigs totalling 6 808 493 bases of sequence and a total of 6183 coding sequences", "token_count": 442, "char_count": 1484, "word_count": 192, "semantic_coherence": 1, "information_density": 0.724, "quality_score": 0.862, "entities": { "genes": [ "MMXDRPA001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:40.599060", "source": { "split": "train_shard_00001", "doc_id": 2735 }, "chunk_id": "train_shard_00001_2735_0", "global_id": 9554 }, { "text": "The isolate belonged to sequence type (ST) 235, contained carbapenemase-encoding gene blaIMP-1 and was clonally related to a previously reported isolate from Thailand.

Conclusion

The identification of an international high-risk clone of ST235 XDR isolate in Myanmar, genomically relating to that from a neighbouring country underscores the need for coordinated AMR surveillance throughout healthcare settings in Myanmar and in the Southeast Asia region.\n\nAn extensively drug-resistant Pseudomonas aeruginosa isolate from Myanmar.", "token_count": 143, "char_count": 547, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7826, "quality_score": 0.8913, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:41.021049", "source": { "split": "train_shard_00001", "doc_id": 2735 }, "chunk_id": "train_shard_00001_2735_1", "global_id": 9555 }, { "text": "Many bacterial species are represented by a pan-genome, whose genetic repertoire far outstrips that of any single bacterial genome. Here we investigate how a bacterial pan-genome might influence gene essentiality, and whether essential genes that are initially critical for the survival of an organism can evolve to become non-essential. By using Tn-Seq, whole-genome sequencing, and RNA-Seq on a set of 36 clinical Streptococcus pneumoniae strains representative of >68% of the species’ pan-genome, we identify a species-wide ‘essentialome’ that can be subdivided into universal, strain-specific and accessory essential genes. By employing ‘forced-evolution experiments’ we show that specific genetic changes allow bacteria to bypass essentiality. Moreover, by untangling several genetic mechanisms we show that gene-essentiality can be highly influenced and/or dependent on: 1) the composition of the accessory genome; 2) the accumulation of toxic intermediates; 3) functional redundancy; 4) efficient recycling of critical metabolites; and 5) pathway rewiring. While this functional characterization underscores the evolvability-potential of many essential genes, we also show that genes with differential essentiality remain important antimicrobial drug target candidates, as their inactivation almost always has a severe fitness cost in vivo .\n\nA bacterial pan-genome makes gene essentiality strain-dependent and evolvable", "token_count": 336, "char_count": 1427, "word_count": 193, "semantic_coherence": 1, "information_density": 0.7047, "quality_score": 0.8523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:41.595519", "source": { "split": "train_shard_00001", "doc_id": 2736 }, "chunk_id": "train_shard_00001_2736_0", "global_id": 9556 }, { "text": "Bacteria sense and respond to environmental stimuli through two-component systems (TCSs), that are composed of histidine kinase sensing and response regulator elements. TCSs are ubiquitous and participate in numerous cellular functions. TCSs across the ESKAPEE pathogens, representing the leading causes of nosocomial infections, were characterized using pangenome analytics, including annotation, mapping, pangenomic status, gene orientation, sequence variation, and structure. Our findings fall into two categories. 1) phylogenetic distribution of TCSs: (i) the number and types of TCSs varies between species of the ESKAPEE pathogens; (ii) TCSs are group-specific, i.e., Gram-positive and Gram-negative, except for KdpDE; (iii) most TCSs are conserved among genomes of an ESKAPEE, except in Pseudomonas aeruginosa . 2) sequence variation: (i) at the operon level, the genomic architecture of a TCS operon stratifies into a few discrete classes; and (ii) at the gene sequence level, histidine kinases, responsible for signal sensing, show sequence and structural variability as compared to response regulators that show a high degree of conservation. Taken together, this first comprehensive pangenomic assessment of TCSs reveals a range of strategies deployed by the ESKAPEE pathogens to manifest pathogenicity and antibiotic resistance. It further suggests that the conserved features of TCSs makes them an attractive group of potential targets with which to address antibiotic resistance.\n\nPangenome analytics reveal two-component systems as conserved targets in ESKAPEE pathogens", "token_count": 384, "char_count": 1585, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:42.211259", "source": { "split": "train_shard_00001", "doc_id": 2737 }, "chunk_id": "train_shard_00001_2737_0", "global_id": 9557 }, { "text": "

What is already known about this topic?

Enterococcus spp., while naturally occurring as commensal bacteria in the gastrointestinal tract of animals and humans, have emerged as significant opportunistic pathogens in healthcare settings.

What is added by this report?

A comprehensive surveillance study revealed enterococci in 14.39% of clinical samples from dogs and cats across China during 2018-2021. Multidrug-resistant enterococcal infections showed significant correlation with urinary tract catheterization and extended hospitalization periods. Notably, pet-derived Enterococcus faecalis isolates demonstrated high genetic similarity with strains isolated from humans, farm animals, and environmental sources.

What are the implications for public health practice?

These findings underscore the critical need for enhanced surveillance of enterococcal infections and implementation of stringent aseptic protocols in veterinary clinical settings. Particular attention should be directed toward linezolid-resistant Enterococcus faecalis infections due to their demonstrated potential for transmission between pets and humans.\n\nPrevalence and Risk Factors of Multidrug-Resistant Enterococcal Infection in Clinical Dogs and Cats - China, 2018-2021.", "token_count": 325, "char_count": 1297, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:42.785389", "source": { "split": "train_shard_00001", "doc_id": 2738 }, "chunk_id": "train_shard_00001_2738_0", "global_id": 9558 }, { "text": "The integrated stress response (ISR) is a central signaling network that enables eukaryotic cells to respond to a variety of different environmental stresses. Such stresses cause ribosome collisions that lead to activation of the kinase Gcn2, resulting in the phosphorylation and inactivation of eukaryotic initiation factor 2 and thereby promoting selective translation of mRNAs to restore homeostasis. Despite the importance of the ISR and intensive study over the past decades, structural insight into how Gcn2 interacts with ribosomal particles has been lacking. Using ex vivo affinity purification approaches, we have obtained a cryoelectron microscopy structure of a yeast Gcn2 dimer in complex with the ribosomal 60S subunit. The Gcn2 dimer is formed by dimerization of the histidine tRNA synthetase-like domains, which establish extensive interactions with the stalk-base and sarcin-ricin loop of the 60S subunit. The C-terminal domain of Gcn2 is also dimerized and occupies the A- and P-site tRNA binding sites at the peptidyl-transferase center of the 60S subunit. Complementary functional studies indicate that binding of Gcn2 to the 60S subunit does not require the coactivators Gcn1 or Gcn20, nor does it lead to phosphorylation of eIF2α. Instead, upon stress, we observe a shift of Gcn2 from the 60S subunit into the colliding ribosome fraction, suggesting that the Gcn2-60S complex represents an inactive stand-by state to enable a rapid redistribution to collided ribosomes, and thereby facilitating a quick and efficient response to stress.\n\nStructure of a Gcn2 dimer in complex with the large 60S ribosomal subunit.", "token_count": 425, "char_count": 1633, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6016, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:43.412414", "source": { "split": "train_shard_00001", "doc_id": 2739 }, "chunk_id": "train_shard_00001_2739_0", "global_id": 9559 }, { "text": "A total of 87 yeast strains were isolated from 28 home-made koumiss samples, a traditional fermented mare milk product in Xinjiang of China. The isolates were identified by standard physiological and biochemical tests and analysis of the large-subunit (26S) rDNA gene D1/D2 domain sequences. They are proved to be Saccharomyces unisporus (48.3% of the isolates), Kluyveromyces marxianus (27.6%) and Pichia membranaefaciens (15.0%), Saccharomyces cerevisiae (9.2%). Among them, six isolates and a standard yeast strain were selected for analysis of D1/D2 domain sequences. They are indicated as S. unisporus, K. marxianus, S. cerevisiae, P. membranifaciens, P. fermentans, P. galeiformis and the standard yeast strain is indicated as K. lactis (100%). The results obtained demonstrate the value of using analysis of D1/D2 domain sequences methods, in conjunction with the traditional taxonomic methods based on phenotypic characteristics. This study forms an essential step towards the preservation and exploitation of the hidden oenological potential of the wealth of yeast biodiversity of the koumiss in Xinjiang Province. The result obtained shown that S. unisporus and K. marxianus were the predominant strains of koumiss in Xingjiang of China.\n\n[Identification and biodiversity of yeasts isolated from Koumiss in Xinjiang of China].", "token_count": 381, "char_count": 1336, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5825, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:43.985414", "source": { "split": "train_shard_00001", "doc_id": 2740 }, "chunk_id": "train_shard_00001_2740_0", "global_id": 9560 }, { "text": "

Objectives

To assess the value of screening for Clostridioides difficile colonization (CDC) at hospital admission in an endemic setting.

Methods

A multi-centre study was conducted at four hospitals located across the Netherlands. Newly admitted patients were screened for CDC. The risk of development of Clostridioides difficile infection (CDI) during admission and 1-year follow-up was assessed in patients with and without colonization. C. difficile isolates from patients with colonization were compared with isolates from incident CDI cases using core genome multi-locus sequence typing to determine whether onwards transmission had occurred.

Results

CDC was present in 108 of 2211 admissions (4.9%), whereas colonization with a toxigenic strain (toxigenic Clostridoides difficile colonization [tCDC]) was present in 68 of 2211 admissions (3.1%). Among these 108 patients with colonization, diverse PCR ribotypes were found and no 'hypervirulent' PCR ribotype 027 (RT027) was detected (95% CI, 0-0.028). None of the patients with colonization developed CDI during admission (0/49; 95% CI, 0-0.073) or 1-year follow-up (0/38; 95% CI, 0-0.93). Core genome multi-locus sequence typing identified six clusters with genetically related isolates from patients with tCDC and CDI; however, in these clusters, only one possible transmission event from a patient with tCDC to a patient with CDI was identified based on epidemiological data.

Conclusion

In this endemic setting with a low prevalence of 'hypervirulent' strains, screening for CDC at admission did not detect any patients with CDC who progressed to symptomatic CDI and detected only one possible transmission event from a patient with colonization to a patient with CDI. Thus, screening for CDC at admission is not useful in this setting.", "token_count": 507, "char_count": 1824, "word_count": 256, "semantic_coherence": 1, "information_density": 0.543, "quality_score": 0.7715, "entities": { "genes": [ "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:44.646213", "source": { "split": "train_shard_00001", "doc_id": 2741 }, "chunk_id": "train_shard_00001_2741_0", "global_id": 9561 }, { "text": "Screening for Clostridioides difficile colonization at admission to the hospital: a multi-centre study.", "token_count": 26, "char_count": 103, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:45.006849", "source": { "split": "train_shard_00001", "doc_id": 2741 }, "chunk_id": "train_shard_00001_2741_1", "global_id": 9562 }, { "text": "The rapid buildup of microbial genomic sequences with a large number of uncharacterized genes has resulted from advances in biological technologies. These genes encode the uncharacterized/ hypothetical and conserved proteins. Orientia tsutsugamushi , a gram negative bacterium causes scrub typhus disease in humans, contains approximately 20% of these proteins which have yet to be annotated. So in the present study, out of 292 hypothetical proteins were chosen to characterize and annotate by using different in silico techniques such as ExPASy ProtParam, VirulentPred, PSROTb, Pfam, InterproScan, PSIPred, SWISS_MODEL, CASTp and STRING. The comparative proteomics analysis revealed that, the protein which are stable, cytoplasmic and virulent, it is non homologous to human genome but essential for the function of the organism. The annotation of these proteins may disclose new information about the pathogen. The actual function of the protein will completely understand by experimental analysis. Prediction of the structure and function of this hypothetical protein should help researchers to uncover and better understand the function of Orientia tsutsugamushi , leading to the discovery of new drug targets.\n\nIdentification and functional annotation of hypothetical protein from the core genome of Orientia tsutsugamushi towards designing a novel drug target", "token_count": 322, "char_count": 1366, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:45.572549", "source": { "split": "train_shard_00001", "doc_id": 2742 }, "chunk_id": "train_shard_00001_2742_0", "global_id": 9563 }, { "text": "Staphylococcus aureus causes persistent clinical and subclinical bovine intramammary infections (IMI) worldwide. However, there is a lack of comprehensive information regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus in bovine milk in Canada. Here, we performed whole-genome sequencing (WGS) of 119 Canadian bovine milk S. aureus isolates and determined they belonged to 8 sequence types (ST151, ST352, ST351, ST2187, ST2270, ST126, ST133, and ST8), 5 clonal complexes (CC151, CC97, CC126, CC133, and CC8), and 18 distinct Spa types. Pan-, core, and accessory genomes were composed of 6,340, 1,279, and 2,431 genes, respectively. Based on phenotypic screening for AMR, resistance was common against beta-lactams (19% of isolates) and sulfonamides (7% of isolates), whereas resistance against pirlimycin, tetracycline, ceftiofur, and erythromycin and to the combination of penicillin and novobiocin was uncommon (3, 3, 3, 2, and 2% of all isolates, respectively). We also determined distributions of 191 virulence factors (VFs) in 119 S. aureus isolates after classifying them into 5 functional categories (adherence [n = 28], exoenzymes [n = 21], immune evasion [n = 20], iron metabolism [n = 29], and toxins [n = 93])", "token_count": 514, "char_count": 1342, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7211, "quality_score": 0.8605, "entities": { "genes": [ "CC126", "ST2270", "CC133", "CC8", "ST351", "CC97", "ST126", "CC151", "ST352", "ST151" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:28:46.231247", "source": { "split": "train_shard_00001", "doc_id": 2743 }, "chunk_id": "train_shard_00001_2743_0", "global_id": 9564 }, { "text": "Additionally, we calculated the pathogenic potential of distinct CCs and STs and determined that CC151 (ST151 and ST351) had the highest pathogenic potential (calculated by subtracting core-VFs from total VFs), followed by CC97 (ST352 and ST2187) and CC126 (ST126 and ST2270), potentially linked to their higher prevalence in bovine IMI worldwide. However, there was no statistically significant link between the presence of VF genes and mastitis.IMPORTANCE Staphylococcus aureus is a major cause of bovine intramammary infections, leading to significant economic losses to dairy industry in Canada and worldwide. There is a lack of knowledge regarding genetic diversity, the presence of antimicrobial resistance (AMR), and virulence genes for S. aureus isolated from bovine milk in Canada. Based on whole-genome sequencing and genomic analysis, we have determined the phylogeny and diversity of S. aureus in bovine milk and concluded that it had a large accessory genome, limited distribution of AMR genes, variable VF gene profiles and sequence types (ST), and clonal complex (CC)-specific pathogenic potentials. Comprehensive information on the population structure, as well as the virulence and resistance characteristics of S. aureus from bovine milk, will allow for source attribution, risk assessment, and improved therapeutic approaches in cattle.\n\nGenomic Analysis of Bovine Staphylococcus aureus Isolates from Milk To Elucidate Diversity and Determine the Distributions of Antimicrobial and Virulence Genes and Their Association with Mastitis.", "token_count": 427, "char_count": 1588, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [ "CC126", "ST2270", "ST351", "CC97", "ST126", "CC151", "ST352", "ST151", "ST2187" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:46.862088", "source": { "split": "train_shard_00001", "doc_id": 2743 }, "chunk_id": "train_shard_00001_2743_1", "global_id": 9565 }, { "text": "The Pangenome: Diversity, Dynamics and Evolution of Genomes", "token_count": 17, "char_count": 59, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:47.221679", "source": { "split": "train_shard_00001", "doc_id": 2744 }, "chunk_id": "train_shard_00001_2744_0", "global_id": 9566 }, { "text": "Mannoprotein with emulsification properties was extracted from the cell walls of Kluyveromyces marxianus grown on a lactose-based medium by autoclaving cells in a citrate buffer at pH 7. The purified product was evaluated for chemical and physical stability to establish its potential use as a natural emulsifier in processed foods. The yield of purified bioemulsifier from this strain of K. marxianus was 4-7% of the original dry cell weight. The purified product, at a concentration of 12 g l(-1), formed emulsions that were stable for 3 months when subjected to a range of pH (3-11) and NaCl concentrations (2-50 g l(-1)). The composition of this mannoprotein was 90% carbohydrate (mannan) and 4-6% protein. These values are similar to mannoprotein extracted from cells of Saccharomyces cerevisiae, which is the traditional source. Consequently K. marxianus cultivated on a low-cost lactose-based medium such as whey, a lactose-rich clean waste of the dairy industry, could be developed as a source of bioemulsifier for use in the food industry.\n\nEvaluation of Kluyveromyces marxianus FII 510700 grown on a lactose-based medium as a source of a natural bioemulsifier.", "token_count": 328, "char_count": 1170, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6044, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:47.791424", "source": { "split": "train_shard_00001", "doc_id": 2745 }, "chunk_id": "train_shard_00001_2745_0", "global_id": 9567 }, { "text": "Increased tolerance to cadmium in Listeria monocytogenes has been suggested to contribute to their persistence in natural and food production environments. This study investigated the phenotypic cadmium response of L. monocytogenes strains with efflux pump cadAC (variants 1-4) and related strains with cadA1C1. Growth of cadAC variant strains (n = 5) in 0 µM-120 µM cadmium salts (CdCl2, CdSO4) in Mueller-Hinton broth (MHB) was evaluated. Additionally, 88 L. monocytogenes strains from dairy processing facilities were exposed to 43.8 µM CdCl2 in MHB, and their lag phase duration (LPD) was measured. Strains with cadA1 through cadA3 showed similar growth trends in the presence of cadmium, while the cadA4 variant (Scott A) had the highest CdCl2 minimum inhibitory concentration (175 µM). Growth varied between the two salts, with CdSO4 significantly increasing LPD (P < 0.05) compared to CdCl2. In 43.8 µM CdCl2, cadA1 strains displayed LPDs ranging from 0.99 ± 0.14 h to 6.44 ± 0.08 h, with no clear genomic differences explaining this variability", "token_count": 458, "char_count": 1220, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7239, "quality_score": 0.862, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:48.430578", "source": { "split": "train_shard_00001", "doc_id": 2746 }, "chunk_id": "train_shard_00001_2746_0", "global_id": 9568 }, { "text": "Strains without cadA did not grow at 43.8 µM CdCl2 but exhibited low tolerance (10.9 µM CdCl2), potentially due to non-specific soft metal ATPases (626 aa; 737 aa) and soft metal resistance proteins encoded by czc genes (289 aa; 291 aa; 303 aa) within their chromosomes. These findings enhance our understanding of L. monocytogenes cadmium tolerance and underscore the need for further research to explore the genetic and physiological factors underlying these trends.

Importance

Mobile genetic elements in Listeria monocytogenes contribute to its survival in natural and food processing environments. This study focused on how different genetic variants of the efflux pump gene cadAC and group of closely related cadA1C1 strains respond to cadmium exposure. When exposed to two cadmium salts, cadmium chloride and cadmium sulfate, we observed varying growth patterns, with a significantly longer lag phase in cadmium sulfate compared to cadmium chloride. Strains with cadA1 to cadA3 had similar growth trends, whereas a strain with the cadA4 variant had the highest minimum inhibitory concentration value. Among 88 strains from dairy processing facilities, significant phenotypic differences were observed despite core genome similarities, indicating other underlying genetic and physiological factors contribute to cadmium tolerance. Since cadmium tolerance studies in L. monocytogenes are limited, with rare phenotypic comparisons between closely related strains, our study makes an important observation and contribution to understanding of L. monocytogenes tolerance to cadmium by providing phenotypic comparisons between numerous strains within the same clonal group (<16 single nucleotide polymorphisms).", "token_count": 506, "char_count": 1817, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6598, "quality_score": 0.8299, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:49.095228", "source": { "split": "train_shard_00001", "doc_id": 2746 }, "chunk_id": "train_shard_00001_2746_1", "global_id": 9569 }, { "text": "Variability in cadmium tolerance of closely related <i>Listeria monocytogenes</i> isolates originating from dairy processing environments.", "token_count": 42, "char_count": 150, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:49.480311", "source": { "split": "train_shard_00001", "doc_id": 2746 }, "chunk_id": "train_shard_00001_2746_2", "global_id": 9570 }, { "text": "

Objectives

We aimed to characterize the vanE cluster and its genetic support in the first Norwegian vanE-type isolates and assess genetic relatedness to other vanE isolates.

Methods

Two vanE-type vancomycin resistant Enterococcus faecalis (vanE-VREfs) isolates (E1 and E2) recovered from the same patient 30 months apart were examined for antimicrobial susceptibility, genome sequence, vancomycin resistance induction, vanE transferability, genome mutation rate, and phylogenetic relationship to E. faecalis closed genomes and two vanE-VREfs from North America.

Results

The ST34 E1 and E2 strains expressed low-level vancomycin resistance and susceptibility to teicoplanin. Their vanE gene clusters were part of a non-transferable Tn6202. The histidine kinase part of vanSE was expressed although a premature stop codon (E1) and insertion of a transposase (E2) truncated their vanSE gene. The vancomycin resistance phenotype in E1 was inducible while constitutive in E2. E1 showed a 125-fold higher mutation rate than E2. Variant calling showed 60 variants but nearly identical chromosomal gene content and synteny between the isolates. Their genomes also showed high similarity to another ST34 vanE-VREfs from Canada.

Conclusion

In-depth genomic analyses of the first two vanE-VREfs found in Europe identified a single chromosomal insertion site of two variants of vanE-conferring Tn6202. Single nucleotide polymorphism (SNP) and core genome multilocus sequence type (cgMLST) analyses show the genomes are different. This can be explained by the high mutation rate of E1 and acquisition of different mobile genetic elements; thus, we believe the two isolates from the same patient are genetically related. Genome similarities also suggest relatedness between the Canadian and Norwegian vanE-VREfs.", "token_count": 516, "char_count": 1849, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [ "ST34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:28:50.137245", "source": { "split": "train_shard_00001", "doc_id": 2747 }, "chunk_id": "train_shard_00001_2747_0", "global_id": 9571 }, { "text": "The first vanE-type vancomycin resistant Enterococcus faecalis isolates in Norway - phenotypic and molecular characteristics.", "token_count": 32, "char_count": 125, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:50.528849", "source": { "split": "train_shard_00001", "doc_id": 2747 }, "chunk_id": "train_shard_00001_2747_1", "global_id": 9572 }, { "text": "The population structure of health care-associated pathogens reflects patterns of diversification, selection, and dispersal over time. Empirical data detailing the long-term population dynamics of nosocomial pathogens provide information about how pathogens adapt in the face of exposure to diverse antimicrobial agents and other host and environmental pressures and can inform infection control priorities. Extensive sequencing of clinical isolates from one hospital spanning a decade and a second hospital in the Cleveland, OH, metropolitan area over a 3-year time period provided high-resolution genomic analysis of the Acinetobacter baumannii metapopulation. Genomic analysis demonstrated an almost complete replacement of the predominant strain groups with a new, genetically distinct strain group during the study period. The new group, termed clade F, differs from other global clone 2 (GC2) strains of A. baumannii in several ways, including its antibiotic resistance and lipooligosaccharide biosynthesis genes. Clade F strains are part of a large phylogenetic group with broad geographic representation. Phylogenetic analysis of single-nucleotide variants in core genome regions showed that although the Cleveland strains are phylogenetically distinct from those isolated from other locations, extensive intermixing of strains from the two hospital systems was apparent, suggesting either substantial exchange of strains or a shared, but geographically restricted, external pool from which infectious isolates were drawn. These findings document the rapid evolution of A. baumannii strains in two hospitals, with replacement of the predominant clade by a new clade with altered lipooligosaccharide loci and resistance gene repertoires.IMPORTANCE Multidrug-resistant (MDR) A. baumannii is a difficult-to-treat health care-associated pathogen. Knowing the resistance genes present in isolates causing infection aids in empirical treatment selection. Furthermore, knowledge of the genetic background can assist in tracking patterns of transmission to limit the spread of infections in hospitals. The appearance of a new genetic background in A", "token_count": 499, "char_count": 2187, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6177, "quality_score": 0.8089, "entities": { "genes": [ "GC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:51.213883", "source": { "split": "train_shard_00001", "doc_id": 2748 }, "chunk_id": "train_shard_00001_2748_0", "global_id": 9573 }, { "text": "baumannii strains with a different set of resistance genes and cell surface structures suggests that strong selective pressures exist, even in highly MDR pathogens. Because the new strains have levels of antimicrobial resistance similar to those of the strains that were displaced, we hypothesize that other features, including host colonization and infection, may confer additional selective advantages and contribute to their increased prevalence.\n\nRapid Replacement of Acinetobacter baumannii Strains Accompanied by Changes in Lipooligosaccharide Loci and Resistance Gene Repertoire.", "token_count": 134, "char_count": 590, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7848, "quality_score": 0.8924, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:51.635292", "source": { "split": "train_shard_00001", "doc_id": 2748 }, "chunk_id": "train_shard_00001_2748_1", "global_id": 9574 }, { "text": "Mycoplasma capricolum subsp. Capricolum (Mcc) is an important member of the Mycoplasma mycoides cluster (Mm cluster) and causes caprine contagious agalactia. Mcc can infect goats of all age groups, especially pregnant ewes and kids. It can cause the abortion in pregnant ewes and the death of goat kids, leading to enormous losses in the goat breeding industry. To date, the prevalence of epidemic Mcc strains on Hainan Island, China, remains unclear. This study aimed to isolate and identify Mcc strains endemic to Hainan Island, China. Genome sequencing and comparative genomic analysis were performed to reveal the molecular characteristics and evolutionary relationships of the isolated strain. Mcc HN-B was isolated and identified in Hainan Island, China. The Mcc HN-B genome consists of a 1,117,925 bp circular chromosome with a 23.79% G + C content. It contains 912 encoding genes, 3 gene islands, and 14 potential virulence genes. The core genome with the features of the Mm cluster and the specific genes of Mcc HN-B were identified by comparative genomic analysis. These results revealed the evolutionary relationship between Mcc HN-B and other members of the Mm cluster. Our findings provide a reference for further studies on the pathogenic mechanism and local vaccine development of Mcc.\n\nFirst Report and Comparative Genomic Analysis of Mycoplasma capricolum subsp. capricolum HN-B in Hainan Island, China.", "token_count": 403, "char_count": 1455, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:52.257225", "source": { "split": "train_shard_00001", "doc_id": 2749 }, "chunk_id": "train_shard_00001_2749_0", "global_id": 9575 }, { "text": "The dynamic interplay between guanine-quadruplex (G4) structures and pathogenicity islands (PAIs) represents a captivating area of research with implications for understanding the molecular mechanisms underlying pathogenicity. This study conducted a comprehensive analysis of a large-scale dataset from reported 89 pathogenic strains of bacteria to investigate the potential interactions between G4 structures and PAIs. G4 structures exhibited an uneven and non-random distribution within the PAIs and were consistently conserved within the same pathogenic strains. Additionally, this investigation identified positive correlations between the number and frequency of G4 structures and the GC content across different genomic features, including the genome, promoters, genes, tRNA, and rRNA regions, indicating a potential relationship between G4 structures and the GC-associated regions of the genome. The observed differences in GC content between PAIs and the core genome further highlight the unique nature of PAIs and underlying factors, such as DNA topology. High-confidence G4 structures within regulatory regions of Escherichia coli were identified, modulating the efficiency or specificity of DNA integration events within PAIs. Collectively, these findings pave the way for future research to unravel the intricate molecular mechanisms and functional implications of G4-PAI interactions, thereby advancing our understanding of bacterial pathogenicity and the role of G4 structures in pathogenic diseases.\n\nThe Intricate Relationship of G-Quadruplexes and Bacterial Pathogenicity Islands", "token_count": 329, "char_count": 1596, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:52.822433", "source": { "split": "train_shard_00001", "doc_id": 2750 }, "chunk_id": "train_shard_00001_2750_0", "global_id": 9576 }, { "text": "Manogepix (APX001A) is the active moiety of the novel drug candidate fosmanogepix (APX001). We previously reported the broad-spectrum activity of manogepix but also observed a correlation between increased manogepix and fluconazole MICs. Here, we extended this study and included isolates with acquired fluconazole resistance. Isolates (n = 835) were identified using CHROMagar, matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), and, when needed, internal transcribed spacer (ITS) sequencing. EUCAST E.Def 7.3.1 susceptibility testing included manogepix, amphotericin B, anidulafungin, micafungin, fluconazole, and voriconazole. Manogepix wild-type-upper-limit (WT-UL) values were established following EUCAST principles for the epidemiological cutoff value (ECOFF) setting allowing wild-type/non-wild-type classification. Drug-specific MIC correlations were investigated using Pearson's correlation. Manogepix modal MICs were low (range, 0.004 to 0.06 mg/liter against 16/20 included species). Exceptions were Candida krusei and Candida inconspicua and, to a lesser extent, Candida kefyr and Pichia kluyveri The activity was independent of Fks echinocandin hot spot alterations (n = 17). Adopting the WT-UL established for Candida albicans, Candida dubliniensis, Candida glabrata, Candida parapsilosis, and Candida tropicalis, 14/724 (1.9%) isolates were non-wild type for manogepix", "token_count": 513, "char_count": 1503, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7374, "quality_score": 0.8687, "entities": { "genes": [ "APX001", "APX001A" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:28:53.828348", "source": { "split": "train_shard_00001", "doc_id": 2751 }, "chunk_id": "train_shard_00001_2751_0", "global_id": 9577 }, { "text": "Twelve of these (85.7%) were also non-wild type for fluconazole. A statistically significant correlation was observed between manogepix and fluconazole MICs for C. albicans, C. dubliniensis, C. glabrata, C. parapsilosis, and C. tropicalis (Pearson's r = 0.401 to 0.575) but not between manogepix and micafungin or amphotericin B MICs for any species except C. tropicalis (r = 0.519 for manogepix versus micafungin). Broad-spectrum activity was confirmed for manogepix against contemporary yeast. However, a 1 to 4 2-fold dilutions increase in manogepix MICs is observed in a subset of isolates with acquired fluconazole resistance. Further studies on the potential underlying mechanism and implication for optimal dosing are warranted.\n\nManogepix (APX001A) Displays Potent In Vitro Activity against Human Pathogenic Yeast, but with an Unexpected Correlation to Fluconazole MICs.", "token_count": 333, "char_count": 941, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6984, "quality_score": 0.8492, "entities": { "genes": [ "APX001A" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:54.396770", "source": { "split": "train_shard_00001", "doc_id": 2751 }, "chunk_id": "train_shard_00001_2751_1", "global_id": 9578 }, { "text": "We hereby present the first descriptions of human invasive infections caused by Escherchia marmotae , a recently described species that encompasses the former “Escherichia cryptic clade V”. We report four cases, one acute sepsis of unknown origin, one post-operative sepsis after cholecystectomy, one spondylodiscitis and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab during six months. Through genome sequencing of the causative strains combined with available genomes from elsewhere we demonstrate E. marmotae to be a likely ubiquitous species containing genotypic virulence traits associated with Escherichia pathogenicity. The invasive isolates were scattered among isolates from a range of non-human sources, thus indicating inherent virulence in multiple phylogenetic lineages. Pan genome analyses indicate that E. marmotae has a large accessory genome and is likely to obtain ecologically advantageous traits like genes encoding antimicrobial resistance. Reliable identification might be possible by MALDI-ToF MS, but relevant spectra are missing in commercial databases. E. marmotae can be identified through 16S rRNA sequencing. Escherichia marmotae could represent a relatively common human pathogen and improved diagnostics will provide a better understanding of its clinical importance.\n\nEscherichia marmotae - a human pathogen easily misidentified as Escherichia coli", "token_count": 346, "char_count": 1445, "word_count": 198, "semantic_coherence": 1, "information_density": 0.7121, "quality_score": 0.8561, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:54.977568", "source": { "split": "train_shard_00001", "doc_id": 2752 }, "chunk_id": "train_shard_00001_2752_0", "global_id": 9579 }, { "text": "

Background

In most of Europe and especially in Germany, there is currently a concerning rise in the number of hospital-acquired infections due to vancomycin-resistant Enterococcus faecium (VREfm). Therefore, there is a need to improve our understanding of the way VREfm spreads in hospitals. In this study, we investigated the molecular epidemiology of VREfm isolates from the first appearance at our university hospital in 2004 until 2010. There is only very scarce information about the molecular epidemiology of VREfm from this early time in Germany.

Methods

Our analysis includes all available first VREfm isolates of each patient at our tertiary care center collected during the years 2004-2010. If available, additional consecutive VREfm isolates from some patients were analyzed. We used multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) for the analysis and description of nosocomial transmission pathways as well as the detection of outbreaks.

Results

VREfm isolates from 158 patients and 76 additional subsequent patient isolates were included in the analysis. Until 2006, detections of VREfm remained singular cases, followed by a peak in the number of VREfm cases in 2007 and 2008 with a subsequent decline to baseline in 2010. MLST and cgMLST analysis show significant changes in the dominant sequence types (STs) and complex types (CTs) over the study period, with ST192 and ST17 being responsible for the peak in VREfm cases in 2007 and 2008. The four largest clusters detected during the study period are comprised of these two STs. Cluster analysis shows a focus on specific wards and departments for each cluster. In the early years of this study (2004-2006), all analyzed VREfm stemmed from clinical specimens, whereas since 2007, approximately half of the VREfm were detected by screening", "token_count": 483, "char_count": 1866, "word_count": 280, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [ "ST17", "ST192" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:55.624305", "source": { "split": "train_shard_00001", "doc_id": 2753 }, "chunk_id": "train_shard_00001_2753_0", "global_id": 9580 }, { "text": "Of the 234 VREfm isolates analyzed, 96% had a vanB and only 4% had a vanA resistance genotype.

Conclusions

This retrospective study contributes significant knowledge about regional VREfm epidemiology from this early VREfm period in Germany. One remarkable finding is the striking dominance of vanB-positive VREfm isolates over the entire study period, which is in contrast with countrywide data. Analysis of cgMLST shows the transition from sporadic VRE cases at our institution to a sharp increase in VRE numbers triggered by oligoclonal spread and specific outbreak clusters with the dominance of ST192 and ST17.\n\nIntroduction and spread of vancomycin-resistant Enterococcus faecium (VREfm) at a German tertiary care medical center from 2004 until 2010: a retrospective whole-genome sequencing (WGS) study of the molecular epidemiology of VREfm.", "token_count": 233, "char_count": 854, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [ "ST17", "ST192" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:56.093808", "source": { "split": "train_shard_00001", "doc_id": 2753 }, "chunk_id": "train_shard_00001_2753_1", "global_id": 9581 }, { "text": "Disposal of lactose in whey and whey permeates is one of the most significant problems with regard to economics and environmental impact faced by the dairy industries. The enzymatic hydrolysis of whey lactose to glucose and galactose by beta-galactosidase constitutes the basis of the most biotechnological processes currently developed to exploit the sugar content of whey. Keeping this in view, lactose hydrolysis in whey was performed using CTAB permeabilized Kluyveromyces marxianus cells. Permeabilization of K. marxianus cells in relation to beta-galactosidase activity was carried out using cetyltrimethyl ammonium bromide (CTAB) to avoid the problem of enzyme extraction. Different process parameters (biomass load, pH, temperature, and incubation time) were optimized to enhance the lactose hydrolysis in whey. Maximum hydrolysis (90.5%) of whey lactose was observed with 200 mg DW yeast biomass after 90 min of incubation period at optimum pH of 6.5 and temperature of 40 degrees C.\n\nHydrolysis of whey lactose using CTAB-permeabilized yeast cells.", "token_count": 298, "char_count": 1058, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6258, "quality_score": 0.8129, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:56.662055", "source": { "split": "train_shard_00001", "doc_id": 2754 }, "chunk_id": "train_shard_00001_2754_0", "global_id": 9582 }, { "text": "

Background

Citric acid is considered as the most economically feasible product of microbiological production, therefore studies on cheap and renewable raw materials for its production are highly desirable. In this study citric acid was synthesized by genetically engineered strains of Yarrowia lipolytica from widely available, renewable polysaccharide - inulin. Hydrolysis of inulin by the Y. lipolytica strains was established by expressing the inulinase gene (INU1 gene; GenBank: X57202.1) with its native secretion signal sequence was amplified from genomic DNA from Kluyveromyces marxianus CBS6432. To ensure the maximum citric acid titer, the optimal cultivation strategy-repeated-batch culture was applied.

Results

The strain Y. lipolytica AWG7 INU 8 secreted more than 200 g dm- 3 of citric acid during repeated-batch culture on inulin, with a productivity of 0.51 g dm- 3 h- 1 and a yield of 0.85 g g- 1.

Conclusions

The citric acid titer obtained in the proposed process is the highest value reported in the literature for Yarrowia yeast. The obtained results suggest that citric acid production from inulin by engineered Y. lipolytica may be a very promising technology for industrial citric acid production.\n\nProduction of high titer of citric acid from inulin.", "token_count": 408, "char_count": 1339, "word_count": 188, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [ "AWG7", "CBS6432", "INU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:57.287634", "source": { "split": "train_shard_00001", "doc_id": 2755 }, "chunk_id": "train_shard_00001_2755_0", "global_id": 9583 }, { "text": "Four vanillic acid-degrading bacterial strains, named LR5S13T, LR5S20, and M4R5S39T and LN1S58, were isolated from Kalidium cuspidatum rhizosphere and bulk soils, respectively. Phylogenetic analysis based on 16S rRNA gene as well as core genome revealed that LR5S13T and LR5S20 clustered closely with each other and with Halomonas ventosae Al12T, and that the two strains shared the highest similarities (both 99.3 %) with H. ventosae Al12T, in contrast, M4R5S39T and LN1S58 clustered together and with Halomonas heilongjiangensis 9-2T, and the two strains shared the highest similarities (99.4 and 99.2 %, respectively) with H. heilongjiangensis 9-2T. The average nucleotides identities based on BLAST (ANIb) and digital DNA-DNA hybridization (dDDH) values of strains LR5S13T to LR5S20, and M4R5S39T to LN1S58, were both higher than the threshold values for delineation of a species. The ANIb and dDDH values of the four strains to their closely relatives were lower than the threshold values. All four strains take phosphatidylethanolamine, phosphatidylglycerol, and diphosphatidylglycerol as the major polar lipids, Summed Feature 8, Summed Feature 3, and C16:0 as the major fatty acids. Based on the phylogenetic and phenotypic results, the four strains should be classified as two novel Halomonas species. Therefore, Halomonas rhizosphaerae sp. nov", "token_count": 513, "char_count": 1474, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5838, "quality_score": 0.7919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:28:57.941355", "source": { "split": "train_shard_00001", "doc_id": 2756 }, "chunk_id": "train_shard_00001_2756_0", "global_id": 9584 }, { "text": "(type strain LR5S13T = KCTC 8016T = CGMCC 1.62049T) and Halomonas kalidii (type strain M4R5S39T = KCTC 8015T = CGMCC 1.62047T) are proposed. The geographical distribution analysis based on 16S rRNA gene revealed that the two novel species are widely distributed across the globe, specifically in highly saline habits, especially in Central and Eastern Asia.\n\nHalomonas rhizosphaerae sp. nov. and Halomonas kalidii sp. nov., two novel moderate halophilic phenolic acid-degrading species isolated from saline soil.", "token_count": 212, "char_count": 578, "word_count": 75, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:58.407218", "source": { "split": "train_shard_00001", "doc_id": 2756 }, "chunk_id": "train_shard_00001_2756_1", "global_id": 9585 }, { "text": "

Background

Muskoxen are important ecosystem components and provide food, economic opportunities, and cultural well-being for Indigenous communities in the Canadian Arctic. Between 2010 and 2021, Erysipelothrix rhusiopathiae was isolated from carcasses of muskoxen, caribou, a seal, and an Arctic fox during multiple large scale mortality events in the Canadian Arctic Archipelago. A single strain ('Arctic clone') of E. rhusiopathiae was associated with the mortalities on Banks, Victoria and Prince Patrick Islands, Northwest Territories and Nunavut, Canada (2010-2017). The objectives of this study were to (i) characterize the genomes of E. rhusiopathiae isolates obtained from more recent muskox mortalities in the Canadian Arctic in 2019 and 2021; (ii) identify and compare common virulence traits associated with the core genome and mobile genetic elements (i.e. pathogenicity islands and prophages) among Arctic clone versus other E. rhusiopathiae genomes; and iii) use pan-genome wide association studies (GWAS) to determine unique genetic contents of the Arctic clone that may encode virulence traits and that could be used for diagnostic purposes.

Results

Phylogenetic analyses revealed that the newly sequenced E. rhusiopathiae isolates from Ellesmere Island, Nunavut (2021) also belong to the Arctic clone. Of 17 virulence genes analysed among 28 Arctic clone isolates, four genes - adhesin, rhusiopathiae surface protein-A (rspA), choline binding protein-B (cbpB) and CDP-glycerol glycerophosphotransferase (tagF) - had amino acid sequence variants unique to this clone when compared to 31 other E. rhusiopathiae genomes. These genes encode proteins that facilitate E. rhusiopathiae to attach to the host endothelial cells and form biofilms", "token_count": 501, "char_count": 1768, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:59.060623", "source": { "split": "train_shard_00001", "doc_id": 2757 }, "chunk_id": "train_shard_00001_2757_0", "global_id": 9586 }, { "text": "GWAS analyses using Scoary found several unique genes to be overrepresented in the Arctic clone.

Conclusions

The Arctic clone of E. rhusiopathiae was associated with multiple muskox mortalities spanning over a decade and multiple Arctic islands with distances over 1000 km, highlighting the extent of its spatiotemporal spread. This clone possesses unique gene content, as well as amino acid variants in multiple virulence genes that are distinct from the other closely related E. rhusiopathiae isolates. This study establishes an essential foundation on which to investigate whether these differences are correlated with the apparent virulence of this specific clone through in vitro and in vivo studies.\n\nGenomic characterization and virulence gene profiling of Erysipelothrix rhusiopathiae isolated from widespread muskox mortalities in the Canadian Arctic Archipelago.", "token_count": 216, "char_count": 879, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6803, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:28:59.527700", "source": { "split": "train_shard_00001", "doc_id": 2757 }, "chunk_id": "train_shard_00001_2757_1", "global_id": 9587 }, { "text": "

Motivation

Horizontal gene transfer (HGT) is a major source of variability in prokaryotic genomes. Regions of Genome Plasticity (RGPs) are clusters of genes located in highly variable genomic regions. Most of them arise from HGT and correspond to Genomic Islands (GIs). The study of those regions at the species level has become increasingly difficult with the data deluge of genomes. To date no methods are available to identify GIs using hundreds of genomes to explore their diversity.

Results

We present here the panRGP method that predicts RGPs using pangenome graphs made of all available genomes for a given species. It allows the study of thousands of genomes in order to access the diversity of RGPs and to predict spots of insertions. It gave the best predictions when benchmarked along other GI detection tools against a reference dataset. In addition, we illustrated its use on Metagenome Assembled Genomes (MAGs) by redefining the borders of the leuX tRNA hotspot, a well studied spot of insertion in Escherichia coli . panRPG is a scalable and reliable tool to predict GIs and spots making it an ideal approach for large comparative studies.

Availability

The methods presented in the current work are available through the following software: https://github.com/labgem/PPanGGOLiN . Detailed results and scripts to compute the benchmark metrics are available at https://github.com/axbazin/panrgp_supdata .

Contact

vallenet@genoscope.cns.fr and acalteau@genoscope.cns.fr

Supplementary information

None.\n\npanRGP: a pangenome-based method to predict genomic islands and explore their diversity", "token_count": 427, "char_count": 1647, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:00.149880", "source": { "split": "train_shard_00001", "doc_id": 2758 }, "chunk_id": "train_shard_00001_2758_0", "global_id": 9588 }, { "text": "In order to provide a method for producing a Kluyveromyces marxianus transformant using a method of easily and efficiently joining the terminals of DNA fragments without using specific restriction enzymes or the recognition sequence thereof, and a method for producing useful substances using said transformant, two or more straight-chain double-stranded DNA fragments that do not contain a autonomously replicating sequence of Kluyveromyces marxianus are introduced into Kluyveromyces marxianus, and a transformant containing a desired concatenated DNA is selected, with the expression of a marker gene that is expressed by the desired concatenated DNA as an indicator, or a straight-chain double-strand DNA fragment containing an autonomously replicating sequence of Kluyveromyces marxianus is combined with one or more types of other straight-chain double-strand DNA fragments and introduced into Kluyveromyces marxianus, and a transformant containing a desired annular concatenated DNA is selected, with the expression of a marker gene expressed by the desired annular concatenated DNA as an indicator.\n\nMETHOD FOR PRODUCING KLUYVEROMYCES MARXIANUS TRANSFORMANT", "token_count": 267, "char_count": 1165, "word_count": 162, "semantic_coherence": 1, "information_density": 0.4259, "quality_score": 0.713, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:00.695498", "source": { "split": "train_shard_00001", "doc_id": 2759 }, "chunk_id": "train_shard_00001_2759_0", "global_id": 9589 }, { "text": "Salmonella enterica is a taxonomically diverse pathogen with over 2600 serovars associated with a wide variety of animal hosts including humans, other mammals, birds and reptiles. Some serovars are host-specific or host-restricted and cause disease in distinct host species, while others, such as serovar S. Typhimurium (STm), are generalists and have the potential to colonize a wide variety of species. However, even within generalist serovars such as STm it is becoming clear that pathovariants exist that differ in tropism and virulence. Identifying the genetic factors underlying host specificity is complex, but the availability of thousands of genome sequences and advances in machine learning have made it possible to build specific host prediction models to aid outbreak control and predict the human pathogenic potential of isolates from animals and other reservoirs. We have advanced this area by building host-association prediction models trained on a wide range of genomic features and compared them with predictions based on nearest-neighbour phylogeny. SNPs, protein variants (PVs), antimicrobial resistance (AMR) profiles and intergenic regions (IGRs) were extracted from 3883 high-quality STm assemblies collected from humans, swine, bovine and poultry in the USA, and used to construct Random Forest (RF) machine learning models. An additional 244 recent STm assemblies from farm animals were used as a test set for further validation. The models based on PVs and IGRs had the best performance in terms of predicting the host of origin of isolates and outperformed nearest-neighbour phylogenetic host prediction as well as models based on SNPs or AMR data. However, the models did not yield reliable predictions when tested with isolates that were phylogenetically distinct from the training set. The IGR and PV models were often able to differentiate human isolates in clusters where the majority of isolates were from a single animal source. Notably, IGRs were the feature with the best performance across multiple models which may be due to IGRs acting as both a representation of their flanking genes, equivalent to PVs, while also capturing genomic regulatory variation, such as altered promoter regions", "token_count": 518, "char_count": 2241, "word_count": 337, "semantic_coherence": 1, "information_density": 0.6053, "quality_score": 0.8027, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:01.396292", "source": { "split": "train_shard_00001", "doc_id": 2760 }, "chunk_id": "train_shard_00001_2760_0", "global_id": 9590 }, { "text": "The IGR and PV models predict that ~45 % of the human infections with STm in the USA originate from bovine, ~40 % from poultry and ~14.5 % from swine, although sequences of isolates from other sources were not used for training. In summary, the research demonstrates a significant gain in accuracy for models with IGRs and PVs as features compared to SNP-based and core genome phylogeny predictions when applied within the existing population structure. This article contains data hosted by Microreact.\n\nThe advantage of intergenic regions as genomic features for machine-learning-based host attribution of Salmonella Typhimurium from the USA.", "token_count": 164, "char_count": 650, "word_count": 100, "semantic_coherence": 1, "information_density": 0.74, "quality_score": 0.87, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:01.850430", "source": { "split": "train_shard_00001", "doc_id": 2760 }, "chunk_id": "train_shard_00001_2760_1", "global_id": 9591 }, { "text": "

Background

Bacterial whole-genome sequencing (WGS) and determination of genetic relatedness is an important tool for investigation of epidemiologically suspected outbreaks.

Aim

This prospective cohort study evaluated a comprehensive, prospective bacterial WGS-based surveillance programme for early detection of transmission of most bacterial pathogens among patients at a paediatric oncology hospital.

Methods

Cultured bacterial isolates from clinical diagnostic specimens collected prospectively from both inpatient and outpatient encounters between January 2019 and December 2021 underwent routine WGS and core genome multi-locus sequence typing to determine isolates' relatedness. Previously collected isolates from January to December 2018 were retrospectively analysed for identification of prior or ongoing transmission. Multi-patient clusters were investigated to identify potential transmission events based on temporal and spatial epidemiological links and interventions were introduced.

Findings

A total of 1497 bacterial isolates from 1025 patients underwent WGS. A total of 259 genetically related clusters were detected, of which 18 (6.9%) multi-patient clusters involving 38 (3.7%) patients were identified. Sixteen clusters involved two patients each, and two clusters involved three patients. Following investigation, epidemiologically plausible transmission links were identified in five (27.8%) multi-patient clusters. None of the multi-patient clusters were suspected by conventional epidemiological surveillance.

Conclusion

Bacterial WGS-based surveillance for early detection of hospital transmission detected several limited multi-patient clusters that were unrecognized by conventional epidemiological methods. Genomic surveillance helped efficiently focus interventions while reducing unnecessary investigations.\n\nA prospective bacterial whole-genome-sequencing-based surveillance programme for comprehensive early detection of healthcare-associated infection transmission in paediatric oncology patients.", "token_count": 451, "char_count": 2066, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:02.518386", "source": { "split": "train_shard_00001", "doc_id": 2761 }, "chunk_id": "train_shard_00001_2761_0", "global_id": 9592 }, { "text": "

Background

Prokaryotes are asexual, but these organisms frequently engage in homologous recombination, a process that differs from meiotic recombination in sexual organisms. Most tools developed to simulate genome evolution either assume sexual reproduction or the complete absence of DNA flux in the population. As a result, very few simulators are adapted to model prokaryotic genome evolution while accounting for recombination. Moreover, many simulators are based on the coalescent, which assumes a neutral model of genomic evolution, and those are best suited for organisms evolving under weak selective pressures, such as animals and plants. In contrast, prokaryotes are thought to be evolving under much stronger selective pressures, suggesting that forward-in-time simulators are better suited for these organisms.

Results

Here, I present CoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection.

Conclusions

CoreSimul is a flexible forward-in-time simulator that constitutes a significant addition to the limited list of available simulators applicable to prokaryote genome evolution.\n\nCoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination.", "token_count": 334, "char_count": 1413, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:03.131468", "source": { "split": "train_shard_00001", "doc_id": 2762 }, "chunk_id": "train_shard_00001_2762_0", "global_id": 9593 }, { "text": "The recent advent of long-read whole genome sequencing has enabled us to create an accurate telomere-to-telomere reference genome, construct pangenome graphs, and compile precise catalogs of genomic structural variations (SVs). These comprehensive SV repositories provide an excellent opportunity to explore the role of SVs in genotype-phenotype associations and examine the mechanisms by which SVs are introduced through double-strand break (DSB) repair. Here, we employed comprehensive SV catalogs identified through various short- and long-read whole genome sequencing efforts to infer the underlying mechanisms of SV introduction based on their genomic and epigenomic profiles. Our findings indicate that high local DNA methylation and DNA shape-related features, such as low variations in propeller twist, support the origins of homology-driven SVs. Subsequently, we utilized an active-learning-based unsupervised clustering approach, revealing that the homology-dependent SVs show greater evidence of retaining ancestral recombination patterns compared to their homology-independent counterparts. Finally, our comparison of inherited and de novo SVs from healthy populations and rare disease cohorts showed distinct upstream H3K27me3 levels in de novo SVs from individuals with ultra-rare disorders. These findings highlight genome-wide characteristics that may influence the choice of repair mechanisms linked to heritable SV origins.\n\nDNA shape and epigenomics distinguish the mechanistic origin of human genomic structural variations", "token_count": 322, "char_count": 1542, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6912, "quality_score": 0.8456, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:03.708251", "source": { "split": "train_shard_00001", "doc_id": 2763 }, "chunk_id": "train_shard_00001_2763_0", "global_id": 9594 }, { "text": "Rationale Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated with poorer outcomes or detect MRSA transmission.

Objectives:

To identify MRSA genes associated with low lung function and identify potential MRSA transmission in CF.

Methods:

We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short-read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies. We classified the MRSA by accessory gene content and correlated the accessory genome to clinical outcomes.

Results:

The most prevalent ST were ST5 (N=55), ST105 (N=14), and ST8 (N=14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three distinct clusters of MRSA were identified by accessory genome content. The first included ST5 and ST105 strains and was common among older patients with lower FEV. The second cluster included ST8, which was generally identified in younger patients. Sputum density of MRSA and Pseudomonas aeruginosa was higher in cultures from patients with ST5/ST105 compared to patients with ST8 at similar ages.

Conclusions:

In this CF cohort, we identified MRSA subtypes that predominate at different ages and differ by accessory gene content. ST5 and ST105 represented the most prevalent cluster of MRSA. ST8 MRSA was more common in younger patients and thus has the potential to rise in prevalence as these patients age.\n\nMRSA Strains with Distinct Accessory Genes Predominate at Different Ages in Cystic Fibrosis", "token_count": 470, "char_count": 1780, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5665, "quality_score": 0.7833, "entities": { "genes": [ "ST5", "ST105", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:04.348961", "source": { "split": "train_shard_00001", "doc_id": 2764 }, "chunk_id": "train_shard_00001_2764_0", "global_id": 9595 }, { "text": "The aim of this study was to investigate the fermentation behaviour, antioxidant activity and rheological behaviour of the sourdoughs prepared with Lactobacillus helveticus and Kluyveromyces marxianus. The final acidity of the sourdough after 18 h of fermentation was higher at higher temperatures (40 °C) and for the formulations with whole rye flour. The highest lactic/acetic acid ratios were obtained in case of more fluid sourdoughs fermented at 40 °C. The antioxidant properties of the sourdoughs are correlated with metabolic activity of the microorganisms, the DPPH radical scavenging activity being higher for optimum conditions of Lactobacillus helveticus growth. On the other hand, the rheological properties of the sourdoughs are not significantly influenced by the temperature. Sourdoughs formulations with whole flour are more viscous, as well as the controls fermented by the spontaneous microflora. The results of the bread-making process simulation by means of Mixolab indicate differences between dough formulations mainly depending on flour type.\n\nStudies concerning the use of Lactobacillus helveticus and Kluyveromyces marxianus for rye sourdough fermentation", "token_count": 306, "char_count": 1185, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5689, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:04.913851", "source": { "split": "train_shard_00001", "doc_id": 2765 }, "chunk_id": "train_shard_00001_2765_0", "global_id": 9596 }, { "text": "

Objectives

Fosfomycin has regained attention for treating infections caused by methicillin-resistant Staphylococcus aureus and multidrug-resistant coagulase-negative staphylococci. In this research, our objective was to investigate the mechanisms underlying fosfomycin resistance in Staphylococcus capitis.

Methods

The minimum inhibitory concentrations (MICs) of fosfomycin were assessed in 109 clinical S. capitis isolates by the agar dilution method. By cloning the fos-like genes into the shuttle vector, pTSSCm-Pcap, and observing the change in fosfomycin MICs, the gene function was verified. Core genome multilocus sequence typing and comparative genomics analysis were conducted to determine the population characteristics of S. capitis isolates and analyse the genetic environment of the fos-like genes.

Results

We identified a novel fosfomycin resistance gene, fosSC, on the chromosome in 58 out of 109 (53.2%) S. capitis isolates. The deduced products of the fosSC genes shared 67.15-67.88% amino acid sequence identity with FosB. The RN-pT-fosSC transformants carrying fosSC showed a 512-fold increase in the fosfomycin MICs. The fosSC gene was embedded in a conserved genetic context, but IS431mec was located to the left of the fosSC gene in cluster L due to the insertion of staphylococcal cassette chromosome mec.

Conclusions

The chromosomal fosSC genes in some lineages of S. capitis explained their high-level fosfomycin resistance. Ongoing surveillance is crucial for monitoring the potential threat of horizontal transfer, which could be facilitated by the presence of mobile genetic elements surrounding the fosSC gene.\n\nIdentification of the novel fosfomycin resistance gene fosSC in Staphylococcus capitis.", "token_count": 487, "char_count": 1757, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:05.562014", "source": { "split": "train_shard_00001", "doc_id": 2766 }, "chunk_id": "train_shard_00001_2766_0", "global_id": 9597 }, { "text": "Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica . We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2 , with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF , a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.\n\nPangenomics provides insights into the role of synanthropy in barn swallow evolution", "token_count": 246, "char_count": 1160, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:06.048536", "source": { "split": "train_shard_00001", "doc_id": 2767 }, "chunk_id": "train_shard_00001_2767_0", "global_id": 9598 }, { "text": "Escherichia albertii is characterized as an emerging pathogen, causing enteric infections. It is responsible for high mortality rate, especially in children, elderly, and immunocompromised people. To the best of our knowledge, no vaccine exists to curb this pathogen. Therefore, in current study, we aimed to identify potential vaccine candidates and design chimeric vaccine models against Escherichia albertii from the analysis of publicly available data of 95 strains, using a reverse vaccinology approach. Outer-membrane proteins (n = 4) were identified from core genome as vaccine candidates. Eventually, outer membrane Fimbrial usher (FimD) protein was selected as a promiscuous vaccine candidate and utilized to construct a potential vaccine model. It resulted in three epitopes, leading to the design of twelve vaccine constructs. Amongst these, V6 construct was found to be highly immunogenic, non-toxic, non-allergenic, antigenic, and most stable. This was utilized for molecular docking and simulation studies against six HLA and two TLR complexes. This construct can therefore be used for pan-therapy against different strains of E. albertii and needs to be tested in vitro and in vivo.\n\nPan-Genome Reverse Vaccinology Approach for the Design of Multi-Epitope Vaccine Construct against Escherichia albertii.", "token_count": 341, "char_count": 1346, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:06.620846", "source": { "split": "train_shard_00001", "doc_id": 2768 }, "chunk_id": "train_shard_00001_2768_0", "global_id": 9599 }, { "text": "Introduction. Klebsiella pneumoniae is a Gram-negative pathogen responsible for community- and nosocomial-acquired infections. The presence of an accessory genome determines the bacterial pathogenicity and the host immune response, and thus indicates multidrug-resistant strains or more virulent groups. Little is known about the virulence genes in K. pneumoniae in Kuwait.Hypothesis/Gap Statement. The diversity of virulence genes and capsule loci in K. pneumoniae isolates warrants further genomic studies to better understand their transmission within the hospitals in Kuwait.Aim. We aimed to investigate the virulence genes harboured by K. pneumoniae isolated from rectal swabs of intensive care unit (ICU) patients in two Kuwaiti teaching hospitals.Methodology. Six isolates from patients in the ICUs of Al Razi and Mubarak hospitals, designated RZH144, RZH132 RZH108 and RZH173, and MKH381 and MKH347, respectively, were subjected to whole-genome sequencing (WGS) assays. RZH144 and RZH132 were non-carbapenemase-producing K. pneumoniae (NCKP) isolates negative for genes encoding carbapenemase production by PCR assays, and the remaining four were carbapenemase-producing K. pneumoniae (CPKP) isolates. Isolates were characterized by phenotypic, PCR and WGS methods. Susceptibility testing was performed by E test and clonality by multilocus sequence typing. Analysis of the isolates' assembled contigs was carried out using Kleborate (https://pathogen.watch).Results. An NCPE RZH132 K", "token_count": 486, "char_count": 1572, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6784, "quality_score": 0.8392, "entities": { "genes": [ "RZH132", "MKH347", "RZH144", "RZH108", "MKH381", "RZH173" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:07.976285", "source": { "split": "train_shard_00001", "doc_id": 2769 }, "chunk_id": "train_shard_00001_2769_0", "global_id": 9600 }, { "text": "pneumoniae isolate belonged to ST231-wzi104 and harboured gene clusters encoding the biosynthesis of the siderophore aerobactin (iuc5) on 62-3LV. The capsular locus variants were KL51 and O locus O1v2. Another NCPKP RZH144 isolate was confirmed as ST43-wzi412 and harboured KL61 and O1v1. The four CPKP isolates harboured two virulence loci - ybt14 and iuc5 - encoding the siderophores yersiniabactin and aerobactin, respectively. They belonged to ST231-wzi104 and harboured yersiniabactin on ICEKp5. The sequence type of ybt was YbST145-1LV. Strain RZ108 was devoid of virulence loci. Its sequence type was ST15-wzi151 and harboured KL48 and O1V1. ST231 clonal lineage isolates shared common virulence plasmid variants.Conclusion. The CPKP ST231 had the highest virulence score and contained iuc5, which was found for the first time in ST231-CPKP isolates in Kuwait.\n\nElucidating the virulence genes harboured by carbapenemase- and non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae rectal isolates from patients admitted to intensive care units using whole-genome sequencing in Kuwait.", "token_count": 427, "char_count": 1153, "word_count": 153, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [ "ST231", "KL61", "RZ108", "RZH144", "ST43", "ST15", "KL48", "KL51" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:08.599724", "source": { "split": "train_shard_00001", "doc_id": 2769 }, "chunk_id": "train_shard_00001_2769_1", "global_id": 9601 }, { "text": "

Background

Population samples show bacterial genomes can be divided into a core of ubiquitous genes and accessory genes that are present in a fraction of isolates. The ecological significance of this variation in gene content remains unclear. However, microbiologists agree that a bacterial species should be 'genomically coherent', even though there is no consensus on how this should be determined.

Results

We use a parsimonious model combining diversification in both the core and accessory genome, including mutation, homologous recombination (HR) and horizontal gene transfer (HGT) introducing new loci, to produce a population of interacting clusters of strains with varying genome content. New loci introduced by HGT may then be transferred on by HR. The model fits well to a systematic population sample of 616 pneumococcal genomes, capturing the major features of the population structure with parameter values that agree well with empirical estimates.

Conclusions

The model does not include explicit selection on individual genes, suggesting that crude comparisons of gene content may be a poor predictor of ecological function. We identify a clearly divergent subpopulation of pneumococci that are inconsistent with the model and may be considered genomically incoherent with the rest of the population. These strains have a distinct disease tropism and may be rationally defined as a separate species. We also find deviations from the model that may be explained by recent population bottlenecks or spatial structure.\n\nRecombination produces coherent bacterial species clusters in both core and accessory genomes.", "token_count": 363, "char_count": 1647, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6186, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:09.195417", "source": { "split": "train_shard_00001", "doc_id": 2770 }, "chunk_id": "train_shard_00001_2770_0", "global_id": 9602 }, { "text": "This study aims to mine a previously developed continuous-flow competitive exclusion culture (CFCEC) originating from the Tilapia gut microbiome as a rational and efficient autochthonous probiotic strain recovery source. Three isolated strains were tested on their adaptability to host gastrointestinal conditions, their antibacterial activities against aquaculture bacterial pathogens, and their antibiotic susceptibility patterns. Their genomes were fully sequenced, assembled, annotated, and relevant functions inferred, such as those related to pinpointed probiotic activities and phylogenomic comparative analyses to the closer reported strains/species relatives. The strains are possible candidates of novel genus/species taxa inside Lactococcus spp. and Priestia spp. (previously known as Bacillus spp.) These results were consistent with reports on strains inside these phyla exhibiting probiotic features, and the strains we found are expanding their known diversity. Furthermore, their pangenomes showed that these bacteria have indeed a set of so far uncharacterized genes that may play a role in the antagonism to competing strains or specific symbiotic adaptations to the fish host. In conclusion, CFCEC proved to effectively allow the enrichment and further pure culture isolation of strains with probiotic potential.\n\nCompetitive Exclusion Bacterial Culture Derived from the Gut Microbiome of Nile Tilapia (Oreochromis niloticus) as a Resource to Efficiently Recover Probiotic Strains: Taxonomic, Genomic, and Functional Proof of Concept.", "token_count": 386, "char_count": 1581, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:09.817945", "source": { "split": "train_shard_00001", "doc_id": 2771 }, "chunk_id": "train_shard_00001_2771_0", "global_id": 9603 }, { "text": "

Purpose

Carbapenem-resistant Acinetobacter baumannii (CRAB) is an urgent concern to public health. This study focuses on exploring the resistance mechanisms and the in vitro results of using rifampicin in combination with conventional antibiotics for the management of CRAB.

Methods

The synergistic and bactericidal effects of rifampicin with conventional antibiotics were evaluated using chequerboard assay and time-kill assay, while the phenotypic and genotypic characteristics of resistant determinants were performed by efflux pump detection and whole genome sequencing on 29 isolates from ICU patients with underlying health diseases.

Results

The isolates showed multidrug resistance, with over 60% showing addictive responses to rifampicin-based combinations at FICI ranging from 0.6 to 0.8. The time-kill assay revealed 99 % killing for rifampicin and minocycline combination in one isolate at 1/4 MIC rifampicin plus 1/4 MIC minocycline, while a bacteriostatic effect was observed at 1/2 MIC rifampici plus 1/2 MIC for a second isolate. Combination with tigecycline resulted in a 99% killing in two out of three isolates with a 2.5-3 log reduction in CFU at 1/4 MIC rifampicin plus 1/4 MIC tigecycline. Rifampicin plus colistin exhibited bactericidal activity against three out of four isolates. The combinations of rifampicin with ciprofloxacin, chloramphenicol, and trimethoprim-sulfamethoxazole were ineffective against the isolates. In addition, a 4-fold reduction in rifampicin MIC was observed in 2 out of 14 isolates in the presence of an efflux pump inhibitor. The pan-genome study demonstrated a progressive evolution with an accessory genome estimated to cover 58% of the matrix", "token_count": 494, "char_count": 1725, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5625, "quality_score": 0.7812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:10.469830", "source": { "split": "train_shard_00001", "doc_id": 2772 }, "chunk_id": "train_shard_00001_2772_0", "global_id": 9604 }, { "text": "Seven of the ten sequenced isolates belong to sequence type 2 (ST2), while one isolate each was assigned to ST164, ST16, and ST25. Furthermore, 11 plasmids, 34 antimicrobial resistance (AMR) genes, and 65 virulence-associated genes were predicted from the whole genome data. The blaOXA-23blaADC-25, blaOXA-66, blaPER-7, aph(6)-Id, armA, and arr-3 were prevalent among the isolates. Sequence alignment of the bacteria genome to the reference strain revealed a deleterious mutation in the rpoB gene of 4 isolates.

Conclusion

The study suggests that rifampicin in combination with either minocycline, tigecycline, or colistin might be a treatment option for CRAB clinical isolates. In addition, genotypic analysis of the bacteria isolates may inform the clinician of the suitable drug regimen for the management of specific bacteria variants.\n\nGenotypic and phenotypic mechanisms underlying antimicrobial resistance and synergistic efficacy of rifampicin-based combinations against carbapenem-resistant Acinetobacter baumannii.", "token_count": 367, "char_count": 1138, "word_count": 138, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [ "ST16", "ST2", "ST164", "ST25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:11.041975", "source": { "split": "train_shard_00001", "doc_id": 2772 }, "chunk_id": "train_shard_00001_2772_1", "global_id": 9605 }, { "text": "

Background

Mycobacteroides abscessus complex (MABC), an emerging pathogen, causes human infections resistant to multiple antibiotics. In this study, the genome data of 1,581 MABC strains were downloaded from NCBI database for phylogenetic relatedness inference, resistance profile identification and the estimation of evolutionary pressure on resistance genes in silico.

Results

From genes associated with resistance to 28 antibiotic classes, 395 putative proteins (ARPs) were identified, based on the information in two antibiotic resistance databases (CARD and ARG-ANNOT). The ARPs most frequently identified in MABC were those associated with resistance to multiple antibiotic classes, beta-lactams and aminoglycosides. After excluding ARPs that had undergone recombination, two ARPs were predicted to be under diversifying selection and 202 under purifying selection. This wide occurrence of purifying selection suggested that the diversity of commonly shared ARPs in MABC have been reduced to achieve stability. The unequal distribution of ARPs in members of the MABC could be due to horizontal gene transfer or ARPs pseudogenization events. Most (81.5%) of the ARPs were observed in the accessory genome and 72.2% ARPs were highly homologous to proteins associated with mobile genetic elements such as plasmids, prophages and viruses. On the other hand, with TBLASTN search, only 18 of the ARPs were identified as pseudogenes.

Conclusion

Altogether, our results suggested an important role of horizontal gene transfer in shaping the resistome of MABC.\n\nThe resistomes of Mycobacteroides abscessus complex and their possible acquisition from horizontal gene transfer.", "token_count": 422, "char_count": 1694, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:11.668935", "source": { "split": "train_shard_00001", "doc_id": 2773 }, "chunk_id": "train_shard_00001_2773_0", "global_id": 9606 }, { "text": "The importance of Xenorhabdus and Photorhabdus symbionts to their respective Steinernema and Heterorhabditis nematode hosts is that they not only contribute to their entomopathogenicity but also to their fecundity through the production of small molecules. Thus, this mini-review gives a brief introductory overview of these nematophilic bacteria. Specifically, their type species, nematode hosts, and geographic region of isolations are tabulated. The use of nucleotide sequence-based techniques for their species delineation and how pangenomes can improve this are highlighted. Using the Steinernema-Xenorhabdus association as an example, the bacterium-nematode lifecycle is visualized with an emphasis on the role of bacterial biomolecules. Those currently in drug development are discussed, and two potential antimalarial lead compounds are highlighted. Thus, this mini-review tabulates forty-eight significant nematophilic bacteria and visualizes the ecological importance of their biomolecules. It further discusses three of these biomolecules that are currently in drug development. Through it, one is introduced to Xenorhabdus and Photorhabdus bacteria, their natural production of biomolecules in the nematode-bacterium lifecycle, and how these molecules are useful in developing novel therapies.\n\nNematophilic bacteria associated with entomopathogenic nematodes and drug development of their biomolecules.", "token_count": 385, "char_count": 1471, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:12.288687", "source": { "split": "train_shard_00001", "doc_id": 2774 }, "chunk_id": "train_shard_00001_2774_0", "global_id": 9607 }, { "text": "During a 2020 routine epidemiological investigation of carbapenem-resistant Enterobacterales at a local food market in Guangzhou, China, two Escherichia coli ST410 isolates coproducing NDM-5 and OXA-181 were obtained from environmental samples. Antimicrobial susceptibility testing, whole-genome sequencing, and conjugation assays were applied to identify their resistance phenotypes, phylogenetic relatedness, and genetic characteristics. Phylogenetic analysis showed that the two isolates were clonally related with only one core-genome single-nucleotide polymorphism (SNP) difference and clustered into a branch with 87 E. coli ST410 isolates deposited in GenBank. These 89 ST410 isolates were closely related (≤51 SNPs), and most were from humans in Southeast Asian countries (n = 47). A Vietnamese clinical isolate collected in 2017 showed the strongest epidemiological link (seven SNPs) to the two ST410 isolates detected in this study. Complete-genome analysis revealed that the carbapenem resistance determinants blaNDM-5 and blaOXA-181 were located on an IncF1:A1:B49-IncQ1 plasmid and IncX3 plasmid, respectively. Conjugation experiments confirmed that the IncX3 plasmid was self-transmissible while the IncF1:A1:B49-IncQ1 plasmid was nonconjugative. BLASTn analysis indicated that the two plasmids showed high similarity to other blaNDM-5-bearing IncF1:A1:B49-IncQ1 and blaOXA-181-bearing IncX3 plasmids from other countries", "token_count": 494, "char_count": 1521, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6576, "quality_score": 0.8288, "entities": { "genes": [ "ST410" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:12.949068", "source": { "split": "train_shard_00001", "doc_id": 2775 }, "chunk_id": "train_shard_00001_2775_0", "global_id": 9608 }, { "text": "Altogether, the high similarity of the core genomes and plasmids between the ST410 isolates found in this study and those human source isolates from foreign countries suggested the clonal spread of E. coli ST410 strains and horizontal transmission of blaOXA-181-bearing IncX3 plasmids across Southeast Asian countries. Stringent sanitary management of food markets is important to prevent the dissemination of high-risk clones to the public. IMPORTANCE This is the first report of an Escherichia coli ST410 clone that coproduces NDM-5 and OXA-181 in China. The high similarity of the core genomes and plasmids between the ST410 isolates characterized in this study and human source isolates from foreign countries strongly suggests that this ST410 lineage is an international high-risk clone, highlighting the need for continuous global surveillance of ST410 clones.\n\nCharacterization of an International High-Risk Escherichia coli ST410 Clone Coproducing NDM-5 and OXA-181 in a Food Market in China.", "token_count": 279, "char_count": 1025, "word_count": 147, "semantic_coherence": 1, "information_density": 0.5238, "quality_score": 0.7619, "entities": { "genes": [ "ST410" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:13.538374", "source": { "split": "train_shard_00001", "doc_id": 2775 }, "chunk_id": "train_shard_00001_2775_1", "global_id": 9609 }, { "text": "Nepeta curvidens is a plant of the mint family and an important species of the genus Nepeta. The main habitat of the N. curvidens in the Garin Mountains in Lorestan Province, Iran. Although locals have used N. curvidens as a food flavoring agent for years, few studies have been conducted on its phytochemical and biological properties. The chemical constituents of N. curvidens essential oil and then its biological properties were studied in detail in this investigation. N. curvidens essential oil was prepared from the aerial parts of the plant using the hydrodistillation method and its chemical composition was analyzed by the GC-MS method. Antimicrobial, antifungal, anti-Leishmania, and cytotoxic activities of the essential oil were investigated in vitro. In addition, antinociceptive and anti-inflammatory effects were evaluated in vivo. Most of N. curvidens essential oil compositions are composed of trans-caryophyllene (17.53%), allo-spathulenol (13.41%), germacrene D (10.12%), bicyclogermacrene (9.36%), α-pinene (9.12%), and β-phellandrene (6.87%). The highest antimicrobial and antifungal effects were observed against L. monocytogenes (MIC=156.25 μg/ml) and K. marxianus (MIC=625 µg/ml), respectively. Concentration-dependent effects were detected in the treatment of L. major, so that the number of macrophages infected with amastigote dropped significantly with higher concentrations. The essential oil showed the highest effect on the lung cancer cell line (A549) with the lowest IC50 (133.2μg/mL). The most resistant cell line to the essential oil was bladder cancer (C450) with an IC50 of 430.69 µg/mL. SI 19.49 index indicated high immunity of the essential oil on macrophage lines. Compared with morphine analgesic, the highest pain control effect of the essential oil was observed in primary and secondary phases at 100 mg/kg concentration in rats", "token_count": 532, "char_count": 1873, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8007, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:14.217711", "source": { "split": "train_shard_00001", "doc_id": 2776 }, "chunk_id": "train_shard_00001_2776_0", "global_id": 9610 }, { "text": "At 100 mg/kg concentration, reduced swelling of the paw and ear was observed in mice compared to the dexamethasone anti-inflammatory drug. The essential oil presents remarkable therapeutic properties such as antifungal, antibacterial, anti-inflammatory properties that probably attributed to the presence of an important trans-caryophyllene compound. Outstandingly, the essential oil has low toxic effects on the normal line and high antitumor properties against cancer cells. Therefore, it is expected to be used in the preparation of less toxic drugs than chemical ones, although more studies are required.\n\nInvestigation of the phytochemicals and bioactivity potential of essential oil from Nepeta curvidens Boiss. & Balansa", "token_count": 170, "char_count": 727, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:14.681387", "source": { "split": "train_shard_00001", "doc_id": 2776 }, "chunk_id": "train_shard_00001_2776_1", "global_id": 9611 }, { "text": "The first eukaryotes emerged from their prokaryotic ancestors more than 1.5 billion years ago and rapidly spread over the planet, first in the ocean, later on as land animals, plants, and fungi. Taking advantage of an expanding genome complexity and flexibility, they invaded almost all known ecological niches, adapting their body plan, physiology, and metabolism to new environments. This increase in genome complexity came along with an increase in gene repertoire, mainly from molecular reassortment of existing protein domains, but sometimes from the capture of a piece of viral genome or of a transposon sequence. With increasing sequencing and computing powers, it has become possible to undertake deciphering eukaryotic genome contents to an unprecedented scale, collecting all genes belonging to a given species, aiming at compiling all essential and dispensable genes making eukaryotic life possible. In this chapter, eukaryotic core- and pangenomes concepts will be described, as well as notions of closed or open genomes. Among all eukaryotes presently sequenced, ascomycetous yeasts are arguably the most well-described clade and the pangenome of Saccharomyces cerevisiae, Candida glabrata, Candida albicans as well as Schizosaccharomyces species will be reviewed. For scientific and economical reasons, many plant genomes have been sequenced too and the gene content of soybean, cabbage, poplar, thale cress, rice, maize, and barley will be outlined. Planktonic life forms, such as Emiliana huxleyi, a chromalveolate or Micromonas pusilla, a green alga, will be detailed and their pangenomes pictured. Mechanisms generating genetic diversity, such as interspecific hybridization, whole-genome duplications, segmental duplications, horizontal gene transfer, and single-gene duplication will be depicted and exemplified. Finally, computing approaches used to calculate core- and pangenome contents will be briefly described, as well as possible future directions in eukaryotic comparative genomics.\n\nEukaryotic Pangenomes", "token_count": 483, "char_count": 2033, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:15.362808", "source": { "split": "train_shard_00001", "doc_id": 2777 }, "chunk_id": "train_shard_00001_2777_0", "global_id": 9612 }, { "text": "Colorectal cancer (CRC) is one of the most prevalent and life-threatening cancer types with limited therapeutic options worldwide. Gut microbiota has been recognized as the pivotal determinant in maintaining gastrointestinal (GI) tract homeostasis, while dysbiosis of gut microbiota contributes to CRC development. Recently, the beneficial role of postbiotics, a new concept in describing microorganism derived substances, in CRC has been uncovered by various studies. However, a comprehensive characterization of the molecular identity, mechanism of action, or routes of administration of postbiotics, particularly their role in CRC, is still lacking. In this review, we outline the current state of research toward the beneficial effects of gut microbiota derived postbiotics against CRC, which will represent the key elements of future precision-medicine approaches in the development of novel therapeutic strategies targeting gut microbiota to improve treatment outcomes in CRC.\n\nBeneficial insights into postbiotics against colorectal cancer.", "token_count": 228, "char_count": 1047, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6783, "quality_score": 0.8392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:15.839084", "source": { "split": "train_shard_00001", "doc_id": 2778 }, "chunk_id": "train_shard_00001_2778_0", "global_id": 9613 }, { "text": "Bifidobacterium longum colonizes mammalian gastrointestinal tracts where it could metabolize host-indigestible oligosaccharides. Although B. longum strains are currently segregated into three subspecies that reflect common metabolic capacities and genetic similarity, heterogeneity within subspecies suggests that these taxonomic boundaries may not be completely resolved. To address this, the B. longum pangenome was analyzed from representative strains isolated from a diverse set of sources. As a result, the B. longum pangenome is open and contains almost 17,000 genes, with over 85% of genes found in ≤28 of 191 strains. B. longum genomes share a small core gene set of only ~500 genes, or ~3% of the total pangenome. Although the individual B. longum subspecies pangenomes share similar relative abundances of clusters of orthologous groups, strains show inter- and intrasubspecies differences with respect to carbohydrate utilization gene content and growth phenotypes.\n\nComparative Pangenomics of the Mammalian Gut Commensal Bifidobacterium longum.", "token_count": 319, "char_count": 1105, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7211, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:16.399252", "source": { "split": "train_shard_00001", "doc_id": 2779 }, "chunk_id": "train_shard_00001_2779_0", "global_id": 9614 }, { "text": "Kefir-a traditional beverage whose consumption has been associated with health benefits-is a logical natural product to investigate for new probiotic strains. The aim of the present work was to isolate and identify kefir yeasts and select those with acid and bile tolerance to study their adhesion to epithelial cells and their transit through mouse gut. From 4 milky and 3 sugary kefir grains, 34 yeast strains were isolated and identified by means of classical microbiological and molecular-genetic methods (whole-cell protein pattern, internal-transcribed-spacer amplification, and analysis of restriction-fragment-length polymorphisms). We identified 4 species belonging to 3 genera-Saccharomyces cerevisiae (15 strains), Saccharomyces unisporus (6 strains), Issatchenkia occidentalis (4 strains), and Kluyveromyces marxianus (9 strains)-and selected 13 strains on the basis of resistance to low pH and bile salts. Among the strains selected, Kluyveromyces marxianus CIDCA 8154 and Saccharomyces cerevisiae CIDCA 8112 were further studied. Both strains evidenced the capacity to adhere to epithelial intestine-derived cells in vitro and to survive passage through the gastrointestinal tract of BALB/c mice. The investigation of the potential probiotic features of these kefir-yeast strains should be useful for the development of novel functional foods.\n\nYeasts from kefir grains: isolation, identification, and probiotic characterization.", "token_count": 383, "char_count": 1443, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:16.981281", "source": { "split": "train_shard_00001", "doc_id": 2780 }, "chunk_id": "train_shard_00001_2780_0", "global_id": 9615 }, { "text": "PURPOSE: Kluyveromyces Marxianus strain with a superior heat resistance and ethanologenic is provided to enable saccharification and fermentation at the same time possible in ethanol manufacturing using fiber based biomass, thereby using for ethanol manufacture. CONSTITUTION: A Kluyveromyces Marxianus mutant strain is manufactured by fusing saccharomyces cerevisiae which has an accession number of KCTC11250BP and Kluyveromyces Marxianus strain which has accession number of KCTC17631. The growth temperature of the Kluyveromyces Marxianus mutant strain is 28-48deg.C, and optimal temperature of ethanol fermentation is 32-45deg.C. 26S rDNA D1/D2 and ITS sequence of the Kluyveromyces Marxianus mutant strain are marked as sequence number 5[SEQ ID NO:5] of DNA sequence. The Kluyveromyces Marxianus mutant strain has an accession number of KCTC 11757BP. An ethanol manufacture method includes a step of saccharizing and fermenting by processing the Kluyveromyces Marxianus mutant strain and diastatic enzyme on Biomass substrate. The biomass is either fiber based biomass or starch based biomass. The saccharification and fermentation are processed at the same time. The ethanol manufacturing method is processed in batch process, semi-continuous operation, or continuous operation.\n\nKLUYVEROMYCES MARXIANUS HAVING SUPERIOR HEAT RESISTANCE AND ETHANOL PRODUCTIVITY", "token_count": 397, "char_count": 1367, "word_count": 186, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [ "KCTC17631" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:17.597279", "source": { "split": "train_shard_00001", "doc_id": 2781 }, "chunk_id": "train_shard_00001_2781_0", "global_id": 9616 }, { "text": "Urinary tract infection (UTI) is a ubiquitous infectious condition, and uropathogenic Escherichia coli (UPEC) is the predominant causative agent of UTI. Copper (Cu) is implicated in innate immunity, including against UPEC. Cu is a trace element utilized as a co-factor, but excess Cu is toxic due to mismetalation of non-cognate proteins. E. coli precisely regulates Cu homeostasis via efflux systems. However, Cu import mechanisms into the bacterial cell are not clear. We hypothesized that Cu import defective mutants would exhibit increased resistance to Cu. This hypothesis was tested in a forward genetic screen with transposon (Tn5) insertion mutants in UPEC strain CFT073, and we identified 32 unique Cu-resistant mutants. Transposon and defined mutants lacking yhiM, which encodes a hypothetical inner membrane protein, were more resistant to Cu than parental strain. Loss of YhiM led to decreased cellular Cu content and increased expression of copA, encoding a Cu efflux pump. The CpxAR envelope stress response system was activated in the ΔyhiM mutant as indicated by increased expression of cpxP. Transcription of yhiM was regulated by CueR and CpxR, and the CpxAR system was essential for increased Cu resistance in the ΔyhiM mutant. Importantly, activation of CpxAR system in the ΔyhiM mutant was independent of NlpE, a known activator of this system. YhiM was required for optimal fitness of UPEC in a mouse model of UTI. Our findings demonstrate that YhiM is a critical mediator of Cu homeostasis and links bacterial adaptation to Cu stress with the CpxAR-dependent envelope stress response in UPEC.IMPORTANCEUPEC is a common bacterial infection. Bacterial pathogens are exposed to host-derived Cu during infection, including UTI. Here, we describe detection of genes involved in Cu homeostasis in UPEC", "token_count": 524, "char_count": 1888, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [ "CFT073" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:18.263486", "source": { "split": "train_shard_00001", "doc_id": 2782 }, "chunk_id": "train_shard_00001_2782_0", "global_id": 9617 }, { "text": "A UPEC mutant lacking YhiM, a membrane protein, exhibited dramatic increase in resistance to Cu. Our study demonstrates YhiM as a nexus between Cu stress and the CpxAR-dependent envelope stress response system. Importantly, our findings establish NlpE-independent activation of CpxAR system during Cu stress in UPEC. Collectively, YhiM emerges as a critical mediator of Cu homeostasis in UPEC and highlights the interlinked nature of bacterial adaptation to survival during Cu and envelope stress.\n\nThe inner membrane protein YhiM links copper and CpxAR envelope stress responses in uropathogenic <i>E. coli</i>.", "token_count": 162, "char_count": 624, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8315, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:18.700919", "source": { "split": "train_shard_00001", "doc_id": 2782 }, "chunk_id": "train_shard_00001_2782_1", "global_id": 9618 }, { "text": "Bradymonabacteria, as the representative of the facultative prey-dependent predators, were re-classified from the preceding Deltaproteobacteria into the phylum Myxococcota and proposed as a novel class named Bradymonadia. However, it was ambiguous whether their predatory pattern and properties were similar to those of the other myxobacterial predators. Therefore, the physiologic features were compared to determine the similarities and differences during the process of group attack and kin discrimination. Comparative genomic analyses were performed to conclude the core genome encoded commonly by bradymonabacteria, Myxococcia, and Polyangia. In conclusion, we proposed that bradymonabacteria have a predation pattern similar to the that of the representative of opportunistic predators like Myxococcus xanthus but with some subtle differences. Their predation was predicted to be initiated by the needle-less T3SS*, and the S-motility mediated by T4P also participated in the process. Meanwhile, their group attacks relied on cell contact and cell destiny. Inter-species (strains) kin discriminations occurred without the existence of T6SS. However, no extracellular lethal substance was detected in the fermentation liquor culture of bradymonabacteria, and the death of prey cells could only be observed when touched by their cells. Moreover, the prey-selective predation was observed when the predator encountered certain prey from Bacillus (G+), Algoriphagus (G-), and Nocardioides (G+). Bradymonabacteria can be regarded as a potential consumer and decomposer, and preying on many sea-dwelling or human pathogenic bacteria allows this group a broad application prospect in marine culture and clinical disease control. Our study will provide more evidence for its exploitations and applications.", "token_count": 488, "char_count": 1900, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6613, "quality_score": 0.8306, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:19.352304", "source": { "split": "train_shard_00001", "doc_id": 2783 }, "chunk_id": "train_shard_00001_2783_0", "global_id": 9619 }, { "text": "The Predatory Properties of Bradymonabacteria, the Representative of Facultative Prey-Dependent Predators.", "token_count": 27, "char_count": 106, "word_count": 11, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:19.703696", "source": { "split": "train_shard_00001", "doc_id": 2783 }, "chunk_id": "train_shard_00001_2783_1", "global_id": 9620 }, { "text": "

Motivation

The pangenome concept describes genetic variability as the union of genes shared in a set of genomes and constitutes the current paradigm for comparative analysis of bacterial populations. However, there is a lack of tools to simulate pangenome variability and structure using defined evolutionary models.

Results

We developed simurg, an R package that allows to simulate bacterial pangenomes using different combinations of evolutionary constraints such as gene gain, gene loss and mutation rates. Our tool allows the straightforward and reproducible simulation of bacterial pangenomes using real sequence data, providing a valuable tool for benchmarking of pangenome software or comparing evolutionary hypotheses.

Availability and implementation

The simurg package is released under the GPL-3 license, and is freely available for download from GitHub (https://github.com/iferres/simurg).

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nsimurg: simulate bacterial pangenomes in R.", "token_count": 248, "char_count": 1059, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:20.191491", "source": { "split": "train_shard_00001", "doc_id": 2784 }, "chunk_id": "train_shard_00001_2784_0", "global_id": 9621 }, { "text": "We examined the genomic adaptations of prevalent bacterial taxa in a highly nutrient- and ion-depleted freshwater environment located in the secondary cooling water system of a nuclear research reactor. Using genome-centric metagenomics, we found that none of the prevalent bacterial taxa were related to typical freshwater bacterial lineages. We also did not identify strong signatures of genome streamlining, which has been shown to be one of the ecoevolutionary forces shaping the genome characteristics of bacterial taxa in nutrient-depleted environments. Instead, focusing on the dominant taxon, a novel Ramlibacter sp. which we propose to name Ramlibacter aquaticus, we detected extensive positive selection on genes involved in phosphorus and carbon scavenging pathways. These genes were involved in the high-affinity phosphate uptake and storage into polyphosphate granules, metabolism of nitrogen-rich organic matter, and carbon/energy storage into polyhydroxyalkanoate. In parallel, comparative genomics revealed a high number of paralogs and an accessory genome significantly enriched in environmental sensing pathways (i.e., chemotaxis and motility), suggesting extensive gene expansions in R. aquaticus The type strain of R. aquaticus (LMG 30558T) displayed optimal growth kinetics and productivity at low nutrient concentrations, as well as substantial cell size plasticity. Our findings with R. aquaticus LMG 30558T demonstrate that positive selection and gene expansions may represent successful adaptive strategies to oligotrophic environments that preserve high growth rates and cellular productivity.IMPORTANCE By combining a genome-centric metagenomic approach with a culture-based approach, we investigated the genomic adaptations of prevalent populations in an engineered oligotrophic freshwater system. We found evidence for widespread positive selection on genes involved in phosphorus and carbon scavenging pathways and for gene expansions in motility and environmental sensing to be important genomic adaptations of the abundant taxon in this system", "token_count": 515, "char_count": 2139, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:20.849301", "source": { "split": "train_shard_00001", "doc_id": 2785 }, "chunk_id": "train_shard_00001_2785_0", "global_id": 9622 }, { "text": "In addition, microscopic and flow cytometric analysis of the first freshwater representative of this population (Ramlibacter aquaticus LMG 30558T) demonstrated phenotypic plasticity, possibly due to the metabolic versatility granted by its larger genome, to be a strategy to cope with nutrient limitation. Our study clearly demonstrates the need for the use of a broad set of genomic tools combined with culture-based physiological characterization assays to investigate and validate genomic adaptations.\n\nGene Expansion and Positive Selection as Bacterial Adaptations to Oligotrophic Conditions.", "token_count": 152, "char_count": 614, "word_count": 81, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:21.293204", "source": { "split": "train_shard_00001", "doc_id": 2785 }, "chunk_id": "train_shard_00001_2785_1", "global_id": 9623 }, { "text": "Food poisoning due to the consumption of Staphylococcus aureus contaminated food is a major health problem worldwide. In this study, we sequenced the genomes of ten plasmid-bearing S. aureus strains isolated from retail beef, chicken, turkey, and pork. The chromosomes of the strains varied in size from 2,654,842 to 2,807,514 bp, and a total of 25 plasmids were identified ranging from 1.4 to 118 kb. Comparative genomic analysis revealed similarities between strains isolated from the same retail meat source, indicating an origin-specific genomic composition. Genes known to modulate attachment, invasion, and toxin production were identified in the 10 genomes. Strains from retail chicken resembled human clinical isolates with respect to virulence factors and genomic islands, and retail turkey and pork isolates shared similarity with S. aureus from livestock. Most chromosomes contained antimicrobial resistance, heavy metal resistance, and stress response genes, and several plasmids contained genes involved in antimicrobial resistance and virulence. In conclusion, the genomes of S. aureus strains isolated from retail meats showed an origin-specific composition and contained virulence and antimicrobial resistance genes similar to those present in human clinical isolates.\n\nComparative Genomics of Plasmid-Bearing Staphylococcus aureus Strains Isolated From Various Retail Meats.", "token_count": 383, "char_count": 1426, "word_count": 194, "semantic_coherence": 1, "information_density": 0.567, "quality_score": 0.7835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:21.871552", "source": { "split": "train_shard_00001", "doc_id": 2786 }, "chunk_id": "train_shard_00001_2786_0", "global_id": 9624 }, { "text": "

Aims

To investigate the effect of total air pressure raise on cell growth and intracellular beta-galactosidase activity in batch cultures of Kluyveromyces marxianus CBS 7894.

Methods and results

A pressurized bioreactor was used for K. marxianus batch cultivation under increased air pressure from 1.2 to 6 bar. Under these conditions no inhibition of cell growth was observed. Moreover, the improvement of the oxygen transfer rate (OTR) from the gas to the culture medium by pressurization led to an enhancement of the cell growth rate obtained at atmospheric pressure without aeration. The specific beta-galactosidase productivity increased from 5.8 to 17.0 U gCD-1 h-1 using a 6-bar air pressure instead of air at atmospheric pressure. The antioxidant enzyme superoxide dismutase (SOD) was slightly induced by the air pressure raise, which indicates that the defensive mechanisms of the cells can cope with an air pressure up to 6 bar.

Conclusions

These experiments showed that the increase of air pressure up to 6 bar is an alternative to other methods of preventing the oxygen limitation and can be applied in the beta-galactosidase production by K. marxianus.

Significance and impact of the study

The results here reported proved that, in what biological aspects are concerned, it is possible to use the air pressure increase as an optimization parameter of beta-galactosidase production in high-density cell cultures of K. marxianus strains.\n\nGrowth and beta-galactosidase activity in cultures of Kluyveromyces marxianus under increased air pressure.", "token_count": 404, "char_count": 1586, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5522, "quality_score": 0.7761, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:22.492793", "source": { "split": "train_shard_00001", "doc_id": 2787 }, "chunk_id": "train_shard_00001_2787_0", "global_id": 9625 }, { "text": "

Background

Thermotolerant yeast has outstanding potential in industrial applications. Komagataella phaffii (Pichia pastoris) is a common cell factory for industrial production of heterologous proteins.

Results

Herein, we obtained a thermotolerant K. phaffii mutant G14 by mutagenesis and adaptive evolution. G14 exhibited oxidative and thermal stress cross-tolerance and high heterologous protein production efficiency. The reactive oxygen species (ROS) level and lipid peroxidation in G14 were reduced compared to the parent. Oxidative stress response (OSR) and heat shock response (HSR) are two major responses to thermal stress, but the activation of them was different in G14 and its parent. Compared with the parent, G14 acquired the better performance owing to its stronger OSR. Peroxisomes, as the main cellular site for cellular ROS generation and detoxification, had larger volume in G14 than the parent. And, the peroxisomal catalase activity and expression level in G14 was also higher than that of the parent. Excitingly, the gene knockdown of CAT encoding peroxisomal catalase by dCas9 severely reduced the oxidative and thermal stress cross-tolerance of G14. These results suggested that the augmented OSR was responsible for the oxidative and thermal stress cross-tolerance of G14. Nevertheless, OSR was not strong enough to protect the parent from thermal stress, even when HSR was initiated. Therefore, the parent cannot recover, thereby inducing the autophagy pathway and resulting in severe cell death.

Conclusions

Our findings indicate the importance of peroxisome and the significance of redox balance in thermotolerance of yeasts.\n\nAugmented peroxisomal ROS buffering capacity renders oxidative and thermal stress cross-tolerance in yeast.", "token_count": 451, "char_count": 1783, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:23.129730", "source": { "split": "train_shard_00001", "doc_id": 2788 }, "chunk_id": "train_shard_00001_2788_0", "global_id": 9626 }, { "text": "Yeast biomass enriched with iron could represent a new and safer solution for prevention from anaemia development. Such an iron source is less toxic and has better absorbability in organisms. The purpose of our research was the determination of the most suitable iron source in the cultivation medium for the yeast Saccharomyces cerevisiae, regarding good growth and iron accumulation in cells. Iron(III) citrate, iron(III) chloride, iron(III) nitrate and Fe-EDTA complex were used. The uptake of the chosen iron compound, Fe(III) citrate, by the yeasts Candida intermedia and Kluyveromyces marxianus was also investigated. Different growth behaviour of the three yeast strains in the presence of Fe(III) citrate was observed. The highest amounts of accumulated iron in S. cerevisiae, C. intermedia and K. marxianus biomass were about 13, 20 and 34mgFeg(-1)dry wt., respectively. To optimise the accumulation of iron in K. marxianus and to characterise iron enriched yeast biomass, further experiments are needed.\n\nIron enriched yeast biomass--a promising mineral feed supplement.", "token_count": 284, "char_count": 1080, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:23.692462", "source": { "split": "train_shard_00001", "doc_id": 2789 }, "chunk_id": "train_shard_00001_2789_0", "global_id": 9627 }, { "text": "

Objectives

Klebsiella pneumoniae is an important opportunistic Gram-negative pathogen. This study describes an outbreak due to colistin-resistant and carbapenem-resistant Klebsiella pneumoniae (ColR-CRKP) in a tertiary hospital related to six patients successively admitted to the department of medical intensive care unit (MICU) between March 11 and April 29, 2021.

Methods

Phenotypic characterization was conducted on 16 ColR-CRKP strains obtained from six infected patients and five ColR-CRKP strains isolated from 48 environmental samples, followed by whole-genome sequencing (WGS) and polymerase chain reaction (PCR) analysis.

Results

All ColR-CRKP strains showed resistance to commonly used antibiotics. Whole-genome sequencing revealed a variety of resistance genes such as blaKPC-2, blaCTX-M-65, and blaTEM-4 present in all strains, which is consistent with their antimicrobial resistance profile. All isolates were identified as the high-risk sequence type 11 (ST11) clonal lineage by multilocus sequencing typing (MLST) and subsequently clustered into a single clonal type by core genome MLST (cgMLST). IS5-like element ISKpn26 family transposase insertion mutations at positions 74 nucleotides in the mgrB gene were the main cause of colistin resistance in these ColR-CRKP. The variations of genes were verified by PCR. SCOTTI analysis demonstrated the transmission pathway of the ColR-CRKP between the patients.

Conclusion

Our study highlights the importance of coordinated efforts between clinical microbiologists and infection control teams to implement aggressive surveillance cultures and proper bacterial genotyping to diagnose nosocomial infections and take control measures. Routine surveillance and the use of advanced sequencing technologies should be implemented to enhance nosocomial infection control and prevention measures.", "token_count": 489, "char_count": 1878, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6917, "quality_score": 0.8458, "entities": { "genes": [ "IS5", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:24.344022", "source": { "split": "train_shard_00001", "doc_id": 2790 }, "chunk_id": "train_shard_00001_2790_0", "global_id": 9628 }, { "text": "Nosocomial outbreak of colistin-resistant, carbapenemase-producing Klebsiella pneumoniae ST11 in a medical intensive care unit.", "token_count": 40, "char_count": 127, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:24.702965", "source": { "split": "train_shard_00001", "doc_id": 2790 }, "chunk_id": "train_shard_00001_2790_1", "global_id": 9629 }, { "text": "

Background

Cellulose, which is the most abundant renewable biomass on earth, is a potential bio-resource of alternative energy. The hydrolysis of plant polysaccharides is catalyzed by microbial cellulases, including endo-β-1,4-glucanases, cellobiohydrolases, cellodextrinases, and β-glucosidases. Converting cellobiose by β-glucosidases is the key factor for reducing cellobiose inhibition and enhancing the efficiency of cellulolytic enzymes for cellulosic ethanol production.

Results

In this study, a cDNA encoding β-glucosidase was isolated from the buffalo rumen fungus Neocallimastix patriciarum W5 and is named NpaBGS. It has a length of 2,331 bp with an open reading frame coding for a protein of 776 amino acid residues, corresponding to a theoretical molecular mass of 85.1 kDa and isoelectric point of 4.4. Two GH3 catalytic domains were found at the N and C terminals of NpaBGS by sequence analysis. The cDNA was expressed in Pichia pastoris and after protein purification, the enzyme displayed a specific activity of 34.5 U/mg against cellobiose as the substrate. Enzymatic assays showed that NpaBGS was active on short cello-oligosaccharides from various substrates. A weak activity in carboxymethyl cellulose (CMC) digestion indicated that the enzyme might also have the function of an endoglucanase. The optimal activity was detected at 40°C and pH 5 ~ 6, showing that the enzyme prefers a weak acid condition. Moreover, its activity could be enhanced at 50°C by adding Mg2+ or Mn2+ ions", "token_count": 465, "char_count": 1517, "word_count": 221, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [ "GH3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:25.345391", "source": { "split": "train_shard_00001", "doc_id": 2791 }, "chunk_id": "train_shard_00001_2791_0", "global_id": 9630 }, { "text": "Interestingly, in simultaneous saccharification and fermentation (SSF) experiments using Saccharomyces cerevisiae BY4741 or Kluyveromyces marxianus KY3 as the fermentation yeast, NpaBGS showed advantages in cell growth, glucose production, and ethanol production over the commercial enzyme Novo 188. Moreover, we showed that the KY3 strain engineered with the NpaNGS gene can utilize 2 % dry napiergrass as the sole carbon source to produce 3.32 mg/ml ethanol when Celluclast 1.5 L was added to the SSF system.

Conclusion

Our characterizations of the novel β-glucosidase NpaBGS revealed that it has a preference of weak acidity for optimal yeast fermentation and an optimal temperature of ~40°C. Since NpaBGS performs better than Novo 188 under the living conditions of fermentation yeasts, it has the potential to be a suitable enzyme for SSF.\n\nA highly efficient β-glucosidase from the buffalo rumen fungus Neocallimastix patriciarum W5.", "token_count": 281, "char_count": 946, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7372, "quality_score": 0.8686, "entities": { "genes": [ "KY3", "BY4741" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:25.918323", "source": { "split": "train_shard_00001", "doc_id": 2791 }, "chunk_id": "train_shard_00001_2791_1", "global_id": 9631 }, { "text": "Staphylococcus pseudintermedius is a major canine pathogen but also occasionally colonizes and infects humans. Multidrug-resistant methicillin-resistant S. pseudintermedius (MDR MRSP) strains have emerged globally, making treatment and control of this pathogen challenging. Sequence type 71 (ST71), ST68, and ST45 are the most widespread and successful MDR MRSP clones. The potential genetic factors underlying the clonal success of these and other predominant clones remain unknown. Characterization of the pangenome, lineage-associated accessory genes, and genes acquired through horizontal gene transfer from other bacteria is important for identifying such factors. Here, we analyzed genome sequence data from 622 S. pseudintermedius isolates to investigate the evolution of pathogenicity across lineages. We show that the predominant clones carry one or more lineage-associated virulence genes. The gene encoding staphylococcal protein A (SpA), a key virulence factor involved in immune evasion and a potential vaccine antigen, is deleted in 62% of isolates. Most importantly, we have discovered that the spa locus is a hot spot for recombination and horizontal gene transfer in S. pseudintermedius, where genes related to restriction modification, prophage immunity, mercury resistance, and nucleotide and carbohydrate metabolism have been acquired in different lineages. Our study also establishes that ST45 is composed of two distinct sublineages that differ in their accessory gene content and virulence potential. Collectively, this study reports several previously undetected lineage-associated genetic factors that may have a role in the clonal success of the major MDR MRSP clones. These data provide a framework for future experimental studies on S. pseudintermedius pathogenesis and for developing novel therapeutics against this pathogen.IMPORTANCEStaphylococcus pseudintermedius is a major canine pathogen but can also occasionally infect humans. Identification of genetic factors contributing to the virulence and clonal success of multidrug-resistant S", "token_count": 523, "char_count": 2130, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5851, "quality_score": 0.7926, "entities": { "genes": [ "ST71", "ST68", "ST45" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:26.593528", "source": { "split": "train_shard_00001", "doc_id": 2792 }, "chunk_id": "train_shard_00001_2792_0", "global_id": 9632 }, { "text": "pseudintermedius clones is critical for the development of therapeutics against this pathogen. Here, we characterized the genome sequences of a global collection of 622 S. pseudintermedius isolates. We show that all major clones, besides carrying core virulence genes, which are present in all strains, carry one or more lineage-specific genes. Many of these genes have been acquired from other bacterial species through a horizontal gene transfer mechanism. Importantly, we have discovered that the staphylococcal protein A gene (spa), a widely used marker for molecular typing of S. pseudintermedius strains and a potential vaccine candidate antigen, is deleted in 62% of strains. Furthermore, the spa locus in S. pseudintermedius acts as a reservoir to accumulate lineage-associated genes with adaptive functions.\n\nStaphylococcal Protein A (spa) Locus Is a Hot Spot for Recombination and Horizontal Gene Transfer in Staphylococcus pseudintermedius.", "token_count": 268, "char_count": 997, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7007, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:27.184931", "source": { "split": "train_shard_00001", "doc_id": 2792 }, "chunk_id": "train_shard_00001_2792_1", "global_id": 9633 }, { "text": "

Background:

Rapid, cost-effective, simple, and reliable bacterial typing methods are essential in clinical infection control. This study aimed to evaluate the clinical applicability and its consistency with conventional typing methods of matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) typing function. Methods Here, we collected 126 carbapenem-resistant Klebsiella pneumoniae (CRKP) strains and 24 Enterobacter cloacae complex (ECC) strains, grouped them according to their strain characteristics, and clustered them using different methods, including MALDI-TOF MS, multi-locus sequence typing (MLST), core genome multi-locus sequence typing (cg-MLST), pulsed-field gel electrophoresis (PFGE). Results The results showed that MALDI-TOF MS was poorly matched with MLST and cg-MLST. MALDI-TOF MS was in relatively high agreement with PFGE for ECC, but for CRKP we concluded that the agreement was poor. We speculated that the reasons for this discrepant result might be the large difference in the number of the two strains and the fact that CRKP strains used to compare PFGE and MALDI-TOF MS were all from the ICU unit, which has a high degree of similarity. In addition, we found three possible outbreaks in our hospital after a small cluster analysis according to the time of strain isolation as well as the departments and wards of patients. Conclusion Therefore, although MALDI-TOF MS is less consistent with traditional methods in typing of these specific species, it may be one of the alternative tools for detecting outbreaks of strains carrying the carbapenemase gene to facilitate rapid clinical measures to prevent further spread of the outbreak.\n\nMALDI-TOF MS as one of the alternative tools for detecting outbreaks of strains carrying the carbapenemase gene", "token_count": 448, "char_count": 1826, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6067, "quality_score": 0.8034, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:27.833524", "source": { "split": "train_shard_00001", "doc_id": 2793 }, "chunk_id": "train_shard_00001_2793_0", "global_id": 9634 }, { "text": "

Background

Despite high vaccination coverage using acellular (ACV) and whole-cell pertussis (WCV) vaccines, the resurgence of pertussis is observed globally. Genetic divergence in circulating strains of Bordetella pertussis has been reported as one of the contributing factors for the resurgence of the disease. Our current knowledge of B. pertussis genetic evolution in circulating strains is mostly based on studies conducted in countries using ACVs targeting only a few antigens used in the production of ACVs. To better understand the adaptation to vaccine-induced selection pressure, it will be essential to study B. pertussis populations in developing countries which are using WCVs. India is a significant user and global supplier of WCVs. We report here comparative genome analyses of vaccine and clinical isolates reported from India. Whole-genome sequences obtained from vaccine strains: WCV (J445, J446, J447 and J448), ACV (BP165) were compared with Tohama-I reference strain and recently reported clinical isolates from India (BPD1, BPD2). Core genome-based phylogenetic analysis was also performed using 166 isolates reported from countries using ACV.

Results

Whole-genome analysis of vaccine and clinical isolates reported from India revealed high genetic similarity and conserved genome among strains. Phylogenetic analysis showed that clinical and vaccine strains share genetic closeness with reference strain Tohama-I. The allelic profile of vaccine strains (J445:ptxP1/ptxA2/prn1/fim2-1/fim3-1; J446: ptxP2/ptxA4/prn7/fim2-2/fim3-1; J447 and J448: ptxP1/ptxA1/ prn1/fim2-1/fim3-1), which matched entirely with clinical isolates (BPD1:ptxP1/ptxA1/prn1/fim2-1 and BPD2: ptxP1/ptxA1/prn1/fim2-1) reported from India", "token_count": 519, "char_count": 1746, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6079, "quality_score": 0.804, "entities": { "genes": [ "BPD2", "BP165", "BPD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:28.487958", "source": { "split": "train_shard_00001", "doc_id": 2794 }, "chunk_id": "train_shard_00001_2794_0", "global_id": 9635 }, { "text": "Multi-locus sequence typing (MLST) demonstrated the presence of dominant sequence types ST2 and primitive ST1 in vaccine strains which will allow better coverage against circulating strains of B. pertussis.

Conclusions

The study provides a detailed characterization of vaccine and clinical strains reported from India, which will further facilitate epidemiological studies on genetic shifts in countries which are using WCVs in their immunization programs.\n\nComparative genomics of whole-cell pertussis vaccine strains from India.", "token_count": 116, "char_count": 537, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7714, "quality_score": 0.8857, "entities": { "genes": [ "ST2", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:28.866148", "source": { "split": "train_shard_00001", "doc_id": 2794 }, "chunk_id": "train_shard_00001_2794_1", "global_id": 9636 }, { "text": "Little is known of the relationships among paediatric upper gastrointestinal microbiotas, and the impact of medication use and disease on their diversity. Here, we investigated the diversity of three microbiotas in the upper gastrointestinal tract of paediatric patients in relation to each other and to host factors. Oral, oesophageal and gastric microbiotas from a prospective paediatric cohort (n=54) were profiled using the 16S rRNA gene and ITS2 amplicon sequencing. 16S rRNA gene amplicon sequencing of oesophageal biopsies from a retrospective paediatric cohort (n=96) and shotgun metagenomics data from oesophageal brushings (n=88) were employed for genomic signature validation. Bacterial diversity and composition showed substantial differences across oral, oesophageal and gastric fluid samples that were not replicated for fungi, and the presence of reflux led to increased homogeneity in the bacterial component of these three microbiotas. The oral and oesophageal microbiotas were associated with age, sex, history of oesophageal atresia and presence of oesophageal metaplasia, with the latter characterized by Prevotella enrichment. Proton pump inhibitor use was associated with increased oral bacterial richness in the gastric fluid, and this correlated with increased levels of gastric pro-inflammatory cytokines. Profiling of oesophageal biopsies from a retrospective paediatric cohort confirmed an increased Prevotella prevalence in samples with metaplasia. Analysis of metagenome-derived oesophageal Prevotella melaninogenica genomes identified strain-specific features that were significantly increased in prevalence in samples with metaplasia", "token_count": 468, "char_count": 1706, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5561, "quality_score": 0.778, "entities": { "genes": [ "ITS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:29.514034", "source": { "split": "train_shard_00001", "doc_id": 2795 }, "chunk_id": "train_shard_00001_2795_0", "global_id": 9637 }, { "text": "Prevotella enrichment is a signature associated with paediatric oesophageal metaplasia, and proton pump inhibitor use substantially alters the paediatric gastric microenvironment.\n\nChanges to the upper gastrointestinal microbiotas of children with reflux oesophagitis and oesophageal metaplasia.", "token_count": 90, "char_count": 302, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:29.882305", "source": { "split": "train_shard_00001", "doc_id": 2795 }, "chunk_id": "train_shard_00001_2795_1", "global_id": 9638 }, { "text": "Faecalibacterium prausnitzii is one of the most prevalent and abundant polyphyletic health-promoting components of the human gut microbiome with a propensity for dysbiotic decreases. To better understand its biology in the human gut, we specifically explored the divergence pressures acting on F. prausnitzii clades on a global scale. Five F. prausnitzii clades were de novo identified from 55 publicly available genomes and 92 high-quality metagenome assembled genomes. Divergence rate indices were constructed and validated to compare the divergence rates among the different clades and between each of the diverging genes. For each clade we identified specific patterns of diverging functionalities, probably reflecting different ecological propensities, in term of inter-host dispersion capacity or exploitation of different substrates in the gut environment. Finally, we speculate that these differences may explain, at least in part, the observed differences in the overall divergence rates of F. prausnitzii clades in human populations.\n\nExploring clade differentiation of the Faecalibacterium prausnitzii complex.", "token_count": 302, "char_count": 1163, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:30.451359", "source": { "split": "train_shard_00001", "doc_id": 2796 }, "chunk_id": "train_shard_00001_2796_0", "global_id": 9639 }, { "text": "Seal finger (sealer's finger, spekk finger), an extremely painful hand infection contracted by individuals handling seals, has previously been associated with Mycoplasma phocacerebrale. From 2000 to 2014, six independent strains of a novel Mycoplasma species were isolated at Statens Serum Institut, Denmark, from Scandinavian patients with seal finger (M5725T, M6447, M6620, M6642 and M6879) or septic arthritis (M6921). Prior to the onset of infection, all patients had reported contact with unspeciated seals. All isolates grew within 2-5 days in Friis' modified broth and metabolized glucose and arginine but not urea. Strains M5725T, M6447, M6642 and M6921 also grew in Hayflick-type media. Colonies on agar media were large (0.5-1.0 mm) and had a typical 'fried egg' appearance, reduced tetrazolium, and were digitonin sensitive. Growth occurred at 32 °C but not at 42 °C. Strains were susceptible to doxycycline and moxifloxacin but resistant to azithromycin and erythromycin. The genomes of the six strains were sequenced and relatedness to all known Mycoplasma species was inferred. Phylogenetic analyses using 16S rRNA gene sequences and core genome single nucleotide polymorphisms showed that the isolated strains were highly similar and phylogenetically distinct from all other species within the genus Mycoplasma. The sizes of the genome sequences of the strains ranged from 744 321 to 772409 bp, with a G+C content of 25.0-25.2 mol%", "token_count": 501, "char_count": 1496, "word_count": 217, "semantic_coherence": 1, "information_density": 0.682, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:31.098890", "source": { "split": "train_shard_00001", "doc_id": 2797 }, "chunk_id": "train_shard_00001_2797_0", "global_id": 9640 }, { "text": "Based on these analyses, we propose a novel species of the genus Mycoplasma with the name Mycoplasma phocimorsus sp. nov. with the first isolate M5725T (NCTC 14922T=DSM 116188T) as the proposed type strain and representative strains M6447, M6620, M6642, M6879 and M6921.\n\nMycoplasma phocimorsus sp. nov., isolated from Scandinavian patients with seal finger or septic arthritis after contact with seals.", "token_count": 180, "char_count": 457, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:31.536610", "source": { "split": "train_shard_00001", "doc_id": 2797 }, "chunk_id": "train_shard_00001_2797_1", "global_id": 9641 }, { "text": "The study of host range determinants within the Pseudomonas syringae complex is gaining renewed attention due to its widespread distribution in non-agricultural environments, evidence of large variability in intra-pathovar host range, and the emergence of new epidemic diseases. This requires the establishment of appropriate model pathosystems facilitating integration of phenotypic, genomic and evolutionary data. Pseudomonas savastanoi pv. savastanoi is a model pathogen of the olive tree, and here we report a closed genome of strain NCPPB 3335, plus draft genome sequences of three strains isolated from oleander (pv. nerii), ash (pv. fraxini) and broom plants (pv. retacarpa). We then conducted a comparative genomic analysis of these four new genomes plus 16 publicly available genomes, representing 20 strains of these four P. savastanoi pathovars of woody hosts. Despite overlapping host ranges, cross-pathogenicity tests using four plant hosts clearly separated these pathovars and lead to pathovar reassignment of two strains. Critically, these functional assays were pivotal to reconcile phylogeny with host range and to define pathovar-specific genes repertoires. We report a pan-genome of 7,953 ortholog gene families and a total of 45 type III secretion system effector genes, including 24 core genes, four genes exclusive of pv. retacarpa and several genes encoding pathovar-specific truncations. Noticeably, the four pathovars corresponded with well-defined genetic lineages, with core genome phylogeny and hierarchical clustering of effector genes closely correlating with pathogenic specialization. Knot-inducing pathovars encode genes absent in the canker-inducing pv. fraxini, such as those related to indole acetic acid, cytokinins, rhizobitoxine, and a bacteriophytochrome", "token_count": 476, "char_count": 1816, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:32.180543", "source": { "split": "train_shard_00001", "doc_id": 2798 }, "chunk_id": "train_shard_00001_2798_0", "global_id": 9642 }, { "text": "Other pathovar-exclusive genes encode type I, type II, type IV, and type VI secretion system proteins, the phytotoxine phevamine A, a siderophore, c-di-GMP-related proteins, methyl chemotaxis proteins, and a broad collection of transcriptional regulators and transporters of eight different superfamilies. Our combination of pathogenicity analyses and genomics tools allowed us to correctly assign strains to pathovars and to propose a repertoire of host range-related genes in the P. syringae complex.\n\nHost Range Determinants of Pseudomonas savastanoi Pathovars of Woody Hosts Revealed by Comparative Genomics and Cross-Pathogenicity Tests.", "token_count": 185, "char_count": 656, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:32.622765", "source": { "split": "train_shard_00001", "doc_id": 2798 }, "chunk_id": "train_shard_00001_2798_1", "global_id": 9643 }, { "text": "The use of comparative genomics for functional, evolutionary, and epidemiological studies requires methods to classify gene families in terms of occurrence in a given species. These methods usually lack multivariate statistical models to infer the partitions and the optimal number of classes and don’t account for genome organization. We introduce a graph structure to model pangenomes in which nodes represent gene families and edges represent genomic neighborhood. Our method, named PPanGGOLiN, partitions nodes using an Expectation-Maximization algorithm based on multivariate Bernoulli Mixture Model coupled with a Markov Random Field. This approach takes into account the topology of the graph and the presence/absence of genes in pangenomes to classify gene families into persistent, cloud, and one or several shell partitions. By analyzing the partitioned pangenome graphs of isolate genomes from 439 species and metagenome-assembled genomes from 78 species, we demonstrate that our method is effective in estimating the persistent genome. Interestingly, it shows that the shell genome is a key element to understand genome dynamics, presumably because it reflects how genes present at intermediate frequencies drive adaptation of species, and its proportion in genomes is independent of genome size. The graph-based approach proposed by PPanGGOLiN is useful to depict the overall genomic diversity of thousands of strains in a compact structure and provides an effective basis for very large scale comparative genomics. The software is freely available at https://github.com/labgem/PPanGGOLiN .

Author summary

Microorganisms have the greatest biodiversity and evolutionary history on earth. At the genomic level, it is reflected by a highly variable gene content even among organisms from the same species which explains the ability of microbes to be pathogenic or to grow in specific environments. We developed a new method called PPanGGOLiN which accurately represent the genomic diversity of a species (i.e. its pangenome) using a compact graph structure. Based on this pangenome graph, we classify genes by a statistical method according to their occurrence in the genomes. This method allowed us to build pangenomes even for uncultivated species at an unprecedented scale. We applied our method on all available genomes in databanks in order to depict the overall diversity of hundreds of species", "token_count": 521, "char_count": 2419, "word_count": 355, "semantic_coherence": 1, "information_density": 0.5408, "quality_score": 0.7704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:33.267360", "source": { "split": "train_shard_00001", "doc_id": 2799 }, "chunk_id": "train_shard_00001_2799_0", "global_id": 9644 }, { "text": "Overall, our work enables microbiologists to explore and visualize pangenomes alike a subway map.\n\nPPanGGOLiN: depicting microbial diversity via a partitioned pangenome graph", "token_count": 46, "char_count": 174, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:33.633994", "source": { "split": "train_shard_00001", "doc_id": 2799 }, "chunk_id": "train_shard_00001_2799_1", "global_id": 9645 }, { "text": "Consolidated bioprocessing represents an attractive approach to converting cellulosic materials into bioethanol, yet is practically unavailable. We developed a ventilation-mediated, simultaneous ethanol fermentation and recovery system. Running the system under air-supplied conditions, apparently pure ethanol (28g) was recovered from cellobiose (100g) by growing recombinant Kluyveromyces marxianus expressing β-glucosidase.\n\nKluyveromyces marxianus-based platform for direct ethanol fermentation and recovery from cellulosic materials under air-ventilated conditions.", "token_count": 148, "char_count": 570, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8413, "quality_score": 0.9206, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:34.066592", "source": { "split": "train_shard_00001", "doc_id": 2800 }, "chunk_id": "train_shard_00001_2800_0", "global_id": 9646 }, { "text": "A current trend in winemaking has highlighted the beneficial contribution of non-Saccharomyces yeasts to wine quality. Hanseniaspora uvarum is one of the more represented non-Saccharomyces species onto grape berries and plays a critical role in influencing the wine sensory profile, in terms of complexity and organoleptic richness. In this work, we analyzed a group of H. uvarum indigenous wine strains as for genetic as for technological traits, such as resistance to SO2 and β-glucosidase activity. Three strains were selected for genome sequencing, assembly and comparative genomic analyses at species and genus level. Hanseniaspora genomes appeared compact and contained a moderate number of genes, while rarefaction analyses suggested an open accessory genome, reflecting a rather incomplete representation of the Hanseniaspora gene pool in the currently available genomes. The analyses of patterns of functional annotation in the three indigenous H. uvarum strains showed distinct enrichment for several PFAM protein domains. In particular, for certain traits, such as flocculation related protein domains, the genetic prediction correlated well with relative flocculation phenotypes at lab-scale. This feature, together with the enrichment for oligo-peptide transport and lipid and amino acid metabolism domains, reveals a promising potential of these indigenous strains to be applied in fermentation processes and modulation of wine flavor and aroma. This study also contributes to increasing the catalog of publicly available genomes from H. uvarum strains isolated from natural grape samples and provides a good roadmap for unraveling the biodiversity and the biotechnological potential of these non-Saccharomyces yeasts.\n\nGenome Sequencing and Comparative Analysis of Three Hanseniaspora uvarum Indigenous Wine Strains Reveal Remarkable Biotechnological Potential.", "token_count": 502, "char_count": 1957, "word_count": 261, "semantic_coherence": 1, "information_density": 0.59, "quality_score": 0.795, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:35.079047", "source": { "split": "train_shard_00001", "doc_id": 2801 }, "chunk_id": "train_shard_00001_2801_0", "global_id": 9647 }, { "text": "This study was conducted to investigate the γ-aminobutyric acid (GABA) production ability of 20 Lactobacillus and 25 Bifidobacterium strains which were previously isolated in our laboratory. Effect of initial pH, incubation time, monosodium glutamate (MSG), and pyridoxal-5'-phosphate (PLP) concentration for highest GABA production by two potent bacterial strains, Levilactobacillus brevis LAB6 and Limosilactobacillus fermentum LAB19 were optimized in the MRS media. A threefold increase in GABA production at an initial pH 4.0, incubation time of 120 h in medium supplemented with 3% MSG and 400 μM of PLP for LAB6 and 300 μM for LAB19 lead to the production of 19.67 ± 0.28 and 20.77 ± 0.14 g/L of GABA, respectively. Coculturing both strains under optimized conditions led to a GABA yield of 20.02 ± 0.17 g/L. Owing to potent anti-inflammatory activity in-vitro, as reported previously, and highest GABA production ability of LAB6 (MTCC 25662), its whole-genome sequencing and bioinformatics analysis was carried out for mining genes related to GABA metabolism. LAB6 harbored a complete glutamate decarboxylase (GAD) gene system comprising gadA, gadB, and gadC as well as genes responsible for the beneficial probiotic traits, such as for acid and bile tolerance and host adhesion", "token_count": 489, "char_count": 1348, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [ "LAB6", "LAB19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:35.731812", "source": { "split": "train_shard_00001", "doc_id": 2802 }, "chunk_id": "train_shard_00001_2802_0", "global_id": 9648 }, { "text": "Comparative genomic analysis of LAB6 with 28 completely sequenced Levilactobacillus brevis strains revealed the presence of 95 strain-specific genes-families that was significantly higher than most other L. brevis strains.

Supplementary information

The online version contains supplementary material available at 10.1007/s13205-024-03918-7.\n\nGABA synthesizing lactic acid bacteria and genomic analysis of Levilactobacillus brevis LAB6.", "token_count": 154, "char_count": 463, "word_count": 50, "semantic_coherence": 1, "information_density": 0.86, "quality_score": 0.93, "entities": { "genes": [ "LAB6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:36.167465", "source": { "split": "train_shard_00001", "doc_id": 2802 }, "chunk_id": "train_shard_00001_2802_1", "global_id": 9649 }, { "text": "

Objectives

The intestinal microflora affects the pathogenesis of several autoimmune diseases by influencing immune system function. Some bacteria, such as lactic acid bacteria, have been reported to have beneficial effects on immune function. However, little is known about the effects of yeasts. Here, we aimed to investigate the effects of various dietary yeasts contained in fermented foods on experimental autoimmune encephalomyelitis (EAE), an animal model of multiple sclerosis (MS), and to elucidate the mechanisms underlying these effects.

Methods

The effects of eight yeasts selected from 18 types of yeasts contained in fermented foods were examined using an EAE model. Of these, Candida kefyr was investigated by analyzing the intestinal microflora and its effects on intestinal and systemic immune states.

Results

Administration of C. kefyr ameliorated the severity of EAE. Reduced numbers of Th17 cells, suppressed interleukin (IL)-6 production by intestinal explants, and increased Tregs and CD103-positive regulatory dendritic cells in mesenteric lymph nodes (MLNs) were observed. Analysis of 16s-rDNA from feces of C. kefyr-treated mice demonstrated increased Lactobacillales and decreased Bacteroides compared to control flora. Transfer of intestinal microbiota also resulted in decreased Bacteroides and ameliorated symptoms of EAE. Thus, oral administration of C. kefyr ameliorated EAE by altering the microflora, accompanied by increased Tregs and CD103-positive regulatory dendritic cells in MLNs and decreased Th17 cells in the intestinal lamina propria.

Interpretation

Oral ingestion of C. kefyr may have beneficial effects on MS by modifying microflora. In addition, our findings also suggested the potential health benefits of dietary yeasts.\n\nDietary Yeasts Reduce Inflammation in Central Nerve System via Microflora.", "token_count": 496, "char_count": 1872, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5794, "quality_score": 0.7897, "entities": { "genes": [ "CD103" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:36.820340", "source": { "split": "train_shard_00001", "doc_id": 2803 }, "chunk_id": "train_shard_00001_2803_0", "global_id": 9650 }, { "text": "The gut microbiome comprised of microbes from multiple kingdoms, including bacteria, fungi, and viruses. Emerging evidence suggests that the intestinal fungi (the gut \"mycobiome\") play an important role in host immunity and inflammation. Advances in next generation sequencing methods to study the fungi in fecal samples and mucosa tissues have expanded our understanding of gut fungi in intestinal homeostasis and systemic immunity in health and their contribution to different human diseases. In this review, the current status of gut mycobiome in health, early life, and different diseases including inflammatory bowel disease, colorectal cancer, and metabolic diseases were summarized.\n\nThe role of gut mycobiome in health and diseases.", "token_count": 172, "char_count": 740, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6542, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:37.266673", "source": { "split": "train_shard_00001", "doc_id": 2804 }, "chunk_id": "train_shard_00001_2804_0", "global_id": 9651 }, { "text": "Abstract

Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhance yield potential. Bi-parental populations were used intensively to map genes controlling flowering. However, the lack of genetic diversity in bi-parental populations can lead to low mapping resolution and low allele richness, rendering the identification of underlying functional alleles difficult. Multiparent mapping populations such as nested association mapping (NAM) and multiparent advanced generation intercross (MAGIC) can overcome these limitations. The higher genetic and phenotypic diversity of multiple parents allows high-resolution quantitative trait loci (QTL) mapping. In this study, we use a MAGIC population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq) and Kompetitive allele-specific polymerase chain reaction (KASP) genotyping. Phenotypic data was collected from 15 trials at different sites, across three consecutive years, various sowing times with/without vernalisation and extended photoperiod. This study detected 14 stable regions associated with flowering time across multiple environments. Minor regions associated with flowering time in certain environmental conditions were also identified. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. These associations provide opportunities to utilise specific genes/alleles to create barley varieties with better grain yield and adaptation to growing conditions.

\n\nMulti-Locus Genome-Wide Association Studies Reveal Novel Alleles for Flowering Time Under Vernalisation and Extended Photoperiod in a Barley MAGIC Population", "token_count": 473, "char_count": 2122, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8296, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:37.938854", "source": { "split": "train_shard_00001", "doc_id": 2805 }, "chunk_id": "train_shard_00001_2805_0", "global_id": 9652 }, { "text": "The effects of probiotics on host gastrointestinal health have become an area of particular interest in the field of probiotic research. However, the impact of the host intestinal environment on genomic changes in probiotic organisms remains largely unknown. To investigate, Lactobacillus plantarum P-8, a well-studied probiotic bacterium, was consumed by healthy human volunteers and rats. Then, the persistence and genomic stability of P-8 in the host gut were surveyed. qPCR results revealed that after the consumption of one dose, P-8 could be detected in the host gastrointestinal tract for 4-5 weeks. By contrast, after 4 successive weeks of consumption, P-8 could be detected for up to 17 weeks after consumption ceased. In total, 92 P-8 derived strains were isolated from fecal samples and their genomes were sequenced and analyzed. Comparative genomic analysis detected 19 SNPs, which showed the characteristics of neutral evolution in the core genome. In nearly half of samples (n = 39, 42%), the loss of one to three plasmids was observed. The frequent loss of plasmids indicated reductive evolution in the accessory genome under selection pressure within the gastrointestinal tract. We also observed a 609-bp 23S rRNA homologous fragment that may have been acquired from other species after intake. Our findings offer insight into the complex reactions of probiotics to the gut environment during survival in the host. The in vivo genomic dynamics of L. plantarum P-8 observed in this study will aid the commercial development of probiotics with more stable characteristics.\n\nGenomic Variations in Probiotic Lactobacillus plantarum P-8 in the Human and Rat Gut.", "token_count": 444, "char_count": 1715, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6124, "quality_score": 0.8062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:38.583242", "source": { "split": "train_shard_00001", "doc_id": 2806 }, "chunk_id": "train_shard_00001_2806_0", "global_id": 9653 }, { "text": "Between January 2015 and October 2022, 38 patients with culture-confirmed melioidosis were identified in the Kowloon West (KW) Region, Hong Kong. Notably, 30 of them were clustered in the Sham Shui Po (SSP) district, which covers an estimated area of 2.5 km2. Between August and October 2022, 18 patients were identified in this district after heavy rainfall and typhoons. The sudden upsurge in cases prompted an environmental investigation, which involved collecting 20 air samples and 72 soil samples from residential areas near the patients. A viable isolate of Burkholderia pseudomallei was obtained from an air sample collected at a building site five days after a typhoon. B. pseudomallei DNA was also detected in 21 soil samples collected from the building site and adjacent gardening areas using full-length 16S rRNA gene sequencing, suggesting that B. psuedomallei is widely distributed in the soil environment surrounding the district. Core genome-multilocus sequence typing showed that the air sample isolate was phylogenetically clustered with the outbreak isolates in KW Region. Multispectral satellite imagery revealed a continuous reduction in vegetation region in SSP district by 162,255 m2 from 2016 to 2022, supporting the hypothesis of inhalation of aerosols from the contaminated soil as the transmission route of melioidosis during extreme weather events. This is because the bacteria in unvegetated soil are more easily spread by winds. In consistent with inhalational melioidosis, 24 (63.2%) patients had pneumonia. Clinicians should be aware of melioidosis during typhoon season and initiate appropriate investigation and treatment for patients with compatible symptoms.\n\nProbable airborne transmission of Burkholderia pseudomallei causing an urban outbreak of melioidosis during typhoon season in Hong Kong, China.", "token_count": 495, "char_count": 1889, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:39.289781", "source": { "split": "train_shard_00001", "doc_id": 2807 }, "chunk_id": "train_shard_00001_2807_0", "global_id": 9654 }, { "text": "

Background

Enterococcus faecium though commensal in the human gut, few strains provide a beneficial effect to humans as probiotics while few are responsible for the nosocomial infection. Comparative genomics of E. faecium can decipher the genomic differences responsible for probiotic, pathogenic and non-pathogenic properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains.

Results

E. faecium 17OM39 was found to be closely related with marketed probiotic strain T110 based on core genome analysis. Strain 17OM39 was devoid of known vancomycin, tetracycline resistance and functional virulence genes. Moreover, E. faecium 17OM39 genome was found to be more stable due to the absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Genes associated with colonization and survival within gastrointestinal tract was also detected across all the strains.

Conclusions

Beyond shared genetic features; this study particularly identified genes that are responsible for imparting probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. Higher genomic stability, absence of known virulence factors and antibiotic resistance genes and close genomic relatedness with marketed probiotics makes E. faecium 17OM39 a potential probiotic candidate. The work presented here demonstrates that comparative genome analyses can be applied to large numbers of genomes, to find potential probiotic candidates.\n\nComparative genome analysis reveals key genetic factors associated with probiotic property in Enterococcus faecium strains.", "token_count": 458, "char_count": 1768, "word_count": 234, "semantic_coherence": 1, "information_density": 0.547, "quality_score": 0.7735, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:39.940851", "source": { "split": "train_shard_00001", "doc_id": 2808 }, "chunk_id": "train_shard_00001_2808_0", "global_id": 9655 }, { "text": "

Background

Biosynthetic gene clusters produce a wide range of metabolites with activities that are of interest to the pharmaceutical industry. Specific interest is shown towards those metabolites that exhibit antimicrobial activities against multidrug-resistant bacteria that have become a global health threat. Genera of the phylum Firmicutes are frequently identified as sources of such metabolites, but the biosynthetic potential of its Virgibacillus genus is not known. Here, we used comparative genomic analysis to determine whether Virgibacillus strains isolated from the Red Sea mangrove mud in Rabigh Harbor Lagoon, Saudi Arabia, may be an attractive source of such novel antimicrobial agents.

Results

A comparative genomics analysis based on Virgibacillus dokdonensis Bac330, Virgibacillus sp. Bac332 and Virgibacillus halodenitrificans Bac324 (isolated from the Red Sea) and six other previously reported Virgibacillus strains was performed. Orthology analysis was used to determine the core genomes as well as the accessory genome of the nine Virgibacillus strains. The analysis shows that the Red Sea strain Virgibacillus sp. Bac332 has the highest number of unique genes and genomic islands compared to other genomes included in this study. Focusing on biosynthetic gene clusters, we show how marine isolates, including those from the Red Sea, are more enriched with nonribosomal peptides compared to the other Virgibacillus species. We also found that most nonribosomal peptide synthases identified in the Virgibacillus strains are part of genomic regions that are potentially horizontally transferred.

Conclusions

The Red Sea Virgibacillus strains have a large number of biosynthetic genes in clusters that are not assigned to known products, indicating significant potential for the discovery of novel bioactive compounds. Also, having more modular synthetase units suggests that these strains are good candidates for experimental characterization of previously identified bioactive compounds as well", "token_count": 506, "char_count": 2038, "word_count": 280, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:40.594696", "source": { "split": "train_shard_00001", "doc_id": 2809 }, "chunk_id": "train_shard_00001_2809_0", "global_id": 9656 }, { "text": "Future efforts will be directed towards establishing the properties of the potentially novel compounds encoded by the Red Sea specific trans-AT PKS/NRPS cluster and the type III PKS/NRPS cluster.\n\nMining biosynthetic gene clusters in Virgibacillus genomes.", "token_count": 62, "char_count": 256, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:40.954502", "source": { "split": "train_shard_00001", "doc_id": 2809 }, "chunk_id": "train_shard_00001_2809_1", "global_id": 9657 }, { "text": "Melioidosis is a bacterial infection caused by Burkholderia pseudomallei (B. pseudomallei), posing a significant threat to public health. Rapid and accurate detection of B. pseudomallei is crucial for preventing and controlling melioidosis. However, identifying B. pseudomallei is challenging due to its high similarity to other species in the same genus. To address this issue, this study proposed a dual-target method that can specifically identify B. pseudomallei in less than 40 min. We analyzed 1722 B. pseudomallei genomes to construct large-scale pan-genomes and selected specific sequence tags in their core genomes that effectively distinguish B. pseudomallei from its closely related species. Specifically, we selected two specific tags, LC1 and LC2, which we combined with the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR associated proteins (Cas12a) system and recombinase polymerase amplification (RPA) pre-amplification. Our analysis showed that the dual-target RPA-CRISPR/Cas12a assay has a sensitivity of approximately 0.2 copies/reaction and 10 fg genomic DNA for LC1, and 2 copies/reaction and 20 fg genomic DNA for LC2. Additionally, our method can accurately and rapidly detect B. pseudomallei in human blood and moist soil samples using the specific sequence tags mentioned above. In conclusion, the dual-target RPA-CRISPR/Cas12a method is a valuable tool for the rapid and accurate identification of B. pseudomallei in clinical and environmental samples, aiding in the prevention and control of melioidosis.\n\nDetection of Burkholderia pseudomallei with CRISPR-Cas12a based on specific sequence tags.", "token_count": 495, "char_count": 1720, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6217, "quality_score": 0.8109, "entities": { "genes": [ "LC1", "LC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:41.599348", "source": { "split": "train_shard_00001", "doc_id": 2810 }, "chunk_id": "train_shard_00001_2810_0", "global_id": 9658 }, { "text": "Vibrio cholerae is a Gram-negative bacterium found in aquatic environments and is the aetiological agent of cholera, characterized by acute watery diarrhoea and severe dehydration. Cholera presents a significant global health burden of an estimated 1.3-5 million annual cases, with the current pandemic caused by a toxigenic lineage of the O1 El Tor biotype called seventh pandemic El Tor (7PET) that is still ongoing. Whilst it is known that non-7PET lineages can cause sporadic disease, little is known about the transmission of these non-epidemic lineages. Thirty-four V. cholerae isolates were obtained from travellers returning from Indonesia to Australia between 2005 and 2017. These were whole genome sequenced, placed into a global phylogenetic context with 883 isolates, and screened for known genes associated with antimicrobial resistance and virulence. This analysis revealed that 30 isolates fell within non-7PET lineages and four within the 7PET lineage. Both 7PET and non-7PET isolates carried genes for resistance to antibiotics that are commonly used in cholera treatment such as tetracyclines and fluoroquinolones. Diverse virulence factors were also present in non-7PET isolates, with two isolates notably carrying toxin-coregulated pilus genes, which are primarily responsible for intestinal colonization in 7PET V. cholerae. This study demonstrates the role of travel in long-range carriage of epidemic and non-epidemic lineages of V. cholerae, and how sentinel travel surveillance can enrich our knowledge of V. cholerae diversity, reveal new biology about the spread of diverse lineages with differing disease potential and illuminate disease presence in endemic regions with limited surveillance data.\n\nSurveillance of travel-associated isolates elucidates the diversity of non-pandemic <i>Vibrio cholerae</i>.", "token_count": 511, "char_count": 1881, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:42.256383", "source": { "split": "train_shard_00001", "doc_id": 2811 }, "chunk_id": "train_shard_00001_2811_0", "global_id": 9659 }, { "text": "Although acute melioidosis is the most common outcome of Burkholderia pseudomallei infection, we have documented a case, P314, where the disease severity lessened with time, and the pathogen evolved towards a commensal relationship with the host. In the current study, we used whole-genome sequencing to monitor this chronic infection to better understand B. pseudomallei persistence in P314’s sputum despite intense and repeated therapeutic regimens. We collected and sequenced 118 B. pseudomallei isolates from P314’s airways over a >16-year period, and also sampled the patient’s home environment, recovering six closely related B. pseudomallei isolates from water. Using comparative genomics, we identified 126 SNPs in the core genome of the 124 isolates or 162 SNPs/indels when the accessory genome was included. The core SNPs were used to construct a phylogenetic tree, which demonstrated a close relationship between environmental and clinical isolates and detailed within-host evolutionary patterns. The phylogeny had little homoplasy, consistent with a single clonal population. Repeated sampling revealed evidence of genetic diversification, but frequent extinctions left only one successful lineage through the first four years and two lineages after that, resulting in a highly linear topology. Although these extinctions and persistence could be explained by genetic drift, we observe phenotypic changes consistent with in situ adaptation. Using a mouse model, P314 isolates caused greatly reduced morbidity and mortality compared to the environmental isolates. Additionally, potentially adaptive phenotypes changed with time and included differences in the O-antigen, capsular polysaccharide, motility, and colony morphology. The >13-year co-existence of two long-lived lineages presents interesting hypotheses that can be tested in future studies to provide additional insights into selective pressures, niche differentiation, and microbial adaptation. This unusual melioidosis case presents a rare example of the evolutionary progression to commensalism by a highly virulent pathogen within a single human host.

Author summary

Pathogens frequently jump between different hosts and associated adaptation may lead to the emergence of new infectious agents", "token_count": 522, "char_count": 2278, "word_count": 315, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:42.917718", "source": { "split": "train_shard_00001", "doc_id": 2812 }, "chunk_id": "train_shard_00001_2812_0", "global_id": 9660 }, { "text": "Such host-jumping evolution is witnessed through endpoint analyses but these cannot capture genetic changes in lineages that have gone extinct. In this study, we have identified and monitored an example of the adaptive evolution of a bacterium often deadly to its mammalian host, in an unprecedented case whereby disease lessened through time and the pathogen adapted to become a part of the commensal human flora. We used genomic analyses to characterize more than 16 years of this evolutionary process and the stepwise mutations that control dictate pathogen interactions with the patient. Soon after infection, mutational changes occurred that allowed the bacterium to remain in the airways without causing disease. This shift towards avirulence was determined based on clinical data and virulence testing in an animal model. In addition, mutations occurred that contributed to the persistence of the bacteria in the patient’s lungs. Finally, we found evidence for the evolutionary emergence and persistence of two distinct lineages of the bacterium over the last 13 years, presenting interesting questions about niche utilization and separation. Bacteria are ubiquitous in the human body and almost all are beneficial or benign. In this study, we document the evolutionary conversion of a normally deadly bacterium into a commensal.\n\nPathogen to commensal: longitudinal within-host population dynamics, evolution, and adaptation during a chronic >16-year Burkholderia pseudomallei infection", "token_count": 325, "char_count": 1501, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:43.479288", "source": { "split": "train_shard_00001", "doc_id": 2812 }, "chunk_id": "train_shard_00001_2812_1", "global_id": 9661 }, { "text": "Recent research has revealed the potential of peptides derived from dairy products preventing cardiovascular disorders, one of the main causes of death worldwide. This review provides an overview of the main cardioprotective effects (assayed in vitro, in vivo, and ex vivo) of bioactive peptides derived from different dairy processing methods (fermentation and enzymatic hydrolysis) and dairy products (yogurt, cheese, and kefir), as well as the beneficial or detrimental effects of the process of gastrointestinal digestion following oral consumption on the biological activities of dairy-derived peptides. The main literature available on the structure-function relationship of dairy bioactive peptides, such as molecular docking and quantitative structure-activity relationships, and their allergenicity and toxicity will also be covered together with the main legislative frameworks governing the commercialization of these compounds. The current products and companies currently commercializing their products as a source of bioactive peptides will also be summarized, emphasizing the main challenges and opportunities for the industrial exploitation of dairy bioactive peptides in the market of functional food and nutraceuticals.\n\nCardioprotective Peptides from Milk Processing and Dairy Products: From Bioactivity to Final Products including Commercialization and Legislation.", "token_count": 292, "char_count": 1385, "word_count": 184, "semantic_coherence": 1, "information_density": 0.5978, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:44.041710", "source": { "split": "train_shard_00001", "doc_id": 2813 }, "chunk_id": "train_shard_00001_2813_0", "global_id": 9662 }, { "text": "

Background

The gut microbiota has been linked to non-communicable diseases, including chronic kidney disease (CKD). However, the relationships between gut microbiome composition changes, uraemic toxins (UTs) accumulation, and diet on CKD severity and progression remain underexplored.

Objective

To characterise relationships between gut microbiome composition and functionality, UTs diet, and CKD severity and progression, as well as assess microbial contributions to UTs accumulation through mice faecal microbiota transplantation (FMT).

Design

This study profiled the gut microbiome of 240 non-dialysis patients with CKD (CKD-REIN cohort) using shotgun metagenomics, with follow-up in 103 patients after 3 years, with comparisons with healthy volunteers from the Milieu Intérieur cohort. A multiomics approach identifies features associated with CKD severity (and progression), with validation in an independent Belgian cohort. Experimental models used FMT to test CKD gut microbiome effects on UTs and kidney fibrosis. Changes in gut microbiome over time were evaluated, and the impact of diet on these changes was assessed.

Results

Compared with matched healthy controls, patients with CKD exhibited gut microbiota alteration, with enrichment of UT precursor-producing species. Patients with severe CKD exhibited higher UT levels and greater enrichment of UT (precursor)-producing species in the microbiota than patients with moderate CKD. Over time, UT (precursor)-producing species increased, and a plant-based low protein diet appeared to mitigate these changes. FMT from patients with CKD to antibiotic-treated CKD model mice increased serum UT levels and exacerbated kidney fibrosis.

Conclusions

This study highlights the role of the microbiome and UTs in CKD, suggesting a potential therapeutic target to slow disease progression.", "token_count": 505, "char_count": 1883, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5796, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:44.694858", "source": { "split": "train_shard_00001", "doc_id": 2814 }, "chunk_id": "train_shard_00001_2814_0", "global_id": 9663 }, { "text": "Toxic microbiome and progression of chronic kidney disease: insights from a longitudinal CKD-Microbiome Study.", "token_count": 30, "char_count": 110, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:45.047106", "source": { "split": "train_shard_00001", "doc_id": 2814 }, "chunk_id": "train_shard_00001_2814_1", "global_id": 9664 }, { "text": "

Aims

This study was aimed to identify yeasts and moulds as well as to detect mycotoxin in corn silages in southern Minas Gerais, Brazil.

Methods and results

Corn silages from 36 farms were sampled to analyse dry matter, crude protein, ether extract, ash, neutral detergent fibre, nonfibre carbohydrates and mycotoxins contents, yeasts and moulds population, pH and temperature values. The mycotoxins found in high frequency were aflatoxin in 77·7% of analysed samples, ochratoxin (33·3%) and zearalenone (22·2%). There was no significant correlation between the mycotoxin concentration and the presence of moulds. The pH was negatively correlated with ochratoxin concentration. Aspergillus fumigatus was identified in all silages that presented growth of moulds. Ten different yeast species were identified using the culture-dependent method: Candida diversa, Candida ethanolica, Candida rugosa, Issatchenkia orientalis, Kluyveromyces marxianus, Pichia manshurica, Pichia membranifaciens, Saccharomyces cerevisiae, Trichosporon asahii and Trichosporon japonicum. Another six different yeast species were identified using the culture-independent method.

Conclusions

A high mycotoxin contamination rate (91·6% of the analysed silages) was observed. The results indicated that conventional culturing and PCR-DGGE should be combined to optimally describe the microbiota associated with corn silage.

Significance and impact of the study

This study provides information about the corn silage fermentation dynamics and our findings are relevant to optimization of this silage fermentation.\n\nOccurrence of mycotoxins and yeasts and moulds identification in corn silages in tropical climate.", "token_count": 475, "char_count": 1711, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6409, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:45.692562", "source": { "split": "train_shard_00001", "doc_id": 2815 }, "chunk_id": "train_shard_00001_2815_0", "global_id": 9665 }, { "text": "Endophytic actinobacteria offer great potential as a source of novel bioactive compounds. In order to investigate the potential for the production of secondary metabolites by endophytes, we recovered a filamentous microorgansism from the tree Antidesma neurocarpum Miq. After phenotypic analysis and whole genome sequencing we demonstrated that this organism, SUK42 was a member of the actinobacterial genus Kitasatospora. This strain has a small genome in comparison with other type strains of this genus and has lost metabolic pathways associated with Stress Response, Nitrogen Metabolism and Secondary Metabolism. Despite this SUK42 can grow well in a laboratory environment and encodes a core genome that is consistent with other members of the genus. Finally, in contrast to other members of Kitasatospora, SUK42 encodes saccharide secondary metabolite biosynthetic gene clusters, one of which with similarity to the acarviostatin cluster, the product of which displays α-amylase inhibitory activity. As extracts of the host plant demonstrate this inhibitory activity, it suggests that the potential medicinal properties of A. neurocarpum Miq might be provided by the endophytic partner and illustrate the potential for exploitation of endophytes for clinical or industrial uses.\n\nAdaptation to Endophytic Lifestyle Through Genome Reduction by Kitasatospora sp. SUK42.", "token_count": 362, "char_count": 1408, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [ "SUK42" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:46.276317", "source": { "split": "train_shard_00001", "doc_id": 2816 }, "chunk_id": "train_shard_00001_2816_0", "global_id": 9666 }, { "text": "Abstract

Background

C. jejuni is the leading cause of bacterial gastroenteritis worldwide. It has been classified as a serious antibiotic resistant threat, causing 13,000 hospitalizations and 120 deaths annually. Our goal was to describe the diversity of clinical C. jejuni using phylogenomics and classify resistance mechanisms.

Methods

Isolates were collected via sentinel surveillance at four hospitals, and demographic and clinical data were obtained. DNA was extracted and sequenced. Raw reads were processed with Trimmomatic and quality checked with FastQC. De novo genome assembly was performed in Spades. Assembled genomes were filtered for quality and completeness; samples of 1.4-2.1MB were annotated in Prokka followed by pangenome and phylogenetic analyses. Multilocus sequence typing loci and virulence and antibiotic resistance genes were extracted from each genome.

Results

Among the 214 C. jejuni isolates recovered, 86 unique sequence types (STs) were identified; five were novel STs with unique allele combinations. ST353 (8.3%: n=18), ST982 (7.4%: n=16), ST50 (5.1 %: n=11) and ST48 (5.1%: n=11) were the most prevalent STs identified, while the majority (50.1%: n=50) of STs were singletons. The pangenome analysis identified 8781, 615, and 1169 total, core, and shell core genes, respectively, which grouped the isolates into three major clades. Most isolates belonged to clade 1. A neighbor-net analysis detected significant recombination among all 86 STs (pairwise homoplasy index p=< 0.00001) and evidence of horizontal gene transfer across clades", "token_count": 461, "char_count": 1598, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7269, "quality_score": 0.8634, "entities": { "genes": [ "ST353", "ST50", "ST48", "ST982" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:46.918953", "source": { "split": "train_shard_00001", "doc_id": 2817 }, "chunk_id": "train_shard_00001_2817_0", "global_id": 9667 }, { "text": "The beta-lactamase gene, blaOXA-605, was the most common resistance gene identified (58.8%: n=125) followed by tet(O) (56.0%: n=121), which mediate resistance to beta-lactams and tetracyclines, respectively. Resistance phenotypes were confirmed using microbroth dilution. Conclusion: Together, these data demonstrate that the C. jejuni population is highly diverse and carries important resistance determinants. The phylogenomic analyses also provide insight into the evolution of this major foodborne pathogen. Future work will focus on identifying molecular and epidemiological factors associated with specific strain types and resistance and virulence profiles circulating in Michigan.

Disclosures

All Authors: No reported disclosures\n\n1199. Phylogenomic analysis of Campylobacter jejuni isolated from gastroenteritis cases in Michigan", "token_count": 216, "char_count": 847, "word_count": 106, "semantic_coherence": 1, "information_density": 0.8491, "quality_score": 0.9245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:47.387177", "source": { "split": "train_shard_00001", "doc_id": 2817 }, "chunk_id": "train_shard_00001_2817_1", "global_id": 9668 }, { "text": "During the 2021 European Food Safety Authority coordinated harmonized monitoring of antimicrobial resistance in Campylobacter species in Slovenia, five Campylobacter-like strains were cultured from caeca of a total of 104 domestic pigs that could not be identified using the standard-prescribed biochemical tests or MALDI-TOF MS. The isolates were obtained using the standard ISO 10272 procedure for the isolation of thermotolerant Campylobacter with prolonged cultivation time. Small Campylobacter-like colonies were observed on mCCDA and CASA agar plates after 2-4 days of incubation; dark-field microscopy revealed relatively big spirilli-shaped bacteria exhibiting characteristic Campylobacter-like motility. The cells were 1.5-3 µm long and 0.5-0.7 µm wide, Gram-negative, oxidase-positive and catalase-positive. MALDI-TOF mass spectra were distinctive and consistent, but with low MALDI-TOF MS log scores and the closest matches being those of Campylobacter hyointestinalis and Campylobacter fetus. All five strains underwent whole-genome sequencing. Analysis of 16S rRNA gene sequences revealed that the isolates were most similar (98.3-98.4 % identity) to Campylobacter lanienae. Pairwise average nucleotide identity (ANI) values revealed that the five studied strains shared pairwise ANI of 96.2-96.5 % but were clearly distinct from the previously described Campylobacter species (ANI ≤72.8 %). The core genome-based phylogeny confirmed that the new strains form a distinct and well-supported clade within the genus Campylobacter", "token_count": 490, "char_count": 1609, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7005, "quality_score": 0.8502, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:48.037590", "source": { "split": "train_shard_00001", "doc_id": 2818 }, "chunk_id": "train_shard_00001_2818_0", "global_id": 9669 }, { "text": "The conducted polyphasic taxonomic analysis confirmed that the five strains represent a novel Campylobacter species for which the name Campylobacter magnus sp. nov. is suggested, with strain 46386T (=DSM 115534T=CCUG 76865T) as the type strain.\n\nCampylobacter magnus sp. nov., isolated from caecal contents of domestic pigs (Sus scrofa domesticus).", "token_count": 148, "char_count": 409, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8776, "quality_score": 0.9388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:48.475590", "source": { "split": "train_shard_00001", "doc_id": 2818 }, "chunk_id": "train_shard_00001_2818_1", "global_id": 9670 }, { "text": "

Background

Candida species are part of the normal human microbiota. However, in recent years, nosocomial bloodstream Candida infections have emerged as a significant problem ranking the fourth common cause of fungemia in intensive care units. Although microdilution methods are the ones recommended for susceptibility testing, they are difficult to undertake in the clinical practice. Thus, an automated commercially available test is ideal.

Aims

To compare minimum inhibitory concentrations (MICs) obtained with the recently introduced Vitek 2 yeast susceptibility system card (AST-YS01) with Etest.

Methods

263 clinical Candida isolates representing six species were included in the study. Categorical agreements (CA) were assessed as described elsewhere.

Results

Irrespective of the Candida species tested, the overall CA between Vitek 2 and Etest ranged between 66.7% and 100%. In general, Etest yielded lower MICs than Vitek 2. For Candida albicans, the CA between Vitek 2 and Etest was >95% for amphotericin B, voriconazole and flucytosine, but only 89% for fluconazole. With respect to Candida glabrata, the CA was between 97% and 100%. The major errors were with Candida krusei and flucytosine and Candida kefyr and amphotericin B. Candida tropicalis susceptibility for fluconazole by Vitek 2 reported more SDD and resistant strains than Etest. Candida parapsilosis showed 100% CA against all the four antifungals tested. No very major errors were detected between the two methods.

Conclusions

Vitek 2 provided comparable results to Etest with quick turnaround for the testing of Candida species susceptibilities.\n\nComparison of the VITEK 2 antifungal susceptibility system with Etest using clinical isolates of Candida species.", "token_count": 485, "char_count": 1772, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [ "YS01" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:49.124324", "source": { "split": "train_shard_00001", "doc_id": 2819 }, "chunk_id": "train_shard_00001_2819_0", "global_id": 9671 }, { "text": "Kluyveromyces marxianus has a high potential for industrial production of aroma compounds, such as 2-phenylethanol, which is derived in a bioconversion from L-phenylalanine. In the present work the product yield of K. marxianus in batch cultivation was estimated as 0.65 mol 2-phenylethanol/mol L-phenylalanine and thus significantly below the theoretical optimum of 1 mol/mol. By a comprehensive approach of stoichiometric balancing and GC-MS analysis of various substrates and products of K. marxianus a detailed insight into its metabolism was gained. For this purpose ring-labelled ((13)C(6)) L-phenylalanine and naturally labelled glucose were applied as substrates in tracer studies in batch culture. The produced aroma compounds 2-phenylethanol and 2-phenylethylacetate stem exclusively from the supplied L-phenylalanine, whereas glucose was not converted into these products because of efficient feed-back inhibition of prephenate dehydratase in the L-phenylalanine biosynthetic pathway. It could be further shown that the supplied L-phenylalanine completely covers the anabolic cellular demand for this amino acid. Quantification of (13)CO(2) in the exhaust gas provided clear evidence for catabolic breakdown of L-phenylalanine during cultivation. Metabolic balancing around the pool of free intracellular L-phenylalanine revealed a significant loss of L-phenylalanine into catabolic and anabolic pathways. While 73.3% of L-phenylalanine was converted into 2-phenylethanol or 2-phenylethylacetate, 22.4% was catabolized through the cinnamate pathway and 4.3% was directed towards protein biosynthesis. Catabolic breakdown of L-phenylalanine via hydroxylation to L-tyrosine could be excluded. In addition to an insight into metabolic functioning and regulation of 2-phenylethanol-producing K", "token_count": 519, "char_count": 1800, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:49.811742", "source": { "split": "train_shard_00001", "doc_id": 2820 }, "chunk_id": "train_shard_00001_2820_0", "global_id": 9672 }, { "text": "marxianus, the approach presented here provides important information on potential targets for genetic optimization of 2-phenylethanol-producing yeasts.\n\nMetabolic physiology of aroma-producing Kluyveromyces marxianus.", "token_count": 57, "char_count": 218, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:50.180685", "source": { "split": "train_shard_00001", "doc_id": 2820 }, "chunk_id": "train_shard_00001_2820_1", "global_id": 9673 }, { "text": "Bacterial spot disease caused by Xanthomonas spp. is a global threat to tomato and pepper plants. A recent classification of these pathogens indicated the need for a diverse dataset of whole-genome resources. We report whole-genome resources of 89 Xanthomonas strains isolated from Canada (n = 44), the United States (n = 29), Argentina (n = 4), Brazil (n = 3), Costa Rica (n = 3), New Zealand (n = 1), Australia (n = 1), Mexico (n = 1), Taiwan (n = 1), Thailand (n = 1), and unknown (n = 1). Of these strains, 48 were previously identified to species-level based on nongenome-based approaches while 41 strains were classified only at the genus level. The average coverage of the sequencing reads was 103×. The draft genome sizes ranged from 4.53 to 5.46 Mbp with a G + C content of 63.53 to 67.78% and comprised 4,233-5,178 protein-coding sequences. Using average nucleotide identity (ANI) and genome-based DNA-DNA hybridization (gDDH) values, the taxonomic classifications were validated for 38 of the 48 strains previously assigned to species level using other methods. Ten strains previously identified as Xanthomonas campestris, X. axonopodis, X. vasicola, and X. arboricola were incorrectly assigned, and new species-level delineations are proposed. Data from ANI, gDDH, and pangenome phylogeny of shared protein families were used to assign the 41 strains, previously identified only to genus level, into five distinct species: X", "token_count": 523, "char_count": 1558, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:29:50.821786", "source": { "split": "train_shard_00001", "doc_id": 2821 }, "chunk_id": "train_shard_00001_2821_0", "global_id": 9674 }, { "text": "euvesicatoria (pv. euvesicatoria or pv. perforans), X. hortorum pv. gardneri, X. vesicatoria, X. campestris, and X. arboricola. These 89 whole-genome sequences of Xanthomonas strains, the majority (49.4%) of which are from Canada, could be useful resources in our understanding of the global population structure and evolution of these pathogens.\n\nWhole-Genome Resources and Species-Level Taxonomic Validation of 89 Plant-Pathogenic Xanthomonas Strains Isolated from Various Host Plants.", "token_count": 200, "char_count": 554, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7385, "quality_score": 0.8692, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:51.315145", "source": { "split": "train_shard_00001", "doc_id": 2821 }, "chunk_id": "train_shard_00001_2821_1", "global_id": 9675 }, { "text": "The search for lactose-fermenting yeast strains has been conducted among 162 strains isolated from various plants and 28 yeast strains isolated from cheese. Four yeast strains have been shown to ferment lactose. They have been identified as Candida kefyr. Specific beta-galactosidase activity of the studied strains grown on lactose-containing medium was 1501-2113 U/g cell. The ethanol production by strains C. kefyr C24 and C30 was significantly inhibited by the increase in substrate concentration (100 g/l).\n\n[Isolation and characterization of lactose-fermenting yeasts Candida kefyr].", "token_count": 168, "char_count": 589, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7349, "quality_score": 0.8675, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:51.778279", "source": { "split": "train_shard_00001", "doc_id": 2822 }, "chunk_id": "train_shard_00001_2822_0", "global_id": 9676 }, { "text": "Vibrio anguillarum is the causative agent of vibriosis in many species important to aquaculture. We generated whole genome sequence (WGS) data on a diverse collection of 64 V. anguillarum strains, which we supplemented with 41 publicly available genomes to produce a combined dataset of 105 strains. These WGS data resolved six major lineages (L1-L6), and the additional use of multilocus sequence analysis (MLSA) clarified the association of L1 with serotype O1 and Salmonidae hosts (salmon/trout), and L2 with serotypes O2a/O2b/O2c and Gadidae hosts (cod). Our analysis also revealed a large-scale homologous replacement of 526-kb of core genome in an L2 strain from a con-specific donor. Although the strains affected by this recombination event are exclusively associated with Gadidae, we find no clear genetic evidence that it has played a causal role in host specialism. Whilst it is established that Vibrio species freely recombine, to our knowledge this is the first report of a contiguous recombinational replacement of this magnitude in any Vibrio genome. We also note a smaller accessory region of high single nucleotide polymorphism (SNP) density and gene content variation that contains lipopolysaccharide biosynthesis genes which may play a role in determining serotype.\n\nA Hopeful Sea-Monster: A Very Large Homologous Recombination Event Impacting the Core Genome of the Marine Pathogen Vibrio anguillarum.", "token_count": 416, "char_count": 1477, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6808, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:52.397751", "source": { "split": "train_shard_00001", "doc_id": 2823 }, "chunk_id": "train_shard_00001_2823_0", "global_id": 9677 }, { "text": "Pseudomonas syringae is a heterogeneous species complex of plant pathogenic bacteria associated with a wide distribution of plant species. Advances in genomics are revealing the complex evolutionary history of this species complex and the wide array of genetic adaptations underpinning their diverse lifestyles. Here, we genomically characterize two P. syringae isolates collected from diseased Callery pears ( Pyrus calleryana ) in Berkeley, California in 2019 and 2022. We also isolated a lytic bacteriophage, which we characterized and evaluated for biocontrol efficiency. Using a multilocus sequence analysis and core genome alignment, we classified the P. syringae isolates as members of phylogroup two, related to other strains previously isolated from Pyrus and Prunus . An analysis of effector proteins demonstrated an evolutionary conservation of effectoromes across isolates classified in PG2, and yet uncovered unique effector profiles for each, including the two newly identified isolates. Whole genome sequencing of the associated phage uncovered a novel phage genus related to Psa phage PHB09 and the Flaundravirus genus. Finally, using in planta infection assays, we demonstrate that the phage was equally useful in symptom mitigation of immature pear fruit regardless of the Pss strain tested. Overall, this study demonstrates the diversity of P. syringae and their viruses associated with ornamental pear trees, posing spill-over risks to commercial pear trees and the possibility of using phages as biocontrol agents to reduce the impact of disease.\n\nGenomic characterization ofPseudomonas syringaepv.syringaefrom Callery pear and the efficiency of associated phages in disease protection", "token_count": 400, "char_count": 1720, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6189, "quality_score": 0.8094, "entities": { "genes": [ "PG2", "PHB09" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:53.010770", "source": { "split": "train_shard_00001", "doc_id": 2824 }, "chunk_id": "train_shard_00001_2824_0", "global_id": 9678 }, { "text": "The accessory genome of many pathogenic bacteria includes ABC transporters that scavenge metal by siderophore uptake and ABC transporters that contribute to antimicrobial resistance by multidrug efflux. There are mechanistic and recently recognised structural similarities between siderophore importer proteins and efflux pumps. Here we investigated the influence of siderophore importer YbtPQ on antimicrobial resistance of Klebsiella pneumoniae . YbtPQ is encoded in the yersiniabactin cluster in a prevalent mobile genetic element ICEKp, and is also common in pathogenicity islands of Escherichia coli and Yersinia species, where yersiniabactin enhances virulence. Deletion of ICEKp increased the sensitivity of K. pneumoniae to all antimicrobials tested. The mechanism was dependent on the yersiniabactin importer YbtPQ and involved antimicrobial efflux, since it was affected by the inhibitor reserpine. The element ICEKp is naturally highly mobile, indeed the accessory genome of K. pneumoniae is recognised as a reservoir of genes for the emergence of hospital outbreak strains and for transfer to other Gram-negative pathogens. Introduction of ICEKp, or a plasmid encoding YbtPQ, to E. coli decreased its sensitivity to a broad range of antimicrobials. Thus, a confirmed siderophore importer, on a rapidly evolving and highly mobile element capable of interspecies transfer, may have a secondary function exporting antimicrobials.\n\nA virulence associated siderophore importer causes antimicrobial efflux inKlebsiella pneumoniae", "token_count": 412, "char_count": 1542, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:53.627493", "source": { "split": "train_shard_00001", "doc_id": 2825 }, "chunk_id": "train_shard_00001_2825_0", "global_id": 9679 }, { "text": "Histone deacetylase activity plays an important role in transcriptional repression. Botrytis cinerea is an important necrotrophic fungal pathogen distributed worldwide and parasites a wide range of hosts. However, the molecular mechanisms of how B. cinerea regulates growth and host infection remain largely unknown. Here, the function of BcRPD3, a histone deacetylase of B. cinerea, was investigated. Overexpression of the BcRPD3 gene resulted in significantly decreased acetylation levels of histone H3 and H4. The BcRPD3 overexpression strains showed slightly delayed vegetative growth, dramatically impaired infection structure formation, oxidative stress response, and virulence. RNA-Seq analysis revealed that enzymatic activity related genes, including 9 genes reported to function as virulence factors, were downregulated in BcRPD3 overexpression strain. Chromatin immunoprecipitation followed by qPCR confirmed the enrichment of BcRPD3 and H3Kac at the promoter regions of these nine genes. These observations indicated that BcRPD3 regulated the transcription of enzymatic activity related genes by controlling the acetylation level of histones, thereby affecting the vegetative growth, infection structure formation, oxidative stress response, and virulence of B. cinerea.\n\nBcRPD3-Mediated Histone Deacetylation Is Involved in Growth and Pathogenicity of Botrytis cinerea.", "token_count": 387, "char_count": 1438, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6319, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:54.246238", "source": { "split": "train_shard_00001", "doc_id": 2826 }, "chunk_id": "train_shard_00001_2826_0", "global_id": 9680 }, { "text": "Cells of Kluyveromyces marxianus FII 510700 and Saccharomyces cerevisiae CBS 1907 were autolysed in phosphate buffer, pH 4.5, for a maximum of 10 days to compare chemical changes that occur in the carbohydrate, protein, amino acid and nucleic acid content. Approximately 2.2-3% carbohydrate, 9.5-12% protein, 0.6-1.0% DNA and 6-7% RNA were recovered in the autolysates. The main amino acids were beta-alanine, phenylalanine, cysteine, methionine, glutamic acid and isoleucine. No significant differences in the yeast autolysates of K. marxianus and S. cerevisiae were observed. Consequently, K. marxianus produced from lactose-based media has potential as a source of yeast autolysates used in the food industry.\n\nEvaluation of Kluyveromyces marxianus as a source of yeast autolysates.", "token_count": 266, "char_count": 785, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:54.800462", "source": { "split": "train_shard_00001", "doc_id": 2827 }, "chunk_id": "train_shard_00001_2827_0", "global_id": 9681 }, { "text": "

Background

A recent study from Taiwan suggested that Clostridium innocuum may be an unrecognized cause of antibiotic-associated diarrhea (AAD) and clinically indistinguishable from Clostridioides difficile infection. Our objective was to compare C. innocuum prevalence and strain between those with AAD and asymptomatic controls.

Methods

In this cross-sectional study, we collected stool from 200 individuals with AAD and 100 asymptomatic controls. We evaluated the association between AAD and C. innocuum in stool using anaerobic culture and quantitative polymerase chain reaction (qPCR). To identify strain-specific associations with AAD, we performed whole-genome sequencing of C. innocuum isolates using Illumina MiSeq and constructed comparative genomics analyses.

Results

C. innocuum was isolated from stool of 126/300 (42%) subjects and more frequently from asymptomatic controls than AAD subjects (50/100 [50%] vs 76/200 [38%], respectively; P = .047). C. innocuum isolation frequency was not associated with AAD in either the adult or pediatric subgroups. C. innocuum and C. difficile were frequently co-prevalent in individuals with and without diarrhea. There were no phylogenetic differences or accessory genome associations between C. innocuum isolates from AAD subjects and asymptomatic controls.

Conclusions

C. innocuum was frequently isolated and at a greater frequency in asymptomatic controls than those with AAD. We did not identify strain lineages or accessory genomic elements associated with AAD. These data highlight that differentiating C. innocuum-associated diarrhea from asymptomatic colonization, and differentiating diarrhea caused by C. difficile from C. innocuum, are clinical microbiology challenges that require additional investigation to identify host-specific factors and/or biomarkers that distinguish these conditions.", "token_count": 485, "char_count": 1885, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:55.444709", "source": { "split": "train_shard_00001", "doc_id": 2828 }, "chunk_id": "train_shard_00001_2828_0", "global_id": 9682 }, { "text": "Association Between Clostridium innocuum and Antibiotic-Associated Diarrhea in Adults and Children: A Cross-sectional Study and Comparative Genomics Analysis.", "token_count": 40, "char_count": 158, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:55.804953", "source": { "split": "train_shard_00001", "doc_id": 2828 }, "chunk_id": "train_shard_00001_2828_1", "global_id": 9683 }, { "text": "Segatella is a prevalent genus within individuals' gut microbiomes worldwide, especially in non-Western populations. Although metagenomic assembly and genome isolation have shed light on its genetic diversity, the lack of available isolates from this genus has resulted in a limited understanding of how members' genetic diversity translates into phenotypic diversity. Within the confines of a single gut microbiome, we have isolated 63 strains from diverse lineages of Segatella. We performed comparative analyses that exposed differences in cellular morphologies, preferences in polysaccharide utilization, yield of short-chain fatty acids, and antibiotic resistance across isolates. We further show that exposure to Segatella isolates either evokes strong or muted transcriptional responses in human intestinal epithelial cells. Our study exposes large phenotypic differences within related Segatella isolates, extending this to host-microbe interactions.\n\nSegatella clades adopt distinct roles within a single individual's gut.", "token_count": 224, "char_count": 1031, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7591, "quality_score": 0.8796, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:56.274320", "source": { "split": "train_shard_00001", "doc_id": 2829 }, "chunk_id": "train_shard_00001_2829_0", "global_id": 9684 }, { "text": "

Aims

To identify the yeast and bacteria present in the mezcal fermentation from Agave salmiana.

Methods and results

The restriction and sequence analysis of the amplified region, between 18S and 28S rDNA and 16S rDNA genes, were used for the identification of yeast and bacteria, respectively. Eleven different micro-organisms were identified in the mezcal fermentation. Three of them were the following yeast: Clavispora lusitaniae, Pichia fermentans and Kluyveromyces marxianus. The bacteria found were Zymomonas mobilis subsp. mobilis and Zymomonas mobilis subsp. pomaceae, Weissella cibaria, Weissella paramesenteroides, Lactobacillus pontis, Lactobacillus kefiri, Lactobacillus plantarum and Lactobacillus farraginis.

Conclusions

The phylogenetic analysis of 16S rDNA and ITS sequences showed that microbial diversity present in mezcal is dominated by bacteria, mainly lactic acid bacteria species and Zymomonas mobilis. Pichia fermentans and K. marxianus could be micro-organisms with high potential for the production of some volatile compounds in mezcal.

Significance and impact of the study

We identified the community of bacteria and yeast present in mezcal fermentation from Agave salmiana.\n\nIdentification of yeast and bacteria involved in the mezcal fermentation of Agave salmiana.", "token_count": 385, "char_count": 1323, "word_count": 171, "semantic_coherence": 1, "information_density": 0.538, "quality_score": 0.769, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:56.899570", "source": { "split": "train_shard_00001", "doc_id": 2830 }, "chunk_id": "train_shard_00001_2830_0", "global_id": 9685 }, { "text": "The human microbiome exhibits intricate populations across the body, with the vaginal tract serving as an ecosystem characterized by the prevalence of the genus Lactobacillus. Disruptions in the vaginal microbiota, which are frequently linked to variables such as sexual activity, hormonal fluctuations, and excessive use of antibiotics, can result in vaginal dysbiosis and the development of diseases such as bacterial vaginosis (BV) and candidiasis. Lactobacillus species, owing to their capacity to create an acidic environment through the production of lactic acid, have a key function within this complex microbial community: they inhibit the growth of harmful microorganisms. This study aimed to investigate the genomic characteristics of L. rhamnosus LR6, a newly discovered strain isolated from the vaginal microbiota of 20 healthy women to assess its potential as a vaginal probiotic. We performed a comparative investigation of the genetic traits of L. rhamnosus using 45 publicly available genomes from various sources. We evaluated the genetic characteristics related to carbohydrate utilization, adhesion to host cells, and the presence of bacteriocin clusters. A comprehensive study was conducted by integrating in silico evaluations with experimental techniques to authenticate the physiological characteristics of strain LR6. We further used a rat model to assess the impact of L. rhamnosus LR6 administration on the changes in the gastrointestinal tract and the vaginal microbiome. The assessments revealed a significantly high inhibitory activity against pathogens, enhanced adherence to host cells, and high lactic acid production. Rat experiments revealed changes in both the fecal and vaginal microbiota; in treated rats, Firmicutes increased in both; Lactobacillaceae increased in the fecal samples; and Enterobacteriaceae decreased but Enterococcaceae, Streptococcaceae, and Morganellaceae increased in the vaginal samples", "token_count": 506, "char_count": 2029, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [ "LR6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:57.558900", "source": { "split": "train_shard_00001", "doc_id": 2831 }, "chunk_id": "train_shard_00001_2831_0", "global_id": 9686 }, { "text": "The study results provide evidence of the genetic characteristics and probiotic properties of LR6, and suggest that oral administration of L. rhamnosus LR6 can alter both gut and vaginal microbiome. Collectively, these findings establish L. rhamnosus LR6 as a highly promising candidate for improving vaginal health.\n\nCharacterization of the probiotic properties of Lacticaseibacillus rhamnosus LR6 isolated from the vaginas of healthy Korean women against vaginal pathogens.", "token_count": 130, "char_count": 496, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7121, "quality_score": 0.8561, "entities": { "genes": [ "LR6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:57.977237", "source": { "split": "train_shard_00001", "doc_id": 2831 }, "chunk_id": "train_shard_00001_2831_1", "global_id": 9687 }, { "text": "Whole-genome sequencing (WGS) is a highly sensitive method for identifying genetic relatedness and transmission of Clostridioides difficile strains. Previous studies suggest that as few as 3 core genome single-nucleotide variants (SNVs) discriminate between genetically distinct isolates. Because a single C. difficile colony is selected from culture for WGS, significant within-host genetic diversity could preclude identification of transmission events. To evaluate the likelihood of missed transmission events using WGS of single colonies from culture, we examined within-host genetic diversity among C. difficile isolates collected from children. We performed WGS using an Illumina MiSeq instrument on 8 C. difficile colonies randomly selected from each culture performed on stool collected from 10 children (8 children diagnosed with C. difficile infection and 2 children with asymptomatic carriage); 77/80 (96%) isolate sequences were successfully assembled. Among 8/10 (80%) children, all isolates were the same sequence type (ST). The other 2 children each had mixed infection with two STs, although one ST predominated. Among 9/10 (90%) children, isotypic isolates differed by ≤2 SNVs; an isotypic isolate in the remaining child differed by 3 to SNVs relative to the other isolates from that child. Overall, among the 77 isolates collected from 10 stool cultures, 74/77 (96%) were clonal (i.e., same ST and ≤2 core genome SNVs) to other isolates in stool culture. In summary, we identified rare C. difficile within-host genetic diversity in children, suggesting that WGS of a single colony from stool is likely to appropriately characterize isolate clonality and putative transmission events in the majority of cases.\n\nClostridioides difficile Whole-Genome Sequencing Reveals Limited Within-Host Genetic Diversity in a Pediatric Cohort.", "token_count": 505, "char_count": 1887, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5547, "quality_score": 0.7774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:58.626210", "source": { "split": "train_shard_00001", "doc_id": 2832 }, "chunk_id": "train_shard_00001_2832_0", "global_id": 9688 }, { "text": "

Background

Though detection of transmission clusters of methicillin-resistant Staphylococcus aureus (MRSA) infections is a priority for infection control personnel in hospitals, the transmission dynamics of MRSA among hospitalized patients with bloodstream infections (BSIs) has not been thoroughly studied. Whole genome sequencing (WGS) of MRSA isolates for surveillance is valuable for detecting outbreaks in hospitals, but the bioinformatic approaches used are diverse and difficult to compare.

Methods

We combined short-read WGS with genotypic, phenotypic, and epidemiological characteristics of 106 MRSA BSI isolates collected for routine microbiological diagnosis from inpatients in two hospitals over 12 months. Clinical data and hospitalization history were abstracted from electronic medical records. We compared three genome sequence alignment strategies to assess similarity in cluster ascertainment. We conducted logistic regression to measure the probability of predicting prior hospital overlap between clustered patient isolates by the genetic distance of their isolates.

Results

While the three alignment approaches detected similar results, they showed some variation. A pangenome-based alignment method was most consistent across MRSA clonal complexes. We identified nine unique clusters of closely-related BSI isolates. Most BSI were healthcare-associated and community-onset. Our logistic model showed that with 13 single nucleotide polymorphisms the likelihood that any two patients in a cluster overlapped in a hospital was 50 percent.

Conclusions

Multiple clusters of closely related MRSA isolates can be identified using WGS among strains cultured from BSI in two hospitals. Genomic clustering of these infections suggest that transmission resulted from a mix of community spread and healthcare exposures long before BSI diagnosis.

Summary

Multiple clusters of closely related MRSA bloodstream infections were identified using WGS in two hospitals using three bioinformatic workflows. Genomic epidemiology suggests that transmission resulted from a mix of community spread and healthcare exposures long before symptom onset.", "token_count": 483, "char_count": 2193, "word_count": 289, "semantic_coherence": 1, "information_density": 0.6021, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:59.279277", "source": { "split": "train_shard_00001", "doc_id": 2833 }, "chunk_id": "train_shard_00001_2833_0", "global_id": 9689 }, { "text": "Unsuspected clonal spread of Methicillin-resistant Staphylococcus aureus causing bloodstream infections in hospitalized adults detected using whole genome sequencing", "token_count": 47, "char_count": 172, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:29:59.636624", "source": { "split": "train_shard_00001", "doc_id": 2833 }, "chunk_id": "train_shard_00001_2833_1", "global_id": 9690 }, { "text": "The antagonistic effect against Salmonella spp. and the immunomodulatory capacity of whey fermented with kefir grains and with three strains isolated from them – Lactobacillus plantarum CIDCA 8327, Lactobacillus kefiri CIDCA 8348 and Kluyveromyces marxianus var. marxianus CIDCA 8154 – were evaluated. Both fermented products interfered with the capacity of Salmonella spp. to associate and invade Caco‐2/TC7 cells and reduced up to the basal level the expression of the CCL20 in response to a pro‐inflammatory stimulus on Caco‐2 CCL20:luc cells. The products with potential application as probiotics obtained by fermentation of whey with kefir micro‐organisms represent an alternative to increase whey economic value.\n\nCheese whey fermented with kefir micro‐organisms: Antagonism against Salmonella and immunomodulatory capacity", "token_count": 246, "char_count": 829, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6348, "quality_score": 0.8174, "entities": { "genes": [ "TC7", "CCL20" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:00.122086", "source": { "split": "train_shard_00001", "doc_id": 2834 }, "chunk_id": "train_shard_00001_2834_0", "global_id": 9691 }, { "text": "

ABSTRACT

Soybean is one of the most important legume crops worldwide. However, soybean yield is dramatically affected by fungal diseases, leading to economic losses of billions of dollars yearly. Here, we integrated publicly available genome-wide association studies and transcriptomic data to prioritize candidate genes associated with resistance to Cadophora gregata, Fusarium graminearum, Fusarium virguliforme, Macrophomina phaseolina , and Phakopsora pachyrhizi . We identified 188, 56, 11, 8, and 3 high-confidence candidates for resistance to F. virguliforme, F. graminearum, C. gregata, M. phaseolina and P. pachyrhizi , respectively. The prioritized candidate genes are highly conserved in the pangenome of cultivated soybeans and are heavily biased towards fungal species-specific defense response. The vast majority of the prioritized candidate resistance genes are related to plant immunity processes, such as recognition, signaling, oxidative stress, systemic acquired resistance, and physical defense. Based on the number of resistance alleles, we selected the five most resistant accessions against each fungal species in the soybean USDA germplasm. Interestingly, the most resistant accessions do not reach the maximum theoretical resistance potential. Hence, they can be further improved to increase resistance in breeding programs or through genetic engineering. Finally, the coexpression network generated here is available in a user-friendly web application ( https://soyfungigcn.venanciogroup.uenf.br/ ) and an R/Shiny package ( https://github.com/almeidasilvaf/SoyFungiGCN ) that serve as a public resource to explore soybean-pathogenic fungi interactions at the transcriptional level.\n\nIntegration of genome-wide association studies and gene coexpression networks unveils promising soybean resistance genes against five common fungal pathogens", "token_count": 459, "char_count": 1875, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6735, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:00.767575", "source": { "split": "train_shard_00001", "doc_id": 2835 }, "chunk_id": "train_shard_00001_2835_0", "global_id": 9692 }, { "text": "The Methylocystis and Methylosinus are two of the five genera that were included in the first taxonomic framework of methanotrophic bacteria created half a century ago. Members of both genera are widely distributed in various environments and play a key role in reducing methane fluxes from soils and wetlands. The original separation of these methanotrophs in two distinct genera was based mainly on their differences in cell morphology. Further comparative studies that explored various single-gene-based phylogenies suggested the monophyletic nature of each of these genera. Current availability of genome sequences from members of the Methylocystis/ Methylosinus clade opens the possibility for in-depth comparison of the genomic potentials of these methanotrophs. Here, we report the finished genome sequence of Methylocystis heyeri H2T and compare it to 23 currently available genomes of Methylocystis and Methylosinus species. The phylogenomic analysis confirmed that members of these genera form two separate clades. The Methylocystis/Methylosinus pan-genome core comprised 1,173 genes, with the accessory genome containing 4,941 and 11,192 genes in the shell and the cloud, respectively. Major differences between the genome-encoded environmental traits of these methanotrophs include a variety of enzymes for methane oxidation and dinitrogen fixation as well as genomic determinants for cell motility and photosynthesis.\n\nPan-Genome-Based Analysis as a Framework for Demarcating Two Closely Related Methanotroph Genera Methylocystis and Methylosinus.", "token_count": 473, "char_count": 1648, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6204, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:01.415223", "source": { "split": "train_shard_00001", "doc_id": 2836 }, "chunk_id": "train_shard_00001_2836_0", "global_id": 9693 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) causes high frequencies of foodborne infections worldwide and has been linked to numerous outbreaks each year. Pulsed-field gel electrophoresis (PFGE) has been the gold standard for surveillance until the recent transition to whole-genome sequencing (WGS). To further understand the genetic diversity and relatedness of outbreak isolates, a retrospective analysis of 510 clinical STEC isolates was conducted. Among the 34 STEC serogroups represented, most (59.6%) belonged to the predominant six non-O157 serogroups. Core genome single nucleotide polymorphism (SNP) analysis differentiated clusters of isolates with similar PFGE patterns and multilocus sequence types (STs). One serogroup O26 outbreak strain and another non-typeable (NT) strain, for instance, were identical by PFGE and clustered together by MLST; however, both were distantly related in the SNP analysis. In contrast, six outbreak-associated serogroup O5 strains clustered with five ST-175 serogroup O5 isolates, which were not part of the same outbreak as determined by PFGE. The use of high-quality SNP analyses enhanced the discrimination of these O5 outbreak strains into a single cluster. In all, this study demonstrates how public health laboratories can more rapidly use WGS and phylogenetics to identify related strains during outbreak investigations while simultaneously uncovering important genetic attributes that can inform treatment practices.\n\nWhole-Genome Sequencing of Shiga Toxin-Producing Escherichia coli for Characterization and Outbreak Investigation.", "token_count": 398, "char_count": 1601, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6898, "quality_score": 0.8449, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:02.087879", "source": { "split": "train_shard_00001", "doc_id": 2837 }, "chunk_id": "train_shard_00001_2837_0", "global_id": 9694 }, { "text": "Invasive Haemophilus influenzae (Hi) disease has decreased in countries that included Hi type b (Hib) vaccination in their childhood immunization programs in the 1990s. Non-typeable (NT) and non-b strains are now the leading causes of invasive Hi disease in Europe, with most cases reported in young children and the elderly. Concerningly, no vaccines toward such strains are available and beta-lactam resistance is increasing. We describe the epidemiology of invasive Hi disease reported to the Norwegian Surveillance System for Communicable Diseases (MSIS) (2017-2021, n = 407). Whole-genome sequencing (WGS) was performed on 245 isolates. We investigated the molecular epidemiology (core genome phylogeny) and the presence of antibiotic resistance markers (including chromosomal mutations associated with beta-lactam or quinolone resistance). For isolates characterized with both WGS and phenotypic antibiotic susceptibility testing (AST) (n = 113) we assessed correlation between resistance markers and susceptibility categorization by calculation of sensitivity, specificity, and predictive values. Incidence rates of invasive Hi disease in Norway ranged from 0.7 to 2.3 per 100,000 inhabitants/year (mean 1.5 per 100,000) and declined during the COVID-19 pandemic. The bacterial population consisted of two major phylogenetic groups with subclustering by serotype and multi-locus sequence type (ST). NTHi accounted for 71.8% (176). The distribution of STs was in line with previous European reports. We identified 13 clusters, including four encapsulated and three previously described international NTHi clones with bla TEM-1 (ST103) or altered PBP3 (rPBP3) (ST14/IIA and ST367/IIA)", "token_count": 495, "char_count": 1728, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7094, "quality_score": 0.8547, "entities": { "genes": [ "ST103", "PBP3", "ST367", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:02.761118", "source": { "split": "train_shard_00001", "doc_id": 2838 }, "chunk_id": "train_shard_00001_2838_0", "global_id": 9695 }, { "text": "Resistance markers were detected in 25.3% (62/245) of the isolates, with bla TEM-1 (31, 50.0%) and rPBP3 (28, 45.2%) being the most frequent. All isolates categorized as resistant to aminopenicillins, tetracycline or chloramphenicol possessed relevant resistance markers, and the absence of relevant substitutions in PBP3 and GyrA/ParC predicted susceptibility to cefotaxime, ceftriaxone, meropenem and quinolones. Among the 132 WGS-only isolates, one isolate had PBP3 substitutions associated with resistance to third-generation cephalosporins, and one isolate had GyrA/ParC alterations associated with quinolone resistance. The detection of international virulent and resistant NTHi clones underlines the need for a global molecular surveillance system. WGS is a useful supplement to AST and should be performed on all invasive isolates.\n\nMolecular epidemiology and antibiotic resistance profiles of invasive Haemophilus influenzae from Norway 2017-2021.", "token_count": 300, "char_count": 981, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [ "PBP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:03.357357", "source": { "split": "train_shard_00001", "doc_id": 2838 }, "chunk_id": "train_shard_00001_2838_1", "global_id": 9696 }, { "text": "Deproteinized sweet and sour cheese whey concentrates were investigated for their suitability as substrates for the production of single-cell protein with Kluyveromyces marxianus CBS 6556 up to a 100-l scale. An important factor for gaining high cell concentrations was the use of the Crabtree-negative strain K. marxianus CBS 6556. Supplements such as trace elements, ammonium and calcium were required for the complete conversion of sweet whey concentrates into biomass, whereas sour whey concentrates had to be supplemented with ammonium, trace elements and vitamins. After improvement, biomass dry concentrations of up to 50 g l-1 could be reached with Yx/s values of 0.52 for sweet whey and of up to 65 g l-1 with Yx/s values of 0.48 for sour whey concentrates. The chemical oxygen demand of the whey concentrates were reduced by 80%. The cells were used for the analysis of amino acid and ash composition, showing a distinct increase of eight out of ten essential amino acids compared to sweet and sour whey protein and exceeding the World Health Organisation guidelines for valine, leucine, isoleucine, threonine, phenylalanine and tyrosine.\n\nMicrobial production of single-cell protein from deproteinized whey concentrates.", "token_count": 324, "char_count": 1231, "word_count": 189, "semantic_coherence": 1, "information_density": 0.582, "quality_score": 0.791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:03.939140", "source": { "split": "train_shard_00001", "doc_id": 2839 }, "chunk_id": "train_shard_00001_2839_0", "global_id": 9697 }, { "text": "Stenotrophomonas maltophilia has been recognized as an emerging multi-drug resistant opportunistic pathogen in cystic fibrosis (CF) patients. We report a comparative genomic and phenotypic analysis of 91 S. maltophilia strains from 10 CF patients over a 12-year period. Draft genome analyses included in silico Multi-Locus Sequence Typing (MLST), Single-Nucleotide Polymorphisms (SNPs), and pangenome characterization. Growth rate, biofilm formation, motility, mutation frequency, in vivo virulence, and in vitro antibiotic susceptibility were determined and compared with population structure over time. The population consisted of 20 different sequence types (STs), 11 of which are new ones. Pangenome and SNPs data showed that this population is composed of three major phylogenetic lineages. All patients were colonized by multiple STs, although most of them were found in a single patient and showed persistence over years. Only few phenotypes showed some correlation with population phylogenetic structure. Our results show that S. maltophilia adaptation to CF lung is associated with consistent genotypic and phenotypic heterogeneity. Stenotrophomonas maltophilia infecting multiple hosts likely experiences different selection pressures depending on the host environment. The poor genotype-phenotype correlation suggests the existence of complex regulatory mechanisms that need to be explored in order to better design therapeutic strategies.\n\nEvolution of Stenotrophomonas maltophilia in Cystic Fibrosis Lung over Chronic Infection: A Genomic and Phenotypic Population Study.", "token_count": 437, "char_count": 1640, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7042, "quality_score": 0.8521, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:04.574179", "source": { "split": "train_shard_00001", "doc_id": 2840 }, "chunk_id": "train_shard_00001_2840_0", "global_id": 9698 }, { "text": "

Background

Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting.

Methods

We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), extended-spectrum beta-lactamase (ESBL-E), and carbapenemase-producing Enterobacterales (CPE) isolated from blood cultures, sterile sites, or screening specimens across three large tertiary referral hospitals (2 adult, 1 paediatric) in Brisbane, Australia. WGS was used to determine in silico multi-locus sequence typing (MLST) and resistance gene profiling via a bespoke genomic analysis pipeline. Putative transmission events were identified by comparison of core genome single nucleotide polymorphisms (SNPs). Relevant clinical meta-data were combined with genomic analyses via customised automation, collated into hospital-specific reports regularly distributed to infection control teams.

Results

Over 4 years (April 2017 to July 2021) 2660 isolates were sequenced. This included MDR gram-negative bacilli (n = 293 CPE, n = 1309 ESBL), MRSA (n = 620), and VRE (n = 433). A total of 379 clinical reports were issued. Core genome SNP data identified that 33% of isolates formed 76 distinct clusters. Of the 76 clusters, 43 were contained to the 3 target hospitals, suggesting ongoing transmission within the clinical environment. The remaining 33 clusters represented possible inter-hospital transmission events or strains circulating in the community", "token_count": 457, "char_count": 1655, "word_count": 209, "semantic_coherence": 1, "information_density": 0.7895, "quality_score": 0.8947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:05.221657", "source": { "split": "train_shard_00001", "doc_id": 2841 }, "chunk_id": "train_shard_00001_2841_0", "global_id": 9699 }, { "text": "In 1 hospital, proven negligible transmission of non-multi-resistant MRSA enabled changes to infection control policy.

Conclusions

Implementation of routine WGS for MDR pathogens in clinical laboratories is feasible and can enable targeted infection prevention and control interventions.\n\nClinical Implementation of Routine Whole-genome Sequencing for Hospital Infection Control of Multi-drug Resistant Pathogens.", "token_count": 99, "char_count": 420, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7551, "quality_score": 0.8776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:05.595153", "source": { "split": "train_shard_00001", "doc_id": 2841 }, "chunk_id": "train_shard_00001_2841_1", "global_id": 9700 }, { "text": "The taxonomic classification of metabolically versatile Paracoccus spp. has been so far performed using polyphasic approach. The topology of single gene phylogenies, however, has highlighted ambiguous species assignments. In the present study, genome based multi-gene phylogenies and overall genome related index were used for species threshold assessment. Comprehensive phylogenomic analysis of Paracoccus genomes (n = 103) showed concordant clustering of strains across multi-gene marker set phylogenies (nMC = 0.08-0.14); as compared to 16S rDNA phylogeny (nMC = 0.37-0.42) suggesting robustness of multi gene phylogenies in drawing phylogenetic inferences. Functional gene content distribution across the genus showed that only 1.7% gene content constitutes the core genome highlighting the significance of extensive genomic variability in the evolution of Paracoccus spp. Further, genome metrics were used to validate characterized strains, identifying classification anomalies (n = 13), and based on this, genome derived taxonomic amendments were notified in present study. Conclusively, validated metric tools can be employed on whole genome sequences, including draft assemblies, for the assessment and assignment of uncharacterized strains and species level ascription of newly isolated Paracoccus strains in future.\n\nPhylogenomic Framework for Taxonomic Delineation of Paracoccus spp. and Exploration of Core-Pan Genome.", "token_count": 437, "char_count": 1486, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:06.236127", "source": { "split": "train_shard_00001", "doc_id": 2842 }, "chunk_id": "train_shard_00001_2842_0", "global_id": 9701 }, { "text": "The ability of six strains of Pichia anomala, four strains of Pichia kluyveri and two strains of Hanseniaspora uvarum predominant during coffee processing to produce polygalacturonase (PG), pectin esterase (PE) and pectin lyase (PL) in yeast polygalacturonic acid medium (YPA) and in coffee broth (CB) was studied. For comparison, a reference strain of Kluyveromyces marxianus CCT 3172 isolated from cocoa and reported to produce high amount of PG was included. Initial screening of PG activity using YPA medium showed that K. marxianus CCT 3172, P. anomala S16 and P. kluyveri S13Y4 had the strongest activity. Enzymatic assays showed that the four yeast species secreted PG, but none of the yeasts investigated was found to produce PE or PL. P. anomala S16 and P. kluyveri S13Y4 were found to produce higher amounts of PG when grown in CB than in YPA. When K. marxianus CCT 3172, P. anomala S16 and P. kluyveri S13Y4 were grown in YPA broth adjusted to pH of 3.0-8.0 and incubated at temperatures of 15-40 degrees C, the three yeast species secreted the highest amount of PG at pH 6.0 and at 30 degrees C. For PG secreted by K. marxianus CCT 3172 and P. anomala S16, the optimum pH and temperature for the enzymatic activity were 5.5 and 40 degrees C, respectively. On the other hand, PG produced by P. kluyveri S13Y4 showed the highest activity at pH 5.0 and 50 degrees C. Significant differences in the extracellular activity of PG were found between the yeasts species as well as between strains within same species. High amounts of PG were produced by two strains of P. anomala and P. kluyveri. It is therefore likely that strains of those two species may be involved in the degradation of pectin during coffee fermentation.", "token_count": 521, "char_count": 1730, "word_count": 295, "semantic_coherence": 1, "information_density": 0.4644, "quality_score": 0.7322, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:30:06.892517", "source": { "split": "train_shard_00001", "doc_id": 2843 }, "chunk_id": "train_shard_00001_2843_0", "global_id": 9702 }, { "text": "Pectin degrading enzymes in yeasts involved in fermentation of Coffea arabica in East Africa.", "token_count": 27, "char_count": 93, "word_count": 14, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:07.252943", "source": { "split": "train_shard_00001", "doc_id": 2843 }, "chunk_id": "train_shard_00001_2843_1", "global_id": 9703 }, { "text": "

ABSTRACT

Whole genome sequencing (WGS) for public health surveillance and epidemiological investigation of foodborne pathogens predominantly relies on sequencing platforms that generate short reads. Continuous improvement of long-read nanopore sequencing such as Oxford Nanopore Technologies (ONT) presents a potential for leveraging multiple advantages of the technology in public health and food industry settings, including rapid turnaround and onsite applicability in addition to superior read length. However, evaluation, standardization and implementation of the ONT approach to WGS-based, strain-level subtyping is challenging, in part due to its relatively high base-calling error rates and frequent iterations of sequencing chemistry and bioinformatic analytics. Using an established cohort of Salmonella Enteritidis isolates for subtyping evaluation, we assessed the technical readiness of ONT for single nucleotide polymorphism (SNP) analysis and core-genome multilocus sequence typing (cgMLST) of a major foodborne pathogen. By multiplexing three isolates per flow cell, we generated sufficient sequencing depths under seven hours of sequencing for robust subtyping. SNP calls by ONT and Illumina reads were highly concordant despite homopolymer errors in ONT reads (R9.4.1 chemistry). In silico correction of such errors allowed accurate allelic calling for cgMLST and allelic difference measurements to facilitate heuristic detection of outbreak isolates. Our study established a baseline for the continuously evolving nanopore technology as a viable solution to high quality subtyping of Salmonella , delivering comparable subtyping performance when used standalone or together with short-read platforms.\n\nSubtyping evaluation of Salmonella Enteritidis using SNP and core genome MLST with nanopore reads", "token_count": 412, "char_count": 1834, "word_count": 243, "semantic_coherence": 1, "information_density": 0.679, "quality_score": 0.8395, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:07.871019", "source": { "split": "train_shard_00001", "doc_id": 2844 }, "chunk_id": "train_shard_00001_2844_0", "global_id": 9704 }, { "text": "Streptococcus thermophilus is a major starter for the dairy industry with great economic importance. In this study we analyzed 23 fully sequenced genomes of S. thermophilus to highlight novel aspects of the evolution, biology and technological properties of this species. Pan/core genome analysis revealed that the species has an important number of conserved genes and that the pan genome is probably going to be closed soon. According to whole genome phylogeny and average nucleotide identity (ANI) analysis, most S. thermophilus strains were grouped in two major clusters (i.e., clusters A and B). More specifically, cluster A includes strains with chromosomes above 1.83 Mbp, while cluster B includes chromosomes below this threshold. This observation suggests that strains belonging to the two clusters may be differentiated by gene gain or gene loss events. Furthermore, certain strains of cluster A could be further subdivided in subgroups, i.e., subgroup I (ASCC 1275, DGCC 7710, KLDS SM, MN-BM-A02, and ND07), II (MN-BM-A01 and MN-ZLW-002), III (LMD-9 and SMQ-301), and IV (APC151 and ND03). In cluster B certain strains formed one distinct subgroup, i.e., subgroup I (CNRZ1066, CS8, EPS, and S9). Clusters and subgroups observed for S. thermophilus indicate the existence of lineages within the species, an observation which was further supported to a variable degree by the distribution and/or the architecture of several genomic traits. These would include exopolysaccharide (EPS) gene clusters, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-CRISPR associated (Cas) systems, as well as restriction-modification (R-M) systems and genomic islands (GIs)", "token_count": 487, "char_count": 1712, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.8381, "entities": { "genes": [ "CS8", "CNRZ1066", "APC151", "ND03", "ND07" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:08.519820", "source": { "split": "train_shard_00001", "doc_id": 2845 }, "chunk_id": "train_shard_00001_2845_0", "global_id": 9705 }, { "text": "Of note, the histidine biosynthetic cluster was found present in all cluster A strains (plus strain NCTC12958T) but was absent from all strains in cluster B. Other loci related to lactose/galactose catabolism and urea metabolism, aminopeptidases, the majority of amino acid and peptide transporters, as well as amino acid biosynthetic pathways were found to be conserved in all strains suggesting their central role for the species. Our study highlights the necessity of sequencing and analyzing more S. thermophilus complete genomes to further elucidate important aspects of strain diversity within this starter culture that may be related to its application in the dairy industry.\n\nComparative Genomics of Streptococcus thermophilus Support Important Traits Concerning the Evolution, Biology and Technological Properties of the Species.", "token_count": 228, "char_count": 863, "word_count": 121, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [ "NCTC12958" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:08.984189", "source": { "split": "train_shard_00001", "doc_id": 2845 }, "chunk_id": "train_shard_00001_2845_1", "global_id": 9706 }, { "text": "Pasteurella multocida, a Gram-negative opportunistic pathogen, has led to a broad range of diseases in mammals and birds, including fowl cholera in poultry, pneumonia and atrophic rhinitis in swine and rabbit, hemorrhagic septicemia in cattle, and bite infections in humans. In order to better interpret the genetic diversity and adaptation evolution of this pathogen, seven genomes of P. multocida strains isolated from fowls, rabbit and pigs were determined by using high-throughput sequencing approach. Together with publicly available P. multocida genomes, evolutionary features were systematically analyzed in this study. Clustering of 70,565 protein-coding genes showed that the pangenome of 33 P. multocida strains was composed of 1,602 core genes, 1,364 dispensable genes, and 1,070 strain-specific genes. Of these, we identified a full spectrum of genes related to virulence factors and revealed genetic diversity of these potential virulence markers across P. multocida strains, e.g., bcbAB, fcbC, lipA, bexDCA, ctrCD, lgtA, lgtC, lic2A involved in biogenesis of surface polysaccharides, hsf encoding autotransporter adhesin, and fhaB encoding filamentous haemagglutinin. Furthermore, based on genome-wide positive selection scanning, a total of 35 genes were subject to strong selection pressure. Extensive analyses of protein subcellular location indicated that membrane-associated genes were highly abundant among all positively selected genes. The detected amino acid sites undergoing adaptive selection were preferably located in extracellular space, perhaps associated with bacterial evasion of host immune responses. Our findings shed more light on conservation and distribution of virulence-associated genes across P. multocida strains", "token_count": 501, "char_count": 1816, "word_count": 240, "semantic_coherence": 1, "information_density": 0.7083, "quality_score": 0.8542, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:09.646067", "source": { "split": "train_shard_00001", "doc_id": 2846 }, "chunk_id": "train_shard_00001_2846_0", "global_id": 9707 }, { "text": "Meanwhile, this study provides a genetic context for future researches on the mechanism of adaptive evolution in P. multocida.\n\nGenome-Wide Analyses Reveal Genes Subject to Positive Selection in Pasteurella multocida.", "token_count": 67, "char_count": 231, "word_count": 30, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:10.009895", "source": { "split": "train_shard_00001", "doc_id": 2846 }, "chunk_id": "train_shard_00001_2846_1", "global_id": 9708 }, { "text": "

Motivation

Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic datasets can be challenging to work at. These challenges have impeded progress in this field.

Results

Here, we present a stack of two C++ libraries, libbdsg and libhandlegraph, which use a simple, field-proven interface, designed to expose elementary features of these graphs while preventing common graph manipulation mistakes. The libraries also provide a Python binding. Using a diverse collection of pangenome graphs, we demonstrate that these tools allow for efficient construction and manipulation of large genome graphs with dense variation. For instance, the speed and memory usage are up to an order of magnitude better than the prior graph implementation in the VG toolkit, which has now transitioned to using libbdsg's implementations.

Availability and implementation

libhandlegraph and libbdsg are available under an MIT License from https://github.com/vgteam/libhandlegraph and https://github.com/vgteam/libbdsg.\n\nEfficient dynamic variation graphs.", "token_count": 281, "char_count": 1243, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7256, "quality_score": 0.8628, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:10.566902", "source": { "split": "train_shard_00001", "doc_id": 2847 }, "chunk_id": "train_shard_00001_2847_0", "global_id": 9709 }, { "text": "Cutibacterium acnes is an important member of the human skin microbiome and plays a critical role in skin health and disease. C. acnes encompasses different phylotypes that have been found to be associated with different skin phenotypes, suggesting a genetic basis for their impact on skin health. Here, we present a comprehensive comparative analysis of 255 C. acnes genomes to provide insights into the species genetic diversity and identify unique features that define various phylotypes. Results revealed a relatively small and open pan genome (6,240 genes) with a large core genome (1,194 genes), and three distinct phylogenetic clades, with multiple robust sub-clades. Furthermore, we identified several unique gene families driving differences between distinct C. acnes clades. Carbohydrate transporters, stress response mechanisms and potential virulence factors, potentially involved in competitive growth and host colonization, were detected in type I strains, which are presumably responsible for acne. Diverse type I-E CRISPR-Cas systems and prophage sequences were detected in select clades, providing insights into strain divergence and adaptive differentiation. Collectively, these results enable to elucidate the fundamental differences among C. acnes phylotypes, characterize genetic elements that potentially contribute to type I-associated dominance and disease, and other key factors that drive the differentiation among clades and sub-clades. These results enable the use of comparative genomics analyses as a robust method to differentiate among the C. acnes genotypes present in the skin microbiome, opening new avenues for the development of biotherapeutics to manipulate the skin microbiota.\n\nComparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications.", "token_count": 459, "char_count": 1915, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6279, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:11.223867", "source": { "split": "train_shard_00001", "doc_id": 2848 }, "chunk_id": "train_shard_00001_2848_0", "global_id": 9710 }, { "text": "Clostridium perfringens has emerged as a growing public health concern due to its ability to cause various infections and its increasing resistance to antibiotics. To assess its current epidemiology in clinical settings, we conducted a survey involving 426 healthy individuals and 273 ICU inpatients at a provincial hospital in China. Our findings revealed a high prevalence of C. perfringens in healthy individuals (45.77%, 95% CI: 41.0%-50.6%) and ICU patients (12.82%, 95% CI: 9.1%-17.4%). The identified 220 C. perfringens isolates displayed substantial resistance to erythromycin (57.9%), clindamycin (50.7%), and tetracycline (32.0%), primarily attributed to the presence of erm(Q) (54.4%), lnu(P) (13.8%), tetB(P) (83.6%), and tetA(P) (66.7%). Notably, C. perfringens isolates from this particular hospital demonstrated a high degree of sequence type diversity and phylogenic variation, suggesting that the potential risk of infection primarily arises from the bacteria's gut colonization rather than clonal transmissions within the clinical environment. This study provides an updated analysis of the current epidemiology of C. perfringens in healthy individuals and ICU patients in China and emphasizes the need to optimize intervention strategies against its public health threat.

Importance

Clostridium perfringens is a bacterium of growing public health concern due to its ability to cause infections and its increasing resistance to antibiotics. Understanding its epidemiology in clinical settings is essential for intervention strategies. This study surveyed healthy individuals and ICU inpatients in a provincial hospital in China. It found a high prevalence of C. perfringens, indicating infection risk", "token_count": 515, "char_count": 1809, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5504, "quality_score": 0.7752, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:30:11.881631", "source": { "split": "train_shard_00001", "doc_id": 2849 }, "chunk_id": "train_shard_00001_2849_0", "global_id": 9711 }, { "text": "The isolates also showed significant antibiotic resistance. Importantly, the study revealed diverse sequence types and phylogenetic variation, suggesting infection risk from intestinal colonization rather than clonal transmission in hospitals. This analysis emphasizes the need to optimize intervention strategies against this public health threat.\n\nHigh intestinal carriage of Clostridium perfringens in healthy individuals and ICU patients in Hangzhou, China.", "token_count": 98, "char_count": 468, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8793, "quality_score": 0.9397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:12.259177", "source": { "split": "train_shard_00001", "doc_id": 2849 }, "chunk_id": "train_shard_00001_2849_1", "global_id": 9712 }, { "text": "The aim of this work was to investigate the physiology of Kluyveromyces marxianus CBS 6556 in terms of its low tendency to form ethanol under exposure to sugar excess, and the split of carbon flux which takes place at the level of glucose-6-phosphate. Measurements were performed in batch cultivations, and after a glucose or a lactose pulse applied to chemostat-grown respiring cells (with a dilution rate of 0.1 h(-1)). No ethanol formation was observed in batch cultivations or during pulse experiments, unless the oxygen supply was shut down, indicating that this organism is more strictly Crabtree-negative than its close relative K. lactis and other known Crabtree-negative yeasts. During the pulse experiments, activities of phosphoglucoisomerase, glucose-6-phosphate dehydrogenase and phosphoglucomutase in cell-free extracts remained rather constant, at higher levels than those of Saccharomyces cerevisiae grown at similar conditions. When cells were exposed to glucose concentrations as high as 26 gl(-1), the activity of phosphoglucomutase was higher than that in cells exposed to 14 gl(-1) glucose, whereas the activities of phosphoglucoisomerase and glucose-6-phosphate dehydrogenase did not change. Our results suggest that the low tendency for ethanol formation in K. marxianus might be a consequence of this yeast's capacity of keeping the glycolytic flux constant, due at least in part to the diversion of carbon flux towards the biosynthesis of carbohydrates and towards the pentose phosphate pathway.\n\nEthanol formation and enzyme activities around glucose-6-phosphate in Kluyveromyces marxianus CBS 6556 exposed to glucose or lactose excess.", "token_count": 445, "char_count": 1662, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5726, "quality_score": 0.7863, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:12.896981", "source": { "split": "train_shard_00001", "doc_id": 2850 }, "chunk_id": "train_shard_00001_2850_0", "global_id": 9713 }, { "text": "Salmonella enterica subsp. enterica serovar Dublin (S. Dublin) is a zoonotic pathogen causing infections in animals, especially in cattle. In this study, we report draft genome sequences of four S. Dublin isolated between 1956 and 1957 from cattle and fox in Poland. Whole genome sequencing was performed on the Illumina platform and the data is available at National Center for Biotechnology Information under the BioProject accession number PRJNA865912. In order to better understand the genetic basis of epidemiology of S. Dublin infection, the obtained sequences were analyzed using the tools which are available at Center of Genomic Epidemiology (https://www.genomicepidemiology.org/) including core genome multilocus sequence typing (cgMLST) and core genome single nucleotide polymorphisms (cgSNPs).\n\nDraft genome sequences data of four Salmonella enterica subsp. enterica serovar Dublin archival strains originating from animals in Poland, 1956 - 1957.", "token_count": 286, "char_count": 1008, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6815, "quality_score": 0.8407, "entities": { "genes": [ "PRJNA865912" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:13.811479", "source": { "split": "train_shard_00001", "doc_id": 2851 }, "chunk_id": "train_shard_00001_2851_0", "global_id": 9714 }, { "text": "Abstract

Mycobacterium abscessus (Mab) is an emerging multidrug-resistant nontuberculous mycobacterium that causes a wide spectrum of infections and has caused several local outbreaks worldwide. To facilitate standardized prospective molecular surveillance, we established a novel core genome multilocus sequence typing (cgMLST) scheme. Over 2000 isolates of Mab, covering all subspecies and main dominant circulating clones as well as extra-pulmonary outbreak strains and sequential isolates of chronically infected cystic fibrosis patients, were used to validate the scheme and set genetic distance thresholds to delineate transmission events and global population structure. Most global clonal complexes previously classified using cgSNP were confirmed by our cgMLST approach, and also correlated well with traditional 7-loci MLST sequence types. 99% of pairwise comparisons between epidemiologically linked isolates were below 25 alleles and 90% below 10 alleles. These thresholds can be used for initial cluster analysis and to guide further epidemiological investigations. Overall, the scheme will help to unravel the apparent global spread of certain clonal complexes and as yet undiscovered transmission routes.

\n\nDelineating Mycobacterium abscessus population structure and transmission employing high-resolution core genome multilocus sequence typing", "token_count": 330, "char_count": 1399, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7486, "quality_score": 0.8743, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:14.403697", "source": { "split": "train_shard_00001", "doc_id": 2852 }, "chunk_id": "train_shard_00001_2852_0", "global_id": 9715 }, { "text": "Marcha, thiat, dawdim, hamei, humao, khekhrii, chowan, and phut are traditionally prepared dried starters used for production of various ethnic alcoholic beverages in North East states of India. The surveillance of mycobiome associated with these starters have been revealed by culture-dependent methods using phenotypic and molecular tools. We identified Wickerhamomyces anomalus, Pichia anomala, Saccharomycopsis fibuligera, Pichia terricola, Pichia kudriavzevii, and Candida glabrata by ITS-PCR. The diversity of yeasts and molds in all 40 samples was also investigated by culture-independent method using PCR-DGGE analysis. The average distributions of yeasts showed Saccharomyces cerevisiae (16.5%), Saccharomycopsis fibuligera (15.3%), Wickerhamomyces anomalus (11.3%), S. malanga (11.7%), Kluyveromyces marxianus (5.3%), Meyerozyma sp. (2.7%), Candida glabrata (2.7%), and many strains below 2%. About 12 strains of molds were also identified based on PCR-DGGE analysis which included Aspergillus penicillioides (5.0%), Rhizopus oryzae (3.3%), and sub-phylum: Mucoromycotina (2.1%). Different techniques used in this paper revealed the diversity and differences of mycobiome species in starter cultures of India which may be referred as baseline data for further research.", "token_count": 483, "char_count": 1377, "word_count": 168, "semantic_coherence": 1, "information_density": 0.756, "quality_score": 0.878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:15.069465", "source": { "split": "train_shard_00001", "doc_id": 2853 }, "chunk_id": "train_shard_00001_2853_0", "global_id": 9716 }, { "text": "Diversity of Yeasts and Molds by Culture-Dependent and Culture-Independent Methods for Mycobiome Surveillance of Traditionally Prepared Dried Starters for the Production of Indian Alcoholic Beverages.", "token_count": 50, "char_count": 200, "word_count": 25, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:15.477673", "source": { "split": "train_shard_00001", "doc_id": 2853 }, "chunk_id": "train_shard_00001_2853_1", "global_id": 9717 }, { "text": "

Introduction

Accurate genotyping of Killer cell Immunoglobulin-like Receptor (KIR) genes plays a pivotal role in enhancing our understanding of innate immune responses, disease correlations, and the advancement of personalized medicine. However, due to the high variability of the KIR region and high level of sequence similarity among different KIR genes, the generic genotyping workflows are unable to accurately infer copy numbers and complete genotypes of individual KIR genes from next-generation sequencing data. Thus, specialized genotyping tools are needed to genotype this complex region.

Methods

Here, we introduce Geny, a new computational tool for precise genotyping of KIR genes. Geny utilizes available KIR allele databases and proposes a novel combination of expectation-maximization filtering schemes and integer linear programming-based combinatorial optimization models to resolve ambiguous reads, provide accurate copy number estimation, and estimate the correct allele of each copy of genes within the KIR region.

Results & discussion

We evaluated Geny on a large set of simulated short-read datasets covering the known validated KIR region assemblies and a set of Illumina short-read samples sequenced from 40 validated samples from the Human Pangenome Reference Consortium collection and showed that it outperforms the existing state-of-the-art KIR genotyping tools in terms of accuracy, precision, and recall. We envision Geny becoming a valuable resource for understanding immune system response and consequently advancing the field of patient-centric medicine.\n\nGeny: a genotyping tool for allelic decomposition of killer cell immunoglobulin-like receptor genes.", "token_count": 398, "char_count": 1709, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:16.098986", "source": { "split": "train_shard_00001", "doc_id": 2854 }, "chunk_id": "train_shard_00001_2854_0", "global_id": 9718 }, { "text": "

ABSTRACT

Extensive gonococcal surveillance has been performed using molecular typing at global, regional, national and local levels. The three main genotyping schemes for this pathogen, Multi-Locus Sequence Typing (MLST), Neisseria gonorrhoeae Multi-Antigen Sequence Typing (NG-MAST) and N. gonorrhoeae Sequence Typing for Antimicrobial Resistance (NG-STAR), allow inter-laboratory and inter-study comparability and reproducibility and provide an approximation to the gonococcal population structure. With high-throughput whole-genome sequencing (WGS), we obtain a substantially higher and more accurate discrimination between strains, i.e., compared to previous molecular typing schemes where isolates with the same sequence type often have a different genomic background. However, WGS remains unavailable or not affordable in many laboratories, accordingly, bioinformatic tools that allow the integration of data among laboratories with and without access to WGS is imperative for a joint effort to increase our understanding of global pathogen threats. Here, we present pyngoST, a command-line Python tool for a fast, simultaneous and accurate sequence typing of the WHO priority pathogen N. gonorrhoeae , from WGS assemblies. pyngoST integrates MLST, NG-MAST and NG-STAR, and can also designate NG-STAR clonal complexes and NG-MAST genogroups, facilitating multiple sequence typing from large WGS assembly collections. Exact matches for existing alleles and STs are reported, but also closest matches of new alleles and STs. The implementation of a fast multi-pattern searching algorithm allows pyngoST to be rapid and report results on 500 WGS assemblies in under 1 minute. The mapping of typing results on a core genome tree of 2,375 gonococcal genomes revealed that NG-STAR is the scheme that best represents the population structure of this pathogen, emphasizing the role of antimicrobial use and antimicrobial resistance (AMR) as a driver of gonococcal evolution.

IMPACT STATEMENT

Molecular typing has been key for N", "token_count": 523, "char_count": 2043, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6456, "quality_score": 0.8228, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:30:16.759631", "source": { "split": "train_shard_00001", "doc_id": 2855 }, "chunk_id": "train_shard_00001_2855_0", "global_id": 9719 }, { "text": "gonorrhoeae epidemiological and AMR surveillance, and WGS has revolutionized this typing. The most frequently used molecular typing schemes include MLST, NG-MAST and NG-STAR, and modifications of those. These schemes can be extracted from WGS assemblies for comparability and reproducibility of results with laboratories that do not have access to WGS technologies. pyngoST is a unique command-line Python tool that integrates all these common typing schemes under the same framework and performs rapid simultaneous user-defined multiple typing of large number of gonococcal genomes through a fast multi-pattern searching algorithm. Typing results on 2,375 gonococcal genomes revealed that NG-STAR best represents the genomic population structure of N. gonorrhoeae , highlighting the importance of antimicrobial use and AMR on the evolution of this pathogen.

DATA SUMMARY

pyngoST is written in Python 3 and is available from Github under the GPL-3.0 License ( https://github.com/leosanbu/pyngoST ). The script can be installed via the Python ‘pip’ package. Genome assemblies used in this study are from the Euro-GASP 2018 WGS survey and are available from Pathogenwatch: https://pathogen.watch/collection/eurogasp2018 (1,2). Pairwise single nucleotide polymorphism (SNP) distances among isolates from this dataset are also available from the same link.

Results:

from running pyngoST on the Euro-GASP 2018 WGS dataset can be explored from Microreact: https://microreact.org/project/wYpBzCs9A6Uf7HEMA6zmmY-eurogasp2018-pyngost .\n\npyngoST: fast, simultaneous and accurate multiple sequence typing ofNeisseria gonorrhoeaegenome collections", "token_count": 474, "char_count": 1661, "word_count": 218, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:17.405282", "source": { "split": "train_shard_00001", "doc_id": 2855 }, "chunk_id": "train_shard_00001_2855_1", "global_id": 9720 }, { "text": "

ABSTRACT

Discovery of influential genetic variants and prediction of phenotypes such as antibiotic resistance are becoming routine tasks in bacterial genomics. Genome-wide association study (GWAS) methods can be applied to study bacterial populations, with a particular emphasis on alignment-free approaches, which are necessitated by the more plastic nature of bacterial genomes. Here we advance bacterial GWAS by introducing a computationally scalable joint modeling framework, where genetic variants covering the entire pangenome are compactly represented by unitigs, and the model fitting is achieved using elastic net penalization. In contrast to current leading GWAS approaches, which test each genotype-phenotype association separately for each variant, our joint modelling approach is shown to lead to increased statistical power while maintaining control of the false positive rate. Our inference procedure also delivers an estimate of the narrow-sense heritability, which is gaining considerable interest in studies of bacteria. Using an extensive set of state-of-the-art bacterial population genomic datasets we demonstrate that our approach performs accurate phenotype prediction, comparable to popular machine learning methods, while retaining both interpretability and computational efficiency. We expect that these advances will pave the way for the next generation of high-powered association and prediction studies for an increasing number of bacterial species.\n\nImproved inference and prediction of bacterial genotype-phenotype associations using pangenome-spanning regressions", "token_count": 319, "char_count": 1604, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:17.966273", "source": { "split": "train_shard_00001", "doc_id": 2856 }, "chunk_id": "train_shard_00001_2856_0", "global_id": 9721 }, { "text": "GET_HOMOLOGUES is an open-source software package that builds on popular orthology-calling approaches making highly customizable and detailed pangenome analyses of microorganisms accessible to nonbioinformaticians. It can cluster homologous gene families using the bidirectional best-hit, COGtriangles, or OrthoMCL clustering algorithms. Clustering stringency can be adjusted by scanning the domain composition of proteins using the HMMER3 package, by imposing desired pairwise alignment coverage cutoffs, or by selecting only syntenic genes. The resulting homologous gene families can be made even more robust by computing consensus clusters from those generated by any combination of the clustering algorithms and filtering criteria. Auxiliary scripts make the construction, interrogation, and graphical display of core genome and pangenome sets easy to perform. Exponential and binomial mixture models can be fitted to the data to estimate theoretical core genome and pangenome sizes, and high-quality graphics can be generated. Furthermore, pangenome trees can be easily computed and basic comparative genomics performed to identify lineage-specific genes or gene family expansions. The software is designed to take advantage of modern multiprocessor personal computers as well as computer clusters to parallelize time-consuming tasks. To demonstrate some of these capabilities, we survey a set of 50 Streptococcus genomes annotated in the Orthologous Matrix (OMA) browser as a benchmark case. The package can be downloaded at http://www.eead.csic.es/compbio/soft/gethoms.php and http://maya.ccg.unam.mx/soft/gethoms.php.\n\nGET_HOMOLOGUES, a versatile software package for scalable and robust microbial pangenome analysis.", "token_count": 400, "char_count": 1725, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6814, "quality_score": 0.8407, "entities": { "genes": [ "HMMER3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:18.585175", "source": { "split": "train_shard_00001", "doc_id": 2857 }, "chunk_id": "train_shard_00001_2857_0", "global_id": 9722 }, { "text": "Bacterial pathogens adapt to host niches because of selective within-host pressures, an evolutionary process that offers invaluable insights into host-pathogen interactions. Here, we retrospectively track the evolution of a single multiresistant Klebsiella pneumoniae clone in 110 patients over a 5-year nosocomial outbreak. We combine comparative genomics with phenotypic characterization of mucoviscosity, serum survival, iron utilization, biofilm formation, and infection potential in Galleria mellonella for all isolates. Strong positive selection within patients targeted key virulence factors. Notably, convergent evolutionary trajectories were dominated by reduced acute virulence and recurrent changes in iron uptake regulation, capsule and lipopolysaccharide, and enhanced biofilm formation. These phenotypic changes likely represent clinical niche adaptations, with some resulting in trade-offs during gastrointestinal colonization. This study underscores the dynamic nature of within-host evolution and its role in shaping virulence in opportunistic pathogens, even on short time scales.\n\nParallel within-host evolution alters virulence factors in an opportunistic Klebsiella pneumoniae during a hospital outbreak.", "token_count": 281, "char_count": 1225, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7582, "quality_score": 0.8791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:19.143874", "source": { "split": "train_shard_00001", "doc_id": 2858 }, "chunk_id": "train_shard_00001_2858_0", "global_id": 9723 }, { "text": "We purified a carboxypeptidase (CPY) from the yeast of Kluyveromyces marxianus. This enzyme was purified 170 times from a soluble extract of 100000 x g. Purification consisted in a fractionated precipitation with ammonium sulfate and two chromatographic steps consisting of anion exchange chromatography and hydrophobic interactions chromatography. The native enzyme depicted a molecular mass of 67 kDa by gel filtration. This serine carboxypeptidase depicted an optimal pH of 8.5 and was stable at a pH ranging from 6.0 to 9.0, its optimal temperature was of 45 degrees C and was unstable at temperatures above 55 degrees C; Michaelis constant and Vmax for N-benzoyl-l-tyrosine-p-nitroanilide were of 29 microM and 612 microM/min mg of protein, respectively. The enzyme was strongly inhibited by phenylmethylsufonyl fluoride (PMSF) and, to a lesser degree, by trans-epoxysuccinyl-l-leucylamido-(4-guanidine)-butane. This study indicated that K. marxianus carboxypeptidase could be an alternative to other animal-source carboxypeptidases in the industry.\n\nPurification and characterization of a serine carboxypeptidase from Kluyveromyces marxianus.", "token_count": 354, "char_count": 1148, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6646, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:19.727997", "source": { "split": "train_shard_00001", "doc_id": 2859 }, "chunk_id": "train_shard_00001_2859_0", "global_id": 9724 }, { "text": "

Background

Haemophilus parasuis is the etiologic agent of Glässer's disease in pigs and causes devastating losses to the farming industry. Whilst some hyper-virulent isolates have been described, the relationship between genetics and disease outcome has been only partially established. In particular, there is weak correlation between serovar and disease phenotype. We sequenced the genomes of 212 isolates of H. parasuis and have used this to describe the pan-genome and to correlate this with clinical and carrier status, as well as with serotype.

Results

Recombination and population structure analyses identified five groups with very high rates of recombination, separated into two clades of H. parasuis with no signs of recombination between them. We used genome-wide association methods including discriminant analysis of principal components (DAPC) and generalised linear modelling (glm) to look for genetic determinants of this population partition, serovar and pathogenicity. We were able to identify genes from the accessory genome that were significantly associated with phenotypes such as potential serovar specific genes including capsule genes, and 48 putative virulence factors that were significantly different between the clinical and non-clinical isolates. We also show that the presence of many previously suggested virulence factors is not an appropriate marker of virulence.

Conclusions

These genes will inform the generation of new molecular diagnostics and vaccines, and refinement of existing typing schemes and show the importance of the accessory genome of a diverse species when investigating the relationship between genotypes and phenotypes.\n\nThe use of genome wide association methods to investigate pathogenicity, population structure and serovar in Haemophilus parasuis.", "token_count": 404, "char_count": 1826, "word_count": 250, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:20.348584", "source": { "split": "train_shard_00001", "doc_id": 2860 }, "chunk_id": "train_shard_00001_2860_0", "global_id": 9725 }, { "text": "This study investigated the yeast community in traditional soft cheese from the Extremadura region to be able to establish possible beneficial properties for human health. A total of 149 yeast isolates were characterised at strain level using the ISSR-PCR technique with the primer (GTG)₅. Forty-three different genetic profiles were obtained, and the yeasts were grouped into 12 species allowing their typification at strain level. Regarding probiotic tests, 54 strains were selected for the study of probiotic properties based on genetic profile and origin. All of them showed adequate tolerance to the most restrictive stomach and bile salts conditions, although strains of Kluyveromyces lactis and Pichia fermentans presented better ability to survive to these stresses. P. fermentans was also the species that showed better antioxidant, auto-aggregation and hydrophobicity capacity, at the same time as antimicrobial activity, followed by Kluyveromyces sp. strains. Thus, considering the probiotic characteristics studied, 15 strains, P. fermentans 1826, 1865, 1859, 1911,1913, 1916 and 1938; P. kudriavzevii 1801, 1809 and 1832; K. marxianus 1886, 1917 and 1919; D. hansenii 1860; and Y. lipolytica 1961, are promising potential probiotic candidates for developing a functional cheese.\n\nIdentification and selection of yeast with functional properties for future application in soft paste cheese", "token_count": 396, "char_count": 1401, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7065, "quality_score": 0.8532, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:20.963063", "source": { "split": "train_shard_00001", "doc_id": 2861 }, "chunk_id": "train_shard_00001_2861_0", "global_id": 9726 }, { "text": "We present polyphasic taxonomic data to demonstrate that strain 125703-2019T, a human blood isolate, represents a novel species within the genus Pseudoclavibacter, and to reclassify the illegitimate Zimmermannella alba Lin et al., 2004 as Pseudoclavibacter albus comb. nov. Upon primary isolation, strain 125703-2019T could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that it belonged to the genus Pseudoclavibacter. Average nucleotide identity and digital DNA-DNA hybridisation analyses confirmed that it represented a novel species within this genus. A detailed physiological characterisation yielded differential tests between the novel species and its nearest neighbor taxa, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify this strain into the novel species Pseudoclavibacter triregionum sp. nov., with strain 125703-2019T (= R-76471T, LMG 31777T, CCUG 74796T) as the type strain. The whole-genome assembly of strain 125703-2019T has a size of 2.4 Mb and a G + C content of 72.74%. A Pseudoclavibacter pangenome analysis revealed that 667 gene clusters were exclusively present in strain 125703-2019T. While these gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that explained the occurrence of this species in human infection", "token_count": 466, "char_count": 1531, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6716, "quality_score": 0.8358, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:21.609722", "source": { "split": "train_shard_00001", "doc_id": 2862 }, "chunk_id": "train_shard_00001_2862_0", "global_id": 9727 }, { "text": "Finally, several phylogenetic and phylogenomic analyses demonstrated that the genus Pseudoclavibacter is polyphyletic with Pseudoclavibacter soli and Pseudoclavibacter caeni representing a unique and deeply branching line of descent within the family Microbacteriaceae. We therefore also propose to reclassify both species into the novel genus Caespitibacter gen. nov. as Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov., respectively, and with C. soli comb. nov. as the type species.\n\nDescription of Pseudoclavibacter triregionum sp. nov. from human blood and Pseudoclavibacter albus comb. nov., and revised classification of the genus Pseudoclavibacter: proposal of Caespitibacter gen. nov., with Caespitibacter soli comb. nov. and Caespitibacter caeni comb. nov.", "token_count": 224, "char_count": 783, "word_count": 104, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:22.072978", "source": { "split": "train_shard_00001", "doc_id": 2862 }, "chunk_id": "train_shard_00001_2862_1", "global_id": 9728 }, { "text": "The Crabtree effect occurs under high-glucose concentrations and is characterized by the increase of the growth and a decrease in mitochondrial respiration of yeasts. Regulation of the Crabtree effect could enhance ethanol production with biotechnological purposes and a better understanding of the etiology of cancer due to its similitude with the Warburg effect. Nonetheless, the conclusive molecular mechanism of the Crabtree effect is still on debate. The pathway Snf1p/Hxk2p/Mig1p has been linked with the transcriptional regulation of the hexose transporters and has also been identified in the modulation of phenotypes related to the Crabtree effect. Nevertheless, it has not been directly identified the genetic regulation of the hexose transporters with modulation of the Crabtree effect phenotypes by Snf1p/Hxk2p/Mig1p pathway. In this sense, we provide evidence that the deletion of the SNF1 and HXK2 genes affects the exponential growth, mitochondrial respiration, and the transcription of hexose transporters in a glucose-dependent manner in Saccharomyces cerevisiae . The Vmax of the main hexose transporters transcribed showed a positive correlation with the exponential growth and a negative correlation with the mitochondrial respiration. Transcription of the gene HXT2 was the most affected by the deletion of the pathway SNF1/HXK2/MIG1 . Deletion of the orthologous genes SNF1 and HXK2 in the Crabtree negative yeast, K. marxianus, has a differential effect in exponential growth and mitochondrial respiration in comparison with S. cerevisiae . Overall, these results indicate that the SNF1/HXK2/MIG1 pathway transcriptionally regulates the hexose transporters having an influence in the exponential growth and mitochondrial respiration in a glucose-dependent manner.\n\nSnf1p/Hxk2p/Mig1p pathway regulates exponential growth, mitochondrial respiration, and hexose transporters transcription inSaccharomyces cerevisiae", "token_count": 504, "char_count": 1942, "word_count": 266, "semantic_coherence": 1, "information_density": 0.4398, "quality_score": 0.7199, "entities": { "genes": [ "SNF1", "HXT2", "HXK2", "MIG1" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:22.736424", "source": { "split": "train_shard_00001", "doc_id": 2863 }, "chunk_id": "train_shard_00001_2863_0", "global_id": 9729 }, { "text": "[Molecular-genetic and physiologic differentiation of yeasts Kluyveromyces lactis and Kluyveromyces marxianus: analysis of strains fron Russian microorganisms collection].", "token_count": 48, "char_count": 171, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:23.105394", "source": { "split": "train_shard_00001", "doc_id": 2864 }, "chunk_id": "train_shard_00001_2864_0", "global_id": 9730 }, { "text": "The objective of this study was to characterize Cronobacter spp. and related organisms isolated from powder dairy products intended for consumption by adults and older adults using whole-genome sequencing (WGS), and to identify genes and traits that encode antibiotic resistance and virulence. Virulence (VGs) and antibiotic resistance genes (ARGs) were detected with the Comprehensive Antibiotic Resistance Database (CARD) platform, ResFinder, and MOB-suite tools. Susceptibility testing was performed using disk diffusion. Five presumptive strains of Cronobacter spp. were identified by MALDI-TOF MS and ribosomal MLST. Three C. sakazakii strains were of the clinical pathovar ST1, one was ST31, and the remaining isolate was C. malonaticus ST60. In addition, Franconibacter helveticus ST345 was identified. The C. sakazakii ST1 strains were further distinguished using core genome MLST based on 2831 loci. Moreover, 100% of the strains were resistant to cefalotin, 75% to ampicillin, and 50% to amikacin. The C. sakazakii ST1 strains were multiresistant (MDR) to four antibiotics. Additionally, all the strains adhered to the N1E-115 cell line, and two invaded it. Eighteen ARGs mainly involved in antibiotic target alteration and antibiotic efflux were detected. Thirty VGs were detected and clustered as flagellar proteins, outer membrane proteins, chemotaxis, hemolysins, and genes involved in metabolism and stress. The pESA3, pSP291-1, and pCMA1 plasmids were detected, and the prevalent mobile genetic elements (MGEs) were ISEsa1, ISEc52, and IS26. The isolates of C. sakazakii and C", "token_count": 524, "char_count": 1651, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6348, "quality_score": 0.8174, "entities": { "genes": [ "IS26", "ST31", "ST60", "ST1", "ST345" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:30:23.737449", "source": { "split": "train_shard_00001", "doc_id": 2865 }, "chunk_id": "train_shard_00001_2865_0", "global_id": 9731 }, { "text": "malonaticus exhibited multiresistance to antibiotics, harbored genes encoding various antibiotic resistance proteins, and various virulence factors. Consequently, these contaminated powdered dairy products pose a risk to the health of hypersensitive adults.\n\nCharacterization of Cronobacter sakazakii and Cronobacter malonaticus Strains Isolated from Powdered Dairy Products Intended for Consumption by Adults and Older Adults.", "token_count": 123, "char_count": 445, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7885, "quality_score": 0.8942, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:24.125658", "source": { "split": "train_shard_00001", "doc_id": 2865 }, "chunk_id": "train_shard_00001_2865_1", "global_id": 9732 }, { "text": "Probiotics are increasingly used as functional food ingredients. The objectives of this study were to isolate and characterise probiotic bacteria from dairy and fermented foods and to use a selected strain for the production of probiotic chèvre cheese. Tolerance to acid (pH 2.0) and bile salt (0.4% (w/v)) were first investigated, and then other probiotic properties were determined. Out of 241 isolates, 35 showed high tolerance to acid and bile salt, and 6 were chosen for further characterisation. They were Lactobacillus plantarum and L. fermentum, and possessed antibacterial activities against foodborne pathogens such as Bacillus cereus, Staphylococcus aureus, Salmonella enterica and Escherichia coli O157:H7. L. plantarum (isolate AD73) showed the highest percentage of adhesion (81.74 ± 0.16%) and was nontoxic to Caco-2 cells at a concentration of 108 CFU/mL. This isolate was therefore selected for the production of probiotic chèvre cheese from goat’s milk and was prepared in a lyophilised form with a concentration of probiotic culture of 8.6 log CFU/g. The cheese had a shelf life of 8 days. On the expiry date, the probiotic, the starter and the yeast contents were 7.56 ± 0.05, 7.81 ± 0.03 and 5.64 log CFU/g, respectively. The level of the probiotics in this chèvre cheese was still sufficiently high to warrant its being a probiotic cheese.\n\nCharacterisation of Lactobacillus plantarum of Dairy-Product Origin for Probiotic Chèvre Cheese Production.", "token_count": 440, "char_count": 1477, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [ "AD73" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:24.756945", "source": { "split": "train_shard_00001", "doc_id": 2866 }, "chunk_id": "train_shard_00001_2866_0", "global_id": 9733 }, { "text": "Three hundred thirty-one yeast and yeast-like isolates were cultivated on eosin methylene blue agar. While the sensitivity rate for Candida kefyr isolates producing a metallic green sheen was 81.8%, the high positive predictive value (100%) for yeast isolates with this phenotype belonging to C. kefyr suggests that these isolates can be presumptively identified as C. kefyr.\n\nPresumptive identification of Candida kefyr on levine formulation of eosin methylene blue agar.", "token_count": 128, "char_count": 472, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7681, "quality_score": 0.8841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:25.181412", "source": { "split": "train_shard_00001", "doc_id": 2867 }, "chunk_id": "train_shard_00001_2867_0", "global_id": 9734 }, { "text": "Until 2019, the human genome was available in only one fully-annotated version, GRCh38, which was the result of 18 years of continuous improvement and revision. Despite dramatic improvements in sequencing technology, no other genome was available as an annotated reference until 2019, when the genome of an Ashkenazi individual, Ash1, was released. In this study, we describe the assembly and annotation of a second individual genome, from a Puerto Rican individual whose DNA was collected as part of the Human Pangenome project. The new genome, called PR1, is the first true reference genome created from an individual of African descent. Due to recent improvements in both sequencing and assembly technology, and particularly to the use of the recently completed CHM13 human genome as a guide to assembly, PR1 is more complete and more contiguous than either GRCh38 or Ash1. Annotation revealed 37,755 genes (of which 19,999 are protein-coding), including 12 additional gene copies that are present in PR1 and missing from CHM13. 57 genes have fewer copies in PR1 than in CHM13, 9 map only partially, and 3 genes (all non-coding) from CHM13 are entirely missing from PR1.\n\nA reference-quality, fully annotated genome from a Puerto Rican individual", "token_count": 315, "char_count": 1249, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.7929, "entities": { "genes": [ "CHM13", "PR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:25.737226", "source": { "split": "train_shard_00001", "doc_id": 2868 }, "chunk_id": "train_shard_00001_2868_0", "global_id": 9735 }, { "text": "DNA sequencing data continues to progress towards longer reads with increasingly lower sequencing error rates. We focus on the problem of assembling such reads into genomes, which poses challenges in terms of accuracy and computational resources when using cutting-edge assembly approaches, e.g. those based on overlapping reads using minimizer sketches. Here, we introduce the concept of minimizer-space sequencing data analysis, where the minimizers rather than DNA nucleotides are the atomic tokens of the alphabet. By projecting DNA sequences into ordered lists of minimizers, our key idea is to enumerate what we call k-min-mers , that are k-mers over a larger alphabet consisting of minimizer tokens. Our approach, mdBG or minimizer-dBG, achieves orders-of-magnitude improvement in both speed and memory usage over existing methods without much loss of accuracy. We demonstrate three uses cases of mdBG: human genome assembly, metagenome assembly, and the representation of large pangenomes. For assembly, we implemented mdBG in software we call rust-mdbg , resulting in ultra-fast, low memory and highly-contiguous assembly of PacBio HiFi reads. A human genome is assembled in under 10 minutes using 8 cores and 10 GB RAM, and 60 Gbp of metagenome reads are assembled in 4 minutes using 1 GB RAM. For pangenome graphs, we newly allow a graphical representation of a collection of 661,405 bacterial genomes as an mdBG and successfully search it (in minimizer-space) for anti-microbial resistance (AMR) genes. We expect our advances to be essential to sequence analysis, given the rise of long-read sequencing in genomics, metagenomics and pangenomics.\n\nMinimizer-space de Bruijn graphs", "token_count": 403, "char_count": 1691, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6614, "quality_score": 0.8307, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:26.374737", "source": { "split": "train_shard_00001", "doc_id": 2869 }, "chunk_id": "train_shard_00001_2869_0", "global_id": 9736 }, { "text": "Xanthomonas spp. infect a wide range of annual and perennial plants. Bacterial blight in young seedlings of Eucalyptus spp. in Indonesia was originally identified as X. perforans. However, these strains failed to elicit a hypersensitive response (HR) on either tomatoes or peppers. Two of the strains, EPK43 and BCC 972, when infiltrated into tomato and pepper leaves, failed to grow to significant levels in comparison with well-characterized X. euvesicatoria pv. perforans (Xp) strains. Furthermore, spray inoculation of 'Bonny Best' tomato plants with a bacterial suspension of the Eucalyptus strains resulted in no obvious symptoms. We sequenced the whole genomes of eight strains isolated from two Eucalyptus species between 2007 and 2015. The strains had average nucleotide identities (ANIs) of at least 97.8 with Xp and X. euvesicatoria pv. euvesicatoria (Xeu) strains, both of which are causal agents of bacterial spot of tomatoes and peppers. A comparison of the Eucalyptus strains revealed that the ANI values were >99.99% with each other. Core genome phylogeny clustered all Eucalyptus strains with X. euvesicatoria pv. rosa. They formed separate clades, which included X. euvesicatoria pv. alangii, X. euvesicatoria pv. citrumelonis, and X. euvesicatoria pv. alfalfae", "token_count": 509, "char_count": 1433, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8194, "entities": { "genes": [ "EPK43" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:27.068937", "source": { "split": "train_shard_00001", "doc_id": 2870 }, "chunk_id": "train_shard_00001_2870_0", "global_id": 9737 }, { "text": "Based on ANI, phylogenetic relationships, and pathogenicity, we designated these Eucalyptus strains as X. euvesicatoria pv. eucalypti (Xee). Comparative analysis of sequenced strains provided unique profiles of type III secretion effectors. Core effector XopD, present in all pathogenic Xp and Xeu strains, was absent in the Xee strains. Comparison of the hrp clusters of Xee, Xp, and Xeu genomes revealed that HrpE in Xee strains was very different from that in Xp and Xeu. To determine if it was functional, we deleted the gene and complemented with the Xee hrpE, confirming it was essential for secretion of type III effectors. HrpE has a hypervariable N-terminus in Xanthomonas spp., in which the N-terminus of Xee strains differs significantly from those of Xeu and Xp strains.\n\nWhole-Genome-Sequence-Based Classification of Xanthomonas euvesicatoria pv. eucalypti and Computational Analysis of the Type III Secretion System.", "token_count": 376, "char_count": 1070, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6143, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:27.684158", "source": { "split": "train_shard_00001", "doc_id": 2870 }, "chunk_id": "train_shard_00001_2870_1", "global_id": 9738 }, { "text": "Haemophilus parasuis is a diverse bacterial species that is found in the upper respiratory tracts of pigs and can also cause Glässer's disease and pneumonia. A previous pangenome study of H. parasuis identified 48 genes that were associated with clinical disease. Here, we describe the development of a generalized linear model (termed a pathotyping model) to predict the potential virulence of isolates of H. parasuis based on a subset of 10 genes from the pangenome. A multiplex PCR (mPCR) was constructed based on these genes, the results of which were entered into the pathotyping model to yield a prediction of virulence. This new diagnostic mPCR was tested on 143 field isolates of H. parasuis that had previously been whole-genome sequenced and a further 84 isolates from the United Kingdom from cases of H. parasuis-related disease in pigs collected between 2013 and 2014. The combination of the mPCR and the pathotyping model predicted the virulence of an isolate with 78% accuracy for the original isolate collection and 90% for the additional isolate collection, providing an overall accuracy of 83% (81% sensitivity and 93% specificity) compared with that of the \"current standard\" of detailed clinical metadata. This new pathotyping assay has the potential to aid surveillance and disease control in addition to serotyping data.\n\n\"Pathotyping\" Multiplex PCR Assay for Haemophilus parasuis: a Tool for Prediction of Virulence.", "token_count": 399, "char_count": 1473, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5689, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:28.312397", "source": { "split": "train_shard_00001", "doc_id": 2871 }, "chunk_id": "train_shard_00001_2871_0", "global_id": 9739 }, { "text": "Recombination is essential to microbial evolution 1–4 , and is involved in the spread of antibiotic resistance, antigenic variation, and adaptation to the host niche 5–8 . Yet quantifying the impact of homologous recombination on different gene classes, which is critical to understanding how selection acts on variation to shape species diversity and genome structure, remains challenging. This is largely due to the dynamic nature of bacterial genomes, whose high intraspecies genome content diversity 9 and complex phylogenetic relationships 10–12 present difficulties for inferring rates of recombination, particularly for rare genes. In this work, we apply a computationally efficient, non-phylogenetic approach 13,14 to measure homologous recombination rates in the core and accessory genome (genes present in all strains and only a subset of strains, respectively) using >100,000 whole genome sequences from 12 microbial species. Our analysis suggests that even well-resolved sequence clusters sampled from global populations interact with overlapping gene pools, which has implications for the role of population structure in genome evolution. We show that in a majority of species, core genes have shorter coalescence times and higher recombination rates than accessory genes, and that gene frequency is often positively correlated with increased recombination. Our results provide a new line of population genomic evidence supporting the hypothesis that core genes are under strong, purifying selection 15–17 , and indicate that homologous recombination may play a key role in increasing the efficiency of selection in those parts of the genome most conserved within each species.\n\nCore genes can have higher recombination rates than accessory genes within global microbial populations", "token_count": 388, "char_count": 1795, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6178, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:28.929121", "source": { "split": "train_shard_00001", "doc_id": 2872 }, "chunk_id": "train_shard_00001_2872_0", "global_id": 9740 }, { "text": "

Background:

Salmonella enterica is a significant public health concern due to its ability to cause foodborne illnesses worldwide. To gain insights into the epidemiology and characteristics of Salmonella strains in China, a total of 20 Salmonella isolates were subjected to phenotypic and molecular analyses. Methods The 20 Salmonella strains were characterized through serotype identification, antimicrobial susceptibility testing (AST), biofilm formation assessment and plasmid transmission studies. Molecular characteristics and relatedness were determined using pulsed-field gel electrophoresis (PFGE) and whole genome sequencing (WGS). Additionally, SNP-based phylogenetic analysis and core genome multilocus sequence typing (cgMLST) were employed to contextualize the strains among previously sequenced S. enterica isolates in China and worldwide. Results The predominant serovar identified was Salmonella enterica serovar Enteritidis ( S. Enteritidis), followed by S. Mbandaka, Thompson, Livingston, Alachua, and Infantis. The SNP-based phylogenetic analysis revealed substantial diversity among S. Enteritidis isolates, with a minimum of 32 SNPs between strains. Conversely, S. Mbandaka isolates were suspected to have originated from a single clonal expansion, displaying a difference within 6 SNPs. SNP-based phylogenetic analysis suggested S. Mbandaka clone in this study was likely to have been derived from a single source that persisted over 5 years in China. S. Mbandaka, Infantis, Livingston, and Alachua exhibited susceptibility to the tested antibiotics, while strains of S. Thompson and Enteritidis demonstrated resistance to ampicillin, quinolone, and sulfamethoxazole/trimethoprim (SMZ/TMP). Particularly concerning was the identification of one S. Enteritidis isolate carrying the highly transferable IncB/O/K/Z plasmid with bla CTX−M15 , conferring cephalosporin resistance. Another isolate, harboring the mrkABCDF operon in an IncX1 plasmid, isolated from cutaneous lesions, demonstrated robust biofilm formation", "token_count": 525, "char_count": 2047, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:30:29.588329", "source": { "split": "train_shard_00001", "doc_id": 2873 }, "chunk_id": "train_shard_00001_2873_0", "global_id": 9741 }, { "text": "Conclusions Our study emphasizes the importance of SNP-based surveillance and prompt response to Salmonella infections to protect public health. The dissemination of bla CTX−M15 -harboring IncB/O/K/Z plasmid and the spread of virulent mrkABCDF operon among S. enterica in China and other global regions warrant close monitoring.\n\nGenomic Diversity of Salmonella Infection from a Tertiary Hospital in China: Insights from Phenotypic and Molecular Analyses", "token_count": 125, "char_count": 455, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:29.970898", "source": { "split": "train_shard_00001", "doc_id": 2873 }, "chunk_id": "train_shard_00001_2873_1", "global_id": 9742 }, { "text": "Provided is a method for expressing a target gene. In said method, a specific promoter derived from Saccharomyces cerevisiae (the TDH3 promoter, ILV5 promoter, or CWP2 promoter) is used in Kluyveromyces marxianus. Also provided is a method for manufacturing the product of a target gene.\n\nTARGET GENE EXPRESSION METHOD USING A SPECIFIC PROMOTER DERIVED FROM SACCHAROMYCES CEREVISIAE IN KLUYVEROMYCES MARXIANUS", "token_count": 134, "char_count": 409, "word_count": 60, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "TDH3", "CWP2", "ILV5" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:30.406706", "source": { "split": "train_shard_00001", "doc_id": 2874 }, "chunk_id": "train_shard_00001_2874_0", "global_id": 9743 }, { "text": "

Background

GRAS transcription factors are crucial for plant development and stress responses but remain poorly characterized in citrus. Soil salinization increasingly threatens sweet orange (Citrus sinensis) yield. Identifying salt-responsive GRAS genes could reveal key tolerance determinants for breeding resistant cultivars.

Methods

We systematically identified and analyzed sweet orange GRAS transcription factors using bioinformatics.

Results

Forty-three CsGRAS genes were identified, phylogenetically classified into ten subfamilies, and found to be structurally conserved. A promoter analysis revealed a high prevalence (58.78%) of hormone- and stress-responsive cis-elements. These genes reside on nine chromosomes, with segmental duplication being the primary evolutionary driver (eight duplicated pairs). Functional enrichment implicated hormone signaling pathways in regulating growth under stress. Transcriptome profiling identified 42 differentially expressed CsGRAS genes (19 upregulated and 23 downregulated) under salt stress. qRT-PCR validated the expression patterns of selected genes (e.g., CsGRAS15 and CsGRAS27). Notably, DELLA subfamily members CsGRAS15 and CsGRAS27, key negative regulators in gibberellin (GA) signaling, were differentially expressed. Modulating these DELLA proteins presents a promising strategy to enhance sweet orange salt tolerance by mitigating GA-mediated growth inhibition during stress.

Conclusion

This study identifies salt-responsive CsGRAS genes, highlighting CsGRAS15 and CsGRAS27 as potential targets for improving salt tolerance in citrus.", "token_count": 477, "char_count": 1700, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7579, "quality_score": 0.8789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:31.047542", "source": { "split": "train_shard_00001", "doc_id": 2875 }, "chunk_id": "train_shard_00001_2875_0", "global_id": 9744 }, { "text": "Genome-Wide Identification of the GRAS Transcription Factor Family in Sweet Orange and the Regulation of Salt Stress-Enhanced Plant Salt Tolerance in Sweet Orange by <i>CsGRAS15</i> and <i>CsGRAS27</i>.", "token_count": 82, "char_count": 226, "word_count": 27, "semantic_coherence": 1, "information_density": 0.7407, "quality_score": 0.8704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:31.416960", "source": { "split": "train_shard_00001", "doc_id": 2875 }, "chunk_id": "train_shard_00001_2875_1", "global_id": 9745 }, { "text": "Galacto-oligosaccharides (GOS) were synthesised from 50% (w/w) lactose with Aspergillus oryzae β-galactosidase. Reacted medium without nutrient supplementation (raw GOS) was fermented with Kluyveromyces marxianus cells obtaining GOS of 95% purity containing mostly tri- and tetrasaccharides with total recovery of GOS after 24 h. The effect of the initial concentration of carbohydrate was assessed in the range of 10–50% (w/w), such purity being obtained even at 50% (w/w) (undiluted raw GOS) though being strongly influenced by the dry cell to total carbohydrate mass ratio (RCC). The process of purification by selective fermentation of raw GOS at 20% (w/w) was optimised in terms of the specific productivity of unwanted carbohydrate removal, considering temperature, pH and RCC as operational variables. According to the experimental design, maximum specific productivity predicted was 0.16 g g−1 h−1, obtained at the optimal operating conditions of 40 °C, pH 3.5 and RCC 1.55 g g−1.\n\nPurification of highly concentrated galacto-oligosaccharide preparations by selective fermentation with yeasts", "token_count": 334, "char_count": 1100, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6709, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:31.988278", "source": { "split": "train_shard_00001", "doc_id": 2876 }, "chunk_id": "train_shard_00001_2876_0", "global_id": 9746 }, { "text": "

Objectives

Using registry data to compare fungaemia caused by uncommon yeast species (UYS; i.e. other than Candida albicans , Candida glabrata , Candida parapsilosis , Candida tropicalis and Candida krusei ) and C. albicans -related fungaemia can reveal specific predisposing factors of UYS with potential impact on treatment strategies.

Methods

We analysed 338 episodes of UYS fungaemia prospectively collected from 27 hospitals (Paris, France; 1 October 2002-31 December 2014) and compared these with 1998 single episodes of C. albicans fungaemia using univariate and multivariate analyses.

Results

The proportion of UYS fungaemia was stable over time. Thirty-five different species were identified (27 ascomycetes, 8 basidiomycetes), 11 had caspofungin MIC 50  >0.25 mg/L and 15 fluconazole MIC 50  >4 mg/L. Haematological malignancies [OR=2.39 (95% CI 1.79-3.18)] and prior exposure to antifungal drugs [OR=1.87 (1.30-2.69)] were independent predisposing factors for UYS infections upon multivariate analysis. However, when considering the genus/species complex level, only infections due to Candida kefyr -related species [OR=4.01 (2.42-6.64)] and to Trichosporon spp. [OR=5.38 (1.72-16.81)] remained associated with haematological malignancies, those due to the GEOTRICHUM group with acute leukaemia [OR=61.29 (19.23-195.36)], and infections with Trichosporon spp", "token_count": 502, "char_count": 1391, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:32.640317", "source": { "split": "train_shard_00001", "doc_id": 2877 }, "chunk_id": "train_shard_00001_2877_0", "global_id": 9747 }, { "text": "or the GEOTRICHUM group with prior exposure to caspofungin [OR=15.67 (3.62-67.80) and OR=13.17 (3.33-52.03), respectively] but not to fluconazole. The global mortality at day 30 for UYS was similar to that for C. albicans (35.4%, and 39.9%, respectively), but very divergent results were observed according to the specific UYS.

Conclusions

UYS encompass a high diversity of species, each with its own behaviour and predisposing factors for human infections. This variety makes it important to rapidly identify an isolate to the species level in order to optimize antifungal treatment.\n\nPredisposing factors and outcome of uncommon yeast species-related fungaemia based on an exhaustive surveillance programme (2002-14).", "token_count": 219, "char_count": 726, "word_count": 102, "semantic_coherence": 1, "information_density": 0.8039, "quality_score": 0.902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:33.102636", "source": { "split": "train_shard_00001", "doc_id": 2877 }, "chunk_id": "train_shard_00001_2877_1", "global_id": 9748 }, { "text": "COMPOSITION COMPRISING KLUYVEROMYCES MARXIANUS FOR PREVENTION AND TREATMENT OF ALLERGY, INFLAMMATION OR ASTHMA DISEASES", "token_count": 52, "char_count": 119, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:33.476590", "source": { "split": "train_shard_00001", "doc_id": 2878 }, "chunk_id": "train_shard_00001_2878_0", "global_id": 9749 }, { "text": "

Introduction

Clostridioides difficile (C. difficile) is a nosocomial bacterial pathogen that causes antibiotic-associated diarrhea mediated by cellular exotoxins secreted into the intestine during bacterial growth. Multilocus sequence typing (MLST) and PCR ribotyping are the main molecular typing for C. difficile. Whole genome sequencing (WGS) core genome multilocus sequence typing (cgMLST) was developed for genetic evolution and outbreak investigation of C. difficile with higher precision and accuracy.

Methods

A total of 699 whole (complete and draft) genome sequences of distinct C. difficile strains were used in this study to identify core gene set (2469 core genes) and the cgMLST scheme for the phylogeny analysis of C. difficile. This cgMLST pipeline was then carried the Chinese Pathogen Identification Net (China PIN) for surveillance of C. difficile in China. Within the China PIN, 195 WGS of C. difficile and an outbreak of CDI with 12 WGS of C. difficile were used to evaluate the cgMLST pipeline.

Results

The result displayed that mostly tested C. difficile isolates could be successfully divided into 5 classic clades and the outbreak event was also successfully identified.

Discussion

The results are meaningful and offer a practicable pipeline for a national-wide surveillance of C. difficile in China.\n\nApplication of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China.", "token_count": 456, "char_count": 1549, "word_count": 207, "semantic_coherence": 1, "information_density": 0.57, "quality_score": 0.785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:34.115269", "source": { "split": "train_shard_00001", "doc_id": 2879 }, "chunk_id": "train_shard_00001_2879_0", "global_id": 9750 }, { "text": "The thermotolerant yeast Kluyveromyces marxianus IMB3 was capable of utilising either iminodiacetate or nitrilotriacetate as a sole source of nitrogen for growth. Cell extracts contained iminodiacetate dehydrogenase and nitrilotriacetate monooxygenase activities, suggesting the presence in the yeast of orthologues of these bacterial enzymes. The activities were not detectable in complete medium-growth cells, nor in nitrogen-starved cells, suggesting an inducible biodedgradation pathway for biodegradation of these xenobiotics, which has not been previously reported in a eukaryotic cell system. This observation emphasises the hitherto unrealised importance of yeast strains in the biodegradation of xenobiotics in the environment.\n\nIminodiacetate and nitrilotriacetate degradation by Kluyveromyces marxianus IMB3.", "token_count": 227, "char_count": 819, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.835, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:34.582494", "source": { "split": "train_shard_00001", "doc_id": 2880 }, "chunk_id": "train_shard_00001_2880_0", "global_id": 9751 }, { "text": "Provided is a novel high-expression promoter, namely a GAL1 promoter, derived from Kluyveromyces marxianus. Also provided are the following, characterized by the use of the provided high-expression promoter: a recombinant polynucleotide containing said high-expression promoter a vector containing said recombinant polynucleotide a transformant obtained by introducing said recombinant polynucleotide or vector into yeast a method using said transformant for high expression of a target gene and a method using said transformant to manufacture the gene product of a target gene.\n\nHIGH-EXPRESSION PROMOTER DERIVED FROM KLUYVEROMYCES MARXIANUS", "token_count": 166, "char_count": 641, "word_count": 86, "semantic_coherence": 1, "information_density": 0.5349, "quality_score": 0.7674, "entities": { "genes": [ "GAL1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:35.023165", "source": { "split": "train_shard_00001", "doc_id": 2881 }, "chunk_id": "train_shard_00001_2881_0", "global_id": 9752 }, { "text": "Gowé is a traditional Beninese fermented red sorghum beverage made from a blend of malted and precooked nonmalted flour. The main objective of this work was to evaluate the degradation of starch during the production of gowé and to characterise the organic acid and sugar profiles of the product obtained using starter cultures. Inoculation was performed with strains of Lactobacillus fermentum or Weissella confusa and of Kluyveromyces marxianus or Pichia anomala used singly or in combination. Size exclusion chromatography revealed that starch was hydrolysed into high molecular weight dextrins (DP over 35), oligosaccharides and glucose, mainly due to the malting and precooking steps. Glucose was the main free sugar, and lactic acid was the main organic acid. The choice of the inoculation strain directly influenced the acidity but also indirectly the sugar content of the resulting gowé and will thus affect consumer acceptability.\n\nDextrin, sugar and organic acid profiles of spontaneous and modified gowe: a malted and fermented sorghum beverage from Benin", "token_count": 265, "char_count": 1066, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6358, "quality_score": 0.8179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:35.571269", "source": { "split": "train_shard_00001", "doc_id": 2882 }, "chunk_id": "train_shard_00001_2882_0", "global_id": 9753 }, { "text": "Serotyping has traditionally been considered the basis for surveillance of Salmonella, but it cannot distinguish distinct lineages sharing the same serovar that vary in host range, pathogenicity and epidemiology. However, polyphyletic serovars have not been extensively investigated. Public health microbiology is currently being transformed by whole-genome sequencing (WGS) data, which promote the lineage determination using a more powerful and accurate technique than serotyping. The focus in this study is to survey and analyze putative polyphyletic serovars. The multi-locus sequence typing (MLST) phylogenetic analysis identified four putative polyphyletic serovars, namely, Montevideo, Bareilly, Saintpaul, and Muenchen. Whole-genome-based phylogeny and population structure highlighted the polyphyletic nature of Bareilly and Saintpaul and the multi-lineage nature of Montevideo and Muenchen. The population of these serovars was defined by extensive genetic diversity, the open pan genome and the small core genome. Source niche metadata revealed putative existence of lineage-specific niche adaptation (host-preference and environmental-preference), exhibited by lineage-specific genomic contents associated with metabolism and transport. Meanwhile, differences in genetic profiles relating to virulence and antimicrobial resistance within each lineage may contribute to pathogenicity and epidemiology. The results also showed that recombination events occurring at the H1-antigen loci may be an important reason for polyphyly. The results presented here provide the genomic basis of simple, rapid, and accurate identification of phylogenetic lineages of these serovars, which could have important implications for public health.\n\nWhole-Genome-Based Survey for Polyphyletic Serovars of Salmonella enterica subsp. enterica Provides New Insights into Public Health Surveillance.", "token_count": 444, "char_count": 1907, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:36.202738", "source": { "split": "train_shard_00001", "doc_id": 2883 }, "chunk_id": "train_shard_00001_2883_0", "global_id": 9754 }, { "text": "

Background and objectives

Oral candidiasis is a serious problem for immunocompromised patients, especially patients with hematological malignancies. After becoming a systemic candidiasis it is difficult to diagnose, control and treat in individuals with hematological malignancies. The aim of this study was to diagnose candidiasis in the oral mucosa of patients with leukemias and lymphomas in a timely manner in order to prevent their progression to systemic candidiasis.

Materials and methods

In this cross sectional study, 50 clinical samples were collected from the mouth of patients with hematological malignancies undergoing chemotherapy from the oncology units of teaching hospitals in Kerman, Iran. Patients were from Kerman, Sistan-Baluchestan and Hormozgan in south-eastern Iran. Sampling was restricted to patients with diagnosed acute lymphoid leukemia (ALL); acute myeloid leukemia (AML); chronic lymphoid leukemia (CLL); chronic myeloid leukemia (CML); Hodgkin's lymphoma (HL) and non-Hodgkin's lymphoma (NHL). Presumptive species identification of fungi was performed using conventional methods like colony characteristics on CHROMagar Candida medium, germ tube production, and assessing the morphology fungi on corn meal agar. Confirmation of presumptive candida isolates was performed using PCR-RFLP.

Results

From a total of 50, 14 patients (28%) had positive oral candidiasis. Candida albicans (57.14%) was the most common species followed by Candida glabrata (14.28%), Candida parapsilosis (14.28%), Candida krusei (7.14%) and Candida kefyr (7.14%)", "token_count": 495, "char_count": 1632, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:36.856306", "source": { "split": "train_shard_00001", "doc_id": 2884 }, "chunk_id": "train_shard_00001_2884_0", "global_id": 9755 }, { "text": "Candida albicans had the highest rate of oral infection in ALL (35.71%) and then NHL (28.57%) patients.

Conclusion

The results indicate that oral candidiasis is a prevalent fungal infection in the patients with hematologic malignancies with C. albicans being the main etiological agent. However, other species of Candida cause similar infections in these patients.\n\nIdentification of Candida spp. isolated from oral mucosa in patients with leukemias and lymphomas in Iran.", "token_count": 156, "char_count": 507, "word_count": 68, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:37.296814", "source": { "split": "train_shard_00001", "doc_id": 2884 }, "chunk_id": "train_shard_00001_2884_1", "global_id": 9756 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) infection can cause mild to severe illness, such as nonbloody or bloody diarrhea, and the fatal hemolytic uremic syndrome (HUS). The molecular mechanism underlying the variable pathogenicity of STEC infection is not fully defined so far. Here, we performed a comparative genomics study on a large collection of clinical STEC strains collected from STEC-infected pediatric patients with and without HUS in Finland over a 16-year period, aiming to identify the bacterial genetic factors that can predict the risk to cause HUS and poor renal outcome. Of 240 STEC strains included in this study, 52 (21.7%) were from pediatric patients with HUS. Serotype O157:H7 was the main cause of HUS, and Shiga toxin gene subtype stx2a was significantly associated with HUS. Comparative genomics and pangenome-wide association studies identified a number of virulence and accessory genes overrepresented in HUS-associated STEC compared to non-HUS STEC strains, including genes encoding cytolethal distending toxins, type III secretion system effectors, adherence factors, etc. No virulence or accessory gene was significantly associated with risk factors for poor renal outcome among HUS patients assessed in this study, including need for and duration of dialysis, presence and duration of anuria, and leukocyte counts. Whole-genome phylogeny and multiple-correspondence analysis of pangenomes could not separate HUS STEC from non-HUS STEC strains, suggesting that STEC strains with diverse genetic backgrounds may independently acquire genetic elements that determine their varied pathogenicity. Our findings indicate that nonbacterial factors, i.e., characteristics of the host immunity, might affect STEC virulence and clinical outcomes", "token_count": 441, "char_count": 1778, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6349, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:37.949248", "source": { "split": "train_shard_00001", "doc_id": 2885 }, "chunk_id": "train_shard_00001_2885_0", "global_id": 9757 }, { "text": "IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) is a serious public health burden worldwide which causes outbreaks of gastrointestinal diseases and the fatal hemolytic uremic syndrome (HUS) characterized by the triad of mechanical hemolytic anemia, thrombocytopenia, and acute renal failure. Understanding the mechanism underlying the disease severity and patient outcome is of high importance. Using comparative genomics on a large collection of clinical STEC strains from STEC-infected patients with and without HUS, our study provides a reference of STEC genetic factors/variants that can be used as predictors of the development of HUS, which will aid risk assessment at the early stage of STEC infection. Additionally, our findings suggest that nonbacterial factors may play a primary role in the renal outcome in STEC-infected patients with HUS; further studies are needed to validate this.\n\nComparative Genomics of Shiga Toxin-Producing Escherichia coli Strains Isolated from Pediatric Patients with and without Hemolytic Uremic Syndrome from 2000 to 2016 in Finland.", "token_count": 280, "char_count": 1090, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6645, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:38.519905", "source": { "split": "train_shard_00001", "doc_id": 2885 }, "chunk_id": "train_shard_00001_2885_1", "global_id": 9758 }, { "text": "

Introduction

The objective of this study was to examine the evolution of carbapenem-resistant Klebsiella pneumoniae (CRKp) infections and their impact at a tertiary care hospital in South India.

Methods

A comparative analysis of clinical data from two prospective cohorts of patients with CRKp bacteremia (C1, 2014-2015; C2, 2021-2022) was carried out. Antimicrobial susceptibilities and whole genome sequencing (WGS) data of selected isolates were also analyzed.

Results

A total of 181 patients were enrolled in the study, 56 from C1 and 125 from C2. CRKp bacteremia shifted from critically ill patients with neutropenia to others (ICU stay: C1, 73%; C2, 54%; p = 0.02). The overall mortality rate was 50% and the introduction of ceftazidime-avibactam did not change mortality significantly (54% versus 48%; p = 0.49). Oxacillinases (OXA) 232 and 181 were the most common mechanisms of resistance. WGS showed the introduction of New Delhi metallo-β-lactamase-5 (NDM-5), higher genetic diversity, accessory genome content, and plasmid burden, as well as increased convergence of hypervirulence and carbapenem resistance in C2.

Conclusions

CRKp continues to pose a significant clinical threat, despite the introduction of new antibiotics. The study highlights the evolution of resistance and virulence in this pathogen and the impact on patient outcomes in South India, providing valuable information for clinicians and researchers.\n\nClinical and Genomic Evolution of Carbapenem-Resistant Klebsiella pneumoniae Bloodstream Infections over Two Time Periods at a Tertiary Care Hospital in South India: A Prospective Cohort Study.", "token_count": 501, "char_count": 1655, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6332, "quality_score": 0.8166, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:39.198280", "source": { "split": "train_shard_00001", "doc_id": 2886 }, "chunk_id": "train_shard_00001_2886_0", "global_id": 9759 }, { "text": "The One Health approach looks after animal welfare and demands constant monitoring of the strains that circulate globally to prevent outbreaks. Anaplasma marginale is the etiologic agent of bovine anaplasmosis and is endemic worldwide. This study aimed to analyze, for the first time, the genetic diversity of seven Mexican strains of A. marginale and their relationship with other strains reported. The main features of A. marginale were obtained by characterizing all 24 genomes reported so far. Genetic diversity and phylogeography were analyzed by characterizing the msp1a gene and 5'-UTR microsatellite sequences and constructing a phylogenetic tree with 540 concatenated genes of the core genome. The Mexican strains show 15 different repeat sequences in six MSP1a structures and have phylogeographic relationships with strains from North America, South America, and Asia, which confirms they are highly variable. Based on our results, we encourage the performance of genome sequencing of A. marginale strains to obtain a high assembly level of molecular markers and the performance of extensive phylogeographic analysis. Undoubtedly, genomic surveillance helps build a picture of how a pathogen changes and evolves in geographical regions. However, we cannot discard the study of relationships pathogens establish with ticks and how they have co-evolved to establish themselves as a successful transmission system.\n\nMexican Strains of Anaplasma marginale: A First Comparative Genomics and Phylogeographic Analysis.", "token_count": 376, "char_count": 1556, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:39.839639", "source": { "split": "train_shard_00001", "doc_id": 2887 }, "chunk_id": "train_shard_00001_2887_0", "global_id": 9760 }, { "text": "

Introduction

Serratia marcescens is a significant causative agent of hospital-acquired infections (HAIs), particularly in intensive care units (ICUs). Carbapenem resistance represents a major concern in HAI management, as carbapenem-resistant bacteria can trigger outbreaks in hospital settings. While molecular evaluation of outbreaks typically relies on pulse field gel electrophoresis (PFGE) or core genome multilocus sequence typing (cgMLST) methods, alternative rapid, reliable, and cost-effective methods for assessing clonal relatedness are needed.

Methods

This study aimed to characterize a carbapenem-resistant S. marcescens outbreak that occurred during the COVID-19 pandemic in a tertiary care hospital, using the flagellin gene as a single-locus sequence typing (SLST) method. In addition, we evaluated the genetic context of carbapenemase genes through whole-genome sequencing (WGS).

Results

Among the 170 carbapenem-resistant Serratia marcescens isolates recovered, high resistance to gentamicin, ciprofloxacin, and cefepime was observed. The predominant carbapenemase gene detected by qPCR-HRM was blaKPC (92.2%). Phylogenetic analysis of the flagellin gene grouped the sequences into two distinct clades, with all outbreak-related bla KPC-positive S. marcescens isolates clustering within clade B. The bla KPC gene was carried on an IncP6 plasmid.

Discussion

Our findings indicate that the flagellin gene serves as an effective marker for characterizing carbapenem-resistant S", "token_count": 466, "char_count": 1588, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7354, "quality_score": 0.8677, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:40.486360", "source": { "split": "train_shard_00001", "doc_id": 2888 }, "chunk_id": "train_shard_00001_2888_0", "global_id": 9761 }, { "text": "marcescens carrying bla KPC, confirming that the outbreak was caused by the clonal expansion of isolates harboring bla KPC on an IncP6 plasmid.\n\nMolecular epidemiology of a carbapenem-resistant <i>Serratia marcescens</i> outbreak during the COVID-19 pandemic.", "token_count": 115, "char_count": 311, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:40.869495", "source": { "split": "train_shard_00001", "doc_id": 2888 }, "chunk_id": "train_shard_00001_2888_1", "global_id": 9762 }, { "text": "The use of flocculating yeast strains has been considered as a convenient approach to obtain high cell densities in bioreactors with increasing productivity in continuous operations. In Kluyveromyces marxianus ATTC 10022, the GAP1 gene encodes an isoform of glyceraldehyde-3-phosphate dehydrogenase-p37-that is accumulated in the cell wall and is involved in flocculation. To test the use of p37 as a tool for engineering Kluyveromyces cells to display a flocculation phenotype, K. marxianus CCT 3172 was transformed with an expression vector containing GAP1. This vector is based on the pY37 previously described, harbouring a S11 Kluyveromyces origin of replication, and the expression of GAP1 is under the control of GAL1. Kluyveromyces cells overexpressing GAP1 acquired a flocculent phenotype together with the accumulation of p37 in the cell wall. The results support the use of GAP1 gene as a molecular tool for inducing flocculation.\n\nAcquisition of flocculation phenotype by Kluyveromyces marxianus when overexpressing GAP1 gene encoding an isoform of glyceraldehyde-3-phosphate dehydrogenase.", "token_count": 317, "char_count": 1102, "word_count": 158, "semantic_coherence": 1, "information_density": 0.5633, "quality_score": 0.7816, "entities": { "genes": [ "GAP1", "GAL1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:41.432133", "source": { "split": "train_shard_00001", "doc_id": 2889 }, "chunk_id": "train_shard_00001_2889_0", "global_id": 9763 }, { "text": "

Background

Pseudomonas aeruginosa is an important cause of serious nosocomial infections. Despite the overall genetic diversity of this species, highly conserved clonal complexes (CCs) have been observed among MDR isolates. Many of these CCs are associated with MBL-producing isolates.

Objectives

To evaluate five P. aeruginosa isolates from Central America that carried IMP-18- and/or VIM-2-encoding genes from the SENTRY Antimicrobial Surveillance Program (2017-2018).

Methods

Susceptibility testing was performed by broth microdilution (CLSI). WGS was performed using MiSeq (Illumina) and MinION (Oxford Nanopore). Assembled contigs from short and long reads were combined for in silico screening of resistance genes, MLST, core genome (cg)MLST and SNP analysis.

Results

The P. aeruginosa isolates were collected in Panama and Mexico from patients with urinary tract infections or pneumonia. Isolates were categorized as XDR (CLSI/EUCAST). All isolates belonged to ST111 but carried different combinations of resistance-encoding genes. Transposon-associated MBL genes, blaIMP-18 and/or blaVIM-2, were chromosomally located. blaIMP-18 was detected in an In1666 integron whereas blaVIM-2 was embedded in an In59-like integron. Isolates were closely related based on cgMLST (average allele distance 2-34) and SNP analysis (5-423 different SNPs).

Conclusions

MBL-producing ST111 P", "token_count": 504, "char_count": 1532, "word_count": 177, "semantic_coherence": 1, "information_density": 0.7797, "quality_score": 0.8898, "entities": { "genes": [ "ST111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:42.082369", "source": { "split": "train_shard_00001", "doc_id": 2890 }, "chunk_id": "train_shard_00001_2890_0", "global_id": 9764 }, { "text": "aeruginosa have become endemic in Panama and may have spread to Mexico via clonal dissemination. Recombination events are apparent in the evolution of this CC. Surveillance is warranted to track the expansion and movement of this clone.\n\nEndemicity of Pseudomonas aeruginosa producing IMP-18 and/or VIM-2 MBLs from the high-risk clone ST111 in Central America.", "token_count": 104, "char_count": 371, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [ "ST111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:42.463179", "source": { "split": "train_shard_00001", "doc_id": 2890 }, "chunk_id": "train_shard_00001_2890_1", "global_id": 9765 }, { "text": "The whole genome of Weissella cibaria strain UTNGt21O isolated from wild fruits of Solanum quitoense (naranjilla) shrub was sequenced and annotated. The similarity proportions based on the genus level, as a result of the best hits for the entire contig, were 54.84% with Weissella, 6.45% with Leuconostoc, 3.23% with Lactococcus, and 35.48% no match. The closest genome was W. cibaria SP7 (GCF_004521965.1) with 86.21% average nucleotide identity (ANI) and 3.2% alignment coverage. The genome contains 1,867 protein-coding genes, among which 1,620 were assigned with the EggNOG database. On the basis of the results, 438 proteins were classified with unknown function from which 247 new hypothetical proteins have no match in the nucleotide Basic Local Alignment Search Tool (BLASTN) database. It also contains 78 tRNAs, six copies of 5S rRNA, one copy of 16S rRNA, one copy of 23S rRNA, and one copy of tmRNA. The W. cibaria UTNGt21O strain harbors several genes responsible for carbohydrate metabolism, cellular process, general stress responses, cofactors, and vitamins, conferring probiotic features. A pangenome analysis indicated the presence of various strain-specific genes encoded for proteins responsible for the defense mechanisms as well as gene encoded for enzymes with biotechnological value, such as penicillin acylase and folates; thus, W. cibaria exhibited high genetic diversity", "token_count": 473, "char_count": 1452, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [ "SP7" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:43.109044", "source": { "split": "train_shard_00001", "doc_id": 2891 }, "chunk_id": "train_shard_00001_2891_0", "global_id": 9766 }, { "text": "The genome characterization indicated the presence of a putative CRISPR-Cas array and five prophage regions and the absence of acquired antibiotic resistance genes, virulence, and pathogenic factors; thus, UTNGt21O might be considered a safe strain. Besides, the interaction between the peptide extracts from UTNGt21O and Staphylococcus aureus results in cell death caused by the target cell integrity loss and the release of aromatic molecules from the cytoplasm. The results indicated that W. cibaria UTNGt21O can be considered a beneficial strain to be further exploited for developing novel antimicrobials and probiotic products with improved technological characteristics.\n\nNext-Generation Sequencing for Whole-Genome Characterization of Weissella cibaria UTNGt21O Strain Originated From Wild Solanum quitoense Lam. Fruits: An Atlas of Metabolites With Biotechnological Significance.", "token_count": 250, "char_count": 916, "word_count": 119, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:43.594634", "source": { "split": "train_shard_00001", "doc_id": 2891 }, "chunk_id": "train_shard_00001_2891_1", "global_id": 9767 }, { "text": "Oral lichen planus (OLP) is a chronic T cell-mediated inflammatory disease that affects the mucus membrane of the oral cavity. We previously proposed a potential role of intracellular bacteria detected within OLP lesions in the pathogenesis of OLP and isolated four Escherichia coli strains from OLP tissues that were phylogenetically close to K-12 MG1655 strain. We sequenced the genomes of the four OLP-isolated E. coli strains and generated 6.71 Gbp of Illumina MiSeq data (166-195x coverage per strain). The size of the assembled draft genomes was 4.69 Mbp, with a GC content of 50.7%, in which 4360 to 4367 protein-coding sequences per strain were annotated. We also identified 368 virulence factors and 53 antibiotic resistance genes. Comparative genomics revealed that the OLP-isolated strains shared more pangenome orthologous groups with pathogenic strains than did the K-12 MG1655 strain, a derivative of K-12 strain isolated from human feces. Although the OLP-isolated strains did not have the major virulence factors (VFs) of the pathogenic strains, a number of VFs involved in adherence/invasion, colonization, or systemic infection were identified. The genomic characteristics of E. coli first isolated from the oral cavity would benefit future investigations on the pathogenic potential of these bacteria.\n\nGenomic characterization of four Escherichia coli strains isolated from oral lichen planus biopsies.", "token_count": 424, "char_count": 1450, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [ "MG1655" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:44.225820", "source": { "split": "train_shard_00001", "doc_id": 2892 }, "chunk_id": "train_shard_00001_2892_0", "global_id": 9768 }, { "text": "The growing number of sequenced genomes enables the study of secondary metabolite biosynthetic gene clusters (BGC) in phyla beyond well-studied soil bacteria. We mined 2627 enterobacterial genomes to detect 8604 BGCs, including nonribosomal peptide synthetases, siderophores, polyketide-nonribosomal peptide hybrids, and 60 other BGC types, with an average of around 3.3 BGCs per genome. These BGCs represented 212 distinct BGC families, of which only 20 have associated products in the MIBiG standard database with functions such as siderophores, antibiotics, and genotoxins. Pangenome analysis identified genes associated with a specific BGC encoding for colon cancer-related colibactin. In one example, we associated genes involved in the type VI secretion system with the presence of a colibactin BGC in Escherichia . This richness of BGCs in enterobacteria opens up the possibility to discover novel secondary metabolites, their physiological roles and provides a guide to identify and understand PKS associated gene sets.\n\nPangenome Analysis of Enterobacteria Reveals Richness of Secondary Metabolite Gene Clusters and their Associated Gene Sets", "token_count": 305, "char_count": 1151, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:44.801504", "source": { "split": "train_shard_00001", "doc_id": 2893 }, "chunk_id": "train_shard_00001_2893_0", "global_id": 9769 }, { "text": "Many fermented foods are known to have beneficial effects on human and animal health, offering anti-aging and immunomodulatory benefits to host. Microorganisms contained in the fermented foods are known to provide metabolic products possibly improving host health. However, despite of a number of studies on the functional effects of the fermented foods, isolation and identification of the effective bacterial strains in the products are still in progress. The objective of this study was to isolate candidate functional strains in various Korean traditional fermented foods, including ganjang, gochujang, doenjang, and jeotgal, and evaluate their beneficial effects on the host, using Caenorhabditis elegans as a surrogate animal model. Among the 30 strains isolated, five Bacillus spp. were selected that increased the expression level of pmk-1, an innate immune gene of C. elegans. These strains extended the nematode lifespan and showed intestinal adhesion to the host. Based on the bioinformatic analyses of whole genome sequences and pangenomes, the five strains of Bacillus subtilis were genetically different from the strains found in East Asian countries and previously reported strains isolated from Korean fermented foods. Our findings suggest that the newly isolated B. subtilis strains can be a good candidate for probiotic with further in-depth investigation on health benefits and safety.\n\nComparative Genomic and Functional Evaluations of Bacillus subtilis Newly Isolated from Korean Traditional Fermented Foods.", "token_count": 392, "char_count": 1578, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6018, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:45.416918", "source": { "split": "train_shard_00001", "doc_id": 2894 }, "chunk_id": "train_shard_00001_2894_0", "global_id": 9770 }, { "text": "Unified strain taxonomies are crucial for fostering international communication in microbiological research and for the epidemiological surveillance of bacterial pathogens. While multilocus sequence typing (MLST) has served as a foundation of strain taxonomy for two decades, whole genome sequencing enables more precise classifications and significantly improves discriminatory resolution. The core genome-wide extension of MLST (known as cgMLST) thus holds great promise for strain genotyping and classification, but its implementation faces challenges that include missing data, potential instability of cluster-based nomenclatures, and the necessity to ensure backwards compatibility with MLST identifiers. Life Identification Number (LIN) codes offer a solution by providing multi-level classification groups that are inherently stable. Here, we present, consolidate, and extend the cgMLST-based LIN code approach. We first develop a nicknaming system for LIN code prefixes, which enables flexible human-readable strain nomenclatures. Using Klebsiella pneumoniae (Kp) as an example, LIN code nicknames were attributed by inheritance from MLST identifiers, thus perpetuating the legacy of MLST nomenclatures in the genomic era. We show that while 7-gene MLST sometimes conflates unrelated sublineages into the same ST, cgMLST-based LIN codes are highly concordant with phylogenetic relationships. We implement this novel LIN code-based nomenclature in the BIGSdb platform, and illustrate, with Pathogenwatch, how it can also be used in other genomic epidemiology platforms. Finally, we demonstrate the value of LIN codes for tracking the strain diversity within high-risk internationally disseminated clonal groups of Kp and protracted outbreaks. Given its stability, precision, and flexibility, we recommend the adoption of the cgMLST-based LIN code taxonomic approach for Kp and suggest that this approach is widely applicable to other bacterial pathogens.\n\nBacterial strain nomenclature in the genomic era: Life Identification Numbers using a gene-by-gene approach", "token_count": 473, "char_count": 2071, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6536, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:46.064177", "source": { "split": "train_shard_00001", "doc_id": 2895 }, "chunk_id": "train_shard_00001_2895_0", "global_id": 9771 }, { "text": "This study was aimed at using nanofiltration to purify the galactooligosaccharides (GOS) found in a commercial mixture containing lactose, glucose and galactose, whose compositions were similar to that obtained through transgalactosylation reactions catalysed by β‐galactosidase from Kluyveromyces marxianus CCT 7082. NP030 polyethersulphone membrane was selected for the purification processes, once it differed statistically from other membranes due to the higher purification factor and permeate flux under the optimised temperature and pressure conditions of 35 °C and 3 MPa, respectively. Results indicate that NP030 membrane can be employed as a preliminary technique for the GOS purification with approximately 61% (w/w) of recovery.\n\nConcentration and purification of galacto‐oligosaccharides using nanofiltration membranes", "token_count": 221, "char_count": 831, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7706, "quality_score": 0.8853, "entities": { "genes": [ "NP030" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:46.530957", "source": { "split": "train_shard_00001", "doc_id": 2896 }, "chunk_id": "train_shard_00001_2896_0", "global_id": 9772 }, { "text": "

ABSTRACT

There has been tremendous progress in the production of phased genome assemblies by combining long-read data with parental information or linking read data. Nevertheless, a typical phased genome assembly generated by trio-hifiasm still generates more than ~140 gaps. We perform a detailed analysis of gaps, assembly breaks, and misorientations from 77 phased and assembled human genomes (154 unique haplotypes). We find that trio-based approaches using HiFi are the current gold standard although chromosome-wide phasing accuracy is comparable when using Strand-seq instead of parental data. We find two-thirds of defined contig ends cluster near the largest and most identical repeats [including segmental duplications (35.4%) or satellite DNA (22.3%) or to regions enriched in GA/AT rich DNA (27.4%)]. As a result, 1513 protein-coding genes overlap assembly gaps in at least one haplotype and 231 are recurrently disrupted or missing from five or more haplotypes. In addition, we estimate that 6-7 Mbp of DNA are incorrectly orientated per haplotype irrespective of whether trio-free or trio-based approaches are employed. 81% of such misorientations correspond to bona fide large inversion polymorphisms in the human species, most of which are flanked by large identical segmental duplications. In addition, we also identify large-scale alignment discontinuities consistent with an 11.9 Mbp deletion and 161.4 Mbp of insertion per human haploid genome. While 99% of this variation corresponds to satellite DNA, we identify 230 regions of the euchromatic DNA with frequent expansions and contractions, nearly half of which overlap with 197 protein-coding genes. Although not completely resolved, these regions include copy number polymorphic and biomedically relevant genic regions where complete resolution and a pangenome representation will be most useful, yet most challenging, to realize.\n\nGaps and complex structurally variant loci in phased genome assemblies", "token_count": 496, "char_count": 1985, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6573, "quality_score": 0.8287, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:47.181226", "source": { "split": "train_shard_00001", "doc_id": 2897 }, "chunk_id": "train_shard_00001_2897_0", "global_id": 9773 }, { "text": "Klebsiella pneumoniae is a prominent etiological agent of healthcare associated infections (HAIs). In this context, multidrug-resistant and biofilm-producing bacteria are of special public health concern due to the difficulties associated with treatment of human infections and eradication from hospital environments. Here, in order to study the impact of medical devices-associated materials on the biofilm dynamics, we performed biofilm phenotypic analyses through a classic and a new scanning electron microscopy (SEM) technique for three multidrug-resistant K. pneumoniae isolates growing on polystyrene and silicone. We also applied whole-genome sequencing (WGS) to search for genetic clues underlying biofilm phenotypic differences. We found major differences in the extracellular polymeric substances (EPS) content among the three strains, which were further corroborated by in-depth EPS composition analysis. WGS analysis revealed a high nucleotide similarity within the core-genome, but relevant differences in the accessory genome that may account for the detected biofilm phenotypic dissimilarities, such as genes already associated with biofilm formation in other pathogenic bacteria (e.g., genes coding haemogglutinins and haemolysins). These data reinforce that the research efforts to defeat bacterial biofilms should take into account that their dynamics may be contingent on the medical devices-associated materials.\n\nInsights on Klebsiella pneumoniae Biofilms Assembled on Different Surfaces Using Phenotypic and Genotypic Approaches.", "token_count": 375, "char_count": 1566, "word_count": 205, "semantic_coherence": 1, "information_density": 0.7122, "quality_score": 0.8561, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:47.768820", "source": { "split": "train_shard_00001", "doc_id": 2898 }, "chunk_id": "train_shard_00001_2898_0", "global_id": 9774 }, { "text": "

Background

Probiotics refer to living microorganisms that exerts a variety of beneficial effects on human health. On the contrary, they also can cause infection, produce toxins within the body, and transfer antibiotic resistant genes to the other microorganisms in the digestive tract necessitating a comprehensive safety assessment. This study aimed to conduct functional genomic analysis to uncover the probiotic potential of Lactobacillus delbrueckii subsp. indicus TY-11 isolated from native yogurt in Bangladesh. We also performed Transmission Electron Microscopic (TEM) analysis, comparative genomic study as well as phylogenetic tree construction with 332 core genes from 262 genomes. These experiments on subspecies indicus were not studied previously.

Results

The strain TY-11 was identified as Lactobacillus delbrueckii subsp. indicus, whose genome (1916674bp) contained genes to adapt to diverse and stressful environments of the human gut, and no gene was identified for either antibiotic resistance or toxic metabolites. It embraced genes for the degradation of toxic metabolites, treatment of lactose intolerance, toll-like receptor 2-dependent innate immune response, heat and cold shock, bile salts tolerance in the gut, and acidic pH tolerance in the stomach. Genes were annotated for inhibiting pathogenic bacteria in the gut by inhibitory substances, (bacteriocin: Helveticin-J (331bp) and Enterolysin-A (275bp), hydrogen peroxide, and acid); blockage of adhesion sites; and competition for nutrients. Its metabolic pathway helped the human gut to recover the digestive disorders and digest indigestible nutrients. The TY-11 genome possessed additional 37 core genes of subspecies indicus which were deficient in the core genome of the most popular subspecies bularicus ", "token_count": 470, "char_count": 1807, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6614, "quality_score": 0.8307, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:48.407327", "source": { "split": "train_shard_00001", "doc_id": 2899 }, "chunk_id": "train_shard_00001_2899_0", "global_id": 9775 }, { "text": "

Conclusions

This is the first study to explore the molecular insights into intestinal residence and probiotic roles including antimicrobial activities of a representative strain (TY-11) of Lactobacillus delbrueckii subsp. indicus .\n\nTEM Experiment and Complete Genome Sequencing with Comparative Genomic Analysis to Uncover Potential Probiotic Features of IsolatedLactobacillus delbrueckiisubsp.indicusTY-11", "token_count": 128, "char_count": 430, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8776, "quality_score": 0.9388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:48.824673", "source": { "split": "train_shard_00001", "doc_id": 2899 }, "chunk_id": "train_shard_00001_2899_1", "global_id": 9776 }, { "text": "The evolution and structure of prokaryotic genomes are largely shaped by horizontal gene transfer. This process is so prevalent that DNA can be seen as a public good—a resource that is shared across individuals, populations, and species. The consequence is a network of DNA sharing across prokaryotic life, whose extent is becoming apparent with increased availability of genomic data. Within prokaryotic species, gene gain (via horizontal gene transfer) and gene loss results in pangenomes, the complete set of genes that make up a species. Pangenomes include core genes present in all genomes, and accessory genes whose presence varies across strains. In this chapter, we discuss how we can understand pangenomes from a network perspective under the view of DNA as a public good, how pangenomes are maintained in terms of drift and selection, and how they may differ between prokaryotic groups. We argue that niche adaptation has a major impact on pangenome structure. We also discuss interactions between accessory genes within genomes, and introduce the concepts of ‘keystone genes’, whose loss leads to concurrent loss of other genes, and ‘event horizon genes’, whose acquisition may lead to adaptation to novel niches and towards a separate, irreversible evolutionary path.\n\nPangenomes and Selection: The Public Goods Hypothesis", "token_count": 280, "char_count": 1334, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:49.378437", "source": { "split": "train_shard_00001", "doc_id": 2900 }, "chunk_id": "train_shard_00001_2900_0", "global_id": 9777 }, { "text": "

Background

Accurate classification of different Burkholderia cepacia complex (BCC) species is essential for therapy, prognosis assessment and research. The taxonomic status of BCC remains problematic and an improved knowledge about the classification of BCC is in particular needed.

Methods

We compared phylogenetic trees of BCC based on 16S rRNA, recA, hisA and MLSA (multilocus sequence analysis). Using the available whole genome sequences of BCC, we inferred a species tree based on estimated single-copy orthologous genes and demarcated species of BCC using dDDH/ANI clustering.

Results

We showed that 16S rRNA, recA, hisA and MLSA have limited resolutions in the taxonomic study of closely related bacteria such as BCC. Our estimated species tree and dDDH/ANI clustering clearly separated 116 BCC strains into 36 clusters. With the appropriate reclassification of misidentified strains, these clusters corresponded to 22 known species as well as 14 putative novel species.

Conclusions

This is the first large-scale and systematic study of the taxonomic status of the BCC and could contribute to further insights into BCC taxonomy. Our study suggested that conjunctive use of core phylogeny based on single-copy orthologous genes, as well as pangenome-based dDDH/ANI clustering would provide a preferable framework for demarcating closely related species.

Reviewer

This article was reviewed by Dr. Xianwen Ren.\n\nGenome-based classification of Burkholderia cepacia complex provides new insight into its taxonomic status.", "token_count": 410, "char_count": 1560, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8104, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:50.367367", "source": { "split": "train_shard_00001", "doc_id": 2901 }, "chunk_id": "train_shard_00001_2901_0", "global_id": 9778 }, { "text": "The global prevalence of obesity is rising year by year, which has become a public health problem worldwide. Many animal and clinical studies have shown that Lactiplantibacillus plantarum is considered an ideal probiotic and potential supplement for the treatment of obesity. In this study, we aimed to complete the genome sequence of L. plantarum HOM2217, which was isolated from human milk, and study its physiological characteristics and anti-obesity effects in 3T3-L1 cells and rats fed a high-fat diet (HFD) to determine its potential as a starter for functional food products. Whole-genome analysis demonstrated that HOM2217 contained a single circular chromosome of 3,267,529 bp with a GC content of 44.5% and one plasmid (62,350 bp) with a GC content of 38.5%. Compared to the reference strains, HOM2217 demonstrated superior tolerance to gastrointestinal conditions, higher adhesion to intestinal epithelial cell lines, potent antimicrobial activity against Enterobacter cloacae ATCC 13047, and effective cholesterol removal ability in vitro. Treatment with heat-killed HOM2217 significantly reduced lipid accumulation and intracellular triglyceride production in 3T3-L1 adipocytes. Daily treatment of HFD-fed rats with HOM2217 for 7 weeks decreased body weight, body weight gain, and body fat without changes in food intake. HOM2217 also significantly increased the serum high-density lipoprotein cholesterol (HDL-C) level, decreased the serum tumor necrosis factor (TNF-α) and increased short-chain fatty acid (SCFA) (formic acid, acetic acid, and butyric acid) levels in the cecum", "token_count": 484, "char_count": 1620, "word_count": 228, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [ "HOM2217" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:51.037989", "source": { "split": "train_shard_00001", "doc_id": 2902 }, "chunk_id": "train_shard_00001_2902_0", "global_id": 9779 }, { "text": "Thus, HOM2217 could potentially prevent obesity in rats by inhibiting inflammatory responses and regulating lipid metabolism and SCFAs expression. Therefore, HOM2217 has potential as an alternative treatment for obesity.\n\nComplete genome sequence and anti-obesity potential of Lactiplantibacillus plantarum HOM2217 in 3T3-L1 cells and high-fat diet-fed rats.", "token_count": 115, "char_count": 365, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8478, "quality_score": 0.9239, "entities": { "genes": [ "HOM2217" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:51.449363", "source": { "split": "train_shard_00001", "doc_id": 2902 }, "chunk_id": "train_shard_00001_2902_1", "global_id": 9780 }, { "text": "A Klebsiella quasipneumoniae subsp. similipneumoniae strain, named S915, belonging to the ST1859 O5:KL35, and harboring the plasmid-mediated quinolone resistance qnrE1 gene, was isolated from a soil sample cultivated with lettuce in Brazil. The core genome multilocus sequence typing analysis revealed that S915 strain was most related to a clinical strain of Brazil. Comparative genomic analysis showed that ST1859 O5:KL35 strains have been circulating in clinical settings and are closely related to multidrug resistance and multimetal tolerance. Strain S915 presented a plasmid contig co-harboring the qnrE1 gene and tellurite tolerance operon. The region harboring the qnrE1 gene (ISEcp1-qnrE1-araJ-ahp) shared high similarity with others from infected humans, ready-to-eat dish, and food-producing animals in Brazil. This is the first report of the plasmid-mediated qnrE1 gene in the environment. Our findings evidence the initial dissemination of the qnrE1 gene in the environment by the introduction of a clinical strain, which may be spread to different sectors, representing a One Health challenge.\n\nKlebsiella quasipneumoniae subsp. similipneumoniae ST1859 O5:KL35 from Soil: First Report of qnrE1 in the Environment.", "token_count": 432, "char_count": 1325, "word_count": 172, "semantic_coherence": 1, "information_density": 0.593, "quality_score": 0.7965, "entities": { "genes": [ "KL35", "ST1859" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:52.106735", "source": { "split": "train_shard_00001", "doc_id": 2903 }, "chunk_id": "train_shard_00001_2903_0", "global_id": 9781 }, { "text": "Iron-rich pelagic aggregates (iron snow) are hot spots for microbial interactions. Using iron snow isolates, we previously demonstrated that the iron-oxidizer Acidithrix sp. C25 triggers Acidiphilium sp. C61 aggregation by producing the infochemical 2-phenethylamine (PEA). Here, we showed slightly enhanced aggregate formation in the presence of PEA on different Acidiphilium spp. but not other iron-snow microorganisms, including Acidocella sp. C78 and Ferrovum sp. PN-J47. Next, we sequenced the Acidiphilium sp. C61 genome to reconstruct its metabolic potential. Pangenome analyses of Acidiphilium spp. genomes revealed the core genome contained 65 gene clusters associated with aggregation, including autoaggregation, motility, and biofilm formation. Screening the Acidiphilium sp. C61 genome revealed the presence of autotransporter, flagellar, and extracellular polymeric substances (EPS) production genes. RNA-seq analyses of Acidiphilium sp. C61 incubations (+/- 10 µM PEA) indicated genes involved in energy production, respiration, and genetic processing were the most upregulated differentially expressed genes in the presence of PEA. Additionally, genes involved in flagellar basal body synthesis were highly upregulated, whereas the expression pattern of biofilm formation-related genes was inconclusive. Our data shows aggregation is a common trait among Acidiphilium spp. and PEA stimulates the central cellular metabolism, potentially advantageous in aggregates rapidly falling through the water column.\n\nMolecular Mechanisms Underpinning Aggregation in Acidiphilium sp. C61 Isolated from Iron-Rich Pelagic Aggregates.", "token_count": 500, "char_count": 1712, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6916, "quality_score": 0.8458, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "respiration" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:52.759310", "source": { "split": "train_shard_00001", "doc_id": 2904 }, "chunk_id": "train_shard_00001_2904_0", "global_id": 9782 }, { "text": "

Background

The importance of pigeons as reservoirs and carriers of Cryptococcus neoformans and other species of this genus is well-known; however, less is known about their role as reservoirs and carriers of other yeasts that impact public health.

Aims

The present study was performed on Gran Canaria Island to define yeasts other than Cryptococcus spp. that have been reported to impact public health and which could be carried by pigeons.

Methods

Samples were obtained from 83 pigeon lofts (Columba livia); moreover, 331 crop samples, 331 cloacal samples and 174 dropping samples were collected. In addition, 17 dropping samples were taken from a total of 17 public squares. Samples were inoculated on Sabouraud dextrose agar with chloramphenicol.

Results

Different yeast species, i.e. Candida guilliermondii (24.36%), Candida kefyr (1.21%), Saccharomyces cerevisiae (2.43%), and Trichosporon asahii (1.21%) were isolated for the first time from the cloaca. The most frequently isolated yeast from the crop, cloaca and dropping samples from lofts was C. guilliermondii (30.46%, 24.36% and 49.37%, respectively). In addition, for the first time, C. kefyr (3.65%), Candida pelliculosa (2.43%), Candida rugosa (1.21%), T. asahii (3.65%), Trichosporon mucoides (3.65%) and Prototheca wickerhamii (1.21%) were obtained from crop samples; Candida pelliculosa (1.20%), T. asahii (9.63%) and T. mucoides (7.22%) were isolated from dropping samples in the lofts", "token_count": 494, "char_count": 1483, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5874, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:53.404502", "source": { "split": "train_shard_00001", "doc_id": 2905 }, "chunk_id": "train_shard_00001_2905_0", "global_id": 9783 }, { "text": "Candida albicans was the most frequently isolated yeast in dropping samples collected in public squares.

Conclusions

It can be assumed that pigeons and their droppings act as carriers and reservoirs of Candida spp. and other zoonotic yeasts.\n\nPigeons and their droppings as reservoirs of Candida and other zoonotic yeasts.", "token_count": 89, "char_count": 329, "word_count": 47, "semantic_coherence": 1, "information_density": 0.6596, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:53.775789", "source": { "split": "train_shard_00001", "doc_id": 2905 }, "chunk_id": "train_shard_00001_2905_1", "global_id": 9784 }, { "text": "Salmonella serovars Heidelberg and Minnesota encoding antimicrobial resistance to third-generation cephalosporins and fluoroquinolones are often detected in poultry/poultry meat. We analysed the genomes of 10 Salmonella Heidelberg (SH) and 4 Salmonella Minnesota (SM) from faecal isolates of Brazilian poultry. These featured virulent and multidrug-resistant characteristics, with AmpC beta-lactamase (blaCMY-2 ) predominance (9/14), for all SM (4/4) and some SH (3/10) located on IncC plasmid replicons. IncC carrying blaCTX-M-2 was only detected among SH (3/10). Mutation in the gyrA/parC genes was present in all SH, whereas SM harboured parC mutation plus qnrB19 on ColRNAI plasmids (3/4). In silico resistance overall corroborated with phenotypic results. Core genome phylogenies showed close clustering and high similarities between the Brazilian and poultry meat/food isolates from Europe, and to human isolates from European countries with documented import of Brazilian poultry meat. Conjugation assays with SM successfully transferred blaCMY-2 , and qnrB19 to an Escherichia coli recipient. The findings reinforce the ongoing antimicrobial resistance acquisition of SH and Minnesota and the risks for disseminating resistant strains and/or mobile elements which may increasingly affect importing countries and the need for controlling AMR in major poultry-exporting countries like Brazil.\n\nSalmonella Heidelberg and Salmonella Minnesota in Brazilian broilers: Genomic characterization of third-generation cephalosporin and fluoroquinolone-resistant strains.", "token_count": 447, "char_count": 1600, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:54.412216", "source": { "split": "train_shard_00001", "doc_id": 2906 }, "chunk_id": "train_shard_00001_2906_0", "global_id": 9785 }, { "text": "The ability of dairy Debaryomyces hansenii, Kluyveromyces lactis and Kluyveromyces marxianus strains to release the casein-derived antihypertensive sequences RYLGY, AYFYPEL, LHLPLP, HLPLP, VPP and/or IPP was examined. Yeast strains were grown in medium with casein as sole nitrogen source and the yeast casein hydrolysates (CSHs) were analysed by HPLC-MS/MS to search for the six antihypertensive sequences. Only LHLPLP and HLPLP were identified in CSHs and exclusively in D. hansenii Dh1 and Dh14 hydrolysates in which both antihypertensive sequences represented approximately 6 (CSH Dh1) and 10% (CSH Dh14) of total peptide content. In addition, a complete analysis of selected CSHs by HPLC-MS/MS allowed the identification of 35 (Dh1) and 46 (Dh14) additional peptides, which could also contribute to the observed in vitro ACE inhibitory potency of both hydrolysates (Dh1, IC50 = 13.6 ± 1.8 μg/mL; Dh14, IC50 = 17.5 ± 2.1 μg/mL) and might confer them multifunctional properties. Finally casein zymography revealed the presence of at least one extracellular protease with a molecular mass of about 50 kDa. In conclusion, the present study contributes to a better insight into bioactive compounds produced by dairy yeasts and shows the feasibility of D. hansenii strains to produce antihypertensive casein-derived peptides.\n\nDairy Debaryomyces hansenii strains produce the antihypertensive casein-derived peptides LHLPLP and HLPLP", "token_count": 470, "char_count": 1431, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6411, "quality_score": 0.8206, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:55.059195", "source": { "split": "train_shard_00001", "doc_id": 2907 }, "chunk_id": "train_shard_00001_2907_0", "global_id": 9786 }, { "text": "Yeast cells of Kluyveromyces marxianus grown in a sterile lactose-based medium, were extracted with sodium hydroxide to give a fraction of alkali-insoluble yeast (AIY) glucan. From ¹H- and ¹³C-NMR characterization it was concluded that the glucan consisted mostly of β(1 → 3) linkages and was similar to that obtained from Saccharomyces cerevisiae used in the preparations for skin revitalization and repair. The molecular weight of the glucan was determined to be approximately 3 × 10⁵ Da. Therefore, K. marxianus grown on a lactose-based medium similar to whey, a waste stream of the dairy industry, could be a commercial source of β(1 → 3) glucans for use in the food and pharmaceutical industries.\n\nNMR confirmation of an alkali-insoluble glucan from Kluyveromyces marxianus cultivated on a lactose-based medium", "token_count": 241, "char_count": 815, "word_count": 126, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:55.545572", "source": { "split": "train_shard_00001", "doc_id": 2908 }, "chunk_id": "train_shard_00001_2908_0", "global_id": 9787 }, { "text": "

Purpose

Despite the existence of a variety of available yeast-identification strategies, easier and more cost-effective methods are required for routine use in clinical laboratories. The internal transcribed spacer (ITS) regions of fungal rRNA genes exhibit variable sizes depending on the yeast species. In the present study, fragment size polymorphism (FSP) analysis of the ITS1 and ITS2 regions for identification of the clinically most important yeast species was assessed.

Methodology

The ITS1 and ITS2 regions of 190 strains, including isolates of 31 standard strains and 159 clinical isolates, were separately PCR amplified with two primer sets: ITS1-ITS2 and ITS3-ITS4. PCR products were mixed and the two-band electrophoretic pattern of each sample was analysed according to the size of the ITS regions as predicted from the GenBank database.

Results

Using this method and avoiding expensive tools such as sequencing or capillary electrophoresis, we were able to differentiate nearly all pathogenic yeast species, including Candida albicans, Candida tropicalis, Candida glabrata, Candida parapsilosis, Candida krusei, Candida guilliermondii, Candida kefyr, Candida lusitaniae, Candida rugosa, Cryptococcus neoformans and Saccharomyces cerevisiae. The method showed limited discriminatory power to differentiate species of the Candida parapsilosis complex. Differentiation of Candida albicans and Candida tropicalis needs already identified controls.

Conclusion

FSP method benefits from advantages such as lower cost, higher speed and wider range of species than some commercial yeast-identification methods. We consider this method as one of the easiest molecular approaches for identifying a wide range of human pathogenic yeast species, applicable to both diagnostic and epidemiological purposes.\n\nUtilization of size polymorphism in ITS1 and ITS2 regions for identification of pathogenic yeast species.", "token_count": 484, "char_count": 1943, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [ "ITS2", "ITS4", "ITS3", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:56.190067", "source": { "split": "train_shard_00001", "doc_id": 2909 }, "chunk_id": "train_shard_00001_2909_0", "global_id": 9788 }, { "text": "

Background

Over the last decades, Candida species have emerged as important pathogens in immunocompromised patients. Nosocomial infections are mainly of endogenous origin. Nevertheless, some cases of exogenous candidiasis have also been reported.

Aims

The aim of this study was to evaluate the genetic relatedness between Candida albicans, Candida glabrata, Candida tropicalis, Candida krusei and Candida kefyr isolates recovered from intensive care unit (ICU) patients.

Methods

A total of 132 Candida clinical isolates (62 C. albicans, 40 C. glabrata, 13 C. tropicalis, 11 C. krusei, 6 C. kefyr), obtained from specimens of endotracheal aspirate, urine and blood taken from patients of a tertiary hospital in Poland, were included in the study. Species identification was performed by PCR method and genetic relatedness was assessed by randomly amplified polymorphic DNA assay (RAPD) with five primers.

Results

The RAPD analysis revealed high genetic diversity among the studied Candida isolates, indicating that most of the strains were from endogenous sources. Only two clonal strains of C. glabrata isolated from different patients were observed, suggesting a possible cross-transmission of these pathogens.

Conclusions

Our study confirmed the high discriminatory power of the RAPD assay. This genotyping method can be applied to local epidemiological studies of Candida species.\n\nMolecular characterization of Candida isolates from intensive care unit patients, Krakow, Poland.", "token_count": 411, "char_count": 1518, "word_count": 203, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:56.808981", "source": { "split": "train_shard_00001", "doc_id": 2910 }, "chunk_id": "train_shard_00001_2910_0", "global_id": 9789 }, { "text": "Flavobacterium psychrophilum is the causative agent of bacterial cold-water disease in salmonids and rainbow trout fry syndrome. This pathogen has attained a global presence and can spread both horizontally and vertically. However, it was not documented in Korea before September 2018. In this study, the objectives were to characterize Flavobacterium psychrophilum strain FPRT1, isolated from diseased rainbow trout genotypically and phenotypically. We also conducted various investigations to better understand its impact and assess potential control measures. We acquired fifty rainbow trout (approximately 70 g in weight) and transferred them to a laboratory aquarium. During the initial acclimation period, we observed mortality and examined affected fish for clinical signs. We isolated the bacterium from the spleen of infected rainbow trout using tryptone yeast extract salts agar supplemented with glucose, naming this FPRT1. Antibiotic susceptibility testing was carried out, and from the result, we selected enrofloxacin to administer to the trout orally to reduce mortality. To evaluate pathogenicity, we exposed the trout to FPRT1 at different water temperatures (8, 15, and 22 °C). Genomic analysis was conducted to identify the serotype and relatedness of FPRT1 to European strains. Affected fish displayed clinical signs, such as ulcerative lesions in the mandible, anemia with pale gills, exophthalmia, and increased mucus secretion. Internal symptoms included pale liver and enlarged spleen. FPRT1 was susceptible to erythromycin, enrofloxacin, florfenicol, oxytetracycline, and gentamicin, but resistant to oxolinic acid and sulfamethoxazole/trimethoprim. Oral administration of enrofloxacin resulted in a decrease in mortality from 28% to 6%. Pathogenicity tests revealed varying mortality rates due to FPRT1 at different temperatures", "token_count": 489, "char_count": 1868, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8353, "entities": { "genes": [ "FPRT1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:57.456981", "source": { "split": "train_shard_00001", "doc_id": 2911 }, "chunk_id": "train_shard_00001_2911_0", "global_id": 9790 }, { "text": "The highest rates were observed at 8 °C (ranging from 43% to 100%) for both intraperitoneal and intramuscular injections, and lower rates occurred at 22 °C (ranging from 0% to 30%), with intramuscular injections displaying higher susceptibility. Genomic analysis identified FPRT1 as serotype 2 and indicated its close genetic relationship with European strains based on the core genome and dispensable genome. The substantial genomic similarity between our strain and European strains suggests the possibility of bacterial spread through the importation of fertilized eggs from Europe. In conclusion, this study highlights the introduction of the previously undocumented pathogen (F. psychrophilum) into Korean rainbow trout populations. The detection of this pathogen and its pathogenicity assessment is not only important for understanding its impact on local aquaculture but also for establishing surveillance and control measures to prevent further transmission and outbreaks in the region.\n\nCharacterization and Pathogenicity of Flavobacterium psychrophilum Isolated from Rainbow Trout (Oncorhynchus mykiss) in Korea.", "token_count": 277, "char_count": 1143, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7032, "quality_score": 0.8516, "entities": { "genes": [ "FPRT1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:58.010077", "source": { "split": "train_shard_00001", "doc_id": 2911 }, "chunk_id": "train_shard_00001_2911_1", "global_id": 9791 }, { "text": "In this paper we report on the effect of different concentrations of lactose and galactose in the production of beta-galactosidase by Kluyveromyces marxianus CBS6556. The results clearly demonstrate a decrease in enzyme specific activity during cultivation at high concentrations of L-lactose or D-galactose, despite the fact that these carbohydrates are normally used for induction of the beta-galactosidase activity. Therefore, maximum induction of beta-galactosidase in K. marxianus batch cultures was obtained at low concentrations of the inducer carbohydrates, in the range between 0.5 to 15 mM. Those informations can help to design low cost medium with higher beta-galactosidase productivity by K. marxianus cells.\n\nThe beta-galactosidase activity in Kluyveromyces marxianus CBS6556 decreases by high concentrations of galactose.", "token_count": 225, "char_count": 836, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8304, "entities": { "genes": [ "CBS6556" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:58.484153", "source": { "split": "train_shard_00001", "doc_id": 2912 }, "chunk_id": "train_shard_00001_2912_0", "global_id": 9792 }, { "text": "Influenza viruses that infect humans are known to swiftly evolve over time. Influenza A virus has a negative single-stranded RNA genome in eight segments. Pangenome analysis of twelve strains of Influenza A viruses H1N1, H1N2, H2N2, H3N2, H5N1, H5N6, H7N2, H7N3, H7N7, H7N9, H9N2, and H10N8 gave insight on the core genes that are conserved and accessory genes that are specific for the strains. The proteins Neuraminidase, Matrix M1 and Nonstructural protein 1 were encoded by the core genes of segments 6, 7, and 8 respectively which proves that they are conserved in almost all the strains of influenza. The 3Dimensional structures of the core genes were interpreted by homology modeling and compared with corresponding Protein Data Bank structures (4MWQ, IEA3, 2GX9). Among several anti-viral phytocompounds that were virtually screened against the modeled and PDB target proteins, three molecules of Indian plant Glycyrrhiza glabra had high scores and interactions. Compounds 2,4,4’ Trihydrochalcone, Davidigenin and Licoflavone B docked well with the Neuraminidase, Matrix protein M1 and Nonstructural Protein NS1 respectively with good scores, minimized energy and interacted with the active sites. The compounds obeyed Lipinski’s Rule of five and exhibited drugability as well. Thus the present study focused on the drugable lead compounds from glabra that has inhibitory activities against the viral attachment, replication and matrix structure.\n\nMolecular Docking of Glycyrrhiza glabra against the Conserved Target M1, NA and NS1 Proteins of Influenza A Viral Strains Identified through Pangenome Analysis", "token_count": 455, "char_count": 1622, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [ "NS1", "IEA3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:59.124234", "source": { "split": "train_shard_00001", "doc_id": 2913 }, "chunk_id": "train_shard_00001_2913_0", "global_id": 9793 }, { "text": "

Background

Listeria monocytogenes consists of four lineages that occupy a wide variety of ecological niches. Sequence type (ST) 87 (serotype 1/2b), belonging to lineage I, is one of the most common STs isolated from food products, food associated environments and sporadic listeriosis in China. Here, we performed a comparative genomic analysis of the L. monocytogenes ST87 clone by sequencing 71 strains representing a diverse range of sources, different geographical locations and isolation years.

Results

The core genome and pan genome of ST87 contained 2667 genes and 3687 genes respectively. Phylogenetic analysis based on core genome SNPs divided the 71 strains into 10 clades. The clinical strains were distributed among multiple clades. Four clades contained strains from multiple geographic regions and showed high genetic diversity. The major gene content variation of ST87 genomes was due to putative prophages, with eleven hotspots of the genome that harbor prophages. All strains carry an intact CRISRP/Cas system. Two major CRISPR spacer profiles were found which were not clustered phylogenetically. A large plasmid of about 90 Kb, which carried heavy metal resistance genes, was found in 32.4% (23/71) of the strains. All ST87 strains harbored the Listeria pathogenicity island (LIPI)-4 and a unique 10-open read frame (ORF) genomic island containing a novel restriction-modification system.

Conclusion

Whole genome sequence analysis of L. monocytogenes ST87 enabled a clearer understanding of the population structure and the evolutionary history of ST87 L. monocytogenes in China. The novel genetic elements identified may contribute to its virulence and adaptation to different environmental niches. Our findings will be useful for the development of effective strategies for the prevention and treatment of listeriosis caused by this prevalent clone.", "token_count": 488, "char_count": 1892, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6519, "quality_score": 0.8259, "entities": { "genes": [ "ST87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:30:59.771992", "source": { "split": "train_shard_00001", "doc_id": 2914 }, "chunk_id": "train_shard_00001_2914_0", "global_id": 9794 }, { "text": "Genomic dissection of the most prevalent Listeria monocytogenes clone, sequence type ST87, in China.", "token_count": 28, "char_count": 100, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:00.123382", "source": { "split": "train_shard_00001", "doc_id": 2914 }, "chunk_id": "train_shard_00001_2914_1", "global_id": 9795 }, { "text": "Abstract

Acinetobacter species are widely distributed in the environment and clinical settings worldwide and serve as natural reservoirs of antimicrobial resistance genes and occasional human pathogens responsible for nosocomial infections. In this study, we performed genomic analysis of Acinetobacter seohaensis DSM 16313, a type strain of the proposed Acinetobacter species. This species was estimated to be evolutionary close to Acinetobacter towneri but the genome sequence of A. seohaensis was not publicly available. Pangenome analysis of the genome sequence of A. seohaensis along with those of genome-available type and reference strains of 82 Acinetobacter species including A. towneri suggested that three groups of Acinetobacter species, A. seohaensis and A. towneri; Acinetobacter pullorum and Acinetobacter portensis; and Acinetobacter idrijaensis, Acinetobacter mesopotamicus, and Acinetobacter lwoffii, were phylogenetically very similar to each other. Genome comparisons based on in silico DNA-DNA hybridization and the average nucleotide identity confirmed that these three groups of Acinetobacter species are conspecific. Based on the rules of priority, A. seohaensis, A. pullorum, and A. idrijaensis/A. mesopotamicus should be reclassified as later heterotypic synonyms of A. towneri, A", "token_count": 520, "char_count": 1724, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:31:00.752984", "source": { "split": "train_shard_00001", "doc_id": 2915 }, "chunk_id": "train_shard_00001_2915_0", "global_id": 9796 }, { "text": "portensis, and A. lwoffii, respectively.

\n\nGenome-based taxonomic reclassification of Acinetobacter species using type and reference strains", "token_count": 49, "char_count": 169, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:01.113623", "source": { "split": "train_shard_00001", "doc_id": 2915 }, "chunk_id": "train_shard_00001_2915_1", "global_id": 9797 }, { "text": "Faecal microbiota transplantation (FMT) is an efficacious therapeutic intervention, but its clinical mode of action and underlying microbiome dynamics remain poorly understood. Here, we analysed the metagenomes associated with 142 FMTs, in a time series-based meta-study across five disease indications. We quantified strain-level dynamics of 1,089 microbial species based on their pangenome, complemented with 47,548 newly constructed metagenome-assembled genomes. Using subsets of procedural-, host- and microbiome-based variables, LASSO-regularised regression models accurately predicted the colonisation and resilience of donor and recipient microbes, as well as turnover of individual species. Linking this to putative ecological mechanisms, we found these sets of variables to be informative of the underlying processes that shape the post-FMT gut microbiome. Recipient factors and complementarity of donor and recipient microbiomes, encompassing entire communities to individual strains, were the main determinants of individual strain population dynamics, and mostly independent of clinical outcomes. Recipient community state and the degree of residual strain depletion provided a neutral baseline for donor strain colonisation success, in addition to inhibitive priority effects between species and conspecific strains, as well as putatively adaptive processes. Our results suggest promising tunable parameters to enhance donor flora colonisation or recipient flora displacement in clinical practice, towards the development of more targeted and personalised therapies.\n\nDrivers and Determinants of Strain Dynamics Following Faecal Microbiota Transplantation", "token_count": 363, "char_count": 1668, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:01.688913", "source": { "split": "train_shard_00001", "doc_id": 2916 }, "chunk_id": "train_shard_00001_2916_0", "global_id": 9798 }, { "text": "In the Antarctic marine ecosystem, krill play a pivotal role, yet the intricate microbial community intertwined with these diminutive crustaceans remains largely unmapped. In this study, we successfully isolated and characterized a unique bacterial strain, Pseudoalteromonas sp. WY3, from Antarctic krill. Genomic analysis revealed that WY3 harbors a multitude of genes associated with cold shock proteins, oxidoreductases, and enzymes involved in the osmotic stress response, equipping it with a robust molecular arsenal to withstand frigid Antarctic conditions. Furthermore, the presence of two distinct biosynthesis-related gene clusters suggests that WY3 has the potential to synthesize diverse secondary metabolites, including aryl polyenes and ribosomally synthesized and post-translationally modified peptides. Notably, the identification of genes encoding enzymes crucial for biological immunity pathways, such as apeH and ubiC, hints at a complex symbiotic relationship between WY3 and its krill host. This comprehensive study highlights the robust potential of WY3 for secondary metabolite production and its remarkable ability to thrive at extremely low temperatures in the Antarctic ecosystem, shedding light on the interplay between culturable microorganisms and their hosts in harsh environments, and providing insights into the underexplored microbial communities associated with Antarctic marine organisms and their role in environmental adaptation and biotechnological applications.\n\nGenomic insights into the cold adaptation and secondary metabolite potential of Pseudoalteromonas sp. WY3 from Antarctic krill.", "token_count": 388, "char_count": 1656, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6435, "quality_score": 0.8218, "entities": { "genes": [ "WY3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:02.363423", "source": { "split": "train_shard_00001", "doc_id": 2917 }, "chunk_id": "train_shard_00001_2917_0", "global_id": 9799 }, { "text": "

Unlabelled

Whole-genome sequence (WGS) data are commonly used to design diagnostic targets for the identification of bacterial pathogens. To do this effectively, genomics databases must be comprehensive to identify the strict core genome that is specific to the target pathogen. As additional genomes are analyzed, the core genome size is reduced and there is erosion of the target-specific regions due to commonality with related species, potentially resulting in the identification of false positives and/or false negatives.

Importance

A comparative analysis of 1,130 Burkholderia genomes identified unique markers for many named species, including the human pathogens B. pseudomallei and B. mallei Due to core genome reduction and signature erosion, only 38 targets specific to B. pseudomallei/mallei were identified. By using only public genomes, a larger number of markers were identified, due to undersampling, and this larger number represents the potential for false positives. This analysis has implications for the design of diagnostics for other species where the genomic space of the target and/or closely related species is not well defined.\n\nThe Effects of Signal Erosion and Core Genome Reduction on the Identification of Diagnostic Markers.", "token_count": 300, "char_count": 1271, "word_count": 181, "semantic_coherence": 1, "information_density": 0.5967, "quality_score": 0.7983, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:03.610647", "source": { "split": "train_shard_00001", "doc_id": 2918 }, "chunk_id": "train_shard_00001_2918_0", "global_id": 9800 }, { "text": "Multilocus sequence typing (MLST) has become a useful tool for studying the genetic diversity of important public health pathogens, such as Chlamydia trachomatis (Ct). Four MLST schemes have been proposed for Ct (data available from Chlamydiales MLST databases). However, the lack of a sole standardized scheme represents the greatest limitation regarding typing this species. This study was thus aimed at evaluating the usefulness of the four MLST schemes available for Ct, describing each molecular marker's pattern and its contribution toward a description of intra-specific genetic diversity and population structure. The markers for each scheme, showed a variable power of dicrimination, exhibiting in some cases over estimation in the determination of Sequence Types (STs). However, individual analysis of each locus's typing efficiency and discrimination power led to identifying 8 markers as having a suitable pattern for intra-specific typing. analyzing the 8 candidate markers gave a combination of 3 of these loci as an optimal scheme for identifying a large amount of STs, maximizing discrimination power whilst maintaining suitable typing efficiency. One scheme was compared against core genome phylogenies, finding a higher typing resolution through the last approach. These results confirm once again that although complete genome data, in particular from core genome MLST (cgMLST) allow a high resolution clustering for Ct isolates. There are combinations of molecular markers that could generate equivalent results, with the advantage of representing an easy implementation strategy and lower costs leading to contribute to the monitoring and molecular epidemiology of Ct.\n\nUnveiling the Multilocus Sequence Typing (MLST) Schemes and Core Genome Phylogenies for Genotyping Chlamydia trachomatis.", "token_count": 422, "char_count": 1861, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:04.241400", "source": { "split": "train_shard_00001", "doc_id": 2919 }, "chunk_id": "train_shard_00001_2919_0", "global_id": 9801 }, { "text": "Genome-scale engineering enables rational removal of dispensable genes in chassis genomes. Deviating from this approach, we applied greedy accumulation of deletions of large dispensable regions in the Bacillus subtilis genome, yielding a library of 298 strains with genomes reduced up to 1.48 Mb in size. High-throughput physiological phenotyping of these strains confirmed that genome reduction is associated with substantial loss of cell fitness and accumulation of synthetic-sick interactions. Transcriptome analysis indicated that <15% of the genes conserved in our genome-reduced strains exhibited a twofold or higher differential expression and revealed a thiol-oxidative stress response. Most transcriptional changes can be explained by loss of known functions and by aberrant transcription at deletion boundaries. Genome-reduced strains exhibited striking new phenotypes relative to wild type, including a very high resistance (increased >300-fold) to the DNA-damaging agent mitomycin C and a very low spontaneous mutagenesis (reduced 100-fold). Adaptive laboratory evolution failed to restore cell fitness, except when coupled with a synthetic increase of the mutation rate, confirming low evolvability. Although mechanisms underlying this emergent phenotype are not understood, we propose that low evolvability can be leveraged in an engineering strategy coupling reductive cycles with evolutive cycles under induced mutagenesis.\n\nGreedy reduction of Bacillus subtilis genome yields emergent phenotypes of high resistance to a DNA damaging agent and low evolvability.", "token_count": 366, "char_count": 1577, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6791, "quality_score": 0.8395, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:04.828742", "source": { "split": "train_shard_00001", "doc_id": 2920 }, "chunk_id": "train_shard_00001_2920_0", "global_id": 9802 }, { "text": "

Objectives

Candidiasis is a common human immunodeficiency virus (HIV)/acquired immunodeficiency syndrome-associated opportunistic mycoses. The present study ascertained the species spectrum of Candida strains recovered from different clinical samples from symptomatic HIV-positive individuals and determined the antifungal susceptibility profile of the isolates.

Materials and methods

A variety of specimens were collected from 234 symptomatic HIV seropositive individuals depending on their clinical manifestations and subjected to direct microscopic examination. Blood samples were inoculated in biphasic blood culture medium and all other specimens on Sabouraud dextrose agar with chloramphenicol and incubated at 35°C-37°C. Species identification of the recovered Candida isolates was attempted on the basis of germ tube production, micromorphology on corn meal agar, color and morphology on HiCrome Candida Differential agar, and carbohydrate fermentation and assimilation tests. Susceptibility testing of the isolates was performed employing the VITEK 2 system.

Results

A total of 167 Candida isolates were obtained; Candida albicans (136), Candida tropicalis (13), Candida krusei (8), Candida parapsilosis (5), Candida glabrata (4), and Candida kefyr (1). Fluconazole resistance was more frequent among nonalbicans species, and significantly higher 5-fluorocytosine resistance compared to C. albicans was also observed. Eight Candida strains (six C. krusei, one C. kefyr, and one C", "token_count": 499, "char_count": 1604, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6771, "quality_score": 0.8385, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:05.482451", "source": { "split": "train_shard_00001", "doc_id": 2921 }, "chunk_id": "train_shard_00001_2921_0", "global_id": 9803 }, { "text": "albicans) were multidrug resistant.

Conclusion

Although C. albicans continues to be the leading etiological agent of candidiasis, the incidence of nonalbicans species among HIV-positive Indian individuals is rising. Antifungal resistance was higher among nonalbicans Candida species. Another issue of therapeutic concern is the possible emergence of multidrug-resistant Candida strains among these patients.\n\nClinico-mycological analysis and antifungal resistance pattern in human immunodeficiency virus-associated candidiasis: An Indian perspective.", "token_count": 161, "char_count": 582, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7969, "quality_score": 0.8984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:05.919282", "source": { "split": "train_shard_00001", "doc_id": 2921 }, "chunk_id": "train_shard_00001_2921_1", "global_id": 9804 }, { "text": "Enhanced abiotic stresses such as increased drought, elevated temperatures, salinity, and extreme weather phenomena severely affect major crops in the Mediterranean area, a 'hot spot' of climate change. Plants have evolved mechanisms to face stressful conditions and adapt to increased environmental pressures. Intricate molecular processes involving genetic and epigenetic factors and plant-microbe interactions have been implicated in the response and tolerance to abiotic stress. Deciphering the molecular mechanisms whereby plants perceive and respond to stress is crucial for developing strategies to counteract climate challenges. Progress in determining genes, complex gene networks, and biochemical pathways, as well as plant-microbiota crosstalk, involved in abiotic stress tolerance has been achieved through the application of molecular tools in diverse genetic resources. This knowledge could be particularly useful for accelerating plant improvement and generating resilient varieties, especially concerning woody perennial crops, where classical breeding is a lengthy and labor-intensive process. Similarly, understanding the mechanisms of plant-microbe interactions could provide insights into innovative approaches to facing stressful conditions. In this review, we provide a comprehensive overview and discuss the recent findings concerning the genetic, epigenetic, and microbial aspects shaping abiotic stress responses, in the context of enhancing resilience in important Mediterranean woody perennial fruit crops.\n\nEnhancing Abiotic Stress Resilience in Mediterranean Woody Perennial Fruit Crops: Genetic, Epigenetic, and Microbial Molecular Perspectives in the Face of Climate Change.", "token_count": 341, "char_count": 1705, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:06.494305", "source": { "split": "train_shard_00001", "doc_id": 2922 }, "chunk_id": "train_shard_00001_2922_0", "global_id": 9805 }, { "text": "

ABSTRACT

The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae , known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly structured in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.\n\nImplications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen", "token_count": 275, "char_count": 1193, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7205, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:07.042145", "source": { "split": "train_shard_00001", "doc_id": 2923 }, "chunk_id": "train_shard_00001_2923_0", "global_id": 9806 }, { "text": "Enteric yersiniosis, the third most common food-borne zoonosis in Europe, is mainly caused by the pathogen Yersinia enterocolitica. In France, the yersiniosis microbiological surveillance is conducted at the Yersinia National Reference Laboratory (YNRL). Since 2017, isolates have been characterized by whole genome sequencing (WGS) followed by a 500-gene Yersinia-cgMLST. We report here the data of the WGS-based surveillance on Y. enterocolitica isolates for the 2017-2021 period. The YNRL characterized 7,642 Y. enterocolitica strains distributed in 2,497 non-pathogenic isolates from lineages 1Aa and 1Ab, and 5,145 specimens belonging to 8 pathogenic lineages. Among pathogenic isolates, lineage 4 was the most common (87.2%) followed by lineages 2/3-9b (10.6%), 2/3-5a (1.2%), 2/3-9a (0.6%), 3-3b, 3-3c, 1B, and 3-3d (0.1% per each). Importantly, we developed a routine surveillance system based on a new typing method consisting of a 1,727-genes core genome Multilocus Sequence Typing (cgMLST) specific to the species Y. enterocolitica followed by isolate clustering. Thresholds of allelic distances (AD) were determined and fixed for the clustering of isolates: AD ≤ 5 for lineages 4, 2/3-5a, and 2/3-9a, and AD ≤ 3 for lineage 2/3-9b. Clustering programs were implemented in 2019 in routine surveillance to detect genomic clusters of pathogenic isolates", "token_count": 497, "char_count": 1411, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6701, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:07.695232", "source": { "split": "train_shard_00001", "doc_id": 2924 }, "chunk_id": "train_shard_00001_2924_0", "global_id": 9807 }, { "text": "In total, 419 clusters with at least 2 isolates were identified, representing 2,504 of the 3,503 isolates characterized between 2019 and 2021. Most clusters (n = 325) comprised 2 to 5 isolates. The new typing method proved to be useful for the molecular investigation of unusual grouping of cases as well as for the detection of genomic clusters in routine surveillance.

Importance

We describe here the new typing method used for molecular surveillance of Yersinia enterocolitica infections in France based on a novel core genome Multilocus Sequence Typing (cgMLST) specific to Y. enterocolitica species. This method can reliably identify the pathogenic Y. enterocolitica subspecies and compare the isolates with a high discriminatory power. Between 2017 and 2021, 5,145 pathogenic isolates belonging to 8 lineages were characterized and lineage 4 was by far the most common followed by lineage 2/3-9b. A clustering program was implemented, and detection thresholds were cross-validated by the molecular and epidemiological investigation of three unusual groups of Y. enterocolitica infections. The routine molecular surveillance system has been able to detect genomic clusters, leading to epidemiological investigations.\n\nA novel cgMLST for genomic surveillance of Yersinia enterocolitica infections in France allowed the detection and investigation of outbreaks in 2017-2021.", "token_count": 393, "char_count": 1426, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5657, "quality_score": 0.7828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:08.308298", "source": { "split": "train_shard_00001", "doc_id": 2924 }, "chunk_id": "train_shard_00001_2924_1", "global_id": 9808 }, { "text": "Ralstonia solanacearum is a destructive plant pathogenic bacterium and the causative agent of bacterial wilt disease, infecting over 200 plant species worldwide. In addition to chromosomal genes, its virulence is mediated by mobile genetic elements including integrated DNA of bacteriophages, i.e ., prophages, which may carry fitness-associated auxiliary genes or modulate host gene expression. Although experimental studies have characterised several prophages that shape R. solanacearum virulence, the global diversity, distribution, and wider functional gene content of R. solanacearum prophages is unknown. In this study, prophages were identified in a diverse collection of 192 R. solanacearum draft genome assemblies originating from six continents. Prophages were identified bioinformatically and their diversity investigated using genetic distance measures, gene content, GC, and total length. Prophage distribution was characterised using metadata on R. solanacearum geographic origin and lineage classification (phylotypes), and their functional gene content was assessed by identifying putative prophage-encoded auxiliary genes. In total, 343 intact prophages were identified, forming ten genetically distinct clusters. These included five prophage clusters belonging to the Inoviridae, Myoviridae , and Siphoviridae phage families, and five uncharacterised clusters, possibly representing novel, previously undescribed phages. The prophages had broad geographical distribution being present across multiple continents. However, they were generally host phylogenetic lineage-specific, and overall, prophage diversity was proportional to the genetic diversity of their hosts. The prophages contained a myriad of auxiliary genes involved in metabolism and virulence of both phage and bacteria. Our results show that while R. solanacearum prophages are highly diverse globally, they make lineage-specific contributions to the R. solanacearum accessory genome, which could have resulted from shared coevolutionary history.\n\nGlobal diversity and distribution of prophages are lineage-specific within the Ralstonia solanacearum plant pathogenic bacterium species complex", "token_count": 504, "char_count": 2183, "word_count": 281, "semantic_coherence": 1, "information_density": 0.637, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:08.960695", "source": { "split": "train_shard_00001", "doc_id": 2925 }, "chunk_id": "train_shard_00001_2925_0", "global_id": 9809 }, { "text": "

Background

Ensete glaucum (2 n = 2 x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana ( Musa ). A high-quality reference genome sequence of E. glaucum offers a vital genomic resource for functional and evolutionary studies of Ensete , the Musaceae, and more widely in the Zingiberales.

Findings

Using a combination of Illumina and Oxford Nanopore Technologies (ONT) sequencing, genome-wide chromosome conformation capture (Hi-C), and RNA survey sequence, we report a high-quality assembly of the 481.5Mb genome with 9 pseudochromosomes and 36,836 genes (BUSCO 94.7%). A total of 55% of the genome is composed of repetitive sequences with LTR-retroelements (37%) and DNA transposons (7%) predominant. The 5S and 45S rDNA were each present at one locus, and the 5S rDNA had an exceptionally long monomer length of c.1,056 bp, contrasting with the c. 450 bp monomer at multiple loci in Musa . A tandemly repeated c. 134 bp satellite, 1.1% of the genome (with no similar sequence in Musa ), was present around all nine centromeres, with a LINE retroelement also found at Musa centromeres. The assembly, including centromeric positions, enabled us to characterize in detail the chromosomal rearrangements occurring between the x = 9 species and x = 11 species of Musa . Only one chromosome has the same gene content as M. acuminata (ma). Three ma chromosomes represent part of only one E. glaucum (eg) chromosome, while the remaining seven ma chromosomes are fusions of parts of two, three, or four eg chromosomes, demonstrating complex and multiple evolutionary rearrangements in the change between x = 9 and x = 11", "token_count": 500, "char_count": 1678, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6384, "quality_score": 0.8192, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:09.615159", "source": { "split": "train_shard_00001", "doc_id": 2926 }, "chunk_id": "train_shard_00001_2926_0", "global_id": 9810 }, { "text": "

Conclusions

The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly show how chromosome number evolves, and features of the rapid evolution of repetitive sequences.\n\nA chromosome-level reference genome of Ensete glaucum gives insight into diversity, chromosomal and repetitive sequence evolution in the Musaceae", "token_count": 122, "char_count": 513, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:09.992377", "source": { "split": "train_shard_00001", "doc_id": 2926 }, "chunk_id": "train_shard_00001_2926_1", "global_id": 9811 }, { "text": "

Aims

Clostridium butyricum has been recognized as a strong candidate for the \"next generation of probiotics\" due to its beneficial roles on humans. Owing to our current understanding of this species is limited, it is imperative to unveil the genetic variety and biological properties of C. butyricum on sufficient strains.

Methods and results

We isolated 53 C. butyricum strains and collected 25 publicly available genomes to comprehensively assess the genomic and phenotypic diversity of this species. Average nucleotide identity and phylogeny suggested that multiple C. butyricum strains might share the same niche. Clostridium butyricum genomes were replete with prophage elements, but the CRISPR-positive strain efficiently inhibited prophage integration. Clostridium butyricum utilizes cellulose, alginate, and soluble starch universally, and shows general resistance to aminoglycoside antibiotics.

Conclusions

Clostridium butyricum exhibited a broad genetic diversity from the extraordinarily open pan-genome, extremely convergent core genome, and ubiquitous prophages. In carbohydrate utilization and antibiotic resistance, partial genotypes have a certain guiding significance for phenotypes.\n\nDiversity within the species Clostridium butyricum: pan-genome, phylogeny, prophage, carbohydrate utilization, and antibiotic resistance.", "token_count": 360, "char_count": 1361, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:10.581102", "source": { "split": "train_shard_00001", "doc_id": 2927 }, "chunk_id": "train_shard_00001_2927_0", "global_id": 9812 }, { "text": "Three bacterial strains, XENO-2T, XENO-7T, and XENO-10T, isolated from Steinernema entomopathogenic nematodes, were found to represent novel Xenorhabdus species. In this study, we describe these new species by whole-genome and whole-proteome phylogenomic reconstructions, by calculating sequence identity scores using core genome sequences, and by phenotypic characterization. Phylogenomic reconstructions using ribosomal and house-keeping genes, and whole-genome and whole-proteome sequences show that XENO-2T and XENO-10T are closely related to Xenorhabdus japonica DSM 16522T and that XENO-7T is closely related to Xenorhabdus bovienii subsp. africana XENO-1T and to X. bovienii subsp. bovienii T228T. The dDDH values between XENO-2T and XENO-10T and between XENO-2T and X. japonica DSM 16522T are 56.4 and 51.8%, respectively. The dDDH value between XENO-10T and X. japonica DSM 16522T is 53.4%. The dDDH values between XENO-7T and X. bovienii subsp. africana XENO-1T and between XENO-7T and X. bovienii subsp. bovienii T228T are 63.6 and 69.4%, respectively. These dDDH values are below the 70% divergence threshold for prokaryotic species delineation", "token_count": 516, "char_count": 1365, "word_count": 160, "semantic_coherence": 1, "information_density": 0.525, "quality_score": 0.7625, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:31:11.235851", "source": { "split": "train_shard_00001", "doc_id": 2928 }, "chunk_id": "train_shard_00001_2928_0", "global_id": 9813 }, { "text": "The newly described species are highly pathogenic to G. mellonella larvae, grow at pH between 5 and 9 (optimum 5-7), at salt concentrations of 1-3% (optimum 1-2%), and temperatures between 20 and 37 °C (optimum 28-30 °C). Biochemical tests such as lysine decarboxylase, ornithine decarboxylase, urease, gelatinase, citrate utilization, indole and acetoin production, and cytochrome oxidase tests allow to differentiate the novel species from their more closely related species. Considering these genetic and phenotypic divergencies, we propose the following new species: Xenorhabdus aichiensis sp. nov. with XENO-7T (= CCM 9233T = CCOS 2024T) as the type strain, Xenorhabdus anantnagensis sp. nov., with XENO-2T (= CCM 9237T = CCOS 2023T) as the type strain, and Xenorhabdus yunnanensis sp. nov., with XENO-10T (= CCM 9322T = CCOS 2071T) as the type strain. Our study contributes to a better understanding of the biodiversity and phylogenetic relationships of entomopathogenic bacteria associated with insect parasitic nematodes.\n\nXenorhabdus aichiensis sp. nov., Xenorhabdus anantnagensis sp. nov., and Xenorhabdus yunnanensis sp. nov., Isolated from Steinernema Entomopathogenic Nematodes.", "token_count": 492, "char_count": 1290, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6331, "quality_score": 0.8166, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:11.884697", "source": { "split": "train_shard_00001", "doc_id": 2928 }, "chunk_id": "train_shard_00001_2928_1", "global_id": 9814 }, { "text": "The bacterial strain PO100/5 was isolated from a skin abscess of a pig ( Sus scrofa domesticus ) in the Alentejo region of southern Portugal. It was identified as Corynebacterium pseudotuberculosis using biochemical tests, multiplex PCR and Pulsed Field Gel Electrophoresis. After genome sequencing and rpoB phylogeny, the strain was classified as C. ulcerans . To better understand the taxonomy of this strain and improve identification methods, we compared strain PO100/5 to other publicly available genomes from the C. diphtheriae group. Taxonomic analysis reclassified it and three others strains as belonging to the recently described C. silvaticum , which have been isolated from wild boar and roe deer in Germany and Austria. The results showed that PO100/5 is the first sequenced genome of a C. silvaticum strain from a domestic animal and a different geographical region, is a putative producer of the diphtheriae toxin, and has a unique sequence type. Genomic analysis of PO100/5 showed four prophages and eight conserved genomic islands when compared to C. ulcerans . Pangenome analysis of 38 C. silvaticum and 76 C. ulcerans samples suggest that C. silvaticum is a clonal species, with 73.6% of conserved genes and a pangenome near to being closed (α > 0.952). 172 conserved genes are unique to C. silvaticum when compared to C. ulcerans , with most related to nutrient uptake and metabolism, prophages or immune evasion. These unique genes could be used as genetic markers for species identification. This information can be useful for identification and surveillance of this pathogen, especially in regard to the possibility of zoonotic transmission.\n\nTaxonomic classification of strain PO100/5 shows a broader geographic distribution and genetic markers of the recently describedCorynebacterium silvaticum", "token_count": 475, "char_count": 1827, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5699, "quality_score": 0.7849, "entities": { "genes": [ "PO100" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:12.531688", "source": { "split": "train_shard_00001", "doc_id": 2929 }, "chunk_id": "train_shard_00001_2929_0", "global_id": 9815 }, { "text": "The mitogen-activated protein kinase Hog1 gene (Kmhog1) was isolated from Kluyveromyces marxianus strain NBRC 1777 by degenerate PCR and genome walking, and then disrupted to construct a mutant strain hog1∆. The mutant was now more sensitive to acetic acid and its growth was nearly completely inhibited by 0.5 M NaCl (97%) and 10 mM H2O2 (93%) as compared with the wild-type cells. However, neither strain grew at 47°C. Kmhog1 may thus be required for adaptation to acetic acid, osmotic, and oxidative stress but is not involved in thermotolerance.\n\nCloning and characterization of Kluyveromyces marxianus Hog1 gene", "token_count": 190, "char_count": 616, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:12.986436", "source": { "split": "train_shard_00001", "doc_id": 2930 }, "chunk_id": "train_shard_00001_2930_0", "global_id": 9816 }, { "text": "Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking. We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST gene diversity among 602 isolates from sporadic clinical cases, small clusters, or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages. The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii. We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed a short-timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500-cgMLST-mismatch threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible (https://bigsdb.pasteur.fr/diphtheria). Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae. The unified genomic taxonomy of C", "token_count": 512, "char_count": 1961, "word_count": 271, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [ "PW8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:13.617963", "source": { "split": "train_shard_00001", "doc_id": 2931 }, "chunk_id": "train_shard_00001_2931_0", "global_id": 9817 }, { "text": "diphtheriae strains provides a common language for studies of ecology, evolution, and virulence heterogeneity among C. diphtheriae sublineages.\n\nGenomic Epidemiology and Strain Taxonomy of Corynebacterium diphtheriae.", "token_count": 69, "char_count": 224, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:14.040380", "source": { "split": "train_shard_00001", "doc_id": 2931 }, "chunk_id": "train_shard_00001_2931_1", "global_id": 9818 }, { "text": "

Background:

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is a serious public health issue. Aim of the study was to identify the antimicrobial resistance and accessory genes, the clonal relatedness and the evolution dynamics of selected CRKP isolates recovered in an adult and a pediatric intensive care unit of a tertiary hospital in Greece.

Methods:

Twenty-four CRKP isolates recovered during 2018-2022 were included in the study. Next-generation sequencing was performed using the Ion Torrent PGM Platform. The identification of the plasmid content, MLST and antimicrobial resistance genes, as well as the comparison of multiple genome alignments and the identification of core genome single-nucleotide polymorphism sites, were performed applying various bioinformatics software.

Results:

The isolates belonged to eight sequence types 11, 15, 30, 35, 39, 307, 323, and 512. A variety of carbapenemases (KPC, VIM, NDM and OXA-48) and resistance genes were detected. CRKP strains shared visually common genomic regions with the reference strain (NTUH-K2044). ST15, ST323, ST39, and ST11 CRKP isolates presented on average 17, 6, 16 and 866 recombined SNPs, respectively. All isolates belonging to ST15, ST323 and ST39 were classified in distinct phylogenetic branches, while ST11 isolates were assigned to a two-subclade branch. For large CRKP sets, the phylogeny seems to change approximately every seven SNPs.

Conclusion:

The current study provides insight into the genetic characterization of CRKP isolates in the ICUs of a tertiary hospital. Our results indicate clonal dispersion of ST15, ST323, and ST39 and highly diverged ST11 isolates.", "token_count": 505, "char_count": 1686, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [ "ST15", "ST39", "ST323", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:14.714510", "source": { "split": "train_shard_00001", "doc_id": 2932 }, "chunk_id": "train_shard_00001_2932_0", "global_id": 9819 }, { "text": "Genetic Characterization of Carbapenem-Resistant Klebsiella pneumoniae Clinical Isolates in a Tertiary Hospital in Greece, 2018-2022", "token_count": 53, "char_count": 141, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:15.097241", "source": { "split": "train_shard_00001", "doc_id": 2932 }, "chunk_id": "train_shard_00001_2932_1", "global_id": 9820 }, { "text": "

Background

Shewanella strains are important dissimilatory metal-reducing bacteria which are widely distributed in diverse habitats. Despite efforts to genomically characterize Shewanella, knowledge of the molecular components, functional information and evolutionary patterns remain lacking, especially for their compatibility in the metal-reducing pathway. The increasing number of genome sequences of Shewanella strains offers a basis for pan-genome studies.

Results

A comparative pan-genome analysis was conducted to study genomic diversity and evolutionary relationships among 24 Shewanella strains. Results revealed an open pan-genome of 13,406 non-redundant genes and a core-genome of 1878 non-redundant genes. Selective pressure acted on the invariant members of core genome, in which purifying selection drove evolution in the housekeeping mechanisms. Shewanella strains exhibited extensive genome variability, with high levels of gene gain and loss during the evolution, which affected variable gene sets and facilitated the rapid evolution. Additionally, genes related to metal reduction were diversely distributed in Shewanella strains and evolved under purifying selection, which highlighted the basic conserved functionality and specificity of respiratory systems.

Conclusions

The diversity of genes present in the accessory and specific genomes of Shewanella strains indicates that each strain uses different strategies to adapt to diverse environments. Horizontal gene transfer is an important evolutionary force in shaping Shewanella genomes. Purifying selection plays an important role in the stability of the core-genome and also drives evolution in mtr-omc cluster of different Shewanella strains.\n\nPan-genome analyses of 24 Shewanella strains re-emphasize the diversification of their functions yet evolutionary dynamics of metal-reducing pathway.", "token_count": 483, "char_count": 1973, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6083, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:15.783361", "source": { "split": "train_shard_00001", "doc_id": 2933 }, "chunk_id": "train_shard_00001_2933_0", "global_id": 9821 }, { "text": "Recent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and the host. In this proof-of-concept study, we proposed a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in the in vitro colon model inoculated with a fecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, while species richness levels decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes. IMPORTANCE Here, we propose a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Our study revealed the importance of integrating the mucus compartment, which retained higher microbial richness during fermentation, showed the preference of oral microbial invaders for the mucosal resources, and indicated potential oral-to-intestinal mucosal competitions", "token_count": 471, "char_count": 1876, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5217, "quality_score": 0.7609, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:16.427610", "source": { "split": "train_shard_00001", "doc_id": 2934 }, "chunk_id": "train_shard_00001_2934_0", "global_id": 9822 }, { "text": "It also underlined promising opportunities to further understand mechanisms of oral invasion into the human gut microbiome, define microbe-microbe and mucus-microbe interactions in a compartmentalized fashion, and help to better characterize the potential of oral microbial invasion and their persistence in the gut.\n\nIn Vitro Modelling of Oral Microbial Invasion in the Human Colon.", "token_count": 94, "char_count": 390, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:16.797505", "source": { "split": "train_shard_00001", "doc_id": 2934 }, "chunk_id": "train_shard_00001_2934_1", "global_id": 9823 }, { "text": "Emm 1 Streptococcus pyogenes is a successful, globally-distributed epidemic clone that is regarded as inherently invasive. An emm 1 sublineage, M1 UK , that expresses increased SpeA toxin, was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1 UK is now dominant in England. To more fully characterise M1 UK , we undertook comparative transcriptomic and proteomic analyses of M1 UK and contemporary non-M1 UK emm 1 strains (M1 global ). Just seven genes were differentially expressed by M1 UK compared with contemporary M1 global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1 UK (gldA, mipB/talC, pflD, and pts system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1 UK strains have a stop codon in gldA. Deletion of the gldA gene in M1 global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm 1 sublineages in England comprising 13/27 (M1 13SNPs ) and 23/27 SNPs (M1 23SNPs ) respectively, that had failed to expand in the population. Proteomic analysis of these four major phylogenetic emm 1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically-defined medium. In rich broth however, transcription and secretion of SpeA was upregulated ~10-fold in both M1 23SNPs and M1 UK sublineages, compared with M1 13SNPs and M1 global . We conclude that stepwise accumulation of SNPs led to the emergence of M1 UK ", "token_count": 507, "char_count": 1762, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5683, "quality_score": 0.7841, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:17.427280", "source": { "split": "train_shard_00001", "doc_id": 2935 }, "chunk_id": "train_shard_00001_2935_0", "global_id": 9824 }, { "text": "While increased expression of SpeA is a key indicator of M1 UK and undoubtedly important, M1 UK strains have outcompeted M1 23SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1 UK on an inherently successful emm 1 streptococcal background.

Data availability

RNAseq. All new RNAseq data are uploaded to the European Nucleotide Archive under project reference PRJEB58303 Genomic data. All genomes listed are available on the European Nucleotide Archive using accession numbers as listed in the appendix, Proteomes. Proteomic data are available on FigShare 10.6084/m9.figshare.21777809 and will be uploaded to PRIDE

Impact Summary

Although the major Streptococcus pyogenes reservoir is in children with pharyngitis and skin infections, S. pyogenes can lead to rarer, invasive infections that are rapidly progressive and associated with high mortality and morbidity. Emm 1 S. pyogenes strains are the single most frequent genotype to cause invasive infections in high income countries and are established worldwide as an epidemic clone. The M1 UK S. pyogenes emm 1 sublineage which is defined by 27 new SNPs in the core genome, and characterised by increased scarlet fever toxin SpeA production, emerged and rose to dominance over a period of 5-6 years since initial recognition, outcompeting other emm 1 strains in England. Increased dominance of emm 1 among invasive infections this winter, on a background of already-increased numbers of S. pyogenes infections, points to a key shift in host-pathogen interaction. We hypothesize that a combination of pathogen fitness, virulence, and host susceptibility have coalesced to account for the excess of circulating S. pyogenes and emm 1 invasive infections", "token_count": 487, "char_count": 1843, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5791, "quality_score": 0.7896, "entities": { "genes": [ "PRJEB58303" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:18.083216", "source": { "split": "train_shard_00001", "doc_id": 2935 }, "chunk_id": "train_shard_00001_2935_1", "global_id": 9825 }, { "text": "In this paper we undertake a systems-based evaluation of M1 UK in comparison to older non-M1 UK emm 1 strains, and identify a number of pathways that are altered in addition to the previously-reported increased SpeA expression. The emergence of a new sublineage within an already virulent clone requires ongoing surveillance, and more detailed investigation of the likely mechanisms leading to increased fitness. The capacity of S. pyogenes to cause outbreaks at national scale highlights a potential need to consider strain-specific public health guidance, underlining the inherent virulence of this exclusively human pathogen.\n\nCharacterisation of emergent toxigenic M1UKStreptococcus pyogenesand associated sublineages", "token_count": 169, "char_count": 739, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7723, "quality_score": 0.8861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:18.525628", "source": { "split": "train_shard_00001", "doc_id": 2935 }, "chunk_id": "train_shard_00001_2935_2", "global_id": 9826 }, { "text": "Recombination and positive selection are two key factors that play a vital role in pathogenic microorganisms' population adaptation and diversification. The Burkholderia cepacia complex (Bcc) represents bacterial species with high similarity, which can cause severe infections among cases suffering from the chronic granulomatous disorder and cystic fibrosis (CF). At present, no genome-wide study has been carried out focusing on investigating the core genome of Bcc associated with the two evolutionary forces. The general characteristics of the core genome of Bcc species remain scarce as well. In this study, we explored the core orthologous genes of 116 Bcc strains using comparative genomic analysis and studied the two adaptive evolutionary forces: recombination and positive selection. We estimated 1005 orthogroups consisting entirely of single copy genes. These single copy orthologous genes in some Cluster of Orthologous Groups (COG) categories showed significant differences in the comparison of several evolutionary properties, and the encoding proteins were relatively simple and compact. Our findings showed that 5.8% of the core orthologous genes strongly supported recombination; in the meantime, 1.1% supported positive selection. We found that genes involved in protein synthesis as well as material transport and metabolism are favored by selection pressure. More importantly, homologous recombination contributed more genetic variation to a large number of genes and largely maintained the genetic cohesion in Bcc. This high level of recombination between Bcc species blurs their taxonomic boundaries, which leads Bcc species to be difficult or impossible to distinguish phenotypically and genotypically.\n\nCharacterization of Burkholderia cepacia Complex Core Genome and the Underlying Recombination and Positive Selection.", "token_count": 409, "char_count": 1859, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:19.151082", "source": { "split": "train_shard_00001", "doc_id": 2936 }, "chunk_id": "train_shard_00001_2936_0", "global_id": 9827 }, { "text": "Fresh vegetables are closely associated with foodborne disease outbreaks; however, systematic analysis of the microbiological quality of fresh vegetables and molecular information on foodborne pathogens in fresh produce are poorly reported in China. Here, we evaluated the epidemiological prevalence of coliforms via the most probable number method and characterized Salmonella and ciprofloxacin-resistant (CIPR) Escherichia coli isolates recovered from retail fresh vegetables in Shaanxi Province, China. Antimicrobial susceptibility testing, serotype determination, multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST), antibiotic resistance encoding gene (ARG) annotation, virulence factor prediction, and functional classification were performed. Between October 2020 and September 2021, 576 samples (i.e., tomatoes, lettuces, spinaches, and cabbages) were found to be positive for coliforms, and the prevalence of coliforms showed a seasonal trend. Coliform counts of vegetables in supermarkets in Xi'an were significantly lower (P < 0.01) than that in other cities. The detection rates of Salmonella and CIPRE. coli-positive vegetables were 1 % (6/576) and 0.7 % (4/576), respectively. All isolates exhibited resistance to ≥1 antibiotics, and 92.9 % (13/14) were multidrug-resistant. One extended spectrum β-lactamase (ESBL)-producing CIPRE. coli isolate in spinach was resistant to not only three third-generation cephalosporins but also to two polymyxins. Among nine Salmonella isolates, five different serovars (S. Enteritidis, S. Indiana, monophasic variant of S. Typhimurium, S. Agona, and S. Gallinarum), four sequence types (STs; ST11, ST13, ST17, and ST34), and seven core genome STs (cgSTs) were identified. Five CIPRE", "token_count": 520, "char_count": 1807, "word_count": 237, "semantic_coherence": 1, "information_density": 0.7215, "quality_score": 0.8608, "entities": { "genes": [ "ST17", "ST34", "ST13", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:31:19.809870", "source": { "split": "train_shard_00001", "doc_id": 2937 }, "chunk_id": "train_shard_00001_2937_0", "global_id": 9828 }, { "text": "coli strains were assigned to three serovars (O101:H4, O8:H18, and O11:H25), three STs (ST44, ST48, and ST457), and four cgSTs. Coexisting amino acid mutations of Thr57Ser/Ser80Arg in ParC and Ser83Phe/Asp87Gly in GyrA in quinolone resistance-determining regions (QRDRs) might be causes for nalidixic acid resistance. Eight definite virulence profiles in eight serovars were identified. Notably, cdtB and pltA only encoded typhoid toxins and were just detected from S. Typhoid isolates were also detected from S. Indiana and monophasic S. Typhimurium, which are closely associated with swine food chain were first detected in fresh vegetables. In conclusion, our findings suggest that coliform contamination on fresh vegetables is prevalent in this province. Most Salmonella and CIPRE. coli isolates were phenotypically and genetically diverse and could resist multiple antibiotics by carrying multiple ARGs and virulence genes.\n\nMicrobiological analysis and characterization of Salmonella and ciprofloxacin-resistant Escherichia coli isolates recovered from retail fresh vegetables in Shaanxi Province, China.", "token_count": 325, "char_count": 1121, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": { "genes": [ "ST48", "ST44", "ST457" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:20.378898", "source": { "split": "train_shard_00001", "doc_id": 2937 }, "chunk_id": "train_shard_00001_2937_1", "global_id": 9829 }, { "text": "The COVID-19 pandemic has intensified the issue of multidrug-resistant (MDR) infections, particularly in intensive care units (ICUs). This study documents the first known case of coinfection with two extensively drug-resistant (XDR) bacterial isolates in a critically ill patient with COVID-19 in Saudi Arabia. Both XDR isolates were recovered from blood and were resistant to all tested antimicrobial agents except colistin. Whole genome sequencing (WGS) revealed that the K. pneumoniae isolate KP-JZ107 had sequence type 11 (ST11) and core genome MLST (cgMLST 304742), while the A. baumannii isolate AB-JZ67 had ST2 and cgMLST 785. KP-JZ107 was found to possess the virulence plasmid KpVP-type-1, carbapenemase genes bla NDM and bla KPC , and numerous antimicrobial-resistant genes (ARGs). The AB-JZ67 isolate had several biofilm-related genes, including biofilm-associated protein (BAP), csuE, and pgaB, and multiple ARGs, including bla ADC-25, bla OXA-23, and bla OXA-66. Our findings suggest that the coexistence of KP-JZ107 and AB-JZ67 isolates may indicate their widespread presence in ICUs, requiring comprehensive surveillance studies across all hospitals.", "token_count": 453, "char_count": 1304, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7394, "quality_score": 0.8697, "entities": { "genes": [ "ST2", "JZ67", "JZ107", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:21.008906", "source": { "split": "train_shard_00001", "doc_id": 2938 }, "chunk_id": "train_shard_00001_2938_0", "global_id": 9830 }, { "text": "Comprehensive Genome Analysis of Colistin-Only-Sensitive KPC-2 and NDM1-1-Coproducing Klebsiella pneumoniae ST11 and Acinetobacter baumannii ST2 From a Critically Ill Patient With COVID-19 in Saudi Arabia: Whole Genome Sequencing (WGS) of K. pneumoniae ST11 and A. baumannii ST2.", "token_count": 123, "char_count": 307, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8108, "quality_score": 0.9054, "entities": { "genes": [ "ST2", "NDM1", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:21.396004", "source": { "split": "train_shard_00001", "doc_id": 2938 }, "chunk_id": "train_shard_00001_2938_1", "global_id": 9831 }, { "text": "

Background

Pandrug-resistant (PDR) Klebsiella pneumoniae has been reported sporadically in many countries and remains rare in Brazil.

Objectives

This study unravelled the genetic determinants involved with the PDR background of a clinical ST11 K. pneumoniae recovered in the Brazilian Amazon Region, where K. pneumoniae genomic and epidemiological information is scarce.

Methods

Kp196 was submitted to the antimicrobial susceptibility test by the disk-diffusion method and minimum inhibitory concentration (MIC) determination. The whole genome sequencing was obtained and the sequence type was determined by core genome multilocus sequence typing (cgMLST). Its intrinsic and acquired resistome was assessed by Comprehensive Antibiotic Resistance Database (CARD) and comparison with wild-type genes.

Findings

The analyses revealed that Kp196 belonged to the pandemic ST11 and presented the PDR phenotype. Its acquired resistome was composed of a huge set of clinically relevant resistance determinants, including bla CTX-M-15 and bla NDM-1, all found in the vicinity of mobile platforms. Considering its intrinsic resistome, the multidrug resistance, especially to colistin, tigecycline and fluoroquinolones, was multifactorial and attributed to modifications (indels, missense mutations, and gene disruption) in several housekeeping genes (arnT/phoQ/mgrB/ramR/acrB/gyrA/parC/ompK35-36-37). The Kp196 intrinsic resistome was also observed in a ST11 environmental strain, although harbouring distinct acquired resistomes.

Conclusions

An accumulation of different resistance mechanisms regarding the intrinsic resistome accounts for a more stable resistome, strongly contributing to the Kp196 PDR phenotype.\n\nUnveiling the genome of a high-risk pandrug-resistant Klebsiella pneumoniae emerging in the Brazilian Amazon Region, 2022.", "token_count": 502, "char_count": 1864, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6272, "quality_score": 0.8136, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:22.047734", "source": { "split": "train_shard_00001", "doc_id": 2939 }, "chunk_id": "train_shard_00001_2939_0", "global_id": 9832 }, { "text": "The epidemiological success of methicillin-resistant Staphylococcus aureus USA300 has been associated with the presence of two mobile elements, the arginine catabolic mobile element (ACME) and the copper and mercury resistance (COMER) element. These two mobile elements are associated with resistance to copper, which has been related to host fitness and survival within macrophages. Several studies found that ACME is more prevalent, and exhibits greater diversity, in Staphylococcus epidermidis while COMER has not been identified in S. epidermidis or any other staphylococcal species. We aimed in this study to evaluate the presence and diversity of ACME and COMER-like elements in our S. epidermidis clinical isolates. The genomes of 58 S. epidermidis clinical isolates, collected between 2009 and 2018 in a Scottish hospital, were sequenced. A core-genome phylogenetic tree and genome based MLST typing showed that more than half of the isolates belong to the clinically predominant sequence type2 (ST2) and these isolates have been found to split into two lineages within the phylogenetic tree. Analysis showed the presence of SCCmec in the majority of isolates. Comparative analysis identified a cluster of ACME-positive isolates with most of them belonging to ST48. ACME showed high variation even between isolates of the same ACME type and ST. COMER-like elements have been identified in one of the two major hospital adapted drug resistant ST2 lineages; and showed high stability. This difference in stability at the genomic level correlates well with the up to one hundred times higher excision frequency found for the SCCmec elements in ACME-containing isolates compared to COMER-like element containing isolates. ACME/COMER-like element positive isolates did not show a significant phenotype of decreased copper susceptibility, while resistance to mercury was over-represented in COMER-like element positive isolates. To the best of our knowledge, this is the first molecular characterization of COMER-like elements in S", "token_count": 525, "char_count": 2085, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5433, "quality_score": 0.7717, "entities": { "genes": [ "USA300", "ST2", "ST48" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:31:22.709445", "source": { "split": "train_shard_00001", "doc_id": 2940 }, "chunk_id": "train_shard_00001_2940_0", "global_id": 9833 }, { "text": "epidermidis isolates. The presence of the COMER-like elements is the most prominent accessory genome feature of these successful lineages suggesting that this chromosomal island contributes to the success and wide clinical distribution of ST2 S. epidermidis.\n\nGenomic Stability of Composite SCCmec ACME and COMER-Like Genetic Elements in Staphylococcus epidermidis Correlates With Rate of Excision.", "token_count": 122, "char_count": 423, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:23.098933", "source": { "split": "train_shard_00001", "doc_id": 2940 }, "chunk_id": "train_shard_00001_2940_1", "global_id": 9834 }, { "text": "Colonization and development of the gut microbiome are crucial for the growth and health of calves. In this review, we summarized the colonization, beneficial nutrition, immune function of gut microbiota, function of the gut barrier, and the evolution of core microbiota in the gut of calves of different ages. Homeostasis of gut microbiome is beneficial for nutritional and immune system development of calves. Disruption of the gut microbiome leads to digestive diseases in calves, such as diarrhea and intestinal inflammation. Microbiota already exists in the gut of calf fetuses, and the colonization of microbiota continues to change dynamically under the influence of various factors, which include probiotics, diet, age, and genotype. Colonization depends on the interaction between the gut microbiota and the immune system of calves. The abundance and diversity of these commensal microbiota stabilize and play a critical role in the health of calves.\n\nColonization and development of the gut microbiome in calves.", "token_count": 233, "char_count": 1022, "word_count": 154, "semantic_coherence": 1, "information_density": 0.4935, "quality_score": 0.7468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:23.570620", "source": { "split": "train_shard_00001", "doc_id": 2941 }, "chunk_id": "train_shard_00001_2941_0", "global_id": 9835 }, { "text": "Lignocellulosic biomass is the most abundant renewable source of energy that has been widely explored as second-generation biofuel feedstock. Despite more than four decades of research, the process of ethanol production from lignocellulosic (LC) biomass remains economically unfeasible. This is due to the high cost of enzymes, end-product inhibition of enzymes, and the need for cost-intensive inputs associated with a separate hydrolysis and fermentation (SHF) process. Thermotolerant yeast strains that can undergo fermentation at temperatures above 40°C are suitable alternatives for developing the simultaneous saccharification and fermentation (SSF) process to overcome the limitations of SHF. This review describes the various approaches to screen and develop thermotolerant yeasts via genetic and metabolic engineering. The advantages and limitations of SSF at high temperatures are also discussed. A critical insight into the effect of high temperatures on yeast morphology and physiology is also included. This can improve our understanding of the development of thermotolerant yeast amenable to the SSF process to make LC ethanol production commercially viable.\n\nThermotolerant fermenting yeasts for simultaneous saccharification fermentation of lignocellulosic biomass", "token_count": 297, "char_count": 1280, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:24.135756", "source": { "split": "train_shard_00001", "doc_id": 2942 }, "chunk_id": "train_shard_00001_2942_0", "global_id": 9836 }, { "text": "Human gut and food microbiomes interact during digestion. The outcome of these interactions influences the taxonomical composition and functional capacity of the resident human gut microbiome, with potential consequential impacts on health and disease. Microbe-microbe interactions between the resident and introduced microbiomes, which likely influence host colonisation, are orchestrated by environmental conditions, elements of the food matrix, host-associated factors as well as social cues from other microorganisms. Quorum sensing is one example of a social cue that allows bacterial communities to regulate genetic expression based on their respective population density and has emerged as an attractive target for therapeutic intervention. By interfering with bacterial quorum sensing, for instance, enzymatic degradation of signalling molecules (quorum quenching) or the application of quorum sensing inhibitory compounds, it may be possible to modulate the microbial composition of communities of interest without incurring negative effects associated with traditional antimicrobial approaches. In this review, we summarise and critically discuss the literature relating to quorum sensing from the perspective of the interactions between the food and human gut microbiome, providing a general overview of the current understanding of the prevalence and influence of quorum sensing in this context, and assessing the potential for therapeutic targeting of quorum sensing mechanisms.\n\nQuorum sensing in human gut and food microbiomes: Significance and potential for therapeutic targeting.", "token_count": 321, "char_count": 1596, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6065, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:24.697854", "source": { "split": "train_shard_00001", "doc_id": 2943 }, "chunk_id": "train_shard_00001_2943_0", "global_id": 9837 }, { "text": "

Background:

Carbapenem-resistant Pseudomonas aeruginosa sequence type 463 (ST463-CRPA) with high-virulence and high-resistance has emerged and spread rapidly in East China. The aim of the study was to investigate the distribution and characteristics of the emerging high-risk ST463-CRPA in intensive care unit (ICU) in East China.

Methods:

: The 11-month-span study investigated the epidemiological characteristics, genetic composition, and transmission pattern of CRPA isolated from patients and environments of 5 different ICUs in a large teaching hospital in East China. Whole-genome sequencing, antibiotic susceptibility testing and biofilm-forming ability testing were performed in all CRPA isolates. The molecular epidemiological characteristics and the phylogenetic relationships of isolates from different sources were assessed using multi-locus sequence typing (MLST) and core genome multi-locus sequence typing (cgMLST). Bacterial virulence was assessed using a Galleria mellonella infection model.

Results:

: According to the MLST scheme, all of CRPA isolates fell into 25 defined STs, of which 24.07% (13/54) CRPA belonged to ST463 as the dominant ST in ICUs. All 13 ST463-CRPA strains, including 4 from patients and 9 from environments mainly in washbasins, carried bla KPC-2 gene with exoU+ / exoS+ virulence genotype showing difficult-to-treat resistance (DTR) phenotype. ST463-CRPA had higher biofilm-forming ability and mortality of infected larvae than non-ST463-CRPA (P<0.05). No differences on virulence were detected between the CRPA from environments and infected patients. CgMLST results revealed that several ST463-CRPA strains isolated from different ICUs had genetic relationship. Notably, 3 ST463 strains harboring both bla AFM-1 and bla KPC-2 genes with 41-59 SNPs difference were isolated from different ICUs", "token_count": 517, "char_count": 1865, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6166, "quality_score": 0.8083, "entities": { "genes": [ "ST463" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:31:25.358254", "source": { "split": "train_shard_00001", "doc_id": 2944 }, "chunk_id": "train_shard_00001_2944_0", "global_id": 9838 }, { "text": "

Conclusions:

: In combination with epidemiological data linked in time and space, the cgMLST results elucidated polyclonal dissemination of CRPA and a distribution of ST463-CRPA among ICUs in a large hospital of East China. As the dominant ST found in ICU especially in environments, KPC-ST463-CRPA might be considered a strain with potential to cause a future outbreak, which could acquire the bla AFM gene additionally, leading to the resistance to last-resort antibiotics. Hence, it’s worth our vigilance about the growing prevalence of ST463-CRPA in ICU of East China. Meanwhile, it’s important to strengthen the management of ICU environment, especially the water reservoirs.\n\nPseudomonas aeruginosa strains isolated from environments and patients analysed by cgMLST: The dominance of the emerging high-risk clone ST463 from intensive care unit in East China", "token_count": 223, "char_count": 872, "word_count": 128, "semantic_coherence": 1, "information_density": 0.7031, "quality_score": 0.8516, "entities": { "genes": [ "ST463" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:25.818840", "source": { "split": "train_shard_00001", "doc_id": 2944 }, "chunk_id": "train_shard_00001_2944_1", "global_id": 9839 }, { "text": "Bacteria of the genus Listeria (phylum Firmicutes) include both human and animal pathogens, as well as saprophytic strains. A common component of Listeria spp. genomes are plasmids, i.e., extrachromosomal replicons that contribute to gene flux in bacteria. This study provides an in-depth insight into the structure, diversity and evolution of plasmids occurring in Listeria strains inhabiting various environments under different anthropogenic pressures. Apart from the components of the conserved plasmid backbone (providing replication, stable maintenance and conjugational transfer functions), these replicons contain numerous adaptive genes possibly involved in: (i) resistance to antibiotics, heavy metals, metalloids and sanitizers, and (ii) responses to heat, oxidative, acid and high salinity stressors. Their genomes are also enriched by numerous transposable elements, which have influenced the plasmid architecture. The plasmidome of Listeria is dominated by a group of related replicons encoding the RepA replication initiation protein. Detailed comparative analyses provide valuable data on the level of conservation of these replicons and their role in shaping the structure of the Listeria pangenome, as well as their relationship to plasmids of other genera of Firmicutes, which demonstrates the range and direction of flow of genetic information in this important group of bacteria.\n\nPlasmidome of Listeria spp.-The repA-Family Business.", "token_count": 395, "char_count": 1518, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6816, "quality_score": 0.8408, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:26.462064", "source": { "split": "train_shard_00001", "doc_id": 2945 }, "chunk_id": "train_shard_00001_2945_0", "global_id": 9840 }, { "text": "Campylobacter jejuni (C. jejuni) is the most common cause of human bacterial gastroenteritis in the world. Food-borne campylobacteriosis is thought to be commonly caused by the handling and consumption of undercooked chicken meat, but the epidemiology of this disease is complex and remains poorly characterized, especially in the Nordic countries. Here, we used state-of-the-art methods in genetic epidemiology combined with patient background and temporal association data to trace domestically acquired human C. jejuni infections (n = 50) to chicken meat, in a midsize Nordic town in Finland during a seasonal peak. Although 59.2% of the human isolates shared a sequence type (ST) with a chicken batch slaughtered prior to the onset of disease, further analysis at the whole-genome level (core genome and whole-genome multilocus sequence typing, cgMLST and wgMLST, respectively) traced a mere nine cases (18.4%) to fresh chicken meat. Human isolates also shared genotypes with isolates collected from chicken batches slaughtered after the onset of the human disease, highlighting the role of alternative transmission pathways from chickens to humans besides the food chain, or a shared third source. The high resolution offered by wgMLST, combined with simple metadata, offers a more accurate way to trace sporadic cases to possible sources and reveal disseminated outbreak clustering in time, confirming the importance of complementing epidemiological investigations with molecular epidemiological data.\n\nHuman Campylobacteriosis Cases Traceable to Chicken Meat-Evidence for Disseminated Outbreaks in Finland.", "token_count": 397, "char_count": 1641, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:27.094769", "source": { "split": "train_shard_00001", "doc_id": 2946 }, "chunk_id": "train_shard_00001_2946_0", "global_id": 9841 }, { "text": "The ST204 subgroup of Listeria monocytogenes is among the most frequently isolated in Australia from a range of environmental niches. In this study we provide a comparative genomics analysis of food and food environment isolates from geographically diverse sources. Analysis of the ST204 genomes showed a highly conserved core genome with the majority of variation seen in mobile genetic elements such as plasmids, transposons and phage insertions. Most strains (13/15) harbored plasmids, which although varying in size contained highly conserved sequences. Interestingly 4 isolates contained a conserved plasmid of 91,396 bp. The strains examined were isolated over a period of 12 years and from different geographic locations suggesting plasmids are an important component of the genetic repertoire of this subgroup and may provide a range of stress tolerance mechanisms. In addition to this 4 phage insertion sites and 2 transposons were identified among isolates, including a novel transposon. These genetic elements were highly conserved across isolates that harbored them, and also contained a range of genetic markers linked to stress tolerance and virulence. The maintenance of conserved mobile genetic elements in the ST204 population suggests these elements may contribute to the diverse range of niches colonized by ST204 isolates. Environmental stress selection may contribute to maintaining these genetic features, which in turn may be co-selecting for virulence markers relevant to clinical infection with ST204 isolates.\n\nComparative Genomics of the Listeria monocytogenes ST204 Subgroup.", "token_count": 374, "char_count": 1617, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5279, "quality_score": 0.7639, "entities": { "genes": [ "ST204" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:27.723243", "source": { "split": "train_shard_00001", "doc_id": 2947 }, "chunk_id": "train_shard_00001_2947_0", "global_id": 9842 }, { "text": "Ten Gram-strain-negative, facultatively anaerobic, moderately halophilic bacterial strains, designated AL184T, IB560, IB563, IC202, IC317, MA421, ML277, ML318, ML328A and ML331, were isolated from water ponds of five salterns located in Spain. The cells were motile, curved rods and oxidase and catalase positive. All of them grew optimally at 37°C, at pH 7.2-7.4 and in the presence of 7.5% (w/v) NaCl. Based on phylogenetic analyses of the 16S rRNA, the isolates were most closely related to Salinivibrio sharmensis BAGT (99.6-98.2% 16S rRNA gene sequence similarity) and Salinivibrio costicola subsp. costicola ATCC 35508T (99.0-98.1%). According to the MLSA analyses based on four (gyrB, recA, rpoA and rpoD) and eight (ftsZ, gapA, gyrB, mreB, pyrH, recA, rpoA and topA) concatenated gene sequences, the most closely relatives were S. siamensis JCM 14472T (96.8-95.4% and 94.9-94.7%, respectively) and S. sharmensis DSM 18182T (94.0-92.6% and 92.9-92.7%, respectively). In silico DNA-DNA hybridization (GGDC) and average nucleotide identity (ANI) showed values of 23.3-44.8% and 80.2-91.8%, respectively with the related species demonstrating that the ten isolates constituted a single novel species of the genus Salinivibrio", "token_count": 508, "char_count": 1284, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7159, "quality_score": 0.858, "entities": { "genes": [ "ML318", "MA421", "IC202", "IC317", "AL184", "IB560", "ML331", "IB563", "ML328A", "ML277" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:28.385080", "source": { "split": "train_shard_00001", "doc_id": 2948 }, "chunk_id": "train_shard_00001_2948_0", "global_id": 9843 }, { "text": "Its pangenome and core genome consist of 6041 and 1230 genes, respectively. The phylogeny based on the concatenated orthologous core genes revealed that the ten strains form a coherent phylogroup well separated from the rest of the species of the genus Salinivibrio. The major cellular fatty acids of strain AL184T were C16:0 and C18:1. The DNA G+C content range was 51.9-52.5mol% (Tm) and 50.2-50.9mol% (genome). Based on the phylogenetic-phylogenomic, phenotypic and chemotaxonomic data, the ten isolates represent a novel species of the genus Salinivibrio, for which the name Salinivibrio kushneri sp. nov. is proposed. The type strain is AL184T (=CECT 9177T=LMG 29817T).\n\nSalinivibrio kushneri sp. nov., a moderately halophilic bacterium isolated from salterns.", "token_count": 305, "char_count": 842, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8451, "entities": { "genes": [ "AL184" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:28.952170", "source": { "split": "train_shard_00001", "doc_id": 2948 }, "chunk_id": "train_shard_00001_2948_1", "global_id": 9844 }, { "text": "Salmonella enterica is one of the most commonly reported foodborne pathogens by public health agencies worldwide. In this study, the multilocus sequence typing (MLST) population structure and frequency of antimicrobial resistance (AMR) genes were evaluated in S. enterica strains from Mexico (n = 2561). The most common sources of isolation were food (44.28%), environment (27.41%), animal-related (24.83%), and human (3.48%). The most prevalent serovars were Newport (8.51%), Oranienburg (7.03%), Anatum (5.78%), Typhimurium (5.12%), and Infantis (4.57%). As determined by the 7-gene MLST scheme, the most frequent sequence types were ST23, ST64, and ST32. The core genome MLST scheme identified 132 HC2000 and 195 HC900 hierarchical clusters, with the HC2000_2 cluster being the most prevalent in Mexico (n = 256). A total of 78 different AMR genes belonging to 13 antimicrobial classes were detected in 638 genomic assemblies of S. enterica. The most frequent class was aminoglycosides (31.76%), followed by tetracyclines (12.53%) and sulfonamides (11.91%). These results can help public health agencies in Mexico prioritize their efforts and resources to increase the genomic sequencing of circulating Salmonella strains. Additionally, they provide valuable information for local and global public health efforts to reduce the impact of foodborne diseases and AMR.\n\nGenomic analysis of the MLST population structure and antimicrobial resistance genes associated with Salmonella enterica in Mexico.", "token_count": 483, "char_count": 1550, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8233, "entities": { "genes": [ "HC900", "ST64", "ST23", "ST32", "HC2000" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:29.602720", "source": { "split": "train_shard_00001", "doc_id": 2949 }, "chunk_id": "train_shard_00001_2949_0", "global_id": 9845 }, { "text": "An experimental design was carried out to evaluate the effect of the concentrations of sodium alginate, glutaraldehyde and activated coal on the immobilization of inulinase from Kluyveromyces marxianus NRRL Y-7571. The experimental condition of 20 g/L of sodium alginate, 50 mL/L of glutaraldehyde and 30 g/L of activated coal led to the highest specific activity (2,063.5 U/mg of protein), corresponding to an enhancement of about 26 times compared to the activity of the free enzyme (79.1 U/mg of protein). The effect of pH and temperature on the immobilized enzyme activity was also evaluated, showing optimal activities at pH of 5.5 and 55 °C. The study of storage of immobilized inulinase in different temperatures showed that the extract kept its initial activity after 43 days of storage at 40 and 50 °C and after 138 days of storage either at 4 or 25 °C.\n\nImmobilization of inulinase from Kluyveromyces marxianus NRRL Y-7571 using modified sodium alginate beads.", "token_count": 296, "char_count": 970, "word_count": 156, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:30.166339", "source": { "split": "train_shard_00001", "doc_id": 2950 }, "chunk_id": "train_shard_00001_2950_0", "global_id": 9846 }, { "text": "

Objectives

To enhance monitoring of high-burden foodborne pathogens, there is opportunity to combine pangenome data with network analysis.

Methods

Salmonella enterica subspecies Enterica serovar Enteritidis isolates were referred to the New South Wales (NSW) Enteric Reference Laboratory between August 2015 and December 2019 (1033 isolates in total), inclusive of a confirmed outbreak. All isolates underwent whole genome sequencing. Distances between genomes were quantified by in silico multiple-locus variable-number tandem repeat analysis (MLVA) as well as core single nucleotide polymorphisms (SNPs), which informed the construction of undirected networks. Centrality-prevalence spaces were generated from the undirected networks. Components on the undirected SNP network were considered alongside a phylogenetic tree representation.

Results

Outbreak isolates were identified as distinct components on the MLVA and SNP networks. The MLVA network-based centrality-prevalence space did not delineate the outbreak, whereas the outbreak was delineated in the SNP network-based centrality-prevalence space. Components on the undirected SNP network showed a high concordance to the SNP clusters based on phylogenetic analysis.

Conclusions

Bacterial whole-genome data in network-based analysis can improve the resolution of population analysis. High concordance of network components and SNP clusters is promising for rapid population analyses of foodborne Salmonella spp. owing to the low overhead of network analysis.\n\nGenome-wide networks reveal emergence of epidemic strains of Salmonella Enteritidis.", "token_count": 404, "char_count": 1633, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6225, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:31.136856", "source": { "split": "train_shard_00001", "doc_id": 2951 }, "chunk_id": "train_shard_00001_2951_0", "global_id": 9847 }, { "text": "Plasmids enable the dissemination of antimicrobial resistance (AMR) in common Enterobacterales pathogens, representing a major public health challenge. However, the extent of plasmid sharing and evolution between Enterobacterales causing human infections and other niches remains unclear, including the emergence of resistance plasmids. Dense, unselected sampling is highly relevant to developing our understanding of plasmid epidemiology and designing appropriate interventions to limit the emergence and dissemination of plasmid-associated AMR. We established a geographically and temporally restricted collection of human bloodstream infection (BSI)-associated, livestock-associated (cattle, pig, poultry, and sheep faeces, farm soils) and wastewater treatment work (WwTW)-associated (influent, effluent, waterways upstream/downstream of effluent outlets) Enterobacterales . Isolates were collected between 2008-2020 from sites <60km apart in Oxfordshire, UK. Pangenome analysis of plasmid clusters revealed shared “backbones”, with phylogenies suggesting an intertwined ecology where well-conserved plasmid backbones carry diverse accessory functions, including AMR genes. Many plasmid “backbones” were seen across species and niches, raising the possibility that plasmid movement between these followed by rapid accessory gene change could be relatively common. Overall, the signature of identical plasmid sharing is likely to be a highly transient one, implying that plasmid movement might be occurring at greater rates than previously estimated, raising a challenge for future genomic One Health studies.

Funding

This study was funded by the Antimicrobial Resistance Cross-council Initiative supported by the seven research councils and the NIHR, UK.\n\nEnterobacteralesplasmid sharing amongst human bloodstream infections, livestock, wastewater, and waterway niches in Oxfordshire, UK", "token_count": 462, "char_count": 1906, "word_count": 240, "semantic_coherence": 1, "information_density": 0.7125, "quality_score": 0.8562, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:31.781863", "source": { "split": "train_shard_00001", "doc_id": 2952 }, "chunk_id": "train_shard_00001_2952_0", "global_id": 9848 }, { "text": "The kinetics and regulation of D-xylose uptake were investigated in the efficient pentose fermentor Candida succiphila, and in Kluyveromyces marxianus, which assimilate but do not ferment pentose sugars. Active high affinity (Km approximately 3.8 mM; Vmax approximately 15 nmol/[mg min]) and putative facilitated diffusion low-affinity (Km approximately 140 mM; Vmax approximately 130 nmol/[mg min]) transport activities were found in C. succiphila grown, respectively, on xylose or glucose. K. marxianus showed facilitated diffusion low-affinity (Km approximately 103 mM; Vmax approximately 190 nmol/[mg min]) transport activity when grown on xylose under microaerobic conditions, and both a low-affinity and an active high-affinity (Km approximately 0.2 mM; Vmax approximately 10 nmol/[mg min]) transport activity when grown on xylose under fully aerobic conditions.\n\nD-Xylose transport by Candida succiphila and Kluyveromyces marxianus.", "token_count": 280, "char_count": 939, "word_count": 126, "semantic_coherence": 1, "information_density": 0.5873, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:32.335247", "source": { "split": "train_shard_00001", "doc_id": 2953 }, "chunk_id": "train_shard_00001_2953_0", "global_id": 9849 }, { "text": "The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common infections. bla KPC, encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn4401, ~10 kb). Here we characterize the genetic features of bla KPC emergence in global E. coli, 2008-2013, using both long- and short-read whole-genome sequencing. Amongst 43/45 successfully sequenced bla KPC-E. coli strains, we identified substantial strain diversity (n = 21 sequence types, 18% of annotated genes in the core genome); substantial plasmid diversity (≥9 replicon types); and substantial bla KPC-associated, mobile genetic element (MGE) diversity (50% not within complete Tn4401 elements). We also found evidence of inter-species, regional and international plasmid spread. In several cases bla KPC was found on high copy number, small Col-like plasmids, previously associated with horizontal transmission of resistance genes in the absence of antimicrobial selection pressures. E. coli is a common human pathogen, but also a commensal in multiple environmental and animal reservoirs, and easily transmissible. The association of bla KPC with a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms (e.g. bla TEM, bla CTX-M) suggests that it may become similarly prevalent.\n\nGenomic epidemiology of global Klebsiella pneumoniae carbapenemase (KPC)-producing Escherichia coli.", "token_count": 474, "char_count": 1645, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:32.983036", "source": { "split": "train_shard_00001", "doc_id": 2954 }, "chunk_id": "train_shard_00001_2954_0", "global_id": 9850 }, { "text": "The purpose of this study was to investigate the yeast population during the processing of green table olives. In the fresh olives, yeast were found at concentrations of around 3.0 log cfu/g, with Cryptococcus spp. being predominant. In the brine, the yeast concentrations were greater than 4.9 log cfu/ml, with Pichia anomala, Kluyveromyces marxianus, and Saccharomyces cerevisiae being the predominant species. Unlike the yeast isolated from the fresh olives, the strains obtained from the olive brine mostly showed low pectolytic but high catalase activities. Some of these strains also exhibited other biochemical desirable properties for the fermentation of green table olives, including their lipolytic activities and their assimilation or production of organic acids in the brine. Seven strains in particular of P. anomala, K. marxianus, S. cerevisiae, and Candida maris showed the best properties for use in trials as starter culture in pilot fermenters.\n\nIdentification and characterization of yeast isolated from the elaboration of seasoned green table olives.", "token_count": 269, "char_count": 1070, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:33.537198", "source": { "split": "train_shard_00001", "doc_id": 2955 }, "chunk_id": "train_shard_00001_2955_0", "global_id": 9851 }, { "text": "Abstract

Background

Nonsusceptibility of Proteus mirabilis to imipenem allows this pathogen evade surveillance for carbapenemases. Metallo-beta-lactamases of the VIM family are widespread among Enterobacterales in Europe. We identified an outbreak of P. mirabilis carrying 2 VIM enzymes among elderly patients from a medical center in Hungary.

Methods

A total of 16 P. mirabilis isolates were received from Hungary during 2020 as part of the SENTRY Antimicrobial Surveillance Program. Isolates were susceptibility tested by the CLSI reference broth microdilution method. Carbapenem-nonsusceptible isolates were submitted to whole genome sequencing, screened for resistance mechanisms, and evaluated for core genome multi-locus sequence typing (cgMLST).

Results

Among the 16 P. mirabilis isolates from Hungary, 5 carbapenem-nonsusceptible, multidrug-resistant isolates (3 from urinary tract infections and 1 each from bloodstream infection and pneumonia) were identified from patients 66-92 years old. Four of these 5 isolates were listed as community acquired. All isolates were resistant to ceftriaxone (MIC, > 8 mg/L), cefepime (16- > 32), imipenem ( > 8), gentamicin ( > 16), levofloxacin (16- > 32), nitrofurantoin ( > 64), trimethoprim/sulfamethoxazole ( > 4), and plazomicin ( > 128), but susceptible to meropenem (0.25-0.5) and ertapenem (0.03-0.25). Isolates carried blaVIM-4 and blaVIM-75 on a class 1 integron within IS26 and separated by aac(6’)-IIc. IS26 was located on a compound plasmid carrying other resistance-encoding genes, including armA", "token_count": 505, "char_count": 1584, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.8311, "entities": { "genes": [ "IS26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:34.185783", "source": { "split": "train_shard_00001", "doc_id": 2956 }, "chunk_id": "train_shard_00001_2956_0", "global_id": 9852 }, { "text": "The integron structure is identical to the blaVIM-4 and blaVIM-1-carrying integron described from a Vibrio cholerae isolated from a seagull in France in 2015 (KR262557). blaVIM-75 is a single amino acid variant (Q60R) of blaVIM-1. All isolates carried mutations in the QRDR (gyrA_S83I, parC_S84I). Based on cgMLST analysis, these 5 P. mirabilis isolates were highly similar, with only 7-19 SNPs detected.

Conclusion

The outbreak of multidrug-resistant P. mirabilis isolates carrying blaVIM-4 and blaVIM-75 in a Hungarian medical center is a cause of concern. Surveillance should be performed to understand the spread of and treatment options for infections caused by carbapenem-nonsusceptible P. mirabilis.

Disclosures

Lalitagauri M. Deshpande, PhD, Melinta: Grant/Research Support|Pfizer: Grant/Research Support Katalin Burián, MD, JMI Laboratories: Grant/Research Support Ilona Dóczi Csányi, MD, JMI Laboratories: Grant/Research Support Mariana Castanheira, PhD, AbbVie: Grant/Research Support|Cidara: Grant/Research Support|GSK: Grant/Research Support|Melinta: Grant/Research Support|Pfizer: Grant/Research Support|Shionogi: Grant/Research Support.\n\n2036. Dual VIM-producing Proteus mirabilis, Including a Novel VIM-75, Among Elderly Patients in a Medical Center from Hungary: Report from the 2020 SENTRY Antimicrobial Surveillance Program", "token_count": 458, "char_count": 1360, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [ "KR262557" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:34.825185", "source": { "split": "train_shard_00001", "doc_id": 2956 }, "chunk_id": "train_shard_00001_2956_1", "global_id": 9853 }, { "text": "The present study aimed to evaluate the genetic diversity of Extended Spectrum Cephalosporin resistant (ESC-R) E. coli isolates obtained from Dutch veal calves during a longitudinal study, to better understand the genetic background behind the persistent ESC-R E. coli colonization in the dairy and veal sectors. Rectal swabs were collected from 683 calves located in 13 Dutch dairy farms 1 day prior to their transportation to 8 veal farms. At the veal farms, rectal swabs were collected at 5 different time points after arrival. A total of 1,202 ESC-R E. coli isolates were obtained through selective isolation. Nine out of 13 dairy farms were positive for ESC-R E. coli (n = 175 isolates), arbitrarily divided in a high prevalence (>50%, n = 7) or low prevalence farms (<5%, n = 2) In three veal farms, a relatively high frequency of ESC-R E. coli was observed (range = 38-84%) while in the remaining five farms, a lower frequency was observed (range = 5-24%). At veal farms, the highest average ESC-R E. coli frequency was detected in week two (57.3%). ESBL/AmpC encoding genes were identified by RT-PCR and amplicon sequencing. ESBL genes (bla CTX-M-1 groups, bla CTX-M-9 group) and specific point mutations in the promotor region of the chromosomal bla ampC gene were identified both at dairy farms and veal farms. A total of 364 ESC-R E", "token_count": 510, "char_count": 1463, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5689, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:35.481145", "source": { "split": "train_shard_00001", "doc_id": 2957 }, "chunk_id": "train_shard_00001_2957_0", "global_id": 9854 }, { "text": "coli isolates were further characterized by WGS to determine the genetic relationship using core genome Multi Locus Sequencing Typing (cgMLST). The ESBL-genes bla CTX-M-1 and bla CTX-M-15 were predominant, the majority in combination with a non-ESBL bla TEM-1 gene. In addition, genes encoding resistance against quinolones, aminoglycosides, phenicols, tetracyclines, sulfonamides, and trimethoprim were identified in these isolates. Finally, phylogenetic analysis showed a diverse pool of E. coli strains carrying the bla CTX-M-1 gene, while two genetically closely related sequence types (STs) were identified in E. coli strains carrying the bla CTX-M-15, being ST 4981 and ST 2325, the most predominant STs identified. Our results revealed a population of ESC-R E. coli which are genetically similar within veal farms and provides evidence of direct transmission and dissemination of ESC-R E. coli between the animals during the rearing process.\n\nLongitudinal study on the genetic diversity of extended-spectrum cephalosporin resistant <i>Escherichia coli</i> in Dutch veal calves.", "token_count": 396, "char_count": 1218, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:36.092475", "source": { "split": "train_shard_00001", "doc_id": 2957 }, "chunk_id": "train_shard_00001_2957_1", "global_id": 9855 }, { "text": "

ABSTRACT

The genus Caldicellulosiruptor are extremely thermophilic, heterotrophic anaerobes that degrade plant biomass using modular, multifunctional enzymes. Prior pangenome analyses determined that this genus is genetically diverse, with the current pangenome remaining open, meaning that new genes are expected with each additional genome sequence added. Given the high biodiversity observed among the genus Caldicellulosiruptor , we have sequenced and added a 14 th species, Caldicellulosiruptor changbaiensis , to the pangenome. The pangenome now includes 3,791 ortholog clusters, 120 of which are unique to C. changbaiensis and may be involved in plant biomass degradation. Comparisons between C. changbaiensis and Caldicellulosiruptor bescii on the basis of growth kinetics, cellulose solubilization and cell attachment to polysaccharides highlighted physiological differences between the two species which are supported by their respective gene inventories. Most significantly, these comparisons indicated that C. changbaiensis possesses unique cellulose attachment mechanisms not observed among the other strongly cellulolytic members of the genus Caldicellulosiruptor .\n\nGenomic and physiological analyses reveal that extremely thermophilicCaldicellulosiruptor changbaiensisdeploys unique cellulose attachment mechanisms", "token_count": 347, "char_count": 1346, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:36.668630", "source": { "split": "train_shard_00001", "doc_id": 2958 }, "chunk_id": "train_shard_00001_2958_0", "global_id": 9856 }, { "text": "In the study, a previously isolated plant beneficial endophytic B. cereus CaB1 was selected for the detailed analysis by whole-genome sequencing. The WGS has generated a total of 1.9 GB high-quality data which was assembled into a 5,257,162 bp genome with G + C content of 35.2%. Interestingly, CaB1 genome was identified to have 40 genes with plant beneficial functions by bioinformatic analysis. At the same time, it also showed the presence of various virulence factors except the diarrhoeal toxin, cereulide. Upon comparative analysis of CaB1 with other B. cereus strains, it was found to have random distributions of virulence and plant growth promoting traits. The core genome phylogenetic analysis of the Bacillus cereus strains further showed the close relation of plant associated strains with isolates from spoiled food products. The observed genome flexibility of B. cereus thus indicates its ability to make use of diverse hosts, which can result either in beneficial or harmful effects.

Supplementary information

The online version contains supplementary material available at 10.1007/s13205-023-03463-9.\n\nGenomic insight into the environmental adaptations and toxigenic features of endophytic Bacillus cereus CaB1 isolated from Capsicum annuum L.", "token_count": 377, "char_count": 1309, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6576, "quality_score": 0.8288, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:37.252990", "source": { "split": "train_shard_00001", "doc_id": 2959 }, "chunk_id": "train_shard_00001_2959_0", "global_id": 9857 }, { "text": "Listerias of the phylogenetic lineage II (PLII) are common in the European environment, and are hypovirulent. Despite this, they caused more than a third of sporadic cases of listeriosis, and multi-country foodborne outbreaks. L. monocytogenes ST37 is one of them. During the COVID-19 pandemic ST37 appeared in the clinical cases and ranked second in occurrence among food isolates in the Moscow region. The aim of this study was to describe the genomic features of ST37 isolates from different sources. All clinical cases of ST37 were in the cohort of male patients (age, 48-81 years) with meningitis-septicemia manifestation, and COVID-19 or Influenza in the anamnesis. The core genomes of the fish isolates were closely related. The clinical and meat isolates revealed a large diversity. Prophages (2-4/genome) were the source of the unique genes. Two clinical isolates displayed the pseudolysogeny, and excided prophages were A006-like. Absence of the plasmids, the assortment of virulence factors and resistance determinants in chromosome corresponded to the hypovirulent characteristics. However, all clinical isolates caused severe disease with deaths in four cases. Thus, these studies allow us to speculate that a previous viral infection increases a human susceptibility to listeriosis.\n\nListeria monocytogenes ST37 Distribution in Russia and Properties of the Clinical and Food-Born Isolates", "token_count": 359, "char_count": 1402, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6165, "quality_score": 0.8083, "entities": { "genes": [ "ST37" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:37.831926", "source": { "split": "train_shard_00001", "doc_id": 2960 }, "chunk_id": "train_shard_00001_2960_0", "global_id": 9858 }, { "text": "Ii.

Summary/Abstract

The annotation of repetitive sequences within plant genomes can help in the interpretation of observed phenotypes. Moreover, repeat masking is required for tasks such as whole-genome alignment, promoter analysis or pangenome exploration. While homology-based annotation methods are computationally expensive, k-mer strategies for masking are orders of magnitude faster. Here we benchmark a two-step approach, where repeats are first called by k-mer counting and then annotated by comparison to curated libraries. This hybrid protocol was tested on 20 plant genomes from Ensembl, using the kmer-based Repeat Detector (Red) and two repeat libraries (REdat and nrTEplants, curated for this work). We obtained repeated genome fractions that match those reported in the literature, but with shorter repeated elements than those produced with conventional annotators. Inspection of masked regions overlapping genes revealed no preference for specific protein domains. Half of Red masked sequences can be successfully classified with nrTEplants, with the complete protocol taking less than 2h on a desktop Linux box. The repeat library and the scripts to mask and annotate plant genomes can be obtained at https://github.com/Ensembl/plant-scripts .\n\nEfficient masking of plant genomes by combining kmer counting and curated repeats", "token_count": 300, "char_count": 1354, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:38.423264", "source": { "split": "train_shard_00001", "doc_id": 2961 }, "chunk_id": "train_shard_00001_2961_0", "global_id": 9859 }, { "text": "The ability of virulent bacteriophages to lyse bacteria influences bacterial evolution, fitness, and population structure. Knowledge of both host susceptibility and resistance factors is crucial for the successful application of bacteriophages as biological control agents in clinical therapy, food processing, and agriculture. In this study, we isolated 12 bacteriophages termed SPLA phage which infect the foodborne pathogen Salmonella enterica. To determine phage host range, a diverse collection of Enterobacteriaceae and Salmonella enterica was used and genes involved in infection by six SPLA phages were identified using Salmonella Typhimurium strain ST4/74. Candidate host receptors included lipopolysaccharide (LPS), cellulose, and BtuB. Lipopolysaccharide was identified as a susceptibility factor for phage SPLA1a and mutations in LPS biosynthesis genes spontaneously emerged during culture with S. Typhimurium. Conversely, LPS was a resistance factor for phage SPLA5b which suggested that emergence of LPS mutations in culture with SPLA1a represented collateral sensitivity to SPLA5b. We show that bacteria-phage co-culture with SPLA1a and SPLA5b was more successful in limiting the emergence of phage resistance compared to single phage co-culture. Identification of host susceptibility and resistance genes and understanding infection dynamics are critical steps in the rationale design of phage cocktails against specific bacterial pathogens.IMPORTANCEAs antibiotic resistance continues to emerge in bacterial pathogens, bacterial viruses (phage) represent a potential alternative or adjunct to antibiotics. One challenge for their implementation is the predisposition of bacteria to rapidly acquire resistance to phages. We describe a functional genomics approach to identify mechanisms of susceptibility and resistance for newly isolated phages that infect and lyse Salmonella enterica and use this information to identify phage combinations that exploit collateral sensitivity, thus increasing efficacy. Collateral sensitivity is a phenomenon where resistance to one class of antibiotics increases sensitivity to a second class of antibiotics", "token_count": 514, "char_count": 2202, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5571, "quality_score": 0.7785, "entities": { "genes": [ "ST4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:31:39.115834", "source": { "split": "train_shard_00001", "doc_id": 2962 }, "chunk_id": "train_shard_00001_2962_0", "global_id": 9860 }, { "text": "We report a functional genomics approach to rationally design a phage combination with a collateral sensitivity dynamic which resulted in increased efficacy. Considering such evolutionary trade-offs has the potential to manipulate the outcome of phage therapy in favor of resolving infection without selecting for escape mutants and is applicable to other virus-host interactions.\n\nCollateral sensitivity increases the efficacy of a rationally designed bacteriophage combination to control Salmonella enterica.", "token_count": 106, "char_count": 517, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:39.530828", "source": { "split": "train_shard_00001", "doc_id": 2962 }, "chunk_id": "train_shard_00001_2962_1", "global_id": 9861 }, { "text": "Lactobacillus helveticus belongs to the large group of lactic acid bacteria (LAB), which are the major players in the fermentation of a wide range of foods. LAB are also present in the human gut, which has often been exploited as a reservoir of potential novel probiotic strains, but several parameters need to be assessed before establishing their safety and potential use for human consumption. In the present study, six L. helveticus strains isolated from natural whey cultures were analyzed for their phenotype and genotype in exopolysaccharide (EPS) production, low pH and bile salt tolerance, bile salt hydrolase (BSH) activity, and antibiotic resistance profile. In addition, a comparative genomic investigation was performed between the six newly sequenced strains and the 51 publicly available genomes of L. helveticus to define the pangenome structure. The results indicate that the newly sequenced strain UC1267 and the deposited strain DSM 20075 can be considered good candidates for gut-adapted strains due to their ability to survive in the presence of 0.2% glycocholic acid (GCA) and 1% taurocholic and taurodeoxycholic acid (TDCA). Moreover, these strains had the highest bile salt deconjugation activity among the tested L. helveticus strains. Considering the safety profile, none of these strains presented antibiotic resistance phenotypically and/or at the genome level. The pangenome analysis revealed genes specific to the new isolates, such as enzymes related to folate biosynthesis in strains UC1266 and UC1267 and an integrated phage in strain UC1035. Finally, the presence of maltose-degrading enzymes and multiple copies of 6-phospho-β-glucosidase genes in our strains indicates the capability to metabolize sugars other than lactose, which is related solely to dairy niches.", "token_count": 488, "char_count": 1829, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6306, "quality_score": 0.8153, "entities": { "genes": [ "UC1267", "UC1035", "UC1266" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:40.189949", "source": { "split": "train_shard_00001", "doc_id": 2963 }, "chunk_id": "train_shard_00001_2963_0", "global_id": 9862 }, { "text": "Genomic Comparison of Lactobacillus helveticus Strains Highlights Probiotic Potential.", "token_count": 30, "char_count": 93, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:40.545361", "source": { "split": "train_shard_00001", "doc_id": 2963 }, "chunk_id": "train_shard_00001_2963_1", "global_id": 9863 }, { "text": "Nanopore sequencing is an increasingly powerful tool for genomics. Recently, computational advances have allowed nanopores to sequence in a targeted fashion; as the sequencer emits data, software can analyze the data in real time and signal the sequencer to eject “non-target” DNA molecules. We present a novel method called SPUMONI, which enables rapid and accurate targeted sequencing with the help of efficient pangenome indexes. SPUMONI uses a compressed index to rapidly generate exact or approximate matching statistics (half-maximal exact matches) in a streaming fashion. When used to target a specific strain in a mock community, SPUMONI has similar accuracy as minimap2 when both are run against an index containing many strains per species. However SPUMONI is 12 times faster than minimap2. SPUMONI’s index and peak memory footprint are also 15 to 4 times smaller than minimap2, respectively. These improvements become even more pronounced with even larger reference databases; SPUMONI’s index size scales sublinearly with the number of reference genomes included. This could enable accurate targeted sequencing even in the case where the targeted strains have not necessarily been sequenced or assembled previously. SPUMONI is open source software available from https://github.com/oma219/spumoni .\n\nPan-genomic Matching Statistics for Targeted Nanopore Sequencing", "token_count": 310, "char_count": 1375, "word_count": 198, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:41.121032", "source": { "split": "train_shard_00001", "doc_id": 2964 }, "chunk_id": "train_shard_00001_2964_0", "global_id": 9864 }, { "text": "The gut microbiota is important for healthy infant development. Part of the initial colonizing microbial strains originate from the maternal gut, and undergo a selective event, termed the \"colonization bottleneck\". While vertical mother-to-infant inheritance and subsequent colonization of bacteria have previously been studied, the role of mobile genetic elements (MGEs) in the infant gut microbiota assembly is unclear. In this perspective article, we discuss how horizontally and vertically transmitted phages and conjugative elements potentially have important roles in infant gut microbiota assembly and colonization through parasitic and mutualistic interactions with their bacterial hosts. While some of these MGEs are likely to be detrimental to their host survival, in other contexts, they may help bacteria colonize new niches, antagonize other bacteria, or protect themselves from other parasitic MGEs in the infant gut. As a result, the horizontal transfer of MGEs likely occurs at high rates in the infant gut, contributing to gene transfer between bacteria and affecting which bacteria can pass the colonization bottleneck. We conclude by highlighting the potential in silico, in vitro, and in vivo methodological approaches that could be employed to study the transmission and colonization dynamics of MGEs and bacteria in the infant gut.\n\nMobile genetic elements: the hidden puppet masters underlying infant gut microbiome assembly?", "token_count": 320, "char_count": 1469, "word_count": 209, "semantic_coherence": 1, "information_density": 0.622, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:41.687217", "source": { "split": "train_shard_00001", "doc_id": 2965 }, "chunk_id": "train_shard_00001_2965_0", "global_id": 9865 }, { "text": "Brucellosis is one of the most common zoonoses in the Middle East. It is causing economic losses to the livestock industry and has a great public health concern. Little is known about the genetic diversity and distribution of brucellae in Iran. Therefore, forty Brucella spp. strains (B. abortus and B. melitensis) isolated from animals and humans were analyzed by whole genome sequencing (WGS) technology using single nucleotide polymorphism (SNP) analysis and core genome multilocus sequence typing (cgMLST). Brucella isolates were obtained from lymph nodes (cows and camels), milk (cows, camels and sheep), and aborted foetus samples (sheep and goats), as well as cerebrospinal fluid and blood of humans. The isolates were originating from thirteen provinces of Iran and isolated between 2015 and 2020. According to in-silico MLST, ST8 and ST2 were the most frequent sequence types in B. melitensis and B. abortus, respectively. Based on phylogeographic reconstruction using cgSNP analysis, the investigated Iranian B. melitensis strains belonged to the American and Mediterranean lineages of the B. melitensis phylogeny. Furthermore, cgSNP analysis revealed a similarity between Iranian B. abortus isolates and strains from Iraq and Egypt. Therefore, the origin of the Iranian strains can be suggested to be strains from neighboring and Middle East countries. Moreover, cgMLST analysis showed that the Iranian B. melitensis strains were closely relative to strains recovered from sheep and humans in Iraq, Afghanistan, Syria, Turkmenistan, and Pakistan. In the current panel of strains, cgMLST and cgSNP analysis provided an appropriate and accurate tool for effective traceback analyses for Brucella spp. from Iran", "token_count": 494, "char_count": 1803, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7988, "entities": { "genes": [ "ST2", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:42.345722", "source": { "split": "train_shard_00001", "doc_id": 2966 }, "chunk_id": "train_shard_00001_2966_0", "global_id": 9866 }, { "text": "The results of cgSNP and cgMLST helped to understand the geographic distribution and interspecies transmission of Iranian strains and highlight the importance of specific brucellosis control measures in Iran with regard to the One-Health approach.\n\nWhole-genome sequencing for genetic diversity analysis of Iranian Brucella spp. isolated from humans and livestock.", "token_count": 88, "char_count": 371, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:42.716255", "source": { "split": "train_shard_00001", "doc_id": 2966 }, "chunk_id": "train_shard_00001_2966_1", "global_id": 9867 }, { "text": "Complementary feeding induces dramatic ecological shifts in the infant gut microbiota toward more diverse compositions and functional metabolic capacities, with potential implications for immune and metabolic health. The aim of this study was to examine whether the age at which solid foods are introduced differentially affects the microbiota in predominantly breastfed infants compared with predominantly formula-fed infants. We performed whole-genome shotgun metagenomic sequencing of infant stool samples from a cohort of six-month-old Australian infants enrolled in a nested study within the ORIGINS Project longitudinal birth cohort. Infants born preterm or those who had been administered antibiotics since birth were excluded. The taxonomic composition was highly variable among individuals at this age. Predominantly formula-fed infants exhibited a higher microbiome diversity than predominantly breastfed infants. Among the predominantly breastfed infants, the introduction of solid foods prior to five months of age was associated with higher alpha diversity than solid food introduction after six months of age, primarily due to the loss of Bifidobacterium infantis. In contrast, the age at which solid food was introduced was not associated with the overall change in diversity among predominantly formula-fed infants but was associated with compositional changes in Escherichia abundance. Examining the functional capacity of the microbiota in relation to these changes, we found that the introduction of solid foods after six months of age was associated with elevated one-carbon compound metabolic pathways in both breastfed and formula-fed infants, although the specific metabolic sub-pathways differed, likely reflecting different taxonomic compositions. Our findings suggest that the age of commencement of solid foods influences the gut microbiota composition differently in predominantly breastfed infants than in predominantly formula-fed infants.\n\nMetagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants.", "token_count": 455, "char_count": 2125, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5192, "quality_score": 0.7596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:43.361935", "source": { "split": "train_shard_00001", "doc_id": 2967 }, "chunk_id": "train_shard_00001_2967_0", "global_id": 9868 }, { "text": "Streptomyces are prolific producers of secondary metabolites from which many clinically useful compounds have been derived. They inhabit diverse habitats but have rarely been reported in vertebrates. Here, we aim to determine to what extent the ecological source (bat host species and cave sites) influence the genomic and biosynthetic diversity of Streptomyces bacteria. We analysed draft genomes of 132 Streptomyces isolates sampled from 11 species of insectivorous bats from six cave sites in Arizona and New Mexico, USA. We delineated 55 species based on the genome-wide average nucleotide identity and core genome phylogenetic tree. Streptomyces isolates that colonize the same bat species or inhabit the same site exhibit greater overall genomic similarity than they do with Streptomyces from other bat species or sites. However, when considering biosynthetic gene clusters (BGCs) alone, BGC distribution is not structured by the ecological or geographical source of the Streptomyces that carry them. Each genome carried between 19-65 BGCs (median=42.5) and varied even among members of the same Streptomyces species. Nine major classes of BGCs were detected in ten of the 11 bat species and in all sites: terpene, non-ribosomal peptide synthetase, polyketide synthase, siderophore, RiPP-like, butyrolactone, lanthipeptide, ectoine, melanin. Finally, Streptomyces genomes carry multiple hybrid BGCs consisting of signature domains from two to seven distinct BGC classes. Taken together, our results bring critical insights to understanding Streptomyces-bat ecology and BGC diversity that may contribute to bat health and in augmenting current efforts in natural product discovery, especially from underexplored or overlooked environments.", "token_count": 494, "char_count": 1807, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6774, "quality_score": 0.8387, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:44.007539", "source": { "split": "train_shard_00001", "doc_id": 2968 }, "chunk_id": "train_shard_00001_2968_0", "global_id": 9869 }, { "text": "Ecology shapes the genomic and biosynthetic diversification of Streptomyces bacteria from insectivorous bats.", "token_count": 34, "char_count": 116, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:44.378052", "source": { "split": "train_shard_00001", "doc_id": 2968 }, "chunk_id": "train_shard_00001_2968_1", "global_id": 9870 }, { "text": "This study reports the first high-quality telomere-to-telomere (T2T) Rhododendron liliiflorum genome with 11 chromosomes that are gap free. The 24 telomeres and all 13 centromeres detected in this genome, which reached the highest quality gold level. In addition, other three Rhododendron species were sequenced and assembled to the chromosomal level. Based on 15 Rhododendron genomes, we conducted a pan-genome analysis of genus Rhododendron. Combining the genome and whole transcriptome sequencing, we identified several key genes and miRNAs related to the heat stress, which were further verified by transgenic experiments. Our findings provide rich resources for comparative and functional genomics studies of Rhododendron species.\n\nT2T genome, pan-genome analysis, and heat stress response genes in <i>Rhododendron</i> species.", "token_count": 265, "char_count": 879, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7652, "quality_score": 0.8826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:44.928376", "source": { "split": "train_shard_00001", "doc_id": 2969 }, "chunk_id": "train_shard_00001_2969_0", "global_id": 9871 }, { "text": "As part of the comparative genomics project 'GENOLEVURES', we studied the Kluyveromyces marxianus var. marxianus strain CBS712 using a partial random sequencing strategy. With a 0.2 x genome equivalent coverage, we identified ca. 1300 novel genes encoding proteins, some containing spliceosomal introns with consensus splice sites identical to those of Saccharomyces cerevisiae, 28 tRNA genes, the whole rDNA repeat, and retrotransposons of the Ty1/2 family of S. cerevisiae with diverged Long Terminal Repeats. Functional classification of the K. marxianus genes, as well as the analysis of the paralogous gene families revealed few differences with respect to S. cerevisiae. Only 42 K. marxianus identified genes are without detectable homolog in the baker's yeast. However, we identified several genetic rearrangements between these two yeast species.\n\nGenomic exploration of the hemiascomycetous yeasts: 12. Kluyveromyces marxianus var. marxianus.", "token_count": 265, "char_count": 951, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7388, "quality_score": 0.8694, "entities": { "genes": [ "CBS712" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:45.478401", "source": { "split": "train_shard_00001", "doc_id": 2970 }, "chunk_id": "train_shard_00001_2970_0", "global_id": 9872 }, { "text": "Kluyveromyces marxianus GX-15 was mutated multiple times by alternately treatment with UV irradiation and NTG for two cycles. Four mutant strains with improved ethanol yield were obtained. The maximum ethanol concentration, ethanol yield coefficient and theoretical ethanol yield of the best mutant strain, GX-UN120, was 69 g/l, 0.46 g/g and 91%, respectively, when fermenting 150 g glucose/l at 40°C. The corresponding values for GX-15 were 58 g/l, 0.39 g/g and 76%, respectively. GX-UN120 grew well in 11% (v/v) of ethanol, while GX-15 could not grow when ethanol was greater than 8% (v/v).\n\nMultiple induced mutagenesis for improvement of ethanol production by Kluyveromyces marxianus", "token_count": 230, "char_count": 687, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8544, "entities": { "genes": [ "UN120" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:45.945067", "source": { "split": "train_shard_00001", "doc_id": 2971 }, "chunk_id": "train_shard_00001_2971_0", "global_id": 9873 }, { "text": "We hypothesize that bacteria isolated from free-ranging animals could potentially be useful for practical applications. To meet this objective a Gram-positive bacterium was isolated from the gastrointestinal (GI) tract of a Gray Wolf (Canis lupus) using Brucella broth with hemin and vitamin K (BBHK). By small ribosomal RNA (16S) gene sequencing the bacterium was initially identified as a novel Carnobacterium maltaromaticum strain. The bacterium could be propagated both anaerobically and aerobically and was both catalase/oxidase negative and negative by the starch hydrolysis as well as negative using lipase assays. The reference whole genome sequence (WGS) was obtained using both Illumina and Nanopore sequencing. The genome assembly was 3,512,202 bp in length, encoding core bacterial genes with a GC% content of 34.48. No lysogenic bacteriophage genes were detected, although the genome harbors genes for the expression of bacteriocin and other secondary metabolites with potential antimicrobial properties. Multilocus sequence typing (MLST), WGS phylogenetics, average nucleotide identity (ANI), and single nucleotide polymorphism (SNP) analyses of the isolate's genome indicate this bacterium is a newly identified Carnobacterium maltaromaticum sequence type (ST). Members of the Carnobacteria have anti-listeria activities, highlighting their potential functional properties. Consequently, the isolate could be a potential probiotic for canids and this is the first report on an axenic C. maltaromaticum culture from the genus Canis.", "token_count": 435, "char_count": 1588, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:46.568847", "source": { "split": "train_shard_00001", "doc_id": 2972 }, "chunk_id": "train_shard_00001_2972_0", "global_id": 9874 }, { "text": "Reference Whole Genome Sequence Analyses and Characterization of a Novel <i>Carnobacterium maltaromaticum</i> Distinct Sequence Type Isolated from a North American Gray Wolf (<i>Canis lupus</i>) Gastrointestinal Tract.", "token_count": 84, "char_count": 242, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:46.940668", "source": { "split": "train_shard_00001", "doc_id": 2972 }, "chunk_id": "train_shard_00001_2972_1", "global_id": 9875 }, { "text": "

SUMMARY

Pseudomonas aeruginosa possesses one of the most complex bacterial regulatory networks, which largely contributes to its success as a human opportunistic pathogen. However, most of its transcription factors (TFs) are still uncharacterized and the potential intra-species variability in regulatory networks has been mostly ignored so far. Here, to provide a first global view of the two-component systems (TCSs) regulatory network in P. aeruginosa , we produced and purified all DNA-binding TCS response regulators (RRs) and used DAP-seq to map the genome-wide binding sites of these 55 TFs across the three major P. aeruginosa lineages. The resulting networks encompass about 40% of all genes in each strain and contain numerous new important regulatory interactions across most major physiological processes, including virulence and antibiotic resistance. Strikingly, the comparison between the three representative strains shows that about half of the detected targets are specific to only one or two of the tested strains, revealing a previously unknown large functional diversity of TFs within a single species. Three main mechanisms were found to drive this diversity, including differences in accessory genome content, as exemplified by the strain-specific plasmid in the IHMA87 outlier strain which harbors numerous binding sites of chromosomally-encoded RRs. Additionally, most RRs display potential auto-regulation or RR-RR cross-regulation, bringing to light the vast complexity of this network. Overall, we provide the first complete delineation of the TCS regulatory network in P. aeruginosa that will represent an important resource for future studies on this pathogen.\n\nDetermination of the Two-Component Systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages", "token_count": 415, "char_count": 1847, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6448, "quality_score": 0.8224, "entities": { "genes": [ "IHMA87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:47.567181", "source": { "split": "train_shard_00001", "doc_id": 2973 }, "chunk_id": "train_shard_00001_2973_0", "global_id": 9876 }, { "text": "Yarrowia lipolytica has been widely used in the food biotech-related industry, where it plays the host's role in producing erythritol. Nevertheless, a temperature of about 28°C-30°C has been estimated as the yeast's optimal growth temperature, leading to the consumption of a considerable quantity of cooling water, especially in summer, which is obligatory for fermentation. Herein is described a method for improving the thermotolerance and erythritol production efficiency at high temperatures of Y. lipolytica. Through screening and testing different heat resistant devices, eight refactored engineered strains showed better growth at higher temperature and the antioxidant properties of the eight engineered strains were also improved. In addition, the erythritol titer, yield and productivity of the strain FOS11-Ctt1 represented the best among the eight strains, reaching at 39.25 g/L, 0.348 g/g glucose, and 0.55 g/L/h respectively, which were increased by 156%, 86% and 161% compared with the control strain, respectively. This study provides insight into an effective heat-resistant device that could enhance the thermotolerance and erythritol production of Y. lipolytica, which might be considered a valued scientific reference for other resistant strains' construction.\n\nEnhancing the thermotolerance and erythritol production of Yarrowia lipolytica by introducing heat-resistant devices.", "token_count": 376, "char_count": 1428, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6788, "quality_score": 0.8394, "entities": { "genes": [ "FOS11" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:48.145614", "source": { "split": "train_shard_00001", "doc_id": 2974 }, "chunk_id": "train_shard_00001_2974_0", "global_id": 9877 }, { "text": "Kefir is a high nutritional fermented dairy beverage associated with a wide range of health benefits. It constitutes a unique symbiotic association, comprising mainly lactic acid bacteria, yeasts, and occasionally acetic acid bacteria, which is strongly influenced by the geographical origin of the grains, the type of milk used, and the manufacture technology applied. Until recently, kefir microbiota has been almost exclusively studied by culture-dependent techniques. However, high-throughput sequencing, alongside omics approaches, has revolutionized the study of food microbial communities. In the present study, the bacterial, and yeast/fungal microbiota of four home-made samples (both grains and drinks), deriving from well spread geographical regions of Greece, and four industrial beverages, was elucidated by culture-dependent and -independent analyses. In all samples, classical microbiological analysis revealed varying populations of LAB and yeasts, ranging from 5.32 to 9.60 log CFU mL-1 or g-1, and 2.49 to 7.80 log CFU mL-1 or g-1, respectively, while in two industrial samples no yeasts were detected. Listeria monocytogenes, Salmonella spp. and Staphylococcus spp. were absent from all the samples analyzed, whereas Enterobacteriaceae were detected in one of them. From a total of 123 isolates, including 91 bacteria and 32 yeasts, Lentilactobacillus kefiri, Leuconostoc mesenteroides, and Lactococcus lactis as well as Kluvyeromyces marxianus and Saccharomyces cerevisiae were the mostly identified bacterial and yeast species, respectively, in the home-made samples", "token_count": 488, "char_count": 1694, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6773, "quality_score": 0.8386, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:48.795081", "source": { "split": "train_shard_00001", "doc_id": 2975 }, "chunk_id": "train_shard_00001_2975_0", "global_id": 9878 }, { "text": "On the contrary, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, and Lacticaseibacillus rhamnosus along with Debaryomyces hansenii and K. marxianus were the main bacterial and yeast species, respectively, isolated from the industrial beverages. In agreement with the identification results obtained from the culture-dependent approaches, amplicon-based metagenomics analysis revealed that the most abundant bacterial genera in almost all home-made samples (both grains and drinks) were Lactobacillus and Lactococcus, while Saccharomyces, Kazachstania, and Kluvyeromyces were the predominant yeasts/fungi. On the other hand, Streptococcus, Lactobacillus, and Lactococcus as well as Kluvyeromyces and Debaryomyces dominated the bacterial and yeast/fungal microbiota, respectively, in the industrial beverages. This is the first report on the microbiota of kefir produced in Greece by a holistic approach combining classical microbiological, molecular, and amplicon-based metagenomics analyses.\n\nZooming Into the Microbiota of Home-Made and Industrial Kefir Produced in Greece Using Classical Microbiological and Amplicon-Based Metagenomics Analyses.", "token_count": 398, "char_count": 1263, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6319, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:49.415054", "source": { "split": "train_shard_00001", "doc_id": 2975 }, "chunk_id": "train_shard_00001_2975_1", "global_id": 9879 }, { "text": "

Background

Many microorganisms possess enzymes that can efficiently degrade lignocellulosic materials, but do not have the capability to produce a large amount of ethanol. Thus, attempts have been made to transform such enzymes into fermentative microbes to serve as hosts for ethanol production. However, an efficient host for a consolidated bioprocess (CBP) remains to be found. For this purpose, a synthetic biology technique that can transform multiple genes into a genome is instrumental. Moreover, a strategy to select cellulases that interact synergistically is needed.

Results

To engineer a yeast for CBP bio-ethanol production, a synthetic biology technique, called \"promoter-based gene assembly and simultaneous overexpression\" (PGASO), that can simultaneously transform and express multiple genes in a kefir yeast, Kluyveromyces marxianus KY3, was recently developed. To formulate an efficient cellulase cocktail, a filter-paper-activity assay for selecting heterologous cellulolytic enzymes was established in this study and used to select five cellulase genes, including two cellobiohydrolases, two endo-β-1,4-glucanases and one beta-glucosidase genes from different fungi. In addition, a fungal cellodextrin transporter gene was chosen to transport cellodextrin into the cytoplasm. These six genes plus a selection marker gene were one-step assembled into the KY3 genome using PGASO. Our experimental data showed that the recombinant strain KR7 could express the five heterologous cellulase genes and that KR7 could convert crystalline cellulose into ethanol.

Conclusion

Seven heterologous genes, including five cellulases, a cellodextrin transporter and a selection marker, were simultaneously transformed into the KY3 genome to derive a new strain, KR7, which could directly convert cellulose to ethanol. The present study demonstrates the potential of our strategy of combining a cocktail formulation protocol and a synthetic biology technique to develop a designer yeast host.", "token_count": 498, "char_count": 2016, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7949, "entities": { "genes": [ "KY3", "KR7" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:50.094166", "source": { "split": "train_shard_00001", "doc_id": 2976 }, "chunk_id": "train_shard_00001_2976_0", "global_id": 9880 }, { "text": "Assembling a cellulase cocktail and a cellodextrin transporter into a yeast host for CBP ethanol production.", "token_count": 31, "char_count": 108, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:50.485288", "source": { "split": "train_shard_00001", "doc_id": 2976 }, "chunk_id": "train_shard_00001_2976_1", "global_id": 9881 }, { "text": "The environmental contamination plays a significant role in the emergence of antimicrobial resistance. In this study, we report a genomic analysis of an extensively drug-resistant and blaNDM-1-producing Klebsiella pneumoniae (EW807) strain recovered from a surface water sample. Strain EW807 belonged to sequence type (ST) 340 and serotype O4:KL15, a high-risk clone of the clonal group 258. This strain carried a broad resistome, including blaNDM-1 and blaCTX-M-15. The core genome multilocus sequence typing phylogenetic analysis revealed that the EW807 strain was most related to strains from Brazil and the USA. An IncX3 plasmid was identified harboring the blaNDM-1 gene, while an IncFIB(K) plasmid was detected carrying the blaCTX-M-15 in addition to multidrug resistance and multimetal tolerance regions. IncX3 and IncFIB(K) plasmids shared high similarity with plasmids from a human in China and a dog in Brazil, respectively. The regions harboring the blaNDM-1 and blaCTX-M-15 genes contained sequences from the Tn3 family. These findings suggest that IncX3 plasmid could play a role in the spread of NDM-1 in a post-pandemic scenario. To the best of our knowledge, this is the first report of blaNDM-1-producing K. pneumoniae ST340 O4:KL15 strain in the environment. Therefore, the presence of high-risk clones of K. pneumoniae carrying carbapenemases in the environment requires strict surveillance.\n\nGenomic features of an extensively drug-resistant and NDM-1-positive Klebsiella pneumoniae ST340 isolated from river water.", "token_count": 491, "char_count": 1623, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [ "ST340", "KL15", "EW807" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:51.147218", "source": { "split": "train_shard_00001", "doc_id": 2977 }, "chunk_id": "train_shard_00001_2977_0", "global_id": 9882 }, { "text": "The possibility of using whey permeate as a raw material for the production of ethanol by continuous fermentation by using Kluyveromyces marxianus was examined. The ethanol formation was investigated as a function of the hydraulic retention time in a UASB reactor. The initial lactose concentration in permeate was 50.0 g L(-1). The hydraulic retention time supplied were 12, 24, 48 h and the daily ethanol formations were 4.46, 8.61, 7.73 g L(-1), respectively. The yield coefficient of ethanol was 0.089 g ethanol g(-1) lactose when the hydraulic retention time was 12 h and raised to 0.325 g g(-1) when the hydraulic retention time was as long as 48 h. The results indicated that in ethanol fermentation the hydraulic retention time should be 24 h to obtain high rates of ethanol formation and to avoid product inhibition.\n\nEthanol production from whey permeate in a continuous anaerobic bioreactor by Kluyveromyces marxianus.", "token_count": 288, "char_count": 929, "word_count": 149, "semantic_coherence": 1, "information_density": 0.5101, "quality_score": 0.755, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:51.753227", "source": { "split": "train_shard_00001", "doc_id": 2978 }, "chunk_id": "train_shard_00001_2978_0", "global_id": 9883 }, { "text": "Perturbations in the gut microbiome have been associated with colorectal cancer (CRC), with the colonic overabundance of Fusobacterium nucleatum shown as the most consistent marker. Despite its significance in the promotion of CRC, genomic studies of Fusobacterium is limited. We enrolled 43 Vietnamese CRC patients and 25 participants with non-cancerous colorectal polyps to study the colonic microbiomes and genomic diversity of Fusobacterium in this population, using a combination of 16S rRNA gene profiling, anaerobic microbiology, and whole genome analysis. Oral bacteria, including F. nucleatum and Leptotrichia, were significantly more abundant in the tumour microbiomes. We obtained 53 Fusobacterium genomes, representing 26 strains, from the saliva, tumour and non-tumour tissues of six CRC patients. Isolates from the gut belonged to diverse F. nucleatum subspecies (nucleatum, animalis, vincentii, polymorphum) and a potential new subspecies of Fusobacterium periodonticum. The Fusobacterium population within each individual was distinct and in some cases diverse, with minimal intra-clonal variation. Phylogenetic analyses showed that within four individuals, tumour-associated Fusobacterium were clonal to those isolated from non-tumour tissues. Genes encoding major virulence factors (Fap2 and RadD) showed evidence of horizontal gene transfer. Our work provides a framework to understand the genomic diversity of Fusobacterium within the CRC patients, which can be exploited for the development of CRC diagnostic and therapeutic options targeting this oncobacterium.\n\nTumour microbiomes and Fusobacterium genomics in Vietnamese colorectal cancer patients.", "token_count": 434, "char_count": 1672, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:52.393737", "source": { "split": "train_shard_00001", "doc_id": 2979 }, "chunk_id": "train_shard_00001_2979_0", "global_id": 9884 }, { "text": "Koumiss is a slightly alcoholic fermented mare's milk beverage, originally obtained by using a natural mixed starter of lactic acid bacteria and yeasts. Yeast is an important component of Koumiss processing which can affect the aroma, texture, as well as the nutrients beneficial to human health, but few reports have examined the yeast ecology of local ecosystems. The purpose of this study was to isolate and identify the yeast present in Koumiss from three representative regions of China using a polyphasic method. A total of 655 yeast isolates were obtained from 96 Koumiss samples collected from three regions in China. Koumiss harbored yeast populations at 5-7 log CFU/ml. Twelve different yeast species belonging to nine genera were detected in the Koumiss samples tested, including Candida pararugosa, Dekkera anomala, Geotrichum sp., Issatchenkia orientalis, Kazachstania unispora, Kluyveromyces marxianus, Pichia deserticola, Pichia fermentans, Pichia manshurica, Pichia membranaefaciens, Saccharomyces cerevisiae and Torulaspora delbrueckii. Kluyveromyces marxianus, Kazachstania unispora and Saccharomyces cerevisiae were the dominant species present in this traditional fermented dairy product. This study is the first to identify the yeast communities associated with Koumiss in China. The results enrich our knowledge of yeast in Koumiss, give us a more complete picture of the microbial diversity in Koumiss and can be used to promote the development of the local dairy industry.\n\nDetection and identification of wild yeast in Koumiss.", "token_count": 404, "char_count": 1552, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6116, "quality_score": 0.8058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:53.014444", "source": { "split": "train_shard_00001", "doc_id": 2980 }, "chunk_id": "train_shard_00001_2980_0", "global_id": 9885 }, { "text": "2. Trimethoprim is a synthetic antibacterial agent that targets folate biosynthesis by competitively binding to the di-hydrofolate reductase enzyme (DHFR). Trimethoprim is often administered synergistically with sulfonamide, another chemotherapeutic agent targeting the di-hydro-pteroate synthase (DHPS) enzyme in the same pathway. Clinical resistance to both drugs is widespread and mediated by enzyme variants capable of performing their biological function without binding to these drugs. These mutant enzymes were assumed to have arisen after the discovery of these synthetic drugs, but recent work has shown that genes conferring resistance to sulfonamide were present in the bacterial pangenome millions of years ago. Here we apply phylogenetics and comparative genomics methods to study the largest family of mobile trimethoprim resistance genes ( dfrA ). We show that most of the dfrA genes identified to date map to two large clades that likely arose from independent mobilization events. In contrast to sulfonamide resistance ( sul ) genes, we find evidence of recurrent mobilization in dfrA genes. Phylogenetic evidence allows us to identify novel dfrA genes in the emerging pathogen Acinetobacter baumannii , and we confirm their resistance phenotype in vitro . We also identify a cluster of dfrA homologs in cryptic plasmid and phage genomes, but we show that these enzymes do not confer resistance to trimethoprim. Our methods also allow us to pinpoint the chromosomal origin of previously reported dfrA genes, and we show that many of these ancient chromosomal genes also confer resistance to trimethoprim. Our work reveals that trimethoprim resistance predated the clinical use of this chemotherapeutic agent, but that novel mutations have likely also arisen and become mobilized following its widespread use within and outside the clinic. This work hence confirms that resistance to novel drugs may already be present in the bacterial pangenome, and stresses the importance of rapid mobilization as a fundamental element in the emergence and global spread of resistance determinants. 3.

Impact statement

Antibiotic resistance is a pressing and global phenomenon", "token_count": 512, "char_count": 2187, "word_count": 324, "semantic_coherence": 1, "information_density": 0.5525, "quality_score": 0.7762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:53.676408", "source": { "split": "train_shard_00001", "doc_id": 2981 }, "chunk_id": "train_shard_00001_2981_0", "global_id": 9886 }, { "text": "It is well-established that resistance to conventional antibiotics emerged millions of years ago in either antibiotic-producing bacteria or their competitors. Resistance to synthetic chemotherapeutic agents cannot be explained by this paradigm, since these drugs are not naturally produced. Resistance is hence assumed to have evolved rapidly following the clinical introduction of these drugs. Recently we showed that resistance to one such drug, sulfonamide, evolved not recently, but millions of years ago, suggesting that the diversity of bacterial genomes may well contain genes conferring resistance to drugs yet to be developed. Here we analyze the origin of resistance to trimethoprim, another chemotherapeutic agent developed in the 1960’s. Using phylogenetic methods, we identify new variants of the trimethoprim resistance genes that had not previously been reported, and we trace the chromosomal origins for a number of already known resistance variants. Our results show that resistance to trimethoprim is very diverse and has originated both from recent mutations and from preexisting ancient variants. These results stress the importance of gene mobilization mechanisms as the main drivers of the current antibiotic resistance phenomenon. 4.

Data summary

- The scripts used for data collection and analysis can be obtained at the GitHub ErillLab repository ( https://github.com/ErillLab/ ). - The Bayesian phylogenetic tree can be visualitzed online on iTOL ( https://itol.embl.de/tree/855674159451585133078 ) [1]. - The authors confirm all other supporting data has been provided within the article or through supplementary data files.\n\nRecurrent mobilization of ancestral and novel variants of the chromosomal di-hydrofolate reductase gene drives the emergence of clinical resistance to trimethoprim", "token_count": 422, "char_count": 1825, "word_count": 257, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:54.305343", "source": { "split": "train_shard_00001", "doc_id": 2981 }, "chunk_id": "train_shard_00001_2981_1", "global_id": 9887 }, { "text": "Three bacterial strains, named hOe-66T, hOe-124 and hOe-125, were isolated from the haemolymph of different specimens of the flat oyster Ostrea edulis collected in Concarneau bay (Finistère, France). These strains were characterized by a polyphasic approach, including (i) whole genome analyses with 16S rRNA gene sequence alignment and pangenome analysis, determination of the G+C content, average nucleotide identity (ANI), and in silico DNA-DNA hybridization (isDDH), and (ii) fatty acid methyl ester and other phenotypic analyses. Strains hOe-66T, hOe-124 and hOe-125 were closely related to both type strains Pseudoalteromonas rhizosphaerae RA15T and Pseudoalteromonas neustonica PAMC 28425T with less than 93.3% ANI and 52.3% isDDH values. Regarding their phenotypic traits, the three strains were Gram-negative, 1-2 µm rod-shaped, aerobic, motile and non-spore-forming bacteria. Cells grew optimally at 25 °C in 2.5% NaCl and at 7-8 pH", "token_count": 417, "char_count": 1070, "word_count": 134, "semantic_coherence": 1, "information_density": 0.791, "quality_score": 0.8955, "entities": { "genes": [ "RA15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:54.936102", "source": { "split": "train_shard_00001", "doc_id": 2982 }, "chunk_id": "train_shard_00001_2982_0", "global_id": 9888 }, { "text": "The most abundant fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c), C16:0 and C17:1 ω8c. The strains carried a genome average size of 4.64 Mb and a G+C content of 40.28 mol%. The genetic and phenotypic results suggested that strains hOe-66T, hOe-124 and hOe-125 belong to a new species of the genus Pseudoalteromonas. In this context, we propose the name Pseudoalteromonas ostreae sp. nov. The type strain is hOe-66T (=CECT 30303T=CIP 111911T).\n\nPseudoalteromonas ostreae sp. nov., a new bacterial species harboured by the flat oyster Ostrea edulis.", "token_count": 343, "char_count": 742, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:55.500124", "source": { "split": "train_shard_00001", "doc_id": 2982 }, "chunk_id": "train_shard_00001_2982_1", "global_id": 9889 }, { "text": "Ethanol production from sugarcane bagasse pith hydrolysate by thermotolerant yeast Kluyveromyces sp. IIPE453 was analyzed using response surface methodology. Variables such as Substrate Concentration, pH, fermentation time and Na2HPO4 concentration were found to influence ethanol production significantly. In a batch fermentation, optimization of key process variables resulted in maximum ethanol concentration of 17.44 g/L which was 88% of the theoretical with specific productivity of 0.36 g/L/h.\n\nDesign and optimization of ethanol production from bagasse pith hydrolysate by a thermotolerant yeast Kluyveromyces sp. IIPE453 using response surface methodology.", "token_count": 177, "char_count": 664, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6552, "quality_score": 0.8276, "entities": { "genes": [ "IIPE453" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:55.944355", "source": { "split": "train_shard_00001", "doc_id": 2983 }, "chunk_id": "train_shard_00001_2983_0", "global_id": 9890 }, { "text": "Acinetobacter baumannii (A. baumannii) attributes 26% of the mortality rate in hospitalized patients, and the percentage can rise to 46 in patients admitted to ICU as it is a major cause of ventilator-associated pneumonia. It has been nominated as the critical priority organism by WHO for which new therapeutic drugs are urgently required. To understand the genomic identification of different strains, antimicrobial resistance patterns, and epidemiological typing of organisms, whole-genome sequencing (WGS) analysis provides insight to explore new epitopes to develop new drugs against the organism. Therefore, the study is aimed at investigating the whole genome sequence of A. baumannii strains to report the new intensifications in its genomic profile. The genome sequences were retrieved from the NCBI database system. Pan-genome BPGA (Bacterial Pan-genome Analysis Tool) was used to analyze the core, pan, and species-specific genome analysis. The pan and core genome curves were extrapolated using the empirical power law equation f(x) = a.xb and the exponential equation f1(x) = c.e (d.x). To identify the resistant genes with resistant mutations against antibiotics, ResFinder and Galaxy Community hub bioinformatics tools were used. According to pan-genome analysis, there were 2227 core genes present in each species of the A. baumannii genome. Furthermore, the number of accessory genes ranged from 1182 to 1460, and the unique genes in the genome were 931. There were 325 exclusively absent genes in the genome of Acinetobacter baumannii. The pan-genome analysis showed that there is a 5-fold increase in the genome of A. baumannii in 5 years, and the genome is still open", "token_count": 525, "char_count": 1799, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:31:56.578740", "source": { "split": "train_shard_00001", "doc_id": 2984 }, "chunk_id": "train_shard_00001_2984_0", "global_id": 9891 }, { "text": "There is the addition of multiple unique genes; among them, genes participating in the function of information and processing are increased.\n\nIntensification in Genetic Information and Acquisition of Resistant Genes in Genome of Acinetobacter baumannii: A Pan-Genomic Analysis.", "token_count": 67, "char_count": 284, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:56.955191", "source": { "split": "train_shard_00001", "doc_id": 2984 }, "chunk_id": "train_shard_00001_2984_1", "global_id": 9892 }, { "text": "

Aims

To identify the dominant micro-organisms involved in the production of gowé, a fermented beverage, and to select the most appropriate species for starter culture development.

Methods and results

Samples of sorghum gowé produced twice at three different production sites were taken at different fermentation times. DNA amplification by internal transcribed spacer-polymerase chain reaction of 288 lactic acid bacteria (LAB) isolates and 16S rRNA gene sequencing of selected strains revealed that the dominant LAB responsible for gowé fermentation were Lactobacillus fermentum, Weissella confusa, Lactobacillus mucosae, Pediococcus acidilactici, Pediococcus pentosaceus and Weissella kimchii. DNA from 200 strains of yeasts was amplified and the D1/D2 domain of the 26S rRNA gene was sequenced for selected isolates, revealing that the yeasts species were Kluyveromyces marxianus, Pichia anomala, Candida krusei and Candida tropicalis.

Conclusions

Gowé processing is characterized by a mixed fermentation dominated by Lact. fermentum, W. confusa and Ped. acidilactici for the LAB and by K. marxianus, P. anomala and C. krusei for the yeasts.

Significance and impact of the study

The diversity of the LAB and yeasts identified offers new opportunities for technology upgrading and products development in gowé production. The identified species can be used as possible starter for a controlled fermentation of gowé.\n\nLactic acid bacteria and yeasts associated with gowé production from sorghum in Bénin.", "token_count": 427, "char_count": 1534, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7967, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:57.584281", "source": { "split": "train_shard_00001", "doc_id": 2985 }, "chunk_id": "train_shard_00001_2985_0", "global_id": 9893 }, { "text": "We report three yellow-pigmented, Gram-negative, aerobic, rod-shaped, motile bacterial isolates designated as PPL1T, PPL2, and PPL3 from healthy basmati rice seeds. Phenotypic and 16S rRNA gene sequence analysis assigned these isolates to the genus Xanthomonas. The 16S rRNA showed a 99.59% similarity with X. sacchari CFBP 4641T, a sugarcane pathogen. Further, biochemical and fatty acid analysis revealed it to be closer to X. sacchari. Still, it differed from other species in general and known rice associated species such as X. oryzae (pathogenic) and X. maliensis (non-pathogenic) in particular. Interestingly, the isolatess in this study were isolated from healthy rice plants but are closely related to species that is pathogenic and isolated from diseased sugarcane. Accordingly, in planta studies revealed that PPL1T, PPL2, and PPL3 are non-pathogenic to rice plants upon leaf inoculation. Taxonogenomic studies based on orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) values with type strains of Xanthomonas species were below the recommended threshold values for species delineation. Whole genome-based phylogenomic analysis revealed that these isolates formed a distinct monophyletic clade with X. sacchari CFBP 4641T as their closest neighbour. Further, pangenome analysis revealed PPL1T, PPL2, and PPL3 isolates to comprise NRPS cluster along with a large number of unique genes associated with the novel species. Based on polyphasic and genomic approaches, a novel lineage and species associated with healthy rice seeds for which the name Xanthomonas sontii sp. nov. is proposed. The type strain for the X. sontii sp. nov", "token_count": 500, "char_count": 1736, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "PPL2", "PPL3", "PPL1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:58.243882", "source": { "split": "train_shard_00001", "doc_id": 2986 }, "chunk_id": "train_shard_00001_2986_0", "global_id": 9894 }, { "text": "is PPL1T (JCM 33631T = CFBP 8688T = ICMP 23426T = MTCC 12491T) and PPL2 (JCM 33632 = CFBP 8689 = ICMP 23427 = MTCC 12492) and PPL3 (JCM 33633 = CFBP 8690 = ICMP 23428 = MTCC 12493) as other strains of the species.\n\nXanthomonas sontii sp. nov., a non-pathogenic bacterium isolated from healthy basmati rice (Oryza sativa) seeds from India.", "token_count": 254, "char_count": 393, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [ "PPL2", "PPL3", "PPL1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:58.725676", "source": { "split": "train_shard_00001", "doc_id": 2986 }, "chunk_id": "train_shard_00001_2986_1", "global_id": 9895 }, { "text": "Extensively drug-resistant (XDR) Klebsiella pneumoniae inflict a notable burden on healthcare worldwide. Of specific concern are strains producing carbapenem-hydrolyzing enzymes, as the therapeutic options for these strains are still very limited. Specific sequence types of K. pneumoniae have been noted for their epidemic occurrence globally, but the mechanisms behind the success of specific clones remain unclear. Herein, we have characterized 20 high-risk clones (HiRCs) and 10 non-HiRCs of XDR K. pneumoniae, exploring factors connected to the epidemiological success of some clones. Isolates were subjected to core genome multilocus sequence typing analysis to determine the clonal relationships of the isolates and subsequently characterized with regard to features known to be linked to overall bacterial fitness and virulence. The genomes were analyzed in silico for capsule types, O antigens, virulence factors, antimicrobial resistance genes, prophages, and CRISPR-Cas loci. In vitro growth experiments were conducted to retrieve proxies for absolute and relative fitness for 11 HiRC and 9 non-HiRC isolates selected based on the clonal groups they belonged to, and infections in a Galleria mellonella insect model were used to evaluate the virulence of the isolates in vivo. This study did not find evidence that virulence factors, prophages, CRISPR-Cas loci, or fitness measured in vitro alone would contribute to the global epidemiological success of specific clones of carbapenemase-producing XDR K. pneumoniae. However, this study did find the HiRC group to be more virulent than the non-HiRC group when measured in vivo in a model with G. mellonella. This suggests that the virulence and epidemiological success of certain clones of K", "token_count": 502, "char_count": 1832, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:59.382453", "source": { "split": "train_shard_00001", "doc_id": 2987 }, "chunk_id": "train_shard_00001_2987_0", "global_id": 9896 }, { "text": "pneumoniae cannot be explained by individual traits investigated in this study and thus warrant further experiments in the future.IMPORTANCEHerein, we explored potential explanations for the successfulness of some epidemic or high-risk clones of carbapenemase-producing Klebsiella pneumoniae. We found differences in mortality in a larva model but found no clear genomic differences in known virulence markers. Most of the research on virulence in K. pneumoniae has been focused on hypervirulent strains, but here, we try to understand differences within the group of highly resistant strains. The results from the larva virulence model could be used to design experiments in higher animals. Moreover, the data could provide further support to a differentiated infection control approach against extensively drug-resistant strains, based on their classification as high-risk clones.\n\nMolecular characteristics, fitness, and virulence of high-risk and non-high-risk clones of carbapenemase-producing Klebsiella pneumoniae.", "token_count": 260, "char_count": 1046, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6594, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:31:59.932642", "source": { "split": "train_shard_00001", "doc_id": 2987 }, "chunk_id": "train_shard_00001_2987_1", "global_id": 9897 }, { "text": "Ethanol and endopolygalacturonase (endoPG) are simultaneously produced by the yeast Kluyveromyces marxianus CCEBI 2011. The aim of this study was to determine the optimal combination of seven environmental and nutritional variables, as well as the influence of each one, with respect to the fermentation process in yeast cultures in which sugarcane juice was the substrate. Simplex sequential optimization showed that after 15 runs the optimal conditions were: pH, 4.6; temperature, 31 ºC; total reducing sugars (TRS), 125 g/l; (NH(4))(2)SO(4), 2.48 g/l; (NH(4))(2)HPO(4), 2.73 g/l; CaCl(2), 0.33 g/l and MgSO(4)·7H(2)O, 0.54 g/l. Under these conditions, the ethanol concentration was 47.6 g/l and endoPG concentration was 9.8 U/ml, which represented increases of 22% and 10%, respectively, over the concentrations obtained under suboptimal conditions. Temperature and (NH(4))(2)SO(4) supplementation were the most significant factors influencing the co-production process.\n\nInfluence of nutritional and environmental factors on ethanol and endopolygalacturonase co-production by Kluyveromyces marxianus CCEBI 2011.", "token_count": 362, "char_count": 1115, "word_count": 150, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:00.507199", "source": { "split": "train_shard_00001", "doc_id": 2988 }, "chunk_id": "train_shard_00001_2988_0", "global_id": 9898 }, { "text": "Polyextremophilic bacteria can thrive in environments with multiple stressors such as the Salar de Huasco (SH). Microbial communities in SH are exposed to low atmospheric pressure, high UV radiation, wide temperature ranges, salinity gradient and the presence of toxic compounds such as arsenic (As). In this work we focus on arsenic stress as one of the main adverse factors in SH and bacteria that belong to the Exiguobacterium genus due to their plasticity and ubiquity. Therefore, our aim was to shed light on the effect of niche conditions pressure (particularly arsenic), on the adaptation and divergence (at genotypic and phenotypic levels) of Exiguobacterium strains from five different SH sites. Also, to capture greater diversity in this genus, we use as outgroup five As(III) sensitive strains isolated from Easter Island (Chile) and The Great Salt Lake (United States). For this, samples were obtained from five different SH sites under an arsenic gradient (9 to 321 mg/kg: sediment) and isolated and sequenced the genomes of 14 Exiguobacterium strains, which had different arsenic tolerance levels. Then, we used comparative genomic analysis to assess the genomic divergence of these strains and their association with phenotypic differences such as arsenic tolerance levels and the ability to resist poly-stress. Phylogenetic analysis showed that SH strains share a common ancestor. Consequently, populations were separated and structured in different SH microenvironments, giving rise to multiple coexisting lineages. Hence, this genotypic variability is also evidenced by the COG (Clusters of Orthologous Groups) composition and the size of their accessory genomes. Interestingly, these observations correlate with physiological traits such as growth patterns, gene expression, and enzyme activity related to arsenic response and/or tolerance. Therefore, Exiguobacterium strains from SH are adapted to physiologically overcome the contrasting environmental conditions, like the arsenic present in their habitat.", "token_count": 489, "char_count": 2055, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:01.155667", "source": { "split": "train_shard_00001", "doc_id": 2989 }, "chunk_id": "train_shard_00001_2989_0", "global_id": 9899 }, { "text": "Genomic Variation and Arsenic Tolerance Emerged as Niche Specific Adaptations by Different Exiguobacterium Strains Isolated From the Extreme Salar de Huasco Environment in Chilean - Altiplano.", "token_count": 58, "char_count": 199, "word_count": 26, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:01.515979", "source": { "split": "train_shard_00001", "doc_id": 2989 }, "chunk_id": "train_shard_00001_2989_1", "global_id": 9900 }, { "text": "Latilactobacillus sakei is a lactic acid bacterium used to produce a wide range of fermented food products. To understand their characteristics and adaptability to various nutrient sources, we applied strain-specific, nucleotide-concatenated (SSC) sequences to the phylogenetic analysis of 32 L. sakei strains isolated from various locations and products. SSC sequences were developed by concatenating the polymorphisms detected by whole-genome sequencing. This enabled us to use sufficient polymorphisms and avoid the bias caused by selecting partial sequences, such as that in core genome and multi-locus sequence typing. SSC sequence-based analysis revealed that the phylogenetic relations for L. sakei are based on the different nutrition sources rather than geographical distance.\n\nPhylogenomic analysis in Latilactobacillus sakei by using polymorphisms detected by next-generation sequencing.", "token_count": 245, "char_count": 940, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:02.018223", "source": { "split": "train_shard_00001", "doc_id": 2990 }, "chunk_id": "train_shard_00001_2990_0", "global_id": 9901 }, { "text": "

Objective of the study

This study aims to characterize phospholipase and proteinase activities of Candida isolates from 82 vulvovaginal candidiasis (VVC) and to study the relationship of these activities with vulvovaginitis.

Methods

Totally 82 Candida isolates from vagina samples of VVC patients were randomly collected over the period between September and December 2014 from hospitalized patients at the general hospitals of Lorestan province, Iran. Isolates were previously identified by conventional mycological methods. The phospholipase and proteinase activities were evaluated by Egg yolk agar, Tween 80 opacity medium and agar plate methods.

Results

The most common Candida species was identified Candida albicans (n=34, 41.5%), followed by Candida famata (n=13, 15.8%), Candida tropicalis (n=11, 13.4%), and Candida parapsilosis (n=9, 11%). The most phospholipase activity was observed in Candida colliculosa (40%), followed by C. famata (38.5%), and Candida krusei (33.3%). The findings revealed that the correlation between phospholipase production by Candida spp. and the presence of VVC was not found to be statistically significant (P=0.91). All Candida spp. exhibited considerable proteinase activity; so that 100% of C. colliculosa, C. parapsilosis, Candida kefyr, and Candida intermedia isolates produced high proteinase activity with Pz 4+ scores. There was a significant correlation between proteinase production by Candida spp. and the presence of VVC (P=0.009).

Conclusion

The obtained findings revealed that Candida spp. isolates may produce both virulence factors, phospholipase and proteinase. Although the phospholipase production was only observed in <40% of the isolates; however there was a significant association between proteinase production by Candida spp. and VVC.", "token_count": 520, "char_count": 1827, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5369, "quality_score": 0.7684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:02.699572", "source": { "split": "train_shard_00001", "doc_id": 2991 }, "chunk_id": "train_shard_00001_2991_0", "global_id": 9902 }, { "text": "Phospholipase and proteinase activities of Candida spp. isolates from vulvovaginitis in Iran.", "token_count": 27, "char_count": 93, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:03.068861", "source": { "split": "train_shard_00001", "doc_id": 2991 }, "chunk_id": "train_shard_00001_2991_1", "global_id": 9903 }, { "text": "

Background and aim

Candida spp. have emerged as successful pathogens both in invasive and mucosal infections. C. albicans is the sixth cause of most common nosocomial infections according to studies by the Centers for Disease Control and Prevention. A shift toward non-albicans species has been reported. There is a dearth of knowledge regarding the virulence factors of Candida, especially from this part of India. The aim was to study the prevalence of Candida, speciate, and determine antifungal sensitivity along with the detection of in vitro production of phospholipases in 100 Candida isolates.

Materials and methods

A total of 100 Candida isolates from various clinical specimens were studied (February 1, 2015-May 31, 2015; 4 months). Speciation was done by conventional methods and antifungal drugs fluconazole and voriconazole tested. Phospholipase activity (Pz value) was determined.

Results

Of the 100 Candida spp., 35% were C. albicans and 65% were nonalbicans Candida (NAC). Species spectrum was of the 100 isolates as follows: 35 were C. albicans, 17 Candida tropicalis, 6 Candida glabrata, 8 Candida guilliermondi, 1 Candida kefyr, 6 Candida krusei, 14 Candida parapsilosis, 2 Candida lusitaniae, and 1 Trichosporon and 10 Candida spp", "token_count": 521, "char_count": 1413, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6811, "quality_score": 0.8405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:03.747624", "source": { "split": "train_shard_00001", "doc_id": 2992 }, "chunk_id": "train_shard_00001_2992_0", "global_id": 9904 }, { "text": "(not speciated). Phospholipase production was seen in 81 (81%) of the total isolates. The majority (63%) of phospholipase producers were NAC. Among NAC spp., the maximum phospholipase activity was seen in C. tropicalis (30%) and C. parapsilosis (24%). Of these, 60% of Candida was from patients admitted to the hospital. Sensitivity rates of C. albicans for fluconazole and voriconazole were 89.5% and 90.5%, respectively.

Conclusion

Increasing usage of devices, total parenteral nutrition, broad-spectrum antibiotics, chemotherapies, and transplantation are factors contributing to the increase of candidal infections. Recent studies underline the increasing frequency of infections by NAC. The present study showcases the increased prevalence as well as virulence of NAC. In addition, early detection of virulence factors by Candida is useful in clinical decision-making.\n\nStudying the Prevalence, Species Distribution, and Detection of In vitro Production of Phospholipase from Candida Isolated from Cases of Invasive Candidiasis.", "token_count": 331, "char_count": 1089, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6479, "quality_score": 0.8239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:04.325326", "source": { "split": "train_shard_00001", "doc_id": 2992 }, "chunk_id": "train_shard_00001_2992_1", "global_id": 9905 }, { "text": "Background.  Within-household sharing of strains from the resistance-associated H30R1 and H30Rx subclones of Escherichia coli sequence type 131 (ST131) has been inferred based on conventional typing data, but it has been assessed minimally using whole genome sequence (WGS) analysis. Methods.  Thirty-three clinical and fecal isolates of ST131-H30R1 and ST131-H30Rx, from 20 humans and pets in 6 households, underwent WGS analysis for comparison with 52 published ST131 genomes. Phylogenetic relationships were inferred using a bootstrapped maximum likelihood tree based on core genome sequence polymorphisms. Accessory traits were compared between phylogenetically similar isolates. Results.  In the WGS-based phylogeny, isolates clustered strictly by household, in clades that were distributed widely across the phylogeny, interspersed between H30R1 and H30Rx comparison genomes. For only 1 household did the core genome phylogeny place epidemiologically unlinked isolates together with household isolates, but even there multiple differences in accessory genome content clearly differentiated these 2 groups. The core genome phylogeny supported within-household strain sharing, fecal-urethral urinary tract infection pathogenesis (with the entire household potentially providing the fecal reservoir), and instances of host-specific microevolution. In 1 instance, the household's index strain persisted for 6 years before causing a new infection in a different household member", "token_count": 451, "char_count": 1570, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8418, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:04.960640", "source": { "split": "train_shard_00001", "doc_id": 2993 }, "chunk_id": "train_shard_00001_2993_0", "global_id": 9906 }, { "text": "Conclusions.  Within-household sharing of E coli ST131 strains was confirmed extensively at the genome level, as was long-term colonization and repeated infections due to an ST131-H30Rx strain. Future efforts toward surveillance and decolonization may need to address not just the affected patient but also other human and animal household members.\n\nHousehold Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis.", "token_count": 155, "char_count": 516, "word_count": 68, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:05.394659", "source": { "split": "train_shard_00001", "doc_id": 2993 }, "chunk_id": "train_shard_00001_2993_1", "global_id": 9907 }, { "text": "The mitogen-activated protein kinase Hog1 gene (Kmhog1) was isolated from Kluyveromyces marxianus strain NBRC 1777 by degenerate PCR and genome walking, and then disrupted to construct a mutant strain hog1∆. The mutant was now more sensitive to acetic acid and its growth was nearly completely inhibited by 0.5 M NaCl (97%) and 10 mM H(2)O(2) (93%) as compared with the wild-type cells. However, neither strain grew at 47°C. Kmhog1 may thus be required for adaptation to acetic acid, osmotic, and oxidative stress but is not involved in thermotolerance.\n\nCloning and characterization of Kluyveromyces marxianus Hog1 gene.", "token_count": 193, "char_count": 621, "word_count": 96, "semantic_coherence": 1, "information_density": 0.8021, "quality_score": 0.901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:05.847030", "source": { "split": "train_shard_00001", "doc_id": 2994 }, "chunk_id": "train_shard_00001_2994_0", "global_id": 9908 }, { "text": "Kluyveromyces marxianus is capable of converting lactose into ethyl acetate offering a chance for an economical reuse of whey. The microbial formation of ethyl acetate as a bulk product calls for an aerobic process and, thus, the highly volatile ethyl acetate is discharged from the aerated bioreactor. This stripping process was modeled and investigated experimentally. The stripping rate was proportional to the gas flow and nearly independent of the stirring rate since the stripping was governed by the absorption capacity of the exhaust gas rather than the phase transfer. Cooling the exhaust gas did not noticeably influence the stripping. One batch experiment is presented in detail to demonstrate the formation of ethyl acetate by K. maxianus DSM 5422 on whey. Further batch experiments showed that a substantial formation of ethyl acetate only occurred when the yeast growth was limited by a lack of trace elements. The highest product yield observed was 0.25 g ethyl acetate per g lactose which is nearly 50% of the theoretical maximum.\n\nFormation of ethyl acetate by Kluyveromyces marxianus on whey: studies of the ester stripping.", "token_count": 277, "char_count": 1142, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:06.401106", "source": { "split": "train_shard_00001", "doc_id": 2995 }, "chunk_id": "train_shard_00001_2995_0", "global_id": 9909 }, { "text": "The use of the thermotolerant yeast Kluyveromyces marxianus IMB3 for ethanol production from whey permeate at 45degC", "token_count": 39, "char_count": 116, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:06.760498", "source": { "split": "train_shard_00001", "doc_id": 2996 }, "chunk_id": "train_shard_00001_2996_0", "global_id": 9910 }, { "text": "Dickeya dianthicola has caused an outbreak of blackleg and soft rot of potato in the eastern half of the United States since 2015. To investigate genetic diversity of the pathogen, a comparative analysis was conducted on genomes of D. dianthicola strains. Whole genomes of 16 strains from the United States outbreak were assembled and compared with 16 previously sequenced genomes of D. dianthicola isolated from potato or carnation. Among the 32 strains, eight distinct clades were distinguished based on phylogenomic analysis. The outbreak strains were grouped into three clades, with the majority of the strains in clade I. Clade I strains were unique and homogeneous, suggesting a recent incursion of this strain into potato production from alternative hosts or environmental sources. The pangenome of the 32 strains contained 6,693 genes, 3,377 of which were core genes. By screening primary protein subunits associated with virulence from all U.S. strains, we found that many virulence-related gene clusters, such as plant cell wall degrading enzyme genes, flagellar and chemotaxis related genes, two-component regulatory genes, and type I/II/III secretion system genes, were highly conserved but that type IV and type VI secretion system genes varied. The clade I strains encoded two clusters of type IV secretion systems, whereas the clade II and III strains encoded only one cluster. Clade I and II strains encoded one more VgrG/PAAR spike protein than did clade III. Thus, we predicted that the presence of additional virulence-related genes may have enabled the unique clade I strain to become predominant in the U.S. outbreak.\n\nPangenomic Analysis of Dickeya dianthicola Strains Related to the Outbreak of Blackleg and Soft Rot of Potato in the United States.", "token_count": 463, "char_count": 1799, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5527, "quality_score": 0.7764, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:07.400961", "source": { "split": "train_shard_00001", "doc_id": 2997 }, "chunk_id": "train_shard_00001_2997_0", "global_id": 9911 }, { "text": "Giant viruses of amoebae were discovered in 2003. Since then, their diversity has greatly expanded. They were suggested to form a fourth branch of life, collectively named 'TRUC' (for \"Things Resisting Uncompleted Classifications\") alongside Bacteria, Archaea, and Eukarya. Their origin and ancestrality remain controversial. Here, we specify the evolution and definition of giant viruses. Phylogenetic and phenetic analyses of informational gene repertoires of giant viruses and selected bacteria, archaea and eukaryota were performed, including structural phylogenomics based on protein structural domains grouped into 289 universal fold superfamilies (FSFs). Hierarchical clustering analysis was performed based on a binary presence/absence matrix constructed using 727 informational COGs from cellular organisms. The presence/absence of 'universal' FSF domains was used to generate an unrooted maximum parsimony phylogenomic tree. Comparison of the gene content of a giant virus with those of a bacterium, an archaeon, and a eukaryote with small genomes was also performed. Overall, both cladistic analyses based on gene sequences of very central and ancient proteins and on highly conserved protein fold structures as well as phenetic analyses were congruent regarding the delineation of a fourth branch of microbes comprised by giant viruses. Giant viruses appeared as a basal group in the tree of all proteomes. A pangenome and core genome determined for Rickettsia bellii (bacteria), Methanomassiliicoccus luminyensis (archaeon), Encephalitozoon intestinalis (eukaryote), and Tupanvirus (giant virus) showed a substantial proportion of Tupanvirus genes that overlap with those of the cellular microbes. In addition, a substantial genome mosaicism was observed, with 51, 11, 8, and 0.2% of Tupanvirus genes best matching with viruses, eukaryota, bacteria, and archaea, respectively", "token_count": 516, "char_count": 1930, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:08.056963", "source": { "split": "train_shard_00001", "doc_id": 2998 }, "chunk_id": "train_shard_00001_2998_0", "global_id": 9912 }, { "text": "Finally, we found that genes themselves may be subject to lateral sequence transfers. In summary, our data highlight the quantum leap between classical and giant viruses. Phylogenetic and phyletic analyses and the study of protein fold superfamilies confirm previous evidence of the existence of a fourth TRUC of life that includes giant viruses, and highlight its ancestrality and mosaicism. They also point out that best evolutionary representations for giant viruses and cellular microorganisms are rhizomes, and that sequence transfers rather than gene transfers have to be considered.\n\nAncestrality and Mosaicism of Giant Viruses Supporting the Definition of the Fourth TRUC of Microbes.", "token_count": 153, "char_count": 692, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:08.490591", "source": { "split": "train_shard_00001", "doc_id": 2998 }, "chunk_id": "train_shard_00001_2998_1", "global_id": 9913 }, { "text": "Cacao (Theobroma cacao), the source of chocolate, is threatened by devastating diseases like frosty pod rot (FPR) and witches' broom disease (WBD), impacting global production and farmer livelihoods. Here, we employ a machine learning-driven genome-wide association study to dissect the genetic architecture of disease resistance and productivity in cacao. Upon analyzing phenotypic data for healthy pod rate along with FPR and WBD resistance across 102 diverse accessions, coupled with single nucleotide polymorphism (SNP) markers mapped to the Criollo and Matina reference genomes, we identified numerous novel candidate genes. These genes are implicated in various biological processes, including cell wall modification, stress response signaling, and defense-related mechanisms. Notably, associations varied between the reference genomes, highlighting the genomic complexity of these traits. Our analyses, using Bootstrap Forest and Boosted Tree models, uncovered loci not previously reported, demonstrating the power of machine learning in uncovering complex genetic interactions. This study offers important insights into the polygenic nature of disease resistance in cacao and presents a genomic roadmap for developing disease-resistant varieties.\n\nMachine learning-driven GWAS uncovers novel candidate genes for resistance to frosty pod rot and witches' broom disease in cacao.", "token_count": 302, "char_count": 1385, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:09.051468", "source": { "split": "train_shard_00001", "doc_id": 2999 }, "chunk_id": "train_shard_00001_2999_0", "global_id": 9914 }, { "text": "Enterococcus lactis and the heterotypic synonym Enterococcus xinjiangensis from dairy origin have recently been identified as a novel species based on 16S rRNA gene sequence analysis. Enterococcus faecium type strain NCTC 7171T was used as the reference genome for determining E. lactis and E. faecium to be separate species. However, this taxonomic classification did not consider the diverse lineages of E. faecium, and the double nature of hospital-associated (clade A) and community-associated (clade B) isolates. Here, we investigated the taxonomic relationship among isolates of E. faecium of different origins and E. lactis, using a genome-based approach. Additional to 16S rRNA gene sequence analysis, we estimated the relatedness among strains and species using phylogenomics based on the core pangenome, multilocus sequence typing, the average nucleotide identity and digital DNA-DNA hybridization. Moreover, following the available safety assessment schemes, we evaluated the virulence profile and the ampicillin resistance of E. lactis and E. faecium clade B strains. Our results confirmed the genetic and evolutionary differences between clade A and the intertwined clade B and E. lactis group. We also confirmed the absence in these strains of virulence gene markers IS16, hylEfm and esp and the lack of the PBP5 allelic profile associated with ampicillin resistance. Taken together, our findings support the reassignment of the strains of E. faecium clade B as E. lactis.", "token_count": 473, "char_count": 1602, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7977, "entities": { "genes": [ "IS16", "PBP5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:09.692137", "source": { "split": "train_shard_00001", "doc_id": 3000 }, "chunk_id": "train_shard_00001_3000_0", "global_id": 9915 }, { "text": "Genome-based studies indicate that the Enterococcus faecium Clade B strains belong to Enterococcus lactis species and lack of the hospital infection associated markers.", "token_count": 52, "char_count": 182, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:10.050486", "source": { "split": "train_shard_00001", "doc_id": 3000 }, "chunk_id": "train_shard_00001_3000_1", "global_id": 9916 }, { "text": "Symbiotic bacteria are responsible for the majority of complex carbohydrate digestion in the human colon. Since the identities and amounts of dietary polysaccharides directly impact the gut microbiota, determining which microorganisms consume specific nutrients is central to defining the relationship between diet and gut microbial ecology. Using a custom phenotyping array, we determined carbohydrate utilization profiles for 354 members of the Bacteroidetes, a dominant saccharolytic phylum. There was wide variation in the numbers and types of substrates degraded by individual bacteria, but phenotype-based clustering grouped members of the same species indicating that each species performs characteristic roles. The ability to utilize dietary polysaccharides and endogenous mucin glycans was negatively correlated, suggesting exclusion between these niches. By analyzing related Bacteroides ovatus/xylanisolvens strains that vary in their ability to utilize mucin glycans, we addressed whether gene clusters that confer this complex, multi-locus trait are being gained or lost in individual strains. Pangenome reconstruction of these strains revealed a remarkably mosaic architecture in which genes involved in polysaccharide metabolism are highly variable and bioinformatics data provide evidence of interspecies gene transfer that might explain this genomic heterogeneity. Global transcriptomic analyses suggest that the ability to utilize mucin has been lost in some lineages of B. ovatus and B. xylanisolvens , which still harbor residual gene clusters that are involved in mucin utilization by strains that still actively express this phenotype. Our data provide insight into the breadth and complexity of carbohydrate metabolism in the microbiome and the underlying genomic events that shape these behaviors.\n\nPhenotypic and genomic diversification in complex carbohydrate degrading human gut bacteria", "token_count": 429, "char_count": 1914, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:11.051993", "source": { "split": "train_shard_00001", "doc_id": 3001 }, "chunk_id": "train_shard_00001_3001_0", "global_id": 9917 }, { "text": "A fructanase, produced by a Kluyveromyces marxianus strain isolated during the fermentation step of the elaboration process of \"Mezcal de Guerrero\" was purified and biochemically characterized. The active protein was a glycosylated dimer with a molecular weight of approximately 250 kDa. The specific enzymatic activity of the protein was determined for different substrates: sucrose, inulin, Agave tequilana fructan, levan and Actilight® and compared with the activity of Fructozyme®. The hydrolysis profile of the different substrates analyzed by HPAEC-PAD showed that the enzyme has different affinities over the substrates tested with a sucrose/inulin enzymatic activity ratio (S/I) of 125. For the hydrolysis of Agave tequilana fructans, the enzyme also showed a higher enzymatic activity and specificity than Fructozyme®, which is important for its potential application in the tequila industry.\n\nPurification and substrate specificities of a fructanase from Kluyveromyces marxianus isolated from the fermentation process of Mezcal.", "token_count": 274, "char_count": 1038, "word_count": 145, "semantic_coherence": 1, "information_density": 0.5931, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:11.601381", "source": { "split": "train_shard_00001", "doc_id": 3002 }, "chunk_id": "train_shard_00001_3002_0", "global_id": 9918 }, { "text": "Klebsiella pneumoniae is a gram-negative, encapsulated, non-motile bacterium that can cause damage to human lungs. Antibiotic resistance of this strain requires constant monitoring and for this purpose, Oxford nanopore mediated whole genome sequencing was done for a strain acquired from the pleural fluid of a diabetic patient suffering from chronic kidney disease. A genome of 5.98 MB was obtained, with 8,869 CDSs and 110 RNAs. Around 96 proteins were seen as involved in virulence, disease or defense, while 25 antibiotic resistance genes were identified. Pan-genome was inferred as open, with 12,857 and 1,303 CDSs forming respective accessory and core genome of antibiotic resistant Pakistani strains (n=168) of this species. Apart from notable antimicrobial resistance genes like beta-lactamases, a gene conferring resistance to colistin was also mined. To the best of our knowledge, this is first report of nanopore mediated long read sequencing of a hypermucoviscous virulent K. pneumoniae from Pakistan.\n\nNanopore sequencing of antibiotic-resistantKlebsiella pneumoniaeJRCGR1 isolate from Pakistan and country scale pan-genomics", "token_count": 321, "char_count": 1145, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [ "JRCGR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:12.165684", "source": { "split": "train_shard_00001", "doc_id": 3003 }, "chunk_id": "train_shard_00001_3003_0", "global_id": 9919 }, { "text": "Somatic mutations in the promoter region of the human telomerase reverse transcriptase (hTERT) gene have been identified in many types of cancer. The hTERT promoter is known to be enriched with sequences that enable the formation of G-quadruplex (G4) structures, whose presence is associated with elevated mutagenicity and genome instability. Here, we used a bioinformatics tool (QGRS mapper) to search for G4-forming sequences (G4 motifs) in the 1000 bp TERT promoter regions of 141 mammalian species belonging to 20 orders, 5 of which, including primates and predators, contain more than 10 species. Groups of conserved G4 motifs and single-nucleotide variants within these groups were discovered using a block alignment approach (based on the Nucleotide PanGenome explorer). It has been shown that: (i) G4 motifs are predominantly located in the region proximal to the transcription start site (up to 400 bp) and are over-represented on the non-coding strand of the TERT promoters, (ii) 11 to 22% of the G4 motifs found are evolutionarily conserved across the related organisms, and (iii) a statistically significant higher frequency of nucleotide substitutions in the conserved G4 motifs compared to the surrounding regions was confirmed only for the order Primates. These data support the assumption that G4s can interfere with the DNA repair process and affect the evolutionary adaptation of organisms and species.\n\nConserved G-Quadruplex-Forming Sequences in Mammalian TERT Promoters and Their Effect on Mutation Frequency.", "token_count": 434, "char_count": 1572, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:12.795305", "source": { "split": "train_shard_00001", "doc_id": 3004 }, "chunk_id": "train_shard_00001_3004_0", "global_id": 9920 }, { "text": "

ABSTRACT

Current studies are shifting from the use of single linear references to representation of multiple genomes organised in pangenome graphs or variation graphs. Meanwhile, in metagenomic samples, resolving strain-level abundances is a major step in microbiome studies, as associations between strain variants and phenotype are of great interest for diagnostic and therapeutic purposes. We developed StrainFLAIR with the aim of showing the feasibility of using variation graphs for indexing highly similar genomic sequences up to the strain level, and for characterizing a set of unknown sequenced genomes by querying this graph. On simulated data composed of mixtures of strains from the same bacterial species Escherichia coli , results show that StrainFLAIR was able to distinguish and estimate the abundances of close strains, as well as to highlight the presence of a new strain close to a referenced one and to estimate its abundance. On a real dataset composed of a mix of several bacterial species and several strains for the same species, results show that in a more complex configuration StrainFLAIR correctly estimates the abundance of each strain. Hence, results demonstrated how graph representation of multiple close genomes can be used as a reference to characterize a sample at the strain level.

Availability

http://github.com/kevsilva/StrainFLAIR\n\nStrainFLAIR: Strain-level profiling of metagenomic samples using variation graphs", "token_count": 325, "char_count": 1470, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:13.371313", "source": { "split": "train_shard_00001", "doc_id": 3005 }, "chunk_id": "train_shard_00001_3005_0", "global_id": 9921 }, { "text": "

ABSTRACT

Enterobacter bugandensis is a recently described species that has been largely associated with nosocomial infections. Here, we report the genome of a non-clinical E. bugandensis strain. We used this and other several publicly available E. bugandensis genomes to obtain the species pangenome, investigate the conservation of important genes, and elucidate general population structure features of the species. Core- and whole-genome multilocus sequence typing (cgMLST and wgMLST, respectively) allowed the detection of five E. bugandensis phylogroups (PG-A to E). We found important antimicrobial resistance and virulence determinants associated with specific PGs, notably PG-A and PG-E. IncFII was the most prevalent plasmid replicon type in this species. We uncovered several extended-spectrum β-lactamases, including bla CTX-M-55 and bla NDM-5 , present in an IncX replicon type plasmid, described here for the first time in E. bugandensis . Genetic context analysis of bla NDM-5 revealed the resemblance of this plasmid with other IncX plasmids isolated from other bacteria from the same country. Further, three distinctive siderophore producing operons were found in the E. bugandensis pangenome: enterobactin ( ent ), aerobactin ( iuc / iut ), and salmochelin ( iro ). The latter operon is conserved in all PG-E isolates. Collectively, our findings provide novel insights on the lifestyle, physiology, antimicrobial, and virulence profiles of E. bugandensis .\n\nPopulation structure and pangenome analysis of Enterobacter bugandensis uncover the presence ofblaCTX-M-55,blaNDM-5andblaIMI-1, along with sophisticated iron acquisition strategies", "token_count": 471, "char_count": 1718, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:14.016787", "source": { "split": "train_shard_00001", "doc_id": 3006 }, "chunk_id": "train_shard_00001_3006_0", "global_id": 9922 }, { "text": "We present genomic, phylogenomic, and phenotypic taxonomic data to demonstrate that three human ear isolates represent a novel species within the genus Gulosibacter. These isolates could not be identified reliably using MALDI-TOF mass spectrometry during routine diagnostic work, but partial 16S rRNA gene sequence analysis revealed that they belonged to the genus Gulosibacter. Overall genomic relatedness indices between the draft genome sequences of the three isolates and of the type strains of established Gulosibacter species confirmed that the three isolates represented a single novel Gulosibacter species. A biochemical characterisation yielded differential tests between the novel and established Gulosibacter species, which could also be differentiated using MALDI-TOF mass spectrometry. We propose to formally classify these three isolates into Gulosibacter hominis sp. nov., with 401352-2018 T (= LMG 31778 T, CCUG 74795 T) as the type strain. The whole-genome sequence of strain 401352-2018 T has a size of 2,340,181 bp and a G+C content of 62.04 mol%. A Gulosibacter pangenome analysis revealed 467 gene clusters that were exclusively present in G. hominis genomes. While these G. hominis specific gene clusters were enriched in several COG functional categories, this analysis did not reveal functions that suggested a role in the human microbiome, nor did it explain the occurrence of G. hominis in ear infections. The absence of acquired antimicrobial resistance determinants and virulence factors in the G. hominis genomes, and an analysis of publicly available 16S rRNA gene sequences and 16S rRNA amplicon sequencing data sets suggested that G. hominis is a member of the human skin microbiota that may occasionally be involved in opportunistic infections.\n\nGulosibacter hominis sp. nov.: a novel human microbiome bacterium that may cause opportunistic infections.", "token_count": 513, "char_count": 1929, "word_count": 277, "semantic_coherence": 1, "information_density": 0.5632, "quality_score": 0.7816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:14.690113", "source": { "split": "train_shard_00001", "doc_id": 3007 }, "chunk_id": "train_shard_00001_3007_0", "global_id": 9923 }, { "text": "Although complete genome sequences hold particular value for an accurate description of core genomes, the identification of strain-specific genes, and as the optimal basis for functional genomics studies, they are still largely underrepresented in public repositories. Based on an assessment of the genome assembly complexity for all lactobacilli, we used Pacific Biosciences' long read technology to sequence and de novo assemble the genomes of three Lactobacillus helveticus starter strains, raising the number of completely sequenced strains to 12. The first comparative genomics study for L. helveticus-to our knowledge-identified a core genome of 988 genes and sets of unique, strain-specific genes ranging from about 30 to more than 200 genes. Importantly, the comparison of MiSeq- and PacBio-based assemblies uncovered that not only accessory but also core genes can be missed in incomplete genome assemblies based on short reads. Analysis of the three genomes revealed that a large number of pseudogenes were enriched for functional Gene Ontology categories such as amino acid transmembrane transport and carbohydrate metabolism, which is in line with a reductive genome evolution in the rich natural habitat of L. helveticus. Notably, the functional Clusters of Orthologous Groups of proteins categories \"cell wall/membrane biogenesis\" and \"defense mechanisms\" were found to be enriched among the strain-specific genes. A genome mining effort uncovered examples where an experimentally observed phenotype could be linked to the underlying genotype, such as for cell envelope proteinase PrtH3 of strain FAM8627. Another possible link identified for peptidoglycan hydrolases will require further experiments. Of note, strain FAM22155 did not harbor a CRISPR/Cas system; its loss was also observed in other L. helveticus strains and lactobacillus species, thus questioning the value of the CRISPR/Cas system for diagnostic purposes", "token_count": 492, "char_count": 1972, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [ "FAM22155", "FAM8627" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:15.374530", "source": { "split": "train_shard_00001", "doc_id": 3008 }, "chunk_id": "train_shard_00001_3008_0", "global_id": 9924 }, { "text": "Importantly, the complete genome sequences proved to be very useful for the analysis of natural whey starter cultures with metagenomics, as a larger percentage of the sequenced reads of these complex mixtures could be unambiguously assigned down to the strain level.\n\nComparative Genomics of Completely Sequenced Lactobacillus helveticus Genomes Provides Insights into Strain-Specific Genes and Resolves Metagenomics Data Down to the Strain Level.", "token_count": 112, "char_count": 454, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:15.797176", "source": { "split": "train_shard_00001", "doc_id": 3008 }, "chunk_id": "train_shard_00001_3008_1", "global_id": 9925 }, { "text": "Population-level comparisons of prokaryotic genomes must take into account the substantial differences in gene content, resulting from frequent horizontal gene transfer, gene duplication and gene loss. However, the automated annotation of prokaryotic genomes is imperfect, and errors due to fragmented assemblies, contamination, diverse gene families and mis-assemblies accumulate over the population, leading to profound consequences when analysing the set of all genes found in a species. Here we introduce Panaroo, a graph based pangenome clustering tool that is able to account for many of the sources of error introduced during the annotation of prokaryotic genome assemblies. We verified our approach through extensive simulations of de novo assemblies using the infinitely many genes model and by analysing a number of publicly available large bacterial genome datasets. Using a highly clonal Mycobacterium tuberculosis dataset as a negative control case, we show that failing to account for annotation errors can lead to pangenome estimates that are dominated by error. We additionally demonstrate the utility of the improved graphical output provided by Panaroo by performing a pan-genome wide association study in Neisseria gonorrhoeae and by analysing gene gain and loss rates across 51 of the major global pneumococcal sequence clusters. Panaroo is freely available under an open source MIT licence at https://github.com/gtonkinhill/panaroo .\n\nProducing Polished Prokaryotic Pangenomes with the Panaroo Pipeline", "token_count": 337, "char_count": 1523, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6728, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:16.370548", "source": { "split": "train_shard_00001", "doc_id": 3009 }, "chunk_id": "train_shard_00001_3009_0", "global_id": 9926 }, { "text": "Through horizontal gene transfer, closely related bacterial strains assimilate distinct sets of genes, resulting in significantly varied lifestyles. However, it remains unclear how strains properly regulate horizontally transferred virulence genes. We hypothesized that strains may use components of the core genome to regulate diverse horizontally acquired genes. To investigate how closely related bacteria assimilate and activate horizontally acquired DNA, we used a model consisting of strains in the brassicacearum/corrugata/mediterranea (BCM) subclade of Pseudomonas fluorescens, including Pseudomonas species N2E2 and N2C3, which exhibit contrasting lifestyles on the model plant Arabidopsis. Pseudomonas sp. N2E2 is a plant commensal and contains genes encoding biosynthetic enzymes for the antifungal compound 2,4-diacetylphloroglucinol (DAPG). In contrast, Pseudomonas sp. N2C3 lacks DAPG biosynthesis and has gained a pathogenic island encoding syringomycin (SYR)- and syringopeptin (SYP)-like toxins from the plant pathogen Pseudomonas syringae. This causes a transition in lifestyle from plant-protective N2E2 to plant-pathogenic N2C3. We found that N2E2 and N2C3 share a highly conserved two-component system GacA/S, a known regulator of DAPG and SYR/SYP. Using knockout mutations, we found that a ΔgacA mutation resulted in loss of expression of SYR/SYP virulence genes and returned pathogenic N2C3 to a plant commensal lifestyle", "token_count": 453, "char_count": 1507, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6546, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:17.007801", "source": { "split": "train_shard_00001", "doc_id": 3010 }, "chunk_id": "train_shard_00001_3010_0", "global_id": 9927 }, { "text": "Our study further explored the conservation of regulatory control across strains by demonstrating that GacA genes from both distant and closely related Pseudomonas strains could functionally complement one another across the genus.IMPORTANCEEmerging pathogens represent a significant threat to humans, agriculture, and natural ecosystems. Bacterial horizontal gene transfer (HGT) aids in the acquisition of novel genes that facilitate adaptation to new environments. Our work shows a novel role for GacA in orchestrating the regulatory changes necessary for virulence and lifestyle transitions facilitated by HGT. These findings suggest that the GacA/S system plays a key role in mediating transitions across diverse Pseudomonas symbiotic lifestyles. This work provides insights into the mechanisms that drive the emergence of pathogenic strains and highlights potential targets for managing bacterial threats to plant health.\n\nGacA regulates symbiosis and mediates lifestyle transitions in <i>Pseudomonas</i>.", "token_count": 231, "char_count": 1036, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6912, "quality_score": 0.8456, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:17.473531", "source": { "split": "train_shard_00001", "doc_id": 3010 }, "chunk_id": "train_shard_00001_3010_1", "global_id": 9928 }, { "text": "Whole-genome sequencing (WGS)-based typing methods have emerged as promising and highly discriminative epidemiological tools. In this study, we combined gene-by-gene allele calling and core genome single nucleotide polymorphism (cgSNP) approaches to investigate the genetic relatedness of a well-characterized collection of OXA-48-producing Klebsiella pneumoniae isolates. We included isolates from the predominant sequence type ST405 (n = 31) OXA-48-producing K. pneumoniae clone and isolates from ST101 (n = 3), ST14 (n = 1), ST17 (n = 1), and ST1233 (n = 1), obtained from eight Catalan hospitals. Core-genome multilocus sequence typing (cgMLST) schemes from Institut Pasteur's BIGSdb-Kp (634 genes) and SeqSphere+ (2,365 genes), and a SeqSphere+ whole-genome MLST (wgMLST) scheme (4,891 genes) were used. Allele differences or allelic mismatches and the genetic distance, as the proportion of allele differences, were used to interpret the results from a gene-by-gene approach, whereas the number of SNPs was used for the cgSNP analysis. We observed between 0-10 and 0-14 allele differences among the predominant ST405 using cgMLST and wgMLST from SeqSphere+, respectively, and <2 allelic mismatches when using Institut Pasteur's BIGSdb-Kp cgMLST scheme. For ST101, we observed 14 and 54 allele differences when using cgMLST and wgMLST SeqSphere+, respectively, and 2-5 allelic mismatches for BIGSdb-Kp cgMLST", "token_count": 499, "char_count": 1469, "word_count": 201, "semantic_coherence": 1, "information_density": 0.5871, "quality_score": 0.7935, "entities": { "genes": [ "ST101", "ST405", "ST17", "ST14", "ST1233" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:18.123534", "source": { "split": "train_shard_00001", "doc_id": 3011 }, "chunk_id": "train_shard_00001_3011_0", "global_id": 9929 }, { "text": "A low genetic distance (<0.0035, a previously established threshold for epidemiological link) was generally in concordance with a low number of allele differences (<8) when using the SeqSphere+ cgMLST scheme. The cgSNP analysis showed 6-29 SNPs in isolates with identical allelic SeqSphere+ cgMLST profiles and 16-61 cgSNPs among ST405 isolates. Furthermore, comparison of WGS-based typing results with previously obtained MLST and pulsed-field gel electrophoresis (PFGE) data showed some differences, demonstrating the different molecular principles underlying these techniques. In conclusion, the use of the different WGS-based typing methods that were used to elucidate the genetic relatedness of clonal OXA-48-producing K. pneumoniae all led to the same conclusions. Furthermore, threshold parameters in WGS-based typing methods should be applied with caution and should be used in combination with clinical epidemiological data and population and species characteristics.\n\nCore/Whole Genome Multilocus Sequence Typing and Core Genome SNP-Based Typing of OXA-48-Producing Klebsiella pneumoniae Clinical Isolates From Spain.", "token_count": 298, "char_count": 1141, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [ "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:18.684444", "source": { "split": "train_shard_00001", "doc_id": 3011 }, "chunk_id": "train_shard_00001_3011_1", "global_id": 9930 }, { "text": "

Introduction

Vancomycin-resistant Enterococcus faecium (VREfm) poses a significant concern in healthcare settings, particularly during outbreaks. Traditional antibiotic susceptibility testing may fail to detect occult vancomycin resistance, and long culture times delay diagnosis. While whole genome sequencing (WGS) is the most accurate method for tracing infectious disease transmissions, its response times are not rapid enough to optimally support controlling of ongoing outbreaks. To address this limitation, we investigated the genomic diversity among outbreak isolates and developed outbreak-specific PCR tests for rapid VREfm carrier screening using strain-specific biomarkers identified through comparative genomics.

Materials and methods

Total DNA from VREfm isolates was sequenced using Oxford Nanopore and Illumina platforms. Multi locus sequence types (MLST-ST) and core genome sequence type clusters (cgMLST-CT) were determined with Ridom SeqSphere + software. Comparative analysis of whole genomes was conducted using Lasergene software (DNASTAR).

Results

A large VREfm outbreak involving 111 patients caused by E. faecium ST117-CT469 was identified in the Northern Netherlands, spanning from August 2021 to September 2024. A subset of 55 E. faecium ST117-CT469 isolates were evaluated by WGS and outbreak specific PCRs. Antibiotic susceptibility testing revealed occult vancomycin resistance in the outbreak strain. Comparative genomics identified unique markers specific to E. faecium ST117-CT469. Two PCR assays were developed for rapid outbreak detection: a traditional PCR assay distinguishing outbreak from non-outbreak strains based on amplicon size and a TaqMan real-time PCR assay. Both assays demonstrated 100% reproducibility and specificity. The TaqMan assay was able to detect as little as 5 fg of bacterial DNA in the presence of human DNA, equivalent to approximately one bacterial genomic copy", "token_count": 495, "char_count": 1946, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6693, "quality_score": 0.8346, "entities": { "genes": [ "ST117", "CT469" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:19.335207", "source": { "split": "train_shard_00001", "doc_id": 3012 }, "chunk_id": "train_shard_00001_3012_0", "global_id": 9931 }, { "text": "Sequence analysis of WGS data for all 55 outbreak isolates showed perfect nucleotide sequence conservation in the regions where the primers and probe hybridized. Sequence comparison against NCBI GenBank entries confirmed the perfect specificity of both PCR assays for detecting the ST117-CT469 outbreak strain.

Conclusions

These PCR tests maintain the accuracy and discriminatory power of WGS for identifying the ST117-CT469 outbreak strain but are more cost-effective, faster, and easier to use compared to WGS. They enhance VREfm outbreak management by providing an efficient method for rapid screening. Application of strain-specific PCR based on WGS data is currently the most effective screening method during large, ongoing outbreaks.\n\nDevelopment of a strain-specific PCR as a diagnostic tool for surveillance, detection, and monitoring of vancomycin-resistant Enterococcus faecium during outbreak.", "token_count": 211, "char_count": 912, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [ "ST117", "CT469" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:19.799925", "source": { "split": "train_shard_00001", "doc_id": 3012 }, "chunk_id": "train_shard_00001_3012_1", "global_id": 9932 }, { "text": "Some well-known Clostridiales species such as Clostridium difficile and C. perfringens are agents of high impact diseases worldwide. Nevertheless, other foreseen Clostridiales species have recently emerged such as Clostridium tertium and C. paraputrificum. Three fecal isolates were identified as Clostridium tertium (Gcol.A2 and Gcol.A43) and C. paraputrificum (Gcol.A11) during public health screening for C. difficile infections in Colombia. C. paraputrificum genomes were highly diverse and contained large numbers of accessory genes. Genetic diversity and accessory gene percentage were lower among the C. tertium genomes than in the C. paraputrificum genomes. C. difficile tcdA and tcdB toxins encoding homologous sequences and other potential virulence factors were also identified. EndoA interferase, a toxic component of the type II toxin-antitoxin system, was found among the C. tertium genomes. toxA was the only toxin encoding gene detected in Gcol.A43, the Colombian isolate with an experimentally-determined high cytotoxic effect. Gcol.A2 and Gcol.A43 had higher sporulation efficiencies than Gcol.A11 (84.5%, 83.8% and 57.0%, respectively), as supported by the greater number of proteins associated with sporulation pathways in the C. tertium genomes compared with the C. paraputrificum genomes (33.3 and 28.4 on average, respectively)", "token_count": 486, "char_count": 1469, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:20.447934", "source": { "split": "train_shard_00001", "doc_id": 3013 }, "chunk_id": "train_shard_00001_3013_0", "global_id": 9933 }, { "text": "This work allowed complete genome description of two clostridiales species revealing high levels of intra-taxa diversity, accessory genomes containing virulence-factors encoding genes (especially in C. paraputrificum), with proteins involved in sporulation processes more highly represented in C. tertium. These finding suggest the need to advance in the study of those species with potential importance at public health level.\n\nComparative genomics identifies potential virulence factors in Clostridium tertium and C. paraputrificum.", "token_count": 142, "char_count": 562, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8286, "quality_score": 0.9143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:20.879375", "source": { "split": "train_shard_00001", "doc_id": 3013 }, "chunk_id": "train_shard_00001_3013_1", "global_id": 9934 }, { "text": "An integrated bioprocess for the production of the natural rose-like aroma compounds, 2-phenylethanol (2-PE) and 2-phenylethylacetate (2-PEAc), from L-phenylalanine (L-phe) with yeasts was investigated. The hydrophobicity of the products leads to product inhibition, which can be compensated by in situ product removal (ISPR). An organophilic pervaporation unit, equipped with a polyoctylmethylsiloxane (POMS) membrane, was coupled via a bypass to a bioreactor and proved to be a suitable technique for the in situ removal of high-boiling products from culture broth. With batch cultures of the thermotolerant yeast Kluyveromyces marxianus CBS 600 in a standard medium at 35 degrees C, the use of pervaporation resulted in a double 2-PE concentration (2.2 g/L) and 1.3 g/L 2-PEAc, which only accumulated transiently in low concentrations during cultivation without ISPR. Using a previously optimized medium, the variation of the temperature from 30 degrees C to 40 degrees C caused an increase in the total conversion yield from 63% to 79%, corresponding to total product concentrations of 5.23 and 5.85 g/L, respectively. In the 40 degrees C batch experiment, the volumetric productivity (2-PE + 2-PEAc) during the exponential phase was 5.2 mmol/L h. While for 2-PE, there is still potential for further optimization, the more hydrophobic 2-PEAc was nearly completely removed from the aqueous culture broth (enrichment factor >400), resulting in highly aroma-enriched permeates. Due to the temperature-correlated performance of the pervaporation, the bioconversion was still efficient even at 45 degrees C (conversion yield: 69%)", "token_count": 464, "char_count": 1630, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:21.524642", "source": { "split": "train_shard_00001", "doc_id": 3014 }, "chunk_id": "train_shard_00001_3014_0", "global_id": 9935 }, { "text": "Surprisingly, at 45 degrees C, the molar ratio of the two products inverted and 2-PEAc turned out to be the main product (4.0 g/L), which opens easy control of the reaction's selectivity by external means. Retrofitting the process with interim heating and cooling equipment to use different temperature levels for cultivation and pervaporation resulted in a decreased yield and product concentration caused by multiple stress factors. The medium composition affected the pervaporation efficiency with molasses acting detrimental.\n\nProduction of 2-phenylethanol and 2-phenylethylacetate from L-phenylalanine by coupling whole-cell biocatalysis with organophilic pervaporation.", "token_count": 171, "char_count": 675, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7912, "quality_score": 0.8956, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:21.963223", "source": { "split": "train_shard_00001", "doc_id": 3014 }, "chunk_id": "train_shard_00001_3014_1", "global_id": 9936 }, { "text": "

Background

Mycoplasma agalactiae, causing agent of contagious agalactia, infects domestic small ruminants such as sheep and goats but also wild Caprinae. M. agalactiae is highly contagious and transmitted through oral, respiratory, and mammary routes spreading rapidly in an infected herd.

Results

In an outbreak of contagious agalactia in a mixed herd of sheep and goats, 80% of the goats were affected displaying swollen udders and loss of milk production but no other symptom such as kerato-conjunctivitis, arthritis or pulmonary distress commonly associated to contagious agalactia. Surprisingly, none of the sheep grazing on a common pasture and belonging to the same farm as the goats were affected. Whole genome sequencing and analysis of M. agalactiae strain GrTh01 isolated from the outbreak, revealed a previously unknown sequence type, ST35, and a particularly small, genome size of 841'635 bp when compared to others available in public databases. Overall, GrTh01 displayed a reduced accessory genome, with repertoires of gene families encoding variable surface proteins involved in host-adhesion and variable antigenicity being scaled down. GrTh01 was also deprived of Integrative Conjugative Element or prophage, and had a single IS element, suggesting that GrTh01 has a limited capacity to adapt and evolve.

Conclusions

The lack of most of the variable antigens and the Integrative Conjugative Element, both major virulence- and host specificity factors of a M. agalactiae strain isolated from an outbreak affecting particularly goats, indicates the implication of these factors in host specificity. Whole genome sequencing and full assembly of bacterial pathogens provides a most valuable tool for epidemiological and virulence studies of M. agalactiae without experimental infections.\n\nMycoplasma agalactiae ST35: a new sequence type with a minimal accessory genome primarily affecting goats.", "token_count": 504, "char_count": 1931, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8114, "entities": { "genes": [ "ST35" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:22.611376", "source": { "split": "train_shard_00001", "doc_id": 3015 }, "chunk_id": "train_shard_00001_3015_0", "global_id": 9937 }, { "text": "Staphylococcus aureus USA300 represents the dominant community-associated methicillin-resistant S. aureus lineage in the USA, where it is a major cause of skin and soft tissue infections. Previous comparative genomic studies have described the population structure and evolution of USA300 based on geographically restricted isolate collections. Here, we investigated the USA300 population by sequencing genomes of a geographically distributed panel of 191 clinical S. aureus isolates belonging to clonal complex 8 (CC8), derived from the Tigecycline Evaluation and Surveillance Trial program. Isolates were collected at 12 healthcare centres across nine USA states in 2004, 2009 or 2010. Reconstruction of evolutionary relationships revealed that CC8 was dominated by USA300 isolates (154/191, 81 %), which were heterogeneous and demonstrated limited phylogeographic clustering. Analysis of the USA300 core genomes revealed an increase in median pairwise SNP distance from 62 to 98 between 2004 and 2010, with a stable pattern of above average dN/dS ratios. The phylogeny of the USA300 population indicated that early diversification events led to the formation of nested clades, which arose through cumulative acquisition of predominantly non-synonymous SNPs in various coding sequences. The accessory genome of USA300 was largely homogenous and consisted of elements previously associated with this lineage. We observed an emergence of SCCmec negative and ACME negative USA300 isolates amongst more recent samples, and an increase in the prevalence of ϕSa5 prophage. Together, the analysed S. aureus USA300 collection revealed an evolving pan-genome through increased core genome heterogeneity and temporal variation in the frequency of certain accessory elements.", "token_count": 490, "char_count": 1815, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8353, "entities": { "genes": [ "USA300", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:23.261945", "source": { "split": "train_shard_00001", "doc_id": 3016 }, "chunk_id": "train_shard_00001_3016_0", "global_id": 9938 }, { "text": "Pan-genomic perspective on the evolution of the Staphylococcus aureus USA300 epidemic.", "token_count": 32, "char_count": 93, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [ "USA300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:23.615063", "source": { "split": "train_shard_00001", "doc_id": 3016 }, "chunk_id": "train_shard_00001_3016_1", "global_id": 9939 }, { "text": "Bioactive peptides are widely used in functional foods due to their remarkable efficacy, selectivity, and low toxicity. However, commercially produced bioactive peptides lack quality stability between batches. Furthermore, the efficacies of bioactive peptides cannot be guaranteed in vivo due to gastrointestinal digestion and rapid plasma, liver, and kidney metabolism. The problem of poor stability has restricted the development of peptides. Bioactive peptide stability assessments use different stability assays, so the results of different studies are not always comparable. This review summarizes the quality stability challenges in the enzymatic hydrolysis production of bioactive peptides and the metabolism stability challenges after oral administration. Future directions on the strategies for improving their stability are provided. It was proposed that we use fingerprinting as a quality control measure using qualitative and quantitative characteristic functional peptide sequences. The chemical modification and encapsulation of bioactive peptides in microcapsules and liposomes are widely used to improve the digestive and metabolic stability of bioactive peptides. Additionally, the establishment of a universal stability test and a unified index would greatly improve uniformity and comparability in research into bioactive peptides. In summary, the reliable evaluation of stability is an essential component of peptide characterization, and these ideas may facilitate further development and utilization of bioactive peptides.\n\nAdvances in the stability challenges of bioactive peptides and improvement strategies.", "token_count": 329, "char_count": 1639, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:24.178205", "source": { "split": "train_shard_00001", "doc_id": 3017 }, "chunk_id": "train_shard_00001_3017_0", "global_id": 9940 }, { "text": "Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two F. oxysporum strains share a core genome of about 46 Mb, in addition to 1,229 and 5,415 unique accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (about 80%) in responding to both fungal inoculums at all timepoints from 12 to 96 h postinoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses functions related to plant growth and development, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest timepoint sampled, and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.\n\nMetatranscriptomic Comparison of Endophytic and Pathogenic Fusarium-Arabidopsis Interactions Reveals Plant Transcriptional Plasticity.", "token_count": 450, "char_count": 1740, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:24.821044", "source": { "split": "train_shard_00001", "doc_id": 3018 }, "chunk_id": "train_shard_00001_3018_0", "global_id": 9941 }, { "text": "Pangenome analyses facilitate the interpretation of genetic diversity and evolutionary history of a taxon. However, there is an urgent and unmet need to develop new tools for advanced pangenome construction and visualization, especially for metagenomic data. Here we present an integrated pipeline, named MetaPGN, for construction and graphical visualization of pangenome network from either microbial genomes or metagenomes. Given either isolated genomes or metagenomic assemblies coupled with a reference genome of the targeted taxon, MetaPGN generates a pangenome in a topological network, consisting of genes (nodes) and gene-gene genomic adjacencies (edges) of which biological information can be easily updated and retrieved. MetaPGN also includes a self-developed Cytoscape plugin for layout of and interaction with the resulting pangenome network, providing an intuitive and interactive interface for full exploration of genetic diversity. We demonstrate the utility of MetaPGN by constructing Escherichia coli ( E. coli ) pangenome networks from five E. coli pathogenic strains and 760 human gut microbiomes respectively, revealing extensive genetic diversity of E. coli within both isolates and gut microbial populations. With the ability to extract and visualize gene contents and gene-gene physical adjacencies of a specific taxon from large-scale metagenomic data, MetaPGN provides advantages in expanding pangenome analysis to uncultured microbial taxa. MetaPGN is available at https://github.com/peng-ye/MetaPGN .\n\nMetaPGN: a pipeline for construction and graphical visualization of annotated pangenome networks", "token_count": 367, "char_count": 1626, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:25.397028", "source": { "split": "train_shard_00001", "doc_id": 3019 }, "chunk_id": "train_shard_00001_3019_0", "global_id": 9942 }, { "text": "Enterococcus faecalis , a major nosocomial pathogen, has become a top leading cause of hospital-acquired infections including urinary tract infections, endocarditis and bacteremia. It is important to study the epidemiology and virulence characteristics of E. faecalis isolates in order to tailor infection prevention and antibiotic prescribing. In this study, comparative genomic analysis was conducted on 537 isolates from different human origins. The isolates from bloodstream and intra-abdominal lining had the largest and smallest average genome size respectively, while the isolates from open natural orifices (gastrointestinal tract, urinary tract, respiratory tract, wound and eye) had medium average genome size. The phylogenetic relationships were expounded that the strain isolation niche is uncorrelated with strain phylogeny. Six clonal complexes generally appeared in different isolation sources. Furthermore, genomic analysis revealed differences at the accessory genome, the functions of different genes mainly pointed to the virulence, drug resistance and metabolism of E. faecalis . Interestingly, fsr quorum sensing system genes affecting biofilm formation had a highest proportion in the blood-derived strains. This study showed the genomic characteristics of different human origins and suggested that fsr quorum-sensing system maybe a contributing factor of bacteremia due to E. faecalis infection.\n\nThe Virulence Associated fsr Quorum Sensing System Play Key Roles in Enterococcus Faecalis", "token_count": 344, "char_count": 1511, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:25.971774", "source": { "split": "train_shard_00001", "doc_id": 3020 }, "chunk_id": "train_shard_00001_3020_0", "global_id": 9943 }, { "text": "

Background

Morganella spp are opportunistic pathogens involved in various infections. Intrinsic resistance to multiple antibiotics (including colistin) combined with the emergence of carbapenemase producers reduces the number of active antimicrobials. The aim of this study was to characterise genetic features related to the spread of carbapenem-resistant Morganella spp.

Methods

This comparative genomic study included extensively drug-resistant Morganella spp isolates collected between Jan 1, 2013, and March 1, 2021, by the French National Reference Center (NRC; n=68) and European antimicrobial resistance reference centres in seven European countries (n=104), as well as one isolate from Canada, two reference strains from the Pasteur Institute collection (Paris, France), and two colistin-susceptible isolates from Bicêtre Hospital (Kremlin-Bicêtre, France). The isolates were characterised by whole-genome sequencing, antimicrobial susceptibility testing, and biochemical tests. Complete genomes from GenBank (n=103) were also included for genomic analysis, including phylogeny and determination of core genomes and resistomes. Genetic distance between different species or subspecies was performed using average nucleotide identity (ANI). Intrinsic resistance mechanisms to polymyxins were investigated by combining genetic analysis with mass spectrometry on lipid A.

Findings

Distance analysis by ANI of 275 isolates identified three groups: Morganella psychrotolerans, Morganella morganii subspecies sibonii, and M morganii subspecies morganii, and a core genome maximum likelihood phylogenetic tree showed that the M morganii isolates can be separated into four subpopulations. On the basis of these findings and of phenotypic divergences between isolates, we propose a modified taxonomy for the Morganella genus including four species, Morganella psychrotolerans, Morganella sibonii, Morganella morganii, and a new species represented by a unique environmental isolate", "token_count": 499, "char_count": 2004, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:26.637484", "source": { "split": "train_shard_00001", "doc_id": 3021 }, "chunk_id": "train_shard_00001_3021_0", "global_id": 9944 }, { "text": "We propose that M morganii include two subspecies: M morganii subspecies morganii (the most prevalent) and M morganii subspecies intermedius. This modified taxonomy was supported by a difference in intrinsic resistance to tetracycline and conservation of metabolic pathways such as trehalose assimilation, both only present in M sibonii. Carbapenemase producers were mostly identified among five high-risk clones of M morganii subspecies morganii. The most prevalent carbapenemase corresponded to NDM-1, followed by KPC-2, and OXA-48. A cefepime-zidebactam combination was the most potent antimicrobial against the 172 extensively drug-resistant Morganella spp isolates in our collection from different European countries, which includes metallo-β-lactamase producers. Lipid A analysis showed that the intrinsic resistance to colistin was associated with the presence of L-ARA4N on lipid A.

Interpretation

This global characterisation of, to our knowledge, the widest collection of extensively drug-resistant Morganella spp highlights the need to clarify the taxonomy and decipher intrinsic resistance mechanisms, and paves the way for further genomic comparisons.

Funding

None.\n\nSpread of carbapenemase-producing Morganella spp from 2013 to 2021: a comparative genomic study.", "token_count": 354, "char_count": 1290, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [ "ARA4N" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:27.244233", "source": { "split": "train_shard_00001", "doc_id": 3021 }, "chunk_id": "train_shard_00001_3021_1", "global_id": 9945 }, { "text": "Dehalococcoidia (Dia) class microorganisms are frequently found in various pristine and contaminated environments. Metagenome-assembled genomes (MAGs) and single-cell amplified genomes (SAGs) studies have substantially improved the understanding of Dia microbial ecology and evolution; however, an updated thorough investigation on the genomic and evolutionary characteristics of Dia microorganisms distributed in geographically distinct environments has not been implemented. In this study, we analyzed available genomic data to unravel Dia evolutionary and metabolic traits. Based on the phylogeny of 16S rRNA genes retrieved from sixty-seven genomes, Dia microorganisms can be categorized into three groups, the terrestrial cluster that contains all Dehalococcoides and Dehalogenimonas strains, the marine cluster I, and the marine cluster II. These results reveal that a higher ratio of horizontally transferred genetic materials was found in the Dia marine clusters compared to that of the Dia terrestrial cluster. Pangenome analysis further suggests that Dia microorganisms have evolved cluster-specific enzymes (e.g., dehalogenase in terrestrial Dia, sulfite reductase in marine Dia) and biosynthesis capabilities (e.g., siroheme biosynthesis in marine Dia). Marine Dia microorganisms are likely adapted to versatile metabolisms for energy conservation besides organohalide respiration. The genomic differences between marine and terrestrial Dia may suggest distinct functions and roles in element cycling (e.g., carbon, sulfur, chlorine), which require interdisciplinary approaches to unravel the physiology and evolution of Dia in various environments.", "token_count": 492, "char_count": 1780, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:27.934059", "source": { "split": "train_shard_00001", "doc_id": 3022 }, "chunk_id": "train_shard_00001_3022_0", "global_id": 9946 }, { "text": "Genomic Characteristics Distinguish Geographically Distributed Dehalococcoidia.", "token_count": 24, "char_count": 86, "word_count": 6, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:28.299702", "source": { "split": "train_shard_00001", "doc_id": 3022 }, "chunk_id": "train_shard_00001_3022_1", "global_id": 9947 }, { "text": "The eradication of Helicobacter pylori (H. pylori) using multiple therapies is used as a prevention strategy. However, its efficacy has been compromised by the emergence of single nucleotide polymorphisms in genes associated with H. pylori's resistance to multiple antibiotics. To estimate antibiotic resistance rates associated with mutations in H. pylori genes in the high-cancer-risk population in Colombia, we included 166 H. pylori whole genome sequences from a cohort of individuals with a high risk of gastric cancer. By using the reference strain ATCC 26695, we identified mutations in specific genes to evaluate resistance rates for different antibiotics: 23S rRNA for clarithromycin, 16S rRNA for tetracycline, pbp1A for amoxicillin, gyrA for levofloxacin, and rdxA for metronidazole. The phylogenomic analysis was conducted using the core genome consisting of 1,594 genes of H. pylori-ATCC 26695. Our findings revealed that the resistance rate of H. pylori to clarithromycin was 3.62%, primarily associated with mutations A2143G and A2142G in the 23S rRNA gene. For tetracycline, the resistance rate was 7.23%, with mutations A926G, A926T, and A928C observed in the 16S rRNA gene. Amoxicillin resistance was found in 25.9% of cases, with observed mutations in the pbp1A gene, including T556S, T593, R649K, R656P, and R656H", "token_count": 514, "char_count": 1438, "word_count": 199, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:28.930055", "source": { "split": "train_shard_00001", "doc_id": 3023 }, "chunk_id": "train_shard_00001_3023_0", "global_id": 9948 }, { "text": "In the gyrA gene, mutations N87K, N87I, D91G, D91N, and D91Y were identified, resulting in a resistance rate of 12.04% to levofloxacin. The most common mutations in the rdxA gene associated with metronidazole resistance were a stop codon, and mutations at D59N and D59S, resulting in a resistance rate of 99.3%. The high resistance rate of H. pylori to metronidazole indicated that this drug should be excluded from the eradication therapy. However, the resistance rates for tetracycline and clarithromycin did not exceed the established resistance threshold in Colombia. The increased resistance rate of H. pylori to levofloxacin and amoxicillin may partially explain the observed therapeutic failures in Colombia. The phylogenomic tree showed that the H. pylori isolate belongs to its own lineage (hspColombia). These findings offer valuable insights to enhance the characterization of treatment protocols for the specific H. pylori lineage (hspColombia) at the local level.\n\nThe Helicobacter pylori single nucleotide polymorphisms SNPs associated with multiple therapy resistance in Colombia.", "token_count": 336, "char_count": 1144, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:29.503240", "source": { "split": "train_shard_00001", "doc_id": 3023 }, "chunk_id": "train_shard_00001_3023_1", "global_id": 9949 }, { "text": "The maize pangenome has demonstrate large amounts of presence/absence variation and it has been hypothesized that presence/absence variation contributes to stress response. To uncover whether the observed genetic variation in physiological response to elevated ozone (a secondary air pollutant that causes significant crop yield losses) concentration is due to variation in genic content, and/or variation in gene expression, we examine the impact of sustained elevated ozone concentration on the leaf tissue from 5 diverse maize inbred genotypes (B73, Mo17, Hp301, C123, NC338). Analysis of long reads from the transcriptomes of the 10 conditions found expressed genes in the leaf are part of the shared genome, with 94.5% of expressed genes from syntenic loci. Quantitative analysis of short reads from 120 plants (twelve from each condition) found limited transcriptional response to sustained ozone stress in the ozone resistant B73 genotype (151 genes), while more than 3,300 genes were significantly differentially expressed in the more sensitive NC338 genotype. The genes underpinning the divergence of B73 from the other 4 genotypes implicates ethylene signaling consistent with some findings in Arabidopsis. For the 82 of the 83 genes differentially expressed among all 5 genotypes and the 788 of 789 genes differentially expressed in 4 genotypes (excluding B73) in sensitivity to ozone is associated with oxidative stress tolerance being associated with a weaker response to a reactive oxygen species (ROS) signal and suggests that genetic variation in downstream processes is key to ozone tolerance.\n\nOzone sensitivity of diverse maize genotypes is associated with differences in gene regulation, not gene content", "token_count": 412, "char_count": 1724, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5647, "quality_score": 0.7824, "entities": { "genes": [ "NC338" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:30.128001", "source": { "split": "train_shard_00001", "doc_id": 3024 }, "chunk_id": "train_shard_00001_3024_0", "global_id": 9950 }, { "text": "Staphylococcus haemolyticus is a major cause of late-onset sepsis in neonates, and endemic clones are often multidrug-resistant. The bacteria can also act as a genetic reservoir for more pathogenic bacteria. Molecular epidemiology is important in understanding bacterial pathogenicity and preventing infection. To describe the molecular epidemiology of S. haemolyticus isolated from neonatal blood cultures at a Swedish neonatal intensive care unit (NICU) over 4 decades, including antibiotic resistance genes (ARGs), virulence factors, and comparison to international isolates. Isolates were whole-genome sequenced, and single nucleotide polymorphisms in the core genome were used to map the relatedness. The occurrence of previously described ARGs and virulence genes were investigated. Disc diffusion and gradient tests were used to determine phenotypic resistance. The results revealed a clonal outbreak of S. haemolyticus at this NICU during the 1990s. Multidrug resistance was present in 28 (82%) of all isolates and concomitant resistance to aminoglycoside and methicillin occurred in 27 (79%). No isolates were vancomycin resistant. Genes encoding ARGs and virulence factors occurred frequently. The isolates in the outbreak were more homogenous in their genotypic and phenotypic patterns. Genotypic and phenotypic resistance combinations were consistent. Pathogenic traits previously described in S. haemolyticus occurred frequently in the present isolates, perhaps due to the hospital selection pressure resulting in epidemiological success. The clonal outbreak revealed by this study emphasizes the importance of adhering to hygiene procedures in order to prevent future endemic outbreaks. IMPORTANCE This study investigated the relatedness of Staphylococcus haemolyticus isolated from neonatal blood and revealed a clonal outbreak in the 1990s at a Swedish neonatal intensive care unit. The outbreak clone has earlier been isolated in Japan and Norway. Virulence and antibiotic resistance genes previously associated with clinical S", "token_count": 516, "char_count": 2075, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5603, "quality_score": 0.7801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:30.784616", "source": { "split": "train_shard_00001", "doc_id": 3025 }, "chunk_id": "train_shard_00001_3025_0", "global_id": 9951 }, { "text": "haemolyticus were frequently occuring in the present study as well. The majority of the isolates were multidrug-resistant. These traits should be considered important for S. haemolyticus epidemiological success and are probably caused by the hospital selection pressure. Thus, this study emphasizes the importance of restrictive antibiotic use and following the hygiene procedures, to prevent further antibiotic resistance spread and future endemic outbreaks.\n\nMolecular Epidemiology of Neonatal-Associated Staphylococcus haemolyticus Reveals Endemic Outbreak.", "token_count": 140, "char_count": 571, "word_count": 71, "semantic_coherence": 1, "information_density": 0.8028, "quality_score": 0.9014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:31.218060", "source": { "split": "train_shard_00001", "doc_id": 3025 }, "chunk_id": "train_shard_00001_3025_1", "global_id": 9952 }, { "text": "

Introduction

Whole genome sequencing (WGS) was introduced into Swiss antimicrobial resistance monitoring in 2022 as an additional method to phenotypic antimicrobial susceptibility testing by broth microdilution to characterize presumptive third-generation cephalosporin-resistant (3GC-R) Escherichia coli. Caecal samples from Swiss slaughter calves and fattening pigs, as well as beef and pork meat from Swiss retail taken in 2021, were analyzed for the presence of 3GC-R E. coli according to European harmonized protocols. In 2021, 3GC-R E. coli was detected in 23,8 % of slaughter calves, 5,9 % of fattening pigs, and 0 % of meat. Comparative analysis of the antimicrobial resistance results obtained by phenotypic measurement and those obtained by the detection of corresponding underlying molecular mechanisms by WGS showed very high agreement (99 %). Resistance to third-generation cephalosporins (3GCs) was mainly associated with the presence of blaCTX-M-15 in E. coli isolates from calves and blaCTX-M-1 in E. coli isolates from pigs and mutations in the ampC-promoter (g.-42 C>T) in E. coli isolates from both animal species. Moreover, WGS data were used for phylogenetic analysis based on multi locus sequence types (MLST) and core genome MLST(cgMLST) revealing that 3GC-R E. coli isolated from Swiss slaughter calves and fattening pigs were genetically diverse. In this study, it was shown that using WGS alone to monitor antimicrobial resistance could detect trends in known molecular antimicrobial resistance mechanisms while also providing other valuable information about the isolates, such as genetic relatedness. However, only by combining phenotypic susceptibility testing and WGS early detection of previously unknown resistance mechanisms will be possible.", "token_count": 488, "char_count": 1783, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:31.866297", "source": { "split": "train_shard_00001", "doc_id": 3026 }, "chunk_id": "train_shard_00001_3026_0", "global_id": 9953 }, { "text": "Characterization of third-generation cephalosporin-resistant Escherichia coli from slaughter calves and fattening pigs: A pilot study for monitoring antimicrobial resistance by whole genome sequencing in Switzerland.", "token_count": 54, "char_count": 216, "word_count": 25, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:32.230989", "source": { "split": "train_shard_00001", "doc_id": 3026 }, "chunk_id": "train_shard_00001_3026_1", "global_id": 9954 }, { "text": "Coagulase-negative Staphylococcus (CoNS) is the most common pathogen causing traumatic endophthalmitis, Staphylococcus epidermidis is the most common species which colonizes human skin, eye surfaces and nasal cavity and is the main cause of nosocomial infection, specially foreign body-related bloodstream infections (FBR-BSIs). Although some studies have reported the genome characteristics of S. epidermidis , a comprehensive understanding of its pathogenicity and the genome of ocular trauma-sourced strains is still lacking. In this study, we sequenced, analyzed and reported the whole genomes of 11 ocular trauma-sourced samples of S. epidermidis that caused traumatic endophthalmitis. By integrating publicly available genomes, we obtained a total of 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract and blood. Combined with pangenome, phylogenetic and comparative genomic analyses, our study supported that S. epidermidis , regardless of niche source, exhibits two founder lineages with different pathogenicities. Moreover, we identified potential biomarkers associated with the virulence of S. epidermidis , namely, essD , uhpt , sdrF , sdrG , fbe and icaABCDR . The essD and uhpt genes have high homology with esaD and hpt in Staphylococcus aureus , showing that the genomes of S. epidermidis and S. aureus may have communicated during evolution, while the sdrF , sdrG , fbe , and icaABCDR genes are related to biofilm formation. Compared to S. epidermidis from blood sources, ocular-sourced strains causing intraocular infection had no direct relationship with biofilm formation. In conclusion, this study not only provided additional data resources for studies on S. epidermidis is, but also improved understanding of the evolution and pathogenicity of different source strains.

Importants

In this study, we comprehensively analysied and reported the whole genome sequence (WGS) of the strains that caused traumatic endophthalmitis", "token_count": 516, "char_count": 1985, "word_count": 284, "semantic_coherence": 1, "information_density": 0.5704, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:32.862282", "source": { "split": "train_shard_00001", "doc_id": 3027 }, "chunk_id": "train_shard_00001_3027_0", "global_id": 9955 }, { "text": "Through comparative genomic analyses among 187 S. epidermidis samples from healthy and diseased eyes, skin, respiratory tract and blood, we identified 10 potential biomarkers of pathogenic strains. Finally, we revealed S. epidermidis -induced traumatic endophthalmitis may be independent of biofilm formation. Overall, our data may facilitate comparative research of S. epidermidis and provide clinical value for identifying pathogenic or contaminating strains.\n\nComparative genomic and pan-genomic characteristion of Staphylococcus epidermidis from different sources unveils the molecular basis and potential biomarkers of pathogenic strains", "token_count": 165, "char_count": 649, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7195, "quality_score": 0.8598, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:33.313301", "source": { "split": "train_shard_00001", "doc_id": 3027 }, "chunk_id": "train_shard_00001_3027_1", "global_id": 9956 }, { "text": "Leptospirosis is a widespread zoonosis caused by spirochaetes belonging to the pathogenic species of Leptospira, which are classified into more than 25 serogroups and 250 serovars. Vaccination can prevent the disease in dogs but offers incomplete efficacy because of a lack of cross-protection between serogroups. The aim of this study was to validate a robust recruitment and sampling process, with the objectives of isolating and typing circulating Leptospira pathogenic strains and then selecting those of proven virulence and pathogenicity for vaccine development. Blood and urine samples from dogs with clinical syndromes compatible with acute leptospirosis were sterilely collected and transported to a reference laboratory for a micro-agglutination test (MAT), PCR, and bacterial isolation. Isolated strains underwent molecular typing using RNA16S, variable-number tandem repeat (VNTR), and pulsed-field gel electrophoresis (PFGE). Subtyping was performed using core genome multilocus sequence typing (CgMLST). Among 64 included dogs, 41 had MAT and/or PCR results compatible with Leptospira infection, and 14 Leptospira strains were isolated. Based on molecular typing, 11 isolates were classified as L. interrogans serogroup Australis, serovar Bratislava, and 3 as serogroup Icterohaemorrhagiae, serovar Icterohaemorrhagiae. CgMLST subtyping revealed a diversity of clonal groups (CGs) distributed in several regional clusters. Besides validating a robust recruitment and sampling process, this study outlines the value of combining PCR and serological testing when suspecting leptospirosis and the usefulness of implementing molecular typing methods to identify circulating field strains. It also confirms the epidemiological importance of the Australis serogroup and allows for the collection of different highly pathogenic strains for vaccine development.", "token_count": 493, "char_count": 1902, "word_count": 253, "semantic_coherence": 1, "information_density": 0.668, "quality_score": 0.834, "entities": { "genes": [ "RNA16S" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:33.961397", "source": { "split": "train_shard_00001", "doc_id": 3028 }, "chunk_id": "train_shard_00001_3028_0", "global_id": 9957 }, { "text": "Isolation of Virulent Leptospira Serogroup Australis Field Strains from Symptomatic Dogs for Canine Leptospiral Vaccine Development.", "token_count": 42, "char_count": 139, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:34.325479", "source": { "split": "train_shard_00001", "doc_id": 3028 }, "chunk_id": "train_shard_00001_3028_1", "global_id": 9958 }, { "text": "BackgroundSince the beginning of the war in Ukraine in February 2022, Ukrainians have been seeking shelter in other European countries.AimWe aimed to investigate the prevalence and the molecular epidemiology of multidrug-resistant Gram-negative (MDRGN) bacteria and meticillin-resistant Staphylococcus aureus (MRSA) in Ukrainian patients at admittance to the University Hospital Frankfurt, Germany.MethodsWe performed screening and observational analysis of all patients from March until June 2022. Genomes of MDRGN isolates were analysed for antimicrobial resistance, virulence genes and phylogenetic relatedness.ResultsWe included 103 patients (median age: 39 ± 23.7 years), 57 of whom were female (55.3%; 95% confidence interval (CI): 45.2-5.1). Patients were most frequently admitted to the Department of Paediatrics (29/103; 28.2%; 95% CI: 19.7-37.9). We found 34 MDRGN isolates in 17 of 103 patients (16.5%; 95% CI: 9.9-25.1). Ten patients carried 21 carbapenem-resistant (CR) bacteria, five of them more than one CR isolate. Four of six patients with war-related injuries carried eight CR isolates. In six of 10 patients, CR isolates caused infections. Genomic characterisation revealed that the CR isolates harboured at least one carbapenemase gene, bla NDM-1 being the most frequent (n = 10). Core genome and plasmid analysis revealed no epidemiological connection between most of these isolates. Hypervirulence marker genes were found in five of six Klebsiella pneumoniae CR isolates", "token_count": 478, "char_count": 1525, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:34.972933", "source": { "split": "train_shard_00001", "doc_id": 3029 }, "chunk_id": "train_shard_00001_3029_0", "global_id": 9959 }, { "text": "No MRSA was found.ConclusionHospitals should consider infection control strategies to cover the elevated prevalence of MDRGN bacteria in Ukrainian patients with war-related injuries and/or hospital pre-treatment and to prevent the spread of hypervirulent CR isolates.\n\nMolecular surveillance of multidrug-resistant Gram-negative bacteria in Ukrainian patients, Germany, March to June 2022.", "token_count": 92, "char_count": 389, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8367, "quality_score": 0.9184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:35.352577", "source": { "split": "train_shard_00001", "doc_id": 3029 }, "chunk_id": "train_shard_00001_3029_1", "global_id": 9960 }, { "text": "Acinetobacter baumannii is especially known as a cause of nosocomial infections worldwide. It shows intrinsic and acquired resistances to numerous antimicrobial agents, which can render the treatment difficult. In contrast to the situation in human medicine, there are only few studies focusing on A. baumannii among livestock. In this study, we have examined 643 samples from turkeys reared for meat production, including 250 environmental and 393 diagnostic samples, for the presence of A. baumannii. In total, 99 isolates were identified, confirmed to species level via MALDI-TOF-MS and characterised with pulsed-field gel electrophoresis. Antimicrobial and biocide susceptibility was tested by broth microdilution methods. Based on the results, 26 representative isolates were selected and subjected to whole-genome sequencing (WGS). In general, A. baumannii was detected at a very low prevalence, except for a high prevalence of 79.7% in chick-box-papers (n = 118) of one-day-old turkey chicks. The distributions of the minimal inhibitory concentration values were unimodal for the four biocides and for most of the antimicrobial agents tested. WGS revealed 16 Pasteur and 18 Oxford sequence types, including new ones. Core genome MLST highlighted the diversity of most isolates. In conclusion, the isolates detected were highly diverse and still susceptible to many antimicrobial agents.\n\nAcinetobacter baumannii from Samples of Commercially Reared Turkeys: Genomic Relationships, Antimicrobial and Biocide Susceptibility.", "token_count": 424, "char_count": 1563, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:35.980695", "source": { "split": "train_shard_00001", "doc_id": 3030 }, "chunk_id": "train_shard_00001_3030_0", "global_id": 9961 }, { "text": "

ABSTRACT

Multicellular animals and bacteria frequently engage in predator-prey and host-pathogen interactions, such as the well-studied relationship between Pseudomonas aeruginosa and the nematode Caenorhabditis elegans . This study investigates the genomic and genetic basis of bacterial-driven variability in P. aeruginosa virulence towards C. elegans . Natural isolates of P. aeruginosa that exhibit diverse genomes display a broad range of virulence towards C. elegans . Using gene association and genetic analysis, we identified accessory genome elements that correlate with virulence, including both known and novel virulence determinants. Among the novel genes, we found a viral-like mobile element, the teg block, that impairs virulence and whose acquisition is restricted by CRISPR-Cas systems. Further genetic and genomic evidence suggests that spacer-targeted elements preferentially associate with lower virulence and suggest a positive, albeit indirect, role for host CRISPR-Cas systems in the restriction of accessory genome elements that may be detrimental to virulence.\n\nThePseudomonas aeruginosaaccessory genome elements influence virulence towardsCaenorhabditis elegans", "token_count": 299, "char_count": 1210, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:36.545742", "source": { "split": "train_shard_00001", "doc_id": 3031 }, "chunk_id": "train_shard_00001_3031_0", "global_id": 9962 }, { "text": "Six pure microbial strains, Kluyveromyces marxianus BD01004, Lactobacillus delbruekii ssp. bulgaricus BD00014, Lactobacillus kefiri BD00002, Streptococcus thermophilus BD00089, Lactococcus lactis BD00736 and Leuconostoc mesenteroides BD01701, previously isolated in our laboratory from diverse sources, were combined in different proportions for the formulation of defined starter cultures for the production of kefir-like beverages in 10% (w/w) reconstituted skim milk. The physicochemical properties of products obtained were analysed by high performance liquid chromatography for ethanol, lactose and lactic acid contents, and by gas chromatography–mass spectrometry for determination of volatile compounds. A comparative study of these products with kefir was further undertaken with the purpose of determining suitable starter culture combinations for production of kefir-like beverages. The results indicated that some of the starter cultures devised were consistent with the production of beverages with characteristics approximating to those of traditional kefir as reported in the literature.\n\nA novel approach of direct formulation of defined starter cultures for different kefir-like beverage production", "token_count": 321, "char_count": 1214, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6688, "quality_score": 0.8344, "entities": { "genes": [ "BD01004", "BD00089", "BD00002", "BD00014", "BD00736", "BD01701" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:37.107914", "source": { "split": "train_shard_00001", "doc_id": 3032 }, "chunk_id": "train_shard_00001_3032_0", "global_id": 9963 }, { "text": "

Background

Carbapenem resistant organisms (CROs) such as Acinetobacter baumannii (CRAb), Pseudomonas aeruginosa (CRPa), Escherichia coli (CREc), and Klebsiella pneumoniae (CRKp) have been identified by the World Health Organization (WHO) as global priority pathogens. The dissemination of these pathogens and clonal outbreaks within healthcare facilities are of serious concern, particularly in regions with limited resources. In Fiji, where healthcare services are primarily provided by public hospitals, understanding the extent and nature of this problem is essential for the development of effective patient management, prevention interventions and control strategies.

Methods

CROs isolated from 211 (77.3%) non-sterile (urinary catheters, urine, sputum, wound swab, and endotracheal tube) and 62 (22.7%) normally sterile (blood, cerebrospinal fluid, intravascular catheter, and aspirates) body sites of 272 patients treated at the three major hospitals in Fiji, the Colonial War Memorial Hospital (CWMH), Lautoka Hospital (LTKH), and Labasa Hospital (LBSH), and outer peripheral health centres around Fiji, were analysed. Clinical and demographic patient data such as age, sex, admission diagnosis, admission and discharge dates, patient outcomes, date of death, start and end date of meropenem and colistin treatment were reviewed. These CRO isolates comprised A. baumannii, P. aeruginosa, E. coli, and K. pneumoniae, that were prospectively collected at the microbiology laboratory of CWMH and LBSH from January 2020 through August 2021 and at the LTKH from January 2020 to December 2021", "token_count": 511, "char_count": 1693, "word_count": 219, "semantic_coherence": 1, "information_density": 0.7443, "quality_score": 0.8721, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:37.777454", "source": { "split": "train_shard_00001", "doc_id": 3033 }, "chunk_id": "train_shard_00001_3033_0", "global_id": 9964 }, { "text": "In addition, 10 retrospectively stored CRPa isolates collected from patients at the CWMH from January through December 2019, were also included in the study. All isolates were characterised using mass spectrometry, antimicrobial susceptibility testing, and whole genome sequencing. Phylogenetic relationships among the CROs were assessed through core genome single nucleotide polymorphism (SNP) analysis. The CRAb isolates were also compared to the CRAb isolates from CWMH isolated in 2016/2017 and 2019, along with CRAb isolates obtained from Fijian patients admitted to New Zealand hospitals in 2020 and 2021 from our retrospective study.

Findings

Of 272 patients, 140 (51.5%) were male, the median (range) age of patients was 45 (<1-89) years, 161 (59.2%) were I-Taukei, 104 (38.2%) Fijians of Indian descent, and 7 (2.6%) were from other ethnic backgrounds. 234 (86.0%) of these 272 patients, had their first positive CRO sample collected ≥72 h following admission and the remaining 38 (14.0%) were isolated within 72 h following admission. Of the 273 CROs, 146 (53.5%) were collected at the CWMH, 66 (24.2%) LTKH, and 61 (22.3%) LBSH, while 62 (22.7%) were isolated from normally sterile sites and 211 (77.3%) from sites that are not sterile", "token_count": 446, "char_count": 1281, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8395, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:38.452109", "source": { "split": "train_shard_00001", "doc_id": 3033 }, "chunk_id": "train_shard_00001_3033_1", "global_id": 9965 }, { "text": "Of 273 isolates, 131 (48.0%) were CRAb, 90 (33.0%) CRPa, 46 (16.8%) CREc, and 6 (2.2%) CRKp. Of 131 CRAb, 108 (82.4%) were ST2, with three distinct clones, all encoding bla OXA-23 and bla OXA - 66, while clone 3 also encoded bla NDM-1; bla OXA-23 was associated with two copies of ISAba1 insertion element, forming the composite transposon Tn2006. The first two CRAb ST2 clones were genetically linked to those isolated at CMWH 2016 through 2019, while the third was genetically linked to isolates from Fijian patients admitted to New Zealand hospitals in 2020 and 2021. Of CRPa, 65 (72.2%) were ST773 and carried β-lactamase genes bla NDM-1, bla OXA-50, and bla OXA-395. Of 10 retrospective CRPa isolates, all belonged to CRPa ST773 and carried bla NDM-1, bla OXA-50, and bla OXA-395", "token_count": 513, "char_count": 1063, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6692, "quality_score": 0.8346, "entities": { "genes": [ "ST2", "ST773" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:39.124768", "source": { "split": "train_shard_00001", "doc_id": 3033 }, "chunk_id": "train_shard_00001_3033_2", "global_id": 9966 }, { "text": "Of 46 CREc, 44 (95.7%) were ST410 and encoded bla NDM-7 on an IncX3 plasmid. Of 6 CRKp, 4 (66.7%) were ST16 and carried bla NDM-5 on an IncX3 plasmid. Other sequence types of CRPa (ST9, ST357, ST654, ST664), CRAb (ST25, ST374, ST499), CREc (ST167), and CRKp (ST45, ST336) were also detected. Of those receiving meropenem treatment in the prospective study, 30 (57.7%) received it inappropriately. Of 272 patients, 65 (23.9%) died within the 30 days after first positive CRO isolation.

Interpretation

We identified nosocomial transmission of distinct clones of CRAb ST2, CRPa ST773, CREc ST410, and CRKp ST16 within and between the three major hospitals in Fiji. Moreover, community onset infections associated with CRPa, CREc, and CRAb were also detected. Of note, cross-border transmission of CRAb ST2 clone 3 strain between Fiji and New Zealand was also detected. These clones encoded an array of carbapenem resistance genes associated with mobile genetic elements, including plasmids, transposons, and integrative and conjugative elements, signifying their potential for increased mobility, further acquisition of resistance genes, and spread. Inappropriate use of meropenem was common. Of note, the majority of patients who died had acquired CRO during their hospital stay", "token_count": 499, "char_count": 1417, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6736, "quality_score": 0.8368, "entities": { "genes": [ "ST410", "ST167", "ST2", "ST773", "ST25", "ST45", "ST664", "ST357", "ST374", "ST16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:39.809452", "source": { "split": "train_shard_00001", "doc_id": 3033 }, "chunk_id": "train_shard_00001_3033_3", "global_id": 9967 }, { "text": "These findings highlight the need for stringent IPC strategies focusing on catheter and ventilator management, meticulous wound care, rigorous sepsis control, consistent hand hygiene, effective use of disinfectants, and thorough sanitisation of both hospital environments and medical equipment in the three major hospitals in Fiji. Additionally, diligent surveillance of AMR and robust antimicrobial stewardship are crucial for effectively managing nosocomial infections.

Funding

This project was funded by the Otago Medical School Foundations Trust (Dean's Bequest Fund) and a Fiji National University seed grant. The funders of the study had no role in the study design, data collection, data analysis, data interpretation, or writing of the report.\n\nMolecular and clinical epidemiology of carbapenem resistant Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacterales in Fiji: a multicentre prospective observational study.", "token_count": 234, "char_count": 958, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7903, "quality_score": 0.8952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:40.298526", "source": { "split": "train_shard_00001", "doc_id": 3033 }, "chunk_id": "train_shard_00001_3033_4", "global_id": 9968 }, { "text": "Mycoplasma pneumoniae causes respiratory infections and other mucous membrane related inflammations. To explore the intra-specific variations and evolution of M. pneumoniae , a pan-genomic analysis was performed on 150 strains. In genome size evaluation of M. pneumoniae , on average 687 genes with low S.D (8.43) showed overall consistency in the gene count of 150 strains. This species is potentially pathogenic and highly evolving as 134 out of 150 showed almost all pathogenic factors with above 90% homology except 16 strains which belong to Spain, USA, China, and Japan. M. pneumoniae pan genome is an open pan genome showed total genes of 103174 in which 70359 (68.19%) core genes, 32241(31.24%) shared genes and 574 (0.55%) unique genes. Adhesin P30, Protein TopJ, ADP-ribosylating toxin CARDS toxin, GLPF, GLPK, GLPO, GLT and IgG-blocking protein M are the part of core genome. Adhesin P1, HMW1 and HMW2 genes are the part of shared genome. HMW3 and Cytadherence-associated protein P65 are the part of the unique genome in some strains. Therefore, comparative neighborhood gene analysis revealed many different neighbor genes pattern for HMW3 and P65. Phylogenetic analysis was exhibited in two main groups/clades of strains and identified major ancestral lineage within M. pneumoniae species.\n\nPan-Genome Analysis of Multiple Strains of Mycoplasma pneumoniae", "token_count": 424, "char_count": 1368, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [ "HMW1", "HMW3", "HMW2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:40.927246", "source": { "split": "train_shard_00001", "doc_id": 3034 }, "chunk_id": "train_shard_00001_3034_0", "global_id": 9969 }, { "text": "Kluyveromyces marxianus GX-15 was mutated multiple times by alternately treatment with UV irradiation and NTG for two cycles. Four mutant strains with improved ethanol yield were obtained. The maximum ethanol concentration, ethanol yield coefficient and theoretical ethanol yield of the best mutant strain, GX-UN120, was 69 g/l, 0.46 g/g and 91%, respectively, when fermenting 150 g glucose/l at 40°C. The corresponding values for GX-15 were 58 g/l, 0.39 g/g and 76%, respectively. GX-UN120 grew well in 11% (v/v) of ethanol, while GX-15 could not grow when ethanol was greater than 8% (v/v).\n\nMultiple induced mutagenesis for improvement of ethanol production by Kluyveromyces marxianus.", "token_count": 239, "char_count": 688, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7184, "quality_score": 0.8592, "entities": { "genes": [ "UN120" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:41.399423", "source": { "split": "train_shard_00001", "doc_id": 3035 }, "chunk_id": "train_shard_00001_3035_0", "global_id": 9970 }, { "text": "Ceftazidime-avibactam (CAZ-AVI) is an active antibiotic combination of a β-lactam-β-lactamase inhibitor against carbapenemase-producing Enterobacterales. Reports of resistance to CAZ-AVI other than metallo-β-lactamases have increased in recent years. The aim of this study was to analyze KPC-Klebsiella pneumoniae (KP) isolates resistant to CAZ-AVI from the intestinal carriage of hospitalized elderly patients in Italy, in February 2018-January 2020. Characterization of CAZ-AVI-resistant KP isolates, including MLST, resistome, virulome and plasmid content, was performed by WGS analysis. Out of six CAZ-AVI-resistant KP isolates, three belonged to ST101 and three to ST512; two isolates produced KPC-3 (both ST512), four had mutated KPC-3 (KPC-31, in ST101 and ST512, and KPC-46, both ST101). All CAZ-AVI-resistant KP isolates were multidrug-resistant and carried several resistance genes. The yersiniabactin ybt9 gene cluster was present in all ST101 isolates, while, in ST512 isolates, no virulence genes were detected. Several plasmids were detected: IncF was present in all isolates, as well as IncR and Col440 in ST101 and IncX3 in ST512 isolates. In conclusion, it is important to monitor the circulation of K. pneumoniae resistant to CAZ-AVI to prevent the spread of clones causing difficult-to-treat infections. The presence of mutated KPC-3 in high-risk K. pneumoniae clones resistant to CAZ-AVI in hospitalized patients deserves attention.", "token_count": 483, "char_count": 1480, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8045, "entities": { "genes": [ "ST512", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:42.046277", "source": { "split": "train_shard_00001", "doc_id": 3036 }, "chunk_id": "train_shard_00001_3036_0", "global_id": 9971 }, { "text": "Whole-Genome Sequencing and Molecular Analysis of Ceftazidime-Avibactam-Resistant KPC-Producing Klebsiella pneumoniae from Intestinal Colonization in Elderly Patients.", "token_count": 60, "char_count": 174, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:42.407557", "source": { "split": "train_shard_00001", "doc_id": 3036 }, "chunk_id": "train_shard_00001_3036_1", "global_id": 9972 }, { "text": "Probiotic microorganisms are used to improve the health and wellness of people and the research on this topic is of current relevance and interest. Fifty-five yeasts, coming from honeybee's ecosystem and belonging to Candida, Debaryomyces, Hanseniaspora, Lachancea, Metschnikowia, Meyerozyma, Starmerella and Zygosacchromyces genera and related different species, were evaluated for the probiotic traits. The resistance to gastrointestinal conditions, auto-aggregation, cell surface hydrophobicity or biofilm formation abilities as well as antimicrobial activity against common human pathogenic bacteria were evaluated. The safety analysis of strains was also carried out to exclude any possible negative effect on the consumer's health. The influence of proteinase treatment of living yeasts and their adhesion to Caco-2 cells were also evaluated. The greatest selection occurred in the first step of survival at the acidic pH and in the presence of bile salts, where more than 50% of the strains were unable to survive. Equally discriminating was the protease test which allowed the survival of only 27 strains belonging to the species Hanseniaspora guilliermondii, Hanseniaspora uvarum, Metschnikowia pulcherrima, Metschnikowia ziziphicola, Meyerozyma caribbica, Meyerozyma guilliermondii, Pichia kluyveri, Pichia kudriavzevii and Pichia terricola. An integrated analysis of the results obtained allowed the detection of seven yeast strains with probiotic aptitudes, all belonging to the Meyerozyma genus, of which three belonging to M. guillermondii and four belonging to M. caribbica species.\n\nAgro-ecosystem of honeybees as source for native probiotic yeasts.", "token_count": 433, "char_count": 1665, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:43.033016", "source": { "split": "train_shard_00001", "doc_id": 3037 }, "chunk_id": "train_shard_00001_3037_0", "global_id": 9973 }, { "text": "

Background

Excrement containing antimicrobial-resistant bacteria (ARB) is discharged from the hospital sewage through wastewater treatment plants (WWTP) into rivers, increasing the antimicrobial resistance (AMR) burden on the environment.

Purpose

We illustrate the contamination of hospital sewage tanks with ARB harboring antimicrobial resistance genes (ARGs) using comprehensive metagenomic sequencing. During the study period, we moved to a new hospital building constructed for renovation. Therefore, we investigated the difference in bacterial flora in the sewage tanks for each building with different departments, and the change in bacterial flora over time in new sewage tanks. Furthermore, we performed a comparative genome analysis of extended spectrum β-lactamase (ESBL)-producing organisms (EPOs) from hospital sewage and clinical samples. Residual antibiotics in the sewage tank were also measured.

Methods

Metagenomic analysis was performed on the hospital sewage samples, followed by whole genome sequencing of EPOs.

Results

The bacterial composition of new sewage tanks was comparable with that of old tanks within 1 month after relocation and was instantly affected by excrement. The bacterial composition of sewage tanks in the old and new buildings, containing rooms where seriously ill patients were treated, was similar. Selection on CHROMagar ESBL allowed detection of EPOs harboring bla CTX-M and carbapenemase genes in all sewage tanks. One of the sewage Escherichia coli strain comprising ST393 harboring bla CTX-M-27 corresponded to the clinical isolates based on core genome analysis", "token_count": 438, "char_count": 1682, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [ "ST393" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:43.669836", "source": { "split": "train_shard_00001", "doc_id": 3038 }, "chunk_id": "train_shard_00001_3038_0", "global_id": 9974 }, { "text": "Moreover, the levels of levofloxacin and clarithromycin in the hospital sewage were 0.0325 and 0.0135 µg/mL, respectively.

Conclusion

Hospital sewage was contaminated with many ARB species, ARGs and residual antibiotics, which can cause a burden on WWTP sewage treatment. The bacterial flora in the sewage tank was rapidly affected, especially by the ward with seriously ill patients. AMR monitoring of hospital sewage may help detect carriers prior to nosocomial ARB-associated outbreaks and control the outbreaks.\n\nComprehensive Genomic Survey of Antimicrobial-Resistance Bacteria in the Sewage Tank Replacement with Hospital Relocation.", "token_count": 186, "char_count": 646, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:44.114115", "source": { "split": "train_shard_00001", "doc_id": 3038 }, "chunk_id": "train_shard_00001_3038_1", "global_id": 9975 }, { "text": "1. The plant microbiome harbors an enormous diversity of fungi, bacteria, and viruses, but little is known on the diversity and function of prophages harbored within plant-associated bacteria. Using “VIP-Seq”, a novel method based on supernatant sequencing, we identified and quantified the activity of 120 spontaneously induced prophages in a collection of 63 Erwinia and Pseudomonas strains isolated from wheat flag leaves collected from the same field. These bacterial strains exhibited high levels of spontaneous prophage induction, with some producing > 10 8 virions/mL in overnight culture. Significant induction in planta also occurred from a lysogenic Erwinia strain inoculated on wheat seedlings. The potential of these active prophages in bacterial warfare was exhibited by their widespread killing of rival bacterial strains. Evidence of transduction was observed, and the prophages were shown to contribute a majority of the non-core genome of E. aphidicola isolates. Many additional prophages were predicted by bioinformatic tools, and we found that the predicted prophages that were not spontaneously induced had a significantly higher number of IS elements. Our results suggest that spontaneous induction of prophages may represent an unknown but wide-spread competition mechanism involved in phyllosphere microbiome assembly and function. This may also have implications for the design and resilience of synthetic bacterial communities used as biocontrol for certain plant diseases.\n\nActivity and diversity of prophages harbored by wheat phyllosphere bacteria", "token_count": 364, "char_count": 1575, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6311, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:44.694737", "source": { "split": "train_shard_00001", "doc_id": 3039 }, "chunk_id": "train_shard_00001_3039_0", "global_id": 9976 }, { "text": "Enzymatic hydrolysis of a cellulosic substrate is the most critical step for the production of bioethanol. In our study, the hydrolysis of steam-exploded sugarcane bagasse (SESB) under optimized conditions (8 % substrate consistency, 22.5 U filter paper cellulase, 0.55 % Tween 80) released a maximum of 461 mg per gram dry substrate sugars. We isolated a thermotolerant yeast strain, Blastobotrys adeninivorans RCKP 2012, from sugarcane bagasse collected from the Cooperative Sugar Mill, Sonepat, Haryana that was found to be capable of fermenting the enzymatic hydrolysate of SESB at 50 °C. When grown under simultaneous saccharification and fermentation conditions, this yeast produced 14.05 g L⁻¹ethanol, which corresponds to a theoretical ethanol yield of 46.87 %.\n\nSimultaneous saccharification and fermentation of pretreated sugarcane bagasse to ethanol using a new thermotolerant yeast", "token_count": 273, "char_count": 893, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7209, "quality_score": 0.8605, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:45.251999", "source": { "split": "train_shard_00001", "doc_id": 3040 }, "chunk_id": "train_shard_00001_3040_0", "global_id": 9977 }, { "text": "

Background

Salmonella enterica subsp. enterica is a public health issue related to food safety, and its adaptation to animal sources remains poorly described at the pangenome scale. Firstly, serovars presenting potential mono- and multi-animal sources were selected from a curated and synthetized subset of Enterobase. The corresponding sequencing reads were downloaded from the European Nucleotide Archive (ENA) providing a balanced dataset of 440 Salmonella genomes in terms of serovars and sources (i). Secondly, the coregenome variants and accessory genes were detected (ii). Thirdly, single nucleotide polymorphisms and small insertions/deletions from the coregenome, as well as the accessory genes were associated to animal sources based on a microbial Genome Wide Association Study (GWAS) integrating an advanced correction of the population structure (iii). Lastly, a Gene Ontology Enrichment Analysis (GOEA) was applied to emphasize metabolic pathways mainly impacted by the pangenomic mutations associated to animal sources (iv).

Results

Based on a genome dataset including Salmonella serovars from mono- and multi-animal sources (i), 19,130 accessory genes and 178,351 coregenome variants were identified (ii). Among these pangenomic mutations, 52 genomic signatures (iii) and 9 over-enriched metabolic signatures (iv) were associated to avian, bovine, swine and fish sources by GWAS and GOEA, respectively.

Conclusions

Our results suggest that the genetic and metabolic determinants of Salmonella adaptation to animal sources may have been driven by the natural feeding environment of the animal, distinct livestock diets modified by human, environmental stimuli, physiological properties of the animal itself, and work habits for health protection of livestock.\n\nGenetic and metabolic signatures of Salmonella enterica subsp. enterica associated with animal sources at the pangenomic scale.", "token_count": 487, "char_count": 1925, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5923, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:45.904535", "source": { "split": "train_shard_00001", "doc_id": 3041 }, "chunk_id": "train_shard_00001_3041_0", "global_id": 9978 }, { "text": "The rise in antimicrobial resistance (AMR) in bacteria is reducing therapeutic options for livestock and human health, with a paucity of information globally. To fill this gap, a One-Health approach was taken by sampling livestock on farms (n = 52), abattoir (n = 8), and animal markets (n = 10), and in-contact humans in Southeast Nigeria. Extended spectrum cephalosporin (ESC)-resistant (ESC-R) Escherichia coli was selectively cultured from 975 healthy livestock faecal swabs, and hand swabs from in-contact humans. Antimicrobial susceptibility testing (AST) was performed on all ESC-R E. coli. For isolates showing a multi-drug resistance (MDR) phenotype (n = 196), quantitative real-time PCR (qPCR) was performed for confirmation of extended-spectrum β-lactamase (ESBL) and carbapenemase genes. Whole-genome sequencing (WGS) was performed on a subset (n = 157) for detailed molecular characterisation. The results showed ESC-R E. coli was present in 41.2% of samples, with AST results indicating 48.8% of isolates were phenotypically MDR. qPCR confirmed presence of ESBL genes, with bla CTX-M present in all but others in a subset [bla TEM (62.8%) and bla SHV (0.5%)] of isolates; none harboured transferable carbapenemase genes", "token_count": 476, "char_count": 1343, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6831, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:46.551178", "source": { "split": "train_shard_00001", "doc_id": 3042 }, "chunk_id": "train_shard_00001_3042_0", "global_id": 9979 }, { "text": "Multi-locus sequence typing identified 34 Sequence Types (ST) distributed among different sampling levels; ST196 carrying bla CTX-M-55 was predominant in chickens. Large numbers of single nucleotide polymorphisms (SNPs) in the core genome of isolates, even within the same clade by phylogenetic analysis, indicated high genetic diversity. AMR genotyping indicated the predominant bla CTX-M variant was bla CTX-M-15 (87.9%), although bla CTX-M-55, bla CTX-M-64, and bla CTX-M-65 were present; it was notable that bla CTX-M-1, common in livestock, was absent. Other predominant AMR genes included: sul2, qnrS1, strB, bla TEM-1b, tetA-v2, and dfrA14, with prevalence varying according to host livestock species. A bla CTX-M-15 harbouring plasmid from livestock isolates in Ebonyi showed high sequence identity to one from river/sewage water in India, indicating this ESBL plasmid to be globally disseminated, being present beyond the river environment. In conclusion, ESC-R E. coli was widespread in livestock and in-contact humans from Southeast Nigeria. WGS data indicated the isolates were genetically highly diverse, probably representing true diversity of wild type E", "token_count": 480, "char_count": 1376, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7365, "quality_score": 0.8683, "entities": { "genes": [ "ST196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:47.191955", "source": { "split": "train_shard_00001", "doc_id": 3042 }, "chunk_id": "train_shard_00001_3042_1", "global_id": 9980 }, { "text": "coli; they were likely to be MDR with several harbouring bla CTX-M-15. Surprisingly, human isolates had highest numbers of AMR genes and pigs the least.\n\nMolecular characterization of extended spectrum cephalosporin resistant Escherichia coli isolated from livestock and in-contact humans in Southeast Nigeria.", "token_count": 104, "char_count": 339, "word_count": 43, "semantic_coherence": 1, "information_density": 0.9535, "quality_score": 0.9767, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:47.563743", "source": { "split": "train_shard_00001", "doc_id": 3042 }, "chunk_id": "train_shard_00001_3042_2", "global_id": 9981 }, { "text": "The degradation of natural phosphorylated compounds (galactose-1-phosphate, N-acetyl-glucosamine-1-phosphate, glycerophosphoethanolamine, and glycerophosphocholine) and added phosphorylated compounds (diphosphate) in milk was investigated by phosphorus 31 nuclear magnetic resonance on the incubation of a sterile milk with Pseudomonas fluorescens CECT381, Lactococcus lactis CECT539, and Kluyveromyces marxianus CECT10584. This preliminary study showed that the degradation of these compounds was dependent on the compound, microorganism, and temperature of incubation. K. marxianus CECT10584 did not show any capability to degrade these compounds, and L. lactis CECT539 was only able to degrade diphosphate at its optimum growth temperature. P. fluorescens CECT381 was the most active strain and possessed more hydrolytic capabilities at 10 degrees C than at its optimum growth temperature. It is suggested that cold-induced enzymes are involved in the ability of P. fluorescens CECT381 to hydrolyze the natural phosphorylated compounds in milk. Consequent potential alterations of dairy products are discussed.\n\nDegradation of natural phosphorylated compounds and added polyphosphates in milk by Pseudomonas fluorescens CECT378, Lactococcus lactis CECT539, and Kluyveromyces marxianus CECT10584.", "token_count": 399, "char_count": 1298, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5964, "quality_score": 0.7982, "entities": { "genes": [ "CECT539", "CECT378", "CECT381", "CECT10584" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:48.177662", "source": { "split": "train_shard_00001", "doc_id": 3043 }, "chunk_id": "train_shard_00001_3043_0", "global_id": 9982 }, { "text": "Food safety is a global concern, with upward of 2.2 million deaths due to enteric disease every year. Current whole-genome sequencing platforms allow routine sequencing of enteric pathogens for surveillance, and during outbreaks; however, a remaining challenge is the identification of genomic markers that are predictive of strain groups that pose the most significant health threats to humans, or that can persist in specific environments. We have previously developed the software program Panseq, which identifies the pan-genome among a group of sequences, and the SuperPhy platform, which utilizes this pan-genome information to identify biomarkers that are predictive of groups of bacterial strains. In this study, we examined the pan-genome of 4893 genomes of Salmonella enterica, an enteric pathogen responsible for the loss of more disability adjusted life years than any other enteric pathogen. We identified a pan-genome of 25.3 Mbp, a strict core of 1.5 Mbp present in all genomes, and a conserved core of 3.2 Mbp found in at least 96% of these genomes. We also identified 404 genomic regions of 1000 bp that were specific to the species S. enterica. These species-specific regions were found to encode mostly hypothetical proteins, effectors, and other proteins related to virulence. For each of the six S. enterica subspecies, markers unique to each were identified. No serovar had pan-genome regions that were present in all of its genomes and absent in all other serovars; however, each serovar did have genomic regions that were universally present among all constituent members, and statistically predictive of the serovar. The phylogeny based on SNPs within the conserved core genome was found to be highly concordant to that produced by a phylogeny using the presence/absence of 1000 bp regions of the entire pan-genome. Future studies could use these predictive regions as components of a vaccine to prevent salmonellosis, as well as in simple and rapid diagnostic tests for both in silico and wet-lab applications, with uses ranging from food safety to public health", "token_count": 521, "char_count": 2115, "word_count": 326, "semantic_coherence": 1, "information_density": 0.5767, "quality_score": 0.7883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:48.839896", "source": { "split": "train_shard_00001", "doc_id": 3044 }, "chunk_id": "train_shard_00001_3044_0", "global_id": 9983 }, { "text": "Lastly, the tools and methods described in this study could be applied as a pan-genomics framework to other population genomic studies seeking to identify markers for other bacterial species and their sub-groups.\n\nPan-genome Analyses of the Species Salmonella enterica, and Identification of Genomic Markers Predictive for Species, Subspecies, and Serovar.", "token_count": 92, "char_count": 363, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:49.214176", "source": { "split": "train_shard_00001", "doc_id": 3044 }, "chunk_id": "train_shard_00001_3044_1", "global_id": 9984 }, { "text": "Yersinia pseudotuberculosis is an enteric pathogen causing mild enteritis that can lead to mesenteric adenitis and septicemia in elderly patients. Most cases are sporadic, but outbreaks have already been described in different countries. We report for the first time a Y. pseudotuberculosis clonal outbreak in France, that occurred in 2020. An epidemiological investigation pointed towards the consumption of tomatoes as the likely source of contamination. The Yersinia National Reference Laboratory (YNRL) developed a new cgMLST scheme with 1,921 genes specific to Y. pseudotuberculosis that identified the clustering of isolates associated to the outbreak and allowed to perform molecular typing in real time. In addition, this method allowed to retrospectively identify isolates belonging to this cluster from earlier in 2020. This method, which does not require specific bioinformatic skills, is now used systematically at the YNRL and proves to display an excellent discriminatory power and is available to the scientific community.\n\nFirst description of aYersinia pseudotuberculosisclonal outbreak in France, confirmed using a new core genome multilocus sequence typing method", "token_count": 276, "char_count": 1189, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:49.773620", "source": { "split": "train_shard_00001", "doc_id": 3045 }, "chunk_id": "train_shard_00001_3045_0", "global_id": 9985 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) O157:H7 is a public health threat and outbreaks occur worldwide. Here, we investigate genomic differences between related STEC O157:H7 that caused two outbreaks, eight weeks apart, at the same restaurant. Short-read genome sequencing divided the outbreak strains into two sub-clusters separated by only three single-nucleotide polymorphisms in the core genome while traditional typing identified them as separate phage types, PT8 and PT54. Isolates did not cluster with local strains but with those associated with foreign travel to the Middle East/North Africa. Combined long-read sequencing approaches and optical mapping revealed that the two outbreak strains had undergone significant microevolution in the accessory genome with prophage gain, loss and recombination. In addition, the PT54 sub-type had acquired a 240 kbp multi-drug resistance (MDR) IncHI2 plasmid responsible for the phage type switch. A PT54 isolate had a general fitness advantage over a PT8 isolate in rich medium, including an increased capacity to use specific amino acids and dipeptides as a nitrogen source. The second outbreak was considerably larger and there were multiple secondary cases indicative of effective human-to-human transmission. We speculate that MDR plasmid acquisition and prophage changes have adapted the PT54 strain for human infection and transmission. Our study shows the added insights provided by combining whole-genome sequencing approaches for outbreak investigations.\n\nShort-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks.", "token_count": 402, "char_count": 1640, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7048, "quality_score": 0.8524, "entities": { "genes": [ "PT8", "PT54" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:50.415070", "source": { "split": "train_shard_00001", "doc_id": 3046 }, "chunk_id": "train_shard_00001_3046_0", "global_id": 9986 }, { "text": "Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a clonal relationship (separated by ≤2 SNVs in their core genome) with one or more porcine strains, consistent with recent inter-host transmission. Clones were spread over a vast geographic area with 50% of the human cases occurring without recent healthcare exposure. These findings suggest a persistent community reservoir with long-range dissemination, potentially due to agricultural recycling of piggery effluent. We also provide the first pan-genome analysis for this lineage, characterizing its resistome, prophage content, and in silico virulence potential. The RT014 is defined by a large \"open\" pan-genome (7587 genes) comprising a core genome of 2296 genes (30.3% of the total gene repertoire) and an accessory genome of 5291 genes. Antimicrobial resistance genotypes and phenotypes varied across host populations and ST lineages and were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P) and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia)", "token_count": 519, "char_count": 1726, "word_count": 238, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [ "RT014" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:32:51.120371", "source": { "split": "train_shard_00001", "doc_id": 3047 }, "chunk_id": "train_shard_00001_3047_0", "global_id": 9987 }, { "text": "Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM). Numerous clinically important prophages (Siphoviridae and Myoviridae) were identified as well as an uncommon accessory gene regulator locus (agr3). Conservation in the pathogenicity locus and S-layer correlated with ST affiliation, further extending the concept of clonal C. difficile lineages. This study provides novel insights on the genetic variability and strain relatedness of C. difficile RT014, a lineage of emerging One Health importance. Ongoing molecular and genomic surveillance of strains in humans, animals, food, and the environment is imperative to identify opportunities to reduce the overall CDI burden.\n\nGenome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission.", "token_count": 306, "char_count": 1039, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7463, "quality_score": 0.8731, "entities": { "genes": [ "RT014" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:51.715597", "source": { "split": "train_shard_00001", "doc_id": 3047 }, "chunk_id": "train_shard_00001_3047_1", "global_id": 9988 }, { "text": "The advent of culture independent approaches has greatly facilitated insights into the vast diversity of bacteria and the ecological importance they hold in nature and human health. Recently, metagenomic surveys and other culture-independent methods have begun to describe the distribution and diversity of microbial metabolism across environmental conditions, often using 16S rRNA gene as a marker to group bacteria into taxonomic units. However, the extent to which similarity at the conserved ribosomal 16S gene correlates with different measures of phylogeny, metabolic diversity, and ecologically relevant gene content remains contentious. Here, we examine the relationship between 16S identity, core genome divergence, and metabolic gene content across the ancient and ecologically important genus Streptomyces. We assessed and quantified the high variability of average nucleotide identity (ANI) and ortholog presence/absence within Streptomyces, even in strains identical by 16S. Furthermore, we identified key differences in shared ecologically important characters, such as antibiotic resistance, carbohydrate metabolism, biosynthetic gene clusters (BGCs), and other metabolic hallmarks, within 16S identities commonly treated as the same operational taxonomic units (OTUs). Differences between common phylogenetic measures and metabolite-gene annotations confirmed this incongruence. Our results highlight the metabolic diversity and variability within OTUs and add to the growing body of work suggesting 16S-based studies of Streptomyces fail to resolve important ecological and metabolic characteristics.\n\nTaxonomic and Metabolic Incongruence in the Ancient Genus Streptomyces.", "token_count": 406, "char_count": 1718, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:52.362176", "source": { "split": "train_shard_00001", "doc_id": 3048 }, "chunk_id": "train_shard_00001_3048_0", "global_id": 9989 }, { "text": "

Objectives

We unexpectedly identified MRSA isolates carrying mecC (mecC-MRSA) from a Danish swine farm located in eastern Zealand. The objective of the present study was to investigate the origin of these isolates and their genetic relatedness to other mecC-MRSA isolates from Zealand.

Methods

WGS was used to infer the phylogenetic relationship between 19 identified mecC-MRSA isolates from the swine farm and 34 additional epidemiologically unrelated human isolates from the same geographical region of Denmark. Variations in the accessory genome were investigated by bioinformatics tools, and antibiotic susceptibility profiles were assessed by MIC determination.

Results

mecC-MRSA was isolated from a domestic swine farm, but not from cattle reared at the same farm. Phylogenetic analysis revealed that all mecC-MRSA isolates from both farm animals and workers formed a separate cluster, whereas human isolates from the same municipality belonged to a closely related cluster. Analysis of the accessory genome supported this relationship.

Conclusions

To the best of our knowledge, this is the first report of mecC-MRSA isolated from domestic swine. The investigation strongly indicates that transmission of mecC-MRSA has taken place on the swine farm between the farmers and swine. The close clustering of farm isolates and isolates from the same municipality suggests a local transmission of mecC-MRSA.\n\nReport of mecC-carrying MRSA in domestic swine.", "token_count": 366, "char_count": 1485, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5512, "quality_score": 0.7756, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:52.949200", "source": { "split": "train_shard_00001", "doc_id": 3049 }, "chunk_id": "train_shard_00001_3049_0", "global_id": 9990 }, { "text": "Salmonella enterica serovar Typhimurium strain ATCC14028s is commercially available from multiple national type culture collections, and has been widely used since 1960 for quality control of growth media and experiments on fitness (\"laboratory evolution\"). ATCC14028s has been implicated in multiple cross-contaminations in the laboratory, and has also caused multiple laboratory infections and one known attempt at bioterrorism. According to hierarchical clustering of 3002 core gene sequences, ATCC14028s belongs to HierCC cluster HC20_373 in which most internal branch lengths are only one to three SNPs long. Many natural Typhimurium isolates from humans, domesticated animals and the environment also belong to HC20_373, and their core genomes are almost indistinguishable from those of laboratory strains. These natural isolates have infected humans in Ireland and Taiwan for decades, and are common in the British Isles as well as the Americas. The isolation history of some of the natural isolates confirms the conclusion that they do not represent recent contamination by the laboratory strain, and 10% carry plasmids or bacteriophages which have been acquired in nature by HGT from unrelated bacteria. We propose that ATCC14028s has repeatedly escaped from the laboratory environment into nature via laboratory accidents or infections, but the escaped micro-lineages have only a limited life span. As a result, there is a genetic gap separating HC20_373 from its closest natural relatives due to a divergence between them in the late 19th century followed by repeated extinction events of escaped HC20_373.\n\nGenomic population structure associated with repeated escape of Salmonella enterica ATCC14028s from the laboratory into nature.", "token_count": 418, "char_count": 1746, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:53.570813", "source": { "split": "train_shard_00001", "doc_id": 3050 }, "chunk_id": "train_shard_00001_3050_0", "global_id": 9991 }, { "text": "Chronic rhinosinusitis (CRS) is a common chronic sinonasal mucosal inflammation associated with Staphylococcus aureus biofilm and relapsing infections. This study aimed to determine rates of S. aureus persistence and pathoadaptation in CRS patients by investigating the genomic relatedness and antibiotic resistance/tolerance in longitudinally collected S. aureus clinical isolates. A total of 68 S. aureus isolates were sourced from 34 CRS patients at least six months apart. Isolates were grown into 48-hour biofilms and tested for tolerance to antibiotics. A hybrid sequencing strategy was used to obtain high-quality reference-grade assemblies of all isolates. Single nucleotide variants (SNV) divergence in the core genome and sequence type clustering were used to analyse the relatedness of the isolate pairs. Single nucleotide and structural genome variations, plasmid similarity, and plasmid copy numbers between pairs were examined. Our analysis revealed that 41% (14/34 pairs) of S. aureus isolates were persisters, while 59% (20/34 pairs) were non-persisters. Persister isolates showed episode-specific mutational changes over time with a bias towards events in genes involved in adhesion to the host and mobile genetic elements such as plasmids, prophages, and insertion sequences. A significant increase in the copy number of conserved plasmids of persister strains (p<0.05) was seen, indicating a role of the “mobilome” in promoting persistence. This was accompanied by a significant increase in biofilm tolerance against all tested antibiotics (p<0.001), which was linked to a significant increase in biofilm biomass (p<0.05) over time, indicating a biofilm central pathoadaptive process in persisters. In conclusion, our study provides important insights into the mutational changes underlying S. aureus persistence in CRS patients highlighting pathoadaptive mechanisms in S. aureus persisters culminating in increased biofilm biomass linked to an increase in plasmid copy number over time.", "token_count": 507, "char_count": 2006, "word_count": 283, "semantic_coherence": 1, "information_density": 0.583, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:54.582309", "source": { "split": "train_shard_00001", "doc_id": 3051 }, "chunk_id": "train_shard_00001_3051_0", "global_id": 9992 }, { "text": "The Intra-Host Evolutionary Landscape And Pathoadaptation Of PersistentStaphylococcus aureusIn Chronic Rhinosinusitis", "token_count": 40, "char_count": 124, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:54.938829", "source": { "split": "train_shard_00001", "doc_id": 3051 }, "chunk_id": "train_shard_00001_3051_1", "global_id": 9993 }, { "text": "The C. perfringens species is associated with various environments, such as soils, sewage, and food. However, it is also a component of the gastrointestinal (GI) microflora (i.e., microbiota) of sick and healthy humans and animals. C. perfringens is linked with different systemic and enteric diseases in livestock and humans, such as gas gangrene, food poisoning, non-foodborne diarrhoea, and enterocolitis. The strains of this opportunistic pathogen are known to secrete over 20 identified toxins that are considered its principal virulence factors. C. perfringens belongs to the anaerobic bacteria community but can also survive in the presence of oxygen. The short time between generations, the multi-production capability of toxins and heat-resistant spores, the location of many virulence genes on mobile genetic elements, and the inhabitance of this opportunistic pathogen in different ecological niches make C. perfringens a very important microorganism for public health protection. The epidemiological evidence for the association of these strains with C. perfringens-meditated food poisoning and some cases of non-foodborne diseases is very clear and well-documented. However, the genetic diversity and physiology of C. perfringens should still be studied in order to confirm the importance of suspected novel virulence traits. A very significant problem is the growing antibiotic resistance of C. perfringens strains. The aim of this review is to show the current basic information about the toxins, epidemiology, and genetic and molecular diversity of this opportunistic pathogen.\n\nClostridium perfringens-Opportunistic Foodborne Pathogen, Its Diversity and Epidemiological Significance.", "token_count": 443, "char_count": 1756, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5966, "quality_score": 0.7983, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:55.569312", "source": { "split": "train_shard_00001", "doc_id": 3052 }, "chunk_id": "train_shard_00001_3052_0", "global_id": 9994 }, { "text": "Pantoea ananatis is ubiquitously found in the environment and causes disease on a wide range of plant hosts. By contrast, its sister species, Pantoea stewartii subsp. stewartii is the host-specific causative agent of the devastating maize disease Stewart's wilt. This pathogen has a restricted lifecycle, overwintering in an insect vector before being introduced into susceptible maize cultivars, causing disease and returning to overwinter in its vector. The other subspecies of P. stewartii subsp. indologenes, has been isolated from different plant hosts and is predicted to proliferate in different environmental niches. Here we have, by the use of comparative genomics and a comprehensive suite of bioinformatic tools, analyzed the genomes of ten P. stewartii and nineteen P. ananatis strains. Our phylogenomic analyses have revealed that there are two distinct clades within P. ananatis while far less phylogenetic diversity was observed among the P. stewartii subspecies. Pan-genome analyses revealed a large core genome comprising of 3,571 protein coding sequences is shared among the twenty-nine compared strains. Furthermore, we showed that an extensive accessory genome made up largely by a mobilome of plasmids, integrated prophages, integrative and conjugative elements and insertion elements has resulted in extensive diversification of P. stewartii and P. ananatis. While these organisms share many pathogenicity determinants, our comparative genomic analyses show that they differ in terms of the secretion systems they encode. The genomic differences identified in this study have allowed us to postulate on the divergent evolutionary histories of the analyzed P. ananatis and P. stewartii strains and on the molecular basis underlying their ecological success and host range.", "token_count": 498, "char_count": 1884, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:56.227292", "source": { "split": "train_shard_00001", "doc_id": 3053 }, "chunk_id": "train_shard_00001_3053_0", "global_id": 9995 }, { "text": "Phylogenomic, Pan-genomic, Pathogenomic and Evolutionary Genomic Insights into the Agronomically Relevant Enterobacteria Pantoea ananatis and Pantoea stewartii.", "token_count": 61, "char_count": 174, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:56.586220", "source": { "split": "train_shard_00001", "doc_id": 3053 }, "chunk_id": "train_shard_00001_3053_1", "global_id": 9996 }, { "text": "

Background

Vibrio cholerae, the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae.

Methods

From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.

Results and conclusions

Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.\n\nArchitecture of the superintegron in Vibrio cholerae: identification of core and unique genes.", "token_count": 468, "char_count": 1863, "word_count": 294, "semantic_coherence": 1, "information_density": 0.5408, "quality_score": 0.7704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:57.234900", "source": { "split": "train_shard_00001", "doc_id": 3054 }, "chunk_id": "train_shard_00001_3054_0", "global_id": 9997 }, { "text": "Antimicrobial resistance (AMR) is an emerging public health threat and is one of the One Health priorities for humans, animals, and environmental health. Red foxes (Vulpes vulpes) are a widespread predator species with great ecological significance, and they may serve as a sentinel of antimicrobial resistance in the general environment. The present study was carried out to detect antimicrobial resistance, antimicrobial resistance genes, and genetic diversity in faecal isolates of red foxes (Vulpes vulpes). In total, 34 Enterococcus isolates, including E. faecium (n = 17), E. faecalis (n = 12), E. durans (n = 3), and E. hirae (n = 2), were isolated. Antimicrobial resistance to 12 antimicrobial agents was detected with EUVENC panels using the minimum inhibitory concentration (MIC). The presence of antimicrobial resistance genes (ARGs) was determined using whole-genome sequencing (WGS). Resistance to tetracycline (6/34), erythromycin (3/34), ciprofloxacin (2/34), tigecycline (2/34), and daptomycin (2/34) was identified in 44% (15/34) of Enterococcus isolates, while all the isolates were found to be susceptible to ampicillin, chloramphenicol, gentamicin, linezolid, teicoplanin, and vancomycin. No multi-resistant Enterococcus spp. were detected. A total of 12 ARGs were identified in Enterococcus spp., with the presence of at least 1 ARG in every isolate", "token_count": 478, "char_count": 1440, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:57.882160", "source": { "split": "train_shard_00001", "doc_id": 3055 }, "chunk_id": "train_shard_00001_3055_0", "global_id": 9998 }, { "text": "The identified ARGs encoded resistance to aminoglycosides (aac(6')-I, ant(6)-Ia, aac(6')-Iih and spw), tetracyclines (tet(M), tet(L) and tet(S)), and macrolide-lincosamide-streptogramin AB (lnu(B,G), lsa(A,E), and msr(C)), and their presence was associated with phenotypical resistance. Core genome multilocus sequence typing (cgMLST) revealed the high diversity of E. faecalis and E. faecium isolates, even within the same geographical area. The distribution of resistant Enterococcus spp. in wild foxes in Latvia highlights the importance of a One Health approach in tackling AMR.\n\nAntimicrobial Resistance in Enterococcus spp. Isolates from Red Foxes (Vulpes vulpes) in Latvia.", "token_count": 304, "char_count": 785, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:58.451084", "source": { "split": "train_shard_00001", "doc_id": 3055 }, "chunk_id": "train_shard_00001_3055_1", "global_id": 9999 }, { "text": "

Rationale

Methicillin resistant Staphylococcus aureus (MRSA) is prevalent and consequential in cystic fibrosis (CF). Whole genome sequencing (WGS) could reveal genomic differences in MRSA associated with poorer outcomes or detect MRSA transmission.

Objectives

To identify MRSA genes associated with low lung function and potential MRSA transmission in CF.

Methods

We collected 97 MRSA isolates from 74 individuals with CF from 2017 and performed short-read WGS. We determined sequence type (ST) and the phylogenetic relationship between isolates. We aligned accessory genes from 25 reference genomes to genome assemblies, classified isolates by accessory gene content, and correlated the accessory genome to clinical outcomes.

Results

The most prevalent ST were ST5 (N = 55), ST8 (N = 15), and ST105 (N = 14). Closely related MRSA strains were shared by family members with CF, but rarely between unrelated individuals. Three clusters of MRSA were identified by accessory genome content. Cluster A, including ST5 and ST105, was highly prevalent at all ages. Cluster B, including ST8, was more limited to younger patients. Cluster C included 6 distantly related strains. Patients 20 years old and younger infected with Cluster A had lower forced expiratory volume in the first second (FEV1 ) and higher sputum biomass compared to similar-aged patients with Cluster B.

Conclusions

In this CF cohort, we identified MRSA subtypes that predominate at different ages and differ by accessory gene content. The most prevalent cluster of MRSA, including ST5 and ST105, was associated with lower FEV1 . ST8 MRSA was more common in younger patients and thus has the potential to rise in prevalence as these patients age.", "token_count": 494, "char_count": 1767, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6235, "quality_score": 0.8118, "entities": { "genes": [ "ST5", "ST105", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:32:59.726866", "source": { "split": "train_shard_00001", "doc_id": 3056 }, "chunk_id": "train_shard_00001_3056_0", "global_id": 10000 }, { "text": "MRSA strains with distinct accessory genes predominate at different ages in cystic fibrosis.", "token_count": 23, "char_count": 92, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:00.079780", "source": { "split": "train_shard_00001", "doc_id": 3056 }, "chunk_id": "train_shard_00001_3056_1", "global_id": 10001 }, { "text": "We hereby present the first descriptions of human-invasive infections caused by Escherichia marmotae, a recently described species that encompasses the former \"Escherichia cryptic clade V.\" We describe four cases, one acute sepsis of unknown origin, one postoperative sepsis after cholecystectomy, one spondylodiscitis, and one upper urinary tract infection. Cases were identified through unsystematic queries in a single clinical lab over 6 months. Through genome sequencing of the causative strains combined with available genomes from elsewhere, we demonstrate Es. marmotae to be a likely ubiquitous species containing genotypic virulence traits associated with Escherichia pathogenicity. The invasive isolates were scattered among isolates from a range of nonhuman sources in the phylogenetic analyses, thus indicating inherent virulence in multiple lineages. Pan genome analyses indicate that Es. marmotae has a large accessory genome and is likely to obtain ecologically advantageous traits, such as genes encoding antimicrobial resistance. Reliable identification might be possible by matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), but relevant spectra are missing in commercial databases. It can be identified through 16S rRNA gene sequencing. Escherichia marmotae could represent a relatively common human pathogen, and improved diagnostics will provide a better understanding of its clinical importance. IMPORTANCE Escherichia coli is the most common pathogen found in blood cultures and urine and among the most important pathogenic species in the realm of human health. The notion that some of these isolates are not Es. coli but rather another species within the same genus may have implications for what Es. coli constitutes. We only recently have obtained methods to separate the two species, which means that possible differences in important clinical aspects, such as antimicrobial resistance rates, virulence, and phylogenetic structure, may exist. We believe that Es", "token_count": 492, "char_count": 2062, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6783, "quality_score": 0.8392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:00.727053", "source": { "split": "train_shard_00001", "doc_id": 3057 }, "chunk_id": "train_shard_00001_3057_0", "global_id": 10002 }, { "text": "marmotae as a common pathogen is new merely because we have not looked or bothered to distinguish between the thousands of invasive Escherichia passing through microbiological laboratories each day.\n\nEscherichia marmotae-a Human Pathogen Easily Misidentified as Escherichia coli.", "token_count": 77, "char_count": 283, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:01.089683", "source": { "split": "train_shard_00001", "doc_id": 3057 }, "chunk_id": "train_shard_00001_3057_1", "global_id": 10003 }, { "text": "Fusobacterium nucleatum (Fn), an oral anaerobic commensal, has recently been identified as a crucial oncogenic contributor to colorectal cancer pathogenesis through its ectopic colonization in the gastrointestinal tract. Accumulating evidence reveals its multifaceted involvement in colorectal cancer initiation, progression, metastasis, and therapeutic resistance to conventional treatments, including chemotherapy, radiotherapy, and immunotherapy. This perspective highlights recent advances in anti-Fn strategies, including small-molecule inhibitors, nanomedicines, and biopharmaceuticals, while critically analyzing the translational barriers in developing targeted antimicrobial interventions. We further propose potential strategies to overcome current challenges in Fn modulation, aiming to pave the way for more effective therapeutic interventions and better clinical outcomes.\n\n<i>Fusobacterium nucleatum</i> in Colorectal Cancer: Ally Mechanism and Targeted Therapy Strategies.", "token_count": 260, "char_count": 1027, "word_count": 113, "semantic_coherence": 1, "information_density": 0.8142, "quality_score": 0.9071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:01.635527", "source": { "split": "train_shard_00001", "doc_id": 3058 }, "chunk_id": "train_shard_00001_3058_0", "global_id": 10004 }, { "text": "Salmonella is a food-borne pathogen often linked to poultry sources, causing gastrointestinal infections in humans, with the numbers of multidrug resistant (MDR) isolates increasing globally. To gain insight into the genomic diversity of common serovars and their potential contribution to disease, we characterized antimicrobial resistance genes, and virulence factors encoded in 88 UK and 55 Thai isolates from poultry; the presence of virulence genes was detected through an extensive virulence determinants database compiled in this study. Long-read sequencing of three MDR isolates, each from a different serovar, was used to explore the links between virulence and resistance. To augment current control methods, we determined the sensitivity of isolates to 22 previously characterized Salmonella bacteriophages. Of the 17 serovars included, Salmonella Typhimurium and its monophasic variants were the most common, followed by S. Enteritidis, S. Mbandaka, and S. Virchow. Phylogenetic analysis of Typhumurium and monophasic variants showed poultry isolates were generally distinct from pigs. Resistance to sulfamethoxazole and ciprofloxacin was highest in isolates from the UK and Thailand, respectively, with 14-15% of all isolates being MDR. We noted that >90% of MDR isolates were likely to carry virulence genes as diverse as the srjF, lpfD, fhuA, and stc operons. Long-read sequencing revealed the presence of global epidemic MDR clones in our dataset, indicating they are possibly widespread in poultry. The clones included MDR ST198 S. Kentucky, harboring a Salmonella Genomic Island-1 (SGI)-K, European ST34 S", "token_count": 498, "char_count": 1714, "word_count": 234, "semantic_coherence": 1, "information_density": 0.641, "quality_score": 0.8205, "entities": { "genes": [ "ST34", "ST198" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:02.294864", "source": { "split": "train_shard_00001", "doc_id": 3059 }, "chunk_id": "train_shard_00001_3059_0", "global_id": 10005 }, { "text": "1,4,[5],12:i:-, harboring SGI-4 and mercury-resistance genes, and a S. 1,4,12:i:- isolate from the Spanish clone harboring an MDR-plasmid. Testing of all isolates against a panel of bacteriophages showed variable sensitivity to phages, with STW-77 found to be the most effective. STW-77 lysed 37.76% of the isolates, including serovars important for human clinical infections: S. Enteritidis (80.95%), S. Typhimurium (66.67%), S. 1,4,[5],12:i:- (83.3%), and S. 1,4,12: i:- (71.43%). Therefore, our study revealed that combining genomics and phage sensitivity assays is promising for accurately identifying and providing biocontrols for Salmonella to prevent its dissemination in poultry flocks and through the food chain to cause infections in humans.\n\nPathogen genomics and phage-based solutions for accurately identifying and controlling Salmonella pathogens.", "token_count": 313, "char_count": 910, "word_count": 117, "semantic_coherence": 1, "information_density": 0.735, "quality_score": 0.8675, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:02.874512", "source": { "split": "train_shard_00001", "doc_id": 3059 }, "chunk_id": "train_shard_00001_3059_1", "global_id": 10006 }, { "text": "In cellulosic ethanol production, use of simultaneous saccharification and fermentation (SSF) has been suggested as the favorable strategy to reduce process costs. Although SSF has many advantages, a significant discrepancy still exists between the appropriate temperature for saccharification (45-50 °C) and fermentation (30-35 °C). In the present study, the potential of temperature-shift as a tool for SSF optimization for bioethanol production from cellulosic biomass was examined. Cellulosic ethanol production of the temperature-shift SSF (TS-SSF) from 16 w/v% biomass increased from 22.2 g/L to 34.3 g/L following a temperature shift from 45 to 35 °C compared with the constant temperature of 45 °C. The glucose conversion yield and ethanol production yield in the TS-SSF were 89.3% and 90.6%, respectively. At higher biomass loading (18 w/v%), ethanol production increased to 40.2 g/L with temperature-shift time within 24 h. These results demonstrated that the temperature-shift process enhances the saccharification ratio and the ethanol production yield in SSF, and the temperature-shift time for TS-SSF process can be changed according to the fermentation condition within 24 h.\n\nCellulosic ethanol production on temperature-shift simultaneous saccharification and fermentation using the thermostable yeast Kluyveromyces marxianus CHY1612.", "token_count": 366, "char_count": 1351, "word_count": 188, "semantic_coherence": 1, "information_density": 0.5532, "quality_score": 0.7766, "entities": { "genes": [ "CHY1612" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:03.477480", "source": { "split": "train_shard_00001", "doc_id": 3060 }, "chunk_id": "train_shard_00001_3060_0", "global_id": 10007 }, { "text": "Genome-wide characterization of genetic variants of a large population of individuals within the same species is essential to have a deeper insight into its evolutionary history as well as the genotype-phenotype relationship. Population genomic surveys have been performed in multiple yeast species, including the two model organisms, Saccharomyces cerevisiae and Schizosaccharomyces pombe . In this context, we sought to explore an uncharacterized yeast species, Brettanomyces bruxellensis , which is a major cause of wine spoilage but also can contribute to the specific flavor profile of some Belgium beers. We have completely sequenced the genome of 53 B. bruxellensis strains isolated worldwide. The annotation of the reference genome allowed us to define the gene content of this species. As previously suggested, our genomic data clearly highlighted that genetic diversity variation is related to ploidy level, which is variable in the B. bruxellensis species. Genomes are punctuated by multiple loss-of-heterozygosity regions while aneuploidies as well as segmental duplications are uncommon. Interestingly, triploid genomes are more prone to gene copy number variation than diploids. Finally, the pangenome of the species was reconstructed and was found to be small with few accessory genes compared to S. cerevisiae . The pangenome is composed of 4,923 core ORFs and 303 ORFs that are variable within the population. All these results highlight the different trajectories of species evolution and consequently the interest of establishing population genomic surveys in more populations.\n\nHigh complexity and degree of genetic variation inBrettanomyces bruxellensispopulation", "token_count": 387, "char_count": 1691, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:04.134024", "source": { "split": "train_shard_00001", "doc_id": 3061 }, "chunk_id": "train_shard_00001_3061_0", "global_id": 10008 }, { "text": "

Objectives

Disease caused by the bacterium Neisseria meningitidis remains a worldwide public health challenge, despite the steadily decreasing incidence in Western countries. The objective of this study was to explore the epidemiology of invasive meningococcal disease in Norway over the last two decades.

Design

All isolates sent to the National Reference Laboratory from patients with invasive meningococcal disease between the years 2000 and 2019 were analyzed using whole genome sequencing (total: 625).

Results

A five-fold decrease in case numbers occurred over this period, and the situation has gone from being dominated by serogroup B to one where serogroups Y and W are more prevalent. Concurrently, the mean age at infection has increased from 18 to 33 years. Among the 350 serogroup B isolates, 87% were an exact match or cross-reactive with one or both the currently available serogroup B vaccines, but the proportion decreased in the past decade. Core genome analyses revealed a high variation in the number of allelic differences accumulated in epidemiologically linked isolates to the point that near-identical isolates were found several years apart.

Conclusion

Allelic distance is an imprecise metric for the degree of epidemiologic linkage between isolates in N. meningitidis.\n\nInvasive meningococcal disease in Norway in the two decades before the COVID-19 pandemic.", "token_count": 361, "char_count": 1414, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6766, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:04.722714", "source": { "split": "train_shard_00001", "doc_id": 3062 }, "chunk_id": "train_shard_00001_3062_0", "global_id": 10009 }, { "text": "Burkholderia (B.) mallei is a host-adapted equine pathogen that causes glanders, a re-emerging zoonotic disease, which is endemic in Pakistan and other developing countries and seriously impacts the global equine movement. Due to globalization, the geographical restriction of diseases vanishes and the lack of awareness of and experience with eradicated diseases in industrialized countries also promotes the re-introduction of infections in these regions. Owing to the high equine population, the Pakistani province Punjab is a potential hotspot where several glanders outbreaks have been seen over last two decades. For determining the genomic diversity of B. mallei in this and other equine-populated prefectures, the genomes of 19 B. mallei strains isolated between 1999 and 2020 in different locations were sequenced and their genotypes were determined. Particularly, for genetically highly homogenous pathogens like B. mallei genotyping techniques require a high discriminatory power for enabling differentiation on the strain level. Thus, core-genome single nucleotide polymorphism (cgSNP) analysis was applied for distinguishing the highly similar strains. Furthermore, a whole-genome sequence-based core genome multi locus sequence typing (cgMLST) scheme, specific to B. mallei, was developed and additionally applied to the data. It was found that B. mallei genotypes in Pakistan persisted over time and space and genotype clusters preferred connection with a time point rather than the place of isolation, probably due to frequent equine movement, which promotes the spread of glanders. The cgMLST approach proved to work in accord with SNP typing and may help to investigate future glanders outbreaks.\n\nSequencing-Based Genotyping of Pakistani Burkholderia mallei Strains: A Useful Way for Investigating Glanders Outbreaks.", "token_count": 495, "char_count": 1899, "word_count": 260, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:05.375218", "source": { "split": "train_shard_00001", "doc_id": 3063 }, "chunk_id": "train_shard_00001_3063_0", "global_id": 10010 }, { "text": "Staphylococcus epidermidis (S. epidermidis) is part of the human skin flora but can also cause nosocomial infections, such as device-associated infections, especially in vulnerable patient groups. Here, we investigated clinical isolates of linezolid-resistant S. epidermidis (LRSE) collected from blood cultures at the University Hospital Münster (UHM) during the period 2020-2022. All detected isolates were subjected to whole genome sequencing (WGS) and the relatedness of the isolates was determined using core genome multilocus sequence typing (cgMLST). The 15 LRSE isolates detected were classified as multilocus sequence type (ST) 2 carrying the staphylococcal cassette chromosome mec (SCCmec) type III. All isolates showed high-level resistance for linezolid by gradient tests. However, no isolate carried the cfr gene that is often associated with linezolid resistance. Analysis of cgMLST data sets revealed a cluster of six closely related LRSE isolates, suggesting a transmission event on a hematological/oncological ward at our hospital. Among the included patients, the majority of patients affected by LRSE infections had underlying hematological malignancies. This confirms previous observations that this patient group is particularly vulnerable to LRSE infection. Our data emphasize that the surveillance of LRSE in the hospital setting is a necessary step to prevent the spread of multidrug-resistant S. epidermidis among vulnerable patient groups, such as patients with hematological malignancies, immunosuppression or patients in intensive care units.\n\nMolecular Characterization of Clinical Linezolid-Resistant Staphylococcus epidermidis in a Tertiary Care Hospital.", "token_count": 459, "char_count": 1742, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6594, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:06.018098", "source": { "split": "train_shard_00001", "doc_id": 3064 }, "chunk_id": "train_shard_00001_3064_0", "global_id": 10011 }, { "text": "Postbiotics are non-viable probiotic preparations that confer a health benefit on the host. In the last years, scientific literature has proved that postbiotics have health-promoting features and technological advantages compared to probiotics, augmenting their full potential application in the food and pharmaceutical industries. The current work comprehensively summarizes the benefits and potential applications of postbiotics and essential mineral-enriched biomass and proposes a new strategy for microbial therapy-mineral-enriched postbiotics. We hypothesize and critically review the relationship between micronutrients (calcium, magnesium, iron, zinc, selenium) and postbiotics with gut microbiota, which has been barely explored yet, and how the new approach could be involved in the gut microbiome modulation to prevent and treat gut dysbiosis. Additionally, the bioactive molecules and minerals from postbiotics could influence the host mineral status, directly or through gut microbiota, which increases the mineral bioavailability. The review increases our understanding of the health improvements of mineral-enriched postbiotics, including antioxidant functions, highlighting their perspective on microbial therapy to prevent and threaten gut-related diseases.\n\nMineral-Enriched Postbiotics: A New Perspective for Microbial Therapy to Prevent and Treat Gut Dysbiosis.", "token_count": 317, "char_count": 1381, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6328, "quality_score": 0.8164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:06.573291", "source": { "split": "train_shard_00001", "doc_id": 3065 }, "chunk_id": "train_shard_00001_3065_0", "global_id": 10012 }, { "text": "It is to provide a novel Kluyveromyces marxianus transformant having thermotolerance and flocculation property, suitable for the industrial production of bioethanol, by introducing a foreign flocculation gene into Kluyveromyces marxianus, and an efficient method for producing the transformant. The present inventors focused on the flocculation gene FLO of Saccharomyces cerevisiae as a foreign gene to confer flocculation property to Kluyveromyces marxianus and produced a linear DNA fragment comprising a known expression promoter sequence and a FLO gene sequence derived from Saccharomyces cerevisiae. As a result of introducing this linear DNA fragment into Kluyveromyces marxianus, the present inventors have confirmed that Kluyveromyces marxianus transformant can be obtained efficiently, and that the flocculation property of the above transformant is unexpectedly and significantly enhanced. The present invention has been thus completed.\n\nFLOCCULENT YEAST AND METHOD FOR PRODUCTION THEREOF", "token_count": 236, "char_count": 998, "word_count": 135, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:07.046273", "source": { "split": "train_shard_00001", "doc_id": 3066 }, "chunk_id": "train_shard_00001_3066_0", "global_id": 10013 }, { "text": "Disclosed is a novel transformant of Kluyveromyces marxianus, which is produced by introducing a foreign flocculation gene into a bacterium Kluyveromyces marxianus, and has suitable levels of heat resistance and flocculating properties for the industrial production of bioethanol. Also disclosed is a method for producing the transformant with efficiency. Attention has focused on a Saccharomyces cerevisiae flocculation gene FLO as a foreign gene for imparting flocculating properties to a bacterium Kluyveromyces marxianus, and a linear DNA fragment containing a known expression promoter sequence and a FLO gene sequence originated from Saccharomyces cerevisiae is produced.; The linear DNA fragment is introduced into a bacterium Kluyveromyces marxianus, and it is confirmed that a transformant of Kluyveromyces marxianus can be produced efficiently and that the flocculating properties of the transformant is significantly improved unexpectedly.\n\nFLOCCULENT YEAST AND METHOD FOR PRODUCTION THEREOF", "token_count": 241, "char_count": 1002, "word_count": 138, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:07.526472", "source": { "split": "train_shard_00001", "doc_id": 3067 }, "chunk_id": "train_shard_00001_3067_0", "global_id": 10014 }, { "text": "Abstract

Staphylococcus aureus colonises the nose in humans, with individuals defined as persistent, intermittent or non-carriers. Unlike the gut microbiome, the nasal microbiome has not been studied in large numbers of people. Here, we define the nasal microbiome in ~ 1,100 individuals and combine this with S. aureus culture data. We identify seven community state types (CST), including two CSTs found more commonly in females. Approximately 70% of those who are persistently colonised with S. aureus have a single CST microbiome dominated by S. aureus, while non-carriers are distributed across the other six CSTs. Intermittent carriers are not a unique state but have microbiomes that resemble either non- or persistent carriers. Persistent carriage is positively associated with S. aureus abundance, and negatively associated with three Corynebacterium species, Dolosigranulum pigrum, Staphylococcus epidermidis, and Moraxella catarrhalis; the microbiome can be exploited with machine learning to accurately predict S. aureus colonisation status. Finally, we find that certain S. aureus lineages are likely better adapted to colonisation. Our data provides a comprehensive view of the nasal microbiome with respect to S. aureus colonisation, describing two key states: a S. aureus dominated CST in which S. aureus shapes the microbiome, and a group of CSTs in which S. aureus is rare or absent.

\n\nThe nasal microbiome redefines Staphylococcus aureus colonisation", "token_count": 511, "char_count": 1746, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6279, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:08.176261", "source": { "split": "train_shard_00001", "doc_id": 3068 }, "chunk_id": "train_shard_00001_3068_0", "global_id": 10015 }, { "text": "Two related anaerobic strains, designated as SWB101512T and SWB19611, were isolated from the bronchoalveolar lavage fluid of two lung cancer patients. Cells were Gram-stain-positive, non-motile and non-spore-forming. Growth could be observed at 26-45 °C (optimum, 37 °C), pH 5.0-8.5 (optimum, pH 7.0) and with 0.5-2.0 % (v/w) NaCl (optimum, 1.0%). The 16S rRNA gene sequences of SWB101512T and SWB19611 showed the highest similarities to Denitrobacterium detoxificans DSM 21843T (91.1 and 91.3 %, respectively). The phylogenetic tree based on the 16S rRNA gene sequences and the core genome sequences demonstrated that the two strains clustered together and formed a distinct lineage within the family Eggerthellaceae. The DNA G+C contents of strains SWB101512T and SWB19611 were 62.0 and 61.9 mol%, respectively. The predominant cellular fatty acids of strains SWB101512T and SWB19611 were C16 : 0 DMA (27.8 and 28.8 %, respectively). The respiratory menaquinone in both strains was menaquinone 6 and the polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, two phospholipids, three glycolipids and three unidentified lipids", "token_count": 478, "char_count": 1231, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6788, "quality_score": 0.8394, "entities": { "genes": [ "SWB19611", "SWB101512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:08.824079", "source": { "split": "train_shard_00001", "doc_id": 3069 }, "chunk_id": "train_shard_00001_3069_0", "global_id": 10016 }, { "text": "Based on evidence from phenotypic, chemotaxonomic and genomic analyses, a new genus and species belonging to the family Eggerthellaceae, named Curtanaerobium respiraculi gen. nov., sp. nov. is proposed. The type strain is SWB101512T (=GDMCC 1.2991T=JCM 35330T).\n\nCurtanaerobium respiraculi gen. nov., sp. nov., a novel anaerobic bacterium isolated from human bronchoalveolar lavage fluid.", "token_count": 169, "char_count": 442, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7885, "quality_score": 0.8942, "entities": { "genes": [ "SWB101512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:09.262384", "source": { "split": "train_shard_00001", "doc_id": 3069 }, "chunk_id": "train_shard_00001_3069_1", "global_id": 10017 }, { "text": "Salmonella strains are traditionally classified into serovars based on their surface antigens. While increasing availability of whole-genome sequences has allowed for more detailed subtyping of strains, links between genotype, serovar, and host remain elusive. Here we reconstruct genome-scale metabolic models for 410 Salmonella strains spanning 64 serovars. Model-predicted growth capabilities in over 530 different environments demonstrate that: (1) the Salmonella accessory metabolic network includes alternative carbon metabolism, and cell wall biosynthesis; (2) metabolic capabilities correspond to each strain's serovar and isolation host; (3) growth predictions agree with 83.1% of experimental outcomes for 12 strains (690 out of 858); (4) 27 strains are auxotrophic for at least one compound, including L-tryptophan, niacin, L-histidine, L-cysteine, and p-aminobenzoate; and (5) the catabolic pathways that are important for fitness in the gastrointestinal environment are lost amongst extraintestinal serovars. Our results reveal growth differences that may reflect adaptation to particular colonization sites.\n\nGenome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.", "token_count": 320, "char_count": 1234, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7658, "quality_score": 0.8829, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:09.828435", "source": { "split": "train_shard_00001", "doc_id": 3070 }, "chunk_id": "train_shard_00001_3070_0", "global_id": 10018 }, { "text": "

Objective

We aimed to investigate the frequency of oral yeast colonization (OYC) and the risk factors for patients who received continuous ambulatory peritoneal dialysis (CAPD) or hemodialysis (HD) or were renal transplant recipients (RTRs). The patients admitted to the Nephrology Clinic at Ataturk University Medical School from January through April 2013 were included in the study. A questionnaire about risk factors was filled out, and swab cultures were taken from the tongue surface of each participant. OYC was detected in 32.1% of the RTRs, 40% of the HD patients, 20.9% of the CAPD patients, and 18% of the healthy control (HC) group. Of the 42 yeast strains isolated from the renal replacement therapy groups, 26 strains (61.9%) were Candida albicans, nine (21.4%) were Candida glabrata, two (4.7%) were Candida krusei, two (4.7%) were Candida kefyr, one (2.38%) was Candida parapsilosis, and two (4.7%) were Geotrichum candidum. Risk factors for OYC in the RTRs group included antibiotic use and the presence of dental prostheses; however, in patients with chronic renal failure undergoing CAPD, only the presence of dental prostheses was found to be a statistically significant risk factor. Although OYC was mostly detected in patients with chronic kidney disease (undergoing HD, a variety of isolated yeast strains in the RTRs was noted. The rates of OYC and isolated Candida species in CAPD were similar to those of the HC group.\n\nOral yeast colonization in peritoneal dialysis and hemodialysis patients and renal transplant recipients.", "token_count": 439, "char_count": 1559, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5394, "quality_score": 0.7697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:10.456609", "source": { "split": "train_shard_00001", "doc_id": 3071 }, "chunk_id": "train_shard_00001_3071_0", "global_id": 10019 }, { "text": "The gut microbiome modulates immunotherapy treatment responses, and this may explain why immune checkpoint inhibitors, such as anti-PD-1, are only effective in some patients. Previous studies correlated lipopolysaccharide (LPS)-producing gut microbes with poorer prognosis; however, LPS from diverse bacterial species can range from immunostimulatory to inhibitory. Here, by functionally analysing faecal metagenomes from 112 patients with melanoma, we found that a subset of LPS-producing bacteria encoding immunostimulatory hexa-acylated LPS was enriched in microbiomes of clinical responders. In an implanted tumour mouse model of anti-PD-1 treatment, microbiota-derived hexa-acylated LPS was required for effective anti-tumour immune responses, and LPS-binding antibiotics and a small-molecule TLR4 antagonist abolished anti-PD-1 efficacy. Conversely, oral administration of hexa-acylated LPS to mice significantly augmented anti-PD-1-mediated anti-tumour immunity. Penta-acylated LPS did not improve anti-PD-1 efficacy in vivo and inhibited hexa-acylated LPS-induced immune activation in vitro. Microbiome hexa-acylated LPS therefore represents an accessible predictor and potential enhancer of immunotherapy responses.\n\nGut microbiota-derived hexa-acylated lipopolysaccharides enhance cancer immunotherapy responses.", "token_count": 361, "char_count": 1322, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7215, "quality_score": 0.8608, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:11.048462", "source": { "split": "train_shard_00001", "doc_id": 3072 }, "chunk_id": "train_shard_00001_3072_0", "global_id": 10020 }, { "text": "Bacteria can acquire an accessory genome through the horizontal transfer of genetic elements from non-parental lineages. This leads to rapid genetic evolution allowing traits such as antibiotic resistance and virulence to spread through bacterial communities. The study of complete genomes of bacterial strains helps to understand the genomic traits associated with virulence and antibiotic resistance. We aimed to investigate the complete accessory genome of an ocular isolate of P. aeruginosa. We obtained the complete genome of the ocular isolate strain PA34 of P. aeruginosa utilising genome sequence reads from Illumina and Oxford Nanopore Technology followed by PCR to close any identified gaps. In-depth genomic analysis was performed using various bioinformatics tools. The phenotypic properties of susceptibility to heavy metals and cytotoxicity were determined to confirm expression of certain traits. The complete genome of PA34 includes a chromosome of 6.8 Mbp and two plasmids of 95.4 Kbp (pMKPA34-1) and 26.8 Kbp (pMKPA34-2). PA34 had a large accessory genome of 1,213 genes and had 543 unique genes not present in other strains. These exclusive genes encoded features related to metal and antibiotic resistance, phage integrase and transposons. At least 24 GIs were predicated in the complete chromosome, of which two were integrated into novel sites. Eleven GIs carried virulence factors or replaced pathogenic genes. A bacteriophage carried the aminoglycoside resistance gene (aac(3)-IId). The two plasmids carried other six antibiotic resistance genes. The large accessory genome of this ocular isolate plays a large role in shaping its virulence and antibiotic resistance.\n\nAccessory genome contributes to the virulence and resistance of the ocular isolate of Pseudomonas aeruginosa: A complete genome analysis", "token_count": 456, "char_count": 1829, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5618, "quality_score": 0.7809, "entities": { "genes": [ "PA34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:11.685002", "source": { "split": "train_shard_00001", "doc_id": 3073 }, "chunk_id": "train_shard_00001_3073_0", "global_id": 10021 }, { "text": "Campylobacter species are among the leading foodborne bacterial agents of human diarrheal illness. The majority of campylobacteriosis has been attributed to Campylobacter jejuni (85% or more), followed by Campylobacter coli (5-10%). The distribution of C. jejuni and C. coli varies by host organism, indicating that the contribution to human infection may differ between isolation sources. To address the relative contribution of each source to C. coli infections in humans, core genome multilocus sequence type with a 200-allele difference scheme (cgMLST200) was used to determine cgMLST type for 3,432 C. coli isolated from food animals (n = 2,613), retail poultry meats (n = 389), human clinical settings (n = 285), and environmental sources (n = 145). Source attribution was determined by analyzing the core genome with a minimal multilocus distance methodology (MMD). Using MMD, a higher proportion of the clinical C. coli population was attributed to poultry (49.6%) and environmental (20.9%) sources than from cattle (9.8%) and swine (3.2%). Within the population of C. coli clinical isolates, 70% of the isolates that were attributed to non-cecal retail poultry, dairy cattle, beef cattle and environmental waters came from two cgMLST200 groups from each source. The most common antibiotic resistance genes among all C", "token_count": 447, "char_count": 1442, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6269, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:12.322019", "source": { "split": "train_shard_00001", "doc_id": 3074 }, "chunk_id": "train_shard_00001_3074_0", "global_id": 10022 }, { "text": "coli were tetO (65.6%), bla OXA - 193 (54.2%), aph(3')-IIIa (23.5%), and aadE-Cc (20.1%). Of the antibiotic resistance determinants, only one gene was isolated from a single source: bla OXA - 61 was only isolated from retail poultry. Within cgMLST200 groups, 17/17 cgMLST200-435 and 89/92 cgMLST200-707 isolates encoded for aph(3')-VIIa and 16/16 cgMLST200-319 harbored aph(2')-If genes. Distribution of bla OXA alleles showed 49/50 cgMLST200-5 isolates contained bla OXA - 498 while bla OXA - 460 was present in 37/38 cgMLST200-650 isolates. The cgMLST200-514 group revealed both ant(6)-Ia and sat4 resistance genes in 23/23 and 22/23 isolates, respectively", "token_count": 514, "char_count": 1008, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7423, "quality_score": 0.8711, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:33:12.975808", "source": { "split": "train_shard_00001", "doc_id": 3074 }, "chunk_id": "train_shard_00001_3074_1", "global_id": 10023 }, { "text": "Also, cgMLST200-266 and cgMLST200-84 had GyrAT86I mutation with 16/16 (100%) and 14/15 (93.3%), respectively. These findings illustrate how cgMLST and MMD methods can be used to evaluate the relative contribution of known sources of C. coli to the human burden of campylobacteriosis and how cgMLST typing can be used as an indicator of antimicrobial resistance in C. coli.\n\nCore Genome MLST for Source Attribution of Campylobacter coli.", "token_count": 175, "char_count": 479, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7612, "quality_score": 0.8806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:13.419740", "source": { "split": "train_shard_00001", "doc_id": 3074 }, "chunk_id": "train_shard_00001_3074_2", "global_id": 10024 }, { "text": "Abstract

BackgroundNew strains of Pseudomonas aeruginosa are continuously being isolated and sequenced to increase the genomic accessibility of this important pathogen. This has led to the generation of an impressive dataset of closed P. aeruginosa genomes. To understand the difference between the strains, investigations are focused on the accessory genome, thereby constantly extending the known pan genome of P. aeruginosa as a species. Apart from follow-up studies, many of the publicly available genomes are only used in their original publication while additional in silico information, based on comparison to previously published genomes, is not being explored. In this study, we defined and investigated the genome of the environmental isolate P. aeruginosa KRP1 and compared it to more than 100 publicly available closed P. aeruginosa genomes. ResultsPseudomonas spp. KRP1 could clearly be identified as a P. aeruginosa isolate, via comparative genomics. By using different genomic island prediction programs, we could identify a total of 25 genomic islands that cover ~12% of the genome of P. aeruginosa KRP1. Based on intra-strain comparisons, we are able to predict the pathogenic potential of this environmental isolate. It shares a substantial amount of its genomic information with the highly virulent PSE9 and LESB58 strains. For both of these clones, their increased virulence has been directly linked to their accessory genome before. ConclusionsHere we show, how the integrated use of previously published genomic data today, can help to replace expensive and time consuming wetlab work to determine the pathogenetic potential of environmental isolates. This knowledge is vital to understand what makes an isolate a potential pathogen as it helps design effective treatment.

", "token_count": 492, "char_count": 2009, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8102, "entities": { "genes": [ "PSE9", "KRP1", "LESB58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:14.072664", "source": { "split": "train_shard_00001", "doc_id": 3075 }, "chunk_id": "train_shard_00001_3075_0", "global_id": 10025 }, { "text": "Estimation of pathogenic potential of an environmental Pseudomonas aeruginosa isolate using comparative genomics", "token_count": 25, "char_count": 112, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:14.441435", "source": { "split": "train_shard_00001", "doc_id": 3075 }, "chunk_id": "train_shard_00001_3075_1", "global_id": 10026 }, { "text": "Starmerella bacillaris is often isolated from environments associated with grape and winemaking. S. bacillaris has many beneficial properties, including the ability to improve the flavor of wine, the production of beneficial metabolites, and the ability to biocontrol. S. bacillaris CC-PT4 (CGMCC No. 23573) was isolated from grape and can inhibit methicillin-resistant Staphylococcus aureus and adaptability to harsh environments. In this paper, the whole genome of S. bacillaris CC-PT4 was sequenced and bioinformatics analyses were performed. The S. bacillaris CC-PT4 genome was finally assembled into five scaffolds with a genome size of 9.45 Mb and a GC content of 39.5%. It was predicted that the strain contained 4150 protein-coding genes, of which two genes encoded killer toxin and one gene encoded lysostaphin. It also contains genes encoding F1F0-ATPases, Na(+)/H(+) antiporter, cation/H(+) antiporter, ATP-dependent bile acid permease, major facilitator superfamily (MFS) antiporters, and stress response protein, which help S. bacillaris CC-PT4 adapt to bile, acid, and other stressful environments. Proteins related to flocculation and adhesion have also been identified in the S. bacillaris CC-PT4 genome. Predicted by antiSMASH, two secondary metabolite biosynthesis gene clusters were found, and the synthesized metabolites may have antimicrobial effects. Furthermore, S. bacillaris CC-PT4 carried genes associated with pathogenicity and drug resistance. Overall, the whole genome sequencing and analysis of S. bacillaris CC-PT4 in this study provide valuable information for understanding the biological characteristics and further development of this strain.", "token_count": 513, "char_count": 1747, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [ "PT4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:33:15.107265", "source": { "split": "train_shard_00001", "doc_id": 3076 }, "chunk_id": "train_shard_00001_3076_0", "global_id": 10027 }, { "text": "Whole-Genome Analysis of Starmerella bacillaris CC-PT4 against MRSA, a Non-Saccharomyces Yeast Isolated from Grape.", "token_count": 52, "char_count": 129, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "PT4" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:15.484705", "source": { "split": "train_shard_00001", "doc_id": 3076 }, "chunk_id": "train_shard_00001_3076_1", "global_id": 10028 }, { "text": "Anaerobic batch fermentations of ricotta cheese whey (i.e. containing lactose) were performed under different operating conditions. Ethanol concentrations of ca. 22g L(-1) were found from whey containing ca. 44g L(-1) lactose, which corresponded to up to 95% of the theoretical ethanol yield within 15h. The experimental data could be explained by means of a simple knowledge-driven biochemically structured model that was built on bioenergetics principles applied to the metabolic pathways through which lactose is converted into major products. Use of the model showed that the observed concentrations of ethanol, lactose, biomass and glycerol during batch fermentation could be described within a ca. 6% deviation, as could the yield coefficients for biomass and ethanol produced on lactose. The model structure confirmed that the thermodynamics considerations on the stoichiometry of the system constrain the metabolic coefficients within a physically meaningful range thereby providing valuable and reliable insight into fermentation processes.\n\nA biochemically structured model for ethanol fermentation by Kluyveromyces marxianus: A batch fermentation and kinetic study.", "token_count": 283, "char_count": 1176, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:16.094462", "source": { "split": "train_shard_00001", "doc_id": 3077 }, "chunk_id": "train_shard_00001_3077_0", "global_id": 10029 }, { "text": "Ligilactobacillus salivarius is a widely used probiotic in human and animal nutrition, particularly for enhancing performance in poultry farming. Supplementing feed with this bacterium has shown benefits such as reducing Salmonella Enteritidis colonization and promoting weight gain. This study investigated the probiotic potential of a newly isolated strain, L. salivarius L33, obtained from the gut of broiler chickens. We employed a series of in vitro tests to assess its probiotic characteristics. These tests evaluated its resistance to simulated digestive conditions, lack of hemolytic activity on blood cells, adherence ability to intestinal surfaces, antibiotic susceptibility, and antimicrobial activity. Whole-genome sequencing of L. salivarius L33 using the Illumina NovaSeq6000 platform revealed 1,870 genes encoding 1,797 proteins. Comparative analysis identified 111 unique genes involved in critical cellular functions such as replication, repair, and defense mechanisms. Additionally, the genome harbored a bacteriocin gene encoding salivaricin, a potent antimicrobial compound. Furthermore, genes associated with key probiotic properties were identified, including stress tolerance, adhesion to gut epithelia, and survival in acidic and bile salt environments. These findings strongly suggest the probiotic potential of L. salivarius L33. The presence of genes linked to established probiotic functionalities and its similarity to known probiotic strains of L. salivarius make it a promising candidate for further research and development as a novel probiotic for poultry applications.IMPORTANCELigilactobacillus salivarius is a well-studied probiotic with proven benefits in poultry farming, including improved growth and reduced pathogen colonization. This study characterizes a novel strain, L. salivarius L33, isolated from broiler chickens, and demonstrates its potential as a probiotic through genomic and functional analyses", "token_count": 507, "char_count": 2011, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:16.752111", "source": { "split": "train_shard_00001", "doc_id": 3078 }, "chunk_id": "train_shard_00001_3078_0", "global_id": 10030 }, { "text": "The strain's genome reveals genes linked to stress tolerance, gut adhesion, and antimicrobial activity, including salivaricin, a bacteriocin with broad anti-pathogen effects. These findings are significant because they highlight L33's promise as a natural, safe alternative to antibiotics in poultry production, aligning with global efforts to reduce antimicrobial resistance. Further development of this strain could enhance animal health, productivity, and food safety, offering economic and public health benefits.\n\nWhole-genome analysis of <i>Ligilactobacillus salivarius</i> L33, a potential probiotic strain isolated from chicken gastrointestinal tract.", "token_count": 165, "char_count": 671, "word_count": 83, "semantic_coherence": 1, "information_density": 0.8795, "quality_score": 0.9398, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:17.195798", "source": { "split": "train_shard_00001", "doc_id": 3078 }, "chunk_id": "train_shard_00001_3078_1", "global_id": 10031 }, { "text": "Bdellovibrio spp. are predatory bacteria with great potential as antimicrobial agents. Studies have shown that members of the genus Bdellovibrio exhibit peculiar characteristics that influence their ecological adaptations. In this study, whole genomes of two different Bdellovibrio spp. designated SKB1291214 and SSB218315 isolated from soil were sequenced. The core genes shared by all the Bdellovibrio spp. considered for the pangenome analysis including the epibiotic B. exovorus were 795. The number of unique genes identified in Bdellovibrio spp. SKB1291214, SSB218315, W, and B. exovorus JJS was 1343, 113, 857, and 1572, respectively. These unique genes encode hydrolytic, chemotaxis, and transporter proteins which might be useful for predation in the Bdellovibrio strains. Furthermore, the two Bdellovibrio strains exhibited differences based on the % GC content, amino acid identity, and 16S rRNA gene sequence. The 16S rRNA gene sequence of Bdellovibrio sp. SKB1291214 shared 99% identity with that of an uncultured Bdellovibrio sp. clone 12L 106 (a pairwise distance of 0.008) and 95-97% identity (a pairwise distance of 0.043) with that of other culturable terrestrial Bdellovibrio spp., including strain SSB218315. In Bdellovibrio sp", "token_count": 488, "char_count": 1338, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6611, "quality_score": 0.8306, "entities": { "genes": [ "SKB1291214", "SSB218315" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:17.842051", "source": { "split": "train_shard_00001", "doc_id": 3079 }, "chunk_id": "train_shard_00001_3079_0", "global_id": 10032 }, { "text": "SKB1291214, 174 bp sequence was inserted at the host interaction (hit) locus region usually attributed to prey attachment, invasion, and development of host independent Bdellovibrio phenotypes. Also, a gene equivalent to Bd0108 in B. bacteriovorus HD100 was not conserved in Bdellovibrio sp. SKB1291214. The results of this study provided information on the genetic characteristics and diversity of the genus Bdellovibrio that can contribute to their successful applications as a biocontrol agent.\n\nWhole-Genome Sequencing and Comparative Genome Analysis Provided Insight into the Predatory Features and Genetic Diversity of Two Bdellovibrio Species Isolated from Soil.", "token_count": 223, "char_count": 718, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7634, "quality_score": 0.8817, "entities": { "genes": [ "SKB1291214", "HD100" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:18.311618", "source": { "split": "train_shard_00001", "doc_id": 3079 }, "chunk_id": "train_shard_00001_3079_1", "global_id": 10033 }, { "text": "

A bstract

Saccharibacteria (formerly TM7) have reduced genomes, a small size, and appear to have a parasitic lifestyle dependent on a bacterial host. Although there are at least 6 major clades of Saccharibacteria inhabiting the human oral cavity, cultured isolates or complete genomes of oral Saccharibacteria have been previously limited to the G1 clade. In this study, nanopore sequencing was used to obtain three complete genome sequences from clade G6. Phylogenetic analysis suggested the presence of at least 3-5 distinct species within G6, with two discrete taxa represented by the 3 complete genomes. G6 Saccharibacteria were highly divergent from the more well-studied clade G1, and had the smallest genomes and lowest GC-content of all Saccharibacteria. Pangenome analysis showed that although 97% of shared pan-Saccharibacteria core genes and 89% of G1-specific Core Genes had putative functions, only 50% of the 244 G6-specific Core Genes had putative functions, highlighting the novelty of this group. Compared to G1, G6 encoded divergent metabolic pathways. G6 genomes lacked an F1F0 ATPase, the pentose phosphate pathway, and several genes involved in nucleotide metabolism, which were all core genes for G1. G6 genomes were also unique compared to G1 in that they encoded lactate dehydrogenase, adenylate cyclase, limited glycerolipid metabolism, a homolog to a lipoarabinomannan biosynthesis enzyme, and the means to degrade starch. These differences at key metabolic steps suggest a distinct lifestyle and ecological niche for clade G6, possibly with alternative hosts and/or host-dependencies, which would have significant ecological, evolutionary, and likely pathogenic, implications.

I mportance

Saccharibacteria are ultrasmall, parasitic bacteria that are common members of the oral microbiota and have been increasingly linked to disease and inflammation", "token_count": 509, "char_count": 1896, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6241, "quality_score": 0.812, "entities": { "genes": [ "TM7" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:18.966509", "source": { "split": "train_shard_00001", "doc_id": 3080 }, "chunk_id": "train_shard_00001_3080_0", "global_id": 10034 }, { "text": "However, the lifestyle and impact on human health of Saccharibacteria remains poorly understood, especially for the 5 clades (G2-G6) with no complete genomes or cultured isolates. Obtaining complete genomes is of particular importance for Saccharibacteria, because they lack many of the “essential” core genes used for determining draft genome completeness and few references exist outside of clade G1. In this study, complete genomes of 3 G6 strains, representing two candidate species, were obtained and analyzed. The G6 genomes were highly divergent from G1, and enigmatic, with 50% of the G6 core genes having no putative functions. The significant difference in encoded functional pathways is suggestive of a distinct lifestyle and ecological niche, probably with alternative hosts and/or host-dependencies, which would have major implications in ecology, evolution, and pathogenesis.\n\nComplete genomes of clade G6 Saccharibacteria suggest a divergent ecological niche and lifestyle", "token_count": 226, "char_count": 987, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6738, "quality_score": 0.8369, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:19.440067", "source": { "split": "train_shard_00001", "doc_id": 3080 }, "chunk_id": "train_shard_00001_3080_1", "global_id": 10035 }, { "text": "Abstract

Background: Host and niche shifts are a source of genomic and phenotypic diversi_cation as evidenced in parasitism. Most characteristic is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversi_cation. However, selective pressures acting on the genome of such organisms are not fully understood. Results: Here, we developed a comparative genomic approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes inhabiting similar niches. We _nd that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes. Discussion: Given the high correlation of lifestyle to genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.

\n\nPredicting Lifestyle and Host From Positive Selection Data and Genome Properties in Oomycetes", "token_count": 327, "char_count": 1411, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:20.003603", "source": { "split": "train_shard_00001", "doc_id": 3081 }, "chunk_id": "train_shard_00001_3081_0", "global_id": 10036 }, { "text": "Brachyspira hyodysenteriae is the principal cause of swine dysentery, a disease that threatens economic productivity of pigs in many countries as it can spread readily within and between farms, and only a small number of antimicrobials are authorized for treatment of pigs. In this study, we performed whole-genome sequencing (WGS) of 81 B. hyodysenteriae archived at the Animal and Plant Health Agency (APHA) from diagnostic submissions and herd monitoring in England and Wales between 2004 and 2015. The resulting genome sequences were analyzed alongside 34 genomes we previously published. Multi-locus sequence typing (MLST) showed a diverse population with 32 sequence types (STs) among the 115 APHA isolates, 25 of them identified only in England; while also confirming that the dominant European clonal complexes, CC8 and CC52, were common in the United Kingdom. A core-genome SNP tree typically clustered the isolates by ST, with isolates from some STs detected only within a specific region in England, although others were more widespread, suggesting transmission between different regions. Also, some STs were more conserved in their core genome than others, despite these isolates being from different holdings, regions and years. Minimum inhibitory concentrations to commonly used antimicrobials (Tiamulin, Valnemulin, Doxycycline, Lincomycin, Tylosin, Tylvalosin) were determined for 82 of the genome-sequenced isolates; genomic analysis revealed mutations generally correlated well with the corresponding resistance phenotype. There was a major swine dysentery intervention program in 2009-2010, and antimicrobial survival curves showed a significant reduction in sensitivity to tiamulin and valnemulin in isolates collected in and after 2010, compared to earlier isolates. This correlated with a significant increase in post-2009 isolates harboring the pleuromutilin resistance gene tva(A), which if present, may facilitate higher levels of resistance", "token_count": 491, "char_count": 1980, "word_count": 279, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [ "CC52", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:20.651757", "source": { "split": "train_shard_00001", "doc_id": 3082 }, "chunk_id": "train_shard_00001_3082_0", "global_id": 10037 }, { "text": "The reduction in susceptibility of Brachyspira from diagnostic submissions to pleuromutilins, emphasizes the need for prudent treatment, control and eradication strategies.\n\nWhole-Genome Sequencing of Brachyspira hyodysenteriae Isolates From England and Wales Reveals Similarities to European Isolates and Mutations Associated With Reduced Sensitivity to Antimicrobials.", "token_count": 107, "char_count": 384, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:21.029512", "source": { "split": "train_shard_00001", "doc_id": 3082 }, "chunk_id": "train_shard_00001_3082_1", "global_id": 10038 }, { "text": "The Arcobacteraceae bacterial family includes species isolated from animals and related food products. Moreover, these species have been found in other ecological niches, including water. Some species, particularly Arcobacter butzleri and Arcobacter cryaerophilus, have been isolated from human clinical cases and linked to gastrointestinal symptoms. The presence of antibiotic-resistant strains is a concern for public health, considering the possible zoonoses and foodborne infections caused by contaminated food containing bacteria resistant to antibiotic treatments. This review aims to highlight the importance of antibiotic resistance in Arcobacter spp. isolates from several sources, including information about antibiotic classes to which this bacterium has shown resistance. Arcobacter spp. demonstrated a wide spectrum of antibiotic resistance, including several antibiotic resistance genes. Antibiotic resistance genomic traits include efflux pumps and mutations in antibiotic target proteins. The literature shows a high proportion of Arcobacter spp. that are multidrug-resistant. However, studies in the literature have primarily focused on the evaluation of antibiotic resistance in A. butzleri and A. cryaerophilus, as these species are frequently isolated from various sources. These aspects underline the necessity of studies focused on several Arcobacter species that could potentially be isolated from several sources.\n\nArcobacteraceae: An Exploration of Antibiotic Resistance Featuring the Latest Research Updates.", "token_count": 383, "char_count": 1604, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:21.617624", "source": { "split": "train_shard_00001", "doc_id": 3083 }, "chunk_id": "train_shard_00001_3083_0", "global_id": 10039 }, { "text": "The study focuses on the in silico analysis of cysteine-rich secretory proteins and PR1-like (CAP) genes in finger lime (Citrus australasica), a citrus species known for its tolerance to Huanglongbing (HLB). We identified several PR1-like genes, all belonging to the CRISP family within the CAP superfamily. Of them, CaCAP2 transcript levels increased by over 300-fold in the finger lime compared to 'Valencia' sweet orange upon infection with 'Candidatus Liberibacter asiaticus' (CaLas). Localization studies using an EGFP fusion showed that the CAP2 protein is predominantly located in the nucleus, extracellular and plasma membrane. The study also examined CAP2 transcript levels in response to cold, drought stress, and salicylic acid application. Despite environmental stress causing apparent damage, CAP genes seem to play a significant role in managing both biotic and abiotic stresses. Analysis of CAP2 gene promoters from finger lime and sweet orange revealed 95.33% sequence identity, with variations in transcription factor-binding sites and cis-acting elements such as Stress Response Element (STRE: AGGGG), which might influence the differential expression of CAP2 between the two species. Additionally, expressing the finger lime-derived CaCAP2 gene in transgenic Nicotiana tabacum induced a strong defense response against Pseudomonas syringae pv. Tabaci., underscoring the CAP gene's crucial role in plant defense mechanisms against bacterial pathogens.\n\nIdentification of CAP genes in finger lime (Citrus australasica) and their role in plant responses to abiotic and biotic stress.", "token_count": 395, "char_count": 1599, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [ "CAP2", "PR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:22.232201", "source": { "split": "train_shard_00001", "doc_id": 3084 }, "chunk_id": "train_shard_00001_3084_0", "global_id": 10040 }, { "text": "A microaerophilic Gram-stain-negative bacilliform bacterial strain, FB-5 T, was isolated from activated sludge in Yokohama, Japan, that exhibited filamentous growth and formed a microtube (sheath). Cells were motile using a single polar flagellum. The optimum growth temperature and pH were 30 °C and 7.5, respectively. Strain FB-5 T was catalase-negative. Peptides and amino acids were utilized as energy and carbon sources. Sugars and organic acids were not utilized. Vitamin B12 enhanced the growth of strain FB-5 T. Sulfur-dependent lithotrophic growth was possible. Major respiratory quinone was UQ-8. Major fatty acids were C16:1ω7 and C16:0. The genomic DNA G + C content was 69.16%. Phylogenetic analysis of the 16S rRNA gene suggested that strain FB-5 T belongs to the genus Sphaerotilus. The close relatives were S. natans subsup. sulfidivorans and S. natans subsup. natans with 98.0% and 97.8% similarity based on the 16S rRNA gene analysis, respectively. The genome size (6.06 Mbp) was larger than that (4.39-5.07 Mbp) of the Sphaerotilus strains. The AAI values against the related strains ranged from 71.0 to 72.5%. The range of ANI values was 81.7 - 82.5%. In addition to these distinguishable features of the genome, the core genome and dDDH analyses suggested that this strain is a novel member of the genus Sphaerotilus", "token_count": 483, "char_count": 1414, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:22.885454", "source": { "split": "train_shard_00001", "doc_id": 3085 }, "chunk_id": "train_shard_00001_3085_0", "global_id": 10041 }, { "text": "Based on its physiological properties and genomic features, strain FB-5 T is considered as a novel species of the genus Sphaerotilus, for which the name S. microaerophilus sp. nov. is proposed. The type strain is FB-5 T (= JCM 35424 T = KACC 23146 T).\n\nTaxonomic characterization of Sphaerotilus microaerophilus sp. nov., a sheath-forming microaerophilic bacterium of activated sludge origin.", "token_count": 164, "char_count": 436, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7833, "quality_score": 0.8917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:23.330706", "source": { "split": "train_shard_00001", "doc_id": 3085 }, "chunk_id": "train_shard_00001_3085_1", "global_id": 10042 }, { "text": "Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen.\n\niCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.", "token_count": 366, "char_count": 1294, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6389, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:23.912264", "source": { "split": "train_shard_00001", "doc_id": 3086 }, "chunk_id": "train_shard_00001_3086_0", "global_id": 10043 }, { "text": "The genomes of different individuals of the same prokaryote species can vary widely in gene content, displaying different proportions of core genes, which are present in all genomes, and accessory genes, whose presence varies between genomes. Together, these core and accessory genes make up a species’ pangenome. The reasons behind this extensive diversity in gene content remain elusive, and there is an ongoing debate about the contribution of accessory genes to fitness, that is, whether their presence is on average advantageous, neutral, or deleterious. In order to explore this issue, we developed a mathematical model to simulate the gene content of prokaryote genomes and pangenomes. Our model focuses on testing how the fitness effects of genes and their rates of gene gain and loss would affect the properties of pangenomes. We first show that pangenomes with large numbers of low-frequency genes can arise due to the gain and loss of neutral and nearly neutral genes in a population. However, pangenomes with large numbers of highly beneficial, low-frequency genes can arise as a consequence of genotype-by-environment interactions when multiple niches are available to a species. Finally, pangenomes can arise, irrespective of the fitness effect of the gained and lost genes, as long as gene gain and loss rates are high. We argue that in order to understand the contribution of different mechanisms to pangenome diversity, it is crucial to have empirical information on population structure, gene-by-environment interactions, the distributions of fitness effects and rates of gene gain and loss in different prokaryote groups.\n\nSelection-based model of prokaryote pangenomes", "token_count": 350, "char_count": 1688, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5253, "quality_score": 0.7626, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:24.494731", "source": { "split": "train_shard_00001", "doc_id": 3087 }, "chunk_id": "train_shard_00001_3087_0", "global_id": 10044 }, { "text": "

Background

Plasmodium vivax is the second most important cause of human malaria worldwide, and accounts for the majority of malaria cases in South America. A high-quality reference genome exists for Papua Indonesia (PvP01) and Thailand (PvW1), but is lacking for South America. A reference genome specifically for South America would be beneficial though, as P. vivax is a genetically diverse parasite with geographical clustering.

Results

This study presents a new high-quality assembly of a South American P. vivax isolate, referred to as PvPAM. The genome was obtained from a low input patient sample from the Peruvian Amazon and sequenced using PacBio technology, resulting in a highly complete assembly with 6497 functional genes. Telomeric ends were present in 17 out of 28 chromosomal ends, and additional (sub)telomeric regions are present in 12 unassigned contigs. A comparison of multigene families between PvPAM and the PvP01 genome revealed remarkable variation in vir genes, and the presence of merozoite surface proteins (MSP) 3.6 and 3.7. Three dhfr and dhps drug resistance associated mutations are present in PvPAM, similar to those found in other Peruvian isolates. Mapping of publicly available South American whole genome sequencing (WGS) data to PvPAM resulted in significantly fewer variants and truncated reads compared to the use of PvP01 or PvW1 as reference genomes. To minimize the number of core genome variants in non-South American samples, PvW1 is most suited for Southeast Asian isolates, both PvPAM and PvW1 are suited for South Asian isolates, and PvPAM is recommended for African isolates. Interestingly, non-South American samples still contained the least subtelomeric variants when mapped to PvPAM, indicating high quality of the PvPAM subtelomeric regions.

Conclusions

Our findings show that the PvPAM reference genome more accurately represents South American P. vivax isolates in comparison to PvP01 and PvW1", "token_count": 517, "char_count": 1976, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5932, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:33:25.151294", "source": { "split": "train_shard_00001", "doc_id": 3088 }, "chunk_id": "train_shard_00001_3088_0", "global_id": 10045 }, { "text": "In addition, PvPAM has a high level of completeness, and contains a similar number of annotated genes as PvP01 or PvW1. The PvPAM genome therefore will be a valuable resource to improve future genomic analyses on P. vivax isolates from the South American continent.\n\nA newPlasmodium vivaxreference genome for South American isolates", "token_count": 94, "char_count": 339, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8077, "quality_score": 0.9038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:25.529801", "source": { "split": "train_shard_00001", "doc_id": 3088 }, "chunk_id": "train_shard_00001_3088_1", "global_id": 10046 }, { "text": "

Background

The emergence and evolution of community-acquired methicillin resistant Staphylococcus aureus (CA-MRSA) strains in Africa is poorly understood. However, one particular MRSA lineage called ST88, appears to be rapidly establishing itself as an \"African\" CA-MRSA clone. In this study, we employed whole genome sequencing to provide more information on the genetic background of ST88 CA-MRSA isolates from Ghana and to describe in detail ST88 CA-MRSA isolates in comparison with other MRSA lineages worldwide.

Methods

We first established a complete ST88 reference genome (AUS0325) using PacBio SMRT sequencing. We then used comparative genomics to assess relatedness among 17 ST88 CA-MRSA isolates recovered from patients attending Buruli ulcer treatment centres in Ghana, three non-African ST88s and 15 other MRSA lineages.

Results

We show that Ghanaian ST88 forms a discrete MRSA lineage (harbouring SCCmec-IV [2B]). Gene content analysis identified five distinct genomic regions enriched among ST88 isolates compared with the other S. aureus lineages. The Ghanaian ST88 isolates had only 658 core genome SNPs and there was no correlation between phylogeny and geography, suggesting the recent spread of this clone. The lineage was also resistant to multiple classes of antibiotics including β-lactams, tetracycline and chloramphenicol.

Discussion

This study reveals that S. aureus ST88-IV is a recently emerging and rapidly spreading CA-MRSA clone in Ghana. The study highlights the capacity of small snapshot genomic studies to provide actionable public health information in resource limited settings. To our knowledge this is the first genomic assessment of the ST88 CA-MRSA clone.", "token_count": 488, "char_count": 1759, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6555, "quality_score": 0.8277, "entities": { "genes": [ "ST88", "AUS0325" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:26.173387", "source": { "split": "train_shard_00001", "doc_id": 3089 }, "chunk_id": "train_shard_00001_3089_0", "global_id": 10047 }, { "text": "Genomic analysis of ST88 community-acquired methicillin resistant Staphylococcus aureus in Ghana.", "token_count": 37, "char_count": 104, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:26.543041", "source": { "split": "train_shard_00001", "doc_id": 3089 }, "chunk_id": "train_shard_00001_3089_1", "global_id": 10048 }, { "text": "The high-pathogenicity island irp-HPI is widespread in Vibrionaceae and encodes the siderophore piscibactin, as well as the regulator PbtA that is essential for its expression. In this work, we aim to study whether PbtA directly interacts with irp-HPI promoters. Furthermore, we hypothesize that PbtA, and thereby the acquisition of irp-HPI island, may also influence the expression of other genes elsewhere in the bacterial genome. To address this question, an RNAseq analysis was conducted to identify differentially expressed genes after pbtA deletion in Vibrio anguillarum RV22 genetic background. The results showed that PbtA not only modulates the irp-HPI genes but also modulates the expression of a plethora of V. anguillarum core genome genes, inducing nitrate, arginine, and sulfate metabolism, T6SS1, and quorum sensing, while repressing lipopolysaccharide (LPS) production, MARTX toxin, and major porins such as OmpV and ChiP. The direct binding of the C-terminal domain of PbtA to piscibactin promoters (PfrpA and PfrpC), quorum sensing (vanT), LPS transporter wza, and T6SS structure- and effector-encoding genes was demonstrated by electrophoretic mobility shift assay (EMSA). The results provide valuable insights into the regulatory mechanisms underlying the expression of irp-HPI island and its impact on Vibrios transcriptome, with implications in pathogenesis.IMPORTANCEHorizontal gene transfer enables bacteria to acquire traits, such as virulence factors, thereby increasing the risk of the emergence of new pathogens", "token_count": 480, "char_count": 1630, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6743, "quality_score": 0.8372, "entities": { "genes": [ "RV22" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:27.215018", "source": { "split": "train_shard_00001", "doc_id": 3090 }, "chunk_id": "train_shard_00001_3090_0", "global_id": 10049 }, { "text": "irp-HPI genomic island has a broad dissemination in Vibrionaceae and is present in numerous potentially pathogenic marine bacteria, some of which can infect humans. Previous works showed that certain V. anguillarum strains exhibit an expanded host range plasticity and heightened virulence, a phenomenon linked to the acquisition of the irp-HPI genomic island. The present work shows that this adaptive capability is likely achieved through comprehensive changes in the transcriptome of the bacteria and that these changes are mediated by the master regulator PbtA encoded within the irp-HPI element. Our results shed light on the broad implications of horizontal gene transfer in bacterial evolution, showing that the acquired DNA can directly mediate changes in the expression of the core genome, with profounds implications in pathogenesis.\n\nRemodulation of bacterial transcriptome after acquisition of foreign DNA: the case of irp-HPI high-pathogenicity island in Vibrio anguillarum.", "token_count": 259, "char_count": 1036, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6831, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:27.792240", "source": { "split": "train_shard_00001", "doc_id": 3090 }, "chunk_id": "train_shard_00001_3090_1", "global_id": 10050 }, { "text": "Uptake of aflatoxin B1 (AFB1) and trichothecene T-2 toxin from growth medium by mycotoxin bioassay strains of Klutyveomyces marxianus and Bacillus megaterium was assessed by incubating, washing, and sonicating the cells, extracting samples with chloroform, and analysing the extracts by a combination of high-performance thin-layer chromatography (HPTLC) and fluorescence densitometry. Using cultures of K. marxianus, the entire AFB1 dose was recovered and no AFB1 metabolites were detected. Less than 1% of the AFB1 was recovered from the cells, and AFB1 did not inhibit growth. Methanol in the incubation medium had no significant effect on the levels of AFB1 associated with K. marxianus cells. The entire dose of T-2 toxin was also recovered from K. marxianus cultures, and no metabolites were detected; again, less than 1% of T-2 toxin was cell-associated, but growth was completely inhibited. AFB1 partially inhibited the growth of B. megaterium; approximately 12% of the dose could not be recovered, and no AFB1-related metabolites were detected. Methanol increased the levels of recoverable AFB1 associated with B. megaterium cells. In the case of T-2 toxin, around 8% of the dose was not recovered, and no metabolites were detected; growth of B. megaterium was stimulated. These results suggest irreversible binding of both toxins, or derivatives of them, to the cells of B. megaterium.\n\nUptake of aflatoxin B1 and T-2 toxin by two mycotoxin bioassay microorganisms: Kluyveromyces marxianus and Bacillus megaterium.", "token_count": 445, "char_count": 1524, "word_count": 230, "semantic_coherence": 1, "information_density": 0.4826, "quality_score": 0.7413, "entities": { "genes": [ "AFB1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:28.456925", "source": { "split": "train_shard_00001", "doc_id": 3091 }, "chunk_id": "train_shard_00001_3091_0", "global_id": 10051 }, { "text": "Rickettsia are intracellular bacteria originally described as arthropod borne pathogens that are emerging as a diverse group of often biologically important, non-pathogenic symbionts of invertebrates and microeukaryotes. However, sparse genomic resources for symbiotic strains and for the sister genus ( Candidatus Megaira) inhibit our understanding of Rickettsia evolution and biology. Here, we present the first closed genomes of Ca . Megaira from an alga ( Mesostigma viride ), and Torix Rickettsia from midge ( Culicoides impunctatus ) and bed bug ( Cimex lectularius ) hosts. Additionally, we sequenced and constructed draft genomes for Ca . Megaira from another alga ( Carteria cerasiformis ), Transitional group Rickettsia from tsetse fly ( Glossina morsitans submorsitans ), and Torix Rickettsia from a spider mite ( Bryobia graminum ). We further extract 22 draft genomes from arthropod genome sequencing projects, including 1 Adalia, 4 Transitional, 1 Spotted Fever, 7 Torix, 7 Belli and the first Rhyzobius and Meloidae Rickettsia group genomes. We used new and existing Rickettsia genomes to estimate the phylogeny and metabolic potential across groups and reveal transitions in genomic properties. These data reveal Torix as unique amongst currently described Rickettsia , with highly distinct and diverse accessory genomes. We confirm the presence of a third subclade of Torix, previously only known from gene marker sequences. Further, Torix share an intact pentose phosphate pathway with Ca . Megaira, not observed in other Rickettsia . Considering the distinctness and diversity of Torix, we propose that the group be named Candidatus Tisiphia. The wide host range of Ca . Tisiphia symbionts necessitates onward research to understand the biological and physiological bases of Ca . Tisiphia-host interactions.

Importance statement

Members of the genus Rickettsia were originally identified as causative agents of mammalian vector-borne disease", "token_count": 508, "char_count": 1969, "word_count": 289, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:29.117803", "source": { "split": "train_shard_00001", "doc_id": 3092 }, "chunk_id": "train_shard_00001_3092_0", "global_id": 10052 }, { "text": "In the last 25 years we have recognised that many Rickettsia are arthropod symbionts, and sit alongside a sister taxon, Ca . Megaira, which are symbiotic associates of microeukaryotes. The lack of genomic information for symbiotic strains affects our ability to determine the evolutionary relationships between strains and understand the biological underpinnings of the different symbioses. We clarify these relationships by assembling 26 genomes of Rickettsia from understudied groups, and the first two Ca . Megaira, from various insects and microeukaryotes. Of note, the accessory genome diversity and broad host range of Torix Rickettsia parallels all other Rickettsia combined. This diversity, alongside the breadth of host species, make the Torix clade an important hidden player in invertebrate biology and physiology. We argue this clade should be given its own genus status, for which we propose Ca . Tisiphia.\n\nLarge-scale comparative genomics unravels great genomic diversity across the Rickettsia and Ca. Megaira genera and identifies Torix group as an evolutionarily distinct clade", "token_count": 283, "char_count": 1108, "word_count": 161, "semantic_coherence": 1, "information_density": 0.677, "quality_score": 0.8385, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:29.678375", "source": { "split": "train_shard_00001", "doc_id": 3092 }, "chunk_id": "train_shard_00001_3092_1", "global_id": 10053 }, { "text": "In September 2017, a cluster of monophasic Salmonella Typhimurium isolates was identified at the National Reference Laboratory for Enteropathogenic Bacteria in Norway. We investigated the cluster to identify the source and implement control measures. We defined a case as a person with laboratory-confirmed salmonellosis with the outbreak strain multiple locus variable-number tandem repeat analysis type. We conducted descriptive epidemiological and environmental investigations and performed whole genome sequencing (WGS) with core and accessory genome multilocus sequence typing of all isolates from cases or the environment connected with this outbreak. We identified 21 cases, residing in 10 geographically dispersed counties, all of whom had consumed food or drinks from a café at Oslo Airport. Case distribution by date of symptom onset suggested that a point source was introduced in mid-August followed by continued environmental contamination. The incubation periods ranged 0-16 days and increased as the outbreak progressed, likely due to increasingly low-dose exposure as control measures were implemented. WGS confirmed an identical cluster type-944 in all cases and six environmental specimens from the café. Control measures, including temporary closure and kitchen refurbishment, failed to eliminate the environmental source. We recommend strengthened hygiene measures for established environmental contamination during an outbreak.\n\nIncreasing incubation periods during a prolonged monophasic Salmonella Typhimurium outbreak with environmental contamination of a commercial kitchen at Oslo Airport, Norway, 2017.", "token_count": 358, "char_count": 1643, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6409, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:30.259744", "source": { "split": "train_shard_00001", "doc_id": 3093 }, "chunk_id": "train_shard_00001_3093_0", "global_id": 10054 }, { "text": "The genus Photobacterium is known for its ecophysiological versatility encompassing free-living, symbiotic, and pathogenic lifestyles. Photobacterium sp. CCB-ST2H9 was isolated from estuarine sediment collected at Matang Mangrove, Malaysia. In this study, the genome of CCB-ST2H9 was sequenced, and the pan-genome of 37 Photobacterium strains was analysed. Phylogeny based on core genes showed that CCB-ST2H9 clustered with P. galatheae, forming a distinct clade with P. halotolerans, P. salinisoli, and P. arenosum. The core genome of Photobacterium was conserved in housekeeping functions, while the flexible genome was well represented by environmental genes related to energy production and carbohydrate metabolism. Genomic metrics including 16S rRNA sequence similarity, average nucleotide identity, and digital DNA-DNA hybridization values were below the cut-off for species delineation, implying that CCB-ST2H9 potentially represents a new species. Genome mining revealed that biosynthetic gene clusters (BGCs) involved in producing antimicrobial compounds such as holomycin in CCB-ST2H9 could contribute to the antagonistic potential. Furthermore, the EtOAc extract from the culture broth of CCB-ST2H9 exhibited antagonistic activity against Vibrio spp. Intriguingly, clustering based on BGCs profiles grouped P. galatheae, P. halotolerans, P. salinisoli, P. arenosum, and CCB-ST2H9 together in the heatmap by the presence of a large number of BGCs. These BGCs-rich Photobacterium strains represent great potential for bioactive secondary metabolites production and sources for novel compounds.", "token_count": 523, "char_count": 1700, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6729, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:33:30.921017", "source": { "split": "train_shard_00001", "doc_id": 3094 }, "chunk_id": "train_shard_00001_3094_0", "global_id": 10055 }, { "text": "Comparative Genomic Analyses of the Genus Photobacterium Illuminate Biosynthetic Gene Clusters Associated with Antagonism.", "token_count": 38, "char_count": 129, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:31.277559", "source": { "split": "train_shard_00001", "doc_id": 3094 }, "chunk_id": "train_shard_00001_3094_1", "global_id": 10056 }, { "text": "The evolution of microbial genome size is driven by gene acquisition and loss events that occur at scales from individual genomes to entire pangenomes. The equilibrium between gene gain and loss is shaped by evolutionary forces, including selection and drift, which are in turn influenced by population demographics. There is a well-known bias towards deletion in microbial genomes, which promotes genome streamlining. Less well described are mechanisms that promote genome expansion, giving rise to the many microbes, such as Streptomyces , that have unusually large genomes. We find evidence of genome expansion in Streptomyces sister-taxa, and we hypothesize that a recent demographic range expansion drove increases in genome size through a non-adaptive mechanism. These Streptomyces sister-taxa, NDR (northern-derived) and SDR (southern-derived), represent recently diverged lineages that occupy distinct geographic ranges. Relative to SDR genomes, NDR genomes are larger, have more genes, and their genomes are enriched in intermediate frequency genes. We also find evidence of relaxed selection in NDR genomes relative to SDR genomes. We hypothesize that geographic range expansion, coupled with relaxed selection, facilitated the introgression of non-adaptive horizontally acquired genes, which accumulated at intermediate frequencies through a mechanism known as genome surfing. We show that similar patterns of pangenome structure and genome expansion occur in a simulation that models the effects of population expansion on genome dynamics. We show that non-adaptive evolutionary phenomena can explain expansion of microbial genome size, and suggest that this mechanism might explain why some bacteria with large genomes can be found in soil.\n\nA non-adaptive demographic mechanism for genome expansion inStreptomyces", "token_count": 409, "char_count": 1834, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5504, "quality_score": 0.7752, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:31.904180", "source": { "split": "train_shard_00001", "doc_id": 3095 }, "chunk_id": "train_shard_00001_3095_0", "global_id": 10057 }, { "text": "

Summary

The Streptococcus pyogenes M1 UK lineage, characterised by an intrinsic ability to express SpeA toxin and defined by 27 single nucleotide polymorphisms in the core genome, dominates the population of emm 1 S. pyogenes isolates in England. The lineage has been identified elsewhere in Europe, North America, and, most recently, Australia. SpeA however may not be the sole deterministic factor underlying success of the M1 UK lineage. Production of SpeA by strains belonging to an intermediate emm 1 sublineage, M1 23SNP , is indistinguishable from M1 UK strains. Despite this, in England at least, M1 UK has outcompeted strains from the M1 23SNP sublineage. We infer that the fitness of M1 UK resides in additional properties that confer an advantage to S. pyogenes , underlining a need for further research. A single nucleotide polymorphism (SNP) in the ssrA leader sequence upstream of speA is one of a limited number of SNPs that distinguish intermediate sublineages that differ in SpeA production. Introduction of the ssrA SNP into representative isolates of the widely disseminated M1 global clone and the intermediate M1 13SNP lineage (that cannot otherwise produce readily-detectable SpeA in culture) resulted in SpeA expression, confirming the importance of the ssrA SNP to SpeA phenotype. However, RNAseq analysis of clinical strains showed that presence of the SNP was not invariably linked to read-through from the ssrA leader sequence or SpeA expression. Literature review suggests that read through and speA mRNA transcript length may be impacted by the two component regulator CovRS, pointing to a complex regulatory network interaction between the bacterial chromosome and phage-encoded superantigens.\n\nTricontinental detection of Streptococcus pyogenes M1UK: A call for wider research and active surveillance", "token_count": 466, "char_count": 1851, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5935, "quality_score": 0.7968, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:32.547208", "source": { "split": "train_shard_00001", "doc_id": 3096 }, "chunk_id": "train_shard_00001_3096_0", "global_id": 10058 }, { "text": "The color of smear cheeses (Muenster) is traditionally thought to be due to the bacterial flora, e.g., Brevibacterium linens. This study was carried out to evaluate indirect effects of yeast on the color of B. linens. A 60% cheese medium was desacidified with Debaryomyces hansenii or Kluyveromyces marxianus until pH 5.8 was reached. After inactivation of the yeast and addition of agar-NaCl, B. linens was inoculated on the medium surface and incubated at 12 degrees C from d 2 to 28. For each bacterial biofilm, color was evaluated by L*C*h(degrees) (brightness, chroma, hue angle) spectrocolorimetry. After d 14 (D. hansenii deacidification) and d 21 (K marxianus desacidification), the color level (as a function of all 3 factors) of B. linens biofilms became maximal and remained so until d 28. Debaryomyces hansenii 304 (LGMPA) was less efficient for deacidification than K. marxianus Laf5. However, color intensity (function of chroma only) was higher when D. hansenii was used. The yeast used had an effect on the composition of the cheese medium in relation to production and consumption of metabolites during deacidification. The results concerning color are discussed with respect to this cheese medium composition.\n\nThe color of Brevibacterium linens depends on the yeast used for cheese deacidification.", "token_count": 377, "char_count": 1317, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:33.128773", "source": { "split": "train_shard_00001", "doc_id": 3097 }, "chunk_id": "train_shard_00001_3097_0", "global_id": 10059 }, { "text": "β-Glucosidase from Kluyveromyces marxianus (KmBglI) belongs to the GH3 (glycoside hydrolase family 3). The enzyme is particularly unusual in that a PA14 domain (pf07691), for which a carbohydrate-binding role has been claimed, is inserted into the catalytic core sequence. In the present study, we determined the enzymatic properties and crystal structure of KmBglI in complex with glucose at a 2.55 A (1 A=0.1 nm) resolution. A striking characteristic of KmBglI was that the enzyme activity is essentially limited to disaccharides, and when trisaccharides were used as the substrates the activity was drastically decreased. This chain-length specificity is in sharp contrast with the preferred action on oligosaccharides of barley β-D-glucan glucohydrolase (ExoI), which does not have a PA14 domain insertion. The structure of subsite (-1) of KmBglI is almost identical with that of Thermotoga neapolitana β-glucosidase and is also similar to that of ExoI, however, the structures of subsite (+1) significantly differ among them. In KmBglI, the loops extending from the PA14 domain cover the catalytic pocket to form subsite (+1), and hence simultaneously become a steric hindrance that could limit the chain length of the substrates to be accommodated. Mutational studies demonstrated the critical role of the loop regions in determining the substrate specificity. The active-site formation mediated by the PA14 domain of KmBglI invokes α-complementation of β-galactosidase exerted by its N-terminal domain, to which the PA14 domain shows structural resemblance. The present study is the first which reveals the structural basis of the interaction between the PA14 domain and a carbohydrate.\n\nRole of a PA14 domain in determining substrate specificity of a glycoside hydrolase family 3 β-glucosidase from Kluyveromyces marxianus.", "token_count": 507, "char_count": 1831, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5683, "quality_score": 0.7841, "entities": { "genes": [ "PA14", "GH3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:33.780230", "source": { "split": "train_shard_00001", "doc_id": 3098 }, "chunk_id": "train_shard_00001_3098_0", "global_id": 10060 }, { "text": "Brucellosis, a zoonosis mainly transmitted by consumption of unpasteurized dairy products, is endemic in Southern Israel, mainly among the Bedouin Arab population. However, the genomic epidemiology of B. melitensis in this region has not yet been elucidated. A cohort of brucellosis cases (n = 118) diagnosed between 2017-2019 was studied using whole-genome sequencing (WGS). Phylogenetic analyses utilized core genome MLST (cgMLST) for all local isolates and core genome SNPs for 347 human-associated B. melitensis genomes, including Israeli and publicly available sequences. Israeli isolates formed two main clusters, presenting a notable diversity, with no clear dominance of a specific strain. On a global scale, the Israeli genomes clustered according to their geographical location, in proximity to genomes originating from the Middle East, and formed the largest cluster in the tree, suggesting relatively high conservation. Our study unveils the genomic epidemiology of B. melitensis in Southern Israel, implicating that rather than a common source, the transmission pattern of brucellosis among Bedouin communities is complex, predominantly local, and household-based. Further, genomic surveillance of B. melitensis is expected to inform future public health and veterinary interventions and clinical care.\n\nGenomic Epidemiology of Clinical Brucella melitensis Isolates from Southern Israel.", "token_count": 372, "char_count": 1442, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:34.375339", "source": { "split": "train_shard_00001", "doc_id": 3099 }, "chunk_id": "train_shard_00001_3099_0", "global_id": 10061 }, { "text": "To evaluate the potential of yeasts of dairy origin as probiotics, we tested 8 species including Candida humilis, Debaryomyces hansenii, Debaryomyces occidentalis, Kluyveromyces lactis, Kluyveromyces lodderae, Kluyveromyces marxianus, Saccharomyces cerevisiae, and Yarrowia lipolytica, isolated from commercial blue cheese and kefir. Strains were randomly selected from each species and tested for their ability to adhere to human enterocyte-like Caco-2 cells in culture. Among the 8 species, K. lactis showed higher adhesive ability than K. marxianus, K. lodderae, and D. hansenii. The other 4 species were poorly adhesive. All species other than K. marxianus and C. humilis were resistant to acidic conditions. In the presence of bile acid, growth inhibition was undetectable when incubation was carried out at 27 degrees C; however, it was evident for C. humilis and a strain of D. occidentalis when incubated at 37 degrees C. Moreover, the influence of proteinase treatment of living cells of K. lactis and K. lodderae on their adhesion to Caco-2 cells was evaluated. Although a slight reduction was recognized when K. lactis was treated with proteinase K, the influence of intestinal protease treatments of pepsin followed by trypsin was negligible. These results indicated that a proteinaceous factor was unlikely to be involved in adhesion of K. lactis and K. lodderae to Caco-2 cells. No stimulation of IL-8 synthesis by Caco-2 cells was recognized in the presence of K. lactis. In conclusion, K. lactis was the most attractive to continue study for use as probiotic microorganisms.\n\nScreening of dairy yeast strains for probiotic applications.", "token_count": 447, "char_count": 1652, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5737, "quality_score": 0.7869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:35.013187", "source": { "split": "train_shard_00001", "doc_id": 3100 }, "chunk_id": "train_shard_00001_3100_0", "global_id": 10062 }, { "text": "UDP-galactose 4-epimerase from yeast Kluyveromyces fragilis (Kluyveromyces marxianus var. marxianus) is a homodimer of molecular mass 75 kDa/subunit and has one mol NAD firmly bound/dimer. The pathway for the assembly of the holoenzyme structure has been studied after dissociating the native epimerase with p-chloromercuribenzoate into inactive mercurated monomers. The process of dissociation was not associated with unfolding of the molecules. Reconstitution of the functional holoenzyme was done by reduction with dithiothreitol and addition of extra NAD. The reaction was thus followed to monitor maturation of the enzyme from the folded monomeric state. The reconstituted enzyme was similar to the native enzyme in terms of a number of physiochemical properties such as secondary, tertiary and quarternary structures, Km for the substrate UDP-galactose, reductive inhibition, interaction with the fluorophore 1-anilino 8-naphthalene sulphonic acid (ANS), etc. Reconstitution under low ionic strength buffer (I = 0.011) shows that the presence of NAD is essential for the formation of a dimeric structure. However, dimeric apoenzyme could also be stabilized under high ionic strength buffer (I = 0.1). Reactivation was strongly dependent on pH, being most effective at pH 8.1. Kinetic evidence suggested that, at low ionic strength, assembly of NAD over dimeric apoenzyme is the rate-limiting step in expressing catalytic activity. This process has a low energy of activation of 27.2 kJ/mol.\n\nUDP-galactose 4-epimerase from Kluyveromyces fragilis: reconstitution of holoenzyme structure after dissociation with parachloromercuribenzoate.", "token_count": 464, "char_count": 1642, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:36.022050", "source": { "split": "train_shard_00001", "doc_id": 3101 }, "chunk_id": "train_shard_00001_3101_0", "global_id": 10063 }, { "text": "

ABSTRACT

Background

Prospective whole-genome sequencing (WGS)-based surveillance may be the optimal approach to rapidly identify transmission of multi-drug resistant (MDR) bacteria in the healthcare setting.

Materials/methods

We prospectively collected methicillin-resistant Staphylococcus aureus (MRSA), vancomycin-resistant enterococci (VRE), carbapenem-resistant Acinetobacter baumannii (CRAB), extended-spectrum beta-lactamase (ESBL-E) and carbapenemase-producing Enterobacterales (CPE) isolated from blood cultures, sterile sites or screening specimens across three large tertiary referral hospitals (2 adult, 1 paediatric) in Brisbane, Australia. WGS was used to determine in silico multi-locus sequence typing (MSLT) and resistance gene profiling via a bespoke genomic analysis pipeline. Putative transmission events were identified by comparison of core genome single nucleotide polymorphisms (SNPs). Relevant clinical meta-data were combined with genomic analyses via customised automation, collated into hospital-specific reports regularly distributed to infection control teams.

Results

Over four years (April 2017 to July 2021) 2,660 isolates were sequenced. This included MDR gram-negative bacilli (n=293 CPE, n=1309 ESBL), MRSA (n=620) and VRE (n=433). A total of 379 clinical reports were issued. Core genome SNP data identified that 33% of isolates formed 76 distinct clusters. Of the 76 clusters, 43 were contained to the three target hospitals, suggesting ongoing transmission within the clinical environment. The remaining 33 clusters represented possible inter-hospital transmission events or strains circulating in the community. In one hospital, proven negligible transmission of non-multi-resistant MRSA enabled changes to infection control policy", "token_count": 491, "char_count": 1806, "word_count": 222, "semantic_coherence": 1, "information_density": 0.7883, "quality_score": 0.8941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:36.676529", "source": { "split": "train_shard_00001", "doc_id": 3102 }, "chunk_id": "train_shard_00001_3102_0", "global_id": 10064 }, { "text": "

Conclusions

Implementation of routine WGS for MDR pathogens in clinical laboratories is feasible and can enable targeted infection prevention and control interventions.

Summary

We initiated a program of routine sequencing of multi-drug resistant organisms. A custom analysis pipeline was used to automate reporting by incorporating clinical meta-data with genomics to define clusters and support infection control interventions.\n\nClinical implementation of routine whole-genome sequencing for hospital infection control of multi-drug resistant pathogens", "token_count": 127, "char_count": 571, "word_count": 71, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:37.065132", "source": { "split": "train_shard_00001", "doc_id": 3102 }, "chunk_id": "train_shard_00001_3102_1", "global_id": 10065 }, { "text": "The appearance of transferable oxazolidinone resistance genes poses a major challenge to public health and environmental safety. These genes not only lead pathogenic bacteria to become resistant to linezolid but also reduce sensitivity to florfenicol, which is widely used in the veterinary field. To verify the dissemination of oxazolidinone resistance genes in enterococcal isolates from pigs at different production stages in a swine farm in China, we collected 355 enterococcal isolates that were resistant to florfenicol from 600 (150 per stage) fresh fecal swabs collected from a swine farm. Through initial PCR screening and whole-genome sequencing, 175 isolates harboring different oxazolidinone resistance genes were identified. All isolates carried the optrA gene. A total of 161 (92%, 161/175) isolates carried only the optrA gene. Three (1.71%, 3/175) isolates carried both the optrA and poxtA genes, and 11 (3.1%, 11/175) isolates contained the optrA gene and poxtA2 and cfr(D) variants. A total of 175 isolates that harbored oxazolidinone resistance genes included 161 E. faecalis, 6 E. faecium, and 8 E. hirae. By sequencing the whole genomes, we found that the 161 isolates of E. faecalis belonged to 28 different STs, including 8 new STs, and the 6 isolates of E. faecium belonged to four different STs, including one new ST. The phylogenetic tree based on SNPs of the core genome showed that both clonal spread and horizontal transfer mediated the diffusion of oxazolidone resistance genes in enterococcal isolates at specific stages in pig farms", "token_count": 511, "char_count": 1648, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5661, "quality_score": 0.7831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:37.706058", "source": { "split": "train_shard_00001", "doc_id": 3103 }, "chunk_id": "train_shard_00001_3103_0", "global_id": 10066 }, { "text": "Moreover, enterococcal isolates carrying oxazolidone resistance genes could spread from breeding pigs to fattening pigs, while transferable oxazolidone resistance genes in enterococcal isolates could persist on a pig farm throughout all production stages. Representative enterococcal isolates with different oxazolidinone resistance genes were further studied through Nanopore sequencing. We identified a novel plasmid, pM4-80 L4 (15,008 bp), carrying the poxtA2 and cfr(D) genes in enterococcal isolates at different stages. We also found three different plasmids harboring the poxtA gene with high genetic variation, and all poxtA genes were flanked by two copies of IS1216E elements. In addition, four genetically distinct plasmids carrying the optrA gene were identified, and Tn554 was found to mediate chromosome-localized optrA gene transfer. Our study highlighted that transferable oxazolidinone resistance genes in enterococcal isolates could persist throughout all production stages on a pig farm, and the prevalence and dissemination of oxazolidinone resistance genes in enterococcal isolates from animal farms should be continually monitored.\n\nPersistence of transferable oxazolidinone resistance genes in enterococcal isolates from a swine farm in China.", "token_count": 366, "char_count": 1322, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:38.292330", "source": { "split": "train_shard_00001", "doc_id": 3103 }, "chunk_id": "train_shard_00001_3103_1", "global_id": 10067 }, { "text": "Abstract

Datamining and metagenomic analyses of 277 open reading frame sequences of bipartite RNA viruses and variants in the genus Nepovirus documented how delicate it can be to unequivocally identify species, in particular subgroup A and C species, based on some of the currently adopted taxonomic demarcation criteria. It suggests a possible need for their amendment to accommodate pangenome information. In addition, we revealed a host-dependent structure of arabis mosaic virus (ArMV) populations at a cladistic level and confirmed a phylogeographic structure of grapevine fanleaf virus (GFLV) populations. We also identified new putative recombinant events for species of subgroups A, B and C. The evolutionary specificity of some capsid regions of ArMV and GFLV that were previously described and biologically validated as vector determinant was circumscribed in silico. Furthermore, a C-terminal segment of the RNA-dependent RNA polymerase of subgroup A species was predicted as a putative host range determinant based on statistically supported higher π values for GFLV and ArMV isolates infecting Vitis spp. compared to non-Vitis infecting ArMV isolates. This study illustrated how sequence information obtained via high throughput sequencing can increase our understanding of mechanisms that modulate virus diversity and evolution and create new opportunities for advancing studies on the biology of economically important plant viruses.

\n\nMetagenomic Analyses of Nepoviruses: Diversity, Evolution and Identification of a Hitherto Undescribed Putative Region for Host Range in Subgroup a Species", "token_count": 379, "char_count": 1628, "word_count": 229, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:38.909414", "source": { "split": "train_shard_00001", "doc_id": 3104 }, "chunk_id": "train_shard_00001_3104_0", "global_id": 10068 }, { "text": "The prevalence and transmission of mobile colistin resistance (mcr) genes have led to a severe threat to humans and animals. Escherichia fergusonii is an emerging pathogen which is closely related to a variety of diseases. However, the report of mcr genes harboring E. fergusonii is still rare. One study in Brazil reported the E. fergusonii isolates with IncHI2-type plasmids harboring mcr-1. A Chinese study reported two strains carrying mcr-1 gene with the same plasmid type IncI2. Here, we identified two strains of E. fergusonii carrying mcr-1 gene from farm environments with IncX4-type and IncI2-type plasmids, respectively. To our best knowledge, this is the first report about mcr-1 gene located on IncX4-type plasmid in E. fergusonii. We investigate the resistance mechanism of colistin-resistant Escherichia fergusonii strains 6S41-1 and 5ZF15-2-1 and elucidate the genetic context of plasmids carrying mcr-1 genes. In addition, we also investigated chromosomal mutations mediated colistin resistance in these two strains. Species identification was performed using MALDI-TOF MS and 16S rRNA gene sequencing. The detection of mcr-1 gene was determined by PCR and Sanger sequencing. S1-pulsed-field gel electrophoresis (PFGE), Southern blotting, antimicrobial susceptibility testing, conjugation experiments, complete genome sequencing, and core genome analysis were conducted to investigate the characteristics of isolates harboring mcr-1", "token_count": 486, "char_count": 1554, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:39.571505", "source": { "split": "train_shard_00001", "doc_id": 3105 }, "chunk_id": "train_shard_00001_3105_0", "global_id": 10069 }, { "text": "The mcr-1 genes on two strains were both plasmids encoded and the typical IS26-parA-mcr-1-pap2 cassette was identified in p6S41-1 while a nikA-nikB-mcr-1 locus sites on the conjugative plasmid p5ZF15-2-1. In addition, Core genome analysis reveals that E. fergusonii 6S41-1 and 5ZF15-2-1 have close genetic relationships. The mcr-1 gene is located on conjugative IncI2-type plasmid p5ZF15-2-1, which provides support for its further transmission. In addition, there's the possibility of mcr-1 spreading to humans through farm environments and thereby threatening public health. Therefore, continuous monitoring and investigations of mcr-1 among Enterobacteriaceae in farm environments are necessary to control the spread.\n\nGenomic Characterization of Two Escherichia fergusonii Isolates Harboring mcr-1 Gene From Farm Environment.", "token_count": 334, "char_count": 934, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7387, "quality_score": 0.8694, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:40.177328", "source": { "split": "train_shard_00001", "doc_id": 3105 }, "chunk_id": "train_shard_00001_3105_1", "global_id": 10070 }, { "text": "Klebsiella pneumoniae is an opportunistic gram-negative bacterium that causes nosocomial infection in healthcare settings. Despite the high morbidity and mortality rate associated with these bacterial infections, no effective vaccine is available to counter the pathogen. In this study, the pangenome of a total of 222 available complete genomes of K. pneumoniae was explored to obtain the core proteome. A reverse vaccinology strategy was applied to the core proteins to identify four antigenic proteins. These proteins were then subjected to epitope mapping and prioritization steps to shortlist nine B-cell derived T-cell epitopes which were linked together using GPGPG linkers. An adjuvant (Cholera Toxin B) was also added at the N-terminal of the vaccine construct to improve its immunogenicity and a stabilized multi-epitope protein structure was obtained using molecular dynamics simulation. The designed vaccine exhibited sustainable and strong bonding interactions with Toll-like receptor 2 and Toll-like receptor 4. In silico reverse translation and codon optimization also confirmed its high expression in E. coli K12 strain. The computer-aided analyses performed in this study imply that the designed multi-epitope vaccine can elicit specific immune responses against K. pneumoniae. However, wet lab validation is necessary to further verify the effectiveness of this proposed vaccine candidate.\n\nImmunoinformatics-Aided Design and Evaluation of a Potential Multi-Epitope Vaccine against Klebsiella Pneumoniae.", "token_count": 386, "char_count": 1564, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:40.796787", "source": { "split": "train_shard_00001", "doc_id": 3106 }, "chunk_id": "train_shard_00001_3106_0", "global_id": 10071 }, { "text": "DNA microarrays of 86 genes from the yeasts Debaryomyces hansenii, Kluyveromyces marxianus, and Yarrowia lipolytica were developed to determine which genes were expressed in a medium mimicking a cheese-ripening environment. These genes were selected for potential involvement in lactose/lactate catabolism and the biosynthesis of sulfur-flavored compounds. Hybridization conditions to follow specifically the expression of homologous genes belonging to different species were set up. The microarray was first validated on pure cultures of each yeast; no interspecies cross-hybridization was observed. Expression patterns of targeted genes were studied in pure cultures of each yeast, as well as in coculture, and compared to biochemical data. As expected, a high expression of the LAC genes of K. marxianus was observed. This is a yeast that efficiently degrades lactose. Several lactate dehydrogenase-encoding genes were also expressed essentially in D. hansenii and K. marxianus, which are two efficient deacidifying yeasts in cheese ripening. A set of genes possibly involved in l-methionine catabolism was also used on the array. Y. lipolytica, which efficiently assimilates l-methionine, also exhibited a high expression of the Saccharomyces cerevisiae orthologs BAT2 and ARO8, which are involved in the l-methionine degradation pathway. Our data provide the first evidence that the use of a multispecies microarray could be a powerful tool to investigate targeted metabolism and possible metabolic interactions between species within microbial cocultures.\n\nGene expression and biochemical analysis of cheese-ripening yeasts: focus on catabolism of L-methionine, lactate, and lactose.", "token_count": 427, "char_count": 1689, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5805, "quality_score": 0.7903, "entities": { "genes": [ "ARO8", "BAT2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:41.421775", "source": { "split": "train_shard_00001", "doc_id": 3107 }, "chunk_id": "train_shard_00001_3107_0", "global_id": 10072 }, { "text": "

Background

Host and niche shifts are a source of genomic and phenotypic diversification as evidenced in parasitism. Exemplary is core metabolism reduction as parasites adapt to a particular host, while the accessory genome often maintains a high degree of diversification. However, selective pressures acting on the genome of organisms that have undergone lifestyle or host change have not been fully investigated.

Results

Here, we developed a comparative genomics approach to study underlying adaptive trends in oomycetes, a eukaryotic phylum with a broad range of economically important plant and animal parasitic lifestyles. Our analysis reveals converging evolution on biological processes for oomycetes that have similar lifestyle. Besides, we find that certain functions, in particular carbohydrate metabolism, transport, and signaling, are important for host and environmental adaption in oomycetes.

Discussion

Given the high correlation between lifestyle and genome properties in our oomycete dataset and the convergent evolution of fungal and oomycete genomes, we have developed a model that predicts plant pathogen lifestyles with high accuracy based on functional annotations. Understanding how genomes and selective pressures correlate with lifestyle may be crucial to identify new emerging diseases and pandemic threats.\n\nPredicting lifestyle and host from positive selection data and genome properties in oomycetes", "token_count": 327, "char_count": 1455, "word_count": 200, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:41.983159", "source": { "split": "train_shard_00001", "doc_id": 3108 }, "chunk_id": "train_shard_00001_3108_0", "global_id": 10073 }, { "text": "Mycoplasma feriruminatoris is a fast-growing Mycoplasma species isolated from wild Caprinae and first described in 2013. M. feriruminatoris isolates have been associated with arthritis, keratoconjunctivitis, pneumonia and septicemia, but were also recovered from apparently healthy animals. To better understand what defines this species, we performed a genomic survey on 14 strains collected from free-ranging or zoo-housed animals between 1987 and 2017. The average chromosome size of the M. feriruminatoris strains was 1,040 ± 0,024 kbp, with 24% G+C and 852 ± 31 CDS. The core genome and pan-genome of the M. feriruminatoris species contained 628 and 1,312 protein families, respectively. The M. feriruminatoris strains displayed a relatively closed pan-genome, with many features and putative virulence factors shared with species from the M. mycoides cluster, including the MIB-MIP Ig cleavage system, a repertoire of DUF285 surface proteins and a complete biosynthetic pathway for galactan. M. feriruminatoris genomes were found to be mostly syntenic, although repertoires of mobile genetic elements, including Mycoplasma Integrative and Conjugative Elements, insertion sequences, and a single plasmid varied. Phylogenetic- and gene content analyzes confirmed that M. feriruminatoris was closer to the M. mycoides cluster than to the ruminant species M. yeatsii and M. putrefaciens . Ancestral genome reconstruction showed that the emergence of the M. feriruminatoris species was associated with the gain of 17 gene families, some of which encode defense enzymes and surface proteins, and the loss of 25 others, some of which are involved in sugar transport and metabolism. This comparative study suggests that the M. mycoides cluster could be extended to include M. feriruminatoris . We also find evidence that the specific organization and structure of the DnaA boxes around the oriC of M", "token_count": 527, "char_count": 1897, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [ "DUF285" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:33:42.632589", "source": { "split": "train_shard_00001", "doc_id": 3109 }, "chunk_id": "train_shard_00001_3109_0", "global_id": 10074 }, { "text": "feriruminatoris may contribute to drive the remarkable fast growth of this minimal bacterium.\n\nComparative genomics ofMycoplasma feriruminatoris, a fast-growing pathogen of wildCaprinae", "token_count": 60, "char_count": 199, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:42.991638", "source": { "split": "train_shard_00001", "doc_id": 3109 }, "chunk_id": "train_shard_00001_3109_1", "global_id": 10075 }, { "text": "Recent pangenome studies have revealed a large fraction of the gene content within a species exhibits presence-absence variation (PAV). However, coding regions alone provide an incomplete assessment of functional genomic sequence variation at the species level. Little to no attention has been paid to noncoding regulatory regions in pangenome studies, though these sequences directly modulate gene expression and phenotype. To uncover regulatory genetic variation, we generated chromosome-scale genome assemblies for thirty Arabidopsis thaliana accessions from multiple distinct habitats and characterized species level variation in Conserved Noncoding Sequences (CNS). Our analyses uncovered not only evidence for PAV and positional variation (PosV) but that diversity in CNS is non-random, with variants shared across different accessions. Using evolutionary analyses and chromatin accessibility data, we provide further evidence supporting roles for conserved and variable CNS in gene regulation. Characterizing species-level diversity in all functional genomic sequences may later uncover previously unknown mechanistic links between genotype and phenotype.\n\nEvolution of conserved noncoding sequences in Arabidopsis thaliana", "token_count": 252, "char_count": 1237, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7205, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:43.480794", "source": { "split": "train_shard_00001", "doc_id": 3110 }, "chunk_id": "train_shard_00001_3110_0", "global_id": 10076 }, { "text": "Large-scale genomic studies have identified within-host adaptation as a hallmark of bacterial infections. However, the impact of physiological, metabolic, and immunological differences between distinct niches on the pathoadaptation of opportunistic pathogens remains elusive. Here, we profile the within-host adaptation and evolutionary trajectories of 976 isolates representing 119 lineages of uropathogenic Escherichia coli (UPEC) sampled longitudinally from both the gastrointestinal and urinary tracts of 123 patients with urinary tract infections. We show that lineages persisting in both niches within a patient exhibit increased allelic diversity. Habitat-specific selection results in niche-specific adaptive mutations and genes, putatively mediating fitness in either environment. Within-lineage inter-habitat genomic plasticity mediated by mobile genetic elements (MGEs) provides the opportunistic pathogen with a mechanism to adapt to the physiological conditions of either habitat, and reduced MGE richness is associated with recurrence in gut-adapted UPEC lineages. Collectively, our results establish niche-specific adaptation as a driver of UPEC within-host evolution.\n\nPersisting uropathogenic Escherichia coli lineages show signatures of niche-specific within-host adaptation mediated by mobile genetic elements.", "token_count": 311, "char_count": 1329, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:44.047268", "source": { "split": "train_shard_00001", "doc_id": 3111 }, "chunk_id": "train_shard_00001_3111_0", "global_id": 10077 }, { "text": "

ABSTRACT

Given their remarkable beneficial effects on plant growth, several Azospirillum isolates currently integrate the formulations of various commercial inoculants. Our research group isolated a new strain, Azospirillum sp. UENF-412522, from passion fruit rhizoplane. This isolate uses carbon sources that are partially distinct from closely-related Azospirillum isolates. Scanning electron microscopy analysis and population counts demonstrate the ability of Azospirillum sp. UENF-412522 to colonize the surface of passion fruit roots. In vitro assays demonstrate the ability of Azospirillum sp. UENF-412522 to fix atmospheric nitrogen, to solubilize phosphate and to produce indole-acetic acid. Passion fruit plantlets inoculated with Azospirillum sp. UENF-41255 showed increased shoot and root fresh matter, as well as root dry matter, further highlighting its biotechnological potential for agriculture. We sequenced the genome of Azospirillum sp. UENF-412522 to investigate the genetic basis of its plant-growth promotion properties. We identified the key nif genes for nitrogen fixation, the complete PQQ operon for phosphate solubilization, the acdS gene that alleviates ethylene effects on plant growth, and the napCAB operon, which produces nitrite under anoxic conditions. We also found several genes conferring resistance to common soil antibiotics, which are critical for Azospirillum sp. UENF-412522 survival in the rhizosphere. Finally, we also assessed the Azospirillum pangenome and highlighted key genes involved in plant growth promotion. A phylogenetic reconstruction of the genus was also conducted. Our results support Azospirillum sp. UENF-412522 as a good candidate for bioinoculant formulations focused on plant growth promotion in sustainable systems.", "token_count": 469, "char_count": 1789, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6224, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:44.687862", "source": { "split": "train_shard_00001", "doc_id": 3112 }, "chunk_id": "train_shard_00001_3112_0", "global_id": 10078 }, { "text": "Characterization of cellular, biochemical and genomic features of the diazotrophic plant growth-promoting bacteriumAzospirillumsp. UENF-412522, a novel member of theAzospirillumgenus", "token_count": 71, "char_count": 196, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:45.051916", "source": { "split": "train_shard_00001", "doc_id": 3112 }, "chunk_id": "train_shard_00001_3112_1", "global_id": 10079 }, { "text": "

Background

The transmission of carbapenem-resistant Enterobacterales pose a significant threat to global public health, which weakens the effectiveness of most antimicrobial agents. The aim of this study is to present the genomic characteristics of a multidrug-resistant Escherichia coli, which contains both blaKPC-2 and blaCTX-M-15 genes, discovered from a respiratory infection in China.

Methods

The antimicrobial susceptibility of E. coli isolate 488 was measured by using the broth microdilution method. The Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms were applied to determine the whole-genome sequence of this isolate. De novo assembly of short Illumina reads and long MinION reads were performed by Unicycler. In silico multilocus sequence typing (MLST), antimicrobial resistance genes and plasmid replicon types were determined using the genome sequencing data. Additionally, a pairwise core genome single nucleotide polymorphism (cgSNP) comparison between E. coli 488 and all ST648 E. coli strains retrieved from NCBI GenBank database were conducted using the BacWGSTdb 2.0 server.

Results

E. coli 488 was resistant to aztreonam, levofloxacin, cefepime, fosfomycin, amikacin, imipenem, cefotaxime, and meropenem. The complete genome sequence of E. coli 488 (belong to ST648) is made up of eleven contigs totaling 5,573,915 bp, including one chromosome and ten plasmids", "token_count": 481, "char_count": 1493, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [ "ST648" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:45.700272", "source": { "split": "train_shard_00001", "doc_id": 3113 }, "chunk_id": "train_shard_00001_3113_0", "global_id": 10080 }, { "text": "Eight antimicrobial resistance genes were identified, including blaKPC-2 located in a 46,161 bp IncI1-type plasmid and the blaCTX-M-15 gene situated in the chromosome. Other two E. coli S617-2 and R616-1 isolates, recovered from China in 2018, are the closest relatives of E. coli 488, with only 52 SNPs difference. The genome also contains at least 57 genomic islands and several IS elements.

Conclusion

Our study reveals the first ST648 E. coli isolate containing both blaKPC-2 and blaCTX-M-15 in China. These results could provide valuable insights into the genetic characteristics, antimicrobial resistance mechanisms, and transmission dynamics of carbapenem-resistant Enterobacterales in clinical settings.\n\nGenomic Characteristics of a Multidrug-Resistant ST648 Escherichia coli Isolate Co-Carrying blaKPC-2 and blaCTX-M-15 Genes Recovered from a Respiratory Infection in China.", "token_count": 363, "char_count": 1027, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6917, "quality_score": 0.8458, "entities": { "genes": [ "ST648" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:46.278846", "source": { "split": "train_shard_00001", "doc_id": 3113 }, "chunk_id": "train_shard_00001_3113_1", "global_id": 10081 }, { "text": "Bacterial genetic variation originates through multiple mechanisms, including mutations during replication, movement of mobile elements, and various forms of recombination. As a result, genomes can be highly divergent with only a small fraction of genes core to all and a large pangenome of genes which have been identified in one or more sequenced samples. In this context, the ability to accurately detect genetic variation throughout the pangenome and compare many genomes remains a difficult problem. Here we present a novel pangenome reference graph structure, which represents the known genetic variation within a species as a collection of `floating' graphs. Each of these represents some homologous region such as a cluster of genes. By approximating a sequenced genome as a mosaic of genomes from the reference panel, this design forms the basis for a systematic framework in which to analyse diverse sets of samples where a single reference would be inappropriate. Applying this method to E. coli, we demonstrate how it enables us to describe genetic variation at both a coarse (gene presence) and a fine (SNP/indel) level. We demonstrate how this enables us to successfully compare divergent genomes within a species, ... (continues)\n\nPan-genomic analysis of clonal bacterial samples using nanopore reads and genome graphs", "token_count": 281, "char_count": 1333, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6293, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:46.835297", "source": { "split": "train_shard_00001", "doc_id": 3114 }, "chunk_id": "train_shard_00001_3114_0", "global_id": 10082 }, { "text": "A novel Neisseria strain, designated CSL10203-ORH2T, was isolated from the oropharynx of a wild California sea lion (Zalophus californianus) that was admitted to The Marine Mammal Center in California, USA. The strain was originally cultured from an oropharyngeal swab on BD Phenylethyl Alcohol (PEA) agar with 5% sheep blood under aerobic conditions. Phylogenetic analyses based on 16S rRNA, rplF, and rpoB gene sequences and the core genome sequences indicated that the strain was most closely related to only N. zalophi CSL 7565T. The average nucleotide identity and digital DNA-DNA hybridization values between strain CSL10203-ORH2T and the closely related species N. zalophi CSL 7565T were 89.84 and 39.70%, respectively, which were significantly lower than the accepted species-defined thresholds for describing novel prokaryotic species at the genomic level. Both type strains were phenotypically similar but can be easily and unambiguously distinguished between each other by the analysis of their housekeeping genes, e.g., rpoB, gyrB, or argF. The major fatty acids in both type strains were C12:0, C16:0, C16:1-c9, and C18:1-c11. Based on the genomic, phenotypic, and phylogenetic properties, the novel strain represents a novel species of the genus Neisseria, for which the name Neisseria montereyensis sp. nov", "token_count": 454, "char_count": 1431, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "CSL10203", "ORH2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:47.479827", "source": { "split": "train_shard_00001", "doc_id": 3115 }, "chunk_id": "train_shard_00001_3115_0", "global_id": 10083 }, { "text": "with the type strain CSL10203-ORH2T (= DSM 114706T = CCUG 76428T = NCTC 14721T) is proposed. The genome G + C content is 45.84% and the complete draft genome size is 2,310,535 bp.\n\nNeisseria montereyensis sp. nov., Isolated from Oropharynx of California Sea Lion (Zalophus californianus): Genomic, Phylogenetic, and Phenotypic Study.", "token_count": 187, "char_count": 377, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8627, "quality_score": 0.9314, "entities": { "genes": [ "CSL10203", "ORH2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:47.918591", "source": { "split": "train_shard_00001", "doc_id": 3115 }, "chunk_id": "train_shard_00001_3115_1", "global_id": 10084 }, { "text": "

Background

Colibacillosis, caused by avian pathogenic Escherichia coli (APEC), is one of the most significant infectious diseases affecting poultry worldwide.

Objectives

This study aimed to determine the genomic diversity, virulence factor genes (VFGs), and antimicrobial resistance genes (ARGs) in the APEC MTR_BAU02 strain isolated from a layer chicken using whole-genome sequencing (WGS).

Methods

Paired-end (2 × 250) WGS was performed using Illumina MiSeq sequencer (Illumina, San Diego, CA) and de novo assembly was performed using SPAdes. Core genome multilocus sequence typing (cgMLST) analysis between APEC MTR_BAU02 and all of the ST1196 E. coli strains retrieved from the National Center for Biotechnology Information (NCBI) GenBank database was performed using the BacWGSTdb 2.0 server. We utilized different databases to detect ARGs, VFGs, and genomic functional features of the APEC MTR_BAU02 strain.

Results

The complete genome of APEC MTR_BAU02 consists of 94 contigs comprising 4,924,680 bp (51.1% guanine-cytosine [GC] content), including 4681 protein-coding sequences, one chromosome, and one plasmid, and was assigned to ST1196. The closest relatives of APEC MTR_BAU02 were four isolates originating from human clinical specimens (diarrhetic stool) in Bangladesh and two clinical isolates originating from chicken in India, which differed by 694 core genome multilocus sequence typing (cgMLST) alleles. One hundred and twenty-two ARGs and 92 VFGs were identified in the APEC MTR_BAU02 genome", "token_count": 485, "char_count": 1539, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8382, "entities": { "genes": [ "ST1196" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:48.571535", "source": { "split": "train_shard_00001", "doc_id": 3116 }, "chunk_id": "train_shard_00001_3116_0", "global_id": 10085 }, { "text": "Metabolic functional annotations detected 380 SEED subsystems including genes coding for carbohydrate metabolism, protein metabolism, cofactors, vitamins, prosthetic groups and pigments, respiration, membrane transport, stress response, motility and chemotaxis, and virulence, disease, and defense.

Conclusion

This study reports the genome sequence of a multidrug-resistant APEC strain isolated from layer birds in Bangladesh. The ARGs and VFGs, widespread in APEC MTR_BAU02, are similar to those found in human isolates, and highlight the growing threat of antimicrobial resistance in both poultry and humans.\n\nGenomic characteristics, virulence, and antimicrobial resistance in avian pathogenic Escherichia coli MTR_BAU02 strain isolated from layer farm in Bangladesh.", "token_count": 211, "char_count": 777, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7449, "quality_score": 0.8724, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "respiration" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:49.030243", "source": { "split": "train_shard_00001", "doc_id": 3116 }, "chunk_id": "train_shard_00001_3116_1", "global_id": 10086 }, { "text": "Global agricultural industries are under pressure to meet the future food demand; however, the existing crop genetic diversity might not be sufficient to meet this expectation. Advances in genome sequencing technologies and availability of reference genomes for over 300 plant species reveals the hidden genetic diversity in crop wild relatives (CWRs), which could have significant impacts in crop improvement. There are many ex-situ and in-situ resources around the world holding rare and valuable wild species, of which many carry agronomically important traits and it is crucial for users to be aware of their availability. Here we aim to explore the available ex-/in- situ resources such as genebanks, botanical gardens, national parks, conservation hotspots and inventories holding CWR accessions. In addition we highlight the advances in availability and use of CWR genomic resources, such as their contribution in pangenome construction and introducing novel genes into crops. We also discuss the potential and challenges of modern breeding experimental approaches (e.g. de novo domestication, genome editing and speed breeding) used in CWRs and the use of computational (e.g. machine learning) approaches that could speed up utilization of CWR species in breeding programs towards crop adaptability and yield improvement.\n\nApplication of crop wild relatives in modern breeding: An overview of resources, experimental and computational methodologies.", "token_count": 317, "char_count": 1485, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:49.583499", "source": { "split": "train_shard_00001", "doc_id": 3117 }, "chunk_id": "train_shard_00001_3117_0", "global_id": 10087 }, { "text": "In this work, production of inulinase was carried out in a packed bed reactor (PBR) under solid state fermentation. Kluyveromyces marxianus var. marxianus was used to produce the inulinase using pressmud as substrate. The parameters like air flow rate, packing density and particle size were optimized using response surface methodology (RSM) to maximize the inulinase production. The optimum conditions for the maximum inulinase production were: air flow rate - 0.82 L/min, packing density - 40 g/L and particle size - 0.0044 mm (mesh - 14/20). At these optimized conditions, the production of inulinase was found to be 300.5 unit/gram of dry substrate (U/gds).\n\nInulinase production in a packed bed reactor by solid state fermentation.", "token_count": 204, "char_count": 737, "word_count": 114, "semantic_coherence": 1, "information_density": 0.6404, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:50.043082", "source": { "split": "train_shard_00001", "doc_id": 3118 }, "chunk_id": "train_shard_00001_3118_0", "global_id": 10088 }, { "text": "The aim of this work was to study the oxidative stress response of Kluyveromyces marxianus to hydrogen peroxide (50 mM), paraquat (1 mM), an increase in air pressure (120 kPa, 600 kPa) and pure oxygen pressure (120-600 kPa) in a pressurized bioreactor. The effect of these oxidants on metabolism and on the induction of antioxidant enzymes was investigated. The exposure for 1 h of K. marxianus at exponential growth phase with either H(2)O(2) or paraquat, under air pressure of 120 kPa or 600 kPa, induced an increase in both superoxide dismutase (SOD) and glutathione reductase (GR) content. SOD induction by the chemical oxidants was independent of the air pressure values used. A 2-fold increase in SOD activity was observed after 1 h of exposure to H(2)O(2) and a 3-fold increase was obtained by the presence of paraquat, with both air pressures studied. In contrast, GR activity was raised 1.7-fold by the exposure to both chemicals with 120 kPa, but a 2.4-fold GR induction was obtained with 600 kPa. As opposed to Saccharomyces cerevisiae, catalase was not induced and was even lower than the normal basal levels. This antioxidant enzyme seemed to be inhibited under increasing oxygen partial pressure. The cells showed a significant increase in SOD and GR activity levels, 4.7-fold and 4.4-fold, when exposed for 24 h to 120 kPa pure oxygen pressure. This behaviour was even more patent with 400 kPa. However, whenever cells were previously exposed to low air pressures, low enzymatic activity levels were measured after subsequent exposure to pure oxygen pressure.\n\nOxidative stress response of Kluyveromyces marxianus to hydrogen peroxide, paraquat and pressure.", "token_count": 489, "char_count": 1673, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5075, "quality_score": 0.7537, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:50.727231", "source": { "split": "train_shard_00001", "doc_id": 3119 }, "chunk_id": "train_shard_00001_3119_0", "global_id": 10089 }, { "text": "Tetragenococcus halophilus (T. halophilus) is a facultative anaerobic, coccus-shaped halophilic lactic acid-producing bacterium previously detected and cultured in various salty foods and credited for beneficial effects on human health. In this study, we investigated the presence of T. halophilus in human samples using a polyphasic approach including scanning electron microscopy, molecular biology methods and microbial culture. This unique investigation yielded the unprecedented presence of T. halophilus in human feces samples, thus enriching the repertoire of halophilic microorganisms colonizing the human gastrointestinal tract with the isolation and culture of T. halophilus for the first time in humans. Using the E-test strips, the MIC was assessed for T. halophilus strain CSURQ6002: rifampicin (MIC at 0.002 μg/mL), benzylpenicillin (MIC at 0.094 μg/mL), amoxicillin (MIC at 0.5 μg/mL), erythromycin (MIC at 2 μg/mL), clindamycin (MIC at 4 μg/mL), and vancomycin (MIC at 8 μg/mL). However, this strain showed a MIC up to 256 μg/mL for ciprofloxacin, fosfomycin, doxycyclin, imipenem, and colistin. In-silico profiling derived from whole genome sequencing (NCBI accession number: PRJNA780809), was confirmed. This discovery suggested that T. halophilus was part of the human digestive microbiota and that its potential role on human health should be considered.\n\nA Tetragenococcus halophilus human gut isolate.", "token_count": 511, "char_count": 1486, "word_count": 200, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "PRJNA780809", "CSURQ6002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:51.409644", "source": { "split": "train_shard_00001", "doc_id": 3120 }, "chunk_id": "train_shard_00001_3120_0", "global_id": 10090 }, { "text": "It has been found using a combination of atomic force microscopy with infrared spectroscopy, gel chromatography, and electrophoresis that inulinase from Kluyveromyces marxianus Y-303 has oligomeric structure, which includes two subunits differing in size, molecular mass, and catalytic activity. It has been shown that the division of the inulinase dimer into monomers leads to an increase in the number of irregular sites by 6% for subunit 1 (54.8 kDa) and by 10% for subunit 2 (8.4 kDa) compared with the native enzyme.\n\n[Oligomeric structure and physicochemical properties of inulinase from Kluyveromyces marxianus Y-303].", "token_count": 184, "char_count": 625, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7312, "quality_score": 0.8656, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:51.880618", "source": { "split": "train_shard_00001", "doc_id": 3121 }, "chunk_id": "train_shard_00001_3121_0", "global_id": 10091 }, { "text": "The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50 % pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple 'omic' strategies, combining Illumina and Pacific Biosciences Single-Molecule Real-Time DNA sequencing and annotation, stranded RNA sequencing and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53 and 74 % of the Sodalis transcriptome remains active in cell-free culture. The mean sense transcription from coding domain sequences (CDSs) is four times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40 % of the 2729 genes in the core genome, suggesting that they are stable and/or that Sodalis is a recent introduction across the genus Glossina as a facultative symbiont. These data shed further light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics gives a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.\n\nLarge-scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont.", "token_count": 434, "char_count": 1663, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6895, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:52.546837", "source": { "split": "train_shard_00001", "doc_id": 3122 }, "chunk_id": "train_shard_00001_3122_0", "global_id": 10092 }, { "text": "ST372 are widely reported as the major Escherichia coli sequence type in dogs globally. They are also a sporadic cause of extraintestinal infections in humans. Despite this, it is unknown whether ST372 strains from dogs and humans represent shared or distinct populations. Furthermore, little is known about genomic traits that might explain the prominence of ST372 in dogs or presence in humans. To address this, we applied a variety of bioinformatics analyses to a global collection of 407 ST372 E. coli whole-genome sequences to characterize their epidemiological features, population structure and associated accessory genomes. We confirm that dogs are the dominant host of ST372 and that clusters within the population structure exhibit distinctive O:H types. One phylogenetic cluster, 'cluster M', comprised almost half of the sequences and showed the divergence of two human-restricted clades that carried different O:H types to the remainder of the cluster. We also present evidence supporting transmission between dogs and humans within different clusters of the phylogeny, including M. We show that multiple acquisitions of the pdu propanediol utilization operon have occurred in clusters dominated by isolates of canine source, possibly linked to diet, whereas loss of the pdu operon and acquisition of K antigen virulence genes characterize human-restricted lineages.\n\nIdentification of genes influencing the evolution of Escherichia coli ST372 in dogs and humans.", "token_count": 367, "char_count": 1511, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6147, "quality_score": 0.8073, "entities": { "genes": [ "ST372" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:53.126184", "source": { "split": "train_shard_00001", "doc_id": 3123 }, "chunk_id": "train_shard_00001_3123_0", "global_id": 10093 }, { "text": "Efficient centromeric and multicopy vectors have been constructed for the yeast Kluyveromyces marxianus using homologous ARS and centromere sequences. A homologous promoter of a purine-cytosine permease gene called PCPL3 has been cloned, using an expression system based on GUS. Its strength has been estimated in K. marxianus by putting the homologous beta-glucosidase gene under its control. This promoter is very efficient as activities higher than the ones obtained with the Saccharomyces cerevisiae PGK promoter were obtained. This promoter appears to be constitutive in various conditions tested. Its five transcription start sites have been mapped, and a derivative expression vector for K. marxianus has been constructed.\n\nConstruction of efficient centromeric, multicopy and expression vectors for the yeast Kluyveromyces marxianus using homologous elements and the promoter of a purine-cytosine-like permease.", "token_count": 228, "char_count": 919, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6172, "quality_score": 0.8086, "entities": { "genes": [ "PCPL3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:53.602449", "source": { "split": "train_shard_00001", "doc_id": 3124 }, "chunk_id": "train_shard_00001_3124_0", "global_id": 10094 }, { "text": "

Background:

Vibrio cholerae , the etiologic agent of cholera, is indigenous to aquatic environments. The V. cholerae genome consists of two chromosomes; the smallest of these harbors a large gene capture and excision system called the superintegron (SI), of ~120 kbp. The flexible nature of the SI that results from gene cassette capture, deletion and rearrangement is thought to make it a hotspot of V. cholerae diversity, but beyond the basic structure it is not clear if there is a core genome in the SI and if so how it is structured. The aim of this study was to explore the core genome structure and the differences in gene content among strains of V. cholerae .

Methods:

: From the complete genomes of seven V. cholerae and one Vibrio mimicus representative strains, we recovered the SI sequences based on the locations of the structural gene IntI4 and the V. cholerae repeats. Analysis of the pangenome, including cluster analysis of functional genes, pangenome profile analysis, genetic variation analysis of functional genes, strain evolution analysis and function enrichment analysis of gene clusters, was performed using a pangenome analysis pipeline in addition to the R scripts, splitsTree4 and genoPlotR.

Results:

and conclusions: Here, we reveal the genetic architecture of the V. cholerae SI. It contains eight core genes when V. mimicus is included and 21 core genes when only V. cholerae strains are considered; many of them are present in several copies. The V. cholerae SI has an open pangenome, which means that V. cholerae may be able to import new gene cassettes to SI. The set of dispensable SI genes is influenced by the niche and type species. The core genes are distributed along the SI, apparently without a position effect.\n\nArchitecture of the superintegron in Vibrio cholerae: identification of core and unique genes", "token_count": 473, "char_count": 1877, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5362, "quality_score": 0.7681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:54.249816", "source": { "split": "train_shard_00001", "doc_id": 3125 }, "chunk_id": "train_shard_00001_3125_0", "global_id": 10095 }, { "text": "Gut microbes and their metabolites maintain the health and homeostasis of the host by communicating with the host via various biochemical and physical factors. Changing lifestyle, chronic intake of foods rich in refined carbohydrates and fats have caused intestinal dysbiosis and other lifestyle-based diseases. Thus, supplementation with probiotics has gained popularity as biotherapies for improving gut health and treating disorders. Research shows that probiotic organisms enhance gastrointestinal health, immunomodulation, generation of essential micronutrients, and prevention of cancer. Ethnically fermented milk and dairy products are hotspots for novel probiotic organisms and bioactive compounds. These ethnic fermented foods have been traditionally prepared by indigenous populations, and have preserved unique microflora for ages. To apply these unique microflora for amelioration of human health, it is important that probiotic properties of the bacterial species are well studied. Majority of the published research and reviews focus on the probiotic organisms and their properties, fermented food products, isolation techniques, and animal studies with their health pathologies. As a consequence, there is a dearth of information about the underlying molecular mechanism behind probiotics associated with ethnically prepared dairy foods. This review is targeted at stimulating research on understanding these mechanisms of bacterial species and beneficial attributes of ethnically fermented dairy products.\n\nMechanistic Insights Into Probiotic Properties of Lactic Acid Bacteria Associated With Ethnic Fermented Dairy Products.", "token_count": 355, "char_count": 1649, "word_count": 219, "semantic_coherence": 1, "information_density": 0.621, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:54.837019", "source": { "split": "train_shard_00001", "doc_id": 3126 }, "chunk_id": "train_shard_00001_3126_0", "global_id": 10096 }, { "text": "Sequence type 59 (ST59) is a predominant clonal lineage of community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) in Asia. Despite its increasing clinical relevance in China, the evolution and geographic expansion of ST59 has been relatively uncared for. Previous study has shown that ST59 was the predominant clone in food-related MRSA in China. This study compared the genomes of 87 clonal complex (CC) 59 S. aureus isolates sourced from food chain and infection cases to reconstruct the molecular evolution and geographical spread of ST59. Accordingly, three major sub-clades of ST59 were identified and these did not correlate with isolation source or location. Phylogenetic analysis estimated that ST59 in mainland China diverged from a most common recent ancestor around 1974, and most of the cases of cross-country transmission occurred between 1987 and 2000. Notably, two recent events of cross-country transmission through the food chain were observed, the isolates from these events diverged within relatively short time intervals. These isolates also showed high similarity in terms of their core genome, accessory genes, and antibiotic resistance patterns. These findings provide a valuable insight into the potential route of ST59 expansion in China and indicate a need for robust food chain surveillance to prevent the spread of this pathogen.\n\nThe Genomic Context for the Evolution and Transmission of Community-Associated Staphylococcus aureus ST59 Through the Food Chain.", "token_count": 378, "char_count": 1528, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [ "ST59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:55.424909", "source": { "split": "train_shard_00001", "doc_id": 3127 }, "chunk_id": "train_shard_00001_3127_0", "global_id": 10097 }, { "text": "Abstract

Background

Vancomycin-resistant enterococci (VRE) are a major cause of nosocomial bloodstream infections. Enterococci exhibit remarkable genomic plasticity and can recombine through the acquisition of genetic material via mobile genetic elements (MGEs), including resistance genes. The accessory genome plays a major role in the evolution of enterococci within the human host. Thus, dissecting the entire genome (pan-genome) is of paramount importance to characterize the population structure of enterococci causing disease.

Methods

VENOUS is an ongoing prospective, observational study of adults with enterococcal bacteremia. From September 2016 to March 2018, E. faecalis (Efs) and E. faecium (Efm) were collected in 14 hospitals of a single hospital system and a major cancer center in Houston, TX, and a general hospital in Detroit, MI. Short- and long-read genomic sequencing were performed with Illumina MiSeq and Oxford Nanopore Technologies GridION X5, respectively. A proprietary bioinformatics pipeline was utilized for genome assembly and further analyses.

Results

156 Efs and 98 Efm isolates from single patients were analyzed. The average proportion of core genes in each genome was 64.6% (53.0–74.1) and 49.1% (45.2–51.0) for Efs and Efm, respectively. The vanA gene cluster was identified in 5.1% (8/157) of Efs and 57.1% (56/98) of Efm. The plasmid-encoded aac(6′)-Ie-aph(2″)-Ia gene conferring high-level resistance to aminoglycosides was found in 37.6% (59/157) Efs, seven of which also possessed vanA. Long-read sequencing of vanA-harboring plasmids from a subset of VRE revealed that the vanA cluster was carried in plasmids ranging from 31.7 to 132.3 kb", "token_count": 515, "char_count": 1710, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6639, "quality_score": 0.832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:33:56.079656", "source": { "split": "train_shard_00001", "doc_id": 3128 }, "chunk_id": "train_shard_00001_3128_0", "global_id": 10098 }, { "text": "Although the vanA operon was fairly conserved, insertions of MGE were identified in the intergenic regions of vanS/vanH and vanX/vanY. Furthermore, a variety of MGE insertions mediated integration of the vanA operon, including IS1216 and IS256 (figure).

Conclusion

Accessory genes, including AMR genes, comprise a significant proportion of the enterococcal pan-genome, indicating major genetic plasticity within these organisms. Acquired resistance genes seem to have a high degree of recombination and play a substantial role in the expansion of the genomic repertoire in clinical isolates.

Disclosures

Samuel L. Aitken, PharmD, Melinta Therapeutics: Grant/Research Support, Research Grant; Merck, Sharpe, and Dohme: Advisory Board; Shionogi: Advisory Board.\n\n622. The Accessory Genome in Enterococcal Bacteremia: Results from the Vancomycin-Resistant Enterococcal Bacteremia Outcomes Study (VENOUS)", "token_count": 258, "char_count": 918, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7417, "quality_score": 0.8708, "entities": { "genes": [ "IS1216", "IS256" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:56.622437", "source": { "split": "train_shard_00001", "doc_id": 3128 }, "chunk_id": "train_shard_00001_3128_1", "global_id": 10099 }, { "text": "Four Gram-stain-positive, aerobic, non-motile and non-spore-forming actinobacterial strains (CPCC 206391T, CPCC 206453T, CPCC 206435T and CPCC 206450T) were isolated from soil samples collected from Tibet Autonomous Region, China. The 16S rRNA gene sequences of these four strains showed close relations to members of the genus Knoellia of the family Intrasporangiaceae, with similarities of 96.1-99.4% to the validly named species of Knoellia. In the phylogenetic trees based on 16S rRNA gene sequences and the core genome, these isolates clustered into the genus Knoellia clade within the lineage of the family Intrasporangiaceae. Genome relatedness index values between these strains and their phylogenetic neighbours, including average nucleotide identity (78.1-91.5%) and digital DNA-DNA hybridization (19.8-41.0%), were all below the species delineation thresholds. These genomic data, combined with their phenotypic characteristics, supported their classification within the genus Knoellia, representing four novel species. Thereby, Knoellia altitudinis sp. nov. (type strain CPCC 206391T=XZ253T=KCTC 59139T), Knoellia pratensis sp. nov. (type strain CPCC 206453T=CXZ644T=KCTC 59274T), Knoellia terrae sp. nov", "token_count": 510, "char_count": 1389, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6625, "quality_score": 0.8313, "entities": { "genes": [ "CXZ644", "XZ253" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:58.002132", "source": { "split": "train_shard_00001", "doc_id": 3129 }, "chunk_id": "train_shard_00001_3129_0", "global_id": 10100 }, { "text": "(type strain CPCC 206435T=CXZ904T=KCTC 59271T) and Knoellia tibetensis sp. nov. (type strain CPCC 206450T=XZ100T=KCTC 59273T) were proposed. These strains exhibited stable growth under high-intensity UV radiation, attributed to the presence of uvrABC and recAFNOQR genes involved in UV resistance and DNA repair. These features indicate the Knoellia spp. adaptation to high UV radiation environments.\n\n<i>Knoellia altitudinis</i> sp. nov., <i>Knoellia pratensis</i> sp. nov., <i>Knoellia terrae</i> sp. nov. and <i>Knoellia tibetensis</i> sp. nov., four novel UV radiation-resistant actinobacteria isolated from Tibet Autonomous Region, China.", "token_count": 322, "char_count": 792, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [ "CXZ904", "XZ100" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:58.568457", "source": { "split": "train_shard_00001", "doc_id": 3129 }, "chunk_id": "train_shard_00001_3129_1", "global_id": 10101 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) isolates remain a serious threat to global health despite a decrease in MRSA infections since 2005. MRSA isolates exhibit great diversity worldwide, and their lineages show geographic variation. In this study, we used whole genome sequencing (WGS) to analyze antibiotic resistance genes and virulence genes, spa, staphylococcal cassette chromosome mec, sequence types (STs), and core genome multilocus sequence typing (cgMLST) of MRSA isolates from patients and environmental surface in hospitals in China to determine their prevalence and molecular traits. The highest number of infections by MRSA isolates was observed in patients aged ≥60 years (69.8%, P < 0.05). We identified a total of 19 STs from 162 MRSA isolates from patients. A significant increase was observed in the incidence of ST764-t002-II MRSA infection, which is replacing ST5-t002-II MRSA as the predominant ST. Similarly, isolates from environmental surface were predominantly ST764-t002-II (47%). Notably, most ST764 isolates (97.7%) carried seb, but not arginine catabolic mobile element (ACME), which differed from ST764 isolates in Japan and Thailand. The potential danger of spreading requires rigorous surveillance of emerging ST764 MRSA isolates. We also found higher resistance to seven antimicrobials [OXA, cefoxitin (FOX), ERY, CFZ, ciprofloxacin (CIP), levofloxacin (LEV), and moxifloxacin (MXF)]. Resistance to gentamicin (38.3%), tetracycline (55.9%), and minocycline (41.5%) were also common. Phenotypic resistance to antimicrobials was associated with resistance genes to its content, and cgMLST clustering suggested a strong link between these strains", "token_count": 520, "char_count": 1724, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6851, "quality_score": 0.8426, "entities": { "genes": [ "ST5", "ST764" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:33:59.226348", "source": { "split": "train_shard_00001", "doc_id": 3130 }, "chunk_id": "train_shard_00001_3130_0", "global_id": 10102 }, { "text": "Overall, our findings revealed the prevalence and molecular characteristics of MRSA isolates in Shanghai, China, providing a theoretical reference for preventing and controlling clonal transmission of MRSA isolates in hospitals in China.\n\nPrevalence and WGS-based characteristics of MRSA isolates in hospitals in Shanghai, China.", "token_count": 65, "char_count": 329, "word_count": 44, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:33:59.587822", "source": { "split": "train_shard_00001", "doc_id": 3130 }, "chunk_id": "train_shard_00001_3130_1", "global_id": 10103 }, { "text": "This is the first reported case of maternal sepsis and placental transmission of Candida kefyr to premature fraternal twins. The mother consumed organic dairy products regularly throughout her pregnancy and developed sepsis with chorioamnionitis caused by C. kefyr. The twins developed respiratory distress at birth. The placenta, fetal membranes, and umbilical cords showed numerous colonies of yeasts, subsequently identified as C. kefyr. C. kefyr sepsis in preterm neonates should be considered when there is a significant maternal history of organic dairy product consumption during pregnancy.\n\nMaternal sepsis, chorioamnionitis, and congenital Candida kefyr infection in premature twins.", "token_count": 172, "char_count": 692, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7292, "quality_score": 0.8646, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:00.033636", "source": { "split": "train_shard_00001", "doc_id": 3131 }, "chunk_id": "train_shard_00001_3131_0", "global_id": 10104 }, { "text": "

Unlabelled

Shiga toxin-producing Escherichia coli (STEC) strains can colonize cattle for several months and may, thus, serve as gene reservoirs for the genesis of highly virulent zoonotic enterohemorrhagic E. coli (EHEC). Attempts to reduce the human risk for acquiring EHEC infections should include strategies to control such STEC strains persisting in cattle. We therefore aimed to identify genetic patterns associated with the STEC colonization type in the bovine host. We included 88 persistent colonizing STEC (STEC(per)) (shedding for ≥4 months) and 74 sporadically colonizing STEC (STEC(spo)) (shedding for ≤2 months) isolates from cattle and 16 bovine STEC isolates with unknown colonization types. Genoserotypes and multilocus sequence types (MLSTs) were determined, and the isolates were probed with a DNA microarray for virulence-associated genes (VAGs). All STEC(per) isolates belonged to only four genoserotypes (O26:H11, O156:H25, O165:H25, O182:H25), which formed three genetic clusters (ST21/396/1705, ST300/688, ST119). In contrast, STEC(spo) isolates were scattered among 28 genoserotypes and 30 MLSTs, with O157:H7 (ST11) and O6:H49 (ST1079) being the most prevalent. The microarray analysis identified 139 unique gene patterns that clustered with the genoserotypes and MLSTs of the strains. While the STEC(per) isolates possessed heterogeneous phylogenetic backgrounds, the accessory genome clustered these isolates together, separating them from the STEC(spo) isolates", "token_count": 472, "char_count": 1498, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6749, "quality_score": 0.8374, "entities": { "genes": [ "ST300", "ST119", "ST1079", "ST21", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:00.676446", "source": { "split": "train_shard_00001", "doc_id": 3132 }, "chunk_id": "train_shard_00001_3132_0", "global_id": 10105 }, { "text": "Given the vast genetic heterogeneity of bovine STEC strains, defining the genetic patterns distinguishing STEC(per) from STEC(spo) isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.

Importance

Ruminants, especially cattle, are sources of food-borne infections by Shiga toxin-producing Escherichia coli (STEC) in humans. Some STEC strains persist in cattle for longer periods of time, while others are detected only sporadically. Persisting strains can serve as gene reservoirs that supply E. coli with virulence factors, thereby generating new outbreak strains. Attempts to reduce the human risk for acquiring STEC infections should therefore include strategies to control such persisting STEC strains. By analyzing representative genes of their core and accessory genomes, we show that bovine STEC with a persistent colonization type emerged independently from sporadically colonizing isolates and evolved in parallel evolutionary branches. However, persistent colonizing strains share similar sets of accessory genes. Defining the genetic patterns that distinguish persistent from sporadically colonizing STEC isolates will facilitate the targeted design of new intervention strategies to counteract these zoonotic pathogens at the farm level.\n\nThe Accessory Genome of Shiga Toxin-Producing Escherichia coli Defines a Persistent Colonization Type in Cattle.", "token_count": 331, "char_count": 1449, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.799, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:01.244174", "source": { "split": "train_shard_00001", "doc_id": 3132 }, "chunk_id": "train_shard_00001_3132_1", "global_id": 10106 }, { "text": "The novel magnetic nanobeads with epoxy groups on the surface were prepared from glycidyl methacrylate (GMA), ethylene glycol dimethacrylate (EGDMA) and hydroxyethyl methacrylate (HEMA) via emulsifier-free emulsion polymerisation, and they were characterized by scanning electron microscopy and vibrating sample magnetometer. The magnetic poly(GMA-EDGMA-HEMA) nanobeads were used as support for covalent immobilization of Kluyveromyces fragilis β-galactosidase, the maximum amount enzyme attached onto the support was 145.6 mg/g with activity recovery of 72.6%. The loading capacity of this novel support for K. fragilis β-galactosidase was improved 2.6-folds compared with Eupergit® C (commercial epoxy support). The immobilized K. fragilis β-galactosidase exhibited high catalytic activity for the reaction of galacto-oligosaccharide (GOS) synthesis, and a total of 2,240 g GOS were produced per gram of immobilized enzyme during consecutive batch reaction of 10 times. The immobilized biocatalyst retained 81.5% of its original activity after 10 reaction cycles.\n\nCovalent immobilization of Kluyveromyces fragilis β-galactosidase on magnetic nanosized epoxy support for synthesis of galacto-oligosaccharide.", "token_count": 356, "char_count": 1210, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6369, "quality_score": 0.8185, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:01.816252", "source": { "split": "train_shard_00001", "doc_id": 3133 }, "chunk_id": "train_shard_00001_3133_0", "global_id": 10107 }, { "text": "Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016-2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequence typing (cgMLST) and high-quality single nucleotide polymorphism (hqSNP) analysis of the sequence data separated the isolates into the same two clades containing minor within-clade differences; however, cgMLST analysis does not require selection of an appropriate reference genome, making the method preferable to hqSNP analysis for Campylobacter surveillance and cluster detection. The isolates were classified as sequence type 2109 (ST2109)-a rarely seen MLST sequence type. PFGE was performed on 38 human and 10 puppy isolates; PFGE patterns did not reliably predict clustering by cgMLST analysis. Genetic detection of antimicrobial resistance determinants predicted that all outbreak-associated isolates would be resistant to six drug classes. Traditional antimicrobial susceptibility testing (AST) confirmed a high correlation between genotypic and phenotypic antimicrobial resistance determinations. WGS analysis linked C. jejuni isolates in humans and pet store puppies even when canine exposure information was unknown, aiding the epidemiological investigation during the outbreak. WGS data were also used to quickly identify the highly drug-resistant profile of these outbreak-associated C. jejuni isolates.", "token_count": 479, "char_count": 1883, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6895, "quality_score": 0.8448, "entities": { "genes": [ "ST2109" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:02.462223", "source": { "split": "train_shard_00001", "doc_id": 3134 }, "chunk_id": "train_shard_00001_3134_0", "global_id": 10108 }, { "text": "Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multistate Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies.", "token_count": 54, "char_count": 207, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:02.865534", "source": { "split": "train_shard_00001", "doc_id": 3134 }, "chunk_id": "train_shard_00001_3134_1", "global_id": 10109 }, { "text": "Structural variants (SVs) remain challenging to represent and study relative to point mutations despite their demonstrated importance. We show that variation graphs, as implemented in the vg toolkit, provide an effective means for leveraging SV catalogs for short-read SV genotyping experiments. We benchmarked vg against state-of-the-art SV genotypers using three sequence-resolved SV catalogs generated by recent long-read sequencing studies. In addition, we use assemblies from 12 yeast strains to show that graphs constructed directly from aligned de novo assemblies improve genotyping compared to graphs built from intermediate SV catalogs in the VCF format.\n\nGenotyping structural variants in pangenome graphs using the vg toolkit", "token_count": 167, "char_count": 736, "word_count": 103, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:03.345186", "source": { "split": "train_shard_00001", "doc_id": 3135 }, "chunk_id": "train_shard_00001_3135_0", "global_id": 10110 }, { "text": "Candida auris is an invasive and multidrug-resistant ascomycetous yeast that is under global surveillance. All clinical cases of C. auris infection diagnosed from 1997 to 2019 in Japan were non-invasive and sporadic otitis media cases. In the present study, we performed whole-genome sequencing of seven C. auris strains isolated from patients with otitis media in Japan, all of which belonged to clade II. Comparative genome analysis using the high-quality draft genome sequences JCM 15448T revealed that single nucleotide variations (SNVs), clade-specific accessory genes, and copy number variations (CNVs) were identified in each C. auris clade. A total of 61 genes involved in cell wall and stress response-related functions was absent in clade II, and the pattern of conserved CNVs in each clade was more stable in clade II than in other clades. Our data suggest that the genomic structural diversity is stable in C. auris isolated from each biogeographic location, and Japanese strains isolated from patients with otitis media might belong to an ancestral type of C. auris. One Japanese strain, TWCC 58362, with reduced susceptibility to fluconazole, exhibited no mutation in ergosterol biosynthesis-related genes (ERG). However, TWCC 58362-specific variations, including SNVs, indels, and CNVs were detected, suggesting that gene duplication events in C. auris might contribute to antifungal drug resistance. Taken together, we demonstrated that genomic structural variations in C. auris could correlate to geographical dissemination, epidemiology, lesions in the host, and antifungal resistance.\n\nClade II Candida auris possess genomic structural variations related to an ancestral strain.", "token_count": 430, "char_count": 1697, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:04.008491", "source": { "split": "train_shard_00001", "doc_id": 3136 }, "chunk_id": "train_shard_00001_3136_0", "global_id": 10111 }, { "text": "Subterranean clover (Trifolium subterraneum L., Ts) is a geocarpic, self-fertile annual forage legume with a compact diploid genome (n = x = 8, 544 Mb/1C). Its resilience and climate adaptivity have made it an economically important species in Mediterranean and temperate zones. Using the cultivar Daliak, we generated higher resolution sequence data, created a new genome assembly TSUd_3.0, and conducted molecular diversity analysis for copy number variant (CNV) and single-nucleotide polymorphism (SNP) among 36 cultivars. TSUd_3.0 substantively improves prior genome assemblies with new Hi-C and long-read sequence data, covering 531 Mb, containing 41,979 annotated genes and generating a 94.4% BUSCO score. Comparative genomic analysis among select members of the tribe Trifolieae indicated TSUd 3.0 corrects six assembly-error inversion/duplications and confirmed phylogenetic relationships. Its synteny with T. pratense, T. repens, Medicago truncatula and Lotus japonicus genomes were assessed, with the more distantly related T. repens and M. truncatula showing higher levels of co-linearity with Ts than between Ts and its close relative T. pratense. Resequencing of 36 cultivars discovered 7,789,537 SNPs subsequently used for genomic diversity assessment and sequence-based clustering. Heterozygosity estimates ranged from 1% to 21% within the 36 cultivars and may be influenced by admixture. Phylogenetic analysis supported subspecific genetic structure, although it indicates four or five groups, rather than the three recognized subspecies. Furthermore, there were incidences where cultivars characterized as belonging to a particular subspecies clustered with another subspecies when using genomic data", "token_count": 513, "char_count": 1780, "word_count": 236, "semantic_coherence": 1, "information_density": 0.7585, "quality_score": 0.8792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:04.691015", "source": { "split": "train_shard_00001", "doc_id": 3137 }, "chunk_id": "train_shard_00001_3137_0", "global_id": 10112 }, { "text": "These outcomes suggest that further investigation of Ts sub-specific classification using molecular and morpho-physiological data is needed to clarify these relationships. This upgraded reference genome, complemented with comprehensive sequence diversity analysis of 36 cultivars, provides a platform for future gene functional analysis of key traits, and genome-based breeding strategies for climate adaptation and agronomic performance. Pangenome analysis, more in-depth intra-specific phylogenomic analysis using the Ts core collection, and functional genetic and genomic studies are needed to further augment knowledge of Trifolium genomes.\n\nAn improved reference genome for Trifolium subterraneum L. provides insight into molecular diversity and intra-specific phylogeny.", "token_count": 172, "char_count": 790, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7551, "quality_score": 0.8776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:05.136558", "source": { "split": "train_shard_00001", "doc_id": 3137 }, "chunk_id": "train_shard_00001_3137_1", "global_id": 10113 }, { "text": "Type II toxin-antitoxin (TA) systems are most commonly composed of two genes encoding a stable toxin, which harms the cell, and an unstable antitoxin that can inactivate it. TA systems were initially characterized as selfish elements, but have recently gained attention for regulating general stress responses responsible for pathogen virulence, formation of drug-tolerant persister cells and biofilms-all implicated in causing recalcitrant chronic infections. We use a bioinformatics approach to explore the distribution and evolution of type II TA loci of the opportunistic pathogen, Pseudomonas aeruginosa, across longitudinally sampled isolates from cystic fibrosis lungs. We identify their location in the genome, mutations, and gain/loss during infection to elucidate their function(s) in stabilizing selfish elements and pathogenesis. We found (1) 26 distinct TA systems, where all isolates harbor four in their core genome and a variable number of the remaining 22 on genomic islands; (2) limited mutations in core genome TA loci, suggesting they are not under negative selection; (3) no evidence for horizontal transmission of elements with TA systems between clone types within patients, despite their ability to mobilize; (4) no gain and limited loss of TA-bearing genomic islands, and of those elements partially lost, the remnant regions carry the TA systems supporting their role in genomic stabilization; (5) no significant correlation between frequency of TA systems and strain ability to establish as chronic infection, but those with a particular TA, are more successful in establishing a chronic infection.\n\nDiversity, Prevalence, and Longitudinal Occurrence of Type II Toxin-Antitoxin Systems of Pseudomonas aeruginosa Infecting Cystic Fibrosis Lungs.", "token_count": 428, "char_count": 1785, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:05.764698", "source": { "split": "train_shard_00001", "doc_id": 3138 }, "chunk_id": "train_shard_00001_3138_0", "global_id": 10114 }, { "text": "The zoonotic pathogen Campylobacter jejuni is among the leading causes of foodborne diseases worldwide. While C. jejuni colonises many wild animals and livestock, persistence mechanisms enabling the bacterium to adapt to host species’ guts are not fully understood. In order to identify putative determinants influencing host preferences of distinct lineages, bootstrapping based on stratified random sampling combined with a k-mer- based genome-wide association was conducted on 490 genomes from diverse origins in Germany and Canada. We show a strong association of both the core and the accessory genome characteristics with distinct host animal species, indicating multiple adaptive trajectories defining the evolution of C. jejuni lifestyle preferences in different ecosystems. Here, we demonstrate that adaptation towards a specific host niche ecology is most likely a long evolutionary and multifactorial process, expressed by gene absence or presence and allele variations of core genes. Several host-specific allelic variants from different phylogenetic backgrounds, including dna E, rpo B, ftsX or pyc B play important roles for genome maintenance and metabolic pathways. Thus, variants of genes important for C. jejuni to cope with specific ecological niches or hosts may be useful markers for both surveillance and future pathogen intervention strategies.\n\nGenome-wide insights into population structure and host specificity ofCampylobacter jejuni", "token_count": 311, "char_count": 1466, "word_count": 205, "semantic_coherence": 1, "information_density": 0.722, "quality_score": 0.861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:06.347990", "source": { "split": "train_shard_00001", "doc_id": 3139 }, "chunk_id": "train_shard_00001_3139_0", "global_id": 10115 }, { "text": "Multidrug-resistant (MDR) Escherichia coli strains that carry extended-spectrum β-lactamases (ESBLs) or colistin resistance gene mcr-1 have been identified in the human gut at an increasing incidence worldwide. In this study, we isolated and characterized MDR Enterobacteriaceae from the gut microbiota of healthy Singaporeans and show that the detection rates for ESBL-producing and mcr-positive Enterobacteriaceae are 25.7% (28/109) and 7.3% (8/109), respectively. Whole-genome sequencing analysis of the 37 E. coli isolates assigned them into 25 sequence types and 6 different phylogroups, suggesting that the MDR E. coli gut colonizers are highly diverse. We then analyzed the genetic context of the resistance genes and found that composite transposons played important roles in the cotransfer of blaCTX-M-15/55 and qnrS1, as well as the acquisition of mcr-1. Furthermore, comparative genomic analysis showed that 12 of the 37 MDR E. coli isolates showed high similarity to ESBL-producing E. coli isolates from raw meat products in local markets. By analyzing the core genome single nucleotide polymorphisms (SNPs) shared by these isolates, we identified possible clonal transmission of an MDR E. coli clone between human and raw meat, as well as a group of highly similar IncI2 (Delta) plasmids that might be responsible for the dissemination of mcr-1 in a much wider geographic region. Together, these results suggest that antibiotic resistance may be transmitted between different environmental settings by the expansion of MDR E. coli clones, as well as by the dissemination of resistance plasmids. IMPORTANCE The human gut can harbor both antibiotic-resistant and virulent Escherichia coli which may subsequently cause infections", "token_count": 513, "char_count": 1813, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6039, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:07.004065", "source": { "split": "train_shard_00001", "doc_id": 3140 }, "chunk_id": "train_shard_00001_3140_0", "global_id": 10116 }, { "text": "In this study, we found that multidrug-resistant (MDR) E. coli isolates from the gut of healthy Singaporeans carry a diverse range of antibiotic resistance mechanisms and virulence factor genes and are highly diverse. By comparing their genomes with the extended-spectrum β-lactamase (ESBL)-producing E. coli isolates from raw meat products that were sampled at a similar time from local markets, we detected an MDR E. coli clone that was possibly transmitted between humans and raw meat products. Furthermore, we also found that a group of resistance plasmids might be responsible for the dissemination of colistin resistance gene mcr-1 in Singapore, Malaysia, and Europe. Our findings call for better countermeasures to block the transmission of antibiotic resistance.\n\nExtended-Spectrum β-Lactamase-Producing and mcr-1-Positive Escherichia coli from the Gut Microbiota of Healthy Singaporeans.", "token_count": 234, "char_count": 910, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:07.472422", "source": { "split": "train_shard_00001", "doc_id": 3140 }, "chunk_id": "train_shard_00001_3140_1", "global_id": 10117 }, { "text": "Grain legumes are a key food source for ensuring global food security and sustaining agriculture. However, grain legume production is challenged by growing disease incidence due to global climate change. Ascochyta blight (AB) is a major disease, causing substantial yield losses in grain legumes worldwide. Harnessing the untapped reserve of global grain legume germplasm, landraces, and crop wild relatives (CWRs) could help minimize yield losses caused by AB infection in grain legumes. Several genetic determinants controlling AB resistance in various grain legumes have been identified following classical genetic and conventional breeding approaches. However, the advent of molecular markers, biparental quantitative trait loci (QTL) mapping, genome-wide association studies, genomic resources developed from various genome sequence assemblies, and whole-genome resequencing of global germplasm has revealed AB-resistant gene(s)/QTL/genomic regions/haplotypes on various linkage groups. These genomics resources allow plant breeders to embrace genomics-assisted selection for developing/transferring AB-resistant genomic regions to elite cultivars with great precision. Likewise, advances in functional genomics, especially transcriptomics and proteomics, have assisted in discovering possible candidate gene(s) and proteins and the underlying molecular mechanisms of AB resistance in various grain legumes. We discuss how emerging cutting-edge next-generation breeding tools, such as rapid generation advancement, field-based high-throughput phenotyping tools, genomic selection, and CRISPR/Cas9, could be used for fast-tracking AB-resistant grain legumes to meet the increasing demand for grain legume-based protein diets and thus ensuring global food security.\n\nBreeding and Genomics Interventions for Developing Ascochyta Blight Resistant Grain Legumes.", "token_count": 408, "char_count": 1862, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6793, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:08.090568", "source": { "split": "train_shard_00001", "doc_id": 3141 }, "chunk_id": "train_shard_00001_3141_0", "global_id": 10118 }, { "text": "Inflammatory bowel disease (IBD) is a chronic inflammatory disease affecting various parts of the gastrointestinal tract. A majority of the current evidence points out the involvement of intestinal dysbiosis in the IBD pathogenesis. Recently, the association of intestinal fungal composition With IBD susceptibility and severity has been reported. These studies suggested gene polymorphisms in the front line of host defense against intestinal microorganisms are considered to play a role in IBD pathogenesis. The studies have also detected increased susceptibility to fungal infections in patients carrying IBD-related mutations. Therefore, a literature search was conducted in related databases to review articles addressing the mycobiota-genotype association in IBD.\n\nThe role of mycobiota-genotype association in inflammatory bowel diseases: a narrative review.", "token_count": 193, "char_count": 865, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6496, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:08.540127", "source": { "split": "train_shard_00001", "doc_id": 3142 }, "chunk_id": "train_shard_00001_3142_0", "global_id": 10119 }, { "text": "Streptococcus suis is a major bacterial pathogen in pigs and an emerging zoonotic pathogen. Different S. suis serotypes exhibit diverse characteristics in population structure and pathogenicity. Surveillance data highlight the significance of S. suis serotype 4 (SS4) in swine streptococcusis, a pathotype causing human infections. However, except for a few epidemiologic studies, the information on SS4 remains limited. In this study, we investigated the population structure, pathogenicity, and antimicrobial characteristics of SS4 based on 126 isolates, including one from a patient with septicemia. We discovered significant diversities within this population, clustering into six minimum core genome (MCG) groups (1, 2, 3, 4, 7-2, and 7-3) and five lineages. Two main clonal complexes (CCs), CC17 and CC94, belong to MCG groups 1 and 3, respectively. Numerous important putative virulence-associated genes are present in these two MCG groups, and 35.00% (7/20) of pig isolates from CC17, CC94, and CC839 (also belonging to MCG group 3) were highly virulent (mortality rate ≥ 80%) in zebrafish and mice, similar to the human isolate ID36054. Cytotoxicity assays showed that the human and pig isolates of SS4 strains exhibit significant cytotoxicity to human cells. Antimicrobial susceptibility testing showed that 95.83% of strains isolated from our labs were classified as multidrug-resistant. Prophages were identified as the primary vehicle for antibiotic resistance genes. Our study demonstrates the public health threat posed by SS4, expanding the understanding of SS4 population structure and pathogenicity characteristics and providing valuable information for its surveillance and prevention.\n\nStreptococcus suis serotype 4: a population with the potential pathogenicity in humans and pigs.", "token_count": 505, "char_count": 1830, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6589, "quality_score": 0.8295, "entities": { "genes": [ "CC94", "CC17", "SS4", "ID36054", "CC839" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:09.193115", "source": { "split": "train_shard_00001", "doc_id": 3143 }, "chunk_id": "train_shard_00001_3143_0", "global_id": 10120 }, { "text": "

Motivation

Bacterial genomes are being deposited into online databases at an increasing rate. Genome annotation represents one of the first efforts to understand organisms and their diseases. Some evolutionary relationships that are capable of being annotated only from genomes are conserved gene neighbourhoods (CNs), phylogenetic profiles (PPs), and gene fusions. At present, there is no standalone software that enables networks of interactions among proteins to be created using these three evolutionary characteristics with efficient and effective results.

Results

We developed GENPPI software for the ab initio prediction of interaction networks using predicted proteins from a genome. In our case study, we employed 50 genomes of the genus Corynebacterium . Based on the PP relationship, GENPPI differentiated genomes between the ovis and equi biovars of the species Corynebacterium pseudotuberculosis and created groups among the other species analysed. If we inspected only the CN relationship, we could not entirely separate biovars, only species. Our software GENPPI was determined to be efficient because, for example, it creates interaction networks from the central genomes of 50 species/lineages with an average size of 2200 genes in less than 40 minutes on a conventional computer. Our software is compelling because the interaction networks that it creates reflect evolutionary relationships among species and were obtained in average nucleotide identity (ANI) analyses. Additionally, this software enables the user to define how he or she intends to explore the PP and CN characteristics through various parameters, enabling the creation of customized interaction networks. For instance, users can set parameters regarding the genus, metagenome, or pangenome. In addition to the parameterization of GENPPI, it is also the user’s choice regarding which set of genomes he or she is going to study.

Availability

The source code in the Common Lisp language, binary files for different operating systems, and GENPPI software tutorials are available at {{github.com/santosardr/genppi}}.

Contact

santosardr@ufu.br

Supplementary information

Supplementary data are available at Bioinformatics online.", "token_count": 520, "char_count": 2254, "word_count": 315, "semantic_coherence": 1, "information_density": 0.6095, "quality_score": 0.8048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:09.851104", "source": { "split": "train_shard_00001", "doc_id": 3144 }, "chunk_id": "train_shard_00001_3144_0", "global_id": 10121 }, { "text": "GENPPI: standalone software for creating protein interaction networks from genomes", "token_count": 15, "char_count": 82, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:10.188633", "source": { "split": "train_shard_00001", "doc_id": 3144 }, "chunk_id": "train_shard_00001_3144_1", "global_id": 10122 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is a gram-positive bacterium and responsible for several infections in the human. Here, Oxford nanopore mediated whole genome sequencing is reported for human host associated strain. The genome size obtained was of ~3 MB, while GC content was 32.9%. Approximately 3600 CDSs, 62 tRNAs and 16 rRNAs were identified. Phage segments were present, with two complete intact phages. Type I and type IV restriction elements were also detected, along with five plasmids. Several antibiotic resistance genes were also mined, with a key mutation in the fluoroquinolone resistant gyrA , phosphonic acid resistant murA transferase and fusidic acid resistant fusA genes. Sequence type was determined as 4803. Comparative analysis with MRSA isolates from Pakistan (n=20) revealed an open pan-genome, with 1,934 CDSs forming core genome.\n\nNanopore sequencing of human associated methicillin-resistant Staphylococcus aureus RWP1 genome for inferring antibiotic resistant gene, plasmid and prophage information", "token_count": 299, "char_count": 1050, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7483, "quality_score": 0.8741, "entities": { "genes": [ "RWP1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:10.748986", "source": { "split": "train_shard_00001", "doc_id": 3145 }, "chunk_id": "train_shard_00001_3145_0", "global_id": 10123 }, { "text": "Human activity directly or indirectly causes climate change, promoting changes in the composition of the atmosphere. This change is beyond the variation of the natural climate. In this manner, climate change could create an environmental pressure which is enough to trigger new fungal diseases. In addition to climate alterations, the onset of the COVID-19 pandemic has also been associated with the emergence of fungal pathogens. Fungi showed that an inability to grow at high temperatures limits the capacity of fungi to infect mammals. However, fungi can develop thermotolerance, gradually adapting to rising temperatures due to climate change, and generating a greater number of disease-causing organisms. In the present study, we reported the detection and identification of Candida palmioleophila isolates recovered from raw sewage samples in Niteroi city, Rio de Janeiro State, Brazil, during a monitoring program for measuring SARS-CoV-2 presence and concentration. Using polyphasic taxonomy to identify the species and evaluating some virulence aspects of this species, such as biofilm formation and extracellular enzyme production, our data highlight this species as a possible emerging pathogen in Brazil, especially in the pandemic context.\n\nCandida palmioleophila: A New Emerging Threat in Brazil?", "token_count": 293, "char_count": 1324, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6895, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:11.329561", "source": { "split": "train_shard_00001", "doc_id": 3146 }, "chunk_id": "train_shard_00001_3146_0", "global_id": 10124 }, { "text": "Streptococcus anginosus is a common isolate of the oral cavity and an opportunistic pathogen for systemic infections. Although the pyogenic infections caused by S. anginosus are similar to those caused by Streptococcus pyogenes, S. anginosus lacks most of the well-characterized virulence factors of S. pyogenes. To investigate the pathogenicity of S. anginosus, we analysed the genome of a newly identified S. anginosus strain, KH1, which was associated with toxic shock-like syndrome in an immunocompetent adolescent. The genome of KH1 contains nine genomic islands, two Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated systems and many phage-related proteins, indicating that the genome is influenced by prophages and horizontal gene transfer. Comparative genome analysis of 355 S. anginosus strains revealed a significant difference between the sizes of the pan genome and core genome, reflecting notable strain variations. We further analysed the transcriptomes of KH1 under conditions mimicking either the oral cavity or the bloodstream. We found that in an artificial saliva medium, the expression of a putative quorum quenching system and pyruvate oxidase for H2O2 production was upregulated, which could optimize the competitiveness of S. anginosus in the oral ecosystem. Conversely, in a modified serum medium, purine and glucan biosynthesis, competence and bacteriocin production were significantly upregulated, likely facilitating the survival of KH1 in the bloodstream. These findings indicate that S. anginosus can utilize diverse mechanisms to adapt to different environmental niches and establish infection, despite its lack of toxin production.", "token_count": 492, "char_count": 1796, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [ "KH1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:11.989169", "source": { "split": "train_shard_00001", "doc_id": 3147 }, "chunk_id": "train_shard_00001_3147_0", "global_id": 10125 }, { "text": "Genomic and transcriptomic insights into the virulence and adaptation of shock syndrome-causing <i>Streptococcus anginosu</i>s.", "token_count": 46, "char_count": 139, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:12.356932", "source": { "split": "train_shard_00001", "doc_id": 3147 }, "chunk_id": "train_shard_00001_3147_1", "global_id": 10126 }, { "text": "The study of the gene repertoires of microbial species, their pangenomes, has become a key topic of study in microbial evolution and genomics. Yet, the increasing number of genomes available complicates the establishment of the basic building blocks of comparative genomics. Here, we present PanACoTA ( https://github.com/gem-pasteur/PanACoTA ), a tool that allows to download all genomes of a species, build a database with those passing quality and redundancy controls, uniformly annotate, and then build their pangenome, several variants of core genomes, their alignments, and a rapid but accurate phylogenetic tree. While many programs building pangenomes have become available in the last few years, we have focused on a modular method, that tackles all the key steps of the process, from download to phylogenetic inference. While all steps are integrated, they can also be run separately and multiple times to allow rapid and extensive exploration of the parameters of interest. The software is built in Python3 and includes features to facilitate its future development. We believe PanACoTa is an interesting addition to the current set of comparative genomics tools, since it will accelerate and standardize the more routine parts of the work, allowing microbial genomicists to more quickly tackle their specific questions.\n\nPanACoTA: A modular tool for massive microbial comparative genomics", "token_count": 313, "char_count": 1400, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:12.913288", "source": { "split": "train_shard_00001", "doc_id": 3148 }, "chunk_id": "train_shard_00001_3148_0", "global_id": 10127 }, { "text": "

Background:

Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance genes. Despite its ongoing threat to human health, surveillance in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention methods. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids).

Results:

: Among 82 of CR-Ec identified between 2017 and 2019, twenty-five sequence types (STs) were detected. ST131 was the most prominent (n=17) followed closely by ST405 (n=12). bla CTX-M were the most common ESBL genes and just over half (18/30) of these genes were predicted to be plasmid-borne by both MOB-suite and mlplasmids. Three genetically related groups of E. coli isolates were identified with cgMLST. One of the groups contained an isolate with a chromosome-borne bla CTX-M-15 gene and an isolate with a plasmid-borne bla CTX-M-15 gene.

Conclusions:

This study provides insights into the dominant clonal groups driving carbapenem resistant E. coli infections in Alameda County, CA, USA clinical sites and highlights the relevance of whole-genome sequencing in routine local genomic surveillance", "token_count": 520, "char_count": 1997, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6431, "quality_score": 0.8216, "entities": { "genes": [ "ST131", "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:13.578386", "source": { "split": "train_shard_00001", "doc_id": 3149 }, "chunk_id": "train_shard_00001_3149_0", "global_id": 10128 }, { "text": "The finding of multi-drug resistant plasmids harboring high-risk resistance genes is of concern as it indicates a risk of dissemination to previously susceptible clonal groups in the community, potentially complicating clinical and public health intervention.\n\nThe Role of Plasmids in Carbapenem Resistant E. coli in Alameda County, California", "token_count": 80, "char_count": 343, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:13.947170", "source": { "split": "train_shard_00001", "doc_id": 3149 }, "chunk_id": "train_shard_00001_3149_1", "global_id": 10129 }, { "text": "Seven novel lactic acid bacterial strains (BF125T, BF186, TKL145, YK3, YK6, YK10 and NSK) were isolated from the fresh faeces of Japanese black beef cattle and weanling piglets, spent mushroom substrates, or steeping water of a corn starch production plant. These strains are rod-shaped, Gram-stain-positive, non-motile, non-spore-forming, catalase-negative, cytochrome oxidase-negative, facultatively anaerobic, and homofermentative. Strain BF125T did not produce any gas from glucose; both d- and l-lactate were produced as end-products of glucose (D/L, 40 : 60). Growth occurred at 30-45 °C (optimum, 37 °C), pH 5.0-8.0 (optimum, pH 6.0), and with NaCl concentration of 1.0-3.0% (w/v). The G+C content of genomic DNA of strain BF125T was 37.8 mol% (whole-genome analysis). The major fatty acids were C16 : 0, C18 : 1 ω9c, C19 cyclopropane 9, 10, and summed feature 10. The 16S rRNA gene in strain BF125T showed high similarity to that of the type strain of Lactobacillus amylovorus (99.93%), and the other isolates were also identified as L. amylovorus based on these similarities. A phylogenetic tree based on the core genomes of L", "token_count": 492, "char_count": 1243, "word_count": 175, "semantic_coherence": 1, "information_density": 0.7714, "quality_score": 0.8857, "entities": { "genes": [ "YK6", "TKL145", "YK3", "BF125", "BF186", "YK10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:14.606001", "source": { "split": "train_shard_00001", "doc_id": 3150 }, "chunk_id": "train_shard_00001_3150_0", "global_id": 10130 }, { "text": "amylovorus strains (n=54), including the seven isolates, showed that they could be divided into two clusters. Strains YK3, YK6, YK10, and NSK were in the first cluster, along with the type strain DSM 20531T, while the second cluster included isolates BF125T, BF186, TKL145, and other strains isolated from various animal origins. Phenotypic differences in fermentability were observed for lactose, salicin, and gentiobiose between these two groups. The intergroup digital DNA-DNA hybridization values (72.9-78.6%) and intergroup average nucleotide identity values (95.64-96.92%) were comparable to values calculated using datasets of other valid subspecies of the genus (ex-) Lactobacillus. In light of the physiological, genotypic, and phylogenetic evidence, we propose a novel subspecies of L. amylovorus, named Lactobacillus amylovorus subsp. animalis subsp. nov. (type strain BF125T=MAFF 212522T=DSM 115528T). Our findings also led to the automatic creation of Lactobacillus amylovorus subsp. amylovorus subsp. nov. and an emended description of the species L. amylovorus.\n\nProposal of <i>Lactobacillus amylovorus</i> subsp. <i>animalis</i> subsp. nov. and an emended description of <i>Lactobacillus amylovorus</i>.", "token_count": 499, "char_count": 1370, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [ "YK6", "TKL145", "YK3", "BF125", "BF186", "YK10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:15.263932", "source": { "split": "train_shard_00001", "doc_id": 3150 }, "chunk_id": "train_shard_00001_3150_1", "global_id": 10131 }, { "text": "To analyse the yeast population diversity during wine fermentations, specific fluorescein-labelled oligonucleotide probes targeted to the D1/D2 region of the 26S rRNA of different yeast species known to occur frequently in this environment were designed and tested with reference strains. The probes were then used to identify wine must isolates and to follow, in combination with plate counts, the evolution of yeast populations in two winery fermentations of white and red grape musts. In both cases, a high diversity of non-Saccharomyces yeast species was detected, including Candida stellata, Hanseniaspora uvarum, H. guilliermondii, Kluyveromyces marxianus, K. thermotolerans and Torulaspora delbrueckii. Some of these species (e.g., K. marxianus, K. thermotolerans and T. delbrueckii) were present in significant amounts during the tumultuous fermentation stage, despite the predominance of Saccharomyces cerevisiae cells following the inoculation of the wine musts with a starter strain. To further clarify the yeast population dynamics at the late phase of the fermentations, and because winery conditions do not allow a reliable control of experimental variables, strains isolated from the industrial musts were used to conduct two laboratory microvinifications in synthetic grape juice, using different ratios of S. cerevisiae/non-Saccharomyces in the inocula. Under these conditions, the results were similar to those obtained in the winery, showing a yeast profile with mixed species throughout the first fermentation stage, i.e. until about 40-50% of the total sugar was consumed. Non-Saccharomyces yeasts were outgrown by S. cerevisiae only after ethanol reached concentrations around 4-5% (v/v), which argues in favour of a potential important role of non-Saccharomyces in the final organoleptic characteristics of the wine.\n\nApplication of fluorescence in situ hybridisation (FISH) to the analysis of yeast population dynamics in winery and laboratory grape must fermentations.", "token_count": 499, "char_count": 1993, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:16.395585", "source": { "split": "train_shard_00001", "doc_id": 3151 }, "chunk_id": "train_shard_00001_3151_0", "global_id": 10132 }, { "text": "

Background

Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities.

Results

In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest - MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii.

Conclusions

Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host's growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii", "token_count": 472, "char_count": 2032, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6196, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:17.043876", "source": { "split": "train_shard_00001", "doc_id": 3152 }, "chunk_id": "train_shard_00001_3152_0", "global_id": 10133 }, { "text": "To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.\n\nPseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience.", "token_count": 140, "char_count": 636, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7949, "quality_score": 0.8974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:17.469800", "source": { "split": "train_shard_00001", "doc_id": 3152 }, "chunk_id": "train_shard_00001_3152_1", "global_id": 10134 }, { "text": "Studies on the bioconversion of cellulosic substrates by the thermotolerant yeast, Kluyveromyces marxianus IMB3 at 45degC", "token_count": 39, "char_count": 121, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:17.832926", "source": { "split": "train_shard_00001", "doc_id": 3153 }, "chunk_id": "train_shard_00001_3153_0", "global_id": 10135 }, { "text": "

ABSTRACT

Clostridioides difficile is the most common cause of antibiotic-associated gastrointestinal infections. Capillary-electrophoresis (CE)-PCR ribotyping is currently the gold standard for C. difficile typing but lacks discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better, but backward compatibility with CE-PCR ribotyping must be assessed. Using a well-characterized collection of diverse strains (N=630; 100 unique ribotypes [RTs]), we aimed to investigate PCR ribotyping prediction from core genome multilocus sequence typing (cgMLST). Additionally, we compared the discriminatory power of cgMLST (SeqSphere & EnteroBase) and whole genome MLST (wgMLST) (EnteroBase) with single nucleotide polymorphism (SNP) analysis). A unique cgMLST profile (>6 allele differences) was observed in 82/100 ribotypes, indicating sufficient backward compatibility. Intra-RT allele difference varied per ribotype and MLST clade. Application of cg/wgMLST and SNP analysis in two outbreak settings with ribotypes RT078 and RT181 (known with a low intra-ribotype allele difference) showed no distinction between outbreak- and non-outbreak strains, in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize and offers higher discrimination. However, in some ribotype complexes adjusted cut-off thresholds and epidemiological data are necessary to recognize outbreaks. We propose to decrease the current threshold of 6 to 3 alleles to better identify outbreaks.\n\nPerformance of Core Genome Multilocus Sequence Typing Compared to Capillary-Electrophoresis PCR Ribotyping and SNP Analysis ofClostridioides difficile", "token_count": 486, "char_count": 1807, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [ "RT078", "RT181" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:18.481646", "source": { "split": "train_shard_00001", "doc_id": 3154 }, "chunk_id": "train_shard_00001_3154_0", "global_id": 10136 }, { "text": "The emergence of extended-spectrum cephalosporin (ESC)-resistant Escherichia coli is a global concern. This study aimed to assess the prevalence and transmission of ESC-resistant E. coli in the Danish broiler production system. Samples from two vertically integrated Production Systems (1 and 2) and two slaughterhouses (A and B) were analyzed (n = 943) for the occurrence of ESC-resistant E. coli from 2015 to 2018. ESC-resistant E. coli isolates were whole-genome sequenced (WGS) for characterization of the multi-locus sequence type (MLST), antibiotic resistance genes, virulence genes, and plasmid replicon types. An ad hoc core genome (cg) MLST based on 2513 alleles was used to examine the genetic relatedness among isolates. The prevalence of ESC-resistant E. coli in the conventional Production System 1 was 2.7%, while in Production System 2 the prevalence was 26.7% and 56.5% for samples from the conventional and organic production, respectively. The overall prevalence of ESC-resistant E. coli in broiler thigh and fecal samples ranged from 19.3% in Slaughterhouse A to 22.4% in Slaughterhouse B. In total, 162 ESC-resistant E. coli were isolated and shown to belong to 16 different sequence types (STs). The most prevalent STs were ST2040 (n = 85) and ST429 (n = 22)", "token_count": 428, "char_count": 1328, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.7929, "entities": { "genes": [ "ST429", "ST2040" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:19.112031", "source": { "split": "train_shard_00001", "doc_id": 3155 }, "chunk_id": "train_shard_00001_3155_0", "global_id": 10137 }, { "text": "Seven ESC resistance genes were detected: blaCMY-2 (n = 119), blaTEM-52B (n = 16), blaCTX-M-1 (n = 5), blaTEM-52C (n = 3), blaCTX-M-14 (n = 1), blaSHV-12 (n = 1), and up-regulation of ampC (n = 16), with an unknown resistance gene in one isolate (n = 1). The carriage of blaCMY-2 in 119 isolates was primarily associated with IncI1 (n = 87), and IncK plasmids (n = 31). Highly similar blaCMY-2 carrying E. coli isolates from ST429 were found in production systems as well as in slaughterhouses. In conclusion, findings from this study indicate that ESC-resistant E. coli are transferred vertically from farms in the production systems to slaughterhouses with the potential to enter the food supply.\n\nPrevalence and Transmission of Extended-Spectrum Cephalosporin (ESC) Resistance Genes in Escherichia coli Isolated from Poultry Production Systems and Slaughterhouses in Denmark.", "token_count": 400, "char_count": 1043, "word_count": 139, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.795, "entities": { "genes": [ "ST429" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:19.731637", "source": { "split": "train_shard_00001", "doc_id": 3155 }, "chunk_id": "train_shard_00001_3155_1", "global_id": 10138 }, { "text": "In the present study, we aim to clarify the taxonomic positions of Anoxybacillus salavatliensis DSM 22626T and Anoxybacillus gonensis G2T by using whole genome phylogenetic analysis, biochemical and chemotaxonomic characteristics. The genome sequences of A. salavatliensis DSM 22626T was not available in any database, so it was sequenced in this study. In phylogenetic trees drawn using whole genome sequences and 16S rRNA gene sequences, A. salavatliensis DSM 22626T and A. gonensis G2T clade together and showed high sequence similarity (99.3%) based on 16S rRNA gene. The average amino acid identity, average nucleotide identity and digital DNA-DNA hybridization values between A. salavatliensis DSM 22626T and A. gonensis G2T were found to be greater than the threshold values for species demarcation. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. salavatliensis DSM 22626T and A. gonensis G2T formed a monophyletic clade. Most phenotypic and chemotaxonomic features between both strains were almost identical except for a few exceptions. The present results show that A. salavatliensis DSM 22626T is a later heterotypic synonym of A. gonensis G2T.\n\nGenome-based reclassification of Anoxybacillus salavatliensis Cihan et al. 2011 as a later heterotypic synonym of Anoxybacillus gonensis Belduz et al. 2003.", "token_count": 498, "char_count": 1491, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5594, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:20.388444", "source": { "split": "train_shard_00001", "doc_id": 3156 }, "chunk_id": "train_shard_00001_3156_0", "global_id": 10139 }, { "text": "Few methicillin-resistant Staphylococcus aureus (MRSA) from the early years of its global emergence have been sequenced. Knowledge about evolutionary factors promoting the success of specific MRSA multi-locus sequence types (MLSTs) remains scarce. We aimed to characterize a legacy MRSA collection isolated from 1965 to 1987 and compare it against publicly available international and local genomes. We accessed 451 ancient (1965-1987) Swiss MRSA isolates, stored in the Culture Collection of Switzerland. We determined phenotypic antimicrobial resistance (AMR) and performed Illumina short-read sequencing on all isolates and long-read sequencing on a selection with Oxford Nanopore Technology. For context, we included 103 publicly available international genomes from 1960 to 1992 and sequenced 1207 modern Swiss MRSA isolates from 2007 to 2022. We analyzed the core genome (cg)MLST and predicted SCC mec cassette types, AMR, and virulence genes. Among the 451 ancient Swiss MRSA isolates, we found 17 sequence types (STs) of which 11 have been previously described. Two STs were novel combinations of known loci and six isolates carried previously unsubmitted MLST alleles, representing five new STs (ST7843, ST7844, ST7837, ST7839, and ST7842). Most isolates (83% 376/451) represented ST247-MRSA-I isolated in the 1960s, followed by ST7844 (6% 25/451), a novel single locus variant (SLV) of ST239. Analysis by cgMLST indicated that isolates belonging to ST7844-MRSA-III cluster within the diversity of ST239-MRSA-IIII. Early MRSA were predominantly from clonal complex (CC) 8. From 1980 to the end of the 20 th century we observed that CC22 and CC5 as well as CC8 were present, both locally and internationally", "token_count": 519, "char_count": 1715, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6917, "quality_score": 0.8458, "entities": { "genes": [ "ST7839", "ST7842", "ST239", "CC22", "CC8", "ST7837", "ST7843", "ST7844", "ST247", "CC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:21.047584", "source": { "split": "train_shard_00001", "doc_id": 3157 }, "chunk_id": "train_shard_00001_3157_0", "global_id": 10140 }, { "text": "The combined analysis of 1761 ancient and contemporary MRSA isolates across more than 50 years uncovered novel STs and allowed us a glimpse into the lineage flux between Swiss and international MRSA across time.\n\nAncient methicillin-resistantStaphylococcus aureus: expanding current knowledge using molecular epidemiological characterization of a Swiss legacy collection", "token_count": 89, "char_count": 377, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8163, "quality_score": 0.9082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:21.421973", "source": { "split": "train_shard_00001", "doc_id": 3157 }, "chunk_id": "train_shard_00001_3157_1", "global_id": 10141 }, { "text": "This work investigated the growth of Kluyveromyces marxianus NRRL Y-7571 in solid-state fermentation in a medium composed of sugarcane bagasse, molasses, corn steep liquor and soybean meal within a packed-bed bioreactor. Seven experimental runs were carried out to evaluate the effects of flow rate and inlet air temperature on the following microbial rates: cell mass production, total reducing sugar and oxygen consumption, carbon dioxide and ethanol production, metabolic heat and water generation. A mathematical model based on an artificial neural network was developed to predict the above-mentioned microbial rates as a function of the fermentation time, initial total reducing sugar concentration, inlet and outlet air temperatures. The results showed that the microbial rates were temperature dependent for the range 27-50 degrees C. The proposed model efficiently predicted the microbial rates, indicating that the neural network approach could be used to simulate the microbial growth in SSF.\n\nMathematical modeling of Kluyveromyces marxianus growth in solid-state fermentation using a packed-bed bioreactor.", "token_count": 254, "char_count": 1119, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:21.917366", "source": { "split": "train_shard_00001", "doc_id": 3158 }, "chunk_id": "train_shard_00001_3158_0", "global_id": 10142 }, { "text": "Aliarcobacter cryaerophilus (formerly Arcobacter cryaerophilus) is a globally emerging foodborne and zoonotic pathogen. However, little is known about the species' genomic features and diversity, antibiotic resistance and virulence. In this study, 27 A. cryaerophilus strains from water poultry in Thuringia, Germany, were investigated using whole-genome sequencing. Four of these strains were sequenced using long- and short-read sequencing methods to obtain circularized genomes. The German strains belong to the A. cryaerophilus cluster I. Cluster I genomes exhibited a high degree of genetic diversity in which variable sites comprised 9.1% of the core genome. The German strains formed three subgroups that contained 2, 6, and 9 strains, respectively. The genomic analysis of cluster I revealed variable presence of mobile elements and that 65% of the strains lack CRISPR systems. The four circularized genomes carried a ∼2 Mbp chromosome and a single megaplasmid (size 98.1-154.5 Kbp). The chromosome was densely packed with coding sequences (∼92%) and showed inversions and shifts in the gene blocks between different strains. Antimicrobial resistance was assessed using a gradient strip diffusion method and showed that all 27 strains were resistant to cefotaxime and susceptible to erythromycin, gentamicin, and ampicillin. Sixteen strains were also resistant to ciprofloxacin, whereas 23 were resistant to streptomycin. The genetic prediction of antibiotic resistance identified numerous efflux pumps similar to those found in A. butzleri. All strains harbored two beta-lactamase genes which may explain the cefotaxime resistance. A correlation between the gyrA point mutation (Thr-85-Ile) and ciprofloxacin resistance was partially discovered in 15 out of 16 strains", "token_count": 512, "char_count": 1819, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6324, "quality_score": 0.8162, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:22.575378", "source": { "split": "train_shard_00001", "doc_id": 3159 }, "chunk_id": "train_shard_00001_3159_0", "global_id": 10143 }, { "text": "In silico virulence profiling showed a wide range of virulence factors including a full chemotaxis system and most of the flagellar genes. In contrast to A. butzleri, no urease cluster was found. This study provides new insights into the genomic variability of A. cryaerophilus strains of cluster I. The different genetic makeup of these strains may contribute to the virulence of strains and the severity of the infections in humans.\n\nGenomic Analysis and Antimicrobial Resistance of Aliarcobacter cryaerophilus Strains From German Water Poultry.", "token_count": 162, "char_count": 575, "word_count": 83, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8434, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:23.016314", "source": { "split": "train_shard_00001", "doc_id": 3159 }, "chunk_id": "train_shard_00001_3159_1", "global_id": 10144 }, { "text": "Salmonella enterica serotype Enteritidis (SE) is a primary pathogen that causes foodborne diseases in humans. Although whole‐genome sequencing (WGS) ‐based typing analyses have been increasingly used to investigate food‐poisoning outbreaks, they are rarely applied to the epidemiology of multiple Salmonella outbreaks in Sichuan, China. This study therefore isolated SE from patients and food of two consecutive food‐poisoning outbreaks during 2020 in Sichuan, China. We tracked outbreak origin using epidemiological investigation, serotyping, antimicrobial susceptibility testing (AST), pulsed‐field gel electrophoresis (PFGE), and WGS. We also determined phylogenetic relationships using PFGE, whole and core genome multilocus sequence typing (wg/cgMLST), and whole‐genome single nucleotide polymorphism (wgSNP) analyses. Epidemiological investigations identified a correlation between cake consumption and food poisoning. Thirteen strains isolated from patients and one strain isolated from the cake were confirmed as SE. Among the 14 strains, only six shared the same AST pattern (AMP‐AMS‐Sul‐STR). Isolates from patients and cakes were indistinguishable in PFGE results. All four methods, namely PFGE, wgMLST, cgMLST, and wgSNP were appropriate for bacterial typing in SE‐related outbreak investigation. However, wgSNP can assign 12 SE strains from the first outbreak to one cluster and assign two SE strains from the second outbreak to another cluster, while PFGE, wgMLST, cgMLST did not successfully distinguish the SE strains from different outbreaks. Thus, we conclude that SNP‐based phylogenetic analysis might be a viable method for differentiating SE strains at the outbreak level.\n\nPhenotypic and genotypic characterization of salmonella Enteritidis isolated from two consecutive Food‐Poisoning outbreaks in Sichuan, China", "token_count": 464, "char_count": 1835, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:23.659675", "source": { "split": "train_shard_00001", "doc_id": 3160 }, "chunk_id": "train_shard_00001_3160_0", "global_id": 10145 }, { "text": "

Background

The purpose of this study was to establish species distribution of Candida isolates from pediatric patients in Istanbul, Turkey, and to determine risk factors associated with nosocomial Candida infections.

Methods

This study was conducted between June 2013 and June 2014 by participation of 7 medical centers in Istanbul. Candida spp strains isolated from the clinical specimens of pediatric patients were included. Clinical features were recorded on a standardized data collection sheet.

Results

A total of 134 systemic Candida infections were identified in 134 patients. The patients were admitted in pediatric and neonatal intensive care units (41.8% and 9.7%, respectively) and in pediatric wards (48.5%). Candida albicans was the most prevalent species (47%), followed by Candida parapsilosis (13.4%), Candida tropicalis (8.2%), Candida glabrata (4.5%), Candida lusitaniae (3.7%), Candida kefyr (2.2%), Candida guilliermondii (1.5%), Candida dubliniensis (0.7%), and Candida krusei (0.7%). Types of Candida infections were candidemia (50.7%), urinary tract infection (33.6%), surgical site infection (4.5%), central nervous system infection (3.7%), catheter infection (3.7%), and intra-abdominal infection (3.7%)", "token_count": 383, "char_count": 1250, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:24.248543", "source": { "split": "train_shard_00001", "doc_id": 3161 }, "chunk_id": "train_shard_00001_3161_0", "global_id": 10146 }, { "text": "In multivariate analysis, younger age (1-24 months) and detection of non-albicans Candida spp was found to be risk factors associated with candidemia (P = 0.040; odds ratio [OR], 4.1; 95% confidence interval [CI], 1.06-15.86; and P = 0.02; OR, 2.4; 95% CI, 1.10-5.53, respectively).

Conclusions

This study provides an update for the epidemiology of nosocomial Candida infections in Istanbul, which is important for the management of patients and implementation of appropriate infection control measures.\n\nEpidemiologic and microbiologic evaluation of nosocomial infections associated with Candida spp in children: A multicenter study from Istanbul, Turkey.", "token_count": 216, "char_count": 663, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7582, "quality_score": 0.8791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:24.709073", "source": { "split": "train_shard_00001", "doc_id": 3161 }, "chunk_id": "train_shard_00001_3161_1", "global_id": 10147 }, { "text": "Whey is a byproduct of the cheese industry, which is potentially dangerous for the environment if it is not treated before its discharge. An alternative use for whey is as raw material to produce compounds with high added value as 2-phenylethanol (2-PE). Experimental production of 2-PE from whey using Kluyveromices marxianus as inoculum was evaluated. Maximum 2-PE concentration obtained was 780mg/L and a lactose removal efficiency of 99.4% with the addition of l-phenylalanine (1g/L) as a precursor and ammonium sulphate (NH4)2SO4 (450mg/L) using a K. marxianus inoculums (1×106CFU/mL) at 30°C/180 rpm. Based on experimental results the process simulation was performed on Aspen Plus V.10. Operation costs were estimated, and fixed costs projection was performed based on essential equipment. Two scenarios were established. In the first one, the sale of the product as an additive with the characteristics of fermentation output was considered; in which case, the breaking point of the process was calculated to obtain the minimal sale price estimate. On the second one, the 2-PE sale as a high purity product was considered and the income from the sale of the product with these characteristics was assessed.\n\nEconomic projection of 2-phenylethanol production from whey", "token_count": 342, "char_count": 1275, "word_count": 195, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7897, "entities": { "genes": [ "NH4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:25.287461", "source": { "split": "train_shard_00001", "doc_id": 3162 }, "chunk_id": "train_shard_00001_3162_0", "global_id": 10148 }, { "text": "Ethanol production by the thermotolerant yeast strain Kluyveromyces marxianus IMB3 during growth on lactose-containing media", "token_count": 35, "char_count": 124, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:25.647468", "source": { "split": "train_shard_00001", "doc_id": 3163 }, "chunk_id": "train_shard_00001_3163_0", "global_id": 10149 }, { "text": "The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.\n\nDisturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.", "token_count": 394, "char_count": 1701, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:26.271463", "source": { "split": "train_shard_00001", "doc_id": 3164 }, "chunk_id": "train_shard_00001_3164_0", "global_id": 10150 }, { "text": "

Background

Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.

Results

In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts.

Conclusions

Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.\n\nImpact of homologous recombination on core genome phylogenies.", "token_count": 414, "char_count": 1789, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5569, "quality_score": 0.7785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:26.928757", "source": { "split": "train_shard_00001", "doc_id": 3165 }, "chunk_id": "train_shard_00001_3165_0", "global_id": 10151 }, { "text": "The role of cell surface hydrophobicity in the adhesion to stainless steel (SS) of 11 wild yeast strains isolated from the ultrafiltration membranes of an apple juice processing plant was investigated. The isolated yeasts belonged to four species: Candida krusei (5 isolates), Candida tropicalis (2 isolates), Kluyveromyces marxianus (3 isolates) and Rhodotorula mucilaginosa (1 isolate). Surface hydrophobicity was measured by the microbial adhesion to solvents method. Yeast cells and surfaces were incubated in apple juice and temporal measurements of the numbers of adherent cells were made. Ten isolates showed moderate to high hydrophobicity and 1 strain was hydrophilic. The hydrophobicity expressed by the yeast surfaces correlated positively with the rate of adhesion of each strain. These results indicated that cell surface hydrophobicity governs the initial attachment of the studied yeast strains to SS surfaces common to apple juice processing plants.\n\nRole of hydrophobicity in adhesion of wild yeast isolated from the ultrafiltration membranes of an apple juice processing plant.", "token_count": 265, "char_count": 1095, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5472, "quality_score": 0.7736, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:27.497042", "source": { "split": "train_shard_00001", "doc_id": 3166 }, "chunk_id": "train_shard_00001_3166_0", "global_id": 10152 }, { "text": "

Background

The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.

Results

We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.

Conclusion

The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1. Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.", "token_count": 500, "char_count": 2194, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5617, "quality_score": 0.7808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:28.196622", "source": { "split": "train_shard_00001", "doc_id": 3167 }, "chunk_id": "train_shard_00001_3167_0", "global_id": 10153 }, { "text": "Vibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement.", "token_count": 40, "char_count": 170, "word_count": 25, "semantic_coherence": 1, "information_density": 0.96, "quality_score": 0.98, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:28.592765", "source": { "split": "train_shard_00001", "doc_id": 3167 }, "chunk_id": "train_shard_00001_3167_1", "global_id": 10154 }, { "text": "

Unlabelled

A major challenge for the production of ethanol from biomass-derived feedstocks is to develop yeasts that can sustain growth under the variety of inhibitory conditions present in the production process, e.g., high osmolality, high ethanol titers, and/or elevated temperatures (≥ 40 °C). Using adaptive laboratory evolution, we previously isolated seven Saccharomyces cerevisiae strains with improved growth at 40 °C. Here, we show that genetic adaptations to high temperature caused a growth trade-off at ancestral temperatures, reduced cellular functions, and improved tolerance of other stresses. Thermotolerant yeast strains showed horizontal displacement of their thermal reaction norms to higher temperatures. Hence, their optimal and maximum growth temperatures increased by about 3 °C, whereas they showed a growth trade-off at temperatures below 34 °C. Computational analysis of the physical properties of proteins showed that the lethal temperature for yeast is around 49 °C, as a large fraction of the yeast proteins denature above this temperature. Our analysis also indicated that the number of functions involved in controlling the growth rate decreased in the thermotolerant strains compared with the number in the ancestral strain. The latter is an advantageous attribute for acquiring thermotolerance and correlates with the reduction of yeast functions associated with loss of respiration capacity. This trait caused glycerol overproduction that was associated with the growth trade-off at ancestral temperatures. In combination with altered sterol composition of cellular membranes, glycerol overproduction was also associated with yeast osmotolerance and improved tolerance of high concentrations of glucose and ethanol. Our study shows that thermal adaptation of yeast is suitable for improving yeast resistance to inhibitory conditions found in industrial ethanol production processes.

Importance

Yeast thermotolerance can significantly reduce the production costs of biomass conversion to ethanol. However, little information is available about the underlying genetic changes and physiological functions required for yeast thermotolerance. We recently revealed the genetic changes of thermotolerance in thermotolerant yeast strains (TTSs) generated through adaptive laboratory evolution", "token_count": 500, "char_count": 2334, "word_count": 315, "semantic_coherence": 1, "information_density": 0.5429, "quality_score": 0.7714, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:29.267098", "source": { "split": "train_shard_00001", "doc_id": 3168 }, "chunk_id": "train_shard_00001_3168_0", "global_id": 10155 }, { "text": "Here, we examined these TTSs' physiology and computed their proteome stability over the entire thermal niche, as well as their preadaptation to other stresses. Using this approach, we showed that TTSs exhibited evolutionary trade-offs in the ancestral thermal niche, as well as reduced numbers of growth functions and preadaptation to other stresses found in ethanol production processes. This information will be useful for rational engineering of yeast thermotolerance for the production of biofuels and chemicals.\n\nThermotolerant Yeast Strains Adapted by Laboratory Evolution Show Trade-Off at Ancestral Temperatures and Preadaptation to Other Stresses.", "token_count": 154, "char_count": 656, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:29.702492", "source": { "split": "train_shard_00001", "doc_id": 3168 }, "chunk_id": "train_shard_00001_3168_1", "global_id": 10156 }, { "text": "The glyceraldehyde-3-phosphate dehydrogenase (GAP) gene from the thermotolerant yeast strain Pichia thermomethanolica BCC16875 was characterized. To investigate the efficiency of the GAP promoter for heterologous expression, especially at high temperature in various carbon sources, the promoter was employed for constitutive expression of a phytase reporter gene. The results showed that this promoter was able to drive efficient expression of phytase at 30 °C; the native promoter was highly robust compared with the heterologous GAP promoter from Pichia pastoris. More importantly, the GAP promoter was shown to be able to function at higher temperatures up to 42 °C, which could be useful for large-scale protein production to help reduce cooling costs in the fermenter. Expression in different carbon sources revealed that the GAP promoter was functional in glucose-, glycerol-, and methanol-containing media, with the highest level of expression in YPD medium. This strong promoter will help promote high expression of heterologous protein expression in P. thermomethanolica, especially in large-scale fermentation. In addition, a new tool for heterologous expression in yeast has been gained.\n\nUse of the glyceraldehyde-3-phosphate dehydrogenase promoter from a thermotolerant yeast, Pichia thermomethanolica, for heterologous gene expression, especially at elevated temperature", "token_count": 345, "char_count": 1385, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5312, "quality_score": 0.7656, "entities": { "genes": [ "BCC16875" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:30.282859", "source": { "split": "train_shard_00001", "doc_id": 3169 }, "chunk_id": "train_shard_00001_3169_0", "global_id": 10157 }, { "text": "The use of molasses as a substrate for ethanol production by the thermotolerant yeast Kluyveromyces marxianus var. marxianus was investigated at 45 degrees C. A maximum ethanol concentration of 7.4% (v/v) was produced from unsupplemented molasses at a concentration of 23% (v/v). The effect on ethanol production of increasing the sucrose concentration in 23% (v/v) molasses was determined. Increased sucrose concentration had a similar detrimental effect on the final ethanol produced as the increase in molasses concentration. This indicated that the effect may be due to increased osmotic activity as opposed to other components in the molasses. The optimum concentration of the supplements nitrogen, magnesium, potassium and fatty acid for maximum ethanol production rate was determined using the Nelder and Mead (Computer J 7:308-313, 1965) simplex optimisation method. The optimum concentration of the supplements were 0.576 g1(-1) magnesium sulphate, 0.288 g1(-1) potassium dihydrogen phosphate and 0.36% (v/v) linseed oil. Added nitrogen in the form of ammonium sulphate did not affect the ethanol production rate.\n\nFermentation of molasses using a thermotolerant yeast, Kluyveromyces marxianus IMB3: simplex optimisation of media supplements.", "token_count": 363, "char_count": 1251, "word_count": 179, "semantic_coherence": 1, "information_density": 0.5698, "quality_score": 0.7849, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:30.857428", "source": { "split": "train_shard_00001", "doc_id": 3170 }, "chunk_id": "train_shard_00001_3170_0", "global_id": 10158 }, { "text": "Abstract

Background. Core genome phylogenies are widely used to build the evolutionary history of individual prokaryote species. By using hundreds or thousands of shared genes, these approaches are the gold standard to reconstruct the relationships of large sets of strains. However, there is growing evidence that bacterial strains exchange DNA through homologous recombination at rates that vary widely across prokaryote species, indicating that core genome phylogenies might not be able to reconstruct true phylogenies when recombination rate is high. Few attempts have been made to evaluate the robustness of core genome phylogenies to recombination, but some analyses suggest that reconstructed trees are not always accurate.Results. In this study, we tested the robustness of core genome phylogenies to various levels of recombination rates. By analyzing simulated and empirical data, we observed that core genome phylogenies are relatively robust to recombination rates; nevertheless, our results suggest that many reconstructed trees are not completely accurate even when bootstrap supports are high. We found that some core genome phylogenies are highly robust to recombination whereas others are strongly impacted by it, and we identified that the robustness of core genome phylogenies to recombination is highly linked to the levels of selective pressures acting on a species. Stronger selective pressures lead to less accurate tree reconstructions, presumably because selective pressures more strongly bias the routes of DNA transfers, thereby causing phylogenetic artifacts. Conclusions. Overall, these results have important implications for the application of core genome phylogenies in prokaryotes.

\n\nImpact of homologous recombination on core genome phylogenies", "token_count": 419, "char_count": 1839, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5538, "quality_score": 0.7769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:31.484132", "source": { "split": "train_shard_00001", "doc_id": 3171 }, "chunk_id": "train_shard_00001_3171_0", "global_id": 10159 }, { "text": "

Background

Chlamydia trachomatis (Ct) plasmid has been shown to encode genes essential for infection. We evaluated the population structure of Ct using whole-genome sequence data (WGS). In particular, the relationship between the Ct genome, plasmid and disease was investigated.

Results

WGS data from 157 Ct isolates deposited in the Chlamydiales pubMLST database ( http://pubMLST.org/chlamydiales/ ) were annotated with 902 genes including the core and accessory genome. Plasmid associated genes were annotated and a plasmid MLST scheme was defined allowing plasmid sequence types to be determined. Plasmid allelic variation was investigated. Phylogenetic relationships were examined using the Genome Comparator tool available in pubMLST. Phylogenetic analyses identified four distinct Ct core genome clusters and six plasmid clusters, with a strong association between the chromosomal genotype and plasmid. This in turn was linked to ompA genovars and disease phenotype. Horizontal genetic transfer of plasmids was observed for three urogenital-associated isolates, which possessed plasmids more commonly found in isolates resulting from ocular infections. The pgp3 gene was identified as the most polymorphic plasmid gene and pgp4 was the most conserved.

Conclusion

A strong association between chromosomal genome, plasmid type and disease was observed, consistent with previous studies. This suggests co-evolution of the Ct chromosome and their plasmids, but we confirmed that plasmid transfer can occur between isolates. These data provide a better understanding of the genetic diversity occurring across the Ct genome in association with the plasmid content.\n\nGenomic analyses of the Chlamydia trachomatis core genome show an association between chromosomal genome, plasmid type and disease.", "token_count": 454, "char_count": 1819, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5749, "quality_score": 0.7874, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:32.128421", "source": { "split": "train_shard_00001", "doc_id": 3172 }, "chunk_id": "train_shard_00001_3172_0", "global_id": 10160 }, { "text": "

Background

Gonorrhea, caused by the bacterium Neisseria gonorrhoeae, is a globally prevalent sexually transmitted infection. The dynamics of gonococcal population biology have been poorly defined due to a lack of resolution in strain typing methods.

Methods

In this study, we assess how the core genome can be used to improve our understanding of gonococcal population structure compared with current typing schemes.

Results

A total of 1668 loci were identified as core to the gonococcal genome. These were organized into a core genome multilocus sequence typing scheme (N gonorrhoeae cgMLST v1.0). A clustering algorithm using a threshold of 400 allelic differences between isolates resolved gonococci into discrete and stable core genome groups, some of which persisted for multiple decades. These groups were associated with antimicrobial genotypes and non-overlapping NG-STAR and NG-MAST sequence types. The MLST-STs were more widely distributed among core genome groups.

Conclusions

Clustering with cgMLST identified globally distributed, persistent, gonococcal lineages improving understanding of the population biology of gonococci and revealing its population structure. These findings have implications for the emergence of antimicrobial resistance in gonococci and how this is associated with lineages, some of which are more predisposed to developing antimicrobial resistance than others.\n\nNeisseria gonorrhoeae Population Genomics: Use of the Gonococcal Core Genome to Improve Surveillance of Antimicrobial Resistance.", "token_count": 407, "char_count": 1559, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5951, "quality_score": 0.7976, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:32.750527", "source": { "split": "train_shard_00001", "doc_id": 3173 }, "chunk_id": "train_shard_00001_3173_0", "global_id": 10161 }, { "text": "

Background

Data from a prospective molecular-epidemiologic study (1997-2021) in Hamburg, Germany, were evaluated to assess the transmission risk of Mycobacterium tuberculosis complex (Mtbc) by children <15 years in a low-incidence setting.

Methods

Isolates of Mtbc were genotyped whole genome sequencing, applying a core genome multilocus sequence typing scheme. Close contacts of culture-confirmed children were examined for latent Mtbc infections (LTBI) with particular focus on IGRA testing.

Results

Out of 3154 culture-confirmed tuberculosis (TB) cases, 79 (2.5%) were children <15 years. Of those, 52 (58%) had pulmonary TB. Genotyping revealed that 35 of the 52 children (67%) were epidemiologically confirmed secondary cluster members; all of their source cases were adults. Six immigrant children presented without a presumed source case; their TB diagnoses came on average 48 weeks (interquartile range [IQR] 71) after their arrival in Germany. Three German-born children were determined to have been infected by adult relatives while visiting their parents' home country. Of the 317 children's close contacts tested with QuantiFERON-TB Gold-In Tube for LTBI, only 21 (6.6%) were positive. Absent a history of prior exposure or immigration from a high-incidence country, none of the contacts of younger (<10 years) TB-afflicted children was latently infected, whereas 2 older children infected 12 of their contacts, children and adults. During a mean observational period of 551 weeks (IQR 735) on average, no secondary TB cases appeared.

Conclusions

Children with pulmonary TB disease, especially those aged below 10 years, rarely transmit Mtbc to their close contacts in a low-incidence setting.\n\nRisk of tuberculosis transmission by children in Hamburg, Germany.", "token_count": 501, "char_count": 1803, "word_count": 250, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:33.412430", "source": { "split": "train_shard_00001", "doc_id": 3174 }, "chunk_id": "train_shard_00001_3174_0", "global_id": 10162 }, { "text": "The human microbiome is a rich factory for metabolite production and emerging data has led to the concept that orally administered microbial strains can synthesize metabolites with neuroactive potential. Recent research from ex vivo and murine models suggests translational potential for microbes to regulate anxiety and depression through the gut-brain axis. However, so far, less emphasis has been placed on the selection of specific microbial strains known to produce the required key metabolites and the formulation in which microbial compositions are delivered to the gut. Here, we describe a double-capsule technology to deliver high numbers of metabolically active cells derived from the 24-strain probiotic product SH-DS01 to the gastrointestinal tract, including the small intestine, where immune responses and adsorption of metabolites into the bloodstream occur. Based on its genome sequence, Limosilactobacillus reuteri SD-LRE2-IT was predicted to have the genetic capacity to de novo produce a specific metabolite of interest to brain health, vitamin B12, which could be confirmed in vitro. Taken together, our data conceptualizes the importance of rationally defined microbial strain characterization based on genomics and metabolomics data, combined with carefully designed capsule technology for delivery of live cells and concomitant functionality in and beyond the gut ecosystem.\n\nDelivery of Metabolically Neuroactive Probiotics to the Human Gut.", "token_count": 350, "char_count": 1486, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [ "LRE2", "DS01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:33.981394", "source": { "split": "train_shard_00001", "doc_id": 3175 }, "chunk_id": "train_shard_00001_3175_0", "global_id": 10163 }, { "text": "Livestock-Associated Methicillin-ResistantStaphylococcus aureus (LA-MRSA) strains of clonal complex (CC) 398 are widely disseminated in pigs and are considered emerging pathogens in human medicine. To investigate the prevalence, genetic characteristics, and zoonotic potential of the pathogen in pig production settings, dust samples were collected from 40 pig operations in Hungary, along with nasal swabs of attending veterinarians and other swine professionals (n = 27) in 2019. MRSA isolates were further characterized by performing whole-genome sequencing and susceptibility testing. The whole-genome sequences of 14 human-derived LA-MRSA clinical isolates from the same year were also included in the study. The proportion of positive farms was 83% (33/40), and 70% (19/27) of the swine professionals carried the pathogen. All but one MRSA strain belonged to CC398, including the human clinical isolates. The core genome multilocus sequence typing (cgMLST) analysis revealed clusters of closely-related isolates of both environmental and human origin with a pairwise allelic distance of ≤24, and both cgMLST and single nucleotide polymorphism (SNP) analyses suggest recent transmission events between the farm environment and humans. Four human clinical isolates harboured the immune-evasion gene cluster, of which one was considered to be closely related to farm isolates. Half of the swine-related strains showed decreased susceptibility to eight or more antimicrobials, and along with human isolates, they carried eight different types of multidrug-resistance genes, including cfr. The results showed a dramatic increase in the occurrence of LA-MRSA in the swine industry in Hungary, compared with the 2% prevalence reported by the European Food Safety Authority baseline study in 2008. The wide range of antimicrobial resistance of the strains, accompanied by the emergence of the pathogen in humans - both asymptomatic carriers and diseased - call for revision of the risk posed by LA-MRSA to the public health.", "token_count": 517, "char_count": 2043, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6267, "quality_score": 0.8134, "entities": { "genes": [ "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:34.636303", "source": { "split": "train_shard_00001", "doc_id": 3176 }, "chunk_id": "train_shard_00001_3176_0", "global_id": 10164 }, { "text": "High Prevalence of Livestock-Associated Methicillin-Resistant <i>Staphylococcus aureus</i> in Hungarian Pig Farms and Genomic Evidence for the Spillover of the Pathogen to Humans.", "token_count": 67, "char_count": 191, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:35.000542", "source": { "split": "train_shard_00001", "doc_id": 3176 }, "chunk_id": "train_shard_00001_3176_1", "global_id": 10165 }, { "text": "

Background

The assembly of animal microbiomes is influenced by multiple environmental factors and host genetics, although the relative importance of these factors remains unclear. Bifidobacteria (genus Bifidobacterium, phylum Actinobacteria) are common first colonizers of gut microbiomes in humans and inhabit other mammals, social insects, food, and sewages. In humans, the presence of bifidobacteria in the gut has been correlated with health-promoting benefits. Here, we compared the genome sequences of a subset of the over 400 Bifidobacterium strains publicly available to investigate the adaptation of bifidobacteria diversity. We tested 1) whether bifidobacteria show a phylogenetic signal with their isolation sources (hosts and environments) and 2) whether key traits encoded by the bifidobacteria genomes depend on the host or environment from which they were isolated. We analyzed Bifidobacterium genomes available in the PATRIC and NCBI repositories and identified the hosts and/or environment from which they were isolated. A multilocus phylogenetic analysis was conducted to compare the genetic relatedness the strains harbored by different hosts and environments. Furthermore, we examined differences in genomic traits and genes related to amino acid biosynthesis and degradation of carbohydrates.

Results

We found that bifidobacteria diversity appears to have evolved with their hosts as strains isolated from the same host were non-randomly associated with their phylogenetic relatedness. Moreover, bifidobacteria isolated from different sources displayed differences in genomic traits such as genome size and accessory gene composition and on particular traits related to amino acid production and degradation of carbohydrates. In contrast, when analyzing diversity within human-derived bifidobacteria, we observed no phylogenetic signal or differences on specific traits (amino acid biosynthesis genes and CAZymes).

Conclusions

Overall, our study shows that bifidobacteria diversity is strongly adapted to specific hosts and environments and that several genomic traits were associated with their isolation sources", "token_count": 510, "char_count": 2156, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5505, "quality_score": 0.7753, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:35.633900", "source": { "split": "train_shard_00001", "doc_id": 3177 }, "chunk_id": "train_shard_00001_3177_0", "global_id": 10166 }, { "text": "However, this signal is not observed in human-derived strains alone. Looking into the genomic signatures of bifidobacteria strains in different environments can give insights into how this bacterial group adapts to their environment and what types of traits are important for these adaptations.\n\nEvolutionary relationships among bifidobacteria and their hosts and environments.", "token_count": 81, "char_count": 377, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8269, "quality_score": 0.9135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:36.006818", "source": { "split": "train_shard_00001", "doc_id": 3177 }, "chunk_id": "train_shard_00001_3177_1", "global_id": 10167 }, { "text": "This study reports the draft genome sequence of Bacillus velezensis strain AAK_S6 as a valuable biocontrol agent with high genetic potential to harbor broad-spectrum secondary metabolite producing capacity. A genome data of 4,430,946 bp were generated with a GC content of 46.4% that comprised a total of 4861 genes including a total of 4757 coding sequences (CDS), 104 rRNAs, 85 tRNAs and 80 pseudo-genes. Based on the overall genome-based relatedness indices (OGRI), the strain AAK_S6 has been reassigned to its correct taxonomic position. The strain shared > 99% OrthoANI, > 98% ANIb, > 99% ANIm, > 0.9900 TETRA, > 93% dDDH and 0.08% GC content difference with model strains B. velezensis FZB42T and B. velezensis NRRL B-41580T thus delineating them as closely related species. The genome was mined for strain-specific secondary metabolites that revealed 20 gene clusters for the biosynthesis of several cyclic lipopeptides, saccharides, polyketides along with bacilysin. Thus, the comparative genome analysis of strain AAK_S6 with members of the genus Bacillus by phylogenomic approach revealed that the genomes were almost similar genetically and contained the core genome for B. velezensis. Genomic data strongly supported that the strain AAK_S6 represented an excellent potential candidate for the production of secondary metabolites that could serve as a basis for developing new biocontrol agents, plant growth promoters, and microbial fertilizers.\n\nIn Silico Genomic Characterization of Bacillus velezensis Strain AAK_S6 for Secondary Metabolite and Biocontrol Potential.", "token_count": 479, "char_count": 1603, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6309, "quality_score": 0.8155, "entities": { "genes": [ "FZB42" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:36.650594", "source": { "split": "train_shard_00001", "doc_id": 3178 }, "chunk_id": "train_shard_00001_3178_0", "global_id": 10168 }, { "text": "

Objectives

To elucidate the molecular epidemiology of tigecycline and carbapenem-resistant Enterobacteriaceae isolates and mechanisms of tigecycline resistance.

Methods

We gathered 31 unduplicated strains of tigecycline-resistant Enterobacteriaceae from six hospitals nationwide. Antimicrobial susceptibility testing, phenotypic detection, and PCR identification were performed first, followed by homology analysis using MLST and PFGE. Conjugation transfer experiments using resistance gene plasmids were carried out, and the conjugates' growth curves were examined. All strains were sequenced using the Illumina HiSeq technology, and we identified a strain KP28 carrying a complete gene cluster tmexCD2-toprJ2. Then, its plasmid was further constructed using the PacBio platforms to complete the frame. The genetic connection of the tmexCD2-toprJ2 gene cluster carried by KP28 was established using core genome analyses.

Results

All 31 tigecycline-resistant Enterobacteriaceae strains (TG-CRE) were multidrug resistant. PFGE classified strains of CRKP, CRECL, and CRKAE into 16 distinct spectra, 6 distinct spectra, and 3 distinct spectra. MLST results showed a high concentration of ST11 in CRKP strains and a predominance of ST116 in CRECL strains, suggesting possible clonal transmission or selective dominance. The findings of the plasmid conjugation assay revealed that three strains expressing carbapenem resistance genes were effectively transmitted to the recipient cell E. coli EC600. WGS data revealed that these 31 strains include 79 resistance genes, with one strain (KP28) carrying the whole tigecycline resistance gene cluster, tmexC2D2-toprJ2", "token_count": 496, "char_count": 1729, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6574, "quality_score": 0.8287, "entities": { "genes": [ "KP28", "EC600", "ST116", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:37.303994", "source": { "split": "train_shard_00001", "doc_id": 3179 }, "chunk_id": "train_shard_00001_3179_0", "global_id": 10169 }, { "text": "This resistance gene is contained in a large IncHI5 plasmid, which is difficult to transfer.

Conclusion

The overall carriage rate of the tmexC2D2-toprJ2 gene cluster was found to be low among the five Chinese hospitals investigated. Conversely, tet(A) mutations were present in most of the strains. Bacteria with the carbapenem resistance genes bla KPC and bla NDM are vulnerable to horizontal transmission. Increasing the risk of transmission of antibiotic-resistant genes.\n\nEpidemiology and resistance mechanisms of tigecycline- and carbapenem-resistant <i>Enterobacteriaceae</i> in China: a multicentre genome-based study.", "token_count": 213, "char_count": 694, "word_count": 83, "semantic_coherence": 1, "information_density": 0.759, "quality_score": 0.8795, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:37.769684", "source": { "split": "train_shard_00001", "doc_id": 3179 }, "chunk_id": "train_shard_00001_3179_1", "global_id": 10170 }, { "text": "Colistin is a last-resort antibiotic used in the treatment of multidrug resistant Gram-negative bacteria. However, the activity and efficacy of colistin has been compromised by the worldwide spread of the mobile colistin resistance genes (mcr-1 to mcr-10). In this study, two clinical Escherichia coli strains, named EcCAI51, and EcCAI73, harbored mcr-1, showed multidrug-resistant phenotypes (with colistin MIC = 4 μg/ml), and belonged to phylogroup D: multilocus sequence type 1011 (ST1011) and phylogroup A: ST744, respectively. Findings revealed the existence of mcr-1 gene on two conjugable plasmids, pAMS-51-MCR1 (∼122 kb IncP) and pAMS-73-MCR1 (∼33 kb IncX4), in EcCAI51, and EcCAI73, respectively. The mcr-1-pap2 element was detected in the two plasmids. Additionally, the composite transposon (ISApl1-IS5D-pap2-mcr-1-ISApl1) was identified only in pAMS-51-MCR1 suggesting the potential for horizontal gene transfer. The two strains carried from 16 to 18 different multiple acquired antimicrobial resistance genes (ARGs)", "token_count": 445, "char_count": 1140, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7234, "quality_score": 0.8617, "entities": { "genes": [ "ST1011", "CAI73", "ST744", "MCR1", "CAI51" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:38.402674", "source": { "split": "train_shard_00001", "doc_id": 3180 }, "chunk_id": "train_shard_00001_3180_0", "global_id": 10171 }, { "text": "Additionally, two different multireplicon virulence plasmids (∼117 kb pAMS-51-Vr and ∼226 kb pAMS-73-Vr) carrying the sit operon, the Salmochelin siderophore iroBCDE operon and other several virulence genes were identified from the two strains. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of EcCAI73, and EcCAI51 with global E. coli lineages at HC levels of 50 (HC50) to 100 (HC100) core genome allelic differences. To the best of our knowledge, this study presented the first complete genomic sequences of mcr-1-carrying IncP and IncX4 plasmids from human clinical E. coli isolates in Egypt. In addition, the study illustrated the mcr-1 broad dissemination in diverse plasmids and dissimilar E. coli clones.\n\nComplete genome sequences of two Escherichia coli clinical isolates from Egypt carrying mcr-1 on IncP and IncX4 plasmids.", "token_count": 337, "char_count": 937, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8228, "entities": { "genes": [ "HC100", "HC50", "CAI73", "CAI51" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:39.009221", "source": { "split": "train_shard_00001", "doc_id": 3180 }, "chunk_id": "train_shard_00001_3180_1", "global_id": 10172 }, { "text": "Chickens infected with Campylobacter jejuni or Campylobacter coli are largely asymptomatic, however, infection with the closely related species, Campylobacter hepaticus, can result in Spotty Liver Disease (SLD). C. hepaticus has been detected in the liver, bile, small intestine and caecum of SLD affected chickens. The survival and colonization mechanisms that C. hepaticus uses to colonize chickens remain unknown. In this study, we compared the genome sequences of 14 newly sequenced Australian isolates of C. hepaticus, isolates from outbreaks in the United Kingdom, and reference strains of C. jejuni and C. coli, with the aim of identifying virulence genes associated with SLD. We also carried out global comparative transcriptomic analysis between C. hepaticus recovered from the bile of SLD infected chickens and C. hepaticus grown in vitro. This revealed how the bacteria adapt to proliferate in the challenging host environment in which they are found. Additionally, biochemical experiments confirmed some in silico metabolic predictions. We found that, unlike other Campylobacter sp., C. hepaticus encodes glucose and polyhydroxybutyrate metabolism pathways. This study demonstrated the metabolic plasticity of C. hepaticus, which may contribute to survival in the competitive, nutrient and energy-limited environment of the chicken. Transcriptomic analysis indicated that gene clusters associated with glucose utilization, stress response, hydrogen metabolism, and sialic acid modification may play an important role in the pathogenicity of C. hepaticus. An understanding of the survival and virulence mechanisms that C. hepaticus uses will help to direct the development of effective intervention methods to protect birds from the debilitating effects of SLD.", "token_count": 513, "char_count": 1891, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:39.695850", "source": { "split": "train_shard_00001", "doc_id": 3181 }, "chunk_id": "train_shard_00001_3181_0", "global_id": 10173 }, { "text": "Survival Mechanisms of Campylobacter hepaticus Identified by Genomic Analysis and Comparative Transcriptomic Analysis of in vivo and in vitro Derived Bacteria.", "token_count": 59, "char_count": 180, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:40.065215", "source": { "split": "train_shard_00001", "doc_id": 3181 }, "chunk_id": "train_shard_00001_3181_1", "global_id": 10174 }, { "text": "Improper use of water resources in irrigation that contain a significant amount of salts, faulty agronomic practices such as improper fertilization, climate change etc. are gradually increasing soil salinity of arable lands across the globe. It is one of the major abiotic factors that inhibits overall plant growth through ionic imbalance, osmotic stress, oxidative stress, and reduced nutrient uptake. Plants have evolved with several adaptation strategies at morphological and molecular levels to withstand salinity stress. Among various approaches, harnessing the crop genetic variability across different genepools and developing salinity tolerant crop plants offer the most sustainable way of salt stress mitigation. Some important major genetic determinants controlling salinity tolerance have been uncovered using classical genetic approaches. However, its complex inheritance pattern makes breeding for salinity tolerance challenging. Subsequently, advances in sequence based breeding approaches and functional genomics have greatly assisted in underpinning novel genetic variants controlling salinity tolerance in plants at the whole genome level. This current review aims to shed light on physiological, biochemical, and molecular responses under salt stress, defense mechanisms of plants, underlying genetics of salt tolerance through bi-parental QTL mapping and Genome Wide Association Studies, and implication of Genomic Selection to breed salt tolerant lines.\n\nImpacts of salinity stress on crop plants: improving salt tolerance through genetic and molecular dissection.", "token_count": 308, "char_count": 1585, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6963, "quality_score": 0.8481, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:40.681260", "source": { "split": "train_shard_00001", "doc_id": 3182 }, "chunk_id": "train_shard_00001_3182_0", "global_id": 10175 }, { "text": "Heat shock protein 20 (HSP20) is a diverse and functionally important protein family that plays a crucial role in plants' tolerance to various abiotic stresses. In this study, we systematically analyzed the structural and functional characteristics of the HSP20 gene family within the Zea pan-genome. By identifying 56 HSP20 pan-genes, we revealed the variation in the number of these genes across different maize inbreds or relatives. Among those 56 genes, only 31 are present in more than 52 inbreds or relatives. Further phylogenetic analysis classified these genes into four major groups (Class A, B, C, D) and explored their diversity in subcellular localization, physicochemical properties, and the terminal structures of those HSP20s. Through collinearity analysis and Ka/Ks ratio calculations, we found that most HSP20 genes underwent purifying selection during maize domestication, although a few genes showed signs of positive selection pressure. Additionally, expression analysis showed that several HSP20 genes were significantly upregulated under high temperatures, particularly in tassels and leaves. Co-expression network analysis revealed that HSP20 genes were significantly enriched in GO terms related to environmental stress responses, suggesting that HSP20 genes not only play key roles in heat stress but may also be involved in regulating various other biological processes, such as secondary metabolism and developmental processes. These findings expand our understanding of the functions of the maize HSP20 family and provide new insights for further research into maize's response mechanisms to environmental stresses.\n\nPan-Genome-Wide Investigation and Co-Expression Network Analysis of HSP20 Gene Family in Maize.", "token_count": 435, "char_count": 1796, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6559, "quality_score": 0.8279, "entities": { "genes": [ "HSP20" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:41.314125", "source": { "split": "train_shard_00001", "doc_id": 3183 }, "chunk_id": "train_shard_00001_3183_0", "global_id": 10176 }, { "text": "

Objectives

From 2012 to 2015, a sudden significant increase in vancomycin-resistant (vanA) Enterococcus faecium (VREfm) was observed in the Capital Region of Denmark. Clonal relatedness of VREfm and vancomycin-susceptible E. faecium (VSEfm) was investigated, transmission events between hospitals were identified and the pan-genome and plasmids from the largest VREfm clonal group were characterized.

Methods

WGS of 1058 E. faecium isolates was carried out on the Illumina platform to perform SNP analysis and to identify the pan-genome. One isolate was also sequenced on the PacBio platform to close the genome. Epidemiological data were collected from laboratory information systems.

Results

Phylogeny of 892 VREfm and 166 VSEfm revealed a polyclonal structure, with a single clonal group (ST80) accounting for 40% of the VREfm isolates. VREfm and VSEfm co-occurred within many clonal groups; however, no VSEfm were related to the dominant VREfm group. A similar vanA plasmid was identified in ≥99% of isolates belonging to the dominant group and 69% of the remaining VREfm. Ten plasmids were identified in the completed genome, and ∼29% of this genome consisted of dispensable accessory genes. The size of the pan-genome among isolates in the dominant group was 5905 genes.

Conclusions

Most probably, VREfm emerged owing to importation of a successful VREfm clone which rapidly transmitted to the majority of hospitals in the region whilst simultaneously disseminating a vanA plasmid to pre-existing VSEfm. Acquisition of a heterogeneous accessory genome may account for the success of this clone by facilitating adaptation to new environmental challenges.", "token_count": 467, "char_count": 1688, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5667, "quality_score": 0.7833, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:41.952346", "source": { "split": "train_shard_00001", "doc_id": 3184 }, "chunk_id": "train_shard_00001_3184_0", "global_id": 10177 }, { "text": "WGS of 1058 Enterococcus faecium from Copenhagen, Denmark, reveals rapid clonal expansion of vancomycin-resistant clone ST80 combined with widespread dissemination of a vanA-containing plasmid and acquisition of a heterogeneous accessory genome.", "token_count": 67, "char_count": 245, "word_count": 31, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:42.319052", "source": { "split": "train_shard_00001", "doc_id": 3184 }, "chunk_id": "train_shard_00001_3184_1", "global_id": 10178 }, { "text": "The empirical and pragmatic nature of diagnostic microbiology has given rise to several different schemes to subtype E.coli, including biotyping, serotyping, and pathotyping. These schemes have proved invaluable in identifying and tracking outbreaks, and for prognostication in individual cases of infection, but they are imprecise and potentially misleading due to the malleability and continuous evolution of E. coli. Whole genome sequencing can be used to accurately determine E. coli subtypes that are based on allelic variation or differences in gene content, such as serotyping and pathotyping. Whole genome sequencing also provides information about single nucleotide polymorphisms in the core genome of E. coli, which form the basis of sequence typing, and is more reliable than other systems for tracking the evolution and spread of individual strains. A typing scheme for E. coli based on genome sequences that includes elements of both the core and accessory genomes, should reduce typing anomalies and promote understanding of how different varieties of E. coli spread and cause disease. Such a scheme could also define pathotypes more precisely than current methods.\n\nAre Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing?", "token_count": 325, "char_count": 1315, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6383, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:42.899390", "source": { "split": "train_shard_00001", "doc_id": 3185 }, "chunk_id": "train_shard_00001_3185_0", "global_id": 10179 }, { "text": "

ABSTRACT

We introduce Giraffe, a pangenome short read mapper that can efficiently map to a collection of haplotypes threaded through a sequence graph. Giraffe, part of the variation graph toolkit (vg) 1 , maps reads to thousands of human genomes at around the same speed BWA-MEM 2 maps reads to a single reference genome, while maintaining comparable accuracy to VG-MAP, vg’s original mapper. We have developed efficient genotyping pipelines using Giraffe. We demonstrate improvements in genotyping for single-nucleotide variants (SNVs), small insertions and deletions (indels) and structural variations (SVs) genome-wide. We use Giraffe to genotype about 167 thousand structural variants ascertained from long read studies in 5,202 human genomes sequenced with short reads, including the complete 1000 Genomes Project dataset, at an average cost of $1.50 per sample. We determine the frequency of these variations in diverse human populations, characterize their complex allelic variations and identify thousands of expression quantitative trait loci (eQTLs) driven by these variations.\n\nGenotyping common, large structural variations in 5,202 genomes using pangenomes, the Giraffe mapper, and the vg toolkit", "token_count": 307, "char_count": 1218, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7011, "quality_score": 0.8506, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:43.468489", "source": { "split": "train_shard_00001", "doc_id": 3186 }, "chunk_id": "train_shard_00001_3186_0", "global_id": 10180 }, { "text": "

Objective

Proteus mirabilis is the one of most important pathogens of catheter-associated urinary tract infections. The emergence of multidrug-resistant (MDR) P. mirabilis severely limits antibiotic treatments, which poses a public health risk. This study aims to investigate the resistance characteristics and virulence potential for a collection of P. mirabilis clinical isolates.

Methods and results

Antibiotic susceptibility testing revealed fourteen MDR strains, which showed high resistance to most β-lactams and trimethoprim/sulfamethoxazole, and a lesser extent to quinolones. All the MDR strains were sensitive to carbapenems (except imipenem), ceftazidime, and amikacin, and most of them were also sensitive to aminoglycosides. The obtained MDR isolates were sequenced using an Illumina HiSeq. The core genome-based phylogenetic tree reveals the high genetic diversity of these MDR P. mirabilis isolates and highlights the possibility of clonal spread of them across China. Mobile genetic elements SXT/R391 ICEs were commonly (10/14) detected in these MDR P. mirabilis strains, whereas the presence of resistance island PmGRI1 and plasmid was sporadic. All ICEs except for ICEPmiChn31006 carried abundant antimicrobial resistance genes (ARGs) in the HS4 region, including the extended-spectrum β-lactamase (ESBL) gene blaCTX-M-65. ICEPmiChn31006 contained the sole ARG blaCMY-2 and was nearly identical to the global epidemic ICEPmiJpn1. The findings highlight the important roles of ICEs in mediating the spread of ARGs in P. mirabilis strains", "token_count": 523, "char_count": 1668, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [ "HS4", "GRI1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:44.123645", "source": { "split": "train_shard_00001", "doc_id": 3187 }, "chunk_id": "train_shard_00001_3187_0", "global_id": 10181 }, { "text": "Additionally, these MDR P. mirabilis strains have great virulence potential as they exhibited significant virulence-related phenotypes including strong crystalline biofilm, hemolysis, urease production, and robust swarming motility, and harbored abundant virulence genes.

Conclusion

In conclusion, the prevalence of MDR P. mirabilis with high virulence potential poses an urgent threat to public health. Intensive monitoring is needed to reduce the incidence of infections by MDR P. mirabilis.\n\nGenetic analysis of resistance and virulence characteristics of clinical multidrug-resistant Proteus mirabilis isolates.", "token_count": 178, "char_count": 650, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7792, "quality_score": 0.8896, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:44.567835", "source": { "split": "train_shard_00001", "doc_id": 3187 }, "chunk_id": "train_shard_00001_3187_1", "global_id": 10182 }, { "text": "Introduction: Genetic plasticity and adaptive camouflage in critical pathogens have contributed to the global surge in multidrug-resistant (MDR) infections, posing a serious threat to public health and therapeutic efficacy. Antimicrobial resistance, now a leading cause of global mortality, demands urgent action through diagnostics, vaccines, and therapeutics. In India, the Indian Council of Medical Research's surveillance network identifies Escherichia coli as a major cause of urinary tract infections, with increasing prevalence in human gut microbiomes, highlighting its significance across One Health domains. Methods: Whole-genome sequencing of E. coli strain ECG015, isolated from a human gut sample, was performed using the Illumina NextSeq platform. Results: Genomic analysis revealed multiple antibiotic resistance genes, virulence factors, and efflux pump components. Phylogenomic comparisons showed close relatedness to pathovars from both human and animal origins. Notably the genome encoded protein tyrosine kinases (Etk/Ptk and Wzc) and displayed variations in the envelope stress-responsive CpxAR two-component system. Promoter analysis identified putative CpxR-binding sites upstream of genes involved in resistance, efflux, protein kinases, and the MazEF toxin-antitoxin module, suggesting a potential regulatory role of CpxAR in stress response and persistence. Conclusions: This study presents a comprehensive genomic profile of E. coli ECG015, a gut-derived isolate exhibiting clinically significant resistance traits. For the first time, it implicates the CpxAR two-component system as a potential central regulator coordinating antimicrobial resistance, stress kinase signaling, and programmed cell death. These findings lay the groundwork for future functional studies aimed at targeting stress-response pathways as novel intervention strategies against antimicrobial resistance.", "token_count": 479, "char_count": 1962, "word_count": 247, "semantic_coherence": 1, "information_density": 0.7409, "quality_score": 0.8704, "entities": { "genes": [ "ECG015" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:45.210926", "source": { "split": "train_shard_00001", "doc_id": 3188 }, "chunk_id": "train_shard_00001_3188_0", "global_id": 10183 }, { "text": "Genomic and Functional Characterization of Multidrug-Resistant <i>E. coli</i>: Insights into Resistome, Virulome, and Signaling Systems.", "token_count": 49, "char_count": 148, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:45.569220", "source": { "split": "train_shard_00001", "doc_id": 3188 }, "chunk_id": "train_shard_00001_3188_1", "global_id": 10184 }, { "text": "Pseudomonas aeruginosa is an opportunistic pathogen of humans and is a major cause of morbidity and mortality in patients with cystic fibrosis (CF). Prolonged infection of the respiratory tract can lead to adaptation of the pathogen to the CF lung environment. To examine the general patterns of adaptation associated with chronic infection, we obtained genome sequences from a collection of P. aeruginosa isolated from airways of patients with CF. Our analyses support a nonclonal epidemic population structure, with a background of unique, recombining genotypes, and the rare occurrence of successful epidemic clones. We present unique genome sequence evidence for the intercontinental spread of an epidemic strain shared between CF clinics in the United Kingdom and North America. Analyses of core and accessory genomes identified candidate genes and important functional pathways associated with adaptive evolution. Many genes of interest were involved in biological functions with obvious roles in this pathosystem, such as biofilm formation, antibiotic metabolism, pathogenesis, transport, reduction/oxidation, and secretion. Key factors driving the adaptive evolution of this pathogen within the host appear to be the presence of oxidative stressors and antibiotics. Regions of the accessory genome unique to the epidemic strain were enriched for genes in transporter families that efflux heavy metals and antibiotics. The epidemic strain was significantly more resistant than nonepidemic strains to three different antibiotics. Multiple lines of evidence suggest that selection imposed by the CF lung environment has a major influence on genomic evolution and the genetic characteristics of P. aeruginosa isolates causing contemporary infection.\n\nEvolutionary genomics of epidemic and nonepidemic strains of Pseudomonas aeruginosa.", "token_count": 391, "char_count": 1839, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6077, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:46.183331", "source": { "split": "train_shard_00001", "doc_id": 3189 }, "chunk_id": "train_shard_00001_3189_0", "global_id": 10185 }, { "text": "The dead Kluyveromyces marxianus biomass, a fermentation industry waste, was used to explore its sorption potential for lead, mercury, arsenic, cobalt, and cadmium as a function of pH, biosorbent dosage, contact time, agitation speed, and initial metal concentration. The equilibrium data fitted the Langmuir model better for cobalt and cadmium, but Freundlich isotherm for all metals tested. At equilibrium, the maximum uptake capacity (Qmax) was highest for lead followed by mercury, arsenic, cobalt, and cadmium. The RL values ranged between 0-1, indicating favorable sorption of all test metals by the biosorbent. The maximum Kf value of Pb showed its efficient removal from the solution. However, multi-metal analysis depicted that sorption of all metals decreased except Pb. The potentiometric titration of biosorbent revealed the presence of functional groups viz. amines, carboxylic acids, phosphates, and sulfhydryl group involved in heavy metal sorption. The extent of contribution of functional groups and lipids to biosorption was in the order: carboxylic>lipids>amines>phosphates. Blocking of sulfhydryl group did not have any significant effect on metal sorption.\n\nMetals sorption from aqueous solutions by Kluyveromyces marxianus: process optimization, equilibrium modeling and chemical characterization.", "token_count": 346, "char_count": 1319, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6793, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:46.761558", "source": { "split": "train_shard_00001", "doc_id": 3190 }, "chunk_id": "train_shard_00001_3190_0", "global_id": 10186 }, { "text": "

Background/objectives

Antimicrobial resistance represents a challenge to public health systems because of the array of resistance and virulence mechanisms that lead to treatment failure and increased mortality rates. Although for years the main driver of carbapenem resistance in Italy has been the Klebsiella pneumoniae KPC carbapenemase, recent years have seen an increase in VIM and NDM metallo-beta-lactamases (MBLs). We conducted a five-year survey of New Delhi Metallo-beta-Lactamase (NDM)-producing Klebsiella pneumoniae (NDM-Kpn) clinical isolates from the Lazio region, Italy; the study aimed to elucidate the molecular mechanisms underpinning their resistant and virulent phenotype.

Methods

Antimicrobial susceptibility was evaluated by automated systems and broth microdilution. In silico analysis of acquired resistance and virulence genes was performed using whole-genome sequencing (WGS), molecular typing through MLST, and core genome multi-locus sequence typing (cgMLST).

Conclusions

A total of 126 clinical NDM-Kpn isolates were collected from 19 distinct hospitals in the Lazio region. Molecular analysis highlighted the existence of NDM-1 (108/126) and NDM-5 (18/126) variants, 18 Sequence Types (STs), and 15 Cluster Types (CTs). Notably, 31/126 isolates displayed a virulence score of 4, carrying ybt, ICEKp, iuc, and rmp genes. This study identified a variety of NDM-Kpn STs, mainly carrying the blaNDM-1 gene, with a significant number linked to high-risk clones", "token_count": 475, "char_count": 1567, "word_count": 200, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:47.401832", "source": { "split": "train_shard_00001", "doc_id": 3191 }, "chunk_id": "train_shard_00001_3191_0", "global_id": 10187 }, { "text": "Of these isolates, 24.6% showed high-level resistance and virulence, emphasizing the risk of the spread of strains that combine multi-drug-resistance (MDR) and virulence. Proactive surveillance and international collaborations are needed to prevent the spread of high-risk clones, as well as further research into new antimicrobial agents to fight antibiotic resistance.\n\nMolecular Characterization of Multidrug-Resistant and Hypervirulent New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae in Lazio, Italy: A Five-Year Retrospective Study.", "token_count": 152, "char_count": 551, "word_count": 68, "semantic_coherence": 1, "information_density": 0.8088, "quality_score": 0.9044, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:47.839391", "source": { "split": "train_shard_00001", "doc_id": 3191 }, "chunk_id": "train_shard_00001_3191_1", "global_id": 10188 }, { "text": "Members of the order Methanomicrobiales are abundant, and sometimes dominant, hydrogenotrophic (H2-CO2 utilizing) methanoarchaea in a broad range of anoxic habitats. Despite their key roles in greenhouse gas emissions and waste conversion to methane, little is known about the physiological and genomic bases for their widespread distribution and abundance. In this study, we compared the genomes of nine diverse Methanomicrobiales strains, examined their pangenomes, reconstructed gene flow and identified genes putatively mediating their success across different habitats. Most strains slowly increased gene content whereas one, Methanocorpusculum labreanum, evidenced genome downsizing. Peat-dwelling Methanomicrobiales showed adaptations centered on improved transport of scarce inorganic nutrients and likely use H+ rather than Na+ transmembrane chemiosmotic gradients during energy conservation. In contrast, other Methanomicrobiales show the potential to concurrently use Na+ and H+ chemiosmotic gradients. Analyses also revealed that the Methanomicrobiales lack a canonical electron bifurcation system (MvhABGD) known to produce low potential electrons in other orders of hydrogenotrophic methanogens. Additional putative differences in anabolic metabolism suggest that the dynamics of interspecies electron transfer from Methanomicrobiales syntrophic partners can also differ considerably. Altogether, these findings suggest profound differences in electron trafficking in the Methanomicrobiales compared with other hydrogenotrophs, and warrant further functional evaluations.\n\nGenomic composition and dynamics among Methanomicrobiales predict adaptation to contrasting environments.", "token_count": 441, "char_count": 1758, "word_count": 209, "semantic_coherence": 1, "information_density": 0.7129, "quality_score": 0.8565, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:48.468579", "source": { "split": "train_shard_00001", "doc_id": 3192 }, "chunk_id": "train_shard_00001_3192_0", "global_id": 10189 }, { "text": "Campylobacter is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multilocus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles at seven MLST loci among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1,810 genes identified by gene-by-gene comparison of 884 genomes of Campylobacter jejuni isolates from animal reservoirs, the environment, and clinical cases. Fifteen loci involved in metabolic activities, protein modification, signal transduction, and stress response or coding for hypothetical proteins were selected as host-segregating markers and used to attribute the source of 42 French and 281 United Kingdom clinical C. jejuni isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the United Kingdom. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs, suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modeling to account for differences in production, behavior, and food consumption.IMPORTANCE Accurately quantifying the relative contribution of different host reservoirs to human Campylobacter infection is an ongoing challenge. This study, based on the development of a novel source attribution approach, provides the first results of source attribution in Campylobacter jejuni in France", "token_count": 510, "char_count": 2335, "word_count": 312, "semantic_coherence": 1, "information_density": 0.5769, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:49.120630", "source": { "split": "train_shard_00001", "doc_id": 3193 }, "chunk_id": "train_shard_00001_3193_0", "global_id": 10190 }, { "text": "A systematic analysis using gene-by-gene comparison of 884 genomes of C. jejuni isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and United Kingdom clinical isolates attributed to each host reservoir illustrate a potential role for local/national variations in C. jejuni transmission dynamics.\n\nGenome-Wide Identification of Host-Segregating Epidemiological Markers for Source Attribution in Campylobacter jejuni.", "token_count": 134, "char_count": 525, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:49.537064", "source": { "split": "train_shard_00001", "doc_id": 3193 }, "chunk_id": "train_shard_00001_3193_1", "global_id": 10191 }, { "text": "In the yeast Kluyveromyces marxianus two forms of inulinase were present, namely, an inulinase secreted into the culture fluid and an inulinase retained in the cell wall. Both forms were purified and analyzed by denaturing and nondenaturing polyacrylamide gel electrophoresis. With the use of endo-beta-N-acetyl-glucosaminidase H, it was established that the enzyme retained in the cell wall and the enzyme secreted into the culture fluid have similar subunits consisting of a 64-kDa polypeptide with varying amounts of carbohydrate (26 to 37% of the molecular mass). The two forms of inulinase differed in size because of their differences in subunit aggregation. The enzyme present in the culture fluid was a dimer, and the enzyme retained in the cell wall was a tetramer. The differences in oligomerization did not affect the apparent Km values towards the substrates sucrose and raffinose. These findings support the hypothesis that the retention of glycoproteins in the yeast cell wall may be caused by a permeability barrier towards larger glycoproteins. The amino-terminal end of inulinase was determined and compared with the amino terminus of the closely related invertase. The kinetic and structural evidence indicates that in yeasts two distinct beta-fructosidases exist, namely, invertase and inulinase.\n\nStructure and properties of the extracellular inulinase of Kluyveromyces marxianus CBS 6556.", "token_count": 368, "char_count": 1409, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5381, "quality_score": 0.769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:50.116570", "source": { "split": "train_shard_00001", "doc_id": 3194 }, "chunk_id": "train_shard_00001_3194_0", "global_id": 10192 }, { "text": "Mangrove ecosystems are characteristic of the high salinity, limited nutrients and S-richness. Marichromatium gracile YL28 (YL28) isolated from mangrove tolerates the high concentrations of nitrite and sulfur compounds and efficiently eliminates them. However, the molecular mechanisms of nitrite and sulfur compounds utilization and the habitat adaptation remain unclear in YL28. We sequenced YL28 genome and further performed the comparative genome analysis in 36 purple bacteria including purple sulfur bacteria (PSB) and purple non-sulfur bacteria (PNSB). YL28 has 6 nitrogen cycle pathways (up to 40 genes), and possibly removes nitrite by denitrification, complete assimilation nitrate reduction and fermentative nitrate reduction (DNRA). Comparative genome analysis showed that more nitrogen utilization genes were detected in PNSB than those in PSB. The partial denitrification pathway and complete assimilation nitrate reduction were reported in PSB and DNRA was reported in purple bacteria for the first time. The three sulfur metabolism genes such as oxidation of sulfide, reversed dissimilatory sulfite reduction and sox system allowed to eliminate toxic sulfur compounds in the mangrove ecosystem. Several unique stress response genes facilitate to the tolerance of the high salinity environment. The CRISPR systems and the transposon components in genomic islands (GIs) likely contribute to the genome plasticity in purple bacteria.\n\nComparative genome analysis of marine purple sulfur bacterium Marichromatium gracile YL28 reveals the diverse nitrogen cycle mechanisms and habitat-specific traits.", "token_count": 384, "char_count": 1612, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5811, "quality_score": 0.7905, "entities": { "genes": [ "YL28" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:50.731731", "source": { "split": "train_shard_00001", "doc_id": 3195 }, "chunk_id": "train_shard_00001_3195_0", "global_id": 10193 }, { "text": "Escherichia coli is a versatile pathogen capable of causing intestinal and extraintestinal infections that result in a huge burden of global human disease. The diversity of E. coli is reflected by its multiple different pathotypes and mosaic genome composition. E. coli strains are also a major driver of antibiotic resistance, emphasizing the urgent need for new treatment and prevention measures. Here, we used a large data set comprising 1,700 draft and complete genomes to define the core and accessory genome of E. coli and demonstrated the overlapping relationship between strains from different pathotypes. In combination with proteomic investigation, this analysis revealed core genes that encode surface-exposed or secreted proteins that represent potential broad-coverage vaccine antigens. One of these antigens, YncE, was characterized as a conserved immunogenic antigen able to protect against acute systemic infection in mice after vaccination. Overall, this work provides a genomic blueprint for future analyses of conserved and accessory E. coli genes. The work also identified YncE as a novel antigen that could be exploited in the development of a vaccine against all pathogenic E. coli strains-an important direction given the high global incidence of infections caused by multidrug-resistant strains for which there are few effective antibiotics. IMPORTANCEE. coli is a multifaceted pathogen of major significance to global human health and an important contributor to increasing antibiotic resistance. Given the paucity of therapies still effective against multidrug-resistant pathogenic E. coli strains, novel treatment and prevention strategies are urgently required. In this study, we defined the core and accessory components of the E. coli genome by examining a large collection of draft and completely sequenced strains available from public databases. This data set was mined by employing a reverse-vaccinology approach in combination with proteomics to identify putative broadly protective vaccine antigens", "token_count": 509, "char_count": 2104, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5836, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:51.414701", "source": { "split": "train_shard_00001", "doc_id": 3196 }, "chunk_id": "train_shard_00001_3196_0", "global_id": 10194 }, { "text": "One such antigen was identified that was highly immunogenic and induced protection in a mouse model of bacteremia. Overall, our study provides a genomic and proteomic framework for the selection of novel vaccine antigens that could mediate broad protection against pathogenic E. coli.\n\nA Novel Protective Vaccine Antigen from the Core Escherichia coli Genome.", "token_count": 98, "char_count": 373, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:51.807218", "source": { "split": "train_shard_00001", "doc_id": 3196 }, "chunk_id": "train_shard_00001_3196_1", "global_id": 10195 }, { "text": "Salmonella enterica subsp. enterica serovar Bovismorbificans has caused multiple outbreaks involving the consumption of produce, hummus, and processed meat products worldwide. To elucidate the intra-serovar genomic structure of S. Bovismorbificans, a core-genome analysis with 2690 loci (based on 150 complete genomes representing Salmonella enterica serovars developed as part of this study) and a k-mer-binning based strategy were carried out on 95 whole genome sequencing (WGS) assemblies from Swiss, Canadian, and USA collections of S. Bovismorbificans strains from foodborne infections. Data mining of a digital DNA tiling array of legacy SARA and SARB strains was conducted to identify near-neighbors of S. Bovismorbificans. The core genome analysis and the k-mer-binning methods identified two polyphyletic clusters, each with emerging evolutionary properties. Four STs (2640, 142, 1499, and 377), which constituted the majority of the publicly available WGS datasets from >260 strains analyzed by k-mer-binning based strategy, contained a conserved core genome backbone with a different evolutionary lineage as compared to strains comprising the other cluster (ST150). In addition, the assortment of genotypic features contributing to pathogenesis and persistence, such as antimicrobial resistance, prophage, plasmid, and virulence factor genes, were assessed to understand the emerging characteristics of this serovar that are relevant clinically and for food safety concerns. The phylogenomic profiling of polyphyletic S. Bovismorbificans in this study corresponds to intra-serovar variations observed in S. Napoli and S. Newport serovars using similar high-resolution genomic profiling approaches and contributes to the understanding of the evolution and sequence divergence of foodborne Salmonellae. These intra-serovar differences may have to be thoroughly understood for the accurate classification of foodborne Salmonella strains needed for the uniform development of future food safety mitigation strategies.", "token_count": 502, "char_count": 2024, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [ "ST150" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:52.491093", "source": { "split": "train_shard_00001", "doc_id": 3197 }, "chunk_id": "train_shard_00001_3197_0", "global_id": 10196 }, { "text": "Phylogenomic Analysis of Salmonella enterica subsp. enterica Serovar Bovismorbificans from Clinical and Food Samples Using Whole Genome Wide Core Genes and kmer Binning Methods to Identify Two Distinct Polyphyletic Genome Pathotypes", "token_count": 65, "char_count": 232, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9032, "quality_score": 0.9516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:52.896623", "source": { "split": "train_shard_00001", "doc_id": 3197 }, "chunk_id": "train_shard_00001_3197_1", "global_id": 10197 }, { "text": "When groups of related bacterial genomes are compared, the number of core genes found in all genomes is usually much less than the mean genome size, whereas the size of the pangenome (the set of genes found on at least one of the genomes) is much larger than the mean size of one genome. We analyze 172 complete genomes of Bacilli and compare the properties of the pangenomes and core genomes of monophyletic subsets taken from this group. We then assess the capabilities of several evolutionary models to predict these properties. The infinitely many genes (IMG) model is based on the assumption that each new gene can arise only once. The predictions of the model depend on the shape of the evolutionary tree that underlies the divergence of the genomes. We calculate results for coalescent trees, star trees, and arbitrary phylogenetic trees of predefined fixed branch length. On a star tree, the pangenome size increases linearly with the number of genomes, as has been suggested in some previous studies, whereas on a coalescent tree, it increases logarithmically. The coalescent tree gives a better fit to the data, for all the examples we consider. In some cases, a fixed phylogenetic tree proved better than the coalescent tree at reproducing structure in the gene frequency spectrum, but little improvement was gained in predictions of the core and pangenome sizes. Most of the data are well explained by a model with three classes of gene: an essential class that is found in all genomes, a slow class whose rate of origination and deletion is slow compared with the time of divergence of the genomes, and a fast class showing rapid origination and deletion. Although the majority of genes originating in a genome are in the fast class, these genes are not retained for long periods, and the majority of genes present in a genome are in the slow or essential classes. In general, we show that the IMG model is useful for comparison with experimental genome data both for species level and widely divergent taxonomic groups. Software implementing the described formulae is provided at http://github.com/rec3141/pangenome.\n\nTesting the infinitely many genes model for the evolution of the bacterial core genome and pangenome.", "token_count": 498, "char_count": 2233, "word_count": 368, "semantic_coherence": 1, "information_density": 0.4946, "quality_score": 0.7473, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:53.555364", "source": { "split": "train_shard_00001", "doc_id": 3198 }, "chunk_id": "train_shard_00001_3198_0", "global_id": 10198 }, { "text": "A versatile plasmid shuttle vector system pKDU7 was constructed, which is useful for the heterologous gene expression in a wide range of Kluyveromyces and Saccharomyces strains. This cloning vector was constructed using the 1.6-µm circular plasmid pKD1 of Kluyveromyces drosophilarum, the URA3 gene of K. marxianus as well as the pUC19 sequences. The stability of vector in transformants strongly depends on the integrity of the functionally important elements of pKD1. It was shown by comparison of three recombinant vectors, which possessed the pKD1 sequence inserted in different ways. The efficient transformation and stability maintenance of the vector constructed in various strains of Kluyveromyces and Saccharomyces was shown by the expression of the EPG1 gene of the Kluyveromyces marxianus encoding pectin-degrading endopolygalacturonase.\n\nHeterologous expression of the Kluyveromyces marxianus endopolygalacturonase gene (EPG1) using versatile autonomously replicating vector for a wide range of host.", "token_count": 264, "char_count": 1012, "word_count": 141, "semantic_coherence": 1, "information_density": 0.539, "quality_score": 0.7695, "entities": { "genes": [ "URA3", "EPG1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:54.110654", "source": { "split": "train_shard_00001", "doc_id": 3199 }, "chunk_id": "train_shard_00001_3199_0", "global_id": 10199 }, { "text": "

Background

Pectobacterium parmentieri is a newly established species within the plant pathogenic family Pectobacteriaceae. Bacteria belonging to this species are causative agents of diseases in economically important crops (e.g. potato) in a wide range of different environmental conditions, encountered in Europe, North America, Africa, and New Zealand. Severe disease symptoms result from the activity of P. parmentieri virulence factors, such as plant cell wall degrading enzymes. Interestingly, we observe significant phenotypic differences among P. parmentieri isolates regarding virulence factors production and the abilities to macerate plants. To establish the possible genomic basis of these differences, we sequenced 12 genomes of P. parmentieri strains (10 isolated in Poland, 2 in Belgium) with the combined use of Illumina and PacBio approaches. De novo genome assembly was performed with the use of SPAdes software, while annotation was conducted by NCBI Prokaryotic Genome Annotation Pipeline.

Results

The pan-genome study was performed on 15 genomes (12 de novo assembled and three reference strains: P. parmentieri CFBP 8475T, P. parmentieri SCC3193, P. parmentieri WPP163). The pan-genome includes 3706 core genes, a high number of accessory (1468) genes, and numerous unique (1847) genes. We identified the presence of well-known genes encoding virulence factors in the core genome fraction, but some of them were located in the dispensable genome. A significant fraction of horizontally transferred genes, virulence-related gene duplications, as well as different CRISPR arrays were found, which can explain the observed phenotypic differences. Finally, we found also, for the first time, the presence of a plasmid in one of the tested P. parmentieri strains isolated in Poland.

Conclusions

We can hypothesize that a large number of the genes in the dispensable genome and significant genomic variation among P. parmentieri strains could be the basis of the potential wide host range and widespread diffusion of P. parmentieri", "token_count": 525, "char_count": 2079, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6088, "quality_score": 0.8044, "entities": { "genes": [ "WPP163", "SCC3193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:55.654166", "source": { "split": "train_shard_00001", "doc_id": 3200 }, "chunk_id": "train_shard_00001_3200_0", "global_id": 10200 }, { "text": "The obtained data on the structure and gene content of P. parmentieri strains enabled us to speculate on the importance of high genomic plasticity for P. parmentieri adaptation to different environments.\n\nHigh genomic variability in the plant pathogenic bacterium Pectobacterium parmentieri deciphered from de novo assembled complete genomes.", "token_count": 77, "char_count": 342, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7708, "quality_score": 0.8854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:56.020949", "source": { "split": "train_shard_00001", "doc_id": 3200 }, "chunk_id": "train_shard_00001_3200_1", "global_id": 10201 }, { "text": "

Background

Ligilactobacillus salivarius has been frequently isolated from the gut microbiota of humans and domesticated animals and has been studied as a candidate probiotic. Badger (Meles meles) is known as a \"generalist\" species that consumes complex foods and exhibits tolerance and resistance to certain pathogens, which can be partly attributed to the beneficial microbes such as L. salivarius in the gut microbiota. However, our understanding of the beneficial traits and genomic features of badger-originated L. salivarius remains elusive.

Results

In this study, nine L. salivarius strains were isolated from wild badgers' feces, one of which exhibited good probiotic properties. Complete genomes of the nine L. salivarius strains were generated, and comparative genomic analysis was performed with the publicly available complete genomes of L. salivarius obtained from humans and domesticated animals. The strains originating from badgers harbored a larger genome, a higher number of protein-coding sequences, and functionally annotated genes than those originating from humans and chickens. The pan-genome phylogenetic tree demonstrated that the strains originating from badgers formed a separate clade, and totally 412 gene families (12.6% of the total gene families in the pan-genome) were identified as genes gained by the last common ancestor of the badger group. The badger group harbored significantly more gene families responsible for the degradation of complex carbohydrate substrates and production of polysaccharides than strains from other hosts; many of these were acquired by gene gain events.

Conclusions

A candidate probiotic and nine L. salivarius complete genomes were obtained from the badgers' gut microbiome, and several beneficial genes were identified to be specifically present in the badger-originated strains that were gained in the evolution. Our study provides novel insights into the adaptation of L. salivarius to the intestinal habitat of wild badgers and provides valuable strain and genome resources for the development of L. salivarius as a probiotic.", "token_count": 494, "char_count": 2116, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5117, "quality_score": 0.7559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:57.045097", "source": { "split": "train_shard_00001", "doc_id": 3201 }, "chunk_id": "train_shard_00001_3201_0", "global_id": 10202 }, { "text": "Assessment of beneficial effects and identification of host adaptation-associated genes of Ligilactobacillus salivarius isolated from badgers.", "token_count": 31, "char_count": 142, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:57.405557", "source": { "split": "train_shard_00001", "doc_id": 3201 }, "chunk_id": "train_shard_00001_3201_1", "global_id": 10203 }, { "text": "Lambdoid (or Lambda-like) phages, are a group of related temperate phages that can infect Escherichia coli and other gut bacteria. A key characteristic of these phages is their mosaic genome structure which served as basis for the “modular genome hypothesis”. Accordingly, lambdoid phages evolve by transferring genomic regions, each of which constitutes a functional unit. Nevertheless, it is unknown which genes are preferentially transferred together and what drives such co-transfer events. Here we aim to characterize genome modularity by studying co-transfer of genes among 95 distantly related lambdoid (pro-)phages. Based on gene content, we observed that the genomes cluster into twelve groups, which are characterized by a highly similar gene content within the groups and highly divergent gene content across groups. Highly similar proteins can occur in genomes of different groups, indicating that they have been transferred. About 26% of homologous protein clusters in the four known operons (i.e., the early left, early right, immunity, and late operon) engage in gene transfer, which affects all operons to a similar extent. We identified pairs of genes that are frequently co-transferred and observed that these pairs tend to be in close proximity to one another on the genome. We find that frequently co-transferred genes are involved in related functions and highlight interesting examples involving structural proteins, the CI repressor and Cro regulator, proteins interacting with DNA, and membrane-interacting proteins. We conclude that epistatic effects, where the functioning of one protein depends on the presence of another, plays an important role in the evolution of the modular structure of these genomes.

Data summary

The genomes used in this research are publicly available (Table S1). All supporting data is available in supplementary tables. Source code and documentation to calculate GRR is available under GPLv2 ( https://github.com/annecmg/GRRpair ).

Impact statement

Temperate phages, viruses that can integrate their own genetic material into bacterial genomes, are pervasive mobile genetic elements that can influence bacterial fitness in manifold ways. The E. coli phage lambda has been a model phage of molecular biology for decades", "token_count": 513, "char_count": 2290, "word_count": 336, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:34:58.041788", "source": { "split": "train_shard_00001", "doc_id": 3202 }, "chunk_id": "train_shard_00001_3202_0", "global_id": 10204 }, { "text": "Lambdoid phages are highly prevalent in Enterobacteria such as E. coli and Salmonella , have a mosaic-like genome, the same genome architecture as lambda, and can recombine with phage lambda. Nevertheless, these phages can be very distinct, and no lambdoid core genome exits. Although lambdoid phage genomes have been studied for decades, we know relatively little about how they evolve. Early observations led to the modular genome hypothesis, according to which, phages are assemblages of genetic modules. But what determines the structure of these modules and which genes do preferentially occur together in modules. In this study, we provide answers to these questions using a novel computational approach that allows to infer gene transfer events between distantly related phages despite the absence of a core genome. We find that co-transfer of functionally related genes is frequent during the evolution of lambdoid phages. This suggests epistatic interactions among these genes, i.e., the co-transferred genes likely need to function together to ensure a viable phage. A prime example is the co-transfer of structural genes, such as genes encoding for the phage capsid or the phage tail. Additionally, we also find co-transfer of known interacting regulatory genes and co-transfer between functionally related genes that have so far been unknown to interact. Together, our analysis provides novel insights into the evolution of temperate phages. Moreover, our approach, which allows to identify gene transfer in the absence of a core phylogeny might be valuable for studying the evolution of other fast-evolving genomes, including viruses of other hosts.\n\nCo-transfer of functionally interdependent genes contributes to genome mosaicism in lambdoid phages", "token_count": 384, "char_count": 1763, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:58.664272", "source": { "split": "train_shard_00001", "doc_id": 3202 }, "chunk_id": "train_shard_00001_3202_1", "global_id": 10205 }, { "text": "Angiotensin-I-Converting Enzyme (ACE) inhibitors peptides were produced from unsupplemented acid goat whey fermented aerobically for 168 h by Kluyveromyces marxianus and Lactobacillus rhamnosus. This yeast-lactobacillus association is GRAS. Two novel lactokinins were identified: NYW and W with IC50 of 20 and 0.86 mum respectively. They both were resistant toward simulated gastrointestinal digestion. In addition, WLAHK was found in the hydrolysate. These three sequences belong to f(99-110) of alpha-la which seems to be a lactokinin cryptic zone. W was the major molecule released by the fermentation process. Considering that W is the precursor of serotonin, the hydrolysate produced could be of interest for the generation of functional health ingredient involved in regulation of affective disorders and hypertension.\n\nGoat whey fermentation by Kluyveromyces marxianus and Lactobacillus rhamnosus release tryptophan and tryptophan-lactokinin from a cryptic zone of alpha-lactalbumin.", "token_count": 293, "char_count": 990, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7111, "quality_score": 0.8556, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:59.238524", "source": { "split": "train_shard_00001", "doc_id": 3203 }, "chunk_id": "train_shard_00001_3203_0", "global_id": 10206 }, { "text": "Plants live in association with microorganisms that positively influence plant development, vigor, and fitness in response to pathogens and abiotic stressors. The bulk of the plant microbiome is concentrated belowground at the plant root-soil interface. Plant roots secrete carbon-rich rhizodeposits containing primary and secondary low molecular-weight metabolites, lysates, and mucilages. These exudates provide nutrients for soil microorganisms and modulate their affinity to host plants, but molecular details of this process are largely unresolved. We addressed this gap by focusing on the molecular dialogue between eight well-characterized beneficial strains of the Pseudomonas fluorescens group and Brachypodium distachyon , a model for economically important food, feed, forage, and biomass crops of the grass family. We collected and analyzed root exudates of B. distachyon and demonstrated the presence of multiple carbohydrates, amino acids, organic acids and phenolic compounds. The subsequent screening of bacteria by Biolog Phenotype MicroArrays revealed that many of these metabolites provide carbon and energy for the Pseudomonas strains. RNA-seq profiling of bacterial cultures amended with root exudates revealed changes in the expression of genes encoding numerous catabolic and anabolic enzymes, transporters, transcriptional regulators, stress response, and conserved hypothetical proteins. Almost half of the differentially expressed genes mapped to the variable part of the strains’ pangenome, reflecting the importance of the variable gene content in the adaptation of P. fluorescens to the rhizosphere lifestyle. Our results collectively reveal the diversity of cellular pathways and physiological responses underlying the establishment of mutualistic interactions between these beneficial rhizobacteria and their plant hosts.\n\nThe effect of root exudates on the transcriptome of rhizospherePseudomonasspp", "token_count": 441, "char_count": 1938, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:34:59.870751", "source": { "split": "train_shard_00001", "doc_id": 3204 }, "chunk_id": "train_shard_00001_3204_0", "global_id": 10207 }, { "text": "

Motivation

Bacterial genomes are composed by a core and an accessory genome. The first composed of housekeeping and essential genes, while the second is composed, in its majority, of mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLIS) on assembled genomes.

Results

We developed ISCompare to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyse multiple ISs at the same time and outputs a list of candidate DLIS. We think that ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.

Availability and implementation

ISCompare was implemented in python3 and its source code is freely available for download at https://github.com/maurijlozano/ISCompare .

Supplementary information

Supplementary data are available at https://github.com/maurijlozano/ISCompare .\n\nEasy identification of insertion sequence mobilization events in related bacterial strains with ISCompare", "token_count": 362, "char_count": 1591, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6226, "quality_score": 0.8113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:00.454309", "source": { "split": "train_shard_00001", "doc_id": 3205 }, "chunk_id": "train_shard_00001_3205_0", "global_id": 10208 }, { "text": "We conducted a prospective, multicenter, specific pilot study on uncomplicated urinary tract infections (uUTI). One-hundred non-duplicated uropathogenic Escherichia coli (UPEC) from uUTI occurred in 2020 in women attending 15 primary care centers of a single health region of northern Spain were characterized using a clonal diagnosis approach. Among the high genetic diversity showed by 59 different phylogroup-clonotype combinations, 11 clones accounted for 46% of the isolates: B2-ST73 (CH24-30); B2-ST73 (CH24-103); B2-ST131 (CH40-30); B2-ST141 (CH52-5); B2-ST372 (CH103-9); B2-ST404 (CH14-27); B2-ST404 (CH14-807); B2-ST1193 (CH14-64); D-ST69 (CH35-27); D-ST349 (CH36-54), and F-ST59 (CH32-41). The screening of the UPEC status found that 69% of isolates carried ≥ 3 of chuA, fyuA, vat, and yfcV genes. Multidrug resistance to at least one antibiotic of ≥ 3 antimicrobial categories were exhibited by 30% of the isolates, with the highest rates of resistance against ampicillin/amoxicillin (48%), trimethoprim (35%), norfloxacin (28%), amoxicillin-clavulanic acid (26%), and trimethoprim-sulfamethoxazole (24%). None extended-spectrum beta-lactamase/carbapenemase producer was recovered. According to our results, fosfomycin and nitrofurantoin should be considered as empirical treatment of choice for uUTI by E", "token_count": 512, "char_count": 1330, "word_count": 173, "semantic_coherence": 1, "information_density": 0.8208, "quality_score": 0.9104, "entities": { "genes": [ "ST141", "ST131", "CH14", "CH35", "CH36", "CH52", "ST73", "ST372", "ST349", "ST59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:01.109345", "source": { "split": "train_shard_00001", "doc_id": 3206 }, "chunk_id": "train_shard_00001_3206_0", "global_id": 10209 }, { "text": "coli (resistance rates 4% and 2%, respectively). We uncover the high prevalence of the pandemic fluoroquinolone-resistant ST1193 clone (6%) in uUTI, which represents the first report in Spain in this pathology. The genomic analysis showed similar key traits than those ST1193 clones disseminated worldwide. Through the SNP comparison based on the core genome, the Spanish ST1193 clustered with isolates retrieved from the Enterobase, showing high genomic similarity than the global ST1193 described in the United States, Canada and Australia. IMPORTANCE Analyzing the clonal structure and antimicrobial resistance of E. coli isolates implicated in uncomplicated urinary tract infections, one of the most frequent visits managed in primary health care, is of interest for clinicians to detect changes in the dynamics of emerging uropathogenic clones associated with the spread of fluoroquinolone resistance. It can also provide consensus concerning optimal control and antibiotic prescribing.\n\nOccurrence and Genomic Characterization of Clone ST1193 Clonotype 14-64 in Uncomplicated Urinary Tract Infections Caused by Escherichia coli in Spain.", "token_count": 291, "char_count": 1150, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.8509, "entities": { "genes": [ "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:01.671455", "source": { "split": "train_shard_00001", "doc_id": 3206 }, "chunk_id": "train_shard_00001_3206_1", "global_id": 10210 }, { "text": "Pulsed electric field (PEF) of 1Hz, 1.5 kV, and 1 ms increased the activities of catalase and inulinase over the whole range of applied Se concentrations compared with the non-treated cultures. A significant effect of selenium concentration (in the range of 5-14 microg/ml) on both intra- and extracellular enzyme activities was noted. At a Se concentration of 10 microg/ml, the activities of intra- and extracellular inulinases and extracellular catalase in the PEF-treated cultures reached the maximum of 71 U/g d.m., 46 U/g d.m., and approx. 8 U/ml, respectively. The maximum activity of intracellular catalase of approx. 6 U/ ml (with and without PEF) was recorded at 5 microg Se/ml. Further increasing of selenium concentration caused a decrease in the activity of the enzymes.\n\nAccumulation of selenium and changes in the activity of inulinase and catalase in the cells of Kluyveromyces marxianus on pulsed electric field treatment.", "token_count": 266, "char_count": 938, "word_count": 146, "semantic_coherence": 1, "information_density": 0.5548, "quality_score": 0.7774, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:02.221572", "source": { "split": "train_shard_00001", "doc_id": 3207 }, "chunk_id": "train_shard_00001_3207_0", "global_id": 10211 }, { "text": "

Objective

To identify Candida species in asymptomatic subjects in Bobo-Dioulasso (Burkina Faso) by the matrix-assisted laser desorption ionization-time of flight mass spectrometry.

Methods

A cross-sectional study was conducted from January to February 2013 in Bobo-Dioulasso to collect fecal and urine specimens from voluntary donors. Fungal strains were isolated on Sabouraud dextrose agar and analyzed using matrix-assisted laser desorption ionisation-time-of-flight mass spectrometry.

Results

A total of 135 samples including stools (78.5%, 106/135) and urine (21.5%, 29/135) were analyzed. The results revealed that fecal specimens contained mainly Candida krusei (C. krusei) (42.5%) followed by Candida albicans (29.3%), Candida glabrata (18.0%) and Candida tropicalis (C. tropicalis) (4.7%). C. krusei (34.6%) was also found to be the most frequently identified in urine samples followed by Candida albicans (27.0%), C. tropicalis (15.4%) and Candida parapsilosis. However, uncommon species such as Candida nivariensis, Candida kefyr, Candida norvegensis, Candida parapsilosis, Candida lusitaniae and Candida robusta were also identified from fecal and urines samples.

Conclusions

This study noted the emergence of species such as C. krusei, Candida glabrata, Candida parapsiolosis, C. tropicalis, Candida nivariensis, Candida norvegensis, and others. It is an imperative to take into account the existence of these species in the therapeutic management of patients in Bobo-Dioulasso.\n\nDigestive fungal flora in asymptomatic subjects in Bobo-Dioulasso, Burkina Faso.", "token_count": 511, "char_count": 1601, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:02.877619", "source": { "split": "train_shard_00001", "doc_id": 3208 }, "chunk_id": "train_shard_00001_3208_0", "global_id": 10212 }, { "text": "

Introduction

Macrococcus species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, Macrococcus spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the Macrococcus genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.

Methods

All high-quality, publicly available Macrococcus genomes (n = 104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).

Results

Overall, the 110 Macrococcus genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for Macrococcus species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across Macrococcus included macrolides, beta-lactams, and aminoglycosides (n = 81, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively)", "token_count": 467, "char_count": 1596, "word_count": 194, "semantic_coherence": 1, "information_density": 0.7113, "quality_score": 0.8557, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:03.543187", "source": { "split": "train_shard_00001", "doc_id": 3209 }, "chunk_id": "train_shard_00001_3209_0", "global_id": 10213 }, { "text": "Genes showing homology to Staphylococcus aureus exoenzyme aureolysin were detected across multiple species (using 90% coverage, n = 40 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). S. aureus Panton-Valentine leucocidin toxin-associated lukF-PV and lukS-PV homologs were identified in eight M. canis genomes (≥40% AA identity, >85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species (M. caseolyticus and M. armenti) were composed of multiple within-species populations. Notably, M. armenti was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT p < 0.05).

Discussion

Overall, this study leverages all publicly available Macrococcus genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.\n\nGenus-wide genomic characterization of Macrococcus: insights into evolution, population structure, and functional potential.", "token_count": 431, "char_count": 1328, "word_count": 165, "semantic_coherence": 1, "information_density": 0.8121, "quality_score": 0.9061, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:04.185272", "source": { "split": "train_shard_00001", "doc_id": 3209 }, "chunk_id": "train_shard_00001_3209_1", "global_id": 10214 }, { "text": "Response: Commentary: Probing Genomic Aspects of the Multi-Host Pathogen <i>Clostridium perfringens</i> Reveals Significant Pangenome Diversity, and a Diverse Array of Virulence Factors.", "token_count": 66, "char_count": 198, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:04.615028", "source": { "split": "train_shard_00001", "doc_id": 3210 }, "chunk_id": "train_shard_00001_3210_0", "global_id": 10215 }, { "text": "Abstract

Background: Streptococcus pneumoniae serotype 1 remains a leading cause of invasive pneumococcal diseases, even in countries with PCV-10/PCV-13 vaccine implementation. The main objective of this study, which is part of the Pneumococcal African Genome project (PAGe), was to determine the phylogenetic relationships of serotype 1 isolates recovered from children patients in Casablanca (Morocco), compared to these from other African countries; and to investigate the contribution of accessory genes and recombination events to the genetic diversity of this serotype.Results: The genome average size of the six-pneumococcus serotype 1 from Casablanca was 2,227,119 bp, and the average content of coding sequences was 2113, ranging from 2041 to 2161. Pangenome analysis of the 80 genomes used in this study revealed 1685 core genes and 1805 accessory genes. The phylogenetic tree based on core genes and the hierarchical bayesian clustering analysis revealed five sublineages with a phylogeographic structure by country. The Moroccan strains cluster in two different lineages, the five invasive strains clusters altogether in a divergent clade distantly related to the non-invasive strain, that cluster with all the serotype 1 genomes from Africa.Conclusions: The whole genome sequencing provides increased resolution analysis of the highly virulent serotype 1 in Casablanca, Morocco. Our results are concordant with previous works, showing that the phylogeography of S. pneumoniae serotype 1 is structured by country, and despite the small size (six isolates) of the Moroccan sample, our analysis shows the genetic cohesion of the Moroccan invasive isolates.

", "token_count": 470, "char_count": 1762, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:05.263860", "source": { "split": "train_shard_00001", "doc_id": 3211 }, "chunk_id": "train_shard_00001_3211_0", "global_id": 10216 }, { "text": "Whole genomic comparative analysis of Streptococcus pneumoniae serotype 1 isolates causing invasive and non-invasive infections among children under 5 years in Casablanca, Morocco", "token_count": 48, "char_count": 179, "word_count": 23, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:05.622437", "source": { "split": "train_shard_00001", "doc_id": 3211 }, "chunk_id": "train_shard_00001_3211_1", "global_id": 10217 }, { "text": "The ectomycorrhizal symbiosis is an essential guild of many forested ecosystems and has a dynamic evolutionary history across kingdom Fungi, having independently evolved from diverse types of saprotrophic ancestors. In this study, we seek to identify genomic features of the transition to the ectomycorrhizal habit within the Russulaceae, one of the most diverse lineages of ectomycorrhizal fungi. We present comparative analyses of the pangenome and gene repertoires of 21 species across the order Russulales, including a closely related saprotrophic member of Russulaceae. The ectomycorrhizal Russulaceae is inferred to have originated around the Cretaceous-Paleogene extinction event (73.6-60.1 million years ago (MY)). The genomes of the ectomycorrhizal Russulaceae are characterized by a loss of genes for plant cell-wall degrading enzymes (PCWDEs), an expansion of genome size through increased transposable element (TE) content, a reduction in secondary metabolism clusters, and an association of genes coding for certain secreted proteins with TE “nests”. The saprotrophic sister group of the ectomycorrhizal Russulaceae, Gloeopeniophorella convolvens , possesses some of these aspects (e.g., loss of some PCWDE and protease orthologs, TE expansion, reduction in secondary metabolism clusters), resulting from an accelerated rate of gene evolution in the shared ancestor of Russulaceae that predates the evolution of the ectomycorrhizal habit. Genomes of Russulaceae possess a high degree of synteny, including a conserved set of terpene secondary metabolite gene clusters. We hypothesize that the evolution of the ectomycorrhizal habit requires premodification of the genome for plant root association followed by an accelerated rate of gene evolution within the secretome for host-defense circumvention and symbiosis establishment.\n\nEvolutionary priming and transition to the ectomycorrhizal habit in an iconic lineage of mushroom-forming fungi: is preadaptation a requirement?", "token_count": 500, "char_count": 1987, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5636, "quality_score": 0.7818, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:06.275305", "source": { "split": "train_shard_00001", "doc_id": 3212 }, "chunk_id": "train_shard_00001_3212_0", "global_id": 10218 }, { "text": "Listeria monocytogenes is an important pathogen, often associated with fish, that can adapt and survive in products and food processing plants, where it can persist for many years. It is a species characterized by diverse genotypic and phenotypic characteristics. Therefore, in this study, a total of 17 L. monocytogenes strains from fish and fish-processing environments in Poland were characterized for their relatedness, virulence profiles, and resistance genes. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IIa and IIb; sequence types (ST) were ST6 and ST121; and clonal complexes (CC) were CC6 and CC121. Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with the publicly available genomes of L. monocytogenes strains recovered in Europe from humans with listeriosis. Despite differential genotypic subtypes, most strains had similar antimicrobial resistance profiles; however, some of genes were located on mobile genetic elements that could be transferred to commensal or pathogenic bacteria. The results of this study showed that molecular clones of tested strains were characteristic for L. monocytogenes isolated from similar sources. Nevertheless, it is worth emphasizing that they could present a major public health risk due to their close relation with strains isolated from human listeriosis.\n\nA Comprehensive Virulence and Resistance Characteristics of Listeria monocytogenes Isolated from Fish and the Fish Industry Environment.", "token_count": 389, "char_count": 1596, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6143, "quality_score": 0.8072, "entities": { "genes": [ "CC121", "ST6", "ST121", "CC6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:06.896940", "source": { "split": "train_shard_00001", "doc_id": 3213 }, "chunk_id": "train_shard_00001_3213_0", "global_id": 10219 }, { "text": "Fungi are being increasingly implicated in etio pathology of rhino sinusitis. Invasive fungal sinusitis occurring in diabetics and immunocompromised patients is notorious for its insidious onset, rapid intra cranial spread and tissue destruction. Candida as a cause of this invasive infection is infrequently reported in India. We report a rare species of Candida, Candida kefyr in a female diabetic patient presenting with invasive fungal sinusitis.\n\nCandida kefyr in Invasive Paranasal Sinusitis.", "token_count": 128, "char_count": 498, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7324, "quality_score": 0.8662, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:07.323671", "source": { "split": "train_shard_00001", "doc_id": 3214 }, "chunk_id": "train_shard_00001_3214_0", "global_id": 10220 }, { "text": "A selective and differential solid medium, called Kluyveromyces Differential Medium (KDM), is described for the isolation of Kluyveromyces marxianus and K. lactis from dairy products. Its discriminative potential is based on the detection of the enzyme beta-galactosidase, in the absence of lactose. Of the more than 95 strains tested, including yeasts, bacteria, and filamentous fungus, only the strains of K. marxianus and K. lactis produced blue colonies on the medium due to the presence of X-Gal/ IPTG. The bacterial strains were not able to grow in KDM. On this basis, the medium was very satisfactory when testing naturally or experimentally contaminated dairy food products. When quality assessment tests were performed, optimal values of productivity (growth and color) and selectivity were obtained for K. marxianus and K. lactis.\n\nA differential medium for the isolation of Kluyveromyces marxianus and Kluyveromyces lactis from dairy products.", "token_count": 249, "char_count": 954, "word_count": 142, "semantic_coherence": 1, "information_density": 0.5775, "quality_score": 0.7887, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:07.813141", "source": { "split": "train_shard_00001", "doc_id": 3215 }, "chunk_id": "train_shard_00001_3215_0", "global_id": 10221 }, { "text": "START proteins, encoded by a plant amplified family of evolutionary conserved genes, are known to bind lipids/sterols in mammals. In the plant kingdom, they have been reported in proteins involved in lipid binding, transport, signaling, as well as modulation of transcriptional activity, but there is very limited information on sub-functionalization or evolution of new function within the amplified gene family. Availability of ten fully annotated wild and cultivated rice varieties enables a comprehensive analysis of this family across the rice pangenome, across functional categories, as well as across START sub-families. The presence of START domains in all seven wild and three cultivated rice genomes suggests low dispensability and critical functional roles for this family, further supported by chromosomal mapping, duplication analysis and conservation of domain structure. Analysis of synteny highlights a preponderance of segmental and dispersed modes of duplication among STARTs, while transcriptomic investigation of the main cultivated variety Oryza sativa var. japonica reveals sub-functionalization among START genes family members in terms of preferential expression across various developmental stages and anatomical parts, especially flowering related parts. Importance of this family was further supported by Ka/Ks ratios confirming strong negative/purifying selection, implying that START family duplication is strongly constrained and evolutionarily stable.\n\nComparative genomics of StAR-related lipid transfer (START) domains across wild and cultivated rice", "token_count": 328, "char_count": 1583, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6589, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:08.377640", "source": { "split": "train_shard_00001", "doc_id": 3216 }, "chunk_id": "train_shard_00001_3216_0", "global_id": 10222 }, { "text": "A cross-sectional study was performed in 325 sheep and 119 goat dairy farms in Greece. Samples of bulk-tank milk were examined by standard microbiological techniques for Listeria spp. Listeria monocytogenes was isolated from one (0.3%) and Listeria ivanovii from three (0.9%) sheep farms. No associations between the isolation of L. monocytogenes or L. ivanovii and milk quality were found. No resistance to antibiotics was identified. Three variables emerged as significant predictors of isolation of the organism: the presence of pigs, low average relative humidity and a high number of ewes on the farm. The three L. ivanovii isolates were assessed in silico for identification of plasmids, prophages, antibiotic resistance genes, virulence factors, CRISPRs and CAS genes. Phylogenetic analysis using the core genome revealed that the three strains belonged to the L. ivanovii subsp. ivanovii branch and were especially close to the PAM 55 strain. All strains of the branch appeared to be very similar, with the distance between them being small.\n\nIsolation of Listeria ivanovii from Bulk-Tank Milk of Sheep and Goat Farms-From Clinical Work to Bioinformatics Studies: Prevalence, Association with Milk Quality, Antibiotic Susceptibility, Predictors, Whole Genome Sequence and Phylogenetic Relationships.", "token_count": 402, "char_count": 1370, "word_count": 192, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:08.995828", "source": { "split": "train_shard_00001", "doc_id": 3217 }, "chunk_id": "train_shard_00001_3217_0", "global_id": 10223 }, { "text": "

Motivation

Routine infectious disease surveillance is increasingly based on large-scale whole-genome sequencing databases. Real-time surveillance would benefit from immediate assignments of each genome assembly to hierarchical population structures. Here we present pHierCC, a pipeline that defines a scalable clustering scheme, HierCC, based on core genome multi-locus typing that allows incremental, static, multi-level cluster assignments of genomes. We also present HCCeval, which identifies optimal thresholds for assigning genomes to cohesive HierCC clusters. HierCC was implemented in EnteroBase in 2018 and has since genotyped >530 000 genomes from Salmonella, Escherichia/Shigella, Streptococcus, Clostridioides, Vibrio and Yersinia.

Availability and implementation

https://enterobase.warwick.ac.uk/ and Source code and instructions: https://github.com/zheminzhou/pHierCC.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nHierCC: a multi-level clustering scheme for population assignments based on core genome MLST.", "token_count": 294, "char_count": 1083, "word_count": 120, "semantic_coherence": 1, "information_density": 0.7583, "quality_score": 0.8792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:09.557112", "source": { "split": "train_shard_00001", "doc_id": 3218 }, "chunk_id": "train_shard_00001_3218_0", "global_id": 10224 }, { "text": "During the past decades considerably large efforts have been made to optimize the production of lignocellulose derived fuel ethanol production in order to develop a process configuration which is economically feasible and competitive with gasoline. One of the process alternatives uses cellulase enzymes for the conversion of cellulose content of lignocellulosic biomass to fermentable glucose. Due to the relatively similar process conditions in the enzymatic hydrolysis and ethanol fermentation, the option of carrying out these two-steps together in one vessel exists. The application of simultaneous saccharification and fermentation (SSF) for the conversion of lignocellulosics to alcohol would result in a more cost-effective process. In the present study various lignocellulosic substrates, i.e. Solka Floc, OCC waste cardboard, and paper sludge, were examined in SSF experiments for the production of ethanol. Two yeast strains were compared, a commercially available baker's yeast and a thermotolerant Kluyveromyces marxianus, in two types of SSF experiments, i.e. isothermal SSF and SSF with temperature profiling. The results showed that OCC waste and paper sludge could be used as substrates for ethanol production in SSF. There was no significant difference observed between Saccharomyces cerevisiae and K. marxianus when the results of SSF were compared. The ethanol yields were in the range of 0.31-0.34 g/g for both strains used. SSF resulted in higher ethanol yields compared to non-isothermal SSF (NSSF; SSF with temperature profiling).\n\nSimultaneous saccharification and fermentation (SSF) of industrial wastes for the production of ethanol", "token_count": 412, "char_count": 1659, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:10.176944", "source": { "split": "train_shard_00001", "doc_id": 3219 }, "chunk_id": "train_shard_00001_3219_0", "global_id": 10225 }, { "text": "Between 2000 and 2017, a total of 236 Legionella species isolates from Arizona were submitted to the CDC for reference testing. Most of these isolates were recovered from bronchoalveolar lavage specimens. Although the incidence of legionellosis in Arizona is less than the overall U.S. incidence, Arizona submits the largest number of isolates to the CDC for testing compared to those from other states. In addition to a higher proportion of culture confirmation of legionellosis cases in Arizona than in other states, all Legionellapneumophila isolates are forwarded to the CDC for confirmatory testing. Compared to that from other states, a higher proportion of isolates from Arizona were identified as belonging to L. pneumophila serogroups 6 (28.2%) and 8 (8.9%). Genome sequencing was conducted on 113 L. pneumophila clinical isolates not known to be associated with outbreaks in order to understand the genomic diversity of strains causing legionellosis in Arizona. Whole-genome multilocus sequence typing (wgMLST) revealed 17 clusters of isolates sharing at least 99% identical allele content. Only two of these clusters contained isolates from more than one individual with exposure at the same facility. Additionally, wgMLST analysis revealed a group of 31 isolates predominantly belonging to serogroup 6 and containing isolates from three separate clusters. Single nucleotide polymorphism (SNP) and pangenome analysis were used to further resolve genome sequences belonging to a subset of isolates. This study demonstrates that culture of clinical specimens for Legionella spp", "token_count": 415, "char_count": 1628, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:10.804596", "source": { "split": "train_shard_00001", "doc_id": 3220 }, "chunk_id": "train_shard_00001_3220_0", "global_id": 10226 }, { "text": "reveals a highly diverse population of strains causing legionellosis in Arizona which could be underappreciated using other diagnostic approaches.IMPORTANCE Culture of clinical specimens from patients with Legionnaires' disease is rarely performed, restricting our understanding of the diversity and ecology of Legionella Culture of Legionella from patient specimens in Arizona revealed a greater proportion of non-serogroup 1 Legionellapneumophila isolates than in other U.S. isolates examined. Disease caused by such isolates may go undetected using other diagnostic methods. Moreover, genome sequence analysis revealed that these isolates were genetically diverse, and understanding these populations may help in future environmental source attribution studies.\n\nCulture of Clinical Specimens Reveals Extensive Diversity of Legionella pneumophila Strains in Arizona.", "token_count": 213, "char_count": 904, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:11.266911", "source": { "split": "train_shard_00001", "doc_id": 3220 }, "chunk_id": "train_shard_00001_3220_1", "global_id": 10227 }, { "text": "Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella, as previous studies have focused on the recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. The aim of this study was to better characterize preterm-associated Klebsiella populations using phenotypic and genotypic approaches. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for Klebsiella spp., and virulence and antimicrobial resistance genes identified. Antibiotic susceptibility profiling and in vitro macrophage and iron assays were undertaken for the Klebsiella strains. Metapangenome analyses with a manually curated genome dataset were undertaken to examine the diversity of Klebsiella oxytoca and related bacteria in a publicly available shotgun metagenome dataset. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. 'healthy') encoded multiple β-lactamases", "token_count": 513, "char_count": 1598, "word_count": 192, "semantic_coherence": 1, "information_density": 0.724, "quality_score": 0.862, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:11.931436", "source": { "split": "train_shard_00001", "doc_id": 3221 }, "chunk_id": "train_shard_00001_3221_0", "global_id": 10228 }, { "text": "No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut. There is little difference in the phenotypic and genomic characteristics of Klebsiella isolates recovered from healthy and sick infants. Identification of β-lactamases in all isolates may prove problematic when defining treatment regimens for NEC or sepsis, and suggests that healthy preterm infants contribute to the resistome. Refined analyses with curated sequence databases are required when studying closely related species present in metagenomic data.\n\nPreterm infants harbour diverse <i>Klebsiella</i> populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors.", "token_count": 321, "char_count": 1208, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6948, "quality_score": 0.8474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:12.497205", "source": { "split": "train_shard_00001", "doc_id": 3221 }, "chunk_id": "train_shard_00001_3221_1", "global_id": 10229 }, { "text": "Horizontal gene transfer accelerates microbial evolution, promoting diversification and adaptation. The globally abundant marine cyanobacterium Prochlorococcus has a highly streamlined genome with frequent gene exchange reflected in its extensive pangenome. The source of its genomic variability, however, remains elusive since most cells lack the common mechanisms that enable horizontal gene transfer, including conjugation, transformation, plasmids and prophages. Examining 623 genomes, we reveal a diverse system of mobile genetic elements – cargo-carrying transposons we named tycheposons – that shape Prochlorococcus ’ genomic plasticity. The excision and integration of tycheposons at seven tRNA genes drive the remodeling of larger genomic islands containing most of Prochlorococcus ’ flexible genes. Most tycheposons carry genes important for niche differentiation through nutrient acquisition; others appear similar to phage parasites. Tycheposons are highly enriched in extracellular vesicles and phage particles in ocean samples, suggesting efficient routes for their dispersal, transmission and propagation. Supported by evidence for similar elements in other marine microbes, our work underpins the role of vesicle- and virus-mediated transfer of mobile genetic elements in the diversification and adaptation of microbes in dilute aquatic environments – adding a significant piece to the puzzle of what governs microbial evolution in the planet’s largest habitat.\n\nNovel integrative elements and genomic plasticity in ocean ecosystems", "token_count": 338, "char_count": 1548, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:13.074055", "source": { "split": "train_shard_00001", "doc_id": 3222 }, "chunk_id": "train_shard_00001_3222_0", "global_id": 10230 }, { "text": "Aeromonas are Gram-negative rods widely distributed in the environment. They can cause severe infections in fish related to financial losses in the fish industry, and are considered opportunistic pathogens of humans causing infections ranging from diarrhea to septicemia. The objective of this study was to determine in silico the contribution of genomic islands to A. hydrophila. The complete genomes of 17 A. hydrophila isolates, which were separated into two phylogenetic groups, were analyzed using a genomic island (GI) predictor. The number of predicted GIs and their characteristics varied among strains. Strains from group 1, which contains mainly fish pathogens, generally have a higher number of predicted GIs, and with larger size, than strains from group 2 constituted by strains recovered from distinct sources. Only a few predicted GIs were shared among them and contained mostly genes from the core genome. Features related to virulence, metabolism, and resistance were found in the predicted GIs, but strains varied in relation to their gene content. In strains from group 1, O Ag biosynthesis clusters OX1 and OX6 were identified, while strains from group 2 each had unique clusters. Metabolic pathways for myo-inositol, L-fucose, sialic acid, and a cluster encoding QueDEC, tgtA5, and proteins related to DNA metabolism were identified in strains of group 1, which share a high number of predicted GIs. No distinctive features of group 2 strains were identified in their predicted GIs, which are more diverse and possibly better represent GIs in this species. However, some strains have several resistance attributes encoded by their predicted GIs. Several predicted GIs encode hypothetical proteins and phage proteins whose functions have not been identified but may contribute to Aeromonas fitness. In summary, features with functions identified on predicted GIs may confer advantages to host colonization and competitiveness in the environment.\n\nPrediction and Analysis in silico of Genomic Islands in Aeromonas hydrophila.", "token_count": 499, "char_count": 2086, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5552, "quality_score": 0.7776, "entities": { "genes": [ "OX1", "OX6" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:13.725443", "source": { "split": "train_shard_00001", "doc_id": 3223 }, "chunk_id": "train_shard_00001_3223_0", "global_id": 10231 }, { "text": "Clostridium perfringens is a spore-forming anaerobic pathogen responsible for a variety of histotoxic and intestinal infections in humans and animals. High-resolution genotyping aiming to identify bacteria at strain level has become increasingly important in modern microbiology to understand pathogen transmission pathways and to tackle infection sources. This study aimed at establishing a publicly available genome-wide multilocus sequence-typing scheme for C. perfringens . 1,431 highly conserved core genes (1.34 megabases; 50% of the reference genome genes) were indexed for a core-genome-based MLST scheme for C. perfringens . As an example, we applied the scheme to 87 poultry and 73 non-poultry strains (total=160). The genotyping results of the 160 genomes were congruent in terms of resolution and tree topology between allele-based and single-nucleotide-polymorphism-based core-genome typing. For the analysis of poultry strains of C. perfringens concerning the country of isolation, NetB-toxin gene carriage and clinical disease, we used 60 allelic differences as a clustering threshold. The results showed that poultry strains from a single country formed a cluster ( n= 17 clusters including 46 strains). Two clusters included six strains from four different countries. These strains were netB -positive, as were seven strains from Denmark and two strains from Finland, possibly indicating common sources of netB -positive strains. In terms of clinical presentation, different clusters of strains were associated with cases of suspected necrotic enteritis. Strains from sick birds grouped with strains from healthy birds or meat samples showing that potentially virulent strains are widespread and that host-related factors contribute significantly to NE. In summary, a publicly available scheme and an allele nomenclature database for genomic typing of C. perfringens has been established and can be used for broad-based and standardised epidemiological studies.\n\nEstablishment of a publicly available core genome multilocus sequence typing scheme forClostridium perfringens", "token_count": 504, "char_count": 2097, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8055, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:14.380907", "source": { "split": "train_shard_00001", "doc_id": 3224 }, "chunk_id": "train_shard_00001_3224_0", "global_id": 10232 }, { "text": "In Saccharomyces cerevisiae, the alcohol dehydrogenase genes ADH1 and ADH5 are part of a duplicated block of genome, thought to originate from a genome-wide duplication posterior to the divergence from the Kluyveromyces lineage. We report here the characterization of Kluyveromyces marxianus ADH2 and the five genes found in its immediate downstream region, MRPS9, YOL087C, RPB5, RIB7 and SPP381. The order of these six genes reflects the structure of the ancestral S. cerevisiae genome before the duplication that formed the blocks including ADH1 on chromosome XV and ADH5 on chromosome II, indicating these ADH genes share a direct ancestor. On the one hand, the two genes found immediately downstream of KmADH2 are located, for the first, downstream ADH5 and, for the second, downstream ADH1 in S. cerevisiae. On the other hand, the order of the paralogs included in the blocks of ADH1 and ADH5 in S. cerevisiae suggests that two of them have been inverted within one block after its formation, and that inversion is confirmed by the gene order observed in K. marxianus.\n\nKluyveromyces marxianus exhibits an ancestral Saccharomyces cerevisiae genome organization downstream of ADH2.", "token_count": 328, "char_count": 1185, "word_count": 185, "semantic_coherence": 1, "information_density": 0.5459, "quality_score": 0.773, "entities": { "genes": [ "YOL087C", "ADH5", "ADH1", "RPB5", "RIB7", "MRPS9", "ADH2", "SPP381" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:14.964674", "source": { "split": "train_shard_00001", "doc_id": 3225 }, "chunk_id": "train_shard_00001_3225_0", "global_id": 10233 }, { "text": "Carbapenem resistant Acinetobacter baumannii is a major global concern, especially in countries of the Middle East and North Africa, where the antibiotic resistance rates are on the rise. The aim of this study was to study the genomic characteristics and antimicrobial susceptibility profile of thirty-six multidrug resistant A. baumannii clinical isolates obtained in hospitals from Alexandria, Egypt. Antibiotic resistance rates were estimated by determination of Minimum Inhibitory Concentrations. Carbapenemase genes, other antibiotic resistance genes and virulence factors were then screened by the use of Whole Genome Sequencing. Isolates were also subjected to Multi Locus Sequence Typing (MLST) using the Pasteur Scheme and to core genome MLST to study their clonal relatedness. In addition, plasmid analysis was performed by the use of a commercial kit and S1- Pulsed Field Gel Electrophoresis, and Hybridization experiments with DIG-labeled DNA probes for bla NDM-1, blaPER-7 and bla GES-like were performed to locate these genes. The majority of isolates were resistant to β-lactams (including carbapenems), fluoroquinolones, aminoglycosides and trimethoprim; and some showed resistance to cefiderocol and minocycline", "token_count": 361, "char_count": 1296, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:15.578441", "source": { "split": "train_shard_00001", "doc_id": 3226 }, "chunk_id": "train_shard_00001_3226_0", "global_id": 10234 }, { "text": "We identified 8 different bla OXA-51-like variants including bla OXA-51, bla OXA-64, bla OXA-65, bla OXA-66, bla OXA-68, bla OXA-91, bla OXA-94 and bla OXA-336; bla OXA-23, bla NDM-1, bla PER-7, bla GES-like and bla ADC-like and other antibiotic resistance genes, some of these genes were within transposons or class 1 integrons. Multiple virulence factors responsible for adherence, biofilm production, type II and type VI secretion systems, exotoxins, exoenzymes, immune modulation and iron uptake were observed and 34 out of 36 isolates showed motility. Thirty-five out of 36 isolates clustered with International Clones 2, 4, 5, 7, 8 and 9; and 9 STs were identified including ST570, ST2, ST600, ST15, ST113, ST613, ST85, ST158, ST164", "token_count": 452, "char_count": 990, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7304, "quality_score": 0.8652, "entities": { "genes": [ "ST2", "ST613", "ST164", "ST113", "ST85", "ST158", "ST15", "ST570", "ST600" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:16.230436", "source": { "split": "train_shard_00001", "doc_id": 3226 }, "chunk_id": "train_shard_00001_3226_1", "global_id": 10235 }, { "text": "Plasmids ranging in size from 1.7 to 70 kb were found; bla NDM-1 and blaPER-7 genes were located in the chromosome and bla GES-like genes were simultaneously located in the chromosome and in a plasmid of 70kb. In conclusion, this study revealed a wide spectrum of antibiotic resistance genes and a variety of lineages among A. baumannii isolated in hospitals from Alexandria, and highlights the importance of investigating the molecular epidemiology to control the spread of multi-drug resistant isolates.\n\nMolecular characterization of multidrug resistant Acinetobacter baumannii clinical isolates from Alexandria, Egypt.", "token_count": 207, "char_count": 690, "word_count": 91, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:16.749364", "source": { "split": "train_shard_00001", "doc_id": 3226 }, "chunk_id": "train_shard_00001_3226_2", "global_id": 10236 }, { "text": "In December 2022, an alert was published in the UK and other European countries reporting an unusual increase in the incidence of Streptococcus pyogenes infections. Our aim was to describe the clinical, microbiological, and molecular characteristics of group A Streptococcus invasive infections (iGAS) in children prospectively recruited in Spain (September 2022-March 2023), and compare invasive strains with strains causing mild infections. One hundred thirty isolates of S. pyogenes causing infection (102 iGAS and 28 mild infections) were included in the microbiological study: emm typing, antimicrobial susceptibility testing, and sequencing for core genome multilocus sequence typing (cgMLST), resistome, and virulome analysis. Clinical data were available from 93 cases and 21 controls. Pneumonia was the most frequent clinical syndrome (41/93; 44.1%), followed by deep tissue abscesses (23/93; 24.7%), and osteoarticular infections (11/93; 11.8%). Forty-six of 93 cases (49.5%) required admission to the pediatric intensive care unit. iGAS isolates mainly belonged to emm1 and emm12; emm12 predominated in 2022 but was surpassed by emm1 in 2023. Spread of M1UK sublineage (28/64 M1 isolates) was communicated for the first time in Spain, but it did not replace the still predominant sublineage M1global (36/64)", "token_count": 456, "char_count": 1396, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7249, "quality_score": 0.8624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:17.397280", "source": { "split": "train_shard_00001", "doc_id": 3227 }, "chunk_id": "train_shard_00001_3227_0", "global_id": 10237 }, { "text": "Furthermore, a difference in emm types compared with the mild cases was observed with predominance of emm1, but also important representativeness of emm12 and emm89 isolates. Pneumonia, the most frequent and severe iGAS diagnosed, was associated with the speA gene, while the ssa superantigen was associated with milder cases. iGAS isolates were mainly susceptible to antimicrobials. cgMLST showed five major clusters: ST28-ST1357/emm1, ST36-ST425/emm12, ST242/emm12.37, ST39/emm4, and ST101-ST1295/emm89 isolates.

Importance

Group A Streptococcus (GAS) is a common bacterial pathogen in the pediatric population. In the last months of 2022, an unusual increase in GAS infections was detected in various countries. Certain strains were overrepresented, although the cause of this raise is not clear. In Spain, a significant increase in mild and severe cases was also observed; this study evaluates the clinical characteristics and the strains involved in both scenarios. Our study showed that the increase in incidence did not correlate with an increase in resistance or with an emm types shift. However, there seemed to be a rise in severity, partly related to a greater rate of pneumonia cases. These findings suggest a general increase in iGAS that highlights the need for surveillance. The introduction of whole genome sequencing in the diagnosis and surveillance of iGAS may improve the understanding of antibiotic resistance, virulence, and clones, facilitating its control and personalized treatment.\n\nClinical, microbiological, and molecular characterization of pediatric invasive infections by Streptococcus pyogenes in Spain in a context of global outbreak.", "token_count": 517, "char_count": 1772, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [ "ST36", "ST28", "ST1295", "ST39", "ST425", "ST101", "ST1357", "ST242" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:18.055198", "source": { "split": "train_shard_00001", "doc_id": 3227 }, "chunk_id": "train_shard_00001_3227_1", "global_id": 10238 }, { "text": "The rose-like aroma compound 2-phenylethanol (2-PE) is an important fragrance and flavor ingredient. Several yeast strains are able to convert l-phenylalanine (l-phe) to 2-PE among which Kluyveromyces marxianus has shown promising results. The limitation of this process is the low product concentration and productivity primarily due to end product inhibition. This study explored the possibility and benefits of using a solid-liquid Two-Phase Partition Bioreactor (TPPB) system as an in situ product removal technique. The system applies polymer beads as the sequestering immiscible phase to partition 2-PE and reduce the aqueous 2-PE concentration to non-inhibitory levels. Among six polymers screened for extracting 2-PE, Hytrel 8206 performed best with a partition coefficient of 79. The desired product stored in the polymer was ultimately extracted using methanol. A 3 L working volume solid-liquid batch mode TPPB using 500 g Hytrel as the sequestering phase generated a final overall 2-PE concentration of 13.7 g/L, the highest reported in the current literature. This was based on a polymer phase concentration of 88.74 g/L and aqueous phase concentration of 1.2 g/L. Even better results were achieved via contact with more polymers (approximately 900 g) with the aqueous phase applying a semi-continuous reactor configuration. In this system, a final 2-PE concentration (overall) of 20.4 g/L was achieved with 1.4 g/L in the aqueous and 97 g/L in the polymer phase. The overall productivities of these two reactor systems were 0.38 and 0.43 g/L h, respectively. This is the first report in the literature of the use of a polymer sequestering phase to enhance the bioproduction of 2-PE, and exceeds the performance of two-liquid phase systems in terms of productivity as well as ease of operation (no emulsions) and ultimate product recovery.", "token_count": 499, "char_count": 1852, "word_count": 284, "semantic_coherence": 1, "information_density": 0.5599, "quality_score": 0.7799, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:18.704478", "source": { "split": "train_shard_00001", "doc_id": 3228 }, "chunk_id": "train_shard_00001_3228_0", "global_id": 10239 }, { "text": "Bioproduction of the aroma compound 2-phenylethanol in a solid-liquid two-phase partitioning bioreactor system by Kluyveromyces marxianus.", "token_count": 43, "char_count": 138, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:19.062954", "source": { "split": "train_shard_00001", "doc_id": 3228 }, "chunk_id": "train_shard_00001_3228_1", "global_id": 10240 }, { "text": "Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is one of the most important foodborne pathogens that infect humans globally. The gastrointestinal tracts of animals like pigs, poultry or cattle are the main reservoirs of Salmonella serotypes. Guinea pig meat is an important protein source for Andean countries, but this animal is commonly infected by S. Typhimurium, producing high mortality rates and generating economic losses. Despite its impact on human health, food security, and economy, there is no genomic information about the S. Typhimurium responsible for the guinea pig infections in Peru. Here, we sequence and characterize 11 S. Typhimurium genomes isolated from guinea pigs from four farms in Lima-Peru. We were able to identify two genetic clusters (HC100_9460 and HC100_9757) distinguishable at the H100 level of the Hierarchical Clustering of Core Genome Multi-Locus Sequence Typing (HierCC-cgMLST) scheme with an average of 608 SNPs of distance. All sequences belonged to sequence type 19 (ST19) and HC100_9460 isolates were typed in silico as monophasic variants (1,4,[5],12:i:-) lacking the fljA and fljB genes. Phylogenomic analysis showed that human isolates from Peru were located within the same genetic clusters as guinea pig isolates, suggesting that these lineages can infect both hosts", "token_count": 422, "char_count": 1403, "word_count": 198, "semantic_coherence": 1, "information_density": 0.7374, "quality_score": 0.8687, "entities": { "genes": [ "ST19" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:19.697178", "source": { "split": "train_shard_00001", "doc_id": 3229 }, "chunk_id": "train_shard_00001_3229_0", "global_id": 10241 }, { "text": "We identified a genetic antimicrobial resistance cassette carrying the ant(3)-Ia, dfrA15, qacE, and sul1 genes associated with transposons TnAs3 and IS21 within an IncI1 plasmid in one guinea pig isolate, while antimicrobial resistance genes (ARGs) for β-lactam (blaCTX-M-65) and colistin (mcr-1) resistance were detected in Peruvian human-derived isolates. The presence of a virulence plasmid highly similar to the pSLT plasmid (LT2 reference strain) containing the spvRABCD operon was found in all guinea pig isolates. Finally, seven phage sequences (STGP_Φ1 to STGP_Φ7) were identified in guinea pig isolates, distributed according to the genetic lineage (H50 clusters level) and forming part of the specific gene content of each cluster. This study presents, for the first time, the genomic characteristics of S. Typhimurium isolated from guinea pigs in South America, showing particular diversity and genetic elements (plasmids and prophages) that require special attention and also broader studies in different periods of time and locations to determine their impact on human health.\n\nGenomic Characterization of Salmonella Typhimurium Isolated from Guinea Pigs with Salmonellosis in Lima, Peru.", "token_count": 375, "char_count": 1275, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.8459, "entities": { "genes": [ "IS21", "LT2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:20.281853", "source": { "split": "train_shard_00001", "doc_id": 3229 }, "chunk_id": "train_shard_00001_3229_1", "global_id": 10242 }, { "text": "Simultaneous saccharification and fermentation (SSF) studies were carried out to produce ethanol from lignocellulosic wastes (sugar cane leaves and Antigonum leptopus leaves) using Trichoderma reesei cellulase and yeast cells. The ability of a thermotolerant yeast, Kluyveromyces fragilis NCIM 3358, was compared with Saccharomyces cerevisiae NRRL-Y-132. K. fragilis was found to perform better in the SSF process and result in high yields of ethanol (2.5-3.5% w/v) compared to S. cerevisiae (2.0-2.5% w/v). Increased ethanol yields were obtained when the cellulase was supplemented with beta-glucosidase. The conversions with K. fragilis were completed in a short time. The substrates were in the following order in terms of fast conversions: Solka floc > A. leptopus > sugar cane.\n\nSimultaneous saccharification and fermentation of lignocellulosic wastes to ethanol using a thermotolerant yeast.", "token_count": 274, "char_count": 897, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6299, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:20.841878", "source": { "split": "train_shard_00001", "doc_id": 3230 }, "chunk_id": "train_shard_00001_3230_0", "global_id": 10243 }, { "text": "Cataloguing the distribution of genes within natural bacterial populations is essential for understanding evolutionary processes and the genetic basis of adaptation. Here we present a pangenomics toolbox, PIRATE (Pangenome Iterative Refinement And Threshold Evaluation), which identifies and classifies orthologous gene families in bacterial pangenomes over a wide range of sequence similarity thresholds. PIRATE builds upon recent scalable software developments to allow for the rapid interrogation of thousands of isolates. PIRATE clusters genes (or other annotated features) over a wide range of amino-acid or nucleotide identity thresholds and uses the clustering information to rapidly classify paralogous gene families into either putative fission/fusion events or gene duplications. Furthermore, PIRATE orders the pangenome using a directed graph, provides a measure of allelic variation and estimates sequence divergence for each gene family. We demonstrate that PIRATE scales linearly with both number of samples and computation resources, allowing for analysis of large genomic datasets, and compares favorably to other popular tools. PIRATE provides a robust framework for analysing bacterial pangenomes, from largely clonal to panmictic species.

Availability

PIRATE is implemented in Perl and is freely available under an GNU GPL 3 open source license from https://github.com/SionBayliss/PIRATE .

Supplementary Information

Supplementary data is available online.\n\nPIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria", "token_count": 360, "char_count": 1589, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6934, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:21.432494", "source": { "split": "train_shard_00001", "doc_id": 3231 }, "chunk_id": "train_shard_00001_3231_0", "global_id": 10244 }, { "text": ": Emaravirus (Order Bunyavirales; Family Fimoviridae) is a genus comprising over 20 emerging plant viruses with a worldwide distribution and economic impact. Emaraviruses infect a variety of host plants and have especially become prevalent in important long-living woody plants. These viruses are enveloped, with a segmented, single-stranded, negative-sense RNA genome and are transmitted by eriophyid mites or mechanical transmission. Emaraviruses have four core genome segments encoding an RNA-dependent RNA polymerase, a glycoprotein precursor, a nucleocapsid protein, and a movement protein. They also have additional genome segments, whose number varies widely. We report here that the proteins encoded by these segments form three main homology groups: a homolog of the sadwavirus Glu2 Pro glutamic protease; a protein involved in pathogenicity, which we named “ABC”; and a protein of unknown function, which we named “P55”. The distribution of these proteins parallels the emaravirus phylogeny and suggests, with other analyses, that emaraviruses should be split into at least two genera. Reliable diagnosis systems are urgently needed to detect emaraviruses, assess their economic and ecological importance, and take appropriate measures to prevent their spread (such as routine testing, hygiene measures, and control of mite vectors). Additional research needs include understanding the function of emaravirus proteins, breeding resistant plants and clarifying transmission modes.\n\nThe Complex World of Emaraviruses – Challenges, Insights and Prospects", "token_count": 387, "char_count": 1585, "word_count": 218, "semantic_coherence": 1, "information_density": 0.711, "quality_score": 0.8555, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:22.051734", "source": { "split": "train_shard_00001", "doc_id": 3232 }, "chunk_id": "train_shard_00001_3232_0", "global_id": 10245 }, { "text": "Yersinia ruckeri is a salmonid pathogen with widespread distribution in cool-temperate waters including Australia and New Zealand, two isolated environments with recently developed salmonid farming industries. Phylogenetic comparison of 58 isolates from Australia, New Zealand, USA, Chile, Finland and China based on non-recombinant core genome SNPs revealed multiple deep-branching lineages, with a most recent common ancestor estimated at 18 500 years BP (12 355-24 757 95% HPD) and evidence of Australasian endemism. Evolution within the Tasmanian Atlantic salmon serotype O1b lineage has been slow, with 63 SNPs describing the variance over 27 years. Isolates from the prevailing lineage are poorly/non-motile compared to a lineage pre-vaccination, introduced in 1997, which is highly motile but has not been isolated since from epizootics. A non-motile phenotype has arisen independently in Tasmania compared to Europe and USA through a frameshift in fliI, encoding the ATPase of the flagella cluster. We report for the first time lipopolysaccharide O-antigen serotype O2 isolates in Tasmania. This phenotype results from deletion of the O-antigen cluster and consequent loss of high-molecular-weight O-antigen. This phenomenon has occurred independently on three occasions on three continents (Australasia, North America and Asia) as O2 isolates from the USA, China and Tasmania share the O-antigen deletion but occupy distant lineages. Despite the European and North American origins of the Australasian salmonid stocks, the lineages of Y. ruckeri in Australia and New Zealand are distinct from those of the northern hemisphere, suggesting they are pre-existing ancient strains that have emerged and evolved with the introduction of susceptible hosts following European colonization.", "token_count": 468, "char_count": 1811, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6523, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:22.696151", "source": { "split": "train_shard_00001", "doc_id": 3233 }, "chunk_id": "train_shard_00001_3233_0", "global_id": 10246 }, { "text": "Whole genome analysis of Yersinia ruckeri isolated over 27 years in Australia and New Zealand reveals geographical endemism over multiple lineages and recent evolution under host selection.", "token_count": 47, "char_count": 196, "word_count": 27, "semantic_coherence": 1, "information_density": 0.9259, "quality_score": 0.963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:23.053949", "source": { "split": "train_shard_00001", "doc_id": 3233 }, "chunk_id": "train_shard_00001_3233_1", "global_id": 10247 }, { "text": "The genus Paenibacillus, known for its diverse sources, is a valuable reservoir of antimicrobial compounds, enzymes and other valuable chemicals, with applications in medicine, agriculture, and bioremediation. Despite this, Paenibacillus strains, particularly those isolated from unique environments, remain underexplored, limiting our understanding of their potential, capabilities and taxonomic classifications. The gut microbiome of large herbivores, such as rhinoceroses, harbors underexplored microbial diversity with unique metabolic capabilities. In this study, a Gram-stain-negative, facultatively aerobic, motile, spore-forming, rod-shaped bacterial strain, NGMCC 1.200843T (= CGMCC 1.64763T = JCM 37214T), was isolated from fresh rhinoceros feces and characterized its taxonomic status and metabolic potential. Phylogenetic, phenotypic, and chemotaxonomic analyses confirmed the isolate as a novel species within the genus Paenibacillus, closely related to Paenibacillus lautus DSM 3035T (98.62% 16S rRNA gene similarity). The average nucleotide identity (ANI) and the digital DNA-DNA hybridization values were below the threshold for species delineation. The major cellular fatty acids were anteiso-C15:0, C16:0 and iso-C16:0 (> 10%) and the polar lipid profile contained diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE), two unidentified phospholipids (PL1-2) and one phosphatidyl choline (PC). The total DNA G + C content was 49.69 mol%", "token_count": 513, "char_count": 1564, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7937, "quality_score": 0.8968, "entities": { "genes": [ "PL1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:23.689350", "source": { "split": "train_shard_00001", "doc_id": 3234 }, "chunk_id": "train_shard_00001_3234_0", "global_id": 10248 }, { "text": "The isolate exhibited significant phosphate solubilization and starch hydrolysis activities in plate assays, suggesting a role in nutrient cycling within the rhinoceros gut. We propose the name Paenibacillus ilasis sp. nov. for this strain. These findings enhance our understanding of gut microbial diversity in herbivores and lay the foundation for future applications in agriculture or industry.\n\nNovel gut bacteria species Paenibacillus ilasis with phosphorus degrading and soluble starch hydrolysis abilities isolated from fresh feces of rhinoceros.", "token_count": 133, "char_count": 553, "word_count": 76, "semantic_coherence": 1, "information_density": 0.8026, "quality_score": 0.9013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:24.115349", "source": { "split": "train_shard_00001", "doc_id": 3234 }, "chunk_id": "train_shard_00001_3234_1", "global_id": 10249 }, { "text": "Members of the bacterial genus Vibrio utilise chitin both as a metabolic substrate and a signal to activate natural competence. Vibrio cholerae is a bacterial enteric pathogen, sub-lineages of which can cause pandemic cholera. However, the chitin metabolic pathway in V. cholerae has been dissected using only a limited number of laboratory strains of this species. Here, we survey the complement of key chitin metabolism genes amongst 195 diverse V. cholerae. We show that the gene encoding GbpA, known to be an important colonisation and virulence factor in pandemic isolates, is not ubiquitous amongst V. cholerae. We also identify a putatively novel chitinase, and present experimental evidence in support of its functionality. Our data indicate that the chitin metabolic pathway within the V. cholerae species is more complex than previously thought, and emphasise the importance of considering genes and functions in the context of a species in its entirety, rather than simply relying on traditional reference strains.

Impact statement

It is thought that the ability to metabolise chitin is ubiquitous amongst Vibrio spp., and that this enables these species to survive in aqueous and estuarine environmental contexts. Although chitin metabolism pathways have been detailed in several members of this genus, little is known about how these processes vary within a single Vibrio species. Here, we present the distribution of genes encoding key chitinase and chitin-binding proteins across diverse Vibrio cholerae , and show that our canonical understanding of this pathway in this species is challenged when isolates from non-pandemic V. cholerae lineages are considered alongside those linked to pandemics. Furthermore, we show that genes previously thought to be species core genes are not in fact ubiquitous, and we identify novel components of the chitin metabolic cascade in this species, and present functional validation for these observations.

Data summary

The authors confirm that all supporting data, code, and protocols have been provided within the article or through supplementary data files. No whole-genome sequencing data were generated in this study", "token_count": 511, "char_count": 2190, "word_count": 328, "semantic_coherence": 1, "information_density": 0.5549, "quality_score": 0.7774, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:24.749182", "source": { "split": "train_shard_00001", "doc_id": 3235 }, "chunk_id": "train_shard_00001_3235_0", "global_id": 10250 }, { "text": "Accession numbers for the publicly-available sequences used for these analyses are listed in Supplementary Table 1, Table 2, and the Methods. All other data which underpin the figures in this manuscript, including pangenome data matrices, modified and unmodified sequence alignments and phylogenetic trees, original images of gels and immunoblots, raw fluorescence data, amplicon sequencing reads, and the R code used to generate Figure 7, are available in Figshare: https://dx.doi.org/10.6084/m9.figshare.13169189 (Note for peer-review: Figshare DOI is inactive but will be activated upon publication, please use temporary URL https://figshare.com/s/7795a2d80c13f694f8fa for review).\n\ngbpAandchiAgenes are not uniformly distributed amongst diverseVibrio cholerae", "token_count": 239, "char_count": 784, "word_count": 97, "semantic_coherence": 1, "information_density": 0.8247, "quality_score": 0.9124, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:25.226702", "source": { "split": "train_shard_00001", "doc_id": 3235 }, "chunk_id": "train_shard_00001_3235_1", "global_id": 10251 }, { "text": "

Objectives

Patients hospitalised abroad can become colonised with multidrug-resistant bacteria and import them to their home countries. In this study, we characterised an OXA-484 carbapenemase-producing Escherichia coli strain from a Swiss patient infected by SARS-CoV-2 and repatriated from India.

Methods

At admission to Switzerland (April 2021), the patient undertook a nasopharyngeal swab to search for SARS-CoV-2 and a rectal swab to detect multidrug-resistant bacteria. Both SARS-CoV-2 and E. coli isolates were whole-genome sequenced and analysed for phylogenetic relatedness.

Results

The patient was infected with the SARS-CoV-2 B.1.617.2 lineage (VOC Delta), a lineage that began to be reported across Switzerland at that time. He was also colonised with a sequence type 410 (ST410) E. coli strain (L3452210II) producing OXA-484, a single amino acid variant of OXA-181. The blaOXA-484 gene was carried by a 51.5 kb IncX3 plasmid identical to those described in blaOXA-181-harbouring ST410 E. coli strains. Core genome analysis showed that L3452210II was identical (ΔSNV ≤23) to two ST410 OXA-484 producers recently reported in Qatar and Germany, but differed from other ST410 OXA-181 producers reported worldwide.

Conclusion

The patient was infected by an emerging SARS-CoV-2 variant and also imported an E. coli producing OXA-484, an OXA-48-like carbapenemase not yet reported in Switzerland", "token_count": 493, "char_count": 1452, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6205, "quality_score": 0.8103, "entities": { "genes": [ "ST410" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:25.876710", "source": { "split": "train_shard_00001", "doc_id": 3236 }, "chunk_id": "train_shard_00001_3236_0", "global_id": 10252 }, { "text": "The genetic background of L3452210II indicated that blaOXA-484 shared the same plasmid as blaOXA-181, but its bacterial host differed from most of the pandemic OXA-181-producing ST410 strains reported previously. This case description underlines that the COVID-19 crisis can contribute to the worldwide spread of emerging carbapenemase producers.\n\nRepatriation of a patient with COVID-19 contributed to the importation of an emerging carbapenemase producer.", "token_count": 138, "char_count": 479, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7742, "quality_score": 0.8871, "entities": { "genes": [ "ST410" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:26.299811", "source": { "split": "train_shard_00001", "doc_id": 3236 }, "chunk_id": "train_shard_00001_3236_1", "global_id": 10253 }, { "text": "Strains within a bacterial species typically have a set of conserved core genes and a variable set of accessory genes. The accessory genes often appear to move laterally between strains, thereby forming new trait combinations. Sometimes, genetic material also moves laterally between species, thereby resulting in diffuse borders between them. The growing number of genome sequences offers new possibilities to study these processes. Ten species for which abundant genomic data exists were here selected for analysis of the species border integrity. The average core genome similarities and relative core genome sizes (RCGSs) were determined for strain pairs within the species and for strain pairs crossing the species border. The variability within the species as well as the border integrity varies for different bacterial species. Some have very distinct borders while others are more or less indefinable. From the growing amount of genomic data, it becomes even clearer that the concept of bacterial species is, in many cases, far from absolute.\n\nThe genetic integrity of bacterial species: the core genome and the accessory genome, two different stories.", "token_count": 227, "char_count": 1160, "word_count": 176, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:26.774119", "source": { "split": "train_shard_00001", "doc_id": 3237 }, "chunk_id": "train_shard_00001_3237_0", "global_id": 10254 }, { "text": "Xylans, a family of xylose-based polysaccharides, are dietary fibers resistant to digestion. They therefore reach the large intestine intact; there, they are utilized by members of the gut microbiota. They are initially broken down by primary degraders that utilize extracellular xylanases to cleave xylan into smaller oligomers. The resulting xylooligosaccharides (XOS) can either be further metabolized directly by primary degraders or cross-feed secondary consumers, including Bifidobacterium. While several Bifidobacterium species have metabolic systems for XOS, most grow poorly on longer-chain XOS and xylan substrates. In this study, we isolated strains of Bifidobacterium pseudocatenulatum and observed that some, including B. pseudocatenulatum ED02, displayed growth on XOS with a high degree of polymerization (DP) and straight-chain xylan, suggesting a primary degrader phenotype that is rare in Bifidobacterium. In silico analyses revealed that only the genomes of these xylan-fermenting (xylan+) strains contained an extracellular GH10 endo-β-1.4 xylanase, a key enzyme for primary degradation of xylan. The presence of an extracellular xylanase was confirmed by the appearance of xylan hydrolysis products in cell-free supernatants. Extracellular xylanolytic activity was only detected in xylan+ strains, as indicated by the production of XOS fragments with a DP of 2 to 6, identified by thin-layer chromatography (TLC) and high-performance liquid chromatography (HPLC). Additionally, in vitro fecal fermentations revealed that strains with a xylan+ phenotype can persist with xylan supplementation. These results indicate that xylan+ B", "token_count": 489, "char_count": 1729, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [ "GH10", "ED02" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:27.451205", "source": { "split": "train_shard_00001", "doc_id": 3238 }, "chunk_id": "train_shard_00001_3238_0", "global_id": 10255 }, { "text": "pseudocatenulatum strains may have a competitive advantage in the complex environment of the gastrointestinal tract, due to their ability to act as primary degraders of xylan through extracellular enzymatic degradation. IMPORTANCE The beneficial health effects of dietary fiber are now well established. Moreover, low fiber consumption is associated with increased risks of metabolic and systemic diseases. This so-called \"fiber gap\" also has a profound impact on the composition of the gut microbiome, leading to a disrupted or dysbiotic microbiota. Therefore, understanding the mechanisms by which keystone bacterial species in the gut utilize xylans and other dietary fibers may provide a basis for developing strategies to restore gut microbiome function. The results described here provide biochemical and genetic evidence for primary xylan utilization by human-derived Bifidobacterium pseudocatenulatum and show also that cooperative utilization of xylans occurs among other members of this species.\n\nRole of Bifidobacterium pseudocatenulatum in Degradation and Consumption of Xylan-Derived Carbohydrates.", "token_count": 262, "char_count": 1118, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:28.012925", "source": { "split": "train_shard_00001", "doc_id": 3238 }, "chunk_id": "train_shard_00001_3238_1", "global_id": 10256 }, { "text": "

Background

The incidence of Clostridioides difficile infection (CDI) has been rising among hospitalized children, with poor understanding of genomic variability of C. difficile isolates in this population.

Methods

This was a retrospective cohort study of CDI in inpatient and outpatient pediatric oncology and cell transplant patients (POTPs) in 2016 and 2017. CDI cases were identified by positive C. difficile toxin polymerase chain reaction tests. Retrieved residual stool specimens were cultured anaerobically and toxin-producing C. difficile isolates underwent whole genome sequencing (WGS) followed by core genome multilocus sequence typing. Plausible time and location epidemiologic links among the closely related strains were evaluated to identify potential transmission events.

Results

Among 226 CDI episodes in 157 patients, 202 stool samples were cultured and had positive cytotoxicity tests. Sequencing identified 33 different strain types in 162 (80%) isolates. Thirty-nine (28%) patients had multiple episodes of CDI, and 31 clusters of related isolates were identified, 15 (47%) of which involved exclusively multiple specimens from the same patient. For the 16 clusters involving multiple patients, epidemiologic investigation revealed only 2 (12.5%) clusters with potential transmission events.

Conclusions

WGS identified a highly diverse group of C. difficile isolates among POTPs with CDI. Although WGS identified clusters of closely related isolates in multiple patients, epidemiologic investigation of shared inpatient exposures identified potential transmission in only 2 clusters. Clostridioides difficile transmission was uncommon in this population. More than 70% of new CDI reinfections in POTPs are actually recurrences caused by a previous CDI strain.\n\nMolecular Epidemiology and Genetic Relatedness of Clostridioides difficile Isolates in Pediatric Oncology and Transplant Patients Using Whole Genome Sequencing.", "token_count": 514, "char_count": 1971, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:28.721155", "source": { "split": "train_shard_00001", "doc_id": 3239 }, "chunk_id": "train_shard_00001_3239_0", "global_id": 10257 }, { "text": "

Objectives

To characterize the genetic environment of metallo-β-lactamases (MBL) in carbapenem-resistant clinical Acinetobacter pittii isolates.

Methods

Seventeen carbapenem-resistant A. pittii isolates harbouring an MBL were collected between 2010 and 2015 in Germany. Antimicrobial susceptibility testing was performed using agar dilution. Presence of MBLs was confirmed by PCR and their genetic location determined by S1-pulsed-field gel electrophoresis followed by Southern blot hybridization. Whole-genome sequencing was performed using the Miseq and MinION platforms. Isolates were typed using an ad hoc core genome MLST scheme. Conjugation into A. baumannii was tested by broth mating.

Results

In 10 isolates the MBL was plasmid-encoded and in seven isolates chromosomally encoded. blaGIM-1 and blaVIM-2 were plasmid-encoded, blaVIM-4 was chromosomally encoded, while blaNDM-1 was chromosomally encoded in four and plasmid-encoded in three isolates. Seven of ten plasmids were conjugative into A. baumannii. Although most isolates were unrelated, the backbones of the MBL-encoding plasmid showed >99% similarity and only differed in the MBL-encoding area. blaNDM-1-harbouring plasmids were highly similar to other plasmids from Acinetobacter isolates worldwide while the blaVIM-2- and blaGIM-1-encoding plasmids have not been described.

Conclusions

These data show the existence of a promiscuous plasmid circulating in A. pittii isolates in Germany that differs only in the MBL-encoding region. Its plasmid backbone has been found globally among multiple Acinetobacter spp. These data should raise awareness of an epidemic conjugative plasmid that has independently acquired MBLs", "token_count": 502, "char_count": 1715, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:29.381611", "source": { "split": "train_shard_00001", "doc_id": 3240 }, "chunk_id": "train_shard_00001_3240_0", "global_id": 10258 }, { "text": "We should also consider that future comparative plasmid analysis will look beyond solely the resistome and include the mobile elements carrying the resistance genes.\n\nCarbapenem resistance in Acinetobacter pittii isolates mediated by metallo-β-lactamases.", "token_count": 60, "char_count": 255, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:29.746956", "source": { "split": "train_shard_00001", "doc_id": 3240 }, "chunk_id": "train_shard_00001_3240_1", "global_id": 10259 }, { "text": "Campylobacter upsaliensis was the most common Campylobacter species in pets' gastrointestinal tracts and has been isolated from patients with bacteremia, hemolytic-uremic syndrome, spontaneous abortion, and Guillain-Barré syndrome. However, the genetic characteristics and the full extent of its significance as a human pathogen remain to be fully understood. This study involved an investigation for genomic analysis of 154 strains from different sources and additional antimicrobial resistance profiles of 26 strains for this species. The genomes contained 1,558-1,971 CDS and the genome sizes were estimated to vary from 1.53 Mb to 1.86 Mb, with an average GC content of  34.71%. The entire analyzed genomes could be divided into three clades (A, B, and C) based on ANI and phylogenomic analysis. Significantly, nearly all strains in Clade B were isolated from patient samples, and the virulence-related sequences FlgD, GmhA, and CdtC might serve as determining factors for the classification of Clade B. Half of the tested isolates had MIC values over 64 μg mL-1 for nalidixic acid, gentamicin, and streptomycin. Isolates from pets in China carried more resistant elements in the genomes. This study both provided a comprehensive profile of C. upsaliensis for its genomic features and suggested some pathogenic agents for human infection with this species.\n\nGenetic characteristics and potential pathogenic agents in Campylobacter upsaliensis based on genomic analysis.", "token_count": 411, "char_count": 1512, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:30.370885", "source": { "split": "train_shard_00001", "doc_id": 3241 }, "chunk_id": "train_shard_00001_3241_0", "global_id": 10260 }, { "text": "Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified as pathotypes of diarrhoeagenic Escherichia coli or Shigella species and is generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated, and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) isolated in Great Britain between 2000 and 2021 and analysed these alongside a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98-35.45 p = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii.\n\nThe genomic epidemiology of Escherichia albertii infecting humans and birds in Great Britain.", "token_count": 387, "char_count": 1333, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:30.990124", "source": { "split": "train_shard_00001", "doc_id": 3242 }, "chunk_id": "train_shard_00001_3242_0", "global_id": 10261 }, { "text": "Abstract

Background Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness. Results Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection. Conclusions The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.

\n\nChromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome", "token_count": 428, "char_count": 1845, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:31.616490", "source": { "split": "train_shard_00001", "doc_id": 3243 }, "chunk_id": "train_shard_00001_3243_0", "global_id": 10262 }, { "text": "A Gram-stain-negative, rod-shaped bacterium, designated HB171785T, was isolated from soil sample collected from Qishui Bay, Hainan, China. The strain grew optimally at pH 7-8, 37-40 °C and with NaCl 3-4%. The predominant isoprenoid quinone was found to be Q-8 and the major fatty acids were C16:0, C16:1 ω7c/C16:1 ω6c, C18:1 ω7c/C18:1 ω6c and C12:0 3OH. The polar lipids contained diphosphatidylglycerol, phosphatidylglycerol, and phosphatidylethanolamine. The size of the draft genome was 4.32 Mbp with G + C content 49.7%. Phylogenetic analysis of 16S rRNA gene sequence indicated that the closest phylogenetically related species were Neiella marina j221T, \"Neiella holothuriorum\" 126 and Echinimonas agarilytica KMM 6351T with the similarities of 98.2, 96.0 and 95.0%, respectively. The phylogenetic tree based on 16S rRNA gene and phylogenomic tree based on core genome showed that strain HB171785T clustered together with N. marina j221T, with the highest values of average nucleotide identity (82.9%) and digital DNA-DNA hybridization (25.4%)", "token_count": 467, "char_count": 1170, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7434, "quality_score": 0.8717, "entities": { "genes": [ "HB171785" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:32.264536", "source": { "split": "train_shard_00001", "doc_id": 3244 }, "chunk_id": "train_shard_00001_3244_0", "global_id": 10263 }, { "text": "The combined phylogenetic relatedness, phenotypic and genotypic features supported the conclusion that strain HB171785T represents a novel species of the genus Neiella, for which the name Neiella litorisoli sp. nov. is proposed. The type strain is HB171785T (= MCCC 1K04625T = KCTC 82319T). In addition, Echinimonadaceae fam. nov. in the order Alteromonadales was proposed.\n\nNeiella litorisoli sp. nov., an alginate lyase: producing bacterium from South China Sea, and proposal of Echinimonadaceae fam. nov. in the order Alteromonadales.", "token_count": 210, "char_count": 581, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "HB171785" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:32.729596", "source": { "split": "train_shard_00001", "doc_id": 3244 }, "chunk_id": "train_shard_00001_3244_1", "global_id": 10264 }, { "text": "Livestock associated methicillin resistant S. aureus (LA-MRSA) are lineages adapted to livestock species. LA-MRSA can be transmitted to humans and public health concerns exist because livestock may be the largest MRSA reservoir outside of hospital settings. Although the predominant European (ST398) and Asian (ST9) lineages of LA-MRSA are considered livestock adapted, North American swine also harbor ST5, a globally disseminated and highly pathogenic lineage. This study applied whole genome sequencing and single nucleotide polymorphism (SNP) typing to compare the population structure and genetic relatedness between swine associated and human clinical MRSA ST5 isolates. The established high-resolution phylogenomic framework revealed that LA-MRSA and human clinical MRSA ST5 are genetically distinct. LA-MRSA isolates were found to be clonal within farms, while greater genome diversity was observed among sampled clinical MRSA ST5. Analysis of the accessory genome demonstrated that LA-MRSA ST5 isolates and clinical MRSA ST5 isolates harbor different AMR genes and virulence factors, consistent with the SNP analysis. Collectively, our data indicate LA-MRSA and clinical MRSA ST5 isolates are distinct and the swine reservoir is likely of minimal significance as a source of clinical MRSA ST5 infections.\n\nSingle Nucleotide Polymorphism Analysis Indicates Genetic Distinction and Reduced Diversity of Swine-Associated Methicillin Resistant Staphylococcus aureus (MRSA) ST5 Isolates Compared to Clinical MRSA ST5 Isolates.", "token_count": 393, "char_count": 1544, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "ST398", "ST5", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:33.349029", "source": { "split": "train_shard_00001", "doc_id": 3245 }, "chunk_id": "train_shard_00001_3245_0", "global_id": 10265 }, { "text": "

Objectives

To reconstruct the evolutionary history and genomic epidemiology of Staphylococcus aureus ST9 in China.

Methods

Using WGS analysis, we described the phylogeny of 131 S. aureus ST9 isolates collected between 2002 and 2016 from 11 provinces in China, including six clinical samples from Taiwan. We also investigated the complex structure and distribution of the lsa(E)-carrying multiresistance gene cluster, and genotyped prophages in the genomes of the ST9 isolates.

Results

ST9 was subdivided into one major (n = 122) and one minor (n = 9) clade. Bayesian phylogeny predicted the divergence of ST9 isolates in pig farming in China as early as 1987, which then evolved rapidly in the following three decades. ST9 isolates shared similar multiresistance properties, which were likely acquired before the ST9 emergence in China. The accessory genome is highly conserved, and ST9 harboured similar sets of phages, but lacked certain virulence genes.

Conclusions

Host exchange and regional transmission of ST9 have occurred between pigs and humans. Pig rearing and trading might have favoured gene exchanges between ST9 isolates. Resistance genes, obtained from the environment and other isolates, were stably integrated into the chromosomal DNA. The abundance of resistance genes among ST9 is likely attributed to the extensive use of antimicrobial agents in livestock. Phages are present in the genomes of ST9 and may play a role in the rapid evolution of this ST. Although human ST9 infections are rare, ST9 isolates may constitute a potential risk to public health as a repository of antimicrobial resistance genes.\n\nEvolution and genomic insight into methicillin-resistant Staphylococcus aureus ST9 in China.", "token_count": 461, "char_count": 1748, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6063, "quality_score": 0.8031, "entities": { "genes": [ "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:33.994108", "source": { "split": "train_shard_00001", "doc_id": 3246 }, "chunk_id": "train_shard_00001_3246_0", "global_id": 10266 }, { "text": "In the present work randomly amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) with primers M13 and RF2 was applied to the identification at species level of yeast strains isolated from cheeses. RAPD-PCR analysis of the type strains of different yeast species gave distinctive band profiles that allowed a clear differentiation of all the considered species. Forty-two of the 48 dairy associated yeasts were clearly assigned to the species Saccharomyces cerevisiae, Kluyveromyces marxianus (anamorph Candida kefyr), Kluyveromyces lactis (anamorph Candida sphaerica), Debaryomyces hansenii (anamorph Candida famata), Yarrowia lipolytica and Torulaspora delbrueckii (anamorph Candida colliculosa). The method, which is rapid and easy to perform, could be a useful tool for the identification of yeasts present in dairy products.\n\nRandomly amplified polymorphic DNA (RAPD) PCR for the identification of yeasts isolated from dairy products.", "token_count": 256, "char_count": 949, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [ "RF2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:34.542039", "source": { "split": "train_shard_00001", "doc_id": 3247 }, "chunk_id": "train_shard_00001_3247_0", "global_id": 10267 }, { "text": "Pseudomonas spp. exhibit considerable differences in host specificity and virulence. Most Pseudomonas species were isolated exclusively from environmental sources, ranging from soil to plants, but some Pseudomonas species have been detected from versatile sources, including both human host and environmental sources. Understanding genome variations that generate the tremendous diversity in Pseudomonas biology is important in controlling the incidence of infections. With a data set of 704 Pseudomonas complete whole genome sequences representing 186 species, Pseudomonas intrageneric structure was investigated by hierarchical clustering based on average nucleotide identity, and by phylogeny analysis based on concatenated core-gene alignment. Further comparative functional analyses indicated that Pseudomonas species only living in natural habitats lack multiple functions that are important in the regulation of bacterial pathogenesis, indicating the possession of these functions might be characteristic of Pseudomonas human pathogens. Moreover, we have performed pangenome based homogeneity analyses, and detected genes with conserved structures but diversified functions across the Pseudomonas genomes, suggesting these genes play a role in driving diversity. In summary, this study provided insights into the dynamics of genome diversity and host-related genetic determinants in Pseudomonas , which might help the development of more targeted antibiotics for the treatment of Pseudomonas infections.\n\nRevisiting the intrageneric structure of the genusPseudomonaswith complete whole genome sequence information: Insights into Diversity and Host-related Genetic Determinants", "token_count": 365, "char_count": 1690, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:35.125922", "source": { "split": "train_shard_00001", "doc_id": 3248 }, "chunk_id": "train_shard_00001_3248_0", "global_id": 10268 }, { "text": "

Aims

The aim of this work was to identify 20 yeasts isolated from autochthonal cheese starters and evaluate their technological and functional properties.

Methods and results

The capacities of the yeasts to grow at different temperatures, pH, NaCl and lactic acid concentrations as well as the proteolytic and lipolytic activities were studied. Moreover, survival to simulated gastrointestinal digestion, hydrophobicity, antimicrobial activity against pathogens and auto- and co-aggregation abilities were evaluated. The sequentiation of a fragment from the 26S rDNA gene indicated that Kluyveromyces marxianus was the predominant species, followed by Saccharomyces cerevisiae, Clavispora lusitaniae, Kluyveromyces lactis and Galactomyces geotrichum. RAPD with primer M13 allowed a good differentiation among strains from the same species. All strains normally grew at pH 4.7-5.5 and temperatures between 15 and 35°C. Most of them tolerated 10% NaCl and 3% lactic acid. Some strains showed proteolytic (eight isolates) and/or lipolytic (four isolates) capacities. All strains evidenced high gastrointestinal resistance, moderate hydrophobicity, intermediate auto-aggregation and variable co-aggregation abilities. No strains inhibited the growth of the pathogens assayed.

Conclusions

Some strains from dairy sources showed interesting functional and technological properties.

Significance and impact of the study

This study has been the first contribution to the identification and characterization of yeasts isolated from autochthonal cheese starters in Argentina. Many strains could be proposed as potential candidates to be used as probiotics and/or as co-starters in cheese productions.\n\nYeasts from autochthonal cheese starters: technological and functional properties.", "token_count": 466, "char_count": 1803, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6391, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:35.774266", "source": { "split": "train_shard_00001", "doc_id": 3249 }, "chunk_id": "train_shard_00001_3249_0", "global_id": 10269 }, { "text": "The study aimed to evaluate the metabolism and resistance to the gastrointestinal tract conditions of Bacillus pumilus UAMX (BP-UAMX) isolated from overweight individuals using genomic tools. Specifically, we assessed its ability to metabolize various carbon sources, its resistance to low pH exposure, and its growth in the presence of bile salts. The genomic and bioinformatic analyses included the prediction of gene and protein metabolic functions, a pan-genome and phylogenomic analysis. BP-UAMX survived at pH 3, while bile salts (0.2-0.3% w/v) increased its growth rate. Moreover, it showed the ability to metabolize simple and complex carbon sources (glucose, starch, carboxymethyl-cellulose, inulin, and tributyrin), showing a differentiated electrophoretic profile. Genome was assembled into a single contig, with a high percentage of genes and proteins associated with the metabolism of amino acids, carbohydrates, and lipids. Antibiotic resistance genes were detected, but only one beta-Lactam resistance protein related to the inhibition of peptidoglycan biosynthesis was identified. The pan-genome of BP-UAMX is still open with phylogenetic similarities with other Bacillus of human origin. Therefore, BP-UAMX seems to be adapted to the intestinal environment, with physiological and genomic analyses demonstrating the ability to metabolize complex carbon sources, the strain has an open pan-genome with continuous evolution and adaptation.\n\nPhysiological and Genomic Analysis of Bacillus pumilus UAMX Isolated from the Gastrointestinal Tract of Overweight Individuals.", "token_count": 438, "char_count": 1611, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5963, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:36.412782", "source": { "split": "train_shard_00001", "doc_id": 3250 }, "chunk_id": "train_shard_00001_3250_0", "global_id": 10270 }, { "text": "Bacteriophages are the most prevalent biological entities impacting on the ecosystem and are characterized by their extensive diversity. However, there are two aspects of phages that have remained largely unexplored: genetic flux by recombination between phage populations and characterization of specific phages in terms of the pan-genome. Here, we examined the recombination and pan-genome in Helicobacter pylori prophages at both the genome and gene level. In the genome-level analysis, we applied, for the first time, chromosome painting and fineSTRUCTURE algorithms to a phage species, and showed novel trends in inter-population genetic flux. Notably, hpEastAsia is a phage population that imported a higher proportion of DNA fragments from other phages, whereas the hpSWEurope phages showed weaker signatures of inter-population recombination, suggesting genetic isolation. The gene-level analysis showed that, after parameter tuning of the prokaryote pan-genome analysis program, H. pylori phages have a pan-genome consisting of 75 genes and a soft-core genome of 10 genes, which includes genes involved in the lytic and lysogenic life cycles. Quantitative analysis of recombination events of the soft-core genes showed no substantial variation in the intensity of recombination across the genes, but rather equally frequent recombination among housekeeping genes that were previously reported to be less prone to recombination. The signature of frequent recombination appears to reflect the host-phage evolutionary arms race, either by contributing to escape from bacterial immunity or by protecting the host by producing defective phages.\n\nAnalysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species.", "token_count": 409, "char_count": 1766, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6138, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:37.390693", "source": { "split": "train_shard_00001", "doc_id": 3251 }, "chunk_id": "train_shard_00001_3251_0", "global_id": 10271 }, { "text": "Ralstonia pickettii is a Gram-negative rod which may cause invasive infections when they contaminate liquid medical products. After R. pickettii was detected in blood cultures and a stem cell product from three patients in a tertiary care hospital in Germany, whole genome sequencing of these three isolates and two water isolates from the environment was performed. Core genome multilocus sequence typing analysis showed that the three patient isolates were closely related and there was a large distance to the environmental isolates. In a genomic comparison, the patients' isolates were distantly related to an R. pickettii strain from a cluster in Australia suspected to be caused by contaminated saline produced in India, while all liquid medical products with a link to all patients were produced in Europe or the United States. Our data point towards an ongoing risk by an unknown common source that could be traced back to medical products contaminated with R. pickettii and potentially distributed worldwide. Investigating invasive R. pickettii infections, identifying and testing medical products administered to the patients and timely whole genome sequencing may help identify the exact source of this potentially global outbreak.\n\nRalstonia pickettii bloodstream infections with potential genomic link to internationally distributed contaminated saline solution, Germany, October 2023.", "token_count": 325, "char_count": 1440, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:37.959781", "source": { "split": "train_shard_00001", "doc_id": 3252 }, "chunk_id": "train_shard_00001_3252_0", "global_id": 10272 }, { "text": "The proteobacterial antimicrobial compound efflux (PACE) family of transport proteins was only recently described. PACE family transport proteins can confer resistance to a range of biocides used as disinfectants and antiseptics, and are encoded by many important Gram-negative human pathogens. However, we are only just beginning to appreciate the range of functions and the mechanism(s) of transport operating in these proteins. Genes encoding PACE family proteins are typically conserved in the core genomes of bacterial species rather than on recently acquired mobile genetic elements, suggesting that they confer important core functions in addition to biocide resistance. Three-dimensional structural information is not yet available for PACE family proteins. However, PACE proteins have several very highly conserved amino acid sequence motifs that are likely to be important for substrate transport. PACE proteins also display strong amino acid sequence conservation between their N and C-terminal halves, suggesting that they evolved by duplication of an ancestral protein comprised of two transmembrane helices. In light of their drug resistance functions in Gram-negative pathogens, PACE proteins should be the subject of detailed future investigation.\n\nPacing across the membrane: the novel PACE family of efflux pumps is widespread in Gram-negative pathogens.", "token_count": 291, "char_count": 1372, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6134, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:38.512727", "source": { "split": "train_shard_00001", "doc_id": 3253 }, "chunk_id": "train_shard_00001_3253_0", "global_id": 10273 }, { "text": "The genomes of bacteria and archaea evolve by extensive loss and gain of genes which, for any group of related prokaryotic genomes, result in the formation of a pangenome with the universal, asymmetrical U-shaped distribution of gene commonality. To elucidate the evolutionary factors that define the specific shape of this distribution, we investigate the fit of simple models of genome evolution to the empirically observed gene commonality distributions and genomes intersections for 33 groups of closely related bacterial genomes. The combined analysis of genome intersections and gene commonality shows that at least one of the two simplifying assumptions that are usually adopted for modeling the evolution of the U-shaped distribution, those of infinitely many genes and constant genome size, is invalid. The violation of both these assumptions stems from the horizontal gene transfer barrier, i.e . the cost of accommodation of foreign genes by prokaryotes.\n\nHorizontal gene transfer barrier shapes the evolution of prokaryotic pangenomes", "token_count": 215, "char_count": 1046, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:38.984009", "source": { "split": "train_shard_00001", "doc_id": 3254 }, "chunk_id": "train_shard_00001_3254_0", "global_id": 10274 }, { "text": "Fecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode of action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre and post intervention, for the treatment of ten different disease indications. We quantified strain-level dynamics of 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. Donor strain colonization and recipient strain resilience were mostly independent of clinical outcomes, but accurately predictable using LASSO-regularized regression models that accounted for host, microbiome and procedural variables. Recipient factors and donor-recipient complementarity, encompassing entire microbial communities to individual strains, were the main determinants of strain population dynamics, providing insights into the underlying processes that shape the post-FMT gut microbiome. Applying an ecology-based framework to our findings indicated parameters that may inform the development of more effective, targeted microbiome therapies in the future, and suggested how patient stratification can be used to enhance donor microbiota colonization or the displacement of recipient microbes in clinical practice.\n\nDrivers and determinants of strain dynamics following fecal microbiota transplantation.", "token_count": 314, "char_count": 1406, "word_count": 178, "semantic_coherence": 1, "information_density": 0.7247, "quality_score": 0.8624, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:39.567579", "source": { "split": "train_shard_00001", "doc_id": 3255 }, "chunk_id": "train_shard_00001_3255_0", "global_id": 10275 }, { "text": "

Background

Carbapenem-resistant Enterobacterales (CRE) are a significant threat to worldwide public health, resulting in increased morbidity, death, hospitalization time and healthcare expenses. Here, the genomic and phylogenetic characteristics of a multidrug-resistant Escherichia coli isolate carrying both the new mcr-1.33 variant and bla NDM-5 gene obtained from a urinary tract infection in China are investigated.

Methods

Antimicrobial susceptibility of E. coli 779 was evaluated by using the broth microdilution method. Short-read Illumina NovaSeq 6000 and long-read Oxford Nanopore MinION platforms were applied to sequence the bacterial whole genomic DNA and then de novo assembled. The genome sequence was annotated using the NCBI Prokaryotic Genome Annotation Pipeline and further subjected to identify the sequence type (ST), capsular type, and antibiotic resistance genes. BacWGSTdb 2.0 was used to perform the core genome multilocus sequence typing (cgMLST) analysis with other closely related E. coli isolates deposited in the public database.

Results

E. coli 779 was resistant to aztreonam, levofloxacin, fosfomycin, cefoxitin, cefepime, cefotaxime, imipenem, meropenem, polymyxin, and tigecycline. The complete genome sequence of E. coli 779 is made up of nine contigs totaling 5,667,876 bp, including one chromosome and eight plasmids. The isolate was assigned to ST101, serotype O-:H31, and phylogroup B1", "token_count": 479, "char_count": 1506, "word_count": 193, "semantic_coherence": 1, "information_density": 0.715, "quality_score": 0.8575, "entities": { "genes": [ "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:40.238570", "source": { "split": "train_shard_00001", "doc_id": 3256 }, "chunk_id": "train_shard_00001_3256_0", "global_id": 10276 }, { "text": "The colistin resistance gene mcr-1.33 (located in a 242,460 bp IncHI2/IncHI2A plasmid) and the β-lactam resistance gene bla NDM-5 (located in a 46,161 bp IncX3 plasmid) were among the 27 antimicrobial resistance genes discovered. The closest relative of E. coli 779, another ST101 strain (E. coli 443) obtained from a sewage sample in Shandong, China in 2015, differs by only 24 cgMLST alleles.

Conclusion

We discovered the first multidrug-resistant ST101 E. coli strain with plasmid-mediated mcr-1.33 variant and bla NDM-5 gene in China. These findings would help us to better understanding the genomic traits, antimicrobial resistance mechanisms and epidemiological aspects of this bacterial pathogen.\n\nEmergence of a Multidrug-Resistant Escherichia coli Co-Carrying a New mcr-1.33 Variant and bla NDM-5 Genes Recovered from a Urinary Tract Infection.", "token_count": 376, "char_count": 963, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": { "genes": [ "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:40.859316", "source": { "split": "train_shard_00001", "doc_id": 3256 }, "chunk_id": "train_shard_00001_3256_1", "global_id": 10277 }, { "text": "Objective: To analyze the drug resistance and genomic characteristics of Salmonella enterica serovar London isolated from clinical and food sources in Hangzhou City from 2017 to 2021. Methods: A total of 91 Salmonella enterica serovar London strains isolated from Hangzhou City from 2017 to 2021 were analyzed for drug susceptibility, pulsed field gel electrophoresis (PFGE) typing and whole genome sequencing. Multilocus sequence typing (MLST), core genome multilocus sequence typing (cgMLST) and detection of drug resistance genes were performed by using the sequencing data. Phylogenetic analysis was conducted to compare the 91 genomes from Hangzhou City with 347 genomes from public databases. Results: No significant difference in the drug resistance rate was observed between clinical strains and food strains to 18 drugs in Hangzhou City(all P>0.05), and the multidrug resistance (MDR) rate was 75.8% (69/91). Most strains were resistant to 7 drug classes simultaneously. One strain was resistant to Polymyxin E as well as positive for mcr-1.1, and 50.5% (46/91) of the strains were resistant to Azithromycin and were positive for mph(A). All 91 Salmonella enterica serovar London strains were ST155, which were subdivided into 44 molecular types by PFGE and 82 types by cgMLST. Phylogenetic analysis showed that most strains from Hangzhou City (83/91) were clustered together, and a small number of human isolates from Europe, North America and pork isolates from Hubei and Shenzhen were mixed in the cluster. Other strains from Hangzhou City (8/91) were closely related to strains from Europe, America and Southeast Asia", "token_count": 514, "char_count": 1700, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5385, "quality_score": 0.7692, "entities": { "genes": [ "ST155" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:41.518410", "source": { "split": "train_shard_00001", "doc_id": 3257 }, "chunk_id": "train_shard_00001_3257_0", "global_id": 10278 }, { "text": "Strains isolated from pork were the most closely related to clinical strains. Conclusion: The epidemic of Salmonella enterica serovar London in Hangzhou City is mainly caused by the spread of ST155 strains, which is mainly transmitted locally. At the same time, cross-region transmission to Europe, North America, Southeast Asia, and other provinces and cities in China may also occur. There is no significant difference in the drug resistance rate between clinical strains and food strains, and a high level of MDR is found in the strains. Clinical infection of Salmonella enterica serovar London may be closely related to pork consumption in Hangzhou City.\n\n[Drug resistance and genomic characteristics of Salmonella enterica serovar London from clinical and food sources in Hangzhou City from 2017 to 2021].", "token_count": 224, "char_count": 845, "word_count": 125, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [ "ST155" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:41.994204", "source": { "split": "train_shard_00001", "doc_id": 3257 }, "chunk_id": "train_shard_00001_3257_1", "global_id": 10279 }, { "text": "

Aims

There are knowledge gaps regarding STEC and EPEC strains in livestock in Jiangsu, China. This study aimed to evaluate the potential public health significance of STEC and EPEC strains isolated from livestock by determining the serotypes, virulence profiles, and genetic relationship with international STEC strains.

Methods and results

A total of 68 STEC and 37 EPEC strains were obtained from 231 faecal sheep samples and 70 faecal cattle samples. By using whole-genome sequencing (WGS) analysis, all STEC belonged to 15 O: H serotypes, and the most prevalent serotypes were O6:H10 (19.1%), O155:H21 (14.7%), and O21:H25 (10.3%). The main Shiga toxin gene subtypes detected were stx1c (41.2%), stx1a (26.5%), stx2b (14.7%), and stx2k (14.7%). Only the STEC from cattle carried eae gene. Other adherence-associated or toxin-related genes, including lpfA (70.6%), iha (48.5%), subA (54.4%), and ehxA (33.8%), were found in STEC. All EPEC strains were bfpA-negative, and the predominant eae variants were eae-β1 (62.2%), eae-ζ (21.6%), and eae-θ (8.1%). The core-genome multi-locus sequence typing (cgMLST) analysis revealed nine scattered clusters in STEC and one dominant cluster in EPEC. The strains with the same serotypes, including O22:H8 and O43:H2 in the two towns, possessed a closely genomic distance", "token_count": 463, "char_count": 1328, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6907, "quality_score": 0.8454, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:42.633987", "source": { "split": "train_shard_00001", "doc_id": 3258 }, "chunk_id": "train_shard_00001_3258_0", "global_id": 10280 }, { "text": "The core genome single-nucleotide polymorphism (cgSNP) showed that part of STEC strains in this study was clustered with isolates possessing the same serotypes from the Netherlands, Sweden, and Xinjiang of China. Five serotypes of STEC isolates were associated with the clinical STEC strains from databases.

Conclusion

This study provided the diverse serotypes and the virulence genes profiles in STEC and EPEC strains. Local strains possessed widely diverse and scattered clusters by cgMLST. Closely genomic correlation with clinical isolates displayed that part of the STEC strains may threaten to public health.

Significance and impact of the study

Non-O157 STEC strains act as important pathogens for human infections. This study supports the increased surveillance work of non-O157 STEC rather than just O157 STEC in this region.\n\nGenetic and phylogenetic characterization of Shiga toxin-producing Escherichia coli and enteropathogenic E. coli from livestock in Jiangsu by using whole-genome sequencing.", "token_count": 275, "char_count": 1022, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6312, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:43.186800", "source": { "split": "train_shard_00001", "doc_id": 3258 }, "chunk_id": "train_shard_00001_3258_1", "global_id": 10281 }, { "text": "Switzerland has one of the highest annual Legionnaires’ disease (LD) notification rates in Europe (7.8 cases/ 100,000 population in 2021). The main sources of infection and the cause for this high rate remain largely unknown. This hampers the implementation of targeted Legionella spp. control efforts. The SwissLEGIO national case-control and molecular source attribution study investigates risk factors and infection sources for community-acquired LD in Switzerland. Over the duration of one year, the study is recruiting 205 newly diagnosed LD patients through a network of 20 university and cantonal hospitals. Healthy controls matched for age, sex, and residence at district level are recruited from the general population. Risk factors for LD are assessed in questionnaire-based interviews. Clinical and environmental Legionella spp. isolates are compared using whole genome sequencing (WGS). Direct comparison of sero- and sequence types (ST), core genome multilocus sequencing types (cgMLST), and single nucleotide polymorphisms (SNPs) between clinical and environmental isolates are used to investigate infection sources and the prevalence and virulence of different Legionella spp. strains detected across Switzerland. The SwissLEGIO study innovates in combining case-control and molecular typing approaches for source attribution on a national level outside an outbreak setting. The study provides a unique platform for national Legionellosis and Legionella research and is conducted in an inter- and transdisciplinary, co-production approach involving various national governmental and national research stakeholders.\n\nLegionnaires’ disease in Switzerland: Rationale and study protocol of a prospective national case-control and molecular source attribution study (SwissLEGIO)", "token_count": 394, "char_count": 1795, "word_count": 242, "semantic_coherence": 1, "information_density": 0.595, "quality_score": 0.7975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:43.807556", "source": { "split": "train_shard_00001", "doc_id": 3259 }, "chunk_id": "train_shard_00001_3259_0", "global_id": 10282 }, { "text": "Pseudomonas aeruginosa is responsible for long-term infections and is particularly resistant to treatments when hiding inside the extracellular matrix or biofilms. Phage therapy might represent an alternative to antibiotic treatment, but up to 10% of clinical strains appear to resist multiple phages. We investigated the characteristics of P. aeruginosa clinical strains naturally resistant to phages and compared them to highly susceptible strains. The phage-resistant strains were defective in lipopolysaccharide (LPS) biosynthesis, were nonmotile and displayed an important degree of autolysis, releasing phages and pyocins. Complete genome sequencing of three resistant strains showed the existence of a large accessory genome made of multiple insertion elements, genomic islands, pyocins and prophages, including two phages performing lateral transduction. Mutations were found in genes responsible for the synthesis of LPS and/or type IV pilus, the major receptors for most phages. CRISPR-Cas systems appeared to be absent or inactive in phage-resistant strains, confirming that they do not play a role in the resistance to lytic phages but control the insertion of exogenous sequences. We show that, despite their apparent weakness, the multiphage-resistant strains described in this study displayed selective advantages through the possession of various functions, including weapons to eliminate other strains of the same or closely related species.\n\nThe Basis for Natural Multiresistance to Phage in Pseudomonas aeruginosa.", "token_count": 368, "char_count": 1554, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:44.395885", "source": { "split": "train_shard_00001", "doc_id": 3260 }, "chunk_id": "train_shard_00001_3260_0", "global_id": 10283 }, { "text": "

Introduction

Streptococcus equi subspecies equi (S. equi) is the causative agent of strangles, which is one of the most common and highly contagious respiratory infectious illnesses in horses. Streptococcus equi (S. equi) is a horse-specific pathogen that originated from the closely related zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). Despite decades of research, the movement of genetic material across host-restricted diseases remains a mystery.

Methods

Three S. equi donkey isolates (HTP133, HTP232, and HT1112) were recently isolated from a strangles epidemic on donkey farms in China's Xinjiang Province. In this study, we performed a comprehensive comparative analysis of these isolates using whole genome sequencing and compared them to the published genomic sequences of equine strain S. equi 4047 to uncover evidence of genetic events that shaped the evolution of these donkey S. equi isolates' genomes.

Results

Whole genome sequencing indicated that both strains were closely related, with comparable gene compositions and a high rate of shared core genomes (1788-2004). Our comparative genomic study indicated that the genome structure is substantially conserved across three donkey strains; however, there are several rearrangements and inversions when compared to the horse isolate S. equi 4047. The virulence factors conveyed by genomic islands and prophages, in particular, played a key role in shaping the pathogenic capacity and genetic diversity of these S. equi strains", "token_count": 486, "char_count": 1640, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6326, "quality_score": 0.8163, "entities": { "genes": [ "HTP232", "HTP133", "HT1112" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:45.047706", "source": { "split": "train_shard_00001", "doc_id": 3261 }, "chunk_id": "train_shard_00001_3261_0", "global_id": 10284 }, { "text": "Furthermore, we discovered that the HT133 isolate had a strong colonization ability and increased motility; the HT1112 isolates had a significantly higher ability for antimicrobial resistance and biofilm formation, and the HT232 isolate gained pathogenic specialization by acquiring a bacteriophage encoding hyaluronate lyase.

Discussion

In summary, our findings show that genetic exchange across S. equi strains influences the development of the donkey S. equi genome, offering important genetic insights for future epidemiological studies of S. equi infection.\n\nComplete genome sequencing and comparative genomic analysis of three donkey Streptococcus equi subsp. equi isolates.", "token_count": 198, "char_count": 722, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7444, "quality_score": 0.8722, "entities": { "genes": [ "HT232", "HT133", "HT1112" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:45.497638", "source": { "split": "train_shard_00001", "doc_id": 3261 }, "chunk_id": "train_shard_00001_3261_1", "global_id": 10285 }, { "text": "Staphylococcus aureus colonizes 30% of the human population, but only a few clones cause severe infections. S. aureus’ virulence varies and partly depends on the presence of prophages, viral DNA embedded in the S. aureus core genome, such as hlb-converting prophage (ϕSa3int). Human-adapted S. aureus often harbours a ϕSa3int group of prophages preferentially integrated into their β-hemolysin ( hlb ) gene that encodes human immune evasion cluster (IEC) genes. Exotoxins and immune modulatory molecules encoded by this prophage can inhibit human innate immunity increasing S. aureus pathogenicity. This study aims to investigate the genomic and phenotypic plasticity of S. aureus and changes in its extracellular proteome after the acquisition of ϕSa3int prophage. To achieve this, we used S. aureus strains isolated from the sinus cavities of a patient with severe chronic rhinosinusitis (CRS) at two different time points ( S. aureus SA222 and S. aureus SA333) and hybrid sequenced the strains using short-read Illumina and long-read Oxford nanopore technology. In silico analysis showed the presence of a ϕSa3int prophage in the later isolate but not in the earlier isolate while most of the core genes remained identical. Using mitomycin C, we induced the ϕSa3int prophage, and transduced it into the Sa3int-prophage-free SA222 isolate to obtain a laboratory generated ‘double lysogen’. We confirmed the successful lysogenisation with culture methods (spot assay, blood agar) and also by sequencing. We compared growth kinetics, biofilm biomass and metabolic activity between parent and the lysogen by establishing growth curves, crystal violet and resazurin assays. Exoproteins were identified and quantified using mass spectrophotometry. Integration of ϕSa3int prophage in SA222 down-regulated the beta-hemolysin expression of the lysogen . In silico analysis of the S", "token_count": 522, "char_count": 1875, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6426, "quality_score": 0.8213, "entities": { "genes": [ "SA222", "SA333" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:46.157474", "source": { "split": "train_shard_00001", "doc_id": 3262 }, "chunk_id": "train_shard_00001_3262_0", "global_id": 10286 }, { "text": "aureus genome confirmed the insertion of a ∼43.8 kb ϕSa3int prophage into hlb gene. Insertion of prophage DNA did not alter the growth kinetics, biofilm formation, adhesion to primary human nasal epithelial cells and the metabolic activity in a biofilm. However, the acquisition of ϕSa3int prophage significantly changed the expression of various secreted proteins, both bacterial and prophage-encoded. Altogether, thirty-eight exoproteins were significantly differentially regulated in the laboratory created lysogen, compared to its recipient strain SA222. Among these proteins, there was significant upregulation of 21 exoproteins (55.3 %) including staphylokinase (sak), SCIN (scn), and intercellular adhesion protein B (icaB) and downregulation of 17 exoproteins (44.7 %), including β-hemolysin (hlb/sph) and outer membrane porin (phoE). Most of the upregulated proteins were involved in immunomodulation that help S. aureus escape human innate immunity and help cause chronic infection. These findings may contribute to the development of novel approaches to render S. aureus susceptible to the immune response by blocking prophage-associated defence mechanisms.

Highlights

A ϕSa3int prophage preferentially integrates into the β-haemolysin gene ( hlb ) gene thereby disrupting the beta-hemolysin function. A ∼43.8 kb ϕSa3int prophage acquisition by S. aureus has no impact on its growth kinetics, biofilm formation and adhesion to primary human nasal epithelial cells (HNECs). The presence of a ϕSa3int group prophage likely enhances Staphylococcus aureus’ human immune evasion capability as the prophage encodes a complete set of immune evasion cluster (IEC) genes. Targeted identification of virulence factors in addition to species and strain identification may lead to better-personalized therapy as not all S. aureus carry the same virulence genes.", "token_count": 518, "char_count": 1869, "word_count": 261, "semantic_coherence": 1, "information_density": 0.613, "quality_score": 0.8065, "entities": { "genes": [ "SA222" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:46.807756", "source": { "split": "train_shard_00001", "doc_id": 3262 }, "chunk_id": "train_shard_00001_3262_1", "global_id": 10287 }, { "text": "Prophage acquisition byStaphylococcus aureuscontributes to the expansion of Staphylococcal immune evasion", "token_count": 35, "char_count": 112, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:47.162443", "source": { "split": "train_shard_00001", "doc_id": 3262 }, "chunk_id": "train_shard_00001_3262_2", "global_id": 10288 }, { "text": "Diarrheal diseases remain one of the leading causes of death for children under 5 globally, disproportionately impacting those living in low- and middle-income countries (LMIC). Campylobacter spp., a zoonotic pathogen, is one of the leading causes of food-borne infection in humans. Yet to be cultured Campylobacter spp. contribute to the total burden in diarrheal disease in children living in LMIC thus hampering interventions. We performed microbiome profiling and metagenomic genome assembly on samples collected from over 100 infant rhesus macaques longitudinally and during cases of clinical diarrhea within the first year of life. Acute diarrhea was associated with long-lasting taxonomic and functional shifts of the infant gut microbiome indicative of microbiome immaturity. We constructed 36 Campylobacter metagenomic assembled genomes (MAGs), many of which fell within 4 yet to be cultured species. Finally, we compared the uncultured Campylobacter MAGs assembled from infant macaques with publicly available human metagenomes to show that these uncultured species are also found in human fecal samples from LMIC. These data highlight the importance of unculturable Campylobacter spp. as an important target for reducing disease burden in LMIC children.\n\nInfant diarrheal disease in rhesus macaques impedes microbiome maturation and is linked to uncultured Campylobacter species.", "token_count": 341, "char_count": 1390, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:47.730597", "source": { "split": "train_shard_00001", "doc_id": 3263 }, "chunk_id": "train_shard_00001_3263_0", "global_id": 10289 }, { "text": "Characterization and stability of lactobacilli and yeasts from kefir grains using culture-dependent and culture-independent methods were investigated in this study. Culture-dependent analysis, followed by sequencing of 16S ribosomal DNA for bacteria and 26S rRNA gene for yeasts, revealed 3 different species of lactobacilli and yeasts, respectively. The most frequently isolated bacterial species were Lactobacillus kefiranofaciens ssp. kefirgranum, Lb. parakefiri, and Lb. kefiri, whereas yeasts belonged to Kluyveromyces marxianus, Kazachstania exigua, and Rhodosporidium kratochvilovae. This study is the first to report on the presence of R. kratochvilovae in kefir grains. On the other hand, PCR-denaturing gradient gel electrophoresis in the culture-independent method showed that the dominant microorganisms were Lb. kefiranofaciens ssp. kefirgranum, Kl. marxianus and Ka. exigua, but did not reveal bands corresponding to Lb. parakefiri, Lb. kefiri, or R. kratochvilovae. Our results support the necessity of combining more techniques for detailed and reliable study of microbial communities in kefir grains. Another interesting finding confirmed that the detected dominant microbiota of kefir grains is very stable and did not change over experimental time. This finding is important to ensure consistent product quality.\n\nCharacterization and stability of lactobacilli and yeast microbiota in kefir grains.", "token_count": 383, "char_count": 1417, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:48.322820", "source": { "split": "train_shard_00001", "doc_id": 3264 }, "chunk_id": "train_shard_00001_3264_0", "global_id": 10290 }, { "text": "Vibrio parahaemolyticus is the leading cause of seafood-borne gastroenteritis worldwide. As reported in other countries, after the rise and fall of the pandemic strain in Chile, other post-pandemic strains have been associated with clinical cases, including strains lacking the major toxins TDH and TRH. Since the presence or absence of tdh and trh genes has been used for diagnostic purposes and as a proxy of the virulence of V. parahaemolyticus isolates, the understanding of virulence in V. parahaemolyticus strains lacking toxins is essential to detect these strains present in water and marine products to avoid possible food-borne infection. In this study, we characterized the genome of four environmental and two clinical non-toxigenic strains (tdh-, trh-, and T3SS2-). Using whole-genome sequencing, phylogenetic, and comparative genome analysis, we identified the core and pan-genome of V. parahaemolyticus of strains of southern Chile. The phylogenetic tree based on the core genome showed low genetic diversity but the analysis of the pan-genome revealed that all strains harbored genomic islands carrying diverse virulence and fitness factors or prophage-like elements that encode toxins like Zot and RTX. Interestingly, the three strains carrying Zot-like toxin have a different sequence, although the alignment showed some conserved areas with the zot sequence found in V. cholerae. In addition, we identified an unexpected diversity in the genetic architecture of the T3SS1 gene cluster and the presence of the T3SS2 gene cluster in a non-pandemic environmental strain. Our study sheds light on the diversity of V. parahaemolyticus strains from the southern Pacific which increases our current knowledge regarding the global diversity of this organism.", "token_count": 485, "char_count": 1846, "word_count": 262, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:48.974187", "source": { "split": "train_shard_00001", "doc_id": 3265 }, "chunk_id": "train_shard_00001_3265_0", "global_id": 10291 }, { "text": "Exploring the Genomic Traits of Non-toxigenic Vibrio parahaemolyticus Strains Isolated in Southern Chile.", "token_count": 38, "char_count": 112, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:49.342013", "source": { "split": "train_shard_00001", "doc_id": 3265 }, "chunk_id": "train_shard_00001_3265_1", "global_id": 10292 }, { "text": "Typhoid fever is transmitted by ingestion of polluted water, contaminated food, and stool of typhoid-infected individuals, mostly in developing countries with poor hygienic environments. To find novel therapeutic targets and inhibitors, We employed a subtractive genomics strategy towards Salmonella Typhi and the complete genomes of eight strains were primarily subjected to the EDGAR tool to predict the core genome (n = 3207). Human non-homology (n = 2450) was followed by essential genes identification (n = 37). The STRING database predicted maximum protein-protein interactions, followed by cellular localization. The virulent/immunogenic ability of predicted genes were checked to differentiate drug and vaccine targets. Furthermore, the 3D models of the identified putative proteins encoded by the respective genes were constructed and subjected to druggability analyses where only “highly druggable” proteins were selected for molecular docking and simulation analyses. The putative targets ATP-dependent CLP protease proteolytic subunit, Imidazole glycerol phosphate synthase hisH, 7,8-dihydropteroate synthase folP and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmI were screened against a drug-like library (n = 12000) and top hits were selected based on H-bonds, RMSD and energy scores. Finally, the ADMET properties for novel inhibitors ZINC19340748, ZINC09319798, ZINC00494142, ZINC32918650 were optimized followed by binding free energy (MM/PBSA) calculation for ligand-receptor complexes. The findings of this work are expected to aid in expediting the identification of novel protein targets and inhibitors in combating typhoid Salmonellosis, in addition to the already existing therapies.", "token_count": 488, "char_count": 1725, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6826, "quality_score": 0.8413, "entities": { "genes": [ "ZINC00494142", "ZINC32918650", "ZINC09319798", "ZINC19340748" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:49.993459", "source": { "split": "train_shard_00001", "doc_id": 3266 }, "chunk_id": "train_shard_00001_3266_0", "global_id": 10293 }, { "text": "Genomic landscape of the emerging XDR Salmonella Typhi for mining druggable targets clpP, hisH, folP and gpmI and screening of novel TCM inhibitors, molecular docking and simulation analyses", "token_count": 48, "char_count": 190, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:50.354510", "source": { "split": "train_shard_00001", "doc_id": 3266 }, "chunk_id": "train_shard_00001_3266_1", "global_id": 10294 }, { "text": "O-antigens are glycopolymers in lipopolysaccharides expressed on the cell surface of Gram-negative bacteria. Variability in the O-antigen structure constitutes the basis for the establishment of the serotyping schema. We pursued a two-pronged approach to define the basis for O-antigen structural diversity. First, we developed a bottom-up systems biology approach to O-antigen metabolism by building a reconstruction of Salmonella O-antigen biosynthesis and used it to (i) update 410 existing Salmonella strain-specific metabolic models, (ii) predict a strain's serogroup and its O-antigen glycan synthesis capability (yielding 98% agreement with experimental data), and (iii) extend our workflow to more than 1,400 Gram-negative strains. Second, we used a top-down pangenome analysis to elucidate the genetic basis for intraserogroup O-antigen structural variations. We assembled a database of O-antigen gene islands from over 11,000 sequenced Salmonella strains, revealing (i) that gene duplication, pseudogene formation, gene deletion, and bacteriophage insertion elements occur ubiquitously across serogroups; (ii) novel serotypes in the group O:4 B2 variant, as well as an additional genotype variant for group O:4, and (iii) two novel O-antigen gene islands in understudied subspecies. We thus comprehensively defined the genetic basis for O-antigen diversity.IMPORTANCE Lipopolysaccharides are a major component of the outer membrane in Gram-negative bacteria. They are composed of a conserved lipid structure that is embedded in the outer leaflet of the outer membrane and a polysaccharide known as the O-antigen. O-antigens are highly variable in structure across strains of a species and are crucial to a bacterium's interactions with its environment. They constitute the first line of defense against both the immune system and bacteriophage infections and have been shown to mediate antimicrobial resistance", "token_count": 504, "char_count": 1948, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:51.017296", "source": { "split": "train_shard_00001", "doc_id": 3267 }, "chunk_id": "train_shard_00001_3267_0", "global_id": 10295 }, { "text": "The significance of our research is in identifying the metabolic and genetic differences within and across O-antigen groups in Salmonella strains. Our effort constitutes a first step toward characterizing the O-antigen metabolic network across Gram-negative organisms and a comprehensive overview of genetic variations in Salmonella.\n\nSystems Biology and Pangenome of Salmonella O-Antigens.", "token_count": 104, "char_count": 411, "word_count": 52, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:51.454703", "source": { "split": "train_shard_00001", "doc_id": 3267 }, "chunk_id": "train_shard_00001_3267_1", "global_id": 10296 }, { "text": "

Objective

Epigallocatechin gallate (EGCG), the major antimicrobial tea polyphenol, has been reported to inhibit the growth of Candida albicans planktonic cells and enhance the antifungal activity of antimycotics. We hypothesised that synergism exists between EGCG and conventional antimycotics against biofilms of Candida species.

Design

The minimal inhibitory concentrations (MIC) of EGCG, miconazole, fluconazole and amphotericin B against planktonic cells and the sessile MIC (SMIC) against biofilms of Candida albicans, Candida parapsilosis, Candida tropicalis, Candida glabrata, Candida kefyr and Candida krusei were determined by a microdilution method. For assessment of biofilm metabolic activity, the 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT) assay was used. The interactions between EGCG and antimycotics were evaluated by checkerboard microdilution assay and determined by fractional inhibitory concentration index (FIC).

Results

Synergism was observed between EGCG and miconazole, fluconazole or amphotericin B against most test planktonic and biofilm cells of Candida species (FIC≤0.5). All biofilm cells were significantly more resistant to EGCG and antimycotics (20-3200 times higher) compared with their planktonic counterparts.

Conclusions

We conclude that EGCG enhances the antifungal effects of miconazole, fluconazole and amphotericin B. Combined treatment with EGCG may lower the dosages of antimycotics, thus preventing adverse effects and the emergence of drug-resistant oral Candida species.", "token_count": 485, "char_count": 1580, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5842, "quality_score": 0.7921, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:52.131922", "source": { "split": "train_shard_00001", "doc_id": 3268 }, "chunk_id": "train_shard_00001_3268_0", "global_id": 10297 }, { "text": "Synergistic effects of tea catechin epigallocatechin gallate and antimycotics against oral Candida species.", "token_count": 30, "char_count": 107, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:52.512226", "source": { "split": "train_shard_00001", "doc_id": 3268 }, "chunk_id": "train_shard_00001_3268_1", "global_id": 10298 }, { "text": "Salmonella enterica serovar Agona has caused multiple food-borne outbreaks of gastroenteritis since it was first isolated in 1952. We analyzed the genomes of 73 isolates from global sources, comparing five distinct outbreaks with sporadic infections as well as food contamination and the environment. Agona consists of three lineages with minimal mutational diversity: only 846 single nucleotide polymorphisms (SNPs) have accumulated in the non-repetitive, core genome since Agona evolved in 1932 and subsequently underwent a major population expansion in the 1960s. Homologous recombination with other serovars of S. enterica imported 42 recombinational tracts (360 kb) in 5/143 nodes within the genealogy, which resulted in 3,164 additional SNPs. In contrast to this paucity of genetic diversity, Agona is highly diverse according to pulsed-field gel electrophoresis (PFGE), which is used to assign isolates to outbreaks. PFGE diversity reflects a highly dynamic accessory genome associated with the gain or loss (indels) of 51 bacteriophages, 10 plasmids, and 6 integrative conjugational elements (ICE/IMEs), but did not correlate uniquely with outbreaks. Unlike the core genome, indels occurred repeatedly in independent nodes (homoplasies), resulting in inaccurate PFGE genealogies. The accessory genome contained only few cargo genes relevant to infection, other than antibiotic resistance. Thus, most of the genetic diversity within this recently emerged pathogen reflects changes in the accessory genome, or is due to recombination, but these changes seemed to reflect neutral processes rather than Darwinian selection. Each outbreak was caused by an independent clade, without universal, outbreak-associated genomic features, and none of the variable genes in the pan-genome seemed to be associated with an ability to cause outbreaks.\n\nNeutral genomic microevolution of a recently emerged pathogen, Salmonella enterica serovar Agona.", "token_count": 480, "char_count": 1942, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:53.186223", "source": { "split": "train_shard_00001", "doc_id": 3269 }, "chunk_id": "train_shard_00001_3269_0", "global_id": 10299 }, { "text": "Yeasts were isolated by the enrichment technique from the phylloplane of 94 samples of sugarcane leaf collected from seven provinces in Thailand. All sugarcane leaf samples contained yeasts and 158 yeast strains were obtained. On the basis of the D1/D2 domain of the large subunit rRNA gene sequence analysis, 144 strains were identified to 24 known species in 14 genera belonging to the Ascomycota viz. Candida akabanensis, Candida dendronema, Candida mesorugosa, Candida michaelii, Candida nivariensis, Candida rugosa, Candida orthopsilosis, Candida quercitrusa, Candida tropicalis, Candida xylopsoci, Cyberlindnera fabianii, Cyberlindnera rhodanensis, Debaryomyces nepalensis, Hannaella aff. coprosmaensis, Hanseniaspora guilliermondii, Kluyveromyces marxianus, Lachancea thermotolerans, Lodderomyces elongisporus, Metschnikowia koreensis, Meyerozyma caribbica, Millerozyma koratensis, Pichia kudriavzevii, Torulaspora delbrueckii and Wickerhamomyces edaphicus, and 12 species in six genera of the Basidiomycota viz . Cryptococcus flavescens, Cryptococcus laurentii, Cryptococcus rajasthanensis, Kwoniella heveanensis, Rhodosporidium fluviale, Rhodosporidium paludigenum, Rhodotorula mucilaginosa, Rhodotorula sesimbrana, Rhodotorula taiwanensis, Sporidiobolus ruineniae, Sporobolomyces carnicolor and Sporobolomyces nylandii. Seven strains were identical or similar to four undescribed species. Another seven strains represented four novels species in the genus Metschnikowia, Nakazawaea, Wickerhamomyces and Yamadazyma", "token_count": 500, "char_count": 1523, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6932, "quality_score": 0.8466, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:54.900652", "source": { "split": "train_shard_00001", "doc_id": 3270 }, "chunk_id": "train_shard_00001_3270_0", "global_id": 10300 }, { "text": "The results revealed 69 % of the isolated strains were ascomycete yeasts and 31 % were basidiomycete yeast. The most prevalent species was M. caribbica with a 23 % frequency of occurrence followed by Rh. taiwanensis (11 %) and C. tropicalis (10 %). All strains were assessed for indole-3-acetic acid (IAA) producing capability showing that 69 strains had the capability of producing IAA when cultivated in yeast extract peptone dextrose broth supplemented with 1 g/L L-tryptophan. The highest IAA concentration of 565.1 mg/L was produced by R. fluviale DMKU-RK253.\n\nDiversity of culturable yeasts in phylloplane of sugarcane in Thailand and their capability to produce indole-3-acetic acid.", "token_count": 218, "char_count": 690, "word_count": 106, "semantic_coherence": 1, "information_density": 0.7264, "quality_score": 0.8632, "entities": { "genes": [ "RK253" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:55.366583", "source": { "split": "train_shard_00001", "doc_id": 3270 }, "chunk_id": "train_shard_00001_3270_1", "global_id": 10301 }, { "text": "Weissella is a genus earlier considered a member of the family Leuconostocaceae, which was reclassified into the family Lactobacillaceae in 1993. Recently, there have been studies emphasizing the probiotic and anti-inflammatory potential of various species of Weissella, of which W. confusa and W. cibaria are the most representative. Other species within this genus include: W. paramesenteroides, W. viridescens, W. halotolerans, W. minor, W. kandleri, W. soli, W. ghanensis, W. hellenica, W. thailandensis, W. fabalis, W. cryptocerci, W. koreensis, W. beninensis, W. fabaria, W. oryzae, W. ceti, W. uvarum, W. bombi, W. sagaensis, W. kimchi, W. muntiaci, W. jogaejeotgali, W. coleopterorum, W. hanii, W. salipiscis, and W. diestrammenae. Weissella confusa, W. paramesenteroides, W. koreensis, and W. cibaria are among the few species that have been isolated from human samples, although the identification of these and other species is possible using metagenomics, as we have shown for inflammatory bowel disease (IBD) and healthy controls. We were able to isolate Weissella in gut-associated bacteria (post 24 h food deprivation and laxatives). Other sources of isolation include fermented food, soil, and skin/gut/saliva of insects/animals. With the potential for hospital and industrial applications, there is a concern about possible infections. Herein, we present the current applications of Weissella on its antimicrobial and anti-inflammatory mechanistic effects, the predisposing factors (e.g., vancomycin) for pathogenicity in humans, and the antimicrobials used in patients. To address the medical concerns, we examined 28 case reports focused on W", "token_count": 486, "char_count": 1660, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:56.017238", "source": { "split": "train_shard_00001", "doc_id": 3271 }, "chunk_id": "train_shard_00001_3271_0", "global_id": 10302 }, { "text": "confusa and found that 78.5% of infections were bacteremia (of which 7 were fatal; 1 for lack of treatment), 8 were associated with underlying malignancies, and 8 with gastrointestinal procedures/diseases of which 2 were Crohn’s disease patients. In cases of a successful resolution, commonly administered antibiotics included: cephalosporin, ampicillin, piperacillin-tazobactam, and daptomycin. Despite reports of Weissella-related infections, the evolving mechanistic findings suggest that Weissella are clinically treatable bacteria with emerging antimicrobial and probiotic benefits ranging from oral health, skin care, obesity, and inflammatory diseases to cancer.\n\nThe Weissella Genus: Clinically Treatable Bacteria with Antimicrobial/Probiotic Effects on Inflammation and Cancer.", "token_count": 211, "char_count": 786, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:56.487374", "source": { "split": "train_shard_00001", "doc_id": 3271 }, "chunk_id": "train_shard_00001_3271_1", "global_id": 10303 }, { "text": "The crude cell-free medium from a culture of Kluyveromyces marxianus var. bulgaricus was immobilized in a gelatin-water support, with an immobilization yield of 82.60% for inulinase activity. The optimum pH for both free and immobilized inulinase was the same (3.5) and the optimum temperatures were 55°C for the free and 60°C for the immobilized enzyme. The Arrhenius plots were linear and activation energies were 56.20 (free enzyme) and 20.27kJ/molK (immobilized enzyme). The kinetic parameters were calculated by Lineweaver-Burk plots and the V max and K m were 37.60IU/mg protein and 61.83mM for the free inulinase and 31.45IU/mg protein and 149.28mM for the immobilized enzyme, respectively. The operational stability of the immobilized inulinase was studied in a continuous fixed-bed column reactor for 33 days, at the end of which the sucrose conversion was 58.12%.\n\nSucrose hydrolysis by gelatin-immobilized inulinase from Kluyveromyces marxianus var. bulgaricus", "token_count": 316, "char_count": 971, "word_count": 143, "semantic_coherence": 1, "information_density": 0.5664, "quality_score": 0.7832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:57.047893", "source": { "split": "train_shard_00001", "doc_id": 3272 }, "chunk_id": "train_shard_00001_3272_0", "global_id": 10304 }, { "text": "In proteomics, peptide information within mass spectrometry data from a specific organism sample is routinely challenged against a protein sequence database that best represent such organism. However, if the species/strain in the sample is unknown or poorly genetically characterized, it becomes challenging to determine a database which can represent such sample. Building customized protein sequence databases merging multiple strains for a given species has become a strategy to overcome such restrictions. However, as more genetic information is publicly available and interesting genetic features such as the existence of pan- and core genes within a species are revealed, we questioned how efficient such merging strategies are to report relevant information. To test this assumption, we constructed databases containing conserved and unique sequences for ten different species. Features that are relevant for probabilistic-based protein identification by proteomics were then monitored. As expected, increase in database complexity correlates with pangenomic complexity. However, Mycobacterium tuberculosis and Bortedella pertusis generated very complex databases even having low pangenomic complexity or no pangenome at all. This suggests that discrepancies in gene annotation is higher than average between strains of those species. We further tested database performance by using mass spectrometry data from eight clinical strains from Mycobacterium tuberculosis , and from two published datasets from Staphylococcus aureus. We show that by using an approach where database size is controlled by removing repeated identical tryptic sequences across strains/species, computational time can be reduced drastically as database complexity increases.\n\nOn the impact of the pangenome and annotation discrepancies while building protein sequence databases for bacteria proteogenomics", "token_count": 365, "char_count": 1886, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:57.628803", "source": { "split": "train_shard_00001", "doc_id": 3273 }, "chunk_id": "train_shard_00001_3273_0", "global_id": 10305 }, { "text": "

Background

Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe.

Results

Genomes were obtained using a hybrid assembly strategy (Illumina and Nanopore) with fine-tuning of settings and inputs used in the Unicycler assembly pipeline, such as size selection of reads and quality trimming of the FASTQ files. The main characteristics and synteny of the genomes were compared. The three genomes mainly differed by their content in terms of mobile genetic elements, i.e. integrative conjugative elements (ICE) and insertion sequences (IS), a feature that impacts their structure. For instance, strain L15527, representing subtype3 (st3), harbours an exceptionally high number of ICEs, which results in a bigger-sized genome than all those previously described and could be associated with the propensity of st3 to gain and fix mutations through chromosomal transfer mechanisms. In contrast, strain F9160, of st1, is very close to the PG45 type strain isolated in 1961 in the USA, and harbours a huge number of IS. These features may be associated with an evolution towards a host-restricted state or in a \"closed\" host or environment reservoir until a recent re-emergence.

Conclusions

Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods.", "token_count": 520, "char_count": 2168, "word_count": 313, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "PG45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:35:58.283371", "source": { "split": "train_shard_00001", "doc_id": 3274 }, "chunk_id": "train_shard_00001_3274_0", "global_id": 10306 }, { "text": "Genomic features of Mycoplasma bovis subtypes currently circulating in France.", "token_count": 19, "char_count": 78, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:58.631798", "source": { "split": "train_shard_00001", "doc_id": 3274 }, "chunk_id": "train_shard_00001_3274_1", "global_id": 10307 }, { "text": "Yarrowia lipolytica ACA-DC 50109 has been reported to be an oleaginous yeast and significant quantities of lipids were accumulated inside the yeast cells. In this study, the INU1 gene encoding exo-inulinase cloned from Kluyveromyces marxianus CBS 6556 was ligated into the expression plasmid pINA1317 and expressed in the cells of the oleaginous yeast. The activity of the inulinase with 6 × His tag secreted by the transformant Z31 obtained was found to be 41.7U mL(-1) after cell growth for 78 h. After optimization of the medium and cultivation conditions for single cell oil production, the transformant could accumulate 46.3% (w/w) oil from inulin in its cells and cell dry weight was 11.6 g L(-1) within 78 h at the flask level. During the 2-L fermentation, the transformant could accumulate 48.3% (w/w) oil from inulin in its cells and cell dry weight was 13.3 g L(-1) within 78 h while the transformant could accumulate 50.6% (w/w) oil from extract of Jerusalem artichoke tubers in its cells and cell dry weight was 14.6 g L(-1) within 78 h. At the end of fermentation, most of the added sugar was utilized by the transformant cells. Over 91.5% of the fatty acids from the transformant cultivated in the extract of Jerusalem artichoke tubercles was C(16:0), C(18:1) and C(18:2), especially C(18:1) (58.5%).\n\nExpression of inulinase gene in the oleaginous yeast Yarrowia lipolytica and single cell oil production from inulin-containing materials.", "token_count": 454, "char_count": 1453, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5064, "quality_score": 0.7532, "entities": { "genes": [ "INU1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:59.266772", "source": { "split": "train_shard_00001", "doc_id": 3275 }, "chunk_id": "train_shard_00001_3275_0", "global_id": 10308 }, { "text": "We investigated the phylogeny of biofilm forming (BF) and non-biofilm forming (NBF) Escherichia coli (n = 114) from beef processing environment and genetic elements in their BF and persistence, by comparative genomic analysis. Phylogroup B1 made up the largest proportion of both BF (73.8%) and NBF (50.9%) groups. E. coli from all sources examined had mixed phylogroups except for those recovered from equipment after cleaning which were exclusively phylogroup B1. Both core genome and gene content trees showed a tree-wide spread of BF strains, with clusters including both BF and NBF strains. Genome wide association studies (GWAS) by Scoary or Pyseer did not find any genes/mutations overrepresented in the BF group. Retrospective analysis of phenotypes found significant correlation (P < 0.05) between BF ability and curli production, cellulose synthesis, and/or mobility. However, the BF group also included strains negative for curli and cellulose and/or missing encoding genes for the two traits. All curli and cellulose encoding genes were present in most genomes, regardless of their BF status. The degree of motility was correlated with both curli and cellulose production, and 80 common genes were overrepresented in all three trait positive groups. A PTS enzyme II and a subsidiary gluconate catabolism pathway, and an iron-dicitrate transport system were more abundant in the persisting E. coli group. These findings suggest gene function redundancy in E. coli for biofilm formation and additional substrate utilization and iron acquisition in its persistence.\n\nComparative genomic analyses of Escherichia coli from meat processing environment in relation to their biofilm formation and persistence", "token_count": 437, "char_count": 1712, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:35:59.901292", "source": { "split": "train_shard_00001", "doc_id": 3276 }, "chunk_id": "train_shard_00001_3276_0", "global_id": 10309 }, { "text": "Akkermansia muciniphila is a commensal bacterium using mucin as its sole carbon and nitrogen source. A. muciniphila is a promising candidate for next-generation probiotics to prevent inflammatory and metabolic disorders, including diabetes and obesity, and to increase the response to cancer immunotherapy. In this study, a comparative pan-genome analysis was conducted to investigate the genomic diversity and evolutionary relationships between complete genomes of 27 A. muciniphila strains, including KGMB strains isolated from healthy Koreans. The analysis showed that A. muciniphila strains formed two clades of group A and B in a phylogenetic tree constructed using 1,219 orthologous single-copy core genes. Interestingly, group A comprised of strains from human feces in Korea, whereas most of group B comprised strains from human feces in Europe and China, and from mouse feces. As group A and B branched, mucin hydrolysis played an important role in the stability of the core genome and drove evolution in the direction of defense against invading pathogens, survival in, and colonization in the mucus layer. In addition, WapA and anSME, which function in competition and post-translational modification of sulfatase, respectively, have been a particularly important selective pressure in the evolution of group A. KGMB strains in group A with anSME gene showed sulfatase activity, but KCTC 15667T in group B without anSME did not. Our findings revealed that KGMB strains evolved to gain an edge in the competition with other gut bacteria by increasing the utilization of sulfated mucin, which will allow it to become highly colonized in the gut environment.\n\nThe evolution and competitive strategies of Akkermansia muciniphila in gut.", "token_count": 466, "char_count": 1789, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5932, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:00.550898", "source": { "split": "train_shard_00001", "doc_id": 3277 }, "chunk_id": "train_shard_00001_3277_0", "global_id": 10310 }, { "text": "BackgroundCarbapenemase-producing Enterobacterales (CPE) are rapidly increasing worldwide, also in Europe. Although prevalence of CPE in Germany is comparatively low, the National Reference Centre for Multidrug-resistant Gram-negative Bacteria noted annually increasing numbers of NDM-5-producing Escherichia coli isolates.AimAs part of our ongoing surveillance programme, we characterised NDM-5-producing E. coli isolates received between 2013 and 2019 using whole genome sequencing (WGS).MethodsFrom 329 identified NDM-5-producing E. coli, 224 isolates from known geographical locations were subjected to Illumina WGS. Analyses of 222 sequenced isolates included multilocus sequence typing (MLST), core genome (cg)MLST and single-nucleotide polymorphism (SNP)-based analyses.ResultsResults of cgMLST revealed genetically distinct clusters for many of the 43 detected sequence types (ST), of which ST167, ST410, ST405 and ST361 predominated. The SNP-based phylogenetic analyses combined with geographical information identified sporadic cases of nosocomial transmission on a small spatial scale. However, we identified large clusters corresponding to clonal dissemination of ST167, ST410, ST405 and ST361 strains in consecutive years in different regions in Germany.ConclusionOccurrence of NDM-5-producing E. coli rose in Germany, which was to a large extent due to the increased prevalence of isolates belonging to the international high-risk clones ST167, ST410, ST405 and ST361. Of particular concern is the supra-regional dissemination of these epidemic clones. Available information suggest community spread of NDM-5-producing E. coli in Germany, highlighting the importance of epidemiological investigation and an integrated surveillance system in the One Health framework.", "token_count": 502, "char_count": 1815, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [ "ST361", "ST167", "ST410", "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:01.205021", "source": { "split": "train_shard_00001", "doc_id": 3278 }, "chunk_id": "train_shard_00001_3278_0", "global_id": 10311 }, { "text": "Molecular surveillance reveals the emergence and dissemination of NDM-5-producing Escherichia coli high-risk clones in Germany, 2013 to 2019.", "token_count": 54, "char_count": 148, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:01.563047", "source": { "split": "train_shard_00001", "doc_id": 3278 }, "chunk_id": "train_shard_00001_3278_1", "global_id": 10312 }, { "text": "Cocoa beans (Theobroma cacao) are the major raw material for chocolate production and fermentation of the beans is essential for the development of chocolate flavor precursors. In this study, a novel approach was used to determine the role of yeasts in cocoa fermentation and their contribution to chocolate quality. Cocoa bean fermentations were conducted with the addition of 200ppm Natamycin to inhibit the growth of yeasts, and the resultant microbial ecology and metabolism, bean chemistry and chocolate quality were compared with those of normal (control) fermentations. The yeasts Hanseniaspora guilliermondii, Pichia kudriavzevii and Kluyveromyces marxianus, the lactic acid bacteria Lactobacillus plantarum and Lactobacillus fermentum and the acetic acid bacteria Acetobacter pasteurianus and Gluconobacter frateurii were the major species found in the control fermentation. In fermentations with the presence of Natamycin, the same bacterial species grew but yeast growth was inhibited. Physical and chemical analyses showed that beans fermented without yeasts had increased shell content, lower production of ethanol, higher alcohols and esters throughout fermentation and lesser presence of pyrazines in the roasted product. Quality tests revealed that beans fermented without yeasts were purplish-violet in color and not fully brown, and chocolate prepared from these beans tasted more acid and lacked characteristic chocolate flavor. Beans fermented with yeast growth were fully brown in color and gave chocolate with typical characters which were clearly preferred by sensory panels. Our findings demonstrate that yeast growth and activity were essential for cocoa bean fermentation and the development of chocolate characteristics.\n\nYeasts are essential for cocoa bean fermentation.", "token_count": 415, "char_count": 1798, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5415, "quality_score": 0.7708, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:02.186839", "source": { "split": "train_shard_00001", "doc_id": 3279 }, "chunk_id": "train_shard_00001_3279_0", "global_id": 10313 }, { "text": "Unsupplemented acid goat whey containing 0.96% protein and 2.76% lactose was fermented aerobically with 32 microflora extracted from various raw milk cheeses and dairy products. These microflora were screened for their ability to hydrolyse whey proteins (alpha-lactalbumin and/or beta-lactoglobulin) and to generate peptides inhibitors of Angiotensin I Converting Enzyme. Five microflora were able to degrade whey protein. The most efficient microflora was able to fully hydrolyse alpha-lactalbumin and to a lesser extend beta-lactoglobulin. It was extracted from Bamalou des Pyrenées cheese. Micro-organisms involved consisted of yeast Kluyveromyces marxianus and lactobacillus Lactobacillus rhamnosus. Both were able to produce ACE inhibitory peptides after whey fermentation.\n\nCrude goat whey fermentation by Kluyveromyces marxianus and Lactobacillus rhamnosus: contribution to proteolysis and ACE inhibitory activity.", "token_count": 273, "char_count": 921, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6917, "quality_score": 0.8458, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:02.744143", "source": { "split": "train_shard_00001", "doc_id": 3280 }, "chunk_id": "train_shard_00001_3280_0", "global_id": 10314 }, { "text": "

Background

The hyperarid core of the Atacama Desert is an extremely harsh environment thought to be colonized by only a few heterotrophic bacterial species. Current concepts for understanding this extreme ecosystem are mainly based on the diversity of these few species, yet a substantial area of the Atacama Desert hyperarid topsoil is covered by expansive boulder accumulations, whose underlying microbiomes have not been investigated so far. With the hypothesis that these sheltered soils harbor uniquely adapted microbiomes, we compared metagenomes and geochemistry between soils below and beside boulders across three distantly located boulder accumulations in the Atacama Desert hyperarid core.

Results

Genome-resolved metagenomics of eleven samples revealed substantially different microbial communities in soils below and beside boulders, despite the presence of shared species. Archaea were found in significantly higher relative abundance below the boulders across all samples within distances of up to 205 km. These key taxa belong to a novel genus of ammonia-oxidizing Thaumarchaeota, Candidatus Nitrosodeserticola. We resolved eight mid-to-high quality genomes of this genus and used comparative genomics to analyze its pangenome and site-specific adaptations. Ca. Nitrosodeserticola genomes contain genes for ammonia oxidation, the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, and acetate utilization indicating a chemolithoautotrophic and mixotrophic lifestyle. They also possess the capacity for tolerating extreme environmental conditions as highlighted by the presence of genes against oxidative stress and DNA damage. Site-specific adaptations of the genomes included the presence of additional genes for heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins.

Conclusion

We provide the first genomic characterization of hyperarid soil microbiomes below the boulders in the Atacama Desert, and report abundant and highly adapted Thaumarchaeaota with ammonia oxidation and carbon fixation potential. Ca", "token_count": 506, "char_count": 2099, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:03.437824", "source": { "split": "train_shard_00001", "doc_id": 3281 }, "chunk_id": "train_shard_00001_3281_0", "global_id": 10315 }, { "text": "Nitrosodeserticola genomes provide the first metabolic and physiological insight into a thaumarchaeal lineage found in globally distributed terrestrial habitats characterized by various environmental stresses. We consequently expand not only the known genetic repertoire of Thaumarchaeota but also the diversity and microbiome functioning in hyperarid ecosystems. Video Abstract.\n\nLeave no stone unturned: individually adapted xerotolerant Thaumarchaeota sheltered below the boulders of the Atacama Desert hyperarid core.", "token_count": 126, "char_count": 521, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8615, "quality_score": 0.9308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:03.831239", "source": { "split": "train_shard_00001", "doc_id": 3281 }, "chunk_id": "train_shard_00001_3281_1", "global_id": 10316 }, { "text": "

Background

Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a Gram-positive bacterium that colonizes the gastrointestinal and genitourinary tract of humans. This bacterium has also been isolated from various animals, such as fish and cattle. Non-coding RNAs (ncRNAs) can act as regulators of gene expression in bacteria, such as Streptococcus pneumoniae and Streptococcus pyogenes. However, little is known about the genomic distribution of ncRNAs and RNA families in S. agalactiae.

Results

Comparative genome analysis of 27 S. agalactiae strains showed more than 5 thousand genomic regions identified and classified as Core, Exclusive, and Shared genome sequences. We identified 27 to 89 RNA families per genome distributed over these regions, from these, 25 were in Core regions while Shared and Exclusive regions showed variations amongst strains. We propose that the amount and type of ncRNA present in each genome can provide a pattern to contribute in the identification of the clonal types.

Conclusions

The identification of RNA families provides an insight over ncRNAs, sRNAs and ribozymes function, that can be further explored as targets for antibiotic development or studied in gene regulation of cellular processes. RNA families could be considered as markers to determine infection capabilities of different strains. Lastly, pan-genome analysis of GBS including the full range of functional transcripts provides a broader approach in the understanding of this pathogen.\n\nFunctional annotation and distribution overview of RNA families in 27 Streptococcus agalactiae genomes.", "token_count": 420, "char_count": 1632, "word_count": 230, "semantic_coherence": 1, "information_density": 0.613, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:04.481387", "source": { "split": "train_shard_00001", "doc_id": 3282 }, "chunk_id": "train_shard_00001_3282_0", "global_id": 10317 }, { "text": "The invention relates to a eukaryon expression method for exoinulinase, which mainly comprises the following steps: firstly, connecting a nucleotide sequence (as shown in SEQ ID No: 1) of the exoinulinase of Kluyveromyces marxianus with pichia expression plasmids pPICZ alpha A through a restricted enzyme site, and obtaining a recombinant expression vector and secondly, introducing the recombinant expression vector into a thermococcus host strain X-33 or SMD1168, and expressing target proteins (the Kluyveromyces marxianus exoinulinase) through induction fermentation. The eukaryon expression method for the exoinulinase lays a foundation for developing the exoinulinase with industrial application value.\n\nSecretory expression method for exoinulinase from Kluyveromyces marxianus", "token_count": 205, "char_count": 784, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [ "SMD1168" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:04.984075", "source": { "split": "train_shard_00001", "doc_id": 3283 }, "chunk_id": "train_shard_00001_3283_0", "global_id": 10318 }, { "text": "In the present work, we analyse the sequences of the 5.8S rRNA gene and the two internal transcribed spacers 1 and 2 (5.8S-ITS region), obtained from 39 strains belonging to the species Kluyveromyces aestuarii, K. dobzhanskii, K. lactis and K. marxianus, K. nonfermentans and K. wickerhamii, to solve the phylogenetic relationships among these species and also to determine the possible genetic basis for the delimitation of the two currently accepted K. lactis varieties: lactis, including lactose-positive strains isolated from dairy products, and drosophilarum, comprising lactose-negative strains isolated from insects and plant exudates. The determination of the phylogenetic relationships within the species K. lactis, together with the examination of the electrophoretic karyotypes and phenotypic characterization of strains representatives of K. lactis var. lactis and var. drosophilarum, allowed differentiation of two groups of strains. The first, and ancestral, group comprises lactose-negative strains isolated from natural habitats in North America. The second, and derived, group includes both lactose-negative strains isolated from natural habitats in Europe and wine fermentation in South Africa, and lactose-positive strains associated with dairy products. These results suggest that the present taxon K. lactis is a complex of different species, subspecies or, at least, genetically structured populations.\n\nAn analysis of inter- and intraspecific genetic variabilities in the Kluyveromyces marxianus group of yeast species for the reconsideration of the K. lactis taxon.", "token_count": 410, "char_count": 1589, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5475, "quality_score": 0.7738, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:05.610197", "source": { "split": "train_shard_00001", "doc_id": 3284 }, "chunk_id": "train_shard_00001_3284_0", "global_id": 10319 }, { "text": "

Unlabelled

The prokaryotic pangenome partitions genes into core and dispensable genes. The order of core genes, albeit assumed to be stable under selection in general, is frequently interrupted by horizontal gene transfer and rearrangement, but how a core-gene-defined genome maintains its stability or flexibility remains to be investigated. Based on data from 30 species, including 425 genomes from six phyla, we grouped core genes into syntenic blocks in the context of a pangenome according to their stability across multiple isolates. A subset of the core genes, often species specific and lineage associated, formed a core-gene-defined genome organizational framework (cGOF). Such cGOFs are either single segmental (one-third of the species analyzed) or multisegmental (the rest). Multisegment cGOFs were further classified into symmetric or asymmetric according to segment orientations toward the origin-terminus axis. The cGOFs in Gram-positive species are exclusively symmetric and often reversible in orientation, as opposed to those of the Gram-negative bacteria, which are all asymmetric and irreversible. Meanwhile, all species showing strong strand-biased gene distribution contain symmetric cGOFs and often specific DnaE (α subunit of DNA polymerase III) isoforms. Furthermore, functional evaluations revealed that cGOF genes are hub associated with regard to cellular activities, and the stability of cGOF provides efficient indexes for scaffold orientation as demonstrated by assembling virtual and empirical genome drafts. cGOFs show species specificity, and the symmetry of multisegmental cGOFs is conserved among taxa and constrained by DNA polymerase-centric strand-biased gene distribution. The definition of species-specific cGOFs provides powerful guidance for genome assembly and other structure-based analysis.

Importance

Prokaryotic genomes are frequently interrupted by horizontal gene transfer (HGT) and rearrangement. To know whether there is a set of genes not only conserved in position among isolates but also functionally essential for a given species and to further evaluate the stability or flexibility of such genome structures across lineages are of importance", "token_count": 505, "char_count": 2213, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5908, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:06.275872", "source": { "split": "train_shard_00001", "doc_id": 3285 }, "chunk_id": "train_shard_00001_3285_0", "global_id": 10320 }, { "text": "Based on a large number of multi-isolate pangenomic data, our analysis reveals that a subset of core genes is organized into a core-gene-defined genome organizational framework, or cGOF. Furthermore, the lineage-associated cGOFs among Gram-positive and Gram-negative bacteria behave differently: the former, composed of 2 to 4 segments, have their fragments symmetrically rearranged around the origin-terminus axis, whereas the latter show more complex segmentation and are partitioned asymmetrically into chromosomal structures. The definition of cGOFs provides new insights into prokaryotic genome organization and efficient guidance for genome assembly and analysis.\n\nFlexibility and symmetry of prokaryotic genome rearrangement reveal lineage-associated core-gene-defined genome organizational frameworks.", "token_count": 185, "char_count": 809, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7549, "quality_score": 0.8775, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:06.712616", "source": { "split": "train_shard_00001", "doc_id": 3285 }, "chunk_id": "train_shard_00001_3285_1", "global_id": 10321 }, { "text": "Carboxypeptidase Y (CPY) is a yeast vacuolar protease with useful applications including C-terminal sequencing of peptides and terminal modification of target proteins. To overexpress CPY with the pro-sequence (proCPY) encoded by the Saccharomyces cerevisiae PRC1 gene in recombinant S. cerevisiae, the proCPY gene was combined with the gene coding for a signal sequence of S. cerevisiae mating factor α (MFα), invertase (SUC2), or Kluyveromyces marxianus inulinase (INU1). Among the three constructs, the MFα signal sequence gave the best specific activity of extracellular CPY. To enhance the CPY expression level, folding accessory proteins of Kar2p, Pdi1p and Ero1p located in the S. cerevisiae endoplasmic reticulum were expressed individually and combinatorially. A single expression of Kar2p led to a 28 % enhancement in extracellular CPY activity, relative to the control strain of S. cerevisiae CEN.PK2-1D/p426Gal1-MFαCPY. Coexpression of Kar2p, Pdi1p and Ero1p gave a synergistic effect on CPY expression, of which activity was 1.7 times higher than that of the control strain. This work showed that engineering of signal sequences and protein-folding proteins would be helpful to overexpress yeast proteins of interest.\n\nEffects of signal sequences and folding accessory proteins on extracellular expression of carboxypeptidase Y in recombinant Saccharomyces cerevisiae.", "token_count": 389, "char_count": 1381, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5888, "quality_score": 0.7944, "entities": { "genes": [ "PRC1", "PK2", "INU1", "SUC2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:07.334727", "source": { "split": "train_shard_00001", "doc_id": 3286 }, "chunk_id": "train_shard_00001_3286_0", "global_id": 10322 }, { "text": "Date palm (Phoenixdactylifera) is the most significant crop across North Africa and the Middle East. However, the crop faces a severe threat from Bayoud disease caused by the fungal pathogen Fusarium oxysporum f. sp. albedinis (FOA). FOA is a soil-borne fungus that infects the roots and vascular system of date palms, leading to widespread destruction of date palm plantations in North Africa over the last century. This is considered the most devastating pathogen of oasis agriculture in North Africa and responsible for loss of 13 million trees in Algeria and Morocco alone. In this study, we present a chromosome-scale high-quality genome assembly of the virulent isolate Foa 44, which provides valuable insights into understanding the genetic basis of Bayoud disease. The genome assembly consists of 11 chromosomes and 40 unplaced contigs, totalling 65,971,825 base pairs in size. It exhibits a GC ratio of 47.77% and a TE (transposable element) content of 17.30%. Through prediction and annotation, we identified 20,416 protein-coding genes. By combining gene and repeat densities analysis with alignment to Fusarium oxysporum f. sp. lycopersici (FOL) 4287 isolate genome sequence, we determined the core and lineage-specific compartments in Foa 44, shedding light on the genome structure of this pathogen. Furthermore, a phylogenomic analysis based on the 3,292 BUSCOs core genome revealed a distinct clade of FOA isolates within the Fusarium oxysporum species complex (FOSC). Notably, the genealogies of the five identified Secreted In Xylem (SIX) genes (1, 6, 9, 11 and 14) in FOA displayed a polyphyletic pattern, suggesting a horizontal inheritance of these effectors", "token_count": 501, "char_count": 1727, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:07.986325", "source": { "split": "train_shard_00001", "doc_id": 3287 }, "chunk_id": "train_shard_00001_3287_0", "global_id": 10323 }, { "text": "These findings provide a valuable genomics toolbox for further research aimed at combatting the serious biotic constraints posed by FOA to date palm. This will pave the way for a deeper understanding of Bayoud disease and facilitate the development of effective diagnostic tools and control measures.\n\nChromosome-scale assembly uncovers genomic compartmentation of Fusarium oxysporum f. sp. albedinis, the causal agent of Bayoud disease in date palm.", "token_count": 112, "char_count": 464, "word_count": 66, "semantic_coherence": 1, "information_density": 0.803, "quality_score": 0.9015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:08.371728", "source": { "split": "train_shard_00001", "doc_id": 3287 }, "chunk_id": "train_shard_00001_3287_1", "global_id": 10324 }, { "text": "

Objectives

The draft genome sequence of Campylobacter jejuni (Cj26) was analysed to investigate genetic mechanisms of antimicrobial resistance, virulence-associated genes, and phylogenetic context.

Methods

Antimicrobial resistance was assessed by agar dilution and disk diffusion. Cj26 was sequenced using NovaSeq 6000 technology. The genome was assembled and annotated. Resistance genes and chromosomal mutations were analysed using the Center for Genomic Epidemiology services, and the multilocus sequence type, SVR-flaA, and porA were determined. The virulome was determined using the Virulence Factor Database. Plasmid detection and assembly were performed using Unicycler v0.5.0 software. To infer the core genome phylogeny, prokka v1.14.5 was employed in conjunction with IQtree v2.0.3.

Results

The Cj26 strain showed a high level of resistance to ciprofloxacin (32 µg/mL) and erythromycin (>128 µg/mL) and resistance to tetracycline and ampicillin. Multilocus sequence typing revealed that the strain belonged to sequence type 353. The substitutions Tre-86-Ile in gyrA and A2075G in 23s RNA were detected, along with the genes tetO, aph(3')-III, ant(6)-Ia, and blaOXA 460. A consistent relationship among accessory and core genes was identified. When compared to other sequence type 353 genomes from Brazil, Cj26 clustered with strains that had more antimicrobial resistance genes than the other clusters.

Conclusion

This report provides insight into the antimicrobial resistance determinants found in a C. jejuni strain and offers a valuable resource for further studies on Campylobacter genomics and antimicrobial resistance.", "token_count": 493, "char_count": 1663, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6273, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:09.018534", "source": { "split": "train_shard_00001", "doc_id": 3288 }, "chunk_id": "train_shard_00001_3288_0", "global_id": 10325 }, { "text": "Genomic characterisation of Campylobacter jejuni Cj26: A high-level ciprofloxacin/erythromycin-resistant strain isolated from a poultry carcass in southern Brazil.", "token_count": 51, "char_count": 163, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:09.381212", "source": { "split": "train_shard_00001", "doc_id": 3288 }, "chunk_id": "train_shard_00001_3288_1", "global_id": 10326 }, { "text": "

Background

The spread of carbapenemase-producing Klebsiella pneumoniae (CP-Kp) strains belonging to high-risk sequence types (STs) is a concern. For Switzerland, national data about the molecular features (especially the STs) of CP-Kp of human origin is not available. In veterinary clinics, ST11 and ST307 blaOXA-48-possessing K. pneumoniae strains have been recently reported.

Methods

We analysed a collection of 285 K. pneumoniae genomes (170 were CP-Kp) isolated in Switzerland from human and non-human sources during 2006-2020. Whole-genome sequencing, core genome phylogenies and public databases were used to present a detailed overview regarding carbapenemases, STs and plasmids.

Results

The top five STs were (main carbapenemase gene) ST512 (blaKPC-3), ST258 (blaKPC-2) and ST101 (blaOXA-48), consisting of strains of human origin only, and ST11 (blaOXA-48) and ST307 (blaOXA-48) strains isolated from human, animal and environmental sources. However, during 2016-2020, the main STs for CP-Kp were ST11 (17.6%), ST307 and ST101 (both 14.7%), whereas ST258 (5.9%) and ST512 (4.4%) significantly declined. Most carbapenemase genes were carried on plasmids already described. Core genome analysis revealed that ST11 K", "token_count": 462, "char_count": 1311, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6807, "quality_score": 0.8404, "entities": { "genes": [ "ST307", "ST11", "ST101", "ST258", "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:10.019459", "source": { "split": "train_shard_00001", "doc_id": 3289 }, "chunk_id": "train_shard_00001_3289_0", "global_id": 10327 }, { "text": "pneumoniae of animal and human origin were closely related, whereas those of ST307 were distant.

Conclusions

We described, for the first time, the features of the CP-Kp circulating in Switzerland in human and non-human settings. Our genomic analysis revealed that the emerging high-risk ST11 and ST307 lineages were often isolated from non-human settings. This study provided a baseline for further whole-genome sequencing-based One-Health surveillance of CP-Kp and emphasized the need for metadata to track dissemination routes between the different settings.\n\nCarbapenemase-producing Klebsiella pneumoniae strains in Switzerland: human and non-human settings may share high-risk clones.", "token_count": 173, "char_count": 695, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [ "ST11", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:10.470477", "source": { "split": "train_shard_00001", "doc_id": 3289 }, "chunk_id": "train_shard_00001_3289_1", "global_id": 10328 }, { "text": "Akkermansia muciniphila has potential as a next-generation probiotic, but few previous studies attempted to analyze its intraspecies population diversity. In this study, we performed a comparative genomic analysis of 112 filtered genomes from the NCBI database. The populations formed three clades (A-C) on the phylogenetic tree, suggesting the existence of three genetic lineages though clades B and C were phylogenetically closer than clade A. The three clades also showed geographic-based clustering, different genetic characteristics, and clade-specific genes. Two putative functional genes (RecD2 and xerD) were specific to clade C due to genomic islands. These lineage-specific genes might be associated with differences in genomic features (number of phages/genomic islands, pan-core genome, recombination rate, genetic diversity) between genetic lineages. The carbohydrate utilization gene profile (particularly for glycolytic hydrolases and carbohydrate esterases) also varied between clades, suggesting different carbohydrate metabolism potential/requirements between genetic lineages. Our findings provide important implications for future research on A. muciniphila. IMPORTANCE Akkermansia muciniphila has been widely accepted as part of the next generation of probiotics. However, most current studies on A. muciniphila have focused on the application of type strain BAA835T in the treatment of diseases, while few studies have reported on the genomic specificity, population structure, and functional characteristics of A. muciniphila species. By comparing the genomes of 112 strains from NCBI which met the quality control conditions, we found that the A. muciniphila population could be divided into three main clades (clades A to C) and presented a certain regional aggregation. There are significant differences among the three clades in their genetic characteristics and functional genes (the type strain BAA835T was located in clade A), especially in genes related to carbohydrate metabolism", "token_count": 523, "char_count": 2082, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6196, "quality_score": 0.8098, "entities": { "genes": [ "BAA835" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:11.106399", "source": { "split": "train_shard_00001", "doc_id": 3290 }, "chunk_id": "train_shard_00001_3290_0", "global_id": 10329 }, { "text": "It should be mentioned that probiotics should be a concept at the strain level rather than at the gut species level, so the probiotic properties of A. muciniphila need to be carefully interpreted.\n\nComparative Genomics Revealed Wide Intra-Species Genetic Heterogeneity and Lineage-Specific Genes of Akkermansia muciniphila.", "token_count": 98, "char_count": 337, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8478, "quality_score": 0.9239, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:11.504437", "source": { "split": "train_shard_00001", "doc_id": 3290 }, "chunk_id": "train_shard_00001_3290_1", "global_id": 10330 }, { "text": "beta-D-galactosidase (EC 3.2.1.23) from Kluyveromyces marxianus YW-1, an isolate from whey, has been studied in terms of cell disruption to liberate the useful enzyme. The enzyme produced in a bioreactor on a wheat bran medium has been successfully immobilized with a view to developing a commercially usable technology for lactose hydrolysis in the food industry. Three chemical and three physical methods of cell disruption were tested and a method of grinding with river sand was found to give highest enzyme activity (720 U). The enzyme was covalently immobilized on gelatin. Immobilized enzyme had optimum pH and temperature of 7.0 and 40 degrees C, respectively and was found to give 49% hydrolysis of lactose in milk after 4 h of incubation. The immobilized enzyme was used for eight hydrolysis batches without appreciable loss in activity. The retention of high catalytic activity compared with the losses experienced with several previously reported immobilized versions of the enzyme is significant. The method of immobilization is simple, effective, and can be used for the immobilization of other enzymes.\n\nCell disruption optimization and covalent immobilization of beta-D-galactosidase from Kluyveromyces marxianus YW-1 for lactose hydrolysis in milk.", "token_count": 336, "char_count": 1265, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5737, "quality_score": 0.7868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:12.090054", "source": { "split": "train_shard_00001", "doc_id": 3291 }, "chunk_id": "train_shard_00001_3291_0", "global_id": 10331 }, { "text": "

Introduction

Listeria monocytogenes is an ubiquitous foodborne pathogen that represents a serious threat to public health and the food industry.

Methods

In this study Whole Genome Sequencing (WGS) was used to characterize 160 L. monocytogenes isolates obtained from 22,593 different food sources in Montenegro during the years 2014-2022.

Results

Isolates belonged to 21 different clonal complexes (CCs), 22 sequence types (STs) and 73 core genome multilocus sequence types (cgMLST) revealing a high diversity. The most prevalent STs were ST8 (n = 29), ST9 (n = 31), ST121 (n = 19) and ST155 (n = 20). All isolates carried virulence genes (VGs), 111 isolates carried mobile genetic elements (MGEs) (ranging from 1 to 7 MGEs) and 101 isolates carried plasmids (ranging from 1 to 3 plasmids). All isolates carried the intrinsic resistance genes fosX and lin. None of the isolates carried acquired antimicrobial resistance genes (ARGs).

Discussion/conclusion

Continuous monitoring and surveillance of L. monocytogenes is needed for improving and ameliorating the public health.\n\nSurveillance and genetic characterization of Listeria monocytogenes in the food chain in Montenegro during the period 2014-2022.", "token_count": 470, "char_count": 1302, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8198, "entities": { "genes": [ "ST155", "ST121", "ST8", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:12.731479", "source": { "split": "train_shard_00001", "doc_id": 3292 }, "chunk_id": "train_shard_00001_3292_0", "global_id": 10332 }, { "text": "

Background

Listeria monocytogenes is a foodborne gram-positive bacterium which causes adverse pregnancy outcomes. Here, the genomic and phylogenetic characteristics of a L. monocytogenes isolate obtained from blood sample of a third trimester pregnant woman with stillbirth are investigated.

Methods

Whole genome DNA of L. monocytogenes ST1 was sequenced with HiSeq X Ten platform. The NCBI Prokaryotic Genome Annotation Pipeline was used to annotate the genome sequence. The sequence type (ST) and antimicrobial resistance genes were then identified. The core genome multilocus sequence typing (cgMLST) analysis with other closely related L. monocytogenes stored in the NCBI GenBank database was performed using BacWGSTdb 2.0.

Results

The complete genome sequence of L. monocytogenes ST1 is made up of 20 contigs totaling 2,914,725 bp, with 2886 protein-coding sequences and a GC content of 37.9%. Fosfomycin [fosX], Lincosamide antibiotic [lin] and peptide antibiotic [mprF] were discovered as antimicrobial resistance genes. In silico serogroup typing prediction revealed that L. monocytogenes ST1 belonged to serotype IVb. The closest relative of L. monocytogenes ST1, obtained from Poland in 2015, differs by only 15 cgMLST alleles.

Conclusion

We identified a L. monocytogenes ST1 strain from blood sample of a woman with third trimester stillbirth in China. These discoveries would aid in our understanding of the genomic characteristics, mechanisms of antimicrobial resistance, and epidemiological features of this pathogen.", "token_count": 513, "char_count": 1637, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:13.395503", "source": { "split": "train_shard_00001", "doc_id": 3293 }, "chunk_id": "train_shard_00001_3293_0", "global_id": 10333 }, { "text": "Genomic Characterization of a Clinical Listeria monocytogenes ST1 Isolate Recovered from the Blood Sample of a Woman with Third Trimester Stillbirth.", "token_count": 45, "char_count": 156, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9048, "quality_score": 0.9524, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:13.754045", "source": { "split": "train_shard_00001", "doc_id": 3293 }, "chunk_id": "train_shard_00001_3293_1", "global_id": 10334 }, { "text": "Dental caries is among the most prevalent chronic diseases worldwide. Streptococcus mutans, the chief causative agent of caries, uses a 25-kDa manganese-dependent SloR protein to coordinate the uptake of essential manganese with the transcription of its virulence attributes. Small non-coding RNAs (sRNAs) can either enhance or repress gene expression, and reports in the literature ascribe an emerging role for sRNAs in the environmental stress response. Herein, we focused our attention on 18-50 nt sRNAs as mediators of the S. mutans SloR and manganese regulons. Specifically, the results of RNA sequencing revealed 19 sRNAs in S. mutans, which were differentially transcribed in the SloR-proficient UA159 and SloR-deficient GMS584 strains, and 10 sRNAs that were differentially expressed in UA159 cells grown in the presence of low vs high manganese. We describe SmsR1532 and SmsR1785 as SloR- and manganese-responsive sRNAs that are processed from large transcripts and that bind SloR directly in their promoter regions. The predicted targets of these sRNAs include regulators of metal ion transport, growth management via a toxin-antitoxin operon, and oxidative stress tolerance. These findings support a role for sRNAs in coordinating intracellular metal ion homeostasis with virulence gene control in an important oral cariogen. IMPORTANCE Small regulatory RNAs (sRNAs) are critical mediators of environmental signaling, particularly in bacterial cells under stress, but their role in Streptococcus mutans is poorly understood. S. mutans, the principal causative agent of dental caries, uses a 25-kDa manganese-dependent protein, called SloR, to coordinate the regulated uptake of essential metal ions with the transcription of its virulence genes", "token_count": 513, "char_count": 1790, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6024, "quality_score": 0.8012, "entities": { "genes": [ "UA159", "GMS584" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:14.387278", "source": { "split": "train_shard_00001", "doc_id": 3294 }, "chunk_id": "train_shard_00001_3294_0", "global_id": 10335 }, { "text": "In the present study, we identified and characterized sRNAs that are both SloR and manganese responsive. Taken together, this research can elucidate the details of regulatory networks that engage sRNAs in an important oral pathogen and that can enable the development of an effective anti-caries therapeutic.\n\nSmall regulatory RNAs are mediators of the Streptococcus mutans SloR regulon.", "token_count": 104, "char_count": 394, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7193, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:14.772374", "source": { "split": "train_shard_00001", "doc_id": 3294 }, "chunk_id": "train_shard_00001_3294_1", "global_id": 10336 }, { "text": "

Objectives

Drug-resistant Neisseria gonorrhoeae are now a global public health threat. Direct transmission of antibiotic-resistant gonococci between individuals has been proposed as a driver for the increased transmission of resistance, but direct evidence of such transmission is limited. Whole-genome sequencing (WGS) has superior resolution to investigate outbreaks and disease transmission compared with traditional molecular typing methods such as multilocus sequence typing (MLST) and N. gonorrhoeae multiantigen sequence (NG-MAST). We therefore aimed to systematically investigate the transmission of N. gonorrhoeae between men in sexual partnerships using WGS to compare isolates and their resistance to antibiotics at a genome level.

Methods

458 couples from a large prospective cohort of men who have sex with men (MSM) tested for gonorrhoea together between 2005 and 2014 were included, and WGS was conducted on all isolates from couples where both men were culture-positive for N. gonorrhoeae. Resistance-determining sequences were identified from genome assemblies, and comparison of isolates between and within individuals was performed by pairwise single nucleotide polymorphism and pangenome comparisons, and in silico predictions of NG-MAST and MLST.

Results

For 33 of 34 (97%; 95% CI 85% to 100%) couples where both partners were positive for gonorrhoea, the resistance-determining genes and mutations were identical in isolates from each partner (94 isolates in total). Resistance determinants in isolates from 23 of 23 (100%; 95% CI 86% to 100%) men with multisite infections were also identical within an individual", "token_count": 465, "char_count": 1686, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:15.450414", "source": { "split": "train_shard_00001", "doc_id": 3295 }, "chunk_id": "train_shard_00001_3295_0", "global_id": 10337 }, { "text": "These partner and within-host isolates were indistinguishable by NG-MAST, MLST and whole genomic comparisons.

Conclusions

These data support the transmission of antibiotic-resistant strains between sexual partners as a key driver of resistance rates in gonorrhoea among MSM. This improved understanding of the transmission dynamics of N. gonorrhoeae between sexual partners will inform treatment and prevention guidelines.\n\nWhole-genome sequencing reveals transmission of gonococcal antibiotic resistance among men who have sex with men: an observational study.", "token_count": 140, "char_count": 575, "word_count": 72, "semantic_coherence": 1, "information_density": 0.8056, "quality_score": 0.9028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:15.887711", "source": { "split": "train_shard_00001", "doc_id": 3295 }, "chunk_id": "train_shard_00001_3295_1", "global_id": 10338 }, { "text": "Typhoid fever is transmitted by ingestion of polluted water, contaminated food, and stool of typhoid-infected individuals, mostly in developing countries with poor hygienic environments. To find novel therapeutic targets and inhibitors, the complete genomes of eight Salmonella Typhi strains were primarily subjected to the EDGAR tool to predict the core genome (n=3207). Human non-homology (n=2450) was followed by essential genes identification (n=37). The STRING database predicted maximum protein-protein interactions, followed by cellular localization. The virulent/immunogenic ability of predicted genes were checked to differentiate drug and vaccine targets. Furthermore, the 3D models of the identified putative proteins encoded by the respective genes were constructed and subjected to druggability analyses where only “highly druggable” proteins were selected for molecular docking and simulation analyses. The putative targets include ATP-dependent CLP protease proteolytic subunit, Imidazole glycerol phosphate synthase hisH, 7,8-dihydropteroate synthase folP and 2,3-bisphosphoglycerate-independent phosphoglycerate mutase gpmI. A ZINC drug-like library (n=12000) was screened against each identified targets and top hits were selected based on H-bonds, RMSD and energy scores. Finally, the ADMET properties for novel inhibitors ZINC19340748, ZINC09319798, ZINC00494142, ZINC32918650 were optimized followed by binding free energy (MM/PBSA) calculation for ligand-receptor complexes. The findings of this work are expected to aid in expediting the identification of novel protein targets and inhibitors in combating typhoid Salmonellosis, in addition to the already existing therapies.\n\nProtocol for expediting drug targets search in S . Typhi through subtractive genomics and the identification of lead-based novel small molecules", "token_count": 493, "char_count": 1845, "word_count": 240, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [ "ZINC00494142", "ZINC32918650", "ZINC09319798", "ZINC19340748" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:16.567558", "source": { "split": "train_shard_00001", "doc_id": 3296 }, "chunk_id": "train_shard_00001_3296_0", "global_id": 10339 }, { "text": "

Objectives

The prevalence of infections caused by OXA-48-like carbapenemase-producing organisms in Ireland has increased dramatically since 2011 and is an urgent public health issue. Genome-based high-resolution genotyping was used to analyse clinical isolates submitted to the Irish Carbapenemase-Producing Enterobacteriaceae Reference Laboratory Service for a 13 month period (2016-17).

Methods

A total of 109 OXA-48-producing non-duplicate clinical isolates from 16 submitting centres were sequenced. Using a gene-by-gene approach, isolate genomes were characterized by MLST and core genome MLST, and the presence of antimicrobial resistance determinants was determined. Reference mapping and a novel plasmid MLST-type approach was applied to determine plasmid background.

Results

The OXA-48-like-producing isolates were Escherichia coli (n = 56), Klebsiella spp. (n = 46) and Enterobacter cloacae (n = 7). Amongst the E. coli isolates there were 37 different STs and amongst the Klebsiella spp. isolates there were 27 different STs. blaOXA-48 was present in 105/109 (96.3%) of isolates. Based on mapping analysis and detection of the pOXA-48 IncL-type plasmid replicon and backbone genes, a pOXA-48-like plasmid was identified in 93/109 isolates (85.3%). The remaining isolates (n = 16; 14.7%) harboured blaOXA-48-like genes in unknown environments", "token_count": 470, "char_count": 1374, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:17.263807", "source": { "split": "train_shard_00001", "doc_id": 3297 }, "chunk_id": "train_shard_00001_3297_0", "global_id": 10340 }, { "text": "Using a gene-by-gene approach two pOXA-48-like plasmid groups with 2/71 pOXA-48-like locus differences between them were identified.

Conclusions

In Ireland we found a diversity of genotypes associated with OXA-48-like-producing clinical isolates with the IncL pOXA-48 plasmid type predominating as the blaOXA-48 genetic environment. A plasmid MLST approach can rapidly identify plasmids associated with outbreaks and monitor spread of types temporally and geographically.\n\nAn MLST approach to support tracking of plasmids carrying OXA-48-like carbapenemase.", "token_count": 170, "char_count": 564, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:17.710057", "source": { "split": "train_shard_00001", "doc_id": 3297 }, "chunk_id": "train_shard_00001_3297_1", "global_id": 10341 }, { "text": "Maintenance of asymmetric ion concentrations across cellular membranes is crucial for proper yeast cellular function. Disruptions of these ionic gradients can significantly impact membrane electrochemical potential and the balance of other ions, particularly under stressful conditions such as exposure to acetic acid. This weak acid, ubiquitous to both yeast metabolism and industrial processes, is a major inhibitor of yeast cell growth in industrial settings and a key determinant of host colonization by pathogenic yeast. Acetic acid toxicity depends on medium composition, especially on the pH (H+ concentration), but also on other ions' concentrations. Regulation of ion fluxes is essential for effective yeast response and adaptation to acetic acid stress. However, the intricate interplay among ion balancing systems and stress response mechanisms still presents significant knowledge gaps. This review offers a comprehensive overview of the mechanisms governing ion homeostasis, including H+, K+, Zn2+, Fe2+/3+, and acetate, in the context of acetic acid toxicity, adaptation, and tolerance. While focus is given on Saccharomyces cerevisiae due to its extensive physiological characterization, insights are also provided for biotechnologically and clinically relevant yeast species whenever available.\n\nThe role of ion homeostasis in adaptation and tolerance to acetic acid stress in yeasts.", "token_count": 301, "char_count": 1400, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:18.278689", "source": { "split": "train_shard_00001", "doc_id": 3298 }, "chunk_id": "train_shard_00001_3298_0", "global_id": 10342 }, { "text": "

Motivation

Pangenomics is a growing field within computational genomics. Many pangenomic analyses use bidirected sequence graphs as their core data model. However, implementing and correctly using this data model can be difficult, and the scale of pangenomic data sets can be challenging to work at. These challenges have impeded progress in this field.

Results

Here we present a stack of two C++ libraries, libbdsg and libhandlegraph , which use a simple, field-proven interface, designed to expose elementary features of these graphs while preventing common graph manipulation mistakes. The libraries also provide a Python binding. Using a diverse collection of pangenome graphs, we demonstrate that these tools allow for efficient construction and manipulation of large genome graphs with dense variation. For instance, the speed and memory usage is up to an order of magnitude better than the prior graph implementation in the vg toolkit, which has now transitioned to using libbdsg ’s implementations.

Availability

libhandlegraph and libbdsg are available under an MIT License from https://github.com/vgteam/libhandlegraph and https://github.com/vgteam/libbdsg .

Contact

erik.garrison@ucsc.edu\n\nSuccinct dynamic variation graphs", "token_count": 300, "char_count": 1269, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7283, "quality_score": 0.8642, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:18.848701", "source": { "split": "train_shard_00001", "doc_id": 3299 }, "chunk_id": "train_shard_00001_3299_0", "global_id": 10343 }, { "text": "From a screening of several Kluyveromyces strains, the yeast Kluyveromyces marxianus CBS 6556 was selected for a study of the parameters relevant to the commercial production of inulinase (EC 3.2.1.7). This yeast exhibited superior properties with respect to growth at elevated temperatures (40 to 45 degrees C), substrate specificity, and inulinase production. In sucrose-limited chemostat cultures growing on mineral medium, the amount of enzyme decreased from 52 U mg of cell dry weight at D = 0.1 h to 2 U mg of cell dry weight at D = 0.8 h. Experiments with nitrogen-limited cultures further confirmed that synthesis of the enzyme is negatively controlled by the residual sugar concentration in the culture. High enzyme activities were observed during growth on nonsugar substrates, indicating that synthesis of the enzyme is a result of a derepression/repression mechanism. A substantial part of the inulinase produced by K. marxianus was associated with the cell wall. The enzyme could be released from the cell wall via a simple chemical treatment of cells. Results are presented on the effect of cultivation conditions on the distribution of the enzyme. Inulinase was active with sucrose, raffinose, stachyose, and inulin as substrates and exhibited an S/I ratio (relative activities with sucrose and inulin) of 15 under standard assay conditions. The enzyme activity decreased with increasing chain length of the substrate.\n\nProduction, Distribution, and Kinetic Properties of Inulinase in Continuous Cultures of Kluyveromyces marxianus CBS 6556.", "token_count": 390, "char_count": 1556, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:19.470764", "source": { "split": "train_shard_00001", "doc_id": 3300 }, "chunk_id": "train_shard_00001_3300_0", "global_id": 10344 }, { "text": "

ABSTRACT

The multipartite genome structure is found in a diverse group of important symbiotic and pathogenic bacteria; however, the advantage of this genome structure remains incompletely understood. Here, we perform comparative genomics of hundreds of finished β-proteobacterial genomes to study the role and emergence of multipartite genomes. Nearly all essential secondary replicons (chromids) of the β-proteobacteria are found in the family Burkholderiaceae . These replicons arose from just two plasmid acquisition events, and they were likely stabilized early in their evolution by the presence of core genes, at least some of which were likely acquired through an inter-replicon translocation event. On average, Burkholderiaceae genera with multipartite genomes had a larger total genome size, but smaller chromosome, than genera without secondary replicons. Pangenome-level functional enrichment analyses suggested that inter-replicon functional biases are partially driven by the enrichment of secondary replicons in the accessory pangenome fraction. Nevertheless, the small overlap in orthologous groups present in each replicon’s pangenome indicates a clear functional separation of the replicons. Chromids appeared biased to environmental adaptation, as the functional categories enriched on chromids were also over-represented on the chromosomes of the environmental genera ( Paraburkholderia, Cupriavidus ) compared to the pathogenic genera ( Burkholderia, Ralstonia ). Using ancestral state reconstruction, it was predicted that the rate of accumulation of modern-day genes by chromids was more rapid than the rate of gene accumulation by the chromosomes. Overall, the data are consistent with a model where the primary advantage of secondary replicons is in facilitating increased rates of gene acquisition through horizontal gene transfer, consequently resulting in a replicon enriched in genes associated with adaptation to novel environments.\n\nEmergence and features of the multipartite genome structure of the family Burkholderiaceae revealed through comparative and evolutionary genomics", "token_count": 483, "char_count": 2124, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5903, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:20.486048", "source": { "split": "train_shard_00001", "doc_id": 3301 }, "chunk_id": "train_shard_00001_3301_0", "global_id": 10345 }, { "text": "Candida albicans typically resides in the human gastrointestinal tract and mucosal membranes as a commensal organism. To adapt and cope with the host immune system, it has evolved a variety of mechanisms of adaptation such as stress-induced mutagenesis and epigenetic regulation. Niche-specific patterns of gene expression also allow the fungus to fine-tune its response to specific microenvironments in the host and switch from harmless commensal to invasive pathogen. Proteome plasticity produced by CUG ambiguity, on the other hand is emerging as a new layer of complexity in C. albicans adaptation, pathogenesis, and drug resistance. Such proteome plasticity is the result of a genetic code alteration where the leucine CUG codon is translated mainly as serine (97%), but maintains some level of leucine (3%) assignment. In this review, we dissect the link between C. albicans non-standard CUG translation, proteome plasticity, host adaptation and pathogenesis. We discuss published work showing how this pathogen uses the fidelity of protein synthesis to spawn novel virulence traits.\n\nThe role of non-standard translation in Candida albicans pathogenesis.", "token_count": 275, "char_count": 1161, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:21.043060", "source": { "split": "train_shard_00001", "doc_id": 3302 }, "chunk_id": "train_shard_00001_3302_0", "global_id": 10346 }, { "text": "Casein phosphatase activities have been identified in five yeast strains grown on Pi-deficient medium. Maximal endocellular activities appeared in the exponential phase. Exocellular phosphatases were significantly produced from Yarrowia lipolytica W-29 and Kluyveromyces marxianus, in the early stationary phase. Major phosphatases from K. marxianus were one heavy acid phosphatase composed of 64-67 kDa subunits, which could be secreted in the medium, and one type 2A protein phosphatase with an apparent molecular mass of 147 kDa and a 52 kDa catalytic subunit dissociated by 80% ethanol treatment. The characteristics of phosphatases purified from K. marxianus were compared with those previously purified from Y. lipolytica.\n\nCharacterization of major protein phosphatases from selected species of Kluyveromyces. Comparison with protein phosphatases from Yarrowia lipolytica.", "token_count": 238, "char_count": 879, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:21.513423", "source": { "split": "train_shard_00001", "doc_id": 3303 }, "chunk_id": "train_shard_00001_3303_0", "global_id": 10347 }, { "text": "Symbiosis with bacteria is common across insects, resulting in adaptive host phenotypes. The recently described bacterial symbionts Lactobacillus micheneri, Lactobacillus timberlakei, and Lactobacillus quenuiae are found in wild bee pollen provisions, bee guts, and flowers but have small genomes in comparison to other lactobacilli. We sequenced, assembled, and analyzed 27 new L. micheneri clade genomes to identify their possible ecological functions in flower and bee hosts. We determined possible key functions for the L. micheneri clade by identifying genes under positive selection, balancing selection, genes gained or lost, and population structure. A host adherence factor shows signatures of positive selection, whereas other orthologous copies are variable within the L. micheneri clade. The host adherence factors serve as strong evidence that these lactobacilli are adapted to animal hosts as their targets are found in the digestive tract of insects. Next, the L. micheneri clade is adapted toward a nutrient-rich environment, corroborating observations of where L. micheneri is most abundant. Additionally, genes involved in osmotolerance, pH tolerance, temperature resistance, detoxification, and oxidative stress response show signatures of selection that allow these bacteria to thrive in pollen and nectar masses in bee nests and in the bee gut. Altogether, these findings not only suggest that the L. micheneri clade is primarily adapted to the wild bee gut but also exhibit genomic features that would be beneficial to survival in flowers.\n\nComparative Genomics of Wild Bee and Flower Isolated Lactobacillus Reveals Potential Adaptation to the Bee Host.", "token_count": 408, "char_count": 1675, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6049, "quality_score": 0.8025, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:22.139295", "source": { "split": "train_shard_00001", "doc_id": 3304 }, "chunk_id": "train_shard_00001_3304_0", "global_id": 10348 }, { "text": "Probiotics are live microorganisms which when administered in adequate amounts confer a health benefit on the host. The concept of individual microorganisms influencing the makeup of T cell subsets via interactions with intestinal dendritic cells (DCs) appears to constitute the foundation for immunoregulatory effects of probiotics, and several studies have reported probiotic strains resulting in reduction of intestinal inflammation through modulation of DC function. Consequent to a focus on Saccharomyces boulardii as the fundamental probiotic yeast, very little is known about hundreds of non-Saccharomyces yeasts in terms of their interaction with the human gastrointestinal immune system. The aim of the present study was to evaluate 170 yeast strains representing 75 diverse species for modulation of inflammatory cytokine secretion by human DCs in vitro, as compared to cytokine responses induced by a S. boulardii reference strain with probiotic properties documented in clinical trials. Furthermore, we investigated whether cytokine inducing interactions between yeasts and human DCs are dependent upon yeast viability or rather a product of membrane interactions regardless of yeast metabolic function. We demonstrate high diversity in yeast induced cytokine profiles and employ multivariate data analysis to reveal distinct clustering of yeasts inducing similar cytokine profiles in DCs, highlighting clear species distinction within specific yeast genera. The observed differences in induced DC cytokine profiles add to the currently very limited knowledge of the cross-talk between yeasts and human immune cells and provide a foundation for selecting yeast strains for further characterization and development toward potentially novel yeast probiotics. Additionally, we present data to support a hypothesis that the interaction between yeasts and human DCs does not solely depend on yeast viability, a concept which may suggest a need for further classifications beyond the current definition of a probiotic.\n\nYeast modulation of human dendritic cell cytokine secretion: an in vitro study.", "token_count": 459, "char_count": 2105, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5819, "quality_score": 0.791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:22.782231", "source": { "split": "train_shard_00001", "doc_id": 3305 }, "chunk_id": "train_shard_00001_3305_0", "global_id": 10349 }, { "text": "The INU1 gene encoding exo-inulinase cloned from Kluyveromyces marxianus CBS 6556 was ligated into the surface display plasmid and expressed in the cells of the marine-derived yeast Yarrowia lipolytica which can produce citric acid. The expressed inulinase was immobilized on the yeast cells. The activity of the immobilized inulinase with 6 x His tag was found to be 22.6 U mg(-1) of cell dry weight after cell growth for 96 h. The optimal pH and temperature of the displayed inulinase were 4.5 and 50 degrees C, respectively and the inulinase was stable in the pH range of 3-8 and in the temperature range of 0-50 degrees C. During the inulin hydrolysis, the optimal inulin concentration was 12.0% and the optimal amount of added inulinase was 181.6 U g(-1) of inulin. Under such conditions, over 77.9% of inulin was hydrolyzed within 10h and the hydrolysate contained main monosaccharides and disaccharides, and minor trisaccharides. During the citric acid production in the flask level, the recombinant yeast could produce 77.9 g L(-1) citric acid and 5.3 g L(-1) iso-citric acid from inulin while 68.9 g L(-1) of citric acid and 4.1 g L(-1) iso-citric acid in the fermented medium were attained within 312 h of the 2-L fermentation, respectively.\n\nInulin hydrolysis and citric acid production from inulin using the surface-engineered Yarrowia lipolytica displaying inulinase.", "token_count": 421, "char_count": 1380, "word_count": 221, "semantic_coherence": 1, "information_density": 0.552, "quality_score": 0.776, "entities": { "genes": [ "INU1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:23.408504", "source": { "split": "train_shard_00001", "doc_id": 3306 }, "chunk_id": "train_shard_00001_3306_0", "global_id": 10350 }, { "text": "

Introduction

There are few studies on paediatric carbapenem-resistant Klebsiella pneumoniae (CRKP) in China. The present study investigated the molecular epidemiological and drug resistance characteristics of CRKP from paediatric patients in China to provide a reference for the prevention and control of CRKP infection.

Methodology

In total, 20 nonrepetitive clinical CRKP isolates were collected between February 2019 and February 2020 in a tertiary hospital in China. Strain identification and drug susceptibility testing were carried out using the VITEK® 2 Compact Bacterial Identification and Monitoring System. Sequence typing, phylogenetic relationships, and antibiotic resistance-associated genes were analysed by whole genome sequencing (WGS).

Results

sequence typing (MLST) and Core genome multilocus sequence typing (cgMLST) analysis revealed the most frequently represented were ST2407-CT3536 (30%), ST76-CT5893 (25%), and ST309-CT7864 (25%). All 20 CRKP isolates were divided into three clusters. All isolates were highly resistant to a variety of β-lactams and were highly susceptible to quinolones, aminoglycosides, and sulphonamides. All isolates mainly carried the carbapenem resistance genes blaNDM-1 and blaKPC-2, among which 10 isolates carried both blaNDM-1 and blaKPC-2 simultaneously.

Conclusions

Sequence typing, phylogenetic relationships, and antibiotic resistance genes can be determined using WGS technology. This can guide CRKP infection control and clinical treatment for paediatric patients.\n\nMolecular typing and drug resistance analysis of carbapenem-resistant Klebsiella pneumoniae from paediatric patients in China.", "token_count": 472, "char_count": 1679, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5913, "quality_score": 0.7957, "entities": { "genes": [ "ST2407", "CT3536", "ST76", "ST309", "CT7864", "CT5893" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:24.056806", "source": { "split": "train_shard_00001", "doc_id": 3307 }, "chunk_id": "train_shard_00001_3307_0", "global_id": 10351 }, { "text": "

Background

Klebsiella oxytoca DSM 29614 - isolated from acid mine drainages - grows anaerobically using Fe(III)-citrate as sole carbon and energy source, unlike other enterobacteria and K. oxytoca clinical isolates. The DSM 29614 strain is multi metal resistant and produces metal nanoparticles that are embedded in its very peculiar capsular exopolysaccharide. These metal nanoparticles were effective as antimicrobial and anticancer compounds, chemical catalysts and nano-fertilizers.

Results

The DSM 29614 strain genome was sequenced and analysed by a combination of in silico procedures. Comparative genomics, performed between 85 K. oxytoca representatives and K. oxytoca DSM 29614, revealed that this bacterial group has an open pangenome, characterized by a very small core genome (1009 genes, about 2%), a high fraction of unique (43,808 genes, about 87%) and accessory genes (5559 genes, about 11%). Proteins belonging to COG categories \"Carbohydrate transport and metabolism\" (G), \"Amino acid transport and metabolism\" (E), \"Coenzyme transport and metabolism\" (H), \"Inorganic ion transport and metabolism\" (P), and \"membrane biogenesis-related proteins\" (M) are particularly abundant in the predicted proteome of DSM 29614 strain. The results of a protein functional enrichment analysis - based on a previous proteomic analysis - revealed metabolic optimization during Fe(III)-citrate anaerobic utilization. In this growth condition, the observed high levels of Fe(II) may be due to different flavin metal reductases and siderophores as inferred form genome analysis. The presence of genes responsible for the synthesis of exopolysaccharide and for the tolerance to heavy metals was highlighted too", "token_count": 485, "char_count": 1723, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:24.705488", "source": { "split": "train_shard_00001", "doc_id": 3308 }, "chunk_id": "train_shard_00001_3308_0", "global_id": 10352 }, { "text": "The inferred genomic insights were confirmed by a set of phenotypic tests showing specific metabolic capability in terms of i) Fe2+ and exopolysaccharide production and ii) phosphatase activity involved in precipitation of metal ion-phosphate salts.

Conclusion

The K. oxytoca DSM 29614 unique capabilities of using Fe(III)-citrate as sole carbon and energy source in anaerobiosis and tolerating diverse metals coincides with the presence at the genomic level of specific genes that can support i) energy metabolism optimization, ii) cell protection by the biosynthesis of a peculiar exopolysaccharide armour entrapping metal ions and iii) general and metal-specific detoxifying activities by different proteins and metabolites.\n\nGenomic traits of Klebsiella oxytoca DSM 29614, an uncommon metal-nanoparticle producer strain isolated from acid mine drainages.", "token_count": 233, "char_count": 876, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:25.176126", "source": { "split": "train_shard_00001", "doc_id": 3308 }, "chunk_id": "train_shard_00001_3308_1", "global_id": 10353 }, { "text": "A unique one-step ethanol fermentation process was developed with the inulinase-producing strain Kluyveromyces marxianus YX01. Firstly, the impact of temperature on ethanol fermentation was investigated through flask fermentation, and the temperature of 35 degrees C was observed to be the optimum to coordinate inulinase production, inulin saccharification and ethanol fermentation. And then, the impact of aeration and substrate concentration was studied through batch fermentation in the 2.5 L fermentor, and the experimental data indicated that the average ethanol fermentation time was decreased at the aeration rates of 50 mL/min and 100 mL/min, but higher ethanol yield was obtained under non-aeration conditions with more substrate directed to ethanol production. The ethanol concentration of 92.2 g/L was achieved with the substrate containing 235 g/L inulin, and the ethanol yield was calculated to be 0.436, equivalent to 85.5% of its theoretical value. Finally, Jerusalem artichoke grown in salina and irrigated with seawater was fermented without sterilization treatment, 84.0 g/L ethanol was obtained with the substrate containing 280 g/L dry Jerusalem artichoke meal, and the ethanol yield was calculated to be 0.405, indicating the Jerusalem artichoke could be an alternative feedstock for grain-based fuel ethanol production.\n\n[One-step ethanol fermentation with Kluyveromyces marxianus YX01 from Jerusalem artichoke].", "token_count": 385, "char_count": 1435, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5545, "quality_score": 0.7772, "entities": { "genes": [ "YX01" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:25.792512", "source": { "split": "train_shard_00001", "doc_id": 3309 }, "chunk_id": "train_shard_00001_3309_0", "global_id": 10354 }, { "text": "Antimicrobial resistance in Shigella spp. is a global public health concern. In this study, the AMR phenotypic profiles of 10 kinds of antibiotics were compared with the genotypic profiles using genomic analysis of 218 Shigella isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016. Core genome Multilocus Sequence Typing (cgMLST) based on the EnteroBase Escherichia/Shigella scheme was used to obtain the genetic relatedness of Shigella isolates. Multiple-drug resistance was observed in 96.79% Shigella spp., and the resistance to antimicrobial agents varied between S. flexneri and S. sonnei. The genotypic results correlated well with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively, from Taiyuan City, Shanxi Province. The sensitivity and specificity of the genotypic antimicrobial susceptibility testing (AST) were 97.56% and 95.34% for S. flexneri, and 95.65% and 93.31% for S. sonnei isolates, respectively. A discrepancy of genotypic and phenotypic AST results existed in some cephalosporin- and azithromycin-resistant Shigella isolates; there were no clear resistance patterns to predict ciprofloxacin resistance. There were major discrepancies between genotypic and phenotypic AST in the genotypically resistant but phenotypically susceptible isolates. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles were the discrepancies between S. flexneri and S. sonnei isolates", "token_count": 492, "char_count": 1569, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5476, "quality_score": 0.7738, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:26.449181", "source": { "split": "train_shard_00001", "doc_id": 3310 }, "chunk_id": "train_shard_00001_3310_0", "global_id": 10355 }, { "text": "Phylogenetic analysis showed that isolates of the same cluster but with different antibiotic-resistance gene patterns occurred because of the loss or gain of antibiotic-resistance genes located in the plasmids and multidrug-resistance islands. IMPORTANCE Antimicrobial resistance in Shigella spp. has become a global public health concern. In this study, we identified the antimicrobial susceptibility testing (AST) characteristics based on genomic sequences of 218 Shigella isolates and analyzed the correlation between genotypic and phenotypic antibiotic resistance profiles of Shigella spp., especially for fluoroquinolone, macrolides, and third-generation cephalosporins. Our results show that the genotypic results correlated with the phenotypic profiles with concordance rates of 96.42% and 94.50% in S. flexneri and S. sonnei isolates, respectively. The drug-resistance patterns and essential drug-resistance genes to predict the phenotypic drug-resistant profiles of S. flexneri and S. sonnei isolates in Taiyuan city were distinct. The discrepancy between genotypic and phenotypic AST was considerable in the genotypically resistant but phenotypically susceptible isolates. The information on drug resistance and resistance genes in this study can offer more details on the prevalence of drug resistance of Shigella spp.\n\nConcordance between Genotypic and Phenotypic Drug-Resistant Profiles of Shigella Isolates from Taiyuan City, Shanxi Province, China, 2005 to 2016.", "token_count": 420, "char_count": 1519, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:27.076631", "source": { "split": "train_shard_00001", "doc_id": 3310 }, "chunk_id": "train_shard_00001_3310_1", "global_id": 10356 }, { "text": "

Background

This study was carried out to determine the prevalence and the genetic background of extended-spectrum β-lactamase-producing Escherichia coli invasive isolates obtained from a tertiary-care hospital in Budapest, Hungary.

Methods

Between October-November 2018, all invasive ESBL-producing E. coli isolates were collected from Central Hospital of Southern Pest. The antimicrobial susceptibility testing was performed according to the EUCAST guidelines. The possible clonal relationships were investigated by core genome (cg)MLST (SeqSphere +) using whole-genome sequencing (WGS) data of isolates obtained from Illumina 251-bp paired-end sequencing. From WGS data acquired antimicrobial resistance genes, virulence genes and replicon types were retrieved using ResFinder3.1, PlasmidFinder2.1, pMLST-2.0, VirulenceFinder2.0 and Virulence Factors Database online tools.

Results

Overall, six E. coli isolates proved to be resistant to third-generation cephalosporins and ESBL-producers in the study period. Full genome sequence analysis showed that five E. coli isolates belonged to the ST131 clone: two to C1-M27 subclade with blaCTX-M-27 and three to C2/H30Rx subclade with blaCTX-M-15. One isolate belonged to ST1193 with blaCTX-M-27. According to cgMLST, all C2/H30Rx isolates formed a cluster (≤ 6 allele differences), while the blaCTX-M-27-producing C1-M27 isolates differed at least 35 alleles from each other. Both C2/H30Rx and C1-M27 ST131 isolates harbored similar antimicrobial resistance gene sets", "token_count": 502, "char_count": 1580, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "ST131", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:27.750395", "source": { "split": "train_shard_00001", "doc_id": 3311 }, "chunk_id": "train_shard_00001_3311_0", "global_id": 10357 }, { "text": "However, only C2/H30Rx isolates had the qnrB and aac(3)-IIa. The isolates carried similar extraintestinal virulence gene set but differed in some genes encoding siderophores, protectins and toxins. Moreover, only one C2/H30Rx isolate carried salmochelin siderophore system and showed virotype B. All isolates showed resistance against ceftriaxone, cefotaxime, and ciprofloxacin, and the C2/H30Rx isolates were also resistant to gentamicin, tobramycin, and ceftazidime.

Conclusions

Out of six ESBL-producing E. coli, five belonged to the ST131 clone. This study indicates, that the C2/H30Rx and C1-M27 subclades of the ST131 appear to be the dominant clones collected in a Hungarian hospital.\n\nPopulation snapshot of the extended-spectrum β-lactamase-producing Escherichia coli invasive strains isolated from a Hungarian hospital.", "token_count": 266, "char_count": 836, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:28.316479", "source": { "split": "train_shard_00001", "doc_id": 3311 }, "chunk_id": "train_shard_00001_3311_1", "global_id": 10358 }, { "text": "Disclosed is a fermented milk product, which is useful for the promotion of good health. The fermented milk product is produced by fermenting a milk raw material with a combination of microorganisms consisting of (1) Lactobacillus kefiri and (2) at least one microorganism selected from the group consisting of Kazachstania turicensis, Kazachstania unispora and Kluyveromyces marxianus. Preferably, the fermented milk product is produced by fermenting the milk raw material with a combination of microorganisms consisting of at least Lactobacillus kefiri strain P-IF, Lactobacillus kefiri strain P-B1, Kazachstania turicensis strain P-Y3, Kazachstania unispora strain P-Y4 and Kluyveromyces marxianus strain P-Y5.\n\nNOVEL FERMENTED MILK PRODUCT AND USE THEREOF", "token_count": 220, "char_count": 759, "word_count": 106, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:28.804787", "source": { "split": "train_shard_00001", "doc_id": 3312 }, "chunk_id": "train_shard_00001_3312_0", "global_id": 10359 }, { "text": "Potential probiotic or immunobiotic effects of lactic acid bacteria (LAB) isolated from the milk of the South American camelid llama (Lama glama) have not been reported in published studies. The aim of the present work was to isolate beneficial LAB from llama milk that can be used as potential probiotics active against bacterial pathogens. LAB strains were isolated from llama milk samples. In vitro functional characterization of the strains was performed by evaluating the resistance against gastrointestinal conditions and inhibition of the pathogen growth. Additionally, the adhesive and immunomodulatory properties of the strains were assessed. The functional studies were complemented with a comparative genomic evaluation and in vivo studies in mice. Ligilactobacillus salivarius TUCO-L2 showed enhanced probiotic/immunobiotic potential compared to that of other tested strains. The TUCO-L2 strain was resistant to pH and high bile salt concentrations and demonstrated antimicrobial activity against Gram-negative intestinal pathogens and adhesion to mucins and epithelial cells. L. salivarius TUCO-L2 modulated the innate immune response triggered by Toll-like receptor (TLR)-4 activation in intestinal epithelial cells. This effect involved differential regulation of the expression of inflammatory cytokines and chemokines mediated by the modulation of the negative regulators of the TLR signaling pathway. Moreover, the TUCO-L2 strain enhanced the resistance of mice to Salmonella infection. This is the first report on the isolation and characterization of a potential probiotic/immunobiotic strain from llama milk. The in vitro, in vivo, and in silico investigation performed in this study reveals several research directions that are needed to characterize the TUCO-L2 strain in detail to position this strain as a probiotic or immunobiotic that can be used against infections in humans or animals, including llama.", "token_count": 507, "char_count": 1987, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:29.479390", "source": { "split": "train_shard_00001", "doc_id": 3313 }, "chunk_id": "train_shard_00001_3313_0", "global_id": 10360 }, { "text": "Functional and Genomic Characterization of Ligilactobacillus salivarius TUCO-L2 Isolated From Lama glama Milk: A Promising Immunobiotic Strain to Combat Infections.", "token_count": 63, "char_count": 178, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:29.837074", "source": { "split": "train_shard_00001", "doc_id": 3313 }, "chunk_id": "train_shard_00001_3313_1", "global_id": 10361 }, { "text": "Glycopeptide antibiotics (GPA) consist of a glycosylated heptapeptide backbone enriched in aromatic residues originating from the shikimate pathway. Since the enzymatic reactions within the shikimate pathway are highly feedback-regulated, this raises the question as to how GPA producers control the delivery of precursors for GPA assembly. We chose Amycolatopsis balhimycina, the producer of balhimycin, as a model strain for analyzing the key enzymes of the shikimate pathway. A. balhimycina contains two copies each of the key enzymes of the shikimate pathway, deoxy-d-arabino-heptulosonate-7-phosphate synthase (Dahp) and prephenate dehydrogenase (Pdh), with one pair (Dahpsec and Pdhsec) encoded within the balhimycin biosynthetic gene cluster and one pair (Dahpprim and Pdhprim) in the core genome. While overexpression of the dahpsec gene resulted in a significant (>4-fold) increase in balhimycin yield, no positive effects were observed after overexpression of the pdhprim or pdhsec genes. Investigation of allosteric enzyme inhibition revealed that cross-regulation between the tyrosine and phenylalanine pathways plays an important role. Tyrosine, a key precursor of GPAs, was found to be a putative activator of prephenate dehydratase (Pdt), which catalyzes the first step reaction from prephenate to phenylalanine in the shikimate pathway. Surprisingly, overexpression of pdt in A. balhimycina led to an increase in antibiotic production in this modified strain. In order to demonstrate that this metabolic engineering approach is generally applicable to GPA producers, we subsequently applied this strategy to Amycolatopsis japonicum and improved the production of ristomycin A, which is used in diagnosis of genetic disorders", "token_count": 501, "char_count": 1817, "word_count": 244, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:30.489072", "source": { "split": "train_shard_00001", "doc_id": 3314 }, "chunk_id": "train_shard_00001_3314_0", "global_id": 10362 }, { "text": "Comparison of \"cluster-specific\" enzymes with the isoenzymes from the primary metabolism's pathway provided insights into the adaptive mechanisms used by producers to ensure adequate precursor supply and GPA yields. These insights further demonstrate the importance of a holistic approach in bioengineering efforts that takes into account not only peptide assembly but also adequate precursor supply.\n\nMetabolic engineering of the shikimate pathway in Amycolatopsis strains for optimized glycopeptide antibiotic production.", "token_count": 115, "char_count": 523, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:30.870186", "source": { "split": "train_shard_00001", "doc_id": 3314 }, "chunk_id": "train_shard_00001_3314_1", "global_id": 10363 }, { "text": "Little is known about zoonotic pathogens and their antimicrobial resistance in South American camelids (SAC) in Germany including Clostridioides (C.) difficile. The aim of this study was to investigate prevalence, molecular characteristics and antimicrobial resistance of C. difficile in SAC. Composite SAC faecal samples were collected in 43 husbandries in Central Germany and cultured for C. difficile. Toxinotyping and ribotyping was done by PCR. Whole genome sequencing was performed with Illumina® Miseq™. The genomes were screened for antimicrobial resistance determinants. Genetic relatedness of the isolates was investigated using core genome multi locus sequence typing (cgMLST) and single nucleotide polymorphism analysis. Antimicrobial susceptibility testing was done using the Etest® method. Eight C. difficile isolates were recovered from seven farms. The isolates belonged to different PCR ribotypes. All isolates were toxinogenic. cgMLST revealed a cluster containing isolates recovered from different farms. Seven isolates showed similar resistance gene patterns. Different phenotypic resistance patterns were found. Agreement between phenotypic and genotypic resistance was identified only in some cases. Consequently, SAC may act as a reservoir for C. difficile. Thus, SAC may pose a risk regarding zoonotic transmission of toxinogenic, potentially human-pathogenic and resistant C. difficile isolates.\n\nClostridioides difficile in South American Camelids in Germany: First Insights into Molecular and Genetic Characteristics and Antimicrobial Resistance.", "token_count": 452, "char_count": 1658, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6238, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:31.508468", "source": { "split": "train_shard_00001", "doc_id": 3315 }, "chunk_id": "train_shard_00001_3315_0", "global_id": 10364 }, { "text": "

Background:

Mycoplasma pneumoniae ( M. pneumoniae ) is an important pathogen of community-acquired pneumonia in children. However, prior to this study, there was a lack of research on the genotypes and macrolide resistance monitoring of M. pneumoniae in Wuhan. The factors contributing to the severity of illness caused by M. pneumoniae infection are still under investigation. We aimed to evaluate the clinical manifestations, genotypes, macrolide resistance, respiratory microenvironment, and their relationship with the severity of illness in children with M. pneumoniae pneumonia in Wuhan.

Results:

Among 1,259 clinical samples, 461 samples were positive for M. pneumoniae via qPCR. We successfully identified the P1 genotypes of 127 samples based on metagenomic and Sanger sequencing, with P1-type 1 (113/127, 88.98%) being the dominant genotype. In addition, we identified the MLST genotypes of 67 samples, with ST-3 being the most common (60/67, 89.6%), followed by ST-14 (5/67, 7.4%) and ST-7 (2/67, 3%). No significant difference in pathogenicity was observed among different genotypes. The macrolide resistance rate of M. pneumoniae isolates was 96% (48/50) and all mutations were A2063G in domain V of 23S rRNA gene. There was no significant difference between the upper respiratory microbiome of patients with mild and severe symptoms. The pan-genome analysis revealed that the genome of M. pneumoniae is highly conserved, with the core genome comprising 79% of the total genome length. In addition, the initial serological test cannot accurately diagnose M. pneumoniae infection. qPCR is suitable for detecting M. pneumoniae infection, while IgM titers greater than 1:160 can be used as a predictor of severity.

Conclusions:

This study is the first to characterize the epidemic and genomic features of M", "token_count": 533, "char_count": 1846, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8055, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:32.165971", "source": { "split": "train_shard_00001", "doc_id": 3316 }, "chunk_id": "train_shard_00001_3316_0", "global_id": 10365 }, { "text": "pneumoniae in Wuhan after the COVID-19 outbreak in 2020, which provides a scientific data basis for monitoring and infection prevention and control of M. pneumoniae in the post-pandemic era.\n\nMolecular epidemiology of Mycoplasma pneumoniae pneumonia in children, Wuhan, 2020-2022", "token_count": 86, "char_count": 279, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7949, "quality_score": 0.8974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:32.538149", "source": { "split": "train_shard_00001", "doc_id": 3316 }, "chunk_id": "train_shard_00001_3316_1", "global_id": 10366 }, { "text": "Abstract

Background: The genome of Vibrionaceae bacteria, which consists of two circular chromosomes, is replicated in a highly ordered fashion. In fast-growing bacteria, multifork replication results in higher gene copy numbers and increased expression of genes located close to the origin of replication of Chr 1 (ori1). This is believed to be a growth optimization strategy to satisfy the high demand of essential growth factors during fast growth. The relationship between ori1-proximate growth-related genes and gene expression during fast growth has been investigated by many researchers. However, it remains unclear which other gene categories that are present close to ori1 and if expression of all ori1-proximate genes is increased during fast growth, or if expression is selectively elevated for certain gene categories.Results: We calculated the pangenome of all complete genomes from the Vibrionaceae family and mapped the four pangene categories, core, softcore, shell and cloud, to their chromosomal positions. This revealed that core and softcore genes were found heavily biased towards ori1, while shell genes were overrepresented at the opposite part of Chr 1 (i.e., close to ter1). RNA-seq of Aliivibrio salmonicida and Vibrio natriegens showed global gene expression patterns that consistently correlated with chromosomal distance to ori1. Despite a biased gene distribution pattern, all pangene categories contributed to a skewed expression pattern at fast-growing conditions, whereas at slow-growing conditions, softcore, shell and cloud genes were responsible for elevated expression.Conclusion: The pangene categories were non-randomly organized on Chr 1, with an overrepresentation of core and softcore genes around ori1, and overrepresentation of shell and cloud genes around ter1", "token_count": 515, "char_count": 2075, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5853, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:33.173520", "source": { "split": "train_shard_00001", "doc_id": 3317 }, "chunk_id": "train_shard_00001_3317_0", "global_id": 10367 }, { "text": "Furthermore, we mapped our gene distribution data on to the intracellular positioning of chromatin described for V. cholerae, and found that core/softcore and shell/cloud genes appear enriched at two spatially separated intracellular regions. Based on these observations, we hypothesize that there is a link between the genomic location of genes and their cellular placement.

\n\nVibrionaceae core, shell and cloud genes are non-randomly distributed on Chr 1: An hypothesis that links the genomic location of genes with their intracellular placement", "token_count": 149, "char_count": 593, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7722, "quality_score": 0.8861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:33.614272", "source": { "split": "train_shard_00001", "doc_id": 3317 }, "chunk_id": "train_shard_00001_3317_1", "global_id": 10368 }, { "text": "

Background

Basenjis are considered an ancient dog breed of central African origins that still live and hunt with tribesmen in the African Congo. Nicknamed the barkless dog, Basenjis possess unique phylogeny, geographical origins and traits, making their genome structure of great interest. The increasing number of available canid reference genomes allows us to examine the impact the choice of reference genome makes with regard to reference genome quality and breed relatedness.

Results

Here, we report two high quality de novo Basenji genome assemblies: a female, China (CanFam_Bas), and a male, Wags. We conduct pairwise comparisons and report structural variations between assembled genomes of three dog breeds: Basenji (CanFam_Bas), Boxer (CanFam3.1) and German Shepherd Dog (GSD) (CanFam_GSD). CanFam_Bas is superior to CanFam3.1 in terms of genome contiguity and comparable overall to the high quality CanFam_GSD assembly. By aligning short read data from 58 representative dog breeds to three reference genomes, we demonstrate how the choice of reference genome significantly impacts both read mapping and variant detection.

Conclusions

The growing number of high-quality canid reference genomes means the choice of reference genome is an increasingly critical decision in subsequent canid variant analyses. The basal position of the Basenji makes it suitable for variant analysis for targeted applications of specific dog breeds. However, we believe more comprehensive analyses across the entire family of canids is more suited to a pangenome approach. Collectively this work highlights the importance the choice of reference genome makes in all variation studies.\n\nChromosome-length genome assembly and structural variations of the primal Basenji dog (Canis lupus familiaris) genome", "token_count": 433, "char_count": 1827, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6023, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:34.242796", "source": { "split": "train_shard_00001", "doc_id": 3318 }, "chunk_id": "train_shard_00001_3318_0", "global_id": 10369 }, { "text": "The hyperarid core of the Atacama Desert is an extremely harsh environment previously thought to be colonized by only a few heterotrophic bacterial species. In addition, carbon and nitrogen cycling in these highly oligotrophic ecosystems are poorly understood. Here we genomically resolved a novel genus of Thaumarchaeota, Ca. Nitrosodesertus , found below boulders of the Atacama hyperarid core, and used comparative genomics to analyze their pangenome and site-specific adaptations. Their genomes contain genes for ammonia oxidation and the 3-hydroxypropionate/4-hydroxybutyrate carbon fixation pathway, indicating a chemolithoautotrophic lifestyle. Ca. Nitrosodesertus possesses the capacity for tolerating extensive environmental stress highlighted by the presence of genes against oxidative stress, DNA damage and genes for the formation of biofilms. These features are likely responsible for their dominance in samples with extremely low water content across three different boulder fields and eight different boulders. Genome-specific adaptations of the genomes included the presence of additional genes for UV resistance, heavy metal transporters, multiple types of ATP synthases, and divergent genes for aquaporins. Our results suggest that Thaumarchaeota mediate important carbon and nitrogen cycling in the hyperarid core of the Atacama and are part of its continuous and indigenous microbiome.\n\nLeave no stone unturned: The hidden potential of carbon and nitrogen cycling by novel, highly adapted Thaumarchaeota in the Atacama Desert hyperarid core", "token_count": 376, "char_count": 1567, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6372, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:34.823951", "source": { "split": "train_shard_00001", "doc_id": 3319 }, "chunk_id": "train_shard_00001_3319_0", "global_id": 10370 }, { "text": "Staphylococcus aureus infections are associated with high mortality rates. Often considered an extracellular pathogen, S. aureus can persist and replicate within host cells, evading immune responses, and causing host cell death. Classical methods for assessing S. aureus cytotoxicity are limited by testing culture supernatants and endpoint measurements that do not capture the phenotypic diversity of intracellular bacteria. Using a well-established epithelial cell line model, we have developed a platform called InToxSa (intracellular toxicity of S. aureus) to quantify intracellular cytotoxic S. aureus phenotypes. Studying a panel of 387 S. aureus bacteraemia isolates, and combined with comparative, statistical, and functional genomics, our platform identified mutations in S. aureus clinical isolates that reduced bacterial cytotoxicity and promoted intracellular persistence. In addition to numerous convergent mutations in the Agr quorum sensing system, our approach detected mutations in other loci that also impacted cytotoxicity and intracellular persistence. We discovered that clinical mutations in ausA, encoding the aureusimine non-ribosomal peptide synthetase, reduced S. aureus cytotoxicity, and increased intracellular persistence. InToxSa is a versatile, high-throughput cell-based phenomics platform and we showcase its utility by identifying clinically relevant S. aureus pathoadaptive mutations that promote intracellular residency.", "token_count": 465, "char_count": 1575, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6772, "quality_score": 0.8386, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:35.467890", "source": { "split": "train_shard_00001", "doc_id": 3320 }, "chunk_id": "train_shard_00001_3320_0", "global_id": 10371 }, { "text": "A high-throughput cytotoxicity screening platform reveals agr-independent mutations in bacteraemia-associated Staphylococcus aureus that promote intracellular persistence.", "token_count": 57, "char_count": 185, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:35.824418", "source": { "split": "train_shard_00001", "doc_id": 3320 }, "chunk_id": "train_shard_00001_3320_1", "global_id": 10372 }, { "text": "This study presents an effective procedure for the determination of a biologically inspired, black-box model of cultures of microorganisms (including yeasts, bacteria, plant and animal cells) in bioreactors. This procedure is based on sets of experimental data measuring the time-evolution of a few extracellular species concentrations, and makes use of maximum likelihood principal component analysis to determine, independently of the kinetics, an appropriate number of macroscopic reactions and their stoichiometry. In addition, this paper provides a discussion of the geometric interpretation of a stoichiometric matrix and the potential equivalent reaction schemes. The procedure is carefully evaluated within the stoichiometric identification framework of the growth of the yeast Kluyveromyces marxianus on cheese whey. Using Monte Carlo studies, it is also compared with two other previously published approaches.\n\nStoichiometric identification with maximum likelihood principal component analysis.", "token_count": 190, "char_count": 1005, "word_count": 134, "semantic_coherence": 1, "information_density": 0.6866, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:36.269652", "source": { "split": "train_shard_00001", "doc_id": 3321 }, "chunk_id": "train_shard_00001_3321_0", "global_id": 10373 }, { "text": "

Background

Multidrug-resistant Enterobacterales (MDR-E), including carbapenem-resistant and third-generation cephalosporin-resistant Enterobacterales (CRE, CefR-E), are major pathogens following solid organ transplantation (SOT).

Methods

We prospectively studied patients who underwent lung, liver, and small bowel transplant from February 2015 through March 2017. Weekly perirectal swabs (up to 100 days post-transplant) were cultured for MDR-E. Whole-genome sequencing (WGS) was performed on gastrointestinal (GI) tract-colonizing and disease-causing isolates.

Results

Twenty-five percent (40 of 162) of patients were MDR-E GI-colonized. Klebsiella pneumoniae was the most common CRE and CefR-E. Klebsiella pneumoniae carbapenemases and CTX-M were leading causes of CR and CefR, respectively. Thirty-five percent of GI colonizers developed MDR-E infection vs 2% of noncolonizers (P < .0001). The attack rate was higher among CRE colonizers than CefR-E colonizers (53% vs 21%, P = .049). GI colonization and high body mass index were independent risk factors for MDR-E infection (P ≤ .004). Thirty-day mortality among infected patients was 6%. However, 44% of survivors developed recurrent infections; 43% of recurrences were late (285 days to 3.9 years after the initial infection). Long-term survival (median, 4.3 years post-transplant) did not differ significantly between MDR-E-infected and MDR-E-noninfected patients (71% vs 77%, P = .56). WGS phylogenetic analyses revealed that infections were caused by GI-colonizing strains and suggested unrecognized transmission of novel clonal group-258 sublineage CR-K", "token_count": 517, "char_count": 1637, "word_count": 210, "semantic_coherence": 1, "information_density": 0.7571, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:36.906671", "source": { "split": "train_shard_00001", "doc_id": 3322 }, "chunk_id": "train_shard_00001_3322_0", "global_id": 10374 }, { "text": "pneumoniae and horizontal transfer of resistance genes.

Conclusions

MDR-E GI colonization was common following SOT and predisposed patients to infections by colonizing strains. MDR-E infections were associated with low short- and long-term mortality, but recurrences were frequent and often occurred years after initial infections. Findings provide support for MDR-E surveillance in our SOT program.\n\nMolecular Epidemiology, Natural History, and Long-Term Outcomes of Multidrug-Resistant Enterobacterales Colonization and Infections Among Solid Organ Transplant Recipients.", "token_count": 144, "char_count": 580, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8143, "quality_score": 0.9071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:37.337299", "source": { "split": "train_shard_00001", "doc_id": 3322 }, "chunk_id": "train_shard_00001_3322_1", "global_id": 10375 }, { "text": "Corn silage juice was found to be a favorable substrate for production of fodder yeasts. Kluyveromyces marxianus NRRL Y-610 yielded significantly more cell dry weight than other cultures examined. In shake-flask experiments, the yeast produced over 13 g of cell dry weight per liter of corn silage juice and completely consumed the organic pollutants (lactic acid, acetic acid, and ethanol). The yeast settled rapidly and had a yeast volume index of 21 ml/g. The results indicate that K. marxianus NRRL Y-610 could be used to efficiently remove lactic acid and other organic compounds from corn silage juice with the concomitant production of fodder yeast.\n\nUtilization of corn silage juice by Klyuveromyces marxianus.", "token_count": 192, "char_count": 718, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:37.785066", "source": { "split": "train_shard_00001", "doc_id": 3323 }, "chunk_id": "train_shard_00001_3323_0", "global_id": 10376 }, { "text": "

Background

In this study, our aim was to identify Candida species isolated from bloodstream infections and to determine their susceptibilities to various antifungal agents to demonstrate the local resistance profiles and to guide empirical treatment for clinicians.

Methods

Two hundred Candida isolates (95 Candida albicans, 105 non-albicans Candida strains) were included in the study. Candida species were identified by conventional, biochemical and molecular methods. Antifungal susceptibility tests for amphotericin B, fluconazole, voriconazole, posaconazole, caspofungin and anidulafungin were performed with broth microdilution method according to the Clinical and Laboratory Standards Institute M27-A3 document.

Results

Of the 200 Candida strains, the most prevalent species were C. albicans (47.5 %), Candida glabrata (18.0 %) and Candida parapsilosis complex (14.0 %). All Candida species except for three (1.5 %) Candida kefyr strains were susceptible to amphotericin B. Only one (2.8 %) C. glabrata was resistant to fluconazole (MIC ≥ 64 μg/ml), and the others (97.2 %) exhibited dose-dependent susceptibility. All species, but C. glabrata strains, were susceptible to fluconazole. Resistance to voriconazole, posaconazole, caspofungin and anidulafungin was not detected in any strain.

Conclusion

Candida albicans were susceptible to all antifungal drugs. Three C. kefyr strains were resistant to amphotericin B. Only one C. glabrata was resistant to fluconazole. All the strains were susceptible to voriconazole, posaconazole, caspofungin and anidulafungin. In vitro antifungal susceptibility tests should be performed to select of appropriate and effective antifungal therapy, and monitor the development of resistance.", "token_count": 517, "char_count": 1761, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5478, "quality_score": 0.7739, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:38.425510", "source": { "split": "train_shard_00001", "doc_id": 3324 }, "chunk_id": "train_shard_00001_3324_0", "global_id": 10377 }, { "text": "Identification and antifungal susceptibility of Candida species isolated from bloodstream infections in Konya, Turkey.", "token_count": 26, "char_count": 118, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:38.787621", "source": { "split": "train_shard_00001", "doc_id": 3324 }, "chunk_id": "train_shard_00001_3324_1", "global_id": 10378 }, { "text": "Consolidated bioprocessing technology can be used for Kluyveromyces marxianus YX01 to produce ethanol from Jerusalem artichoke, which is one of the potential processes to produce biofuel from non-cereal crops. In this study, we combined the aeration rate with the substrate concentration to conduct cross-over experiments for K. marxinaus YX01, and studied ethanol fermentation and the influence of inulin enzyme activity. The substrate concentration had a little repressive effect on ethanol productivity. When substrate concentration reached 250 g/L under anaerobic conditions, ethanol concentration was 84.8 g/L, and ethanol yield was reduced from 86.4% (50 g/L substrate concentration) to 84.7% of the theoretical value. Aeration rate could accelerate K. marxinaus YX01 ethanol fermentation, but reduced ethanol yield. When substrate concentration reached 250 g/L under aeration at 1.0 vvm, ethanol yield was reduced from 84.7% under anaerobic conditions to 73.3% of the theoretical value. With increased concentration of the carbon source and reduced aeration rate, the inulinase of K. marxinaus YX01 reduced and the concentration of glycerol increased, however, the acetic acid increased with the increased concentration of the carbon source and aeration rate. When substrate concentration reached 250 g/L under anaerobic conditions, inulinase activity was only 6.59 U/mL; when substrate concentration reached 50 g/L under aeration at 1.0 vvm, inulinase activity was 21.54 U/mL.\n\n[Effect of aeration and inulin concentration on ethanol production by Kluyveromyces marxinaus YX01].", "token_count": 446, "char_count": 1586, "word_count": 225, "semantic_coherence": 1, "information_density": 0.4711, "quality_score": 0.7356, "entities": { "genes": [ "YX01" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:39.429152", "source": { "split": "train_shard_00001", "doc_id": 3325 }, "chunk_id": "train_shard_00001_3325_0", "global_id": 10379 }, { "text": "Nontyphoidal Salmonella (NTS) in children remains a growing burden on public health and often causes children to be hospitalized with diarrheic symptoms. In this work, 260 strains of human Salmonella isolated from Jilin, China were characterized by serotypes and antimicrobial resistance using whole genome sequencing (WGS). The most prevalent serotype was Salmonella enteritidis (47.3%), followed by S. I 4,[5],12:i:- (33.1%), and Salmonella Typhimurium (7.3%). Furthermore, the consistency between resistance phenotype and genotype was confirmed. Similarly, strains harbored bla TEM-1B and tetA genes were detected, which verified the level of resistant phenotype in β-lactams and tetracyclines. The presence of a single mutation in parC, gyrA, and qnrS1 genes corresponding to quinolones was also observed. In our work, multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) were found to have a high resolution to molecular traceability, and the combination of both was conducive to practical application in an actual situation. Taking all of this into account, we suggested that the comprehensive surveillance of Salmonella infection in children should be carried out to monitor antimicrobial-resistant trends from various sources and to alert on outbreaks of foodborne diseases to protect public health.\n\nWhole Genome Sequencing, Antibiotic Resistance, and Epidemiology Features of Nontyphoidal Salmonella Isolated From Diarrheic Children: Evidence From North China.", "token_count": 468, "char_count": 1605, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:40.089617", "source": { "split": "train_shard_00001", "doc_id": 3326 }, "chunk_id": "train_shard_00001_3326_0", "global_id": 10380 }, { "text": "A non-flocculent strain of Saccharomyces cerevisiae was transformed with the GAP1 gene which encodes p37, a GAPDH-like protein present in the cell wall of Kluyveromyces marxianus flocculent cells. The transformed cells were characterized with respect to flocculation behaviour, morphology, growth, cell wall integrity and GAPDH activity. A flocculent phenotype was acquired by the transformed cells, showing a behaviour in respect to flocculation/deflocculation very similar to that of K. marxianus. The presence of p37 in the cell wall was assessed by immunoprecipitation of biotinylated cell wall proteins and an accumulation of p37 was evident in the cell wall of transformed cells. This result was confirmed by studies using a chimeric protein resulting from fusing the p37 with a yeast-enhanced green fluorescent protein, yEGFP. The recombinant protein was localized mainly in the cell wall of the transformed strain, although the presence of p37 in the cytosol was indicated by an increase in GAPDH activity. Calcofluor white sensitivity tests indicated that the cell wall structure is affected by the accumulation of p37. These results provided further evidence of p37 function regarding flocculation and that although lacking a N-terminal signal peptide p37 is targeted to the cell wall.\n\nFlocculation of Saccharomyces cerevisiae is induced by transformation with the GAP1 gene from Kluyveromyces marxianus.", "token_count": 361, "char_count": 1415, "word_count": 209, "semantic_coherence": 1, "information_density": 0.4976, "quality_score": 0.7488, "entities": { "genes": [ "GAP1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:40.692304", "source": { "split": "train_shard_00001", "doc_id": 3327 }, "chunk_id": "train_shard_00001_3327_0", "global_id": 10381 }, { "text": "Understanding the functional potential of the gut microbiome is of primary importance for the design of innovative strategies for allergy treatment and prevention. Here we report the gut microbiome features of 90 children affected by food (FA) or respiratory (RA) allergies and 30 age-matched, healthy controls (CT). We identify specific microbial signatures in the gut microbiome of allergic children, such as higher abundance of Ruminococcus gnavus and Faecalibacterium prausnitzii, and a depletion of Bifidobacterium longum, Bacteroides dorei, B. vulgatus and fiber-degrading taxa. The metagenome of allergic children shows a pro-inflammatory potential, with an enrichment of genes involved in the production of bacterial lipo-polysaccharides and urease. We demonstrate that specific gut microbiome signatures at baseline can be predictable of immune tolerance acquisition. Finally, a strain-level selection occurring in the gut microbiome of allergic subjects is identified. R. gnavus strains enriched in FA and RA showed lower ability to degrade fiber, and genes involved in the production of a pro-inflammatory polysaccharide. We demonstrate that a gut microbiome dysbiosis occurs in allergic children, with R. gnavus emerging as a main player in pediatric allergy. These findings may open new strategies in the development of innovative preventive and therapeutic approaches. Trial: NCT04750980.\n\nSpecific gut microbiome signatures and the associated pro-inflamatory functions are linked to pediatric allergy and acquisition of immune tolerance.", "token_count": 383, "char_count": 1552, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.7949, "entities": { "genes": [ "NCT04750980" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:41.320218", "source": { "split": "train_shard_00001", "doc_id": 3328 }, "chunk_id": "train_shard_00001_3328_0", "global_id": 10382 }, { "text": "The dramatic increase in genome sequencing during the last years has changed our ideas about bacterial diversity, from single gene to whole community DNA surveys; we have learned that nature's lagest gene repository resides in bacteria resides in bacteria. Comparison of bacteria genomes has contributed to understand the flexibility in size and gene content as well as the gene movement due to gene family expansions and Horizontal Gene Transfer. Bacteria species are currently defined by means of 16S rRNA sequence comparisons and some limited phenotypic traits. There is an ongoing debate about the biological and evolutive significance of the bacteria species, and thus the need to refine the definition of it using the most of the genomic shared information across any taxonomic range. When comparing multiple genomes of related strains we can distinguish a set of common shared features which are known as the core genome. In the other hand, the set of strain specific genes are known as accessory genome. The accessory and core genome conform the total of the genetic composition, and are known as pan-genome. Here we present the possibilities using pan-genomics as a workhorse to describe both taxonomical and functional diversity within bacteria.\n\nPan-genomics: Unmasking the gene diversity hidden in the bacteria species", "token_count": 276, "char_count": 1330, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6184, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:41.877939", "source": { "split": "train_shard_00001", "doc_id": 3329 }, "chunk_id": "train_shard_00001_3329_0", "global_id": 10383 }, { "text": "

Background

In September 2018, Burkholderia cepacia complex (BCC) infections in 3 patients associated with exposure to a mouthwash solution (MWS) were reported to the Robert Koch Institute (RKI). As the product was still on the market and the scale of the outbreak was unclear, a nation-wide investigation was initiated.

Methods

We aimed to investigate BCC infections/colonizations associated with MWS. Hospitals, laboratories, and public health services were informed that BCC isolates should be sent to the RKI. These isolates were typed by pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing (WGS) including development of an ad hoc core genome MLST (cgMLST) scheme.

Results

In total, 36 patients from 6 hospitals met the case definition, the last patient in November 2018. Twenty-nine isolates from 26 of these patients were available for typing. WGS analysis revealed 2 distinct cgMLST clusters. Cluster 1 (Burkholderia arboris) contained isolates from patients and MWS obtained from 4 hospitals and isolates provided by the manufacturer. Patient and MWS isolates from another hospital were assigned to cluster 2 (B. cepacia).

Conclusions

The combined clinical, epidemiological, and microbiological investigation, including whole-genome analysis, allowed for uncovering a supraregional BCC outbreak in health care settings. Strains of B. arboris and B. cepacia were identified as contaminating species of MWS bottles and subsequent colonization and putative infection of patients in several hospitals. Despite a recall of the product by the manufacturer in August 2018, the outbreak lasted until December 2018. Reporting of contaminated medical products and recalls should be optimized to protect patients.", "token_count": 479, "char_count": 1790, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6405, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:42.518229", "source": { "split": "train_shard_00001", "doc_id": 3330 }, "chunk_id": "train_shard_00001_3330_0", "global_id": 10384 }, { "text": "Combined Clinical, Epidemiological, and Genome-Based Analysis Identified a Nationwide Outbreak of Burkholderia cepacia Complex Infections Caused by Contaminated Mouthwash Solutions.", "token_count": 54, "char_count": 188, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:42.881351", "source": { "split": "train_shard_00001", "doc_id": 3330 }, "chunk_id": "train_shard_00001_3330_1", "global_id": 10385 }, { "text": "Host-adapted microorganisms are generally assumed to have evolved from free-living, environmental microorganisms, as examples of the reverse process are rare. In the phylum Gammaproteobacteria, family Moraxellaceae, the genus Psychrobacter includes strains from a broad ecological distribution including animal bodies as well as sea ice and other nonhost environments. To elucidate the relationship between these ecological niches and Psychrobacter's evolutionary history, we performed tandem genomic analyses with phenotyping of 85 Psychrobacter accessions. Phylogenomic analysis of the family Moraxellaceae reveals that basal members of the Psychrobacter clade are Moraxella spp., a group of often-pathogenic organisms. Psychrobacter exhibited two broad growth patterns in our phenotypic screen: one group that we called the \"flexible ecotype\" (FE) had the ability to grow between 4 and 37°C, and the other, which we called the \"restricted ecotype\" (RE), could grow between 4 and 25°C. The FE group includes phylogenetically basal strains, and FE strains exhibit increased transposon copy numbers, smaller genomes, and a higher likelihood to be bile salt resistant. The RE group contains only phylogenetically derived strains and has increased proportions of lipid metabolism and biofilm formation genes, functions that are adaptive to cold stress. In a 16S rRNA gene survey of polar bear fecal samples, we detect both FE and RE strains, but in in vivo colonizations of gnotobiotic mice, only FE strains persist", "token_count": 448, "char_count": 1583, "word_count": 219, "semantic_coherence": 1, "information_density": 0.653, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:43.516608", "source": { "split": "train_shard_00001", "doc_id": 3331 }, "chunk_id": "train_shard_00001_3331_0", "global_id": 10386 }, { "text": "Our results indicate the ability to grow at 37°C, seemingly necessary for mammalian gut colonization, is an ancestral trait for Psychrobacter, which likely evolved from a pathobiont.IMPORTANCE Host-associated microbes are generally assumed to have evolved from free-living ones. The evolutionary transition of microbes in the opposite direction, from host associated toward free living, has been predicted based on phylogenetic data but not studied in depth. Here, we provide evidence that the genus Psychrobacter, particularly well known for inhabiting low-temperature, high-salt environments such as sea ice, permafrost soils, and frozen foodstuffs, has evolved from a mammalian-associated ancestor. We show that some Psychrobacter strains retain seemingly ancestral genomic and phenotypic traits that correspond with host association while others have diverged to psychrotrophic or psychrophilic lifestyles.\n\nFree-Living, Psychrotrophic Bacteria of the Genus Psychrobacter Are Descendants of Pathobionts.", "token_count": 274, "char_count": 1042, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7612, "quality_score": 0.8806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:44.066890", "source": { "split": "train_shard_00001", "doc_id": 3331 }, "chunk_id": "train_shard_00001_3331_1", "global_id": 10387 }, { "text": "The yeast Kluyveromyces marxianus strain BKM Y-719 produces an efficient pectin-degrading endopolygalacturonase (EPG) that cleaves the internal alpha-1,4-D-glycosidic linkages to yield oligomers of varying sizes. The EPG1 gene encoding this industrially important EPG was cloned by using the polymerase chain reaction (PCR) technique and degenerate primers to generate a 135 bp DNA fragment with which a genomic library was screened. The cloned fragment contained an open reading frame (ORF) of 1083 bp, encoding a 361 amino acid polypeptide. The predicted amino acid (aa) sequence of EPG showed similarity with polygalacturonases (PGs) of fungi. Analysis of the aa sequence indicated that the first 25 aa constitute a signal sequence and a motif (C218XGGHGXSIGSVG230) that is usually associated with a PG active site. Pulsed-field gel electrophoresis resolved chromosomal bands for K. marxianus BKM Y-719 and using chromoblotting it seems that EPG1 is present as only a single copy in the genome.\n\nCloning, targeted disruption and heterologous expression of the Kluyveromyces marxianus endopolygalacturonase gene (EPG1).", "token_count": 337, "char_count": 1121, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6914, "quality_score": 0.8457, "entities": { "genes": [ "EPG1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:44.634492", "source": { "split": "train_shard_00001", "doc_id": 3332 }, "chunk_id": "train_shard_00001_3332_0", "global_id": 10388 }, { "text": "

Objectives

To highlight the importance of molecular testing in characterizing extensively drug-resistant (XDR) Salmonella Typhi (S. Typhi), and linking it to the current outbreak in Sindh, Pakistan.

Methods

Our study reports three travel-related typhoid fever cases caused by XDR S. Typhi that presented between January 2019 and August 2019. Antimicrobial susceptibility and genotyping with pulse-field gel electrophoresis (PFGE) were carried out. Whole-genome sequencing (WGS) was performed to characterize the genomic clonality in relation to the emerging outbreak of S. Typhi in Sindh, Pakistan, and to study the molecular resistance profiles.

Results

Laboratory testing revealed resistance to all first-line antibiotics (i.e ampicillin, chloramphenicol, and trimethoprim-sulfamethoxazole), as well as to quinolones and third-generation cephalosporins, leading to a change in the patients' therapy to the use of carbapenems. Classical MLST (cMLST) revealed that the strains were of sequence type 1 (ST1) and the core genome sequence (cgWGS) analysis closely clustered our strains with internationally reported strains from Pakistan, India, and the UK. The strains were found to carry a bla CTX-15 gene-harbouring IncY plasmid, which encodes resistance to ceftriaxone.

Conclusions

Our report alerts clinicians to the use of appropriate empirical treatments in such scenarios, and highlights the significance of the global spread of XDR S. Typhi.\n\nGenomic analysis of the first cases of extensively drug-resistant, travel-related Salmonella enterica serovar Typhi in Oman.", "token_count": 483, "char_count": 1662, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:45.285617", "source": { "split": "train_shard_00001", "doc_id": 3333 }, "chunk_id": "train_shard_00001_3333_0", "global_id": 10389 }, { "text": "

Aims

E. coli are ubiquitously present bacterial pathogens that cause septicaemia, diarrhoea and other clinical illness in farm animals. Many pathogen factors can be associated with disease conditions. Currently, studies inferring E. coli genetic factors associated with infection in bovines are limited. Hence, the present study envisaged to determine the pathogen genetic factors associated with bovine disease conditions.

Method and results

The comparative genomic analysis involved genome sequence data of 135 diseased and 145 healthy bovine origin E. coli strains. Phylogroups A and C, as well as pathotypes ExPEC and EPEC, were found to have a strong connection with bovine disease strains. STEC strains, including EHEC, seem to play a less important role in bovine disease. Sequence types (STs) predominant among strains from diarrhoeal origin were ST 301 (CC 165) and ST 342. Correlation of core genome phylogeny with accessory gene-based clustering, phylogroups and pathotypes indicated lineage-specific virulence factors mostly associated with disease conditions.

Conclusions

Comparative genomic analysis was applied to infer genetic factors significant in bovine disease origin E. coli strains. Isolates from bovine disease origin were enriched for the phylogroups A and C, and for the pathotypes ExPEC and EPEC. However, there was minimal evidence of STEC involvement. The study also indicated predominant genetic lineages and virulence genes (pap, sfa and afa) associated with disease origin strains.

Significance and impact of study

The study revealed significant pathotypes, phylogroups, serotypes and sequence types associated with bovine disease conditions. These identified genetic factors can be applied for disease diagnosis, implementing vaccines and therapeutic measures. In addition, E. coli isolates from the bovine species revealed a complex pattern of disease epidemiology.", "token_count": 486, "char_count": 1927, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5399, "quality_score": 0.77, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:45.936742", "source": { "split": "train_shard_00001", "doc_id": 3334 }, "chunk_id": "train_shard_00001_3334_0", "global_id": 10390 }, { "text": "A comparative genomics approach for identifying genetic factors in Escherichia coli isolates associated with bovine diseases.", "token_count": 27, "char_count": 125, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:46.295016", "source": { "split": "train_shard_00001", "doc_id": 3334 }, "chunk_id": "train_shard_00001_3334_1", "global_id": 10391 }, { "text": "Increased efficiency of substrate utilization by exposure of the thermotolerant yeast strain, Kluyveromyces marxianus IMB3 to electric-field stimulation.", "token_count": 39, "char_count": 153, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:46.654599", "source": { "split": "train_shard_00001", "doc_id": 3335 }, "chunk_id": "train_shard_00001_3335_0", "global_id": 10392 }, { "text": "Since the spread of multidrug-resistant Klebsiella pneumoniae (MDRKP) strains is considered as a challenge for patients with weakened or suppressed immunity, the emergence of isolates carrying determinants of hypervirulent phenotypes in addition may become a serious problem even for healthy individuals. The aim of this study is an investigation of the nonoutbreak K. pneumoniae emergence occurred in early 2017 at a maternity hospital of Kazan, Russia. Ten bacterial isolates demonstrating multiple drug resistance phenotypes were collected from eight healthy full-term breastfed neonates, observed at the maternity hospital of Kazan, Russia. All the infants and their mothers were dismissed without symptoms or complaints, in a satisfactory condition. Whole-genome shotgun (WGS) sequencing was performed with the purpose to track down a possible spread source(s) and obtain detailed information about resistance determinants and pathogenic potential of the collected isolates. Microdilution tests have confirmed production of extended-spectrum β-lactamases (ESBL) and their resistance to aminoglycoside, β-lactam, fluoroquinolone, sulfonamide, nitrofurantoin, trimethoprim, and fosfomycin antibiotics and Klebsiella phage. The WGS analysis has revealed the genes that are resistant to aminoglycosides, fluoroquinolones, macrolides, sulfonamides, chloramphenicols, tetracyclines, and trimethoprim and ESBL determinants. The pangenome analysis had split the isolates into two phylogenetic clades. The first group, a more heterogeneous clade, was represented by 5 isolates with 4 different in silico multilocus sequence types (MLSTs)", "token_count": 448, "char_count": 1675, "word_count": 215, "semantic_coherence": 1, "information_density": 0.7116, "quality_score": 0.8558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:47.294148", "source": { "split": "train_shard_00001", "doc_id": 3336 }, "chunk_id": "train_shard_00001_3336_0", "global_id": 10393 }, { "text": "The second group contained 5 isolates from infants born vaginally with the single MLST ST23, positive for genes corresponding to hypervirulent phenotypes: yersiniabactin, aerobactin, salmochelin, colibactin, hypermucoid determinants, and specific alleles of K- and O-antigens. The source of the MDRKP spread was not defined. Infected infants have shown no developed disease symptoms.\n\nMultidrug-Resistant Hypervirulent Klebsiella pneumoniae Found Persisting Silently in Infant Gut Microbiota.", "token_count": 145, "char_count": 499, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [ "ST23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:47.716292", "source": { "split": "train_shard_00001", "doc_id": 3336 }, "chunk_id": "train_shard_00001_3336_1", "global_id": 10394 }, { "text": "Streptococcus agalactiae is an invasive multi-host pathogen that causes invasive diseases mainly in newborns, elderly, and individuals with underlying health complications. In fish, S. agalactiae causes streptococcosis, which is characterized by septicemia and neurological signs, and leads to great economic losses to the fish farming industry worldwide. These bacteria can be classified into different serotypes based on capsular antigens, and into different sequence types (ST) based on multilocus sequence typing (MLST). In 2015, serotype III ST283 was identified to be associated with a foodborne invasive disease in non-pregnant immunocompetent humans in Singapore, and the infection was related to raw fish consumption. In addition, a serotype III strain isolated from tilapia in Brazil has been reported to be resistant to five antibiotic classes. This specific serotype can serve as a reservoir of resistance genes and pose a serious threat to public health. Thus, new approaches for the control and treatment of S. agalactiae infections are needed. In the present study, 24 S. agalactiae serotype III complete genomes, isolated from human and fish hosts, were compared. The core genome was identified, and, using bioinformatics tools and subtractive criteria, five proteins were identified as potential drug targets. Furthermore, 5,008 drug-like natural compounds were virtually screened against the identified targets. The ligands with the best binding properties are suggested for further in vitro and in vivo analysis.\n\nIn silico Prediction of New Drug Candidates Against the Multidrug-Resistant and Potentially Zoonotic Fish Pathogen Serotype III Streptococcus agalactiae.", "token_count": 446, "char_count": 1742, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [ "ST283" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:48.350534", "source": { "split": "train_shard_00001", "doc_id": 3337 }, "chunk_id": "train_shard_00001_3337_0", "global_id": 10395 }, { "text": "

Summary

PanViz is a novel, interactive, visualization tool for pangenome analysis. PanViz allows visualization of changes in gene group (groups of similar genes across genomes) classification as different subsets of pangenomes are selected, as well as comparisons of individual genomes to pangenomes with gene ontology based navigation of gene groups. Furthermore it allows for rich and complex visual querying of gene groups in the pangenome. PanViz visualizations require no external programs and are easily sharable, allowing for rapid pangenome analyses.

Availability and implementation

PanViz is written entirely in JavaScript and is available on https://github.com/thomasp85/PanViz . A companion R package that facilitates the creation of PanViz visualizations from a range of data formats is released through Bioconductor and is available at https://bioconductor.org/packages/PanVizGenerator .

Contact

thomasp85@gmail.com.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nPanViz: interactive visualization of the structure of functionally annotated pangenomes.", "token_count": 278, "char_count": 1133, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:48.900764", "source": { "split": "train_shard_00001", "doc_id": 3338 }, "chunk_id": "train_shard_00001_3338_0", "global_id": 10396 }, { "text": "

Background

Illumina technology currently dominates bacterial genomics due to its high read accuracy and low sequencing cost. However, the incompleteness of draft genomes generated by Illumina reads limits their application in comprehensive genomics analyses. Alternatively, hybrid assembly using both Illumina short reads and long reads generated by single molecule sequencing technologies can enable assembly of complete bacterial genomes, yet the high per-genome cost of long-read sequencing limits the widespread use of this approach in bacterial genomics. Here we developed a protocol for hybrid assembly of complete bacterial genomes using miniaturized multiplexed Illumina sequencing and non-barcoded PacBio sequencing of a synthetic genomic pool (SGP), thus significantly decreasing the overall per-genome cost of sequencing.

Results

We evaluated the performance of SGP hybrid assembly on the genomes of 20 bacterial isolates with different genome sizes, a wide range of GC contents, and varying levels of phylogenetic relatedness. By improving the contiguity of Illumina assemblies, SGP hybrid assembly generated 17 complete and 3 nearly complete bacterial genomes. Increased contiguity of SGP hybrid assemblies resulted in considerable improvement in gene prediction and annotation. In addition, SGP hybrid assembly was able to resolve repeat elements and identify intragenomic heterogeneities, e.g. different copies of 16S rRNA genes, that would otherwise go undetected by short-read-only assembly. Comprehensive comparison of SGP hybrid assemblies with those generated using multiplexed PacBio long reads (long-read-only assembly) also revealed the relative advantage of SGP hybrid assembly in terms of assembly quality. In particular, we observed that SGP hybrid assemblies were completely devoid of both small (i.e. single base substitutions) and large assembly errors. Finally, we show the ability of SGP hybrid assembly to differentiate genomes of closely related bacterial isolates, suggesting its potential application in comparative genomics and pangenome analysis.

Conclusion

Our results indicate the superiority of SGP hybrid assembly over both short-read and long-read assemblies with respect to completeness, contiguity, accuracy, and recovery of small replicons", "token_count": 520, "char_count": 2306, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5566, "quality_score": 0.7783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:49.555256", "source": { "split": "train_shard_00001", "doc_id": 3339 }, "chunk_id": "train_shard_00001_3339_0", "global_id": 10397 }, { "text": "By lowering the per-genome cost of sequencing, our parallel sequencing and hybrid assembly pipeline could serve as a cost effective and high throughput approach for completing high-quality bacterial genomes.\n\nCompletion of draft bacterial genomes by long-read sequencing of synthetic genomic pools.", "token_count": 64, "char_count": 298, "word_count": 41, "semantic_coherence": 1, "information_density": 0.8293, "quality_score": 0.9146, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:49.922401", "source": { "split": "train_shard_00001", "doc_id": 3339 }, "chunk_id": "train_shard_00001_3339_1", "global_id": 10398 }, { "text": "

Objectives

An increasing number of isolations of Corynebacterium diphtheriae has been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples with C. diphtheriae .

Methods

All C. diphtheriae isolates identified in New Caledonia from May 2015 to May 2019 were included. For each case, a retrospective consultation of the patient files was conducted. Antimicrobial susceptibility phenotypes, tox gene and diphtheria toxin expression, biovar and the genomic sequence were determined. Core genome multilocus sequence typing (cgMLST), 7-gene MLST and search of genes of interest were performed from genomic assemblies.

Results

58 isolates were included, with a median age of patients of 28 years (range: 9 days to 78 years). Cutaneous origin accounted for 51 of 58 (87.9%) isolates, and C. diphtheriae was associated with Staphylococcus aureus and/or Streptococcus pyogenes in three quarters of cases. Half of cases came either from the main city Noumea (24%, 14/58) or from the sparsely populated island of Lifou (26%, 15/58). Six tox-positive isolates were identified, associated with recent travel to Vanuatu; 5 of these cases were linked and cgMLST confirmed recent transmission. Two cases of endocarditis in young female patients with a history of rheumatic fever involved tox-negative isolates. The 58 isolates were mostly susceptible to commonly used antibiotics. In particular, no isolate was resistant to the first-line molecules amoxicillin or erythromycin. Resistance to tetracycline was found in a genomic cluster of 17 (29%) isolates, 16 of which carried the tetO gene. There were 13 cgMLST sublineages, most of which were also observed in the neighboring country Australia", "token_count": 515, "char_count": 1787, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:50.554639", "source": { "split": "train_shard_00001", "doc_id": 3340 }, "chunk_id": "train_shard_00001_3340_0", "global_id": 10399 }, { "text": "

Conclusions

Cutaneous infections may harbor non-toxigenic C. diphtheriae isolates, which circulate largely silently in non-specific wounds. The possible introduction of tox-positive strains from a neighboring island illustrates that diphtheria surveillance should be maintained in New Caledonia, and that immunization in neighboring islands must be improved. Genomic sequencing uncovers how genotypes circulate locally and across neighboring countries.\n\nGenomic epidemiology ofCorynebacterium diphtheriaein New Caledonia", "token_count": 141, "char_count": 536, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:50.988749", "source": { "split": "train_shard_00001", "doc_id": 3340 }, "chunk_id": "train_shard_00001_3340_1", "global_id": 10400 }, { "text": "Cronobacter sakazakii continues to be isolated from ready-to-eat fresh and frozen produce, flours, dairy powders, cereals, nuts, and spices, in addition to the conventional sources of powdered infant formulae (PIF) and PIF production environments. To understand the sequence diversity, phylogenetic relationship, and virulence of C. sakazakii originating from plant-origin foods, comparative molecular and genomic analyses, and zebrafish infection (ZI) studies were applied to 88 strains. Whole genome sequences of the strains were generated for detailed bioinformatic analysis. PCR analysis showed that all strains possessed a pESA3-like virulence plasmid similar to reference C. sakazakii clinical strain BAA-894. Core genome analysis confirmed a shared genomic backbone with other C. sakazakii strains from food, clinical and environmental strains. Emerging nucleotide diversity in these plant-origin strains was highlighted using single nucleotide polymorphic alleles in 2000 core genes. DNA hybridization analyses using a pan-genomic microarray showed that these strains clustered according to sequence types (STs) identified by multi-locus sequence typing (MLST). PHASTER analysis identified 185 intact prophage gene clusters encompassing 22 different prophages, including three intact Cronobacter prophages: ENT47670, ENT39118, and phiES15. AMRFinderPlus analysis identified the CSA family class C β-lactamase gene in all strains and a plasmid-borne mcr-9.1 gene was identified in three strains. ZI studies showed that some plant-origin C. sakazakii display virulence comparable to clinical strains. Finding virulent plant-origin C. sakazakii possessing significant genomic features of clinically relevant STs suggests that these foods can serve as potential transmission vehicles and supports widening the scope of continued surveillance for this important foodborne pathogen.", "token_count": 525, "char_count": 1940, "word_count": 250, "semantic_coherence": 1, "information_density": 0.656, "quality_score": 0.828, "entities": { "genes": [ "ENT39118", "ENT47670" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:36:51.648390", "source": { "split": "train_shard_00001", "doc_id": 3341 }, "chunk_id": "train_shard_00001_3341_0", "global_id": 10401 }, { "text": "Characterization of Cronobacter sakazakii Strains Originating from Plant-Origin Foods Using Comparative Genomic Analyses and Zebrafish Infectivity Studies.", "token_count": 46, "char_count": 162, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:52.034406", "source": { "split": "train_shard_00001", "doc_id": 3341 }, "chunk_id": "train_shard_00001_3341_1", "global_id": 10402 }, { "text": "

Aims

To examine how storage temperatures influence ensiling fermentation, aerobic stability and microbial communities of total mixed ration (TMR) silage.

Methods and results

Laboratory-scale silos were stored at 5, 15, 25 and 35°C for 10, 30 and 90 days. If silage was stored at 5°C, fermentation was weak until day 30, but acceptable lactic acid production was observed on day 90. The ethanol content was higher than the acetic acid content when stored at 15 and 25°C, whereas the ethanol content was lower when stored at 35 than at 25°C. Aerobic deterioration did not occur when silage was exposed to air at the same temperature at which it was stored. Although 10-day silages stored at 5 and 15°C deteriorated when the aerobic stability test was conducted at 25°C, heating was not observed in silages stored at 25 or 35°C or in any 90-day silages regardless of storage temperature. Denaturing gradient gel electrophoresis demonstrated that bands indicative of Lactobacillus plantarum and Lactobacillus delbrueckii were less prominent, while bands indicative of Lactobacillus panis became more distinct in silages stored at high temperatures. Bands of Kluyveromyces marxianus were seen exclusively in silages that were spoiled at 25°C.

Conclusion

High ambient temperature enhances acetic acid production in TMR silage. Lactobacillus panis may be associated with changes in the fermentation products due to differences in storage temperature.

Significance and impact of the study

The role of Lacto. panis in ensiling fermentation and aerobic stability is worth examining.\n\nEffects of storage temperature and ensiling period on fermentation products, aerobic stability and microbial communities of total mixed ration silage.", "token_count": 493, "char_count": 1753, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5451, "quality_score": 0.7725, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:52.694382", "source": { "split": "train_shard_00001", "doc_id": 3342 }, "chunk_id": "train_shard_00001_3342_0", "global_id": 10403 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) O26 is the predominant non-O157 serogroup causing hemolytic uremic syndrome worldwide. Moreover, the serogroup is highly dynamic and harbors several pathogenic clones. Here, we investigated the phylogenetic relationship of STEC O26 at a global level based on 1,367 strains from 20 countries deposited in NCBI and Enterobase databases. The whole-genome-based analysis identified a new genetic clade, called ST29C4. The new clade was unique in terms of multilocus sequence type (ST29), CRISPR (group Ia), and dominant plasmid gene profile (ehxA+/katP-/espP-/etpD-). Moreover, the combination of multiple typing methods (core genome single nucleotide polymorphism [SNP] typing, CRISPR typing, and virulence genes analysis) demonstrated that this new lineage ST29C4 was in the intermediate phylogenetic position between ST29C3 and other non-ST29C3 strains. Besides, we observed that ST29C4 harbored extraintestinal pathogenic E. coli (ExPEC)-related virulence gene (VG), tsh, and STEC-associated VG, stx2a, suggesting the emergence of a hybrid pathogen. The ST29C4 strains also exhibited high similarity in stx2a-prophage and integrase with the O104:H4 strain, further demonstrating its potential risk to human health. Collectively, the large-scale phylogenetic analysis extends the understanding of the clonal structure of O26 strains and provides new insights for O26 strain microevolution", "token_count": 456, "char_count": 1482, "word_count": 194, "semantic_coherence": 1, "information_density": 0.7216, "quality_score": 0.8608, "entities": { "genes": [ "ST29" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:53.395608", "source": { "split": "train_shard_00001", "doc_id": 3343 }, "chunk_id": "train_shard_00001_3343_0", "global_id": 10404 }, { "text": "IMPORTANCE Shiga toxin-producing Escherichia coli (STEC) O26 is the second prevalent STEC serogroup only to O157, which can cause a series of diseases ranging from mild diarrhea to life-threatening hemolytic uremic syndrome (HUS). The serogroup is highly diverse and multiple clones are characterized, including ST29C1-C3 and ST21C1-C2. However, the phylogenetic relationship of these clones remains fully unclear. In this study, we revealed a new genetic clade among O26 strains, ST29C4, which was unique in terms of CRISPR, multilocus sequence type (MLST), and plasmid gene profile (PGP). Moreover, the combination of multiple typing methods demonstrated that this new clone was located in the intermediate phylogenetic position between ST29C3 and other non-ST29C3 strains (i.e., ST29C1-C2 and ST21C1-C2). Overall, the large-scale phylogenetic analysis extends our current understanding of O26 microevolution.\n\nLarge-Scale Phylogenetic Analysis Reveals a New Genetic Clade among Escherichia coli O26 Strains.", "token_count": 305, "char_count": 1017, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:53.954463", "source": { "split": "train_shard_00001", "doc_id": 3343 }, "chunk_id": "train_shard_00001_3343_1", "global_id": 10405 }, { "text": "Candida kefyr fungal enteritis following autologous BMT.", "token_count": 16, "char_count": 56, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:54.315949", "source": { "split": "train_shard_00001", "doc_id": 3344 }, "chunk_id": "train_shard_00001_3344_0", "global_id": 10406 }, { "text": "Listeria monocytogenes, a foodborne bacterial pathogen, is comprised of four phylogenetic lineages that vary with regard to their serotypes and distribution among sources. In order to characterize lineage-specific genomic diversity within L. monocytogenes, we sequenced the genomes of eight strains from several lineages and serotypes, and characterized the accessory genome, which was hypothesized to contribute to phenotypic differences across lineages. The eight L. monocytogenes genomes sequenced range in size from 2.85-3.14 Mb, encode 2,822-3,187 genes, and include the first publicly available sequenced representatives of serotypes 1/2c, 3a and 4c. Mapping of the distribution of accessory genes revealed two distinct regions of the L. monocytogenes chromosome: an accessory-rich region in the first 65° adjacent to the origin of replication and a more stable region in the remaining 295°. This pattern of genome organization is distinct from that of related bacteria Staphylococcus aureus and Bacillus cereus. The accessory genome of all lineages is enriched for cell surface-related genes and phosphotransferase systems, and transcriptional regulators, highlighting the selective pressures faced by contemporary strains from their hosts, other microbes, and their environment. Phylogenetic analysis of O-antigen genes and gene clusters predicts that serotype 4 was ancestral in L. monocytogenes and serotype 1/2 associated gene clusters were putatively introduced through horizontal gene transfer in the ancestral population of L. monocytogenes lineage I and II.\n\nEvolutionary dynamics of the accessory genome of Listeria monocytogenes.", "token_count": 421, "char_count": 1646, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:54.936959", "source": { "split": "train_shard_00001", "doc_id": 3345 }, "chunk_id": "train_shard_00001_3345_0", "global_id": 10407 }, { "text": "The objective of this study was to use whole-genome sequencing (WGS) to screen for genes encoding for antibiotic resistance, fitness and virulence in Cronobacter sakazakii strains that had been isolated from food and powdered-milk-producing environments. Virulence (VGs) and antibiotic-resistance genes (ARGs) were detected with the Comprehensive Antibiotic Resistance Database (CARD) platform, ResFinder and PlasmidFinder tools. Susceptibility testing was performed using disk diffusion. Fifteen presumptive strains of Cronobacter spp. were identified by MALDI-TOF MS and ribosomal-MLST. Nine C. sakazakii strains were found in the meningitic pathovar ST4: two were ST83 and one was ST1. The C. sakazakii ST4 strains were further distinguished using core genome MLST based on 3678 loci. Almost all (93%) strains were resistant to cephalotin and 33% were resistant to ampicillin. In addition, 20 ARGs, mainly involved in regulatory and efflux antibiotics, were detected. Ninety-nine VGs were detected that encoded for OmpA, siderophores and genes involved in metabolism and stress. The IncFIB (pCTU3) plasmid was detected, and the prevalent mobile genetic elements (MGEs) were ISEsa1, ISEc52 and ISEhe3. The C. sakazakii isolates analyzed in this study harbored ARGs and VGs, which could have contributed to their persistence in powdered-milk-producing environments, and increase the risk of infection in susceptible population groups.\n\nScreening of Antibiotic and Virulence Genes from Whole Genome Sequenced Cronobacter sakazakii Isolated from Food and Milk-Producing Environments.", "token_count": 496, "char_count": 1624, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6273, "quality_score": 0.8136, "entities": { "genes": [ "ST83", "ST4", "ST1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:55.590583", "source": { "split": "train_shard_00001", "doc_id": 3346 }, "chunk_id": "train_shard_00001_3346_0", "global_id": 10408 }, { "text": "

Background

Dispensability of genes in a phylogenetic lineage, e.g. a species, genus, or higher-level clade, is gaining relevance as most genome sequencing projects move to a pangenome level. Most analyses classify genes as core genes, which are present in all investigated individual genomes, and dispensable genes, which only occur in a single or a few investigated genomes. The binary classification as ‘core’ or ‘dispensable’ is often based on arbitrary cutoffs of presence/absence in the analysed genomes. Even when extended to ‘conditionally dispensable’, this concept still requires the assignment of genes to distinct groups.

Results

Here, we present a new method which overcomes this distinct classification by quantifying gene dispensability and present a dedicated tool for reference-based QUantification Of gene Dispensability (QUOD). As a proof of concept, sequence data of 966 Arabidopsis thaliana accessions (Ath-966) were processed to calculate a gene-specific dispensability score for each gene based on normalised coverage in read mappings. We validated this score by comparison of highly conserved Benchmarking Universal Single Copy Orthologs (BUSCOs) to all other genes. The average scores of BUSCOs were significantly lower than the scores of non-BUSCOs. Analysis of variation demonstrated lower variation values between replicates of a single accession than between iteratively, randomly selected accessions from the whole dataset Ath-966. Functional investigations revealed defense and antimicrobial response genes among the genes with high-dispensability scores.

Conclusions

Instead of classifying a gene as core or dispensable, QUOD assigns a dispensability score to each gene. Hence, QUOD facilitates the identification of candidate dispensable genes, associated with high dispensability scores, which often underlie lineage-specific adaptation to varying environmental conditions.\n\nReference-based QUantification Of gene Dispensability (QUOD)", "token_count": 468, "char_count": 1995, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6134, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:56.241655", "source": { "split": "train_shard_00001", "doc_id": 3347 }, "chunk_id": "train_shard_00001_3347_0", "global_id": 10409 }, { "text": "Late blight caused by the oomycete pathogen Phytophthora infestans continues to cause major worldwide losses in potato and tomato. Most accessions of Solanum americanum , a globally distributed, wild Solanaceae plant, are highly resistant to late blight. We generated high-quality reference genomes of four S. americanum accessions, re-sequenced 52 accessions, and we defined variation in the NLR immune receptor genes (the S. americanum NLRome). We further screened for variation in recognition of ∼315 P. infestans RXLR effectors in 52 S. americanum accessions. Using these genotypic and phenotypic data, we cloned three novel NLR-encoding genes Rpi-amr4, Rpi-amr16 and Rpi-amr17 , and determined their corresponding RXLR effector genes Avramr4 ( PITG_22825 ), Avramr16 ( PITG_02860 ) and Avramr17 ( PITG_04373 ) from P. infestans . These genomic resources and methodology will support efforts to convert potato into a “nonhost” of late blight and can be applied to diseases of other crops.\n\nTheSolanum americanumpangenome and effectoromics reveal new resistance genes against potato late blight", "token_count": 326, "char_count": 1104, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6894, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:56.809301", "source": { "split": "train_shard_00001", "doc_id": 3348 }, "chunk_id": "train_shard_00001_3348_0", "global_id": 10410 }, { "text": "

Objectives

A previous study showed higher prevalence of Escherichia coli (E. coli) expressing extended-spectrum β-lactamases (ESBL-Ec) among men who have sex with men (MSM) in Amsterdam, the Netherlands, compared with the general Dutch population. This study genetically characterised the ESBL-Ec isolates and investigated whether the increased prevalence could be explained by transmission between participants.

Methods

Whole-genome sequences were obtained from 93 unique ESBL-Ec isolates that were cultured from rectal swabs of 79 participants. Isolates were typed according to the Achtman MLST scheme and ESBL and virulence genes were identified. Pairwise SNP distances were determined between isolates. Isolate pairs with ≤ 25 SNPs were considered part of a putative transmission event, and events between multiple participants formed putative transmission clusters. To investigate whether putatively transmitted isolates belonged to globally expanded lineages, the level of hierarchical clustering with international isolates was assessed using core genome MLST (cgMLST) implemented on the Enterobase platform.

Results

The most frequently detected E. coli types were ST131:blaCTX-M-15 (16 of 117, 13.5%), ST131:blaCTX-M-27, ST3075:blaCTX-M-15 and ST14:blaSHV-12 (all six of 117, 6.5%). Fourteen putative transmission events were identified, forming four putative transmission clusters. The largest putative transmission cluster contained ST131 isolates, which clustered with multiple international isolates in SNP and cgMLST analysis", "token_count": 441, "char_count": 1604, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6919, "quality_score": 0.846, "entities": { "genes": [ "ST131", "ST3075", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:57.442268", "source": { "split": "train_shard_00001", "doc_id": 3349 }, "chunk_id": "train_shard_00001_3349_0", "global_id": 10411 }, { "text": "One other transmission cluster (ST14:blaSHV-12) and two transmission events (ST14:blaSHV-12 and ST394:blaCTX-M-15) contained very rarely reported strains.

Conclusions

The identification of unique ESBL-Ec strains involved in putative transmission and carried by multiple participants demonstrated a high probability of ESBL-Ec transmission between MSM in Amsterdam; therefore, ESBL-Ec infection should be considered in cases of sexually active MSM having associated symptoms.\n\nPutative transmission of extended-spectrum β-lactamase-producing Escherichia coli among men who have sex with men in Amsterdam, the Netherlands.", "token_count": 182, "char_count": 660, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7733, "quality_score": 0.8867, "entities": { "genes": [ "ST394", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:57.884093", "source": { "split": "train_shard_00001", "doc_id": 3349 }, "chunk_id": "train_shard_00001_3349_1", "global_id": 10412 }, { "text": "The maize based ogi and mawè and the sorghum based gowé and tchoukoutou are traditional, spontaneously fermented products widely consumed by the population of Benin (West Africa). Yeast occurrence in the products, as sold on local markets at different locations, was studied using a combination of culture-dependent and independent methods. Number of yeasts is varied from 3.75 log10 colony forming units (cfu)/g for ogi to 5.60 log10 cfu/g for tchoukoutou. Isolated yeasts (236) were identified based on different migration profiles on denaturing gradient gel electrophoresis (DGGE) and 26S rRNA gene sequencing. Candida krusei was the yeast most frequently isolated with strongest predominance in the maize based products. Other predominant yeast present at equal or lower incidence were Clavispora lusitaniae and Saccharomyces cerevisiae in ogi and mawè, Cl. lusitaniae, Candida tropicalis and Kluyveromyces marxianus in gowè and Cl. lusitaniae, S. cerevisiae and Candida rugosa in tchoukoutou. Grouping of C. krusei isolates (164) by rep-PCR analysis indicated that several biotypes were involved in fermentation of the four products. The DGGE analysis on the DNA directly extracted from the food matrices demonstrated the presence of Dekkera bruxellensis and Debaryomyces hansenii, not detected by the culture-based approach. This is the first study combining culture-dependent and independent methods to reveal predominant yeast species and biotypes in traditional foods from Benin.\n\nDetermination of yeast diversity in ogi, mawè, gowé and tchoukoutou by using culture-dependent and -independent methods.", "token_count": 437, "char_count": 1610, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6234, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:58.518652", "source": { "split": "train_shard_00001", "doc_id": 3350 }, "chunk_id": "train_shard_00001_3350_0", "global_id": 10413 }, { "text": "Powdery mildew resistance genes restrict infection attempts at different stages of pathogenesis. Here, a strong and rapid powdery mildew resistance phenotype was discovered from Vitis amurensis 'PI 588631' that rapidly stopped over 97% of Erysiphe necator conidia, before or immediately after emergence of a secondary hypha from appressoria. This resistance was effective across multiple years of vineyard evaluation on leaves, stems, rachises, and fruit and against a diverse array of E. necator laboratory isolates. Using core genome rhAmpSeq markers, resistance mapped to a single dominant locus (here named REN12) on chromosome 13 near 22.8-27.0 Mb, irrespective of tissue type, explaining up to 86.9% of the phenotypic variation observed on leaves. Shotgun sequencing of recombinant vines using skim-seq technology enabled the locus to be further resolved to a 780 kb region, from 25.15 to 25.93 Mb. RNASeq analysis indicated the allele-specific expression of four resistance genes (NLRs) from the resistant parent. REN12 is one of the strongest powdery mildew resistance loci in grapevine yet documented, and the rhAmpSeq sequences presented here can be directly used for marker-assisted selection or converted to other genotyping platforms. While no virulent isolates were identified among the genetically diverse isolates and wild populations of E. necator tested here, NLR loci like REN12 are often race-specific. Thus, stacking of multiple resistance genes and minimal use of fungicides should enhance the durability of resistance and could enable a 90% reduction in fungicides in low-rainfall climates where few other pathogens attack the foliage or fruit.", "token_count": 479, "char_count": 1716, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [ "REN12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:59.512213", "source": { "split": "train_shard_00001", "doc_id": 3351 }, "chunk_id": "train_shard_00001_3351_0", "global_id": 10414 }, { "text": "Discovery and genome-guided mapping of REN12 from Vitis amurensis, conferring strong, rapid resistance to grapevine powdery mildew.", "token_count": 49, "char_count": 145, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "REN12" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:36:59.869239", "source": { "split": "train_shard_00001", "doc_id": 3351 }, "chunk_id": "train_shard_00001_3351_1", "global_id": 10415 }, { "text": "

Motivation

The increase in available microbial genome sequences has resulted in an increase in the size of the pangenomes being analyzed. Current pangenome visualizations are not intended for the pangenome sizes possible today and new approaches are necessary in order to convert the increase in available information to increase in knowledge. As the pangenome data structure is essentially a collection of sets we explore the potential for scalable set visualization as a tool for pangenome analysis.

Results

We present a new hierarchical clustering algorithm based on set arithmetics that optimizes the intersection sizes along the branches. The intersection and union sizes along the hierarchy are visualized using a composite dendrogram and icicle plot, which, in pangenome context, shows the evolution of pangenome and core size along the evolutionary hierarchy. Outlying elements, i.e. elements whose presence pattern do not correspond with the hierarchy, can be visualized using hierarchical edge bundles. When applied to pangenome data this plot shows putative horizontal gene transfers between the genomes and can highlight relationships between genomes that is not represented by the hierarchy. We illustrate the utility of hierarchical sets by applying it to a pangenome based on 113 Escherichia and Shigella genomes and find it provides a powerful addition to pangenome analysis.

Availability and implementation

The described clustering algorithm and visualizations are implemented in the hierarchicalSets R package available from CRAN ( https://cran.r-project.org/web/packages/hierarchicalSets ).

Contact

thomasp85@gmail.com.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nHierarchical sets: analyzing pangenome structure through scalable set visualizations.", "token_count": 423, "char_count": 1846, "word_count": 240, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:00.499065", "source": { "split": "train_shard_00001", "doc_id": 3352 }, "chunk_id": "train_shard_00001_3352_0", "global_id": 10416 }, { "text": "Intestinal inflammation, caused by impaired intestinal homeostasis, is a serious condition in both animals and humans. The use of conventional extracted soybean meal (SBM) in diets for Atlantic salmon and several other fish species is known to induce enteropathy in the distal intestine, a condition often referred to as SBM induced enteropathy (SBMIE). In the present study, we investigated the potential of different microbial ingredients to alleviate SBMIE in Atlantic salmon, as a model of feed-induced inflammation. The dietary treatments consisted of a negative control based on fish meal (FM), a positive control based on 20% SBM, and four experimental diets combining 20% SBM with either one of the three yeasts Candida utilis (CU), Kluyveromyces marxianus (KM), Saccharomyces cerevisiae (SC) or the microalgae Chlorella vulgaris (CV). Histopathological examination of the distal intestine showed that all fish fed the SC or SBM diets developed characteristic signs of SBMIE, while those fed the FM, CV or CU diets showed a healthy intestine. Fish fed the KM diet showed intermediate signs of SBMIE. Corroborating results were obtained when measuring the relative length of PCNA positive cells in the crypts of the distal intestine. Gene set enrichment analysis revealed decreased expression of amino acid, fat and drug metabolism pathways as well as increased expression of the pathways for NOD-like receptor signalling and chemokine signalling in both the SC and SBM groups while CV and CU were similar to FM and KM was intermediate. Gene expression of antimicrobial peptides was reduced in the groups showing SBMIE. The characterisation of microbial communities using PCR-DGGE showed a relative increased abundance of Firmicutes bacteria in fish fed the SC or SBM diets. Overall, our results show that both CU and CV were highly effective to counteract SBMIE, while KM had less effect and SC had no functional effects.\n\nCandida utilis and Chlorella vulgaris counteract intestinal inflammation in Atlantic salmon (Salmo salar L.).", "token_count": 507, "char_count": 2040, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5605, "quality_score": 0.7803, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:01.152870", "source": { "split": "train_shard_00001", "doc_id": 3353 }, "chunk_id": "train_shard_00001_3353_0", "global_id": 10417 }, { "text": "

Background:

The Salmonella enterica serovar Newport red onion outbreak of 2020 was the largest foodborne outbreak of Salmonella in over a decade. The epidemiological investigation suggested two farms as the likely source of contamination. However, single nucleotide polymorphism (SNP) analysis of the whole genome sequencing data did not find any Salmonella isolates from the farm regions that were closely related to the clinical isolates—preventing the use of phylogenetics in source identification. Here, we explored an alternative method for analyzing the whole genome sequencing data driven by the hypothesis that if the outbreak strain had come from the farm regions, then the clinical isolates would disproportionately contain plasmids found in isolates from the farm regions due to recent horizontal transfer. Results SNP analysis confirmed that the clinical isolates formed a highly related clade with evidence for ancestry in California going back a decade. The clinical isolates not only had a large and highly conserved core genome (4,399 genes), but also 2,577 sparsely distributed accessory genes—at least 64% of which were carried on plasmids. Amongst the clinical isolates and Salmonella isolates from the farm regions were 2,187 and 503 putative plasmids, respectively. High similarity was observed between 17 plasmids from 8 farm isolates and 14 plasmids from 13 clinical isolates. Phylogenetic analysis suggested the highly similar plasmids shared a recent common ancestor and might have been transferred via intermediary species, but the seeming promiscuity of the plasmids prevented any conclusions about geographic location, isolation source, and time since transfer. Our sampling analysis suggested that observing a similar number and combination of highly similar plasmids in random samples of environmental Salmonella enterica within NCBI Pathogen Detection database was unlikely, supporting a connection between the outbreak strain and the farms implicated by the epidemiological investigation. Conclusion Horizontally transferred plasmids provided evidence for a connection between clinical isolates and the farms implicated as the source of the outbreak", "token_count": 484, "char_count": 2193, "word_count": 314, "semantic_coherence": 1, "information_density": 0.551, "quality_score": 0.7755, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:01.809000", "source": { "split": "train_shard_00001", "doc_id": 3354 }, "chunk_id": "train_shard_00001_3354_0", "global_id": 10418 }, { "text": "Our case study suggests that such analyses might add a new dimension to source tracking investigations, but highlights the need for detailed and accurate metadata, more extensive environmental sampling, and a better understanding of plasmid molecular evolution.\n\nAssessment of plasmids for relating the 2020 Salmonella enterica serovar Newport onion outbreak to farms implicated by the outbreak investigation", "token_count": 82, "char_count": 408, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8596, "quality_score": 0.9298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:02.181285", "source": { "split": "train_shard_00001", "doc_id": 3354 }, "chunk_id": "train_shard_00001_3354_1", "global_id": 10419 }, { "text": "The use of air pressure as a way of improving oxygen transfer in aerobic bioreactors was investigated. To compare the air pressure effects with traditional air bubbled cultures, experiments using a pressure reactor and a stirred flask, with the same oxygen transfer rate, were made. Kluyveromyces marxianus is an important industrial yeast and some of it show a \"Kluyver effect\" for lactose: even under oxygen limited growth conditions, certain disaccharides that support aerobic, respiratory growth, are not fermented. This study deals with the effect of increased pressure on the physiological behavior of two Kluyveromyces strains: K. marxianus ATCC10022 is a lactose-fermenting strain, whereas K. marxianus CBS 7894 has a Kluyver-effect for lactose. For K. marxianus ATCC10022 an air pressure increase of 2 bar led to a 3-fold increase in biomass yield. When air pressure increased an enhancement of ethanol oxidation of cell yeasts was also observed. Batch cultures of K. marxianus CBS 7894 exhibited different growth behaviour. Its metabolism was always oxidative and ethanol was never produced. With the increase in air pressure, it was possible to increase the productivity in biomass of K. marxianus CBS 7894. As a response to high oxygen concentrations, due to the increase in oxygen partial pressure, oxidative stress in the cells was also studied. Antioxidant defences, such as superoxide dismutase, catalase, and glutathione reductase, were at high activity levels, suggesting that these yeast strains could tolerate the increased pressures applied.\n\nAir pressure effects on biomass yield of two different Kluyveromyces strains.", "token_count": 424, "char_count": 1641, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5668, "quality_score": 0.7834, "entities": { "genes": [ "ATCC10022" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:02.804663", "source": { "split": "train_shard_00001", "doc_id": 3355 }, "chunk_id": "train_shard_00001_3355_0", "global_id": 10420 }, { "text": "The pangenome is the collection of all groups of orthologous genes (OGGs) from a set of genomes. We apply the pangenome analysis to propose a definition of prokaryotic species based on identification of lineage-specific gene sets. While being similar to the classical biological definition based on allele flow, it does not rely on DNA similarity levels and does not require analysis of homologous recombination. Hence this definition is relatively objective and independent of arbitrary thresholds. A systematic analysis of 110 accepted species with the largest numbers of sequenced strains yields results largely consistent with the existing nomenclature. However, it has revealed that abundant marine cyanobacteria Prochlorococcus marinus should be divided into two species. As a control we have confirmed the paraphyletic origin of Yersinia pseudotuberculosis (with embedded, monophyletic Y. pestis) and Burkholderia pseudomallei (with B. mallei). We also demonstrate that by our definition and in accordance with recent studies Escherichia coli and Shigella spp. are one species.\n\nPangenomic Definition of Prokaryotic Species and the Phylogenetic Structure of Prochlorococcus spp.", "token_count": 331, "char_count": 1241, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:03.374463", "source": { "split": "train_shard_00001", "doc_id": 3356 }, "chunk_id": "train_shard_00001_3356_0", "global_id": 10421 }, { "text": "Seven Helicobacter-like isolates were cultured from caecal contents of 100 domestic pigs (Sus scrofa domesticus) sampled as part of the EFSA-coordinated harmonized monitoring of antimicrobial resistance in Campylobacter sp. in 2015. The bacteria were isolated using the standard ISO 10272 procedure for the isolation of thermotolerant Campylobacter with extended incubation time and formed small, grey, moist and flat colonies with a metallic sheen (small Campylobacter-like colonies) on modified Charcoal-Cefoperazone-Deoxycholate Agar (mCCDA) and Skirow agar plates. Morphologically, the bacterial cells were spirilli-shaped and highly motile, 1-2 µm long and ≤0.5 µm wide, Gram-negative, oxidase-positive and catalase-positive. They could not be identified using the standard-prescribed biochemical tests and had uniform, unique and reproducible MALDI-TOF mass spectra that most closely matched those of Helicobacter pullorum. Three strains (11154-15T, 14348-15 and 16470-15) underwent whole-genome sequencing. Analysis of 16S rRNA gene sequences revealed a high similarity (≥99.8 % identity) to Helicobacter canadensis. Pairwise average nucleotide identity (ANI) values revealed that the three studied strains were closely related (ANI ≥98.9 %), but distinct from the previously described Helicobacter species (ANI ≤90.6 %). The core genome-based phylogeny confirmed that the new strains form a distinct clade most closely related to H. canadensis", "token_count": 492, "char_count": 1525, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7538, "quality_score": 0.8769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:04.045906", "source": { "split": "train_shard_00001", "doc_id": 3357 }, "chunk_id": "train_shard_00001_3357_0", "global_id": 10422 }, { "text": "The conducted polyphasic taxonomic analysis confirmed that the three strains represent a novel Helicobacter species for which the name Helicobacter colisuis sp. nov. is suggested, with strain 11154-15T (= DSM 113688T = CCUG 76053T) as the type strain.\n\nHelicobacter colisuis sp. nov., isolated from caecal contents of domestic pigs (Sus scrofa domesticus).", "token_count": 154, "char_count": 417, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:04.502302", "source": { "split": "train_shard_00001", "doc_id": 3357 }, "chunk_id": "train_shard_00001_3357_1", "global_id": 10423 }, { "text": "

Unlabelled

Staphylococcus aureus is an important pathogen of humans and animals. We genome sequenced 90 S. aureus isolates from The Gambia: 46 isolates from invasive disease in humans, 13 human carriage isolates, and 31 monkey carriage isolates. We inferred multiple anthroponotic transmissions of S. aureus from humans to green monkeys (Chlorocebus sabaeus) in The Gambia over different time scales. We report a novel monkey-associated clade of S. aureus that emerged from a human-to-monkey switch estimated to have occurred 2,700 years ago. Adaptation of this lineage to the monkey host is accompanied by the loss of phage-carrying genes that are known to play an important role in human colonization. We also report recent anthroponotic transmission of the well-characterized human lineages sequence type 6 (ST6) and ST15 to monkeys, probably because of steadily increasing encroachment of humans into the monkeys' habitat. Although we have found no evidence of transmission of S. aureus from monkeys to humans, as the two species come into ever-closer contact, there might be an increased risk of additional interspecies exchanges of potential pathogens.

Importance

The population structures of Staphylococcus aureus in humans and monkeys in sub-Saharan Africa have been previously described using multilocus sequence typing (MLST). However, these data lack the power to accurately infer details regarding the origin and maintenance of new adaptive lineages. Here, we describe the use of whole-genome sequencing to detect transmission of S. aureus between humans and nonhuman primates and to document the genetic changes accompanying host adaptation. We note that human-to-monkey switches tend to be more common than the reverse and that a novel monkey-associated clade is likely to have emerged from such a switch approximately 2,700 years ago. Moreover, analysis of the accessory genome provides important clues as to the genetic changes underpinning host adaptation and, in particular, shows that human-to-monkey switches tend to be associated with the loss of genes known to confer adaptation to the human host.", "token_count": 519, "char_count": 2134, "word_count": 315, "semantic_coherence": 1, "information_density": 0.5587, "quality_score": 0.7794, "entities": { "genes": [ "ST15", "ST6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:05.174279", "source": { "split": "train_shard_00001", "doc_id": 3358 }, "chunk_id": "train_shard_00001_3358_0", "global_id": 10424 }, { "text": "Transmission of Staphylococcus aureus from Humans to Green Monkeys in The Gambia as Revealed by Whole-Genome Sequencing.", "token_count": 37, "char_count": 120, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:05.576438", "source": { "split": "train_shard_00001", "doc_id": 3358 }, "chunk_id": "train_shard_00001_3358_1", "global_id": 10425 }, { "text": "Streptococcus gallolyticus is an opportunistic pathogen and plays important role in various ecological niches, particularly in the intestinal tract of mammals. Obtaining the composition of S. gallolyticus strains from multiple perspectives is beneficial to broadening the knowledge of S. gallolyticus . Hence, we collected the genomic datasets of 31 S. gallolyticus strains and conducted the pan-genome analysis to systemically illustrate the genetic features and investigate the mechanism of its pathogenicity. Our results showed that the pan-genome of S. gallolyticus is composed of 4,606 homologous clusters and presented an open pan-genome structure. The phylogenetic analysis revealed the complicated relationship among S. gallolyticus strains. Six CAZyme families were identified from 182 orthologous genes that mainly derived from the core genome to clarify the carbohydrate metabolism of S. gallolyticus strains. The results showed that the metabolic ability of carbohydrates of 31 S. gallolyticus strains was different and these strains preferred glycosides and a crucial influence on the formation and modification of glycans and glycoconjugates. Particularly, the results of virulence factors indicated that the pathogenicity of S. gallolyticus strains was related to immunity, bile acid metabolism, and membrane synthesis. Besides, to guide the clinical treatment, we investigated the composition of antibiotic resistance genes of S. gallolyticus strains and claimed that these strains are resistant to antibiotics. Overall, our work systematically explores the genetic background of S. gallolyticus , provides an in-depth understanding of the biological characteristics of S. gallolyticus , and sheds light on the clinical detection and prevention of S. gallolyticus .\n\nComparative analysis of 31 Streptococcus gallolyticus strains uncovers their potential risks from the perspectives of virulence factors and antibiotic resistance genes", "token_count": 465, "char_count": 1950, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5185, "quality_score": 0.7593, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:06.230758", "source": { "split": "train_shard_00001", "doc_id": 3359 }, "chunk_id": "train_shard_00001_3359_0", "global_id": 10426 }, { "text": "

Objectives

Vancomycin-resistant Enterococcus faecium (VRE) belonging to sequence type 80 (ST80) have been successfully disseminating in hospital settings. This study aimed to explore whole-genome sequencing (WGS)-based approaches in epidemiological typing of VRE by investigating a collection of ST80 strains.

Methods

In total, 41 VRE ST80 isolates in three suspected transmission chains were subjected to WGS. The genetic relationship of the isolates was analysed by core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based typing. The published genome sequence of a predominant ST80 clone in Copenhagen was also included in the analyses.

Results

Group 1 isolates (n = 10) were recovered in the same geographic area, including two isolates from an outbreak of vanA genotype. Group 2 isolates (n = 4) were detected from another outbreak. Group 3 consisted of 3 non-outbreak isolates and 24 representative isolates from an outbreak of vanB genotype. Our findings indicated ≥24 allelic difference and >16 SNPs as the cut-off for excluding VRE strains from an outbreak. cgMLST identified >200 differing alleles between genomes of the Copenhagen clone and outbreak strains in this study. Our findings also demonstrated that SNP analysis was not suitable for typing samples from different groups, even with the same ST, owing to lack of an optimal reference genome.

Conclusion

cgMLST and SNPs provided comparable epidemiological discrimination for isolates with a suspected transmission chain. For diverse isolates, SNP analysis could be suboptimal. An approach applying cgMLST as the first-line typing method and SNPs as a complementary tool is suggested.\n\nEpidemiological typing of ST80 vancomycin-resistant Enterococcus faecium: core genome multilocus sequence typing versus single nucleotide polymorphism-based typing.", "token_count": 491, "char_count": 1884, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:06.884559", "source": { "split": "train_shard_00001", "doc_id": 3360 }, "chunk_id": "train_shard_00001_3360_0", "global_id": 10427 }, { "text": "The Sporothrix schenckii complex is the etiologic agent of sporotrichosis, a subacute or chronic mycosis which can affect humans and animals. Killer yeasts have been used in the medical field for development of novel antimycotics and biotyping of pathogenic fungi. The action of 18 killer yeasts on the growth of 88 characterized S. schenckii, Sporothrix globosa, Sporothrix brasiliensis, and Sporothrix mexicana clinical and environmental isolates was evaluated. Killer studies were performed on Petri dishes containing cheese black starch agar. The yeasts Candida catenulata (QU26, QU31, QU127, LV102); Trichosporon faecale (QU100); Trichosporon japonicum (QU139); Kluyveromyces lactis (QU30, QU99, QU73); Kazachstania unispora (QU49), Trichosporon insectorum (QU89), and Kluyveromyces marxianus (QU103) showed activity against all strains of the S. schenckii complex tested. Observation by optical microscopy of S. brasiliensis 61 within the inhibition haloes around the colonies of the killer yeasts QU100, QU139, and LV102 showed that there was no conidiation, but there was hyphal proliferation. The toxins were fungistatic against S. brasiliensis 61. There was no difference in susceptibility to the toxins among the S. schenckii species complex. Further investigations are necessary to clearly establish the mechanism of action of the toxins.\n\nSusceptibility of species within the Sporothrix schenckii complex to a panel of killer yeasts.", "token_count": 442, "char_count": 1446, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6373, "quality_score": 0.8186, "entities": { "genes": [ "LV102", "QU30", "QU139", "QU26", "QU31", "QU99", "QU89", "QU103", "QU127", "QU100" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:07.515631", "source": { "split": "train_shard_00001", "doc_id": 3361 }, "chunk_id": "train_shard_00001_3361_0", "global_id": 10428 }, { "text": "

ABSTRACT

Streptococci are the major etiology in mastitis, a cause of huge economic losses in the dairy industries. Streptococcus ( S .) agalactiae, S. dysagalactiae and S. uberis are mostly encountered in bovine mastitis; however, data on the diversity and characteristics of Streptococcus in clinical mastitis of cattle in Bangladesh is lacking. Thus, the present study was aimed to determine the diversity and antimicrobial resistance pattern of Streptococcus spp. isolated from clinical mastitis of cattle reared in Bangladesh. A total of 105 milk samples comprising eighty (80) from cattle with clinical mastitis (CCM) and twenty-five (25) from apparently healthy cattle (AHC) in four prominent dairy farms and one dairy community were purposively collected and examined in this study. Milk samples were enriched in Luria Bertani broth (LB) and Streptococcus spp. was isolated on Modified Edwards Medium and identified by 16S rRNA gene sequencing. Among eighty (80) clinical samples, eighteen (18) were positive for Streptococcus spp. while none of the milk from AHC revealed Streptococcus by cultural and molecular examination. Sequencing and phylogenetic analysis identified 55.6%, 33.3%, 5.6% and 5.6% of the Streptococcus isolates as S. uberis, S. agalactiae, S. hyovaginalis and S. urinalis , respectively. Antibiotic sensitivity testing with antimicrobials commonly used to treat clinical mastitis revealed 100%, 100%, and 30% of the S. agalactiae , S. hyovaginalis , and S. uberis as multidrug-resistant, respectively. Molecular characterization through whole genome sequencing of five (5) S. uberis isolates identified at least two novel ST types of S. uberis circulating in the study areas with one ST (4/5 isolates) clustered with the isolates from China, India and Thailand, and the other (1/5) with UK, Ireland and Australia", "token_count": 527, "char_count": 1849, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5673, "quality_score": 0.7836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:08.171586", "source": { "split": "train_shard_00001", "doc_id": 3362 }, "chunk_id": "train_shard_00001_3362_0", "global_id": 10429 }, { "text": "Pan-genome analysis and phylogeny of the core genome sequences also clustered the isolates into two sub-clusters, indicating the presence of at least two different subtypes of S. uberis in the study area. On virulence profiling, all the isolates of this study were found to harbor at least 35 virulence and putative virulence genes probably associated with intramammary infection (IMI) indicating all the S. uberis isolated in this study as potential pathogen. From the overall findings it was evident that Strepococcus occurring in bovine mastitis are diverse and S. uberis genome carries an array of putative virulence factors which need to be investigated genotypically and phenotypically to identify a specific trait or determinant governing the virulence and fitness of this bacterium. Moreover, Streptococcus isolated in this study carried multidrug resistance which needs careful consideration during the selection of a treatment regimen for mastitis.\n\nGenomic diversity ofStreptococcus uberisisolated from clinical mastitis of cattle in selected areas of Bangladesh", "token_count": 256, "char_count": 1080, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6603, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:08.719562", "source": { "split": "train_shard_00001", "doc_id": 3362 }, "chunk_id": "train_shard_00001_3362_1", "global_id": 10430 }, { "text": "Methicillin resistance, mediated by the mecA gene in staphylococci and mammaliicocci, has caused tremendous setbacks in the use of antibiotics in human and veterinary medicine due to its high potential of presenting the multidrug resistance (MDR) phenotype. Three other mec analogs exist, of which the mecC has evolutionary been associated with methicillin-resistant Staphylococcus aureus (MRSA) in wild animals, thus loosely referred to as the wild MRSA. In this study, we present an epidemiological review and genomic analysis of non-aureus staphylococci and mammaliicocci that carry the mecC-mediated methicillin resistance trait and determine whether this trait has any relevant link with the One Health niches. All previous studies (2007 till 2023) that described the mecC gene in non-aureus staphylococci and mammaliicocci were obtained from bibliometric databases, reviewed, and systematically analyzed to obtain the antimicrobial resistance (AMR) and virulence determinants, mobilome, and other genetic contents. Moreover, core genome single-nucleotide polymorphism analysis was used to assess the relatedness of these strains. Of the 533 articles analyzed, only 16 studies (on livestock, environmental samples, milk bulk tanks, and wild animals) were eligible for inclusion, of which 17 genomes from 6 studies were used for various in silico genetic analyses. Findings from this systematic review show that all mecC-carrying non-aureus staphylococci were resistant to only beta-lactam antibiotics and associated with the classical SCCmec XI of S. aureusLGA251", "token_count": 492, "char_count": 1663, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "LGA251" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:09.371742", "source": { "split": "train_shard_00001", "doc_id": 3363 }, "chunk_id": "train_shard_00001_3363_0", "global_id": 10431 }, { "text": "Similarly, two studies on wild animals reported mecC-carrying Mammaliicoccus stepanovicii associated with SCCmec XI. Nevertheless, most of the mecC-carrying Mammaliicoccus species presented an MDR phenotype (including linezolid) and carried the SCCmec-mecC hybrid associated with mecA. The phylogenetic analysis of the 17 genomes revealed close relatedness (<20 SNPs) and potential transmission of M. sciuri and M. lentus strains in livestock farms in Algeria, Tunisia, and Brazil. Furthermore, closely related M. sciuri strains from Austria, Brazil, and Tunisia (<40 SNPs) were identified. This systematic review enhances our comprehension of the epidemiology and genetic organization of mecC within the non-aureus staphylococci and mammaliicocci. It could be hypothesized that the mecC-carrying non-aureus staphylococci are evolutionarily related to the wild MRSA-mecC. The potential implications of clonal development of a lineage of mecA/mecC carrying strains across multiple dairy farms in a vast geographical region with the dissemination of MDR phenotype is envisaged. It was observed that most mecC-carrying non-aureus staphylococci and mammaliicocci were reported in mastitis cases. Therefore, veterinarians and veterinary microbiology laboratories must remain vigilant regarding the potential existence of mecA/mecC strains originating from mastitis as a potential niche for this resistance trait.", "token_count": 497, "char_count": 1547, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6489, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:10.017755", "source": { "split": "train_shard_00001", "doc_id": 3363 }, "chunk_id": "train_shard_00001_3363_1", "global_id": 10432 }, { "text": "Beyond the Wild MRSA: Genetic Features and Phylogenomic Review of mecC-Mediated Methicillin Resistance in Non-aureus Staphylococci and Mammaliicocci.", "token_count": 63, "char_count": 163, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:10.375515", "source": { "split": "train_shard_00001", "doc_id": 3363 }, "chunk_id": "train_shard_00001_3363_2", "global_id": 10433 }, { "text": "A thermotolerant Saccharomyces cerevisiae yeast strain, YK60-1, was bred from a parental strain, MT8-1, via stepwise adaptation. YK60-1 grew at 40°C, a temperature at which MT8-1 could not grow at all. YK60-1 exhibited faster growth than MT8-1 at 30°C. To investigate the mechanisms how MT8-1 acquired thermotolerance, DNA microarray analysis was performed. The analysis revealed the induction of stress-responsive genes such as those encoding heat shock proteins and trehalose biosynthetic enzymes in YK60-1. Furthermore, nontargeting metabolome analysis showed that YK60-1 accumulated more trehalose, a metabolite that contributes to stress tolerance in yeast, than MT8-1. In conclusion, S. cerevisiae MT8-1 acquired thermotolerance by induction of specific stress-responsive genes and enhanced intracellular trehalose levels.\n\nAcquisition of thermotolerant yeast Saccharomyces cerevisiae by breeding via stepwise adaptation.", "token_count": 267, "char_count": 927, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [ "MT8", "YK60" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:10.933285", "source": { "split": "train_shard_00001", "doc_id": 3364 }, "chunk_id": "train_shard_00001_3364_0", "global_id": 10434 }, { "text": "A closed-loop vertical tubular photobioreactor (PBR), specially designed to operate under conditions of scarce flat land availability and irregular solar irradiance conditions, was used to study the potential of Scenedesmus obliquus biomass/sugar production. The results obtained were compared to those from an open-raceway pond and a closed-bubble column. The influence of the type of light source and the regime (natural vs artificial and continuous vs light/dark cycles) on the growth of the microalga and the extent of the sugar accumulation was studied in both PBRs. The best type of reactor studied was a closed-loop PBR illuminated with natural light/dark cycles. In all the cases, the relationship between the nitrate depletion and the sugar accumulation was observed. The microalga Scenedesmus was cultivated for 53 days in a raceway pond (4,500 L) and accumulated a maximum sugar content of 29 % g/g. It was pre-treated for carrying out ethanol fermentation assays, and the highest ethanol concentration obtained in the hydrolysate fermented by Kluyveromyces marxianus was 11.7 g/L.\n\nBioethanol production from Scenedesmus obliquus sugars: the influence of photobioreactors and culture conditions on biomass production.", "token_count": 318, "char_count": 1229, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:11.496538", "source": { "split": "train_shard_00001", "doc_id": 3365 }, "chunk_id": "train_shard_00001_3365_0", "global_id": 10435 }, { "text": "

Introduction

Citrus is an important fruit crop for human health. The sensitivity of citrus trees to a wide range of abiotic stresses is a major challenge for their overall growth and productivity. Among these abiotic stresses, salinity results in a significant loss of global citrus yield. In order to find straightforward and sustainable solutions for the future and to ensure citrus productivity, it is of paramount importance to decipher the mechanisms responsible for salinity stress tolerance. Thisstudy aimed to investigate how ploidy levels influence salt stress tolerance in citrus by comparing the transcriptomic responses of diploid and tetraploid genotypes. In a previous article we investigated the physiological and biochemical response of four genotypes with different ploidy levels: diploid trifoliate orange (Poncirus trifoliata [L.] Raf.) (PO2x) and Cleopatra mandarin (Citrus reshni Hort. Ex Tan.) (CL2x) and their respective tetraploids (PO4x, CL4x).

Methods

In this study, we useda multifactorial gene selection and gene clustering approach to finely dissect the influence of ploidy level on the salt stress response of each genotype. Following transcriptome sequencing, differentially expressed genes (DEGs) were identified in response to salt stress in leaves and roots of the different citrus genotypes.

Result and discussion

Gene expression profiles and functional characterization of genes involved in the response to salt stress, as a function of ploidy level and the interaction between stress response and ploidy level, have enabled us to highlight the mechanisms involved in the varieties tested. Saltstress induced overexpression of carbohydrate biosynthesis and cell wall remodelling- related genes specifically in CL4x Ploidy level enhanced oxidative stress response in PO and ion management capacity in both genotypes. Results further highlighted that under stress conditions, only the CL4x genotype up- regulated genes involved in sugar biosynthesis, transport management, cell wall remodelling, hormone signalling, enzyme regulation and antioxidant metabolism. These findings provide crucial insights that could inform breeding strategies for developing salt-tolerant citrus varieties.", "token_count": 519, "char_count": 2242, "word_count": 307, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:12.153430", "source": { "split": "train_shard_00001", "doc_id": 3366 }, "chunk_id": "train_shard_00001_3366_0", "global_id": 10436 }, { "text": "Comparative transcriptomic analyses of diploid and tetraploid citrus reveal how ploidy level influences salt stress tolerance.", "token_count": 30, "char_count": 126, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:12.505130", "source": { "split": "train_shard_00001", "doc_id": 3366 }, "chunk_id": "train_shard_00001_3366_1", "global_id": 10437 }, { "text": "

Background

Heterogeneous vancomycin-intermediate Staphylococcus aureus (hVISA) compromise the clinical efficacy of vancomycin. The hVISA isolates spontaneously produce vancomycin-intermediate Staphylococcus aureus (VISA) cells generated by diverse and intriguing mechanisms.

Objective

To characterize the biomolecular profile of clinical hVISA applying genomic, transcriptomic and metabolomic approaches.

Methods

39 hVISA and 305 VSSA and their genomes were included. Core genome-based Bayesian phylogenetic reconstructions were built and alterations in predicted proteins in VISA/hVISA were interrogated. Linear discriminant analysis and a Genome-Wide Association Study were performed. Differentially expressed genes were identified in hVISA-VSSA by RNA-sequencing. The undirected profiles of metabolites were determined by liquid chromatography and hydrophilic interaction in six CC5-MRSA.

Results

Genomic relatedness of MRSA associated to hVISA phenotype was not detected. The change Try38 → His in Atl (autolysin) was identified in 92% of the hVISA. We identified SNPs and k-mers associated to hVISA in 11 coding regions with predicted functions in virulence, transport systems, carbohydrate metabolism and tRNA synthesis. Further, capABCDE, sdrD, esaA, esaD, essA and ssaA genes were overexpressed in hVISA, while lacABCDEFG genes were downregulated. Additionally, valine, threonine, leucine tyrosine, FAD and NADH were more abundant in VSSA, while arginine, glycine and betaine were more abundant in hVISA", "token_count": 455, "char_count": 1540, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8395, "entities": { "genes": [ "CC5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:13.147377", "source": { "split": "train_shard_00001", "doc_id": 3367 }, "chunk_id": "train_shard_00001_3367_0", "global_id": 10438 }, { "text": "Finally, we observed altered metabolic pathways in hVISA, including purine and pyrimidine pathway, CoA biosynthesis, amino acid metabolism and aminoacyl tRNA biosynthesis.

Conclusions

Our results show that the mechanism of hVISA involves major changes in regulatory systems, expression of virulence factors and reduction in glycolysis via TCA cycle. This work contributes to the understanding of the development of this complex resistance mechanism in regional strains.\n\nMultiomics characterization of methicillin-resistant Staphylococcus aureus (MRSA) isolates with heterogeneous intermediate resistance to vancomycin (hVISA) in Latin America.", "token_count": 169, "char_count": 651, "word_count": 81, "semantic_coherence": 1, "information_density": 0.8025, "quality_score": 0.9012, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis", "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:13.585138", "source": { "split": "train_shard_00001", "doc_id": 3367 }, "chunk_id": "train_shard_00001_3367_1", "global_id": 10439 }, { "text": "The lactic yeast Kluyveromyces marxianus var.marxianus (formerly K. fragilis) autolyzates at faster rate than Saccharomyces cerevisiae. During K. marxianus autolysis, quite similar release kinetics were observed for intracellular space markers (potassium ions, nucleotides), cell-wall components (polysaccharides, N-acetyl-D-Glucosamine) and non specific products (amino nitrogen). By Scanning Electronic Microscopy examination, no cell burst was observed, but a variation in cell shape (from ellipsoîdal to cylindrical), as well as a 43% decrease in the internal volume were observed. The mechanism proposed for S. cerevisiae autolysis appeared also likely for K. marxianus.\n\nBehaviour of the yeast Kluyveromyces marxianus var. marxianus during its autolysis.", "token_count": 221, "char_count": 760, "word_count": 99, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:14.050739", "source": { "split": "train_shard_00001", "doc_id": 3368 }, "chunk_id": "train_shard_00001_3368_0", "global_id": 10440 }, { "text": "Strangles, caused by Streptococcus equi ssp. equi (S. equi equi), is a highly infectious and frequent disease of equines worldwide. No data are available regarding the molecular epidemiology of strangles in Indonesia. This study aimed to characterize S. equi equi isolates obtained from suspected strangles cases in Indonesia in 2018. Isolates originated from seven diseased horses on four different farms located in three provinces of Indonesia. Whole genome sequences of these isolates were determined and used for seM typing, multilocus sequence typing (MLST), and core genome MLS typing (cgMLST). Genomes were also screened for known antimicrobial resistance genes and genes encoding for the recombinant antigens used in the commercial Strangvac® subunit vaccine. All seven S. equi equi isolates from Indonesia belonged to ST179 and carried seM allele 166. Isolates differed from each other by only 2 to 14 cgSNPs and built an exclusive sub-cluster within the Bayesian Analysis of Population Structure (BAPS) cluster 2 (BAPS-2) of the S. equi equi cgMLST scheme. All isolates revealed predicted amino acid sequence identity to seven and high similarity to one of the eight antigen fragments contained in Strangvac®. Furthermore, all isolates were susceptible to beta-lactam antibiotics penicillin G, ampicillin, and ceftiofur. Our data suggest that the horses from this study were affected by strains of the same novel sublineage within globally distributed BAPS-2 of S. equi equi. Nevertheless, penicillin G can be used as a first-choice antibiotic against these strains and Strangvac® may also be protective against Indonesian strains.", "token_count": 492, "char_count": 1737, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": { "genes": [ "ST179" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:14.699338", "source": { "split": "train_shard_00001", "doc_id": 3369 }, "chunk_id": "train_shard_00001_3369_0", "global_id": 10441 }, { "text": "Molecular Features and Antimicrobial Susceptibilities of Streptococcus equi ssp. equi Isolates from Strangles Cases in Indonesia.", "token_count": 50, "char_count": 143, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:15.057470", "source": { "split": "train_shard_00001", "doc_id": 3369 }, "chunk_id": "train_shard_00001_3369_1", "global_id": 10442 }, { "text": "

ABSTRACT

Cyanide is widely used in industry as a potent lixiviant due to its capacity to tightly bind metals. This property imparts cyanide enormous toxicity to all known organisms. Thus, industries that utilize this compound must reduce its concentration in recycled or waste waters. Physical, chemical, and biological treatments have been used for cyanide remediation; however, none of them meet all the desired characteristics: efficiency, low cost and low environmental impact. A better understanding of metabolic pathways and biochemistry of enzymes involved in cyanide degradation is a necessary step to improve cyanide bioremediation efficacy to satisfy the industry requirements. Here, we used several approaches to explore this topic. We have isolated three cyanide-degrading Bacillus strains from water in contact with mine tailings from Lima, Peru, and classified them as Bacillus safensis PER-URP-08, Bacillus licheniformis PER-URP-12, and Bacillus subtilis PER-URP-17 based on 16S rRNA gene sequencing and core genome analyses. Additionally, core genome analyses of 132 publicly available genomes of Bacillus pumilus group including B. safensis and B. altitudinis allowed us to reclassify some strains and identify two strains that did not match with any known species of the Bacillus pumilus group. We searched for possible routes of cyanide-degradation in the genomes of these three strains and identified putative B. licheniformis PER-URP-12 and B. subtilis PER-URP-17 rhodaneses and B. safensis PER-URP-08 cyanide dihydratase (CynD) sequences possibly involved cyanide degradation. We identified characteristic C-terminal residues that differentiate CynD from B. pumilus and B. safensis , and showed that, differently from CynD from B. pumilus C1, recombinant CynD from the Bacillus safensis PER-URP-08 strain remains active up to pH 9 and presents a distinct oligomerization pattern at pH 8 and 9", "token_count": 524, "char_count": 1923, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6151, "quality_score": 0.8076, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:15.706815", "source": { "split": "train_shard_00001", "doc_id": 3370 }, "chunk_id": "train_shard_00001_3370_0", "global_id": 10443 }, { "text": "Moreover, transcripts of B. safensis PER-URP-08 CynD (CynD PER-URP-08 ) are strongly induced in the presence of cyanide. Our results warrant further investigation of B. safensis PER-URP-08 and CynD PER-URP-08 as potential tools for cyanide-bioremediation.\n\nIsolation of a Bacillus safensis from mine tailings in Peru, genomic characterization and characterization of its cyanide-degrading enzyme CynD", "token_count": 131, "char_count": 407, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7407, "quality_score": 0.8704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:16.172596", "source": { "split": "train_shard_00001", "doc_id": 3370 }, "chunk_id": "train_shard_00001_3370_1", "global_id": 10444 }, { "text": "A 2³ factorial design was employed to find the best conditions of pH, l-phenylalanine concentration and temperature for the production of 2-phenylethanol by Kluyveromyces marxianus CBS 6556. The cultivation was carried out on grape must, which contains a great amount of nitrogen compounds. Central composite design (CCD) was used for the analysis of treatment combinations. Results showed a second-degree polynomial regression model with good agreement of experimental data, with R ² = 0.92015 (p < 0.05). The maximum production of 2-phenylethanol was found at pH 7.0, temperature of 37 °C, and a concentration of 3.0 g of l-phenylalanine L-¹. Further experiments in bioreactors showed that oxygen concentration is also important to 2-phenylethanol production, with best results obtained at oxygen mass transfer rates of 2.0 h-¹.\n\nBioconversion of l-phenylalanine into 2-phenylethanol by Kluyveromyces marxianus in grape must cultures", "token_count": 269, "char_count": 935, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6715, "quality_score": 0.8358, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:16.736050", "source": { "split": "train_shard_00001", "doc_id": 3371 }, "chunk_id": "train_shard_00001_3371_0", "global_id": 10445 }, { "text": "Chlamydomonas reinhardtii is a unicellular eukaryotic alga that has been studied as a model organism for decades. Despite an extensive history as a model system, phylogenetic and genetic characteristics of viruses infecting this alga have remained elusive. We analyzed high-throughput genome sequence data of C. reinhardtii field isolates, and in six we discovered sequences belonging to endogenous giant viruses that reach up to several 100 kb in length. In addition, we have also discovered the entire genome of a closely related giant virus that is endogenized within the genome of Chlamydomonas incerta, the closest sequenced relative of C. reinhardtii. Endogenous giant viruses add hundreds of new gene families to the host strains, highlighting their contribution to the pangenome dynamics and interstrain genomic variability of C. reinhardtii. Our findings suggest that the endogenization of giant viruses may have important implications for structuring the population dynamics and ecology of protists in the environment.\n\nEndogenous giant viruses contribute to intraspecies genomic variability in the model green alga Chlamydomonas reinhardtii.", "token_count": 305, "char_count": 1194, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5964, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:17.357059", "source": { "split": "train_shard_00001", "doc_id": 3372 }, "chunk_id": "train_shard_00001_3372_0", "global_id": 10446 }, { "text": "

Objectives

Antimicrobial-resistant bacteria of the order Enterobacterales are emerging threats to global public and animal health, leading to morbidity and mortality. The emergence of antimicrobial-resistant, livestock-associated pathogens is a great public health concern. The genera Enterobacter and Lelliottia are ubiquitous, facultatively anaerobic, motile, non-spore-forming, rod-shaped Gram-negative bacteria belonging to the Enterobacteriaceae family and include pathogens of public health importance. Here, we report the first draft genome sequences of a rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 in Africa.

Methods

The bacteria were isolated from environmental wastewater samples. Bacteria were cultured on nutrient agar, and the pure cultures were subjected to whole-genome sequencing. Genomic DNA was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and subjected to de novo assembly. The assembled contigs were analysed for virulence genes, antimicrobial resistance genes, and extra-chromosomal plasmids, and multilocus sequence typing was performed. To compare the sequenced strains with other, previously sequenced E. kobei and L. nimipressuralis strains, available raw read sequences were downloaded, and all sequence files were treated identically to generate core genome bootstrapped maximum likelihood phylogenetic trees.

Results

Whole-genome sequencing analyses identified strain MEZLN61 as L. nimipressuralis and strains MEZEK193 and MEZEK194 as E. kobei. MEZEK193 and MEZEK194 carried genes encoding resistance to fosfomycin (fosA), beta-lactam antibiotics (blaACT-9), and colistin (mcr-9). Additionally, MEZEK193 harboured nine different virulence genes, while MEZEK194 harboured eleven different virulence genes", "token_count": 523, "char_count": 1853, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6476, "quality_score": 0.8238, "entities": { "genes": [ "MEZEK193", "MEZLN61", "MEZEK194" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:18.025343", "source": { "split": "train_shard_00001", "doc_id": 3373 }, "chunk_id": "train_shard_00001_3373_0", "global_id": 10447 }, { "text": "The phenotypic analysis showed that L. nimipressuralis strain MEZLN61 was susceptible to colistin (2 μg/mL), while E. kobei MEZEK193 (64 μg/mL) and MEZEK194 (32 μg/mL) were resistant to colistin.

Conclusion

The genome sequences of strains L. nimipressuralis MEZLN6, E. kobei MEZEK193, and E. kobei MEZEK194 will serve as a reference point for molecular epidemiological studies of L. nimipressuralis and E. kobei in Africa. In addition, this study provides an in-depth analysis of the genomic structure and offers important information that helps clarify the pathogenesis and antimicrobial resistance of L. nimipressuralis and E. kobei. The detection of mcr-9, which is associated with very low-level colistin resistance in Enterobacter species, is alarming and may indicate the undetected dissemination of mcr genes in bacteria of the order Enterobacterales. Continuous monitoring and surveillance of the prevalence of mcr genes and their associated phenotypic changes in clinically important pathogens and environmentally associated bacteria is necessary to control and prevent the spread of colistin resistance.\n\nDraft genome sequences of rare Lelliottia nimipressuralis strain MEZLN61 and two Enterobacter kobei strains MEZEK193 and MEZEK194 carrying mobile colistin resistance gene mcr-9 isolated from wastewater in South Africa.", "token_count": 391, "char_count": 1340, "word_count": 186, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [ "MEZEK193", "MEZLN6", "MEZLN61", "MEZEK194" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:18.641633", "source": { "split": "train_shard_00001", "doc_id": 3373 }, "chunk_id": "train_shard_00001_3373_1", "global_id": 10448 }, { "text": "

Background

RNA-sequencing (RNA-seq) has been widely used to study the dynamic expression patterns of transcribed genes, which can lead to new biological insights. However, processing and analyzing these huge amounts of histological data remains a great challenge for wet labs and field researchers who lack bioinformatics experience and computational resources.

Results

We present BarleyExpDB, an easy-to-operate, free, and web-accessible database that integrates transcriptional profiles of barley at different growth and developmental stages, tissues, and stress conditions, as well as differential expression of mutants and populations to build a platform for barley expression and visualization. The expression of a gene of interest can be easily queried by searching by known gene ID or sequence similarity. Expression data can be displayed as a heat map, along with functional descriptions as well as Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, Proteins Families Database, and Simple Modular Architecture Research Tool annotations.

Conclusions

BarleyExpDB will serve as a valuable resource for the barley research community to leverage the vast publicly available RNA-seq datasets for functional genomics research and crop molecular breeding.\n\nBarleyExpDB: an integrative gene expression database for barley.", "token_count": 296, "char_count": 1348, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:19.215297", "source": { "split": "train_shard_00001", "doc_id": 3374 }, "chunk_id": "train_shard_00001_3374_0", "global_id": 10449 }, { "text": "Heme consists of a tetrapyrrole ring ligating an iron ion and has important roles in biological systems. While well-known as the oxygen-binding molecule within hemoglobin of mammals, heme is also cofactor for several enzymes and a major iron source for bacteria within the host. The enterococci are a diverse group of Gram-positive bacteria that exist primarily within the gastrointestinal tract of animals. However, some species within this genus can transform into formidable opportunistic pathogens, largely owing to their extraordinary adaptability to hostile environments. Although enterococci cannot synthesize heme nor depend on heme to grow, several species within the genus encode proteins that utilize heme as a cofactor, which appears to increase their fitness and ability to thrive in challenging environments. This includes more efficient energy generation via aerobic respiration and protection from reactive oxygen species. Here, we review the significance of heme to enterococci, primarily the major human pathogen Enterococcus faecalis, use bioinformatics to assess the prevalence of hemoproteins throughout the genus, and highlight recent studies that underscore the central role of the heme-E. faecalis relationship in host-pathogen dynamics and interspecies bacterial interactions.\n\nHeme utilization by the enterococci.", "token_count": 305, "char_count": 1353, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6915, "quality_score": 0.8457, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:19.788530", "source": { "split": "train_shard_00001", "doc_id": 3375 }, "chunk_id": "train_shard_00001_3375_0", "global_id": 10450 }, { "text": "Mule duck is vitally important to the production of global duck meat. Here, we present two high-quality haplotypes of a female mule duck (haplotype 1 (H1):1.28 Gb, haplotype 2 (H2): 1.40 Gb). The continuity (H1: contig N50 = 14.90 Mb, H2: contig N50 = 15.70 Mb) and completeness (BUSCO: H1 = 96.9%, H2 = 97.3%) are substantially better than those of other duck genomes. We detected the structural variations (SVs) in H1 and H2. We observed a positive correlation between autosome length and the number of SVs. Z chromosome was some deficient in deletions and insertions, but W chromosome was some excessive. A total of 1,451 genes were haplotype specific expression (HSEs). Among them, 737 specifically expressed in H1, and 714 specifically expressed in H2. We found that H1 and H2 HSEs tended to be involved in similar biological processes, such as myometrial relaxation and contraction pathways, muscle structure development and phosphorylation. Our haplotype-resolved genome assembly provides a powerful platform for future functional genomics, molecular breeding, and genome editing in mule duck.\n\nHaplotype-resolved assembly of the mule duck genome using high-fidelity sequencing technology.", "token_count": 350, "char_count": 1196, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:20.378157", "source": { "split": "train_shard_00001", "doc_id": 3376 }, "chunk_id": "train_shard_00001_3376_0", "global_id": 10451 }, { "text": "The present invention is directed to processes, combinations, uses and biomass comprising a combination of yeasts and bacterial strains, for the production of consumable biomass from substrates comprising a simple sugar. More particularly, the claimed subject matter includes the use of Lactobacillus fermentum, Kluyveromyces marxianus and Saccharomyces unisporus. The process intends to fix an environmental problem.\n\nFERMENTATION PROCESS OF A SUBSTRATE USING A MIXED CULTURE FOR THE PRODUCTION OF AN EDIBLE BIOMASS FOR ANIMAL AND/OR HUMAN CONSUMPTION", "token_count": 146, "char_count": 552, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7013, "quality_score": 0.8506, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:20.811392", "source": { "split": "train_shard_00001", "doc_id": 3377 }, "chunk_id": "train_shard_00001_3377_0", "global_id": 10452 }, { "text": "Kombucha, a beverage traditionally obtained through the fermentation of tea, is believed to have beneficial health properties. Therefore, characterizing the microorganisms responsible for this fermentation is essential to demonstrate its potential health benefits and to identify candidates for new probiotics. In this study, four probiotic yeast strains isolated from kombucha tea were identified, by the PCR-RFLP analysis of the ribosomal ITS region and the sequence of the D1/D2 domain of the 26S rDNA, as Brettanomyces bruxellensis (UVI55 and UVI56) and B. anomalus (UVI57 and UVI58). Properties relevant to probiotics were also studied in these strains. All of them showed excellent survival in simulated gastric (99%-100%) and duodenal (95%-100%) juices. The ability to self-aggregate (38%-100%), adhesion to xylene (15%-50%) and, above all, adhesion to Caco-2 cells (4%-21%), revealed its potential capacity to adhere to the intestinal epithelium. In addition, the tested strains showed excellent antioxidant capacity (82%-94%), antimicrobial activity against different pathogens (Escherichia coli, Staphylococcus aureus, Salmonella enterica, Listeria monocytogenes, and Bacillus cereus), as well as remarkable cytotoxic activity against colon, melanoma and ovarian tumor cell lines. Finally, using Caenorhabditis elegans as a model, strain UVI56 exhibited ability to both extend the lifespan of the nematode and protect it against infection by S. enterica. These results support the probiotic and functional properties of the analyzed strains", "token_count": 494, "char_count": 1613, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6884, "quality_score": 0.8442, "entities": { "genes": [ "UVI55", "UVI58", "UVI57", "UVI56" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:21.465005", "source": { "split": "train_shard_00001", "doc_id": 3378 }, "chunk_id": "train_shard_00001_3378_0", "global_id": 10453 }, { "text": "In conclusion, the study revealed that kombucha tea could be a source of potential probiotics that contribute to its health-promoting properties and that the characterized Brettanomyces strains could be exploited directly as probiotics or for the development of new functional foods.\n\nPotential probiotic and functional properties of Brettanomyces strains isolated from kombucha tea.", "token_count": 98, "char_count": 397, "word_count": 53, "semantic_coherence": 1, "information_density": 0.6981, "quality_score": 0.8491, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:21.838193", "source": { "split": "train_shard_00001", "doc_id": 3378 }, "chunk_id": "train_shard_00001_3378_1", "global_id": 10454 }, { "text": "The genetic heterogeneity of Heyndrickxia sporothermodurans (formerly Bacillussporothermodurans) was evaluated using whole genome sequencing. The genomes of 29 previously identified Heyndrickxiasporothermodurans and two Heyndrickxia vini strains isolated from ultra-high-temperature (UHT)-treated milk were sequenced by short-read (Illumina) sequencing. After sequence analysis, the two H. vini strains could be reclassified as H. sporothermodurans. In addition, the genomes of the H.sporothermodurans type strain (DSM 10599T) and the closest phylogenetic neighbors Heyndrickxiaoleronia (DSM 9356T) and Heyndrickxia vini (JCM 19841T) were also sequenced using both long (MinION) and short-read (Illumina) sequencing. By hybrid sequence assembly, the genome of the H. sporothermodurans type strain was enlarged by 15% relative to the short-read assembly. This noticeable increase was probably due to numerous mobile elements in the genome that are presumptively related to spore heat tolerance. Phylogenetic studies based on 16S rDNA gene sequence, core genome, single-nucleotide polymorphisms and ANI/dDDH, showed that H. vini is highly related to H. sporothermodurans. When examining the genome sequences of all H.sporothermodurans strains from this study, together with 4 H", "token_count": 493, "char_count": 1437, "word_count": 168, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:22.495108", "source": { "split": "train_shard_00001", "doc_id": 3379 }, "chunk_id": "train_shard_00001_3379_0", "global_id": 10455 }, { "text": "sporothermodurans genomes available in the GenBank database, the majority of the 36 strains examined occurred in a clonal lineage with less than 100 SNPs. These data substantiate previous reports on the existence and spread of a genetically highly homogenous and heat resistant spore clone, i.e., the HRS-clone.\n\nTaxonomic Evaluation of the Heyndrickxia (Basonym Bacillus) sporothermodurans Group (H. sporothermodurans, H. vini, H. oleronia) Based on Whole Genome Sequences.", "token_count": 185, "char_count": 534, "word_count": 67, "semantic_coherence": 1, "information_density": 0.8358, "quality_score": 0.9179, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:22.933143", "source": { "split": "train_shard_00001", "doc_id": 3379 }, "chunk_id": "train_shard_00001_3379_1", "global_id": 10456 }, { "text": "The INU1 gene (Accession number: JX073660) encoding exo-inulinase from Cryptococcus aureus HYA was cloned and characterized. The gene had an open reading frame (ORF) of 1653 bp long encoding an inulinase. The coding region of the gene was not interrupted by any intron. It encoded 551 amino acid residues of a protein with a putative signal peptide of 23 amino acids and the calculated molecular mass of 59.5 kDa. The protein sequence deduced from the inulinase structural gene contained the inulinase consensus sequences (WMNDPNGL), (RDP), ECP, FS and Q. It also had two conserved putative N-glycosylation sites. The inulinase from C. aureus HYA was found to be closely related to that from Kluyveromyces marxianus and Pichia guilliermondii. The inulinase gene without the signal sequence was subcloned into pPICZaA expression vector and expressed in Pichia pastoris X-33. The expressed fusion protein was analyzed by SDS-PAGE and western blotting and a specific band with molecular mass of about 60 kDa was found. Enzyme activity assay verified the recombinant protein as an inulinase. A maximum inulinase activity of 16.3±0.24 U/ml was obtained from the culture supernatant of P. pastoris X-33 harboring the inulinase gene. The optimal temperature and pH for action of the enzyme were 50 °C and 5.0, respectively. A large amount of monosaccharides were detected after the hydrolysis of inulin with the purified recombinant inulinase.\n\nCloning, characterization and heterelogous expression of the INU1 gene from Cryptococcus aureus HYA.", "token_count": 447, "char_count": 1538, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [ "JX073660", "INU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:23.566646", "source": { "split": "train_shard_00001", "doc_id": 3380 }, "chunk_id": "train_shard_00001_3380_0", "global_id": 10457 }, { "text": "IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly in Enterobacteriaceae . Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.\n\nGenomic network analysis of an environmental and livestock IncF plasmid population", "token_count": 316, "char_count": 1498, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6601, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:24.123946", "source": { "split": "train_shard_00001", "doc_id": 3381 }, "chunk_id": "train_shard_00001_3381_0", "global_id": 10458 }, { "text": "The persistent edaphic stress on microbial succession due to dynamic changes during composting was explored for selection of multi-stress tolerant microbe(s) desirable for ethanol production. A total of 23 strains were isolated from mango compost using four successive enrichments in YP broth (g l(-1)): glucose, 100; 150; 250 with ethanol (40) and cycloheximide (0.4) at 40 °C, pH 6.0. Based on multi-gene ribotyping, 14 yeasts (61 %) of Saccharomycetaceae, 2 filamentous fungi (8.6 %) and 7 bacteria (30.4 %) were obtained. Phenetic and phylogenetic analysis of the 14 yeasts revealed 64.3 % tolerant to 500 g l(-1) glucose, growth at 45 °C and resemblance to Candida sp. (14.3 %), Kluyveromyces marxianus (35.7 %), Pichia kudriavzevii (21.4 %) and Saccharomyces cerevisiae (28.6 %). Assessment of the 14 yeasts in glucose fermentation medium (pH 4.5 at 40 °C) showed ethanol productivity of ≥92 % by 12 yeasts with theoretical yields of 90-97 %. Fermentation of molasses (150 g l(-1) glucose equivalent) by P. kudriavzevii D1C at 40 °C resulted in 73.70 ± 0.02 g l(-1) ethanol and productivity of 4.91 ± 0.01 g l(-1) h(-1). Assessment of P", "token_count": 444, "char_count": 1142, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:24.751566", "source": { "split": "train_shard_00001", "doc_id": 3382 }, "chunk_id": "train_shard_00001_3382_0", "global_id": 10459 }, { "text": "kudriavzevii D1C revealed multi-stress tolerance towards 5-hydroxymethyl furfural, ethanol (20 %, v/v), high gravity and H2O2 (0.3 M) indicating suitability for ethanol production using high gravity molasses and pre-treated lignocellulosic biomass fermentation.\n\nBioprospecting of thermo- and osmo-tolerant fungi from mango pulp-peel compost for bioethanol production.", "token_count": 124, "char_count": 368, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:25.132436", "source": { "split": "train_shard_00001", "doc_id": 3382 }, "chunk_id": "train_shard_00001_3382_1", "global_id": 10460 }, { "text": "

Aims

Phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) using whole-genome sequencing (WGS) is increasingly used in epidemiological investigations of bacteria. The approach, however, is both resource intensive and time-consuming. Oxford Nanopore Technologies (ONT) sequencing is capable of real-time data analysis but the high error rate hampers its application in cgSNP-based phylogenetic analysis. Here, we developed a cgSNP-independent phylogenetic analysis method using ONT read assemblies by focusing on open reading frame (ORF) content patterns.

Methods and results

WGS data of 66 Enterobacter hormaechei strains acquired by both ONT and Illumina sequencing and 162 strains obtained from NCBI database were converted to binary sequences based on the presence or absence of ORFs using BLASTn. Phylogenetic trees calculated from binary sequences (ORF trees) were compared with cgSNP trees derived from Illumina sequences. Clusters of closely related strains in the cgSNP trees formed comparable clusters in the ORF trees built with binary sequences, and the tree topologies between them were similar based on Fowlkes-Mallows index.

Conclusions

The ORF-based phylogenetic analysis using ONT sequencing may be useful in epidemiological investigations and offer advantages over the cgSNP-based approach.

Significance and impact of the study

Conversion of assembled WGS data to binary sequences based on the presence or absence of ORFs circumvents read error concerns with ONT sequencing. Since ONT sequencing generates data in real time and does not require major investment, this ORF-based phylogenetic analysis method has the potential to enable phylogenetic and epidemiological analysis at the point of care.\n\nRapid phylogenetic analysis using open reading frame content patterns acquired by Oxford nanopore sequencing.", "token_count": 474, "char_count": 1885, "word_count": 254, "semantic_coherence": 1, "information_density": 0.563, "quality_score": 0.7815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:25.775268", "source": { "split": "train_shard_00001", "doc_id": 3383 }, "chunk_id": "train_shard_00001_3383_0", "global_id": 10461 }, { "text": "Streptococcus pneumoniae can be split into multiple strains, each with a characteristic combination of core and accessory genome variation, able to co-circulate and compete within the same hosts. Previous analyses of epidemiological datasets suggested the short-term vaccine-associated dynamics of S. pneumoniae strains may be mediated through multi-locus negative frequency-dependent selection (NFDS), acting to maintain accessory loci at equilibrium frequencies. To test whether this model could explain how such multi-strain populations were generated, it was modified to incorporate recombination. The outputs of simulations featuring symmetrical recombination were compared with genomic data on locus frequencies and distributions between genotypes, pairwise genetic distances and tree shape. These demonstrated NFDS prevented the loss of variation through neutral drift, but generated unstructured populations of diverse isolates. Making recombination asymmetrical, favouring deletion of accessory loci over insertion, alongside multi-locus NFDS significantly improved the fit to genomic data. In a population at equilibrium, structuring into multiple strains was stable due to outbreeding depression, resulting from recombinants with reduced accessory genomes having lower fitness than their parental genotypes. As many bacteria inhibit the integration of insertions into their chromosomes, this combination of asymmetrical recombination and multi-locus NFDS may underlie the co-existence of strains within a single ecological niche.\n\nNegative frequency-dependent selection and asymmetrical transformation stabilise multi-strain bacterial population structures", "token_count": 344, "char_count": 1667, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:26.354132", "source": { "split": "train_shard_00001", "doc_id": 3384 }, "chunk_id": "train_shard_00001_3384_0", "global_id": 10462 }, { "text": "The tracking of a pathogen's evolution over different timescales is essential: for the design of vaccines, to control antibiotic resistance, for the surveillance of disease, to identify transmission chains and to understand the mechanisms behind the pathogen’s evolution. Although the first bacterial genome was sequenced in 1995, techniques and costs have only recently enabled the large scale study of the evolution of pathogens in human populations over short timescales. This thesis begins by developing methods for the analysis of pathogen genomes, including the identification of population structure, characterisation of gene content and tracking of transmission. These techniques are then applied to the analysis of two large pathogen sequencing studies investigating the evolution of Streptococcus pneumoniae and SARS-CoV-2 within the host and during transmission. Initially, a fast solution to the problem of clustering pathogen genomes is presented. An approximation to a Dirichlet process mixture model is shown to produce accurate genome clusterings 10-100 times faster than existing methods. Next, the problem of identifying the pangenome (the set of all genes that have been found in a species) is considered ... (continues)\n\nPathogen evolution within and between hosts with applications to the pneumococcus and SARS-CoV-2", "token_count": 286, "char_count": 1337, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:26.905858", "source": { "split": "train_shard_00001", "doc_id": 3385 }, "chunk_id": "train_shard_00001_3385_0", "global_id": 10463 }, { "text": "An effective and ecological method for liberation of pectin-derived oligosaccharides (POS) from sugar beet pulp (SBP) was developed using enzymatic and microorganism-mediated biomass conversion. The POS may be applied in the production of prebiotic feed additives. Various yeast strains were screened for their capacity for protein synthesis and monosaccharide assimilation. Combined yeast cultivation and pectin hydrolysis were found to be an effective method of producing prebiotics. Separate enzymatic hydrolysis and fermentation of SBP resulted in the release of 3.6 g of POS per 100 g d.w., whereas the yield of POS acquired after the combined process was 17.9% higher, giving 4.2 g of POS per 100 g d.w. Introducing the yeast into the process improved hydrolysis performance due to lower enzyme inhibition by mono- and disaccharides. The prebiotic effect of the POS was assessed by in vitro fermentation using individual cultures of gastrointestinal bacteria. The POS in the SBP hydrolysate effectively promoted the growth of lactobacilli and bifidobacteria. A large increase in adherence to Caco-2 cells in the presence of POS was noted for beneficial Lactobacillus brevis strains, whereas pathogenic bacteria and yeast (C. albicans, C. lusitanie, C. pelliculosa), responsible for infections in breeding animals, showed much weaker adhesion.\n\nCombined Yeast Cultivation and Pectin Hydrolysis as an Effective Method of Producing Prebiotic Animal Feed from Sugar Beet Pulp.", "token_count": 432, "char_count": 1499, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5826, "quality_score": 0.7913, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:27.538416", "source": { "split": "train_shard_00001", "doc_id": 3386 }, "chunk_id": "train_shard_00001_3386_0", "global_id": 10464 }, { "text": "The hypervirulent lineages of Klebsiella pneumoniae (HvKp) cause invasive infections such as Klebsiella-liver abscess. Invasive infection often occurs after initial colonization of the host gastrointestinal tract by HvKp. Over 80% of HvKp isolates belong to the clonal group 23 sublineage I that has acquired genomic islands (GIs) GIE492 and ICEKp10. Our analysis of 12 361 K. pneumoniae genomes revealed that GIs GIE492 and ICEKp10 are co-associated with the CG23-I and CG10118 HvKp lineages. GIE492 and ICEKp10 enable HvKp to make a functional bacteriocin microcin E492 (mccE492) and the genotoxin colibactin, respectively. We discovered that GIE492 and ICEKp10 play cooperative roles and enhance gastrointestinal colonization by HvKp. Colibactin is the primary driver of this effect, modifying gut microbiome diversity. Our in vitro assays demonstrate that colibactin and mccE492 kill or inhibit a range of Gram-negative Klebsiella species and Escherichia coli strains, including Gram-positive bacteria, sometimes cooperatively. Moreover, mccE492 and colibactin kill human anaerobic gut commensals that are similar to the taxa found altered by colibactin in the mouse intestines. Our findings suggest that GIs GIE492 and ICEKp10 enable HvKp to kill several commensal bacterial taxa during interspecies interactions in the gut. Thus, acquisition of GIE492 and ICEKp10 could enable better carriage in host populations and explain the dominance of the CG23-I HvKp lineage.\n\nHypervirulent Klebsiella pneumoniae employs genomic island encoded toxins against bacterial competitors in the gut.", "token_count": 499, "char_count": 1589, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8097, "entities": { "genes": [ "CG23", "GIE492", "CG10118" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:28.203276", "source": { "split": "train_shard_00001", "doc_id": 3387 }, "chunk_id": "train_shard_00001_3387_0", "global_id": 10465 }, { "text": "

Motivation

Routine infectious disease surveillance is increasingly based on large-scale whole genome sequencing databases. Real-time surveillance would benefit from immediate assignments of each genome assembly to hierarchical population structures. Here we present HierCC, a scalable clustering scheme based on core genome multi-locus typing that allows incremental, static, multi-level cluster assignments of genomes. We also present HCCeval, which identifies optimal thresholds for assigning genomes to cohesive HierCC clusters. HierCC was implemented in EnteroBase in 2018, and has since genotyped >400,000 genomes from Salmonella, Escherichia, Yersinia and Clostridioides .

Availability

Implementation: http://enterobase.warwick.ac.uk/ and Source codes: https://github.com/zheminzhou/HierCC

Contact

zhemin.zhou@warwick.ac.uk

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nHierCC: A multi-level clustering scheme for population assignments based on core genome MLST", "token_count": 290, "char_count": 1044, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7712, "quality_score": 0.8856, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:28.788635", "source": { "split": "train_shard_00001", "doc_id": 3388 }, "chunk_id": "train_shard_00001_3388_0", "global_id": 10466 }, { "text": "Objective: To investigate the molecular characteristics of ciprofloxacin-cefotaxime-azithromycin co-resistant Salmonella enterica serovar Thompson (S. Thompson) isolates from sporadic cases of foodborne diseases and aquatic foods in Hunan province. Methods: Ciprofloxacin-cefotaxime-azithromycin co-resistant S. Thompson isolates were selected from samples, and broth microdilution method was used to determine the resistance to 11 antibiotics of these isolates in vitro. Whole genome sequencing was used for investigating antimicrobial resistance gene patterns and phylogenetic relationships of strains. Results: Nine ciprofloxacin-cefotaxime-azithromycin co-resistant isolates were recovered from 19 S. Thompson isolates. Among nine ciprofloxacin-cefotaxime-azithromycin co-resistant isolates, eight of them harbored IncC plasmids, simultaneously carrying plasmid-mediated quinolone resistance (PMQR) genes qepA and qnrS1, β-lactamase resistance gene blaCMY-2, azithromycin resistance gene mph(A), and one isolate harbored IncR plasmid, and carried PMQR genes qnrB4 and aac(6')-Ib-cr, blaOXA-10 and mph(A)", "token_count": 452, "char_count": 1248, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6899, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:29.475623", "source": { "split": "train_shard_00001", "doc_id": 3389 }, "chunk_id": "train_shard_00001_3389_0", "global_id": 10467 }, { "text": "Genetic environment analysis showed that qnrS1, qepA, mph(A) and blaCMY-2 genes might be integrated on genomes of strains by ISKra4, IS91, IS6100 and ISEcp1, respectively. Phylogenetic core genome comparisons demonstrated that ciprofloxacin-cefotaxime-azithromycin co-resistant isolates from patients and aquatic foods were genetically similar and clustered together. Conclusion: Ciprofloxacin-cefotaxime-azithromycin co-resistant S. Thompson isolates have been isolated from both human and aquatic food samples, suggesting that the spread of multidrug resistant Salmonella between human and aquatic animals.\n\n[Molecular characteristics of ciprofloxacin-cefotaxime-azithromycin co-resistant Salmonella enterica Serovar Thompson in foodborne diseases in Hunan Province].", "token_count": 290, "char_count": 850, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7753, "quality_score": 0.8876, "entities": { "genes": [ "IS6100", "IS91" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:30.036726", "source": { "split": "train_shard_00001", "doc_id": 3389 }, "chunk_id": "train_shard_00001_3389_1", "global_id": 10468 }, { "text": "The reconstruction of the evolutionary histories of pathogen populations in space and time has greatly improved our understanding of their epidemiology. However, analyses are usually restricted to the non-recombining genomic regions and, thus, fail to inform on the dynamics of the accessory genome. Yet, horizontal gene transfer is of striking importance to the evolution of bacteria as it can redistribute phenotypically important genes. For bacterial pathogens, those include resistance to antimicrobial compounds and virulence factors. Understanding the gene turnover in genomes at microevolutionary scales is key to apprehend the pace of this evolutionary process. Here we addressed this question for the epidemic lineage of a major bacterial plant pathogen, relying on a dense geographic sampling spanning 39 years of evolution. Gene turnover rate exceeded SNP mutation rates by three orders of magnitude. Accessory genes were preferentially plasmid-encoded, but we evidenced a highly plastic chromosomal region hosting ecologically important genes such as transcription activator-like effectors. We argue that turnover of accessory genes provides a potent evolutionary force in monomorphic bacteria, and exemplify this statement retracing the history of a mobile element conferring resistance to copper compounds widely used for the management of plant bacterial pathogens.\n\nTime-calibrated genomic evolution of a monomorphic bacterium during its establishment as an endemic crop pathogen", "token_count": 314, "char_count": 1495, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:30.604393", "source": { "split": "train_shard_00001", "doc_id": 3390 }, "chunk_id": "train_shard_00001_3390_0", "global_id": 10469 }, { "text": "Currently, the pathogenesis of acute myelocytic leukemia(AML) is still unclear. We found the core genome M5C plays a vital role in methylation modification and immune infiltration of AML. At the same time, we created a new M5C score model to define the high and low-risk groups of AML.Our research showed the expression levels of the three molecular subtypes of M5C (C1, C2 and C3);as well as different clinical features ,the results showed significant differences in age\\RUNX1-RUNX1T1 fusion, but not in RUNX1 mutation group.We constructed a prognostic risk model based on m5C phenotype from 417 samples in the GSE37642 data set and found 5 differential genes using lasso regression method. And the prognostic KM curve of the 5-gene signature was obtained, from which it can be seen that: all the five genes could significantly reduce the high and low risk of GSE37642 training set samples ( P  < 0.05).Finally, the robustness of M5C related 5-gene signature for AML prediction was verified by internal and external data using single factor and multifactor COX regression analysis.5-gene signature has strong robustness and can play a stable prediction performance in external validation data sets (GSE12417, TCGA-LAML).\n\nThe core genome M5C plays an important role in methylation modification and immune infiltration of acute myelocytic leukemia samples", "token_count": 374, "char_count": 1355, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [ "GSE37642", "GSE12417", "RUNX1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:31.186567", "source": { "split": "train_shard_00001", "doc_id": 3391 }, "chunk_id": "train_shard_00001_3391_0", "global_id": 10470 }, { "text": "Viburnum opulus is a plant with fruits that are rich in biologically active substances, making it valuable to the food and pharmaceutical industries. Here, we present our study of the total phenolic and anthocyanin contents and antimicrobial activity in the fruit juice of six V. opulus L. accessions. The cultivar 'Krasnaya Grozd' was notable for its exceptionally large amount of total phenolics, 1168 mg/100 g, with anthocyanins comprising 3-5 % of the total phenolic content. The evaluation of the antimicrobial properties confirmed that the juice of V. opulus fruits strongly inhibited the growth of a wide range of human pathogenic bacteria, both Gram-negative (Salmonella typhimurium and S. agona) and Gram-positive (Staphylococcus aureus, Lysteria monocytogenes, and Enterococcus faecalis) organisms. Conversely, the yeasts Debaryomyces hansenii and Torulaspora delbrueckii showed complete resistance to the fruit juice, whereas a low sensitivity was demonstrated by Trichosporon cutaneum, Kluyveromyces marxianus var. lactis, Saccharomyces cerevisiae, S. cerevisiae 12R, and Candida parapsilosis.\n\nDetermination of the total phenolic and anthocyanin contents and antimicrobial activity of Viburnum opulus fruit juice.", "token_count": 347, "char_count": 1226, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6706, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:31.761712", "source": { "split": "train_shard_00001", "doc_id": 3392 }, "chunk_id": "train_shard_00001_3392_0", "global_id": 10471 }, { "text": "Probiotic microorganisms are generally considered to beneficially affect host health when used in adequate amounts. Although generally used in dairy products, they are also widely used in various commercial food products such as fermented meats, cereals, baby foods, fruit juices, and ice creams. Among lactic acid bacteria, Lactobacillus and Bifidobacterium are the most commonly used bacteria in probiotic foods, but they are not resistant to heat treatment. Probiotic food diversity is expected to be greater with the use of probiotics, which are resistant to heat treatment and gastrointestinal system conditions. Bacillus coagulans (B. coagulans) has recently attracted the attention of researchers and food manufacturers, as it exhibits characteristics of both the Bacillus and Lactobacillus genera. B. coagulans is a spore-forming bacterium which is resistant to high temperatures with its probiotic activity. In addition, a large number of studies have been carried out on the low-cost microbial production of industrially valuable products such as lactic acid and various enzymes of B. coagulans which have been used in food production. In this review, the importance of B. coagulans in food industry is discussed. Moreover, some studies on B. coagulans products and the use of B. coagulans as a probiotic in food products are summarized.\n\nPotential Use of Bacillus coagulans in the Food Industry.", "token_count": 411, "char_count": 1490, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5498, "quality_score": 0.7749, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:32.383222", "source": { "split": "train_shard_00001", "doc_id": 3393 }, "chunk_id": "train_shard_00001_3393_0", "global_id": 10472 }, { "text": "Among more than twenty species belonging to the class Mollecutes, Mycoplasma bovis is the most common cause of bovine mycoplasmosis in North America and Europe. Bovine mycoplasmosis causes significant economic loss in the cattle industry. The number of M. bovis positive herds has recently increased in North America and Europe. Since antibiotic treatment is ineffective and no efficient vaccine is available, M. bovis -induced mycoplasmosis is primarily controlled by herd management measures such as the restriction of moving infected animals out of the herds and culling of infected animals or shedders. To better understand the population structure and genomic factors that may contribute to its transmission, we sequenced 147 M. bovis strains isolated from four different countries and hosts, primarily cattle. We performed a large-scale comparative analysis of M. bovis genomes by integrating 104 publicly available genomes and our dataset (251 total genomes). A whole genome-single nucleotide polymorphism (SNP)-based phylogeny revealed that M. bovis population structure is composed of five clades with one of the isolates clustering with the outgroup M. agalactiae . These isolates were found to cluster with those from Canada, Israel, Lithuania, and Switzerland, suggesting trans-continental transmission of the strains. We also validated a previous report suggesting minimum divergence in isolates of Australian origin, which grouped within a single clade along with strains from China and Israel. However, no observable pattern of host association in M. bovis genomes was found in this study. Our comparative genome analysis also revealed that M. bovis has an open pangenome with a large breadth of unexplored diversity of genes. Analysis of vsp gene-host association revealed a single vsp significantly associated with bovine isolates that may be targeted for diagnostics or vaccine development. Our study also found that M. bovis genome harbors a large number of IS elements, including a novel 1624 bp IS element, and ISMbov9. Collectively, the genome data and the whole genome-based population analysis in this study may help to develop control measures to reduce the incidence of M", "token_count": 509, "char_count": 2197, "word_count": 330, "semantic_coherence": 1, "information_density": 0.5727, "quality_score": 0.7864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:33.040860", "source": { "split": "train_shard_00001", "doc_id": 3394 }, "chunk_id": "train_shard_00001_3394_0", "global_id": 10473 }, { "text": "bovis -induced mycoplasmosis in cattle and/or to identify candidate genes for vaccine development.\n\nGlobal population genomic analysis ofMycoplasma bovisisolates reveals transcontinental variations and potential virulence genes", "token_count": 59, "char_count": 234, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:33.397902", "source": { "split": "train_shard_00001", "doc_id": 3394 }, "chunk_id": "train_shard_00001_3394_1", "global_id": 10474 }, { "text": "Kefir grains might have different ratios and/or content of microflora according to their origin. The purpose of this study was to determine microbial flora of kefir grains produced in three regional universities in Turkey using polymerase chain reaction (PCR) and consensus sequence primers. According to the results of PCR products with the specific primers, the following were identified as the natural inhabitants of the kefir grains: Lactobacillus acidophilus, Lactobacillus helveticus, Streptococcus thermophilus, Bifidobacterium bifidum and Kluyveromyces marxianus kefir. The results of this study revealed that traditional kefir produced by using kefir grains as natural starter cultures contains lactic acid bacteria especially Lactobacillus spp. One of the sources also contained B. bifidum. This is the first record on the presence of B. bifidum in kefir grains.\n\nIdentification of microbial flora in kefir grains produced in Turkey using PCR", "token_count": 250, "char_count": 954, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6204, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:33.890793", "source": { "split": "train_shard_00001", "doc_id": 3395 }, "chunk_id": "train_shard_00001_3395_0", "global_id": 10475 }, { "text": "Biosorption capacities and rates of different kinds of dried yeasts (Saccharomyces cerevisiae, Schizosaccharomyces pombe, Kluyveromyces marxianus, Candida sp., C. tropicalis, C. lipolytica, C. utilis, C. quilliermendii and C. membranaefaciens) for Remazol Blue reactive dye from aqueous solutions were compared under laboratory conditions as a function of initial pH and initial dye concentration. Optimum initial biosorption pH was determined as 2 for all the yeasts. All the yeast species showed comparable and very high dye sorption at 100 mg/l initial dye concentration. The equilibrium sorption capacity of the biomass increased with increasing initial dye concentration up to 400 mg/l for Candida sp. C. lipolytica and C. tropicalis; up to 300 mg/l for C. quilliermendii and C. utilis and up to 200 mg/l for S. cerevisiae, S. pombe, K. marxianus and C. membranaefaciens while the adsorption yield of dye showed the opposite trend for all the yeasts. Among the nine yeast species, C. lipolytica exhibited the highest dye uptake capacity (Q(0) = 250 mg/g). Both the Freundlich and Langmuir adsorption models were found suitable for describing the biosorption of the dye by all the Candida yeasts (except C. membranaefaciens). The results indicated that the dye uptake process followed the pseudo-second-order kinetics for each dye-yeast system.\n\nA comparative study on the biosorption characteristics of some yeasts for Remazol Blue reactive dye.", "token_count": 421, "char_count": 1450, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5505, "quality_score": 0.7752, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:34.516454", "source": { "split": "train_shard_00001", "doc_id": 3396 }, "chunk_id": "train_shard_00001_3396_0", "global_id": 10476 }, { "text": "

Background

Global tuberculosis (TB) control is challenged by uncontrolled transmission of Mycobacterium tuberculosis complex (Mtbc) strains, esp. of multidrug (MDR) or extensively resistant (XDR) variants. Precise analysis of transmission networks is the basis to trace outbreak M/XDR clones and improve TB control. However, classical genotyping tools lack discriminatory power due to the high similarity of strains of particular successful lineages, e.g. Beijing or outbreak strains. This can be overcome by whole genome sequencing (WGS) approaches, but these are not yet standardized to facilitate larger investigations encompassing different laboratories or outbreak tracing across borders.

Methods

We established and improved a whole genome gene-by-gene multi locus sequence typing approach encompassing a stable set of core genome genes (cgMLST) and linked it to a web-based nomenclature server (cgMLST.org) facilitating assignment and storage of allele numbers.

Findings

We evaluated and refined a previously suggested cgMLST schema by using a reference strain set (n = 251) reflecting the global diversity of the Mtbc. A set of 2891 genes showed excellent performance with at least 97% of the genes reliably identified in strains of all Mtbc lineages and in discriminating outbreak strains. cgMLST allele numbers were automatically retrieved from and stored at cgMLST.org.

Interpretation

The refined cgMLST schema provides high resolution genome-based typing of clinical strains of all Mtbc lineages. Combined with a web-based nomenclature server, it facilitates rapid, high-resolution, and harmonized tracing of clinical Mtbc strains needed for prospective local and global surveillance.\n\nHarmonized Genome Wide Typing of Tubercle Bacilli Using a Web-Based Gene-By-Gene Nomenclature System.", "token_count": 480, "char_count": 1827, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:35.160068", "source": { "split": "train_shard_00001", "doc_id": 3397 }, "chunk_id": "train_shard_00001_3397_0", "global_id": 10477 }, { "text": "Whole-genome sequencing of non-model organisms is now widely accessible and has allowed a range of questions in the field of molecular ecology to be investigated with greater power. However, some genomic regions that are of high biological interest remain problematic for assembly and data-handling. Three such regions are the major histocompatibility complex (MHC), sex-determining regions (SDRs) and the plant self-incompatibility locus (S-locus). Using these as examples, we illustrate the challenges of both assembling and resequencing these highly polymorphic regions and how bioinformatic and technological developments are enabling new approaches to their study. Mapping short-read sequences against multiple alternative references improves genotyping comprehensiveness at the S-locus thereby contributing to more accurate assessments of allelic frequencies. Long-read sequencing, producing reads of several tens to hundreds of kilobase pairs in length, facilitates the assembly of such regions as single sequences can span the multiple duplicated gene copies of the MHC region, and sequence through repetitive stretches and translocations in SDRs and S-locus haplotypes. These advances are adding value to short-read genome resequencing approaches by allowing, for example, more accurate haplotype phasing across longer regions. Finally, we assessed further technical improvements, such as nanopore adaptive sequencing and bioinformatic tools using pangenomes, which have the potential to further expand our knowledge of a number of genomic regions that remain challenging to study with classical resequencing approaches.\n\nWhole-genome sequencing and genome regions of special interest: Lessons from major histocompatibility complex, sex determination, and plant self-incompatibility.", "token_count": 381, "char_count": 1792, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6611, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:35.739436", "source": { "split": "train_shard_00001", "doc_id": 3398 }, "chunk_id": "train_shard_00001_3398_0", "global_id": 10478 }, { "text": "

Objectives

Vancomycin-resistant enterococci (VRE) are one of the most important bacterial causes of healthcare-associated infections (HAIs). In China, the detection rate of VRE Enterococcus faecium (VREfm) is low, although VREfm had a high prevalence in our hospitals between 2013-2015. In this study, we used molecular typing methods combined with epidemiological data to investigate the spread of VREfm in our hospital.

Methods

The characteristics of E. faecium strains isolated from 89 patients with HAIs, including antibiotic susceptibility and virulence genes, were analyzed. This study analyzed 50 E. faecium strains isolated from 47 intensive care unit and Emergency ward patients using core genome Multilocus Sequence Typing and transposon typing. Epidemiological information about those patients was also analyzed.

Results

Twenty-seven E. faecium isolates containing the vanA gene were identified as VREfm in 89 non-duplicate E. faecium isolates. The major clonal VREfm strains that persisted from 2013-2015 were CT1/ST78/PFGE cluster A that contained transposon type Ⅰ. The other CT4/ST363/PFGE cluster of VREfm strains also contained transposon type Ⅰ. Three patients acquired different clonal E. faecium strains during the hospital period, and the VREfm strain infected one patient.

Conclusions

In this study, we report the spread caused by vanA vancomycin-resistant E. faecium strains of different cluster types with the same type of transposon in a tertiary hospital. Our literature review revealed that this is the first report of the HAIs caused by ST363/CT4 VREfm strains.\n\nA molecular study regarding the spread of vanA vancomycin-resistant Enterococcus faecium in a tertiary hospital in China.", "token_count": 490, "char_count": 1741, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5542, "quality_score": 0.7771, "entities": { "genes": [ "CT1", "ST363", "CT4", "ST78" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:36.385672", "source": { "split": "train_shard_00001", "doc_id": 3399 }, "chunk_id": "train_shard_00001_3399_0", "global_id": 10479 }, { "text": "Whey waste is a major problem for the dairy industry. Finding alternative means to reduce its pollution potential and produce high value-added bioingredients has been attempted by many researchers. Kluyveromyces marxianus var. marxianus is a dairy yeast that produces beta-galactosidase, allowing for whey fermentation. Also, K. marxianus has been proposed as a source of: (1) oligonucleotides, used as flavor enhancers in food products; (2) oligosaccharides, used as prebiotics to stimulate the growth of Bifidobacterium sp. in the animal and human intestines; and (3) oligopeptides, immunostimulators added to dairy products that are released in the wort after whey protein proteolysis. Fed-batch fermentation can be used as an alternative process to avoid increases in lactose concentration and prevent the catabolite repression of the respiratory enzyme synthesis during aerobic fermentation, thus allowing for high biomass yields. The relevance of these factors on yeast fermentation of whey is summarized in this critical review.\n\nProduction of bioingredients from Kluyveromyces marxianus grown on whey: an alternative.", "token_count": 295, "char_count": 1125, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:36.951358", "source": { "split": "train_shard_00001", "doc_id": 3400 }, "chunk_id": "train_shard_00001_3400_0", "global_id": 10480 }, { "text": "Disclosed is a preparation method of a milk beer drink. The method is as follows: preparing by weight proportions 10 to 70 servings of a yogurt, 15 to 80 servings of water, 5 to 20 servings of a juice, 3 to 10 servings of a sweetener, 0.3 to 0.6 servings of a stabilizer, and 0.1 to 0.3 servings of an acidifier mixing before preheating to a temperature between 55 and 60 DEG C homogeneously performing pasteurization cooling to a temperature between 20 to 50 DEG C adding 1 to 3 servings of a yeast maintaining a temperature between 20 to 50 DEG C fermenting for 6 to 24 hours pouring the mixture into a sealed container maintaining a temperature between 20 to 40 DEG C refermenting for 4 to 10 hours obtaining the milk beer drink after sterilization. The yeast is a preservation registered yeast, Kluyveromyces marxianus var.marxianus (CGMCC NO. 3781), or a mixture thereof with a brewer's yeast and a fermented milk Candida.\n\nHIGH-QUALITY YEAST AND PREPARATION OF MILK BEER DRINK THEREOF", "token_count": 314, "char_count": 990, "word_count": 173, "semantic_coherence": 1, "information_density": 0.5029, "quality_score": 0.7514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:37.874459", "source": { "split": "train_shard_00001", "doc_id": 3401 }, "chunk_id": "train_shard_00001_3401_0", "global_id": 10481 }, { "text": "Corynebacterium diphtheriae is one of the most prominent human pathogens and the causative agent of the communicable disease diphtheria. The genomes of 12 strains isolated from patients with classical diphtheria, endocarditis, and pneumonia were completely sequenced and annotated. Including the genome of C. diphtheriae NCTC 13129, we herewith present a comprehensive comparative analysis of 13 strains and the first characterization of the pangenome of the species C. diphtheriae. Comparative genomics showed extensive synteny and revealed a core genome consisting of 1,632 conserved genes. The pangenome currently comprises 4,786 protein-coding regions and increases at an average of 65 unique genes per newly sequenced strain. Analysis of prophages carrying the diphtheria toxin gene tox revealed that the toxoid vaccine producer C. diphtheriae Park-Williams no. 8 has been lysogenized by two copies of the ω(tox)(+) phage, whereas C. diphtheriae 31A harbors a hitherto-unknown tox(+) corynephage. DNA binding sites of the tox-controlling regulator DtxR were detected by genome-wide motif searches. Comparative content analysis showed that the DtxR regulons exhibit marked differences due to gene gain, gene loss, partial gene deletion, and DtxR binding site depletion. Most predicted pathogenicity islands of C. diphtheriae revealed characteristics of horizontal gene transfer. The majority of these islands encode subunits of adhesive pili, which can play important roles in adhesion of C. diphtheriae to different host tissues. All sequenced isolates contain at least two pilus gene clusters. It appears that variation in the distributed genome is a common strategy of C. diphtheriae to establish differences in host-pathogen interactions.\n\nPangenomic study of Corynebacterium diphtheriae that provides insights into the genomic diversity of pathogenic isolates from cases of classical diphtheria, endocarditis, and pneumonia.", "token_count": 508, "char_count": 1933, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:38.529169", "source": { "split": "train_shard_00001", "doc_id": 3402 }, "chunk_id": "train_shard_00001_3402_0", "global_id": 10482 }, { "text": "Cultivations of Kluyveromyces marxianus var. bulgaricus ATCC 16045 were performed on both minimal and complex media using different carbon and nitrogen sources either in the presence or absence of aeration. The results collected were worked out and compared so as to provide a useful contribution to the optimization of inulinase production. Kinetics of extracellular inulinase release were similar on glucose, fructose, and sucrose. Inulinase was detected at basal level since the beginning of batch runs on these three carbon sources and overproduced after their depletion. The highest inulinase activity in minimal medium containing 10 g/l sucrose (6.4 IU/ml) was obtained at an initial (NH(4))(2)SO(4) concentration of 5 g/l, whereas it was reduced to about one fourth of this value and detected only at the beginning under nitrogen-limited conditions. The best sucrose concentrations for the enzyme production were 30 and 20 g/l in minimal and complex media, yielding 15.4 and 208 IU/ml, respectively. In general, the enzyme activity was much higher in complex than in minimal medium under all conditions. O(2)-enriched air neither improved inulinase production nor prevented ethanol formation.\n\nEffects of carbon and nitrogen sources and oxygenation on the production of inulinase by Kluyveromyces marxianus.", "token_count": 329, "char_count": 1314, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6308, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:39.105784", "source": { "split": "train_shard_00001", "doc_id": 3403 }, "chunk_id": "train_shard_00001_3403_0", "global_id": 10483 }, { "text": "

ABSTRACT

Bacteria of the genus Flavobacterium are recovered from a large variety of environments. Among the described species, Flavobacterium psychrophilum and Flavobacterium columnare are causing considerable losses in fish farms. Alongside these well-known fish-pathogenic species, isolates belonging to the same genus recovered from diseased or apparently healthy wild, feral, and farmed fish have been suspected to be pathogenic. Here, we report the identification and genomic characterization of a F. collinsii isolate (TRV642) retrieved from rainbow trout spleen. A phylogenetic tree of the genus built by aligning the core genome of 195 Flavobacterium species revealed that F. collinsii is standing within a cluster of species associated to diseased fish, the closest one being F. tructae which was recently confirmed as pathogenic. We evaluated the pathogenicity of F. collinsii TRV642 as well as of F. bernardetii F-372 T , another recently described species reported as a possible emerging pathogen. Following intramuscular injection challenges in rainbow trout, no clinical signs nor mortalities were observed. However, F. collinsii was isolated from the internal organs of wounded fish, suggesting that the bacterium could invade fish under compromised conditions such as stress and/or wounds. Our results suggest that some fish-associated Flavobacterium species should be considered as opportunistic fish pathogens causing disease under specific circumstances.

IMPORTANCE

Aquaculture has expanded significantly worldwide in the last decades and accounts for half of human fish consumption. However, infectious fish diseases are a major bottleneck for its sustainable development and an increasing number of bacterial species from diseased fish raise a great concern. The current study revealed phylogenetic associations with ecological niches among the Flavobacterium species. We also focused on Flavobacterium collinsii that belongs to a group of putative pathogenic species. The genome contents revealed a versatile metabolic repertoire suggesting the use of diverse nutrient sources, a characteristic of saprophytic or commensal bacteria. In a rainbow trout experimental challenge, the bacterium colonized only oppressed fish facing stressful conditions suggesting opportunistic pathogenic behavior", "token_count": 529, "char_count": 2332, "word_count": 321, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.81, "entities": { "genes": [ "TRV642" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:39.781402", "source": { "split": "train_shard_00001", "doc_id": 3404 }, "chunk_id": "train_shard_00001_3404_0", "global_id": 10484 }, { "text": "This study highlights the importance of experimentally evaluating the pathogenicity of the numerous bacterial species retrieved from diseased fish.\n\nInvestigation of the genus Flavobacterium as a reservoir for fish-pathogenic bacterial species: the case of Flavobacterium collinsii", "token_count": 77, "char_count": 295, "word_count": 36, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:40.179511", "source": { "split": "train_shard_00001", "doc_id": 3404 }, "chunk_id": "train_shard_00001_3404_1", "global_id": 10485 }, { "text": "A correct identification of Streptococcus pseudopneumoniae is a prerequisite for investigating the clinical impact of the bacterium. The identification has traditionally relied on phenotypic methods. However, these phenotypic traits have been shown to be unreliable, with some S. pseudopneumoniae strains giving conflicting results. Therefore, sequence-based identification methods have increasingly been used for identification of S. pseudopneumoniae In this study, we used 64 S. pseudopneumoniae strains, 59 S. pneumoniae strains, 22 S. mitis strains, 24 S. oralis strains, 6 S. infantis strains, and 1 S. peroris strain to test the capability of three single genes (rpoB, gyrB, and recA), two multilocus sequence analysis (MLSA) schemes, the single nucleotide polymorphism (SNP)-based phylogeny tool CSI phylogeny, a k-mer-based identification method (KmerFinder), average nucleotide identity (ANI) using fastANI, and core genome analysis to identify S. pseudopneumoniae Core genome analysis and CSI phylogeny were able to cluster all strains into distinct clusters related to their respective species. It was not possible to identify all S. pseudopneumoniae strains correctly using only one of the single genes. The MLSA schemes were unable to identify some of the S. pseudopneumoniae strains, which could be misidentified. KmerFinder identified all S. pseudopneumoniae strains but misidentified one S. mitis strain as S. pseudopneumoniae, and fastANI differentiated between S. pseudopneumoniae and S. pneumoniae using an ANI cutoff of 96%.", "token_count": 531, "char_count": 1684, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5945, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:40.828339", "source": { "split": "train_shard_00001", "doc_id": 3405 }, "chunk_id": "train_shard_00001_3405_0", "global_id": 10486 }, { "text": "Streptococcus pseudopneumoniae: Use of Whole-Genome Sequences To Validate Species Identification Methods.", "token_count": 29, "char_count": 105, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:41.230630", "source": { "split": "train_shard_00001", "doc_id": 3405 }, "chunk_id": "train_shard_00001_3405_1", "global_id": 10487 }, { "text": "

Background

Over the past two decades, livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) has become widely prevalent in pig production in Europe. The carriage status of LA-MRSA is known to vary among individual pigs, but bacterial load in pigs has rarely been studied. We assessed the quantity of LA-MRSA in nasal and skin samples of pigs and investigated the genetic diversity of the strains together with sequenced strains from national surveillance and pathology samples from the Finnish Food Authority. On two farms with assumed MRSA-positive status, farm 1 and farm 2, 10 healthy pigs were sampled three times during 2 weeks from the nares and skin (study A). On farm 1, 54 additional pigs were sampled and from confirmed MRSA-positive animals, 10 were randomly selected and transported to a clean, controlled environment for further sampling (study B). From the samples taken on farms 1 and 2 and in the controlled environment, MRSA was isolated both by direct plating and enrichment on selective media. spa types, multilocus sequence types, staphylococcal cassette chromosome mec types, resistance and virulence genes were determined. Core genome multilocus sequence typing (cgMLST) analysis was performed, including the sequences deriving from the surveillance/pathology samples from the Finnish Food Authority.

Results

All pigs on farm 1 carried LA-MRSA in the nares at all three time points and five pigs on farm 2 at one time point. Nasal quantity varied between 10 and 103 CFU/swab and quantity on the skin between 10 and 102 CFU/swab. In the controlled environment, MRSA was detected in at least one of the nasal samples from each animal. spa type t034 was predominant", "token_count": 460, "char_count": 1742, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5665, "quality_score": 0.7833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:41.889431", "source": { "split": "train_shard_00001", "doc_id": 3406 }, "chunk_id": "train_shard_00001_3406_0", "global_id": 10488 }, { "text": "cgMLST showed one cluster with minimum allele differences between 0 and 11.

Conclusions

The study shows predominantly low-level carriage (< 103 CFU/swab) of LA-MRSA on farms. In the controlled environment we observed a decline in nasal carriage but constant skin carriage. cgMLST showed that strains of spa type t034 are closely related at the national level.\n\nLow-level colonization of methicillin-resistant Staphylococcus aureus in pigs is maintained by slowly evolving, closely related strains in Finnish pig farms.", "token_count": 153, "char_count": 536, "word_count": 74, "semantic_coherence": 1, "information_density": 0.8108, "quality_score": 0.9054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:42.328380", "source": { "split": "train_shard_00001", "doc_id": 3406 }, "chunk_id": "train_shard_00001_3406_1", "global_id": 10489 }, { "text": "178 yeasts isolated from various foods were identified using ID32 C strip; Saccharomyces cerevisiae (47), Rhodotorula mucilaginosa (19), Candida kefyr (33), Candida krusei (37), Candida lusitaniae (28), Cndida lipolytica (14). The yeasts were harvested, saponified, derivatized, and extracted, and fatty acid analysis was performed by Gas Chromatography Mass Spectrometry. The yeast lipids contained Decanoic acid (C10:0), Luaric acid (C12:0), Myristoleic acid (C14:1), Myristic acid (C14:0), Pentadecanoic acid (C15:0), Palmitoleic acid C16:1), Pamitic acid (C16:0), Heptadecenoic acid (C17:1), Linoleic acid (C18:2), Linolenic acid (C18:3), Oleic acid (C18:1) and Stearic acid (C 18:0). The differences in the composition of these fatty acids could be used to identify the species as an accurate, efficient and relatively rapid method.\n\nIdentification of some yeasts by fatty acid profiles.", "token_count": 310, "char_count": 892, "word_count": 123, "semantic_coherence": 1, "information_density": 0.7642, "quality_score": 0.8821, "entities": { "genes": [ "ID32" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:42.907308", "source": { "split": "train_shard_00001", "doc_id": 3407 }, "chunk_id": "train_shard_00001_3407_0", "global_id": 10490 }, { "text": "

Background

Adaptation of Pseudomonas aeruginosa to different living conditions is accompanied by microevolution resulting in genomic diversity between strains of the same clonal lineage. In order to detect the impact of colonized habitats on P. aeruginosa microevolution we determined the genomic diversity between the highly virulent cystic fibrosis (CF) isolate CHA and two temporally and geographically unrelated clonal variants. The outcome was compared with the intraclonal genome diversity between three more closely related isolates of another clonal complex.

Results

The three clone CHA isolates differed in their core genome in several dozen strain specific nucleotide exchanges and small deletions from each other. Loss of function mutations and non-conservative amino acid replacements affected several habitat- and lifestyle-associated traits, for example, the key regulator GacS of the switch between acute and chronic disease phenotypes was disrupted in strain CHA. Intraclonal genome diversity manifested in an individual composition of the respective accessory genome whereby the highest number of accessory DNA elements was observed for isolate PT22 from a polluted aquatic habitat. Little intraclonal diversity was observed between three spatiotemporally related outbreak isolates of clone TB. Although phenotypically different, only a few individual SNPs and deletions were detected in the clone TB isolates. Their accessory genome mainly differed in prophage-like DNA elements taken up by one of the strains.

Conclusions

The higher geographical and temporal distance of the clone CHA isolates was associated with an increased intraclonal genome diversity compared to the more closely related clone TB isolates derived from a common source demonstrating the impact of habitat adaptation on the microevolution of P. aeruginosa. However, even short-term habitat differentiation can cause major phenotypic diversification driven by single genomic variation events and uptake of phage DNA.\n\nIntraclonal genome diversity of Pseudomonas aeruginosa clones CHA and TB.", "token_count": 480, "char_count": 2101, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5645, "quality_score": 0.7822, "entities": { "genes": [ "PT22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:43.550692", "source": { "split": "train_shard_00001", "doc_id": 3408 }, "chunk_id": "train_shard_00001_3408_0", "global_id": 10491 }, { "text": "Two lactose-consuming diploid Saccharomyces cerevisiae strains, AY-51024A and AY-51024M, were constructed by expressing the LAC4 and LAC12 genes of Kluyveromyces marxianus in the host strain AY-5. In AY-51024A, both genes were targeted to the ATH1 and NTH1 gene-encoding regions to abolish the activity of acid/neutral trehalase. In AY-51024M, both genes were respectively integrated into the MIG1 and NTH1 gene-encoding regions to relieve glucose repression. Physiologic studies of the two transformants under anaerobic cultivations in glucose and galactose media indicated that the expression of both LAC genes did not physiologically burden the cells, except for AY-51024A in glucose medium. Galactose consumption was initiated at higher glucose concentrations in the MIG1 deletion strain AY-51024M than in the corresponding wild-type strain and AY-51024A, wherein galactose was consumed until glucose was completely depleted in the mixture. In lactose medium, the Sp. growth rates of AY-51024A and AY-51024M under anaerobic shake-flasks were 0.025 and 0.067 h(-1), respectively. The specific lactose uptake rate and ethanol production of AY-51024M were 2.50 g lactose g CDW(-1) h(-1) and 23.4 g l(-1), respectively, whereas those of AY-51024A were 0.98 g lactose g CDW(-1) h(-1) and 24.3 g lactose g CDW(-1) h(-1), respectively", "token_count": 468, "char_count": 1331, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5492, "quality_score": 0.7746, "entities": { "genes": [ "NTH1", "LAC12", "LAC4", "MIG1", "ATH1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:44.195753", "source": { "split": "train_shard_00001", "doc_id": 3409 }, "chunk_id": "train_shard_00001_3409_0", "global_id": 10492 }, { "text": "In concentrated cheese whey powder solutions, AY-51024M produced 63.3 g l(-1) ethanol from approximately 150 g l(-1) initial lactose in 120 h, conversely, AY-51024A consumed 63.7 % of the initial lactose and produced 35.9 g l(-1) ethanol. Therefore, relieving glucose repression is an effective strategy for constructing lactose-consuming S. cerevisiae.\n\nConstruction of lactose-consuming Saccharomyces cerevisiae for lactose fermentation into ethanol fuel.", "token_count": 163, "char_count": 457, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7869, "quality_score": 0.8934, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:44.633371", "source": { "split": "train_shard_00001", "doc_id": 3409 }, "chunk_id": "train_shard_00001_3409_1", "global_id": 10493 }, { "text": "This work is focussed on the evaluation of enzymatic synthesis of galactooligosaccharides (GOS) catalysed by β-galactosidase from permeabilized cell of Kluyveromyces marxianus in different compressed fluids. The experiments were performed in a batch mode reactor, where the effects of enzyme and lactose concentrations and system pressure were evaluated. Results showed significant differences in the maximum GOS concentration among the experimental conditions, where the lactose concentration and enzyme activity were found to be statistically significant. Comparing the GOS productions in the three reaction systems, the supercritical CO₂ led to the best results, where the maximum production was 83gl⁻¹ while, for propane and n-butane, values of 63.0 and 75.0gl⁻¹ were verified, respectively. According to the kinetic results of GOS production in supercritical CO₂, a promising route is noted for this system, since the competition between synthesis and hydrolysis was less pronounced compared to the other tested fluids.\n\nEnzymatic synthesis of galactooligosaccharides using pressurised fluids as reaction medium", "token_count": 271, "char_count": 1116, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:45.187605", "source": { "split": "train_shard_00001", "doc_id": 3410 }, "chunk_id": "train_shard_00001_3410_0", "global_id": 10494 }, { "text": "Genome methylation in bacteria is an area of intense interest because it has broad implications for bacteriophage resistance, replication, genomic diversity via replication fidelity, response to stress, gene expression regulation, and virulence. Increasing interest in bacterial DNA modification is coming about with investigation of host/microbe interactions and the microbiome association and coevolution with the host organism. Since the recognition of DNA methylation being important in Escherichia coli and bacteriophage resistance using restriction/modification systems, more than 43,600 restriction enzymes have been cataloged in more than 3600 different bacteria. While DNA sequencing methods have made great advances there is a dearth of method advances to examine these modifications in situ. However, the large increase in whole genome sequences has led to advances in defining the modification status of single genomes as well as mining new restriction enzymes, methyltransferases, and modification motifs. These advances provide the basis for the study of pan-epigenomes, population-scale comparisons among pangenomes to link replication fidelity and methylation status along with mutational analysis of mutLS. Newer DNA sequencing methods that include SMRT and nanopore sequencing will aid the detection of DNA modifications on the ever-increasing whole genome and metagenome sequences that are being produced. As more sequences become available, larger analyses are being done to provide insight into the role and guidance of bacterial DNA modification to bacterial survival and physiology.\n\nBacterial Epigenomics: Epigenetics in the Age of Population Genomics", "token_count": 357, "char_count": 1675, "word_count": 231, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:45.768366", "source": { "split": "train_shard_00001", "doc_id": 3411 }, "chunk_id": "train_shard_00001_3411_0", "global_id": 10495 }, { "text": "Endosomally produced by eukaryotic cells, exosomes are microvesicles involved in cell-to-cell communication. Exosomes have shown a wide range of therapeutic potential as a drug or vaccine delivery system, and they are useful as biomarkers in several disease processes. Another biological function described is pathogen dissemination through host-derived molecules released during infection, thus modulating the immune response in the host. This work characterizes the exosomal fraction recovered from serum of Piscirickttesia salmonis-challenged Salmo salar specimens and from the corresponding non-challenged controls. Exosomes presented a spherical morphology and particle size distribution within 50–125 nm, showing similar parameters in both groups. The mass spectrometry analysis of exosomes isolated at 14 and 21 d post-challenge showed the presence of peptides corresponding to the three proteins of Hsp70/DnaK chaperone system (DnaK, DnaJ, and GrpE). BLAST search of these peptides showed the specificity to P. salmonis. Data are available via ProteomeXchange with identifier PXD023594. The chaperones were found with >95% identity in the core genome when aligned to 73 genomes of P. salmonis. The proteins also showed a high degree of similarity with other microorganisms, where this system has proven to be vital for their survival under stress conditions. The presence of these three proteins in exosomes isolated from challenged fish sera calls for further study into their potential role in bacterium pathogenicity. How to cite: Muñoz C, Carmona M, Luna O, et al. Serum-isolated exosomes from Piscirickettsia salmonis-infected Salmo salar specimens enclose bacterial DnaK, DnaJ and GrpE chaperones. Electron J Biotechnol 2022;59. https://doi.org/10.1016/j.ejbt.2022.07.003.", "token_count": 495, "char_count": 1786, "word_count": 248, "semantic_coherence": 1, "information_density": 0.7177, "quality_score": 0.8589, "entities": { "genes": [ "PXD023594" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:46.421426", "source": { "split": "train_shard_00001", "doc_id": 3412 }, "chunk_id": "train_shard_00001_3412_0", "global_id": 10496 }, { "text": "Serum-isolated exosomes from Piscirickettsia salmonis-infected Salmo salar specimens enclose bacterial DnaK, DnaJ and GrpE chaperones", "token_count": 48, "char_count": 133, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:46.779015", "source": { "split": "train_shard_00001", "doc_id": 3412 }, "chunk_id": "train_shard_00001_3412_1", "global_id": 10497 }, { "text": "Despite its low morbidity, listeriosis has a high mortality rate due to the severity of its clinical manifestations. The source of human listeriosis is often unclear. In this study, we investigate the ability of machine learning to predict the food source from which clinical Listeria monocytogenes isolates originated. Four machine learning classification algorithms were trained on core genome multilocus sequence typing data of 1212 L. monocytogenes isolates from various food sources. The average accuracies of random forest, support vector machine radial kernel, stochastic gradient boosting, and logit boost were found to be 0.72, 0.61, 0.7, and 0.73, respectively. Logit boost showed the best performance and was used in model testing on 154 L. monocytogenes clinical isolates. The model attributed 17.5 % of human clinical cases to dairy, 32.5% to fruits, 14.3% to leafy greens, 9.7% to meat, 4.6% to poultry, and 18.8% to vegetables. The final model also provided us with genetic features that were predictive of specific sources. Thus, this combination of genomic data and machine learning-based models can greatly enhance our ability to track L. monocytogenes from different food sources.\n\nA Machine Learning Model for Food Source Attribution of Listeria monocytogenes.", "token_count": 361, "char_count": 1315, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:47.370630", "source": { "split": "train_shard_00001", "doc_id": 3413 }, "chunk_id": "train_shard_00001_3413_0", "global_id": 10498 }, { "text": "Streptococcus mutans is a keystone pathogen of dental caries, and the ability to form biofilms is essential for its pathogenicity. We identified a glycosylation machinery (Pgf) in S. mutans that post-translationally modifies two surface-associated adhesins, Cnm and WapA. The four pgf genes ( pgfS , pgfM1 , pgfE, and pgfM2 ) are part of S. mutans core genome and we hypothesized that the scope of Pgf goes beyond Cnm and WapA. By inactivating each pgf gene individually or creating a quadruple pgf mutant in S. mutans OMZ175, we showed that the Pgf machinery is important for biofilm formation. Compared to OMZ175, differences in surface charge, membrane stability, and genetic competence were also observed for most mutants. Importantly, in silico analyses and tunicamycin MIC assays suggest a functional redundancy between the Pgf machinery and the rhamnose-glucose polysaccharide synthesis pathway. Using a rat oral colonization model, we showed a 10-fold reduction in recovered CFUs for the pgf quadruple mutant compared to OMZ175. Finally, using Cnm as a model, we showed by glycoproteomics analyses that Cnm is heavily modified with N-acetyl hexosamine in OMZ175 whereas phosphorylations were observed for the pgfS mutant. Our findings indicate that the Pgf machinery participates in important aspects of S. mutans pathobiology.

Graphical Abstract

Abbreviated summary

In this study, we demonstrate that the Pgf glycosylation machinery of Streptococcus mutans , a keystone pathogen of dental caries, regulates several aspects of bacterial pathophysiology that ultimately contribute to S. mutans fitness in oral colonization experiments", "token_count": 466, "char_count": 1659, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5551, "quality_score": 0.7776, "entities": { "genes": [ "OMZ175" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:48.013209", "source": { "split": "train_shard_00001", "doc_id": 3414 }, "chunk_id": "train_shard_00001_3414_0", "global_id": 10499 }, { "text": "Using the heavily glycosylated Cnm adhesin as a model, we found that inactivation of the glycosyltransferase PgfS results in loss of Cnm glycosylation, but instead, Cnm became heavily phosphorylated, suggesting a crosstalk/competition between these two post-translational modification mechanisms.\n\nPost-translational modification by the Pgf glycosylation machinery modulatesStreptococcus mutansphysiology and virulence", "token_count": 120, "char_count": 425, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8163, "quality_score": 0.9082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:48.396493", "source": { "split": "train_shard_00001", "doc_id": 3414 }, "chunk_id": "train_shard_00001_3414_1", "global_id": 10500 }, { "text": "Root tubers of Asparagus officinalis were used as a source of raw inulin for the production of exoinulinase (EC 3.2.1.7) from Kluyveromyces marxianus YS-1. Root extract prepared at 10kg/cm2 pressure for 10min showed maximum inulinase production. Medium components and process parameters were standardized to improve the enzyme production. Inulinase yield of 40.2IU/mL in a medium containing raw inulin (3.5%), beef extract (2%), SDS (0.001%), Mn2+ (2.0mM), Mg2+ (1.5mM), Co2+ (2mM) and pH 6.5 has been obtained under agitation (150rpm) after 60h of incubation at 30 degrees C at shake flask level. After optimization, the enzyme production was 4.8 times more than the basal medium. To test the feasibility of raw inulin from A. officinalis for the production of inulinase, trials were also made in a bioreactor (1.5L). Inulinase activity of 50.2IU/mL was obtained from raw inulin (4.0%) under agitation (200rpm) and aeration (0.75vvm) at 30 degrees C after 60h of fermentation. Inulinase yield in bioreactor was almost six times higher than the basal medium used initially in shake flask.\n\nProduction of extracellular exoinulinase from Kluyveromyces marxianus YS-1 using root tubers of Asparagus officinalis.", "token_count": 399, "char_count": 1208, "word_count": 183, "semantic_coherence": 1, "information_density": 0.5792, "quality_score": 0.7896, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:49.020728", "source": { "split": "train_shard_00001", "doc_id": 3415 }, "chunk_id": "train_shard_00001_3415_0", "global_id": 10501 }, { "text": "Sellimonas intestinalis is a Gram positive and anaerobic bacterial species previously considered as uncultivable. Although little is known about this Lachnospiraceae family member, its increased abundance has been reported in patients who recovered intestinal homeostasis after dysbiosis events. In this context, the aim of this work was taken advantage of a culturomics protocol that allowed the recovery species extremely oxygen-sensitive from faecal samples, which led to the establishment of an S. intestinalis isolate. Whole genome sequencing and taxonomic allocation confirmation were the base to develop comparative analyses including 11 public genomes closely related. Phylogeographic analysis revealed the existence of three lineages (linage-I including isolates from Chile and France, linage-II from South Korea and Finland, and linage-III from China and one isolate from USA). Pangenome analysis on the established dataset revealed that although S. intestinalis seems to have a highly conserved genome (with 50.1% of its coding potential being part of the coregenome), some recombination signals were evidenced. The identification of cluster of orthologous groups revealed a high number of genes involved in metabolism, including amino acid and carbohydrate transport as well as energy production and conversion, which matches with the metabolic profile previously reported for healthy microbiota. Additionally, virulence factors and antimicrobial resistance genes were found (mainly in linage-III), which could favour their survival during antibiotic-induced dysbiosis. These findings provide the basis of knowledge about this species with potential as a bioindicator of intestinal homeostasis recovery and contribute to advance in the characterization of gut microbiota members with beneficial potential.\n\nComprehensive genome analyses ofSellimonas intestinalis, a potential biomarker of homeostasis gut recovery", "token_count": 435, "char_count": 1932, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.8321, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:49.653349", "source": { "split": "train_shard_00001", "doc_id": 3416 }, "chunk_id": "train_shard_00001_3416_0", "global_id": 10502 }, { "text": "The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.\n\nInsights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.", "token_count": 398, "char_count": 1651, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:50.274094", "source": { "split": "train_shard_00001", "doc_id": 3417 }, "chunk_id": "train_shard_00001_3417_0", "global_id": 10503 }, { "text": "Bacillus coagulans, a Gram-positive thermophilic bacterium, is recognized for its probiotic properties and recent development as a microbial cell factory. Despite its importance for biotechnological applications, the current understanding of B. coagulans' robustness is limited, especially for undomesticated strains. To fill this knowledge gap, we characterized the metabolic capability and performed functional genomics and systems analysis of a novel, robust strain, B. coagulans B-768. Genome sequencing revealed that B-768 has the largest B. coagulans genome known to date (3.94 Mbp), about 0.63 Mbp larger than the average genome of sequenced B. coagulans strains, with expanded carbohydrate metabolism and mobilome. Functional genomics identified a well-equipped genetic portfolio for utilizing a wide range of C5 (xylose, arabinose), C6 (glucose, mannose, galactose), and C12 (cellobiose) sugars present in biomass hydrolysates, which was validated experimentally. For growth on individual xylose and glucose, the dominant sugars in biomass hydrolysates, B-768 exhibited distinct phenotypes and proteome profiles. Faster growth and glucose uptake rates resulted in lactate overflow metabolism, which makes B. coagulans a lactate overproducer; however, slower growth and xylose uptake diminished overflow metabolism due to the high energy demand for sugar assimilation. Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) made up 60%-65% of the measured proteomes but were allocated differently when growing on xylose and glucose", "token_count": 469, "char_count": 1639, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6912, "quality_score": 0.8456, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:50.921385", "source": { "split": "train_shard_00001", "doc_id": 3418 }, "chunk_id": "train_shard_00001_3418_0", "global_id": 10504 }, { "text": "The trade-off in proteome reallocation, with high investment in COG-C over COG-G, explains the xylose growth phenotype with significant upregulation of xylose metabolism, pyruvate metabolism, and tricarboxylic acid (TCA) cycle. Strain B-768 tolerates and effectively utilizes inhibitory biomass hydrolysates containing mixed sugars and exhibits hierarchical sugar utilization with glucose as the preferential substrate.IMPORTANCEThe robustness of B. coagulans makes it a valuable microorganism for biotechnology applications; yet, this phenotype is not well understood at the cellular level. Through phenotypic characterization and systems analysis, this study elucidates the functional genomics and robustness of a novel, undomesticated strain, B. coagulans B-768, capable of utilizing inhibitory switchgrass biomass hydrolysates. The genome of B-768, enriched with carbohydrate metabolism genes, demonstrates high regulatory capacity. The coordination of proteome reallocation in Carbohydrate Transport and Metabolism (COG-G), Translation (COG-J), and Energy Conversion and Production (COG-C) is critical for effective cell growth, sugar utilization, and lactate production via overflow metabolism. Overall, B-768 is a novel, robust, and promising B. coagulans strain that can be harnessed as a microbial biomanufacturing platform to produce chemicals and fuels from biomass hydrolysates.\n\nExpanded genome and proteome reallocation in a novel, robust Bacillus coagulans strain capable of utilizing pentose and hexose sugars.", "token_count": 436, "char_count": 1561, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:51.551042", "source": { "split": "train_shard_00001", "doc_id": 3418 }, "chunk_id": "train_shard_00001_3418_1", "global_id": 10505 }, { "text": "The potential probiotic benefits of Bifidobacterium bifidum have received increasing attention recently. We used comparative genomic analysis to explore the differences in the genome and the physiological characteristics of B. bifidum isolated from the fecal samples of Chinese adults and infants. The relationships between genotypes and phenotypes were analyzed to assess the effects of isolation sources on the genetic variation of B. bifidum. The phylogenetic tree results indicated that the phylogeny of B. bifidum may be related to the geographical features of its isolation source. B. bifidum was found to have an open pan-genome and a conserved core genome. The genetic diversity of B. bifidum is mainly reflected in carbohydrate metabolism- and immune/competition-related factors, such as the glycoside hydrolase gene family, bacteriocin operons, antibiotic resistance genes, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. Additionally, the type III A CRISPR-Cas system was discovered in B. bifidum for the first time. B. bifidum strains exhibited niche-specific characteristics, and the results of this study provide an improved understanding of the genetics of this species.\n\nComparative Genomic Analysis of Bifidobacterium bifidum Strains Isolated from Different Niches.", "token_count": 376, "char_count": 1373, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:52.161220", "source": { "split": "train_shard_00001", "doc_id": 3419 }, "chunk_id": "train_shard_00001_3419_0", "global_id": 10506 }, { "text": "Bacillus species are among the most promising plant growth-promoting bacteria (PGPB) due to their adaptability to various environmental niches and extensive biosynthetic capabilities. Despite the available data on the PGP-traits (PGPTs) of Bacillus, the genetic basis underlying their beneficial effects remains largely unexplored. In this study, a comparative genomic analysis of three B. pumilus and one B. pseudomycoides strains, isolated from the maize rhizosphere, is presented to elucidate the molecular mechanisms behind their PGP-traits. All strains exhibited multiple PGP-traits, including phosphate solubilization, phytohormone and siderophore production, growth in nitrogen-free medium, stress tolerance, and biofilm formation. Phylogenomic analysis revealed that plant-associated strains have higher genetic similarity, emphasizing niche-specific evolution. Genome analyses revealed strain- and species-specific adaptations, particularly in relation to nutrient acquisition and abiotic stress response mechanisms. B. pumilus strains encoded alternative sigma factors (SigB, SigM, SigW) enabling enhanced salt tolerance, whereas B. pseudomycoides lacked this system and relied on conventional osmoprotective strategies. The strains utilized different tryptophan-dependent (IAN, IAM or IPyA) pathways for auxin biosynthesis and differed in phosphate solubilization ability, which can be attributed to upstream and missense variants in genes affecting acid metabolism (gltA, acnA, acnB, citM, and citS) and phosphatase (phoA) activity. Iron uptake via bacillibactin-siderophores was exclusive to B. pumilus. The inability of the B", "token_count": 486, "char_count": 1719, "word_count": 209, "semantic_coherence": 1, "information_density": 0.7703, "quality_score": 0.8852, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:52.837865", "source": { "split": "train_shard_00001", "doc_id": 3420 }, "chunk_id": "train_shard_00001_3420_0", "global_id": 10507 }, { "text": "pseudomycoides strain to acquire iron was associated with structural variants (absence of bsaA gene) within the bacillibactin biosynthetic gene cluster. This work provides new insights into the molecular basis of PGP traits in Bacillus and supports the development of Bacillus-based bioinoculants for sustainable agriculture.\n\nUnveiling the genetic basis of biochemical pathways of plant growth promotion in <i>Bacillus pumilus</i> and the first genomic insights into <i>B. pseudomycoides</i> as a biostimulant.", "token_count": 177, "char_count": 560, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8116, "quality_score": 0.9058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:53.316149", "source": { "split": "train_shard_00001", "doc_id": 3420 }, "chunk_id": "train_shard_00001_3420_1", "global_id": 10508 }, { "text": "We determined the nucleotide sequence of the URA3 gene encoding orotidine-5'-phosphate decarboxylase (OMPDCase) of the erythritol-producing osmotolerant yeast Candida magnoliae by degenerate polymerase chain reaction and genome walking. Sequence analysis revealed the presence of an uninterrupted open-reading frame of 795 bp, encoding a 264 amino acid residue protein with the highest identity to the OMPDCase of the yeast Kluyveromyces marxianus. Phylogenetic analysis of the deduced amino acid sequence revealed that it shared a high degree of identity with other yeast OMPDCase homologs. The cloned URA3 gene successfully complemented the ura3 null mutation in Saccharomyces cerevisiae, revealing that it encodes a functional OMPDCase in C. magnoliae. An enzyme activity assay and reverse transcription polymerase chain reaction indicated that the expression level of the C. magnoliae URA3 gene in S. cerevisiae was not as high as that of the S. cerevisiae URA3 gene. The GenBank accession number for C. magnoliae URA3 is JF521441.\n\nCloning and characterization of the orotidine-5'-phosphate decarboxylase gene (URA3) from the osmotolerant yeast Candida magnoliae.", "token_count": 340, "char_count": 1168, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [ "URA3", "JF521441" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:53.911387", "source": { "split": "train_shard_00001", "doc_id": 3421 }, "chunk_id": "train_shard_00001_3421_0", "global_id": 10509 }, { "text": "Production of inulinase by solid state fermentation always involves an extraction step, which dictates enzyme recovery yield and is related to cultivation conditions and control of process parameters. This work is focused on the study of extraction conditions aiming to maximize yield of an inulinase obtained by solid state fermentation of sugar cane bagasse and Kluyveromyces marxianus NRRL Y-7571. Kinetics of extraction was followed varying the kind of solvent used. After determining the best solvent, an experimental design was carried out to study the effect of the solid/liquid ratio (1:10-1:20), extraction temperature (20-53 degrees C), and stirring rate (50-177 rpm). Results showed that maximum yield was obtained when sodium acetate buffer 0.1 M pH 4.8 was used, using a solid/liquid ratio of 1:10, at 53 degrees C and 150 rpm for 40 min.\n\nExtraction of inulinase obtained by solid state fermentation of sugarcane bagasse by Kluyveromyces marxianus NRRL Y-7571.", "token_count": 276, "char_count": 974, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6309, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:54.455382", "source": { "split": "train_shard_00001", "doc_id": 3422 }, "chunk_id": "train_shard_00001_3422_0", "global_id": 10510 }, { "text": "Enterohaemorrhagic Escherichia coli (EHEC) O157 is a zoonotic pathogen for which colonization of cattle and virulence in humans is associated with multiple horizontally acquired genes, the majority present in active or cryptic prophages. Our understanding of the evolution and phylogeny of EHEC O157 continues to develop primarily based on core genome analyses; however, such short-read sequences have limited value for the analysis of prophage content and its chromosomal location. In this study, we applied Single Molecule Real Time (SMRT) sequencing, using the Pacific Biosciences long-read sequencing platform, to isolates selected from the main sub-clusters of this clonal group. Prophage regions were extracted from these sequences and from published reference strains. Genome position and prophage diversity were analysed along with genetic content. Prophages could be assigned to clusters, with smaller prophages generally exhibiting less diversity and preferential loss of structural genes. Prophages encoding Shiga toxin (Stx) 2a and Stx1a were the most diverse, and more variable compared to prophages encoding Stx2c, further supporting the hypothesis that Stx2c-prophage integration was ancestral to acquisition of other Stx types. The concept that phage type (PT) 21/28 (Stx2a+, Stx2c+) strains evolved from PT32 (Stx2c+) was supported by analysis of strains with excised Stx-encoding prophages. Insertion sequence elements were over-represented in prophage sequences compared to the rest of the genome, showing integration in key genes such as stx and an excisionase, the latter potentially acting to capture the bacteriophage into the genome. Prophage profiling should allow more accurate prediction of the pathogenic potential of isolates.\n\nEvolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing.", "token_count": 493, "char_count": 1913, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6679, "quality_score": 0.834, "entities": { "genes": [ "PT32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:55.099706", "source": { "split": "train_shard_00001", "doc_id": 3423 }, "chunk_id": "train_shard_00001_3423_0", "global_id": 10511 }, { "text": "

Background

There is a need to characterize genomes of the foodborne pathogen, Salmonella enterica serovar Enteritidis (SE) and identify genetic information that could be ultimately deployed for differentiating strains of the organism, a need that is yet to be addressed mainly because of the high degree of clonality of the organism. In an effort to achieve the first characterization of the genomes of SE of Canadian origin, we carried out massively parallel sequencing of the nucleotide sequence of 11 SE isolates obtained from poultry production environments (n = 9), a clam and a chicken, assembled finished genomes and investigated diversity of the SE genome.

Results

The median genome size was 4,678,683 bp. A total of 4,833 chromosomal genes defined the pan genome of our field SE isolates consisting of 4,600 genes present in all the genomes, i.e., core genome, and 233 genes absent in at least one genome (accessory genome). Genome diversity was demonstrable by the presence of 1,360 loci showing single nucleotide polymorphism (SNP) in the core genome which was used to portray the genetic distances by means of a phylogenetic tree for the SE isolates. The accessory genome consisted mostly of previously identified SE prophage sequences as well as two, apparently full-sized, novel prophages namely a 28 kb sequence provisionally designated as SE-OLF-10058 (3) prophage and a 43 kb sequence provisionally designated as SE-OLF-10012 prophage.

Conclusions

The number of SNPs identified in the relatively large core genome of SE is a reflection of substantial diversity that could be exploited for strain differentiation as shown by the development of an informative phylogenetic tree. Prophage sequences can also be exploited for SE strain differentiation and lineage tracking. This work has laid the ground work for further studies to develop a readily adoptable laboratory test for the subtyping of SE.", "token_count": 501, "char_count": 1935, "word_count": 294, "semantic_coherence": 1, "information_density": 0.585, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:55.754147", "source": { "split": "train_shard_00001", "doc_id": 3424 }, "chunk_id": "train_shard_00001_3424_0", "global_id": 10512 }, { "text": "High resolution assembly and characterization of genomes of Canadian isolates of Salmonella Enteritidis.", "token_count": 22, "char_count": 104, "word_count": 13, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:56.111889", "source": { "split": "train_shard_00001", "doc_id": 3424 }, "chunk_id": "train_shard_00001_3424_1", "global_id": 10513 }, { "text": "The hydrolysis of lactose in skimmed milk and β‐galactosidase inactivation studies were carried out in three different devices – bioreactor, sonicator and homogeniser – to evaluate the performance of such reactors that have different operational systems. The experiments were carried out using β‐galactosidase produced from Kluyveromyces marxianus lactis. At the optimum process conditions obtained from the experiments performed in bioreactor, sonicator and homogeniser, 89%, 90% and 54% of lactose were hydrolysed and the enzyme lost its activity by 14%, 13% and 24%, respectively, at the end of the processing time of 30 min. The commercial milk lactose content (1 g/L lactose) was reached at 60 min for bioreactor and sonicator. After evaluation of the data, it was found that the kinetics of hydrolysis and enzyme inactivation could be represented by a first‐order kinetic model and a single‐step non‐first‐order enzyme inactivation kinetic model, respectively, for all process conditions applied. The activation energy for hydrolysis reaction and the enzymatic inactivation energy values were also calculated.\n\nAModelling study on skimmed milk lactose hydrolysis and β‐galactosidase stability using three reactor types", "token_count": 347, "char_count": 1251, "word_count": 174, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:56.684766", "source": { "split": "train_shard_00001", "doc_id": 3425 }, "chunk_id": "train_shard_00001_3425_0", "global_id": 10514 }, { "text": "Many bacteria are known to inhibit food pathogens, such as Listeria monocytogenes, by secreting a variety of bactericidal and bacteriostatic substances. In sharp contrast, it is unknown whether yeast has an inhibitory potential for the growth of pathogenic bacteria in food. A total of 404 yeasts were screened for inhibitory activity against five Listeria monocytogenes strains. Three hundred and four of these yeasts were isolated from smear-ripened cheeses. Most of the yeasts were identified by Fourier transform infrared spectroscopy. Using an agar-membrane screening assay, a fraction of approximately 4% of the 304 red smear cheese isolates clearly inhibited growth of L. monocytogenes. Furthermore, 14 out of these 304 cheese yeasts were cocultivated with L. monocytogenes WSLC 1364 on solid medium to test the antilisterial activity of yeast in direct cell contact with Listeria. All yeasts inhibited L. monocytogenes to a low degree, which is most probably due to competition for nutrients. However, one Candida intermedia strain was able to reduce the listerial cell count by 4 log units. Another four yeasts, assigned to C. intermedia (three strains) and Kluyveromyces marxianus (one strain), repressed growth of L. monocytogenes by 3 log units. Inhibition of L. monocytogenes was clearly pronounced in the cocultivation assay, which simulates the conditions and contamination rates present on smear cheese surfaces. We found no evidence that the unknown inhibitory molecule is able to diffuse through soft agar.\n\nInhibition of Listeria monocytogenes by food-borne yeasts.", "token_count": 418, "char_count": 1584, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:57.313926", "source": { "split": "train_shard_00001", "doc_id": 3426 }, "chunk_id": "train_shard_00001_3426_0", "global_id": 10515 }, { "text": "

Background

Coxiella burnetii is a zoonotic pathogen that resides in wild and domesticated animals across the globe and causes a febrile illness, Q fever, in humans. An improved understanding of the genetic diversity of C. burnetii is essential for the development of diagnostics, vaccines and therapeutics, but genotyping data is lacking from many parts of the world. Sporadic outbreaks of Q fever have occurred in the United Kingdom, but the local genetic make-up of C. burnetii has not been studied in detail.

Results

Here, we report whole genome data for nine C. burnetii sequences obtained in the UK. All four genomes of C. burnetii from cattle, as well as one sheep sample, belonged to Multi-spacer sequence type (MST) 20, whereas the goat samples were MST33 (three genomes) and MST32 (one genome), two genotypes that have not been described to be present in the UK to date. We established the phylogenetic relationship between the UK genomes and 67 publically available genomes based on single nucleotide polymorphisms (SNPs) in the core genome, which confirmed tight clustering of strains within genomic groups, but also indicated that sub-groups exist within those groups. Variation is mainly achieved through SNPs, many of which are non-synonymous, thereby confirming that evolution of C. burnetii is based on modification of existing genes. Finally, we discovered genomic-group specific genome content, which supports a model of clonal expansion of previously established genotypes, with large scale dissemination of some of these genotypes across continents being observed.

Conclusions

The genetic make-up of C. burnetii in the UK is similar to the one in neighboring European countries. As a species, C. burnetii has been considered a clonal pathogen with low genetic diversity at the nucleotide level. Here, we present evidence for significant variation at the protein level between isolates of different genomic groups, which mainly affects secreted and membrane-associated proteins. Our results thereby increase our understanding of the global genetic diversity of C. burnetii and provide new insights into the evolution of this emerging zoonotic pathogen.", "token_count": 522, "char_count": 2193, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5841, "quality_score": 0.792, "entities": { "genes": [ "MST33", "MST32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:37:57.975770", "source": { "split": "train_shard_00001", "doc_id": 3427 }, "chunk_id": "train_shard_00001_3427_0", "global_id": 10516 }, { "text": "Extensive genome analysis of Coxiella burnetii reveals limited evolution within genomic groups.", "token_count": 21, "char_count": 95, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:58.329208", "source": { "split": "train_shard_00001", "doc_id": 3427 }, "chunk_id": "train_shard_00001_3427_1", "global_id": 10517 }, { "text": "

Background

Bifidobacterium longum is a common member of the human gut microbiota and is frequently present at high numbers in the gut microbiota of humans throughout life, thus indicative of a close symbiotic host-microbe relationship. Different mechanisms may be responsible for the high competitiveness of this taxon in its human host to allow stable establishment in the complex and dynamic intestinal microbiota environment. The objective of this study was to assess the genetic and metabolic diversity in a set of 20 B. longum strains, most of which had previously been isolated from infants, by performing whole genome sequencing and comparative analysis, and to analyse their carbohydrate utilization abilities using a gene-trait matching approach.

Results

We analysed their pan-genome and their phylogenetic relatedness. All strains clustered in the B. longum ssp. longum phylogenetic subgroup, except for one individual strain which was found to cluster in the B. longum ssp. suis phylogenetic group. The examined strains exhibit genomic diversity, while they also varied in their sugar utilization profiles. This allowed us to perform a gene-trait matching exercise enabling the identification of five gene clusters involved in the utilization of xylo-oligosaccharides, arabinan, arabinoxylan, galactan and fucosyllactose, the latter of which is an abundant human milk oligosaccharide (HMO).

Conclusions

The results showed high diversity in terms of genes and predicted glycosyl-hydrolases, as well as the ability to metabolize a large range of sugars. Moreover, we corroborate the capability of B. longum ssp. longum to metabolise HMOs. Ultimately, their intraspecific genomic diversity and the ability to consume a wide assortment of carbohydrates, ranging from plant-derived carbohydrates to HMOs, may provide an explanation for the competitive advantage and persistence of B. longum in the human gut microbiome.", "token_count": 489, "char_count": 1947, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5942, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:58.980455", "source": { "split": "train_shard_00001", "doc_id": 3428 }, "chunk_id": "train_shard_00001_3428_0", "global_id": 10518 }, { "text": "Gene-trait matching across the Bifidobacterium longum pan-genome reveals considerable diversity in carbohydrate catabolism among human infant strains.", "token_count": 36, "char_count": 150, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:59.344863", "source": { "split": "train_shard_00001", "doc_id": 3428 }, "chunk_id": "train_shard_00001_3428_1", "global_id": 10519 }, { "text": "Treatment failure of methicillin-resistant Staphylococcus aureus (MRSA) infections remains problematic in clinical practice because therapeutic options are limited. Penicillin plus potassium clavulanate combination (PENC) was shown to have potential for treating some MRSA infections. We investigated the susceptibility of MRSA isolates and constructed a drug susceptibility prediction model for the phenotype of the PENC. We determined the minimum inhibitory concentration of PENC for MRSA (n=284) in a teaching hospital (SRRSH-MRSA). PENC susceptibility genotypes were analysed using a published genotyping scheme based on the mecA sequence. mecA expression in MRSA isolates was analysed by qPCR. We established a random forest model for predicting PENC-susceptible phenotypes using core genome allelic profiles from cgMLST analysis. We identified S2-R isolates with susceptible mecA genotypes but PENC-resistant phenotypes; these isolates expressed mecA at higher levels than did S2 MRSA (2.61 vs 0.98, P<0.05), indicating the limitation of using a single factor for predicting drug susceptibility. Using the data of selected UK-sourced MRSA (n=74) and MRSA collected in a previous national survey (NA-MRSA, n=471) as a training set, we built a model with accuracies of 0.94 and 0.93 for SRRSH-MRSA and UK-sourced MRSA (n=287, NAM-MRSA) validation sets. The AUROC of this model for SRRSH-MRSA and NAM-MRSA was 0.96 and 0.97. Although the source of the training set data affects the scope of application of the prediction model, our data demonstrated the power of the machine learning approach in predicting susceptibility from cgMLST results.", "token_count": 505, "char_count": 1715, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:37:59.994551", "source": { "split": "train_shard_00001", "doc_id": 3429 }, "chunk_id": "train_shard_00001_3429_0", "global_id": 10520 }, { "text": "A random forest model based on core genome allelic profiles of MRSA for penicillin plus potassium clavulanate susceptibility prediction.", "token_count": 33, "char_count": 136, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:00.351778", "source": { "split": "train_shard_00001", "doc_id": 3429 }, "chunk_id": "train_shard_00001_3429_1", "global_id": 10521 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) is a leading cause of foodborne infections. Cattle are an important STEC reservoir, although little is known about specific pathogen traits that impact persistence in the farm environment. Hence, we sought to evaluate STEC isolates recovered from beef cattle in a single herd in Michigan. To do this, we collected fecal grabs from 26 cattle and resampled 13 of these animals at 3 additional visits over a 3-month period. In all, 66 STEC isolates were recovered for genomics and biofilm quantification using crystal violet assays. The STEC population was diverse, representing seven serotypes, including O157:H7, O26:H11, and O103:H2, which are commonly associated with human infections. Although a core genome analysis of 2,933 genes grouped isolates into clusters based on serogroups, some isolates within each cluster had variable biofilm levels and virulence gene profiles. Most (77.8%; n = 49) isolates harbored stx2a, while 38 (57.5%) isolates formed strong biofilms. Isolates belonging to the predominant serogroup O6 (n = 36; 54.5%) were more likely to form strong biofilms, persistently colonize multiple cattle, and be acquired over time. A high-quality single nucleotide polymorphism (SNP) analysis of 33 O6 isolates detected between 0 and 13 single nucleotide polymorphism (SNP) differences between strains, indicating that highly similar strain types were persisting in this herd. Similar findings were observed for other persistent serogroups, although key genes were found to differ among strong and weak biofilm producers", "token_count": 454, "char_count": 1621, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7149, "quality_score": 0.8574, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:00.995099", "source": { "split": "train_shard_00001", "doc_id": 3430 }, "chunk_id": "train_shard_00001_3430_0", "global_id": 10522 }, { "text": "Together, these data highlight the diversity and persistent nature of some STEC types in this important food animal reservoir.IMPORTANCE Food animal reservoirs contribute to Shiga toxin-producing Escherichia coli (STEC) evolution via the acquisition of horizontally acquired elements like Shiga toxin bacteriophages that enhance pathogenicity. In cattle, persistent fecal shedding of STEC contributes to contamination of beef and dairy products and to crops being exposed to contaminated water systems. Hence, identifying factors important for STEC persistence is critical. This longitudinal study enhances our understanding of the genetic diversity of STEC types circulating in a cattle herd and identifies genotypic and phenotypic traits associated with persistence. Key findings demonstrate that multiple STEC types readily persist in and are transmitted across cattle in a shared environment. These dynamics also enhance the persistence of virulence genes that can be transferred between bacterial hosts, resulting in the emergence of novel STEC strain types. Understanding how pathogens persist and diversify in reservoirs is important for guiding new preharvest prevention strategies aimed at reducing foodborne transmission to humans.\n\nGenetic and Phenotypic Factors Associated with Persistent Shedding of Shiga Toxin-Producing Escherichia coli by Beef Cattle.", "token_count": 309, "char_count": 1381, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:01.560231", "source": { "split": "train_shard_00001", "doc_id": 3430 }, "chunk_id": "train_shard_00001_3430_1", "global_id": 10523 }, { "text": "An extracellular endo-polygalacturonase (PGase) produced by a mutant of Saccharomyces cerevisiae was isolated. The enzyme was regarded, immunologically, as a PGase belonging to the Kluyveromyces marxianus group. The enzyme had properties similar to the PGase from K. marxianus in heat and pH stability, and N-terminal amino acid sequence. However, the enzyme showed different properties in optimum pH and temperature, molecular weight, and reactivity in antiserum against PGase from K. marxianus, indicating that the enzyme has a different molecular structure from the PGase from K. marxianus.\n\nPurification and characterization of an endo-polygalacturonase from a mutant of Saccharomyces cerevisiae.", "token_count": 193, "char_count": 700, "word_count": 97, "semantic_coherence": 1, "information_density": 0.5876, "quality_score": 0.7938, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:02.014814", "source": { "split": "train_shard_00001", "doc_id": 3431 }, "chunk_id": "train_shard_00001_3431_0", "global_id": 10524 }, { "text": "The objective of this work was to test the protective effect of a mixture (MM) constituted by kefir-isolated microorganisms (Lactobacillus plantarum, Lactobacillus kefir, Lc. lactis, Kluyveromyces marxianus and Saccharomyces cerevisiae) in a hamster model of infection with Clostridium difficile, an anaerobic Gram-positive bacterium that causes diarrhoea. Placebo or MM was administered ad libitum in drinking water from day 0 to the end of treatment. Hamsters received orally 200 μg of clyndamicin at day 7 and then were infected with 1 × 10(8) CFU of C. difficile by gavage. Development of diarrhoea and death was registered until the end of the protocol. Surviving animals were sacrificed at day 16, and a test for biological activity of clostridial toxins and histological stainings were performed in caecum samples. Six of seven infected animals developed diarrhoea and 5/7 died at the end of the experimental protocol. The histological sections showed oedema and inflammatory infiltrates with neutrophils and crypt abscesses. In the group of animals infected and treated with MM1/1000, only 1 of 7 hamsters showed diarrhoea and none of them died. The histological sections showed only a slight thickening of the mucosa with presence of lymphocytic infiltrate. These results demonstrate that an oral treatment with a mixture of kefir-isolated bacteria and yeasts was able to prevent diarrhoea and enterocolitis triggered by C. difficile.\n\nProtective effect of a mixture of kefir-isolated lactic acid bacteria and yeasts in a hamster model of Clostridium difficile infection.", "token_count": 443, "char_count": 1580, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5649, "quality_score": 0.7824, "entities": { "genes": [ "MM1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:02.644509", "source": { "split": "train_shard_00001", "doc_id": 3432 }, "chunk_id": "train_shard_00001_3432_0", "global_id": 10525 }, { "text": "Among the numerous yeasts able to produce flavor compounds, several strains of Kluyveromyces species are known for the synthesis of large amounts of aromatic compounds. In particular, the accumulation of 2-phenylethyl alcohol in liquid cultures of Kluyveromyces marxianus was observed after incubation on a semisynthetic medium at 30 degrees C, 125 rpm. Changes in the carbon sources led to a significant modification of the amount of this aromatic compound; moreover, the variations in the level of DL-phenylalanine and the exclusive use of a precursor isomer (L) also affected the synthesis of 2-phenylethyl alcohol. Finally, this study revealed the growth inhibition of K. marxianus when the concentration of 2-phenylethyl alcohol reached a critical value near 1.4 g/L; the use of an exponential model allowed the inhibition constant ki to be determined (ki = 0.35 g/L).\n\nProduction of 2-phenylethyl alcohol by Kluyveromyces marxianus.", "token_count": 253, "char_count": 938, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6738, "quality_score": 0.8369, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:03.143316", "source": { "split": "train_shard_00001", "doc_id": 3433 }, "chunk_id": "train_shard_00001_3433_0", "global_id": 10526 }, { "text": "

Objectives

Until July 2016, vancomycin-resistantEnterococcus faecium (VREfm) was sporadically detected in Odense University Hospital, Denmark. After July 2016, the number of VREfm cases increased. This study aimed to apply a core genome multilocus sequence typing (cgMLST) scheme for E. faecium to type and analyse VREfm isolates collected at a single Danish hospital and to compare the results with cgMLST data from other regions of Denmark to trace transmission.

Methods

A total of 38 VREfm clinical isolates from inpatients at the hospital in the period January 2014 through June 2017 were included in the study and analysed using whole-genome sequencing. Use of SeqSphere + software was initiated from the beginning of June 2017 to obtain MLST, cgMLST and epi curves. Admission histories were incorporated and national surveillance data on cgMLST were used to identify transmission routes.

Results

Six different sequence types (STs) were identified, the most frequent being ST80, ST117 and ST203. cgMLST subdivided the 38 isolates into 18 different complex types (CTs) with 13 isolates (34%) belonging to ST80-CT993. Epi curves indicated transmission of ST80-CT993 in several departments. Transmission from patients transferred from other hospitals was not identifiable. Infection control interventions launched in one department ended the outbreak.

Conclusion

The high resolution of cgMLST allowed for detailed interpretation with evidence of nosocomial transmission of specific CTs. cgMLST made it easy to compare our local isolates with national findings, thereby clarifying transmission routes. Supplemented with admission histories, cgMLST targeted the epidemiological investigation and delineated the expensive and time-consuming infection control interventions.\n\nUsing core genome multilocus sequence typing (cgMLST) for vancomycin-resistant Enterococcus faecium isolates to guide infection control interventions and end an outbreak.", "token_count": 507, "char_count": 1973, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6136, "quality_score": 0.8068, "entities": { "genes": [ "CT993", "ST80", "ST117", "ST203" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:03.796804", "source": { "split": "train_shard_00001", "doc_id": 3434 }, "chunk_id": "train_shard_00001_3434_0", "global_id": 10527 }, { "text": "South Asian (SA) Canadian immigrants have a higher risk of developing certain immune-mediated inflammatory diseases compared to non-migrant SAs. We sought to investigate the effect of migration on the gut metagenome and to identify microbiological associations between migration and conditions that may influence the development of immune-mediated inflammatory diseases. Metagenomic analysis of 58 first-generation (GEN1) SA immigrants and 38 unrelated Canadian born children-of-immigrants (GEN2) determined that the time lived in Canada was associated with continued changes in gut microbial communities. Migration of GEN1 to Canada early in life results in a gut community with similarities to GEN2 SA Canadians and non-SA North Americans. Conversely, GEN1 immigrants who arrived recently to Canada exhibited pronounced differences from GEN2, while displaying microbial similarities to a non-migrating SA cohort. Multivariate analysis identified that community composition was primarily influenced by high abundance taxa. Prevotella copri dominated in GEN1 and non-migrant SAs. Clostridia and functionally related Bacteroidia spp. replaced P. copri dominance over generations in Canada. Mutually exclusive Dialister species occurred at differing relative abundances over time and generations in Canada. This shift in species composition is accompanied by a change in genes associated with carbohydrate utilization and short-chain fatty acid production. Total energy derived from carbohydrates compared to protein consumption was significantly higher for GEN1 recent immigrants, which may influence the functional requirements of the gut community. This study demonstrates the associations between migration and the gut microbiome, which may be further associated with the altered risk of immune-mediated inflammatory diseases observed for SA Canadians.\n\nThe Impact of Migration on the Gut Metagenome of South Asian Canadians.", "token_count": 435, "char_count": 1962, "word_count": 262, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [ "GEN2", "GEN1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:04.439033", "source": { "split": "train_shard_00001", "doc_id": 3435 }, "chunk_id": "train_shard_00001_3435_0", "global_id": 10528 }, { "text": "This study investigated the possibility of using yeast strains in fermented milks to obtain products with high Angiotensin I-converting enzyme (ACE) inhibitory activity and low bitter taste. Ninety-three yeast strains isolated from Colombian Kumis in different geographic regions were molecularly identified, and their milk fermentation performances were determined. Molecular identification evidenced that Galactomyces geotrichum, Pichia kudriavzevii, Clavispora lusitaniae and Candida tropicalis, were the dominant species. Eighteen out of 93 strains produced fermented milk with ACE-inhibitory (ACEI) activity values ranging from 8.69 to 88.19%. Digestion of fermented milk samples by pepsin and pancreatin demonstrated an increase in ACEI activity, with C. lusitaniae KL4A as the best producer of ACEI peptides. Moreover, sensory analysis of the products containing the major ACE-inhibitory activity pointed out that P. kudriavzevii KL84A and Kluyveromyces marxianus KL26A could be selected as potential adjunct starter cultures in Kumis, since they made a considerable contribution to the ACE inhibitory activity and produced fermented milk without bitter taste. In this study we observed that Colombian Kumis can be an excellent vehicle for the isolation of yeasts with a potential to enhance bioactive peptides produced during milk fermentation.\n\nYeasts from Colombian Kumis as source of peptides with Angiotensin I converting enzyme (ACE) inhibitory activity in milk.", "token_count": 381, "char_count": 1475, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [ "KL26A", "KL84A", "KL4A" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:05.044595", "source": { "split": "train_shard_00001", "doc_id": 3436 }, "chunk_id": "train_shard_00001_3436_0", "global_id": 10529 }, { "text": "A Gram-stain-negative, aerobic, non-motile, non-haemolytic, oxidase-negative, catalase-positive bacillus strain (A3.8T) was isolated from beach sediment from Zhairuo Island, PR China. The strain grew at pH 6.0-9.0 (optimum, 7.0), with 0-4.5 % NaCl (optimum, 2 %) and at 10-35 °C (optimum, 30 °C). Its whole-genome sequence was 2.5 Mb in size, with a DNA G+C content of 41.6 mol%. On the basis of the results of core genome phylogenetic analysis, A3.8T represents a separate branch within the clade formed by five species of the genus Acinetobacter with 'Acinetobacter marinus' as the most closely related species. The average nucleotide identity compared with the closely related species of the genus Acinetobacter was below 83.66 % and digital DNA-DNA hybridization values were less than 28.80 %. The predominant fatty acids included C18 : 1ω9c, C16 : 0 and summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c). Q-9 was the major respiratory quinone. The polar lipids are mainly composed of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two phospholipids, an aminolipid and four unknown lipids", "token_count": 466, "char_count": 1223, "word_count": 168, "semantic_coherence": 1, "information_density": 0.744, "quality_score": 0.872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:05.725273", "source": { "split": "train_shard_00001", "doc_id": 3437 }, "chunk_id": "train_shard_00001_3437_0", "global_id": 10530 }, { "text": "A3.8T cannot assimilate dl-lactate and weakly utilizes l-glutamate, l-leucine, l-phenylalanine and l-tartrate, which distinguishes it from other species of the genus Acinetobacter. On the basis of the genotype, phenotype and biochemical data, strain A3.8T represents a novel species of the genus Acinetobacter, for which the name Acinetobacter sedimenti sp. nov. is proposed. The type strain is A3.8T (=MCCC 1K07161T=LMG 32568T).\n\nAcinetobacter sedimenti sp. nov., isolated from beach sediment.", "token_count": 219, "char_count": 577, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:06.191747", "source": { "split": "train_shard_00001", "doc_id": 3437 }, "chunk_id": "train_shard_00001_3437_1", "global_id": 10531 }, { "text": "Whipple's disease is a rare chronic systemic disease that affects almost any organ system of the body caused by the intracellular bacterium Tropheryma whipplei, which is found ubiquitously in the environment. Sequencing of the T. whipplei genome has revealed that it has a reduced genome (0.93 Mbp), a characteristic shared with other intracellular bacteria. Until our research started, 19 T. whipplei strains had been sequenced from cultures originated in France, Canada, and Germany. The genome of T. whipplei bacterium has not been studied in Asia yet. Here, two metagenome-assembled genomes (MAGs) of T. whipplei from China were reconstructed through metagenomic next-generation sequencing (mNGS) and genome binning. We also provided genomic insights into the geographical role and genomic features by analyzing the whole genome. The whole-genome phylogenetic tree was constructed based on single-nucleotide polymorphism (SNP) distance calculations and then grouped by distance similarity. The phylogenetic tree shows inconsistencies with geographic origins, thus suggesting that the variations in geographical origins cannot explain the phylogenetic relationships among the 21 T. whipplei strains. The two Chinese strains were closely related to each other, and also found to be related to strains from Germany (T. whipplei TW08/27) and France (T. whipplei Bcu26 and T. whipplei Neuro1). Furthermore, the Average Nucleotide Identity (ANI) matrix also showed no association between geographic origins and genomic similarities. The pan-genome analysis revealed that T. whipplei has a closed pan-genome composed of big core-genomes and small accessory genomes, like other intracellular bacteria. By examining the genotypes of the sequenced strains, all 21 T", "token_count": 520, "char_count": 1832, "word_count": 252, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [ "TW08" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:06.862059", "source": { "split": "train_shard_00001", "doc_id": 3438 }, "chunk_id": "train_shard_00001_3438_0", "global_id": 10532 }, { "text": "whipplei strains were found to be resistant to fluoroquinolones, due to the genetic mutations in genes gyrA, gyrB, parC, and parE. The 21 T. Whipplei strains shared the same virulence factors, except for the alpC gene, which existed in 7 out of the 21 T. whipplei strains. When comparing 21 entire T. whipplei pan-genomes from various nations, it was discovered that the bacterium also possessed a closed genome, which was a trait shared by intracellular pathogens.\n\nGenomic characterization of two metagenome-assembled genomes of Tropheryma whipplei from China.", "token_count": 220, "char_count": 629, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:07.333521", "source": { "split": "train_shard_00001", "doc_id": 3438 }, "chunk_id": "train_shard_00001_3438_1", "global_id": 10533 }, { "text": "Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of “Virus” and the existence of a fourth domain of life 1-3 . While increasing knowledge of genome diversity has accumulated 4 , functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and its host Acanthamoeba castellanii using CRISPR/Cas9, allowing us to uncover the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the evolutionary intermediate mollivirus highlights a stepwise transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. Genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and demonstrate that viral gigantism can arise as an emerging trait.\n\nEvolution of giant pandoravirus from small icosahedral viruses revealed by CRISPR/Cas9", "token_count": 269, "char_count": 1175, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:07.884771", "source": { "split": "train_shard_00001", "doc_id": 3439 }, "chunk_id": "train_shard_00001_3439_0", "global_id": 10534 }, { "text": "To control the pH during antimicrobial peptide (nisin) production by a lactic acid bacterium, Lactococcus lactis subsp. lactis (ATCC11454), a novel method involving neither addition of alkali nor a separation system such as a ceramic membrane filter and electrodialyzer was developed. A mixed culture of L. lactis and Kluyveromyces marxianus, which was isolated from kefir grains, was utilized in the developed system. The interaction between lactate production by L. lactis and its assimilation by K. marxianus was used to control the pH. To utilize the interaction of these microorganisms to maintain high-level production of nisin, the kinetics of growth of, and production of lactate, acetate, and nisin by, L. lactis were investigated. The kinetics of growth of and lactic acid consumption by K. marxianus were also investigated. Because the pH of the medium could be controlled by the lactate consumption of K. marxianus and the specific lactate consumption rate of K. marxianus could be controlled by changing the dissolved oxygen (DO) concentration, a cascade pH controller coupled with DO control was developed. As a result, the pH was kept constant because the lactate level was kept low and nisin accumulated in the medium to a high level compared with that attained using other pH control strategies, such as with processes lacking pH control and those in which pH is controlled by addition of alkali.\n\nNisin production by a mixed-culture system consisting of Lactococcus lactis and Kluyveromyces marxianus.", "token_count": 394, "char_count": 1519, "word_count": 237, "semantic_coherence": 1, "information_density": 0.4852, "quality_score": 0.7426, "entities": { "genes": [ "ATCC11454" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:08.505462", "source": { "split": "train_shard_00001", "doc_id": 3440 }, "chunk_id": "train_shard_00001_3440_0", "global_id": 10535 }, { "text": "The thermotolerant yeast, Kluyveromyces marxianus IMB3, was grown in batch culture at 45°C on cellulose-containing media, supplemented with exogenous cellulase activity. At various stages during fermentation, both substrate and enzyme were added in batch mode and fermentation was continued for 220 h. Ethanol production increased to 20 g/l at 200 h, representing 45% of the maximum theoretical yield. In subsequent experiments, the organism was immobilized in calcium alginate beads and these were used in a similar, batch-fed system at 45°C. Again, fermentation was continued for 220 h and ethanol production increased to its maximum, of 28 g/l, within 100 h and this represented in excess of 60% of the maximum theoretical yield.\n\nShort communication: Ethanol production from cellulose at 45°C using a batch-fed system containing alginate-immobilized Kluyveromyces marxianus IMB3.", "token_count": 250, "char_count": 883, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6589, "quality_score": 0.8295, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:08.990547", "source": { "split": "train_shard_00001", "doc_id": 3441 }, "chunk_id": "train_shard_00001_3441_0", "global_id": 10536 }, { "text": "Livestock have been proposed as a reservoir for drug-resistant Escherichia coli that infect humans. We isolated and sequenced 431 E. coli isolates (including 155 extended-spectrum β-lactamase [ESBL]-producing isolates) from cross-sectional surveys of livestock farms and retail meat in the East of England. These were compared with the genomes of 1,517 E. coli bacteria associated with bloodstream infection in the United Kingdom. Phylogenetic core genome comparisons demonstrated that livestock and patient isolates were genetically distinct, suggesting that E. coli causing serious human infection had not directly originated from livestock. In contrast, we observed highly related isolates from the same animal species on different farms. Screening all 1,948 isolates for accessory genes encoding antibiotic resistance revealed 41 different genes present in variable proportions in human and livestock isolates. Overall, we identified a low prevalence of shared antimicrobial resistance genes between livestock and humans based on analysis of mobile genetic elements and long-read sequencing. We conclude that within the confines of our sampling framework, there was limited evidence that antimicrobial-resistant pathogens associated with serious human infection had originated from livestock in our region.IMPORTANCE The increasing prevalence of E. coli bloodstream infections is a serious public health problem. We used genomic epidemiology in a One Health study conducted in the East of England to examine putative sources of E. coli associated with serious human disease. E. coli from 1,517 patients with bloodstream infections were compared with 431 isolates from livestock farms and meat. Livestock-associated and bloodstream isolates were genetically distinct populations based on core genome and accessory genome analyses. Identical antimicrobial resistance genes were found in livestock and human isolates, but there was limited overlap in the mobile elements carrying these genes. Within the limitations of sampling, our findings do not support the idea that E", "token_count": 519, "char_count": 2132, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5377, "quality_score": 0.7688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:09.643911", "source": { "split": "train_shard_00001", "doc_id": 3442 }, "chunk_id": "train_shard_00001_3442_0", "global_id": 10537 }, { "text": "coli causing invasive disease or their resistance genes are commonly acquired from livestock in our region.\n\nOne Health Genomic Surveillance of Escherichia coli Demonstrates Distinct Lineages and Mobile Genetic Elements in Isolates from Humans versus Livestock.", "token_count": 67, "char_count": 265, "word_count": 36, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:10.016801", "source": { "split": "train_shard_00001", "doc_id": 3442 }, "chunk_id": "train_shard_00001_3442_1", "global_id": 10538 }, { "text": "Microbial spoilage of raw meat causes huge economic losses every year. An understanding of the microbial ecology associated with the spoilage and its dynamics during the refrigerated storage of meat can help in preventing and delaying the spoilage-related activities. The raw meat microbiota is usually complex, but only a few members will develop during storage and cause spoilage upon the pressure from several external factors, such as temperature and oxygen availability. We characterized the metagenome of beef packed aerobically or under vacuum during refrigerated storage to explore how different packaging conditions may influence the microbial composition and potential spoilage-associated activities. Different population dynamics and spoilage-associated genomic repertoires occurred in beef stored aerobically or in vacuum packaging. Moreover, the pangenomes of Pseudomonas fragi strains were extracted from metagenomes. We demonstrated the presence of specific, storage-driven strain-level profiles of Pseudomonas fragi, characterized by different gene repertoires and thus potentially able to act differently during meat spoilage. The results provide new knowledge on strain-level microbial ecology associated with meat spoilage and may be of value for future strategies of spoilage prevention and food waste reduction.IMPORTANCE This work provides insights on the mechanisms involved in raw beef spoilage during refrigerated storage and on the selective pressure exerted by the packaging conditions. We highlighted the presence of different microbial metagenomes during the spoilage of beef packaged aerobically or under vacuum. The packaging condition was able to select specific Pseudomonas fragi strains with distinctive genomic repertoires. This study may help in deciphering the behavior of different biomes directly in situ in food and in understanding the specific contribution of different strains to food spoilage.\n\nStrain-Level Diversity Analysis of Pseudomonas fragi after In Situ Pangenome Reconstruction Shows Distinctive Spoilage-Associated Metabolic Traits Clearly Selected by Different Storage Conditions.", "token_count": 476, "char_count": 2177, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5345, "quality_score": 0.7672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:10.660079", "source": { "split": "train_shard_00001", "doc_id": 3443 }, "chunk_id": "train_shard_00001_3443_0", "global_id": 10539 }, { "text": "

Summary

Genome-wide association studies (GWAS) in microbes have different challenges to GWAS in eukaryotes. These have been addressed by a number of different methods. pyseer brings these techniques together in one package tailored to microbial GWAS, allows greater flexibility of the input data used, and adds new methods to interpret the association results.

Availability and implementation

pyseer is written in python and is freely available at https://github.com/mgalardini/pyseer, or can be installed through pip. Documentation and a tutorial are available at http://pyseer.readthedocs.io.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\npyseer: a comprehensive tool for microbial pangenome-wide association studies.", "token_count": 198, "char_count": 781, "word_count": 94, "semantic_coherence": 1, "information_density": 0.734, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:11.110189", "source": { "split": "train_shard_00001", "doc_id": 3444 }, "chunk_id": "train_shard_00001_3444_0", "global_id": 10540 }, { "text": "Kefir is a dairy product obtained by fermentation of milk with a complex microbial population and several health-promoting properties have been attributed to its consumption. In this work, we tested the ability of different kefir-isolated bacterial and yeast strains (Lactobacillus kefir, Lb. plantarum, Lactococcus lactis subps. lactis, Saccharomyces cerevisiae and Kluyveromyces marxianus) or a mixture of them (MM) to antagonise the cytopathic effect of toxins from Clostridium difficile (TcdA and TcdB). Cell detachment assays and F-actin network staining using Vero cell line were performed. Although incubation with microbial cells did not reduce the damage induced by C. difficile spent culture supernatant (SCS), Lc. lactis CIDCA 8221 and MM supernatants were able to inhibit the cytotoxicity of SCS to Vero cells. Fraction of Lc. lactis CIDCA 8221 supernatant containing components higher than 10 kDa were responsible for the inhibitory activity and heating of this fraction for 15 min at 100 °C completely abrogated this ability. By dot-blot assay with anti-TcdA or anti-TcdB antibodies, concentration of both toxins seems to be reduced in SCS treated with Lc. lactis CIDCA 8221 supernatant. However, protective effect was not affected by treatment with proteases or proteases-inhibitors tested. In conclusion, we demonstrated that kefir-isolated Lc. lactis CIDCA 8221 secreted heat-sensitive products able to protect eukaryotic cells from cytopathic effect of C. difficile toxins in vitro. Our findings provide new insights into the probiotic action of microorganisms isolated from kefir against virulence factors from intestinal pathogens.\n\nKefir-isolated Lactococcus lactis subsp. lactis inhibits the cytotoxic effect of Clostridium difficile in vitro.", "token_count": 514, "char_count": 1765, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:11.762090", "source": { "split": "train_shard_00001", "doc_id": 3445 }, "chunk_id": "train_shard_00001_3445_0", "global_id": 10541 }, { "text": "

ABSTRACT

Campylobacter jejuni and Campylobacter coli are the leading cause of human gastroenteritis in the industrialized world and an emerging threat in developing countries. The incidence of campylobacteriosis in South America is greatly underestimated, mostly due to the lack of adequate diagnostic methods. Accordingly, there is limited genomic and epidemiological data from this region. In the present study, we performed a genome-wide analysis of the genetic diversity, virulence, and antimicrobial resistance of the largest collection of clinical C. jejuni and C. coli strains from Chile available to date (n=81), collected in 2017-2019 in Santiago, Chile. This culture collection accounts for over a third of the genome sequences available of clinical strains from South America. cgMLST analysis identified high genetic diversity as well as 13 novel STs and alleles in both C. jejuni and C. coli . Pangenome and virulome analyses showed a differential distribution of virulence factors, including both plasmid and chromosomally encoded T6SSs and T4SSs. Resistome analysis predicted widespread resistance to fluoroquinolones, but low rates of erythromycin resistance. This study provides valuable genomic and epidemiological data and highlights the need for further genomic epidemiology studies in Chile and other South American countries to better understand molecular epidemiology and antimicrobial resistance of this emerging intestinal pathogen.

AUTHOR SUMMARY

Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. In this study, we performed an in-depth analysis of the genome sequences of 69 C. jejuni and 12 C. coli clinical strains isolated from Chile, which account for over a third of the sequences from clinical strains available from South America. We identified a high genetic diversity among C. jejuni strains and the unexpected identification of clade 3 C. coli strains, which are infrequently isolated from humans in other regions of the world. Most strains harbored the virulence factors described for Campylobacter ", "token_count": 502, "char_count": 2135, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:12.418500", "source": { "split": "train_shard_00001", "doc_id": 3446 }, "chunk_id": "train_shard_00001_3446_0", "global_id": 10542 }, { "text": "While ∼40% of strains harbored mutation in the gyrA gene described to confer fluoroquinolone resistance, very few strains encoded the determinants linked to macrolide resistance, currently used for the treatment of campylobacteriosis. Our study contributes to our knowledge of this important foodborne pathogen providing valuable data from South America.\n\nGenomic analysis of the diversity, antimicrobial resistance and virulence potential of clinical Campylobacter jejuni and Campylobacter coli strains from Chile", "token_count": 130, "char_count": 528, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7681, "quality_score": 0.8841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:12.843136", "source": { "split": "train_shard_00001", "doc_id": 3446 }, "chunk_id": "train_shard_00001_3446_1", "global_id": 10543 }, { "text": "Motile Aeromonad septicemia (MAS) outbreaks caused by hypervirulent Aeromonas hydrophila (vAh) strains belonging to sequence type (ST) 251, have been reported and investigated widely in China and United States (US). In this study, for the first time, two genomes of vAh strains isolated from striped catfish in Vietnam have been identified and characterized. These two vAh strains caused catfish mortalities of 51.7–86.7% post immersion challenge with 2 × 10⁸ CFU mL⁻¹ or intraperitoneal injection challenge with 1 × 10³ CFU fish⁻¹, while no mortalities were observed in catfish challenged with regular A. hydrophila (rAh) strains (p < 0.05). These challenge trials indicate that vAh virulence is impacted by different degrees of penetration into the fish host and suggest that disease outbreaks in production ponds are affected by other pathogens or factors that contribute to vAh invasiveness. Comparative genomic analyses of vAh and rAh strains from Vietnam, together with reference A. hydrophila strains from China and US, were performed to gain an insight into the pathogenicity of the epidemic A. hydrophila strains collected from various locations worldwide. Besides the myo-inositol utilization and mobile genetic elements identified by previous studies, this work found that attachment and motility mediated by pili /fimbriae are also key factors underlying the hypervirulent nature of vAh strains. The vAh heterogeneity was observed on the core genome phylogenetic tree and the O-antigen gene clusters, where Vietnamese vAh strains showed closer genetic relationship with vAh strains isolated from carp species in China compared to vAh strains isolated from catfish in the US. The persistent occurrence of ST251 strains has been responsible for MAS outbreaks occurring frequently in Vietnamese catfish farms since 2013. This study provides important information about the spread of vAh in farmed catfish in Vietnam, its virulence in fish and the highly clonal nature of vAh strains identified in multiple countries.", "token_count": 504, "char_count": 2025, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5855, "quality_score": 0.7928, "entities": { "genes": [ "ST251" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:13.500338", "source": { "split": "train_shard_00001", "doc_id": 3447 }, "chunk_id": "train_shard_00001_3447_0", "global_id": 10544 }, { "text": "Comparative genomic analysis of hypervirulent Aeromonas hydrophila strains from striped catfish (Pangasianodon hypophthalmus) in Vietnam", "token_count": 37, "char_count": 136, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:13.853666", "source": { "split": "train_shard_00001", "doc_id": 3447 }, "chunk_id": "train_shard_00001_3447_1", "global_id": 10545 }, { "text": "In this study, a 4-year-old girl presented with a case of septic arthritis and fever. Salmonella was isolated from her knee effusion and feces; isolates were confirmed to be a novel S. Virchow monophasic variant (Salmonella 6,7,14:r:-) based on core genome MLST (cgMLST), CRISPR typing combined with analysis of the fljAB operon. Whole-genome sequencing analysis revealed that replacement of the fljAB operon by a 4.8 kb cassette from E. coli caused the nonexpression of phase-2 flagellar antigen in S. Virchow monophasic variant. Additionally, the acquisition of Salmonella genomic island 2 (SGI2) with an antimicrobial resistance gene cassette enabled the isolates to be multidrug-resistant (MDR) to chloramphenicol, tetracycline, trimethoprim, and sulfamethoxazole. The emerging of MDR S. Virchow monophasic variant causing human infection should be concerned in the national Salmonella surveillance system.\n\nGenomic identification of the emerging multidrug-resistant Salmonella Virchow monophasic variant causing septic arthritis of the knee joint", "token_count": 299, "char_count": 1051, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6395, "quality_score": 0.8197, "entities": { "genes": [ "SGI2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:14.418888", "source": { "split": "train_shard_00001", "doc_id": 3448 }, "chunk_id": "train_shard_00001_3448_0", "global_id": 10546 }, { "text": "

ABSTRACT

Rhizobium – legume symbioses serve as a paradigmatic example for the study of mutualism evolution. The genus Ensifer (syn. Sinorhizobium ) contains diverse plant-associated bacteria, a subset of which can fix nitrogen in symbiosis with legumes. To gain insights into the evolution of symbiotic nitrogen fixation (SNF), and inter-kingdom mutualisms more generally, we performed extensive phenotypic, genomic, and phylogenetic analyses of the genus Ensifer . The data suggest that SNF emerged several times within the genus Ensifer , likely through independent horizontal gene transfer events. Yet, the majority (105 of 106) of the Ensifer strains with the nodABC and nifHDK nodulation and nitrogen fixation genes were found within a single, monophyletic clade. Comparative genomics highlighted several differences between the “symbiotic” and “non-symbiotic” clades, including divergences in their pangenome content. Additionally, strains of the symbiotic clade carried 325 fewer genes, on average, and appeared to have fewer rRNA operons than strains of the non-symbiotic clade. Characterizing a subset of ten Ensifer strains identified several phenotypic differences between the clades. Strains of the non-symbiotic clade could catabolize 25% more carbon sources, on average, than strains of the symbiotic clade, and they were better able to grow in LB medium and tolerate alkaline conditions. On the other hand, strains of the symbiotic clade were better able to tolerate heat stress and acidic conditions. We suggest that these data support the division of the genus Ensifer into two main subgroups, as well as the hypothesis that pre-existing genetic features are required to facilitate the evolution of SNF in bacteria.\n\nSymbiotic and non-symbiotic members of the genusEnsifer(syn.Sinorhizobium) are separated into two clades based on comparative genomics and high-throughput phenotyping", "token_count": 497, "char_count": 1923, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5782, "quality_score": 0.7891, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:15.070091", "source": { "split": "train_shard_00001", "doc_id": 3449 }, "chunk_id": "train_shard_00001_3449_0", "global_id": 10547 }, { "text": "Ethanol production was studied in simultaneous saccharification and fermentation (SSF) of steam-pretreated spruce at 42 degrees C, using a thermotolerant yeast. Three yeast strains of Kluyveromyces marxianus were compared in test fermentations. SSF experiments were performed with the best of these on 5% (w/w) of substrate, at a cellulase loading of 37 filter paper units/g of cellulose, and a beta-glucosidase loading of 38 IU/g of cellulose. The detoxification of the substrate and the lack of pH control in the experiments increased the final ethanol concentration. The final ethanol yield was 15% lower compared to SSF with Saccharomyces cerevisiae at 37 degrees C, owing to the cessation of ethanol fermentation after the first 10 h.\n\nSimultaneous saccharification and fermentation of steam-pretreated spruce to ethanol.", "token_count": 238, "char_count": 826, "word_count": 123, "semantic_coherence": 1, "information_density": 0.5935, "quality_score": 0.7967, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:15.545269", "source": { "split": "train_shard_00001", "doc_id": 3450 }, "chunk_id": "train_shard_00001_3450_0", "global_id": 10548 }, { "text": "Pseudomonas aeruginosa AG1 (PaeAG1) is a Costa Rican strain that was isolated in 2010 in a major Hospital. This strain has resistance to multiple antibiotics such as β-lactams (including carbapenems), aminoglycosides, and fluoroquinolones. PaeAG1 is considered critical (Priority 1) due to its resistance to carbapenems, and it was the first report of a P. aeruginosa isolate carrying both VIM-2 and IMP-18 genes encoding for metallo-β-lactamases (MBL) enzymes (both with carbapenemase activity). Owing to these traits, we have studied this model for 10 years using diverse approaches including multi-omics. In this review, we summarize the main points of the different steps that we have studied in PaeAG1: preliminary analyses of this strain at the genomic and phenomic levels revealed that this microorganism has particular features of antibiotic resistance. In the multi-omics approach, the genome assembly was the initial step to identify the genomic determinants of this strain, including virulence factors, antibiotic resistance genes, as well as a complex accessory genome. Second, a comparative genomic approach was implemented to define and update the phylogenetic relationship among complete P. aeruginosa genomes, the genomic island content in other strains, and the architecture of the two MBL-carrying integrons. Third, the proteomic profile of PaeAG1 was studied after exposure to antibiotics using 2-dimensional gel electrophoresis (2D-GE). Fourth, to study the central response to multiple perturbations in P. aeruginosa, i.e., the core perturbome, a machine learning approach was used. The analysis revealed biological functions and determinants that are shared by different disturbances. Finally, to evaluate the effects of ciprofloxacin (CIP) on PaeAG1, a growth curve comparison, differential expression analysis (RNA-Seq), and network analysis were performed", "token_count": 487, "char_count": 1908, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [ "AG1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:16.605994", "source": { "split": "train_shard_00001", "doc_id": 3451 }, "chunk_id": "train_shard_00001_3451_0", "global_id": 10549 }, { "text": "Using the results of the core perturbome (pathways that also were found in this perturbation with CIP), it was possible to identify the \"exclusive\" response and determinants of PaeAG1 after exposure to CIP. Altogether, after a decade of study using a multi-omics approach (at genomics, comparative genomics, perturbomics, transcriptomics, proteomics, and phenomics levels), we have provided new insights about the genomic and transcriptomic determinants associated with antibiotic resistance in PaeAG1. These results not only partially explain the high-risk condition of this strain that enables it to conquer nosocomial environments and its multi-resistance profile, but also this information may eventually be used as part of the strategies to fight this pathogen.

Supplementary information

The online version contains supplementary material available at 10.1007/s43657-021-00016-z.\n\nMolecular Determinants of Antibiotic Resistance in the Costa Rican Pseudomonas aeruginosa AG1 by a Multi-omics Approach: A Review of 10 Years of Study.", "token_count": 280, "char_count": 1051, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7183, "quality_score": 0.8592, "entities": { "genes": [ "AG1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:17.181062", "source": { "split": "train_shard_00001", "doc_id": 3451 }, "chunk_id": "train_shard_00001_3451_1", "global_id": 10550 }, { "text": "Streptococcus pneumoniae is a normal commensal of the upper respiratory tract but can also invade the bloodstream or CSF (cerebrospinal fluid), causing invasive pneumococcal disease (IPD). In this study, we attempt to identify genes associated with IPD by applying a random forest machine-learning algorithm to whole genome sequence (WGS) data. We find 43 genes consistently associated with IPD across three geographically distinct WGS data sets of pneumococcal carriage isolates. Of these genes, 23 genes have previously shown to be directly relevant to IPD, while the other 18 are uncharacterized.\n\nIdentifyingStreptococcus pneumoniaegenes associated with invasive disease using pangenome-based whole genome sequence typing", "token_count": 186, "char_count": 732, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7822, "quality_score": 0.8911, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:17.669776", "source": { "split": "train_shard_00001", "doc_id": 3452 }, "chunk_id": "train_shard_00001_3452_0", "global_id": 10551 }, { "text": "Two Legionella-like strains isolated from hot water distribution systems in 2012 have been characterized phenotypically, biochemically and genomically in terms of DNA relatedness. Both strains, HCPI-6T and EUR-108, exhibited biochemical phenotypic profiles typical of Legionella species. Cells were Gram-negative motile rods which grew on BCYEα agar but not on blood agar and displayed phenotypic characteristics typical of the family Legionellaceae, including a requirement for l-cysteine and testing catalase positive. Both strains were negative for oxidase, urease, nitrate reduction and hippurate negative, and non-fermentative. The major ubiquinone was Q12 (59.4 % HCPI-6T) and the dominant fatty acids were C16 : 1 ω7c (28.4 % HCPI-6T, ≈16 % EUR-108), C16 : 0 iso (≈22.5 % and ≈13 %) and C15 : 0 anteiso (19.5 % and ≈23.5 %, respectively). The percent G+C content of genomic DNA was determined to be 39.3 mol %. The 16S rRNA gene, mip sequence and comparative genome sequence-based analyses (average nucleotide identity, ANI; digital DNA-DNA hybridization, dDDH; and phylogenomic treeing) demonstrated that the strains represent a new species of the genus Legionella. The analysis based on the 16S rRNA gene sequences showed that the sequence similarities for both strains ranged from 98.8-90.1 % to other members of the genus", "token_count": 499, "char_count": 1440, "word_count": 202, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:18.327007", "source": { "split": "train_shard_00001", "doc_id": 3453 }, "chunk_id": "train_shard_00001_3453_0", "global_id": 10552 }, { "text": "The core genome-based phylogenomic tree (protein-concatemer tree based on concatenation of 418 proteins present in single copy) revealed that these two strains clearly form a separate cluster within the genus Legionella. ANI and dDDH values confirmed the distinctiveness of the strains. Based on the genomic, genotypic and phenotypic findings from a polyphasic study, the isolates are considered to represent a single novel species, for which the name Legionella maioricensis sp. nov. is proposed. The type strain is HCPI-6T (=CCUG 75071T=CECT 30569T).\n\nLegionella maioricensis sp. nov., a new species isolated from the hot water distribution systems of a hospital and a shopping center during routine sampling.", "token_count": 222, "char_count": 765, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7524, "quality_score": 0.8762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:18.793398", "source": { "split": "train_shard_00001", "doc_id": 3453 }, "chunk_id": "train_shard_00001_3453_1", "global_id": 10553 }, { "text": "Most foodborne salmonellosis outbreaks are linked to agricultural animal products with a few serovars accounting for most Salmonella isolated from specific animal products, suggesting an adaptation to the corresponding animal hosts and their respective environments. Here, we utilized whole-genome sequence (WGS) data to analyze the evolution and population genetics of seven serovars frequently isolated from ground beef (Montevideo, Cerro, and Dublin), chicken (Kentucky, Infantis, and Enteritidis), and turkey (Reading) in the United States. In addition, publicly available metadata were used to characterize major clades within each serovar with regard to public health significance. Except for Dublin, all serovars were polyphyletic, comprising 2-6 phylogenetic groups. Further partitioning of the phylogenies identified 25 major clades, including 12 associated with animal or environmental niches. These 12 clades differed in evolutionary parameters (e.g., substitution rates) as well as public health relevant characteristics (e.g., association with human illness, antimicrobial resistance). Overall, our results highlight several critical trends: (i) the Salmonella generation time appears to be more dependent on source than serovar and (ii) all serovars contain clades and sub-clades that are estimated to have emerged after the year 1940 and that are enriched for isolates associated with humans, agricultural animals, antimicrobial resistance (AMR), and/or specific geographical regions. These findings suggest that serotyping alone does not provide enough resolution to differentiate isolates that may have evolved independently, present distinct geographic distribution and host association, and possibly have distinct public health significance.

Importance

Non-typhoidal Salmonella are major foodborne bacterial pathogens estimated to cause more than one million illnesses, thousands of hospitalizations, and hundreds of deaths annually in the United States. More than 70% of Salmonella outbreaks in the United States have been associated with agricultural animals. Certain serovars include persistent strains that have repeatedly contaminated beef, chicken, and turkey, causing outbreaks and sporadic cases over many years", "token_count": 513, "char_count": 2273, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6644, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:19.447394", "source": { "split": "train_shard_00001", "doc_id": 3454 }, "chunk_id": "train_shard_00001_3454_0", "global_id": 10554 }, { "text": "These persistent strains represent a particular challenge to public health, as they are genetically clonal and widespread, making it difficult to differentiate distinct outbreak and contamination events using whole-genome sequence (WGS)-based subtyping methods (e.g., core genome allelic typing). Our results indicate that a phylogenetic approach is needed to investigate persistent strains and suggest that the association between a Salmonella serovar and an agricultural animal is driven by the expansion of clonal subtypes that likely became adapted to specific animals and associated environments.\n\nSalmonella associated with agricultural animals exhibit diverse evolutionary rates and show evidence of recent clonal expansion.", "token_count": 153, "char_count": 745, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7653, "quality_score": 0.8827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:19.887673", "source": { "split": "train_shard_00001", "doc_id": 3454 }, "chunk_id": "train_shard_00001_3454_1", "global_id": 10555 }, { "text": "An intracellular esterase from the yeast Kluyveromyces marxianus CBS 1553 with interesting enantioselective hydrolytic activity towards racemic esters of 1,2-O-isopropylidene glycerol (IPG) was purified and characterized. Optimal culture conditions for the obtainment of the enantioselective esterase on a 5 l-fermentation scale were investigated. Two esterase activities (EST1 and EST2) in the crude cell extract were identified by native PAGE with specific activity staining and separated from each other by anion-exchange chromatography. EST1 showed higher activity and enantioselectivity than EST2 in the resolution of racemic IPG acetate and was further purified by hydrophobic interaction chromatography and preparative electrophoresis (final specific activity approximately = 300 U mg(-1), showing a main protein band with a molecular mass of 29 kDa. EST1 showed optimal activity between pH 8.0 and 10.0 and was stable in the pH range 7.0-10.0. Moreover, it was rather thermostable and active up to 80 degrees C, and retained most of its activity in the presence of 15% (v/v) of various organic solvents. The enzyme showed similar Vmax in the hydrolysis of the acetate esters of IPG, whereas the Km value towards (S)-IPG acetate was significantly lower than the one towards the (R)-enantiomer (5.3 and 70 microM, respectively). Finally, comparison of EST1 activity in the presence of different glycerol esters and synthetic substrates with different chain lengths showed a strong preference of this biocatalyst for short-chain substrates.\n\nPurification and characterization of the enantioselective esterase from Kluyveromyces marxianus CBS 1553.", "token_count": 451, "char_count": 1652, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [ "EST1", "EST2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:20.525340", "source": { "split": "train_shard_00001", "doc_id": 3455 }, "chunk_id": "train_shard_00001_3455_0", "global_id": 10556 }, { "text": "Cells are unceasingly confronted by oxidative stresses that oxidize proteins on their cysteines. The thioredoxin (Trx) system, which is a ubiquitous system for thiol and protein repair, is composed of a thioredoxin (TrxA) and a thioredoxin reductase (TrxB). TrxAs reduce disulfide bonds of oxidized proteins and are then usually recycled by a single pleiotropic NAD(P)H-dependent TrxB (NTR). In this work, we first analyzed the composition of Trx systems across Bacteria. Most bacteria have only one NTR, but organisms in some Phyla have several TrxBs. In Firmicutes, multiple TrxBs are observed only in Clostridia, with another peculiarity being the existence of ferredoxin-dependent TrxBs. We used Clostridioides difficile, a pathogenic sporulating anaerobic Firmicutes, as a model to investigate the biological relevance of TrxB multiplicity. Three TrxAs and three TrxBs are present in the 630Δerm strain. We showed that two systems are involved in the response to infection-related stresses, allowing the survival of vegetative cells exposed to oxygen, inflammation-related molecules and bile salts. A fourth TrxB copy present in some strains also contributes to the stress-response arsenal. One of the conserved stress-response Trx system was found to be present both in vegetative cells and in the spores and is under a dual transcriptional control by vegetative cell and sporulation sigma factors. This Trx system contributes to spore survival to hypochlorite and ensure proper germination in the presence of oxygen. Finally, we found that the third Trx system contributes to sporulation through the recycling of the glycine-reductase, a Stickland pathway enzyme that allows the consumption of glycine and contributes to sporulation. Altogether, we showed that Trx systems are produced under the control of various regulatory signals and respond to different regulatory networks. The multiplicity of Trx systems and the diversity of TrxBs most likely meet specific needs of Clostridia in adaptation to strong stress exposure, sporulation and Stickland pathways.", "token_count": 522, "char_count": 2068, "word_count": 305, "semantic_coherence": 1, "information_density": 0.5607, "quality_score": 0.7803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:21.177320", "source": { "split": "train_shard_00001", "doc_id": 3456 }, "chunk_id": "train_shard_00001_3456_0", "global_id": 10557 }, { "text": "The multiplicity of thioredoxin systems meets the specific lifestyles of Clostridia.", "token_count": 22, "char_count": 84, "word_count": 11, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:21.527548", "source": { "split": "train_shard_00001", "doc_id": 3456 }, "chunk_id": "train_shard_00001_3456_1", "global_id": 10558 }, { "text": "Pathogenic Leptospira , the causative agents of leptospirosis, comprise >200 serotypes (called serovars). Most have a restricted reservoir-host range, and some, e.g., serovar Copenhageni, are cosmopolitan and of public health importance owing to their propensity to produce severe, fatal disease in humans. Available serotyping approaches—such as multi-locus sequence typing, core genome sequence typing, pulsed-field gel electrophoresis, and the cross-agglutination absorption test—are tedious and expensive, and require isolation of the organisms in culture media—a protracted and incredibly inefficient process— precluding their use in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. Here, we have developed a simple yet specific real-time qPCR assay—targeting a Leptospira -unique gene encoding a putative polysaccharide flippase—that provides intra-species, serotype-defining (i.e., epidemiologically useful) information, and improves upon the sensitivity of preferred lipL32 -based qPCR-based diagnostic tests. The assay, dubbed RAgI (“rage one”), is r apid and a ffordable, and reliably and specifically detects g roup I pathogenic Leptospira in culture, serum and urine, with no detectable off-target amplification—even of the genetically related but low virulence group II pathogenic (formerly “intermediate”) or non-pathogenic Leptospira . It retained 100% diagnostic specificity when tested against difficult sample types, including field-collected dog urine-samples and environmental samples containing varied and complex microbial species-consortia. And holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies.\n\nCulture-Independent Detection and Identification of Leptospira Serovars", "token_count": 473, "char_count": 1902, "word_count": 238, "semantic_coherence": 1, "information_density": 0.7605, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:22.169913", "source": { "split": "train_shard_00001", "doc_id": 3457 }, "chunk_id": "train_shard_00001_3457_0", "global_id": 10559 }, { "text": "Lactobacillus acidophilus has been extensively applied in plentiful probiotic products and is mostly found in the gastrointestinal tract, vagina, and oral cavity of human and animal, and fermented foods. Although several studies have been performed to investigate the beneficial characteristics and genome function of L. acidophilus , comparative genomic analysis remains scarce. In this study, we collected 74 L. acidophilus genomes from our gut bacterial genome collection and the public database and conducted a comprehensive comparative genomic analysis. The analysis of average nucleotide identity (ANI), phylogenetic, gene distribution of COG and KEGG database, carbohydrates utilization, and secondary metabolites revealed the potential correlation of the genomic diversity and niches adaptation of L. acidophilus from different perspectives. In addition, the pan-genome of L. acidophilus was found to be open, with metabolism, information storage and processing genes mainly distributed in the core genome. Phage- and peptidase-associated genes were found in the genome of the specificity of animal-derived strains, which were related to adaptation of animal gut. SNP analysis showed the differences of the utilization of Vitamin B12 in cellular of L. acidophilus strains from animal gut and others. This work provides new insights for the genomic diversity analysis of Lactobacillus acidophilus and uncovers the ecological adaptation of the specific strains.\n\nComparative Genome Analysis of Lactobacillus acidophilus Isolates from Different Ecological Niches", "token_count": 367, "char_count": 1567, "word_count": 218, "semantic_coherence": 1, "information_density": 0.578, "quality_score": 0.789, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:22.753118", "source": { "split": "train_shard_00001", "doc_id": 3458 }, "chunk_id": "train_shard_00001_3458_0", "global_id": 10560 }, { "text": "Providencia alcalifaciens is a Gram-negative bacterium found in various water and land environments and organisms, including insects and mammals. Some P. alcalifaciens strains encode gene homologs of virulence factors found in pathogenic Enterobacterales members, such as Salmonella enterica serovar Typhimurium and Shigella flexneri. Whether these genes are pathogenic determinants in P. alcalifaciens is not known. In this study, we investigated P. alcalifaciens-host interactions at the cellular level, focusing on the role of two type III secretion systems (T3SS) belonging to the Inv-Mxi/Spa family. T3SS1b is widespread in Providencia spp. and encoded on the chromosome. A large plasmid that is present in a subset of P. alcalifaciens strains, primarily isolated from diarrheal patients, encodes for T3SS1a. We show that P. alcalifaciens 205/92 is internalized into eukaryotic cells, lyses its internalization vacuole, and proliferates in the cytosol. This triggers caspase-4-dependent inflammasome responses in gut epithelial cells. The requirement for the T3SS1a in entry, vacuole lysis, and cytosolic proliferation is host cell type-specific, playing a more prominent role in intestinal epithelial cells than in macrophages or insect cells. In a bovine ligated intestinal loop model, P. alcalifaciens colonizes the intestinal mucosa and induces mild epithelial damage with negligible fluid accumulation in a T3SS1a- and T3SS1b-independent manner", "token_count": 497, "char_count": 1579, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6946, "quality_score": 0.8473, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:23.403064", "source": { "split": "train_shard_00001", "doc_id": 3459 }, "chunk_id": "train_shard_00001_3459_0", "global_id": 10561 }, { "text": "However, T3SS1b was required for the rapid killing of Drosophila melanogaster. We propose that the acquisition of two T3SS has allowed P. alcalifaciens to diversify its host range, from a highly virulent pathogen of insects to an opportunistic gastrointestinal pathogen of animals.\n\nPathogenic diversification of the gut commensal Providencia alcalifaciens via acquisition of a second type III secretion system.", "token_count": 128, "char_count": 443, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7966, "quality_score": 0.8983, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:23.817208", "source": { "split": "train_shard_00001", "doc_id": 3459 }, "chunk_id": "train_shard_00001_3459_1", "global_id": 10562 }, { "text": "Pseudomonas aeruginosa is an opportunistic pathogen with multiple strategies to interact with other microbes and host cells, gaining fitness in complicated infection sites. The contact-dependent type VI secretion system (T6SS) is one critical secretion apparatus involved in both interbacterial competition and pathogenesis. To date, only limited numbers of T6SS-effectors have been clearly characterized in P. aeruginosa laboratory strains, and the importance of T6SS diversity in the evolution of clinical P. aeruginosa remains unclear. Recently, we characterized a P. aeruginosa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. Bioinformatic analysis has revealed a putative type VI secretion system (T6SS) dependent lipase effector in LYSZa7, which is a homologue of TseL in Vibrio cholerae and is widely distributed in pathogens. We experimentally validated that this TseL homologue belongs to the Tle2, a subfamily of T6SS-lipase effectors; thereby, we name this effector TseL (TseLPA in this work). Further, we showed the lipase-dependent bacterial toxicity of TseLPA, which primarily targets bacterial periplasm. The toxicity of TseLPA can be neutralized by two immunity proteins, TsiP1 and TsiP2, which are encoded upstream of tseL. In addition, we proved this TseLPA contributes to bacterial pathogenesis by promoting bacterial internalization into host cells. Our study suggests that clinical bacterial strains employ a diversified group of T6SS effectors for interbacterial competition and might contribute to emerging of new epidemic clonal lineages. IMPORTANCE Pseudomonas aeruginosa is one predominant pathogen that causes hospital-acquired infections and is one of the commonest coinfecting bacteria in immunocompromised patients and chronic wounds. This bacterium harbors a diverse accessory genome with a high frequency of gene recombination, rendering its population highly heterogeneous", "token_count": 512, "char_count": 2032, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6374, "quality_score": 0.8187, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:24.449292", "source": { "split": "train_shard_00001", "doc_id": 3460 }, "chunk_id": "train_shard_00001_3460_0", "global_id": 10563 }, { "text": "Numerous Pa lineages coexist in the biofilm, where successful epidemic clonal lineage or strain-specific type commonly acquires genes to increase its fitness over the other organisms. Current studies of Pa genomic diversity commonly focused on antibiotic resistant genes and novel phages, overlooking the contribution of type VI secretion system (T6SS). We characterized a Pa clinical strain LYSZa7 from a COVID-19 patient, which adopted complex genetic adaptations toward chronic infections. We report, in this study, a novel T6SS-lipase effector that is broadly distributed in Pa clinical isolates and other predominant pathogens. The study suggests that hospital transmission may raise the emergence of new epidemic clonal lineages with specified T6SS effectors.\n\nAcquisition of T6SS Effector TseL Contributes to the Emerging of Novel Epidemic Strains of Pseudomonas aeruginosa.", "token_count": 236, "char_count": 909, "word_count": 125, "semantic_coherence": 1, "information_density": 0.728, "quality_score": 0.864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:24.924032", "source": { "split": "train_shard_00001", "doc_id": 3460 }, "chunk_id": "train_shard_00001_3460_1", "global_id": 10564 }, { "text": "

Background

As whole-genome sequencing for pathogen genomes becomes increasingly popular, the typing methods of gene-by-gene comparison, such as core genome multilocus sequence typing (cgMLST) and whole-genome multilocus sequence typing (wgMLST), are being routinely implemented in molecular epidemiology. However, some intrinsic problems remain. For example, genomic sequences with varying read depths, read lengths, and assemblers influence the genome assemblies, introducing error or missing alleles into the generated allelic profiles. These errors and missing alleles might create \"specious discrepancy\" among closely related isolates, thus making accurate epidemiological interpretation challenging. In addition, the rapid growth of the cgMLST allelic profile database can cause problems related to storage and maintenance as well as long query search times.

Methods

We attempted to resolve these issues by decreasing the scheme size to reduce the occurrence of error and missing alleles, alleviate the storage burden, and improve the query search time. The challenge in this approach is maintaining the typing resolution when using fewer loci. We achieved this by using a popular artificial intelligence technique, XGBoost, coupled with Shapley additive explanations for feature selection. Finally, 370 loci from the original 1701 cgMLST loci of Listeria monocytogenes were selected.

Results

Although the size of the final scheme (LmScheme_370) was approximately 80% lower than that of the original cgMLST scheme, its discriminatory power, tested for 35 outbreaks, was concordant with that of the original cgMLST scheme. Although we used L. monocytogenes as a demonstration in this study, the approach can be applied to other schemes and pathogens. Our findings might help elucidate gene-by-gene-based epidemiology.\n\nA machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking.", "token_count": 477, "char_count": 2028, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:25.569378", "source": { "split": "train_shard_00001", "doc_id": 3461 }, "chunk_id": "train_shard_00001_3461_0", "global_id": 10565 }, { "text": "Diversity and dynamics of microbial cultures were studied during the production of May bryndza cheese, a traditional Slovak cheese produced from unpasteurized ewes' milk. Quantitative culture-based data were obtained for lactobacilli, lactococci, total mesophilic aerobic counts, coliforms, E. coli, staphylococci, coagulase-positive staphylococci, yeasts, fungi and Geotrichum spp. in ewes' milk, curd produced from it and ripened for 0 - 10 days, and in bryndza cheese produced from the curd, in three consecutive batches. Diversity of prokaryotes and eukaryotes in selected stages of the production was studied by non-culture approach based on amplification of 16S rDNA and internal transcribed spacer region, coupled to denaturing gradient gel electrophoresis and sequencing. The culture-based data demonstrated an overall trend of growth of the microbial population contributing to lactic acid production and to ripening of the cheese, lactobacilli, lactococci and Geotrichum spp. growing up to densities of 10(8) CFU/g, 10(9) CFU/g and 10(5) CFU/g, respectively, in all three consecutive batches of bryndza cheese. The diversity of bacteria encompassed Acinetobacter calcoaceticus, Acinetobacter guillouiae, Acinetobacter sp., Acinetobacter johnsonii, Citrobacter braakii, Clostridium bartlettii, Corynebacterium callunae, Corynebacterium maris, Enterobacter aerogenes, Enterobacter asburiae, Enterobacter hormaechei, Enterococcus faecium, Enterococcus pallens, Escherichia coli, Haemophilus haemolyticus, Hafnia alvei, Kluyvera cryocrescens, Lactobacillus helveticus, Lactococcus garvieae, Lc. lactis subsp. cremoris, Lc. lactis subsp", "token_count": 519, "char_count": 1641, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:26.233220", "source": { "split": "train_shard_00001", "doc_id": 3462 }, "chunk_id": "train_shard_00001_3462_0", "global_id": 10566 }, { "text": "lactis, \"Leuconostoc garlicum\", Mannheimia glucosida, Mannheimia haemolytica, Pseudomonas sp., Ps. fluorescens, \"Ps. reactans\", Raoultella ornithinolytica, R. terrigena, \"Rothia arfidiae\", Staphylococcus aureus, Staph. epidermidis, Staph. felis, Staph. pasteuri, Staph. sciuri, Staph. xylosus, Streptococcus parauberis, Str. thermophilus and Variovorax paradoxus. The diversity of yeasts and fungi encompassed Alternaria alternata, \"Ascomycete sp.\", Aspergillus fumigatus, Beauveria brongniartii, Candida xylopsoci, C. inconspicua, Cladosporium cladosporioides, Debaromyces hansenii, Fomes fomentarius, Galactomyces candidus, Gymnoascus reesii, Chaetomium globosum, Kluyveromyces marxianus, Metarhizium anisopliae, Penicillium aurantiogriseum, P. camemberti, P. freii, P. polonicum, P. viridicatum, Pichia kudriavzevii, Sordaria alcina, Trichosporon lactis and Yarrowia lipolytica.\n\nMicrobial diversity and dynamics during the production of May bryndza cheese.", "token_count": 362, "char_count": 960, "word_count": 103, "semantic_coherence": 1, "information_density": 0.8641, "quality_score": 0.932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:26.810314", "source": { "split": "train_shard_00001", "doc_id": 3462 }, "chunk_id": "train_shard_00001_3462_1", "global_id": 10567 }, { "text": "

Background

Aggregatibacter actinomycetemcomitans is genetically heterogeneous and comprises distinct clonal lineages that may have different virulence potentials. However, limited information of the strain-to-strain genomic variations is available.

Methodology/principal findings

The genome sequences of 11 A. actinomycetemcomitans strains (serotypes a-f) were generated de novo, annotated and combined with three previously sequenced genomes (serotypes a-c) for comparative genomic analysis. Two major groups were identified; serotypes a, d, e, and f, and serotypes b and c. A serotype e strain was found to be distinct from both groups. The size of the pangenome was 3,301 genes, which included 2,034 core genes and 1,267 flexible genes. The number of core genes is estimated to stabilize at 2,060, while the size of the pangenome is estimated to increase by 16 genes with every additional strain sequenced in the future. Within each strain 16.7-29.4% of the genome belonged to the flexible gene pool. Between any two strains 0.4-19.5% of the genomes were different. The genomic differences were occasionally greater for strains of the same serotypes than strains of different serotypes. Furthermore, 171 genomic islands were identified. Cumulatively, 777 strain-specific genes were found on these islands and represented 61% of the flexible gene pool.

Conclusions/significance

Substantial genomic differences were detected among A. actinomycetemcomitans strains. Genomic islands account for more than half of the flexible genes. The phenotype and virulence of A. actinomycetemcomitans may not be defined by any single strain. Moreover, the genomic variation within each clonal lineage of A. actinomycetemcomitans (as defined by serotype grouping) may be greater than between clonal lineages. The large genomic data set in this study will be useful to further examine the molecular basis of variable virulence among A", "token_count": 520, "char_count": 1941, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5568, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:27.456071", "source": { "split": "train_shard_00001", "doc_id": 3463 }, "chunk_id": "train_shard_00001_3463_0", "global_id": 10568 }, { "text": "actinomycetemcomitans strains.\n\nIdentification of the pangenome and its components in 14 distinct Aggregatibacter actinomycetemcomitans strains by comparative genomic analysis.", "token_count": 52, "char_count": 176, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:27.812556", "source": { "split": "train_shard_00001", "doc_id": 3463 }, "chunk_id": "train_shard_00001_3463_1", "global_id": 10569 }, { "text": "

Background

Pairwise single nucleotide polymorphisms (SNPs) are a cornerstone of genomic approaches to the inference of transmission of multidrug-resistant (MDR) organisms in hospitals. However, the impact of many key analytical approaches on these inferences has not yet been systematically assessed. This study aims to make such a systematic assessment.

Methods

We conducted a 15-month prospective study (2-month pilot phase, 13-month implementation phase), across four hospital networks including eight hospitals in Melbourne, VIC, Australia. Patient clinical and screening samples containing one or more isolates of meticillin-resistant Staphylococcus aureus, vancomycin-resistant Enterococcus faecium, and extended-spectrum β-lactamase-producing Escherichia coli and Klebsiella pneumoniae were collected and underwent whole genome sequencing. Using the genome data from the top four most numerous sequence types from each species, 16 in total, we systematically assessed the: (1) impact of sample and reference genome diversity through multiple core genome alignments using different data subsets and reference genomes, (2) effect of masking of prophage and regions of recombination in the core genome alignments by assessing SNP distances before and after masking, (3) differences between a cumulative versus a 3-month sliding-window approach to sample genome inclusion in the dataset over time, and (4) the comparative effects each of these approaches had when applying a previously defined SNP threshold for inferring likely transmission.

Findings

2275 samples were collected (397 during the pilot phase from April 4 to June 18, 2017; 1878 during the implementation phase from Oct 30, 2017, to Nov 30, 2018) from 1870 patients", "token_count": 453, "char_count": 1755, "word_count": 238, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:28.470521", "source": { "split": "train_shard_00001", "doc_id": 3464 }, "chunk_id": "train_shard_00001_3464_0", "global_id": 10570 }, { "text": "Of these 2275 samples, 1537 were identified as arising from the four most numerous sequence types from each of the four target species of MDR organisms in this dataset (16 sequence types in total: S aureus ST5, ST22, ST45, and ST93; E faecium ST80, ST203, ST1421, and ST1424; K pneumoniae ST15, ST17, ST307, and ST323; and E coli ST38, ST131, ST648, and ST1193). Across the species, using a reference genome of the same sequence type provided a greater degree of pairwise SNP resolution, compared with species and outgroup-reference alignments that mostly resulted in inflated SNP distances and the possibility of missed transmission events. Omitting prophage regions had minimal effect; however, omitting recombination regions had a highly variable effect, often inflating the number of closely related pairs. Estimated SNP distances between isolate pairs over time were more consistent using a sliding-window than a cumulative approach.

Interpretation

We propose that the use of a closely related reference genome, without masking of prophage or recombination regions, and of a sliding-window approach for isolate inclusion is best for accurate and consistent MDR organism transmission inference, when using core genome alignments and SNP thresholds. These approaches provide increased stability and resolution, so SNP thresholds can be more reliably applied for putative transmission inference among diverse MDR organisms, reducing the chance of incorrectly inferring the presence or absence of close genetic relatedness and, therefore, transmission. The establishment of a broadly applicable and standardised approach, as proposed here, is necessary to implement widespread prospective genomic surveillance for MDR organism transmission.

Funding

Melbourne Genomics Health Alliance, and National Health and Medical Research Council of Australia.\n\nKey parameters for genomics-based real-time detection and tracking of multidrug-resistant bacteria: a systematic analysis.", "token_count": 477, "char_count": 1986, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6643, "quality_score": 0.8321, "entities": { "genes": [ "ST131", "ST1424", "ST22", "ST17", "ST45", "ST323", "ST648", "ST307", "ST5", "ST1421" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:29.138963", "source": { "split": "train_shard_00001", "doc_id": 3464 }, "chunk_id": "train_shard_00001_3464_1", "global_id": 10571 }, { "text": "Astaxanthin (AXT) is a red fat-soluble pigment found naturally in aquatic animals, plants, and various microorganisms and can be manufactured artificially using chemical catalysis. AXT is a xanthophyll carotenoid with a high potential for scavenging free radicals. Several studies have investigated AXT efficacy against diseases such as neurodegenerative, ocular, skin, and cardiovascular hypertension, diabetes, gastrointestinal and liver diseases, and immuno-protective functions. However, its poor solubility, low stability to light and oxygen, and limited bioavailability are major obstacles hindering its wide applications as a therapeutic agent or nutritional supplement. Incorporating AXT with nanocarriers holds great promise in enhancing its physiochemical properties. Nanocarriers are delivery systems with several benefits, including surface modification, bioactivity, and targeted medication delivery and release. Many approaches have been applied to enhance AXT's medicinal effect, including solid lipid nanoparticles, nanostructured lipid carriers (NLCs) and polymeric nanospheres. AXT nano-formulations have demonstrated a high antioxidant and anti-inflammatory effect, significantly affecting cancer in different organs. This review summarizes the most recent data on AXT production, characterization, biological activity, and therapeutic usage, focusing on its uses in the nanotechnology era.\n\nProduction and therapeutic use of astaxanthin in the nanotechnology era.", "token_count": 348, "char_count": 1483, "word_count": 188, "semantic_coherence": 1, "information_density": 0.734, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:29.748826", "source": { "split": "train_shard_00001", "doc_id": 3465 }, "chunk_id": "train_shard_00001_3465_0", "global_id": 10572 }, { "text": "

Introduction

Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It is mainly caused by consuming contaminated food, with retail food considered the primary source.

Methods

In Guizhou, China, 102 Salmonella strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing and whole-genome sequencing (WGS) to understand Salmonella diversity, including serotypes, sequencing types (STs), antimicrobial genes, virulence genes, plasmid types, multi-locus sequence types (MLST), and core genome MLST (cgMLST).

Results and discussion

S.Typhimurium was the dominant serotype, and O:4(B) was the leading serogroup. The most prevalent genotype was ST40. Phenotypic antimicrobial resistance identified 66.7% of the sampled isolates as multi-drug resistant (MDR). S.Enteritidis (n = 7), S.Typhimurium (n = 1), S.Indiana (n = 1), S.Kentucky (n = 1), S.Uganda (n = 1), all of which were MDR, were resistant to Colistin. Resistance rates varied significantly across different strains and food types, particularly meat products exhibiting higher resistance", "token_count": 444, "char_count": 1222, "word_count": 147, "semantic_coherence": 1, "information_density": 0.7279, "quality_score": 0.8639, "entities": { "genes": [ "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:30.396346", "source": { "split": "train_shard_00001", "doc_id": 3466 }, "chunk_id": "train_shard_00001_3466_0", "global_id": 10573 }, { "text": "Notably, significant increases in resistance were observed from 2016 to 2021 for the following: ≥ 1 resistant (P = 0.001), MDR (P = 0.001), ampicillin (P = 0.001), tetracycline (P < 0.001), chloramphenicol (P = 0.030), and trimethoprim/sulfamethoxazole (P = 0.003). The marked escalation in drug resistance over the recent years, coupled with the varying resistance rates among food sources, underscores the growing public health concern. Our findings highlight the need for a coordinated approach to effectively monitor and respond to Salmonella infections in Guizhou, China.\n\nAntimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China.", "token_count": 280, "char_count": 737, "word_count": 100, "semantic_coherence": 1, "information_density": 0.69, "quality_score": 0.845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:30.953965", "source": { "split": "train_shard_00001", "doc_id": 3466 }, "chunk_id": "train_shard_00001_3466_1", "global_id": 10574 }, { "text": "The green alga Chlamydomonas is an important and versatile model organism for research topics ranging from photosynthesis and metabolism, cilia, and basal bodies to cellular communication and the cellular cycle and is of significant interest for green bioengineering processes. The genome in this unicellular green alga is contained in 17 haploid chromosomes and codes for 16 883 protein coding genes. Functional genomics, as well as biotechnological applications, rely on the ability to remove, add, and change these genes in a controlled and efficient manner. In this review, the history of gene editing in Chlamydomonas is put in the context of the wider developments in genetics to demonstrate how many of the key developments to engineer these algae follow the global trends and the availability of technology. Building on this background, an overview of the state of the art in Chlamydomonas engineering is given, focusing primarily on the practical aspects while giving examples of recent applications. Commonly encountered Chlamydomonas-specific challenges, recent developments, and community resources are presented, and finally, a comprehensive discussion on the emergence and evolution of CRISPR/Cas-based precision gene editing is given. An outline of possible future paths for gene editing based on current global trends in genetic engineering and tools for gene editing is presented.\n\nGenome editing in the green alga Chlamydomonas: past, present practice and future prospects.", "token_count": 324, "char_count": 1491, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5864, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:31.524651", "source": { "split": "train_shard_00001", "doc_id": 3467 }, "chunk_id": "train_shard_00001_3467_0", "global_id": 10575 }, { "text": "Clostridioides difficile is a gastrointestinal pathogen of both humans and agricultural animals and thus a major One Health threat. The C. difficile species consists of five main clades, with Clade 5 currently undergoing speciation from Clades 1-4. Since Clade 5 strains are highly prevalent in agricultural animals and a frequent cause of zoonotic infections, these strains may have evolved phenotypes that distinguish them from Clade 1-4 strains. Here, we compare the growth properties of Clade 5 strains to those of Clade 1-4 strains using anaerobic time-lapse microscopy coupled with automated image analysis. Our analyses indicate that Clade 5 strains grow faster and are more likely to form long chains of cells than Clade 1-4 strains. Using comparative genomic and CRISPRi analyses, we show that the chaining phenotype of Clade 5 strains is driven by the orientation of the invertible cmr switch sequence, with chaining strains exhibiting a bias to the cmr-ON state. Interestingly, Clade 5 strains with a bias towards the cmr-ON state shifted to a largely cmr-OFF state during murine infection, suggesting that the cmr-OFF state is under positive selection during infection. Collectively, our data reveal that Clade 5 strains have distinct growth properties, which may allow them to inhabit diverse ecological niches.\n\nUnique growth and morphology properties of Clade 5 Clostridioides difficile strains revealed by single-cell time-lapse microscopy.", "token_count": 361, "char_count": 1456, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5818, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:32.102844", "source": { "split": "train_shard_00001", "doc_id": 3468 }, "chunk_id": "train_shard_00001_3468_0", "global_id": 10576 }, { "text": "Self-synthesizing transposons are integrative mobile genetic elements (MGEs) that encode their own B-family DNA polymerase (PolB). Discovered a few years ago, they are proposed as key players in the evolution of several groups of DNA viruses and virus-host interaction machinery. Pipolins are the most recent addition to the group, are integrated in the genomes of bacteria from diverse phyla and also present as circular plasmids in mitochondria. Remarkably, pipolins-encoded PolBs are proficient DNA polymerases endowed with DNA priming capacity, hence the name, primer-independent PolB (piPolB). We have now surveyed the presence of pipolins in a collection of 2238 human and animal pathogenic Escherichia coli strains and found that, although detected in only 25 new isolates (1.1%), they are present in E. coli strains from a wide variety of pathotypes, serotypes, phylogenetic groups and sequence types. Overall, the pangenome of strains carrying pipolins is highly diverse, despite the fact that a considerable number of strains belongs to only three clonal complexes (CC10, CC23 and CC32). Comparative analysis with a set of 67 additional pipolin-harboring strains from GenBank further confirmed these results. The genetic structure of pipolins shows great flexibility and variability, with the piPolB gene and the attachment sites being the only common features. Most pipolins contain one or more recombinases that would be involved in excision/integration of the element in the same conserved tRNA gene. This mobilization mechanism might explain the apparent incompatibility of pipolins with other integrative MGEs such as integrons. In addition, analysis of cophylogeny between pipolins and pipolin-harboring strains showed a lack of congruence between several pipolins and their host strains, in agreement with horizontal transfer between hosts. Overall, these results indicate that pipolins can serve as a vehicle for genetic transfer among circulating E. coli and possibly also among other pathogenic bacteria.", "token_count": 485, "char_count": 2024, "word_count": 296, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "CC10", "CC32", "CC23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:32.752500", "source": { "split": "train_shard_00001", "doc_id": 3469 }, "chunk_id": "train_shard_00001_3469_0", "global_id": 10577 }, { "text": "High diversity and variability of pipolins among a wide range of pathogenicEscherichia colistrains", "token_count": 32, "char_count": 105, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:33.104180", "source": { "split": "train_shard_00001", "doc_id": 3469 }, "chunk_id": "train_shard_00001_3469_1", "global_id": 10578 }, { "text": "

Objectives

Cronobacter sakazakii is an emerging opportunistic foodborne pathogen that is frequently associated with life-threatening infections such as infantile septicemia, meningitis, and necrotizing enterocolitis. The emergence of antimicrobial-resistant, livestock-associated C. sakazakii is a great public health concern. Here, we report on the first draft genome sequence of C. sakazakii strain MEZCS99 sequence type 3 (ST3) isolated from feces from a healthy chicken in KwaZulu-Natal Province, South Africa.

Methods

The genomic DNA of C. sakazakii was sequenced using an Illumina MiSeq platform (Illumina Inc., San Diego, CA). Generated reads were trimmed and de novo assembled. The assembled contigs were analyzed for virulence and antimicrobial resistance genes, extra-chromosomal plasmids, and multilocus sequence type (MLST). To compare the sequenced strains to other previously sequenced C. sakazakii strains, available raw read sequences of C. sakazakii were downloaded and all sequence files were treated identically to generate a core genome phylogenetic tree.

Results

Intrinsic beta-lactam resistance gene blaCSA-1 was detected in MEZCS99. No colistin or other antibiotic resistance genes were detected. MEZCS99 belonged to ST3 and harbored an extra-chromosomal plasmid (IncFIB (pCTU3)). The genome of MEZCS99 strain showed two CRISPR/Cas cluster arrays of I-E (n = 1) and I-F (n = 1) type.

Conclusion

The genome sequence of strain MEZCS99 will serve as a reference point for molecular epidemiological studies of livestock-associated C. sakazakii in Africa. In addition, this study allows in-depth analysis of the genomic structure and will provide valuable information that helps understand the pathogenesis and antimicrobial resistance of livestock-associated C. sakazakii.", "token_count": 525, "char_count": 1820, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [ "MEZCS99", "ST3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:33.735440", "source": { "split": "train_shard_00001", "doc_id": 3470 }, "chunk_id": "train_shard_00001_3470_0", "global_id": 10579 }, { "text": "Draft genome sequence of Cronobacter sakazakii strain MEZCS99 sequence type 3 isolated from chicken in South Africa.", "token_count": 32, "char_count": 116, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [ "MEZCS99" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:34.100649", "source": { "split": "train_shard_00001", "doc_id": 3470 }, "chunk_id": "train_shard_00001_3470_1", "global_id": 10580 }, { "text": "A foodborne outbreak related to milk cartons served in school lunches occurred in June 2021, which involved more than 1,800 cases from 25 schools. The major symptoms were abdominal pain, diarrhoea, vomiting, and fever. Although major foodborne toxins and pathogens were not detected, a specific Escherichia coli strain, serotype OUT (OgGp9):H18, was predominantly isolated from milk samples related to the outbreak and most patients tested. The strains from milk and patient stool samples were identified as the same clone by core genome multilocus sequence typing and single-nucleotide polymorphism analysis. The strain was detected in milk samples served for two days related to the foodborne outbreak at a rate of 69.6% and levels of less than ten most probable number/100 mL but not on days unrelated to the outbreak. The acid tolerance of the strain for survival in the stomach was similar to that of enterohaemorrhagic E. coli O157:H7, and the same inserts in the chu gene cluster in the acid fitness island were genetically revealed. The pathogenicity of the strain was not clear; however, it was indicated that the causative pathogen was atypical diarrhoeagenic E. coli OUT (OgGp9):H18.\n\nAtypical diarrhoeagenic Escherichia coli in milk related to a large foodborne outbreak.", "token_count": 372, "char_count": 1318, "word_count": 200, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:34.678365", "source": { "split": "train_shard_00001", "doc_id": 3471 }, "chunk_id": "train_shard_00001_3471_0", "global_id": 10581 }, { "text": "During a 2018 antimicrobial resistance surveillance of Escherichia coli isolates from diarrheal calves in Xinjiang Province, China, an unexpectedly high prevalence (48.5%) of fosfomycin resistance was observed. This study aimed to reveal the determinants of fosfomycin resistance and the underlying transmission mechanism. Polymerase chain reaction (PCR) screening showed that all fosfomycin-resistant E. coli carried the fosA3 gene. Pulsed-field gel electrophoresis (PFGE) and southern blot hybridization revealed that the 16 fosA3-positive isolates belonged to four different PFGE patterns (i.e., A, B, C, D). The fosA3 genes of 11 clonally related strains (pattern D) were located on the chromosome, while others were carried by plasmids. Whole-genome and long-read sequencing indicated that the pattern D strains were E. coli O101: H9-ST10, and the pattern C, B, and A strains were O101: H9-ST167, O8: H30-ST1431, and O101: H9 with unknown ST, respectively. Among the pattern C strains, the bla CTX-M-14 gene was co-localized with the fosA3 gene on the F18: A-: B1 plasmids. Interestingly, phylogenetic analysis based on core genome single nucleotide polymorphisms (cgSNPs) showed that the O101: H9-ST10 strains were closely related to a Australian-isolated Chroicocephalus-origin E. coli O101: H9-ST10 strain producing CTX-M-14 and FosA3, with a difference of only 11 SNPs", "token_count": 505, "char_count": 1458, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6583, "quality_score": 0.8291, "entities": { "genes": [ "ST167", "ST10", "ST1431" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:35.335401", "source": { "split": "train_shard_00001", "doc_id": 3472 }, "chunk_id": "train_shard_00001_3472_0", "global_id": 10582 }, { "text": "These results indicate possible international dissemination of the high-risk E. coli clone O101: H9-ST10 by migratory birds.\n\nClonal spread of Escherichia coli O101: H9-ST10 and O101: H9-ST167 strains carrying fosA3 and bla CTX-M-14 among diarrheal calves in a Chinese farm, with Australian Chroicocephalus as the possible origin of E. coli O101: H9-ST10.", "token_count": 172, "char_count": 408, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [ "ST167", "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:35.776735", "source": { "split": "train_shard_00001", "doc_id": 3472 }, "chunk_id": "train_shard_00001_3472_1", "global_id": 10583 }, { "text": "Severe Helicobacter pylori-linked gastric disorders are especially prevalent in the East Asia region. The ability of H. pylori to cause different clinical outcomes is thought to be associated with unique sets of its genetic features. However, only few genetic features have been definitively linked to specific gastrointestinal pathologies. Genome heterogeneity of clinical H. pylori strains from patients with four different gastric disorders was studied to explore the population structure and molecular genomic features and their association with pathogenicity. Population analysis showed that 92.9% of the Shanghai H. pylori isolates were clustered in the East Asia group. Among 2,866 genes detected in all genomes, 1,146 genes formed the core genome, whereas 209 unique genes were detected in individual disease groups. The unique genes of peptic ulcer and gastric cancer groups represented the inorganic ion transport and metabolism function gene clusters. Sixteen virulence genes were detected with statistically different detection rates among the four disease groups. Furthermore, 127 clustered regularly interspaced short palindromic repeats were found with significantly different rates in the four disease groups. A total of 337 putative genomic islands were identified, and three genomic islands were individually found in more than 10% of strains. The genomic islands included several metabolism-associated genes and many genes with unknown function. In total, 88 sequence types were detected among the 112 Shanghai H. pylori isolates. Our study provides an essential milestone in the mapping of specific genomic features and their functions to identify factors needed to induce specific gastric disorders in H. pylori.\n\nGenomic population structure of Helicobacter pylori Shanghai isolates and identification of genomic features uniquely linked with pathogenicity.", "token_count": 456, "char_count": 1928, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5581, "quality_score": 0.779, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:36.415776", "source": { "split": "train_shard_00001", "doc_id": 3473 }, "chunk_id": "train_shard_00001_3473_0", "global_id": 10584 }, { "text": "

Abstract

Public health and regulatory agencies worldwide sequence all Listeria monocytogenes isolates obtained as part of routine surveillance and outbreak investigations. Many of these entities submit the sequences to the National Center for Biotechnology Information Pathogen Detection (NCBI PD) database, which groups the L. monocytogenes isolates into single nucleotide polymorphism (SNP) clusters based on a pairwise SNP difference threshold of 50 SNPs. Our goal was to assess whether isolates with metadata that suggest different sources or locations could show evidence for close genetic relatedness indicating a recent common ancestor and a possible unknown common source. We compared the whole genome sequencing (WGS) data of 249 L. monocytogenes isolates sequenced here, which have detailed metadata, with WGS data of nonclinical isolates on NCBI PD. The 249 L. monocytogenes isolates originated from natural environments (n = 91) as well as from smoked fish (n = 62), dairy (n = 56), and deli meat (n = 40) operations in the United States. Using a combination of subtyping by core genome multilocus sequence typing and high-quality SNP, we observed five SNP clusters in which study isolates and SNP cluster isolates seemed to be closely related and either (i) shared the same geolocation but showed different source types (one SNP cluster); (ii) shared the same source type but showed different geolocations (two SNP clusters); or (iii) shared neither source type nor geolocation (two SNP clusters). For one of the two clusters under (iii), there was, however, no strong bootstrap support for a common ancestor shared between the study isolates and SNP cluster isolates, indicating the value of in-depth evolutionary analyses when WGS data are used for traceback and epidemiological investigations. Overall, our results demonstrate that some L. monocytogenes subtypes may be associated with specific locations or commodities; these associations can help in investigations involving multi-ingredient foods such as sandwiches. However, at least some L", "token_count": 486, "char_count": 2068, "word_count": 308, "semantic_coherence": 1, "information_density": 0.6396, "quality_score": 0.8198, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:37.067065", "source": { "split": "train_shard_00001", "doc_id": 3474 }, "chunk_id": "train_shard_00001_3474_0", "global_id": 10585 }, { "text": "monocytogenes subtypes can be widespread geographically and can be associated with different sources, which may present a challenge to traceback investigations involving these subtypes.

Highlights

\n\nIdentification of Closely Related Listeria monocytogenes Isolates with No Apparent Evidence for a Common Source or Location: A Retrospective Whole Genome Sequencing Analysis.", "token_count": 90, "char_count": 380, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8723, "quality_score": 0.9362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:37.438560", "source": { "split": "train_shard_00001", "doc_id": 3474 }, "chunk_id": "train_shard_00001_3474_1", "global_id": 10586 }, { "text": "The distributed genome hypothesis states that the gene pool of a bacterial taxon is much more complex than that found in a single individual genome. However, the possible fitness advantage, why such genomic diversity is maintained, whether this variation is largely adaptive or neutral, and why these distinct individuals can coexist, remains poorly understood. Here, we present the infinitely many genes (IMG) model, which is a quantitative, evolutionary model for the distributed genome. It is based on a genealogy of individual genomes and the possibility of gene gain (from an unbounded reservoir of novel genes, e.g., by horizontal gene transfer from distant taxa) and gene loss, for example, by pseudogenization and deletion of genes, during reproduction. By implementing these mechanisms, the IMG model differs from existing concepts for the distributed genome, which cannot differentiate between neutral evolution and adaptation as drivers of the observed genomic diversity. Using the IMG model, we tested whether the distributed genome of 22 full genomes of picocyanobacteria (Prochlorococcus and Synechococcus) shows signs of adaptation or neutrality. We calculated the effective population size of Prochlorococcus at 1.01 × 10(11) and predicted 18 distinct clades for this population, only six of which have been isolated and cultured thus far. We predicted that the Prochlorococcus pangenome contains 57,792 genes and found that the evolution of the distributed genome of Prochlorococcus was possibly neutral, whereas that of Synechococcus and the combined sample shows a clear deviation from neutrality.\n\nThe infinitely many genes model for the distributed genome of bacteria.", "token_count": 383, "char_count": 1689, "word_count": 250, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:38.020068", "source": { "split": "train_shard_00001", "doc_id": 3475 }, "chunk_id": "train_shard_00001_3475_0", "global_id": 10587 }, { "text": "The aim of the study was to evaluate enzymatic activities of yeasts isolated from inflammatory mammary secretion. The yeasts isolated from cows with clinical and sub-clinical mastitis (134 strains) included: Candida krusei (62 strains), Candida kefyr (48 strains), Candida lusitaniae (17 strains) and Candida famata (7 strains). The API ZYM system was used containing substrates to assess 19 hydrolytic enzymes. Substantial differences in the number and activity of hydrolyses were demonstrated in individual species. In Candida krusei, acid phosphatase showed the highest activity (4.36 points), in Candida kefyr and Candida lusitaniae--leucine arylamidase (4.93 and 4.25 points, respectively), in Candida famata--alpha-glucosidase (4.75 points). No activity of trypsin, chymotrypsin, alpha-galactosidase, beta-glucuronidase, alpha-mannosidase or alpha-fucosidase was observed in any of the yeasts examined.\n\nEnzymatic activity of yeasts isolated from the inflamed mammary secretion in dairy cows.", "token_count": 304, "char_count": 998, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6466, "quality_score": 0.8233, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:38.593435", "source": { "split": "train_shard_00001", "doc_id": 3476 }, "chunk_id": "train_shard_00001_3476_0", "global_id": 10588 }, { "text": "Candida kefyr is a common yeast species that can be found in fermented milk and cheeses. As a first step to developing a gene transfer system for C. kefyr, the orotidine-5'-phosphate decarboxylase (URA3) gene was cloned, using degenerate PCR and genome walking. The uninterrupted open reading frame of the C. kefyr URA3 gene spans 801 bp, corresponding to 267 amino acid residues. The functionality of the gene was confirmed by complementation of ura3 auxotrophs of C. albicans and Saccharomyces cerevisiae. Phylogenetic analysis of the deduced amino acid sequence indicated that it shares a high degree of homology with other Candida URA3 homologues.\n\nIsolation and characterization of Candida kefyr orotidine-5'-phosphate decarboxylase (URA3) gene.", "token_count": 224, "char_count": 750, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:39.069915", "source": { "split": "train_shard_00001", "doc_id": 3477 }, "chunk_id": "train_shard_00001_3477_0", "global_id": 10589 }, { "text": "

Background

Salmonella enterica is a significant foodborne pathogen, which can be transmitted via several distinct routes, and reports on acquisition of antimicrobial resistance (AMR) are increasing. To better understand the association between human Salmonella clinical isolates and the potential environmental/animal reservoirs, whole genome sequencing (WGS) was used to investigate the epidemiology and AMR patterns within Salmonella isolates from two adjacent US states.

Results

WGS data of 200 S. enterica isolates recovered from human (n = 44), swine (n = 32), poultry (n = 22), and farm environment (n = 102) were used for in silico prediction of serovar, distribution of virulence genes, and phylogenetically clustered using core genome single nucleotide polymorphism (SNP) and feature frequency profiling (FFP). Furthermore, AMR was studied both by genotypic prediction using five curated AMR databases, and compared to phenotypic AMR using broth microdilution. Core genome SNP-based and FFP-based phylogenetic trees showed consistent clustering of isolates into the respective serovars, and suggested clustering of isolates based on the source of isolation. The overall correlation of phenotypic and genotypic AMR was 87.61% and 97.13% for sensitivity and specificity, respectively. AMR and virulence genes clustered with the Salmonella serovars, while there were also associations between the presence of virulence genes in both animal/environmental isolates and human clinical samples.

Conclusions

WGS is a helpful tool for Salmonella phylogenetic analysis, AMR and virulence gene predictions. The clinical isolates clustered closely with animal and environmental isolates, suggesting that animals and environment are potential sources for dissemination of AMR and virulence genes between Salmonella serovars.", "token_count": 493, "char_count": 1842, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5887, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:39.723339", "source": { "split": "train_shard_00001", "doc_id": 3478 }, "chunk_id": "train_shard_00001_3478_0", "global_id": 10590 }, { "text": "Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources.", "token_count": 49, "char_count": 228, "word_count": 26, "semantic_coherence": 1, "information_density": 0.9615, "quality_score": 0.9808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:40.122449", "source": { "split": "train_shard_00001", "doc_id": 3478 }, "chunk_id": "train_shard_00001_3478_1", "global_id": 10591 }, { "text": "

Background

Pantoea ananatis is found in a wide range of natural environments, including water, soil, as part of the epi- and endophytic flora of various plant hosts, and in the insect gut. Some strains have proven effective as biological control agents and plant-growth promoters, while other strains have been implicated in diseases of a broad range of plant hosts and humans. By analysing the pan-genome of eight sequenced P. ananatis strains isolated from different sources we identified factors potentially underlying its ability to colonize and interact with hosts in both the plant and animal Kingdoms.

Results

The pan-genome of the eight compared P. ananatis strains consisted of a core genome comprised of 3,876 protein coding sequences (CDSs) and a sizeable accessory genome consisting of 1,690 CDSs. We estimate that ~106 unique CDSs would be added to the pan-genome with each additional P. ananatis genome sequenced in the future. The accessory fraction is derived mainly from integrated prophages and codes mostly for proteins of unknown function. Comparison of the translated CDSs on the P. ananatis pan-genome with the proteins encoded on all sequenced bacterial genomes currently available revealed that P. ananatis carries a number of CDSs with orthologs restricted to bacteria associated with distinct hosts, namely plant-, animal- and insect-associated bacteria. These CDSs encode proteins with putative roles in transport and metabolism of carbohydrate and amino acid substrates, adherence to host tissues, protection against plant and animal defense mechanisms and the biosynthesis of potential pathogenicity determinants including insecticidal peptides, phytotoxins and type VI secretion system effectors.

Conclusions

P. ananatis has an 'open' pan-genome typical of bacterial species that colonize several different environments. The pan-genome incorporates a large number of genes encoding proteins that may enable P. ananatis to colonize, persist in and potentially cause disease symptoms in a wide range of plant and animal hosts.", "token_count": 499, "char_count": 2076, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5853, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:40.811465", "source": { "split": "train_shard_00001", "doc_id": 3479 }, "chunk_id": "train_shard_00001_3479_0", "global_id": 10592 }, { "text": "Analysis of the Pantoea ananatis pan-genome reveals factors underlying its ability to colonize and interact with plant, insect and vertebrate hosts.", "token_count": 35, "char_count": 148, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:41.184347", "source": { "split": "train_shard_00001", "doc_id": 3479 }, "chunk_id": "train_shard_00001_3479_1", "global_id": 10593 }, { "text": "

Background

Streptococcus uberis, a Gram-positive, catalase-negative member of the family Streptococcaceae is an important environmental pathogen responsible for a significant proportion of subclinical and clinical bovine intramammary infections. Currently, the genome of only a single reference strain (0140J) has been described. Here we present a comparative analysis of complete draft genome sequences of an additional twelve S. uberis strains.

Results

Pan and core genome analysis revealed the core genome common to all strains to be 1,550 genes in 1,509 orthologous clusters, complemented by 115-246 accessory genes present in one or more S. uberis strains but absent in the reference strain 0140J. Most of the previously predicted virulent genes were present in the core genome of all 13 strains but gene gain/loss was observed between the isolates in CDS associated with clustered regularly interspaced short palindromic repeats (CRISPRs), prophage and bacteriocin production. Experimental challenge experiments confirmed strain EF20 as non-virulent; only able to infect in a transient manner that did not result in clinical mastitis. Comparison of the genome sequence of EF20 with the validated virulent strain 0140J identified genes associated with virulence, however these did not relate clearly with clinical/non-clinical status of infection.

Conclusion

The gain/loss of mobile genetic elements such as CRISPRs and prophage are a potential driving force for evolutionary change. This first \"whole-genome\" comparison of strains isolated from clinical vs non-clinical intramammary infections including the type virulent vs non-virulent strains did not identify simple gene gain/loss rules that readily explain, or be confidently associated with, differences in virulence. This suggests that a more complex dynamic determines infection potential and clinical outcome not simply gene content.\n\nVirulence related sequences; insights provided by comparative genomics of Streptococcus uberis of differing virulence.", "token_count": 502, "char_count": 2040, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8105, "entities": { "genes": [ "EF20" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:41.889306", "source": { "split": "train_shard_00001", "doc_id": 3480 }, "chunk_id": "train_shard_00001_3480_0", "global_id": 10594 }, { "text": "Introduction. Invasive meningococcal disease (IMD) caused by Neisseria meningitidis may show temporal and geographical changes in both the epidemiology and the characteristics of the strains involved.Gap statement. A study that examined invasive N. meningitidis causing IMD in Atlantic Canada from 2009 to 2013 was published in 2014. Data from subsequent years have not been described.Aim. This study examined the molecular epidemiology of IMD in four Atlantic Provinces of Canada as well as potential serogroup B (MenB) vaccine coverage.Methods. Individual IMD case isolates recovered from 2014 to 2020 were analysed for serotype and serosubtype antigens as well as by whole-genome sequencing (WGS) for prediction of potential MenB vaccine coverage.Results. Of the 56 IMD isolates, 42, 8, 5 and 1 were MenB, serogroup Y, serogroup W (MenW) and serogroup C, respectively. Geographical differences in the distribution of MenB clones revealed concentration of sequence type (ST)-269 clonal complex (cc) and ST-60 cc in Newfoundland and Labrador, while ST-41/44 cc (particularly ST-154) was predominantly found in New Brunswick and Nova Scotia. Core genome multi-locus sequence typing (cgMLST) also separated the New Brunswick and Nova Scotia ST-154 isolates into two clusters, with differences in their nhba and penA alleles. Furthermore, cgMLST also separated the ST-269 cc isolates in Atlantic Canada into the ST-1611 and the ST-269/ST-8924 clusters, with the latter showing high similarity to the ST-269 that first emerged in the Province of Quebec", "token_count": 482, "char_count": 1612, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:42.543614", "source": { "split": "train_shard_00001", "doc_id": 3481 }, "chunk_id": "train_shard_00001_3481_0", "global_id": 10595 }, { "text": "Genetic Meningococcal Antigen Typing System showed that 54.8 % of MenB were predicted to be covered by the MenB vaccine Bexsero, with a further 38.1 % potentially covered by virtue of the presence of genes that encoded factor H-binding protein variant 1 proteins. Meningococcal deduced vaccine antigen reactivity predicted from WGS data showed that 95.3 % of MenB were covered by Trumenba. Four cases of IMD due to MenW ST-11 cc were also identified, with the first case found in 2018.Conclusions. This study provided evidence concerning the dynamics of N. meningitidis strains causing IMD in Atlantic Canada, with both geographical and temporal differences found. MenB vaccine appeared to provide good coverage of MenB IMD, especially towards the predominant strain of ST-154.\n\nCharacterization of invasive meningococcal disease case isolates in Atlantic Canada, 2014 to 2020: spatial-temporal variations of clones and predicted meningococcal B vaccine coverage.", "token_count": 263, "char_count": 977, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6597, "quality_score": 0.8299, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:43.084932", "source": { "split": "train_shard_00001", "doc_id": 3481 }, "chunk_id": "train_shard_00001_3481_1", "global_id": 10596 }, { "text": "PURPOSE: Endophytic Streptomyces parvulus VCCM 22513 isolated from Bruguiera gymnorrhiza in Quang Ninh mangrove forest, northern Vietnam showed abiotic stress tolerance consisting of antioxidant, salt-tolerant, and aromatic-compound degrading activities. The goal of this study was to shed light on genomic bases rendering mangrove endophytic S. parvulus more resilient to environmental stressors. METHODS: Phenotypic analysis including antioxidant activities, hydrogen peroxide and sodium chloride resistance, and aromatic compound utilization were evaluated. The genome of strain VCCM 22513 was sequenced using Illumina Miseq sequencing platform and assembled using SPAdes. RESULTS: Out of 15 endophytic actinomycetes associated with B. gymnorrhiza in Quang Ninh mangrove, northern Vietnam, VCCM 22513 extract showed remarkable antioxidant activities through (1,1-diphenyl-2-picrylhydrazyl) DPPH and superoxide radical scavenging assays of 72.1 ± 0.04% and 38.3 ± 0.16% at 1.6 mg/ml, respectively. The genome consists of a 7,688,855 bp linear chromosome, 6782 protein-coding sequences, and 68 tRNAs. Genomic analysis identified strain VCCM 22513 as Streptomyces parvulus and confirmed a highly conserved core genome and stability of S. parvulus under natural selection. Genome mining revealed the presence of genetic determinants involved in mycothiol and ergothioneine biosynthesis (26 genes), oxidative stress resistance (43 genes), osmoadaptation (87 genes), heat and cold stress (34 genes), aromatic compound degradation (55 genes). Further genome-wide comparison between S", "token_count": 484, "char_count": 1579, "word_count": 208, "semantic_coherence": 1, "information_density": 0.7115, "quality_score": 0.8558, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:43.734485", "source": { "split": "train_shard_00001", "doc_id": 3482 }, "chunk_id": "train_shard_00001_3482_0", "global_id": 10597 }, { "text": "parvulus VCCM 22513 and 11 Streptomyces genomes showed that VCCM 22513 possesses significantly higher copies of genes involved in mycothiol and ergothioneine biosynthesis. In support of this finding, the strain exhibited much resistance to 0.6–1.0 M H₂O₂ and 6% (w/v) NaCl as compared to Streptomyces cavourensis YBQ59 isolated from Cinnamomum cassia Prels. In addition, the complete pathways for degradation of aromatic compounds including protocatechuate, gentisate, 4-hydroxyphenylpyruvate, cinnamate, 3-phenylpropionate, and styrene were only identified in the genome of VCCM 22513. CONCLUSIONS: The present study revealed for the first time adaptive responses of mangrove endophytic S. parvulus VCCM 22513 to survive in hostile environment. The information shown here provided better understanding of underlying mechanisms related to adaptation and partially plant-microbe interaction of Streptomyces associated with mangrove plants.\n\nGenomic and physiological traits provide insights into ecological niche adaptations of mangrove endophytic Streptomyces parvulus VCCM 22513", "token_count": 326, "char_count": 1079, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7183, "quality_score": 0.8592, "entities": { "genes": [ "YBQ59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:44.298693", "source": { "split": "train_shard_00001", "doc_id": 3482 }, "chunk_id": "train_shard_00001_3482_1", "global_id": 10598 }, { "text": "

Background

Accumulating evidence shows a role of the hospital wastewater system in the spread of multidrug-resistant organisms, such as carbapenemase producing Enterobacterales (CPE). Several sequential outbreaks of CPE on the geriatric ward of the Ghent University hospital have led to an outbreak investigation. Focusing on OXA-48 producing Citrobacter freundii, the most prevalent species, we aimed to track clonal relatedness using whole genome sequencing (WGS). By exploring transmission routes we wanted to improve understanding and (re)introduce targeted preventive measures.

Methods

Environmental screening (toilet water, sink and shower drains) was performed between 2017 and 2021. A retrospective selection was made of 53 Citrobacter freundii screening isolates (30 patients and 23 environmental samples). DNA from frozen bacterial isolates was extracted and prepped for shotgun WGS. Core genome multilocus sequence typing was performed with an in-house developed scheme using 3,004 loci.

Results

The CPE positivity rate of environmental screening samples was 19.0% (73/385). Highest percentages were found in the shower drain samples (38.2%) and the toilet water samples (25.0%). Sink drain samples showed least CPE positivity (3.3%). The WGS data revealed long-term co-existence of three patient sample derived C. freundii clusters. The biggest cluster (ST22) connects 12 patients and 8 environmental isolates taken between 2018 and 2021 spread across the ward. In an overlapping period, another cluster (ST170) links eight patients and four toilet water isolates connected to the same room. The third C. freundii cluster (ST421) connects two patients hospitalised in the same room but over a period of one and a half year", "token_count": 457, "char_count": 1756, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [ "ST170", "ST421", "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:44.942358", "source": { "split": "train_shard_00001", "doc_id": 3483 }, "chunk_id": "train_shard_00001_3483_0", "global_id": 10599 }, { "text": "Additional sampling in 2022 revealed clonal isolates linked to the two largest clusters (ST22, ST170) in the wastewater collection pipes connecting the rooms.

Conclusions

Our findings suggest long-term circulation and transmission of carbapenemase producing C. freundii clones in hospital sanitary installations despite surveillance, daily cleaning and intermittent disinfection protocols. We propose a role for the wastewater drainage system in the spread within and between rooms and for the sanitary installations in the indirect transmission via bioaerosol plumes. To tackle this problem, a multidisciplinary approach is necessary including careful design and maintenance of the plumbing system.\n\nSanitary installations and wastewater plumbing as reservoir for the long-term circulation and transmission of carbapenemase producing Citrobacter freundii clones in a hospital setting.", "token_count": 198, "char_count": 892, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [ "ST170", "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:45.390883", "source": { "split": "train_shard_00001", "doc_id": 3483 }, "chunk_id": "train_shard_00001_3483_1", "global_id": 10600 }, { "text": "2. The accessory genes of prokaryote and eukaryote pangenomes accumulate by horizontal gene transfer, differential gene loss, and the effects of selection and drift. We have developed Coinfinder, a software program that assesses whether sets of homologous genes (gene families) in pangenomes associate or dissociate with each other (i.e. are “coincident”) more often than would be expected by chance. Coinfinder employs a user-supplied phylogenetic tree in order to assess the lineage-dependence (i.e. the phylogenetic distribution) of each accessory gene, allowing Coinfinder to focus on coincident gene pairs whose joint presence is not simply because they happened to appear in the same clade, but rather that they tend to appear together more often than expected across the phylogeny. Coinfinder is implemented in C++, Python3, and R and is freely available under the GPU license from https://github.com/fwhelan/coinfinder . 3.

Impact statement

Coinfinder identifies genes that co-occur (associate) or avoid (dissociate) with each other across the accessory genomes of a pangenome of interest. Genes that associate or dissociate more often than expected by chance, suggests that those genes have a connection (attraction or repulsion) that is interesting to explore. Identification of these groups of genes will further the field’s understanding of the importance of accessory genes. Coinfinder is a freely available, open-source software which can identify gene patterns locally on a personal computer in a matter of hours. 4.

Data summary

Coinfinder is freely available at https://github.com/fwhelan/coinfinder . A list of the Identifiers of the genomes used within as well as all input/output files are available at https://github.com/fwhelan/coinfinder-manuscript . The authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.\n\nCoinfinder: Detecting Significant Associations and Dissociations in Pangenomes", "token_count": 483, "char_count": 2006, "word_count": 284, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:46.042482", "source": { "split": "train_shard_00001", "doc_id": 3484 }, "chunk_id": "train_shard_00001_3484_0", "global_id": 10601 }, { "text": "

Introduction

Infections caused by carbapenemase-producing Enterobacteriaceae (CPE) pose a significant threat, leading to severe morbidity and mortality among newborns.

Methods

This study, conducted at Franceville hospital's maternity and neonatology wards from February 22nd to June 20th, 2022, investigated the prevalence of CPE in 197 parturients and 203 newborns. Rectal swabs were taken from parturients before delivery and from newborns 30 minutes after birth. Blood culture samples were collected if signs of infection were observed in newborns during a 28-day follow-up. A total of 152 environmental samples were obtained, comprising 18 from sinks, 14 from incubators, 27 from cradles, 39 from maternal beds, 14 from tables and desks, four from the two baby scales and 36 from bedside furniture.

Results

None of the 203 newborns were found to be CPE carriers 30 minutes after delivery. CPE carriage was found in 4.6% of mothers. When comparing colonized and uncolonized parturients, well-established risk factors for CPE carriage, such as recent hospitalization and antibiotic therapy, were more frequently observed among CPE carriers (33.3 vs 10.6% for hospitalization in the past 15 days; 55.5 vs 30.3% for hospitalization during pregnancy, and 55.5 vs 35.1% for antibiotic therapy during pregnancy). Notably, the prevalence of treatment with amoxicillin and clavulanic acid was 44.4% in CPE carriers compared to 17.0% in non-carriers. The incidence density of CPE-associated bloodstream infection was 0.49 per 100 newborns, accounting for a fatal case of CPE-associated bacteremia identified in one of the 203 newborns. Seven environmental samples returned positive for CPE (5 sinks and two pieces of furniture)", "token_count": 512, "char_count": 1743, "word_count": 250, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:46.701454", "source": { "split": "train_shard_00001", "doc_id": 3485 }, "chunk_id": "train_shard_00001_3485_0", "global_id": 10602 }, { "text": "Whole genome sequencing, performed on the 25 CPE isolates, revealed isolates carrying blaNDM-7 (n=10), blaNDM-5 (n=3), blaOXA181 (n=10), blaOXA48 (n=2) or blaOXA244 (n=1), along with genetic traits associated with the ability to cause severe and difficult-to-treat infections in newborns. Core genome comparison revealed nine CPE belonging to three international high-risk clones: E. coli ST410 (four mothers and a sink), two E. coli ST167 (a mother and a piece of furniture), and K. pneumoniae ST307 (a sink and a piece of furniture), with highly similar genetic backgrounds shared by maternal and environmental isolates, suggesting maternal contamination originating from the environment.

Discussion

Our study reveals key findings may guide the implementation of infection control measures to prevent nosocomial infections in newborns: the prevalence of CPE carriage in one out of 20 parturients, an infection occurring in one out of 400 newborns, substantial contamination of the care environment, clinical and environmental CPE isolates possessing genetic traits associated with the ability to cause severe and challenging infections, and clonal relationships between clinical and environmental isolates suggesting CPE spread within the wards, likely contributing to the acquisition and colonization of CPE by parturients during pregnancy.\n\nCarbapenem-producing Enterobacteriaceae in mothers and newborns in southeast Gabon, 2022.", "token_count": 382, "char_count": 1448, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6212, "quality_score": 0.8106, "entities": { "genes": [ "ST410", "ST167", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:47.276044", "source": { "split": "train_shard_00001", "doc_id": 3485 }, "chunk_id": "train_shard_00001_3485_1", "global_id": 10603 }, { "text": "Listeria monocytogenes is an important foodborne pathogen which has the ability to adapt and survive in food and food processing facilities where it can persist for years. In this study, a total of 143 L. monocytogenes isolates in South Africa (SA) were characterized for their strain's genetic relatedness, virulence profiles, stress tolerance and resistance genes associated with L. monocytogenes. The Core Genome Multilocus Sequence Typing (cgMLST) analysis revealed that the most frequent serogroups were IVb and IIa; Sequence Types (ST) were ST204, ST2, and ST1; and Clonal Complexes (CC) were CC204, CC1, and CC2. Examination of genes involved in adaptation and survival of L. monocytogenes in SA showed that ST1, ST2, ST121, ST204, and ST321 are well adapted in food processing environments due to the significant over-representation of Benzalkonium chloride (BC) resistance genes (bcrABC cassette, ermC, mdrL and Ide), stress tolerance genes (SSI-1 and SSI-2), Prophage (φ) profiles (LP_101, vB LmoS 188, vB_LmoS_293, and B054 phage), plasmids profiles (N1-011A, J1776, and pLM5578) and biofilm formation associated genes. Furthermore, the L. monocytogenes strains that showed hyper-virulent potential were ST1, ST2 and ST204, and hypo-virulent were ST121 and ST321 because of the presence and absence of major virulence factors such as LIPI-1, LIPI-3, LIPI-4 and the internalin gene family members including inlABCEFJ", "token_count": 492, "char_count": 1489, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6762, "quality_score": 0.8381, "entities": { "genes": [ "ST2", "ST204", "ST321", "CC204", "ST1", "CC2", "CC1", "ST121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:47.927119", "source": { "split": "train_shard_00001", "doc_id": 3486 }, "chunk_id": "train_shard_00001_3486_0", "global_id": 10604 }, { "text": "The information provided in this study revealed that hyper-virulent strains ST1, ST2, and ST204 could present a major public health risk due to their association with meat products and food processing environments in SA.\n\nWhole Genome-Based Characterization of Listeria monocytogenes Isolates Recovered From the Food Chain in South Africa.", "token_count": 85, "char_count": 346, "word_count": 49, "semantic_coherence": 1, "information_density": 0.898, "quality_score": 0.949, "entities": { "genes": [ "ST2", "ST204", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:48.305909", "source": { "split": "train_shard_00001", "doc_id": 3486 }, "chunk_id": "train_shard_00001_3486_1", "global_id": 10605 }, { "text": "CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics.\n\nAnalysis of metagenome-assembled viral genomes from the human gut reveals diverse putative CrAss-like phages with unique genomic features.", "token_count": 374, "char_count": 1473, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6175, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:48.884608", "source": { "split": "train_shard_00001", "doc_id": 3487 }, "chunk_id": "train_shard_00001_3487_0", "global_id": 10606 }, { "text": "In this paper, four nonionic surfactants with different hydrophilic-lipophilic balance (HLB) based on sorbitan monolaurate were synthesized by introducing ethylene oxide gas (n = 20, 40, 60, and 80 ethylene oxide units). The chemical structure of the prepared ethoxylated surfactants was confirmed using Fourier transform-infrared and (1)H NMR spectroscopes. The surface tension and thermodynamic properties of the prepared surfactants have been studied. The simultaneous saccharification and fermentation (SSF) process for ethanol production from microwave/alkali pretreated wheat straw has been assayed using nonionic surfactants have different ethylene oxide units. Ethanol yield was 82% and 61% for Kluyveromyces marxianus and Saccharomyces cerevisiae, respectively, with the addition of 2.5 g/l of the prepared nonionic surfactant (HLB = 18.2). Results show that the production of ethanol from microwave/alkali pretreated wheat straw increased with increasing the (HLB) value of the nonionic surfactant.\n\nThe effect of different ethoxylations for sorbitan monolaurate on enhancing simultaneous saccharification and fermentation (SSF) of wheat straw to ethanol.", "token_count": 339, "char_count": 1165, "word_count": 157, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:49.463638", "source": { "split": "train_shard_00001", "doc_id": 3488 }, "chunk_id": "train_shard_00001_3488_0", "global_id": 10607 }, { "text": "

ABSTRACT

A novel bacterium, strain RR6 T of the genus Halopseudomonas , was isolated from the sea sand from Paradip port area, India. Cells are Gram-stain-negative, rod-shaped, aerobic, non-sporulating and motile. The major cellular fatty acids of RR6 T were C 10:0 3OH, C 12:0 , C 16:1 w7c/16:1 w6c, 18:1 w7c and/or 18:1 w6c and C 16:0. The predominant polar lipids were phosphatidylglycerol (PG), diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylcholine (PC), unidentified phospholipid (PL) and unidentified lipids (L1-L2). The genome size of the strain RR6 was 3.93 Mb. The genomic G+C content was 61.3%. Gene ontology study showed a significant fraction of genes were associated with biological processes (53%), followed by molecular function (36%) and cellular components (11%). Comparisons of 16S rRNA gene sequences revealed 99.73 - 99.87 % sequence similarity with the closely related type strains of the genus Halopseudomonas . The average nucleotide identity (ANI) and average amino acid identity (AAI) of RR6 T with reference strains of closely related species of the genus Halopseudomonas were below 95–96, and the corresponding in-silico DNA–DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of RR6 T indicate that the strain represents a novel species of the genus Halopseudomonas and the name Halopseudomonas maritima sp. nov. is proposed. The type strain is RR6 T (= NBRC 115418 T = TBRC 15628 T ).", "token_count": 518, "char_count": 1561, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [ "RR6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:50.121433", "source": { "split": "train_shard_00001", "doc_id": 3489 }, "chunk_id": "train_shard_00001_3489_0", "global_id": 10608 }, { "text": "Description of Halopseudomonas maritima sp. nov., based on phylogenomic analysis", "token_count": 29, "char_count": 87, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:50.475214", "source": { "split": "train_shard_00001", "doc_id": 3489 }, "chunk_id": "train_shard_00001_3489_1", "global_id": 10609 }, { "text": "The gastrointestinal tracts of dairy calves and cows are reservoirs of antimicrobial-resistant bacteria (ARB), which are present regardless of previous antimicrobial therapy. Young calves harbor a greater abundance of resistant bacteria than older cows, but the factors driving this high abundance are unknown. Here, we aimed to fully characterize the genomes of multidrug-resistant (MDR) and antimicrobial-susceptible Escherichia coli strains isolated from pre-weaned calves, post-weaned calves, dry cows, and lactating cows and to identify the accessory genes that are associated with the MDR genotype to discover genetic targets that can be exploited to mitigate antimicrobial resistance in dairy farms. Results indicated that both susceptible and resistant E. coli isolates recovered from animals on commercial dairy operations were highly diverse and encoded a large pool of virulence factors. In total, 838 transferrable antimicrobial resistance genes (ARGs) were detected, with genes conferring resistance to aminoglycosides being the most common. Multiple sequence types (STs) associated with mild to severe human gastrointestinal and extraintestinal infections were identified. A Fisher's Exact Test identified 619 genes (ARGs and non-ARGs) that were significantly enriched in MDR isolates and 147 genes that were significantly enriched in susceptible isolates. Significantly enriched genes in MDR isolates included the iron scavenging aerobactin synthesis and receptor genes (iucABCD-iutA) and the sitABCD system, as well as the P fimbriae pap genes, myo-inositol catabolism (iolABCDEG-iatA), and ascorbate transport genes (ulaABC). The results of this study demonstrate a highly diverse population of E", "token_count": 496, "char_count": 1779, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:51.132058", "source": { "split": "train_shard_00001", "doc_id": 3490 }, "chunk_id": "train_shard_00001_3490_0", "global_id": 10610 }, { "text": "coli in commercial dairy operations, some of which encode virulence genes responsible for severe human infections and resistance to antibiotics of human health significance. Further, the enriched accessory genes in MDR isolates (aerobactin, sit, P fimbriae, and myo-inositol catabolism and ascorbate transport genes) represent potential targets for reducing colonization of antimicrobial-resistant bacteria in the calf gut.\n\nGenome-Wide Analysis of Escherichia coli Isolated from Dairy Animals Identifies Virulence Factors and Genes Enriched in Multidrug-Resistant Strains.", "token_count": 171, "char_count": 598, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7568, "quality_score": 0.8784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:51.571678", "source": { "split": "train_shard_00001", "doc_id": 3490 }, "chunk_id": "train_shard_00001_3490_1", "global_id": 10611 }, { "text": "We report an uncommon but emerging fungal pathogen, Candida kefyr, as a causative agent of infective endocarditis in a patient with a known history of hypertrophic obstructive cardiomyopathy. A 74-year-old woman with diabetes type II, hypertrophic obstructive cardiomyopathy, presented with gross hematuria and abdominal pain. Computed tomography scan revealed a hemorrhagic mass in the superior pole of the right kidney, with a thrombus extending from the ureter to the bladder. She underwent cryotherapy of the renal mass, together with retrograde ureteral stent placement, developed hypotension and respiratory distress, spiked high-grade fever, and had a new pansystolic murmur over the mitral and aortic areas. Urine and blood culture grew C. kefyr. Transthoracic echocardiogram revealed large mitral valve vegetation with moderate regurgitation. Micafungin was started, patient responded, and fungemia cleared. Repeat echocardiogram showed small vegetation, preserved leaflet mobility and mild regurgitation. Patient received 10 days of micafungin, followed by 6 weeks of fluconazole.\n\nCandida kefyr endocarditis in a patient with hypertrophic obstructive cardiomyopathy.", "token_count": 325, "char_count": 1177, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7205, "quality_score": 0.8602, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:52.177713", "source": { "split": "train_shard_00001", "doc_id": 3491 }, "chunk_id": "train_shard_00001_3491_0", "global_id": 10612 }, { "text": "Extracellular exoinulinase from Kluyveromyces marxianus YS-1, which hydrolyzes inulin into fructose, was immobilized on Duolite A568 after partial purification by ethanol precipitation and gel exclusion chromatography on Sephadex G-100. Optimum temperature of immobilized enzyme was 55 degrees C, which was 5 degrees C higher than the free enzyme and optimal pH was 5.5. Immobilized biocatalyst retained more than 90% of its original activity after incubation at 60 degrees C for 3 h, whereas in free form its activity was reduced to 10% under same conditions, showing a significant improvement in the thermal stability of the biocatalyst after immobilization. Apparent K (m) values for inulin, raffinose and sucrose were found to be 3.75, 28.5 and 30.7 mM, respectively. Activation energy (E (a)) of the immobilized biocatalyst was found to be 46.8 kJ/mol. Metal ions like Co(2+) and Mn(2+) enhanced the activity, whereas Hg(2+) and Ag(2+) were found to be potent inhibitors even at lower concentrations of 1 mM. Immobilized biocatalyst was effectively used in batch preparation of high fructose syrup from Asparagus racemosus raw inulin and pure inulin, which yielded 39.2 and 40.2 g/L of fructose in 4 h; it was 85.5 and 92.6% of total reducing sugars produced, respectively.\n\nProduction of high fructose syrup from Asparagus inulin using immobilized exoinulinase from Kluyveromyces marxianus YS-1.", "token_count": 439, "char_count": 1401, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:52.833806", "source": { "split": "train_shard_00001", "doc_id": 3492 }, "chunk_id": "train_shard_00001_3492_0", "global_id": 10613 }, { "text": "

Summary

Genome-wide association studies (GWAS) in microbes face different challenges to eukaryotes and have been addressed by a number of different methods. pyseer brings these techniques together in one package tailored to microbial GWAS, allows greater flexibility of the input data used, and adds new methods to interpret the association results.

Availability and Implementation

pyseer is written in python and is freely available at https://github.com/mgalardini/pyseer , or can be installed through pip . Documentation and a tutorial are available at http://pyseer.readthedocs.io .

Contact

john.lees@nyumc.org and marco@ebi.ac.uk

Supplementary information

Supplementary data are available online.\n\npyseer: a comprehensive tool for microbial pangenome-wide association studies", "token_count": 220, "char_count": 816, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7451, "quality_score": 0.8725, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:53.335304", "source": { "split": "train_shard_00001", "doc_id": 3493 }, "chunk_id": "train_shard_00001_3493_0", "global_id": 10614 }, { "text": "The invention creates a basis for the development of a technology for obtaining a complex of enzymes (D-aminooxidase, catalase, superoxide dismutase, and beta- galactosidase) from a microbial producer, which finds application in biotechnology, medicine, and food industry. The selected lactose-absorbing yeast strain Kluyveromyces marxianus 8362 possesses the necessary technological properties (thermal tolerance, high assimilation ability with regard to lactose) and a capability of producing thermostable enzymes - D-aminooxidase, catalase, superoxide dismutase. The Kluyveromyces marxianus 8362 strain is registered with the National Bank for Industrial Microorganisms and Cell Cultures for obtaining D-aminooxidase and concomitant enzymes. There is a suitable nutrient medium and conditions forcultivation of the selected strain and for induction of the synthesis of D-aminooxidase. When cultivating nutrient medium containing permeate and 30mM D-alanine, there is a yield coefficient 0,37 g dry substance/g consumed substrate and high specific activity of D-aminooxidase û 0,545 U/mg protein. Under these conditions, the strain synthesizes as concomitant enzymes thermostable catalase (8.12 deltaE/min/mg protein), thermostable superoxide dismutase (86.4 U/mg protein), and the enzyme beta- galactosidase (0.843 U/mg protein). The biomass rich in such enzymes may be used for obtaining them in pure or technical form.\n\nKLUYVEROMYCES MARXIANUS STRAIN FOR OBTAINING D-AMINOOXIDASE AND CONCOMINANT ENZYMS", "token_count": 438, "char_count": 1507, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6231, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:54.008010", "source": { "split": "train_shard_00001", "doc_id": 3494 }, "chunk_id": "train_shard_00001_3494_0", "global_id": 10615 }, { "text": "In malic acid-grown cells of the strains ATCC 10022 and KMS3 of Kluyveromyces marxianus the transport of malic acid occurred by a malate-proton symport, which accepted L-malic, D-malic, succinic and fumaric acids, but not tartaric, malonic or maleic acids. The system was inducible and subjected to glucose repression. Mutants of the strain KMS3, unable to grow in a medium with malic acid, were isolated and checked for their capacity to utilize several carbon sources and to transport dicarboxylic acids by the malate-proton symport. Two distinct clones affected on malate transport were obtained. Both were able to grow on a medium with glycerol or ethanol but not with DL-malic, succinic, oxoglutaric and oxaloacetic acids as the sole carbon and energy sources. However, while one of the mutants (Mal7) displayed activity levels for the enzymes malate dehydrogenase, isocitrate lyase, and phosphoenolpyruvate carboxykinase similar to those of the wild strain, in the other mutant type (Mal6) the activities for the same enzymes were significantly reduced. Plasma membranes from derepressed cells of the wild strain and of the mutants Mal6 and Mal7 were isolated and the protein analysed by SDS-PAGE. The electrophoretic patterns of these preparations differed in a polypeptide with an apparent molecular mass of about 28 kDa, which was absent only in the mutant Mal7. The results indicated that Mal7 can be affected in a gene that encodes a malate carrier in K. marxianus.\n\nIsolation and characterization of Kluyveromyces marxianus mutants deficient in malate transport.", "token_count": 427, "char_count": 1574, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5967, "quality_score": 0.7984, "entities": { "genes": [ "KMS3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:54.634964", "source": { "split": "train_shard_00001", "doc_id": 3495 }, "chunk_id": "train_shard_00001_3495_0", "global_id": 10616 }, { "text": "In recent years, there has been an observed increase in infections caused by carbapenem-resistant Klebsiella pneumonia (Kp) strains. The aim of this study was the phenotypic and genotypic analysis of eight K. pneumoniae NDM (Kp NDM) isolates, recovered in Poland during the years 2016 and 2018 from seven patients with urinary tract infections (UTIs), asymptomatic bacteriuria (ABU), or colonization of the gut. PCR melting profile genotyping indicated a close relationship between the strains derived from 2018, which were not related to the strain isolated in 2016. WGS results were analyzed in relation to international Kp isolates. Clonal and phylogenetic analyses were performed based on multilocus sequence typing (MLST) and single nucleotide polymorphisms (SNPs) of the core genome. The metallo-β-lactamase was assigned to the NDM-1 type and the sequence was identified as ST11. Eleven antimicrobial resistance genes were detected, mostly from plasmid contigs. Unprecedented profiles of plasmid replicons were described with the IncFII/pKPX-1 dominant replicon. In terms of the KL24 and O2v1 capsular antigen profiles, these isolates corresponded to Greek strains. Strains isolated from UTI, ABU, and colonization GI tract patients were not carrying environment-specific virulence genes. Based on the assessment of strain relationships at the genome level and their direction of evolution, the international character of the sublines was demonstrated, with a documented epidemic potential in Poland and Greece. In conclusion, some groups of patients, e.g., renal transplant recipients or those with complicated UTIs, who are frequently hospitalized and undergoing antibiotic therapy, should be monitored not only for the risk of UTI, but also for colonization by Kp NDM strains.", "token_count": 471, "char_count": 1799, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6769, "quality_score": 0.8385, "entities": { "genes": [ "KL24", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:55.277345", "source": { "split": "train_shard_00001", "doc_id": 3496 }, "chunk_id": "train_shard_00001_3496_0", "global_id": 10617 }, { "text": "Genetic Background and Antibiotic Resistance Profiles of K. pneumoniae NDM-1 Strains Isolated from UTI, ABU, and the GI Tract, from One Hospital in Poland, in Relation to Strains Nationally and Worldwide.", "token_count": 66, "char_count": 211, "word_count": 31, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:55.637254", "source": { "split": "train_shard_00001", "doc_id": 3496 }, "chunk_id": "train_shard_00001_3496_1", "global_id": 10618 }, { "text": "Whey containing 4.4% (w/v) lactose was inoculated with Kluyveromyces marxianus MTCC 1389 for carrying out studies related to β-galactosidase production. β-galactosidase activity was found to be maximum after 30 h and further incubation resulted in decline in activity. The maximum cell biomass of 2.54 mg mL(-1) was observed after 36 h of incubation. Lactose concentration dropped drastically to 0.04 % from 4.40% after 36 h of incubation. Out of the four methods tested for extraction of enzyme, SDS - Chlorofom method was found to be best followed by Toluene - Acetone, sonication and homogenization with glass beads in that order. It could be concluded through this study that SDS - Chloroform is cheap and simple method for enzyme extraction from Kluyveromyces cells, which resulted in higher enzyme activity as compared to the activity observed using the remaining extraction methods. The study could also establish that whey could effectively be utilized for β-galactosidase production thus alleviating water pollution problems caused due to its disposal into the water streams.\n\nProduction of β-galactosidase by Kluyveromyces marxianus MTCC 1388 using whey and effect of four different methods of enzyme extraction on β-galactosidase activity.", "token_count": 347, "char_count": 1250, "word_count": 189, "semantic_coherence": 1, "information_density": 0.582, "quality_score": 0.791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:56.214855", "source": { "split": "train_shard_00001", "doc_id": 3497 }, "chunk_id": "train_shard_00001_3497_0", "global_id": 10619 }, { "text": "

Key message

Key genes controlling flowering and interactions of different photoperiod alleles with various environments were identified in a barley MAGIC population. A new candidate gene for vernalisation requirements was also detected. Optimal flowering time has a major impact on grain yield in crop species, including the globally important temperate cereal crop barley (Hordeum vulgare L.). Understanding the genetics of flowering is a key avenue to enhancing yield potential. Although bi-parental populations were used intensively to map genes controlling flowering, their lack of genetic diversity requires additional work to obtain desired gene combinations in the selected lines, especially when the two parental cultivars did not carry the genes. Multi-parent mapping populations, which use a combination of four or eight parental cultivars, have higher genetic and phenotypic diversity and can provide novel genetic combinations that cannot be achieved using bi-parental populations. This study uses a Multi-parent advanced generation intercross (MAGIC) population from four commercial barley cultivars to identify genes controlling flowering time in different environmental conditions. Genome-wide association studies (GWAS) were performed using 5,112 high-quality markers from Diversity Arrays Technology sequencing (DArT-seq), and Kompetitive allele-specific polymerase chain reaction (KASP) genetic markers were developed. Phenotypic data were collected from fifteen different field trials for three consecutive years. Planting was conducted at various sowing times, and plants were grown with/without additional vernalisation and extended photoperiod treatments. This study detected fourteen stable regions associated with flowering time across multiple environments. GWAS combined with pangenome data highlighted the role of CEN gene in flowering and enabled the prediction of different CEN alleles from parental lines. As the founder lines of the multi-parental population are elite germplasm, the favourable alleles identified in this study are directly relevant to breeding, increasing the efficiency of subsequent breeding strategies and offering better grain yield and adaptation to growing conditions.\n\nMulti-locus genome-wide association studies reveal novel alleles for flowering time under vernalisation and extended photoperiod in a barley MAGIC population.", "token_count": 486, "char_count": 2391, "word_count": 319, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:56.865983", "source": { "split": "train_shard_00001", "doc_id": 3498 }, "chunk_id": "train_shard_00001_3498_0", "global_id": 10620 }, { "text": "Anthropogenic perturbations such as water overexploitation introduce novel selective pressures to the natural environments, impacting on the genomic variability of organisms and thus altering the evolutionary trajectory of its populations. Bad agricultural practices and defective policies in Cuatro Cienegas, Coahuila, Mexico, have strongly impacted its water reservoir, pushing entire hydrological systems to the brink of extinction together with their native populations. Here, we studied the effects of continuous water overexploitation on an environmental aquatic lineage of Pseudomonas otitidis , inhabitant to a particularly affected lagoon of an exhaustively studied system in the middle of the desert, over a 13 year period which encompasses three desiccation events. By comparing the genomes of a population sample from 2003 (original state) and 2015 (perturbed state), we analyzed the demographic history and evolutionary response of this bacterial lineage to the perturbation. Through coalescent simulations, we obtained a demographic model of contraction-expansion-contraction which, alongside an increment in mean Tajima’s D and recombination rate, loss of genetic and nucleotidic variation and a single amino acid under positive selection, points the occurrence of an evolutionary rescue event, possibly potentiated by horizontal gene transfer, where the population nearly went extinct during the first desiccation event but sharply recovered in the second and adapted to its new environment. Furthermore, the gain of phosphorylation, DNA recombination and small-molecule metabolism and loss of biosynthetic and regulation genes on the exclusive accessory genome suggest a functional shift to a more generalist scavenger lifestyle in an environment that went from oligotrophic to nutrient-rich.\n\nFast eco-evolutionary changes in bacterial genomes after anthropogenic perturbation", "token_count": 418, "char_count": 1894, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:57.496885", "source": { "split": "train_shard_00001", "doc_id": 3499 }, "chunk_id": "train_shard_00001_3499_0", "global_id": 10621 }, { "text": "Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and the genomic determinants of disease outcomes. Across two wards over 6 months, we selectively cultured C. difficile from patients (n = 384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n = 79), 19 (24%) patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤2 core gene single nucleotide polymorphisms; two of these networks contain strains from different patients. Strain networks were temporally linked (P < 0.0001). To understand the genomic correlates of the disease, we conducted WGS on an additional cohort of C. difficile (n = 102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR, nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes (tcdABER and cdtR) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate that toxigenic and nontoxigenic C. difficile contamination persist in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C", "token_count": 522, "char_count": 1773, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8044, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:38:58.149575", "source": { "split": "train_shard_00001", "doc_id": 3500 }, "chunk_id": "train_shard_00001_3500_0", "global_id": 10622 }, { "text": "difficile colonization and disease.

Importance

Clostridioides difficile infection remains a leading cause of hospital-associated diarrhea, despite increased antibiotic stewardship and transmission prevention strategies. This suggests a changing genomic landscape of C. difficile. Our study provides insight into the nature of prevalent C. difficile strains in a hospital setting and transmission patterns among carriers. Longitudinal sampling of surfaces and patient stool revealed that both toxigenic and nontoxigenic strains of C. difficile clade 1 dominate these two wards. Moreover, quantification of transmission in carriers of these clade 1 isolates underscores the need to revisit infection prevention measures in this patient group. We identified unique genetic signatures associated with virulence in this clade. Our data highlight the complexities of preventing transmission of this pathogen in a hospital setting and the need to investigate the mechanisms of in vivo persistence and virulence of prevalent lineages in the host gut microbiome.\n\nGenomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting.", "token_count": 294, "char_count": 1208, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6026, "quality_score": 0.8013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:58.705926", "source": { "split": "train_shard_00001", "doc_id": 3500 }, "chunk_id": "train_shard_00001_3500_1", "global_id": 10623 }, { "text": "

Background

Legionella pneumophila is the main cause of a severe pneumonic illness known as Legionnaires' disease and is a global public health threat. Whole-genome sequencing (WGS) can be applied to trace environmental origins of L pneumophila infections, providing information to guide appropriate interventions. We aim to explore the evolutionary and epidemiological relationships in a 36-year Scottish L pneumophila reference isolate collection.

Methods

We investigated the genomic epidemiology of Legionnaires' disease over 36 years in Scotland, comparing genome sequences for all clinical L pneumophila isolates (1984-2020) with a sequence dataset of 3211 local and globally representative isolates. We used a stratified clustering approach to capture epidemiological relationships by core genome Multi-locus Sequence Typing, followed by high-resolution phylogenetic analysis of clusters to measure diversity and evolutionary relatedness in context with epidemiological metadata.

Findings

Clustering analysis showed that 111 (57·5 %) of 193 of L pneumophila infections in Scotland were caused by ten endemic lineages with a wide temporal and geographical distribution. Phylogenetic analysis of L pneumophila identified hospital-associated sublineages that had been detected in the hospital environment up to 19 years. Furthermore, 12 (30·0%) of 40 community-associated infections (excluding a single, large outbreak) that occurred over a 13 year period (from 2000 to 2013) were caused by a single widely distributed endemic clone (ST37), consistent with enhanced human pathogenicity. Finally, our analysis revealed clusters linked by national or international travel to distinct geographical regions, indicating several previously unrecognised travel links between closely related isolates (fewer than five single nucleotide polymorphisms) connected by geography.

Interpretation

Our analysis reveals the existence of previously undetected endemic clones of L pneumophila that existed for many years in hospital, community, and travel-associated environments", "token_count": 508, "char_count": 2091, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6654, "quality_score": 0.8327, "entities": { "genes": [ "ST37" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:38:59.720873", "source": { "split": "train_shard_00001", "doc_id": 3501 }, "chunk_id": "train_shard_00001_3501_0", "global_id": 10624 }, { "text": "In light of these findings, we propose that cluster and outbreak definitions should be reconsidered, and propose WGS-based surveillance as a critical public health tool for real-time identification and mitigation of clinically important endemic clones.

Funding

Chief Scientist Office, Biotechnology and Biological Sciences Research Council (UK), Medical Research Council Precision Medicine Doctoral Training Programme, Wellcome Trust, and Medical Research Council (UK).\n\nEpidemiological analysis of Legionnaires' disease in Scotland: a genomic study.", "token_count": 124, "char_count": 557, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7971, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:00.100228", "source": { "split": "train_shard_00001", "doc_id": 3501 }, "chunk_id": "train_shard_00001_3501_1", "global_id": 10625 }, { "text": "Four strains of bifidobacteria (B. bifidum 93, B. infantis ATCC 17930, B. longum ATCC 15707, and B. longum JR) cultivated in MRS broth modified by the addition of cysteine-hydrochloride (0.05%) were serially subcultured in unsupplemented cow milk alone or in combination with Kluyveromyces marxianus var. marxianus 269 under aerobic conditions. In monoculture, bifidobacteria did not multiply after the second subculture. In contrast, in coculture with yeast bifidobacteria reached counts about 8 log CFU/g even during 15 subcultures. In addition, K. marxianus var. marxianus 269 significantly prolonged the survival of bifidobacteria in milk at 4 degrees C. The most susceptible strains (B. longum JR and B. infantis ATCC 17,930) completely lost their viability within 5 and 12 d of storage, respectively, while in coculture with yeasts all bifidobacteria cultures tested survived for at least 40 d. The results could be useful in producing kefir-like fermented milks containing bifidobacteria.\n\nEffect of Kluyveromyces marxianus on the growth and survival of bifidobacteria in milk.", "token_count": 347, "char_count": 1084, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:00.676695", "source": { "split": "train_shard_00001", "doc_id": 3502 }, "chunk_id": "train_shard_00001_3502_0", "global_id": 10626 }, { "text": "

Background

The ST313 sequence type of Salmonella Typhimurium causes invasive non-typhoidal salmonellosis and was thought to be confined to sub-Saharan Africa. Two distinct phylogenetic lineages of African ST313 have been identified.

Methods

We analysed the whole genome sequences of S. Typhimurium isolates from UK patients that were generated following the introduction of routine whole-genome sequencing (WGS) of Salmonella enterica by Public Health England in 2014.

Results

We found that 2.7% (84/3147) of S. Typhimurium from patients in England and Wales were ST313 and were associated with gastrointestinal infection. Phylogenetic analysis revealed novel diversity of ST313 that distinguished UK-linked gastrointestinal isolates from African-associated extra-intestinal isolates. The majority of genome degradation of African ST313 lineage 2 was conserved in the UK-ST313, but the African lineages carried a characteristic prophage and antibiotic resistance gene repertoire. These findings suggest that a strong selection pressure exists for certain horizontally acquired genetic elements in the African setting. One UK-isolated lineage 2 strain that probably originated in Kenya carried a chromosomally located bla CTX-M-15, demonstrating the continual evolution of this sequence type in Africa in response to widespread antibiotic usage.

Conclusions

The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. This study highlights the power of routine WGS by public health agencies to make epidemiologically significant deductions that would be missed by conventional microbiological methods. We speculate that the niche specialisation of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.\n\nPublic health surveillance in the UK revolutionises our understanding of the invasive Salmonella Typhimurium epidemic in Africa.", "token_count": 497, "char_count": 1987, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5885, "quality_score": 0.7942, "entities": { "genes": [ "ST313" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:01.331056", "source": { "split": "train_shard_00001", "doc_id": 3503 }, "chunk_id": "train_shard_00001_3503_0", "global_id": 10627 }, { "text": "A phylogenetic analysis of 17 species belonging to the genus Kluyveromyces and 12 reference and outgroup species was performed using mitochondrial cytochrome-c oxidase II gene sequences. The genus Kluyveromyces appears as a polyphyletic taxon formed by species included within the following four main groups. The Kluyveromyces phaffii group encompasses the species Kluyveromyces blattae, K. phaffii and Kluyveromyces yarrowii. The Kluyveromyces marxianus group is a monophyletic group consisting of the species Kluyveromyces aestuarii, Kluyveromyces dobzhanskii, Kluyveromyces lactis, K. marxianus and Kluyveromyces wickerhamii. The monophyletic Kluyveromyces thermotolerans group is formed by K. thermotolerans, Kluyveromyces waltii and Saccharomyces kluyveri (which appears in the mitochondrial tree as the sister clade of the K. marxianus group). Finally, the Saccharomyces cerevisiae group contains the remaining Kluyveromyces species, as well as the reference Saccharomyces species (sensu lato and sensu stricto) and Candida glabrata (the phylogenetic relationships within this group are unclear according to the bootstrap test). The phylogenetic relationships obtained for this mitochondrial gene are, for the most part, congruent with previous trees based on nuclear rRNA sequences, except for the position of K. yarrowii and the close relationship between the K. marxianus and K. thermotolerans groups. These differences, as well as the existence of these groups, are discussed in the context of previous studies based on phenotypic, genetic and molecular data. Although additional studies are required to decipher the phylogenetic relationships between the genus Kluyveromyces and the closely related genera Saccharomyces, Torulaspora and Zygosaccharomyces, future changes to their taxonomic status should take account of the existence of these four groups of Kluyveromyces species.", "token_count": 498, "char_count": 1891, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5136, "quality_score": 0.7568, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:01.979260", "source": { "split": "train_shard_00001", "doc_id": 3504 }, "chunk_id": "train_shard_00001_3504_0", "global_id": 10628 }, { "text": "Phylogeny of the genus Kluyveromyces inferred from the mitochondrial cytochrome-c oxidase II gene.", "token_count": 31, "char_count": 98, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:02.336121", "source": { "split": "train_shard_00001", "doc_id": 3504 }, "chunk_id": "train_shard_00001_3504_1", "global_id": 10629 }, { "text": "

ABSTRACT

Lactobacillus acidophilus has been extensively applied in plentiful probiotic products and is mostly found in the gastrointestinal tract, vagina, and oral cavity of human and animal, and fermented foods. Although several studies have been performed to investigate the beneficial characteristics and genome function of L. acidophilus , comparative genomic analysis remains scarce. In this study, we collected 74 L. acidophilus genomes from our gut bacterial genome collection and the public database and conducted a comprehensive comparative genomic analysis. The analysis of average nucleotide identity (ANI), phylogenetic, gene distribution of COG and KEGG database, carbohydrates utilization, and secondary metabolites revealed the potential correlation of the genomic diversity and niches adaptation of L. acidophilus from different perspectives. In addition, the pan-genome of L. acidophilus was found to be open, with metabolism, information storage and processing genes mainly distributed in the core genome. Phage- and peptidase-associated genes were found in the genome of the specificity of animal-derived strains, which were related to adaptation of animal gut. SNP analysis showed the differences of the utilization of Vitamin B12 in cellular of L. acidophilus strains from animal gut and others. This work provides new insights for the genomic diversity analysis of Lactobacillus acidophilus and uncovers the ecological adaptation of the specific strains.\n\nComparative Genome Analysis ofLactobacillus acidophilusIsolates from Different Ecological Niches", "token_count": 384, "char_count": 1590, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:02.947752", "source": { "split": "train_shard_00001", "doc_id": 3505 }, "chunk_id": "train_shard_00001_3505_0", "global_id": 10630 }, { "text": "Brucellosis, caused by the bacteria of the genus Brucella, is one of the most neglected common zoonotic diseases globally with a public health significance and a high economic loss among the livestock industry worldwide. Since little is known about the distribution of B. abortus in Egypt, a total of 46 B. abortus isolates recovered between 2012-2020, plus one animal isolate from 2006, were analyzed by examining the whole core genome single nucleotide polymorphism (cgSNP) in comparison to the in silico multilocus variable number of tandem repeat analysis (MLVA). Both cgSNP analysis and MLVA revealed three clusters and one isolate only was distantly related to the others. One cluster identified a rather widely distributed outbreak strain which is repeatedly occurring for at least 16 years with marginal deviations in cgSNP analysis. The other cluster of isolates represents a rather newly introduced outbreak strain. A separate cluster comprised RB51 vaccine related strains, isolated from aborted material. The comparison with MLVA data sets from public databases reveals one near relative from Argentina to the oldest outbreak strain and a related strain from Spain to a newly introduced outbreak strain in Egypt. The distantly related isolate matches with a strain from Portugal in the MLVA profile. Based on cgSNP analysis the oldest outbreak strain clusters with strains from the UK. Compared to the in silico analysis of MLVA, cgSNP analysis using WGS data provides a much higher resolution of genotypes and, when correlated to the associated epidemiological metadata, cgSNP analysis allows the differentiation of outbreaks by defining different outbreak strains. In this respect, MLVA data are error-prone and can lead to incorrect interpretations of outbreak events.\n\nTracking the Distribution of Brucella abortus in Egypt Based on Core Genome SNP Analysis and In Silico MLVA-16.", "token_count": 450, "char_count": 1924, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5621, "quality_score": 0.781, "entities": { "genes": [ "RB51" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:03.587100", "source": { "split": "train_shard_00001", "doc_id": 3506 }, "chunk_id": "train_shard_00001_3506_0", "global_id": 10631 }, { "text": "

Background

The pan-genome of a bacterial species consists of a core and an accessory gene pool. The accessory genome is thought to be an important source of genetic variability in bacterial populations and is gained through lateral gene transfer, allowing subpopulations of bacteria to better adapt to specific niches. Low-cost and high-throughput sequencing platforms have created an exponential increase in genome sequence data and an opportunity to study the pan-genomes of many bacterial species. In this study, we describe a new online pan-genome sequence analysis program, Panseq.

Results

Panseq was used to identify Escherichia coli O157:H7 and E. coli K-12 genomic islands. Within a population of 60 E. coli O157:H7 strains, the existence of 65 accessory genomic regions identified by Panseq analysis was confirmed by PCR. The accessory genome and binary presence/absence data, and core genome and single nucleotide polymorphisms (SNPs) of six L. monocytogenes strains were extracted with Panseq and hierarchically clustered and visualized. The nucleotide core and binary accessory data were also used to construct maximum parsimony (MP) trees, which were compared to the MP tree generated by multi-locus sequence typing (MLST). The topology of the accessory and core trees was identical but differed from the tree produced using seven MLST loci. The Loci Selector module found the most variable and discriminatory combinations of four loci within a 100 loci set among 10 strains in 1 s, compared to the 449 s required to exhaustively search for all possible combinations; it also found the most discriminatory 20 loci from a 96 loci E. coli O157:H7 SNP dataset.

Conclusion

Panseq determines the core and accessory regions among a collection of genomic sequences based on user-defined parameters", "token_count": 464, "char_count": 1825, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:04.262739", "source": { "split": "train_shard_00001", "doc_id": 3507 }, "chunk_id": "train_shard_00001_3507_0", "global_id": 10632 }, { "text": "It readily extracts regions unique to a genome or group of genomes, identifies SNPs within shared core genomic regions, constructs files for use in phylogeny programs based on both the presence/absence of accessory regions and SNPs within core regions and produces a graphical overview of the output. Panseq also includes a loci selector that calculates the most variable and discriminatory loci among sets of accessory loci or core gene SNPs.

Availability

Panseq is freely available online at http://76.70.11.198/panseq. Panseq is written in Perl.\n\nPan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions.", "token_count": 169, "char_count": 676, "word_count": 99, "semantic_coherence": 1, "information_density": 0.6869, "quality_score": 0.8434, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:04.723939", "source": { "split": "train_shard_00001", "doc_id": 3507 }, "chunk_id": "train_shard_00001_3507_1", "global_id": 10633 }, { "text": "The accessory genome as a cradle for adaptive evolution in pathogens.", "token_count": 19, "char_count": 69, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:05.093831", "source": { "split": "train_shard_00001", "doc_id": 3508 }, "chunk_id": "train_shard_00001_3508_0", "global_id": 10634 }, { "text": "Candida kefyr has been increasingly associated with bloodstream infections. This study reports on the identification and antifungal susceptibility pattern of 33 Candida isolates, identified biochemically as C. kefyr. One strain was finally identified as Candida sphaerica (Kluyveromyces lactis) by ITS sequencing. Both species seem to be emerging pathogens and highly susceptible in vitro to currently licensed antifungal compounds.\n\nMolecular identification and susceptibility profile in vitro of the emerging pathogen Candida kefyr.", "token_count": 129, "char_count": 534, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7606, "quality_score": 0.8803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:05.540840", "source": { "split": "train_shard_00001", "doc_id": 3509 }, "chunk_id": "train_shard_00001_3509_0", "global_id": 10635 }, { "text": "It is well known that large genomic variations can greatly impact the phenotype of an organism. Structural Variants (SVs) encompass any genomic variation larger than 30 base pairs, and include changes caused by deletions, inversions, duplications, transversions, and other genome modifications. Due to their size and complex nature, until recently, it has been difficult to truly capture these variations. Recent advances in sequencing technology and computational analyses now permit more extensive studies of SVs in plant genomes. In tomato, advances in sequencing technology have allowed researchers to sequence hundreds of genomes from tomatoes, and tomato relatives. These studies have identified SVs related to fruit size and flavor, as well as plant disease response, resistance/susceptibility, and the ability of plants to detect pathogens (immunity). In this review, we discuss the implications for genomic structural variation in plants with a focus on its role in tomato immunity. We also discuss how advances in sequencing technology have led to new discoveries of SVs in more complex genomes, the current evidence for the role of SVs in biotic and abiotic stress responses, and the outlook for genetic modification of SVs to advance plant breeding objectives.\n\nGenomic structural variation in tomato and its role in plant immunity.", "token_count": 282, "char_count": 1344, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.8069, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:06.130442", "source": { "split": "train_shard_00001", "doc_id": 3510 }, "chunk_id": "train_shard_00001_3510_0", "global_id": 10636 }, { "text": "The mammalian target of rapamycin (mTOR) and the phosphatidylinositol-3-kinase (PI3K)/protein kinase B or Akt (PKB/Akt) signaling pathways are considered as two but somewhat interconnected significant immune pathways which play complex roles in a variety of physiological processes as well as pathological conditions. Aberrant activation of PI3K/Akt/mTOR signaling pathways has been reported to be associated in a wide variety of human diseases. Over the past few years, growing evidence in in vitro and in vivo models suggest that this sophisticated and subtle cascade mediates the orchestration of the immune response in health and disease through exposure to probiotics. An expanding body of literature has highlighted the contribution of probiotics and PI3K/Akt/mTOR signaling pathways in gastrointestinal disorders, metabolic syndrome, skin diseases, allergy, salmonella infection, and aging. However, longitudinal human studies are possibly required to verify more conclusively whether the investigational tools used to understand the regulation of these pathways might provide effective approaches in the prevention and treatment of various disorders. In this Review, we summarize the experimental evidence from recent peer-reviewed studies and provide a brief overview of the causal relationship between the effects of probiotics and their metabolites on the components of PI3K/Akt/mTOR signaling pathways and human disease.\n\nModulation of the PI3K/Akt/mTOR signaling pathway by probiotics as a fruitful target for orchestrating the immune response.", "token_count": 369, "char_count": 1571, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [ "PI3K" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:06.707585", "source": { "split": "train_shard_00001", "doc_id": 3511 }, "chunk_id": "train_shard_00001_3511_0", "global_id": 10637 }, { "text": "Enzymatic library preparation kits are increasingly used for bacterial whole genome sequencing. While they offer a rapid workflow, the transposases used in the kits are recognized to be somewhat biased. The aim of this study was to optimize and validate a protocol for the Illumina DNA Prep kit (formerly Nextera DNA Flex) for sequencing enteric pathogens and compare its performance against the Nextera XT kit. One hundred forty-three strains of Campylobacter, Escherichia, Listeria, Salmonella, Shigella, and Vibrio were prepared with both methods and sequenced on the Illumina MiSeq using 300 and/or 500 cycle chemistries. Sequences were compared using core genome multilocus sequence typing (cgMLST), 7-gene multilocus sequence typing (MLST), and detection of markers encoding serotype, virulence, and antimicrobial resistance. Sequences for one Escherichia strain were downsampled to determine the minimum coverage required for the analyses. While organism-specific differences were observed, the Prep libraries generated longer average read lengths and less fragmented assemblies compared to the XT libraries. In downstream analysis, the most notable difference between the kits was observed for Escherichia, particularly for the 300 cycle sequences. The O group was not predicted in 32% and 4% of XT sequences when using blast and kmer algorithms, respectively, while the O group was predicted from all Prep sequences regardless of the algorithm. In addition, the ehxA gene was not detected in 6% of XT sequences and 34% were missing one or more of the type III secretion systems and/or plasmid-associated genes, which were detected in the Prep sequences. The coverage downsampling revealed that acceptable assembly quality and allele detection was achieved at 30 × coverage with the Prep libraries, whereas 40-50 × coverage was required for the XT libraries", "token_count": 512, "char_count": 1928, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5971, "quality_score": 0.7986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:07.367344", "source": { "split": "train_shard_00001", "doc_id": 3512 }, "chunk_id": "train_shard_00001_3512_0", "global_id": 10638 }, { "text": "The better performance of the Prep libraries was attributed to more even coverage, particularly in genome regions low in GC content.\n\nSequencing of Enteric Bacteria: Library Preparation Procedure Matters for Accurate Identification and Characterization.", "token_count": 54, "char_count": 253, "word_count": 34, "semantic_coherence": 1, "information_density": 0.9118, "quality_score": 0.9559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:07.723949", "source": { "split": "train_shard_00001", "doc_id": 3512 }, "chunk_id": "train_shard_00001_3512_1", "global_id": 10639 }, { "text": "An extracellular exoinulinase (2,1-beta-D fructan fructanohydrolase, EC 3.2.1.7), which catalyzes the hydrolysis of inulin into fructose and glucose, was purified 23.5-fold by ethanol precipitation, followed by Sephadex G-100 gel permeation from a cell-free extract of Kluyveromyces marxianus YS-1. The partially purified enzyme exhibited considerable activity between pH 5 to 6, with an optimum pH of 5.5, while it remained stable (100%) for 3 h at the optimum temperature of 50 degrees C. Mn2+ and Ca2+ produced a 2.4-fold and 1.2-fold enhancement in enzyme activity, whereas Hg2+ and Ag2+ completely inhibited the inulinase. A preparation of the partially purified enzyme effectively hydrolyzed inulin, sucrose, and raffinose, yet no activity was found with starch, lactose, and maltose. The enzyme preparation was then successfully used to hydrolyze pure inulin and raw inulin from Asparagus racemosus for the preparation of a high-fructose syrup. In a batch system, the exoinulinase hydrolyzed 84.8% of the pure inulin and 86.7% of the raw Asparagus racemosus inulin, where fructose represented 43.6 mg/ml and 41.3 mg/ml, respectively.\n\nPartial purification and characterization of exoinulinase from Kluyveromyces marxianus YS-1 for preparation of high-fructose syrup.", "token_count": 408, "char_count": 1273, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6175, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:08.343059", "source": { "split": "train_shard_00001", "doc_id": 3513 }, "chunk_id": "train_shard_00001_3513_0", "global_id": 10640 }, { "text": "The commercial sources of microbial beta-galactosidases (lactases) include the yeasts species Kluyveromyces marxianus, Kluyveromyces lactis and Candida kefyr which are used to hydrolyse lactose in milk due to their optimum pH. On the other hand, lactases obtained from the moulds Aspergillus niger and Aspergillus oryzae have an acid optimum pH and therefore are used to hydrolyse lactose in whey to obtain whey syrups to be used as raw materials in the food industry. The lactose intolerance problem has led to many studies concerning lactose hydrolysis by means of these microbial enzymes to obtain milk suitable for people with lactose maldigestion and special diets for ill persons, elderly population and intolerant babies due to secondary deficiency of lactose. Most industries obtain hydrolyzed lactose milk with free enzyme; however, there are some developments of immobilized lactase catalysts which are being used mainly in whey.\n\n[Uses of microbial beta-galactosidases to reduce lactose content in milk and dairy products].", "token_count": 278, "char_count": 1034, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:08.905133", "source": { "split": "train_shard_00001", "doc_id": 3514 }, "chunk_id": "train_shard_00001_3514_0", "global_id": 10641 }, { "text": "Lyme disease, initially described as Lyme arthritis, was reported before nucleic-acid based detection technologies were available. The most widely used diagnostic tests for Lyme disease are based on the serologic detection of antibodies produced against antigens derived from a single strain of Borrelia burgdorferi. The poor diagnostic accuracy of serological tests early in the infection process has been noted most recently in the 2018 Report to Congress issued by the U.S. Department of Health and Human Services Tick-Borne Disease Working Group. Clinical Lyme disease may be caused by a diversity of borreliae, including those classified as relapsing fever species, in the United States and in Europe. It is widely accepted that antibiotic treatment of Lyme disease is most successful during this critical early stage of infection. While genomic sequencing is recognized as an irrefutable direct detection method for laboratory diagnosis of Lyme borreliosis, development of a molecular diagnostic tool for all clinical forms of borreliosis is challenging because a \"core genome\" shared by all pathogenic borreliae has not yet been identified. After a diligent search of the GenBank database, we identified two highly conserved segments of DNA sequence among the borrelial 16S rRNA genes. We further developed a pair of Borrelia genus-specific PCR primers for amplification of a segment of borrelial 16S rRNA gene as a \"core genome\" to be used as the template for routine Sanger sequencing-based metagenomic direct detection test. This study presented examples of base-calling DNA sequencing electropherograms routinely generated in a clinical diagnostic laboratory on DNA extracts of human blood specimens and ticks collected from human skin bites and from the environment. Since some of the tick samples tested were collected in Ireland, borrelial species or strains not known to exist in the United States were also detected by analysis of this 16S rRNA \"core genome\". We recommend that hospital laboratories located in Lyme disease endemic areas begin to use a \"core genome\" sequencing test to routinely diagnose spirochetemia caused by various species of borreliae for timely management of patients at the early stage of infection.", "token_count": 512, "char_count": 2254, "word_count": 340, "semantic_coherence": 1, "information_density": 0.5824, "quality_score": 0.7912, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:09.555558", "source": { "split": "train_shard_00001", "doc_id": 3515 }, "chunk_id": "train_shard_00001_3515_0", "global_id": 10642 }, { "text": "Single Core Genome Sequencing for Detection of both Borrelia burgdorferi Sensu Lato and Relapsing Fever Borrelia Species.", "token_count": 44, "char_count": 128, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:09.912556", "source": { "split": "train_shard_00001", "doc_id": 3515 }, "chunk_id": "train_shard_00001_3515_1", "global_id": 10643 }, { "text": "

Background

Understanding pairwise bacterial interactions in the human gut is crucial for deciphering the complex networks of bacterial interactions and their contributions to host health. However, there is a lack of large-scale experiments focusing on bacterial interactions within the human gut microbiome.

Methods

We investigated the pairwise interactions of 113 bacterial strains isolated from healthy Chinese volunteers, selected for their high abundance and functional representation of the human gut microbiome. Using mGAM agar plates, a rich medium designed to maintain community structure, we established the \"PairInteraX\" dataset, which includes 3233 pair combinations of culturable human gut bacteria. This dataset was analyzed to identify interaction patterns and the key factors influencing these patterns.

Results

Our analysis revealed that negative interactions were predominant among the bacteria in the PairInteraX dataset. When combined with in vivo gut metagenome datasets, we noted a diminishing mutualism and an increasing competition as microbial abundances increased; consequently, the maintenance of community diversity requires the participation of various types of interactions, especially the negative interactions. We also identified key factors influencing these interaction patterns including metabolic capacity and motility.

Conclusions

This study provides a comprehensive overview of pairwise bacterial interactions within the human gut microbiome, revealing a dominance of negative interactions. Besides, metabolic capacity and motility were identified as the key factors to influence the pairwise interaction patterns. This large-scale dataset and analysis offer valuable insights for further research on microbial community dynamics and their implications for host health. Video Abstract.\n\nSystematic pairwise co-cultures uncover predominant negative interactions among human gut bacteria.", "token_count": 383, "char_count": 1952, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:10.494513", "source": { "split": "train_shard_00001", "doc_id": 3516 }, "chunk_id": "train_shard_00001_3516_0", "global_id": 10644 }, { "text": "Pseudomonas aeruginosa is a ubiquitous microorganism and an important opportunistic pathogen responsible for a broad spectrum of infections mainly in immunosuppressed and critically ill patients. Molecular investigations traditionally rely on pulsed field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). In this work we propose a core genome multilocus sequence typing (cgMLST) scheme for P. aeruginosa, a methodology that combines traditional MLST principles with whole genome sequencing data. All publicly available complete P. aeruginosa genomes, representing the diversity of this species, were used to establish a cgMLST scheme targeting 2,653 genes. The scheme was then tested using genomes available at contig, chromosome and scaffold levels. The proposed cgMLST scheme for P. aeruginosa typed over 99% (2,314/2,325) of the genomes available for this study considering at least 95% of the cgMLST target genes present. The absence of a certain number gene targets at the threshold considered for both the creation and validation steps due to low genome sequence quality is possibly the main reason for this result. The cgMLST scheme was compared with previously published whole genome single nucleotide polymorphism analysis for the characterization of the population structure of the epidemic clone ST235 and results were highly similar. In order to evaluate the typing resolution of the proposed scheme, collections of isolates belonging to two important STs associated with cystic fibrosis, ST146 and ST274, were typed using this scheme, and ST235 isolates associated with an outbreak were evaluated. Besides confirming the relatedness of all the isolates, earlier determined by MLST, the higher resolution of cgMLST denotes that it may be suitable for surveillance programs, overcoming possible shortcomings of classical MLST. The proposed scheme is publicly available at: https://github.com/BioinformaticsHIAEMolecularMicrobiology/cgMLST-Pseudomonas-aeruginosa.", "token_count": 493, "char_count": 2018, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.8051, "entities": { "genes": [ "ST274", "ST235", "ST146" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:11.149065", "source": { "split": "train_shard_00001", "doc_id": 3517 }, "chunk_id": "train_shard_00001_3517_0", "global_id": 10645 }, { "text": "A Core Genome Multilocus Sequence Typing Scheme for Pseudomonas aeruginosa.", "token_count": 27, "char_count": 82, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:11.503544", "source": { "split": "train_shard_00001", "doc_id": 3517 }, "chunk_id": "train_shard_00001_3517_1", "global_id": 10646 }, { "text": "Rapid low-cost whole-genome sequencing (WGS) is revolutionizing microbiology; however, complementary advances in accessible, reproducible, and rapid analysis techniques are required to realize the potential of these data. Here, investigations of the genus Neisseria illustrated the gene-by-gene conceptual approach to the organization and analysis of WGS data. Using the gene and its link to phenotype as a starting point, the BIGSdb database, which powers the PubMLST databases, enables the assembly of large open-access collections of annotated genomes that provide insight into the evolution of the Neisseria, the epidemiology of meningococcal and gonococcal disease, and mechanisms of Neisseria pathogenicity.\n\nPopulation and Functional Genomics of Neisseria Revealed with Gene-by-Gene Approaches.", "token_count": 196, "char_count": 801, "word_count": 107, "semantic_coherence": 1, "information_density": 0.7103, "quality_score": 0.8551, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:11.950450", "source": { "split": "train_shard_00001", "doc_id": 3518 }, "chunk_id": "train_shard_00001_3518_0", "global_id": 10647 }, { "text": "A method of producing fuel ethanol by whey especially relates to the mixed fermentation of Kluyveromyces marxianus and saccharomyces cerevisiae and a method of producing the fuel ethanol by solidifying fermented whey thereof, which can shorten the fermentation period of the whey and improve the substrate utilization rate. Base on the prior yeast strain, the present invention uses the technical measures of fluid culture, cell solidification, proliferation culture, fermentations (mixed fermentation, mixed solidification fermentation and solidification serial fermentation), etc., to ensure that the period that the yeast uses the whey fermentation to produce the fuel ethanol is shorted to 48 hours the alcohol degree is 5.0 percent (V.V) the substrate utilization rate is 98.2 percent compared with the single Kluyveromyces marxianus fermentation, the fermentation period is shortened by 50 percent and the wine yield is improved by 31.6 percent.\n\nMethod for producing fuel ethanol by yeast hybrid fermentation whey", "token_count": 256, "char_count": 1020, "word_count": 149, "semantic_coherence": 1, "information_density": 0.5235, "quality_score": 0.7617, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:12.496986", "source": { "split": "train_shard_00001", "doc_id": 3519 }, "chunk_id": "train_shard_00001_3519_0", "global_id": 10648 }, { "text": "The spread of multidrug-resistant bacteria from humans or livestock is a critical issue. However, the epidemiology of resistant pathogens across wastewater pathways is poorly understood. Therefore, we performed a detailed comparison of third-generation cephalosporin-resistant Escherichia coli (3GCREC) from wastewater treatment plants (WWTPs) to analyze dissemination pathways. A total of 172 3GCREC isolated from four WWTPs were characterized via whole genome sequencing. Clonal relatedness was determined using multi-locus sequence typing (MLST) and core genome MLST. Resistance genotypes and plasmid replicons were determined. A total of 68 MLST sequence types were observed with 28 closely related clusters. Resistance genes to eight antibiotic classes were detected. In fluoroquinolone-resistant isolates, resistance was associated with three-or-more point mutations in target genes. Typing revealed high genetic diversity with only a few clonal lineages present in all WWTPs. The distribution paths of individual lines could only be traced in exceptional cases with a lack of enrichment of certain lineages. Varying resistance genes and plasmids, as well as fluoroquinolone resistance-associated point mutations in individual isolates, further corroborated the high diversity of 3GCREC in WWTPs. In total, we observed high diversity of 3GCREC inside the tested WWTPs with proof of resistant strains being released into the environment even after treatment processes.\n\nHigh Genetic Diversity in Third-Generation Cephalosporin-Resistant <i>Escherichia coli</i> in Wastewater Systems of Schleswig-Holstein.", "token_count": 417, "char_count": 1629, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:13.123982", "source": { "split": "train_shard_00001", "doc_id": 3520 }, "chunk_id": "train_shard_00001_3520_0", "global_id": 10649 }, { "text": "The invention provides a method for preparing whey nutrient vinegar, which comprises the following steps of: firstly, hydrolyzing whey which has 8 percent of solid content after concentration by using Novozymes Alcalace protease secondly, preparing Kluyveromyces Marxianus yeast and acetobacter freeze-dried strains and thirdly, activating the freeze-dried strains, sequentially applying the activated strains to alcoholic fermentation and acetic fermentation of whey hydrolysis liquid, and performing prebiotic blending and membrane separation refining on fermentation liquor to prepare the whey nutrient vinegar containing whey protein peptide and xylooligosaccharide.\n\nMethod for preparing whey nutrient vinegar", "token_count": 173, "char_count": 714, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:13.578791", "source": { "split": "train_shard_00001", "doc_id": 3521 }, "chunk_id": "train_shard_00001_3521_0", "global_id": 10650 }, { "text": "The hypocholesterolemic effects of Kluyveromyces marxianus YIT 8292 crude cell wall (KM-CW) were examined. In pilot studies, KM-CW tablets were administered to mildly hypercholesterolemic subjects at doses of 8.0, 4.0, 2.0, or 1.0 g/d for 4 weeks. Total cholesterol (TC) and low-density lipoprotein cholesterol (LDL-C) decreased at doses above 2.0 and 4.0 g/d, respectively. Further, we examined the effect of intake of yogurt containing 3.0 or 4.0 g of KM-CW/d for 8 weeks in normal and hypercholesterolemic subjects in a double-blind placebo-controlled study. The intake of either of the KM-CW-containing yogurts was associated with significantly improved TC and LDL-C in hypercholesterolemic subjects, but had no effect on these levels in normal subjects. TC was significantly lower at week 8 in the hypercholesterolemic subjects who ingested yogurt containing 3.0 or 4.0 g of KM-CW than in those who consumed placebo yogurt. Intake of KM-CW might contribute to the prevention of hypercholesterolemia.\n\nEffect of Kluyveromyces marxianus YIT 8292 crude cell wall fraction on serum lipids in normocholesterolemic and mildly hypercholesterolemic subjects.", "token_count": 374, "char_count": 1155, "word_count": 169, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7959, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:14.164308", "source": { "split": "train_shard_00001", "doc_id": 3522 }, "chunk_id": "train_shard_00001_3522_0", "global_id": 10651 }, { "text": "Salmonella enterica serovar Rissen is recognized as one of the most common serotypes in pigs and pig products in many countries and can be transmitted to human through the consumption of contaminated food. To reveal the genetic characteristics of S. Rissen, 39 isolates from human and animal food were subjected to whole-genome sequencing analysis combined with 337 genome sequences downloaded from the NCBI Assembly database. Core genome single nucleotide polymorphism (cgSNP) divided these S. Rissen isolates into two clusters, of which cluster A included 78.3% of American isolates, while cluster B was mainly composed of isolates from China, Asia, and the UK. The 39 S. Rissen isolates located in cluster B were further divided into two subclusters with cluster B-1 of 26 isolates from both humans and food, while cluster B-2 consisted of 13 isolates from animal food, mainly pork. CRISPR typing and cgMLST of the 39 isolates showed perfect correspondence to cgSNP results of their phylogenetic relationship. Virulence factors analysis revealed that ABZJ_0085 and ABZJ_0086 genes presenting in cluster B-2 were lost in cluster B-1. Additionally, antimicrobial resistance gene profiles showed qnrS1, cmlA1, and tet(M) could be detected in cluster B-2 other than cluster B-1. The findings of the divergent difference between cluster B-1 and cluster B-2 demonstrated that S. Rissen was continuously evolved through the pork production chain. In conclusion, pigs are the main reservoir for S. Rissen capable of causing human nontyphoid salmonellosis.\n\nWhole-genome sequencing analysis reveals pig as the main reservoir for persistent evolution of Salmonella enterica serovar Rissen causing human salmonellosis", "token_count": 431, "char_count": 1709, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5703, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:14.789952", "source": { "split": "train_shard_00001", "doc_id": 3523 }, "chunk_id": "train_shard_00001_3523_0", "global_id": 10652 }, { "text": "Most clinical drugs are based on microbial natural products, with compound classes including polyketides (PKS), non-ribosomal peptides (NRPS), fluoroquinones and ribosomally synthesized and post-translationally modified peptides (RiPPs). While variants of biosynthetic gene clusters (BGCs) for known classes of natural products are easy to identify in genome sequences, BGCs for new compound classes escape attention. In particular, evidence is accumulating that for RiPPs, subclasses known thus far may only represent the tip of an iceberg. Here, we present decRiPPter (Data-driven Exploratory Class-independent RiPP TrackER), a RiPP genome mining algorithm aimed at the discovery of novel RiPP classes. DecRiPPter combines a Support Vector Machine (SVM) that identifies candidate RiPP precursors with pan-genomic analyses to identify which of these are encoded within operon-like structures that are part of the accessory genome of a genus. Subsequently, it prioritizes such regions based on the presence of new enzymology and based on patterns of gene cluster and precursor peptide conservation across species. We then applied decRiPPter to mine 1,295 Streptomyces genomes, which led to the identification of 42 new candidate RiPP families that could not be found by existing programs. One of these was studied further and elucidated as a novel subfamily of lanthipeptides, designated Class V. Two previously unidentified modifying enzymes are proposed to create the hallmark lanthionine bridges. Taken together, our work highlights how novel natural product families can be discovered by methods going beyond sequence similarity searches to integrate multiple pathway discovery criteria.

Code and data availability

The source code of DecRiPPter is freely available online at https://github.com/Alexamk/decRiPPter ", "token_count": 443, "char_count": 1826, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6941, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:15.425234", "source": { "split": "train_shard_00001", "doc_id": 3524 }, "chunk_id": "train_shard_00001_3524_0", "global_id": 10653 }, { "text": "Results of the data analysis are available online at http://www.bioinformatics.nl/~medem005/decRiPPter_strict/index.html and http://www.bioinformatics.nl/~medem005/decRiPPter_mild/index.html (for the strict and mild filters, respectively). All training data and code used to generate these, as well as outputs of the data analyses, are available on Zenodo at doi:10.5281/zenodo.3834818 .\n\nIntegration of machine learning and pan-genomics expands the biosynthetic landscape of RiPP natural products", "token_count": 155, "char_count": 497, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:15.859867", "source": { "split": "train_shard_00001", "doc_id": 3524 }, "chunk_id": "train_shard_00001_3524_1", "global_id": 10654 }, { "text": "Non-typhoidal Salmonella enterica is a leading cause of gastrointestinal illnesses in the United States. Among the 2,600 different S. enterica serovars, Infantis has been significantly linked to human illnesses and is frequently recovered from broilers and chicken parts in the U.S. A key virulence determinant in serovar Infantis is the presence of the megaplasmid pESI, conferring multidrug resistance. To further characterize the virulence potential of this serovar, the present study identified the types of plasmids harbored by Infantis strains, recovered from surface waters adjacent to leafy greens farms in California. Sequencing analysis showed that each of the examined 12 Infantis strains had a large plasmid ranging in size from 78 kb to 125 kb. In addition, a second 4-kb plasmid was detected in two strains. Plasmid nucleotide queries did not identify the emerging megaplasmid pESI in the examined Infantis strains; however, the detected plasmids each had similarity to a plasmid sequence already cataloged in the nucleotide databases. Subsequent comparative analyses, based on gene presence or absence, divided the detected plasmids into five distinct clusters, and the phylogram revealed these Infantis plasmids were clustered based either on the plasmid conjugation system, IncI and IncF, or on the presence of plasmid phage genes. Assignment of the putative genes to functional categories revealed that the large plasmids contained genes implicated in cell cycle control and division, replication and recombination and defense mechanisms. Further analysis of the mobilome, including prophages and transposons, demonstrated the presence of genes implicated in the release of the bactericidal peptide microcin in the IncF plasmids and identified a Tn10 transposon conferring tetracycline resistance in one of the IncI1 plasmids. These findings indicated that the plasmids in the environmental S. enterica serovar Infantis strains from surface waters harbored a wide variety of genes associated with adaptation, survivability and antimicrobial resistance.", "token_count": 504, "char_count": 2070, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5633, "quality_score": 0.7817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:16.547938", "source": { "split": "train_shard_00001", "doc_id": 3525 }, "chunk_id": "train_shard_00001_3525_0", "global_id": 10655 }, { "text": "Plasmidome of Salmonella enterica serovar Infantis recovered from surface waters in a major agricultural region for leafy greens in California.", "token_count": 33, "char_count": 143, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:16.930420", "source": { "split": "train_shard_00001", "doc_id": 3525 }, "chunk_id": "train_shard_00001_3525_1", "global_id": 10656 }, { "text": "Salmonella enterica is a leading cause of human gastrointestinal disease worldwide. Given that Salmonella is persistent in aquatic environments, this study examined the prevalence, levels and genotypic diversity of Salmonella isolates recovered from major rivers in an important agricultural region in northwestern Mexico. During a 13-month period, a total of 143 river water samples were collected and subjected to size-exclusion ultrafiltration, followed by enrichment, and selective media for Salmonella isolation and quantitation. The recovered Salmonella isolates were examined by next-generation sequencing for genome characterization. Salmonella prevalence in river water was lower in the winter months (0.65 MPN/100 mL) and significantly higher in the summer months (13.98 MPN/100 mL), and a Poisson regression model indicated a negative effect of pH and salinity and a positive effect of river water temperature (p = 0.00) on Salmonella levels. Molecular subtyping revealed Oranienburg, Anatum and Saintpaul were the most predominant Salmonella serovars. Single nucleotide polymorphism (SNP)-based phylogeny revealed that the detected 27 distinct serovars from river water clustered in two major clades. Multiple nonsynonymous SNPs were detected in stiA, sivH, and ratA, genes required for Salmonella fitness and survival, and these findings identified relevant markers to potentially develop improved methods for characterizing this pathogen.\n\nPrevalence and Genomic Diversity of Salmonella enterica Recovered from River Water in a Major Agricultural Region in Northwestern Mexico.", "token_count": 468, "char_count": 1689, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:17.605257", "source": { "split": "train_shard_00001", "doc_id": 3526 }, "chunk_id": "train_shard_00001_3526_0", "global_id": 10657 }, { "text": "Pseudomonas syringae sensu stricto (phylogroup 2; referred to as P. syringae) consists of an environmentally ubiquitous bacterial population associated with diseases of numerous plant species. Recent studies using multilocus sequence analysis have indicated the clonal expansion of several P. syringae lineages, located in phylogroups 2a and 2b, in association with outbreaks of bacterial spot disease of watermelon, cantaloupe, and squash in the United States. To investigate the evolutionary processes that led to the emergence of these epidemic lineages, we sequenced the genomes of six P. syringae strains that were isolated from cucurbits grown in the United States, Europe, and China over a period of more than a decade, as well as eight strains that were isolated from watermelon and squash grown in six different Florida counties during the 2013 and 2014 seasons. These data were subjected to comparative analyses along with 42 previously sequenced genomes of P. syringae stains collected from diverse plant species and environments available from GenBank. Maximum likelihood reconstruction of the P. syringae core genome revealed the presence of a hybrid phylogenetic group, comprised of cucurbit strains collected in Florida, Italy, Serbia, and France, which emerged through genome-wide homologous recombination between phylogroups 2a and 2b. Functional analysis of the recombinant core genome showed that pathways involved in the ATP-dependent transport and metabolism of amino acids, bacterial motility, and secretion systems were enriched for recombination. A survey of described virulence factors indicated the convergent acquisition of several accessory type 3 secreted effectors (T3SEs) among phylogenetically distinct lineages through integrative and conjugative element and plasmid loci. Finally, pathogenicity assays on watermelon and squash showed qualitative differences in virulence between strains of the same clonal lineage, which correlated with T3SEs acquired through various mechanisms of horizontal gene transfer (HGT)", "token_count": 520, "char_count": 2088, "word_count": 289, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:18.298527", "source": { "split": "train_shard_00001", "doc_id": 3527 }, "chunk_id": "train_shard_00001_3527_0", "global_id": 10658 }, { "text": "This study provides novel insights into the interplay of homologous recombination and HGT toward pathogen emergence and highlights the dynamic nature of P. syringae sensu lato genomes.\n\nInference of Convergent Gene Acquisition Among Pseudomonas syringae Strains Isolated From Watermelon, Cantaloupe, and Squash.", "token_count": 94, "char_count": 325, "word_count": 42, "semantic_coherence": 1, "information_density": 0.881, "quality_score": 0.9405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:18.674104", "source": { "split": "train_shard_00001", "doc_id": 3527 }, "chunk_id": "train_shard_00001_3527_1", "global_id": 10659 }, { "text": "UDP-galactose 4-epimerase from Kluyveromyces fragilis is a homodimer containing one catalytic site and one NAD(+) as cofactor per subunit. One 5'-UMP, a competitive inhibitor, binds per dimer of epimerase as isolated and causes inactivation. Addition of 0.2 mm inhibitor to the enzyme in vitro leads to three sequential steps: first, the inhibitor binds to the unoccupied site; second, the inhibitor bound ex vivo is displaced allosterically; and finally, both sites are occupied by the inhibitor. These reactions have been monitored by kinetic lag in substrate conversion, coenzyme fluorescence, protection against trypsin digestion, and reductive inhibition. The transition profiles indicate the existence of a stable intermediate with one inhibitor-binding site remaining unoccupied. Reductive inhibition of this intermediate reduced the activity to 58% +/- 2%, with modification of one catalytic site. A change of conformation of the epimerase upon binding with substrate or inhibitor was evident from fluorescence emission spectra. The epimerase demonstrated a biphasic Michaelis-Menten dependency. The epimerase devoid of 5'-UMP showed a Michaelis-Menten dependency that can be explained by assuming simultaneous operation of two catalytic sites. A monomeric form of the epimerase was devoid of such regulation. The inhibitory profile of 5'-UMP also suggested negative cooperativity. Incubation of the epimerase with combinations of substrate analogs rendered one of the sites inactive, supporting the presence of two functional and regulated catalytic sites. Dissimilar kinetic patterns of the reconstituted enzyme after treatment with p-chloromercuribenzoate indicated stability of the dimeric enzyme against fast association-dissociation, which could otherwise generate multiple forms of the enzyme with functional heterogeneity.\n\nUDP-galactose 4-epimerase from Kluyveromyces fragilis--catalytic sites of the homodimeric enzyme are functional and regulated.", "token_count": 498, "char_count": 1966, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:19.332133", "source": { "split": "train_shard_00001", "doc_id": 3528 }, "chunk_id": "train_shard_00001_3528_0", "global_id": 10660 }, { "text": "BACKGROUND Lactobacillus johnsonii is a probiotic bacterium commonly found in the gastrointestinal tracts of humans and other animals. It is non-pathogenic and plays a crucial role in maintaining gut health. L. johnsonii is often associated with beneficial effects on the host immune system and digestion.         However, reports of L. johnsonii infections are rare, and their clinical characteristics remain poorly understood. This article reports a case of L. johnsonii isolated from a patient's blood - the first such case documented in Thailand. Whole-genome sequencing (WGS) was performed on the isolate (LJ-PSU-blood) to investigate its genomic characteristics. CASE REPORT A 25-year-old Thai woman with a large abdominal mass was diagnosed with diffuse large B-cell lymphoma, and she was started on rituximab-cyclophosphamide, hydroxydaunorubicin, oncovin, and prednisolone chemotherapy. During her first rituximab infusion, she developed a fever, tachypnea, and tachycardia. Her blood cultures revealed an organism after 1 day. L. johnsonii was initially identified and subjected to WGS, and the sequence data were analyzed using bioinformatics tools. The findings demonstrated that the LJ-PSU-blood isolate possessed antibiotic resistance and virulence-associated genes. In addition, this isolate harbored bacteriocin-encoding genes and integrated bacteriophage sequences. Our genome was compared with 21 published genomes from various countries, hosts, and isolation sources. They were grouped into 3 monophyletic clades based on single-nucleotide polymorphism distances. CONCLUSIONS This case report describes the characteristics of L. johnsonii isolated from the blood of a Thai patient. Clinical and WGS data highlight important public health concerns associated with L. johnsonii infections.\n\nWhole-Genome Sequencing of Blood-Isolated Lactobacillus johnsonii in Thailand: Clinical Implications and Public Health Relevance.", "token_count": 503, "char_count": 1937, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:19.981574", "source": { "split": "train_shard_00001", "doc_id": 3529 }, "chunk_id": "train_shard_00001_3529_0", "global_id": 10661 }, { "text": "Understanding the structure of a bacterial population is essential in order to understand bacterial evolution. Estimating the core genome (those genes common to all, or nearly all, strains of a species) is a key component of such analyses. The size and composition of the core genome varies by dataset, but we hypothesized that the variation between different collections of the same bacterial species would be minimal. To investigate this, we analyzed the genome sequences of 3,118 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (United States), and Maela (Thailand). The analyses revealed a \"supercore\" genome (genes shared by all 3,118 pneumococci) of 558 genes, although an additional 354 core genes were shared by pneumococci from Reykjavik, Southampton, and Boston. Overall, the size and composition of the core and pan-genomes among pneumococci recovered in Reykjavik, Southampton, and Boston were similar. Maela pneumococci were distinctly different in that they had a smaller core genome and larger pan-genome. The pan-genome of Maela pneumococci contained several >25 Kb sequence regions (flanked by pneumococcal genes) that were homologous to genomic regions found in other bacterial species. Overall, our work revealed that some subsets of the global pneumococcal population are highly heterogeneous, and our hypothesis was rejected. This is an important finding in terms of understanding genetic variation among pneumococci and is also an essential point of consideration before generalizing the findings from a single dataset to the wider pneumococcal population.\n\nGenomic Analyses of >3,100 Nasopharyngeal Pneumococci Revealed Significant Differences Between Pneumococci Recovered in Four Different Geographical Regions.", "token_count": 447, "char_count": 1799, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5547, "quality_score": 0.7773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:20.616087", "source": { "split": "train_shard_00001", "doc_id": 3530 }, "chunk_id": "train_shard_00001_3530_0", "global_id": 10662 }, { "text": "Shared bikes as a public transport provide convenience for short-distance travel. Whilst they also act as a potential vector for antimicrobial resistant (AR) bacteria and antimicrobial resistance genes (ARGs). However, the understanding of the whole genome sequence of AR strains and ARGs-carrying plasmids collected from shared bikes is still lacking. Here, we used the HiSeq platform to sequence and analyze 24 Escherichia coli isolated from shared bikes around Metro Stations in Beijing. The isolates from shared bikes showed 14 STs and various genotypes. Two blaNDM-5 and blaCTX-M-199-producing ST167 E. coli have 16 resistance genes, four plasmid types and show >95% of similarities in core genomes compared with the ST167 E. coli strains from different origins. The blaNDM-5- or blaCTX-M-199-carrying plasmids sequencing by Nanopore were compared to plasmids with blaNDM-5- or blaCTX-M-199 originated from humans and animals. These two ST167 E. coli show high similarities in core genomes and the plasmid profiles with strains from hospital inpatients and farm animals. Our study indicated that ST167 E. coli is retained in diverse environments and carried with various plasmids. The analysis of strains such as ST167 can provide useful information for preventing or controlling the spread of AR bacteria between animals, humans and environments.\n\nCharacterization of blaNDM-5-and blaCTX-M-199-Producing ST167 Escherichia coli Isolated from Shared Bikes.", "token_count": 432, "char_count": 1503, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": { "genes": [ "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:21.251845", "source": { "split": "train_shard_00001", "doc_id": 3531 }, "chunk_id": "train_shard_00001_3531_0", "global_id": 10663 }, { "text": "Serovars of the genus Salmonella primarily evolved as gastrointestinal pathogens in a wide range of hosts. Some serotypes later evolved further, adopting a more invasive lifestyle in a narrower host range associated with systemic infections. A system-level knowledge of these pathogens could identify the complex adaptations associated with the evolution of serovars with distinct pathogenicity, host range, and risk to human health. This promises to aid the design of interventions and serve as a knowledge base in the Salmonella research community. Here, we present SalmoNet2, a major update to SalmoNet1, the first multilayered interaction resource for Salmonella strains, containing protein-protein, transcriptional regulatory, and enzyme-enzyme interactions. The new version extends the number of Salmonella networks from 11 to 20. We now include a strain from the second species in the Salmonella genus, a strain from the Salmonella enterica subspecies arizonae and additional strains of importance from the subspecies enterica, including S. Typhimurium strain D23580, an epidemic multidrug-resistant strain associated with invasive nontyphoidal salmonellosis (iNTS). The database now uses strain specific metabolic models instead of a generalized model to highlight differences between strains. The update has increased the coverage of high-quality protein-protein interactions, and enhanced interoperability with other computational resources by adopting standardized formats. The resource website has been updated with tutorials to help researchers analyze their Salmonella data using molecular interaction networks from SalmoNet2. SalmoNet2 is accessible at http://salmonet.org/. IMPORTANCE Multilayered network databases collate interaction information from multiple sources, and are powerful both as a knowledge base and subject of analysis. Here, we present SalmoNet2, an integrated network resource containing protein-protein, transcriptional regulatory, and metabolic interactions for 20 Salmonella strains", "token_count": 467, "char_count": 2042, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6022, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:21.895458", "source": { "split": "train_shard_00001", "doc_id": 3532 }, "chunk_id": "train_shard_00001_3532_0", "global_id": 10664 }, { "text": "Key improvements to the update include expanding the number of strains, strain-specific metabolic networks, an increase in high-quality protein-protein interactions, community standard computational formats to help interoperability, and online tutorials to help users analyze their data using SalmoNet2.\n\nMultilayered Networks of SalmoNet2 Enable Strain Comparisons of the Salmonella Genus on a Molecular Level.", "token_count": 92, "char_count": 411, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8679, "quality_score": 0.934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:22.268588", "source": { "split": "train_shard_00001", "doc_id": 3532 }, "chunk_id": "train_shard_00001_3532_1", "global_id": 10665 }, { "text": "In an investigation of the changes in the microflora along the pathway: kefir grains (A)-->kefir made from kefir grains (B)-->kefir made from kefir as inoculum (C), the following species of lactic acid bacteria (83-90%) of the microbial count in the grains) were identified: Lactococcus lactis subsp. lactis, Streptococcus thermophilus, Lactobacillus delbrueckii subsp. bulgaricus, Lactobacillus helveticus, Lactobacillus casei subsp. pseudoplantarum and Lactobacillus brevis. Yeasts (10-17%) identified were Kluyveromyces marxianus var. lactis, Saccharomyces cerevisiae, Candida inconspicua and Candida maris. In the microbial population of kefir grains and kefir made from them the homofermentative lactic streptococci (52-65% and 79-86%, respectively) predominated. Within the group of lactobacilli, the homofermentative thermophilic species L. delbrueckii subsp. bulgaricus and L. helveticus (70-87% of the isolated bacilli) predominated. Along the pathway A-->B-->C, the streptococcal proportion in the total kefir microflora increased by 26-30% whereas the lactobacilli decreased by 13-23%. K. marxianus var. lactis was permanently present in kefir grains and kefirs, whereas the dominant lactose-negative yeast in the total yeast flora of the kefir grains dramatically decreased in kefir C.\n\nLactic acid bacteria and yeasts in kefir grains and kefir made from them.", "token_count": 456, "char_count": 1372, "word_count": 185, "semantic_coherence": 1, "information_density": 0.5189, "quality_score": 0.7595, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:22.907607", "source": { "split": "train_shard_00001", "doc_id": 3533 }, "chunk_id": "train_shard_00001_3533_0", "global_id": 10666 }, { "text": "Staphylococcus saprophyticus is a Gram-positive coccus responsible for the occurrence of cystitis in sexually active, young females. While effective antibiotics against this organism exist, resistant strains are on the rise. Therefore, prevention via vaccines appears to be a viable solution to address this problem. In comparison to traditional techniques of vaccine design, computationally aided vaccine development demonstrates marked specificity, efficiency, stability, and safety. In the present study, a novel, multi-epitope vaccine construct was developed against S. saprophyticus by targeting fully sequenced proteomes of its five different strains, which were examined using a pangenome and subtractive proteomic strategy to characterize prospective vaccination targets. The three immunogenic vaccine targets which were utilized to map the probable immune epitopes were verified by annotating the entire proteome. The predicted epitopes were further screened on the basis of antigenicity, allergenicity, water solubility, toxicity, virulence, and binding affinity towards the DRB*0101 allele, resulting in 11 potential epitopes, i.e., DLKKQKEKL, NKDLKKQKE, QDKLKDKSD, NVMDNKDLE, TSGTPDSQA, NANSDGSSS, GSDSSSSNN, DSSSSNNDS, DSSSSDRNN, SSSDRNNGD, and SSDDKSKDS. All these epitopes have the efficacy to cover 99.74% of populations globally. Finally, shortlisted epitopes were joined together with linkers and three different adjuvants to find the most stable and immunogenic vaccine construct. The top-ranked vaccine construct was further scrutinized on the basis of its physicochemical characterization and immunological profile. The non-allergenic and antigenic features of modeled vaccine constructs were initially validated and then subjected to docking with immune receptor major histocompatibility complex I and II (MHC-I and II), resulting in strong contact. In silico cloning validations yielded a codon adaptation index (CAI) value of 1 and an ideal percentage of GC contents (46.717%), indicating a putative expression of the vaccine in E", "token_count": 524, "char_count": 2054, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8466, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:23.568312", "source": { "split": "train_shard_00001", "doc_id": 3534 }, "chunk_id": "train_shard_00001_3534_0", "global_id": 10667 }, { "text": "coli. Furthermore, immune simulation demonstrated that, after injecting the proposed MEVC, powerful antibodies were produced, resulting in the sharpest peaks of IgM + IgG formation (>11,500) within 5 to 15 days. Experimental testing against S. saprophyticus can evaluate the safety and efficacy of these prophylactic vaccination designs.\n\nDesign of Multi-Epitope Vaccine for Staphylococcus saprophyticus: Pan-Genome and Reverse Vaccinology Approach.", "token_count": 132, "char_count": 456, "word_count": 59, "semantic_coherence": 1, "information_density": 0.9153, "quality_score": 0.9576, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:23.993303", "source": { "split": "train_shard_00001", "doc_id": 3534 }, "chunk_id": "train_shard_00001_3534_1", "global_id": 10668 }, { "text": "We tested a novel colorimetric toxicity test, based on inhibition of beta-galactosidase activity in the yeast Kluyveromyces marxianus, for sensitivity to a range of mycotoxins. A variety of trichothecene mycotoxins could be detected. The order of toxicity established with this bioassay was verrucarin A > roridin A > T-2 toxin > diacetoxyscirpenol > HT-2 toxin > acetyl T-2 toxin > neosolaniol > fusarenon X > T-2 triol > scirpentriol > nivalenol > deoxynivalenol > T-2 tetraol. The sensitivity of detection was high, with the most potent trichothecene tested, verrucarin A, having a 50% effective concentration (concentration of toxin causing 50% inhibition) of 2 ng/ml. Other mycotoxins (cyclopiazonic acid, fumonisin B1, ochratoxin A, patulin, sterigmatocystin, tenuazonic acid, and zearalenone) could not be detected at up to 10 micrograms/ml, nor could aflatoxins B1 and M1 be detected at concentrations up to 25 micrograms/ml. This test should be useful for trichothecene detection and for studies of relevant interactions-both between trichothecenes themselves and between trichothecenes and other food constituents.\n\nA colorimetric technique for detecting trichothecenes and assessing relative potencies.", "token_count": 378, "char_count": 1213, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6057, "quality_score": 0.8029, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:24.583013", "source": { "split": "train_shard_00001", "doc_id": 3535 }, "chunk_id": "train_shard_00001_3535_0", "global_id": 10669 }, { "text": "Shrimp farming is one of the fastest-growing food production sectors but disease related mortality remains a limitation to industry expansion. Bacterial species belonging to the Harveyi clade, such as Vibrio harveyi and Vibrio parahaemolyticus, have long been implicated as agents of disease in shrimp aquaculture but traditional methods cannot accurately differentiate these species. Following a vibriosis outbreak in Pacific white shrimp, Penaeus (litopenaeus) vannamei, we hypothesized that infection promoted the co-occurrence of multiple Harveyi clade species. The shrimp were reared in a zero-exchange raceway using biofloc technology and presumptive Vibrio species were isolated from the hepatopancreases of moribund shrimp by culture on a Vibrio-selective agar. Isolates were identified and characterized by PCR-based genotyping and whole-genome sequencing. A phylogenetic tree based on a 43-genome pangenome analysis revealed the presence of five known shrimp pathogens: Photobacterium damselae, Vibrio alginolyticus, V. harveyi, V. parahaemolyticus, Vibrio rotiferianus, and a potentially novel Vibrio species (Vibrio sp. Hep-1b-8). Multilocus sequence typing revealed that P. damselae and V. parahaemolyticus isolates exhibited novel allelic profiles, although the V. parahaemolyticus isolates were closely related to strains isolated from Southeastern Asia. Further, a novel comparative analysis of 23 type VI secretion systems revealed three phylogenetically distinct systems, which suggests that co-occurring bacteria possess diverse mechanisms for interspecies competition. These results highlight whole-genome sequencing as an invaluable tool for identifying and characterizing co-occurring, infection-associated bacteria at the species, strain and molecular level.\n\nGenomic identification and characterization of co-occurring Harveyi clade species following a vibriosis outbreak in Pacific white shrimp, Penaeus (litopenaeus) vannamei", "token_count": 499, "char_count": 1951, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:25.235707", "source": { "split": "train_shard_00001", "doc_id": 3536 }, "chunk_id": "train_shard_00001_3536_0", "global_id": 10670 }, { "text": "

Background

Large scale metagenome assembly and binning to generate metagenome-assembled genomes (MAGs) has become possible in the past five years. As a result, millions of MAGs have been produced and increasingly included in pan-genomics workflow. However, pan-genome analyses of MAGs may suffer from the known issues with MAGs: fragmentation, incompleteness, and contamination, due to mis-assembly and mis-binning. Here, we conducted a critical assessment of including MAGs in pan-genome analysis, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs.

Results

We found that incompleteness led to more significant core gene loss than fragmentation. Contamination had little effect on core genome size but had major influence on accessory genomes. The core gene loss remained when using different pan-genome analysis tools and when using a mixture of MAGs and complete genomes. Importantly, the core gene loss was partially alleviated by lowering the core gene threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The core gene loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees.

Conclusions

We conclude that lowering core gene threshold and predicting genes in metagenome mode (as Anvi’o does with Prodigal) are necessary in pan-genome analysis of MAGs to alleviate the accuracy loss. Better quality control of MAGs and development of new pan-genome analysis tools specifically designed for MAGs are needed in future studies.\n\nCritical assessment of pan-genomics of metagenome-assembled genomes", "token_count": 410, "char_count": 1689, "word_count": 239, "semantic_coherence": 1, "information_density": 0.59, "quality_score": 0.795, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:25.858375", "source": { "split": "train_shard_00001", "doc_id": 3537 }, "chunk_id": "train_shard_00001_3537_0", "global_id": 10671 }, { "text": "Old yellow enzymes (OYEs, EC 1.6.99.1) are flavin-dependent oxidoreductases that catalyze the stereoselective trans-hydrogenation of the double bond, representing a promising alternative to metal-based catalysis. Bioconversion of ketoisophorone (KIP) by 28 non-conventional yeasts belonging to 16 different species was investigated. Growing cells of most of the strains reduced KIP via OYE and showed high stereoselectivity, producing R-levodione as major product. Competition by carbonyl reductase (CR) activity was observed in several strains. The best performing yeasts belong to Candida castellii, Kazachstania spencerorum and Kluyveromyces marxianus exhibited yields of levodione ≥77% up to 95% e.e., and. Candida freyschussii, the sole strain lacking the OYE gene, reduced KIP only to unsaturated alcohols via CR. Nine unedited OYE genes were cloned, sequenced, and heterologously expressed in Saccharomyces cerevisiae BY4741ΔOye2, a mutant that showed negligible OYE and CR activities. Compared with the corresponding wild-type yeasts, growing cells of the recombinant strains bioconverted KIP with improved yields of OYE products, minor competition by CR activity, and lower enantioselectivity. In particular, resting cells of recombinant S. cerevisae presented the best performance in KIP bioconversion. Based on the results herein reported, selected strains of non-conventional yeasts and novel OYE genes can be profitably used as innovative biocatalysts in asymmetric reductions.\n\nEnoate reductases from non conventional yeasts: bioconversion, cloning, and functional expression in Saccharomyces cerevisiae.", "token_count": 442, "char_count": 1618, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:26.496092", "source": { "split": "train_shard_00001", "doc_id": 3538 }, "chunk_id": "train_shard_00001_3538_0", "global_id": 10672 }, { "text": "Candidiasis is the most common fungal infection in immunocompromised patients who are at greater risk for developing disseminated disease. Renal transplant recipients often are administered immunosuppressants and therefore are at an increased risk for developing disseminated candidal infections. Disseminated candidiasis generally does not present with cutaneous lesions, but when present, lesions usually are generalized or limited to the trunk and limbs. We describe the case of an immunosuppressed renal transplant recipient who developed a disseminated Candida kefyr infection and presented with oral mucosal lesions and cutaneous lesions limited to the left lower extremity. The lesions were localized due to a thrombus that was subsequently found in the patient's left external iliac artery.\n\nUnilateral presentation of disseminated candidiasis: case report and review of the literature.", "token_count": 200, "char_count": 894, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:26.947920", "source": { "split": "train_shard_00001", "doc_id": 3539 }, "chunk_id": "train_shard_00001_3539_0", "global_id": 10673 }, { "text": "The phenotype-genotype landscape is a projection coming from detailed phenotypic and genotypic data under environmental pressure. Although phenome of microbes or microbial consortia mirrors the functional expression of a genome or set of genomes, metabolic traits rely on the phenotype. Phenomics has the potential to revolution functional genomics. In this review, we discuss why and how phenomics was developed. We described how phenomics may extend our understanding of the assembly of microbial consortia and their functionality, and then we outlined the novel applications within the study of phenomes using Omnilog platform together with a revision of its current application to study lactic acid bacteria (LAB) metabolic traits during food processing. LAB were proposed as a suitable model system to analyze and discuss the implementation and exploitation of this emerging omics approach. We introduced the 'phenotype switching', as a new phenotype microarray approach to get insights in bacterial physiology. An overview of methodologies and tools to manage and analyze the generated data was provided. Finally, pro and cons of pipelines developed so far, including the most innovative ones were critically analyzed. We propose an R pipeline, recently deposited, which allows to automatically analyze Omnilog data integrating the latest approaches and implementing the new concepts described here.\n\nMicrobial high throughput phenomics: The potential of an irreplaceable omics.", "token_count": 306, "char_count": 1484, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:27.518129", "source": { "split": "train_shard_00001", "doc_id": 3540 }, "chunk_id": "train_shard_00001_3540_0", "global_id": 10674 }, { "text": "

Background

Wildlife zoos provide the opportunity for children and adults to interact with animals, However, it's unknown that the risk of contact with animals, which carried zoonotic pathogens and antimicrobial resistant bacteria.

Objectives

This study aimed to investigate the prevalence and antimicrobial susceptibility of extended-spectrum β-lactamases Escherichia coli (ESBLs-EC) from a wildlife zoo in China.

Methods

A total of 93 wildlife faecal samples were collected from a wildlife zoo. Agar dilution method was used to determine the resistant phenotype. Whole genomes sequencing and bioinformatic analysis were employed to evaluate the molecular typing and genetic relationships of ESBLs-EC.

Results

A total of 23 CTX-M-positive ESBLs-EC were isolated from swan (n = 14), squirrel monkey (n = 5), black hat hanging monkey (n = 2), gibbon monkey (n = 1) and phoenicopteridae (n = 1) respectively. All ESBLs-EC strains were resistant to cefotaxime, tetracycline, ciprofloxacin and trimethoprim-sulfamethoxazole, but susceptible to colistin, tigecycline, meropenem and amikacin. By screening whole genome sequences, ESBLs-EC strains main carried blaCTX-M-55 (34.8%, 8/23) and blaCTX-M-14 (26.0%, 6/23), following by blaCTX-M-27 (21.7%, 5/23), blaCTX-M-15 (13.0%, 3/23) and blaCTX-M-121 (4.3%, 1/23)", "token_count": 497, "char_count": 1389, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6954, "quality_score": 0.8477, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:28.175261", "source": { "split": "train_shard_00001", "doc_id": 3541 }, "chunk_id": "train_shard_00001_3541_0", "global_id": 10675 }, { "text": "ESBLs-EC strains mainly belonged to phylogroup A (60.9%, 14/23), and ST48, ST746 and ST616 (3 strains respectively, 13.0%) were major ST types. Core genome-based single nucleotide polymorphism (SNP) analysis suggested that strains from the swan, over the phylogenetic tree, have a closer genetic relationship with strains from other animals (black hat hanging monkey, gibbon monkey, phoenicopteridae and squirrel monkey).

Conclusions

CTX-M type ESBLs-EC can transmit between animals in wildlife zoos, which may be a risk of spread to animal keepers, veterinarians and visitors when contact with animals. Our study provides that the importance of hygiene measures to minimise the risk of transmission of ESBLs-EC to visitors in wildlife zoos.\n\nPrevalence and antimicrobial susceptibility of CTX-M-type-producing Escherichia coli from a wildlife zoo in China.", "token_count": 251, "char_count": 864, "word_count": 121, "semantic_coherence": 1, "information_density": 0.719, "quality_score": 0.8595, "entities": { "genes": [ "ST48", "ST616", "ST746" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:28.692910", "source": { "split": "train_shard_00001", "doc_id": 3541 }, "chunk_id": "train_shard_00001_3541_1", "global_id": 10676 }, { "text": "Although irrigation water is frequently assessed for the presence of plant pathogens, large spatial and temporal surveys that provide clues on the diversity and circulation of pathogens are missing. We evaluate the diversity of soft rot Pectobacteriaceae (SRP) of the genera Dickeya and Pectobacterium over 2 years in a temperate, mixed-use watershed. The abundance of isolated strains correlates with the agricultural gradient along the watershed with a positive correlation found with temperature, nitrate, and dissolved organic carbon water concentration. We characterized 582 strains by amplification and sequencing of the gapA gene. Multilocus sequence analysis, performed with three housekeeping genes for 99 strains, and core genome analysis of 38 sequenced strains, confirmed for all the strains but one, the taxonomic assignation obtained with the sole gapA sequence. Pectobacterium spp. (549 isolates) were far more abundant than Dickeya spp. (33 isolates). Dickeya spp. were only observed in the lower part of the river when water temperature was >19°C, and we experimentally confirmed a decreased fitness of several Dickeya spp. at 8°C in river water. D. oryzae dominates the Dickeya spp. and P. versatile and P. aquaticum dominate the Pectobacterium spp., but their repartition along the watershed was different, with P. versatile being the only species regularly recovered all along the watershed. Excepting P. versatile, the Dickeya and Pectobacterium spp. responsible for disease outbreak on crops were less abundant or rarely detected", "token_count": 508, "char_count": 1698, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:29.376062", "source": { "split": "train_shard_00001", "doc_id": 3542 }, "chunk_id": "train_shard_00001_3542_0", "global_id": 10677 }, { "text": "This work sheds light on the various ecological behaviors of different SRP types in stream water and indicates that SRP occupation is geographically structured.\n\nThe Diversity and Abundance of Soft Rot Pectobacteriaceae Along the Durance River Stream in the Southeast of France Revealed by Multiple Seasonal Surveys.", "token_count": 80, "char_count": 323, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:29.791208", "source": { "split": "train_shard_00001", "doc_id": 3542 }, "chunk_id": "train_shard_00001_3542_1", "global_id": 10678 }, { "text": "In spring 2022, an increase in metallo-β-lactamase-producing Pseudomonas aeruginosa (MBL-Pa) infections was detected in a hospital in Upper Austria. To identify the source of infection and to stop further transmissions, an epidemiological outbreak investigation including whole-genome sequencing (WGS)-based typing was conducted. The final case definition included cases admitted to the hospital between 2020 and 2023 with an MBL-Pa in one of the three genomic clusters identified. In addition, the investigation was extended to include historical cases from 2017. Core genome multilocus sequence typing was performed to assess the genetic relatedness between the isolates. Fifty-four clinical P. aeruginosa isolates and eight P. aeruginosa isolates from the hospital environment were obtained. All but nine isolates grouped into one of three genomic clusters (ST235/blaVIM-1, ST111/blaVIM-2, or ST621/blaIMP-13), which were considered to be distinct, prolonged outbreaks involving 47 out of 52 cases. The most likely source of infection for cluster 1 (ST111/blaVIM-2) and cluster 2 (ST235/blaVIM-1) was sinks in the intensive care unit (ICU) washroom. Cluster 3 clone (ST621/blaIMP-13) could have originated in the urology ward in 2020 and then spread to the ICU years later. However, the nosocomial origin of this clone could not be proven. In March 2023, following the implementation of control measures (gowning, patient isolation, screening, and daily disinfection), no further MLB-Pa was detected, and the outbreaks were considered to be over. As ICUs play an important role in the transmission of P", "token_count": 522, "char_count": 1737, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [ "ST621", "ST111", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:30.432260", "source": { "split": "train_shard_00001", "doc_id": 3543 }, "chunk_id": "train_shard_00001_3543_0", "global_id": 10679 }, { "text": "aeruginosa, emphasis should be placed on genomic surveillance, infection prevention, and control in such wards.

Importance

The significance of our work lies in the successful resolution of three prolonged outbreaks of MBL-Pa infections in a hospital in Upper Austria. Through a comprehensive epidemiological investigation coupled with WGS-based typing of P. aeruginosa isolates, the study identified three distinct genomic clusters responsible for prolonged outbreaks involving 47 cases. The investigation pinpointed sinks in the ICU washroom as the likely source of infection for two of the clusters. The study demonstrates the effectiveness of control measures such as hand hygiene, gowning, patient isolation, screening, and disinfection in stopping further transmission and bringing the outbreaks to a close. This underscores the critical role of genomic surveillance and control measures, particularly in high-risk settings like ICUs, in reducing nosocomial transmission of MBL-Pa infections.\n\nThree prolonged outbreaks of metallo-β-lactamase-producing Pseudomonas aeruginosa in an Upper Austrian hospital, 2017-2023.", "token_count": 272, "char_count": 1147, "word_count": 149, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:30.991192", "source": { "split": "train_shard_00001", "doc_id": 3543 }, "chunk_id": "train_shard_00001_3543_1", "global_id": 10680 }, { "text": "The definition of bacterial species is traditionally a taxonomic issue while bacterial populations are identified by population genetics. These assignments are species specific, and depend on the practitioner. Legacy multilocus sequence typing is commonly used to identify sequence types (STs) and clusters (ST Complexes). However, these approaches are not adequate for the millions of genomic sequences from bacterial pathogens that have been generated since 2012. EnteroBase ( http://enterobase.warwick.ac.uk ) automatically clusters core genome MLST allelic profiles into hierarchical clusters (HierCC) after assembling annotated draft genomes from short read sequences. HierCC clusters span core sequence diversity from the species level down to individual transmission chains. Here we evaluate HierCC’s ability to correctly assign 100,000s of genomes to the species/subspecies and population levels for Salmonella, Escherichia, Clostridoides, Yersinia, Vibrio and Streptococcus . HierCC assignments were more consistent with maximum-likelihood super-trees of core SNPs or presence/absence of accessory genes than classical taxonomic assignments or 95% ANI. However, neither HierCC nor ANI were uniformly consistent with classical taxonomy of Streptococcus. HierCC was also consistent with legacy eBGs/ST Complexes in Salmonella or Escherichia and with O serogroups in Salmonella . Thus, EnteroBase HierCC supports the automated identification of and assignment to species/subspecies and populations for multiple genera.\n\nEnteroBase: Hierarchical clustering of 100,000s of bacterial genomes into species/sub-species and populations", "token_count": 391, "char_count": 1635, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6495, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:31.607528", "source": { "split": "train_shard_00001", "doc_id": 3544 }, "chunk_id": "train_shard_00001_3544_0", "global_id": 10681 }, { "text": "The vaginal microbiome plays an important role in human health and species of vaginal bacteria have been associated with reproductive disease. Strain-level variation is also thought to be important, but the diversity, structure and evolutionary history of vaginal strains is not as well characterized. We developed and validated an approach to measure strain variation from metagenomic data based on SNPs within the core genomes for six species of vaginal bacteria: Gardnerella vaginalis, Lactobacillus crispatus, Lactobacillus iners, Lactobacillus jensenii, Lactobacillus gasseri and Atopobium vaginae. Despite inhabiting the same environment, strain diversity and structure varies across species. All species except L. iners are characterized by multiple distinct groups of strains. Even so, strain diversity is lower in the Lactobacillus species, consistent with a more recent colonization of the human vaginal microbiome. Both strain diversity and the frequency of multi-strain samples is related to species-level diversity of the microbiome in which they occur, suggesting similar ecological factors influencing diversity within the vaginal niche. We conclude that the structure of strain-level variation provides both the motivation and means of testing whether strain-level differences contribute to the function and health consequences of the vaginal microbiome.\n\nThe structure and diversity of strain-level variation in vaginal bacteria.", "token_count": 354, "char_count": 1502, "word_count": 200, "semantic_coherence": 1, "information_density": 0.61, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:32.186296", "source": { "split": "train_shard_00001", "doc_id": 3545 }, "chunk_id": "train_shard_00001_3545_0", "global_id": 10682 }, { "text": "Although the beneficial effects of probiotics are likely to be associated with their ability to colonize the gut, little is known about the characteristics of good colonizers. In a systematic analysis of the comparative genomics, we tried to elucidate the genomic contents that account for the distinct host adaptability patterns of Lactobacillus and Bifidobacterium species. The Bifidobacterium species, with species-level phylogenetic structures affected by recombination among strains, broad mucin-foraging activity, and dietary-fibre-degrading ability, represented niche conservatism and tended to be host-adapted. The Lactobacillus species stretched across three lifestyles, namely free-living, nomadic and host-adapted, as characterized by the variations of bacterial occurrence time, guanine-cytosine (GC) content and genome size, evolution event frequency, and the presence of human-adapted bacterial genes. The numbers and activity of host-adapted factors, such as bile salt hydrolase and intestinal tissue-anchored elements, were distinctly distributed among the three lifestyles. The strains of the three lifestyles could be separated with such a collection of colonization-related genomic content (genes, genome size and GC content). Thus, our work provided valuable information for rational selection and gut engraftment prediction of probiotics. Here, we have found many interesting predictive results for bacterial gut fitness, which will be validated in vitro and in vivo.\n\nMining genome traits that determine the different gut colonization potential of Lactobacillus and Bifidobacterium species.", "token_count": 427, "char_count": 1668, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:32.812796", "source": { "split": "train_shard_00001", "doc_id": 3546 }, "chunk_id": "train_shard_00001_3546_0", "global_id": 10683 }, { "text": "A newly isolated strain of Kluyveromyces marxianus YS-1 was used for the production of extra cellular inulinase in a medium containing inulin, meat extract, CaCl2 and sodium dodecyl sulphate (SDS). Fermentation medium pH 6.5, cultivation temperature 30 degrees C and 5% (v/v) inoculum of 12 h-old culture were optimal for enzyme production (30.8 IU/ml) with a fermentation time of 72 h at shake flask level. Raw inulin (2%, w/v) extracted from dahlia tubers by processing at 15 kg/cm2 for 10 min was optimum for bioreactor studies. Maximum enzyme production (55.4 IU/ml) was obtained at an agitation rate of 200 rpm and aeration of 0.75 vvm in a stirred tank reactor with a fermentation time of 60 h.\n\nOptimization of medium and process parameters for the production of inulinase from a newly isolated Kluyveromyces marxianus YS-1.", "token_count": 266, "char_count": 831, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6815, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:33.368625", "source": { "split": "train_shard_00001", "doc_id": 3547 }, "chunk_id": "train_shard_00001_3547_0", "global_id": 10684 }, { "text": "

ABSTRACT

Lactococcus garvieae is an emerging zoonotic pathogen, but there are few reports regarding bovine mastitis. The recent prevalence of L. garvieae poses an increasing disease threat and global public health risk. A total of 39 L. garvieae isolates were obtained from 2899 bovine clinical mastitis milk samples in 6 provinces of China from 2017 to 2021. Five clonal complexes were determined from 32 MLST types of L. garvieae ; ST46 was the predominant sequence type and 13 novel MLST types were identified. All isolates were resistant to chloramphenicol and clindamycin, but susceptible to penicillin, ampicillin, amoxicillin-clavulanic acid, imipenem, ceftiofur, enrofloxacin, and marbofloxacin. Based on genomic analyses, L. garvieae had 6310 genes, including 1015, 3641 and 1654 core, accessory and unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, Glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase and NADH oxidase. Most isolates had lsaD and mdtA AMR genes. Based on COG results, the functions of defense, transcription and replication, recombination and repair were enhanced in unique genes, whereas functions of translation, ribosomal structure and biogenesis were enhanced in core genes. The KEGG functional categories enriched in unique genes included human disease and membrane transport, whereas COG functional categories enriched in core genes included energy metabolism, nucleotide metabolism and translation. No gene was significantly associated with host specificity. In addition, core genome SNPs analysis suggested potential host adaptation of some isolates in several sequence types. Therefore, this study characterized L. garvieae isolated from mastitis and assessed host adaptation of L. garvieae to various hosts", "token_count": 501, "char_count": 1812, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [ "ST46" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:34.028634", "source": { "split": "train_shard_00001", "doc_id": 3548 }, "chunk_id": "train_shard_00001_3548_0", "global_id": 10685 }, { "text": "

IMPORTANCE

This study provides important insights on bovine mastitis key topic pathogen Lactococcus garvieae , which constitutes mastitis concerns. However, comprehensive genomic analyses of L. garvieae from dairy farms have not been performed. This study gives a detailed and comprehensive novel feature in L. garvieae , an important but poorly characterized bacterium, recovered in the past 5 years in 6 Chinese provinces. We documented diverse contributory genetic processes, including predominant sequence type ST46 and 13 novel MLST types. L. garvieae had 6310 genes, including 1015, 3641 and 1654 core, accessory and unique genes. All isolates had virulence genes coding for collagenase, fibronectin-binding protein, Glyceraldehyde-3-phosphate dehydrogenase, superoxide dismutase and NADH oxidase, and resistant to chloramphenicol and clindamycin. Most isolates had lsaD and mdtA antimicrobial resistance genes. No gene was significantly associated with host specificity. This is the first absolute quantification of L. garvieae isolated from mastitis and identified host adaptation of L. garvieae to various hosts.\n\nComparative genomic analyses of Lactococcus garvieae isolated from bovine mastitis in China", "token_count": 334, "char_count": 1230, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7186, "quality_score": 0.8593, "entities": { "genes": [ "ST46" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:34.591075", "source": { "split": "train_shard_00001", "doc_id": 3548 }, "chunk_id": "train_shard_00001_3548_1", "global_id": 10686 }, { "text": "Escherichia coli comprises of diverse strains with a large accessory genome, indicating functional diversity and the ability to adapt to a range of niches. Specific strains would display greatest fitness in niches matching their combination of phenotypic traits. Given this hypothesis, we sought to determine whether E. coli in a peri-urban pond and associated cattle pasture display niche preference. Samples were collected from water, sediment, aquatic plants, water snails associated with the pond as well as bovine feces from cattle in an adjacent pasture. Isolates (120) were obtained after plating on Membrane Lactose Glucuronide Agar (MLGA). We used the uidA and mutS sequences for all isolates to determine phylogeny by maximum likelihood, and population structure through gene flow analysis. PCR was used to allocate isolates to phylogroups and to determine the presence of pathogenicity / virulence genes ( stxI, stxII, eaeA, hlyA , ST and LT). Antimicrobial resistance was determined using a disk diffusion assay for Tetracycline, Gentamicin, Ciprofloxacin, Meropenem, Ceftriaxone, and Azitrhomycin. Our results showed that isolates from water, sediment and water plants were similar by phylogroup distribution, virulence gene distribution and antibiotic resistance while both snail and feces populations were significantly different. Few of the feces isolates were significantly similar to aquatic ones, and most of the snail isolates were also different. Population structure analysis indicated three genetic backgrounds associated with bovine, snail and aquatic environments. Collectively these data support niche preference of E. coli isolates occurring in this ecosystem.\n\nNiche preference ofEscherichia coliin a peri-urban pond ecosystem", "token_count": 432, "char_count": 1761, "word_count": 250, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:35.241477", "source": { "split": "train_shard_00001", "doc_id": 3549 }, "chunk_id": "train_shard_00001_3549_0", "global_id": 10687 }, { "text": "Ethanol fermentation from Jerusalem artichoke tubers by recombinant Saccharomyces cerevisiae strains expressing the inulinase gene (inu) from Kluyveromyces marxianus was investigated. The inu native and pgk promoters were used to drive the expression of the inu gene, and the inulinase was expressed as an extracellular enzyme. All positive clones (confirmed by PCR) were able to express inulinase as measured by enzyme activity in the culture supernatant, among which two clones HI6/6 and HPI6/3 were selected, and their inulinase activity and ethanol fermentation performance were compared with their wild type. The inulinase activities of 86 and 23.8 U/mL were achieved, which were 4.6-fold and 1.5-fold higher than that of the wild type. Furthermore, ethanol fermentation was carried out with the recombinants and medium containing 200 g/L raw Jerusalem artichoke meal, and ethanol concentrations of 55 g/L and 52 g/L were obtained, with ethanol yields of 0.495 and 0.453, respectively, equivalent to 96.9% and 88.6% of the theoretical value.\n\n[Ethanol fermentation from Jerusalem artichoke tubers by a genetically-modified Saccharomyces cerevisiae strain capable of secreting inulinase].", "token_count": 346, "char_count": 1192, "word_count": 173, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [ "HI6", "HPI6" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:35.808479", "source": { "split": "train_shard_00001", "doc_id": 3550 }, "chunk_id": "train_shard_00001_3550_0", "global_id": 10688 }, { "text": "A fundamental requisite for genetic studies is an accurate determination of sequence variation. While human genome sequence diversity is increasingly well characterized, there is a need for efficient ways to utilize this knowledge in sequence analysis. Here we present Graphtyper, a publicly available novel algorithm and software for discovering and genotyping sequence variants. Graphtyper realigns short-read sequence data to a pangenome, a variation-aware graph structure that encodes sequence variation within a population by representing possible haplotypes as graph paths. Our results show that Graphtyper is fast, highly scalable, and provides sensitive and accurate genotype calls. Graphtyper genotyped 89.4 million sequence variants in whole-genomes of 28,075 Icelanders using less than 100,000 CPU days, including detailed genotyping of six human leukocyte antigen (HLA) genes. We show that Graphtyper is a valuable tool in characterizing sequence variation in population-scale sequencing studies.\n\nGraphtyper: Population-scale genotyping using pangenome graphs", "token_count": 255, "char_count": 1072, "word_count": 144, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:36.661017", "source": { "split": "train_shard_00001", "doc_id": 3551 }, "chunk_id": "train_shard_00001_3551_0", "global_id": 10689 }, { "text": "In this work, four nonionic surfactants based on sorbitan monolaurate (Span 20) were synthesized by introducing ethylene oxide gas (n = 20, 40, 60, 80 ethylene oxide units) into Span 20 to give four new surfactants with different hydrophilic-lipophilic balance (HLB), namely, E(20), E(40), E(60), and E(80). The structures of the prepared nonionic surfactants were elucidated using Fourier-transform infrared (FT-IR) and (1)H-nuclear magnetic resonance (NMR) spectroscopy. The surface-tension measurements were recorded. The effects of the prepared nonionic surfactants on the simultaneous saccharification and fermentation (SSF) of microwave/alkali-pretreated rice straw to produce ethanol were investigated. From the obtained data, it was found that the addition of the nonionic surfactants at 2.5 g/L had a positive effect on SSF. The maximum ethanol yield (76 and 55%) was obtained after 72 hr for rice straw using Kluyveromyces marxianus and Saccharomyces cerevisiae, respectively. Also, it was found that the ethanol yield increases with increasing HLB of the prepared nonionic surfactants by increasing ethylene oxide units. The adsorption of nonionic surfactants on lignocelluloses is proposed to be due to hydrophobic and hydrogen bonding interactions between nonionic surfactants and the lignin part in the lignocelulose. It can be concluded that additions of surface-active compounds, such as nonionic surfactants, increase enzymatic conversion of rice straw for bioethanol purposes.\n\nEnhancement of ethanol production by simultaneous saccharification and fermentation (SSF) of rice straw using ethoxylated span 20.", "token_count": 471, "char_count": 1626, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:37.310286", "source": { "split": "train_shard_00001", "doc_id": 3552 }, "chunk_id": "train_shard_00001_3552_0", "global_id": 10690 }, { "text": "Liver cirrhosis is one of the most prevalent chronic liver disorders with high mortality. We aimed to explore changed gut microbiome and urine metabolome in compensatory liver cirrhosis (CLC) patients, thus providing novel diagnostic biomarkers for CLC. Forty fecal samples from healthy volunteers (control: 19) and CLC patients (patient: 21) were undertaken 16S rDNA sequencing. Chromatography-mass spectrometry was performed on 40 urine samples (20 controls and 20 patients). Microbiome and metabolome data were separately analyzed using corresponding bioinformatics approaches. The diagnostic model was constructed using the least absolute shrinkage and selection operator regression. The optimal diagnostic model was determined by five-fold cross-validation. Pearson correlation analysis was applied to clarify the relations among the diagnostic markers. 16S rDNA sequencing analyses showed changed overall alpha diversity and beta diversity in patient samples compared with those of controls. Similarly, we identified 841 changed metabolites. Pathway analysis revealed that the differential metabolites were mainly associated with pathways, such as tryptophan metabolism, purine metabolism, and steroid hormone biosynthesis. A 9-maker diagnostic model for CLC was determined, including 7 microorganisms and 2 metabolites. In this model, there were multiple correlations between microorganisms and metabolites. Subdoligranulum, Agathobacter, norank_f_Eubacterium_coprostanoligenes_group, Butyricicoccus, Lachnospiraceae_UCG_004, and L-2,3-Dihydrodipicolinate were elevated in CLC patients, whereas Blautia, Monoglobus, and 5-Acetamidovalerate were reduced. A novel diagnostic model for CLC was constructed and verified to be reliable, which provides new strategies for the diagnosis and treatment of CLC.\n\nIdentification of Diagnostic Biomarkers for Compensatory Liver Cirrhosis Based on Gut Microbiota and Urine Metabolomics Analyses.", "token_count": 487, "char_count": 1939, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6437, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:37.958255", "source": { "split": "train_shard_00001", "doc_id": 3553 }, "chunk_id": "train_shard_00001_3553_0", "global_id": 10691 }, { "text": "The URA3 gene, coding for orotidine-5'-phosphate decarboxylase, from Kluyveromyces marxianus CBS 6556, was isolated from a genomic DNA library. The K. marxianus URA3 gene encodes a protein of 267 amino acids with a calculated molecular weight of 29.3 kDa. Comparison of the K. marxianus protein with the corresponding enzymes of Saccharomyces cerevisiae and Kluyveromyces lactis showed amino acid sequence identities of 81% and 88%, respectively. Using contour-clamped homogenous electric field gel electrophoresis, the genomic copy was found to be located on chromosome VI. We have used the cloned gene for the construction of a K. marxianus leu2 mutant. This mutant contains no heterologous sequences, which is essential to make it acceptable for application in the food industry.\n\nCloning and sequencing of the URA3 gene of Kluyveromyces marxianus CBS 6556.", "token_count": 253, "char_count": 860, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [ "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:38.448501", "source": { "split": "train_shard_00001", "doc_id": 3554 }, "chunk_id": "train_shard_00001_3554_0", "global_id": 10692 }, { "text": "The gut microbiota evolves rapidly after birth, responding dynamically to environmental factors and playing a key role in short- and long-term health. Lifestyle and rurality have been shown to contribute to differences in the gut microbiome, including Bifidobacterium levels, between infants. We studied the composition, function and variability of the gut microbiomes of 6- to 11-month-old Kenyan infants (n = 105). Shotgun metagenomics showed Bifidobacterium longum to be the dominant species. A pangenomic analysis of B. longum in gut metagenomes revealed a high prevalence of B. longum subsp. infantis (B. infantis) in Kenyan infants (80%), and possible co-existence of this subspecies with B. longum subsp. longum. Stratification of the gut microbiome into community (GMC) types revealed differences in composition and functional features. GMC types with a higher prevalence of B. infantis and abundance of B. breve also had a lower pH and a lower abundance of genes encoding pathogenic features. An analysis of human milk oligosaccharides (HMOs) classified the human milk (HM) samples into four groups defined on the basis of secretor and Lewis polymorphisms revealed a higher prevalence of HM group III (Se+, Le-) (22%) than in most previously studied populations, with an enrichment in 2'-fucosyllactose. Our results show that the gut microbiome of partially breastfed Kenyan infants over the age of six months is enriched in bacteria from the Bifidobacterium community, including B. infantis, and that the high prevalence of a specific HM group may indicate a specific HMO-gut microbiome association. This study sheds light on gut microbiome variation in an understudied population with limited exposure to modern microbiome-altering factors.", "token_count": 523, "char_count": 1849, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5916, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:39.105993", "source": { "split": "train_shard_00001", "doc_id": 3555 }, "chunk_id": "train_shard_00001_3555_0", "global_id": 10693 }, { "text": "Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides.", "token_count": 26, "char_count": 117, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:39.465613", "source": { "split": "train_shard_00001", "doc_id": 3555 }, "chunk_id": "train_shard_00001_3555_1", "global_id": 10694 }, { "text": "We report here a comparative analysis of the growth, acidification capacity, and chemical and microbiologic composition between kefir grains after 20 subcultures in whey at 20, 30, and 37°C and the original kefir grains coming from milk along with a determination of the microbiological composition of the fermented whey as compared with that of traditional fermented milk. When fermentation was carried out repeatedly at 30 or 37°C, kefir grains changed their kefir-like appearance, exhibited reduced growth rates, had a lower diversity of yeasts and water content, and a higher protein-to-polysaccharide ratio compared with the original kefir grains. In contrast, at 20°C kefir grains could remain in whey for prolonged periods without altering their acidification capacity, growth rate, macroscopic appearance or chemical and microbiologic composition-with the only difference being a reduction in certain yeast populations after 20 subcultures in whey. At this incubation temperature, the presence of Lactobacillus kefiranofaciens, Lb. kefir, Lb. parakefir, Lactococcus lactis, Kluyveromyces marxianus, Saccharomyces unisporus, and Sac. cerevisiae was detected in kefir grains and in fermented whey by denaturing-gradient-gel electrophoresis (DGGE). In whey fermented at 20°C the number of lactic-acid bacteria (LAB) was significantly lower (P<0·05) and the number of yeast significantly higher (P<0·05) than in fermented milk. Since the DGGE profiles were similar for both products, at this temperature the microbiologic composition of fermented whey is similar to that of fermented milk. We therefore suggest a temperature of 20°C to preserve kefir grains as whey-fermentation starters.\n\nKefir grains as a starter for whey fermentation at different temperatures: chemical and microbiological characterisation.", "token_count": 498, "char_count": 1826, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5373, "quality_score": 0.7686, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:40.115759", "source": { "split": "train_shard_00001", "doc_id": 3556 }, "chunk_id": "train_shard_00001_3556_0", "global_id": 10695 }, { "text": "Steak tartare is a raw, ready-to-eat meal popular in European countries, the safety of which is often discussed due to the risk of foodborne illness. The aim of this study was to determine the prevalence of Listeria monocytogenes in vacuum-packed steak tartare from retailers in the Czech Republic, characterize the strains obtained by typing methods and to evaluate the efficacy of ListexTM P100 against L. monocytogenes artificially inoculated into steak tartare samples. The prevalence of L. monocytogenes was 55% and 17 isolates belonging mostly to serotype 1/2a were obtained. Altogether 11 sequence types and 11 clonal complexes were assigned based on the whole genome sequencing (WGS) signifying the high diversity of L. monocytogenes isolates obtained. Core genome multi-locus sequence typing (cgMLST) did not confirm an epidemiological connection with human cases of listeriosis. The efficacy of ListexTM P100 treatment at concentrations of 108 and 109 PFU/g on artificially inoculated beef steak tartare samples was not efficient. Based on the results of this study, steak tartare from retailers can be considered as a source of L. monocytogenes that remains a challenge to the food industry.\n\nVacuum-Packed Steak Tartare: Prevalence of Listeria monocytogenes and Evaluation of Efficacy of ListexTM P100.", "token_count": 423, "char_count": 1411, "word_count": 197, "semantic_coherence": 1, "information_density": 0.5787, "quality_score": 0.7893, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:40.756027", "source": { "split": "train_shard_00001", "doc_id": 3557 }, "chunk_id": "train_shard_00001_3557_0", "global_id": 10696 }, { "text": "Group B Streptococcus (GBS) is a commensal of the gastrointestinal and genitourinary tracts, while a prevailing cause of neonatal disease worldwide. Of the various clonal complexes (CCs), CC17 is overrepresented in GBS-infected newborns for reasons that are still largely unknown. Here, we report a comprehensive genomic analysis of 626 CC17 isolates collected worldwide, identifying the genetic traits behind their successful adaptation to humans and the underlying differences between carriage and clinical strains. Comparative analysis with 923 GBS genomes belonging to CC1, CC19, and CC23 revealed that the evolution of CC17 is distinct from that of other human-adapted lineages and recurrently targets functions related to nucleotide and amino acid metabolism, cell adhesion, regulation, and immune evasion. We show that the most distinctive features of disease-specific CC17 isolates were frequent mutations in the virulence-associated CovS and Stk1 kinases, underscoring the crucial role of the entire CovRS regulatory pathway in modulating the pathogenicity of GBS. Importantly, parallel and convergent evolution of major components of the bacterial cell envelope, such as the capsule biosynthesis operon, the pilus, and Rib, reflects adaptation to host immune pressures and should be taken into account in the ongoing development of a GBS vaccine. The presence of recurrent targets of evolution not previously implicated in virulence also opens the way for uncovering new functions involved in host colonization and GBS pathogenesis. IMPORTANCE The incidence of group B Streptococcus (GBS) neonatal disease continues to be a significant cause of concern worldwide. Strains belonging to clonal complex 17 (CC17) are the most frequently responsible for GBS infections in neonates, especially among late-onset disease cases. Therefore, we undertook the largest genomic study of GBS CC17 strains to date to decipher the genetic bases of their remarkable colonization and infection ability", "token_count": 487, "char_count": 2014, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6146, "quality_score": 0.8073, "entities": { "genes": [ "CC19", "CC1", "CC23", "CC17" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:41.443031", "source": { "split": "train_shard_00001", "doc_id": 3558 }, "chunk_id": "train_shard_00001_3558_0", "global_id": 10697 }, { "text": "We show that crucial functions involved in different steps of the colonization or infection process of GBS are distinctly mutated during the adaptation of CC17 to the human host. In particular, our results implicate the CovRS two-component regulator of virulence in the differentiation between carriage- and disease-associated isolates. Not only does this work raise important implications for the ongoing development of a vaccine against GBS but might also drive the discovery of key functions for GBS adaptation and pathogenesis that have been overlooked until now. Author Video: An author video summary of this article is available.\n\nParallel Evolution of Group B Streptococcus Hypervirulent Clonal Complex 17 Unveils New Pathoadaptive Mutations.", "token_count": 172, "char_count": 763, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7909, "quality_score": 0.8955, "entities": { "genes": [ "CC17" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:41.926597", "source": { "split": "train_shard_00001", "doc_id": 3558 }, "chunk_id": "train_shard_00001_3558_1", "global_id": 10698 }, { "text": "The aim of the present work was to evaluate the use of the kefir grains as a starter culture for new cocoa (Theobroma cacao L.) beverages. Fermentation was performed by inoculating kefir grains in cocoa pulp. Flasks containing kefir grains and different substrates were statically incubated at 10 and 25°C for 48 and 72h. The microbiota of Brazilian kefir grains and kefir cocoa beverages was characterized using molecular techniques. Denaturing gradient gel electrophoresis displayed communities included yeasts: Kluyveromyces marxianus, Saccharomyces cerevisiae, Kazachstania unispora, and bacteria: Lactobacillus kefiranofaciens subsp. kefirgranum, Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactobacillus plantarum, Lactobacillus fermentum, and a bacterium related to the genus Acetobacter. A microbial steady structure was detected in the analyzed kefir cocoa beverages and kefir grains. This robustness is determinant for future implementation of cocoa-based kefir beverages. The lactic, acetic, malic, propionic and citric acid contents increased during the 72h of fermentation process in kefir beverages, reaching maximum value of ~5.55gL⁻¹, ~1.0gL⁻¹, ~0.3gL⁻¹, ~1.0gL⁻¹ and ~3.0gL⁻¹ respectively. Oxalic, tartaric, butyric acids and glycerol were detected in similar concentrations. These compounds were found during the 48 and 72h fermentation period at 10 and 25°C in low concentration of ~1.4gL⁻¹. Methanol also was detected in low concentration of ~0.8gL⁻¹", "token_count": 503, "char_count": 1503, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6219, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:42.588348", "source": { "split": "train_shard_00001", "doc_id": 3559 }, "chunk_id": "train_shard_00001_3559_0", "global_id": 10699 }, { "text": "The beverages fermented at 10°C during 48 and 72h produce lower amounts of ethanol ~4.5gL⁻¹ (0.36% v/v). These beverages had the greater acceptance (92% and 100% of the panelist, respectively) based on taste, odor, and appearance of the beverages. The best acceptance may be due to low acidity/alcoholic concentration in the beverages. In this study it was possible to produce alcoholic kefir beverages (ethanol concentration of, ~45.0gL⁻¹ (3.6% v/v)) with cocoa pulp fermentation for a period of 48 and 72h at 25°C. These beverages had acceptance by 80% of the panelist. This study is the first to report the alcoholic kefir beverage production from cocoa. Based on the chemical characteristics and acceptance in the sensory analysis, these results open up perspectives for this innovative application of kefir grains for developing cocoa pulp-based beverages.\n\nNew cocoa pulp-based kefir beverages: Microbiological, chemical composition and sensory analysis", "token_count": 291, "char_count": 967, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:43.143989", "source": { "split": "train_shard_00001", "doc_id": 3559 }, "chunk_id": "train_shard_00001_3559_1", "global_id": 10700 }, { "text": "Bloodstream infection (BSI) caused by Acinetobacter baumannii poses a serious threat to health and is correlated with high mortality in patients with hospital-acquired infections, so the molecular epidemiology and antimicrobial resistance characteristics of this pathogen urgently need to be explored. A. baumannii isolates from BSI patients were collected in three tertiary hospitals in northwest China from 2009 to 2018. Antimicrobial susceptibility testing was used to determine the MICs of the A. baumannii isolates. Whole-genome sequencing based on the Illumina platform was performed for molecular epidemiological analyses and acquired resistance gene screening. The efflux pump phenotype was detected by examining the influence of an efflux pump inhibitor. The expression of efflux pump genes was evaluated by RT-PCR. In total, 47 A. baumannii isolates causing BSI were collected and they presented multidrug resistance, including resistance to carbapenems. Clone complex (CC) 92 was the most prevalent with 30 isolates, among which a cluster was observed in the phylogenetic tree based on the core genome multi-locus sequence type, indicating the dissemination of a dominant clone. BSI-related A. baumannii isolates normally harbour multiple resistance determinants, of which oxacillinase genes are most common. Except for the intrinsic bla OXA-51 family, there are some carbapenem-resistant determinants in these A. baumannii isolates, including bla OXA-23, which is encoded within the Tn2006, Tn2008 or Tn2009 transposon structures and bla OXA-72", "token_count": 500, "char_count": 1673, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6425, "quality_score": 0.8213, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:43.808328", "source": { "split": "train_shard_00001", "doc_id": 3560 }, "chunk_id": "train_shard_00001_3560_0", "global_id": 10701 }, { "text": "The transfer of bla OXA-72 was suggested by XerC/D site-specific recombination. The AdeABC efflux pump system contributed to carbapenem resistance in A. baumannii isolates, as evidenced by the high expression of some of its encoding genes. Both the clone dissemination and carbapenem resistance mediated by oxacillinase or efflux pumps suggest an effective strategy for hospital infection control.\n\nMolecular epidemiology and carbapenem resistance characteristics of Acinetobacter baumannii causing bloodstream infection from 2009 to 2018 in northwest China.", "token_count": 172, "char_count": 590, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:44.249214", "source": { "split": "train_shard_00001", "doc_id": 3560 }, "chunk_id": "train_shard_00001_3560_1", "global_id": 10702 }, { "text": "We report here the draft genome sequence of a Listeria monocytogenes strain, core genome multilocus sequence typing (cgMLST) complex type 2521 (CT2521), isolated from ready-to-eat meat sausage related to a protracted and supraregional listeriosis outbreak (Sigma1) in Germany from 2014 to 2019.\n\nDraft Genome Sequence of a Listeria monocytogenes Isolate of Core Genome Multilocus Sequence Typing Complex Type 2521 from Ready-to-Eat Meat Sausage Related to an Outbreak (Sigma1) in Germany.", "token_count": 163, "char_count": 495, "word_count": 70, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "CT2521" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:44.688346", "source": { "split": "train_shard_00001", "doc_id": 3561 }, "chunk_id": "train_shard_00001_3561_0", "global_id": 10703 }, { "text": "Lactic acid bacteria (LAB) are indigenous microorganisms that have been involved in food fermentations throughout history to preserve food and also to give special characteristics to them. The traditional fermented foods that are still being elaborated in indigenous populations around the world are a potential source of LAB with important biotechnological properties and/or beneficial to health. In a previous work, LAB biodiversity associated with chicha, a traditional maize-based fermented beverage from Northwestern Argentina, was studied, both by culture dependent and independent methods. From that study, 392 isolates were recovered, mostly members of Lactobacillus and Leuconostoc. Biotechnological characterization of representative isolates led to the selection of five strains belonging to the species Lactobacillus plantarum for their ability to produce vitamin B2 (riboflavin) and vitamin B9 (folates), their antimicrobial properties and antibiotics susceptibility. In this work, we present the Whole Genome Sequences (WGS) of these five strains that have been deposited in the Spanish Type Culture Collection: M5MA1 (= CECT 8962), M9MM1 (= CECT 8963), M9MM4 (= CECT 8964), M9MG6 (= CECT 8965), and M9Y2 (= CECT 8966), and a detailed description of their characterization, through a genomic approach, analyzing the genes responsible for these biotechnological properties, making a comparative study of the five genomes and reporting the aspects related to food safety, in accordance with the recommendations of the European Food Safety Authority (EFSA FEEDAP Panel, 2018) aiming at their use in the design of functional foods", "token_count": 428, "char_count": 1668, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:45.318037", "source": { "split": "train_shard_00001", "doc_id": 3562 }, "chunk_id": "train_shard_00001_3562_0", "global_id": 10704 }, { "text": "The analysis unveiled, for the five strains, the complete set of genes for folate and riboflavin biosynthesis, the absence of pathogenic factors, the presence of CRISPR and cas genes, phage sequences, insertion elements and an aminoglycosides resistance gene, aadA, whose resistance could not be proved phenotypically in any strain. Genomic comparisons showed that strain CECT 8962 was significantly different in terms of genetic content and allowed the identification of carbohydrates metabolism and membrane transport related genes as the main components of the unique and accessory genome.\n\nGenomic Insights Into Five Strains of Lactobacillus plantarum With Biotechnological Potential Isolated From chicha, a Traditional Maize-Based Fermented Beverage From Northwestern Argentina.", "token_count": 213, "char_count": 811, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7685, "quality_score": 0.8843, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:45.786015", "source": { "split": "train_shard_00001", "doc_id": 3562 }, "chunk_id": "train_shard_00001_3562_1", "global_id": 10705 }, { "text": "During the growth of Kluyveromyces marxianus var. marxianus ATCC 10022 on lactose, peaks of glucose, but not beta-galactosidase activity, were detected in culture medium. Harvested and washed whole cells produced glucose and galactose from lactose, or ortho-nitro-phenol from the chromogenic substrate ortho-nitro-phenyl-beta-D-galactopyranoside (ONPG), indicating that beta-galactosidase is physically associated with cells. ONPG hydrolysis by whole cells presented a monophasic kinetics (Km 36.6 mM) in lactose exponential growth phase cells, but a biphasic kinetics (Km 0.2 and 36.6 mM) in stationary growth phase cells. Permeabilization with digitonin or disruption of cells from both growth phases led to monosite ONPG hydrolysis (Km 2.2 to 2.5 mM), indicating that beta-galactosidase is not located in the periplasm. In addition, the energy inhibitors fluoride or arsenate, as well as the uncoupler carbonyl cyanide m-chlorophenylhydrazone (CCCP) prevented ONPG hydrolysis by whole cells. These findings indicate that energy coupled transmembrane transport is the rate-limiting step for intracellular ONPG cleavage. The taxonomic and physiologic implications of the exclusive intracellular location of beta-galactosidase of K. marxianus var. marxianus ATCC 10022 are discussed.\n\nLocation of the beta-galactosidase of the yeast Kluyveromyces marxianus var. marxianus ATCC 10022.", "token_count": 434, "char_count": 1383, "word_count": 186, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:46.422173", "source": { "split": "train_shard_00001", "doc_id": 3563 }, "chunk_id": "train_shard_00001_3563_0", "global_id": 10706 }, { "text": "Cholera is a life-threatening gastrointestinal infection caused by a toxigenic bacterium, Vibrio cholerae. After a lull of almost 30 years, a first case of cholera was detected in Lebanon in October 2022. The outbreak lasted three months, with 8007 suspected cases (671 laboratory-confirmed) and 23 deaths. In this study, we use phenotypic methods and microbial genomics to study 34 clinical and environmental Vibrio cholerae isolates collected throughout this outbreak. All isolates are identified as V. cholerae O1, serotype Ogawa strains from wave 3 of the seventh pandemic El Tor (7PET) lineage. Phylogenomic analysis unexpectedly reveals the presence of two different strains of the seventh pandemic El Tor (7PET) lineage. The dominant strain has a narrow antibiotic resistance profile and is phylogenetically related to South Asian V. cholerae isolates and derived African isolates from the AFR15 sublineage. The second strain is geographically restricted and extensively drug-resistant. It belongs to the AFR13 sublineage and clusters with V. cholerae isolates collected in Yemen. In conclusion, the 2022-2023 Lebanese cholera outbreak is caused by the simultaneous introduction of two different 7PET strains. Genomic surveillance with cross-border collaboration is therefore crucial for the identification of new introductions and routes of circulation of cholera, improving our understanding of cholera epidemiology.\n\nAn unusual two-strain cholera outbreak in Lebanon, 2022-2023: a genomic epidemiology study.", "token_count": 402, "char_count": 1518, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [ "AFR13", "AFR15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:47.043299", "source": { "split": "train_shard_00001", "doc_id": 3564 }, "chunk_id": "train_shard_00001_3564_0", "global_id": 10707 }, { "text": "

Background

Aeromonas veronii is a Gram-negative rod-shaped motile bacterium that inhabits mainly freshwater environments. A. veronii is a pathogen of aquatic animals, causing diseases in fish. A. veronii is also an emerging human enteric pathogen, causing mainly gastroenteritis with various severities and also often being detected in patients with inflammatory bowel disease. Currently, limited information is available on the genomic information of A. veronii strains that cause human gastrointestinal diseases. Here we sequenced, assembled and analysed 25 genomes (one complete genome and 24 draft genomes) of A. veronii strains isolated from patients with gastrointestinal diseases using combine sequencing technologies from Illumina and Oxford Nanopore. We also conducted comparative analysis of genomes of 168 global A. veronii strains isolated from different sources.

Results

We found that most of the A. veronii strains isolated from patients with gastrointestinal diseases were closely related to each other, and the remaining were closely related to strains from other sources. Nearly 300 putative virulence factors were identified. Aerolysin, microbial collagenase and multiple hemolysins were present in all strains isolated from patients with gastrointestinal diseases. Type III Secretory System (T3SS) in A. veronii was in AVI-1 genomic island identified in this study, most likely acquired via horizontal transfer from other Aeromonas species. T3SS was significantly less present in A. veronii strains isolated from patients with gastrointestinal diseases as compared to strains isolated from fish and domestic animals.

Conclusions

This study provides novel information on source of infection and virulence of A. veronii in human gastrointestinal diseases.\n\nAnalysis of global Aeromonas veronii genomes provides novel information on source of infection and virulence in human gastrointestinal diseases.", "token_count": 467, "char_count": 1940, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5133, "quality_score": 0.7567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:47.687843", "source": { "split": "train_shard_00001", "doc_id": 3565 }, "chunk_id": "train_shard_00001_3565_0", "global_id": 10708 }, { "text": "Knowledge of fungal diversity in the environment is poor compared with bacterial biodiversity. In this study, we applied the denaturing high-performance liquid chromatography (D-HPLC) technique, combined with the amplification of the ITS1 region from fungal rDNA, for the rapid identification of major fungal species in 9 raw milk samples from cow, ewe and goat, collected at different periods of the year. A total of 27 fungal species were identified. Yeast species belonged to Candida, Cryptococcus, Debaryomyces, Geotrichum, Kluyveromyces, Malassezia, Pichia, Rhodotorula and Trichosporon genera; and mold species belonged to Aspergillus, Chrysosporium, Cladosporium, Engyodontium, Fusarium, Penicillium and Torrubiella genera. Cow milk samples harbored the highest fungal diversity with a maximum of 15 species in a single sample, whereas a maximum of 4 and 6 different species were recovered in goat and ewe milk respectively. Commonly encountered genera in cow and goat milk were Geotrichum candidum, Kluyveromyces marxianus and Candida spp. (C. catenulata and C. inconspicua); whereas Candida parapsilosis was frequently found in ewe milk samples. Most of detected species were previously described in literature data. A few species were uncultured fungi and others (Torrubiella and Malassezia) were described for the first time in milk.\n\nFungal diversity in cow, goat and ewe milk.", "token_count": 375, "char_count": 1389, "word_count": 201, "semantic_coherence": 1, "information_density": 0.597, "quality_score": 0.7985, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:48.263803", "source": { "split": "train_shard_00001", "doc_id": 3566 }, "chunk_id": "train_shard_00001_3566_0", "global_id": 10709 }, { "text": "Mycoplasma bovis is a significant pathogen of feedlot cattle, responsible for chronic pneumonia and polyarthritis syndrome (CPPS). M. bovis isolates (n = 129) were used to compare four methods of phylogenetic analysis and to determine if the isolates' genotypes were associated with phenotypes. Metadata included the health status of the animal from which an isolate was derived (healthy, diseased, or dead), anatomical location (nasopharynx, lung, or joint), feedlot, and production year (2006 to 2018). Four in silico phylogenetic typing methods were used: multilocus sequence typing (MLST), core genome MLST (cgMLST), core genome single nucleotide variant (cgSNV) analysis, and whole-genome SNV (wgSNV) analysis. Using Simpson's diversity index (D) as a proxy for resolution, MLST had the lowest resolution (D = 0.932); cgSNV (D = 0.984) and cgMLST (D = 0.987) generated comparable results; and wgSNV (D = 1.000) provided the highest resolution. Visual inspection of the minimum spanning trees found that the memberships of the clonal complexes and clades had similar structural appearances. Although MLST had the lowest resolution, this methodology was intuitive and easy to apply, and the PubMLST database facilitates the comparison of sequence types across studies. The cg methods had higher resolution than MLST, and the graphical interface software was user-friendly for nonbioinformaticians, but the proprietary software is relatively expensive. The wgSNV approach was the most robust for processing poor-quality sequence data while offering the highest resolution; however, application of its software requires specialized training. None of the four methods could associate genotypes with phenotypes.", "token_count": 500, "char_count": 1759, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:48.916227", "source": { "split": "train_shard_00001", "doc_id": 3567 }, "chunk_id": "train_shard_00001_3567_0", "global_id": 10710 }, { "text": "Application of Four Genotyping Methods to Mycoplasma bovis Isolates Derived from Western Canadian Feedlot Cattle.", "token_count": 31, "char_count": 113, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:49.269642", "source": { "split": "train_shard_00001", "doc_id": 3567 }, "chunk_id": "train_shard_00001_3567_1", "global_id": 10711 }, { "text": "The gut microbiome of companion animals is relatively underexplored, despite its relevance to animal health, pet owner health, and basic microbial community biology. Here, we provide the most comprehensive analysis of the canine and feline gut microbiomes to date, incorporating 2639 stool shotgun metagenomes (2272 dog and 367 cat) spanning 14 publicly available datasets (n = 730) and 8 new study populations (n = 1909). These are compared with 238 and 112 baseline human gut metagenomes from the Human Microbiome Project 1-II and a traditionally living Malagasy cohort, respectively, processed in a manner identical to the animal metagenomes. All microbiomes were characterized using reference-based taxonomic and functional profiling, as well as de novo assembly yielding metagenomic assembled genomes clustered into species-level genome bins. Companion animals shared 184 species-level genome bins not found in humans, whereas 198 were found in all three hosts. We applied novel methodology to distinguish strains of these shared organisms either transferred or unique to host species, with phylogenetic patterns suggesting host-specific adaptation of microbial lineages. This corresponded with functional divergence of these lineages by host (e.g. differences in metabolic and antibiotic resistance genes) likely important to companion animal health. This study provides the largest resource to date of companion animal gut metagenomes and greatly contributes to our understanding of the \"One Health\" concept of a shared microbial environment among humans and companion animals, affecting infectious diseases, immune response, and specific genetic elements.\n\nComprehensive profile of the companion animal gut microbiome integrating reference-based and reference-free methods.", "token_count": 419, "char_count": 1781, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:49.891885", "source": { "split": "train_shard_00001", "doc_id": 3568 }, "chunk_id": "train_shard_00001_3568_0", "global_id": 10712 }, { "text": "When examining bacterial genomes for evidence of past selection, the results depend heavily on the mutational distance between chosen genomes. Even within a bacterial species, genomes separated by larger mutational distances exhibit stronger evidence of purifying selection as assessed by dN/dS, the normalized ratio of nonsynonymous to synonymous mutations. Here, we show that the classical interpretation of this scale dependence, weak purifying selection, leads to problematic mutation accumulation when applied to available gut microbiome data. We propose an alternative, adaptive reversion model with opposite implications for dynamical intuition and applications of dN/dS. Reversions that occur and sweep within-host populations are nearly guaranteed in microbiomes due to large population sizes, short generation times, and variable environments. Using analytical and simulation approaches, we show that adaptive reversion can explain the dN/dS decay given only dozens of locally fluctuating selective pressures, which is realistic in the context of Bacteroides genomes. The success of the adaptive reversion model argues for interpreting low values of dN/dS obtained from long timescales with caution as they may emerge even when adaptive sweeps are frequent. Our work thus inverts the interpretation of an old observation in bacterial evolution, illustrates the potential of mutational reversions to shape genomic landscapes over time, and highlights the importance of studying bacterial genomic evolution on short timescales.\n\nReversions mask the contribution of adaptive evolution in microbiomes.", "token_count": 375, "char_count": 1702, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:50.480695", "source": { "split": "train_shard_00001", "doc_id": 3569 }, "chunk_id": "train_shard_00001_3569_0", "global_id": 10713 }, { "text": "

Background

The 16S rRNA gene is used extensively in bacterial phylogenetics, in species delineation, and now widely in microbiome studies. However, the gene suffers from intragenomic heterogeneity, and reports of recombination and an unreliable phylogenetic signal are accumulating. Here, we compare core gene phylogenies to phylogenies constructed using core gene concatenations to estimate the strength of signal for the 16S rRNA gene, its hypervariable regions, and all core genes at the intra- and inter-genus levels. Specifically, we perform four intra-genus analyses (Clostridium, n = 65; Legionella, n = 47; Staphylococcus, n = 36; and Campylobacter, n = 17) and one inter-genus analysis [41 core genera of the human gut microbiome (31 families, 17 orders, and 12 classes), n = 82].

Results

At both taxonomic levels, the 16S rRNA gene was recombinant and subject to horizontal gene transfer. At the intra-genus level, the gene showed one of the lowest levels of concordance with the core genome phylogeny (50.7% average). Concordance for hypervariable regions was lower still, with entropy masking providing little to no benefit. A major factor influencing concordance was SNP count, which showed a positive logarithmic association. Using this relationship, we determined that 690 ± 110 SNPs were required for 80% concordance (average 16S rRNA gene SNP count was 254). We also found a wide range in 16S-23S-5S rRNA operon copy number among genomes (1-27)", "token_count": 475, "char_count": 1476, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:51.122545", "source": { "split": "train_shard_00001", "doc_id": 3570 }, "chunk_id": "train_shard_00001_3570_0", "global_id": 10714 }, { "text": "At the inter-genus level, concordance for the whole 16S rRNA gene was markedly higher (73.8% - 10th out of 49 loci); however, the most concordant hypervariable regions (V4, V3-V4, and V1-V2) ranked in the third quartile (62.5 to 60.0%).

Conclusions

Ramifications of a poor phylogenetic performance for the 16S rRNA gene are far reaching. For example, in addition to incorrect species/strain delineation and phylogenetic inference, it has the potential to confound community diversity metrics if phylogenetic information is incorporated - for example, with popular approaches such as Faith's phylogenetic diversity and UniFrac. Our results highlight the problematic nature of these approaches and their use (along with entropy masking) is discouraged. Lastly, the wide range in 16S rRNA gene copy number among genomes also has a strong potential to confound diversity metrics. Video Abstract.\n\nPhylogenies of the 16S rRNA gene and its hypervariable regions lack concordance with core genome phylogenies.", "token_count": 290, "char_count": 1009, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6599, "quality_score": 0.8299, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:51.685135", "source": { "split": "train_shard_00001", "doc_id": 3570 }, "chunk_id": "train_shard_00001_3570_1", "global_id": 10715 }, { "text": "

Background and objective

The presence of carbapenemase enzymes among Enterobacterales is the main mechanism to reduce susceptibility to a wide range of antibiotics. Carbapenemase enzymes such as the Klebsiella pneumoniae carbapenemase (KPC) hydrolyse beta-lactam antibiotics group, which includes carbapenem, leads to fewer treatment options. We aim to describe the first report of carbapenem-resistant K. pneumoniae (CRKP) sequence type (ST) 11 harbouring KPC in Oman.

Material and methods

Five confirmed CRKP isolates were isolated from clinical samples during the period of January 2019 till December 2019. Strains were genotyped by pulse field gel electrophoresis (PFGE) for genetic relatedness. Whole genome sequencing (WGS) was performed to observe relationships with global strains using multilocus sequence typing (MLST). Antimicrobial genes, capsular loci-K-types, plasmids types and virulence genes were also identified using whole genome sequence data.

Results

All five CRKP were determined to have blaKPC-2 with or without blaOX-A48 and blaNDM-2. The molecular genotyping by PFGE showed 100% similarity among the five isolates. The MLST allelic profile analysis clonally clustered our strains with SL-258, CG-11 and ST11 mainly reported from South Asia. Further molecular characterization of the capsular K-locus and O-locus genes, revealed the strains to belong to KL-47 type and OL101 type respectively. The core genome typing suggests that our strains were clonally related to Chinese strains with less than five chromosomal nucleotides differences.

Conclusion

Epidemiological and molecular analyses confirmed that these KPC-producing K. pneumoniae strains are from a single clone that caused multiple nosocomial infections in one health institution", "token_count": 515, "char_count": 1826, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6904, "quality_score": 0.8452, "entities": { "genes": [ "OL101", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:52.375426", "source": { "split": "train_shard_00001", "doc_id": 3571 }, "chunk_id": "train_shard_00001_3571_0", "global_id": 10716 }, { "text": "This finding highlights the importance to sustain the surveillance and infection prevention efforts and to step up active screening to prevent the spread of nosocomial infection.\n\nGenomic analysis of the emerging carbapenem-resistant Klebsiella pneumoniae sequence type 11 harbouring Klebsiella pneumoniae carbapenemase (KPC) in Oman.", "token_count": 81, "char_count": 334, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7955, "quality_score": 0.8977, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:52.767270", "source": { "split": "train_shard_00001", "doc_id": 3571 }, "chunk_id": "train_shard_00001_3571_1", "global_id": 10717 }, { "text": "2. Healthcare-associated wastewater reservoirs and asymptomatic gastrointestinal patient colonisation by carbapenemase-producing Enterobacterales (CPE) contribute to nosocomial CPE dissemination. We systematically sampled wastewater sites (n=4488 sampling events; 349 sites) and patients (n=1247) across six wards over 6-12 months in 2016 to better understand bla KPC -associated CPE (KPC-E) diversity within these niches and transmission potential in an endemic healthcare setting. Up to five isolates in KPC-E-positive samples were sequenced (Illumina). Recombination-adjusted phylogenies were used to define genetically related strains; assembly and mapping-based typing approaches were used to characterise antimicrobial resistance genes, insertion sequences, and Tn4401 types/target site sequences. The wider accessory genome was evaluated in a subset of the largest clusters, and those crossing niches. Wastewater site KPC-E-positivity was substantial (101/349 sites [28.9%] positive); 228/5,601 (4.1%) patients cultured were CPE culture-positive over the same timeframe. At a genomic-level, 13 KPC-E species and 109 strains were identified, and 24% of wastewater and 26% of patient KPC-E-positive samples harboured ≥1 strain. Most diversity was explained by the individual niche, suggesting localised factors are important in selection and spread. Tn4401+target site sequence diversity was greater in wastewater sites (p<0.001), which might favour Tn4401-associated transposition/evolution. Shower/bath and sluice/mop-associated sites were more likely to be KPC-E-positive (Adjusted Odds Ratio [95% CI]: 2.69 [1.44-5.01], p=0.0019 and 2.60 [1.04-6.52], p=0.0410, respectively)", "token_count": 517, "char_count": 1683, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7371, "quality_score": 0.8685, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:53.417837", "source": { "split": "train_shard_00001", "doc_id": 3572 }, "chunk_id": "train_shard_00001_3572_0", "global_id": 10718 }, { "text": "Different strains had different transmission and bla KPC dissemination dynamics. There may be substantial KPC-E colonisation of wastewater sites and patients in KPC-E-endemic healthcare settings. Niche-specific factors (e.g. microbial interactions, selection pressure) likely affect carbapenemase gene persistence and evolution, and different strains and mobile genetic elements with different transmission dynamics influence carbapenemase gene dissemination; these factors should be considered in surveillance and control strategies.\n\nGenomic epidemiology and longitudinal sampling of ward wastewater environments and patients reveals complexity of the transmission dynamics of blaKPC-carbapenemase-producing Enterobacterales in a hospital setting", "token_count": 161, "char_count": 759, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7159, "quality_score": 0.858, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:53.909507", "source": { "split": "train_shard_00001", "doc_id": 3572 }, "chunk_id": "train_shard_00001_3572_1", "global_id": 10719 }, { "text": "Effect of sourdough fermentation, by different starter culture (lactic acid bacteria Lactococcus lactis ssp. Lactis, Weissella confusa, Lactobacillus plantarum, Lactobacillus brevis, Lactobacillus helveticus, and yeast Kluyveromyces marxianus subsp. Marxianus), on antioxidant capacity of rye dough and bread was determined and compared with spontaneous fermentation. The total phenolic content and antioxidant activities assessed using Trolox equivalent antioxidant capacity (TEAC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity expressed in terms of Trolox equivalents and of percentage of discoloration, were measured. The results indicate that antioxidant activity of the rye sourdough highly depends on the type of inoculum used for fermentation and the levels of bioactive compounds change during the bread making process. Fermentation process and type of starter culture are tools to increase the bioactive compounds with antioxidant activities of the rye bread.\n\nEffect of Lactic Fermentation on Antioxidant Capacity of Rye Sourdough and Bread", "token_count": 295, "char_count": 1070, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:54.473526", "source": { "split": "train_shard_00001", "doc_id": 3573 }, "chunk_id": "train_shard_00001_3573_0", "global_id": 10720 }, { "text": "Staphylococcus epidermidis is a pathogen emerging worldwide as a leading cause of health care-associated infections. A standardized high-resolution typing method to document transmission and dissemination of multidrug-resistant S. epidermidis strains is needed. Our aim was to provide a core genome multilocus sequence typing (cgMLST) scheme for S. epidermidis to improve the international surveillance of S. epidermidis We defined a cgMLST scheme based on 699 core genes and used it to investigate the population structure of the species and the genetic relatedness of isolates recovered from infants hospitalized in several wards of a French hospital. Our results show the long-lasting endemic persistence of S. epidermidis clones within and across wards of hospitals and demonstrate the ability of our cgMLST approach to identify and track these clones. We made the scheme publicly available through the Institut Pasteur BIGSdb server (http://bigsdb.pasteur.fr/epidermidis/). This tool should enable international harmonization of the epidemiological surveillance of multidrug-resistant S. epidermidis clones. By comparing gene distribution among infection and commensal isolates, we also confirmed the association of the mecA locus with infection isolates and of the fdh gene with commensal isolates. (This study has been registered at ClinicalTrials.gov under registration no. NCT03374371.).\n\nHigh-Resolution Typing of Staphylococcus epidermidis Based on Core Genome Multilocus Sequence Typing To Investigate the Hospital Spread of Multidrug-Resistant Clones.", "token_count": 437, "char_count": 1627, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [ "NCT03374371" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:55.102977", "source": { "split": "train_shard_00001", "doc_id": 3574 }, "chunk_id": "train_shard_00001_3574_0", "global_id": 10721 }, { "text": "

Background

Acinetobacter baumannii is one of the most problematic nosocomial pathogens that can efficiently thrive within hospital settings, mainly due to resistances towards antibiotics, desiccation, disinfectants, human serum and oxidative stress. Recently, increased resistance against last resort antibiotics earns this bacterium the highest priority concern classified by the CDC and the WHO. An obvious hallmark of this bacterium is the high heterogeneity observed amongst A. baumannii isolates, with a limited core genome. This feature complexifies the study of A. baumannii bacteria as an entity, subsequently reflected in a diversity of phenotypes of not only antimicrobial and environmental resistance but also virulence.

Main body

High degree of genome plasticity, along with the use of a limited subset of established reference strains, can lead to strain-specific observations, decreasing the global understanding of this pathogenic agent. Phenotypic variability of A. baumannii strains is easily observable such as with the macrocolony morphologies, in vitro and in vivo virulence, natural competence level, production of different capsular polysaccharide structures and cellular densities. Some strains encode an extensive amount of virulence factors while other, including the reference strains, lack several key ones. The lack/excess of genes or specific physiological processes might interfere with in vivo and in vitro experiments, thus providing limited impact on the global understanding of Acinetobacter bacteria as a whole.

Conclusion

As an answer to the high heterogeneity amongst A. baumannii strains, we propose a first comprehensive database that includes the bacterial strains and the associated phenotypic and genetic data. This new repository, freely accessible to the entire scientific community, allow selecting the best bacterial isolate(s) related to any biological question, using an efficient and fast exchange platform.\n\nAcinetobase: the comprehensive database and repository of Acinetobacter strains", "token_count": 473, "char_count": 2071, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6431, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:55.749311", "source": { "split": "train_shard_00001", "doc_id": 3575 }, "chunk_id": "train_shard_00001_3575_0", "global_id": 10722 }, { "text": "

Objectives

To reconstruct the genomic epidemiology and evolution of MDR Salmonella Indiana in China.

Methods

A total of 108 Salmonella Indiana strains were collected from humans and livestock in China. All isolates were subjected to WGS and antimicrobial susceptibility testing. Phylogenetic relationships and evolutionary analyses were conducted using WGS data from this study and the NCBI database.

Results

Almost all 108 Salmonella Indiana strains displayed the MDR phenotype. Importantly, 84 isolates possessed concurrent resistance to ciprofloxacin and cefotaxime. WGS analysis revealed that class 1 integrons on the chromosome and IncHI2 plasmids were the key vectors responsible for multiple antibiotic resistance gene (ARG) [including ESBL and plasmid-mediated quinolone resistance (PMQR) genes] transmission among Salmonella Indiana. The 108 Salmonella Indiana dataset displayed a relatively large core genome and ST17 was the predominant ST. Moreover, the global ST17 Salmonella Indiana strains could be divided into five distinct lineages, each of which was significantly associated with a geographical distribution. Genomic analysis revealed multiple antimicrobial resistance determinants and QRDR mutations in Chinese lineages, which almost did not occur in other global lineages. Using molecular clock analysis, we hypothesized that ST17 isolates have existed since 1956 and underwent a major population expansion from the 1980s to the 2000s and the genetic diversity started to decrease around 2011, probably due to geographical barriers, antimicrobial selective pressure and MDR, favouring the establishment of this prevalent multiple antibiotic-resistant lineage and local epidemics.

Conclusions

This study revealed that adaptation to antimicrobial pressure was possibly pivotal in the recent evolutionary trajectory for the clonal spread of ST17 Salmonella Indiana in China.\n\nPhylogenomic analysis of Salmonella Indiana ST17, an emerging MDR clonal group in China.", "token_count": 506, "char_count": 2011, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7989, "entities": { "genes": [ "ST17" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:56.417289", "source": { "split": "train_shard_00001", "doc_id": 3576 }, "chunk_id": "train_shard_00001_3576_0", "global_id": 10723 }, { "text": "

Background

In bacteria, pan-genomes are the result of an evolutionary \"tug of war\" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.

Results

We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport.

Conclusions

Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments", "token_count": 520, "char_count": 2115, "word_count": 305, "semantic_coherence": 1, "information_density": 0.577, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:57.080316", "source": { "split": "train_shard_00001", "doc_id": 3577 }, "chunk_id": "train_shard_00001_3577_0", "global_id": 10724 }, { "text": "This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.\n\nPopulation genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.", "token_count": 49, "char_count": 238, "word_count": 31, "semantic_coherence": 1, "information_density": 0.8387, "quality_score": 0.9194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:57.438447", "source": { "split": "train_shard_00001", "doc_id": 3577 }, "chunk_id": "train_shard_00001_3577_1", "global_id": 10725 }, { "text": "

ABSTRACT

Background

Bioaugmentation is now a well-established approach for attenuating toxic groundwater and soil contaminants, particularly for chlorinated ethenes and ethanes. The KB-1 and WBC-2 consortia are cultures used for this purpose. These consortia contain organisms belonging to the Dehalococcoidia, including strains of Dehalococcoides mccartyi in KB-1 and of both D. mccartyi and Dehalogenimonas in WBC-2. These tiny anaerobic bacteria couple respiratory reductive dechlorination to growth and harbour multiple reductive dehalogenase genes ( rdhA ) in their genomes, the majority of which have yet to be characterized.

Results

Using a combination of Illumina mate-pair and paired-end sequencing we closed the genomes of eight new strains of Dehalococcoides mccartyi found in three related KB-1 sub-cultures that were enriched on trichloroethene (TCE), 1,2-dichloroethane (1,2-DCA) and vinyl chloride (VC), bringing the total number of genomes available in NCBI to 24. A pangenome analysis was conducted on 24 Dehalococcoides genomes and five Dehalogenimonas genomes (2 in draft) currently available in NCBI. This Dehalococcoidia pangenome generated 2875 protein families comprising of 623 core, 2203 accessory, and 49 unique protein families. In Dehalococcoides mccartyi the complement of reductive dehalogenase genes varies by strain, but what was most surprising was how the majority of rdhA sequences actually exhibit a remarkable degree of synteny across all D. mccartyi genomes. Several homologous sequences are also shared with Dehalogenimonas genomes. Nucleotide and predicted protein sequences for all reductive dehalogenases were aligned to begin to decode the evolutionary history of reductive dehalogenases in the Dehalococcoidia", "token_count": 518, "char_count": 1780, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6311, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:39:58.070524", "source": { "split": "train_shard_00001", "doc_id": 3578 }, "chunk_id": "train_shard_00001_3578_0", "global_id": 10726 }, { "text": "

Conclusions

The conserved synteny of the rdhA genes observed across Dehalococcoides genomes indicates that the major differences between strain rdhA gene complement has resulted from gene loss rather than recombination. These rdhA have a long evolutionary history and trace their origin in the Dehalococcoidia prior to the speciation of Dehalococcoides and Dehalogenimonas. The only rdhA genes suspected to have been acquired by lateral gene transfer are protein-coding rdhA that have been identified to catalyze dehalogenation of industrial pollutants. Sequence analysis suggests that evolutionary pressures resulting in new rdhA genes involve adaptation of existing dehalogenases to new substrates, mobilization of rdhA between genomes or within a genome, and to a lesser degree manipulation of regulatory regions to alter expression.\n\nEight new genomes of organohalide-respiring Dehalococcoides mccartyi reveal evolutionary trends in reductive dehalogenase enzymes", "token_count": 244, "char_count": 983, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:58.559806", "source": { "split": "train_shard_00001", "doc_id": 3578 }, "chunk_id": "train_shard_00001_3578_1", "global_id": 10727 }, { "text": "Three strains (H4-D09T, S2-D11 and S9-F39) of a member of the genus Paracoccus attributed to a novel species were isolated from topsoil of temperate grasslands. The genome sequence of the type strain H4-D09T exhibited a complete set of genes required for denitrification as well as methylotrophy. The genome of H4-D09T included genes for two alternative pathways of formaldehyde oxidation. Besides the genes for the canonical glutathione (GSH)-dependent formaldehyde oxidation pathway, all genes for the tetrahydrofolate-formaldehyde oxidation pathway were identified. The strain has the potential to utilize methanol and/or methylamine as a single carbon source as evidenced by the presence of methanol dehydrogenase (mxaFI) and methylamine dehydrogenase (mau) genes. Apart from dissimilatory denitrification genes (narA, nirS, norBC and nosZ), genes for assimilatory nitrate (nasA) and nitrite reductases (nirBD) were also identified. The results of phylogenetic analysis based on 16S rRNA genes coupled with riboprinting revealed that all three strains represented the same species of genus Paracoccus. Core genome phylogeny of the type strain H4-D09T indicated that Paracoccus thiocyanatus and Paracoccus denitrificans are the closest phylogenetic neighbours. The average nucleotide index (ANI) and digital DNA-DNA hybridization (dDDH) with the closest phylogenetic neighbours revealed genetic differences at the species level, which were further substantiated by differences in several physiological characteristics", "token_count": 505, "char_count": 1648, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:59.211802", "source": { "split": "train_shard_00001", "doc_id": 3579 }, "chunk_id": "train_shard_00001_3579_0", "global_id": 10728 }, { "text": "The major respiratory quinone is Q-10, and the predominant cellular fatty acids are C18 : 1ω7c, C19 : 0cyclo ω7c, and C16 : 0, which correspond to those detected in other members of the genus. The polar lipid profile consists of a diphosphatidylglycerol (DPG), phosphatidylethanolamine (PE), phosphatidylglycerol (PG), phosphatidylcholine (PC), aminolipid (AL), glycolipid (GL) and an unidentified lipid (L).On the basis of our results, we concluded that the investigated isolates represent a novel species of the genus Paracoccus, for which the name Paracoccus methylovorus sp. nov. (type strain H4-D09T=LMG 31941T= DSM 111585T) is proposed.\n\nGenomic evidence for two pathways of formaldehyde oxidation and denitrification capabilities of the species Paracoccus methylovorus sp. nov.", "token_count": 323, "char_count": 885, "word_count": 112, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:39:59.776586", "source": { "split": "train_shard_00001", "doc_id": 3579 }, "chunk_id": "train_shard_00001_3579_1", "global_id": 10729 }, { "text": "Gardnerella vaginalis is described as a common anaerobic vaginal bacterium whose presence may correlate with vaginal dysbiotic conditions. In the current study, we performed phylogenomic analyses of 72 G. vaginalis genome sequences, revealing noteworthy genome differences underlying a polyphyletic organization of this taxon. Particularly, the genomic survey revealed that this species may actually include nine distinct genotypes (GGtype1 to GGtype9). Furthermore, the observed link between sialidase and phylogenomic grouping provided clues of a connection between virulence potential and the evolutionary history of this microbial taxon. Specifically, based on the outcomes of these in silico analyses, GGtype3, GGtype7, GGtype8, and GGtype9 appear to have virulence potential since they exhibited the sialidase gene in their genomes. Notably, the analysis of 34 publicly available vaginal metagenomic samples allowed us to trace the distribution of the nine G. vaginalis genotypes identified in this study among the human population, highlighting how differences in genetic makeup could be related to specific ecological properties. Furthermore, comparative genomic analyses provided details about the G. vaginalis pan- and core genome contents, including putative genetic elements involved in the adaptation to the ecological niche as well as many putative virulence factors. Among these putative virulence factors, particularly noteworthy genes identified were the gene encoding cholesterol-dependent cytolysin (CDC) toxin vaginolysin and genes related to microbial biofilm formation, iron uptake, adhesion to the vaginal epithelium, as well as macrolide antibiotic resistance.IMPORTANCE The identification of nine different genotypes among members of G. vaginalis allowed us to distinguish an uneven distribution of virulence-associated genetic traits within this taxon and thus suggest the potential occurrence of putative pathogen and commensal G. vaginalis strains", "token_count": 512, "char_count": 2031, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:00.431566", "source": { "split": "train_shard_00001", "doc_id": 3580 }, "chunk_id": "train_shard_00001_3580_0", "global_id": 10730 }, { "text": "These findings, coupled with metagenomics microbial profiling of human vaginal microbiota, permitted us to get insights into the distribution of the genotypes among the human population, highlighting the presence of different structural communities in terms of G. vaginalis genotypes.\n\nAssessing the Genomic Variability of Gardnerella vaginalis through Comparative Genomic Analyses: Evolutionary and Ecological Implications.", "token_count": 101, "char_count": 431, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:00.807214", "source": { "split": "train_shard_00001", "doc_id": 3580 }, "chunk_id": "train_shard_00001_3580_1", "global_id": 10731 }, { "text": "Vibrio parahaemolyticus has caused widespread mortality in Indian shrimp aquaculture in recent years. However, there are insufficient genome data for the isolates from Indian shrimp vibriosis to analyze genetic diversity and track the acquisition of genetic features that could be involved in virulence and fitness. In this study, we have performed genome analysis of V. parahaemolyticus isolated from moribund shrimps collected from shrimp farms along coastal Karnataka, India, for better understanding of their diversity and virulence. Five newly sequenced genomes of V. parahaemolyticus along with 40 genomes retrieved from NCBI were subjected to comparative genome analysis. The sequenced genomes had an overall genome size of 5.2 Mb. MLST analysis and core genome phylogenomic analysis revealed considerable genetic diversity among the isolates obtained from the moribund shrimps. Interestingly, none of the V. parahaemolyticus isolates possessed the classical features (PirAB) of the strains associated with Acute Hepatopancreatic Necrosis Disease (AHPND). This study also revealed the presence of multiple virulence attributes, including ZOT, ACE and RTX toxins, secretion systems, and mobile genetic elements. The findings of this study provide insights into the possible transition of an environmental V. parahaemolyticus to emerge as pathogens of aquaculture species by increasing its virulence and host adaptation. Future studies focusing on continuous genomic surveillance of V. parahaemolyticus are required to study the evolution and transmission of new variants in shrimp aquaculture, as well as to design and implement biosecurity programs to prevent disease outbreaks.\n\nWhole genome analysis unveils genetic diversity and potential virulence determinants in Vibrio parahaemolyticus associated with disease outbreak among cultured Litopenaeus vannamei (Pacific white shrimp) in India.", "token_count": 499, "char_count": 1956, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:01.459666", "source": { "split": "train_shard_00001", "doc_id": 3581 }, "chunk_id": "train_shard_00001_3581_0", "global_id": 10732 }, { "text": "Biological reaction calorimetry, also known as biocalorimetry, has led to extensive applications in monitoring and control of different bioprocesses. A simple real-time estimator for biomass and growth rate was formulated, based on in-line measured metabolic heat flow values. The performance of the estimator was tested in a unique bench-scale calorimeter (BioRC1), improved to a sensitivity range of 8 mW l(-1) in order to facilitate the monitoring of even weakly exothermic biochemical reactions. A proportional-integral feedback control strategy based on these estimators was designed and implemented to control the growth rate of Candida utilis, Kluyveromyces marxianus and Pichia pastoris by regulating an exponential substrate feed. Maintaining a particular specific growth rate throughout a culture is essential for reproducible product quality in industrial bioprocesses and therefore a key sequence for the step from quality by analysis to quality by design. The potential of biocalorimetry as a reliable biomass monitoring tool and as a key part of a robust control strategy for aerobic fed-batch cultures of Crabtree-negative yeast cells in defined growth medium was investigated. Presenting controller errors of less than 4% in the best cases, the approach paves the way for the development of a generally applicable process analytical technology platform for monitoring and control of microbial fed-batch cultures.\n\nInvestigation of the potential of biocalorimetry as a process analytical technology (PAT) tool for monitoring and control of Crabtree-negative yeast cultures.", "token_count": 354, "char_count": 1588, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:02.040281", "source": { "split": "train_shard_00001", "doc_id": 3582 }, "chunk_id": "train_shard_00001_3582_0", "global_id": 10733 }, { "text": "

Background

Yersiniabactin, a siderophore with a high affinity to iron, has been described as a potential virulence factor in Enterobacteriaceae. Klebsiella aerogenes is a Gram-negative rod known to cause invasive infection in very low birth weight infants but is an unusual pathogen to cause outbreaks in neonatal intensive care units (NICU).

Methods

We performed a retrospective analysis of all patients colonized with K. aerogenes in our NICU from September to December 2018. Each infant with an occurrence of K. aerogenes in any microbiological culture was defined as a case. Clinical data were taken from medical charts. K. aerogenes isolates were genotyped using whole-genome sequencing combined with core genome multilocus sequencing type analysis. Yersiniabactin production was evaluated by luciferase assay.

Results

In total 16 patients were colonized with K. aerogenes over the 3-month period and 13 patients remained asymptomatic or developed late-onset neonatal sepsis from another pathogen. Three patients developed necrotizing enterocolitis, 2 complicated by sepsis and 1 of them died. All symptomatic patients were premature infants with low birth weight. Genetic sequencing confirmed an outbreak with the same strain, all samples expressed the high-pathogenicity island, necessary for the production of yersiniabactin. Six exemplary cases were proven to produce yersiniabactin in vitro.

Conclusion

This is the first report of an outbreak of a yersiniabactin-producing K. aerogenes strain causing invasive infection in preterm infants. We hypothesize that, due to improved iron uptake, this strain was associated with higher virulence than non-yersiniabactin-producing strains. Extended search for virulence factors and genetic sequencing could be pivotal in the management of NICU outbreaks in the future.", "token_count": 478, "char_count": 1849, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6324, "quality_score": 0.8162, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:02.687924", "source": { "split": "train_shard_00001", "doc_id": 3583 }, "chunk_id": "train_shard_00001_3583_0", "global_id": 10734 }, { "text": "A Yersiniabactin-producing Klebsiella aerogenes Strain Causing an Outbreak in an Austrian Neonatal Intensive Care Unit.", "token_count": 37, "char_count": 119, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:03.042853", "source": { "split": "train_shard_00001", "doc_id": 3583 }, "chunk_id": "train_shard_00001_3583_1", "global_id": 10735 }, { "text": "We report herein the results of antifungal activity of fifteen 1,2,3-triazoles against Candida albicans, Candida krusei, Candida parapsilosis, Candida kefyr, Candida tropicalis, Candida dubliniensis, Tricophyton rubrum, Microporum canis and Aspergillus niger. All of the 1,2,3-triazoles were prepared from 1,3-dipolar cyclizations between aryl azides and alkynes catalyzed by Cu(I), and several of the compounds exhibited antifungal activity with low cytotoxicity. The results demonstrated the potential and importance of developing new 1,2,3-triazoles compounds with antifungal activity.\n\nSynthesis of 1H-1,2,3-triazoles and study of their antifungal and cytotoxicity activities.", "token_count": 212, "char_count": 680, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:03.512443", "source": { "split": "train_shard_00001", "doc_id": 3584 }, "chunk_id": "train_shard_00001_3584_0", "global_id": 10736 }, { "text": "The human microbiome contributes significantly to the genetic content of the human body. Genetic and environmental factors help shape the microbiome, and as such, the microbiome can be unique to an individual. Previous studies have demonstrated the potential to use microbiome profiling for forensic applications; however, a method has yet to identify stable features of skin microbiomes that produce high classification accuracies for samples collected over reasonably long time intervals. A novel approach is described here to classify skin microbiomes to their donors by comparing two feature types: Propionibacterium acnes pangenome presence/absence features and nucleotide diversities of stable clade-specific markers. Supervised learning was used to attribute skin microbiomes from 14 skin body sites from 12 healthy individuals sampled at three time points over a >2.5-year period with accuracies of up to 100% for three body sites. Feature selection identified a reduced subset of markers from each body site that are highly individualizing, identifying 187 markers from 12 clades. Classification accuracies were compared in a formal model testing framework, and the results of this analysis indicate that learners trained on nucleotide diversity perform significantly better than those trained on presence/absence encodings. This study used supervised learning to identify individuals with high accuracy and associated stable features from skin microbiomes over a period of up to almost 3 years. These selected features provide a preliminary marker panel for future development of a robust and reproducible method for skin microbiome profiling for forensic human identification.IMPORTANCE A novel approach is described to attribute skin microbiomes, collected over a period of >2.5 years, to their individual hosts with a high degree of accuracy. Nucleotide diversities of stable clade-specific markers with supervised learning were used to classify skin microbiomes from a particular individual with up to 100% classification accuracy for three body sites. Attribute selection was used to identify 187 genetic markers from 12 clades which provide the greatest differentiation of individual skin microbiomes from 14 skin sites. This study performs skin microbiome profiling from a supervised learning approach and obtains high classification accuracy for samples collected from individuals over a relatively long time period for potential application to forensic human identification.", "token_count": 520, "char_count": 2507, "word_count": 356, "semantic_coherence": 1, "information_density": 0.4635, "quality_score": 0.7317, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:40:04.174068", "source": { "split": "train_shard_00001", "doc_id": 3585 }, "chunk_id": "train_shard_00001_3585_0", "global_id": 10737 }, { "text": "Forensic Human Identification Using Skin Microbiomes.", "token_count": 13, "char_count": 53, "word_count": 6, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:04.568698", "source": { "split": "train_shard_00001", "doc_id": 3585 }, "chunk_id": "train_shard_00001_3585_1", "global_id": 10738 }, { "text": "Staphylococcus haemolyticus is one of the most important nosocomial human pathogens frequently isolated in bloodstream and medical devices related infections. This species is notorious for its multidrug resistance and genome plasticity. However, its mechanisms of evolution and adaptation are still poorly explored. In this study we aimed to characterize the strategies of genetic and phenotypic diversity in S. haemolyticus . Here, we analyzed an invasive S. haemolyticus strain, recovered from a bloodstream infection, for genetic and phenotypic stability after serial passage in vitro (>400 generations) in the absence and presence of sub-inhibitory concentrations of a beta-lactam antibiotic. We performed PFGE of the culture and five colonies at seven time points during stability assays were analyzed for beta-lactams susceptibility, hemolysis, mannitol fermentation and biofilm production. We compared their whole genome regarding chromosomal structure, gene content and mutations and preformed phylogenetic analysis based on core SNPs. We observed a high instability in the PFGE profiles at the different time points during serial passage in vitro in the absence of antibiotic. However, no variation was observed in PFGE patterns in the presence of beta-lactams. Analysis of WGS data for individual colonies collected at different time points showed the occurrence of six large-scale genomic deletions within the oriC environ (36 kbp-348 kbp) in the cell populations analyzed, smaller deletions in non-OriC environ region as well as non-synonymous mutations in clinically relevant genes. The regions of deletion and point mutations included genes encoding amino acid and metal transporters, resistance to environmental stress and beta-lactams, virulence, mannitol fermentation, metabolic processes and IS elements. A parallel variation was additionally detected in clinically significant phenotypic traits such as mannitol fermentation, beta-lactams resistance, hemolysis and biofilm formation. All the genetic variants analyzed were closely related in their core genome (13-292 SNPs). Our results suggest that S", "token_count": 488, "char_count": 2120, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:05.264253", "source": { "split": "train_shard_00001", "doc_id": 3586 }, "chunk_id": "train_shard_00001_3586_0", "global_id": 10739 }, { "text": "haemolyticus populations are composed of subpopulations of genetic and phenotypic variants that might be affected in antibiotic and stress resistance, specific metabolic processes and virulence. The maintenance of subpopulations in different physiological states might be a strategy to adapt rapidly to a stress situation imposed by the host particularly in the hospital environment.\n\nSpontaneous genomic variation as a survival strategy of nosocomial S. haemolyticus", "token_count": 105, "char_count": 474, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:05.665124", "source": { "split": "train_shard_00001", "doc_id": 3586 }, "chunk_id": "train_shard_00001_3586_1", "global_id": 10740 }, { "text": "

Introduction

Commensal and pathogenic strains of multidrug-resistant (MDR) Escherichia coli and non-typhoid strains of Salmonella represent a growing foodborne threat from foods of poultry origin. MDR strains of Salmonella Infantis and E. coli are frequently isolated from broiler chicks and the simultaneous presence of these two enteric bacterial species would potentially allow the exchange of mobile resistance determinants.

Objectives

In order to understand possible genomic relations and to obtain a first insight into the potential interplay of resistance genes between enteric bacteria, we compared genomic diversity and mobile resistomes of S. Infantis and E. coli from broiler sources.

Results

The core genome MLST analysis of 56 S. Infantis and 90 E. coli contemporary strains revealed a high genomic heterogeneity of broiler E. coli. It also allowed the first insight into the genomic diversity of the MDR clone B2 of S. Infantis, which is endemic in Hungary. We also identified new MDR lineages for S. Infantis (ST7081 and ST7082) and for E. coli (ST8702 and ST10088). Comparative analysis of antibiotic resistance genes and plasmid types revealed a relatively narrow interface between the mobile resistomes of E. coli and S. Infantis. The mobile resistance genes tet(A), aadA1, and sul1 were identified at an overall high prevalence in both species. This gene association is characteristic to the plasmid pSI54/04 of the epidemic clone B2 of S. Infantis", "token_count": 497, "char_count": 1615, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5388, "quality_score": 0.7694, "entities": { "genes": [ "ST7082", "ST8702", "ST7081", "ST10088" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:06.373421", "source": { "split": "train_shard_00001", "doc_id": 3587 }, "chunk_id": "train_shard_00001_3587_0", "global_id": 10741 }, { "text": "Simultaneous presence of these genes and of IncI plasmids of the same subtype in cohabitant caecal strains of E. coli and S. Infantis suggests an important role of these plasmid families in a possible interplay of resistance genes between S. Infantis and E. coli in broilers.

Conclusion

This is the first comparative genomic analysis of contemporary broiler strains of S. Infantis and E. coli. The diversity of mobile resistomes suggests that commensal E. coli could be potential reservoirs of resistance for S. Infantis, but so far only a few plasmid types and mobile resistance genes could be considered as potentially exchangeable between these two species. Among these, IncI1 plasmids could make the greatest contribution to the microevolution and genetic interaction between E. coli and S. Infantis.\n\nComparative Genomics of Emerging Lineages and Mobile Resistomes of Contemporary Broiler Strains of Salmonella Infantis and E. coli.", "token_count": 300, "char_count": 1028, "word_count": 142, "semantic_coherence": 1, "information_density": 0.5423, "quality_score": 0.7711, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:06.931514", "source": { "split": "train_shard_00001", "doc_id": 3587 }, "chunk_id": "train_shard_00001_3587_1", "global_id": 10742 }, { "text": "

Background

With the rapid development of accurate sequencing and assembly technologies, an increasing number of high-quality chromosome-level and haplotype-resolved assemblies of genomic sequences have been derived, from which there will be great opportunities for computational pangenomics. Although genome graphs are among the most useful models for pangenome representation, their structural complexity makes it difficult to present genome information intuitively, such as the linear reference genome. Thus, efficiently and accurately analyzing the genome graph spatial structure and coordinating the information remains a substantial challenge.

Results

We developed a new method, a colored superbubble (cSupB), that can overcome the complexity of graphs and organize a set of species- or population-specific haplotype sequences of interest. Based on this model, we propose a tri-tuple coordinate system that combines an offset value, topological structure and sample information. Additionally, cSupB provides a novel method that utilizes complete topological information and efficiently detects small indels (< 50 bp) for highly similar samples, which can be validated by simulated datasets. Moreover, we demonstrated that cSupB can adapt to the complex cycle structure.

Conclusions

Although the solution is made suitable for increasingly complex genome graphs by relaxing the constraint, the directed acyclic graph, the motif cSupB and the cSupB method can be extended to any colored directed acyclic graph. We anticipate that our method will facilitate the analysis of individual haplotype variants and population genomic diversity. We have developed a C +  + program for implementing our method that is available at https://github.com/eggleader/cSupB .\n\nA tri-tuple coordinate system derived for fast and accurate analysis of the colored de Bruijn graph-based pangenomes.", "token_count": 421, "char_count": 1900, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:07.560228", "source": { "split": "train_shard_00001", "doc_id": 3588 }, "chunk_id": "train_shard_00001_3588_0", "global_id": 10743 }, { "text": "In this study, the lactic fermentation of immature tomatoes as a tool for food ingredient production was evaluated as a circular economy-oriented alternative for valorising industrial tomatoes that are unsuitable for processing and which have wasted away in large quantities in the field. Two lactic acid bacteria (LAB) were assessed as starter cultures in an immature tomato pulp fermentation to produce functional food ingredients with probiotic potential. The first trial evaluated the probiotic character of Lactiplantibacillus plantarum (LAB97, isolated from immature tomato microbiota) and Weissella paramesenteroides (C1090, from the INIAV collection) through in vitro gastrointestinal digestion simulation. The results showed that LAB97 and C1090 met the probiotic potential viability criterion by maintaining 6 log10 CFU/mL counts after in vitro simulation. The second trial assessed the LAB starters' fermentative ability. Partially decontaminated (110 °C/2 min) immature tomato pulp was used to prepare the individually inoculated samples (Id: LAB97 and C1090). Non-inoculated samples, both with and without thermal treatment (Id: CTR-TT and CTR-NTT, respectively), were prepared as the controls. Fermentation was undertaken (25 °C, 100 rpm) for 14 days. Throughout storage (0, 24, 48, 72 h, 7, and 14 days), all the samples were tested for LAB and Y&M counts, titratable acidity (TA), solid soluble content (SSC), total phenolic content (TPC), antioxidant capacity (AOx), as well as for organic acids and phenolic profiles, and CIELab colour and sensory evaluation (14th day). The LAB growth reached ca. 9 log10 CFU/mL for all samples after 72 h. The LAB97 samples had an earlier and higher acidification rate than the remaining ones, and they were highly correlated to lactic acid increments", "token_count": 518, "char_count": 1840, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [ "LAB97" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:40:08.214250", "source": { "split": "train_shard_00001", "doc_id": 3589 }, "chunk_id": "train_shard_00001_3589_0", "global_id": 10744 }, { "text": "The inoculated samples showed a faster and higher decrease rate in their SSC levels when compared to the controls. A nearly two-fold increase (p < 0.05) during the fermentation, over time, was observed in all samples' AOx and TPC (p < 0.05, r = 0.93; similar pattern). The LAB97 samples obtained the best sensory acceptance for flavour and overall appreciation scores when compared to the others. In conclusion, the L. plantarum LAB97 starter culture was selected as a novel probiotic candidate to obtain a potential probiotic ingredient from immature tomato fruits.\n\nValorisation of Wasted Immature Tomato to Innovative Fermented Functional Foods.", "token_count": 186, "char_count": 669, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7426, "quality_score": 0.8713, "entities": { "genes": [ "LAB97" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:08.661376", "source": { "split": "train_shard_00001", "doc_id": 3589 }, "chunk_id": "train_shard_00001_3589_1", "global_id": 10745 }, { "text": "beta-Galactosidase production by K. marxianus was studied in shake flasks. Enzyme production was strongly influenced by culture conditions determining oxygen transfer rates. Working volume turned out to be the most significant parameter affecting enzyme yields: the higher the volume, the higher the specific activity of the enzyme. The use of dehydrated whey (as the source of lactose) resulted in a large increase in the specific enzyme activity as compared with the use of pure lactose. This effect is likely due to a lower dissolved oxygen concentration along the fermentation. In the range of kL a between 40 and 90 h-1, enzyme activity did not seem to depend on kL a, whereas a drastic drop in the final specific enzyme activity was observed for kL a values above 90 h-1.\n\nbeta-Galactosidase production by Kluyveromyces marxianus cultured in shake flasks.", "token_count": 220, "char_count": 861, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6232, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:09.121497", "source": { "split": "train_shard_00001", "doc_id": 3590 }, "chunk_id": "train_shard_00001_3590_0", "global_id": 10746 }, { "text": "Homologous recombination is expected to increase natural selection efficacy by decoupling the fate of beneficial and deleterious mutations and by readily creating new combinations of beneficial alleles. Here, we investigate how the proportion of amino acid substitutions fixed by adaptive evolution ( α ) depends on the recombination rate in bacteria. We analyze 3086 core protein-coding sequences from 196 genomes belonging to five closely-related species of the genus Rhizobium . These genes are found in all species and do not display any signs of introgression between species. We estimate α using the site frequency spectrum (SFS) and divergence data for all pairs of species. We evaluate the impact of recombination within each species by dividing genes into three equally sized recombination classes based on their average level of intragenic linkage disequilibrium. We find that α varies from 0.07 to 0.39 across species and is positively correlated with the level of recombination. This is both due to a higher estimated rate of adaptive evolution and a lower estimated rate of non-adaptive evolution, suggesting that recombination both increases the fixation probability of advantageous variants and decreases the probability of fixation of deleterious variants. Our results demonstrate that homologous recombination facilitates adaptive evolution measured by α in the core genome of prokaryote species in agreement with studies in eukaryotes.

Significance statement

Whether intraspecific homologous recombination has a net beneficial or detrimental effect on adaptive evolution is largely unexplored in natural bacterial populations. We address this question by evaluating polymorphism and divergence data across the core genomes of 196 bacterial sequences––belonging to five closely related species of the genus Rhizobium . We show that the proportion of amino acid changes fixed due to adaptive evolution ( α ) increases with an increased recombination rate. This correlation is observed both in the interspecies and intraspecific comparisons. By using a population genetics approach our results demonstrate that homologous recombination directly impacts the efficacy of natural selection in the core genome of prokaryotes, as previously reported in eukaryotes.", "token_count": 511, "char_count": 2283, "word_count": 331, "semantic_coherence": 1, "information_density": 0.5196, "quality_score": 0.7598, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:09.775821", "source": { "split": "train_shard_00001", "doc_id": 3591 }, "chunk_id": "train_shard_00001_3591_0", "global_id": 10747 }, { "text": "Recombination facilitates adaptive evolution in rhizobial soil bacteria", "token_count": 16, "char_count": 71, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:10.126359", "source": { "split": "train_shard_00001", "doc_id": 3591 }, "chunk_id": "train_shard_00001_3591_1", "global_id": 10748 }, { "text": "Clostridioides difficile is the most important pathogen causing antimicrobial-associated diarrhea and has recently been recognized as a cause of community-associated C. difficile infection (CA-CDI). This study aimed to characterize virulence factors, antimicrobial resistance (AMR), ribotype (RT) distribution and genetic relationship of C. difficile isolates from diverse fecally contaminated environmental sources. C. difficile isolates were recovered from different environmental samples in Northern Germany. Antimicrobial susceptibility testing was determined by E-test or disk diffusion method. Toxin genes (tcdA and tcdB), genes coding for binary toxins (cdtAB) and ribotyping were determined by PCR. Furthermore, 166 isolates were subjected to whole genome sequencing (WGS) for core genome multi-locus sequence typing (cgMLST) and extraction of AMR and virulence-encoding genes. Eighty-nine percent (148/166) of isolates were toxigenic, and 51% (76/148) were positive for cdtAB. Eighteen isolates (11%) were non-toxigenic. Thirty distinct RTs were identified. The most common RTs were RT127, RT126, RT001, RT078, and RT014. MLST identified 32 different sequence types (ST). The dominant STs were ST11, followed by ST2, ST3, and ST109. All isolates were susceptible to vancomycin and metronidazole and displayed a variable rate of resistance to moxifloxacin (14%), clarithromycin (26%) and rifampicin (2%)", "token_count": 458, "char_count": 1467, "word_count": 190, "semantic_coherence": 1, "information_density": 0.7105, "quality_score": 0.8553, "entities": { "genes": [ "ST2", "RT078", "ST3", "RT014", "ST109", "RT001", "ST11", "RT127", "RT126" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:10.761848", "source": { "split": "train_shard_00001", "doc_id": 3592 }, "chunk_id": "train_shard_00001_3592_0", "global_id": 10749 }, { "text": "AMR genes, such as gyrA/B, blaCDD-1/2, aph(3')-llla-sat-4-ant(6)-la cassette, ermB, tet(M), tet(40), and tetA/B(P), conferring resistance toward fluoroquinolone, beta-lactam, aminoglycoside, macrolide and tetracycline antimicrobials, were found in 166, 137, 29, 32, 21, 72, 17, and 9 isolates, respectively. Eleven \"hypervirulent\" RT078 strains were detected, and several isolates belonged to RTs (i.e., RT127, RT126, RT023, RT017, RT001, RT014, RT020, and RT106) associated with CA-CDI, indicating possible transmission between humans and environmental sources pointing out to a zoonotic potential.\n\nClostridioides difficile from Fecally Contaminated Environmental Sources: Resistance and Genetic Relatedness from a Molecular Epidemiological Perspective.", "token_count": 332, "char_count": 825, "word_count": 92, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [ "RT106", "RT078", "RT014", "RT017", "RT023", "RT020", "RT001", "RT127", "RT126" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:11.327402", "source": { "split": "train_shard_00001", "doc_id": 3592 }, "chunk_id": "train_shard_00001_3592_1", "global_id": 10750 }, { "text": "The current study evaluates antibiotic susceptibility and Extended Spectrum β-Lactamase (ESBL) production of 557 Escherichia coli isolates obtained from clean catch midstream urine samples using VITEK 2 compact automated microbial identification system. Different classes of drugs were used to determine the Minimum inhibitory concentration (MIC). In our study, 50.45% of isolates were ESBL producers. There is a higher incidence of UTI in females (77.4%) than in males (22.6%). The isolates reveal a high percentage of resistance to antibiotics like nalidixic acid (89.59%), ampicillin (75.76%), ticarcillin (73.43%), cefalotin (67.68%), cefixime (65.17%), ciprofloxacin (58.35%) and ceftriaxone (56.37%). An increased susceptibility pattern was observed for the isolates against drug classes like fosfomycin (98.03%) and nitrofurantoin (91.02%). Among the isolates, 395 (70.91%) were classified as Multidrug-resistant organisms based on the resistance pattern observed against three or more classes of antibiotics. One of the isolates resistant to fluoroquinolones, penicillins, penicillins along with β-lactamase inhibitor, aminoglycosides, third-generation cephalosporins and carbapenems was subjected to Whole genome sequencing (WGS)", "token_count": 395, "char_count": 1245, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7702, "quality_score": 0.8851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:11.938826", "source": { "split": "train_shard_00001", "doc_id": 3593 }, "chunk_id": "train_shard_00001_3593_0", "global_id": 10751 }, { "text": "WGS data revealed the isolate to be a high-risk clone ST410, which contains antimicrobial-resistance genes (blaTEM-1B, blaCTX-M-15, blaNDM-5, aac(3)-IId, armA, gyrA(p.S83L), gyrA(p.D87N)) conferring resistance to β-lactam, cephalosporins, carbapenem, aminoglycoside and fluoroquinolone class of antibiotics. The core genome MLST was carried out using BacWGSTdb to assess the global phylogenetic relationship of the genome sequence.

Supplementary information

The online version contains supplementary material available at 10.1007/s12088-023-01125-1.\n\nThe Prevalence of Multidrug-Resistant <i>Escherichia coli</i> in Chennai and Whole Genome Sequence Analysis of Carbapenem-Resistant <i>Escherichia coli</i> ST410.", "token_count": 322, "char_count": 786, "word_count": 80, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [ "ST410" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:12.503884", "source": { "split": "train_shard_00001", "doc_id": 3593 }, "chunk_id": "train_shard_00001_3593_1", "global_id": 10752 }, { "text": "Thermal inactivation of the Kluyveromyces marxianus inulinase in a free form and immobilized on VION KN-1 cation exchange fiber was studied. Atomic force microscopy demonstrated an oligomeric structure of this enzyme, composed of two subunits differing in their size. It was assumed that the intersubunit contacts were destroyed at 60 degrees C, and the inulinase molecule dissociated into two monomers located separately.\n\n[Thermal inactivation of free and immobilized inulinase].", "token_count": 127, "char_count": 481, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7971, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:12.894328", "source": { "split": "train_shard_00001", "doc_id": 3594 }, "chunk_id": "train_shard_00001_3594_0", "global_id": 10753 }, { "text": "

Background

Cases of Clostridiodes difficile infection (CDI) diagnosed after hospital discharge account for a substantial proportion of new infections. It is unclear whether post-discharge infections originate from hospital-based transmission.

Methods

This was a Retrospective cohort study at a tertiary-care cancer center (non-outbreak setting). For all laboratory-identified cases of CDI in 2015-2016, patients with post-discharge (PD) CDI within eight weeks of their hospital stay were included in the study. Isolates from PD-CDI cases and their CDI-positive unit-based contacts were first genotyped by multilocus sequence typing (MLST). Common strains were further examined by core genome sequencing (CGS) to evaluate transmission links.

Results

Of 173 cases examined by MLST, 50% of PD cases matched previous unit contacts. Next, 34 isolates, including 16 PD cases and their 18-unit contacts were examined by CGS. None were ≤3 single-nucleotide variants apart. Seventy percent of PD cases had in-hospital antibiotic exposure before CDI onset in the community.

Conclusion

Our study results suggest that symptomatic CDI cases are not a substantial source of transmission to PD cases. Frequent antibiotic exposure in post-discharge CDI cases is an important target for surveillance and stewardship efforts.\n\nGenotypic correlation between post discharge Clostridiodes difficle infection (CDI) and previous unit-based contacts.", "token_count": 385, "char_count": 1455, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6754, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:13.513177", "source": { "split": "train_shard_00001", "doc_id": 3595 }, "chunk_id": "train_shard_00001_3595_0", "global_id": 10754 }, { "text": "Pneumococcal conjugate vaccines (PCV) have reduced pneumococcal diseases globally. Despite this, much remains to be learned about their effect on pathogen population structure. Here we undertook whole genome sequencing of 660 pneumococcal strains from asymptomatic carriers to investigate population restructuring in pneumococcal strains sampled before and after PCV13 introduction in a previously vaccine-naïve setting. We show substantial decreasing frequency of vaccine-type (VT) strains and their strain diversity post-vaccination in the vaccinated but not unvaccinated age groups indicative of direct but limited or delayed indirect effect of vaccination. Clearance of identical VT serotypes associated with multiple lineages occurred regardless of their genetic background. Interestingly, despite the increasing frequency of non-vaccine type (NVT) strains through serotype replacement, the serotype diversity was not fully restored to the levels observed prior to vaccination implying limited serotype replacement. The frequency of antibiotic resistant strains was low and remained largely unchanged post-vaccination but intermediate-penicillin-resistant lineages were reduced in the post vaccine population. Significant perturbations marked by changing frequency of accessory genes associated with diverse functions especially mobile genetic elements and bacteriocin activity were detected. This phylogenomic analysis demonstrates early vaccine-induced pneumococcal population restructuring not only at serotype but also accessory genome level.

Author summary

Different formulations of PCVs have been effective in reducing the invasive pneumococcal disease burden globally. Clinical trials have started to indicate high impact and effectiveness of PCV13 in Sub Saharan Africa (SSA) but there is limited understanding of how the introduction of PCVs alters the population structure of pneumococcal strains at serotype and genomic level. Here we investigated this using pneumococcal strains sampled pre‐ and post-PCV13 introduction from a previously vaccine naïve setting in Northern Malawi. Our findings reveal decrease in frequency of VT serotypes and their associated lineages in the largely vaccinated under-five population but not older individuals indicating a direct but limited or delayed indirect protection", "token_count": 499, "char_count": 2330, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [ "PCV13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:14.164430", "source": { "split": "train_shard_00001", "doc_id": 3596 }, "chunk_id": "train_shard_00001_3596_0", "global_id": 10755 }, { "text": "The diversity of serotypes also decreased post-vaccination in VT strains in the under-fives but there was no change in NVT strains suggesting incomplete serotype replacement. At the genomic level, logistic regression revealed changing frequency of accessory genes largely associated with mobile genetic elements but such changes did not include any antibiotic resistance genes. These findings show significant perturbations at serotype and accessory genome level in carried pneumococcal population after two years from PCV13 introduction but the pneumococcal population was still perturbed and had not returned to a new equilibrium state.\n\nEarly signals of vaccine driven perturbation seen in pneumococcal carriage population genomic data", "token_count": 153, "char_count": 738, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7767, "quality_score": 0.8883, "entities": { "genes": [ "PCV13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:14.603183", "source": { "split": "train_shard_00001", "doc_id": 3596 }, "chunk_id": "train_shard_00001_3596_1", "global_id": 10756 }, { "text": "Through preliminary plate tests, Kluyveromyces marxianus was found to be much more resistant to toxic heavy metals compared to a CUP1R strain of Saccharomyces cerevisiae. Specific growth rate and maximum dry weights affected by increasing metal concentrations were determined to obtain precise patterns of resistance. Metal biosorption was also monitored during the course of growth in synthetic media containing respective metals at 0.5 mM final concentration. Although Zn- and Co-binding was negligible, as much as 90% of silver, 60% of copper, and 65% of cadmium were found to be absorbed by the end of active growth. Analysis of the protein profiles of S. cerevisiae and K. marxianus on metal exposure suggested constitutive production of metallothionein in K. marxianus. Furthermore, a smaller protein synthesized by K. marxianus on induction by silver or cadmium accounts for the high resistance of the organism to these metals.\n\nStudies on metal resistance system in Kluyveromyces marxianus.", "token_count": 247, "char_count": 998, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8311, "entities": { "genes": [ "CUP1R" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:15.088046", "source": { "split": "train_shard_00001", "doc_id": 3597 }, "chunk_id": "train_shard_00001_3597_0", "global_id": 10757 }, { "text": "Salmonella is a prevalent zoonotic foodborne pathogen. Swine and pork are implicated as important sources of salmonellosis in humans. In Chiang Mai and Lamphun Provinces in northern Thailand, there has been a high prevalence of Salmonella persistence for over a decade. Infection is usually with dominant S. enterica serotypes, including serotypes Rissen and 1,4,[5],12:i:-. However, other serotypes also contribute to disease but are less well characterized. The whole genome sequencing data of 43 S. enterica serotypes isolated from pork production chain through 2011-2014, were used to evaluate genetic diversity and ascertain the possible source of Salmonella contamination based on Core Genome Multilocus Sequence Typing (cgMLST) approach. The Salmonella serotypes recovered from farms and slaughterhouses were re-circulating by swine environmental contamination. Conversely, the Salmonella contamination in the retail market represents cross-contamination from multiple sources, including contaminated foodstuffs. Salmonella contamination in the pork production chain has the competency for host cell adhesion, host cell invasion, and intracellular survival, which is enough for the pathogenicity of salmonellosis. In addition, all of these isolates were multi-drug resistant Salmonella, which contained at least 10 antimicrobial resistance genes. This result indicated that these S. enterica serotypes also pose a significant public health risk. Our findings support the need for appropriate surveillance of food-animal products going to market to reduce public exposure to highly pathogenic, multi-drug resistant Salmonella. Acquiring information would motivate all stakeholders to reinforce sanitation standards throughout the pork production chain in order to eradicate Salmonella contamination and reduce the risk of salmonellosis in humans.", "token_count": 501, "char_count": 1936, "word_count": 250, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:15.746270", "source": { "split": "train_shard_00001", "doc_id": 3598 }, "chunk_id": "train_shard_00001_3598_0", "global_id": 10758 }, { "text": "Genome-based analysis of infrequent <i>Salmonella</i> serotypes through the Thai pork production chain.", "token_count": 38, "char_count": 115, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:16.104596", "source": { "split": "train_shard_00001", "doc_id": 3598 }, "chunk_id": "train_shard_00001_3598_1", "global_id": 10759 }, { "text": "A two-strain starter culture containing Lactobacillus plantarum CIDCA 83114, a potential probiotic strain isolated from kefir grains, and Streptococcus thermophilus CIDCA 321 was tested for the preparation of a fermented milk product. Kluyveromyces marxianus CIDCA 8154, a yeast with immunomodulatory properties was included to formulate a three-strain starter culture. Supernatants of enterohaemorragic Escherichia coli, shiga-toxin-producing strain, along with a two-strain or a three-strain starter culture were included in the medium of Vero-cell surface cultures. The results demonstrated that these combinations of microorganisms antagonize the cytopathic action of shiga toxins. The cell concentration of Lb. plantarum did not decrease during fermentation, indicating that the viability of this strain was not affected by low pH, nor did the number of viable bacteria change during 21 days of storage in either fermented products. The number of viable yeasts increases during fermentation and storage. Trained assessors analyzed the general acceptability of fresh fermented milks and considered both acceptable. The milk fermented with the two-strain starter culture was considered acceptable after two week of storage, while the product fermented with the three-strain starter culture remained acceptable for less than one week. The main changes in sensory attributes detected by the trained panel were in sour taste, milky taste and also in fermented attributes. The correlation between different sensory attributes and acceptability indicated that the panel was positively influenced by milky attributes (taste, odour, and flavour) as well as the intensity of flavour. In conclusion, the two-strain starter culture would be the more promising alternative for inclusion of that potential probiotic lactobacillus in a fermented milk product.\n\nPhysicochemical, microbiological and sensory profiles of fermented milk containing probiotic strains isolated from kefir.", "token_count": 477, "char_count": 1972, "word_count": 275, "semantic_coherence": 1, "information_density": 0.56, "quality_score": 0.78, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:16.790111", "source": { "split": "train_shard_00001", "doc_id": 3599 }, "chunk_id": "train_shard_00001_3599_0", "global_id": 10760 }, { "text": "Microcystis aeruginosa is one of the most common bloom-forming cyanobacteria in freshwater ecosystems worldwide. This species produces numerous secondary metabolites, including microcystins, which are harmful to human health. We sequenced the genomes of ten strains of M. aeruginosa in order to explore the genomic basis of their ability to occupy varied environments and proliferate. Our findings show that M. aeruginosa genomes are characterized by having a large open pangenome, and that each genome contains similar proportions of core and flexible genes. By comparing the GC content of each gene to the mean value of the whole genome, we estimated that in each genome, around 11% of the genes seem to result from recent horizontal gene transfer events. Moreover, several large gene clusters resulting from HGT (up to 19 kb) have been found, illustrating the ability of this species to integrate such large DNA molecules. It appeared also that all M. aeruginosa displays a large genomic plasticity, which is characterized by a high proportion of repeat sequences and by low synteny values between the strains. Finally, we identified 13 secondary metabolite gene clusters, including three new putative clusters. When comparing the genomes of Microcystis and Prochlorococcus, one of the dominant picocyanobacteria living in marine ecosystems, our findings show that they are characterized by having almost opposite evolutionary strategies, both of which have led to ecological success in their respective environments.\n\nA tribute to disorder in the genome of the bloom-forming freshwater cyanobacterium Microcystis aeruginosa.", "token_count": 362, "char_count": 1628, "word_count": 243, "semantic_coherence": 1, "information_density": 0.5967, "quality_score": 0.7984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:17.398325", "source": { "split": "train_shard_00001", "doc_id": 3600 }, "chunk_id": "train_shard_00001_3600_0", "global_id": 10761 }, { "text": "

Unlabelled

Three batches of soft smear-ripened Taleggio PDO cheese were made in Northern Italy during the summertime 2010. A total of 129 isolates cultured from cheese surface were examined by using PCR-based methods and sequencing of both the ITS1 region and D1 and D2 domains of the 26S rRNA gene. Sequence analysis of isolates brought to the identification of 6 species: Debaryomyces hansenii, Kluyveromyces lactis, Kluyveromyces marxianus, Yarrowia lipolytica, Pichia guilliermondii, and Torulaspora delbrueckii. Analysis of DNA directly extracted from 45 cheese surfaces permitted to detect 2 additional species Candida sake and Candida etchellsii. D. hansenii was predominant and widespread whereas the other yeast species were detected less frequently. To determine the relationships between yeast community and the environment, 39 isolates from wooden boxes used for dry salting of cheese were analyzed as well. Sequencing of ITS1 region allowed to identify D. hansenii, T. delbrueckii, and K. lactis. ITS1 multiple sequence alignments of D. hansenii detected in wooden boxes showed an in-del polymorphism at position 169. ITS1 secondary structures of yeasts were modeled to explore new applications of this region for molecular identification purposes.

Practical application

This study used molecular analysis to identify adventitious yeast population present in the surface of Taleggio smear-ripened cheese. D. hansenii was found predominant in pasteurized milk, in dry salting equipment, and in all cheese samples until the end of ripening.\n\nInternal transcribed spacer as a target to assess yeast biodiversity in Italian Taleggio PDO cheese.", "token_count": 434, "char_count": 1668, "word_count": 238, "semantic_coherence": 1, "information_density": 0.605, "quality_score": 0.8025, "entities": { "genes": [ "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:18.520586", "source": { "split": "train_shard_00001", "doc_id": 3601 }, "chunk_id": "train_shard_00001_3601_0", "global_id": 10762 }, { "text": "The purpose of this study was to characterize microbial biofilms from 'gerles' (wooden vats for making PDO Salers cheese) and identify their role in milk inoculation and in preventing pathogen development. Gerles from ten farms producing PDO Salers cheese were subjected to microbial analysis during at least 4 periods spread over two years. They were distinguished by their levels of Lactobacillus (between 4.50 and 6.01 log CFU/cm(2)), Gram negative bacteria (between 1.45 and 4.56 log CFU/cm(2)), yeasts (between 2.91 and 5.57 log CFU/cm(2)), and moulds (between 1.72 and 4.52 log CFU/cm(2)). They were then classed into 4 groups according their microbial characteristics. These 4 groups were characterized by different milk inoculations (with either sour whey or starter culture, daily or not), and different washing procedures (with water or whey from cheese making). The farm gerles were not contaminated by Salmonella, Listeria monocytogenes or Staphylococcus aureus. Only one slight, punctual contamination was found on one gerle among the ten studied. Even when the milk was deliberately contaminated with L. monocytogenes and S. aureus in the 40 L experimental gerles, these pathogens were found neither on the gerle surfaces nor in the cheeses. Using 40 L experimental gerles it was shown that the microbial biofilms on the gerle surfaces formed in less than one week and then remained stable", "token_count": 380, "char_count": 1403, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6221, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:19.107348", "source": { "split": "train_shard_00001", "doc_id": 3602 }, "chunk_id": "train_shard_00001_3602_0", "global_id": 10763 }, { "text": "They were mainly composed of a great diversity of lactic acid bacteria (Leuconostoc pseudomesenteroides, Lactococcus lactis, Lactobacillus casei, Lactobacillus plantarum, Lactobacillus hilgardii,…), Gram positive catalase positive bacteria (Curtobacterium flaccumfaciens, Curtobacterium oceanosedimentum Citrococcus spp., Brachybacterium rhamnosum, Kocuria rhizophila, Arthrobacter spp.…) and yeast (Kluyveromyces lactis, Kluyveromyces marxianus). In less than 1 min, even in a 500 L farm gerle, the gerle's microbial biofilm can inoculate pasteurized milk with micro-organisms at levels superior to those in raw milk.\n\nCharacteristics of microbial biofilm on wooden vats ('gerles') in PDO Salers cheese.", "token_count": 229, "char_count": 704, "word_count": 87, "semantic_coherence": 1, "information_density": 0.8506, "quality_score": 0.9253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:19.574173", "source": { "split": "train_shard_00001", "doc_id": 3602 }, "chunk_id": "train_shard_00001_3602_1", "global_id": 10764 }, { "text": "Pseudomonas aeruginosa is an opportunistic human pathogen that frequently causes health care-associated infections (HAIs). Due to its metabolic diversity and ability to form biofilms, this Gram-negative nonfermenting bacterium can persist in the health care environment, which can lead to prolonged HAI outbreaks. We describe the creation of a core genome multilocus sequence typing (cgMLST) scheme to provide a stable platform for the rapid comparison of P. aeruginosa isolates using whole-genome sequencing (WGS) data. We used a diverse set of 58 complete P. aeruginosa genomes to curate a set of 4,440 core genes found in each isolate, representing ∼64% of the average genome size. We then expanded the alleles for each gene using 1,991 contig-level genome sequences. The scheme was used to analyze genomes from four historical HAI outbreaks to compare the phylogenies generated using cgMLST to those of other means (traditional MLST, pulsed-field gel electrophoresis [PFGE], and single-nucleotide variant [SNV] analysis). The cgMLST scheme provides sufficient resolution for analyzing individual outbreaks, as well as the stability for comparisons across a variety of isolates encountered in surveillance studies, making it a valuable tool for the rapid analysis of P. aeruginosa genomes.\n\nDevelopment and Application of a Core Genome Multilocus Sequence Typing Scheme for the Health Care-Associated Pathogen Pseudomonas aeruginosa.", "token_count": 383, "char_count": 1464, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:20.158518", "source": { "split": "train_shard_00001", "doc_id": 3603 }, "chunk_id": "train_shard_00001_3603_0", "global_id": 10765 }, { "text": "

Background

Hypervirulent Klebsiella pneumoniae (hvKP) infections can have high morbidity and mortality rates owing to their invasiveness and virulence. However, there are no effective tools or biomarkers to discriminate between hvKP and nonhypervirulent K. pneumoniae (nhvKP) strains. We aimed to use a random forest algorithm to predict hvKP based on core-genome data.

Methods

In total, 272 K. pneumoniae strains were collected from 20 tertiary hospitals in China and divided into hvKP and nhvKP groups according to clinical criteria. Clinical data comparisons, whole-genome sequencing, virulence profile analysis, and core genome multilocus sequence typing (cgMLST) were performed. We then established a random forest predictive model based on the cgMLST scheme to prospectively identify hvKP. The random forest is an ensemble learning method that generates multiple decision trees during the training process and each decision tree will output its own prediction results corresponding to the input. The predictive ability of the model was assessed by means of area under the receiver operating characteristic curve.

Results

Patients in the hvKP group were younger than those in the nhvKP group (median age, 58.0 and 68.0 years, respectively; P < .001). More patients in the hvKP group had underlying diabetes mellitus (43.1% vs 20.1%; P < .001). Clinically, carbapenem-resistant K. pneumoniae was less common in the hvKP group (4.1% vs 63.8%; P < .001), whereas the K1/K2 serotype, sequence type (ST) 23, and positive string tests were significantly higher in the hvKP group. A cgMLST-based minimal spanning tree revealed that hvKP strains were scattered sporadically within nhvKP clusters. ST23 showed greater genome diversification than did ST11, according to cgMLST-based allelic differences", "token_count": 512, "char_count": 1819, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [ "ST23", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:20.817942", "source": { "split": "train_shard_00001", "doc_id": 3604 }, "chunk_id": "train_shard_00001_3604_0", "global_id": 10766 }, { "text": "Primary virulence factors (rmpA, iucA, positive string test result, and the presence of virulence plasmid pLVPK) were poor predictors of the hypervirulence phenotype. The random forest model based on the core genome allelic profile presented excellent predictive power, both in the training and validating sets (area under receiver operating characteristic curve, 0.987 and 0.999 in the training and validating sets, respectively).

Conclusions

A random forest algorithm predictive model based on the core genome allelic profiles of K. pneumoniae was accurate to identify the hypervirulent isolates.\n\nCore Genome Allelic Profiles of Clinical Klebsiella pneumoniae Strains Using a Random Forest Algorithm Based on Multilocus Sequence Typing Scheme for Hypervirulence Analysis.", "token_count": 198, "char_count": 781, "word_count": 106, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:21.266593", "source": { "split": "train_shard_00001", "doc_id": 3604 }, "chunk_id": "train_shard_00001_3604_1", "global_id": 10767 }, { "text": "Two bacterial strains designated NKC220-2T and NKC851-2 were isolated from commercial kimchi from different areas in Korea. The strains were Gram-positive, aerobic, oxidaseand catalase-positive, rod-shaped, spore-forming, non-motile, and halophilic bacteria. Both strains grew without NaCl, unlike type species in the genus Lentibacillus. The optimal pH for growth was 8.0, higher than that of the type species in the genus Lentibacillus, although growth was observed at pH 5.5-9.0. 16S rRNA gene sequence-based phylogenetic analysis indicated that the two strains (99.3-99.9% similarity) are grouped within the genus Lentibacillus and most closely related to Lentibacillus juripiscarius IS40-3T (97.4-97.6% similarity) isolated from fish sauce in Thailand. OrthoANI value between two novel strains and Lentibacillus lipolyticus SSKP1-9T (79.5-79.6% similarity) was far lower than the species demarcation threshold. Comparative genomic analysis displayed differences between the two strains as well as among other strains belonging to Lentibacillus. Furthermore, each isolate had strain-specific groups of orthologous genes based on pangenome analysis. Genomic G + C contents of strains NKC-220-2T and NKC851-2 were 41.9 and 42.2 mol%, respectively. The strains contained meso-diaminopimelic acid in their cell walls, and the major menaquinone was menaquinone-7. Phosphatidylglycerol, diphosphatidylglycerol, and an unidentified glycolipid, aminophospholipid, and phospholipid were the major polar lipid components of both strains", "token_count": 499, "char_count": 1574, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [ "SSKP1", "IS40", "NKC220", "NKC851" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:21.920043", "source": { "split": "train_shard_00001", "doc_id": 3605 }, "chunk_id": "train_shard_00001_3605_0", "global_id": 10768 }, { "text": "The major cellular fatty acids of the strains were anteiso-C15:0 and anteiso-C17:0. Based on phenotypic, genomic, phylogenetic, and chemotaxonomic features, strains NKC220-2T and NKC851-2 represent novel species of the genus Lentibacillus, for which the name Lentibacillus cibarius sp. nov. is proposed. The type strain is NKC220-2T (= KACC 21232T = JCM 33390T).\n\nLentibacillus cibarius sp. nov., isolated from kimchi, a Korean fermented food.", "token_count": 206, "char_count": 509, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7937, "quality_score": 0.8968, "entities": { "genes": [ "NKC220", "NKC851" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:22.383955", "source": { "split": "train_shard_00001", "doc_id": 3605 }, "chunk_id": "train_shard_00001_3605_1", "global_id": 10769 }, { "text": "A fast and sensitive reverse transcriptase PCR (RT-PCR) method was developed for the detection of viable Kluyveromyces marxianus in yoghurt. Yeast-specific primers were used with the RT-PCR to evaluate the suitability of 18S rRNA as a target for the detection of viable yeasts in pure culture and yoghurt. The RT-PCR assay was able to detect down to 10(2) CFU ml(-1) in yoghurt samples contaminated with viable yeast cells. Application of the RT-PCR method to commercial yoghurt samples demonstrated the utility of this technique for detection of low concentrations of viable yeast cells in naturally contaminated dairy products. The 18S rRNA molecule is an appropriate target for cell viability assessment because of its limited persistence after cell death and the resultant high level of sensitivity of the assay.\n\nA reverse transcriptase PCR technique for the detection and viability assessment of Kluyveromyces marxianus in yoghurt.", "token_count": 240, "char_count": 937, "word_count": 143, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:22.851809", "source": { "split": "train_shard_00001", "doc_id": 3606 }, "chunk_id": "train_shard_00001_3606_0", "global_id": 10770 }, { "text": "Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of nosocomial infections and hospital outbreaks worldwide, remaining a critical clinical concern. Here we characterized and investigated the phylogenetic relationships of 105 CRAB isolates from an intensive care unit from one hospital in China collected over six years. All strains carried blaOXA-23 , blaOXA-66 genes for carbapenem resistance, also had high resistance gene, virulence factor, and insertion sequence burdens. Whole-genome sequencing revealed all strains belonged to ST2, the global clone CC2. The phylogenetic analysis based on the core genome showed all isolates were dominated by a single lineage of three clusters and eight different clones. Two clones were popular during the collection time. Using chi-square test to identify the epidemiologically meaningful groupings, we found the significant difference in community structure only existed in strains from separation time. The haplotype and median-joining network analysis revealed genetic differences appeared among clusters and changes occurred overtime in the dominating cluster. Our results highlighted substantial multidrug-resistant CRAB burden in the hospital ICU environment demonstrating potential clone outbreak in the hospital.\n\nMolecular Epidemiology and Clone Transmission of Carbapenem-Resistant Acinetobacter baumannii in ICU Rooms.", "token_count": 352, "char_count": 1440, "word_count": 186, "semantic_coherence": 1, "information_density": 0.7258, "quality_score": 0.8629, "entities": { "genes": [ "ST2", "CC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:23.430900", "source": { "split": "train_shard_00001", "doc_id": 3607 }, "chunk_id": "train_shard_00001_3607_0", "global_id": 10771 }, { "text": "Kluyveromyces fragilis KCTC 7260 and Saccharomyces cerevisiae KCTC 7904, which both grew well in pear marc extract, were selected and their growth profiles and physiological functionalities were determined. Both of the selected yeasts established maximal growth by 20 hr of cultivation at 30℃ in pear marc extract. The cell-free extracts showed high antihypertensive angiotensin I-converting enzyme inhibitory activity of 68.9% and 52.1%, respectively. The extracts also displayed 9.2 U/mL and 12.0 U/mL of protease activity, respectively.\n\nGrowth characteristics and physiological functionality of yeasts in pear marc extracts.", "token_count": 181, "char_count": 628, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6782, "quality_score": 0.8391, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:23.868149", "source": { "split": "train_shard_00001", "doc_id": 3608 }, "chunk_id": "train_shard_00001_3608_0", "global_id": 10772 }, { "text": "

Introduction

Yeast pathogens are emerging agents of nosocomial as well as community-acquired infections and their rapid and accurate identification is crucial for a better management of high-risk patients and for an adequate treatment.

Methods

We performed a retrospective review of 156 yeast isolates collected during a 17 months' period of regular clinical practice at the Microbiology Department of San Camillo Hospital in Treviso, Italy and analyzed by the traditional culture-based method combined with matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS).

Results

Out of all the samples collected MALDI-TOF MS was able to characterize with a MT score ≥1.7 (accurate result at species level) 12 different yeast and yeast-like species from 140 samples: Candida albicans (63.7%), Candida glabrata (13.6%), Saccharomyces cerevisiae (6.5%), Candida parapsilosis (5.7%), Candida tropicalis (2.1%), Candida pararugosa (2.1%), Candida guilliermondii (2.1%), Candida kefyr (1.4%), Candida lusitaniae (0.7%), Candida palmioleophila (0.7%), Geotrichum silvicola (0.7%), Rhodotorula mucilaginosa (0.7%). Susceptibility testing toward seven common antifungal agents showed a characteristic MIC distribution of C. albicans isolates for echinocandins: particularly we noticed that 72% and 46% of C", "token_count": 504, "char_count": 1443, "word_count": 173, "semantic_coherence": 1, "information_density": 0.7572, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:24.518549", "source": { "split": "train_shard_00001", "doc_id": 3609 }, "chunk_id": "train_shard_00001_3609_0", "global_id": 10773 }, { "text": "albicans showed an MIC value close to clinical breakpoint as defined by EUCAST, respectively for anidulafungin and micafungin.

Conclusion

Accurate identification of microorganisms and the study of their antifungal susceptibility allow to understand the epidemiology of a particular area, permitting the choice of the most appropriate early antifungal treatment.\n\nPhenotypic typing and epidemiological survey of antifungal resistance of Candida species detected in clinical samples of Italian patients in a 17 months' period.", "token_count": 138, "char_count": 542, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7571, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:24.943360", "source": { "split": "train_shard_00001", "doc_id": 3609 }, "chunk_id": "train_shard_00001_3609_1", "global_id": 10774 }, { "text": "Saccharomyces cerevisiae cells, Kluyveromyces marxianus cells, inulase, glucose oxidase, chloroplasts, and mitochondria were immobilized in calcium alginate gels. Ethanol production from glucose solutions by an immobilized preparation of S. cerevisiae was demonstrated over a total of twenty-three days, and the half-life of such a preparation was shown to be about ten days. Immobilized K. marxianus, inulase, and glucose oxidase preparations were used to demonstrate the porosity and retraining properties of calcium alginate gels. Calcium alginate-immobilized chloroplasts were shown to perform the Hill reaction. Some experiments with immobilized mitochondria are reported.\n\nThe immobilization of microbial cells, subcellular organelles, and enzymes in calcium alginate gels. Reprinted from Biotechnology and Bioengineering, Vol. XIX, No. 3, Pages 387-397 (1977).", "token_count": 250, "char_count": 867, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:25.432931", "source": { "split": "train_shard_00001", "doc_id": 3610 }, "chunk_id": "train_shard_00001_3610_0", "global_id": 10775 }, { "text": "

Background

Candidemia represents a significant cause of morbidity and mortality in children. We examined the epidemiology and associated risk factors of candidemia at a Canadian tertiary care paediatric hospital over an 11-year period.

Methods

A retrospective chart review was conducted on children with positive blood culture for Candida species between January 1, 2007 and December 31, 2018. Patient demographics, previously described candidemia risk factors, Candida species, follow-up investigations, interventions, and outcome data were included in the analysis.

Results

Sixty-one candidemia episodes were reported with an overall incidence rate of 5.1 cases per 10,000 patient admissions. Of the 66 species identified, the most common was Candida albicans (53%, 35), followed by Candida parapsilosis (18%, 12), and Candida glabrata (8%, 5). Mixed candidemia was noted in 8% (5/61) of episodes. The most common risk factors included presence of central venous catheter (95%, 58/61) and receipt of antibiotics in the last 30 days (92%, 56/61). Majority of patients received abdominal imaging (89%, 54/61), ophthalmology consult (84%, 51/61), and echocardiogram (70%, 43/61), regardless of age. Line removal was performed in 81% (47/58) of cases. Evidence of disseminated fungal disease on abdominal imaging was observed in 11% (6/54) of patients, all in non-neonates but with risk factors including immunosuppression and gastrointestinal abnormalities", "token_count": 484, "char_count": 1512, "word_count": 202, "semantic_coherence": 1, "information_density": 0.7178, "quality_score": 0.8589, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:26.084260", "source": { "split": "train_shard_00001", "doc_id": 3611 }, "chunk_id": "train_shard_00001_3611_0", "global_id": 10776 }, { "text": "The overall 30-day case fatality rate was 8% (5/61).

Conclusions

C. albicans was the most commonly isolated species. Disseminated candidiasis was demonstrated mainly on abdominal imaging in patients with relevant risk factors, including immunosuppression and gastrointestinal abnormalities.\n\nEpidemiology and associated risk factors for candidemia in a Canadian tertiary paediatric hospital: An 11-year review.", "token_count": 123, "char_count": 424, "word_count": 51, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:26.469771", "source": { "split": "train_shard_00001", "doc_id": 3611 }, "chunk_id": "train_shard_00001_3611_1", "global_id": 10777 }, { "text": "This study aimed to examine the effect of Debaryomyces hansenii CBS 8339 on innate immune responses in mice. Thirty BALB/c mice were randomly treated with phosphate buffered saline (PBS) (control) and two D. hansenii (Dh) doses: Dh 10ˆ6 CFU (colony forming units) and Dh 10ˆ8 CFU daily for 15 days. Spleen, blood, and gut samples were taken on days 7 and 15. Mouse splenocytes were isolated and challenged with Escherichia coli. Immunological assays and immune-related gene expressions were performed. Serum was obtained from blood for total IgA and IgG antibody titer determination. Gut samples were taken for yeast colonization assessment. Phagocytosis, respiratory burst activity, and nitric oxide production in mice were mainly enhanced (p < 0.05) upon 7 days of D. hansenii intake at a concentration of 10ˆ8 CFU before and after bacterial challenge. Moreover, oral D. hansenii in mice upregulated (p < 0.05) gene expression of pro-inflammatory cytokines (INF-γ, IL-6 and IL-1β) before or after E. coli challenge on day 7 but downregulated (p < 0.05) on day 15. Furthermore, total serum IgG and IgA titers were higher (p < 0.05) in Dh 10ˆ8 CFU at days 7 and 15, and only at day 7, respectively, than that in the other dose and control groups. Finally, D. hansenii was detected in the gut of mice that received the treatments, suggesting that yeast survived gastrointestinal transit", "token_count": 515, "char_count": 1462, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:40:27.109379", "source": { "split": "train_shard_00001", "doc_id": 3612 }, "chunk_id": "train_shard_00001_3612_0", "global_id": 10778 }, { "text": "Altogether, a short period (7 days) of D. hansenii CBS 8339 oral delivery improved immune innate response on mice.\n\nProbiotic Debaryomyces hansenii CBS 8339 yeast enhanced immune responses in mice.", "token_count": 74, "char_count": 211, "word_count": 30, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:27.481272", "source": { "split": "train_shard_00001", "doc_id": 3612 }, "chunk_id": "train_shard_00001_3612_1", "global_id": 10779 }, { "text": "Akkermansia muciniphila is a human microbial symbiont residing in the mucosal layer of the large intestine. Its main carbon source is the highly heterogeneous mucin glycoprotein, and it uses an array of carbohydrate-active enzymes and sulfatases to access this complex energy source. Here we describe the biochemical characterization of 54 glycoside hydrolases, 11 sulfatases and 1 polysaccharide lyase from A. muciniphila to provide a holistic understanding of their carbohydrate-degrading activities. This was achieved using a variety of liquid chromatography techniques, mass spectrometry, enzyme kinetics and thin-layer chromatography. These results are supported with A. muciniphila growth and whole-cell assays. We find that these enzymes can act synergistically to degrade the O-glycans on the mucin polypeptide to completion, down to the core N-acetylgalactosaime. In addition, these enzymes can break down human breast milk oligosaccharide, ganglioside and globoside glycan structures, showing their capacity to target a variety of host glycans. These data provide a resource to understand the full degradative capability of the gut microbiome member A. muciniphila.\n\nCarbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion.", "token_count": 359, "char_count": 1275, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:28.064762", "source": { "split": "train_shard_00001", "doc_id": 3613 }, "chunk_id": "train_shard_00001_3613_0", "global_id": 10780 }, { "text": "A series of (1-substituted aryl)-3-(1H-imidazol-1-yl)-1-propanones was synthesized through the N-alkylation of imidazole with 3-dimethylamino-1-(substituted aryl)-1-propanone hydrochlorides (ketonic Mannich bases). A second series of N(1) -substituted imidazoles was obtained by the reduction of the carbonyl function of the imidazole-ketones in the previous series by means of NaBH(4) . All of the compounds were evaluated for antifungal activity against 16 strains of Candida, and 3-(1H-imidazol-1-yl)-1-(4-biphenylyl)-1-propanone emerged as a broad-spectrum antifungal agent. Several 3-(1H-imidazol-1-yl)-1-(2'-(substituted benzyl)oxyphenyl)-1-propanones were also active towards Candida kefyr.\n\nA novel antifungal agent with broad spectrum: 1-(4-biphenylyl)-3-(1H-imidazol-1-yl)-1-propanone.", "token_count": 292, "char_count": 795, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7326, "quality_score": 0.8663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:28.652309", "source": { "split": "train_shard_00001", "doc_id": 3614 }, "chunk_id": "train_shard_00001_3614_0", "global_id": 10781 }, { "text": "Agriculturally important genes are often introgressed into crops from closely related donor species or landraces. The gene pool of hexaploid bread wheat ( Triticum aestivum) is known to contain numerous such “alien” introgressions. Recently established high-quality reference genome sequences allow prediction of the size, frequency, and identity of introgressed chromosome regions. Here, we characterise chromosomal introgressions in bread wheat using exome capture data from the WHEALBI collection. We identified 26,664 putative introgression segments of at least 2 Mb across 434 wheat accessions. Detailed study of the most frequent introgressions identified T. timophevii or its close relatives as a frequent donor species. Importantly, 118 introgressions of at least 10 Mb were exclusive to single wheat accessions, revealing that large populations need to be studied to assess the total diversity of the wheat pangenome. In one case, a 14 Mb introgression in chromosome 7D, exclusive to cultivar Pamukale, was shown by QTL mapping to harbor a recessive powdery mildew resistance gene. We identified multiple events where distal chromosomal segments of one subgenome were duplicated in the genome and replaced the homoeologous segment in another subgenome. We propose that these examples are the results of inter-homoeolog recombination. Our study produced an extensive catalogue of the wheat introgression landscape, providing a resource for wheat breeding. Of note, the finding that the wheat gene pool contains numerous rare, but potentially important introgressions and chromosomal rearrangements has implications for future breeding.

Key message

This study highlights the potential of rare introgressions, as demonstrated by a major QTL for powdery mildew resistance on chromosome 7D. It further shows evidence for inter-homoeolog recombination in wheat.\n\nAnalysis of a diverse wheat germplasm panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeolog chromosomal recombination", "token_count": 476, "char_count": 2035, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6272, "quality_score": 0.8136, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:29.330612", "source": { "split": "train_shard_00001", "doc_id": 3615 }, "chunk_id": "train_shard_00001_3615_0", "global_id": 10782 }, { "text": "A US collection of invasive Escherichia coli serotype O1 bloodstream infection (BSI) isolates were assessed for genotypic and phenotypic diversity as the basis for designing a broadly protective O-antigen vaccine. Eighty percent of the BSI isolate serotype O1 strains were genotypically ST95 O1:K1:H7. The carbohydrate repeat unit structure of the O1a subtype was conserved in the three strains tested representing core genome multi-locus sequence types (MLST) sequence types ST95, ST38, and ST59. A long-chain O1a CRM197 lattice glycoconjugate antigen was generated using oxidized polysaccharide and reductive amination chemistry. Two ST95 strains were investigated for use in opsonophagocytic assays (OPA) with immune sera from vaccinated animals and in murine lethal challenge models. Both strains were susceptible to OPA killing with O1a glycoconjugate post-immune sera. One of these, a neonatal sepsis strain, was found to be highly lethal in the murine challenge model for which virulence was shown to be dependent on the presence of the K1 capsule. Mice immunized with the O1a glycoconjugate were protected from challenges with this strain or a second, genotypically related, and similarly virulent neonatal isolate. This long-chain O1a CRM197 lattice glycoconjugate shows promise as a component of a multi-valent vaccine to prevent invasive E. coli infections.

Importance

The Escherichia coli serotype O1 O-antigen serogroup is a common cause of invasive bloodstream infections (BSI) in populations at risk such as newborns and the elderly. Sequencing of US BSI isolates and structural analysis of O polysaccharide antigens purified from strains that are representative of genotypic sub-groups confirmed the relevance of the O1a subtype as a vaccine antigen", "token_count": 521, "char_count": 1815, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5914, "quality_score": 0.7957, "entities": { "genes": [ "ST95", "ST59", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:40:30.025445", "source": { "split": "train_shard_00001", "doc_id": 3616 }, "chunk_id": "train_shard_00001_3616_0", "global_id": 10783 }, { "text": "O polysaccharide was purified from a strain engineered to produce long-chain O1a O-antigen and was chemically conjugated to CRM197 carrier protein. The resulting glycoconjugate elicited functional antibodies and was protective in mice against lethal challenges with virulent K1-encapsulated O1a isolates.\n\nPreclinical validation of an Escherichia coli O-antigen glycoconjugate for the prevention of serotype O1 invasive disease.", "token_count": 134, "char_count": 446, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8393, "quality_score": 0.9196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:30.487903", "source": { "split": "train_shard_00001", "doc_id": 3616 }, "chunk_id": "train_shard_00001_3616_1", "global_id": 10784 }, { "text": "The diversity of populations of yeast and lactic acid bacteria (LAB) in pig feeds fermented at 10, 15, or 20 degrees C was characterized by rRNA gene sequencing of isolates. The feeds consisted of a cereal grain mix blended with wet wheat distillers' grains (WWDG feed), whey (W feed), or tap water (WAT feed). Fermentation proceeded for 5 days without disturbance, followed by 14 days of daily simulated feed outtakes, in which 80% of the contents were replaced with fresh feed mixtures. In WWDG feed, Pichia galeiformis became the dominant yeast species, independent of the fermentation temperature and feed change. The LAB population was dominated by Pediococcus pentosaceus at the start of the fermentation period. After 3 days, the Lactobacillus plantarum population started to increase in feeds at all temperatures. The diversity of LAB increased after the addition of fresh feed components. In W feed, Kluyveromyces marxianus dominated, but after the feed change, the population diversity increased. With increasing fermentation temperatures, there was a shift toward Pichia membranifaciens as the dominant species. L. plantarum was the most prevalent LAB in W feed. The WAT feed had a diverse microbial flora, and the yeast population changed throughout the whole fermentation period. Pichia anomala was the most prevalent yeast species, with increasing occurrence at higher fermentation temperatures. Pediococcus pentosaceus was the most prevalent LAB, but after the feed change, L. plantarum started to proliferate. The present study demonstrates that the species composition in fermented pig feed may vary considerably, even if viable cell counts indicate stable microbial populations.\n\nPopulation diversity of yeasts and lactic acid bacteria in pig feed fermented with whey, wet wheat distillers' grains, or water at different temperatures.", "token_count": 453, "char_count": 1852, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5376, "quality_score": 0.7688, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:31.129776", "source": { "split": "train_shard_00001", "doc_id": 3617 }, "chunk_id": "train_shard_00001_3617_0", "global_id": 10785 }, { "text": "Four methicillin-resistant Staphylococcus sciuri (MRSS) strains isolated from stranded dogs showed trimethoprim (TMP) resistance, while all staphylococcal TMP resistant dihydrofolate reductase genes ( dfr ) were negative. An in-depth whole-genome-sequencing approach on strain C2865 was followed for resistome and mobilome profiling, and for comparative genomics with S. sciuri group available genomes. Lack of species host tropism was observed, with MRSS C2865 placed at a separate sub-branch within S. sciuri species, close to the average nucleotide identity to be considered a different species (95-96%). S. sciuri proved a pronounced accessory genome (73% of genes), while MRSS C2865 distinctively harboured the highest total gene number and highest number of unique genes, with 75% associated to the recognised mobilome . A novel multidrug resistance mosaic plasmid (pUR2865-34) with several adaptive, mobilization ( oriT mimic) and segregational stability (Type Ib par system) traits and two small single resistance plasmids were identified. Plasmid pUR2865-34 enclosed a novel staphylococcal TMP resistance gene, named dfrE , which shared highest identity with dfr of soil-related Paenibacillus anaericanus (68%). DfrE conferred high-level TMP resistance in S. aureus and Escherichia coli . Database searches revealed that dfrE was formerly denoted ( dfr_like ) in an Exiguobacterium spp. from a fish-farm sediment and that was present but unnoticed in several staphylococcal and onemacrococcal genomes with different epidemiological backgrounds", "token_count": 437, "char_count": 1552, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6866, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:31.763528", "source": { "split": "train_shard_00001", "doc_id": 3618 }, "chunk_id": "train_shard_00001_3618_0", "global_id": 10786 }, { "text": "Novel chromosomal site-specific mobile islands with resourceful traits were identified, including a multidrug-resistant SCC mec cassette lacking cassette chromosome recombinase (Ccr) genes, a staphylococcal pathogenicity island of the SaPI4 family, and three unrelated siphoviridae prophages, two of which enclosed recombinases with the conserved Ccr-motif. We reveal a novel staphylococcal TMP resistance dfrE gene already present in diverse bacterial backgrounds. We confirm the ubiquity, high genome plasticity and low host tropism of S. sciuri highlighting its role as a resourceful reservoir for evolutionary novel features contributing to its extraordinary versatility and adaptability.

Author summary

Staphylococcus spp. are ubiquitous bacteria present in diverse ecological niches, including humans, animals and the environment. They are clinically relevant opportunistic pathogens and are notorious for their ability to acquire antimicrobial resistance (AMR) and virulence properties, resulting in a significant impact for Public Health. Mobile genetic elements (MGEs) play a central role in this adaptation process and are a means to transfer genetic information across bacterial species. Staphylococcus sciuri represents one of the most ancestral species in the genus and has been suggested a reservoir for AMR genes. Here, following a refined whole genome sequencing approach we determined the entire genome of an animal and environment-associated multidrug resistant (MDR) S. sciuri strain uncovering a novel acquired staphylococcal TMP resistance gene already spread among different bacterial species from different epidemiological backgrounds. We also reveal several additional MGEs, including a novel MDR mobilizable plasmid that encloses several adaptive and stabilization features, and novel mobilizable chromosomal islands with resourceful traits, including three unrelated prophages. Together with comparative genomics, we confirm the ubiquity, high intraspecies heterogenicity, genome plasticity and low host tropism of this species, highlighting its role as resourceful reservoir for evolutionary novel features contributing to its extraordinary versatility and adaptability.", "token_count": 507, "char_count": 2206, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5842, "quality_score": 0.7921, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:32.416239", "source": { "split": "train_shard_00001", "doc_id": 3618 }, "chunk_id": "train_shard_00001_3618_1", "global_id": 10787 }, { "text": "Staphylococcus sciuriC2865 from a distinct subspecies cluster as reservoir of the novel transferable trimethoprim resistance gene,dfrE,and adaptation driving mobile elements", "token_count": 57, "char_count": 187, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:32.775386", "source": { "split": "train_shard_00001", "doc_id": 3618 }, "chunk_id": "train_shard_00001_3618_2", "global_id": 10788 }, { "text": "

Summary

Members of the bacterial genus Pseudomonas form mutualistic, commensal and pathogenic associations with diverse hosts. The prevalence of host association across the genus suggests that symbiosis may be a conserved ancestral trait and that distinct symbiotic lifestyles may be more recently evolved. Here we show that the ColR/S two-component system, part of the Pseudomonas core genome, is functionally conserved between Pseudomonas aeruginosa and Pseudomonas fluorescens . Using plant rhizosphere colonization and virulence in a murine abscess model, we show that colR is required for commensalism with plants and virulence in animals. Comparative transcriptomics revealed that the ColR regulon has diverged between P. aeruginosa and P. fluorescens and deleting components of the ColR regulon revealed strain-specific, but not hostspecific, requirements for ColR-dependent genes. Collectively, our results suggest that ColR/S allows Pseudomonas to sense and respond to a host, but that the ColR-regulon has diverged between Pseudomonas strains with distinct lifestyles.\n\nThe ColR/S two-component system is a conserved determinant of host association across Pseudomonas species", "token_count": 307, "char_count": 1201, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:33.339412", "source": { "split": "train_shard_00001", "doc_id": 3619 }, "chunk_id": "train_shard_00001_3619_0", "global_id": 10789 }, { "text": "Of three β-galactosidases from Aspergillus oryzae, Kluyveromyces lactis and Bacillus sp., used for the production of low-content galacto- oligosaccharides (GOS) from lactose, the latter produced the highest yield of trisaccharides and tetrasaccharides. GOS production was enhanced by mixing β-galactosidase glucose oxidase. The low-content GOS syrups, produced either by β-galactosidase alone or by the mixed enzyme system, were subjected to the fermentation by Kluyveromyces marxianus, whereby glucose, galactose, lactose and other disaccharides were depleted, resulting in up to 97% and 98% on a dry weight basis of high-content GOS with the yields of 31% and 32%, respectively.\n\nProduction of High-content Galacto-oligosaccharide by Enzyme Catalysis and Fermentation with Kluyveromyces marxianus", "token_count": 254, "char_count": 798, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:33.829270", "source": { "split": "train_shard_00001", "doc_id": 3620 }, "chunk_id": "train_shard_00001_3620_0", "global_id": 10790 }, { "text": "A number of yeast strains, isolated from sugar cane mills and identified as strains of Kluyveromyces marxianus var. marxianus, were examined for their ability to ferment glucose and cane syrup to ethanol at high temperatures. Several strains were capable of rapid fermentation at temperatures up to 47 degrees C. At 43 degrees C, >6% (wt/vol) ethanol was produced after 12 to 14 h of fermentation, concurrent with retention of high cell viability (>80%). Although the type strain (CBS 712) of K. marxianus var. marxianus produced up to 6% (wt/vol) ethanol at 43 degrees C, cell viability was low, 30 to 50%, and the fermentation time was 24 to 30 h. On the basis of currently available strains, we suggest that it may be possible by genetic engineering to construct yeasts capable of fermenting carbohydrates at temperatures close to 50 degrees C to produce 10 to 15% (wt/vol) ethanol in 12 to 18 h with retention of cell viability.\n\nHigh-Efficiency Carbohydrate Fermentation to Ethanol at Temperatures above 40 degrees C by Kluyveromyces marxianus var. marxianus Isolated from Sugar Mills.", "token_count": 338, "char_count": 1090, "word_count": 178, "semantic_coherence": 1, "information_density": 0.5787, "quality_score": 0.7893, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:34.398138", "source": { "split": "train_shard_00001", "doc_id": 3621 }, "chunk_id": "train_shard_00001_3621_0", "global_id": 10791 }, { "text": "Acidobacteriota are abundant in soil, peatlands, and sediments, but their ecology in freshwater environments remains understudied. UBA12189, an Acidobacteriota genus, is an uncultivated, genome-streamlined lineage with a small genome size found in aquatic environments where detailed genomic analyses are lacking. Here, we analyzed 66 MAGs of UBA12189 (including one complete genome) from freshwater lakes and rivers in Europe, North America, and Asia. UBA12189 has small genome sizes (<1.4 Mbp), low GC content, and a highly diverse pangenome. In freshwater lakes, this bacterial lineage is abundant from the surface waters (epilimnion) down to a 300-m depth (hypolimnion). UBA12189 appears to be free-living from CARD-FISH analysis. When compared to other genome-streamlined bacteria such as Nanopelagicales and Methylopumilus, genome reduction has caused UBA12189 to have a more limited metabolic repertoire in carbon, sulfur, and nitrogen metabolisms, limited numbers of membrane transporters, as well as a higher degree of auxotrophy for various amino acids, vitamins, and reduced sulfur. Despite having reduced genomes, UBA12189 encodes proteorhodopsin, complete biosynthesis pathways for heme and vitamin K2, cbb3-type cytochrome c oxidases, and heme-requiring enzymes. These genes may give a selective advantage during the genome streamlining process. We propose the new genus Acidiparvus, with two new species named \"A. lacustris\" and \"A. fluvialis\"", "token_count": 486, "char_count": 1536, "word_count": 204, "semantic_coherence": 1, "information_density": 0.7206, "quality_score": 0.8603, "entities": { "genes": [ "UBA12189" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:35.046614", "source": { "split": "train_shard_00001", "doc_id": 3622 }, "chunk_id": "train_shard_00001_3622_0", "global_id": 10792 }, { "text": "Acidiparvus is the first described genome-streamlined lineage under the phylum Acidobacteriota, which is a free-living, slow-growing scavenger in freshwater environments.\n\nUbiquitous genome streamlined Acidobacteriota in freshwater environments.", "token_count": 88, "char_count": 266, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:35.418393", "source": { "split": "train_shard_00001", "doc_id": 3622 }, "chunk_id": "train_shard_00001_3622_1", "global_id": 10793 }, { "text": "This work sought to develop a fermentative process for the microbial production of superoxide dismutase (SOD), to overcome extraction from animal tissues. Twenty-eight wild-type yeast strains were screened for SOD productivity. Kluyveromyces marxianus L3 showed the highest SOD activity (62 U mg(-1)) and was used for process development. Oxidative stress conditions and parameters affecting oxygen transfer rate were exploited to improve production. The effects of dilution rate (0.067 vs 0.2 h(-1)), aeration pressure (0.3 vs 1.2 bar) and H(2)O(2) (0 vs 50 mM) were studied during chemostat experiments. Low dilution rate, high pressure and H(2)O(2) resulted in an increase in CuZn-SOD up to 475 U mg(-1). When a regulation of oxygen saturation was applied during batch cultures, CuZn-SOD was progressively higher at 60, 80 and 90% dissolved oxygen tension (DOT) (250, 330 and 630 U mg(-1), respectively). Furthermore, the highest growth rate and biomass yield were achieved at 90% DOT, this being therefore the best DOT condition for high overall productivity. Growth and productivity on different carbon sources were compared. Specific activity was higher on glycerol than on lactose or glucose (496, 454 and 341 U mg(-1), respectively). The highest biomass yield was achieved on lactose. It may be therefore the best substrate for SOD production.\n\nFermentative production of superoxide dismutase with Kluyveromyces marxianus.", "token_count": 402, "char_count": 1430, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:36.040824", "source": { "split": "train_shard_00001", "doc_id": 3623 }, "chunk_id": "train_shard_00001_3623_0", "global_id": 10794 }, { "text": "Leptospira weilii belongs to the pathogenic Leptospira group and is a causal agent of human and animal leptospirosis in many world regions. L. weilii can produce varied clinical presentations from asymptomatic through acute to chronic infections and occupy several ecological niches. Nevertheless, the genomic feature and genetic basis behind the host adaptability of L. weilii remain elusive due to limited information. Therefore, this study aimed to examine the complete circular genomes of two new L. weilii serogroup Mini strains (CUDO6 and CUD13) recovered from the urine of asymptomatic dogs in Thailand and then compared with the 17 genomes available for L. weilii. Variant calling analysis (VCA) was also undertaken to gain potential insight into the missense mutations, focusing on the known pathogenesis-related genes. Whole genome sequences revealed that the CUDO6 and CUD13 strains each contained two chromosomes and one plasmid, with average genome size and G+C content of 4.37 Mbp and 40.7%, respectively. Both strains harbored almost all the confirmed pathogenesis-related genes in Leptospira. Two novel plasmid sequences, pDO6 and pD13, were identified in the strains CUDO6 and CUD13. Both plasmids contained genes responsible for stress response that may play important roles in bacterial adaptation during persistence in the kidneys. The core-single nucleotide polymorphisms phylogeny demonstrated that both strains had a close genetic relationship. Amongst the 19 L. weilii strains analyzed, the pan-genome analysis showed an open pan-genome structure, correlated with their high genetic diversity. VCA identified missense mutations in genes involved in endoflagella, lipopolysaccharide (LPS) structure, mammalian cell entry protein, and hemolytic activities, and may be associated with host-adaptation in the strains", "token_count": 503, "char_count": 1892, "word_count": 263, "semantic_coherence": 1, "information_density": 0.673, "quality_score": 0.8365, "entities": { "genes": [ "CUDO6", "CUD13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:36.702187", "source": { "split": "train_shard_00001", "doc_id": 3624 }, "chunk_id": "train_shard_00001_3624_0", "global_id": 10795 }, { "text": "Missense mutations of the endoflagella genes of CUDO6 and CUD13 were associated with loss of motility. These findings extend the knowledge about the pathogenic molecular mechanisms and genomic evolution of this important zoonotic pathogen.\n\nComparative Genomic Analysis and a Novel Set of Missense Mutation of the Leptospira weilii Serogroup Mini From the Urine of Asymptomatic Dogs in Thailand.", "token_count": 105, "char_count": 402, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7586, "quality_score": 0.8793, "entities": { "genes": [ "CUDO6", "CUD13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:37.078932", "source": { "split": "train_shard_00001", "doc_id": 3624 }, "chunk_id": "train_shard_00001_3624_1", "global_id": 10796 }, { "text": "

Background

Enteric fever is a serious public health concern. The causative agents, Salmonella enterica serovars Typhi and Paratyphi A, frequently have antimicrobial resistance (AMR), leading to limited treatment options and poorer clinical outcomes. We investigated the genomic epidemiology, resistance mechanisms, and transmission dynamics of these pathogens at three urban sites in Africa and Asia.

Methods

S Typhi and S Paratyphi A bacteria isolated from blood cultures of febrile children and adults at study sites in Dhaka (Bangladesh), Kathmandu (Nepal), and Blantyre (Malawi) during STRATAA surveillance were sequenced. Isolates were charactered in terms of their serotypes, genotypes (according to GenoTyphi and Paratype), molecular determinants of AMR, and population structure. We used phylogenomic analyses incorporating globally representative genomic data from previously published surveillance studies and ancestral state reconstruction to differentiate locally circulating from imported pathogen AMR variants. Clusters of sequences without any single-nucleotide variants in their core genome were identified and used to explore spatiotemporal patterns and transmission dynamics.

Findings

We sequenced 731 genomes from isolates obtained during surveillance across the three sites between Oct 1, 2016, and Aug 31, 2019 (24 months in Dhaka and Kathmandu and 34 months in Blantyre). S Paratyphi A was present in Dhaka and Kathmandu but not Blantyre. S Typhi genotype 4.3.1 (H58) was common in all sites, but with different dominant variants (4.3.1.1.EA1 in Blantyre, 4.3.1.1 in Dhaka, and 4.3.1.2 in Kathmandu)", "token_count": 460, "char_count": 1643, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6847, "quality_score": 0.8423, "entities": { "genes": [ "EA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:37.732637", "source": { "split": "train_shard_00001", "doc_id": 3625 }, "chunk_id": "train_shard_00001_3625_0", "global_id": 10797 }, { "text": "Multidrug resistance (ie, resistance to chloramphenicol, co-trimoxazole, and ampicillin) was common in Blantyre (138 [98%] of 141 cases) and Dhaka (143 [32%] of 452), but absent from Kathmandu. Quinolone-resistance mutations were common in Dhaka (451 [>99%] of 452) and Kathmandu (123 [89%] of 138), but not in Blantyre (three [2%] of 141). Azithromycin-resistance mutations in acrB were rare, appearing only in Dhaka (five [1%] of 452). Phylogenetic analyses showed that most cases derived from pre-existing, locally established pathogen variants; 702 (98%) of 713 drug-resistant infections resulted from local circulation of AMR variants, not imported variants or recent de novo emergence; and pathogen variants circulated across age groups. 479 (66%) of 731 cases clustered with others that were indistinguishable by point mutations; individual clusters included multiple age groups and persisted for up to 2·3 years, and AMR determinants were invariant within clusters.

Interpretation

Enteric fever was associated with locally established pathogen variants that circulate across age groups. AMR infections resulted from local transmission of resistant strains. These results form a baseline against which to monitor the impacts of control measures.

Funding

Wellcome Trust, Bill & Melinda Gates Foundation, EU Horizon 2020, and UK National Institute for Health and Care Research.\n\nPathogen diversity and antimicrobial resistance transmission of Salmonella enterica serovars Typhi and Paratyphi A in Bangladesh, Nepal, and Malawi: a genomic epidemiological study.", "token_count": 472, "char_count": 1579, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6881, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:38.375747", "source": { "split": "train_shard_00001", "doc_id": 3625 }, "chunk_id": "train_shard_00001_3625_1", "global_id": 10798 }, { "text": "Ethanol can be produced from cellulosic biomass in a process known as simultaneous saccharification and fermentation (SSF). The presence of yeast together with the cellulolytic enzyme complex reduces the accumulation of sugars within the reactor, increasing the ethanol yield and saccharification rate. This paper reports the isolation of Saccharomyces cerevisiae LBM-1, a strain capable of growth at 42 °C. In addition, S. cerevisiae LBM-1 and Kluyveromyces marxianus UFV-3 were able to ferment sugar cane bagasse in SSF processes at 37 and 42 °C. Higher ethanol yields were observed when fermentation was initiated after presaccharification at 50°C than at 37 or 42° C. Furthermore, the volumetric productivity of fermentation increased with presaccharification time, from 0.43 g/L/h at 0 h to 1.79 g/L/h after 72 h of presaccharification. The results suggest that the use of thermotolerant yeasts and a presaccharification stage are key to increasing yields in this process.\n\nThe influence of presaccharification, fermentation temperature and yeast strain on ethanol production from sugarcane bagasse.", "token_count": 308, "char_count": 1104, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6481, "quality_score": 0.8241, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:38.941093", "source": { "split": "train_shard_00001", "doc_id": 3626 }, "chunk_id": "train_shard_00001_3626_0", "global_id": 10799 }, { "text": "Diet-microbe interactions play an important role in modulating the early life microbiota, with Bifidobacterium strains and species dominating the gut microbiota of breast-fed infants. Here, we sought to explore how infant diet drives distinct bifidobacterial community composition and dynamics within individual infant ecosystems. Genomic characterisation of 19 strains isolated from breast-fed infants revealed a diverse genomic architecture enriched in carbohydrate metabolism genes, which was distinct to each strain, but collectively formed a pangenome across infants. Presence of gene clusters implicated in digestion of human milk oligosaccharides (HMOs) varied between species, with growth studies indicating within infant differences in the ability to utilise 2’FL and LNnT HMOs between strains. We also performed cross-feeding experiments using metabolic products from growth on 2’FL or LNnT for non-HMO degrading isolates, these compounds were identified to include fucose, galactose, acetate and N-acetylglucosamine. These data highlight the cooperative nature of individual bifidobacterial ‘founder’ strains within an infant ecosystem, and how sharing resources maximises nutrient consumption from the diet. We propose that this social behaviour contributes to the diversity and dominance of Bifidobacterium in early life and suggests avenues for development of new diet and microbiota based therapies to promote infant health.\n\nInfant diet promotesBifidobacteriumcommunity cooperation within a single ecosystem", "token_count": 361, "char_count": 1530, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6847, "quality_score": 0.8424, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:40.237723", "source": { "split": "train_shard_00001", "doc_id": 3627 }, "chunk_id": "train_shard_00001_3627_0", "global_id": 10800 }, { "text": "Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common including against World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, evolutionary history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a most recent common ancestor in 2018 carrying a low-fitness cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.\n\nThe evolution and international spread of extensively drug resistant Shigella sonnei.", "token_count": 276, "char_count": 1212, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:40.839008", "source": { "split": "train_shard_00001", "doc_id": 3628 }, "chunk_id": "train_shard_00001_3628_0", "global_id": 10801 }, { "text": "

Objectives

The genomic epidemiology of group b streptococcal (GBS) isolates from the Rotunda maternity hospital, Dublin, 2008-2017, was investigated.

Methods

Whole genome sequences of isolates (invasive, n = 114; non-invasive, n = 76) from infants and women were analysed using the PubMLST database (https://pubmlst.org/sagalactiae/).

Results

Serotypes III (36%), Ia (18%), V (17%), II (11%) and Ib, (9%) and sequence types (ST) 17 (23%), ST-23 (14%), ST-1 (12%) and ST-19 (7%) were most common. Core genome MLST (cgMLST) differentiated isolates of the same ST, grouped STs into five lineages congruent with known clonal complexes and identified known mother-baby pairs and suspected linked infant cases. Clonal complex (CC) 17 accounted for 40% and 22% of infant and maternal invasive cases, respectively and 21% of non-invasive isolates. CC23 and CC19 were associated with maternal disease (30%) and carriage (24%), respectively. Erythromycin (26%) and clindamycin (18%) resistance increased over the study period and was associated with presence of the erm(B) gene (55%), CC1 (33%) and CC19 (24%). A multi-resistant integrative conjugative element incorporated in the PI-1 locus was detected in CC17, an ST-12 and ST-23 isolate confirming the global dissemination of this element. All isolates possessed one or more pilus islands. Genes encoding other potential protective proteins including Sip, C5a peptidase and Srr1 were present in 100%, 99.5% and 65.8% of isolates, respectively", "token_count": 509, "char_count": 1508, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7477, "quality_score": 0.8738, "entities": { "genes": [ "CC19", "CC17", "CC1", "CC23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:41.511919", "source": { "split": "train_shard_00001", "doc_id": 3629 }, "chunk_id": "train_shard_00001_3629_0", "global_id": 10802 }, { "text": "The srr2 gene was unique to CC17.

Conclusions

The PubMLST.org website provides a valuable framework for genomic GBS surveillance to inform on local and global GBS epidemiology, preventive and control measures.\n\nGenomic epidemiology of group B streptococci spanning 10 years in an Irish maternity hospital, 2008-2017.", "token_count": 97, "char_count": 323, "word_count": 44, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [ "CC17" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:41.916580", "source": { "split": "train_shard_00001", "doc_id": 3629 }, "chunk_id": "train_shard_00001_3629_1", "global_id": 10803 }, { "text": "Of three beta-galactosidases from Aspergillus oryzae, Kluyveromyces lactis and Bacillus sp., used for the production of low-content galacto- oligosaccharides (GOS) from lactose, the latter produced the highest yield of trisaccharides and tetrasaccharides. GOS production was enhanced by mixing beta-galactosidase glucose oxidase. The low-content GOS syrups, produced either by beta-galactosidase alone or by the mixed enzyme system, were subjected to the fermentation by Kluyveromyces marxianus, whereby glucose, galactose, lactose and other disaccharides were depleted, resulting in up to 97% and 98% on a dry weight basis of high-content GOS with the yields of 31% and 32%, respectively.\n\nProduction of high-content galacto-oligosaccharide by enzyme catalysis and fermentation with Kluyveromyces marxianus.", "token_count": 252, "char_count": 808, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:42.447583", "source": { "split": "train_shard_00001", "doc_id": 3630 }, "chunk_id": "train_shard_00001_3630_0", "global_id": 10804 }, { "text": "The genomes of three representatives of the family Methylophilaceae, Methylotenera mobilis JLW8, Methylotenera versatilis 301, and Methylovorus glucosetrophus SIP3-4, all isolated from a single study site, Lake Washington in Seattle, WA, were completely sequenced. These were compared to each other and to the previously published genomes of Methylobacillus flagellatus KT and an unclassified Methylophilales strain, HTCC2181. Comparative analysis revealed that the core genome of Methylophilaceae may be as small as approximately 600 genes, while the pangenome may be as large as approximately 6,000 genes. Significant divergence between the genomes in terms of both gene content and gene and protein conservation was uncovered, including the varied presence of certain genes involved in methylotrophy. Overall, our data demonstrate that metabolic potentials can vary significantly between different species of Methylophilaceae, including organisms inhabiting the very same environment. These data suggest that genetic divergence among the members of this family may be responsible for their specialized and nonredundant functions in C₁ cycling, which in turn suggests means for their successful coexistence in their specific ecological niches.\n\nGenomes of three methylotrophs from a single niche reveal the genetic and metabolic divergence of the methylophilaceae.", "token_count": 333, "char_count": 1366, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6614, "quality_score": 0.8307, "entities": { "genes": [ "JLW8", "HTCC2181", "SIP3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:43.023138", "source": { "split": "train_shard_00001", "doc_id": 3631 }, "chunk_id": "train_shard_00001_3631_0", "global_id": 10805 }, { "text": "SAR86 is an abundant and ubiquitous heterotroph in the surface ocean that plays a central role in the function of marine ecosystems. We hypothesized that despite its ubiquity, different SAR86 subgroups may be endemic to specific ocean regions and functionally specialized for unique marine environments. However, the global biogeographical distributions of SAR86 genes, and the manner in which these distributions correlate with marine environments, have not been investigated. We quantified SAR86 gene content across globally-distributed metagenomic samples and modeled these gene distributions as a function of 51 environmental variables. We identified five distinct clusters of genes within the SAR86 pangenome, each with a unique geographic distribution associated with specific environmental characteristics. Gene clusters are characterized by strong taxonomic enrichment of distinct SAR86 genomes and partial assemblies, as well as differential enrichment of certain functional groups, suggesting differing functional and ecological roles of SAR86 ecotypes. We then leveraged our models and high-resolution, remote sensing-derived environmental data to predict the distributions of SAR86 gene clusters across the world’s oceans, creating global maps of SAR86 ecotype distributions. Our results reveal that SAR86 exhibits previously unknown, complex biogeography, and provide a framework for exploring geographic distributions of genetic diversity from other microbial clades.\n\nGlobal ecotypes in the ubiquitous marine clade SAR86", "token_count": 330, "char_count": 1535, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6232, "quality_score": 0.8116, "entities": { "genes": [ "SAR86" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:43.584653", "source": { "split": "train_shard_00001", "doc_id": 3632 }, "chunk_id": "train_shard_00001_3632_0", "global_id": 10806 }, { "text": "In vivo hydrolysis of inulin and sucrose was examined in selected yeasts of the genus Kluyveromyces. Cells, grown in sucrose-limited chemostat cultures, were subjected to treatments for the removal of inulinase, the enzyme responsible for the hydrolysis of both inulin and sucrose. The effects of these treatments were studied by measurement of inulin-dependent and sucrose-dependent oxygen consumption by cell suspensions. In Kluyveromyces marxianus var. marxianus, inulinase was partially secreted into the culture fluid. Removal of culture fluid inulinase by washing had no effect on sucrose-dependent oxygen consumption by this yeast. However, this treatment drastically reduced inulin-dependent oxygen consumption. Treatment of washed cells with sulfhydryls removed part of the cell wall-retained inulinase and reduced inulin-dependent oxygen consumption by another 80%. Sucrose-dependent oxygen consumption was less affected, decreasing by 40%. Cell suspensions of K. marxianus var. drosophilarum, K. marxianus var. vanudenii, and Saccharomyces kluyveri rapidly utilized sucrose but not inulin. This is in accordance with the classification of these yeasts as inulin negative. Supernatants of cultures grown at pH 5.5 did not catalyze the hydrolysis of inulin and sucrose. This suggested that these yeasts contained a strictly cell-bound invertase, an enzyme not capable of inulin hydrolysis. However, upon washing, cells became able to utilize inulin. The inulin-dependent oxygen consumption further increased after treatment of the cells with sulfhydryls. These treatments did not affect the sucrose-dependent oxygen consumption of the cells. Apparently, these treatments removed a permeability barrier for inulin that does not exist for sucrose.(ABSTRACT TRUNCATED AT 250 WORDS)\n\nLocalization of inulinase and invertase in Kluyveromyces species.", "token_count": 453, "char_count": 1854, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5216, "quality_score": 0.7608, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:44.223341", "source": { "split": "train_shard_00001", "doc_id": 3633 }, "chunk_id": "train_shard_00001_3633_0", "global_id": 10807 }, { "text": "This review aims to systematically dissect the genetic regulatory mechanisms of plant secondary metabolites in the era of genomics, while comprehensively summarizing the progress and potential impact of genomics in plant secondary metabolism research. By integrating methodologies such as high-throughput sequencing, structural genomics, comparative genomics, and functional genomics, we elucidate the principles underlying plant secondary metabolism and identify functional genes. The application of these technologies has deepened our understanding of secondary metabolic pathways and driven advancements in plant molecular genetics and genomics. The development of genomics has enabled scientists to gain profound insights into the biosynthetic pathways of secondary metabolites in plants such as ginseng (Panax ginseng) and grapevine (Vitis vinifera), while offering novel possibilities for precise regulation of these pathways. Despite remarkable progress in studying the genetic regulation of plant secondary metabolites, significant challenges persist. Future research must focus on integrating multi-omics data, developing advanced bioinformatics tools, and exploring effective genetic improvement strategies to fully harness the medicinal potential of plants and enhance their capacity to synthesize secondary metabolites.\n\nApplication and Progress of Genomics in Deciphering the Genetic Regulation Mechanisms of Plant Secondary Metabolites.", "token_count": 294, "char_count": 1464, "word_count": 185, "semantic_coherence": 1, "information_density": 0.5946, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:44.789755", "source": { "split": "train_shard_00001", "doc_id": 3634 }, "chunk_id": "train_shard_00001_3634_0", "global_id": 10808 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) carrying mecC gene (mecC-MRSA) is frequently reported among European hedgehogs (Europeaus erineaus) due to co-evolutionary adaptation to dermatophyte infection in European hedgehogs. The occurrence of MRSA in European hedgehogs in Finland is unknown. Consequently, we investigated the occurrence of MRSA in wild hedgehogs from urban Helsinki metropolitan area in 2020-2021 and applied whole genome sequencing (WGS) to further characterize the studied isolates and compared them with human clinical MRSA isolates. Altogether 115 dead hedgehogs were screened for MRSA using selective cultivation methods. Presumptive MRSA isolates were tested for antimicrobial susceptibility and confirmed MRSA isolates were further characterized by spa-typing and WGS. Hedgehog derived MRSA isolates were compared with clinical human MRSA isolates using core genome multilocus sequence typing (cgMLST). In total MRSA was recovered from 11 out of 115 (10%) hedgehogs. Among these four different spa types (t304; n = 4, t8835; n = 4, t5133; n = 2 and t622; n = 1) and three different sequence types (STs) (ST6; n = 6, ST7663; n = 4 and ST2840; n = 1) were identified. From the studied MRSA isolates seven harboured the mecA gene (mecA-MRSA) and four were identified as mecC-MRSA. All mecA-MRSA isolates carried immune evasion cluster genes, and one isolate was positive for Panton-Valentine leukocidin", "token_count": 516, "char_count": 1517, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6132, "quality_score": 0.8066, "entities": { "genes": [ "ST2840", "ST6", "ST7663" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:40:45.450054", "source": { "split": "train_shard_00001", "doc_id": 3635 }, "chunk_id": "train_shard_00001_3635_0", "global_id": 10809 }, { "text": "cgMLST comparison revealed close genetic relatedness among three hedgehog and two human mecA-MRSA isolates all belonging to t304/ST6. Our results suggest a clonal dissemination of a successful MRSA clone among humans and hedgehogs. Further studies are warranted to investigate the sources and dissemination of such clone in urban environments. We observed a relatively low occurrence of mecC-MRSA in Finnish hedgehogs.\n\nClonal dissemination of successful emerging clone mecA-MRSA t304/ST6 among humans and hedgehogs in the Helsinki metropolitan area in Finland.", "token_count": 158, "char_count": 575, "word_count": 79, "semantic_coherence": 1, "information_density": 0.6962, "quality_score": 0.8481, "entities": { "genes": [ "ST6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:45.890674", "source": { "split": "train_shard_00001", "doc_id": 3635 }, "chunk_id": "train_shard_00001_3635_1", "global_id": 10810 }, { "text": "Acid goat whey fermentation by a co-culture of Kluyveromyces marxianus and Lactobacillus rhamnosus yielded a hydrolysate inhibitory for the angiotensin-I-converting enzyme. The potential of this hydrolysate and its main lactokinin tryptophan against accumulation of lipid was investigated at different stages of immortalised human adipocytes development using Oil Red O staining and compared with that of captopril. A slight reduction of lipid content (8%) was observed when mature adipocytes were incubated with the whole hydrolysate at the concentration of 587 μg mL⁻¹. Proliferation of pre-adipocytes was also reduced after incubation with this hydrolysate, which was not cytotoxic. Tryptophan induced a reduction of lipid content of 18% and was cytotoxic towards adipocytes at the concentration found in the hydrolysate: 25.7 μg mL⁻¹. A decrease of the lipid content of mature adipocytes of 28% was observed with 2.9 ng mL⁻¹ of captopril, which was also cytotoxic.\n\nEffects of lactokinins from fermented acid goat whey on lipid content and adipogenesis of immortalised human adipocytes", "token_count": 332, "char_count": 1089, "word_count": 160, "semantic_coherence": 1, "information_density": 0.5687, "quality_score": 0.7844, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:46.461460", "source": { "split": "train_shard_00001", "doc_id": 3636 }, "chunk_id": "train_shard_00001_3636_0", "global_id": 10811 }, { "text": "Genomic characterization of Furfurilactobacillus rossiae revealed that strains which were previously identified as F. rossiae are genetically heterogeneous. The 16S rRNA gene sequences of strains FUA3430, FUA3583, C5, FUA3115 and FUA3119, were 99.6 % identical to F. rossiae but the core genome analysis revealed that these strains share less than 93 % average nucleotide identity (ANI) with the F. rossiae type strain DSM 15814T. Because the ANI value is below the threshold for delineation of bacterial species, we propose the novel species Furfurilactobacillus milii sp. nov. with the type strain FUA3430T (=DSM 113338T=LMG 32478T). Strains of F. milii have smaller genomes than F. rossiae, lack the pdu-cbi-cob-hem cluster which is responsible for 1,2-propanediol utilization in F. rossiae, and lack genes involved in ethanolamine utilization. Two strains of the novel species (FUA3430T and FUA3583) were compared to F. rossiae FUA3214. Analysis of the cellular fatty acid composition and metabolite analysis did not reveal significant differences between F. milii sp. nov. and F. rossiae FUA3124. Although the growth requirements with respect to temperature and pH were very similar, only the strain of F. rossiae utilized melibiose and d-xylose. Morphological differences were also seen in the colony and cell size of the novel compared to F", "token_count": 531, "char_count": 1496, "word_count": 203, "semantic_coherence": 1, "information_density": 0.601, "quality_score": 0.8005, "entities": { "genes": [ "FUA3430", "FUA3124", "FUA3583", "FUA3115", "FUA3119", "FUA3214" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:40:47.120571", "source": { "split": "train_shard_00001", "doc_id": 3637 }, "chunk_id": "train_shard_00001_3637_0", "global_id": 10812 }, { "text": "rossiae.\n\nFurfurilactobacillus milii sp. nov., isolated from fermented cereal foods.", "token_count": 39, "char_count": 95, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:47.477417", "source": { "split": "train_shard_00001", "doc_id": 3637 }, "chunk_id": "train_shard_00001_3637_1", "global_id": 10813 }, { "text": "

Background

Inflammatory bowel disease (IBD) is characterized by chronic inflammation of the gastrointestinal tract that is associated with changes in the gut microbiome. Here, we sought to identify strain-specific functional correlates with IBD outcomes.

Methods

We performed metagenomic sequencing of monthly stool samples from 20 IBD patients and 12 controls (266 total samples). These were taxonomically profiled with MetaPhlAn2 and functionally profiled using HUMAnN2. Differentially abundant species were identified using MaAsLin and strain-specific pangenome haplotypes were analyzed using PanPhlAn.

Results

We found a significantly higher abundance in patients of facultative anaerobes that can tolerate the increased oxidative stress of the IBD gut. We also detected dramatic, yet transient, blooms of Ruminococcus gnavus in IBD patients, often co-occurring with increased disease activity. We identified two distinct clades of R. gnavus strains, one of which is enriched in IBD patients. To study functional differences between these two clades, we augmented the R. gnavus pangenome by sequencing nine isolates from IBD patients. We identified 199 IBD-specific, strain-specific genes involved in oxidative stress responses, adhesion, iron-acquisition, and mucus utilization, potentially conferring an adaptive advantage for this R. gnavus clade in the IBD gut.

Conclusions

This study adds further evidence to the hypothesis that increased oxidative stress may be a major factor shaping the dysbiosis of the microbiome observed in IBD and suggests that R. gnavus may be an important member of the altered gut community in IBD.\n\nA novel Ruminococcus gnavus clade enriched in inflammatory bowel disease patients.", "token_count": 454, "char_count": 1747, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5949, "quality_score": 0.7975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:48.118344", "source": { "split": "train_shard_00001", "doc_id": 3638 }, "chunk_id": "train_shard_00001_3638_0", "global_id": 10814 }, { "text": "Functional profiles of microbial communities are typically generated using comprehensive metagenomic or metatranscriptomic sequence read searches, which are time-consuming, prone to spurious mapping, and often limited to community-level quantification. We developed HUMAnN2, a tiered search strategy that enables fast, accurate, and species-resolved functional profiling of host-associated and environmental communities. HUMAnN2 identifies a community's known species, aligns reads to their pangenomes, performs translated search on unclassified reads, and finally quantifies gene families and pathways. Relative to pure translated search, HUMAnN2 is faster and produces more accurate gene family profiles. We applied HUMAnN2 to study clinal variation in marine metabolism, ecological contribution patterns among human microbiome pathways, variation in species' genomic versus transcriptional contributions, and strain profiling. Further, we introduce 'contributional diversity' to explain patterns of ecological assembly across different microbial community types.\n\nSpecies-level functional profiling of metagenomes and metatranscriptomes.", "token_count": 246, "char_count": 1140, "word_count": 138, "semantic_coherence": 1, "information_density": 0.7681, "quality_score": 0.8841, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:48.601694", "source": { "split": "train_shard_00001", "doc_id": 3639 }, "chunk_id": "train_shard_00001_3639_0", "global_id": 10815 }, { "text": "Lactobacillus acidophilus is a common kind of lactic acid bacteria usually found in the human gastrointestinal tract, oral cavity, vagina, and various fermented foods. At present, many studies have focused on the probiotic function and industrial application of L. acidophilus. Additionally, dozens of L. acidophilus strains have been genome sequenced, but there has been no research to compare them at the genomic level. In this study, 46 strains of L. acidophilus were performed comparative analyses to explore their genetic diversity. The results showed that all the L. acidophilus strains were divided into two clusters based on ANI values, phylogenetic analysis and whole genome comparison, due to the difference of their predicted gene composition of bacteriocin operon, CRISPR-Cas systems and prophages mainly. Additionally, L. acidophilus was a pan-genome open species with a difference in carbohydrates utilization, antibiotic resistance, EPS operon, surface layer protein operon and other functional gene composition. This work provides a better understanding of L. acidophilus from a genetic perspective, and offers a frame for the biotechnological potentiality of this species.\n\nComparative Genomics and Specific Functional Characteristics Analysis of Lactobacillus acidophilus.", "token_count": 352, "char_count": 1346, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6703, "quality_score": 0.8352, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:49.187701", "source": { "split": "train_shard_00001", "doc_id": 3640 }, "chunk_id": "train_shard_00001_3640_0", "global_id": 10816 }, { "text": "

Background

Colistin serves as the last line of defense against multidrug resistant Gram-negative bacterial infections in both human and veterinary medicine. This study aimed to investigate the occurrence and spread of colistin-resistant Enterobacterales (ColR-E) using a One Health approach in Belgium and in the Netherlands.

Methods

In a transnational research project, a total of 998 hospitalized patients, 1430 long-term care facility (LTCF) residents, 947 children attending day care centres, 1597 pigs and 1691 broilers were sampled for the presence of ColR-E in 2017 and 2018, followed by a second round twelve months later for hospitalized patients and animals. Colistin treatment incidence in livestock farms was used to determine the association between colistin use and resistance. Selective cultures and colistin minimum inhibitory concentrations (MIC) were employed to identify ColR-E. A combination of short-read and long-read sequencing was utilized to investigate the molecular characteristics of 562 colistin-resistant isolates. Core genome multi-locus sequence typing (cgMLST) was applied to examine potential transmission events.

Results

The presence of ColR-E was observed in all One Health sectors. In Dutch hospitalized patients, ColR-E proportions (11.3 and 11.8% in both measurements) were higher than in Belgian patients (4.4 and 7.9% in both measurements), while the occurrence of ColR-E in Belgian LTCF residents (10.2%) and children in day care centres (17.6%) was higher than in their Dutch counterparts (5.6% and 12.8%, respectively). Colistin use in pig farms was associated with the occurrence of colistin resistance. The percentage of pigs carrying ColR-E was 21.8 and 23.3% in Belgium and 14.6% and 8.9% in the Netherlands during both measurements", "token_count": 484, "char_count": 1802, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:49.837009", "source": { "split": "train_shard_00001", "doc_id": 3641 }, "chunk_id": "train_shard_00001_3641_0", "global_id": 10817 }, { "text": "The proportion of broilers carrying ColR-E in the Netherlands (5.3 and 1.5%) was higher compared to Belgium (1.5 and 0.7%) in both measurements. mcr-harboring E. coli were detected in 17.4% (31/178) of the screened pigs from 7 Belgian pig farms. Concurrently, four human-related Enterobacter spp. isolates harbored mcr-9.1 and mcr-10 genes. The majority of colistin-resistant isolates (419/473, 88.6% E. coli; 126/166, 75.9% Klebsiella spp.; 50/75, 66.7% Enterobacter spp.) were susceptible to the critically important antibiotics (extended-spectrum cephalosporins, fluoroquinolones, carbapenems and aminoglycosides). Chromosomal colistin resistance mutations have been identified in globally prevalent high-risk clonal lineages, including E. coli ST131 (n = 17) and ST1193 (n = 4). Clonally related isolates were detected in different patients, healthy individuals and livestock animals of the same site suggesting local transmission. Clonal clustering of E. coli ST10 and K. pneumoniae ST45 was identified in different sites from both countries suggesting that these clones have the potential to spread colistin resistance through the human population or were acquired by exposure to a common (food) source. In pig farms, the continuous circulation of related isolates was observed over time. Inter-host transmission between humans and livestock animals was not detected.

Conclusions

The findings of this study contribute to a broader understanding of ColR-E prevalence and the possible pathways of transmission, offering insights valuable to both academic research and public health policy development.\n\nOne Health surveillance of colistin-resistant Enterobacterales in Belgium and the Netherlands between 2017 and 2019.", "token_count": 488, "char_count": 1730, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6582, "quality_score": 0.8291, "entities": { "genes": [ "ST131", "ST45", "ST10", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:50.484211", "source": { "split": "train_shard_00001", "doc_id": 3641 }, "chunk_id": "train_shard_00001_3641_1", "global_id": 10818 }, { "text": "In symbiotic processes, different organisms coexist stably and interact by sharing the same metabolites and environmental conditions. The robustness of a symbiotic nisin production process system composed of the lactic acid bacterium Lactococcus lactis subsp. lactis (ATCC11454) and dairy yeast Kluyveromyces marxianus (MS1) was studied. It was found that this symbiotic process system was robust to the initial disturbance in the inoculum sizes of both microorganisms and pH.\n\nRobustness of cascade pH and dissolved oxygen control in symbiotic nisin production process system of Lactococcus lactis and Kluyveromyces marxianus.", "token_count": 170, "char_count": 627, "word_count": 88, "semantic_coherence": 1, "information_density": 0.6477, "quality_score": 0.8239, "entities": { "genes": [ "MS1", "ATCC11454" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:50.932245", "source": { "split": "train_shard_00001", "doc_id": 3642 }, "chunk_id": "train_shard_00001_3642_0", "global_id": 10819 }, { "text": "The emergence of carbapenem-resistant, hypervirulent Klebsiella pneumoniae is a new threat to health care. We studied the molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Qatar using whole-genome sequence data. We also characterized the prevalence and genetic basis of hypervirulent phenotypes and established the virulence potential using a Galleria mellonella model. Of 100 Klebsiella isolates studied, NDM and OXA-48 were the most common carbapenemases. Core genome single-nucleotide polymorphism (SNP) analysis indicated the presence of diverse sequence types and clonal lineages; isolates belonging to Klebsiella quasipneumoniae subsp. quasipneumoniae sequence type 196 (ST196) and ST1416 may be disseminated among several health care centers. Ten K. pneumoniae isolates carried rmpA and/or truncated rmpA2, and 2 isolates belonged to KL2, indicating low prevalence of classical hypervirulent isolates. Isolates carrying both carbapenem resistance and hypervirulence genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated that blaNDM was located on an IncHI1B-type plasmid (pFQ61_ST383_NDM-5) which coharbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from recombination events. Comparative genomics indicated that this hybrid plasmid may be present in two additional Qatari ST383 isolates. Carbapenem-resistant, hypervirulent K", "token_count": 512, "char_count": 1671, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [ "ST231", "KL2", "ST196", "ST383", "ST1416" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:51.560394", "source": { "split": "train_shard_00001", "doc_id": 3643 }, "chunk_id": "train_shard_00001_3643_0", "global_id": 10820 }, { "text": "pneumoniae ST383 isolates pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.\n\nGenomic Epidemiology of Carbapenem-Resistant Klebsiella in Qatar: Emergence and Dissemination of Hypervirulent Klebsiella pneumoniae Sequence Type 383 Strains.", "token_count": 94, "char_count": 301, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [ "ST383" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:51.939231", "source": { "split": "train_shard_00001", "doc_id": 3643 }, "chunk_id": "train_shard_00001_3643_1", "global_id": 10821 }, { "text": "The present work investigates, as a first step, the influences of pressure, exposure time and depressurisation rate on the β-galactosidase activity of permeabilized cells of Kluyveromyces marxianus CCT 7082 submitted to treatment with compressed carbon dioxide, propane and n-butane. In general, results showed that the enzyme activity changes significantly, depending on the experimental conditions investigated, allowing the selection of proper operating conditions for advantageous application of this biocatalyst in hydrolysis reactions. Further, the stability of the enzyme, after high-pressure pre-treatment, was also experimentally monitored, and the results demonstrated that the activities of this biocatalyst were always higher than those of the non-treated one. Finally, evaluation of synthesis of galactooligosaccharides (GOS), using β-galactosidase without treatment and after treatment in compressed fluids, was carried out. Results indicated promising possibilities since the use of n-butane-pre-treated enzyme led to very satisfactory reaction conversions and selectivity.\n\nEffect of compressed fluids treatment on the activity, stability and enzymatic reaction performance of β-galactosidase", "token_count": 278, "char_count": 1211, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6603, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:52.494502", "source": { "split": "train_shard_00001", "doc_id": 3644 }, "chunk_id": "train_shard_00001_3644_0", "global_id": 10822 }, { "text": "Production of inulinase from Kluyveromyces marxianus YS-1 using root extract of Asparagus racemosus", "token_count": 31, "char_count": 99, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:52.880643", "source": { "split": "train_shard_00001", "doc_id": 3645 }, "chunk_id": "train_shard_00001_3645_0", "global_id": 10823 }, { "text": "Mangabeira (Hancornia speciosa) is a Brazilian tree and a socioeconomic key due to the commercialization of its food products and tree parts to treat health conditions empirically. This review gathers the main chemical, and microbiological characteristics of the mangabeira tree parts (leaves, fruits, tree bark, latex, and seeds), emphasizing its applicability in food science and focusing on its bioapplicability in health conditions. Leaves, fruits, and tree bark can be used to develop functional foods, and phytochemical products; the tree latex have great potential in the bioengineering material field; and the seeds in sustainable energy production. Leaves and fruits were the main samples bioapplied in health conditions in vitro (oxidative stress and chemopreventive effect) and in vivo (gastrointestinal and cardiovascular health, anti-inflammatory, and antidiabetic effect), whereas tree bark and latex also exhibited health effects and seeds showed low cytotoxicity. All parts of the mangabeira tree can be explored by extractivist families and industries from a sustainable point of view.\n\nBiotechnological potential of Hancornia speciosa whole tree: A narrative review from composition to health applicability.", "token_count": 305, "char_count": 1253, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6127, "quality_score": 0.8064, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:53.484312", "source": { "split": "train_shard_00001", "doc_id": 3646 }, "chunk_id": "train_shard_00001_3646_0", "global_id": 10824 }, { "text": "

Introduction

Cold-blooded hosts, particularly exotic frogs, have become a newly recognized reservoir for atypical Brucella species and strains worldwide, but their pathogenicity to humans remains largely unknown. Here we report the isolation and molecular characterization of a B. inopinata strain (FO700662) cultured from clinical samples taken from a captive diseased White's Tree Frog (Litoria caerulea) in Switzerland. The isolation of B. inopinata from a frog along with other reports of human infection by atypical Brucella raises the question of whether atypical Brucella could pose a risk to human health and deserves further attention.

Methods

The investigations included histopathological analysis of the frog, bacterial culture and in-depth molecular characterization of strain FO700662 based on genome sequencing data.

Results and discussion

Originally identified as Ochrobactrum based on its rapid growth and biochemical profile, strain FO700622 was positive for the Brucella- specific markers bcsp31 and IS711. It showed the specific banding pattern of B. inopinata in conventional Bruce-ladder multiplex PCR and also had identical 16S rRNA and recA gene sequences as B. inopinata. Subsequent genome sequencing followed by core genome-based MLST (cgMLST) analysis using 2704 targets (74% of the total chromosome) revealed only 173 allelic differences compared to the type strain of B. inopinata BO1T, while previously considered the closest related strain BO2 differed in 2046 alleles. The overall average nucleotide identity (ANI) between the type strain BO1T and FO700622 was 99,89%, confirming that both strains were almost identical", "token_count": 519, "char_count": 1771, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6926, "quality_score": 0.8463, "entities": { "genes": [ "FO700662", "IS711", "BO1", "BO2", "FO700622" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:40:54.184293", "source": { "split": "train_shard_00001", "doc_id": 3647 }, "chunk_id": "train_shard_00001_3647_0", "global_id": 10825 }, { "text": "In silico MLST-21 and MLVA-16 also identified strain FO700662 as B. inopinata. The nucleotide and amino acid-based phylogenetic reconstruction and comparative genome analysis again placed the isolate together with B. inopinata with 100% support. In conclusion, our data unequivocally classified strain FO700622, isolated from an exotic frog, as belonging to B. inopinata.\n\nIsolation of Brucella inopinata from a White's tree frog (Litoria caerulea): pose exotic frogs a potential risk to human health?", "token_count": 187, "char_count": 543, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [ "FO700662", "FO700622" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:54.658389", "source": { "split": "train_shard_00001", "doc_id": 3647 }, "chunk_id": "train_shard_00001_3647_1", "global_id": 10826 }, { "text": "Nomimicin (1), a new spirotetronate-class polyketide, was isolated from the culture broth of an actinomycete of the genus Actinomadura. Its structure was established by spectroscopic methods, and the absolute configuration was determined by a combination of NOESY experiment, J-based configuration analysis and the modified Mosher method. Nomimicin (1) showed antimicrobial activity against Micrococcus luteus, Candida albicans and Kluyveromyces fragilis.\n\nNomimicin, a new spirotetronate-class polyketide from an actinomycete of the genus Actinomadura.", "token_count": 156, "char_count": 553, "word_count": 71, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:55.099062", "source": { "split": "train_shard_00001", "doc_id": 3648 }, "chunk_id": "train_shard_00001_3648_0", "global_id": 10827 }, { "text": "In this study, 37 yeast strains belonging to 19 different species, which had been isolated from various Turkish sugary foods, were characterized by molecular methods. Identification of yeast isolates at the species level was performed with restriction fragment length polymorphism–polymerase chain reaction (RFLP-PCR) by using five different restriction enzymes (MspI, HaeIII, AluI, RsaI, and ScrFI). For each enzyme, different restriction patterns obtained for endogenic yeast strains were compared to those obtained for the control (type or reference) strains. The strains could be identified when their digestion profiles obtained by all of the enzymes matched those of the control strains. Among the yeast strains, 16 could be identified adequately by RFLP-PCR. Tested yeast species were determined as Candida colliculosa, Candida guilliermondii, Candida kefyr, Candida lambica, Candida parapsilosis, Candida pelliculosa, Candida pulcherrima, Pichia anomala, Saccharomyces cerevisiae, Torulaspora delbrueckii and Zygosaccharomyces rouxii. Strain variation was determined by randomly amplified polymorphic DNA (RAPD-PCR) analysis by using (GTG)₃ and M13 primers. The discrimination among the strains were detected by cluster analysis. Generally, strains of the same species clustered together with a few exceptions. By this way, all the strains in the same species could be differentiated by using both the primers.\n\nMolecular identification of some yeast strains isolated from various sugary foods", "token_count": 387, "char_count": 1501, "word_count": 207, "semantic_coherence": 1, "information_density": 0.599, "quality_score": 0.7995, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:55.711171", "source": { "split": "train_shard_00001", "doc_id": 3649 }, "chunk_id": "train_shard_00001_3649_0", "global_id": 10828 }, { "text": "

Background

Public health is seriously threatened by the rise of carbapenem-resistant Enterobacterales (CRE). However, the genomic characteristics of CRE detected in pediatric patients are largely unknown. Here, we reported the genomic characteristics of a multidrug-resistant Escherichia coli strain containing the plasmid-borne bla NDM-5 and bla CTX-M-14 genes recovered from a Chinese pediatric patient.

Methods

The genome sequence of E. coli strain B379 was determined using Illumina NovaSeq 6000 and Oxford Nanopore MinION. Multiple bioinformatics tools were used to annotate the genome sequence, identify antimicrobial resistance genes and plasmid replicons and perform the in silico multilocus sequence typing (MLST) analysis. Using BacWGSTdb 2.0 server, a core genome MLST (cgMLST) comparison was made between E. coli B379 and all ST746 E. coli strains downloaded from the public database.

Results

The E. coli B379 genome sequence is comprised of six contigs totaling 5,152,502 bp, including one chromosome and five plasmids. Nineteen antimicrobial resistance genes were predicted. The bla NDM-5, which is located on a 46,161 bp IncX3 plasmid and the bla CTX-M-14 gene which is located on a 147,204 bp IncFII/IncFIA/IncFIB plasmid are two examples of these 19 genes. E", "token_count": 484, "char_count": 1407, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [ "ST746" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:56.360581", "source": { "split": "train_shard_00001", "doc_id": 3650 }, "chunk_id": "train_shard_00001_3650_0", "global_id": 10829 }, { "text": "coli B379 was resistant to ampicillin, ampicillin/sulbactam, ceftriaxone, ceftazidime, imipenem, cefepime, ciprofloxacin, ertapenem, trimethoprim-sulfamethoxazole. This isolate belonged to ST746 and the closest relative was another one originating from a human material specimen in Denmark, which differed by 273 cgMLST alleles.

Conclusion

Our study reports the emergence of a multidrug-resistant E. coli strain co-carrying bla NDM-5 and bla CTX-M-14 recovered from a pediatric patient in China. These data would help us better understand the prevalence, genetic characteristics, and mechanisms of antimicrobial resistance of this recently identified multidrug-resistant bacteria in children.\n\nGenomic Characterization of a Multidrug-Resistant Escherichia coli Isolate Co-Carrying bla NDM-5 and bla CTX-M-14 Genes Recovered from a Pediatric Patient in China.", "token_count": 332, "char_count": 955, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8394, "entities": { "genes": [ "ST746" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:56.930183", "source": { "split": "train_shard_00001", "doc_id": 3650 }, "chunk_id": "train_shard_00001_3650_1", "global_id": 10830 }, { "text": "A method to obtain K. marxianus mutants has been developed. Different auxotrophic mutants were isolated by nystatin and snail-enzyme enrichment procedures using an incubation time of 2 h before adding the antibiotic or the enzyme respectively. All his mutants analyzed by complementation tests turned out to belong to the same complementation group. Some of them were transformed and complemented by the S. cerevisiae HIS3 gene. These non-reverting his3 mutants contain no heterologous sequence, which is essential to make them acceptable for application in the food industry.\n\nIsolation and characterization of mutants as an approach to a transformation system in Kluyveromyces marxianus.", "token_count": 163, "char_count": 689, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7525, "quality_score": 0.8762, "entities": { "genes": [ "HIS3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:57.725189", "source": { "split": "train_shard_00001", "doc_id": 3651 }, "chunk_id": "train_shard_00001_3651_0", "global_id": 10831 }, { "text": "A central composite design (CCD) was performed to evaluate the effects of four factors, i.e. temperature (T), pH, agitation rate (K) and initial lactose concentration (L), on ricotta cheese whey batch fermentation and to optimize the process leading to the formation of bio-ethanol. Anaerobic batch fermentation experiments were carried out by using the yeast Kluyveromyces marxianus. After a preliminary experimental analysis, the values of the chosen factors were 32 and 40 degrees C for T, 4 and 6 for pH, 100 and 300 rpm for K, 40 and 80 g L(-1) for L. Response surface methodology (RSM) was used to optimize the fermentation process and an empirical polynomial model was used to fit the experimental data. The best operating conditions resulted to be T=32.35 degrees C, pH 5.41, K=195.56 rpm and L=40 g L(-1) and the model ensured a good fitting of the observed data.\n\nOptimization of ricotta cheese whey (RCW) fermentation by response surface methodology.", "token_count": 276, "char_count": 961, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:58.277902", "source": { "split": "train_shard_00001", "doc_id": 3652 }, "chunk_id": "train_shard_00001_3652_0", "global_id": 10832 }, { "text": "The vast majority of clinical human listeriosis cases are caused by serotype 1/2a, 1/2b, 1/2c, and 4b isolates of Listeria monocytogenes. The ability of L. monocytogenes to establish a systemic listeriosis infection within a host organism relies on a combination of genes that are involved in cell recognition, internalization, evasion of host defenses, and in vitro survival and growth. Recently, whole genome sequencing and comparative genomic analysis have proven to be powerful tools for the identification of these virulence-associated genes in L. monocytogenes. In this study, two serotype 1/2b strains of L. monocytogenes with analogous isolation sources, but differing infection abilities, were subjected to comparative genomic analysis. The results from this comparison highlight the importance of accessory genes (genes that are not part of the conserved core genome) in L. monocytogenes pathogenesis. In addition, a number of factors, which may account for the perceived inability of one of the strains to establish a systemic infection within its host, have been identified. These factors include the notable absence of the Listeria pathogenicity island 3 and the stress survival islet, of which the latter has been demonstrated to enhance the survival ability of L. monocytogenes during its passage through the host intestinal tract, leading to a higher infection rate. The findings from this research demonstrate the influence of hypervariable hotspots in defining the physiological characteristics of a L. monocytogenes strain and indicate that the emergence of a non-pathogenic isolate of L. monocytogenes may result from a cumulative loss of functionality rather than by a single isolated genetic event.", "token_count": 458, "char_count": 1790, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:58.909408", "source": { "split": "train_shard_00001", "doc_id": 3653 }, "chunk_id": "train_shard_00001_3653_0", "global_id": 10833 }, { "text": "Comparative Genomic Analysis of Two Serotype 1/2b Listeria monocytogenes Isolates from Analogous Environmental Niches Demonstrates the Influence of Hypervariable Hotspots in Defining Pathogenesis.", "token_count": 60, "char_count": 203, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:59.268095", "source": { "split": "train_shard_00001", "doc_id": 3653 }, "chunk_id": "train_shard_00001_3653_1", "global_id": 10834 }, { "text": "The presence of Saccharomyces cerevisiae in grape berries and fresh musts is usually very low. However, as fermentation progresses, the population levels of this species considerably increase. In this study, we use the concept of fitness advantage to measure how increasing ethanol concentrations (0-25%) and temperature values (4-46 °C) in wine fermentations affects competition between S. cerevisiae and several non-Saccharomyces yeasts (Hanseniaspora uvarum, Torulaspora delbrueckii, Candida zemplinina, Pichia fermentans and Kluyveromyces marxianus). We used a mathematical approach to model the hypothetical time needed for S. cerevisiae to impose itself on a mixed population of the non-Saccharomyces species described above. This approach also took into consideration the influence of environmental factors and the initial population levels of S. cerevisiae (0.1, 1.0 and 10.0%). Our results suggest that Saccharomyces niche construction via ethanol production does not provide a clear ecological advantage (at least not until the ethanol concentration exceeds 9%), whereas a temperature rise (above 15 °C) does give S. cerevisiae a considerable advantage. The initial frequency of S. cerevisiae considerably influences the time it needs to impose itself (until it reaches a final frequency of 99% in the mixed culture), the lowest time values being found at the highest initial frequency. In light of these results, the application of low temperatures in the wine industry could favor the growth and survival of non-Saccharomyces species for a longer period of time.\n\nQuantifying the individual effects of ethanol and temperature on the fitness advantage of Saccharomyces cerevisiae.", "token_count": 422, "char_count": 1691, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:40:59.889274", "source": { "split": "train_shard_00001", "doc_id": 3654 }, "chunk_id": "train_shard_00001_3654_0", "global_id": 10835 }, { "text": "

Background

Cholera, a rapidly dehydrating diarrheal disease caused by toxigenic Vibrio cholerae, is a leading cause of morbidity and mortality in some regions of the world. Core genome multilocus sequence typing (cgMLST) is a promising approach in generating genetic fingerprints from whole-genome sequencing (WGS) data for strain comparison among laboratories.

Methods

We constructed a V. cholerae core gene allele database using an in-house developed computational pipeline, a database with cgMLST profiles converted from genomic sequences from the National Center for Biotechnology Information, and built a REST-based web accessible via the Internet.

Results

We built a web service platform-cgMLST@Taiwan and installed a V. cholerae allele database, a cgMLST profile database, and computational tools for generating V. cholerae cgMLST profiles (based on 3,017 core genes), performing rapid global strain tracking, and clustering analysis of cgMLST profiles. This web-based platform provides services to researchers, public health microbiologists, and physicians who use WGS data for the investigation of cholera outbreaks and tracking of V. cholerae strain transmission across countries and geographic regions. The cgMLST@Taiwan is accessible at http://rdvd.cdc.gov.tw/cgMLST.\n\ncgMLST@Taiwan: A web service platform for Vibrio cholerae cgMLST profiling and global strain tracking.", "token_count": 369, "char_count": 1405, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6448, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:00.469702", "source": { "split": "train_shard_00001", "doc_id": 3655 }, "chunk_id": "train_shard_00001_3655_0", "global_id": 10836 }, { "text": "

ABSTRACT

Carbapenem-resistant Klebsiella pneumoniae (CRKP) are major pathogens globally. It is unknown whether bloodstream infections (BSIs) by CRKP and other bacteria are commonly caused by single organisms or mixed microbial populations. We hypothesized that contemporaneous CRKP from blood cultures of individual patients are genetically and phenotypically distinct. We determined short-read whole genome sequences of 10 strains from single colonies from CRKP-positive blood cultures in each of 6 patients (Illumina HiSeq). All strains were sequence type (ST)-258 K. pneumoniae that were unique by core genome single nucleotide polymorphism phylogeny, antibiotic resistance and virulence genes, capsular polysaccharide (CPS) gene mutations, and/or plasmid loss. Strains from each of 3 patients that differed in antibiotic resistance, virulence and/or CPS gene content underwent long-read sequencing for genome completion (Oxford Nanopore), and were tested for phenotypes in vitro and pathogenicity during mouse BSIs. Genetically distinct strains within individual patients exhibited significant differences in carbapenem, beta-lactam/beta-lactamase inhibitor and other antibiotic responses, CPS production, mucoviscosity, and susceptibility to serum killing. In 2 patients, strains differed significantly in their ability to infect organs and cause mortality in mice. In conclusion, we identified genotypic and phenotypic variant ST258 K. pneumoniae strains from blood cultures of individual patients, which were not detected by the clinical laboratory at time of BSI diagnosis. The data support a new paradigm of CRKP population diversity during BSIs. If validated for other BSIs, within-host bacterial diversity may have profound implications for medical, microbiology laboratory and infection prevention practices, and for understanding emergence of antibiotic resistance and pathogenesis.

IMPORTANCE

In processing positive microbiologic cultures, standard clinical laboratory practice is to test a single bacterial strain from each morphologically distinct colony", "token_count": 511, "char_count": 2088, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6374, "quality_score": 0.8187, "entities": { "genes": [ "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:01.127713", "source": { "split": "train_shard_00001", "doc_id": 3656 }, "chunk_id": "train_shard_00001_3656_0", "global_id": 10837 }, { "text": "We performed comprehensive whole genome sequence analyses on 10 carbapenem-resistant Klebsiella pneumoniae (CRKP) strains from positive blood cultures from each of 6 patients. Our findings that all strains were genetically unique and that genetic variants manifested differences in phenotypes like antibiotic responsiveness and virulence suggest that CRKP bloodstream infections may be commonly caused by mixed bacterial populations. Results raise questions about laboratory protocols and treatment decisions that are directed against a single strain. The observation that pan-genome analyses revealed inter-strain differences that were not evident by studying core genomes has important implications for investigating nosocomial outbreaks and transmission. Data also suggest a model of pathogenesis of CRKP infections, in which environmental pressures in vivo may select for outgrowth of variants that manifest antibiotic resistance, tolerance or specific virulence attributes.\n\nWithin-host genotypic and phenotypic diversity of contemporaneous carbapenem-resistant Klebsiella pneumoniae from blood cultures of patients with bacteremia", "token_count": 252, "char_count": 1143, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7603, "quality_score": 0.8801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:01.618894", "source": { "split": "train_shard_00001", "doc_id": 3656 }, "chunk_id": "train_shard_00001_3656_1", "global_id": 10838 }, { "text": "

Background

ST11 is the most prevalent sequence type of clinical Klebsiella pneumoniae in China.

Methods

We investigated the characteristics of the ST11 subclones using core genome multi-locus sequence typing (cgMLST). Ninety-three carbapenemase-producing K. pneumoniae isolates were collected at Shenzhen People's Hospital. Then, whole-genome sequencing and cgMLST were used to discriminate apparent subclones within the ST11 group.

Results

We analyzed the prevalence and genetic relationships of these subclones. ST11 and K. pneumoniae carbapenemase (KPC-2) were the predominant genotype and carbapenemase, respectively, in the clinical carbapenemase-producing K. pneumoniae strains. cgMLST scheme genotyping divided the ST11 group into two clades across seven complex types (CTs). CT1313 was the most prevalent subclone. The deletion of galF and a high frequency of SNPs in genes associated with the stress- and SOS-responses were found in CT1291 and CT2405 over time, respectively.

Conclusion

Our results indicated that the subclones of the ST11 group had different patterns of prevalence. Highly discriminatory genotyping techniques, such as cgMLST scheme, should be used in further molecular epidemiology investigations.\n\nExpanding of ST11 Carbapenemase-Producing Klebsiella pneumoniae Subclones in a Chinese Hospital, Shenzhen, China.", "token_count": 431, "char_count": 1411, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [ "CT1313", "CT1291", "CT2405", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:02.243143", "source": { "split": "train_shard_00001", "doc_id": 3657 }, "chunk_id": "train_shard_00001_3657_0", "global_id": 10839 }, { "text": "Edible coatings and films represent an alternative packaging system characterized by being more environment- and customer-friendly than conventional systems of food protection. Research on edible coatings requires multidisciplinary efforts by food engineers, biopolymer specialists and biotechnologists. Entrapment of probiotic cells in edible films or coatings is a favorable approach that may overcome the limitations linked with the use of bioactive compounds in or on food products. The recognition of several health advantages associated with probiotics ingestion is worldwide accepted and well documented. Nevertheless, due to the low stability of probiotics in the food processing steps, in the food matrices and in the gastrointestinal tract, this kind of encapsulation is of high relevance. The development of new and functional edible packaging may lead to new functional foods. This review will focus on edible coatings and films containing probiotic cells (obtaining techniques, materials, characteristics, and applications) and the innovative entrapment techniques use to obtained such packaging.\n\nEdible Films and Coatings Functionalization by Probiotic Incorporation: A Review.", "token_count": 243, "char_count": 1192, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5976, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:02.727633", "source": { "split": "train_shard_00001", "doc_id": 3658 }, "chunk_id": "train_shard_00001_3658_0", "global_id": 10840 }, { "text": "Xanthomonas arboricola comprises a number of economically important fruit tree pathogens classified within different pathovars. Dozens of nonpathogenic and taxonomically unvalidated strains are also designated as X. arboricola, leading to a complicated taxonomic status in the species. In this study, we have evaluated the whole-genome resources of all available Xanthomonas spp. strains designated as X. arboricola in the public databases to refine the members of the species based on DNA similarity indexes and core genome-based phylogeny. Our results show that, of the nine validly described pathovars within X. arboricola, pathotype strains of seven pathovars are taxonomically genuine, belonging to the core clade of the species regardless of their pathogenicity on the host of isolation (thus the validity of pathovar status). However, strains of X. arboricola pv. guizotiae and X. arboricola pv. populi do not belong to X. arboricola because of the low DNA similarities between the type strain of the species and the pathotype strains of these two pathovars. Thus, we propose to elevate the two pathovars to the rank of a species as X. guizotiae sp. nov. with the type strain CFBP 7408T and X. populina sp. nov. with the type strain CFBP 3123T. In addition, other mislabeled strains of X. arboricola were scattered within Xanthomonas spp. that belong to previously described species or represent novel species that await formal description.\n\nTaxonomic Refinement of Xanthomonas arboricola.", "token_count": 488, "char_count": 1623, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5419, "quality_score": 0.7709, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:03.374174", "source": { "split": "train_shard_00001", "doc_id": 3659 }, "chunk_id": "train_shard_00001_3659_0", "global_id": 10841 }, { "text": "

Aims

The goal was to explore the effects of subinhibitory concentration (SIC) (0·5 MIC = 20 µg l-1 ) of ciprofloxacin on the transcriptome of enterohaemorrhagic Escherichia coli O26:H11 isolate by 60 minutes of exposure.

Materials and results

We used a combination of comparative genomic and transcriptomic (RNAseq) analyses. The whole genome of the E. coli O26:H11 #30934 strain of bovine origin was sequenced and assembled. This genome was next used as reference for the differential gene expression analysis. A whole-genome-based analysis of 36 publicly available E. coli O26:H11 genomes was performed to define the core and the accessory transcriptome of E. coli O26:H11. Using RNAseq and RT-qPCR analysis we observed overexpression of the SOS response and of T3SS effectors, together with the inhibition of specific motility-associated genes. Among the large set of transposases present, only three were activated, suggesting moderate transposition of genes with low doses of ciprofloxacin. Our results illustrated that transcriptional repressors, such as the CopG family protein, belonging to the core genome of E. coli O26:H11, are altered in response to fluoroquinolone exposure. The gene ontology enrichment analysis showed SIC of ciprofloxacin induced binding functions and catalytic activities, including mostly transferase and hydrolase proteins. The amino acid pathways involved in metabolic processes were significantly enhanced after the treatment.

Conclusions

Although the core genome of E. coli O26:H11 constituted only 54·5% of the whole genome, we demonstrated that most differentially expressed genes were associated with the core genome of E", "token_count": 482, "char_count": 1695, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6345, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:04.022060", "source": { "split": "train_shard_00001", "doc_id": 3660 }, "chunk_id": "train_shard_00001_3660_0", "global_id": 10842 }, { "text": "coli O26:H11, and that effects on the mobile genetic element, phage, and plasmid-related genes were rare.

Significance and impact of the study

For the first time the effect of low dose of ciprofloxacin on the core transcriptome of E. coli O26:H11 was described. The effects on the main biological functions and protein classes including transcriptional regulators were illustrated.\n\nOverall changes in the transcriptome of Escherichia coli O26:H11 induced by a subinhibitory concentration of ciprofloxacin.", "token_count": 148, "char_count": 513, "word_count": 72, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:04.458380", "source": { "split": "train_shard_00001", "doc_id": 3660 }, "chunk_id": "train_shard_00001_3660_1", "global_id": 10843 }, { "text": "Abstract

Background Genomics-informed pathogen surveillance strengthens public health decision-making, playing an important role in infectious diseases’ prevention and control. A pivotal outcome of genomics surveillance is the identification of pathogen genetic clusters and their characterization in terms of geotemporal spread or linkage to clinical and demographic data. This task often consists of the visual exploration of (large) phylogenetic trees and associated metadata, being time consuming and difficult to reproduce. Results We developed ReporTree, a flexible bioinformatics pipeline that allows diving into the complexity of pathogen diversity to rapidly identify genetic clusters at any (or all) distance thresholds (e.g., high resolution thresholds used for outbreak detection or stable threshold ranges for nomenclature design) and to generate surveillance-oriented reports based on the available metadata, such as timespan, geography or vaccination/clinical status. By handling several input formats (SNP/allele matrices, trees/dendrograms, multiple sequence alignments, VCF files or distance matrices) and clustering methods, ReporTree is applicable to multiple pathogens, thus constituting a flexible resource that can be smoothly deployed in routine surveillance bioinformatics workflows with negligible computational and time costs. This is demonstrated through a benchmarking using core genome- (cg) or whole genome- (wg) Multiple Locus Sequence Type (MLST) (cg/wgMLST) datasets of four foodborne bacterial pathogens (each comprising more than a thousand isolates), in which genetic clusters at possible outbreak level were identified and reported in a matter of seconds. To further validate this tool, we reproduced a previous large-scale study on Neisseria gonorrhoeae, demonstrating how ReporTree is able to rapidly identify the main species genogroups and characterize them with key surveillance metadata (e.g, antibiotic resistance data). By providing examples for SARS-CoV-2 and the foodborne bacterial pathogen Listeria monocytogenes, we show how this tool is currently a useful asset in genomics-informed routine surveillance and outbreak detection of a wide variety of species", "token_count": 505, "char_count": 2262, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6734, "quality_score": 0.8367, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:05.156393", "source": { "split": "train_shard_00001", "doc_id": 3661 }, "chunk_id": "train_shard_00001_3661_0", "global_id": 10844 }, { "text": "Conclusions In summary, ReporTree is a pan-pathogen tool for automated and reproducible identification and characterization of genetic clusters that contributes to a sustainable and efficient public health genomics-informed pathogen surveillance. ReporTree is implemented in python 3.8 and is freely available at https://github.com/insapathogenomics/ReporTree or as a Docker image at insapathogenomics/reportree.

\n\nReporTree: a surveillance-oriented tool to strengthen the linkage between pathogen genetic clusters and epidemiological data", "token_count": 127, "char_count": 543, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:05.557864", "source": { "split": "train_shard_00001", "doc_id": 3661 }, "chunk_id": "train_shard_00001_3661_1", "global_id": 10845 }, { "text": "The vaginal microbiota, normally characterized by lactobacilli presence, is crucial for vaginal health. Members belonging to L. crispatus and L. gasseri species exert crucial protective functions against pathogens, although a total comprehension of factors that influence their dominance in healthy women is still lacking. Here we investigated the complete genome sequence and comprehensive phenotypic profile of L. crispatus strain BC5 and L. gasseri strain BC12, two vaginal strains featured by anti-bacterial and anti-viral activities. Phenotype microarray (PM) results revealed an improved capacity of BC5 to utilize different carbon sources as compared to BC12, although some specific carbon sources that can be associated to the human diet were only metabolized by BC12, i.e. uridine, amygdalin, tagatose. Additionally, the two strains were mostly distinct in the capacity to utilize the nitrogen sources under analysis. On the other hand, BC12 showed tolerance/resistance towards twice the number of stressors (i.e. antibiotics, toxic metals etc.) with respect to BC5. The divergent phenotypes observed in PM were supported by the identification in either BC5 or BC12 of specific genetic determinants that were found to be part of the core genome of each species. The PM results in combination with comparative genome data provide insights into the possible environmental factors and genetic traits supporting the predominance of either L. crispatus BC5 or L. gasseri BC12 in the vaginal niche, giving also indications for metabolic predictions at the species level.\n\nInsight into phenotypic and genotypic differences between vaginal Lactobacillus crispatus BC5 and Lactobacillus gasseri BC12 to unravel nutritional and stress factors influencing their metabolic activity.", "token_count": 466, "char_count": 1835, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [ "BC12", "BC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:06.226185", "source": { "split": "train_shard_00001", "doc_id": 3662 }, "chunk_id": "train_shard_00001_3662_0", "global_id": 10846 }, { "text": "Listeria monocytogenes is a foodborne pathogen of concern in dairy processing facilities, with the potential to cause human illness and trigger regulatory actions if found in the product. Monitoring for Listeria spp. through environmental sampling is recommended to prevent establishment of these microorganisms in dairy processing environments, thereby reducing the risk of product contamination. To inform on L. monocytogenes diversity and transmission, we analyzed genome sequences of L. monocytogenes strains (n = 88) obtained through the British Columbia Dairy Inspection Program. Strains were recovered from five different dairy processing facilities over a 10 year period (2007-2017). Analysis of whole genome sequences (WGS) grouped the isolates into nine sequence types and 11 cgMLST types (CT). The majority of isolates (93%) belonged to lineage II. Within each CT, single nucleotide polymorphism (SNP) differences ranged from 0 to 237 between isolates. A highly similar (0-16 SNPs) cluster of over 60 isolates, collected over 9 years within one facility (#71), was identified suggesting a possible persistent population. Analyses of genome content revealed a low frequency of genes associated with stress tolerance, with the exception of widely disseminated cadmium resistance genes cadA1 and cadA2. The distribution of virulence genes and mutations within internalin genes varied across the isolates and facilities. Further studies are needed to elucidate their phenotypic effect on pathogenicity and stress response. These findings demonstrate the diversity of L. monocytogenes isolates across dairy facilities in the same region. Findings also showed the utility of using WGS to discern potential persistence events within a single facility over time.\n\nGenomic characterization of Listeria monocytogenes recovered from dairy facilities in British Columbia, Canada from 2007 to 2017.", "token_count": 500, "char_count": 1959, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6421, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:06.906589", "source": { "split": "train_shard_00001", "doc_id": 3663 }, "chunk_id": "train_shard_00001_3663_0", "global_id": 10847 }, { "text": "Grape must fermentation performance and volatiles formation by simultaneously cryophilic and thermotolerant yeast (strain AXAZ-1), isolated from grapes in Greece, was evaluated in a wide temperature range (5-40°C). Yeast strain was immobilized on brewer's spent grains (BSG) and the formed biocatalyst was introduced into a Multi-Stage Fixed Bed Tower (MFBT) bioreactor. Almost complete sugar utilization from the aforementioned biocatalyst was observed in a wide temperature spectrum, ranging from 5 °C to 37 °C, while at 40 °C residual sugar was up to 29 g/l. Time to complete fermentation with the immobilized yeast ranged from 290 h at 5 °C and 120 h at 40 °C to 25 h at 33 °C. The daily ethanol productivity reached maximum (88.6 g/l) and minimum (5.6 g/l) levels at 33 °C and 5 °C, respectively. The aroma-related compounds' profiles of immobilized cells at different fermentation temperatures were evaluated by using solid phase microextraction (SPME) gas chromatography/mass spectrometry (GC/MS). Must fermentation resulted in a high-quality fermentation product due to the low concentrations of higher and amyl alcohols at all temperatures tested. AXAZ-1 is a very promising strain for quality wine production, as it is capable of performing fermentations of high ethanol concentration and productivities in both low and high temperatures.\n\nVolatiles formation from grape must fermentation using a cryophilic and thermotolerant yeast.", "token_count": 413, "char_count": 1443, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6037, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:07.528445", "source": { "split": "train_shard_00001", "doc_id": 3664 }, "chunk_id": "train_shard_00001_3664_0", "global_id": 10848 }, { "text": "Here, we report the first complete genomes of three cultivable treponeme species from bovine digital dermatitis (DD) skin lesions, two comparative human treponemes, considered indistinguishable from bovine DD species, and a bovine gastrointestinal (GI) treponeme isolate. Key genomic differences between bovine and human treponemes implicate microbial mechanisms that enhance knowledge of how DD, a severe disease of ruminants, has emerged into a prolific, worldwide disease. Bovine DD treponemes have additional oxidative stress genes compared to nearest human-isolated relatives, suggesting better oxidative stress tolerance, and potentially explaining how bovine strains can colonize skin surfaces. Comparison of both bovine DD and GI treponemes as well as bovine pathogenic and human non-pathogenic saprophyte Treponema phagedenis strains indicates genes encoding a five-enzyme biosynthetic pathway for production of 2,3-diacetamido-2,3-dideoxy-d-mannuronic acid, a rare di-N-acetylated mannuronic acid sugar, as important for pathogenesis. Bovine T. phagedenis strains further differed from human strains by having unique genetic clusters including components of a type IV secretion system and a phosphate utilisation system including phoU, a gene associated with osmotic stress survival. Proteomic analyses confirmed bovine derived T. phagedenis exhibits expression of PhoU but not the putative secretion system, whilst the novel mannuronic acid pathway was expressed in near entirety across the DD treponemes. Analysis of osmotic stress response in water identified a difference between bovine and human T. phagedenis with bovine strains exhibiting enhanced survival. This novel mechanism could enable a selective advantage, allowing environmental persistence and transmission of bovine T. phagedenis. Finally, we investigated putative outer membrane protein (OMP) ortholog families across the DD treponemes and identified several families as multi-specific adhesins capable of binding extra cellular matrix (ECM) components", "token_count": 505, "char_count": 2031, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6494, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:08.183470", "source": { "split": "train_shard_00001", "doc_id": 3665 }, "chunk_id": "train_shard_00001_3665_0", "global_id": 10849 }, { "text": "One bovine pathogen specific adhesin ortholog family showed considerable serodiagnostic potential with the Treponema medium representative demonstrating considerable disease specificity (91.6%). This work has shed light on treponeme host adaptation and has identified candidate molecules for future diagnostics, vaccination and therapeutic intervention.\n\nDissecting the molecular diversity and commonality of bovine and human treponemes identifies key survival and adhesion mechanisms.", "token_count": 100, "char_count": 485, "word_count": 59, "semantic_coherence": 1, "information_density": 0.8644, "quality_score": 0.9322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:08.557833", "source": { "split": "train_shard_00001", "doc_id": 3665 }, "chunk_id": "train_shard_00001_3665_1", "global_id": 10850 }, { "text": "Zucchini plants with symptoms including twisted petioles, necrotic leaves, crown rot, and internal fruit rot were found in Bundaberg, Australia, at a commercial field for the first time during late autumn 2016, resulting in direct yield losses of 70 to 80%. Three Pseudomonas syringae strains isolated from symptomatic leaf (KL004-k1), crown (77-4C), and fruit (KFR003-1) were characterized and their pathogenicity evaluated on pumpkin, rockmelon, squash, and zucchini. Biochemical assays showed typical results for P. syringae. The three isolates differed, however, in that two produced fluorescent pigment (KFR003-1 and 77-4C) whereas the third, KL004-k1, was nonfluorescent. Multilocus sequence analysis classified the isolates to phylogroup 2b. The single-nucleotide polymorphism analysis of core genome from the Australian and closely related international isolates of P. syringae showed two separate clusters. The Australian isolates were clustered based on fluorescent phenotype. Pathogenicity tests demonstrated that all three isolates moved systemically within the inoculated plants and induced necrotic leaf symptoms in zucchini plants. Their identities were confirmed with specific PCR assays for P. syringae and phylogroup 2. Pathogenicity experiments also showed that the Eva variety of zucchini was more susceptible than the Rosa variety for all three isolates. Isolate KL004-k1 was more virulent than 77-4C on pumpkin, rockmelon, squash, and zucchini. This study expands the knowledge of P. syringae isolates that infect cucurbits and provides useful information for growers about the relative susceptibility of a range of cucurbit species.\n\nCharacterization of Pseudomonas syringae Isolated from Systemic Infection of Zucchini in Australia.", "token_count": 505, "char_count": 1798, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [ "KFR003", "KL004" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:09.211535", "source": { "split": "train_shard_00001", "doc_id": 3666 }, "chunk_id": "train_shard_00001_3666_0", "global_id": 10851 }, { "text": "Plesiomonas shigelloides is an emerging pathogen that has been shown to be involved in gastrointestinal diseases and extraintestinal infections in humans. However, the taxonomic position, evolutionary dynamics, and pathogenesis of P. shigelloides remain unclear. We reported the draft genome sequences of 12 P. shigelloides strains representing different serogroups. We were able to determine a clear distinction between P. shigelloides and other members of Enterobacterales via core genome phylogeny, Neighbor-Net network, and average genome identity analysis. The pan-genome analysis of P. shigelloides revealed extensive genetic diversity and presented large flexible gene repertoires, while the core genome phylogeny exhibited a low level of clonality. The discordance between the core genome phylogeny and the pan-genome phylogeny indicated that flexible accessory genomes account for an important proportion of the evolution of P. shigelloides, which was subsequently characterized by determinations of hundreds of horizontally transferred genes (horizontal genes), massive gene expansions and contractions, and diverse mobile genetic elements (MGEs). The apparently high levels of horizontal gene transfer (HGT) in P. shigelloides were conferred from bacteria with novel properties from other taxa (mainly Vibrionaceae and Aeromonadaceae), which caused the historical taxonomic confusion and shaped the virulence gene pools. Furthermore, P. shigelloides genomes contain many macromolecular secretion system genes, virulence factor genes, and resistance genes, indicating its potential to cause intestinal and invasive infections. Collectively, our work provides insights into the phylogenetic position, evolutionary dynamic, and pathogenesis of P. shigelloides at the genomic level, which could facilitate the observation and research of this important pathogen.IMPORTANCE The taxonomic position of P", "token_count": 519, "char_count": 2001, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:09.871838", "source": { "split": "train_shard_00001", "doc_id": 3667 }, "chunk_id": "train_shard_00001_3667_0", "global_id": 10852 }, { "text": "shigelloides has been the subject of debate for a long time, and until now, the evolutionary dynamics and pathogenesis of P. shigelloides were unclear. In this study, pan-genome analysis indicated extensive genetic diversity and the presence of large and variable gene repertoires. Our results revealed that horizontal gene transfer was the focal driving force for the genetic diversity of the P. shigelloides pan-genome and might have contributed to the emergence of novel properties. Vibrionaceae and Aeromonadaceae were found to be the predominant donor taxa for horizontal genes, which might have caused the taxonomic confusion historically. Comparative genomic analysis revealed the potential of P. shigelloides to cause intestinal and invasive diseases. Our results could advance the understanding of the evolution and pathogenesis of P. shigelloides, particularly in elucidating the role of horizontal gene transfer and investigating virulence-related elements.\n\nHorizontal Gene Transfer Clarifies Taxonomic Confusion and Promotes the Genetic Diversity and Pathogenicity of Plesiomonas shigelloides.", "token_count": 290, "char_count": 1152, "word_count": 153, "semantic_coherence": 1, "information_density": 0.5686, "quality_score": 0.7843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:10.430881", "source": { "split": "train_shard_00001", "doc_id": 3667 }, "chunk_id": "train_shard_00001_3667_1", "global_id": 10853 }, { "text": "Due to the public health importance of flagellar genes for typing, it is important to understand mechanisms that could alter their expression or presence. Phenotypic novelty in flagellar genes arise predominately through accumulation of mutations but horizontal transfer is known to occur. A linear plasmid termed pBSSB1 previously identified in Salmonella Typhi, was found to encode a flagellar operon that can mediate phase variation, which results in the rare z66 flagella phenotype. The identification and tracking of homologs of pBSSB1 is limited because it falls outside the normal replicon typing schemes for plasmids. Here we report the generation of nine new pBSSB1-family sequences using Illumina and Nanopore sequence data. Homologs of pBSSB1 were identified in 154 genomes representing 25 distinct serotypes from 67,758 Salmonella public genomes. Pangenome analysis of pBSSB1-family contigs was performed using Roary and we identified three core genes amenable to a minimal MLST scheme. Population structure analysis based on the newly developed MLST scheme identified three major lineages representing 35 sequence types, and the distribution of these sequence types was found to span multiple serovars across the globe. This MLST scheme has shown utility in tracking and subtyping pBSSB1-family plasmids and it has been incorporated into the plasmid MLST database under the name “pBSSB1-family”.\n\nDevelopment of a multi-locus typing scheme for anEnterobacteriaceaelinear plasmid that mediates inter-species transfer of flagella", "token_count": 376, "char_count": 1547, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6441, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:11.020538", "source": { "split": "train_shard_00001", "doc_id": 3668 }, "chunk_id": "train_shard_00001_3668_0", "global_id": 10854 }, { "text": "

Background

Antimicrobial resistant infections continue to be a leading global public health crisis. Mobile genetic elements, such as plasmids, have been shown to play a major role in the dissemination of antimicrobial resistance (AMR) genes. Despite its ongoing threat to human health, surveillance of AMR in the United States is often limited to phenotypic resistance. Genomic analyses are important to better understand the underlying resistance mechanisms, assess risk, and implement appropriate prevention strategies. This study aimed to investigate the extent of plasmid mediated antimicrobial resistance that can be inferred from short read sequences of carbapenem resistant E. coli (CR-Ec) in Alameda County, California. E. coli isolates from healthcare locations in Alameda County were sequenced using an Illumina MiSeq and assembled with Unicycler. Genomes were categorized according to predefined multilocus sequence typing (MLST) and core genome multilocus sequence typing (cgMLST) schemes. Resistance genes were identified and corresponding contigs were predicted to be plasmid-borne or chromosome-borne using two bioinformatic tools (MOB-suite and mlplasmids).

Results

Among 82 of CR-Ec identified between 2017 and 2019, twenty-five sequence types (STs) were detected. ST131 was the most prominent (n = 17) followed closely by ST405 (n = 12). blaCTX-M were the most common ESBL genes and just over half (18/30) of these genes were predicted to be plasmid-borne by both MOB-suite and mlplasmids. Three genetically related groups of E. coli isolates were identified with cgMLST. One of the groups contained an isolate with a chromosome-borne blaCTX-M-15 gene and an isolate with a plasmid-borne blaCTX-M-15 gene.

Conclusions

This study provides insights into the dominant clonal groups driving carbapenem resistant E", "token_count": 517, "char_count": 1882, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6628, "quality_score": 0.8314, "entities": { "genes": [ "ST131", "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:11.672396", "source": { "split": "train_shard_00001", "doc_id": 3669 }, "chunk_id": "train_shard_00001_3669_0", "global_id": 10855 }, { "text": "coli infections in Alameda County, CA, USA clinical sites and highlights the relevance of whole-genome sequencing in routine local genomic surveillance. The finding of multi-drug resistant plasmids harboring high-risk resistance genes is of concern as it indicates a risk of dissemination to previously susceptible clonal groups, potentially complicating clinical and public health intervention.\n\nThe role of plasmids in carbapenem resistant E. coli in Alameda County, California.", "token_count": 111, "char_count": 480, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7576, "quality_score": 0.8788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:12.055457", "source": { "split": "train_shard_00001", "doc_id": 3669 }, "chunk_id": "train_shard_00001_3669_1", "global_id": 10856 }, { "text": "An estimated 50% of all people carry the stomach bacterium Helicobacter pylori (H. pylori). This organism is responsible for gastric problems like gastritis and gastric ulcers, and is one of the major causes of gastric cancer worldwide. Large numbers of people carry this organism asymptomatically and many questions remain about why serious symptoms develop in a subset of infected humans. These extremely recombinant bacteria may take different evolutionary trajectories in different people, and some genomic changes may be associated with gastric cancer. To test this, and learn more about the genetics of cancer-associated H. pylori, different approaches were used. First, evolution of H. pylori populations was investigated looking at both core and accessory genomes and revealed traces of the long and complex history of the Americas in the bacterial genomes, as well as a similar evolution in core and accessory genome. This was the first time accessory genome of H. pylori was studied that way. Secondly, evolution occurring in the bacterial genome during colonisation of a single host was studied in mice model. This analysis revealed small changes during the passage from a human host to a mice host, and during the ... (continues)\n\nGenome evolution and virulence in H. pylori : identifying the genes/alleles underlying phenotype variation", "token_count": 301, "char_count": 1349, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6106, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:12.626873", "source": { "split": "train_shard_00001", "doc_id": 3670 }, "chunk_id": "train_shard_00001_3670_0", "global_id": 10857 }, { "text": "Plant growth-promoting bacteria can confer a range of health benefits to plants, and are increasingly being used in agriculture as bioinoculants to enhance crop performance and prevent diseases. However, within complex rhizosphere communities, their success as bioinoculants depends heavily on their capacity to competitively colonise root systems. Here, we uncover genetic determinants of root colonisation by the biocontrol agent Pseudomonas protegens Pf-5, known for its ability to suppress multiple plant diseases. Using Transposon-Directed Insertion Site Sequencing (TraDIS), we systematically assayed the entire P. protegens Pf-5 genome to determine genes involved in colonising the rhizoplane of two key agricultural crops, cotton (n = 153 Pf-5 genes) and wheat (n = 110 Pf-5 genes). We find a large overlap of 80 P. protegens Pf-5 genes which are important for colonisation fitness in both plants, suggesting that these encode core traits linked to root colonisation. In-depth functional annotation of these genes, leveraging both protein sequence and structure, reveals key traits that promote P. protegens Pf-5 rhizoplane fitness, including biofilm formation, surface motility, nucleotide and amino acid biosynthesis, sugar catabolism, iron uptake, low-oxygen growth, and stress response mechanisms. These findings can help guide future design and selection of microbial inoculants with improved capacity for competitive root colonisation.\n\nGenetic Drivers of Plant Root Colonisation by the Biocontrol Agent Pseudomonas protegens Pf-5.", "token_count": 373, "char_count": 1545, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:13.219479", "source": { "split": "train_shard_00001", "doc_id": 3671 }, "chunk_id": "train_shard_00001_3671_0", "global_id": 10858 }, { "text": "

Objectives

Pseudomonas is a Gram-negative bacterial genus with numerous member species. In this study, using whole-genome sequencing, we characterized a novel Pseudomonas sp. strain TUM18999, isolated as a pathogen from a human patient.

Methods

The TUM18999 strain was isolated from a patient's burn wound. Minimum inhibitory concentrations (MICs) were determined using the broth microdilution method. The whole-genome sequence was obtained using Miseq and MinION, and we conducted phylogenetic analysis based on single nucleotide polymorphisms of the core genome.

Results

Antimicrobial susceptibility testing revealed a high ceftazidime MIC (32 mg/L). Moreover, carbapenemase production was confirmed using the modified carbapenem inactivation method. We found that the complete genome of TUM18999 was 6,826,062 bp long, with 6175 coding sequences (CDS) and a DNA G+C content (non-plasmid) of 66.4 mol%. Consistent with the high similarities with the 16S rRNA sequences of P. otitidis MCC10330 (98.6%) and P. alcaligenes NBRC 14159 (99.2%), similarities (<90%) were also observed with the gyrB genes of both strains. The average nucleotide identities for P. alcaligenes NBRC 14159 and P. otitidis MCC10330 were also <90%. The core-genome single nucleotide polymorphism phylogenetic tree indicated that the TUM18999 strain was most closely related to P. otitidis MCC10330. In addition, the TUM18999 strain carried the novel gene, species-specific subclass B3 metallo-β-lactamase (MBL), and its similarities with P. alcaligenes metallo-β-lactamase-1 (PAM-1) and P", "token_count": 519, "char_count": 1584, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6355, "quality_score": 0.8178, "entities": { "genes": [ "TUM18999", "MCC10330" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:13.870727", "source": { "split": "train_shard_00001", "doc_id": 3672 }, "chunk_id": "train_shard_00001_3672_0", "global_id": 10859 }, { "text": "otitidis metallo-β-lactamase-1 (POM-1) were 90.24% and 73.14%, respectively.

Conclusion

We characterized the complete whole genome sequence of the novel Pseudomonas sp. TUM18999 carrying the novel gene species-specific subclass B3 MBL.\n\nComplete whole-genome sequence of the novel Pseudomonas species strain TUM18999, isolated from a patient with a burn wound in Japan.", "token_count": 124, "char_count": 376, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [ "TUM18999" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:14.260691", "source": { "split": "train_shard_00001", "doc_id": 3672 }, "chunk_id": "train_shard_00001_3672_1", "global_id": 10860 }, { "text": "Vancomycin-resistant Enterococcus faecium (VREfm) bloodstream infections are associated with high recurrence rates. This study used genome sequencing to accurately distinguish the frequency of relapse and reinfection in patients with recurrent E. faecium bacteremia and to investigate strain relatedness in patients with apparent VREfm and vancomycin-susceptible E. faecium (VSEfm) mixed infection. A retrospective study was performed at the Cambridge University Hospitals NHS Foundation Trust (CUH) between November 2006 and December 2012. We analyzed the genomes of 44 E. faecium isolates from 21 patients (26 VREfm isolates from 12 patients with recurrent bacteremia and 18 isolates from 9 patients with putative VREfm/VSEfm mixed infection). Phenotypic antibiotic susceptibility was determined using a Vitek2 instrument. Genomes were compared with those of a further 263 E. faecium isolates associated with bacteremia in patients at CUH over the same time period. Pairwise comparison of core genomes indicated that 10 (71%) episodes of recurrent VREfm bacteremia were due to reinfection with a new strain, with reinfection being more likely with increasing time between the two positive cultures. The majority (78%) of patients with a mixed VREfm and VSEfm infection had unrelated strains. More than half (59%) of study isolates were closely related to another isolate associated with bacteremia from CUH. This included 60% of isolates associated with reinfection, indicating acquisition in the hospital. This study provides the first high-resolution insights into recurrence and mixed infection by E. faecium and demonstrates that reinfection with a new strain, often acquired from the hospital, is a driver of recurrence.\n\nGenome-Based Analysis of Enterococcus faecium Bacteremia Associated with Recurrent and Mixed-Strain Infection.", "token_count": 496, "char_count": 1881, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:14.916034", "source": { "split": "train_shard_00001", "doc_id": 3673 }, "chunk_id": "train_shard_00001_3673_0", "global_id": 10861 }, { "text": "An unstructured model for an integrated fermentation/membrane extraction process for the production of the aroma compounds 2-phenylethanol and 2-phenylethylacetate by Kluyveromyces marxianus CBS 600 was developed. The extent to which this model, based only on data from the conventional fermentation and separation processes, provided an estimation of the integrated process was evaluated. The effect of product inhibition on specific growth rate and on biomass yield by both aroma compounds was approximated by multivariate regression. Simulations of the respective submodels for fermentation and the separation process matched well with experimental results. With respect to the in situ product removal (ISPR) process, the effect of reduced product inhibition due to product removal on specific growth rate and biomass yield was predicted adequately by the model simulations. Overall product yields were increased considerably in this process (4.0 g/L 2-PE+2-PEA vs. 1.4 g/L in conventional fermentation) and were even higher than predicted by the model. To describe the effect of product concentration on product formation itself, the model was extended using results from the conventional and the ISPR process, thus agreement between model and experimental data improved notably. Therefore, this model can be a useful tool for the development and optimization of an efficient integrated bioprocess.\n\nModeling of an integrated fermentation/membrane extraction process for the production of 2-phenylethanol and 2-phenylethylacetate.", "token_count": 346, "char_count": 1534, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5139, "quality_score": 0.7569, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:15.498322", "source": { "split": "train_shard_00001", "doc_id": 3674 }, "chunk_id": "train_shard_00001_3674_0", "global_id": 10862 }, { "text": "Sixty yeast cultures were isolated from samples of water buffalo Mozzarella, a popular \"pasta filata\" cheese, originating on 16 farms located in the provinces of Salerno, Caserta, and Frosinone (Italy). Strains were identified by means of 5.8S internal transcribed spacer rDNA PCR-RFLP combined with 26S rRNA gene partial sequencing and characterized for their ability to exert biochemical properties of technological interest. The recorded dominance of fermenting yeasts such as the lactose-fermenting Kluyveromyces marxianus (38.3% of the total isolates) and the galactose-fermenting Saccharomyces cerevisiae (21.6% of the total isolates) suggests that these yeasts contribute to the organoleptic definition of the water buffalo Mozzarella. The speciographic analysis revealed the presence of 7 other species rarely or never reported in a dairy environment belonging to the genera Pichia and Candida, whose role in Mozzarella cheese organoleptic properties need to be further investigated.\n\nShort communication: Identification and technological characterization of yeast strains isolated from samples of water buffalo Mozzarella cheese.", "token_count": 287, "char_count": 1138, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6987, "quality_score": 0.8494, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:16.056123", "source": { "split": "train_shard_00001", "doc_id": 3675 }, "chunk_id": "train_shard_00001_3675_0", "global_id": 10863 }, { "text": "Thermophilic microorganisms are expected to have smaller cells and genomes compared with mesophiles, a higher proportion of horizontally acquired genes, and distinct nucleotide and amino acid composition signatures. Here, we took an integrative approach to investigate these apparent correlates of thermophily for Synechococcus A/B cyanobacteria, which include the most heat-tolerant phototrophs on the planet. Phylogenomics confirmed a unique origin of different thermotolerance ecotypes, with low levels of continued gene flow between ecologically divergent but overlapping populations, which has shaped the distribution of phenotypic traits along these geothermal gradients. More thermotolerant strains do have smaller genomes, but genome reduction is associated with a decrease in community richness and metabolic diversity, rather than with cell size. Horizontal gene transfer played only a limited role during Synechococcus evolution, but, the most thermotolerant strains have acquired a Thermus tRNA modification enzyme that may stabilize translation at high temperatures. Although nucleotide base composition was not associated with thermotolerance, we found a general replacement of aspartate with glutamate, as well as a dramatic remodeling of amino acid composition at the highest temperatures that substantially differed from previous predictions. We conclude that Synechococcus A/B genome diversification largely does not conform to the standard view of temperature adaptation. In addition, carbon fixation was more thermolabile than photosynthetic oxygen evolution for the most thermotolerant strains compared with less tolerant lineages. This suggests that increased flow of reducing power generated during the light reactions to an electron sink(s) beyond carbon dioxide has emerged during temperature adaptation of these bacteria.\n\nIdiosyncratic genome evolution of the thermophilic cyanobacterium Synechococcus at the limits of phototrophy.", "token_count": 431, "char_count": 1958, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6603, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:16.684913", "source": { "split": "train_shard_00001", "doc_id": 3676 }, "chunk_id": "train_shard_00001_3676_0", "global_id": 10864 }, { "text": "Kluyveromyces marxianus Y-8281 yeast culture was utilized for the biological treatment of deproteinated whey wastewater in a batch system. Removal of lactose was optimized by the utilization of response surface methodology, RSM. The empirical model developed through RSM in terms of effective operational factors of medium pH, temperature, lactose and ammonia concentrations was found adequate to describe the treatment of deproteinated whey. Through the analysis, medium pH and temperature were found to be the most significant factors and an increment in both had a positive effect on lactose utilization, while lactose and ammonia concentrations had the least weight within the ranges investigated. Based on contour plots and variance analysis, optimum operational conditions for maximizing lactose removal were found to be 31 degrees C, 45 g/L whey powder concentration, 4 g/L total ammonium salt concentration and medium pH 6. Under the optimum operating conditions determined, 95% lactose removal was achieved after an 18-h fermentation.\n\nOptimization of lactose utilization in deproteinated whey by Kluyveromyces marxianus using response surface methodology (RSM).", "token_count": 280, "char_count": 1171, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6012, "quality_score": 0.8006, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:17.283024", "source": { "split": "train_shard_00001", "doc_id": 3677 }, "chunk_id": "train_shard_00001_3677_0", "global_id": 10865 }, { "text": "Failure of food preservation is frequently caused by thermostable spores of members of the Bacillaceae family, which show a wide spectrum of resistance to cleaning and preservation treatments. We constructed and validated a mixed-species genotyping array for 6 Bacillus species, including Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus sporothermodurans, Bacillus cereus and Bacillus coagulans, and 4 Geobacillus species, including Geobacillus stearothermophilus, Geobacillus thermocatenulatus, Geobacillus toebii and Geobacillus sp., in order to track food spoilage isolates from ingredient to product. The discriminating power of the array was evaluated with sets of 42 reference and 20 test strains. Bacterial isolates contain a within-species-conserved core genome comprising 68–88% of the entire genome and a non-conserved accessory genome comprising 7–22%. The majority of the core genome markers do not hybridise between species, thus they allow for efficient discrimination at the species level. The accessory genome array markers provide high-resolution discrimination at the level of individual isolates from a single species. In conclusion, the reported mixed-species microarray contains discriminating markers that allow rapid and cost-effective typing of Bacillus food spoilage bacteria in a wide variety of food products.\n\nA mixed-species microarray for identification of food spoilage bacilli", "token_count": 374, "char_count": 1430, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:17.892804", "source": { "split": "train_shard_00001", "doc_id": 3678 }, "chunk_id": "train_shard_00001_3678_0", "global_id": 10866 }, { "text": "

Objectives

The Enterobacter cloacae complex is responsible for a variety of infections in hospitalized patients and is resistant to β-lactam antibiotics owing to the expression of AmpC β-lactamase. We report emerging resistance in Enterobacter roggenkampii exposed to ceftriaxone and explore the mechanism underlying mutations responsible for this resistance.

Methods

Three strains were derived from different samples from one patient (blood and liver abscess fluid). Antimicrobial susceptibility was evaluated by standard broth microdilution, while ampC expression was determined via RT-PCR. Genetic relatedness was evaluated via pulsed-field gel electrophoresis (PFGE). Species identification and comparative genome analysis were performed via genome sequencing. Mutation rate testing and selection of AmpC-derepressed mutants were conducted to explore the mutation mechanism.

Results

E. roggenkampii F1247 was susceptible to third-generation cephalosporins (3GCs); F95 and F1057, found in blood sample on day 11 and liver abscess drainage fluid on day 25, were resistant. ampC expression was 341- and 642-fold higher in F95 and F1057, respectively, than in F1247. Three isolates were the same PFGE and sequence types (ST1778) and were highly homologous (2 and 4 core genome single nucleotide polymorphism differences). Compared to F1247, F95 possessed a 575 bp deletion, including 537 bp of ampD, whereas F1057 harbored only one amino acid mutation (Leu140Pro in ampD)", "token_count": 436, "char_count": 1493, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6832, "quality_score": 0.8416, "entities": { "genes": [ "ST1778" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:18.575091", "source": { "split": "train_shard_00001", "doc_id": 3679 }, "chunk_id": "train_shard_00001_3679_0", "global_id": 10867 }, { "text": "The mutation rates from F1247 exposure to cefotaxime, ceftazidime, ceftriaxone, piperacillin-tazobactam, and cefepime were (1.90 ± 0.21) × 10-8, (3.18 ± 0.43) × 10-8, (2.00 ± 0.20) × 10-8, (2.92 ± 0.29) × 10-9, and zero, respectively. In vitro-selected mutations responsible for resistance were identified in ampD, ampR, and dacB.

Conclusions

E. roggenkampii may develop resistance in vivo and in vitro upon exposure to 3GCs and to a lesser extent to piperacillin-tazobactam. 3GCs should not be used as a monotherapy for E. roggenkampii infections. Therapy using cefepime or carbapenems may be preferred to piperacillin-tazobactam in the treatment of E. roggenkampii, especially if source control is difficult.\n\nEmerging resistance to ceftriaxone treatment owing to different ampD mutations in Enterobacter roggenkampii.", "token_count": 336, "char_count": 871, "word_count": 117, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:19.149423", "source": { "split": "train_shard_00001", "doc_id": 3679 }, "chunk_id": "train_shard_00001_3679_1", "global_id": 10868 }, { "text": "Whole-genome sequencing was carried out on 30 Staphylococcus (S.) aureus isolates from dairy cows with subclinical mastitis from all five provinces of Rwanda. Twenty-five of the isolates produced enough sequence to be analyzed using core genome multilocus sequence typing (cg-MLST). The isolates group into three main clusters. The largest cluster contain isolates of sequence type (ST) 152 (n = 6) and the closely related ST1633 (n = 2). These sequence types have previously mainly been encountered in humans. The isolates of the second-largest cluster belong to ST5477 (n = 5),so far exclusively isolated from cows in Rwanda. The third cluster consists of isolates of ST97 (n = 4), which is a well-known bovine-adapted sequence type. These three clusters were all widespread over the country. Isolates of the usually human-adapted sequence types 1 (n = 2) and 5 (n= 1) were found and a single isolate of ST2430, previously found among humans in Africa. Finally, four isolates of novel sequence types were found: ST7108 (n = 2), ST7109 (n = 1), and ST7110 (n = 1). The blaZ penicillin resistance gene was found in 84% of the isolates and was in all cases corroborated by phenotypic resistance determination. Five (20%) of the isolates carried a tetracycline resistance gene, tet(K) or tetM, and three of these five also displayed phenotypic resistance while two isolates carried a tetM-gene but were yet tetracycline susceptible. Seven (28%) isolates carried the dfrG gene conferring resistance to trimethoprim. Four of these isolates indeed were resistant to trimethoprim while three isolates were sensitive", "token_count": 513, "char_count": 1679, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5608, "quality_score": 0.7804, "entities": { "genes": [ "ST2430", "ST7110", "ST1633", "ST7108", "ST97", "ST5477", "ST7109" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:19.805906", "source": { "split": "train_shard_00001", "doc_id": 3680 }, "chunk_id": "train_shard_00001_3680_0", "global_id": 10869 }, { "text": "The str gene conferring resistance to aminoglycosides was found in three isolates; however, none of these displayed resistance to gentamycin. Our data revealed a high diversity of the sequence types of S. aureus isolates from cows with subclinical mastitis in Rwanda. Two major clusters of ST97 and ST5477 are likely to be bovine adapted and cause mastitis while the third cluster of ST152 usually have been found in humans and may signify a recent transmission of these types from human to cows, for example from hand milking. The high prevalence of this sequence type among dairy cows may pose zoonotic threat. The sequence types were widely distributed without any geographic correlation. Penicillin resistance, the most common type of resistance with a prevalence over 80%, but also tetracycline and trimethoprim resistance were displayed by several isolates.\n\nGenetic Characterization of Staphylococcus aureus From Subclinical Mastitis Cases in Dairy Cows in Rwanda.", "token_count": 249, "char_count": 985, "word_count": 149, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [ "ST152", "ST97", "ST5477" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:20.294091", "source": { "split": "train_shard_00001", "doc_id": 3680 }, "chunk_id": "train_shard_00001_3680_1", "global_id": 10870 }, { "text": "Streptococcus mutans is one of the primary pathogens responsible for the development of dental caries. Recent whole-genome sequencing (WGS)-based core genome multilocus sequence typing (cgMLST) approaches have been employed in epidemiological studies of specific human pathogens. However, this approach has not been reported in studies of S. mutans Here, we therefore developed a cgMLST scheme for S. mutans We surveyed 199 available S. mutans genomes as a means of identifying cgMLST targets, developing a scheme that incorporated 594 targets from the S. mutans UA159 reference genome. Sixty-eight sequence types (STs) were identified in this cgMLST scheme (cgSTs) in 80 S. mutans isolates from 40 children that were sequenced in this study, compared to 35 STs identified by multilocus sequence typing (MLST). Fifty-six cgSTs (82.35%) were associated with a single isolate based on our cgMLST scheme, which is significantly higher than in the MLST scheme (11.43%). In addition, 58.06% of all MLST profiles with ≥2 isolates were further differentiated by our cgMLST scheme. Topological analyses of the maximum likelihood phylogenetic trees revealed that our cgMLST scheme was more reliable than the MLST scheme. A minimum spanning tree of 145 S. mutans isolates from 10 countries developed based upon the cgMLST scheme highlighted the diverse population structure of S. mutans This cgMLST scheme thus offers a new molecular typing method suitable for evaluating the epidemiological distribution of this pathogen and has the potential to serve as a benchmark for future global studies of the epidemiological nature of dental caries.IMPORTANCEStreptococcus mutans is regarded as a major pathogen responsible for the onset of dental caries. S. mutans can transmit among people, especially within families", "token_count": 522, "char_count": 1878, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5741, "quality_score": 0.787, "entities": { "genes": [ "UA159" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:20.950931", "source": { "split": "train_shard_00001", "doc_id": 3681 }, "chunk_id": "train_shard_00001_3681_0", "global_id": 10871 }, { "text": "In this study, we established a new epidemiological approach to S. mutans classification. This approach can effectively differentiate among closely related isolates and offers superior reliability relative to that of the traditional MLST molecular typing method. As such, it has the potential to better support effective public health strategies centered around this bacterium that are aimed at preventing and treating dental caries.\n\nA Core Genome Multilocus Sequence Typing Scheme for Streptococcus mutans.", "token_count": 107, "char_count": 515, "word_count": 72, "semantic_coherence": 1, "information_density": 0.8611, "quality_score": 0.9306, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:21.333277", "source": { "split": "train_shard_00001", "doc_id": 3681 }, "chunk_id": "train_shard_00001_3681_1", "global_id": 10872 }, { "text": "In this work the cell growth and inulinase production by Kluyveromyces marxianus NRRL Y-7571 were investigated in a packed-bed bioreactor. For this purpose, seven experimental runs were carried out in order to verify the influence of the inlet air temperature and volumetric air flow rate on the process dynamics. The results showed that the manipulated variables affected significantly the process performance. The best condition for enzyme production was an inlet air temperature and volumetric flow rate of 30°C and 3m³ h⁻¹, respectively, reaching an activity of around 463Ugds⁻¹. The results obtained here can be useful in the scale-up and optimisation of packed-bed bioreactors configuration for inulinase production.\n\nKinetics of inulinase production by solid-state fermentation in a packed-bed bioreactor", "token_count": 200, "char_count": 811, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:21.792391", "source": { "split": "train_shard_00001", "doc_id": 3682 }, "chunk_id": "train_shard_00001_3682_0", "global_id": 10873 }, { "text": "Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi, and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98 Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism, and defense functions. L. sakei has open pan-genomic characteristics, and its pan-gene curve shows an upward trend. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.\n\nIntegrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches.", "token_count": 344, "char_count": 1144, "word_count": 148, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:22.364314", "source": { "split": "train_shard_00001", "doc_id": 3683 }, "chunk_id": "train_shard_00001_3683_0", "global_id": 10874 }, { "text": "In this work, we report 2 cases of vancomycin-resistant Enterococcus faecium bacteremia with development of daptomycin resistance in 2 patients with acute myeloid leukemia and myelodysplastic syndrome. Mutations related to daptomycin-nonsusceptible phenotype in liaSR genes were found in all strains of the study, including those with a minimum inhibitory concentration <1 µg/mL collected before daptomycin therapy. Epidemiological investigation using core genome single nucleotide polymorphism and core genome multilocus sequence typing revealed clonality of all the isolates. In this study, we conclude that real-time genome sequencing of clinical isolates can provide rapid access to timely information on daptomycin-resistant genotypes that would help clinicians speed up and optimize the selection of the antibiotic for treatment.\n\nTwo Cases of Vancomycin-Resistant Enterococcus faecium Bacteremia With Development of Daptomycin-Resistant Phenotype and its Detection Using Oxford Nanopore Sequencing.", "token_count": 276, "char_count": 1026, "word_count": 132, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:22.915361", "source": { "split": "train_shard_00001", "doc_id": 3684 }, "chunk_id": "train_shard_00001_3684_0", "global_id": 10875 }, { "text": "The antimicrobial activities of the ethyl acetate, acetone and methanol extract of 12 plant species were studied. The extract of Capsicum annuum (red pepper) (fruit) Zingiber officinale (ginger) (root), Cuminum cyminum (cumin), Alpinia ficinarum (galingale), Coriandrum sativum (coriander), Cinnamomun zeylanicum Nees (cinnamomun), Origanum onites L. (thyme), Folium sennae (senna), Eugenia caryophyllata (cloves), Flos tiliae (lime), Folium menthae crispae (peppermint) and Piper nigrum (blackpepper) were tested in vitro against 2 fungi and 8 bacterial species by the disc diffusion method. Klebsiella pneumonia 13883, Bacillus megaterium NRS, Pseudomonas aeroginosa ATCC 27859, Staphylococcus aureus 6538 P, Escherichia coil ATCC 8739, Enterobacter cloaca ATCC 13047, Corynebacterium xerosis UC 9165, Streptococcus faecalis DC 74, Kluyveromyces marxianus, Rhodotorula rubra were used in this investigation", "token_count": 342, "char_count": 908, "word_count": 118, "semantic_coherence": 1, "information_density": 0.8729, "quality_score": 0.9364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:23.495888", "source": { "split": "train_shard_00001", "doc_id": 3685 }, "chunk_id": "train_shard_00001_3685_0", "global_id": 10876 }, { "text": "The results indicated that extracts of different spices has shown antibacterial activity in the range of 7-24 mm 30 microl(-1) inhibition zone Eugenia caryophyllata (clove), 7-20 mm 30microl(-1) inhibition zone Capsicum annum (red pepper) and Cinnamomun zeylanicum (cinnamon) bark, 7-18 mm 30microl(-1) inhibition zone Folium sennae (senna) leaves, 7-16 mm 30 microl(-1) inhibition zone Zingiber officinale (ginger) root, 7-15 mm 30microl(-1) inhibition zone Cuminum cyminum (cumin) seed, 7-14 mm 30 microl(-1) inhibition zone Folium menthae crispae (peppermint), Origanum onites (thyme) leaves and Alpinia ficinarum (galingale) root, 7-12 mm 30 microl(-1) inhibiton zone Piper nigrum (blackpepper), 7-11 mm 30microl(-1) inhibition zone Flos tiliae (lime) leaves, 7-8 mm 30microl(-1) inhibition zone Coriandrum sativum (coriander) to the microorganisms tested.\n\nStudies on antimicrobial activities of solvent extracts of different spices.", "token_count": 349, "char_count": 938, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6508, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:24.060208", "source": { "split": "train_shard_00001", "doc_id": 3685 }, "chunk_id": "train_shard_00001_3685_1", "global_id": 10877 }, { "text": "Introduction. Pseudomonas syringae pv. actinidiae (Psa) has emerged as a major bacterial pathogen of kiwifruit cultivation throughout the world.Aim. We aim to introduce a CRISPR-Cas9 system, a commonly used genome editing tool, into Psa. The protocols may also be useful in other Pseudomonas species.Methodology. Using standard molecular biology techniques, we modified plasmid pCas9, which carries the CRISPR-Cas9 sequences from Streptococcus pyogenes, for use in Psa. The final plasmid, pJH1, was produced in a series of steps and is maintained with selection in both Escherichia coli and Psa.Results. We have constructed plasmids carrying a CRISPR-Cas9 system based on that of S. pyogenes, which can be maintained, under selection, in Psa. We have shown that the gene targeting capacity of the CRISPR-Cas9 system is active and that the Cas9 protein is able to cleave the targeted sites. The Cas9 was directed to several different sites in the P. syringae genome. Using Cas9 we have generated Psa transformants that no longer carry the native plasmid present in Psa, and other transformants that lack the integrative, conjugative element, Pac_ICE1. Targeting of a specific gene, a chromosomal non-ribosomal peptide synthetase, led to gene knockouts with the transformants having deletions encompassing the target site.Conclusion. We have constructed shuttle plasmids carrying a CRISPR-Cas9 system that are maintained in both E. coli and P. syringae pv. actinidiae. We have used this gene editing system to eliminate features of the accessory genome (plasmids or ICEs) from Psa and to target a single chromosomal gene.", "token_count": 504, "char_count": 1710, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:24.718052", "source": { "split": "train_shard_00001", "doc_id": 3686 }, "chunk_id": "train_shard_00001_3686_0", "global_id": 10878 }, { "text": "The application of the CRISPR-Cas9 system in Pseudomonas syringae pv. actinidiae.", "token_count": 35, "char_count": 88, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:25.074574", "source": { "split": "train_shard_00001", "doc_id": 3686 }, "chunk_id": "train_shard_00001_3686_1", "global_id": 10879 }, { "text": "Background and aimThe trend in reported case counts of invasive Listeria monocytogenes (Lm), a potentially severe food-borne disease, has been increasing since 2008. In 2015, 2,224 cases were reported in the European Union/European Economic Area (EU/EEA). We aimed to validate the microbiological and epidemiological aspects of an envisaged EU/EEA-wide surveillance system enhanced by routine whole genome sequencing (WGS). Methods: WGS and core genome multilocus sequence typing (cgMLST) were performed on isolates from 2,726 cases from 27 EU/EEA countries from 2010-15. Results: Quality controls for contamination, mixed Lm cultures and sequence quality classified nearly all isolates with a minimum average coverage of the genome of 55x as acceptable for analysis. Assessment of the cgMLST variation between six different pipelines revealed slightly less variation associated with assembly-based analysis compared to reads-based analysis. Epidemiological concordance, based on 152 isolates from 19 confirmed outbreaks and a cluster cutoff of seven allelic differences, was good (sensitivity > 95% for two cgMLST schemes of 1,748 and 1,701 loci each; PPV 58‒68%). The proportion of sporadic cases was slightly below 50%. Of remaining isolates, around one third were in clusters involving more than one country, often spanning several years. Detection of multi-country clusters was on average several months earlier when pooling the data at EU/EEA level, compared with first detection at national level. Conclusions: These findings provide a good basis for comprehensive EU/EEA-wide, WGS-enhanced surveillance of listeriosis. Time limits should not be used for hypothesis generation during outbreak investigations, but should be for analytical studies.\n\nRetrospective validation of whole genome sequencing-enhanced surveillance of listeriosis in Europe, 2010 to 2015.", "token_count": 505, "char_count": 1910, "word_count": 262, "semantic_coherence": 1, "information_density": 0.7099, "quality_score": 0.855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:25.743284", "source": { "split": "train_shard_00001", "doc_id": 3687 }, "chunk_id": "train_shard_00001_3687_0", "global_id": 10880 }, { "text": "

Background

Wastewater treatment plants (WWTPs) are considered hotspots for the environmental dissemination of antimicrobial resistance (AMR) determinants. Vancomycin-Resistant Enterococcus (VRE) are candidates for gauging the degree of AMR bacteria in wastewater. Enterococcus faecalis and Enterococcus faecium are recognized indicators of fecal contamination in water. Comparative genomics of enterococci isolated from conventional activated sludge (CAS) and biological aerated filter (BAF) WWTPs was conducted.

Results

VRE isolates, including E. faecalis (n = 24), E. faecium (n = 11), E. casseliflavus (n = 2) and E. gallinarum (n = 2) were selected for sequencing based on WWTP source, species and AMR phenotype. The pangenomes of E. faecium and E. faecalis were both open. The genomic fraction related to the mobilome was positively correlated with genome size in E. faecium (p < 0.001) and E. faecalis (p < 0.001) and with the number of AMR genes in E. faecium (p = 0.005). Genes conferring vancomycin resistance, including vanA and vanM (E. faecium), vanG (E. faecalis), and vanC (E. casseliflavus/E. gallinarum), were detected in 20 genomes. The most prominent functional AMR genes were efflux pumps and transporters. A minimum of 16, 6, 5 and 3 virulence genes were detected in E. faecium, E. faecalis, E. casseliflavus and E. gallinarum, respectively. Virulence genes were more common in E. faecalis and E. faecium, than E. casseliflavus and E. gallinarum. A number of mobile genetic elements were shared among species. Functional CRISPR/Cas arrays were detected in 13 E", "token_count": 536, "char_count": 1595, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5654, "quality_score": 0.7827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:26.404332", "source": { "split": "train_shard_00001", "doc_id": 3688 }, "chunk_id": "train_shard_00001_3688_0", "global_id": 10881 }, { "text": "faecalis genomes, with all but one also containing a prophage. The lack of a functional CRISPR/Cas arrays was associated with multi-drug resistance in E. faecium. Phylogenetic analysis demonstrated differential clustering of isolates based on original source but not WWTP. Genes related to phage and CRISPR/Cas arrays could potentially serve as environmental biomarkers.

Conclusions

There was no discernible difference between enterococcal genomes from the CAS and BAF WWTPs. E. faecalis and E. faecium have smaller genomes and harbor more virulence, AMR, and mobile genetic elements than other Enterococcus spp.\n\nComparative genomics of multidrug-resistant Enterococcus spp. isolated from wastewater treatment plants.", "token_count": 194, "char_count": 725, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7938, "quality_score": 0.8969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:26.856636", "source": { "split": "train_shard_00001", "doc_id": 3688 }, "chunk_id": "train_shard_00001_3688_1", "global_id": 10882 }, { "text": "D-allulose, a rare sugar with emerging potential as a low-calorie sweetener, has garnered attention as an alternative to other commercially available alternative sweeteners, such as sugar alcohols, which often cause severe gastrointestinal discomfort. D-allulose-6-phosphate 3-epimerase (AlsE) is a prokaryotic enzyme that converts D-allulose-6-phosphate into D-fructose-6-phosphate, enabling its use as a carbon source. However, the taxonomic breadth of AlsE across gut bacteria remains poorly understood, hindering insights into the utilization of D-allulose by microbial communities. In this study, we provide experimental evidence showing that Clostridium innocuum is capable of D-allulose metabolism via a homologous AlsE. A bioinformatics search of 85,202 bacterial genomes identified 116 bacterial species with AlsE homologs, suggesting a limited distribution of AlsE in bacteria. Additionally, Escherichia coli contains a copy of alsE, but it does not grow on D-allulose as a sole carbon source unless alsE is heterologously expressed. A metagenomic analysis revealed that 15.8% of 3079 adult healthy human metagenomic samples that we analyzed contained alsE, suggesting a limited prevalence of the enzyme in the gut microbiome. These results suggest that the gut microbiome has limited capacity to metabolize D-allulose via alsE, supporting its use as an alternative sweetener with minimal impact on microbial composition and gastrointestinal symptoms. This finding also enables personalized nutrition, allowing diabetic individuals to assess their gut microbiota for alsE, and manage glycemic response while reducing gastrointestinal distress.\n\nGut microbial utilization of the alternative sweetener, D-allulose, via AlsE.", "token_count": 443, "char_count": 1732, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6426, "quality_score": 0.8213, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:27.488252", "source": { "split": "train_shard_00001", "doc_id": 3689 }, "chunk_id": "train_shard_00001_3689_0", "global_id": 10883 }, { "text": "Reliable control of the specific growth rate (μ) in fed-batch fermentations depends on the availability of accurate online estimations of the controlled variable. Due to difficulties in measuring biomass, μ is typically estimated using reference models relating measurements of substrate consumption or oxygen uptake rate to biomass growth. However, as culture conditions vary, these models are adapted dynamically, resulting in complex algorithms that lack the necessary robustness for industrial applicability. A simpler approach is presented where biomass is monitored using dielectric spectroscopy. The measurements are subjected to online balances and reconciled in real time against metabolite concentrations and off-gas composition. The reconciled biomass values serve to estimate the growth rate and a simple control scheme is implemented to maintain the desired value of μ. The methodology is developed with the yeast Kluyveromyces marxianus, tested for disturbance rejection and validated with two other strains. It is applicable to other cellular systems with minor modifications.\n\nSimple control of specific growth rate in biotechnological fed-batch processes based on enhanced online measurements of biomass.", "token_count": 247, "char_count": 1221, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:27.977699", "source": { "split": "train_shard_00001", "doc_id": 3690 }, "chunk_id": "train_shard_00001_3690_0", "global_id": 10884 }, { "text": "

Background

Acinetobacter baumannii has emerged as a significant nosocomial pathogen during the last few years, exhibiting resistance to almost all major classes of antibiotics. Alternative treatment options such as vaccines tend to be most promising and cost effective approaches against this resistant pathogen. In the current study, we have explored the pan-genome of A. baumannii followed by immune-proteomics and reverse vaccinology approaches to identify potential core vaccine targets.

Results

The pan-genome of all available A. baumannii strains (30 complete genomes) is estimated to contain 7,606 gene families and the core genome consists of 2,445 gene families (~32 % of the pan-genome). Phylogenetic tree, comparative genomic and proteomic analysis revealed both intra- and inter genomic similarities and evolutionary relationships. Among the conserved core genome, thirteen proteins, including P pilus assembly protein, pili assembly chaperone, AdeK, PonA, OmpA, general secretion pathway protein D, FhuE receptor, Type VI secretion system OmpA/MotB, TonB dependent siderophore receptor, general secretion pathway protein D, outer membrane protein, peptidoglycan associated lipoprotein and peptidyl-prolyl cis-trans isomerase are identified as highly antigenic. Epitope mapping of the target proteins revealed the presence of antigenic surface exposed 9-mer T-cell epitopes. Protein-protein interaction and functional annotation have shown their involvement in significant biological and molecular processes. The pipeline is validated by predicting already known immunogenic targets against Gram negative pathogen Helicobacter pylori as a positive control.

Conclusion

The study, based upon combinatorial approach of pan-genomics, core genomics, proteomics and reverse vaccinology led us to find out potential vaccine candidates against A. baumannii. The comprehensive analysis of all the completely sequenced genomes revealed thirteen putative antigens which could elicit substantial immune response", "token_count": 495, "char_count": 2033, "word_count": 263, "semantic_coherence": 1, "information_density": 0.7148, "quality_score": 0.8574, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:28.630176", "source": { "split": "train_shard_00001", "doc_id": 3691 }, "chunk_id": "train_shard_00001_3691_0", "global_id": 10885 }, { "text": "The integration of computational vaccinology strategies would facilitate in tackling the rapid dissemination of resistant A.baumannii strains. The scarcity of effective antibiotics and the global expansion of sequencing data making this approach desirable in the development of effective vaccines against A. baumannii and other bacterial pathogens.\n\nPangenome and immuno-proteomics analysis of Acinetobacter baumannii strains revealed the core peptide vaccine targets.", "token_count": 107, "char_count": 468, "word_count": 60, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:29.026343", "source": { "split": "train_shard_00001", "doc_id": 3691 }, "chunk_id": "train_shard_00001_3691_1", "global_id": 10886 }, { "text": "The invention provides a nucleic acid sequence derivable from a yeast, e.g. from a Kluyveromyces yeast, preferably from the strain K. marxianus var. marxianus (CBS 6556), and comprising at least a regulatory region derivable from a gene encoding a polypeptide having inulinase activity or a functional modification thereof. Regulatory regions comprise a promoter, a terminator, and a sequence encoding a secretory signal necessary for secreting a gene product from a yeast. The DNA sequence of the inulinase gene from K. marxianus var. marxianus (CBS 6556) is given, including its regulatory regions. The regulatory regions can be used for preparing vectors suitable for transforming a host, preferably a yeast, for the production of desired expression products, e.g. proteins, RNA suitable for flavouring purposes, and metabolites. A process for production of an expression product is also provided.\n\nTHE USE OF THE KLUYVEROMYCES MARXIANUS INULINASE GENE PROMOTER FOR PROTEIN PRODUCTION", "token_count": 260, "char_count": 987, "word_count": 147, "semantic_coherence": 1, "information_density": 0.5306, "quality_score": 0.7653, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:29.595375", "source": { "split": "train_shard_00001", "doc_id": 3692 }, "chunk_id": "train_shard_00001_3692_0", "global_id": 10887 }, { "text": "

Objectives

To evaluate and characterise meningococcal carriage among healthy men who have sex with men (MSM) within a screening programme for Neisseria gonorrhoeae infection at the San Gallicano Dermatological Institute, Italy.

Methods

A total of 441 MSM attending the STI/HIV Centre of the San Gallicano Institute, Rome, Italy, in 2016 were routinely screened for N. gonorrhoeae infection by pharyngeal and rectal swabs. N. meningitidis isolates were evaluated for antibiotic susceptibility and characterised by whole genome sequencing. Genetic relationships among the meningococcal carriage isolates were determined using core genome multilocus sequence typing analysis. The soluble domain of AniA (sAniA) protein expression by western blotting was also evaluated.

Results

A total of 62 (14.1%, 95% CI 11.1 to 17.6) carriage meningococci were found among 441 MSM. Forty-three viable N. meningitidis isolates were cultivated (42 from pharyngeal and 1 from rectal swabs). All the viable isolates were susceptible to cefotaxime, ceftriaxone, ciprofloxacin and rifampicin. Four isolates were penicillin G-resistant and 73% of those penicillin G-susceptible showed a minimum inhibitory concentration from 0.064 μg/mL to 0.25 μg/mL. Serogroup B was the most frequent (44.2%), followed by Z (16.3%), E (9.3%), and Y and W (2.3%), respectively. Multilocus sequence typing analysis identified 29 sequence types belonging to 12 clonal complexes", "token_count": 487, "char_count": 1486, "word_count": 200, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:30.274430", "source": { "split": "train_shard_00001", "doc_id": 3693 }, "chunk_id": "train_shard_00001_3693_0", "global_id": 10888 }, { "text": "The sAniA protein was expressed in 8 out of 28 (29%) screened meningococcal carriage isolates.

Conclusions

Serogroup B meningococcal carriage identified from oral and anal specimens among healthy MSM was the most frequent serogroup identified in this study. Molecular evaluation revealed a degree of similarity among strains belonging to the same clonal complex.\n\nMolecular characterisation and antibiotic susceptibility of meningococcal isolates from healthy men who have sex with men.", "token_count": 126, "char_count": 493, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7761, "quality_score": 0.8881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:30.696550", "source": { "split": "train_shard_00001", "doc_id": 3693 }, "chunk_id": "train_shard_00001_3693_1", "global_id": 10889 }, { "text": "

Objectives

Vancomycin-resistant Enterococcus faecium and Enterococcus faecalis (VRE) are a common cause of healthcare-associated infections. Whole genome sequencing-based typing methods yield the highest discriminatory power for outbreak surveillance in the hospital. We analysed the clonal composition of enteric VRE populations of at-risk patients over several weeks to characterise VRE population diversity and dynamics.

Methods

Five bone marrow transplant recipients (three colonised with vanA-positive isolates, two colonised with vanB-positive isolates) contributed three rectal swabs over a course of several weeks. Fourteen VRE colonies per swab were analysed by core genome multi locus sequence typing (cgMLST) and typing of the van-element.

Results

VRE populations were clonally diverse in three of five patients, and population composition changed dynamically over the time of observation. Besides new acquisition of VRE isolates, shared van-elements localised on nearly identical plasmids between clonally different isolates indicate horizontal gene transfer as a mechanism behind VRE population diversity within single patients.

Conclusion

Outbreak detection relies on typing of isolates, usually by analysing one isolate per patient. We here show that this approach is insufficient for outbreak surveillance of VRE in highly vulnerable patients, as it does not take into account VRE population heterogeneity and horizontal gene transfer of the resistance element.\n\nPopulation dynamics in colonizing vancomycin-resistant Enterococcus faecium isolated from immunosuppressed patients.", "token_count": 375, "char_count": 1624, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6732, "quality_score": 0.8366, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:31.294591", "source": { "split": "train_shard_00001", "doc_id": 3694 }, "chunk_id": "train_shard_00001_3694_0", "global_id": 10890 }, { "text": "Multi-drug resistant S. aureus is a leading concern worldwide. Coagulase-Negative Staphylococci (CoNS) are claimed to be the reservoir and source of important resistant elements in S. aureus . However, the origin and evolutionary route of resistant genes in S. aureus are still remaining unknown. Here, we performed a detailed phylogenomic analysis of 152 completely sequenced S. aureus strains in comparison with 7,529 non- S. aureus reference bacterial genomes. Our results reveal s that S. aureus has a large open pan-genome where 97 (55%) of its known resistant related genes belonging to its accessory genome. Among these genes, 47 (27%) were located within the Staphylococcal Cassette Chromosome (SCCmec), a transposable element responsible for resistance against major classes of antibiotics including beta-lactams, macrolides and aminoglycosides. However, the physically linked mec-box genes ( MecA-MecR-MecI) that are responsible for the maintenance of SCCmec elements is not unique to S. aureus , instead it is widely distributed within Staphylococcaceae family. The phyletic patterns of SCCmec encoded resistant genes in Staphylococcus species are significantly different from that of its core genes indicating frequent exchange of these genes between Staphylococcus species. Our in-depth analysis of SCCmec resistant gene phylogenies reveals that genes such as blaZ , ble, kmA and tetK that are responsible for beta-lactam, bleomycin, kanamycin and tetracycline resistance in S. aureus were laterally transferred from non- Staphylococcus sources. In addition, at least 11 non-SCCmec encoded resistant genes in S. aureus , mostly present in plasmid are laterally acquired from distantly related species. Our study evidently shows that gene transfers played a crucial role in shaping the evolution of antibiotic resistance in S. aureus .", "token_count": 491, "char_count": 1847, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5948, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:31.950109", "source": { "split": "train_shard_00001", "doc_id": 3695 }, "chunk_id": "train_shard_00001_3695_0", "global_id": 10891 }, { "text": "Evolutionary route of resistant genes in Staphylococcus aureus", "token_count": 24, "char_count": 69, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:32.309450", "source": { "split": "train_shard_00001", "doc_id": 3695 }, "chunk_id": "train_shard_00001_3695_1", "global_id": 10892 }, { "text": "

Motivation

The progress of High Throughput Sequencing (HTS) technologies and the reduction in the sequencing costs are such that Whole Genome Sequencing (WGS) could replace many traditional laboratory assays and procedures. Exploiting the volume of data produced by HTS platforms requires substantial computing skills and this is the main bottleneck in the implementation of WGS as a routine laboratory technique. The way in which the vast amount of results are presented to researchers and clinicians with no specialist knowledge of genome sequencing is also a significant issue.

Results

Here we present TORMES, a user-friendly pipeline for WGS analysis of bacteria from any origin generated by HTS on Illumina platforms. TORMES is designed for non-bioinformatician users, and automates the steps required for WGS analysis directly from the raw sequence data: sequence quality filtering, de novo assembly, draft genome ordering against a reference, genome annotation, multi-locus sequence typing (MLST), searching for antibiotic resistance and virulence genes, and pangenome comparisons. Once the analysis is finished, TORMES generates and interactive web-like report that can be opened in any web browser and shared and revised by researchers in a simple manner. TORMES can be run by using very simple commands and represent a quick an easy way to perform WGS analysis.

Availability and implementation

TORMES is free available at https://github.com/nmquijada/tormes.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nTORMES: an automated pipeline for whole bacterial genome analysis.", "token_count": 386, "char_count": 1650, "word_count": 226, "semantic_coherence": 1, "information_density": 0.646, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:32.922859", "source": { "split": "train_shard_00001", "doc_id": 3696 }, "chunk_id": "train_shard_00001_3696_0", "global_id": 10893 }, { "text": "Introduction. Molecular epidemiological and phenotypic analyses of Listeria monocytogenes strains can inform our understanding of factors that influence onward transmission, virulence potential and ability to control the pathogen in foods or in clinical settings. Bile acids represent a host-specific barrier to microbial colonization of the gastrointestinal tract and are, therefore, not encountered in the external environment. We tested the hypothesis that tolerance of bile acids may be an evolutionary adaptation across L. monocytogenes clonal complexes (CCs), which varies with genotype and/or is associated with clinical isolates.Hypothesis. We hypothesized that strains of L. monocytogenes may differ in bile tolerance (a potential virulence-associated trait) and herein examine this phenomenon according to CC, strain origin and genotype.Aim. To assess 205 genome-sequenced isolates of L. monocytogenes for tolerance of porcine bile acids and bile salt hydrolase (BSH) activity.Methodology. Survival of L. monocytogenes strains was determined following exposure to porcine bile acids under conditions that mimic the small intestinal environment. BSH activity was assayed against pure taurodeoxycholic acid and glycodeoxycholic acid using an agar plate deconjugation assay. Genomes were analysed for polymorphisms in known bile tolerance loci.Results. Isolates demonstrated distinct inter-individual variances in bile tolerance under anaerobic conditions that mimic the intestinal environment. Strains isolated from cases of human disease were significantly more bile-tolerant than those isolated from natural environments or foods. There was no correlation between levels of bile tolerance and the size of bile precipitation zones on the BSH agar plate assay", "token_count": 474, "char_count": 1837, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:33.569839", "source": { "split": "train_shard_00001", "doc_id": 3697 }, "chunk_id": "train_shard_00001_3697_0", "global_id": 10894 }, { "text": "No significant patterns were seen upon analysis of known or putative bile tolerance loci; however, individual strains with naturally occurring sigB operon mutations demonstrated reduced bile tolerance.Conclusion. L. monocytogenes strains isolated from clinical cases of listeriosis demonstrated elevated bile resistance consistent with a likely enhanced capacity to cause gastrointestinal infection preceding invasive disease. The data suggest the potential importance of bile tolerance in L. monocytogenes infection and highlight underlying molecular mechanisms by which strains vary in their natural levels of bile tolerance.\n\nPhenotypic and phylogenetic analyses of <i>Listeria monocytogenes</i> strains reveal enhanced bile tolerance in clinical isolates.", "token_count": 195, "char_count": 799, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7423, "quality_score": 0.8711, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:34.022596", "source": { "split": "train_shard_00001", "doc_id": 3697 }, "chunk_id": "train_shard_00001_3697_1", "global_id": 10895 }, { "text": "

Importance

The travelers' gut microbiome is potentially assaulted by acute and chronic perturbations (e.g., diarrhea, antibiotic use, and different environments). Prior studies of the impact of travel and travelers' diarrhea (TD) on the microbiome have not directly compared antibiotic regimens, and studies of different antibiotic regimens have not considered travelers' microbiomes. This gap is important to be addressed as the use of antibiotics to treat or prevent TD-even in moderate to severe cases or in regions with high infectious disease burden-is controversial based on the concerns for unintended consequences to the gut microbiome and antimicrobial resistance (AMR) emergence. Our study addresses this by evaluating the impact of defined antibiotic regimens (single-dose treatment or daily prophylaxis) on the gut microbiome and resistomes of deployed servicemembers, using samples collected during clinical trials. Our findings indicate that the antibiotic treatment regimens that were studied generally do not lead to adverse effects on the gut microbiome and resistome and identify the relative risks associated with prophylaxis. These results can be used to inform therapeutic guidelines for the prevention and treatment of TD and make progress toward using microbiome information in personalized medical care.\n\nGut microbiome and antibiotic resistance effects during travelers' diarrhea treatment and prevention.", "token_count": 325, "char_count": 1438, "word_count": 200, "semantic_coherence": 1, "information_density": 0.595, "quality_score": 0.7975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:34.587804", "source": { "split": "train_shard_00001", "doc_id": 3698 }, "chunk_id": "train_shard_00001_3698_0", "global_id": 10896 }, { "text": "

ABSTRACT

Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae , a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive dataset of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates which could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST ( https://pubmlst.org/vcholerae/ ).

IMPORTANCE

Toxigenic Vibrio cholerae of the O1 and O139 serogroups are the causative agent of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing (cgMLST) scheme for V. cholerae ", "token_count": 506, "char_count": 2109, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6263, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:35.253152", "source": { "split": "train_shard_00001", "doc_id": 3699 }, "chunk_id": "train_shard_00001_3699_0", "global_id": 10897 }, { "text": "Using cgMLST, we established an outbreak threshold that can efficiently identify outbreak related strains and potential sources of introduction. We also defined a sublineage threshold that is similar to traditional MLST sequence type which will provide context to this new typing method by relating it to previous MLST results. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease-of-use, making this scheme the most suitable method for V. cholerae typing and surveillance worldwide.\n\nAVibrio choleraeCore Genome Multilocus Sequence Typing Scheme to Facilitate the Epidemiological Study of Cholera", "token_count": 146, "char_count": 641, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7865, "quality_score": 0.8933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:35.688557", "source": { "split": "train_shard_00001", "doc_id": 3699 }, "chunk_id": "train_shard_00001_3699_1", "global_id": 10898 }, { "text": "Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 has spread rapidly across North America, and CA-MRSA is also increasing in Australia. However, the dominant Australian CA-MRSA strain, ST93-IV [2B] appears distantly related to USA300 despite strikingly similar clinical and epidemiological profiles. Here, we compared the virulence of a recent Australian ST93 isolate (JKD6159) to other MRSA, including USA300, and found that JKD6159 was the most virulent in a mouse skin infection model. We fully sequenced the genome of JKD6159 and confirmed that JKD6159 is a distinct clone with 7616 single nucleotide polymorphisms (SNPs) distinguishing this strain from all other S. aureus genomes. Despite its high virulence there were surprisingly few virulence determinants. However, genes encoding α-hemolysin, Panton-Valentine leukocidin (PVL) and α-type phenol soluble modulins were present. Genome comparisons revealed 32 additional CDS in JKD6159 but none appeared to encode new virulence factors, suggesting that this clone's enhanced pathogenicity could lie within subtler genome changes, such as SNPs within regulatory genes. To investigate the role of accessory genome elements in CA-MRSA epidemiology, we next sequenced three additional Australian non-ST93 CA-MRSA strains and compared them with JKD6159, 19 completed S. aureus genomes and 59 additional S. aureus genomes for which unassembled genome sequence data was publicly available (82 genomes in total). These comparisons showed that despite its distinctive genotype, JKD6159 and other CA-MRSA clones (including USA300) share a conserved repertoire of three notable accessory elements (SSCmecIV, PVL prophage, and pMW2). This study demonstrates that the genetically distinct ST93 CA-MRSA from Australia is highly virulent", "token_count": 507, "char_count": 1811, "word_count": 250, "semantic_coherence": 1, "information_density": 0.664, "quality_score": 0.832, "entities": { "genes": [ "USA300", "JKD6159", "ST93" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:36.338042", "source": { "split": "train_shard_00001", "doc_id": 3700 }, "chunk_id": "train_shard_00001_3700_0", "global_id": 10899 }, { "text": "Our comparisons of geographically and genetically diverse CA-MRSA genomes suggest that apparent convergent evolution in CA-MRSA may be better explained by the rapid dissemination of a highly conserved accessory genome from a common source.\n\nThe dominant Australian community-acquired methicillin-resistant Staphylococcus aureus clone ST93-IV [2B] is highly virulent and genetically distinct.", "token_count": 99, "char_count": 391, "word_count": 50, "semantic_coherence": 1, "information_density": 0.86, "quality_score": 0.93, "entities": { "genes": [ "ST93" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:36.724717", "source": { "split": "train_shard_00001", "doc_id": 3700 }, "chunk_id": "train_shard_00001_3700_1", "global_id": 10900 }, { "text": "

Background

Enterococcus species account for most of the human enterococcal HAI and multidrug-resistant infections and have become a major threat to modern public health. We examine the rise in the number of vancomycin resistant E. faecium blood stream and urinary tract infections in a COVID-19 department during an epidemiologic outbreak investigation to detect and eliminate nosocomial clusters of the bacteria.

Methods

 Strain identification was performed by classical isolation and biochemical and cultivation methods. Antibiotic testing results were interpreted according to European committee on antimicrobial susceptibility testing (EUCAST) guidelines. Six isolated samples underwent the whole genome sequencing (WGS) during the outbreak investigation. Isolate relatedness was determined using the core genome multi-locus sequence typing.

Results

 WGS revealed two genotypically distinct VRE clusters, one of which had genetically closely related patients and environmental isolates. The cluster was terminated by enhanced infection control strategies.

Conclusions

 This study provides the first description of an outbreak caused by vanB-ST117 and vanA-ST17 E. faecium strains among COVID-19 patients in Slovakia. This study can help to raise the awareness about the need for strict adherence to infection control measures and the implementation of rational antimicrobial stewardship as a routine part of COVID-19 management (Tab. 3, Fig. 3, Ref. 27). Text in PDF www.elis.sk Keywords: vancomycin-resistant Enterococcus faecium, antibiotic resistant, COVID-19, SARS-CoV-2, bacterial outbreak, healthcare-associated infection.\n\nFirst report of nosocomial outbreak of vancomycin-resistant Enterococcus faecium infection among COVID-19 patients hospitalized in a non-intensive care unit ward in Slovakia.", "token_count": 474, "char_count": 1837, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6851, "quality_score": 0.8426, "entities": { "genes": [ "ST17", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:37.743760", "source": { "split": "train_shard_00001", "doc_id": 3701 }, "chunk_id": "train_shard_00001_3701_0", "global_id": 10901 }, { "text": "

ABSTRACT

Protein misfolding affects cellular fitness. This can be caused due to the toxic aggregation of one species of protein or global protein misfolding events. Since the fitness defect arises due to the multi-modal effect of misfolding, there is no consensus mechanism to alleviate this fitness defect. Here, we used adaptive laboratory evolution of thermotolerance to identify pathways contributing to proteotoxic stress resistance in S. cerevisiae . Our results suggest a link between thermotolerance and proteotoxicity resistance, majorly routed through the loss of mitochondrial DNA. Loss of mitochondrial DNA decreased the association of mistargeted misfolded proteins on the mitochondrial surface and altered the cellular response to proteostasis to enhance protein quality control associated degradation. We show that a decrease in the abundance of import channels is sufficient to mimic the loss of mtDNA and increase cellular proteostasis. Thus, we uncover a cryptic interorganellar cooperation in combating proteotoxicity in yeast.\n\nFitness defects due to cytosolic protein misfolding inS. cerevisiaecan be alleviated by decreasing mitochondrial protein import capacity", "token_count": 284, "char_count": 1200, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6566, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:38.307416", "source": { "split": "train_shard_00001", "doc_id": 3702 }, "chunk_id": "train_shard_00001_3702_0", "global_id": 10902 }, { "text": "

Study aim

To determine the genetic diversity of human isolates of Listeria monocytogenes obtained in 2016-2020 from clinical laboratories in various locations of the Czech Republic with a focus on their possible epidemic links and virulence using whole genome sequencing data.

Methods

A total of 102 human L. monocytogenes isolates, serotyped by slide agglutination in combination with multiplex PCR serotyping, were used in this study. Whole genome sequencing was performed retrospectively, and based on the obtained data, the clonal relatedness of the tested strains and the presence of virulence genes were assessed using the Ridom SeqSphere+ software.

Results

In 2016-2020, 102 human isolates of L. monocytogenes were characterized, which represented 65% of all cases of listeriosis reported to the ISIN/EPIDAT systems in the Czech Republic in the monitored period. Serotype 1/2a (57%) was dominant, followed by serotype 4b (30%). Strains of serotype 1/2b (12%) and 1/2c (1%) were rarely detected. Based on the analysis of whole genome sequencing data, the strains were assigned to 26 clonal complexes and 27 sequence types. The cgMLST (core genome Multi-Locus Sequence Typing) analysis revealed four clusters of more than three strains, showing high relatedness (differences up to 10 alleles) with a possible epidemic link. The presence of all key virulence genes was confirmed in all strains. Only three strains (of serotypes 1/2a, 1/2b, and 1/2c) carried a point mutation in the inlA gene responsible for the expression of truncated internalin A protein, which is involved in the mechanism of intestinal barrier crossing by L. monocytogenes.

Conclusion

Molecular epidemiology based on whole genome sequencing is an effective tool to study the population structure of L. monocytogenes strains", "token_count": 520, "char_count": 1827, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5774, "quality_score": 0.7887, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:38.961846", "source": { "split": "train_shard_00001", "doc_id": 3703 }, "chunk_id": "train_shard_00001_3703_0", "global_id": 10903 }, { "text": "This study found high heterogeneity of human L. monocytogenes strains, especially for serotype 1/2a, dominant in the Czech Republic. Several clusters with a possible epidemic link have been identified, and their occurrence will be further monitored.\n\nGenetic diversity of human strains of Listeria monocytogenes in the Czech Republic in 2016-2020.", "token_count": 92, "char_count": 347, "word_count": 50, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:39.339896", "source": { "split": "train_shard_00001", "doc_id": 3703 }, "chunk_id": "train_shard_00001_3703_1", "global_id": 10904 }, { "text": "The CDC's Emerging Infections Program (EIP) conducted population- and laboratory-based surveillance of US carbapenem-resistant Pseudomonas aeruginosa (CRPA) from 2016 through 2018. To characterize the pathotype, 1,019 isolates collected through this project underwent antimicrobial susceptibility testing and whole-genome sequencing. Sequenced genomes were classified using the seven-gene multilocus sequence typing (MLST) scheme and a core genome (cg)MLST scheme was used to determine phylogeny. Both chromosomal and horizontally transmitted mechanisms of carbapenem resistance were assessed. There were 336 sequence types (STs) among the 1,019 sequenced genomes, and the genomes varied by an average of 84.7% of the cgMLST alleles used. Mutations associated with dysfunction of the porin OprD were found in 888 (87.1%) of the genomes and were correlated with carbapenem resistance, and a machine learning model incorporating hundreds of genetic variations among the chromosomal mechanisms of resistance was able to classify resistant genomes. While only 7 (0.1%) isolates harbored carbapenemase genes, 66 (6.5%) had acquired non-carbapenemase β-lactamase genes, and these were more likely to have OprD dysfunction and be resistant to all carbapenems tested. The genetic diversity demonstrates that the pathotype includes a variety of strains, and clones previously identified as high-risk make up only a minority of CRPA strains in the United States. The increased carbapenem resistance in isolates with acquired non-carbapenemase β-lactamase genes suggests that horizontally transmitted mechanisms aside from carbapenemases themselves may be important drivers of the spread of carbapenem resistance in P. aeruginosa.", "token_count": 456, "char_count": 1719, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6426, "quality_score": 0.8213, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:39.972892", "source": { "split": "train_shard_00001", "doc_id": 3704 }, "chunk_id": "train_shard_00001_3704_0", "global_id": 10905 }, { "text": "Whole-Genome Sequencing Reveals Diversity of Carbapenem-Resistant Pseudomonas aeruginosa Collected through CDC's Emerging Infections Program, United States, 2016-2018.", "token_count": 62, "char_count": 174, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:40.338151", "source": { "split": "train_shard_00001", "doc_id": 3704 }, "chunk_id": "train_shard_00001_3704_1", "global_id": 10906 }, { "text": "The increasing prevalence of multidrug-resistant (MDR) pathogens, particularly ESKAPE bacteria, necessitates alternative antimicrobial strategies. Probiotics, particularly lactic acid bacteria, protect against pathogenic infections. This study aimed to characterize Schleiferilactobacillus harbinensis WU01, isolated from fermented palm sap, and evaluate its probiotic potential and antimicrobial activity. Its probiotic characteristics were assessed based on low-pH and bile tolerance, auto-aggregation, hydrophobicity, and adhesion to Caco-2 cells. Antimicrobial activity against ESKAPE pathogens was evaluated using the agar well diffusion assay. Whole-genome sequencing (WGS) and in silico analysis were performed to identify bacteriocin-related genes, virulence factors, and antibiotic-resistance genes. WU01 exhibited a strong tolerance to gastrointestinal conditions, with high survival rates under acidic and bile-salt environments. S. harbinensis WU01 demonstrated significant auto-aggregation, high hydrophobicity, and strong adhesion to Caco-2 cells. Antimicrobial assays revealed inhibitory activity against MDR ESKAPE pathogens, which correlated with the presence of bacteriocin-related genes, including those homologous to Carnocin_CP52. Molecular dynamics (MDs) simulations confirmed the interaction of Carnocin_CP52 with bacterial membranes, suggesting a mechanism for pathogen disruption. WGS confirmed the absence of virulence and antimicrobial-resistance genes, confirming its safety for probiotic applications. These findings suggest that S. harbinensis WU01 possesses probiotic properties and antimicrobial activity against ESKAPE pathogens. The combined results highlight its potential application in functional foods and therapeutic interventions.", "token_count": 459, "char_count": 1791, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [ "WU01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:40.977039", "source": { "split": "train_shard_00001", "doc_id": 3705 }, "chunk_id": "train_shard_00001_3705_0", "global_id": 10907 }, { "text": "Phenotypic and Genomic Insights into <i>Schleiferilactobacillus harbinensis</i> WU01, a Candidate Probiotic with Broad-Spectrum Antimicrobial Activity Against ESKAPE (<i>Enterococcus faecium</i>, <i>Staphylococcus aureus</i>, <i>Klebsiella pneumoniae</i>, <i>Acinetobacter baumannii</i>, <i>Pseudomonas aeruginosa</i>, and <i>Enterobacter</i>) Pathogens.", "token_count": 202, "char_count": 438, "word_count": 30, "semantic_coherence": 1, "information_density": 0.9667, "quality_score": 0.9833, "entities": { "genes": [ "WU01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:41.469932", "source": { "split": "train_shard_00001", "doc_id": 3705 }, "chunk_id": "train_shard_00001_3705_1", "global_id": 10908 }, { "text": "

Background

During a meticillin-resistant Staphylococcus aureus contact tracing and screening investigation, two borderline oxacillin-resistant Staphylococcus aureus (BORSA)-positive screening cultures were encountered among neonatal intensive care unit (NICU) healthcare workers (HCWs). This finding led to further investigations.

Aim

To assess the likelihood of an outbreak with direct transmission among HCWs.

Methods

An infection control team was initiated after the discovery. The team initiated additional infection control measures and evaluated new findings. All NICUs and paediatric ward HCWs were screened for BORSA carriage, and a prospective BORSA seven-week monitoring period for patients was observed. To assess the likelihood of an outbreak with direct transmission among HCWs, the BORSA isolates were analysed using augmented fragment length polymorphism and whole-genome sequencing (WGS).

Findings

Positive HCWs were prohibited from clinical work while awaiting the results from the screening programme. In all, 127 NICU and 77 general paediatric ward HCWs were screened for BORSA carriage; five HCWs were BORSA positive. Seventy-two patients were screened during the seven-week period yielding a total of 138 cultures, ranging from one to nine cultures per patient. No spread from HCWs to patients occurred, and the BORSA screening programme was discontinued. WGS analysis with core genome multi-locus sequence typing of all five BORSA strains showed relatedness between two NICU strains.

Conclusion

During a seven-week period, no transmission from BORSA-positive HCWs to neonates was observed in either screening or clinical cultures. More vigilance and experience is needed to design adequate evidence-based interventions in the future for this vulnerable population.\n\nBorderline oxacillin-resistant Staphylococcus aureus carriage among healthcare workers at neonatal intensive care unit and paediatric ward.", "token_count": 504, "char_count": 1963, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5787, "quality_score": 0.7894, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:42.137029", "source": { "split": "train_shard_00001", "doc_id": 3706 }, "chunk_id": "train_shard_00001_3706_0", "global_id": 10909 }, { "text": "Inulinase is an enzyme relevant to fructose production by enzymatic hydrolysis of inulin. This enzyme is also applied in the production of fructo-oligosaccharides that may be used as a new food functional ingredient. Commercial inulinase is currently obtained using inulin as substrate, which is a relatively expensive raw material. In Brazil, the production of this enzyme using residues of sugarcane and corn industry (sugarcane bagasse, molasses, and corn steep liquor) is economically attractive, owing to the high amount and low cost of such residues. In this context, the aim of this work was the assessment of inulinase production by solid state fermentation using by Kluyveromyces marxianus NRRL Y-7571. The solid medium consisted of sugar cane bagasse supplemented with molasses and corn steep liquor. The production of inulinase was carried out using experimental design technique. The effect of temperature, moisture, and supplements content were investigated. The enzymatic activity reached a maximum of 445 units of inulinase per gram of dry substrate.\n\nInulinase production by Kluyveromyces marxianus NRRL Y-7571 using solid state fermentation.", "token_count": 287, "char_count": 1158, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:42.733286", "source": { "split": "train_shard_00001", "doc_id": 3707 }, "chunk_id": "train_shard_00001_3707_0", "global_id": 10910 }, { "text": "To better understand the effects of endophytic bacteria on halophytes, a bacteria that produced indole-3-acetic acid and 1-aminocyclopropane-1-carboxylic acid deaminase, designated HD2P242T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. The cells of strain HD2P242T were Gram-stain-negative, strictly aerobic, motile by gliding, non-spore-forming and rod-shaped. Strain HD2P242T grew at pH 6.0-9.0 (optimum, pH 7.0) and 10-45 °C (optimum 37 °C), in the presence of 0-8 % (w/v) NaCl (optimum, 4 %). The strain was positive for oxidase and catalase. The phylogenetic trees based on the 16S rRNA gene sequences and the whole genome sequences both showed that strain HD2P242T clustered with Sinomicrobium pectinilyticum 5DNS001T and S. oceani SCSIO 03483T, and had 95.6, 94.3 and <94.3 % 16S rRNA gene similarities to S. pectinilyticum 5DNS001T, S. oceani SCSIO 03483T and all the other current type strains. Strain HD2P242T contained menaquinone 6 as its sole respiratory quinone", "token_count": 485, "char_count": 1171, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7078, "quality_score": 0.8539, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:43.394285", "source": { "split": "train_shard_00001", "doc_id": 3708 }, "chunk_id": "train_shard_00001_3708_0", "global_id": 10911 }, { "text": "Its major polar lipids were phosphatidylethanolamine, two unidentified aminolipids, two unidentified phospholipids and an unidentified lipid. The major fatty acids were iso-C17 : 0, iso-C16 : 0 3-OH, anteiso-C17 : 0 and summed feature 6 (C19 : 1  ω9c and/or C19 : 1  ω11c). The genome consisted of a 5 364 211 bp circular chromosome, with a G+C content of 45.1 mol%, predicting 4391 coding sequence genes, 47 tRNA genes and two rRNA operons. The average nucleotide identity based on blast and the digital DNA-DNA hybridization values of strain HD2P242T with S. oceani SCSIO 03483T and S. pectinilyticum 5DNS001T were 73.8 and 77.0%, and 22.3 and 22.2%, respectively. The comparative genome analysis showed that the pan-genomes of strain HD2P242T and three Sinomicrobium type strains possessed 4236 clusters, whereas the core genome possessed 2162 clusters, which accounted for 52.3 % of all the clusters. The genomic analysis revealed that all four Sinomicrobium members could utilize d-glucose by the glycolysis-gluconeogenesis pathway or the pentose phosphate pathway. The tricarboxylic acid cycle was utilized as a metabolic centre", "token_count": 520, "char_count": 1289, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7102, "quality_score": 0.8551, "entities": { "genes": [], "proteins": [], "pathways": [ "glycolysis" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:44.044461", "source": { "split": "train_shard_00001", "doc_id": 3708 }, "chunk_id": "train_shard_00001_3708_1", "global_id": 10912 }, { "text": "The phylogenetic, physiological and phenotypic characteristics allowed the discrimination of strain HD2P242T from its phylogenetic relatives. Therefore, Sinomicrobium kalidii sp. nov. is proposed, and the type strain is HD2P242T (=CGMCC 1.19025T=KCTC 92136T).\n\nSinomicrobium kalidii sp. nov., an indole-3-acetic acid-producing endophyte from a shoot of halophyte Kalidium cuspidatum.", "token_count": 184, "char_count": 448, "word_count": 47, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:44.492413", "source": { "split": "train_shard_00001", "doc_id": 3708 }, "chunk_id": "train_shard_00001_3708_2", "global_id": 10913 }, { "text": "Three glyceraldehyde-3-phosphate dehydrogenase (GAPDH) genes from Kluyveromyces marxianus were identified and characterized. The coding region of two of them (GAP2 and GAP3) is very similar (99.6% homology). The other gene (GAP1) is only 86% homologous to GAP2 or GAP3 and is responsible for the expression of Gap1p. This protein is extremely homologous to the K. marxianus cell wall protein p37, presumably involved in flocculation. However, no leader sequence could be detected in this gene. The identification of the three genes was possible with the use of polymerase chain reaction-single-strand conformation polymorphism (PCR-SSCP), as it permits us to overcome the difficulties caused by the high homology amongst the genes. Expression of the GAPDH genes under different carbon sources (glucose or ethanol) was assessed either by Northern blot or reverse transcription-PCR-SSCP analysis, revealing that genes GAP1 and GAP2, but not GAP3, are transcribed. The results also indicate that the transcription of the gene encoding the cell wall protein p37 (Gap1p) is not dependent on the carbon source, in contrast with the expression of the gene GAP2, which is affected in cells growing in a glucose-depleted medium.\n\nCharacterization of the glyceraldehyde-3-phosphate dehydrogenase gene family from Kluyveromyces marxianus--polymerase chain reaction-single-strand conformation polymorphism as a tool for the study of multigenic families.", "token_count": 389, "char_count": 1441, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6232, "quality_score": 0.8116, "entities": { "genes": [ "GAP1", "GAP2", "GAP3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:45.111720", "source": { "split": "train_shard_00001", "doc_id": 3709 }, "chunk_id": "train_shard_00001_3709_0", "global_id": 10914 }, { "text": "Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated clade A1, and that plasmids are major contributors to the emergence of nosocomial E. faecium. Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving single-nucleotide polymorphisms (SNPs). We identified three genomic regions harbouring large numbers of SNPs in tight linkage that are not proximal to each other based on the completely assembled chromosome of the clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS30-like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS30-like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.", "token_count": 478, "char_count": 1932, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5824, "quality_score": 0.7912, "entities": { "genes": [ "AUS0004" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:45.753902", "source": { "split": "train_shard_00001", "doc_id": 3710 }, "chunk_id": "train_shard_00001_3710_0", "global_id": 10915 }, { "text": "Genomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogen, Enterococcus faecium.", "token_count": 40, "char_count": 130, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:46.109095", "source": { "split": "train_shard_00001", "doc_id": 3710 }, "chunk_id": "train_shard_00001_3710_1", "global_id": 10916 }, { "text": "The invention discloses a preparation method of natural spice 2-phenethyl alcohol, which is implemented by selecting Candida drusei, Saccharomyces cerevisiae, Kluyveromyces marxianus, inoculating cultivated seed liquid or active dried yeast powder into fermentation culture medium, taking L-PHE produced by fermentation method or enzyme method as substrate, performing liquid aerobic fermentation in a fermentation shake flask or a fermentation tank, adding solid phase absorption medium, L-PHE and glucose in the process of fermentation, obtaining the solid phase absorption medium in a filtration or centrifugation manner, then adopting an elution solvent to carry out elution on the absorption medium, further distilling the eluent to obtain the natural 2-phenethyl alcohol with purity of 97.5-99.5%. The invention combines the fermentation and absorption separation of 2-phenethyl alcohol, has low production cost and excellent aroma quality of the product.\n\nPreparation method of natural spice 2-phenethyl alcohol", "token_count": 258, "char_count": 1018, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6214, "quality_score": 0.8107, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:46.657379", "source": { "split": "train_shard_00001", "doc_id": 3711 }, "chunk_id": "train_shard_00001_3711_0", "global_id": 10917 }, { "text": "

Objectives

The occurrence of OXA-232-producing carbapenem-resistant Klebsiella pneumoniae (CRKP) has been increasing in China during the last five years. The blaOXA-232-carrying CRKP strain's clonal propagation can readily lead to nosocomial epidemics. Here, we report the genome sequence of an OXA-232 and CTX-M-15 co-producing K. pneumoniae strain isolated from a gallbladder infection in China.

Methods

The genome sequence of K. pneumoniae S105 was determined using the Illumina NovaSeq 6000 platform. Antimicrobial resistance genes (ARGs), multilocus sequence typing (MLST) and plasmid replicons were identified using the BacWGSTdb server. The phylogenetic relationship between S105 and other K. pneumoniae strains was analysed using the core genome multilocus sequence typing (cgMLST) strategy.

Results

The genomic sequence of K. pneumoniae S105 is made up of 111 contigs with a total length of 5 748 752 bp. According to the Pasteur MLST scheme, S105 belongs to sequence type (ST) 15. Fifteen ARGs were discovered in the genome, including the beta-lactam resistance genes blaOXA-232 and blaCTX-M-15. The blaOXA-232 gene was located in a ColKP3 plasmid. KL112 was anticipated to be the capsule and lipopolysaccharide serotype", "token_count": 439, "char_count": 1296, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [ "KL112" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:47.295131", "source": { "split": "train_shard_00001", "doc_id": 3712 }, "chunk_id": "train_shard_00001_3712_0", "global_id": 10918 }, { "text": "A total of 73 phylogenetically related strains were found from 19 nations across four continents; 22 of them were from China, with 21 strains harbouring the blaOXA-232 gene, and the majority of them diverged by just 6-37 cgMLST alleles.

Conclusion

In summary, we reported the genomic sequencing of a K. pneumoniae ST15 clinical strain co-carrying the blaOXA-232 and blaCTX-M-15 genes. The clonal dissemination of OXA-232-producing K. pneumoniae ST15 strains in China needs our attention.\n\nGenomic and phylogenetic analysis of a multidrug-resistant Klebsiella pneumoniae ST15 strain co-carrying blaOXA-232 and blaCTX-M-15 recovered from a gallbladder infection in China.", "token_count": 263, "char_count": 731, "word_count": 94, "semantic_coherence": 1, "information_density": 0.6489, "quality_score": 0.8245, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:47.835253", "source": { "split": "train_shard_00001", "doc_id": 3712 }, "chunk_id": "train_shard_00001_3712_1", "global_id": 10919 }, { "text": "

Background

The role of meticillin-susceptible Staphylococcus aureus (MSSA) colonization of healthcare workers (HCWs), patients and the hospital environment in MSSA transmission events (TEs) is poorly understood.

Aims

The role of meticillin-resistant Staphylococcus aureus (MRSA) was investigated recently under non-outbreak conditions in a large hospital with a history of endemic MRSA over 2 years using whole-genome sequencing (WGS). Numerous potential MRSA TEs were identified. The present study investigated MSSA TEs from the same sources during the same 2-year hospital study.

Methods

HCW (N=326) and patient (N=388) volunteers on nine wards were tested for nasal and oral MSSA colonization over 2 years. Near-patient environment (N=1164), high-frequency touch sites (N=810) and air (N=445) samples were screened for MSSA. Representative MSSA and clinical isolates were sequenced and analysed by core genome multi-locus sequence typing. Closely related isolates (≤24 allelic differences) were segregated into related isolate groups (RIGs). Potential TEs involving MSSA in RIGs from HCWs, patients and patient infections were identified in combination with epidemiological data.

Findings

In total, 635 MSSA were recovered: clinical isolates (N=82), HCWs (N=170), patients (N=120), and environmental isolates (N=263). Twenty-four clonal complexes (CCs) were identified among 406/635 MSSA sequenced, of which 183/406 segregated into 59 RIGs. Numerous potential HCW-to-patient, HCW-to-HCW and patient-to-patient TEs were identified, predominantly among CC5-MSSA, CC30-MSSA and CC45-MSSA", "token_count": 509, "char_count": 1616, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6732, "quality_score": 0.8366, "entities": { "genes": [ "CC45", "CC5", "CC30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:48.492408", "source": { "split": "train_shard_00001", "doc_id": 3713 }, "chunk_id": "train_shard_00001_3713_0", "global_id": 10920 }, { "text": "HCW, patient, clinical and environmental isolates were identified in 33, 24, six and 32 RIGs, respectively, with 19/32 of these containing MSSA related to HCW and/or patient isolates.

Conclusions

WGS detected numerous potential hospital MSSA TEs involving HCWs, patients and environmental contamination under non-outbreak conditions.\n\nMeticillin-susceptible Staphylococcus aureus transmission among healthcare workers, patients and the environment in a large acute hospital under non-outbreak conditions investigated using whole-genome sequencing.", "token_count": 147, "char_count": 554, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8485, "quality_score": 0.9242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:48.921411", "source": { "split": "train_shard_00001", "doc_id": 3713 }, "chunk_id": "train_shard_00001_3713_1", "global_id": 10921 }, { "text": "Eremothecium ashbyi is a phytopathogenic fungus infesting cotton, soybeans and several other plants. This highly flavinogenic fungus has been phylogenetically characterized, but the genetic aspects of its central metabolic and riboflavin biosynthetic pathways are unknown. An ORF of 996 bp was obtained from E. ashbyi by using degenerate primers for glyceraldehyde-3-phosphate dehydrogenase (GPD) through reverse transcriptase polymerase chain reaction (RT-PCR) and 5'-3' rapid amplification of cDNA ends (RACE-PCR). This nucleotide sequence had a high similarity of 88% with GPD sequence of Ashbya gossypii. The putative GPD peptide of 331-aa had a high similarity of 85% with the GPD sequence from other ascomycetes. The ORF had an unusually strong codon bias with 5 amino acids showing strict preference of a single codon. The theoretical molecular weight for the putative peptide was 35.58 kDa with an estimated pI of 5.7. A neighbor-joining tree showed that the putative peptide from E. ashbyi displayed the highest similarity to GPD of A. gossypii. The gene sequence is available at the GenBank, accession number EU717696. Homology modeling done with Kluyveromyces marxianus GPD (PDB: 2I5P) as template indicated high structural similarity.\n\nSequence analysis and structural characterization of a glyceraldehyde-3-phosphate dehydrogenase gene from the phytopathogenic fungus Eremothecium ashbyi.", "token_count": 425, "char_count": 1401, "word_count": 200, "semantic_coherence": 1, "information_density": 0.635, "quality_score": 0.8175, "entities": { "genes": [ "EU717696" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:49.543114", "source": { "split": "train_shard_00001", "doc_id": 3714 }, "chunk_id": "train_shard_00001_3714_0", "global_id": 10922 }, { "text": "Enterococcus faecalis is a commensal pathogenic bacterium commonly found in the human gastrointestinal tract and a cause of opportunistic infections typically associated with multidrug resistance. The E. faecalis genetic changes associated with pathogenicity and extraintestinal infection, particularly through gut-to-bloodstream translocation, are poorly understood. Here, we investigate the E. faecalis genetic signatures associated with intestinal colonisation and extraintestinal infection and infection of hospitalised and non-hospitalised individuals using heritability estimation and a genome-wide association study (GWAS). We analysed 750 whole-genome sequences of faecal and bloodstream E. faecalis isolates from hospitalised patients and non-hospitalised individuals, respectively, predominantly in Europe. We found that E. faecalis infection of individuals depending on their hospitalisation status and extraintestinal infection are heritable traits and that ∼24% and ∼34% of their variation is explained by the considered genetic effects, respectively. Further, a GWAS using linear mixed models did not pinpoint any clear enrichment of individual genetic changes in isolates from different isolation sites and individuals with varying hospitalisation statuses, suggesting that these traits are highly polygenic. Altogether, our findings indicate that E. faecalis infection and extraintestinal infection are influenced by variation in genetic, host, and environmental factors, and ultimately the opportunistic pathogenic lifestyle of this versatile host generalist bacterium.\n\nThe population-level impact of Enterococcus faecalis genetics on intestinal colonisation and extraintestinal infection", "token_count": 369, "char_count": 1713, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:50.124546", "source": { "split": "train_shard_00001", "doc_id": 3715 }, "chunk_id": "train_shard_00001_3715_0", "global_id": 10923 }, { "text": "Abstract

Background

The molecular epidemiology of carbapenem-resistant Klebsiella species is not well investigated in Qatar. The objective of this work was to characterize the genetic context of carbapenemase-producing Klebsiella isolates recovered from clinical specimens.

Methods

Klebsiella isolates (n=100) were collected at 7 tertiary hospitals from 2015-2017. Identification and susceptibility testing were performed using MALDI-TOF MS and BD Phoenix system, respectively. Whole Genome Sequencing was performed on the Illumina NextSeq platform. Phylogenomic analysis, screening of resistance and virulence genes, and comparison of genetic environment of carbapenemase were carried out.

Results

Klebsiella pneumoniae was common (80), followed by K. quasipneumoniae (16), K. aerogenes (3) and K. oxytoca (1). The most prevalent were genes encoding NDM-1 (39), OXA-48 (20), OXA-232 (10) and OXA-181 (12). KPC-2 (3) and KPC-3 (2) were also identified; no carbapenemase-encoding genes could be identified in 15 isolates. Plasmid locations of 24 carbapenemase-encoding genes were determined; blaNDM-1 was localized on IncFII replicon, while blaOXA-181 and blaOXA-232 were commonly associated with ColKP3 plasmids. pOXA-48-like plasmid was detected in 17/20 isolates harboring blaOXA-48. blaKPC-3 was located on a contig with ‘traditional’ Tn4401a mobile genetic element. Sequence types (STs) were diverse and the ‘traditional’ clonal group (CG) 258 was rare. K. pneumoniae ST147 was predominant (13), followed by ST231 (7) and ST11 (5). Nine K", "token_count": 524, "char_count": 1569, "word_count": 212, "semantic_coherence": 1, "information_density": 0.717, "quality_score": 0.8585, "entities": { "genes": [ "ST231", "ST147", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:50.781186", "source": { "split": "train_shard_00001", "doc_id": 3716 }, "chunk_id": "train_shard_00001_3716_0", "global_id": 10924 }, { "text": "quasipneumoniae isolates belonged to ST196 and were highly clonal. The virulence loci such as yersiniabactin (ybt) and rmpA were not detected within the study’s K. quasipneumoniae isolates. Amongst K. pneumoniae, there were 50 ybt+ isolates; 8 isolates had rmpA, and of these, 3 belonged to ST383. K. pneumoniae serotype K2, the capsular serotype associated with invasive liver abscess syndrome, was detected in 5 isolates. Genetic relationship of carbapenem-resistant Klebsiella pneumoniae and K. quasipneumoniae isolates in Qatar inferred from core genome SNPs. The tree is overlaid with predicted antimicrobial resistance genes and virulence factors for each isolate.

Conclusion

The predominant carbapenemases among clinical Klebsiella species isolates in Qatar are NDM and OXA-48 like enzymes, disseminated through various plasmids. The detection of carbapenemase-producing isolate bearing rmpA and serotype K2 reflect the presence of both multidrug resistance and hypervirulence in K. pneumoniae", "token_count": 301, "char_count": 1009, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8417, "entities": { "genes": [ "ST196", "ST383" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:51.336891", "source": { "split": "train_shard_00001", "doc_id": 3716 }, "chunk_id": "train_shard_00001_3716_1", "global_id": 10925 }, { "text": "

Disclosures

Yohei Doi, MD, PhD, AstraZeneca (Speaker’s Bureau)bioMerieux (Consultant)FujiFilm (Advisor or Review Panel member, Speaker’s Bureau)Gilead (Consultant)GSK (Consultant)Meiji (Consultant)MSD (Consultant)Shionogi (Consultant) Yohei Doi, MD, PhD, Astellas (Individual(s) Involved: Self): Grant/Research Support; AstraZeneca (Individual(s) Involved: Self): Speakers’ bureau; bioMerieux (Individual(s) Involved: Self): Consultant, Speakers’ bureau; Chugai (Individual(s) Involved: Self): Consultant; Entasis (Individual(s) Involved: Self): Consultant; FujiFilm (Individual(s) Involved: Self): Advisor or Review Panel member; Gilead (Individual(s) Involved: Self): Consultant; GSK (Individual(s) Involved: Self): Consultant; Kanto Chemical (Individual(s) Involved: Self): Grant/Research Support; MSD (Individual(s) Involved: Self): Speaking Fee; Pfizer (Individual(s) Involved: Self): Grant/Research Support; Shionogi (Individual(s) Involved: Self): Grant/Research Support, Speakers’ bureau; Teijin Healthcare (Individual(s) Involved: Self): Speakers’ bureau; VenatoRx (Individual(s) Involved: Self): Consultant\n\n1247. Molecular Epidemiology of Multi-drug Resistant Klebsiella pneumoniae and K. quasipneumoniae in Qatar", "token_count": 451, "char_count": 1233, "word_count": 125, "semantic_coherence": 1, "information_density": 0.512, "quality_score": 0.756, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:51.969410", "source": { "split": "train_shard_00001", "doc_id": 3716 }, "chunk_id": "train_shard_00001_3716_2", "global_id": 10926 }, { "text": "

Aims

The aim of this work was to refine the taxonomy and the functional characterization of publicly available Lactiplantibacillus plantarum complete genomes through a pan-genome analysis. Particular attention was paid in depicting the probiotic potential of each strain.

Methods and results

Complete genome sequence of 127 L. plantarum strains, without detected anomalies, was downloaded from NCBI. Roary analysis of L. plantarum pan-genome identified 1436 core, 414 soft core, 1858 shell and 13,203 cloud genes, highlighting the 'open' nature of L. plantarum pan-genome. Identification and characterization of plasmid content, mobile genetic elements, adaptative immune system and probiotic marker genes (PMGs) revealed unique features across all the L. plantarum strains included in the present study. Considering our updated list of PMGs, we determined that approximatively 70% of the PMGs belongs to the core/soft-core genome.

Conclusions

The comparative genomic analysis conducted in this study provide new insights into the genomic content and variability of L. plantarum.

Significance and impact of the study

This study provides a comprehensive pan-genome analysis of L. plantarum, including the largest number (N = 127) of complete L. plantarum genomes retrieved from publicly available repositories. Our effort aimed to determine a solid reference panel for the future characterization of newly sequenced L. plantarum strains useful as probiotic supplements.\n\nComprehensive pan-genome analysis of Lactiplantibacillus plantarum complete genomes.", "token_count": 423, "char_count": 1583, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:52.596943", "source": { "split": "train_shard_00001", "doc_id": 3717 }, "chunk_id": "train_shard_00001_3717_0", "global_id": 10927 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) presenting spa type t899 is commonly associated with sequence type 9 (ST9) but is also increasingly linked to ST398. This study provides genomic insight into the diversity of t899 isolates using core genome multilocus sequence typing (cgMLST), single nucleotide polymorphism (SNP)-based phylogeny, and the description of selected antimicrobial resistance and virulence markers. The SNP-based phylogenic tree showed that isolates sharing the same spa type (t899) but different STs highly diverged in their core and accessory genomes, revealing discriminant antimicrobial resistance (AMR) and virulence markers. Our results highlighted the idea that in a surveillance context where only spa typing is used, an additional multiplex PCR for the detection of the tet(M), sak, and seg genes would be valuable in helping distinguish ST9 from ST398 isolates on a routine basis.IMPORTANCE This study showed the genetic diversity and population structure of S. aureus presenting the same spa type, t899, but belonging to different STs. Our findings revealed that these isolates vary deeply in their core and accessory genomes, contrary to what is regularly inferred from studies using spa typing only. Given that identical spa types can be associated with different STs and that spa typing only is not appropriate for S. aureus isolates that have undergone major recombination events which include the passage of the spa gene (such as in t899-positive MRSA), the combination of both MLST and spa typing methods is recommended. However, spa typing alone is still largely used in surveillance studies and basic characterization", "token_count": 504, "char_count": 1785, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [ "ST398", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:53.296243", "source": { "split": "train_shard_00001", "doc_id": 3718 }, "chunk_id": "train_shard_00001_3718_0", "global_id": 10928 }, { "text": "Our data suggest that additional markers, such as tet(M), sak, and seg genes, could be implemented in an easy and inexpensive manner in order to identify S. aureus lineages with a higher accuracy.\n\nGenomic Insights into Methicillin-Resistant Staphylococcus aureus spa Type t899 Isolates Belonging to Different Sequence Types.", "token_count": 120, "char_count": 360, "word_count": 48, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:53.693249", "source": { "split": "train_shard_00001", "doc_id": 3718 }, "chunk_id": "train_shard_00001_3718_1", "global_id": 10929 }, { "text": "Endosymbiotic theory in eukaryotic-cell evolution rests upon a foundation of three cornerstone partners--the plastid (a cyanobacterium), the mitochondrion (a proteobacterium), and its host (an archaeon)--and carries a corollary that, over time, the majority of genes once present in the organelle genomes were relinquished to the chromosomes of the host (endosymbiotic gene transfer). However, notwithstanding eukaryote-specific gene inventions, single-gene phylogenies have never traced eukaryotic genes to three single prokaryotic sources, an issue that hinges crucially upon factors influencing phylogenetic inference. In the age of genomes, single-gene trees, once used to test the predictions of endosymbiotic theory, now spawn new theories that stand to eventually replace endosymbiotic theory with descriptive, gene tree-based variants featuring supernumerary symbionts: prokaryotic partners distinct from the cornerstone trio and whose existence is inferred solely from single-gene trees. We reason that the endosymbiotic ancestors of mitochondria and chloroplasts brought into the eukaryotic--and plant and algal--lineage a genome-sized sample of genes from the proteobacterial and cyanobacterial pangenomes of their respective day and that, even if molecular phylogeny were artifact-free, sampling prokaryotic pangenomes through endosymbiotic gene transfer would lead to inherited chimerism. Recombination in prokaryotes (transduction, conjugation, transformation) differs from recombination in eukaryotes (sex). Prokaryotic recombination leads to pangenomes, and eukaryotic recombination leads to vertical inheritance. Viewed from the perspective of endosymbiotic theory, the critical transition at the eukaryote origin that allowed escape from Muller's ratchet--the origin of eukaryotic recombination, or sex--might have required surprisingly little evolutionary innovation.\n\nEndosymbiotic gene transfer from prokaryotic pangenomes: Inherited chimerism in eukaryotes.", "token_count": 505, "char_count": 1979, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6411, "quality_score": 0.8206, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:54.376590", "source": { "split": "train_shard_00001", "doc_id": 3719 }, "chunk_id": "train_shard_00001_3719_0", "global_id": 10930 }, { "text": "Ruminococcus gnavus is a prevalent gut microbe reported to occur in higher abundance among individuals with inflammatory bowel disease (IBD). This study reports the isolation and characterization of six bacteriophages (phages) isolated from human fecal material and environmental samples that infect this species. Isolated phages have a siphovirus morphology, with genomes ranging between 36.5 and 37.8 kbp. Genome analysis indicates that the phages have a temperate lifestyle, which was confirmed by their ability to form lysogens on their host bacterial species. In contrast to the finding that phages lyse their host in liquid medium, results from a mouse trial indicate these phages can co-exist with the host bacterium in the gut without causing a significant reduction of R. gnavus. The bacterial counts in the feces of phage-treated mice did not significantly differ in the presence of phage. Furthermore, analysis of publicly available gut virome sequence data indicates a high abundance of these phages among individuals suffering from IBD. This work provides the first insight into how phages interact with R. gnavus in the human gut microbiome.\n\nTemperate bacteriophages infecting the mucin-degrading bacterium Ruminococcus gnavus from the human gut.", "token_count": 317, "char_count": 1289, "word_count": 188, "semantic_coherence": 1, "information_density": 0.617, "quality_score": 0.8085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:54.975745", "source": { "split": "train_shard_00001", "doc_id": 3720 }, "chunk_id": "train_shard_00001_3720_0", "global_id": 10931 }, { "text": "Campylobacter spp. are a leading and increasing cause of gastrointestinal infections worldwide. Source attribution, which apportions human infection cases to different animal species and food reservoirs, has been instrumental in control- and evidence-based intervention efforts. The rapid increase in whole-genome sequencing data provides an opportunity for higher-resolution source attribution models. Important challenges, including the high dimension and complex structure of WGS data, have inspired concerted research efforts to develop new models. We propose network analysis models as an accurate, high-resolution source attribution approach for the sources of human campylobacteriosis. A weighted network analysis approach was used in this study for source attribution comparing different WGS data inputs. The compared model inputs consisted of cgMLST and wgMLST distance matrices from 717 human and 717 animal isolates from cattle, chickens, dogs, ducks, pigs and turkeys. SNP distance matrices from 720 human and 720 animal isolates were also used. The data were collected from 2015 to 2017 in Denmark, with the animal sources consisting of domestic and imports from 7 European countries. Clusters consisted of network nodes representing respective genomes and links representing distances between genomes. Based on the results, animal sources were the main driving factor for cluster formation, followed by type of species and sampling year. The coherence source clustering (CSC) values based on animal sources were 78%, 81% and 78% for cgMLST, wgMLST and SNP, respectively. The CSC values based on Campylobacter species were 78%, 79% and 69% for cgMLST, wgMLST and SNP, respectively. Including human isolates in the network resulted in 88%, 77% and 88% of the total human isolates being clustered with the different animal sources for cgMLST, wgMLST and SNP, respectively. Between 12% and 23% of human isolates were not attributed to any animal source", "token_count": 480, "char_count": 1976, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:55.622580", "source": { "split": "train_shard_00001", "doc_id": 3721 }, "chunk_id": "train_shard_00001_3721_0", "global_id": 10932 }, { "text": "Most of the human genomes were attributed to chickens from Denmark, with an average attribution percentage of 52.8%, 52.2% and 51.2% for cgMLST, wgMLST and SNP distance matrices respectively, while ducks from Denmark showed the least attribution of 0% for all three distance matrices. The best-performing model was the one using wgMLST distance matrix as input data, which had a CSC value of 81%. Results from our study show that the weighted network-based approach for source attribution is reliable and can be used as an alternative method for source attribution considering the high performance of the model. The model is also robust across the different Campylobacter species, animal sources and WGS data types used as input.\n\nSource Attribution of Human Campylobacteriosis Using Whole-Genome Sequencing Data and Network Analysis.", "token_count": 205, "char_count": 841, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:56.085271", "source": { "split": "train_shard_00001", "doc_id": 3721 }, "chunk_id": "train_shard_00001_3721_1", "global_id": 10933 }, { "text": "

Background

Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, can cause significant economic losses and is present worldwide. With the advance of whole genome sequencing technologies, new methods are available for the researchers; one emerging methodology is the core genome Multi-Locus Sequence Typing (cgMLST). The core genome contains a high percentage of the coding DNA sequence (CDS) set of the studied strains. The cgMLST schemas are powerful genotyping tools allowing for the investigation of potential epidemics, and precise and reliable classification of the strains. Although whole genome sequences of M. anserisalpingitidis strains are available, to date, no cgMLST schema has been published for this species.

Results

In this study, Illumina short reads of 81 M. anserisalpingitidis strains were used, including samples from Hungary, Poland, Sweden, and China. Draft genomes were assembled with the SPAdes software and analysed with the online available chewBBACA program. User made modifications in the program enabled analysis of mycoplasmas and provided similar results as the conventional SeqSphere+ software. The threshold of the presence of CDS in the strains was set to 93% due to the quality of the draft genomes, resulting in the most accurate and robust schema. Three hundred thirty-one CDSs constituted our cgMLST schema (representing 42,77% of the whole CDS set of M. anserisalpingitidis ATCC BAA-2147), and a Neighbor joining tree was created using the allelic profiles. The correlation was observed between the strains' cgMLST profile and geographical origin; however, strains from the same integration but different locations also showed close relationship. Strains isolated from different tissue samples of the same animal revealed highly similar cgMLST profiles.

Conclusions

The Neighbor joining tree from the cgMLST schema closely resembled the real-life spatial and temporal relationships of the strains. The incongruences between background data and the cgMLST profile in the strains from the same integration can be because of the higher probability of contacts between the flocks", "token_count": 521, "char_count": 2165, "word_count": 308, "semantic_coherence": 1, "information_density": 0.5877, "quality_score": 0.7938, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:41:56.740585", "source": { "split": "train_shard_00001", "doc_id": 3722 }, "chunk_id": "train_shard_00001_3722_0", "global_id": 10934 }, { "text": "This schema can help with the epidemiological investigation and can be used as a basis for further studies.\n\nThe core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis.", "token_count": 47, "char_count": 187, "word_count": 27, "semantic_coherence": 1, "information_density": 0.9259, "quality_score": 0.963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:57.102858", "source": { "split": "train_shard_00001", "doc_id": 3722 }, "chunk_id": "train_shard_00001_3722_1", "global_id": 10935 }, { "text": "Chlamydia pecorum is a common gastrointestinal inhabitant of livestock but infections can manifest in a broad array of clinical presentations and in a range of host species. While C. pecorum is a known cause of ovine abortion, clinical cases have only recently been described in detail. Here, the prevalence and sequence types (STs) of C. pecorum in ewes from a property experiencing high levels of perinatal mortality (PNM) in New South Wales (NSW), Australia, were investigated using serological and molecular methods. Ewes that were PNM+ were statistically more likely to test seropositive compared to PNM- ewes and displayed higher antibody titres; however, an increase in chlamydial shedding from either the rectum, vagina or conjunctiva of PNM+ ewes was not observed. Multilocus sequence typing (MLST) indicated that C. pecorum ST23 was the major ST shed by ewes in the flock, was the only ST identified from the vaginal site, and was the same ST detected within aborted foetal tissues. Whole genome sequencing of C. pecorum isolated from one abortion case revealed that the C. pecorum plasmid (pCpec) contained a unique deletion in coding sequence 1 (CDS1) that was also present in C. pecorum ST23 shed from the ewes. A further unique deletion was noted in a polymorphic membrane protein gene (pmpG) of the C. pecorum chromosome, which warrants further investigation given the role of PmpG in host cell adherence and tissue tropism.This study describes novel infection parameters in a sheep flock experiencing C. pecorum-associated perinatal mortality, provides the first genomic data from an abortigenic C. pecorum strain, and raises questions about possible links between unique genetic features of this strain and C. pecorum abortion.", "token_count": 509, "char_count": 1821, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8114, "entities": { "genes": [ "ST23", "CDS1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:57.731828", "source": { "split": "train_shard_00001", "doc_id": 3723 }, "chunk_id": "train_shard_00001_3723_0", "global_id": 10936 }, { "text": "Chlamydia pecorum Ovine Abortion: Associations between Maternal Infection and Perinatal Mortality.", "token_count": 34, "char_count": 105, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:58.095896", "source": { "split": "train_shard_00001", "doc_id": 3723 }, "chunk_id": "train_shard_00001_3723_1", "global_id": 10937 }, { "text": "The presence of adenylate cyclase activity was first demonstrated in membrane fractions from the budding yeast Kluyveromyces marxianus. The enzyme showed a Mn(2+)- and Mg(2+)-dependent activity, with optimal pH at around 6 as observed in other yeast species. As in Saccharomyces cerevisiae, where adenylate cyclase is regulated by RAS1 and RAS2, we detected a guanyl nucleotide-dependent activity. Interestingly Y13-259 monoclonal antibody, raised against mammalian p21Ha-ras, inhibited Mg2+ plus GTP-gamma-S-dependent cAMP production, suggesting that the GTP binding proteins involved in adenylate cyclase regulation could be Ras proteins. The same antibody recognized on Western blot and immunoprecipitated a 40 kDa polypeptide from K. marxianus crude membranes. This polypeptide was not detected by an anti-RAS2 polyclonal antibody raised against S. cerevisiae RAS2 protein, suggesting that Ras proteins from the two species could be structurally different.\n\nIn the budding yeast Kluyveromyces marxianus, adenylate cyclase is regulated by Ras protein(s) in vitro.", "token_count": 312, "char_count": 1066, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6939, "quality_score": 0.8469, "entities": { "genes": [ "RAS1", "RAS2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:58.657445", "source": { "split": "train_shard_00001", "doc_id": 3724 }, "chunk_id": "train_shard_00001_3724_0", "global_id": 10938 }, { "text": "Fungal genomes encode highly organized gene clusters that underlie the production of specialized (or secondary) metabolites. Gene clusters encode key functions to exploit plant hosts or environmental niches. Promiscuous exchange among species and frequent reconfigurations make gene clusters some of the most dynamic elements of fungal genomes. Despite evidence for high diversity in gene cluster content among closely related strains, the microevolutionary processes driving gene cluster gain, loss and neofunctionalization are largely unknown. We analyzed the Fusarium graminearum species complex (FGSC) composed of plant pathogens producing potent mycotoxins and causing Fusarium head blight on cereals. We de novo assembled genomes of previously uncharacterized FGSC members (two strains of F. austroamericanum , F. cortaderiae and F. meridionale ). Our analyses of eight species of the FGSC in addition to 15 other Fusarium species identified a pangenome of 54 gene clusters within FGSC. We found that multiple independent losses were a key factor generating extant cluster diversity within the FGSC and the Fusarium genus. We identified a modular gene cluster conserved among distantly related fungi, which was likely reconfigured to encode different functions. We also found strong evidence that a rare cluster in FGSC was gained through an ancient horizontal transfer between bacteria and fungi. Chromosomal rearrangements underlying cluster loss were often complex and were likely facilitated by an enrichment in specific transposable elements. Our findings identify important transitory stages in the birth and death process of specialized metabolism gene clusters among very closely related species.\n\nComplex evolutionary origins of specialized metabolite gene cluster diversity among the plant pathogenic fungi of theFusarium graminearumspecies complex", "token_count": 405, "char_count": 1871, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:59.274677", "source": { "split": "train_shard_00001", "doc_id": 3725 }, "chunk_id": "train_shard_00001_3725_0", "global_id": 10939 }, { "text": "Production of high-content galacto-oligosaccharide by enzyme catalysis and fermentation with Kluyveromyces marxianus", "token_count": 34, "char_count": 116, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:41:59.633446", "source": { "split": "train_shard_00001", "doc_id": 3726 }, "chunk_id": "train_shard_00001_3726_0", "global_id": 10940 }, { "text": "

Background

Previous studies have demonstrated the beneficial effects of Ligilactobacillus salivarius A3iob on honeybee (Apis mellifera) colonies' health and honey production. The present work aimed to assess the genomic characteristics of the A3iob strain to understand its ability to improve bees' health.

Methods

The comparative genomic analysis was performed with the A3iob genome and the genomes of probiotic L. salivarius strains of human, porcine, and chicken origin, as well as bacteria isolated from the bees' gut. The analysis included the examination of metabolic genes and functional genes related to adhesion, the production of bioactive compounds, the modulation of the host's immune system, and antimicrobial substances. Genes associated with antimicrobial resistance and virulence were also analyzed.

Results

In silico studies revealed that L. salivarius A3iob possesses genes for glycosyltransferases (GTs) from the families GT2 and GT4, like Bombella apis and Bombella intestinalis, and glycosylhydrolases (GH) from the families GH1, GH2, GH13, GH36, GH65, and GH177, similar to Apilactobacillus kunkeei, Enterococcus durans, and bifidobacteria isolated from the bee intestine. The A3iob strain also has a unique genetic profile with a high number of secretion system genes and adhesion genes, including the ones coding for the SecA2/Y2 system, the mucus-binding proteins MucBP1, MucBP2, and MucBP3, and a pilus cluster (pilA, SpaA, SpaB, and sorteaseA) that has only been described in five strains of the L", "token_count": 497, "char_count": 1605, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [ "GT2", "GH2", "GH65", "GH177", "GT4", "GH36", "GH1", "GH13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:00.289162", "source": { "split": "train_shard_00001", "doc_id": 3727 }, "chunk_id": "train_shard_00001_3727_0", "global_id": 10941 }, { "text": "salivarius species and in the intestinal bee-derived strain E. durans EDD2, which could be involved in the successful colonization of the A3iob strain in the bee gastrointestinal tract. Additionally, L. salivarius A3iob showed the presence of exopolysaccharide biosynthesis clusters described in the probiotic L. salivarius UCC118. Genes related to oxidative stress response (thioredoxin and NrdH-redoxin systems) and the bacteriocin genes abp118A and abp118B were found in the A3iob genome. L. salivarius A3iob does not harbor virulence or antibiotic resistance genes.

Conclusions

The genomic characterization of L. salivarius A3iob performed in this work provides some clues about the genetic mechanisms underlying its probiotic properties, paving the way for future research aimed at improving bees' health and productivity in the face of environmental challenges.\n\nGenomic Characterization of the Honeybee-Probiotic Strain <i>Ligilactobacillus salivarius</i> A3iob.", "token_count": 320, "char_count": 1027, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [ "UCC118", "EDD2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:00.857263", "source": { "split": "train_shard_00001", "doc_id": 3727 }, "chunk_id": "train_shard_00001_3727_1", "global_id": 10942 }, { "text": "Pseudomonas aeruginosa strains exhibit significant variability in pathogenicity and ecological flexibility. Such interstrain differences reflect the dynamic nature of the P. aeruginosa genome, which is composed of a relatively invariable \"core genome\" and a highly variable \"accessory genome.\" Here we review the major classes of genetic elements comprising the P. aeruginosa accessory genome and highlight emerging themes in the acquisition and functional importance of these elements. Although the precise phenotypes endowed by the majority of the P. aeruginosa accessory genome have yet to be determined, rapid progress is being made, and a clearer understanding of the role of the P. aeruginosa accessory genome in ecology and infection is emerging.\n\nThe accessory genome of Pseudomonas aeruginosa.", "token_count": 178, "char_count": 802, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6348, "quality_score": 0.8174, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:01.309422", "source": { "split": "train_shard_00001", "doc_id": 3728 }, "chunk_id": "train_shard_00001_3728_0", "global_id": 10943 }, { "text": "Rapid identification of clinically important yeasts can facilitate the initiation of anti-fungal therapy, since susceptibility is largely species-dependent. We evaluated melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA) as an identification tool for distinguishing between 16 Candida spp., i.e. Candida albicans, Candida bracarensis, Candida dubliniensis, Candida famata, Candida glabrata, Candida guilliermondii, Candida inconspicua, Candida kefyr, Candida krusei, Candida lipolytica, Candida lusitaniae, Candida nivariensis, Candida norvegensis, Candida parapsilosis, Candida tropicalis and Candida sojae, and Saccharomyces cerevisiae and one species pair, i.e. Candida metapsilosis/Candida orthopsilosis. Starting from a cultured isolate, ITS2-MCA led to differentiation of these species within 6 h. According to our findings, ITS2-MCA offers a simple, rapid and cost-effective method for identification of cultured isolates of the clinically most relevant and prevalent Candida species. Further studies will be necessary to evaluate how it performs on mixed samples and clinical samples.\n\nRapid and accurate identification of isolates of Candida species by melting peak and melting curve analysis of the internally transcribed spacer region 2 fragment (ITS2-MCA).", "token_count": 348, "char_count": 1323, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8081, "entities": { "genes": [ "ITS2" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:01.878209", "source": { "split": "train_shard_00001", "doc_id": 3729 }, "chunk_id": "train_shard_00001_3729_0", "global_id": 10944 }, { "text": "Cheese whey, the main dairy by-product, is increasingly recognized as a source of many bioactive valuable compounds. Nevertheless, the most abundant component in whey is lactose (ca. 5% w/v), which represents a significant environmental problem. Due to the large lactose surplus generated, its conversion to bio-ethanol has long been considered as a possible solution for whey bioremediation. In this review, fermentation of lactose to ethanol is discussed, focusing on wild lactose-fermenting yeasts, particularly Kluyveromyces marxianus, and recombinant Saccharomyces cerevisiae strains. The early efforts in the screening and characterization of the fermentation properties of wild lactose-consuming yeasts are reviewed. Furthermore, emphasis is given on the latter advances in engineering S. cerevisiae strains for efficient whey-to-ethanol bioprocesses. Examples of industrial implementation are briefly discussed, illustrating the viability of whey-to-ethanol systems. Current developments on strain engineering together with the growing market for biofuels will likely boost the industrial interest in such processes.\n\nFermentation of lactose to bio-ethanol by yeasts as part of integrated solutions for the valorisation of cheese whey.", "token_count": 295, "char_count": 1243, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6766, "quality_score": 0.8383, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:02.440431", "source": { "split": "train_shard_00001", "doc_id": 3730 }, "chunk_id": "train_shard_00001_3730_0", "global_id": 10945 }, { "text": "The thermophilic bacterium Thermosulfidibacter takaii is affiliated to the deep-branching bacterial lineage in the phylum Aquificota. However, the recent taxonomic study of the phylum Aquificota revealed that T. takaii has no specific association with the phylum. The fact that T. takaii is considered an important model organism for studying the evolution and kinetics of ancestral carbon metabolism pathways, its proper classification is therefore of significant interest. In this work, phylogenomics and comparative genomic analyses were employed to ascertain the taxonomic placement of T. takaii. Results from the phylogenetic analyses based on 16S rRNA gene and core genome sequences confirmed the exclusion of T. takaii from the phylum Aquificota and further revealed a phylum-level lineage for T. takaii. The analysis of conserved signature indels (CSIs) specific for the phylum Aquificota also supported the exclusion of T. takaii from the phylum. Pan-genome analysis of T. takaii along with the members of the closely related clade from the phylum Thermodesulfobacteriota revealed that T. takaii was indeed distinct, supporting its phylum-level placement. Furthermore, the presence of CSIs specific to T. takaii, and the results from the average nucleotide identity and average amino acid identity analyses, together with the unique characteristic of T. takaii also provided evidence supporting its assignment to a novel phylum. Based on these results, T. takaii is proposed to be transferred to a novel family, Thermosulfidibacteraceae fam. nov., of a novel order, Thermosulfidibacterales ord", "token_count": 525, "char_count": 1742, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5408, "quality_score": 0.7704, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:03.095213", "source": { "split": "train_shard_00001", "doc_id": 3731 }, "chunk_id": "train_shard_00001_3731_0", "global_id": 10946 }, { "text": "nov., and a novel class, Thermosulfidibacteria classis nov., within a novel phylum Thermosulfidibacterota phyl. nov.

Supplementary information

The online version contains supplementary material available at 10.1007/s12088-024-01214-9.\n\nGenomics of the Thermophilic Bacterium <i>Thermosulfidibacter takaii</i> Reveals Novel Lineage of Deep-Branching Bacterial Phylum.", "token_count": 156, "char_count": 399, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8684, "quality_score": 0.9342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:03.534700", "source": { "split": "train_shard_00001", "doc_id": 3731 }, "chunk_id": "train_shard_00001_3731_1", "global_id": 10947 }, { "text": "A tetracycline repressible promoter system designed for Saccharomyces cerevisiae was evaluated for use in Kluyveromyces marxianus. A plasmid was constructed containing the Escherichia coli beta-glucuronidase (gus) gene cloned downstream of the yeast tet-off promoter, the tetR-VP16 activator protein gene, and the URA3 gene for selection. The tet-off promoter-gus construct was integrated into the chromosomal DNA and tested under varying growth conditions in complex medium. The repressors tetracycline and doxycycline were both found to be effective for inhibiting gene expression. Doxycycline levels of 0.5 microg/mL or greater were sufficient to nearly completely suppress Gus synthesis. For most transformants, the induction ratio was approximately 2,000-fold. The tet-off promoter was effective at 30, 37, and 42 degrees C, although the overall Gus activity was highest at 37 degrees C. During exponential growth, little product was formed; expression increased dramatically in late exponential and early stationary phase. The promoter thus shows promise for protein synthesis following cell growth. No inducer is required and the repressor is only needed to prevent expression during the seed culture.\n\nEvaluation of the tetracycline promoter system for regulated gene expression in Kluyveromyces marxianus.", "token_count": 334, "char_count": 1314, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6576, "quality_score": 0.8288, "entities": { "genes": [ "VP16", "URA3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:04.097059", "source": { "split": "train_shard_00001", "doc_id": 3732 }, "chunk_id": "train_shard_00001_3732_0", "global_id": 10948 }, { "text": "Vancomycin-resistant enterococci (VRE) are one of the leading causes of nosocomial infections in health care facilities around the globe. In particular, infections caused by vancomycin-resistant Enterococcus faecium are becoming increasingly common. Comparative and functional genomic studies of E. faecium isolates have so far been limited owing to the lack of a fully assembled E. faecium genome sequence. Here we address this issue and report the complete 3.0-Mb genome sequence of the multilocus sequence type 17 vancomycin-resistant Enterococcus faecium strain Aus0004, isolated from the bloodstream of a patient in Melbourne, Australia, in 1998. The genome comprises a 2.9-Mb circular chromosome and three circular plasmids. The chromosome harbors putative E. faecium virulence factors such as enterococcal surface protein, hemolysin, and collagen-binding adhesin. Aus0004 has a very large accessory genome (38%) that includes three prophage and two genomic islands absent among 22 other E. faecium genomes. One of the prophage was present as inverted 50-kb repeats that appear to have facilitated a 683-kb chromosomal inversion across the replication terminus, resulting in a striking replichore imbalance. Other distinctive features include 76 insertion sequence elements and a single chromosomal copy of Tn1549 containing the vanB vancomycin resistance element. A complete E. faecium genome will be a useful resource to assist our understanding of this emerging nosocomial pathogen.\n\nComparative analysis of the first complete Enterococcus faecium genome.", "token_count": 413, "char_count": 1564, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:04.716368", "source": { "split": "train_shard_00001", "doc_id": 3733 }, "chunk_id": "train_shard_00001_3733_0", "global_id": 10949 }, { "text": "Pseudomonas aeruginosa is an environmental bacterium and a nosocomial pathogen with clone C one of the most prevalent clonal groups. The P. aeruginosa clone C specific genomic island PACGI-1 harbors a xenolog of ftsH encoding a functionally diverse membrane-spanning ATP-dependent metalloprotease on the core genome. In the aquatic isolate P. aeruginosa SG17M, the core genome copy ftsH1 significantly affects growth and dominantly mediates a broad range of phenotypes, such as secretion of secondary metabolites, swimming and twitching motility and resistance to aminoglycosides, while the PACGI-1 xenolog ftsH2 backs up the phenotypes in the ftsH1 mutant background. The two proteins, with conserved motifs for disaggregase and protease activity present in FtsH1 and FtsH2, have the ability to form homo- and hetero-oligomers with ftsH2 distinctively expressed in the late stationary phase of growth. However, mainly FtsH1 degrades a major substrate, the heat shock transcription factor RpoH. Pull-down experiments with substrate trap-variants inactive in proteolytic activity indicate both FtsH1 and FtsH2 to interact with the inhibitory protein HflC, while the phenazine biosynthesis protein PhzC was identified as a substrate of FtsH1. In summary, as an exception in P. aeruginosa, clone C harbors two copies of the ftsH metallo-protease, which cumulatively are required for the expression of a diversity of phenotypes.\n\nTwo FtsH Proteases Contribute to Fitness and Adaptation of Pseudomonas aeruginosa Clone C Strains.", "token_count": 481, "char_count": 1601, "word_count": 221, "semantic_coherence": 1, "information_density": 0.629, "quality_score": 0.8145, "entities": { "genes": [ "SG17M" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:05.429855", "source": { "split": "train_shard_00001", "doc_id": 3734 }, "chunk_id": "train_shard_00001_3734_0", "global_id": 10950 }, { "text": "Successful management and utilization of increasingly large genomic datasets is essential for breeding programs to increase genetic gain and accelerate cultivar development. To help with data management and storage, we developed a sorghum Practical Haplotype Graph (PHG) pangenome database that stores all identified haplotypes and variant information for a given set of individuals. We developed two PHGs in sorghum, one with 24 individuals and another with 398 individuals, that reflect the diversity across genic regions of the sorghum genome. 24 founders of the Chibas sorghum breeding program were sequenced at low coverage (0.01x) and processed through the PHG to identify genome-wide variants. The PHG called SNPs with only 5.9% error at 0.01x coverage - only 3% lower than its accuracy when calling SNPs from 8x coverage sequence. Additionally, 207 progeny from the Chibas genomic selection (GS) training population were sequenced and processed through the PHG. Missing genotypes in the progeny were imputed from the parental haplotypes available in the PHG and used for genomic prediction. Mean prediction accuracies with PHG SNP calls range from 0.57-0.73 for different traits, and are similar to prediction accuracies obtained with genotyping-by-sequencing (GBS) or markers from sequencing targeted amplicons (rhAmpSeq). This study provides a proof of concept for using a sorghum PHG to call and impute SNPs from low-coverage sequence data and also shows that the PHG can unify genotype calls from different sequencing platforms. By reducing the amount of input sequence needed, the PHG has the potential to decrease the cost of genotyping for genomic selection, making GS more feasible and facilitating larger breeding populations that can capture maximum recombination. Our results demonstrate that the PHG is a useful research and breeding tool that can maintain variant information from a diverse group of taxa, store sequence data in a condensed but readily accessible format, unify genotypes from different genotyping methods, and provide a cost-effective option for genomic selection for any species.", "token_count": 500, "char_count": 2118, "word_count": 317, "semantic_coherence": 1, "information_density": 0.5931, "quality_score": 0.7965, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:06.101620", "source": { "split": "train_shard_00001", "doc_id": 3735 }, "chunk_id": "train_shard_00001_3735_0", "global_id": 10951 }, { "text": "A sorghum Practical Haplotype Graph facilitates genome-wide imputation and cost-effective genomic prediction", "token_count": 28, "char_count": 108, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:06.481672", "source": { "split": "train_shard_00001", "doc_id": 3735 }, "chunk_id": "train_shard_00001_3735_1", "global_id": 10952 }, { "text": "

Background:

The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria order and are soil-borne pathogens causing the vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a “species complex”,” gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. T3Es are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology).

Methods:

. Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors.

Results:

. We curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.\n\nPangenomic type III effector database of the plant pathogenic Ralstonia spp.", "token_count": 432, "char_count": 1707, "word_count": 243, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:07.142415", "source": { "split": "train_shard_00001", "doc_id": 3736 }, "chunk_id": "train_shard_00001_3736_0", "global_id": 10953 }, { "text": "A lactose amount in cheese whey is 1 to 5% (w/v), which is low, and when cheese whey is fermented as such, an ethanol concentration results in only 0.5 to 2.5% (w/v), and production efficiency is low. It is possible to increase a sugar concentration in a medium using whey powder, however, fossil energy is consumed in a production step of the whey powder, therefore, the cost tends to be high. By utilizing a yeast strain of Kluyveromyces marxianus which is resistant to 2-deoxyglucose, ethanol is promptly and efficiently produced from a raw material containing lactose and a sugar other than lactose as a sugar source.\n\nMETHOD FOR PRODUCING ETHANOL", "token_count": 180, "char_count": 651, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:07.588690", "source": { "split": "train_shard_00001", "doc_id": 3737 }, "chunk_id": "train_shard_00001_3737_0", "global_id": 10954 }, { "text": "Edwardsiella ictaluri and Edwardsiella piscicida are important fish pathogens affecting cultured and wild fish worldwide. To investigate the genome-level differences and similarities between catfish-adapted strains in these two species, the complete E. ictaluri 93-146 and E. piscicida C07-087 genomes were evaluated by applying comparative genomics analysis. All available complete (10) and non-complete (19) genomes from five Edwardsiella species were also included in a systematic analysis. Average nucleotide identity and core-genome phylogenetic tree analyses indicated that the five Edwardsiella species were separated from each other. Pan-/core-genome analyses for the 29 strains from the five species showed that genus Edwardsiella members have 9474 genes in their pan genome, while the core genome consists of 1421 genes. Orthology cluster analysis showed that E. ictaluri and E. piscicida genomes have the greatest number of shared clusters. However, E. ictaluri and E. piscicida also have unique features; for example, the E. ictaluri genome encodes urease enzymes and cytochrome o ubiquinol oxidase subunits, whereas E. piscicida genomes encode tetrathionate reductase operons, capsular polysaccharide synthesis enzymes and vibrioferrin-related genes. Additionally, we report for what is believed to be the first time that E. ictaluri 93-146 and three other E. ictaluri genomes encode a type IV secretion system (T4SS), whereas none of the E. piscicida genomes encode this system. Additionally, the E", "token_count": 525, "char_count": 1640, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:08.216905", "source": { "split": "train_shard_00001", "doc_id": 3738 }, "chunk_id": "train_shard_00001_3738_0", "global_id": 10955 }, { "text": "piscicida C07-087 genome encodes two different type VI secretion systems. E. ictaluri genomes tend to encode more insertion elements, phage regions and genomic islands than E. piscicida. We speculate that the T4SS could contribute to the increased number of mobilome elements in E. ictaluri compared to E. piscicida. Two of the E. piscicida genomes encode full CRISPR-Cas regions, whereas none of the E. ictaluri genomes encode Cas proteins. Overall, comparison of the E. ictaluri and E. piscicida genomes reveals unique features and provides new insights on pathogenicity that may reflect the host adaptation of the two species.\n\nComparative genomics of the fish pathogens Edwardsiella ictaluri 93-146 and Edwardsiella piscicida C07-087.", "token_count": 280, "char_count": 817, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:08.773935", "source": { "split": "train_shard_00001", "doc_id": 3738 }, "chunk_id": "train_shard_00001_3738_1", "global_id": 10956 }, { "text": "Bread wheat is an allohexaploid species originating from two successive and recent rounds of hybridization between three diploid species that were very similar in terms of chromosome number, genome size, TE content, gene content and synteny. As a result, it has long been considered that most of the genes were in three pairs of homoeologous copies. However, these so-called triads represent only one half of wheat genes, while the remaining half belong to homoeologous groups with various number of copies across subgenomes. In this study, we examined and compared the distribution, conservation, function, expression and epigenetic profiles of triads with homoeologous groups having undergone a deletion (dyads) or a duplication (tetrads) in one subgenome. We show that dyads and tetrads are mostly located in distal regions and have lower expression level and breadth than triads. Moreover, they are enriched in functions related to adaptation and more associated with the repressive H3K27me3 modification. Altogether, these results suggest that triads mainly correspond to housekeeping genes and are part of the core genome, while dyads and tetrads belong to the Triticeae dispensable genome. In addition, by comparing the different categories of dyads and tetrads, we hypothesize that, unlike most of the allopolyploid species, subgenome dominance and biased fractionation are absent in hexaploid wheat. Differences observed between the three subgenomes are more likely related to two successive and ongoing waves of post-polyploid diploidization, that had impacted A and B more significantly than D, as a result of the evolutionary history of hexaploid wheat.

Core ideas

Only one half of hexaploid wheat genes are in triads, i.e . in a 1:1:1 ratio across subgenomes Triads are likely part of the core genome; dyads and tetrads belong to the dispensable genome Subgenome dominance and biased fractionation are absent in hexaploid wheat Subgenome differences are related to two successive waves of post-polyploid diploidization", "token_count": 496, "char_count": 2040, "word_count": 306, "semantic_coherence": 1, "information_density": 0.5425, "quality_score": 0.7712, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:09.425496", "source": { "split": "train_shard_00001", "doc_id": 3739 }, "chunk_id": "train_shard_00001_3739_0", "global_id": 10957 }, { "text": "New insights into homoeologous copy number variations in the hexaploid wheat genome", "token_count": 19, "char_count": 83, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:09.779291", "source": { "split": "train_shard_00001", "doc_id": 3739 }, "chunk_id": "train_shard_00001_3739_1", "global_id": 10958 }, { "text": "Shigellosis is a highly infectious disease that are mainly transmitted via faecal-oral contact of the bacteria Shigella. Four species have been identified in Shigella genus, among which S. flexneri is used to be the most prevalent species globally and commonly isolated from developing countries. However, it is being replaced by S. sonnei that is currently the main causative agent for dysentery pandemic in many emerging industrialized countries such as Asia and the Middle East with unclear reasons. For a better understanding of S. sonnei virulence and antibiotic resistance, we sequenced 12 clinical S. sonnei strains with varied antibiotic-resistance profiles collected from four cities in Jiangsu Province, China. Phylogenomic analysis clustered antibiotic sensitive and resistant S. sonnei into two distinct groups while pangenome analysis reveals the presence and absence of featured genes in each group. Screening of 31 classes of virulence factors found out that type 2 secretion system is doubled in resistant strains. Further principle component analysis based on the interactions between virulence and resistance indicated that abundant virulence factors are associated with higher resistant phenotypes. The result present here is based on statistical analysis of a small sample size and serves basically as a guidance for further experimental and theoretical studies.\n\nComparative genome analysis of 12 Shigella sonnei strains: virulence, resistance, and their interactions", "token_count": 328, "char_count": 1495, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6837, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:10.347640", "source": { "split": "train_shard_00001", "doc_id": 3740 }, "chunk_id": "train_shard_00001_3740_0", "global_id": 10959 }, { "text": "Multiple \"omics\" approaches have emerged as successful technologies for plant systems over the last few decades. Advances in next-generation sequencing (NGS) have paved a way for a new generation of different omics, such as genomics, transcriptomics, and proteomics. However, metabolomics, ionomics, and phenomics have also been well-documented in crop science. Multi-omics approaches with high throughput techniques have played an important role in elucidating growth, senescence, yield, and the responses to biotic and abiotic stress in numerous crops. These omics approaches have been implemented in some important crops including wheat (Triticum aestivum L.), soybean (Glycine max), tomato (Solanum lycopersicum), barley (Hordeum vulgare L.), maize (Zea mays L.), millet (Setaria italica L.), cotton (Gossypium hirsutum L.), Medicago truncatula, and rice (Oryza sativa L.). The integration of functional genomics with other omics highlights the relationships between crop genomes and phenotypes under specific physiological and environmental conditions. The purpose of this review is to dissect the role and integration of multi-omics technologies for crop breeding science. We highlight the applications of various omics approaches, such as genomics, transcriptomics, proteomics, metabolomics, phenomics, and ionomics, and the implementation of robust methods to improve crop genetics and breeding science. Potential challenges that confront the integration of multi-omics with regard to the functional analysis of genes and their networks as well as the development of potential traits for crop improvement are discussed. The panomics platform allows for the integration of complex omics to construct models that can be used to predict complex traits. Systems biology integration with multi-omics datasets can enhance our understanding of molecular regulator networks for crop improvement. In this context, we suggest the integration of entire omics by employing the \"phenotype to genotype\" and \"genotype to phenotype\" concept", "token_count": 515, "char_count": 2095, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6113, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:11.000798", "source": { "split": "train_shard_00001", "doc_id": 3741 }, "chunk_id": "train_shard_00001_3741_0", "global_id": 10960 }, { "text": "Hence, top-down (phenotype to genotype) and bottom-up (genotype to phenotype) model through integration of multi-omics with systems biology may be beneficial for crop breeding improvement under conditions of environmental stresses.\n\nApplications of Multi-Omics Technologies for Crop Improvement.", "token_count": 68, "char_count": 295, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8378, "quality_score": 0.9189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:11.364848", "source": { "split": "train_shard_00001", "doc_id": 3741 }, "chunk_id": "train_shard_00001_3741_1", "global_id": 10961 }, { "text": "Phylosymbiosis is a cross-system trend whereby microbial community relationships recapitulate the host phylogeny. In Nasonia parasitoid wasps, phylosymbiosis occurs throughout development, is distinguishable between sexes, and benefits host development and survival. Moreover, the microbiome shifts in hybrids as a rare Proteus bacterium in the microbiome becomes dominant. The larval hybrids then catastrophically succumb to bacterium-assisted lethality and reproductive isolation between the species. Two important questions for understanding phylosymbiosis and bacterium-assisted lethality in hybrids are (i) do the Nasonia bacterial genomes differ from other animal isolates and (ii) are the hybrid bacterial genomes the same as those in the parental species. Here, we report the cultivation, whole-genome sequencing, and comparative analyses of the most abundant gut bacteria in Nasonia larvae, Providencia rettgeri and Proteus mirabilis Characterization of new isolates shows Proteus mirabilis forms a more robust biofilm than Providencia rettgeri and that, when grown in coculture, Proteus mirabilis significantly outcompetes Providencia rettgeri Providencia rettgeri genomes from Nasonia are similar to each other and more divergent from pathogenic, human associates. Proteus mirabilis from Nasonia vitripennis, Nasonia giraulti, and their hybrid offspring are nearly identical and relatively distinct from human isolates. These results indicate that members of the larval gut microbiome within Nasonia are most similar to each other, and the strain of the dominant Proteus mirabilis in hybrids is resident in parental species", "token_count": 502, "char_count": 1753, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5701, "quality_score": 0.7851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:12.014095", "source": { "split": "train_shard_00001", "doc_id": 3742 }, "chunk_id": "train_shard_00001_3742_0", "global_id": 10962 }, { "text": "Holobiont interactions between shared, resident members of the wasp microbiome and the host underpin phylosymbiosis and hybrid breakdown.IMPORTANCE Animal and plant hosts often establish intimate relationships with their microbiomes. In varied environments, closely related host species share more similar microbiomes, a pattern termed phylosymbiosis. When phylosymbiosis is functionally significant and beneficial, microbial transplants between host species and host hybridization can have detrimental consequences on host biology. In the Nasonia parasitoid wasp genus, which contains a phylosymbiotic gut community, both effects occur and provide evidence for selective pressures on the holobiont. Here, we show that bacterial genomes in Nasonia differ from other environments and harbor genes with unique functions that may regulate phylosymbiotic relationships. Furthermore, the bacteria in hybrids are identical to those in parental species, thus supporting a hologenomic tenet that the same members of the microbiome and the host genome impact phylosymbiosis, hybrid breakdown, and speciation.\n\nGenomes of Gut Bacteria from Nasonia Wasps Shed Light on Phylosymbiosis and Microbe-Assisted Hybrid Breakdown.", "token_count": 310, "char_count": 1239, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6914, "quality_score": 0.8457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:12.580603", "source": { "split": "train_shard_00001", "doc_id": 3742 }, "chunk_id": "train_shard_00001_3742_1", "global_id": 10963 }, { "text": "The partitioning behaviour of endo-polygalacturonase (endo-PG) and total protein from a clarified Kluyveromyces marxianus fermentation broth in polyethylene glycol (PEG)-ammonium sulfate and PEG-potassium phosphate (pH=7) aqueous two-phase systems was experimentally investigated. Both the enzyme and total protein partitioned in the bottom phase for these two kinds of systems. The enzyme partitioning coefficient can be lower than 0.01 in PEG8000-(NH4)2SO4 ATPS with a large phase volume ratio and a moderate tie-line length, which implies the possibility of concentration operation using aqueous two phase partitioning. An ion-exchange separation of high purification efficiency was applied to analyze the clarified and dialyzed fermentation broth. A total purification factor of only 2.3 was obtained, which indicated the high enzyme protein content in the total protein of the fermentation broth. Consequently, the main purpose for separating endo-PG is concentration rather than purification. A separation scheme using an aqueous two-phase extraction process with polymer recycling and a dialysis was proposed to recover endo-PG from the fermentation supernatant of K. marxianus for commercial purpose. A high enzyme recovery up to 95% and a concentration factor of 5 to 8 with a purification factor of about 1.25 were obtained using the single aqueous two-phase extraction process. More than 95% polymer recycled will not affect the enzyme recovery and purification factor. Dialysis was used mainly to remove salts in the bottom phase. The dialysis step has no enzyme loss and can further remove small bulk proteins. The total purification factor for the scheme is about 1.7.\n\nRecovery of endo-polygalacturonase using polyethylene glycol-salt aqueous two-phase extraction with polymer recycling.", "token_count": 463, "char_count": 1802, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5116, "quality_score": 0.7558, "entities": { "genes": [ "PEG8000", "NH4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:13.223476", "source": { "split": "train_shard_00001", "doc_id": 3743 }, "chunk_id": "train_shard_00001_3743_0", "global_id": 10964 }, { "text": "Water systems in health care facilities can form reservoirs for Gram-negative bacteria. While planning a new neonatal intensive care unit (NICU), we performed a retrospective evaluation of potential risks from water-diverting systems on the existing NICU of our tertiary care University Hospital. During 2017 to 2023, we recorded nine nosocomial cluster events with bacterial pathogens in our NICU. Of these, three clusters of Gram-negative bacteria were potentially related to sink drains: A Klebsiella oxytoca, a Pseudomonas aeruginosa, and an Enterobacter hormaechei cluster were uncovered by clinical routine screening of patients and breastmilk samples. They were confirmed using whole-genome sequencing and a subsequent core genome multilocus sequence typing (cgMLST) algorithm. Our observations highlight that the implementation of sink drains in a NICU may have negative effects on patients' safety. Construction planning should concentrate on the avoidance of washbasins in patient rooms when redesigning sensitive areas such as NICUs.\n\nSink Drains in a Neonatal Intensive Care Unit: A Retrospective Risk Assessment and Evaluation.", "token_count": 283, "char_count": 1161, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7267, "quality_score": 0.8634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:13.792318", "source": { "split": "train_shard_00001", "doc_id": 3744 }, "chunk_id": "train_shard_00001_3744_0", "global_id": 10965 }, { "text": "

Background

Salmonella Enteritidis and Salmonella Typhimurium are major causes of bloodstream infection and diarrheal disease in East Africa. Sources of human infection, including the role of the meat pathway, are poorly understood.

Methods

We collected cattle, goat, and poultry meat pathway samples from December 2015 through August 2017 in Tanzania and isolated Salmonella using standard methods. Meat pathway isolates were compared with nontyphoidal serovars of Salmonella enterica (NTS) isolated from persons with bloodstream infections and diarrheal disease from 2007 through 2017 from Kenya by core genome multi-locus sequence typing (cgMLST). Isolates were characterized for antimicrobial resistance, virulence genes, and diversity.

Results

We isolated NTS from 164 meat pathway samples. Of 172 human NTS isolates, 90 (52.3%) from stool and 82 (47.7%) from blood, 53 (30.8%) were Salmonella Enteritidis sequence type (ST) 11 and 62 (36.0%) were Salmonella Typhimurium ST313. We identified cgMLST clusters within Salmonella Enteritidis ST11, Salmonella Heidelberg ST15, Salmonella Typhimurium ST19, and Salmonella II 42:r:- ST1208 that included both human and meat pathway isolates. Salmonella Typhimurium ST313 was isolated exclusively from human samples. Human and poultry isolates bore more antimicrobial resistance and virulence genes and were less diverse than isolates from other sources.

Conclusions

Our findings suggest that the meat pathway may be an important source of human infection with some clades of Salmonella Enteritidis ST11 in East Africa, but not of human infection by Salmonella Typhimurium ST313", "token_count": 491, "char_count": 1653, "word_count": 223, "semantic_coherence": 1, "information_density": 0.5785, "quality_score": 0.7892, "entities": { "genes": [ "ST19", "ST313", "ST11", "ST15", "ST1208" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:14.439542", "source": { "split": "train_shard_00001", "doc_id": 3745 }, "chunk_id": "train_shard_00001_3745_0", "global_id": 10966 }, { "text": "Research is needed to systematically examine the contributions of other types of meat, animal products, produce, water, and the environment to nontyphoidal Salmonella disease in East Africa.\n\nInvestigating the Meat Pathway as a Source of Human Nontyphoidal Salmonella Bloodstream Infections and Diarrhea in East Africa.", "token_count": 78, "char_count": 319, "word_count": 45, "semantic_coherence": 1, "information_density": 0.7556, "quality_score": 0.8778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:14.813988", "source": { "split": "train_shard_00001", "doc_id": 3745 }, "chunk_id": "train_shard_00001_3745_1", "global_id": 10967 }, { "text": "A combined PCR-culture technique was developed for the detection of viable yeasts in yoghurt samples. Yoghurt samples were inoculated with either viable or heat-inactivated Kluyveromyces marxianus cells, and analyzed before and after incubation for 24 h at 25 degrees C under agitation. DNA was extracted from the samples and amplified using yeast-specific primers targeted at the gene coding for the 18S rRNA. A 251-bp fragment was amplified by the Polymerase Chain Reaction from the yoghurt samples containing initial yeasts counts of 10 cfu g(-1) or higher, whereas no PCR product was generated from control uninoculated yoghurt samples. Comparison of PCR results obtained before and after the incubation step was used to assess yeast viability. Viability was also confirmed by plating on Sabouraud-Dextrose-Chloramphenicol Agar. Moreover, comparison of the results obtained using PCR-culture and plate count methods for the analysis of commercial yoghurt samples, demonstrated that the PCR-culture technique developed in this work can be very useful for the rapid detection of viable spoilage yeasts in dairy industries.\n\nDetection of Kluyveromyces marxianus and other spoilage yeasts in yoghurt using a PCR-culture technique.", "token_count": 315, "char_count": 1230, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5944, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:15.379171", "source": { "split": "train_shard_00001", "doc_id": 3746 }, "chunk_id": "train_shard_00001_3746_0", "global_id": 10968 }, { "text": "Whey valorization concerns have led to recent interest on the production of whey beverage simulating kefir. In this study, the structure and microbiota of Brazilian kefir grains and beverages obtained from milk and whole/deproteinised whey was characterized using microscopy and molecular techniques. The aim was to evaluate its stability and possible shift of probiotic bacteria to the beverages. Fluorescence staining in combination with Confocal Laser Scanning Microscopy showed distribution of yeasts in macro-clusters among the grain's matrix essentially composed of polysaccharides (kefiran) and bacteria. Denaturing gradient gel electrophoresis displayed communities included yeast affiliated to Kluyveromyces marxianus, Saccharomyces cerevisiae, Kazachatania unispora, bacteria affiliated to Lactobacillus kefiranofaciens subsp. Kefirgranum, Lactobacillus kefiranofaciens subsp. Kefiranofaciens and an uncultured bacterium also related to the genus Lactobacillus. A steady structure and dominant microbiota, including probiotic bacteria, was detected in the analyzed kefir beverages and grains. This robustness is determinant for future implementation of whey-based kefir beverages.\n\nProduction of fermented cheese whey-based beverage using kefir grains as starter culture: evaluation of morphological and microbial variations.", "token_count": 342, "char_count": 1335, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:15.952163", "source": { "split": "train_shard_00001", "doc_id": 3747 }, "chunk_id": "train_shard_00001_3747_0", "global_id": 10969 }, { "text": "Kluyveromyces marxianus can be transformed with an efficiency of 10(5) transformants/microgram of DNA by a replicative plasmid using electroporation. In order to obtain this efficiency, we isolated ura- mutants cells which can be complemented by the URA3 gene from Saccharomyces cerevisiae. The URA3 gene and KARS2, a replicative origin from Kluyveromyces lactis which functions in K. marxianus, were ligated together in a plasmid which can be used as a vector to transform this strain.\n\nHigh efficiency transformation of Kluyveromyces marxianus by a replicative plasmid.", "token_count": 159, "char_count": 571, "word_count": 84, "semantic_coherence": 1, "information_density": 0.6548, "quality_score": 0.8274, "entities": { "genes": [ "URA3", "KARS2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:16.390959", "source": { "split": "train_shard_00001", "doc_id": 3748 }, "chunk_id": "train_shard_00001_3748_0", "global_id": 10970 }, { "text": "This study aimed to characterize the dominant microflora in shubat, a special fermented product prepared from unheated two-humped camel milk. In the seven investigated samples of shubat, lactic acid bacteria and yeasts were the dominant microorganisms with the number ranging from log 6.8 to 7.6 cfu/ml and from log 4.3 to 4.7 cfu/ml, respectively. Using phenotypic and molecular methods, a total of 48 LAB isolates were identified as Lactobacillus sakei, Enterococcus faecium, Lactobacillus helveticus, Leuconstoc lactis, Enterococcus feacalis, Lactobacillus brevis and Weissella hellenica, whereas 15 yeast isolates were identified as Kluyveromyces marxianus, Kazahstan uiosporus, and Candida ethanolica. Results showed also that Lactobacillus and Enterococcus as well as Kluyveromyces were the predominant genera, with the most frequently isolated species being Lactobacillus sakei and Enterococcus faecium as well as Kluyveromyces maxius, respectively. This is the first report on the characterization of dominant microflora of shubat in China.\n\nCharacterization of the dominant microflora in naturally fermented camel milk shubat", "token_count": 322, "char_count": 1134, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:16.956470", "source": { "split": "train_shard_00001", "doc_id": 3749 }, "chunk_id": "train_shard_00001_3749_0", "global_id": 10971 }, { "text": "We compared genomes from multiple isolations of Shiga toxin-producing Escherichia coli (STEC) O157:H7 from the same patient, in cases notified to Public Health England (PHE) between 2015 and 2019. There were 261 cases where multiple isolates were sequenced from the same patient comprising 589 isolates. Serial isolates from the same patient fell within five single nucleotide polymorphisms (SNPs) of each other for 260/261 (99.6%) of the cases, indicating that there was little evidence of within host variation. The investigation into the 13 SNP discrepancy between one isolate pair revealed the cause to be a recombination event within a stx2a-encoding prophage resulting in the insertion/deletion of a fragment of the genome. This 50 kbp prophage fragment was homologous to a prophage in the reference genome, and the short reads from the isolate that had the 50 kbp fragment, mapped unambiguously to this region. The discrepant variants in the isolate without the 50 kbp fragment were attributed to ambiguous mapping of the short reads from other prophage regions to the 50 kbp fragment in the reference genome. Identification of such recombination events in this dataset appeared to be rare, most likely because the majority of prophage regions in the Sakai reference genome are masked during the analysis. Identification of SNPs under neutral selection, and masking recombination events, is a requirement for phylogenetic analysis used for public health surveillance, and for the detection of point source outbreaks. However, assaying the accessory genome by combining the use of short and long read technologies for public health surveillance may provide insight into how recombination events impact on the evolutionary course of STEC O157:H7.\n\nA Shiga Toxin-Encoding Prophage Recombination Event Confounds the Phylogenetic Relationship Between Two Isolates of Escherichia coli O157:H7 From the Same Patient.", "token_count": 505, "char_count": 1937, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5398, "quality_score": 0.7699, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:17.628738", "source": { "split": "train_shard_00001", "doc_id": 3750 }, "chunk_id": "train_shard_00001_3750_0", "global_id": 10972 }, { "text": "The survival of undesirable micro-organisms Yersinia enterocolitica, Escherichia coli, Rhodotorula mucilaginosa, Kluyveromyces marxianus in fruit yoghurts after inoculation at two different levels (10(2)-10(3) cfu/ml and 10(4)-10(6) cfu/ml) was investigated during storage at 4 and 8 degrees C. When stored at 4 degrees C, the survival of Y. enterocolitica was not significant (3 days) except when the size of the initial inoculum was larger than 10(5) cfu/ml: in this case, viable cells of the pathogen were still recovered after 17 days of storage. Cells of E. coli were detected in the yoghurt samples after 24-48 days at 4 degrees C, regardless of the inoculum size. The growth of yeasts easily occurred at 4 degrees C; R. mucilaginosa showed an increase of 10-100 fold and K. marxianus was able to grow from 10(2) to 10(5)-10(6) cfu/ml during the 30 days of storage. Similar trends were noted with 8 degrees C storage. The survival of both contaminants was longer than 8-10 days and yeasts were able to grow remarkably well, with microbial values of 10(6) cfu/ml R. mucilaginosa and 10(8) cfu/ml K. marxianus in the case of the large inoculum. Throughout the whole experiment, the counts for lactic streptococci were around 10(8)-10(9) cfu/ml whereas lactobacilli levels were 10(6) cfu/ml, and viability declined after 15 days of storage. The competition in vitro between both Lactobacillus and Streptococcus strains isolated from yoghurt and E. coli was also investigated. With Lactobacillus, the inhibition of E. coli was very effective; no viable E. coli cells were detected after 24 h incubation", "token_count": 516, "char_count": 1604, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5551, "quality_score": 0.7776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:18.764133", "source": { "split": "train_shard_00001", "doc_id": 3751 }, "chunk_id": "train_shard_00001_3751_0", "global_id": 10973 }, { "text": "The Streptococcus strain was also able to inhibit E. coli but not so rapidly; slight growth of E. coli was observed during the first 3 h, followed by a marked decrease in the number of cells.\n\nSurvival of undesirable micro-organisms in fruit yoghurts during storage at different temperatures", "token_count": 74, "char_count": 291, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:19.167018", "source": { "split": "train_shard_00001", "doc_id": 3751 }, "chunk_id": "train_shard_00001_3751_1", "global_id": 10974 }, { "text": "

Objectives

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is increasingly reported worldwide and has posed a serious challenge for public health. Here we report the complete genome sequence of a multidrug-resistant (MDR) K. pneumoniae carrying one blaNDM-1 and two copies of blaKPC-2 genes isolated from a cerebrospinal fluid specimen in China.

Methods

The minimal inhibitory concentrations (MICs) of 26 antimicrobial agents against K. pneumoniae strain KP46 were measured. The complete genome sequence of KP46 was determined using Illumina and Nanopore platforms. The derived short and long reads were assembled using Unicycler. Multilocus sequence typing (MLST), antimicrobial resistance genes, virulence genes, and plasmid replicons were predicted in silico using the BacWGSTdb server. The phylogenetic relationship between KP46 and 454 ST15 K. pneumoniae strains obtained from NCBI GenBank database was analysed based on a core genome MLST (cgMLST) strategy.

Results

K. pneumoniae strain KP46 was resistant to all antimicrobial agents tested, except for tigecycline, colistin, cefiderocol, and fosfomycin. The genome sequence of KP46 belonged to sequence type 15 (ST15), which contained seven circularized contigs comprising 5 674 521 bp, including one chromosome and six plasmids. Serval antimicrobial resistance genes were identified, including a blaNDM-1 gene located in a 53 096 bp IncX3 plasmid, and two copies of blaKPC-2 gene located both in a 103 807 bp IncX6 and an 88 164 bp IncFII plasmid, respectively", "token_count": 502, "char_count": 1586, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6512, "quality_score": 0.8256, "entities": { "genes": [ "ST15", "KP46" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:19.826329", "source": { "split": "train_shard_00001", "doc_id": 3752 }, "chunk_id": "train_shard_00001_3752_0", "global_id": 10975 }, { "text": "The most closely related strain was another ST15 strain also isolated from China with five cgMLST loci differences.

Conclusion

We reported the first complete genome sequence of a K. pneumoniae ST15 clinical isolate coharbouring blaNDM-1 and two copies of blaKPC-2 in China. This study will provide insight into the antimicrobial resistance mechanisms and phylogeny of carbapenem-resistant ST15 K. pneumoniae.\n\nCoexistence of two blaKPC-2 genes in a blaNDM-1-carrying multidrug-resistant ST15 Klebsiella pneumoniae isolate recovered from cerebrospinal fluid in China.", "token_count": 194, "char_count": 617, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7368, "quality_score": 0.8684, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:20.274650", "source": { "split": "train_shard_00001", "doc_id": 3752 }, "chunk_id": "train_shard_00001_3752_1", "global_id": 10976 }, { "text": "Disclosed is a Kluyveromyces marxianus yeast fermented drink and its preparation method, wherein a strain of separated Kluyveromyces marxianus Van der walf is employed for the preparing process which comprises, screening culture medium at 25-30 deg. C, carrying out fermentation culturing, degerming, filtering and subsequent conventional processing procedures.\n\nKluyveromyces marxianus yeast fermented drink and its preparation method", "token_count": 108, "char_count": 435, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7719, "quality_score": 0.886, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:20.657284", "source": { "split": "train_shard_00001", "doc_id": 3753 }, "chunk_id": "train_shard_00001_3753_0", "global_id": 10977 }, { "text": "

Background

In March 2022, an outbreak investigation was initiated in Ireland after identifying a cluster of monophasic Salmonella Typhimurium cases, affecting primarily small children. Microbiological investigations revealed that the cluster was part of a wider international outbreak.

Methods

A total of 18 Irish outbreak cases were identified. We undertook a matched case-control study using the case-case method to determine if exposure to the implicated products was associated with illness.

Results

In univariable analysis, the highest odds of disease due to monophasic S. Typhimurium versus other gastrointestinal disease were obtained for a chocolate Product A of Brand A [matched odds ratio (mOR) = 7.77, 95% confidence intervals (CI): 0.89-67.20]. When grouping the implicated products in a composite variable, the odds of disease due to monophasic S. Typhimurium versus other gastrointestinal disease were 10.5 times higher with a consumption of at least one of the implicated products [mOR = 10.50, 95% CI: 1.24-88.60, p = 0.031].

Conclusion

This analytical study supported the internationally generated hypothesis which led to the implementation of control measures. Owing to the high levels of chocolate purchasing with Easter approaching, early outbreak identification and involvement in the internationally coordinated investigation was essential to an efficient response and to minimise the risk of further harm to a particularly vulnerable population group.\n\nInvestigation of a monophasic <i>Salmonella</i> Typhimurium outbreak linked to chocolate products as part of wider international outbreak: A matched case-control study, Ireland, 2022.", "token_count": 459, "char_count": 1728, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:21.299164", "source": { "split": "train_shard_00001", "doc_id": 3754 }, "chunk_id": "train_shard_00001_3754_0", "global_id": 10978 }, { "text": "Abstract

Background

K. pneumoniae (KPN) has emerged as a major hospital associated pathogen in the recent years. Clonal complex (CC) 258 constitutes an international epidemic clone responsible for spread of extended spectrum beta-lactamases (ESBL) and carbapenemases. We evaluated the core genome (cg) MLST, resistance (R) gene and plasmid profiles of a worldwide collection of KPN using the 1928 bioinformatic cloud platform.

Methods

A total of 155 KPN clinical isolates (CC258, n=129; non-CC258, n=26) collected from 19 countries during 2018 of SENTRY Program were analyzed. Isolates included carbapenem resistant (CR; n=120) and non-CR (n=35). Whole genome sequencing FASTQ files were uploaded to the 1928 pipeline for analysis.

Results

Most CC258 isolates belonged to ST258, ST11 and ST512 (Table), and separated from unrelated ST by allelic distance (ad) > 2000. cgMLST grouped together isolates from the same STs, and those from similar geographies had greater homology, except isolates from US showed greater heterogenicity (ad 620). Applying an ad cutoff of < 100, ST258 isolates grouped in 4 clades with a predominance of either KPC-2 or -3. An ad cutoff of < 200 identified 7 clades within ST11 that were related by geography and R genes. Among CC258 isolates KPC was the major carbapenemase (58.1%) and associated with Tn4401 (a or b in 84% KPC); NDM-1 was detected (8.5%) only in ST11 and ST395. KPC-2 was more prevalent in Latin America and the isolates were closely related (ad 104) among ST258 compared to ST11 (ad 355)", "token_count": 509, "char_count": 1561, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6955, "quality_score": 0.8477, "entities": { "genes": [ "ST395", "ST11", "CC258", "ST258", "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:21.957174", "source": { "split": "train_shard_00001", "doc_id": 3755 }, "chunk_id": "train_shard_00001_3755_0", "global_id": 10979 }, { "text": "KPC-3 CC258 isolates showed ad of 164 and were from Italy, Russia, Greece, and US. CTX-M-14 was prevalent in ST258 while CTX-M-15 was common in other STs, except ST512 which carried no CTX-M despite clustering within ST258.

Conclusion

1928 generated cgMLST showed good correlation with MLST in classifying all KPN isolates. ST258 isolates showed tight clustering, no NDM genes and distribution in the Americas while ST11 showed global dissemination and diversity of carbapenemases. Table 1

Disclosures

Fredrik Dyrkell, n/a, 1928 Diagnostics (Employee) Dimitrios Arnellos, n/a, 1928 Diagnostics (Employee) Mariana Castanheira, PhD, 1928 Diagnostics (Research Grant or Support)A. Menarini Industrie Farmaceutiche Riunite S.R.L. (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Amplyx Pharmaceuticals (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Fox Chase Chemical Diversity Center (Research Grant or Support)GlaxoSmithKline (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Merck (Research Grant or Support)Merck (Research Grant or Support)Merck & Co, Inc. (Research Grant or Support)Merck & Co, Inc. (Research Grant or Support)Paratek Pharma, LLC (Research Grant or Support)Pfizer (Research Grant or Support)Qpex Biopharma (Research Grant or Support)", "token_count": 514, "char_count": 1608, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5097, "quality_score": 0.7549, "entities": { "genes": [ "ST11", "CC258", "ST258", "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:22.608037", "source": { "split": "train_shard_00001", "doc_id": 3755 }, "chunk_id": "train_shard_00001_3755_1", "global_id": 10980 }, { "text": "831. Analysis of a Worldwide Collection of Klebsiella pneumoniae CC258 with Reference to Carbapenemase Production Using the 1928 Core Genome (cg) Multilocus Sequence Type (MLST) Reveals Endemicity and Global Dissemination of Clones", "token_count": 72, "char_count": 231, "word_count": 32, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [ "CC258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:22.976207", "source": { "split": "train_shard_00001", "doc_id": 3755 }, "chunk_id": "train_shard_00001_3755_2", "global_id": 10981 }, { "text": "The interaction between nine lactic acid bacteria (LAB) and five yeast strains isolated from airag of Inner Mongolia Autonomic Region, China was investigated. Three representative LAB and two yeasts showed symbioses were selected and incubated in 10% (w/v) reconstituted skim milk as single and mixed cultures to measure viable count, titratable acidity, ethanol and sugar content every 24 h for 1 week. LAB and yeasts showed high viable counts in the mixed cultures compared to the single cultures. Titratable acidity of the mixed cultures was obviously enhanced compared with that of the single cultures, except for the combinations of Lactobacillus reuteri 940B3 with Saccharomyces cerevisiae 4C and Lactobacillus helveticus 130B4 with Candida kefyr 2Y305. C. kefyr 2Y305 produced large amounts of ethanol (maximum 1.35 g/L), whereas non-lactose-fermenting S. cerevisiae 4C produced large amounts of ethanol only in the mixed cultures. Total glucose and galactose content increased while lactose content decreased in the single cultures of Leuconostoc mesenteroides 6B2081 and Lb. helveticus 130B4. However, both glucose and galactose were completely consumed and lactose was markedly reduced in the mixed cultures with yeasts. The result suggests that yeasts utilize glucose and galactose produced by LAB lactase to promote cell growth.\n\nInteraction between lactic acid bacteria and yeasts in airag, an alcoholic fermented milk.", "token_count": 404, "char_count": 1432, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:23.597160", "source": { "split": "train_shard_00001", "doc_id": 3756 }, "chunk_id": "train_shard_00001_3756_0", "global_id": 10982 }, { "text": "Kordiimonas pumila N18T (=KCTC 62164T = MCCC 1K03436T) was isolated from coastal sediments collected in Zhoushan, P. R. China. Ensuing genome sequencing revealed that it consists of a single chromosome with a size of 4,041,658 bp and a DNA G+C content of 47.4%. The genomic annotations further identified 3724 open reading frames (ORFs), 4 rRNA genes, and 43 tRNA genes in the Kordiimonas pumila N18T genome. The percentages of ORFs assigned to the CAZy, COG, GO, and KEGG databases were 1.0, 84.8, 19.9, and 59.3%, respectively. Comparative genomic analysis with four other Kordiimonas genomes indicated that the pan- and core-genomes of the genus Kordiimonas consists of 8985 and 1470 orthologous clusters, respectively. Functional annotations of the genus Kordiimonas core genome further revealed that they utilize monosaccharides, peptides, and esters as energy substrates because of the absence of several glycoside hydrolases, glycosyl transferases, aminopeptidases, carbohydrate esterase coding genes, and polysaccharide lyases coding genes in their genomes. Moreover, the genus Kordiimonas possesses survival advantages in ammonium-, phosphorus-, and iron- deficient environments, which are vital for inhabiting marine environments. Overall, this study reports the complete genome of the order Kordiimonadales and broadens the understanding of its ecological roles.\n\nComplete genome sequence of Kordiimonas pumila N18T sheds light on biogeochemical roles of the genus Kordiimonas.", "token_count": 497, "char_count": 1543, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:24.256998", "source": { "split": "train_shard_00001", "doc_id": 3757 }, "chunk_id": "train_shard_00001_3757_0", "global_id": 10983 }, { "text": "The gene encoding inulase of the yeast Kluyveromyces marxianus (INU1Km) was cloned and expressed in the inulin-negative yeast Saccharomyces cerevisiae. Cells of S. cerevisiae transformed with the INU1Km gene have acquired extracellular inulase activity and were able to grow in the medium with inulin as a sole carbon source. The S. cerevisiae strain was constructed that is capable of heterologous expression of secreted K. marxianus inulase and is defective in fructose uptake due to null-mutations of the hexokinase structural genes HXK1 and HXK2. When grown in inulin-containing media, this strain is capable of accumulating at least 10% glucose-free fructose in the culture liquid.\n\nInulase-secreting strain of Saccharomyces cerevisiae produces fructose.", "token_count": 218, "char_count": 759, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8273, "entities": { "genes": [ "HXK1", "HXK2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:24.722928", "source": { "split": "train_shard_00001", "doc_id": 3758 }, "chunk_id": "train_shard_00001_3758_0", "global_id": 10984 }, { "text": "The accessory genomes of many pathogenic bacteria include ABC transporters that scavenge metal by siderophore uptake and ABC transporters that contribute to antimicrobial resistance by multidrug efflux. There are mechanistic and recently recognized structural similarities between siderophore importer proteins and efflux pumps. Here we investigated the influence of siderophore importer YbtPQ on antimicrobial resistance of Klebsiella pneumoniae. YbtPQ is encoded in the yersiniabactin cluster in a prevalent mobile genetic element ICEKp, and is also common in pathogenicity islands of Escherichia coli and Yersinia species, where yersiniabactin enhances virulence. Deletion of ICEKp increased the susceptibility of K. pneumoniae to all antimicrobials tested. The mechanism was dependent on the yersiniabactin importer YbtPQ and may involve antimicrobial efflux, since it was affected by the inhibitor reserpine. The element ICEKp is naturally highly mobile, indeed the accessory genome of K. pneumoniae is recognized as a reservoir of genes for the emergence of hospital outbreak strains and for transfer to other Gram-negative pathogens. Introduction of ICEKp, or a plasmid encoding YbtPQ, to E. coli decreased its susceptibility to a broad range of antimicrobials. Thus a confirmed siderophore importer, on a rapidly evolving and highly mobile element capable of interspecies transfer, may have a secondary function exporting antimicrobials.\n\nA Virulence Associated Siderophore Importer Reduces Antimicrobial Susceptibility of Klebsiella pneumoniae.", "token_count": 453, "char_count": 1602, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6009, "quality_score": 0.8005, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:25.360910", "source": { "split": "train_shard_00001", "doc_id": 3759 }, "chunk_id": "train_shard_00001_3759_0", "global_id": 10985 }, { "text": "On 6 June 2019, the Norwegian Institute of Public Health was notified of more than 50 cases of gastroenteritis in Askøy. A reservoir in a water supply system was suspected as the source of the outbreak because of the acute onset and geographical distribution of cases. We investigated the outbreak to confirm the source, extent of the outbreak and effect of control measures. A case was defined as a person in a household served by Water Supply System A (WSS-A) who had gastroenteritis for more than 24 h between 1 and 19 June 2019. We conducted pilot interviews, a telephone survey and an SMS-based cohort study of residents served by WSS-A. System information of WSS-A was collected. Whole genome sequencing on human and environmental isolates was performed. Among 6,108 individuals, 1,573 fulfilled the case definition. Residents served by the reservoir had a 4.6× higher risk of illness than others. Campylobacter jejuni isolated from cases (n = 24) and water samples (n = 4) had identical core genome MLST profiles. Contamination through cracks in the reservoir most probably occurred during heavy rainfall. Water supply systems are susceptible to contamination, particularly to certain weather conditions. This highlights the importance of water safety planning and risk-based surveillance to mitigate risks.\n\nLarge waterborne Campylobacter outbreak: use of multiple approaches to investigate contamination of the drinking water supply system, Norway, June 2019.", "token_count": 379, "char_count": 1482, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:25.946011", "source": { "split": "train_shard_00001", "doc_id": 3760 }, "chunk_id": "train_shard_00001_3760_0", "global_id": 10986 }, { "text": "The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1-3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029-base-pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, showing the complete ampliconic structures of gene families TSPY, DAZ and RBMY; 41 additional protein-coding genes, mostly from the TSPY family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a previous assembly of the CHM13 genome4 and mapped available population variation, clinical variants and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.\n\nThe complete sequence of a human Y chromosome.", "token_count": 333, "char_count": 1183, "word_count": 173, "semantic_coherence": 1, "information_density": 0.659, "quality_score": 0.8295, "entities": { "genes": [ "CHM13", "HG002" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:26.512652", "source": { "split": "train_shard_00001", "doc_id": 3761 }, "chunk_id": "train_shard_00001_3761_0", "global_id": 10987 }, { "text": "Arthropods, such as houseflies, play a significant role in the dissemination of antimicrobial resistance (AMR); however, their impact has often been overlooked in comparison to other AMR vectors. Understanding the contribution of arthropods to the spread of AMR is critical for implementing robust policies to mitigate the spread of AMR across One Health sectors, affecting animals and environmental habitats as well as humans. In this study, we investigated the in situ transfer of a gfp-labelled AMR plasmid (IncA/C carrying an mcr-8 gene, pA/C_MCR-8) in the gut microbiota of houseflies (Musca domestica) by applying single-cell sorting, 16S rRNA gene amplicon sequencing and whole-genome sequencing. Our findings demonstrate that the pA/C_MCR-8-positive Escherichia coli donor strain is capable of colonizing the gut microbiome of houseflies and persists in the housefly intestine for 5 days; however, no transfer was detectable above the detection threshold of 10-5 per cell. The conjugative plasmid pA/C_MCR-8 demonstrated a high transfer frequency ranging from 4.1 × 10-3 to 5.0 × 10-3 per cell in vitro and exhibited transfer across various bacterial phyla, primarily encompassing Pseudomonadota and Bacillota. Phylogenic analysis has revealed that Providencia stuartii, a human opportunistic pathogen, is a notable recipient of pA/C_MCR-8. The conjugation assays further revealed that newly formed P. stuartii transconjugants readily transfer pA/C_MCR-8 to other clinically relevant pathogens (e.g. Klebsiella pneumoniae). Our findings indicate the potential transfer of AMR plasmids from houseflies to human opportunistic pathogens and further support the adoption of a One Health approach in developing infection control policies that address AMR across clinical settings.\n\nHousefly gut microbiomes as a reservoir and facilitator for the spread of antibiotic resistance.", "token_count": 514, "char_count": 1881, "word_count": 267, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:27.168250", "source": { "split": "train_shard_00001", "doc_id": 3762 }, "chunk_id": "train_shard_00001_3762_0", "global_id": 10988 }, { "text": "Plant AT-rich sequence and zinc-binding proteins (PLATZs) are a novel category of plant-specific transcription factors involved in growth, development, and abiotic stress responses. However, the PLATZ gene family has not been identified in barley. In this study, a total of 11 HvPLATZs were identified in barley, and they were unevenly distributed on five of the seven chromosomes. The phylogenetic tree, incorporating PLATZs from Arabidopsis, rice, maize, wheat, and barley, could be classified into six clusters, in which HvPLATZs are absent in Cluster VI. HvPLATZs exhibited conserved motif arrangements with a characteristic PLATZ domain. Two segmental duplication events were observed among HvPLATZs. All HvPLATZs were core genes present in 20 genotypes of the barley pan-genome. The HvPLATZ5 coding sequences were conserved among 20 barley genotypes, whereas HvPLATZ4/9/10 exhibited synonymous single nucleotide polymorphisms (SNPs); the remaining ones showed nonsynonymous variations. The expression of HvPLATZ2/3/8 was ubiquitous in various tissues, whereas HvPLATZ7 appeared transcriptionally silent; the remaining genes displayed tissue-specific expression. The expression of HvPLATZs was modulated by salt stress, potassium deficiency, and osmotic stress, with response patterns being time-, tissue-, and stress type-dependent. The heterologous expression of HvPLATZ3/5/6/8/9/10/11 in yeast enhanced tolerance to salt and osmotic stress, whereas the expression of HvPLATZ2 compromised tolerance. These results advance our comprehension and facilitate further functional characterization of HvPLATZs.", "token_count": 513, "char_count": 1708, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6963, "quality_score": 0.8481, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:27.823671", "source": { "split": "train_shard_00001", "doc_id": 3763 }, "chunk_id": "train_shard_00001_3763_0", "global_id": 10989 }, { "text": "Identification and Functional Characterization of Abiotic Stress Tolerance-Related PLATZ Transcription Factor Family in Barley (Hordeum vulgare L.).", "token_count": 51, "char_count": 162, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:28.184728", "source": { "split": "train_shard_00001", "doc_id": 3763 }, "chunk_id": "train_shard_00001_3763_1", "global_id": 10990 }, { "text": "Change in global climate has started to show its effect in the form of extremes of temperatures and water scarcity which is bound to impact adversely the global food security in near future. In the current review we discuss the impact of drought on plants and highlight the ability of endophytes, microbes that inhabit the plants asymptomatically, to confer stress tolerance to their host. For this we first describe the symbiotic association between plant and the endophytes and then focus on the molecular and physiological strategies/mechanisms adopted by these endophytes to confer stress tolerance. These include root alteration, osmotic adjustment, ROS scavenging, detoxification, production of phytohormones, and promoting plant growth under adverse conditions. The review further elaborates on how omics-based techniques have advanced our understanding of molecular basis of endophyte mediated drought tolerance of host plant. Detailed analysis of whole genome sequences of endophytes followed by comparative genomics facilitates in identification of genes involved in endophyte-host interaction while functional genomics further unveils the microbial targets that can be exploited for enhancing the stress tolerance of the host. Thus, an amalgamation of endophytes with other sustainable agricultural practices seems to be an appeasing approach to produce climate-resilient crops.\n\nAdvancement in the molecular perspective of plant-endophytic interaction to mitigate drought stress in plants.", "token_count": 319, "char_count": 1501, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:28.743547", "source": { "split": "train_shard_00001", "doc_id": 3764 }, "chunk_id": "train_shard_00001_3764_0", "global_id": 10991 }, { "text": "

Introduction

Carbapenem-resistant Klebsiella pneumoniae (CRKP) causes life-threatening hospital-acquired infections. KPC and VIM carbapenemase production is the main molecular mechanism for carbapenem resistance. The aim of the current study was the genetic characterization of four ST39 CRKP isolates simultaneously producing VIM-1 and KPC-2, obtained in a Greek tertiary hospital.

Methods

Identification and antimicrobial susceptibility testing were performed through VITEK 2. Multiplex PCR, multiplex lateral flow immunoassay, phenotypic tests and next generation sequencing were applied. The sequence reads were de novo assembled and annotated, while antimicrobial resistance genes and plasmids were identified using bioinformatics software. Genomic comparison and core genome single-nucleotide polymorphism-based phylogenetic analysis were also performed.

Results

Three isolates were pandrug-resistant, and one was extensively drug-resistant; they all carried blaVIM-1 and blaKPC-2 genes and were assigned to ST39. BlaVIM-1 was integrated in a class 1 integron. They all harboured many antimicrobial resistance genes and various plasmids. The mgrB gene of all isolates was disrupted by an insertion sequence (ISKpn14). Genome comparison and phylogenetic analysis revealed that the isolates were closely related.

Conclusion

To our knowledge this is the first report on detection of CRKP ST39 isolates simultaneously producing VIM-1 and KPC-2 in addition to colistin resistance. The knowledge of the clonal relatedness of the isolates can lead to the implementation of strict infection control measures absolutely needed to eliminate their spread.\n\nEmergence of ST39 carbapenem-resistant Klebsiella pneumoniae producing VIM-1 and KPC-2.", "token_count": 491, "char_count": 1801, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6413, "quality_score": 0.8206, "entities": { "genes": [ "ST39" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:29.419333", "source": { "split": "train_shard_00001", "doc_id": 3765 }, "chunk_id": "train_shard_00001_3765_0", "global_id": 10992 }, { "text": "

ABSTRACT

Saccharomyces eubayanus represents missing cryotolerant ancestor of lager yeast hybrid and can be found in Patagonia in association with Nothofagus forests. The limited number of isolates and associated genomes available has prevented to resolve the S. eubayanus origin and evolution. Here, we present a sampling effort at an unprecedented scale and report the isolation of 160 strains from ten sampling sites along 2,000 km distance in South America. We sequenced the genome of 82 strains and, together with other 25 available genomes, performed comprehensive phylogenetic analysis. Our results revealed the presence of three main Patagonia-B lineages together with dozens of admixed strains distributed in three mosaic clusters. The PB-1 lineage isolated from Tierra del Fuego exhibited the highest genetic diversity, lowest LD blocks and highest F is values compared to the other lineages, suggesting a successful adaptation to cold temperatures in extreme environments and greater inbreeding rates in Tierra del Fuego. Differences between lineages and strains were found in terms of aneuploidy and pangenome content, evidencing a lateral gene transfer event in PB-2 strains from an unknown donor species. Overall, the Patagonian lineages, particularly southern populations, showed a greater global genetic diversity compared to Holarctic and Chinese lineages, supporting the scenario of a S. eubayanus colonization from Patagonia and then spread towards northern and western regions, including the Holarctic (North America and China) and New Zealand. Interestingly, fermentative capacity and maltose consumption resulted negatively correlated with latitude, indicating a better fermentative performance in norther populations. Our genome analysis together with previous reports in the sister species S. uvarum strongly suggests that the S. eubayanus ancestor could have originated in Patagonia or the Southern Hemisphere, rather than China, yet further studies are needed to resolve this conflicting scenario. Understanding S. eubayanus evolutionary history is crucial to resolve the unknown origin of the lager yeast and might open new avenues for biotechnological applications.", "token_count": 497, "char_count": 2201, "word_count": 312, "semantic_coherence": 1, "information_density": 0.6474, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:30.102221", "source": { "split": "train_shard_00001", "doc_id": 3766 }, "chunk_id": "train_shard_00001_3766_0", "global_id": 10993 }, { "text": "An Out-of-Patagonia dispersal explains most of the worldwide genetic distribution in Saccharomyces eubayanus", "token_count": 34, "char_count": 115, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:30.494439", "source": { "split": "train_shard_00001", "doc_id": 3766 }, "chunk_id": "train_shard_00001_3766_1", "global_id": 10994 }, { "text": "Hyper-production of a thermotolerant beta-xylosidase by a deoxy-D-glucose and cycloheximide resistant mutant derivative of Kluyveromyces marxianus PPY 125", "token_count": 54, "char_count": 154, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:30.900156", "source": { "split": "train_shard_00001", "doc_id": 3767 }, "chunk_id": "train_shard_00001_3767_0", "global_id": 10995 }, { "text": "Campylobacter jejuni is a major foodborne pathogen and common cause of bacterial enteritis worldwide. A total of 622 C. jejuni isolates recovered from food animals and retail meats in the United States through the National Antimicrobial Resistance Monitoring System between 2013 and 2017 were sequenced using an Illumina MiSeq. Sequences were combined with WGS data of 222 human isolates downloaded from NCBI and analyzed by core genome multilocus sequence typing (cgMLST) and traditional MLST. cgMLST allelic difference (AD) thresholds of 0, 5, 10, 25, 50, 100 and 200 identified 828, 734, 652, 543, 422, 298 and 197 cgMLST types among the 844 isolates, respectively, and traditional MLST identified 174 ST. The cgMLST scheme allowing an AD of 200 (cgMLST200) revealed strong correlation with MLST. cgMLST200 showed 40.5% retail chicken isolates, 56.5% swine, 77.4% dairy cattle and 78.9% beef cattle isolates shared cgMLST sequence type with human isolates. All ST-8 had the same cgMLST200 type (cgMLST200-12) and 74.3% of ST-8 and 75% cgMLST200-12 were confirmed as sheep abortion virulence clones by PorA analysis", "token_count": 425, "char_count": 1186, "word_count": 172, "semantic_coherence": 1, "information_density": 0.7384, "quality_score": 0.8692, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:31.537078", "source": { "split": "train_shard_00001", "doc_id": 3768 }, "chunk_id": "train_shard_00001_3768_0", "global_id": 10996 }, { "text": "Twenty-nine acquired resistance genes, including 21 alleles of blaOXA, tetO, aph(3')-IIIa, ant(6)-Ia, aadE, aad9, aph(2')-Ig, aph(2')-Ih, sat4 plus mutations in gyrA, 23SrRNA and L22 were identified. Resistance genotypes were strongly linked with cgMLST200 type for certain groups including 12/12 cgMLST200-510 with the A103V substitution in L22 and 10/11 cgMLST200-608 with the T86I GyrA substitution associated with macrolide and quinolone resistance, respectively. In summary, the cgMLST200 threshold scheme combined with resistance genotype information could provide an excellent subtyping scheme for source attribution of human C. jejuni infections.\n\nCore Genome Multilocus Sequence Typing for Food Animal Source Attribution of Human Campylobacter jejuni Infections.", "token_count": 344, "char_count": 910, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7327, "quality_score": 0.8663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:32.106558", "source": { "split": "train_shard_00001", "doc_id": 3768 }, "chunk_id": "train_shard_00001_3768_1", "global_id": 10997 }, { "text": "Despite insights gained through experimental models, the set of bacterial genes important for human infection is unclear for many of our most threatening pathogens. Klebsiella pneumoniae is a leading cause of health care-associated infections (HAIs) and commonly colonizes hospitalized patients, but the factors that determine whether a particular isolate causes disease or remains a colonizer are poorly understood. To identify bacterial genes associated with K. pneumoniae infection, a case-control study was performed comparing infected and asymptomatic colonized patients. Comparative bacterial genomics was combined with a conditional logit model that identified patient factors differentiating cases from controls. This method identified five gene loci associated with infection after adjustment for patient factors, including a psicose sugar utilization locus that was validated as a fitness factor during mouse lung infection. These results indicate that bacterial genome-wide association studies of patients can identify loci associated with HAIs and important in infection models. IMPORTANCE Klebsiella pneumoniae is a common cause of infections in the health care setting. This work supports a paradigm for K. pneumoniae pathogenesis where the accessory genome, composed of genes present in some but not all isolates, influences whether a strain causes infection or asymptomatic colonization, after accounting for patient-level factors. Identification of patients at high risk of infection could allow interventions to prevent or rapidly treat K. pneumoniae infections.\n\nIdentification of Pathogenicity-Associated Loci in Klebsiella pneumoniae from Hospitalized Patients.", "token_count": 353, "char_count": 1689, "word_count": 228, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:32.680365", "source": { "split": "train_shard_00001", "doc_id": 3769 }, "chunk_id": "train_shard_00001_3769_0", "global_id": 10998 }, { "text": "Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree", "token_count": 507, "char_count": 1760, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "ST8016", "ST11", "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:33.337615", "source": { "split": "train_shard_00001", "doc_id": 3770 }, "chunk_id": "train_shard_00001_3770_0", "global_id": 10999 }, { "text": "In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004-2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.\n\nSerotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004-2019.", "token_count": 192, "char_count": 736, "word_count": 94, "semantic_coherence": 1, "information_density": 0.6809, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:33.784690", "source": { "split": "train_shard_00001", "doc_id": 3770 }, "chunk_id": "train_shard_00001_3770_1", "global_id": 11000 }, { "text": "Trichoderma brevicompactum produces trichodermin, a simple trichothecene-type toxin that shares the first steps of the sesquiterpene biosynthetic pathway with other phytotoxic trichothecenes from Fusarium spp. Trichodiene synthase catalyses the conversion of farnesyl pyrophosphate to trichodiene and it is encoded by the tri5 gene that was cloned and analysed functionally by homologous overexpression in T. brevicompactum. tri5 expression was up-regulated in media with glucose, H(2)O(2) or glycerol. tri5 repression was observed in cultures supplemented with the antioxidants ferulic acid and tyrosol. Acetone extracts of tri5-overexpressing transformants displayed higher antifungal activity than those from the wild-type. Chromatographic and spectroscopic analyses revealed that tri5 overexpression led to an increased production of trichodermin and tyrosol. Agar diffusion assays with these two purified metabolites from the tri5-overexpressing transformant T. brevicompactum Tb41tri5 showed that only trichodermin had antifungal activity against Saccharomyces cerevisiae, Kluyveromyces marxianus, Candida albicans, Candida glabrata, Candida tropicalis and Aspergillus fumigatus, in most cases such activity being higher than that observed for amphotericin B and hygromycin. Our results point to the significant role of tri5 in the production of trichodermin and in the antifungal activity of T. brevicompactum.\n\nOverexpression of the trichodiene synthase gene tri5 increases trichodermin production and antimicrobial activity in Trichoderma brevicompactum.", "token_count": 447, "char_count": 1563, "word_count": 200, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:34.410665", "source": { "split": "train_shard_00001", "doc_id": 3771 }, "chunk_id": "train_shard_00001_3771_0", "global_id": 11001 }, { "text": "

Objective

Urinary catheters are colonized by a wide range of microorganisms, including numerous yeasts. The catheters are usually colonized by more microbial species forming a community - multispecies biofilm. Catheter colonization usually does not affect the patient's clinical status in any significant way. On the other hand, the biofilm can become a source of endogenous infection and its presence can affect functionality of the catheter and formation of urinary stones. Material a

Methods

A total of 721 urinary catheters were studied. Microorganisms were released from catheters by sonication and subsequently cultured. Their identification was performed with the use of common phenotypic tests, as well as using MALDI TOF. Yeasts whose identification was ambiguous were recognized by sequencing. Biofilm formation was assessed by growth in a microtiter plate.

Results and conclusion

Yeast colonization was proved in 244 urinary catheters. However, a total of 274 yeast strains were isolated. Most of them occurred together with other yeast species and/or bacteria on the catheters, producing multispecies biofilm there. The most frequent species was Candida albicans (a total of 144 isolated strains), followed by Candida glabrata (41), Candida tropicalis (41) and Candida parapsilosis sensu stricto (14). Other isolated species were as follows: Candida kefyr (10), Candida krusei (9), Candida fabianii (6), Candida lusitaniae (5), Candida dubliniensis (3) and Saccharomyces cerevisiae (one case). Most of the yeasts rather readily formed a firmly adhering biofilm layer on artificial surfaces.\n\n[Yeast colonization of urinary catheters and the significance of biofilm formation].", "token_count": 445, "char_count": 1710, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:35.043888", "source": { "split": "train_shard_00001", "doc_id": 3772 }, "chunk_id": "train_shard_00001_3772_0", "global_id": 11002 }, { "text": "Eusocial bees (such as honey bees and bumble bees) harbor core gut microbiomes that are transmitted through social interaction between nestmates. Carpenter bees are not eusocial; however, recent microbiome analyses found that Xylocopa species harbor distinctive core gut microbiomes. In this study, we analyzed the gut microbiomes of three Xylocopa species in Japan between 2016 and 2021 by V1 to V2 region-based 16S rDNA amplicon sequencing, and 14 candidate novel species were detected based on the full-length 16S rRNA gene sequences. All Xylocopa species harbor core gut microbiomes consisting of primarily lactic acid bacteria (LAB) that were phylogenetically distant from known species. Although they were difficult to cultivate, two LAB species from two different Xylocopa species were isolated by supplementing bacterial culture supernatants. Both genomes exhibited an average LAB genome size with a large set of genes for carbohydrate utilization but lacked genes to synthesize an essential coenzyme NAD, which is unique among known insect symbionts. Our findings of phylogenetically distinct core LAB of NAD auxotrophy reflected the evolution of Xylocopa-restricted bacteria retention and maintenance through vertical transmission of microbes during solitary life. We propose five candidate novel species belonging to the families Lactobacillaceae and Bifidobacteriaceae, including a novel genus, and their potential functions in carbohydrate utilization. IMPORTANCE Recent investigations found unique microbiomes in carpenter bees, but the description of individual microbes, including isolation and genomics, remains largely unknown. Here, we found that the Japanese Xylocopa species also harbor core gut microbiomes. Although most of them were difficult to isolate a pure colony, we successfully isolated several strains", "token_count": 484, "char_count": 1882, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:35.697617", "source": { "split": "train_shard_00001", "doc_id": 3773 }, "chunk_id": "train_shard_00001_3773_0", "global_id": 11003 }, { "text": "We performed whole-genome sequencing of the isolated candidate novel species and found that the two Lactobacillaceae strains belonging to the Xylocopa-specific novel LAB clade lack the genes for synthesizing NAD, a coenzyme central to metabolism in all living organisms. Here, we propose a novel genus for the two LAB species based on very low 16S rRNA gene sequence similarities and genotypic characters.\n\nSymbiosis of Carpenter Bees with Uncharacterized Lactic Acid Bacteria Showing NAD Auxotrophy.", "token_count": 141, "char_count": 507, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7973, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:36.121926", "source": { "split": "train_shard_00001", "doc_id": 3773 }, "chunk_id": "train_shard_00001_3773_1", "global_id": 11004 }, { "text": "

Key message

This study highlights the agronomic potential of rare introgressions, as demonstrated by a major QTL for powdery mildew resistance on chromosome 7D. It further shows evidence for inter-homoeologue recombination in wheat. Agriculturally important genes are often introgressed into crops from closely related donor species or landraces. The gene pool of hexaploid bread wheat (Triticum aestivum) is known to contain numerous such \"alien\" introgressions. Recently established high-quality reference genome sequences allow prediction of the size, frequency and identity of introgressed chromosome regions. Here, we characterise chromosomal introgressions in bread wheat using exome capture data from the WHEALBI collection. We identified 24,981 putative introgression segments of at least 2 Mb across 434 wheat accessions. Detailed study of the most frequent introgressions identified T. timopheevii or its close relatives as a frequent donor species. Importantly, 118 introgressions of at least 10 Mb were exclusive to single wheat accessions, revealing that large populations need to be studied to assess the total diversity of the wheat pangenome. In one case, a 14 Mb introgression in chromosome 7D, exclusive to cultivar Pamukale, was shown by QTL mapping to harbour a recessive powdery mildew resistance gene. We identified multiple events where distal chromosomal segments of one subgenome were duplicated in the genome and replaced the homoeologous segment in another subgenome. We propose that these examples are the results of inter-homoeologue recombination. Our study produced an extensive catalogue of the wheat introgression landscape, providing a resource for wheat breeding. Of note, the finding that the wheat gene pool contains numerous rare, but potentially important introgressions and chromosomal rearrangements has implications for future breeding.\n\nAnalysis of a global wheat panel reveals a highly diverse introgression landscape and provides evidence for inter-homoeologue chromosomal recombination.", "token_count": 482, "char_count": 2040, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6281, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:36.772781", "source": { "split": "train_shard_00001", "doc_id": 3774 }, "chunk_id": "train_shard_00001_3774_0", "global_id": 11005 }, { "text": "The emergence of multidrug-resistant Pseudomonas spp. in the clinical settings has heightened public awareness. Here, we described the genomic characteristics of a P. putida isolate co-carrying five β-lactam resistance genes recovered from a urinary tract infection in China. Whole-genome sequencing was performed using Illumina NovaSeq 6000 and Oxford Nanopore MinION platforms. The genome sequence was annotated and further subjected to identify the sequence type (ST), antibiotic resistance and virulence genes. Phylogenetic analysis of 193 P. putida strains stored in NCBI public database based on core genome single nucleotide polymorphism (cgSNP) strategy were also performed and visualized. Our study indicated that P. putida PP_2463 was resistant to a wide range of antimicrobial agents tested, including aminoglycosides, carbapenems and fluoroquinolones. The complete genome sequence of P. putida PP_2463 is made up of one chromosome and two plasmids, which could be assigned to a new sequence type (ST) 148. The co-occurrence of β-lactam resistance genes bla IPM-15, bla PME-1, bla CARB-2, and bla NDM-1 were first identified in P. putida, and a novel β-lactamase gene located in the chromosome were among the antimicrobial resistance genes discovered. The closest relative of P. putida PP_2463 was identified in 2012 from a urine sample in China, with a difference of 143 SNPs", "token_count": 479, "char_count": 1508, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:37.416406", "source": { "split": "train_shard_00001", "doc_id": 3775 }, "chunk_id": "train_shard_00001_3775_0", "global_id": 11006 }, { "text": "Along with the presence of multiple β-lactamase genes and mobile genetic elements, the multidrug-resistant phenotype suggests a significant potential as an antibiotic resistance reservoir for Pseudomonas spp.\n\nFirst Identification of a Multidrug-Resistant Pseudomonas putida Co-Carrying Five β-Lactam Resistance Genes Recovered from a Urinary Tract Infection in China.", "token_count": 108, "char_count": 382, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:37.796213", "source": { "split": "train_shard_00001", "doc_id": 3775 }, "chunk_id": "train_shard_00001_3775_1", "global_id": 11007 }, { "text": "

Justification

The frequency of candidiasis has increased dramatically in recent years. Candida albicans is the most common species. However, other species which are pathogenic and resistant to usual antifungal agents beginning to emerge. These include Candida dubliniensis and Candida africana, which share morphological similarities with Candida albicans. Thus, it is of interest to correctly identify the fungal isolates.

Objective

To seek these new species among Candida strains isolated in Dakar.

Material and methods

Oropharyngeal and vaginal swabs were performed at Fann Universitary Hospital in Dakar. The strains were identified by the germ tube test, the chlamydospore production test and an auxanogram. Then identification by PCR targeting the hyphal wall protein 1(hwp1) gene, was performed for the discrimination between Candida albicans, Candida dubliniensis and Candida africana.

Results

In total, 243 yeasts were isolated from samples including 231 in vaginal swab and 12 in oropharyngeal swab. Species identified by phenotypic methods are Candida albicans, which is the most frequent, Candida tropicalis, Candida glabrata, Candida dubliniensis, Candida kefyr and Candida lusitaniae. PCR performed on the 150 strains germ tube test positive identifies three Candida africana, 109 Candida albicans and no strain of Candida dubliniensis.

Conclusion

This study isolates Candida africana for the first time in Senegal. Further studies on a larger sample will better know the actual proportion of these three species among the isolated yeasts.\n\n[Identification of three Candida africana strains in Senegal].", "token_count": 447, "char_count": 1653, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6081, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:38.431868", "source": { "split": "train_shard_00001", "doc_id": 3776 }, "chunk_id": "train_shard_00001_3776_0", "global_id": 11008 }, { "text": "A lysine aminopeptidase was purified from the yeast Kluyveromyces marxianus. This enzyme was purified 100-fold from a soluble extract obtained at 100,000g. The purification procedure consisted in fractionated precipitation with ammonium sulfate and five chromatography steps. The native enzyme had a molecular mass of 46 kDa assessed through gel filtration. This aminopeptidase depicted an optimal pH of 7.0 and was stable at a pH range of 4-8, its optimal temperature was 45 degrees C and the enzyme became unstable at temperatures above 55 degrees C. The isoelectric point of the purified enzyme was 4.4. Michaelis constant and Vmax for L-lysine-p-nitroanilide were 0.33 mM and 2.2 mM min(-1) per milligram of protein, respectively. The enzyme was strongly inhibited by bestatin, o-phenanthroline and, to a lesser extent, by EDTA, suggesting that this enzyme is a metalloprotease. Our results suggest that the lysine aminopeptidase from Kluyveromyces marxianus might be of biotechnological relevance.\n\nPurification and characterization of a lysine aminopeptidase from Kluyveromyces marxianus.", "token_count": 336, "char_count": 1094, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6352, "quality_score": 0.8176, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:38.996849", "source": { "split": "train_shard_00001", "doc_id": 3777 }, "chunk_id": "train_shard_00001_3777_0", "global_id": 11009 }, { "text": "

Background

Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood.

Results

Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states.

Conclusions

Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.\n\nTurnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers.", "token_count": 267, "char_count": 1268, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:39.544759", "source": { "split": "train_shard_00001", "doc_id": 3778 }, "chunk_id": "train_shard_00001_3778_0", "global_id": 11010 }, { "text": "Helicobacter pylori have coevolved with mankind since its origins, adapting to different human groups. In America H. pylori has evolved in several subpopulations specific for regions or even countries. In this study we analyzed the genome of 163 Colombian strains along with 1,113 strains that represent worldwide H. pylori populations to better discern the ancestry and adaption to Colombian people. Population structure was inferred with FineStructure and chromosome painting identifying the proportion of ancestries in Colombian isolates. Phylogenetic relationship was analyzed using the SNPs present in the core genome. Also, a Fst analysis was done to identify the gene variants with the strongest fixation in the identified Colombian subpopulations in relation to their parent population hspSWEurope . Worldwide, population structure analysis allowed the identification of two Colombian subpopulations, the previously described hspSWEuropeColombia and a novel subpopulation named hspColombia . In addition, three subgroups of H. pylori were identified within hspColombia that follow their geographic origin. The Colombian H. pylori subpopulations represent an admixture of European, African and Native indigenous ancestry; although some genomes showed a high proportion of self-identity, suggesting a strong adaption to these mestizo Colombian groups. The Fst analysis identified 82 SNPs significantly fixed in 26 genes of the hspColombia subpopulation that encode mainly for outer membrane proteins and proteins involved in central metabolism. The strongest fixation indices were identified in genes encoding the membrane proteins HofC, HopE, FrpB-4 and Sialidase A. These findings demonstrate that H. pylori has evolved in Colombia to give rise to subpopulations following a geographical structure, evolving to an autochthonous genetic pool, drive by a positive selective pressure especially on genes encoding for outer membrane proteins.\n\nSelective pressure on membrane proteins drives the evolution of Helicobacter pylori Colombian subpopulations", "token_count": 470, "char_count": 2063, "word_count": 286, "semantic_coherence": 1, "information_density": 0.5734, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:40.185402", "source": { "split": "train_shard_00001", "doc_id": 3779 }, "chunk_id": "train_shard_00001_3779_0", "global_id": 11011 }, { "text": "The study was performed to provide an overview of the molecular epidemiology of carbapenem-resistant Acinetobacter baumannii in Afghanistan isolated by the German military medical service during the Afghanistan conflict. A total of 18 isolates were collected between 2012 and 2018 at the microbiological laboratory of the field hospital in Camp Marmal near Mazar-e Sharif, Afghanistan, from Afghan patients. The isolates were subjected to phenotypic and genotypic differentiation and antimicrobial susceptibility testing as well as to a core genome multi-locus sequence typing (cgMLST) approach based on whole-genome next-generation sequence (wgNGS) data. Next to several sporadic isolates, four transmission clusters comprising strains from the international clonal lineages IC1, IC2, and IC9 were identified. Acquired carbapenem resistance was due to blaOXA-23 in 17/18 isolates, while genes mediating resistance against sulfonamides, macrolides, tetracyclines, and aminoglycosides were frequently identified as well. In conclusion, the assessment confirmed both the frequent occurrence of A. baumannii associated with outbreak events and a variety of different clones in Afghanistan. The fact that acquired carbapenem resistance was almost exclusively associated with blaOXA-23 may facilitate molecular resistance screening based on rapid molecular assays targeting this resistance determinant.\n\nMolecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Strains Isolated at the German Military Field Laboratory in Mazar-e Sharif, Afghanistan.", "token_count": 419, "char_count": 1615, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6373, "quality_score": 0.8186, "entities": { "genes": [ "IC2", "IC1", "IC9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:40.819906", "source": { "split": "train_shard_00001", "doc_id": 3780 }, "chunk_id": "train_shard_00001_3780_0", "global_id": 11012 }, { "text": "Salmonella enterica is a major foodborne pathogen, and contaminated beef products have been identified as the primary source of Salmonella -related outbreaks. Pathogenicity and antibiotic resistance of Salmonella are highly serotype- and subpopulation-specific, which makes it essential to understand high-resolution Salmonella population dynamics in cattle. Time of year, source of cattle, pen, and sample type(i.e., feces, hide or lymph nodes) have previously been identified as important factors influencing the serotype distribution of Salmonella (e.g., Anatum, Lubbock, Cerro, Montevideo, Kentucky, Newport, and Norwich) that were isolated from a longitudinal sampling design in a research feedlot. In this study, we performed high-resolution genomic comparisons of Salmonella isolates within each serotype using both single-nucleotide polymorphism (SNP)-based maximum likelihood phylogeny and hierarchical clustering of core-genome multi-locus sequence typing. The importance of the aforementioned features on clonal Salmonella expansion was further explored using a supervised machine learning algorithm. In addition, we identified and compared the resistance genes, plasmids, and pathogenicity island profiles of the isolates within each sub-population. Our findings indicate that clonal expansion of Salmonella strains in cattle was mainly influenced by the randomization of block and pen, as well as the origin/source of the cattle; that is, regardless of sampling time and sample type (i.e., feces, lymph node or hide). Further research is needed concerning the role of the feedlot pen environment prior to cattle placement to better understand carry-over contributions of existing strains of Salmonella and their bacteriophages.

Importance

Salmonella serotypes isolated from outbreaks in humans can also be found in beef cattle and feedlots. Virulence factors and antibiotic resistance are among the primary defense mechanisms of Salmonella , and are often associated with clonal expansion. This makes understanding the subpopulation dynamics of Salmonella in cattle critical for effective mitigation. There remains a gap in the literature concerning subpopulation dynamics within Salmonella serotypes in feedlot cattle from the beginning of feeding up until slaughter", "token_count": 507, "char_count": 2289, "word_count": 312, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:41.517297", "source": { "split": "train_shard_00001", "doc_id": 3781 }, "chunk_id": "train_shard_00001_3781_0", "global_id": 11013 }, { "text": "Here, we explore Salmonella population dynamics within each serotype using core genome phylogeny and hierarchical classifications. We used machine-learning to quantitatively parse the relative importance of both hierarchical and longitudinal clustering among cattle host samples. Our results reveal that Salmonella populations in cattle are highly clonal over a 6-month study period, and that clonal dissemination of Salmonella in cattle is mainly influenced spatially by experimental block and pen, as well by the geographical origin of the cattle.\n\nHigh-resolution genomic comparisons within Salmonella enterica serotypes derived from beef feedlot cattle: parsing the roles of cattle source, pen, animal, sample type and production period", "token_count": 164, "char_count": 747, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7745, "quality_score": 0.8873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:41.977285", "source": { "split": "train_shard_00001", "doc_id": 3781 }, "chunk_id": "train_shard_00001_3781_1", "global_id": 11014 }, { "text": "The gut microbiome is a potentially important mechanism that links prenatal disaster exposures with increased disease risks. However, whether prenatal disaster exposures are associated with alterations in the infant's gut microbiome remains unknown. We established a birth cohort study named Hurricane as the Origin of Later Alterations in Microbiome (HOLA) after Hurricane Maria struck Puerto Rico in 2017. We enrolled vaginally born Latino term infants aged 2 to 6 months, including n = 29 infants who were exposed in utero to Hurricane Maria in Puerto Rico and n = 34 infants who were conceived at least 5 months after the hurricane as controls. Shotgun metagenomic sequencing was performed on infant stool swabs. Infants exposed in utero to Hurricane Maria had a reduced diversity in their gut microbiome compared to the control infants, which was mainly seen in the exclusively formula-fed group (P = 0.02). Four bacterial species, including Bacteroides vulgatus, Clostridium innocuum, Bifidobacterium pseudocatenulatum, and Clostridium neonatale, were depleted in the exposure group compared to the control group. Compositional differences in the microbial community and metabolic genes between the exposure and control groups were significant, which were driven by the formula feeding group (P = 0.02 for the microbial community and P = 0.008 for the metabolic genes). Metabolic modules involved in carbohydrate metabolism were reduced in the exposure group. Prenatal maternal exposure to Hurricane Maria was associated with a reduced gut commensal and an altered microbial composition and metabolic potential in the offspring's gut. Breastfeeding can adjust the composition of the gut microbiomes of exposed infants. IMPORTANCE Climate change is a serious issue that is affecting human health", "token_count": 495, "char_count": 1877, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5651, "quality_score": 0.7825, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:42.674216", "source": { "split": "train_shard_00001", "doc_id": 3782 }, "chunk_id": "train_shard_00001_3782_0", "global_id": 11015 }, { "text": "With more frequent and intense weather disasters due to climate change, there is an urgent need to evaluate and understand the impacts of prenatal disaster exposures on the offspring. The prenatal stage is a particularly vulnerable stage for disease origination. However, the impact of prenatal weather disaster exposures on the offspring's gut microbiome has not been evaluated. Our HOLA study starts to fill this knowledge gap and provides novel insights into the microbiome as a mechanism that links prenatal disaster exposures with elevated disease risks. Our major finding that reduced microbial diversity and altered metabolic capacity are associated with prenatal hurricane exposures warrants further studies to evaluate the impact of weather disasters on the unborn.\n\nInfants exposed in utero to Hurricane Maria have gut microbiomes with reduced diversity and altered metabolic capacity.", "token_count": 191, "char_count": 902, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6288, "quality_score": 0.8144, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:43.153621", "source": { "split": "train_shard_00001", "doc_id": 3782 }, "chunk_id": "train_shard_00001_3782_1", "global_id": 11016 }, { "text": "

Background

The gut microbiome is believed to contribute to bloodstream infection (BSI) via translocation of dominant gut bacteria in vulnerable patient populations. However, conclusively linking gut and blood organisms requires stringent approaches to establish strain-level identity.

Methods

We enrolled a convenience cohort of critically ill patients and investigated 86 bloodstream infection episodes that occurred in 57 patients. Shotgun metagenomic sequencing was used to define constituents of their gut microbiomes, and whole genome sequencing and assembly was done on 23 unique bloodstream isolates that were available from 21 patients. Whole genome sequences were downloaded from public databases and used to establish sequence-identity distribution and define thresholds for unrelated genomes of BSI species. Gut microbiome reads were then aligned to whole genome sequences of the cognate bloodstream isolate and unrelated database isolates to assess identity.

Results

Gut microbiome constituents matching the bloodstream infection species were present in half of BSI episodes, and represented >30% relative abundance of gut sequences in 10% of episodes. Among the 23 unique bloodstream organisms that were available for whole genome sequencing, 14 were present in gut at the species level. Sequence alignment applying defined thresholds for identity revealed that 6 met criteria for identical strains in blood and gut, but 8 did not. Sequence identity between BSI isolates and gut microbiome reads was more likely when the species was present at higher relative abundance in gut.

Conclusion

In assessing potential gut source for BSI, stringent sequence-based approaches are essential to determine if organisms responsible for BSI are identical to those in gut: of 14 evaluable patients in which the same species was present in both sites, they were identical in 6/14, but were non-identical in 8/14 and thus inconsistent with gut source. This report demonstrates application of sequencing as a key tool to investigate infection tracking within patients.\n\nTracking gut microbiome and bloodstream infection in critically ill adults.", "token_count": 484, "char_count": 2170, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5296, "quality_score": 0.7648, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:43.800275", "source": { "split": "train_shard_00001", "doc_id": 3783 }, "chunk_id": "train_shard_00001_3783_0", "global_id": 11017 }, { "text": "For expression of the alpha-galactosidase gene from Cyamopsis tetragonoloba in Kluyveromyces marxianus CBS 6556 we have used the promoter of the homologous inulinase-encoding gene (INU1). The INU1 gene has been cloned and sequenced and the coding region shows an identity of 59% with the Saccharomyces cerevisiae invertase gene (SUC2). In the 5'-flanking region of INU1 we found a sequence (TAAATCCGGGG) that perfectly matches to the MIG1 binding consensus sequence (WWWWTSYGGGG) of the S. cerevisiae GAL1, GAL4 and SUC2 genes. Using the K. marxianus INU1 promoter and prepro-signal sequence, we obtained a high alpha-galactosidase production level (153 mg/l) and a secretion efficiency of 99%. Both the production level and the secretion efficiency were significantly reduced when the INU1 pro-peptide was deleted. With either the S. cerevisiae PGK or GAL7 promoter we could obtain only low alpha-galactosidase production levels (2 mg/l).\n\nExpression of an alpha-galactosidase gene under control of the homologous inulinase promoter in Kluyveromyces marxianus.", "token_count": 317, "char_count": 1061, "word_count": 154, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [ "GAL4", "GAL1", "SUC2", "MIG1", "GAL7", "INU1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:44.368915", "source": { "split": "train_shard_00001", "doc_id": 3784 }, "chunk_id": "train_shard_00001_3784_0", "global_id": 11018 }, { "text": "The effects of Nd:YAG laser irradiations at different power settings on several oral pathogens were evaluated. A total of 252 dentin samples were divided into seven groups consisting of 36 dentin specimens each. In each group, 9 of the 36 specimens were used as controls, thereby including a control in every group. The remaining 27 specimens were divided into three subgroups consisting of nine specimens according to different Nd:YAG laser settings (1.5, 1.8, and 2 W). Each group was inoculated on the nonpulpal side with one of the following microorganisms: Candida glabrata, Candida tropicalis, Candida krusei, Candida sake, Candida lusitaniae, Candida kefyr, and Rhodotorula mucilaginosa. The following irradiation procedure was used: the specimens were irradiated on the bacteria-free side (the side consisting of the pulpal wall) using contact mode under the constant scanning movement of the optical fiber at an angle of 10°. One lasing cycle consisted of four irradiation cycles of 10 s each, with 15-s intervals in between each irradiation cycle. The remainder of the controls and the lased specimens of each group were prepared for the microbiological investigation. After incubation for 24 h at 37 °C, the colonies were counted, and the total number of surviving microorganisms was statistically assessed. Microorganisms irradiated with Nd:YAG laser at power settings 2 W, 15 pps did not survive. Although there was a significant reduction of microorganisms at 1.5 and 1.8 W, when comparing Nd:YAG laser irradiation with the control group, sterilization did not occur.\n\nDetermination of the effect of Nd:YAG laser irradiation through dentinal tubules on several oral pathogens.", "token_count": 448, "char_count": 1690, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5598, "quality_score": 0.7799, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:45.012184", "source": { "split": "train_shard_00001", "doc_id": 3785 }, "chunk_id": "train_shard_00001_3785_0", "global_id": 11019 }, { "text": "

Background

Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae .

Results

Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro . Whereas, robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together, and not either alone. D. pigrum L-lactic-acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum encoded a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions.

Conclusions

These new insights into D. pigrum ’s functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments.\n\nDolosigranulum pigrum cooperation and competition in human nasal microbiota", "token_count": 461, "char_count": 1775, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6183, "quality_score": 0.8091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:45.654059", "source": { "split": "train_shard_00001", "doc_id": 3786 }, "chunk_id": "train_shard_00001_3786_0", "global_id": 11020 }, { "text": "

Background

Vancomycin-resistant Enterococcus faecium (VREfm) strains are one of the most important pathogens causing nosocomial infections in Germany. Due to limited treatment options and an increased risk for acquisition in immunocompromised children, surveillance to monitor occurrence of VREfm in paediatric clinical facilities is of critical importance. Following an unusual accumulation of VREfm positive patients between April 2019 and August 2020 at Dr. von Hauner Children's Hospital in Munich, Germany, our study aimed to identify dynamics and routes of transmission, and analyse the affected population in view of previously described host risk factors for VREfm colonisation or infection.

Methods

The hospital database was used to collect epidemiological and clinical data of VREfm cases. Descriptive statistical analyses were conducted to outline patient characteristics and depict possible differences between VREfm-colonised and -infected children. An outbreak investigation determining genetic relatedness among VREfm isolates was performed by core genome multilocus sequence typing (cgMLST). To examine potential transmission pathways, results of genome analysis were compared with epidemiological and clinical data of VREfm positive patients.

Results

VREfm acquisition was documented in a total of 33 children (< 18 years). Seven VREfm-colonised patients (21.2%), especially those with a haemato-oncological disease (4/7; p = 0.011), showed signs of clinical infection. cgMLST analysis revealed seven distinct clusters, demonstrating a possible connection within each clonal lineage. Additional eight singletons were identified. Comparison with epidemiological and clinical data provided strong evidence for a link between several VREfm positive patients within the hospital.

Conclusions

A nosocomial spread-at least in part-was the most likely reason for the unusual accumulation of VREfm cases. The study highlights that there is a constant need to increase efforts in hygiene measures, infection control and antibiotic stewardship to combat VREfm transmission events within German paediatric hospitals", "token_count": 499, "char_count": 2150, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:46.308957", "source": { "split": "train_shard_00001", "doc_id": 3787 }, "chunk_id": "train_shard_00001_3787_0", "global_id": 11021 }, { "text": "Continuous monitoring of adherence to respective policies might reduce the occurrence of clustered cases and prevent future outbreaks.\n\nEpidemiological and genetic characteristics of vancomycin-resistant Enterococcus faecium isolates in a University Children's Hospital in Germany: 2019 to 2020.", "token_count": 74, "char_count": 295, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8649, "quality_score": 0.9324, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:46.678039", "source": { "split": "train_shard_00001", "doc_id": 3787 }, "chunk_id": "train_shard_00001_3787_1", "global_id": 11022 }, { "text": "Increasing attention has been paid to the potential probiotic effects of Latilactobacillus sakei. To explore the genetic diversity of L. sakei, 14 strains isolated from different niches (feces, fermented kimchi and meat products) and 54 published strains were compared and analyzed. The results showed that the average genome size and GC content of L. sakei were 1.98Mb and 41.22%, respectively. Its core genome mainly encodes translation and transcription, amino acid synthesis, glucose metabolism and defense functions. L. sakei has an open pan-genomic characteristics, and its pan-gene curve shows an upward trend. L. sakei has open pan-genome feature, and its pan-genome curve is on the rise. The genetic diversity of L. sakei is mainly reflected in carbohydrate utilization, antibiotic tolerance, and immune/competition-related factors, such as clustering regular interval short palindromic repeat sequence (CRISPR)-Cas. The CRISPR system is mainly IIA type, and a few are IIC types. This work provides a basis for the study of this species.\n\nIntegrated Phenotypic-Genotypic Analysis of Latilactobacillus sakei from Different Niches", "token_count": 300, "char_count": 1137, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6727, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:47.242242", "source": { "split": "train_shard_00001", "doc_id": 3788 }, "chunk_id": "train_shard_00001_3788_0", "global_id": 11023 }, { "text": "In fed-batch fermentation by Kluyveromyces marxianus var. marxianus, whey-soluble proteins were converted into oligopeptides. To assess whether bioactive peptides could be produced during whey fermentation, K. marxianus was cultured in batch in deproteinized media containing 5 or 15% (wt/vol) dehydrated whey for 20 h and then was in fed-batch mode for 50 h. After harvesting the biomass (25,000 x g, 15 min), at 6-h intervals, the wort was analyzed to determine protein consumption and oligopeptide production by HPLC. The proteins in the wort showed an oscillatory degradation with a constant increase in the production of oligopeptides. Four major peaks were collected and were analyzed by API mass spectroscopy. Sequences of fermented peptides were compared with sequences of known bioactive peptides. On the basis of their molecular weights, two amino acid sequences were proposed. The presence of sites containing the peptide sequence of beta-lactorphin (YLLF) suggests that these oligopeptides may have antihypertensive properties.\n\nProposing sequences for peptides derived from whey fermentation with potential bioactive sites.", "token_count": 306, "char_count": 1136, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:47.813468", "source": { "split": "train_shard_00001", "doc_id": 3789 }, "chunk_id": "train_shard_00001_3789_0", "global_id": 11024 }, { "text": "The cellular components involved in the hypocholesterolemic activity of Kluyveromyces marxianus YIT 8292 were examined in rats fed on a high-cholesterol diet. Whole cells (KM) were heated at 115 degrees C for 10 minutes and fractionated into water-soluble extract 1 and the insoluble residue (KM-CW). After mechanical disruption by glass beads, KM-CW was separated into the cell wall (KM-W) and water-soluble extract 2. Plasma total cholesterol was decreased by feeding KM-CW or KM-W, but was not changed by feeding extract 1 or extract 2. Feeding KM-CW and KM-W increased the fecal sterol excretion and concentration of short-chain fatty acids (SCFA) in the cecum. The hypocholesterolemic activity of KM-CW was completely abolished by the enzymatic degradation of alpha-mannan and beta-glucan. These results suggest that alpha-mannan and beta-glucan were the major active components of KM, and that its hypocholesterolemic activity may be attributable to the increasing fecal sterol excretion and/or production of SCFA.\n\nEffects of the cell wall of Kluyveromyces marxianus YIT 8292 on the plasma cholesterol and fecal sterol excretion in rats fed on a high-cholesterol diet.", "token_count": 355, "char_count": 1175, "word_count": 176, "semantic_coherence": 1, "information_density": 0.5568, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:48.387299", "source": { "split": "train_shard_00001", "doc_id": 3790 }, "chunk_id": "train_shard_00001_3790_0", "global_id": 11025 }, { "text": "

Background

NDM-producing Acinetobacter baumannii (NDMAb) were reported sporadically worldwide but little is known about the transmission, epidemiology and clinical features of NDMAb-infected patients. The goals of this study were to characterize (1) the epidemiology and clinical features of NDMAb-infected patients; (2) the microbiological and molecular features of NDMAb isolates and (3) the transmission networks of NDMAb within healthcare facilities.

Methods

The study was conducted at the Tel-Aviv Sourasky, Rambam and Sha'are-Zedek Medical centers (TASMC, RMC and SZMC, respectively) in Israel. All cases detected between January 2018 and July 2019 were included. Phylogenetic analysis was based on core genome SNP distances. Clonal transmission was defined according to molecular (≤ 5 SNP) and epidemiological criteria (overlapping hospital stay). NDMAb cases were compared at a ratio of 1:2 with non-NDM carbapenem-resistant A. baumannii (CRAb) cases.

Results

The study included 54 NDMAb-positive out of 857 CRAb patients, including 6/179 (3.3%) in TASMC, 18/441 (4.0%) in SZMC and 30/237 (12.6%) in RMC. Patients infected by NDMAb had similar clinical features and risk factors as patients with non-NDM CRAb. The length-of-stay was higher in NDMAb cases (48.5 days vs. 36 days, respectively, p = 0.097) and the in-hospital mortality was similarly high in both groups. Most isolates (41/54, 76%) were first detected from surveillance culture", "token_count": 460, "char_count": 1471, "word_count": 204, "semantic_coherence": 1, "information_density": 0.701, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:49.029362", "source": { "split": "train_shard_00001", "doc_id": 3791 }, "chunk_id": "train_shard_00001_3791_0", "global_id": 11026 }, { "text": "The majority of isolates harbored the blaNDM-2 gene allele (n = 33), followed by the blaNDM-1 (n = 20) allele and the blaNDM-4 allele (n = 1). The majority of isolates were related within the ST level to other isolates in SZMC and RMC: 17/18 and 27/30 isolates, respectfully. The common ST's were the blaNDM-1 harboring ST-2 (n = 3) and ST-107 (n = 8) in SZMC and the blaNDM-2 harboring ST-103 in SZMC (n = 6) and in RMC (n = 27). All blaNDM alleles were located within a conserved mobile genetic environment flanked by the ISAb125 and IS91 family transposon. Clonal transmission was identified in most hospital-acquired cases in RMC and SZMC.

Conclusion

NDMAb constitutes a minor part of CRAb cases and are clinically similar to non-NDM CRAb. Transmission of NDMAb occurs mostly by clonal spread.\n\nClinical and molecular features of NDM-producing Acinetobacter baumannii in a multicenter study in Israel.", "token_count": 385, "char_count": 978, "word_count": 150, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7933, "entities": { "genes": [ "IS91" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:49.640722", "source": { "split": "train_shard_00001", "doc_id": 3791 }, "chunk_id": "train_shard_00001_3791_1", "global_id": 11027 }, { "text": "To determine which yeasts are present in the naturally fermented milks of China, 69 samples made by the nomads of Tibet were collected from the Tibetan Plateau in China. From these samples, 225 strains of yeast were isolated and identified using conventional microbiological analysis and gene sequencing analysis of the D1/D2 domain of the large subunit (26S) ribosomal DNA. The results showed that the total concentration of yeasts in these samples ranged from 5.01 to 8.97 log10 colony-forming units (CFU)/mL (6.91 ± 1.02 log10 CFU/mL; mean ± SD). The number of cultivable yeasts was higher in the samples from Qinghai (7.55 ± 0.75 log10 CFU/mL) than those from Tibet (6.21 ± 0.79 log10 CFU/mL, P < 0.05). Moreover, there were 15 phylotypes in these 69 samples. Among these phylotypes, Kluyveromyces marxianus (49.3%, frequency percentage), Saccharomyces cerevisiae (62.3%), and Pichia fermentans (46.4%) appeared frequently and can be considered the most common culturable species in naturally fermented milk products. Traditional fermented Mongolian cow milk featured a wide diversity of yeast species, including Issatchenkia orientalis, Kazachstania unisporus, Rhodotorula mucilaginosa, Candida pararugosa, Torulaspora delbrueckii, Geotrichum sp., Kazachstania unisporus, Geotrichum fragrans, Debaryomyces hansenii, Yarrowia lipolytica, Trichosporon gracile, and Pichia membranifaciens. This study provides new data on yeast composition in naturally fermented milk and shows the yeast biodiversity of fermented milk products from the Tibetan Plateau of China.\n\nOccurrence and dominance of yeast species in naturally fermented milk from the Tibetan Plateau of China.", "token_count": 513, "char_count": 1670, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:50.301289", "source": { "split": "train_shard_00001", "doc_id": 3792 }, "chunk_id": "train_shard_00001_3792_0", "global_id": 11028 }, { "text": "A molecular systematic investigation of members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces was performed by using 18S rRNA gene sequence analysis. Our comparative sequence analysis revealed that Brettanomyces anomalus and Brettanomyces bruxellensis were closely related to one another and also to their teleomorphs, Dekkera anomala and Dekkera bruxellensis, respectively. Together with Dekkera custersiana and Dekkera naardenensis, these four species formed a stable and distinct phylogenetic group. The three representative species of the genus Debaryomyces examined (viz., Debaryomyces castellii, Debaryomyces hansenii, and Debaryomyces udenii) were found to be genealogically highly related to each other and exhibited a specific phylogenetic affinity (level of sequence similarity, approximately 99.2%) with Candida guilliermondii (teleomorph, Pichia guilliermondii). Debaryomyces species and C. guilliermondii formed a distinct phylogenetic group, which displayed a significant association with a phylogenetically coherent cluster encompassing Lodderomyces elongisporus, Candida albicans, and four other Candida species. In contrast to the situation with the genera Brettanomyces and Debaryomyces, the genus Kluyveromyces displayed very marked phylogenetic heterogeneity. Kluyveromyces polysporus, the type species of the genus Kluyveromyces, and six other Kluyveromyces species (viz., Kluyveromyces africanus, Kluyveromyces delphensis, Kluyveromyces lodderae, Kluyveromyces thermotolerans, Kluyveromyces waltii, and Kluyveromyces yarrowii) were phylogenetically intermixed with species of the genera Zygosaccharomyces, Saccharomyces, and Torulaspora", "token_count": 477, "char_count": 1701, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5784, "quality_score": 0.7892, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:50.947776", "source": { "split": "train_shard_00001", "doc_id": 3793 }, "chunk_id": "train_shard_00001_3793_0", "global_id": 11029 }, { "text": "In contrast, Kluyveromyces aestuarii, Kluyveromyces dobzhanskii, Kluyveromyces lactis, Kluyveromyces wickerhamii, and three Kluyveromyces marxianus varieties, along with their anamorph, Candida kefyr, formed a highly stable monophyletic group worthy of separate generic status. Kluyveromyces blattae and Kluyveromyces phaffii formed two distinct phylogenetic lines that did not exhibit particularly close affinity with each other or other ascomycetous yeast genera. Our phylogenetic findings are discussed in the context of the results of other genotypic and phenotypic studies.\n\nPhylogenetic relationships among members of the ascomycetous yeast genera Brettanomyces, Debaryomyces, Dekkera, and Kluyveromyces deduced by small-subunit rRNA gene sequences.", "token_count": 218, "char_count": 755, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7447, "quality_score": 0.8723, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:51.411562", "source": { "split": "train_shard_00001", "doc_id": 3793 }, "chunk_id": "train_shard_00001_3793_1", "global_id": 11030 }, { "text": "

Objective

Gut microbiome dysbiosis has previously been reported in spondyloarthritis (SpA) patients and could be critically involved in the pathogenesis of this disorder. The objectives of this study were to further characterize the microbiota structure in SpA patients and to investigate the relationship between dysbiosis and disease activity in light of the putative influence of the genetic background.

Methods

Shotgun sequencing was performed on fecal DNA isolated from stool samples from 2 groups of adult volunteers: SpA patients (n = 102) and healthy controls (n = 63). A subset of the healthy controls comprised the age-matched siblings of patients whose HLA-B27 status was known. Changes in gut microbiota composition were assessed based on species diversity, enterotypes, and taxonomic and functional differences.

Results

Dysbiosis was confirmed in SpA patients as compared to healthy controls. The restriction of microbiota diversity was detected in patients with the most active disease, and the abundance of several bacterial species was correlated with Bath Ankylosing Spondylitis Disease Activity Index score. Among healthy controls, significant differences in microbiota composition were also detected between the HLA-B27-positive and the HLA-B27-negative siblings of SpA patients. We highlighted a decreased abundance of several species of bacteria in SpA patients, especially those bacteria belonging to the Clostridiales order. Among the few species of bacteria showing increased abundance, Ruminococcus gnavus was one of the top differentiating species.

Conclusion

These findings reveal that genetic background and level of disease activity are likely to influence the composition of the gut microbiota of patients with SpA. It may be appropriate for further research on chronic arthritis to focus on these key parameters.\n\nBoth Disease Activity and HLA-B27 Status Are Associated With Gut Microbiome Dysbiosis in Spondyloarthritis Patients.", "token_count": 468, "char_count": 1990, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5438, "quality_score": 0.7719, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:52.055315", "source": { "split": "train_shard_00001", "doc_id": 3794 }, "chunk_id": "train_shard_00001_3794_0", "global_id": 11031 }, { "text": "The maximum volumetric productivity of β-galactosidase by a Kluyveromyces marxianus mutant, grown on lactose/corn steep liquor medium for 3 d, was 150 IU l-1 h-1 which is twice that of the parent organism. During product formation, mutated cells provided more resistance against thermal inactivation.\n\nKinetics of improved productivity of beta-galactosidase by a cycloheximide-resistant mutant of Kluyveromyces marxianus", "token_count": 123, "char_count": 420, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8246, "quality_score": 0.9123, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:52.447367", "source": { "split": "train_shard_00001", "doc_id": 3795 }, "chunk_id": "train_shard_00001_3795_0", "global_id": 11032 }, { "text": "

Objectives

To assess the current prevalence, distribution, and main clonal types of carbapenem-resistant Enterobacterales (CRE) in the United Arab Emirates.

Methods

A total of 504 CRE collected over a 9-month period in 15 hospitals were studied. Antibiotic susceptibility and the presence of common carbapenemase, 16S methylase, and mobile colistin resistance genes were assessed. Selected strains forming larger clusters by pulsed field gel electrophoresis were subjected to whole genome sequencing to identify their sequence types and core genome MLST.

Results

Strains expressing OXA and NDM type carbapenemases and 16S methylases were present in all major hospitals. Considerable interhospital differences were noticed, suggesting the role of specific clones. A total of three major Klebsiella pneumoniae clones (CC14, ST231, and CC147) were identified, accounting for 48.6% of all CRE. All clones were significantly more resistant than sporadic isolates. CC14 strains exhibited a significant association with Emirati patients.

Conclusions

Nearly half of CRE infections in the country are due to a limited number of clones. The data indicate the possibility of interhospital transmission, combined in some hospitals with inadequate stewardship practices. The study also revealed an association of the largest, most resistant clone (CC14) with Emirati patients. The specific reasons for it should be clarified by further investigations.\n\nThe first nationwide surveillance of carbapenem-resistant Enterobacterales in the United Arab Emirates - increased association of Klebsiella pneumoniae CC14 clone with Emirati patients.", "token_count": 431, "char_count": 1654, "word_count": 220, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [ "ST231", "CC14", "CC147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:53.078052", "source": { "split": "train_shard_00001", "doc_id": 3796 }, "chunk_id": "train_shard_00001_3796_0", "global_id": 11033 }, { "text": "

Background

In the past decade, several countries have seen gradual replacement of endemic multi-resistant healthcare-associated methicillin-resistant Staphylococcus aureus (MRSA) with clones that are more susceptible to antibiotic treatment. One example is Singapore, where MRSA ST239, the dominant clone since molecular profiling of MRSA began in the mid-1980s, has been replaced by ST22 isolates belonging to EMRSA-15, a recently emerged pandemic lineage originating from Europe.

Results

We investigated the population structure of MRSA in Singaporean hospitals spanning three decades, using whole genome sequencing. Applying Bayesian phylogenetic methods we report that prior to the introduction of ST22, the ST239 MRSA population in Singapore originated from multiple introductions from the surrounding region; it was frequently transferred within the healthcare system resulting in a heterogeneous hospital population. Following the introduction of ST22 around the beginning of the millennium, this clone spread rapidly through Singaporean hospitals, supplanting the endemic ST239 population. Coalescent analysis revealed that although the genetic diversity of ST239 initially decreased as ST22 became more dominant, from 2007 onwards the genetic diversity of ST239 began to increase once more, which was not associated with the emergence of a sub-clone of ST239. Comparative genomic analysis of the accessory genome of the extant ST239 population identified that the Arginine Catabolic Mobile Element arose multiple times, thereby introducing genes associated with enhanced skin colonization into this population.

Conclusions

Our results clearly demonstrate that, alongside clinical practice and antibiotic usage, competition between clones also has an important role in driving the evolution of nosocomial pathogen populations.\n\nEvolutionary dynamics of methicillin-resistant Staphylococcus aureus within a healthcare system.", "token_count": 447, "char_count": 1954, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6732, "quality_score": 0.8366, "entities": { "genes": [ "ST22", "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:53.739645", "source": { "split": "train_shard_00001", "doc_id": 3797 }, "chunk_id": "train_shard_00001_3797_0", "global_id": 11034 }, { "text": "Abstract

Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the pathogenic agents. In this study, metagenomic sequencing was conducted to investigate the microbiome of the vitreous of an endophthalmitis patient whose disease progressed rapidly and was accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome. The main antibiotic resistance gene (ARG) types included beta-lactam, macrolide-lincosamide-streptogramin, and multidrug resistance genes. Additionally, the metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was isolated. The average nucleotide identities (ANI) and DNA–DNA hybridization (DDH) analysis between the genomes of Streptococcus sp. v1. nov and related species revealed that Streptococcus sp. v1. nov belongs to a new species. Pan/core genome analysis for Streptococcus sp. v1. nov. and tetra correlation search (TCS) top 25 hit strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to the ABC transporter system, which could indicate the unique virulence and pathogenic potential of Streptococcus sp. v1. nov. In addition, 7 virulence factors were identified in total, and most of them were classified as “offensive virulence factors”. The high pathogenicity of Streptococcus sp. v1. nov. could explain the patient's rapid disease progression. Our study first isolated an ocular pathogen with high virulence based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patients in the future.

", "token_count": 528, "char_count": 1956, "word_count": 250, "semantic_coherence": 1, "information_density": 0.604, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:54.425704", "source": { "split": "train_shard_00001", "doc_id": 3798 }, "chunk_id": "train_shard_00001_3798_0", "global_id": 11035 }, { "text": "Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis patient", "token_count": 33, "char_count": 121, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:54.824737", "source": { "split": "train_shard_00001", "doc_id": 3798 }, "chunk_id": "train_shard_00001_3798_1", "global_id": 11036 }, { "text": "The natural environment represents a complex reservoir of antibiotic-resistant bacteria as a consequence of different wastewater discharges including anthropogenic and agricultural. Therefore, the aim of this study was to examine sewage and waters across Ireland for the presence of antibiotic-resistant Enterobacterales. Samples were collected from the West, East and South of Ireland. Two periods of sampling took place between July 2019 and November 2020, during which 118 water (30 L) and 36 sewage samples (200 mL) were collected. Waters were filtered using the CapE method, followed by enrichment and culturing. Sewage samples were directly cultured on selective agars. Isolates were identified by MALDI-TOF and antibiotic susceptibility testing was performed in accordance with EUCAST criteria. Selected isolates were examined for blaCTX-M, blaVIM, blaIMP, blaOXA-48, blaNDM, and blaKPC by real time PCR and whole genome sequencing (n = 146). A total of 419 Enterobacterales (348 water, 71 sewage) were isolated from all samples. Hospital sewage isolates displayed the highest percentage resistance to many beta-lactam and aminoglycoside antibiotics. Extended-spectrum beta-lactamase-producers were identified in 78% of water and 50% of sewage samples. One or more carbapenemase-producing Enterobacterales were identified at 23 individual sampling sites (18 water, 5 sewage). This included the detection of blaOXA-48 (n = 18), blaNDM (n = 14), blaKPC (n = 4) and blaOXA-484 (n = 1). All NDM-producing isolates harbored the ble-MBL bleomycin resistance gene", "token_count": 514, "char_count": 1673, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8356, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:42:55.488656", "source": { "split": "train_shard_00001", "doc_id": 3799 }, "chunk_id": "train_shard_00001_3799_0", "global_id": 11037 }, { "text": "Commonly detected sequence types included Klebsiella ST323, ST17, and ST405 as well as E. coli ST131, ST38 and ST10. Core genome MLST comparisons detected identical E. coli isolates from wastewater treatment plant (WWTP) influent and nursing home sewage, and the surrounding waters. Similarly, one Klebsiella pneumoniae isolated from WWTP influent and the surrounding estuarine water were identical. These results highlight the need for regular monitoring of the aquatic environment for the presence of antibiotic-resistant organisms to adequately inform public health policies.\n\nA Longitudinal Survey of Antibiotic-Resistant Enterobacterales in the Irish Environment, 2019-2020.", "token_count": 179, "char_count": 679, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7717, "quality_score": 0.8859, "entities": { "genes": [ "ST131", "ST405", "ST323", "ST17", "ST10", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:55.935222", "source": { "split": "train_shard_00001", "doc_id": 3799 }, "chunk_id": "train_shard_00001_3799_1", "global_id": 11038 }, { "text": "Koalas (Phascolarctos cinereus) are highly specialized herbivorous marsupials that feed almost exclusively on Eucalyptus leaves, which are known to contain varying concentrations of many different toxic chemical compounds. The literature suggests that Lonepinella koalarum, a bacterium in the Pasteurellaceae family, can break down some of these toxic chemical compounds. Furthermore, in a previous study, we identified L. koalarum as the most predictive taxon of koala survival during antibiotic treatment. Therefore, we believe that this bacterium may be important for koala health. Here, we isolated a strain of L. koalarum from a healthy koala female and sequenced its genome using a combination of short-read and long-read sequencing. We placed the genome assembly into a phylogenetic tree based on 120 genome markers using the Genome Taxonomy Database (GTDB), which currently does not include any L. koalarum assemblies. Our genome assembly fell in the middle of a group of Haemophilus, Pasteurella and Basfia species. According to average nucleotide identity and a 16S rRNA gene tree, the closest relative of our isolate is L. koalarum strain Y17189. Then, we annotated the gene sequences and compared them to 55 closely related, publicly available genomes. Several genes that are known to be involved in carbohydrate metabolism could exclusively be found in L. koalarum relative to the other taxa in the pangenome, including glycoside hydrolase families GH2, GH31, GH32, GH43 and GH77. Among the predicted genes of L. koalarum were 79 candidates putatively involved in the degradation of plant secondary metabolites", "token_count": 492, "char_count": 1707, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6516, "quality_score": 0.8258, "entities": { "genes": [ "GH2", "GH32", "GH77", "GH43", "GH31" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:56.586160", "source": { "split": "train_shard_00001", "doc_id": 3800 }, "chunk_id": "train_shard_00001_3800_0", "global_id": 11039 }, { "text": "Additionally, several genes coding for amino acid variants were found that had been shown to confer antibiotic resistance in other bacterial species against pulvomycin, beta-lactam antibiotics and the antibiotic efflux pump KpnH. In summary, this genetic characterization allows us to build hypotheses to explore the potentially beneficial role that L. koalarum might play in the koala intestinal microbiome. Characterizing and understanding beneficial symbionts at the whole genome level is important for the development of anti- and probiotic treatments for koalas, a highly threatened species due to habitat loss, wildfires, and high prevalence of Chlamydia infections.\n\nIsolation and sequence-based characterization of a koala symbiont: Lonepinella koalarum.", "token_count": 197, "char_count": 783, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7714, "quality_score": 0.8857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:57.032262", "source": { "split": "train_shard_00001", "doc_id": 3800 }, "chunk_id": "train_shard_00001_3800_1", "global_id": 11040 }, { "text": "

Aims

The aim of this study was to investigate the behaviour of a Serratia marcescens-Kluyveromyces fragilis mixed culture in whey, with the objective of proteases production and organic waste reduction.

Methods and results

Discontinuous aerobic fermentations in whey were carried out using individual pure cultures and mixed cultures of S. marcescens and K. fragilis. Cell growth, protease production, lactose and proteins consumption and COD/TOC reduction were monitored. Lactose and protein content of the fermenting medium was almost depleted in the mixed cultures, achieving a reduction in the organic content much higher than in both pure cultures. Interestingly, proteolytic activity in the mixed cultures was similar to that obtained for S. marcescens in pure culture. In addition, protease stability was increased in the mixed cultures. Kinetic models were developed fitting well with the experimental results.

Conclusions

Mixed cultures were found to maintain the achievements of each individual fermentation, yielding a high and stable production of proteases and a significant reduction of COD/TOC.

Significance and impact of the study

Mixed cultures tested in this work have shown a synergistic effect with possible industrial applications. These results lead to a gain in the chain value for enzyme production with an environmentally friendly operation.\n\nMixed cultures of Serratia marcescens and Kluyveromyces fragilis for simultaneous protease production and COD removal of whey.", "token_count": 357, "char_count": 1523, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5667, "quality_score": 0.7833, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:57.975610", "source": { "split": "train_shard_00001", "doc_id": 3801 }, "chunk_id": "train_shard_00001_3801_0", "global_id": 11041 }, { "text": "A dataset of four draft genome sequences of Bifidobacterium strains is presented. All four genome assemblies are high-quality drafts characterized by high completeness and low contamination levels. GC content of the genomes varied in the range between 59.27% and 62.77%. Genome sequences were annotated for further functional and taxonomical analyses of the respective Bifidobacterium strains. Genetic determinants of probiotic capabilities, including the genes, related to utilization of human milk oligosaccharides and mucin, as well as the genes, encoding bile salt hydrolase were identified. The genome of B. bifidum VKPM=Ac-1784 has been shown to possess two bacteriocin gene clusters. The dataset expands knowledge on genomic diversity of probiotic strains of Bifidobacterium genus. The dataset is available under PRJNA656137 accession number in NCBI database and under zyv26t6x5r accession number in Mendeley Data repository.\n\nA dataset of four probiotic Bifidobacterium strains genome assemblies.", "token_count": 298, "char_count": 1039, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6571, "quality_score": 0.8286, "entities": { "genes": [ "PRJNA656137" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:58.541903", "source": { "split": "train_shard_00001", "doc_id": 3802 }, "chunk_id": "train_shard_00001_3802_0", "global_id": 11042 }, { "text": "Sublineages within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and industrial or public health applications. Whereas the classification and naming of prokaryotes is unified at the species level and higher taxonomic ranks, universally accepted definitions of sublineages within species are largely missing, which introduces confusion in population biology and epidemiological surveillance. Here we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LIN). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infra-specific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL sublineages (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform ( https://bigsdb.pasteur.fr/klebsiella ), which also enables external users’ genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcodes systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.\n\nA dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy ofKlebsiella pneumoniaestrains", "token_count": 484, "char_count": 2045, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:59.187480", "source": { "split": "train_shard_00001", "doc_id": 3803 }, "chunk_id": "train_shard_00001_3803_0", "global_id": 11043 }, { "text": "Salmonella has been known as the most important foodborne pathogen, which can infect humans via consuming contaminated food. Chicken meat has been known as an important vehicle to transmit Salmonella by the food supply chain. This study determined the prevalence, antimicrobial resistance, and genetic characteristics of Salmonella at different chicken slaughtering stages in East China. In total, 114 out of 200 (57%) samples were Salmonella positive, while Salmonella contamination was gradually increasing from the scalding and unhairing stage (17.5%) to the subdividing stage (70%) throughout the slaughtering. Whole-genome sequencing (WGS) was then performed to analyze the serotype, antimicrobial resistance gene profiles, and genetic relationship of all Salmonella isolates. The most common serotypes were S. Kentucky (51/114, 44.7%) and S. Enteritidis (37/114, 32.5%), which were distributed throughout the four slaughtering stages, and were also identified in the corresponding environments. The multilocus sequence typing (MLST) analysis revealed that seven sequence types (STs) were occupied by six different serotypes, respectively. Only S. Kentucky had two STs, ST314 was the predominant ST shared by 50 isolates, while the ST198 has 1 isolate. The antimicrobial resistance gene analysis demonstrated that most of the strains belonging to S. Kentucky (39/51, 76.5%) and S. Indiana (15, 100%) contained over five groups of antimicrobial resistance genes. Based on the core genome analysis, 50 S. Kentucky isolates were genetically identical, indicating that one S. Kentucky strain with the same genetic background was prevalent in the chicken slaughtering line. Although 37 S", "token_count": 503, "char_count": 1785, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6405, "quality_score": 0.8202, "entities": { "genes": [ "ST198", "ST314" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:42:59.842351", "source": { "split": "train_shard_00001", "doc_id": 3804 }, "chunk_id": "train_shard_00001_3804_0", "global_id": 11044 }, { "text": "Enteritidis isolates only had three different antimicrobial resistance gene profiles, the core genome sequence analysis subtyped these S. Enteritidis isolates into five different clusters, which revealed the diverse genetic background of S. Enteritidis in the slaughterhouse. The antimicrobial resistance phenotypes were consistent with the presence of the corresponding resistance genes of S. Kentucky and S. Enteritidis, including tetA, floR, blaTEM-1B, strA/B, sul1/sul2, and gyrA (D87Y). Our study observed a high prevalence of Salmonella in the chicken slaughter line and identified the slaughtering environment as a main source of causing Salmonella cross-contamination during chicken slaughtering. Further studies will be needed to limit the transmission of Salmonella in the slaughterhouse.\n\nPrevalence of Salmonella Isolates and Their Distribution Based on Whole-Genome Sequence in a Chicken Slaughterhouse in Jiangsu, China.", "token_count": 286, "char_count": 1011, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:00.402785", "source": { "split": "train_shard_00001", "doc_id": 3804 }, "chunk_id": "train_shard_00001_3804_1", "global_id": 11045 }, { "text": "

Background

VanD is a rare type of vancomycin resistance worldwide. However, the host diversity of the vanD gene cluster and the structural similarity of their genomic islands are not well understood.

Methods

Three VanD-type Enterococcus faecium strains (AA620, AA622 and AA624) isolated from a Japanese patient who underwent vancomycin treatment in 2017 were analysed. This study utilized WGS analysis to characterize the three VanD-type E. faecium strains and describes the diversity of hosts possessing VanD-carrying genomic islands.

Results

The three isolates exhibited variable MICs of vancomycin. In the relatively vancomycin-resistant AA620, mutations were identified in vanSD and ddl. The strains AA622 and AA624 had intact ddl and harboured two vanD gene clusters. qRT-PCR results revealed the ddl mutation to be a factor affecting the high vancomycin resistance range of AA620. WGS data showed the 155 kb and 185 kb genomic islands harbouring the vanD gene cluster inserted in the coding region of the lysS gene, located in the chromosome in AA620 and AA622/624, respectively. Comparing the VanD-carrying genomic islands to available sequences of other enterococci and enteric anaerobes revealed how the genomic islands of these organisms isolated worldwide shared similar core genes and backbones. These anaerobes belonged to various genera within the order Eubacteriales", "token_count": 455, "char_count": 1484, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6281, "quality_score": 0.8141, "entities": { "genes": [ "AA622", "AA624", "AA620" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:01.038850", "source": { "split": "train_shard_00001", "doc_id": 3805 }, "chunk_id": "train_shard_00001_3805_0", "global_id": 11046 }, { "text": "The phylogenetic cluster of the genomic island core genome alignment did not correlate with the host-species lineage, indicating horizontal gene transfer in the gut microbiota.

Conclusions

By horizontal gene transfer, various bacteria forming the gut microbiota maintain VanD-carrying genomic islands.\n\nElucidation of host diversity of the VanD-carrying genomic islands in enterococci and anaerobes.", "token_count": 104, "char_count": 406, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7255, "quality_score": 0.8627, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:01.418768", "source": { "split": "train_shard_00001", "doc_id": 3805 }, "chunk_id": "train_shard_00001_3805_1", "global_id": 11047 }, { "text": "IntroductionWhole genome sequencing (WGS) is increasingly used in Legionnaires' disease (LD) outbreak investigations, owing to its higher resolution than sequence-based typing, the gold standard typing method for Legionella pneumophila, in the analysis of endemic strains. Recently, a gene-by-gene typing approach based on 1,521 core genes called core genome multilocus sequence typing (cgMLST) was described that enables a robust and standardised typing of L. pneumophila. Methods: We applied this cgMLST scheme to isolates obtained during the largest outbreak of LD reported so far in Germany. In this outbreak, the epidemic clone ST345 had been isolated from patients and four different environmental sources. In total 42 clinical and environmental isolates were retrospectively typed. Results: Epidemiologically unrelated ST345 isolates were clearly distinguishable from the epidemic clone. Remarkably, epidemic isolates split up into two distinct clusters, ST345-A and ST345-B, each respectively containing a mix of clinical and epidemiologically-related environmental samples. Discussion/conclusion: The outbreak was therefore likely caused by both variants of the single sequence type, which pre-existed in the environmental reservoirs. The two clusters differed by 40 alleles located in two neighbouring genomic regions of ca 42 and 26 kb. Additional analysis supported horizontal gene transfer of the two regions as responsible for the difference between the variants. Both regions comprise virulence genes and have previously been reported to be involved in recombination events. This corroborates the notion that genomic outbreak investigations should always take epidemiological information into consideration when making inferences. Overall, cgMLST proved helpful in disentangling the complex genomic epidemiology of the outbreak.\n\nEpidemiological information is key when interpreting whole genome sequence data - lessons learned from a large Legionella pneumophila outbreak in Warstein, Germany, 2013.", "token_count": 487, "char_count": 2057, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6642, "quality_score": 0.8321, "entities": { "genes": [ "ST345" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:02.070314", "source": { "split": "train_shard_00001", "doc_id": 3806 }, "chunk_id": "train_shard_00001_3806_0", "global_id": 11048 }, { "text": "Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen", "token_count": 517, "char_count": 1862, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8353, "entities": { "genes": [ "CC152" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:43:02.732345", "source": { "split": "train_shard_00001", "doc_id": 3807 }, "chunk_id": "train_shard_00001_3807_0", "global_id": 11049 }, { "text": "By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.\n\nAntibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda.", "token_count": 109, "char_count": 440, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:03.111339", "source": { "split": "train_shard_00001", "doc_id": 3807 }, "chunk_id": "train_shard_00001_3807_1", "global_id": 11050 }, { "text": "

Objective

This paper aimed to identify and quantify Candida on head and neck irradiated patients with two comparative elderly populations.

Materials and methods

Saliva was sampled from 29 head and neck irradiated patients (group 1) 34 non-institutionalized elderly patients (group 2) and 29 institutionalized elders (group 3) and matched by age. For quantification, the obtained saliva was sewed on CHROMagar Candida(®), which was used also for presumptive identification of Candida, API 20C AUX(®), microculture and RAPD (OPE-18) were used for the final identification.

Results

Among the 92 patients surveyed, 51 (55.4%) had scores classified as positive for Candida, and among individuals of groups 1 and 3, 58.6% had Candida. There was higher positive/carrier conditions (CFU/sample) in groups 1 and 3, comparing with group 2 (P=0.011). Gender was not associated with Candida portability (P=0.334). Candida portability was significantly associated with the presence of candidosis (P=0.031) and xerostomic state (P=0.007). The isolates and definitive confirmed colonies were Candida albicans, Candida dubliniensis, Candida tropicalis, Candida krusei, Candida glabrata, Candida parapsilosis, Candida guilliermondii, Candida lusitaniae, and Candida kefyr. Among the species identified, C. albicans was the most frequent, followed by C. tropicalis, C. parapsilosis and C. glabrata. C. albicans was more prevalent in group 2 and 3, 45% and 41.2%, respectively, whereas, the most prevalent species in group 1 were C. tropicalis (27%), C. albicans and C. parapsilosis (16.2% for both)", "token_count": 494, "char_count": 1602, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5766, "quality_score": 0.7883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:03.769894", "source": { "split": "train_shard_00001", "doc_id": 3808 }, "chunk_id": "train_shard_00001_3808_0", "global_id": 11051 }, { "text": "On multiple statistical models, only radiotherapic treatment was associated with positiveness to Candida.

Conclusions

Diversification and major prevalence of non-albicans species were observed in irradiated patients on head and neck and this treatment is straightly associated with fungus positiveness.\n\nOral Candida species in head and neck cancer patients treated by radiotherapy.", "token_count": 87, "char_count": 389, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7551, "quality_score": 0.8776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:04.139887", "source": { "split": "train_shard_00001", "doc_id": 3808 }, "chunk_id": "train_shard_00001_3808_1", "global_id": 11052 }, { "text": "Sterol composition plays a crucial role in determining the ability of yeast cells to withstand high temperatures, an essential trait in biotechnology. Using a targeted evolution strategy involving fluconazole (FCNZ), an inhibitor of the sterol biosynthesis pathway, and the immunosuppressant FK506, we aimed to enhance thermotolerance in an industrial baker's yeast population by modifying their sterol composition. This approach yielded six isolates capable of proliferating in liquid YPD with μmax values ranging from 0.072 to 0.236 h-1 at 41.5°C, a temperature that completely inhibits the growth of the parental strain. The clones were categorised into two groups based on their respiratory competence or deficiency, the latter associated with mtDNA loss, an event seemingly linked to FCNZ and heat tolerance. Genome sequencing and ploidy-level analysis of all strains revealed aneuploidies, copy number variations (CNVs), and single nucleotide polymorphisms (SNPs). Notably, all evolved clones exhibited specific point mutations in MPM1 (P50S) and PDR1 (F749S). CRISPR-Cas9 experiments confirmed the role of the pdr1F749S mutation in the FCNZ-tolerance phenotype and demonstrated that Mpm1 is required for growth at high temperatures. However, no apparent heat tolerance benefit was observed from single or combined mutations in these genes, supporting the hypothesis that thermotolerance is mediated by multiple interacting mechanisms. In this context, all evolved clones exhibited altered sterol profiles, with differences observed between respiratory-competent and -deficient strains. In conclusion, our experimental evolution generated thermotolerant and fully competent strains and identified factors that could influence fluconazole and heat growth.\n\nSterol-Targeted Laboratory Evolution Allows the Isolation of Thermotolerant and Respiratory-Competent Clones of the Industrial Yeast Saccharomyces cerevisiae.", "token_count": 497, "char_count": 1953, "word_count": 259, "semantic_coherence": 1, "information_density": 0.668, "quality_score": 0.834, "entities": { "genes": [ "PDR1", "MPM1", "FK506" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:04.801825", "source": { "split": "train_shard_00001", "doc_id": 3809 }, "chunk_id": "train_shard_00001_3809_0", "global_id": 11053 }, { "text": "The bacterial genus Methylococcus, which comprises aerobic thermotolerant methanotrophic cocci, was described half-a-century ago. Over the years, a member of this genus, Methylococcus capsulatus Bath, has become a major model organism to study genomic and metabolic basis of obligate methanotrophy. High biotechnological potential of fast-growing Methylococcus species, mainly as a promising source of feed protein, has also been recognized. Despite this big research attention, the currently cultured Methylococcus diversity is represented by members of the two species, M. capsulatus and M. geothermalis, while finished genome sequences are available only for two strains of these methanotrophs. This study extends the pool of phenotypically characterized Methylococcus strains with good-quality genome sequences by contributing four novel isolates of these bacteria from activated sludge, landfill cover soil, and freshwater sediments. The determined genome sizes of novel isolates varied between 3.2 and 4.0Mb. As revealed by the phylogenomic analysis, strains IO1, BH, and KN2 affiliate with M. capsulatus, while strain Mc7 may potentially represent a novel species. Highest temperature optima (45-50°C) and highest growth rates in bioreactor cultures (up to 0.3h-1) were recorded for strains obtained from activated sludge. The comparative analysis of all complete genomes of Methylococcus species revealed 4,485 gene clusters. Of these, pan-genome core comprised 2,331 genes (on average 51.9% of each genome), with the accessory genome containing 846 and 1,308 genes in the shell and the cloud, respectively. Independently of the isolation source, all strains of M. capsulatus displayed surprisingly high genome synteny and a striking similarity in gene content", "token_count": 518, "char_count": 1849, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8353, "entities": { "genes": [ "IO1", "KN2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:43:05.483360", "source": { "split": "train_shard_00001", "doc_id": 3810 }, "chunk_id": "train_shard_00001_3810_0", "global_id": 11054 }, { "text": "Strain Mc7 from a landfill cover soil differed from other isolates by the high content of mobile genetic elements in the genome and a number of genome-encoded features missing in M. capsulatus, such as sucrose biosynthesis and the ability to scavenge phosphorus and sulfur from the environment.\n\nExpanding Characterized Diversity and the Pool of Complete Genome Sequences of Methylococcus Species, the Bacteria of High Environmental and Biotechnological Relevance.", "token_count": 127, "char_count": 478, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7206, "quality_score": 0.8603, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:05.914472", "source": { "split": "train_shard_00001", "doc_id": 3810 }, "chunk_id": "train_shard_00001_3810_1", "global_id": 11055 }, { "text": "

Background

Corynebacterium diphtheriae is the main etiological agent of diphtheria, a global disease causing life-threatening infections, particularly in infants and children. Vaccination with diphtheria toxoid protects against infection with potent toxin producing strains. However a growing number of apparently non-toxigenic but potentially invasive C. diphtheriae strains are identified in countries with low prevalence of diphtheria, raising key questions about genomic structures and population dynamics of the species. This study examined genomic diversity among 48 C. diphtheriae isolates collected in Australia over a 12-year period using whole genome sequencing. Phylogeny was determined using SNP-based mapping and genome wide analysis.

Results

C. diphtheriae sequence type (ST) 32, a non-toxigenic clone with evidence of enhanced virulence that has been also circulating in Europe, appears to be endemic in Australia. Isolates from temporospatially related patients displayed the same ST and similarity in their core genomes. The genome-wide analysis highlighted a role of pilins, adhesion factors and iron utilization in infections caused by non-toxigenic strains.

Conclusions

The genomic diversity of toxigenic and non-toxigenic strains of C. diphtheriae in Australia suggests multiple sources of infection and colonisation. Genomic surveillance of co-circulating toxigenic and non-toxigenic C. diphtheriae offer new insights into the evolution and virulence of pathogenic clones and can inform targeted public health actions and policy. The genomes presented in this investigation will contribute to the global surveillance of C. diphtheriae both for the monitoring of antibiotic resistance genes and virulent strains such as those belonging to ST32.\n\nGenome-wide comparison of Corynebacterium diphtheriae isolates from Australia identifies differences in the Pan-genomes between respiratory and cutaneous strains.", "token_count": 486, "char_count": 1951, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8275, "entities": { "genes": [ "ST32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:06.584108", "source": { "split": "train_shard_00001", "doc_id": 3811 }, "chunk_id": "train_shard_00001_3811_0", "global_id": 11056 }, { "text": "The process of ethanol fermentation has a long history in the production of alcoholic drinks, but much larger scale production of ethanol is now required to enable its use as a substituent of gasoline fuels at 3%, 10%, or 85% (referred to as E3, E10, and E85, respectively). Compared with fossil fuels, the production costs are a major issue for the production of fuel ethanol. There are a number of possible approaches to delivering cost-effective fuel ethanol production from different biomass sources, but we focus in our current report on high-temperature fermentation using a newly isolated thermotolerant strain of the yeast Kluyveromyces marxianus. We demonstrate that a 5 degrees C increase only in the fermentation temperature can greatly affect the fuel ethanol production costs. We contend that this approach may also be applicable to the other microbial fermentations systems and propose that thermotolerant mesophilic microorganisms have considerable potential for the development of future fermentation technologies.\n\nHigh-temperature fermentation: how can processes for ethanol production at high temperatures become superior to the traditional process using mesophilic yeast?", "token_count": 274, "char_count": 1191, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:07.177285", "source": { "split": "train_shard_00001", "doc_id": 3812 }, "chunk_id": "train_shard_00001_3812_0", "global_id": 11057 }, { "text": "

Background and objectives

The incidence of fungal infections in immunocompromised patients, especially by Candida species, has increased in recent years. This study was designed to identify Candida species and determine antifungal susceptibility patterns of 595 yeast strains isolated from various clinical specimens.

Material and methods

Identification of the isolates were determined by the API 20 C AUX kit and antifungal susceptibilities of the species to fluconazole, amphotericin B, ketoconazole, itraconazole, voriconazole, and caspofungin were determined by the agar-based E-test method.

Results

Candida albicans (48%) was the most frequently isolated species, followed by Candida kruzei (16.1%), Candida glabrata (13.5%), Candida kefyr (7.4%), Candida parapsilosis (4.8%), Candida tropicalis (1.7%) and other species (8.5%). Resistance varies depending on the species and the respective antifungal agents. Comparing the MIC90 for all the strains, the lower MIC90 was observed for caspofungin (0.5 µg/ml). The MIC90 for all Candida species were 64 µg/ml for fluconazole, 0.75 µg/ml for amphotericin B, 4 µg/ml for ketoconazole, 4 µg/ml for itraconazole, and 2 µg/ml for voriconazole.

Conclusions

Species definition and determination of antifungal susceptibility patterns are advised for the proper management and treatment of patients at risk for systemic candidiasis. Resistance to antifungal agents is an alarming sign for the emerging common nosocomial fungal infections.\n\nSusceptibility of clinical Candida species isolates to antifungal agents by E-test, Southern Iran: A five year study.", "token_count": 492, "char_count": 1630, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5741, "quality_score": 0.787, "entities": { "genes": [ "MIC90" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:07.836267", "source": { "split": "train_shard_00001", "doc_id": 3813 }, "chunk_id": "train_shard_00001_3813_0", "global_id": 11058 }, { "text": "

Background:

Shotgun metagenomic sequencing has the potential to provide bacterial strain-level resolution which is of key importance to tackle a host of clinical questions. While bioinformatics tools that achieve strain-level resolution are available, thorough benchmarking is needed to validate their use for less investigated and low biomass microbiomes like those from the upper respiratory tract.

Methods:

: We analyzed a previously published dataset of longitudinally collected nasopharyngeal samples from Bangladeshi infants (Microbiota & Health study) and a novel dataset of oropharyngeal samples from Swiss children with cystic fibrosis. Data from bacterial cultures were used for benchmarking the parameters of StrainPhlAn 3, a bioinformatic tool designed for strain-level resolution. In addition, StrainPhlAn 3 results were compared to metagenomic assemblies and whole-genome sequencing data of S. aureus strains. Finally, strain retention analyses were performed.

Results:

: After optimizing the analytical parameters, we compared our results to culture gold standard methods and achieved sensitivity values of 87% ( S. pneumoniae ), 80% ( M. catarrhalis ), 75% ( H. influenzae ) and 57% ( S. aureus ) for 420 nasopharyngeal and 75% ( H. influenzae ) and 46% ( S. aureus ) for 260 oropharyngeal samples. Comparing the phylogenetic tree of the core genome of 50 S. aureus isolates with a corresponding marker gene tree generated by StrainPhlAn 3 revealed a striking similarity in tree topology for all but three samples indicating adequate strain resolution. Quantitative analyses of longitudinally collected samples revealed clear signatures of strain retention for the four analyzed species.

Conclusions:

: Comparison of StrainPhlAn 3 results to data from bacterial cultures revealed that strain-level tracking of the respiratory microbiome is feasible despite high content of host DNA when parameters are carefully optimized to fit low biomass microbiomes", "token_count": 513, "char_count": 2005, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5799, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:43:08.499516", "source": { "split": "train_shard_00001", "doc_id": 3814 }, "chunk_id": "train_shard_00001_3814_0", "global_id": 11059 }, { "text": "This allowed to perform strain retention analyses applied to relevant pathobionts which will help to better understand the longitudinal dynamics of the upper respiratory microbiome during health and disease.\n\nInformed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome", "token_count": 70, "char_count": 332, "word_count": 45, "semantic_coherence": 1, "information_density": 0.7556, "quality_score": 0.8778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:08.866902", "source": { "split": "train_shard_00001", "doc_id": 3814 }, "chunk_id": "train_shard_00001_3814_1", "global_id": 11060 }, { "text": "Salmonella enterica resistant to fluoroquinolones (FQs) and extended-spectrum cephalosporins (ESCs) has been deemed a high-priority pathogen by the WHO. Salmonella enterica serovar Saintpaul (S. Saintpaul) co-resistant to ESCs and FQs and harboring corresponding resistance genes (bla CTX-M-55 and qnrS1) have been previously reported. However, they have not been reported in China. Moreover, the genetic context and transferability of ESCs and FQs resistance genes in S. Saintpaul remain obscure. This study is the first study to characterize a multidrug-resistant (MDR) S. Saintpaul isolate (16Sal016) harboring plasmid-mediated bla CTX-M-55 and qnrS1 genes recovered from weever fish in China. The whole genome short- and long-read sequencing results identified the presence of 15 acquired antibiotic resistance genes encoding resistance to nine classes of antibiotics, as well as abundant mobile genetic elements residing on a 259,529 bp IncHI2 plasmid. The bla CTX-M-55 and qnrS1 genes were located in a 12,865 bp region, IS26-orf-orf-ISKpn19-qnrS1-IS3-Tn3-orf-bla CTX-M-55-ISEc9-orf-IS26", "token_count": 503, "char_count": 1291, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6577, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:09.522413", "source": { "split": "train_shard_00001", "doc_id": 3815 }, "chunk_id": "train_shard_00001_3815_0", "global_id": 11061 }, { "text": "Similar structures have been identified in various bacterial species, indicating a high transferability of bla CTX-M-55 and qnrS1 genes within this gene cluster. The plasmid was found to be transferable to Escherichia coli (E. coli) J53 by conjugation and resulted in the acquisition of multiple resistances by the transconjugants. Genome sequence comparisons by core genome multilocus sequence typing (cgMLST) based on global 2,947 S. Saintpaul isolates indicated that strain 16Sal016 was epidemiologically linked with an isolate from the United Kingdom (UK). Our findings suggest that plasmids and IS26-mediated mobile genetic elements are carriers of bla CTX-M-55 and qnrS1 genes in S. Saintpaul, and highlight their potential transmission, which needs continuous investigations.\n\nGenetic context of bla CTX-M-55 and qnrS1 genes in a foodborne Salmonella enterica serotype Saintpaul isolate from China.", "token_count": 325, "char_count": 1022, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7287, "quality_score": 0.8643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:10.084041", "source": { "split": "train_shard_00001", "doc_id": 3815 }, "chunk_id": "train_shard_00001_3815_1", "global_id": 11062 }, { "text": "Advanced multi-omics technologies offer much information that can uncover the regulatory mechanisms from genotype to phenotype. In soybean, numerous multi-omics databases have been published. Although they cover multiple omics, there are still limitations when it comes to the types and scales of omics datasets and analysis methods utilized. This study aims to address these limitations by collecting and integrating a comprehensive set of multi-omics datasets. This includes 38 genomes, transcriptomes from 435 tissue samples, 125 phenotypes from 6686 accessions, epigenome data involving histone modification, transcription factor binding, chromosomal accessibility and chromosomal interaction, as well as genetic variation data from 24 501 soybean accessions. Then, common analysis pipelines and statistical methods were applied to mine information from these multi-omics datasets, resulting in the successful establishment of a user-friendly multi-omics database called SoyMD (https://yanglab.hzau.edu.cn/SoyMD/#/). SoyMD provides researchers with efficient query options and analysis tools, allowing them to swiftly access relevant omics information and conduct comprehensive multi-omics data analyses. Another notable feature of SoyMD is its capability to facilitate the analysis of candidate genes, as demonstrated in the case study on seed oil content. This highlights the immense potential of SoyMD in soybean genetic breeding and functional genomics research.\n\nSoyMD: a platform combining multi-omics data with various tools for soybean research and breeding.", "token_count": 345, "char_count": 1570, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6952, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:10.658993", "source": { "split": "train_shard_00001", "doc_id": 3816 }, "chunk_id": "train_shard_00001_3816_0", "global_id": 11063 }, { "text": "In the Netherlands, more than half of domestic shigellosis cases are among men who have sex with men (MSM), particularly in the Amsterdam region. However, there is limited insight into which Shigella strains circulate in the Netherlands. Our objective was to assess the added value of whole-genome sequencing (WGS)-based surveillance for Shigella. To this end, we determined the relatedness among Shigella spp. isolates from patients in the Amsterdam region, as well as in an international context, including antimicrobial resistance markers, using WGS. The following criteria were used: it should provide insight into (1) clustering of shigellosis cases and the affected population, (2) the extent of admixture of MSM-associated isolates with those from the broader population and (3) the presence of antimicrobial resistance. It should then lead to more opportunities for targeted control measures. For this study, Shigella isolates from three laboratories in the Amsterdam region obtained between February 2019 and October 2021 were subjected to Illumina WGS at the National Institute for Public Health and the Environment (RIVM). Raw data were quality-checked and assembled, the Shigella serotype was determined with ShigaTyper, and antimicrobial resistance markers were detected using ResFinder and PointFinder. For Shigella sonnei, subclades were determined using Mykrobe. Relatedness of isolates, including 21 international reference genomes, was assessed with core genome multilocus sequence typing. In total, 109 isolates were included, of which 27 were from females (25 %) and 66 were from males (61 %), with which the majority (n=48, 73 %) being from MSM. No information on sex was available for the remaining 16 cases. The WGS data for all isolates, comprising 55 S", "token_count": 482, "char_count": 1833, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:11.308446", "source": { "split": "train_shard_00001", "doc_id": 3817 }, "chunk_id": "train_shard_00001_3817_0", "global_id": 11064 }, { "text": "sonnei, 52 Shigella flexneri, 1 Shigella boydii and 1 Shigella dysenteriae, met the quality criteria. In total, 14 clusters containing 51 isolates (49 %) were identified, with a median cluster size of 2.5 cases (range: 2-15). Nine out of 14 clusters were MSM-associated, and 8 clusters (57 %) were travel-related. Six of the MSM clusters were related to international reference genomes. The prevalence of antimicrobial resistance markers was higher among isolates from MSM than non-MSM patients, particularly for ciprofloxacin (89 vs 33 %) and azithromycin (58 vs 17 %). In conclusion, about half of Shigella spp. patients were part of a cluster, of which a substantial part were related to international reference genomes, particularly among MSM, and a high prevalence of antimicrobial resistance markers was found. These findings indicate widespread international circulation of Shigella spp., particularly among MSM, with multidrug resistance that hampers treatment of patients. Moreover, the results of this study led to the implementation of a national WGS-based laboratory surveillance programme for Shigella spp. that started in April 2022.\n\nWhole-genome sequencing of Shigella for surveillance purposes shows (inter)national relatedness and multidrug resistance in isolates from men who have sex with men.", "token_count": 403, "char_count": 1369, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6062, "quality_score": 0.8031, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:11.926777", "source": { "split": "train_shard_00001", "doc_id": 3817 }, "chunk_id": "train_shard_00001_3817_1", "global_id": 11065 }, { "text": "Strains of the same bacterial species often show considerable genomic variation. To examine the extent of such variation in Rhizobium etli, the complete genome sequence of R. etli CIAT652 and the partial genomic sequences of six additional R. etli strains having different geographical origins were determined. The sequences were compared with each other and with the previously reported genome sequence of R. etli CFN42. DNA sequences common to all strains constituted the greater part of these genomes and were localized in both the chromosome and large plasmids. About 700 to 1,000 kb of DNA that did not match sequences of the complete genomes of strains CIAT652 and CFN42 was unique to each R. etli strain. These sequences were distributed throughout the chromosome as individual genes or chromosomal islands and in plasmids, and they encoded accessory functions, such as transport of sugars and amino acids, or secondary metabolism; they also included mobile elements and hypothetical genes. Sequences corresponding to symbiotic plasmids showed high levels of nucleotide identity (about 98 to 99%), whereas chromosomal sequences and the sequences with matches to other plasmids showed lower levels of identity (on average, about 90 to 95%). We concluded that R. etli has a pangenomic structure with a core genome composed of both chromosomal and plasmid sequences, including a highly conserved symbiotic plasmid, despite the overall genomic divergence.\n\nConserved symbiotic plasmid DNA sequences in the multireplicon pangenomic structure of Rhizobium etli.", "token_count": 383, "char_count": 1562, "word_count": 236, "semantic_coherence": 1, "information_density": 0.5508, "quality_score": 0.7754, "entities": { "genes": [ "CIAT652", "CFN42" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:12.509180", "source": { "split": "train_shard_00001", "doc_id": 3818 }, "chunk_id": "train_shard_00001_3818_0", "global_id": 11066 }, { "text": "

Background

Metagenomic approaches have revealed the complexity of environmental microbiomes with the advancement in whole genome sequencing displaying a significant level of genetic heterogeneity on the species level. It has become apparent that patterns of superior bioactivity of bacteria applicable in biotechnology as well as the enhanced virulence of pathogens often requires distinguishing between closely related species or sub-species. Current methods for binning of metagenomic reads usually do not allow for identification below the genus level and generally stops at the family level.

Results

In this work, an attempt was made to improve metagenomic binning resolution by creating genome specific barcodes based on the core and accessory genomes. This protocol was implemented in novel software tools available for use and download from http://bargene.bi.up.ac.za /. The most abundant barcode genes from the core genomes were found to encode for ribosomal proteins, certain central metabolic genes and ABC transporters. Performance of metabarcode sequences created by this package was evaluated using artificially generated and publically available metagenomic datasets. Furthermore, a program (Barcoding 2.0) was developed to align reads against barcode sequences and thereafter calculate various parameters to score the alignments and the individual barcodes. Taxonomic units were identified in metagenomic samples by comparison of the calculated barcode scores to set cut-off values. In this study, it was found that varying sample sizes, i.e. number of reads in a metagenome and metabarcode lengths, had no significant effect on the sensitivity and specificity of the algorithm. Receiver operating characteristics (ROC) curves were calculated for different taxonomic groups based on the results of identification of the corresponding genomes in artificial metagenomic datasets. The reliability of distinguishing between species of the same genus or family by the program was nearly perfect.

Conclusions

The results showed that the novel online tool BarcodeGenerator ( http://bargene.bi.up.ac.za /) is an efficient approach for generating barcode sequences from a set of complete genomes provided by users. Another program, Barcoder 2.0 is available from the same resource to enable an efficient and practical use of metabarcodes for visualization of the distribution of organisms of interest in environmental and clinical samples.", "token_count": 520, "char_count": 2467, "word_count": 342, "semantic_coherence": 1, "information_density": 0.5877, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:43:13.169807", "source": { "split": "train_shard_00001", "doc_id": 3819 }, "chunk_id": "train_shard_00001_3819_0", "global_id": 11067 }, { "text": "Selection of marker genes for genetic barcoding of microorganisms and binning of metagenomic reads by Barcoder software tools.", "token_count": 28, "char_count": 126, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:13.524760", "source": { "split": "train_shard_00001", "doc_id": 3819 }, "chunk_id": "train_shard_00001_3819_1", "global_id": 11068 }, { "text": "Methanol quenching and fast filtration, the two most common sampling protocols in microbial metabolome analysis, were validated for intracellular amino acid analysis in phylogenetically different yeast strains comprising Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia pastoris, Schizosaccharomyces pombe and Zygosaccharomyces bailii. With only few exceptions for selected amino acids, all yeasts exhibited negligible metabolite leakage during quenching with 60% cold buffered methanol. Slightly higher leakage was observed with increasing methanol content in the quenching solution. Fast filtration resulted in identical levels for intracellular amino acids in all strains tested. The results clearly demonstrate the validity of both approaches for leakage-free sampling of amino acids in yeast.\n\nAppropriate sampling for intracellular amino acid analysis in five phylogenetically different yeasts", "token_count": 235, "char_count": 908, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6724, "quality_score": 0.8362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:13.991678", "source": { "split": "train_shard_00001", "doc_id": 3820 }, "chunk_id": "train_shard_00001_3820_0", "global_id": 11069 }, { "text": "Where classical epidemiology has proven to be inadequate for surveillance and control of foodborne pathogens, molecular epidemiology, using genomic typing methods, can add value. However, the analysis of whole genome sequencing (WGS) data varies widely and is not yet fully harmonised. We used genomic data on 494 Listeria monocytogenes isolates from ready-to-eat food products and food processing environments deposited in the strain collection of the German National Reference Laboratory to compare various procedures for WGS data analysis and to evaluate compatibility of results. Two different core genome multilocus sequence typing (cgMLST) schemes, different reference genomes in single nucleotide polymorphism (SNP) analysis and commercial as well as open-source software were compared. Correlation of allele distances from the different cgMLST approaches was high, ranging from 0.97 to 1, and unified thresholds yielded higher clustering concordance than scheme-specific thresholds. The number of detected SNP differences could be increased up to a factor of 3.9 using a specific reference genome compared with a general one. Additionally, specific reference genomes improved comparability of SNP analysis results obtained using different software tools. The use of a closed or a draft specific reference genome did not make a difference. The harmonisation of WGS data analysis will finally guarantee seamless data exchange, but, in the meantime, knowledge on threshold values that lead to comparable clustering of isolates by different methods may improve communication between laboratories. We therefore established a translation code between commonly applied cgMLST and SNP methods based on optimised clustering concordances. This code can work as a first filter to identify WGS-based typing matches resulting from different methods, which opens up a new perspective for data exchange and thereby accelerates time-critical analyses, such as in outbreak investigations.\n\nTranslatability of WGS typing results can simplify data exchange for surveillance and control of Listeria monocytogenes.", "token_count": 455, "char_count": 2115, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6263, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:14.627014", "source": { "split": "train_shard_00001", "doc_id": 3821 }, "chunk_id": "train_shard_00001_3821_0", "global_id": 11070 }, { "text": "Bacillus velezensis strain WRN014 was isolated from banana fields in Hainan, China. Bacillus velezensis is an important member of the plant growth-promoting rhizobacteria (PGPR) which can enhance plant growth and control soil-borne disease. The complete genome of Bacillus velezensis WRN014 was sequenced by combining Illumina Hiseq 2500 system and Pacific Biosciences SMRT high-throughput sequencing technologies. Then, the genome of Bacillus velezensis WRN014, together with 45 other completed genome sequences of the Bacillus velezensis strains, were comparatively studied. The genome of Bacillus velezensis WRN014 was 4,063,541bp in length and contained 4,062 coding sequences, 9 genomic islands and 13 gene clusters. The results of comparative genomic analysis provide evidence that (i) The 46 Bacillus velezensis strains formed 2 obviously closely related clades in phylogenetic trees. (ii) The pangenome in this study is open and is increasing with the addition of new sequenced genomes. (iii) Analysis of single nucleotide polymorphisms (SNPs) revealed local diversification of the 46 Bacillus velezensis genomes. Surprisingly, SNPs were not evenly distributed throughout the whole genome. (iv) Analysis of gene clusters revealed that rich gene clusters spread over Bacillus velezensis strains and some gene clusters are conserved in different strains. This study reveals that the strain WRN014 and other Bacillus velezensis strains have potential to be used as PGPR and biopesticide.\n\nComplete Genome Sequencing of Bacillus velezensis WRN014, and Comparison with Genome Sequences of other Bacillus velezensis Strains.", "token_count": 508, "char_count": 1696, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5808, "quality_score": 0.7904, "entities": { "genes": [ "WRN014" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:15.285378", "source": { "split": "train_shard_00001", "doc_id": 3822 }, "chunk_id": "train_shard_00001_3822_0", "global_id": 11071 }, { "text": "The invention relates to a method for preparing cholesterol reducing eggnog fermenting drink by utilizing lactobacillus and microzyme which produce bile salt hydrolase, belonging to a functional drinkwhich is prepared from the following ingredients: 15% of whole egg pulp, 35% of milk, 7% of saccharose, 0.3% of CMC-Na. and 0.2% of carrageenin, wherein the ratio of the raw materials (the whole eggplug and the milk) to water is 1:1 (W/V). The primary fermentation condition is described as following: streptococcus thermophilus Tx, Lactococcus lactis subsp.lactis KS4 and Lactobacillus casei KL1 are mixed in proportion of 1:1:1, the inoculum size is 3%, and then the mixture is fermented for 8h at the temperature of 43 DEG C. The secondary fermentation condition is described as following: Kluyveromyces marxianus M3 and K1 are compounded in proportion of 1:1 or the inoculum size of the single strain is 1%, and then the composite is fermented for 24-26 h at the temperature of 30 DEG C (mixture strain) or 32-34 DEG C after ripening is carried out for 1 day at the temperature of 4 DEG C, the reducing rate of raw material cholesterol reaches as high as 89.3%. By utilizing the characteristics of strain high-yielding BSH, exopolysaccharide and the like, the invention has the efficiencies of immunological regulation, cholesterol reducing, tumor prevention and the like, and the problem of egg smell is not only solved, but also the content of raw material cholesterol is efficiently reduced through egg pulp proper sterilization and eggnog secondary fermentation. The eggnog drink preparedby the invention has simple fermentation process, short period and lower cost and is suitable for industrialized production.\n\nMethod for preparing cholesterol reducing eggnog fermenting drink by utilizing lactobacillus and microzyme which produce bile salt hydrolase", "token_count": 512, "char_count": 1862, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5363, "quality_score": 0.7682, "entities": { "genes": [ "KS4", "KL1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:15.949313", "source": { "split": "train_shard_00001", "doc_id": 3823 }, "chunk_id": "train_shard_00001_3823_0", "global_id": 11072 }, { "text": "

Background

Legionella pneumophila subsp. pneumophila is a gram-negative gamma-Proteobacterium and the causative agent of Legionnaires' disease, a form of epidemic pneumonia. It has a water-related life cycle. In industrialized cities L. pneumophila is commonly encountered in refrigeration towers and water pipes. Infection is always via infected aerosols to humans. Although many efforts have been made to eradicate Legionella from buildings, it still contaminates the water systems. The town of Alcoy (Valencian Region, Spain) has had recurrent outbreaks since 1999. The strain \"Alcoy 2300/99\" is a particularly persistent and recurrent strain that was isolated during one of the most significant outbreaks between the years 1999-2000.

Results

We have sequenced the genome of the particularly persistent L. pneumophila strain Alcoy 2300/99 and have compared it with four previously sequenced strains known as Philadelphia (USA), Lens (France), Paris (France) and Corby (England).Pangenome analysis facilitated the identification of strain-specific features, as well as some that are shared by two or more strains. We identified: (1) three islands related to anti-drug resistance systems; (2) a system for transport and secretion of heavy metals; (3) three systems related to DNA transfer; (4) two CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) systems, known to provide resistance against phage infections, one similar in the Lens and Alcoy strains, and another specific to the Paris strain; and (5) seven islands of phage-related proteins, five of which seem to be strain-specific and two shared.

Conclusions

The dispensable genome disclosed by the pangenomic analysis seems to be a reservoir of new traits that have mainly been acquired by horizontal gene transfer and could confer evolutionary advantages over strains lacking them.\n\nLegionella pneumophila pangenome reveals strain-specific virulence factors.", "token_count": 503, "char_count": 1955, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8303, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:16.605013", "source": { "split": "train_shard_00001", "doc_id": 3824 }, "chunk_id": "train_shard_00001_3824_0", "global_id": 11073 }, { "text": "Infections with antibiotic resistant pathogens threaten lives and cause substantial costs. For effective interventions, knowledge of the transmission paths of resistant bacteria to humans is essential. In this study, carbapenem resistant bacteria were isolated from the wastewater of a maximum care hospital during a period of two years, starting in the patient rooms and following the sewer system to the effluent of the wastewater treatment plant (WWTP). The bacteria belonged to six different species and 44 different sequence types (STs). The most frequent STs, ST147 K. pneumoniae (blaNDM/blaOXA-48) and ST235 P. aeruginosa (blaVIM) strains, were present at nearly all sampling sites from the hospital to the WWTP effluent. After core genome multi-locus sequence typing (cgMLST), all ST147 K. pneumoniae strains presented a single epidemiological cluster. In contrast, ST235 P. aeruginosa formed five cgMLST clusters and the largest cluster contained the strain from the WWTP effluent, indicating without doubt, a direct dissemination of both high-risk clones into the environment. Thus, there are - at least two - possible transmission pathways to humans, (i) within the hospital by contact with the drains of the sanitary installations and (ii) by recreational or irrigation use of surface waters that have received WWTP effluent. In conclusion, remediation measures must be installed at both ends of the wastewater system, targeting the drains of the hospital as well as at the effluent of the WWTP.\n\nDissemination of carbapenem resistant bacteria from hospital wastewater into the environment.", "token_count": 409, "char_count": 1635, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [ "ST147", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:17.231909", "source": { "split": "train_shard_00001", "doc_id": 3825 }, "chunk_id": "train_shard_00001_3825_0", "global_id": 11074 }, { "text": "The maximum volumetric productivity of beta-galactosidase by a Kluyveromyces marxianus mutant, grown on lactose/corn steep liquor medium for 3 d, was 150 IU l(-1) h(-1) which is twice that of the parent organism. During product formation, mutated cells provided more resistance against thermal inactivation.\n\nKinetics of improved productivity of beta-galactosidase by a cycloheximide-resistant mutant of Kluyveromyces marxianus.", "token_count": 125, "char_count": 428, "word_count": 57, "semantic_coherence": 1, "information_density": 0.8246, "quality_score": 0.9123, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:17.639865", "source": { "split": "train_shard_00001", "doc_id": 3826 }, "chunk_id": "train_shard_00001_3826_0", "global_id": 11075 }, { "text": "A Gram-negative bacterium, designated strain Marseille-Q3452T, was isolated from subgingival dental plaque of a subject suffering from dental plaque biofilm-induced gingivitis on an intact periodontium in Marseille, France. The strain was characterized by 16S rRNA and atpA gene sequence analysis and by conventional phenotypic and chemotaxonomic testing. The average nucleotide identity (ANI) and core genome phylogeny were determined using whole-genome sequences. Although strain Marseille-Q3452T showed 99.72 % 16S rRNA gene sequence similarity with Campylobacter showae strain ATCC 51146T, atpA and ANI analyses revealed divergence between the two strains. The two species could also be distinguished phenotypically on the basis of the absence of flagella and nitrate reduction. On the basis of the results from phenotypic, chemotaxonomic, genomic and phylogenetic analyses and data, we concluded that strain Marseille-Q3452T represents a novel species of the genus Campylobacter, for which the name Campylobacter massiliensis sp. nov. is proposed (=CSUR Q3452=CECT 30263).\n\nIsolation and characterization of Campylobacter massiliensis sp. nov., a novel Campylobacter species detected in a gingivitis subject.", "token_count": 402, "char_count": 1305, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6606, "quality_score": 0.8303, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:18.301997", "source": { "split": "train_shard_00001", "doc_id": 3827 }, "chunk_id": "train_shard_00001_3827_0", "global_id": 11076 }, { "text": "Yacon (Polymnia sanchifolia) extract as a substrate to produce inulinase by Kluyveromyces marxianus var. bulgaricus.", "token_count": 37, "char_count": 116, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:18.681527", "source": { "split": "train_shard_00001", "doc_id": 3828 }, "chunk_id": "train_shard_00001_3828_0", "global_id": 11077 }, { "text": "A mutant strain is provided to produce lactase having excellent lactose decomposing capability with high yield. And a method for mass-producing lactase using the same and a lactase produced therefrom are provided. A lactase highly producing Kluyveromyces fragilis 1-36 mutant is deposited as a deposition number of KCTC 10912BP. To mass-produce lactase, the Kluyveromyces fragilis 1-36 mutant is cultured in a liquid culture medium at a temperature of 25-30 deg.C under pH of 5.0-6.5 for 30-48 hours, wherein the liquid culture medium contains 0.5-1.0%(w/w) of yeast extract, 2.0-4.0%(w/w) of lactose and 1.0-2.0%(w/w) of bacto-peptone.\n\nKLUYVEROMYCES FRAGILIS MUTANT STRAIN AND LACTASE PRODUCED THEREFROM", "token_count": 253, "char_count": 705, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:19.200806", "source": { "split": "train_shard_00001", "doc_id": 3829 }, "chunk_id": "train_shard_00001_3829_0", "global_id": 11078 }, { "text": "

Background

Aeromonas hydrophila infections can cause gastrointestinal symptoms such as diarrhea; however, deep infections are rarely reported. Outbreaks of A. hydrophila are reported more frequently in fish, poultry, and snakes than in humans. This study aimed to track clonal relatedness of deep infections caused by A. hydrophila using whole genome sequencing (WGS).

Methods

We collected three isolates of A. hydrophila in July 19 to August 29, 2019, from patients that underwent spine surgery. Accurate species identification was performed using whole-genome average nucleotide identity (ANI). Antimicrobial susceptibility testing was performed using a VITEK 2 automated AST-N334 Gram-negative susceptibility card system. Antimicrobial resistance and virulence genes were identified using the Comprehensive Antibiotic Resistance Database and Virulence Factor Database VFanalyzer.

Results

All three isolates were identified as A. hydrophila based on ANI and multilocus sequence typing analysis revealed that A. hydrophila belonged to a novel sequence type (ST1172). All three isolates were susceptible to amikacin and levofloxacin; however, they were resistant to piperacillin/tazobactam, ceftriaxone, cefuroxime, cefoxitin, and imipenem. Isolate 19W05620 (patient 3) showed increased ceftazidime resistance (minimum inhibitory concentration ≥ 64 µg/mL). All three isolates possessed the same chromosomally encoded β-lactamases, including blaOXA-724 (β-lactamase), imiH (metallo-β-lactamase), and blaMOX-13 (AmpC) in plasmids.

Conclusions

Our study validated the transmission of a novel carbapenem-resistant A", "token_count": 506, "char_count": 1662, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8465, "entities": { "genes": [ "ST1172" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:19.866162", "source": { "split": "train_shard_00001", "doc_id": 3830 }, "chunk_id": "train_shard_00001_3830_0", "global_id": 11079 }, { "text": "hydrophila sequence type (ST1172) in patients that underwent spine surgery. Control measures should be developed to prevent dissemination of A. hydrophila in the hospital setting.\n\nEmergence and clonal expansion of Aeromonas hydrophila ST1172 that simultaneously produces MOX-13 and OXA-724.", "token_count": 81, "char_count": 291, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [ "ST1172" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:20.237934", "source": { "split": "train_shard_00001", "doc_id": 3830 }, "chunk_id": "train_shard_00001_3830_1", "global_id": 11080 }, { "text": "By transformation of a Saccharomyces cerevisiae mutant strain conditionally expressing the ABF1-gene, a Kluyveromyces marxianus DNA fragment carrying the gene encoding the ABF1-homologue of this yeast strain (KmABF1) was selected. Comparison of the sequence of the KmABF1 gene with that encoding Saccharomyces cerevisiae ABF1 and the previously isolated ABF1-gene from Kluyveromyces lactis (KlABF1) revealed distinct regions displaying considerable homology and therefore most likely representing sequences encoding essential domains. In addition to the domains putatively involved in DNA binding of the protein factor, two short conserved amino acid sequence elements at the C-termini of the homologous proteins were identified, which are proposed to play a part in their trans-acting functions. This is the first report on the structure of a regulatory protein factor from K. marxianus.\n\nStructure of the ABF1-homologue from Kluyveromyces marxianus.", "token_count": 237, "char_count": 951, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6742, "quality_score": 0.8371, "entities": { "genes": [ "ABF1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:20.709522", "source": { "split": "train_shard_00001", "doc_id": 3831 }, "chunk_id": "train_shard_00001_3831_0", "global_id": 11081 }, { "text": "

Background

The bacterial genus Listeria contains pathogenic and non-pathogenic species, including the pathogens L. monocytogenes and L. ivanovii, both of which carry homologous virulence gene clusters such as the prfA cluster and clusters of internalin genes. Initial evidence for multiple deletions of the prfA cluster during the evolution of Listeria indicates that this genus provides an interesting model for studying the evolution of virulence and also presents practical challenges with regard to definition of pathogenic strains.

Results

To better understand genome evolution and evolution of virulence characteristics in Listeria, we used a next generation sequencing approach to generate draft genomes for seven strains representing Listeria species or clades for which genome sequences were not available. Comparative analyses of these draft genomes and six publicly available genomes, which together represent the main Listeria species, showed evidence for (i) a pangenome with 2,032 core and 2,918 accessory genes identified to date, (ii) a critical role of gene loss events in transition of Listeria species from facultative pathogen to saprotroph, even though a consistent pattern of gene loss seemed to be absent, and a number of isolates representing non-pathogenic species still carried some virulence associated genes, and (iii) divergence of modern pathogenic and non-pathogenic Listeria species and strains, most likely circa 47 million years ago, from a pathogenic common ancestor that contained key virulence genes.

Conclusions

Genome evolution in Listeria involved limited gene loss and acquisition as supported by (i) a relatively high coverage of the predicted pan-genome by the observed pan-genome, (ii) conserved genome size (between 2.8 and 3.2 Mb), and (iii) a highly syntenic genome. Limited gene loss in Listeria did include loss of virulence associated genes, likely associated with multiple transitions to a saprotrophic lifestyle. The genus Listeria thus provides an example of a group of bacteria that appears to evolve through a loss of virulence rather than acquisition of virulence characteristics", "token_count": 505, "char_count": 2157, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5668, "quality_score": 0.7834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:21.364417", "source": { "split": "train_shard_00001", "doc_id": 3832 }, "chunk_id": "train_shard_00001_3832_0", "global_id": 11082 }, { "text": "While Listeria includes a number of species-like clades, many of these putative species include clades or strains with atypical virulence associated characteristics. This information will allow for the development of genetic and genomic criteria for pathogenic strains, including development of assays that specifically detect pathogenic Listeria strains.\n\nComparative genomics of the bacterial genus Listeria: Genome evolution is characterized by limited gene acquisition and limited gene loss.", "token_count": 102, "char_count": 495, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:21.741055", "source": { "split": "train_shard_00001", "doc_id": 3832 }, "chunk_id": "train_shard_00001_3832_1", "global_id": 11083 }, { "text": "The plant pathogen Erwinia amylovora can be divided into two host-specific groupings; strains infecting a broad range of hosts within the Rosaceae subfamily Spiraeoideae (e.g., Malus, Pyrus, Crataegus, Sorbus) and strains infecting Rubus (raspberries and blackberries). Comparative genomic analysis of 12 strains representing distinct populations (e.g., geographic, temporal, host origin) of E. amylovora was used to describe the pan-genome of this major pathogen. The pan-genome contains 5751 coding sequences and is highly conserved relative to other phytopathogenic bacteria comprising on average 89% conserved, core genes. The chromosomes of Spiraeoideae-infecting strains were highly homogeneous, while greater genetic diversity was observed between Spiraeoideae- and Rubus-infecting strains (and among individual Rubus-infecting strains), the majority of which was attributed to variable genomic islands. Based on genomic distance scores and phylogenetic analysis, the Rubus-infecting strain ATCC BAA-2158 was genetically more closely related to the Spiraeoideae-infecting strains of E. amylovora than it was to the other Rubus-infecting strains. Analysis of the accessory genomes of Spiraeoideae- and Rubus-infecting strains has identified putative host-specific determinants including variation in the effector protein HopX1(Ea) and a putative secondary metabolite pathway only present in Rubus-infecting strains.\n\nComparative genomics of 12 strains of Erwinia amylovora identifies a pan-genome with a large conserved core.", "token_count": 416, "char_count": 1531, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:22.364907", "source": { "split": "train_shard_00001", "doc_id": 3833 }, "chunk_id": "train_shard_00001_3833_0", "global_id": 11084 }, { "text": "The effect of freeze-drying on viability and probiotic properties of a microbial mixture containing selected bacterial and yeast strains isolated from kefir grains (Lactobacillus kefir, Lactobacillus plantarum, Lactococcus lactis, Saccharomyces cerevisiae and Kluyveromyces marxianus) was studied. The microorganisms were selected according to their potentially probiotic properties in vitro already reported. Two types of formulations were performed, a microbial mixture (MM) suspended in milk and a milk product fermented with MM (FMM). To test the effect of storage on viability of microorganisms, MM and FMM were freeze-dried and maintained at 4°C for six months. After 180 days of storage at 4°C, freeze-dried MM showed better survival rates for each strain than freeze-dried FMM. The addition of sugars (trehalose or sucrose) did not improve the survival rates of any of the microorganisms after freeze-drying. Freeze-drying did not affect the capacity of MM to inhibit growth of Shigella sonnei in vitro, since the co-incubation of this pathogen with freeze-dried MM produced a decrease of 2 log in Shigella viability. The safety of freeze-dried MM was tested in mice and non-translocation of microorganisms to liver or spleen was observed in BALB/c mice feed ad libitum during 7 or 20 days. To our knowledge, this is the first report about the effect of freeze-drying on viability, in vitro probiotic properties and microbial translocation of a mixture containing different strains of both bacteria and yeasts isolated from kefir.\n\nEffect of freeze-drying on viability and in vitro probiotic properties of a mixture of lactic acid bacteria and yeasts isolated from kefir.", "token_count": 445, "char_count": 1679, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5276, "quality_score": 0.7638, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:22.993486", "source": { "split": "train_shard_00001", "doc_id": 3834 }, "chunk_id": "train_shard_00001_3834_0", "global_id": 11085 }, { "text": "Staphylococcus aureus can colonize the human vestibulum nasi for many years. It is unknown whether and, how S. aureus adapts to this ecological niche during colonization. We determined the short (1 and 3 months) and mid-term (36 months) genomic evolution of S. aureus in natural carriers and artificially colonized volunteers. Eighty-five S. aureus strains were collected from 6 natural carriers during 3 years and 6 artificially colonized volunteers during 1 month. Multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis based on whole-genome sequencing (WGS) were carried out. Mutation frequencies within resident bacterial populations over time were quantified using core genome SNP counts (comparing groups of genomes) and pairwise SNP divergence assessment (comparing two genomes from strains originating from one host and sharing identical MLST). SNP counts (within 1-3 months) in all naturally colonizing strains varied from 0 to 757 (median 4). These strains showed random and independent patterns of pairwise SNP divergence (0 to 44 SNPs, median 7). When the different core genome SNP counts over a period of 3 years were considered, the median SNP count was 4 (range 0-26). Host-specific pairwise SNP divergence for the same period ranged from 9 to 57 SNPs (median 20). During short term artificial colonization the mutation frequency was even lower (0-7 SNPs, median 2) and the pairwise SNP distances were 0 to 5 SNPs (median 2). Quantifying mutation frequencies is important for the longitudinal follow-up of epidemics of infections and outbreak management. Random pattern of pairwise SNP divergence between the strains isolated from single carriers suggested that the WGS of multiple colonies is necessary in this context. Over periods up to 3 years, maximum median core genome SNP counts and SNP divergence for the strains studied were 4 and 20 SNPs or lower", "token_count": 514, "char_count": 1930, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5802, "quality_score": 0.7901, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:43:23.659296", "source": { "split": "train_shard_00001", "doc_id": 3835 }, "chunk_id": "train_shard_00001_3835_0", "global_id": 11086 }, { "text": "During artificial colonization, where median core genome SNP and pairwise SNP distance scores were 2, there is no early stage selection of different genotypes. Therefore, we suggest an epidemiological cut off value of 20 SNPs as a marker of S. aureus strain identity during studies on nasal colonization and also outbreaks of infection.\n\nGenomic Evolution of Staphylococcus aureus During Artificial and Natural Colonization of the Human Nose.", "token_count": 119, "char_count": 456, "word_count": 67, "semantic_coherence": 1, "information_density": 0.806, "quality_score": 0.903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:24.040614", "source": { "split": "train_shard_00001", "doc_id": 3835 }, "chunk_id": "train_shard_00001_3835_1", "global_id": 11087 }, { "text": "Using a Saccharomyces cerevisiae ADH1 probe, a gene coding for a cytoplasmic alcohol dehydrogenase from Kluyveromyces marxianus ATCC 12424 (formerly K. fragilis) has been cloned. This gene is able to restore alcoholic fermentation in an ADH-null strain of S. cerevisiae and its encoded protein shows strong similarity with other yeast alcohol dehydrogenases (from S. cerevisiae, Schizosaccharomyces pombe and its close relative K. lactis). The product of the gene expressed in S. cerevisiae co-migrates on native gel with a K. marxianus ADH isozyme which is more active in cells growing on non-fermentable carbon sources than on glucose. This behaviour is in contrast with that of the two cytoplasmic ADH isozymes of K. lactis which are both more active in glucose-growing than in ethanol-growing cells.\n\nSequence of a gene coding for a cytoplasmic alcohol dehydrogenase from Kluyveromyces marxianus ATCC 12424.", "token_count": 275, "char_count": 911, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6232, "quality_score": 0.8116, "entities": { "genes": [ "ADH1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:24.595780", "source": { "split": "train_shard_00001", "doc_id": 3836 }, "chunk_id": "train_shard_00001_3836_0", "global_id": 11088 }, { "text": "Listeria monocytogenes is a foodborne pathogen that causes listeriosis in humans with severe symptoms. In South Korea, listeriosis had only been reported sporadically among hospitalized patients until the first foodborne outbreak occurred in 2018. In this study, a L. monocytogenes strain responsible for this outbreak (FSCNU0110) was characterized via whole genome sequencing and compared with publicly available L. monocytogenes genomes of the same clonal complex (CC). Strain FSCNU0110 belonged to multilocus sequence typing (MLST)-based sequence type 224 and CC224, and core genome MLST-based sublineage 6,178. The strain harbored tetracycline resistance gene tetM, four other antibiotic resistance genes, and 64 virulence genes, including Listeria pathogenicity island 1 (LIPI-1) and LIPI-3. Interestingly, llsX in LIPI-3 exhibited a characteristic SNP (deletion of A in position 4, resulting in a premature stop codon) that was missing among all CC224 strains isolated overseas but was conserved among those from South Korea. In addition, the tetM gene was also detected only in a subset of CC224 strains from South Korea. These findings will provide an essential basis for assessing the characteristics of CC224 strains in South Korea that have shown a potential to cause listeriosis outbreaks.\n\nWhole-genome sequencing of Listeria monocytogenes isolated from the first listeriosis foodborne outbreak in South Korea.", "token_count": 428, "char_count": 1479, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [ "FSCNU0110", "CC224" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:25.222702", "source": { "split": "train_shard_00001", "doc_id": 3837 }, "chunk_id": "train_shard_00001_3837_0", "global_id": 11089 }, { "text": "

Introduction

New Delhi metallo-β-lactamase producing Klebsiella pneumoniae (NDM-Kpn) strains have been causing healthcare-associated infections worldwide. The aim of this study was to describe the molecular mechanisms of antimicrobial resistance and to analyze the clonality of NDM-Kpn isolates collected between January 2019 and June 2020 from patients admitted to hospitals from the Lazio region, Italy.

Methods

We performed a retrospective cohort study. Whole-genome sequencing (WGS) was performed on all NDM-Kpn strains; clonality and genetic relationships were further investigated.

Results

During the surveillance period, 17 NDM-Kpn isolates were obtained from 17 patients admitted to seven different hospitals. Eight different sequence types (STs) were detected: ST147 (n = 4), ST383 (n = 4), ST15 (n = 3), ST11 (n = 2), ST17 (n = 1), ST29 (n = 1), ST307 (n = 1) and the newly identified ST4853 (n = 1). Genetic relationships were further investigated by the WGS-based core genome MLST (cgMLST) scheme, and 5 cluster types (CTs) were identified. Whereas a substantial overall heterogeneity among isolates was detected (8 different STs were identified out of 17 isolates), the strains within each cluster showed a very high level of genome similarity.

Discussion

Our study highlights the key role of surveillance, which allowed taking a picture of a part of the NDM-Kpn strains circulating in Italy, adding further insight into their molecular features.\n\nImportance of Surveillance of New Delhi Metallo-Beta-Lactamase Klebsiella pneumoniae: Molecular Characterization and Clonality of Strains Isolated in the Lazio Region, Italy.", "token_count": 488, "char_count": 1678, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [ "ST29", "ST17", "ST4853", "ST307", "ST383", "ST11", "ST15", "ST147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:25.867547", "source": { "split": "train_shard_00001", "doc_id": 3838 }, "chunk_id": "train_shard_00001_3838_0", "global_id": 11090 }, { "text": "Streptococcus agalactiae is an emerging pathogen of nonpregnant human adults worldwide and a reemerging pathogen of dairy cattle in parts of Europe. To learn more about interspecies transmission of this bacterium, we compared contemporaneously collected isolates from humans and cattle in Finland and Sweden. Multilocus sequence typing identified 5 sequence types (STs) (ST1, 8, 12, 23, and 196) shared across the 2 host species, suggesting possible interspecies transmission. More than 54% of the isolates belonged to those STs. Molecular serotyping and pilus island typing of those isolates did not differentiate between populations isolated from different host species. Isolates from humans and cattle differed in lactose fermentation, which is encoded on the accessory genome and represents an adaptation to the bovine mammary gland. Serotype IV-ST196 isolates were obtained from multiple dairy herds in both countries. Cattle may constitute a previously unknown reservoir of this strain.\n\nStreptococcus agalactiae Serotype IV in Humans and Cattle, Northern Europe1.", "token_count": 273, "char_count": 1081, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [ "ST196", "ST1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:26.429420", "source": { "split": "train_shard_00001", "doc_id": 3839 }, "chunk_id": "train_shard_00001_3839_0", "global_id": 11091 }, { "text": "

Background

Livestock-associated meticillin-resistant Staphylococcus aureus (LA-MRSA) clonal complex (CC) 398 may be transmitted and cause morbidity and mortality in hospitals. The economic cost of stopping hospital transmission of LA-MRSA CC398 is poorly described. Early detection of transmission may limit the extent of the intervention.

Aim

To evaluate core genome multi-locus sequence typing (cgMLST) for detecting transmission chains and to estimate the costs for interventions to prevent further spread after discovery of hospital transmission of LA-MRSA CC398.

Methods

Five patients were involved in two episodes of transmission of LA-MRSA CC398 in a hospital. Standard interventions including MRSA screening of patients and healthcare workers were initiated. Whole genome sequences of the five isolates and 17 epidemiologically unrelated MRSA CC398 isolates from other hospitalized patients were analysed by single nucleotide polymorphism (SNP) comparisons and cgMLST. The economic costs of constraining transmission were calculated from relevant sources.

Findings

The five isolates suspected to be involved in hospital transmission clustered with ≤2 SNPs in the draft genome sequences with some distance to other isolates. cgMLST allocated the five isolates to the same type, which was different from all but two of the sporadic isolates. Furthermore, cgMLST separated the five transmission isolates from all other isolates. The economic costs of the outbreak interventions exceeded €11,000 per patient.

Conclusion

LA-MRSA CC398 is transmittable in hospitals, and intervention against transmission may reach considerable costs. cgMLST is useful in surveillance of hospital transmission of LA-MRSA.\n\nCore genome multi-locus sequence typing as an essential tool in a high-cost livestock-associated meticillin-resistant Staphylococcus aureus CC398 hospital outbreak.", "token_count": 477, "char_count": 1908, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5447, "quality_score": 0.7724, "entities": { "genes": [ "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:27.075949", "source": { "split": "train_shard_00001", "doc_id": 3840 }, "chunk_id": "train_shard_00001_3840_0", "global_id": 11092 }, { "text": "Under bile salt treatment, strains display significant differences in their tolerance ability, suggesting the existence of diverse resistance mechanisms in Lactobacillus; however, the genes involved in this protective process are not fully understood. In this study, novel target genes associated with bile salt tolerance in Lactobacillus were identified using comparative genomics for PCR detection and the rapid screening of tolerant strains. The bile salt tolerance of 107 lactobacilli isolated from different origins was assessed, and 26 strains with comparatively large differences were selected for further comparative genomic analysis. Tolerant strains had 112 specific genes that were enriched in the phosphotransferase system, the two-component system, carbohydrate metabolism, and the ATP-binding cassette transporter. Six genes from Lactobacillus were cloned into the inducible lactobacillal expression vector pSIP403. Overexpression in the host strain increased its tolerance ability by 11.86-18.08%. The novel genes identified here can be used as targets to design primers for the rapid screening of bile salt-tolerant lactobacilli. Altogether, these results deepen our understanding of bile salt tolerance mechanisms in Lactobacillus and provide a basis for further rapid assessments of tolerant strains.\n\nIdentification of Novel Bile Salt-Tolerant Genes in Lactobacillus Using Comparative Genomics and Its Application in the Rapid Screening of Tolerant Strains.", "token_count": 397, "char_count": 1525, "word_count": 201, "semantic_coherence": 1, "information_density": 0.5771, "quality_score": 0.7886, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:27.698481", "source": { "split": "train_shard_00001", "doc_id": 3841 }, "chunk_id": "train_shard_00001_3841_0", "global_id": 11093 }, { "text": "

Objective

To investigate the biochemical characteristics of the chitosanase from Fusarium solani, and its application in chitooligosaccharides production, and express the chitosanase gene (csn) in a Saccharomyces cerevisiae industrial strain.

Methods

The chitosanase cDNA (EU263917) was amplified by reverse transcription-mediated PCR (RT-PCR). A His-chitosanase fusion protein was expressed in E. coli DE3. This protein was purified and characterized. Thin-layer chromatography (TLC) and high performance liquid chromatography (HPLC) were used to analyze the hydrolysates of this enzyme when it acted on 85% deacetylated chitosan. In addition, the csn cDNA was also fused to the inulinase (INU1A) signal sequence from Kluyveromyces marxianus. The fusion sequence was transferred into S. cerevisiae industrial strain N-27.

Results

The purified chitosanase had a specific activity of 2.5 U/mg. The enzyme showed the maximum activity at 50 degrees C, which was different from the first reported chitosanase that from F. solanif. sp. Phaseoli. TLC and HPLC results indicated that most of the hydrolysis products were chitooligosaccharides with a polymerization below 10, and no monomers were detected. Furthermore, chitosanase activity was detected in the culture medium of the recombinant S. cerevisiae cultures, and the volume activity reached 50.2 mU/mL. This result indicated that the recombinant protein was secretively expressed in S. cerevisiae.

Conclusion

The chitosanase from F. solani 0114 is an endochitosanase. Because of its special characteristics, this enzyme is very useful in chitooligosaccharides production, and the construction of recombinant S. cerevisiae made a step towards the large-scale production of this enzyme.", "token_count": 508, "char_count": 1765, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [ "EU263917", "DE3", "INU1A" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:28.360240", "source": { "split": "train_shard_00001", "doc_id": 3842 }, "chunk_id": "train_shard_00001_3842_0", "global_id": 11094 }, { "text": "[Characterization of a chitosanase from Fusarium solani and its expression in an industrial strain of Saccharomyces cerevisiae].", "token_count": 32, "char_count": 128, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:28.720169", "source": { "split": "train_shard_00001", "doc_id": 3842 }, "chunk_id": "train_shard_00001_3842_1", "global_id": 11095 }, { "text": "Background: Fermentable oligosaccharides, disaccharides, monosaccharides and polyols (FODMAPs) are an heterogeneous group of compounds that can be poorly digested and may have a range of effects on gastrointestinal processes. FODMAPs are found in a wide variety of foods, including bread. FODMAPs' intake is associated with the onset of symptoms of irritable bowel syndrome (IBS). On the other hand, some FODMAPs contribute to the healthy maintenance of intestinal microbiota. Volume increase of bread dough commonly relies on the use of two biological leavening agents, sourdough and baker's yeast and, in some cases, a combination of both. Scope and Approach: The main objective of this review is to discuss the association between FODMAPs and IBS, beneficial effects of FODMAPs on healthy subjects and potential impact of biological leavening agents on FODMAPs content of bread. Key Findings and Conclusion: Given that yeasts and lactic acid bacteria, the dominant microorganisms in sourdough, may degrade FODMAPs, it would be possible to modulate the FODMAPs concentration in bread, thus positively affecting consumers' health.\n\nEffects of Sourdough on FODMAPs in Bread and Potential Outcomes on Irritable Bowel Syndrome Patients and Healthy Subjects.", "token_count": 329, "char_count": 1276, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6324, "quality_score": 0.8162, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:29.284406", "source": { "split": "train_shard_00001", "doc_id": 3843 }, "chunk_id": "train_shard_00001_3843_0", "global_id": 11096 }, { "text": "

Background

Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species.

Results

We report new high-quality genomes of O. tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene islands and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia.

Conclusions

Complete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have larger genomes compared with most other Rickettsiaceae, with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.\n\nLong-read whole genome sequencing and comparative analysis of six strains of the human pathogen Orientia tsutsugamushi.", "token_count": 471, "char_count": 1984, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6231, "quality_score": 0.8116, "entities": { "genes": [ "UT176", "TA686", "UT76" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:29.968756", "source": { "split": "train_shard_00001", "doc_id": 3844 }, "chunk_id": "train_shard_00001_3844_0", "global_id": 11097 }, { "text": "

Background

Corynebacterium diphtheriae is highly transmissible and can cause large diphtheria outbreaks where vaccination coverage is insufficient. Sporadic cases or small clusters are observed in high-vaccination settings. The phylogeography and short timescale evolution of C. diphtheriae are not well understood, in part due to a lack of harmonized analytical approaches of genomic surveillance and strain tracking.

Methods

We combined 1,305 genes with highly reproducible allele calls into a core genome multilocus sequence typing (cgMLST) scheme. We analyzed cgMLST genes diversity among 602 isolates from sporadic clinical cases, small clusters or large outbreaks. We defined sublineages based on the phylogenetic structure within C. diphtheriae and strains based on the highest number of cgMLST mismatches within documented outbreaks. We performed time-scaled phylogenetic analyses of major sublineages.

Results

The cgMLST scheme showed high allele call rate in C. diphtheriae and the closely related species C. belfantii and C. rouxii . We demonstrate its utility to delineate epidemiological case clusters and outbreaks using a 25 mismatches threshold, and reveal a number of cryptic transmission chains, most of which are geographically restricted to one or a few adjacent countries. Subcultures of the vaccine strain PW8 differed by up to 20 cgMLST mismatches. Phylogenetic analyses revealed short timescale evolutionary gain or loss of the diphtheria toxin and biovar-associated genes. We devised a genomic taxonomy of strains and deeper sublineages (defined using a 500 cgMLST mismatches threshold), currently comprising 151 sublineages, only a few of which are geographically widespread based on current sampling. The cgMLST genotyping tool and nomenclature was made publicly accessible at https://bigsdb.pasteur.fr/diphtheria ", "token_count": 499, "char_count": 1868, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [ "PW8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:30.643567", "source": { "split": "train_shard_00001", "doc_id": 3845 }, "chunk_id": "train_shard_00001_3845_0", "global_id": 11098 }, { "text": "

Conclusions

Standardized genome-scale strain genotyping will help tracing transmission and geographic spread of C. diphtheriae . The unified genomic taxonomy of C. diphtheriae strains provides a common language for studies into the ecology, evolution and virulence heterogeneity among C. diphtheriae sublineages.\n\nGenomic epidemiology and strain taxonomy ofCorynebacterium diphtheriae", "token_count": 116, "char_count": 400, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7708, "quality_score": 0.8854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:31.058632", "source": { "split": "train_shard_00001", "doc_id": 3845 }, "chunk_id": "train_shard_00001_3845_1", "global_id": 11099 }, { "text": "Failure of food preservation is frequently caused by thermostable spores of members of the Bacillaceae family, which show a wide spectrum of resistance to cleaning and preservation treatments. We constructed and validated a mixed-species genotyping array for 6 Bacillus species, including Bacillus subtilis, Bacillus licheniformis, Bacillus pumilus, Bacillus sporothermodurans, Bacillus cereus and Bacillus coagulans, and 4 Geobacillus species, including Geobacillus stearothermophilus, Geobacillus thermocatenulatus, Geobacillus toebii and Geobacillus sp., in order to track food spoilage isolates from ingredient to product. The discriminating power of the array was evaluated with sets of 42 reference and 20 test strains. Bacterial isolates contain a within-species-conserved core genome comprising 68-88% of the entire genome and a non-conserved accessory genome comprising 7-22%. The majority of the core genome markers do not hybridise between species, thus they allow for efficient discrimination at the species level. The accessory genome array markers provide high-resolution discrimination at the level of individual isolates from a single species. In conclusion, the reported mixed-species microarray contains discriminating markers that allow rapid and cost-effective typing of Bacillus food spoilage bacteria in a wide variety of food products.\n\nA mixed-species microarray for identification of food spoilage bacilli.", "token_count": 375, "char_count": 1431, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:32.360895", "source": { "split": "train_shard_00001", "doc_id": 3846 }, "chunk_id": "train_shard_00001_3846_0", "global_id": 11100 }, { "text": "Antistress effect of extracellular peptides on UV irradiated yeast of different phylogenetic groups was studied. Yeast from different ecotopes and taxonomic groups exposed to UV radiation of a lethal intensity showed a protective effect and reactivating effect with participation of extracellular peptides. The highest protective activity was found in peptide reactivation factors (RFs) of bakery yeast-Saccharomyces cerevisiae, Kluyveromyces fragilis, and Candida utilis; the highest reactivating activity was exhibited by factors of the above-mentioned cultures and Debariomyces hansenii. Cross-protective and reactivating effects of RFs of yeast belonging to different taxonomic groups were demonstrated. Cross-protection increased two to three times after preexposure of reactivation factors to UV light (activation) in contrast to their reactivating effect.\n\n[Antistress cross-protection of UV irradiated yeast cells with participation of extracellular peptide factors].", "token_count": 238, "char_count": 975, "word_count": 126, "semantic_coherence": 1, "information_density": 0.5794, "quality_score": 0.7897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:32.835339", "source": { "split": "train_shard_00001", "doc_id": 3847 }, "chunk_id": "train_shard_00001_3847_0", "global_id": 11101 }, { "text": "International travel contributes to the global spread of antimicrobial resistance. Travelers' diarrhea exacerbates the risk of acquiring multidrug-resistant organisms and can lead to persistent gastrointestinal disturbance post-travel. However, little is known about the impact of diarrhea on travelers' gut microbiomes, and the dynamics of these changes throughout travel. Here, we assembled a cohort of 159 international students visiting the Andean city of Cusco, Peru and applied next-generation sequencing techniques to 718 longitudinally-collected stool samples. We find that gut microbiome composition changed significantly throughout travel, but taxonomic diversity remained stable. However, diarrhea disrupted this stability and resulted in an increased abundance of antimicrobial resistance genes that can remain high for weeks. We also identified taxa differentially abundant between diarrheal and non-diarrheal samples, which were used to develop a classification model that distinguishes between these disease states. Additionally, we sequenced the genomes of 212 diarrheagenic Escherichia coli isolates and found those from travelers who experienced diarrhea encoded more antimicrobial resistance genes than those who did not. In this work, we find the gut microbiomes of international travelers' are resilient to dysbiosis; however, they are also susceptible to colonization by multidrug-resistant bacteria, a risk that is more pronounced in travelers with diarrhea.\n\nImpact of international travel and diarrhea on gut microbiome and resistome dynamics.", "token_count": 366, "char_count": 1568, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:33.411804", "source": { "split": "train_shard_00001", "doc_id": 3848 }, "chunk_id": "train_shard_00001_3848_0", "global_id": 11102 }, { "text": "

Background

Neisseria meningitidis is a naturally transformable, facultative pathogen colonizing the human nasopharynx. Here, we analyze on a genome-wide level the impact of recombination on gene-complement diversity and virulence evolution in N. meningitidis. We combined comparative genome hybridization using microarrays (mCGH) and multilocus sequence typing (MLST) of 29 meningococcal isolates with computational comparison of a subset of seven meningococcal genome sequences.

Principal findings

We found that lateral gene transfer of minimal mobile elements as well as prophages are major forces shaping meningococcal population structure. Extensive gene content comparison revealed novel associations of virulence with genetic elements besides the recently discovered meningococcal disease associated (MDA) island. In particular, we identified an association of virulence with a recently described canonical genomic island termed IHT-E and a differential distribution of genes encoding RTX toxin- and two-partner secretion systems among hyperinvasive and non-hyperinvasive lineages. By computationally screening also the core genome for signs of recombination, we provided evidence that about 40% of the meningococcal core genes are affected by recombination primarily within metabolic genes as well as genes involved in DNA replication and repair. By comparison with the results of previous mCGH studies, our data indicated that genetic structuring as revealed by mCGH is stable over time and highly similar for isolates from different geographic origins.

Conclusions

Recombination comprising lateral transfer of entire genes as well as homologous intragenic recombination has a profound impact on meningococcal population structure and genome composition. Our data support the hypothesis that meningococcal virulence is polygenic in nature and that differences in metabolism might contribute to virulence.\n\nVirulence evolution of the human pathogen Neisseria meningitidis by recombination in the core and accessory genome.", "token_count": 481, "char_count": 2051, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:34.063510", "source": { "split": "train_shard_00001", "doc_id": 3849 }, "chunk_id": "train_shard_00001_3849_0", "global_id": 11103 }, { "text": "

Background

Staphylococcus aureus (S. aureus) is a main pathogen associated with different types of hospital acquired infections. There are various factors associated with the virulence of S. aureus. Among these factors are biofilm formation, antibiotics resistance, alpha-toxin, and phenol-soluble modulins (PSMs) which are encoded by genes within the core genome. The aims of the present study were to identify the prevalence psm-mec gene in MRSA isolated from different types of hospital acquired infections and to study the association of this gene with biofilm formation capacity in S. aureus.

Methods

The study was a retrospective, cross-sectional study that included 150 isolates of MRSA isolated from different clinical samples. Methicillin resistant S. aureus was identified as resistance to cefoxitin disc by disc diffusion method, biofilm detection by microplate method, and polymerase chain reaction (PCR) was used for detection of PSMα gene.

Results

MRSA was identified by phenotypic detection with resistance to cefoxitin disc in 64.7% of the isolated S. aureus. Biofilm formation was detected in 70 isolates (46.7%) with high titer in 61 isolates, intermediate titer in 6 isolates and low titer in 4 isolates. PSMα gene detected in 65 (43.3%) of the isolates, Table 1. There was significant association between the presence of PSMα gene and formation of biofilm (p = 0.0001). All detected PSMα genes were present in 65 (92.8%) of positive S. aureus isolates for biofilm formation.

Conclusions

There was high prevalence of the PSMα gene in MRSA with association with high titer biofilm forming S. aureus. The absence of PSMα gene in MRSA strains may reduce the ability of MRSA to form biofilm.", "token_count": 482, "char_count": 1735, "word_count": 258, "semantic_coherence": 1, "information_density": 0.4845, "quality_score": 0.7422, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:34.711167", "source": { "split": "train_shard_00001", "doc_id": 3850 }, "chunk_id": "train_shard_00001_3850_0", "global_id": 11104 }, { "text": "Molecular Study of Mec-Phenol Soluble Modulin Gene in Methicillin Resistant Staphylococcus Aureus.", "token_count": 35, "char_count": 98, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:35.068330", "source": { "split": "train_shard_00001", "doc_id": 3850 }, "chunk_id": "train_shard_00001_3850_1", "global_id": 11105 }, { "text": "Extracellular beta-galactosidase produced by a strain of Aspergillus niger van Tiegh was purified to homogeneity using a combination of gel filtration, ion-exchange, chromatofocusing, and hydrophobic interaction chromatographies. The enzyme displayed a temperature optimum of 65 degrees C and a low pH optimum of between 2.0 and 4.0. The monomeric glycosylated enzyme displayed a molecular mass of 129 kDa and an isoelectric point of 4.7. Protein database similarity searching using mass spectrometry-derived sequence data indicate that the enzyme shares homology with a previously sequenced A. niger beta-galactosidase. Unlike currently commercialised products, the enzyme displayed a high level of stability when exposed to simulated gastric conditions in vitro, retaining 68+/-2% of original activity levels. This acid-stable, acid-active beta-galactosidase was formulated, along with a neutral beta-galactosidase from Kluyveromyces marxianus DSM5418, in a novel two-segment capsule system designed to ensure delivery of enzymes of appropriate physicochemical properties to both stomach and small intestine. When subjected to simulated full digestive tract conditions, the twin lactase-containing capsule hydrolyzed, per unit activity, some 3.5-fold more lactose than did the commercial supplemental enzyme. The acid-stable, acid-active enzyme, along with the novel two-segment delivery system, may prove beneficial in the more effective treatment of lactose intolerance.\n\nA novel acid-stable, acid-active beta-galactosidase potentially suited to the alleviation of lactose intolerance.", "token_count": 425, "char_count": 1589, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.831, "entities": { "genes": [ "DSM5418" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:36.055836", "source": { "split": "train_shard_00001", "doc_id": 3851 }, "chunk_id": "train_shard_00001_3851_0", "global_id": 11106 }, { "text": "

Aims

To investigate if Clostridium (Clostridioides) difficile infection (CDI), traditionally thought of as hospital-acquired, can be genomically linked to hospital or community environmental sources, and to define possible importation routes from the community to the hospital.

Methods and results

In 2019, C. difficile was isolated from 89/300 (29.7%) floor and 96/300 (32.0%) shoe sole samples at a tertiary hospital in Western Australia. Non-toxigenic C. difficile ribotype (RT) 010 predominated among floor (96.6%) and shoe sole (73.2%) isolates, while toxigenic RT 014/020 was most prevalent among contemporaneous clinical cases (33.0%) at the hospital. Whole-genome sequencing and high-resolution core genome single nucleotide polymorphism (cgSNP) analysis on C. difficile strains from hospital and community sources showed no clinical C. difficile RT 014/020 strains were genetically related, and evidence of frequent long-distance, multi-directional spread between humans, animals and the environment. In addition, cgSNP analysis of environmental RT 010 strains suggested transportation of C. difficile via shoe soles.

Conclusions

While C. difficile RT 014/020 appears to spread via routes outside the healthcare system, RT 010 displayed a pattern of possible importation from the community into the hospital.

Significance and impact of study

These findings suggest developing community-based infection prevention and control strategies could significantly lower rates of CDI in the hospital setting.\n\nWhole-genome sequencing links Clostridium (Clostridioides) difficile in a single hospital to diverse environmental sources in the community.", "token_count": 464, "char_count": 1679, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5945, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:36.695294", "source": { "split": "train_shard_00001", "doc_id": 3852 }, "chunk_id": "train_shard_00001_3852_0", "global_id": 11107 }, { "text": "Hypogammaglobulinemia (HG) predisposes patients to gastrointestinal Campylobacter infections. This prospective study determined the prevalence of Campylobacter in stool samples from patients with immunoglobulin (Ig)-substituted HG at Bordeaux University Hospital. 73 patients (42 women, median age: 61) receiving Ig substitution therapy were enrolled from July 2022 to July 2024. Stool samples were analysed with culture, PCR, faecal calprotectin levels, and immune profiles were also assessed. A second stool sample was collected from 38 patients after 6-12 months, totalling 111 samples. 53 patients had primary HG (32 common variable immunodeficiency, 7 IgG subclass deficiencies, 4 Bruton's agammaglobulinemias) and 20 had secondary HG (7 drug-induced, 8 lymphoid hemopathy-related, 5 mixed). Campylobacter were detected in 11 patients (15.1%), with species identified as Campylobacter jejuni, Campylobacter coli, and Aliarcobacter butzleri. Diarrhea was reported in 42% of Campylobacter-positive patients versus 15% of negative patients. Campylobacter-positive patients exhibited higher median faecal calprotectin levels (255 µg/g vs. 52 µg/g). Among positive patients, 44% (versus 34% in negative patients) had non-infectious complications such as immune complications. Mean residual IgG levels were similar between groups, although IgA and IgM were lower in Campylobacter-positive patients (0 vs. 0.36 g/L and 0.17 vs. 0.40 g/L, respectively). The mean CD4/CD8 ratio was also lower in the positive group (1.71 ± 0.85 vs. 2.06 ± 1.18)", "token_count": 509, "char_count": 1540, "word_count": 212, "semantic_coherence": 1, "information_density": 0.7028, "quality_score": 0.8514, "entities": { "genes": [ "CD8", "CD4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:37.354148", "source": { "split": "train_shard_00001", "doc_id": 3853 }, "chunk_id": "train_shard_00001_3853_0", "global_id": 11108 }, { "text": "This study reveals a high prevalence of Campylobacter in HG patients despite receiving Ig therapy. Elevated faecal levels of calprotectin in symptomatic patients suggests active infection. Screening for Campylobacter should be considered in HG patients presenting with digestive symptoms.\n\nStool Screening for Campylobacter Species in Hypogammaglobulinemic Patients Receiving Immunoglobulin Therapy.", "token_count": 100, "char_count": 399, "word_count": 50, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:37.728696", "source": { "split": "train_shard_00001", "doc_id": 3853 }, "chunk_id": "train_shard_00001_3853_1", "global_id": 11109 }, { "text": "The sum of unique genes in all genomes of a bacterial species is referred to as the pan-genome and is comprised of variably absent or present accessory genes and universally present core genes. The accessory genome is an important source of genetic variability in bacterial populations, allowing sub-populations of bacteria to better adapt to specific niches. Such subgroups may themselves have a relatively stable core genome that may influence host preference, virulence, or an association with specific disease syndromes. The core genome provides a useful means of phylogenetic reconstruction as well as contributing to phenotypic heterogeneity. Variation within the pan-genome forms the basis of comparative genotyping techniques, which have evolved alongside technology. Current high-throughput sequencing platforms have created an unprecedented opportunity for comparisons among multiple, closely related genomes. The computer algorithms and software for such comparisons continue to evolve and promise exciting advances in the world of bacterial comparative genomics. We review genotyping techniques based upon phenotypic traits, both core and accessory genomes, and look at some of the software programs currently available to perform whole-genome comparative analyses.\n\nEverything at once: comparative analysis of the genomes of bacterial pathogens.", "token_count": 281, "char_count": 1358, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:38.290245", "source": { "split": "train_shard_00001", "doc_id": 3854 }, "chunk_id": "train_shard_00001_3854_0", "global_id": 11110 }, { "text": "Whole genome sequencing (WGS) is increasingly used for epidemiological investigations of pathogens. While SNP variant calling is currently considered as the most suitable method, the choice of a representative reference genome and the isolate dependency of results limit standardization and affect resolution in an unknown manner. Whole or core genome Multi Locus Sequence Typing (wg-, cg-MLST) represents an attractive alternative. Here, we assess the accuracy of wg- and cg-MLST by comparing results of four Pseudomonas aeruginosa datasets for which epidemiological and genomic data were previously described. Three datasets included 155 isolates from three different sequence types (ST) of P. aeruginosa collected in our ICUs over a 5-year period. The fourth dataset consisted of 10 isolates from an investigation of P. aeruginosa contaminated hand soap. All isolates were previously analyzed by a core SNP approach. In this study, wg- and cg-MLST were performed in BioNumericsTM using a scheme developed by Applied-Maths. Correlation between SNP calling and wg- or cg-MLST results were evaluated by calculating linear regressions and their coefficient of correlations (R 2) between the number of SNPs and the number of allele differences in pairwise comparison of isolates. The number of SNPs and allele difference between isolates with close epidemiological linkage varies between 0-26 and 0-13, respectively. When compared to core-SNP calling, a higher coefficient of correlation was obtained with cgMLST (R 2 of 0.92-0.99) than with wgMLST (0.78-0.99). In one dataset, a putative homologous recombination of a large DNA fragment (202 loci) was identified among these isolates, affecting its phylogeny, but with no impact on the epidemiological analysis of outbreak isolates. In conclusion, we showed that the P", "token_count": 497, "char_count": 1888, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6283, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:38.941363", "source": { "split": "train_shard_00001", "doc_id": 3855 }, "chunk_id": "train_shard_00001_3855_0", "global_id": 11111 }, { "text": "aeruginosa wgMLST scheme in BioNumericsTM is as discriminatory as the core-SNP calling approach and apparently useful for outbreak investigations. We also showed that epidemiological linked isolates showed less than 26 SNPs or 13 allele differences. These are important figures for the distinction between outbreak and non-outbreak isolates when interpreting WGS results. However, as P. aeruginosa is highly recombinant, a cgMLST approach is preferable and caution should be addressed to possible recombination of large DNA fragments.\n\nComparison of Whole Genome (wg-) and Core Genome (cg-) MLST (BioNumericsTM) Versus SNP Variant Calling for Epidemiological Investigation of Pseudomonas aeruginosa.", "token_count": 202, "char_count": 739, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:39.401346", "source": { "split": "train_shard_00001", "doc_id": 3855 }, "chunk_id": "train_shard_00001_3855_1", "global_id": 11112 }, { "text": "Contaminated environments can pose new challenges when new contaminants appear and can select organisms with new genetic and metabolic strategies. The increased presence of Te(IV) in the environment is becoming more important. This highlights how underexplored the investigation of how bacteria molecularly respond to less common environmental contaminants, such as tellurite when compared to other metals/ metalloids. Understanding what tools an organism uses from its genetic pool when responding to a new contaminant requires a multiple-technique approach, such as metabolic tests and differential omics analysis. These analyses provide a full metabolic and phenotypical map of stress response that can include new resistance mechanisms, whether specific or not. This study aimed to determine if Bacillus altitudinis strain 3W19, isolated from a Te(IV) contaminated site, presents specific changes at the proteomic level when exposed to the metalloid. In strain 3W19, growth in the presence of Te(IV) upregulated pathways of amino acid metabolism and membrane transport and downregulated pathways of carbohydrate metabolism. Growth in the presence of Te(IV) also induced the formation of reactive oxygen species and lowered the metabolic activity of the strain. This metal led to the overexpression of the proteins of the ter gene cluster. When compared with other strains, the ter system identified in this strain differed in genomic organization from related Bacillus sp. strains. Together, these strain-specificities can contribute to understanding its Te(IV) resistance phenotype.\n\nMetabolic response of tellurite resistant Bacillus altitudinis strain 3W19 highlights the potential as a model organism for bioremediation.", "token_count": 386, "char_count": 1728, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5918, "quality_score": 0.7959, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:40.020211", "source": { "split": "train_shard_00001", "doc_id": 3856 }, "chunk_id": "train_shard_00001_3856_0", "global_id": 11113 }, { "text": "We present the genome sequences of Salmonella enterica tailed phages Sasha, Sergei, and Solent. These phages, along with Salmonella phages 9NA, FSL_SP-062, and FSL_SP-069 and the more distantly related Proteus phage PmiS-Isfahan, have similarly sized genomes of between 52 and 57 kbp in length that are largely syntenic. Their genomes also show substantial genome mosaicism relative to one another, which is common within tailed phage clusters. Their gene content ranges from 80 to 99 predicted genes, of which 40 are common to all seven and form the core genome, which includes all identifiable virion assembly and DNA replication genes. The total number of gene types (pangenome) in the seven phages is 176, and 59 of these are unique to individual phages. Their core genomes are much more closely related to one another than to the genome of any other known phage, and they comprise a well-defined cluster within the family Siphoviridae To begin to characterize this group of phages in more experimental detail, we identified the genes that encode the major virion proteins and examined the DNA packaging of the prototypic member, phage 9NA. We show that it uses a pac site-directed headful packaging mechanism that results in virion chromosomes that are circularly permuted and about 13% terminally redundant. We also show that its packaging series initiates with double-stranded DNA cleavages that are scattered across a 170-bp region and that its headful measuring device has a precision of ±1.8%.IMPORTANCE The 9NA-like phages are clearly highly related to each other but are not closely related to any other known phage type. This work describes the genomes of three new 9NA-like phages and the results of experimental analysis of the proteome of the 9NA virion and DNA packaging into the 9NA phage head", "token_count": 496, "char_count": 1853, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5533, "quality_score": 0.7766, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:40.672893", "source": { "split": "train_shard_00001", "doc_id": 3857 }, "chunk_id": "train_shard_00001_3857_0", "global_id": 11114 }, { "text": "There is increasing interest in the biology of phages because of their potential for use as antibacterial agents and for their ecological roles in bacterial communities. 9NA-like phages that infect two bacterial genera have been identified to date, and related phages infecting additional Gram-negative bacterial hosts are likely to be found in the future. This work provides a foundation for the study of these phages, which will facilitate their study and potential use.\n\nDNA Packaging and Genomics of the Salmonella 9NA-Like Phages.", "token_count": 126, "char_count": 542, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7195, "quality_score": 0.8598, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:41.056286", "source": { "split": "train_shard_00001", "doc_id": 3857 }, "chunk_id": "train_shard_00001_3857_1", "global_id": 11115 }, { "text": "The microflora of Tibetan kefir grains was investigated by culture- independent methods. Denaturing gradient gel electrophoresis (DGGE) of partially amplified 16S rRNA for bacteria and 26S rRNA for yeasts, followed by sequencing of the most intense bands, showed that the dominant microorganisms were Pseudomonas sp., Leuconostoc mesenteroides, Lactobacillus helveticus, Lactobacillus kefiranofaciens, Lactococcus lactis, Lactobacillus kefiri, Lactobacillus casei, Kazachstania unispora, Kluyveromyces marxianus, Saccharomyces cerevisiae, and Kazachstania exigua. The bacterial communities between three kinds of Tibetan kefir grains showed 78-84% similarity, and yeasts 80-92%. The microflora is held together in the matrix of fibrillar material composed largely of a water-insoluble polysaccharide.\n\nAnalysis of the microflora in Tibetan kefir grains using denaturing gradient gel electrophoresis.", "token_count": 277, "char_count": 899, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6964, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:41.634775", "source": { "split": "train_shard_00001", "doc_id": 3858 }, "chunk_id": "train_shard_00001_3858_0", "global_id": 11116 }, { "text": "A new cytosine deaminase gene and protein from Candida kefyr are provided. This protein has increased ability to convert the 5-fluorocytosine prodrug to its toxic form when compared against the E. coli enzyme.\n\nCandida Kefyr Cytosine Deaminase", "token_count": 71, "char_count": 243, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8108, "quality_score": 0.9054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:42.038749", "source": { "split": "train_shard_00001", "doc_id": 3859 }, "chunk_id": "train_shard_00001_3859_0", "global_id": 11117 }, { "text": "

Background

Next-generation sequencing (NGS) is now a commonplace tool for molecular characterisation of virtually any species of interest. Despite the ever-increasing use of NGS in laboratories worldwide, analysis of whole genome re-sequencing (WGS) datasets from start to finish remains nontrivial due to the fragmented nature of NGS software and the lack of experienced bioinformaticists in many research teams.

Findings

We describe SPANDx (Synergised Pipeline for Analysis of NGS Data in Linux), a new tool for high-throughput comparative analysis of haploid WGS datasets comprising one through thousands of genomes. SPANDx consolidates several well-validated, open-source packages into a single tool, mitigating the need to learn and manipulate individual NGS programs. SPANDx incorporates BWA for alignment of raw NGS reads against a reference genome or pan-genome, followed by data filtering, variant calling and annotation using Picard, GATK, SAMtools and SnpEff. BEDTools has also been included for genetic locus presence/absence (P/A) determination to easily visualise the core and accessory genomes. Additional SPANDx features include construction of error-corrected single-nucleotide polymorphism (SNP) and insertion-deletion matrices, and P/A matrices, to enable user-friendly visualisation of genetic variants. The SNP matrices generated using VCFtools and GATK are directly importable into PAUP*, PHYLIP or RAxML for downstream phylogenetic analysis. SPANDx has been developed to handle NGS data from Illumina, Ion Personal Genome Machine (PGM) and 454 platforms, and we demonstrate that it has comparable performance across Illumina MiSeq/HiSeq2000 and Ion PGM data.

Conclusion

SPANDx is an all-in-one tool for comprehensive haploid WGS analysis. SPANDx is open source and is freely available at: http://sourceforge.net/projects/spandx/.", "token_count": 491, "char_count": 1874, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6815, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:42.711456", "source": { "split": "train_shard_00001", "doc_id": 3860 }, "chunk_id": "train_shard_00001_3860_0", "global_id": 11118 }, { "text": "SPANDx: a genomics pipeline for comparative analysis of large haploid whole genome re-sequencing datasets.", "token_count": 27, "char_count": 106, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:43.099734", "source": { "split": "train_shard_00001", "doc_id": 3860 }, "chunk_id": "train_shard_00001_3860_1", "global_id": 11119 }, { "text": "

ABSTRACT

In diverse mutualistic relationships, genetic variations in impact on the growth of interacting partners—variations in partner quality—are common, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variations. Here, we investigated how variations in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variations in the core genome and the contrastingly similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using nine sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variations represented by plant growth phenotypes, including genotype-by-genotype interactions. Quality variations were not associated with the presence/absence variations of known symbiosis-related genes in the symbiosis island, but rather, showed significant correlations with the core genome variations, supported by SNP- and kinship matrix-based association analyses. These findings highlight the novel role of HGT of symbiosis islands, which indirectly supply mutations of core genomes into L. japonicus -associated bacteria, thereby contributing to the maintenance of variations in partner quality.\n\nMassive rhizobial genomic variations associated with partner quality inLotus–Mesorhizobiumsymbiosis", "token_count": 355, "char_count": 1577, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:43.704918", "source": { "split": "train_shard_00001", "doc_id": 3861 }, "chunk_id": "train_shard_00001_3861_0", "global_id": 11120 }, { "text": "Small regulatory RNAs (sRNAs) play a critical role in bacterial gene expression, modulating various cellular processes, including stress responses, metabolism, virulence, and many others. While well-characterized in bacterial systems, an emerging class of phage-derived sRNAs has been identified, suggesting an underexplored regulatory network at phage-host interactions. These sRNAs, encoded within phage genomes, influence both bacterial and viral life cycles by modulating transcriptional and post-transcriptional gene expression processes. The interplay between phage-derived sRNAs and the host genome reveals a complex network of gene regulation, with an impact on bacterial fitness, pathogenesis, and horizontal gene transfer. This review explores the diverse functions of phage-encoded sRNAs, highlighting recent discoveries and their impact on bacterial physiology and phage-host interactions.\n\nThe Role of Bacteriophage-Derived Small RNA Molecules in Bacterial and Phage Interactions.", "token_count": 235, "char_count": 993, "word_count": 127, "semantic_coherence": 1, "information_density": 0.685, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:44.175531", "source": { "split": "train_shard_00001", "doc_id": 3862 }, "chunk_id": "train_shard_00001_3862_0", "global_id": 11121 }, { "text": "A thermotolerant yeast capable of fermenting xylose to xylitol at 40°C was isolated and identified as a strain of Debaryomyces hansenii by ITS sequencing. This paper reports the production of xylitol from D-xylose and sugarcane bagasse hemicellulose by free and Ca-alginate immobilized cells of D. hansenii. The efficiency of free and immobilized cells were compared for xylitol production from D-xylose and hemicellulose in batch culture at 40°C. The maximum xylitol produced by free cells was 68.6 g/L from 100 g/L of xylose, with a yield of 0.76 g/g and volumetric productivity 0.44 g/L/h. The yield of xylitol and volumetric productivity were 0.69 g/g and 0.28 g/L/h respectively from hemicellulosic hydrolysate of sugarcane bagasse after detoxification with activated charcoal and ion exchange resins. The Ca-alginate immobilized D. hansenii cells produced 73.8 g of xylitol from 100 g/L of xylose with a yield of 0.82 g/g and volumetric productivity of 0.46 g/L/h and were reused for five batches with steady bioconversion rates and yields.\n\nMicrobial production of xylitol from D-xylose and sugarcane bagasse hemicellulose using newly isolated thermotolerant yeast Debaryomyces hansenii.", "token_count": 377, "char_count": 1194, "word_count": 179, "semantic_coherence": 1, "information_density": 0.486, "quality_score": 0.743, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:44.752940", "source": { "split": "train_shard_00001", "doc_id": 3863 }, "chunk_id": "train_shard_00001_3863_0", "global_id": 11122 }, { "text": "METHOD FOR PRODUCING CEREBROSIDE HAVING 4-TRANS, 8-TRANS-SPHINGADIENINE AS PRIMARY SPHINGOID BASE BY KLUYVEROMYCES MARXIANUS", "token_count": 61, "char_count": 124, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:45.118872", "source": { "split": "train_shard_00001", "doc_id": 3864 }, "chunk_id": "train_shard_00001_3864_0", "global_id": 11123 }, { "text": "Enterobacter cloacae (EC) is a significant emerging pathogen that is occasionally associated with lung infection, surgical site infection, urinary infection, sepsis, and outbreaks in neonatal intensive care units. In light of the fact that there is currently no approved vaccine or therapeutic option for the treatment of EC, the current study was developed to concentrate on applications based on modern computational approaches to design a multi-epitope-based E. cloacae peptide vaccine (MEBEPV) expressing the antigenic determinants prioritized from the EC genome. Integrated computational analyses identified two potential protein targets (phosphoporin protein-PhoE and putative outer-membrane porin protein) for further exploration on the basis of pangenome subtractive proteomics and immunoinformatic in-depth examination of the core proteomes. Then, a multi-epitope peptide vaccine was designed, which comprised shortlisted epitopes that were capable of eliciting both innate and adaptive immunity, as well as the cholera toxin's B-subunit, which was used as an adjuvant in the vaccine formulation. To ensure maximum expression, the vaccine's 3D structure was developed and the loop was refined, improving the stability by disulfide engineering, and the physicochemical characteristics of the recombinant vaccine sequence were found to be ideal for both in vitro and in vivo experimentation. Blind docking was then used for the prediction of the MEBEPV predominant blinding mode with MHCI, MHCII, and TLR3 innate immune receptors, with lowest global energy of -18.64 kJ/mol, -48.25 kJ/mol, and -5.20 kJ/mol for MHC-I, MHC-II, and TLR-4, respectively, with docked complexes considered for simulation. In MD and MMGBSA investigations, the docked models of MEBEPV-TLR3, MEBEPV-MHCI, and MEBEPV-MHCII were found to be stable during the course of the simulation", "token_count": 502, "char_count": 1877, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [ "TLR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:45.784275", "source": { "split": "train_shard_00001", "doc_id": 3865 }, "chunk_id": "train_shard_00001_3865_0", "global_id": 11124 }, { "text": "MM-GBSA analysis calculated -122.17 total net binding free energies for the TLR3-vaccine complex, -125.4 for the MHC I-vaccine complex, and -187.94 for the MHC II-vaccine complex. Next, MM-PBSA analysis calculated -115.63 binding free energy for the TLR3-vaccine complex, -118.19 for the MHC I-vaccine complex, and -184.61 for the MHC II-vaccine complex. When the vaccine was tested in silico, researchers discovered that it was capable of inducing both types of immune responses (cell mediated and humoral) at the same time. Even though the suggested MEBEPV has the potential to be a powerful contender against E. cloacae-associated illnesses, further testing in the laboratory will be required before it can be declared safe and immunogenic.\n\nDesign of a Multi-Epitopes Based Chimeric Vaccine against Enterobacter cloacae Using Pan-Genome and Reverse Vaccinology Approaches.", "token_count": 269, "char_count": 890, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.832, "entities": { "genes": [ "TLR3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:46.333225", "source": { "split": "train_shard_00001", "doc_id": 3865 }, "chunk_id": "train_shard_00001_3865_1", "global_id": 11125 }, { "text": "The invention relates to a method for obtaining the endopolygalacturonase enzyme by means of cultivating recombinant microbial strains overexpressing gene epg2 of Kluyveromyces marxianus. Disclosed is the cloning and sequencing of gene EPG2 and the construction of yeast strains producing and secreting the endopolygalacturonase enzyme in large amounts and in a very stable manner. The produced enzyme can be used in the depectinization of fruit juice, vegetables and garden produces, the maceration of vegetables and for increasing juice yields, animal feed formulation and the degradation of vegetable residues.\n\nMETHOD FOR OBTAINING THE ENDOPOLYGALACTURONASE ENZYME BY CULTIVATING RECOMBINANT MICROBIAL STRAINS OVEREXPRESSING GENE EPG2 OF KLUYVEROMYCES MARXIANUS.", "token_count": 221, "char_count": 766, "word_count": 105, "semantic_coherence": 1, "information_density": 0.5429, "quality_score": 0.7714, "entities": { "genes": [ "EPG2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:46.800530", "source": { "split": "train_shard_00001", "doc_id": 3866 }, "chunk_id": "train_shard_00001_3866_0", "global_id": 11126 }, { "text": "

Background

Paraburkholderia fungorum (P. fungorum) is a Gram-negative environmental species that has been commonly used as a beneficial microorganism in agriculture as an agent for biocontrol and bioremediation. Its use in agriculture is controversial as many people believe that it could harm human health; however, there is no clear evidence to support.

Methodology

The pangolin P. fungorum (pangolin Pf) genome has a genomic size of approximately 7.7 Mbps with N50 of 69,666 bps. Our study showed that pangolin Pf is a Paraburkholderia fungorum supported by evidence from the core genome SNP-based phylogenetic analysis and the ANI analysis. Functional analysis has shown that the presence of a considerably large number of genes related to stress response, virulence, disease, and defence. Interestingly, we identified different types of secretion systems in the genome of pangolin Pf, which are highly specialized and responsible for a bacterium's response to its environment and in physiological processes such as survival, adhesion, and adaptation. The pangolin Pf also shared some common virulence genes with the known pathogenic member of the Burkholderiales. These genes play important roles in adhesion, motility, and invasion.

Conclusion

This study may provide better insights into the functions, secretion systems and virulence of this pangolin-associated bacterial strain. The addition of this genome sequence is also important for future comparative analysis and functional work of P. fungorum.\n\nComprehensive genome analysis of a pangolin-associated Paraburkholderia fungorum provides new insights into its secretion systems and virulence.", "token_count": 440, "char_count": 1712, "word_count": 233, "semantic_coherence": 1, "information_density": 0.618, "quality_score": 0.809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:47.435370", "source": { "split": "train_shard_00001", "doc_id": 3867 }, "chunk_id": "train_shard_00001_3867_0", "global_id": 11127 }, { "text": "Molecular typing methods are used to characterize the relatedness between bacterial isolates involved in infections. These approaches rely mostly on discrete loci or whole genome sequences (WGS) analyses of pure cultures. On the other hand, their application to environmental DNA profiling to evaluate epidemiological relatedness amongst patients and environments has received less attention. We developed a specific, high-throughput short sequence typing (HiSST) method for the opportunistic human pathogen Serratia marcescens . Genes displaying the highest polymorphism were retrieved from the core genome of 60 S. marcescens strains. Bioinformatics analyses showed that use of only three loci (within bssA, gabR and dhaM ) distinguished strains with the same level of efficiency than average nucleotide identity scores of whole genomes. This HiSST scheme was applied to an epidemiological survey of S. marcescens in a neonatal intensive care unit (NICU). In a first case study, a strain responsible for an outbreak in the NICU was found in a sink drain of this unit, by using HiSST scheme and confirmed by WGS. The HiSST scheme was also applied to environmental DNA extracted from sink-environment samples. Diversity of S. marcescens was modest, with 11, 6 and 4 different sequence types (ST) of gabR, bssA and dhaM loci amongst 19 sink drains, respectively. Epidemiological relationships amongst sinks were inferred on the basis of pairwise comparisons of ST profiles. Further research aimed at relating ST distribution patterns to environmental features encompassing sink location, utilization and microbial diversity is needed to improve the surveillance and management of opportunistic pathogens.\n\nDevelopment and Validation of a High-Throughput Short Sequence Typing Scheme forSerratia marcescensPure Culture and Environmental DNA", "token_count": 437, "char_count": 1845, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6479, "quality_score": 0.824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:48.066804", "source": { "split": "train_shard_00001", "doc_id": 3868 }, "chunk_id": "train_shard_00001_3868_0", "global_id": 11128 }, { "text": "Delftia tsuruhatensis has become an emerging pathogen in humans. There is scant information on the genomic characteristics of this microorganism. In this study, we determined the complete genome sequence of a clinical D. tsuruhatensis strain, TR1180, isolated from a sputum specimen of a female patient in China in 2019. Phylogenetic and average nucleotide identity analysis demonstrated that TR1180 is a member of D. tsuruhatensis. TR1180 exhibited resistance to β-lactam, aminoglycoside, tetracycline and sulphonamide antibiotics, but was susceptible to phenicols, fluoroquinolones and macrolides. Its genome is a single, circular chromosome measuring 6,711,018 bp in size. Whole-genome analysis identified 17 antibiotic resistance-related genes, which match the antimicrobial susceptibility profile of this strain, as well as 24 potential virulence factors and a number of metal resistance genes. Our data showed that Delftia possessed an open pan-genome and the genes in the core genome contributed to the pathogenicity and resistance of Delftia strains. Comparative genomics analysis of TR1180 with other publicly available genomes of Delftia showed diverse genomic features among these strains. D. tsuruhatensis TR1180 harbored a unique 38-kb genomic island flanked by a pair of 29-bp direct repeats with the insertion of a novel In4-like integron containing most of the specific antibiotic resistance genes within the genome. This study reports the findings of a fully sequenced genome from clinical D. tsuruhatensis, which provide researchers and clinicians with valuable insights into this uncommon species.", "token_count": 472, "char_count": 1672, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6435, "quality_score": 0.8217, "entities": { "genes": [ "TR1180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:48.709416", "source": { "split": "train_shard_00001", "doc_id": 3869 }, "chunk_id": "train_shard_00001_3869_0", "global_id": 11129 }, { "text": "Genomic Analysis of Delftia tsuruhatensis Strain TR1180 Isolated From A Patient From China With In4-Like Integron-Associated Antimicrobial Resistance.", "token_count": 53, "char_count": 157, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [ "TR1180" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:49.065885", "source": { "split": "train_shard_00001", "doc_id": 3869 }, "chunk_id": "train_shard_00001_3869_1", "global_id": 11130 }, { "text": "A new cytosine deaminase gene and protein from Candida kefyr are provided. This protein has increased ability to convert the 5-fluorocytosine prodrug to its toxic form when compared against the E. coli enzyme.\n\nNucleic acids encoding Candida kefyr cytosine deaminase", "token_count": 77, "char_count": 266, "word_count": 40, "semantic_coherence": 1, "information_density": 0.825, "quality_score": 0.9125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:49.435606", "source": { "split": "train_shard_00001", "doc_id": 3870 }, "chunk_id": "train_shard_00001_3870_0", "global_id": 11131 }, { "text": "Genomic analyses on versatility of the ubiquitous opportunistic pathogen Pseudomonas aeruginosa have been focusing on clinical strains from humans but much less on animal and environmental strains. Here, we aimed to compare genomic patterns of bovine, environmental, and human strains of P. aeruginosa. A collection of 71 strains, equally representing bovine (non-clinical), environmental (aquatic), and human (clinical) isolates from all main subregions of Hungary was genotyped by PCR microarray. Results were interpreted in comparison with internationally established human clinical and environmental clones, based on single nucleotide polymorphisms, on di- and multiallelic loci (fliC and fpvA) of the conserved core genome, and on genetic markers for the flexible accessory genome. As a result, a total of 33 clones were identified, with one bovine, 10 environmental, and five human clones regarded as new ones. In spite of general clonal diversity, bovine and human clones seemed to be habitat related. Bovine strains were characterized by significant overrepresentation of type III FpvA pyoverdine receptor, while the environmental and human strains showed the dominance of type I FpvA. Genotypes of non-clinical bovine strains of P. aeruginosa differed from those of human clinical strains, supporting the hypothesis about specific groups of strains colonizing specific habitats.\n\nComparative genomic analysis of bovine, environmental, and human strains of Pseudomonas aeruginosa.", "token_count": 367, "char_count": 1488, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:50.014804", "source": { "split": "train_shard_00001", "doc_id": 3871 }, "chunk_id": "train_shard_00001_3871_0", "global_id": 11132 }, { "text": "

Background

Proteus spp. have long been recognized for their role in urinary tract infections, while recent evidence disclosed their implications in gastrointestinal diseases. Despite this, the taxonomy of clinically-derived Proteus spp., particularly those from gastrointestinal samples, remains understudied and is frequently mis-assigned, which limits our understanding of infections caused by these species.

Results

Four Proteus strains (i.e., DFP240708, LHD240705, TSJ240517 and WDL240414) were isolated from the appendiceal pus of patients with acute appendicitis, whole-genome average nucleotide identity (ANI) analysis identified all of them as Proteus genomosp. 6, different from that identified using the automated bacterial identification instrument (VITEK®-32). Based on ANI and the core-genomic phylogenetic tree, we found that 87.5% of clinically-related strains previously identified as P. columbae should be re-classified as Proteus genomosp. 6. Additionally, the Proteus genomosp. 6 genomes all carry one or more beta-lactam resistance genes, but none carry aminoglycoside resistance genes, and antibiotic susceptibility testing conducted on the four strains isolated in this study confirmed these findings. Among the genomes analyzed, only four (two from this study (TSJ240517 and WDL240414)) carried virulence genes, specifically the hlyA, hlyB, and hlyD genes encoding hemolysin.

Conclusion

Our study highlights inaccuracies in the taxa classification of Proteus species under clinical settings, underscoring the necessity of using genomic-based taxonomic assignment methods. We revealed that the prevalence of Proteus genomosp. 6 in clinical infections has likely been underestimated. Furthermore, given the resistance-gene absence and their sensitivity to aminoglycosides, aminoglycosides may serve as a promising first-line treatment option for infections caused by this species.", "token_count": 508, "char_count": 1934, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6911, "quality_score": 0.8455, "entities": { "genes": [ "TSJ240517", "LHD240705", "WDL240414", "DFP240708" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:50.675079", "source": { "split": "train_shard_00001", "doc_id": 3872 }, "chunk_id": "train_shard_00001_3872_0", "global_id": 11133 }, { "text": "Genome-based analyses from four clinically-isolated strains refined the taxonomy of Proteus genomosp. 6 and revealed their underestimated role in gastrointestinal diseases.", "token_count": 44, "char_count": 172, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:51.035735", "source": { "split": "train_shard_00001", "doc_id": 3872 }, "chunk_id": "train_shard_00001_3872_1", "global_id": 11134 }, { "text": "Sulfonamides are synthetic chemotherapeutic agents that work as competitive inhibitors of the di-hydro-pteroate synthase (DHPS) enzyme, encoded by the folP gene. Resistance to sulfonamides is widespread in the clinical setting and predominantly mediated by plasmid- and integron-borne sul1-3 genes encoding mutant DHPS enzymes that do not bind sulfonamides. In spite of their clinical importance, the genetic origin of sul1-3 genes remains unknown. Here we analyze sul genes and their genetic neighborhoods to uncover sul signature elements that enable the elucidation of their genetic origin. We identify a protein sequence Sul motif associated with sul-encoded proteins, as well as consistent association of a phosphoglucosamine mutase gene ( glmM ) with the sul2 gene. We identify chromosomal folP genes bearing these genetic markers in two bacterial families: the Rhodobiaceae and the Leptospiraceae . Bayesian phylogenetic inference of FolP/Sul and GlmM protein sequences clearly establishes that sul1-2 and sul3 genes originated as a mobilization of folP genes present in, respectively, the Rhodobiaceae and the Leptospiraceae , and indicate that the Rhodobiaceae folP gene was transferred from the Leptospiraceae . Analysis of %GC content in folP / sul gene sequences supports the phylogenetic inference results and indicates that the emergence of the Sul motif in chromosomally-encoded FolP proteins is ancient and considerably predates the clinical introduction of sulfonamides. In vitro assays reveal that both the Rhodobiaceae and the Leptospiraceae , but not other related chromosomally-encoded FolP proteins confer resistance in a sulfonamide-sensitive Escherichia coli background, indicating that the Sul motif is associated with sulfonamide resistance. Given the absence of any known natural sulfonamides targeting DHPS, these results provide a novel perspective on the emergence of resistance to synthetic chemotherapeutic agents, whereby preexisting resistant variants in the vast bacterial pangenome may be rapidly selected for and mobilized upon the clinical introduction of novel chemotherapeuticals.", "token_count": 509, "char_count": 2120, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5452, "quality_score": 0.7726, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:51.668355", "source": { "split": "train_shard_00001", "doc_id": 3873 }, "chunk_id": "train_shard_00001_3873_0", "global_id": 11135 }, { "text": "Origin of the mobile di-hydro-pteroate synthase gene determining sulfonamide resistance in clinical isolates", "token_count": 27, "char_count": 108, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:52.030374", "source": { "split": "train_shard_00001", "doc_id": 3873 }, "chunk_id": "train_shard_00001_3873_1", "global_id": 11136 }, { "text": "

Objectives

The aim of this study was to identify clonally-related carbapenemase-producing Klebsiella pneumoniae complex members that could be involved in outbreaks among hospitalized patients in Denmark, and to identify possible epidemiological links.

Methods

From January 2014 to June 2018, 103 isolates belonging to the K. pneumoniae complex were collected from 102 patients. From the whole-genome sequencing (WGS) data, presence of genes encoding carbapenemase and multilocal sequence typing (MLST) data were extracted. Core genome MLST (cgMLST) cluster analysis was performed. Using data from the Danish National Patient Registry (DNPR) and reported travel history, presumptive outbreaks were investigated for possible epidemiological links.

Results

The most common detected carbapenemase gene was blaOXA-48, followed by blaNDM-1. The 103 K. pneumoniae complex isolates belonged to 47 sequence types (STs) and cgMLST subdivided the isolates into 80 different complex types. cgMLST identified 13 clusters with 2-4 isolates per cluster. For five of the 13 clusters, a direct link (the patients stayed at the same ward on the same day) could be detected between at least some of the patients. In two clusters, the patients resided simultaneously at the same hospital, but not the same ward. A possible link (same ward within 1-13 days) was detected for the patients in one cluster. For five clusters detected by cgMLST, no epidemiological link could be detected using data from DNPR.

Conclusion

In this study, cgMLST combined with patient hospital admission data and travel information was found to be a reliable and detailed approach to detect possible clonal transmission of carbapenemase-producing K. pneumoniae complex members.", "token_count": 473, "char_count": 1783, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:52.677445", "source": { "split": "train_shard_00001", "doc_id": 3874 }, "chunk_id": "train_shard_00001_3874_0", "global_id": 11137 }, { "text": "Investigation of possible clonal transmission of carbapenemase-producing Klebsiella pneumoniae complex member isolates in Denmark using core genome MLST and National Patient Registry Data.", "token_count": 44, "char_count": 188, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:53.036503", "source": { "split": "train_shard_00001", "doc_id": 3874 }, "chunk_id": "train_shard_00001_3874_1", "global_id": 11138 }, { "text": "Xanthomonas oryzae is a devastating pathogen of rice worldwide, however, X. sontii and X. maliensis are its non-pathogenic counterparts from the same host. So far, these non-pathogenic isolates were overlooked due to their less economic importance and lack of genomic information. We have carried out detailed ecological and evolutionary study focusing on diverse lifestyles of these strains. Phylogenomic analysis revealed two major lineages corresponding to X. sontii (ML-I) and X. oryzae (ML-II) species. Interestingly, one of the non-pathogenic Xanthomonas strains belonging to X. maliensis is intermediary to both the major lineages/species suggesting on-going diversification and selection. Accordingly, pangenome analysis revealed large number of lifestyle specific genes with atypical GC content indicating role of horizontal gene transfer in genome diversification. Our comprehensive comparative genomic investigation of major lineages has revealed that impact of recombination is more for X. sontii as compared to X. oryzae . Acquisition of type III secretion system and its effectome along with a type VI secretion system also seem to have played a major role in the pathogenic lineage. Other known key pathogenicity clusters or genes like biofilm forming cluster, cellobiohydrolase and non-fimbrial adhesin ( yapH) are exclusive to pathogenic lineage. However, commonality of loci encoding exopolysacharide, rpf signalling molecule, iron-uptake, xanthomonadin pigment, etc. suggests their essentiality in host adaptation. Overall, this study reveals evolutionary history of pathogenic and non-pathogenic strains and will further open up a new avenue for better management of pathogenic strains for sustainable cultivation of a major staple food crop.\n\nEcological and evolutionary insights into pathogenic and non-pathogenic rice associatedXanthomonas", "token_count": 452, "char_count": 1869, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:53.690416", "source": { "split": "train_shard_00001", "doc_id": 3875 }, "chunk_id": "train_shard_00001_3875_0", "global_id": 11139 }, { "text": "

Background

The criteria for defining bacterial species and even the concept of bacterial species itself are under debate, and the discussion is apparently intensifying as more genome sequence data is becoming available. However, it is still unclear how the new advances in genomics should be used most efficiently to address this question. In this study we identify genes that are common to any group of genomes in our dataset, to determine whether genes specific to a particular taxon exist and to investigate their potential role in adaptation of bacteria to their specific niche. These genes were named unique core genes. Additionally, we investigate the existence and importance of unique core genes that are found in isolates of phylogenetically non-coherent groups. These groups of isolates, that share a genetic feature without sharing a closest common ancestor, are termed genophyletic groups.

Results

The bacterial family Vibrionaceae was used as the model, and we compiled and compared genome sequences of 64 different isolates. Using the software orthoMCL we determined clusters of homologous genes among the investigated genome sequences. We used multilocus sequence analysis to build a host phylogeny and mapped the numbers of unique core genes of all distinct groups of isolates onto the tree. The results show that unique core genes are more likely to be found in monophyletic groups of isolates. Genophyletic groups of isolates, in contrast, are less common especially for large groups of isolate. The subsequent annotation of unique core genes that are present in genophyletic groups indicate a high degree of horizontally transferred genes. Finally, the annotation of the unique core genes of Vibrio cholerae revealed genes involved in aerotaxis and biosynthesis of the iron-chelator vibriobactin.

Conclusion

The presented work indicates that genes specific for any taxon inside the bacterial family Vibrionaceae exist. These unique core genes encode conserved metabolic functions that can shed light on the adaptation of a species to its ecological niche. Additionally, our study suggests that unique core genes can be used to aid classification of bacteria and contribute to a bacterial species definition on a genomic level. Furthermore, these genes may be of importance in clinical diagnostics and drug development.", "token_count": 505, "char_count": 2359, "word_count": 352, "semantic_coherence": 1, "information_density": 0.5085, "quality_score": 0.7543, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:54.366452", "source": { "split": "train_shard_00001", "doc_id": 3876 }, "chunk_id": "train_shard_00001_3876_0", "global_id": 11140 }, { "text": "Unique core genomes of the bacterial family vibrionaceae: insights into niche adaptation and speciation.", "token_count": 23, "char_count": 104, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:54.734054", "source": { "split": "train_shard_00001", "doc_id": 3876 }, "chunk_id": "train_shard_00001_3876_1", "global_id": 11141 }, { "text": "

Introduction

Shiga toxin-producing Escherichia coli (STEC) is a gastrointestinal pathogen causing foodborne outbreaks. Whole Genome Sequencing (WGS) in STEC surveillance holds promise in outbreak prevention and confinement, in broadening STEC epidemiology and in contributing to risk assessment and source attribution. However, despite international recommendations, WGS is often restricted to assist outbreak investigation and is not yet fully implemented in food safety surveillance across all European countries, in contrast to for example in the United States.

Methods

In this study, WGS was retrospectively applied to isolates collected within the context of Belgian food safety surveillance and combined with data from clinical isolates to evaluate its benefits. A cross-sector WGS-based collection of 754 strains from 1998 to 2020 was analyzed.

Results

We confirmed that WGS in food safety surveillance allows accurate detection of genomic relationships between human cases and strains isolated from food samples, including those dispersed over time and geographical locations. Identifying these links can reveal new insights into outbreaks and direct epidemiological investigations to facilitate outbreak management. Complete WGS-based isolate characterization enabled expanding epidemiological insights related to circulating serotypes, virulence genes and antimicrobial resistance across different reservoirs. Moreover, associations between virulence genes and severe disease were determined by incorporating human metadata into the data analysis. Gaps in the surveillance system were identified and suggestions for optimization related to sample centralization, harmonizing isolation methods, and expanding sampling strategies were formulated.

Discussion

This study contributes to developing a representative WGS-based collection of circulating STEC strains and by illustrating its benefits, it aims to incite policymakers to support WGS uptake in food safety surveillance.\n\nTransforming Shiga toxin-producing Escherichia coli surveillance through whole genome sequencing in food safety practices.", "token_count": 464, "char_count": 2151, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:55.408834", "source": { "split": "train_shard_00001", "doc_id": 3877 }, "chunk_id": "train_shard_00001_3877_0", "global_id": 11142 }, { "text": "Neisseria meningitidis and Neisseria gonorrhoeae are pathogenic bacteria that can cause human infections. While N. meningitidis infections are associated with bacterial meningitis and bacteremia, a strain of N. meningitidis, isolated from the urogenital system, has recently been associated with urethritis. As this strain is becoming prominent as an emerging pathogen, it is essential to assess identification tools for N. meningitidis and N. gonorrhoeae urogenital isolates. Consecutive N. meningitidis isolates recovered from urogenital cultures of symptomatic patients with presumptive diagnoses of gonorrhea and a random selection of N. gonorrhoeae isolates recovered from the same population within the same time frame were characterized with routine identification systems, antimicrobial susceptibility testing, and whole-genome sequencing. Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS), multilocus sequence typing, 16S rRNA gene sequence, and average nucleotide identity methods accurately identified 95% (18/19) of N. meningitidis and N. gonorrhoeae isolates. With the Aptima Combo 2 CT/NG test, 30% (3/10) of N. meningitidis isolates were misidentified as N. gonorrhoeae, but no misidentifications were found with the Xpert CT/NG nucleic acid amplification test (NAAT). Phylogenetic core genome and single nucleotide polymorphism (SNP)-based grouping analyses showed that urogenital N. meningitidis isolates were highly related and phylogenetically distinct from N. gonorrhoeae and respiratory N", "token_count": 516, "char_count": 1652, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:43:56.083252", "source": { "split": "train_shard_00001", "doc_id": 3878 }, "chunk_id": "train_shard_00001_3878_0", "global_id": 11143 }, { "text": "meningitidis isolates but similar to urogenital N. meningitidis isolates from patients with urethritis in the United States. Urogenital N. meningitidis isolates were predominantly azithromycin resistant, while N. gonorrhoeae isolates were azithromycin susceptible. These data indicate that urogenital isolates of N. meningitidis can cause false-positive detections with N. gonorrhoeae diagnostic assays. Misidentification of urogenital N. meningitidis isolates may confound public health-related activities for gonorrhea, and future studies are needed to understand the impact on clinical outcome of N. meningitidis urogenital infection.\n\nGenomic Characterization of Emerging Bacterial Uropathogen Neisseria meningitidis, Which Was Misidentified as Neisseria gonorrhoeae by Nucleic Acid Amplification Testing.", "token_count": 273, "char_count": 862, "word_count": 99, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:56.630731", "source": { "split": "train_shard_00001", "doc_id": 3878 }, "chunk_id": "train_shard_00001_3878_1", "global_id": 11144 }, { "text": "The effect of carbon source and its concentration, inoculum size, yeast extract concentration, nitrogen source, pH of the fermentation medium, and fermentation temperature on beta-glucosidase production by Kluyveromyces marxianus in shake-flask culture was investigated. These were the independent variables that directly regulated the specific growth and beta-glucosidase production rate. The highest product yield, specific product yield, and productivity of beta-glucosidase occurred in the medium (pH 5.5) inoculated with 10% (v/v) inoculum of the culture. Cellobiose (20 g/L) significantly improved beta-glucosidase production measured as product yield (YP/S) and volumetric productivity (QP) followed by sucrose, lactose, and xylose. The highest levels of productivity (144 IU/[L.h]) of beta-glucosidase occurred on cellobiose in the presence of CSL at 35 degrees C and are significantly higher than the values reported by other researchers on almost all other organisms. The thermodynamics and kinetics of beta-glucosidase production and its deactivation are also reported. The enzyme was substantially stable at 60 degrees C and may find application in some industrial processes.\n\nInfluence of carbon and nitrogen sources and temperature on hyperproduction of a thermotolerant beta-glucosidase from synthetic medium by Kluyveromyces marxianus.", "token_count": 343, "char_count": 1351, "word_count": 183, "semantic_coherence": 1, "information_density": 0.5956, "quality_score": 0.7978, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:57.195878", "source": { "split": "train_shard_00001", "doc_id": 3879 }, "chunk_id": "train_shard_00001_3879_0", "global_id": 11145 }, { "text": "In this work we analyzed the ability of three Arthrobacter strains (namely TB23, TB26 and CAL618), which were isolated from the Antarctic sponges Haliclonissa verrucosa and Lyssodendrix nobilis, to specifically inhibit the growth of a panel of 40 Burkholderia cepacia complex strains, representing a major cause of infections in patients that are affected by Cystic Fibrosis. The inhibitory activity was due to the synthesis of antimicrobial compounds, very likely volatile organic compounds (VOCs), and was partially dependent on the growth media that were used for Antarctic strains growth. The phylogenetic analysis revealed that two of them (i.e. CAL 618 and TB23) were very close and very likely belonged to the same Arthrobacter species, whereas the strain TB26 was placed in a distant branch. The genome of the strains TB26 and CAL618 was also sequenced and compared with that of the strain TB23. The analysis revealed that TB23 and CAL618 shared more genomic properties (GC content, genome size, number of genes) than with TB26. Since the three strains exhibited very similar inhibition pattern vs Bcc strains, it is quite possible that genes involved in the biosynthesis of antimicrobial compounds very likely belong to the core genome.\n\nGenomic analysis of three sponge-associated Arthrobacter Antarctic strains, inhibiting the growth of Burkholderia cepacia complex bacteria by synthesizing volatile organic compounds.", "token_count": 381, "char_count": 1429, "word_count": 216, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [ "TB23", "CAL618", "TB26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:57.775812", "source": { "split": "train_shard_00001", "doc_id": 3880 }, "chunk_id": "train_shard_00001_3880_0", "global_id": 11146 }, { "text": "

Background

The Streptococcus genus is relevant to both public health and food safety because of its ability to cause pathogenic infections. It is well-represented (>100 genomes) in publicly available databases. Streptococci are ubiquitous, with multiple sources of isolation, from human pathogens to dairy products. The Streptococcus genus has traditionally been classified by morphology, serum types, the 16S ribosomal RNA (rRNA) gene, and multi-locus sequence types subject to in-depth comparative genomic analysis.

Methods

Core and pan-genomes described the genomic diversity of 108 strains belonging to 16 Streptococcus species. The core genome nucleotide diversity was calculated and compared to phylogenomic distances within the genus Streptococcus. The core genome was also used as a resource to recruit metagenomic fragment reads from streptococci dominated environments. A conventional 16S rRNA gene phylogeny reconstruction was used as a reference to compare the resulting dendrograms of average nucleotide identity (ANI) and genome similarity score (GSS) dendrograms.

Results

The core genome, in this work, consists of 404 proteins that are shared by all 108 Streptococcus. The average identity of the pairwise compared core proteins decreases proportionally to GSS lower scores, across species. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes). The GSS is a distance metric that can reflect evolutionary history comparing orthologous proteins", "token_count": 450, "char_count": 1603, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6542, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:58.422811", "source": { "split": "train_shard_00001", "doc_id": 3881 }, "chunk_id": "train_shard_00001_3881_0", "global_id": 11147 }, { "text": "Additionally, GSS resulted in the most useful metric for genus and species comparisons, where ANI metrics failed due to false positives when comparing different species.

Discussion

Understanding of genomic variability and species relatedness is the goal of tools like GSS, which makes use of the maximum pairwise shared orthologous sequences for its calculation. It allows for long evolutionary distances (above species) to be included because of the use of amino acid alignment scores, rather than nucleotides, and normalizing by positive matches. Newly sequenced species and strains could be easily placed into GSS dendrograms to infer overall genomic relatedness. The GSS is not restricted to ubiquitous conservancy of gene features; thus, it reflects the mosaic-structure and dynamism of gene acquisition and loss in bacterial genomes.\n\nGlobal genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments.", "token_count": 229, "char_count": 1026, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7192, "quality_score": 0.8596, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:58.890770", "source": { "split": "train_shard_00001", "doc_id": 3881 }, "chunk_id": "train_shard_00001_3881_1", "global_id": 11148 }, { "text": "Rare information is available on clinical Enterococcus faecium encountered in Sardinia, Italy. This study investigated the antimicrobial susceptibility profiles and genotypic characteristics of E. faecium isolated at the University Hospital of Sassari, Italy, using the Vitek2 system and PCR, MLST, or WGS. Vitek2 revealed two VanB-type vancomycin-resistant Enterococcus faecium (VREfm) isolates (MICs mg/L = 8 and ≥32) but failed to detect vancomycin resistance in one isolate (MIC mg/L ≤ 1) despite positive genotypic confirmation of vanB gene, which proved to be vancomycin resistant by additional phenotypic methods (MICs mg/L = 8). This vanB isolate was able to increase its vancomycin MIC after exposure to vancomycin, unlike the \"classic\" occult vanB-carrying E. faecium, becoming detectable by Vitek 2 (MICs mg/L ≥ 32). All three E. faecium had highly mutated vanB2 operons, as part of a chromosomally integrated Tn1549 transposon, with common missense mutations in VanH and VanB2 resistance proteins and specific missense mutations in the VanW accessory protein. There were additional missense mutations in VanS, VanH, and VanB proteins in the vanB2-carrying VREfm isolates compared to Vitek2. The molecular typing revealed a polyclonal hospital-associated E. faecium population from Clade A1, and that vanB2-VREfm, and nearly half of vancomycin-susceptible E", "token_count": 507, "char_count": 1506, "word_count": 198, "semantic_coherence": 1, "information_density": 0.7071, "quality_score": 0.8535, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:59.541885", "source": { "split": "train_shard_00001", "doc_id": 3882 }, "chunk_id": "train_shard_00001_3882_0", "global_id": 11149 }, { "text": "faecium (VSEfm) analyzed, belonged to ST117. Based on core genome-MLST, ST117 strains had different clonal types (CT), excluding nosocomial transmission of specific CT. Detecting vanB2-carrying VREfm isolates by Vitek2 may be problematic, and alternative methods are needed to prevent therapeutic failure and spread.\n\nOccult Vancomycin-Resistant Enterococcus faecium ST117 Displaying a Highly Mutated vanB2 Operon.", "token_count": 153, "char_count": 461, "word_count": 54, "semantic_coherence": 1, "information_density": 0.9259, "quality_score": 0.963, "entities": { "genes": [ "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:43:59.979747", "source": { "split": "train_shard_00001", "doc_id": 3882 }, "chunk_id": "train_shard_00001_3882_1", "global_id": 11150 }, { "text": "Streptococcus pyogenes genotype emm1 is a successful, globally distributed epidemic clone that is regarded as inherently virulent. An emm1 sublineage, M1UK, that produces increased levels of SpeA toxin was associated with increased scarlet fever and invasive infections in England in 2015/2016. Defined by 27 SNPs in the core genome, M1UK is now dominant in England. To more fully characterize M1UK, we undertook comparative transcriptomic and proteomic analyses of M1UK and contemporary non-M1UK emm1 strains (M1global). Just seven genes were differentially expressed by M1UK compared with contemporary M1global strains. In addition to speA, five genes in the operon that includes glycerol dehydrogenase were upregulated in M1UK (gldA, mipB/talC, pflD, and phosphotransferase system IIC and IIB components), while aquaporin (glpF2) was downregulated. M1UK strains have a stop codon in gldA. Deletion of gldA in M1global abrogated glycerol dehydrogenase activity, and recapitulated upregulation of gene expression within the operon that includes gldA, consistent with a feedback effect. Phylogenetic analysis identified two intermediate emm1 sublineages in England comprising 13/27 (M113SNPs) and 23/27 SNPs (M123SNPs), respectively, that had failed to expand in the population", "token_count": 509, "char_count": 1497, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:00.614401", "source": { "split": "train_shard_00001", "doc_id": 3883 }, "chunk_id": "train_shard_00001_3883_0", "global_id": 11151 }, { "text": "Proteomic analysis of invasive strains from the four phylogenetic emm1 groups highlighted sublineage-specific changes in carbohydrate metabolism, protein synthesis and protein processing; upregulation of SpeA was not observed in chemically defined medium. In rich broth, however, expression of SpeA was upregulated ~10-fold in both M123SNPs and M1UK sublineages, compared with M113SNPs and M1global. We conclude that stepwise accumulation of SNPs led to the emergence of M1UK. While increased expression of SpeA is a key indicator of M1UK and undoubtedly important, M1UK strains have outcompeted M123SNPs and other emm types that produce similar or more superantigen toxin. We speculate that an accumulation of adaptive SNPs has contributed to a wider fitness advantage in M1UK on an inherently successful emm1 streptococcal background.\n\nCharacterization of emergent toxigenic M1<sub>UK</sub> <i>Streptococcus pyogenes</i> and associated sublineages.", "token_count": 344, "char_count": 1094, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7154, "quality_score": 0.8577, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:01.187291", "source": { "split": "train_shard_00001", "doc_id": 3883 }, "chunk_id": "train_shard_00001_3883_1", "global_id": 11152 }, { "text": "We present draft whole-genome sequences of seven Streptococcus agalactiae strains isolated from Camelus dromedarius in Kenya and Somalia. These data are an extension to the group B Streptococcus (GBS) pangenome and might provide more insight into the underlying mechanisms of pathogenicity and antibiotic resistance of camel GBS.\n\nDraft Genome Sequences of Seven Streptococcus agalactiae Strains Isolated from Camelus dromedarius at the Horn of Africa.", "token_count": 154, "char_count": 487, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:01.623540", "source": { "split": "train_shard_00001", "doc_id": 3884 }, "chunk_id": "train_shard_00001_3884_0", "global_id": 11153 }, { "text": "Abstract Global meat and milk demands are projected to increase by 50% by the year 2050, making a highly efficient cattle industry a top priority. Widespread use of antibiotics over the last 70 years has led to increases in antibiotic resistance genes (ARGs) in microbial populations, posing health risks to animal and human populations. Thus, a thorough understanding of where antibiotic resistance genes reside in microbial ecosystems surrounding livestock is paramount in developing strategies to mitigate transfer of antibiotic resistance. Recent advances in metagenome sequencing have made it possible to predict microbial genomes from shotgun metagenome datasets. However, genomes binned from metagenome data are often smaller than genomes from pure cultures, omitting genetic information that is not part of the core genome e.g. antibiotic resistance. This study uses a new linked-read metagenome sequencing approach, partitioning long fragments of DNA (>40Kbp) into millions of droplets which are individually barcoded giving each strand a unique index, improving metagenome assembly and increasing access to genetic information pertaining to antibiotic resistance. Rumen samples from four animals which received daily antibiotics in feed as well as antibiotic injections were pooled for linked-read metagenome sequencing. Additionally, soil samples from the animal pen were collected from three locations and pooled for analysis. Linked-read sequencing reads were assembled using MEGAHIT and ATHENA assemblers (N50 > 2702bp, 578,838 contigs >1000bp). Metagenome assembled genomes (MAGs) were binned using MetaBAT2, yielding 341 genome bins. Of these, 144 bins were of intermediate to high quality (>70% completeness, < 10% contamination), 79 genomes from rumen and 65 from soil samples, respectively. Genomes were scanned for ARGs (ABRicate), revealing 12 genomes containing ARGs, 5 from rumen, 7 from soil", "token_count": 474, "char_count": 1915, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6618, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:02.279675", "source": { "split": "train_shard_00001", "doc_id": 3885 }, "chunk_id": "train_shard_00001_3885_0", "global_id": 11154 }, { "text": "MAGs possessed genes conferring resistance to penicillin, macrolide, nitroimidazole, aminoglycoside, and tetracycline class antibiotics, helping uncover information about where ARGs are sequestered in their respective environments. USDA is an equal opportunity provider and employer.\n\nPSV-14 Genome Centric Approaches to Understand Antimicrobial Resistance in the Rumen Microbiome", "token_count": 101, "char_count": 380, "word_count": 46, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:02.656321", "source": { "split": "train_shard_00001", "doc_id": 3885 }, "chunk_id": "train_shard_00001_3885_1", "global_id": 11155 }, { "text": "Game meat is becoming increasingly popular but may be contaminated with pathogenic bacteria such as Shiga toxin-producing Escherichia coli (STEC). STEC cause gastrointestinal illnesses including diarrhoea, haemorrhagic colitis (HC), and the haemolytic uremic syndrome (HUS). The aim of this study was to assess the occurrence of STEC in 92 meat samples from chamois (n = 2), red deer (n = 27), roe deer (n = 38), and wild boar (n = 25), from Switzerland and other European countries. After enrichment, Shiga-toxin encoding genes (stx) were detected by PCR in 78 (84%) of the samples and STEC were isolated from 23 (25%) of the same samples. Nine different serotypes and eight different sequence types (STs) were found, with O146:H28 ST738 (n = 10) and O110:H31 ST812 (n = 5) predominating. None of the STEC belonged to the so-called top-five serogroups O26, O103, O111, O145, and O157. Subtyping of stx identified stx1c (n = 9), stx2a (n = 1), stx2b (n = 19), stx2e (n = 2), and stx2g (n = 1). Additional virulence factors (VFs) comprised ehx (n = 12), iha (n = 21), sta1 (n = 1), and subAB (n = 19). None of the isolates contained the eae gene. Twenty-one STEC contained VFs associated with extra-intestinal pathogenic E", "token_count": 514, "char_count": 1221, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6603, "quality_score": 0.8301, "entities": { "genes": [ "ST812", "ST738" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:03.294384", "source": { "split": "train_shard_00001", "doc_id": 3886 }, "chunk_id": "train_shard_00001_3886_0", "global_id": 11156 }, { "text": "coli (ExPEC). Overall, the pathogenic potential of STEC in game meat is moderate, though the isolation of one STEC strain carrying stx2a, and of STEC/ExPEC hybrids suggests a role of game meat as a potential source of STEC infections in humans. Therefore, detailed knowledge of the safe handling and preparation of game meat is needed to prevent foodborne infections.\n\nWhole genome sequence-based characterisation of Shiga toxin-producing Escherichia coli isolated from game meat originating from several European countries.", "token_count": 126, "char_count": 524, "word_count": 77, "semantic_coherence": 1, "information_density": 0.6883, "quality_score": 0.8442, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:03.684509", "source": { "split": "train_shard_00001", "doc_id": 3886 }, "chunk_id": "train_shard_00001_3886_1", "global_id": 11157 }, { "text": "The genus Lactobacillus is a diverse group with a combined species count of over 200. They are the largest group within the lactic acid bacteria and one of the most important bacterial groups involved in food microbiology and human nutrition because of their fermentative and probiotic properties. Lactobacillus salivarius, a species commonly isolated from the gastrointestinal tract of humans and animals, has been described as having potential probiotic properties and results of previous studies have revealed considerable functional diversity existing on both the chromosomes and plasmids. Our study consists of comparative genomic analyses of the functional and phylogenomic diversity of 42 genomes of strains of L. salivarius using bioinformatic techniques. The main aim of the study was to describe intra-species diversity and to determine how this diversity is spread across the replicons. We found that multiple phylogenomic and non-phylogenomic methods used for reconstructing trees all converge on similar tree topologies, showing that different metrics largely agree on the evolutionary history of the species. The greatest genomic variation lies on the small plasmids, followed by the repA-type circular megaplasmid, with the chromosome varying least of all. Additionally, the presence of extra linear and circular megaplasmids is noted in several strains, while small plasmids are not always present. Glycosyl hydrolases, bacteriocins and proteases vary considerably on all replicons while two exopolysaccharide clusters and several clustered regularly interspaced short palindromic repeats-associated systems show a lot of variation on the chromosome. Overall, despite its reputation as a mammalian gastrointestinal tract specialist, the intra-specific variation of L. salivarius reveals potential strain-dependant effects on human health.\n\nPhylogenomics and comparative genomics of Lactobacillus salivarius, a mammalian gut commensal.", "token_count": 483, "char_count": 1999, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6642, "quality_score": 0.8321, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:04.340866", "source": { "split": "train_shard_00001", "doc_id": 3887 }, "chunk_id": "train_shard_00001_3887_0", "global_id": 11158 }, { "text": "This study aimed to examine the diversity and ecology of yeasts associated with traditional Egyptian dairy products employing molecular techniques in yeast identification. A total of 120 samples of fresh and stored Domiati cheese, kariesh cheese, and \"Matared\" cream were collected from local markets and examined. Forty yeast isolates were cultured from these samples and identified using the restriction-fragment length polymorphism (RFLPs) of 5.8S-ITS rDNA region and sequencing of the domains D1 and D2 of the 26S rRNA gene. Yeasts were identified as Issatchenkia orientalis (13 isolates), Candida albicans (4 isolates), Clavispora lusitaniae (Candida lusitaniae) (9 isolates), Kodamaea ohmeri (Pichia ohmeri) (1 isolate), Kluyveromyces marxianus (6 isolates), and Candida catenulata (7 isolates). With the exception of C. lusitaniae, the D1/D2 26S rRNA gene sequences were 100% identical for the yeast isolates within the same species. Phylogenetic reconstruction of C. lusitaniae isolates grouped them into 3 distinguished clusters. Kariesh cheese was found to be the most diverse in its yeast floras and contained the highest total yeast count compared with other examined dairy products. This was linked to the acidic pH and lower salt content of this cheese, which favor the growth and survival of yeasts in foodstuffs. Stored Domiati cheese also contained diverse yeast species involving isolates of the pathogenic yeast C. albicans. This raises the possibility of dairy products being vehicles of transmission of pathogenic yeasts.\n\nMolecular identification of yeasts associated with traditional Egyptian dairy products.", "token_count": 425, "char_count": 1631, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6034, "quality_score": 0.8017, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:04.966163", "source": { "split": "train_shard_00001", "doc_id": 3888 }, "chunk_id": "train_shard_00001_3888_0", "global_id": 11159 }, { "text": "Antimicrobial resistance (AMR) is a growing concern in public health, particularly for the clinically relevant extended-spectrum beta-lactamase (ESBL) and AmpC-producing Enterobacteriaceae. Studies describing ESBL-producing Escherichia coli clinical samples from Finland to the genomic level and investigation of possible zoonotic transmission routes are scarce. This study characterizes ESBL-producing E. coli from clinical samples in Finland using whole genome sequencing (WGS). Comparison is made between animal, food, and environmental sources in Finland to gain insight into potential zoonotic transmission routes and to recognize successful AMR genes, bacterial sequence types (STs), and plasmids. ESBL-producing E. coli isolates (n = 30) obtained from the Eastern Finland healthcare district between 2018 and 2020 underwent WGS and were compared to sequences from non-human and healthy human sources (n = 67) isolated in Finland between 2012 and 2018. A majority of the clinical isolates belonged to ST131 (n = 21; 70%), of which 19 represented O25:H4 and fimH30 allele, and 2 O16:H5 and fimH41 allele. Multidrug resistance was common, and the most common bla gene identified was bla CTX-M-27 (n = 14; 47%) followed by bla CTX-M-15 (n = 10; 33%). bla CTX-M-27 was identified in 13 out of 21 isolates representing ST131, with 12 isolates belonging to a recently discovered international E", "token_count": 516, "char_count": 1549, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:05.622938", "source": { "split": "train_shard_00001", "doc_id": 3889 }, "chunk_id": "train_shard_00001_3889_0", "global_id": 11160 }, { "text": "coli ST131 C1-M27 subclade. Isolates were found to be genetically distinct from non-human sources with core genome multilocus sequence typing based analysis. Most isolates (n = 26; 87%) possessed multiple replicons, with IncF family plasmids appearing in 27 (90%) and IncI1 in 5 (17%) isolates. IncF[F1:A2:B20] replicon was identified in 11, and IncF[F-:A2:B20] in 4 isolates. The results indicate the ST131-C1-M27 clade gaining prevalence in Europe and provide further evidence of the concerning spread of this globally successful pathogenic clonal group. This study is the first to describe ESBL-producing E. coli in human infections with WGS in Finland and provides important information on global level of the spread of ESBL-producing E. coli belonging to the C1-M27 subclade. The results will help guide public health actions and guide future research.\n\nWhole-Genome Sequencing of Extended-Spectrum Beta-Lactamase-Producing Escherichia coli From Human Infections in Finland Revealed Isolates Belonging to Internationally Successful ST131-C1-M27 Subclade but Distinct From Non-human Sources.", "token_count": 355, "char_count": 1127, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:06.221686", "source": { "split": "train_shard_00001", "doc_id": 3889 }, "chunk_id": "train_shard_00001_3889_1", "global_id": 11161 }, { "text": "Abstract

Sphingobium yanoikuyae S72 was isolated from the rhizosphere of sorghum plant, Mexico. Its role on the degradation of polycyclic aromatic hydrocarbon (PAH) was evaluated in a minimal medium containing one of biphenyl, naphthalene, phenanthrene, xylene and Toluene as the only carbon source. It grew effectively in each minimal medium (Bushnell Haas, BH). Gas column chromatography–mass spectrometry (GC-MS) analysis on the metabolite recovered after S72’s growth in BH showed that it successfully degraded the PAHs tested resulting in the degradation of biphenyl (85%), phenanthrene (93%), naphthalene (81%), xylene (19%) and toluene (30%). The complete genome of the S72 was sequenced to evaluate the genetic bases of S72`s degradation of PAH. The genome was assembled de novo and reduced to 1 contig and consists of 5,532,623 bp, 5005 protein-coding genes. The analysis of the COG categories in S72 in comparison with other Sphingobium yanoikuyae and other PAH degrading gene, showed that it has in higher abundance in some categories that have been associated with the degradation of PAH (energy production and conversion (COG C, 6.35), carbohydrate transport and metabolism (COG G, 6.20%), lipid transport and metabolism (COG I, 6.99), secondary metabolites biosynthesis (COG Q, 4.52%), general function prediction only in transport and catabolism (COG R, 9.93),) Pan-core genome analysis revealed that about 126 unique genes in S72 are associated with the degradation of xenobiotics and PAHs. Most gene found in S72 are associated with the peripheral degradation pathway for PAH", "token_count": 515, "char_count": 1662, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:06.896415", "source": { "split": "train_shard_00001", "doc_id": 3890 }, "chunk_id": "train_shard_00001_3890_0", "global_id": 11162 }, { "text": "Based on our observation we proposed a possible benzoate degradation pathway.

\n\nComplete Genome Report of Sphingobium Yanoikuyae S72: A Bacterium Capable of Degrading Hydrocarbons", "token_count": 55, "char_count": 182, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:07.301340", "source": { "split": "train_shard_00001", "doc_id": 3890 }, "chunk_id": "train_shard_00001_3890_1", "global_id": 11163 }, { "text": "The present invention provides a novel yeast strain capable of producing ethanol through fermentation with a high degree of efficiency at a temperature of 37 DEG C. or higher, preferably a temperature ranging from 40 to 49 DEG C. or higher, and also a method for producing ethanol by utilizing the yeast strain, and further, ethanol produced by the method. Therefore, in the present invention, an yeast strain (Deposit No. NITE BP-283, etc) belonging to species Kluyveromyces marxianus isolated by a screening step using a culture medium containing sugar in a high concentration and ethanol, is cultured in a culture solution supplemented with 10 to 100 mM of sorbitol at 40 to 49 DEG C.\n\nTHERMOTOLERANT ETHANOL-PRODUCING YEAST AND ETHANOL PRODUCTION METHOD UTILIZING THE SAME", "token_count": 221, "char_count": 776, "word_count": 125, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:07.792939", "source": { "split": "train_shard_00001", "doc_id": 3891 }, "chunk_id": "train_shard_00001_3891_0", "global_id": 11164 }, { "text": "Methanol quenching and fast filtration, the two most common sampling protocols in microbial metabolome analysis, were validated for intracellular amino acid analysis in phylogenetically different yeast strains comprising Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia pastoris, Schizosaccharomyces pombe and Zygosaccharomyces bailii. With only few exceptions for selected amino acids, all yeasts exhibited negligible metabolite leakage during quenching with 60% cold buffered methanol. Slightly higher leakage was observed with increasing methanol content in the quenching solution. Fast filtration resulted in identical levels for intracellular amino acids in all strains tested. The results clearly demonstrate the validity of both approaches for leakage-free sampling of amino acids in yeast.\n\nAppropriate sampling for intracellular amino acid analysis in five phylogenetically different yeasts.", "token_count": 236, "char_count": 909, "word_count": 116, "semantic_coherence": 1, "information_density": 0.681, "quality_score": 0.8405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:08.268489", "source": { "split": "train_shard_00001", "doc_id": 3892 }, "chunk_id": "train_shard_00001_3892_0", "global_id": 11165 }, { "text": "Through this study, we established the taxonomic status of seven strains belonging to the genus Pectobacterium (A477-S1-J17T, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17) collected from four different river streams and an artificial lake in south-east France between 2016 and 2017. Ecological surveys in rivers and lakes pointed out different repartition of strains belonging to this clade compared to the closest species, Pectobacterium aquaticum. The main phenotypic difference observed between these strains and the P. aquaticum type strain was strongly impaired growth with rhamnose as the sole carbon source. This correlates with three different forms of pseudogenization of the l-rhamnose/proton symporter gene rhaT in the genomes of strains belonging to this clade. Phylogenetic analysis using gapA gene sequences and multi locus sequence analysis of the core genome showed that these strains formed a distinct clade within the genus Pectobacterium closely related to P. aquaticum. Digital DNA-DNA hybridization (dDDH) and average nucleotide identity (ANI) values showed a clear discontinuity between the new clade and P. aquaticum. However, the calculated values are potentially consistent with either splitting or merging of this new clade with P. aquaticum. In support of the split, ANI coverages were higher within this new clade than between this new clade and P. aquaticum. The split is also consistent with the range of observed ANI or dDDH values that currently separate several accepted species within the genus Pectobacterium", "token_count": 491, "char_count": 1662, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5983, "quality_score": 0.7991, "entities": { "genes": [ "FL63", "FL60" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:08.917234", "source": { "split": "train_shard_00001", "doc_id": 3893 }, "chunk_id": "train_shard_00001_3893_0", "global_id": 11166 }, { "text": "On the basis of these data,strains A477-S1-J17T, A398-S21-F17, A535-S3-A17, A411-S4-F17, A113-S21-F16, FL63-S17 and FL60-S17 represent a novel species of the genus Pectobacterium, for which the name Pectobacterium quasiaquaticum sp. nov. is proposed. The type strain is A477-S1-J17T (=CFBP 8805T=LMG 32181T).\n\nPectobacterium quasiaquaticum sp. nov., isolated from waterways.", "token_count": 218, "char_count": 439, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8298, "quality_score": 0.9149, "entities": { "genes": [ "FL63", "FL60" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:09.384293", "source": { "split": "train_shard_00001", "doc_id": 3893 }, "chunk_id": "train_shard_00001_3893_1", "global_id": 11167 }, { "text": "In this work, the agitation and aeration effects in the maximization of the beta-galactosidase production from Kluyveromyces marxianus CCT 7082 were investigated simultaneously, in relation to the volumetric enzyme activity and the productivity, as well as the analysis of the lactose consumption and production of glucose, and galactose of this process. Agitation and aeration effects were studied in a 2 L batch stirred reactor. A central composite design (2(2) trials plus three central points) was carried out. Agitation speed varied from 200 to 500 rpm and aeration rate from 0.5 to 1.5 vvm. It has been shown in this study that the volumetric enzyme production was strongly influenced by mixing conditions, while aeration was shown to be less significant. Linear models for activity and productivity due to agitation and aeration were obtained. The favorable condition was 500 rpm and 1.5 vvm, which lead to the best production of 17 U mL(-1) for enzymatic activity, 1.2 U mL(-1) h(-1) for productivity in 14 h of process, a cellular concentration of 11 mg mL(-1), and a 167.2 h(-1) volumetric oxygen transfer coefficient.\n\nMaximization of beta-galactosidase production: a simultaneous investigation of agitation and aeration effects.", "token_count": 333, "char_count": 1240, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5781, "quality_score": 0.7891, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:09.957589", "source": { "split": "train_shard_00001", "doc_id": 3894 }, "chunk_id": "train_shard_00001_3894_0", "global_id": 11168 }, { "text": "

Introduction

Healthcare associated infections due to carbapenem-resistant Klebsiella pneumoniae (CRKP) are a major concern in Portuguese hospitals. Whole genome sequencing (WGS) can improve infection control, but this practice is not routinely used by hospital clinical laboratories in Portugal. We simulated the investigation of a CRKP outbreak based on WGS, with the aim of determining, in the minimum possible time, genetic relatedness between CRKP clinical and environmental isolates.

Material and methods

Ten CRKP clinical isolates routinely obtained in the hospital laboratory were used. Forty environmental samples - from sinks and sink drains of ward rooms - were collected. Environmental samples were plated on selective media and presumptive CRKP colonies were isolated. Total DNA was extracted from all putative CRKP isolates and sequenced. Clonal relatedness was determined by multi-locus sequence typing and core genome single nucleotide polymorphism analysis; the presence of carbapenemase genes was evaluated.

Results

Clinical isolates were characterized in 48 hours: eight strains were confirmed as CRKP, of which six were of ST13 and carried blaKPC-3. Environmental samples results were obtained in six days: eight CRKP were isolated from which five were of ST13 and carried blaKPC-3. Clinical and environmental ST13 isolates were highly related: ten (of 11) isolates differed from each other in < 0.001% of 2 172 367 core nucleotides.

Discussion

WGS can be used as a high-resolution effective tool to investigate healthcare associated infections and track routes of dissemination in real-time.

Conclusion

In Portugal, routine use of WGS to improve infection control could thrive through collaborative initiatives between hospitals and research institutes.\n\nUsing Whole Genome Sequencing to Investigate a Mock-Outbreak of Carbapenem-Resistant Klebsiella pneumoniae in Real-Time.", "token_count": 486, "char_count": 1931, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6077, "quality_score": 0.8038, "entities": { "genes": [ "ST13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:10.606222", "source": { "split": "train_shard_00001", "doc_id": 3895 }, "chunk_id": "train_shard_00001_3895_0", "global_id": 11169 }, { "text": "A protein with an apparent molecular weight of 37,000 (p37) is present in very large amounts in the cell wall of Kluyveromyces marxianus, after the induction of flocculation of the yeast. This protein was isolated by preparative gel electrophoresis and its purity checked by SDS-PAGE and reverse-phase HPLC. SDS-PAGE, endoglycosidase-H treatment and peptide sequencing indicated that p37 is a glycoprotein with a high identity to cytosolic glyceraldehyde-3-phosphate dehydrogenase from Saccharomyces cerevisiae. Polyclonal antibodies were used for Western blot analysis and immunocytochemistry, which showed that p37 is present in the cell wall of non-flocculent K. marxianus and, therefore, is a constitutive protein of the cell wall.\n\nA protein homologous to glyceraldehyde-3-phosphate dehydrogenase is induced in the cell wall of a flocculent Kluyveromyces marxianus.", "token_count": 264, "char_count": 870, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:11.152445", "source": { "split": "train_shard_00001", "doc_id": 3896 }, "chunk_id": "train_shard_00001_3896_0", "global_id": 11170 }, { "text": "

Background and objectives

Colonization of Candida species is common in pediatric patients admitted to hematology-oncology wards. The aim of this study was to identify colonized Candida species and their susceptibility patterns in hematologic pediatric patients.

Materials and methods

Samples were collected from mouth, nose, urine and stool of the patients admitted to five university hospitals and cultured on sabouraud dextrose agar. The isolates were identified by API 20 C AUX system and their susceptibility patterns were evaluated by CLSI M27-A3 and S4.

Results

From 650 patients, 320 (49.2%) were colonized with 387 Candida species. Candida albicans was the most prevalent isolated species, followed by Candida glabrata, Candida tropicalis, Candida famata, Candida kefyr and Candida kuresi. The epidemiological cut off value (ECV) for all Candida species to amphotericin B was ≤0.25 μg except C. krusei (4 μg). The resistance rate to fluconazole in this study in C. albicans was 4.9% with ECV 8 μg/ml, followed by C. tropicalis 8.8% with ECV 0.5 μg/ml. Voriconazole and posaconazole were effective antifungal agents for all Candida isolates. The ECV of C. albicans, Candida parapsilosis, C. tropicalis, C. glabrata and C. krusei for itraconazole were 0.5, 0.25, 0.5, 1 and 2 μg, respectively", "token_count": 506, "char_count": 1411, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6166, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:11.805384", "source": { "split": "train_shard_00001", "doc_id": 3897 }, "chunk_id": "train_shard_00001_3897_0", "global_id": 11171 }, { "text": "The resistant and intermediate rates of Candida species to caspofungin in this study were 2.9%, 5.9%, 18.8%, 47.9%, 0.0% and 16.7% in C. tropicalis, C. glabrata and C. parapsilosis respectively.

Conclusion

C. albicans was the most prevalent species in pediatric colonized patients. New azole agents like voriconazole and posaconazole are effective against non-albicans Candida species. Increase in intermediate species is alarming to future emerging resistant species.\n\nAntifungal susceptibility patterns of colonized Candida species isolates from immunocompromised pediatric patients in five university hospitals.", "token_count": 214, "char_count": 663, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7375, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:12.269696", "source": { "split": "train_shard_00001", "doc_id": 3897 }, "chunk_id": "train_shard_00001_3897_1", "global_id": 11172 }, { "text": "To understand the molecular mechanisms that contribute to the stress responses of the important foodborne pathogen Listeria monocytogenes, we collected 139 strains (meat, n = 25; dairy, n = 10; vegetable, n = 8; seafood, n = 14; mixed food, n = 4; and food processing environments, n = 78), mostly isolated in Ireland, and subjected them to whole-genome sequencing. These strains were compared to 25 Irish clinical isolates and 4 well-studied reference strains. Core genome and pan-genome analysis confirmed a highly clonal and deeply branched population structure. Multilocus sequence typing showed that this collection contained a diverse range of strains from L. monocytogenes lineages I and II. Several groups of isolates with highly similar genome content were traced to single or multiple food business operators, providing evidence of strain persistence or prevalence, respectively. Phenotypic screening assays for tolerance to salt stress and resistance to acid stress revealed variants within several clonal complexes that were phenotypically distinct. Five of these phenotypic outliers were found to carry mutations in the sigB operon, which encodes the stress-inducible sigma factor sigma B. Transcriptional analysis confirmed that three of the strains that carried mutations in sigB, rsbV, or rsbU had reduced SigB activity, as predicted. These strains exhibited increased tolerance to salt stress and displayed decreased resistance to low pH stress. Overall, this study shows that loss-of-function mutations in the sigB operon are comparatively common in field isolates, probably reflecting the cost of the general stress response to reproductive fitness in this pathogen", "token_count": 489, "char_count": 1761, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6546, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:12.922590", "source": { "split": "train_shard_00001", "doc_id": 3898 }, "chunk_id": "train_shard_00001_3898_0", "global_id": 11173 }, { "text": "IMPORTANCE The bacterial foodborne pathogen Listeria monocytogenes frequently contaminates various categories of food products and is able to cause life-threatening infections when ingested by humans. Thus, it is important to control the growth of this bacterium in food by understanding the mechanisms that allow its proliferation under suboptimal conditions. In this study, intraspecies heterogeneity in stress response was observed across a collection consisting of mainly Irish L. monocytogenes isolates. Through comparisons of genome sequence and phenotypes observed, we identified three strains with impairment of the general stress response regulator SigB. Two of these strains are used widely in food challenge studies for evaluating the growth potential of L. monocytogenes. Given that loss of SigB function is associated with atypical phenotypic properties, the use of these strains in food challenge studies should be re-evaluated.\n\nPhylogenetic and Phenotypic Analyses of a Collection of Food and Clinical Listeria monocytogenes Isolates Reveal Loss of Function of Sigma B from Several Clonal Complexes.", "token_count": 261, "char_count": 1122, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6709, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:13.473201", "source": { "split": "train_shard_00001", "doc_id": 3898 }, "chunk_id": "train_shard_00001_3898_1", "global_id": 11174 }, { "text": "Probiotic organisms are increasingly being incorporated into foods in order to develop products to prevent and reduce many diseases. Saccharomyces boulardii, a probiotic yeast with unique properties, such as viability over a wide pH range, antibiotic resistance, and the ability to reach a steady state, has an advantage over bacterial probiotics. The present review highlights the potential application of S. boulardii in functional fermented dairy products and the genetic engineering of this probiotic microorganism as a therapeutic agent for the treatment of various infectious diseases. It was found that probiotic yeast stimulates the growth of lactic acid bacteria in dairy products, creating favorable conditions and positively affecting the product's sensory characteristics. Moreover, its viability of more than 106 cfu/mL at the end of the yogurt shelf life confirms its probiotic effect. On the other hand, there is a growing interest in the design of probiotic strains to improve their characteristics and fill existing gaps in their spectrum of action such as the inhibition of some bacterial toxins, as well as anti-inflammatory and immunomodulatory effects. The strengthening of immune functions and effective therapies against various diseases by S. boulardii was confirmed. However, considering this yeast species' potential, further research is necessary to accurately determine the functional properties in terms of incorporation into food matrices and from the aspect of health and well-being claims.\n\nNovel Insights in the Application of Probiotic Yeast Saccharomyces boulardii in Dairy Products and Health Promotion.", "token_count": 391, "char_count": 1678, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6345, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:14.093134", "source": { "split": "train_shard_00001", "doc_id": 3899 }, "chunk_id": "train_shard_00001_3899_0", "global_id": 11175 }, { "text": "Rhodococcus equi, a member of the Rhodococcus genus, is a gram-positive pathogenic bacterium. Rhodococcus possesses an open pan-genome that constitutes the basis of its high genomic diversity and allows for adaptation to specific niche conditions and the changing host environments. Our analysis further showed that the core genome of R. equi contributes to the pathogenicity and niche adaptation of R. equi. Comparative genomic analysis revealed that the genomes of R. equi shared identical collinearity relationship, and heterogeneity was mainly acquired by means of genomic islands and prophages. Moreover, genomic islands in R. equi were always involved in virulence, resistance, or niche adaptation and possibly working with prophages to cause the majority of genome expansion. These findings provide an insight into the genomic diversity, evolution, and structural variation of R. equi and a valuable resource for functional genomic studies.\n\nComparative Genomic Analysis of Rhodococcus equi: An Insight into Genomic Diversity and Genome Evolution.", "token_count": 298, "char_count": 1117, "word_count": 152, "semantic_coherence": 1, "information_density": 0.5921, "quality_score": 0.7961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:14.656107", "source": { "split": "train_shard_00001", "doc_id": 3900 }, "chunk_id": "train_shard_00001_3900_0", "global_id": 11176 }, { "text": "

Background and aim

Clinical strains of microorganisms, including pathogenic yeast-like fungi (YLF), are resistant to currently used antifungal agents. Thus, it is relevant to study the combinations of existing antimicrobial drugs and a medicinal extract of plant origin (farnesol). In previous studies, farnesol showed a relatively strong anti-biofilm effect against Candida albicans. This study aimed to determine how much the resistance profile of non-biofilm microorganisms can change.

Materials and methods

Six clinical isolates of C. albicans and one reference strain were used to study the interaction of farnesol with the most used antimycotics. To determine the sensitivity of YLF to antimycotic drugs, such as nystatin (50 μg), amphotericin B (10 μg), ketoconazole (10 μg), clotrimazole (10 μg), voriconazole (10 μg), fluconazole (25 μg), miconazole (10 μg), and intraconazole (10 μg), the classic disk diffusion method was used. In the second stage, one of the six strains was used to simulate candidiasis of the gastrointestinal tract in an in vivo quail model. As an unusual experimental design, this study investigated the effects of pretreated C. albicans in quails, not the in vivo pathogenicity of C. albicans, after treatment with farnesol.

Results

The resistance profiles of Candida strains did not improve with farnesol in all strains. All concentrations of farnesol (100, 50, and 25 μM) demonstrated a fungistatic effect (i.e., an increase in drug sensitivity) in 23 of 56 (7×8) cases (41%)", "token_count": 503, "char_count": 1581, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6311, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:15.667117", "source": { "split": "train_shard_00001", "doc_id": 3901 }, "chunk_id": "train_shard_00001_3901_0", "global_id": 11177 }, { "text": "The remaining 54% demonstrated no changes in the resistance to antifungal drugs or deterioration of the indicators in rare cases (5%). At 100 μM farnesol, sensitivity improved in 33 of 56 cases (59%). Candidiasis or the severity of clinical disease of the quail digestive tract developed to a lesser extent if fungi were treated with farnesol.

Conclusion

Farnesol does not always show a positive result on single cells without biofilm in the laboratory. However, in a biofilm or an in vivo model with biofilms, farnesol can be considered a new antimycotic drug or an additive to existing antimycotics.\n\nEnhancement of the antifungal activity of some antimycotics by farnesol and reduction of Candida albicans pathogenicity in a quail model experiment.", "token_count": 225, "char_count": 772, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7094, "quality_score": 0.8547, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:16.139041", "source": { "split": "train_shard_00001", "doc_id": 3901 }, "chunk_id": "train_shard_00001_3901_1", "global_id": 11178 }, { "text": "Kluyveromyces marxianus was grown in submerged culture in a complex medium with several potential inducers of lipolytic activity (triacylglycerols, fatty acids). The highest extracellular lipolytic enzyme production (about 80 U ml(-1) in 3 d) was obtained when the medium was supplemented with 2 g urea l(-1) plus 5 g tributyrin l(-1). Addition of surfactants (1 g l(-1)) did not improve production. The lipase had a high thermal stability in aqueous solution (73% residual activity after 9 d at 50 degrees C, 16 min half-life time at 100 degrees C). It was also stable at acidic pH and showed good tolerance to organic solvents (70% residual activity after 2 d in n-hexane of cyclohexane).\n\nProduction of a thermostable extracellular lipase by Kluyveromyces marxianus", "token_count": 234, "char_count": 768, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7295, "quality_score": 0.8648, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:16.609483", "source": { "split": "train_shard_00001", "doc_id": 3902 }, "chunk_id": "train_shard_00001_3902_0", "global_id": 11179 }, { "text": "The compound 2-phenylethanol (2-PE) is a bulk flavor and fragrance with a rose-like aroma that can be produced by microbial cell factories, but its cellular toxicity inhibits cellular growth and limits strain performance. Specifically, the microbe Bacillus licheniformis has shown a strong tolerance to 2-PE. Understanding these tolerance mechanisms is crucial for achieving the hyperproduction of 2-PE. In this report, the mechanisms of B. licheniformis DW2 resistance to 2-PE were studied by multi-omics technology coupled with physiological and molecular biological approaches. 2-PE induced reactive oxygen species formation and affected nucleic acid, ribosome, and cell wall synthesis. To manage 2-PE stress, the antioxidant and global stress response systems were activated; the repair system of proteins and homeostasis of the ion and osmotic were initiated. Furthermore, the tricarboxylic acid cycle and NADPH synthesis pathways were upregulated; correspondingly, scanning electron microscopy revealed that cell morphology was changed. These results provide deeper insights into the adaptive mechanisms of B. licheniformis to 2-PE and highlight the potential targets for genetic manipulation to enhance 2-PE resistance. IMPORTANCE The ability to tolerate organic solvents is essential for bacteria producing these chemicals with high titer, yield, and productivity. As exemplified by 2-PE, bioproduction of 2-PE represents a promising alternative to chemical synthesis and plant extraction approaches, but its toxicity hinders successful large-scale microbial production. Here, a multi-omics approach is employed to systematically study the mechanisms of B. licheniformis DW2 resistance to 2-PE. As a 2-PE-tolerant strain, B. licheniformis displays multifactorial mechanisms of 2-PE tolerance, including activating global stress response and repair systems, increasing NADPH supply, changing cell morphology and membrane composition, and remodeling metabolic pathways. The current work yields novel insights into the mechanisms of B. licheniformis resistance to 2-PE", "token_count": 490, "char_count": 2080, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.805, "entities": { "genes": [ "DW2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:17.263253", "source": { "split": "train_shard_00001", "doc_id": 3903 }, "chunk_id": "train_shard_00001_3903_0", "global_id": 11180 }, { "text": "This knowledge can also be used as a clue for improving bacterial performances to achieve industrial-scale production of 2-PE and potentially applied to the production of other relevant organic solvents, such as tyrosol and hydroxytyrosol.\n\nSystematic Adaptation of Bacillus licheniformis to 2-Phenylethanol Stress.", "token_count": 79, "char_count": 315, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:17.631790", "source": { "split": "train_shard_00001", "doc_id": 3903 }, "chunk_id": "train_shard_00001_3903_1", "global_id": 11181 }, { "text": "The interleukin-17 (IL-17) family consists of proinflammatory cytokines conserved during evolution. A comparative genomics approach was applied to examine IL-17 throughout evolution from poriferans to higher vertebrates. Cnidaria was highlighted as the most ancient diverged phylum, and several evolutionary patterns were revealed. Large expansions of the IL-17 repertoire were observed in marine molluscs and echinoderm species. We further studied this expansion in filter-fed Mytilus galloprovincialis, which is a bivalve with a highly effective innate immune system supported by a variable pangenome. We recovered 379 unique IL-17 sequences and 96 receptors from individual genomes that were classified into 23 and 6 isoforms after phylogenetic analyses. Mussel IL-17 isoforms were conserved among individuals and shared between closely related Mytilidae species. Certain isoforms were specifically implicated in the response to a waterborne infection with Vibrio splendidus in mussel gills. The involvement of IL-17 in mucosal immune responses could be conserved in higher vertebrates from these ancestral lineages.\n\nThe Evolution and Diversity of Interleukin-17 Highlight an Expansion in Marine Invertebrates and Its Conserved Role in Mucosal Immunity.", "token_count": 336, "char_count": 1271, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.8439, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:18.234855", "source": { "split": "train_shard_00001", "doc_id": 3904 }, "chunk_id": "train_shard_00001_3904_0", "global_id": 11182 }, { "text": "The LEU2 gene, coding for beta-isopropylmalate dehydrogenase, of the yeast Kluyveromyces marxianus was isolated and sequenced. An open reading frame, coding for a protein with a molecular weight of 38 kDa was found. Comparison of the deduced amino acid sequence of the LEU2 gene with the corresponding enzymes of three other yeasts and two thermophilic bacteria, revealed extensive sequence similarities. The cloned gene could complement a leuB mutation of Escherichia coli and a leu2 mutation of Saccharomyces cerevisiae. Using orthogonal field alternation gel electrophoresis, the genomic copy of the gene was found to be located at chromosome VI or VII. Analysis of the 5'-untranslated region indicated the presence of a putative binding site for the LEU3 protein, which is involved in the leucine-specific regulation of transcription. We show that the cloned gene can be used for the construction of a non-reverting K. marxianus leu2 mutant.\n\nCloning and disruption of the LEU2 gene of Kluyveromyces marxianus CBS 6556.", "token_count": 278, "char_count": 1023, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6369, "quality_score": 0.8185, "entities": { "genes": [ "LEU3", "LEU2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:18.801562", "source": { "split": "train_shard_00001", "doc_id": 3905 }, "chunk_id": "train_shard_00001_3905_0", "global_id": 11183 }, { "text": "Helicobacter cinaedi is a Gram-negative bacterium from the family Helicobacteraceae and genus Helicobacter. The pathogen is a causative agent of gastroenteritis, cellulitis, and bacteremia. The increasing antibiotic resistance pattern of the pathogen prompts the efforts to develop a vaccine to prevent dissemination of the bacteria and stop the spread of antibiotic resistance (AR) determinants. Herein, a pan-genome analysis of the pathogen strains was performed to shed light on its core genome and its exploration for potential vaccine targets. In total, four vaccine candidates (TonB dependent receptor, flagellar hook protein FlgE, Hcp family type VI secretion system effector, flagellar motor protein MotB) were identified as promising vaccine candidates and subsequently subjected to an epitopes' mapping phase. These vaccine candidates are part of the pathogen core genome: they are essential, localized at the pathogen surface, and are antigenic. Immunoinformatics was further applied on the selected vaccine proteins to predict potential antigenic, non-allergic, non-toxic, virulent, and DRB*0101 epitopes. The selected epitopes were then fused using linkers to structure a multi-epitopes' vaccine construct. Molecular docking simulations were conducted to determine a designed vaccine binding stability with TLR5 innate immune receptor. Further, binding free energy by MMGB/PBSA and WaterSwap was employed to examine atomic level interaction energies. The designed vaccine also stimulated strong humoral and cellular immune responses as well as interferon and cytokines' production. In a nutshell, the designed vaccine is promising in terms of immune responses' stimulation and could be an ideal candidate for experimental analysis due to favorable physicochemical properties.\n\nPan-Genome-Assisted Computational Design of a Multi-Epitopes-Based Vaccine Candidate against Helicobacter cinaedi.", "token_count": 462, "char_count": 1932, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6371, "quality_score": 0.8185, "entities": { "genes": [ "TLR5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:19.479635", "source": { "split": "train_shard_00001", "doc_id": 3906 }, "chunk_id": "train_shard_00001_3906_0", "global_id": 11184 }, { "text": "Regulation of transport of D-glucose and D-fructose was studied in Kluyveromyces marxianus grown in continuous culture. Both substrates could be transported by at least two different transport systems, low-affinity transport and high-affinity proton-sugar symport. The low-affinity transporter, specific for both glucose and fructose, was constitutively present and was apparently not regulated by carbon catabolite repression. Regulation of the activity of the glucose- and fructose-specific proton symport systems appeared to proceed mainly through catabolite repression. Activation of symport did not need the presence of specific inductor molecules in the medium. Nevertheless, the capacities of the proton-sugar symporters varied in cells grown on a wide variety of carbon sources. The possibility that the control of proton symport activity is related to the presence of specific intracellular metabolites is discussed.\n\nContinuous-culture study of the regulation of glucose and fructose transport in Kluyveromyces marxianus CBS 6556.", "token_count": 249, "char_count": 1040, "word_count": 142, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:19.986491", "source": { "split": "train_shard_00001", "doc_id": 3907 }, "chunk_id": "train_shard_00001_3907_0", "global_id": 11185 }, { "text": "Bacteriophages (phages) are bacterial parasites that can themselves be parasitized by phage satellites. The molecular mechanisms used by satellites to hijack phages are sometimes understood in great detail, but the origins, abundance, distribution, and composition of these elements are poorly known. Here, we show that P4-like elements are present in more than 10% of the genomes of Enterobacterales, and in almost half of those of Escherichia coli , sometimes in multiple distinct copies. We identified over 1000 P4-like elements with very conserved genetic organization of the core genome and a few hotspots with highly variable genes. These elements are never found in plasmids and have very little homology to known phages, suggesting an independent evolutionary origin. Instead, they are scattered across chromosomes, possibly because their integrases are often exchanged with other elements. The rooted phylogenies of hijacking functions are correlated and suggest longstanding co-evolution. They also reveal broad host ranges in P4-like elements, since almost identical elements can be found in distinct bacterial genuses. Our results show that P4-like phage satellites constitute a very distinct, widespread and ancient family of mobile genetic elements. They pave the way for studying the molecular evolution of antagonistic interactions between phages and their satellites.\n\nTo catch a hijacker: abundance, evolution and genetic diversity of P4-like bacteriophage satellites", "token_count": 324, "char_count": 1485, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6338, "quality_score": 0.8169, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:20.542360", "source": { "split": "train_shard_00001", "doc_id": 3908 }, "chunk_id": "train_shard_00001_3908_0", "global_id": 11186 }, { "text": "

ABSTRACT

Biological hydrolysis of cellulose above 70°C involves microorganisms that secrete free enzymes, and deploy separate protein systems to adhere to their substrate. Strongly cellulolytic Caldicellulosiruptor bescii is one such extreme thermophile, which deploys modular, multi-functional carbohydrate acting enzymes to deconstruct plant biomass. Additionally, C. bescii also encodes for non-catalytic carbohydrate binding proteins, which likely evolved as a mechanism to compete against other heterotrophs in carbon limited biotopes that these bacteria inhabit. Analysis of the Caldicellulosiruptor pangenome identified a type IV pilus (T4P) locus encoded upstream of the tāpirins, that is encoded for by all Caldicellulosiruptor species. In this study, we sought to determine if the C. bescii T4P plays a role in attachment to plant polysaccharides. The major C. bescii pilin (CbPilA) was identified by the presence of pilin-like protein domains, paired with transcriptomics and proteomics data. Using immuno-dot blots, we determined that the plant polysaccharide, xylan, induced production of CbPilA 10 to 14-fold higher than glucomannan or xylose. Furthermore, we are able to demonstrate that recombinant CbPilA directly interacts with xylan, and cellulose at elevated temperatures. Localization of CbPilA at the cell surface was confirmed by immunofluorescence microscopy. Lastly, a direct role for CbPilA in cell adhesion was demonstrated using recombinant CbPilA or anti-CbPilA antibodies to reduce C. bescii cell adhesion to xylan and crystalline cellulose up to 4.5 and 2-fold, respectively. Based on these observations, we propose that CbPilA and by extension, the T4P, plays a role in Caldicellulosiruptor cell attachment to plant biomass", "token_count": 510, "char_count": 1764, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:21.197508", "source": { "split": "train_shard_00001", "doc_id": 3909 }, "chunk_id": "train_shard_00001_3909_0", "global_id": 11187 }, { "text": "

IMPORTANCE

Most microorganisms are capable of attaching to surfaces in part to persist in their environment. Here, we describe that the thermophilic, plant degrading bacterium, Caldicellulosiruptor bescii , uses type IV pili to attach to carbohydrates found in plant biomass. This ability is likely key to survival in environments where carbon sources are limiting, allowing C. bescii to compete against other plant degrading microorganisms. Interestingly, the carbohydrate that induced the highest expression of pilin protein was xylan, a hemicellulose that is not the majority polysaccharide in plant biomass. Not only do we demonstrate a direct interaction of the pilin with the polysaccharides, but also that cell attachment to polysaccharides can be disrupted by the addition of recombinant pilin and notably by antibody neutralization of the native pilin. This mechanism mirrors those recently described in pathogenic Gram-positive bacteria, and further supports the ancient origins of type IV pilus systems.\n\nCaldicellulosiruptor besciiregulates pilus expression in response to the polysaccharide, xylan", "token_count": 281, "char_count": 1126, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6835, "quality_score": 0.8418, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:21.751562", "source": { "split": "train_shard_00001", "doc_id": 3909 }, "chunk_id": "train_shard_00001_3909_1", "global_id": 11188 }, { "text": "In this study, our objective was to evaluate the genetic stability of foodborne bacterial pathogens during serial passage in vitro and persistent in vivo carriage. Six strains of Listeria, Campylobacter, Escherichia, Salmonella, and Vibrio were serially passaged 20 times. Three colonies were picked for whole-genome sequencing (WGS) from passes P0, P5, P10, P15, and P20. In addition, isolates of Salmonella and Escherichia from three patients with persistent infections were sequenced. Genetic stability was evaluated in terms of variations detected in high-quality single-nucleotide polymorphism (hqSNP), core genome multilocus sequence typing (cgMLST), seven-gene MLST, and determinants encoding serotype, antimicrobial resistance (AMR), and virulence. During serial passage, increasing diversity was observed in Listeria, Salmonella, and Vibrio as measured by hqSNPs (from median of 0 SNPs to median of 3-5 SNPs, depending on the organism) and to a lesser extent with cgMLST (from median of 0 alleles to median of 0-5 alleles), while Escherichia and Campylobacter genomes showed minimal variation. The serotype, AMR, and virulence markers remained stable in all organisms. Isolates from persistent infections lasting up to 10 weeks remained genetically stable. However, isolates from a persistent Salmonella enterica ser. Montevideo infection spanning 9 years showed early heterogeneity leading to the emergence of one predominant genotype that continued to evolve over the years, including gains and losses of AMR markers. While the hqSNP and cgMLST variation observed during the serial passage was minimal, culture passages should be limited to as few times as possible before WGS", "token_count": 519, "char_count": 1792, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6708, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:22.408455", "source": { "split": "train_shard_00001", "doc_id": 3910 }, "chunk_id": "train_shard_00001_3910_0", "global_id": 11189 }, { "text": "Our WGS data show that in vivo carriage lasting for a few weeks did not appear to alter the genotype. Longer persistent infections spanning for years, particularly in the presence of selective pressure, may cause changes in the genotype making it challenging to differentiate persistent infections from reinfections.\n\nAssessment of Genetic Stability During Serial In Vitro Passage and In Vivo Carriage.", "token_count": 104, "char_count": 423, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8197, "quality_score": 0.9098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:22.793212", "source": { "split": "train_shard_00001", "doc_id": 3910 }, "chunk_id": "train_shard_00001_3910_1", "global_id": 11190 }, { "text": "Francisella tularensis can cause the zoonotic disease tularemia and is partitioned into subspecies due to differences in chromosomal organization and virulence. The subspecies holarctica (type B) is generally considered more clonal than the other subpopulations with moderate virulence compared to the hypervirulent A.I clade. We performed whole genome sequencing (WGS) on six type B strains isolated from the blood of patients with tularemia within a one-year period from the same United States region, to better understand the associated pathogenicity. The WGS data were compared to the prototype strain for this subspecies, specifically FSC200, which was isolated from a patient with tularemia in Europe. These findings revealed 520-528 single nucleotide polymorphisms (SNPs) between the six United States type B strains compared to FSC200, with slightly higher A+T content in the latter strain. In contrast, comparisons between the six type B isolates showed that five of the six type B isolates had only 4-22 SNPs, while one of the strains had 47-53 SNPs. Analysis of SNPs in the core genome for the six United States type B isolates and the FSC200 strain gave similar results, suggesting that some of these mutations may have been nonsynonymous, resulting in altered protein function and pathogenicity.\n\nDifferences in Blood-derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia.", "token_count": 380, "char_count": 1431, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8052, "entities": { "genes": [ "FSC200" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:23.381385", "source": { "split": "train_shard_00001", "doc_id": 3911 }, "chunk_id": "train_shard_00001_3911_0", "global_id": 11191 }, { "text": "Asparagus bean (Vigna unguiculata ssp. sesquipedialis) is an important cowpea subspecies. We assembled the genomes of Ningjiang 3 (NJ, 550.31 Mb) and Dubai bean (DB, 564.12 Mb) for comparative genomics analysis. The whole-genome duplication events of DB and NJ occurred at 64.55 and 64.81 Mya, respectively, while the divergence between soybean and Vigna occurred in the Paleogene period. NJ genes underwent positive selection and amplification in response to temperature and abiotic stress. In species-specific gene families, NJ is mainly enriched in response to abiotic stress, while DB is primarily enriched in respiration and photosynthesis. We established the pan-genomes of four accessions (NJ, DB, IT97K-499-35 and Xiabao II) and identified 20,336 (70.5%) core genes present in all the accessions, 6,507 (55.56%) variable genes in two individuals, and 2,004 (6.95%) unique genes. The final pan genome is 616.35 Mb, and the core genome is 399.78 Mb. The variable genes are manifested mainly in stress response functions, ABC transporters, seed storage, and dormancy control. In the pan-genome sequence variation analysis, genes affected by presence/absence variants were enriched in biological processes associated with defense responses, immune system processes, signal transduction, and agronomic traits. The results of the present study provide genetic data that could facilitate efficient asparagus bean genetic improvement, especially in producing cold-adapted asparagus bean.\n\nGenome and pan-genome assembly of asparagus bean (Vigna unguiculata ssp. sesquipedialis) reveal the genetic basis of cold adaptation.", "token_count": 498, "char_count": 1657, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6478, "quality_score": 0.8239, "entities": { "genes": [ "IT97K" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:24.041015", "source": { "split": "train_shard_00001", "doc_id": 3912 }, "chunk_id": "train_shard_00001_3912_0", "global_id": 11192 }, { "text": "

Objectives

The global increase in carbapenem-resistant Enterobacteriaceae (CRE) is a growing health concern. Infections caused by CRE are associated with increased mortality and length of hospital stay, emphasising the health and economic burden posed by these pathogens. Although CRE can inhabit the human gut asymptomatically, colonisation with CRE is associated with an increased risk of CRE infection and mortality. In this study, we investigated the occurrence and characteristics of CRE in faecal samples from healthy persons in 12 villages in Shandong Province, China.

Methods

Screening for CRE in faecal samples was performed by selective cultivation. Minimum inhibitory concentrations (MICs) of meropenem were determined by the agar dilution method. Multilocus sequence typing (MLST) and carbapenemase gene carriage of the isolates were determined by whole-genome sequencing. Genetic relatedness of Escherichia coli isolates was determined by core genome MLST.

Results

CRE carriage increased from 2.4% in 2015 to 13.4% in 2017. Most CRE isolates (93.0%) were E. coli and all carried NDM-type carbapenemases. Sequence types (STs) among the E. coli isolates were diverse. The single most common ST was the highly epidemic strain ST167, which was only observed in 2017.

Conclusion

We report a rapid increase in occurrence of CRE (from 2.4% to 13.4%) among faecal samples collected from healthy rural residents of Shandong Province from 2015 to 2017. Colonisation with CRE is known to increase the risk of CRE infection, and the worrying deterioration of the epidemiological situation in the region reported here indicates a need for further monitoring and possible interventions.\n\nRapid increase in occurrence of carbapenem-resistant Enterobacteriaceae in healthy rural residents in Shandong Province, China, from 2015 to 2017.", "token_count": 505, "char_count": 1862, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5458, "quality_score": 0.7729, "entities": { "genes": [ "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:24.692502", "source": { "split": "train_shard_00001", "doc_id": 3913 }, "chunk_id": "train_shard_00001_3913_0", "global_id": 11193 }, { "text": "The coproduction of ethanol and polygalacturonase (PG) in a pilot-scale batch fermentor using yeast extract--glucose (YD)--and sugar beet molasses (SBM)-based media was implemented utilizing a new high-PG-producing strain of Kluyveromyces marxianus. A certain growth inhibition was observed in SBM medium, causing ethanol and PG production to be lower. Ethanol productivity and accumulation values of 1.94 g/(L x h) and 40 g/L, respectively, were attained in YD, whereas the best fermentation efficiency (95.1%) was achieved with SBM medium. Maximal PG synthesis occurred at the end of cell growth, with values of 1.08 and 0.46 U/(mg x h) for the YD and SBM media, respectively. When the cultures reached stationary phase, PG production stopped. The highest accumulation level (17 U/mL) occurred in YD medium, in agreement with previous laboratory-scale studies carried out for this strain. The potential applications of the crude enzyme preparations were evaluated with different fruit juices and vegetable slices. The enzyme was able to increase the filtration rate of orange, pear, and apple juices by twofold. Additionally, complete clarification of apple juice was readily accomplished, whereas cucumber, carrot, and banana tissues were macerated to a lesser extent.\n\nPolygalacturonase and ethanol production in Kluyveromyces marxianus: potential use of polygalacturonase in foodstuffs.", "token_count": 366, "char_count": 1391, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:25.276730", "source": { "split": "train_shard_00001", "doc_id": 3914 }, "chunk_id": "train_shard_00001_3914_0", "global_id": 11194 }, { "text": "We performed whole-genome sequencing of Vibrio cholerae O1 isolates from Laos, Thailand, and Vietnam, where cholera outbreaks occurred, to determine their genetic lineages. Core genome phylogenetic analysis revealed that the isolates located in same lineage without regional clusters, which suggests that closely related strains circulated in Southeast Asia.\n\nPhylogenetic Analysis Revealed the Dissemination of Closely Related Epidemic Vibrio cholerae O1 Isolates in Laos, Thailand, and Vietnam.", "token_count": 138, "char_count": 510, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:25.703936", "source": { "split": "train_shard_00001", "doc_id": 3915 }, "chunk_id": "train_shard_00001_3915_0", "global_id": 11195 }, { "text": "Antimicrobial resistant Salmonella enterica serovar Concord (S. Concord) is known to cause severe gastrointestinal and bloodstream infections in patients from Ethiopia and Ethiopian adoptees, and occasional records exist of S. Concord linked to other countries. The evolution and geographical distribution of S. Concord remained unclear. Here, we provide a genomic overview of the population structure and antimicrobial resistance (AMR) of S. Concord by analysing genomes from 284 historical and contemporary isolates obtained between 1944 and 2022 across the globe. We demonstrate that S. Concord is a polyphyletic serovar distributed among three Salmonella super-lineages. Super-lineage A is composed of eight S. Concord lineages, of which four are associated with multiple countries and low levels of AMR. Other lineages are restricted to Ethiopia and horizontally acquired resistance to most antimicrobials used for treating invasive Salmonella infections in low- and middle-income countries. By reconstructing complete genomes for 10 representative strains, we demonstrate the presence of AMR markers integrated in structurally diverse IncHI2 and IncA/C2 plasmids, and/or the chromosome. Molecular surveillance of pathogens such as S. Concord supports the understanding of AMR and the multi-sector response to the global AMR threat. This study provides a comprehensive baseline data set essential for future molecular surveillance.\n\nA global genomic analysis of Salmonella Concord reveals lineages with high antimicrobial resistance in Ethiopia.", "token_count": 370, "char_count": 1550, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:26.292784", "source": { "split": "train_shard_00001", "doc_id": 3916 }, "chunk_id": "train_shard_00001_3916_0", "global_id": 11196 }, { "text": "This work presents a multi-route, non-structured kinetic model for determination of microbial growth and substrate consumption in an experimental batch bioreactor in which beta-galactosidase is produced by Kluyveromyces marxianus growing on cheese whey. The main metabolic routes for lactose, and oxygen consumption, cell growth, and ethanol production are derived based on experimental data. When these individual rates are combined into a single growth rate, by rewriting the model equations, the model re-interpretation has a complexity similar to that of the usual variations of the Monod kinetic model, available in the literature. Furthermore, the proposed model is in good agreement with the experimental data for different growth temperatures, being acceptable for dynamic simulations, processes optimization, and implementations of model-based control technologies.\n\nA growth kinetic model of Kluyveromyces marxianus cultures on cheese whey as substrate.", "token_count": 204, "char_count": 963, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:26.755334", "source": { "split": "train_shard_00001", "doc_id": 3917 }, "chunk_id": "train_shard_00001_3917_0", "global_id": 11197 }, { "text": "At the Bundeswehr Hospitals of Hamburg and Westerstede, patients repatriated from subtropical war and crisis zones of Northern Africa and the Middle East were medically treated, including microbiological assessment. Within a six-year interval, 16 Acinetobacter spp. strains, including 14 Acinetobacter baumannii (Ab) isolates with resistance against carbapenems and origins in Afghanistan (n = 4), Iraq (n = 2), Libya (n = 2), and Syria (n = 8) were collected. While clonal relationships of Libyan and Syrian strains had been assessed by superficial next generation sequencing (NGS) and \"DiversiLab\" repetitive elements sequence-based (rep-)PCR so far, this study provides core genome-based sequence typing and thus more detailed epidemiological information. In detail, sequencing allowed a definitive species identification and comparison with international outbreak-associated Ab strains by core genome multi locus sequence typing (cgMLST) and the identification of MLST lineages, as well as the identification of known resistance genes. The sequence analysis allowed for the confirmation of outbreak-associated clonal clusters among the Syrian and Afghan Ab isolates, indicating likely transmission events. The identified acquired carbapenem resistance genes comprised blaOXA-23, blaOXA-58, blaNDM-1, and blaGES-11, next to other intrinsic and acquired, partly mobile resistance-associated genes. Eleven out of 14 Ab isolates clustered with the previously described international clonal lineages IC1 (4 Afghan strains), IC2 (6 Syrian strains), and IC7 (1 Syrian strain)", "token_count": 466, "char_count": 1686, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [ "IC2", "IC1", "IC7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:27.397898", "source": { "split": "train_shard_00001", "doc_id": 3918 }, "chunk_id": "train_shard_00001_3918_0", "global_id": 11198 }, { "text": "Identified Pasteur sequence types of the 14 Ab strains comprised ST2 (Syrian), ST25 (Libyan), ST32 (Iraqi), ST81 (Afghan), ST85 (Libyan), and ST1112 (Syrian), respectively. In conclusion, the study revealed a broad spectrum of resistance genes in Ab isolated from war-injured patients from Northern Africa and the Middle East, thereby broadening the scarcely available data on locally abundant clonal lineages and resistance mechanisms.\n\nMolecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolates from Northern Africa and the Middle East.", "token_count": 158, "char_count": 566, "word_count": 76, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "ST1112", "ST2", "ST81", "ST25", "ST32", "ST85" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:27.836393", "source": { "split": "train_shard_00001", "doc_id": 3918 }, "chunk_id": "train_shard_00001_3918_1", "global_id": 11199 }, { "text": "Staphylococcus aureus superantigens (SAgs) have been reported to aggravate atopic dermatitis. However, comprehensive analyses of these molecules in multiple microniches are lacking. The present study involved 50 adult patients with active atopic dermatitis. S. aureus was isolated from the lesional skin, nonlesional skin, and anterior nares. Multiplex-PCR was performed to identify genes encoding (1) selX (core genome); (2) seg, selI, selM, selN, selO, selU (enterotoxin gene cluster, EGC); and (3) sea, seb, sec, sed, see, tstH (classic SAgs encoded on other mobile genetic elements). The results were correlated to clinical parameters of the study group. selx and EGC were the most prevalent in all microniches. The number of SAg-encoding genes correlated between the anterior nares and nonlesional skin, and between the nonlesional and lesional skin. On lesional skin, the total number of SAg genes correlated with disease severity (total and objective SCORAD, intensity, erythema, edema/papulation, lichenification and dryness). Linear regression revealed that AD severity was predicted only by selx and EGC. This study revealed that selX and EGC are associated with atopic dermatitis severity. Anterior nares and nonlesional skin could be reservoirs of SAg-positive S. aureus. Restoring the physiological microbiome could reduce the SAg burden and alleviate syndromes of atopic dermatitis.\n\nEnterotoxin Gene Cluster and selX Are Associated with Atopic Dermatitis Severity-A Cross-Sectional Molecular Study of Staphylococcus aureus Superantigens.", "token_count": 488, "char_count": 1629, "word_count": 219, "semantic_coherence": 1, "information_density": 0.621, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:29.128402", "source": { "split": "train_shard_00001", "doc_id": 3919 }, "chunk_id": "train_shard_00001_3919_0", "global_id": 11200 }, { "text": "Disclosed is a novel yeast strain capable of producing ethanol through fermentation with a high degree of efficiency at a temperature of 37 DEG C or higher, preferably a temperature ranging from 40 to 49 DEG C or higher. Also disclosed is a method for producing ethanol by utilizing the yeast strain. Further disclosed is ethanol produced by the method. An yeast strain (Deposition No. NITE BP-283 or the like) belonging to a kind of yeast Kluyveromyces marxianus which can be isolated through a screening step using a culture medium supplemented with a saccharide in a high concentration and ethanol is cultured in a culture liquid supplemented with 10 to 100 mM of sorbitol at 40 to 49 DEG C.\n\nTHERMOTOLERANT ETHANOL-PRODUCING YEAST AND ETHANOL PRODUCTION METHOD UTILIZING THE SAME", "token_count": 226, "char_count": 783, "word_count": 130, "semantic_coherence": 1, "information_density": 0.5769, "quality_score": 0.7885, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:29.596355", "source": { "split": "train_shard_00001", "doc_id": 3920 }, "chunk_id": "train_shard_00001_3920_0", "global_id": 11201 }, { "text": "A potential application of inulinase in the food industry is the production of fructoligosaccharides (FOS) by the transfructosilation of sucrose. The FOSs present many interesting functional properties besides their ability to increase the shelf-life and flavor of many products. The use of an industrial medium represents a good alternative to producing inulinase at low cost, since the activity may improve, or at least remain the same, as that obtained using a synthetic medium. This work was an optimization study of the inulinase production by Kluyveromyces marxianus NRRL Y-7571 using industrial pre-treated culture medium in a bioreactor employing a sequential strategy of experimental design. Initially, a Plackett-Burman (Screening Design) design was used, where the studied variables were molasses, corn steep liquor, yeast extract concentration, and agitation and aeration rates. After the analysis of the effects, a central composite rotational design (CCRD) was carried out. The optimized condition for the inulinase production was: 250 g/l of molasses, 80 g/l of corn steep liquor, 6 g/l of yeast extract, 300 rpm of agitation and 1.5 vvm aeration rate, which resulted in an enzymatic activity of 1,317 +/- 65 U/ml.\n\nUse of a sequential strategy of experimental design to optimize the inulinase production in a batch bioreactor.", "token_count": 341, "char_count": 1342, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:30.201396", "source": { "split": "train_shard_00001", "doc_id": 3921 }, "chunk_id": "train_shard_00001_3921_0", "global_id": 11202 }, { "text": "Bacterial species are hosts to horizontally acquired mobile genetic elements (MGEs), which encode virulence, toxin, antimicrobial resistance, and other metabolic functions. The bipartite genome of Vibrio cholerae harbors sporadic and conserved MGEs that contribute in the disease development and survival of the pathogens. For a comprehensive understanding of dynamics of MGEs in the bacterial genome, we engineered the genome of V. cholerae and examined in vitro and in vivo stability of genomic islands (GIs), integrative conjugative elements (ICEs), and prophages. Recombinant vectors carrying the integration module of these GIs, ICE and CTXΦ, helped us to understand the efficiency of integrations of MGEs in the V. cholerae chromosome. We have deleted more than 250 acquired genes from 6 different loci in the V. cholerae chromosome and showed contribution of CTX prophage in the essentiality of SOS response master regulator LexA, which is otherwise not essential for viability in other bacteria, including Escherichia coli In addition, we observed that the core genome-encoded RecA helps CTXΦ to bypass V. cholerae immunity and allow it to replicate in the host bacterium in the presence of similar prophage in the chromosome. Finally, our proteomics analysis reveals the importance of MGEs in modulating the levels of cellular proteome. This study engineered the genome of V. cholerae to remove all of the GIs, ICEs, and prophages and revealed important interactions between core and acquired genomes.\n\nMolecular insights into the genome dynamics and interactions between core and acquired genomes of <i>Vibrio cholerae</i>.", "token_count": 468, "char_count": 1694, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:30.867461", "source": { "split": "train_shard_00001", "doc_id": 3922 }, "chunk_id": "train_shard_00001_3922_0", "global_id": 11203 }, { "text": "

A bstract

Fungal pathogens represent a serious threat towards agriculture, health, and environment. Control of fungal diseases on crops necessitates a global understanding of fungal pathogenicity determinants and their expression during infection. Genomes of phytopathogenic fungi are often compartmentalized: the core genome contains housekeeping genes whereas the fast-evolving genome mainly contains transposable elements and species-specific genes. In this study, we analysed nucleosome landscapes of four phytopathogenic fungi with contrasted genome organizations to describe and compare nucleosome repartition patterns in relation with genome structure and gene expression level. We combined MNase-seq and RNA-seq analyses to concomitantly map nucleosome-rich and transcriptionally active regions during fungal growth in axenic culture; we developed the MNase-seq Tool Suite (MSTS) to analyse and visualise data obtained from MNase-seq experiments in combination with other genomic data and notably RNA-seq expression data. We observed different characteristics of nucleosome profiles between species, as well as between genomic regions within the same species. We further linked nucleosome repartition and gene expression. Our findings support that nucleosome positioning and occupancies are subjected to evolution, in relation with underlying genome sequence modifications. Understanding genomic organization and its role in expression regulation is the next gear to understand complex cellular mechanisms and their evolution.\n\nNucleosome patterns in four plant pathogenic fungi with contrasted genome structures", "token_count": 350, "char_count": 1630, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6338, "quality_score": 0.8169, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:31.500906", "source": { "split": "train_shard_00001", "doc_id": 3923 }, "chunk_id": "train_shard_00001_3923_0", "global_id": 11204 }, { "text": "Listeria monocytogenes is causing listeriosis, a rare but severe foodborne infection. Listeriosis affects pregnant women, newborns, older adults, and immunocompromised individuals. Ready-to-eat (RTE) foods are the most common sources of transmission of the pathogen This study explored the virulence factors and antibiotic resistance in L. monocytogenes strains isolated from ready-to-eat (RTE) foods through in vitro and in silico testing by whole-genome sequencing (WGS). The overall positivity of L. monocytogenes in RTE food samples was 3.1% and 14 strains were isolated. L. monocytogenes ST8, ST2763, ST1, ST3, ST5, ST7, ST9, ST14, ST193, and ST451 sequence types were identified by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST. Seven isolates had serotype 1/2a, five 1/2b, one 4b, and one 1/2c. Three strains exhibited in vitro resistance to ampicillin and 100% of the strains carried the fosX, lin, norB, mprF, tetA, and tetC resistance genes. In addition, the arsBC, bcrBC, and clpL genes were detected, which conferred resistance to stress and disinfectants", "token_count": 435, "char_count": 1229, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7301, "quality_score": 0.865, "entities": { "genes": [ "ST3", "ST193", "ST2763", "ST14", "ST5", "ST451", "ST7", "ST1", "ST8", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:32.134621", "source": { "split": "train_shard_00001", "doc_id": 3924 }, "chunk_id": "train_shard_00001_3924_0", "global_id": 11205 }, { "text": "All strains harbored hlyA, prfA, and inlA genes almost thirty-two the showed the bsh, clpCEP, hly, hpt, iap/cwhA, inlA, inlB, ipeA, lspA, mpl, plcA, pclB, oat, pdgA, and prfA genes. One isolate exhibited a type 11 premature stop codon (PMSC) in the inlA gene and another isolate a new mutation (deletion of A in position 819). The Inc18(rep25), Inc18(rep26), and N1011A plasmids and MGEs were found in nine isolates. Ten isolates showed CAS-Type II-B systems; in addition, Anti-CRISPR AcrIIA1 and AcrIIA3 phage-associated systems were detected in three genomes. These virulence and antibiotic resistance traits in the strains isolated in the RTE foods indicate a potential public health risk for consumers.\n\nVirulence and Antibiotic Resistance Genes in Listeria monocytogenes Strains Isolated From Ready-to-Eat Foods in Chile.", "token_count": 326, "char_count": 875, "word_count": 125, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:32.696318", "source": { "split": "train_shard_00001", "doc_id": 3924 }, "chunk_id": "train_shard_00001_3924_1", "global_id": 11206 }, { "text": "The bread wheat (Triticum aestivum) pangenome is a patchwork of variable regions, including translocations and introgressions from progenitors and wild relatives. Although a large number of these have been documented, it is likely that many more remain unknown. To map these variable regions and make them more traceable in breeding programs, wheat accessions need to be genotyped or sequenced. The wheat genome is large and complex and consequently, sequencing efforts are often targeted through exome capture. In this study, we employed exome capture prior to sequencing 12 wheat varieties; 10 elite T. aestivum cultivars and two T. aestivum landrace accessions. Sequence coverage across chromosomes was greater toward distal regions of chromosome arms and lower in centromeric regions, reflecting the capture probe distribution which itself is determined by the known telomere to centromere gene gradient. Superimposed on this general pattern, numerous drops in sequence coverage were observed. Several of these corresponded with reported introgressions. Other drops in coverage could not be readily explained and may point to introgressions that have not, to date, been documented.\n\nThe Use and Limitations of Exome Capture to Detect Novel Variation in the Hexaploid Wheat Genome.", "token_count": 305, "char_count": 1305, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:33.267265", "source": { "split": "train_shard_00001", "doc_id": 3925 }, "chunk_id": "train_shard_00001_3925_0", "global_id": 11207 }, { "text": "A respiratory deficient mutant of Kluyveromyces fragilis was isolated using ethidium bromide mutagenesis. It was characterized by a loss of cytochromes a + a3 and deficiency in cytochrome b. This petite mutant has brought about modifications in the excretion pattern of beta-fructosidase active on saccharose and inulin. The mutant practically no longer excretes the enzyme, and is incapable of growth and fermentation in the presence of inulin. The study of the activities of different enzyme extracts (culture medium, whole and disrupted cells) on inulin and saccharose suggests the existence of an unique enzyme system capable of taking several forms, and also shows the influence of the growth substrate on the I/S activity ratio.\n\nImpairment of insulin assimilation and beta-fructosidase activity due to a petite mutation in Kluyveromyces marxianus.", "token_count": 219, "char_count": 854, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:33.733164", "source": { "split": "train_shard_00001", "doc_id": 3926 }, "chunk_id": "train_shard_00001_3926_0", "global_id": 11208 }, { "text": "

Background

Colistin is used against multi-drug resistant pathogens, yet resistance emerges through dissemination of plasmid-mediated genes (mcr) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challenging due to poor diffusion of colistin in agar media, leading to an underestimation of resistance. Performance of five phenotypic approaches was compared in the context of different molecular mechanisms of resistance. We evaluated Vitek 2® (bioMérieux, AST N242), Colistin MIC Test Strip (Liofilchem Diagnostici), UMIC (Biocentric), and Rapid Polymyxin™ NP test (ELITechGroup) against the standard broth microdilution (BMD) method. We used whole genome sequencing (WGS) to infer molecular resistance mechanisms. We analysed 97 Enterobacterales and non-fermenting bacterial isolates, largely clinical isolates collected up to 2018. Data was analysed by comparing susceptibility categories (susceptible or resistant) and minimal inhibitory concentrations (MIC). Susceptibility category concordance is the percentage of test results sharing the same category to BMD. MIC concordance was calculated similarly but considering ±1 MIC titre error range. We determined genomic diversity by core genome multi locus sequencing typing (cgMLST) and identified putative antimicrobial resistance genes using NCBI and CARD databases, and manual annotation.

Results

Of 97 isolates, 54 (56%) were resistant with standard BMD. Highest susceptibility category concordance was achieved by Rapid Polymyxin™ NP (98.8%) followed by UMIC (97.9%), Colistin E-test MIC strip (96.9%) and Vitek 2® (95.6%)", "token_count": 474, "char_count": 1683, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6727, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:34.382058", "source": { "split": "train_shard_00001", "doc_id": 3927 }, "chunk_id": "train_shard_00001_3927_0", "global_id": 11209 }, { "text": "Highest MIC concordance was achieved by UMIC (80.4%), followed by Vitek 2® (72.5%) and Colistin E-test MIC strip (62.9%). Among resistant isolates, 23/54 (43%) were intrinsically resistant to colistin, whereas 31/54 (57%) isolates had acquired colistin resistance. Of these, mcr-1 was detected in four isolates and mcr-2 in one isolate. Non-synonymous mutations in mgrB, phoQ, pmrA, pmrB, and pmrC genes were encountered in Klebsiella pneumoniae, Escherichia coli, and Acinetobacter bereziniae resistant isolates. Mutations found in mgrB and pmrB were only identified in isolates exhibiting MICs of ≥16 mg/L.

Conclusions

The Rapid Polymyxin™ NP test showed highest categorical concordance and the UMIC test provided MIC values with high concordance to BMD. We found colistin resistance in diverse species occurred predominantly through spontaneous chromosomal mutation rather than plasmid-mediated resistance.\n\nColistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms.", "token_count": 327, "char_count": 1050, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7183, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:34.950185", "source": { "split": "train_shard_00001", "doc_id": 3927 }, "chunk_id": "train_shard_00001_3927_1", "global_id": 11210 }, { "text": "Abstract

Background

The long-standing paradigm is that almost all BSIs stem from a single, clonal organism (“single-organism” hypothesis). We hypothesized that CG-positive BCs were comprised of genetically diverse strain variants.

Methods

Five to ten CG colonies were isolated from positive BC bottles from ten distinct patients (pts) for a total of 94 clones, which underwent NextGen short-read sequencing (Illumina). Variants were analyzed using SNPeff, and a phylogeny was constructed with Maximum Likelihood method.

Results

BCs harbored a diverse population of CG strains that were unique to each pt [Fig. 1]. All strains were genetically distinct, differing by unique SNPs and insertions-deletions (indels) [Fig. 2-3]. SNPs were ~8-fold more common than indels. Individual genomes from the same time point in the same pt exhibited consistent magnitude of variations relative to reference genome; however, variations were unique, pointing to significant genomic variability that could be both intra- and interclonal. The number of variant sites for within-pt pairwise clone comparisons ranged from 1924-8500. There were 124,145 variant sites when all clones are compared. Roughly half of all SNPs were identical in different samples from a given pt; the remainder were present/absent in at least one sample per pt. Long-read WGS revealed strains with structural variants in each pt, including chromosomal recombinations and gene duplications that were not evident by short-read WGS. A genomic phylogeny construction showed that 94 clones spanned 3 distinct clades that were distinct from the reference strain. Finally, comparison of non-synonymous mutations among intra-pt clones showed overwhelming overrepresentation of adhesin and adhesin-like genes, pointing to possible importance in host adaptation. Venn diagram of core genome SNPs of 5 Candida glabrata recovered from blood cultures of patient C.

Conclusion

Preliminary analyses revealed genetically diverse populations of C. glabrata in BCs of individuals with BSIs", "token_count": 526, "char_count": 2064, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6485, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:35.611581", "source": { "split": "train_shard_00001", "doc_id": 3928 }, "chunk_id": "train_shard_00001_3928_0", "global_id": 11211 }, { "text": "We are studying phenotypic diversity of strain variants, and the clinical implications of genetically diverse Candida BSIs.

Disclosures

Cornelius J. Clancy, MD, Merck (Grant/Research Support) Minh-Hong Nguyen, MD, Merck (Grant/Research Support)\n\n215. Candida glabrata (CG) Bloodstream Infections (BSIs) Are Characterized by Genetically Diverse Populations of Strain Variants Recovered from Positive Blood Cultures (BCs)", "token_count": 133, "char_count": 428, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7925, "quality_score": 0.8962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:36.040266", "source": { "split": "train_shard_00001", "doc_id": 3928 }, "chunk_id": "train_shard_00001_3928_1", "global_id": 11212 }, { "text": "An amine oxidase from the yeast Kluyveromyces marxianus was induced, purified and completely characterized; it was shown to belong to the class of copper-containing amine oxidases (E.C. 1.4.3.6). The enzyme was induced by putrescine and, very strongly, by copper(II); structural-functional characterization of the enzyme was performed, including determination of molecular weight, glycosylation, copper and TPQ content, isoelectric point, K(M) and k(CAT) (with benzylamine as substrate), pH, temperature and ionic strength effect on catalysis, substrate and inhibitor specificity. A 700 bp clone was isolated containing the cDNA that encodes for the C-terminus of the enzyme; the amino acid sequence deduced (the first available for a benzylamine oxidase from yeast) was compared to that of other copper amine oxidases from microorganisms and higher organisms. From the results obtained, the putrescine/benzylamine oxidase from Kluyveromyces marxianus was found to have a good homology with other enzymes of this class from microorganisms, and particularly with AO I from Aspergillus niger. Nonetheless, some features resulted closer to those of animal amine oxidases and histaminases. Some potential biotechnological applications are proposed. The cDNA Accession No. is AJ320485.\n\nInduction and characterization of a novel amine oxidase from the yeast Kluyveromyces marxianus.", "token_count": 376, "char_count": 1377, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6321, "quality_score": 0.8161, "entities": { "genes": [ "AJ320485" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:36.628666", "source": { "split": "train_shard_00001", "doc_id": 3929 }, "chunk_id": "train_shard_00001_3929_0", "global_id": 11213 }, { "text": "Recently, a total of 32 carbapenem- and fluoroquinolone-resistant Acinetobacter baumannii (Ab) isolates was isolated from war-injured patients who were treated at German Bundeswehr Hospitals, and preliminarily typed by \"DiversiLab\" repetitive elements sequence-based (rep-) PCR. Core genome-based sequence typing was also used to provide more detailed epidemiological information. From the clusters observed by rep-PCR, selected Ab strains were subjected to Next Generation Sequencing (NGS) in order to compare them with international outbreak-associated Ab strains and to identify MLST (multi-locus sequence type) lineages, as well as to identify known resistance genes. Accordingly, NGS indicated higher diversity than rep-PCR, but also confirmed likely transmission events. The identified acquired carbapenem-resistant genes comprised blaOXA-23, blaOXA-72 and blaGES-12, as well as various other intrinsic and acquired resistance-associated genetic elements. All isolates clustered with the previously identified international clonal lineages IC1, IC2, IC6 and IC7, with corresponding Pasteur sequence types ST1, ST2, ST78 and ST25, respectively. In conclusion, the assessment confirmed a broad spectrum of resistance-associated genes in Ab isolated from war-injured patients from the Eastern Ukraine, and provided the first insights into locally abundant clonal lineages.\n\nMolecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii Isolated from War-Injured Patients from the Eastern Ukraine.", "token_count": 421, "char_count": 1576, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [ "ST2", "IC6", "IC7", "ST25", "ST78", "IC2", "ST1", "IC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:37.257591", "source": { "split": "train_shard_00001", "doc_id": 3930 }, "chunk_id": "train_shard_00001_3930_0", "global_id": 11214 }, { "text": "Host-associated microbiomes can be critical for the health and proper development of animals and plants. The answers to many fundamental questions regarding the modes of acquisition and microevolution of microbiome communities remain to be established. Deciphering strain-level dynamics is essential to fully understand how microbial communities evolve, but the forces shaping the strain-level dynamics of microbial communities remain largely unexplored, mostly because of methodological issues and cost. Here, we used targeted strain-level deep sequencing to uncover the strain dynamics within a host-associated microbial community using the honey bee gut microbiome as a model system. Our results revealed that amplicon sequencing of conserved protein-coding gene regions using species-specific primers is a cost-effective and accurate method for exploring strain-level diversity. In fact, using this method we were able to confirm strain-level results that have been obtained from whole-genome shotgun sequencing of the honey bee gut microbiome but with a much higher resolution. Importantly, our deep sequencing approach allowed us to explore the impact of low-frequency strains (i.e., cryptic strains) on microbiome dynamics. Results show that cryptic strain diversity is not responsible for the observed variations in microbiome composition across bees. Altogether, the findings revealed new fundamental insights regarding strain dynamics of host-associated microbiomes.IMPORTANCE The factors driving fine-scale composition and dynamics of gut microbial communities are poorly understood. In this study, we used metagenomic amplicon deep sequencing to decipher the strain dynamics of two key members of the honey bee gut microbiome. Using this high-throughput and cost-effective approach, we were able to confirm results from previous large-scale whole-genome shotgun (WGS) metagenomic sequencing studies while also gaining additional insights into the community dynamics of two core members of the honey bee gut microbiome. Moreover, we were able to show that cryptic strains are not responsible for the observed variations in microbiome composition across bees.\n\nStrain Structure and Dynamics Revealed by Targeted Deep Sequencing of the Honey Bee Gut Microbiome.", "token_count": 482, "char_count": 2277, "word_count": 315, "semantic_coherence": 1, "information_density": 0.4825, "quality_score": 0.7413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:37.899584", "source": { "split": "train_shard_00001", "doc_id": 3931 }, "chunk_id": "train_shard_00001_3931_0", "global_id": 11215 }, { "text": "Kluyveromyces marxianus was grown in submerged culture in a complex medium with several potential inducers of lipolytic activity (triacylglycerols, fatty acids). The highest extracellular lipolytic enzyme production (about 80 U ml(-1) in 3 d) was obtained when the medium was supplemented with 2 g urea l(-1) plus 5 g tributyrin l(-1). Addition of surfactants (1 g l(-1)) did not improve production. The lipase had a high thermal stability in aqueous solution (73% residual activity after 9 d at 50 degrees C, 16 min half-life time at 100 degrees C). It was also stable at acidic pH and showed good tolerance to organic solvents (70% residual activity after 2 d in n-hexane of cyclohexane).\n\nProduction of a thermostable extracellular lipase by Kluyveromyces marxianus.", "token_count": 235, "char_count": 769, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7377, "quality_score": 0.8689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:38.370079", "source": { "split": "train_shard_00001", "doc_id": 3932 }, "chunk_id": "train_shard_00001_3932_0", "global_id": 11216 }, { "text": "Microbial pectinolytic enzymes are known to play a commercially important role in a number of industrial processes. The objective of this study was to investigate the extracellular polygalacturonases of yeasts isolated from Brazilian semi-arid environments. Among the 250 colonies tested, only 33 produced extracellular polygalacturonases: Aureobasidium pullulans (18 isolates), Candida boidinii (one isolate), Trichosporonoides sp. (three isolates), Kluyveromyces marxianus (one isolate), Cryptococcus liquefaciens (one isolate), Pseudozyma sp. (four isolates), and yeast-like related to fungal endophyte (five isolates). The highest activity of polygalacturonase was observed in Pseudozyma sp. CCMB 300 (14.17+/-0.08 micromol acid galacturonic released/min/mg protein). This study shows the potential of yeasts and yeast-like organisms isolated from Brazilian semi-arid environments to produce pectinolytic enzymes.\n\nPolygalacturonase secreted by yeasts from Brazilian semi-arid environments.", "token_count": 297, "char_count": 994, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.8361, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:38.935631", "source": { "split": "train_shard_00001", "doc_id": 3933 }, "chunk_id": "train_shard_00001_3933_0", "global_id": 11217 }, { "text": "

Background

High-temperature bioethanol production benefits from yeast thermotolerance. Salt stress could induce obvious cross-protection against heat stress of Pichia kudriavzevii, contributing to the improvement of its thermotolerance and bioethanol fermentation. However, the underlying mechanisms of the cross-protection remain poorly understood.

Results

Salt stress showed obvious cross-protection for thermotolerance and high-temperature ethanol production of P. kudriavzevii observed by biomass, cell morphology and bioethanol production capacity. The biomass and ethanol production of P. kudriavzevii at 45 °C were, respectively, improved by 2.6 and 3.9 times by 300 mmol/L NaCl. Metabolic network map showed that salt stress obviously improved the key enzymes and intermediates in carbohydrate metabolism, contributing to the synthesis of bioethanol, ATP, amino acids, nucleotides, and unsaturated fatty acids, as well as subsequent intracellular metabolisms. The increasing trehalose, glycerol, HSPs, and ergosterol helped maintain the normal function of cell components. Heat stress induced serious oxidative stress that the ROS-positive cell rate and dead cell rate, respectively, rose from 0.5% and 2.4% to 28.2% and 69.2%, with the incubation temperature increasing from 30 to 45 °C. The heat-induced ROS outburst, oxidative damage, and cell death were obviously inhibited by salt stress, especially the dead cell rate which fell to only 20.3% at 300 mmol/L NaCl. The inhibiting oxidative damage mainly resulted from the abundant synthesis of GSH and GST, which, respectively, increased by 4.8 and 76.1 times after addition of 300 mmol/L NaCl", "token_count": 480, "char_count": 1670, "word_count": 228, "semantic_coherence": 1, "information_density": 0.5921, "quality_score": 0.7961, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:39.583818", "source": { "split": "train_shard_00001", "doc_id": 3934 }, "chunk_id": "train_shard_00001_3934_0", "global_id": 11218 }, { "text": "The improved bioethanol production was not only due to the improved thermotolerance, but resulted from the up-regulated alcohol dehydrogenases and down-regulated aldehyde dehydrogenases by salt stress.

Conclusion

The results provide a first insight into the mechanisms of the improved thermotolerance and high-temperature bioethanol production of P. kudriavzevii by salt stress, and provide important information to construct genetic engineering yeasts for high-temperature bioethanol production.\n\nSalt stress improves thermotolerance and high-temperature bioethanol production of multi-stress-tolerant Pichia kudriavzevii by stimulating intracellular metabolism and inhibiting oxidative damage.", "token_count": 179, "char_count": 702, "word_count": 81, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8272, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:40.030476", "source": { "split": "train_shard_00001", "doc_id": 3934 }, "chunk_id": "train_shard_00001_3934_1", "global_id": 11219 }, { "text": "Abstract

Pseudomonas stutzeri A1501 is the model strain for studying associative nitrogen fixation and possesses the nitrogen regulatory NtrC protein in the core genome. Nitrogen source is one of the important factors affecting the efficiency of biological nitrogen fixation in the natural environment. However, the regulation of NtrC in nitrogen metabolism of P. stutzeri A1501 is not clear. In this work, phenotypic analysis of the ntrC mutant characterized the roles of NtrC for the nitrogen metabolism and oxidative stress response of P. stutzeri A1501. To systematically identify NtrC-controlled gene expression, RNA-seq was performed to further analyze the gene expression differences between the wild type strain and the ∆ntrC mutant under nitrogen fixation conditions. A total of 1431 genes were found to be significantly altered by the ntrC deletion, among which 147 associative genes had NtrC-binding sites, and pathways for nitrogen fixation regulation, the acquisition and catabolism of nitrogenous compounds and nitrate assimilation were particularly discussed. Furthermore, the oxidative stress-related gene (katB), upregulated by the ntrC deletion, was suggested to be the potential target gene of NtrC, underlining the importance of NtrC to nitrogenase protection against oxygen damage. Based on these findings, we propose that NtrC is a high-ranked element in the regulatory network of P. stutzeri A1501 that controls a variety of nitrogen metabolic and oxidative stress responsive traits required for adaptation to complex rhizosphere environment.

\n\nNtrC, The Master Regulator Controls the Utilization of Alternative Nitrogen Sources in Pseudomonas Stutzeri A1501", "token_count": 505, "char_count": 1856, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7842, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:40.688248", "source": { "split": "train_shard_00001", "doc_id": 3935 }, "chunk_id": "train_shard_00001_3935_0", "global_id": 11220 }, { "text": "Meiosis, the key process underlying sexual reproduction, is generally a fair process: each chromosome has a 50% chance of being included into each gamete. However in some organisms meiosis has become highly aberrant with some chromosomes having a higher chance of making it into gametes than others. Yet why and how such systems evolve remains unclear. Here we study the unusual reproductive genetics of mealybugs, in which only maternal-origin chromosomes are included into the gametes during male meiosis, while paternally-derived chromosomes degrade. This “whole genome meiotic drive” occurs in all males and is evolutionarily conserved. However one species - the obscure mealybug Pseudococcus viburni - has a segregating B chromosome that increases in frequency by escaping paternal genome elimination. Here we present whole-genome and gene expression data from laboratory lines with and without B chromosomes. These data allow us to identify B-linked sequences including >70 protein-coding genes as well as a B-specific satellite repeat that makes up a significant proportion of the chromosome. We also used these data to investigate the evolutionary origin of the B chromosome. The few paralogs between the B and the core genome are distributed throughout the genome, showing that it is unlikely that the B originated through a simple duplication of one of the autosomes. We also find that while many of the B-linked genes do not have paralogs within the P . viburni genome, but they do show orthology with genes in other hemipteran insects suggesting that the B might have originated from fission of one of the autosomes, possibly followed by further translocations of individual genes. Finally in order to understand the mechanisms by which the B is able to escape elimination when paternally-derived we generated gene expression data for males and females with and without B chromosomes. We find that at the developmental stage when meiosis is taking place only a small number of B-linked genes show significant expression. Only one gene was significantly over-expressed during male meiosis, which is when the drive occurs: a acetyltransferase involved in H3K56Ac, which has a putative role in meiosis and is therefore a promising candidate for further studies", "token_count": 522, "char_count": 2269, "word_count": 353, "semantic_coherence": 1, "information_density": 0.5609, "quality_score": 0.7805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:41.358362", "source": { "split": "train_shard_00001", "doc_id": 3936 }, "chunk_id": "train_shard_00001_3936_0", "global_id": 11221 }, { "text": "Together, these results form a promising foundation for studying the mechanisms of meiotic drive in a system that is uniquely suited for this approach.\n\nThe B chromosome of Pseudococcus viburni: a selfish chromosome that exploits whole-genome meiotic drive", "token_count": 68, "char_count": 263, "word_count": 38, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:41.730430", "source": { "split": "train_shard_00001", "doc_id": 3936 }, "chunk_id": "train_shard_00001_3936_1", "global_id": 11222 }, { "text": "Background:Klebsiella pneumoniae is an opportunistic pathogen associated with community-acquired and nosocomial infections. Since 2010, K. pneumoniae testing has been included into an existing diarrhea-syndrome surveillance system for estimating the prevalence of K. pneumoniae in diarrhea-syndrome patients, assessing antibiotic susceptibility, and investigating molecular characteristics of K. pneumoniae. Methods:Klebsiella pneumoniae strains were isolated from stool specimens from diarrhea-syndrome outpatients in Beijing, China. Isolates were tested for antibiotic susceptibility, and phylogenetic relationships were explored though whole genome sequence analysis. Multi-locus sequence type (MLST) alleles were extracted from the whole genome sequence (WGS) data. A maximum likelihood tree was generated by MEGAX. Genomes were annotated by Prokka; core genes were produced by Roary; a maximum likelihood phylogenetic tree was generated using FastTree. Results: Forty-four K. pnuemoniae strains were isolated from 2010 to July 2019; of these 37 were K. pneumoniae and seven were K. variicola. Antibiotic susceptibility testing showed that all 44 strains were sensitive to gentamicin, imipenem, amikacin, meropenem, kanamycin; 97.73% were sensitive to cefoxitin andlavo-ofloxacin; the highest antibiotic resistance rate was 79.55%, which was to ampicillin. We found three extended-spectrum beta-lactamase (ESBL) producing strains; we identified high-virulence ST types, including ST307 and ST65; and we found that ST23 has been the epidemic clone since 2010. MLST and core genome sequence analysis showed two distinct clusters of 44 K", "token_count": 523, "char_count": 1718, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6389, "quality_score": 0.8194, "entities": { "genes": [ "ST23", "ST65", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:42.395270", "source": { "split": "train_shard_00001", "doc_id": 3937 }, "chunk_id": "train_shard_00001_3937_0", "global_id": 11223 }, { "text": "pnuemoniae; 40 alleles were identified in core genome sequence analysis, while 36 alleles were identified in MLST typing. Conclusions: There is an urgent need for epidemiological and molecular studies to understand the dynamics of antibiotic resistance and virulence gene transmission to guide strategies for K. pneumoniae surveillance. WGS analysis provided high discrimination power and reliable and robust data useful for molecular epidemiology.\n\nMolecular Characteristics of Klebsiella pneumoniae Isolates From Outpatients in Sentinel Hospitals, Beijing, China, 2010-2019.", "token_count": 161, "char_count": 601, "word_count": 76, "semantic_coherence": 1, "information_density": 0.8026, "quality_score": 0.9013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:42.871125", "source": { "split": "train_shard_00001", "doc_id": 3937 }, "chunk_id": "train_shard_00001_3937_1", "global_id": 11224 }, { "text": "

Introduction

Nasal carriage of coagulase-positive staphylococci (CoPS) in healthy dogs could indicate increased risks of colonization for in-contact people or vice versa. This study determined the nasal carriage rate of CoPS among healthy dogs and in-contact people, their genotypic characteristics and phylogenetic relatedness.

Methods

Nasal samples were collected from 27 households (34 dogs and 41 humans) in Spain. Staphylococci were identified by MALDI-TOF-MS, their antimicrobial resistance (AMR) genes and spa-types were tested by PCR/sequencing. The relatedness of CoPS from the same households was assessed by core genome single nucleotide polymorphisms (SNPs) analyses.

Results

Staphylococcus aureus carriage was found in 34.1% of humans (including one methicillin-resistant S. aureus MRSA-CC5-t2220-SCCmec type-IV2B) and 5.9% of dogs; Staphylococcus pseudintermedius in 2.4% of humans and 32.4% of dogs; while Staphylococcus coagulans was only detected in dogs (5.4%). Remarkably, one human co-carried S. aureus/S. pseudintermedius, while a dog co-carried the three CoPS species. Household density was significantly associated with S. pseudintermedius carriage in households with > than 1 dog and >than 1 human (OR = 18.10, 95% CI: 1.24-260.93, p = 0.034). Closely related (<15 SNPs) S. aureus or S", "token_count": 516, "char_count": 1411, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6592, "quality_score": 0.8296, "entities": { "genes": [ "CC5", "IV2B" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:43.540882", "source": { "split": "train_shard_00001", "doc_id": 3938 }, "chunk_id": "train_shard_00001_3938_0", "global_id": 11225 }, { "text": "pseudintermedius were found in humans or dogs in three households. About 56.3% S. aureus carriers (dog or human) harboured diverse within-host spa-types or AMR genotypes. Ten clonal complexes (CCs) were detected among the S. aureus, of which methicillin-susceptible S. aureus-CC398-IEC-type C (t1451 and t571) was the most frequent, but exclusive to humans. S. aureus and S. pseudintermedius isolates harboured resistance genes or mutations associated to 9 classes of antimicrobials including linezolid (G2261A & T1584A point mutations in 23S rDNA). The S. coagulans isolates were susceptible to all antimicrobials. Most of the S. pseudintermedius carried lukS/F-I, siet, and sient genes, and all S. aureus were negative for lukS/F-PV, tst-1, eta and etb genes.

Discussion

Clonally related human-to-human MSSA and dog-to-human MSSP were found. The detection of the MSSA-CC398 clade highlights the need for its continuous surveillance from One Health perspective.\n\nClonal relatedness of coagulase-positive staphylococci among healthy dogs and dog-owners in Spain. Detection of multidrug-resistant-MSSA-CC398 and novel linezolid-resistant-MRSA-CC5.", "token_count": 466, "char_count": 1255, "word_count": 155, "semantic_coherence": 1, "information_density": 0.671, "quality_score": 0.8355, "entities": { "genes": [ "CC5", "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:44.195628", "source": { "split": "train_shard_00001", "doc_id": 3938 }, "chunk_id": "train_shard_00001_3938_1", "global_id": 11226 }, { "text": "

Objectives

The emergence and dissemination of colistin-resistant Enterobacterales has become a major global public-health threat. Here we investigated the genomic and phylogenetic characteristics of a multidrug-resistant Klebsiella pneumoniae strain (KP4823) carrying the mcr-1 gene recovered from a urinary tract infection in China.

Methods

Antimicrobial susceptibility of K. pneumoniae KP4823 was determined by broth microdilution. Whole genomic DNA was extracted and sequenced using Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. Hybrid assembly with long and short reads was performed using Unicycler, and the genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The sequence type (ST), capsular type, and antimicrobial resistance and virulence genes were identified from the genome sequence. Core genome multilocus sequence typing (cgMLST) analysis was performed by BacWGSTdb 2.0 server.

Results

Klebsiella pneumoniae KP4823 was resistant to colistin, ceftazidime, cefepime, cefotaxime, fosfomycin and aztreonam. The complete genome sequence of KP4823 consists of five contigs comprising 5 445 519 bp, including one chromosome and four plasmids. The isolate was assigned to ST101 with capsular serotype KL106. Several antimicrobial resistance genes were identified, including the colistin resistance gene mcr-1, which was located on a 34 685-bp IncX4 plasmid. The closest relative of K. pneumoniae KP4823 was another ST101 isolate (08EU827) recovered from Sweden in 2008, which differed by 191 cgMLST loci.

Conclusion

Our study reports the genome sequence of a multidrug-resistant mcr-1-carrying K", "token_count": 520, "char_count": 1674, "word_count": 219, "semantic_coherence": 1, "information_density": 0.653, "quality_score": 0.8265, "entities": { "genes": [ "KP4823", "KL106", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:44.856357", "source": { "split": "train_shard_00001", "doc_id": 3939 }, "chunk_id": "train_shard_00001_3939_0", "global_id": 11227 }, { "text": "pneumoniae in China. These data may help to understand the antimicrobial resistance mechanisms, genomic features and transmission dynamics of colistin resistance in clinical settings.\n\nGenomic and phylogenetic analysis of a multidrug-resistant mcr-1-carrying Klebsiella pneumoniae recovered from a urinary tract infection in China.", "token_count": 81, "char_count": 331, "word_count": 42, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:45.230554", "source": { "split": "train_shard_00001", "doc_id": 3939 }, "chunk_id": "train_shard_00001_3939_1", "global_id": 11228 }, { "text": "The objective of this study was to elucidate the genetic and evolutionary relatedness of blaCMY-2- and blaSHV-12-carrying IncI1-Iγ plasmids. Phylogenomic analysis based on core genome alignments and gene presence/absence was performed for different IncI1-Iγ sequence types (STs). Most IncI1-Iγ/ST12 and IncI1-Iγ/ST231 plasmids had near-identical core genomes. The data suggest that widely occurring blaCMY-2-carrying IncI1-Iγ/ST12 plasmids originate from a common ancestor. In contrast, blaSHV-12 was inserted independently into different IncI1-Iγ/ST231-related plasmids.\n\nPhylogenomic Investigation of IncI1-Iγ Plasmids Harboring blaCMY-2 and blaSHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries.", "token_count": 306, "char_count": 828, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7386, "quality_score": 0.8693, "entities": { "genes": [ "ST12", "ST231" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:45.802162", "source": { "split": "train_shard_00001", "doc_id": 3940 }, "chunk_id": "train_shard_00001_3940_0", "global_id": 11229 }, { "text": "Whey is the major by-product of the dairy industry, produced in large quantities and usually disposed off causing major environmental pollution, due to its high organic load that makes treatment cost prohibitive. This paper comprises a contribution on the valorisation of this high polluting liquid waste of the dairy industry, based on research for the production of novel dairy starter cultures using whey as raw material. Starter cultures are used for cheese ripening in order to: (i) accelerate ripening, (ii) improve quality and (iii) increase shelf-life. The developed technology involves biomass production from whey followed by thermal drying of cultures. Specifically, Kluyveromyces marxianus, Lactobacillus bulgaricus and kefir yeasts were thermally dried, and their efficiency in lactose and milk whey fermentations was studied. The most suitable culture regarding its technological properties was kefir, which was used for cheese ripening in freeze-dried and thermally dried form. Besides the reduction of production cost, which is an essential requirement for the food industry, the use of thermally dried kefir displayed several other advantages such as acceleration of ripening, increase of shelf-life, and improvement of hard-type cheese quality.\n\nWhey valorisation: a complete and novel technology development for dairy industry starter culture production.", "token_count": 299, "char_count": 1373, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6447, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:46.372157", "source": { "split": "train_shard_00001", "doc_id": 3941 }, "chunk_id": "train_shard_00001_3941_0", "global_id": 11230 }, { "text": "Abstract

Background

Increasing antimicrobial resistance (R) among Escherichia coli (EC) isolates can be associated with the expansion of the pandemic sequence type (ST) 131 that harbors virulence factors and causes more severe infections when compared with other antimicrobial-R EC. We evaluated the core genome MLST (cgMLST) profiles and R genes using the bioinformatics tool 1928D to evaluate the epidemiology of a global ST131 EC collection and unrelated STs.

Methods

A total of 259 EC clinical isolates belonging to ST131 (n = 206), ST131-single loci variant (SLV; n = 25), and 28 non-ST131 isolates collected from 27 countries during 2016–2018 were selected. Whole-genome sequencing FASTQ files were uploaded to the 1928D pipeline to generate MLST, cgMLST and R gene prediction. cgMLST assignment was based on comparing >2,500 genes.

Results

Among 231 ST131 and SLV EC isolates, 7 clades were identified (3 major [178 isolates]; Table) applying cgMLST allele distance (ad) of ≤50 as a cutoff. A total of 21 isolates were not assigned to clades (>50 ad from ST131 and SLV). Based on >95% concordance, 11 alleles differentiated clades II and III from clade I, while 6 alleles separated clades I and III from clade II", "token_count": 403, "char_count": 1246, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7179, "quality_score": 0.859, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:47.000041", "source": { "split": "train_shard_00001", "doc_id": 3942 }, "chunk_id": "train_shard_00001_3942_0", "global_id": 11231 }, { "text": "Isolates in clades I to IV were ciprofloxacin R (MIC, ≥4 mg/L); clades I and III predominantly carried blaCTX-M-15 (39/43 and 61/66), blaOXA-1 (35/43 and 43/66), and aac(6’)-Ib-cr (39/43, 45/66) while clade II carried blaCTX-M-14-like and rarely aac(6’)Ib-cr (3/69). The most ad between the 7 ST131 clades was 216, while unrelated STs showed variable ad among isolates within that ST. Isolates bellowing to ST1193 were closely related genetically (ad of 30), but other STs had more variability among isolates (ST167, ad 552; ST38, ad 150; and ST69, ad 179).

Conclusion

1928D is a robust platform for epidemiological analysis of isolates, providing additional granularity when compared with MLST. Clades II and III were closely related, but carried different blaCTX-M genes, while clades I and III were not as closely related, but both carried blaCTX-M-15, blaOXA-1, and aac(6’)Ib-cr. These findings suggest that these clades might have acquired R genes at different points in their genetic evolution. A threshold of ≤50 (cgMLST distance) was useful for classifying isolates into clades.

Disclosures

All authors: No reported disclosures.\n\n239. Epidemiologic Analysis of a Worldwide Collection of Escherichia coli ST131 Using the 1928D Core Genome (cg) Multilocus Sequence Type (MLST) Reveals Country Specific and Globally Disseminated Clades", "token_count": 477, "char_count": 1358, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6915, "quality_score": 0.8458, "entities": { "genes": [ "ST167", "ST131", "ST1193", "ST69", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:47.645199", "source": { "split": "train_shard_00001", "doc_id": 3942 }, "chunk_id": "train_shard_00001_3942_1", "global_id": 11232 }, { "text": "Carbonyl reductase (CR) of a yeast strain, Kluyveromyces marxianus, and its isolation and purification method thereof is provided. The reduction reaction by the reductase obtained in the present invention is more stereospecific and requires less cost and time than the reduction reactions by the microorganisms or by the reducing enzymes obtained from a chemical synthesis.\n\nCarbonyl reductase of kluyveromyces marxianus and its isolation and purification method", "token_count": 112, "char_count": 462, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6212, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:48.030852", "source": { "split": "train_shard_00001", "doc_id": 3943 }, "chunk_id": "train_shard_00001_3943_0", "global_id": 11233 }, { "text": "The focus of the present investigation was on the Tanzanian fermented food togwa as a source for dietary iron and zinc, and the potential for mineral availability improvements using selected yeasts. To establish the content of target minerals and main inhibitor for intestinal uptake, iron and zinc as well as the mineral chelating phytic acid, (IP(6) or phytate) were determined in naturally fermented togwa. Yeasts were isolated from sorghum, maize and cassava based togwa, and identified by sequencing the D1/D2 region of the LSU rRNA gene. The isolated yeasts were subsequently screened for phytase activity. The total iron content in sorghum, maize and cassava based togwa were 41.5 (+/-7.2), 85.4 (+/-31.9) and 28.6 (+/-3.8) microg/g dw (dry weight) respectively. The zinc content was 12.3 (+/-3.1), 11.0 (+/-1.1) and 6.4 (+/-4.5) microg/g dw in sorghum, maize and cassava based togwa, and the phytate content in the three varieties were 2.6+/-1.2, 4.7+/-0.8 and 0.4+/-0.4 micromol/g dw respectively. The phytate levels in the sorghum and maize based togwa are expected to substantially reduce the availability of iron. The molar ratio phytate to iron for these two varieties were estimated to be 3.5:1 and 3.1:1 respectively. In general, a phytate to iron molar ratio below 1 is needed to increase the availability of iron. Among 26 isolates, 9 different species could be distinguished: Issatchenkia orientalis, Pichia anomala, Pichia norvegensis, Pichia burtonii, Pichia guilliermondii, Kluyveromyces marxianus, Saccharomyces cerevisiae, Hanseniaspora guilliermondii and Candida glabrata", "token_count": 512, "char_count": 1595, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5756, "quality_score": 0.7878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:48.667386", "source": { "split": "train_shard_00001", "doc_id": 3944 }, "chunk_id": "train_shard_00001_3944_0", "global_id": 11234 }, { "text": "The strains were screened for phytase activity in YPD supplemented with 0.5 mM IP(6). Of 26 screened strains, the phytase activity was most prominent in strains of I. orientalis and H. guilliermondii. The strains and data constitute a basis for further improvements of iron and zinc bioavailability in togwa.\n\nBiodiversity and phytase capacity of yeasts isolated from Tanzanian togwa.", "token_count": 110, "char_count": 384, "word_count": 59, "semantic_coherence": 1, "information_density": 0.6949, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:49.054506", "source": { "split": "train_shard_00001", "doc_id": 3944 }, "chunk_id": "train_shard_00001_3944_1", "global_id": 11235 }, { "text": "The effects of pH, concentration of NaCl, concentration of sucrose and concentrations of sorbic and benzoic acids on growth were examined for 30 strains of food spoilage yeasts, representing Debaryomyces hansenii, Yarrowia lipolytica, Kloeckera apiculata, Zygosaccharomyces bailii, Zygosaccharomyces rouxii, Kluyveromyces marxianus, Pichia membranaefaciens, Pichia anomala and Saccharomyces cerevisiae. Zygosaccharomyces bailii did not grow at pH 7.0 and Z. rouxii, Kl. apiculata and P. membranaefaciens did not grow at pH 8.0. Only Kl. apiculata grew at pH 1.5-2.0. The remaining species grew at pH 2.5-8.0. None of the species grew at 20% NaCl but strains of D. hansenii, Z. rouxii and P. anomala grew at 15% NaCl. S. cerevisiae and K. marxianus were the least salt tolerant, showing no growth at 7.5% NaCl and 10% NaCl, respectively. Medium pH influenced growth in the presence of NaCl. For Y. lipolytica, D. hansenii and S. cerevisiae, greatest tolerance of NaCl occurred at pH 5.0-7.0, but for Kl. apiculata, D. membranaefaciens and Z. bailii best tolerance occurred at pH 3.0. K. apiculata grew in the presence of 12.5% NaCl at pH 2.0. All yeasts grew at 50% sucrose, with Z. rouxii, Z. bailii and P. anomala and D. hansenii growing at 60-70% sucrose. Medium pH in the range 2.0-7.0 had little effect on ability to grow in the presence of high sucrose concentrations. Z. bailii and Y. lipolytica were the species most tolerant of sorbate and benzoate preservatives (750-1200 mg l-1) at pH 5.0.", "token_count": 534, "char_count": 1499, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:44:49.694135", "source": { "split": "train_shard_00001", "doc_id": 3945 }, "chunk_id": "train_shard_00001_3945_0", "global_id": 11236 }, { "text": "The effect of pH, sodium chloride, sucrose, sorbate and benzoate on the growth of food spoilage yeasts", "token_count": 32, "char_count": 102, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:50.056664", "source": { "split": "train_shard_00001", "doc_id": 3945 }, "chunk_id": "train_shard_00001_3945_1", "global_id": 11237 }, { "text": "Chryseobacterium spp. are Gram-negative rods found ubiquitously in the environment, with certain species being reported as having unusual degrading properties. Polyvinyl alcohol (PVA) is used widely in industry but causes serious global environmental pollution. Here, we report the complete genome sequence of a novel bacterium, AC3, that efficiently degrades PVA. As the representative genome of Chryseobacterium nepalense, key genomic characteristics (e.g., mobile genetic elements, horizontal genes, genome-scale metabolic network, secondary metabolite biosynthesis gene clusters, and carbohydrate-active enzymes) were comprehensively investigated to reveal the potential genetic features of this species. Core genome phylogenetic analysis in combination with average nucleotide identity, average amino acid identity, and in silico DNA-DNA hybridization values provided an accurate taxonomic position of C. nepalense in the genus Chryseobacterium. Comparative genomic analysis of AC3 with closely related species suggested evolutionary dynamics characterized by a species-specific genetic repertoire, dramatic rearrangements, and evolutionary constraints driven by selective pressure, which facilitated the speciation and adaptative evolution of C. nepalense. Biogeographic characterization indicated that this species is ubiquitously distributed not only in soil habitats but also in a variety of other source niches. Bioinformatic analysis revealed the potential genetic basis of PVA degradation in AC3, which included six putative genes associated with the synthesis of PVA dehydrogenase, cytochrome c, oxidized PVA hydrolase, and secondary alcohol dehydrogenase. Our study reports the first complete genome of C. nepalense with PVA-degrading properties, providing comprehensive insights into the genomic characteristics of this species and increasing our understanding of the microbial degradation of PVA. IMPORTANCE Although PVA is a biodegradable polymer, the widespread use of PVA in global industrialization has resulted in serious environmental problems", "token_count": 499, "char_count": 2121, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6679, "quality_score": 0.834, "entities": { "genes": [ "AC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:50.709190", "source": { "split": "train_shard_00001", "doc_id": 3946 }, "chunk_id": "train_shard_00001_3946_0", "global_id": 11238 }, { "text": "To date, knowledge of effective and applicable PVA-degrading bacteria is limited, and thus, the discovery of novel PVA biodegraders is pertinent. Here, we isolated a novel bacterial strain, AC3, which efficiently degraded PVA. The complete genome of AC3 was sequenced as the first genome sequence of the species C. nepalense. Comparative genomic analysis was performed to comprehensively investigate the phylogenetic relationships, genome-scale metabolic network, key genomic characteristics associated with genomic evolution, evolutionary dynamics between AC3 and its close relatives, and biogeographic characterization of C. nepalense, particularly regarding the potential genetic basis of PVA degradation. These findings could advance our understanding of the genomic characteristics of C. nepalense and PVA bioremediation.\n\nInsights into Evolutionary, Genomic, and Biogeographic Characterizations of Chryseobacterium nepalense Represented by a Polyvinyl Alcohol-Degrading Bacterium, AC3.", "token_count": 245, "char_count": 1012, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7244, "quality_score": 0.8622, "entities": { "genes": [ "AC3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:51.194770", "source": { "split": "train_shard_00001", "doc_id": 3946 }, "chunk_id": "train_shard_00001_3946_1", "global_id": 11239 }, { "text": "Huntington's disease (HD) is a neurodegenerative disorder caused by a trinucleotide expansion in the HTT gene, which is expressed throughout the brain and body, including the gut epithelium and enteric nervous system. Afflicted individuals suffer from progressive impairments in motor, psychiatric, and cognitive faculties, as well as peripheral deficits, including the alteration of the gut microbiome. However, studies characterizing the gut microbiome in HD have focused entirely on the bacterial component, while the fungal community (mycobiome) has been overlooked. The gut mycobiome has gained recognition for its role in host homeostasis and maintenance of the gut epithelial barrier. We aimed to characterize the gut mycobiome profile in HD using fecal samples collected from the R6/1 transgenic mouse model (and wild-type littermate controls) from 4 to 12 weeks of age, corresponding to presymptomatic through to early disease stages. Shotgun sequencing was performed on fecal DNA samples, followed by metagenomic analyses. The HD gut mycobiome beta diversity was significantly different from that of wild-type littermates at 12 weeks of age, while no genotype differences were observed at the earlier time points. Similarly, greater alpha diversity was observed in the HD mice by 12 weeks of age. Key taxa, including Malassezia restricta, Yarrowia lipolytica, and Aspergillus species, were identified as having a negative association with HD. Furthermore, integration of the bacterial and fungal data sets at 12 weeks of age identified negative correlations between the HD-associated fungal species and Lactobacillus reuteri. These findings provide new insights into gut microbiome alterations in HD and may help identify novel therapeutic targets. IMPORTANCE Huntington's disease (HD) is a fatal neurodegenerative disorder affecting both the mind and body. We have recently discovered that gut bacteria are disrupted in HD. The present study provides the first evidence of an altered gut fungal community (mycobiome) in HD", "token_count": 495, "char_count": 2040, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:51.850415", "source": { "split": "train_shard_00001", "doc_id": 3947 }, "chunk_id": "train_shard_00001_3947_0", "global_id": 11240 }, { "text": "The genomes of many thousands of gut microbes were sequenced and used to assess \"metagenomics\" in particular the different types of fungal species in the HD versus control gut, in a mouse model. At an early disease stage, before the onset of symptoms, the overall gut mycobiome structure (array of fungi) in HD mice was distinct from that of their wild-type littermates. Alterations of multiple key fungi species were identified as being associated with the onset of disease symptoms, some of which showed strong correlations with the gut bacterial community. This study highlights the potential role of gut fungi in HD and may facilitate the development of novel therapeutic approaches.\n\nAlterations in the Gut Fungal Community in a Mouse Model of Huntington's Disease.", "token_count": 173, "char_count": 770, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:52.301362", "source": { "split": "train_shard_00001", "doc_id": 3947 }, "chunk_id": "train_shard_00001_3947_1", "global_id": 11241 }, { "text": "Non-typhoidal Salmonella (NTS) is a common cause for self-limiting gastroenteritis, representing a public health concern globally. NTS is one of the leading causes of foodborne illnesses in China; however, the invasive infection caused by NTS is largely underappreciated. Here, we reported an NTS invasive infection caused by an infrequently reported serovar Telelkebir (13,23:d:e,n,z15) strain FJ001 in China, which carries antimicrobial-resistant genes [fosA7 and aac(6')-Iaa] and typhoid-toxin genes (cdtB, pltA, and pltB). By conducting the whole genomic sequencing, we also investigated the relatedness of this strain with an additional 120 global contextual Salmonella enterica serovar Telelkebir (S. Telelkebir) isolates, and assessed the antimicrobial-resistant determinants and key virulence factors using the available genomic dataset. Notably, all 121 (100%) of the S. Telelkebir strains possessed the typhoid toxin genes cdtB, pltA, and pltB, and 58.67% (71/121) of S. Telelkebir harbored antimicrobial-resistant gene fosaA7. The study by core genome multilocus sequence typing (cgMLST) and core single-nucleotide polymorphism (SNP)-based phylogenomic analysis demonstrated that the S. Telelkebir isolates from different sources and locations clustered together. This suggests that regular international travels might increase the likelihood of rapid and extensive transmissions of potentially pathogenic bacteria", "token_count": 499, "char_count": 1530, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6968, "quality_score": 0.8484, "entities": { "genes": [ "FJ001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:52.948346", "source": { "split": "train_shard_00001", "doc_id": 3948 }, "chunk_id": "train_shard_00001_3948_0", "global_id": 11242 }, { "text": "For the first time, our study revealed the antimicrobial resistance, virulence patterns, and genetic diversity of the serovar S. Telelkebir isolate in humans and similar isolates over the world. The present study also suggests that genomic investigation can facilitate surveillance and could offer added knowledge of a previously unknown threat with the unique combination of virulent and antimicrobial-resistant determinants.\n\nGlobal Genomic Characterization of Salmonella enterica Serovar Telelkebir.", "token_count": 122, "char_count": 516, "word_count": 67, "semantic_coherence": 1, "information_density": 0.791, "quality_score": 0.8955, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:53.341236", "source": { "split": "train_shard_00001", "doc_id": 3948 }, "chunk_id": "train_shard_00001_3948_1", "global_id": 11243 }, { "text": "Food contamination by staphylococcal enterotoxins (SEs) is responsible for many food poisoning outbreaks (FPOs) each year, and they represent the third leading cause of FPOs in Europe. SEs constitute a protein family with 27 proteins. However, enzyme immunoassays can only detect directly in food the five classical SEs (SEA-SEE). Thus, molecular characterization methods of strains found in food are now used for FPO investigations. Here, we describe the development and implementation of a genomic analysis tool called NAuRA (Nice automatic Research of alleles) that can detect the presence of 27 SEs genes in just one analysis- and create a database of allelic data and protein variants for harmonizing analyses. This tool uses genome assembly data and the 27 protein sequences of SEs. To include the different divergence levels between SE-coding genes, parameters of coverage and identity were generated from 10,000 simulations and a dataset of 244 assembled genomes from strains responsible for outbreaks in Europe as well as the RefSeq reference database. Based on phylogenetic inference performed using maximum-likelihood on the core genomes of the strains in this collection, we demonstrated that strains responsible for FPOs are distributed throughout the phylogenetic tree. Moreover, 71 toxin profiles were obtained using the NAuRA pipeline and these profiles do not follow the evolutionary history of strains. This study presents a pioneering method to investigate strains isolated from food at the genomic level and to analyze the diversity of all 27 SE-coding genes together.\n\nNAuRA: Genomic Tool to Identify Staphylococcal Enterotoxins in Staphylococcus aureus Strains Responsible for FoodBorne Outbreaks.", "token_count": 416, "char_count": 1726, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6196, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:53.965299", "source": { "split": "train_shard_00001", "doc_id": 3949 }, "chunk_id": "train_shard_00001_3949_0", "global_id": 11244 }, { "text": "Most urinary tract infections (UTIs) are caused by uropathogenic Escherichia coli (UPEC), which depend on an extracellular organelle (Type 1 pili) for adherence to bladder cells during infection. Type 1 pilus expression is partially regulated by inversion of a piece of DNA referred to as fimS, which contains the promoter for the fim operon encoding Type 1 pili. fimS inversion is regulated by up to five recombinases collectively known as Fim recombinases. These Fim recombinases are currently known to regulate two other switches: the ipuS and hyxS switches. A long-standing question has been whether the Fim recombinases regulate the inversion of other switches, perhaps to coordinate expression for adhesion or virulence. We answered this question using whole genome sequencing with a newly developed algorithm (Structural Variation detection using Relative Entropy, SVRE) for calling structural variations using paired-end short read sequencing. SVRE identified all of the previously known switches, refining the specificity of which recombinases act at which switches. Strikingly, we found no new inversions that were mediated by the Fim recombinases. We conclude that the Fim recombinases are each highly specific for a small number of switches. We hypothesize that the unlinked Fim recombinases have been recruited to regulate fimS, and fimS only, as a secondary locus; this further implies that regulation of Type 1 pilus expression (and its role in gastrointestinal and/or genitourinary colonization) is important enough, on its own, to influence the evolution and maintenance of multiple additional genes within the accessory genome of E. coli.\n\nComprehensive Identification of Fim-Mediated Inversions in Uropathogenic Escherichia coli with Structural Variation Detection Using Relative Entropy", "token_count": 454, "char_count": 1806, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:54.618632", "source": { "split": "train_shard_00001", "doc_id": 3950 }, "chunk_id": "train_shard_00001_3950_0", "global_id": 11245 }, { "text": "The global prevalence of infections caused by extended-spectrum β-lactamase-producing Enterobacterales (ESBL-E) is increasing, and for Escherichia coli, observations indicate that this is partly driven by community-onset cases. The ESBL-E population structure in the community is scarcely described, and data on risk factors for carriage are conflicting. Here, we report the prevalence and population structure of fecal ESBL-producing E. coli and Klebsiella pneumoniae (ESBL-Ec/Kp) in a general adult population, examine risk factors, and compare carriage isolates with contemporary clinical isolates. Fecal samples obtained from 4,999 participants (54% women) ≥40 years in the seventh survey of the population-based Tromsø Study, Norway (2015, 2016), were screened for ESBL-Ec/Kp. In addition, we included 118 ESBL-Ec clinical isolates from the Norwegian surveillance program in 2014. All isolates were whole-genome sequenced. Risk factors associated with carriage were analyzed using multivariable logistic regression. ESBL-Ec gastrointestinal carriage prevalence was 3.3% [95% confidence interval (CI) 2.8%-3.9%, no sex difference] and 0.08% (0.02%-0.20%) for ESBL-Kp. For ESBL-Ec, travel to Asia was the only independent risk factor (adjusted odds ratio 3.46, 95% CI 2.18-5.49). E. coli ST131 was most prevalent in both collections. However, the ST131 proportion was significantly lower in carriage (24%) versus clinical isolates (58%, P < 0.001)", "token_count": 464, "char_count": 1485, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7085, "quality_score": 0.8543, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:55.730520", "source": { "split": "train_shard_00001", "doc_id": 3951 }, "chunk_id": "train_shard_00001_3951_0", "global_id": 11246 }, { "text": "Carriage isolates were genetically more diverse with a higher proportion of phylogroup A (26%) than clinical isolates (5%, P < 0.001), indicating that ESBL gene acquisition occurs in a variety of E. coli lineages colonizing the gut. STs commonly related to extraintestinal infections were more frequent in clinical isolates also carrying a higher prevalence of antimicrobial resistance, which could indicate clone-associated pathogenicity.IMPORTANCEESBL-Ec and ESBL-Kp are major pathogens in the global burden of antimicrobial resistance. However, there is a gap in knowledge concerning the bacterial population structure of human ESBL-Ec/Kp carriage isolates in the community. We have examined ESBL-Ec/Kp isolates from a population-based study and compared these to contemporary clinical isolates. The large genetic diversity of carriage isolates indicates frequent ESBL gene acquisition, while those causing invasive infections are more clone dependent and associated with a higher prevalence of antibiotic resistance. The knowledge of factors associated with ESBL carriage helps to identify patients at risk to combat the spread of resistant bacteria within the healthcare system. Particularly, previous travel to Asia stands out as a major risk factor for carriage and should be considered in selecting empirical antibiotic treatment in critically ill patients.\n\nCommunity carriage of ESBL-producing Escherichia coli and Klebsiella pneumoniae: a cross-sectional study of risk factors and comparative genomics of carriage and clinical isolates.", "token_count": 369, "char_count": 1575, "word_count": 215, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:56.315760", "source": { "split": "train_shard_00001", "doc_id": 3951 }, "chunk_id": "train_shard_00001_3951_1", "global_id": 11247 }, { "text": "

Background

E. faecium is a gut commensal of humans and animals. In addition, it has recently emerged as an important nosocomial pathogen through the acquisition of genetic elements that confer resistance to antibiotics and virulence. We performed a whole-genome sequencing based study on 96 multidrug-resistant E. faecium strains that asymptomatically colonized five patients with the aim to describe the genome dynamics of this species.

Results

The patients were hospitalized on multiple occasions and isolates were collected over periods ranging from 15 months to 6.5 years. Ninety-five of the sequenced isolates belonged to E. faecium clade A1, which was previously determined to be responsible for the vast majority of clinical infections. The clade A1 strains clustered into six clonal groups of highly similar isolates, three of which entirely consisted of isolates from a single patient. We also found evidence of concurrent colonization of patients by multiple distinct lineages and transfer of strains between patients during hospitalisation. We estimated the evolutionary rate of two clonal groups that colonized a single patient at 12.6 and 25.2 single nucleotide polymorphisms (SNPs)/genome/year. A detailed analysis of the accessory genome of one of the clonal groups revealed considerable variation due to gene gain and loss events, including the chromosomal acquisition of a 37 kbp prophage and the loss of an element containing carbohydrate metabolism-related genes. We determined the presence and location of twelve different Insertion Sequence (IS) elements, with IS Efa5 showing a unique pattern of location in 24 of the 25 isolates, suggesting widespread IS Efa5 excision and insertion into the genome during gut colonization.

Conclusions

Our findings show that the E. faecium genome is highly dynamic during asymptomatic colonization of the patient gut. We observe considerable genomic flexibility due to frequent horizontal gene transfer and recombination, which can contribute to the generation of genetic diversity within the species and, ultimately, can contribute to its success as a nosocomial pathogen.", "token_count": 496, "char_count": 2157, "word_count": 315, "semantic_coherence": 1, "information_density": 0.5905, "quality_score": 0.7952, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:56.967342", "source": { "split": "train_shard_00001", "doc_id": 3952 }, "chunk_id": "train_shard_00001_3952_0", "global_id": 11248 }, { "text": "Enterococcus faeciumgenome dynamics during long-term asymptomatic patient gut colonization", "token_count": 27, "char_count": 97, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:57.325778", "source": { "split": "train_shard_00001", "doc_id": 3952 }, "chunk_id": "train_shard_00001_3952_1", "global_id": 11249 }, { "text": "The invention is a gene coding for a quinone oxidoreductase from Kluyveromyces marxianus and a protein having an amino acid sequence expressed therefrom, which can be advantageously used in a reduction reaction of a quinone compound and synthesis of intermediates for a biologically active compound.\n\nGene coding for quinone oxidoreductase of kluyveromyces marxianus and protein expressed therefrom", "token_count": 98, "char_count": 398, "word_count": 57, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:57.705706", "source": { "split": "train_shard_00001", "doc_id": 3953 }, "chunk_id": "train_shard_00001_3953_0", "global_id": 11250 }, { "text": "The environmental bacterium Pseudomonas aeruginosa, particularly multidrug-resistant clones, is often associated with nosocomial infections and outbreaks. Today, core genome multilocus sequence typing (cgMLST) is frequently applied to delineate sporadic cases from nosocomial transmissions. However, until recently, no cgMLST scheme for a standardized typing of P. aeruginosa was available. To establish a novel cgMLST scheme for P. aeruginosa, we initially determined the breadth of the P. aeruginosa population based on MLST data with a Bayesian approach (BAPS). Using genomic data of representative isolates for the whole population and all 12 serogroups, we extracted target genes and further refined them using a random data set of 1,000 P. aeruginosa genomes. Subsequently, we investigated reproducibility and discriminatory ability with repeatedly sequenced isolates and isolates from well-defined outbreak scenarios, respectively, and compared clustering applying two recently published cgMLST schemes. BAPS generated seven P. aeruginosa groups. To cover these and all serogroups, 15 reference strains were used to determine genes common in all strains. After refinement with the data set of 1,000 genomes, the cgMLST scheme consisted of 3,867 target genes, which are representative of the P. aeruginosa population and highly reproducible using biological replicates. We finally evaluated the scheme by reanalyzing two published outbreaks where the authors used single-nucleotide polymorphism (SNP) typing. In both cases, cgMLST was concordant with the previous SNP results and the results of the two other cgMLST schemes. In conclusion, the highly reproducible novel P. aeruginosa cgMLST scheme facilitates outbreak investigations due to the publicly available cgMLST nomenclature.", "token_count": 482, "char_count": 1846, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5927, "quality_score": 0.7964, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:58.353508", "source": { "split": "train_shard_00001", "doc_id": 3954 }, "chunk_id": "train_shard_00001_3954_0", "global_id": 11251 }, { "text": "Establishment and Evaluation of a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Pseudomonas aeruginosa.", "token_count": 42, "char_count": 145, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:58.716766", "source": { "split": "train_shard_00001", "doc_id": 3954 }, "chunk_id": "train_shard_00001_3954_1", "global_id": 11252 }, { "text": "The invention is a gene coding for a quinone oxidoreductase from Kluyveromyces marxianus and a protein having an amino acid sequence expressed therefrom, which can be advantageously used in a reduction reaction of a quinone compound and synthesis of intermediates for a biologically active compound.\n\nGene coding for quinone oxidoreductase of kluyveromyces marxianus and protein expressed therefrom", "token_count": 102, "char_count": 402, "word_count": 57, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:59.095804", "source": { "split": "train_shard_00001", "doc_id": 3955 }, "chunk_id": "train_shard_00001_3955_0", "global_id": 11253 }, { "text": "A Gram-stain-positive, strictly aerobic, motile, endospore-forming, milk-white, indole acetic acid-producing, rod-shaped bacterial strain, designated as HU2P27T, was isolated from a shoot of Kalidium cuspidatum collected in Tumd Right Banner, Inner Mongolia, PR China. Strain grew at 10-40 °C (optimum, 30 °C), at pH 6.0-9.0 (optimum, pH 7.0) and with 0-14.0 % NaCl (optimum, 5.0-8.0 %). The strain tested positive for oxidase, catalase and nitrate reductase. The phylogenetic trees based on the 16S rRNA gene sequence and the core genome both showed that strain HU2P27T clustered with Aquibacillus koreensis BH30097T, sharing 97.7 % and <97.0 % of 16S rRNA gene similarity with A. koreensis BH30097T and any other type strain. Strain HU2P27T contained MK-7 as the major respiratory quinone. Its major fatty acids were anteiso-C15 : 0 and iso-C15 : 0, and the major polar lipids were phosphatidylglycerol, diphosphatidylglycerol and four unidentified phospholipids. The genomic DNA G+C content was 36.0 mol%. The average nucleotide identity, amino acid identity and digital DNA-DNA hybridization values of strain HU2P27T with A", "token_count": 486, "char_count": 1239, "word_count": 167, "semantic_coherence": 1, "information_density": 0.7425, "quality_score": 0.8713, "entities": { "genes": [ "BH30097" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:44:59.752192", "source": { "split": "train_shard_00001", "doc_id": 3956 }, "chunk_id": "train_shard_00001_3956_0", "global_id": 11254 }, { "text": "koreensis BH30097T were 71.7, 69.2 and 19.4%, respectively. The phylogenetic, physiological and phenotypic results allowed the discrimination of strain HU2P27T from its phylogenetic relatives. The name Aquibacillus kalidii sp. nov. is therefore proposed. The type strain is strain HU2P27T (=CGMCC 1.18646T=KCTC 43248T). Based on the results of 16S rRNA gene and genome analyses, we propose the reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.\n\nAquibacillus kalidii sp. nov., an indole acetic acid-producing endophyte from a shoot of Kalidium cuspidatum, and reclassification of Virgibacillus campisalis Lee et al. 2012 as a later heterotypic synonym of Virgibacillus alimentarius Kim et al. 2011.", "token_count": 390, "char_count": 922, "word_count": 112, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [ "BH30097" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:00.369386", "source": { "split": "train_shard_00001", "doc_id": 3956 }, "chunk_id": "train_shard_00001_3956_1", "global_id": 11255 }, { "text": "It includes the stages of grinding the lignocellulosic biomass to a size of 15-30 mm, subjecting the product obtained to steam explosion pre-treatment at a temperature of 190-230 DEG C. for between 1 and 10 minutes in a reactor (2), collecting the pre-treated material in a cyclone (3) and separating the liquid and solid fractions by filtration in a filter press (9), introducing the solid fraction in a fermentation deposit (10), adding a cellulase at a concentration of 15 UFP per gram of cellulose and 12.6 International Units of beta-glucosidase enzyme dissolved in citrate buffer pH 4.8, inoculating the fermentation deposit (10) with a culture of the heat-tolerant bacteria Kluyveromyces marxianus CECT 10875, obtained by chemical mutagenesis from strain DER-26 of Kluyveromyces marxianus and shaking the mixture for 72 hours at 42 DEG C.\n\nProcedure for the production of ethanol from lignocellulosic biomass using a new heat-tolerant yeast", "token_count": 288, "char_count": 949, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:00.926139", "source": { "split": "train_shard_00001", "doc_id": 3957 }, "chunk_id": "train_shard_00001_3957_0", "global_id": 11256 }, { "text": "

Background

Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely-related genomes among a background of thousands of other genomes is challenging.

Methods

We describe a refinement to core-genome multi-locus sequence typing (cgMLST) where alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralised database of sequentially-numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to mapping-based approaches in Clostridium difficile using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals.

Results

Hash-cgMLST provided the same results as standard cgMLST with minimal performance penalty. Comparing 272 pairs of replicate sequences, using reference-based mapping there were 0, 1 or 2 SNPs between 262(96%), 5(2%) and 1(<1%) pairs respectively. Using hash-cgMLST or standard cgMLST, 197(72%) replicate pairs had zero gene differences, 37(14%), 8(3%) and 30(11%) pairs had 1, 2 and >2 differences respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies. Considering 413 pairs of infections within ≤2 SNPS, i.e. consistent with recent transmission, 266(64%) had ≤2 gene differences and 50(12%) ≥5 differences. Comparing a genome to 100,000 others took <1 minute using hash-cgMLST.

Conclusion

Hash-cgMLST is an effective surveillance tool that can rapidly identify clusters of related genomes. However, cgMLST/hash-cgMLST generates potentially more false variants than mapping-based analysis. Refined mapping-based variant calling is likely required to precisely define close genetic relationships.", "token_count": 511, "char_count": 1909, "word_count": 250, "semantic_coherence": 1, "information_density": 0.712, "quality_score": 0.856, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:01.588204", "source": { "split": "train_shard_00001", "doc_id": 3958 }, "chunk_id": "train_shard_00001_3958_0", "global_id": 11257 }, { "text": "Hash-based core genome multi-locus sequencing typing for Clostridium difficile", "token_count": 27, "char_count": 85, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:01.952243", "source": { "split": "train_shard_00001", "doc_id": 3958 }, "chunk_id": "train_shard_00001_3958_1", "global_id": 11258 }, { "text": "Investigating fitness interactions in natural populations remains a considerable challenge. We take advantage of the unique population structure of Vibrio parahaemolyticus , a bacterial pathogen of humans and shrimp, to perform a genome-wide screen for coadapted genetic elements. We identified 90 interaction groups involving 1,560 coding genes. 82 of these interaction groups are between accessory genes, many of which have functions related to carbohydrate transport and metabolism. Only 8 interaction groups involve both core and accessory genomes. The largest includes 1,540 SNPs in 82 genes and 338 accessory genome elements, many involved in lateral flagella and cell wall biogenesis. The interactions have a complex hierarchical structure encoding at least four distinct ecological strategies. Preliminary experiments imply that the strategies influence biofilm formation and bacterial growth rate in vitro. One strategy involves a divergent profile in multiple genome regions, implying that strains have irreversibly specialized, while the others involve fewer genes and are more plastic. Our results imply that most genetic alliances are ephemeral but that increasingly complex strategies can evolve and eventually cause speciation.\n\nThe landscape of coadaptation in Vibrio parahaemolyticus", "token_count": 288, "char_count": 1307, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7072, "quality_score": 0.8536, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:02.517562", "source": { "split": "train_shard_00001", "doc_id": 3959 }, "chunk_id": "train_shard_00001_3959_0", "global_id": 11259 }, { "text": "

Background

For decades there has been increasing interest in understanding the relationships between microbial communities and ecosystem functions. Current DNA sequencing technologies allows for the exploration of microbial communities in two principle ways: targeted rRNA gene surveys and shotgun metagenomics. For large study designs, it is often still prohibitively expensive to sequence metagenomes at both the breadth and depth necessary to statistically capture the true functional diversity of a community. Although rRNA gene surveys provide no direct evidence of function, they do provide a reasonable estimation of microbial diversity, while being a very cost-effective way to screen samples of interest for later shotgun metagenomic analyses. However, there is a great deal of 16S rRNA gene survey data currently available from diverse environments, and thus a need for tools to infer functional composition of environmental samples based on 16S rRNA gene survey data.

Results

We present a computational method called pangenome-based functional profiles (PanFP), which infers functional profiles of microbial communities from 16S rRNA gene survey data for Bacteria and Archaea. PanFP is based on pangenome reconstruction of a 16S rRNA gene operational taxonomic unit (OTU) from known genes and genomes pooled from the OTU's taxonomic lineage. From this lineage, we derive an OTU functional profile by weighting a pangenome's functional profile with the OTUs abundance observed in a given sample. We validated our method by comparing PanFP to the functional profiles obtained from the direct shotgun metagenomic measurement of 65 diverse communities via Spearman correlation coefficients. These correlations improved with increasing sequencing depth, within the range of 0.8-0.9 for the most deeply sequenced Human Microbiome Project mock community samples. PanFP is very similar in performance to another recently released tool, PICRUSt, for almost all of survey data analysed here", "token_count": 440, "char_count": 2006, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:03.148001", "source": { "split": "train_shard_00001", "doc_id": 3960 }, "chunk_id": "train_shard_00001_3960_0", "global_id": 11260 }, { "text": "But, our method is unique in that any OTU building method can be used, as opposed to being limited to closed-reference OTU picking strategies against specific reference sequence databases.

Conclusions

We developed an automated computational method, which derives an inferred functional profile based on the 16S rRNA gene surveys of microbial communities. The inferred functional profile provides a cost effective way to study complex ecosystems through predicted comparative functional metagenomes and metadata analysis. All PanFP source code and additional documentation are freely available online at GitHub ( https://github.com/srjun/PanFP ).\n\nPanFP: pangenome-based functional profiles for microbial communities.", "token_count": 157, "char_count": 723, "word_count": 94, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:03.585200", "source": { "split": "train_shard_00001", "doc_id": 3960 }, "chunk_id": "train_shard_00001_3960_1", "global_id": 11261 }, { "text": "Colistin is an important antimicrobial agent in the treatment of infections caused by multidrug resistant (MDR) Gram-negative bacteria. The horizontal transfer of mobile colistin resistance gene (mcr) poses a major threat to the public health worldwide. In this study, a total of thirteen mcr-carrying Escherichia coli (MCREC) strains were recovered from a tertiary hospital in Zhejiang, China, between 2016 and 2019. The minimum inhibitory concentration (MIC) of antimicrobial agents, epidemiological characteristics, and transmission dynamics of mcr-carrying isolates were analyzed using antimicrobial susceptibility testing, whole-genome sequencing, S1 nuclease pulsed-field gel electrophoresis (S1-PFGE), and southern blotting analysis. All strains were discovered to be resistant to colistin, and the majority displayed MDR phenotype. However, none of the 13 MCREC strains were resistant to carbapenems. The 13 MCREC isolates were divided into 10 different STs, including ST744, ST156, ST453, ST410, ST57, ST131, ST7034, ST2599, ST457, and ST13239, in which ST13239 was discovered for the first time. Based on core genome single nucleotide polymorphism (cgSNP) analysis, no clear epidemiological link was discovered in these strains with the exception of EC2118 and EC3807, which differ by just one SNP. A total of 35 antimicrobial resistance genes which can be divided into 14 classes were identified from the 13 MCREC isolates. According to S1-PFGE and southern blotting analyses, all 13 MCREC strains had plasmid-mediated mcr-1, and nine of them carried conjugative plasmids. In conclusion, our study revealed the emergence and dissemination of colistin-resistant E", "token_count": 519, "char_count": 1711, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6709, "quality_score": 0.8354, "entities": { "genes": [ "ST410", "ST131", "ST2599", "ST13239", "EC2118", "ST57", "ST7034", "ST156", "EC3807", "ST744" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:04.222250", "source": { "split": "train_shard_00001", "doc_id": 3961 }, "chunk_id": "train_shard_00001_3961_0", "global_id": 11262 }, { "text": "coli isolates carrying mcr-1 in a Chinese hospital, which poses a potential risk to anti-infective therapy. More efforts should be taken to monitor the prevalence of mcr-1-carrying bacteria in China.\n\nGenomic Insights into the Colistin Resistant mcr-Carrying Escherichia coli Strains in a Tertiary Hospital in China.", "token_count": 114, "char_count": 348, "word_count": 46, "semantic_coherence": 1, "information_density": 0.8043, "quality_score": 0.9022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:04.610815", "source": { "split": "train_shard_00001", "doc_id": 3961 }, "chunk_id": "train_shard_00001_3961_1", "global_id": 11263 }, { "text": "A compound represented by a genera formula (Ia) or (Ib) and a stereo-selective preparation method thereof using a carbonyl reductase which is separated from Kluyveromyces marxianus. The compound can be prepared by reduction of substituted beta-keto ester and can be used as an intermediate in preparing beta-lactam group antibiotics.\n\nReduction of carbonyl compounds using the carbonyl reductase of kluyveromyces marxianus", "token_count": 118, "char_count": 427, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:04.989023", "source": { "split": "train_shard_00001", "doc_id": 3962 }, "chunk_id": "train_shard_00001_3962_0", "global_id": 11264 }, { "text": "

Background

The genus Neisseria contains two important yet very different pathogens, N. meningitidis and N. gonorrhoeae, in addition to non-pathogenic species, of which N. lactamica is the best characterized. Genomic comparisons of these three bacteria will provide insights into the mechanisms and evolution of pathogenesis in this group of organisms, which are applicable to understanding these processes more generally.

Results

Non-pathogenic N. lactamica exhibits very similar population structure and levels of diversity to the meningococcus, whilst gonococci are essentially recent descendents of a single clone. All three species share a common core gene set estimated to comprise around 1190 CDSs, corresponding to about 60% of the genome. However, some of the nucleotide sequence diversity within this core genome is particular to each group, indicating that cross-species recombination is rare in this shared core gene set. Other than the meningococcal cps region, which encodes the polysaccharide capsule, relatively few members of the large accessory gene pool are exclusive to one species group, and cross-species recombination within this accessory genome is frequent.

Conclusion

The three Neisseria species groups represent coherent biological and genetic groupings which appear to be maintained by low rates of inter-species horizontal genetic exchange within the core genome. There is extensive evidence for exchange among positively selected genes and the accessory genome and some evidence of hitch-hiking of housekeeping genes with other loci. It is not possible to define a 'pathogenome' for this group of organisms and the disease causing phenotypes are therefore likely to be complex, polygenic, and different among the various disease-associated phenotypes observed.\n\nIndependent evolution of the core and accessory gene sets in the genus Neisseria: insights gained from the genome of Neisseria lactamica isolate 020-06.", "token_count": 466, "char_count": 1965, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5855, "quality_score": 0.7927, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:05.630777", "source": { "split": "train_shard_00001", "doc_id": 3963 }, "chunk_id": "train_shard_00001_3963_0", "global_id": 11265 }, { "text": "The availability and aggressive use of chemotherapeutic and immunosuppressive agents as well as broad-spectrum antibacterial agents have created a large population of patients who are at increased risk of acquiring infections with fungal organisms, especially Candida species. Present work was undertaken to study the epidemiology and microbiology of candidemia and Candida colonization in hospitalized children. A total of 323 suspected cases of septicemia were enrolled, of which blood culture from 7.4% subjects was positive for Candida species. In total, 57.3% subjects were colonized by Candida species at least at one of the tested sites. Of 337 isolates, 24.3, 71.5, 2.9, 0.59, and 0.59% were Candida albicans, Candida tropicalis, Candida krusei, Candida kefyr, and Candida lusitaniae, respectively. Antifungal susceptibility results show that fluconazole, itraconazole, and amphotericin B resistance is prevalent in 18.2, 2.4, and 3.6% of C. albicans isolates, and 21.1, 4.6, and 0.04% of C. tropicalis isolates, respectively. In a large number of cases, source of blood infection was patient's own colonizers, as shown by genetic matching. It was also noted that some strain types are circulating within the ward. High prevalence of non-albicans candidemia with high resistance to fluconazole is prevalent in North Indian hospitalized children.\n\nEpidemiology and microbiology of nosocomial pediatric candidemia at a northern Indian tertiary care hospital.", "token_count": 410, "char_count": 1464, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:06.290774", "source": { "split": "train_shard_00001", "doc_id": 3964 }, "chunk_id": "train_shard_00001_3964_0", "global_id": 11266 }, { "text": "Aquatic environments are important reservoirs for drug resistance. Aquatic foods may act as carriers to lead antibiotic-resistant commensal bacteria into the human gastrointestinal system, then contacting gut microbiota and spreading antibiotic resistance. Here, several shrimp farms were investigated to identify colistin resistance among commensal bacteria of aquaculture. A total of 884 (41.6%) colistin-resistant isolates were identified among 2126 strains. Electroporation demonstrated that colistin-resistant fragments were present in some commensal bacteria that could be transferred to other bacteria. Most of the resistant bacteria were Bacillus spp., with 69.3% of the Bacillus species exhibiting multiple drug resistance. Bacillus licheniformis was prevalent, with 58 strains identified that comprised six sequence types (ST) based on multilocus sequence typing. Whole-genome sequencing and comparisons with previous B. licheniformis genomes revealed a high degree of genomic similarity among isolates from different regions. Thus, this species is widely distributed, and this study provides new insights into global antibiotic-resistant characteristics of B. licheniformis. Sequence analyses further revealed some of these strains are even pathogenic and virulent, suggesting the antibiotic resistance and hazards of commensal bacteria in aquaculture should be considered. Considering the \"One Health\" perspective, improved monitoring of aquatic food is needed to prevent the spread of drug-resistant commensal bacteria from food-associated bacteria to humans.\n\nSurvey of Colistin Resistance in Commensal Bacteria from Penaeus vannamei Farms in China.", "token_count": 424, "char_count": 1705, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:06.968855", "source": { "split": "train_shard_00001", "doc_id": 3965 }, "chunk_id": "train_shard_00001_3965_0", "global_id": 11267 }, { "text": "Multiple epidemiological studies identify Dolosigranulum pigrum as a candidate beneficial bacterium based on its positive association with health, including negative associations with nasal/nasopharyngeal colonization by the pathogenic species Staphylococcus aureus and Streptococcus pneumoniae Using a multipronged approach to gain new insights into D. pigrum function, we observed phenotypic interactions and predictions of genomic capacity that support the idea of a role for microbe-microbe interactions involving D. pigrum in shaping the composition of human nasal microbiota. We identified in vivo community-level and in vitro phenotypic cooperation by specific nasal Corynebacterium species. Also, D. pigrum inhibited S. aureus growth in vitro, whereas robust inhibition of S. pneumoniae required both D. pigrum and a nasal Corynebacterium together. D. pigrum l-lactic acid production was insufficient to account for these inhibitions. Genomic analysis of 11 strains revealed that D. pigrum has a small genome (average 1.86 Mb) and multiple predicted auxotrophies consistent with D. pigrum relying on its human host and on cocolonizing bacteria for key nutrients. Further, the accessory genome of D. pigrum harbored a diverse repertoire of biosynthetic gene clusters, some of which may have a role in microbe-microbe interactions. These new insights into D", "token_count": 466, "char_count": 1492, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:07.653275", "source": { "split": "train_shard_00001", "doc_id": 3966 }, "chunk_id": "train_shard_00001_3966_0", "global_id": 11268 }, { "text": "pigrum's functions advance the field from compositional analysis to genomic and phenotypic experimentation on a potentially beneficial bacterial resident of the human upper respiratory tract and lay the foundation for future animal and clinical experiments.IMPORTANCEStaphylococcus aureus and Streptococcus pneumoniae infections cause significant morbidity and mortality in humans. For both, nasal colonization is a risk factor for infection. Studies of nasal microbiota identify Dolosigranulum pigrum as a benign bacterium present when adults are free of S. aureus or when children are free of S. pneumoniae Here, we validated these in vivo associations with functional assays. We found that D. pigrum inhibited S. aureusin vitro and, together with a specific nasal Corynebacterium species, also inhibited S. pneumoniae Furthermore, genomic analysis of D. pigrum indicated that it must obtain key nutrients from other nasal bacteria or from humans. These phenotypic interactions support the idea of a role for microbe-microbe interactions in shaping the composition of human nasal microbiota and implicate D. pigrum as a mutualist of humans. These findings support the feasibility of future development of microbe-targeted interventions to reshape nasal microbiota composition to exclude S. aureus and/or S. pneumoniae.\n\nDolosigranulum pigrum Cooperation and Competition in Human Nasal Microbiota.", "token_count": 440, "char_count": 1514, "word_count": 196, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:08.304350", "source": { "split": "train_shard_00001", "doc_id": 3966 }, "chunk_id": "train_shard_00001_3966_1", "global_id": 11269 }, { "text": "The number of bacterial genomes deposited each year in public databases is growing exponentially. However, efforts to use these genomes to track trends in antimicrobial resistance (AMR) have been limited thus far. We used 22,102 genomes from public databases to track AMR trends in nontyphoidal Salmonella in food animals in the United States. In 2018, genomes deposited in public databases carried genes conferring resistance, on average, to 2.08 antimicrobial classes in poultry, 1.74 in bovines, and 1.28 in swine. This represents a decline in AMR of over 70% compared to the levels in 2000 in bovines and swine, and an increase of 13% for poultry. Trends in resistance inferred from genomic data showed good agreement with U.S. phenotypic surveillance data (weighted mean absolute difference ± standard deviation, 5.86% ± 8.11%). In 2018, resistance to 3rd-generation cephalosporins in bovines, swine, and poultry decreased to 9.97% on average, whereas in quinolones and 4th-generation cephalosporins, resistance increased to 12.53% and 3.87%, respectively. This was concomitant with a decrease of blaCMY-2 but an increase in blaCTX-M-65 and gyrA D87Y (encoding a change of D to Y at position 87). Core genome single-nucleotide polymorphism (SNP) phylogenies show that resistance to these antimicrobial classes was predominantly associated with Salmonella enterica serovar Infantis and, to a lesser extent, S. enterica serovar Typhimurium and its monophasic variant I 4,[5],12:i:-, whereas quinolone resistance was also associated with S. enterica serovar Dublin", "token_count": 510, "char_count": 1609, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:08.970133", "source": { "split": "train_shard_00001", "doc_id": 3967 }, "chunk_id": "train_shard_00001_3967_0", "global_id": 11270 }, { "text": "Between 2000 and 2018, trends in serovar prevalence showed a composition shift where S. Typhimurium decreased while S. Infantis increased. Our findings illustrate the growing potential of using genomes in public databases to track AMR in regions where sequencing capacities are currently expanding. IMPORTANCE Next-generation sequencing has led to an exponential increase in the number of genomes deposited in public repositories. This growing volume of information presents opportunities to track the prevalence of genes conferring antimicrobial resistance (AMR), a growing threat to the health of humans and animals. Using 22,102 public genomes, we estimated that the prevalence of multidrug resistance (MDR) in the United States decreased in nontyphoidal Salmonella isolates recovered from bovines and swine between 2000 and 2018, whereas it increased in poultry. These trends are consistent with those detected by national surveillance systems that monitor resistance using phenotypic testing. However, using genomes, we identified that genes conferring resistance to critically important antimicrobials were associated with specific MDR serovars that could be the focus for future interventions. Our analysis illustrates the growing potential of public repositories to monitor AMR trends and shows that similar efforts could soon be carried out in other regions where genomic surveillance is increasing.\n\nMultidrug Resistance Dynamics in Salmonella in Food Animals in the United States: An Analysis of Genomes from Public Databases.", "token_count": 359, "char_count": 1558, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7959, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:09.550725", "source": { "split": "train_shard_00001", "doc_id": 3967 }, "chunk_id": "train_shard_00001_3967_1", "global_id": 11271 }, { "text": "Although anthropogenic activities contribute to the selection and spread of antibiotic resistance in aquatic environments, limited information is available from countries with absent or incomplete sewage treatment systems and the impact of their discharges onto water bodies. This study therefore aimed to characterize the genetic structure of colistin resistance (mcr) genes among Escherichia coli isolates recovered from surface waters and sediments in Ecuador. Out of 459 isolates, four Escherichia coli showed multidrug-resistant phenotypes, which harbored the mcr-1 gene and β-lactamases, such as blaTEM, blaCTX-M-15, blaCTX-M-55, or blaCTX-M-65 genes. Three E. coli isolates (U20, U30 and U144) shared a similar genetic environment surrounding the mcr-1 gene, which was located on plasmids. Only one E. coli isolate (U175) showed that the mcr-1 gene was chromosomally located. Moreover, the core genome multilocus sequence typing (cgMLST) analysis revealed that these isolates belong to different lineages. This study represents the first detection of the mcr-1 gene in multidrug-resistant E. coli isolates from environmental samples in Ecuador.\n\nCharacterization of the genetic structure of mcr-1 gene among Escherichia coli isolates recovered from surface waters and sediments from Ecuador.", "token_count": 365, "char_count": 1342, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8122, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:10.135977", "source": { "split": "train_shard_00001", "doc_id": 3968 }, "chunk_id": "train_shard_00001_3968_0", "global_id": 11272 }, { "text": "Staphylococcus epidermidis is a leading cause of nosocomial infections in patients with a compromised immune system and/or an implanted medical device. Seventy to 90% of S. epidermidis clinical isolates are methicillin resistant and carry the mecA gene, present in a mobile genetic element (MGE) called the staphylococcal cassette chromosome mec (SCCmec) element. Along with the presence of antibiotic and heavy metal resistance genes, MGEs can also contain genes encoding secreted or cell wall-anchored virulence factors. In our earlier studies of S. epidermidis clinical isolates, we discovered S. epidermidis surface protein J (SesJ), a prototype of a recently discovered subfamily of the microbial surface component recognizing adhesive matrix molecule (MSCRAMM) group. MSCRAMMs are major virulence factors of pathogenic Gram-positive bacteria. Here, we report that the sesJ gene is always accompanied by two glycosyltransferase genes, gtfA and gtfB, and is present in two MGEs, called the arginine catabolic mobile element (ACME) and the staphylococcal cassette chromosome (SCC) element. The presence of the sesJ gene was associated with the left-hand direct repeat DR_B or DR_E. When inserted via DR_E, the sesJ gene was encoded in the SCC element. When inserted via DR_B, the sesJ gene was accompanied by the genes for the type 1 restriction modification system and was encoded in the ACME. Additionally, the SCC element and ACME carry different isoforms of the SesJ protein. To date, the genes encoding MSCRAMMs have been seen to be located in the bacterial core genome. Here, we report the presence of an MSCRAMM in an MGE in S", "token_count": 515, "char_count": 1730, "word_count": 253, "semantic_coherence": 1, "information_density": 0.581, "quality_score": 0.7905, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:10.791207", "source": { "split": "train_shard_00001", "doc_id": 3969 }, "chunk_id": "train_shard_00001_3969_0", "global_id": 11273 }, { "text": "epidermidis clinical isolates.IMPORTANCES. epidermidis is an opportunistic bacterium that has established itself as a successful nosocomial pathogen. The modern era of novel therapeutics and medical devices has extended the longevity of human life, but at the same time, we also witness the evolution of pathogens to adapt to newly available niches in the host. Increasing antibiotic resistance among pathogens provides an example of such pathogen adaptation. With limited opportunities to modify the core genome, most of the adaptation occurs by acquiring new genes, such as virulence factors and antibiotic resistance determinants present in MGEs. In this study, we describe that the sesJ gene, encoding a recently discovered cell wall-anchored protein in S. epidermidis, is present in both ACME and the SCC element. The presence of virulence factors in MGEs can influence the virulence potential of a specific strain. Therefore, it is critical to study the virulence factors found in MGEs in emerging pathogenic bacteria or strains to understand the mechanisms used by these bacteria to cause infections.\n\nStaphylococcus epidermidis MSCRAMM SesJ Is Encoded in Composite Islands.", "token_count": 298, "char_count": 1213, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.8381, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:11.351834", "source": { "split": "train_shard_00001", "doc_id": 3969 }, "chunk_id": "train_shard_00001_3969_1", "global_id": 11274 }, { "text": "Transjugation is an unconventional conjugation mechanism in Thermus thermophilus (Tth) that involves the active participation of both mating partners, encompassing a DNA secretion system (DSS) in the donor and an active natural competence apparatus (NCA) in the recipient cells. DSS is encoded within an integrative and conjugative element (ICETh1) in the strain Tth HB27, whereas the NCA is constitutively expressed in both mates. Previous experiments suggested the presence of multiple origins of transfer along the genome, which could generate genomic mosaicity among the progeny. Here, we designed transjugation experiments between two closely related strains of Tth with highly syntenic genomes, containing enough single nucleotide polymorphisms to allow precise parenthood analysis. Individual clones from the progeny were sequenced, revealing their origin as derivatives of our ICETh1-containing intended \"donor\" strain (HB27), which had acquired separate fragments from the genome of the ICETh1-free HB8 cells, which are our intended recipient. Due to the bidirectional nature of transjugation, only assays employing competence-defective HB27 derivatives as donors allowed the recovery of HB8-derived progeny. These results show a preference for a retrotransfer mechanism in transjugation in ICETh1-bearing strains, supporting an inter-strain gene-capture function for ICETh1. This function could benefit the donor-capable host by facilitating the acquisition of adaptive traits from external sources, ultimately increasing the open pangenome of Thermus, maximizing the potential repertoire of physiological and phenotypical traits related to adaptation and speciation.\n\nIntegrative and Conjugative Element ICETh1 Functions as a Pangenomic DNA Capture Module in Thermus thermophilus.", "token_count": 465, "char_count": 1826, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6901, "quality_score": 0.845, "entities": { "genes": [ "HB8", "HB27" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:11.998211", "source": { "split": "train_shard_00001", "doc_id": 3970 }, "chunk_id": "train_shard_00001_3970_0", "global_id": 11275 }, { "text": "The metabolically versatile Gram-negative bacterium Pseudomonas aeruginosa inhabits terrestrial, aquatic, animal-, human-, and plant-host-associated environments and is an important causative agent of nosocomial infections, particularly in intensive-care units. The population genetics of P. aeruginosa was investigated by an approach that is generally applicable to the rapid, robust, and informative genotyping of bacteria. DNA, amplified from the bacterial colony by circles of multiplex primer extension, is hybridized onto a microarray to yield an electronically portable binary multimarker genotype that represents the core genome by single nucleotide polymorphisms and the accessory genome by markers of genomic islets and islands. The 240 typed P. aeruginosa strains of diverse habitats and geographic origin segregated into two large nonoverlapping clusters and 45 isolated clonal complexes with few or no partners. The majority of strains belonged to few dominant clones widespread in disease and environmental habitats. The most frequent genotype was represented by the sequenced strain PA14. Core and accessory genome were found to be nonrandomly assembled in P. aeruginosa. Individual clones preferred a specific repertoire of accessory segments. Even the most promiscuous genomic island, pKLC102, had integrated preferentially into a subset of clones. Moreover, some physically distant loci of the core genome, including oriC, showed nonrandom associations of genotypes, whereas other segments in between were freely recombining. Thus, the P. aeruginosa genome is made up of clone-typical segments in core and accessory genome and of blocks in the core with unrestricted gene flow in the population.\n\nPopulation structure of Pseudomonas aeruginosa.", "token_count": 407, "char_count": 1762, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:12.618188", "source": { "split": "train_shard_00001", "doc_id": 3971 }, "chunk_id": "train_shard_00001_3971_0", "global_id": 11276 }, { "text": "The Mig1 repressor is a key effector in glucose repression in the yeast Saccharomyces cerevisiae. To gain further insights into structure-function relationships, we have now cloned the MIG1 homologue from the yeast Kluyveromyces marxianus. The amino acid sequence deduced from KmMIG1 differs significantly from ScMig1p outside the highly conserved zinc fingers. However, 12 discrete conserved motifs could be identified in a multiple alignment that also included the K. lactis Mig1p sequence. We further found that KmMig1p is fully functional when expressed in S. cerevisiae. First, it represses the SUC2 promoter almost as well as ScMig1p. This repression requires the Cyc8 and Tup1 proteins and is dependent on a C-terminal region comprising several conserved leucine-proline repeats. Second, KmMig1p is regulated by glucose in S. cerevisiae, and a KmMig1-VP16 hybrid activator is inhibited by the ScSnf1p kinase in the absence of glucose. This suggests that KmMig1p has retained the ability to interact with several S. cerevisiae proteins, and reinforces the notion that the conserved motifs are functionally important. Finally, we found that the physiological role of Mig1p also is conserved in K. marxianus, since KmMig1p represses INU1, the counterpart of SUC2 in this organism.\n\nComparative analysis in three fungi reveals structurally and functionally conserved regions in the Mig1 repressor.", "token_count": 390, "char_count": 1400, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6232, "quality_score": 0.8116, "entities": { "genes": [ "MIG1", "INU1", "SUC2", "VP16" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:13.239714", "source": { "split": "train_shard_00001", "doc_id": 3972 }, "chunk_id": "train_shard_00001_3972_0", "global_id": 11277 }, { "text": "The taxonomic status of six strains of Acinetobacter obtained from meat samples, collected from supermarkets in Porto, Portugal, was investigated using polyphasic analysis. Partial rpoB sequence similarities lower than 95 % to other Acinetobacter species with validly published names led to the hypothesis that these strains represented novel species. This was confirmed based on comparative multilocus sequence analysis, which included the gyrB, recA and 16S rRNA genes, revealing that these strains represented two coherent lineages that were distinct from each other and from all known species. The names Acinetobacter portensis sp. nov. (comprising four strains) and Acinetobacter guerrae sp. nov. (comprising two strains) are proposed for these novel species. The species status of these two groups was confirmed by low (below 95 %) whole-genome sequence average nucleotide identity values and low (below 70 %) digital DNA-DNA hybridization similarities between the whole-genome sequences of the proposed type strains of each novel species and the representatives of the known Acinetobacter species. Phylogenomic treeing from core genome analysis supported these results. The coherence of each new species lineage was supported by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry differentiation of the species at the protein level, by cellular fatty acid profiles, and by unique and differential combinations of metabolic and physiological properties shared by each novel species. The type strain of A. portensis sp. nov. is AC 877T (=CCUG 68672T=CCM 8789T) and the type strain of A. guerrae sp. nov. is AC 1271T (=CCUG 68674T=CCM 8791T).", "token_count": 518, "char_count": 1808, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5702, "quality_score": 0.7851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:13.899630", "source": { "split": "train_shard_00001", "doc_id": 3973 }, "chunk_id": "train_shard_00001_3973_0", "global_id": 11278 }, { "text": "Acinetobacter portensis sp. nov. and Acinetobacter guerrae sp. nov., isolated from raw meat.", "token_count": 38, "char_count": 106, "word_count": 13, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:14.263651", "source": { "split": "train_shard_00001", "doc_id": 3973 }, "chunk_id": "train_shard_00001_3973_1", "global_id": 11279 }, { "text": "The type VIIb protein secretion system (T7SSb) is found in Bacillota (firmicute) bacteria and has been shown to mediate interbacterial competition. EssC is a membrane-bound ATPase that is a critical component of the T7SSb and plays a key role in substrate recognition. Prior analysis of available genome sequences of the foodborne bacterial pathogen Listeria monocytogenes has shown that although the T7SSb was encoded as part of the core genome, EssC could be found as one of seven different sequence variants. While each sequence variant was associated with a specific suite of candidate substrate proteins encoded immediately downstream of essC, many LXG-domain proteins were encoded across multiple essC sequence variants. Here, we have extended this analysis using a diverse collection of 37 930 L. monocytogenes genomes. We have identified a rare eighth variant of EssC present in ten L. monocytogenes lineage III genomes. These genomes also encode a large toxin of the rearrangement hotspot (Rhs) repeat family adjacent to essC8, along with a probable immunity protein and three small accessory proteins. We have further identified nine novel LXG-domain proteins, and four additional chromosomal hotspots across L. monocytogenes genomes where LXG proteins can be encoded. The eight L. monocytogenes EssC variants were also found in other Listeria species, with additional novel EssC types also identified. Across the genus, species frequently encoded multiple EssC types, indicating that T7SSb diversity is a primary feature of the genus Listeria.\n\nA novel variant of the Listeria monocytogenes type VII secretion system EssC component is associated with an Rhs toxin.", "token_count": 486, "char_count": 1766, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5968, "quality_score": 0.7984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:14.911861", "source": { "split": "train_shard_00001", "doc_id": 3974 }, "chunk_id": "train_shard_00001_3974_0", "global_id": 11280 }, { "text": "The sexual or teleomorphic state of yeasts has only been described in a few clinically involved species, mainly those of the Saccharomycetaceae family. With the aim of gathering information on their incidence in human pathology, a study has been made of a total of 2,135 strains isolated from clinical samples and cultivated in McClary agar. From these, 8 strains in teleomorphic state were identified: Kluyveromyces marxianus [1], Pichia anomala [2], Pichia farinosa [1], Pichia membranaefaciens [1] and Saccharomyces cerevisiae [3]. The two strains of P. anomala were responsible for fungemia; K, marxianus and the two strains of S. cerevisiae produced vaginitis; the other strains were oral cavity colonizers.\n\nSexual forms of yeasts in clinical samples.", "token_count": 208, "char_count": 757, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6435, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:15.383693", "source": { "split": "train_shard_00001", "doc_id": 3975 }, "chunk_id": "train_shard_00001_3975_0", "global_id": 11281 }, { "text": "The Lactobacillus genus encompasses a genetically and functionally diverse group of species, and contains many strains widely formulated in the human food supply chain as probiotics and starter cultures. Within this genetically expansive group, there are several distinct clades that have high levels of homology, one of which is the Lactobacillus acidophilus group. Of the uniting features, small genomes, low GC content, adaptation to dairy environments, and fastidious growth requirements, are some of the most defining characteristics of this group. To better understand what truly links and defines this clade, we sought to characterize the genomic organization and content of the genomes of several members of this group. Through core genome analysis we explored the synteny and intrinsic genetic underpinnings of the L. acidophilus clade, and observed key features related to the evolution and adaptation of these organisms. While genetic content is able to provide a large map of the potential of each organism, it does not always reflect their functionality. Through transcriptomic data we inferred the core transcriptome of the L. acidophilus complex to better define the true metabolic capabilities that unite this clade. Using this approach we have identified seven small ORFs that are both highly conserved and transcribed in diverse members of this clade and could be potential novel small peptide or untranslated RNA regulators. Overall, our results reveal the core features of the L. acidophilus complex and open new avenues for the enhancement and formulation and of next generation probiotics and starter cultures.\n\nConserved Genome Organization and Core Transcriptome of the Lactobacillus acidophilus Complex.", "token_count": 414, "char_count": 1770, "word_count": 258, "semantic_coherence": 1, "information_density": 0.593, "quality_score": 0.7965, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:16.009095", "source": { "split": "train_shard_00001", "doc_id": 3976 }, "chunk_id": "train_shard_00001_3976_0", "global_id": 11282 }, { "text": "Shewanella baltica was the dominant culturable nitrate-reducing bacterium in the eutrophic and strongly stratified Baltic Sea in the 1980s, where it primarily inhabited the oxic-anoxic transition zone. The genomic structures of 46 of these isolates were investigated through comparative genomic hybridization (CGH), which revealed a gradient of genomic similarity, ranging from 65% to as high as 99%. The core genome of the S. baltica species was enriched in anaerobic respiration-associated genes. Auxiliary genes, most of which locate within a few genomic islands (GIs), were nonuniformly distributed among the isolates. Specifically, hypothetical and mobile genetic element (MGE)-associated genes dominated intraclade gene content differences, whereas gain/loss of functional genes drove gene content differences among less related strains. Among the major S. baltica clades, gene signatures related to specific redox-driven and spatial niches within the water column were identified. For instance, genes involved in anaerobic respiration of sulfur compounds may provide key adaptive advantages for clade A strains in anoxic waters where sulfur-containing electron acceptors are present. Genes involved in cell motility, in particular, a secondary flagellar biosynthesis system, may be associated with the free-living lifestyle by clade E strains. Collectively, this study revealed characteristics of genome variations present in the water column and active speciation of S. baltica strains, driven by niche partitioning and horizontal gene transfer (HGT).IMPORTANCE Speciation in nature is a fundamental process driving the formation of the vast microbial diversity on Earth. In the central Baltic Sea, the long-term stratification of water led to formation of a large-scale vertical redoxcline that provided a gradient of environmental niches with respect to the availability of electron acceptors and donors. The region was home to Shewanella baltica populations, which composed the dominant culturable nitrate-reducing bacteria, particularly in the oxic-anoxic transition zone. Using the collection of S", "token_count": 522, "char_count": 2155, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:16.668320", "source": { "split": "train_shard_00001", "doc_id": 3977 }, "chunk_id": "train_shard_00001_3977_0", "global_id": 11283 }, { "text": "baltica isolates as a model system, genomic variations showed contrasting gene-sharing patterns within versus among S. baltica clades and revealed genomic signatures of S. baltica clades related to redox niche specialization as well as particle association. This study provides important insights into genomic mechanisms underlying bacterial speciation within this unique natural redoxcline.\n\nGenomic Variations Underlying Speciation and Niche Specialization of Shewanella baltica.", "token_count": 125, "char_count": 506, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:17.052400", "source": { "split": "train_shard_00001", "doc_id": 3977 }, "chunk_id": "train_shard_00001_3977_1", "global_id": 11284 }, { "text": "This strategic plan summarizes the major accomplishments achieved in the last quinquennial by the soybean [Glycine max (L.) Merr.] genetics and genomics research community and outlines key priorities for the next 5 years (2024-2028). This work is the result of deliberations among over 50 soybean researchers during a 2-day workshop in St Louis, MO, USA, at the end of 2022. The plan is divided into seven traditional areas/disciplines: Breeding, Biotic Interactions, Physiology and Abiotic Stress, Functional Genomics, Biotechnology, Genomic Resources and Datasets, and Computational Resources. One additional section was added, Training the Next Generation of Soybean Researchers, when it was identified as a pressing issue during the workshop. This installment of the soybean genomics strategic plan provides a snapshot of recent progress while looking at future goals that will improve resources and enable innovation among the community of basic and applied soybean researchers. We hope that this work will inform our community and increase support for soybean research.\n\nSoybean genomics research community strategic plan: A vision for 2024-2028.", "token_count": 277, "char_count": 1152, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:17.609900", "source": { "split": "train_shard_00001", "doc_id": 3978 }, "chunk_id": "train_shard_00001_3978_0", "global_id": 11285 }, { "text": "

Background

The prevalence of multidrug-resistant Klebsiella pneumoniae is increasingly being implicated worldwide in a variety of infections with high mortalities. Here, we report the complete genome sequence of K. pneumoniae strain KP58, a pandrug-resistant K. pneumoniae strain that exhibits high levels of resistance to colistin and tigecycline in China.

Methods

The K. pneumoniae strain KP58 was recovered from a urine sample of a female patient hospitalized in a tertiary hospital in Hangzhou, China. Antimicrobial susceptibility testing was performed and the minimum inhibitory concentrations (MICs) were determined. Whole-genome sequencing was performed using Illumina and Oxford nanopore sequencing technologies. Genomic features, antimicrobial resistance genes and virulence genes were comprehensively analysed by various bioinformatics approaches. In addition, genomic epidemiological and phylogenetic analyses of K. pneumoniae KP58 and closely related isolates were performed using the core genome multilocus sequence typing (cgMLST) analysis in BacWGSTdb, an online bacterial whole-genome sequence typing and source tracking database.

Results

K. pneumoniae KP58 was resistant to all antimicrobial agents tested, including tigecycline and colistin. Combining the two sequencing technologies allowed a high-quality complete genome sequence of K. pneumoniae KP58 comprising one circular chromosome and five circular plasmids to be obtained. This strain harbours a variety of acquired antimicrobial resistance and virulence determinants. It also carried an ISKpn26-like insertion in the disrupted mgrB gene, which confers colistin resistance. The tigecycline resistance was associated with overexpression of the AcrAB efflux system. The closest relative of K", "token_count": 518, "char_count": 1854, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6043, "quality_score": 0.8022, "entities": { "genes": [ "KP58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:18.288305", "source": { "split": "train_shard_00001", "doc_id": 3979 }, "chunk_id": "train_shard_00001_3979_0", "global_id": 11286 }, { "text": "pneumoniae KP58 was another clinical isolate recovered from Hangzhou that differed by only 10 cgMLST loci.

Conclusion

The dataset presented in this study provides essential insights into the evolution of antimicrobial-resistant K. pneumoniae in hospital settings and assists in the development of effective control strategies. Appropriate surveillance and control measures are essential to prevent its further dissemination.\n\nHybrid Genome Assembly and Annotation of a Pandrug-Resistant Klebsiella pneumoniae Strain Using Nanopore and Illumina Sequencing.", "token_count": 156, "char_count": 580, "word_count": 71, "semantic_coherence": 1, "information_density": 0.831, "quality_score": 0.9155, "entities": { "genes": [ "KP58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:18.745723", "source": { "split": "train_shard_00001", "doc_id": 3979 }, "chunk_id": "train_shard_00001_3979_1", "global_id": 11287 }, { "text": "EnteroBase is an integrated software environment that supports the identification of global population structures within several bacterial genera that include pathogens. Here, we provide an overview of how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridioides, Helicobacter, Vibrio, and Moraxella and genotyped those assemblies by core genome multilocus sequence typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case Study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports single nucleotide polymorphism (SNP) calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by Case Study 2 which summarizes the microevolution of Yersinia pestis over the last 5000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by Case Study 3, which presents a novel, global overview of the population structure of all of the species, subspecies, and clades within Escherichia.\n\nThe EnteroBase user's guide, with case studies on <i>Salmonella</i> transmissions, <i>Yersinia pestis</i> phylogeny, and <i>Escherichia</i> core genomic diversity.", "token_count": 477, "char_count": 1700, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:19.410818", "source": { "split": "train_shard_00001", "doc_id": 3980 }, "chunk_id": "train_shard_00001_3980_0", "global_id": 11288 }, { "text": "Listeria monocytogenes sequence type 1247 clonal complex 8 caused a prolonged multicountry outbreak in five EU countries: Denmark, Estonia, Finland, France, and Sweden. A total of 22 disease cases were identified with onset of symptoms between July 2014 and February 2019. Five patients died due to, or with, the disease. The retrospective analysis of L. monocytogenes isolate VLTRLM2013 revealed the presence of an outbreak-related strain (cgMLST type L2-SL8-ST1247-CT4158) in ready-to-eat fish product more than a year prior to the first outbreak-related cases. Reference outbreak strain and VLTRLM2013 strain were compared using core genome and whole-genome multilocus sequence typing analyses. Genomic level differences of the persistent L. monocytogenes strains associated with a prolonged multicountry foodborne listeriosis outbreak are described. It was concluded that the persistent nature of the multicountry outbreak-related L. monocytogenes strain VLTRLM2013 together with stress island, virulence, and antibiotic resistance genes could potentially be the determining factors for the extensive and prolonged outbreak affecting five European Union countries. Our results support the systematic application of whole-genome sequencing in food and public health surveillance and further encourages its wide adoption.\n\nRetrospective Use of Whole-Genome Sequencing Expands the Multicountry Outbreak Cluster of Listeria monocytogenes ST1247.", "token_count": 396, "char_count": 1487, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8376, "entities": { "genes": [ "ST1247", "CT4158", "SL8", "VLTRLM2013" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:20.067175", "source": { "split": "train_shard_00001", "doc_id": 3981 }, "chunk_id": "train_shard_00001_3981_0", "global_id": 11289 }, { "text": "

ABSTRACT

The present study described the comparative genomic analysis of the validly named species of the genus Pseudomonas to define the taxonomic assignment. Genomic information for 208 type strains was available in the NCBI genome database at the time of conducting this analysis. The ANI, AAI and in silico DNA DNA hybridization (isDDH) data were higher than the threshold values for the twelve strains with their closely related type species. Whole genome comparisons shared 97 - 99 % average nucleotide identity, 97.85 to 99.19 % average amino acid identity and 72.80 to 90.40 % digital DNA DNA hybridization values. Further, the phylogenomic analysis based on the core genome confirmed that P. humi CCA1 and P. citronellolis LMG 18378, P. zeshuii KACC 15471 and P. luteola NBRC 103146, P. oryzihabitans DSM 6835 and P. psychrotolerans DSM 15758, P. nitroreducens DSM 14399 and P. nitritireducens WZBFD3-5A2, P. fluvialis CCM 8778 and P. pharmacofabricae ZYSR67-Z, P. panacis DSM 18529 and P. marginalis DSM 13124 formed a monophyletic clade. Thus, we proposed six type species viz., P. humi CCA1, P. zeshuii KACC 15471, P. psychrotolerans DSM 15758, P. nitritireducens WZBFD3 5A2, P. pharmacofabricae ZYSR67 Z and P. panacis DSM 18529 are the later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P", "token_count": 527, "char_count": 1392, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [ "ZYSR67", "CCA1", "WZBFD3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:20.727144", "source": { "split": "train_shard_00001", "doc_id": 3982 }, "chunk_id": "train_shard_00001_3982_0", "global_id": 11290 }, { "text": "marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively considering the priority date of publication.\n\nPhylogenomic analysis of the genus Pseudomonas and reclassification of P. humi, P. zeshuii, P. psychrotolerans, P. nitritireducens, P. pharmacofabricae and P. panacis are later heterotypic synonym of P. citronellolis Lang 2007, P. luteola, P. oryzihabitans, P. nitroreducens Lang 2007, P. fluvialis and P. marginalis (Brown 1918) Stevens 1925 (Approved Lists 1980), respectively", "token_count": 229, "char_count": 547, "word_count": 67, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:21.189276", "source": { "split": "train_shard_00001", "doc_id": 3982 }, "chunk_id": "train_shard_00001_3982_1", "global_id": 11291 }, { "text": "A strategy to optimize biotechnological process design is illustrated for the production of fructose-rich syrups via enzymatic hydrolysis of agave fructo-oligosaccharides. The optimization process includes ecological studies from natural fermentations leading to the selection of a strain with capacity for inulinase synthesis, and variable optimization for the synthesis, and enzymatic hydrolysis using the response surface methodology. The results lead to the selection of Kluyveromyces marxianus , endogenous strains isolated from aguamiel (natural fermented sugary sap from agave plants), as the main strain with high capacity for enzyme synthesis with inulinase activity. Production optimization at bioreactor level revealed that operation at 30.6 degrees C, 152 rpm, 1.3 VVM of aeration, and pH 6.3 leads to maximum inulinase synthesis, whereas 31 degrees C, 50 rpm, and pH 6.2 leads to maximum hydrolysis of agave fructo-oligosaccharides. HPLC analysis of the fructose-rich syrups obtained at these optimal conditions showed an average composition of 95% of fructose and 5% of glucose and the absence of sucrose. The analysis also revealed that the syrups are free of residues and toxic compounds, an undesirable occurrence often present when traditional methods based on thermal or acid hydrolysis are applied for their obtainment. Therefore, the product may be suitable for use as additive in many applications in the food and beverage industries.\n\nStrategy for biotechnological process design applied to the enzymatic hydrolysis of agave fructo-oligosaccharides to obtain fructose-rich syrups.", "token_count": 403, "char_count": 1603, "word_count": 230, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:21.806697", "source": { "split": "train_shard_00001", "doc_id": 3983 }, "chunk_id": "train_shard_00001_3983_0", "global_id": 11292 }, { "text": "Antimicrobial resistance-encoding mobile genetic elements (MGEs) may contribute to the disease potential of bacterial pathogens. We previously described the association of Group A Streptococcus (GAS) derived from invasive disease with increasingly frequent antimicrobial resistance (AMR). We hypothesized that a 65-kb AMR-encoding MGE (ICESpyM92), highly conserved among closely related emergent invasive emm92 GAS, contributes to GAS disease potential. Here, we provide evidence that a combination of ICESpyM92- and core genome-dependent differential gene expression (DGE) contributes to invasive disease phenotypes of emergent emm92 GAS. Using isogenic ICESpyM92 mutants generated in distinct emm92 genomic backgrounds, we determined the presence of ICESpyM92 enhances GAS virulence in a mouse subcutaneous infection model. Measurement of in vitro and ex vivo DGE indicates ICESpyM92 influences GAS global gene expression in a background-dependent manner. Our study links virulence and AMR on a unique MGE via MGE-related DGE and highlights the importance of investigating associations between AMR-encoding MGEs and pathogenicity.\n\nThe Integrative Conjugative Element ICESpyM92 Contributes to Pathogenicity of Emergent Antimicrobial-Resistant emm92 Group A Streptococcus.", "token_count": 367, "char_count": 1315, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8343, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:22.388737", "source": { "split": "train_shard_00001", "doc_id": 3984 }, "chunk_id": "train_shard_00001_3984_0", "global_id": 11293 }, { "text": "Sourdough is the oldest form of leavened bread used as early as 2000 BC by the ancient Egyptians. It may have been discovered by accident when wild yeast drifted into dough that had been left out resulting in fermentation of good microorganisms, which made bread with better flavour and texture. The discovery was continued where sourdough was produced as a means of reducing wastage with little known (at that point of time) beneficial effects to health. With the progress and advent of science and technology in nutrition, sourdough fermentation is now known to possess many desirable attributes in terms of health benefits. It has become the focus of attention and practice in modern healthy eating lifestyles when linked to the secret of good health. The sourdough starter is an excellent habitat where natural and wild yeast plus beneficial bacteria grow by ingesting only water and flour. As each sourdough starter is unique, with different activities, populations and interactions of yeast and bacteria due to different ingredients, environment, fermentation time and its carbohydrate fermentation pattern, there is no exact elucidation on the complete make-up of the sourdough microbiome. Some lactic acid bacteria (LAB) strains that are part of the sourdough starter are considered as probiotics which have great potential for improving gastrointestinal health. Hence, from a wide literature surveyed, this paper gives an overview of microbial communities found in different sourdough starters. This review also provides a systematic analysis that identifies, categorises and compares these microbes in the effort of linking them to specific functions, particularly to unlock their health benefits.\n\nSourdough Microbiome Comparison and Benefits.", "token_count": 377, "char_count": 1754, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:22.974113", "source": { "split": "train_shard_00001", "doc_id": 3985 }, "chunk_id": "train_shard_00001_3985_0", "global_id": 11294 }, { "text": "Salmonella enterica subspecies arizonae is frequently associated with animal reservoirs, particularly reptiles, and can cause illness in some mammals, including humans. Using whole-genome sequencing data, core genome phylogenetic analyses were performed using 112 S. enterica subsp. arizonae isolates, representing 46 of 102 described serovars. Nearly one-third of these are polyphyletic, including two serovars that appear in four and five distinct evolutionary lineages. Subspecies arizonae has a monophasic H antigen. Among the 46 serovars investigated, only 8 phase 1 H antigens were identified, demonstrating high conservation for this antigen. Prophages and plasmids were found throughout this subspecies, including five novel prophages. Polyphyly was also reflected in prophage content, although some clade-specific enrichment for some phages was observed. IncFII(S) was the most frequent plasmid replicon identified and was found in a quarter of S. enterica subsp. arizonae genomes. Salmonella pathogenicity islands (SPIs) 1 and 2 are present across all Salmonella, including this subspecies, although effectors sipA, sptP and arvA in SPI-1 and sseG and ssaI in SPI-2 appear to be lost in this lineage. SPI-20, encoding a type VI secretion system, is exclusive to this subspecies and is well maintained in all genomes sampled. A number of fimbral operons were identified, including the sas operon that appears to be a synapomorphy for this subspecies, while others exhibited more clade-specific patterns. This work reveals evolutionary patterns in S. enterica subsp", "token_count": 525, "char_count": 1699, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:23.635707", "source": { "split": "train_shard_00001", "doc_id": 3986 }, "chunk_id": "train_shard_00001_3986_0", "global_id": 11295 }, { "text": "arizonae that make this subspecies a unique lineage within this very diverse species.\n\nPhylogeny of Salmonella enterica subspecies arizonae by whole-genome sequencing reveals high incidence of polyphyly and low phase 1 H antigen variability.", "token_count": 83, "char_count": 262, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:24.005766", "source": { "split": "train_shard_00001", "doc_id": 3986 }, "chunk_id": "train_shard_00001_3986_1", "global_id": 11296 }, { "text": "Bacterial pathogens can undergo striking adaptive evolutionary change in the context of infection, driven by selection forces associated with host defenses and antibiotic treatment. In this work, we analyze the transcriptional landscape associated with adaptation in an emerging zoonotic pathogen, Bordetella hinzii, as it evolved during a 45-month infection in an IL12Rβ1-deficient immunocompromised host. We find evidence of multiple niche-specific modifications in the intravascular and gastrointestinal compartments, involving the superoxide dismutase system, glutamate and ectoine metabolism, chaperone-mediated protein folding, pilus organization, and peptide transport. Individual blood lineages displayed modifications in glutathione, phenylacetate, and 3-phenylpropionate metabolism, iron cluster assembly, and electron transport, whereas individual gastrointestinal lineages demonstrated changes relating to gluconeogenesis, de novo pyrimidine synthesis, and transport of peptides and phosphate ions. Down regulation of the flagellar operon with corresponding loss of flagellar structures occurred in multiple lineages, suggesting an evolutionary tradeoff between motility and host immune evasion. Finally, methylome analysis demonstrates alteration of global genome methylation associated with loss of a Type III methyltransferase. Our findings reveal striking plasticity in how pathogen transcriptomes explore functional space as they evolve in the context of host infection, and demonstrate that such analysis may uncover phenotypic adaptations not apparent from genomic analysis alone.\n\nTranscriptional diversification in a human-adapting zoonotic pathogen drives niche-specific evolution.", "token_count": 389, "char_count": 1703, "word_count": 210, "semantic_coherence": 1, "information_density": 0.7095, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:24.625943", "source": { "split": "train_shard_00001", "doc_id": 3987 }, "chunk_id": "train_shard_00001_3987_0", "global_id": 11297 }, { "text": "Deinococcus species are widely studied due to their utility in bioremediation of sites contaminated with radioactive elements. In the present study, we re-evaluated the taxonomic placement of two species of the genus Deinococcus namely D. swuensis DY59T and D. radiopugnans ATCC 19172T based on whole genome analyses. The 16S rRNA gene analysis revealed a 99.58% sequence similarity between this species pair that is above the recommended threshold value for species delineation. These two species also clustered together in both the 16S rRNA gene and core genome based phylogenies depicting their close relatedness. Furthermore, more than 98% of genes were shared between D. swuensis DY59T and D. radiopugnans ATCC 19172T. Interestingly, D. swuensis DY59T and D. radiopugnans ATCC 19172T shared high genome similarity in different genomic indices. They displayed an average nucleotide identity value of 97.63%, an average amino acid identity value of 97% and a digital DNA-DNA hybridization value equal to 79.50%, all of which are well above the cut-off for species delineation. Altogether, based on these evidences, D. swuensis DY59T and D. radiopugnans ATCC 19172T constitute a single species", "token_count": 464, "char_count": 1353, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5889, "quality_score": 0.7944, "entities": { "genes": [ "DY59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:25.276824", "source": { "split": "train_shard_00001", "doc_id": 3988 }, "chunk_id": "train_shard_00001_3988_0", "global_id": 11298 }, { "text": "Hence, as per the priority of publication, we propose that Deinococcus swuensis Lee et al. 2015 should be reclassified as a later heterotypic synonym of Deinococcus radiopugnans.\n\nGenome based reclassification of Deinococcus swuensis as a heterotypic synonym of Deinococcus radiopugnans.", "token_count": 119, "char_count": 322, "word_count": 40, "semantic_coherence": 1, "information_density": 0.675, "quality_score": 0.8375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:25.663385", "source": { "split": "train_shard_00001", "doc_id": 3988 }, "chunk_id": "train_shard_00001_3988_1", "global_id": 11299 }, { "text": "The economically important plant pathogen Xylella fastidiosa has been reported in multiple regions of the globe during the last two decades, threatening a growing list of crops and industries. Xylella fastidiosa subspecies fastidiosa causes disease in grapevines (Pierce’s disease of grapevines, PD), a current problem in the United States (US), Spain, and Taiwan. We studied PD-causing subsp. fastidiosa populations and compared the genome sequences of 33 isolates found in Central Taiwan with 171 isolates from the US and two from Spain. Phylogenetic relationships, haplotype network, and genetic diversity analyses confirm that subsp. fastidiosa was recently introduced into Taiwan from the Southeast US (i.e., the PD-I lineage in Georgia based on available data). Recent core genome recombination events were detected among introduced subsp. fastidiosa isolates in Taiwan and contributed to the development of genetic diversity, particularly in the Houli District of Taichung City in Central Taiwan. Unexpectedly, despite comprehensive sampling of all regions with high PD incidences in Taiwan, the genetic diversity observed include contributions through recombination from unknown donors, suggesting that higher diversity exists in the region. Nevertheless, no recombination event was detected between X. fastidiosa subsp. fastidiosa and the endemic sister species Xylella taiwanensis . In summary, this study improved our understanding of the genetic diversity of PD-causing subsp. fastidiosa after invasion to a new region.\n\nGenetic differentiation ofXylella fastidiosafollowing the introduction into Taiwan", "token_count": 373, "char_count": 1622, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:26.905143", "source": { "split": "train_shard_00001", "doc_id": 3989 }, "chunk_id": "train_shard_00001_3989_0", "global_id": 11300 }, { "text": "We successfully expressed the neutral β-glucosidase (BGL4) from Scytalidium thermophilum in the thermotolerant yeast Candida glabrata. Compared to the strain expressing Aspergillus acidic β-glucosidase (BGL1), the BGL4-expressing strain showed a higher cellobiose fermentation ability at pH 6.0 and 40°C, leading to a higher ethanol production from alkaline-pretreated rice straw.\n\nExpression of neutral β-glucosidase from Scytalidium thermophilum in Candida glabrata for ethanol production from alkaline-pretreated rice straw.", "token_count": 165, "char_count": 527, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "BGL4", "BGL1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:27.350336", "source": { "split": "train_shard_00001", "doc_id": 3990 }, "chunk_id": "train_shard_00001_3990_0", "global_id": 11301 }, { "text": "Vancomycin-resistant Enterococcus faecium (VREfm) is a globally significant nosocomial pathogen with a rapidly increasing prevalence. The objectives were to investigate VREfm outbreak duration and study the additional impact that infection control bundle strategies (ICBSs) set up to curb coronavirus disease 2019 (COVID-19) spreading had on VREfm outbreaks. Outbreak data set were collected prospectively from April 2, 2014 to August 13, 2020 at Copenhagen University Hospital Bispebjerg, Denmark. All VREfm samples had polymerase chain reaction performed for vanA/vanB genes before whole genome sequencing using the Illumina MiSeq platform. The relatedness of isolates was studied by core genome multilocus sequence typing (cgMLST) using Ridom SeqSphere. Eighty-one outbreaks had a median outbreak duration of 32.5 days (range 5-204 days) and 1,161 VREfm isolates were sequenced. The same cgMLST cluster types reappeared after outbreaks were terminated. When comparing the first 5 months of the COVID-19 pandemic with the corresponding period in 2019, we found a 10-fold decrease in VREfm outbreak patients and median outbreak duration decreased from 56 to 7 days (88%). Several COVID-19 ICBSs were implemented from March 13 through summer 2020. VREfm outbreaks lasted up to 204 days, but our findings suggest that outbreaks might last longer since the same cgMLST persisted in the same wards for years implying an endemic situation with recurrent outbreaks caused by hospital reservoirs or readmittance of unknown VREfm carriers. The sharp decline in VREfm outbreaks during the COVID-19 pandemic was most likely due to the ICBSs, resulting in a decrease in VREfm transmission.", "token_count": 464, "char_count": 1700, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:27.987912", "source": { "split": "train_shard_00001", "doc_id": 3991 }, "chunk_id": "train_shard_00001_3991_0", "global_id": 11302 }, { "text": "Substantial Decrease in Vancomycin-Resistant Enterococcus faecium Outbreak Duration and Number of Patients During the Danish COVID-19 Lockdown: A Prospective Observational Study.", "token_count": 55, "char_count": 185, "word_count": 21, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:28.352479", "source": { "split": "train_shard_00001", "doc_id": 3991 }, "chunk_id": "train_shard_00001_3991_1", "global_id": 11303 }, { "text": "

Background

Probiotic strains are incorporated into food substrates to contribute to fermentation process. The technological suitability of such strains to improve the flavor and nutritional value of fermented food is strain-specific. Potentially probiotic yeasts isolated from Nigerian traditional fermented foods were assessed for production of volatile compounds by gas chromatography-mass spectrophotometry. Phytases were characterized for activity and stability at different pH (3-8) and temperatures (25-50 °C).

Results

A total of 45 volatiles compounds were identified from intracellular cell-free extracts of Pichia kluyveri LKC17, Issatchenkia orientalis OSL11, P. kudriavzevii OG32, P. kudriavzevii ROM11, and Candida tropicalis BOM21. They include alcohols (14), carbonyls (13), esters (10), and organic acids (8). Phenylethyl alcohol was the highest higher-alcohol in Issatchenkia orientalis OSL11 (27.51 %). The largest proportion of esters was detected in P. kudriavzevii OG32 (17.38 %). Pichia kudriavzevii OG32 and C. tropicalis BOM21 showed vigorous gowth in minimal medium supplemented with sodium phytate (2 g L-1). Extracellular phytases from P. kudriavzevii OG32 and Candida tropicalis BOM2 showed optimal activiy at pH 4.6 (104.28 U) and pH 3.6 (81.43 U) respectively.

Conclusions

Results obtained revealed species- and strain-specific potentials of the yeast strains to improve flavor and mineral bioavailability of fermented food products", "token_count": 489, "char_count": 1494, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8376, "entities": { "genes": [ "OSL11", "ROM11", "OG32", "BOM2", "LKC17", "BOM21" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:29.002457", "source": { "split": "train_shard_00001", "doc_id": 3992 }, "chunk_id": "train_shard_00001_3992_0", "global_id": 11304 }, { "text": "Therefore, the application of these yeasts as starter cultures during food fermentation process is a very promising method to enhance the flavor profile and enhance mineral bioavailability in indigenous cereal-based fermented food products.\n\nProduction and characterization of volatile compounds and phytase from potentially probiotic yeasts isolated from traditional fermented cereal foods in Nigeria.", "token_count": 81, "char_count": 402, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8113, "quality_score": 0.9057, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:29.374710", "source": { "split": "train_shard_00001", "doc_id": 3992 }, "chunk_id": "train_shard_00001_3992_1", "global_id": 11305 }, { "text": "

Background

Improving probiotic engraftment in the human gut requires a thorough understanding of the in vivo adaptive strategies of probiotics in diverse contexts. However, for most probiotic strains, these in vivo genetic processes are still poorly characterized. Here, we investigated the effects of gut selection pressures from human, mice, and zebrafish on the genetic stability of a candidate probiotic Lactiplantibacillus plantarum HNU082 (Lp082) as well as its ecological and evolutionary impacts on the indigenous gut microbiota using shotgun metagenomic sequencing in combination with isolate resequencing methods.

Results

We combined both metagenomics and isolate whole genome sequencing approaches to systematically study the gut-adaptive evolution of probiotic L. plantarum and the ecological and evolutionary changes of resident gut microbiomes in response to probiotic ingestion in multiple host species. Independent of host model, Lp082 colonized and adapted to the gut by acquiring highly consistent single-nucleotide mutations, which primarily modulated carbohydrate utilization and acid tolerance. We cultivated the probiotic mutants and validated that these gut-adapted mutations were genetically stable for at least 3 months and improved their fitness in vitro. In turn, resident gut microbial strains, especially competing strains with Lp082 (e.g., Bacteroides spp. and Bifidobacterium spp.), actively responded to Lp082 engraftment by accumulating 10-70 times more evolutionary changes than usual. Human gut microbiota exhibited a higher ecological and genetic stability than that of mice.

Conclusions

Collectively, our results suggest a highly convergent adaptation strategy of Lp082 across three different host environments. In contrast, the evolutionary changes within the resident gut microbes in response to Lp082 were more divergent and host-specific; however, these changes were not associated with any adverse outcomes. This work lays a theoretical foundation for leveraging animal models for ex vivo engineering of probiotics to improve engraftment outcomes in humans. Video abstract.", "token_count": 515, "char_count": 2137, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6119, "quality_score": 0.8059, "entities": { "genes": [ "HNU082" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:30.006108", "source": { "split": "train_shard_00001", "doc_id": 3993 }, "chunk_id": "train_shard_00001_3993_0", "global_id": 11306 }, { "text": "Candidate probiotic Lactiplantibacillus plantarum HNU082 rapidly and convergently evolves within human, mice, and zebrafish gut but differentially influences the resident microbiome.", "token_count": 49, "char_count": 182, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [ "HNU082" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:30.372136", "source": { "split": "train_shard_00001", "doc_id": 3993 }, "chunk_id": "train_shard_00001_3993_1", "global_id": 11307 }, { "text": "Xanthomonas perforans is the predominant pathogen responsible for bacterial leaf spot of tomato and X. euvesicatoria for that of pepper in the southeast United States. Previous studies have indicated significant changes in the X. perforans population collected from Florida tomato fields over the span of 2 decades, including a shift in race and diversification into three phylogenetic groups driven by genome-wide homologous-recombination events derived from X. euvesicatoria In our sampling of Xanthomonas strains associated with bacterial spot disease in Alabama, we were readily able to isolate X. perforans from symptomatic pepper plants grown in several Alabama counties, indicating a recent shift in the host range of the pathogen. To investigate the diversity of these pepper-pathogenic strains and their relation to populations associated with tomatoes grown in the southeast United States, we sequenced the genomes of eight X. perforans strains isolated from tomatoes and peppers grown in Alabama and compared them with previously published genome data available from GenBank. Surprisingly, reconstruction of the X. perforans core genome revealed the presence of two novel genetic groups in Alabama that each harbored a different transcription activation-like effector (TALE). While one TALE, AvrHah1, was associated with an emergent lineage pathogenic to both tomato and pepper, the other was identified as a new class within the AvrBs3 family, here designated PthXp1, and was associated with enhanced symptom development on tomato. Examination of patterns of homologous recombination across the larger X. euvesicatoria species complex revealed a dynamic pattern of gene flow, with multiple donors of Xanthomonas spp. associated with diverse hosts of isolation.IMPORTANCE Bacterial leaf spot of tomato and pepper is an endemic plant disease with a global distribution. In this study, we investigated the evolutionary processes leading to the emergence of novel X. perforans lineages identified in Alabama", "token_count": 514, "char_count": 2099, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5836, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:31.046018", "source": { "split": "train_shard_00001", "doc_id": 3994 }, "chunk_id": "train_shard_00001_3994_0", "global_id": 11308 }, { "text": "While one lineage was isolated from symptomatic tomato and pepper plants, confirming the host range expansion of X. perforans, the other lineage was isolated from tomato and acquired a novel transcription activation-like effector, here designated PthXp1. Functional analysis of PthXp1 indicated that it does not induce Bs4-mediated resistance in tomato and contributes to virulence, providing an adaptive advantage to strains on tomato. Our findings also show that different phylogenetic groups of the pathogen have experienced independent recombination events originating from multiple Xanthomonas species. This suggests a continuous gene flux between related xanthomonads associated with diverse plant hosts that results in the emergence of novel pathogen lineages and associated phenotypes, including host range.\n\nIndependent Evolution with the Gene Flux Originating from Multiple Xanthomonas Species Explains Genomic Heterogeneity in Xanthomonas perforans.", "token_count": 239, "char_count": 988, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7287, "quality_score": 0.8643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:31.535561", "source": { "split": "train_shard_00001", "doc_id": 3994 }, "chunk_id": "train_shard_00001_3994_1", "global_id": 11309 }, { "text": "This study aims at obtaining a probiotic product based on viable biomass from 6 yeast strains and 2 strains of lactic bacteria used for nutrition of animals. The strains are subjected to some resistance tests, at temperature, pH, pepsin, pancreatin and biliary salts so as to make obvious their viability. Tests were done by comparison to the witness strain and respectively a protective solution based on mucin and casein. Based on the resulted viabilities 2 products are formulated. Their effect is tested by inoculating fresh rumen content and supervising the microbic balance for a period of 12 days. After the final tests, it resulted that the product Fpl (20% Saccharomyces cerevisiae 1-29, 10% Kluyveromyces marxianus R-CS, 20% Issatchenkia orientalis R-BC, 30% Lactobacillus paracasei CMGB16, 20% Enterococcus faecium GM8) was chosen because anaerobic strains were preponderant as a consequence of the tests performed with rumen.\n\nEffect of the yeast and bacteria biomass on the microbiota in the rumen.", "token_count": 286, "char_count": 1011, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.8439, "entities": { "genes": [ "CMGB16", "GM8" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:32.154876", "source": { "split": "train_shard_00001", "doc_id": 3995 }, "chunk_id": "train_shard_00001_3995_0", "global_id": 11310 }, { "text": "Random genomic DNA fragments from Kluyveromyces marxianus were cloned in order to identify chromosomal bands in pulsed field electrophoresis patterns of intergneric hybrid strains which were obtained by protoplast fusion. Molecular hybridization data indicated that the K. marxianus parental strain might be triploid, and it showed strong chromosome length polymorphism. We analyzed the karyotype of two Saccharomyces cerevisiae/K. marxianus hybrid strains (St. 1.St.46) with our DNA probes and with a Ty1 specific probe. We found indications for recombinational events which lead to the formation of hybrid chromosomal DNA molecules.\n\nMolecular probes for the detection of Kluyveromyces marxianus chromosomal DNA in electrophoretic karyotypes of intergeneric protoplast fusion products.", "token_count": 208, "char_count": 787, "word_count": 107, "semantic_coherence": 1, "information_density": 0.7103, "quality_score": 0.8551, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:32.625618", "source": { "split": "train_shard_00001", "doc_id": 3996 }, "chunk_id": "train_shard_00001_3996_0", "global_id": 11311 }, { "text": "

Importance

Klebsiella pneumoniae is a common cause of difficult-to-treat infections due to its propensity to express resistance to many antibiotics. For example, carbapenem-resistant K. pneumoniae has been named an urgent threat by the United States Centers for Disease Control and Prevention. Gastrointestinal colonization in patients with K. pneumoniae has been linked to subsequent infection, making it a key process to control in the prevention of multidrug-resistant infections. However, the bacterial factors which contribute to K. pneumoniae colonization are not well understood. Additionally, individual strains exhibit large amounts of genetic diversity, begging the question of whether some colonization factors are strain dependent. This study identifies the enteric colonization factors of three classical strains using transposon mutant screens to define a core colonization program for K. pneumoniae as well as detecting strain-to-strain differences in colonization strategies.\n\nGenome-wide screens reveal shared and strain-specific genes that facilitate enteric colonization by <i>Klebsiella pneumoniae</i>.", "token_count": 300, "char_count": 1177, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6871, "quality_score": 0.8435, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:33.192512", "source": { "split": "train_shard_00001", "doc_id": 3997 }, "chunk_id": "train_shard_00001_3997_0", "global_id": 11312 }, { "text": "The availability of multiple wheat genome sequences enables us to identify core genes and characterize their genetic and epigenetic features, thereby advancing our understanding of their biological implications within individual plant species. It is, however, largely understudied in wheat. To this end, we reanalyzed genome sequences from 16 different wheat varieties and identified 62,299 core genes. We found that core and non-core genes have different roles in subgenome differentiation. Meanwhile, according to their expression profiles, these core genes can be classified into genes related to tissue development and stress responses, including 3376 genes highly expressed in both spikelets and at high temperatures. After associating with six histone marks and open chromatin, we found that these core genes can be divided into eight sub-clusters with distinct epigenomic features. Furthermore, we found that ca. 51% of the expressed transcription factors (TFs) were marked with both H3K27me3 and H3K4me3, indicative of the bivalency feature, which can be involved in tissue development through the TF-centered regulatory network. Thus, our study provides a valuable resource for the functional characterization of core genes in stress responses and tissue development in wheat.\n\nCharacterization of Expression and Epigenetic Features of Core Genes in Common Wheat.", "token_count": 288, "char_count": 1372, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6193, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:33.750693", "source": { "split": "train_shard_00001", "doc_id": 3998 }, "chunk_id": "train_shard_00001_3998_0", "global_id": 11313 }, { "text": "NAD(P)H quinone oxidoreductase is a ubiquitous enzyme that is known to directly reduce quinone substrates to hydroquinones by a two-electron reaction. We report the identification of NADPH quinone oxidoreductase from Kluyveromyces marxianus (KmQOR), which reduces quinone substrates directly to hydroquinones. The KmQOR gene was sequenced, expressed in Escherichia coli, purified, and characterized. The open-reading frame of the KmQOR gene consists of 1143 nucleotides, encoding a 380 amino acid polypeptide. The nucleotide sequence of the KmQOR gene was assigned to EMBL under accession number AY040868. The M(r) that was determined by SDS-PAGE for the protein subunit was about 42 kDa, and the molecular mass of the native KmQOR was 84 kDa, as determined by column calibration, indicating that the native protein is a homodimer. The KmQOR protein efficiently reduced 1,4-benzoquinone, whereas no activities were found for menadiones and methoxyquinones. These observations, and the result of an extended sequence analysis of known NADPH quinone oxidoreductase, suggest that KmQOR possesses a different action mechanism.\n\nMolecular cloning and characterization of an NADPH quinone oxidoreductase from Kluyveromyces marxianus.", "token_count": 353, "char_count": 1227, "word_count": 173, "semantic_coherence": 1, "information_density": 0.5896, "quality_score": 0.7948, "entities": { "genes": [ "AY040868" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:34.334409", "source": { "split": "train_shard_00001", "doc_id": 3999 }, "chunk_id": "train_shard_00001_3999_0", "global_id": 11314 }, { "text": "Otomycosis, which is otitis externa caused by fungi, is common throughout the world especially in tropical and subtropical countries. However, the epidemiologic data about the etiologic agents of otomycosis in Turkey is limited. The aim of this retrospective study was to evaluate the agents of otomycosis in patients living at Manisa region (located at western Anatolia of Turkey). A total of 2279 cases [1465 male, 813 female; age range 1-87 (mean: 41.7) years] who were clinically prediagnosed as otomycosis at Celal Bayar University Hospital, between February 1995 and July 2011, were included in the study. External ear swab samples from patients with suspicion of otomycosis have been evaluated by routine mycological methods. Identification of mold-like fungi was based on colony morphology and microscopic examination of fungal structure, whereas germ tube test, growth characteristics on cornmeal-Tween 80 agar and API 20C AUX (bio-Mérieux, France) system were used for the identification of yeast-like fungi. Of the samples, 28% (638/2279) were found positive by direct microscopy and 24% (544/2279) by culture methods. Among culture-positive cases the isolation rates of mold-like and yeast-like fungi were 66% (359/544) and 34% (185/544), respectively. The number of distribution of the molds were as follows; Aspergillus niger (180), Aspergillus fumigatus (95), Aspergillus terreus (32), Aspergillus flavus (23), Aspergillus spp. (14), Penicillium spp. (13), Trichophyton spp", "token_count": 458, "char_count": 1488, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:34.972398", "source": { "split": "train_shard_00001", "doc_id": 4000 }, "chunk_id": "train_shard_00001_4000_0", "global_id": 11315 }, { "text": "(T.rubrum 1, T.mentagrophytes 1); while this distribution was as follows for the yeasts; Candida tropicalis (97), Candida albicans (39), Candida parapsilosis (21), Candida glabrata (19), Candida kefyr (4), C.guilliermondii (2), Candida krusei (1), Geotrichum candidum (1) and Trichosporon capitatum (1). It was notable that 96% (344/359) of mold-like fungi were Aspergillus spp., and 99% (183/185) of yeast-like fungi were Candida spp. The results of this study indicated that the most frequent agents of otomycosis were non-dermatophyte species such as Aspergillus, followed by Candida. Dermatophytes were isolated in a small number of otomycosis cases. These data will provide support to the establishment of antifungal therapy guidelines for otomycosis.\n\n[Agents of otomycosis in Manisa region, Turkey, 1995-2011].", "token_count": 279, "char_count": 817, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7565, "quality_score": 0.8783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:35.524307", "source": { "split": "train_shard_00001", "doc_id": 4000 }, "chunk_id": "train_shard_00001_4000_1", "global_id": 11316 }, { "text": "

Objectives

Carbapenemase-producing Enterobacterales (CPE) have spread widely into health care facilities (HCF) but clusters caused by carbapenemase-producing (CP) Citrobacter freundii have been uncommon until recent years. Here we describe CP C. freundii clusters detected in Finland during 2016-20.

Methods

As a part of the national CPE surveillance, clinical microbiology laboratories send potential CP C. freundii isolates to the reference laboratory for confirmation and further characterization. Whole genome sequencing (WGS) with Illumina MiSeq sequencer was used to detect clusters. Resistance genes and STs were analysed using SRST2 and typing with core genome (cg) MLST. A case was defined as a patient with a CP C. freundii isolate belonging to one of the detected clusters.

Results

We detected three CP C. freundii clusters: cluster 1 included 16 cases in five HCFs during 2016-20, cluster 2 had two cases in two HCFs during 2018-19 and cluster 3 had two cases in one HCF in 2020. The isolates (11 clinical and 5 screening) in cluster 1 had KPC-2 carbapenemase and were sequence type (ST)18. Cluster 2 (2 clinical isolates) had OXA-181/GES-5 carbapenemases and were ST604 and cluster 3 (two screening isolates) had KPC-3 carbapenemase and were ST116. None of the cases had a history of recent travel abroad.

Conclusions

CP C. freundii also causes outbreaks and can be a reservoir of carbapenemase genes. The long intervals between successive cases, mostly found in clinical specimens in two clusters, suggest that besides unknown carriers, environmental contamination may play a role in transmission.\n\nThree clusters of carbapenemase-producing Citrobacter freundii in Finland, 2016-20.", "token_count": 500, "char_count": 1725, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8085, "entities": { "genes": [ "SRST2", "ST604", "ST116" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:36.551514", "source": { "split": "train_shard_00001", "doc_id": 4001 }, "chunk_id": "train_shard_00001_4001_0", "global_id": 11317 }, { "text": "Along with affecting oral health, oral microbial communities may also be endogenously translocated to the gut, thereby mediating the development of a range of malignancies in that habitat. While species-level studies have proven the capability of oral pathogens to migrate to the intestine, genetic evidence supporting this mechanism remains insufficient. In this study, we identified over 55,000 oral translocation genes (OTGs) associated with colorectal cancer (CRC) and inflammatory bowel disease (IBD). These genes are primarily involved in signal transduction and cell wall biosynthesis and show consistency in their functions between IBD and CRC. Furthermore, we found that Leclercia adecarboxylata, a newly discovered opportunistic pathogen, has a significantly high abundance in the gut microbiota of colorectal cancer patients. OTGs of this pathogen were enriched in 15 metabolic pathways, including those associated with amino acid and cofactor metabolism. These findings, for the first time, provide evidence at the genetic level of the transfer of oral pathogens to the intestine and offer new insights into the understanding of the roles of oral pathogens in the development of gastrointestinal cancers.\n\nOral Microbial Translocation Genes in Gastrointestinal Cancers: Insights from Metagenomic Analysis.", "token_count": 313, "char_count": 1324, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6578, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:37.112160", "source": { "split": "train_shard_00001", "doc_id": 4002 }, "chunk_id": "train_shard_00001_4002_0", "global_id": 11318 }, { "text": "Pseudomonas corrugata constitute one of the phylogenomic subgroups within the Pseudomonas fluorescens species complex and include both plant growth-promoting rhizobacteria (PGPR) and plant pathogenic bacteria. Previous studies suggest that the species diversity of this group remains largely unexplored together with frequent misclassification of strains. Using more than 1800 sequenced Pseudomonas genomes we identified 121 genomes belonging to the P. corrugata subgroup. Intergenomic distances obtained using the genome-to-genome blast distance (GBDP) algorithm and the determination of digital DNA-DNA hybridization values were further used for phylogenomic and clustering analyses, which revealed 29 putative species clusters, of which only five correspond to currently named species within the subgroup. Comparative and functional genome-scale analyses also support the species status of these clusters. The search for PGPR and plant pathogenic determinants showed that approximately half of the genomes analysed could have a pathogenic behaviour based on the presence of a pathogenicity genetic island, while all analysed genomes possess PGPR traits. Finally, this information together with the characterization of phenotypic traits, allows the reclassification proposal of Pseudomonas fluorescens F113 as Pseudomonas ogarae sp. nov., nom rev., type strain F113T (=DSM 112162T=CECT 30235T), which is substantiated by genomic, functional genomics and phenotypic differences with their closest type strains.\n\nComparative genomics of the Pseudomonas corrugata subgroup reveals high species diversity and allows the description of Pseudomonas ogarae sp. nov.", "token_count": 467, "char_count": 1749, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:37.755362", "source": { "split": "train_shard_00001", "doc_id": 4003 }, "chunk_id": "train_shard_00001_4003_0", "global_id": 11319 }, { "text": "Listeria monocytogenes, a foodborne pathogen, and other Listeria spp. are present in natural environments. Isolating and characterizing strains from natural reservoirs can provide insight into the prevalence and diversity of Listeria spp. in these environments, elucidate their contribution to contamination of agricultural and food processing environments and food products, and lead to the discovery of novel species. In this study, we evaluated the diversity of Listeria spp. isolated from soil in a small region of the Great Smoky Mountains National Park, the most biodiverse national park in the U.S. National Park system. Of the 17 Listeria isolates recovered, whole-genome sequencing revealed that 14 were distinct strains. The strains represented a diversity of Listeria species (L. monocytogenes [n = 9], L. cossartiae subsp. cossartiae [n = 1], L. marthii [n = 1], L. booriae [n = 1], and a potentially novel Listeria sp. [n = 2]), as well as a diversity of sequence types based on multilocus sequence typing (MLST) and core genome MLST, including many novel designations. The isolates were not closely related (≥99.99% average nucleotide identity) to any isolates in public databases (NCBI, PATRIC), which also indicated novelty. The Listeria samples isolated in this study were collected from high-elevation sites near a creek that ultimately leads to the Mississippi River; thus, Listeria present in this natural environment could potentially travel downstream to a large region that includes portions of nine southeastern and midwestern U.S. states. This study provides insight into the diversity of Listeria spp", "token_count": 519, "char_count": 1731, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5894, "quality_score": 0.7947, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:38.418155", "source": { "split": "train_shard_00001", "doc_id": 4004 }, "chunk_id": "train_shard_00001_4004_0", "global_id": 11320 }, { "text": "in the Great Smoky Mountains and indicates that this environment is a reservoir of novel Listeria spp. IMPORTANCE Listeria monocytogenes is a foodborne pathogen that can cause serious systemic illness that, although rare, usually results in hospitalization and has a relatively high mortality rate compared to other foodborne pathogens. Identification of novel and diverse Listeria spp. can provide insights into the genomic evolution, ecology, and evolution and variance of pathogenicity of this genus, especially in natural environments. Comparing L. monocytogenes and Listeria spp. isolates from natural environments, such as those recovered in this study, to contamination and/or outbreak strains may provide more information about the original natural sources of these strains and the pathways and mechanisms that lead to contamination of food products and agricultural or food processing environments.\n\nSoil Collected from a Single Great Smoky Mountains Trail Contains a Diversity of Listeria monocytogenes and Listeria spp.", "token_count": 255, "char_count": 1065, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6259, "quality_score": 0.8129, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:38.906048", "source": { "split": "train_shard_00001", "doc_id": 4004 }, "chunk_id": "train_shard_00001_4004_1", "global_id": 11321 }, { "text": "Aim: Carbapenemase-resistant Enterobacteriaceae represents a major concern in hospital setting. Materials & methods: The evolutionary history of carbapenem-resistant Klebsiella pneumonia strains was analyzed by core genome multilocus sequence typing and Bayesian phylogenesis by whole genomes sequencing. Results: A great increase carbapenem-resistant K.pneumoniae causing blood stream infection was observed in the years 2015-2016. At multilocus sequence typing (MLST), they were prevalently ST512 and ST101. ST512 were core genome (cg)MLST 53, while ST101 mainly cgMLST453. The minimum-spanning tree, based on cgMLST, showed strains clustering based on the different STs. By Bayesian phylogenetic analysis, maximum clade credibility tree showed that strains were introduced in the year 2005 with the most probable location in the ICU ward. Two outbreaks by ST101 and ST512 strains with Tower T8 as the probable location were evidenced. Conclusion: Molecular epidemiology is a powerful tool to track the way of transmission of resistant bacteria within the hospital setting.\n\nWhole genome sequencing of carbapenem-resistant Klebsiella pneumoniae: evolutionary analysis for outbreak investigation.", "token_count": 375, "char_count": 1260, "word_count": 161, "semantic_coherence": 1, "information_density": 0.677, "quality_score": 0.8385, "entities": { "genes": [ "ST512", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:39.490438", "source": { "split": "train_shard_00001", "doc_id": 4005 }, "chunk_id": "train_shard_00001_4005_0", "global_id": 11322 }, { "text": "Finding strategies for decolonizing gut carriers of multidrug-resistant Escherichia coli (MDR-Ec) is a public-health priority. In this context, novel approaches should be validated in preclinical in vivo gut colonization models before being translated to humans. However, the use of mice presents limitations. Here, we used for the first time Zophobas morio larvae to design a new model of intestinal colonization (28-days duration, T28). Three hyperepidemic MDR-Ec producing extended-spectrum β-lactamases (ESBLs) or carbapenemases were administered via contaminated food to larvae for the first 7 days (T7): Ec-4901.28 (ST131, CTX-M-15), Ec-042 (ST410, OXA-181) and Ec-050 (ST167, NDM-5). Growth curve analyses showed that larvae became rapidly colonized with all strains (T7, ~106-7 CFU/mL), but bacterial load remained high after the removal of contaminated food only in Ec-4901.28 and Ec-042 (T28, ~103-4 CFU/mL)", "token_count": 394, "char_count": 1009, "word_count": 129, "semantic_coherence": 1, "information_density": 0.8217, "quality_score": 0.9109, "entities": { "genes": [ "ST131", "ST410", "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:40.109859", "source": { "split": "train_shard_00001", "doc_id": 4006 }, "chunk_id": "train_shard_00001_4006_0", "global_id": 11323 }, { "text": "Moreover, larvae receiving a force-feeding treatment with INTESTI bacteriophage cocktail (on T7 and T10 via gauge needle) were decolonized by Ec-4901.28 (INTESTI-susceptible); however, Ec-042 and Ec-050 (INTESTI-resistant) did not. Initial microbiota (before administering contaminated food) was very rich of bacterial genera (e.g., Lactococcus, Enterococcus, Spiroplasma), but patterns were heterogeneous (Shannon diversity index: range 1.1-2.7) and diverse to each other (Bray-Curtis dissimilarity index ≥30%). However, when larvae were challenged with the MDR-Ec with or without administering bacteriophages the microbiota showed a non-significant reduction of the diversity during the 28-day experiments. In conclusion, the Z. morio larvae model promises to be a feasible and high-throughput approach to study novel gut decolonization strategies for MDR-Ec reducing the number of subsequent confirmatory mammalian experiments.\n\nA new in vivo model of intestinal colonization using Zophobas morio larvae: testing hyperepidemic ESBL- and carbapenemase-producing Escherichia coli clones.", "token_count": 410, "char_count": 1186, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7786, "quality_score": 0.8893, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:40.731665", "source": { "split": "train_shard_00001", "doc_id": 4006 }, "chunk_id": "train_shard_00001_4006_1", "global_id": 11324 }, { "text": "

Background

Musa beccarii (Musaceae) is a banana species native to Borneo, sometimes grown as an ornamental plant. The basic chromosome number of Musa species is x = 7, 10, or 11; however, M. beccarii has a basic chromosome number of x = 9 (2n = 2x = 18), which is the same basic chromosome number of species in the sister genera Ensete and Musella. Musa beccarii is in the section Callimusa, which is sister to the section Musa. We generated a high-quality chromosome-scale genome assembly of M. beccarii to better understand the evolution and diversity of genomes within the family Musaceae.

Findings

The M. beccarii genome was assembled by long-read and Hi-C sequencing, and genes were annotated using both long Iso-seq and short RNA-seq reads. The size of M. beccarii was the largest among all known Musaceae assemblies (∼570 Mbp) due to the expansion of transposable elements and increased 45S ribosomal DNA sites. By synteny analysis, we detected extensive genome-wide chromosome fusions and fissions between M. beccarii and the other Musa and Ensete species, far beyond those expected from differences in chromosome number. Within Musaceae, M. beccarii showed a reduced number of terpenoid synthase genes, which are related to chemical defense, and enrichment in lipid metabolism genes linked to the physical defense of the cell wall. Furthermore, type III polyketide synthase was the most abundant biosynthetic gene cluster (BGC) in M. beccarii. BGCs were not conserved in Musaceae genomes.

Conclusions

The genome assembly of M. beccarii is the first chromosome-scale genome assembly in the Callimusa section in Musa, which provides an important genetic resource that aids our understanding of the evolution of Musaceae genomes and enhances our knowledge of the pangenome.", "token_count": 500, "char_count": 1801, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5725, "quality_score": 0.7862, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:41.388078", "source": { "split": "train_shard_00001", "doc_id": 4007 }, "chunk_id": "train_shard_00001_4007_0", "global_id": 11325 }, { "text": "Genome assembly of Musa beccarii shows extensive chromosomal rearrangements and genome expansion during evolution of Musaceae genomes.", "token_count": 32, "char_count": 134, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:41.744859", "source": { "split": "train_shard_00001", "doc_id": 4007 }, "chunk_id": "train_shard_00001_4007_1", "global_id": 11326 }, { "text": "Abstract

Background

The global spread of methicillin-resistant Staphylococcus aureus (MRSA) is associated with distinct genetic lineages that predominate in specific geographical regions. Available evidence suggests the Chilean-Cordobes clone (ChC), an ST5-SCCmecI lineage, has largely predominated in Chilean hospitals since its first description in the late 1990’s. Although the circulation of other MRSA lineages, including community-associated clones, has been well documented, the dynamics of clonal replacement over time has not been explored. Therefore, we aimed to study the molecular epidemiology and dynamics of clonal replacement using a large collection of clinical MRSA strains recovered from Chile during the last two decades.

Methods

We used whole-genome sequencing (WGS) and core-based phylogenomic analysis to identify genetic lineages and explore their relationship in 798 MRSA isolates obtained between 1999-2018 from two tertiary-care Chilean hospitals.

Results

Overall, the most frequently identified clones were the ST5-SCCmecI ChC (n=476, 60%), followed by ST105-SCCmecII (n=119, 15%), ST72-SCCmecIV (n=74, 9%), and ST8-SCCmecII (n=26, 3%). Phylogenomic reconstruction demonstrated 7 major clades: Clade I (CC30); Clade II (CC22); Clade III (CC97); Clade IV (CC8); Clade V (ST72); Clade VI (CC5/ST225 and ST105) and Clade VII (CC5/ST5-SCCmecI) (Fig. 1). The ChC clone remained the most frequent MRSA lineage throughout the study period (Fig. 2). However, its relative abundance decreased from >90% of isolates in 1999 to ca. 40% in 2018", "token_count": 499, "char_count": 1586, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7294, "quality_score": 0.8647, "entities": { "genes": [ "ST72", "CC22", "ST105", "CC8", "CC97", "ST5", "ST225", "CC5", "CC30", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:42.403526", "source": { "split": "train_shard_00001", "doc_id": 4008 }, "chunk_id": "train_shard_00001_4008_0", "global_id": 11327 }, { "text": "This decrease began around 2005 and was associated with a progressive expansion of the ST105-SCCmecII and ST72-SCCmecIV lineages (Fig. 2). A Bayesian molecular clock analysis established the most recent common ancestor in 1964 (95% HPD interval=1961.975-1966.218) and corroborated a CC5 expansion event starting in Chile in 1999 (Fig. 3). Interestingly, our analyses revealed two branches within the ST5-SCCmecI lineage: one predominating in 1999-2006, and a more recent branch (related to the ST105-SCCmecII clone) that emerged around 2008. Figure 1. Core genome phylogenomic reconstruction of the 798 MRSA isolates. The seven major clades are represented by colored sections. The Clade I (purple section) was composed of isolates belonging to the CC30. Clade II (cyan section) includes four isolates of CC22. Clade III (red section) is composed of isolates of CC97. Clade IV (blue section) grouped isolates of different ST239 and ST8, belonging to the CC8. Clade V (orange section) includes isolates of ST72. Clade VI (yellow section) includes isolates of ST225 and ST105, both belonging to CC5. Clade VII (green section) is mostly composed of isolates of ST5-SCCmecI. The inner ring shows the ST of the isolates; the external ring shows the staphylococcal chromosomal cassette mec (SCCmec) type. Figure 2. Relative frequency of MRSA clones from 1999 to 2018. The genomes were grouped according to their isolation dates. Most frequent MRSA clones are represented by colored sections. Figure 3. Maximum clade credibility tree from the molecular clock analysis of the 798 MRSA genomes. A Bayesian molecular clock analysis was performed with BEAST using the isolation date of each genome as a calibrator. The colored strip showed the most frequent clones. The red dot shows a major event of divergence in 2008", "token_count": 534, "char_count": 1808, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5643, "quality_score": 0.7821, "entities": { "genes": [ "ST72", "CC22", "ST105", "ST239", "CC8", "CC97", "ST5", "ST225", "CC5", "CC30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:43.082528", "source": { "split": "train_shard_00001", "doc_id": 4008 }, "chunk_id": "train_shard_00001_4008_1", "global_id": 11328 }, { "text": "

Conclusion

The ChC clone remains the most prevalent MRSA in Chile. However, our data is consistent with the evolution of this clone and a progressive replacement of with ST105 and ST72 genetic lineages.

Disclosures

Lorena Diaz, PhD , Nothing to disclose Cesar A. Arias, M.D., MSc, Ph.D., FIDSA, Entasis Therapeutics (Grant/Research Support)MeMed Diagnostics (Grant/Research Support)Merk (Grant/Research Support)\n\n666. Molecular Epidemiology of Methicillin-Resistant Staphylococcus aureus in Chile between 1999-2018", "token_count": 178, "char_count": 532, "word_count": 68, "semantic_coherence": 1, "information_density": 0.8529, "quality_score": 0.9265, "entities": { "genes": [ "ST105", "ST72" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:43.540108", "source": { "split": "train_shard_00001", "doc_id": 4008 }, "chunk_id": "train_shard_00001_4008_2", "global_id": 11329 }, { "text": "

Introduction

Drug resistance (DR) of pathogens remains a global healthcare concern. In contrast to other bacteria, acquiring mutations in the core genome is the main mechanism of drug resistance for Mycobacterium tuberculosis (MTB). For some antibiotics, the resistance of a particular isolate can be reliably predicted by identifying specific mutations, while for other antibiotics the knowledge of resistance mechanisms is limited. Statistical machine learning (ML) methods are used to infer new genes implicated in drug resistance leveraging large collections of isolates with known whole-genome sequences and phenotypic states for different drugs. However, high correlations between the phenotypic states for commonly used drugs complicate the inference of true associations of mutations with drug phenotypes by ML approaches.

Methods

Recently, several new methods have been developed to select a small subset of reliable predictors of the dependent variable, which may help reduce the number of spurious associations identified. In this study, we evaluated several such methods, namely, logistic regression with different regularization penalty functions, a recently introduced algorithm for solving the best-subset selection problem (ABESS) and \"Hungry, Hungry SNPos\" (HHS) a heuristic algorithm specifically developed to identify resistance-associated genetic variants in the presence of resistance co-occurrence. We assessed their ability to select known causal mutations for resistance to a specific drug while avoiding the selection of mutations in genes associated with resistance to other drugs, thus we compared selected ML models for their applicability for MTB genome wide association studies.

Results and discussion

In our analysis, ABESS significantly outperformed the other methods, selecting more relevant sets of mutations. Additionally, we demonstrated that aggregating rare mutations within protein-coding genes into markers indicative of changes in PFAM domains improved prediction quality, and these markers were predominantly selected by ABESS, suggesting their high informativeness. However, ABESS yielded lower prediction accuracy compared to logistic regression methods with regularization.\n\nFeature selection and aggregation for antibiotic resistance GWAS in <i>Mycobacterium tuberculosis</i>: a comparative study.", "token_count": 514, "char_count": 2384, "word_count": 311, "semantic_coherence": 1, "information_density": 0.6206, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:44.213627", "source": { "split": "train_shard_00001", "doc_id": 4009 }, "chunk_id": "train_shard_00001_4009_0", "global_id": 11330 }, { "text": "The widespread use and abuse of antibiotic therapy has evolutionary and ecological consequences, some of which are only just beginning to be examined. One well known consequence is the fixation of mutations and lateral gene transfer (LGT) events that confer antibiotic resistance. Sequential selection events, driven by different classes of antibiotics, have resulted in the assembly of diverse resistance determinants and mobile DNAs into novel genetic elements of ever-growing complexity and flexibility. These novel plasmids, integrons, and genomic islands have now become fixed at high frequency in diverse cell lineages by human antibiotic use. Consequently they can be regarded as xenogenetic pollutants, analogous to xenobiotic compounds, but with the critical distinction that they replicate rather than degrade when released to pollute natural environments. Antibiotics themselves must also be regarded as pollutants, since human production overwhelms natural synthesis, and a major proportion of ingested antibiotic is excreted unchanged into waste streams. Such antibiotic pollutants have non-target effects, raising the general rates of mutation, recombination, and LGT in all the microbiome, and simultaneously providing the selective force to fix such changes. This has the consequence of recruiting more genes into the resistome and mobilome, and of increasing the overlap between these two components of microbial genomes. Thus the human use and environmental release of antibiotics is having second order effects on the microbial world, because these small molecules act as drivers of bacterial evolution. Continued pollution with both xenogenetic elements and the selective agents that fix such elements in populations has potentially adverse consequences for human welfare.\n\nEvolutionary consequences of antibiotic use for the resistome, mobilome and microbial pangenome.", "token_count": 392, "char_count": 1890, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6517, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:44.833928", "source": { "split": "train_shard_00001", "doc_id": 4010 }, "chunk_id": "train_shard_00001_4010_0", "global_id": 11331 }, { "text": "Lactiplantibacillus plantarum is a widely studied species known for its probiotic properties that can help alleviate serum cholesterol levels. Whole-genome sequencing provides genetic information on probiotic attributes, metabolic activities and safety assessment. This study investigates the probiotic properties of strain CRM56-2, isolated from Thai fermented tea leaves, using Whole-Genome Sequencing (WGS) to evaluate the safety, health-promoting genes and functional analysis. Strain CRM56-2 showed bile salt hydrolase (BSH) activity, assimilated cholesterol at a rate of 75.94%, tolerated acidic and bile environments and attached to Caco-2 cells. Based on ANIb (98.9%), ANIm (99.2%), and digital DNA-DNA hybridisation (98.3%), strain CRM56-2 was identified as L. plantarum. In silico analysis revealed that it was not pathogenic and contained no antibiotic-resistance genes or plasmids. L. plantarum CRM56-2 possessed genes linked to several probiotic properties and beneficial impacts. The genome of strain CRM56-2 suggested that L. plantarum CRM56-2 is non-hazardous, with potential probiotic characteristics and beneficial impacts, which could enhance its probiotic application. Consequently, L. plantarum CRM56-2 demonstrated excellent cholesterol-lowering activity and probiotic properties.\n\nGenomic Assessment of Potential Probiotic Lactiplantibacillus plantarum CRM56-2 Isolated from Fermented Tea Leaves.", "token_count": 437, "char_count": 1468, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8343, "entities": { "genes": [ "CRM56" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:45.472275", "source": { "split": "train_shard_00001", "doc_id": 4011 }, "chunk_id": "train_shard_00001_4011_0", "global_id": 11332 }, { "text": "Ghee is widely produced from a traditional fermented butter-like product named mashita in western Uganda. However, no detailed studies have been done to identify the microorganisms involved in mashita fermentation. The aim of this study was to identify the microorganisms present at the end of mashita ripening using culture-dependent and culture-independent techniques. The most commonly identified species of lactic acid bacteria (LAB) in mashita using culture-dependent techniques were Lactobacillus paracasei, Lactobacillus helveticus, Lactobacillus plantarum and Lactobacillus perolens constituting 37.3%, 10.1%, 8.1% and 7.7% of total bacterial colonies isolated respectively. L. paracasei was the only bacterial species identified in all mashita samples by culture-dependent technique. Two of the four most commonly isolated LAB species (L. helveticus and L. plantarum) were also identified in mashita by a culture-independent method (PCR-DGGE). Other main LAB species identified in mashita by PCR-DGGE were Bifidobacterium sp., Enterococcus faecium, Lactobacillus brevis, Lactobacillus acetotolerans, Lactobacillus sp., Lactococcus raffinolactis, Lactococcus lactis subsp. lactis and Streptococcus salivarius. The main species of acetic acid bacteria (AAB) identified in the mashita using PCR-DGGE method were Acetobacter aceti, Acetobacter lovaniensis, Acetobacter orientalis and Acetobacter pasteurianus. PCR-DGGE identification of yeasts showed that Brettanomyces custersianus, Candida silvae, Geotrichum sp., Issatchenkia occidentalis, Issatchenkia orientalis, Kluyveromyces marxianus, Saccharomyces cerevisiae, and Trichosporon asahii were main yeast species in mashita. A. lovaniensis, A. aceti, and I", "token_count": 510, "char_count": 1715, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5853, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:46.140230", "source": { "split": "train_shard_00001", "doc_id": 4012 }, "chunk_id": "train_shard_00001_4012_0", "global_id": 11333 }, { "text": "orientalis were identified in all the six mashita samples analyzed using PCR-DGGE method. Other microbial species were only found in some samples. These results indicate that LAB and yeasts, as in similar fermentation products, but also AAB are main microbial groups involved in mashita fermentation.\n\nMain microorganisms involved in the fermentation of Ugandan ghee.", "token_count": 92, "char_count": 367, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7963, "quality_score": 0.8981, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:46.539686", "source": { "split": "train_shard_00001", "doc_id": 4012 }, "chunk_id": "train_shard_00001_4012_1", "global_id": 11334 }, { "text": "

Objectives

To describe the prevalence of poxtA among clinical linezolid-resistant enterococci (LRE) collected in France from 2016 to 2020 and to extensively characterize its genetic supports and environments.

Methods

All LRE clinical isolates received at the National Reference Centre for Enterococci from French hospitals between 2016 and 2020 were included. LRE isolates were screened for linezolid resistance genes (cfr-like, optrA and poxtA) by real-time PCR and phenotypically characterized. A collection of 11 representative poxtA-positive isolates (10 Enterococcus faecium and 1 Enterococcus faecalis) underwent WGS by hybrid assembly combining short-read (Illumina MiSeq) and long-read (MinION) approaches. Transferability of poxtA was attempted by filter-mating experiments.

Results

Out of 466 LRE received at the National Reference Centre for Enterococci over the period, 47 (10.1%) were poxtA-positive, including 42 E. faecium. The 11 isolates characterized by WGS were confirmed to be epidemiologically unrelated by core genome analysis and eight different STs were assigned to E. faecium isolates. The poxtA gene was found to be plasmid carried and flanked by IS1216E transposase genes in all isolates and frequently linked with fexB, tet(M) and tet(L). A total of seven distinct poxtA-harbouring plasmids were obtained after hybrid assembly and plasmid transfer of poxtA was successful in three cases. For the two poxtA/optrA-positive isolates, those genes were carried by different plasmids.

Conclusions

The poxtA gene has been circulating among clinical enterococci in France since at least 2016, mostly in E. faecium and independently from optrA", "token_count": 482, "char_count": 1691, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5957, "quality_score": 0.7978, "entities": { "genes": [ "IS1216E" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:47.188063", "source": { "split": "train_shard_00001", "doc_id": 4013 }, "chunk_id": "train_shard_00001_4013_0", "global_id": 11335 }, { "text": "The poxtA-carrying plasmids often co-carried resistance genes to phenicols and tetracyclines, and could have been co-selected through their veterinary use.\n\nGenetic features of the poxtA linezolid resistance gene in human enterococci from France.", "token_count": 65, "char_count": 246, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:47.555907", "source": { "split": "train_shard_00001", "doc_id": 4013 }, "chunk_id": "train_shard_00001_4013_1", "global_id": 11336 }, { "text": "What is the highest possible replication rate for living organisms? The cellular growth rate is controlled by a variety of processes. Therefore, it is unclear which metabolic process or group of processes should be activated to increase growth rate. An organism that is already growing fast may already have optimized through evolution all processes that could be optimized readily, but may be confronted with a more generic limitation. Here we introduce a method called 'cell selection' to select for highest growth rate, and show how such a cellular site of 'growth control' was identified. By applying pH-auxostat cultivation to the already fast-growing yeast Kluyveromyces marxianus for a sufficiently long time, we selected a strain with a 30% increased growth rate; its cell-cycle time decreased to 52 min, much below that reported to date for any eukaryote. The increase in growth rate was accompanied by a 40% increase in cell surface at a fairly constant cell volume. We show how the increase in growth rate can be explained by a dominant (80%) limitation of growth by the group of membrane processes (a 0.7% increase of specific growth rate to a 1% increase in membrane surface area). Simultaneous activation of membrane processes may be what is required to accelerate growth of the fastest-growing form of eukaryotic life to growth rates that are even faster, and may be of potential interest for single-cell protein production in industrial 'White' biotechnology processes.\n\nSuper life--how and why 'cell selection' leads to the fastest-growing eukaryote.", "token_count": 353, "char_count": 1567, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5726, "quality_score": 0.7863, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:48.134858", "source": { "split": "train_shard_00001", "doc_id": 4014 }, "chunk_id": "train_shard_00001_4014_0", "global_id": 11337 }, { "text": "The bulk of higher order organismal genomes is comprised of transposable element (TE) copies, i.e. genetic parasites. The host-parasite relation is multi-faceted, varying across genomic region (genic versus intergenic), life-cycle stages, tissue-type and of course in health versus pathological state. The reach of functional genomics though, in investigating genotype-to-phenotype relations, has been limited when TEs are involved. The aim of this review is to highlight recent progress made in understanding how TE origin biochemical activity interacts with the central dogma stages of the host genome. Such interaction can also bring about modulation of the immune context and this could have important repercussions in disease state where immunity has a role to play. Thus, the review is to instigate ideas and action points around identifying evolutionary adaptations that the host genome and the genetic parasite have evolved and why they could be relevant.\n\nRecent insights into crosstalk between genetic parasites and their host genome.", "token_count": 230, "char_count": 1044, "word_count": 153, "semantic_coherence": 1, "information_density": 0.7386, "quality_score": 0.8693, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:48.609374", "source": { "split": "train_shard_00001", "doc_id": 4015 }, "chunk_id": "train_shard_00001_4015_0", "global_id": 11338 }, { "text": "A 23.5-fold purified exoinulinase with a specific activity of 413 IU/mg and covalently immobilized on Duolite A568 has been used for the development of a continuous flow immobilized enzyme reactor for the hydrolysis of inulin. In a packed bed reactor containing 72 IU of exoinulinase from Kluyveromyces marxianus YS-1, inulin solution (5%, pH 5.5) with a flow rate of 4 mL/h was completely hydrolyzed at 55 degrees C. The reactor was run continuously for 75 days and its experimental half-life was 72 days under the optimized operational conditions. The volumetric productivity and fructose yield of the reactor were 44.5 g reducing sugars/L/h and 53.3 g/L, respectively. The hydrolyzed product was a mixture of fructose (95.8%) and glucose (4.2%) having an average fructose/glucose ratio of 24. An attempt has also been made to substitute pure inulin with raw Asparagus racemosus inulin to determine the operational stability of the developed reactor. The system remained operational only for 11 days, where 85.9% hydrolysis of raw inulin was achieved.\n\nDevelopment of a stable continuous flow immobilized enzyme reactor for the hydrolysis of inulin.", "token_count": 339, "char_count": 1151, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8045, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:49.186261", "source": { "split": "train_shard_00001", "doc_id": 4016 }, "chunk_id": "train_shard_00001_4016_0", "global_id": 11339 }, { "text": "Leptospira is a zoonotic pathogen causing significant morbidity and mortality both in animals and humans. Although several surface proteins have been identified as vaccine candidate, they failed to induce sterilizing immunity and cross protection against different serovars. Thus, identification of highly immunogenic antigens that are conserved among pathogenic serovars would be first step towards development of universal vaccine for Leptospirosis. Here we used reverse vaccinology pipeline to screen core genome of pathogenic Leptospira spp.in order to identify suitable vaccine candidates. Based on properties like sub cellular localization, adhesin, homology to human proteins, antigenicity and allergenicity, 18 antigenic proteins were identified and were further investigated for immunological properties. Based on immunogenicity, Protegenicity, Antigenicity, B-cell and promiscuous T-cell epitopes, 6 Potential Vaccine Candidates (PVCs) were finally selected which covered most of the affected world population. For designing a Multi-Epitope Vaccine (MEV), 6 B-cell and 6 promiscuous MHC-I and MHC-II epitopes from each candidate were clustered with linkers in between and stitched along with a TLR4 adjuvant (APPHALS) at the N-terminal to form a construct of 361 amino acids. The physiochemical properties, secondary and tertiary structure analysis revealed that MEV was highly stable. Molecular docking analysis revealed the deep binding interactions of the MEV construct within the grooves of human TLR4 (4G8A). In-silico codon optimization and cloning of the vaccine construct assured good expression. Further, immune simulations have shown that MEV could induce strong and diverse B and T cell responses. Taken together our results indicate that the designed MEV could be a promising subunit vaccine candidate against Leptospirosis, however it requires experimental validation.\n\nDesigning of multiepitope-based vaccine against Leptospirosis using Immuno-Informatics approaches", "token_count": 477, "char_count": 1990, "word_count": 270, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:49.837959", "source": { "split": "train_shard_00001", "doc_id": 4017 }, "chunk_id": "train_shard_00001_4017_0", "global_id": 11340 }, { "text": "PURPOSE: A quinone oxidoreductase gene from Kluyveromyces marxianus is provided to be used for the reduction reaction of the quinone compounds and for the intermediate synthesis of the biologically active compounds by way of the excellent quinone reduction activity thereof. CONSTITUTION: A gene codes the amino acid sequence of Kluyveromyces marxianus quinone oxidoreductase(kmQOR) presented at the sequence No. 2. The kmQOR has a molecular weight of about 42kDa. A recombinant vector contains the gene coded with the kmQOR, and is determined to be plasmid pQOR22b. An E. coli is transformed into the recombinant vector. In a method of preparing the kmQOR, the transformed E. coli is first cultured, and [beta]-D-isopropyl-D-thiogalactopyranoside (IPTG) is then added to the cultured E. coli to induce the expression of kmQOR therefrom. The expressed kmQOR is collected, and purified.\n\nQUINONE OXIDOREDUCTASE GENE FROM KLUYVEROMYCES MARXIANUS AND PROTEIN EXPRESSED THEREFROM", "token_count": 299, "char_count": 975, "word_count": 143, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:50.409147", "source": { "split": "train_shard_00001", "doc_id": 4018 }, "chunk_id": "train_shard_00001_4018_0", "global_id": 11341 }, { "text": "Abstract

PurposeHaemophilus influenzae is a common cause of mucosal infections that warrants accurate surveillance. We aimed to assess the prevalence of the species in clinical specimens, and characterise population structure and resistance to aminopenicillins by whole genome sequencing.MethodsWe assessed the point prevalence by entering the database records of one day in Denmark, and examined the genome sequences of nationwide, collected isolates from the same day. ResultsThe prevalence of H. influenzae in clinical samples on the 10th of January 2018 was 1.78 per 100,000 person-days (all samples), and 2.47 per 1,000 hospital bed-days (hospital samples). Of 2,009 bacteria deemed clinically relevant and collected in a concerted action by the Danish departments of clinical microbiology, 62 (3.1%) were H. influenzae. All 62 isolates belonged to phylogenetic group I and were unencapsulated. Three strains from separate Danish regions had identical core genome sequences, but a small number of intergenic mutations testified to circulating clones, rather than individual cases of patient-to-patient transmission. The TEM-1 β-lactamase gene was present in 24 strains, while 13 strains were genetically categorised as ampicillin-resistant due to substitutions in penicillin-binding protein 3; shared patterns of amino acid substitutions in unrelated strains indicated putative lateral transfer of chromosomal resistance. ConclusionsCirculating clones of H. influenzae are frequent, and host factors, rather than direct transmission of epidemic strains, may be the primary cause of infection. The bleak presence of ampicillin resistance revealed by sequencing of point prevalence strains underscores the necessity for close examination of testing methods.

\n\nHaemophilus Influenzae One Day in Denmark: Prevalence, Circulating Clones, and Dismal Resistance to Aminopenicillins", "token_count": 500, "char_count": 1912, "word_count": 258, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:51.063577", "source": { "split": "train_shard_00001", "doc_id": 4019 }, "chunk_id": "train_shard_00001_4019_0", "global_id": 11342 }, { "text": "The thermotolerant yeast Pichia etchellsii produces multiple cell bound β-glucosidases that can be used for synthesis of important alkyl- and aryl-glucosides. Present work focuses on enhancement of β-glucosidase I (BGLI) production in Pichia pastoris. In the first step, one-factor-at-a-time experimentation was used to investigate the effect of aeration, antifoam addition, casamino acid addition, medium pH, methanol concentration, and mixed feed components on BGLI production. Among these, initial medium pH, methanol concentration, and mixed feed in the induction phase were found to affect BGLI production. A 3.3-fold improvement in β-glucosidase expression was obtained at pH 7.5 as compared to pH 6.0 on induction with 1 % methanol. Addition of sorbitol, a non-repressing substrate, led to further enhancement in β-glucosidase production by 1.4-fold at pH 7.5. These factors were optimized with response surface methodology using Box-Behnken design. Empirical model obtained was used to define the optimum \"operating space\" for fermentation which was a pH of 7.5, methanol concentration of 1.29 %, and sorbitol concentration of 1.28 %. Interaction of pH and sorbitol had maximum effect leading to the production of 4,400 IU/L. The conditions were validated in a 3-L bioreactor with accumulation of 88 g/L biomass and 2,560 IU/L β-glucosidase activity.\n\nResponse surface methodology based optimization of β-glucosidase production from Pichia pastoris.", "token_count": 430, "char_count": 1457, "word_count": 210, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:51.692120", "source": { "split": "train_shard_00001", "doc_id": 4020 }, "chunk_id": "train_shard_00001_4020_0", "global_id": 11343 }, { "text": "

Background

Cefiderocol (CFDC) is a promising antimicrobial agent against multidrug resistant Gram-negative bacteria. However, CFDC resistance has emerged in carbapenem-resistant Acinetobacter baumannii (CR-AB) but the underlying mechanisms remain unclear.

Methods

Whole-genome sequencing and transcriptome sequencing were performed on CFDC-non-susceptible and CFDC-susceptible isolates. Two different recombinant plasmids was electro-transformed into the E. coli BL21 strain to determine the impact of blaPER and the combined impact of blaPER-1 and blaOXA-23 on CFDC resistance.

Results

Fifty-five CR-AB isolates with minimum inhibitory concentrations (MICs) ranged from 0.06 mg/L to >256 mg/L were sequenced, including 47 CFDC-non-susceptible and eight CFDC-susceptible isolates. Two CFDC-non-susceptible isolates belonged to ST104 whereas the remaining isolates belonged to ST2, and blaPER-1 was present only in CFDC-non-susceptible isolates. Amino acid substitutions were noted in penicillin-binding proteins (PBPs) in four CFDC-susceptible isolates, with slightly elevated MICs. The MICs of recombinant E. coli BL21 carrying the blaPER-1 gene increased 64-fold and recombinant E. coli BL21 carrying both the blaPER-1 and blaOXA-23 genes increased 8-fold but both remained within the susceptibility range", "token_count": 517, "char_count": 1483, "word_count": 163, "semantic_coherence": 1, "information_density": 0.638, "quality_score": 0.819, "entities": { "genes": [ "BL21", "ST2", "ST104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:52.344362", "source": { "split": "train_shard_00001", "doc_id": 4021 }, "chunk_id": "train_shard_00001_4021_0", "global_id": 11344 }, { "text": "Transcriptome sequencing of 17 CFDC-non-susceptible isolates and eight CFDC-susceptible isolates revealed that transcriptional levels of various iron transport proteins, such as fiu, feoA, and feoB, and the energy transduction system, TonB-ExbB-ExbD, were relatively downregulated in CFDC-non-susceptible isolates. GO enrichment analysis revealed that the upregulated genes in CFDC-non-susceptible isolates were mainly associated with redox homeostasis and stress response. Besides, the expression levels of the blaOXA-23 and exbD genes were negatively correlated with the MICs.

Conclusion

PER-1 production, iron transport system downregulation, and mutations in PBPs may synergistically impart high-level resistance to CFDC in CR-AB.\n\nResistance to Cefiderocol Involved Expression of PER-1 β-Lactamase and Downregulation of Iron Transporter System in Carbapenem-Resistant Acinetobacter baumannii.", "token_count": 286, "char_count": 943, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6697, "quality_score": 0.8349, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:52.900055", "source": { "split": "train_shard_00001", "doc_id": 4021 }, "chunk_id": "train_shard_00001_4021_1", "global_id": 11345 }, { "text": "Breastfeeding and microbial colonization during infancy occur within a critical time window for development, and both are thought to influence the risk of respiratory illness. However, the mechanisms underlying the protective effects of breastfeeding and the regulation of microbial colonization are poorly understood. Here, we profiled the nasal and gut microbiomes, breastfeeding characteristics, and maternal milk composition of 2,227 children from the CHILD Cohort Study. We identified robust colonization patterns that, together with milk components, predict preschool asthma and mediate the protective effects of breastfeeding. We found that early cessation of breastfeeding (before 3 months) leads to the premature acquisition of microbial species and functions, including Ruminococcus gnavus and tryptophan biosynthesis, which were previously linked to immune modulation and asthma. Conversely, longer exclusive breastfeeding supports a paced microbial development, protecting against asthma. These findings underscore the importance of extended breastfeeding for respiratory health and highlight potential microbial targets for intervention.\n\nMicrobial colonization programs are structured by breastfeeding and guide healthy respiratory development.", "token_count": 272, "char_count": 1258, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:53.453371", "source": { "split": "train_shard_00001", "doc_id": 4022 }, "chunk_id": "train_shard_00001_4022_0", "global_id": 11346 }, { "text": "Listeria monocytogenes is a highly fatal foodborne causative agent that has been implicated in numerous outbreaks and related deaths of listeriosis in the world. In this study, six L. monocytogenes isolated from ready-to-eat (RTE) meat products were analysed using Whole Genome Sequencing (WGS) to identify virulence and resistance genes, prophage sequences, PCR-serogroups, and sequence types (STs). The WGS identified four different STs (ST1, ST121, ST204, and ST876) that belonged to serogroup 4b (lineage I) and 1/2a (lineage II). Core genome, and average nucleotide identity (ANI) phylogenetic analyses showed that the majority of strains from serogroup 4b (lineage I) clustered together. However, two isolates that belong to serogroup 1/2a (lineage II) grouped far from each other and the other strains. Examination of reference-guided scaffolds for the presence of prophages using the PHAge Search Tool Enhanced Release (PHASTER) software identified 24 diverse prophages, which were either intact or incomplete/questionable. The National Center for Biotechnology Information- Nucleotide Basic Local Alignment Search Tool (NCBI-BLASTn) revealed that Listeria monocytogenes strains in this study shared some known major virulence genes that are encoded in Listeria pathogenicity islands 1 and 3. In general, the resistance profiles for all the isolates were similar and encoded for multidrug, heavy metal, antibiotic, and sanitizer resistance genes. All the isolates in this study possessed genes that code for resistance to common food processing antiseptics such as Benzalkonium chloride.\n\nGenomic Diversity of Common Sequence Types of Listeria monocytogenes Isolated from Ready-to-Eat Products of Animal Origin in South Africa.", "token_count": 496, "char_count": 1770, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6463, "quality_score": 0.8232, "entities": { "genes": [ "ST876", "ST204", "ST121", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:54.100251", "source": { "split": "train_shard_00001", "doc_id": 4023 }, "chunk_id": "train_shard_00001_4023_0", "global_id": 11347 }, { "text": "

Objectives

Community-onset bloodstream infections (BSIs) caused by carbapenemase-producing Enterobacter cloacae complex (ECC) species are increasing internationally. This observation suggests that ECC are emerging pathogens, requiring for detailed understanding on their genomic epidemiology including transmission dynamics and antimicrobial resistance profiles.

Patients and methods

We performed WGS on 79 Enterobacter spp. isolated from the patients with clinically significant BSIs and admitted to emergency department of a major tertiary hospital in Nepal between April 2016 and October 2017.

Results

We identified 5 species and 13 STs of ECC. Enterobacter xiangfangensis ST171, one of the globally emerging carbapenem resistant ECC clones with epidemic potential, was the most prevalent (42%). Phylogenetic analysis showed a large (>19 400 SNPs) core genome SNP distance across major STs, which was minimal (<30 SNPs) among the isolates of each prevalent ST, suggesting the relatively recent importation of major STs followed by local clonal expansions. Genomic evidence for resistance to all major antimicrobial classes except for colistin and macrolides was detected. A limited number of isolates also carried bla NDM-1 (n = 2) and bla OXA-48 (n = 1) carbapenemase genes. Virulence factors encoding siderophores (24%), T6SSD (25%) and fimbriae (54%) were detected.

Conclusions

Our study highlighted that MDR ECC clones are important pathogens of BSIs in community", "token_count": 474, "char_count": 1570, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7463, "quality_score": 0.8731, "entities": { "genes": [ "ST171" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:54.787009", "source": { "split": "train_shard_00001", "doc_id": 4024 }, "chunk_id": "train_shard_00001_4024_0", "global_id": 11348 }, { "text": "Though of low prevalence, carbapenem resistance observed in our ECC isolates raised concern about further community dissemination, underscoring the need for community surveillance to identify MDR ECC clones with epidemic potential.\n\nGenomic epidemiology, antimicrobial resistance and virulence factors of <i>Enterobacter cloacae</i> complex causing potential community-onset bloodstream infections in a tertiary care hospital of Nepal.", "token_count": 111, "char_count": 447, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:55.181066", "source": { "split": "train_shard_00001", "doc_id": 4024 }, "chunk_id": "train_shard_00001_4024_1", "global_id": 11349 }, { "text": "

Background

Lactobacillus crispatus is a ubiquitous micro-organism encountered in a wide range of host-associated habitats. It can be recovered from the gastrointestinal tract of animals and it is a common constituent of the vaginal microbiota of humans. Moreover, L. crispatus can contribute to the urogenital health of the host through competitive exclusion and the production of antimicrobial agents. In order to investigate the genetic diversity of this important urogenital species, we performed a comparative genomic analysis of L. crispatus.

Results

Utilizing the completed genome sequence of a strain ST1 and the draft genome sequences of nine other L. crispatus isolates, we defined the scale and scope of the pan- and core genomic potential of L. crispatus. Our comparative analysis identified 1,224 and 2,705 ortholog groups present in all or only some of the ten strains, respectively. Based on mathematical modeling, sequencing of additional L. crispatus isolates would result in the identification of new genes and functions, whereas the conserved core of the ten strains was a good representation of the final L. crispatus core genome, estimated to level at about 1,116 ortholog groups. Importantly, the current core was observed to encode bacterial components potentially promoting urogenital health. Using antibody fragments specific for one of the conserved L. crispatus adhesins, we demonstrated that the L. crispatus core proteins have a potential to reduce the ability of Gardnerella vaginalis to adhere to epithelial cells. These findings thereby suggest that L. crispatus core proteins could protect the vagina from G. vaginalis and bacterial vaginosis.

Conclusions

Our pan-genome analysis provides insights into the intraspecific genome variability and the collective molecular mechanisms of the species L. crispatus. Using this approach, we described the differences and similarities between the genomes and identified features likely to be important for urogenital health. Notably, the conserved genetic backbone of L. crispatus accounted for close to 60% of the ortholog groups of an average L. crispatus strain and included factors for the competitive exclusion of G", "token_count": 522, "char_count": 2215, "word_count": 321, "semantic_coherence": 1, "information_density": 0.5483, "quality_score": 0.7741, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:45:55.838868", "source": { "split": "train_shard_00001", "doc_id": 4025 }, "chunk_id": "train_shard_00001_4025_0", "global_id": 11350 }, { "text": "vaginalis, providing an explanation on how this urogenital species could improve vaginal health.\n\nComparative genomics of Lactobacillus crispatus suggests novel mechanisms for the competitive exclusion of Gardnerella vaginalis.", "token_count": 52, "char_count": 227, "word_count": 28, "semantic_coherence": 1, "information_density": 0.9643, "quality_score": 0.9821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:56.246479", "source": { "split": "train_shard_00001", "doc_id": 4025 }, "chunk_id": "train_shard_00001_4025_1", "global_id": 11351 }, { "text": "

Objectives

Isolation of colistin- and carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) is increasing in hospital settings worldwide, which is related to increased morbidity, mortality and healthcare costs. The aim of this work was to perform whole-genome sequencing (WGS), genomic and phylogenetic analysis, and conjugation assays of an extensively drug-resistant (XDR) CCR-Kp isolate from Argentina.

Methods

WGS of strain KpS26 isolated from a bloodstream infection was performed using Illumina MiSeq-I, and de novo assembly was achieved using SPAdes v.3.11. A maximum likelihood tree was created using MEGA7 based on core genome single nucleotide polymorphisms from whole-genome alignment of K. pneumoniae isolates identified in silico as sequence type 15 (ST15). The resistome, plasmids and integrons were analysed using ResFinder, AMRFinderPlus, ISfinder, plasmidSPAdes, PlasmidFinder and IntegronFinder. Standard conjugation was performed.

Results

KpS26 belonged to ST15, which is less common than ST258, ST25 and ST11 that are globally reported as responsible for CCR-Kp outbreaks. Fourteen transferable antimicrobial resistance genes (ARGs), including blaKPC-2 in a novel genetic platform transferable by conjugation, were detected contributing to the XDR phenotype. The amino acid substitution T157P in the protein encoded by the pmrB gene of KpS26, previously reported as being responsible for resistance to colistin in K. pneumoniae lineages globally disseminated, was also identified in this strain.

Conclusion

The XDR CCR-Kp isolate analysed here shows that ST15 is also disseminating blaKPC-2 in Argentina alongside other ARGs, evidencing that KPC epidemiology continues to be shaped by intricate and assorted ways of lateral gene transfer.", "token_count": 512, "char_count": 1807, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [ "ST25", "ST11", "ST15", "MEGA7", "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:56.883255", "source": { "split": "train_shard_00001", "doc_id": 4026 }, "chunk_id": "train_shard_00001_4026_0", "global_id": 11352 }, { "text": "Emergence of colistin resistance in Klebsiella pneumoniae ST15 disseminating blaKPC-2 in a novel genetic platform.", "token_count": 40, "char_count": 125, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:57.253787", "source": { "split": "train_shard_00001", "doc_id": 4026 }, "chunk_id": "train_shard_00001_4026_1", "global_id": 11353 }, { "text": "Avian pathogenic Escherichia coli (APEC) is one of the most important bacterial pathogens affecting poultry worldwide. The emergence of multidrug-resistant pathogens has renewed the interest in the therapeutic use of bacteriophages (phages). However, a major concern for the successful implementation of phage therapy is the emergence of phage-resistant mutants. The understanding of the phage-host interactions, as well as underlying mechanisms of resistance, have shown to be essential for the development of a successful phage therapy. Here, we demonstrate that the strictly lytic Escherichia phage vB_EcoM-P10 rapidly selected for resistance in the APEC ST95 O1 strain AM621. Whole-genome sequence analysis of 109 spontaneous phage-resistant mutant strains revealed 41 mutants with single-nucleotide polymorphisms (SNPs) in their core genome. In 32 of these, a single SNP was detected while two SNPs were identified in a total of nine strains. In total, 34 unique SNPs were detected. In 42 strains, including 18 strains with SNP(s), gene losses spanning 17 different genes were detected. Affected by genetic changes were genes known to be involved in phage resistance (outer membrane protein A, lipopolysaccharide-, O- antigen-, or cell wall-related genes) as well as genes not previously linked to phage resistance, including two hypothetical genes. In several strains, we did not detect any genetic changes. Infecting phages were not able to overcome the phage resistance in host strains. However, interestingly the initial infection was shown to have a great fitness cost for several mutant strains, with up to ∼65% decrease in overall growth. In conclusion, this study provides valuable insights into the phage-host interaction and phage resistance in APEC. Although acquired resistance to phages is frequently observed in pathogenic E. coli, it may be associated with loss of fitness, which could be exploited in phage therapy.", "token_count": 501, "char_count": 1957, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6285, "quality_score": 0.8142, "entities": { "genes": [ "ST95", "AM621" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:57.903709", "source": { "split": "train_shard_00001", "doc_id": 4027 }, "chunk_id": "train_shard_00001_4027_0", "global_id": 11354 }, { "text": "Spontaneous Phage Resistance in Avian Pathogenic Escherichia coli.", "token_count": 26, "char_count": 73, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:58.268209", "source": { "split": "train_shard_00001", "doc_id": 4027 }, "chunk_id": "train_shard_00001_4027_1", "global_id": 11355 }, { "text": "Lactobacillaceae are an important family of lactic acid bacteria that play key roles in the gut microbiome of many animal species. In the honey bee (Apis mellifera) gut microbiome, many species of Lactobacillaceae are found, and there is functionally important strain-level variation in the bacteria. In this study, we completed whole-genome sequencing of 3 unique Lactobacillaceae isolates collected from hives in Virginia, USA. Using 107 genomes of known bee-associated Lactobacillaceae and Limosilactobacillus reuteri as an outgroup, the phylogenetics of the 3 isolates was assessed, and these isolates were identified as novel strains of Apilactobacillus kunkeei, Lactobacillus kullabergensis, and Bombilactobacillus mellis. Genome rearrangements, conserved orthologous genes (COG) categories and potential prophage regions were identified across the 3 novel strains. The new A. kunkeei strain was enriched in genes related to replication, recombination and repair, the L. kullabergensis strain was enriched for carbohydrate transport, and the B. mellis strain was enriched in transcription or transcriptional regulation and in some genes with unknown functions. Prophage regions were identified in the A. kunkeei and L. kullabergensis isolates. These new bee-associated strains add to our growing knowledge of the honey bee gut microbiome, and to Lactobacillaceae genomics more broadly.\n\nComparative genomics of Lactobacillaceae from the gut of honey bees, Apis mellifera, from the Eastern United States.", "token_count": 410, "char_count": 1509, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:58.880204", "source": { "split": "train_shard_00001", "doc_id": 4028 }, "chunk_id": "train_shard_00001_4028_0", "global_id": 11356 }, { "text": "

Background

Transfusion-transmitted bacterial infection is a rare occurrence but the most feared complication in transfusion practices. Between 2012 and 2017, five cases of platelet concentrates (PCs) contaminated with the bacterial pathogen Citrobacter koseri (PC-Ck) have been reported in France, with two leading to the death of the recipients. We tested the possibilities of the emergence of a PC-specific clone of C. koseri (Ck) and of specific bacterial genes associated with PC contamination.

Study design and methods

The phylogenetic network, based on a homemade Ck core genome scheme, inferred from the genomes of 20 worldwide Ck isolates unrelated to PC contamination taken as controls (U-Ck) and the genomes of the five PC-Ck, explored the clonal relationship between the genomes and evaluated the distribution of PC-Ck throughout the species. Along with this core genome multilocus sequence typing approach, a Ck pan genome has been used to seek genes specific to PC-Ck isolates.

Results

Our genomic approach suggested that the population of C. koseri is nonclonal, although it also identified a cluster containing three PC-Ck and eight U-Ck. Indeed, the PC-Ck did not share any specific genes.

Conclusion

The elevated incidence of PCs contaminated by C. koseri in France between 2012 and 2017 was not due to the dissemination of a clone. The determinants of the recent outbreaks of PC contamination with C. koseri are still unknown.\n\nGenotypic study of Citrobacter koseri, an emergent platelet contaminant since 2012 in France.", "token_count": 429, "char_count": 1568, "word_count": 230, "semantic_coherence": 1, "information_density": 0.613, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:45:59.505184", "source": { "split": "train_shard_00001", "doc_id": 4029 }, "chunk_id": "train_shard_00001_4029_0", "global_id": 11357 }, { "text": "Small subunit rRNA sequences have been determined for 10 of the most clinically important pathogenic species of the yeast genus Candida (including Torulopsis [Candida] glabrata and Yarrowia [Candida] lipolytica) and for Hansenula polymorpha. Phylogenetic analyses of these sequences and those of Saccharomyces cerevisiae, Kluyveromyces marxianus var. lactis, and Aspergillus fumigatus indicate that Candida albicans, C. tropicalis, C. parapsilosis, and C. viswanathii form a subgroup within the genus. The remaining significant pathogen, T. glabrata, falls into a second, distinct subgroup and is specifically related to S. cerevisiae and more distantly related to C. kefyr (psuedotropicalis) and K. marxianus var. lactis. The 18S rRNA sequence of Y. lipolytica has evolved rapidly in relation to the other Candida sequences examined and appears to be only distantly related to them. As anticipated, species of several other genera appear to bear specific relationships to members of the genus Candida.\n\nEvolutionary relationships among pathogenic Candida species and relatives.", "token_count": 292, "char_count": 1078, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6645, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:00.061381", "source": { "split": "train_shard_00001", "doc_id": 4030 }, "chunk_id": "train_shard_00001_4030_0", "global_id": 11358 }, { "text": "Is Candida kefyr an emerging pathogen in patients with oncohematological diseases?", "token_count": 19, "char_count": 82, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:00.414900", "source": { "split": "train_shard_00001", "doc_id": 4031 }, "chunk_id": "train_shard_00001_4031_0", "global_id": 11359 }, { "text": "Here we discuss the evolution of the northern Australian Staphylococcus aureus isolate MSHR1132 genome. MSHR1132 belongs to the divergent clonal complex 75 lineage. The average nucleotide divergence between orthologous genes in MSHR1132 and typical S. aureus is approximately sevenfold greater than the maximum divergence observed in this species to date. MSHR1132 has a small accessory genome, which includes the well-characterized genomic islands, νSAα and νSaβ, suggesting that these elements were acquired well before the expansion of the typical S. aureus population. Other mobile elements show mosaic structure (the prophage ϕSa3) or evidence of recent acquisition from a typical S. aureus lineage (SCCmec, ICE6013 and plasmid pMSHR1132). There are two differences in gene repertoire compared with typical S. aureus that may be significant clues as to the genetic basis underlying the successful emergence of S. aureus as a pathogen. First, MSHR1132 lacks the genes for production of staphyloxanthin, the carotenoid pigment that confers upon S. aureus its characteristic golden color and protects against oxidative stress. The lack of pigment was demonstrated in 126 of 126 CC75 isolates. Second, a mobile clustered regularly interspaced short palindromic repeat (CRISPR) element is inserted into orfX of MSHR1132. Although common in other staphylococcal species, these elements are very rare within S. aureus and may impact accessory genome acquisition. The CRISPR spacer sequences reveal a history of attempted invasion by known S. aureus mobile elements. There is a case for the creation of a new taxon to accommodate this and related isolates.\n\nA very early-branching Staphylococcus aureus lineage lacking the carotenoid pigment staphyloxanthin.", "token_count": 477, "char_count": 1755, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.8191, "entities": { "genes": [ "MSHR1132", "CC75", "ICE6013" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:01.052135", "source": { "split": "train_shard_00001", "doc_id": 4032 }, "chunk_id": "train_shard_00001_4032_0", "global_id": 11360 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) is a common pathogen contributing to healthcare-associated infections, which can result in multiple sites infections. The epidemiological characteristics of MRSA exhibit variability among distinct regions and healthcare facilities. The aim of this study was to investigate the molecular epidemiology and nosocomial outbreak characteristics of MRSA in a county-level hospital in China. A total of 130 non-repetitive MRSA strains were collected from December 2020 to November 2021. Whole-genome sequencing (WGS) was performed to identify antimicrobial resistance and virulence factors. Phylogenetic analysis was conducted to ascertain genetic diversity and phylogenetic relationships. Independent transmission scenarios were determined by the phylogeny derived from single nucleotide polymorphisms (SNPs) within the core genome. All the MRSA isolates were collected from the intensive care unit (30.00%, 39/130), the department of otorhinolaryngology (10.00%, 13/130) and the department of burn unit (9.23%, 12/130). The clinical samples mainly included phlegm (53.85%, 70/130), purulent fluid (24.62%, 32/130), and secretions (8.46%, 11/130). The resistance rates to erythromycin, clindamycin and ciprofloxacin were 75.38, 40.00, and 39.23%, respectively. All the isolates belonged to 11 clonal complexes (CCs), with the major prevalent types were CC5, CC59, and CC398, accounting for 30.00% (39/130), 29.23% (38/130), and 16.92% (22/130), respectively", "token_count": 478, "char_count": 1509, "word_count": 197, "semantic_coherence": 1, "information_density": 0.7208, "quality_score": 0.8604, "entities": { "genes": [ "CC5", "CC59", "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:01.702435", "source": { "split": "train_shard_00001", "doc_id": 4033 }, "chunk_id": "train_shard_00001_4033_0", "global_id": 11361 }, { "text": "Twenty sequence types (STs) were identified, and ST59 (25.38%, 33/130) was the dominant lineage, followed by ST5 (23.84%, 31/130) and ST398 (16.92%, 22/130). Three different SCCmec types were investigated, most of isolates were type IV (33.85%, 44/130), followed by type II (27.69%, 36/130) and type III (0.77%, 1/130). The common clonal structures included CC5-ST5-t2460-SCCmec IIa, CC59-ST59-t437-SCCmec IV and CC398-ST398-t034-SCCmec (-), with rates of 16.92% (22/130), 14.62% (19/130), and 13.84% (18/130), respectively. Only 12 panton-valentine leucocidin (PVL) positive strains were identified. Two independent clonal outbreaks were detected, one consisting of 22 PVL-negative strains belongs to CC5-ST5-t2460-SCCmec IIa and the other consisting of 8 PVL-negative strains belongs to CC5-ST5-t311-SCCmec IIa. Overall, our study indicated that the CC5 lineage emerged as the predominant epidemic clone of MRSA, responsible for nosocomial outbreaks and transmission within a county-level hospital in China, highlighting the necessity to strengthen infection control measures for MRSA in such healthcare facilities.\n\nGenomic characterization and outbreak investigations of methicillin-resistant Staphylococcus aureus in a county-level hospital in China.", "token_count": 456, "char_count": 1262, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [ "ST398", "ST5", "CC5", "ST59", "CC398", "CC59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:02.349301", "source": { "split": "train_shard_00001", "doc_id": 4033 }, "chunk_id": "train_shard_00001_4033_1", "global_id": 11362 }, { "text": "Molecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. The genetic relatedness of M. bovis isolates from cattle and wildlife have also suggested sustained transmission within this multi-host system. However, while previous surveillance highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric and provided valuable information on the prevalence and spatial occurrence of TB, links at the wildlife-livestock interfaces were established mainly via genotype associations. Therefore, evidence at a local fine scale of transmission events linking wildlife hosts and cattle remains lacking. Here, we explore the advantages of whole genome sequencing (WGS) applied to cattle, red deer and wild boar isolates to reconstruct the evolutionary dynamics of M. bovis and to identify putative pathogen transmission events. Whole genome sequences of 44 representative M. bovis isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this M. bovis population into five genetic clades, three with geographic specificities, as well as the establishment of a SNPs catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to reconstruct transmission networks, which together with inferred secondary cases, further structured this M. bovis population by host species and geographic location. WGS of M. bovis isolates from Portugal is reported for the first time, refining the spatiotemporal context of transmission events and providing further support to the key role of red deer and wild boar on the persistence of animal TB in this Iberian multi-host system.", "token_count": 504, "char_count": 2203, "word_count": 312, "semantic_coherence": 1, "information_density": 0.6442, "quality_score": 0.8221, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:03.007110", "source": { "split": "train_shard_00001", "doc_id": 4034 }, "chunk_id": "train_shard_00001_4034_0", "global_id": 11363 }, { "text": "Phylogenomics Sheds Light on the population structure ofMycobacterium bovisfrom a Multi-Host Tuberculosis System", "token_count": 39, "char_count": 119, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:03.374306", "source": { "split": "train_shard_00001", "doc_id": 4034 }, "chunk_id": "train_shard_00001_4034_1", "global_id": 11364 }, { "text": "Prior to the identification of Xanthomonas perforans associated with bacterial spot of tomato in 1991, X. euvesicatoria was the only known species in Florida. Currently, X. perforans is the Xanthomonas sp. associated with tomato in Florida. Changes in pathogenic race and sequence alleles over time signify shifts in the dominant X. perforans genotype in Florida. We previously reported recombination of X. perforans strains with closely related Xanthomonas species as a potential driving factor for X. perforans evolution. However, the extent of recombination across the X. perforans genomes was unknown. We used a core genome multilocus sequence analysis approach to identify conserved genes and evaluated recombination-associated evolution of these genes in X. perforans. A total of 1,356 genes were determined to be \"core\" genes conserved among the 58 X. perforans genomes used in the study. Our approach identified three genetic groups of X. perforans in Florida based on the principal component analysis (PCA) using core genes. Nucleotide variation in 241 genes defined these groups, that are referred as Phylogenetic-group Defining (PgD) genes. Furthermore, alleles of many of these PgD genes showed 100% sequence identity with X. euvesicatoria, suggesting that variation likely has been introduced by recombination at multiple locations throughout the bacterial chromosome. Site-specific recombinase genes along with plasmid mobilization and phage associated genes were observed at different frequencies in the three phylogenetic groups and were associated with clusters of recombinant genes. Our analysis of core genes revealed the extent, source, and mechanisms of recombination events that shaped the current population and genomic structure of X. perforans in Florida.", "token_count": 497, "char_count": 1878, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5543, "quality_score": 0.7771, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:04.027069", "source": { "split": "train_shard_00001", "doc_id": 4035 }, "chunk_id": "train_shard_00001_4035_0", "global_id": 11365 }, { "text": "Multiple Recombination Events Drive the Current Genetic Structure of Xanthomonas perforans in Florida.", "token_count": 30, "char_count": 109, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:04.389743", "source": { "split": "train_shard_00001", "doc_id": 4035 }, "chunk_id": "train_shard_00001_4035_1", "global_id": 11366 }, { "text": "Race-specific resistance loci, whether having qualitative or quantitative effects, present plant-breeding challenges for phenotypic selection and deciding which loci to select or stack with other resistance loci for improved durability. Previously, resistance to grapevine powdery mildew (GPM, caused by Erysiphe necator) was predicted to be conferred by at least three race-specific loci in the mapping family B37-28 × C56-11 segregating for GPM resistance from Vitis aestivalis. In this study, 9 years of vineyard GPM disease severity ratings plus a greenhouse and laboratory assays were genetically mapped, using a rhAmpSeq core genome marker platform with 2,000 local haplotype markers. A new qualitative resistance locus, named REN11, on the chromosome (Chr) 15 was found to be effective in nearly all (11 of 12) vineyard environments on leaves, rachis, berries, and most of the time (7 of 12) stems. REN11 was independently validated in a pseudo-testcross with the grandparent source of resistance, \"Tamiami.\" Five other loci significantly predicted GPM severity on leaves in only one or two environments, which could indicate race-specific resistance or their roles in different timepoints in epidemic progress. Loci on Chr 8 and 9 reproducibly predicted disease severity on stems but not on other tissues and had additive effects with REN11 on the stems. The rhAmpSeq local haplotype sequences published in this study for REN11 and Chr 8 and 9 stem quantitative trait locus (QTL) can be used directly for marker-assisted selection or converted to SNP assays. In screening for REN11 in a diversity panel of 20,651 vines representing the diversity of Vitis, this rhAmpSeq haplotype had a false positive rate of 0.034% or less", "token_count": 505, "char_count": 1787, "word_count": 266, "semantic_coherence": 1, "information_density": 0.609, "quality_score": 0.8045, "entities": { "genes": [ "REN11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:05.041483", "source": { "split": "train_shard_00001", "doc_id": 4036 }, "chunk_id": "train_shard_00001_4036_0", "global_id": 11367 }, { "text": "The effects of the other foliar resistance loci detected in this study seem too unstable for genetic improvement regardless of quantitative effect size, whether due to race specificity or other environmental variables.\n\nDiscovery of the REN11 Locus From Vitis aestivalis for Stable Resistance to Grapevine Powdery Mildew in a Family Segregating for Several Unstable and Tissue-Specific Quantitative Resistance Loci.", "token_count": 108, "char_count": 429, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7797, "quality_score": 0.8898, "entities": { "genes": [ "REN11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:05.430695", "source": { "split": "train_shard_00001", "doc_id": 4036 }, "chunk_id": "train_shard_00001_4036_1", "global_id": 11368 }, { "text": "Staphylococcus epidermidis has been recently recognized as an emerging nosocomial pathogen. There are concerns over the increasing virulence potential of this commensal due to the capabilities of transferring mobile genetic elements to Staphylococcus aureus through staphylococcal chromosomal cassette (SCCmec) and the closely related arginine catabolic mobile element (ACME) and the copper and mercury resistance island (COMER). The potential pathogenicity of S. epidermidis, particularly from blood stream infections, has been poorly investigated. In this study, 24 S. epidermidis isolated from blood stream infections from Oman were investigated using whole genome sequence analysis. Core genome phylogenetic trees revealed one third of the isolates belong to the multidrug resistance ST-2. Genomic analysis unraveled a common occurrence of SCCmec type IV and ACME element predominantly type I arranged in a composite island. The genetic composition of ACME was highly variable among isolates of same or different STs. The COMER-like island was absent in all of our isolates. Reduced copper susceptibility was observed among isolates of ST-2 and ACME type I, followed by ACME type V. In conclusion, in this work, we identify a prevalent occurrence of highly variable ACME elements in different hospital STs of S. epidermidis in Oman, thus strongly suggesting the hypothesis that ACME types evolved from closely related STs.\n\nWhole Genome Sequencing of Methicillin-Resistant Staphylococcus epidermidis Clinical Isolates Reveals Variable Composite SCCmec ACME among Different STs in a Tertiary Care Hospital in Oman.", "token_count": 447, "char_count": 1680, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5991, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:06.063187", "source": { "split": "train_shard_00001", "doc_id": 4037 }, "chunk_id": "train_shard_00001_4037_0", "global_id": 11369 }, { "text": "Abstract

Background Colistin is used against multi-drug resistant pathogens, yet resistance emerges either through dissemination of plasmid-mediated genes (mcr) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challenging due to poor diffusion of colistin in agar media, leading to an underestimation of resistance. We aimed to compare the performance of four different phenotypic approaches in the context of different molecular mechanism of resistance. Methods We compared the performance of Vitek 2® (bioMérieux, AST N242), Colistin MIC Test Strip (Liofilchem Diagnostici), UMIC (Biocentric), and Rapid Polymyxin NP Test (ELITechGroup) against the standard broth microdilution (BDM) method. We used whole genome sequencing (WGS) to infer the molecular mechanisms of resistance. A total of 97 Enterobacterales and non-fermenting bacterial isolates were collected from clinical samples during 2016–2017 and tested for colistin susceptibility. Data was analysed by comparing the susceptibility category (susceptible or resistant) and minimal inhibitory concentrations (MIC). We determined diversity of isolates by core genome multi locus sequencing typing (cgMLST) and identified antimicrobial resistance genes using NCBI and CARD databases. Results Of the 97 clinical isolates, 54 (56%) were resistant by the standard broth microdilution. The highest susceptibility category concordance was achieved by the Rapid Polymyxin NP test (98.8%) followed by UMIC (97.9%), E-test MIC strip (96.9%) and Vitek 2 (95.6%)", "token_count": 477, "char_count": 1673, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6514, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:06.735691", "source": { "split": "train_shard_00001", "doc_id": 4038 }, "chunk_id": "train_shard_00001_4038_0", "global_id": 11370 }, { "text": "The highest MIC concordance was achieved by UMIC (80.4%), followed by Vitek 2 (72.5%) and E-test MIC strip (62.9%). Among the resistant isolates, 23/54 (43%) were intrinsically resistant to colistin, whereas 31/54 (57%) isolates had acquired colistin resistance. Of these, mcr-1 was detected in four isolates and mcr-2 in one isolate. Mutations in mgrB, phoQ, pmrA, pmrB, and pmrC genes that led to amino acid changes were encountered in Klebsiella pneumoniae, Escherichia coli, and Acinetobacter bereziniae resistant isolates. Conclusions The Rapid Polymyxin NP test showed the highest categorical concordance and the UMIC test provided MIC values with a high concordance to the standard method. We found colistin resistance in diverse species occurred predominantly through spontaneous chromosomal mutation rather than plasmid-mediated resistance.

\n\nColistin resistance in Gram-negative bacteria analysed by five phenotypic assays and inference of the underlying genomic mechanisms", "token_count": 336, "char_count": 1089, "word_count": 138, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:07.332128", "source": { "split": "train_shard_00001", "doc_id": 4038 }, "chunk_id": "train_shard_00001_4038_1", "global_id": 11371 }, { "text": "Samples of the traditional Sudanese fermented camel's milk product Gariss representing 9 different regions in Sudan were microbiologically characterized using an integrated approach including phenotypic and genotypic methods. Lactic acid bacteria [log(CFU/g)=7.76-8.66] and yeasts [log(CFU/g)=6.05-7.79] were detected in high numbers. A total of 180 LAB isolates were identified of which 123 isolates were found to belong to the Streptococcus bovis group. Thirteen representative isolates were characterized by PCR amplification and sequencing of the housekeeping genes rpoB and sodA and the streptococcal glucosyltransferase gene (gtf). All thirteen isolates were identified as Streptococcus infantarius subsp. infantarius, a potential human pathogen. The gene encoding the virulence determinant gtf was detected in 10 of the 13 tested strains. The same isolates were able to survive exposure to 0.3% (w/v) oxgall for 4 h and pH=2.7 for 1-4 h. Also Lactobacillus fermentum were detected in high numbers, whereas Enterococcus faecium and Lactobacillus helveticus were detected more occasionally. The yeast microflora in all Gariss samples consisted of Kluyveromyces marxianus and Issatchenkia orientalis with the former being predominant in 7 out of 9 samples.\n\nA traditional Sudanese fermented camel's milk product, Gariss, as a habitat of Streptococcus infantarius subsp. infantarius.", "token_count": 392, "char_count": 1386, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6373, "quality_score": 0.8187, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:07.973158", "source": { "split": "train_shard_00001", "doc_id": 4039 }, "chunk_id": "train_shard_00001_4039_0", "global_id": 11372 }, { "text": "

Importance

Extensively drug-resistant Campylobacter jejuni infections cannot be treated with any commonly recommended antibiotics and pose an increasing public health threat.

Objectives

To investigate cases of extensively drug-resistant C jejuni associated with pet store puppies and describe the epidemiologic and laboratory characteristics of these infections.

Design, setting, and participants

In August 2017, health officials identified, via survey, patients with C jejuni infections who reported contact with puppies sold by pet stores. In conjunction with state and federal partners, the Centers for Disease Control and Prevention investigated cases of culture-confirmed C jejuni infections in US patients with an epidemiologic or molecular association with pet store puppies between January 1, 2016, and February 29, 2020. Available records from cases occurring before 2016 with genetically related isolates were also obtained.

Main outcomes and measures

Patients were interviewed about demographic characteristics, health outcomes, and dog exposure during the 7 days before illness onset. Core genome multilocus sequence typing was used to assess isolate relatedness, and genomes were screened for resistance determinants to predict antibiotic resistance. Isolates resistant to fluoroquinolones, macrolides, and 3 or more additional antibiotic classes were considered to be extensively drug resistant. Cases before 2016 were identified by screening all sequenced isolates submitted for surveillance using core genome multilocus sequence typing.

Results

A total of 168 patients (median [interquartile range] age, 37 [19.5-51.0] years; 105 of 163 female [64%]) with an epidemiologic or molecular association with pet store puppies were studied. A total of 137 cases occurred from January 1, 2016, to February 29, 2020, with 31 additional cases dating back to 2011", "token_count": 483, "char_count": 1905, "word_count": 252, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:08.665281", "source": { "split": "train_shard_00001", "doc_id": 4040 }, "chunk_id": "train_shard_00001_4040_0", "global_id": 11373 }, { "text": "Overall, 117 of 121 patients (97%) reported contact with a dog in the week before symptom onset, of whom 69 of 78 (88%) with additional information reported contact with a pet store puppy; 168 isolates (88%) were extensively drug resistant. Traceback investigation did not implicate any particular breeder, transporter, distributer, store, or chain.

Conclusions and relevance

Strains of extensively drug-resistant C jejuni have been circulating since at least 2011 and are associated with illness among pet store customers, employees, and others who come into contact with pet store puppies. The results of this study suggest that practitioners should ask about puppy exposure when treating patients with Campylobacter infection, especially when they do not improve with routine antibiotics, and that the commercial dog industry should take action to help prevent the spread of extensively drug-resistant C jejuni from pet store puppies to people.\n\nOngoing Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Associated With US Pet Store Puppies, 2016-2020.", "token_count": 270, "char_count": 1083, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:09.220227", "source": { "split": "train_shard_00001", "doc_id": 4040 }, "chunk_id": "train_shard_00001_4040_1", "global_id": 11374 }, { "text": "The objective of the present study was to investigate yeast communities in kefir grains and viili starters in Taiwan through conventional microbiological cultivation and polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The DNA sequencing was used as a validity technique to ensure that all isolates within each group belonged to just one species, and to confirm the identified results of PCR-DGGE. Results indicated that a combination of conventional microbiological cultivation with PCR-DGGE and sequencing could successfully identify 4 yeast species from both types of cultures in Taiwan. Kluyveromyces marxianus, Saccharomyces turicensis, and Pichia fermentans were found in Taiwanese kefir grains with a distribution of 76, 22, and 2%, respectively, whereas Klu. marxianus, Saccharomyces unisporus and P. fermentans were identified in viili starters corresponding to 58, 11, and 31% of the total cell counts, respectively. Furthermore, the culture-independent method was applied to identify the yeast species using DGGE. Only 2 yeast species, Klu. marxianus and S. turicensis, were found in kefir grains and 2, Klu. marxianus and P. fermentans, in viili starters. These results suggest that in samples containing multiple species, PCR-DGGE may fail to detect some species. Sequences of yeast isolates reported in this study have been deposited in the GenBank database under accession nos. DQ139802, AF398485, DQ377652, and AY007920.\n\nIdentification of yeasts and evaluation of their distribution in Taiwanese Kefir and Viili starters.", "token_count": 422, "char_count": 1567, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5893, "quality_score": 0.7946, "entities": { "genes": [ "DQ377652", "AY007920", "DQ139802", "AF398485" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:09.841868", "source": { "split": "train_shard_00001", "doc_id": 4041 }, "chunk_id": "train_shard_00001_4041_0", "global_id": 11375 }, { "text": "Salmonellosis is a major cause of bacterial foodborne infection. Since 2016, an increased number of cases of gastroenteritis caused by Salmonella enterica serovar Enteritidis linked to eggs produced in Poland has been reported in Europe. In Italy, S. Enteritidis is one of the three most commonly reported serotypes, associated mainly with the consumption of contaminated eggs and derived products. In our work, we analysed 61 strains of S. Enteritidis obtained from humans and farms in the Abruzzi region, Italy, in 2018. We used Multiple-Loci Variable-Number Tandem Repeat (VNTR) analysis (MLVA)-based typing and Whole-Genome Sequencing (WGS) tools to identify closely related strains and perform cluster analysis. We found two clusters of genetically similar strains. The first one was present in the local farms and isolated from human cases and had single-linkage distance of no more than two core genes and less than five Single-Nucleotide Polymorphisms (SNPs). The second cluster contained strains isolated from humans and from a dessert (tiramisù) sample that shared identical core genome and were assigned the same SNP address. Cluster 2 isolates were found to be genetically similar to an S. Enteritidis strain from a multi-country outbreak linked to Polish eggs.\n\nGenomic Comparison of Salmonella Enteritidis Strains Isolated from Laying Hens and Humans in the Abruzzi Region during 2018.", "token_count": 384, "char_count": 1434, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6351, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:10.460268", "source": { "split": "train_shard_00001", "doc_id": 4042 }, "chunk_id": "train_shard_00001_4042_0", "global_id": 11376 }, { "text": "Escherichia coli sequence type 131 (ST131), a pandemic clone responsible for the high incidence of extraintestinal pathogenic E. coli (ExPEC) infections, has been known widely for its contribution to the worldwide dissemination of multidrug resistance. Although other ExPEC-associated and extended-spectrum-β-lactamase (ESBL)-producing E. coli clones, such as ST38, ST405, and ST648 have been studied widely, no comparative genomic data with respect to other genotypes exist for ST131. In this study, comparative genomic analysis was performed for 99 ST131 E. coli strains with 40 genomes from three other STs, including ST38 (n = 12), ST405 (n = 10), and ST648 (n = 18), and functional studies were performed on five in-house strains corresponding to the four STs. Phylogenomic analysis results from this study corroborated with the sequence type-specific clonality. Results from the genome-wide resistance profiling confirmed that all strains were inherently multidrug resistant. ST131 genomes showed unique virulence profiles, and analysis of mobile genetic elements and their associated methyltransferases (MTases) has revealed that several of them were missing from the majority of the non-ST131 strains. Despite the fact that non-ST131 strains lacked few essential genes belonging to the serum resistome, the in-house strains representing all four STs demonstrated similar resistance levels to serum antibactericidal activity. Core genome analysis data revealed that non-ST131 strains usually lacked several ST131-defined genomic coordinates, and a significant number of genes were missing from the core of the ST131 genomes. Data from this study reinforce adaptive diversification of E", "token_count": 485, "char_count": 1744, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [ "ST648", "ST131", "ST38", "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:11.109086", "source": { "split": "train_shard_00001", "doc_id": 4043 }, "chunk_id": "train_shard_00001_4043_0", "global_id": 11377 }, { "text": "coli strains belonging to the ST131 lineage and provide new insights into the molecular mechanisms underlying clonal diversification of the ST131 lineage.IMPORTANCEE. coli, particularly the ST131 extraintestinal pathogenic E. coli (ExPEC) lineage, is an important cause of community- and hospital-acquired infections, such as urinary tract infections, surgical site infections, bloodstream infections, and sepsis. The treatment of infections caused by ExPEC has become very challenging due to the emergence of resistance to the first-line as well as the last-resort antibiotics. This study analyzes E. coli ST131 against three other important and globally distributed ExPEC lineages (ST38, ST405, and ST648) that also produced extended-spectrum β-lactamase (ESBL). This is perhaps the first study that employs the high-throughput whole-genome sequence-based approach to compare and study the genomic features of these four ExPEC lineages in relation to their functional properties. Findings from this study highlight the differences in the genomic coordinates of ST131 with respect to the other STs considered here. Results from this comparative genomics study can help in advancing the understanding of ST131 evolution and also offer a framework towards future developments in pathogen identification and targeted therapeutics to prevent diseases caused by this pandemic E. coli ST131 clone.\n\nComparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages.", "token_count": 418, "char_count": 1603, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.8061, "entities": { "genes": [ "ST648", "ST131", "ST38", "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:11.734925", "source": { "split": "train_shard_00001", "doc_id": 4043 }, "chunk_id": "train_shard_00001_4043_1", "global_id": 11378 }, { "text": "Bordetella pertussis is the primary causative agent of pertussis, a highly infectious respiratory disease associated with prolonged coughing episodes. Pertussis infections are typically mild in adults, however in neonates, infections can be fatal. Despite successful vaccine uptake, the disease is re-emerging across the globe, therefore it is critical to determine the mechanism by which B. pertussis is escaping vaccination control. Studies have suggested that significant changes have occurred in B. pertussis genomes in response to whole cell and acellular vaccines. Continued molecular monitoring is therefore crucial for public health surveillance. High-resolution molecular surveillance of B. pertussis can be achieved through the sequencing of the whole genome. In public health laboratories, whole genome sequencing is primarily performed by short-read sequencing technologies as they are most cost-effective. However short read sequencing does not resolve the extensive genomic rearrangement evident in Bordetella genomes. This is because repeat regions present in Bordetella genomes are collapsed by downstream analysis. For example, the B. pertussis genome contains more than 200 copies of the IS 481 insertion element, hence assemblies generally consist of >200 contigs. Advancements in long-read technologies however increase the potential to circularise and close genomes by bridging the locations of the IS 481 insertion element. In this study, we aimed to contextualise the Bordetella spp. circulating in NSW, Australia and assess their relationship with global isolates utilising core genome, SNP and structural clustering analysis using long read technology. We report five closed genomes of Bordetella spp. isolated from Australian patients. Two of the three B. pertussis closed isolates, were unique with their own genomic structure, while the other structurally clustered with global isolates. We found that Australian B. holmesii and B. parapertussis strains cluster with global isolates and do not appear to be unique to Australia. Australian draft B. holmesii SNP analysis showed that between 1999 and 2007, isolates were relatively similar, however post-2012, isolates were distinct from each other. The closed isolates can also be used as high-quality reference sequences for both surveillance and other investigations into pertussis spread.", "token_count": 534, "char_count": 2368, "word_count": 336, "semantic_coherence": 1, "information_density": 0.5923, "quality_score": 0.7961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:46:12.397696", "source": { "split": "train_shard_00001", "doc_id": 4044 }, "chunk_id": "train_shard_00001_4044_0", "global_id": 11379 }, { "text": "Genomic evaluation ofBordetella spp. originating from Australia", "token_count": 20, "char_count": 70, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:12.757496", "source": { "split": "train_shard_00001", "doc_id": 4044 }, "chunk_id": "train_shard_00001_4044_1", "global_id": 11380 }, { "text": "

ABSTRACT

Plants are continuously exposed to beneficial and pathogenic microbes, but how plants recognize and respond to friends versus foes remains poorly understood. Here, we compared the molecular response of Arabidopsis thaliana independently challenged with a Fusarium oxysporum endophyte Fo47 versus a pathogen Fo5176. These two Fusarium oxysporum strains share a core genome of about 46 Mb, in addition to unique 1,229 and 5,415 accessory genes. Metatranscriptomic data reveal a shared pattern of expression for most plant genes (∼80%) in responding to both fungal inoculums at all time points from 12 to 96 h post inoculation (HPI). However, the distinct responding genes depict transcriptional plasticity, as the pathogenic interaction activates plant stress responses and suppresses plant growth/development related functions, while the endophytic interaction attenuates host immunity but activates plant nitrogen assimilation. The differences in reprogramming of the plant transcriptome are most obvious in 12 HPI, the earliest time point sampled and are linked to accessory genes in both fungal genomes. Collectively, our results indicate that the A. thaliana and F. oxysporum interaction displays both transcriptome conservation and plasticity in the early stages of infection, providing insights into the fine-tuning of gene regulation underlying plant differential responses to fungal endophytes and pathogens.

One-sentence summary

Multiomics analysis reveals the regulatory plasticity of plants in response to beneficial and antagonistic microbes, resulting in distinct phenotypes and rewired transcriptional networks.\n\nMetatranscriptomic comparison of endophytic and pathogenicFusarium–Arabidopsis interactions reveals plant transcriptional plasticity", "token_count": 433, "char_count": 1792, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6287, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:13.389074", "source": { "split": "train_shard_00001", "doc_id": 4045 }, "chunk_id": "train_shard_00001_4045_0", "global_id": 11381 }, { "text": "Microbial cells (Kluyveromyces fragilis and Chlorella vulgaris) efficiently interacted with maghemite nanoparticles stabilized as low-pH ionic magnetic fluid, leading to the formation of magnetically labeled cells. This simple procedure allows to use the prepared materials as new cheap and easy to get magnetic affinity adsorbents to the removal of water-soluble dyes from polluted water sources using magnetic separation techniques. Magnetically modified cells were investigated by means of electron spin resonance spectroscopy and conventional magnetic methods over the temperature range 4-300 K. The magnetic behavior of these materials was dominated by the superparamagnetic relaxation of isolated single domain maghemite particles although a little amount of agglomerates was also present on the cell surface. However, these agglomerates were sufficiently small to show at static conditions the superparamagnetic behavior at room temperature. Therefore, the ferrofluid-modified microbial cells represent new interesting magnetic affinity adsorbents which could be applied for large-scale magnetic separation processes.\n\nMagnetic studies of ferrofluid-modified microbial cells.", "token_count": 251, "char_count": 1182, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6839, "quality_score": 0.8419, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:13.888753", "source": { "split": "train_shard_00001", "doc_id": 4046 }, "chunk_id": "train_shard_00001_4046_0", "global_id": 11382 }, { "text": "Campylobacter spp. are a common cause of bacterial gastroenteritis in Australia, primarily acquired from contaminated meat. We investigated the relationship between genomic virulence characteristics and the severity of campylobacteriosis, hospitalisation, and other host factors.We recruited 571 campylobacteriosis cases from three Australian states and territories (2018-2019). We collected demographic, health status, risk factors, and self-reported disease data. We whole genome sequenced 422 C. jejuni and 84 C. coli case isolates along with 616 retail meat isolates. We classified case illness severity using a modified Vesikari scoring system, performed phylogenomic analysis, and explored risk factors for hospitalisation and illness severity.On average, cases experienced a 7.5 day diarrhoeal illness with additional symptoms including stomach cramps (87.1 %), fever (75.6 %), and nausea (72.0 %). Cases aged ≥75 years had milder symptoms, lower Vesikari scores, and higher odds of hospitalisation compared to younger cases. Chronic gastrointestinal illnesses also increased odds of hospitalisation. We observed significant diversity among isolates, with 65 C. jejuni and 21 C. coli sequence types. Antimicrobial resistance genes were detected in 20.4 % of isolates, but multidrug resistance was rare (0.04 %). Key virulence genes such as cdtABC (C. jejuni) and cadF were prevalent (>90 % presence) but did not correlate with disease severity or hospitalisation. However, certain genes (e.g. fliK, Cj1136, and Cj1138) appeared to distinguish human C", "token_count": 518, "char_count": 1665, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7431, "quality_score": 0.8716, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:46:14.548347", "source": { "split": "train_shard_00001", "doc_id": 4047 }, "chunk_id": "train_shard_00001_4047_0", "global_id": 11383 }, { "text": "jejuni cases from food source isolates.Campylobacteriosis generally presents similarly across cases, though some are more severe. Genotypic virulence factors identified in the literature to-date do not predict disease severity but may differentiate human C. jejuni cases from food source isolates. Host factors like age and comorbidities have a greater influence on health outcomes than virulence factors.\n\nGenomic and clinical characteristics of campylobacteriosis in Australia.", "token_count": 112, "char_count": 490, "word_count": 64, "semantic_coherence": 1, "information_density": 0.8594, "quality_score": 0.9297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:14.936041", "source": { "split": "train_shard_00001", "doc_id": 4047 }, "chunk_id": "train_shard_00001_4047_1", "global_id": 11384 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) sequence type (ST)398 is a livestock associated (LA) lineage with zoonotic potential, especially in humans with live pig contact. The objective of this study was to characterize two S. aureus strains of lineage ST398 (one methicillin-resistant (MRSA), one methicillin-susceptible (MSSA)) isolated from the same nasal sample of a patient admitted in the Intensive-Care Unit of a Spanish Hospital, and with previous occupational exposure to live pigs, by whole-genome-sequencing (WGS). The sample was obtained during routine surveillance for MRSA colonization. Purified genomic DNA was sequenced using Illumina HiSeq 2000 and processed using conventional bioinformatics software. The two isolates recovered were both S. aureus t011/ST398 and showed similar resistance-phenotypes, other than methicillin susceptibility. The possession of antibiotic resistance genes was the same, except for the mecA-gene located in SCCmecV in the MRSA isolate. The MSSA isolate harbored remnants of a SCCmec following the deletion of 17342bp from a recombination between two putative primases. Both isolates belonged to the livestock-associated clade as defined by three canonical single-nucleotide-polymorphisms, and neither possessed the human immune evasion cluster genes, chp, scn, or sak. The core genome alignment showed a similarity of 99.6%, and both isolates harbored the same mobile genetic elements. The two nasal ST398 isolates recovered from the patient with previous occupational exposure to pigs appeared to have a livestock origin and could represent different evolutionary steps of animal-human interface lineage", "token_count": 499, "char_count": 1738, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6478, "quality_score": 0.8239, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:15.587567", "source": { "split": "train_shard_00001", "doc_id": 4048 }, "chunk_id": "train_shard_00001_4048_0", "global_id": 11385 }, { "text": "The MSSA strain was formed as a result of the loss of the mecA gene from the livestock-associated-MRSA lineage.\n\nSimultaneous Nasal Carriage by Methicillin-Resistant and Methicillin Susceptible <i>Staphylococcus aureus</i> of Lineage ST398 in a Live Pig Transporter.", "token_count": 104, "char_count": 285, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8378, "quality_score": 0.9189, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:15.969165", "source": { "split": "train_shard_00001", "doc_id": 4048 }, "chunk_id": "train_shard_00001_4048_1", "global_id": 11386 }, { "text": "USA300 is a pandemic clonal lineage of hypervirulent, community-acquired, methicillin-resistant Staphylococcus aureus (CA-MRSA) with specific molecular characteristics. Despite its high clinical relevance, the evolutionary origin of USA300 remained unclear. We used comparative genomics of 224 temporal and spatial diverse S. aureus isolates of multilocus sequence type (ST) 8 to reconstruct the molecular evolution and global dissemination of ST8, including USA300. Analyses of core SNP diversity and accessory genome variations showed that the ancestor of all ST8 S. aureus most likely emerged in Central Europe in the mid-19th century. From here, ST8 was exported to North America in the early 20th century and progressively acquired the USA300 characteristics Panton-Valentine leukocidin (PVL), SCCmec IVa, the arginine catabolic mobile element (ACME), and a specific mutation in capsular polysaccharide gene cap5E Although the PVL-encoding phage ϕSa2USA was introduced into the ST8 background only once, various SCCmec types were introduced to ST8 at different times and places. Starting from North America, USA300 spread globally, including Africa. African USA300 isolates have aberrant spa-types (t112, t121) and form a monophyletic group within the clade of North American USA300. Large parts of ST8 methicillin-susceptible S. aureus (MSSA) isolated in Africa represent a symplesiomorphic group of ST8 (i.e., a group representing the characteristics of the ancestor), which are rarely found in other world regions. Isolates previously discussed as USA300 ancestors, including USA500 and a \"historic\" CA-MRSA from Western Australia, were shown to be only distantly related to recent USA300 clones.", "token_count": 508, "char_count": 1760, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6805, "quality_score": 0.8402, "entities": { "genes": [ "USA300", "USA500", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:16.609852", "source": { "split": "train_shard_00001", "doc_id": 4049 }, "chunk_id": "train_shard_00001_4049_0", "global_id": 11387 }, { "text": "Origin, evolution, and global transmission of community-acquired Staphylococcus aureus ST8.", "token_count": 31, "char_count": 98, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:16.975158", "source": { "split": "train_shard_00001", "doc_id": 4049 }, "chunk_id": "train_shard_00001_4049_1", "global_id": 11388 }, { "text": "Whole-genome sequencing is increasingly adopted in clinical settings to identify pathogen transmissions. Currently, such studies are performed largely retrospectively, but to be actionable they need to be carried out prospectively, in which samples are continuously added and compared to previous samples. To enable prospective pathogen comparison, genomic relatedness metrics based on single nucleotide differences must be consistent across time, efficient to compute and reliable for a large variety of samples. The choice of genomic regions to compare, i.e. , the core genome , is critical to obtain a good metric. We propose a novel core genome method that selects conserved sequences in the reference genome by comparing its k-mer content to that of publicly available genome assemblies. The conserved-sequence genome is sample set-independent, which enables prospective pathogen monitoring. Based on clinical data sets of 3436 S. aureus , 1362 K. pneumoniae and 348 E. faecium samples, we show that the conserved-sequence genome disambiguates same-patient samples better than a core genome consisting of conserved genes. The conserved-sequence genome confirms outbreak samples with high accuracy: in a set of 2335 S. aureus samples, it correctly identifies 44 out of 45 outbreak samples, whereas the conserved gene method confirms 38 out of 45 outbreak samples.\n\nA novel core genome approach to enable prospective and dynamic monitoring of infectious outbreaks", "token_count": 338, "char_count": 1466, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6065, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:17.542612", "source": { "split": "train_shard_00001", "doc_id": 4050 }, "chunk_id": "train_shard_00001_4050_0", "global_id": 11389 }, { "text": "Methanotrophs play key roles in global methane cycling and are promising platforms for methane bioconversion. However, major gaps existing in fundamental knowledge undermines understanding of these methane-consuming microorganisms. To associate genes with a phenotype at the genome-wide level, we developed a Cre/lox-mediated method for constructing a large-scale CRISPRi library in a model methanotroph Methylotuvimicrobium buryatense 5GB1C. The efficiency of this Cre mediated integration method was up to a level of 105 CFU/μg DNA. Targeting 4,100 predicted protein-coding genes, our CRISPRi pooled screening uncovered 788 core genes for the growth of strain 5GB1C using methane. The core genes are highly consistent with the gene knockout results, indicating the reliability of the CRISPRi screen. Insights from the core genes include that annotated isozymes generally exist in metabolic pathways and many core genes are hypothetical genes. This work not only provides functional genomic data for both fundamental research and metabolic engineering of methanotrophs, but also offers a method for CRISPRi library construction. IMPORTANCE Due to their key role in methane cycling and their industrial potential, methanotrophs have drawn increasing attention. Genome-wide experimental approaches for gene-phenotype mapping accelerate our understanding and engineering of a bacterium. However, these approaches are still unavailable in methanotrophs. This work has two significant implications. First, the core genes identified here provide functional genetic basics for complete reconstruction of the metabolic network and afford more clues for knowledge gaps. Second, the Cre-mediated knock-in method developed in this work enables large-scale DNA library construction in methanotrophs; the CRISPRi library can be used to screen the genes associated with special culture conditions.", "token_count": 462, "char_count": 1916, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6269, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:18.545218", "source": { "split": "train_shard_00001", "doc_id": 4051 }, "chunk_id": "train_shard_00001_4051_0", "global_id": 11390 }, { "text": "Cre/lox-Mediated CRISPRi Library Reveals Core Genome of a Type I Methanotroph Methylotuvimicrobium buryatense 5GB1C.", "token_count": 60, "char_count": 130, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:18.953977", "source": { "split": "train_shard_00001", "doc_id": 4051 }, "chunk_id": "train_shard_00001_4051_1", "global_id": 11391 }, { "text": "Ethanol stimulated the leakage of amino acids and 260-nm-light-absorbing compounds from cells of Saccharomyces cerevisiae. The efflux followed first-order kinetics over an initial period. In the presence of lethal concentrations of ethanol, the efflux rates at 30 and 36 degrees C were an exponential function of ethanol concentration: k(e) = k(e)e, where k(e) and k(e) are the efflux rate constants, respectively, in the presence of a concentration X of ethanol or the minimal concentration of ethanol, X(m), above which the equation was applicable, coincident with the minimal lethal concentration of ethanol. E is the enhancement constant. At 36 degrees C, as compared with the corresponding values at 30 degrees C, the efflux rates were higher and the minimal concentration of ethanol (X(m)) was lower. The exponential constants for the enhancement of the rate of leakage (E) had similar values at 30 or 36 degrees C and were of the same order of magnitude as the corresponding exponential constants for ethanol-induced death. Under isothermic conditions (30 degrees C) and up to 22% (vol/vol) ethanol, the resistance to ethanol-induced leakage of 260-nm-light-absorbing compounds was found to be closely related with the ethanol tolerance of three strains of yeasts, Kluyveromyces marxianus, Saccharomyces cerevisiae, and Saccharomyces bayanus. The resistance to ethanol-induced leakage indicates the possible adoption of the present method for the rapid screening of ethanol-tolerant strains. The addition to a fermentation medium of the intracellular material obtained by ethanol permeabilization of yeast cells led to improvements in alcohol fermentation by S. cerevisiae and S. bayanus. The action of the intracellular material, by improving yeast ethanol tolerance, and the advantages of partially recycling the fermented medium after distillation were discussed.", "token_count": 494, "char_count": 1873, "word_count": 276, "semantic_coherence": 1, "information_density": 0.4964, "quality_score": 0.7482, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:19.624269", "source": { "split": "train_shard_00001", "doc_id": 4052 }, "chunk_id": "train_shard_00001_4052_0", "global_id": 11392 }, { "text": "Ethanol-Induced Leakage in Saccharomyces cerevisiae: Kinetics and Relationship to Yeast Ethanol Tolerance and Alcohol Fermentation Productivity.", "token_count": 43, "char_count": 144, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:20.025168", "source": { "split": "train_shard_00001", "doc_id": 4052 }, "chunk_id": "train_shard_00001_4052_1", "global_id": 11393 }, { "text": "The gut microbiota plays a crucial role in health and is significantly modulated by human diets. In addition to Western diets which are rich in proteins, high-protein diets are used for specific populations or indications, mainly weight loss. In this study, we investigated the effect of protein supplementation on Bacteroides caccae, a Gram-negative gut symbiont. The supplementation with whey proteins led to a significant increase in growth rate, final biomass, and short-chain fatty acids production. A comprehensive genomic analysis revealed that B. caccae possesses a set of 156 proteases with putative intracellular and extracellular localization and allowed to identify amino acid transporters and metabolic pathways. We developed a fully curated genome-scale metabolic model of B. caccae that incorporated its proteolytic activity and simulated its growth and production of fermentation-related metabolites in response to the different growth media. We validated the model by comparing the predicted phenotype to experimental data. The model accurately predicted B. caccae's growth and metabolite production (R2 = 0.92 for the training set and R2 = 0.89 for the validation set). We found that accounting for both ATP consumption related to proteolysis, and whey protein accessibility is necessary for accurate predictions of metabolites production. These results provide insights into B. caccae's adaptation to a high-protein diet and its ability to utilize proteins as a source of nutrition. The proposed model provides a useful tool for understanding the feeding mechanism of B. caccae in the gut microbiome.IMPORTANCEMicrobial proteolysis is understudied despite the availability of dietary proteins for the gut microbiota. Here, the proteolytic potential of the gut symbiont Bacteroides caccae was analyzed for the first time using pan-genomics", "token_count": 501, "char_count": 1942, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:20.714766", "source": { "split": "train_shard_00001", "doc_id": 4053 }, "chunk_id": "train_shard_00001_4053_0", "global_id": 11394 }, { "text": "This sketches a well-equipped bacteria for protein breakdown, capable of producing 156 different proteases with a broad spectrum of cleavage targets. This functional potential was confirmed by the enhancement of growth and metabolic activities at high protein levels. Proteolysis was included in a B. caccae metabolic model which was fitted with the experiments and validated on external data. This model pinpoints the links between protein availability and short-chain fatty acids production, and the importance for B. caccae to gain access to glutamate and asparagine to promote growth. This integrated approach can be generalized to other symbionts and upscaled to complex microbiota to get insights into the ecological impact of proteins on the gut microbiota.\n\nDesign of a proteolytic module for improved metabolic modeling of Bacteroides caccae.", "token_count": 212, "char_count": 872, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6905, "quality_score": 0.8452, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:21.187267", "source": { "split": "train_shard_00001", "doc_id": 4053 }, "chunk_id": "train_shard_00001_4053_1", "global_id": 11395 }, { "text": "An extensive body of evidence documents the importance of the gut microbiome both in health and in a variety of human diseases. Cell and animal studies describing this relationship abound, whilst clinical studies exploring the associations between changes in gut microbiota and the corresponding metabolites with neurodegeneration in the human brain have only begun to emerge more recently. Further, the findings of such studies are often difficult to translate into simple clinical applications that result in measurable health outcomes. The purpose of this paper is to appraise the literature on a select set of faecal biomarkers from a clinician’s perspective. This practical review aims to examine key physiological processes that influence both gastrointestinal, as well as brain health, and to discuss how tools such as the characterisation of commensal bacteria, the identification of potential opportunistic, pathogenic and parasitic organisms and the quantification of gut microbiome biomarkers and metabolites can help inform clinical decisions of nutrition and lifestyle medicine practitioners.\n\nHarnessing the Power of Microbiome Assessment Tools as Part of Neuroprotective Nutrition and Lifestyle Medicine Interventions.", "token_count": 250, "char_count": 1239, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6286, "quality_score": 0.8143, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:21.670142", "source": { "split": "train_shard_00001", "doc_id": 4054 }, "chunk_id": "train_shard_00001_4054_0", "global_id": 11396 }, { "text": "

Background

Lysobacter species are Gram-negative bacteria widely distributed in soil, plant and freshwater habitats. Lysobacter owes its name to the lytic effects on other microorganisms. To better understand their ecology and interactions with other (micro)organisms, five Lysobacter strains representing the four species L. enzymogenes, L. capsici, L. gummosus and L. antibioticus were subjected to genomics and metabolomics analyses.

Results

Comparative genomics revealed a diverse genome content among the Lysobacter species with a core genome of 2,891 and a pangenome of 10,028 coding sequences. Genes encoding type I, II, III, IV, V secretion systems and type IV pili were highly conserved in all five genomes, whereas type VI secretion systems were only found in L. enzymogenes and L. gummosus. Genes encoding components of the flagellar apparatus were absent in the two sequenced L. antibioticus strains. The genomes contained a large number of genes encoding extracellular enzymes including chitinases, glucanases and peptidases. Various nonribosomal peptide synthase (NRPS) and polyketide synthase (PKS) gene clusters encoding putative bioactive metabolites were identified but only few of these clusters were shared between the different species. Metabolic profiling by imaging mass spectrometry complemented, in part, the in silico genome analyses and allowed visualisation of the spatial distribution patterns of several secondary metabolites produced by or induced in Lysobacter species during interactions with the soil-borne fungus Rhizoctonia solani.

Conclusions

Our work shows that mining the genomes of Lysobacter species in combination with metabolic profiling provides novel insights into the genomic and metabolic potential of this widely distributed but understudied and versatile bacterial genus.\n\nComparative genomics and metabolic profiling of the genus Lysobacter.", "token_count": 487, "char_count": 1912, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:22.321571", "source": { "split": "train_shard_00001", "doc_id": 4055 }, "chunk_id": "train_shard_00001_4055_0", "global_id": 11397 }, { "text": "The prevalence of diabetes mellitus is increasing globally. Probiotics have been shown to be an effective intervention for diabetes. This study focused on the relieving effects and possible mechanisms of 16 strains of two dominant Bifidobacterium species (B. bifidum and B. adolescentis, which exist in the human gut at different life stages) on type 2 diabetes (T2D). The results indicated that more B. adolescentis strains appeared to be superior in alleviating T2D symptoms than B. bifidum strains. This effect was closely related to the ability of B. adolescentis to restore the homeostasis of the gut microbiota, increase the abundance of short-chain fatty acid-producing flora, and alleviate inflammation in mice with T2D. In addition, compared with B. bifidum, B. adolescentis had a higher number of core genes, and these genes were more evolutionarily stable, including unique environmental tolerance, carbon and nitrogen utilization genes, and a blood sugar regulation gene, glgP. This may be one of the reasons why B. adolescentis is more likely to colonize in the adult gut and show a superior ability to relieve T2D. This study provides insights into future studies aimed at investigating probiotics for the treatment of metabolic diseases.\n\nBifidobacterium adolescentis Is Effective in Relieving Type 2 Diabetes and May Be Related to Its Dominant Core Genome and Gut Microbiota Modulation Capacity.", "token_count": 409, "char_count": 1488, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:22.943154", "source": { "split": "train_shard_00001", "doc_id": 4056 }, "chunk_id": "train_shard_00001_4056_0", "global_id": 11398 }, { "text": "Acinetobacter species assigned to the Acinetobacter calcoaceticus-baumannii (Acb) complex, are Gram-negative bacteria responsible for a large number of human infections. The population structure of Acb has been studied using two 7-gene MLST schemes, introduced by Bartual and coworkers (Oxford scheme) and by Diancourt and coworkers (Pasteur scheme). The schemes have three genes in common but underlie two coexisting nomenclatures of sequence types and clonal complexes, which complicates communication on A. baumannii genotypes. The aim of this study was to compare the characteristics of the two schemes to make a recommendation about their usage. Using genome sequences of 730 strains of the Acb complex, we evaluated the phylogenetic congruence of MLST schemes, the correspondence between sequence types, their discriminative power and genotyping reliability from genomic sequences. In silico ST re-assignments highlighted the presence of a second copy of the Oxford gdhB locus, present in 553/730 genomes that has led to the creation of artefactual profiles and STs. The reliability of the two MLST schemes was tested statistically comparing MLST-based phylogenies to two reference phylogenies (core-genome genes and genome-wide SNPs) using topology-based and likelihood-based tests. Additionally, each MLST gene fragment was evaluated by correlating the pairwise nucleotide distances between each pair of genomes calculated on the core-genome and on each single gene fragment. The Pasteur scheme appears to be less discriminant among closely related isolates, but less affected by homologous recombination and more appropriate for precise strain classification in clonal groups, which within this scheme are more often correctly monophyletic. Statistical tests evaluate the tree deriving from the Oxford scheme as more similar to the reference genome trees. Our results, together with previous work, indicate that the Oxford scheme has important issues: gdhB paralogy, recombination, primers sequences, position of the genes on the genome", "token_count": 510, "char_count": 2087, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6199, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:23.594201", "source": { "split": "train_shard_00001", "doc_id": 4057 }, "chunk_id": "train_shard_00001_4057_0", "global_id": 11399 }, { "text": "While there is no complete agreement in all analyses, when considered as a whole the above results indicate that the Pasteur scheme is more appropriate for population biology and epidemiological studies of A. baumannii and related species and we propose that it should be the scheme of choice during the transition toward, and in parallel with, core genome MLST.\n\nComparative Analysis of the Two Acinetobacter baumannii Multilocus Sequence Typing (MLST) Schemes.", "token_count": 117, "char_count": 476, "word_count": 71, "semantic_coherence": 1, "information_density": 0.8028, "quality_score": 0.9014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:23.978645", "source": { "split": "train_shard_00001", "doc_id": 4057 }, "chunk_id": "train_shard_00001_4057_1", "global_id": 11400 }, { "text": "A novel strain of a member of the genus Acinetobacter, strain PS-1T, was isolated from the skin of fresh water pufferfish (Tetraodon cutcutia) collected from Mahanadi River, India. Cells were Gram-stain-negative, aerobic, coccoid and non-motile. The predominant polar lipids were diphosphatidylglycerol (DPG), phosphatidylglycerol (PG), phosphatidylethanolamine (PE) and phospholipid (PL) and the cell wall sugars were glucose, galactose and ribose. The major cellular fatty acids of PS-1T were C18 : 1ω9c (30.67 %), C16 : 1ω7c (19.54 %), C16 : 0 (15.87 %), C12 : 0 (7.35 %) and C12 : 0 3-OH (6.77 %). The genome size was 3.5 Mbp and the DNA G+C content was 41.97 %. Gene ontology study revealed that the major fraction of genes were associated with biological processes (53.99 %) followed by molecular function (30.42 %) and cellular components (15.58 %). Comparisons of 16S rRNA gene sequences revealed 97.94-97.05 % sequence similarity with the closely related type strains of species of the genus Acinetobacter", "token_count": 440, "char_count": 1126, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6855, "quality_score": 0.8428, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:24.615134", "source": { "split": "train_shard_00001", "doc_id": 4058 }, "chunk_id": "train_shard_00001_4058_0", "global_id": 11401 }, { "text": "The average nucleotide identity (ANI) and average amino acid identity (AAI) of PS-1T with reference strains of species of the genus Acinetobacter with validly published names were bellow 95-96 and the corresponding in-silico DNA-DNA hybridization (DDH) values were below 70 %. A phylogenomic tree based on core genome analysis supported these results. Genotypic and phenotypic characteristics of PS-1T indicate that the strain represents a novel species of the genus Acinetobacter and the name Acinetobacter kanungonis sp. nov. is proposed. The type strain is PS-1T (=JCM 34131T=NCIMB 15260T).\n\nDescription of Acinetobacter kanungonis sp. nov., based on phylogenomic analysis.", "token_count": 257, "char_count": 766, "word_count": 97, "semantic_coherence": 1, "information_density": 0.6701, "quality_score": 0.8351, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:25.156536", "source": { "split": "train_shard_00001", "doc_id": 4058 }, "chunk_id": "train_shard_00001_4058_1", "global_id": 11402 }, { "text": "Abstract

Background:This study was carried out to determine the prevalence and the genetic background of extended-spectrum β-lactamase-producing Escherichia coli invasive isolates obtained from a tertiary-care hospital in Budapest, Hungary. MethodsBetween October-November 2018, all invasive ESBL-producing E. coli isolates were collected from Central Hospital of Southern Pest. The antimicrobial susceptibility testing was performed according to the EUCAST guidelines. The possible clonal relationships were investigated by core genome (cg)MLST (SeqSphere+) using whole-genome sequencing (WGS) data of isolates obtained from Illumina 251-bp paired-end sequencing. From WGS data acquired antimicrobial resistance genes and replicon types were retrieved using ResFinder3.1, PlasmidFinder2.1, and pMLST-2.0 online tools.ResultsOverall, 25 E. coli isolates were detected and six proved to be resistant to third-generation cephalosporins. Full genome sequence analysis showed that five E. coli isolates belonged to the ST131 clone: two to C1-M27 subclade with blaCTX-M-27 and three to C2/H30Rx subclade with blaCTX-M-15. One isolate belonged to ST1193 with blaCTX-M-27. According to cgMLST, all C2/H30Rx isolates formed a cluster (≤6 allele differences), while the blaCTX-M-27-producing C1-M27 isolates differed at least 35 alleles from each other", "token_count": 505, "char_count": 1574, "word_count": 175, "semantic_coherence": 1, "information_density": 0.7029, "quality_score": 0.8514, "entities": { "genes": [ "ST131", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:25.818841", "source": { "split": "train_shard_00001", "doc_id": 4059 }, "chunk_id": "train_shard_00001_4059_0", "global_id": 11403 }, { "text": "Both C2/H30Rx and C1-M27 ST131 isolates harbored similar antimicrobial resistance gene sets. However, only C2/H30Rx isolates had the qnrB and aac(3)-IIa. All isolates showed resistance against ceftriaxone, cefotaxime, and ciprofloxacin, and the C2/H30Rx isolates were also resistant to gentamicin, tobramycin, and ceftazidime.ConclusionsOut of six third-generation cephalosporins-resistant, invasive E. coli, five belonged to the S131clone. This study indicates, that the C2/H30Rx and C1-M27 subclades of the ST131 appear to be the dominant clones collected in a Hungarian hospital.

\n\nPopulation Snapshot of the Extended-spectrum β-lactamase-producing Escherichia Coli Invasive Strains Isolated From a Hungarian Hospital", "token_count": 273, "char_count": 783, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7174, "quality_score": 0.8587, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:26.374618", "source": { "split": "train_shard_00001", "doc_id": 4059 }, "chunk_id": "train_shard_00001_4059_1", "global_id": 11404 }, { "text": "The aim of this study was to develop and validate a novel bioassay for determining serum voriconazole (VRC) concentrations and to compare its routine clinical performance with that of high-performance liquid chromatography (HPLC). The biological activity of VRC was measured by a plate diffusion assay using a VRC-hypersusceptible Candida kefyr strain. The bioassay's utility was tested by measuring steady-state VRC concentrations in 100 serum probes from VRC-treated patients. The HPLC system used solvent extraction with hexane:dichloromethane followed by reversed-phase HPLC with ultraviolet detection. The intra-day and inter-day accuracy of the bioassay was <5%, while that of HPLC was <1%. The precision (mean coefficient of variation, 3.5%) was equal for both the methods. The limit of quantification was lower for HPLC (0.2 mg l(-1)) than for the bioassay (0.5 mg l(-1)). The result of linear regression analysis was HPLC = 1.0178 (bioassay) + 0.328; R(2) = 0.88; n = 100. Results of the serum panel ranged from 0.5 to more than 8.0 mg l(-1) for the bioassay and from 0.26 to 10.1 mg l(-1) for HPLC. Especially in laboratories without access to HPLC, the bioassay may be a clinically useful tool for therapeutic drug monitoring.\n\nComparison and evaluation of a novel bioassay and high-performance liquid chromatography for the clinical measurement of serum voriconazole concentrations.", "token_count": 406, "char_count": 1394, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:26.995941", "source": { "split": "train_shard_00001", "doc_id": 4060 }, "chunk_id": "train_shard_00001_4060_0", "global_id": 11405 }, { "text": "Researchers contest the importance of gene flow in bacterial core genomes, as traditionalists view microbes as predominantly clonal, asexually reproducing organisms. Contrary to the traditional perspective, Escherichia coli core genes vary greatly in their levels of synonymous genetic diversity. This observation indicates that the relative importance of evolutionary forces such as mutation, selection, and recombination varies from gene to gene. In this paper, I highlight why the synonymous diversity observation is broadly relevant to researchers interested in the evolutionary dynamics of microbial populations and communities. I explain how a model of evolution called the coalescent relates neutral diversity (i.e. mutations with negligible fitness effects) to mutation rates, evolutionary time, and a parameter called effective population size. I then describe the possible ways in which mutation, selection, and recombination can explain observed patterns of synonymous diversity in E. coli. Finally, I describe a model for E. coli genome evolution in which different loci are subject to varying levels of gene flow among co-occurring microbes and viruses in the environment. Researchers can falsify the gene flow hypothesis by sequencing genes and strains isolated from stable microbiomes or by carrying out evolution experiments that trace gene genealogies in real-time.\n\nGene flow in microbial communities could explain unexpected patterns of synonymous variation in the Escherichia coli core genome.", "token_count": 336, "char_count": 1541, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5888, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:27.567583", "source": { "split": "train_shard_00001", "doc_id": 4061 }, "chunk_id": "train_shard_00001_4061_0", "global_id": 11406 }, { "text": "Separation of yeast cells using a co-flocculation process was investigated. Co-flocculation is a fast process (within few minutes), occurs in a broad pH range (3.0-8.0) and requires a small amount of calcium (0.1 mM). Agitation affects yeast aggregation; however, an agitation between 60 rev/min and 160 rev/min has only a little influence on the co-flocculation process. The ratio flocculent/non-flocculent cells that induced the settling of 50 and 90% of the cells of S. cerevisiae was 1:7 and 1:1, respectively. Separation of non-flocculent cells can be carried out at any time of the growth cycle. No difference in the efficiency of co-flocculation carried out in buffer (pH 4.0 with 10 mM calcium) or in 48 h-fermented broth was observed. Flocculent cells of Saccharomyces cerevisiae had the ability to sediment non-flocculent cells of S. cerevisiae and Kluyveromyces marxianus, which shows the suitability of the co-flocculation process for separation of different kinds of non-flocculent cells.\n\nSeparation of yeasts by addition of flocculent cells of Saccharomyces cerevisiae", "token_count": 325, "char_count": 1083, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:28.130908", "source": { "split": "train_shard_00001", "doc_id": 4062 }, "chunk_id": "train_shard_00001_4062_0", "global_id": 11407 }, { "text": "Lafun is a fermented cassava food product consumed in parts of West Africa. In the present work the microorganisms (aerobic bacteria (AB), lactic acid bacteria (LAB) and yeasts) associated with the fermentation of Lafun under traditional conditions have for the first time been studied using a combination of pheno- and genotypic methods. During Lafun fermentation the AB count ranged from 6-7 log(10) CFU/g at the beginning to 9 log(10) CFU/g at the end. Similarly, the number of LAB increased from 5 log(10) CFU/g to 9 log(10) CFU/g during the process while the yeast load increased from 3 log(10) CFU/g at the onset of the fermentation to 5-6 log(10) CFU/g at the end of the fermentation. A total of 168 isolates (31 AB, 88 LAB, and 49 yeasts) were isolated and identified by means of phenotypic tests, PCR-based methods and 16S rRNA gene sequencing. The aerobic bacteria were mostly identified as belonging to the Bacillus cereus group (71%). The B. cereus isolates lacked the genetic determinant specific for cereulide producers but harboured several genes encoding the heat-labile toxins hemolysin BL and nonhemolytic enterotoxin as detected by PCR. The other aerobic bacteria isolated were Gram negative and identified as Klebsiella pneumoniae and Pantoea agglomerans. The dominant LAB were identified as Lactobacillus fermentum (42% of LAB isolates) followed by Lactobacillus plantarum (30%) and Weissella confusa (18%). Seven isolates remained unidentified and constitute probably a novel LAB species", "token_count": 444, "char_count": 1509, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:28.767011", "source": { "split": "train_shard_00001", "doc_id": 4063 }, "chunk_id": "train_shard_00001_4063_0", "global_id": 11408 }, { "text": "The predominant yeast species associated with Lafun fermentation were Saccharomyces cerevisiae (22% of yeast isolates), Pichia scutulata (20%), Kluyveromyces marxianus (18%), Hanseniaspora guilliermondii (12%), Pichia rhodanensis (8%) and Candida glabrata (8%) as well as Pichia kudriavzevii, Candida tropicalis and Trichosporon asahii at lower incidence (<5% each).\n\nThe microbiota of Lafun, an African traditional cassava food product.", "token_count": 149, "char_count": 437, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8393, "quality_score": 0.9196, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:29.201136", "source": { "split": "train_shard_00001", "doc_id": 4063 }, "chunk_id": "train_shard_00001_4063_1", "global_id": 11409 }, { "text": "Microbial organisms inhabit virtually all environments and encompass a vast biological diversity. The pan-genome concept aims to facilitate an understanding of diversity within defined phylogenetic groups. Hence, pan-genomes are increasingly used to characterize the strain diversity of prokaryotic species. To understand the interdependency of pan-genome features (such as numbers of core and accessory genes) and to study the impact of environmental and phylogenetic constraints on the evolution of conspecific strains, we computed pan-genomes for 155 phylogenetically diverse species using 7000 high-quality genomes. We show that many pan-genome features such as functional diversity and core genome nucleotide diversity are correlated to each other. Further, habitat flexibility as approximated by species ubiquity is associated with several pan-genome features, particularly core genome size. In general, environment had a stronger impact on pan-genome features than phylogenetic signal. Similar environmental preferences led to convergent evolution of pan-genomic features in distant phylogenetic clades. For example, the soil environment promotes expansion of pan-genome size, while host-associated habitats lead to its reduction.\n\nDisentangling the impact of environmental and phylogenetic constraints on prokaryotic strain diversity", "token_count": 293, "char_count": 1341, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:29.755612", "source": { "split": "train_shard_00001", "doc_id": 4064 }, "chunk_id": "train_shard_00001_4064_0", "global_id": 11410 }, { "text": "Sequence comparisons between Saccharomyces cerevisiae ScMig1 and Aspergillus nidulans CREA proteins allowed us to design two sets of degenerate primers from the conserved zinc finger loops. PCR amplification on Kluyveromyces marxianus and K. lactis genomic DNA yielded single products with sequences closely related to each other and to the corresponding regions of ScMig1 and CREA. The KIMIG1 gene of K. lactis was cloned from a genomic library using the K. marxianus PCR fragment as probe. KIMIG1 encodes a 474-amino acid protein 55% similar to ScMig1. Besides their highly conserved zinc fingers, the two proteins display short conserved motifs of possible significance in glucose repression. Heterologous complementation of a mig1 mutant of S. cerevisiae by the K. lactis gene demonstrates that the function of the Mig1 protein is conserved in these two distantly related yeasts.\n\nThe MIG1 repressor from Kluyveromyces lactis: cloning, sequencing and functional analysis in Saccharomyces cerevisiae.", "token_count": 277, "char_count": 1003, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [ "MIG1", "KIMIG1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:30.311310", "source": { "split": "train_shard_00001", "doc_id": 4065 }, "chunk_id": "train_shard_00001_4065_0", "global_id": 11411 }, { "text": "Humans, like all mammals, depend on the gut microbiome for digestion of cellulose, the main component of plant fiber. However, evidence for cellulose fermentation in the human gut is scarce. We have identified ruminococcal species in the gut microbiota of human populations that assemble functional multienzymatic cellulosome structures capable of degrading plant cell wall polysaccharides. One of these species, which is strongly associated with humans, likely originated in the ruminant gut and was subsequently transferred to the human gut, potentially during domestication where it underwent diversification and diet-related adaptation through the acquisition of genes from other gut microbes. Collectively, these species are abundant and widespread among ancient humans, hunter-gatherers, and rural populations but are rare in populations from industrialized societies thus indicating potential disappearance in response to the westernized lifestyle.\n\nCryptic diversity of cellulose-degrading gut bacteria in industrialized humans.", "token_count": 216, "char_count": 1036, "word_count": 139, "semantic_coherence": 1, "information_density": 0.705, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:30.776716", "source": { "split": "train_shard_00001", "doc_id": 4066 }, "chunk_id": "train_shard_00001_4066_0", "global_id": 11412 }, { "text": "1. Since the introduction of the White-Kauffmann-Le Minor (WKL) scheme for Salmonella serotyping, the nomenclature remains the most widely used for reporting the disease prevalence of Salmonella enterica across the globe. With the advent of whole genome sequencing (WGS), traditional serotyping has been increasingly replaced by in-silico methods that couple the detection of genetic variations in antigenic determinants with sequence-based typing. However, despite the integration of genomic-based typing by in-silico serotyping tools such as SeqSero2 and SISTR, in-silico serotyping in certain contexts remains ambiguous and insufficiently informative due to polyphyletic serovars. Furthermore, in spite of the widespread acknowledgement of polyphyly from genomic studies, the serotyping nomenclature remains unaltered. To prompt refinements to the Salmonella typing nomenclature for disease reporting, we herein performed a systematic characterization of putative polyphyletic serovars and the global Salmonella population structure by comparing 180,098 Salmonella genomes (representing 723 predicted serovars) from GenomeTrakr and PubMLST databases. We identified a range of core genome MLST typing thresholds that result in stable population structure, potentially suitable as the foundation of a genomic-based typing nomenclature for longitudinal surveillance. From the genomic comparisons of hundreds of predicted serovars, we demonstrated that in-silico serotyping classifications do not consistently reflect the population divergence observed at the genomic level. The organization of Salmonella subpopulations based on antigenic determinants can be confounded by homologous recombination and niche adaptation, resulting in shared classification of highly divergent genomes and misleading distinction between highly similar genomes. In consideration of the pivotal role of Salmonella serotyping, a compendium of putative polyphyletic serovars was compiled and made publicly available to provide additional context for future interpretations of in-silico serotyping results in disease surveillance settings", "token_count": 483, "char_count": 2114, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6022, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:31.482674", "source": { "split": "train_shard_00001", "doc_id": 4067 }, "chunk_id": "train_shard_00001_4067_0", "global_id": 11413 }, { "text": "To refine the typing nomenclatures used in Salmonella surveillance reports, we foresee an improved typing scheme to be a hybrid that integrates both genomic and antigenic information such that the resolution from WGS is leveraged to improve the precision of subpopulation classifications while preserving the common names defined by the WKL scheme. Lastly, we stress the importance of controlled vocabulary integration for typing information in open data settings in order for the global Salmonella population dynamics to be fully trackable. 2.

Impact Statement

Salmonella enterica ( S. enterica ) is a major foodborne pathogen responsible for an annual incidence rate of more than 90 million cases of foodborne illnesses worldwide. To surveil the high order Salmonella lineages, compare disease prevalence across jurisdictions worldwide, and inform risk assessments, in-silico serotyping has been established as the gold standard for typing the bacteria. However, despite previous Salmonella genomic studies reporting discordance between phylogenomic clades and serovars, refinements have yet been made to the serotyping scheme. Here, we analyzed over 180,000 Salmonella genomes representing 723 predicted serovars to subdivide the population into evolutionarily stable clusters in order to propose a stable organization of the Salmonella population structure that can form the basis of a genomic-based typing scheme for the pathogen. We described numerous instances in which genomes between serotypes are more similar than genomes within a serotype to reflect the inconsistencies of subpopulation classifications based on antigenic determinants. Moreover, we found inconsistencies between predicted serovars and reported serovars which highlighted potential errors in existing in-silico serotyping tools and the need to implement controlled vocabularies for reporting Salmonella subtypes in public databases. The findings of our study aim to motivate the future development of a standardized genomic-based typing nomenclature that more accurately captures the natural populations of S. enterica . 3.

Data Summary

The assembly accession numbers of the genomes analyzed in this study (n = 204,952) and the associated metadata (e.g. sampling location, collection date, FTP address for retrieval) are documented in Table S1", "token_count": 523, "char_count": 2339, "word_count": 330, "semantic_coherence": 1, "information_density": 0.6152, "quality_score": 0.8076, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:46:32.151509", "source": { "split": "train_shard_00001", "doc_id": 4067 }, "chunk_id": "train_shard_00001_4067_1", "global_id": 11414 }, { "text": "The GenomeTrakr genomes were retrieved from the National Center for Biological Information GenBank database. The PubMLST genomes were retrieved using the BIGSdb API.\n\nLarge-scale comparative genomics of Salmonella enterica to refine the organization of the global Salmonella population structure", "token_count": 80, "char_count": 309, "word_count": 39, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:32.571565", "source": { "split": "train_shard_00001", "doc_id": 4067 }, "chunk_id": "train_shard_00001_4067_2", "global_id": 11415 }, { "text": "Leptospirosis is an emerging zoonotic and neglected disease across the world causing huge loss of life and economy. The disease is caused by Leptospira of which 605 sequenced genomes representing 72 species are available in RefSeq database. A comparative genomics approach based on Average Amino acid Identity (AAI), Average Nucleotide Identity (ANI), and Insilco DNA-DNA hybridization provide insight that taxonomic and evolutionary position of few genomes needs to be changed and reclassified. Clustering on the basis of AAI of core and pan-genome contradict clustering pattern on basis of ANI into 4 clusters. Amino acid identity based hierarchical clustering clearly established 3 clusters of Leptospira correlating with level of virulence. Whole genome tree supported three cluster classifications and grouped Leptospira into three clades termed as pathogenic, intermediate and saprophytic. Leptospira genus consist of diverse species and exist in heterogeneous environment, it contains relatively large and closed core genome of 1038 genes. Analysis provided pan genome remains open with 20822 genes. COG analysis revealed that mobilome related genes were found mainly in pan-genome of pathogenic clade. Clade specific genes mined in the study can be used as marker for determining clade and associating level of virulence of any new Leptospira species. Many known Leptospira virulent genes were absent in set of 78 virulent factors mined using Virulence Factor database. A deep search approach provided a repertoire of 496 virulent genes in pan-genome. Further validation of virulent genes will help in accurately targeting pathogenic Leptospira and controlling leptospirosis.

Graphical Abstract

\n\nComparative analysis of whole genome sequences ofLeptospiraspp. from RefSeq database provide interspecific divergence and repertoire of virulence factors", "token_count": 461, "char_count": 1873, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6302, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:33.221652", "source": { "split": "train_shard_00001", "doc_id": 4068 }, "chunk_id": "train_shard_00001_4068_0", "global_id": 11416 }, { "text": "Spent grains (SG), the residue remaining after extraction of wort, are a major by-product of brewing. This lignocelluose-rich biomass may provide a source of sugars for fuel ethanol fermentations. Dilute acid and enzyme treatments were developed to convert the hemicellulose and cellulose fractions to glucose, xylose and arabinose. Pretreatment of dried, milled grains with 0.16 N HNO(3) at 121 degrees C for 15 min was chosen as the most suitable method for solubilizing grains before enzymatic digestion with cellulase and hemicellulase preparations. Solids loading concentrations (10%, 15% and 20% w/v) were compared and reducing sugar between 40 and 48 g (100 g SG)(-1) was extracted. Hydrolysate, prepared from 20% SG, pretreated with 0.16 N HNO(3), partially neutralized to pH 5-6 and digested with enzymes for 18 h, contained 27 g L(-1) glucose, 16.7 g L(-1) xylose and 11.9 g L(-1) arabinose. Fermentation of this hydrolysate for 48 h by Pichia stipitis and Kluyveromyces marxianus resulted in 8.3 and 5.9 g L(-1) ethanol corresponding to ethanol conversion yields of 0.32 and 0.23 g ethanol (g substrate)(-1), respectively. Substrate utilization efficiency was less when compared with glucose/xylose mixtures in synthetic media, suggesting that yeast inhibitory compounds derived from SG were present in the hydrolysate.\n\nBioconversion of brewer's spent grains to bioethanol.", "token_count": 456, "char_count": 1385, "word_count": 209, "semantic_coherence": 1, "information_density": 0.689, "quality_score": 0.8445, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:33.863853", "source": { "split": "train_shard_00001", "doc_id": 4069 }, "chunk_id": "train_shard_00001_4069_0", "global_id": 11417 }, { "text": "

Motivation

High-resolution microbial strain typing is essential for various clinical purposes, including disease outbreak investigation, tracking of microbial transmission events and epidemiological surveillance of bacterial infections. The widely used approach for multilocus sequence typing (MLST) that is based on the core genome, cgMLST, has the advantage of a high level of typeability and maximal discriminatory power. Yet, the transition from a seven loci-based scheme to cgMLST involves several challenges, that include the need by some users to maintain backward compatibility, growing difficulties in the day-to-day communication within the microbiology community with respect to nomenclature and ontology, issues with typeability, especially if a more stringent approach to loci presence is used, and computational requirements concerning laboratory data management and sharing with end-users. Hence, methods for optimizing cgMLST schemes through careful reduction of the number of loci are expected to be beneficial for practical needs in different settings.

Results

We present a new machine learning-based methodology, minMLST, for minimizing the number of genes in cgMLST schemes by identifying subsets of informative genes and analyzing the trade-off between gene reduction and typing performance. The results achieved with minMLST over eight bacterial species show that despite the reduction in the number of genes up to a factor of 10, the typing performance remains very high and significant with an Adjusted Rand Index that ranges between 0.4 and 0.93 in different species and a P-value < 10-3. The identification of such optimized MLST schemes for bacterial strain typing is expected to improve the implementation of cgMLST by improving interlaboratory agreement and communication.

Availability and implementation

The python package minMLST is available at https://PyPi.org/project/minmlst/PyPI and supported on Linux and Windows.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nminMLST: machine learning for optimization of bacterial strain typing.", "token_count": 471, "char_count": 2136, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6175, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:34.514395", "source": { "split": "train_shard_00001", "doc_id": 4070 }, "chunk_id": "train_shard_00001_4070_0", "global_id": 11418 }, { "text": "The production of inulinase employing agroindustrial residues as the substrate is a good alternative to reduce production costs and to minimize the environmental impact of disposing these residues in the environment. This study focused on the use of a phenomenological model and an artificial neural network (ANN) to simulate the inulinase production during the batch cultivation of the yeast Kluyveromyces marxianus NRRL Y-7571, employing a medium containing agroindustrial residues such as molasses, corn steep liquor and yeast extract. It was concluded that due to the complexity of the medium composition it was rather difficult to use a phenomenological model with sufficient accuracy. For this reason, an alternative and more cost-effective methodology based on ANN was adopted. The predictive capacity of the ANN was superior to that of the phenomenological model, indicating that the neural network approach could be used as an alternative in the predictive modeling of complex batch cultivations.\n\nInulinase production in a batch bioreactor using agroindustrial residues as the substrate: experimental data and modeling.", "token_count": 240, "char_count": 1129, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5482, "quality_score": 0.7741, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:34.991299", "source": { "split": "train_shard_00001", "doc_id": 4071 }, "chunk_id": "train_shard_00001_4071_0", "global_id": 11419 }, { "text": "Lactobacillus acidophilus is a gram-positive, microaerophilic, and acidophilic bacterial species. L. acidophilus strains in the gastrointestinal tracts of humans and other animals have been profiled, but strains found in the canine gut have not been studied yet. Our study helps in understanding the genetic features of the L. acidophilus C5 strain found in the canine gut, determining its adaptive features evolved to survive in the canine gut environment, and in elucidating its probiotic functions. To examine the canine L. acidophilus C5 genome, we isolated the C5 strain from a Korean dog and sequenced it using PacBio SMRT sequencing technology. A comparative genomic approach was used to assess genetic relationships between C5 and six other strains and study the distinguishing features related to different hosts. We found that most genes in the C5 strain were related to carbohydrate transport and metabolism. The pan-genome of seven L. acidophilus strains contained 2,254 gene families, and the core genome contained 1,726 gene families. The phylogenetic tree of the core genes in the canine L. acidophilus C5 strain was very close to that of two strains (DSM20079 and NCFM) from humans. We identified 30 evolutionarily accelerated genes in the L. acidophilus C5 strain in the ratio of non-synonymous to synonymous substitutions (dN/dS) analysis. Five of these thirty genes were associated with carbohydrate transport and metabolism. This study provides insights into genetic features and adaptations of the L. acidophilus C5 strain to survive the canine intestinal environment. It also suggests that the evolution of the L. acidophilus genome is closely related to the host's evolutionary adaptation process.", "token_count": 489, "char_count": 1783, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5019, "quality_score": 0.751, "entities": { "genes": [ "DSM20079" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:35.643797", "source": { "split": "train_shard_00001", "doc_id": 4072 }, "chunk_id": "train_shard_00001_4072_0", "global_id": 11420 }, { "text": "Complete genome sequencing and comparative genomic analysis of Lactobacillus acidophilus C5 as a potential canine probiotics.", "token_count": 39, "char_count": 132, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:36.002911", "source": { "split": "train_shard_00001", "doc_id": 4072 }, "chunk_id": "train_shard_00001_4072_1", "global_id": 11421 }, { "text": "The thermophilic bacterium Rhodothermus marinus has mainly been studied for its thermostable enzymes. More recently, the potential of using the species as a cell factory and in biorefinery platforms has been explored, due to the elevated growth temperature, native production of compounds such as carotenoids and EPSs, the ability to grow on a wide range of carbon sources including polysaccharides, and available genetic tools. A comprehensive understanding of the metabolism of production organisms is crucial. Here, we report a genome-scale metabolic model of R. marinus DSM 4252 T . Moreover, the genome of the genetically amenable R. marinus ISCaR-493 was sequenced and the analysis of the core genome indicated that the model could be used for both strains. Bioreactor growth data was obtained, used for constraining the model and the predicted and experimental growth rates were compared. The model correctly predicted the growth rates of both strains. During the reconstruction process, different aspects of the R. marinus metabolism were reviewed and subsequently, both cell densities and carotenoid production were investigated for strain ISCaR-493 under different growth conditions. Additionally, the dxs gene, which was not found in the R. marinus genomes, from Thermus thermophilus was cloned on a shuttle vector into strain ISCaR-493 resulting in a higher yield of carotenoids.

Importance

A biorefinery converting biomass into fuels and value-added chemicals is a sustainable alternative to fossil fuel-based chemical synthesis. Rhodothermus marinus is a bacterium that is potentially well suited for biorefineries. It possesses various enzymes that degrade biomass, such as macroalgae and parts of plants (e.g. starch and xylan) and grows at high temperatures (55-77°C) which is beneficial in biorefinery processes. In this study, we reviewed the metabolism of R. marinus and constructed a metabolic model. Such a model can be used to predict phenotypes, e.g. growth under different environmental and genetic conditions. We focused specifically on metabolic features that are of interest in biotechnology, including carotenoid pigments which are used in many different industries", "token_count": 528, "char_count": 2203, "word_count": 324, "semantic_coherence": 1, "information_density": 0.5494, "quality_score": 0.7747, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:46:36.638654", "source": { "split": "train_shard_00001", "doc_id": 4073 }, "chunk_id": "train_shard_00001_4073_0", "global_id": 11422 }, { "text": "We described cultivations of R. marinus and the resulting carotenoid production in different growth conditions, which aids in understanding how carotenoid yields can be increased in the bacterium.\n\nA genome-scale metabolic reconstruction provides insight into the metabolism of the thermophilic bacteriumRhodothermus marinus", "token_count": 80, "char_count": 331, "word_count": 42, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:37.019801", "source": { "split": "train_shard_00001", "doc_id": 4073 }, "chunk_id": "train_shard_00001_4073_1", "global_id": 11423 }, { "text": "

Purpose

Three NDM-5-producing Enterobacteriaceae (Escherichia coli, Klebsiella pneumoniae, and Citrobacter braakii, one each) were isolated during a screening study for the presence of carbapenemase-producing Enterobacteriaceae (CPE) strains in urban rivers in China. The aim of the present study was to characterize these NDM-5-producing isolates by using whole-genome analysis.

Methods

In vitro susceptibility testing was performed using the broth microdilution method. Conjugation assay was carried out to investigate the transferability of bla NDM-5-harboring plasmids. Whole-genome sequencing was performed using an Illumina HiSeq combined with the PacBio RSII system. The genetic characteristics of the bla NDM-5-harboring plasmids were analyzed. Antimicrobial resistance genes and virulence genes were identified from the genome sequences. Phylogenetic analysis was performed based on core genome.

Results

Antimicrobial susceptibility testing showed that all three isolates were resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, and susceptible to colistin. Whole-genome sequencing showed that each isolate carried multiple antibiotic resistance genes mediating multidrug resistance, and harbored numerous virulence genes, some of which were located on plasmids. In these isolates, bla NDM-5 was carried by an IncX3 plasmid in K. pneumoniae and C. braakii, and on an IncR/IncX1 plasmid in E. coli. Conjugation experiments showed that these bla NDM-5-haboring plasmids were successfully transferred to E. coli J53", "token_count": 519, "char_count": 1673, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6181, "quality_score": 0.809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:46:37.652541", "source": { "split": "train_shard_00001", "doc_id": 4074 }, "chunk_id": "train_shard_00001_4074_0", "global_id": 11424 }, { "text": "Phylogenetic analysis revealed that E. coli SCLZR49 was present in a cluster with isolates of different origin, K. pneumoniae SCLZR50 was mainly clustered with clinical isolates, and C. braakii SCLZR53 had closely genetic relationship with environmental isolates.

Conclusion

This study revealed contamination of the urban river ecosystems by clinically significant carbapenemase gene bla NDM-5, raising the possibility of plasmid transmission into the environmental from humans and highlighting the need for a constant surveillance of CPE in the environment under the \"One-Health\" perspective.\n\nWhole-Genomic Analysis of NDM-5-Producing Enterobacteriaceae Recovered from an Urban River in China.", "token_count": 207, "char_count": 741, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7609, "quality_score": 0.8804, "entities": { "genes": [ "SCLZR50", "SCLZR49", "SCLZR53" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:38.118829", "source": { "split": "train_shard_00001", "doc_id": 4074 }, "chunk_id": "train_shard_00001_4074_1", "global_id": 11425 }, { "text": "

Background

The growing importance of the ubiquitous fungal genus Trichoderma (Hypocreales, Ascomycota) requires understanding of its biology and evolution. Many Trichoderma species are used as biofertilizers and biofungicides and T. reesei is the model organism for industrial production of cellulolytic enzymes. In addition, some highly opportunistic species devastate mushroom farms and can become pathogens of humans. A comparative analysis of the first three whole genomes revealed mycoparasitism as the innate feature of Trichoderma. However, the evolution of these traits is not yet understood.

Results

We selected 12 most commonly occurring Trichoderma species and studied the evolution of their genome sequences. Trichoderma evolved in the time of the Cretaceous-Palaeogene extinction event 66 (±15) mya, but the formation of extant sections (Longibrachiatum, Trichoderma) or clades (Harzianum/Virens) happened in Oligocene. The evolution of the Harzianum clade and section Trichoderma was accompanied by significant gene gain, but the ancestor of section Longibrachiatum experienced rapid gene loss. The highest number of genes gained encoded ankyrins, HET domain proteins and transcription factors. We also identified the Trichoderma core genome, completely curated its annotation, investigated several gene families in detail and compared the results to those of other fungi. Eighty percent of those genes for which a function could be predicted were also found in other fungi, but only 67% of those without a predictable function.

Conclusions

Our study presents a time scaled pattern of genome evolution in 12 Trichoderma species from three phylogenetically distant clades/sections and a comprehensive analysis of their genes. The data offer insights in the evolution of a mycoparasite towards a generalist.\n\nEvolution and comparative genomics of the most common Trichoderma species.", "token_count": 477, "char_count": 1917, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:38.764396", "source": { "split": "train_shard_00001", "doc_id": 4075 }, "chunk_id": "train_shard_00001_4075_0", "global_id": 11426 }, { "text": "

Background

There is a significant gap in our understanding of the sources of multidrug-resistant bacteria and resistance genes in community settings where human-animal interfaces exist.

Objectives

This study characterized the relationship of third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) isolated from animal feces in the environment and child feces based on phenotypic antimicrobial resistance (AMR) and whole genome sequencing (WGS).

Methods

We examined 3GCR-EC isolated from environmental fecal samples of domestic animals and child fecal samples in Ecuador. We analyzed phenotypic and genotypic AMR, as well as clonal relationships (CRs) based on pairwise single-nucleotide polymorphisms (SNPs) analysis of 3GCR-EC core genomes. CRs were defined as isolates with fewer than 100 different SNPs.

Results

A total of 264 3GCR-EC isolates from children (n=21), dogs (n=20), and chickens (n=18) living in the same region of Quito, Ecuador, were identified. We detected 16 CRs total, which were found between 7 children and 5 domestic animals (5 CRs) and between 19 domestic animals (11 CRs). We observed that several clonally related 3GCR-EC isolates had acquired different plasmids and AMR genes. Most CRs were observed in different homes (n=14) at relatively large distances. Isolates from children and domestic animals shared the same blaCTX-M allelic variants, and the most prevalent were blaCTX-M-55 and blaCTX-M-65, which were found in isolates from children, dogs, and chickens.

Discussion

This study provides evidence of highly dynamic horizontal transfer of AMR genes and mobile genetic elements (MGEs) in the E", "token_count": 483, "char_count": 1686, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:39.409698", "source": { "split": "train_shard_00001", "doc_id": 4076 }, "chunk_id": "train_shard_00001_4076_0", "global_id": 11427 }, { "text": "coli community and shows that some 3GCR-EC and (extended-spectrum β-lactamase) ESBL genes may have moved relatively large distances among domestic animals and children in semirural communities near Quito, Ecuador. Child-animal contact and the presence of domestic animal feces in the environment potentially serve as important sources of drug-resistant bacteria and ESBL genes. https://doi.org/10.1289/EHP7729.\n\nEnvironmental Spread of Extended Spectrum Beta-Lactamase (ESBL) Producing Escherichia coli and ESBL Genes among Children and Domestic Animals in Ecuador.", "token_count": 166, "char_count": 576, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7123, "quality_score": 0.8562, "entities": { "genes": [ "EHP7729" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:39.857438", "source": { "split": "train_shard_00001", "doc_id": 4076 }, "chunk_id": "train_shard_00001_4076_1", "global_id": 11428 }, { "text": "Our knowledge and understanding of how bacterial pathogens have evolved has been limited by inadequate information on the full ecology of these organisms. Large-scale population genomic analyses have enabled a high-resolution view of variation at the core and accessory genome level, within and between bacterial populations, revealing previously hidden patterns of variation among microorganisms. This sheds light on the evolution and maintenance of ecologically distinct populations of bacteria and has raised the question of whether the same approach can uncover novel information on the ecology of established, clinically important pathogens. Yersinia pseudotuberculosis and Escherichia coli represent 'model' organisms in the study of microbial evolution, but given the high degree of niche overlap in both species, their ecology is largely unknown. In this study, genomic analyses of Y. pseudotuberculosis strains, obtained from various habitats worldwide, revealed a phylogeographic split within the population, with an Asian ancestry and subsequent dispersal of successful clonal lineages across the rest of the world. These lineages were differentiated by CRISPR arrays and we demonstrated that genetic exchange between ... (continues)\n\nElucidating the unknown ecology of bacterial pathogens from genomic data", "token_count": 277, "char_count": 1318, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6902, "quality_score": 0.8451, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:40.412803", "source": { "split": "train_shard_00001", "doc_id": 4077 }, "chunk_id": "train_shard_00001_4077_0", "global_id": 11429 }, { "text": "The present study was carried out to clarify the taxonomic assignment of two closely related Amycolatopsis species. Genomic information for 48 type strains was available at the time of conducting this analysis. Our analysis showed that two species, viz. Amycolatopsis eurytherma Kim et al. 2002 and Amycolatopsis thermoflava Chun et al. 1999, are conspecific. The 16S rRNA gene sequences of the two species possess 98.85 % sequence similarity. Further, whole-genome comparisons showed that A. eurytherma DSM 44348T and A. thermoflava N1165T shared 98.75 % average nucleotide identity, 98.63 % average amino acid identity and 87.8 % digital DNA-DNA hybridization values. These values exceed the threshold values for bacterial species delineation, indicating that they belong to the same species. Further, the phylogenomic analysis based on the core genome of the strains under study confirmed that A. eurytherma DSM 44348T and A. thermoflava N1165T formed a monophyletic clade. Based on this evidence we propose the reclassification of Amycolatopsis eurytherma Kim et al. 2002 as a later heterotypic synonym of Amycolatopsis thermoflava Chun et al. 1999.\n\nGenome-based reclassification of Amycolatopsis eurytherma as a later heterotypic synonym of Amycolatopsis thermoflava.", "token_count": 505, "char_count": 1429, "word_count": 186, "semantic_coherence": 1, "information_density": 0.586, "quality_score": 0.793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:41.072161", "source": { "split": "train_shard_00001", "doc_id": 4078 }, "chunk_id": "train_shard_00001_4078_0", "global_id": 11430 }, { "text": "Photodynamic treatment of the yeast Kluyveromyces marxianus with the sensitizer aluminum phthalocyanine results in loss of clonogenicity. In this paper the effect of this treatment on DNA of this yeast was investigated by searching for single strand breaks and forward mutations. Using the alkaline step elution technique it was found that illumination of the yeast in the presence of aluminum phthalocyanine resulted in an increase in single strand breaks. These could, partially, be repaired by post-incubating illuminated cells in growth medium. At comparable survival levels, photodynamic treatment with aluminum phthalocyanine induced fewer single strand breaks than X-ray treatment. By using a medium containing 5-fluoroorotic acid, mutants in the uracil biosynthetic pathway were selected. Photodynamic treatment resulted in a light dose dependent increase of the mutation frequency. The observed mutagenicity of photodynamic treatment of the yeast with phthalocyanine was lower than the mutagenicity of UVC and X-ray treatment at equal colony forming capacity, indicating that photodynamic treatment is the least mutagenic of those treatments. It is concluded that photodynamic treatment of K. marxianus results in DNA damage. Saccharomyces cerevisiae rad14 and rad52 mutants were used to determine the effect of the nucleotide excision repair and recombinational repair pathways, respectively, on survival after photodynamic treatment. Our data indicate that DNA damage is not the main determinant for cell killing by photodynamic treatment and that the type of damage induced is apparently not subject to RAD14- or RAD52 controlled repair.\n\nSingle strand breaks and mutagenesis in yeast induced by photodynamic treatment with chloroaluminum phthalocyanine.", "token_count": 410, "char_count": 1766, "word_count": 251, "semantic_coherence": 1, "information_density": 0.5179, "quality_score": 0.759, "entities": { "genes": [ "RAD52", "RAD14" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:41.697803", "source": { "split": "train_shard_00001", "doc_id": 4079 }, "chunk_id": "train_shard_00001_4079_0", "global_id": 11431 }, { "text": "Sorghum ( Sorghum bicolor L.) is one of the most important food crops in the arid and rainfed production ecologies. It is a part of resilient farming and is projected as a smart crop to overcome the food and nutritional challenges in the developing world. The development and characterisation of the sorghum pan-genome will provide insight into genome diversity and functionality, supporting sorghum improvement. We built a sorghum pan-genome using reference genomes as well as 354 genetically diverse sorghum accessions belonging to different races. We explored the structural and functional characteristics of the pan-genome and explain its utility in supporting genetic gain. The newly-developed pan-genome has a total of 35,719 genes, a core genome of 16,821 genes and an average of 32,795 genes in each cultivar. The variable genes are enriched with environment responsive genes and classify the sorghum accessions according to their race. We show that 53% of genes display presence-absence variation, and some of these variable genes are predicted to be functionally associated with drought traits. Using more than two million SNPs from the pan-genome, association analysis identified 398 SNPs significantly associated with important agronomic traits, of which, 92 were in genes. Drought gene expression analysis identified 1,788 genes that are functionally linked to different conditions, of which 79 were absent from the reference genome assembly. This study provides comprehensive genomic diversity resources in sorghum which can be used in genome assisted crop improvement.\n\nSorghum pan-genome explores the functional utility to accelerate the genetic gain", "token_count": 383, "char_count": 1666, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:42.293032", "source": { "split": "train_shard_00001", "doc_id": 4080 }, "chunk_id": "train_shard_00001_4080_0", "global_id": 11432 }, { "text": "We used culture- and molecular-biology-based methods to investigate microbial diversity in the traditional Mongolian fermented milks “Airag” (fermented mare's milk) and “Tarag” (fermented milk of cows, yaks, goats, or camels). By rRNA or functional gene sequencing, we identified 367 lactic acid bacteria (LAB) strains and 152 yeast strains isolated from 22 Airag and 31 Tarag samples. The total concentration of LAB in Airag (10⁷.⁷⁸ ± ⁰.⁵⁰ c.f.u. ml⁻¹; mean ± SD) was significantly lower (P < 0.01) than in Tarag (10⁸.³⁵ ± ⁰.⁶² c.f.u. ml⁻¹), whereas the total concentration of yeasts in Airag (10⁷.⁴¹ ± ⁰.⁶¹ c.f.u. ml⁻¹) was significantly higher (P < 0.01) than in Tarag (10⁵.⁸⁶ ± ¹.²⁹ c.f.u. ml⁻¹). Lactobacillus helveticus and Lactobacillus kefiranofaciens were isolated from Airag as the predominant LAB strains at levels of about 10⁷ c.f.u. ml⁻¹, whereas Lactobacillus delbrueckii subsp. bulgaricus, L. helveticus, and Streptococcus thermophilus were the predominant isolates from Tarag at about 10⁷ c.f.u. ml⁻¹. The lactose-fermenting Kluyveromyces marxianus was isolated predominantly from Airag as its major alcoholic fermentation component", "token_count": 462, "char_count": 1148, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6331, "quality_score": 0.8166, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:42.956628", "source": { "split": "train_shard_00001", "doc_id": 4081 }, "chunk_id": "train_shard_00001_4081_0", "global_id": 11433 }, { "text": "Non-lactose-fermenting yeasts such as Saccharomyces cerevisiae, Issatchenkia orientalis, and Kazachstania unispora were the predominant isolates from Tarag, at about 10⁵ c.f.u. ml⁻¹. The apparent geographic differences in the L. kefiranofaciens and S. thermophilus contents of Tarag strongly suggested that differences among the animal species from which the milk was sourced, rather than geographic distances, were the most important factors influencing the diversity of the microbial composition of traditional fermented milks in Mongolia.\n\nDiversity of lactic acid bacteria and yeasts in Airag and Tarag, traditional fermented milk products of Mongolia", "token_count": 173, "char_count": 655, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7079, "quality_score": 0.8539, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:43.425112", "source": { "split": "train_shard_00001", "doc_id": 4081 }, "chunk_id": "train_shard_00001_4081_1", "global_id": 11434 }, { "text": "Ulcerative colitis (UC) is a chronic inflammatory bowel disease. The purpose of this study was to investigate the ameliorating effects of three yeast strains, Saccharomyces cerevisiae I4, Clavispora lusitaniae 30 and Pichia kudriavzevii 11, isolated from traditional fermented dairy food in Xinjiang, China, on the ulcerative colitis symptoms of Balb/c mice treated by dextran sulfate sodium (DSS). Among which, S. cerevisiae I4 had good tolerance to simulated gastrointestinal juice and strong adhesion to HT-29 cells monolayers. Furthermore, the three yeast strains were oral administered to Balb/c mice with DSS induced colitis. The weight loss, colon shortening and histological injury of colitis mice were ameliorated. Then, oral administration of S. cerevisiae I4 improved the immune state by reducing the contents of TNF-α, IL-6 and IL-1β and increasing immunoglobulin. The relative expression of intestinal barrier proteins Claudin-1, Occludin and Zonula Occludins-1 (ZO-1) of the mice enhanced, and the short chain fatty acids (SCFAs) content such as Propionic acid, Butyric acid, Isobutyric acid and Isovaleric acid in the feces of the mice increased to varying degrees, after S. cerevisiae I4 treatment compared with the model group of drinking 3% DSS water without yeast treatment. Moreover, S. cerevisiae I4 treatment lifted the proportion of beneficial bacteria such as Muribaculaceae, Lactobacillaceae and Rikenellaceae in the intestinal tract of the mice, the abundance of harmful bacteria such as Staphylococcus aureus and Turicibacter was decreased. These results suggested that S", "token_count": 512, "char_count": 1664, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6609, "quality_score": 0.8305, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:44.084835", "source": { "split": "train_shard_00001", "doc_id": 4082 }, "chunk_id": "train_shard_00001_4082_0", "global_id": 11435 }, { "text": "cerevisiae I4 could alleviate DSS induced colitis in mice by enhancing intestinal barrier function and regulating intestinal flora balance.\n\nSaccharomyces cerevisiae I4 Showed Alleviating Effects on Dextran Sulfate Sodium-Induced Colitis of Balb/c Mice.", "token_count": 89, "char_count": 264, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8788, "quality_score": 0.9394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:44.500352", "source": { "split": "train_shard_00001", "doc_id": 4082 }, "chunk_id": "train_shard_00001_4082_1", "global_id": 11436 }, { "text": "The enzyme ADH1 has been extracted and purified from the budding yeast Kluyveromyces marxianus, and its enzymatic activity has been compared, with the ADH1 extracted and purified in the same way from the well known yeast Saccharomyces cerevisiae. K. marxianus ADH1 has an optimal temperature higher than the S. cerevisiae enzyme (45-50 degrees vs 35 degrees C), a better stability to pH variations in the oxidative reaction (pH optimum 7.5), a lower Michaelis constant for acetaldehyde, and a good catalytic activity both for fermentative and oxidative reactions. In fact, while in Saccharomyces the constants ratio (velocity constant fermentation/velocity constant oxidation) is about 20,000, in Kluyveromyces the same ratio is only 15. Even if these two Genera are quite related (they belong to the same subfamily) it seems that their ADH1s possess different catalytic properties.\n\nExtraction, purification and characterization of ADH1 from the budding yeast Kluyveromyces marxianus.", "token_count": 276, "char_count": 985, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6575, "quality_score": 0.8288, "entities": { "genes": [ "ADH1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:45.084099", "source": { "split": "train_shard_00001", "doc_id": 4083 }, "chunk_id": "train_shard_00001_4083_0", "global_id": 11437 }, { "text": "The lactose-utilizing Kluyveromyces fragilis SS-437 was found to have an associative temperature profile, but a thermotolerant growth yield behaviour. Cardinal growth temperatures were: 3 degrees C minimum for growth; 41.5 degrees C optimum; 44.5 degrees C final maximum (growth and death rates equalize); 46.1 degrees C initial maximum (maximum limit for growth).\n\nKluyveromyces fragilis SS-437: an associatively-profiled thermotolerant yeast.", "token_count": 127, "char_count": 444, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7797, "quality_score": 0.8898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:45.472838", "source": { "split": "train_shard_00001", "doc_id": 4084 }, "chunk_id": "train_shard_00001_4084_0", "global_id": 11438 }, { "text": "

Objectives

Carbapenem-resistant Acinetobacter baumannii (CRAB) is a serious nosocomial pathogen that causes a variety of serious, often life-threatening, infections and outbreaks. This study aimed to investigate the molecular epidemiology of clinical CRAB isolates from an outbreak that occurred in the intensive care unit (ICU) of an Italian hospital.

Methods

From December 2016 to April 2017, 13 CRAB isolates were collected from seven patients treated in the ICU at 'L. Spallanzani' Hospital (Rome, Italy). Typing was performed by repetitive extragenic palindromic PCR (rep-PCR) using a DiversiLab® system. Whole-genome sequencing (WGS) data were used for in silico analysis of traditional multilocus sequence typing (MLST) results, to identify resistance genes and for core genome MLST (cgMLST) analysis. Epidemiological data were obtained from hospital records.

Results

All isolates showed a carbapenem-resistant profile and carried the blaOXA-23 carbapenemase gene. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group, whilst the cgMLST approach, which uses 2390 gene targets to characterise the gene-by-gene allelic profile, highlighted the presence of two cluster types. These results allowed us to identify two patients who were likely to be the source of two separate transmission chains.

Conclusion

These results show that WGS by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.\n\nEpidemiological investigation of an Acinetobacter baumannii outbreak using core genome multilocus sequence typing.", "token_count": 458, "char_count": 1737, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6754, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:46.121998", "source": { "split": "train_shard_00001", "doc_id": 4085 }, "chunk_id": "train_shard_00001_4085_0", "global_id": 11439 }, { "text": "

Background:

Colistin is used against multi-drug resistant pathogens, yet resistance emerges either through dissemination of plasmid-mediated genes ( mcr ) or chromosomal mutation of genes involved in lipopolysaccharide synthesis (i.e. mgrB, phoPQ, pmrCAB). Phenotypic susceptibility testing is challenging due to poor diffusion of colistin in agar media, leading to an underestimation of resistance. We aimed to compare the performance of four different phenotypic approaches in the context of different molecular mechanism of resistance.

Methods:

: We compared the performance of Vitek 2® (bioMérieux, AST N242), Colistin MIC Test Strip (Liofilchem Diagnostici), UMIC (Biocentric), and Rapid Polymyxin NP Test (ELITechGroup) against the standard broth microdilution (BDM) method. We used whole genome sequencing (WGS) to infer the molecular mechanisms of resistance. A total of 97 Enterobacterales and non-fermenting bacterial isolates were collected from clinical samples during 2016-2017 and tested for colistin susceptibility. Data was analysed by comparing the susceptibility category (susceptible or resistant) and minimal inhibitory concentrations (MIC). We determined diversity of isolates by core genome multi locus sequencing typing (cgMLST) and identified antimicrobial resistance genes using NCBI and CARD databases.

Results:

: Of the 97 clinical isolates, 54 (56%) were resistant by the standard broth microdilution. The highest susceptibility category concordance was achieved by the Rapid Polymyxin NP test (98.8%) followed by UMIC (97.9%), E-test MIC strip (96.9%) and Vitek 2 (95.6%). The highest MIC concordance was achieved by UMIC (80.4%), followed by Vitek 2 (72.5%) and E-test MIC strip (62.9%)", "token_count": 514, "char_count": 1744, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:46:46.808744", "source": { "split": "train_shard_00001", "doc_id": 4086 }, "chunk_id": "train_shard_00001_4086_0", "global_id": 11440 }, { "text": "Among the resistant isolates, 23/54 (43%) were intrinsically resistant to colistin, whereas 31/54 (57%) isolates had acquired colistin resistance. Of these, mcr-1 was detected in four isolates and mcr-2 in one isolate. Mutations in mgrB, phoQ, pmrA, pmrB , and pmrC genes that led to amino acid changes were encountered in Klebsiella pneumoniae, Escherichia coli, and Acinetobacter bereziniae resistant isolates.

Conclusions:

: The Rapid Polymyxin NP test showed the highest categorical concordance and the UMIC test provided MIC values with a high concordance to the standard method. We found colistin resistance in diverse species occurred predominantly through spontaneous chromosomal mutation rather than plasmid-mediated resistance.\n\nDetermination of Colistin Resistance in Gram-negative Bacteria by Four Phenotypic Assays and Inference of the Underlying Molecular Mechanisms", "token_count": 258, "char_count": 889, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7623, "quality_score": 0.8811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:47.355515", "source": { "split": "train_shard_00001", "doc_id": 4086 }, "chunk_id": "train_shard_00001_4086_1", "global_id": 11441 }, { "text": "

Background:

Comparative genomics between closely related bacterial strains can distinguish important features determining pathogenesis, antibiotic resistance, and phylogenetic structure. The Streptococcus genus is relevant to public health and food safety and it is well-represented (>100 genomes) in databases of publicly available databases. Streptococci are cosmopolitan, with multiple sources of isolation, from humans to dairy products. The Streptococcus genus has been classified by morphology, serotypes, 16S rRNA gene, and Multi Locus Sequence Types (MLST). The Genomic Similarity Score (GSS) is proposed as a tool to quantify genome level relatedness between species of Streptococcus. The Streptococcus core genome can be used to assess strain specific abundances in metagenomic sequences.

Methods:

. A 16S rRNA gene phylogeny was calculated for 108 strains, belonging to 16 Streptococcus species and compared to a dendrogram using GSS pairwise distances for the same genomes. The core and pan-genome were calculated for these 108 genomes. The core genome sequences were analyzed and used as a resource to discriminate homologous fragment reads from closely related strains in metagenomic samples.

Results:

. A total of 404 proteins are shared by all 108 Streptococcus genomes, which is the core genome. The pairwise amino acid identity values of the core proteins for all the compared strains and outgroups are reported. Lower sequence identity variation (90-100%) is predominantly found in core clusters containing ribosomal and translation-related proteins. For 48 core proteins (11.8%) no functional assignment could be made and those proteins have larger sequence identity variations than other core proteins. The sequence identity of the core genome diminishes as GSS score between species decreases. The GSS dendrogram recovers most of the clades in the 16S rRNA gene phylogeny while distinguishing between 16S polytomies (unresolved nodes)", "token_count": 510, "char_count": 1984, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5866, "quality_score": 0.7933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:48.025009", "source": { "split": "train_shard_00001", "doc_id": 4087 }, "chunk_id": "train_shard_00001_4087_0", "global_id": 11442 }, { "text": "Finally, the core genome was used to distinguish between closely related species within human oral metagenomes.

Discussion:

. The Streptococcus genus provides a benchmark dataset for comparative genomic studies due to the breath depth of genomic coverage. Comparing metagenomic shotgun fragment reads to the core genome using rapid alignment tools allows species-specific abundance estimates in metagenomic samples. Understanding of genomic variability and strains relatedness is the goal of tools like GSS, which make use of both pairwise shared core and pan-genomic homologous shared sequences for its calculation.\n\nGlobal genomic similarity and core genome sequence diversity of the Streptococcus genus as a toolkit to identify closely related bacterial species in complex environments.", "token_count": 171, "char_count": 799, "word_count": 112, "semantic_coherence": 1, "information_density": 0.7054, "quality_score": 0.8527, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:48.468848", "source": { "split": "train_shard_00001", "doc_id": 4087 }, "chunk_id": "train_shard_00001_4087_1", "global_id": 11443 }, { "text": "The extracellular inulinase structural gene was isolated from the genomic DNA of the marine yeast Pichia guilliermondii strain 1 by PCR. The gene had an open reading frame of 1,542 bp long encoding an inulinase. The coding region of the gene was not interrupted by any intron. It encoded 514 amino acid residues of a protein with a putative signal peptide of 18 amino acids and the calculated molecular mass of 58.04 kDa. The protein sequence deduced from the inulinase structural gene contained the inulinase consensus sequences (WMNXPNGL) and (RDPKVF). It also had ten conserved putative N-glycosylation sites. The inulinase from P. guilliermondii strain 1 was found to be closely related to that from Kluyveromyces marxianus. The inulinase gene without the signal sequence was subcloned into pPICZalphaA expression vector and expressed in Pichia pastoris X-33. The expressed fusion protein was analyzed by SDS-PAGE and western blotting and a specific band with molecular mass of about 60 kDa was found. Enzyme activity assay verified the recombinant protein as an inulinase. A maximum activity of 58.7 +/- 0.12 U/ml was obtained from the culture supernatant of P. pastoris X-33 harboring the inulinase gene. A large amount of monosaccharides, disaccharides and oligosaccharides were detected after the hydrolysis of inulin with the crude recombinant inulinase.\n\nCloning and characterization of the inulinase gene from a marine yeast Pichia guilliermondii and its expression in Pichia pastoris.", "token_count": 417, "char_count": 1496, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5609, "quality_score": 0.7804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:49.092127", "source": { "split": "train_shard_00001", "doc_id": 4088 }, "chunk_id": "train_shard_00001_4088_0", "global_id": 11444 }, { "text": "

ABSTRACT

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)’s 2013-2017 sample collection.

Methods

A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10 ® Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of AMR, and AGROSAVIA.

Results

Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases bla KPC-3 , bla KPC-2 , bla NDM-1 , bla NDM-9 , bla VIM-2 , bla VIM-4 , and bla VIM-24 , and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin ( clb3 ) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI> 99.9%).

Conclusions

The study outlines complex CRKP epidemiology in Colombia", "token_count": 483, "char_count": 1488, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [ "CG258", "ST4851", "CG380", "ST512", "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:49.743355", "source": { "split": "train_shard_00001", "doc_id": 4089 }, "chunk_id": "train_shard_00001_4089_0", "global_id": 11445 }, { "text": "CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of STs, MGE, and resistance and virulence genes.

summary

In Colombia, the dissemination of carbapenemases in carbapenem-resistant Klebsiella pneumoniae is attributed to horizontal gene transfer and successful circulation of CG258, and, to a lesser extent, other clones such as ST307, ST147, and ST152.\n\nComplexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs", "token_count": 242, "char_count": 809, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "CG258", "CG307", "ST307", "CG152", "ST152", "ST147", "CG147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:50.229939", "source": { "split": "train_shard_00001", "doc_id": 4089 }, "chunk_id": "train_shard_00001_4089_1", "global_id": 11446 }, { "text": "

Summary

Trace metals are essential to all domains of life but toxic when found at high concentrations. While the importance of iron in host-pathogen interactions is firmly established, contemporary studies indicate that other trace metals, including manganese and zinc, are also critical to the infectious process. In this study, we sought to identify and characterize the zinc uptake system(s) of S. mutans , a keystone pathogen in dental caries and a causative agent of bacterial endocarditis. Different than other pathogenic bacteria, including several streptococci, that encode multiple zinc import systems, bioinformatic analysis indicated that the S. mutans core genome encodes a single, highly conserved, zinc importer commonly known as AdcABC. Inactivation of the genes coding for the metal-binding AdcA (Δ adcA ) or both AdcC ATPase and AdcB permease (Δ adcCB ) severely impaired the ability of S. mutans to grow under zinc-depleted conditions. Intracellular metal quantifications revealed that both mutants accumulated less zinc when grown in the presence of a sub-inhibitory concentration of a zinc-specific chelator. Notably, the Δ adcCB strain displayed a severe colonization defect in a rat oral infection model. Both Δ adc strains were hypersensitive to high concentrations of manganese, showed reduced peroxide tolerance, and formed less biofilm in sucrose-containing media when cultivated in the presence of the lowest amount of zinc that support their growth, but not when zinc was supplied in excess. Collectively, this study identifies AdcABC as the lone high affinity zinc importer of S. mutans and provides preliminary evidence that zinc is a growth-limiting factor within the dental biofilm.\n\nZinc Import Mediated by AdcABC is Critical for Colonization of the Dental Biofilm byStreptococcus mutansin an Animal Model", "token_count": 466, "char_count": 1854, "word_count": 275, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:50.874995", "source": { "split": "train_shard_00001", "doc_id": 4090 }, "chunk_id": "train_shard_00001_4090_0", "global_id": 11447 }, { "text": "The family Enterobacteriaceae is a taxonomically diverse and widely distributed family containing many human commensal and pathogenic species that are known to carry transferable antibiotic resistance determinants. Characterization of novel taxa within this family is of great importance in order to understand the associated health risk and provide better treatment options. The aim of the present study was to characterize a Gram-negative bacterial strain (CCUG 66741) belonging to the family Enterobacteriaceae, isolated from a wound infection of an adult patient, in Sweden. Initial phenotypic and genotypic analyses identified the strain as a member of the family Enterobacteriaceae but could not assign it to any previously described species. The complete 16S rRNA gene sequence showed highest similarity (98.8%) to four species. Whole genome sequencing followed by in silico DNA-DNA similarity analysis and average nucleotide identity (ANI) analysis confirmed that strain CCUG 66741 represents a novel taxon. Sequence comparisons of six house-keeping genes (16S rRNA, atpD, dnaJ, gyrB, infB, rpoB) with those of the type strains of the type species of related genera within the family Enterobacteriaceae indicated that the strain embodies a novel species within the family. Phylogenomic analyses (ANI-based and core genome-based phylogeny) showed that strain CCUG 66741 forms a distinct clade, representing a novel species of a distinct, new genus within the family Enterobacteriaceae, for which the name Scandinavium goeteborgense gen. nov., sp. nov. is proposed, with CCUG 66741T as the type strain (= CECT 9823T = NCTC 14286T). S", "token_count": 502, "char_count": 1752, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:51.538838", "source": { "split": "train_shard_00001", "doc_id": 4091 }, "chunk_id": "train_shard_00001_4091_0", "global_id": 11448 }, { "text": "goeteborgense CCUG 66741T carries a novel variant of a chromosomally-encoded quinolone resistance gene (proposed qnrB96). When expressed in Escherichia coli, the qnrB96 gene conferred five-fold increase in minimum inhibitory concentration against ciprofloxacin. This study highlights the importance and the utility of whole genome sequencing for pathogen identification in clinical settings.\n\nScandinavium goeteborgense gen. nov., sp. nov., a New Member of the Family Enterobacteriaceae Isolated From a Wound Infection, Carries a Novel Quinolone Resistance Gene Variant.", "token_count": 196, "char_count": 620, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7467, "quality_score": 0.8733, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:51.984011", "source": { "split": "train_shard_00001", "doc_id": 4091 }, "chunk_id": "train_shard_00001_4091_1", "global_id": 11449 }, { "text": "PROBLEM TO BE SOLVED: To provide a quinone oxide reductase useful for the reduction reaction of a quinone compound and the synthesis of an intermediate for a biologically active compound.\n\nGENE CODING KLUYVEROMYCES MARXIANUS QUINONE OXIDE REDUCTASE AND PROTEIN EXPRESSED THEREFROM", "token_count": 92, "char_count": 280, "word_count": 41, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:52.365492", "source": { "split": "train_shard_00001", "doc_id": 4092 }, "chunk_id": "train_shard_00001_4092_0", "global_id": 11450 }, { "text": "

Objectives

Approximately 75% of the genome of Staphylococcus aureus (the 'core' genome) is highly conserved between strains, whereas the remaining 25% (the 'accessory' genome) is composed of mobile genetic elements (MGEs), containing virulence and resistance genes. We developed a composite microarray focused on resistance and virulence genes located on the accessory or core-variable genome to characterize a collection of Belgian community-acquired methicillin-resistant S. aureus (CA-MRSA) strains.

Methods

Oligonucleotide probes targeting 403 genes encoding antimicrobial resistance (35%), virulence (28%) and adhesion (31%) factors were designed among eight S. aureus sequenced genomes. The StaphVar Array was validated by testing five of the strains used for the design and utilized to characterize 13 CA-MRSA strains representative of the multilocus sequence typing (MLST) sequence types circulating in Belgium.

Results

Analysis of the gene content of the five reference strains by the StaphVar Array matched 90% to 97% of the theoretical results. Analysis of CA-MRSA strains showed that 54.4% of the genes tested were strain-dependent. Strains presented specific exotoxin, enterotoxin, cytolysin and adhesin gene profiles by MLST lineage. One exception to these 'lineage-specific' profiles was the variable presence of the arginine catabolic mobile element (characteristic of the USA300 clone) within ST8 strains.

Conclusions

The StaphVar Array enables the characterization of approximately 400 variable resistance and virulence determinants in S. aureus. CA-MRSA strains displayed extensive diversity in virulence and resistance profiles. The presence of the USA300 clone in Belgium was confirmed. Although mainly located on MGEs, associations of virulence genes were highly conserved within strains of the same MLST lineage.", "token_count": 497, "char_count": 1864, "word_count": 247, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [ "USA300", "ST8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:53.023265", "source": { "split": "train_shard_00001", "doc_id": 4093 }, "chunk_id": "train_shard_00001_4093_0", "global_id": 11451 }, { "text": "StaphVar-DNA microarray analysis of accessory genome elements of community-acquired methicillin-resistant Staphylococcus aureus.", "token_count": 38, "char_count": 128, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:53.389534", "source": { "split": "train_shard_00001", "doc_id": 4093 }, "chunk_id": "train_shard_00001_4093_1", "global_id": 11452 }, { "text": "Cell wall proteins of Kluyveromyces fragilis: surface and emulsifying properties.", "token_count": 20, "char_count": 81, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:53.741546", "source": { "split": "train_shard_00001", "doc_id": 4094 }, "chunk_id": "train_shard_00001_4094_0", "global_id": 11453 }, { "text": "BackgroundIn 2017, a food-borne Salmonella Agona outbreak caused by infant milk products from a French supplier occurred in Europe. Simultaneously, S. Agona was detected in animal feed samples in Bavaria.AimUsing next generation sequencing (NGS) and three data analysis methods, this study's objectives were to verify clonality of the Bavarian feed strains, rule out their connection to the outbreak, explore the genetic diversity of Bavarian S. Agona isolates from 1993 to 2018 and compare the analysis approaches employed, for practicality and ability to delineate outbreaks caused by the genetically monomorphic Agona serovar.MethodsIn this observational retrospective study, three 2017 Bavarian feed isolates were compared to a French outbreak isolate and 48 S. Agona isolates from our strain collections. The later included human, food, feed, veterinary and environmental isolates, of which 28 were epidemiologically outbreak related. All isolates were subjected to NGS and analysed by: (i) a publicly available species-specific core genome multilocus sequence typing (cgMLST) scheme, (ii) single nucleotide polymorphism phylogeny and (iii) an in-house serovar-specific cgMLST scheme. Using additional international S. Agona outbreak NGS data, the cluster resolution capacity of the two cgMLST schemes was assessed.ResultsWe could prove clonality of the feed isolates and exclude their relation to the French outbreak. All approaches confirmed former Bavarian epidemiological clusters.ConclusionEven for S. Agona, species-level cgMLST can produce reasonable resolution, being standardisable by public health laboratories. For single samples or homogeneous sample sets, higher resolution by serovar-specific cgMLST or SNP genotyping can facilitate outbreak investigations.\n\nGenetic diversity and delineation of Salmonella Agona outbreak strains by next generation sequencing, Bavaria, Germany, 1993 to 2018.", "token_count": 504, "char_count": 1960, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:54.393297", "source": { "split": "train_shard_00001", "doc_id": 4095 }, "chunk_id": "train_shard_00001_4095_0", "global_id": 11454 }, { "text": "To overcome the problem of enzyme extraction and poor permeability of cell membrane to lactose, experimentation was carried to permeabilize Kluyveromyces marxianus NCIM 3465 cells for their subsequent use for the production of lactose-hydrolyzed milk. Different process parameters, such as biomass load, temperature, agitation and treatment time, were optimized for maximum lactose hydrolysis in skim milk using these cells. The ethanol-permeabilized yeast cells gave 89% hydrolysis of milk lactose under optimized conditions.\n\nProduction of lactose-hydrolyzed milk using ethanol permeabilized yeast cells", "token_count": 161, "char_count": 605, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7284, "quality_score": 0.8642, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:54.834816", "source": { "split": "train_shard_00001", "doc_id": 4096 }, "chunk_id": "train_shard_00001_4096_0", "global_id": 11455 }, { "text": "Neisseria meningitidis and N. gonorrhoeae are closely related pathogenic bacteria. To compare their population genetics, we compiled a dataset of 1,145 genes found across 20 N. meningitidis and 15 N. gonorrhoeae genomes. We find that N. meningitidis is seven-times more diverse than N. gonorrhoeae in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however, we find that N. meningitidis has acquired more of its diversity by recombination than N. gonorrhoeae. We find that linkage disequilibrium (LD) declines rapidly across the genomes of both species. Several observations suggest that N. meningitidis has a higher effective population size than N. gonorrhoeae; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote in N. meningitidis. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome using a McDonald-Kreitman test and by considering the diversity around non-synonymous sites that are fixed for different alleles in the two species. We find some evidence for adaptive evolution using both approaches.\n\nThe comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae.", "token_count": 482, "char_count": 1765, "word_count": 256, "semantic_coherence": 1, "information_density": 0.4922, "quality_score": 0.7461, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:55.516798", "source": { "split": "train_shard_00001", "doc_id": 4097 }, "chunk_id": "train_shard_00001_4097_0", "global_id": 11456 }, { "text": "Galactose transport was studied in membrane vesicles, prepared by fusion of plasma membranes from the yeast Kluyveromyces marxianus with proteoliposomes containing beef heart cytochrome c oxidase as a proton-motive force-generating system. Sugar transport studies performed under nonenergized conditions revealed that, even at high protein to phospholipid ratios, not all vesicles contained a D-galactose-specific transporter. The amount of vesicles containing an active carrier proved to be proportional to the amount of plasma membrane protein present in the fusion mixture. By addition of a suitable electron donor system a proton-motive force of -160 mV could be generated, inside alkaline and negative. Moreover, D-galactose accumulation was observed. It was found that D-galactose accumulation was highly dependent on the phospholipid composition of the vesicles, whereas generation of a proton-motive force was not. Best results were obtained with vesicles prepared with Escherichia coli phospholipid, giving a galactose accumulation of 14 times. Uphill transport could be established under conditions where only the pH gradient or the electrical gradient was present. Moreover, kinetic analysis of the galactose transport activity in energized vesicles revealed influx with a Km value of 540 microM, which is in good agreement with the apparent affinity constant obtained with whole cells. These results establish that galactose transport of K. marxianus is a proton-motive force-driven process. Moreover it demonstrates that plasma membrane vesicles co-reconstituted with cytochrome c oxidase are a valuable resource for the analysis of proton-motive force-driven sugar transport systems of yeast.\n\nProton-motive force-driven D-galactose transport in plasma membrane vesicles from the yeast Kluyveromyces marxianus.", "token_count": 441, "char_count": 1824, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5595, "quality_score": 0.7798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:56.164445", "source": { "split": "train_shard_00001", "doc_id": 4098 }, "chunk_id": "train_shard_00001_4098_0", "global_id": 11457 }, { "text": "A novel system for high-temperature alcoholic fermentation of whey is described. This system consists of Kluyveromyces marxianus yeast immobilized on delignified cellulosic material (DCM). The effect of pH, initial lactose concentration and temperature on the fermentation of a synthetic medium containing lactose was studied. Batch fermentations of whey were also carried out and the formation of volatile by-products was examined. The concentrations of higher alcohols were found to be in very low levels leading to a product of improved quality. The fermented whey had an improved characteristic aroma compared to unfermented whey. The possibility to use fermented whey as raw material for the production of a novel, low alcohol content drink was also investigated.\n\nHigh-temperature alcoholic fermentation of whey using Kluyveromyces marxianus IMB3 yeast immobilized on delignified cellulosic material.", "token_count": 213, "char_count": 906, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:56.673866", "source": { "split": "train_shard_00001", "doc_id": 4099 }, "chunk_id": "train_shard_00001_4099_0", "global_id": 11458 }, { "text": "Pasteurella multocida is a zoonotic pathogen whose genetic heterogeneity is well known. Five serogroups (A, B, D, E, and F) and 16 serotypes of P. multocida have been recognized thus far based on capsular polysaccharide typing and lipopolysaccharide typing, respectively. Progressive atrophic rhinitis in domestic pigs is caused by P. multocida strains containing toxA, which encodes a 146 kDa heat-labile toxin. Among the five serogroups, only some strains of serogroups A and D are toxigenic. In this study, by comparative analyses of the genomes of many strains, it has been shown that toxA is sparsely distributed in P. multocida. Furthermore, full-length homologs of P. multocida toxA were found only in two other bacterial species. It has also been shown that toxA is usually associated with a prophage, and that some strains contain an orthologous prophage but not toxA. Among the toxA-containing prophages that were compared, an operon putatively encoding a type II restriction-modification system was present only in strains LFB3, HN01, and HN06. These results indicate that the selection and maintenance of the heat-labile toxin and the type II restriction-modification system are evolutionarily less favorable among P. multocida strains. Phylogenetic analysis using the alignment- and parameter-free method CVTree3 showed that deduced proteome sequences can be used as effectively as whole/core genome single nucleotide polymorphisms to group P. multocida strains in relation to their serotypes and (or) genotypes", "token_count": 472, "char_count": 1608, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6652, "quality_score": 0.8326, "entities": { "genes": [ "HN01", "LFB3", "HN06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:57.331112", "source": { "split": "train_shard_00001", "doc_id": 4100 }, "chunk_id": "train_shard_00001_4100_0", "global_id": 11459 }, { "text": "It remains to be determined if the toxA-containing prophages in strains HN01 and HN06 are inducible, and if they can be used for lysogenic transfer of toxA to other bacteria.\n\nComparative genomics of the Pasteurella multocida toxin.", "token_count": 88, "char_count": 253, "word_count": 37, "semantic_coherence": 1, "information_density": 0.8378, "quality_score": 0.9189, "entities": { "genes": [ "HN01", "HN06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:57.708729", "source": { "split": "train_shard_00001", "doc_id": 4100 }, "chunk_id": "train_shard_00001_4100_1", "global_id": 11460 }, { "text": "Natural isolates of Burkholderia pseudomallei (Bp), the causative agent of melioidosis, can exhibit significant ecological flexibility that is likely reflective of a dynamic genome. Using whole-genome Bp microarrays, we examined patterns of gene presence and absence across 94 South East Asian strains isolated from a variety of clinical, environmental, or animal sources. 86% of the Bp K96243 reference genome was common to all the strains representing the Bp \"core genome\", comprising genes largely involved in essential functions (eg amino acid metabolism, protein translation). In contrast, 14% of the K96243 genome was variably present across the isolates. This Bp accessory genome encompassed multiple genomic islands (GIs), paralogous genes, and insertions/deletions, including three distinct lipopolysaccharide (LPS)-related gene clusters. Strikingly, strains recovered from cases of human melioidosis clustered on a tree based on accessory gene content, and were significantly more likely to harbor certain GIs compared to animal and environmental isolates. Consistent with the inference that the GIs may contribute to pathogenesis, experimental mutation of BPSS2053, a GI gene, reduced microbial adherence to human epithelial cells. Our results suggest that the Bp accessory genome is likely to play an important role in microbial adaptation and virulence.\n\nThe core and accessory genomes of Burkholderia pseudomallei: implications for human melioidosis.", "token_count": 363, "char_count": 1464, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6878, "quality_score": 0.8439, "entities": { "genes": [ "BPSS2053" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:58.642488", "source": { "split": "train_shard_00001", "doc_id": 4101 }, "chunk_id": "train_shard_00001_4101_0", "global_id": 11461 }, { "text": "Rathayibacter toxicus is a Gram-positive, nematode-vectored bacterium that infects several grass species in the family Poaceae. Unique in its genus, R. toxicus has the smallest genome, possesses a complete CRISPR-Cas system, a vancomycin-resistance cassette, produces tunicamycin, a corynetoxin responsible for livestock deaths in Australia, and is designated a Select Agent in the United States. In-depth, genome-wide analyses performed in this study support the previously designated five genetic populations, with a core genome comprising approximately 80% of the genome for all populations. Results varied as a function of the type of analysis and when using different bioinformatics tools for the same analysis; e.g., some programs failed to identify specific genomic regions that were actually present. The software variance highlights the need to verify bioinformatics results by additional methods; e.g., PCR, mapping genes to genomes, use of multiple algorithms). These analyses suggest the following relationships among populations: RT-IV ↔ RT-I ↔ RT-II ↔ RT-III ↔ RT-V, with RT-IV and RT-V being the most unrelated. This is the most comprehensive analysis of R. toxicus that included populations RT-I and RT-V. Future studies require underrepresented populations and more recent isolates from varied hosts and geographic locations.\n\nComparative Genomic Analysis Confirms Five Genetic Populations of the Select Agent, Rathayibacter toxicus.", "token_count": 368, "char_count": 1478, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6732, "quality_score": 0.8366, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:59.227331", "source": { "split": "train_shard_00001", "doc_id": 4102 }, "chunk_id": "train_shard_00001_4102_0", "global_id": 11462 }, { "text": "

Background

The purpose of the present study was to examine the GC content of substituted bases (sbGC) in the core genomes of 35 bacterial species. Each species, or core genome, constituted genomes from at least 10 strains. We also wanted to explore whether sbGC for each strain was associated with the corresponding species' core genome GC content (cgGC). We present a simple mathematical model that estimates sbGC from cgGC. The model assumes only that the estimated sbGC is a function of cgGC proportional to fixed AT→GC (α) and GC → AT (β) mutation rates. Non-linear regression was used to estimate parameters α and β from the empirical data described above.

Results

We found that sbGC for each strain showed a non-linear association with the corresponding cgGC with a bias towards higher GC content for most core genomes (66.3% of the strains), assuming as a null-hypothesis that sbGC should be approximately equal to cgGC. The most GC rich core genomes (i.e. approximately %GC > 60), on the other hand, exhibited slightly less GC-biased sbGC than expected. The best fitted regression model indicates that GC → AT mutation rates β = (1.91 ± 0.13) p < 0.001 are approximately (1.91/0.79) = 2.42 times as high, on average, as AT→GC α = (- 0.79 ± 0.25) p < 0.001 mutation rates. Whether the observed sbGC GC-bias for all but the most GC-rich prokaryotic species is due to selection, compensating for the GC → AT mutation bias, and/or selective neutral processes is currently debated", "token_count": 476, "char_count": 1498, "word_count": 247, "semantic_coherence": 1, "information_density": 0.583, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:46:59.873871", "source": { "split": "train_shard_00001", "doc_id": 4103 }, "chunk_id": "train_shard_00001_4103_0", "global_id": 11463 }, { "text": "Residual standard error was found to be σ = 0.076 indicating estimated errors of sbGC to be approximately within ±15.2% GC (95% confidence interval) for the strains of all species in the study.

Conclusion

Not only did our mathematical model give reasonable estimates of sbGC it also provides further support to previous observations that mutation rates in prokaryotes exhibit a universal GC → AT bias that appears to be remarkably consistent between taxa.\n\nModeling of the GC content of the substituted bases in bacterial core genomes.", "token_count": 140, "char_count": 542, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:00.303705", "source": { "split": "train_shard_00001", "doc_id": 4103 }, "chunk_id": "train_shard_00001_4103_1", "global_id": 11464 }, { "text": "Campylobacter is one of the most important foodborne pathogens worldwide, and poultry is regarded as the main reservoir of Campylobacter. The contamination of Campylobacter in broiler chickens at the farm level is closely related to the transmission of Campylobacter in the poultry production chain. This study identified 464 Campylobacter isolates from 1,534 samples from broiler rearing period and slaughtering process including 233 Campylobacter jejuni isolates and 231 Campylobacter coli isolates. We have observed a dynamic distribution of Campylobacter during broiler chicken production, that 66.3% of Campylobacter isolates were C. jejuni during broiler rearing period, while C. coli occupied 60.4% of Campylobacter isolates during the broiler slaughtering process. A tag-label method allowed us to track the dynamic of Campylobacter in each broiler chicken from 31-day age at rearing to the partition step in the slaughterhouse. At the 31-day during rearing, 150 broiler chicken were labeled, and was tracked for Campylobacter positive from rearing period to slaughtering process. Among the labeled broiler, 11 of the tracking broiler samples were able to detect Campylobacter from rearing period to slaughtering. All Campylobacter isolates from the 11 tracking samples were sequenced and analyzed. C. jejuni isolates were divided into four STs and C. coli isolates were divided into six STs. Isolates with identical core genome were observed from the same tag-labeled samples at different stages indicating a vertical transmission of Campylobacter in the early broiler meat production. Meanwhile, the core genome analysis elucidated the cross-contamination of Campylobacter during the rearing period and the slaughtering process", "token_count": 525, "char_count": 1856, "word_count": 250, "semantic_coherence": 1, "information_density": 0.48, "quality_score": 0.74, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:00.940873", "source": { "split": "train_shard_00001", "doc_id": 4104 }, "chunk_id": "train_shard_00001_4104_0", "global_id": 11465 }, { "text": "The virulotyping analysis revealed that all C. jejuni isolates shared the same virulotypes, while C. coli isolates were divided into three different virulotypes. The antimicrobial resistance gene analysis demonstrated that all Campylobacter isolates contained at least two antibiotic resistance genes (ARGs), and the ARG profiles were well-corresponding to each ST type. Our study observed a high prevalence of Campylobacter during the early chicken meat production, and further studies will be needed to investigate the diversity and transmission of Campylobacter in the poultry production chain.\n\nCharacterization and Prevalence of Campylobacter spp. From Broiler Chicken Rearing Period to the Slaughtering Process in Eastern China.", "token_count": 202, "char_count": 776, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7255, "quality_score": 0.8627, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:01.407029", "source": { "split": "train_shard_00001", "doc_id": 4104 }, "chunk_id": "train_shard_00001_4104_1", "global_id": 11466 }, { "text": "

Objective

The aim of this study was to evaluate the influence of pharmacophores having naphthylamine and nitro groups on the antimicrobial (antibacterial and antifungal) activity of thiazolidinone derivatives.

Materials and methods

The initial 5-substituted-2-methylmercaptothiazolidin-4-ones were subjected to S-demethylation to yield 2-amino-substituted thiazolidinones. 4-Nitro-1-naphthylamine, nitrofuran aldehydes, and nitrobenzene aldehydes were used as pharmacophoric compounds having amino or aldehyde groups. Antimicrobial (antibacterial and antifungal) activity of the new compounds was tested in vitro against bacterial cultures - Staphylococcus aureus, Escherichia coli, Bacillus subtilis, Klebsiella pneumoniae - and fungal cultures - Candida albicans, Candida glabrata, Candida krusei, Candida kefyr, Candida tropicalis, and Candida parapsilosis.

Results

Microbiological analysis showed that all new thiazolidinone derivatives with nitronaphthylamine substituent possessed antibacterial and antifungal properties. New compounds 2a-b showed similar antibacterial activity in vitro against S. aureus and B. subtilis as aminopenicillins. The lowest antibacterial activity of all newly synthesized compounds was against capsule-forming bacteria K. pneumoniae and against gram-negative bacteria E. coli (minimum inhibitory concentration range, 500-1000 μg/mL).

Conclusions

The minimum inhibitory concentration of naphthylamine derivatives varied in the range of 0.4-1000 μg/mL, and activity of some newly synthesized compounds was similar to the activity of aminopenicillins and fluconazole, an antifungal preparation", "token_count": 514, "char_count": 1655, "word_count": 189, "semantic_coherence": 1, "information_density": 0.5979, "quality_score": 0.7989, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:02.066931", "source": { "split": "train_shard_00001", "doc_id": 4105 }, "chunk_id": "train_shard_00001_4105_0", "global_id": 11467 }, { "text": "Based on the results, it is possible to separate the perspective group of potential antimicrobial compounds.\n\nSynthesis and antimicrobial properties of naphthylamine derivatives having a thiazolidinone moiety.", "token_count": 53, "char_count": 209, "word_count": 27, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:02.430194", "source": { "split": "train_shard_00001", "doc_id": 4105 }, "chunk_id": "train_shard_00001_4105_1", "global_id": 11468 }, { "text": "Editorial: Pseudomonas aeruginosa Pathogenesis: Virulence, Antibiotic Tolerance and Resistance, Stress Responses and Host-Pathogen Interactions.", "token_count": 48, "char_count": 151, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:02.792289", "source": { "split": "train_shard_00001", "doc_id": 4106 }, "chunk_id": "train_shard_00001_4106_0", "global_id": 11469 }, { "text": "Due to the potential of enterohemorrhagic Escherichia coli (EHEC) serogroup O157 to cause large food borne outbreaks, national and international surveillance is necessary. For developing an effective method of molecular surveillance, a conventional method, multilocus variable-number tandem-repeat analysis (MLVA), and whole-genome sequencing (WGS) analysis were compared. WGS of 369 isolates of EHEC O157 belonging to 7 major MLVA types and their relatives were subjected to comprehensive in silico typing, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) analyses. The typing resolution was the highest in cgSNP analysis. However, determination of the sequence of the mismatch repair protein gene mutS is necessary because spontaneous deletion of the gene could lead to a hypermutator phenotype. MLVA had sufficient typing resolution for a short-term outbreak investigation and had advantages in rapidity and high throughput. cgMLST showed less typing resolution than cgSNP, but it is less time-consuming and does not require as much computer power. Therefore, cgMLST is suitable for comparisons using large data sets (e.g., international comparison using public databases). In conclusion, screening using MLVA followed by cgMLST and cgSNP analyses would provide the highest typing resolution and improve the accuracy and cost-effectiveness of EHEC O157 surveillance.IMPORTANCE Intensive surveillance for enterohemorrhagic Escherichia coli (EHEC) serogroup O157 is important to detect outbreaks and to prevent the spread of the bacterium. Recent advances in sequencing technology made molecular surveillance using whole-genome sequence (WGS) realistic. To develop rapid, high-throughput, and cost-effective typing methods for real-time surveillance, typing resolution of WGS and a conventional typing method, multilocus variable-number tandem-repeat analysis (MLVA), was evaluated", "token_count": 483, "char_count": 1972, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5862, "quality_score": 0.7931, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:03.442047", "source": { "split": "train_shard_00001", "doc_id": 4107 }, "chunk_id": "train_shard_00001_4107_0", "global_id": 11470 }, { "text": "Nation-level systematic comparison of MLVA, core genome single nucleotide polymorphism (cgSNP), and core genome multilocus sequence typing (cgMLST) indicated that a combination of WGS and MLVA is a realistic approach to improve EHEC O157 surveillance.\n\nEffective Surveillance Using Multilocus Variable-Number Tandem-Repeat Analysis and Whole-Genome Sequencing for Enterohemorrhagic Escherichia coli O157.", "token_count": 114, "char_count": 404, "word_count": 50, "semantic_coherence": 1, "information_density": 0.86, "quality_score": 0.93, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:03.824525", "source": { "split": "train_shard_00001", "doc_id": 4107 }, "chunk_id": "train_shard_00001_4107_1", "global_id": 11471 }, { "text": "

Synopsis

Background

Our primary aim was to test whether cattle-associated fluoroquinolone-resistant (FQ-R) Escherichia coli found on dairy farms were a significant cause of bacteriuria in humans living in the same 50 × 50 km geographical region located in South West England. Another aim was to identify risk factors for the presence of FQ-R E. coli on dairy farms.

Methods

FQ-R E. coli were isolated during 2017-18 from 42 dairy farms and from community urine samples. Forty-two cattle and 489 human urinary isolates were subjected to WGS, allowing phylogenetic comparisons. Risk factors were identified using a Bayesian regularisation approach.

Results

Of 489 FQ-R human isolates, 255 were also 3 rd generation cephalosporin-resistant (3GC-R), with strong genetic linkage between aac(6’)Ib-cr and bla CTX-M-15 . We identified possible farm-to-human sharing for pairs of ST744 and ST162 isolates, but core genome SNP distances (71 and 63, respectively) were smaller in pairs of ST744 and ST162 isolates from different farms (7 and 3 SNPs, respectively). Total farm fluoroquinolone use showed a positive association with the odds of isolating FQ-R E. coli while total dry cow therapy use showed a negative association.

Conclusions

This work suggests that FQ-R E. coli found on dairy farms have a limited impact on community bacteriuria within the local human population, however, this appears greater than observed for 3GC-R E. coli when studied in parallel. Reducing fluoroquinolone use may reduce the on-farm prevalence of FQ-R E. coli , and this reduction may be greater when dry cow therapy is targeted to the ecology of resistant E. coli on the farm.", "token_count": 502, "char_count": 1700, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6139, "quality_score": 0.8069, "entities": { "genes": [ "ST162", "ST744" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:04.479104", "source": { "split": "train_shard_00001", "doc_id": 4108 }, "chunk_id": "train_shard_00001_4108_0", "global_id": 11472 }, { "text": "Limited Phylogenetic Overlap Between Fluoroquinolone-Resistant Escherichia coli Isolated on Dairy Farms and those Causing Bacteriuria in Humans Living in the Same Geographical Region", "token_count": 53, "char_count": 182, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:04.835364", "source": { "split": "train_shard_00001", "doc_id": 4108 }, "chunk_id": "train_shard_00001_4108_1", "global_id": 11473 }, { "text": "

ABSTRACT

With the exponential increase in the number of bacterial taxa with genome sequence data, a new standardized method is needed to assign bacterial species designations using genomic data that is consistent with the classically-obtained taxonomy. This is particularly acute for unculturable obligate intracellular bacteria like those in the Rickettsiales, where classical methods like DNA-DNA hybridization cannot be used to define species. Within the Rickettsiales, species designations have been applied inconsistently, often obfuscating the relationship between organisms and the context for experimental results. In this study, we generated core genome alignments for a wide range of genera with classically defined species, including Arcobacter , Caulobacter , Erwinia , Neisseria , Polaribacter , Ralstonia , Thermus , as well as genera within the Rickettsiales including Rickettsia , Orientia , Ehrlichia , Neoehrlichia , Anaplasma , eorickettsia , and Wolbachia . A core genome alignment sequence identity (CGASI) threshold of 96.8% was found to maximize the prediction of classically-defined species. Using the CGASI cutoff, the Wolbachia genus can be delineated into species that differ from the currently used supergroup designations, while the Rickettsia genus is delineated into nine species, as opposed to the current 27 species. Additionally, we find that core genome alignments cannot be constructed between genomes belonging to different genera, establishing a bacterial genus cutoff that suggests the need to create new genera from the Anaplasma and Neorickettsia . By using core genome alignments to assign taxonomic designations, we aim to provide a high-resolution, robust method for bacterial nomenclature that is aligned with classically-obtained results.\n\nUsing Core Genome Alignments to Assign Bacterial Species", "token_count": 451, "char_count": 1851, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5437, "quality_score": 0.7719, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:05.475447", "source": { "split": "train_shard_00001", "doc_id": 4109 }, "chunk_id": "train_shard_00001_4109_0", "global_id": 11474 }, { "text": "Methicillin-resistant Staphylococcus aureus (MRSA) are a major threat to human and animal health, causing difficult-to-treat infections. The aim of our study was to evaluate the intra-farm transmission of livestock-associated (LA) MRSA sequence type (ST) 398 isolates on German dairy farms. A total of 115 LA-MRSA ST398 isolates originating from animals, humans and the environment of six dairy farms were analyzed by whole-genome sequencing and core genome multilocus sequence typing. Phylogenetic clusters of high allelic similarity were detected on all dairy farms, suggesting a MRSA transmission across the different niches. On one farm, closely related isolates from quarter milk samples (QMS), suckers of calf feeders and nasal cavities of calves indicate that MRSA may be transferred by feeding contaminated milk to calves. Detection of related MRSA isolates in QMS and teat cups (4/6 farms) or QMS and human samples (3/4 farms) pointed out a transmission of MRSA between cows during the milking process and a potential zoonotic risk. In conclusion, LA-MRSA ST398 isolates may spread between animals, humans and the environment on dairy farms. Milking time hygiene and other internal biosecurity measures on farms and pre-treatment of milk before feeding it to calves may reduce the risk of MRSA transmission.\n\nPhylogenetic Tracking of LA-MRSA ST398 Intra-Farm Transmission among Animals, Humans and the Environment on German Dairy Farms.", "token_count": 390, "char_count": 1464, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:06.095018", "source": { "split": "train_shard_00001", "doc_id": 4110 }, "chunk_id": "train_shard_00001_4110_0", "global_id": 11475 }, { "text": "The presence and dissemination of carbapenem-resistant Klebsiella pneumoniae (CRKP) often cause life-threatening infections worldwide, but the therapeutic option is limited. In this study, whole-genome sequencing (WGS) was applied to assess the epidemiological characteristics and transmission dynamics of CRKP isolates recovered from two fetal outbreaks of nosocomial infections. Between April 2016 and March 2018, a total of 70 isolates of K. pneumoniae were collected from sterile samples in a tertiary hospital in Hangzhou, China. The minimal inhibitory concentrations (MICs) of 21 antimicrobial agents were determined using the broth microdilution methods. Pulsed-field gel electrophoresis (PFGE) was performed on 47 CRKP isolates, and 16 clonally related isolates were further characterized by Illumina sequencing. In addition, the complete genome sequences of three representative isolates (KP12, KP36, and KP37) were determined by Oxford Nanopore sequencing. The K. pneumoniae isolates were recovered from patients diagnosed with pulmonary infection, cancer, or encephalopathy. For all CRKP isolates, PFGE separated three clusters among all strains. The most predominant PFGE cluster contained 16 isolates collected from patients who shared close hospital units and represented a potential outbreak. All 16 isolates showed an extremely high resistance level (≥87.5%) to 18 antimicrobials tested but remain susceptible to colistin (CST). Multiple antimicrobial resistance and virulence determinants, such as the carbapenem resistance gene bla KPC-2, and genes encoding the virulence factor aerobactin and the regulator of the mucoid phenotype (rmpA and rmpA2), were observed in the 16 CRKP isolates", "token_count": 500, "char_count": 1758, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.834, "entities": { "genes": [ "KP37", "KP12", "KP36" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:06.746369", "source": { "split": "train_shard_00001", "doc_id": 4111 }, "chunk_id": "train_shard_00001_4111_0", "global_id": 11476 }, { "text": "These isolates belonged to sequence type 11 (ST11) and capsular serotype KL64. A core genome single nucleotide polymorphism (cgSNP)-based phylogenetic analysis indicated that the 16 CRKP isolates could be partitioned into two separate clades (≤15 SNPs), suggesting the two independent transmission scenarios co-occurred. Moreover, a high prevalence of IncFIB/IncHI1B type virulence plasmid with the iroBCDN locus deleted, and an IncFII/IncR type bla KPC-2-bearing plasmid was co-harbored in ST11-KL64 CRKP isolates. In conclusion, our data indicated that the nosocomial dissemination of ST11-KL64 CRKP clone is a potential threat to anti-infective therapy. The development of novel strategies for surveillance, diagnosis, and treatment of this high-risk CRKP clone is urgently needed.\n\nTransmission Dynamics of Carbapenem-Resistant Klebsiella pneumoniae Sequence Type 11 Strains Carrying Capsular Loci KL64 and rmpA/rmpA2 Genes.", "token_count": 319, "char_count": 974, "word_count": 125, "semantic_coherence": 1, "information_density": 0.736, "quality_score": 0.868, "entities": { "genes": [ "KL64", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:07.339550", "source": { "split": "train_shard_00001", "doc_id": 4111 }, "chunk_id": "train_shard_00001_4111_1", "global_id": 11477 }, { "text": "The invention relates to a method for extracting bile salt hydrolase (BSH) of two kinds of yeasts and a production technology of functional kefir, applicable to the production of functional kefir and sour kefir in fermented dairy products. The invention adopts high-throughput screening technique and phthalic aldehyde method to acquire two kinds of yeasts which can lower cholesterol efficiently and have higher capacity of fermenting lactose, and Oxford cup method to acquire strains yielding the BSH highly through secondary screening. The invention optimizes the fermentation conditions and extraction method for the two kinds of yeasts to produce the BSH, and adopts proper cracking method by ultrasonic wave, which solves the problem that the cell walls of the yeasts are difficult to be cracked, and the cracking effect can be compared with that of the high pressure cell cracker. Kluyveromyces Marxianus K1 (CGMCC No 1812) and M3 (CGMCC No 1811) which can lower the cholesterol efficiently can yield the BSH highly and can ferment lactose to yield ethanol highly, are adopted to prepare the kefir of high quality that has the function of lowering the cholesterol. The fermentation process of preparing the functional kefir is simple with shorter fermentation period and lower cost. Thus, the fermentation process is applicable to mass industrial production.\n\nProcess for extracting two kinds of yeast bilesalt hydrolase and production technology of functional posset", "token_count": 349, "char_count": 1474, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5022, "quality_score": 0.7511, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:07.932852", "source": { "split": "train_shard_00001", "doc_id": 4112 }, "chunk_id": "train_shard_00001_4112_0", "global_id": 11478 }, { "text": "Gene essentiality studies have been performed on numerous bacterial pathogens, but essential gene sets have been determined for only a few plant-associated bacteria. Pseudomonas protegens Pf-5 is a plant-commensal, biocontrol bacterium that can control disease-causing pathogens on a wide range of crops. Work on Pf-5 has mostly focused on secondary metabolism and biocontrol genes, but genome-wide approaches such as high-throughput transposon mutagenesis have not yet been used for this species. In this study, we generated a dense P. protegens Pf-5 transposon mutant library and used transposon-directed insertion site sequencing (TraDIS) to identify 446 genes essential for growth on rich media. Genes required for fundamental cellular machinery were enriched in the essential gene set, while genes related to nutrient biosynthesis, stress responses, and transport were underrepresented. The majority of Pf-5 essential genes were part of the P. protegens core genome. Comparison of the essential gene set of Pf-5 with those of two plant-associated pseudomonads, P. simiae and P. syringae, and the well-studied opportunistic human pathogen P. aeruginosa PA14 showed that the four species share a large number of essential genes, but each species also had uniquely essential genes. Comparison of the Pf-5 in silico-predicted and in vitro-determined essential gene sets highlighted the essential cellular functions that are over- and underestimated by each method. Expanding essentiality studies into bacteria with a range of lifestyles may improve our understanding of the biological processes important for bacterial survival and growth.IMPORTANCE Essential genes are those crucial for survival or normal growth rates in an organism. Essential gene sets have been identified in numerous bacterial pathogens but only a few plant-associated bacteria. Employing genome-wide approaches, such as transposon insertion sequencing, allows for the concurrent analyses of all genes of a bacterial species and rapid determination of essential gene sets", "token_count": 519, "char_count": 2107, "word_count": 293, "semantic_coherence": 1, "information_density": 0.5461, "quality_score": 0.773, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:08.614795", "source": { "split": "train_shard_00001", "doc_id": 4113 }, "chunk_id": "train_shard_00001_4113_0", "global_id": 11479 }, { "text": "We have used transposon insertion sequencing to systematically analyze thousands of Pseudomonas protegens Pf-5 genes and gain insights into gene functions and interactions that are not readily available using traditional methods. Comparing Pf-5 essential genes with those of three other pseudomonads highlights how gene essentiality varies between closely related species.\n\nElucidating Essential Genes in Plant-Associated Pseudomonas protegens Pf-5 Using Transposon Insertion Sequencing.", "token_count": 109, "char_count": 494, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8226, "quality_score": 0.9113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:09.038517", "source": { "split": "train_shard_00001", "doc_id": 4113 }, "chunk_id": "train_shard_00001_4113_1", "global_id": 11480 }, { "text": "ENGINEERING OF XYLOSE REDUCTASE AND OVEREXPRESSION OF XYLITOL DEHYDROGENASE AND XYLULOKINASE IMPROVES XYLOSE ALCOHOLIC FERMENTATION IN THE THERMOTOLERANT YEAST HANSENULA POLYMORPHA", "token_count": 83, "char_count": 180, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:09.444166", "source": { "split": "train_shard_00001", "doc_id": 4114 }, "chunk_id": "train_shard_00001_4114_0", "global_id": 11481 }, { "text": "

Summary

Metagenomics revolutionized the field of microbial ecology, giving access to Gb-sized datasets of microbial communities under natural conditions. This enables fine-grained analyses of the functions of community members, studies of their association with phenotypes and environments, as well as of their microevolution and adaptation to changing environmental conditions. However, phylogenetic methods for studying adaptation and evolutionary dynamics are not able to cope with big data. EDEN is the first software for the rapid detection of protein families and regions under positive selection, as well as their associated biological processes, from meta- and pangenome data. It provides an interactive result visualization for detailed comparative analyses.

Availability and implementation

EDEN is available as a Docker installation under the GPL 3.0 license, allowing its use on common operating systems, at http://www.github.com/hzi-bifo/eden.

Contact

alice.mchardy@helmholtz-hzi.de.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nEDEN: evolutionary dynamics within environments.", "token_count": 272, "char_count": 1159, "word_count": 138, "semantic_coherence": 1, "information_density": 0.7174, "quality_score": 0.8587, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:09.995923", "source": { "split": "train_shard_00001", "doc_id": 4115 }, "chunk_id": "train_shard_00001_4115_0", "global_id": 11482 }, { "text": "Malate is a major contributor to the sourness of grape berries ( Vitis spp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wild Vitis grapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecific Vitis family that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on the Vitis collinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for over two-fold and 6.9 g/L differences in ripe fruit malate, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%) and their associated QTL overlapped on chromosome 7, indicating a common genetic basis. However, use of transferable markers on a closely related Vitis family did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate the levels of this key metabolite in the Vitis genus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.\n\nStable QTL for malate levels in ripe fruit and their transferability acrossVitisspecies", "token_count": 413, "char_count": 1668, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:10.621740", "source": { "split": "train_shard_00001", "doc_id": 4116 }, "chunk_id": "train_shard_00001_4116_0", "global_id": 11483 }, { "text": "Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem around the world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone and displays significantly greater virulence than other S. aureus. Here, we have examined the evolution of ST93 via genomic analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from around Australia over a 17-year period. Comparative analysis revealed a core genome of 2.6 Mb, sharing greater than 99.7% nucleotide identity. The accessory genome was 0.45 Mb and comprised additional mobile DNA elements, harboring resistance to erythromycin, trimethoprim, and tetracycline. Phylogenetic inference revealed a molecular clock and suggested that a single clone of methicillin susceptible, Panton-Valentine leukocidin (PVL) positive, ST93 S. aureus likely spread from North Western Australia in the early 1970s, acquiring methicillin resistance at least twice in the mid 1990s. We also explored associations between genotype and important MRSA phenotypes including oxacillin MIC and production of exotoxins (α-hemolysin [Hla], δ-hemolysin [Hld], PSMα3, and PVL). High-level expression of Hla is a signature feature of ST93 and reduced expression in eight isolates was readily explained by mutations in the agr locus. However, subtle but significant decreases in Hld were also noted over time that coincided with decreasing oxacillin resistance and were independent of agr mutations. The evolution of ST93 S. aureus is thus associated with a reduction in both exotoxin expression and oxacillin MIC, suggesting MRSA ST93 isolates are under pressure for adaptive change.\n\nAdaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus.", "token_count": 501, "char_count": 1816, "word_count": 255, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [ "ST93" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:11.284237", "source": { "split": "train_shard_00001", "doc_id": 4117 }, "chunk_id": "train_shard_00001_4117_0", "global_id": 11484 }, { "text": "Salmonella is among the most common foodborne pathogens worldwide, and can lead to acute gastroenteritis. Along with poultry, cattle production is recognized as an important source of human infection. Salmonella transmission from cattle to humans can occur through the environment, or through close contact with sick animals or their derived products. This study aimed to investigate the intestinal carriage of Salmonella spp. within French cattle production. A total of 959 cattle intestinal samples, from one of the largest French slaughterhouses, were analyzed. Isolated strains were genotyped by pulsed field gel electrophoresis (PFGE), and a sub-selection was taken by whole genome sequencing (WGS). Twenty-nine samples were positive for Salmonella spp., yielding an estimated prevalence of 3% in cattle production. Eight different Salmonella serotypes were found: Montevideo was the most prevalent (34%), followed by Mbandaka (24%) and Anatum (14%). PFGE genotyping allowed the clustering of Salmonella isolates according to their serotype. Within the clusters, some isolates presented 100% similarity. To investigate potential epidemiological links between them, WGS and core genome multilocus sequence typing (cgMLST) were used, revealing identical profiles between isolates originating from different areas and/or different animal breeds. This investigation provides new insights on Salmonella serotype epidemiology in cattle production in France.\n\nOccurrence of Salmonella in the Cattle Production in France.", "token_count": 400, "char_count": 1574, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:11.902081", "source": { "split": "train_shard_00001", "doc_id": 4118 }, "chunk_id": "train_shard_00001_4118_0", "global_id": 11485 }, { "text": "Extremely thermophilic bacteria of the genus Caldicellulosiruptor utilize carbohydrate components of plant cell walls, including cellulose and hemicellulose, facilitated by a diverse set of glycoside hydrolases (GHs). From a biofuel perspective, this capability is crucial for deconstruction of plant biomass into fermentable sugars. While all species from the genus grow on xylan and acid-pretreated switchgrass, growth on crystalline cellulose is variable. The basis for this variability was examined using microbiological, genomic, and proteomic analyses of eight globally diverse Caldicellulosiruptor species. The open Caldicellulosiruptor pangenome (4,009 open reading frames [ORFs]) encodes 106 GHs, representing 43 GH families, but only 26 GHs from 17 families are included in the core (noncellulosic) genome (1,543 ORFs). Differentiating the strongly cellulolytic Caldicellulosiruptor species from the others is a specific genomic locus that encodes multidomain cellulases from GH families 9 and 48, which are associated with cellulose-binding modules. This locus also encodes a novel adhesin associated with type IV pili, which was identified in the exoproteome bound to crystalline cellulose. Taking into account the core genomes, pangenomes, and individual genomes, the ancestral Caldicellulosiruptor was likely cellulolytic and evolved, in some cases, into species that lost the ability to degrade crystalline cellulose while maintaining the capacity to hydrolyze amorphous cellulose and hemicellulose.\n\nCaldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass.", "token_count": 446, "char_count": 1642, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:12.535610", "source": { "split": "train_shard_00001", "doc_id": 4119 }, "chunk_id": "train_shard_00001_4119_0", "global_id": 11486 }, { "text": "Campylobacteriosis is among the world’s most common foodborne illnesses, caused predominantly by the bacterium Campylobacter jejuni . Effective interventions require determination of the infection source which is challenging as transmission occurs via multiple sources such as contaminated meat, poultry, and drinking water. Strain variation has allowed source tracking based upon allelic variation in multi-locus sequence typing (MLST) genes allowing isolates from infected individuals to be attributed to specific animal or environmental reservoirs. However, the accuracy of probabilistic attribution models has been limited by the ability to differentiate isolates based upon just 7 MLST genes. Here, we broaden the input data spectrum to include core genome MLST (cgMLST) and whole genome sequences (WGS), and implement multiple machine learning algorithms, allowing more accurate source attribution. We increase attribution accuracy from 64% using the standard iSource population genetic approach to 71% for MLST, 85% for cgMLST and 78% for kmerized WGS data using machine learning. To gain insight beyond the source model prediction, we use Bayesian inference to analyse the relative affinity of C. jejuni strains to infect humans and identified potential differences, in source-human transmission ability among clonally related isolates in the most common disease causing lineage (ST-21 clonal complex). Providing generalizable computationally efficient methods, based upon machine learning and population genetics, we provide a scalable approach to global disease surveillance that can continuously incorporate novel samples for source attribution and identify fine-scale variation in transmission potential.

Author summary

C. jejuni are the most common cause of food-borne bacterial gastroenteritis but the relative contribution of different sources are incompletely understood. We traced the origin of human C. jejuni infections using machine learning algorithms that compare the DNA sequences of bacteria sampled from infected people, contaminated chickens, cattle, sheep, wild birds and the environment. This approach achieved improvement in accuracy of source attribution by 33% over existing methods that use only a subset of genes within the genome and provided evidence for the relative contribution of different infection sources", "token_count": 479, "char_count": 2355, "word_count": 326, "semantic_coherence": 1, "information_density": 0.6196, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:13.185167", "source": { "split": "train_shard_00001", "doc_id": 4120 }, "chunk_id": "train_shard_00001_4120_0", "global_id": 11487 }, { "text": "Sometimes even very similar bacteria showed differences, demonstrating the value of basing analyses on the entire genome when developing this algorithm that can be used for understanding the global epidemiology and other important bacterial infections.\n\nMachine learning to predict the source of campylobacteriosis using whole genome data", "token_count": 65, "char_count": 338, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8936, "quality_score": 0.9468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:13.555803", "source": { "split": "train_shard_00001", "doc_id": 4120 }, "chunk_id": "train_shard_00001_4120_1", "global_id": 11488 }, { "text": "DEVELOPMENT OF STRAINS OF THE THERMOTOLERANT YEAST HANSENULA POLYMORPHA CAPABLE OF ALCOHOLIC FERMENTATION OF STARCH AND XYLAN BY EXPRESSION OF STARCH AND XYLAN DEGRADING ENZYMES", "token_count": 74, "char_count": 177, "word_count": 25, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:13.922859", "source": { "split": "train_shard_00001", "doc_id": 4121 }, "chunk_id": "train_shard_00001_4121_0", "global_id": 11489 }, { "text": "An in-depth analysis was performed on Swedish broiler producers that had delivered chickens with Campylobacter to slaughter over several years, in order to identify possible transmission routes and formulate effective measures to prevent chickens being colonized with Campylobacter. Between 2017 and 2019, 626 samples were collected at farm level and Campylobacter was isolated from 133 (21.2%). All C. jejuni and C. coli isolated from these samples were whole-genome sequenced, together with isolates from the corresponding cecum samples at slaughter (n = 256). Core genome multi-locus sequence typing (cgMLST) analysis, using schemes consisting of 1140 and 529 genes for C. jejuni and C. coli, respectively, revealed that nearby cattle, contaminated drinking water, water ponds, transport crates, and parent flocks were potential reservoirs of Campylobacter. A novel feature compared with previous studies is that measures were implemented and tested during the work. These contributed to a nationwide decrease in Campylobacter-positive flocks from 15.4% in 2016 to 4.6% in 2019, which is the lowest ever rate in Sweden. To conclude, there are different sources and routes of Campylobacter transmission to chickens from different broiler producers, and individual measures must be taken by each producer to prevent Campylobacter colonization of chickens.\n\nIdentification of Transmission Routes of Campylobacter and On-Farm Measures to Reduce Campylobacter in Chicken.", "token_count": 443, "char_count": 1567, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:14.568107", "source": { "split": "train_shard_00001", "doc_id": 4122 }, "chunk_id": "train_shard_00001_4122_0", "global_id": 11490 }, { "text": "

Background

Antimicrobial resistance (AMR) in Helicobacter pylori is increasing globally and can result in treatment failure and inappropriate antibiotic usage. This study used whole genome sequencing (WGS) to conduct an analysis of the H. pylori resistome and phylogeny.

Materials/methods

A total of 1040 H. pylori isolate sequences were retrieved. Analysis was conducted via an in-house bioinformatics pipeline targeting point mutations in selected genes frequently associated with AMR (pbp1A, 23S rRNA, gyrA, rdxA, frxA, and rpoB) and phylogenomic analyses using core genome multilocus sequence typing (cgMLST).

Results

Phylogenomic analysis revealed a notable geographical clustering of H. pylori genomes across world regions, but large distances of more than 1000 loci between isolates on individual branches were observed. Resistome analysis revealed the prevalence of common mutations which have previously been found to correlate with phenotypic antibiotic resistance; the most common point mutations for each gene were S589G (pbp1A, 48.8% of perfect aligned sequences), A2143G (23S rRNA, 27.4% of perfectly aligned sequences), N87 K\\I\\Y (gyrA, 14.7% of perfectly aligned sequences), R131K (rdxA, 65.7% of perfectly aligned sequences), and C193S (frxA, 62.6% of perfectly aligned sequences).

Conclusions

This is the largest study to date featuring the global phylogeny of H. pylori in conjunction with a global snapshot of the H. pylori resistome based on >1000 genomes. Further analyses that combine WGS and phenotypic methods will provide further understanding of the association between the mutations and resistance.", "token_count": 485, "char_count": 1655, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6473, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:15.212824", "source": { "split": "train_shard_00001", "doc_id": 4123 }, "chunk_id": "train_shard_00001_4123_0", "global_id": 11491 }, { "text": "Unraveling antimicrobial resistance in Helicobacter pylori: Global resistome meets global phylogeny.", "token_count": 29, "char_count": 100, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:15.572096", "source": { "split": "train_shard_00001", "doc_id": 4123 }, "chunk_id": "train_shard_00001_4123_1", "global_id": 11492 }, { "text": "Idiopathic normal pressure hydrocephalus (iNPH), a leading cause of reversible dementia in older adults, is marked by ventriculomegaly, gait disturbances, cognitive decline, and urinary incontinence. Emerging evidence suggests that gut dysbiosis (microbial imbalance) may influence neuroinflammation and cerebrospinal fluid dynamics, potentially contributing to glymphatic system dysfunction and ventricular enlargement. This study used shotgun metagenomics to analyze the gut microbiome in iNPH patients (n = 18) compared to healthy controls (n = 50), individuals with ventriculomegaly but no iNPH symptoms (n = 50), and Alzheimer's disease patients (n = 50). Microbiome analysis showed an enrichment of species previously linked to various disease states, such as Enterocloster bolteae and Ruminococcus gnavus, indicating general dysbiosis. In contrast, enrichment of specific taxa, including Evtepia gabavorous and Cuneatibacter sp., were specifically associated with iNPH clinical traits, pointing to possible disease-specific microbial markers. Functional analysis showed enrichment of pathways related to carbohydrate and amino acid metabolism, including the S-adenosyl-L-methionine superpathway, implicating inflammatory and immune processes. These findings suggest distinct gut microbiome signatures in iNPH, offering insights into potential gut-brain interactions that may contribute to the disorder's pathophysiology and highlighting possible targets for future therapeutic strategies.\n\nGut microbiome signatures in iNPH: Insights from a shotgun metagenomics study.", "token_count": 422, "char_count": 1575, "word_count": 200, "semantic_coherence": 1, "information_density": 0.73, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:16.192134", "source": { "split": "train_shard_00001", "doc_id": 4124 }, "chunk_id": "train_shard_00001_4124_0", "global_id": 11493 }, { "text": "Currently, the mechanism of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) transmission mechanism is unclear; however, it must be considered in conjunction with asymptomatic S. aureus strains colonization dynamics. This epidemiological study aimed to determine the role of the household in CA-MRSA transmission in China. Five patients with culture-confirmed CA-MRSA infection and five control patients were recruited from the Sir Run Run Shaw Hospital in Zhejiang, China, between December 2019 and January 2020. The household members of the patients, their pets, and environmental surfaces were sampled and screened for MRSA colonization. Mass spectrometry identification and antimicrobial susceptibility testing were performed on the MRSA isolates. Whole-genome sequencing and core genome multilocus sequence typing (cgMLST) were performed to determine the origin and transmission of the MRSA isolates in the households. Overall, 14 S. aureus-positive specimens (14.1%, 14/99) were obtained from the five households of patients with CA-MRSA infections, of which 12 (85.7%) were MRSA. The overall positivity of MRSA was 12.1% (12/99) among the samples from the CA-MRSA households, while no MRSA isolates were detected in the five control households. Most MRSA isolates belonged to epidemic CA-MRSA clones, such as ST59 (15/35, 42.9%) and ST508 (15/35, 42.9%). The cgMLST results confirmed that MRSA was transmitted among patients, contacts, and pets in the households and was present on environmental surfaces in the CA-MRSA patients' households. In conclusion, the study revealed that the home environment was an important MRSA reservoir. Therefore, focusing on MRSA decolonization in patients alone is not sufficient for infection control of CA-MRSA.\n\nHousehold Transmission of Community-Associated Methicillin-Resistant Staphylococcus Aureus.", "token_count": 513, "char_count": 1901, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5642, "quality_score": 0.7821, "entities": { "genes": [ "ST59", "ST508" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:16.847306", "source": { "split": "train_shard_00001", "doc_id": 4125 }, "chunk_id": "train_shard_00001_4125_0", "global_id": 11494 }, { "text": "Functional-based screening of crude beta-galactosidase activities from 42 yeast strains resulted in the selection of a single enzyme of potential interest as a digestive supplement. beta-Galactosidase produced by Kluyveromyces marxianus DSM5418 was purified to homogeneity by a combination of gel filtration, ion-exchange, and hydroxylapatite chromatographies. The denatured (123 kDa) and native molecular masses (251 kDa) suggest that the enzyme is a homodimer. The optimum pH and temperature of the purified enzyme were 6.8 and 37 degrees C, respectively. The unpurified beta-galactosidase in particular displayed a high level of stability when exposed to simulated intestinal conditions in vitro for 4 h. Matrix-assisted laser desorption ionization mass sectrometry analysis revealed that the enzyme's trypsin-generated peptide mass fingerprint shares several peptide fragment hits with beta-galactosidases from Kluyveromyces lactis. This confirms the enzyme's identity and indicates that significant sequence homology exists between these enzymes.\n\nPurification and properties of a beta-galactosidase with potential application as a digestive supplement.", "token_count": 308, "char_count": 1158, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6928, "quality_score": 0.8464, "entities": { "genes": [ "DSM5418" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:17.427025", "source": { "split": "train_shard_00001", "doc_id": 4126 }, "chunk_id": "train_shard_00001_4126_0", "global_id": 11495 }, { "text": "The application of high-throughput DNA sequencing technologies (WGS) data remain an increasingly discussed but vastly unexplored resource in the public health domain of quantitative microbial risk assessment (QMRA). This is due to challenges including high dimensionality of WGS data and heterogeneity of microbial growth phenotype data. This study provides an innovative approach for modeling the impact of population heterogeneity in microbial phenotypic stress response and integrates this into predictive models inputting a high-dimensional WGS data for increased precision exposure assessment using an example of Listeria monocytogenes. Finite mixture models were used to distinguish the number of sub-populations for each of the stress phenotypes, acid, cold, salt and desiccation. Machine learning predictive models were selected from six algorithms by inputting WGS data to predict the sub-population membership of new strains with unknown stress response data. An example QMRA was conducted for cultured milk products using the strains of unknown stress phenotype to illustrate the significance of the findings of this study. Increased resistance to stress conditions leads to increased growth, the likelihood of higher exposure and probability of illness. Neglecting within-species genetic and phenotypic heterogeneity in microbial stress response may over or underestimate microbial exposure and eventual risk during QMRA.\n\nQuantitative Microbial Risk Assessment Based on Whole Genome Sequencing Data: Case of Listeria monocytogenes.", "token_count": 337, "char_count": 1558, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:17.993339", "source": { "split": "train_shard_00001", "doc_id": 4127 }, "chunk_id": "train_shard_00001_4127_0", "global_id": 11496 }, { "text": "Kluyveromyces marxianus NRRL Y-1196 produced the highest inulinase activity (38 U/mg protein) of six yeasts examined after 24 h growth in sauerkraut brine in shaking flasks at 30°C with 0.3% inulin as an enzyme inducer. The enzyme was recovered by acetone fractionation, with a yield of 81%. It had maximum activity at pH 4.4 and 55°C with K m values for inulin and sucrose of 3.92 mM and 11.9 mM, respectively. The yeast raised the pH from 3.4 to above 7.0, using all the lactic acid in the brine. Growth of K. marxianus in sauerkraut brine with a small amount of inulin may usefully decrease the BOD and concomitantly produce inulinase.\n\nEffect of inulin on yeast inulinase production in sauerkraut brine.", "token_count": 236, "char_count": 707, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:18.468897", "source": { "split": "train_shard_00001", "doc_id": 4128 }, "chunk_id": "train_shard_00001_4128_0", "global_id": 11497 }, { "text": "Yeasts Candida kefyr NCYC143, Candida utilis CUM, Kluyveromyces lactis KL71, Saccharomyces bayanus SB1, Saccharomyces cerevisiae EC1118, Saccharomyces chevalieri CCICC1028, Candida famata (previously Torulopsis candida) CCICC1041 and Williopsis saturnus var. saturnus CBS254 were screened for their ability to produce flavour-active methionol (3-methylthio-1-propanol) in coconut cream supplemented with l-methionine. The yeasts varied with their ability to produce methionol from methionine with Saccharomyces cerevisiae EC1118 producing the most, followed by Kluyveromyces lactis KL71. Little methionol was produced by the other yeasts. Methionol production by Kluyveromyces lactis KL71 was subjected to further studies under different conditions of initial pH (4.0-6.3), temperature (20-33 °C), l-methionine concentration (0.05-0.25%) and yeast extract concentration (0-0.50%); optimal conditions were established at pH 5.0, 33.0 °C, 0.15% l-methionine and 0.05% yeast extract. CharmAnalysis™ using SPME-GC-MS was conducted on the coconut cream ferment; methional (3-methylthio-1-propanal), methionol and 2-phenylethyl acetate were found to be the most potent aroma-active compounds. The product of coconut cream fermentation by Kluyveromyces lactis KL71 may be considered as a novel, plant-based, natural and complex flavoring bioingredient in food applications.\n\nProduction of flavour-active methionol from methionine metabolism by yeasts in coconut cream.", "token_count": 483, "char_count": 1461, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6467, "quality_score": 0.8234, "entities": { "genes": [ "CBS254", "EC1118", "CCICC1041", "SB1", "NCYC143", "KL71", "CCICC1028" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:19.116381", "source": { "split": "train_shard_00001", "doc_id": 4129 }, "chunk_id": "train_shard_00001_4129_0", "global_id": 11498 }, { "text": "Multidrug-resistant (MDR) Shigella sonnei have become prevalent among men who have sex with men and have become a global public health concern. From June 2017 to April 2019, 32 men were infected with MDR S. sonnei acquired locally, in Montréal, which was suggestive of an outbreak. Antimicrobial susceptibility testing, whole-genome sequencing (WGS), phylogenetic analysis, antimicrobial resistance and virulence characterization, and association to international clusters were performed. The outbreak strain was ceftriaxone- and azithromycin-resistant due to the acquisition of blaCTX-M-27, and mphA and ermB genes, respectively, with reduced susceptibility to ciprofloxacin due to a single point mutation (gyrA S83L). One out of 27 patients treated with a fluoroquinolone experienced microbiological failure. Epidemiological evidence first supported by a rare unique MDR Shigella sonnei documented only in men in 2017 followed by similar pulsed-field gel electrophoresis profiles was confirmed by WGS. A core genome high-quality single-nucleotide variant (hqSNV)-based phylogeny found a median of 6 hqSNV differences among isolates. Virulence gene content was investigated, but no Shiga toxins were detected. An international cluster of highly related isolates was identified (PDS000019750.208) and belonged to the 3.7.29.1.4.1 S. sonnei genotype (Global III VN2.KH1.Aus). Genomic analysis revealed that this Montréal cluster was connected to other documented outbreaks in Australia, the United States, and the United Kingdom. This study highlights the urgent need for public health measures to focus on the prevention and the early detection of S. sonnei, since global transmission patterns of MDR strains is concerning and few antimicrobial treatment options are available", "token_count": 499, "char_count": 1815, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [ "KH1", "VN2", "PDS000019750" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:19.804217", "source": { "split": "train_shard_00001", "doc_id": 4130 }, "chunk_id": "train_shard_00001_4130_0", "global_id": 11499 }, { "text": "IMPORTANCE Shigella sonnei, an important foodborne pathogen, recently became a frequent sexually transmitted agent involved in large and persistent outbreaks globally among men who have sex with men. Most strains also harbor several multidrug-resistant (MDR) determinants of particular concern. This study characterizes an outbreak strain at the source of an important MDR cluster identified in Montréal in 2017. Associations were made to many high-profile international outbreaks, and the causative S. sonnei lineage of these clusters was identified, which was not evident in past reports. The worldwide occurrence of this strain is of concern since treatment with antimicrobials like ceftriaxone and azithromycin may not be effective, and rare microbiological failures have been documented in patients treated with ciprofloxacin. Our investigation highlights the threats of Shigella spp. infection and the necessity for antimicrobial susceptibility monitoring in order to mitigate S. sonnei's impact on public health and to avoid transmission to other at-risk communities.\n\nClinical and Genomic Investigation of an International Ceftriaxone- and Azithromycin-Resistant Shigella sonnei Cluster among Men Who Have Sex with Men, Montréal, Canada 2017-2019.", "token_count": 313, "char_count": 1269, "word_count": 174, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:20.373930", "source": { "split": "train_shard_00001", "doc_id": 4130 }, "chunk_id": "train_shard_00001_4130_1", "global_id": 11500 }, { "text": "A hydrolysis of 62% and 50% for OSX (Oat spelt xylan) and WBH (Wheat bran hemicellulose) were obtained in 36h and 48h using Accellerase 1000 at 50 degrees C wherein thermostable xylanase from alkalothermophilic Thermomonospora sp. yielded 67% (OSX) in 3h and 58% (WBH) in 24h at 60 degrees C, favouring a reduction in process time and enzyme dosage. The rate of hydrolysis with thermostable xylanase was increased by 20% with the addition of nonionic surfactant tween 80 or biosurfactant sophorolipid. The simultaneous saccharification and fermentation (SSF) of OSX and WBH using thermostable xylanase and D. hansenii in batch cultures produced 9.1g/L and 9.5 g/L of ethanol, respectively and had a shorter overall process time than the separate hydrolysis and fermentation (SHF). The immobilized yeast cells in Ca-alginate matrix produced ethanol with a yield of 0.46 g/g from hemicellulosic hydrolysates and were reused six times with 100% fermentation efficiency.\n\nBiocatalytic approach for the utilization of hemicellulose for ethanol production from agricultural residue using thermostable xylanase and thermotolerant yeast.", "token_count": 365, "char_count": 1129, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6488, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:20.986481", "source": { "split": "train_shard_00001", "doc_id": 4131 }, "chunk_id": "train_shard_00001_4131_0", "global_id": 11501 }, { "text": "

Background

Campylobacter jejuni and C. coli share a multitude of risk factors associated with human gastrointestinal disease, yet their phylogeny differs significantly. C. jejuni is scattered into several lineages, with no apparent linkage, whereas C. coli clusters into three distinct phylogenetic groups (clades) of which clade 1 has shown extensive genome-wide introgression with C. jejuni, yet the other two clades (2 and 3) have less than 2% of C. jejuni ancestry. We characterized a C. coli strain (76339) with four novel multilocus sequence type alleles (ST-5088) and having the capability to express gamma-glutamyltranspeptidase (GGT); an accessory feature in C. jejuni. Our aim was to further characterize unintrogressed C. coli clades 2 and 3, using comparative genomics and with additional genome sequences available, to investigate the impact of horizontal gene transfer in shaping the accessory and core gene pools in unintrogressed C. coli.

Results

Here, we present the first fully closed C. coli clade 3 genome (76339). The phylogenomic analysis of strain 76339, revealed that it belonged to clade 3 of unintrogressed C. coli. A more extensive respiratory metabolism among unintrogressed C. coli strains was found compared to introgressed C. coli (clade 1). We also identified other genes, such as serine proteases and an active sialyltransferase in the lipooligosaccharide locus, not present in C. coli clade 1 and we further propose a unique scenario for the evolution of Campylobacter ggt.

Conclusions

We propose new insights into the evolution of the accessory genome of C. coli clade 3 and C. jejuni. Also, in silico analysis of the gene content revealed that C. coli clades 2 and 3 have genes associated with infection, suggesting they are a potent human pathogen, and may currently be underreported in human infections due to niche separation.", "token_count": 524, "char_count": 1887, "word_count": 284, "semantic_coherence": 1, "information_density": 0.581, "quality_score": 0.7905, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:21.650930", "source": { "split": "train_shard_00001", "doc_id": 4132 }, "chunk_id": "train_shard_00001_4132_0", "global_id": 11502 }, { "text": "Comparative genomics of unintrogressed Campylobacter coli clades 2 and 3.", "token_count": 24, "char_count": 73, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:22.008309", "source": { "split": "train_shard_00001", "doc_id": 4132 }, "chunk_id": "train_shard_00001_4132_1", "global_id": 11503 }, { "text": "The process of solid-state fermentation was used to produce a cocktail enzyme of Trichoderma reesei ATCC 66587 and Aspergillus tubingensis KRCF 700-33. Wheat bran, corncob, and sugi pulp were supplemented with ammonium sulfate as an enzyme-producing medium using T. reesei and A. tubingensis. The corncob blend ratio, duration of incubation, and ammonium sulfate concentration were optimized for enhancing cellulase production from T. reesei using a Box-Behnken design. Filter paper degrading activity more than tripled when T. reesei was grown in the optimized medium, as compared with the initial medium. The highest activity of 4.03 FPU/ml (about 29 FPU/g of dry material) was obtained with a cocktail enzyme having a 25 % content of A. tubingensis and 75 % of T. reesei. The sugi pulp was then fermented to ethanol with the cocktail enzyme and thermotolerant yeast (Saccharomyces cerevisiae BA-11) under simultaneous saccharification and fermentation (SSF) at 40 °C. An ethanol concentration of 4.48 % (w/v) was achieved using the cocktail enzyme (4 FPU/g-pulp) that was produced on-site with a substrate loading level of 12.5 wt %, which achieved an ethanol yield of 76 % after 72 h.\n\nEthanol production from sugi pulp under simultaneous saccharification and fermentation using a cocktail enzyme of T. reesei and A. tubingensis produced by solid-state fermentation", "token_count": 432, "char_count": 1369, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5592, "quality_score": 0.7796, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:22.636891", "source": { "split": "train_shard_00001", "doc_id": 4133 }, "chunk_id": "train_shard_00001_4133_0", "global_id": 11504 }, { "text": "The Roseobacter group comprises a significant group of marine bacteria which are involved in global carbon and sulfur cycles. Some members are methylotrophs, using one-carbon compounds as a carbon and energy source. It has recently been shown that methylotrophs generally require a rare earth element when using the methanol dehydrogenase enzyme XoxF for growth on methanol. Addition of lanthanum to methanol enrichments of coastal seawater facilitated the isolation of a novel methylotroph in the Roseobacter group: Marinibacterium anthonyi strain La 6. Mutation of xoxF5 revealed the essential nature of this gene during growth on methanol and ethanol. Physiological characterization demonstrated the metabolic versatility of this strain. Genome sequencing revealed that strain La 6 has the largest genome of all Roseobacter group members sequenced to date, at 7.18 Mbp. Multilocus sequence analysis (MLSA) showed that whilst it displays the highest core gene sequence similarity with subgroup 1 of the Roseobacter group, it shares very little of its pangenome, suggesting unique genetic adaptations. This research revealed that the addition of lanthanides to isolation procedures was key to cultivating novel XoxF-utilizing methylotrophs from the marine environment, whilst genome sequencing and MLSA provided insights into their potential genetic adaptations and relationship to the wider community.\n\nComparative Genomics and Mutational Analysis Reveals a Novel XoxF-Utilizing Methylotroph in the Roseobacter Group Isolated From the Marine Environment.", "token_count": 383, "char_count": 1570, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6227, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:23.227704", "source": { "split": "train_shard_00001", "doc_id": 4134 }, "chunk_id": "train_shard_00001_4134_0", "global_id": 11505 }, { "text": "Biocontrol formulations prepared from biocontrol bacteria are increasingly applied in sustainable agriculture. Notably, inoculants prepared from Bacillus strains have been proven efficient and environmentally friendly alternatives to chemical bactericides. The bacterium Bacillus velezensis HAB-2 (formerly classified as B. amyloliquefaciens HAB-2) is used as a biological control agent in agricultural fields. In this study, we reported a high-quality genome sequence of HAB-2 using third-generation sequencing technology (PacBio RS II). The 3.89 Mb genome encoded 3,820 predicted genes. Comparative analysis among the genome sequences of reference strains B. velezensis FZB42, B. amyloliquefaciens DSM7 and B. subtilis 168 with the HAB-2 genome revealed obvious differences in the variable part of the genomes, while the core genome shared by FZB42 and HAB-2 was similar (96.14%). However, there were differences in the prophage region among the four strains. The numbers of prophage regions and coding genes in HAB-2 and FZB42 were smaller than the other two strains. The HAB-2 genome showed superior ability to produce secondary metabolites and harbored 13 gene clusters involved in synthesis of antifungal and antibacterial acting secondary metabolites. Furthermore, there were two unique clusters: one cluster which encoded lanthipeptide was involved in mersacidin synthesis and another cluster which encoded ladderane was shown to direct an unknown compound. Multidomain enzymes, such as non-ribosomal peptide synthetase and polyketide synthase, control the biosynthesis of secondary metabolites and rely on 4'-phosphopantetheinyl transferases (PPTases). Key genes lpaH2 and a encoded PPTases in HAB-2 encoded 224 and 120 amino acids, respectively", "token_count": 518, "char_count": 1810, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6516, "quality_score": 0.8258, "entities": { "genes": [ "FZB42", "DSM7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:23.888430", "source": { "split": "train_shard_00001", "doc_id": 4135 }, "chunk_id": "train_shard_00001_4135_0", "global_id": 11506 }, { "text": "The genomic features revealed that HAB-2 possesses immense potential to synthesize antimicrobial acting secondary metabolites by regulating and controlling gene clusters. The prophage regions and genes encoding PPTases may provide novel insight for the bacteriostatic mechanism of Bacillus in the biological control of plant diseases.\n\nComparative Genomics Analysis Provides New Strategies for Bacteriostatic Ability of Bacillus velezensis HAB-2.", "token_count": 117, "char_count": 460, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8621, "quality_score": 0.931, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:24.271535", "source": { "split": "train_shard_00001", "doc_id": 4135 }, "chunk_id": "train_shard_00001_4135_1", "global_id": 11507 }, { "text": "Campylobacteriosis typically manifests as a short-lived, self-limiting gastrointestinal infection in humans, however prolonged infection can be seen in cases with underlying immunodeficiency. Public Health England received 25 isolates of Campylobacter jejuni from an individual with combined variable immunodeficiency over a period of 15 years. All isolates were typed and archived at the time of receipt. Whole genome sequencing (WGS) and antimicrobial susceptibility testing were performed to examine the relatedness of the isolates and to investigate the changes in the genome that had taken place over the course of the infection. Genomic typing methods were compared to conventional phenotypic methods, and revealed that the infection was caused by a single, persistent strain of C. jejuni belonging to clonal complex ST-45, with evidence of adaptation and selection in the genome over the course of the infection. Genomic analysis of sequence variants associated with antimicrobial resistance identified the genetic background behind rRNA gene mutations causing variable levels of resistance to erythromycin. This application of WGS to examine a persistent case of campylobacteriosis provides insight into the mutations and selective pressures occurring over the course of an infection, some of which have important clinical relevance.\n\nMicroevolution of Campylobacter jejuni during long-term infection in an immunocompromised host.", "token_count": 317, "char_count": 1438, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6238, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:24.838935", "source": { "split": "train_shard_00001", "doc_id": 4136 }, "chunk_id": "train_shard_00001_4136_0", "global_id": 11508 }, { "text": "A beige-pigmented, oxidase-positive bacterial isolate, Wesi-4T, isolated from charcoal in 2012, was examined in detail by applying a polyphasic taxonomic approach. Cells of the isolates were rod shaped and Gram-stain negative. Examination of the 16S rRNA gene sequence of the isolate revealed highest sequence similarities to the type strains of Pseudomonas matsuisoli and Pseudomonas nosocomialis (both 97.3 %). Phylogenetic analyses on the basis of the 16S rRNA gene sequences indicated a separate position of Wesi-4T, which was confirmed by multilocus sequence analyses (MLSA) based on the three loci gyrB, rpoB and rpoD and a core genome-based phylogenetic tree. Genome sequence based comparison of Wesi-4T and the type strains of P. matsuisoli and P. nosocomialis yielded average nucleotide identity values <95 % and in silico DNA-DNA hybridization values <70 %, respectively. The polyamine pattern contains the major amines putrescine, cadaverine and spermidine. The quinone system contains predominantly ubiquinone Q-9 and in the polar lipid profile diphosphatidylglycerol, phosphatidylglycerol and phosphatidylethanolamine are the major lipids", "token_count": 402, "char_count": 1240, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6605, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:25.466702", "source": { "split": "train_shard_00001", "doc_id": 4137 }, "chunk_id": "train_shard_00001_4137_0", "global_id": 11509 }, { "text": "The fatty acid contains predominantly C16 : 0, summed feature 3 (C16 : 1ω7c and/or C16 : 1ω6c) and summed feature 8 (C18 : 1ω7c and/or C18 : 1 ω6c). In addition, physiological and biochemical tests revealed a clear phenotypic difference from P. matsuisoli. These cumulative data indicate that the isolate represents a novel species of the genus Pseudomonas for which the name Pseudomonas carbonaria sp. nov. is proposed with Wesi-4T (=DSM 110367T=CIP 111764T=CCM 9017T) as the type strain.\n\nPseudomonas carbonaria sp. nov., isolated from charcoal.", "token_count": 301, "char_count": 702, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7791, "quality_score": 0.8895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:26.029868", "source": { "split": "train_shard_00001", "doc_id": 4137 }, "chunk_id": "train_shard_00001_4137_1", "global_id": 11510 }, { "text": "Mycoplasma mycoides subspecies capri (Mmc) is one of the six Mycoplasma mycoides cluster (Mm cluster) members, which can cause \"MAKePS\" (Mastitis, Arthritis, Keratoconjunctivitis, Pneumonia, Septicemia) syndrome in ruminants. These symptoms can occur alone or together in individuals or flocks of goats. However, little is known about the epidemic Mmc strains in Hainan Island, China. We aimed to isolate the endemic Mmc strains in Hainan Island and reveal their molecular characteristics by genomic sequencing and comparative genomics to mitigate the impact of Mmc on local ruminant farming. Here, the Mmc HN-A strain was isolated and identified for the first time in Hainan Island, China. The genome of Mmc HN-A was sequenced. It contains a 1,084,691 bp-long circular chromosome and 848 coding genes. The genomic analysis of Mmc HN-A revealed 16 virulence factors, 2 gene islands, and a bacterial type IV secretion system protein VirD4. Comparative genomics showed that the core genome of the five Mycoplasma mycoides contained 611 genes that could be exploited to develop drugs and endemic vaccines. Additionally, 36 specific genes were included in the Mmc HN-A genome, which could provide the possibility for the further control and prevention of the Mmc effects on local ruminants and enrich the information on Mmc strains.\n\nFirst Report and Comparative Genomic Analysis of a Mycoplasma mycoides Subspecies capri HN-A in Hainan Island.", "token_count": 435, "char_count": 1482, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6091, "quality_score": 0.8045, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:26.657219", "source": { "split": "train_shard_00001", "doc_id": 4138 }, "chunk_id": "train_shard_00001_4138_0", "global_id": 11511 }, { "text": "The thermotolerant yeast Hansenula polymorpha ferments glucose and xylose to ethanol at high temperatures. However, H. polymorpha cannot utilize starchy materials or xylans. Heterologous amylolytic and xylanolytic enzymes have to be expressed in this yeast to provide for utilization and growth on starch and xylan. Genes SWA2 and GAM1 from the yeast Schwanniomyces occidentalis, encoding alpha-amylase and glucoamylase, respectively, were expressed in H. polymorpha. The expression was achieved by integration of the SWA2 and GAM1 genes under the strong constitutive promoter of the H. polymorpha glyceraldehyde-3-phosphate dehydrogenase gene (HpGAP) into H. polymorpha genome. Resulting transformants acquired the ability to grow on a minimal medium containing soluble starch as a sole carbon source. Ethanol production at high-temperature fermentation from starch by the recombinant strains was up to 10 g/L. The XYN2 gene encoding endoxylanase of the fungus Trichoderma reseei was expressed in H. polymorpha. Co-expression of xlnD gene coding for beta-xylosidase of the fungus Aspergillus niger and the XYN2 gene in H. polymorpha was achieved by integration of these genes under control of the HpGAP promoter. Resulting transformants were capable of growth and alcoholic fermentation on a minimal medium supplemented with birchwood xylan as a sole carbon source at 48 degrees C.\n\nDevelopment of strains of the thermotolerant yeast Hansenula polymorpha capable of alcoholic fermentation of starch and xylan.", "token_count": 430, "char_count": 1510, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5229, "quality_score": 0.7615, "entities": { "genes": [ "SWA2", "GAM1", "XYN2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:27.286275", "source": { "split": "train_shard_00001", "doc_id": 4139 }, "chunk_id": "train_shard_00001_4139_0", "global_id": 11512 }, { "text": "

Objectives

The global spread of carbapenem-resistant Enterobacterales is a leading public-health threat. Lack of effective treatment has resulted in use of colistin as a last-resort therapeutic option for multidrug-resistant (MDR) bacterial infections. Here we report the complete genome sequence of a MDR Escherichia coli strain carrying a plasmid-mediated colistin resistance gene mcr-1 recovered from a Chinese paediatric patient.

Methods

Whole-genome sequencing of E. coli strain 1506 was performed using both Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. De novo hybrid assembly of short Illumina reads and long MinION reads was performed using Unicycler. In silico multilocus sequence typing (MLST), antimicrobial resistance genes (ARGs) and plasmid replicons were identified from the genome sequence. Core genome multilocus sequence typing (cgMLST) analysis between E. coli 1506 and all of the ST48 E. coli strains retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server.

Results

The complete genome sequence of E. coli 1506 consists of six contigs comprising 4 849 058 bp, including one chromosome and five plasmids, and was assigned to ST48. Fourteen ARGs were identified, including mcr-1 located on a 33 309-bp IncX4 plasmid. The closest relative of E. coli 1506 was another isolate originating from livestock in Australia, which differed by 614 cgMLST alleles.

Conclusion

Our study reports the genome sequence of a MDR E. coli carrying mcr-1 isolated from a Chinese paediatric patient. These data may help to understand the antimicrobial resistance mechanisms and genomic features and highlight the growing threat of antimicrobial resistance in children.", "token_count": 499, "char_count": 1734, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8128, "entities": { "genes": [ "ST48" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:27.938179", "source": { "split": "train_shard_00001", "doc_id": 4140 }, "chunk_id": "train_shard_00001_4140_0", "global_id": 11513 }, { "text": "Genomic characterisation of a multidrug-resistant Escherichia coli strain carrying the mcr-1 gene recovered from a paediatric patient in China.", "token_count": 38, "char_count": 143, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:28.297824", "source": { "split": "train_shard_00001", "doc_id": 4140 }, "chunk_id": "train_shard_00001_4140_1", "global_id": 11514 }, { "text": "Continuous ethanol fermentation of cheese whey powder solution was realized using pure culture of Kluyveromyces marxianus (DSMZ 7239) at hydraulic residence times (HRT) between 12.5 and 60 h. Sugar utilization, ethanol and biomass formation were investigated as functions of HRT. Effluent sugar concentration decreased, but percent sugar utilization, ethanol and biomass concentrations increased with HRT. Ethanol productivity was maximum (0.745 gE l(-1)h(-1)) at an HRT of 43.2 h where the biomass productivity was almost minimum (0.18 gX l(-1) h(-1)). The ethanol yield coefficient was almost constant at 0.4 gE g(-1)S up to HRT of 43.2 h and the growth yield coefficient was minimum at HRT of 43.2 h. Kinetic models were developed and the constants were determined by using the experimental data.\n\nContinuous ethanol fermentation of cheese whey powder solution: effects of hydraulic residence time.", "token_count": 260, "char_count": 901, "word_count": 135, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:28.849094", "source": { "split": "train_shard_00001", "doc_id": 4141 }, "chunk_id": "train_shard_00001_4141_0", "global_id": 11515 }, { "text": "The aim of this study was to assess the potential of four yeast strains to initiate a biofilm on stainless steel. The yeasts were isolated from apple juice and were identified as Kluyveromyces marxianus, Candida krusei, Zygosaccharomyces sp. and Rhodotorula rubra. The physiochemical properties of cell surface were determined under different conditions. The adhesion capacity of the yeast strains to stainless steel was assayed in presence of apple juice. Cell surfaces were always negatively charged except for Zygosaccharomyces sp., whose isoelectric point was around 3.0. Neither electrophoretic mobility nor flocculation coefficient correlated with the capacity of attachment to stainless steel. The hydrophobicity expressed by the yeast surfaces at pH 3.0, correlated positively with the rate of adhesion (number of cells/min) of each strain. These results indicated that cell surface hydrophobicity governs the initial attachment of the studied contaminant yeast strains to stainless steel surfaces common to the apple juice processing plant.\n\nPotential of yeast isolated from apple juice to adhere to stainless steel surfaces in the apple juice processing industry", "token_count": 273, "char_count": 1172, "word_count": 170, "semantic_coherence": 1, "information_density": 0.5647, "quality_score": 0.7824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:29.405064", "source": { "split": "train_shard_00001", "doc_id": 4142 }, "chunk_id": "train_shard_00001_4142_0", "global_id": 11516 }, { "text": "This study was focused on characterization of the genetic diversity of Listeria monocytogenes isolated from packed fresh rabbit meat obtained from one producer via retail outlets. The partial aim was to compare the characteristics of a suspect persistent strain with strains from human cases. The occurrence of L. monocytogenes in vacuum-packed rabbit meat was monitored during 2013 to 2016. All strains were characterized by serotyping, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST). Selected strains, which represented each year, were analyzed using the whole genome sequencing method. L. monocytogenes was detected in 21 (38%) of 56 originally packed rabbit meat samples from one food producer during the whole monitored period. All strains showed the identical serotype (1/2a), AscI/ApaI pulsotype (735/2), and sequence type (ST451). The clonal similarity of strains from rabbit meat was also confirmed on the basis of core genome MLST (on 1,701 loci). This fact suggests the occurrence of a suspect persistent strain in the meat processing plant. Results of core genome MLST enabled us to unambiguously exclude rabbit meat as a source of listeriosis in humans caused by the indistinguishable AscI/ApaI pulsotype and sequence type, although all strains carried all genes important for the virulence of L. monocytogenes. No specific genes that may be associated with its persistence in the food processing environment were detected among the tested strains of ST451.\n\nPrediction of Persistence of Listeria monocytogenes ST451 in a Rabbit Meat Processing Plant in the Czech Republic.", "token_count": 433, "char_count": 1646, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7842, "entities": { "genes": [ "ST451" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:30.037779", "source": { "split": "train_shard_00001", "doc_id": 4143 }, "chunk_id": "train_shard_00001_4143_0", "global_id": 11517 }, { "text": "Akkermansia muciniphila is a mucin-degrading bacterium found in the gut of most humans and is considered a \"next-generation probiotic.\" However, knowledge of the genomic and physiological diversity of human-associated Akkermansia sp. strains is limited. Here, we reconstructed 35 metagenome-assembled genomes and combined them with 40 publicly available genomes for comparative genomic analysis. We identified at least four species-level phylogroups (AmI to AmIV), with distinct functional potentials. Most notably, we identified genes for cobalamin (vitamin B12) biosynthesis within the AmII and AmIII phylogroups. To verify these predictions, 10 Akkermansia strains were isolated from adults and screened for vitamin B12 biosynthesis genes via PCR. Two AmII strains were positive for the presence of cobalamin biosynthesis genes, while all 9 AmI strains tested were negative. To demonstrate vitamin B12 biosynthesis, we measured the production of acetate, succinate, and propionate in the presence and absence of vitamin supplementation in representative strains of the AmI and AmII phylogroups, since cobalamin is an essential cofactor in propionate metabolism. Results showed that the AmII strain produced acetate and propionate in the absence of supplementation, which is indicative of vitamin B12 biosynthesis. In contrast, acetate and succinate were the main fermentation products for the AmI strains when vitamin B12 was not supplied in the culture medium. Lastly, two bioassays were used to confirm vitamin B12 production by the AmII phylogroup", "token_count": 460, "char_count": 1640, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5856, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:30.678563", "source": { "split": "train_shard_00001", "doc_id": 4144 }, "chunk_id": "train_shard_00001_4144_0", "global_id": 11518 }, { "text": "This novel physiological trait of human-associated Akkermansia strains may affect how these bacteria interact with the human host and other members of the human gut microbiome.IMPORTANCE There is significant interest in the therapeutic and probiotic potential of the common gut bacterium Akkermansia muciniphila However, knowledge of both the genomic and physiological diversity of this bacterial lineage is limited. Using a combination of genomic, molecular biological, and traditional microbiological approaches, we identified at least four species-level phylogroups with differing functional potentials that affect how these bacteria interact with both their human host and other members of the human gut microbiome. Specifically, we identified and isolated Akkermansia strains that were able to synthesize vitamin B12 The ability to synthesize this important cofactor broadens the physiological capabilities of human-associated Akkermansia strains, fundamentally altering our understanding of how this important bacterial lineage may affect human health.\n\nComparative Genomics Guides Elucidation of Vitamin B12 Biosynthesis in Novel Human-Associated Akkermansia Strains.", "token_count": 311, "char_count": 1238, "word_count": 155, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:31.251226", "source": { "split": "train_shard_00001", "doc_id": 4144 }, "chunk_id": "train_shard_00001_4144_1", "global_id": 11519 }, { "text": "Cyanobacteria thrive in very diverse environments. However, questions remain about possible growth limitations in ancient environmental conditions. As a single genus, the Thermosynechococcus are cosmopolitan and live in chemically diverse habitats. To understand the genetic basis for this, we compared the protein coding component of Thermosynechococcus genomes. Supplementing the known genetic diversity of Thermosynechococcus , we report draft metagenome-assembled genomes of two Thermosynechococcus recovered from ferrous carbonate hot springs in Japan. We find that as a genus, Thermosynechococcus is genomically conserved, having a small pan-genome with few accessory genes per individual strain and only 14 putative orthologous protein groups appearing in all Thermosynechococcus but not in any other cyanobacteria in our analysis. Furthermore, by comparing orthologous protein groups, including an analysis of genes encoding proteins with an iron related function (uptake, storage or utilization), no clear differences in genetic content, or adaptive mechanisms could be detected between genus members, despite the range of environments they inhabit. Overall, our results highlight a seemingly innate ability for Thermosynechococcus to inhabit diverse habitats without having undergone substantial genomic adaptation to accommodate this. The finding of Thermosynechococcus in both hot and high iron environments without adaptation recognizable from the perspective of the proteome has implications for understanding the basis of thermophily within this clade, and also for understanding the possible genetic basis for high iron tolerance in cyanobacteria on early Earth. The conserved core genome may be indicative of an allopatric lifestyle – or reduced genetic complexity of hot spring habitats relative to other environments.\n\nTheThermosynechococcusgenus: wide environmental distribution, but a highly conserved genomic core", "token_count": 435, "char_count": 1942, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:31.911748", "source": { "split": "train_shard_00001", "doc_id": 4145 }, "chunk_id": "train_shard_00001_4145_0", "global_id": 11520 }, { "text": "Owing to the increasing number of infections in hospitalised patients caused by resistant strains of fungi, there is a need to develop new therapeutic agents for these infections. Naturally occurring antimicrobial peptides may constitute models for developing such agents. A modified peptide sequence (CFQWKRAMRKVR; HLopt2) based on amino acid residues 20-31 of the N-terminal end of human lactoferrin (hLF) as well as a double-sized human lactoferricin-like peptide (amino acid residues 16-40; HLBD1) were investigated for their antifungal activities in vitro and in vivo. By in vitro assay, HLopt2 was fungicidal at concentrations of 12.5-25 μg/mL against Cryptococcus neoformans, Candida albicans, Candida krusei, Candida kefyr and Candida parapsilosis, but not against Candida glabrata. HLopt2 was demonstrated to have ≥ 16-fold greater killing activity than HLBD1. By inducing some helical formation caused by lactam bridges or by extending the assay time (from 2h to 20 h), HLBD1 became almost comparable with HLopt2 in its fungicidal activity. Killing of C. albicans yeast cells by HLopt2 was rapid and was accompanied by cytoplasmic and mitochondrial membrane permeabilisation as well as formation of deep pits on the yeast cell surface. In a murine C. albicans skin infection model, atopic treatment with the peptides resulted in significantly reduced yields of Candida from the infected skin areas. The antifungal activities of HLopt2 in vitro and in vivo suggest possible potential as a therapeutic agent against most Candida spp. and C. neoformans. The greatly improved antifungal effect of the lactam-modified HLBD1 indicates the importance of amphipathic helix formation for lethal activity.", "token_count": 490, "char_count": 1705, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6324, "quality_score": 0.8162, "entities": { "genes": [ "HLBD1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:32.582663", "source": { "split": "train_shard_00001", "doc_id": 4146 }, "chunk_id": "train_shard_00001_4146_0", "global_id": 11521 }, { "text": "Fungicidal activity of human lactoferrin-derived peptides based on the antimicrobial αβ region.", "token_count": 31, "char_count": 95, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:32.976294", "source": { "split": "train_shard_00001", "doc_id": 4146 }, "chunk_id": "train_shard_00001_4146_1", "global_id": 11522 }, { "text": "

Motivation

Genome-wide association study (GWAS) methods applied to bacterial genomes have shown promising results for genetic marker discovery or fine-assessment of marker effect. Recently, alignment-free methods based on kmer composition have proven their ability to explore the accessory genome. However, they lead to redundant descriptions and results which are hard to interpret.

Methods

Here, we introduce DBGWAS, an extended kmer-based GWAS method producing interpretable genetic variants associated with pheno-types. Relying on compacted De Bruijn graphs (cDBG), our method gathers cDBG nodes identified by the association model into subgraphs defined from their neighbourhood in the initial cDBG. DBGWAS is fast, alignment-free and only requires a set of contigs and phenotypes. It produces annotated subgraphs representing local polymorphisms as well as mobile genetic elements (MGE) and offers a graphical framework to interpret GWAS results.

Results

We validated our method using antibiotic resistance phenotypes for three bacterial species. DBGWAS recovered known resistance determinants such as mutations in core genes in Mycobacterium tuberculosis and genes acquired by horizontal transfer in Staphylococcus aureus and Pseudomonas aeruginosa – along with their MGE context. It also enabled us to formulate new hypotheses involving genetic variants not yet described in the antibiotic resistance literature.

Conclusion

Our novel method proved its efficiency to retrieve any type of phenotype-associated genetic variant without prior knowledge. All experiments were computed in less than two hours and produced a compact set of meaningful subgraphs, thereby outperforming other GWAS approaches and facilitating the interpretation of the results.

Availability

Open-source tool available at https://gitlab.com/leoisl/dbgwas\n\nA fast and agnostic method for bacterial genome-wide association studies: bridging the gap between kmers and genetic events", "token_count": 470, "char_count": 2003, "word_count": 267, "semantic_coherence": 1, "information_density": 0.7154, "quality_score": 0.8577, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:33.649276", "source": { "split": "train_shard_00001", "doc_id": 4147 }, "chunk_id": "train_shard_00001_4147_0", "global_id": 11523 }, { "text": "Over the last few years, the application of nanotechnology to nutraceuticals has been rapidly growing due to its ability to enhance the bioavailability of the loaded active ingredients, resulting in improved therapeutic/nutraceutical outcomes. The focus of this work is nanoprebiotics and nanoprobiotics, terms which stand for the loading of a set of compounds (e.g., prebiotics, probiotics, and synbiotics) in nanoparticles that work as absorption enhancers in the gastrointestinal tract. In this manuscript, the main features of prebiotics and probiotics are highlighted, together with the discussion of emerging applications of nanotechnologies in their formulation. Current research strategies are also discussed, in particular the promising use of nanofibers for the delivery of probiotics. Synbiotic-based nanoparticles represent an innovative trend within this area of interest. As only few experimental studies on nanoprebiotics and nanoprobiotics are available in the scientific literature, research on this prominent field is needed, covering effectiveness, bioavailability, and safety aspects.\n\nAn Updated Overview on Nanonutraceuticals: Focus on Nanoprebiotics and Nanoprobiotics.", "token_count": 280, "char_count": 1192, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6687, "quality_score": 0.8344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:34.209486", "source": { "split": "train_shard_00001", "doc_id": 4148 }, "chunk_id": "train_shard_00001_4148_0", "global_id": 11524 }, { "text": "

Objectives

To investigate the antimycotic activity of the plant alkaloid berberine (BBR), alone and in combination with antifungal azoles, against planktonic and biofilm Candida cultures.

Design

The minimum inhibitory concentrations (MICs) of BBR, miconazole (MCZ), and fluconazole (FLC) towards Candida albicans, Candida glabrata, Candida kefyr, Candida krusei, Candida parapsilosis, and Candida tropicalis were determined by a microdilution method. For C. albicans, the synergistic effects of BBR combined with MCZ or FLC were examined in a paper disc agar diffusion assay and checkerboard microdilution assay. The effect of the BBR/MCZ combination was further investigated in a C. albicans biofilm formation model with a dual-chamber flow cell. The effect on metabolic activity of biofilm cells was established using 2,3-bis(2-methoxy-4-nitro-5-sulfophenyl)-2H-tetrazolium-5-carboxanilide (XTT)/menadione.

Results

Berberine inhibited the growth of various Candida species (MICs 0.98-31.25mg/L) in the following order of susceptibility: C. krusei > C. kefyr > C. glabrata > C. tropicalis > C. parapsilosis and C. albicans. Synergism between BBR and MCZ or FLC was observed in the disc diffusion assay as well as in suspension showing an FIC index <0.5 (∑FIC=0.19). Whilst neither BBR (16 mg/L) nor MCZ (0.8 mg/L) alone significantly inhibited biofilm formation of C. albicans, their combination reduced biofilm formation by >91% after 24 h, as established from the reduction in surface area coverage (P<0.01). The BBR/MCZ combination also exhibited synergy against the metabolic activity of pre-formed C", "token_count": 509, "char_count": 1627, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5856, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:34.867538", "source": { "split": "train_shard_00001", "doc_id": 4149 }, "chunk_id": "train_shard_00001_4149_0", "global_id": 11525 }, { "text": "albicans biofilms in polystyrene microtiter plates (∑FIC=0.25).

Conclusion

Berberine exhibits synergistic effects with commonly used antimycotic drugs against C. albicans, either in planktonic or in biofilm growth phases.\n\nIn vitro synergism between berberine and miconazole against planktonic and biofilm Candida cultures.", "token_count": 102, "char_count": 330, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8205, "quality_score": 0.9103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:35.248430", "source": { "split": "train_shard_00001", "doc_id": 4149 }, "chunk_id": "train_shard_00001_4149_1", "global_id": 11526 }, { "text": "Vertical transmission of bacterial endosymbionts is accompanied by virtually irreversible gene loss that can provide insights into adaptation to divergent ecological niches. While patterns of genome reduction have been well described in some terrestrial symbioses, they are less understood in marine systems where vertical transmission is relatively rare. The association between deep-sea vesicomyid clams and chemosynthetic Gammaproteobacteria is one example of maternally inherited symbioses in the ocean. Differences in nitrogen and sulfur physiology between the two dominant symbiont groups, Ca. Ruthia and Ca. Vesicomyosocius, have been hypothesized to influence niche exploitation, which likely affects gene content evolution in these symbionts. However, genomic data are currently limited to confirm this assumption. In the present study we sequenced and compared 11 vesicomyid symbiont genomes with existing assemblies for Ca . Vesicomyosocius okutanii and Ca . Ruthia magnifica. Our analyses indicate that the two vesicomyid symbiont groups have a common core genome related to chemosynthetic metabolism, but differ in their potential for nitrate respiration and flexibility to environmental sulfide concentrations. Moreover, Ca . Vesicomyosocius and Ca . Ruthia have different enzymatic requirements for cobalamin and nickel and show contrasting capacities to acquire foreign genetic material. Tests for site-specific positive selection in metabolic candidate genes imply that the observed physiological differences are adaptive and thus likely correspond to ecological niches available to each symbiont group. These findings highlight the role of niche differentiation in creating divergent paths of reductive genome evolution in vertically transmitted symbionts.\n\nDifferences in cofactor, oxygen and sulfur requirements influence niche adaptation in deep-sea vesicomyid clam symbioses", "token_count": 436, "char_count": 1896, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6445, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "respiration" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:35.885166", "source": { "split": "train_shard_00001", "doc_id": 4150 }, "chunk_id": "train_shard_00001_4150_0", "global_id": 11527 }, { "text": "A new high polygalacturonase (PG)-producing Kluyveromyces marxianus strain was isolated from coffee wet-processing wastewater. PG production in this strain is not repressed in the presence of 100 g/L of glucose and, being growth-associated, reached its maximum accumulation in the culture medium at the beginning of the stationary phase. Oxygen and galacturonic acid negatively regulated enzyme synthesis, and glucose as the carbon source afforded better enzyme yields than lactose. The data reported here show that this strain exhibits the highest index of PG production among the wild-type strains reported so far (18.8 U/mL). PG was readily purified by ion-exchange chromatography on SP-Sepharose FF. The activity corresponded to a single protein with an M(r) of 41.7kDa according to sodium dodecyl sulfatepolyacrylamide gel electrophoresis. The enzyme was stable in the pH range of 3.0-5.0 and displayed an optimal temperature of 55 degrees C; it showed a typical endosplitting way of substrate hydrolysis and exhibited a fair degree of activity on pectin with a high degree of esterification.\n\nProduction, purification, and characterization of a polygalacturonase from a new strain of Kluyveromyces marxianus isolated from coffee wet-processing wastewater.", "token_count": 334, "char_count": 1261, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6503, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:36.826895", "source": { "split": "train_shard_00001", "doc_id": 4151 }, "chunk_id": "train_shard_00001_4151_0", "global_id": 11528 }, { "text": "

Purpose

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is one of the leading causes of healthcare-associated infections (HAIs) and is particularly pervasive in intensive care units (ICUs). This study takes ICU layout as the research object, and integrates clinical data and bacterial genome analysis to clarify the role of separate, small wards within the ICU in controlling the transmission of CRKP.

Methods

This study prospectively observed the carriage and spread of CRKP from a long-term in-hospital patient (hereafter called the Patient) colonized with CRKP in the gut and located in a separate, small ward within the ICU. The study also retrospectively investigated CRKP-HAIs in the same ICU. The relationship and transmission between CRKP isolates from the Patient and HAI events in the ICU were explored with comparative genomics.

Results

In this study, 65 CRKP-HAI cases occurred during the investigation period. Seven CRKP-HAI outbreaks were also observed. A total of 95 nonrepetitive CRKP isolates were collected, including 32 strains from the Patient in the separate small ward. Phylogenetic analysis based on core genome single-nucleotide polymorphism (cgSNP) showed that there were five possible CRKP clonal transmission events and two clonal outbreaks (A1, A2) during the study. CRKP strains from the Patient did not cause CRKP between-patient transmission or outbreaks in the ICU during the 5-year study period.

Conclusion

The presence of a long-term hospitalized patient carrying CRKP and positioned in a separate, small ward did not lead to CRKP transmission or infection outbreaks in the ICU. Combining a small-ward ICU layout with normative HAI control measures for multidrug-resistant pathogen infection was effective in reducing CRKP transmission.\n\nSmall wards in the ICU: a favorable measure for controlling the transmission of carbapenem-resistant Klebsiella pneumoniae.", "token_count": 506, "char_count": 1926, "word_count": 270, "semantic_coherence": 1, "information_density": 0.537, "quality_score": 0.7685, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:37.486589", "source": { "split": "train_shard_00001", "doc_id": 4152 }, "chunk_id": "train_shard_00001_4152_0", "global_id": 11529 }, { "text": "Clostridioides difficile infection (CDI) is the leading cause of life-threatening health care-related gastrointestinal illness worldwide. Phylogenetically appropriate closed reference genomes are essential for studies of C. difficile transmission and evolution. Here, we provide high-quality complete hybrid genome assemblies for the three most prevalent C. difficile strains causing CDI in Australia.\n\nComplete Genome Assemblies of Three Highly Prevalent, Toxigenic Clostridioides difficile Strains Causing Health Care-Associated Infections in Australia.", "token_count": 136, "char_count": 555, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:37.910831", "source": { "split": "train_shard_00001", "doc_id": 4153 }, "chunk_id": "train_shard_00001_4153_0", "global_id": 11530 }, { "text": "Salmonella spp. is an important foodborne pathogen associated with consumption of contaminated food, especially livestock products. Antimicrobial resistance (AMR) in Salmonella has been reported globally and increasing AMR in food production is a major public health issue worldwide. The objective of this study was to describe the genetic relatedness among Salmonella enterica isolates, which displayed identical DNA fingerprint profiles. Ten S. enterica isolates were selected from meat and human cases with an identical rep-PCR profile of serovars Rissen (n=4), Weltevreden (n=4), and Stanley (n=2). We used long-read whole genome sequencing (WGS) on the MinION sequencing platform to type isolates and investigate in silico the presence of specific AMR genes. Antimicrobial susceptibility testing was tested by disk diffusion and gradient diffusion method to corroborate the AMR phenotype. Multidrug resistance and resistance to more than one antimicrobial agent were observed in eight and nine isolates, respectively. Resistance to colistin with an accompanying mcr -1 gene was observed among the Salmonella isolates. The analysis of core genome and whole genome MLST revealed that the Salmonella from meat and human salmonellosis were closely genetic related. Hence, it could be concluded that meat is one of the important sources for Salmonella infection in human.

Highlights

Colistin resistance detected in 2 clones from 2 different Salmonella enterica serovars (Rissen and Weltevreden) with accompanying plasmid-borne mcr -1 gene from the food production chain and human clinical salmonellosis. High prevalence of multidrug resistant isolates and resistance to more than one antimicrobial agent. MinION has potential for mobile, rapid and accurate application in veterinary genomic epidemiology studies.\n\nMultiple clones of colistin-resistantSalmonella entericacarryingmcr-1plasmids in meat products and patients in Northern Thailand", "token_count": 469, "char_count": 1965, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:38.554875", "source": { "split": "train_shard_00001", "doc_id": 4154 }, "chunk_id": "train_shard_00001_4154_0", "global_id": 11531 }, { "text": "Microcystis aeruginosa is a bloom-forming cyanobacterium found in eutrophic fresh-and brackish water bodies worldwide. As typical for cyanobacteria, most M. aeruginosa strains are blue-green in color owing to the concomitance of two photosynthetic pigments, phycocyanin (PC) and chlorophyll a . Although less common, M. aeruginosa strains that are brownish in color owing to the presence of another pigment phycoerythrin (PE) have been documented. However, the genomic basis, phylogeny, and evolutionary origin of PE pigmentation in M. aeruginosa have only been poorly characterized until date. In the present study, we sequenced and characterized the genomes of five PE-containing M. aeruginosa strains. Putative PE synthesis and regulation genes (the cpe cluster) were identified in all five sequenced genomes as well as in three previously published M. aeruginosa genomes. Of note, Absorption spectra indicated that the PE content, but not PC content, was markedly altered in response to availability of red/green light in all PE-containing strains. This was consistent with the presence of ccaS / ccaR , a hallmark of type II chromatic adapter, in the cpe cluster. Phylogenetic analyses of core genome genes indicated that PE-containing genotypes were located in three different phylogenetic groups. In contrast, the genomic organization of the cpe cluster was mostly conserved regardless of genomic background. Additionally, the phylogenies of PE genes were found to be congruent, consistent with the core genome phylogeny. A comparison of core genome and PE genes showed a similar level of genetic divergence between two PE-containing groups. These results suggest that genes responsible for PE pigmentation were introduced into M. aeruginosa early during evolution and were repeatedly lost thereafter possibly due to ecological adaptation. Additional horizontal gene transfer (HGT) later during evolution also contributed to the present phylogenetic distribution of PE in M. aeruginosa .", "token_count": 476, "char_count": 1994, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:39.200827", "source": { "split": "train_shard_00001", "doc_id": 4155 }, "chunk_id": "train_shard_00001_4155_0", "global_id": 11532 }, { "text": "Evolutionary history of phycoerythrin pigmentation in the water bloom-forming cyanobacteriumMicrocystis aeruginosa", "token_count": 40, "char_count": 121, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:39.566040", "source": { "split": "train_shard_00001", "doc_id": 4155 }, "chunk_id": "train_shard_00001_4155_1", "global_id": 11533 }, { "text": "Commercial production of the ornamental plant dipladenia (Mandevilla spp.) is threatened by dipladenia leaf and stem spot disease, caused by the bacterium Pseudomonas savastanoi. P. savastanoi includes four pathovars of woody hosts differentiated by a characteristic host range in olive, oleander, ash, and broom plants. However, isolates from dipladenia have not been ascribed to any particular lineage or P. savastanoi pathovar. Here we report that isolates from dipladenia represent a distinct, clonal lineage. First, dipladenia isolates display very similar plasmid profiles, including a plasmid encoding the iaaM gene for biosynthesis of indole-3-acetic acid. Second, multilocus sequence analysis and core genome single-nucleotide polymorphisms phylogenies showed a monophyletic origin for dipladenia isolates, which cluster with isolates from oleander (pathovar nerii) in a distinct clade well separated from other P. savastanoi strains. Metabolic profiling and cross-pathogenicity tests in olive, oleander, ash, broom, and dipladenia clearly distinguished dipladenia isolates from the four P. savastanoi pathovars. Comparative genomics of the draft genome sequence of the dipladenia strain Ph3 with the other four pathovars showed that Ph3 encodes very few strain-specific genes and a similar set of virulence genes to pv. nerii, including its repertoire of type III secretion system effectors. However, hierarchical clustering based on the catalog of effectors and their allelic variants clearly separated Ph3 from pv. nerii strains. Based on their distinctive pathogenicity profile, we propose a de novo pathovar for P. savastanoi isolates from dipladenia, P. savastanoi pv. mandevillae pv", "token_count": 528, "char_count": 1789, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:40.202947", "source": { "split": "train_shard_00001", "doc_id": 4156 }, "chunk_id": "train_shard_00001_4156_0", "global_id": 11534 }, { "text": "nov., for which strain Ph3 (CFBP 8832PT) has been designated as the pathotype strain.\n\nPseudomonas savastanoi pv. mandevillae pv. nov., a Clonal Pathogen Causing an Emerging, Devastating Disease of the Ornamental Plant Mandevilla spp.", "token_count": 101, "char_count": 266, "word_count": 34, "semantic_coherence": 1, "information_density": 0.9118, "quality_score": 0.9559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:40.591553", "source": { "split": "train_shard_00001", "doc_id": 4156 }, "chunk_id": "train_shard_00001_4156_1", "global_id": 11535 }, { "text": "Serotyping has traditionally been used for subtyping of non-typhoidal Salmonella (NTS) isolates. However, its discriminatory power is limited, which impairs its use for epidemiological investigations of source attribution. Whole-genome sequencing (WGS) analysis allows more accurate subtyping of strains. However, because of the relative newness and cost of routine WGS, large-scale studies involving NTS WGS are still rare. We aimed to revisit the big picture of subtyping NTS with a public health impact by using traditional serotyping (i.e. reaction between antisera and surface antigens) and comparing the results with those obtained using WGS. For this purpose, we analysed 18 282 sequences of isolates belonging to 37 serotypes with a public health impact that were recovered in the USA between 2006 and 2017 from multiple sources, and were available at the National Center for Biotechnology Information (NCBI). Phylogenetic trees were reconstructed for each serotype using the core genome for the identification of genetic subpopulations. We demonstrated that WGS-based subtyping allows better identification of sources potentially linked with human infection and emerging subpopulations, along with providing information on the risk of dissemination of plasmids and acquired antimicrobial resistance genes (AARGs). In addition, by reconstructing a phylogenetic tree with representative isolates from all serotypes (n=370), we demonstrated genetic variability within and between serotypes, which formed monophyletic, polyphyletic and paraphyletic clades. Moreover, we found (in the entire data set) an increased detection rate for AARGs linked to key antimicrobials (such as quinolones and extended-spectrum cephalosporins) over time. The outputs of this large-scale analysis reveal new insights into the genetic diversity within and between serotypes; the polyphyly and paraphyly of certain serotypes may suggest that the subtyping of NTS to serotypes may not be sufficient", "token_count": 489, "char_count": 1995, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6487, "quality_score": 0.8244, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:41.250895", "source": { "split": "train_shard_00001", "doc_id": 4157 }, "chunk_id": "train_shard_00001_4157_0", "global_id": 11536 }, { "text": "Moreover, the results and the methods presented here, leading to differentiation between genetic subpopulations based on their potential risk to public health, as well as narrowing down the possible sources of these infections, may be used as a baseline for subtyping of future NTS infections and help efforts to mitigate and prevent infections in the USA and globally.\n\nComparing serotyping with whole-genome sequencing for subtyping of non-typhoidal Salmonella enterica: a large-scale analysis of 37 serotypes with a public health impact in the USA.", "token_count": 133, "char_count": 558, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7349, "quality_score": 0.8675, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:41.679339", "source": { "split": "train_shard_00001", "doc_id": 4157 }, "chunk_id": "train_shard_00001_4157_1", "global_id": 11537 }, { "text": "Due to Australia's management of antimicrobial use in poultry, particularly the discontinued use of avoparcin for nearly 20 years, it is hypothesized that vancomycin-resistant enterococci associated with human disease are not derived from poultry isolates. This study evaluated antimicrobial resistance (AMR) of five enterococcal species isolated from Australian meat chickens, genomic features of Enterococcus faecium and Enterococcus faecalis, and the phylogenetic relationship of the poultry-derived E. faecium with isolates from human sepsis cases. All enterococcal isolates from chicken ceca were subjected to antimicrobial susceptibility testing. E. faecium and E. faecalis underwent whole-genome sequencing. E. faecium was compared at the core genome level to a collection of human isolates (n = 677) obtained from cases of sepsis over a 2-year period spanning 2015 to 2016. Overall, 205 enterococci were isolated consisting of five different species. E. faecium was the most frequently isolated species (37.6%), followed by E. durans (29.7%), E. faecalis (20%), E. hirae (12.2%), and E. gallinarum (0.5%). All isolates were susceptible to vancomycin and gentamicin, while one isolate was linezolid resistant (MIC 16 mg/liter). Core genome analysis of the E. faecium demonstrated two clades consisting predominantly of human or chicken isolates in each clade, with minimal overlap", "token_count": 485, "char_count": 1478, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:42.331021", "source": { "split": "train_shard_00001", "doc_id": 4158 }, "chunk_id": "train_shard_00001_4158_0", "global_id": 11538 }, { "text": "Principal component analysis for total gene content revealed three clusters comprised of vanA-positive, vanB-positive, and both vanA- and vanB-negative E. faecium populations. The results of this study provide strong evidence that Australian chicken E. faecium isolates are unlikely to be precursor strains to the currently circulating vancomycin-resistant strains being isolated in Australian hospitals.\n\nGenomic, Antimicrobial Resistance, and Public Health Insights into Enterococcus spp. from Australian Chickens.", "token_count": 163, "char_count": 565, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8485, "quality_score": 0.9242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:42.775802", "source": { "split": "train_shard_00001", "doc_id": 4158 }, "chunk_id": "train_shard_00001_4158_1", "global_id": 11539 }, { "text": "Woesearchaeota is a newly proposed archaeal phylum frequently detected in various environments. Due to the limited systematical study, little is known about their distribution, taxonomy, and metabolism. Here, we conducted a comprehensive study for Woesearchaeota with 16S ribosomal RNA (rRNA) gene sequencing data of 27,709 samples and metagenomic whole genome sequencing (WGS) data of 1,266 samples. We find that apart from free-living environments, Woesearchaeota also widely distribute in host-associated environments. And host-associated environmental parameters greatly affect their distribution. 81 Woesearchaeota genomes, including 33 genomes firstly reconstructed in this project, were assigned to 59 Woesearchaeota species, suggesting their high taxonomic diversity. Comparative analysis indicated that Woesearchaeota have an open pan-genome with small core genome. Metabolic reconstruction showed that particular metabolic pathway absence in specific environments, demonstrated the metabolic diversity of Woesearchaeota varies in differences environments. These results have placed host-associated environments into the global biogeography of Woesearchaeota and have demonstrated their genomic diversity for future investigation of adaptive evolution.\n\nDiversity and biogeography of Woesearchaeota: A comprehensive analysis of multi-environment data", "token_count": 311, "char_count": 1359, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6864, "quality_score": 0.8432, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:43.352132", "source": { "split": "train_shard_00001", "doc_id": 4159 }, "chunk_id": "train_shard_00001_4159_0", "global_id": 11540 }, { "text": "In 2019, two distinct bacterial isolates were independently isolated from the fecal samples of separate dogs in Beijing, China. These cells exhibit microaerobic, are Gram-negative, motile, and possess a characteristic spiral shape with bipolar single flagellum. They display positive results for the oxidase test while being negative for both catalase and urease. These organisms measure approximately 0.2-0.3 μm in width and 4.5-6 μm in length. The colonies are wet, flat, grey, circular, and smooth with sizes ranging from 1 to 2 mm in diameter after 2 days of growth. However, strains may exhibit variations in size and morphology following extended incubation. Phylogenetic analyses based on the 16S rRNA gene and core genome indicated that these two isolates belong to the genus Helicobacter and formed a robust clade that was remains distinctly separate from currently recognized species. These two isolates shared low dDDH relatedness and ANI values with their closest species Helicobacter canis CCUG 32756T, with these values falling below the commonly cutoff values for strains of the same species. The genomic DNA G + C contents of strain XJK30-2 were 44.93 mol%. Comparing the phenotypic and phylogenetic features between these two isolates and their closely related species, XJK30-2 represents a novel species within the genus Helicobacter, for which the name Helicobacter zhangjianzhongii sp. nov. (Type strain XJK30-2T = GDMCC 1.3695T) is proposed.\n\nHelicobacter zhangjianzhongii sp. nov., isolated from dog feces.", "token_count": 460, "char_count": 1596, "word_count": 230, "semantic_coherence": 1, "information_density": 0.687, "quality_score": 0.8435, "entities": { "genes": [ "XJK30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:44.016485", "source": { "split": "train_shard_00001", "doc_id": 4160 }, "chunk_id": "train_shard_00001_4160_0", "global_id": 11541 }, { "text": "Listeria monocytogenes is an etiologic agent of listeriosis, and has emerged as an important foodborne pathogen worldwide. In this study, the molecular characteristics of 155 L. monocytogenes isolates from seven food groups in Shanghai, the biggest city in China, were identified using whole-genome sequencing (WGS). Most L. monocytogenes isolates (79.3%) were obtained between May and October from 2009 to 2019. The serogroups and clonal complexes (CCs) of L. monocytogenes were found useful for identifying potential health risks linked to foods. Differences in distributions of serogroups and CCs among different food groups were analyzed using t-test. The results showed that the IIa and IVb serogroups were identified among most of food groups. However, the prevalence of serogroup IIb was significantly higher in ready-to-eat (RTE) food and raw seafood than in other food groups, similar to group IIc in raw meat and raw poultry than others. Meanwhile, the prevalence of CC9 in raw meat and raw poultry, CC8 in raw poultry, and CC87 in raw seafood significantly exceeded that of in other food groups. Specially, CC87 was the predominant CC in foodborne and clinical isolates in China, indicating that raw seafood may induce a high-risk to food safety. Also, hypervirulence pathogenicity islands LIPI-3 and LIPI-4 were found in CC3, CC1, and CC87, respectively. The clonal group CC619 carried LIPI-3 and LIPI-4, as previously reported in China. Core genome multilocus sequence typing (cgMLST) analysis suggested that CC87 isolates from the same food groups in different years had no allelic differences, indicating that L. monocytogenes could persist over years. These 10-year results in Shanghai underscore the significance of molecular epidemiological surveillance of L", "token_count": 499, "char_count": 1821, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5613, "quality_score": 0.7807, "entities": { "genes": [ "CC8", "CC9", "CC3", "CC619", "CC1", "CC87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:44.692568", "source": { "split": "train_shard_00001", "doc_id": 4161 }, "chunk_id": "train_shard_00001_4161_0", "global_id": 11542 }, { "text": "monocytogenes in foodborne products in assessing the potential risk of this pathogen, and further address food safety issues in China.\n\n10-Year Molecular Surveillance of Listeria monocytogenes Using Whole-Genome Sequencing in Shanghai, China, 2009-2019.", "token_count": 83, "char_count": 264, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8485, "quality_score": 0.9242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:45.093079", "source": { "split": "train_shard_00001", "doc_id": 4161 }, "chunk_id": "train_shard_00001_4161_1", "global_id": 11543 }, { "text": "We demonstrate the value of the thermotolerant yeast Issatchenkia orientalis as a candidate microorganism for bioethanol production from lignocellulosic biomass with the goal of consolidated bioprocessing. The I. orientalis MF-121 strain is acid tolerant, ethanol tolerant, and thermotolerant, and is thus a multistress-tolerant yeast. To express heterologous proteins in I. orientalis, we constructed a transformation system for the MF-121 strain and then isolated the promoters of TDH1 and PGK1, two genes that were found to be strongly expressed during ethanol fermentation. As a result, expression of beta-glucosidase from Aspergillus aculeatus could be achieved with I. orientalis, demonstrating successful heterologous gene expression in I. orientalis for the first time. The transformant could convert cellobiose to ethanol under acidic conditions and at high temperature. Simultaneous saccharification and fermentation (SSF) was performed with the transformant, which produced 29 g l(-1) of ethanol in 72 h at 40 degrees C even without addition of beta-glucosidase when SSF was carried out in medium containing 100 g l(-1) of microcrystalline cellulose and a commercial cellulase preparation. These results suggest that using a genetically engineered thermotolerant yeast such as I. orientalis in SSF could lead to cost reduction because less saccharification enzymes are required.\n\nConstruction of a beta-glucosidase expression system using the multistress-tolerant yeast Issatchenkia orientalis.", "token_count": 394, "char_count": 1505, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6172, "quality_score": 0.8086, "entities": { "genes": [ "TDH1", "PGK1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:45.728029", "source": { "split": "train_shard_00001", "doc_id": 4162 }, "chunk_id": "train_shard_00001_4162_0", "global_id": 11544 }, { "text": "The rapidly increasing availability of whole genomes provides the opportunity to reach an updated comprehensive view of bacterial evolution. The staggered diversification of evolutionary processes, based on the combined strategy of layered phylogenomics and polymorphism fingerprinting, give a new perspective in phylogenetic reconstructions. Layered phylogenomics is based on the assignation of genes according to five different evolutionary layers: minimal genome, genus-core genome, species-core genome, phylogroup-core genome and phylogroup-flexible genome. Polymorphism fingerprinting is based on the detection of conserved positions in each phylogenetic group but differing from those of their hypothetical ancestors. This approach was applied to Escherichia coli because there are unresolved evolutionary questions, although has been highly studied. Phylogenetic analysis based on 6,220 full genomes, identified three E. coli root lineages, defined as D, EB1A and FGB2. A new phylogroup, called G was detected near to phylogroup B2. The closest phylogroup to ancestral E. coli was phylogroup D, whereas E and F were the closest ones in their respective lineages; moreover, A and B2 were the most distant phylogroups in EB1A and FGB2 respectively. We suspect that EB1A and FGB2 lineages represent different adaptive strategies. In the deepest branch of EB1A lineage, the number of accumulated mutations was lower than in recent branches, whereas in FGB2 lineage the opposite occurred. The FGB2 lineage was enriched in genes related to host colonization-pathogenicity and toxin-antitoxin systems (such as hipA), whereas B1A sub-lineage acquired functions related to uptake and metabolism of carbohydrates (such as bgl, mng or xlyE). This new combined strategy shows a detailed staggered evolutionary reconstruction, which help us to understand the deepest events and the selection forces have driven E. coli diversification. This approach could add resolution in the reconstruction of the evolutionary trajectories of other microorganisms.", "token_count": 500, "char_count": 2044, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6146, "quality_score": 0.8073, "entities": { "genes": [ "FGB2", "EB1A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:46.385948", "source": { "split": "train_shard_00001", "doc_id": 4163 }, "chunk_id": "train_shard_00001_4163_0", "global_id": 11545 }, { "text": "Reconstruction of Escherichia coli ancient diversification by layered phylogenomics and polymorphism fingerprinting", "token_count": 30, "char_count": 115, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:46.738414", "source": { "split": "train_shard_00001", "doc_id": 4163 }, "chunk_id": "train_shard_00001_4163_1", "global_id": 11546 }, { "text": "

Background

The gut microbiota is considered a rich source for potential novel probiotics. Enterococcus genus is a normal component of a healthy gut microbiota, suggesting its vital role. Nosocomial infections caused mainly by E. facalis and E. faecium have been attributed to the plasticity of the Enterococcus genomes. In this study, we assessed the probiotic and safety characteristics of two E. lactis strains isolated from the human gut microbiota using in-vitro and in silico approaches. Additionally, the safety of the E. lactis species was evaluated using comparative genomics analysis.

Results

The two E. lactis strains 10NA and 50NA showed resistance to bile salts and acid tolerance with antibacterial activity against Escherichia coli, Salmonella typhi, and Clostridioides difficile. For safety assays, the two strains did not display any type of hemolysis on blood agar, and the survival of Caco-2 cells was not significantly different (P-value > 0.05) compared to the control using cell free supernatants at 100% (v/v), 50% (v/v), 10% (v/v), and 5% (v/v) concentrations. Regarding antibiotic susceptibility, both strains were sensitive to vancomycin, tetracycline, and chloramphenicol. Comprehensive whole-genome analysis revealed no concerning associations between virulence or antibiotic resistance genes and any of the identified mobile genetic elements. Comparative genome analysis with closely related E. faecium species genomes revealed the distinctive genomic safety of the E. lactis species.

Conclusions

Our two E. lactis strains showed promising probiotic properties in-vitro. Their genomes were devoid of any transferable antibiotic resistance genes. In silico comparative analysis confirmed the safety of the E. lactis species. These results suggest that E. lactis species could be a potential source for safer Enterococcus probiotic supplements.", "token_count": 503, "char_count": 1892, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:47.399084", "source": { "split": "train_shard_00001", "doc_id": 4164 }, "chunk_id": "train_shard_00001_4164_0", "global_id": 11547 }, { "text": "Safety assessment of Enterococcus lactis strains complemented with comparative genomics analysis reveals probiotic and safety characteristics of the entire species.", "token_count": 32, "char_count": 164, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:47.757000", "source": { "split": "train_shard_00001", "doc_id": 4164 }, "chunk_id": "train_shard_00001_4164_1", "global_id": 11548 }, { "text": "A Gram-stain-negative, coccus-shaped, obligately anaerobic, non-motile and non-spore-forming bacterium, designated strain JN500902T, was isolated from the mud in a fermentation cellar used continuously over 30 years for Chinese strong-flavour baijiu production. Colonies were white, circular, convex and smooth-edged. Growth was observed at 20-40 °C (optimum, 37 °C), at pH 5.0-10 (optimum, pH 7.5), with 0-2 % (w/v) NaCl and with 0-4 % (v/v) ethanol. The Biolog assay demonstrated positive reactions of strain JN500902T in the metabolism of l-fucose and pyruvate. The predominant cellular fatty acids (>10 %) consisted of C16 : 0 and C14 : 0. The major end metabolites of strain JN500902T were acetic acid and ethanol when incubated anaerobically in liquid reinforced clostridial medium. Acetate was the major organic acid end product. The complete genome size of strain JN500902T was 3 420 321 bp with 3327 identified genes. The G+C content was 43.5 mol%. Phylogenetic analysis based on 16S rRNA gene sequences affiliated strain JN500902T with the family Lachnospiraceae, having low sequence similarity (92.8 %) to the nearest type strain, Syntrophococcus sucromutans DSM 3224T and forming a clearly distinct branch", "token_count": 505, "char_count": 1326, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7418, "quality_score": 0.8709, "entities": { "genes": [ "JN500902" ], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:48.407394", "source": { "split": "train_shard_00001", "doc_id": 4165 }, "chunk_id": "train_shard_00001_4165_0", "global_id": 11549 }, { "text": "Core genome phylogenetic analysis of the isolate and 134 strains belonging to the family Lachnospiraceae also revealed that strain JN500902T was well-separated from other genera of this family as a monophyletic clade. The average nucleotide identity and amino acid identity values between strain JN500902T and 134 Lachnospiraceae strains were less than 74 and 65 %, respectively. Considering its polyphasic characteristics, strain JN500902T represents a novel genus and species within the family Lachnospiraceae, for which the name Novisyntrophococcus fermenticellae gen. nov., sp. nov. is proposed. The type strain is JN500902T (=CICC 24502T=JCM 33939T).\n\nNovisyntrophococcus fermenticellae gen. nov., sp. nov., isolated from an anaerobic fermentation cellar of Chinese strong-flavour baijiu.", "token_count": 331, "char_count": 901, "word_count": 108, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [ "JN500902" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:48.978412", "source": { "split": "train_shard_00001", "doc_id": 4165 }, "chunk_id": "train_shard_00001_4165_1", "global_id": 11550 }, { "text": "Objective: To analyze the molecular characteristics of Listeria monocytogenes strains from ready-to eat food in China. Methods: A total of 239 Listeria monocytogenes strains isolated from ready-to-eat food in 2017, all strains underwent whole-genome sequencing (WGS) , and comparisons uncovered population structure derived from lineages, clonal complex, serogroups, antimicrobial susceptibility and virulence, which were inferred in silico from the WGS data. Core genome multilocus sequence typing was used to subtype isolates. Results: All strains were categorized into three different lineages, lineage Ⅱ was the predominant types in food, and IIa was the main serogroups. CC8, CC101 and CC87 were the first three prevalent CCs among 23 detected CCs, accounting for 49.4%. Only 4.6% (11 isolates) of tested strains harbored antibiotic resistance genes, which were mostly trimethoprim genes (7 isolates, 2.9%). All strains were positive for LIPI-1, and only a part of strains harbored LIPI-3 and LIPI-4, accounting for 13.8% (33 isolates) and 14.2% (34 isolates), respectively. ST619 carried both LIPI-3 and LIPI-4. 51.5% (123 isolates) of strains carried SSI-1, and all CC121 strains harbored SSI-2. Different lineages, serogroups and CCs can be separated obviously through cgMLST analysis, and 24 sublineages were highly concordant with CCs", "token_count": 440, "char_count": 1379, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [ "CC8", "CC121", "ST619", "CC101", "CC87" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:49.610873", "source": { "split": "train_shard_00001", "doc_id": 4166 }, "chunk_id": "train_shard_00001_4166_0", "global_id": 11551 }, { "text": "Conclusion: Ⅱa was the main serogroups in ready-to-eat food isolates in China; CC8, CC101 and CC87 were the prevalent CCs, and CC87 isolates was hypervirulent isolates, cgMLST method can be adopted for prospective foodborne disease surveillance and outbreaks detection.\n\n[Molecular epidemiology of Listeria monocytogenes isolated from ready-to-eat food in 2017 in China].", "token_count": 119, "char_count": 378, "word_count": 52, "semantic_coherence": 1, "information_density": 0.7885, "quality_score": 0.8942, "entities": { "genes": [ "CC101", "CC87", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:49.990865", "source": { "split": "train_shard_00001", "doc_id": 4166 }, "chunk_id": "train_shard_00001_4166_1", "global_id": 11552 }, { "text": "

Background

Plague is a highly dangerous vector-borne infectious disease that has left a significant mark on history of humankind. There are 13 natural plague foci in the Caucasus, located on the territory of the Russian Federation, Azerbaijan, Armenia and Georgia. We performed whole-genome sequencing of Y. pestis strains, isolated in the natural foci of the Caucasus and Transcaucasia. Using the data of whole-genome SNP analysis and Bayesian phylogeny methods, we carried out an evolutionary-phylogeographic analysis of modern population of the plague pathogen in order to determine the phylogenetic relationships of Y. pestis strains from the Caucasus with the strains from other countries.

Results

We used 345 Y. pestis genomes to construct a global evolutionary phylogenetic reconstruction of species based on whole-genome SNP analysis. The genomes of 16 isolates were sequenced in this study, the remaining 329 genomes were obtained from the GenBank database. Analysis of the core genome revealed 3315 SNPs that allow differentiation of strains. The evolutionary phylogeographic analysis showed that the studied Y. pestis strains belong to the genetic lineages 0.PE2, 2.MED0, and 2.MED1. It was shown that the Y. pestis strains isolated on the territory of the East Caucasian high-mountain, the Transcaucasian high-mountain and the Priaraksinsky low-mountain plague foci belong to the most ancient of all existing genetic lineages - 0.PE2.

Conclusions

On the basis of the whole-genome SNP analysis of 345 Y. pestis strains, we describe the modern population structure of the plague pathogen and specify the place of the strains isolated in the natural foci of the Caucasus and Transcaucasia in the structure of the global population of Y. pestis. As a result of the retrospective evolutionary-phylogeographic analysis of the current population of the pathogen, we determined the probable time frame of the divergence of the genetic lineages of Y", "token_count": 524, "char_count": 1974, "word_count": 290, "semantic_coherence": 1, "information_density": 0.4828, "quality_score": 0.7414, "entities": { "genes": [ "MED0", "MED1", "PE2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:47:50.622742", "source": { "split": "train_shard_00001", "doc_id": 4167 }, "chunk_id": "train_shard_00001_4167_0", "global_id": 11553 }, { "text": "pestis, as well as suggested the possible paths of the historical spread of the plague pathogen.\n\nYersinia pestis strains isolated in natural plague foci of Caucasus and Transcaucasia in the context of the global evolution of species.", "token_count": 61, "char_count": 234, "word_count": 37, "semantic_coherence": 1, "information_density": 0.7027, "quality_score": 0.8514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:50.998583", "source": { "split": "train_shard_00001", "doc_id": 4167 }, "chunk_id": "train_shard_00001_4167_1", "global_id": 11554 }, { "text": "The Salmonella Enterica subsp. Enterica serovar Enteritidis is one of main serovars isolated from human patients with food poisoning and poultry without clinical signs. Consumption of poultry products contaminated with Salmonella Enteritidis is a common source of human salmonellosis; 82 Salmonella spp. were isolated from 291 samples of retail chicken meat, 201 one-day-old chicks, 30 internal organs of chickens, 156 chicken eggs, 100 duck eggs, 38 straw bedding samples, 18 samples of retail duck meat, and 19 swab samples from slaughterhouses in 2019 and 2020. An antibiotic susceptibility test was performed for all isolates, revealing 33 multidrug-resistant (MDR) strains. The whole genome of 33 MDR strains isolated in 2019 and 2020 and 10 strains isolated in 2011, 2012, and 2017 was sequenced using the MinION sequencing protocol. Within these 43 samples, 5 serovars were identified: S. Enteritidis, S. Agona, S. Virchow, S. Albany, and S. Bareilly. The most common serovar was S. Enteritidis (26/43), which showed the highest resistance to ampicillin (100%), followed by nalidixic acid (90%) and colistin (83%). Core genome multilocus sequence typing analysis showed that the S. Enteritidis strains isolated from different sources and in different years were clustered together. In addition, the S. Enteritidis strains isolated since 2011 consistently harbored the same antibiotic resistance patterns.", "token_count": 488, "char_count": 1488, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:51.643703", "source": { "split": "train_shard_00001", "doc_id": 4168 }, "chunk_id": "train_shard_00001_4168_0", "global_id": 11555 }, { "text": "Whole-Genome Analysis of Multidrug-Resistant Salmonella Enteritidis Strains Isolated from Poultry Sources in Korea.", "token_count": 40, "char_count": 122, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:52.005083", "source": { "split": "train_shard_00001", "doc_id": 4168 }, "chunk_id": "train_shard_00001_4168_1", "global_id": 11556 }, { "text": "Diphtheria is a vaccine-preventable disease with a high potential for reemergence. One of its causative agents is Corynebacterium diphtheriae, with some strains producing diphtheria toxin. From 2011 to 2019, 57 clinical C. diphtheriae strains were isolated in Austria, either from the respiratory tract or from skin infections. The aim of this study was to investigate the genetic diversity of these C. diphtheriae isolates using whole-genome sequencing. Isolates were characterized by genome-wide comparisons using single nucleotide polymorphism analysis or core genome multilocus sequence typing and by searching sequence data for antimicrobial resistance genes and genes involved in diphtheria toxin production. The genetic diversity among the isolates was high, with no clear distribution over time or place. Corynebacterium belfantii isolates were separated from other strains and were strongly associated with respiratory infections (odds ratio [OR] = 57). Two clusters, limited in time and space, were identified. Almost 40% of strains carried resistance genes against tetracycline or sulfonamides, mostly from skin infections. Microbiological tests showed that 55% of isolates were resistant to penicillin but did not carry genes conferring β-lactam resistance. A diphtheria toxin gene with no nonsynonymous mutation was found in three isolates only. This study showed that sequencing can provide valuable information complementing routine microbiological and epidemiological investigations. It allowed us to identify unknown clusters, evaluate antimicrobial resistance more broadly, and support toxigenicity results obtained by PCR. For these reasons, C. diphtheriae surveillance could strongly benefit from the routine implementation of whole-genome sequencing.\n\nAssessing the Genetic Diversity of Austrian Corynebacterium diphtheriae Clinical Isolates, 2011 to 2019.", "token_count": 502, "char_count": 1912, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6196, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:52.658532", "source": { "split": "train_shard_00001", "doc_id": 4169 }, "chunk_id": "train_shard_00001_4169_0", "global_id": 11557 }, { "text": "

Background

Shigellosis (previously bacillary dysentery) was the primary diarrhoeal disease of World War 1, but outbreaks still occur in military operations, and shigellosis causes hundreds of thousands of deaths per year in developing nations. We aimed to generate a high-quality reference genome of the historical Shigella flexneri isolate NCTC1 and to examine the isolate for resistance to antimicrobials.

Methods

In this genomic analysis, we sequenced the oldest extant Shigella flexneri serotype 2a isolate using single-molecule real-time (SMRT) sequencing technology. Isolated from a soldier with dysentery from the British forces fighting on the Western Front in World War 1, this bacterium, NCTC1, was the first isolate accessioned into the National Collection of Type Cultures. We created a reference sequence for NCTC1, investigated the isolate for antimicrobial resistance, and undertook comparative genetics with S flexneri reference strains isolated during the 100 years since World War 1.

Findings

We discovered that NCTC1 belonged to a 2a lineage of S flexneri, with which it shares common characteristics and a large core genome. NCTC1 was resistant to penicillin and erythromycin, and contained a complement of chromosomal antimicrobial resistance genes similar to that of more recent isolates. Genomic islands gained in the S flexneri 2a lineage over time were predominately associated with additional antimicrobial resistances, virulence, and serotype conversion.

Interpretation

This S flexneri 2a lineage is a well adapted pathogen that has continued to respond to selective pressures. We have created a valuable historical benchmark for shigellae in the form of a high-quality reference sequence for a publicly available isolate.

Funding

The Wellcome Trust.\n\nThe extant World War 1 dysentery bacillus NCTC1: a genomic analysis.", "token_count": 498, "char_count": 1883, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5923, "quality_score": 0.7962, "entities": { "genes": [ "NCTC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:53.321006", "source": { "split": "train_shard_00001", "doc_id": 4170 }, "chunk_id": "train_shard_00001_4170_0", "global_id": 11558 }, { "text": "Recent work performed by Sberro et al. (2019) revealed a vast unexplored space of small proteins existing within the human microbiome. At present, these small open reading frames (smORFs) are unannotated in existing reference genomes and standard genome annotation tools are not able to accurately predict them. In this study, we introduce an annotation tool named SmORFinder that predicts small proteins based on those identified by Sberro et al. This tool combines profile Hidden Markov models (pHMMs) of each small protein family and deep learning models that may better generalize to smORF families not seen in the training set. We find that combining predictions of both pHMM and deep learning models leads to more precise smORF predictions and that these predicted smORFs are enriched for Ribo-Seq or MetaRibo-Seq translation signals. Feature importance analysis reveals that the deep learning models learned to identify Shine-Dalgarno sequences, deprioritize the wobble position in each codon, and group codons in a way that strongly corresponds to the codon synonyms found in the codon table. We perform a core genome analysis of 26 bacterial species and identify many core smORFs of unknown function. We pre-compute small protein annotations for thousands of RefSeq isolate genomes and HMP metagenomes, and we make these data available through a web portal along with other useful tools for small protein annotation and analysis. The systematic identification and annotation of those important small proteins will help researchers to expand our understanding of this exciting field of biology.\n\nAutomated prediction and annotation of small proteins in microbial genomes", "token_count": 373, "char_count": 1678, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6118, "quality_score": 0.8059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:53.909527", "source": { "split": "train_shard_00001", "doc_id": 4171 }, "chunk_id": "train_shard_00001_4171_0", "global_id": 11559 }, { "text": "An aerobic, Gram-stain-negative, non-sporulating, flagellated and spindle-like bacterium, designated HY14T, was isolated from a pickle-processing factory wastewater sample. The isolate chemoheterotrophically grew at 4-42 °C (optimum, 35 °C) and pH 5.5-9.0 (optimum, pH 6.0-6.5). Salt was required for growth (0.5-12 % NaCl, w/v). A deep brown and water-soluble uncharacterized pigment was produced when grown in certain media. The predominant fatty acids (>5 %) included C16 : 0, C18 : 1  ω7c, 11-methyl C18 : 1  ω7c and C19 : 0 cyclo ω8c. The polar lipid profile consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylcholine, two unidentified aminolipids, two unidentified phospholipids, two unidentified glycolipids and five unknown lipids. The major isoprenoid quinone was ubiquinone-10. Pairwise alignment based on 16S rRNA gene sequences indicated that strain HY14T had the highest sequence similarity to genera Maritimibacter (95.61-96.05 %) and Boseongicola (95.82 %)", "token_count": 459, "char_count": 1113, "word_count": 138, "semantic_coherence": 1, "information_density": 0.8043, "quality_score": 0.9022, "entities": { "genes": [ "HY14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:54.548477", "source": { "split": "train_shard_00001", "doc_id": 4172 }, "chunk_id": "train_shard_00001_4172_0", "global_id": 11560 }, { "text": "Phylogenetic analysis based on core genome illustrated that strain HY14T formed a monophyletic lineage with members of the genus Maritimibacter in the clade of the Roseobacter group in the family Rhodobacteraeceae. The core-gene average amino acid identity used to define bacterial genera by a threshold of 60-80 % was calculated to be 68.56-76.5 % between HY14T and closely related taxa. Several genomic characteristics, such as carrying two RuBisCO-mediated pathways and different osmoprotectant transport pathways, exhibited the genotypic discrepancies of strain HY14T. Based on the polyphasic taxonomic characterization, strain HY14T is considered to represent a novel species of a novel genus belonging to the family Rhodobacteraeceae, for which the name Muriiphilus fusiformis gen. nov., sp. nov. is proposed. The type strain is HY14T (=CGMCC 1.15973T=KCTC 52499T). Maritimibacter lacisalsi (Zhong et al. 2015) is considered to diverge from Maritimibacter alkaliphilus at the genus level, and should be reassigned as a novel genus, for which the name Muriicola lacisalsi gen. nov., comb. nov. is proposed.", "token_count": 436, "char_count": 1251, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8272, "entities": { "genes": [ "HY14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:55.177193", "source": { "split": "train_shard_00001", "doc_id": 4172 }, "chunk_id": "train_shard_00001_4172_1", "global_id": 11561 }, { "text": "Muriiphilus fusiformis gen. nov., sp. nov., a novel non-marine bacterium belonging to the Roseobacter group, and reclassification of Maritimibacter lacisalsi (Zhong et al. 2015) as Muriicola lacisalsi gen. nov., comb. nov.", "token_count": 106, "char_count": 257, "word_count": 31, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:55.554458", "source": { "split": "train_shard_00001", "doc_id": 4172 }, "chunk_id": "train_shard_00001_4172_2", "global_id": 11562 }, { "text": "Although homologous recombination is accepted to be common in bacteria, so far it has been challenging to accurately quantify its impact on genome evolution within bacterial species. We here introduce methods that use the statistics of single-nucleotide polymorphism (SNP) splits in the core genome alignment of a set of strains to show that, for many bacterial species, recombination dominates genome evolution. Each genomic locus has been overwritten so many times by recombination that it is impossible to reconstruct the clonal phylogeny and, instead of a consensus phylogeny, the phylogeny typically changes many thousands of times along the core genome alignment. We also show how SNP splits can be used to quantify the relative rates with which different subsets of strains have recombined in the past. We find that virtually every strain has a unique pattern of frequencies with which its lineages have recombined with those of other strains, and that the relative rates with which different subsets of strains share SNPs follow long-tailed distributions. Our findings show that bacterial populations are neither clonal nor freely recombining, but structured such that recombination rates between different lineages vary along a continuum spanning several orders of magnitude, with a unique pattern of rates for each lineage. Thus, rather than reflecting clonal ancestry, whole genome phylogenies reflect these long-tailed distributions of recombination rates.\n\nWhole genome phylogenies reflect long-tailed distributions of recombination rates in many bacterial species", "token_count": 347, "char_count": 1577, "word_count": 232, "semantic_coherence": 1, "information_density": 0.569, "quality_score": 0.7845, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:56.145594", "source": { "split": "train_shard_00001", "doc_id": 4173 }, "chunk_id": "train_shard_00001_4173_0", "global_id": 11563 }, { "text": "In Pichia stipitis, fermentative and pyruvate decarboxylase (PDC) activities increase with diminished oxygen rather than in response to fermentable sugars. To better characterize PDC expression and regulation, two genes for PDC (PsPDC1 and PsPDC2) were cloned and sequenced from P. stipitis CBS 6054. Aside from Saccharomyces cerevisiae, from which three PDC genes have been characterized, P. stipitis is the only organism from which multiple genes for PDC have been identified and characterized. PsPDC1 and PsPDC2 have diverged almost as far from one another as they have from the next most closely related known yeast gene. PsPDC1 contains an open reading frame of 1,791 nucleotides encoding 597 amino acids. PsPDC2 contains a reading frame of 1,710 nucleotides encoding 570 amino acids. An 81-nucleotide segment in the middle of the beta domain of PsPDC1 codes for a unique segment of 27 amino acids, which may play a role in allosteric regulation. The 5' regions of both P. stipitis genes include two putative TATA elements that make them similar to the PDC genes from S. cerevisiae, Kluyveromyces marxianus, and Hanseniaspora uvarum.\n\nCloning and characterization of two pyruvate decarboxylase genes from Pichia stipitis CBS 6054.", "token_count": 365, "char_count": 1235, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6021, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:56.740407", "source": { "split": "train_shard_00001", "doc_id": 4174 }, "chunk_id": "train_shard_00001_4174_0", "global_id": 11564 }, { "text": "Candida kefyr as an emerging pathogen causing nosocomial bloodstream infections in neutropenic leukemia patients.", "token_count": 29, "char_count": 113, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:57.137087", "source": { "split": "train_shard_00001", "doc_id": 4175 }, "chunk_id": "train_shard_00001_4175_0", "global_id": 11565 }, { "text": "

Background

Clostridioides difficile infection (CDI) caused by toxigenic strains leads to antibiotic-related diarrhea, colitis, or even fatal pseudomembranous enteritis. Previously, we conducted a cross-sectional study on prevalence of CDI in southwest China. However, the antibiotics resistance and characteristics of genomes of these isolates are still unknown.

Methods

Antibiotic susceptibility testing with E-test strips and whole genome sequence analysis were used to characterize the features of these C. difficile isolates.

Results

Forty-nine strains of C. difficile were used in this study. Five isolates were non-toxigenic and the rest carried toxigenic genes. We have previously reported that ST35/RT046, ST3/RT001 and ST3/RT009 were the mostly distributed genotypes of strains in the children group. In this study, all the C. difficile isolates were sensitive to metronidazole, meropenem, amoxicillin/clavulanic acid and vancomycin. Most of the strains were resistant to erythromycin, gentamicin and clindamycin. The annotated resistant genes, such as macB, vanRA, vanRG, vanRM, arlR, and efrB were mostly identified related to macrolide, glycopeptide, and fluoroquinolone resistance. Interestingly, 77.55% of the strains were considered as multi-drug resistant (MDR). Phylogenetic analysis based on core genome of bacteria revealed all the strains were divided into clade 1 and clade 4. The characteristics of genome diversity for clade 1 could be found", "token_count": 482, "char_count": 1556, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "ST3", "ST35", "RT046", "RT009", "RT001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:57.811587", "source": { "split": "train_shard_00001", "doc_id": 4176 }, "chunk_id": "train_shard_00001_4176_0", "global_id": 11566 }, { "text": "None of the isolates showed 18-bp deletion of tcdC as RT027 strain as described before, and polymorphism of tcdB showed a high degree of conservation than tcdA gene.

Conclusions

Most of the C. difficile isolates in this study were resistant to macrolide and aminoglycoside antibiotics. Moreover, the MDR strains were commonly found. All the isolates belonged to clade 1 and clade 4 according to phylogenetic analysis of bacterial genome, and highly genomic diversity of clade 1 was identified for these strains.\n\nAntibiotic resistance and genomic features of Clostridioides difficile in southwest China.", "token_count": 201, "char_count": 645, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [ "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:58.271327", "source": { "split": "train_shard_00001", "doc_id": 4176 }, "chunk_id": "train_shard_00001_4176_1", "global_id": 11567 }, { "text": "The genus Populus comprises a complex amalgam of ancient and modern species that has become a prime model for evolutionary and taxonomic studies. Here we sequenced the genomes of 10 species from five sections of the genus Populus, identified 71 million genomic variations, and observed new correlations between the single-nucleotide polymorphism-structural variation (SNP-SV) density and indel-SV density to complement the SNP-indel density correlation reported in mammals. Disease resistance genes (R genes) with heterozygous loss-of-function (LOF) were significantly enriched in the 10 species, which increased the diversity of poplar R genes during evolution. Heterozygous LOF mutations in the self-incompatibility genes were closely related to the self-fertilization of poplar, suggestive of genomic control of self-fertilization in dioecious plants. The phylogenetic genome-wide SNPs tree also showed possible ancient hybridization among species in sections Tacamahaca, Aigeiros, and Leucoides. The pangenome resource also provided information for poplar genetics and breeding.\n\nThe poplar pangenome provides insights into the evolutionary history of the genus.", "token_count": 294, "char_count": 1180, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:58.837583", "source": { "split": "train_shard_00001", "doc_id": 4177 }, "chunk_id": "train_shard_00001_4177_0", "global_id": 11568 }, { "text": "Listeria monocytogenes is one of the most important foodborne pathogens that may be present in food and in food processing environments. In the present study, 91 L. monocytogenes isolates of serogroup IVb from raw meat, ready-to-eat food and food production environments in Poland were characterized by whole genome sequencing (WGS). The strains were also compared, using core genome multi-locus sequence typing (cgMLST) analysis, with 186 genomes of L. monocytogenes recovered worldwide from food, environments, and from humans with listeriosis. The L. monocytogenes examined belonged to three MLST clonal complexes: CC1 (10; 11.0% isolates), CC2 (70; 76.9%), and CC6 (11; 12.1%). CC1 comprised of two STs (ST1 and ST515) which could be divided into five cgMLST, CC2 covered two STs (ST2 and ST145) with a total of 20 cgMLST types, whereas CC6 consisted of only one ST (ST6) classified as one cgMLST. WGS sequences of the tested strains revealed that they had several pathogenic markers making them potentially hazardous for public health. Molecular comparison of L. monocytogenes strains tested in the present study with those isolated from food and human listeriosis showed a relationship between the isolates from Poland, but not from other countries.\n\nMolecular Typing of Listeria monocytogenes IVb Serogroup Isolated from Food and Food Production Environments in Poland.", "token_count": 420, "char_count": 1418, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6411, "quality_score": 0.8206, "entities": { "genes": [ "ST145", "ST2", "ST6", "ST515", "ST1", "CC6", "CC2", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:47:59.467620", "source": { "split": "train_shard_00001", "doc_id": 4178 }, "chunk_id": "train_shard_00001_4178_0", "global_id": 11569 }, { "text": "Elizabethkingia bruuniana is a novel species of the Elizabethkingia genus. There is scant information on this microorganism. Here, we report the whole-genome features and antimicrobial susceptibility patterns of E. bruuniana strain EM798-26. Elizabethkingia strain EM798-26 was initially identified as E. miricola. This isolate contained a circular genome of 4,393,011 bp. The whole-genome sequence-based phylogeny revealed that Elizabethkingia strain EM798-26 was in the same group of the type strain E. bruuniana G0146T. Both in silico DNA-DNA hybridization and average nucleotide identity analysis clearly demonstrated that Elizabethkingia strain EM798-26 was a species of E. bruuniana. The pan-genome analysis identified 2,875 gene families in the core genome and 5,199 gene families in the pan genome of eight publicly available E. bruuniana genome sequences. The unique genes accounted for 0.2-12.1% of the pan genome in each E. bruuniana. A total of 59 potential virulence factor homologs were predicted in the whole-genome of E. bruuniana strain EM798-26. This isolate was nonsusceptible to multiple antibiotics, but susceptible to aminoglycosides, minocycline, and levofloxacin. The whole-genome sequence analysis of E. bruuniana EM798-26 revealed 29 homologs of antibiotic resistance-related genes. This study presents the genomic features of E. bruuniana. Knowledge of the genomic characteristics provides valuable insights into a novel species.\n\nGenomic Features, Comparative Genomics, and Antimicrobial Susceptibility Patterns of Elizabethkingia bruuniana.", "token_count": 446, "char_count": 1580, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5211, "quality_score": 0.7606, "entities": { "genes": [ "EM798" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:00.100159", "source": { "split": "train_shard_00001", "doc_id": 4179 }, "chunk_id": "train_shard_00001_4179_0", "global_id": 11570 }, { "text": "

Background

The resistance of Streptococcus pneumoniae to macrolides is becoming an increasingly important issue and thus it is important to understand the genetics related to adaptation of this species to the widespread use of antibiotics in Europe. The 58 isolates of S. pneumoniae belonging to sequence type (ST) 416 and serotype 19A and to several different phenotypes originated from Italy, Portugal and Czech Republic were thus sequenced on Illumina MiSeq. The aim of the study was to describe genetical origine of isolates, investigate their macrolide resistance and suggest reasons for spread of ST416 in the Czech Republic.

Results

Investigation of genes associated with serotype determined serotype switch between 15B and 19A serotypes and core genome multilocus sequence typing (cgMLST) confirmed the origine of concerned isolates in Netherlands15B-37 clone. Inspected genomes proved variability of genes associated with the macrolide resistance even within closely genetically relative isolates.

Conclusions

Participation of 19A/ST416 on the spread of Netherlands15B-37 is accompanied by serotype switch between 19A and 15B serotypes and with acquisition of genes involved in macrolide resistance to the clone that was originally macrolide susceptible. There is evident tendency to interchanging and modifications of these and surrounding genes, that could lead to accelerate spreading of this sequence type in regions with high macrolide consumption.\n\nWhole genome sequencing of macrolide resistant Streptococcus pneumoniae serotype 19A sequence type 416.", "token_count": 405, "char_count": 1611, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5642, "quality_score": 0.7821, "entities": { "genes": [ "ST416" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:00.720712", "source": { "split": "train_shard_00001", "doc_id": 4180 }, "chunk_id": "train_shard_00001_4180_0", "global_id": 11571 }, { "text": "Shigella spp. and entero-invasive Escherichia coli (EIEC) can cause mild diarrhea to dysentery. In Netherlands, although shigellosis is a notifiable disease, there is no laboratory surveillance for Shigella spp. and EIEC in place. Consequently, the population structure for circulating Shigella spp. and EIEC isolates is not known. This study describes the phenotypic and serological characteristics, the phenotypic and genetic antimicrobial resistance (AMR) profiles, the virulence gene profiles, the classic multi-locus sequence types (MLST) and core genome (cg)MLST types, and the epidemiology of 414 Shigella spp. and EIEC isolates collected during a cross-sectional study in Netherlands in 2016 and 2017. S. sonnei (56%), S. flexneri (25%), and EIEC (15%) were detected predominantly in Netherlands, of which the EIEC isolates were most diverse according to their phenotypical profile, O-types, MLST types, and cgMLST clades. Virulence gene profiling showed that none of the isolates harbored Shiga toxin genes. Most S. flexneri and EIEC isolates possessed nearly all virulence genes examined, while these genes were only detected in approximately half of the S. sonnei isolates, probably due to loss of the large invasion plasmid upon subculturing. Phenotypical resistance correlated well with the resistant genotype, except for the genes involved in resistance to aminoglycosides. A substantial part of the characterized isolates was resistant to antimicrobials advised for treatment, i.e., 73% was phenotypically resistant to co-trimoxazole and 19% to ciprofloxacin. AMR was particularly observed in isolates from male patients who had sex with men (MSM) or from patients that had traveled to Asia", "token_count": 523, "char_count": 1768, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:01.383229", "source": { "split": "train_shard_00001", "doc_id": 4181 }, "chunk_id": "train_shard_00001_4181_0", "global_id": 11572 }, { "text": "Furthermore, isolates related to international clusters were also circulating in Netherlands. Travel-related isolates formed clusters with isolates from patients without travel history, indicating their emergence into the Dutch population. In conclusion, laboratory surveillance using whole genome sequencing as high-resolution typing technique and for genetic characterization of isolates complements the current epidemiological surveillance, as the latter is not sufficient to detect all (inter)national clusters, emphasizing the importance of multifactorial public health approaches.\n\nA Multifactorial Approach for Surveillance of Shigella spp. and Entero-Invasive Escherichia coli Is Important for Detecting (Inter)national Clusters.", "token_count": 164, "char_count": 751, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7865, "quality_score": 0.8933, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:01.826211", "source": { "split": "train_shard_00001", "doc_id": 4181 }, "chunk_id": "train_shard_00001_4181_1", "global_id": 11573 }, { "text": "Global spread of Escherichia coli strains carrying the mobilized colistin resistance gene mcr-1.1 (MCR1-EC) poses serious threats to public health. Colistin has been generally prescribed for swine colibacillosis, having made swine farms as major reservoirs of MCR1-EC. The present study aimed to understand characteristic differences of MCR1-EC, including prevalence, antimicrobial resistance, and virulence, according to swine production stages. In addition, genetic relatedness was evaluated between MCR1-EC isolated from this study as well as pig-, human-, and chicken-derived strains published in the National Center for Biotechnology Information (NCBI), based on the multi-locus sequence types (MLSTs) and whole-genome sequences (WGS). Individual fecal samples (n = 331) were collected from asymptomatic weaning-piglets, growers, finishers, and sows from 10 farrow-to-finishing farms in South Korea between 2017 and 2019. The weighted prevalence of MCR1-EC was 11.6% (95% CI: 8.9%-15.0%, 55/331), with the highest prevalence at weaning stage. The 96.2% of MCR1-EC showed multi-drug resistance. Notably, weaning stage-derived MCR1-EC showed higher resistance rates (e.g., against extended-spectrum β-lactams or quinolones) than those from other stages. MCR1-EC with virulence advantages (e.g., intestinal/extraintestinal pathogenic E. coli or robust biofilm formation) were identified from all pig stages, accounting for nearly half of the total strains. WGS-based in-depth characterization showed that intestinal pathogenic MCR1-EC harbored multi-drug resistance and multiple virulence factors, which were highly shared between strains isolated from pigs of different stages. The clonal distribution of MCR1-EC was shared within swine farms but rarely across farms", "token_count": 520, "char_count": 1797, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6949, "quality_score": 0.8475, "entities": { "genes": [ "MCR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:02.464802", "source": { "split": "train_shard_00001", "doc_id": 4182 }, "chunk_id": "train_shard_00001_4182_0", "global_id": 11574 }, { "text": "The major clonal type of MCR1-EC from swine farms and NCBI database was ST10-A. Core genomes of MCR1-EC isolated from individuals within closed environments (same farms or human hospitals) were highly shared (genetic distance < 0.01), suggesting a high probability of clonal expansion of MCR1-EC within closed environments such as livestock husbandry. To the best of our knowledge, this is the first study to analyze the differences in the characteristics and clonal distribution of MCR1-EC according to production stages in swine farms, an important reservoir of MCR1-EC. Our results highlight the need to establish MCR1-EC control plans in swine farms based on an in-depth understanding of MCR1-EC characteristics according to swine production stages, focusing especially on the weaning stages.\n\nPrevalence, Characteristics, and Clonal Distribution of Escherichia coli Carrying Mobilized Colistin Resistance Gene mcr-1.1 in Swine Farms and Their Differences According to Swine Production Stages.", "token_count": 256, "char_count": 1011, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [ "MCR1", "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:03.008781", "source": { "split": "train_shard_00001", "doc_id": 4182 }, "chunk_id": "train_shard_00001_4182_1", "global_id": 11575 }, { "text": "Although Yarrowia lipolytica is a model yeast for the study of lipid metabolism, its diversity is poorly known, as studies generally consider only a few standard laboratory strains. To extend our knowledge of this biotechnological workhorse, we investigated the genomic and phenotypic diversity of 56 natural isolates. Y. lipolytica is classified into five clades with no correlation between clade membership and geographic or ecological origin. A low genetic diversity (π = 0.0017) and a pan-genome (6528 genes) barely different from the core genome (6315 genes) suggest Y. lipolytica is a recently evolving species. Large segmental duplications were detected, totaling 892 genes. With three new LTR-retrotransposons of the Gypsy family (Tyl4, Tyl9, and Tyl10), the transposable element content of genomes appeared diversified but still low (from 0.36% to 3.62%). We quantified 34 traits with substantial phenotypic diversity, but genome-wide association studies failed to evidence any associations. Instead, we investigated known genes and found four mutational events leading to XPR2 protease inactivation. Regarding lipid metabolism, most high-impact mutations were found in family-belonging genes, such as ALK or LIP, and therefore had a low phenotypic impact, suggesting that the huge diversity of lipid synthesis and accumulation is multifactorial or due to complex regulations.\n\nInsights into the Genomic and Phenotypic Landscape of the Oleaginous Yeast Yarrowia lipolytica.", "token_count": 434, "char_count": 1538, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8498, "entities": { "genes": [ "XPR2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:03.644004", "source": { "split": "train_shard_00001", "doc_id": 4183 }, "chunk_id": "train_shard_00001_4183_0", "global_id": 11576 }, { "text": "Cholera caused by pathogenic Vibrio cholerae is still considered one of the major health problems in developing countries including those in Asia and Africa. Australia is known to have unique V. cholerae strains in Queensland waterways, resulting in sporadic cholera-like disease being reported in Queensland each year. We conducted virulence and antimicrobial genetic characterization of O1 and non-O1, non-O139 V. cholerae (NOVC) strains (1983 to 2020) from Queensland with clinical significance and compared these to environmental strains that were collected as part of a V. cholerae monitoring project in 2012 of Queensland waterways. In this study, 87 V. cholerae strains were analyzed where O1 (n = 5) and NOVC (n = 54) strains from Queensland and international travel-associated NOVC (n = 2) (61 in total) strains were sequenced, characterized, and compared with seven previously sequenced O1 strains and 18 other publicly available NOVC strains from Australia and overseas to visualize the genetic context among them. Of the 61 strains, three clinical and environmental NOVC serogroup strains had cholera toxin-producing genes, namely, the CTX phage (identified in previous outbreaks) and the complete Vibrio pathogenicity island 1. Phylogenetic analysis based on core genome analysis showed more than 10 distinct clusters and interrelatedness between clinical and environmental V. cholerae strains from Australia. Moreover, 30 (55%) NOVC strains had the cholix toxin gene (chxA) while only 11 (20%) strains had the mshA gene. In addition, 18 (34%) NOVC strains from Australia had the type three secretion system and discrete expression of type six secretion system genes. Interestingly, four NOVC strains from Australia and one NOVC strain from Indonesia had intSXT, a mobile genetic element", "token_count": 524, "char_count": 1849, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:04.303561", "source": { "split": "train_shard_00001", "doc_id": 4184 }, "chunk_id": "train_shard_00001_4184_0", "global_id": 11577 }, { "text": "Several strains were found to have beta-lactamase (blaCARB-9) and chloramphenicol acetyltransferase (catB9) genes. Our study suggests that Queensland waterways can harbor highly divergent V. cholerae strains and serve as a reservoir for various V. cholerae-associated virulence genes which could be shared among O1 and NOVC V. cholerae strains via mobile genetic elements or horizontal gene transfer. IMPORTANCE Australia has its own V. cholerae strains, both toxigenic and nontoxigenic, that are associated with cholera disease. This study aimed to characterize a collection of clinical and environmental NOVC strains from Australia to understand their virulence and antimicrobial resistance profile and to place strains from Australia in the genetic context of international strains. The findings from this study suggest the toxigenic V. cholerae strains in the Queensland River water system are of public health concern. Therefore, ongoing monitoring and genomic characterization of V. cholerae strains from the Queensland environment are important and would assist public health departments to track the source of cholera infection early and implement prevention strategies for future outbreaks. Understanding the genomics of V. cholerae could also inform the natural ecology and evolution of this bacterium in natural environments.\n\nClinical and Environmental Vibrio cholerae Non-O1, Non-O139 Strains from Australia Have Similar Virulence and Antimicrobial Resistance Gene Profiles.", "token_count": 368, "char_count": 1519, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5942, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:04.882956", "source": { "split": "train_shard_00001", "doc_id": 4184 }, "chunk_id": "train_shard_00001_4184_1", "global_id": 11578 }, { "text": "

Background

Although generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunocompromized patients. Infections are often caused by multidrug-resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients' quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities.

Results

Based on an assessment of > 800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico, and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis. The approach was validated on isolates representing skin commensals and on genomic mock communities with a sensitivity of < 10 copies/μL. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis populations. Additionally, the qPCR showed a high degree of variation in absolute abundance of S. epidermidis.

Conclusions

The Epidome method is designed for use on primary samples to obtain important information on S. epidermidis abundance and diversity beyond species-level to answer questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection", "token_count": 496, "char_count": 2161, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6014, "quality_score": 0.8007, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:05.537577", "source": { "split": "train_shard_00001", "doc_id": 4185 }, "chunk_id": "train_shard_00001_4185_0", "global_id": 11579 }, { "text": "Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in low-biomass samples such as skin samples.\n\nThe Epidome - a species-specific approach to assess the population structure and heterogeneity of Staphylococcus epidermidis colonization and infection.", "token_count": 70, "char_count": 321, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8974, "quality_score": 0.9487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:05.907361", "source": { "split": "train_shard_00001", "doc_id": 4185 }, "chunk_id": "train_shard_00001_4185_1", "global_id": 11580 }, { "text": "Removal of skim milk lactose by fermentation using free and immobilized Kluyveromyces marxianus cells.", "token_count": 30, "char_count": 102, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:06.270712", "source": { "split": "train_shard_00001", "doc_id": 4186 }, "chunk_id": "train_shard_00001_4186_0", "global_id": 11581 }, { "text": "Abstract

BackgroundPseudomonas aeruginosa is a ubiquitous environmental microorganism and also a common cause of infection. Its ability to survive in many different environments and persistently colonize humans is linked to its presence in biofilms formed on indwelling device surfaces. Biofilm promotes adhesion to, and survival on surfaces, protects from desiccation and the actions of antibiotics and disinfectants. ResultsWe examined the genetic basis for biofilm production on polystyrene at room (22°C) and body temperature (37°C) within 280 P. aeruginosa. 69% of isolates (n=193) produced more biofilm at 22°C, whilst those producing more biofilm at 37°C had reduced genetic diversity. Using GWAS and pan-GWAS, we found a number of accessory genes significantly associated with this phenotype. Many of these are present on a 165kb region containing genes for heavy metal resistance (arsenic, copper, mercury and cadmium) transcriptional regulators and methytransferases. We also discovered multiple core genome SNPs in the A-type flagellin gene and Type II secretion system gene xpsD. Analysis of biofilm production of isolates of the MDR ST111 and ST235 lineages on stainless-steel revealed several accessory genes associated with enhanced biofilm production. These include a putative translocase with homology to a Helicobacter pylori type IV secretion system protein, a TA system II toxin gene and the alginate biosynthesis gene algA, several transcriptional regulators and methytransferases as well as core SNPs in genes involved in quorum sensing and protein translocation. ConclusionsGWAS and pan-GWAS approaches have great potential as a first step in characterizing the genetic basis of novel bacterial phenotypes.

", "token_count": 489, "char_count": 1859, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6532, "quality_score": 0.8266, "entities": { "genes": [ "ST111", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:06.919122", "source": { "split": "train_shard_00001", "doc_id": 4187 }, "chunk_id": "train_shard_00001_4187_0", "global_id": 11582 }, { "text": "Biofilm Associated Genotypes of Multiple Antibiotic Resistant Pseudomonas Aeruginosa", "token_count": 25, "char_count": 84, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:07.277507", "source": { "split": "train_shard_00001", "doc_id": 4187 }, "chunk_id": "train_shard_00001_4187_1", "global_id": 11583 }, { "text": "Children with inflammatory bowel diseases (IBD) are particularly vulnerable to infection with Clostridioides difficile (CDI). IBD and IBD + CDI have overlapping symptoms but respond to distinctive treatments, highlighting the need for diagnostic biomarkers. Here, we studied pediatric patients with IBD and IBD + CDI, comparing longitudinal data on the gut microbiome, metabolome, and other measures. The microbiome is dysbiotic and heterogeneous in both disease states, but the metabolome reveals disease-specific patterns. The IBD group shows increased concentrations of markers of inflammation and tissue damage compared with healthy controls, and metabolic changes associate with susceptibility to CDI. In IBD + CDI, we detect both metabolites associated with inflammation/tissue damage and fermentation products produced by C. difficile. The most discriminating metabolite found is isocaproyltaurine, a covalent conjugate of a distinctive C. difficile fermentation product (isocaproate) and an amino acid associated with tissue damage (taurine), which may be useful as a joint marker of the two disease processes.\n\nMulti-omic Analysis of the Interaction between Clostridioides difficile Infection and Pediatric Inflammatory Bowel Disease.", "token_count": 307, "char_count": 1243, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6647, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:07.870648", "source": { "split": "train_shard_00001", "doc_id": 4188 }, "chunk_id": "train_shard_00001_4188_0", "global_id": 11584 }, { "text": "Jerusalem artichoke mashed tubers were fermented using single yeasts and a bacterium as well as mixed culture of microorganisms. Kluyveromyces fragilis, a yeast with an active inulinase, was used together with either a commercial distillery yeast, Saccharomyces cerevisiae, or the bacterium Zymomonas mobilis. After batch fermentation the best ethanol concentration of 0.48 g g-1 for the mixed population and 0.46 g g-1 for the single population can be obtained. The theoretical yield of the mixed cultures was 2-12% higher than for the single microorganism.\n\nUse of Zymomonas mobilis and Saccharomyces cerevisiae mixed with Kluyveromyces fragilis for improved ethanol production from Jerusalem artichoke tubers", "token_count": 187, "char_count": 711, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:08.335773", "source": { "split": "train_shard_00001", "doc_id": 4189 }, "chunk_id": "train_shard_00001_4189_0", "global_id": 11585 }, { "text": "

Objectives

The emergence of carbapenem-resistant Enterobacteriaceae has become a serious public-health threat. Here we report the complete genome sequence of a multidrug-resistant (MDR) Escherichia coli carrying blaNDM-5 and two copies of blaCTX-M-14 recovered from a bloodstream infection in China.

Methods

Whole-genome sequencing of E. coli strain 2D was performed both using Oxford Nanopore MinION and Illumina NovaSeq 6000 platforms. De novo hybrid assembly of short Illumina reads and long MinION reads was performed using Unicycler. In silico multilocus sequence typing (MLST), antimicrobial resistance genes and plasmid replicons were identified from the genome sequence. Core genome MLST (cgMLST) analysis between E. coli 2D and all ST354 E. coli strains retrieved from the NCBI GenBank database was performed using BacWGSTdb 2.0 server.

Results

The complete genome sequence of E. coli 2D consists of six contigs comprising 5 363 300 bp, including one chromosome and five plasmids, and was assigned to ST354. Six antimicrobial resistance genes were identified, including blaNDM-5 located in a 46 161-bp IncX3 plasmid and two copies of the blaCTX-M-14 gene located both in the chromosome and in a 96 499-bp IncB plasmid. The closest relative of E. coli 2D was another isolate recovered from Lebanon, which differed by 162 cgMLST loci.

Conclusion

This study reports the first genome sequence of a MDR E. coli carrying blaNDM-5 and two copies of blaCTX-M-14 in China", "token_count": 504, "char_count": 1566, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5806, "quality_score": 0.7903, "entities": { "genes": [ "ST354" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:09.011328", "source": { "split": "train_shard_00001", "doc_id": 4190 }, "chunk_id": "train_shard_00001_4190_0", "global_id": 11586 }, { "text": "These data may help to understand the antimicrobial resistance mechanisms and transmission dynamics of carbapenem-resistant Enterobacteriaceae in clinical settings.\n\nCoexistence of two blaCTX-M-14 genes in a blaNDM-5-carrying multidrug-resistant Escherichia coli strain recovered from a bloodstream infection in China.", "token_count": 96, "char_count": 340, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:09.432182", "source": { "split": "train_shard_00001", "doc_id": 4190 }, "chunk_id": "train_shard_00001_4190_1", "global_id": 11587 }, { "text": "Abstract

Background

A 60-year-old woman with acute myeloid leukemia developed fever and cough post induction chemotherapy. Meropenem and vancomycin were administered as empiric therapy. A bloodstream infection due to resistant E. meningoseptica was initially identified. Ceftazidime-avibactam and aztreonam (ATM) were next administered. Minocycline and trimethoprim/sulfamethoxazole (TMP/SMX) were added as the patient deteriorated and died ten days later.

Methods

MIC testing /disc diffusion assays were done according to CLSI guidelines. Whole genome sequencing (WGS) was performed, assembled, and annotated using PATRIC.org and compared to Institute Pasteur cgMLST instance of the BIGSdb database tool. Resistant genes and plasmids were identified by the Center for Genomic epidemiology.

Results

Core genome MLST and average nucleotide identity of 99.46% revealed the organism as E. anophelis, not E. meningoseptica. The WGS assembly resulted in 118 contigs with a chromosome of 4,110,726 bp. Plasmids were not identified. Resistance genes blaB11, blaGOB-13 (a metallo beta-lactamase) and blaCME-1 were detected. E. anophelis was resistant to multiple drug classes including aminoglycosides, vancomycin, cephalosporins, and carbapenems. Mechanism based susceptibility testing using double-disc diffusion assays demonstrated susceptibility to cefiderocol (MIC 1 µg/ml), minocycline, TMP/SMX, linezolid, and modestly wider zones of inhibition with the addition of ATM. Susceptibility results are shown in Table 1. Antimicrobial susceptibility testing using various BLIs and combinations with Aztreonam

Conclusion

This is one of the first reports describing E. anophelis in immunocompromised hosts", "token_count": 517, "char_count": 1733, "word_count": 225, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:10.069166", "source": { "split": "train_shard_00001", "doc_id": 4191 }, "chunk_id": "train_shard_00001_4191_0", "global_id": 11588 }, { "text": "More thorough testing methods are needed for distinguishing between species in the Elizabethkingia genus in hospital settings as there is concern that this may represent a novel opportunistic infection. Per CDC, E. anophelis outbreaks have occurred in three Midwestern states in 2016. Vigilance is warranted to the role of this pathogen in immunocompromised hosts.

Disclosures

Robert A. Bonomo, MD, Entasis, Merck, Venatorx (Research Grant or Support)\n\n1444. Characterization of a Novel Pathogen in Immunocompromised Patients: Elizabethkingia Anopheles", "token_count": 149, "char_count": 561, "word_count": 77, "semantic_coherence": 1, "information_density": 0.8182, "quality_score": 0.9091, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:10.508851", "source": { "split": "train_shard_00001", "doc_id": 4191 }, "chunk_id": "train_shard_00001_4191_1", "global_id": 11589 }, { "text": "Eight strains of Kluyveromyces marxianus were screened, and all of them were found to ferment the aldopentose d-xylose directly to ethanol under aerobic conditions. One of these strains, K. marxianus SUB-80-S, was grown in a medium containing 20 g of d-xylose per liter, and the following results were obtained: maximum ethanol concentration, 5.6 g/liter; ethanol yield, 0.28 g of ethanol per g of d-xylose (55% of theoretical); maximum specific growth rate, 0.12 h; 100% d-xylose utilization was completed in 48 h.\n\nDirect Fermentation of d-Xylose to Ethanol by Kluyveromyces marxianus Strains.", "token_count": 198, "char_count": 595, "word_count": 91, "semantic_coherence": 1, "information_density": 0.6703, "quality_score": 0.8352, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:10.961284", "source": { "split": "train_shard_00001", "doc_id": 4192 }, "chunk_id": "train_shard_00001_4192_0", "global_id": 11590 }, { "text": "We present a novel method for taxon selection, the aim being to minimize problems arising from highly recombinant species such as Helicobacter pylori. Helicobacter pylori has accompanied modern-human migration out of Africa and is marked by a phylogeographic strain distribution, which has been exploited to add an extra layer of information about human migrations to that obtained from human sources. However, H. pylori's genome has high sequence heterogeneity combined with a very high rate of recombination, causing major allelic diversification across strains. On the other hand, recombination events that have become preserved in sub-populations are a useful source of phylogenetic information. This creates a potential problem in selecting representative strains for particular genetic or phylogeographic clusters and generally ameliorating the impact on analyses of extensive low-level recombination. To address this issue, we perform multiple population structure-based analyses on core genomes to select exemplar strains, called 'quintessents', which exhibit limited recombination. In essence, quintessent strains are representative of their specific phylogenetic clades and can be used to refine the current MLST concatenation-based population structure classification system. The use of quintessents reduces the noise due to local recombination events, while preserving recombination events that have become fixed in sub-populations. We illustrate the method with an analysis of core genome concatenations from 185 H. pylori strains, which reveals a recent speciation event resulting from the recombination of strains from phylogeographic clade hpSahul, carried by Aboriginal Australians, and hpEurope, carried by some of the people who arrived in Australia over the past 200 years. The signal is much clearer when based on quintessent strains, but absent from the analysis based on MLST concatenations.\n\nA novel taxon selection method, aimed at minimizing recombination, clarifies the discovery of a new sub-population of Helicobacter pylori from Australia.", "token_count": 500, "char_count": 2104, "word_count": 290, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:11.610257", "source": { "split": "train_shard_00001", "doc_id": 4193 }, "chunk_id": "train_shard_00001_4193_0", "global_id": 11591 }, { "text": "Small millets, also known as nutri-cereals, are smart foods that are expected to dominate food industries and diets to achieve nutritional security. Nutri-cereals are climate resilient and nutritious. Small millet-based foods are becoming popular in markets and are preferred for patients with celiac and diabetes. These crops once ruled as food and fodder but were pushed out of mainstream cultivation with shifts in dietary habits to staple crops during the green revolution. Nevertheless, small millets are rich in micronutrients and essential amino acids for regulatory activities. Hence, international and national organizations have recently aimed to restore these lost crops for their desirable traits. The major goal in reviving these crops is to boost the immune system of the upcoming generations to tackle emerging pandemics and disease infestations in crops. Earlier periods of civilization consumed these crops, which had a greater significance in ethnobotanical values. Along with nutrition, these crops also possess therapeutic traits and have shown vast medicinal use in tribal communities for the treatment of diseases like cancer, cardiovascular disease, and gastrointestinal issues. This review highlights the significance of small millets, their values in cultural heritage, and their prospects. Furthermore, this review dissects the nutritional and therapeutic traits of small millets for developing sustainable diets in near future.\n\nRevitalization of small millets for nutritional and food security by advanced genetics and genomics approaches.", "token_count": 322, "char_count": 1567, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6339, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:12.187280", "source": { "split": "train_shard_00001", "doc_id": 4194 }, "chunk_id": "train_shard_00001_4194_0", "global_id": 11592 }, { "text": "Yeast single-cell protein and yeast extract, in particular, are two products which have many feed, food, pharmaceutical, and biotechnological applications. However, many of these applications are limited by their market price. Specifically, the yeast extract requirements for culture media are one of the major technical hurdles to be overcome for the development of low-cost fermentation routes for several top value chemicals in a biorefinery framework. A potential biotechnical solution is the production of yeast biomass from the hemicellulosic fraction stream. The growth of three pentose-assimilating yeast cell factories, Debaryomyces hansenii, Kluyveromyces marxianus, and Pichia stipitis was compared using non-detoxified brewery's spent grains hemicellulosic hydrolyzate supplemented with mineral nutrients. The yeasts exhibited different specific growth rates, biomass productivities, and yields being D. hansenii as the yeast species that presented the best performance, assimilating all sugars and noteworthy consuming most of the hydrolyzate inhibitors. Under optimized conditions, D. hansenii displayed a maximum specific growth rate, biomass yield, and productivity of 0.34 h(-1), 0.61 g g(-1), and 0.56 g l(-1) h(-1), respectively. The nutritional profile of D. hansenii was thoroughly evaluated, and it compares favorably to others reported in literature. It contains considerable amounts of some essential amino acids and a high ratio of unsaturated over saturated fatty acids.\n\nYeast biomass production in brewery's spent grains hemicellulosic hydrolyzate.", "token_count": 395, "char_count": 1576, "word_count": 215, "semantic_coherence": 1, "information_density": 0.693, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:12.803739", "source": { "split": "train_shard_00001", "doc_id": 4195 }, "chunk_id": "train_shard_00001_4195_0", "global_id": 11593 }, { "text": "In this study, multidrug-resistant (MDR) Escherichia coli isolates from retail food and humans assigned into similar Multilocus Sequence Types (MLST) were analyzed using whole genome sequencing (WGS). In silico analysis of assembled sequences revealed the existence of multiple resistance genes among the examined E. coli isolates. Of the six CTX-M-producing isolates from retail food, blaCTX-M-14 was the prevalent variant identified (83.3%, 5/6). Two plasmid-mediated fosfomycin resistance genes, fosA3, and fosA4, were detected from retail food isolates (one each from chicken and beef), where fosA4 was identified in the chicken isolate 82CH that also carried the colistin resistance gene mcr-1. The blaCTX-M-14 and fosA genes in retail food isolates were located adjacent to insertion sequences ISEcp1 and IS26, respectively. Sequence analysis of the reconstructed mcr-1 plasmid (p82CH) showed 96-97% identity to mcr-1-carrying IncI2 plasmids previously identified in human and food E. coli isolates from Egypt. Hierarchical clustering of core genome MLST (HierCC) revealed clustering of chicken isolate 82CH, co-harboring mcr-1 and fosA4 genes, with a chicken E. coli isolate from China at the HC200 level (≤200 core genome allelic differences). As E", "token_count": 483, "char_count": 1407, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6243, "quality_score": 0.8122, "entities": { "genes": [ "HC200" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:13.454043", "source": { "split": "train_shard_00001", "doc_id": 4196 }, "chunk_id": "train_shard_00001_4196_0", "global_id": 11594 }, { "text": "coli co-harboring mcr-1 and fosA4 genes has only been recently reported, this study shows rapid spread of this genotype that shares similar genetic structures with regional and international E. coli lineages originating from both humans and food animals. Adopting WGS-based surveillance system is warranted to facilitate monitoring the international spread of MDR pathogens.\n\nEmergence of Multidrug-Resistant Escherichia coli Producing CTX-M, MCR-1, and FosA in Retail Food From Egypt.", "token_count": 150, "char_count": 517, "word_count": 68, "semantic_coherence": 1, "information_density": 0.8235, "quality_score": 0.9118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:13.885607", "source": { "split": "train_shard_00001", "doc_id": 4196 }, "chunk_id": "train_shard_00001_4196_1", "global_id": 11595 }, { "text": "Prokaryote genome evolution is characterized by the frequent gain of genes through horizontal gene transfer (HGT). For a gene, being horizontally transferred can represent a strong change in its genomic and physiological context. If the codon usage of a transferred gene deviates from that of the receiving organism, the fitness benefits it provides can be reduced due to a mismatch with the expression machinery. Consequently, transferred genes with a deviating codon usage can be selected against or elicit evolutionary responses that enhance their integration. In this study, a comparative genomics approach was used to investigate evolutionary responses after the horizontal transfer of genes with diverse degrees of codon usage mismatch in Pseudomonas aeruginosa . Selection on codon usage of genes acquired through HGT was observed, with the overall codon usage converging towards that of the core genome over evolutionary time. This pattern seemed to be mainly driven by selective retention of transferred genes with an initial codon usage similar to that of the core genes. Gene amelioration, through the accumulation of synonymous mutations after HGT, did not seem to systematically affect transferred genes. Additionally, variation in the copy number of tRNA genes was often associated with the acquisition of genes for which the observed variation could enhance their expression. This provides evidence that compensatory evolution might be an important mechanism for the integration of horizontally transferred genes.\n\nEvolutionary responses to codon usage of horizontally transferred genes inPseudomonas aeruginosa", "token_count": 329, "char_count": 1633, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5378, "quality_score": 0.7689, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:14.451412", "source": { "split": "train_shard_00001", "doc_id": 4197 }, "chunk_id": "train_shard_00001_4197_0", "global_id": 11596 }, { "text": "Mycobacterium chelonae is a rapidly growing nontuberculous mycobacterium that is a common cause of nosocomial infections. Here we describe investigation of a possible nosocomial transmission of M. chelonae at the Hospital of the University of Pennsylvania (HUP). M. chelonae strains with similar high-level antibiotic resistance patterns were isolated from two patients who developed post-operative infections at HUP in 2017, suggesting a possible point source infection. The isolates, along with other clinical isolates from other patients, were sequenced using the Illumina and Oxford Nanopore technologies. The resulting short and long reads were hybrid assembled into draft genomes. The genomes were compared by quantifying single nucleotide variants in the core genome and assessed using a control dataset for identity. We show that that all M. chelonae isolates tested were highly divergent, consistent with environmental acquisition. Additionally, antibiotic resistance genes were predicted for our isolates, and several single nucleotide variants identified with the potential to modulated drug susceptibility, providing candidate resistance mechanisms.\n\nInvestigating hospitalMycobacterium chelonaeinfection using whole genome sequencing and hybrid assembly", "token_count": 281, "char_count": 1273, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6686, "quality_score": 0.8343, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:15.008036", "source": { "split": "train_shard_00001", "doc_id": 4198 }, "chunk_id": "train_shard_00001_4198_0", "global_id": 11597 }, { "text": "

Background

Neonatal Staphylococcus aureus (S. aureus) bacteremia is an important cause of morbidity and mortality. In this study, we examined whether methicillin-susceptible S. aureus (MSSA) transmission and genetic makeup contribute to the occurrence of neonatal S. aureus bacteremia.

Methods

A retrospective, single-centre study was performed. All patients were included who suffered from S. aureus bacteremia in the neonatal intensive care unit (NICU), Erasmus MC-Sophia, Rotterdam, the Netherlands, between January 2011 and November 2017. Whole-genome sequencing (WGS) was used to characterize the S. aureus isolates, as was also done in comparison to reference genomes. Transmission was considered likely in case of genetically indistinguishable S. aureus isolates.

Results

Excluding coagulase-negative staphylococci (CoNS), S. aureus was the most common cause of neonatal bacteremia. Twelve percent (n = 112) of all 926 positive blood cultures from neonates grew S. aureus. Based on core genome multilocus sequence typing (cgMLST), 12 clusters of genetically indistinguishable MSSA isolates were found, containing 33 isolates in total (2-4 isolates per cluster). In seven of these clusters, at least two of the identified MSSA isolates were collected within a time period of one month. Six virulence genes were present in 98-100% of all MSSA isolates. In comparison to S. aureus reference genomes, toxin genes encoding staphylococcal enterotoxin A (sea) and toxic shock syndrome toxin 1 (tsst-1) were present more often in the genomes of bacteremia isolates.

Conclusion

Transmission of MSSA is a contributing factor to the occurrence of S. aureus bacteremia in neonates. Sea and tsst-1 might play a role in neonatal S", "token_count": 530, "char_count": 1752, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:15.661093", "source": { "split": "train_shard_00001", "doc_id": 4199 }, "chunk_id": "train_shard_00001_4199_0", "global_id": 11598 }, { "text": "aureus bacteremia.\n\nWhole-genome sequencing to explore nosocomial transmission and virulence in neonatal methicillin-susceptible Staphylococcus aureus bacteremia.", "token_count": 52, "char_count": 162, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:16.024390", "source": { "split": "train_shard_00001", "doc_id": 4199 }, "chunk_id": "train_shard_00001_4199_1", "global_id": 11599 }, { "text": "Bacillus anthracis plasmids pXO1 and pXO2 carry the main virulence factors responsible for anthrax. However, the extent of copy number variation within the species and how the plasmids are related to pXO1/pXO2-like plasmids in other species of the Bacillus cereus sensu lato group remain unclear. To gain new insights into these issues, we sequenced 412 B. anthracis strains representing the total phylogenetic and ecological diversity of the species. Our results revealed that B. anthracis genomes carried, on average, 3.86 and 2.29 copies of pXO1 and pXO2, respectively, and also revealed a positive linear correlation between the copy numbers of pXO1 and pXO2. No correlation between the plasmid copy number and the phylogenetic relatedness of the strains was observed. However, genomes of strains isolated from animal tissues generally maintained a higher plasmid copy number than genomes of strains from environmental sources (P < 0.05 [Welch two-sample t test]). Comparisons against B. cereus genomes carrying complete or partial pXO1-like and pXO2-like plasmids showed that the plasmid-based phylogeny recapitulated that of the main chromosome, indicating limited plasmid horizontal transfer between or within these species. Comparisons of gene content revealed a closed pXO1 and pXO2 pangenome; e.g., plasmids encode <8 unique genes, on average, and a single large fragment deletion of pXO1 in one B. anthracis strain (2000031682) was detected. Collectively, our results provide a more complete view of the genomic diversity of B. anthracis plasmids, their copy number variation, and the virulence potential of other Bacillus species carrying pXO1/pXO2-like plasmids. IMPORTANCE Bacillus anthracis microorganisms are of historical and epidemiological importance and are among the most homogenous bacterial groups known, even though the B", "token_count": 520, "char_count": 1873, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5704, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:17.433546", "source": { "split": "train_shard_00001", "doc_id": 4200 }, "chunk_id": "train_shard_00001_4200_0", "global_id": 11600 }, { "text": "anthracis genome is rich in mobile elements. Mobile elements can trigger the diversification of lineages; therefore, characterizing the extent of genomic variation in a large collection of strains is critical for a complete understanding of the diversity and evolution of the species. Here, we sequenced a large collection of B. anthracis strains (>400) that were recovered from human, animal, and environmental sources around the world. Our results confirmed the remarkable stability of gene content and synteny of the anthrax plasmids and revealed no signal of plasmid exchange between B. anthracis and pathogenic B. cereus isolates but rather predominantly vertical descent. These findings advance our understanding of the biology and pathogenomic evolution of B. anthracis and its plasmids.\n\nGenomic Characterization and Copy Number Variation of Bacillus anthracis Plasmids pXO1 and pXO2 in a Historical Collection of 412 Strains.", "token_count": 218, "char_count": 941, "word_count": 137, "semantic_coherence": 1, "information_density": 0.635, "quality_score": 0.8175, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:17.902104", "source": { "split": "train_shard_00001", "doc_id": 4200 }, "chunk_id": "train_shard_00001_4200_1", "global_id": 11601 }, { "text": "Klebsiella aerogenes, is a Gram-negative bacterium, which was previously known as Enterobacter aerogenes. It is present in all environments such as water, soil, air and hospitals; and is an opportunistic pathogen that causes several types of infections. As compared to other clinically important pathogens included in the ESKAPE category (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species), the pangenome and population structure of Klebsiella aerogenes is still poorly understood. For the present study, the bacterial sample was isolated from agricultural soils of Haryana, India. With an aim to identify the occurrence of multi-drug resistance genes in the agricultural field soil bacterial isolate, whole genome sequencing (WGS) of the bacteria was performed; and the antibiotic resistance causing genes, along with the genes responsible for other major functions of the cell; and the different Single Nuceotide Polymorphisms (SNPs) and Insertions and deletions (InDels) were identified. The data presented in this manuscript can be reused by researchers as a reference for determining the antibiotic resistance genes that could be present in different bacterial isolates, and it would also help in determination of functions of various other genes present in other genomes of Klebsiella species.\n\nWhole genome sequencing data of Klebsiella aerogenes isolated from agricultural soil of Haryana, India.", "token_count": 394, "char_count": 1538, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6048, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:18.889775", "source": { "split": "train_shard_00001", "doc_id": 4201 }, "chunk_id": "train_shard_00001_4201_0", "global_id": 11602 }, { "text": "The invention relates to a DNA sequence comprising the triosephosphate isomerase gene including its regulatory sequences, to a DNA sequence, which is an active promoter, to expression and secretion systems containing said promoter sequence and to the use thereof and a method for producing proteins.\n\nDNA SEQUENCE FROM KLUYVEROMYCES MARXIANUS COMPRISING REGULATORY REGIONS FOR EXPRESSING PROTEINS", "token_count": 102, "char_count": 396, "word_count": 56, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:19.275656", "source": { "split": "train_shard_00001", "doc_id": 4202 }, "chunk_id": "train_shard_00001_4202_0", "global_id": 11603 }, { "text": "The OsTHION family represents a class of cysteine-rich signal peptides widely recognized for their significant roles in plant disease resistance and immunity. While members of this family are known to be induced under various biotic and abiotic stresses, their responses to environmental stressors beyond disease resistance remain underexplored. This study investigates the evolution, expression patterns, and functional roles of the OsTHION gene family in rice (Oryza sativa) under diverse stress conditions. Using sequence data from the Phytozome database, we identified 44 OsTHION family members and classified them into four groups based on phylogenetic analysis. Cis-acting element analysis revealed that the promoter regions of OsTHION genes are enriched with regulatory elements associated with light response, hormone signaling, plant growth, and stress responses. The OsTHION genes exhibit complex organ-specific expression patterns, with OsTHION30 and OsTHION36 showing ubiquitous expression, while other members are highly expressed in specific tissues or developmental stages. Under drought, salt, and low-temperature stress, OsTHION genes undergo significant expression changes, underscoring their critical role in plant adaptation to environmental challenges. Notably, OsTHION15 was markedly upregulated under drought stress, and the Osthion15 mutant displayed heightened sensitivity to drought and ABA stress, confirming its pivotal role in stress resistance. RNA sequencing analysis identified many differentially expressed genes (DEGs), primarily enriched in pathways related to ribosomal function and plant hormone signaling, suggesting that OsTHION15 may regulate stress responses through multiple mechanisms. In summary, this study advances our understanding of the OsTHION gene family and highlights its intricate involvement in regulating rice growth, development, and environmental stress responses. These findings offer valuable insights and technical support for crop improvement, with potential applications in enhancing environmental adaptability and yield stability in crops.", "token_count": 515, "char_count": 2201, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6282, "quality_score": 0.8141, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:19.927874", "source": { "split": "train_shard_00001", "doc_id": 4203 }, "chunk_id": "train_shard_00001_4203_0", "global_id": 11604 }, { "text": "Genome-Wide Identification and Expression Analysis of Thionin Family in Rice (<i>Oryza sativa</i>) and Functional Characterization of <i>OsTHION15</i> in Drought Stress and ABA Stress.", "token_count": 73, "char_count": 208, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8261, "quality_score": 0.913, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:20.333815", "source": { "split": "train_shard_00001", "doc_id": 4203 }, "chunk_id": "train_shard_00001_4203_1", "global_id": 11605 }, { "text": "In this study, identification of 207 Candida isolates, previously isolated from mastitic bovine quarter milk samples at the level of genus, was made using API 20 C AUX system. The most frequently isolated species were Candida krusei (34.8%), followed by Candida rugosa (16.4%), Candida kefyr (12.6%), Candida albicans (10.1%), and Candida tropicalis (9.2%). Less common isolates were Candida zeylanoides (5.8%), Candida parapsilosis (4.3%), Candida guilliermondii (3.4%), Candida famata (1.9%), and Candida glabrata (1.5%). Additionally, in vitro hemolytic activity of all Candida strains were also examined in the present study. C. krusei (72 isolates), C. kefyr (26), C. albicans (21), C. tropicalis (19), C. zeylanoides (12), and C. glabrata (3) demonstrated both alpha and beta hemolysis at 48-h postinoculation. Only alpha hemolysis was detected in C. rugosa (34), C. guilliermondii (7), and C. famata (4), while C. parapsilosis (9) did not show any hemolytic activity after incubation for 72 h. Statistically significant difference (P < 0.001) was determined between the beta-hemolytic activities of Candida strains. The hemolytic activities of C. zeylanoides, C. albicans and C. kefyr were higher than other strains. This is the first study to describe variable hemolysis types exhibited by different Candida strains isolated from bovine mastitic milk in Turkey.\n\nIdentification of Candida species isolated from bovine mastitic milk and their in vitro hemolytic activity in Western Turkey.", "token_count": 470, "char_count": 1496, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5727, "quality_score": 0.7864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:20.985126", "source": { "split": "train_shard_00001", "doc_id": 4204 }, "chunk_id": "train_shard_00001_4204_0", "global_id": 11606 }, { "text": "Invasive alien species often have reduced genetic diversity and must adapt to new environments. Given the success of many invasions, this is sometimes called the genetic paradox of invasion. Phytophthora ramorum is invasive, limited to asexual reproduction within four lineages, and presumed clonal. It is responsible for sudden oak death in the United States, sudden larch death in Europe, and ramorum blight in North America and Europe. We sequenced the genomes of 107 isolates to determine how this pathogen can overcome the invasion paradox. Mitotic recombination (MR) associated with transposons and low gene density has generated runs of homozygosity (ROH) affecting 2,698 genes, resulting in novel genotypic diversity within the lineages. One ROH enriched in effectors was fixed in the NA1 lineage. An independent ROH affected the same scaffold in the EU1 lineage, suggesting an MR hot spot and a selection target. Differences in host infection between EU1 isolates with and without the ROH suggest that they may differ in aggressiveness. Non-core regions (not shared by all lineages) had signatures of accelerated evolution and were enriched in putative pathogenicity genes and transposons. There was a striking pattern of gene loss, including all effectors, in the non-core EU2 genome. Positive selection was observed in 8.0% of RxLR and 18.8% of Crinkler effector genes compared with 0.9% of the core eukaryotic gene set. We conclude that the P. ramorum lineages are diverging via a rapidly evolving non-core genome and that the invasive asexual lineages are not clonal, but display genotypic diversity caused by MR.IMPORTANCE Alien species are often successful invaders in new environments, despite the introduction of a few isolates with a reduced genetic pool. This is called the genetic paradox of invasion. We found two mechanisms by which the invasive forest pathogen causing sudden oak and sudden larch death can evolve", "token_count": 478, "char_count": 1957, "word_count": 300, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [ "EU1", "NA1", "EU2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:21.674820", "source": { "split": "train_shard_00001", "doc_id": 4205 }, "chunk_id": "train_shard_00001_4205_0", "global_id": 11607 }, { "text": "Extensive mitotic recombination producing runs of homozygosity generates genotypic diversity even in the absence of sexual reproduction, and rapid turnover of genes in the non-core, or nonessential portion of genome not shared by all isolates, allows pathogenicity genes to evolve rapidly or be eliminated while retaining essential genes. Mitotic recombination events occur in genomic hot spots, resulting in similar ROH patterns in different isolates or groups; one ROH, independently generated in two different groups, was enriched in pathogenicity genes and may be a target for selection. This provides important insights into the evolution of invasive alien pathogens and their potential for adaptation and future persistence.\n\nMitotic Recombination and Rapid Genome Evolution in the Invasive Forest Pathogen Phytophthora ramorum.", "token_count": 189, "char_count": 841, "word_count": 118, "semantic_coherence": 1, "information_density": 0.7119, "quality_score": 0.8559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:22.137385", "source": { "split": "train_shard_00001", "doc_id": 4205 }, "chunk_id": "train_shard_00001_4205_1", "global_id": 11608 }, { "text": "

Objectives

To analyse the strains collected during a 1-year survey of ceftazidime-avibactam-resistant KPC-producing Klebsiella pneumoniae, in order to investigate the molecular mechanisms potentially responsible for their resistant phenotype.

Methods

Clinical KPC-producing K. pneumoniae isolates were collected from 31 patients in six different hospitals in Rome. For eight of the patients, an additional strain grown before the start of treatment was also available, bringing the total of isolates studied to 39. Antimicrobial susceptibility was determined by automated system, broth microdiluition and E-test as appropriate. In silico analysis of acquired resistance genes was achieved by whole-genome sequencing, while multilocus sequence typing and core genome multilocus sequence typing were employed for molecular typing. Mutations associated with ceftazidime-avibactam resistance were identified by Sanger sequencing of the blaKPC gene. Possible mutations in OmpK35 and OmpK36 outer membrane proteins were also investigated.

Results

Molecular analyses highlighted the circulation of the ST512, 101 and 307 high-risk clones; 26 of the 31 patients carried a mutated KPC variant, five had a wild-type KPC-3. Among the KPC variants detected, 11 were different mutations within the blaKPC-3 gene, four of which were novel mutational changes.

Conclusions

Different mutations including single amino-acid substitutions, insertions or deletions within the blaKPC gene were found in 26/31 ceftazidime-avibactam-resistant KPC-producing K. pneumoniae strains belonging to high-risk clones circulating in Italy. Of note, in 14/31 cases the isolates displayed resistance to both ceftazidime-avibactam and carbapenems, raising concerns for the possible selection of a multidrug-resistant phenotype.", "token_count": 513, "char_count": 1853, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8254, "entities": { "genes": [ "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:22.770631", "source": { "split": "train_shard_00001", "doc_id": 4206 }, "chunk_id": "train_shard_00001_4206_0", "global_id": 11609 }, { "text": "Molecular analysis of clinical isolates of ceftazidime-avibactam-resistant Klebsiella pneumoniae.", "token_count": 31, "char_count": 97, "word_count": 9, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:23.136608", "source": { "split": "train_shard_00001", "doc_id": 4206 }, "chunk_id": "train_shard_00001_4206_1", "global_id": 11610 }, { "text": "The host-specific Salmonella serovar S. Pullorum (SP) modulates the chicken immune response to a Th2-biased response associated with persistent infection. This is different from the Th1-biased immune response induced by the genetically close serovar, S. Enteritidis (SE). Based on core genome differences between SP and SE, we used three complementary bioinformatics approaches to identify SP genes, which may be important for stimulation of the immune response. Defined mutants were constructed in selected genes, and the infection potential and ability of mutants to stimulate cytokine production in avian derived HD11 macrophages were determined. Deletion of large genomic regions unique to SP did not change infection potential nor immune stimulation significantly. Mutants in genes with conserved single nucleotide polymorphisms (SNPs) between the two serovars in the region 100 bp upstream of the start codon (conserved upstream SNPs [CuSNPs]) such as sseE, osmB, tolQ, a putative immune antigen, and a putative persistent infection factor, exhibited differences in induction of inflammatory cytokines compared to wild-type SP, suggesting a possible role of these CuSNPs in immune regulation. Single nucleotide SP mutants correcting for the CuSNP difference were constructed in the upstream region of sifA and pipA. The SNP corrected pipA mutant expressed pipA at a higher level than the wild-type SP strain, and the mutant differentially caused upregulation of proinflammatory cytokines. It suggests that this CuSNP is important for the suppression of proinflammatory responses. In conclusion, this study has identified putative immune stimulating factors of relevance to the difference in infection dynamics between SP and SE in avian macrophages. IMPORTANCE Salmonella Pullorum is host specific to avian species, where it causes life-threatening infection in young birds", "token_count": 500, "char_count": 1949, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6052, "quality_score": 0.8026, "entities": { "genes": [ "HD11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:23.784861", "source": { "split": "train_shard_00001", "doc_id": 4207 }, "chunk_id": "train_shard_00001_4207_0", "global_id": 11611 }, { "text": "It is unknown why it is host restricted and causes systemic disease, rather than gastroenteritis normally seen with Salmonella. In the present study, we identified genes and single nucleotide polymorphisms (SNPs; relative to the broad-host-range type Salmonella Enteritidis), which affected survival and immune induction in macrophages from hens suggesting a role in development of the host specific infection. Further studies of such genes may enable understanding of which genetic factors determine the development of host specific infection by S. Pullorum. In this study, we developed an in silico approach to predict candidate genes and SNPs for development of the host-specific infection and the specific induction of immunity associated with this infection. This study flow can be used in similar studies in other clades of bacteria.\n\nIdentification of Salmonella Pullorum Factors Affecting Immune Reaction in Macrophages from the Avian Host.", "token_count": 218, "char_count": 969, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6547, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:24.247814", "source": { "split": "train_shard_00001", "doc_id": 4207 }, "chunk_id": "train_shard_00001_4207_1", "global_id": 11612 }, { "text": "UDP-galactose 4-epimerase from Kluyveromyces fragilis is a stable homodimer of 75 kDa/subunit with non-covalently bound NAD acting as cofactor. Partial proteolysis with trypsin in the presence of 5'-UMP, a strong competitive inhibitor, led to a degraded product which was purified. Results from SDS-PAGE, size-exclusion (SE)-HPLC and ultracentrifugation indicated its monomeric status and size between 43 and 45 kDa. 'Two-step assay' with UDP-glucose dehydrogenase as coupling enzyme in the presence of NAD ensured epimerase activity of the monomer. The possibility of transient dimerization of monomeric epimerase during catalysis was excluded by SE-HPLC in the presence of excess substrate and NAD. This truncated enzyme retained catalytic site related properties like Km for UDP-galactose, 'NADH-like coenzyme fluorescence' and 'reductive inhibition' similar to its dimeric counterpart. Reversible reactivation of the monomer was achieved up to 95% within 3 min from 8 M urea induced unfolded state, indicating that the catalytic site could form independent of its quaternary structure. Equilibrium unfolding between 0 and 8 M urea indicated that the monomer was less stable compared to the dimer. Chemical modification of amino acids and reconstitution with etheno-NAD suggested that the architecture around the catalytic site of the monomer was conserved. Specific modification reagents further confirmed that the cysteine residues required for catalysis and coenzyme fluorophore reside exclusively on a single subunit negating a 'subunit sharing model' of its catalytic site.\n\nUDP-galactose 4-epimerase from Kluyveromyces fragilis: existence of subunit independent functional site.", "token_count": 458, "char_count": 1687, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:24.884755", "source": { "split": "train_shard_00001", "doc_id": 4208 }, "chunk_id": "train_shard_00001_4208_0", "global_id": 11613 }, { "text": "

ABSTRACT

Although the adaptation strategies of bacteria to specific environmental conditions are widely reported, fewer studies have addressed how microbe with cosmopolitan distribution adapted to diverse habitats. Exiguobacterium is a versatile genus whose members have been commonly found in great variety of habitats. To understand the mechanism behind the universally of Exiguobacterium, we isolated 103 strains from diverse environments, and performed large-scale metabolic and adaptive ability tests. We found that the capacities of survival in a wide range of temperature, salinity and pH are common for most Exiguobacterium members. According to the core genome based phylogeny and ANI analysis, 26 putative species including 13 putative new ones were identified and two genetic groups were classified as Group I and II. Comparative genomic analysis revealed that Exiguobacterium members can not only utilize a variety of complex polysaccharides and proteins that are ubiquitous in both terrestrial and marine environments, but also have a number of chaperonins and transporters which could support them to survive in different extreme environments. In addition, we found that the species from Group I can be found in more diverse environments with larger genome size compared to those of Group II. Twenty-five transporter families involved in transport of organic or inorganic substrates and environments stresses resistance were predicted to be enriched in Group I strains. This study provided the comprehensive insight into general genetic basis of the cosmopolitan distribution of a bacteria genus and deciphered putative determinants behind the ecological difference of different groups belonging to the same genus.

IMPORTANCE

The wide distribution characteristics make Exiguobacterium a valuable model for studying adaptive strategy of bacteria adapted to multiple habitats. In this study, we found that comprehensive capacity of diverse polysaccharides utilization and environmental stress resistance is the important basis for survival, and selective expansion of transporters is an evolution and adaptation strategy for extensive distribution. Our findings are significant for understanding the adaptation and evolution mechanisms of cosmopolitan bacteria and explaining the vital genomic traits that facilitate niches adaptation.\n\nComparative genomics of Exiguobacterium reveals what makes a cosmopolitan bacterium", "token_count": 497, "char_count": 2457, "word_count": 341, "semantic_coherence": 1, "information_density": 0.5718, "quality_score": 0.7859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:25.540422", "source": { "split": "train_shard_00001", "doc_id": 4209 }, "chunk_id": "train_shard_00001_4209_0", "global_id": 11614 }, { "text": "

Introduction

Tuberculosis (TB) is the leading cause of morbidity and mortality globally, responsible for an estimated annual 10.0 million new cases and 1.3 million deaths among infectious diseases with Africa contributing a quarter of these cases in 2019. Classification of Mycobacterium tuberculosis (MTB) strains is important in understanding their geographical predominance and pathogenicity. Different studies have gone ahead to classify MTB using different methods. Some of these include; RFLP, spoligotyping, MIRU-VNTR and SNP set based phylogeny. The SNP set based classification has been found to be in concordance with the region of difference (RD) analysis of MTB complex classification system. In Uganda, the most common cause of pulmonary tuberculosis (PTB) is Uganda genotype of MTB and accounts for up to 70 % of isolates.

Methods

Sequenced MTB genome samples were retrieved from NCBI and others from local sequencing projects. The genomes were subjected to snippy (a rapid haploid variant calling and core genome alignment) to call variants and annotate them. Outputs from snippy were used to classify the isolates into Uganda genotypes and Non Ugandan genotypes based on 62 SNP set. The Ugandan genotype isolates were later subjected to 413 SNP set and then to a pan genome wide association analysis.

Results

6 Uganda genotype isolates were found not to classify as either Uganda I or II genotypes based on the 62 SNP set. Using the 413 SNP set, the 6 Uganda genotype isolates were found to have only one SNP out of the 7 SNPs that classify the Uganda I genotypes. They were also found to have both missense and frameshift mutations within the ctpH gene whereas the rest of Uganda I that had a mutation within this gene, was a missense.

Conclusion

Among the Uganda genotypes genomes, Uganda I genomes are unstable", "token_count": 524, "char_count": 1865, "word_count": 294, "semantic_coherence": 1, "information_density": 0.5646, "quality_score": 0.7823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:26.196962", "source": { "split": "train_shard_00001", "doc_id": 4210 }, "chunk_id": "train_shard_00001_4210_0", "global_id": 11615 }, { "text": "We used publicly available datasets to perform analysis like mapping, variant calling, mixed infection, pan-genome analysis to investigate and compare evolution of the Ugandan genotype.\n\nComparative genomic analysis ofMycobacterium tuberculosisreveals evolution and genomic instability within Uganda I sub-lineage", "token_count": 77, "char_count": 320, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:26.568994", "source": { "split": "train_shard_00001", "doc_id": 4210 }, "chunk_id": "train_shard_00001_4210_1", "global_id": 11616 }, { "text": "A new cytosine deaminase gene and protein from Candida kefyr are provided. This protein has increased ability to convert the 5-fluorocytosine prodrug t o its toxic form when compared against the E. coli enzyme.\n\nCANDIDA KEFYR CYTOSINE DEAMINASE", "token_count": 76, "char_count": 244, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:26.937157", "source": { "split": "train_shard_00001", "doc_id": 4211 }, "chunk_id": "train_shard_00001_4211_0", "global_id": 11617 }, { "text": "Autophagy requires ubiquitin-like Atg8 and Atg12 conjugation systems, where Atg7 has a critical role as the sole E1 enzyme. Although Atg7 recognizes two distinct E2s, Atg3 and Atg10, it is not understood how Atg7 correctly loads these E2s with their cognate ubiquitin-like proteins, Atg8 and Atg12. Here, we report the crystal structures of the N-terminal domain of Atg7 bound to Atg10 or Atg3 of thermotolerant yeast and plant homologs. The observed Atg7-Atg10 and Atg7-Atg3 interactions, which resemble each other but are quite distinct from the canonical E1-E2 interaction, makes Atg7 suitable for transferring Atg12 to Atg10 and Atg8 to Atg3 by a trans mechanism. Notably, in vitro experiments showed that Atg7 loads Atg3 and Atg10 with Atg8 and Atg12 in a nonspecific manner, which suggests that cognate conjugate formation in vivo is not an intrinsic quality of Atg7.\n\nNoncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.", "token_count": 293, "char_count": 960, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6644, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:27.506645", "source": { "split": "train_shard_00001", "doc_id": 4212 }, "chunk_id": "train_shard_00001_4212_0", "global_id": 11618 }, { "text": "Introduction. Staphylococcus aureus is a major cause of hospital infections worldwide. Awareness towards methicillin-resistant S. aureus (MRSA) infections is high but attention towards borderline oxacillin-resistant S. aureus (BORSA) is limited, possibly due to an underestimated clinical relevance, presumption of low incidence and diagnostic limitations.Gap statement. BORSA surveillance has not been routinely implemented, and thus consensus with regard to a definition and infection control measures is lacking.Aim. Our goals were to investigate the occurrence, molecular characteristics and clinical manifestations of BORSA infections in the hospital setting.Methodology. Following an increased incidence in 2016, BORSA cases in 2014/2016 (in our institution) were more specifically evaluated. Medical records were reviewed to investigate epidemiological links, clinical characteristics and outcomes. Resistance and virulence markers were assessed by whole genome sequencing (WGS). Conventional methods: amplified fragment length polymorphism (AFLP) ; multilocus sequence typing (MLST) and multiple locus variable-number tandem repeat analysis (MLVA) were compared with core genome MLST (cgMLST) and whole-genome single nucleotide polymorphism (wgSNP) analysis to confirm genetic clusters.Results. From 2009 to 2013, BORSA comprised 0.1 % of all clinical S. aureus strains. In 2016, the incidence was six-fold higher in comparison to the baseline. Whole-genome SNP and cgMLST confirmed two BORSA clusters among patients with dermatological conditions. Patients with BORSA presented with skin infections, and one case developed a severe invasive infection with a fatal outcome. Infection control measures successfully prevented further transmission in both clusters", "token_count": 474, "char_count": 1832, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:28.148912", "source": { "split": "train_shard_00001", "doc_id": 4213 }, "chunk_id": "train_shard_00001_4213_0", "global_id": 11619 }, { "text": "WGS findings showed that BORSA strains carried multiple resistance and virulence genes with increased pathogenic potential.Conclusion. WGS and cgMLST effectively characterized and confirmed BORSA clusters among at-risk patients with clinical manifestations ranging from mild skin infections to life-threatening bacteraemia. Clinical awareness and active monitoring are therefore warranted for the timely implementation of infection control measures to prevent BORSA transmission in high-risk patients.\n\nHospital transmission of borderline oxacillin-resistant Staphylococcus aureus evaluated by whole-genome sequencing.", "token_count": 146, "char_count": 632, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8493, "quality_score": 0.9247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:28.586026", "source": { "split": "train_shard_00001", "doc_id": 4213 }, "chunk_id": "train_shard_00001_4213_1", "global_id": 11620 }, { "text": "Antimicrobial resistance (AMR) in Mycoplasma bovis has previously been associated with mutations within topoisomerases and ribosomal genes rather than specific resistance-conferring genes. This study used whole genome sequencing (WGS) to identify potential new AMR mechanisms. It was found that a 2019 clinical isolate with high MIC (2019-043682) had a new core genome multilocus sequencing (cgMLST) type (ST10-like) and 91% homology with the published genome of M. bovis PG45. Closely related to PG45, a 1982 isolate (1982-M6152) shared the same cgMLST type (ST17), 97.2% homology and similar low MIC results. Known and potential AMR-associated genetic events were identified through comparison with the published M. bovis PG45 genome. Isolate 2019-043682 had 507 genes with non-synonymous mutations (NSMs) and 67 genes disrupted. Isolate 1982-M6152 had 81 NSMs and 20 disruptions. Based on functional roles and known mechanisms of antimicrobials, a 55 gene subset was assessed for potential AMR mechanisms. Of these, 14 were previously identified from other bacteria as sites of AMR mutation, 41 shared similar functions to them, and 11 contained gene-disrupting mutations. This study indicated that M. bovis may obtain high AMR characteristics by mutating or disrupting other functional genes, in addition to topoisomerases and ribosomal genes.\n\nIdentification of antimicrobial resistance-associated genes through whole genome sequencing of high and low MIC isolates ofMycoplasma bovis", "token_count": 448, "char_count": 1495, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6291, "quality_score": 0.8146, "entities": { "genes": [ "ST17", "ST10", "PG45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:29.223481", "source": { "split": "train_shard_00001", "doc_id": 4214 }, "chunk_id": "train_shard_00001_4214_0", "global_id": 11621 }, { "text": "

ABSTRACT

Acinetobacter baumannii is an important human pathogen due to its multi-drug resistance, but is usually with low-grade virulence. Although a mouse model revealed different virulence grades of clinical carbapenem-resistant A. baumannii (CRAB) strains, the genetic basis remains unknown. We collected 61 CRAB isolates from intensive care unit of Shenzhen People’s Hospital (Shenzhen, China), and analyzed them used whole genome sequencing (WGS), multilocus sequence typing (MLST) and core genome MLST (cgMLST), transmission chain reconstruction and Comparative genomic tools. A mouse pneumonia model was used to confirm the hypervirulent phenotype. Eleven complex types (CT) were identified based on core genome multilocus sequence typing scheme. CT512 showed higher transmissibility and bloodstream infection rates than other CTs. A genomic region Lyb-2-4 was shared by CT512 and CT2092 but not CT2085. The mortality rates of patient infected with CRAB harboring Lyb-2-4 was significantly higher than those infected with CRAB isolates without Lyb-2-4 (77.8% vs 24.5%, p < 0.01). In the mouse model, the survival rates of strains containing the Lyb-2-4 region (LAC-4, 5122 and 2092) were significantly lower than for strains without Lyb-2-4 (7152, 71517, 20859 and ATCC17978). One open reading frame (ORF) was a marker for the presence of Lyb-2-4, and PCR of a segment of this ORF, designated as hvcT , served as a tag for hypervirulent CRAB. Our study should be very useful in advising the clinician to implement medical intervention earlier, and also making the worldwide surveillance of these hypervirulent CRAB strains easier.

IMPORTANCE

Hypervirulent CRAB strains are expected to pose a threat to human health because infection of these strains is associated with high mortality and multidrug resistance", "token_count": 512, "char_count": 1833, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6617, "quality_score": 0.8309, "entities": { "genes": [ "ATCC17978", "CT2085", "CT2092", "CT512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:29.882442", "source": { "split": "train_shard_00001", "doc_id": 4215 }, "chunk_id": "train_shard_00001_4215_0", "global_id": 11622 }, { "text": "The rapid hypervirulent CRAB identification assay will facilitate prompt medical intervention. Our findings should provoke surveillance for hypervirulent CRAB strains harboring Lyb-2-4 in other countries. Further research should focus on the mechanism of hypervirulence, the acquisition of this genomic region and the development of control measures to prevent further dissemination.\n\nLyb-2-4, a unique genomic region of hypervirulent carbapenem-resistant Acinetobacter baumannii", "token_count": 116, "char_count": 486, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7833, "quality_score": 0.8917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:30.263149", "source": { "split": "train_shard_00001", "doc_id": 4215 }, "chunk_id": "train_shard_00001_4215_1", "global_id": 11623 }, { "text": "Factorial design and response surface techniques were used to optimize the culture medium for the production of inulinase by Kluyveromyces marxianus. Sucrose was used as the carbon source instead of inulin. Initially, a fractional factorial design (2(5-1)) was used in order to determine the most relevant variables for enzyme production. Five parameters were studied (sucrose, peptone, yeast extract, pH, and K2HPO4), and all were shown to be significant. Sucrose concentration and pH had negative effects on inulinase production, whereas peptone, yeast extract, and K2HPO4 had positive ones. The pH was shown to be the most significant variable and should be preferentially maintained at 3.5. According to the results from the first factorial design, sucrose, peptone, and yeast extract concentrations were selected to be utilized in a full factorial design. The optimum conditions for a higher enzymatic activity were then determined: 14 g/L of sucrose, 10 g/L of yeast extract, 20 g/L of peptone, 1 g/L of K2HPO4. The enzymatic activity in the culture conditions was 127 U/mL, about six times higher than before the optimization.\n\nOptimization of inulinase production by Kluyveromyces marxianus using factorial design.", "token_count": 321, "char_count": 1222, "word_count": 185, "semantic_coherence": 1, "information_density": 0.573, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:30.843126", "source": { "split": "train_shard_00001", "doc_id": 4216 }, "chunk_id": "train_shard_00001_4216_0", "global_id": 11624 }, { "text": "Immobilization system of Kluyveromyces marxianus cells in barium alginate for inulin hydrolysis.", "token_count": 27, "char_count": 96, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:31.203921", "source": { "split": "train_shard_00001", "doc_id": 4217 }, "chunk_id": "train_shard_00001_4217_0", "global_id": 11625 }, { "text": "The high background of host RNA poses a major challenge to metatranscriptome analysis of human samples. Hence, metatranscriptomics has been mainly applied to microbe-rich samples, while its application in human tissues with low ratio of microbial to host cells has yet to be explored. Since there is no computational workflow specifically designed for the taxonomic and functional analysis of this type of samples, we propose an effective metatranscriptomics strategy to accurately characterize the microbiome in human tissues with a low ratio of microbial to host content. We experimentally generated synthetic samples with well-characterized bacterial and host cell compositions, and mimicking human samples with high and low microbial loads. These synthetic samples were used for optimizing and establishing the workflow in a controlled setting. Our results show that the integration of the taxonomic analysis of optimized Kraken 2/Bracken with the functional analysis of HUMAnN 3 in samples with low microbial content, enables the accurate identification of a large number of microbial species with a low false-positive rate, while improving the detection of microbial functions. The effectiveness of our metatranscriptomics workflow was demonstrated in synthetic samples, simulated datasets, and most importantly, human gastric tissue specimens, thus providing a proof of concept for its applicability on mucosal tissues of the gastrointestinal tract. The use of an accurate and reliable metatranscriptomics approach for human tissues with low microbial content will expand our understanding of the functional activity of the mucosal microbiome, uncovering critical interactions between the microbiome and the host in health and disease.\n\nA metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass.", "token_count": 404, "char_count": 1868, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5075, "quality_score": 0.7538, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:31.827766", "source": { "split": "train_shard_00001", "doc_id": 4218 }, "chunk_id": "train_shard_00001_4218_0", "global_id": 11626 }, { "text": "Antimicrobial resistance has become a major public health threat. Food-related Staphylococcus species have received much attention due to their multidrug resistance. The cfr gene associated with multidrug resistance has been consistently detected in food-derived Staphylococcus species. In this retrospective study, we examined the prevalence of cfr-positive Staphylococcus strains isolated from poultry meat in different geographical areas of China from 2011 to 2016. Two cfr-positive Staphylococcus delphini strains were identified from poultry meat in China. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in the two S. delphini isolates 245-1 and 2794-1. Whole-genome sequencing showed that they both harbored a novel 20,258-bp cfr-carrying Tn558 transposon derivative on their chromosomes. The Tn558 derivative harbors multiple antimicrobial resistance genes, including the transferable multiresistance gene cfr, chloramphenicol resistance gene fexA, aminoglycoside resistance genes aacA-aphD and aadD, and bleomycin resistance gene ble. Surprisingly, within the Tn558 derivative, an active unconventional circularizable structure containing various resistance genes and a copy of a direct repeat sequence was identified by two-step PCR. Furthermore, core genome phylogenetic analysis revealed that the cfr-positive S. delphini strains were most closely related to S", "token_count": 495, "char_count": 1593, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6684, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:32.495574", "source": { "split": "train_shard_00001", "doc_id": 4219 }, "chunk_id": "train_shard_00001_4219_0", "global_id": 11627 }, { "text": "delphini 14S03313-1 isolated from Japan in 2017 and 14S03319-1 isolated from Switzerland in 2017. This study is the first report of S. delphini harboring a novel cfr-carrying Tn558 derivative isolated from retail food. This finding raises further concerns regarding the potential threat to food safety and public health safety. The occurrence and dissemination of similar cfr-carrying transposons from diverse Staphylococcus species need further surveillance.\n\nPresence and Characterization of a Novel cfr-Carrying Tn558 Transposon Derivative in Staphylococcus delphini Isolated From Retail Food.", "token_count": 215, "char_count": 649, "word_count": 81, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:32.983618", "source": { "split": "train_shard_00001", "doc_id": 4219 }, "chunk_id": "train_shard_00001_4219_1", "global_id": 11628 }, { "text": "

Unlabelled

Bacterial evolution is accelerated by mobile genetic elements. To spread horizontally and to benefit the recipient bacteria, genes encoded on these elements must be properly regulated. Among the legionellae are multiple integrative conjugative elements (ICEs) that each encode a paralog of the broadly conserved regulator csrA. Using bioinformatic analyses, we deduced that specific csrA paralogs are coinherited with particular lineages of the type IV secretion system that mediates horizontal spread of its ICE, suggesting a conserved regulatory interaction. As a first step to investigate the contribution of csrA regulators to this class of mobile genetic elements, we analyzed here the activity of the csrA paralog encoded on Legionella pneumophila ICE-βox. Deletion of this gene, which we name csrT, had no observed effect under laboratory conditions. However, ectopic expression of csrT abrogated the protection to hydrogen peroxide and macrophage degradation that ICE-βox confers to L. pneumophila. When ectopically expressed, csrT also repressed L. pneumophila flagellin production and motility, a function similar to the core genome's canonical csrA. Moreover, csrT restored the repression of motility to csrA mutants of Bacillus subtilis, a finding consistent with the predicted function of CsrT as an mRNA binding protein. Since all known ICEs of legionellae encode coinherited csrA-type IV secretion system pairs, we postulate that CsrA superfamily proteins regulate ICE activity to increase their horizontal spread, thereby expanding L. pneumophila versatility.

Importance

ICEs are mobile DNA elements whose type IV secretion machineries mediate spread among bacterial populations. All surveyed ICEs within the Legionella genus also carry paralogs of the essential life cycle regulator csrA. It is striking that the csrA loci could be classified into distinct families based on either their sequence or the subtype of the adjacent type IV secretion system locus. To investigate whether ICE-encoded csrA paralogs are bona fide regulators, we analyzed ICE-βox as a model system", "token_count": 525, "char_count": 2115, "word_count": 302, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:33.681568", "source": { "split": "train_shard_00001", "doc_id": 4220 }, "chunk_id": "train_shard_00001_4220_0", "global_id": 11629 }, { "text": "When expressed ectopically, its csrA paralog inhibited multiple ICE-βox phenotypes, as well as the motility of not only Legionella but also Bacillus subtilis. Accordingly, we predict that CsrA regulators equip legionellae ICEs to promote their spread via dedicated type IV secretion systems.\n\ncsrT Represents a New Class of csrA-Like Regulatory Genes Associated with Integrative Conjugative Elements of Legionella pneumophila.", "token_count": 120, "char_count": 426, "word_count": 59, "semantic_coherence": 1, "information_density": 0.9153, "quality_score": 0.9576, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:34.095912", "source": { "split": "train_shard_00001", "doc_id": 4220 }, "chunk_id": "train_shard_00001_4220_1", "global_id": 11630 }, { "text": "Despite hundreds of sequenced Arabidopsis genomes, very little is known about the degree of genomic collinearity within single species, due to the low number of chromosome-level assemblies. Here, we report chromosome-level reference-quality assemblies of seven Arabidopsis thaliana accessions selected across its global range. Each genome reveals between 13-17 Mb rearranged, and 5-6 Mb non-reference sequences introducing copy-number changes in ~5000 genes, including ~1900 non-reference genes. Quantifying the collinearity between the genomes reveals ~350 euchromatic regions, where accession-specific tandem duplications destroy the collinearity between the genomes. These hotspots of rearrangements are characterized by reduced meiotic recombination in hybrids and genes implicated in biotic stress response. This suggests that hotspots of rearrangements undergo altered evolutionary dynamics, as compared to the rest of the genome, which are mostly based on the accumulation of new mutations and not on the recombination of existing variation, and thereby enable a quick response to the biotic stress.\n\nChromosome-level assemblies of multiple Arabidopsis genomes reveal hotspots of rearrangements with altered evolutionary dynamics.", "token_count": 301, "char_count": 1237, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:34.662309", "source": { "split": "train_shard_00001", "doc_id": 4221 }, "chunk_id": "train_shard_00001_4221_0", "global_id": 11631 }, { "text": "This research aimed to evaluate the diversity of yeasts recovered from fermented foods gathered from some areas of Northeastern Thailand. The fermented food items included Pla-som, Nham-pla, Kem-buknud, Isan-sausage, Pla-ra, Mhum-neu, Mhum-Khai-pla, Nham-neu, Nham-mu, Kung-joom, Som-pla-noi, and Poo-dong. Their probiotic characteristics were also investigated. A total of 103 yeast isolates of nine genera were identified using 28S rDNA sequencing. The yeast genera were Candida (20.3%), Diutina (2.9%), Filobasidium (1.0%), Kazachstania (33.0%), Pichia (3.9%), Saccharomyces (1.0%), Starmerella (28.2%), Torulaspora (2.9%), and Yarrowia (6.8%). Based on probiotic characteristic analysis of ten selected yeast strains, Kazachstania bulderi KKKS4-1 showed the strongest probiotic characteristics in terms of hemolytic activity, antimicrobial activity against pathogenic bacteria, tolerance to low pH and bile salt and hydrophobicity. Isolated yeasts with probiotic characteristics may be useful in fermented food and animal feed production to improve their nutritional values.\n\nDiversity of fermentative yeasts with probiotic potential isolated from Thai fermented food products.", "token_count": 435, "char_count": 1251, "word_count": 152, "semantic_coherence": 1, "information_density": 0.7237, "quality_score": 0.8618, "entities": { "genes": [ "KKKS4" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:35.290459", "source": { "split": "train_shard_00001", "doc_id": 4222 }, "chunk_id": "train_shard_00001_4222_0", "global_id": 11632 }, { "text": "Methods and compositions for the production of ethanol from lignocellulosic starting materials are provided herein. Embodiments provide yeast cells of the genus H. polymorpha with one or more modifications, including, for example, an inactive acid trehalase gene, overexpression of xylulokinase, and/or overexpression of heat-shock protein 104.\n\nALCOHOLIC XYLOSE FERMENTATION AT HIGH TEMPERATURES BY THE THERMOTOLERANT YEAST HANSENULA POLYMORPHA", "token_count": 136, "char_count": 445, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8448, "quality_score": 0.9224, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:35.719233", "source": { "split": "train_shard_00001", "doc_id": 4223 }, "chunk_id": "train_shard_00001_4223_0", "global_id": 11633 }, { "text": "Five novel bacterial strains, Marseille-P1476T (=CSURP1476T=DSM 100642T), Marseille-P3256T (=CSURP3256T=CECT 9977T), Marseille-P2936T (=CSURP2936T=DSM 103159T), Marseille-P2912T (=CSURP2912T=DSM 103345T) and Marseille-P3197T (=CSURP3197T=CCUG 71847T), were isolated from various human specimens. These five strains were not identified at the species level by matrix-assisted laser desorption/ionization time of flight mass spectrometry. Following 16S rRNA gene sequence comparisons with the GenBank database, the highest nucleotide sequence similarities of all studied strains were obtained to members of the paraphyletic genus Olsenella. A polyphasic taxono-genomic strategy (16S rRNA gene-based and core genome-based phylogeny, genomic comparison, phenotypic and biochemical characteristics) enabled us to better classify these strains and reclassify Olsenella species. Among the studied strains, Marseille-P1476T, Marseille-P2936T and Marseille-P3197T belonged to new species of the genus Olsenella for which we propose the names Olsenella massiliensis sp", "token_count": 505, "char_count": 1284, "word_count": 126, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [ "CSURP2912", "CSURP3256", "CSURP2936", "CSURP1476", "CSURP3197" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:36.372781", "source": { "split": "train_shard_00001", "doc_id": 4224 }, "chunk_id": "train_shard_00001_4224_0", "global_id": 11634 }, { "text": "nov., Olsenella phocaeensis sp. nov. and Olsenella urininfantis sp. nov., respectively. Strains Marseille-P2912T and Marseille-P3256T belonged to a new genus for which the names Thermophilibacter provencensis gen. nov., sp. nov. and Thermophilibacter mediterraneus gen. nov., sp. nov. are proposed, respectively. We also propose the creation of the genera Parafannyhessea gen. nov., Tractidigestivibacter gen. nov. and Paratractidigestivibacter gen. nov. and the reclassification of Olsenella umbonata as Parafannyhessea umbonata comb. nov., Olsenella scatoligenes as Tractidigestivibacter scatoligenes comb. nov., and Olsenella faecalis as Paratractidigestivibacter faecalis comb. nov.\n\nNew human-associated species of the family Atopobiaceae and proposal to reclassify members of the genus Olsenella.", "token_count": 358, "char_count": 929, "word_count": 100, "semantic_coherence": 1, "information_density": 0.52, "quality_score": 0.76, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:36.955802", "source": { "split": "train_shard_00001", "doc_id": 4224 }, "chunk_id": "train_shard_00001_4224_1", "global_id": 11635 }, { "text": "Staphylococcus aureus is a major human and animal pathogen although the animal-associated S. aureus can be a potential risk of human zoonoses. Acquisition of phage-related genomic islands determines the S. aureus species diversity. This study characterized and compared the genome architecture, distribution nature, and evolutionary relationship of 65 complete prophages carried by human and animal-associated S. aureus strains spreading across the European regions. The analyzed prophage genomes showed mosaic architecture with extensive variation in genome size. The phylogenetic analyses generated seven clades in which prophages of the animal-associated S. aureus scattered in all the clades. The S. aureus strains with the same SCCmec type, and clonal complex favored the harboring of similar prophage sequences and suggested that the frequency of phage-mediated horizontal gene transfer is higher between them. The presence of various virulence factors in prophages of animal-associated S. aureus suggested that these prophages could have more pathogenic potential than prophages of human-associated S. aureus. This study showed that the S. aureus phages are dispersed among the several S. aureus serotypes and around the European regions. Further, understanding the phage functional genomics is necessary for the phage-host interactions and could be used for tracing the S. aureus strains transmission.\n\nComparative analysis of prophages carried by human and animal-associated Staphylococcus aureus strains spreading across the European regions.", "token_count": 363, "char_count": 1552, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5463, "quality_score": 0.7731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:37.535636", "source": { "split": "train_shard_00001", "doc_id": 4225 }, "chunk_id": "train_shard_00001_4225_0", "global_id": 11636 }, { "text": "Jerusalem artichoke mashed tubers were fermented using single yeasts and a bacterium as well as mixed culture of microorganisms. Kluyveromyces fragilis, a yeast with an active inulinase, was used together with either a commercial distillery yeast, Saccharomyces cerevisiae, or the bacterium Zymomonas mobilis. After batch fermentation the best ethanol concentration of 0.48 g g(-1) for the mixed population and 0.46 g g(-1) for the single population can be obtained. The theoretical yield of the mixed cultures was 2-12% higher than for the single microorganism.\n\nUse of Zymomonas mobilis and Saccharomyces cerevisiae mixed with Kluyveromyces fragilis for improved ethanol production from Jerusalem artichoke tubers.", "token_count": 190, "char_count": 716, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:37.989362", "source": { "split": "train_shard_00001", "doc_id": 4226 }, "chunk_id": "train_shard_00001_4226_0", "global_id": 11637 }, { "text": "The era of antibiotics as a cure-all for bacterial infections appears to be coming to an end. The emergence of multidrug resistance in many hospital-associated pathogens has resulted in \"superbugs\" that are effectively untreatable. Multidrug efflux pumps are well known mediators of bacterial drug resistance. Genome sequencing efforts have highlighted an abundance of putative efflux pump genes in bacteria. However, it is not clear how many of these pumps play a role in antimicrobial resistance. Efflux pump genes that participate in drug resistance can be under tight regulatory control and expressed only in response to substrates. Consequently, changes in gene expression following antimicrobial shock may be used to identify efflux pumps that mediate antimicrobial resistance. Using this approach we have characterized several novel efflux pumps in bacteria. In one example we recently identified the Acinetobacterchlorhexidine efflux protein (AceI) efflux pump in Acinetobacter. AceI is a prototype for a novel family of multidrug efflux pumps conserved in many proteobacterial lineages. The discovery of this family raises the possibility that additional undiscovered intrinsic resistance proteins may be encoded in the core genomes of pathogenic bacteria.\n\nAn ace up their sleeve: a transcriptomic approach exposes the AceI efflux protein of Acinetobacter baumannii and reveals the drug efflux potential hidden in many microbial pathogens.", "token_count": 360, "char_count": 1429, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:38.563067", "source": { "split": "train_shard_00001", "doc_id": 4227 }, "chunk_id": "train_shard_00001_4227_0", "global_id": 11638 }, { "text": "

Background:

There are increasing researches on whole-genome sequences for clinical strains of Elizabethkingia genus which can cause severe infection in humans, while few studies on the comparative genomics of species in the Elizabethkingia genus in China have been conducted.

Methods:

: The Elizabethkingia genus, isolated in a tertiary hospital of Beijing, China, were re-identified and analyzed through in silico DNA-DNA hybridization (DDH), whole-genome sequence-based phylogeny. Antibiotic resistance genes, antimicrobial resistance-associated proteins, virulence factors were identified, and clusters of orthologous groups were evaluated by Kyoto Encyclopedia of Genes and Genomes (KEGG). The clinical information of patients infected by these organisms was collected and the characteristics were analyzed.

Results:

: There were three species among 20 clinical isolates of Elizabethkingia genus: E. meningoseptica , E. anophelis and E. miricola . E. anophelis accounted for the majority. E. meningoseptica exhibited higher GC content and possessed carbapenemase-encoding genes of bla GOB-16 and bla B-12 while E. anophelis carried genes of bla CME-1 . Multiple kinds of antimicrobial resistance-associated proteins were predicted and the virulence factors about adherence, biofilm formation, iron and magnesium uptake, stress adaptation, and immune evasion were discovered. Among 2622 clusters of core genomes identified from the three species of the Elizabethkingia genus, the majority of genes were metabolism-related. Pan genome displayed an upregulation, while the core genome displayed a downregulation with the addition of new genes for the 20 Elizabethkingia strains.

Conclusions:

: The composition was different in antimicrobial resistance-related, virulence-related and metabolism-related genes depending upon species of Elizabethkingia . An adaptive evolution of Elizabethkingia to environmental change including hospital settings has been developed.", "token_count": 494, "char_count": 2002, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5871, "quality_score": 0.7936, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:39.216505", "source": { "split": "train_shard_00001", "doc_id": 4228 }, "chunk_id": "train_shard_00001_4228_0", "global_id": 11639 }, { "text": "Comparison of Whole-Genome Sequences for Three Species of the Elizabethkingia Genus", "token_count": 29, "char_count": 93, "word_count": 9, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:39.570893", "source": { "split": "train_shard_00001", "doc_id": 4228 }, "chunk_id": "train_shard_00001_4228_1", "global_id": 11640 }, { "text": "Recombinant genetic constructs and strains of H. polymorpha having significantly increased ethanol productivity with a simultaneous decreased production of xylitol during high- temperature xylose fermentation are disclosed. The constructs include a H. polymorpha XYLl gene encoding xylose reductase mutated to decrease affinity of the enzyme toward NADP?. The modified version of XYLl gene under control of a strong constitutive HpGAP promoter was overexpressed in a ?xyll background. A recombinant H. polymorpha strain overexpressing the mutated enzyme together with native xylitol dehydrogenase and xylulokinase in the ?xyll background was also constructed. Xylose consumption, ethanol and xylitol production by the constructed strain were evaluated during high-temperature xylose fermentation (48 DEG C). A significant increase in ethanol productivity (up to 7.4 times) was shown in the recombinant strain as compared with the wild type strain. Moreover, the xylitol production by the recombinant strain was reduced considerably: 0.9 mg?(L?h)-1 versus 4.2 mg?(Lxh)-1 by the wild type strain.\n\nENGINEERING OF XYLOSE REDUCTASE AND OVEREXPRESSION OF XYLITOL DEHYDROGENASE AND XYLULOKINASE IMPROVES XYLOSE ALCOHOLIC FERMENTATION IN THE THERMOTOLERANT YEAST HANSENULA POLYMORPHA", "token_count": 374, "char_count": 1276, "word_count": 174, "semantic_coherence": 1, "information_density": 0.5517, "quality_score": 0.7759, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:40.156223", "source": { "split": "train_shard_00001", "doc_id": 4229 }, "chunk_id": "train_shard_00001_4229_0", "global_id": 11641 }, { "text": "Recombinant genetic constructs and strains of H. polymorpha having significantly increased ethanol productivity with a simultaneous decreased production of xylitol during high-temperature xylose fermentation are disclosed. The constructs include a H. polymorpha XYL1 gene encoding xylose reductase mutated to decrease affinity of the enzyme toward NADPH. The modified version of XYL1 gene under control of a strong constitutive HpGAP promoter was overexpressed in a [Delta]xyll background. A recombinant H. polymorpha strain overexpressing the mutated enzyme together with native xylitol dehydrogenase and xylulokinase in the [Delta]xyll background was also constructed. Xylose consumption, ethanol and xylitol production by the constructed strain were evaluated during high-temperature xylose fermentation (48 DEG C.). A significant increase in ethanol productivity (up to 7.4 times) was shown in the recombinant strain as compared with the wild type strain. Moreover, the xylitol production by the recombinant strain was reduced considerably: 0.9 mg[chi] (L[chi]h)-1 versus 4.2 mg[chi] (Lxh)-1 by the wild type strain.\n\nENGINEERING OF XYLOSE REDUCTASE AND OVEREXPRESSION OF XYLITOL DEHYDROGENASE AND XYLULOKINASE IMPROVES XYLOSE ALCOHOLIC FERMENTATION IN THE THERMOTOLERANT YEAST HANSENULA POLYMORPHA", "token_count": 387, "char_count": 1302, "word_count": 175, "semantic_coherence": 1, "information_density": 0.5429, "quality_score": 0.7714, "entities": { "genes": [ "XYL1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:40.773792", "source": { "split": "train_shard_00001", "doc_id": 4230 }, "chunk_id": "train_shard_00001_4230_0", "global_id": 11642 }, { "text": "Acanthamoeba polyphaga mimivirus, Marseillevirus, and Sputnik, a virophage, are intra-amoebal viruses that have been isolated from water collected in cooling towers. They have provided fascinating data and have raised exciting questions about viruses definition and evolution. Mimivirus and Marseillevirus have been classified in the nucleo-cytoplasmic large DNA viruses (NCLDVs) class. Their genomes are the largest and fifth largest viral genomes sequenced so far. The gene repertoire of these amoeba-associated viruses can be divided into four groups: the core genome, genes acquired by lateral gene transfer, duplicated genes, and ORFans. Open reading frames (ORFs) that have homologs in the NCLDVs core gene set represent 2.9 and 6.1% of the Mimivirus and Marseillevirus gene contents, respectively. A substantial proportion of the Mimivirus, Marseillevirus and Sputnik ORFs exhibit sequence similarities to homologs found in bacteria, archaea, eukaryotes or viruses. The large amount of chimeric genes in these viral genomes might have resulted from acquisitions by lateral gene transfers, implicating sympatric bacteria and viruses with an intra-amoebal lifestyle. In addition, lineage-specific gene expansion may have played a major role in the genome shaping. Altogether, the data so far accumulated on amoeba-associated giant viruses are a powerful incentive to isolate and study additional strains to gain better understanding of their pangenome.\n\nGene repertoire of amoeba-associated giant viruses.", "token_count": 394, "char_count": 1510, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:41.390380", "source": { "split": "train_shard_00001", "doc_id": 4231 }, "chunk_id": "train_shard_00001_4231_0", "global_id": 11643 }, { "text": "The gene encoding endopolygalacturonase (EC 3.2.1.15) has been cloned, sequenced and expressed from three strains of Saccharomyces cerevisiae (including nonsecretors) and three strains of Kluyveromyces marxianus. Both control and coding regions showed small differences within each species, one including loss of a potential glycosylation site. Two non-secreting S. cerevisiae strains (FY1679 and var. uvarum) had non-transcribed copies of functional genes. Maximum enzyme activity was achieved with the S. cerevisiae FY1679 gene in an expressing vector, with an enzyme activity of 51 micromol of reducing sugar released from polygalacturonic acid microg protein(-1) min(-1), the highest so far reported for a yeast.\n\nEndopolygalacturonase genes and enzymes from Saccharomyces cerevisiae and Kluyveromyces marxianus.", "token_count": 238, "char_count": 816, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7182, "quality_score": 0.8591, "entities": { "genes": [ "FY1679" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:41.863661", "source": { "split": "train_shard_00001", "doc_id": 4232 }, "chunk_id": "train_shard_00001_4232_0", "global_id": 11644 }, { "text": "Using mRNA transcript levels for key functional enzymes as proxies for the organohalide respiration (OHR) rate, is a promising approach for monitoring bioremediation populations in situ at chlorinated solvent-contaminated field sites. However, to date, no correlations have been empirically derived for chlorinated solvent respiring, Dehalococcoides mccartyi (DMC) containing, bioaugmentation cultures. In the current study, genome-wide transcriptome and proteome data were first used to confirm the most highly expressed OHR-related enzymes in the bioaugmentation culture, KB-1TM, including several reductive dehalogenases (RDases) and a Ni-Fe hydrogenase, Hup. Different KB-1™ DMC strains could be resolved at the RNA and protein level through differences in the sequence of a common RDase (DET1545-like homologs) and differences in expression of their vinyl chloride-respiring RDases. The dominant strain expresses VcrA, whereas the minor strain utilizes BvcA. We then used quantitative reverse-transcriptase PCR (qRT-PCR) as a targeted approach for quantifying transcript copies in the KB-1TM consortium operated under a range of TCE respiration rates in continuously-fed, pseudo-steady-state reactors. These candidate biomarkers from KB-1TM demonstrated a variety of trends in terms of transcript abundance as a function of respiration rate over the range: 7.7 × 10-12 to 5.9 × 10-10 microelectron equivalents per cell per hour (μeeq/cell∙h)", "token_count": 428, "char_count": 1508, "word_count": 198, "semantic_coherence": 1, "information_density": 0.7323, "quality_score": 0.8662, "entities": { "genes": [ "DET1545" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:42.494850", "source": { "split": "train_shard_00001", "doc_id": 4233 }, "chunk_id": "train_shard_00001_4233_0", "global_id": 11645 }, { "text": "Power law trends were observed between the respiration rate and transcript abundance for the main DMC RDase (VcrA) and the hydrogenase HupL (R² = 0.83 and 0.88, respectively), but not transcripts for 16S rRNA or three other RDases examined: TceA, BvcA or the RDase DET1545 homologs in KB1TM. Overall, HupL transcripts appear to be the most robust activity biomarker across multiple DMC strains and in mixed communities including DMC co-cultures such as KB1TM. The addition of oxygen induced cell stress that caused respiration rates to decline immediately (>95% decline within one hour). Although transcript levels did decline, they did so more slowly than the respiration rate observed (transcript decay rates between 0.02 and 0.03 per hour). Data from strain-specific probes on the pangenome array strains suggest that a minor DMC strain in KB-1™ that harbors a bvcA homolog preferentially recovered following oxygen stress relative to the dominant, vcrA-containing strain.\n\nBiomarkers' Responses to Reductive Dechlorination Rates and Oxygen Stress in Bioaugmentation Culture KB-1TM.", "token_count": 329, "char_count": 1132, "word_count": 162, "semantic_coherence": 1, "information_density": 0.7099, "quality_score": 0.8549, "entities": { "genes": [ "KB1", "DET1545" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:43.059892", "source": { "split": "train_shard_00001", "doc_id": 4233 }, "chunk_id": "train_shard_00001_4233_1", "global_id": 11646 }, { "text": "To gain insights into the origin and genome evolution of the plague bacterium Yersinia pestis, we have sequenced the deep-rooted strain Angola, a virulent Pestoides isolate. Its ancient nature makes this atypical isolate of particular importance in understanding the evolution of plague pathogenicity. Its chromosome features a unique genetic make-up intermediate between modern Y. pestis isolates and its evolutionary ancestor, Y. pseudotuberculosis. Our genotypic and phenotypic analyses led us to conclude that Angola belongs to one of the most ancient Y. pestis lineages thus far sequenced. The mobilome carries the first reported chimeric plasmid combining the two species-specific virulence plasmids. Genomic findings were validated in virulence assays demonstrating that its pathogenic potential is distinct from modern Y. pestis isolates. Human infection with this particular isolate would not be diagnosed by the standard clinical tests, as Angola lacks the plasmid-borne capsule, and a possible emergence of this genotype raises major public health concerns. To assess the genomic plasticity in Y. pestis, we investigated the global gene reservoir and estimated the pangenome at 4,844 unique protein-coding genes. As shown by the genomic analysis of this evolutionary key isolate, we found that the genomic plasticity within Y. pestis clearly was not as limited as previously thought, which is strengthened by the detection of the largest number of isolate-specific single-nucleotide polymorphisms (SNPs) currently reported in the species. This study identified numerous novel genetic signatures, some of which seem to be intimately associated with plague virulence. These markers are valuable in the development of a robust typing system critical for forensic, diagnostic, and epidemiological studies.\n\nGenome sequence of the deep-rooted Yersinia pestis strain Angola reveals new insights into the evolution and pangenome of the plague bacterium.", "token_count": 455, "char_count": 1957, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:43.702822", "source": { "split": "train_shard_00001", "doc_id": 4234 }, "chunk_id": "train_shard_00001_4234_0", "global_id": 11647 }, { "text": "The protozoan Trypanosoma cruzi almost invariably establishes life-long infections in humans and other mammals, despite the development of potent host immune responses that constrain parasite numbers. The consistent, decades-long persistence of T. cruzi in human hosts arises at least in part from the remarkable level of genetic diversity in multiple families of genes encoding the primary target antigens of anti-parasite immune responses. However, the highly repetitive nature of the genome – largely a result of these same extensive families of genes – have prevented a full understanding of the extent of gene diversity and its maintenance in T. cruzi . In this study, we have combined long-read sequencing and proximity ligation mapping to generate very high-quality assemblies of two T. cruzi strains representing the apparent ancestral lineages of the species. These assemblies reveal not only the full repertoire of gene family members in the two strains, demonstrating extreme diversity within and between isolates, but also provide evidence of the processes that generate and maintain that diversity, including extensive gene amplification, dispersion of copies throughout the genome and diversification via recombination and in situ mutations. These processes also impact genes not required for or involved in immune evasion, creating unique challenges with respect to preserving core genome function while maximizing genetic diversity.\n\nStrain-specific genome evolution inTrypanosoma cruzi, the agent of Chagas disease", "token_count": 319, "char_count": 1538, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6516, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:44.323188", "source": { "split": "train_shard_00001", "doc_id": 4235 }, "chunk_id": "train_shard_00001_4235_0", "global_id": 11648 }, { "text": "Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) of clonal complex CC398 typically carry various antimicrobial resistance genes, many of them located on plasmids. In the bovine LA-MRSA isolate Rd11, we previously identified plasmid pAFS11 in which resistance genes are co-localized with a novel ica-like gene cluster, harboring genes required for polysaccharide intercellular adhesin (PIA)-mediated biofilm formation. The ica genes on pAFS11 were acquired in addition to a pre-existing ica locus on the S. aureus Rd11 chromosomal DNA. Both loci consist of an icaADBC operon and icaR, encoding a corresponding icaADBC repressor. Despite carrying two biofilm gene copies, strain Rd11 did not produce PIA and transformation of pAFS11 into another S. aureus strain even slightly diminished PIA-mediated biofilm formation. By focusing on the molecular background of the biofilm-negative phenotype of pAFS11-carrying S. aureus, we identified the pAFS11-borne ica locus copy as functionally fully active. However, transcription of both plasmid- and core genome-derived icaADBC operons were efficiently suppressed involving IcaR. Surprisingly, although being different on the amino acid sequence level, the two IcaR repressor proteins are mutually replaceable and are able to interact with the icaA promoter region of the other copy. We speculate that this regulatory crosstalk causes the biofilm-negative phenotype in S. aureus Rd11. The data shed light on an unexpected regulatory interplay between pre-existing and newly acquired DNA traits in S", "token_count": 503, "char_count": 1667, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6773, "quality_score": 0.8386, "entities": { "genes": [ "CC398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:44.994905", "source": { "split": "train_shard_00001", "doc_id": 4236 }, "chunk_id": "train_shard_00001_4236_0", "global_id": 11649 }, { "text": "aureus. This also raises interesting general questions regarding functional consequences of gene transfer events and their putative implications for the adaptation and evolution of bacterial pathogens.\n\nPlasmid-Chromosome Crosstalk in Staphylococcus aureus: A Horizontally Acquired Transcription Regulator Controls Polysaccharide Intercellular Adhesin-Mediated Biofilm Formation.", "token_count": 99, "char_count": 390, "word_count": 42, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:45.392101", "source": { "split": "train_shard_00001", "doc_id": 4236 }, "chunk_id": "train_shard_00001_4236_1", "global_id": 11650 }, { "text": "Resistance to third-generation cephalosporins (3GC) in Escherichia coli has been reported worldwide from humans and animals, but the situation in Cuba is still poorly understood. This study aimed to gain new insights into the phenotypic and genotypic characteristics of third-generation cephalosporin-resistant (3GC-R) E. coli isolated from pigs in Cuba. Rectal swabs from 215 healthy pigs were taken from different municipalities in the western region of Cuba and spread on MacConkey agar supplemented with cefotaxime and ceftazidime. Ninety-six isolates were identified as 3GC-R E. coli and 87.5% of them were resistant to at least three antibiotic classes as determined by the measurement of the minimum inhibitory concentration (MIC) of 14 antibiotics. Twenty-seven different isolates were selected for Illumina next-generation sequencing, and subsequent in silico analysis was performed for the detection of antibiotic resistance and virulence genes, plasmid incompatibility (Inc) groups, multilocus sequence typing (MLST), and core genome MLST (cgMLST). The sequenced isolates contained extended-spectrum β-lactamase genes blaCTX-M-32 (n = 17), blaCTX-M-15 (n = 5), and blaCTX-M-55 (n = 4) as well as with pAmpC gene blaCMY-2 (n = 2). They also harbored genes for resistance to other clinically important classes of antibiotics, as well as several diverse virulence factors. The 3GC-R E", "token_count": 509, "char_count": 1523, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6816, "quality_score": 0.8408, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:46.070484", "source": { "split": "train_shard_00001", "doc_id": 4237 }, "chunk_id": "train_shard_00001_4237_0", "global_id": 11651 }, { "text": "coli were genetically highly diverse, belonging to 16 different sequence types. IncX1 was the most frequent Inc group. The presence of 3GC-R E. coli in pigs from Cuba containing several different antibiotic resistance mechanisms emphasizes the need for surveillance programs and the establishment of strategies for the prudent use of antibiotics in food-producing animals.\n\nCharacterization of Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Pigs in Cuba Using Next-Generation Sequencing.", "token_count": 136, "char_count": 530, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:46.511740", "source": { "split": "train_shard_00001", "doc_id": 4237 }, "chunk_id": "train_shard_00001_4237_1", "global_id": 11652 }, { "text": "Due to the evident demand for probiotic microorganisms, a growing number of scientific studies have involved the preliminary selection of new strains, but deeper studies for knowing specific functional and biotechnological properties are needed. In the present work, twenty yeasts (Saccharomyces and non-Saccharomyces) with potential probiotic characteristics, selected in previous works, were evaluated. The following assays were realized: adhesion to Caco-2/TC7 cells, prebiotic metabolisms, assimilation of cholesterol, enzymatic and antioxidant activity, and antifungal resistance. In addition, the effect of ultrasonic treatment was evaluated for attenuating the cultures before their possible incorporation into a food or supplement. In all of the cases, the unique commercial probiotic yeast (S. boulardii CNM I-745) was used as positive control. Results show different capabilities depending on the property studied. In general, no Saccharomyces yeasts were better in the adhesion to Caco cells, prebiotic metabolism, and presented higher variability of enzymatic activities. The ones related to cholesterol assimilation and antioxidant capability did not show a marked trend, and with respect to the attenuation process, the Saccharomyces yeasts were more resistant. For selecting the potential probiotic yeasts with better balance among all characteristics, a principal component analysis (PCA) was carried out. The most promising yeasts for use as health-promoting probiotics are Hanseniaspora osmophila 1056 and 1094, Lachancea thermotolerans 1039, and S. cerevisiae 3 and 146.\n\nPotential Probiotic Strains of Saccharomyces and Non-Saccharomyces: Functional and Biotechnological Characteristics.", "token_count": 490, "char_count": 1777, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6463, "quality_score": 0.8231, "entities": { "genes": [ "TC7" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:47.160843", "source": { "split": "train_shard_00001", "doc_id": 4238 }, "chunk_id": "train_shard_00001_4238_0", "global_id": 11653 }, { "text": "The pathogenic profiles of seven Shewanella spp. positive cases identified during diarrhea surveillance in Beijing, China, in 2023 were characterised. Sentinel hospitals collected patient information and stool samples, while regional centres for disease control (CDC) performed cultures and real time PCR. Whole-genome sequencing (WGS), average nucleotide identity (ANI) analysis, phylogenetic analysis, virulence gene and resistance gene analysis of the Shewanella spp. isolates were conducted, as well as phenotypic resistance analysis. The detection rate in the stool samples collected from 354 diarrhea patients was 1.98% (7/354). The time of disease onset of six out of the seven patients ranged from July 17-22, 2023. The incubation period ranged from 8 to 12 h with 3-50 episodes/day. Three subjects reported having consumed potentially contaminated seafood. The seven isolated strains of Shewanella spp. (named as S1-S7) were closely related to S. algae, belonged to the algae clade, and were all novel ST (sequence typing) strains. A total of 125,738 SNPs (single nucleotide polymorphism) were identified in the core genomes of the seven Shewanella strains. Twenty-six virulence-related genes in five categories were identified, with chemotaxis and flagella-related genes being the most abundant (26.92%, 7/26), followed by secretion system- and serum resistance-related genes at 23.08% (6/26) and 15.38% (4/26), respectively. Shewanella spp. were detected in patients with diarrhea at a certain level. Seafood should be the key food category for monitoring and seafood markets should become a key monitoring site for Shewanella spp. The novel STs of the algae clade isolated from diarrhea patients in this study may potentially help in tracking circulating strains. Further in-depth investigations are required to precisely elucidate the correlation between Shewanella infections and human diarrhea and the pathogenic characteristics of this infection.", "token_count": 522, "char_count": 1962, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6228, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:47.831677", "source": { "split": "train_shard_00001", "doc_id": 4239 }, "chunk_id": "train_shard_00001_4239_0", "global_id": 11654 }, { "text": "Investigation and pathogenetic testing of Shewanella spp. positive diarrhea cases in Beijing, China.", "token_count": 25, "char_count": 100, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:48.190130", "source": { "split": "train_shard_00001", "doc_id": 4239 }, "chunk_id": "train_shard_00001_4239_1", "global_id": 11655 }, { "text": "The abundant multifunctional protein ABF1 of Saccharomyces cerevisiae binds to the upstream region of several genes, including some ribosomal protein genes like the one encoding protein S33. Deletion of the ABF1-binding sequence lowers the transcription of these genes three- to more than ten-fold. We have isolated the S33 genes of two related yeast species, Kluyveromyces lactis and Kluyveromyces marxianus. Comparison of the nucleotide sequences of these S33 genes with their counterpart from S. cerevisiae shows a strong sequence similarity covering the whole of the coding regions. In contrast, little or no sequence similarity is found in the 5'-flanking regions of the three genes. Also the trailer regions differ considerably in both length and sequence from one species to another. An ABF1-binding site is present in the upstream region of the S33 gene of K. marxianus. Retardation analyses showed that this sequence is able to bind a protein present in Kluyveromyces cells with a molecular mass somewhat lower than that of S. cerevisiae ABF1. Functional analyses, using a beta-glucuronidase reporter system, showed that the ABF1-binding site is indeed involved in transcription activation of the K. marxianus S33 gene in Kluyveromyces cells. A S. cerevisiae ABF1-gene-specific probe showed only weak hybridization with Kluyveromyces DNA and Northern blots did not show a signal. These results indicate that S. cerevisiae and Kluyveromyces contain functionally related but structurally dissimilar ABF1-type proteins.\n\nStructure and expression of the ABF1-regulated ribosomal protein S33 gene in Kluyveromyces.", "token_count": 418, "char_count": 1618, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5588, "quality_score": 0.7794, "entities": { "genes": [ "ABF1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:48.815050", "source": { "split": "train_shard_00001", "doc_id": 4240 }, "chunk_id": "train_shard_00001_4240_0", "global_id": 11656 }, { "text": "Previous papers in this series described the “evolutionary genetic species concept” which is based on population genetic theory and should be applicable to any organism. Also described was a species criterion, the K/θ ratio, that delimits independently evolving evolutionary species based on single-gene sequences, and its application to sexual and asexual eukaryotes was illustrated. Here, we show how the evolutionary genetic species concept and the K/θ ratio can be applied to bacteria, using the sequences from some genes of the core genome that are rarely, if ever, transferred horizontally between different species. This completes the demonstration that K/θ is a general method for species delimitation, applicable to all organisms. Also, it adds to the evidence that bacteria have species in the most general sense, even though they have the ability to exchange genes across species boundaries. Finally, we show that a published critique of the use of K/θ ≥ 4 as a criterion for independently evolving species rests on two errors in the application of population/evolutionary genetic theory.\n\nEvolutionary Genetic Species Detected in Prokaryotes by Applying the K/θ Ratio to DNA Sequences", "token_count": 261, "char_count": 1196, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6044, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:49.366914", "source": { "split": "train_shard_00001", "doc_id": 4241 }, "chunk_id": "train_shard_00001_4241_0", "global_id": 11657 }, { "text": "The coinage \"pan-genome\" was first introduced dating back to 2005, and was used to elaborate the entire gene repertoire of any given species. Core genome consists of genes shared by all bacterial strains studied and is considered to encode essential functions associated with species' basic biology and phenotypes, yet its relatedness with bacterial lifestyle of the species remains elusive. We performed the pan-genome analysis of sulfur-oxidizing acidophile Acidithiobacillus thiooxidans as a case study to highlight species' core genome and its relevance with autotrophic lifestyle of bacterial species. The mathematical modeling based on bacterial genomes of A. thiooxidans species, including a novel strain ZBY isolated from Zambian copper mine plus eight other recognized strains, was attempted to extrapolate the expansion of its pan-genome, suggesting that A. thiooxidans pan-genome is closed. Further investigation revealed a common set of genes, many of which were assigned to metabolic profiles, notably with respect to energy metabolism, amino acid metabolism, and carbohydrate metabolism. The predicted metabolic profiles of A. thiooxidans were characterized by the fixation of inorganic carbon, assimilation of nitrogen compounds, and aerobic oxidation of various sulfur species. Notably, several hydrogenase (H2ase)-like genes dispersed in core genome might represent the novel classes due to the potential functional disparities, despite being closely related homologous genes that code for H2ase. Overall, the findings shed light on the distinguishing features of A. thiooxidans genomes on a global scale, and extend the understanding of its conserved core genome pertaining to autotrophic lifestyle.\n\nIn Silico Genome-Wide Analysis Reveals the Potential Links Between Core Genome of Acidithiobacillus thiooxidans and Its Autotrophic Lifestyle.", "token_count": 504, "char_count": 1932, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:50.018280", "source": { "split": "train_shard_00001", "doc_id": 4242 }, "chunk_id": "train_shard_00001_4242_0", "global_id": 11658 }, { "text": "Changes in Xanthomonas race and species composition causing bacterial spot of tomato have occurred throughout the world and are often associated with epidemics. Knowledge of bacterial population structure is key for resistance discovery and deployment. We surveyed Xanthomonas spp. composition from processing tomato fields in the Midwestern United States over a 4-year period between 2017 and 2020, compared these to strains collected previously, and found that X. perforans is currently the most prevalent species. We characterized 564 X. perforans isolates for sequence variation in avrXv3 to distinguish between race T3 and T4 and validated race designation using hypersensitive response (HR) assays for 106 isolates. Race T4 accounted for over 95% of X. perforans isolates collected in the Midwest between 2017 and 2020. Whole genome sequencing, Average Nucleotide Identity (ANI) analysis, core genome alignment and single nucleotide polymorphism (SNP) detection relative to a reference strain, and phylogenomic analysis suggest that the majority of Midwestern X. perforans strains collected between 2017 and 2020 were nearly identical, with greater than 99.99% ANI to X. perforans isolates collected from Collier County, Florida in 2012. These isolates shared a common SNP variant resulting an a premature stop codon in avrXv3. One sequenced isolate was identified with a deletion of avrXv3 and shared 99.99% ANI with a strain collected in Collier Co., Florida in 2006. A population shift to X. perforans T4 occurred in the absence of widely deployed resistance, with only 7% of tomato varieties tested having the resistant allele at the Xv3/Rx-4 locus", "token_count": 512, "char_count": 1749, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6024, "quality_score": 0.8012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:50.682387", "source": { "split": "train_shard_00001", "doc_id": 4243 }, "chunk_id": "train_shard_00001_4243_0", "global_id": 11659 }, { "text": "The persistence of nearly identical strains over multiple years suggests that migration led to the establishment of an endemic population. Our findings validate a genomics-based framework to track shifts in X. perforans populations due to migration, mutation, drift, or selection based on comparisons to 146 genomes.\n\nMigration Drives the Replacement of Xanthomonas perforans Races in the Absence of Widely Deployed Resistance.", "token_count": 110, "char_count": 441, "word_count": 61, "semantic_coherence": 1, "information_density": 0.8033, "quality_score": 0.9016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:51.062194", "source": { "split": "train_shard_00001", "doc_id": 4243 }, "chunk_id": "train_shard_00001_4243_1", "global_id": 11660 }, { "text": "Although Candida species are present as normal microflora of the human host, alterations in host defenses can lead to development of disease. Candida infections, ranging from urinary tract infections to bloodstream infections, are common in patients in the intensive care unit. Infections with non-albicans Candida sp are becoming more frequent, and resistance among these isolates is concerning. Candida kefyr is an uncommonly documented fungal pathogen. We report two cases of infection resulting from C. kefyr in our institution. The two patients had underlying disease states and drug therapies that increased the likelihood of developing an immunocompromised state. The C. kefyr isolates obtained from both patients were susceptible to amphotericin B, fluconazole, and itraconazole. Both patients had resolution of infection, one after receiving treatment with amphotericin B and the other with voriconazole.\n\nCandida kefyr, an uncommon but emerging fungal pathogen: report of two cases.", "token_count": 227, "char_count": 992, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6713, "quality_score": 0.8357, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:51.533531", "source": { "split": "train_shard_00001", "doc_id": 4244 }, "chunk_id": "train_shard_00001_4244_0", "global_id": 11661 }, { "text": "Enterococcus species are an emerging group of bacterial pathogens that have a significant role in hospital-associated infections and are associated with higher mortality and morbidity rates. Among these pathogens, Enterococcus mundtii is one of the causative agents of multiple hospital associated infections. Currently, no commercially available licensed vaccine is present, and multi-drug resistant strains of the pathogen are prominent. Due to several limitations of experimental vaccinology, computational vaccine designing proved to be helpful in vaccine designing against several bacterial pathogens. Herein, we designed a multi-epitope-based vaccine against E. mundtii using in silico approaches. After an in-depth analysis of the core genome, three probable antigenic proteins (lytic polysaccharide monooxygenase, siderophore ABC transporter substrate-binding protein, and lytic polysaccharide monooxygenase) were shortlisted for epitope prediction. Among predicted epitopes, ten epitopes-GPADGRIAS, TTINHGGAQA, SERTALSVTT, GDGGNGGGEV, GIKEPDLEK, KQADDRIEA, QAIGGDTSN, EPLDEQTASR, AQWEPQSIEA, QPLKFSDFEL-were selected for multi-epitope vaccine construct designing. The screened B- and T-cell epitopes were joined with each other via specific linkers and linked to the cholera toxin B subunit as an adjuvant to enhance vaccine immune protection efficacy. The designed vaccine construct induced cellular and humoral immune responses. Blind docking with immune cell receptors, followed by molecular dynamic simulation results confirms the good binding potency and stability of the vaccine in providing protection against the pathogen.\n\nDesigning of a Recombinant Multi-Epitopes Based Vaccine against Enterococcus mundtii Using Bioinformatics and Immunoinformatics Approaches.", "token_count": 478, "char_count": 1801, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6991, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:52.172315", "source": { "split": "train_shard_00001", "doc_id": 4245 }, "chunk_id": "train_shard_00001_4245_0", "global_id": 11662 }, { "text": "Mycoplasma gallisepticum is the most virulent and economically important Mycoplasma species for poultry worldwide. Currently, M. gallisepticum strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been successfully used for microbial outbreak investigations. However, the massive sequence data and the diverse properties of different genes within bacterial genomes results in a lack of standard reproducible methods for comparisons among M. gallisepticum whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for M. gallisepticum strains and field isolates. For development of this scheme, a diverse collection of 37 M. gallisepticum genomes was used to identify cgMLST targets. A total of 425 M. gallisepticum conserved genes (49.85% of M. gallisepticum genome) were selected as core genome targets. A total of 81 M. gallisepticum genomes from 5 countries on 4 continents were typed using M. gallisepticum cgMLST. Analyses of phylogenetic trees generated by cgMLST displayed a high degree of agreement with geographical and temporal information. Moreover, the high discriminatory power of cgMLST allowed differentiation between M. gallisepticum strains of the same outbreak. M. gallisepticum cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among M. gallisepticum isolates. cgMLST provides stable and expandable nomenclature, allowing for comparison and sharing of typing results among laboratories worldwide. cgMLST offers an opportunity to harness the tremendous power of next-generation sequencing technology in applied avian mycoplasma epidemiology at both local and global levels.", "token_count": 520, "char_count": 1937, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:52.829949", "source": { "split": "train_shard_00001", "doc_id": 4246 }, "chunk_id": "train_shard_00001_4246_0", "global_id": 11663 }, { "text": "Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum.", "token_count": 32, "char_count": 113, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:53.184120", "source": { "split": "train_shard_00001", "doc_id": 4246 }, "chunk_id": "train_shard_00001_4246_1", "global_id": 11664 }, { "text": "In this work 51 yeasts strains isolated from seasoned green table olives and belonging to the Candida, Debaryomyces, Kluyveromyces, Pichia, and Saccharomyces genera were characterized by their killer activity in different conditions. Killer activity of isolates was analyzed in a medium with different pH's (3.5 to 8.5) and NaCl concentrations (5, 8, and 10%). At every pH tested, all the genera studied had killer strains, although the smallest percentages of killer yeasts were found at the highest pH (8.5). The presence of 5 and 8% NaCl increased the detected killer percentage, but the highest salt concentration (10%) decreased it. The interaction between the reference killer yeasts and yeasts isolated from olives was analyzed. Most isolates were killer-sensitive to one or more killer reference strains. Only 2 of the 51 strains tested were considered killer-neutral. Cross-reaction trials between isolates and spoilage yeasts showed that, of the isolates, nine killer strains, belonging to Debaryomyces hansenii, Kluyveromyces marxianus, Pichia anomala, Pichia guilliermondii, and Saccharomyces cerevisiae, had the broadest spectra of action against yeasts that cause spoilage. These killer yeasts and the toxins that they produce are candidates for further investigation as suppressors of indigenous olive table yeast growth. The results confirmed the highly polymorphic expression of the killing activity, with each strain showing different killer activities. This method may thus be very useful for simple and rapid characterization of yeast strains of industrial interest.\n\nDetermination of killer activity in yeasts isolated from the elaboration of seasoned green table olives.", "token_count": 407, "char_count": 1692, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6016, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:53.812265", "source": { "split": "train_shard_00001", "doc_id": 4247 }, "chunk_id": "train_shard_00001_4247_0", "global_id": 11665 }, { "text": "

Background

Propionibacterium freudenreichii (PF) is an actinobacterium used in cheese technology and for its probiotic properties. PF is also extremely adaptable to several ecological niches and can grow on a variety of carbon and nitrogen sources. The aim of this work was to discover the genetic basis for strain-dependent traits related to its ability to use specific carbon sources. High-throughput sequencing technologies were ideal for this purpose as they have the potential to decipher genomic diversity at a moderate cost.

Results

21 strains of PF were sequenced and the genomes were assembled de novo. Scaffolds were ordered by comparison with the complete reference genome CIRM-BIA1, obtained previously using traditional Sanger sequencing. Automatic functional annotation and manual curation were performed. Each gene was attributed to either the core genome or an accessory genome. The ability of the 21 strains to degrade 50 different sugars was evaluated. Thirty-three sugars were degraded by none of the sequenced strains whereas eight sugars were degraded by all of them. The corresponding genes were present in the core genome. Lactose, melibiose and xylitol were only used by some strains. In this case, the presence/absence of genes responsible for carbon uptake and degradation correlated well with the phenotypes, with the exception of xylitol. Furthermore, the simultaneous presence of these genes was in line the metabolic pathways described previously in other species. We also considered the genetic origin (transduction, rearrangement) of the corresponding genomic islands. Ribose and gluconate were degraded to a greater or lesser extent (quantitative phenotype) by some strains. For these sugars, the phenotypes could not be explained by the presence/absence of a gene but correlated with the premature appearance of a stop codon interrupting protein synthesis and preventing the catabolism of corresponding carbon sources.

Conclusion

These results illustrate (i) the power of correlation studies to discover the genetic basis of binary strain-dependent traits, and (ii) the plasticity of PF chromosomes, probably resulting from horizontal transfers, duplications, transpositions and an accumulation of mutations", "token_count": 520, "char_count": 2263, "word_count": 322, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [ "BIA1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:48:54.470091", "source": { "split": "train_shard_00001", "doc_id": 4248 }, "chunk_id": "train_shard_00001_4248_0", "global_id": 11666 }, { "text": "Knowledge of the genetic basis of nitrogen and sugar degradation opens up new strategies for the screening of PF strain collections to enable optimum cheese starter, probiotic and white biotechnology applications.\n\nMutations and genomic islands can explain the strain dependency of sugar utilization in 21 strains of Propionibacterium freudenreichii.", "token_count": 80, "char_count": 350, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:54.848350", "source": { "split": "train_shard_00001", "doc_id": 4248 }, "chunk_id": "train_shard_00001_4248_1", "global_id": 11667 }, { "text": "Carbapenem-resistant Acinetobacter baumannii (CRAB) is a major cause of nosocomial infections and hospital outbreaks worldwide, remaining a critical clinical concern. Here we characterized and investigated the phylogenetic relationships of 105 CRAB isolates on intensive care unit surfaces from one hospital in China collected over six years. All strains carried bla OXA-23 , bla OXA-66 genes for carbapenem resistance, also had high resistance gene, virulence factor and insertion sequences burdens. Whole-genome sequencing revealed all strains belonged to ST2, the global clone CC2. The phylogenetic analysis based on the core genome showed all isolates was dominated by a single lineage of three clusters and eight different clones. Two clones were popular during the collection time. Using chi-square test to identify the epidemiologically meaningful groupings, we found the significant difference in community structure only present in strains from separation time. The haplotype and median-joining network analysis revealed genetic differences among clusters and changes occurred overtime in the dominating cluster. Our results highlighted substantial multidrug-resistant CRAB burden in hospital ICU environment, demonstrated potential clone outbreak in hospital.\n\nMolecular epidemiology and clone transmission of carbapenem-resistantAcinetobacter baumanniiin ICU rooms", "token_count": 314, "char_count": 1382, "word_count": 183, "semantic_coherence": 1, "information_density": 0.7541, "quality_score": 0.877, "entities": { "genes": [ "ST2", "CC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:55.407465", "source": { "split": "train_shard_00001", "doc_id": 4249 }, "chunk_id": "train_shard_00001_4249_0", "global_id": 11668 }, { "text": "Passage through the birth canal and consequent exposure to the mother's microbiota is considered to represent the initiating event for microbial colonization of the gastrointestinal tract of the newborn. However, a precise evaluation of such suspected vertical microbiota transmission has yet to be performed. Here, we evaluated the microbiomes of four sample sets, each consisting of a mother's fecal and milk samples and the corresponding infant's fecal sample, by means of amplicon-based profiling supported by shotgun metagenomics data for two key samples. Notably, targeted genome reconstruction from microbiome data revealed vertical transmission of a Bifidobacterium breve strain and a Bifidobacterium longum subsp. longum strain from mother to infant, a notion confirmed by strain isolation and genome sequencing. Furthermore, PCR analyses targeting unique genes from these two strains highlighted their persistence in the infant gut at 6 months. Thus, this study demonstrates the existence of specific bifidobacterial strains that are common to mother and child and thus indicative of vertical transmission and that are maintained in the infant for at least relatively short time spans.\n\nExploring Vertical Transmission of Bifidobacteria from Mother to Child.", "token_count": 279, "char_count": 1268, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6448, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:55.959587", "source": { "split": "train_shard_00001", "doc_id": 4250 }, "chunk_id": "train_shard_00001_4250_0", "global_id": 11669 }, { "text": "The activity of caspofungin (CSP) combined with terbinafine (TRB) against Candida dubliniensis, Candida kefyr and azole-resistant Candida albicans was evaluated in vitro by checkerboard analysis. The combination of CSP with TRB resulted in positive interactive effects in vitro against C. albicans and C. kefyr but not against C. dubliniensis. Moreover, true synergism was observed only against TRB resistant strains which became susceptible to this drug in the presence of CSP. In contrast, indifference was observed against strains that were already sensitive to TRB indicating that CSP may inhibit resistance to TRB.\n\nDifferential effects of the combination of caspofungin and terbinafine against Candida albicans, Candida dubliniensis and Candida kefyr.", "token_count": 196, "char_count": 757, "word_count": 108, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:56.816963", "source": { "split": "train_shard_00001", "doc_id": 4251 }, "chunk_id": "train_shard_00001_4251_0", "global_id": 11670 }, { "text": "Dehalococcoides spp. are an industrially relevant group of Chloroflexi bacteria capable of reductively dechlorinating contaminants in groundwater environments. Existing Dehalococcoides genomes revealed a high level of sequence identity within this group, including 98 to 100% 16S rRNA sequence identity between strains with diverse substrate specificities. Common molecular techniques for identification of microbial populations are often not applicable for distinguishing Dehalococcoides strains. Here we describe an oligonucleotide microarray probe set designed based on clustered Dehalococcoides genes from five different sources (strain DET195, CBDB1, BAV1, and VS genomes and the KB-1 metagenome). This \"pangenome\" probe set provides coverage of core Dehalococcoides genes as well as strain-specific genes while optimizing the potential for hybridization to closely related, previously unknown Dehalococcoides strains. The pangenome probe set was compared to probe sets designed independently for each of the five Dehalococcoides strains. The pangenome probe set demonstrated better predictability and higher detection of Dehalococcoides genes than strain-specific probe sets on nontarget strains with <99% average nucleotide identity. An in silico analysis of the expected probe hybridization against the recently released Dehalococcoides strain GT genome and additional KB-1 metagenome sequence data indicated that the pangenome probe set performs more robustly than the combined strain-specific probe sets in the detection of genes not included in the original design. The pangenome probe set represents a highly specific, universal tool for the detection and characterization of Dehalococcoides from contaminated sites. It has the potential to become a common platform for Dehalococcoides-focused research, allowing meaningful comparisons between microarray experiments regardless of the strain examined.\n\nDesign and verification of a pangenome microarray oligonucleotide probe set for Dehalococcoides spp.", "token_count": 466, "char_count": 2015, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [ "CBDB1", "DET195", "BAV1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:57.472078", "source": { "split": "train_shard_00001", "doc_id": 4252 }, "chunk_id": "train_shard_00001_4252_0", "global_id": 11671 }, { "text": "The incidence of infections caused by extraintestinal Escherichia coli (ExPEC) is rising globally, which is a major public health concern. ExPEC strains that are resistant to antimicrobials have been associated with excess mortality, prolonged hospital stays, and higher health care costs. E. coli sequence type 131 (ST131) is a major ExPEC clonal group worldwide, with variable plasmid composition, and has an array of genes enabling antimicrobial resistance (AMR). ST131 isolates frequently encode the AMR genes blaCTX-M-14, blaCTX-M-15, and blaCTX-M-27, which are often rearranged, amplified, and translocated by mobile genetic elements (MGEs). Short DNA reads do not fully resolve the architecture of repetitive elements on plasmids to allow MGE structures encoding blaCTX-M genes to be fully determined. Here, we performed long-read sequencing to decipher the genome structures of six E. coli ST131 isolates from six patients. Most long-read assemblies generated entire chromosomes and plasmids as single contigs, in contrast to more fragmented assemblies created with short reads alone. The long-read assemblies highlighted diverse accessory genomes with blaCTX-M-15, blaCTX-M-14, and blaCTX-M-27 genes identified in three, one, and one isolates, respectively. One sample had no blaCTX-M gene", "token_count": 453, "char_count": 1463, "word_count": 184, "semantic_coherence": 1, "information_density": 0.712, "quality_score": 0.856, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:58.152788", "source": { "split": "train_shard_00001", "doc_id": 4253 }, "chunk_id": "train_shard_00001_4253_0", "global_id": 11672 }, { "text": "Two samples had chromosomal blaCTX-M-14 and blaCTX-M-15 genes, and the latter was at three distinct locations, likely transposed by the adjacent MGEs: ISEcp1, IS903B, and Tn2 This study showed that AMR genes exist in multiple different chromosomal and plasmid contexts, even between closely related isolates within a clonal group such as E. coli ST131.IMPORTANCE Drug-resistant bacteria are a major cause of illness worldwide, and a specific subtype called Escherichia coli ST131 causes a significant number of these infections. ST131 bacteria become resistant to treatments by modifying their DNA and by transferring genes among one another via large packages of genes called plasmids, like a game of pass-the-parcel. Tackling infections more effectively requires a better understanding of what plasmids are being exchanged and their exact contents. To achieve this, we applied new high-resolution DNA sequencing technology to six ST131 samples from infected patients and compared the output to that of an existing approach. A combination of methods shows that drug resistance genes on plasmids are highly mobile because they can jump into ST131's chromosomes. We found that the plasmids are very elastic and undergo extensive rearrangements even in closely related samples. This application of DNA sequencing technologies illustrates at a new level the highly dynamic nature of ST131 genomes.\n\nComplete Assembly of Escherichia coli Sequence Type 131 Genomes Using Long Reads Demonstrates Antibiotic Resistance Gene Variation within Diverse Plasmid and Chromosomal Contexts.", "token_count": 440, "char_count": 1653, "word_count": 231, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:58.783384", "source": { "split": "train_shard_00001", "doc_id": 4253 }, "chunk_id": "train_shard_00001_4253_1", "global_id": 11673 }, { "text": "

Background

Antibiotic-resistant (AR) bacteria are a global threat. AR bacteria can be acquired in early life and have long-term sequelae. Limiting the spread of antibiotic resistance without triggering the development of additional resistance mechanisms is of immense clinical value. Here, we show how the infant gut microbiome can be modified, resulting in a significant reduction of AR genes (ARGs) and the potentially pathogenic bacteria that harbor them.

Methods

The gut microbiome was characterized using shotgun metagenomics of fecal samples from two groups of healthy, term breastfed infants. One group was fed B. infantis EVC001 in addition to receiving lactation support (n = 29, EVC001-fed), while the other received lactation support alone (n = 31, controls). Coliforms were isolated from fecal samples and genome sequenced, as well as tested for minimal inhibitory concentrations against clinically relevant antibiotics.

Results

Infants fed B. infantis EVC001 exhibited a change to the gut microbiome, resulting in a 90% lower level of ARGs compared to controls. ARGs that differed significantly between groups were predicted to confer resistance to beta lactams, fluoroquinolones, or multiple drug classes, the majority of which belonged to Escherichia, Clostridium, and Staphylococcus. Minimal inhibitory concentration assays confirmed the resistance phenotypes among isolates with these genes. Notably, we found extended-spectrum beta lactamases among healthy, vaginally delivered breastfed infants who had never been exposed to antibiotics.

Conclusions

Colonization of the gut of breastfed infants by a single strain of B. longum subsp. infantis had a profound impact on the fecal metagenome, including a reduction in ARGs", "token_count": 506, "char_count": 1830, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6639, "quality_score": 0.832, "entities": { "genes": [ "EVC001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:59.441259", "source": { "split": "train_shard_00001", "doc_id": 4254 }, "chunk_id": "train_shard_00001_4254_0", "global_id": 11674 }, { "text": "This highlights the importance of developing novel approaches to limit the spread of these genes among clinically relevant bacteria. Future studies are needed to determine whether colonization with B. infantis EVC001 decreases the incidence of AR infections in breastfed infants.

Trial registration

This clinical trial was registered at ClinicalTrials.gov, NCT02457338.\n\nEarly-life gut microbiome modulation reduces the abundance of antibiotic-resistant bacteria.", "token_count": 119, "char_count": 477, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8621, "quality_score": 0.931, "entities": { "genes": [ "NCT02457338", "EVC001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:48:59.824703", "source": { "split": "train_shard_00001", "doc_id": 4254 }, "chunk_id": "train_shard_00001_4254_1", "global_id": 11675 }, { "text": "

Background

The worldwide emergence and diffusion of extended-spectrum β-lactamase-K. pneumoniae (ESBL-KP) is of particular concern. Although ESBL-KP can inhabit the human gut asymptomatically, colonization with ESBL-KP is associated with an increased risk of ESBL-KP infection and mortality. In this study, we investigated the prevalence and characteristics of ESBL-KP in fecal samples from healthy persons in 12 villages in Shandong Province, China.

Methods

Screening for ESBL-KP in fecal samples was performed by selective cultivation. The bacterial species were identified using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and 16S rDNA sequence analysis. Minimum inhibitory concentrations (MICs) of 16 antibiotics were determined by the agar dilution method. Plasmid replicons, antimicrobial resistance genes and Sequence types (STs) of the isolates were determined by whole-genome sequencing (WGS). Genetic relatedness of ESBL-KP isolates was determined by the single nucleotide polymorphisms (SNP). The S1 nuclease-pulsed-field gel electrophoresis (S1-PFGE) was used to characterize the plasmids carried by ESBL-KP isolates. Conjugation assays was used to verify the transferability of bla CTX - M.

Results

ESBL-KP prevalence rates increased from 12.0% in 2015 to 27.5% in 2017. The experimental results showed that 97% of isolates had multi-drug resistance. Multiple ESBL resistance genotypes were commonly detected in the isolates. STs among the ESBL-KP isolates were diverse. All 69 bla CTX-M-3-positive isolates were located on plasmids, and these genes could be transferred with plasmids between different strains", "token_count": 517, "char_count": 1736, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6712, "quality_score": 0.8356, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:00.464383", "source": { "split": "train_shard_00001", "doc_id": 4255 }, "chunk_id": "train_shard_00001_4255_0", "global_id": 11676 }, { "text": "Phylogenetic analysis showed the possibility of transmission among some isolates.

Conclusion

This study obtained the drug resistance patterns, the drug resistance phenotype and molecular characteristics of fecal-derived ESBL-KP in rural communities in Shandong Province, China. We report a rapid increase in occurrence of ESBL-KP among fecal samples collected from healthy rural residents of Shandong Province from 2015 to 2017. The carriage rate of multidrug-resistant bacteria in healthy residents is increasing. Thus, a need for further monitoring and possible interventions of ESBL-KP in this region is warranted.\n\nIntestinal colonization with ESBL-producing Klebsiella pneumoniae in healthy rural villager: A genomic surveillance study in China, 2015-2017.", "token_count": 198, "char_count": 775, "word_count": 101, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:00.922953", "source": { "split": "train_shard_00001", "doc_id": 4255 }, "chunk_id": "train_shard_00001_4255_1", "global_id": 11677 }, { "text": "While the major virulence factors for Vibrio cholerae, the cause of the devastating diarrheal disease cholera, have been extensively studied, the initial intestinal colonization of the bacterium is not well understood because non-human adult animals are refractory to its colonization. Recent studies suggest the involvement of an interbacterial killing device known as the type VI secretion system (T6SS). Here, we tested the T6SS-dependent interaction of V. cholerae with a selection of human gut commensal isolates. We show that the pathogen efficiently depleted representative genera of the Proteobacteria in vitro, while members of the Enterobacter cloacae complex and several Klebsiella species remained unaffected. We demonstrate that this resistance against T6SS assaults was mediated by the production of superior T6SS machinery or a barrier exerted by group I capsules. Collectively, our data provide new insights into immunity protein-independent T6SS resistance employed by the human microbiota and colonization resistance in general.\n\nHuman commensal gut Proteobacteria withstand type VI secretion attacks through immunity protein-independent mechanisms.", "token_count": 264, "char_count": 1167, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7329, "quality_score": 0.8665, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:01.475165", "source": { "split": "train_shard_00001", "doc_id": 4256 }, "chunk_id": "train_shard_00001_4256_0", "global_id": 11678 }, { "text": "

ABSTRACT

Complex structural variants (cxSVs), e.g. inversions with flanking deletions or interspersed inverted duplications, are part of human genetic diversity but their characteristics are not well delineated. Because their structures are difficult to resolve, cxSVs have been largely excluded from genome analysis and population-scale association studies. To permit large-scale detection of cxSVs from paired-end whole-genome sequencing, we developed Automated Reconstruction of Complex Variants (ARC-SV) using a novel probabilistic algorithm and a machine learning approach that leverages the new Human Pangenome Reference Consortium diploid assemblies. Using ARC-SV, we resolved, across 4,262 human genomes spanning all continental super-populations, 8,493 cxSVs belonging to 12 subclasses. Some cxSVs with population-specific signatures are shared with Neanderthals. Overall cxSVs are significantly enriched in regions prone to recombination and germline de novo mutations. Many cxSVs mark phenotypic hotspots (each significantly associated with ≥ 20 traits) identified in genome-wide association studies (GWAS), and 46.4% of all significant GWAS-SNPs catalogued to date reside within ±125 kb of at least one cxSV locus. Common SNPs near cxSVs show significant trait heritability enrichment. Genomic regions affected by cxSVs are enriched for bivalent chromatin states. Rare cxSVs are enriched in neural genes and loci undergoing rapid or accelerated evolution and recently evolved cis -regulatory regions for human corticogenesis. We also identified 41 fixed loci where divergence from our most recent common ancestor is via localized cxSV. Our method and analysis framework allow for the accurate, efficient, and automatic identification of cxSVs for future population-scale studies of human disease and genome biology.\n\nAutomatic detection of complex structural genome variation across world populations", "token_count": 468, "char_count": 1921, "word_count": 259, "semantic_coherence": 1, "information_density": 0.695, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:02.130001", "source": { "split": "train_shard_00001", "doc_id": 4257 }, "chunk_id": "train_shard_00001_4257_0", "global_id": 11679 }, { "text": "Syphilis is an important sexually transmitted infection caused by the bacterium Treponema pallidum subspecies pallidum . The last two decades have seen syphilis incidence rise in many high-income countries, yet the evolutionary and epidemiological relationships that underpin this are poorly understood, as is the global T. pallidum population structure. We assembled a geographically and temporally diverse collection of clinical and laboratory samples comprising 726 T. pallidum genomes. We used detailed phylogenetic analysis and clustering to show that syphilis globally can be described by only two deeply branching lineages, Nichols and SS14. We show that both of these lineages can be found circulating concurrently in 12 of the 23 countries sampled. To provide further phylodynamic resolution we subdivided Treponema pallidum subspecies pallidum into 17 distinct sublineages. Importantly, like SS14, we provide evidence that two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analysis showed that recent isolates circulating in 14 different countries were genetically identical in their core genome to those from other countries, suggesting frequent exchange through international transmission pathways. This contrasts with the majority of samples collected prior to 1983, which are phylogenetically distinct from these more recently isolated sublineages. Bayesian temporal analysis provided evidence of a population bottleneck and decline occurring during the late 1990s, followed by a rapid population expansion a decade later. This was driven by the dominant T. pallidum sublineages circulating today, many of which are resistant to macrolides. Combined we show that the population of contemporary syphilis in high-income countries has undergone a recent and rapid global expansion.\n\nContemporary syphilis is characterised by rapid global spread of pandemicTreponema pallidumlineages", "token_count": 457, "char_count": 1971, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6089, "quality_score": 0.8044, "entities": { "genes": [ "SS14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:02.766374", "source": { "split": "train_shard_00001", "doc_id": 4258 }, "chunk_id": "train_shard_00001_4258_0", "global_id": 11680 }, { "text": "Aroma compounds produced Kluyveromyces marxianus in solid state fermentation on a packed bed column bioreactor.", "token_count": 30, "char_count": 111, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:03.131225", "source": { "split": "train_shard_00001", "doc_id": 4259 }, "chunk_id": "train_shard_00001_4259_0", "global_id": 11681 }, { "text": "In this work, a novel method is proposed to establish the most suitable operational temperature for an enzyme reactor. The method was based on mathematical modelling of the thermal stability and activity of the enzyme and was developed using thermodynamic concepts and experimental data from free and immobilized inulinases (2,1-beta-D fructan frutanohydrolase, EC 3.2.1.7) from Kluyveromyces marxianus, which were used as examples. The model was, therefore, designed to predict the enzyme activity with respect to the temperature and time course of the enzymatic process, as well as its half-life, in a broad temperature range. The knowledge and information provided by the model could be used to design the operational temperature conditions, leading to higher enzyme activities, while preserving acceptable stability levels, which represent the link between higher productivity and lower process costs. For the inulinase used in this study, the optimum temperature conditions leading to higher enzyme activities were shown to be 63 degrees C and 57.5 degrees C for the free and immobilized inulinases, respectively. However, according to the novel method of approach used here, the more appropriate operating temperatures would be 52 degrees C for free and 42 degrees C for immobilized inulinases, showing that the working temperature is not necessarily the same as the maximum reaction rate temperature, but preferably a lower temperature where the enzyme is much more stable.\n\nModelling thermal stability and activity of free and immobilized enzymes as a novel tool for enzyme reactor design.", "token_count": 351, "char_count": 1597, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5436, "quality_score": 0.7718, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:03.702137", "source": { "split": "train_shard_00001", "doc_id": 4260 }, "chunk_id": "train_shard_00001_4260_0", "global_id": 11682 }, { "text": "Escherichia coli is a highly diverse group of pathogens ranging from commensal of the intestinal tract, through to intestinal pathogen, and extraintestinal pathogen. Here, we present data on the population diversity of E. coli, using Bayesian analysis to identify 13 distinct clusters within the population from multilocus sequence typing data, which map onto a whole-genome-derived phylogeny based on 62 genome sequences. Bayesian analysis of recombination within the core genome identified reduction in detectable core genome recombination as one moves from the commensals, through the intestinal pathogens down to the multidrug-resistant extraintestinal pathogenic clone E. coli ST131. Our data show that the emergence of a multidrug-resistant, extraintestinal pathogenic lineage of E. coli is marked by substantial reduction in detectable core genome recombination, resulting in a lineage which is phylogenetically distinct and sexually isolated in terms of core genome recombination.\n\nThe evolutionary path to extraintestinal pathogenic, drug-resistant Escherichia coli is marked by drastic reduction in detectable recombination within the core genome.", "token_count": 288, "char_count": 1157, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5535, "quality_score": 0.7767, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:04.263295", "source": { "split": "train_shard_00001", "doc_id": 4261 }, "chunk_id": "train_shard_00001_4261_0", "global_id": 11683 }, { "text": "Genes SWA2 and GAMl from the yeast, Schwanniomyces occidentalis, encoding a- amylase and glucoamylase, respectively, were cloned and expressed in H. polymorpha. The expression was achieved by integration of the SWA2 and GAMl genes into the chromosome of H. polymorpha under operably linked to a strong constitutive promoter of the H. polymorpha - glyceraldehyde-3 -phosphate dehydrogenase gene (HpGAP. Resulting transformants acquired the ability to grow on a minimal medium containing soluble starch as a sole carbon source and can produce Ethanol at high-temperature fermentation from starch up to 10 g/L. A XYN2 gene encoding endoxylanase was obtained from the fungus Trichoderma resee, and a xlnD gene coding for ss-xylosidase was obtained from the fungus Aspergillus niger. Co-expression of these genes was also achieved by integration into the H. polymorpha chromosome under control of the HpGAP promoter. The resulting transformants were capable of growth on a minimal medium supplemented with birchwood xylan as a sole carbon source. Successful expression of xylanolytic enzymes resulted in a recipient strain capable of fermentation of birchwood xylan to ethanol at 48 DEG C. Further with co expression of the forgoing genes in a H. polymorpha strain that overexpresses a pyruvate decarboxylase gene further improved ethanol production.\n\nDEVELOPMENT OF STRAINS OF THE THERMOTOLERANT YEAST HANSENULA POLYMORPHA CAPABLE OF ALCOHOLIC FERMENTATION OF STARCH AND XYLAN BY EXPRESSION OF STARCH AND XYLAN DEGRADING ENZYMES", "token_count": 446, "char_count": 1524, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5177, "quality_score": 0.7588, "entities": { "genes": [ "SWA2", "XYN2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:04.891166", "source": { "split": "train_shard_00001", "doc_id": 4262 }, "chunk_id": "train_shard_00001_4262_0", "global_id": 11684 }, { "text": "

Objectives

Achromobacter xylosoxidans is widely distributed in the environment and is increasingly recognised as a significant nosocomial pathogen in healthcare settings. However, the genomic and phylogenetic characteristics of this pathogen are not fully understood. Here we report the first genome sequence of a multidrug-resistant A. xylosoxidans ST273 strain (MTYH1) isolated from a wound infection in China.

Methods

Whole-genome sequencing of the strain was performed using an Illumina NovaSeq 6000 platform. Generated short reads were de novo assembled into contigs using SPAdes v.3.13.0. Antimicrobial resistance genes (ARGs) were identified using ResFinder 4.0. Phylogenetic analysis was conducted using NJ/UPGMA phylogeny (MAFFT v.7) based on core genome single nucleotide polymorphism data.

Results

The draft genome sequence of A. xylosoxidans ST273 strain MTYH1 consists of 45 contigs comprising 6 643 045 bp with a GC content of 67.5%. According to the Achromobacter spp. multilocus sequence typing (MLST) scheme, MTYH1 belongs to ST273. MTYH1 is resistant to aminoglycosides, ciprofloxacin, aztreonam and cephalosporins. Five ARGs belonging to three different classes were identified in the genome, namely aac(6')-IIa, ant(2'')-Ia, blaCARB-2, blaOXA-114g and sul1. Phylogenetic analysis showed that MTYH1 was not epidemiologically related to any of the strains retrieved from the NCBI GenBank database.

Conclusion

We unravelled the genome sequence of multidrug-resistant A. xylosoxidans ST273 clinical strain MTYH1 recovered from a wound infection in China", "token_count": 511, "char_count": 1620, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6619, "quality_score": 0.831, "entities": { "genes": [ "ST273", "MTYH1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:05.554939", "source": { "split": "train_shard_00001", "doc_id": 4263 }, "chunk_id": "train_shard_00001_4263_0", "global_id": 11685 }, { "text": "Our data may help to understand the antimicrobial resistance mechanisms, genomic features and phylogenetic characteristic of this bacterial pathogen.\n\nGenomic and phylogenetic analysis of multidrug-resistant Achromobacter xylosoxidans ST273 strain MTYH1 co-carrying blaOXA-114g and blaCARB-2 recovered from a wound infection in China.", "token_count": 110, "char_count": 356, "word_count": 41, "semantic_coherence": 1, "information_density": 0.878, "quality_score": 0.939, "entities": { "genes": [ "ST273", "MTYH1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:05.935784", "source": { "split": "train_shard_00001", "doc_id": 4263 }, "chunk_id": "train_shard_00001_4263_1", "global_id": 11686 }, { "text": "In the current study, we aimed to elucidate the plant growth-promoting characteristics of Pseudomonas psychrotolerans CS51 under heavy metal stress conditions (Zn, Cu, and Cd) and determine the genetic makeup of the CS51 genome using the single-molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that inoculation with CS51 induced endogenous indole-3-acetic acid (IAA) and gibberellins (GAs), which significantly enhanced cucumber growth (root shoot length) and increased the heavy metal tolerance of cucumber plants. Moreover, genomic analysis revealed that the CS51 genome consisted of a circular chromosome of 5,364,174 base pairs with an average G+C content of 64.71%. There were around 4774 predicted protein-coding sequences (CDSs) in 4859 genes, 15 rRNA genes, and 67 tRNA genes. Around 3950 protein-coding genes with function prediction and 733 genes without function prediction were identified. Furthermore, functional analyses predicted that the CS51 genome could encode genes required for auxin biosynthesis, nitrate and nitrite ammonification, the phosphate-specific transport system, and the sulfate transport system, which are beneficial for plant growth promotion. The heavy metal resistance of CS51 was confirmed by the presence of genes responsible for cobalt-zinc-cadmium resistance, nickel transport, and copper homeostasis in the CS51 genome. The extrapolation of the curve showed that the core genome contained a minimum of 2122 genes (95% confidence interval = 2034.24 to 2080.215). Our findings indicated that the genome sequence of CS51 may be used as an eco-friendly bioresource to promote plant growth in heavy metal-contaminated areas.\n\nComplete Genome Sequence of Pseudomonas psychrotolerans CS51, a Plant Growth-Promoting Bacterium, Under Heavy Metal Stress Conditions.", "token_count": 504, "char_count": 1854, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [ "CS51" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:06.588765", "source": { "split": "train_shard_00001", "doc_id": 4264 }, "chunk_id": "train_shard_00001_4264_0", "global_id": 11687 }, { "text": "

Unlabelled

Prior to the epidemic that emerged in Haiti in October of 2010, cholera had not been documented in this country. After its introduction, a strain of Vibrio cholerae O1 spread rapidly throughout Haiti, where it caused over 600,000 cases of disease and >7,500 deaths in the first two years of the epidemic. We applied whole-genome sequencing to a temporal series of V. cholerae isolates from Haiti to gain insight into the mode and tempo of evolution in this isolated population of V. cholerae O1. Phylogenetic and Bayesian analyses supported the hypothesis that all isolates in the sample set diverged from a common ancestor within a time frame that is consistent with epidemiological observations. A pangenome analysis showed nearly homogeneous genomic content, with no evidence of gene acquisition among Haiti isolates. Nine nearly closed genomes assembled from continuous-long-read data showed evidence of genome rearrangements and supported the observation of no gene acquisition among isolates. Thus, intrinsic mutational processes can account for virtually all of the observed genetic polymorphism, with no demonstrable contribution from horizontal gene transfer (HGT). Consistent with this, the 12 Haiti isolates tested by laboratory HGT assays were severely impaired for transformation, although unlike previously characterized noncompetent V. cholerae isolates, each expressed hapR and possessed a functional quorum-sensing system. Continued monitoring of V. cholerae in Haiti will illuminate the processes influencing the origin and fate of genome variants, which will facilitate interpretation of genetic variation in future epidemics.

Importance

Vibrio cholerae is the cause of substantial morbidity and mortality worldwide, with over three million cases of disease each year. An understanding of the mode and rate of evolutionary change is critical for proper interpretation of genome sequence data and attribution of outbreak sources. The Haiti epidemic provides an unprecedented opportunity to study an isolated, single-source outbreak of Vibrio cholerae O1 over an established time frame", "token_count": 491, "char_count": 2128, "word_count": 304, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:07.247130", "source": { "split": "train_shard_00001", "doc_id": 4265 }, "chunk_id": "train_shard_00001_4265_0", "global_id": 11688 }, { "text": "By using multiple approaches to assay genetic variation, we found no evidence that the Haiti strain has acquired any genes by horizontal gene transfer, an observation that led us to discover that it is also poorly transformable. We have found no evidence that environmental strains have played a role in the evolution of the outbreak strain.\n\nEvolutionary dynamics of Vibrio cholerae O1 following a single-source introduction to Haiti.", "token_count": 92, "char_count": 435, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7794, "quality_score": 0.8897, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:07.621252", "source": { "split": "train_shard_00001", "doc_id": 4265 }, "chunk_id": "train_shard_00001_4265_1", "global_id": 11689 }, { "text": "During a study investigating the microbiota of raw milk and its semi-finished products, strains WS 5106T and WS 5096 were isolated from cream and skimmed milk concentrate. They could be assigned to the genus Pseudomonas by their 16S rRNA sequences, but not to any validly named species. In this work, a polyphasic approach was used to characterize the novel strains and to investigate their taxonomic status. Examinations based on the topology of core genome phylogenomy as well as average nucleotide identity (ANIm) comparisons suggested a novel Pseudomonas species within the Pseudomonas fluorescens subgroup. With pairwise ANIm values of 90.1 and 89.8 %, WS 5106T was most closely related to Pseudomonas nabeulensis CECT 9765T and Pseudomonas kairouanensis CECT 9766T. The G+C content of strain WS 5106T was 60.1 mol%. Morphologic analyses revealed Gram-stain-negative, aerobic, catalase and oxidase positive, rod-shaped and motile cells. Proteolysis on skimmed milk agar as well as lipolysis on tributyrin agar occurred at both 28 and 6 °C. Tolerated growth conditions were temperatures between 4 and 34 °C, pH values between 6.0 and 8.0, and salt concentrations of up to 5 %. Fatty acid profiles showed a pattern typical for Pseudomonas, with C16 : 0 as the dominant component. The major cellular polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol and the dominating quinone was Q-9", "token_count": 513, "char_count": 1536, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7051, "quality_score": 0.8525, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:08.263515", "source": { "split": "train_shard_00001", "doc_id": 4266 }, "chunk_id": "train_shard_00001_4266_0", "global_id": 11690 }, { "text": "Based on these results, it is proposed to classify the strains as a novel species, Pseudomonas cremoris sp. nov., with WS 5106T (=DSM 111143T=LMG 31863T) as type strain and WS 5096 (=DSM 111129=LMG 31864) as an additional strain.\n\nPseudomonas cremoris sp. nov., a novel proteolytic species isolated from cream.", "token_count": 151, "char_count": 357, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:08.747333", "source": { "split": "train_shard_00001", "doc_id": 4266 }, "chunk_id": "train_shard_00001_4266_1", "global_id": 11691 }, { "text": "Sugarcane Grassy Shoot (SCGS) disease is known to be related to Rice Yellow Dwarf (RYD) phytoplasmas (16SrXI-B group) which are found predominantly in sugarcane growing areas of the Indian subcontinent and South-East Asia. The 16S rRNA gene sequences of SCGS phytoplasma strains belonging to the 16SrXI-B group share 98.07 % similarity with 'Ca. Phytoplasma cynodontis' strain BGWL-C1 followed by 97.65 % similarity with 'Ca. P. oryzae' strain RYD-J. Being placed distinctly away from both the phylogenetically related species, the taxonomic identity of SCGS phytoplasma is unclear and confusing. We attempted to resolve the phylogenetic positions of SCGS phytoplasma based on the phylogenetic analysis of 16S rRNA gene (>1500 bp), nine housekeeping genes (>3500 aa), core genome phylogeny (>10 000 aa) and OGRI values. The draft genome sequences of SCGS phytoplasma (strain SCGS) and Bermuda Grass White leaf (BGWL) phytoplasma (strain LW01), closely related to 'Ca. P. cynodontis', were obtained. The SCGS genome was comprised of 29 scaffolds corresponding to 505 173 bp while LW01 assembly contained 21 scaffolds corresponding to 483 935 bp with the fold coverages over 330× and completeness over 90 % for both the genomes. The G+C content of SCGS was 19.86 % while that of LW01 was 20.46 %. The orthoANI values for the strain SCGS against strains LW01 was 79.42 %, and dDDH values were 22", "token_count": 516, "char_count": 1413, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [ "LW01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:09.417568", "source": { "split": "train_shard_00001", "doc_id": 4267 }, "chunk_id": "train_shard_00001_4267_0", "global_id": 11692 }, { "text": "Overall analysis reveals that SCGS phytoplasma forms a distant clade in RYD group of phytoplasmas. Based on phylogenetic analyses and OGRI values obtained from the genome sequences, a novel taxon 'Candidatus Phytoplasma sacchari' is proposed.\n\n'Candidatus Phytoplasma sacchari', a novel taxon - associated with Sugarcane Grassy Shoot (SCGS) disease.", "token_count": 115, "char_count": 363, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8776, "quality_score": 0.9388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:09.824656", "source": { "split": "train_shard_00001", "doc_id": 4267 }, "chunk_id": "train_shard_00001_4267_1", "global_id": 11693 }, { "text": "Abstract

Background

Clostridioides difficile infection rates are subject to infection prevention surveillance as a quality measure within the hospital setting. A large spike in Clostridioides difficile infections in post-operative patients, the majority of whom were gastrointestinal surgery (GIS) patients, was noted within a six month period (June through November 2019) at our comprehensive cancer center. These patients had been housed in one of two inpatient units and there was appropriate concern that this represented a C. difficile outbreak possibly related some type of infection control breach.

Methods

In an effort to query case relatedness, whole genome sequencing was performed using Illumina MiSeq instrumentation and chemistry with Illumina Nextera XT library chemistry. Assembly and core genome multilocus sequence typing analysis were performed with Ridom SeqSphere+ software. Cases were classified as community or hospital acquired based on the National Healthcare Safety Network (NHSN) definitions.

Results

There were 23 samples submitted for possible whole genome sequencing (WGS). 5 samples were unable to be grown therefore WGS was not completed; 16 were found to be unrelated (51 or more allelic differences); 2 of the 18 isolates were found to be possibly related (7 to 50 allelic differences). There were no isolates found to be definitively related (zero to 6 allelic differences).

Conclusion

Given the overwhelming unrelatedness of the isolates via whole genome sequencing, this increase of C. difficile cases, identified by routine surveillance within two inpatient units, was determined to be representative of a pseudo-outbreak rather than an outbreak. This study has implications on public health reporting. National Healthcare Safety Network definitions are used to identify healthcare facility-onset C. difficile infections (CDI). The majority of cases in this study met the definition of healthcare facility-onset, and thus were reported as such, despite being genetically unrelated. This raises the concern that a significant percentage of C. difficile infections may be currently misclassified as hospital-associated and this may have negative, unfair consequences for hospitals, such as implications on reimbursement", "token_count": 513, "char_count": 2290, "word_count": 323, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:10.504113", "source": { "split": "train_shard_00001", "doc_id": 4268 }, "chunk_id": "train_shard_00001_4268_0", "global_id": 11694 }, { "text": "

Disclosures

Robin Patel, MD, Accelerate Diagnostics (Grant/Research Support)CD Diagnostics (Grant/Research Support)Contrafect (Grant/Research Support)Curetis (Consultant)GenMark Diagnostics (Consultant)Heraeus Medical (Consultant)Hutchison Biofilm Medical Solutions (Grant/Research Support)Merck (Grant/Research Support)Next Gen Diagnostics (Consultant)PathoQuest (Consultant)Qvella (Consultant)Samsung (Other Financial or Material Support, Dr. Patel has a patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an anti-biofilm substance issued.)Selux Dx (Consultant)Shionogi (Grant/Research Support)Specific Technologies (Consultant)\n\n875. Pseudo-outbreak of Clostridioides (Clostridium) difficile amongst post-operative Oncology Patients", "token_count": 268, "char_count": 856, "word_count": 84, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:11.055006", "source": { "split": "train_shard_00001", "doc_id": 4268 }, "chunk_id": "train_shard_00001_4268_1", "global_id": 11695 }, { "text": "Abstract

Background

The transmission dynamics of Acinetobacter baumannii (Ab) outside the setting of hospital outbreaks is underinvestigated. The BJC Healthcare System in St. Louis, MO has not experienced an Ab hospital outbreak since 2012. Despite this, nearly 60% of all BJC Ab isolates are carbapenem-resistant Ab (CrAb).

Methods

We acquired whole genome sequences (WGSs) of 110 Ab isolates identified in five BJC hospitals from July 2017 to May 2019. We performed multilocus sequence typing, core genome alignment and pairwise average nucleotide identity analysis to compare WGSs from BJC isolates and GenBank-available WGSs of Ab isolates from other US hospitals. Further epidemiologic characterization was performed using BJC electronic medical records and detailed chart review.

Results

Though the majority of CrAb isolates in other US studies belonged to globally-prevalent sequence type 2 (ST2 [Pasteur scheme]), 62% and 26% of BJC CrAb index isolates belonged to the unrelated ST499 and ST406, respectively. BJC ST499 and ST406 isolates were phylogenetically distinct compared to corresponding isolates from other US hospitals. Under the assumption that Ab transmission occurs primarily through nosocomial spread, we expected BJC isolates from the same hospital and timespan to share the highest degree of homogeneity. However, geotemporal proximity between ST499 or ST406 BJC isolates was a poor predictor of their genetic relatedness, according to multiple comparative methods. Review of patient metadata did not identify epidemiological links between BJC isolates within phylogenetic subgroups.

Conclusion

We combined comparative genomics and detailed clinical chart review to characterize the transmission dynamics of two emerging US CrAb sequence types, ST499 and ST406. Though these highly homogeneous Ab isolates were identified over two years in multiple BJC hospitals, we found no evidence of robust intra-hospital transmission networks", "token_count": 508, "char_count": 1991, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [ "ST499", "ST2", "ST406" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:11.706206", "source": { "split": "train_shard_00001", "doc_id": 4269 }, "chunk_id": "train_shard_00001_4269_0", "global_id": 11696 }, { "text": "Instead, it appears that these CrAb isolates independently emerged from yet-to-be-identified regional, extra-hospital Ab populations. To neutralize the threat of drug-resistant infections in the US, it is essential to identify, characterize and disrupt emergent CrAb transmission networks that exist outside of hospital environments.

Disclosures

All Authors: No reported disclosures\n\n154. comparative Genomics Reveals Extra-hospital Transmission Networks of Carbapenem-resistant acinetobacter Baumannii sustained over Multiple Years in a US Midwest City", "token_count": 138, "char_count": 562, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8406, "quality_score": 0.9203, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:12.133273", "source": { "split": "train_shard_00001", "doc_id": 4269 }, "chunk_id": "train_shard_00001_4269_1", "global_id": 11697 }, { "text": "Different mixed cultures of Trichoderma reesei and a yeast were cultivated on beet pulp (BP)-containing medium. T. reesei and Kluyveromyces marxianus offered a combination that gave high SCP yields (51%) and efficiently converted BP into proteins (39.4%). The yeast extract in the basal medium could be substituted and the BP level multiplicated from 2 to 4% upon using mixed culture of T. reesei and K. marxianus. Under these conditions the protein yields reached to a maximum value of 54% and highest efficiency of BP conversion into proteins (41.8%). The obtained protein proved to contain all essential amino acids, which compared favourably with those of the FAO guideline and soy bean oil meal.\n\nSingle cell protein production from beet pulp by mixed culture.", "token_count": 198, "char_count": 765, "word_count": 122, "semantic_coherence": 1, "information_density": 0.7131, "quality_score": 0.8566, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:12.585761", "source": { "split": "train_shard_00001", "doc_id": 4270 }, "chunk_id": "train_shard_00001_4270_0", "global_id": 11698 }, { "text": "NorA is the best studied efflux system of Staphylococcus aureus and therefore frequently used as a model for investigating efflux-mediated resistance in this pathogen. NorA activity is associated with resistance to fluoroquinolones, several antiseptics and disinfectants and several reports have pointed out the role of efflux systems, including NorA, as a first-line response to antimicrobials in S. aureus. Genetic diversity studies of the gene norA have described three alleles; norAI, norAII and norAIII. However, the epidemiology of these alleles and their impact on NorA activity remains unclear. Additionally, increasing studies do not account for norA variability when establishing relations between resistance phenotypes and norA presence or reported absence, which actually corresponds, as we now demonstrate, to different norA alleles. In the present study we assessed the variability of the norA gene present in the genome of over 1,000 S. aureus isolates, corresponding to 112 S. aureus strains with whole genome sequences publicly available; 917 MRSA strains sourced from a London-based study and nine MRSA isolates collected in a major Hospital in Lisbon, Portugal. Our analyses show that norA is part of the core genome of S. aureus. It also suggests that occurrence of norA variants reflects the population structure of this major pathogen. Overall, this work highlights the ubiquitous nature of norA in S. aureus which must be taken into account when studying the role played by this important determinant on S. aureus resistance to antimicrobials.", "token_count": 480, "char_count": 1692, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:13.235765", "source": { "split": "train_shard_00001", "doc_id": 4271 }, "chunk_id": "train_shard_00001_4271_0", "global_id": 11699 }, { "text": "Genetic Diversity of <i>norA</i>, Coding for a Main Efflux Pump of <i>Staphylococcus aureus</i>.", "token_count": 58, "char_count": 120, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:13.602604", "source": { "split": "train_shard_00001", "doc_id": 4271 }, "chunk_id": "train_shard_00001_4271_1", "global_id": 11700 }, { "text": "Carbapenem resistant Acinetobacter baumannii (CRAb) is an important global pathogen contributing to increased morbidity and mortality in hospitalized patients, due to limited alternative treatment options. Nine international clonal (IC) lineages have been identified in many countries worldwide, however, data still lacks from some parts of the world, particularly in Africa. We hereby present the molecular epidemiology of MDR A. baumannii from four hospitals in Khartoum, Sudan, collected from 2017 to 2018. Forty-two isolates were whole-genome sequenced, and subsequent molecular epidemiology was determined by core genome MLST (cgMLST), and their resistomes identified. All isolates had an array of diverse antibiotic resistance mechanisms conferring resistance to multiple classes of antibiotics. We found a predominance (88%) of IC2 (with the intrinsic OXA-66 and acquired OXA-23), and some with NDM-1. IC2 isolates were sub-divided into 4 STs separated by 5 to 431 allelic differences, and with evidence of seven transmission clusters. Isolates belonging to IC1, IC5, and IC9 were also identified. These data illustrate that MDR IC2 A. baumannii are widely distributed in Khartoum hospitals and are in possession of multiple antibiotic resistance determinants.\n\nMolecular Epidemiology of Carbapenem-Resistant Acinetobacter baumannii From Khartoum State, Sudan.", "token_count": 379, "char_count": 1395, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [ "IC2", "IC1", "IC9", "IC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:14.188701", "source": { "split": "train_shard_00001", "doc_id": 4272 }, "chunk_id": "train_shard_00001_4272_0", "global_id": 11701 }, { "text": "

Background

Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios.

Results

We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, < or = 10 genome signature dissimilarity, and > 61% proteome identity", "token_count": 478, "char_count": 1663, "word_count": 250, "semantic_coherence": 1, "information_density": 0.632, "quality_score": 0.816, "entities": { "genes": [ "VM573", "VM603" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:14.836298", "source": { "split": "train_shard_00001", "doc_id": 4273 }, "chunk_id": "train_shard_00001_4273_0", "global_id": 11702 }, { "text": "Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree.

Conclusion

The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding.\n\nGenomic taxonomy of Vibrios.", "token_count": 147, "char_count": 665, "word_count": 91, "semantic_coherence": 1, "information_density": 0.6593, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:15.268811", "source": { "split": "train_shard_00001", "doc_id": 4273 }, "chunk_id": "train_shard_00001_4273_1", "global_id": 11703 }, { "text": "Salmonella is an important agent of gastrointestinal disease in humans. While livestock, such as cattle, poultry, and pigs, are well-recognised animal reservoirs of Salmonella, there is a lack of data on Salmonella in edible frogs, even though frog meat is a popular food worldwide. In this study, 103 live edible Chinese frogs (Hoplobatrachus rugulosus) were collected from wet markets throughout Hong Kong. After euthanasia, faeces or cloacal swabs were examined for Salmonella. Overall, Salmonella spp. were isolated from 67 (65%, CI: 0.554-0.736) of the samples. The serotypes included S. Saintpaul (33%), S. Newport (24%), S. Bareilly (7%), S. Braenderup (4%), S. Hvittingfoss (4%), S. Stanley (10%), and S. Wandsworth (16%). Many isolates were phylogenetically related. A high number of genes encoding for resistance to clinically relevant antimicrobials, and a high number of virulence determinants, were identified. Antimicrobial susceptibility testing (AST) identified multidrug resistance (MDR) in 21% of the isolates. Resistance to ampicillin, ciprofloxacin, nalidixic acid, and tetracycline was common. These results demonstrate that a high percentage of live frogs sold for human consumption in wet markets are carriers of multidrug-resistant Salmonella. Public health recommendations for handling edible frogs should be considered, to mitigate the risk of Salmonella transmission to humans.", "token_count": 485, "char_count": 1509, "word_count": 200, "semantic_coherence": 1, "information_density": 0.695, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:15.910195", "source": { "split": "train_shard_00001", "doc_id": 4274 }, "chunk_id": "train_shard_00001_4274_0", "global_id": 11704 }, { "text": "Serotypes, Antimicrobial Resistance Profiles, and Virulence Factors of Salmonella Isolates in Chinese Edible Frogs (Hoplobatrachus rugulosus) Collected from Wet Markets in Hong Kong.", "token_count": 67, "char_count": 196, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:16.290151", "source": { "split": "train_shard_00001", "doc_id": 4274 }, "chunk_id": "train_shard_00001_4274_1", "global_id": 11705 }, { "text": "Genes SWA2 and GAMl from the yeast, Schwanniomyces occidentalis, encoding [alpha]-amylase and glucoamylase, respectively, were cloned and expressed in H. polymorpha. The expression was achieved by integration of the SWA2 and GAM1 genes into the chromosome of H. polymorpha under operably linked to a strong constitutive promoter of the H. polymorpha-glyceraldehyde-3-phosphate dehydrogenase gene (HpGAP. Resulting transformants acquired the ability to grow on a minimal medium containing soluble starch as a sole carbon source and can produce Ethanol at high-temperature fermentation from starch up to 10 g/L. A XYN2 gene encoding endoxylanase was obtained from the fungus Trichoderma resee, and a xlnD gene coding for [beta]-xylosidase was obtained from the fungus Aspergillus niger. Co-expression of these genes was also achieved by integration into the H. polymorpha chromosome under control of the HpGAP promoter. The resulting transformants were capable of growth on a minimal medium supplemented with birchwood xylan as a sole carbon source. Successful expression of xylanolytic enzymes resulted in a recipient strain capable of fermentation of birchwood xylan to ethanol at 48 DEG C. Further with co expression of the for-going genes in a H. polymorpha strain that overexpresses a pyruvate decarboxylase gene further improved ethanol production.\n\nDevelopment of Strains of the Thermotolerant Yeast Hansenula Polymorpha Capable of Alcoholic Fermentation of Starch and Xylan by Expression of Starch and Xylan Degrading Enzymes", "token_count": 428, "char_count": 1531, "word_count": 222, "semantic_coherence": 1, "information_density": 0.518, "quality_score": 0.759, "entities": { "genes": [ "SWA2", "GAM1", "XYN2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:16.917260", "source": { "split": "train_shard_00001", "doc_id": 4275 }, "chunk_id": "train_shard_00001_4275_0", "global_id": 11706 }, { "text": "Water bodies worldwide have proven to be vast reservoirs of clinically significant antibiotic resistant organisms. Contamination of waters by anthropogenic discharges is a significant contributor to the widespread dissemination of antibiotic resistance. The aim of this research was to investigate multiple different anthropogenic sources on a national scale for the role they play in the environmental propagation of antibiotic resistance. A total of 39 water and 25 sewage samples were collected across four local authority areas in the West, East and South of Ireland. In total, 211 Enterobacterales were isolated (139 water, 72 sewage) and characterised. A subset of isolates (n=60) were chosen for whole genome sequencing. Direct comparisons of the water versus sewage isolate collections revealed a higher percentage of sewage isolates displayed resistance to cefoxitin (46%) and ertapenem (32%), while a higher percentage of water isolates displayed resistance to tetracycline (55%) and ciprofloxacin (71%). Half of all isolates displayed extended spectrum beta-lactamase (ESBL) production phenotypically (n = 105/211; 50%), with blaCTX-M detected in 99/105 isolates by PCR. Carbapenemase genes were identified in 11 isolates (6 sewage, 5 water). The most common variant was blaOXA-48 (n=6), followed by blaNDM-5 (n=2) and blaKPC-2 (n=2). Whole genome sequencing analysis revealed numerous different sequence types in circulation in both waters and sewage including E. coli ST131 (n=15), ST38 (n=8), ST10 (n=4) along with Klebsiella ST405 (n=3) and ST11 (n=2). Core genome MLST (cgMLST) comparisons uncovered three highly similar Klebsiella isolates originating from hospital sewage and two nearby waters", "token_count": 511, "char_count": 1755, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [ "ST131", "ST405", "ST10", "ST11", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:17.579675", "source": { "split": "train_shard_00001", "doc_id": 4276 }, "chunk_id": "train_shard_00001_4276_0", "global_id": 11707 }, { "text": "The Klebsiella isolates from an estuary and seawater displayed 99.1% and 98.8% cgMLST identity to the hospital sewage isolate respectively. In addition, three pairs of E. coli isolates from different waters also revealed cgMLST similarities, indicating widespread dissemination and persistence of certain strains in the aquatic environment. These findings highlight the need for routine monitoring of water bodies used for recreational and drinking purposes for the presence of multi-drug resistant organisms.\n\nA Point Prevalence Survey of Antibiotic Resistance in the Irish Environment, 2018-2019.", "token_count": 149, "char_count": 598, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7711, "quality_score": 0.8855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:18.030079", "source": { "split": "train_shard_00001", "doc_id": 4276 }, "chunk_id": "train_shard_00001_4276_1", "global_id": 11708 }, { "text": "Giant viruses (GVs) are a hotspot of unresolved controversies since their discovery, including the definition of \"Virus\" and their origin. While increasing knowledge of genome diversity has accumulated, GV functional genomics was largely neglected. Here, we describe an experimental framework to genetically modify nuclear GVs and their host Acanthamoeba castellanii using CRISPR/Cas9, shedding light on the evolution from small icosahedral viruses to amphora-shaped GVs. Ablation of the icosahedral major capsid protein in the phylogenetically-related mollivirus highlights a transition in virion shape and size. We additionally demonstrate the existence of a reduced core essential genome in pandoravirus, reminiscent of their proposed smaller ancestors. This proposed genetic expansion led to increased genome robustness, indicating selective pressures for adaptation to uncertain environments. Overall, we introduce new tools for manipulation of the unexplored genome of nuclear GVs and provide experimental evidence suggesting that viral gigantism has aroused as an emerging trait.\n\nEvolution of giant pandoravirus revealed by CRISPR/Cas9.", "token_count": 262, "char_count": 1144, "word_count": 154, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:18.582659", "source": { "split": "train_shard_00001", "doc_id": 4277 }, "chunk_id": "train_shard_00001_4277_0", "global_id": 11709 }, { "text": "

Background

Staphylococcus aureus is a major bacterial pathogen that causes a variety of diseases, ranging from wound infections to severe bacteremia or food poisoning. The course and severity of the disease are mainly dependent on the bacterium genotype as well as host factors. Whole-genome sequencing (WGS) is currently the most extensive genotyping method available, followed by bioinformatic sequence analysis.

Methods

A total of 253 uncharacterized staphylococcus genome sequences were downloaded from the National Center for Biotechnology Information (NCBI) (August 2012 to March 2020) from different studies. Samples were clustered based on core and accessory pairwise distances between isolates and then analyzed by multilocus sequence typing tool (MLST). Staphylococcal Cassette Chromosome mec (SCC mec ), spa typing, variant calling, core genome alignment, and recombination sites prediction were performed on detected S. aureus isolates. S. aureus isolates were also analyzed for the presence of genes coding for virulence factors and antibiotic resistance.

Results and conclusion

Uncategorized genome sequences were clustered into 24 groups. About 182 uncharacterized Staphylococcus genomes were identified at the species level based on MLST, including 32 S. lugdunensis genome sequence, thus doubling the number of the publicly accessible S. lugdunensis genome sequence in Genbank. MLST identified another four species ( S. epidermidis (33/253), S. lugdunensis (32/253), S. haemolyticus (41/253), S. hominis (24/253) and S. aureus (52/253)). Among the 52 S. aureus isolates, 21 (40.38%) isolates carried mec A gene, with 57.14% classified as SCC mec IV. The results of this study provide knowledge that facilitates evolutionary studies of staphylococcal species and other bacteria at the genome level.", "token_count": 521, "char_count": 1841, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8353, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:19.243993", "source": { "split": "train_shard_00001", "doc_id": 4278 }, "chunk_id": "train_shard_00001_4278_0", "global_id": 11710 }, { "text": "Comparative Genomic Analysis of Fifty-TwoStaphylococcus aureusIsolates Identified from Uncharacterized Staphylococcus Genomes in the NCBI database", "token_count": 47, "char_count": 153, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:19.606958", "source": { "split": "train_shard_00001", "doc_id": 4278 }, "chunk_id": "train_shard_00001_4278_1", "global_id": 11711 }, { "text": "

Background

Species of the family Vibrionaceae are ubiquitous in marine environments. Several of these species are important pathogens of humans and marine species. Evidence indicates that genetic exchange plays an important role in the emergence of new pathogenic strains within this family. Data from the sequenced genomes of strains in this family could show how the genes encoded by all these strains, known as the pangenome, are distributed. Information about the core, accessory and panproteome of this family can show how, for example, genes encoding virulence-associated proteins are distributed and help us understand how virulence emerges.

Results

We deduced the complete set of orthologs for eleven strains from this family. The core proteome consists of 1,882 orthologous groups, which is 28% of the 6,629 orthologous groups in this family. There were 4,411 accessory orthologous groups (i.e., proteins that occurred in from 2 to 10 proteomes) and 5,584 unique proteins (encoded once on only one of the eleven genomes). Proteins that have been associated with virulence in V. cholerae were widely distributed across the eleven genomes, but the majority was found only on the genomes of the two V. cholerae strains examined.

Conclusions

The proteomes are reflective of the differing evolutionary trajectories followed by different strains to similar phenotypes. The composition of the proteomes supports the notion that genetic exchange among species of the Vibrionaceae is widespread and that this exchange aids these species in adapting to their environments.\n\nComparative genomics of the family Vibrionaceae reveals the wide distribution of genes encoding virulence-associated proteins.", "token_count": 418, "char_count": 1721, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5565, "quality_score": 0.7782, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:20.237908", "source": { "split": "train_shard_00001", "doc_id": 4279 }, "chunk_id": "train_shard_00001_4279_0", "global_id": 11712 }, { "text": "

Unlabelled

Unraveling the drivers controlling the response and adaptation of biological communities to environmental change, especially anthropogenic activities, is a central but poorly understood issue in ecology and evolution. Comparative genomics studies suggest that lateral gene transfer (LGT) is a major force driving microbial genome evolution, but its role in the evolution of microbial communities remains elusive. To delineate the importance of LGT in mediating the response of a groundwater microbial community to heavy metal contamination, representative Rhodanobacter reference genomes were sequenced and compared to shotgun metagenome sequences. 16S rRNA gene-based amplicon sequence analysis indicated that Rhodanobacter populations were highly abundant in contaminated wells with low pHs and high levels of nitrate and heavy metals but remained rare in the uncontaminated wells. Sequence comparisons revealed that multiple geochemically important genes, including genes encoding Fe(2+)/Pb(2+) permeases, most denitrification enzymes, and cytochrome c553, were native to Rhodanobacter and not subjected to LGT. In contrast, the Rhodanobacter pangenome contained a recombinational hot spot in which numerous metal resistance genes were subjected to LGT and/or duplication. In particular, Co(2+)/Zn(2+)/Cd(2+) efflux and mercuric resistance operon genes appeared to be highly mobile within Rhodanobacter populations. Evidence of multiple duplications of a mercuric resistance operon common to most Rhodanobacter strains was also observed. Collectively, our analyses indicated the importance of LGT during the evolution of groundwater microbial communities in response to heavy metal contamination, and a conceptual model was developed to display such adaptive evolutionary processes for explaining the extreme dominance of Rhodanobacter populations in the contaminated groundwater microbiome.

Importance

Lateral gene transfer (LGT), along with positive selection and gene duplication, are the three main mechanisms that drive adaptive evolution of microbial genomes and communities, but their relative importance is unclear", "token_count": 497, "char_count": 2151, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5943, "quality_score": 0.7972, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:20.955414", "source": { "split": "train_shard_00001", "doc_id": 4280 }, "chunk_id": "train_shard_00001_4280_0", "global_id": 11713 }, { "text": "Some recent studies suggested that LGT is a major adaptive mechanism for microbial populations in response to changing environments, and hence, it could also be critical in shaping microbial community structure. However, direct evidence of LGT and its rates in extant natural microbial communities in response to changing environments is still lacking. Our results presented in this study provide explicit evidence that LGT played a crucial role in driving the evolution of a groundwater microbial community in response to extreme heavy metal contamination. It appears that acquisition of genes critical for survival, growth, and reproduction via LGT is the most rapid and effective way to enable microorganisms and associated microbial communities to quickly adapt to abrupt harsh environmental stresses.\n\nLateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community.", "token_count": 174, "char_count": 891, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:21.417812", "source": { "split": "train_shard_00001", "doc_id": 4280 }, "chunk_id": "train_shard_00001_4280_1", "global_id": 11714 }, { "text": "A lactose utilizing yeast strain, Kluyveromyces marxianus DSMZ-7239 was used for ethanol formation from cheese-whey powder (CWP) solution in batch experiments. Effects of initial substrate (CWP) and yeast concentrations on the rate and extent of ethanol formation were investigated. The initial pH and oxidation-reduction potential (ORP) was kept at 5 and -250 mV, respectively. The rate and extent of ethanol formation increased with increasing CWP concentration up to 156 g l(-1) (75 g l(-1) sugar) and then decreased for larger CWP concentrations due to substrate inhibition at high sugar concentrations. The ethanol yield coefficient was also maximum (0.54 g EtOH/g sugar) and equal to the theoretical yield at CWP concentration of 156 g l(-1). The growth yield coefficient was found to be Y(x/s)=1.2+/-0.1g biomass g sugar(-1). The rate of sugar utilization and ethanol formation also increased linearly with increasing initial biomass concentrations. A kinetic model describing the rate of sugar utilization and substrate inhibition as function of the initial substrate and the biomass concentrations was developed. The kinetic constants were determined using the experimental data. Model predictions of sugar utilization rates were in good agreement with the experimental data. The results indicated that the initial sugar concentration should be below 75 g l(-1) (CWP<156 g l(-1)) and the initial biomass should be above 850 mg l(-1) to obtain high rates and yields of ethanol formation and to avoid substrate inhibition.\n\nKinetics of batch ethanol fermentation of cheese-whey powder (CWP) solution as function of substrate and yeast concentrations.", "token_count": 428, "char_count": 1657, "word_count": 247, "semantic_coherence": 1, "information_density": 0.4534, "quality_score": 0.7267, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:22.076818", "source": { "split": "train_shard_00001", "doc_id": 4281 }, "chunk_id": "train_shard_00001_4281_0", "global_id": 11715 }, { "text": "

Background

In the course of replication of eukaryotic chromosomes, the telomere length is maintained due to activity of telomerase, the ribonucleoprotein reverse transcriptase. Abolishing telomerase function causes progressive shortening of telomeres and, ultimately, cell cycle arrest and replicative senescence. To better understand the cellular response to telomerase deficiency, we performed a transcriptomic study for the thermotolerant methylotrophic yeast Hansenula polymorpha DL-1 lacking telomerase activity.

Results

Mutant strain of H. polymorpha carrying a disrupted telomerase RNA gene was produced, grown to senescence and analyzed by RNA-seq along with wild type strain. Telomere shortening induced a transcriptional response involving genes relevant to telomere structure and maintenance, DNA damage response, information processing, and some metabolic pathways. Genes involved in DNA replication and repair, response to environmental stresses and intracellular traffic were up-regulated in senescent H. polymorpha cells, while strong down-regulation was observed for genes involved in transcription and translation, as well as core histones.

Conclusions

Comparison of the telomerase deletion transcription responses by Saccharomyces cerevisiae and H. polymorpha demonstrates that senescence makes different impact on the main metabolic pathways of these yeast species but induces similar changes in processes related to nucleic acids metabolism and protein synthesis. Up-regulation of a subunit of the TORC1 complex is clearly relevant for both types of yeast.\n\nThe genome-wide transcription response to telomerase deficiency in the thermotolerant yeast Hansenula polymorpha DL-1.", "token_count": 421, "char_count": 1718, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [ "TORC1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:22.724057", "source": { "split": "train_shard_00001", "doc_id": 4282 }, "chunk_id": "train_shard_00001_4282_0", "global_id": 11716 }, { "text": "Streptomycetaceae is one of the oldest families within phylum Actinobacteria and it is large and diverse in terms of number of described taxa. The members of the family are known for their ability to produce medically important secondary metabolites and antibiotics. In this study, strains showing low 16S rRNA gene similarity (<97.3 %) with other members of Streptomycetaceae were identified and subjected to phylogenomic analysis using 33 orthologous gene clusters (OGC) for accurate taxonomic reassignment resulted in identification of eight distinct and deeply branching clades, further average amino acid identity (AAI) analysis showed lower AAI values or AAI within the range of 60-80 % which was previously observed in related but different genera of bacteria. The whole genome phylogeny based on concatenated core genes and AAI analyses supported the claim that those phylogenetically distinct members may be assigned to 8 novel genera namely Actinoacidiphila, Actinomesophilus, Charcoactinospora, Curviacidiphilus, Kafeoacidiphilus, Mangroviactinospora, Peterkaempfera, and Streptantibioticus. In addition, based on the core genome phylogeny and 16S rRNA tree topology and distinct chemotaxonomic and physiological properties, the sequence belonged to Streptomyces thermoautotrophicus was assigned to a novel genera Charcoactinospora which is placed under novel family Charcoactinosporaceae . Lastly, a clade comprising of strains that showed high 16S rRNA gene similarity (100 %) with similar tree topology in phylogenetic trees was subjected to overall genome related indices analyses such as digital DNA – DNA hybridization, and average nucleotide identity that supported the claim that Streptomyces asterosporus is a later heterotypic synonym of Streptomyces calvus.", "token_count": 466, "char_count": 1779, "word_count": 248, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:23.364036", "source": { "split": "train_shard_00001", "doc_id": 4283 }, "chunk_id": "train_shard_00001_4283_0", "global_id": 11717 }, { "text": "Genomic and phylogenomic insights into the familyStreptomycetaceaelead to proposal ofCharcoactinosporaceaefam. nov. and 8 novel genera with emended descriptions ofStreptomyces calvus", "token_count": 72, "char_count": 203, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:23.730738", "source": { "split": "train_shard_00001", "doc_id": 4283 }, "chunk_id": "train_shard_00001_4283_1", "global_id": 11718 }, { "text": "

Background

Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents exploration of their genomic functions, including those that convey (human) health benefits.

Methods

PacBio SMRT sequencing was used to determine the whole genome seqeunces of two B. longum subsp. longum strains. The B. longum pan-genome was computed using PGAP v1.2 and the core B. longum phylogenetic tree was constructed using a maximum-likelihood based approach in PhyML v3.0. M.blmNCII was cloned in E. coli and an internal fragment if arfBarfB was cloned into pORI19 for insertion mutagenesis.

Results

In this study we present the complete genome sequences of two Bifidobacterium longum subsp. longum strains. Comparative analysis with thirty one publicly available B. longum genomes allowed the definition of the B. longum core and dispensable genomes. This analysis also highlighted differences in particular metabolic abilities between members of the B. longum subspecies infantis, longum and suis. Furthermore, phylogenetic analysis of the B. longum core genome indicated the existence of a novel subspecies. Methylome data, coupled to the analysis of restriction-modification systems, allowed us to substantially increase the genetic accessibility of B. longum subsp. longum NCIMB 8809 to a level that was shown to permit site-directed mutagenesis.

Conclusions

Comparative genomic analysis of thirty three B. longum representatives revealed a closed pan-genome for this bifidobacterial species. Phylogenetic analysis of the B. longum core genome also provides evidence for a novel fifth B. longum subspecies. Finally, we improved genetic accessibility for the strain B. longum subsp. longum NCIMB 8809, which allowed the generation of a mutant of this strain.", "token_count": 527, "char_count": 2012, "word_count": 279, "semantic_coherence": 1, "information_density": 0.5448, "quality_score": 0.7724, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:24.363155", "source": { "split": "train_shard_00001", "doc_id": 4284 }, "chunk_id": "train_shard_00001_4284_0", "global_id": 11719 }, { "text": "Pangenome analysis of Bifidobacterium longum and site-directed mutagenesis through by-pass of restriction-modification systems.", "token_count": 32, "char_count": 127, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:24.722602", "source": { "split": "train_shard_00001", "doc_id": 4284 }, "chunk_id": "train_shard_00001_4284_1", "global_id": 11720 }, { "text": "Candida auris is an emerging, multidrug-resistant fungal pathogen that has become a public health threat with an increasing incidence of infections worldwide. Candida auris spreads easily among patients within and between hospitals. Infections and outbreaks caused by C. auris have been reported in the Middle East region including Oman, Kuwait, Saudi Arabia, and Qatar; however, the origin of these isolates is largely unknown. Pathogen whole genome sequencing (WGS) was used to determine the epidemiology and drug resistance mutations of C. auris in Qatar. Forty-four samples isolated from patients in three hospitals and the hospital environment were sequenced by Illumina NextSeq. Core genome single nucleotide polymorphisms (SNPs) revealed that all isolates belonged to the South Asian lineage with genetic heterogeneity that suggests previous acquisition from foreign healthcare. The genetic variability among the outbreak isolates in the two hospitals (A and B) was low. Four environmental isolates clustered with the related clinical isolates, and epidemiologically linked isolates clustered together, suggesting that the ongoing transmission of C. auris could be linked to infected/colonized patients and the hospital environment. Prominent mutations Y132F and K143R in ERG11 linked to increased fluconazole resistance were detected.\n\nGenomic Epidemiology of Candida auris in Qatar Reveals Hospital Transmission Dynamics and a South Asian Origin.", "token_count": 369, "char_count": 1504, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [ "ERG11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:25.299636", "source": { "split": "train_shard_00001", "doc_id": 4285 }, "chunk_id": "train_shard_00001_4285_0", "global_id": 11721 }, { "text": "An understanding of why certain Acinetobacter species are more successful in causing nosocomial infections, transmission and epidemic spread in healthcare institutions compared with other species is lacking. We used genomic, phenotypic and virulence studies to identify differences between Acinetobacter species. Fourteen strains representing nine species were examined. Genomic analysis of six strains showed that the A. baumannii core genome contains many genes important for diverse metabolism and survival in the host. Most of the A. baumannii core genes were also present in one or more of the less clinically successful species. In contrast, when the accessory genome of an individual A. baumannii strain was compared to a strain of a less successful species (A. calcoaceticus RUH2202), many operons with putative virulence function were found to be present only in the A. baumannii strain, including the csu operon, the acinetobactin chromosomal cluster, and bacterial defence mechanisms. Phenotype microarray analysis showed that compared to A. calcoaceticus (RUH2202), A. baumannii ATCC 19606(T) was able to utilise nitrogen sources more effectively and was more tolerant to pH, osmotic and antimicrobial stress. Virulence differences were also observed, with A. baumannii ATCC 19606(T), A. pittii SH024, and A. nosocomialis RUH2624 persisting and forming larger biofilms on human skin than A. calcoaceticus. A. baumannii ATCC 19606(T) and A. pittii SH024 were also able to survive in a murine thigh infection model, whereas the other two species were eradicated. The current study provides important insights into the elucidation of differences in clinical relevance among Acinetobacter species.\n\nThe success of acinetobacter species; genetic, metabolic and virulence attributes.", "token_count": 465, "char_count": 1789, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5698, "quality_score": 0.7849, "entities": { "genes": [ "RUH2624", "RUH2202", "SH024" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:25.937517", "source": { "split": "train_shard_00001", "doc_id": 4286 }, "chunk_id": "train_shard_00001_4286_0", "global_id": 11722 }, { "text": "Eleven completely sequenced Chlorobi genomes were compared in oligonucleotide usage, gene contents, and synteny. The green sulfur bacteria (GSB) are equipped with a core genome that sustains their anoxygenic phototrophic lifestyle by photosynthesis, sulfur oxidation, and CO(2) fixation. Whole-genome gene family and single gene sequence comparisons yielded similar phylogenetic trees of the sequenced chromosomes indicating a concerted vertical evolution of large gene sets. Chromosomal synteny of genes is not preserved in the phylum Chlorobi. The accessory genome is characterized by anomalous oligonucleotide usage and endows the strains with individual features for transport, secretion, cell wall, extracellular constituents, and a few elements of the biosynthetic apparatus. Giant genes are a peculiar feature of the genera Chlorobium and Prosthecochloris. The predicted proteins have a huge molecular weight of 10(6), and are probably instrumental for the bacteria to generate their own intimate (micro)environment.\n\nComparative genomics of green sulfur bacteria.", "token_count": 267, "char_count": 1071, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7055, "quality_score": 0.8527, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:26.490921", "source": { "split": "train_shard_00001", "doc_id": 4287 }, "chunk_id": "train_shard_00001_4287_0", "global_id": 11723 }, { "text": "Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that dominates microbial mats in Asian non-acidic hot springs. These cyanobacteria are the major primary producers in their ecological niches and are promising sources of thermostable enzymes for biotechnology applications. To improve our understanding of these organisms, we conducted whole-genome sequencing of a novel strain for comparative analysis with other representatives in the same genus. This newly characterized strain, Thermosynechococcus sp. TA-1, was isolated from the Taian hot springs in Taiwan. Analyses based on average nucleotide identity (ANI) and genome-scale phylogeny suggested that TA-1 and another Taiwanese strain CL-1 belong to a novel species-level taxon. Two metagenome-assembled genomes (MAGs) originated from India represent the sister group, and Thermosynechococcus elongatus PKUAC-SCTE542 from China is the next closest lineage. All cultivated strains and MAGs from Japan form a separate monophyletic clade and could be classified into two species-level taxa. Intriguingly, although TA-1 and CL-1 share 97.0% ANI, the genome alignment identified at least 16 synteny breakpoints that are mostly associated with transposase genes, which illustrates the dynamic nature of their chromosomal evolution. Gene content comparisons identified multiple features distinct at species- or strain-level among these Thermosynechococcus representatives. Examples include genes involved in bicarbonate transportation, nitric oxide protection, urea utilization, kanamycin resistance, restriction-modification system, and chemotaxis. Moreover, we observed the insertion of type II inteins in multiple genes of the two Taiwanese strains and inferred putative horizontal transfer of an asparagine synthase gene (asnB) associated with exopolysaccharides gene cluster", "token_count": 491, "char_count": 1886, "word_count": 244, "semantic_coherence": 1, "information_density": 0.7254, "quality_score": 0.8627, "entities": { "genes": [ "SCTE542" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:27.151397", "source": { "split": "train_shard_00001", "doc_id": 4288 }, "chunk_id": "train_shard_00001_4288_0", "global_id": 11724 }, { "text": "Taken together, while previous work suggested that strains in this genus share a highly conserved genomic core and no clear genetic differentiation could be linked to environmental factors, we found that the overall pattern of gene content divergence is largely congruent with core genome phylogeny. However, it is difficult to distinguish between the roles of phylogenetic relatedness and geographic proximity in shaping the genetic differentiation. In conclusion, knowledge of the genomic differentiation among these strains provides valuable resources for future functional characterization.\n\nComparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. TA-1.", "token_count": 156, "char_count": 726, "word_count": 95, "semantic_coherence": 1, "information_density": 0.8105, "quality_score": 0.9053, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:27.587390", "source": { "split": "train_shard_00001", "doc_id": 4288 }, "chunk_id": "train_shard_00001_4288_1", "global_id": 11725 }, { "text": "Neisseria meningitidis (Nm) and N. gonorrhoeae (Ng) are closely related pathogenic bacteria. Using those genes found across 20 Nm and 15 Ng genomes we find that Nm is 7x more diverse than Ng in their combined core genome. Both species have acquired the majority of their diversity by recombination with divergent strains, however we find that Nm has acquired more of its diversity by recombination than Ng. We find that linkage disequilibrium declines rapidly across both species. Several observations suggest that Nm has a higher effective population size than Ng; it is more diverse, the ratio of non-synonymous to synonymous polymorphism is lower, and LD declines more rapidly to a lower asymptote. The two species share a modest amount of variation, half of which seems to have been acquired by lateral gene transfer and half from their common ancestor. We investigate whether diversity varies across the genome of each species and find that it does. Much of this variation is due to different levels of lateral gene transfer. However, we also find some evidence that the effective population size varies across the genome. We test for adaptive evolution in the core genome and found some evidence.\n\nThe comparative population genetics of Neisseria meningitidis and Neisseria gonorrhoeae", "token_count": 313, "char_count": 1305, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5777, "quality_score": 0.7888, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:28.145608", "source": { "split": "train_shard_00001", "doc_id": 4289 }, "chunk_id": "train_shard_00001_4289_0", "global_id": 11726 }, { "text": "Based on previous studies, Candida utilis pyruvate decarboxylase (PDC) proved to be a stable and high productivity enzyme for the production (R)-phenylacetylcarbinol (PAC), a pharmaceutical precursor. However, a portion of the substrate pyruvate was lost to by-product formation. To identify a source of PDC which might overcome this problem, strains of four yeasts -- C. utilis, Candida tropicalis, Saccharomyces cerevisiae and Kluyveromyces marxianus -- were investigated for their PDC biocatalytic properties. Biotransformations were conducted with benzaldehyde and pyruvate as substrates and three experimental systems were employed (in the order of increasing benzaldehyde concentrations): (I) aqueous (soluble benzaldehyde), (II) aqueous/benzaldehyde emulsion, and (III) aqueous/octanol-benzaldehyde emulsion. Although C. utilis PDC resulted in the highest concentrations of PAC and was the most stable enzyme, C. tropicalis PDC was associated with the lowest acetoin formation. For example, in system (III) the ratio of PAC over acetoin was 35 g g(-1) for C. tropicalis PDC and 9.2 g g(-1) for C. utilis PDC. The study thereby opens up the potential to design a PDC with both high productivity and high yield characteristics.\n\nYeast pyruvate decarboxylases: variation in biocatalytic characteristics for (R)-phenylacetylcarbinol production.", "token_count": 385, "char_count": 1347, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:28.759382", "source": { "split": "train_shard_00001", "doc_id": 4290 }, "chunk_id": "train_shard_00001_4290_0", "global_id": 11727 }, { "text": "Everyday actions such as eating, tooth brushing or applying cosmetics inherently modulate our microbiome. Advances in sequencing technologies now facilitate detailed microbial profiling, driving intentional microbiome-targeted product development. Inspired by an academic-industry workshop held in January 2024, this review explores the oral, skin and gut microbiomes, focussing on the potential long-term implications of perturbations. Key challenges in microbiome safety assessment include confounding factors (ecological variability, host influences and external conditions like geography and diet) and biases from experimental measurements and bioinformatics analyses. The taxonomic composition of the microbiome has been associated with both health and disease, and perturbations like regular disruption of the dental biofilm are essential for preventing caries and inflammatory gum disease. However, further research is required to understand the potential long-term impacts of microbiome disturbances, particularly in vulnerable populations including infants. We propose that emerging technologies, such as omics technologies to characterize microbiome functions rather than taxa, leveraging artificial intelligence to interpret clinical study data and in vitro models to characterize and measure host-microbiome interaction endpoints, could all enhance the risk assessments. The workshop emphasized the importance of detailed documentation, transparency and openness in computational models to reduce uncertainties. Harmonisation of methods could help bridge regulatory gaps and streamline safety assessments but should remain flexible enough to allow innovation and technological advancements. Continued scientific collaboration and public engagement are critical for long-term microbiome monitoring, which is essential to advancing safety assessments of microbiome perturbations.\n\nAssessing the safety of microbiome perturbations.", "token_count": 386, "char_count": 1947, "word_count": 243, "semantic_coherence": 1, "information_density": 0.7243, "quality_score": 0.8621, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:29.380593", "source": { "split": "train_shard_00001", "doc_id": 4291 }, "chunk_id": "train_shard_00001_4291_0", "global_id": 11728 }, { "text": "

Objective

To evaluate the efficacy and safety of ibrexafungerp versus placebo for acute vulvovaginal candidiasis (VVC) treatment.

Design

Global phase 3, randomised, placebo-controlled superiority study.

Setting

Study sites in the USA (n = 19) and Bulgaria (n = 18).

Population

Female patients aged ≥12 years with acute VVC and a vulvovaginal signs and symptoms (VSS) score ≥4 at baseline.

Methods

Patients were randomly assigned 2:1 to ibrexafungerp (300 mg twice for 1 day) or placebo.

Main outcome measures

The primary endpoint was the percentage of patients with a clinical cure (VSS = 0) at the test-of-cure visit (day 11 ± 3)", "token_count": 265, "char_count": 673, "word_count": 90, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:29.929717", "source": { "split": "train_shard_00001", "doc_id": 4292 }, "chunk_id": "train_shard_00001_4292_0", "global_id": 11729 }, { "text": "Secondary endpoints included percentages of patients with mycological eradication, clinical cure and mycological eradication (overall success), clinical improvement (VSS ≤1) at test-of-cure visit, and complete resolution of symptoms at follow-up visit (day 25 ± 4).

Results

At the test-of-cure visit, patients receiving ibrexafungerp had significantly higher rates of clinical cure (63.3% [119/188] versus 44.0% [37/84]; P = 0.007), mycological eradication (58.5% [110/188] versus 29.8% [25/84]; P < 0.001), overall success (46.1% [82/188] versus 28.4% [23/84]; P = 0.022) and clinical improvement (72.3% [136/188] versus 54.8% [46/84]; P = 0.01) versus those receiving placebo. Symptom resolution was sustained and further increased with ibrexafungerp (73.9%) versus placebo (52.4%) at follow-up (P = 0.001). Ibrexafungerp was generally well tolerated. Adverse events were primarily gastrointestinal and were mild to moderate in severity.

Conclusions

Ibrexafungerp demonstrated statistical superiority over placebo for the primary and secondary endpoints. Ibrexafungerp is a promising novel, well-tolerated and effective oral 1-day treatment for acute VVC.

Tweetable abstract

Ibrexafungerp is statistically superior to placebo for the treatment of vulvovaginal candidiasis.", "token_count": 481, "char_count": 1295, "word_count": 163, "semantic_coherence": 1, "information_density": 0.681, "quality_score": 0.8405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:30.572458", "source": { "split": "train_shard_00001", "doc_id": 4292 }, "chunk_id": "train_shard_00001_4292_1", "global_id": 11730 }, { "text": "Efficacy and safety of oral ibrexafungerp for the treatment of acute vulvovaginal candidiasis: a global phase 3, randomised, placebo-controlled superiority study (VANISH 306).", "token_count": 58, "char_count": 175, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:30.937936", "source": { "split": "train_shard_00001", "doc_id": 4292 }, "chunk_id": "train_shard_00001_4292_2", "global_id": 11731 }, { "text": "Microscopic colitis (MC) is a chronic inflammatory disease of the large intestine that primarily affects older adults and presents with chronic diarrhea. The etiology is unknown and there are currently no FDA approved medications or biomarkers for treatment or monitoring of the disease. Emerging evidence have implicated the gut microbiome and metabolome disturbances in MC pathogenesis. We conduct a comprehensive analysis of gut microbial and metabolic changes in a cohort of 683 participants, including 131 patients with active MC, 159 with chronic diarrhea, and 393 age- and sex-matched controls without diarrhea. Stool microbiome and metabolome are profiled using whole-genome shotgun metagenomic sequencing and ultra-high performance liquid chromatography-mass spectrometry, respectively. Compared to controls, eight microbial species including pro-inflammatory oral-typical Veillonella dispar and Haemophilus parainfluenzae, and 11 species, including anti-inflammatory Blautia glucerasea and Bacteroides stercoris are enriched and depleted in MC, respectively. Pro-inflammatory metabolites, including lactosylceramides, ceramides, lysophospholipids, and lysoplasmalogens, are enriched in active MC. Multi-omics analyses reveal robust associations between microbial species, metabolic pathways, and metabolites, suggesting concordant disruptions in MC. Here, we show distinct shifts in gut microbiome and metabolome in MC that can inform the development of non-invasive biomarkers and novel therapeutics.\n\nAssociation of distinct microbial and metabolic signatures with microscopic colitis.", "token_count": 417, "char_count": 1597, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:31.563719", "source": { "split": "train_shard_00001", "doc_id": 4293 }, "chunk_id": "train_shard_00001_4293_0", "global_id": 11732 }, { "text": "Quantifying patterns of adaptive divergence between taxa is a major goal in the comparative and evolutionary study of prokaryote genomes. When applied appropriately, the McDonald-Kreitman (MK) test is a powerful test of selection based on the relative frequency of non-synonymous and synonymous substitutions between species compared to non-synonymous and synonymous polymorphisms within species. The webserver ODoSE (Ortholog Direction of Selection Engine) allows the calculation of a novel extension of the MK test, the Direction of Selection (DoS) statistic, as well as the calculation of a weighted-average Neutrality Index (NI) statistic for the entire core genome, allowing for systematic analysis of the evolutionary forces shaping core genome divergence in prokaryotes. ODoSE is hosted in a Galaxy environment, which makes it easy to use and amenable to customization and is freely available at www.odose.nl.\n\nODoSE: a webserver for genome-wide calculation of adaptive divergence in prokaryotes.", "token_count": 240, "char_count": 1003, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6084, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:32.038276", "source": { "split": "train_shard_00001", "doc_id": 4294 }, "chunk_id": "train_shard_00001_4294_0", "global_id": 11733 }, { "text": "The invention relates to a method for producing inulinase through solid state fermentation, namely using a solid state bioreactor to produce the inulinase through fermentation. The method comprises the following steps: (1) inoculating Kluyveromyces fragilis strains onto the agar slant of yeast powder, peptone and inulin, cultivating the strains for four to six days at a constant temperature of 30 DEG C, and adding 0.75 percent (W/W) of normal saline to wash mycelium so as to obtain bacteria suspension the spore content of which is between 10<5> and 10<6> (2) inoculating the bacteria suspension to the solid culture medium after sterilization to be cultivated into solid seeds or cultivated into liquid seeds through liquid expansion again (3) adding the liquid seeds in the solid culture medium by 5ml to 10ml per 100 grams or adding the solid seeds in the solid culture medium by 5mg to 10mg per 100 grams, sufficiently stirring and mixing the mixture to obtain the thickness of between 0.5 and 3.0 centimeters, the humidity of between 50 percent and 80 percent, introducing 0.2 to 1.5V/(V. min) of sterile air, keeping the temperature between 25 and 45 DEG C, and making the mixture keep stand for 4 to 6 days to ferment and (4) diluting the products, collecting the supernatant containing the inulinase through centrifugation, and drying and pulverizing the products to obtain an inulinase preparation. The method effectively improves the yield of the inulinase, shortens the fermentation cycle, reduces pollution discharge, and is advantageous to environmental protection.\n\nMethod for producing inulase by solid fermentation", "token_count": 423, "char_count": 1635, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5504, "quality_score": 0.7752, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:32.664559", "source": { "split": "train_shard_00001", "doc_id": 4295 }, "chunk_id": "train_shard_00001_4295_0", "global_id": 11734 }, { "text": "We studied the utilization of protein-hydrolyzed sweet cheese whey as a medium for the production of beta-galactosidase by the yeasts Kluyveromyces marxianus CBS 712 and CBS 6556. The conditions for growth were determined in shake cultures. The best growth occurred at pH 5.5 and 37 degrees C. Strain CBS 6556 grew in cheese whey in natura, while strain CBS 712 needed cheese whey supplemented with yeast extract. Each yeast was grown in a bioreactor under these conditions. The strains produced equivalent amounts of beta-galactosidase. To optimize the process, strain CBS 6556 was grown in concentrated cheese whey, resulting in a higher beta-galactosidase production. The beta-galactosidase produced by strain CBS 6556 produced maximum activity at 37 degrees C, and had low stability at room temperature (30 degrees C) as well as at a storage temperature of 4 degrees C. At -4 degrees C and -18 degrees C, the enzyme maintained its activity for over 9 weeks.\n\nUtilization of protein-hydrolyzed cheese whey for production of beta-galactosidase by Kluyveromyces marxianus.", "token_count": 295, "char_count": 1073, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5449, "quality_score": 0.7725, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:33.250363", "source": { "split": "train_shard_00001", "doc_id": 4296 }, "chunk_id": "train_shard_00001_4296_0", "global_id": 11735 }, { "text": "Escherichia coli exhibits a wide range of lifestyles encompassing commensalism and various pathogenic behaviors which its highly dynamic genome contributes to develop. How environmental and host factors shape the genetic structure of E. coli strains remains, however, largely unknown. Following a previous study of E. coli genomic diversity, we investigated its diversity at the metabolic level by building and analyzing the genome-scale metabolic networks of 29 E. coli strains (8 commensal and 21 pathogenic strains, including 6 Shigella strains). Using a tailor-made reconstruction strategy, we significantly improved the completeness and accuracy of the metabolic networks over default automatic reconstruction processes. Among the 1,545 reactions forming E. coli panmetabolism, 885 reactions were common to all strains. This high proportion of core reactions (57%) was found to be in sharp contrast to the low proportion (13%) of core genes in the E. coli pangenome, suggesting less diversity of metabolic functions compared to that of all gene functions. Core reactions were significantly overrepresented among biosynthetic reactions compared to the more variable degradation processes. Differences between metabolic networks were found to follow E. coli phylogeny rather than pathogenic phenotypes, except for Shigella networks, which were significantly more distant from the others. This suggests that most metabolic changes in non-Shigella strains were not driven by their pathogenic phenotypes. Using a supervised method, we were yet able to identify small sets of reactions related to pathogenicity or commensalism. The quality of our reconstructed networks also makes them reliable bases for building metabolic models.\n\nCore and panmetabolism in Escherichia coli.", "token_count": 410, "char_count": 1775, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:33.893915", "source": { "split": "train_shard_00001", "doc_id": 4297 }, "chunk_id": "train_shard_00001_4297_0", "global_id": 11736 }, { "text": "Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an urgent public health problem worldwide, and its rapid evolution in the clinical environment has been a major concern. A total of 99 CRKP isolates spreading in the intensive care unit (ICU) setting were included and subjected to whole-genome sequencing, and their sequence types (STs), serotype loci, and virulence determinants were screened based on genome data. The phylogenetic structure was reconstructed based on the core genome multilocus sequence typing method. Regions of recombination were assessed. Biofilm formation, serum resistance assays, and a Galleria mellonella infection model were used to evaluate strain virulence. A novel ST, designated ST4496, emerged in the ICU and spread for 6 months before its disappearance. ST4496 was closely related to ST11, with only a single-allele variant, and ST11 is the most dominant clinical clone in China. Recombination events occurred at capsule biosynthesis loci and divided the strains of ST11 and its derivative ST4496 into three clusters, including ST11-KL47, ST11-KL64, and ST4496-KL47. The phylogenetic structure indicated that ST11-KL47 was probably the origin of ST11-related strain evolution and presented more diversity in terms of both sequence similarity and phenotypes. ST4496-KL47 cluster strains presented less virulence than ST11-KL64, which was probably one of the factors preventing the former from spreading widely. In conclusion, ST4496-KL47 was probably derived from ST11-KL47 via intraspecies shifting but was less competitive than ST11-KL64, which also evolved from ST11-KL47 and developed increased virulence via capsule biosynthesis locus recombination. ST11-KL64 has the potential to be the predominant CRKP clone in China.", "token_count": 500, "char_count": 1774, "word_count": 250, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [ "ST4496", "KL47", "KL64", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:34.607089", "source": { "split": "train_shard_00001", "doc_id": 4298 }, "chunk_id": "train_shard_00001_4298_0", "global_id": 11737 }, { "text": "The Emergence of Novel Sequence Type Strains Reveals an Evolutionary Process of Intraspecies Clone Shifting in ICU-Spreading Carbapenem-Resistant Klebsiella pneumoniae.", "token_count": 58, "char_count": 175, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:34.972573", "source": { "split": "train_shard_00001", "doc_id": 4298 }, "chunk_id": "train_shard_00001_4298_1", "global_id": 11738 }, { "text": "The natural aroma chemicals 2-phenylethanol (2-PE) and 2-phenylethylacetate (2-PEAc) are of high industrial relevance and can be produced from L-phenylalanine in a yeast-based process with growth-associated product formation. Due to product inhibition, in situ product removal is mandatory to obtain economically interesting concentrations. A fed-batch approach using polypropylene glycol 1200 as in situ extractant and the precursor in a saturated concentration led to the highest 2-PE productivity reported for a bioprocess so far. With Kluyveromyces marxianus CBS 600, 26.5 g/l 2-PE and 6.1 g/l 2-PEAc in the organic phase were obtained, corresponding to space-time yields of 0.33 and 0.08 g/l h, respectively.\n\nAn aqueous-organic two-phase bioprocess for efficient production of the natural aroma chemicals 2-phenylethanol and 2-phenylethylacetate with yeast.", "token_count": 264, "char_count": 863, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6975, "quality_score": 0.8487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:35.524541", "source": { "split": "train_shard_00001", "doc_id": 4299 }, "chunk_id": "train_shard_00001_4299_0", "global_id": 11739 }, { "text": "The prevalence of fecal colonization with extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) among children in low- and middle-income countries is alarmingly high. This study aimed to identify the sources of ESBL-Ec colonization in children < 1 year old through comparative analysis of E. coli isolates from child stool, child's mother stool, and point-of-use drinking water from 46 rural households in Bangladesh. The pairwise similarity in antibiotic susceptibility of E. coli from all three sources was evaluated, followed by phylogenetic clustering using enterobacterial repetitive intergenic consensus polymerase chain reaction and whole-genome sequence analysis of the isolates. Matching antibiotic susceptibility and enterobacterial repetitive intergenic consensus polymerase chain reaction patterns were found among ESBL-Ec isolates from child-mother dyads of 24 and 11 households, respectively, from child-water dyads of 5 and 4 households, respectively, and from child-mother-water triads of 3 and 4 households, respectively. Whole-genome sequence analysis of 30 isolates from 10 households revealed that ESBL-Ec from children in five households (50%) was clonally related to ESBL-Ec either from their mothers (2 households), drinking water sources (2 households), or both mother and drinking-water sources (1 household) based on serotype, phylogroup, sequence type, antibiotic resistance genes, mobile genetic elements, core single-nucleotide polymorphisms, and whole-genome multilocus sequence typing. Overall, this study provides empirical evidence that ESBL-Ec colonization in children is linked to the colonization status of mothers and exposure to the household environments contaminated with ESBL-Ec. Interventions such as improved hygiene practices and a safe drinking water supply may help reduce the transmission of ESBL-Ec at the household level.", "token_count": 475, "char_count": 1904, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5873, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:36.169252", "source": { "split": "train_shard_00001", "doc_id": 4300 }, "chunk_id": "train_shard_00001_4300_0", "global_id": 11740 }, { "text": "Identifying the Sources of Intestinal Colonization With Extended-Spectrum β-Lactamase-Producing Escherichia coli in Healthy Infants in the Community.", "token_count": 51, "char_count": 156, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:36.534039", "source": { "split": "train_shard_00001", "doc_id": 4300 }, "chunk_id": "train_shard_00001_4300_1", "global_id": 11741 }, { "text": "Microbacterium species have been isolated from a wide range of hosts and environments, including heavy metal-contaminated sites. Here, we present a comprehensive analysis on the phylogenetic distribution and the genetic potential of 70 Microbacterium belonging to 20 different species isolated from heavy metal-contaminated and non-contaminated sites with particular attention to secondary metabolites gene clusters. The analyzed Microbacterium species are divided in three main functional clades. They share a small core genome (331 gene families covering basic functions) pointing to high genetic diversity. The most common secondary metabolite gene clusters encode pathways for the production of terpenoids, type III polyketide synthases and non-ribosomal peptide synthetases, potentially responsible of the synthesis of siderophore-like compounds. In vitro tests showed that many Microbacterium strains produce siderophores, ACC deaminase, auxins (IAA) and are able to solubilize phosphate. Microbacterium isolates from heavy metal contaminated sites are on average more resistant to heavy metals and harbor more genes related to metal homeostasis (e.g., metalloregulators). On the other hand, the ability to increase the metal mobility in a contaminated soil through the secretion of specific molecules seems to be widespread among all. Despite the widespread capacity of strains to mobilize several metals, plants inoculated with selected Microbacterium isolates showed only slightly increased iron concentrations, whereas concentrations of zinc, cadmium and lead were decreased.\n\nComparative Genomics of Microbacterium Species to Reveal Diversity, Potential for Secondary Metabolites and Heavy Metal Resistance.", "token_count": 446, "char_count": 1774, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6623, "quality_score": 0.8312, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:37.532825", "source": { "split": "train_shard_00001", "doc_id": 4301 }, "chunk_id": "train_shard_00001_4301_0", "global_id": 11742 }, { "text": "

Background

The Dickeya genus is part of the Pectobacteriaceae family that is included in the newly described enterobacterales order. It comprises a group of aggressive soft rot pathogens with wide geographic distribution and host range. Among them, the new Dickeya fangzhongdai species groups causative agents of maceration-associated diseases that impact a wide variety of crops and ornamentals. It affects mainly monocot plants, but D. fangzhongdai strains have also been isolated from pear trees and water sources. Here, we analysed which genetic novelty exists in this new species, what are the D. fangzhongdai-specific traits and what is the intra-specific diversity.

Results

The genomes of eight D. fangzhongdai strains isolated from diverse environments were compared to 31 genomes of strains belonging to other Dickeya species. The D. fangzhongdai core genome regroups approximately 3500 common genes, including most genes that encode virulence factors and regulators characterised in the D. dadantii 3937 model strain. Only 38 genes are present in D. fangzhongdai and absent in all other Dickeyas. One of them encodes a pectate lyase of the PL10 family of polysaccharide lyases that is found only in a few bacteria from the plant environment, soil or human gut. Other D. fangzhongdai-specific genes with a known or predicted function are involved in regulation or metabolism. The intra-species diversity analysis revealed that seven of the studied D. fangzhongdai strains were grouped into two distinct clades. Each clade possesses a pool of 100-150 genes that are shared by the clade members, but absent from the other D. fangzhongdai strains and several of these genes are clustered into genomic regions. At the strain level, diversity resides mainly in the arsenal of T5SS- and T6SS-related toxin-antitoxin systems and in secondary metabolite biogenesis pathways.

Conclusion

This study identified the genome-specific traits of the new D. fangzhongdai species and highlighted the intra-species diversity of this species", "token_count": 529, "char_count": 2052, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5867, "quality_score": 0.7933, "entities": { "genes": [ "PL10" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:38.200723", "source": { "split": "train_shard_00001", "doc_id": 4302 }, "chunk_id": "train_shard_00001_4302_0", "global_id": 11743 }, { "text": "This diversity encompasses secondary metabolites biosynthetic pathways and toxins or the repertoire of genes of extrachromosomal origin. We however didn't find any relationship between gene content and phenotypic differences or sharing of environmental habitats.\n\nGenomic characterisation of the new Dickeya fangzhongdai species regrouping plant pathogens and environmental isolates.", "token_count": 91, "char_count": 383, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:38.581857", "source": { "split": "train_shard_00001", "doc_id": 4302 }, "chunk_id": "train_shard_00001_4302_1", "global_id": 11744 }, { "text": "Anamorphic basidiomycetous yeast strains M9962T and M9963 were isolated from water samples collected from a small stream in Ohwakudani, Hakone, a hot-spring area in Japan. These belonged to a single species and were phylogenetically closely related to Bullera lagerstroemiae, although the ability to form ballistoconidia was not observed. Based on sequence analyses of the D1/D2 domain of the LSU rDNA and ITS regions and differences in G+C content, the name Cryptococcus tepidarius sp. nov. Takashima, Sugita, Toriumi et Nakase (Trichosporonales, Tremellomycetes, Basiomycota) is proposed for these isolates, with strain M9962T (=SP-5T =JCM 11965T =CBS 9427T) as the type strain. The strains grew in YM broth at 47 degrees C and in YM broth with the pH adjusted to 1.5 by HCl, indicating that the species is thermotolerant and acid-tolerant.\n\nCryptococcus tepidarius sp. nov., a thermotolerant yeast species isolated from a stream from a hot-spring area in Japan.", "token_count": 311, "char_count": 964, "word_count": 147, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:39.157711", "source": { "split": "train_shard_00001", "doc_id": 4303 }, "chunk_id": "train_shard_00001_4303_0", "global_id": 11745 }, { "text": "The intrasubspecies diversity of six strains of Lactococcus lactis subsp. lactis was investigated at the genomic level and in terms of phenotypic and transcriptomic profiles in an ultrafiltration cheese model. The six strains were isolated from various sources, but all exhibited a dairy phenotype (growth in ultrafiltration cheese model and high acidification rate). The six strains exhibited similar behaviors in terms of growth during cheese ripening, while different acidification capabilities were detected. Even if all strains displayed large genomic similarities, sharing a large core genome of almost 2,000 genes, the expression of this core genome directly in the cheese matrix revealed major strain-specific differences that potentially could account for the observed different acidification capabilities. This work demonstrated that significant transcriptomic polymorphisms exist even among Lactococcus lactis subsp. lactis strains with the same dairy origin.\n\nAssessment of the diversity of dairy Lactococcus lactis subsp. lactis isolates by an integrated approach combining phenotypic, genomic, and transcriptomic analyses.", "token_count": 258, "char_count": 1136, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:39.698577", "source": { "split": "train_shard_00001", "doc_id": 4304 }, "chunk_id": "train_shard_00001_4304_0", "global_id": 11746 }, { "text": "

ABSTRACT

Salmonella enterica serotype Dublin ( S. Dublin) is a bovine-adapted serotype that can cause serious systemic infections in humans. Despite the increasing prevalence of human infections and the negative impact on agricultural processes, little is known about the population structure of the serotype. To this end, we compiled a manually curated dataset comprising of 880 S. Dublin genomes. Core genome phylogeny and ancestral state reconstruction revealed that region-specific clades dominate the global population structure of S. Dublin. Strains of S. Dublin in the UK are genomically distinct from US, Brazilian and African strains. The geographical partitioning impacts the composition of the core genome as well as the ancillary genome. Antibiotic resistance genes are almost exclusively found in US genomes and is mediated by an IncA/C2 plasmid. Phage content and the S. Dublin virulence plasmid were strongly conserved in the serotype. Comparison of S. Dublin to a closely related serotype, Salmonella enterica serotype Enteritidis, revealed that S. Dublin contains 82 serotype specific genes that are not found in S. Enteritidis . Said genes encode metabolic functions involved in the uptake and catabolism of carbohydrates and virulence genes associated with type VI secretion systems and fimbria assembly respectively.

IMPORTANCE

S. Dublin is a bovine-adapted strain that can also cause human infections. Typical S. Dublin human infections are characterized by invasion of tissue that ultimately traverses to the bloodstream causing life-threatening systemic cases. The preferred course of treatment for such infection is the administration of antibiotics. Thus, it is important to study the population structure of the serotype to monitor and identify which strains present the greatest threats to public health. Consequently, in this work, it was found that S. Dublin genomic features are greatly influenced by the region in which they populate. Our analysis found that most S. Dublin isolates from the US are distinct and have gained multidrug resistance through a new hybrid plasmid. Thus, it would be expected that infections in the US would respond less favorably to the first line of therapy and the region acts as the major source of a multidrug-resistant S. Dublin.", "token_count": 530, "char_count": 2310, "word_count": 347, "semantic_coherence": 1, "information_density": 0.5562, "quality_score": 0.7781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:40.353319", "source": { "split": "train_shard_00001", "doc_id": 4305 }, "chunk_id": "train_shard_00001_4305_0", "global_id": 11747 }, { "text": "Geography Shapes the Population Genomics ofSalmonella entericaDublin", "token_count": 25, "char_count": 75, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:40.712956", "source": { "split": "train_shard_00001", "doc_id": 4305 }, "chunk_id": "train_shard_00001_4305_1", "global_id": 11748 }, { "text": "Despite their relevance to human health, not all staphylococcal species have been characterized. As such, the potential zoonotic threats posed by uninvestigated species and their contribution to the staphylococcal pangenome are unclear. Here, we report the complete genome sequence of Staphylococcus lutrae ATCC 700373, a coagulase-positive species isolated from deceased otters.\n\nComplete Genome Sequence of Staphylococcus lutrae ATCC 700373, a Potential Pathogen Isolated from Deceased Otters.", "token_count": 156, "char_count": 509, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:41.149182", "source": { "split": "train_shard_00001", "doc_id": 4306 }, "chunk_id": "train_shard_00001_4306_0", "global_id": 11749 }, { "text": "UDP-galactose 4-epimerase serves as a prototype model of class II oxidoreductases that use bound NAD as a cofactor. This enzyme from Kluyveromyces fragilis is a homodimer with a molecular mass of 75 kDa/subunit. Continuous monitoring of the conversion of UDP-galactose (UDP-gal) to UDP-glucose (UDP-glu) by the epimerase in the presence of the coupling enzyme UDP-glucose dehydrogenase and NAD shows a kinetic lag of up to 80 s before a steady state is reached. The disappearance of the lag follows first-order kinetics (k = 3.22 x 10(-2) s(-1)) at 25 degrees C at enzyme and substrate concentrations of 1.0 nM and 1 mM, respectively. The observed lag is not due to factors such as insufficient activity of the coupling enzyme, association or dissociation or incomplete recruitment of NAD by epimerase, product activation, etc., but was a true expression of the activity of the prepared enzyme. Dissociation of the bound ligand(s) by heat followed by analysis with reverse-phase HPLC, TLC, UV-absorption spectrometry, mass spectrometry, and NMR showed that in addition to 1.78 mol of NAD/dimer, the epimerase also contains 0.77 mol of 5'-UMP/dimer. The latter is a strong competitive inhibitor. Preincubation of the epimerase with the substrate UDP-gal or UDP-glu replaces the inhibitor and also abolishes the lag, which reappeared after the enzyme was treated with 5'-UMP. The lag was not observed as long as the cells were in the growing phase and galactose in the growth medium was limiting, suggesting that association with 5'-UMP is a late log-phase phenomenon. The stoichiometry and conserved amino acid sequence around the NAD binding site of multimeric class I (classical dehydrogenases) and class II oxidoreductases, as reported in the literature, have been compared", "token_count": 510, "char_count": 1775, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5899, "quality_score": 0.795, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:41.787868", "source": { "split": "train_shard_00001", "doc_id": 4307 }, "chunk_id": "train_shard_00001_4307_0", "global_id": 11750 }, { "text": "It shows that each subunit is independently capable of being associated with one molecule of NAD, suggestive of two NAD binding sites of epimerase per dimer.\n\nUDP-galactose 4-epimerase from Kluyveromyces fragilis: analysis of its hysteretic behavior during catalysis.", "token_count": 70, "char_count": 267, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:42.161511", "source": { "split": "train_shard_00001", "doc_id": 4307 }, "chunk_id": "train_shard_00001_4307_1", "global_id": 11751 }, { "text": "

Background

Autographa californica Multiple Nucleopolyhedrovirus (AcMNPV) is a baculovirus with a high potential for its use as a biopesticide against arthropod pests. The budded form of the virus causes a systemic infection when it escapes the midgut to enter the hemolymph of susceptible hosts. Yet, the specific molecular processes underlying the biocidal activity of AcMNPV on its insect hosts are largely unknown.

Results

In this study, we describe the transcriptional responses in two major pests, Spodoptera frugiperda and Trichoplusia ni , to determine the host-pathogen responses during AcMNPV infection, concurrently with the viral response to the host. We assembled species-specific de novo reference transcriptomes of the hemolymph to identify key transcripts that respond during pathogenesis in these arthropod models where genomic resources are sparse. We found that the suppression of transcriptional processes related to chitin, a metabolite critical for basement membrane stability and tracheal development are central in establishing a systemic infection. Synergistic transcriptional support was observed to suggest suppression of immune responses and induction of oxidative stress indicating disease progression in the host. The entire AcMNPV core genome was expressed in the host hemolymph and viral genes predominantly associated with the budded virus replication, structure, and movement were more abundant than those associated with the occlusion-derived virus. Genes known to directly arrest host cell cycle and development were among the most abundant AcMNPV transcripts in infected hosts. Interestingly, several of the host genes (e.g. Chitin synthase ) that were targeted by the pathogen as revealed by our study are also targets of several chemical insecticides currently used commercially to control arthropod pests.

Conclusions

Our results reveal an extensive overlap between biological processes represented by genes differently expressed in both hosts, as well as convergence on highly abundant viral genes expressed in the two hosts, providing an overview of the host-pathogen transcriptomic landscape during systemic infection", "token_count": 501, "char_count": 2186, "word_count": 306, "semantic_coherence": 1, "information_density": 0.6046, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:42.820255", "source": { "split": "train_shard_00001", "doc_id": 4309 }, "chunk_id": "train_shard_00001_4309_0", "global_id": 11752 }, { "text": "Given the diversity of AcMNPV strains that infect a wide range of insect hosts, our study provides a framework where pathogen strains could be selected to target specific host genes that facilitates modulation of the infection strength and specificity of the susceptible hosts.\n\nA tale of two transcriptomic responses in agricultural pests via host defenses and viral replication", "token_count": 79, "char_count": 379, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7931, "quality_score": 0.8966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:43.188967", "source": { "split": "train_shard_00001", "doc_id": 4309 }, "chunk_id": "train_shard_00001_4309_1", "global_id": 11753 }, { "text": "The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.", "token_count": 512, "char_count": 2251, "word_count": 315, "semantic_coherence": 1, "information_density": 0.527, "quality_score": 0.7635, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:43.825196", "source": { "split": "train_shard_00001", "doc_id": 4310 }, "chunk_id": "train_shard_00001_4310_0", "global_id": 11754 }, { "text": "Microbiome \"Inception\": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host.", "token_count": 31, "char_count": 113, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:44.188928", "source": { "split": "train_shard_00001", "doc_id": 4310 }, "chunk_id": "train_shard_00001_4310_1", "global_id": 11755 }, { "text": "

Objectives

Salmonella enterica serovar Goldcoast has been identified as the agent responsible for multistate epidemic outbreaks in humans. However, knowledge regarding the antimicrobial resistance and transmission of S. Goldcoast is scarce. This study aimed to investigate the genomic features of a multidrug-resistant S. Goldcoast sequence type 358 strain in China.

Methods

Antimicrobial susceptibility of S. enterica strain SalGC_ZJ_53 was determined by microdilution broth assay. Whole genomic DNA was extracted and sequenced using the Illumina NovaSeq platform. De novo genome assembly was performed using Unicycler and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline. The sequence type (ST), antimicrobial resistance genes and Salmonella pathogenicity islands were identified from the genome sequence. The core genome multilocus sequence typing (cgMLST) analysis between S. enterica SalGC_ZJ_53 and all of the S. Goldcoast strains retrieved from the public database was performed using BacWGSTdb server.

Results

Salmonella enterica SalGC_ZJ_53 was resistant to ampicillin, amikacin, cefotetan, cefazolin, ciprofloxacin, gentamicin and tetracycline. The genome size was calculated as 4,904,788 bp, with 4595 protein-coding sequences and GC content of 52.0%. This isolate was assigned to ST358. Several antimicrobial resistance genes and salmonella pathogenicity islands, as well as multiple insertion sequences were identified. The closest relative of S. enterica SalGC_ZJ_53 was another isolate recovered from the UK, differing by only six cgMLST loci.

Conclusions

This study reports the first genome sequence of a multidrug-resistant S. Goldcoast isolate in China. These data may help to understand the antimicrobial resistance mechanisms and transmission dynamics of this rare serovar of Salmonella infection in humans.", "token_count": 526, "char_count": 1892, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5685, "quality_score": 0.7843, "entities": { "genes": [ "ST358" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:44.841400", "source": { "split": "train_shard_00001", "doc_id": 4311 }, "chunk_id": "train_shard_00001_4311_0", "global_id": 11756 }, { "text": "Genomic characterization of a multidrug-resistant Salmonella enterica serovar Goldcoast sequence type 358 strain in China.", "token_count": 33, "char_count": 122, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:45.239256", "source": { "split": "train_shard_00001", "doc_id": 4311 }, "chunk_id": "train_shard_00001_4311_1", "global_id": 11757 }, { "text": "An improved disc diffusion type bioassay was developed for T-2 toxin (T-2), HT-2 toxin (HT-2), diacetoxyscirpenol (DAS), deoxynivalenol (DON), nivalenol (NIV), neosolaniol (NSL), fusarenon-X (FUS-X), trichothecin (TIN), roridin A (RDA) and verrucarin A (VCA) using the yeast, Kluyveromyces marxianus . Factors such as type of medium, agar volume per plate, preincubation time and temperature, incubation temperature, inoculum size and pH had variable, and in some cases a dramatic effect on the sensitivity of the assay. The effect of pH of the assay medium was particularly pronounced. The highest sensitivity was obtained when 6 ml per plate of a tryptic-soy-agar (TSA) medium (pH 7.5) containing 105 CFU inoculum per ml was incubated at 38°C for 18 h. All of the trichothecenes (TNN) were able to inhibit the growth of the yeast with the detection limit being 0.005, 0.01, 0.02, 0.02, 0.1, 0.5, 10, 10, 10 and 50 μg/disc for VCA, RDA, T-2, TTN, DAS, HT-2, DON, NSL, FUS-X and NIV, respectively. The detection limits for corn and wheat spiked with T-2 were 0.1 and 0.2 μg/g, respectively", "token_count": 413, "char_count": 1100, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7216, "quality_score": 0.8608, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:45.873512", "source": { "split": "train_shard_00001", "doc_id": 4312 }, "chunk_id": "train_shard_00001_4312_0", "global_id": 11758 }, { "text": "Non-TNN mycotoxins that did not inhibit yeast at a concentration of 200 μg/disc were aflatoxin B1 (AFB1), ochratoxin A (OA), citrinin (CT), penicillic acid (PA), cyclopiazonic acid (CPA), penitrem-A (PTA) and zearalenone (ZEE). These results indicate that disc diffusion assay using K. marxianus under optimized conditions provides a sensitive method for the detection of low concentrations of several TNN.\n\nOptimization of Yeast Bioassay for Trichothecene Mycotoxins.", "token_count": 162, "char_count": 490, "word_count": 66, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:46.349403", "source": { "split": "train_shard_00001", "doc_id": 4312 }, "chunk_id": "train_shard_00001_4312_1", "global_id": 11759 }, { "text": "Residents in long-term care facilities (LTCFs) are frequently colonized by multidrug-resistant Gram-negative bacteria, putting them at risk for subsequent infections. We aimed to evaluate the effect of the multispecies probiotic Omnibiotic10AAD® on the intestinal and inguinal skin colonization of patients by multidrug-resistant Gram-negative bacteria in LTCFs. Patients colonized by multidrug-resistant Gram-negative bacteria received a 12 week oral course of Omnibiotic10AAD®. Inguinal swabs and stool samples were collected during and after treatment for microbiological and microbiome analysis. The median age of patients was 76 years. Twelve patients completed the pilot study. Intestinal colonization was reduced to 42% of patients 8 weeks after the end of treatment, but increased to 66% 24 weeks after the end of probiotic treatment. Colonization of inguinal skin was lowest during probiotic treatment and increased thereafter. Fecal microbiome analysis revealed statistically significant increases of the genus Enterococcus comparing start and end of probiotic treatment. In conclusion, a 12 week course of a multispecies probiotic led to a transient reduction of intestinal colonization 8 weeks after the end of treatment. The findings of our pilot study warrant further research in the area of probiotics and intestinal colonization by multidrug-resistant bacteria.\n\nEffect of a Multispecies Probiotic on Intestinal and Skin Colonization by Multidrug-Resistant Gram-Negative Bacteria in Patients in a Long-Term Care Facility: A Pilot Study.", "token_count": 405, "char_count": 1581, "word_count": 216, "semantic_coherence": 1, "information_density": 0.4769, "quality_score": 0.7384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:46.984518", "source": { "split": "train_shard_00001", "doc_id": 4313 }, "chunk_id": "train_shard_00001_4313_0", "global_id": 11760 }, { "text": "

Background

The genus Ehrlichia consists of tick-borne obligatory intracellular bacteria that can cause deadly diseases of medical and agricultural importance. Ehrlichia sp. HF, isolated from Ixodes ovatus ticks in Japan [also referred to as I. ovatus Ehrlichia (IOE) agent], causes acute fatal infection in laboratory mice that resembles acute fatal human monocytic ehrlichiosis caused by Ehrlichia chaffeensis. As there is no small laboratory animal model to study fatal human ehrlichiosis, Ehrlichia sp. HF provides a needed disease model. However, the inability to culture Ehrlichia sp. HF and the lack of genomic information have been a barrier to advance this animal model. In addition, Ehrlichia sp. HF has several designations in the literature as it lacks a taxonomically recognized name.

Results

We stably cultured Ehrlichia sp. HF in canine histiocytic leukemia DH82 cells from the HF strain-infected mice, and determined its complete genome sequence. Ehrlichia sp. HF has a single double-stranded circular chromosome of 1,148,904 bp, which encodes 866 proteins with a similar metabolic potential as E. chaffeensis. Ehrlichia sp. HF encodes homologs of all virulence factors identified in E. chaffeensis, including 23 paralogs of P28/OMP-1 family outer membrane proteins, type IV secretion system apparatus and effector proteins, two-component systems, ankyrin-repeat proteins, and tandem repeat proteins. Ehrlichia sp. HF is a novel species in the genus Ehrlichia, as demonstrated through whole genome comparisons with six representative Ehrlichia species, subspecies, and strains, using average nucleotide identity, digital DNA-DNA hybridization, and core genome alignment sequence identity.

Conclusions

The genome of Ehrlichia sp. HF encodes all known virulence factors found in E. chaffeensis, substantiating it as a model Ehrlichia species to study fatal human ehrlichiosis", "token_count": 530, "char_count": 1910, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6165, "quality_score": 0.8083, "entities": { "genes": [ "DH82" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:47.645236", "source": { "split": "train_shard_00001", "doc_id": 4314 }, "chunk_id": "train_shard_00001_4314_0", "global_id": 11761 }, { "text": "Comparisons between Ehrlichia sp. HF and E. chaffeensis will enable identification of in vivo virulence factors that are related to host specificity, disease severity, and host inflammatory responses. We propose to name Ehrlichia sp. HF as Ehrlichia japonica sp. nov. (type strain HF), to denote the geographic region where this bacterium was initially isolated.\n\nComparative Analysis of Genome of Ehrlichia sp. HF, a Model Bacterium to Study Fatal Human Ehrlichiosis.", "token_count": 126, "char_count": 468, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:48.049166", "source": { "split": "train_shard_00001", "doc_id": 4314 }, "chunk_id": "train_shard_00001_4314_1", "global_id": 11762 }, { "text": "A known furanocoumarin, 8-geranyloxy psoralen, was isolated from n-hexane extract of Prangos uloptera roots by the TLC method. Its structure was determined by comparison of the spectral data with the literature. Cytotoxic effects of the isolated compound were determined by MTT and Tripan blue assays. The antioxidant and antimicrobial potential of the compound were evaluated by DPPH assay and agar dilution method, respectively. The MTT assay results showed that 8-geranyloxy psoralen reduced cell viability of Hela and Mc-Coy cell lines with IC(50) values of 0.792 and 0.835 mM, respectively. Based on the Tripan blue assay, the compound has cytotoxic effects, with an IC(50) value of 1.26 mM for Mc-Coy cell line. The compound exhibited weak antioxidant potential, with an RC(50) value of 0.262 mg mL(-1) and high antimicrobial effects against Staphylococcus epidermidis and Candida kefyr.\n\nA furanocoumarin from Prangos uloptera roots, biological effects.", "token_count": 290, "char_count": 960, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:48.613929", "source": { "split": "train_shard_00001", "doc_id": 4315 }, "chunk_id": "train_shard_00001_4315_0", "global_id": 11763 }, { "text": "The state of Florida reports a high burden of non-typhoidal Salmonella enterica with approximately two times higher than the national incidence. We retrospectively analyzed the population structure and molecular epidemiology of 1,709 clinical isolates from 2017 and 2018. We found 115 different serotypes. Rarefaction suggested that the serotype richness did not differ between children under 2 years of age and older children and adults and, there are ~22 well-characterized dominant serotypes. There were distinct differences in dominant serotypes between Florida and the USA as a whole, even though S. Enteritidis and S. Newport were the dominant serotypes in Florida and nationally. S. Javiana, S. Sandiego, and S. IV 50:z4, z23:- occurred more frequently in Florida than nationally. Legacy Multi Locus Sequence Typing (MLST) was of limited use for differentiating clinical Salmonella isolates beyond the serotype level. We utilized core genome MLST (cgMLST) hierarchical clusters (HC) to identify potential outbreaks and compared them to outbreaks detected by Pulse Field Gel Electrophoresis (PFGE) surveillance for five dominant serotypes (Enteritidis, Newport, Javiana, Typhimurium, and Bareilly). Single nucleotide polymorphism (SNP) phylogenetic-analysis of cgMLST HC at allelic distance 5 or less (HC5) corroborated PFGE detected outbreaks and generated well-segregated SNP distance-based clades for all studied serotypes. We propose \"combination approach\" comprising \"HC5 clustering,\" as efficient tool to trigger Salmonella outbreak investigations, and \"SNP-based analysis,\" for higher resolution phylogeny to confirm an outbreak", "token_count": 478, "char_count": 1711, "word_count": 227, "semantic_coherence": 1, "information_density": 0.7137, "quality_score": 0.8568, "entities": { "genes": [ "HC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:49.269026", "source": { "split": "train_shard_00001", "doc_id": 4316 }, "chunk_id": "train_shard_00001_4316_0", "global_id": 11764 }, { "text": "We also applied this approach to identify case clusters, more distant in time and place than traditional outbreaks but may have been infected from a common source, comparing 176 Florida clinical isolates and 1,341 non-clinical isolates across USA, of most prevalent serotype Enteritidis collected during 2017-2018. Several clusters of closely related isolates (0-4 SNP apart) within HC5 clusters were detected and some included isolates from poultry from different states in the US, spanning time periods over 1 year. Two SNP-clusters within the same HC5 cluster included isolates with the same multidrug-resistant profile from both humans and poultry, supporting the epidemiological link. These clusters likely reflect the vertical transmission of Salmonella clones from higher levels in the breeding pyramid to production flocks.\n\nMolecular Epidemiology of Salmonellosis in Florida, USA, 2017-2018.", "token_count": 231, "char_count": 907, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7519, "quality_score": 0.876, "entities": { "genes": [ "HC5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:49.734634", "source": { "split": "train_shard_00001", "doc_id": 4316 }, "chunk_id": "train_shard_00001_4316_1", "global_id": 11765 }, { "text": "BackgroundCampylobacter is the main cause of bacterial gastroenteritis worldwide. The main transmission route is through consumption of food contaminated with Campylobacter species or contact with infected animals. In Latvia, the prevalence of campylobacteriosis is reported to be low (4.6 cases per 100,000 population in 2016).AimTo determine prevalence, species spectrum and antimicrobial resistance (AMR) of Campylobacter spp. in Latvia, using data from various livestock and human clinical samples.MethodsWe analysed data of Campylobacter microbiological monitoring and AMR (2008 and 2014-16) in Latvia. Data from broilers, poultry, pigs, calves and humans were used to determine prevalence of Campylobacter. Additionally, 45 different origin isolates (22 human) were sequenced on the Illumina MiSeq platform; for each isolate core genome multilocus sequence typing was used and relevant antimicrobial resistance mechanisms were identified.ResultsOverall, Campylobacter prevalence in was 83.3% in pigs, 50.2% in broilers, 16.1% in calves and 5.3% in humans; C. jejuni was the predominant species in all sources except pigs where C. coli was main species. High level of resistance in Campylobacter were observed against fluoroquinolones, tetracycline and streptomycin, in most of sequenced isolates genetic determinants of relevant AMR profiles were identified.ConclusionsIn Latvia, prevalence of Campylobacter in livestock is high, especially in pigs and broilers; prevalence in poultry and humans were lower than in other European countries. AMR analysis reveals increase of streptomycin and tetracycline resistant broiler origin C. jejuni strains", "token_count": 501, "char_count": 1729, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5956, "quality_score": 0.7978, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:50.399535", "source": { "split": "train_shard_00001", "doc_id": 4317 }, "chunk_id": "train_shard_00001_4317_0", "global_id": 11766 }, { "text": "WGS demonstrates a high compliance between resistance phenotype and genotype for quinolones and tetracyclines.\n\nCampylobacter species prevalence, characterisation of antimicrobial resistance and analysis of whole-genome sequence of isolates from livestock and humans, Latvia, 2008 to 2016.", "token_count": 84, "char_count": 296, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:50.771304", "source": { "split": "train_shard_00001", "doc_id": 4317 }, "chunk_id": "train_shard_00001_4317_1", "global_id": 11767 }, { "text": "Vibrio vulnificus (Vv) is a multi-host pathogenic species currently subdivided into three biotypes (Bts). The three Bts are human-pathogens, but only Bt2 is also a fish-pathogen, an ability that is conferred by a transferable virulence-plasmid (pVvbt2). Here we present a phylogenomic analysis from the core genome of 80 Vv strains belonging to the three Bts recovered from a wide range of geographical and ecological sources. We have identified five well-supported phylogenetic groups or lineages (L). L1 comprises a mixture of clinical and environmental Bt1 strains, most of them involved in human clinical cases related to raw seafood ingestion. L2 is formed by a mixture of Bt1 and Bt2 strains from various sources, including diseased fish, and is related to the aquaculture industry. L3 is also linked to the aquaculture industry and includes Bt3 strains exclusively, mostly related to wound infections or secondary septicemia after farmed-fish handling. Lastly, L4 and L5 include a few strains of Bt1 associated with specific geographical areas. The phylogenetic trees for ChrI and II are not congruent to one another, which suggests that inter- and/or intra-chromosomal rearrangements have been produced along Vv evolution. Further, the phylogenetic trees for each chromosome and the virulence plasmid were also not congruent, which also suggests that pVvbt2 has been acquired independently by different clones, probably in fish farms. From all these clones, the one with zoonotic capabilities (Bt2-Serovar E) has successfully spread worldwide. Based on these results, we propose a new updated classification of the species based on phylogenetic lineages rather than on Bts, as well as the inclusion of all Bt2 strains in a pathovar with the particular ability to cause fish vibriosis, for which we suggest the name \"piscis.\"", "token_count": 479, "char_count": 1839, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:51.417145", "source": { "split": "train_shard_00001", "doc_id": 4318 }, "chunk_id": "train_shard_00001_4318_0", "global_id": 11768 }, { "text": "Phylogeny of Vibrio vulnificus from the Analysis of the Core-Genome: Implications for Intra-Species Taxonomy.", "token_count": 39, "char_count": 116, "word_count": 14, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:51.773179", "source": { "split": "train_shard_00001", "doc_id": 4318 }, "chunk_id": "train_shard_00001_4318_1", "global_id": 11769 }, { "text": "Vibrio parahaemolyticus can cause gastrointestinal illness through consumption of seafood. Despite frequent food-borne outbreaks of V. parahaemolyticus, only 19 strains have subjected to complete whole-genome analysis. In this study, a novel strain of V. parahaemolyticus, designated FORC_022 (Food-borne pathogen Omics Research Center_022), was isolated from soy sauce marinated crabs, and its genome and transcriptome were analyzed to elucidate the pathogenic mechanisms. FORC_022 did not include major virulence factors of thermostable direct hemolysin (tdh) and TDH-related hemolysin (trh). However, FORC_022 showed high cytotoxicity and had several V. parahaemolyticus islands (VPaIs) and other virulence factors, such as various secretion systems (types I, II, III, IV, and VI), in comparative genome analysis with CDC_K4557 (the most similar strain) and RIMD2210633 (genome island marker strain). FORC_022 harbored additional virulence genes, including accessory cholera enterotoxin, zona occludens toxin, and tight adhesion (tad) locus, compared with CDC_K4557. In addition, O3 serotype specific gene and the marker gene of pandemic O3:K6 serotype (toxRS) were detected in FORC_022. The expressions levels of genes involved in adherence and carbohydrate transporter were high, whereas those of genes involved in motility, arginine biosynthesis, and proline metabolism were low after exposure to crabs. Moreover, the virulence factors of the type III secretion system, tad locus, and thermolabile hemolysin were overexpressed. Therefore, the risk of foodborne-illness may be high following consumption of FORC_022 contaminated crab", "token_count": 511, "char_count": 1687, "word_count": 222, "semantic_coherence": 1, "information_density": 0.7252, "quality_score": 0.8626, "entities": { "genes": [ "RIMD2210633" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:52.407468", "source": { "split": "train_shard_00001", "doc_id": 4319 }, "chunk_id": "train_shard_00001_4319_0", "global_id": 11770 }, { "text": "These results provided molecular information regarding the survival and pathogenesis of V. parahaemolyticus FORC_022 strain in contaminated crab and may have applications in food safety.\n\nPotential Survival and Pathogenesis of a Novel Strain, Vibrio parahaemolyticus FORC_022, Isolated From a Soy Sauce Marinated Crab by Genome and Transcriptome Analyses.", "token_count": 113, "char_count": 369, "word_count": 48, "semantic_coherence": 1, "information_density": 0.7917, "quality_score": 0.8958, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:52.793097", "source": { "split": "train_shard_00001", "doc_id": 4319 }, "chunk_id": "train_shard_00001_4319_1", "global_id": 11771 }, { "text": "

Background

Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only sporadic cases of ceftriaxone resistant S . Typhi are reported. This study aimed at elucidating the phylogenetic evolutionary framework of ceftriaxone resistant S . Typhi isolates from India to predict their potential dissemination in endemic regions.

Methods

Five ceftriaxone resistant S . Typhi isolates from three tertiary care hospitals in India were sequenced on an Ion Torrent Personal Genome Machine (PGM). A core genome single-nucleotide-polymorphism (SNP) based phylogeny of the isolates in comparison to the global collection of MDR and XDR S . Typhi isolates was built. Two of five isolates were additionally sequenced using Oxford Nanopore MinION to completely characterize the plasmid and understand its transmission dynamics within Enterobacteriaceae.

Results

Comparative genomic analysis and detailed plasmid characterization indicate that while in Pakistan (4.3.1 lineage I) the XDR trait is associated with bla CTX-M-15 gene on IncY plasmid, in India (4.3.1 lineage II), the ceftriaxone resistance is due to short term adaptation of resistance plasmids such as IncX3 or IncN.

Conclusion

Since the bacterial acquisition of smaller resistance plasmids such as IncX3 or IncN from other Enterobacteriaceae can be much faster than the larger IncY plasmids, the rapid expansion of these genotypically novel XDR S . Typhi could potentially cause large outbreaks. Therefore, continuous monitoring of S . Typhi lineages carrying cephalosporin resistance on IncX3 or IncN plasmids is vital not just for India but globally.

Importance

Genomic analysis of cephalosporin resistant S . Typhi isolated from India indicates the potential of S ", "token_count": 501, "char_count": 1886, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:53.453488", "source": { "split": "train_shard_00001", "doc_id": 4320 }, "chunk_id": "train_shard_00001_4320_0", "global_id": 11772 }, { "text": "Typhi to develop cephalosporin resistance by acquiring diverse plasmids from other Enterobacteriaceae. We identified the occurrence of independent acquisition of drug-resistant plasmids such as IncX3 and IncN with genes encoding beta-lactamases in H58/4.3.1.2 lineage. A short term adaptation of drug-resistant plasmids in H58/4.3.1.2 lineage can be the reason for the sporadic cases cephalosporin resistant S . Typhi in India. However, the IncY plasmid acquired by isolates that belong to H58/4.3.1.1 lineage appeared to be well adapted as observed in XDR S. Typhi outbreak in Pakistan. Plasmid acquisition and maintenance of cephalosporin resistant S . Typhi appears to be specific to the phylogenetic lineage as lineages differ in compensating the initial cost imposed by the plasmid. The stable maintenance of these resistance plasmids without a fitness cost, are determinant in understanding the future spread of cephalosporin resistance in S . Typhi. Therefore, critical strategies in monitoring and control of cephalosporin resistant S . Typhi is needed to tackle further public health crisis.\n\nSalmonellaTyphi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance", "token_count": 322, "char_count": 1216, "word_count": 172, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:54.013764", "source": { "split": "train_shard_00001", "doc_id": 4320 }, "chunk_id": "train_shard_00001_4320_1", "global_id": 11773 }, { "text": "Legionella pneumophila is a bacterial pathogen present in aquatic environments that can cause a severe pneumonia called Legionnaires' disease. Soon after its recognition, it was shown that Legionella replicates inside amoeba, suggesting that bacteria replicating in environmental protozoa are able to exploit conserved signaling pathways in human phagocytic cells. Comparative, evolutionary, and functional genomics suggests that the Legionella-amoeba interaction has shaped this pathogen more than previously thought. A complex evolutionary scenario involving mobile genetic elements, type IV secretion systems, and horizontal gene transfer among Legionella, amoeba, and other organisms seems to take place. This long-lasting coevolution led to the development of very sophisticated virulence strategies and a high level of temporal and spatial fine-tuning of bacteria host-cell interactions. We will discuss current knowledge of the evolution of virulence of Legionella from a genomics perspective and propose our vision of the emergence of this human pathogen from the environment.\n\nGenome dynamics in Legionella: the basis of versatility and adaptation to intracellular replication.", "token_count": 258, "char_count": 1186, "word_count": 161, "semantic_coherence": 1, "information_density": 0.7267, "quality_score": 0.8634, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:54.562443", "source": { "split": "train_shard_00001", "doc_id": 4321 }, "chunk_id": "train_shard_00001_4321_0", "global_id": 11774 }, { "text": "Clostridioides difficile causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C", "token_count": 522, "char_count": 2358, "word_count": 318, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [ "RT106", "RT078" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:49:55.227398", "source": { "split": "train_shard_00001", "doc_id": 4322 }, "chunk_id": "train_shard_00001_4322_0", "global_id": 11775 }, { "text": "difficile.\n\nTransition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile.", "token_count": 43, "char_count": 122, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:55.589067", "source": { "split": "train_shard_00001", "doc_id": 4322 }, "chunk_id": "train_shard_00001_4322_1", "global_id": 11776 }, { "text": "Sethemi, a South African traditional fermented milk, was prepared in the laboratory by spontaneously fermenting raw milk in four different types of containers; namely, a clay pot, gourd, nickel jar and plastic bowl. The development of bacteria and yeasts in the different containers was followed by taking samples at 24 h intervals for 7 days. The predominating microorganisms in all cases were the aerobic mesophilic bacteria, lactobacilli-leuconostocs (LAB on MRS) and lactococci (LAB on M17). No significant (p > 0.05) differences were found in the number of microorganisms between the different containers. However, there were significant (p < 0.05) differences with respect to the types of dominant yeast species, and the diversity of yeast species. The least time to attain maximum LAB counts was recorded for the nickel container. In milk fermented in the clay pot and gourd the most dominant yeast species were Debaryomyces hansenii and Saccharomyces cerevisiae, respectively, while Cryptococcus curvatus predominated in both the nickel and plastic containers. The highest yeast diversity was obtained from milk samples fermented in the clay pot represented by 15 species. Of the 23 species isolated from all the containers and raw milk, only D. hansenii, Cryptococcus humicola and Kluyveromyces marxianus were isolated from both raw and naturally fermented milks of all containers. The use of different types of containers therefore influenced the diversity of yeasts in the fermented milk and may influence the characteristics of the fermented milk product. The clay pot offered the greatest yeast diversity suggesting that it could be the best suited for preparing traditional fermented milk.\n\nThe effect of container type on the growth of yeast and lactic acid bacteria during production of Sethemi, South African spontaneously fermented milk", "token_count": 440, "char_count": 1854, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5071, "quality_score": 0.7535, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:56.220869", "source": { "split": "train_shard_00001", "doc_id": 4323 }, "chunk_id": "train_shard_00001_4323_0", "global_id": 11777 }, { "text": "Multilocus sequence typing (MLST) is a standard tool in population genetics and bacterial epidemiology that assesses the genetic variation present in a reduced number of housekeeping genes (typically seven) along the genome. This methodology assigns arbitrary integer identifiers to genetic variations at these loci allowing to efficiently compare bacterial isolates using allele-based methods. Now, the increasing availability of whole-genome sequences for hundreds to thousands of strains from the same bacterial species has motivated to upgrade the resolution of traditional MLST schemes using larger gene sets or even the core genome (cgMLST). The PubMLST database is the most comprehensive resource of described MLST and cgMLST schemes available for a wide variety of species. Here we present MLSTar as the first R package that allows to i) connect with the PubMLST database to select a target scheme, ii) screen a desired set of genomes to assign alleles and sequence types and iii) interact with other widely used R packages to analyze and produce graphical representations of the data. We applied MLSTar to analyze a set of 400 Campylobacter coli genomes, showing great accuracy and comparable performance with previously published command-line tools. MLSTar can be freely downloaded from http://github.com/iferres/MLSTar .\n\nMLSTar: automatic multilocus and core genome sequence typing in R", "token_count": 301, "char_count": 1398, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6763, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:56.788471", "source": { "split": "train_shard_00001", "doc_id": 4324 }, "chunk_id": "train_shard_00001_4324_0", "global_id": 11778 }, { "text": "The genus Methanosphaera is a well-recognized but poorly characterized member of the mammalian gut microbiome, and distinctive from Methanobrevibacter smithii for its ability to induce a pro-inflammatory response in humans. Here we have used a combination of culture- and metagenomics-based approaches to expand the representation and information for the genus, which has supported the examination of their phylogeny and physiological capacity. Novel isolates of the genus Methanosphaera were recovered from bovine rumen digesta and human stool, with the bovine isolate remarkable for its large genome size relative to other Methanosphaera isolates from monogastric hosts. To substantiate this observation, we then recovered seven high-quality Methanosphaera-affiliated population genomes from ruminant and human gut metagenomic datasets. Our analyses confirm a monophyletic origin of Methanosphaera spp. and that the colonization of monogastric and ruminant hosts favors representatives of the genus with different genome sizes, reflecting differences in the genome content needed to persist in these different habitats.\n\nCulture- and metagenomics-enabled analyses of the Methanosphaera genus reveals their monophyletic origin and differentiation according to genome size.", "token_count": 299, "char_count": 1273, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:57.375960", "source": { "split": "train_shard_00001", "doc_id": 4325 }, "chunk_id": "train_shard_00001_4325_0", "global_id": 11779 }, { "text": "The objective of this study was to determine whether β1-4 galacto-oligosaccharides (GOS) and Candida kefyr combined with nitrate as manipulators could suppress rumen methanogenesis without nitrate poisoning in sheep. Four rumen fistulated wethers were allocated to a 4×4 Latin square design. Nitrate (1.3 g NaNO3 kg-0.75 body weight) with and without GOS and C. kefyr were administered into the rumen through fistula as a single dose 30 min after the morning meal. GOS and C. kefyr were supplemented by sprinkling into the feed and through rumen fistula, respectively. The four treatments consisted of saline, nitrate, nitrate plus GOS, and nitrate plus GOS plus C. kefyr. Physiological saline was used as the control treatment. Compared to saline treatment, the administration of nitrate alone resulted in a very marked decrease in rumen methanogenesis and an increase in rumen and plasma nitrite production and blood methaemoglobin formation consequently causing a decline in oxygen consumption, carbon dioxide production and metabolic rate. When compared to nitrate alone, the simultaneous administration of nitrate with GOS decreased nitrite accumulation in rumen and plasma and nitrate-induced methaemoglobin, while retaining low methane production. However, GOS could not fully restore metabolic parameters reduced by nitrate. When compared to the simultaneous administration of nitrate with GOS, the simultaneous administration of nitrate with GOS plus C. kefyr lowered rumen methanogenesis to a negligible level, but did not decrease rumen and plasma nitrite accumulation as well as blood methaemoglobin formation. These results suggest that combination of nitrate with GOS may be a potent manipulator to suppress rumen methanogenesis while abating the hazards of nitrate-nitrite toxicity in ruminants.\n\nEffects of combination of nitrate with beta1-4 galacto-oligosaccharides and yeast (Candida kefyr) on methane emission from sheep.", "token_count": 506, "char_count": 1973, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5267, "quality_score": 0.7633, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:58.037654", "source": { "split": "train_shard_00001", "doc_id": 4326 }, "chunk_id": "train_shard_00001_4326_0", "global_id": 11780 }, { "text": "

A bstract

Case numbers of listeriosis have been increasing in Germany and the European Union during the last decade. In addition reports on the occurrence of antibiotic resistance in Listeria monocytogenes in clinical and environmental isolates are accumulating. The susceptibility towards 14 antibiotics was tested in a selection of clinical L. monocytogenes isolates to get a more precise picture of the development and manifestation of antibiotic resistance in the L. monocytogenes population. Based on the population structure determined by core genome multi locus sequence typing (cgMLST) 544 out of 1,220 sequenced strains collected in Germany between 2009 and 2019 were selected to cover the phylogenetic diversity observed in the clinical L. monocytogenes population. All isolates tested were susceptible towards ampicillin, penicillin and co-trimoxazole - the most relevant antibiotics in the treatment of listeriosis. Resistance to daptomycin and ciprofloxacin was observed in 493 (91%) and in 71 (13%) of 544 isolates, respectively. While all tested strains showed resistance towards ceftriaxone, the minimal inhibitory concentrations (MIC) observed varied widely between 4 mg/L up to >128 mg/L. An allelic variation of the penicillin binding protein gene pbpB3 could be identified as the cause of this difference in ceftriaxone resistance levels. This study is the first population structure-guided analysis of antimicrobial resistance in recent clinical isolates and confirms the importance of penicillin binding protein B3 (PBP B3) for the high level of intrinsic cephalosporin resistance of L. monocytogenes on a population-wide scale.\n\nPopulation structure-guided profiling of antibiotic resistance patterns in clinicalListeria monocytogenesisolates from Germany identifiespbpB3alleles associated with low levels of cephalosporin resistance", "token_count": 492, "char_count": 1880, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:58.726076", "source": { "split": "train_shard_00001", "doc_id": 4327 }, "chunk_id": "train_shard_00001_4327_0", "global_id": 11781 }, { "text": "

Background

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an emerging public health problem. This study explores the specifics of CRKP epidemiology in Colombia based on whole genome sequencing (WGS) of the National Reference Laboratory at Instituto Nacional de Salud (INS)'s 2013-2017 sample collection.

Methods

A total of 425 CRKP isolates from 21 departments were analyzed by HiSeq-X10®Illumina high-throughput sequencing. Bioinformatic analysis was performed, primarily using the pipelines developed collaboratively by the National Institute for Health Research Global Health Research Unit (GHRU) on Genomic Surveillance of Antimicrobial Resistance (AMR), and AGROSAVIA.

Results

Of the 425 CRKP isolates, 91.5% were carbapenemase-producing strains. The data support a recent expansion and the endemicity of CRKP in Colombia with the circulation of 7 high-risk clones, the most frequent being CG258 (48.39% of isolates). We identified genes encoding carbapenemases blaKPC-3, blaKPC-2, blaNDM-1, blaNDM-9, blaVIM-2, blaVIM-4, and blaVIM-24, and various mobile genetic elements (MGE). The virulence of CRKP isolates was low, but colibactin (clb3) was present in 25.2% of isolates, and a hypervirulent CRKP clone (CG380) was reported for the first time in Colombia. ST258, ST512, and ST4851 were characterized by low levels of diversity in the core genome (ANI > 99.9%).

Conclusions

The study outlines complex CRKP epidemiology in Colombia", "token_count": 476, "char_count": 1473, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7026, "quality_score": 0.8513, "entities": { "genes": [ "CG258", "ST4851", "CG380", "ST512", "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:59.378261", "source": { "split": "train_shard_00001", "doc_id": 4328 }, "chunk_id": "train_shard_00001_4328_0", "global_id": 11782 }, { "text": "CG258 expanded clonally and carries specific carbapenemases in specific MGEs, while the other high-risk clones (CG147, CG307, and CG152) present a more diverse complement of carbapenemases. The specifics of the Colombian situation stress the importance of WGS-based surveillance to monitor evolutionary trends of sequence types (STs), MGE, and resistance and virulence genes.\n\nComplexity of Genomic Epidemiology of Carbapenem-Resistant Klebsiella pneumoniae Isolates in Colombia Urges the Reinforcement of Whole Genome Sequencing-Based Surveillance Programs.", "token_count": 157, "char_count": 558, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [ "CG152", "CG147", "CG258", "CG307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:49:59.815842", "source": { "split": "train_shard_00001", "doc_id": 4328 }, "chunk_id": "train_shard_00001_4328_1", "global_id": 11783 }, { "text": "Campylobacter is among the four main causes of gastroenteritis worldwide. Most reported Campylobacter infections are caused by C. jejuni and C. coli. However, other emerging Campylobacter pathogens have been recognized as important pathogens in humans and animals. A novel bacterial strain, PS10T, was isolated from the gastric mucous of pigs in 2022 in Beijing, China. The cell was Gram-negative, microaerobic, motile, and negative for catalase, oxidase, and urease. Phylogenetic and phylogenomic analyses based on the 16S rRNA gene and core genome indicated that this isolate belongs to the genus Campylobacter. There were low dDDH relatedness and ANI values shared within this strain and its closest species C. mucosalis below the cut-off values generally recognized for isolates of the same species. The draft genome size of PS10T is 2,240,910 bp in length with a percentage of DNA G+C contents of 37.72%. Comparing the phenotypic and phylogenetic features among this isolate and its related organisms, strain PS10T represents a novel species within the genus Campylobacter, for which the name Campylobacter gastrosuis sp. nov. (Type strain PS10T = GDMCC 1.3686T = JCM 35849T) is proposed.\n\nPhenotypic and Genomic Characteristics of Campylobacter gastrosuis sp. nov. Isolated from the Stomachs of Pigs in Beijing.", "token_count": 475, "char_count": 1453, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6482, "quality_score": 0.8241, "entities": { "genes": [ "PS10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:00.470613", "source": { "split": "train_shard_00001", "doc_id": 4329 }, "chunk_id": "train_shard_00001_4329_0", "global_id": 11784 }, { "text": "

ABSTRACT

Carbapenem-resistant (CR) Acinetobacter baumannii is a serious nosocomial pathogen able to cause a variety of serious, often life-threatening infections and outbreaks. We aimed to investigate the molecular epidemiology of clinical isolates of CR- A. baumannii from an outbreak occurred in the intensive care unit (ICU) of our hospital. From January to April 2017, 13 CR- A. baumannii isolates were collected at the “L. Spallanzani” hospital, Rome, Italy; typing was performed by repetitive extragenetic palindromic-based (rep)- PCR-based DiversiLab system and WGS data were used for in silico analysis of traditional MLST types, for identifying resistance genes and for core genome multi locus sequence typing (cgMLST) analysis. Epidemiological data were obtained from hospital records. Strains were cultured from 7 patients treated in the ICU of our hospital; all isolates showed a multi-drug resistant (MDR) profile, carrying the bla OXA-23 carbapenemase. Typing performed by rep-PCR and MLST showed that the isolates clustered into one group while the cgMLST approach, which uses 2690 gene targets to characterize the gene-by-gene allelic profile of A. baumannii, highlighted the presence of two cluster types. These results allowed us to identify two patients who entered the ICU already colonized by two different strains of CR- A. baumannii ; we hypothesize that these two patients could be the source of two separate transmission chains. Our results show that whole-genome-DNA sequencing by cgMLST is a valuable tool, better suited for prompt epidemiological investigations than traditional typing methods because of its higher discriminatory ability in determining clonal relatedness.\n\nEpidemiologal investigation of anAcinetobacter baumanniioutbreak using Core Genome Multilocus Sequence Typing", "token_count": 472, "char_count": 1828, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6641, "quality_score": 0.832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:01.119601", "source": { "split": "train_shard_00001", "doc_id": 4330 }, "chunk_id": "train_shard_00001_4330_0", "global_id": 11785 }, { "text": "A total of 110 strains belonging to seven species of Candida were isolated from various forms of candidiasis in diabetic patients. They were Candida albicans 53 (47%), Candida tropicalis 36 (33%), Candida glabrata 9 (8%), Candida parapsilosis 4 (4%), Candida guilliermondii 2 (2%), Candida krusei 5 (5%) and Candida kefyr 1 (1%). All 53 strains of C. albicans isolated were observed to express virulence factors such as cell surface hydrophobicity (CSH), adherence to human buccal epithelial cell (BEC) and proteinase activity (100%), while phospholipase activity was observed in 52 (98%). Phenotypic switching and its influence on the pathogenicity of C. albicans were studied. Two C. albicans strains isolated from oral and vaginal thrush, respectively, in diabetic individuals, and the control strain C. albicans NCPF 3153A were induced to undergo phenotypic switching by exposure to UV light and the degree of expression of virulence factors by the different morphological forms was determined. Three different morphological forms of C. albicans were obtained, namely Star (S), Wrinkled (W) and Ring (R) types from the original Smooth (O) variety. It was found that proteinase activity was greatest with the W type followed by the R type then the O type. The S type produced the least proteinase. The phospholipase activity was greatest with O type followed by R type. The W and S types produced the least phospholipase. Expression of CSH and adherence was greatest in the O type followed by the R and then the W type and finally the S type. Differential expression of virulence factors occurs with different phenotypic forms of C. albicans and this may provide a particular morphological type with a distinct advantage over other types in causing candidiasis.\n\nEffect of phenotypic switching on expression of virulence factors by Candida albicans causing candidiasis in diabetic patients.", "token_count": 503, "char_count": 1893, "word_count": 297, "semantic_coherence": 1, "information_density": 0.4781, "quality_score": 0.7391, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:01.775908", "source": { "split": "train_shard_00001", "doc_id": 4331 }, "chunk_id": "train_shard_00001_4331_0", "global_id": 11786 }, { "text": "Bacteria from the same species can differ widely in their gene content. In E. coli , the set of genes shared by all strains, known as the core genome, represents about half the number of genes present in any strain. While recent advances in bacterial genomics have enabled to unravel genes required for fitness in various experimental conditions at the genome scale, most studies have focused on model strains. As a result, the impact of this genetic diversity on core processes of the bacterial cell largely remains to be investigated. Here, we developed a new CRISPR interference platform for high-throughput gene repression that is compatible with most E. coli isolates and closely-related species. We applied it to assess the importance of ∼3,400 nearly ubiquitous genes in 3 growth media in 18 representative E. coli strains spanning most common phylogroups and lifestyles of the species. Our screens highlighted extensive variations in gene essentiality between strains and conditions. Unlike variations in gene expression level, variations in gene essentiality do not recapitulate the strains’ phylogeny. Investigation of the genetic determinants for these variations highlighted the importance of epistatic interactions with mobile genetic elements. In particular, we showed how mobile genetic elements can trigger the essentiality of core genes that are usually nonessential. This study provides new insights into the evolvability of gene essentiality and argues for the importance of studying various isolates from the same species in bacterial genomics.\n\nThe impact of genetic diversity on gene essentiality within theE. colispecies", "token_count": 349, "char_count": 1650, "word_count": 247, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:02.352425", "source": { "split": "train_shard_00001", "doc_id": 4332 }, "chunk_id": "train_shard_00001_4332_0", "global_id": 11787 }, { "text": "

Background

Sigma factor B (SigB) is the central regulator of the general stress response in Bacillus subtilis and regulates a group of genes in response to various stressors, known as the SigB regulon members. Genes that are directly regulated by SigB contain a promotor binding motif (PBM) with a previously identified consensus sequence.

Results

In this study, refined SigB PBMs were derived and different spacer compositions and lengths (N12-N17) were taken into account. These were used to identify putative SigB-regulated genes in the B. subtilis genome, revealing 255 genes: 99 had been described in the literature and 156 genes were newly identified, increasing the number of SigB putative regulon members (with and without a SigB PBM) to > 500 in B. subtilis. The 255 genes were assigned to five categories (I-V) based on their similarity to the original SigB consensus sequences. The functionalities of selected representatives per category were assessed using promoter-reporter fusions in wt and ΔsigB mutants upon exposure to heat, ethanol, and salt stress. The activity of the PrsbV (I) positive control was induced upon exposure to all three stressors. PytoQ (II) showed SigB-dependent activity only upon exposure to ethanol, whereas PpucI (II) with a N17 spacer and PylaL (III) with a N16 spacer showed mild induction regardless of heat/ethanol/salt stress. PywzA (III) and PyaaI (IV) displayed ethanol-specific SigB-dependent activities despite a lower-level conserved - 10 binding motif. PgtaB (V) was SigB-induced under ethanol and salt stress while lacking a conserved - 10 binding region", "token_count": 517, "char_count": 1742, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:03.004742", "source": { "split": "train_shard_00001", "doc_id": 4333 }, "chunk_id": "train_shard_00001_4333_0", "global_id": 11788 }, { "text": "The activities of PygaO and PykaA (III) did not show evident changes under the conditions tested despite having a SigB PBM that highly resembled the consensus. The identified extended SigB regulon candidates in B. subtilis are mainly involved in coping with stress but are also engaged in other cellular processes. Orthologs of SigB regulon candidates with SigB PBMs were identified in other Bacillales genomes, but not all showed a SigB PBM. Additionally, genes involved in the integration of stress signals to activate SigB were predicted in these genomes, indicating that SigB signaling and regulon genes are species-specific.

Conclusion

The entire SigB regulatory network is sophisticated and not yet fully understood even for the well-characterized organism B. subtilis 168. Knowledge and information gained in this study can be used in further SigB studies to uncover a complete picture of the role of SigB in B. subtilis and other species.\n\nPrediction and validation of novel SigB regulon members in Bacillus subtilis and regulon structure comparison to Bacillales members.", "token_count": 266, "char_count": 1109, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5976, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:03.544322", "source": { "split": "train_shard_00001", "doc_id": 4333 }, "chunk_id": "train_shard_00001_4333_1", "global_id": 11789 }, { "text": "Antimicrobial resistance genes (ARGs) and the bacteria that harbor them are widely distributed in the environment, especially in surface water, sewage treatment plant effluent, soil, and animal waste. In this study, we isolated a KPC-2-producing Klebsiella pneumoniae strain (GSU10-3) from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP) and determined its complete genome sequence. Strain GSU10-3 is resistant to most β-lactam antibiotics and other antimicrobial agents (quinolones and aminoglycosides). This strain is classified as sequence type 11 (ST11), and a core genome phylogenetic analysis indicated that strain GSU10-3 is closely related to KPC-2-positive Chinese clinical isolates from 2011 to 2017 and is clearly distinct from strains isolated from the European Union (EU), United States, and other Asian countries. Strain GSU10-3 harbors four plasmids, including a blaKPC-2-positive plasmid, pGSU10-3-3 (66.2 kb), which is smaller than other blaKPC-2-positive plasmids and notably carries dual replicons (IncFII [pHN7A8] and IncN). Such downsizing and the presence of dual replicons may promote its maintenance and stable replication, contributing to its broad host range with low fitness costs", "token_count": 383, "char_count": 1280, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7102, "quality_score": 0.8551, "entities": { "genes": [ "GSU10", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:04.128394", "source": { "split": "train_shard_00001", "doc_id": 4334 }, "chunk_id": "train_shard_00001_4334_0", "global_id": 11790 }, { "text": "A second plasmid, pGSU10-3-1 (159.0 kb), an IncA/C2 replicon, carries a class 1 integron (containing intI1, dfrA12, aadA2, qacEΔ1, and sul1) with a high degree of similarity to a broad-host-range plasmid present in the family Enterobacteriaceae The plasmid pGSU10-3-2 (134.8 kb), an IncFII(K) replicon, carries the IS26-mediated ARGs [aac(6')Ib-cr,blaOXA-1, catB4 (truncated), and aac(3)-IId], tet(A), and a copper/arsenate resistance locus. GSU10-3 is the first nonclinical KPC-2-producing environmental Enterobacteriaceae isolate from Japan for which the whole genome has been sequenced.IMPORTANCE We isolated and determined the complete genome sequence of a KPC-2-producing K. pneumoniae strain from a sampling site in Tokyo Bay, Japan, near a wastewater treatment plant (WWTP). In Japan, the KPC type has been very rarely detected, while IMP is the most predominant type of carbapenemase in clinical carbapenemase-producing Enterobacteriaceae (CPE) isolates. Although laboratory testing thus far suggested that Japan may be virtually free of KPC-producing Enterobacteriaceae, we have detected it from effluent from a WWTP", "token_count": 488, "char_count": 1283, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7226, "quality_score": 0.8613, "entities": { "genes": [ "GSU10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:04.771994", "source": { "split": "train_shard_00001", "doc_id": 4334 }, "chunk_id": "train_shard_00001_4334_1", "global_id": 11791 }, { "text": "Antimicrobial resistance (AMR) monitoring of WWTP effluent may contribute to the early detection of future AMR bacterial dissemination in clinical settings and communities; indeed, it will help illuminate the whole picture in which environmental contamination through WWTP effluent plays a part.\n\nComplete Genome Sequence of a blaKPC-2-Positive Klebsiella pneumoniae Strain Isolated from the Effluent of an Urban Sewage Treatment Plant in Japan.", "token_count": 124, "char_count": 463, "word_count": 62, "semantic_coherence": 1, "information_density": 0.8226, "quality_score": 0.9113, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:05.159661", "source": { "split": "train_shard_00001", "doc_id": 4334 }, "chunk_id": "train_shard_00001_4334_2", "global_id": 11792 }, { "text": "ppGpp is an intracellular sensor that, in response to different types of stress, coordinates the rearrangement of the gene expression pattern of bacteria to promote adaptation and survival to new environmental conditions. First described to modulate metabolic adaptive responses, ppGpp modulates the expression of genes belonging to very diverse functional categories. In Escherichia coli, ppGpp regulates the expression of cellular factors that are important during urinary tract infections. Here, we characterize the role of this alarmone in the regulation of the hlyCABDII operon of the UPEC isolate J96, encoding the toxin α-hemolysin that induces cytotoxicity during infection of bladder epithelial cells. ppGpp is required for the expression of the α-hemolysin encoded in hlyCABDII by stimulating its transcriptional expression. Prototrophy suppressor mutations in a ppGpp-deficient strain restore the α-hemolysin expression from this operon to wild-type levels, confirming the requirement of ppGpp for its expression. ppGpp stimulates hlyCABDII expression independently of RpoS, RfaH, Zur, and H-NS. The expression of hlyCABDII is promoted at 37 °C and at low osmolarity. ppGpp is required for the thermoregulation but not for the osmoregulation of the hlyCABDII operon. Studies in both commensal and UPEC isolates demonstrate that no UPEC specific factor is strictly required for the ppGpp-mediated regulation described. Our data further support the role of ppGpp participating in the coordinated regulation of the expression of bacterial factors required during infection.", "token_count": 456, "char_count": 1678, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5733, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:05.799081", "source": { "split": "train_shard_00001", "doc_id": 4335 }, "chunk_id": "train_shard_00001_4335_0", "global_id": 11793 }, { "text": "ppGpp, the General Stress Response Alarmone, Is Required for the Expression of the α-Hemolysin Toxin in the Uropathogenic Escherichia coli Isolate, J96.", "token_count": 58, "char_count": 159, "word_count": 22, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:06.160889", "source": { "split": "train_shard_00001", "doc_id": 4335 }, "chunk_id": "train_shard_00001_4335_1", "global_id": 11794 }, { "text": "Studies were carried out for the production of aroma compounds in solid-state fermentation using factorial design and response surface methodology (RSM) experiments. Five agro-industrial residues were evaluated as substrate for cultivating a strain of Kluyveromyces marxianus. The results proved the feasibility of using cassava bagasse and giant palm bran (Opuntia ficus indica) as substrates to produce fruity aroma compounds by the yeast culture. In order to test the influence of the process parameters on the culture to produce volatile compounds, two statistical experimental designs were performed. The parameters studied were initial substrate pH, addition of glucose, cultivation temperature, initial substrate moisture and inoculum size. Using a 2(5) factorial design, addition of glucose and initial pH of the substrate was found statistically significant for aroma compounds production on palm bran. Although this experimental design showed that addition of glucose did not have a significant role with cassava bagasse, 2(2) factorial design revealed that glucose addition was significant at higher concentrations. Head-space analysis of the culture by gas chromatography showed the production of nine and eleven compounds from palm bran and cassava bagasse, respectively, which included alcohols, esters and aldehyde. In both the cases, two compounds remained unidentified and ethyl acetate, ethanol and acetaldehyde were the major compounds produced. Esters produced were responsible for the fruity aroma in both the cases. With palm bran, ethanol was the compound produced in highest concentration, and with cassava bagasse (both supplemented with 10% glucose), ethyl acetate was produced at highest concentration, accumulating 418 and 1395µmoll(-1) head-spaceg(-1) substrate in 72h, respectively.\n\nOptimization of the production of aroma compounds by Kluyveromyces marxianus in solid-state fermentation using factorial design and response surface methodology.", "token_count": 469, "char_count": 1975, "word_count": 275, "semantic_coherence": 1, "information_density": 0.52, "quality_score": 0.76, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:06.801002", "source": { "split": "train_shard_00001", "doc_id": 4336 }, "chunk_id": "train_shard_00001_4336_0", "global_id": 11795 }, { "text": "The slow-growing, anaerobic, coagulase-negative species Staphylococcus saccharolyticus is found on human skin and in clinical specimens but its pathogenic potential is unclear. Here, we investigated clinical isolates and sequenced the genomes of seven strains of S. saccharolyticus. Phylogenomic analyses showed that the closest relative of S. saccharolyticus is Staphylococcus capitis with an average nucleotide identity of 80%. Previously sequenced strains assigned to S. saccharolyticus are misclassified and belong to S. capitis. Based on single nucleotide polymorphisms of the core genome, the population of S. saccharolyticus can be divided into two clades that also differ in a few larger genomic islands as part of the flexible genome. An unexpected feature of S. saccharolyticus is extensive genome decay, with over 300 pseudogenes, indicating ongoing reductive evolution. Many genes of the core metabolism are not functional, rendering the species auxotrophic for several amino acids, which could explain its slow growth and need for fastidious growth conditions. Secreted proteins of S. saccharolyticus were determined; they include stress response proteins such as heat and oxidative stress-related factors, as well as immunodominant staphylococcal surface antigens and enzymes that can degrade host tissue components. The strains secrete lipases and a hyaluronic acid lyase. Hyaluronidase as well as urease activities were detected in biochemical assays, with clade-specific differences. Our study revealed that S. saccharolyticus has adapted its genome, possibly due to a recent change of habitat; moreover, the data imply that the species has tissue-invasive potential and might cause prosthetic joint infections.", "token_count": 491, "char_count": 1798, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6598, "quality_score": 0.8299, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:07.447109", "source": { "split": "train_shard_00001", "doc_id": 4337 }, "chunk_id": "train_shard_00001_4337_0", "global_id": 11796 }, { "text": "Staphylococcus saccharolyticus Isolated From Blood Cultures and Prosthetic Joint Infections Exhibits Excessive Genome Decay.", "token_count": 43, "char_count": 131, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:07.806011", "source": { "split": "train_shard_00001", "doc_id": 4337 }, "chunk_id": "train_shard_00001_4337_1", "global_id": 11797 }, { "text": "C-repeat binding factor (CBF) transcription factors can activate the expression of a series of cold regulation-related genes, thereby improving the cold resistance of plants. However, no detailed information is known about the biological functions of CBF proteins in yellowhorn (Xanthoceras sorbifolium). In this study, a total of 59 CBF gene family members were identified in five yellowhorn cultivars (WF18, Zhongshi 4, Jinguanxipei 2021, Zhong Guan NO.2, and XsoG11), revealing their intraspecific structural and functional diversity, with 8 core genes present in all cultivars. Phylogenetic and motif analyses highlighted conserved features and species-specific adaptations. Gene duplication events revealed that tandem duplicates are major factors involved in the expansion of this gene family in yellowhorn. Expression profiling under stress conditions demonstrated the involvement of these genes in stress responses. Of particular interest was Xg11_CBF11, which showed strong induction by low-temperature stress. Overexpression of Xg11_CBF11 in Arabidopsis thaliana was performed to validate its cold resistance function. The wild-type and T2 transgenic A. thaliana plants were subjected to low-temperature stress at 4°C for 0, 24, and 48 h, and physiological indexes related to antioxidant enzyme activity, photosynthesis, and cell membrane permeability were determined by comparative test. The results were as follows: the POD and SOD activities of transgenic lines were significantly higher than those of wild-type lines, indicating Xg11_CBF11 improved the adaptability of A", "token_count": 452, "char_count": 1657, "word_count": 220, "semantic_coherence": 1, "information_density": 0.7227, "quality_score": 0.8614, "entities": { "genes": [ "WF18" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:08.445916", "source": { "split": "train_shard_00001", "doc_id": 4338 }, "chunk_id": "train_shard_00001_4338_0", "global_id": 11798 }, { "text": "thaliana to low-temperature; The increase of relative conductivity and malondialdehyde, the decrease of chlorophyll content in transgenic lines were smaller than those of wild-type lines, indicating Xg11_CBF11 enhanced the resistance of A. thaliana to low-temperature stress. These results implied that Xg11_CBF11 has a positive regulatory effect on A. thaliana 's response to low-temperature stress.\n\nComparative genomic profiling of CBFs pan-gene family in five yellowhorn cultivars and functional identification of Xg11_CBF11.", "token_count": 181, "char_count": 575, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7571, "quality_score": 0.8786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:08.883044", "source": { "split": "train_shard_00001", "doc_id": 4338 }, "chunk_id": "train_shard_00001_4338_1", "global_id": 11799 }, { "text": "Abstract

Background

Epidemiological (EPI) analyses of bacterial pathogens play an important role in infection control practices during suspected outbreaks. Pulsed field gel electrophoresis (PFGE) is the gold standard for EPI typing of most bacterial organisms, but this method has been slowly replaced by sequencing-based methods, such as multilocus sequence typing (MLST) and core genome (cg)MLST that uses whole genome sequencing (WGS) data. We evaluated the utility of WGS ad hoc schemas to predict relatedness among Serratia marcescens (SM) clinical strains.

Methods

A total of 19 SM clinical isolates collected as part of the SENTRY Program and JMI worldwide collections were selected. Isolates were typed by PFGE and analyzed using GelCompar II (100% similarity scored as identical, > 85% and < 100% as genetically related and < 85% as unrelated). WGS was performed using MiSeq (Illumina) and contigs generated using SPAdes. Raw reads and assembled contigs were used to generate phylogenetic trees using kWIP and progressiveMauve (pMauve), respectively. Similarity matrices and dendrograms created by the three protocols were compared.

Results

Based on PFGE analysis, 19 isolates were classified into 10 pulsotypes, A through J, and 1 subtype, A1 (Fig.1A). Among dendrograms generated based on WGS, analysis of short k-mers (Fig.1B) inaccurately showed phylogenetic separation among isolates in A/A1, C and G types, while analysis of much longer contigs (Fig.1C) accurately clustered isolates according to groups defined using PFGE. One isolate in the A/A1 group (517323) was separated from the group using kWIP; however, using the more sophisticated pMauve, this isolate was accurately clustered within the A/A1 isolates", "token_count": 486, "char_count": 1754, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6992, "quality_score": 0.8496, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:10.283956", "source": { "split": "train_shard_00001", "doc_id": 4339 }, "chunk_id": "train_shard_00001_4339_0", "global_id": 11800 }, { "text": "

Conclusion

Concordance was observed between PFGE- and WGS-based phylogenetic analysis of SM for genetic relatedness. Based on this analysis, WGS data can be used to predict EPI of this bacterial species on an ad hoc basis. This methodology can be expanded to other species. Figure 1

Disclosures

Rodrigo E. Mendes, PhD, A. Menarini Industrie Farmaceutiche Riunite S.R.L. (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Basilea Pharmaceutica International, Ltd (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Department of Health and Human Services (Research Grant or Support)GlaxoSmithKline (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Merck (Research Grant or Support)Merck (Research Grant or Support)Pfizer (Research Grant or Support) Mariana Castanheira, PhD, 1928 Diagnostics (Research Grant or Support)A. Menarini Industrie Farmaceutiche Riunite S.R.L. (Research Grant or Support)Allergan (Research Grant or Support)Allergan (Research Grant or Support)Amplyx Pharmaceuticals (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cidara Therapeutics (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Cipla Ltd. (Research Grant or Support)Fox Chase Chemical Diversity Center (Research Grant or Support)GlaxoSmithKline (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Melinta Therapeutics, Inc. (Research Grant or Support)Merck (Research Grant or Support)Merck (Research Grant or Support)Merck & Co, Inc. (Research Grant or Support)Merck & Co, Inc", "token_count": 500, "char_count": 1691, "word_count": 211, "semantic_coherence": 1, "information_density": 0.4171, "quality_score": 0.7085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:10.944163", "source": { "split": "train_shard_00001", "doc_id": 4339 }, "chunk_id": "train_shard_00001_4339_1", "global_id": 11801 }, { "text": "(Research Grant or Support)Paratek Pharma, LLC (Research Grant or Support)Pfizer (Research Grant or Support)Qpex Biopharma (Research Grant or Support)\n\n826. Comparative Epidemiological Analysis of Serratia marcescens using PFGE and Whole Genome Sequence Methods", "token_count": 81, "char_count": 261, "word_count": 33, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:11.321413", "source": { "split": "train_shard_00001", "doc_id": 4339 }, "chunk_id": "train_shard_00001_4339_2", "global_id": 11802 }, { "text": "The fermentation of whey by Kluyveromyces marxianus strain MTCC 1288 was studied using varying lactose concentrations at constant temperature and pH. The increase in substrate concentration up to a certain limit was accompanied by an increase in ethanol formation, for example, at a substrate concentration of 10 g L-1, the production of ethanol was 0.618 g L-1 whereas at 50 g L-1 it was 3.98 g L-1. However, an increase in lactose concentration to 100 g L-1 led to a drastic decrease in product formation and substrate utilization. The maximum ethanol yield was obtained with an initial lactose concentration of 50 g L-1. A method of batch kinetics was utilized to formulate a mathematical model using substrate and product inhibition constants. The model successfully simulated the batch kinetics observed at S0 = 10 and 50 g L-1 but failed in case of S0 = 100 g L-1 because of strong substrate inhibition.\n\nBatch kinetics and modelling of ethanolic fermentation of whey", "token_count": 268, "char_count": 973, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5093, "quality_score": 0.7547, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:11.876166", "source": { "split": "train_shard_00001", "doc_id": 4340 }, "chunk_id": "train_shard_00001_4340_0", "global_id": 11803 }, { "text": "The effect of changing environmental conditions on the morphology of the yeast Kluyveromyces marxianus var. marxianus NRRLy2415 was investigated in batch and continuous culture, using a previously developed computer-aided image analysis protocol [O'Shea and Walsh (1996) Biotechnol Bioeng 51: 679 690]. The morphology of the organism is primarily controlled by the specific growth rate, mu. This finding was contrary to a previous investigation [Walker and O'Neill (1990) J Chem Tech Biotechnol 49: 75-89]. When the organism is cultured in batch with excess oxygen, mu can approach the maximum specific growth rate, microm, and the primary morphology of the culture is yeast-like. However, if the organism is cultured in a chemostat, thereby controlling the growth rate, the morphology reverts to a pseudohyphal form. This response is thought to be an adaptation by the organism to its environment, whereby it assumes a foraging form under adverse environmental conditions. The use of computer-aided image analysis made possible the discrimination of subtle morphological differences between samples and the determination of the relationship between morphology and growth rate.\n\nThe effect of culture conditions on the morphology of the dimorphic yeast Kluyveromyces marxianus var. marxianus NRRLy2415: a study incorporating image analysis.", "token_count": 333, "char_count": 1340, "word_count": 195, "semantic_coherence": 1, "information_density": 0.5744, "quality_score": 0.7872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:12.450307", "source": { "split": "train_shard_00001", "doc_id": 4341 }, "chunk_id": "train_shard_00001_4341_0", "global_id": 11804 }, { "text": "Leptospirosis is a ubiquitous disease and a major clinical challenge owing to the multitude of clinical presentations and manifestations that are possibly attributable to the diversity of Leptospira , the understanding of which is key to study the epidemiology of this emerging global disease threat. Sri Lanka is a hotspot for leptospirosis with high levels of endemic disease as well as annual epidemics. We carried out a prospective study of Leptospira diversity in Sri Lanka, covering the full range of climatic zones, geography, and clinical severity. Samples were collected for leptospiral culture from 1192 patients from 15 of 25 districts in Sri Lanka over two and half years period. Twenty-five isolates belonging to four pathogenic Leptospira species were identified: L. interrogans , L. borgpetersenii , L. weilii , and L. kirschneri . At least six serogroups were identified among the isolates: Autumnalis (6), Pyrogenes (4), Icterohaemorrhagiae (2), Celledoni (1), Grippotyphosa (2) and Bataviae (1). Seven isolates did not agglutinate using available antisera panels, suggesting new serogroups. Isolates were sequenced by Illumina. These data add 25 new core genome sequence types and were clustered in 15 clonal groups, including 12 new clonal groups. L. borgpetersenii was found only in the dry zone and L. weilii only in the wet zone. Acute kidney injury and cardiovascular involvement were seen only with L. interrogans infections. Thrombocytopenia and liver impairment were seen in both L. interrogans and L. borgpetersenii infections. The inadequate sensitivity of culture isolation to identify infecting Leptospira species underscores the need for culture-independent typing methods for Leptospira .

Author Summary

There is a huge diversity in pathogenic Leptospira species worldwide, and our knowledge of the currently circulating species is deficient owing to limited isolation and identification of Leptospira species from endemic countries", "token_count": 512, "char_count": 1973, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5945, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:13.113855", "source": { "split": "train_shard_00001", "doc_id": 4342 }, "chunk_id": "train_shard_00001_4342_0", "global_id": 11805 }, { "text": "This prospective study reveals the wide pathogen diversity that causes human leptospirosis in Sri Lanka, representing four species, more than eight serogroups, and fifteen clonal groups. Further, the different geographic and climatic zone distributions and clinical manifestations observed underscores the need for prospective studies to expand the molecular epidemiological approaches to combat leptospirosis\n\n12 Novel Clonal Groups of Leptospira Infecting Humans in Multiple Contrasting Epidemiological Contexts in Sri Lanka", "token_count": 124, "char_count": 533, "word_count": 69, "semantic_coherence": 1, "information_density": 0.8116, "quality_score": 0.9058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:13.503933", "source": { "split": "train_shard_00001", "doc_id": 4342 }, "chunk_id": "train_shard_00001_4342_1", "global_id": 11806 }, { "text": "

Background

Streptococcus dysgalactiae subspecies equisimilis (SDSE) is an emerging global pathogen, yet the epidemiology and population genetics of SDSE species have not been extensively characterized.

Methods

We carried out whole genome sequencing to characterize 274 SDSE isolates causing bloodstream infections obtained through national surveillance program in 2018. We conducted multilocus sequence typing (MLST), emm-typing, core genome phylogeny, as well as investigated key features associated with virulence. Moreover, comparison to SDSE from other geographic regions were performed in order to gain more insight in the evolutionary dynamics in SDSE.

Results

The phylogenetic analysis indicated a substantial diversity of emm-types and sequence types (STs). Briefly, 17 emm-types and 58 STs were identified that formed 10 clonal complexes (CCs). The predominant ST-types were ST20 (20%), ST17 (17%), and ST29 (11%). While CC17 and CC29 clades showed a substantial heterogeneity with well-separated emm-associated subclades, the CC20 clade harboring the stG62647 emm-type was more homogenous and the most prevalent in the present study. Moreover, we observed notable differences in the distribution of clades within Norway, as well as several disseminated CCs and also distinct geographic variations when compared to data from other countries. We also revealed extensive intra-species recombination events involving surface exposed virulence factors, including the emm gene important for phylogenetic profiling.

Conclusion

Recombination events involving the emm as well as other virulence genes in SDSE, are important mechanisms in shaping the genetic variability in the SDSE population, potentially offering selective advantages to certain lineages", "token_count": 509, "char_count": 1848, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [ "ST20", "CC17", "ST17", "ST29", "CC29", "CC20" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:14.136155", "source": { "split": "train_shard_00001", "doc_id": 4343 }, "chunk_id": "train_shard_00001_4343_0", "global_id": 11807 }, { "text": "The enhanced phylogenetic resolution offered by whole genome sequencing is necessary to identify and delimitate outbreaks, monitor and properly characterize emerging strains, as well as elucidate bacterial population dynamics.\n\nGenomic epidemiology of Streptococcus dysgalactiae subsp. equisimilis strains causing invasive disease in Norway during 2018.", "token_count": 100, "char_count": 367, "word_count": 44, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:14.522519", "source": { "split": "train_shard_00001", "doc_id": 4343 }, "chunk_id": "train_shard_00001_4343_1", "global_id": 11808 }, { "text": "

ABSTRACT

The Type VIIb protein secretion system (T7SSb) is found in Bacillota (firmicute) bacteria and has been shown to mediate interbacterial competition. EssC is a membrane-bound ATPase that is a critical component of the T7SSb and plays a key role in substrate recognition. Prior analysis of available genome sequences of the foodborne bacterial pathogen Listeria monocytogenes has shown that although the T7SSb was encoded as part of the core genome, EssC could be found as one of seven different sequence variants. While each sequence variant was associated with a specific suite of candidate substrate proteins encoded immediately downstream of essC , many LXG-domain proteins were encoded across multiple essC sequence variants. Here we have extended this analysis using a diverse collection of 37,930 L. monocytogenes genomes. We have identified a rare eighth variant of EssC present in ten L. monocytogenes Lineage III genomes. These genomes also encode a large toxin of the rearrangement hotspot (Rhs) repeat family adjacent to essC8 , along with a probable immunity protein and three small accessory proteins. We have further identified nine novel LXG-domain proteins, and four additional chromosomal hotspots across L. monocytogenes genomes where LXG proteins can be encoded. The eight L. monocytogenes EssC variants were also found in other Listeria species, with additional novel EssC types also identified. Across the genus, species frequently encoded multiple EssC types, indicating that T7SSb diversity is a primary feature of the genus Listeria .

DATA SUMMARY

All genome sequences used in this study are available via Genbank, and the assembly accession numbers are provided in Table S1. This file also lists relevant metadata (name, source category, country, year and clonal complex).

IMPACT STATEMENT

Listeria monocytogenes is a soil-borne saprophytic bacterium and a food-borne pathogen of humans. Decomposing plant matter and the human GI tract are rich in diverse microbial species and to colonise these niches L", "token_count": 519, "char_count": 2063, "word_count": 309, "semantic_coherence": 1, "information_density": 0.6019, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:15.156217", "source": { "split": "train_shard_00001", "doc_id": 4344 }, "chunk_id": "train_shard_00001_4344_0", "global_id": 11809 }, { "text": "monocytogenes must be able to compete with other bacteria. The type VII secretion system (T7SS) of Bacillota has been shown to secrete protein toxins that target other bacteria. In this study we have analysed a diverse collection of L. monocytogenes genome sequences to study the diversity of the Listeria T7SS and its putative effector proteins. We show that the EssC component of the L. monocytogenes T7SS is highly diverse, clustering into one of eight sequence variants. Each EssC variant is associated with a specific toxin candidate, and the EssC8 variant T7SS likely secretes a novel rearrangement hotspot (Rhs) repeat toxin. We also identify multiple new LXG-families of T7SS toxins and describe genomic hotspots where they are encoded. We find no link between EssC variants and clinical outcome. In agreement with this, analysis of EssC variability in available genomes of other Listeria species showed that all eight L. monocytogenes EssC variants are present in non-monocytogenes Listeria species.\n\nA novel variant of theListeria monocytogenestype VII secretion system EssC component is associated with an Rhs toxin", "token_count": 297, "char_count": 1133, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:15.726778", "source": { "split": "train_shard_00001", "doc_id": 4344 }, "chunk_id": "train_shard_00001_4344_1", "global_id": 11810 }, { "text": "Two Gram-stain-negative, aerobic, rod-shaped, orange-coloured bacterial strains, designated strain C216T and strain M2295, were isolated from mature mushroom compost from composting facilities in Victoria and South Australia, Australia, respectively. External structures such as flagella or pili were not observed on the cells under scanning electron microscopy. Optimal growth was found to occur at 45 °C, at pH 7.25 and in the absence of NaCl on Emerson's 350 YpSs medium. The genome sequence of strain C216T was 3 342 126 bp long with a G+C content of 40.5 mol%. Functional analysis of the genome of strain C216T revealed genes encoding chitinolytic and hemi-cellulolytic functions, with 166 predicted genes associated with carbohydrate metabolism (8.9% of the predicted genes). These functions are important for survival in the mushroom compost environment, which is rich in hemicelluloses. No antibiotic resistance genes were found in the genome sequence. The major fatty acids of strain C216T were iso-C15 : 0 (56.7%), iso-C17 : 0 3-OH (15.6%), C16 : 1  ω7c/iso-C15 : 0 2-OH (7.3%) and iso-C15 : 1 G (6.1%). The only respiratory quinone was MK-7", "token_count": 456, "char_count": 1264, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6889, "quality_score": 0.8444, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:16.376187", "source": { "split": "train_shard_00001", "doc_id": 4345 }, "chunk_id": "train_shard_00001_4345_0", "global_id": 11811 }, { "text": "The major polar lipid of strain C216T was phosphatidylethanolamine, but three unidentified phospholipids, four unidentified aminophospholipids/aminolipids and one unidentified glycolipid were also detected. Phylogenetic analysis based on proteins encoded by the core genome (bac120, 120 conserved bacterial genes) showed that strain C216T forms a distinct lineage in the family Chitinophagaceae and that the closest identified relative is Niabella soli (69.69% ANI). These data demonstrate that strain C216T represents a novel genus and novel species within the family Chitinophagaceae, for which we propose the name Mycovorax composti. The type strain is C216T (=DSM 114558T=LMG 32998T).\n\n<i>Mycovorax composti</i> gen. nov., sp. nov., a member of the family <i>Chitinophagaceae</i> isolated from button mushroom compost.", "token_count": 333, "char_count": 940, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7568, "quality_score": 0.8784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:16.942260", "source": { "split": "train_shard_00001", "doc_id": 4345 }, "chunk_id": "train_shard_00001_4345_1", "global_id": 11812 }, { "text": "Piscirickettsia salmonis is an intracellular bacterial fish pathogen that causes piscirickettsiosis, a disease with highly adverse impact in the Chilean salmon farming industry. The development of effective treatment and control methods for piscireckttsiosis is still a challenge. To meet it the number of studies on P. salmonis has grown in the last couple of years but many aspects of the pathogen's biology are still poorly understood. Studies on its metabolism are scarce and only recently a metabolic model for reference strain LF-89 was developed. We present a new genome-scale model for P. salmonis LF-89 with more than twice as many genes as in the previous model and incorporating specific elements of the fish pathogen metabolism. Comparative analysis with models of different bacterial pathogens revealed a lower flexibility in P. salmonis metabolic network. Through constraint-based analysis, we determined essential metabolites required for its growth and showed that it can benefit from different carbon sources tested experimentally in new defined media. We also built an additional model for strain A1-15972, and together with an analysis of P. salmonis pangenome, we identified metabolic features that differentiate two main species clades. Both models constitute a knowledge-base for P. salmonis metabolism and can be used to guide the efficient culture of the pathogen and the identification of specific drug targets.\n\nAnalysis of Piscirickettsia salmonis Metabolism Using Genome-Scale Reconstruction, Modeling, and Testing.", "token_count": 398, "char_count": 1592, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5973, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:17.555181", "source": { "split": "train_shard_00001", "doc_id": 4346 }, "chunk_id": "train_shard_00001_4346_0", "global_id": 11813 }, { "text": "Inflammatory bowel disease (IBD) is a chronic inflammation of the gastrointestinal tract (GIT), including Crohn's disease (CD) and ulcerative colitis (UC), which differ in the location and lesion extensions. Both diseases are associated with microbiota dysbiosis, with a reduced population of butyrate-producing species, abnormal inflammatory response, and micronutrient deficiency (e.g., vitamin D hypovitaminosis). Vitamin D (VitD) is involved in immune cell differentiation, gut microbiota modulation, gene transcription, and barrier integrity. Vitamin D receptor (VDR) regulates the biological actions of the active VitD (1α,25-dihydroxyvitamin D3), and is involved in the genetic, environmental, immune, and microbial aspects of IBD. VitD deficiency is correlated with disease activity and its administration targeting a concentration of 30 ng/mL may have the potential to reduce disease activity. Moreover, VDR regulates functions of T cells and Paneth cells and modulates release of antimicrobial peptides in gut microbiota-host interactions. Meanwhile, beneficial microbial metabolites, e.g., butyrate, upregulate the VDR signaling. In this review, we summarize the clinical progress and mechanism studies on VitD/VDR related to gut microbiota modulation in IBD. We also discuss epigenetics in IBD and the probiotic regulation of VDR. Furthermore, we discuss the existing challenges and future directions. There is a lack of well-designed clinical trials exploring the appropriate dose and the influence of gender, age, ethnicity, genetics, microbiome, and metabolic disorders in IBD subtypes. To move forward, we need well-designed therapeutic studies to examine whether enhanced vitamin D will restore functions of VDR and microbiome in inhibiting chronic inflammation.\n\nVitamin D Modulates Intestinal Microbiota in Inflammatory Bowel Diseases.", "token_count": 467, "char_count": 1854, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8123, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:18.192917", "source": { "split": "train_shard_00001", "doc_id": 4347 }, "chunk_id": "train_shard_00001_4347_0", "global_id": 11814 }, { "text": "

Background

In 2015, in addition to a United States multistate outbreak linked to contaminated ice cream, another outbreak linked to ice cream was reported in the Pacific Northwest of the United States. It was a hospital-acquired outbreak linked to milkshakes, made from contaminated ice cream mixes and milkshake maker, served to patients. Here we performed multiple analyses on isolates associated with this outbreak: pulsed-field gel electrophoresis (PFGE), whole genome single nucleotide polymorphism (SNP) analysis, species-specific core genome multilocus sequence typing (cgMLST), lineage-specific cgMLST and whole genome-specific MLST (wgsMLST)/outbreak-specific cgMLST. We also analyzed the prophages and virulence genes.

Results

The outbreak isolates belonged to sequence type 1038, clonal complex 101, genetic lineage II. There were no pre-mature stop codons in inlA. Isolates contained Listeria Pathogenicity Island 1 and multiple internalins. PFGE and multiple whole genome sequencing (WGS) analyses all clustered together food, environmental and clinical isolates when compared to outgroup from the same clonal complex, which supported the finding that L. monocytogenes likely persisted in the soft serve ice cream/milkshake maker from November 2014 to November 2015 and caused 3 illnesses, and that the outbreak strain was transmitted between two ice cream production facilities. The whole genome SNP analysis, one of the two species-specific cgMLST, the lineage II-specific cgMLST and the wgsMLST/outbreak-specific cgMLST showed that L. monocytogenes cells persistent in the milkshake maker for a year formed a unique clade inside the outbreak cluster. This clustering was consistent with the cleaning practice after the outbreak was initially recognized in late 2014 and early 2015. Putative prophages were conserved among prophage-containing isolates", "token_count": 482, "char_count": 1881, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:18.841431", "source": { "split": "train_shard_00001", "doc_id": 4348 }, "chunk_id": "train_shard_00001_4348_0", "global_id": 11815 }, { "text": "The loss of a putative prophage in two isolates resulted in the loss of the AscI restriction site in the prophage, which contributed to their AscI-PFGE banding pattern differences from other isolates.

Conclusions

The high resolution of WGS analyses allowed the differentiation of epidemiologically unrelated isolates, as well as the elucidation of the microevolution and persistence of isolates within the scope of one outbreak. We applied a wgsMLST scheme which is essentially the outbreak-specific cgMLST. This scheme can be combined with lineage-specific cgMLST and species-specific cgMLST to maximize the resolution of WGS.\n\nWhole genome sequencing analyses of Listeria monocytogenes that persisted in a milkshake machine for a year and caused illnesses in Washington State.", "token_count": 193, "char_count": 785, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:19.288904", "source": { "split": "train_shard_00001", "doc_id": 4348 }, "chunk_id": "train_shard_00001_4348_1", "global_id": 11816 }, { "text": "An increasing number of isolations of Corynebacterium diphtheriae has been observed in recent years in the archipelago of New Caledonia. We aimed to analyze the clinical and microbiological features of samples with C. diphtheriae. All C. diphtheriae isolates identified in New Caledonia from May 2015 to May 2019 were included. For each case, a retrospective consultation of the patient files was conducted. Antimicrobial susceptibility phenotypes, tox gene and diphtheria toxin expression, biovar, and the genomic sequence were determined. Core genome multilocus sequence typing (cgMLST), 7-gene MLST, and search of genes of interest were performed from genomic assemblies. Fifty-eight isolates were included, with a median age of patients of 28 years (range: 9 days to 78 years). Cutaneous origin accounted for 51 of 58 (87.9%) isolates, and C. diphtheriae was associated with Staphylococcus aureus and/or Streptococcus pyogenes in three-quarters of cases. Half of cases came either from the main city Noumea (24%, 14/58) or from the sparsely populated island of Lifou (26%, 15/58). Six tox-positive isolates were identified, associated with recent travel to Vanuatu; 5 of these cases were linked and cgMLST confirmed recent transmission. Two cases of endocarditis in young female patients with a history of rheumatic fever involved tox-negative isolates. The 58 isolates were mostly susceptible to commonly used antibiotics. In particular, no isolate was resistant to the first-line molecules amoxicillin or erythromycin. Resistance to tetracycline was found in a genomic cluster of 17 (29%) isolates, 16 of which carried the tetO gene. There were 13 cgMLST sublineages, most of which were also observed in the neighboring country Australia", "token_count": 526, "char_count": 1771, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6462, "quality_score": 0.8231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:19.920065", "source": { "split": "train_shard_00001", "doc_id": 4349 }, "chunk_id": "train_shard_00001_4349_0", "global_id": 11817 }, { "text": "Cutaneous infections may harbor nontoxigenic C. diphtheriae isolates, which circulate largely silently in nonspecific wounds. The possible introduction of tox-positive strains from a neighboring island illustrates that diphtheria surveillance should be maintained in New Caledonia, and that immunization in neighboring islands must be improved. Genomic sequencing uncovers how genotypes circulate locally and across neighboring countries. IMPORTANCE The analysis of C. diphtheriae from the tropical archipelago of New Caledonia revealed a high genetic diversity with sublineages that may be linked to Polynesia, Australia, or metropolitan France. Genomic typing allowed confirming or excluding suspected transmission events among cases and contacts. A highly prevalent tetracycline-resistant sublineage harboring the tetO gene was uncovered. Toxigenic isolates were observed from patients returning from Vanuatu, showing the importance of improving vaccination coverage in settings where it is insufficient. This study also illustrates the importance for diphtheria surveillance of the inclusion of isolates from cutaneous sources in addition to respiratory cases, in order to provide a more complete epidemiological picture of the diversity and transmission of C. diphtheriae.\n\nGenomic Epidemiology of Corynebacterium diphtheriae in New Caledonia.", "token_count": 325, "char_count": 1369, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6742, "quality_score": 0.8371, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:20.493858", "source": { "split": "train_shard_00001", "doc_id": 4349 }, "chunk_id": "train_shard_00001_4349_1", "global_id": 11818 }, { "text": "To induce extracellular secretion of beta-galactosidase synthesised by Kluyveromyces fragilis 28, it was used glycine, L-asparagine, L-leucine, dimethyl fluoride, dimethyl sulfoxide, cetyldimethylethylammonium bromide, penicillin G and glycolipids from Candida antarctica. The highest increase in the secretion of beta-galactosidase was obtained in the yeast culture cultivated in the medium with polypeptone when glycine was used as the secretion inductor. The extracellular activity of beta-galactosidase reached 0.416 A.U./ml, and was 10-fold higher than the beta-galactosidase activity reported in the control group.\n\nThe effect of some conditions on the secretion of extracellular beta-galactosidase synthesised by Kluyveromyces fragilis 28.", "token_count": 235, "char_count": 746, "word_count": 95, "semantic_coherence": 1, "information_density": 0.6211, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:21.011035", "source": { "split": "train_shard_00001", "doc_id": 4350 }, "chunk_id": "train_shard_00001_4350_0", "global_id": 11819 }, { "text": "The reclassification of Streptobacillus hongkongensis as Pseudostreptobacillus hongkongensis gen. nov., comb. nov. is proposed because of the separate phylogenetic position on the basis of the 16S rRNA gene sequence phylogeny, the combined analysis of the three protein-coding housekeeping genes groEL, gyrB and recA and a core genome sequence phylogeny to all other Streptobacillus species that is supported by phenotypic differences. The species Pseudostreptobacillus hongkongensis is the type species of the genus. The type strain is HKU33T, JCM 18691T, NCTC 13659T, DSM 26322T.\n\nProposal to reclassify Streptobacillus hongkongensis into a novel genus as Pseudostreptobacillus hongkongensis gen. nov., comb. nov.", "token_count": 310, "char_count": 822, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [ "HKU33" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:22.063432", "source": { "split": "train_shard_00001", "doc_id": 4351 }, "chunk_id": "train_shard_00001_4351_0", "global_id": 11820 }, { "text": "The human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. Here we report a whole genome sequencing metagenomic study of the intestinal microbiota changes caused by Helicobacter pylori eradication therapy. We have found the decrease in taxonomic alpha-diversity due to the therapy. The changes observed were more extensive for patients with duodenal ulcer and female ones. As well across the patients under the therapy we have detected the shifts in the metabolic potential and resistome. Seven KEGG pathways associated with quorum sensing, genetic Information processing and environmental Information processing were increased, while metabolic pathways related with metabolism of cofactors and vitamins and glycan biosynthesis and metabolism decreased. Changes in the resistome profile have also been identified. We observed perturbations in intraspecies structures, which were higher in group of patients under the therapy than in control group of people without treatment. The Eubacterium rectale pangenome extracted from metagenomic data were changed. We also isolated and sequenced Enterococcus faecium strains from two patients before and after eradication therapy. After the therapy this bacterium increased as the antibiotic resistance in vitro, as well the number of ARGs to macrolides and tetracyclines and metagenomic relative abundance in comparison with strains before therapy. In summary, microbial community demonstrated shift to reduce metabolic potential and to increased mechanisms, which mediate more survival condition through intraspecies perturbations.

Importance

The human gut microbiome plays an important role both in health and disease. The use of antibiotics can alter gut microbiota composition, which can cause complications of various kinds. H. pylori eradication therapy causes multiple shifts and alterations (including intraspecies changes) of the intestinal microbiota structure and leads to the accumulation of genes which determine resistance to macrolides. Since these changes are not the same for patients with various diseases, patients with duodenal ulcer may be further paid special attention for reducing side effects, such as antibiotic-induced dysbiosis", "token_count": 502, "char_count": 2333, "word_count": 328, "semantic_coherence": 1, "information_density": 0.5335, "quality_score": 0.7668, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:22.769854", "source": { "split": "train_shard_00001", "doc_id": 4352 }, "chunk_id": "train_shard_00001_4352_0", "global_id": 11821 }, { "text": "Also, study of antibiotic treatment in terms of its impact upon the human gut microbiota allows shedding light on of the complex processes that cause accumulation and spread of antibiotic resistance. An identification and understanding of these complicated processes may help to constrain antibiotic resistance spread, which is of great importance for human health care.\n\nShifts in the gut microbiota structure caused byHelicobacter pylorieradication therapy", "token_count": 101, "char_count": 465, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:23.147992", "source": { "split": "train_shard_00001", "doc_id": 4352 }, "chunk_id": "train_shard_00001_4352_1", "global_id": 11822 }, { "text": "We determined the prevalence and genetic characteristics of methicillin-resistant Staphylococcus aureus (MRSA) isolated from pigs and humans between September 2013 and February 2015 in Kogi State, a central region in Nigeria. A total of 680 nasal swabs were collected and analyzed from pigs (n = 425) and \"pig-contact\" humans (n = 55) on 35 farms, and \"non-pig-contact\" humans (n = 200). MRSA was recovered from 20 (4.7%) pigs on 12 farms and 18 (7.0%) humans. Six (2.4%) of the human isolates were recovered from \"pig-contact\" humans, of which only three work on farms also harboring MRSA positive pigs. All 38 MRSA were resistant to β-lactams only, belonged to spa type t1603, sequence type (ST) 88, and mecA was associated with a SCCmec IVa element. Four isolates from a pig, a pig-contact human from the same farm, a pig-contact human from a pig farm in a different district, and a non-pig-contact human were subjected to whole genome sequencing (WGS). Core genome SNP analysis revealed high genetic similarity between strains (3-11 SNP differences), despite the temporal (2 year gap) and geographic (165 km) differences between isolates. Furthermore, these Nigerian isolates form a distinct clade when compared to other African MRSA ST88 isolates. All but one porcine strain was positive for scn suggesting a possible human origin and that pigs were either transiently contaminated by humans or result of a very recent human-to-pig transmission event. To our knowledge, this is the first report of genetically confirmed MRSA in pigs in Nigeria, which appear to be a typical CA-MRSA clone present in the human population.", "token_count": 506, "char_count": 1681, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [ "ST88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:23.781138", "source": { "split": "train_shard_00001", "doc_id": 4353 }, "chunk_id": "train_shard_00001_4353_0", "global_id": 11823 }, { "text": "High Genetic Similarity of MRSA ST88 Isolated From Pigs and Humans in Kogi State, Nigeria.", "token_count": 28, "char_count": 90, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:24.136211", "source": { "split": "train_shard_00001", "doc_id": 4353 }, "chunk_id": "train_shard_00001_4353_1", "global_id": 11824 }, { "text": "The number of nosocomial blood stream infections due to Candida species has increased over the past few decades. In order to establish an infection, opportunistic pathogens have to evade the immune system, survive, divide in the host environment, and spread to other tissues. Proteinase and phospholipase secretion has been implicated as potential virulence factors for some Candida species responsible for catheter related candidemia in intensive care unit (ICU) patients with indwelling devices. We therefore have aimed at demonstrating the secretion of proteinase and phospholipase enzymes as virulent factors by Candida species isolated from blood samples collected from ICUs, dialysis units and oncology units. One hundred and fourteen isolates of Candida species were obtained from the blood samples and the isolates include 37 Candida albicans, 7 Candida glabrata, 5 Candida guilliermondii, 3 Candida kefyr, 45 Candida krusei, 5 Candida parapsilosis, and 12 Candida tropicalis. Proteinase assay was performed by using the Staib et al method. Phospholipase assay was performed by using the method of Samaranayake et al. Precipitation zone (Pz value) was determined. The percentage of isolates which produced detectable amounts of proteinase is 74.56% and 44.73% of isolates produced detectable amounts of phospholipase. We believe that production of both phospholipase and proteinase enzimes could be an important virulence factor for several Candida species.\n\nProteinase and phospholipase activity as virulence factors in Candida species isolated from blood.", "token_count": 390, "char_count": 1565, "word_count": 226, "semantic_coherence": 1, "information_density": 0.5929, "quality_score": 0.7965, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:24.753076", "source": { "split": "train_shard_00001", "doc_id": 4354 }, "chunk_id": "train_shard_00001_4354_0", "global_id": 11825 }, { "text": "A genomic cluster of Salmonella Braenderup ST22, a serovar of Salmonella enterica subsp. enterica which causes symptoms of gastrointestinal illness, was notified by Danish authorities to the European Centre for Disease Prevention and Control (ECDC) on 3 May 2021. By 6 July 2021, S. Braenderup outbreak cases (n = 348) had been reported from 12 countries in the European Union/European Economic Area (EU/EEA) and the United Kingdom (UK), including 68 hospitalised cases. With support from affected EU/EEA countries, and in partnership with the European Food Safety Authority (EFSA), ECDC established an international outbreak investigation team to rapidly identify the source and prevent outbreak spread. Consumption information was shared with affected countries through a standard line list, revealing that 124 of 197 cases (63%) reported having eaten (any) melons within 7 days prior to disease onset. The speed and completeness of the investigation, which identified the outbreak vehicle as galia melons imported from Honduras in June 2021, was a direct result of extensive collaboration and information sharing between countries' national food safety and public health authorities. This article describes the outbreak and the benefits, successes, and challenges of multi-country collaboration for consideration in future large foodborne outbreaks across Europe.\n\nMultinational collaboration in solving a European Salmonella Braenderup outbreak linked to imported melons, 2021.", "token_count": 372, "char_count": 1516, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6792, "quality_score": 0.8396, "entities": { "genes": [ "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:25.336446", "source": { "split": "train_shard_00001", "doc_id": 4355 }, "chunk_id": "train_shard_00001_4355_0", "global_id": 11826 }, { "text": "A novel Kluyveromyces marxianus gene that encodes an acid phosphatase, Pho610, was cloned in Saccharomyces cerevisiae. The deduced amino acid sequence was distinct from S. cerevisiae phosphatases but similar to some fungal enzymes. A peculiar feature of the sequence is that it has hydrophobic stretches both at the N- and C-termini, which is a characteristic of the precursors of glycosylphosphatidylinositol(GPI)-anchored proteins. When the gene was expressed in S. cerevisiae, the active enzyme was recovered in the periplasmic fraction by glucanase digestion. The Pho610 polypeptide was highly glycosylated and a significant portion was covalently linked to the cell-wall glucan. The enzyme was secreted when the C-terminal region was truncated to remove the GPI signal. Therefore, Pho610 is a novel cell-wall protein having an enzyme activity.\n\nMolecular characterization of a novel yeast cell-wall acid phosphatase cloned from Kluyveromyces marxianus.", "token_count": 277, "char_count": 957, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6277, "quality_score": 0.8139, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:25.894853", "source": { "split": "train_shard_00001", "doc_id": 4356 }, "chunk_id": "train_shard_00001_4356_0", "global_id": 11827 }, { "text": "Most genomes within the species complex of Fusarium oxysporum are organized into two compartments: the core chromosomes (CCs) and accessory chromosomes (ACs). As opposed to CCs, which are conserved and vertically transmitted to carry out essential housekeeping functions, lineage- or strain-specific ACs are believed to be initially horizontally acquired through unclear mechanisms. These two genomic compartments are different in terms of gene density, the distribution of transposable elements, and epigenetic markers. Although common in eukaryotes, the functional importance of ACs is uniquely emphasized among fungal species, specifically in relationship to fungal pathogenicity and their adaptation to diverse hosts. With a focus on the cross-kingdom fungal pathogen F. oxysporum, this review provides a summary of the differences between CCs and ACs based on current knowledge of gene functions, genome structures, and epigenetic signatures, and explores the transcriptional crosstalk between the core and accessory genomes.\n\nAccessory Chromosomes in Fusarium oxysporum.", "token_count": 264, "char_count": 1097, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:26.453121", "source": { "split": "train_shard_00001", "doc_id": 4357 }, "chunk_id": "train_shard_00001_4357_0", "global_id": 11828 }, { "text": "Cheese flavour is the result of complex biochemical transformations attributed to bacteria and yeasts grown on the curd of smear-ripened cheeses. Volatile sulphur compounds (VSCs) are responsible for the characteristic aromatic notes of several cheeses. In the present study, we have assessed the ability of Kluyveromyces lactis, Kluyveromyces marxianus and Saccharomyces cerevisiae strains, which are frequently isolated from smear-ripened cheeses, to grow and deacidify a cheese medium and generate VSCs resulting from L-methionine degradation. The Kluyveromyces strains produced a wider variety and higher amounts of VSCs than the S. cerevisiae ones. We have shown that the pathway is likely to be proceeding differently in these two yeast genera. The VSCs are mainly generated through the degradation of 4-methylthio-oxobutyric acid in the Kluyveromyces strains, in contrast to the S. cerevisiae ones which have higher L-methionine demethiolating activity, resulting in a direct conversion of L-methionine to methanethiol. The deacidification activity which is of major importance in the early stages of cheese-ripening was also compared in S. cerevisiae and Kluyveromyces strains.\n\nKluyveromyces lactis and Saccharomyces cerevisiae, two potent deacidifying and volatile-sulphur-aroma-producing microorganisms of the cheese ecosystem.", "token_count": 368, "char_count": 1338, "word_count": 183, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:27.043471", "source": { "split": "train_shard_00001", "doc_id": 4358 }, "chunk_id": "train_shard_00001_4358_0", "global_id": 11829 }, { "text": "Lactobacillus paracasei are diverse Gram-positive bacteria that are very closely related to Lactobacillus casei, belonging to the Lactobacillus casei group. Due to extreme genome similarities between L. casei and L. paracasei, many strains have been cross placed in the other group. We had earlier sequenced and analyzed the genome of Lactobacillus paracasei Lbs2, but mistakenly identified it as L. casei. We re-analyzed Lbs2 reads into a 2.5 MB genome that is 91.28% complete with 0.8% contamination, which is now suitably placed under L. paracasei based on Average Nucleotide Identity and Average Amino Acid Identity. We took 74 sequenced genomes of L. paracasei from GenBank with assembly sizes ranging from 2.3 to 3.3 MB and genome completeness between 88% and 100% for comparison. The pan-genome of 75 L. paracasei strains hold 15,945 gene families (21,5232 genes), while the core genome contained about 8.4% of the total genes (243 gene families with 18,225 genes) of pan-genome. Phylogenomic analysis based on core gene families revealed that the Lbs2 strain has a closer relationship with L. paracasei subsp. tolerans DSM20258. Finally, the in-silico analysis of the L. paracasei Lbs2 genome revealed an important pathway that could underpin the production of thiamin, which may contribute to the host energy metabolism.", "token_count": 476, "char_count": 1420, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6244, "quality_score": 0.8122, "entities": { "genes": [ "DSM20258" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:27.683880", "source": { "split": "train_shard_00001", "doc_id": 4359 }, "chunk_id": "train_shard_00001_4359_0", "global_id": 11830 }, { "text": "Reanalysis of Lactobacillus paracasei Lbs2 Strain and Large-Scale Comparative Genomics Places Many Strains into Their Correct Taxonomic Position.", "token_count": 47, "char_count": 152, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:28.042400", "source": { "split": "train_shard_00001", "doc_id": 4359 }, "chunk_id": "train_shard_00001_4359_1", "global_id": 11831 }, { "text": "In this study, rDNA ITS restriction analysis was used to identify yeasts from two naturally fermented products: French ciders and black olives. In cider musts and bottled ciders, the PCR-RFLP method generated 15 different ITS/RFLP profiles for a total of 208 isolates. The predominant yeasts corresponded to Saccharomyces bayanus, Saccharomyces cerevisiae, Lachancea cidri and Dekkera anomala. Three identified species: Candida sake, Candida tropicalis and Kluyveromyces marxianus had never been described before in ciders. For the black olive fermentation, the method allowed for identification of 11 profiles for a total of 137 isolates. A sequential apparition of yeasts was observed with Pichia anomala, Candida boidinii and Debaryomyces etchellsii being the predominant species. Four isolates did not correspond to any known species based on the sequencing of the D1/D2 region of the 26S rRNA gene. By using the rDNA ITS method, valuable information on yeast population biodiversity and dynamics in the naturally fermented food products studied was obtained.\n\nYeast ecology in French cider and black olive natural fermentations.", "token_count": 299, "char_count": 1133, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6747, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:28.602646", "source": { "split": "train_shard_00001", "doc_id": 4360 }, "chunk_id": "train_shard_00001_4360_0", "global_id": 11832 }, { "text": "A human anti-haemophilic factor IX gene (h-FIX) was fussed to a secretion signal peptide sequence from the yeast Kluyveromyces lactis and controlled under the regulatory promoter of LAC4 gene from K. fragilis to form an h-FIX gene expression cassette. By inserting the cassette into a yeast integrating plasmid, a high-stable h-FIX gene expression vector, pHKB202-FP, was constructed. After induction with galactose, the h-FIX was first successfully expressed and secreted in yeast K. fragils transformed by the pHKB202-FP. The expression level was up to 200 rig/ml in the culture supernatant determined by ELISA method. The result was significant to promotion of the h-FIX production in biotech industry scale.\n\nExpression and Secretion of Human Anti-haemophilic Factor IX in Yeast Kluyveromyces fragilis", "token_count": 224, "char_count": 805, "word_count": 119, "semantic_coherence": 1, "information_density": 0.5966, "quality_score": 0.7983, "entities": { "genes": [ "LAC4" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:29.074742", "source": { "split": "train_shard_00001", "doc_id": 4361 }, "chunk_id": "train_shard_00001_4361_0", "global_id": 11833 }, { "text": "The use of stalks instead of tubers as a source of carbohydrates for ethanol production has been investigated. The inulin present in the stalks of Jerusalem artichoke was extracted with water and the effect of solid-liquid ratio, temperature, and acid addition was studied and optimized in order to attain a high-fructose fermentable extract. The maximum extraction efficiency (corresponding to 35 g/L) of soluble sugars was obtained at 1/6 solid-liquid ratio. Fermentations of hydrolyzed extracts by baker's yeast and direct fermentation by an inulinase activity yeast were also performed and the potential to use this feedstock for bioethanol production assessed. The results show that the carbohydrates derived from Jerusalem artichoke stalks can be converted efficiently to ethanol by acidic hydrolysis followed by fermentation with Saccharomyces cerevisiae or by direct fermentation of inulin using Kluyveromyces marxianus strains. In this last case about 30 h to complete fermentation was required in comparison with 8-9 h obtained in experiments with S. cerevisiae growth on acid extracted juices.\n\nInulin-containing biomass for ethanol production: carbohydrate extraction and ethanol fermentation.", "token_count": 307, "char_count": 1205, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.815, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:29.645063", "source": { "split": "train_shard_00001", "doc_id": 4362 }, "chunk_id": "train_shard_00001_4362_0", "global_id": 11834 }, { "text": "The kinetics of ethanol inhibition on cell growth and ethanol production by Kluyveromyces marxianus UCD (FST) 55-82 were studied during batch growth. The liquid medium contained 10% (wt/vol) inulin-type sugars derived from an extract of Jerusalem artichoke (Helianthus tuberosus) tubers, supplemented with small amounts of Tween 80, oleic acid, and corn steep liquor. Initial ethanol concentrations ranging from 0 to 80 g/liter in the liquid medium were used to study the inhibitory effect of ethanol on the following parameters: maximum specific growth rate (mu(max)), cell and ethanol yields, and sugar utilization. It was found that as the initial ethanol concentration increased from 0 to 80 g/liter, and maximum specific growth rate of K. marxianus cells decreased from 0.42 to 0.09 h, whereas the ethanol and cell yields and sugar utilization remained almost constant. A simple kinetic model was used to correlate the mu(max) results and the rates of cell and ethanol production, and the appropriate constants were evaluated.\n\nEthanol Inhibition Kinetics of Kluyveromyces marxianus Grown on Jerusalem Artichoke Juice.", "token_count": 302, "char_count": 1123, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6095, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:30.209183", "source": { "split": "train_shard_00001", "doc_id": 4363 }, "chunk_id": "train_shard_00001_4363_0", "global_id": 11835 }, { "text": "A kind of genes associated with the thermotolerance of yeast, especially two novel ESTs associated with the thermotolerance of Kluyveromyces marxianus is disclosed. A process for finding out them is also disclosed.\n\nYeast heat resistant related gene and its use", "token_count": 65, "char_count": 261, "word_count": 40, "semantic_coherence": 1, "information_density": 0.775, "quality_score": 0.8875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:30.577983", "source": { "split": "train_shard_00001", "doc_id": 4364 }, "chunk_id": "train_shard_00001_4364_0", "global_id": 11836 }, { "text": "The epidemiology of patients with gastrointestinal colonization of carbapenem-resistant Acinetobacter baumannii (CRAB) has not been systematically analyzed. We aimed to analyze the incidence, risk factors, and clinical outcomes of patients with newly identified gastrointestinal colonization of CRAB in a healthcare region in Hong Kong, where a multi-pronged screening strategy for gastrointestinal colonization of CRAB, together with other multidrug-resistant organisms (MDROs), was conducted by collecting fecal specimens (rectal swab or stool) upon admission and during hospitalization. From 1 October 2015 to 31 December 2019, a total of 161,339 fecal specimens from 63,588 patients, 61,856 (97.3%) of whom were hospitalized patients, and 54,525 (88.1%) were screened upon admission, with 1309 positive for CRAB (2.4% prevalence). Among patients positive for CRAB in fecal specimens, 698 (53.3%) had newly detected gastrointestinal colonization of CRAB, giving an incidence of 10.03 per 10,000 patient admissions and constituting 2646 CRAB colonization days in the general wards. Excluding the 164 patients with co-colonization of other MDROs, 534 patients had gastrointestinal colonization with only CRAB, and 12.5% (67/534) developed symptomatic CRAB infections at a median of 61 days (range: 2 to 671 days), during prospective follow-up for 2 years. Compared with age- and sex-matched controls, patients being referred from residential care homes for the elderly, the presence of indwelling devices, use of beta-lactam/beta-lactamase inhibitors, carbapenems, and proton pump inhibitors in the preceding 6 months, and history of hospitalization in the past 6 months were significantly associated with gastrointestinal colonization with CRAB, as shown by multivariable analysis", "token_count": 515, "char_count": 1782, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:31.209549", "source": { "split": "train_shard_00001", "doc_id": 4365 }, "chunk_id": "train_shard_00001_4365_0", "global_id": 11837 }, { "text": "Log-rank test showed that cases had significantly shorter survival duration than controls (p < 0.001). The adjusted hazard ratio of gastrointestinal colonization of CRAB was 1.8 (95% CI: 1.5−2.2; p < 0.001), as shown by Cox regression analysis. Whole-genome sequencing of eight patients with CRAB isolates in their blood cultures and rectal swabs during the same episode of hospitalization revealed ST-195 as the predominant type, as shown by multilocus sequencing type. Gastrointestinal colonization of CRAB poses a considerable challenge for infection prevention and control.\n\nGastrointestinal Colonization of Carbapenem-Resistant Acinetobacter baumannii: What Is the Implication for Infection Control?", "token_count": 196, "char_count": 711, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7629, "quality_score": 0.8814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:31.667004", "source": { "split": "train_shard_00001", "doc_id": 4365 }, "chunk_id": "train_shard_00001_4365_1", "global_id": 11838 }, { "text": "

Aim

Evaluation of Lantana camara's use as feedstock for fuel ethanol production.

Methods and results

Lantana camara plant material was hydrolysed with 1% sulfuric acid for 18 h at room temperature, followed by heat treatment of 121 degrees C for 20 min. Hemicellulosic hydrolyzate was separated and used for detoxification by ethyl acetate and overliming. Cellulosic fraction was hydrolysed with Aspergillus niger crude cellulase enzyme for 18 h at 55 degrees C. Using 15% (dw/v) substrate 73 g l(-1) total reducing sugars were obtained to give 78.7% hydrolysis of carbohydrate content. Acid and enzyme hydrolyzates were mixed equally and used for fermentation with thermotolerant Saccharomyces cerevisiae (VS(3)). Yeast fermented L. camara hydrolyzate well with a fermentation efficiency of 83.7% to give an ethanol yield of 0.431 +/- 0.018 g ethanol pre g sugar and productivity of 0.5 +/- 0.021 g l(-1) h(-1).

Conclusions

Even though inhibitors were present in L. camara hydrolyzate, maximum sugars were utilized by thermotolerant yeast.

Significance and impact of the study

Use of L. camara for fuel ethanol production with improved strains and detoxification can be recommended.\n\nLantana camara for fuel ethanol production using thermotolerant yeast.", "token_count": 414, "char_count": 1284, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6284, "quality_score": 0.8142, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:32.300861", "source": { "split": "train_shard_00001", "doc_id": 4366 }, "chunk_id": "train_shard_00001_4366_0", "global_id": 11839 }, { "text": "It includes the stages of grinding the lignocellulosic biomass to a size of 15-30 mm, subjecting the product obtained to steam explosion pre-treatment at a temperature of 190-230ºC for between 1 and 10 minutes in a reactor (2), collecting the pre-treated material in a cyclone (3) and separating the liquid and solid fractions by filtration in a filter press (9), introducing the solid fraction in a fermentation deposit (10), adding a cellulase at a concentration of 15 UFP per gram of cellulose and 12.6 International Units of beta-glucosidase enzyme dissolved in citrate buffer pH 4.8, inoculating the fermentation deposit (10) with a culture of the heat-tolerant bacteria Kluyveromyces marxianus CECT 10875, obtained by chemical mutagenesis from strain DER-26 of Kluyveromyces marxianus and shaking the mixture for 72 hours at 42ºC.\n\nProcedure for the production of ethanol from lignocellulosic biomass using a heat-tolerant yeast", "token_count": 282, "char_count": 934, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6503, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:32.851292", "source": { "split": "train_shard_00001", "doc_id": 4367 }, "chunk_id": "train_shard_00001_4367_0", "global_id": 11840 }, { "text": "

Background

The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart.

Results

The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S", "token_count": 478, "char_count": 1944, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6842, "quality_score": 0.8421, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:33.520458", "source": { "split": "train_shard_00001", "doc_id": 4368 }, "chunk_id": "train_shard_00001_4368_0", "global_id": 11841 }, { "text": "constellatus we were able to determine important SNPs and changes in VNTR numbers that occurred over the course of one year.

Conclusions

The comparative genomic analysis of the SAG clarifies the phylogenetics of these bacteria and supports the distinct species classification. Numerous potential virulence determinants were identified and provide a foundation for further studies into SAG pathogenesis. Furthermore, the data may be used to enable the development of rapid diagnostic assays and therapeutics for these pathogens.\n\nPhylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation.", "token_count": 159, "char_count": 714, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:33.978503", "source": { "split": "train_shard_00001", "doc_id": 4368 }, "chunk_id": "train_shard_00001_4368_1", "global_id": 11842 }, { "text": "Multiresistance plasmids belonging to the IncI incompatibility group have become one of the most pervasive plasmid types in extended-spectrum beta-lactamase-producing Escherichia coli of animal origin. The extent of the burden imposed on the bacterial cell by these plasmids seems to modulate the emergence of \"epidemic\" plasmids. However, in vivo data in the natural environment of the strains are scarce. Here, we investigated the cost of a bla CTX-M-1-IncI1 epidemic plasmid in a commensal E. coli animal strain, UB12-RC, before and after oral inoculation of 15 6- to 8-week- old specific-pathogen-free pigs. Growth rate in rich medium was determined on (i) UB12-RC and derivatives, with or without plasmid, in vivo and/or in vitro evolved, and (ii) strains that acquired the plasmid in the gut during the experiment. Although bla CTX-M-1-IncI1 plasmid imposed no measurable burden on the recipient strain after conjugation and during the longitudinal carriage in the pig's gut, we observed a significant difference in the bacterial growth rate between IncI1 plasmid-carrying and plasmid-free isolates collected during in vivo carriage. Only a few mutations on the chromosome of the UB12-RC derivatives were detected by whole-genome sequencing. RNA-Seq analysis of a selected set of these strains showed that transcriptional responses to the bla CTX-M-1-IncI1 acquisition were limited, affecting metabolism, stress response, and motility functions. Our data suggest that the effect of IncI plasmid on host cells is limited, fitness cost being insufficient to act as a barrier to IncI plasmid spread among natural population of E. coli in the gut niche.", "token_count": 522, "char_count": 1758, "word_count": 250, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "UB12" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:34.647346", "source": { "split": "train_shard_00001", "doc_id": 4369 }, "chunk_id": "train_shard_00001_4369_0", "global_id": 11843 }, { "text": "Dissemination of IncI plasmid encoding bla CTX-M-1 is not hampered by its fitness cost in the pig's gut.", "token_count": 46, "char_count": 122, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:35.041101", "source": { "split": "train_shard_00001", "doc_id": 4369 }, "chunk_id": "train_shard_00001_4369_1", "global_id": 11844 }, { "text": "The U3 snoRNA coding sequences from the genomic DNAs of Kluyveromyces delphensis and four variants of the Kluyveromyces marxianus species were cloned by PCR amplification. Nucleotide sequence analysis of the amplification products revealed a unique U3 snoRNA gene sequence in all the strains studied, except for K. marxianus var. fragilis. The K. marxianus U3 genes were intronless, whereas an intron similar to those of the Saccharomyces cerevisiae U3 genes was found in K. delphensis. Hence, U3 genes with and without intron are found in yeasts of the Saccharomycetoideae subfamily. The secondary structure of the K. delphensis pre-U3 snoRNA and of the K. marxianus mature snoRNAs were studied experimentally. They revealed a strong conservation in yeasts of (1) the architecture of U3 snoRNA introns, (2) the 5'-terminal domain of the mature snoRNA, and (3) the protein-anchoring regions of the U3 snoRNA 3' domain. In contrast, stem-loop structures 2, 3, and 4 of the 3' domain showed great variations in size, sequence, and structure. Using a genetic test, we show that, in spite of these variations, the Kluyveromyces U3 snoRNAs are functional in S. cerevisiae. We also show that S. cerevisiae U3A snoRNAs lacking the stem-loop structure 2 or 4 are functional. Hence, U3 snoRNA function can accommodate great variations of the RNA 3'-terminal domain.\n\nU3 snoRNA genes with and without intron in the Kluyveromyces genus: yeasts can accommodate great variations of the U3 snoRNA 3'-terminal domain.", "token_count": 444, "char_count": 1502, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5021, "quality_score": 0.7511, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:35.670368", "source": { "split": "train_shard_00001", "doc_id": 4370 }, "chunk_id": "train_shard_00001_4370_0", "global_id": 11845 }, { "text": "Kefir is a dairy product that can be prepared from different milk types, such as goat, buffalo, sheep, camel, or cow via microbial fermentation (inoculating milk with kefir grains). As such, kefir contains various bacteria and yeasts which influence its chemical and sensory characteristics. A mixture of two kinds of milk promotes kefir sensory and rheological properties aside from improving its nutritional value. Additives such as inulin can also enrich kefir's health qualities and organoleptic characters. Several metabolic products are generated during kefir production and account for its distinct flavour and aroma: Lactic acid, ethanol, carbon dioxide, and aroma compounds such as acetoin and acetaldehyde. During the storage process, microbiological, physicochemical, and sensory characteristics of kefir can further undergo changes, some of which improve its shelf life. Kefir exhibits many health benefits owing to its antimicrobial, anticancer, gastrointestinal tract effects, gut microbiota modulation and anti-diabetic effects. The current review presents the state of the art relating to the role of probiotics, prebiotics, additives, and different manufacturing practices in the context of kefir's physicochemical, sensory, and chemical properties. A review of kefir's many nutritional and health benefits, underlying chemistry and limitations for usage is presented.\n\nThe Many Faces of Kefir Fermented Dairy Products: Quality Characteristics, Flavour Chemistry, Nutritional Value, Health Benefits, and Safety.", "token_count": 376, "char_count": 1528, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6509, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:36.266395", "source": { "split": "train_shard_00001", "doc_id": 4371 }, "chunk_id": "train_shard_00001_4371_0", "global_id": 11846 }, { "text": "The use of whole genome sequencing (WGS) using next generation sequencing (NGS) technology has become a widely accepted method for microbiology laboratories in the application of molecular typing for outbreak tracing and genomic epidemiology. Several studies demonstrated the usefulness of WGS data analysis through Single Nucleotide Polymorphism (SNP) calling from a reference sequence analysis for Brucella melitensis , whereas gene-by-gene comparison through core-genome Multilocus Sequence Typing (cgMLST) has not been explored so far. The current study developed an allele-based method cgMLST and compared its performance to the genome-wide SNP approach and the traditional MLVA on a defined sample collection. The dataset comprised of 37 epidemiologically linked animal cases of brucellosis as well as 71 epidemiologically unrelated human and animal isolates collected in Italy. The cgMLST scheme generated in this study contained 2,687 targets of the B. melitensis 16M reference genome (75.4% of the complete genome). We established the potential criteria necessary for inclusion of an isolate into a brucellosis outbreak cluster to be ≤4 loci in the cgMLST and ≤10 in WGS SNP analysis. CgMLST and SNP analysis provided much higher phylogenetic distance resolution than MLVA, particularly for strains belonging to the same lineage thus allowing diverse and unrelated genotypes to be identified with greater confidence. The application of this cgMLST scheme to the characterization of B. melitensis strains provided insights into the epidemiology of this pathogen and it is a candidate to be a benchmark tool for outbreak investigations in human and animal brucellosis.\n\nCore Genome Multi Locus Sequence Typing and Single Nucleotide Polymorphism Analysis in the Epidemiology of Brucella melitensis Infections", "token_count": 436, "char_count": 1821, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6008, "quality_score": 0.8004, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:36.898733", "source": { "split": "train_shard_00001", "doc_id": 4372 }, "chunk_id": "train_shard_00001_4372_0", "global_id": 11847 }, { "text": "

Background

A huge and continuous increase in the number of completely sequenced chloroplast genomes, available for evolutionary and functional studies in plants, has been observed during the past years. Consequently, it appears possible to build large-scale phylogenetic trees of plant species. However, building such a tree that is well-supported can be a difficult task, even when a subset of close plant species is considered. Usually, the difficulty raises from a few core genes disturbing the phylogenetic information, due for example from problems of homoplasy. Fortunately, a reliable phylogenetic tree can be obtained once these problematic genes are identified and removed from the analysis.Therefore, in this paper we address the problem of finding the largest subset of core genomes which allows to build the best supported tree.

Results

As an exhaustive study of all core genes combination is untractable in practice, since the combinatorics of the situation made it computationally infeasible, we investigate three well-known metaheuristics to solve this optimization problem. More precisely, we design and compare distributed approaches using genetic algorithm, particle swarm optimization, and simulated annealing. The latter approach is a new contribution and therefore is described in details, whereas the two former ones have been already studied in previous works. They have been designed de novo in a new platform, and new experiments have been achieved on a larger set of chloroplasts, to compare together these three metaheuristics.

Conclusions

The ways genes affect both tree topology and supports are assessed using statistical tools like Lasso or dummy logistic regression, in an hybrid approach of the genetic algorithm. By doing so, we are able to provide the most supported trees based on the largest subsets of core genes.\n\nComparison of metaheuristics to measure gene effects on phylogenetic supports and topologies.", "token_count": 419, "char_count": 1968, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6399, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:37.525567", "source": { "split": "train_shard_00001", "doc_id": 4373 }, "chunk_id": "train_shard_00001_4373_0", "global_id": 11848 }, { "text": "Carbapenem-resistant pathogens mediated by metallo-beta-lactamases (MBLs) have spread worldwide, where NDM-1 is a typical and key MBL. Here, we firstly discussed the distribution characterization of NDM-1, which produces multidrug-resistant Proteus mirabilis among broilers in China. From January to April 2019, 40 (18.1%, 40/221) blaNDM-1-carrying P. mirabilis strains were recovered from commercial broilers in slaughterhouse B in China. All the isolates were resistant to imipenem, meropenem and other β-lactams. These isolates belong to five clusters identified via pulsed field gel electrophoresis (PFGE). Further studies on twenty representative strains revealed that seven blaNDM-1 genes were located on plasmids with sizes of 104.5-138.9 kb. Notably, only three strains (PB72, PB96 and PB109) were successfully transferred to Escherichia coli J53, while the other four isolates were located in nontransferable plasmids. The rest were harbored in chromosomes. Ulteriorly, based on whole genome sequencing (WGS), these twenty isolates showed four typical phylogenetic clades according to single nucleotide polymorphisms (SNPs) of a core genome and presented four main genomic backbone profiles, in which type II/III strains shared a similar genetic context. All of the above is evidence of blaNDM-1 transmission and evolution in P. mirabilis, suggesting that the prevalence may be more diverse in broiler farms. Accordingly, as intestinal and environmental symbiotic pathogens, blaNDM-1-positive P. mirabilis will pose greater threats to the environment and public health.", "token_count": 516, "char_count": 1696, "word_count": 219, "semantic_coherence": 1, "information_density": 0.7169, "quality_score": 0.8584, "entities": { "genes": [ "PB72", "PB96", "PB109" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:38.177617", "source": { "split": "train_shard_00001", "doc_id": 4374 }, "chunk_id": "train_shard_00001_4374_0", "global_id": 11849 }, { "text": "Characterization of NDM-1-Producing Carbapenemase in Proteus mirabilis among Broilers in China.", "token_count": 34, "char_count": 102, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:38.538370", "source": { "split": "train_shard_00001", "doc_id": 4374 }, "chunk_id": "train_shard_00001_4374_1", "global_id": 11850 }, { "text": "The human gut microbiome includes beneficial, commensal and pathogenic bacteria that possess antimicrobial resistance (AMR) genes and exchange these predominantly through conjugative plasmids. Escherichia coli is a significant component of the gastrointestinal microbiome and is typically non-pathogenic in this niche. In contrast, extra-intestinal pathogenic E. coli (ExPEC) including ST131 may occupy other environments like the urinary tract or bloodstream where they express genes enabling AMR and host adhesion like type 1 fimbriae. The extent to which non-pathogenic gut E. coli and infectious ST131 share AMR genes and key associated plasmids remains understudied at a genomic level. Here, we examined AMR gene sharing between gut E. coli and ST131 to discover an extensive shared preterm infant resistome. In addition, individual ST131 show extensive AMR gene diversity highlighting that analyses restricted to the core genome may be limiting and could miss AMR gene transfer patterns. We show that pEK499-like segments are ancestral to most ST131 Clade C isolates, contrasting with a minority with substantial pEK204-like regions encoding a type IV fimbriae operon. Moreover, ST131 possess extensive diversity at genes encoding type 1, type IV, P and F17-like fimbriae, particular within subclade C2. The type, structure and composition of AMR genes, plasmids and fimbriae varies widely in ST131 and this may mediate pathogenicity and infection outcomes.\n\nPlasmids Shape the Diverse Accessory Resistomes of Escherichia coli ST131", "token_count": 402, "char_count": 1538, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6413, "quality_score": 0.8206, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:39.157056", "source": { "split": "train_shard_00001", "doc_id": 4375 }, "chunk_id": "train_shard_00001_4375_0", "global_id": 11851 }, { "text": "The presence of an isoform of glyceraldehyde-3-phosphate dehydrogenase (kmGAPDH1p) associated with the cell wall of a flocculent strain of Kluyveromyces marxianus was the first report of a non-cytosolic localization of a glycolytic enzyme, but the mechanism by which the protein is transported to the cell surface is not known. To identify structural features that could account for the multiple localizations of the protein, the three-dimensional structure of kmGAPDH1p was determined by x-ray crystallography and small angle x-ray scattering. The x-ray crystallographic structure of kmGAPDH1p revealed a dimer, although all GAPDH homologs studied thus far have a tetrameric structure with 222 symmetry. Interestingly, the structure of kmGAPDH1p in solution revealed a tetramer with a 70 degrees tilt angle between the dimers. Moreover, the separation between the centers of the dimers composing the kmGAPDH1p tetramer diminished from 34 to 30 A upon NAD(+) binding, this latter value being similar to the observed in the crystallographic models of GAPDH homologs. The less compact structure of apo-kmGAPDH1p could already be the first image of the transition intermediate between the tetramer observed in solution and the dimeric form found in the crystal structure, which we postulate to exist in vivo because of the protein's multiple subcellular localizations in this yeast species.\n\nThe crystal and solution structures of glyceraldehyde-3-phosphate dehydrogenase reveal different quaternary structures.", "token_count": 400, "char_count": 1508, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5734, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:39.773848", "source": { "split": "train_shard_00001", "doc_id": 4376 }, "chunk_id": "train_shard_00001_4376_0", "global_id": 11852 }, { "text": "

Introduction

The introduction of pneumococcal conjugate vaccines (PCV) into the national immunization programs (NIPs) has significantly reduced the number of pneumococcal infections. However, infections caused by isolates of non-vaccine serotypes (NVT) started spreading shortly thereafter and strains of NVT 19A have become the main cause of invasive pneumococcal disease burden worldwide. The aim of the study was to characterize serotype 19A invasive pneumococci of GPSC1/CC320 circulating in Poland before the introduction of PCV into the Polish NIP in 2017 and to compare them to isolates from other countries where PCVs were implemented much earlier than in Poland.

Methods

All the GPSC1/CC320 isolates were analyzed by serotyping, susceptibility testing, and whole genome sequencing followed by analyses of resistome, virulome, and core genome multilocus sequence typing (cgMLST), including comparative analysis with isolates with publicly accessible genomic sequences (PubMLST).

Results

During continuous surveillance the NRCBM collected 4237 invasive Streptococcus pneumoniae isolates between 1997 and 2016, including 200 isolates (4.7%) of serotype 19A. The most prevalent among 19A pneumococci were highly resistant representatives of Global Pneumococcal Sequence Cluster 1/Clonal Complex 320, GPSC1/CC320 (n = 97, 48.5%). Isolates of GPSC1/CC320 belonged to three sequence types (STs): ST320 (75.2%) ST4768 (23.7%), and ST15047 (1.0%), which all represented the 19A-III cps subtype and had complete loci for both PI-1 and PI-2 pili types", "token_count": 485, "char_count": 1571, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7014, "quality_score": 0.8507, "entities": { "genes": [ "ST4768", "ST15047", "ST320", "CC320", "GPSC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:40.428778", "source": { "split": "train_shard_00001", "doc_id": 4377 }, "chunk_id": "train_shard_00001_4377_0", "global_id": 11853 }, { "text": "On the basis of the cgMLST analysis the majority of Polish GPSC1/CC320 isolates formed a group clearly distinct from pneumococci of this clone observed in other countries.

Conclusion

Before introduction of PCV in the Polish NIP we noticed an unexpected increase of serotype 19A in invasive pneumococcal infections, with the most common being representatives of highly drug-resistant GPSC1/CC320 clone, rarely identified in Europe both before and even after PCV introduction.\n\nHighly Resistant Serotype 19A Streptococcus pneumoniae of the GPSC1/CC320 Clone from Invasive Infections in Poland Prior to Antipneumococcal Vaccination of Children.", "token_count": 175, "char_count": 648, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7079, "quality_score": 0.8539, "entities": { "genes": [ "CC320", "GPSC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:40.869767", "source": { "split": "train_shard_00001", "doc_id": 4377 }, "chunk_id": "train_shard_00001_4377_1", "global_id": 11854 }, { "text": "Thirty isolates of Pseudomonas syringae other than pathovar (pv.) phaseolicola, recovered from beans (18) and weeds (12) in a Northern Spanish region, were studied by a polyphasic approach, including phenotypic tests, detection of levansucrase and toxin (syringomycin and syringopeptin) genes, typing by RAPD (Random Amplified Polymorphic DNA) and PFGE (Pulsed-Field Gel Electrophoresis). The isolates were phenotypically heterogeneous, and both RAPD and PFGE, probed to be highly discriminative, as they were almost able to differentiate at the level of isolate. Phylogenetic analysis based on conserved genes of the core genome (rpoD, gltA and gyrB) distributed the isolates in three different clades (2A, 2B and 2C) belonging to phylogroup 2 of the P. syringae complex. According to toxin production, 18 of them, within clade 2B, were assigned to P. syringae pv. syringae and five of these caused symptoms after experimental inoculation on bean pods. Four of the five pathogenic isolates were obtained from weeds, supporting the role of weeds associated with bean crops, particularly Cyperus rotundus, Malva sylvestris, and Polygonum lapathifolium, as a reservoir of the pathogen. In conclusion, results of this study suggest that apart from P. syringae pv. phaseolicola, P. syringae isolates circulating in our region are mostly epiphytes, and support the role of weeds associated with bean crops as reservoir of pathogenic strains of P. syringae pv. syringae.\n\nPhenotypic and genotypic analysis of Pseudomonas syringae recovered from symptomatic beans and associated weeds in Northern Spain", "token_count": 450, "char_count": 1595, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:41.505320", "source": { "split": "train_shard_00001", "doc_id": 4378 }, "chunk_id": "train_shard_00001_4378_0", "global_id": 11855 }, { "text": "This invention relates to a process for the synthesis of (S)-1,2-O-isopropylidene glycerol by hydrolysis of a racemic mixture of (R,S)-1,2-O-isopropylidene glycerol acetate catalysed by Kluyveromyces marxianus, recovery of the unreacted (R)-1,2-O-isopropylidene glycerol acetate, and hydrolysis thereof.\n\nEnzymatic synthesis of (S)-1,2-O-isopropylidene glycerol", "token_count": 142, "char_count": 361, "word_count": 41, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:41.934236", "source": { "split": "train_shard_00001", "doc_id": 4379 }, "chunk_id": "train_shard_00001_4379_0", "global_id": 11856 }, { "text": "Salmonella is one of the primary causes of foodborne disease, especially Salmonella enterica subsp. enterica (I) which has caused ~99% of clinical salmonellosis cases for humans and domestic mammals. The flagella genes, fliC and fljB, which encode the Salmonella phase 1 and phase 2 antigens respectively, are considered as the Salmonella serotype determinant genes, and contribute to the virulence of Salmonella. However, the evolution of the two flagellin genes is still not well-understood. In this study, the fliC and fljB gene clusters were analyzed among 205 S. enterica subspecies I genomes. The dataset covered 87 different serovars of S. enterica subsp. enterica and included 9 genomes (six serovars) of four other Salmonella subspecies. Based on a pan-genome definition and flanked gene linkages, the fliC and fljB gene clusters were identified in 207 (91 serovars) and 138 (61 serovars) genomes, respectively. A phylogenetic tree constructed based on SNPs (Single Nucleotide Polymorphisms) of core genes were used to reflect the essential evolutionary relationships among various serovars. Congruence analysis was performed among the core genome and each gene of fliC and fljB gene clusters, with only fliA and fliS showing congruence to Salmonella core genome", "token_count": 465, "char_count": 1418, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6354, "quality_score": 0.8177, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:42.579139", "source": { "split": "train_shard_00001", "doc_id": 4380 }, "chunk_id": "train_shard_00001_4380_0", "global_id": 11857 }, { "text": "Congruence was also observed among fliB, fliC/fljB, and fliD genes, and their phylogeny revealed a division into two major groups, which strongly corresponded to monophasic and biphasic serovars. Besides, homologous recombination events referring fliB, fliC, and fliD were found to have mainly occurred within each group. These results suggested two distinct evolutionary patterns of Salmonella flagellin gene clusters. Further insight on the evolutionary implication of the two patterns and a framework for phase variation mechanism are needed to be further processed.\n\nComprehensive Analysis Reveals Two Distinct Evolution Patterns of Salmonella Flagellin Gene Clusters.", "token_count": 195, "char_count": 714, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7419, "quality_score": 0.871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:43.027122", "source": { "split": "train_shard_00001", "doc_id": 4380 }, "chunk_id": "train_shard_00001_4380_1", "global_id": 11858 }, { "text": "

Background

Multidrug-resistant (MDR) Mycobacterium tuberculosis complex (MTBC) strains are a serious health problem in India, also contributing to one-fourth of the global MDR tuberculosis (TB) burden. About 36% of the MDR MTBC strains are reported fluoroquinolone (FQ) resistant leading to high pre-extensively drug-resistant (pre-XDR) and XDR-TB (further resistance against bedaquiline and/or linezolid) rates. Still, factors driving the MDR/pre-XDR epidemic in India are not well defined.

Methods

In a retrospective study, we analyzed 1852 consecutive MTBC strains obtained from patients from a tertiary care hospital laboratory in Mumbai by whole genome sequencing (WGS). Univariate and multivariate statistics was used to investigate factors associated with pre-XDR. Core genome multi locus sequence typing, time scaled haplotypic density (THD) method and homoplasy analysis were used to analyze epidemiological success, and positive selection in different strain groups, respectively.

Results

In total, 1016 MTBC strains were MDR, out of which 703 (69.2%) were pre-XDR and 45 (4.4%) were XDR. Cluster rates were high among MDR (57.8%) and pre-XDR/XDR (79%) strains with three dominant L2 (Beijing) strain clusters (Cl 1-3) representing half of the pre-XDR and 40% of the XDR-TB cases. L2 strains were associated with pre-XDR/XDR-TB (P < 0.001) and, particularly Cl 1-3 strains, had high first-line and FQ resistance rates (81.6-90.6%). Epidemic success analysis using THD showed that L2 strains outperformed L1, L3, and L4 strains in short- and long-term time scales", "token_count": 501, "char_count": 1594, "word_count": 222, "semantic_coherence": 1, "information_density": 0.7117, "quality_score": 0.8559, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:43.681943", "source": { "split": "train_shard_00001", "doc_id": 4381 }, "chunk_id": "train_shard_00001_4381_0", "global_id": 11859 }, { "text": "More importantly, L2 MDR and MDR + strains had higher THD success indices than their not-MDR counterparts. Overall, compensatory mutation rates were highest in L2 strains and positive selection was detected in genes of L2 strains associated with drug tolerance (prpB and ppsA) and virulence (Rv2828c). Compensatory mutations in L2 strains were associated with a threefold increase of THD indices, suggesting improved transmissibility.

Conclusions

Our data indicate a drastic increase of FQ resistance, as well as emerging bedaquiline resistance which endangers the success of newly endorsed MDR-TB treatment regimens. Rapid changes in treatment and control strategies are required to contain transmission of highly successful pre-XDR L2 strains in the Mumbai Metropolitan region but presumably also India-wide.\n\nHigh fluoroquinolone resistance proportions among multidrug-resistant tuberculosis driven by dominant L2 Mycobacterium tuberculosis clones in the Mumbai Metropolitan Region.", "token_count": 251, "char_count": 992, "word_count": 133, "semantic_coherence": 1, "information_density": 0.7068, "quality_score": 0.8534, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:44.170035", "source": { "split": "train_shard_00001", "doc_id": 4381 }, "chunk_id": "train_shard_00001_4381_1", "global_id": 11860 }, { "text": "A new cytosine deaminase gene and protein from Candida kefyr are provided. This protein has increased ability to convert the 5-fluorocytosine prodrug to its toxic form when compared against the E. coli enzyme.\n\nAntibody that specifically binds to BackgroundCampylobacter jejuni is the most common bacterial cause of human infectious intestinal disease.

Methods

We genome sequenced 601 human C. jejuni isolates, obtained from two large prospective studies of infectious intestinal disease (IID1 [isolates from 1993-1996; n = 293] and IID2 [isolates from 2008-2009; n = 93]), the INTEGRATE project [isolates from 2016-2017; n = 52] and the ENIGMA project [isolates from 2017; n = 163].

Results

There was a significant increase in the prevalence of the T86I mutation conferring resistance to fluoroquinolone between each of the three later studies (IID2, INTEGRATE and ENIGMA) and IID1. Although the distribution of major multilocus sequence types (STs) was similar between the studies, there were changes in both the abundance of minority STs associated with the T86I mutation, and the abundance of clones within single STs associated with the T86I mutation.

Discussion

Four population-based studies of community diarrhoea over a 25 year period revealed an increase over time in the prevalence of the T86I amongst isolates of C. jejuni associated with human gastrointestinal disease in the UK. Although associated with many STs, much of the increase is due to the expansion of clones associated with the resistance mutation.\n\nIncreasing prevalence of a fluoroquinolone resistance mutation amongst Campylobacter jejuni isolates from four human infectious intestinal disease studies in the United Kingdom.", "token_count": 428, "char_count": 1484, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5166, "quality_score": 0.7583, "entities": { "genes": [ "IID2", "IID1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:45.203438", "source": { "split": "train_shard_00001", "doc_id": 4383 }, "chunk_id": "train_shard_00001_4383_0", "global_id": 11862 }, { "text": "

Aim

To determine whether pulsed-field gel electrophoresis (PFGE) accurately recognizes isolates belonging to clusters defined by techniques based on whole-genome sequencing (WGS) using Pseudomonas aeruginosa as a model.

Methods

We selected 65 isolates of ST395 P. aeruginosa isolated in seven European hospitals between 1998 and 2012. Isolates were typed by PFGE and sequenced by WGS. A core genome multi-locus sequence typing (cgMLST) analysis based on 3831 genes was performed with a homemade pipeline.

Findings

PFGE identified eight pulsotypes and cgMLST differentiated nine clusters and nine singletons. Five cgMLST clusters and pulsotypes (31/65 isolates) coincided perfectly. Isolates without evident epidemiological links grouped by PFGE were separated by cgMLST (16/65 isolates) differentiating cities, suggesting that PFGE should be kept for the investigation of local outbreaks. Importantly, hypermutator isolates still shared the pulsotype with their parents (16/65 isolates), whereas they were not recognized by cgMLST. This shows that PFGE was less affected than WGS-based typing by the accelerated genetic drift that occurs in epidemic P. aeruginosa.

Conclusions

although WGS-based typing has logically become the new reference standard, we show here that the PFGE can be used with confidence for the investigation of local outbreaks caused by P. aeruginosa.\n\nComparison of pulsed-field gel electrophoresis and whole-genome-sequencing-based typing confirms the accuracy of pulsed-field gel electrophoresis for the investigation of local Pseudomonas aeruginosa outbreaks.", "token_count": 441, "char_count": 1613, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [ "ST395" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:45.863739", "source": { "split": "train_shard_00001", "doc_id": 4384 }, "chunk_id": "train_shard_00001_4384_0", "global_id": 11863 }, { "text": "Whole-genome sequencing (WGS) is the method of choice for bacterial subtyping and it is rapidly replacing the more traditional methods such as pulsed-field gel electrophoresis (PFGE). Here we used the high-resolution core genome single nucleotide variant (cgSNV) typing method to characterize clinical and food from Salmonella enterica serovar Heidelberg isolates in the context of source attribution. Additionally, clustered regularly interspaced short palindromic repeats (CRISPR) analysis was included to further support this method. Our results revealed that cgSNV was highly discriminatory and separated the outbreak isolates into distinct clusters (0-4 SNVs). CRISPR analysis was also able to distinguish outbreak strains from epidemiologically unrelated isolates. Specifically, our data clearly demonstrated the strength of these two methods to determine the probable source(s) of a 2012 epidemiologically characterized outbreak of S. Heidelberg. Using molecular cut-off of 0-10 SNVs, the cgSNV analysis of 246 clinical and food isolates of S. Heidelberg collected in Québec, in the same year of the outbreak event, revealed that retail and abattoir chicken isolates likely represent an important source of human infection to S. Heidelberg. Interestingly, the isolates genetically related by cgSNV also harbored the same CRISPR as outbreak isolates and clusters. This indicates that CRISPR profiles can be useful as a complementary approach to determine source attribution in foodborne outbreaks. Use of the genomic analysis also allowed to identify a large number of cases that were missed by PFGE, indicating that most outbreaks are probably underestimated. Although epidemiological information must still support WGS-based results, cgSNV method is a highly discriminatory method for the resolution of outbreak events and the attribution of these events to their respective sources. CRISPR typing can serve as a complimentary tool to this analysis during source tracking.", "token_count": 469, "char_count": 2008, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6064, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:46.553684", "source": { "split": "train_shard_00001", "doc_id": 4385 }, "chunk_id": "train_shard_00001_4385_0", "global_id": 11864 }, { "text": "Source Tracking Based on Core Genome SNV and CRISPR Typing of Salmonella enterica Serovar Heidelberg Isolates Involved in Foodborne Outbreaks in Québec, 2012.", "token_count": 57, "char_count": 165, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:46.959695", "source": { "split": "train_shard_00001", "doc_id": 4385 }, "chunk_id": "train_shard_00001_4385_1", "global_id": 11865 }, { "text": "Shigella flexneri is a major health burden in low- and middle-income countries, where it is a leading cause of mortality associated with diarrhoea in children, and shows an increasing incidence among travellers and men having sex with men. Like all Shigella spp., S. flexneri has evolved from commensal Escherichia coli following the acquisition of a large plasmid pINV, which contains genes essential for virulence. Current sequence typing schemes of Shigella are based on combinations of chromosomal genetic loci, since pINV-encoded virulence genes are often lost during growth in the laboratory, making these elements inappropriate for sequence typing. By performing comparative analysis of pINVs from S. flexneri strains isolated from different geographical regions and belonging to different serotypes, we found that in contrast to plasmid-encoded virulence genes, plasmid maintenance genes are highly stable pINV-encoded elements. For the first time, to our knowledge, we have developed a S. flexneri plasmid multilocus sequence typing (pMLST) method based on different combinations of alleles of the vapBC and yacAB toxin-antitoxin (TA) systems, and the parAB partitioning system. This enables typing of S. flexneri pINV plasmids into distinct 'virulence sequence types' (vSTs). Furthermore, the phylogenies of vST alleles and bacterial host core genomes suggests an intimate co-evolution of pINV with the chromosome of its bacterial host, consistent with previous findings. This work demonstrates the potential of plasmid maintenance loci as genetic characteristics to study as well as to trace the molecular phylogenesis of S. flexneri pINV and the phylogenetic relationship of this plasmid with its bacterial host.", "token_count": 491, "char_count": 1808, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:47.617831", "source": { "split": "train_shard_00001", "doc_id": 4386 }, "chunk_id": "train_shard_00001_4386_0", "global_id": 11866 }, { "text": "Virulence plasmid pINV as a genetic signature for <i>Shigella flexneri</i> phylogeny.", "token_count": 39, "char_count": 97, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:47.975217", "source": { "split": "train_shard_00001", "doc_id": 4386 }, "chunk_id": "train_shard_00001_4386_1", "global_id": 11867 }, { "text": "Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient organism’s physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ~12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative and positive selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths.

Significance statement

In a parallel evolution experiment, we probe lateral gene transfer between two Bacillus subtilis lineages close to the species boundary. We show that laboratory evolution by horizontal gene transfer can rapidly generate hybrid organisms with broad genomic and functional alterations. By combining genomics, transcriptomics, fitness assays and statistical modeling, we map the selective effects underlying gene transfer. We show that transfer takes place under genome-wide positive and negative selection, generating a net fitness increase in hybrids. The evolutionary dynamics efficiently navigates this fitness landscape, finding viable paths with increasing fraction of transferred genes.\n\nAdaptive evolution of hybrid bacteria by horizontal gene transfer", "token_count": 443, "char_count": 2177, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5644, "quality_score": 0.7822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:48.615651", "source": { "split": "train_shard_00001", "doc_id": 4387 }, "chunk_id": "train_shard_00001_4387_0", "global_id": 11868 }, { "text": "The gut commensal bacteria Christensenellaceae species are negatively associated with many metabolic diseases, and have been seen as promising next-generation probiotics. However, the cultured Christensenellaceae strain resources were limited, and their beneficial mechanisms for improving metabolic diseases have yet to be explored. In this study, we developed a method that enabled the enrichment and cultivation of Christensenellaceae strains from fecal samples. Using this method, a collection of Christensenellaceae Gut Microbial Biobank (ChrisGMB) was established, composed of 87 strains and genomes that represent 14 species of 8 genera. Seven species were first described and the cultured Christensenellaceae resources have been significantly expanded at species and strain levels. Christensenella strains exerted different abilities in utilization of various complex polysaccharides and other carbon sources, exhibited host-adaptation capabilities such as acid tolerance and bile tolerance, produced a wide range of volatile probiotic metabolites and secondary bile acids. Cohort analyses demonstrated that Christensenellaceae and Christensenella were prevalent in various cohorts and the abundances were significantly reduced in T2D and OB cohorts. At species level, Christensenellaceae showed different changes among healthy and disease cohorts. C. faecalis, F. tenuis, L. tenuis, and Guo. tenuis significantly reduced in all the metabolic disease cohorts. The relative abundances of C. minuta, C. hongkongensis and C. massiliensis showed no significant change in NAFLD and ACVD. and C. tenuis and C. acetigenes showed no significant change in ACVD, and Q. tenuis and Geh. tenuis showed no significant change in NAFLD, when compared with the HC cohort", "token_count": 520, "char_count": 1895, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:49.277291", "source": { "split": "train_shard_00001", "doc_id": 4388 }, "chunk_id": "train_shard_00001_4388_0", "global_id": 11869 }, { "text": "So far as we know, this is the largest collection of cultured resource and first exploration of Christensenellaceae prevalences and abundances at species level.\n\nChristensenella strain resources, genomic/metabolomic profiling, and association with host at species level.", "token_count": 63, "char_count": 277, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:49.639775", "source": { "split": "train_shard_00001", "doc_id": 4388 }, "chunk_id": "train_shard_00001_4388_1", "global_id": 11870 }, { "text": "The present invention relates to a process which is specific to determine and number the yeast Kluyveromyces marxianus. The process involves the addition to a culture medium used as a base for yeasts of a chromogenic substrate, an inductor substrate and a bacterial growth inhibitor antibiotic. When said medium is subjected to the 'beta'-galactosidase activity of Kluyveromyces marxianus, it produces a blue coloration exclusively in the colonies of said yeasts. The usefulness of the culture medium object of the invention is the detection of the kluyveromyces marxianus yeast in the food industry.\n\nPROCESS FOR OBTAINING AND USING A CULTURE MEDIUM IN ORDER TO DETECT DIFFERENTIALLY AND TO NUMBER KLUYVEROMYCES MARXIANUS FOOD CONTAMINANTS", "token_count": 206, "char_count": 740, "word_count": 112, "semantic_coherence": 1, "information_density": 0.5446, "quality_score": 0.7723, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:50.110570", "source": { "split": "train_shard_00001", "doc_id": 4389 }, "chunk_id": "train_shard_00001_4389_0", "global_id": 11871 }, { "text": "Electrophoretic karyotypes of yeasts belonging to the species Saccharomyces cerevisiae, Kluyveromyces marxianus and Candida macedoniensis were established by means of OFAGE. Hybrids between S. cerevisiae and K. marxianus as well as between K. marxianus and C. macedoniensis were analyzed by comparing their OFAGE-banding-pattern with the parental banding-patterns. Thus, evidence for exchanges of intact chromosomes and for chromosomal rearrangements could be gained on a molecular level.\n\nOFAGE banding patterns of different yeast genera and of intergeneric hybrids.", "token_count": 155, "char_count": 567, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:50.550965", "source": { "split": "train_shard_00001", "doc_id": 4390 }, "chunk_id": "train_shard_00001_4390_0", "global_id": 11872 }, { "text": "

ABSTRACT

Helicobacter pylori encodes a large number of Restriction-Modification (R-M) systems despite its small genome.R-M systems have been described as “primitive immune systems” in bacteria, but the role of methylation in bacterial gene regulation and other processes is increasingly accepted. Every H.pylori strain harbours a unique set of R-M systems resulting in a highly diverse methylome. We identified a highly conserved GCGC-specific m5 C MTase (JHP1050) that was predicted to be active in all of 459 H.pylori genome sequences analyzed. Transcriptome analysis of two H.pylori strains and their respective MTase mutants showed that inactivation of the MTase led to changes in the expression of 225 genes in strain J99, and 29 genes in strain BCM-300.10 genes were differentially expressed in both mutated strains. Combining bioinformatic analysis and site-directed mutagenesis, we demonstrated that motifs overlapping the promoter influence the expression of genes directly, while methylation of other motifs might cause secondary effects.Thus, m5 C methylation modifies the transcription of multiple genes, affecting important phenotypic traits that include adherence to host cells, natural competence for DNA uptake, bacterial cell shape, and susceptibility to copper.\n\nThe core genome m5C methyltransferase JHP1050 (M.Hpy99III) plays an important role in orchestrating gene expression in Helicobacter pylori", "token_count": 384, "char_count": 1446, "word_count": 200, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [ "JHP1050" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:51.169589", "source": { "split": "train_shard_00001", "doc_id": 4391 }, "chunk_id": "train_shard_00001_4391_0", "global_id": 11873 }, { "text": "A rapid assay for detection of yeast species in vacuum packed ham has been developed based on the polymerase chain reaction (PCR) coupled to a 24 h pre-enrichment at 25 °C. DNA was isolated from yeast inoculated ham samples and amplified using primers specific for the 18S rRNA gene sequences of yeasts. A detection limit of 10(2) CFU/cm(2) was achieved following enrichment of samples experimentally inoculated with three yeast species frequently associated with meat products spoilage: Debaryomyces hansenii, Yarrowia lipolytica, and Kluyveromyces marxianus. Likewise, commercial sliced and vacuum packed ham samples were analysed using the PCR-culture technique. The results obtained in this work show that PCR amplification of a conserved region of the 18S rRNA gene in the yeast species could be potentially used as a rapid tool for detection of low levels of viable spoilage yeasts in meat products.\n\nDevelopment of a PCR-culture technique for rapid detection of yeast species in vacuum packed ham.", "token_count": 257, "char_count": 1004, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6323, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:51.712127", "source": { "split": "train_shard_00001", "doc_id": 4392 }, "chunk_id": "train_shard_00001_4392_0", "global_id": 11874 }, { "text": "

Background

The role played by airway infections with Pseudomonas aeruginosa in the course and pathogenesis of chronic obstructive pulmonary disease (COPD) has not yet been resolved. We report on the molecular epidemiology and population biology of P. aeruginosa in COPD.

Methods

P. aeruginosa isolates collected from adults with COPD during a 10-year prospective study were genotyped in 56 binary marker loci of core and accessory genomes.

Results

The typing of 134 P. aeruginosa COPD isolates uncovered 60 unrelated bacterial clones. The worldwide dominant clones in the P. aeruginosa population were also the most abundant clones among the COPD isolates. Sporadic or intermittent infection with P. aeruginosa was typical for the airways of patients with COPD. Sequential isolates with the same genotype of the core genome diversified the composition of their accessory genome during the course of the infection.

Conclusions

Intraclonal microevolution and the frequent turnover or loss of clones are typical for infections with P. aeruginosa in COPD. This epidemiological signature differs from that of the chronic carriage of the same P. aeruginosa clone in patients with cystic fibrosis.\n\nPseudomonas aeruginosa population biology in chronic obstructive pulmonary disease.", "token_count": 344, "char_count": 1304, "word_count": 181, "semantic_coherence": 1, "information_density": 0.558, "quality_score": 0.779, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:52.287954", "source": { "split": "train_shard_00001", "doc_id": 4393 }, "chunk_id": "train_shard_00001_4393_0", "global_id": 11875 }, { "text": "

Objectives

Invasive listeriosis is a severe foodborne infection caused by Listeria(L.)monocytogenes. The aim of this investigation was to verify and describe a molecular cluster of listeriosis patients and identify factors leading to this outbreak.

Methods

Whole genome sequencing and core genome multilocus sequence typing were used for subtyping L. monocytogenes isolates from listeriosis cases and food samples in Germany. Patient interviews and investigational tracing of foodstuffs offered in health-care facilities (HCF), where some of the cases occurred, were conducted.

Results

We identified a German-wide listeriosis outbreak with 39 genetically related cases occurring between 2014 and 2019. Three patients died as a result of listeriosis. After identification of HCF in different regions of Germany for at least 13 cases as places of exposure, investigational tracing of food supplies in six prioritized HCF revealed meat products from one company (X) as a commonality. Subsequently the outbreak strain was analysed in six isolates from ready-to-eat meat products and one isolate from the production environment of company X. No further Sigma1 cases were detected after recall of the meat products from the market and closure of company X (as of August 2020).

Conclusions

Interdisciplinary efforts including whole genome sequencing, epidemiological investigations in patients and investigational tracing of foods were essential to identify the source of infections, and thereby prevent further illnesses and deaths. This outbreak underlines the vulnerability of hospitalized patients for foodborne diseases, such as listeriosis. Food producers and HCF should minimize the risk of microbiological hazards when producing, selecting and preparing food for patients.\n\nNationwide outbreak of invasive listeriosis associated with consumption of meat products in health care facilities, Germany, 2014-2019.", "token_count": 454, "char_count": 1939, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:52.925310", "source": { "split": "train_shard_00001", "doc_id": 4394 }, "chunk_id": "train_shard_00001_4394_0", "global_id": 11876 }, { "text": "Metagenomic assembly enables novel organism discovery from microbial communities, but from most metagenomes it can only capture few abundant organisms. Here, we present a method - MetaPhlAn 4 - to integrate information from both metagenome assemblies and microbial isolate genomes for improved and more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01M prokaryotic reference and metagenome-assembled genomes, we defined unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ∼20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome, and proved more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlighted previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mice microbiomes, and showed that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains. MetaPhlAn 4 thus integrates the novelty of metagenomic assemblies with the sensitivity and fidelity of reference-based analyses, providing efficient metagenomic profiling of uncharacterized species and enabling deeper and more comprehensive microbiome biomarker detection.\n\nExtending and improving metagenomic taxonomic profiling with uncharacterized species with MetaPhlAn 4", "token_count": 371, "char_count": 1562, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6618, "quality_score": 0.8309, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:53.507481", "source": { "split": "train_shard_00001", "doc_id": 4395 }, "chunk_id": "train_shard_00001_4395_0", "global_id": 11877 }, { "text": "Twelve species of bacteria and two species of yeast were tested for sensitivity against 11 different mycotoxins using a disc diffusion assay. Among the bacterial species, Bacillus brevis appeared to be the most sensitive microorganism, being sensitive to eight mycotoxins (AFB1, ochratoxin A [OA], citrinin [CT], patulin [PAT], penicillic acid [PA], cyclopiazonic acid [CPA], penitrem A [PT-A], and zearalenone [ZEE]). This microorganism was not affected by a high concentration (500 μg per disc) of any of the trichothecenes (T-2 toxin, HT-2 toxin, diacetoxyscirpenol, and deoxynivalenol). Kluyveromyces marxianus , a species of yeast, was the only microorganism that was inhibited by all four of the trichothecenes but was not inhibited by the other mycotoxins. The area of the inhibition zone produced by some of the mycotoxins such as OA with the B. brevis assay was dramatically influenced by the pH of the medium, while the toxicity of other mycotoxins such as AFB1 was relatively pH independent. The sensitivity of the B. brevis assay also tended to decrease at agar volumes above 6 ml and as the number of microbes per plate increased. The lowest amounts of the different ochratoxins; OA, OB and OC (OA ethyl ester) that could be detected under optimal conditions were 0.5, 20, and 2 μg per disc, respectively. The lowest amounts of CPA, AFB1 CT, PAT, PA, PT-A, and ZEE that were detectable were 0.5, 1, 1, 1, 1, 1, and 10 μg per disc, respectively. These results demonstrate that B. brevis can be used as a positive indicator organism to detect the presence of several common non-trichothecene mycotoxins. The results demonstrate that, used together, B. brevis and K", "token_count": 515, "char_count": 1708, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5809, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:50:54.172987", "source": { "split": "train_shard_00001", "doc_id": 4396 }, "chunk_id": "train_shard_00001_4396_0", "global_id": 11878 }, { "text": "marxianus can be used as indicator organisms in a bioassay approach to the detection of several of the most common mycotoxins.\n\nComparison of Toxicity of Different Mycotoxins to Several Species of Bacteria and Yeasts: Use of Bacillus brevis in a Disc Diffusion Assay.", "token_count": 74, "char_count": 267, "word_count": 43, "semantic_coherence": 1, "information_density": 0.7674, "quality_score": 0.8837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:54.541918", "source": { "split": "train_shard_00001", "doc_id": 4396 }, "chunk_id": "train_shard_00001_4396_1", "global_id": 11879 }, { "text": "Colistin is still commonly used and misused in animal husbandry driving the evolution and dissemination of transmissible plasmid-mediated colistin resistance (mcr). mcr-1.26 is a rare variant and, so far, has only been detected in Escherichia coli obtained from a hospitalized patient in Germany in 2018. Recently, it was also notified in fecal samples from a pigeon in Lebanon. We report on the presence of 16 colistin-resistant, mcr-1.26-carrying extended-spectrum beta-lactamase (ESBL)-producing and commensal E. coli isolated from poultry samples in Germany, of which retail meat was the most common source. Short- and long-read genome sequencing and bioinformatic analyses revealed the location of mcr-1.26 exclusively on IncX4 plasmids. mcr-1.26 was identified on two different IncX4 plasmid types of 33 and 38 kb and was associated with an IS6-like element. Based on the genetic diversity of E. coli isolates, transmission of the mcr-1.26 resistance determinant is mediated by horizontal transfer of IncX4 plasmids, as confirmed by conjugation experiments. Notably, the 33-kb plasmid is highly similar to the plasmid reported for the human sample. Furthermore, we identified the acquisition of an additional beta-lactam resistance linked to a Tn2 transposon on the mcr-1.26 IncX4 plasmids of three isolates, indicating progressive plasmid evolution. Overall, all described mcr-1.26-carrying plasmids contain a highly conserved core genome necessary for colistin resistance development, transmission, replication, and maintenance. Variations in the plasmid sequences are mainly caused by the acquisition of insertion sequences and alteration in intergenic sequences or genes of unknown function", "token_count": 507, "char_count": 1770, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:55.176810", "source": { "split": "train_shard_00001", "doc_id": 4397 }, "chunk_id": "train_shard_00001_4397_0", "global_id": 11880 }, { "text": "IMPORTANCE Evolutionary events causing the emergence of new resistances/variants are usually rare and challenging to predict. Conversely, common transmission events of widespread resistance determinants are quantifiable and predictable. One such example is the transmissible plasmid-mediated colistin resistance. The main determinant, mcr-1, has been notified in 2016 but has successfully established itself in multiple plasmid backbones in diverse bacterial species across all One Health sectors. So far, 34 variants of mcr-1 are described, of which some can be used for epidemiological tracing-back analysis to identify the origin and transmission dynamics of these genes. Here, we report the presence of the rare mcr-1.26 gene in E. coli isolated from poultry since 2014. Based on the temporal occurrence and high similarity of the plasmids between poultry and human isolates, our study provides first indications for poultry husbandry as the primary source of mcr-1.26 and its transmission between different niches.\n\nGenomic Evidence of mcr-1.26 IncX4 Plasmid Transmission between Poultry and Humans.", "token_count": 303, "char_count": 1146, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7197, "quality_score": 0.8599, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:55.741957", "source": { "split": "train_shard_00001", "doc_id": 4397 }, "chunk_id": "train_shard_00001_4397_1", "global_id": 11881 }, { "text": "

Objective

To investigate the molecular epidemiology of methicillin-susceptible Staphylococcus aureus (MSSA) in infants in a neonatal intensive care unit (NICU) using whole-genome sequencing.

Design

Investigation of MSSA epidemiology in a NICU.

Setting

Single-center, level IV NICU.

Methods

Universal S. aureus screening was done using a single swab obtained from the anterior nares, axilla, and groin area of infants in the NICU on a weekly basis. Core genome multilocus sequence type (cgMLST) analysis was performed on MSSA isolates detected over 1 year (2018-2019).

Results

In total, 68 MSSA-colonized infants were identified, and cgMLSTs of 67 MSSA isolates were analyzed. Overall, we identified 11 cgMLST isolate groups comprising 39 isolates (58%), with group sizes ranging from 2 to 10 isolates, and 28 isolates (42%) were unrelated to each other or any of the isolate groups. Cases of infants colonized by MSSA were scattered throughout the 1-year study period, and isolates belonging to the same cgMLST group were typically detected contemporaneously, over a few weeks or a few months. Overall, 13 infants (19.7%) developed MSSA infections: bacteremia (n = 3), wound infection (n = 5), conjunctivitis (n = 4), and cellulitis (n = 1). We detected no association between these clinically manifest infections and specific cgMLST groups.

Conclusions

Although MSSA isolates in infants in a NICU showed high diversity, most were related to other isolates, albeit within small groups. cgMLST facilitates an understanding of the complex transmission dynamics of MSSA in NICUs, and these data can be used to inform better control strategies.", "token_count": 508, "char_count": 1683, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:56.391771", "source": { "split": "train_shard_00001", "doc_id": 4398 }, "chunk_id": "train_shard_00001_4398_0", "global_id": 11882 }, { "text": "Molecular epidemiology of methicillin-susceptible Staphylococcus aureus in infants in a neonatal intensive care unit.", "token_count": 44, "char_count": 124, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:56.753122", "source": { "split": "train_shard_00001", "doc_id": 4398 }, "chunk_id": "train_shard_00001_4398_1", "global_id": 11883 }, { "text": "Streptococcus agalactiae (GBS) causes disease in a wide range of animals. The serotype 1b lineage is highly adapted to aquatic hosts, exhibiting substantial genome reduction compared with terrestrial con-specifics. Here we sequence genomes from 40 GBS isolates including 25 from wild fish and captive stingrays in Australia, six local veterinary or human clinical isolates, and nine isolates from farmed tilapia in Honduras and compare with 42 genomes from public databases. Phylogenetic analysis based on non-recombinant core genome SNPs indicated that aquatic serotype Ib isolates from Queensland were distantly related to local veterinary and human clinical isolates. In contrast, Australian aquatic isolates are most closely related to a tilapia isolate from Israel, differing by only 63 core-genome SNPs. A consensus minimum spanning tree based on core genome SNPs indicates dissemination of ST-261 from an ancestral tilapia strain, which is congruent with several introductions of tilapia into Australia from Israel during the 1970s and 1980s. Pan-genome analysis identified 1,440 genes as core with the majority being dispensable or strain-specific with non-protein-coding intergenic regions (IGRs) divided amongst core and strain-specific genes. Aquatic serotype Ib strains have lost many virulence factors during adaptation, but six adhesins were well conserved across the aquatic isolates and might be critical for virulence in fish and targets for vaccine development. The close relationship amongst recent ST-261 isolates from Ghana, USA and China with the Israeli tilapia isolate from 1988 implicates the global trade in tilapia seed for aquaculture in the widespread dissemination of serotype Ib fish-adapted GBS.

Importance

Streptococcus agalactiae (GBS) is a significant pathogen of humans and animals. Some lineages have become adapted to particular hosts and serotype Ib is highly specialized to fish", "token_count": 489, "char_count": 1927, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:57.433504", "source": { "split": "train_shard_00001", "doc_id": 4399 }, "chunk_id": "train_shard_00001_4399_0", "global_id": 11884 }, { "text": "Here we show that this lineage is likely to have been distributed widely by the global trade in tilapia for aquaculture, with probable introduction into Australia in the 1970s and subsequent dissemination in wild fish populations. We report variability in the polysaccharide capsule amongst this lineage, but identify a cohort common surface proteins that may be a focus of future vaccine development to reduce the biosecurity risk in international fish trade.\n\nMicroevolution of aquaticStreptococcus agalactiaeST-261 from Australia indicates dissemination via imported tilapia and ongoing adaptation to marine hosts or environment", "token_count": 149, "char_count": 638, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7889, "quality_score": 0.8944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:57.881563", "source": { "split": "train_shard_00001", "doc_id": 4399 }, "chunk_id": "train_shard_00001_4399_1", "global_id": 11885 }, { "text": "A genome-based systematic analysis was conducted to characterize the metabolic, probiotic, fitness, and safety properties of Limosilactobacillus fermentum LAB-1, a lactic acid bacterium demonstrating strong antimicrobial effects against clinical pathogens. Gene functional characterization revealed a large number of genes for carbohydrate metabolism and a heterofermentative system for carbon dissimilation. Genes for intact pyruvate oxidation, pentose phosphate, and PRPP biosynthetic pathways were identified. Substantial carbohydrate-active enzymes and transporters were also predicted. Metabolic reconstruction revealed complete sets of enzymes for arginine, lysine, methionine, threonine, proline, and ornithine biosynthesis. The bacterium harbors a diverse range of peptidases, and a large variety of peptide and amino acid uptake systems. It encodes restriction-modification and CRISPR-Cas systems for protection against phage infections and carries a wide spectrum of stress proteins for adaptation in the gut and industrial conditions. Genes related to the biosynthesis of B-group and K vitamins were identified allowing its application for novel bio-enriched food production. Other beneficial traits of probiotic and industrial importance such as production of flavor compounds, exopolysaccharide, acetoin, and butanediol were identified. Three antimicrobial peptides were predicted which showed >98% sequence-identity to experimentally validated bacteriocins. Negative traits such as transmissible antibiotic resistance, pathogenicity or virulence appeared to be absent suggesting the strain to be considered safe. The genome analysis will allow precisely targeted laboratory research and full exploitation of the probiotic potentials towards functional-food, biotechnology and health-related applications.\n\nFunctional genomics of the lactic acid bacterium Limosilactobacillus fermentum LAB-1: metabolic, probiotic and biotechnological perspectives.", "token_count": 488, "char_count": 1975, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6831, "quality_score": 0.8416, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:58.553450", "source": { "split": "train_shard_00001", "doc_id": 4400 }, "chunk_id": "train_shard_00001_4400_0", "global_id": 11886 }, { "text": "BackgroundWhole genome sequencing (WGS) is a reliable tool for studying tuberculosis (TB) transmission. WGS data are usually processed by custom-built analysis pipelines with little standardisation between them.AimTo compare the impact of variability of several WGS analysis pipelines used internationally to detect epidemiologically linked TB cases.MethodsFrom the Netherlands, 535 Mycobacterium tuberculosis complex (MTBC) strains from 2016 were included. Epidemiological information obtained from municipal health services was available for all mycobacterial interspersed repeat unit-variable number of tandem repeat (MIRU-VNTR) clustered cases. WGS data was analysed using five different pipelines: one core genome multilocus sequence typing (cgMLST) approach and four single nucleotide polymorphism (SNP)-based pipelines developed in Oxford, United Kingdom; Borstel, Germany; Bilthoven, the Netherlands and Copenhagen, Denmark. WGS clusters were defined using a maximum pairwise distance of 12 SNPs/alleles.ResultsThe cgMLST approach and Oxford pipeline clustered all epidemiologically linked cases, however, in the other three SNP-based pipelines one epidemiological link was missed due to insufficient coverage. In general, the genetic distances varied between pipelines, reflecting different clustering rates: the cgMLST approach clustered 92 cases, followed by 84, 83, 83 and 82 cases in the SNP-based pipelines from Copenhagen, Oxford, Borstel and Bilthoven respectively.ConclusionConcordance in ruling out epidemiological links was high between pipelines, which is an important step in the international validation of WGS data analysis. To increase accuracy in identifying TB transmission clusters, standardisation of crucial WGS criteria and creation of a reference database of representative MTBC sequences would be advisable.\n\nTowards standardisation: comparison of five whole genome sequencing (WGS) analysis pipelines for detection of epidemiologically linked tuberculosis cases.", "token_count": 477, "char_count": 2002, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:50:59.678390", "source": { "split": "train_shard_00001", "doc_id": 4401 }, "chunk_id": "train_shard_00001_4401_0", "global_id": 11887 }, { "text": "The effect of inulin sugars concentration on the growth and ethanol production by Kluyveromyces marxianus UCD (FST) 55-82 was studied. A maximum ethanol concentration of 102 g/liter was obtained from 250 g of sugars per liter initial concentration. The maximum specific growth rate varied from 0.44 h at 50 g of sugar per liter to 0.13 h at 300 g of sugar per liter, whereas the ethanol yield remained almost constant at 0.45 g of ethanol per g of sugars utilized.\n\nEffect of Sugar Concentration in Jerusalem Artichoke Extract on Kluyveromyces marxianus Growth and Ethanol Production.", "token_count": 172, "char_count": 584, "word_count": 96, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:00.127329", "source": { "split": "train_shard_00001", "doc_id": 4402 }, "chunk_id": "train_shard_00001_4402_0", "global_id": 11888 }, { "text": "The body-wide human microbiome plays a role in health, but its full diversity remains uncharacterized, particularly outside of the gut and in international populations. We leveraged 9,428 metagenomes to reconstruct 154,723 microbial genomes (45% of high quality) spanning body sites, ages, countries, and lifestyles. We recapitulated 4,930 species-level genome bins (SGBs), 77% without genomes in public repositories (unknown SGBs [uSGBs]). uSGBs are prevalent (in 93% of well-assembled samples), expand underrepresented phyla, and are enriched in non-Westernized populations (40% of the total SGBs). We annotated 2.85 M genes in SGBs, many associated with conditions including infant development (94,000) or Westernization (106,000). SGBs and uSGBs permit deeper microbiome analyses and increase the average mappability of metagenomic reads from 67.76% to 87.51% in the gut (median 94.26%) and 65.14% to 82.34% in the mouth. We thus identify thousands of microbial genomes from yet-to-be-named species, expand the pangenomes of human-associated microbes, and allow better exploitation of metagenomic technologies.\n\nExtensive Unexplored Human Microbiome Diversity Revealed by Over 150,000 Genomes from Metagenomes Spanning Age, Geography, and Lifestyle.", "token_count": 391, "char_count": 1253, "word_count": 171, "semantic_coherence": 1, "information_density": 0.7135, "quality_score": 0.8567, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:00.743651", "source": { "split": "train_shard_00001", "doc_id": 4403 }, "chunk_id": "train_shard_00001_4403_0", "global_id": 11889 }, { "text": "

Background

Our primary aim was to test whether cattle-associated fluoroquinolone-resistant (FQ-R) Escherichia coli found on dairy farms are closely phylogenetically related to those causing bacteriuria in humans living in the same 50 × 50 km geographical region suggestive of farm-human sharing. Another aim was to identify risk factors for the presence of FQ-R E. coli on dairy farms.

Methods

FQ-R E. coli were isolated during 2017-18 from 42 dairy farms and from community urine samples. Forty-two cattle and 489 human urinary isolates were subjected to WGS, allowing phylogenetic comparisons. Risk factors were identified using a Bayesian regularization approach.

Results

Of 489 FQ-R human isolates, 255 were also third-generation-cephalosporin-resistant, with strong genetic linkage between aac(6')Ib-cr and blaCTX-M-15. We identified possible farm-human sharing for pairs of ST744 and ST162 isolates, but minimal core genome SNP distances were larger between farm-human pairs of ST744 and ST162 isolates (71 and 63 SNPs, respectively) than between pairs of isolates from different farms (7 and 3 SNPs, respectively). Total farm fluoroquinolone use showed a positive association with the odds of isolating FQ-R E. coli, while total dry cow therapy use showed a negative association.

Conclusions

This work suggests that FQ-R E. coli found on dairy farms have a limited impact on community bacteriuria within the local human population. Reducing fluoroquinolone use may reduce the on-farm prevalence of FQ-R E. coli and this reduction may be greater when dry cow therapy is targeted to the ecology of resistant E. coli on the farm.", "token_count": 486, "char_count": 1662, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6109, "quality_score": 0.8054, "entities": { "genes": [ "ST162", "ST744" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:01.399372", "source": { "split": "train_shard_00001", "doc_id": 4404 }, "chunk_id": "train_shard_00001_4404_0", "global_id": 11890 }, { "text": "Limited phylogenetic overlap between fluoroquinolone-resistant Escherichia coli isolated on dairy farms and those causing bacteriuria in humans living in the same geographical region.", "token_count": 45, "char_count": 183, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:01.760099", "source": { "split": "train_shard_00001", "doc_id": 4404 }, "chunk_id": "train_shard_00001_4404_1", "global_id": 11891 }, { "text": "Although the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from more than 700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from those of adults. We find evidence for more than a 10-fold increase in the rate of evolution and strain turnover in the infant gut compared with healthy adults, with the mother-infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.\n\nRapid evolution and strain turnover in the infant gut microbiome.", "token_count": 284, "char_count": 1375, "word_count": 212, "semantic_coherence": 1, "information_density": 0.5849, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:02.324090", "source": { "split": "train_shard_00001", "doc_id": 4405 }, "chunk_id": "train_shard_00001_4405_0", "global_id": 11892 }, { "text": "Phylogenetic analyses based on 16S rRNA gene sequences of members of the family Staphylococcaceae showed the presence of para- and polyphyletic genera. This finding prompted a thorough investigation into the taxonomy of the Staphylococcaceae family by analysing their core genome phylogeny complemented with genome-based indices such as digital DNA-DNA hybridization, average nucleotide identity and average amino acid identity. The resulting data suggested the following proposals: Auricoccus indicus was reduced in taxonomic rank as a later heterotypic synonym of Abyssicoccus albus; Staphylococcus petrasii subsp. jettensis as a later heterotypic synonym of Staphylococcus petrasii subsp. petrasii; the unification of Staphylococcus aureus subsp. anaerobius and Staphylococcus aureus subsp. aureus as Staphylococcus aureus; the unification of Staphylococcus carnosus subsp. utilis and Staphylococcus carnosus subsp. carnosus as Staphylococcus carnosus; the unification of Staphylococcus saprophyticus subsp. bovis and Staphylococcus saprophyticus subsp. saprophyticus as Staphylococcus saprophyticus; Staphylococcus succinis subsp", "token_count": 482, "char_count": 1301, "word_count": 142, "semantic_coherence": 1, "information_density": 0.5986, "quality_score": 0.7993, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:02.967112", "source": { "split": "train_shard_00001", "doc_id": 4406 }, "chunk_id": "train_shard_00001_4406_0", "global_id": 11893 }, { "text": "casei as the novel species Staphylococcus casei; Staphylococcus schleiferi subsp. coagulans as the novel species Staphylococcus coagulans; Staphylococcus petrasii subsp. croceilyticus as the novel species Staphylococcus croceilyticus; Staphylococcus petrasii subsp. pragensis as the novel species Staphylococcus pragensis; Staphylococcus cohnii subsp. urealyticus as the novel species Staphylococcus urealyticus; the reassignment of Staphylococcus sciuri, Staphylococcus fleurettii, Staphylococcus lentus, Staphylococcus stepanovicii and Staphylococcus vitulinus to the novel genus Mammaliicoccus with Mammaliicoccus sciuri as the type species; and the formal assignment of Nosocomiicoccus as a member of the family Staphylococcaceae.\n\nPhylogenomic analyses of the Staphylococcaceae family suggest the reclassification of five species within the genus Staphylococcus as heterotypic synonyms, the promotion of five subspecies to novel species, the taxonomic reassignment of five Staphylococcus species to Mammaliicoccus gen. nov., and the formal assignment of Nosocomiicoccus to the family Staphylococcaceae.", "token_count": 513, "char_count": 1310, "word_count": 134, "semantic_coherence": 1, "information_density": 0.4328, "quality_score": 0.7164, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:03.618007", "source": { "split": "train_shard_00001", "doc_id": 4406 }, "chunk_id": "train_shard_00001_4406_1", "global_id": 11894 }, { "text": "

Objectives

To describe and analyse erythromycin resistance trends in blood isolates of Staphylococcus aureus (EARS-Net Spain, 2004-2020) and the association of these trends with the consumption of macrolide, lincosamide, and streptogramin B (MLSB) antibiotics. To assess molecular changes that could be involved in erythromycin resistance trends by whole genome analysis of representative isolates.

Materials and methods

We collected antibiotic susceptibility data for all first-blood S. aureus isolates in patients from 47 Spanish hospitals according to EARS-Net criteria. MLSB antibiotic consumption was obtained from the Spanish Agency for Medicines and Medical Devices (2008-2020). We sequenced 137 representative isolates for core genome multilocus sequence typing, resistome and virulome analysis.

Results

For the 36,612 invasive S. aureus isolates, methicillin resistance decreased from 26.4% in 2004 to 22.4% in 2020. Erythromycin resistance in methicillin-susceptible S. aureus (MSSA) increased from 13.6% in 2004 to 28.9% in 2020 (p < 0.001); however, it decreased from 68.7 to 61.8% (p < 0.0001) in methicillin-resistant S. aureus (MRSA). Total consumption of MLSB antibiotics increased from 2.72 defined daily doses per 1,000 inhabitants per day (DID) in 2014 to 3.24 DID in 2016", "token_count": 519, "char_count": 1395, "word_count": 179, "semantic_coherence": 1, "information_density": 0.648, "quality_score": 0.824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:04.275321", "source": { "split": "train_shard_00001", "doc_id": 4407 }, "chunk_id": "train_shard_00001_4407_0", "global_id": 11895 }, { "text": "By WGS, the macrolide resistance genes detected were erm (59.8%), msrA (46%), and mphC (45.2%). The erm genes were more prevalent in MSSA (44/57, 77.2%) than in MRSA (38/80, 47.5%). Most of the erm genes identified in MSSA after 2013 differed from the predominant ermC gene (17/22, 77.3%), largely because ermT was significantly associated with MSSA after 2013 (11/29, 37.9%). All 13 ermT isolates in this study, except one, belonged to ST398 and came from 10 hospitals and six Spanish provinces.

Conclusion

The significant increase in erythromycin resistance in blood MSSA correlated with the consumption of the MLSB antibiotics in Spain. These preliminary data seem support the hypothesis that the human ST398 MSSA clade with ermT-mediated resistance to erythromycin may be involved in this trend.\n\nAn increase in erythromycin resistance in methicillin-susceptible Staphylococcus aureus from blood correlates with the use of macrolide/lincosamide/streptogramin antibiotics. EARS-Net Spain (2004-2020).", "token_count": 407, "char_count": 1091, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:04.885643", "source": { "split": "train_shard_00001", "doc_id": 4407 }, "chunk_id": "train_shard_00001_4407_1", "global_id": 11896 }, { "text": "Data on typical surface microflora of smeared semi-soft, soft and acid curd cheeses and the minimal composition of suitable surface starter cultures are reviewed. Cultures for semi-soft cheeses should contain Debaryomyces hansenii, Staphylococcus equorum, Corynebacterium casei, Microbacterium gubbeenense (or Arthrobacter nicotianae), and Brevibacterium linens. Apart from D. hansenii, soft cheese surface cultures should contain Geotrichum candidum, which is responsible for the typical appearance and aroma development. M. gubbeenense or A. nicotianae and B. linens are essential for soft cheese ripening, but C. casei is not. S. equorum, not regularly found on the surface of commercial soft cheeses, accelerated deacidification and smear development. Cultures for acid curd cheeses, produced from quarg, should contain Kluyveromyces marxianus and Candida krusei. Staphylococci seem to be essential for ripening. S. equorum can replace the non-food-grade S. saprophyticus that is always present on commercial acid curd cheeses. Suitable corynebacteria for spraying of cheeses are B. linens and C. variabile.\n\nCultures for the ripening of smear cheeses", "token_count": 325, "char_count": 1155, "word_count": 160, "semantic_coherence": 1, "information_density": 0.5938, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:05.453777", "source": { "split": "train_shard_00001", "doc_id": 4408 }, "chunk_id": "train_shard_00001_4408_0", "global_id": 11897 }, { "text": "Different surveillance studies (2005-2015) on the presence of ESBL-producing E. coli in the northwest Spain revealed that eae-positive isolates of serotype O153:H10 were periodically detected in meat (of beef, chicken and pork), and also implicated in human diarrhea. This study aimed: i) to characterize the degree of relatedness between human and animal isolates; ii) to know if this was a geographically restricted or disseminated genetic lineage. Thirty-two isolates were conventionally typified as O153:H10-A-ST10 fimH54, fimAvMT78, traT and eae-beta1, being 21 of those CTX-M-32 or SHV-12 producers. PFGE comparison of their macrorestriction profiles showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like. Besides, the core genome investigation based on the cgMLST scheme from Enterobase, proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of clonal group O153:H10-A-ST10 (CH11-54) would be playing a successful role in spreading ESBLs (CTX-M-32) in our region within different hosts, including wildlife. It would be potentially implicated in human diarrhea via food (meat) transmission. Importantly, we proved genomic evidence of a related hybrid aEPEC/ExPEC in other countries.\n\nGenomic Characterization of ESBL-producing Escherichia coli Isolates Belonging to a Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Human Diarrheagenic Isolates, Meat, Poultry and Wildlife", "token_count": 490, "char_count": 1603, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7018, "quality_score": 0.8509, "entities": { "genes": [ "ST10", "CH11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:06.102302", "source": { "split": "train_shard_00001", "doc_id": 4409 }, "chunk_id": "train_shard_00001_4409_0", "global_id": 11898 }, { "text": "The thermotolerant yeast Candida thermophila SRY-09 isolated from Thailand produces an extracellular lipase that hydrolyses various triglycerides. To clone the gene encoding the lipase, Saccharomyces cerevisiae was transformed with a C. thermophila genomic library and screened for lipase activity on medium containing olive oil emulsion and rhodamine B. One C. thermophila lipase gene (CtLIP) was found that contained an ORF of 1317 bp encoding a deduced polypeptide of 438 amino acids. Candida thermophila lipase contained a Gly-Asp-Ser-Gln-Gly motif which matched the consensus Gly-X-Ser-X-Gly conserved among lipolytic enzymes. Heterologous expression of the cloned CtLIP under the control of the alcohol oxidase gene (AOX1) promoter in the methylotrophic yeast Pichia pastoris, and enzymatic measurements confirmed the function of the respective protein as a lipase. The recombinant CtLIP could hydrolyse various substrates at high temperature (55 degrees C) with higher efficiency than at 37 or 45 degrees C and preferentially hydrolysed two-positional ester bonds. As with C. thermophila, the heterologously expressed lipase was secreted into the medium by Pichia pastoris.\n\nMolecular cloning and functional expression of a novel extracellular lipase from the thermotolerant yeast Candida thermophila.", "token_count": 365, "char_count": 1308, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "AOX1" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:06.687793", "source": { "split": "train_shard_00001", "doc_id": 4410 }, "chunk_id": "train_shard_00001_4410_0", "global_id": 11899 }, { "text": "Listeria monocytogenes is a major human and animal foodborne pathogen. However, data from environmental reservoirs remain scarce. Here, we used whole-genome sequencing to characterize Listeria species isolates recovered over 1 year from wild animals in their natural habitats in Spain. Three different Listeria spp. (L. monocytogenes [n = 19], Listeria ivanovii subsp. londoniensis [n = 4], and Listeria innocua [n = 3]) were detected in 23 animal tonsils (9 deer, 14 wild boars) and 2 feeding troughs. No Listeria species was detected in feces. L. monocytogenes was detected in tonsils of 44.4% (8 out of 18) of deer and 40.7% (11 out of 27) of wild boars. L. monocytogenes isolates belonged to 3 different core genome multilocus sequence typing (cgMLST) types (CTs) of 3 distinct sublineages (SL1, SL387, and SL155) from lineages I and II. While cgMLST type L1-SL1-ST1-CT5279 (IVb; clonal complex 1 [CC1]) occurred only in one animal, types L1-SL387-ST388-CT5239 (IVb; CC388) and L2-SL155-ST155-CT1170 (IIa; CC155) were retrieved from multiple animals. In addition, L1-SL387-ST388-CT5239 (IVb; CC388) isolates were collected 1 year apart, revealing their long-term occurrence within the animal population and/or environmental reservoir", "token_count": 524, "char_count": 1328, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6793, "quality_score": 0.8397, "entities": { "genes": [ "ST388", "CT5239", "CT1170", "ST155", "SL387", "CT5279", "ST1", "CC388", "SL155", "CC155" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:08.088613", "source": { "split": "train_shard_00001", "doc_id": 4411 }, "chunk_id": "train_shard_00001_4411_0", "global_id": 11900 }, { "text": "The presence of identical L. monocytogenes strains in deer and wild boars suggests contamination from a common food or environmental source, although interhost transmission cannot be excluded. Pathogenicity islands LIPI-1, LIPI-3, and LIPI-4 were present in 100%, 5%, and 79% of the L. monocytogenes isolates, respectively, and all L. monocytogenes lineage II isolates (n = 3) carried SSI-1 stress islands. This study highlights the need for monitoring L. monocytogenes environmental contamination and the importance of tonsils as a possible L. monocytogenes intrahost reservoir.IMPORTANCEListeria monocytogenes is a foodborne bacterial pathogen responsible for listeriosis. Whole-genome sequencing has been extensively used in public health and food industries to characterize circulating Listeria isolates, but genomic data on isolates occurring in natural environments and wild animals are still scarce. Here, we show that wild animals carry pathogenic Listeria and that the same genotypes can be found at different time points in different host species. This work highlights the need of Listeria species monitoring of environmental contamination and the importance of tonsils as a possible L. monocytogenes intrahost reservoir.\n\nListeria spp. Isolated from Tonsils of Wild Deer and Boars: Genomic Characterization.", "token_count": 409, "char_count": 1409, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6216, "quality_score": 0.8108, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:08.712345", "source": { "split": "train_shard_00001", "doc_id": 4411 }, "chunk_id": "train_shard_00001_4411_1", "global_id": 11901 }, { "text": "Streptococcus dysgalactiae subsp. dysgalactiae (SDSD) is one of the most prevalent pathogens causing bovine mastitis worldwide. However, there is a lack of comprehensive information regarding genetic diversity, complete profiles of virulence factors (VFs), and antimicrobial resistance (AMR) genes for SDSD associated with bovine mastitis in China. In this study, a total of 674 milk samples, including samples from 509 clinical and 165 subclinical mastitis cases, were collected from 17 herds in 7 provinces in China from November 2016 to June 2019. All SDSD isolates were included in phylogenetic analysis based on 16S rRNA and multi-locus sequence typing (MLST). In addition, whole genome sequencing was performed on 12 representative SDSD isolates to screen for VFs and AMR genes and to define pan-, core and accessory genomes. The prevalence of SDSD from mastitis milk samples was 7.57% (51/674). According to phylogenetic analysis based on 16S rRNA, 51 SDSD isolates were divided into 4 clusters, whereas based on MLST, 51 SDSD isolates were identified as 11 sequence types, including 6 registered STs and 5 novel STs (ST521, ST523, ST526, ST527, ST529) that belonged to 2 distinct clonal complexes (CCs) and 4 singletons. Based on WGS information, 108 VFs genes in 12 isolates were determined in 11 categories. In addition, 23 AMR genes were identified in 11 categories. Pan-, core and accessory genomes were composed of 2,663, 1,633 and 699 genes, respectively. These results provided a comprehensive profiles of SDSD virulence and resistance genes as well as phylogenetic relationships among mastitis associated SDSD in North China.", "token_count": 494, "char_count": 1655, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5952, "quality_score": 0.7976, "entities": { "genes": [ "ST527", "ST526", "ST523", "ST529", "ST521" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:09.393578", "source": { "split": "train_shard_00001", "doc_id": 4412 }, "chunk_id": "train_shard_00001_4412_0", "global_id": 11902 }, { "text": "Comparative Genomic Analysis of Streptococcus dysgalactiae subspecies dysgalactiae Isolated From Bovine Mastitis in China.", "token_count": 44, "char_count": 129, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:09.788928", "source": { "split": "train_shard_00001", "doc_id": 4412 }, "chunk_id": "train_shard_00001_4412_1", "global_id": 11903 }, { "text": "

ABSTRACT

Understanding the complex information stored in a genome remains challenging since multiple connected regulatory mechanisms act at various scales to determine function. Increased comprehension of genome function at scales beyond contiguous nucleotides will help understand genetic diseases, the emergence of pathogenesis, and more broadly the genomics of adaptation. Here we report the analysis of DNA methylation, histone modification, and DNA accessibility in the plant pathogenic vascular wilt fungus Verticillium dahliae . Functional analysis details that DNA methylation is restricted to repetitive elements, such as transposable element DNA, but interestingly only some repetitive DNA is methylated. This incomplete DNA methylation is associated with repetitive DNA residing in specific compartments of the genome that were previously defined as Lineage-Specific (LS) regions. These regions are hypervariable between V. dahliae isolates and contain genes that support host colonization and adaptive traits. LS regions are associated with H3 Lys-27 methylated histones (H3K27me3), and repetitive DNA within LS regions are more transcriptionally active and have increased DNA accessibility, representing a hybrid chromatin state when compared to repetitive regions within the core genome. We used machine learning algorithms trained on epigenetic and DNA accessibility data to predict LS regions with high recall, identifying approximately twice as much LS DNA in the V. dahliae genome as previously recognized. Collectively, these results characterize LS regions in an intermediate chromatin state and provide evidence that links chromatin features and genome architecture to adaptive regions within the genome.\n\nChromatin features define adaptive genomic regions in a fungal plant pathogen", "token_count": 389, "char_count": 1813, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6145, "quality_score": 0.8072, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:10.422736", "source": { "split": "train_shard_00001", "doc_id": 4413 }, "chunk_id": "train_shard_00001_4413_0", "global_id": 11904 }, { "text": "A method for preparing yeast containing ginsenoside Rg3 is provided to increase usefulness of conventionally discarded side products, capable of inducing environment contamination, by using effluent generated from red ginseng preparation as a culture medium and produce the yeast containing a large amount of the ginsenoside Rg3 with useful activities. A method for preparing yeast containing ginsenoside Rg3 comprises the steps of: (a) culturing yeast selected from the group consisting of Pichia sp., Saccharomyces sp., Kluyveromyces sp., Zygosaccharomyces sp., and Lipomyces sp. at a temperature of 25-35 deg.C for 6 to 80 hours using the remnant effluent after distilling fresh ginseng as a culture medium remaining and (b) recovering the cultured yeast from the culture medium. A health functional food comprises the yeast containing ginsenoside Rg3 ginsenoside as an effective ingredient. Further, the yeast is selected from a group consisting of Pichia anomala, Saccharomyces cerevisiae, Saccharomyces pastorianus, Kluyveromyces fragilis, Zygosaccharomyces rouxii and Lipomyces starkeyi.\n\nMETHOD FOR PRODUCING YEAST CONTAINING GINSENOSIDE RG3", "token_count": 313, "char_count": 1149, "word_count": 161, "semantic_coherence": 1, "information_density": 0.5342, "quality_score": 0.7671, "entities": { "genes": [ "RG3" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:11.019630", "source": { "split": "train_shard_00001", "doc_id": 4414 }, "chunk_id": "train_shard_00001_4414_0", "global_id": 11905 }, { "text": "The reactive oxygen species hydrogen peroxide is a byproduct of the β-oxidation process that occurs in peroxisomes. Since reactive oxygen species can cause serious damage to biomolecules, a number of scavengers control their intracellular levels. One such scavenger that is present in the peroxisome is the oxidoreductase catalase. In this study, the crystal structure of heterologously expressed peroxisomal catalase from the thermotolerant yeast Hansenula polymorpha has been determined at 2.9 Å resolution. H. polymorpha catalase is a typical peroxisomal catalase; it is tetrameric and is highly similar to catalases from other organisms. However, its hydrogen peroxide-degrading activity is higher than those of a number of other catalases for which structural data are available. Structural superimpositions indicate that the nature of the major channel, the path for hydrogen peroxide to the active site, varies from those seen in other catalase structures, an observation that may account for the high activity of H. polymorpha catalase.\n\nStructural features of peroxisomal catalase from the yeast Hansenula polymorpha.", "token_count": 283, "char_count": 1126, "word_count": 163, "semantic_coherence": 1, "information_density": 0.6012, "quality_score": 0.8006, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:11.585148", "source": { "split": "train_shard_00001", "doc_id": 4415 }, "chunk_id": "train_shard_00001_4415_0", "global_id": 11906 }, { "text": "Since March 2020, the COVID-19 pandemic forced hospitals worldwide to intensify their infection control measures to prevent health care-associated transmission of SARS-CoV-2. The correct use of personal protective equipment, especially the application of masks, was quickly identified as priority to reduce transmission with this pathogen. Here, we report a nosocomial cluster of methicillin-resistant Staphylococcus aureus (MRSA) that occurred during the COVID-19 pandemic in a gynecology/obstetrics department, despite these intensified contact precautions. Five MRSA originating from clinical samples after surgical intervention led to an outbreak investigation. Firstly, this included environmental sampling of the operation theatre (OT) and, secondly, a point prevalence screening of patients and health care workers (HCW). All detected MRSA were subjected to whole genome sequencing (WGS) and isolate relatedness was determined using core genome multilocus sequence typing (cgMLST). WGS revealed one MRSA cluster with genetically closely related five patient and two HCW isolates differing in a single cgMLST allele at maximum. The outbreak was terminated after implementation of infection control bundle strategies. Although contact precaution measures, which are also part of MRSA prevention bundle strategies, were intensified during the COVID-19 pandemic, this MRSA outbreak could take place. This illustrates the importance of adherence to classical infection prevention strategies.\n\nOutbreak of MRSA in a Gynecology/Obstetrics Department during the COVID-19 Pandemic: A Cautionary Tale.", "token_count": 363, "char_count": 1605, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6869, "quality_score": 0.8435, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:12.171354", "source": { "split": "train_shard_00001", "doc_id": 4416 }, "chunk_id": "train_shard_00001_4416_0", "global_id": 11907 }, { "text": "

Aims

The aim of this study was to analyse the current situation of Contagious Bovine Pleuropneumonia (CBPP) in the Central African Republic (CAR) by seroprevalence analysis, as well as isolation and characterization of strains of the etiologic agent, Mycoplasma mycoides mycoides (Mmm), circulating in livestock breeding regions.

Material and methods

The strains obtained were subjected to whole genome sequencing by Illumina technology and genotyped using the eMLST technique based on 62 genes of the Mmm core genome. Their sensitivity to tetracycline was assessed by determination of the minimum inhibitory concentration (MIC) on agar. A seroprevalence analysis by competitive ELISA was conducted in livestock breeding regions (West, Centre and East CAR), including both zebu and taurine cattle breeds, and both males and females.

Results

The three strains isolated in the three regions of the CAR shared exactly the same genomic sequence. Phylogenetic analysis showed that they were closely related to a strain isolated in the CAR in 1991, also sequenced in this study, and clustered with Mmm strains originating from East and Central Africa. The recent isolates presented increased MIC values, though they were still sensitive to tetracycline. The global CBPP prevalence in the CAR was estimated at 12.5% with no significant differences observed between cattle breeding regions, nor between males and females. However, a significantly higher prevalence was observed in zebu compared to taurine cattle, most likely in relation to their herding system based on cattle transhumance and nomadic pastoralism.

Conclusion

CBPP is enzootic in the CAR in spite of control campaigns based on use of the live T1 vaccines, which have shown little efficacy due to poor implementation in the field. New strategies combining controlled use of antibiotics and inactivated vaccines, with increased thermostability, should be well received by livestock keepers and allow a better control of CBPP in the region", "token_count": 508, "char_count": 2031, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:12.832163", "source": { "split": "train_shard_00001", "doc_id": 4417 }, "chunk_id": "train_shard_00001_4417_0", "global_id": 11908 }, { "text": "The fact that the recent Mmm isolates are still resistant to tetracycles is encouraging.\n\n[Present Situation of Contagious Bovine Pleuropneumonia in Central African Republic].", "token_count": 43, "char_count": 175, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9583, "quality_score": 0.9792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:13.191546", "source": { "split": "train_shard_00001", "doc_id": 4417 }, "chunk_id": "train_shard_00001_4417_1", "global_id": 11909 }, { "text": "Abstract

BackgroundAlthough generally known as a human commensal, Staphylococcus epidermidis is also an opportunistic pathogen that can cause nosocomial infections related to foreign body materials and immunicompromized patients. Infections are often caused by multidrug resistant (MDR) lineages that are difficult and costly to treat, and can have a major adverse impact on patients’ quality of life. Heterogeneity is a common phenomenon in both carriage and infection, but present methodology for detection of this is laborious or expensive. In this study, we present a culture-independent method, labelled Epidome, based on an amplicon sequencing-approach to deliver information beyond species level on primary samples and to elucidate clonality, population structure and temporal stability or niche selection of S. epidermidis communities. MethodsBased on an assessment of >800 genes from the S. epidermidis core genome, we identified genes with variable regions, which in combination facilitated the differentiation of phylogenetic clusters observed in silico, and allowed classification down to lineage level. A duplex PCR, combined with an amplicon sequencing protocol, and a downstream analysis pipeline were designed to provide subspecies information from primary samples. Additionally, a probe-based qPCR was designed to provide valuable absolute abundance quantification of S. epidermidis. ResultsA combined laboratory and bioinformatic approach was successfully designed and validated on isolates representing skin commensals and on genomic mock communities to validate primer specificity and reproducibility using technical replicates. The method was furthermore applied to a sample set of primary skin and nasal samples, revealing a high degree of heterogeneity in the S. epidermidis population at both sampling sites with resolution down to distinct lineages. Additionally, the qPCR, with a detection limit of <10 copies/µL, showed a high degree of variation in absolute abundance of S", "token_count": 508, "char_count": 2168, "word_count": 280, "semantic_coherence": 1, "information_density": 0.6536, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:13.828666", "source": { "split": "train_shard_00001", "doc_id": 4418 }, "chunk_id": "train_shard_00001_4418_0", "global_id": 11910 }, { "text": "epidermidis.ConclusionsThe Epidome method is designed for use on primary samples to obtain information on S. epidermidis abundance and diversity beyond species-level to answer important questions regarding the emergence and dissemination of nosocomial lineages, investigating clonality of S. epidermidis communities, population dynamics, and niche selection. Our targeted-sequencing method allows rapid differentiation and identification of clinically important nosocomial lineages in primary low-biomass samples such as skin samples.

\n\nThe Epidome - A species-specific Approach to Assess the Population Structure and Heterogeneity of Staphylococcus Epidermidis Colonization and Infection", "token_count": 184, "char_count": 747, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:14.283633", "source": { "split": "train_shard_00001", "doc_id": 4418 }, "chunk_id": "train_shard_00001_4418_1", "global_id": 11911 }, { "text": "The application of Fenton's reaction to enhance the fermentability of prehydrolysates obtained from steam explosion pretreatment of poplar biomass was studied. Reaction conditions of temperature and H2O2 and Fe(II) concentrations were studied. The fermentability of prehydrolysate treated by Fenton's reaction was tested by using different inoculum sizes of thermotolerant strain Kluyveromyces marxianus CECT 10875. The highest percentages of toxic compound degradation (ranging from 71 to 93% removal) were obtained at the highest H2O2 concentration tested (50 mM). However, a negative effect on fermentability was observed at this H2O2 concentration at the lower inoculum loading. An increase in inoculum size to 0.6 g/L resulted in an enhanced ethanol fermentation yield of 95% relative to control.\n\nApplication of Fenton's reaction to steam explosion prehydrolysates from poplar biomass.", "token_count": 238, "char_count": 891, "word_count": 125, "semantic_coherence": 1, "information_density": 0.608, "quality_score": 0.804, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:14.756556", "source": { "split": "train_shard_00001", "doc_id": 4419 }, "chunk_id": "train_shard_00001_4419_0", "global_id": 11912 }, { "text": "The rhizobium-legume symbiosis has been widely studied as the model of mutualistic evolution and the essential component of sustainable agriculture. Extensive genetic and recent genomic studies have led to the hypothesis that many distinct strategies, regardless of rhizobial phylogeny, contributed to the varied rhizobium-legume symbiosis. We sequenced 26 genomes of Sinorhizobium and Bradyrhizobium nodulating soybean to test this hypothesis. The Bradyrhizobium core genome is disproportionally enriched in lipid and secondary metabolism, whereas several gene clusters known to be involved in osmoprotection and adaptation to alkaline pH are specific to the Sinorhizobium core genome. These features are consistent with biogeographic patterns of these bacteria. Surprisingly, no genes are specifically shared by these soybean microsymbionts compared with other legume microsymbionts. On the other hand, phyletic patterns of 561 known symbiosis genes of rhizobia reflected the species phylogeny of these soybean microsymbionts and other rhizobia. Similar analyses with 887 known functional genes or the whole pan genome of rhizobia revealed that only the phyletic distribution of functional genes was consistent with the species tree of rhizobia. Further evolutionary genetics revealed that recombination dominated the evolution of core genome. Taken together, our results suggested that faithfully vertical genes were rare compared with those with history of recombination including lateral gene transfer, although rhizobial adaptations to symbiotic interactions and other environmental conditions extensively recruited lineage-specific shell genes under direct or indirect control through the speciation process.\n\nComparative genomics of rhizobia nodulating soybean suggests extensive recruitment of lineage-specific genes in adaptations.", "token_count": 429, "char_count": 1841, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:15.385519", "source": { "split": "train_shard_00001", "doc_id": 4420 }, "chunk_id": "train_shard_00001_4420_0", "global_id": 11913 }, { "text": "Enterococcus faecium is a gut commensal of the gastro-digestive tract, but also known as nosocomial pathogen among hospitalized patients. Population genetics based on whole-genome sequencing has revealed that E. faecium strains from hospitalized patients form a distinct clade, designated as clade A1 and that plasmids are major contributors to the emergence of nosocomial E. faecium . Here we further explored the adaptive evolution of E. faecium using a genome-wide co-evolution study (GWES) to identify co-evolving SNPs. We identified three genomic regions harboring large numbers of SNPs in tight linkage which are not proximal to each other based on the completely assembled chromosome of clade A1 reference hospital isolate AUS0004. Close examination of these regions revealed that they are located at the borders of four different types of large-scale genomic rearrangements, insertion sites of two different genomic islands and an IS 30 -like transposon. In non-clade A1 isolates, these regions are adjacent to each other and they lack the insertions of the genomic islands and IS 30 -like transposon. Additionally, among the clade A1 isolates there is one group of pet isolates lacking the genomic rearrangement and insertion of the genomic islands, suggesting a distinct evolutionary trajectory. In silico analysis of the biological functions of the genes encoded in three regions revealed a common link to a stress response. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed. In conclusion, to our knowledge, this is the first study using GWES to identify genomic rearrangements, suggesting that there is considerable untapped potential to unravel hidden evolutionary signals from population genomic data.

Impact statement

Enterococcus faecium has emerged as an important nosocomial pathogen around the world. Population genetics revealed that clinical E. faecium strains form a distinct clade, designated as clade A1 and that plasmids are major contributors to the emergence of nosocomial E. faecium . Here, the adaptive evolution of E", "token_count": 514, "char_count": 2192, "word_count": 326, "semantic_coherence": 1, "information_density": 0.5061, "quality_score": 0.7531, "entities": { "genes": [ "AUS0004" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:16.047942", "source": { "split": "train_shard_00001", "doc_id": 4421 }, "chunk_id": "train_shard_00001_4421_0", "global_id": 11914 }, { "text": "faecium was further explored using an unsupervised machine learning method (SuperDCA) to identify genome-wide co-evolving SNPs. We identified three genomic regions harboring large numbers of SNPs in tight linkage which are separated by a large chromosomal distance in a clinical clade A1 reference isolate, but appeared adjacent to each other in non-clade A1 isolates. We identified four different types of large-scale genomic rearrangements and in all cases, we found insertion of two different genomic islands and an insertion element at the border. In contrast, no genomic rearrangement and insertions were identified among a group of clade A1 pet isolates, suggesting a distinct evolutionary trajectory. Based on the in silico predicted biological functions, we found a common link to a stress response for the genes encoded in three regions. This suggests that these rearrangements may reflect adaptation to the stringent conditions in the hospital environment, such as antibiotics and detergents, to which bacteria are exposed.

Data summary

Raw core-genome alignment (1.1 MB, Harvest suite v1.1.2), including the 1,644 Clade A isolates and the complete E. faecium AUS0004 (accession number CP003351 ) as a reference is available under the following gitlab repository https://gitlab.com/sirarredondo/efm_gwes .\n\nGenomic rearrangements uncovered by genome-wide co-evolution analysis of a major nosocomial pathogenEnterococcus faecium", "token_count": 369, "char_count": 1453, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6976, "quality_score": 0.8488, "entities": { "genes": [ "AUS0004", "CP003351" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:16.625005", "source": { "split": "train_shard_00001", "doc_id": 4421 }, "chunk_id": "train_shard_00001_4421_1", "global_id": 11915 }, { "text": "

Introduction

Although carbapenem-resistant Enterobacteriaceae (CRE) have been thoroughly investigated as the pathogens most commonly associated with clinical infections, data on Serratia marcescens are inadequate and superficial.

Methods

In this study, we characterized 36 carbapenem-resistant Serratia marcescens (CRSM) isolates in our hospital from April 2018 to March 2019 by analysing whole-genome sequencing (WGS) data. The molecular typing of the isolates was performed using both pulsed-field gel electrophoresis (PFGE) and core genome multilocus sequence typing (cgMLST).

Results

Thirty-three of the 36 isolates showed carbapenem resistance conferred by a bla KPC-2-harbouring plasmid, while the remaining three isolates were characterized by overexpression of beta-lactamase combined with porin loss. The bla KPC-2 genes in all the isolates were located on a plasmid of ~103 kb, except one, which was on a plasmid of ~94 kb. The gene structure surrounding bla KPC-2 in the plasmids was confirmed by integration of a partial Tn4401 structure and an intact IS26 as previously reported. Most of the plasmids also contained a mobile genetic element (MGE) comprising qnr and ISKpn19, which provided evidence of horizontal transfer of antibiotic resistance genes.

Conclusion

The thirty-six CRSM isolates were mainly clonally disseminated with a bla KPC-2-harbouring plasmid in our hospital", "token_count": 465, "char_count": 1507, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [ "IS26" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:17.273021", "source": { "split": "train_shard_00001", "doc_id": 4422 }, "chunk_id": "train_shard_00001_4422_0", "global_id": 11916 }, { "text": "The gene structure surrounding bla KPC-2 as an MGE, as well as the qnr segment, might be acquired by horizontal gene transfer, and it could aggravate the infection and increase the difficulty of clinical treatment.\n\nMolecular Characterization of Carbapenem-Resistant Serratia marcescens Clinical Isolates in a Tertiary Hospital in Hangzhou, China.", "token_count": 109, "char_count": 372, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:17.652751", "source": { "split": "train_shard_00001", "doc_id": 4422 }, "chunk_id": "train_shard_00001_4422_1", "global_id": 11917 }, { "text": "Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.\n\nDeciphering the gastrointestinal carriage of Klebsiella pneumoniae.", "token_count": 346, "char_count": 1349, "word_count": 160, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:18.228488", "source": { "split": "train_shard_00001", "doc_id": 4423 }, "chunk_id": "train_shard_00001_4423_0", "global_id": 11918 }, { "text": "Populus trichocarpa, a pivotal model organism for woody transgenic research, not only garners substantial scientific interest but plays an integral role in forestry economics. Previous genomic assemblies of P. trichocarpa predominantly treated its heterozygous genome as homozygous, thereby neglecting crucial haplotypic diversity. Leveraging the high-fidelity (HiFi) sequencing capabilities of PacBio sequencing and the chromosome conformation capture insights provided by Illumina's Hi-C technique, this study is the first to achieve a near telomere-to-telomere assembly of both paternal and maternal haplotypes in P. trichocarpa. Comparative genomic analysis between these haplotypes has uncovered several allelic variants and pathways critical for trait determination through allele-specific expression. Furthermore, utilizing RNA-seq data from multiple tissues, this investigation has detailed the tissue-specific expression patterns of the leucine-rich repeat gene family, which are essential in mediating plant signal transduction and developmental regulation. Our results not only illuminate the functional genomics landscape of P. trichocarpa but also provide invaluable theoretical underpinnings for the genetic improvement of woody plants and a robust framework for exploring genetic variability and allelic expression disparities in arboreal species.\n\nChromosome-scale and haplotype-resolved genome assembly of <i>Populus trichocarpa</i>.", "token_count": 375, "char_count": 1490, "word_count": 182, "semantic_coherence": 1, "information_density": 0.7637, "quality_score": 0.8819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:18.807545", "source": { "split": "train_shard_00001", "doc_id": 4424 }, "chunk_id": "train_shard_00001_4424_0", "global_id": 11919 }, { "text": "Bacteria and yeasts are important sensory factors of raw-milk cheeses as they contribute to the sensory richness and diversity of these products. The diversity and succession of yeast populations in three traditional Registered Designation of Origin (R.D.O.) Salers cheeses have been determined by using phenotypic diagnoses and Single-Strand Conformation Polymorphism (SSCP) analysis. Isolates were identified by phenotypic tests and the sequencing of the D1-D2 domains of the 26S rRNA gene. Ninety-two percent of the isolates were identified as the same species in both tests. Yeast-specific primers were designed to amplify the V4 region of the 18S rRNA gene for SSCP analysis. The yeast species most frequently encountered in the three cheeses were Kluyveromyces lactis, Kluyveromyces marxianus, Saccharomyces cerevisiae, Candida zeylanoides and Debaryomyces hansenii. Detection of less common species, including Candida parapsilosis, Candida silvae, Candida intermedia, Candida rugosa, Saccharomyces unisporus, and Pichia guilliermondii was more efficient with the conventional method. SSCP analysis was accurate and could be used to rapidly assess the proportions and dynamics of the various species during cheese ripening. Each cheese was clearly distinguished by its own microbial community dynamics.\n\nApplication of SSCP-PCR fingerprinting to profile the yeast community in raw milk Salers cheeses.", "token_count": 361, "char_count": 1407, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:19.384761", "source": { "split": "train_shard_00001", "doc_id": 4425 }, "chunk_id": "train_shard_00001_4425_0", "global_id": 11920 }, { "text": "Abstract

Background: Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation.

Methods:

Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively.

Results:

Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined", "token_count": 345, "char_count": 1505, "word_count": 189, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:19.960713", "source": { "split": "train_shard_00001", "doc_id": 4426 }, "chunk_id": "train_shard_00001_4426_0", "global_id": 11921 }, { "text": "The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak.

Conclusions:

Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time.

\n\nEvaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.", "token_count": 314, "char_count": 1320, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6171, "quality_score": 0.8086, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:20.519806", "source": { "split": "train_shard_00001", "doc_id": 4426 }, "chunk_id": "train_shard_00001_4426_1", "global_id": 11922 }, { "text": "Nontuberculous mycobacterial infection (NTM) such as endophthalmitis, dacryocystitis, canaliculitis are pervasive across the globe and are currently managed by antibiotics such as cefoxitin/imipenem and azithromycin/clarithromycin. However, the recent cases of Mycobacteroides developing drug resistance reported along with the improper practice of medicine intrigued us to explore its genomic and proteomic canvas at a global scale. A timely developed vaccine against Mycobacteroides is, therefore, a much requirement. Consequently, we carried out a vivid Genomic study on five recently sequenced strains of Mycobacteroides and explored their Pan-Core genome/ proteome. The promiscuous antigenic proteins were identified via a subtractive proteomics approach that qualified for virulence causation, resistance and essentiality factors for this notorious bacterium. An integrated pipeline was developed for the identification of B Cell, MHC class I, II epitopes. Our final vaccine construct, V6 qualified for all tests such as absence for allergenicity, presence of antigenicity, etc. and contains β defensin adjuvant, linkers, LAMP1 signal peptide, and PADRE (Pan HLA-DR epitopes) amino acid sequence. The vaccine construct, V6 also interacts with a maximum number of MHC molecules, and the TLR4/MD2 complex confirmed by docking and molecular dynamics simulation studies. The knowledge harnessed from the current study can help improve the current treatment regimens and propel further related studies.\n\nTowards a Chimeric Vaccine against Multiple Isolates ofMycobacteroides- An Integrative Approach", "token_count": 404, "char_count": 1607, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7327, "quality_score": 0.8664, "entities": { "genes": [ "LAMP1", "TLR4", "MD2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:21.145208", "source": { "split": "train_shard_00001", "doc_id": 4427 }, "chunk_id": "train_shard_00001_4427_0", "global_id": 11923 }, { "text": "Myxobacteria are recognized for fascinating social behaviors and producing diverse extracellular active substances. Isolating novel myxobacteria is of great interest in the exploitation of new antibiotics and extracellular enzymes. Herein, four novel strains were isolated from Dinghu Mountain Biosphere Reserve, Guangdong province, and Qinghai virgin forest soils, Qinghai province, China. The phylogenetic analysis based on 16S rRNA gene and genomic sequences indicated that the four strains belong to the genera Myxococcus and Pyxidicoccus, sharing the highly similarities of 16S rRNA gene with the genera Myxococcus and Pyxidicoccus (99.3-99.6%, respectively). The four strains had average nucleotide identity (ANI) values of 82.8-94.5%, digital DNA-DNA hybridization (dDDH) values of 22.2-56.6%, average amino acid identity (AAI) values of 75.8-79.1% and percentage of conserved protein (POCP) values of 66.4-74.9% to members of the genera Myxococcus and Pyxidicoccus. Based on phylogenetic analyses, physiological and biochemical characteristics, and comparative genomic analyses, we propose four novel species of the genera Myxococcus and Pyxidicoccus and further supported the two genera above represented the same genus. Description of the four novel species is Myxococcus guangdongensis sp. nov. (K38C18041901T = GDMCC 1.2320T = JCM 39260T), Myxococcus qinghaiensis sp. nov", "token_count": 506, "char_count": 1486, "word_count": 188, "semantic_coherence": 1, "information_density": 0.617, "quality_score": 0.8085, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:21.823588", "source": { "split": "train_shard_00001", "doc_id": 4428 }, "chunk_id": "train_shard_00001_4428_0", "global_id": 11924 }, { "text": "(QH3KD-4-1T = GDMCC 1.2316T = JCM 39262T), Myxococcus dinghuensis sp. nov. (K15C18031901T = GDMCC 1.2319T = JCM 39259T), and Pyxidicoccus xibeiensis sp. nov. (QH1ED-7-1T = GDMCC 1.2315T = JCM 39261T), respectively. Furthermore, comparative genomics of all 15 species of the genera Myxococcus and Pyxidicoccus revealed extensive genetic diversity. Core genomes enriched more genes associated with housekeeping functional classes while accessory genomes enriched more genes related to environmental interactions, indicating the former is relatively indispensable compared to signaling pathway genes. The 15 species of Myxococcus and Pyxidicoccus also exhibited great gene diversity of carbohydrate-active enzymes (CAZymes) and secondary metabolite biosynthesis gene clusters (BGCs), especially related to glycosyl transferases (GT2 and GT4), glycoside hydrolases (GH13 and GH23), non-ribosomal peptide synthetases (NRPS), and Type I polyketide synthase (PKS)/NRPS hybrids.", "token_count": 427, "char_count": 1111, "word_count": 126, "semantic_coherence": 1, "information_density": 0.7302, "quality_score": 0.8651, "entities": { "genes": [ "GH23", "GH13", "GT2", "GT4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:22.466399", "source": { "split": "train_shard_00001", "doc_id": 4428 }, "chunk_id": "train_shard_00001_4428_1", "global_id": 11925 }, { "text": "Comparative genomics of Myxococcus and Pyxidicoccus, including the description of four novel species: Myxococcus guangdongensis sp. nov., Myxococcus qinghaiensis sp. nov., Myxococcus dinghuensis sp. nov., and Pyxidicoccus xibeiensis sp. nov.", "token_count": 115, "char_count": 283, "word_count": 30, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:22.884597", "source": { "split": "train_shard_00001", "doc_id": 4428 }, "chunk_id": "train_shard_00001_4428_2", "global_id": 11926 }, { "text": "A simple and rapid method for lithium acetate-mediated transformation of Kluyveromyces marxianus cells.", "token_count": 28, "char_count": 103, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:23.302093", "source": { "split": "train_shard_00001", "doc_id": 4429 }, "chunk_id": "train_shard_00001_4429_0", "global_id": 11927 }, { "text": "On the basis of two other publications (Yarza et al. 2013; Nemec et al. 2019) and on the basis of resequencing of the 16S rRNA gene of Prolinoborus fasciculus CIP 103579T it is concluded that Prolinoborus fasciculus CIP 103579T, which is the only available strain of the species from culture collections, does not conform to the original description given by Pot et al. (1992). The strain investigated is a member of the genus Acinetobacter within the Moraxellaceae, a family of the Gammaproteobacteria and not a member of the Betaproteobacteria as originally proposed. Prolinoborus fasciculus CIP 103579T shared 99.8 % 16S rRNA gene sequence similarity with Acinetobacter lwoffii DSM 2403T. The two strains clustered together by rpoB- and core genome-based phylogenetic analyses and shared an average nucleotide identity of 96.47% (reciprocal, 96.56 %) and a digital genome distance calculation (GGDC) value of 66.9 %. Furthermore, the two strains shared matrix-assisted laser desorption/ionization time of flight MS profiles to a high extent and showed highly similar cellular fatty acid profiles and physiological substrate utilization patterns", "token_count": 435, "char_count": 1275, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6474, "quality_score": 0.8237, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:23.938600", "source": { "split": "train_shard_00001", "doc_id": 4430 }, "chunk_id": "train_shard_00001_4430_0", "global_id": 11928 }, { "text": "It is proposed that the Judicial commission consider (1) that the strain currently deposited as CIP 103579 be recognized as a member of Acinetobacter lwoffii; (2) placing Prolinoborus fasciculus (Pot et al. 1992) on the list of rejected names if a suitable replacement strain, or a neotype strain cannot be found within 2 years of publication of this request; and (3) place the genus name Prolinoborus (Pot et al. 1992) on the list of rejected names [Recommendation 20D (3) of the Code].\n\nThe status of the genus Prolinoborus (Pot et al. 1992) and the species Prolinoborus fasciculus (Pot et al. 1992).", "token_count": 240, "char_count": 665, "word_count": 101, "semantic_coherence": 1, "information_density": 0.5941, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:24.416957", "source": { "split": "train_shard_00001", "doc_id": 4430 }, "chunk_id": "train_shard_00001_4430_1", "global_id": 11929 }, { "text": "

Objectives

Genomic characterization of the internationally spread sequence type (ST) 16 carbapenem-resistant Klebsiella pneumoniae.

Methods

The complete genomes of three carbapenem producing ST16 K. pneumoniae from Italian patients were analysed by single-nucleotide polymorphism-based phylogeny, core genome multilocus sequence typing, resistance, plasmid, and virulence content and compared with ten genomes of ST16 strains isolated in other countries. Plasmids carrying blaNDM-1 or blaOXA-232 carbapenemase genes were assembled and sequences were analysed.

Results

The internationally spread ST16 K. pneumoniae clone showed variability in terms of distribution of NDM-1 and OXA-232 type carbapenemases. In some ST16 strains, up to six plasmids can be simultaneously present in the same cell, including ColE-like plasmids carrying blaOXA-232 and IncF plasmids carrying blaNDM-1. The differences observed in plasmid, resistance, and virulence content and core genome suggested that there is not a unique, highly conserved ST16 clone, but instead different variants of this lineage circulate worldwide.

Conclusions

The ST16 K. pneumoniae clone has spread worldwide and may become a high-risk clone.\n\nGenomics of Klebsiella pneumoniae ST16 producing NDM-1, CTX-M-15, and OXA-232.", "token_count": 419, "char_count": 1351, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "ST16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:25.039916", "source": { "split": "train_shard_00001", "doc_id": 4431 }, "chunk_id": "train_shard_00001_4431_0", "global_id": 11930 }, { "text": "Twelve isolates recovered from 10 cystic fibrosis/other patient types and a variety of clinical sources, were referred to Canada's National Microbiology Laboratory over 7 years. These were assignable to the genus Pseudoxanthomonas but were unidentifiable to species level. Patients included five males and five females from two geographically separated provinces, ranging in age from 2 months to 84 years. In contrast, most Pseudoxanthomonas species described to date have been derived from water, plants or contaminated soils. By 16S rRNA gene sequencing, the patient strains had ≥99.4 % similarity to each other but only 97.73-98.29 % to their closest relatives, Pseudoxanthomonas spadix or Pseudoxanthomonas helianthi. Bacteria were studied by whole genome sequencing using average nucleotide identity by Blastn, digital DNA-DNA hybridization, average amino acid identity, core genome and single nucleotide variant analyses, MALDI-TOF, biochemical and cellular fatty acid analyses, and by antimicrobial susceptibility testing. Bacterial structures were assessed using scanning and transmission electron microscopy. Strains were strict aerobes, yellowish-pigmented, oxidative, non-motile, Gram-stain-negative bacilli and generally unable to reduce nitrate. Strains were susceptible to most of the antibiotics tested; some resistance was observed towards carbapenems, several cephems and uniformly to nitrofurantoin. The single taxon group observed by 16S rRNA gene sequencing was supported by whole genome sequencing; genomes ranged in size from 4.36 to 4.73 Mb and had an average G+C content of 69.12 mol%. Based on this study we propose the name Pseudoxanthomonas winnipegensis sp. nov. for this cluster", "token_count": 506, "char_count": 1742, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6975, "quality_score": 0.8487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:25.693369", "source": { "split": "train_shard_00001", "doc_id": 4432 }, "chunk_id": "train_shard_00001_4432_0", "global_id": 11931 }, { "text": "Pseudoxanthomonas spadix DSM 18855T, acquired for this study, was found to be non-motile phenotypically and by electron microscopy; we therefore propose the emendation of Pseudoxanthomonas spadix Young et al. 2007 to document that observation.\n\nPseudoxanthomonas winnipegensis sp. nov., derived from human clinical materials and recovered from cystic fibrosis and other patient types in Canada, and emendation of Pseudoxanthomonas spadix Young et al. 2007.", "token_count": 175, "char_count": 509, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7619, "quality_score": 0.881, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:26.132701", "source": { "split": "train_shard_00001", "doc_id": 4432 }, "chunk_id": "train_shard_00001_4432_1", "global_id": 11932 }, { "text": "Irritable bowel syndrome (IBS) is still a common functional gastrointestinal disease that presents chronic abdominal symptoms but with a pathophysiology that is not yet fully elucidated. Moreover, the use of the synergistic combination of prebiotics and probiotics, known as synbiotics, for IBS therapy is still in the early stages. Advancements in technology led to determining the important role played by probiotics in IBS, whereas the present paper focuses on the detailed review of the various pathophysiologic mechanisms of action of probiotics, prebiotics, and synbiotics via multidisciplinary domains involving the gastroenterology (microbiota modulation, alteration of gut barrier function, visceral hypersensitivity, and gastrointestinal dysmotility) immunology (intestinal immunological modulation), and neurology (microbiota-gut-brain axis communication and co-morbidities) in mitigating the symptoms of IBS. In addition, this review synthesizes literature about the mechanisms involved in the beneficial effects of prebiotics and synbiotics for patients with IBS, discussing clinical studies testing the efficiency and outcomes of synbiotics used as therapy for IBS.\n\nProbiotics, Prebiotics, and Synbiotics: Implications and Beneficial Effects against Irritable Bowel Syndrome.", "token_count": 321, "char_count": 1290, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6548, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:26.692347", "source": { "split": "train_shard_00001", "doc_id": 4433 }, "chunk_id": "train_shard_00001_4433_0", "global_id": 11933 }, { "text": "A Kluyveromyces marxianus mutant deficient in p37, a glyceraldehyde-3-phosphate dehydrogenase (GAPDH)-like protein, was obtained and characterized with respect to flocculation behaviour, resistance to temperatures above the optimum for growth, morphology, growth, calcofluor white sensitivity and GAPDH activity. In YPD media, the mutant cells were unable to flocculate and were thermosensitive. However, this thermosensitivity could be overcome by the presence of calcium. Calcofluor white was toxic to the mutant, indicating that the mutation affects cell wall structure. The contribution of p37 to total GAPDH activity was 25% when cells were using glucose as carbon source and 50% when cells were growing in 3% ethanol. These results indicate that p37 is likely to be involved in thermotolerance and flocculation, which can be related to its contribution to cell wall integrity.\n\nKluyveromyces marxianus flocculence and growth at high temperature is dependent on the presence of the protein p37.", "token_count": 275, "char_count": 1013, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:27.240691", "source": { "split": "train_shard_00001", "doc_id": 4434 }, "chunk_id": "train_shard_00001_4434_0", "global_id": 11934 }, { "text": "Listeria monocytogenes, an important foodborne pathogen, may be present in different kinds of food and in food processing environments where it can persist for a long time. In this study, 28 L. monocytogenes isolates from fish and fish manufactures were characterized by whole genome sequencing (WGS). Core genome multilocus sequence typing (cgMLST) analysis was applied to compare the present isolates with publicly available genomes of L. monocytogenes strains recovered worldwide from food and from humans with listeriosis. All but one (96.4%) of the examined isolates belonged to molecular serogroup IIa, and one isolate (3.6%) was classified to serogroup IVb. The isolates of group IIa were mainly of MLST sequence types ST121 (13 strains) and ST8 (four strains) whereas the isolate of serogroup IVb was classified to ST1. Strains of serogroup IIa were further subtyped into eight different sublineages with the most numerous being SL121 (13; 48.1% strains) which belonged to six cgMLST types. The majority of strains, irrespective of the genotypic subtype, had the same antimicrobial resistance profile. The cluster analysis identified several molecular clones typical for L. monocytogenes isolated from similar sources in other countries; however, novel molecular cgMLST types not present in the Listeria database were also identified.\n\nWhole-Genome Sequencing-Based Characterization of Listeria monocytogenes from Fish and Fish Production Environments in Poland.", "token_count": 406, "char_count": 1512, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6262, "quality_score": 0.8131, "entities": { "genes": [ "ST8", "ST1", "ST121", "SL121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:27.857312", "source": { "split": "train_shard_00001", "doc_id": 4435 }, "chunk_id": "train_shard_00001_4435_0", "global_id": 11935 }, { "text": "A new α-haemolytic streptococcal strain has been isolated from the dental plaque of a teenager with Down syndrome. Genetic and taxonomic analyses place this Streptococcus within the oralis group. It is a Gram-stain-positive, non-motile, non-spore-forming spherical alpha-haemolytic coccus arranged in chains, and it ferments a large number of monosaccharides and disaccharides, as well as polymeric carbohydrates. It differs biochemically from closely related species of Streptococcus due to its production of α-galactosidase, β-galactosidase and N-acetyl-β-d-glucosaminidase and by the absence of arginine dihydrolase deiminase and IgA1-protease. It grows in a temperature range of 25 to 40 °C (optimal growth temperature at 37 °C) and in a pH range of 4.5 to 8 (optimal pH at 7.0). A phylogenetic analysis based on its 16S and 23S rRNA gene sequences placed it close to Streptococcus dentisani CECT 7747T. The ANIb and ANIm values were 93.19 and 93.61 %, respectively, both below the accepted threshold to designate it as a new species of bacteria. A phylogenetic tree based on its core genome placed it close to Streptococcus oralis subsp. dentisani strain CECT 7747T with a distance in the expanded core phylogeny of 0.1298. The in silico DNA-DNA hybridization value was 52.2 % with respect to the closest species, S. oralis subsp", "token_count": 504, "char_count": 1412, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6456, "quality_score": 0.8228, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:28.517027", "source": { "split": "train_shard_00001", "doc_id": 4436 }, "chunk_id": "train_shard_00001_4436_0", "global_id": 11936 }, { "text": "dentisani CECT 7747T. Based on these data, a new species of bacteria within the genus Streptococcus, family Streptococcaceae and order Lactobacillales is described, for which the name of Streptococcus downii sp. nov. is proposed (type strain CECT 9732T=CCUG 73139T).\n\nStreptococcus downii sp. nov., isolated from the oral cavity of a teenager with Down syndrome.", "token_count": 170, "char_count": 437, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8148, "quality_score": 0.9074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:28.957384", "source": { "split": "train_shard_00001", "doc_id": 4436 }, "chunk_id": "train_shard_00001_4436_1", "global_id": 11937 }, { "text": "

ABSTRACT

Background

Mass drug administration (MDA) with azithromycin for trachoma elimination reduces nasopharyngeal carriage of Streptococcus pneumoniae in the short term. We evaluated S. pneumoniae carried in the nasopharynx before and after a round of azithromycin MDA to determine whether MDA was associated with changes in pneumococcal population structure.

Methods

We analysed 514 pneumococcal isolates cultured from nasopharyngeal samples collected in Gambian villages that received MDA for trachoma elimination. The samples were collected during three cross-sectional surveys conducted before the third round of MDA (CSS-1) and at one (CSS-2) and six (CSS-3) months after MDA. Whole genome sequencing was conducted on randomly selected isolates. Bayesian Analysis of Population Structure (BAPS) was used to cluster related isolates by capturing variation in the core genome. Serotype and multi-locus sequence type were inferred from the genotype. The Antimicrobial Resistance Identification by Assembly (ARIBA) tool was used to identify macrolide resistance genes.

Results

Twenty-seven BAPS clusters were assigned. These consisted of 81 sequence types (STs), 15 of which were novel additions to pubMLST. Two BAPS clusters, BAPS20 (p-value<=0.016) and BAPS22 (p-value<=0.032) showed an increase in frequency at CSS-3 not associated with antimicrobial resistance. Macrolide resistance within BASP17 increased after treatment (p<0.05) and was carried on a mobile transposable element that also conferred resistance to tetracycline.

Conclusions

Limited changes in pneumococcal population structure were observed after the third round of MDA suggesting treatment had little effect on the circulating lineages. An increase in macrolide resistance within one BAPS highlights the need for antimicrobial resistance surveillance in treated villages.", "token_count": 505, "char_count": 1892, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6166, "quality_score": 0.8083, "entities": { "genes": [ "BASP17", "BAPS22", "BAPS20" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:29.614469", "source": { "split": "train_shard_00001", "doc_id": 4437 }, "chunk_id": "train_shard_00001_4437_0", "global_id": 11938 }, { "text": "Mass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx", "token_count": 35, "char_count": 143, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:29.971411", "source": { "split": "train_shard_00001", "doc_id": 4437 }, "chunk_id": "train_shard_00001_4437_1", "global_id": 11939 }, { "text": "The probiotics market is one of the fastest growing segments of the food industry as there is growing scientific evidence of the positive health effects of probiotics on consumers. Currently, there are various forms of probiotic products and they can be categorized according to dosage form and the site of action. To increase the effectiveness of probiotic preparations, they need to be specifically designed so they can target different sites, such as the oral, upper respiratory or gastrointestinal tracts. Here we review the characteristics of different dosage forms of probiotics and discuss methods to improve their bioavailability in detail, in the hope that this article will provide a reference for the development of probiotic products.\n\nCharacteristics of Probiotic Preparations and Their Applications.", "token_count": 165, "char_count": 813, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6393, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:30.415878", "source": { "split": "train_shard_00001", "doc_id": 4438 }, "chunk_id": "train_shard_00001_4438_0", "global_id": 11940 }, { "text": "

Objectives

To describe the propensity of carbapenem-resistant Pseudomonas aeruginosa to spread within a hospital critical care setting.

Methods

The study was conducted in a 700-bed tertiary centre in Cologne, Germany. P. aeruginosa resistant to piperacillin, ceftazidime, cefepime, imipenem, meropenem and ciprofloxacin, isolated from clinical and screening specimens from four critical care units from 2015 to 2020 were analysed. Genotyping was carried out by WGS (Illumina and MinION). MLST, core genome MLST (cgMLST) and resistome analysis was performed and merged with epidemiological data.

Results

Fifty-five out of 79 non-duplicate P. aeruginosa isolates were available, of which 20 were carbapenemase producers as follows: bla VIM-1 (n = 1), bla VIM-2 (n = 17), bla VIM-4 (n = 1), and bla NDM-1/bla GES-5 (n = 1). Forty-two of 55 isolates were hospital-acquired", "token_count": 409, "char_count": 1029, "word_count": 124, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:31.039775", "source": { "split": "train_shard_00001", "doc_id": 4439 }, "chunk_id": "train_shard_00001_4439_0", "global_id": 11941 }, { "text": "cgMLST revealed three clusters: Cluster 1 (n = 15, ST111, bla VIM-2, recovered between 2015 and 2020); Cluster 2 (n = 4, ST970, carbapenemase negative); and Cluster 3 (n = 2, ST357, carbapenemase negative). The bla VIM-2 gene of Cluster 1 was integrated on the chromosome in a class 1 integron (type In59). Using conventional epidemiology, we were only able to confirm two patient-to-patient transmissions and one room-to-patient transmission on three different ICUs within Cluster 1. Isolates from Cluster 2 represented an outbreak occurring in 2019.

Conclusions

These data give insight into the epidemiology of carbapenem-resistant P. aeruginosa. Transmission dynamics differed between carbapenemase- and non-carbapenemase-producing isolates. A continuous acquisition of clonally related ST111 VIM-2 P. aeruginosa, being the main carbapenemase-producing strain, was observed over the whole study period, as well as an overall higher genomic diversity among non-carbapenemase-producing P. aeruginosa.\n\nGenomic-based transmission analysis of carbapenem-resistant Pseudomonas aeruginosa at a tertiary care centre in Cologne (Germany) from 2015 to 2020.", "token_count": 426, "char_count": 1243, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7197, "quality_score": 0.8599, "entities": { "genes": [ "ST357", "ST111", "ST970" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:31.667685", "source": { "split": "train_shard_00001", "doc_id": 4439 }, "chunk_id": "train_shard_00001_4439_1", "global_id": 11942 }, { "text": "Listeria monocytogenes is a Gram-positive bacterium that can be found in a broad range of environments, including soil, food, animals, and humans. L. monocytogenes can cause a foodborne disease manifesting as sepsis and meningo-encephalitis. To evaluate signals of selection within the core genome of neuroinvasive L. monocytogenes strains, we sequenced 122 L. monocytogenes strains from cerebrospinal fluid (CSF) of Dutch meningitis patients and performed a genome-wide analysis using Tajima's D and ω (dN/dS). We also evaluated the residual variation intolerance score (RVIS), a computationally less demanding methodology, to identify loci under selection. Results show that the large genetic distance between the listerial lineages influences the Tajima's D and ω (dN/dS) outcome. Within genetic lineages we detected signals of selection in 6 of 2327 loci (<1%), which were replicated in an external cohort of 105 listerial CSF isolates from France. Functions of identified loci under selection were within metabolism pathways (lmo2476, encoding aldose 1-epimerase), putative antimicrobial resistance mechanisms (lmo1855, encoding PBPD3), and virulence factors (lmo0549, internalin-like protein; lmo1482, encoding comEC). RVIS over the two genetic lineages showed signals of selection in internalin-like proteins loci potentially involved in pathogen-host interaction (lmo0549, lmo0610, and lmo1290). Our results show that RVIS can be used to detect bacterial loci under selection.", "token_count": 478, "char_count": 1561, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8252, "entities": { "genes": [ "PBPD3" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:32.320538", "source": { "split": "train_shard_00001", "doc_id": 4440 }, "chunk_id": "train_shard_00001_4440_0", "global_id": 11943 }, { "text": "Residual Variation Intolerance Score Detects Loci Under Selection in Neuroinvasive Listeria monocytogenes.", "token_count": 35, "char_count": 113, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:32.682770", "source": { "split": "train_shard_00001", "doc_id": 4440 }, "chunk_id": "train_shard_00001_4440_1", "global_id": 11944 }, { "text": "Among enterococci, Enterococcus faecalis occurs ubiquitously, with the highest incidence of human and animal infections. The high genetic plasticity of E. faecalis complicates both molecular investigations and phylogenetic analyses. Whole-genome sequencing (WGS) enables unraveling of epidemiological linkages and putative transmission events between humans, animals, and food. Core genome multilocus sequence typing (cgMLST) aims to combine the discriminatory power of classical multilocus sequence typing (MLST) with the extensive genetic data obtained by WGS. By sequencing a representative collection of 146 E. faecalis strains isolated from hospital outbreaks, food, animals, and colonization of healthy human individuals, we established a novel cgMLST scheme with 1,972 gene targets within the Ridom SeqSphere+ software. To test the E. faecalis cgMLST scheme and assess the typing performance, different collections comprising environmental and bacteremia isolates, as well as all publicly available genome sequences from the NCBI and SRA databases, were analyzed. In more than 98.6% of the tested genomes, >95% good cgMLST target genes were detected (mean, 99.2% target genes). Our genotyping results not only corroborate the known epidemiological background of the isolates but exceed previous typing resolution. In conclusion, we have created a powerful typing scheme, hence providing an international standardized nomenclature that is suitable for surveillance approaches in various sectors, linking public health, veterinary public health, and food safety in a true One Health fashion.\n\nA Core Genome Multilocus Sequence Typing Scheme for Enterococcus faecalis.", "token_count": 426, "char_count": 1711, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:33.310696", "source": { "split": "train_shard_00001", "doc_id": 4441 }, "chunk_id": "train_shard_00001_4441_0", "global_id": 11945 }, { "text": "

Objectives

The emergence of antimicrobial-resistant livestock-associated Escherichia coli represents a great public health concern. Here we report the draft genome sequences of two multidrug-resistant livestock-associated E. coli strains MEZEC8 and MEZEC10 isolated from sheep in South Africa.

Methods

Genomic DNA of E. coli strains MEZEC8 and MEZEC10 was sequenced using an Illumina MiSeq platform. Generated reads were trimmed and de novo assembled. The assembled contigs were analysed for antimicrobial resistance genes, chromosomal mutations and extrachromosomal plasmids, and the sequence type (ST) was determined by multilocus sequence typing (MLST). To compare strains MEZEC8 and MEZEC10 with other previously published sequences of E. coli strains, raw read sequences of E. coli from livestock were downloaded from the NCBI's Sequence Read Archive and all sequence files were treated identically to generate a core genome bootstrapped maximum likelihood phylogenetic tree.

Results

Antimicrobial resistance genes were detected in MEZEC8 and MEZEC10 conferring resistance to tetracycline and macrolides. MEZEC10 harboured two extrachromosomal plasmids (pO111 and Incl2), while MEZEC8 did not contain any extrachromosomal plasmids. Strain MEZEC8 belonged to serotype H25:O9 and ST58, whereas strain MEZEC10 belonged to serotype H49:O8 and ST1844.

Conclusion

The genome sequences of E. coli strains MEZEC8 and MEZEC10 will serve as a reference point for molecular epidemiological studies of antimicrobial-resistant livestock-associated E. coli in Africa. In addition, this study allows in-depth analysis of genomic structure and will provide valuable information enabling us understand the antimicrobial resistance of livestock-associated E. coli.", "token_count": 509, "char_count": 1780, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [ "MEZEC10", "ST1844", "ST58", "MEZEC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:33.988057", "source": { "split": "train_shard_00001", "doc_id": 4442 }, "chunk_id": "train_shard_00001_4442_0", "global_id": 11946 }, { "text": "Genome sequences of two multidrug-resistant Escherichia coli strains MEZEC8 and MEZEC10 isolated from livestock in South Africa.", "token_count": 39, "char_count": 128, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "MEZEC10", "MEZEC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:34.370286", "source": { "split": "train_shard_00001", "doc_id": 4442 }, "chunk_id": "train_shard_00001_4442_1", "global_id": 11947 }, { "text": "Abstract

Escherichia albertii is a recently identified gastrointestinal bacterial pathogen of humans and animals which is typically misidentified and generally only detected during genomic surveillance of other Enterobacteriaceae. The incidence of E. albertii is likely underestimated and its epidemiology and clinical relevance are poorly characterised. Here, we whole genome sequenced E. albertii isolates from humans (n = 83) and birds (n = 79) in Great Britain and analysed a broader public dataset (n = 475) to address these gaps. We found human and avian isolates typically (90%; 148/164) belonged to host-associated monophyletic groups with distinct virulence and antimicrobial resistance profiles. Overlaid patient epidemiological data suggested that human infection was likely related to travel and possibly foodborne transmission. The Shiga toxin encoding stx2f gene was associated with clinical disease (OR = 10.27, 95% CI = 2.98–35.45 p = 0.0002) in finches. Our results suggest that improved future surveillance will further elucidate disease ecology and public and animal health risks associated with E. albertii.

\n\nThe genomic epidemiology of Escherichia albertii", "token_count": 414, "char_count": 1336, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:35.024286", "source": { "split": "train_shard_00001", "doc_id": 4443 }, "chunk_id": "train_shard_00001_4443_0", "global_id": 11948 }, { "text": "

Unlabelled

The O-specific antigen (OSA) in Pseudomonas aeruginosa lipopolysaccharide is highly varied by sugar identity, side chains, and bond between O-repeats. These differences classified P. aeruginosa into 20 distinct serotypes. In the past few decades, O12 has emerged as the predominant serotype in clinical settings and outbreaks. These serotype O12 isolates exhibit high levels of resistance to various classes of antibiotics. Here, we explore how the P. aeruginosa OSA biosynthesis gene clusters evolve in the population by investigating the association between the phylogenetic relationships among 83 P. aeruginosa strains and their serotypes. While most serotypes were closely linked to the core genome phylogeny, we observed horizontal exchange of OSA biosynthesis genes among phylogenetically distinct P. aeruginosa strains. Specifically, we identified a \"serotype island\" ranging from 62 kb to 185 kb containing the P. aeruginosa O12 OSA gene cluster, an antibiotic resistance determinant (gyrA(C248T)), and other genes that have been transferred between P. aeruginosa strains with distinct core genome architectures. We showed that these genes were likely acquired from an O12 serotype strain that is closely related to P. aeruginosa PA7. Acquisition and recombination of the \"serotype island\" resulted in displacement of the native OSA gene cluster and expression of the O12 serotype in the recipients. Serotype switching by recombination has apparently occurred multiple times involving bacteria of various genomic backgrounds. In conclusion, serotype switching in combination with acquisition of an antibiotic resistance determinant most likely contributed to the dissemination of the O12 serotype in clinical settings.

Importance

Infection rates in hospital settings by multidrug-resistant (MDR) Pseudomonas aeruginosa clones have increased during the past decades, and serotype O12 is predominant among these epidemic strains. It is not known why the MDR phenotype is associated with serotype O12 and how this clone type has emerged", "token_count": 510, "char_count": 2067, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5276, "quality_score": 0.7638, "entities": { "genes": [ "PA7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:35.704552", "source": { "split": "train_shard_00001", "doc_id": 4444 }, "chunk_id": "train_shard_00001_4444_0", "global_id": 11949 }, { "text": "This study shows that evolution of MDR O12 strains involved a switch from an ancestral O4 serotype to O12. Serotype switching was the result of horizontal transfer and genetic recombination of lipopolysaccharide (LPS) biosynthesis genes originating from an MDR taxonomic outlier P. aeruginosa strain. Moreover, the recombination event also resulted in acquisition of antibiotic resistance genes. These results impact on our understanding of MDR outbreak strain and serotype evolution and can potentially assist in better monitoring and prevention.\n\nThe Widespread Multidrug-Resistant Serotype O12 Pseudomonas aeruginosa Clone Emerged through Concomitant Horizontal Transfer of Serotype Antigen and Antibiotic Resistance Gene Clusters.", "token_count": 175, "char_count": 734, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7172, "quality_score": 0.8586, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:36.154019", "source": { "split": "train_shard_00001", "doc_id": 4444 }, "chunk_id": "train_shard_00001_4444_1", "global_id": 11950 }, { "text": "

Background

Streptococcus agalactiae (Group B Streptococcus, (GBS)) is the leading cause of mastitis (inflammation of the mammary gland) among dairy camels in Sub-Saharan Africa, with negative implications for milk production and quality and animal welfare. Camel milk is often consumed raw and presence of GBS in milk may pose a public health threat. Little is known about the population structure or virulence factors of camel GBS. We investigated the molecular epidemiology of camel GBS and its implications for mastitis control and public health.

Results

Using whole genome sequencing, we analysed 65 camel milk GBS isolates from 19 herds in Isiolo, Kenya. Six sequence types (STs) were identified, mostly belonging to previously described camel-specific STs. One isolate belonged to ST1, a predominantly human-associated lineage, possibly as a result of interspecies transmission. Most (54/65) isolates belonged to ST616, indicative of contagious transmission. Phylogenetic analysis of GBS core genomes showed similar levels of heterogeneity within- and between herds, suggesting ongoing between-herd transmission. The lactose operon, a marker of GBS adaptation to the mammary niche, was found in 75 % of the isolates, and tetracycline resistance gene tet(M) in all but two isolates. Only the ST1 isolate harboured virulence genes scpB and lmb, which are associated with human host adaptation.

Conclusions

GBS in milk from Kenyan camel herds largely belongs to ST616 and shows signatures of adaptation to the udder. The finding of similar levels of within- and between herd heterogeneity of GBS in camel herds, as well as potential human-camel transmission highlights the need for improved internal as well as external biosecurity to curb disease transmission and increase milk production.\n\nGenomic analysis of group B Streptococcus from milk demonstrates the need for improved biosecurity: a cross-sectional study of pastoralist camels in Kenya.", "token_count": 508, "char_count": 1972, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [ "ST1", "ST616" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:36.787552", "source": { "split": "train_shard_00001", "doc_id": 4445 }, "chunk_id": "train_shard_00001_4445_0", "global_id": 11951 }, { "text": "The ability of macroencapsulated Saccharomyces cerevisiae CBS 8066 to produce ethanol at elevated temperatures was investigated in consecutive batch and continuous cultures. Prior to cultivation yeast was confined inside alginate-chitosan capsules composed of an outer semi-permeable membrane and an inner liquid core. The encapsulated yeast could successfully ferment 30 g/L glucose and produce ethanol at a high yield in five consecutive batches of 12 h duration at 42°C, while freely suspended yeast was completely inactive already in the third batch. A high ethanol production was observed also through the first 48 h at 40°C during continuous cultivation at D=0.2 h(-1) when using encapsulated cells. The ethanol production slowly decreased in the following days at 40°C. The ethanol production was also measured in a continuous cultivation in which the temperature was periodically increased to 42-45°C and lowered to 37°C again in periods of 12h. Our investigation shows that a non-thermotolerant yeast strain improved its heat tolerance upon encapsulation, and could produce ethanol at temperatures as high as 45°C for a short time. The possibility of performing fermentations at higher temperatures would greatly improve the enzymatic hydrolysis in simultaneous saccharification and fermentation (SSF) processes and thereby make the bioethanol production process more economically feasible.\n\nEthanol production at elevated temperatures using encapsulation of yeast.", "token_count": 357, "char_count": 1474, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6161, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:37.379627", "source": { "split": "train_shard_00001", "doc_id": 4446 }, "chunk_id": "train_shard_00001_4446_0", "global_id": 11952 }, { "text": "High-throughput comparative genomics has changed our view of bacterial evolution and relatedness. Many genomic comparisons, especially those regarding the accessory genome that is variably conserved across strains in a species, are performed using assembled genomes. For completed genomes, an assumption is made that the entire genome was incorporated into the genome assembly, while for draft assemblies, often constructed from short sequence reads, an assumption is made that genome assembly is an approximation of the entire genome. To understand the potential effects of short read assemblies on the estimation of the complete genome, we downloaded all completed bacterial genomes from GenBank, simulated short reads, assembled the simulated short reads and compared the resulting assembly to the completed assembly. Although most simulated assemblies demonstrated little reduction, others were reduced by as much as 25%, which was correlated with the repeat structure of the genome. A comparative analysis of lost coding region sequences demonstrated that up to 48 CDSs or up to ~112,000 bases of coding region sequence, were missing from some draft assemblies compared to their finished counterparts. Although this effect was observed to some extent in 32% of genomes, only minimal effects were observed on pan-genome statistics when using simulated draft genome assemblies. The benefits and limitations of using draft genome assemblies should be fully realized before interpreting data from assembly-based comparative analyses.\n\nBacterial genome reduction as a result of short read sequence assembly", "token_count": 332, "char_count": 1606, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:37.958089", "source": { "split": "train_shard_00001", "doc_id": 4447 }, "chunk_id": "train_shard_00001_4447_0", "global_id": 11953 }, { "text": "Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) ST398 was recovered from infections in humans exposed to animals, raising public health concerns. However, contact with food producing chain as a means of transmission of LA-MRSA to humans remains poorly understood. We aimed to assess if pork production chain is a source of MRSA ST398 for human colonization and infection. MRSA from live pigs, meat, the environment, and slaughterhouse workers were analyzed by Pulsed-Field Gel Electrophoresis (PFGE), spa, MLST typing, SNPs and for antibiotic resistance and virulence gene profiles. We compared core and accessory genomes of MRSA ST398 isolated from slaughterhouse and hospital. We detected MRSA ST398 (t011, t108, t1451) along the entire pork production chain (live pigs: 60%; equipment: 38%; meat: 23%) and in workers (40%). All MRSA ST398 were multidrug resistant, and the majority carried genes encoding biocide resistance and enterotoxins. We found 23 cross-transmission events between live pigs, meat, and workers (6-55 SNPs). MRSA ST398 from infection and slaughterhouse environment belonged to the same clonal type (ST398, t011, SCCmec V), but differed in 321-378 SNPs. Pork production chain can be a source of MRSA ST398 for colonization of human slaughterhouse workers, which can represent a risk of subsequent meat contamination and human infection.\n\nEvidence for the Dissemination to Humans of Methicillin-Resistant Staphylococcus aureus ST398 through the Pork Production Chain: A Study in a Portuguese Slaughterhouse.", "token_count": 456, "char_count": 1585, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6116, "quality_score": 0.8058, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:38.593727", "source": { "split": "train_shard_00001", "doc_id": 4448 }, "chunk_id": "train_shard_00001_4448_0", "global_id": 11954 }, { "text": "Why microbes harm their hosts is a fundamental question in evolutionary biology with broad relevance to our understanding of infectious diseases. Several hypotheses have been proposed to explain this \"evolution of virulence.\" In this perspective, we reexamine one of these hypotheses in the specific context of the human gut microbiome, namely short-sighted evolution. According to the short-sighted evolution hypothesis, virulence is a product of niche expansion within a colonized host, whereby variants of commensal microbes establish populations in tissues and sites where the infection causes morbidity or mortality. This evolution is short-sighted in that the evolved variants that infect those tissues and sites are not transmitted to other hosts. The specific hypothesis that we propose is that some bacteria responsible for invasive infections and disease are the products of the short-sighted evolution of commensal bacteria residing in the gut microbiota. We present observations in support of this hypothesis and discuss the challenges inherent in assessing its general application to infections and diseases associated with specific members of the gut microbiota. We then describe how this hypothesis can be tested using genomic data and animal model experiments and outline how such studies will serve to provide fundamental information about both the evolution and genetic basis of virulence, and the bacteria of intensively studied yet poorly understood habitats including the gut microbiomes of humans and other mammals.\n\nShort-sighted evolution of virulence for invasive gut microbes: From hypothesis to tests.", "token_count": 329, "char_count": 1628, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5865, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:39.165322", "source": { "split": "train_shard_00001", "doc_id": 4449 }, "chunk_id": "train_shard_00001_4449_0", "global_id": 11955 }, { "text": "From 2015 onwards, the number of vancomycin-resistant Enterococcus faecium (VREfm) isolates increased in Tasmania. Previously, we examined the transmission of VREfm at the Royal Hobart Hospital (RHH). In this study, we performed a state-wide analysis of VREfm from Tasmania's four public acute hospitals. Whole-genome analysis was performed on 331 isolates collected from screening and clinical specimens of VREfm. In silico multi-locus sequence typing (MLST) was used to determine the relative abundance of broad sequence types (ST) across the state. Core genome MLST (cgMLST) was then applied to identify potential clades within the ST groupings followed by single-nucleotide polymorphic (SNP) analysis. This work revealed that differences in VREfm profiles are evident between the state's two largest hospitals with the dominant vanA types being ST80 at the RHH and ST1421 at Launceston General Hospital (LGH). A higher number of VREfm cases were recorded at LGH (n = 54 clinical, n = 122 colonization) compared to the RHH (n = 14 clinical, n = 67 colonization) during the same time period, 2014-2016. Eleven of the clinical isolates from LGH were vanA and belonged to ST1421 (n = 8), ST1489 (n = 1), ST233 (n = 1), and ST80 (n = 1) whereas none of the clinical isolates from the RHH were vanA. For the recently described ST1421, cgMLST established the presence of individual clusters within this sequence type that were common to more than one hospital and that included isolates with a low amount of SNP variance (≤16 SNPs)", "token_count": 511, "char_count": 1619, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.8089, "entities": { "genes": [ "ST1421", "ST80", "ST233", "ST1489" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:39.824424", "source": { "split": "train_shard_00001", "doc_id": 4450 }, "chunk_id": "train_shard_00001_4450_0", "global_id": 11956 }, { "text": "A spatio-temporal analysis revealed that VREfm vanA ST1421 was first detected at the RHH in 2014 and an isolate belonging to the same cgMLST cluster was later collected at LGH in 2016. Inclusion of isolates from two smaller hospitals, the North West Regional Hospital (NRH) and the Mersey Community Hospital (MCH) found that ST1421 was present in both of these institutions in 2017. These findings illustrate the spread of a recently described sequence type of VREfm, ST1421, to multiple hospitals in an Australian state within a relatively short time span.\n\nState-Wide Genomic and Epidemiological Analyses of Vancomycin-Resistant Enterococcus faecium in Tasmania's Public Hospitals.", "token_count": 201, "char_count": 697, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7476, "quality_score": 0.8738, "entities": { "genes": [ "ST1421" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:40.285332", "source": { "split": "train_shard_00001", "doc_id": 4450 }, "chunk_id": "train_shard_00001_4450_1", "global_id": 11957 }, { "text": "

Introduction

The emergence of carbapenem-resistant bacteria causing serious infections may lead to more frequent use of previously abandoned antibiotics like colistin. However, mobile colistin resistance genes (mcr) can jeopardise its effectiveness in both human and veterinary medicine. In Germany, turkeys have been identified as the food-producing animal most likely to harbour mcr-positive colistin-resistant Enterobacterales (mcr-Col-E). Therefore, the aim of the present study was to assess the prevalence of both mcr-Col-E and carbapenemase-producing Enterobacterales (CPE) in German turkey herds and humans in contact with these herds.

Methods

In 2018 and 2019, 175 environmental (boot swabs of turkey faeces) and 46 human stool samples were analysed using a combination of enrichment-based culture, PCR, core genome multilocus sequence typing (cgMLST) and plasmid typing.

Results

mcr-Col-E were detected in 123 of the 175 turkey farms in this study (70.3%). mcr-Col-E isolates were Escherichia coli (98.4%) and Klebsiella spp. (1.6%). Herds that had been treated with colistin were more likely to harbour mcr-Col-E, with 82.2% compared to 66.2% in untreated herds (p = 0.0298). Prevalence also depended on husbandry, with 7.1% mcr-Col-E in organic farms compared to 74.5% in conventional ones (p < 0.001)", "token_count": 494, "char_count": 1419, "word_count": 184, "semantic_coherence": 1, "information_density": 0.7011, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:41.306348", "source": { "split": "train_shard_00001", "doc_id": 4451 }, "chunk_id": "train_shard_00001_4451_0", "global_id": 11958 }, { "text": "In addition, four of the 46 (8.7%) human participants were colonised with mcr-Col-E. mcr-Col-E isolates from stables had minimum inhibitory concentrations (MICs) from 4 to ≥ 32 mg/l, human isolates ranged from 4 to 8 mg/l. cgMLST showed no clonal transmission of isolates. For one farm, plasmid typing revealed great similarities between plasmids from an environmental and a human sample. No CPE were found in turkey herds or humans.

Discussion

These findings confirm that mcr-Col-E-prevalence is high in turkey farms, but no evidence of direct zoonotic transmission of clonal mcr-Col-E strains was found. However, the results indicate that plasmids may be transmitted between E. coli isolates from animals and humans.\n\nEpidemiology and zoonotic transmission of mcr-positive and carbapenemase-producing Enterobacterales on German turkey farms.", "token_count": 277, "char_count": 892, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:41.855254", "source": { "split": "train_shard_00001", "doc_id": 4451 }, "chunk_id": "train_shard_00001_4451_1", "global_id": 11959 }, { "text": "

Background

Lactobacillus reuteri is a gram-positive, non-motile bacterial species that has been used as a representative microorganism model to describe the ecology and evolution of vertebrate gut symbionts.

Objective

Because the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of canines remain unknown, we tried to construct draft genome canine L. reuteri and investigate modified, acquired, or lost genetic features that have facilitated the evolution and adaptation of strains to specific environmental niches by this study.

Methods

To examine canine L. reuteri, we sequenced an L. reuteri strain isolated from a dog in Korea. A comparative genomic approach was used to assess genetic diversity and gain insight into the distinguishing features related to different hosts based on 27 published genomic sequences.

Results

The pan-genome of 28 L. reuteri strains contained 7,369 gene families, and the core genome contained 1070 gene families. The ANI tree based on the core genes in the canine L. reuteri strain (C1) was very close to those for three strains (IRT, DSM20016, JCM1112) from humans. Evolutionarily, these four strains formed one clade, which we regarded as C1-clade in this study. We could investigate a total of 32,050 amino acid substitutions among the 28 L. reuteri strain genomes. In this comparison, 283 amino acid substitutions were specific to strain C1 and four strains in C1-clade shared most of these 283 C1-strain specific amino acid substitutions, suggesting strongly similar selective pressure. In accessory genes, we could identify 127 C1-clade host-specific genes and found that several genes were closely related to replication, recombination, and repair.

Conclusion

This study provides new insights into the adaptation of L. reuteri to the canine intestinal habitat, and suggests that the genome of L", "token_count": 510, "char_count": 1913, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5709, "quality_score": 0.7855, "entities": { "genes": [ "JCM1112", "DSM20016" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:42.509933", "source": { "split": "train_shard_00001", "doc_id": 4452 }, "chunk_id": "train_shard_00001_4452_0", "global_id": 11960 }, { "text": "reuteri from canines is closely associated with their living and shared environment with humans.\n\nComparative genomics of canine Lactobacillus reuteri reveals adaptation to a shared environment with humans.", "token_count": 45, "char_count": 206, "word_count": 28, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:42.870131", "source": { "split": "train_shard_00001", "doc_id": 4452 }, "chunk_id": "train_shard_00001_4452_1", "global_id": 11961 }, { "text": "Background. Shigella species are pathogenic bacteria that cause gastrointestinal symptoms ranging from mild watery diarrhoea to bacillary dysentery. Transmission is faecal-oral and historically associated with international travel. Recently, sexual transmission has been documented among gay, bisexual and other men who have sex with men (GBMSM). Through routine surveillance, we observed an increase in notifications of S. flexneri serotype 1b. We investigated the emergence of this serotype and examined possible drivers of transmission.Methods. We used historical data and whole-genome sequencing data from S. flexneri 1b isolates submitted to the United Kingdom Health Security Agency (UKHSA) to determine the relatedness of isolates and describe the population structure using phylogenetics. We tested for associations with possible epidemiological, biological and genetic drivers.Results. Between 1 January 2004 and 30 June 2024, 1,672 isolates of S. flexneri 1b were identified. Prior to 2019, there was a median of 12.5 [interquartile range (IQR) 10-17] notifications per quarter, rising to a median of 39.5 (IQR 23-58) notifications from 2019 to 2024. The rise was predominantly among adult males, consistent with patterns seen in prior sexually transmitted shigellosis epidemics among GBMSM. Unlike previous outbreaks of shigellosis among GBMSM, the emergence of S. flexneri 1b showed no evidence of an association with the acquisition of antimicrobial resistance determinants.Conclusions. Shigellosis can have severe clinical outcomes, and the repeated emergence of Shigella variants among GBMSM highlights the significance of the sexual transmission pathway. Continued surveillance of Shigella subtypes is necessary to inform public health interventions aimed at preventing sexual transmission of enteric pathogens in the GBMSM community.", "token_count": 514, "char_count": 1927, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8275, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:43.504989", "source": { "split": "train_shard_00001", "doc_id": 4453 }, "chunk_id": "train_shard_00001_4453_0", "global_id": 11962 }, { "text": "The emergence of sexually transmissible <i>Shigella flexneri</i> serotype 1b between 2019 and 2024 in England: a descriptive epidemiological study.", "token_count": 58, "char_count": 159, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:43.872449", "source": { "split": "train_shard_00001", "doc_id": 4453 }, "chunk_id": "train_shard_00001_4453_1", "global_id": 11963 }, { "text": "Public health agencies are increasingly relying on genomics during Legionnaires' disease investigations. However, the causative bacterium (Legionella pneumophila) has an unusual population structure, with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires' disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based on L. pneumophila core genome single nucleotide polymorphism (SNP) comparisons eliminates ambiguity for defining outbreak clusters and accurately predicts exposure sources for clinical cases. We illustrate the performance of our method by genome comparisons of 234 L. pneumophila isolates obtained from patients and cooling towers in Melbourne, Australia, between 1994 and 2014. This collection included one of the largest reported Legionnaires' disease outbreaks, which involved 125 cases at an aquarium. Using only sequence data from L. pneumophila cooling tower isolates and including all core genome variation, we built a multivariate model using discriminant analysis of principal components (DAPC) to find cooling tower-specific genomic signatures and then used it to predict the origin of clinical isolates. Model assignments were 93% congruent with epidemiological data, including the aquarium Legionnaires' disease outbreak and three other unrelated outbreak investigations. We applied the same approach to a recently described investigation of Legionnaires' disease within a UK hospital and observed a model predictive ability of 86%. We have developed a promising means to breach L. pneumophila genetic diversity extremes and provide objective source attribution data for outbreak investigations.IMPORTANCE Microbial outbreak investigations are moving to a paradigm where whole-genome sequencing and phylogenetic trees are used to support epidemiological investigations. It is critical that outbreak source predictions are accurate, particularly for pathogens, like Legionella pneumophila, which can spread widely and rapidly via cooling system aerosols, causing Legionnaires' disease", "token_count": 524, "char_count": 2275, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6588, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:44.505815", "source": { "split": "train_shard_00001", "doc_id": 4454 }, "chunk_id": "train_shard_00001_4454_0", "global_id": 11964 }, { "text": "Here, by studying hundreds of Legionella pneumophila genomes collected over 21 years around a major Australian city, we uncovered limitations with the phylogenetic approach that could lead to a misidentification of outbreak sources. We implement instead a statistical learning technique that eliminates the ambiguity of inferring disease transmission from phylogenies. Our approach takes geolocation information and core genome variation from environmental L. pneumophila isolates to build statistical models that predict with high confidence the environmental source of clinical L. pneumophila during disease outbreaks. We show the versatility of the technique by applying it to unrelated Legionnaires' disease outbreaks in Australia and the UK.\n\nA Supervised Statistical Learning Approach for Accurate Legionella pneumophila Source Attribution during Outbreaks.", "token_count": 201, "char_count": 884, "word_count": 116, "semantic_coherence": 1, "information_density": 0.681, "quality_score": 0.8405, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:44.967468", "source": { "split": "train_shard_00001", "doc_id": 4454 }, "chunk_id": "train_shard_00001_4454_1", "global_id": 11965 }, { "text": "Several families of water soluble dendrimers were synthesized based on poly(propyleneoxide) amines (Jeffamines) (P(1)). P(1)-core and branched units were constructed from both methylacrylate and ethylenediamine (P(2)-P(9), and generations 0-3 with -NH(2), -COOH functionalities). They were characterized by elemental analysis (EA), gel permeation chromatography (GPC), FT-IR, (1)H, and (13)C NMR. The antimicrobial activities of only water soluble compounds (P(1), P(3), P(4), P(6), P(7) and P(9)) were evaluated using disk diffusion method in water as well as the minimal inhibitory concentration (MIC) dilution method against 9 bacteria. The obtained results from disk diffusion method are assessed in side-by-side comparison with those of Penicillin-g, Ampicillin, Cefotaxime, Vancomycin, Oflaxacin, and Tetracycline, well-known antibacterial agents. The results from dilution procedure are compared with Gentamycin as antibacterial and Nystatin as antifungal. The antifungal activities are reported on five yeast cultures namely, Candida albicans, Kluyveromyces fragilis, Rhodotorula rubra, Debaryomyces hansenii, and Hanseniaspora guilliermondii, and the results are referenced with Nystatin, Ketaconazole, and Clotrimazole, commercial antifungal agents. In most cases, the compounds show broad-spectrum (gram-positive and gram-negative bacteria) activities that are comparatively higher or equipotent to the antibiotic and antifungal agents in the comparison tests.\n\nSynthesis, characterization and antimicrobial activity of water soluble dendritic macromolecules.", "token_count": 457, "char_count": 1570, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:45.619752", "source": { "split": "train_shard_00001", "doc_id": 4455 }, "chunk_id": "train_shard_00001_4455_0", "global_id": 11966 }, { "text": "

Background

The natural environment serves as a potential reservoir for Campylobacter, the leading cause of bacterial gastroenteritis in humans. However, little is understood about the mechanisms underlying variations in survival characteristics between different strains of C. jejuni in natural environments, including water.

Results

We identified three Campylobacter jejuni strains that exhibited variability in their ability to retain culturability after suspension in water at two different temperatures (4°C and 25°C). Of the three, strains C. jejuni M1 exhibited the most rapid loss of culturability whilst retaining viability. Using RNAseq transcriptomics, we characterised C. jejuni M1 gene expression in response to suspension in water by analyzing bacterial suspensions recovered immediately after introduction into water (Time 0), and from two sampling time/temperature combinations where considerable loss of culturability was evident, namely (i) after 24 h at 25°C, and (ii) after 72 h at 4°C. Transcript data were compared with a culture-grown control. Some gene expression characteristics were shared amongst the three populations recovered from water, with more genes being up-regulated than down. Many of the up-regulated genes were identified in the Time 0 sample, whereas the majority of down-regulated genes occurred in the 25°C (24 h) sample.

Conclusions

Variations in expression were found amongst genes associated with oxygen tolerance, starvation and osmotic stress. However, we also found upregulation of flagellar assembly genes, accompanied by down-regulation of genes involved in chemotaxis. Our data also suggested a switch from secretion via the sec system to via the tat system, and that the quorum sensing gene luxS may be implicated in the survival of strain M1 in water. Variations in gene expression also occurred in accessory genome regions. Our data suggest that despite the loss of culturability, C. jejuni M1 remains viable and adapts via specific changes in gene expression.\n\nCampylobacter jejunitranscriptome changes during loss of culturability in water", "token_count": 496, "char_count": 2128, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5809, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:46.332494", "source": { "split": "train_shard_00001", "doc_id": 4456 }, "chunk_id": "train_shard_00001_4456_0", "global_id": 11967 }, { "text": "Objective: This study aimed to determine the prevalence of fecal carriage of antibiotic-resistant Escherichia coli of healthy household dogs with an emphasis on extended-spectrum β-lactamases (ESBL), AmpC-type β-lactamases and resistance to quinolones. Materials and Methods: Rectal swabs were collected from 74 dogs without any clinical evidence of gastrointestinal disease. Samples were cultured on MacConkey agar plates and MacConkey supplemented with 2 μg/mL cefotaxime or 5 μg/mL ciprofloxacin. Isolates were identified with Vitek 2 Compact and susceptibility testing performed by Kirby Bauer disk diffusion method. Minimal inhibitory concentration (MIC) was done on isolates resistant to cefotaxime, ciprofloxacin, and nalidixic acid. PCR amplification was performed to detect CTX-M and CMY-2. Isolates positive for CTX-M and/or CMY-2 were selected for whole-genome sequencing. Results: Multiresistance was detected in 56% of the isolates. A high percentage of resistance was detected for cefazolin (63%), ampicillin (54%), streptomycin (49%), nalidixic acid (42%) and tetracycline (38%). The MIC50 and MIC90 for isolates resistant to cefotaxime (24%) was determined as 16 and >250 μg/mL, respectively; for ciprofloxacin (18%), 125 and 250 μg/mL, respectively. ESBL (CTX-M type) and AmpC (CMY-2 type) were detected in 6 (7.1%) and 14 (19%) of the isolates, respectively", "token_count": 513, "char_count": 1453, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6943, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:47.022962", "source": { "split": "train_shard_00001", "doc_id": 4457 }, "chunk_id": "train_shard_00001_4457_0", "global_id": 11968 }, { "text": "Whole-genome sequence analysis showed high genetic diversity in most of the isolates and a large variety of resistance mechanisms, including mobile genetic elements. Conclusion: The frequency of multidrug-resistant E. coli is worrying, mainly because of the presence of many isolates producing ESBL and AmpC β-lactamases. Based on the \"One Health\" concept, considering the relationships between animals, humans, and the environment, these data support the notion that companion animals are important reservoirs of multidrug-resistant bacteria.\n\nMultidrug-Resistant CTX-M and CMY-2 Producing Escherichia coli Isolated from Healthy Household Dogs from the Great Metropolitan Area, Costa Rica.", "token_count": 183, "char_count": 718, "word_count": 93, "semantic_coherence": 1, "information_density": 0.7634, "quality_score": 0.8817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:47.510772", "source": { "split": "train_shard_00001", "doc_id": 4457 }, "chunk_id": "train_shard_00001_4457_1", "global_id": 11969 }, { "text": "The bacterial family Brucellaceae is currently composed of seven genera, including species of the genus Brucella, a number of which are significant veterinary and zoonotic pathogens. The bacteriological identification of pathogenic Brucella spp. may be hindered by their close phenotypic similarity to other members of the Brucellaceae, particularly of the genus Ochrobactrum. Additionally, a number of novel atypical Brucella taxa have recently been identified, which exhibit greater genetic diversity than observed within the previously described species, and which share genomic features with organisms outside of the genus. Furthermore, previous work has indicated that the genus Ochrobactrum is polyphyletic, raising further questions regarding the relationship between the genus Brucella and wider Brucellaceae. We have applied whole genome sequencing (WGS) and pan-family multi-locus sequence analysis (MLSA) approaches to a comprehensive panel of Brucellaceae type strains, in order to characterize relationships within the family. Phylogenies based on WGS core genome alignments were able to resolve phylogenetic relationships of 31 non-Brucella spp. type strains from within the family, alongside type strains of twelve Brucella species. A phylogeny based on concatenated pan-family MLSA data was largely consistent with WGS based analyses. Notably, recently described atypical Brucella isolates were consistently placed in a single clade with existing species, clearly distinct from all members of the genus Ochrobactrum and wider family. Both WGS and MLSA methods closely grouped Brucella spp. with a sub-set of Ochrobactrum species. However, results also confirmed that the genus Ochrobactrum is polyphyletic, with seven species forming a separate grouping", "token_count": 509, "char_count": 1888, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6179, "quality_score": 0.8089, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:48.153634", "source": { "split": "train_shard_00001", "doc_id": 4458 }, "chunk_id": "train_shard_00001_4458_0", "global_id": 11970 }, { "text": "The pan-family MLSA scheme was subsequently applied to a panel of 50 field strains of the family Brucellaceae, isolated from a wide variety of sources. This analysis confirmed the utility of the pan-Brucellaceae MLSA scheme in placing field isolates in relation to recognized type strains. However, a significant number of these isolates did not cluster with currently identified type strains, suggesting the existence of additional taxonomic diversity within some members of the Brucellaceae. The WGS and pan-family MLSA approaches applied here provide valuable tools for resolving the identity and phylogenetic relationships of isolates from an expanding bacterial family containing a number of important pathogens.\n\nApplication of Whole Genome Sequencing and Pan-Family Multi-Locus Sequence Analysis to Characterize Relationships Within the Family Brucellaceae.", "token_count": 204, "char_count": 892, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6446, "quality_score": 0.8223, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:48.621021", "source": { "split": "train_shard_00001", "doc_id": 4458 }, "chunk_id": "train_shard_00001_4458_1", "global_id": 11971 }, { "text": "

Background

Pseudomonas aeruginosa is an opportunistic pathogen with a high incidence of hospital infections that represents a threat to immune compromised patients. Genomic studies have shown that, in contrast to other pathogenic bacteria, clinical and environmental isolates do not show particular genomic differences. In addition, genetic variability of all the P. aeruginosa strains whose genomes have been sequenced is extremely low. This low genomic variability might be explained if clinical strains constitute a subpopulation of this bacterial species present in environments that are close to human populations, which preferentially produce virulence associated traits.

Results

In this work, we sequenced the genomes and performed phenotypic descriptions for four non-human P. aeruginosa isolates collected from a plant, the ocean, a water-spring, and from dolphin stomach. We show that the four strains are phenotypically diverse and that this is not reflected in genomic variability, since their genomes are almost identical. Furthermore, we performed a detailed comparative genomic analysis of the four strains studied in this work with the thirteen previously reported P. aeruginosa genomes by means of describing their core and pan-genomes.

Conclusions

Contrary to what has been described for other bacteria we have found that the P. aeruginosa core genome is constituted by a high proportion of genes and that its pan-genome is thus relatively small. Considering the high degree of genomic conservation between isolates of P. aeruginosa from diverse environments, including human tissues, some implications for the treatment of infections are discussed. This work also represents a methodological contribution for the genomic study of P. aeruginosa, since we provide a database of the comparison of all the proteins encoded by the seventeen strains analyzed.\n\nPseudomonas aeruginosa clinical and environmental isolates constitute a single population with high phenotypic diversity.", "token_count": 437, "char_count": 2017, "word_count": 282, "semantic_coherence": 1, "information_density": 0.539, "quality_score": 0.7695, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:49.274036", "source": { "split": "train_shard_00001", "doc_id": 4459 }, "chunk_id": "train_shard_00001_4459_0", "global_id": 11972 }, { "text": "Honey is well known to possess a broad spectrum of activity against medically important organisms. The purpose of this study was to investigate the anti-candidal activity of 28 locally produced honeys from two floral sources, 14 from southern and 14 from northern Iran, against some pathogenic Candida species such as Candida albicans, C. parapsilosis, C. tropicalis, C. kefyr, C. glabrata, and C. dubliniensis. A microdilution broth method was used to assess the activity of the selected honeys against six Candida species. The honeys were tested at 40 concentrations ranging from 20 to 60 % (v/v). Both northern and southern honeys possessed in vitro antifungal activity against the six Candida species tested. Little or no anti-candidal activity was seen at concentrations lower than 24 %. Increased honey concentrations resulted in reduced growth of Candida species. The highest inhibitory effect of different honeys was demonstrated in C. tropicalis, C. glabrata and C. dubliniensis. Candida kefyr and C. albicans showed more resistance to fungicidal activity of honeys, whereas C. glabrata was least affected. All honeys were able to produce complete inhibition of candidal growth with minimum fungicidal concentrations ranging from 29 to 56 %. Overall, varying sensitivities to the anti-candidal properties of different honeys were observed with six species of Candida emphasizing the variability in the antifungal effect of honey samples. Further research is needed to assess the efficacy of honey as an inhibitor of candidal growth in clinical trials, especially in treatment of patients with candidiasis.\n\nFungicidal potential of different Iranian honeys against some pathogenic Candida species", "token_count": 423, "char_count": 1704, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5176, "quality_score": 0.7588, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:49.900823", "source": { "split": "train_shard_00001", "doc_id": 4460 }, "chunk_id": "train_shard_00001_4460_0", "global_id": 11973 }, { "text": "Novel catalase-negative, Gram-stain-positive, beta-haemolytic, coccus-shaped organisms were isolated from Chacoan peccaries that died from respiratory disease. The initial API 20 Strep profiles suggested Streptococcus agalactiae with acceptable identification scores, but the 16S rRNA gene similarity (1548 bp) to available sequences of streptococci was below 98 %. Next taxa of the genus Streptococcus, displaying highest similarities to the strains from this study, were S. bovimastitidis NZ1587T (97.5 %), S. iniae ATCC 29178T (97.5 %), S. hongkongensis HKU30T (97.4 %), S. parauberis DSM 6631T (97.1 %), S. penaeicida CAIM 1838T (97.1 %), S. pseudoporcinus DSM 18513T (97.0 %), S. didelphis DSM 15616T (96.6 %), S. ictaluri 707-05T (96.6 %), S. uberis JCM 5709T (96.5 %) and S. porcinus NCTC 10999T (96.4 %). All other Streptococcus species had sequence similarities of below 96.4 %", "token_count": 521, "char_count": 1087, "word_count": 131, "semantic_coherence": 1, "information_density": 0.7557, "quality_score": 0.8779, "entities": { "genes": [ "NZ1587", "HKU30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:50.566907", "source": { "split": "train_shard_00001", "doc_id": 4461 }, "chunk_id": "train_shard_00001_4461_0", "global_id": 11974 }, { "text": "A sodA gene as well as whole genome-based core genome phylogeny of three representative strains and 145 available Streptococcus genomes confirmed the unique taxonomic position. Interstrain average nucleotide identity (ANI) and amino acid identity (AAI) values were high (ANI >96 %; AAI 100%), but for other streptococci clearly below the proposed species boundary of 95-96 % (ANI <75 %; AAI <83 %). Results were confirmed by genome-to-genome distance calculations. Pairwise digital DNA-DNA hybridization estimates were high (>90 %) between the novel strains, but well below the species boundary of 70 % for closely related Streptococcus type strains (23.5-19.7 %). Phenotypic properties as obtained from extended biochemical profiles and MALDI-TOF mass spectrometry supported the outstanding rank. Based on the presented molecular and physiological data of the six strains, we propose a novel taxon for which we suggest the name Streptococcus catagoni sp. nov. with the type strain 99-1/2017T (=DSM 110457T=CCUG 74072T) and five reference strains.\n\nStreptococcus catagoni sp. nov., isolated from the respiratory tract of diseased Chacoan peccaries (Catagonus wagneri).", "token_count": 409, "char_count": 1243, "word_count": 169, "semantic_coherence": 1, "information_density": 0.7219, "quality_score": 0.8609, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:51.188043", "source": { "split": "train_shard_00001", "doc_id": 4461 }, "chunk_id": "train_shard_00001_4461_1", "global_id": 11975 }, { "text": "

Objectives

To characterize one OXA-232-producing wzi93-KL112-O1 carbapenem-resistant Klebsiella pneumoniae (CRKP) co-harboring chromosomal bla CTX-M-15 and one rmpA2-associated virulence plasmid.

Methods

Minimum inhibitory concentrations (MICs) were measured via broth microdilution method. Conjugation, chemical transformation, string test and Galleria mellonella infection model experiments were also conducted. Whole-genome sequencing (WGS) was performed on the Illumina and Nanopore platforms. Antimicrobial resistance determinants were identified using ABRicate program with ResFinder database. Insertion sequences (ISs) were identified using ISfinder. Bacterial virulence factors were identified using virulence factor database (VFDB). Wzi, capsular polysaccharide (KL) and lipoolygosaccharide (OCL) were analyzed using Kleborate with Kaptive. Phylogenetic analysis of 109 ST15 K. pneumoniae strains was performed using core genome multilocus sequence typing (cgMLST) on the Ridom SeqSphere+ server. MLST, replicons type, SNP strategies and another cgMLST analysis for 45 OXA-232-producing K. pneumoniae strains were further conducted using BacWGSTdb server.

Results

K. pneumoniae KPTCM strain belongs to ST15 with wzi93, KL112 and O1. It possessed a multidrug-resistant (MDR) profile and was resistant to carbapenems (meropenem and ertapenem), ciprofloxacin and amikacin", "token_count": 516, "char_count": 1487, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7561, "quality_score": 0.878, "entities": { "genes": [ "ST15", "KL112" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:51.847964", "source": { "split": "train_shard_00001", "doc_id": 4462 }, "chunk_id": "train_shard_00001_4462_0", "global_id": 11976 }, { "text": "Virulence assays demonstrated KPTCM strain possesses a low virulence phenotype. WGS revealed it contained one circular chromosome and nine plasmids. The carbapenemase-encoding gene bla OXA-232 was located in a 6141-bp ColKP3-type non-conjugative plasmid and flanked by ΔISEcp1 and ΔlysR-ΔereA. Interestingly, bla CTX-M-15 was located in the chromosome mediated by ISEcp1-based transposon Tn2012. Importantly, it harbored a rmpA2-associated pLVPK-like virulence plasmid with iutA-iucABCD gene cluster and one IS26-mediated MDR fusion plasmid according to 8-bp (AGCTGCAC or GGCCTTTG) target site duplications (TSD). Based on the cgMLST and SNP analysis, data showed OXA-232-producing ST15 K. pneumoniae isolates were mainly isolated from China and have evolved in recent years.

Conclusions

Early detection of CRKP strains carrying chromosomal bla CTX-M-15, OXA-232 carbapenemase and pLVPK-like virulence plasmid is recommended to avoid the extensive spread of this high-risk clone.", "token_count": 429, "char_count": 1110, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7615, "quality_score": 0.8808, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:52.478350", "source": { "split": "train_shard_00001", "doc_id": 4462 }, "chunk_id": "train_shard_00001_4462_1", "global_id": 11977 }, { "text": "Whole genome sequencing of OXA-232-producing wzi93-KL112-O1 carbapenem-resistant Klebsiella pneumoniae in human bloodstream infection co-harboring chromosomal ISEcp1-based bla CTX-M-15 and one rmpA2-associated virulence plasmid.", "token_count": 126, "char_count": 274, "word_count": 23, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "KL112" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:52.862959", "source": { "split": "train_shard_00001", "doc_id": 4462 }, "chunk_id": "train_shard_00001_4462_2", "global_id": 11978 }, { "text": "

Objectives

The antiviral zidovudine has been recently identified as an active drug against resistant Enterobacteriaceae, but prevalence of resistance to this compound remains unknown. The aim was to estimate the prevalence of clinical Escherichia coli isolates resistant to zidovudine and to decipher the mechanism of zidovudine resistance.

Methods

We screened 537 isolates on zidovudine-containing agar plates and studied their thymidine kinase (tdk) gene sequences, the putative target involved in zidovudine resistance. Moreover, sequence analysis of 633 complete genomes of E. coli was performed to investigate mutation in the tdk gene. A comparative genomic analysis was done on an in vitro zidovudine-resistant mutant.

Results

After screening on our medium containing 2.7 mg/L (10 μM) zidovudine, nine strains had a zidovudine MIC >26.7 mg/L. The gene was absent in three isolates, inactivated by an IS (IS1X2 and ISApl1) in two isolates and mutated in four isolates. A genomic analysis of 633 E. coli genomes showed heterogeneity of the tdk gene sequence, with 27 different sequences. Among them, three genomes showed an inactivation of the gene (IS, stop codon and no tdk gene sequence). The in vitro mutant E. coli had 27 SNPs in eight genes of the core genome compared with the initial strain.

Conclusions

Our study reports zidovudine-resistant clinical isolates of E. coli, presumably related to tdk inactivation. Diversity of Tdk in bacterial genomes can be large. Other mechanisms need to be considered in zidovudine resistance. The use of zidovudine in antibiotic-resistant infections needs to be in combination and should be tested before clinical administration.", "token_count": 488, "char_count": 1707, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5951, "quality_score": 0.7976, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:53.519125", "source": { "split": "train_shard_00001", "doc_id": 4463 }, "chunk_id": "train_shard_00001_4463_0", "global_id": 11979 }, { "text": "Inactivation of thymidine kinase as a cause of resistance to zidovudine in clinical isolates of Escherichia coli: a phenotypic and genomic study.", "token_count": 44, "char_count": 145, "word_count": 22, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:53.882788", "source": { "split": "train_shard_00001", "doc_id": 4463 }, "chunk_id": "train_shard_00001_4463_1", "global_id": 11980 }, { "text": "UDP-galactose 4-epimerases from the yeast Kluyvero-myces fragilis and Escherichia coli are both homodimers but the molecular mass of the former (75 kDa/subunit) is nearly double that of the latter (39 kDa/subunit). Protein databank sequence homology revealed the possibility of mutarotase activity in the excess mass of the yeast enzyme. This was confirmed by three independent assay protocols. With the help of specific inhibitors and chemical modification reagents, the catalytic sites of epimerase and mutarotase were shown to be distinct and independent. Partial proteolysis with trypsin in the presence of specific inhibitors, 5'-UMP for epimerase and galactose for mutarotase, protected the respective activities. Similar digestion with double inhibitors cleaved the molecule into two fragments of 45 and 30 kDa. After separation by size-exclusion HPLC, they manifested exclusively epimerase and mutarotase activities, respectively. Epimerases from Kluyveromyces lactis var lactis, Pachysolen tannophilus and Schizosaccharomyces pombi also showed associated mutarotase activity distinct from the constitutively formed mutarotase activity. Thus, the bifunctionality of homodimeric yeast epimerases of 65-75 kDa/subunit appears to be universal. In addition to the inducible bifunctional epimerase/mutarotase, K. fragilis contained a smaller constitutive monomeric mutarotase of approximately 35 kDa.\n\nUDP-galactose 4-epimerase from Kluyveromyces fragilis. Evidence for independent mutarotation site.", "token_count": 411, "char_count": 1503, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6701, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:54.507723", "source": { "split": "train_shard_00001", "doc_id": 4464 }, "chunk_id": "train_shard_00001_4464_0", "global_id": 11981 }, { "text": "Lactococcus garvieae is a major pathogen for fish. Two complete (ATCC 49156 and Lg2) and three draft (UNIUD074, 8831, and 21881) genome sequences of L. garvieae have recently been released. We here present the results of a comparative genomic analysis of these fish and human isolates of L. garvieae. The pangenome comprised 1,542 core and 1,378 dispensable genes. The sequenced L. garvieae strains shared most of the possible virulence genes, but the capsule gene cluster was found only in fish-pathogenic strain Lg2. The absence of the capsule gene cluster in other nonpathogenic strains isolated from mastitis and vegetable was also confirmed by PCR. The fish and human isolates of L. garvieae contained the specific two and four adhesin genes, respectively, indicating that these adhesion proteins may be involved in the host specificity differences of L. garvieae. The discoveries revealed by the pangenomic analysis may provide significant insights into the biology of L. garvieae.\n\nComparative Genomic Analysis of Lactococcus garvieae Strains Isolated from Different Sources Reveals Candidate Virulence Genes.", "token_count": 309, "char_count": 1116, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8065, "entities": { "genes": [ "UNIUD074" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:55.076057", "source": { "split": "train_shard_00001", "doc_id": 4465 }, "chunk_id": "train_shard_00001_4465_0", "global_id": 11982 }, { "text": "Clostridioides difficile is an important nosocomial pathogen increasingly observed in the community and in different non-human reservoirs. The epidemiology and transmissibility of C. difficile has been studied using a variety of typing methods, including more recently developed whole-genome sequence (WGS) analysis that is becoming used routinely for bacterial typing worldwide. Here we review the schemes for WGS-based typing methods available for C. difficile and their applications in the field of human C. difficile infection (CDI). The two main approaches to discover genomic variations are single nucleotide variant (SNV) analysis and methods based on gene-by-gene comparisons (frequently called core genome or whole genome MLST, cgMLST, or wgMLST). SNV analysis currently provides the ultimate resolution, however, typing nomenclature and standardized methodology are missing. On the other hand, gene-by-gene approaches allow portability and standardized nomenclature, and are therefore becoming increasingly popular in bacterial epidemiology and outbreak investigation. Two commercial software packages (BioNumerics and Ridom SeqSphere+) and an open source database (EnteroBase) for allele and sequence type determination for C. difficile are currently available. Proof-of-concept WGS studies have already enabled advances in the investigation of the population structure of C. difficile species, microevolution within the epidemic strains, intercontinental transmission over time and in tracking of transmission events. WGS of clinical C. difficile isolates demonstrated a considerable genetic diversity suggesting diverse reservoirs for CDI. WGS was also shown to aid in resolving relapses and reinfections in recurrent CDI and has potential for use as a tool for assessing hospital infection prevention and control performance.\n\nDevelopment and Implementation of Whole Genome Sequencing-Based Typing Schemes for Clostridioides difficile.", "token_count": 479, "char_count": 2005, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:55.726437", "source": { "split": "train_shard_00001", "doc_id": 4466 }, "chunk_id": "train_shard_00001_4466_0", "global_id": 11983 }, { "text": "Currently, only 5 (SEA to SEE) out of 27 known staphylococcal enterotoxins can be analyzed using commercially available kits. Six genes (seg, sei, sem, sen, seo, and seu), encoding putative and undetectable enterotoxins, are located on the enterotoxin gene cluster (egc), which is part of the Staphylococcus aureus genomic island vSaβ. These enterotoxins have been described as likely being involved in staphylococcal food-poisoning outbreaks. The aim of the present study was to determine if whole-genome data can be used for the prediction of staphylococcal egc enterotoxin production, particularly enterotoxin G (SEG) and enterotoxin I (SEI). For this purpose, whole-genome sequences of 75 Staphylococcus aureus strains from different origins (food-poisoning outbreaks, human, and animal) were investigated by applying bioinformatics methods (phylogenetic analysis using the core genome and different alignments). SEG and SEI expression was tested in vitro using a sandwich enzyme-linked immunosorbent assay method. Strains could be allocated to 14 different vSaβ types, each type being associated with a single clonal complex (CC). In addition, the vSaβ type and CC were associated with the origin of the strain (human or cattle derived). The amount of SEG and SEI produced also correlated with the vSaβ type and the CC of a strain. The present results show promising indications that the in vitro production of SEG and SEI can be predicted based on the vSaβ type or CC of a strain. IMPORTANCE Besides having infectious properties in human and animals, S. aureus can produce different enterotoxins in food", "token_count": 512, "char_count": 1721, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:56.384298", "source": { "split": "train_shard_00001", "doc_id": 4467 }, "chunk_id": "train_shard_00001_4467_0", "global_id": 11984 }, { "text": "The enterotoxins can cause vomiting and diarrhea, often involving many people. Most of these outbreaks remain undiscovered, as detection methods for enterotoxins are only available for a few enterotoxins but not for the more recently discovered enterotoxins G (SEG) and I (SEI). In this study, we show promising results that in vitro production of SEG and SEI can be predicted based on the whole-genome sequencing data of a strain. In addition, these data could be used to find the source (human or cattle derived) of an outbreak strain, which is the key for a better understanding of the role SEG and SEI play in foodborne outbreaks caused by S. aureus.\n\nStaphylococcal Enterotoxin Gene Cluster: Prediction of Enterotoxin (SEG and SEI) Production and of the Source of Food Poisoning on the Basis of vSaβ Typing.", "token_count": 222, "char_count": 826, "word_count": 134, "semantic_coherence": 1, "information_density": 0.694, "quality_score": 0.847, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:56.850266", "source": { "split": "train_shard_00001", "doc_id": 4467 }, "chunk_id": "train_shard_00001_4467_1", "global_id": 11985 }, { "text": "

Motivation

Variant calling workflows that utilize a single reference sequence are the de facto standard elementary genomic analysis routine for resequencing projects. Various ways to enhance the reference with pangenomic information have been proposed, but scalability combined with seamless integration to existing workflows remains a challenge.

Results

We present PanVC with founder sequences, a scalable and accurate variant calling workflow based on a multiple alignment of reference sequences. Scalability is achieved by removing duplicate parts up to a limit into a founder multiple alignment, that is then indexed using a hybrid scheme that exploits general purpose read aligners. Our implemented workflow uses GATK or BCFtools for variant calling, but the various steps of our workflow (e.g. vcf2multialign tool, founder reconstruction) can be of independent interest as a basis for creating novel pangenome analysis workflows beyond variant calling.

Availability and implementation

Our open access tools and instructions how to reproduce our experiments are available at the following address: https://github.com/algbio/panvc-founders.

Supplementary information

Supplementary data are available at Bioinformatics online.\n\nFounder reconstruction enables scalable and seamless pangenomic analysis.", "token_count": 289, "char_count": 1333, "word_count": 168, "semantic_coherence": 1, "information_density": 0.6964, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:57.409686", "source": { "split": "train_shard_00001", "doc_id": 4468 }, "chunk_id": "train_shard_00001_4468_0", "global_id": 11986 }, { "text": "Mycobacterium avium subspecies paratuberculosis (MAP) is the aetiological agent of Johne's disease (JD), a chronic enteritis that causes major losses to the global livestock industry. Further, it has been associated with human Crohn's disease. Several strains of MAP have been identified, the two major groups being sheep strain MAP, which includes the Type I and Type III sub-lineages, and the cattle strain or Type II MAP lineage, of which bison strains are a sub-grouping. Major genotypic, phenotypic and pathogenic variations have been identified in prior comparisons, but the research has predominately focused on cattle strains of MAP. In countries where the sheep industries are more prevalent, however, such as Australia and New Zealand, ovine JD is a substantial burden. An information gap exists regarding the genomic differences between sheep strain sub-lineages and the relevance of Type I and Type III MAP in terms of epidemiology and/or pathogenicity. We therefore investigated sheep MAP isolates from Australia and New Zealand using whole genome sequencing. For additional context, sheep MAP genome datasets were downloaded from the Sequence Read Archive and GenBank. The final dataset contained 18 Type III and 16 Type I isolates and the K10 cattle strain MAP reference genome. Using a pan-genome approach, an updated global phylogeny for sheep MAP from de novo assemblies was produced. When rooted with the K10 cattle reference strain, two distinct clades representing the lineages were apparent. The Australian and New Zealand isolates formed a distinct sub-clade within the type I lineage, while the European type I isolates formed another less closely related group. Within the type III lineage, isolates appeared more genetically diverse and were from a greater number of continents. Querying of the pan-genome and verification using BLAST analysis revealed lineage-specific variations (n = 13) including genes responsible for metabolism and stress responses. The genetic differences identified may represent important epidemiological and virulence traits specific to sheep MAP. This knowledge will potentially contribute to improved vaccine development and control measures for these strains.", "token_count": 516, "char_count": 2242, "word_count": 329, "semantic_coherence": 1, "information_density": 0.6018, "quality_score": 0.8009, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:51:58.099522", "source": { "split": "train_shard_00001", "doc_id": 4469 }, "chunk_id": "train_shard_00001_4469_0", "global_id": 11987 }, { "text": "Comparative Genomics of Mycobacterium avium Subspecies Paratuberculosis Sheep Strains.", "token_count": 38, "char_count": 100, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:58.483428", "source": { "split": "train_shard_00001", "doc_id": 4469 }, "chunk_id": "train_shard_00001_4469_1", "global_id": 11988 }, { "text": "Carbonyl reductase (CR) of a yeast strain, Kluyveromyces marxianus, and its isolation and purification method thereof is provided. The reduction reaction by the reductase obtained in the present invention is more stereospecific and requires less cost and time than the reduction reactions by the microorganisms or by the reducing enzymes obtained from a chemical synthesis.\n\nCarbonyl reductase of Saccharomyces and non-Saccharomyces yeasts. Before safety evaluation, differentiation of Saccharomyces cerevisiae strains was done by PCR amplification of inter-δ region with pairs of primers δ2-12 and δ12-21, which showed that they were all different from each other and also had different profiles to Saccharomyces boulardii (the only commercial probiotic yeast). The non-Saccharomyces ones were already known. The evaluation tests carried out were antibiotic and antifungal resistance, production of biogenic amines, deconjugation activity of bile salts, and different enzymatic activities: coagulase, deoxyribonuclease, hemolysin, proteolytic, and phospholipase. None of the studied strains demonstrated coagulase, hemolytic or DNase capacity (clear virulence factors), although all of them showed protease activity, some showed phospholipase activity, and half of the yeasts were capable of conjugating bile salts. Regarding antimicrobial compounds, all were resistant to antibiotics but showed sensitivity to the antimycotics used. Nevertheless, only one strain of Hanseniaspora osmophila was excluded for use in the food industry, due to its high production of tyramine.\n\nSafety Evaluation of Yeasts With Probiotic Potential.", "token_count": 408, "char_count": 1471, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6769, "quality_score": 0.8385, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:51:59.574502", "source": { "split": "train_shard_00001", "doc_id": 4471 }, "chunk_id": "train_shard_00001_4471_0", "global_id": 11990 }, { "text": "

Objectives

Staphylococcus aureus skin and soft tissue infection (Sa-SSTI) places a significant burden on healthcare systems. New Zealand has a high incidence of Sa-SSTI, and here most morbidity is caused by a polyclonal methicillin-susceptible (MSSA) bacterial population. However, MSSA also colonise asymptomatically the cornified epithelia of approximately 20% of the population, and their divide between commensalism and pathogenicity is poorly understood. We aimed to see whether MSSA are genetically differentiated across colonisation and SSTI; and given the close interactions between people and pets, whether strains isolated from pets differ from human strains.

Methods

We compared the genomes of contemporaneous colonisation and clinical MSSA isolates obtained in New Zealand from humans and pets.

Results

Core and accessory genome comparisons revealed a homogeneous bacterial population across colonisation, disease, humans, and pets. The rate of MSSA colonisation in dogs was comparatively low (5.4%).

Conclusions

In New Zealand, most Sa-SSTI morbidity is caused by a random sample of the colonising MSSA population, consistent with the opportunistic infection model rather than the paradigm distinguishing strains according to their pathogenicity. Thus, studies of the factors determining colonisation and immune-escape may be more beneficial than comparative virulence studies. Contact with house-hold pets may pose low zoonotic risk.\n\nGenomic epidemiology of methicillin-susceptible Staphylococcus aureus across colonisation and skin and soft tissue infection.", "token_count": 398, "char_count": 1603, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:00.200267", "source": { "split": "train_shard_00001", "doc_id": 4472 }, "chunk_id": "train_shard_00001_4472_0", "global_id": 11991 }, { "text": "The mucophilic anaerobic bacterium Akkermansia muciniphila is a prominent member of the gastrointestinal (GI) microbiota and the only known species of the Verrucomicrobia phylum in the mammalian gut. A high prevalence of A. muciniphila in adult humans is associated with leanness and a lower risk for the development of obesity and diabetes. Four distinct A. muciniphila phylogenetic groups have been described, but little is known about their relative abundance in humans or how they impact human metabolic health. In this study, we isolated and characterized 71 new A. muciniphila strains from a cohort of children and adolescents undergoing treatment for obesity. Based on genomic and phenotypic analysis of these strains, we found several phylogroup-specific phenotypes that may impact the colonization of the GI tract or modulate host functions, such as oxygen tolerance, adherence to epithelial cells, iron and sulfur metabolism, and bacterial aggregation. In antibiotic-treated mice, phylogroups AmIV and AmII outcompeted AmI strains. In children and adolescents, AmI strains were most prominent, but we observed high variance in A. muciniphila abundance and single phylogroup dominance, with phylogroup switching occurring in a small subset of patients. Overall, these results highlight that the ecological principles determining which A. muciniphila phylogroup predominates in humans are complex and that A. muciniphila strain genetic and phenotypic diversity may represent an important variable that should be taken into account when making inferences as to this microbe's impact on its host's health.IMPORTANCE The abundance of Akkermansia muciniphila in the gastrointestinal (GI) tract is linked to multiple positive health outcomes. There are four known A", "token_count": 506, "char_count": 1841, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6304, "quality_score": 0.8152, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:00.864022", "source": { "split": "train_shard_00001", "doc_id": 4473 }, "chunk_id": "train_shard_00001_4473_0", "global_id": 11992 }, { "text": "muciniphila phylogroups, yet the prevalence of these phylogroups and how they vary in their ability to influence human health is largely unknown. In this study, we performed a genomic and phenotypic analysis of 71 A. muciniphila strains and identified phylogroup-specific traits such as oxygen tolerance, adherence, and sulfur acquisition that likely influence colonization of the GI tract and differentially impact metabolic and immunological health. In humans, we observed that single Akkermansia phylogroups predominate at a given time but that the phylotype can switch in an individual. This collection of strains provides the foundation for the functional characterization of A. muciniphila phylogroup-specific effects on the multitude of host outcomes associated with Akkermansia colonization, including protection from obesity, diabetes, colitis, and neurological diseases, as well as enhanced responses to cancer immunotherapies.\n\nGenotypic and Phenotypic Diversity among Human Isolates of Akkermansia muciniphila.", "token_count": 278, "char_count": 1054, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7194, "quality_score": 0.8597, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:01.413294", "source": { "split": "train_shard_00001", "doc_id": 4473 }, "chunk_id": "train_shard_00001_4473_1", "global_id": 11993 }, { "text": "

Objectives

Intestinal colonization with extended-spectrum cephalosporin-resistant (ESC-R) and colistin-resistant (CST-R) Enterobacterales (Ent) can be driven by contact with colonized animals and/or contamination of the food chain. We studied the ESC-R-Ent and COL-R-Ent colonizing poultry as well as contaminating chicken meat in Zanzibar (Tanzania). Results were compared with recently published data obtained from rectal swabs of people in the community.

Methods

During June and July 2018, we collected poultry faecal material (n = 62) and retail chicken meat (n = 37) samples. ESC-R and CST-R strains were isolated implementing selective approaches and characterized with different molecular methods, including WGS coupled with core-genome analyses.

Results

The prevalence of ESC-R-Ent and CST-R-Ent, respectively, were: 88.7% and 48.4% in poultry; and 43.2% and 18.9% in chicken meat. Overall, the following strains and main resistance mechanisms were found in the two settings: 69 ESC-R Escherichia coli (CTX-M-15 subgroup, 75%), 34 ESC-R Klebsiella pneumoniae (CTX-M-9 group, 54.5%), 24 non-ESC-R but CST-R E. coli (mcr-1, 95.8%) and 17 non-ESC-R but CST-R K. pneumoniae (D150G substitution in PhoQ). Several clones (differing by only 0-13 single nucleotide variants) were concomitantly and frequently found in human and non-human settings: mcr-1-carrying E. coli ST46; CTX-M-15-producing E. coli ST361; CTX-M-14-producing K", "token_count": 513, "char_count": 1453, "word_count": 194, "semantic_coherence": 1, "information_density": 0.7062, "quality_score": 0.8531, "entities": { "genes": [ "ST361", "ST46" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:52:02.076297", "source": { "split": "train_shard_00001", "doc_id": 4474 }, "chunk_id": "train_shard_00001_4474_0", "global_id": 11994 }, { "text": "pneumoniae ST17; and CTX-M-15-producing K. pneumoniae ST1741.

Conclusions

This is one of the few studies that have assessed the occurrence of identical MDR Enterobacterales in human and non-human settings. The frequent human gut colonization observed in the community might be favoured by the spread of ESC-R-Ent and CST-R-Ent in poultry and chicken meat. Further studies with a One Health approach should be carried out to better investigate this phenomenon.\n\nOn the island of Zanzibar people in the community are frequently colonized with the same MDR Enterobacterales found in poultry and retailed chicken meat.", "token_count": 165, "char_count": 621, "word_count": 91, "semantic_coherence": 1, "information_density": 0.6703, "quality_score": 0.8352, "entities": { "genes": [ "ST17", "ST1741" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:02.517392", "source": { "split": "train_shard_00001", "doc_id": 4474 }, "chunk_id": "train_shard_00001_4474_1", "global_id": 11995 }, { "text": "The invention is about the production method for the immobilized lactase. It includes: (1) prepare the kluyveromyces Fragilis suspension, (2) breaking the cell wall by the enzyme, (3) breaking the cell wall by freeze-thaw, (4) breaking the cell wall by high-pressure homogenizer, (5) preparing the immobilized carrier liquid, (6) preparing the immobilized carrier liquid for lactase, (7) preparing the immobile liquid, (8) immobilization. So the low lactin milk is produced by the immobilized lactase, it can treat it continuously and the enzyme caní t run off. So it can decrease the cost.\n\nProduction of curing lactase", "token_count": 169, "char_count": 620, "word_count": 96, "semantic_coherence": 1, "information_density": 0.5938, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:02.966345", "source": { "split": "train_shard_00001", "doc_id": 4475 }, "chunk_id": "train_shard_00001_4475_0", "global_id": 11996 }, { "text": "An integrated approach including phenotypic (morphological, biochemical and physiological characterization) and genotypic (RAPD-PCR, sequencing of D1/D2 domain of 26S rRNA encoding gene) methods was used for the identification of yeasts isolated from different milk products. There were 513 isolates in all, 460 ascomycetous and 53 basidiomycetous yeasts. The yeast isolates were characterized on the basis of their biochemical and physiological properties, and the D1/D2 domain of 26S rDNA was sequenced in selected strains. Relying on the obtained results from both the data-sets, corresponding type strains were selected and compared with the respective yeast isolates from milk products by RAPD fingerprinting. The strains showing a degree of similarity >80% were considered conspecific. By means of the applied techniques it was possible to identify 92% yeast isolates at species level. Debaryomyces hansenii, Geotrichum candidum, Kluyveromyces marxianus, Yarrowia lipolytica and Candida zeylanoides are the most frequently isolated species. The majority of the yeasts were isolated from fresh and sour curd cheese. A comparison of the results obtained by phenotypic and genotypic investigation revealed that the identification based on classical methods was supported by genotypic characterization in only 54% of examined isolates. The results described in this work show that the applied molecular identification is a reliable approach to the identification of yeasts associated with milk products in contrast to the conventional biochemical and physiological tests. The identification of new yeast species requires additional genetic markers such as sequencing of different genes or DNA:DNA hybridization.\n\nIdentification of yeasts associated with milk products using traditional and molecular techniques.", "token_count": 426, "char_count": 1813, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5613, "quality_score": 0.7806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:03.590185", "source": { "split": "train_shard_00001", "doc_id": 4476 }, "chunk_id": "train_shard_00001_4476_0", "global_id": 11997 }, { "text": "

ABSTRACT

The Bacillus cereus group comprises numerous closely related species, including bioterrorism agent B. anthracis, foodborne pathogen B. cereus , and biopescticide B. thuringiensis . Differentiating organisms capable of causing illness or death from those used in industry is essential for risk assessment and outbreak preparedness. However, current species definitions facilitate species-phenotype incongruencies, particularly when horizontally acquired genes are responsible for a phenotype. Using all publicly available B. cereus group genomes ( n = 2,231), we show that current genomospecies definitions lead to overlapping species clusters, and that an average nucleotide identity (ANI) genomospecies threshold of ≈92.5 reflects a natural gap in core genome similarity. We propose a taxonomy for the B. cereus group which accounts for (i) genomospecies using separable species clusters formed at a threshold of ≈92.5 ANI, and (ii) phenotypes relevant to public health and industry. We anticipate that the proposed nomenclature will remain interpretable to clinicians, without sacrificing genomic species definitions, which can in turn aid in pathogen surveillance, early detection of emerging, high-risk genotypes, and outbreak preparedness. Furthermore, the nomenclatural framework outlined here serves as a model for genomics-based bacterial taxonomy which moves beyond arbitrarily set genomospecies thresholds, while maintaining congruence with phenotypes and historically important species names.\n\nProposal of a taxonomic nomenclature for theBacillus cereusgroup which reconciles genomic definitions of bacterial species with clinical and industrial phenotypes", "token_count": 395, "char_count": 1692, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6861, "quality_score": 0.843, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:04.212813", "source": { "split": "train_shard_00001", "doc_id": 4477 }, "chunk_id": "train_shard_00001_4477_0", "global_id": 11998 }, { "text": "Abstract

Background

MRSA BSIs have 15-50% mortality and are commonly diagnosed in US hospitals. However, the frequency of hospital transmission of MRSA causing BSI is unknown.

Methods

We performed Illumina shotgun whole genome sequencing (WGS) of 106 sequential MRSA isolates from different adults with a BSI at two Philadelphia academic hospitals in a single health system in July 2018-June 2019. We abstracted clinical data from the electronic medical record. Genomic data were analyzed preliminarily using the Staphopia Analysis Pipeline.

Results

Among 106 subjects, 51.9% were male, 47.2% were white, 46.2% were black, 23.6% were < 40 years of age, and mean age was 53.1 years (s.d. 17 years). One isolate had WGS data that were inadequate for analysis. Of 105 genomes, 52 were clonal cluster (CC) 8, 22 were sequence type (ST) 5, and 16 were ST105; the remaining 15 strains belonged to 8 other CCs. Of CC8 strains, 44 were USA300 and 6 were USA500. There were 6 clusters (i.e., < 35 SNP differences in the core genome) among the 105 isolates. Four clusters were CC5 and two were CC8 strains. One cluster of CC5 strains involved 3 subjects, and 5 clusters involved 2 subjects. One cluster of ST8/USA300 strains were separated by only 1 SNP (Fig a). This and two other clustered pairs were from subjects who had overlapping hospital stays. Two of these paired subjects had an overlap in the same unit while the third pair was in the hospital together on a number of occasions (total of 40 days overlap) but never simultaneously in the same unit. The other three clustered pairs did not have temporally overlapping hospital stays, suggesting transmission via a hospital reservoir", "token_count": 497, "char_count": 1708, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6523, "quality_score": 0.8262, "entities": { "genes": [ "CC8", "ST105", "USA500", "CC5", "ST8", "USA300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:04.874043", "source": { "split": "train_shard_00001", "doc_id": 4478 }, "chunk_id": "train_shard_00001_4478_0", "global_id": 11999 }, { "text": "One of these three pairs had hospitalizations overlapping in time, one at each study hospital, before each of them had infections with the related MRSA strains. There was not a clear-cut clustering of SNP distances among the isolate genomes into transmission and non-transmission groups, with some pairs of patient isolates separated by 40-80 SNPs (Fig. b). Figure 1.

Conclusion

We were able to discern from WGS data alone that some MRSA BSIs in 2 hospitals were likely due to strains transmitted between patients. Universal WGS of BSI strains may detect MRSA outbreaks in real time, even in the absence of overlapping hospitalizations, and is an emerging strategy to detect healthcare transmission of MRSA.

Disclosures

Michael Z. David, MD PhD, GSK (Consultant)\n\n852. Genomic Clusters of Methicillin-Resistant Staphylococcus aureus (MRSA) Causing Bloodstream Infections (BSIs) in Hospitalized Adults, 2018-19", "token_count": 255, "char_count": 927, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7664, "quality_score": 0.8832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:05.365392", "source": { "split": "train_shard_00001", "doc_id": 4478 }, "chunk_id": "train_shard_00001_4478_1", "global_id": 12000 }, { "text": "The anaerobic Gram-positive coccus Finegoldia magna is a rare cause of infections of bone and joints. The aim of this study was to describe the microbiological and clinical characteristics of orthopedic implant-associated infections caused by F. magna We retrospectively analyzed samples consisting of anaerobic Gram-positive cocci and samples already identified as F. magna from patients with orthopedic infections. The isolates found were determined to the species level using matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). The antibiotic susceptibility pattern was determined by Etest. Whole-genome sequencing (WGS) was performed. Clinical data were extracted from each patient's journal. In nine patients, orthopedic joint implant-associated infections were identified as being caused by F. magna The isolates were susceptible to most of the antibiotics tested, with the exception of rifampin and moxifloxacin in a few cases. Five of the nine infections were monomicrobial. The most common antibiotic used to treat the infection was penicillin V, but five of the nine patients received a combination of antibiotics. Eight patients underwent surgical treatment, with extraction of the implant performed in seven cases and reimplantation in only two cases. The WGS showed a relatively small core genome, with 126,647 single nucleotide polymorphisms identified within the core genome. A phylogenomic analysis revealed that the isolates clustered into two distinct clades. Orthopedic implant-associated infections caused by F. magna are rare, but the bacteria are generally susceptible to antibiotics. Despite this, surgical treatment combined with long-term antibiotics is often necessary. The WGS analysis revealed a high heterogeneity and suggested the existence of at least two different Finegoldia species.\n\nFinegoldia magna Isolated from Orthopedic Joint Implant-Associated Infections.", "token_count": 505, "char_count": 1979, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5651, "quality_score": 0.7825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:06.017902", "source": { "split": "train_shard_00001", "doc_id": 4479 }, "chunk_id": "train_shard_00001_4479_0", "global_id": 12001 }, { "text": "

Background

Gastrointestinal infections are a global public health problem. In Burkina Faso, West Africa, exposure to Salmonella through the consumption of unhygienic street food represents a major risk of infection requiring detailed evaluation.

Methods

Between June 2017 and July 2018, we sampled 201 street food stalls, in 11 geographic sectors of Ouagadougou, Burkina Faso. We checked for Salmonella contamination in 201 sandwiches (one per seller), according to the ISO 6579:2002 standard. All Salmonella isolates were characterized by serotyping and antimicrobial susceptibility testing, and whole-genome sequencing was performed on a subset of isolates, to investigate their phylogenetic relationships and antimicrobial resistance determinants.

Results

The prevalence of Salmonella enterica was 17.9% (36/201) and the Salmonella isolates belonged to 16 different serotypes, the most frequent being Kentucky, Derby and Tennessee, with five isolates each. Six Salmonella isolates from serotypes Brancaster and Kentucky were multidrug-resistant (MDR). Whole-genome sequencing revealed that four of these MDR isolates belonged to the emergent S. enterica serotype Kentucky clone ST198-X1 and to an invasive lineage of S. enterica serotype Enteritidis (West African clade).

Conclusion

This study reveals a high prevalence of Salmonella spp. in sandwiches sold in Ouagadougou. The presence of MDR Salmonella in food on sale detected in this study is also matter of concern.\n\nContamination of street food with multidrug-resistant Salmonella, in Ouagadougou, Burkina Faso.", "token_count": 460, "char_count": 1599, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8152, "entities": { "genes": [ "ST198" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:06.663851", "source": { "split": "train_shard_00001", "doc_id": 4480 }, "chunk_id": "train_shard_00001_4480_0", "global_id": 12002 }, { "text": "Methanogenic archaea are a group of microorganisms found in the gastrointestinal tract of various herbivores and humans; however, the quantity (intensity) of methane emissions during feed digestion varies. Macropodids, such as the Eastern Gray Kangaroo (Macropus giganteus), are considered to be low methane-emitting animals, but their gut methanogenic archaea remain poorly characterized. Characterizing methanogens from animals with low methane emissions offers the potential to develop strategies and interventions that reduce methane emissions from livestock. In this study, we describe a novel strain of Methanobrevibacter gottschalkii (EGK), the first Methanobrevibacter isolate from a marsupial host. Comparative analyses with other M. gottschalkii genomes revealed a high degree of gene conservation, along with strain-specific differences in genes related to membrane transport, xenobiotic metabolism, nucleotide metabolism, and the metabolism of cofactors and vitamins. Notably, the M. gottschalkii EGK genome contains multiple copies of large proviral elements, likely acquired through integration events in this strain. M. gottschalkii EGK is the first isolated representative of Methanobrevibacter from a low methane-emitting animal, providing a valuable reference genome to identify metabolic targets for methane mitigation.\n\nIsolation of a Methanobrevibacter gottschalkii strain from an Eastern Gray Kangaroo.", "token_count": 401, "char_count": 1480, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6649, "quality_score": 0.8324, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:07.293315", "source": { "split": "train_shard_00001", "doc_id": 4481 }, "chunk_id": "train_shard_00001_4481_0", "global_id": 12003 }, { "text": "An expert panel was convened in September 2019 by The International Scientific Association for Probiotics and Prebiotics (ISAPP) to develop a definition for fermented foods and to describe their role in the human diet. Although these foods have been consumed for thousands of years, they are receiving increased attention among biologists, nutritionists, technologists, clinicians and consumers. Despite this interest, inconsistencies related to the use of the term 'fermented' led the panel to define fermented foods and beverages as \"foods made through desired microbial growth and enzymatic conversions of food components\". This definition, encompassing the many varieties of fermented foods, is intended to clarify what is (and is not) a fermented food. The distinction between fermented foods and probiotics is further clarified. The panel also addressed the current state of knowledge on the safety, risks and health benefits, including an assessment of the nutritional attributes and a mechanistic rationale for how fermented foods could improve gastrointestinal and general health. The latest advancements in our understanding of the microbial ecology and systems biology of these foods were discussed. Finally, the panel reviewed how fermented foods are regulated and discussed efforts to include them as a separate category in national dietary guidelines.\n\nThe International Scientific Association for Probiotics and Prebiotics (ISAPP) consensus statement on fermented foods.", "token_count": 318, "char_count": 1485, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:07.859536", "source": { "split": "train_shard_00001", "doc_id": 4482 }, "chunk_id": "train_shard_00001_4482_0", "global_id": 12004 }, { "text": "By complementation the ode - mutation of K. lactis, the KfADES, 7 gene was cloned from K. fragilis DNA library. The full length of this gene is 4975bp which encodes 793 amino acid residues. There is 68.3% identity at amino acid sequence between K. fragilis and S. cerevisiae. Deletion analysis on the fused KfADES, 7-lacZ gene revealed that two regions of KfADES, 7 can enhance the transcription and other two regions can attenuate the transcription, and the promoter region can assure the initiation of transcription.\n\nCloning of ADE5,7 Gene from Kluyveromyces fragilis and Struc- tural and Functional Study on its 5' Untranslated Region", "token_count": 193, "char_count": 638, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6602, "quality_score": 0.8301, "entities": { "genes": [ "ADE5" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:08.313200", "source": { "split": "train_shard_00001", "doc_id": 4483 }, "chunk_id": "train_shard_00001_4483_0", "global_id": 12005 }, { "text": "Biomass of food yeast Kluyveromyces fragilis (MTCC 188) grown on deproteinized whey supplemented with 0.8% diammonium hydrogen phosphate and 10 ppm indole-3-acetic acid, had a crude protein content of 37%. The true protein content based on nitrogen fractionation procedure was 28.1%. Total nucleic acid content was 4.82%. This amount does not appear to be toxicologically offensive. Crude fiber, ash, and lipid content of K.fragilis dry cells were found to be 4.9%, 16%, and 7.8%, respectively. Essential fatty acids of both omega-3 and omega-6 series were found present in the fat of the yeast and represented 21.5% of the total fatty acids. All the essential amino acids were present in the proteins of K. fragilis; however, sulfur containing amino acids were found in lower amounts. Calculated protein scores indicate moderate biological value. B vitamins in the biomass were present as expected, but folic acid and pyridoxine were present in high concentration.\n\nNutritional profile of food yeast Kluyveromyces fragilis biomass grown on whey.", "token_count": 294, "char_count": 1046, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:08.875252", "source": { "split": "train_shard_00001", "doc_id": 4484 }, "chunk_id": "train_shard_00001_4484_0", "global_id": 12006 }, { "text": "

Background

Lactobacillus reuteri is a gut symbiont of a wide variety of vertebrate species that has diversified into distinct phylogenetic clades which are to a large degree host-specific. Previous work demonstrated host specificity in mice and begun to determine the mechanisms by which gut colonisation and host restriction is achieved. However, how L. reuteri strains colonise the gastrointestinal (GI) tract of pigs is unknown.

Results

To gain insight into the ecology of L. reuteri in the pig gut, the genome sequence of the porcine small intestinal isolate L. reuteri ATCC 53608 was completed and consisted of a chromosome of 1.94 Mbp and two plasmids of 138.5 kbp and 9.09 kbp, respectively. Furthermore, we generated draft genomes of four additional L. reuteri strains isolated from pig faeces or lower GI tract, lp167-67, pg-3b, 20-2 and 3c6, and subjected all five genomes to a comparative genomic analysis together with the previously completed genome of strain I5007. A phylogenetic analysis based on whole genomes showed that porcine L. reuteri strains fall into two distinct clades, as previously suggested by multi-locus sequence analysis. These six pig L. reuteri genomes contained a core set of 1364 orthologous gene clusters, as determined by OrthoMCL analysis, that contributed to a pan-genome totalling 3373 gene clusters. Genome comparisons of the six pig L. reuteri strains with 14 L. reuteri strains from other host origins gave a total pan-genome of 5225 gene clusters that included a core genome of 851 gene clusters but revealed that there were no pig-specific genes per se", "token_count": 459, "char_count": 1614, "word_count": 250, "semantic_coherence": 1, "information_density": 0.604, "quality_score": 0.802, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:09.523202", "source": { "split": "train_shard_00001", "doc_id": 4485 }, "chunk_id": "train_shard_00001_4485_0", "global_id": 12007 }, { "text": "However, genes specific for and conserved among strains of the two pig phylogenetic lineages were detected, some of which encoded cell surface proteins that could contribute to the diversification of the two lineages and their observed host specificity.

Conclusions

This study extends the phylogenetic analysis of L. reuteri strains at a genome-wide level, pointing to distinct evolutionary trajectories of porcine L. reuteri lineages, and providing new insights into the genomic events in L. reuteri that occurred during specialisation to their hosts. The occurrence of two distinct pig-derived clades may reflect differences in host genotype, environmental factors such as dietary components or to evolution from ancestral strains of human and rodent origin following contact with pig populations.\n\nThe pan-genome of Lactobacillus reuteri strains originating from the pig gastrointestinal tract.", "token_count": 209, "char_count": 904, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6825, "quality_score": 0.8413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:10.006432", "source": { "split": "train_shard_00001", "doc_id": 4485 }, "chunk_id": "train_shard_00001_4485_1", "global_id": 12008 }, { "text": "Klebsiella pneumoniae is one of the leading causes of nosocomial infections. Carbapenem-resistant (CR) K. pneumoniae are on the rise in India. The biofilm forming ability of K. pneumoni ae further complicates patient management. There is still a knowledge gap on the association of biofilm formation with patient outcome and carbapenem susceptibility, which is investigated in the present study. K. pneumoniae isolates from patients admitted in critical care units with catheters and ventilators were included. K. pneumoniae ( n = 72) were tested for antimicrobial susceptibility as recommended by CLSI 2019 and subjected to 96-well microtitre plate biofilm formation assay. Based on optical density at 570 nm isolates were graded as strong, moderate and weak biofilm formers. Subset of strong biofilm formers were subjected to whole genome sequencing and a core genome phylogenetic analysis in comparison with global isolates were performed. Biofilm formation was compared for an association with the carbapenem susceptibility and with patient outcome. Statistical significance, correlations and graphical representation were performed using SPSS v23.0. Phenotypic analyses showed a positive correlation between biofilm formation and carbapenem resistance. Planktonic cells observed to be susceptible in vitro exhibited higher MICs in biofilm structure. The biofilm forming ability had a significant association with the morbidity/mortality. Infections by stronger biofilm forming pathogens significantly (P<0.05) resulted in fewer ‘average days alive’ for the patient (3.33) in comparison to those negative for biofilms (11.33). Phylogenetic analysis including global isolates revealed the clear association of sequence types with genes for biofilm mechanism and carbapenem resistance. Carbapenemase genes were found specific to each clade. The known hypervirulent clone-ST23 with wcaG , magA , rmpA , rmpA2 and wzc with a lack of mutation for hyper-capsulation might be poor biofilm formers", "token_count": 492, "char_count": 1993, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6007, "quality_score": 0.8004, "entities": { "genes": [ "ST23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:10.686524", "source": { "split": "train_shard_00001", "doc_id": 4486 }, "chunk_id": "train_shard_00001_4486_0", "global_id": 12009 }, { "text": "Interestingly, ST15, ST16, ST307 and ST258 – reported global high-risk clones were wcaJ negative indicating the high potential of biofilm forming capacity. Genes wabG and treC for CPS, bcsA and pgaC for adhesins, luxS for quorum sensing were common in all clades in addition to genes for aerobactin ( iutA ), allantoin ( allS ), type I and III fimbriae ( fimA , fimH , mrkD ) and pili ( pilQ , ecpA ). This study is the first of its kind to compare genetic features of antimicrobial resistance with a spectrum covering most of the genetic factors for K. pneumoniae biofilm. These results highlight the importance of biofilm screening to effectively manage nosocomial infections by K. pneumoniae . Further, data obtained on epidemiology and associations of biofilm and antimicrobial resistance genetic factors will serve to enhance our understanding on biofilm mechanisms in K. pneumoniae .\n\nThe influence of biofilm formation on carbapenem resistance in clinicalKlebsiella pneumoniaeinfections: phenotype vs genome-wide analysis", "token_count": 280, "char_count": 1035, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6832, "quality_score": 0.8416, "entities": { "genes": [ "ST15", "ST16", "ST258", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:11.267869", "source": { "split": "train_shard_00001", "doc_id": 4486 }, "chunk_id": "train_shard_00001_4486_1", "global_id": 12010 }, { "text": "Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug-resistant (MDR) strains. During the COVID-19 pandemic, MDR A. baumannii clones have caused several outbreaks worldwide. Here, we describe a detailed investigation of an MDR A. baumannii outbreak that occurred at Policlinico San Matteo (Pavia, Italy). A total of 96 A. baumannii strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive and negative) in different wards, were characterized by phenotypic and genomic analyses combining Illumina and Nanopore sequencing. Antibiotic susceptibility testing revealed that all isolates were resistant to carbapenems, and the sequence analysis attributed this to the carbapenemase gene blaOXA-23. Virulence factor screening unveiled that all strains carried determinants for biofilm formation, while plasmid analysis revealed the presence of two plasmids, one of which was ~100 kbp long and encoded a phage sequence. A core genome-based phylogeny was inferred to integrate outbreak strain genomes with background genomes from public databases and the local surveillance program. All strains belonged to the globally disseminated sequence type 2 (ST2) clone and were mainly divided into two clades. Isolates from the outbreak clustered with surveillance isolates from 2019, suggesting that the outbreak was caused by two strains that were already circulating in the hospital before the start of the pandemic. The intensive spread of A. baumannii in the hospital was enhanced by the extreme emergency situation of the first COVID-19 pandemic wave that resulted in reduced attention to infection prevention and control practices. IMPORTANCE The COVID-19 pandemic, especially during the first wave, posed a great challenge to the hospital management and generally promoted nosocomial pathogen dissemination. MDR A. baumannii can easily spread and persist for a long time on surfaces, causing outbreaks in health care settings", "token_count": 502, "char_count": 2042, "word_count": 294, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:11.965437", "source": { "split": "train_shard_00001", "doc_id": 4487 }, "chunk_id": "train_shard_00001_4487_0", "global_id": 12011 }, { "text": "Infection prevention and control practices, epidemiological surveillance, and microbiological screening are fundamental in order to control such outbreaks. Here, we sequenced the genomes of 96 isolates from an outbreak of MDR A. baumannii strains using both short- and long-read technology in order to reconstruct the outbreak events in fine detail. The sequence data demonstrated that two endemic clones of MDR A. baumannii were the source of this large hospital outbreak during the first COVID-19 pandemic wave, confirming the effect of COVID-19 emergency disrupting the protection provided by the use of the standard prevention procedures.\n\nThe COVID-19 Pandemic Sparked Off a Large-Scale Outbreak of Carbapenem-Resistant Acinetobacter baumannii from the Endemic Strains at an Italian Hospital.", "token_count": 184, "char_count": 797, "word_count": 114, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:12.410055", "source": { "split": "train_shard_00001", "doc_id": 4487 }, "chunk_id": "train_shard_00001_4487_1", "global_id": 12012 }, { "text": "

ABSTRACT

Background

A variety of rapid molecular PCR tests has been developed and commercialised that interrogate the junction site between the staphylococcal core genome, and the mobile genetic element (SCC mec ) which harbours the gene responsible for methicillin-/beta-lactam-resistance.

Aim

The purpose of the present study was to investigate why a clinical MRSA isolate yielded false negative test results with widely used, commercial orfX /SCC mec junction site PCR tests.

Methods

A collection of isolates that belonged to the same epidemic strain as the index isolate were investigated with commercial MRSA assays and all isolates were sequenced in order to explain this observation.

Results

It was found that isolates of the epidemic “European CC1-MRSA-IV” clone, which likely originated in South-Eastern Europe and subsequently spread to Western Europe, generally exhibit this behaviour. The failure of the assays was attributable to a characteristic large insertion in the orfX /SCC mec integration site presumably targeted by such tests. In contrast to MW2 (GenBank BA000033.2 , a CC1 “USA400” strain which also harbours SCC mec IVa), the European CC1 clone harbours an insertion of ca . 5,350 nucleotides adjacent to orfX . This sequence starts with a novel SCC terminal sequence alternate to dcs and encodes six different hypothetical proteins (E7MHX1, ydiL 2, C5QAP8, A8YYX4, npd- SCC, H4AYD7; nucleotide positions 280,690–286,024 of GenBank RBVO000005.1). An SCC mec element with the same insertion was previously found in a Staphylococcus epidermidis isolate (GenBank MH188467.1 ) suggesting transfer between staphylococcal species", "token_count": 496, "char_count": 1692, "word_count": 244, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [ "RBVO000005", "MH188467", "MW2", "USA400", "BA000033", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:13.057470", "source": { "split": "train_shard_00001", "doc_id": 4488 }, "chunk_id": "train_shard_00001_4488_0", "global_id": 12013 }, { "text": "

Conclusion

In order to ensure the reliability of molecular MRSA tests, it is vital to monitor the emergence of new SCC mec junction sites, not only in Staphylococcus aureus but also in coagulase-negative staphylococci.\n\nAn epidemic CC1-MRSA-IV clone yields false negative test results in molecular MRSA identification assays: a note of caution", "token_count": 99, "char_count": 352, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8269, "quality_score": 0.9135, "entities": { "genes": [ "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:13.444568", "source": { "split": "train_shard_00001", "doc_id": 4488 }, "chunk_id": "train_shard_00001_4488_1", "global_id": 12014 }, { "text": "Abstract

Background: In bacteria, pan-genomes are the result of an evolutionary \"tug of war\" between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size (Ne), resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT and mutation, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses, elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes. Results: We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high Ne estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low Ne, suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.005 to 2.725, which are similar to oceanic Vibrionaceae estimations. However, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation, purging the genomes and keeping closed pan-genome patterns", "token_count": 461, "char_count": 1796, "word_count": 241, "semantic_coherence": 1, "information_density": 0.6224, "quality_score": 0.8112, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:14.093598", "source": { "split": "train_shard_00001", "doc_id": 4489 }, "chunk_id": "train_shard_00001_4489_0", "global_id": 12015 }, { "text": "Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes associated with these SNPs were related to sodium transport.Conclusions: Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported for the first time. Most Vibrionaceae lineages of CCB are adapted to their micro-habitats rather than to the sampled environments. This pattern of adaptation is concordant with the association of closed pan-genomes and local adaptation.

\n\nPopulation genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation.", "token_count": 161, "char_count": 727, "word_count": 100, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:14.537063", "source": { "split": "train_shard_00001", "doc_id": 4489 }, "chunk_id": "train_shard_00001_4489_1", "global_id": 12016 }, { "text": "High temperature and agitation are advantageous for ethanol production from insoluble feedstock when using the simultaneous saccharification and fermentation (SSF) technique. To construct an effective SSF system, a respiratory-deficient mutant was isolated from the thermotolerant yeast Candida glabrata. Our results suggest that this respiratory-deficient mutant has higher ethanol production abilities in SSF.\n\nStrategy for simultaneous saccharification and fermentation using a respiratory-deficient mutant of Candida glabrata for bioethanol production.", "token_count": 133, "char_count": 556, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7353, "quality_score": 0.8676, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:14.963487", "source": { "split": "train_shard_00001", "doc_id": 4490 }, "chunk_id": "train_shard_00001_4490_0", "global_id": 12017 }, { "text": "The airways of individuals with cystic fibrosis (CF) often become chronically infected with unique strains of the opportunistic pathogen Pseudomonas aeruginosa. Several lines of evidence suggest that the infecting P. aeruginosa lineage diversifies in the CF lung niche, yet so far this contemporary diversity has not been investigated at a genomic level. In this work, we sequenced the genomes of pairs of randomly selected contemporary isolates sampled from the expectorated sputum of three chronically infected adult CF patients. Each patient was infected by a distinct strain of P. aeruginosa. Single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) were identified in the DNA common to the paired isolates from different patients. The paired isolates from one patient differed due to just 1 SNP and 8 indels. The paired isolates from a second patient differed due to 54 SNPs and 38 indels. The pair of isolates from the third patient both contained a mutS mutation, which conferred a hypermutator phenotype; these isolates cumulatively differed due to 344 SNPs and 93 indels. In two of the pairs of isolates, a different accessory genome composition, specifically integrated prophage, was identified in one but not the other isolate of each pair. We conclude that contemporary isolates from a single sputum sample can differ at the SNP, indel, and accessory genome levels and that the cross-sectional genomic variation among coeval pairs of P. aeruginosa CF isolates can be comparable to the variation previously reported to differentiate between paired longitudinally sampled isolates.\n\nGenomic variation among contemporary Pseudomonas aeruginosa isolates from chronically infected cystic fibrosis patients.", "token_count": 409, "char_count": 1729, "word_count": 257, "semantic_coherence": 1, "information_density": 0.537, "quality_score": 0.7685, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:15.589976", "source": { "split": "train_shard_00001", "doc_id": 4491 }, "chunk_id": "train_shard_00001_4491_0", "global_id": 12018 }, { "text": "

Background

Currently, hospitals have been forced to divert substantial resources to cope with the ongoing coronavirus disease 2019 (COVID-19) pandemic. It is unclear if this situation will affect long-standing infection prevention practices and impact on healthcare associated infections. Here, we report a nosocomial cluster of vancomycin-resistant enterococci (VRE) that occurred on a COVID-19 dedicated intensive care unit (ICU) despite intensified contact precautions during the current pandemic. Whole genome sequence-based typing (WGS) was used to investigate genetic relatedness of VRE isolates collected from COVID-19 and non-COVID-19 patients during the outbreak and to compare them to environmental VRE samples.

Methods

Five VRE isolated from patients (three clinical and two screening samples) as well as 11 VRE and six vancomycin susceptible Enterococcus faecium (E. faecium) samples from environmental sites underwent WGS during the outbreak investigation. Isolate relatedness was determined using core genome multilocus sequence typing (cgMLST).

Results

WGS revealed two genotypic distinct VRE clusters with genetically closely related patient and environmental isolates. The cluster was terminated by enhanced infection control bundle strategies.

Conclusions

Our results illustrate the importance of continued adherence to infection prevention and control measures during the COVID-19 pandemic to prevent VRE transmission and healthcare associated infections.\n\nA nosocomial cluster of vancomycin resistant enterococci among COVID-19 patients in an intensive care unit.", "token_count": 380, "char_count": 1612, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:16.179379", "source": { "split": "train_shard_00001", "doc_id": 4492 }, "chunk_id": "train_shard_00001_4492_0", "global_id": 12019 }, { "text": "The thermotolerant yeast strain isolated from sugarcane juice through enrichment technique was identified as a strain of Pichiakudriavzevii (Issatchenkiaorientalis) through molecular characterization. The P. kudriavzevii cells adapted to galactose medium produced about 30% more ethanol from sugarcane juice than the non-adapted cells. The recycled cells could be used for four successive cycles without a significant drop in ethanol production. Fermentation in a laboratory fermenter with galactose adapted P. kudriavzevii cells at 40°C resulted in an ethanol concentration and productivity of 71.9 g L(-1) and 4.0 g L(-1)h(-1), respectively from sugarcane juice composed of about 14% (w/v) sucrose, 2% (w/v) glucose and 1% (w/v) fructose. In addition to ethanol, 3.30 g L(-1) arabitol and 4.19 g L(-1) glycerol were also produced, whereas sorbitol and xylitol were not formed during fermentation. Use of galactose adapted P. kudriavzevii cells for ethanol production from sugarcane juice holds potential for scale-up studies.\n\nEnhanced ethanol production from sugarcane juice by galactose adaptation of a newly isolated thermotolerant strain of Pichia kudriavzevii.", "token_count": 349, "char_count": 1167, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.8061, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:16.760835", "source": { "split": "train_shard_00001", "doc_id": 4493 }, "chunk_id": "train_shard_00001_4493_0", "global_id": 12020 }, { "text": "

Purpose of review

Largely due to its recognition as a biological threat agent, current knowledge on melioidosis, caused by the Gram-negative bacterium Burkholderia pseudomallei, has increased tremendously over the last years. This review summarizes current understanding on the molecular characterization of B. pseudomallei and the immunology of melioidosis.

Recent findings

The genome of B. pseudomallei is composed of two chromosomes of which the largest part represents the B. pseudomallei core genome, whereas the remaining accessory genome has been associated with bacterial virulence. Virulence factors, most notably quorum sensing, type III secretion system, lipopolysaccharide and other surface polysaccharides, flagella and various factors essential for the intracellular life cycle of B. pseudomallei, have been further characterized. The neutrophils play a critical in host defense, which is initiated by the Toll-like receptors. The proinflammatory immune response--including the activation of coagulation-- and its regulation have been further dissected.

Summary

Severe melioidosis can probably be seen as the clinical manifestation of a pathogen recognition receptor mediated dysregulation of the immune response to invading B. pseudomallei. B. pseudomallei employs numerous tactics to evade the immune response. Studies on host-pathogen interactions in melioidosis have identified a whole range of potential new treatment targets.\n\nImmunity to Burkholderia pseudomallei.", "token_count": 367, "char_count": 1507, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:17.339929", "source": { "split": "train_shard_00001", "doc_id": 4494 }, "chunk_id": "train_shard_00001_4494_0", "global_id": 12021 }, { "text": "Mixed aza-oxo-thia macrocyclic ligands 1,3,5,11,13,15-hexaaza-6,10,16,20-tetraoxo-8,18-dithia-2,3,4:12,13,14-dipyridine cyclocosane (L(1)); 1,3,5,12,14,16-hexeaza-6,11,17,22-tetraoxo-8,9,19,20-tetrathia-2,3,4:13,14,15-dipyridine cyclodocosane (L(2)); 1,3,5,13,15,17-hexaaza-6,12,18,24-tetraoxo-9,21-dithia-2,3,4:14,15,16-dipyridine cyclotetracosane (L(3)) and 1,3,5,14,16,18-hexaaza-6,13,19,26-tetraoxo-9,10,22,23-tetrathia-2,3,4:15,16,17-dipyridine cyclohexacosane (L(4)) were synthesised. The structural features of the ligands have been studied by elemental analyses, Raman, IR, (1)H and (13)C NMR spectroscopy. The antimicrobial activities of the ligands were evaluated using disk diffusion method in dimethyl sulfoxide (DMSO) as well as the minimal inhibitory concentration (MIC) dilution method, against nine bacteria. The obtained results from disk diffusion method were assessed in side-by-side comparison with those of penicillin G, ampicillin, cefotaxime, vancomycin, ofloxacin, and tetracycline well known antibacterial agents. The results from dilution procedure were compared with gentamycin as antibacterial and nystatin as antifungal", "token_count": 512, "char_count": 1148, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7339, "quality_score": 0.867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:17.993827", "source": { "split": "train_shard_00001", "doc_id": 4495 }, "chunk_id": "train_shard_00001_4495_0", "global_id": 12022 }, { "text": "The antifungal activities are reported on five yeast cultures namely Candida albicans, Kluyveromyces fragilis, Rhodotorula rubra, Debaryomyces hansenii, and Hanseniaspora guilliermondii, and the results are referenced with nystatin, Ketoconazole, and clotrimazole, commercial antifungal agents. In most cases, the compounds show broad-spectrum (Gram(+) and Gram(-) bacteria) activities that were more active or equipotent to the antibiotic and antifungal agents in the comparison tests.\n\nSynthesis, Raman, FT-IR, NMR spectroscopic data and antimicrobial activity of mixed aza-oxo-thia macrocyclic compounds.", "token_count": 178, "char_count": 607, "word_count": 76, "semantic_coherence": 1, "information_density": 0.8158, "quality_score": 0.9079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:18.437816", "source": { "split": "train_shard_00001", "doc_id": 4495 }, "chunk_id": "train_shard_00001_4495_1", "global_id": 12023 }, { "text": "This study characterized five Cronobacter spp. and six Salmonella spp. strains that had been isolated from 155 samples of powdered infant formula (PIF) sold in Chile and manufactured in Chile and Mexico in 2018-2020. Two strains of Cronobacter sakazakii sequence type (ST) ST1 and ST31 (serotypes O:1 and O:2) and one strain of Cronobacter malonaticus ST60 (O:1) were identified. All Salmonella strains were identified as Salmonella Typhimurium ST19 (serotype O:4) by average nucleotide identity, ribosomal multilocus sequence typing (rMLST), and core genome MLST (cgMLST). The C. sakazakii and C. malonaticus isolates were resistant to cephalothin, whereas the Salmonella isolates were resistant to oxacillin and ampicillin. Nineteen antibiotic resistance genes were detected in the C. sakazakii and C. malonaticus isolates; the most prevalent were mcr-9.1, blaCSA , and blaCMA . In Salmonella, 30 genes encoding for aminoglycoside and cephalosporin resistance were identified, including aac(6')-Iaa, β-lactamases ampH, ampC1, and marA", "token_count": 449, "char_count": 1184, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [ "ST60", "ST19", "ST1", "ST31" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:19.076457", "source": { "split": "train_shard_00001", "doc_id": 4496 }, "chunk_id": "train_shard_00001_4496_0", "global_id": 12024 }, { "text": "In the Cronobacter isolates, 32 virulence-associated genes were detected by WGS and clustered as flagellar proteins, outer membrane proteins, chemotaxis, hemolysins, invasion, plasminogen activator, colonization, transcriptional regulator, survival in macrophages, use of sialic acid, and toxin-antitoxin genes. In the Salmonella strains, 120 virulence associated genes were detected, adherence, magnesium uptake, resistance to antimicrobial peptides, secretion system, stress protein, toxin, resistance to complement killing, and eight pathogenicity islands. The C. sakazakii and C. malonaticus strains harbored I-E and I-F CRISPR-Cas systems and carried Col(pHHAD28) and IncFIB(pCTU1) plasmids, respectively. The Salmonella strains harbored type I-E CRISPR-Cas systems and carried IncFII(S) plasmids. The presence of C. sakazakii and Salmonella in PIF is a health risk for infants aged less than 6 months. For this reason, sanitary practices should be reinforced for its production and retail surveillance.\n\nGenomic Characterization of Cronobacter spp. and Salmonella spp. Strains Isolated From Powdered Infant Formula in Chile.", "token_count": 392, "char_count": 1193, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7181, "quality_score": 0.8591, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:19.692839", "source": { "split": "train_shard_00001", "doc_id": 4496 }, "chunk_id": "train_shard_00001_4496_1", "global_id": 12025 }, { "text": "Epidemiological projections point to acquisition of ever-expanding multidrug resistance (MDR) by Escherichia coli, a commensal of the digestive tract and a source of urinary tract pathogens. Bioinformatics analyses of a large collection of E. coli genomes from EnteroBase, enriched in clinical isolates of worldwide origins, suggest the Cytotoxic Necrotizing Factor 1 (CNF1)-toxin encoding gene, cnf1, is preferentially distributed in four common sequence types (ST) encompassing the pandemic E. coli MDR lineage ST131. This lineage is responsible for a majority of extraintestinal infections that escape first-line antibiotic treatment, with known enhanced capacities to colonize the gastrointestinal tract. Statistical projections based on this dataset point to a global expansion of cnf1-positive multidrug-resistant ST131 strains from subclade H30Rx/C2, accounting for a rising prevalence of cnf1-positive strains in ST131. Despite the absence of phylogeographical signals, cnf1-positive isolates segregated into clusters in the ST131-H30Rx/C2 phylogeny, sharing a similar profile of virulence factors and the same cnf1 allele. The suggested dominant expansion of cnf1-positive strains in ST131-H30Rx/C2 led us to uncover the competitive advantage conferred by cnf1 for gut colonization to the clinical strain EC131GY ST131-H30Rx/C2 versus cnf1-deleted isogenic strain. Complementation experiments showed that colon tissue invasion was compromised in the absence of deamidase activity on Rho GTPases by CNF1", "token_count": 507, "char_count": 1616, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [ "ST131", "CNF1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:20.348317", "source": { "split": "train_shard_00001", "doc_id": 4497 }, "chunk_id": "train_shard_00001_4497_0", "global_id": 12026 }, { "text": "Hence, gut colonization factor function of cnf1 was confirmed for another clinical strain ST131-H30Rx/C2. In addition, functional analysis of the cnf1-positive clinical strain EC131GY ST131-H30Rx/C2 and a cnf1-deleted isogenic strain showed no detectable impact of the CNF1 gene on bacterial fitness and inflammation during the acute phase of bladder monoinfection. Together these data argue for an absence of role of CNF1 in virulence during UTI, while enhancing gut colonization capacities of ST131-H30Rx/C2 and suggested expansion of cnf1-positive MDR isolates in subclade ST131-H30Rx/C2.\n\nThe cnf1 gene is associated with an expanding Escherichia coli ST131 H30Rx/C2 subclade and confers a competitive advantage for gut colonization.", "token_count": 289, "char_count": 814, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6796, "quality_score": 0.8398, "entities": { "genes": [ "ST131", "CNF1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:20.903064", "source": { "split": "train_shard_00001", "doc_id": 4497 }, "chunk_id": "train_shard_00001_4497_1", "global_id": 12027 }, { "text": "Solar crystallizer ponds are characterized by high population density with a relatively simple community structure in terms of species composition. The microbial community in the solar saltern of Santa Pola (Alicante, Spain), is largely dominated by the hyperhalophilic square archaeon Haloquadratum walsbyi. Here we studied metatranscriptomes retrieved from a crystallizer pond during the winter of 2012 and summer of 2014 and compared Hqr. walsbyi's transcription patterns with that of the cultured strain Hqr. walsbyi HBSQ001. Significant differences were found between natural and the cultured grown strain in the distribution of transcript levels per gene. This likely reflects the adaptation of the cultured strain to the relative homogeneous growth conditions while the natural species, which is represented by multiple ecotypes, is adapted to heterogeneous environmental conditions and challenges of nutrient competition, viral attack, and other stressors. An important consequence of this study is that expression patterns obtained under artificial cultivation conditions cannot be directly extrapolated to gene expression under natural conditions. Moreover, we found 195 significantly differential expressed genes between the seasons, with 140 genes being higher expressed in winter and mainly encode proteins involved in energy and carbon source acquiring processes, and in stress responses.\n\nDifferences in gene expression patterns between cultured and natural Haloquadratum walsbyi ecotypes.", "token_count": 343, "char_count": 1532, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6377, "quality_score": 0.8188, "entities": { "genes": [ "HBSQ001" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:21.477698", "source": { "split": "train_shard_00001", "doc_id": 4498 }, "chunk_id": "train_shard_00001_4498_0", "global_id": 12028 }, { "text": "Fermented dairy products (e.g., yogurt, kefir, and buttermilk) are significant in the dairy industry. They are less immunoreactive than the raw materials from which they are derived. The attractiveness of these products is based on their bioactivity and properties that induce immune or anti-inflammatory processes. In the search for new solutions, plant raw materials with beneficial effects have been combined to multiply their effects or obtain new properties. Polyphenols (e.g., flavonoids, phenolic acids, lignans, and stilbenes) are present in fruit and vegetables, but also in coffee, tea, or wine. They reduce the risk of chronic diseases, such as cancer, diabetes, or inflammation. Hence, it is becoming valuable to combine dairy proteins with polyphenols, of which epigallocatechin-3-gallate (EGCG) and chlorogenic acid (CGA) show a particular predisposition to bind to milk proteins (e.g., α-lactalbumin β-lactoglobulin, αs1-casein, and κ-casein). Reducing the allergenicity of milk proteins by combining them with polyphenols is an essential issue. As potential 'metabolic prebiotics', they also contribute to stimulating the growth of beneficial bacteria and inhibiting pathogenic bacteria in the human gastrointestinal tract. In silico methods, mainly docking, assess the new structures of conjugates and the consequences of the interactions that are formed between proteins and polyphenols, as well as to predict their action in the body.\n\nBioactive Dairy-Fermented Products and Phenolic Compounds: Together or Apart.", "token_count": 396, "char_count": 1532, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8157, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:22.108452", "source": { "split": "train_shard_00001", "doc_id": 4499 }, "chunk_id": "train_shard_00001_4499_0", "global_id": 12029 }, { "text": "Streptococcus suis is a major zoonotic pathogen that causes severe disease in both humans and pigs. In this study, we investigated S. suis from 148 cases of clinical disease in pigs from 46 pig herds over a period of seven years. These isolates underwent whole genome sequencing, genome analysis and antimicrobial susceptibility testing. Genome sequence data of Australian isolates was compared at the core genome level to clinical isolates from overseas. Results demonstrated eight predominant multi-locus sequence types and two major cps gene types (cps2 and 3). At the core genome level Australian isolates clustered predominantly within one large clade consisting of isolates from the UK, Canada and North America. In particular, serotype 2 MLST25 strains were very closely associated with Canadian and North American strains. A very small proportion of Australian swine isolates (5%) were phylogenetically associated with south-east Asian and UK isolates, many of which were classified as causing systemic disease, and derived from cases of human and swine disease. In addition, we show that ST1 clones carry a constellation of putative virulence genes not present in other Australian STs, and that this is mirrored in overseas ST1 clones. Based on this dataset we provide a comprehensive outline of the current S. suis clones associated with disease in Australian pigs and their global context, and discuss the implications this has on antimicrobial therapy, potential vaccine candidates and public health.

Importance

In this study, we examine in detail, the genomic characteristics of 148 Streptococcus suis isolates from clinically diseased Australian pigs. We report the antimicrobial susceptibility profiles, virulence gene analysis and relationship to isolates from other regions of the world. We also demonstrate that ST1 clones, regardless of serotype, carry a large array of putative virulence genes while maintaining a small total gene content. This compilation of data has major ramifications for vaccine development, and refines the understanding of the distribution of various strains of this potentially-fatal zoonotic agent in the global pig industry", "token_count": 488, "char_count": 2179, "word_count": 325, "semantic_coherence": 1, "information_density": 0.5446, "quality_score": 0.7723, "entities": { "genes": [ "ST1", "MLST25" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:22.788489", "source": { "split": "train_shard_00001", "doc_id": 4500 }, "chunk_id": "train_shard_00001_4500_0", "global_id": 12030 }, { "text": "Examination of AustralianStreptococcus suisIsolates From Clinically Affected Pigs in a Global Context and the Genomic Characterisation of ST1 as a Predictor of Virulence", "token_count": 51, "char_count": 176, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [ "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:23.170904", "source": { "split": "train_shard_00001", "doc_id": 4500 }, "chunk_id": "train_shard_00001_4500_1", "global_id": 12031 }, { "text": "In 1986, Bouvet and Grimont delineated two related taxa of the genus Acinetobacter termed genospecies (GS) 8 and 9. They proposed the name Acinetobacter lwoffii for GS8, which included the supposed type strain (CIP 64.10). As the authenticity of CIP 64.10 was later questioned, this study aimed at reassessing the taxonomy of these genospecies. We investigated 52 strains of GS8 or GS9, including CIP 64.10 and the genuine type strain of A. lwoffii (NCTC 5866T). All strains were subjected to the genus-wide comparative analyses of MALDI-TOF whole-cell mass spectra, rpoB gene sequences and metabolic traits while whole-genome sequences were analysed for 16 strains. The strains were classified into two distinct groups corresponding to GS8 (n=15) and GS9 (n=37). CIP 64.10 fell within GS8 whereas NCTC 5866T belonged to GS9. Intraspecies ANIb values for the genomes of GS8 (n=6) and GS9 (n=10) were ≥96.1% and ≥95.4%, respectively, whereas the ANIb values between them were 86.8-88.6%. Based on core genome phylogeny, GS8 and GS9 formed a distinct clade within the genus, with two respective, strongly supported subclades. GS8 and GS9 were similar in physiological and catabolic properties but were separable by MALDI-TOF MS. We conclude that the name A. lwoffii pertains to GS9 and not to GS8 as originally assumed and that these groups represent two species. We propose the name Acinetobacter pseudolwoffii sp. nov", "token_count": 468, "char_count": 1439, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [ "GS9", "GS8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:24.295352", "source": { "split": "train_shard_00001", "doc_id": 4501 }, "chunk_id": "train_shard_00001_4501_0", "global_id": 12032 }, { "text": "for GS8, with ANC 5044T (=CCM 8638T=CCUG 67963T=CIP 111642T) as the type strain, and provide the emended description of A. lwoffii.\n\nRevising the taxonomy of the Acinetobacter lwoffii group: The description of Acinetobacter pseudolwoffii sp. nov. and emended description of Acinetobacter lwoffii.", "token_count": 135, "char_count": 340, "word_count": 42, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "GS8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:24.715086", "source": { "split": "train_shard_00001", "doc_id": 4501 }, "chunk_id": "train_shard_00001_4501_1", "global_id": 12033 }, { "text": "Serotype M28 isolates of the group A Streptococcus (GAS; Streptococcus pyogenes) are nonrandomly associated with cases of puerperal sepsis, a potentially life-threatening infection that can occur in women following childbirth. Previously, we discovered that the 36.3-kb RD2 pathogenicity island, which is present in serotype M28 isolates but lacking from most other isolates, promotes the ability of M28 GAS to colonize the female reproductive tract. Here, we performed a gain-of-function study in which we introduced RD2 into representative serotype M1, M49, and M59 isolates and assessed the phenotypic consequences of RD2 acquisition. All RD2-containing derivatives colonized a higher percentage of mice, and at higher CFU levels, than did the parental isolates in a mouse vaginal colonization model. However, for two additional phenotypes, survival in heparinized whole human blood and adherence to two human vaginal epithelial cell lines, there were serotype-specific differences from RD2 acquisition. Using transcriptomic comparisons, we identified that such differences may be a consequence of RD2 altering the abundance of transcripts from select core genome genes along serotype-specific lines. Our study is the first that interrogates RD2 function in GAS serotypes other than M28 isolates, shedding light on variability in the phenotypic consequences of RD2 acquisition and informing on why this mobile genetic element is not ubiquitous in the GAS population.\n\nThe RD2 Pathogenicity Island Modifies the Disease Potential of the Group A <i>Streptococcus</i>.", "token_count": 418, "char_count": 1586, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6356, "quality_score": 0.8178, "entities": { "genes": [ "RD2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:25.336577", "source": { "split": "train_shard_00001", "doc_id": 4502 }, "chunk_id": "train_shard_00001_4502_0", "global_id": 12034 }, { "text": "Gut microbiota are shaped by a combination of ecological and evolutionary forces. While the ecological dynamics have been extensively studied, much less is known about how species of gut bacteria evolve over time. Here, we introduce a model-based framework for quantifying evolutionary dynamics within and across hosts using a panel of metagenomic samples. We use this approach to study evolution in approximately 40 prevalent species in the human gut. Although the patterns of between-host diversity are consistent with quasi-sexual evolution and purifying selection on long timescales, we identify new genealogical signatures that challenge standard population genetic models of these processes. Within hosts, we find that genetic differences that accumulate over 6-month timescales are only rarely attributable to replacement by distantly related strains. Instead, the resident strains more commonly acquire a smaller number of putative evolutionary changes, in which nucleotide variants or gene gains or losses rapidly sweep to high frequency. By comparing these mutations with the typical between-host differences, we find evidence that some sweeps may be seeded by recombination, in addition to new mutations. However, comparisons of adult twins suggest that replacement eventually overwhelms evolution over multi-decade timescales, hinting at fundamental limits to the extent of local adaptation. Together, our results suggest that gut bacteria can evolve on human-relevant timescales, and they highlight the connections between these short-term evolutionary dynamics and longer-term evolution across hosts.\n\nEvolutionary dynamics of bacteria in the gut microbiome within and across hosts.", "token_count": 339, "char_count": 1696, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8256, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:25.906869", "source": { "split": "train_shard_00001", "doc_id": 4503 }, "chunk_id": "train_shard_00001_4503_0", "global_id": 12035 }, { "text": "Campylobacter spp. are the most common cause of bacterial gastrointestinal infection in humans both in Denmark and worldwide. Studies have found microbial subtyping to be a powerful tool for source attribution, but comparisons of different methodologies are limited. In this study, we compare three source attribution approaches (Machine Learning, Network Analysis, and Bayesian modeling) using three types of whole genome sequences (WGS) data inputs (cgMLST, 5-Mers and 7-Mers). We predicted and compared the sources of human campylobacteriosis cases in Denmark. Using 7mer as an input feature provided the best model performance. The network analysis algorithm had a CSC value of 78.99% and an F1-score value of 67%, while the machine-learning algorithm showed the highest accuracy (98%). The models attributed between 965 and all of the 1224 human cases to a source (network applying 5mer and machine learning applying 7mer, respectively). Chicken from Denmark was the primary source of human campylobacteriosis with an average percentage probability of attribution of 45.8% to 65.4%, representing Bayesian with 7mer and machine learning with cgMLST, respectively. Our results indicate that the different source attribution methodologies based on WGS have great potential for the surveillance and source tracking of Campylobacter. The results of such models may support decision makers to prioritize and target interventions.\n\nComparison of Source Attribution Methodologies for Human Campylobacteriosis.", "token_count": 355, "char_count": 1513, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6343, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:26.482916", "source": { "split": "train_shard_00001", "doc_id": 4504 }, "chunk_id": "train_shard_00001_4504_0", "global_id": 12036 }, { "text": "Frequency-dependent lactose uptake via the H+/lactose symporter in an externally applied low-intensity alternating electric field was demonstrated, using tracer flux experiments. The uptake of radiolabeled lactose was significantly inhibited with the electric field-strength of 30 V/cm and at frequencies below 10 Hz.\n\nLow frequency alternating electric fields inhibit lactose uptake in Kluyveromyces marxianus.", "token_count": 109, "char_count": 411, "word_count": 53, "semantic_coherence": 1, "information_density": 0.7736, "quality_score": 0.8868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:26.865625", "source": { "split": "train_shard_00001", "doc_id": 4505 }, "chunk_id": "train_shard_00001_4505_0", "global_id": 12037 }, { "text": "Listeria monocytogenes is one of the most important foodborne pathogens responsible for listeriosis, a severe disease with symptoms ranging from septicemia, meningoencephalitis, and abortion. Given the strong impact of listeriosis on human health and the difficulty of controlling L. monocytogenes along the food production chain, listeriosis has become a priority subjected to molecular surveillance in European Union/European Economic Area since 2007. From 2018, surveillance is based on whole-genome sequence using the core genome multilocus sequence type. The complete sequences of 132 clinical strains were used to define the evolutionary relatedness among subtypes of L. monocytogenes isolated in Italy from 2010 to 2016, allowing the identification of clades and/or clusters associated with outbreaks or sporadic cases of listeriosis. All the strains analyzed are clustered in lineages I and II, and the majority of the strains were classified as lineage II. A probable epidemic entrance in different years for every clade and cluster from each different region was defined. The persistence of the same specific clonal complexes of L. monocytogenes has been found over long periods; this may be related to the fact that some strains are able to survive better than others in a food production environment. Phylogenic studies, using whole-genome sequence data, are able to identify the emergence of highly persistent pathogenic variants, contributing to improving the hazard characterization of L. monocytogenes.\n\nPhylogenetic and Evolutionary Genomic Analysis of Listeria monocytogenes Clinical Strains in the Framework of Foodborne Listeriosis Risk Assessment.", "token_count": 433, "char_count": 1710, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:27.499906", "source": { "split": "train_shard_00001", "doc_id": 4506 }, "chunk_id": "train_shard_00001_4506_0", "global_id": 12038 }, { "text": "PURPOSE: Alcohol dehydrogenase-producing microorganisms for the synthesis of optically active ethyl 3-hydroxy-3-phenylpropionate from ethyl benzoylacetate are provided, which microorganisms environment-friendly and simply produces higher purity of optically active ethyl 3-hydroxy-3-phenylpropionate. CONSTITUTION: The alcohol dehydrogenase-producing microorganisms for the synthesis of optically active ethyl 3-hydroxy-3-phenylpropionate from ethyl benzoylacetate are Candida parapsilosis IFO 0708, Candida parapsilosis KCTC 7653, Geotrichum candidum IFO 4597, Kluyveromyces lactis KCTC 7133, Kluyveromyces marxianus KCTC 7524, Saccharomyces cerevisiae KCTC 1218, Saccharomyces cerevisiae KCTC 1552 and Saccharomyces cerevisiae KCTC 7917 and the optically active ethyl 3-hydroxy-3-phenylpropionate is (R)- and (S)-ethyl 3-hydroxy-3-phenylpropionate.\n\nALCOHOL DEHYDROGENASE-PRODUCING MICROORGANISMS FOR THE SYNTHESIS OF OPTICALLY ACTIVE ETHYL 3-HYDROXY-3-PHENYLPROPIONATE FROM ETHYL BENZOYLACETATE", "token_count": 393, "char_count": 997, "word_count": 105, "semantic_coherence": 1, "information_density": 0.4476, "quality_score": 0.7238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:28.119190", "source": { "split": "train_shard_00001", "doc_id": 4507 }, "chunk_id": "train_shard_00001_4507_0", "global_id": 12039 }, { "text": "Pediococcus pentosaceus isolated from fermented food and the gastrointestinal tracts of humans and animals have been widely identified, and some strains have been reported to reduce inflammation, encephalopathy, obesity and fatty liver in animals. In this study, the genomes of 65 P. pentosaceus strains isolated from human and animal feces and different fermented food were sequenced and comparative genomics analysis was performed on all strains along with nine sequenced representative strains to preliminarily reveal the lifestyle of P. pentosaceus, and investigate the genomic diversity within this species. The results reveal that P. pentosaceus is not host-specific, and shares core genes encoding proteins related to translation, ribosomal structure and biogenesis and signal transduction mechanisms, while its genetic diversity relates mainly to carbohydrate metabolism, and horizontally transferred DNA, especially prophages and bacteriocins encoded on plasmids. Additionally, this is the first report of a type IIA CRISPR/Cas system in P. pentosaceus. This work provides expanded resources of P. pentosaceus genomes, and offers a framework for understanding the biotechnological potential of this species.\n\nComparative Genomics of Pediococcus pentosaceus Isolated From Different Niches Reveals Genetic Diversity in Carbohydrate Metabolism and Immune System.", "token_count": 370, "char_count": 1417, "word_count": 187, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:28.699103", "source": { "split": "train_shard_00001", "doc_id": 4508 }, "chunk_id": "train_shard_00001_4508_0", "global_id": 12040 }, { "text": "Corynebacterium striatum is an emerging multidrug-resistant (MDR) pathogen that occurs primarily among immunocompromised and chronically ill patients. However, little is known about the genomic diversity of C. striatum, which contributes to its long-term persistence and transmission in hospitals. In this study, a total of 192 C. striatum isolates obtained from 14 September 2017 to 29 March 2018 in a hospital in Beijing, China, were analyzed by antimicrobial susceptibility testing and pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing was conducted on 91 isolates. Nearly all isolates (96.3%, 183/190) were MDR. The highest resistance rate was observed for ciprofloxacin (99.0%, 190/192), followed by cefotaxime (90.6%, 174/192) and erythromycin (89.1%, 171/192). PFGE separated the 192 isolates into 79 pulsotypes, and differences in core genome single-nucleotide polymorphisms (SNPs) partitioned the 91 isolates sequenced into four clades. Isolates of the same pulsotype were identical or nearly identical at the genome level, with some exceptions. Two dominant subclones, clade 3a, and clade 4a, were responsible for the hospital-wide dissemination. Genomic analysis further revealed nine resistance genes mobilized by eight unique cassettes. PFGE and whole-genome sequencing revealed that the C. striatum isolates studied were the result mainly of predominant clones spreading in the hospital. C. striatum isolates in the hospital progressively acquired resistance to antimicrobial agents, demonstrating that isolates of C. striatum may adapt rapidly through the acquisition and accumulation of resistance genes and thus evolve into dominant and persistent clones. These insights will be useful for the prevention of C", "token_count": 524, "char_count": 1786, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:52:29.358562", "source": { "split": "train_shard_00001", "doc_id": 4509 }, "chunk_id": "train_shard_00001_4509_0", "global_id": 12041 }, { "text": "striatum infection in hospitals.\n\nWhole-Genome Sequencing Reveals a Prolonged and Persistent Intrahospital Transmission of Corynebacterium striatum, an Emerging Multidrug-Resistant Pathogen.", "token_count": 58, "char_count": 194, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:29.718656", "source": { "split": "train_shard_00001", "doc_id": 4509 }, "chunk_id": "train_shard_00001_4509_1", "global_id": 12042 }, { "text": "Horizontal gene transfer (HGT) is an important force in evolution, which may lead, among other things, to the adaptation to new environments by the import of new metabolic functions. Recent studies based on phylogenetic analyses of a few genome fragments containing archaeal 16S rRNA genes and fosmid-end sequences from deep-sea metagenomic libraries have suggested that marine planktonic archaea could be affected by high HGT frequency. Likewise, a composite genome of an uncultured marine euryarchaeote showed high levels of gene sequence similarity to bacterial genes. In this work, we ask whether HGT is frequent and widespread in genomes of these marine archaea, and whether HGT is an ancient and/or recurrent phenomenon. To answer these questions, we sequenced 997 fosmid archaeal clones from metagenomic libraries of deep-Mediterranean waters (1,000 and 3,000 m depth) and built comprehensive pangenomes for planktonic Thaumarchaeota (Group I archaea) and Euryarchaeota belonging to the uncultured Groups II and III Euryarchaeota (GII/III-Euryarchaeota). Comparison with available reference genomes of Thaumarchaeota and a composite marine surface euryarchaeote genome allowed us to define sets of core, lineage-specific core, and shell gene ortholog clusters for the two archaeal lineages. Molecular phylogenetic analyses of all gene clusters showed that 23.9% of marine Thaumarchaeota genes and 29.7% of GII/III-Euryarchaeota genes had been horizontally acquired from bacteria. HGT is not only extensive and directional but also ongoing, with high HGT levels in lineage-specific core (ancient transfers) and shell (recent transfers) genes. Many of the acquired genes are related to metabolism and membrane biogenesis, suggesting an adaptive value for life in cold, oligotrophic oceans. We hypothesize that the acquisition of an important amount of foreign genes by the ancestors of these archaeal groups significantly contributed to their divergence and ecological success.", "token_count": 495, "char_count": 1982, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6021, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:30.374475", "source": { "split": "train_shard_00001", "doc_id": 4510 }, "chunk_id": "train_shard_00001_4510_0", "global_id": 12043 }, { "text": "Pangenome Evidence for Extensive Interdomain Horizontal Transfer Affecting Lineage Core and Shell Genes in Uncultured Planktonic Thaumarchaeota and Euryarchaeota", "token_count": 44, "char_count": 161, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:30.735629", "source": { "split": "train_shard_00001", "doc_id": 4510 }, "chunk_id": "train_shard_00001_4510_1", "global_id": 12044 }, { "text": "Candida albicans is the species most frequently isolated from oral specimens, but the recovery of other Candida species such as Candida dubliniensis is increasing. Differentiation of C. dubliniensis from C. albicans requires special tests and both species are misidentified in some studies. CHROM-Pal (CH-P) is a novel chromogenic medium used in our laboratory for differentiation between C. albicans and C. dubliniensis on the basis of colony colour and morphology, and chlamydospore production. The performance of CH-P and CHROMagar Candida (CAC) was compared for primary isolation and presumptive identification of yeasts from oral specimens from human immunodeficiency virus (HIV)-infected and uninfected individuals. The identification of Candida species on both media was compared with two reference identification methods (API ID 32 C and multiplex PCR). A total of 137/205 oral swabs (66.8 %) plated onto CH-P and CAC media were positive by culture and resulted in the growth of 171 isolates of Candida species on CH-P, whilst only 159 isolates grew on CAC. C. albicans was the most frequently isolated species in both groups of patients, followed by Candida parapsilosis in the HIV-negative group, and by C. dubliniensis in the HIV-infected group. The other Candida species isolated were Candida guilliermondii, Candida glabrata, Candida krusei, Candida tropicalis, Candida famata, Candida rugosa, Candida kefyr, Candida pelliculosa and Candida pulcherrima. The sensitivity and specificity for identifying C. albicans, C. krusei, C. tropicalis and C. dubliniensis on CH-P were over 98.5 %, always equal to or higher than those obtained when CAC was used. CH-P is a simple reliable medium for primary isolation and presumptive identification of yeast isolates from oral samples. The ability of CH-P to discriminate between C. dubliniensis and C. albicans was significantly higher (P <0.05) than that of CAC.", "token_count": 509, "char_count": 1915, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5052, "quality_score": 0.7526, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:31.370555", "source": { "split": "train_shard_00001", "doc_id": 4511 }, "chunk_id": "train_shard_00001_4511_0", "global_id": 12045 }, { "text": "Evaluation of CHROM-Pal medium for the isolation and direct identification of Candida dubliniensis in primary cultures from the oral cavity.", "token_count": 30, "char_count": 140, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:31.729843", "source": { "split": "train_shard_00001", "doc_id": 4511 }, "chunk_id": "train_shard_00001_4511_1", "global_id": 12046 }, { "text": "Since the introduction of pneumococcal conjugate vaccines, the prevalence of non-meropenem-susceptible pneumococci has been increasing in Japan. In an earlier study, we demonstrated that multidrug-resistant serotype 15A-ST63 in Japan has a specific pbp1a sequence (pbp1a-13) that could promote meropenem resistance. To trace the origin of pbp1a, we analyzed isolates of serotype 19A-CC3111, which is the most prevalent non-meropenem-susceptible clone in Japan. We analyzed a total of 119 serotype 19A-CC3111 strains recovered in Japan using whole-genome sequencing. Of the 119 isolates, 53 (44.5%) harbored pbp1a-13, indicating that the clone may be the primary reservoir of the pbp1a type and that the pbp1a region may be horizontally transferred between different serotype strains. The single acquisition of pbp1a-13 seemed to cause only penicillin resistance and not multidrug resistance; a combination of penicillin-binding protein (PBP) recombination in the pbp2b and/or pbp2x region(s) with acquisition of pbp1a-13 caused multidrug resistance. Conserved amino acid motif analysis suggested that the pbp1a 370SXXK, pbp2b 448SXN, and pbp2x 337SXXN motifs were the candidates for amino acid substitutions increasing the MICs of meropenem, cefotaxime, and penicillin", "token_count": 474, "char_count": 1359, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6307, "quality_score": 0.8153, "entities": { "genes": [ "CC3111", "ST63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:32.377114", "source": { "split": "train_shard_00001", "doc_id": 4512 }, "chunk_id": "train_shard_00001_4512_0", "global_id": 12047 }, { "text": "We identified a specific clone that was correlated with multidrug resistance, although no correlation was observed between phylogenetic trees generated using core genomes and those generated with only the cps locus. All tested isolates were highly erythromycin resistant, and most harbored mefE within macrolide efflux genetic assembly (MEGA) elements and ermB within Tn917, which was inserted within Tn916 and exhibited a structure identical to that of Tn2017.\n\nPenicillin-Binding Protein Typing, Antibiotic Resistance Gene Identification, and Molecular Phylogenetic Analysis of Meropenem-Resistant Streptococcus pneumoniae Serotype 19A-CC3111 Strains in Japan.", "token_count": 215, "char_count": 704, "word_count": 87, "semantic_coherence": 1, "information_density": 0.8391, "quality_score": 0.9195, "entities": { "genes": [ "CC3111" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:32.837618", "source": { "split": "train_shard_00001", "doc_id": 4512 }, "chunk_id": "train_shard_00001_4512_1", "global_id": 12048 }, { "text": "Zearalenone (ZEN) is considered one of the most serious mycotoxins contaminating grains and their by-products, causing significant economic losses in the feed and food industries. Biodegradation pathways are currently considered the most efficient solution to remove ZEN contamination from foods. However, low degradation rates and vulnerability to environmental impacts limit the application of biodegradation pathways. Therefore, the main research objective of this article was to screen strains that can efficiently degrade ZEN and survive under harsh conditions. This study successfully isolated a new strain L9 which can efficiently degrade ZEN from 108 food ingredients. The results of sequence alignment showed that L9 is Bacillus velezensis. Meanwhile, we found that the L9 degradation rate reached 91.14% at 24 h and confirmed that the primary degradation mechanism of this strain is biodegradation. The strain exhibits resistance to high temperature, acid, and 0.3% bile salts. The results of whole-genome sequencing analysis showed that, it is possible that the strain encodes the key enzyme, such as chitinase, carboxylesterases, and lactone hydrolase, that work together to degrade ZEN. In addition, 227 unique genes in this strain are primarily involved in its replication, recombination, repair, and protective mechanisms. In summary, we successfully excavated a ZEN-degrading, genetically distinct strain of Bacillus velezensis that provides a solid foundation for the detoxification of feed and food contamination in the natural environment.\n\nA Novel Bacillus Velezensis for Efficient Degradation of Zearalenone.", "token_count": 395, "char_count": 1643, "word_count": 231, "semantic_coherence": 1, "information_density": 0.632, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:33.459963", "source": { "split": "train_shard_00001", "doc_id": 4513 }, "chunk_id": "train_shard_00001_4513_0", "global_id": 12049 }, { "text": "Understanding the biochemistry and metabolic pathways of cyanide degradation is necessary to improve the efficacy of cyanide bioremediation processes and industrial requirements. We have isolated and sequenced the genome of a cyanide-degrading Bacillus strain from water in contact with mine tailings from Lima, Peru. This strain was classified as Bacillus safensis based on 16S rRNA gene sequencing and core genome analyses and named B. safensis PER-URP-08. We searched for possible cyanide-degradation enzymes in the genome of this strain and identified a putative cyanide dihydratase (CynD) gene similar to a previously characterized CynD from Bacillus pumilus C1. Sequence analysis of CynD from B. safensis and B. pumilus allow us to identify C-terminal residues that differentiate both CynDs. We then cloned, expressed in Escherichia coli, and purified recombinant CynD from B. safensis PER-URP-08 (CynDPER-URP-08) and showed that in contrast to CynD from B. pumilus C1, this recombinant CynD remains active at up to pH 9. We also showed that oligomerization of CynDPER-URP-08 decreases as a function of increased pH. Finally, we demonstrated that transcripts of CynDPER-URP-08 in B. safensis PER-URP-08 are strongly induced in the presence of cyanide. Our results suggest that the use of B. safensis PER-URP-08 and CynDPER-URP-08 as potential tool for cyanide bioremediation warrants further investigation. IMPORTANCE Despite being of environmental concern around the world due to its toxicity, cyanide continues to be used in many important industrial processes", "token_count": 521, "char_count": 1668, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6043, "quality_score": 0.8022, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:52:34.129040", "source": { "split": "train_shard_00001", "doc_id": 4514 }, "chunk_id": "train_shard_00001_4514_0", "global_id": 12050 }, { "text": "Thus, searching for cyanide bioremediation methods is a matter of societal concern and must be present on the political agenda of all governments. Here, we report the isolation, genome sequencing and characterization of cyanide degradation capacity of a bacterial strain isolated from an industrial mining site in Peru. We characterize a cyanide dehydratase (CynD) homolog from one of these bacteria, Bacillus safensis PER-URP-08.\n\nGenomic Characterization of Bacillus safensis Isolated from Mine Tailings in Peru and Evaluation of Its Cyanide-Degrading Enzyme CynD.", "token_count": 155, "char_count": 573, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7654, "quality_score": 0.8827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:34.597402", "source": { "split": "train_shard_00001", "doc_id": 4514 }, "chunk_id": "train_shard_00001_4514_1", "global_id": 12051 }, { "text": "Hospitalized preterm infants receive frequent and often prolonged exposures to antibiotics because they are vulnerable to infection. It is not known whether the short-term effects of antibiotics on the preterm infant gut microbiota and resistome persist after discharge from neonatal intensive care units. Here, we use complementary metagenomic, culture-based and machine learning techniques to study the gut microbiota and resistome of antibiotic-exposed preterm infants during and after hospitalization, and we compare these readouts to antibiotic-naive healthy infants sampled synchronously. We find a persistently enriched gastrointestinal antibiotic resistome, prolonged carriage of multidrug-resistant Enterobacteriaceae and distinct antibiotic-driven patterns of microbiota and resistome assembly in extremely preterm infants that received early-life antibiotics. The collateral damage of early-life antibiotic treatment and hospitalization in preterm infants is long lasting. We urge the development of strategies to reduce these consequences in highly vulnerable neonatal populations.\n\nPersistent metagenomic signatures of early-life hospitalization and antibiotic treatment in the infant gut microbiota and resistome.", "token_count": 269, "char_count": 1227, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:35.164657", "source": { "split": "train_shard_00001", "doc_id": 4515 }, "chunk_id": "train_shard_00001_4515_0", "global_id": 12052 }, { "text": "

Background

Understanding the structure of a bacterial population is essential in order to understand bacterial evolution, or which genetic lineages cause disease, or the consequences of perturbations to the bacterial population. Estimating the core genome, the genes common to all or nearly all strains of a species, is an essential component of such analyses. The size and composition of the core genome varies by dataset, but our hypothesis was that variation between different collections of the same bacterial species should be minimal. To test this, the genome sequences of 3,121 pneumococci recovered from healthy individuals in Reykjavik (Iceland), Southampton (United Kingdom), Boston (USA) and Maela (Thailand) were analysed.

Results

The analyses revealed a ‘supercore’ genome (genes shared by all 3,121 pneumococci) of only 303 genes, although 461 additional core genes were shared by pneumococci from Reykjavik, Southampton and Boston. Overall, the size and composition of the core genomes and pan-genomes among pneumococci recovered in Reykjavik, Southampton and Boston were very similar, but pneumococci from Maela were distinctly different. Inspection of the pan-genome of Maela pneumococci revealed several >25 Kb sequence regions that were homologous to genomic regions found in other bacterial species.

Conclusions

Some subsets of the global pneumococcal population are highly heterogeneous and thus our hypothesis was rejected. This is an essential point of consideration before generalising the findings from a single dataset to the wider pneumococcal population.\n\nHeterogeneity among estimates of the core genome and pan-genome in different pneumococcal populations", "token_count": 421, "char_count": 1712, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5579, "quality_score": 0.7789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:35.825002", "source": { "split": "train_shard_00001", "doc_id": 4516 }, "chunk_id": "train_shard_00001_4516_0", "global_id": 12053 }, { "text": "In Austria, all laboratories are legally obligated to forward human and food/environmental L. monocytogenes isolates to the National Reference Laboratory/Center (NRL) for Listeria. Two invasive human isolates of L. monocytogenes serotype 1/2a of the same pulsed-field gel electrophoresis (PFGE) pattern, previously unknown in Austria, were cultured for the first time in January 2016. Five further human isolates, obtained from patients with invasive listeriosis between April 2016 and September 2017, showed this PFGE pattern. In Austria the NRL started to use whole-genome sequencing (WGS) based typing in 2016, using a core genome MLST (cgMLST) scheme developed by Ruppitsch et al. 2015, which contains 1701 target genes. Sequence data are submitted to a publicly available nomenclature server (Ridom GmbH, Münster, Germany) for allocation of the core genome complex type (CT). The seven invasive human isolates differed from each other with zero to two alleles and were allocated to CT1234 (declared as outbreak strain). Among the Austrian strain collection of about 6,000 cgMLST-characterized non-human isolates (i.e., food/environmental isolates) 90 isolates shared CT1234. Out of these, 83 isolates were traced back to one meat processing-company. They differed from the outbreak strain by up to seven alleles; one isolate originated from the company's industrial slicer. The remaining seven CT1234-isolates were obtained from food products of four other companies (five fish-products, one ready-to-eat dumpling and one deer-meat) and differed from the outbreak strain by six to eleven alleles. The outbreak described shows the considerable potential of WGS to identify the source of a listeriosis outbreak. Compared to PFGE analysis, WGS-based typing has higher discriminatory power, yields better data accuracy, and allows higher laboratory through-put at lower cost", "token_count": 509, "char_count": 1896, "word_count": 271, "semantic_coherence": 1, "information_density": 0.6642, "quality_score": 0.8321, "entities": { "genes": [ "CT1234" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:36.495165", "source": { "split": "train_shard_00001", "doc_id": 4517 }, "chunk_id": "train_shard_00001_4517_0", "global_id": 12054 }, { "text": "Utilization of WGS-based typing results of human and food/ environmental L. monocytogenes isolates by appropriate public health analysts and epidemiologists is indispensable to support a successful outbreak investigation.\n\nWhole Genome Sequencing Based Surveillance of L. monocytogenes for Early Detection and Investigations of Listeriosis Outbreaks.", "token_count": 95, "char_count": 364, "word_count": 44, "semantic_coherence": 1, "information_density": 0.8409, "quality_score": 0.9205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:36.870332", "source": { "split": "train_shard_00001", "doc_id": 4517 }, "chunk_id": "train_shard_00001_4517_1", "global_id": 12055 }, { "text": "Streptococcus suis is a zoonotic pathogen that causes invasive infections in humans and pigs. Although S. suis serotype 2 is prevalent among patient and swine infections, other serotypes are occasionally detected in humans. Of these, serotype 24 clonal complex (CC) 221/234 are recognized as emerging clones of human infection. Genomic exploration of three S. suis serotype 24 CC221/234 strains revealed antimicrobial resistance genes, pathotyping, virulence-associated gene (VAG) profiles, minimum core genome (MCG) typing, and comparison of the genomes. Based on these analyzes, all three serotype 24 strains were MCG7-3 and should be classified in the intermediate/weakly virulent (I/WV) group. All selected serotype 24 strains were susceptible to several antibiotics including β-lactam, fluoroquinolone, and chloramphenicol. Resistance to tetracycline, macrolide, and clindamycin was observed and attributed to the genes tet(O) and erm(B). Genomic comparison revealed the strains S12X, LSS66, LS0L, LS0E, 92-4,172, and IMT40201 that had phylogenetic affinity with serotype 24 CC221/234", "token_count": 367, "char_count": 1124, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [ "LSS66", "IMT40201", "LS0E", "CC221", "MCG7", "LS0L" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:37.461409", "source": { "split": "train_shard_00001", "doc_id": 4518 }, "chunk_id": "train_shard_00001_4518_0", "global_id": 12056 }, { "text": "Analysis of 80 virulence-associated genes (VAG) showed that all three serotype 24 strains lacked 24 genes consisting of adhesin P, epf, hyl, ihk, irr, mrp, nadR, neuB, NisK/R, ofs, permease (SSU0835), rgg, revS, salK/R, sao, sly, spyM3_0908, srtBCD, srtF, srtG, SSU05_0473, virA, virB4, and virD4. Eleven specific sequences were identified in the 3 serotype 24 genomes that differed from the genomes of the representative strains of epidemic (E; SC84), highly virulent (HV; P1/7), I/WV (89-1,591), and avirulent (T15 and 05HAS68).\n\nGenomic Characterization of Streptococcus suis Serotype 24 Clonal Complex 221/234 From Human Patients.", "token_count": 278, "char_count": 662, "word_count": 93, "semantic_coherence": 1, "information_density": 0.8065, "quality_score": 0.9032, "entities": { "genes": [ "SSU0835", "SC84" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:38.010643", "source": { "split": "train_shard_00001", "doc_id": 4518 }, "chunk_id": "train_shard_00001_4518_1", "global_id": 12057 }, { "text": "The exceptional diversity of maize ( Zea mays ) is the backbone of modern heterotic patterns and hybrid breeding. Historically, US farmers exploited this variability to establish today’s highly productive Corn Belt inbred lines from blends of dent and flint germplasm pools. Here, we report high quality de novo genome sequences of the four European flint lines EP1, F7, DK105 and PE0075 assembled to pseudomolecules with scaffold N50 ranging between 6.1 to 10.4 Mb. Comparative analyses with the two US Corn Belt genomes B73 and PH207 elucidates the pronounced differences between both germplasm groups. While overall syntenic order and consolidated gene annotations reveal only moderate pan-genomic differences, whole genome alignments delineating the core and dispensable genome, and the analysis of repeat structures, heterochromatic knobs and orthologous long terminal repeat retrotransposons (LTRs) unveil the extreme dynamics of the maize genome. Haplotypes derived from core genome SNPs demonstrate the tessellation of modern maize resulting from a complex breeding history. The high quality genome sequences of the flint pool are a crucial complement to the maize pan-genome and provide an important tool to study maize improvement at a genome scale and to enhance modern hybrid breeding.\n\nEuropean maize genomes unveil pan-genomic dynamics of repeats and genes", "token_count": 339, "char_count": 1370, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [ "DK105", "EP1", "PH207", "PE0075" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:38.589262", "source": { "split": "train_shard_00001", "doc_id": 4519 }, "chunk_id": "train_shard_00001_4519_0", "global_id": 12058 }, { "text": "Taxonomic relationships between Lactobacillus casei, Lactobacillus paracasei and Lactobacillus zeae have long been debated. Results of previous analyses have shown that overall genome relatedness indices (such as average nucleotide identity and core nucleotide identity) between the type strains L. casei ATCC 393T and L. zeae ATCC 15820T were 94.6 and 95.3 %, respectively, which are borderline for species definition. However, the digital DNA‒DNA hybridization value was 57.3 %, which was clearly lower than the species delineation threshold of 70 %, and hence raised the possibility that L. casei could be reclassified into two species. To re-evaluate the taxonomic relationship of these taxa, multilocus sequence analysis (MLSA) based on the concatenated five housekeeping gene (dnaJ, dnaK, mutL, pheS and yycH) sequences, phylogenomic and core genome multilocus sequence typing analyses, gene presence and absence profiles using pan-genome analysis, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) profiling analysis, cellular fatty acid compositions, and phenotype analysis were carried out. The results of phenotypic characterization, MLSA, whole-genome sequence-based analyses and MALDI-TOF MS profiling justified an independent species designation for the L. zeae strains, and supported an emended the description of the name of Lactobacillus zeae (ex Kuznetsov 1956) Dicks et al", "token_count": 486, "char_count": 1552, "word_count": 197, "semantic_coherence": 1, "information_density": 0.7005, "quality_score": 0.8503, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:39.243325", "source": { "split": "train_shard_00001", "doc_id": 4520 }, "chunk_id": "train_shard_00001_4520_0", "global_id": 12059 }, { "text": "1996, with ATCC 15820T (=DSM 20178T=BCRC 17942T) as the type strain.\n\nGenome-based reclassification of Lactobacillus casei: emended classification and description of the species Lactobacillus zeae.", "token_count": 105, "char_count": 244, "word_count": 25, "semantic_coherence": 1, "information_density": 0.88, "quality_score": 0.94, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:39.625979", "source": { "split": "train_shard_00001", "doc_id": 4520 }, "chunk_id": "train_shard_00001_4520_1", "global_id": 12060 }, { "text": "

Background

Members of the genus Bacillus are important plant growth-promoting rhizobacteria that serve as biocontrol agents. Bacillus paralicheniformis MDJK30 is a PGPR isolated from the peony rhizosphere and can suppress plant-pathogenic bacteria and fungi. To further uncover the genetic mechanism of the plant growth-promoting traits of MDJK30 and its closely related strains, we used comparative genomics to provide insights into the genetic diversity and evolutionary relationship between B. paralicheniformis and B. licheniformis.

Results

A comparative genomics analysis based on B. paralicheniformis MDJK30 and 55 other previously reported Bacillus strains was performed. The evolutionary position of MDJK30 and the evolutionary relationship between B. paralicheniformis and B. licheniformis were evaluated by studying the phylogeny of the core genomes, a population structure analysis and ANI results. Comparative genomic analysis revealed various features of B. paralicheniformis that contribute to its commensal lifestyle in the rhizosphere, including an opening pan genome, a diversity of transport and the metabolism of the carbohydrates and amino acids. There are notable differences in the numbers and locations of the insertion sequences, prophages, genomic islands and secondary metabolic synthase operons between B. paralicheniformis and B. licheniformis. In particular, we found most gene clusters of Fengycin, Bacitracin and Lantipeptide were only present in B. paralicheniformis and were obtained by horizontal gene transfer (HGT), and these clusters may be used as genetic markers for distinguishing B. paralicheniformis and B. licheniformis.

Conclusions

This study reveals that MDJK30 and the other strains of lineage paralicheniformis present plant growth-promoting traits at the genetic level and can be developed and commercially formulated in agriculture as PGPR. Core genome phylogenies and population structure analysis has proven to be a powerful tool for differentiating B. paralicheniformis and B. licheniformis", "token_count": 516, "char_count": 2064, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5326, "quality_score": 0.7663, "entities": { "genes": [ "MDJK30" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:52:40.264711", "source": { "split": "train_shard_00001", "doc_id": 4521 }, "chunk_id": "train_shard_00001_4521_0", "global_id": 12061 }, { "text": "Comparative genomic analyses illustrate the genetic differences between the paralicheniformis-licheniformis group with respect to rhizosphere adaptation.\n\nComparative genomic analysis of Bacillus paralicheniformis MDJK30 with its closely related species reveals an evolutionary relationship between B. paralicheniformis and B. licheniformis.", "token_count": 80, "char_count": 341, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8158, "quality_score": 0.9079, "entities": { "genes": [ "MDJK30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:40.644579", "source": { "split": "train_shard_00001", "doc_id": 4521 }, "chunk_id": "train_shard_00001_4521_1", "global_id": 12062 }, { "text": "The study of microbial pangenomes relies on the computation of gene families, i.e. the clustering of coding sequences into groups of essentially similar genes. There is no standard approach to obtain such gene families. Ideally, the gene family computations should be robust against errors in the annotation of genes in various genomes. In an attempt to achieve this robustness, we propose to cluster sequences by their domain sequence, i.e. the ordered sequence of domains in their protein sequence. In a study of 347 genomes from Escherichia coli we find on average around 4500 proteins having hits in Pfam-A in every genome, clustering into around 2500 distinct domain sequence families in each genome. Across all genomes we find a total of 5724 such families. A binomial mixture model approach indicates this is around 95% of all domain sequences we would expect to see in E. coli in the future. A Heaps law analysis indicates the population of domain sequences is larger, but this analysis is also very sensitive to smaller changes in the computation procedure. The resolution between strains is good despite the coarse grouping obtained by domain sequence families. Clustering sequences by their ordered domain content give us domain sequence families, who are robust to errors in the gene prediction step. The computational load of the procedure scales linearly with the number of genomes, which is needed for the future explosion in the number of re-sequenced strains. The use of domain sequence families for a functional classification of strains clearly has some potential to be explored.\n\nA domain sequence approach to pangenomics: applications to Escherichia coli.", "token_count": 368, "char_count": 1676, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5489, "quality_score": 0.7744, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:41.233349", "source": { "split": "train_shard_00001", "doc_id": 4522 }, "chunk_id": "train_shard_00001_4522_0", "global_id": 12063 }, { "text": "

Objective

The aim of this study was to evaluate the prevalence of Candida spp. and presence of oral lesions in Brazilian leprosy patients under multidrug therapy (MDT).

Methods

Thirty-eight individuals (18 males and 20 females, median age 53 years) clinically and microbiologically diagnosed as leprosy (lepromatous variant), and under MDT for at least 45 days were studied. The control group constituted by 38 healthy individuals (median age 53.5), matched to the test group in relation to age, gender and oral conditions. Oral rinses were collected and the Candida identification was performed by phenotypic tests. The existence of Candida dubliniensis among the isolates was analyzed using a validated multiplex PCR assay. Twenty-nine leprosy patients were examined intra-orally for the presence of lesions. Data were analyzed by z- and Mann-Whitney tests (alpha = 5%).

Results

Yeast carriage rate between leprosy patients (65.8%) and controls (47.4%) was similar (P = 0.099), and no significant difference between yeast counts was observed (P = 0.1004). Candida albicans was the most frequently isolated species in both groups. In the leprosy group, Candida tropicalis and Candida parapsilosis were also identified. In the control group, we additionally identified Candida tropicalis, Candida glabrata and Candida kefyr. Candida dubliniensis was not detected. No leprosy-related oral lesion was registered.

Conclusion

Within the limits of the study, we concluded that Brazilian leprosy patients under MDT showed similar levels of carriage and Candida species distribution in relation to the controls.\n\nOral distribution of Candida species and presence of oral lesions in Brazilian leprosy patients under multidrug therapy.", "token_count": 460, "char_count": 1755, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5547, "quality_score": 0.7773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:41.872751", "source": { "split": "train_shard_00001", "doc_id": 4523 }, "chunk_id": "train_shard_00001_4523_0", "global_id": 12064 }, { "text": "Lactic acid bacteria (LAB) and yeasts constitute part of the microflora in Zimbabwean traditional fermented cows' milk, amasi. The present study was carried out to investigate the growth characteristics of Candida kefyr 23, Lactococcus lactis subsp. lactis biovar. diacetylactis C1 and L. lactis subsp. lactis Lc261, previously isolated from amasi, in ultrahigh temperature (UHT)-treated cows' milk. The strains were inoculated into the UHT milk as both single and yeast\n\nGrowth characteristics of Candida kefyr and two strains of Lactococcus lactis subsp. lactis isolated from Zimbabwean naturally fermented milk.", "token_count": 186, "char_count": 614, "word_count": 88, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:42.325182", "source": { "split": "train_shard_00001", "doc_id": 4524 }, "chunk_id": "train_shard_00001_4524_0", "global_id": 12065 }, { "text": "Yeast isolates from flowers and fruits from a Brazilian forest were studied. The yeasts were identified at species and strain level by PCR-RFLP and PCR-RAPD, respectively. The 46 isolated yeasts were classified into 11 different species belonging to the genera Candida, Diutina, Hanseniaspora, Meyerozyma, Pichia, Rhodotorula, and Torulaspora. A total of 20 different strains were found. In order to ascertain the probiotic potential, the resistance to gastrointestinal conditions, autoaggregation, and hydrophobicity assays were studied, along with the capacity to form biofilm. The results indicate that, although most of the strains presented better results than Saccharomyces boulardii (the only strain recognized as a probiotic yeast), four strains were the most promising, namely, Rhodotorula mucilaginosa 32, Meyerozyma caribbica 35, and Diutina rugosa 12 and 45, according to the Duncan test. Several biotechnological properties were evaluated. D. rugosa inhibited Dekkera bruxellensis. The assimilation or fermentation of seven sugars was tested, and only five of the yeasts did not show a capacity to assimilate any of the sugars under aerobic conditions. However, all strains were able to ferment at least one of the sugars under anaerobic conditions. As far as enzyme production is concerned, positive results were only found for the enzymes' amylase, pectinase, and protease. D. rugosa 42 and Hanseniaspora opuntiae 18, followed of Pichia kluyveri 26, showed high values for the production of melatonin. In conclusion, the results of this study show that several non-Saccharomyces present probiotic characteristics, and these have good potential for industrial applications in the food or biotechnology industries.\n\nStudy of potential probiotic and biotechnological properties of non-Saccharomyces yeasts from fruit Brazilian ecosystems.", "token_count": 488, "char_count": 1850, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6212, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:42.972180", "source": { "split": "train_shard_00001", "doc_id": 4525 }, "chunk_id": "train_shard_00001_4525_0", "global_id": 12066 }, { "text": "

Background

ESBL and AmpC β-lactamases are an increasing concern for public health. Studies suggest that ESBL/pAmpC-producing Escherichia coli and their plasmids carrying antibiotic resistance genes can spread from broilers to humans working or living on broiler farms. These studies used traditional typing methods, which may not have provided sufficient resolution to reliably assess the relatedness of these isolates.

Methods

Eleven suspected transmission events among broilers and humans living/working on eight broiler farms were investigated using whole-genome short-read (Illumina) and long-read sequencing (PacBio). Core genome MLST (cgMLST) was performed to investigate the occurrence of strain transmission. Horizontal plasmid and gene transfer were analysed using BLAST.

Results

Of eight suspected strain transmission events, six were confirmed. The isolate pairs had identical ESBL/AmpC genes and fewer than eight allelic differences according to the cgMLST, and five had an almost identical plasmid composition. On one of the farms, cgMLST revealed that the isolate pairs belonging to ST10 from a broiler and a household member of the farmer had 475 different alleles, but that the plasmids were identical, indicating horizontal transfer of mobile elements rather than strain transfer. Of three suspected horizontal plasmid transmission events, one was confirmed. In addition, gene transfer between plasmids was found.

Conclusions

The present study confirms transmission of strains as well as horizontal plasmid and gene transfer between broilers and farmers and household members on the same farm. WGS is an important tool to confirm suspected zoonotic strain and resistance gene transmission.\n\nTransmission of ESBL-producing Escherichia coli between broilers and humans on broiler farms.", "token_count": 425, "char_count": 1830, "word_count": 247, "semantic_coherence": 1, "information_density": 0.583, "quality_score": 0.7915, "entities": { "genes": [ "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:43.600851", "source": { "split": "train_shard_00001", "doc_id": 4526 }, "chunk_id": "train_shard_00001_4526_0", "global_id": 12067 }, { "text": "Invasive listeriosis, caused by Listeria (L.) monocytogenes, is a severe foodborne infection, especially for immunocompromised individuals. The aim of our investigation was the identification and analysis of listeriosis outbreaks in Germany with smoked and graved salmon products as the most likely source of infection using whole-genome sequencing (WGS) and patient interviews. In a national surveillance programme, WGS was used for subtyping and core genome multi locus sequence typing (cgMLST) for cluster detection of L. monocytogenes isolates from listeriosis cases as well as food and environmental samples in Germany. Patient interviews were conducted to complement the molecular typing. We identified 22 independent listeriosis outbreaks occurring between 2010 and 2021 that were most likely associated with the consumption of smoked and graved salmon products. In Germany, 228 cases were identified, of 50 deaths (22%) reported 17 were confirmed to have died from listeriosis. Many of these 22 outbreaks were cross-border outbreaks with further cases in other countries. This report shows that smoked and graved salmon products contaminated with L. monocytogenes pose a serious risk for listeriosis infection in Germany. Interdisciplinary efforts including WGS and epidemiological investigations were essential to identifying the source of infection. Uncooked salmon products are high-risk foods frequently contaminated with L. monocytogenes. In order to minimize the risk of infection for consumers, food producers need to improve hygiene measures and reduce the entry of pathogens into food processing. Furthermore, susceptible individuals should be better informed of the risk of acquiring listeriosis from consuming smoked and graved salmon products.\n\nInvasive listeriosis outbreaks and salmon products: a genomic, epidemiological study.", "token_count": 449, "char_count": 1878, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:44.247061", "source": { "split": "train_shard_00001", "doc_id": 4527 }, "chunk_id": "train_shard_00001_4527_0", "global_id": 12068 }, { "text": "The optimized protocols of the bioanalytes separation, proteins and yeasts, dynamically modified by the nonionogenic tenside PEG pyrenebutanoate, were applied in CZE and CIEF with the acidic gradient in pH range 2-5.5, both with fluorescence detection. PEG pyrenebutanoate was used as a buffer additive for a dynamic modification of proteins and/or yeast samples. The narrow peaks of modified analytes were detected. The values of the pI's of the labeled proteins were calculated using new fluorescent pI markers in CIEF and they were found to be comparable with pI's of the native compounds. As an example of the possible use of the suggested CIEF technique, the mixed cultures of yeasts, Candida albicans, Candida glabrata, Candida kefyr, Candida krusei, Candida lusitaniae, Candida parapsilosis, Candida tropicalis, Candida zeylanoides, Geotrichum candidum, Saccharomyces cerevisiae, Trichosporon asahii and Yarrowia lipolytica, were reproducibly focused and separated with high sensitivity. Using UV excitation for the on-column fluorometric detection, the minimum detectable amounts of analytes, femtograms of proteins and down to ten cells injected on the separation capillary, were estimated.\n\nCE separation of proteins and yeasts dynamically modified by PEG pyrenebutanoate with fluorescence detection.", "token_count": 353, "char_count": 1310, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:44.825614", "source": { "split": "train_shard_00001", "doc_id": 4528 }, "chunk_id": "train_shard_00001_4528_0", "global_id": 12069 }, { "text": "Review: Ethanol production at elevated temperatures and alcohol concentrations. II. Use of Kluyveromyces marxianus IMB3.", "token_count": 32, "char_count": 120, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:45.186742", "source": { "split": "train_shard_00001", "doc_id": 4529 }, "chunk_id": "train_shard_00001_4529_0", "global_id": 12070 }, { "text": "

Background

Neisseria gonorrhoeae causes gonorrhoea, the second most commonly notified sexually transmitted infection in Australia. One of the highest notification rates of gonorrhoea is found in the remote regions of Western Australia (WA). Unlike isolates from the major Australian population centres, the remote community isolates have low rates of antimicrobial resistance (AMR). Population structure and whole-genome comparison of 59 isolates from the Western Australian N. gonorrhoeae collection were used to investigate relatedness of isolates cultured in the metropolitan and remote areas. Core genome phylogeny, multilocus sequencing typing (MLST), N. gonorrhoeae multi-antigen sequence typing (NG-MAST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) in addition to hierarchical clustering of sequences were used to characterize the isolates.

Results

Population structure analysis of the 59 isolates together with 72 isolates from an international collection, revealed six population groups suggesting that N. gonorrhoeae is a weakly clonal species. Two distinct population groups, Aus1 and Aus2, represented 63% of WA isolates and were mostly composed of the remote community isolates that carried no chromosomal AMR genotypes. In contrast, the Western Australian metropolitan isolates were frequently multi-drug resistant and belonged to population groups found in the international database, suggesting international transmission of the isolates.

Conclusions

Our study suggests that the population structure of N. gonorrhoeae is distinct between the communities in remote and metropolitan WA. Given the high rate of AMR in metropolitan regions, ongoing surveillance is essential to ensure the enduring efficacy of the empiric gonorrhoea treatment in remote WA.\n\nGenomic epidemiology and population structure of Neisseria gonorrhoeae from remote highly endemic Western Australian populations.", "token_count": 463, "char_count": 1951, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5273, "quality_score": 0.7637, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:45.832342", "source": { "split": "train_shard_00001", "doc_id": 4530 }, "chunk_id": "train_shard_00001_4530_0", "global_id": 12071 }, { "text": "PURPOSE: A method for purifying a polygalacturonase is provided of which the steps are simplified. Thereby, the purified polygalacturonase, for example, Kluyveromyces marxianus IFO 0288, is provided. The purification method allows to design a primer by sequencing N-terminal amino acids-based sequences and increases an availability of the polygalacturonase. CONSTITUTION: Polygalacturonase is purified by the steps of: applying a concentrated culture medium containing a microorganism that secretes the polygalacturonase, to an ion-exchange column using 10-100 mM of sodium acetate (pH 5.0) as buffer and 10-100 mM of sodium acetate with a linear gradient of 0-0.2 M NaCl as an eluate to carry out a fast protein liquid chromatography(FPLC).The ion-exchange column is preferably mono S ion exchange column and the concentrated culture medium is obtained by a membrane filter thickener for centrifugation. Also, the microorganism is preferably Kluyveromyces marxianus IFO 0288 and the polygalacturonase has preferably a sequence set forth in SEQ ID NO : 1 at N-terminal thereof.\n\nMETHOD FOR PURIFYING POLYGALACTURONASE AND PURIFIED POLYGALACTURONASE", "token_count": 339, "char_count": 1149, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5915, "quality_score": 0.7957, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:46.441083", "source": { "split": "train_shard_00001", "doc_id": 4531 }, "chunk_id": "train_shard_00001_4531_0", "global_id": 12072 }, { "text": "Fusarium oxysporum ff. sp. canariensis (Foc) and palmarum (Fop) cause lethal fusarium wilt on ornamental palms. Foc infects Phoenix canariensis and has a worldwide presence, whereas Fop primarily infects Washingtonia robusta and Syagrus romanzoffiana and is currently primarily restricted to Florida (USA). A Secreted in Xylem (SIX) gene profile was obtained for Fop and Foc isolates from the USA. SIX1, SIX7, SIX10 and SIX12 were detected in most Foc isolates and, with the exception of SIX12, with minimal sequence polymorphism. SIX8 and SIX9 were detected in all Fop isolates, with no sequence polymorphism. SIX10 was also present in seven of the Fop isolates. Phylogenetic trees were constructed using EF-1α‐, SIX1, SIX7 and SIX10 gene sequences from this study and previously derived sequences from Foc isolates obtained in Australia, the Canary Islands and Japan. The topology of the housekeeping EF‐1α gene indicated Foc is polyphyletic, with the Australian isolates separating into a distinct group from all other Foc isolates. However, the topologies of SIX1, SIX7 and SIX10 phylogenetic trees for Foc indicate monophyly. As has been proposed previously, this suggests the core genome of Foc evolved into a separate lineage after the SIX genes were conserved within the whole genome. This study is the first to generate SIX12 sequences for Foc. Interestingly, the topology of the SIX12 phylogenetic tree suggests polyphyly. For Fop, the topologies of the EF‐1α, SIX8 and SIX9 phylogenetic trees support monophyly. The distinct SIX gene profile and EF‐1α sequence of Fop demonstrates an independent evolutionary origin from Foc.\n\nComparison of Secreted in Xylem (SIX) genes in two fusarium wilt pathogens of ornamental palms", "token_count": 487, "char_count": 1732, "word_count": 266, "semantic_coherence": 1, "information_density": 0.515, "quality_score": 0.7575, "entities": { "genes": [ "SIX10", "SIX12", "SIX8", "SIX7", "SIX1", "SIX9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:47.111712", "source": { "split": "train_shard_00001", "doc_id": 4532 }, "chunk_id": "train_shard_00001_4532_0", "global_id": 12073 }, { "text": "Mycoplasma gallisepticum (MG) is the most pathogenic avian mycoplasma species. It affects commercial and noncommercial poultry and wild birds. Current MG sequence typing methods rely on the partial sequence of one or more surface antigen genes. Multilocus sequence typing (MLST), a widely used typing method for many human and animal pathogens, relies on conserved housekeeping genes. Recently, MLST assays have been developed for Mycoplasma synoviae (MS) and Mycoplasma iowae. Additionally, a whole genome-based core genome MLST (cgMLST) assay has been developed for MG and MS. However, cgMLST can be implemented only on pure isolates and cannot be applied to clinical samples. Here, we have developed a seven-locus-based MLST scheme for MG that can be applied directly on clinical samples without the need for isolation. The seven loci were selected from 425 genes recently used for the cgMLST assay. A total of 101 diverse MG samples, including isolates and clinical samples, were typed with the newly developed seven-locus MLST. The phylogeny and discriminatory power of the seven-locus MLST were evaluated and compared with the cgMLST and gene-targeted sequencing methods currently used for MG sequence typing. The seven-locus MLST provided optimum discriminatory power and congruent phylogeny to cgMLST. Additionally, a database for MG MLST was created and is currently available for public use online. This assay will increase accessibility to MG sequence typing and provide a stable and expandable nomenclature compatible with cgMLST. The seven-locus MLST assay represents an important tool for epidemiologic investigation of MG that can contribute to better control and eradication efforts.\n\nDevelopment of a Multilocus Sequence Typing Assay for Mycoplasma gallisepticum.", "token_count": 464, "char_count": 1808, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5665, "quality_score": 0.7833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:47.787121", "source": { "split": "train_shard_00001", "doc_id": 4533 }, "chunk_id": "train_shard_00001_4533_0", "global_id": 12074 }, { "text": "

Background

Linezolid is an antibiotic used to treat infections caused by multi-drug-resistant Gram-positive bacteria. Linezolid resistance in enterococci has been reported with increasing frequency, with a recent rise in resistance encoded by optrA, poxtA or cfr.

Aim

To investigate a hospital outbreak of linezolid- and vancomycin-resistant Enterococcus faecium (LVREfm) using whole-genome sequencing (WGS).

Methods

Thirty-nine VREfm from patient screening (19 isolates, 17 patients) and environmental sites (20 isolates) recovered in October 2019 were investigated. Isolates were screened using polymerase chain reaction for optrA, poxtA and cfr, and underwent Illumina MiSeq WGS. Isolate relatedness was assessed using E. faecium core genome multi-locus sequence typing (cgMLST). One LVREfm underwent MinION long-read WGS (Oxford Nanopore Technologies) and hybrid assembly with MiSeq short-read sequences to resolve an optrA-encoding plasmid.

Findings

Twenty isolates (51.3%) were LVREfm and optrA-positive, including the LVREfm from the index patient. A closely related cluster of 28 sequence type (ST) 80 isolates was identified by cgMLST, including all 20 LVREfm and eight linezolid-susceptible VREfm, with an average allelic difference of two (range 0-10), indicating an outbreak. Nineteen (95%) LVREfm harboured a 56,684-bp conjugative plasmid (pEfmO_03). The remaining LVREfm exhibited 44.1% sequence coverage to pEfmO_03. The presence of pEfmO_03 in LVREfm and the close relatedness of the outbreak cluster isolates indicated the spread of a single strain", "token_count": 494, "char_count": 1594, "word_count": 208, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:48.464492", "source": { "split": "train_shard_00001", "doc_id": 4534 }, "chunk_id": "train_shard_00001_4534_0", "global_id": 12075 }, { "text": "The outbreak was terminated by enhanced infection prevention and control (IPC) and environmental cleaning measures, ceasing ward admissions and ward-dedicated staff.

Conclusion

WGS was central in investigating an outbreak of ST80 LVREfm. The rapid implementation of enhanced IPC measures terminated the outbreak.\n\nHospital outbreak of linezolid-resistant and vancomycin-resistant ST80 Enterococcus faecium harbouring an optrA-encoding conjugative plasmid investigated by whole-genome sequencing.", "token_count": 126, "char_count": 502, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7414, "quality_score": 0.8707, "entities": { "genes": [ "ST80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:48.849500", "source": { "split": "train_shard_00001", "doc_id": 4534 }, "chunk_id": "train_shard_00001_4534_1", "global_id": 12076 }, { "text": "Tea plant (Camellia sinensis) is a widely cultivated cash crop and tea is a favorite functional food in the world. Fresh tea leaves (FTLs) play a critical role in bridging the two fields closely related to tea cultivation and tea processing, those are, tea plant biology and tea biochemistry. To provide a comprehensive overview of the development stages, authorship collaboration, research topics, and hotspots and their temporal evolution trends in the field of FTLs research, we conducted a bibliometric analysis, based on 971 publications on FTLs-related research published during 2001-2021 from Web of Science Core Collection. CiteSpace, R package Bibliometrix, and VOSviewer were employed in this research. The results revealed that the development history can be roughly divided into three stages, namely initial stage, slow development stage and rapid development stage. Journal of Agricultural & Food Chemistry published most articles in this field, while Frontiers in Plant Science held the highest total citations and h-index. The most influential country, institution, and author in this field was identified as China, the Chinese Academy of Agricultural Sciences, and Xiaochun Wan, respectively. FTLs-related research can be categorized into three main topics: the regulation mechanism of key genes, the metabolism and features of essential compounds, and tea plants' growth and stress responses. The most concerning hotspots are the application of advanced technologies, essential metabolites, leaf color variants, and effective cultivation treatments. There has been a shift from basic biochemical and enzymatic studies to studies of molecular mechanisms that depend on multi-omics technologies. We also discussed the future development in this field. This study provides a comprehensive summary of the research field, making it easier for researchers to be informed about its development history, status, and trends.\n\nTopics and trends in fresh tea (Camellia sinensis) leaf research: A comprehensive bibliometric study.", "token_count": 448, "char_count": 2063, "word_count": 296, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:49.498121", "source": { "split": "train_shard_00001", "doc_id": 4535 }, "chunk_id": "train_shard_00001_4535_0", "global_id": 12077 }, { "text": "Cattle harbor Shiga toxin-producing Escherichia coli (STEC) in their intestinal tract, thereby providing these microorganisms with an ecological niche, but without this colonization leading to any clinical signs. In a preceding study, genotypic characterization of bovine STEC isolates unveiled that their ability to colonize cattle persistently (STECper) or only sporadically (STECspo) is more closely associated with the overall composition of the accessory rather than the core genome. However, the colonization pattern could not be unequivocally linked to the possession of classical virulence genes. This study aimed at assessing, therefore, if the presence of certain phenotypic traits in the strains determines their colonization pattern and if these can be traced back to distinctive genetic features. STECspo strains produced significantly more biofilm than STECper when incubated at lower temperatures. Key substrates, the metabolism of which showed a significant association with colonization type, were glyoxylic acid and L-rhamnose, which were utilized by STECspo, but not or only by some STECper. Genomic sequences of the respective glc and rha operons contained mutations and frameshifts in uptake and/or regulatory genes, particularly in STECper. These findings suggest that STECspo conserved features leveraging survival in the environment, whereas the acquisition of a persistent colonization phenotype in the cattle reservoir was accompanied by the loss of metabolic properties and genomic mutations in the underlying genetic pathways.\n\nMetabolic Traits of Bovine Shiga Toxin-Producing Escherichia Coli (STEC) Strains with Different Colonization Properties.", "token_count": 461, "char_count": 1792, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6466, "quality_score": 0.8233, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:50.146395", "source": { "split": "train_shard_00001", "doc_id": 4536 }, "chunk_id": "train_shard_00001_4536_0", "global_id": 12078 }, { "text": "

Background

Whole-genome \"shotgun\" (WGS) metagenomic sequencing is an increasingly widely used tool for analyzing the metagenomic content of microbiome samples. While WGS data contains gene-level information, it can be challenging to analyze the millions of microbial genes which are typically found in microbiome experiments. To mitigate the ultrahigh dimensionality challenge of gene-level metagenomics, it has been proposed to cluster genes by co-abundance to form Co-Abundant Gene groups (CAGs). However, exhaustive co-abundance clustering of millions of microbial genes across thousands of biological samples has previously been intractable purely due to the computational challenge of performing trillions of pairwise comparisons.

Results

Here we present a novel computational approach to the analysis of WGS datasets in which microbial gene groups are the fundamental unit of analysis. We use the Approximate Nearest Neighbor heuristic for near-exhaustive average linkage clustering to group millions of genes by co-abundance. This results in thousands of high-quality CAGs representing complete and partial microbial genomes. We applied this method to publicly available WGS microbiome surveys and found that the resulting microbial CAGs associated with inflammatory bowel disease (IBD) and colorectal cancer (CRC) were highly reproducible and could be validated independently using multiple independent cohorts.

Conclusions

This powerful approach to gene-level metagenomics provides a powerful path forward for identifying the biological links between the microbiome and human health. By proposing a new computational approach for handling high dimensional metagenomics data, we identified specific microbial gene groups that are associated with disease that can be used to identify strains of interest for further preclinical and mechanistic experimentation.\n\nClustering co-abundant genes identifies components of the gut microbiome that are reproducibly associated with colorectal cancer and inflammatory bowel disease.", "token_count": 471, "char_count": 2051, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5778, "quality_score": 0.7889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:50.790021", "source": { "split": "train_shard_00001", "doc_id": 4537 }, "chunk_id": "train_shard_00001_4537_0", "global_id": 12079 }, { "text": "FIELD: food industry. ^ SUBSTANCE: invention relates to technology for inverting sugar syrups used in non-alcoholic, liqueur and vodka, confectionary and baking industry. Method involves preparing sugar syrup with the concentration 75-80%, addition of the dried preparation of beta-fructofuranosidase to syrup and hydrolysis of sucrose. The latter is carried out for a single stage. The enzyme preparation obtained from yeast Kluyveromyces marxianus Y-303 is used for hydrolysis taken in the amount 9-10 U per g of sucrose and the hydrolysis process is carried out at pH value of syrup 3.9-4.4 and temperature 65-70 C for 304 h. Invention provides reducing the time process, enhancing degree of sucrose hydrolysis and elevating content of invert sugar and syrup. ^ EFFECT: improved preparing method. ^ 5 ex\n\nMETHOD FOR PREPARING INVERT SYRUP", "token_count": 237, "char_count": 841, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:51.271473", "source": { "split": "train_shard_00001", "doc_id": 4538 }, "chunk_id": "train_shard_00001_4538_0", "global_id": 12080 }, { "text": "Strains belonging to the genus Amycolatopsis are well known for the production of a number of important antimicrobials and other bioactive molecules. In this study, we have sequenced the genomes of five Amycolatopsis strains including Amycolatopsis circi DSM 45561T, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis thermalba NRRL B-24845T. The genome sequences were analyzed with 52 other publically available Amycolatopsis genomes, representing 34 species, and 12 representatives from related genera including Saccharomonospora, Saccharopolyspora, Saccharothrix, Pseudonocardia and Thermobispora. Based on the core genome phylogeny, Amycolatopsis strains were subdivided into four major clades and several singletons. The genus Amycolatopsis is homogeneous with only three strains noted to group with other genera. Amycolatopsis halophila YIM93223T is quite distinct from other Amycolatopsis strains, both phylogenetically and taxonomically, and belongs to a distinct genus. In addition, Amycolatopsis palatopharyngis DSM 44832T and Amycolatopsis marina CGMCC4 3568T grouped in a clade with Saccharomonospora strains and showed similar taxogenomic differences to this genus as well as other Amycolatopsis strains", "token_count": 512, "char_count": 1423, "word_count": 160, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "CGMCC4", "YIM93223" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:51.926835", "source": { "split": "train_shard_00001", "doc_id": 4539 }, "chunk_id": "train_shard_00001_4539_0", "global_id": 12081 }, { "text": "The study found a number of strains, particularly those identified as Amycolatopsis orientalis, whose incorrect identification could be resolved by taxogenomic analyses. Similarly, some unclassified strains could be assigned with species designations. The genome sequences of some strains that were independently sequenced by different laboratories were almost identical (99-100% average nucleotide and amino acid identities) consistent with them being the same strain, and confirming the reproducibility and robustness of genomic data. These analyses further demonstrate that whole genome sequencing can reliably resolve intra- and, inter-generic structures and should be incorporated into prokaryotic systematics.\n\nRevisiting the Taxonomic Status of the Biomedically and Industrially Important Genus Amycolatopsis, Using a Phylogenomic Approach.", "token_count": 200, "char_count": 861, "word_count": 109, "semantic_coherence": 1, "information_density": 0.789, "quality_score": 0.8945, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:52.378044", "source": { "split": "train_shard_00001", "doc_id": 4539 }, "chunk_id": "train_shard_00001_4539_1", "global_id": 12082 }, { "text": "

Introduction

Aging and comorbidities such as diabetes and vascular problems contribute to the increasing occurrence of chronic wounds. From the beginning of 2016, a marked increase in Arcanobacterium haemolyticum (ARH) in chronic wound cultures was noted among patients visiting a wound expertise centre in The Netherlands.

Aim

To report the outbreak investigation of ARH cultured from chronic wounds and describe the implemented infection prevention measures.

Methods

In total, 50 ARH isolates were sent to a reference laboratory for molecular typing. Samples for bacterial culture and ARH polymerase chain reaction were taken from care workers, the environment and items used for wound care. Infection prevention measures were implemented in a bundled approach, involving education, better aseptic wound care conditions and hygienic precautions. Before and after the implementation of infection prevention measures, two screening rounds of ARH testing were performed among all patients receiving home care.

Results

ARH isolates from wound care patients were found to be identical by core genome multi-locus sequence typing. No definite outbreak source could be determined by culture. However, three pairs of forceps, used by two nurses on multiple patients, were found to be ARH positive by polymerase chain reaction. In the two screening rounds before and after the implementation of infection prevention measures, the proportion of ARH-positive patients decreased significantly from 20% (20/99) to 3% (3/104). Subsequently, no new cases occurred.

Conclusion

This first ARH outbreak was likely caused by re-using contaminated instruments. Through the implementation of improved infection prevention measures and re-education of all employees involved, the outbreak was controlled. With the current trend of care transition, infection control must be a major concern.\n\nOutbreak of Arcanobacterium haemolyticum in chronic wounds in The Netherlands.", "token_count": 442, "char_count": 1985, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:53.013106", "source": { "split": "train_shard_00001", "doc_id": 4540 }, "chunk_id": "train_shard_00001_4540_0", "global_id": 12083 }, { "text": "The human small-intestinal microbiota is characterised by relatively large and dynamic Streptococcus populations. In this study, genome sequences of small-intestinal streptococci from S. mitis, S. bovis, and S. salivarius species-groups were determined and compared with those from 58 Streptococcus strains in public databases. The Streptococcus pangenome consists of 12,403 orthologous groups of which 574 are shared among all sequenced streptococci and are defined as the Streptococcus core genome. Genome mining of the small-intestinal streptococci focused on functions playing an important role in the interaction of these streptococci in the small-intestinal ecosystem, including natural competence and nutrient-transport and metabolism. Analysis of the small-intestinal Streptococcus genomes predicts a high capacity to synthesize amino acids and various vitamins as well as substantial divergence in their carbohydrate transport and metabolic capacities, which is in agreement with observed physiological differences between these Streptococcus strains. Gene-specific PCR-strategies enabled evaluation of conservation of Streptococcus populations in intestinal samples from different human individuals, revealing that the S. salivarius strains were frequently detected in the small-intestine microbiota, supporting the representative value of the genomes provided in this study. Finally, the Streptococcus genomes allow prediction of the effect of dietary substances on Streptococcus population dynamics in the human small-intestine.\n\nComparative genomics analysis of Streptococcus isolates from the human small intestine reveals their adaptation to a highly dynamic ecosystem.", "token_count": 403, "char_count": 1684, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6055, "quality_score": 0.8028, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:53.634791", "source": { "split": "train_shard_00001", "doc_id": 4541 }, "chunk_id": "train_shard_00001_4541_0", "global_id": 12084 }, { "text": "Fourteen yeast strains were screened for production of 2-phenylethanol from l-phenylalanine with molasses as carbon source. Up to 1 g 2-phenylethanol l-1 was obtained. Using oleyl alcohol as a second phase for in situ product removal to enhance the production of 2-phenylethanol increased the yield to about 3 g 2-phenylethanol l-1 at 35 degrees C. The most productive strains were Kluyveromyces marxianus CBS 600 and CBS 397.\n\nScreening of yeasts for the production of the aroma compound 2-phenylethanol in a molasses-based medium", "token_count": 168, "char_count": 531, "word_count": 82, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:54.082958", "source": { "split": "train_shard_00001", "doc_id": 4542 }, "chunk_id": "train_shard_00001_4542_0", "global_id": 12085 }, { "text": "

Background

Neisseria meningitidis can cause sporadic cases and outbreaks of invasive disease, including meningitis and sepsis. The meningococcal serogroup C (MenC) is the second most common serogroup in Italy after MenB. In this study we have estimated the reproductive numbers and the demographic reconstruction on the genomes of invasive N. meningitidis C:P1.5-1,10-8:F3-6:ST-11(cc11) strains isolated in Italy in 2012 - 2017, a period that includes the outbreak in Tuscany.

Methods

The genomes of N. meningitidis were sequenced using the Illumina MiSeq platform, through the whole genome sequencing (WGS) method and were analyzed by the core genome MLST (cgMLST) approach, using the BIGSdb Genome Comparator tool implemented on the PubMLST website. A Bayesian method was applied to study population dynamics across the entire N. meningitidis dataset. The basic reproduction number R0, which indicates the average number of secondary cases generated by a single primary case, was calculated using a Bayesian method, on the dataset and on the two subsets. The effective reproduction number R(t), defined as the average number of secondary cases per infectious case in a population, made up of susceptible and non-susceptible hosts was studied on the Tuscany dataset, with a Bayesian method.

Results

An increase in the effective number of the N. meningitidis infections was observed between 2013 and 2016. The estimated R0 parameter was 1.31 (95% HPD: 1.03 - 1.64), 1.22 (95% HPD: 0.90 - 1.64) and 1.4 (95% HPD: 0.91 - 1.9) for the entire dataset, first and second subset, respectively", "token_count": 492, "char_count": 1629, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5941, "quality_score": 0.7971, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:54.736062", "source": { "split": "train_shard_00001", "doc_id": 4543 }, "chunk_id": "train_shard_00001_4543_0", "global_id": 12086 }, { "text": "The BDSKY estimated an initial R(t) of about 2.0 (95% HPD: 0.04 - 5.0), which showed a growing trend at the end of 2014, reaching an average value of 3.22 in 2015, and then declining below 1 from the year 2016.

Conclusion

Monitoring the effective reproduction number can help to inform future vaccination strategies. The increase in the reproductive number for the Tuscany dataset, was consistent with the amplification event that led to the Tuscany outbreak. Subsequently, the intervention that led to the decline of the cases was followed, suggesting a high effectiveness of the vaccination campaign.\n\nEstimates of the reproductive numbers and demographic reconstruction of outbreak associated with C:P1.5-1,10-8:F3-6:ST-11(cc11) Neisseria meningitidis strains.", "token_count": 225, "char_count": 770, "word_count": 111, "semantic_coherence": 1, "information_density": 0.7027, "quality_score": 0.8514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:55.208874", "source": { "split": "train_shard_00001", "doc_id": 4543 }, "chunk_id": "train_shard_00001_4543_1", "global_id": 12087 }, { "text": "

Background

Despite the availability of numerous complete genome sequences from E. coli strains, published genome-scale metabolic models exist only for two commensal E. coli strains. These models have proven useful for many applications, such as engineering strains for desired product formation, and we sought to explore how constructing and evaluating additional metabolic models for E. coli strains could enhance these efforts.

Results

We used the genomic information from 16 E. coli strains to generate an E. coli pangenome metabolic network by evaluating their collective 76,990 ORFs. Each of these ORFs was assigned to one of 17,647 ortholog groups including ORFs associated with reactions in the most recent metabolic model for E. coli K-12. For orthologous groups that contain an ORF already represented in the MG1655 model, the gene to protein to reaction associations represented in this model could then be easily propagated to other E. coli strain models. All remaining orthologous groups were evaluated to see if new metabolic reactions could be added to generate a pangenome-scale metabolic model (iEco1712_pan). The pangenome model included reactions from a metabolic model update for E. coli K-12 MG1655 (iEco1339_MG1655) and enabled development of five additional strain-specific genome-scale metabolic models. These additional models include a second K-12 strain (iEco1335_W3110) and four pathogenic strains (two enterohemorrhagic E. coli O157:H7 and two uropathogens). When compared to the E. coli K-12 models, the metabolic models for the enterohemorrhagic (iEco1344_EDL933 and iEco1345_Sakai) and uropathogenic strains (iEco1288_CFT073 and iEco1301_UTI89) contained numerous lineage-specific gene and reaction differences. All six E", "token_count": 515, "char_count": 1767, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5587, "quality_score": 0.7794, "entities": { "genes": [ "MG1655" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:52:55.868278", "source": { "split": "train_shard_00001", "doc_id": 4544 }, "chunk_id": "train_shard_00001_4544_0", "global_id": 12088 }, { "text": "coli models were evaluated by comparing model predictions to carbon source utilization measurements under aerobic and anaerobic conditions, and to batch growth profiles in minimal media with 0.2% (w/v) glucose. An ancestral genome-scale metabolic model based on conserved ortholog groups in all 16 E. coli genomes was also constructed, reflecting the conserved ancestral core of E. coli metabolism (iEco1053_core). Comparative analysis of all six strain-specific E. coli models revealed that some of the pathogenic E. coli strains possess reactions in their metabolic networks enabling higher biomass yields on glucose. Finally the lineage-specific metabolic traits were compared to the ancestral core model predictions to derive new insight into the evolution of metabolism within this species.

Conclusion

Our findings demonstrate that a pangenome-scale metabolic model can be used to rapidly construct additional E. coli strain-specific models, and that quantitative models of different strains of E. coli can accurately predict strain-specific phenotypes. Such pangenome and strain-specific models can be further used to engineer metabolic phenotypes of interest, such as designing new industrial E. coli strains.\n\nThe evolution of metabolic networks of E. coli.", "token_count": 305, "char_count": 1272, "word_count": 178, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7978, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:56.438534", "source": { "split": "train_shard_00001", "doc_id": 4544 }, "chunk_id": "train_shard_00001_4544_1", "global_id": 12089 }, { "text": "Lipid peroxidation may be one of the main manifestations of cellular damage in the toxicity of several mycotoxins. A species of yeast, Kluyveromyces marxianus, was used in this study to determine the oxidative damage induced by T-2 toxin (T-2). Malondialdehyde (MDA), produced from the decomposition of lipid peroxides, was monitored using the thiobarbituric acid reaction. The yeast showed a high sensitivity to T-2 because the addition of 25 ng T-2/mL medium greatly reduced the multiplication rate of yeast. In addition, the MDA content increased when the concentration of T-2 was increased in the growth medium. Preincubation of the yeast with linoleic and linolenic acids in the medium enhanced the effects of T-2. The addition of the antioxidant dl-alpha-tocopherol acetate completely quenched the effects of T-2 whereas ascorbic acid and reduced glutathione (GSH) acted as prooxidants in this system. Electron paramagnetic resonance (EPR) spin trapping technique using lipid soluble N-tert-butyl-alpha-phenylnitrone (PNB) or more water soluble alpha-(4-pyridyl-1-oxide)-N-tert-butylnitrone (4-POBN) as free radical spin traps showed that free radical production was promoted by T-2. Vitamin E effectively quenched the EPR signals of the spin adducts. The observed spin adduct hyperfine splitting constants were consistent with those of alpha-hydroxyethyl radicals. The spin trapping data strongly suggest that initially generated hydroxyl radicals react with ethanol that is present in the samples, and the alpha-hydroxyethyl radicals formed in this process are then trapped. These data demonstrate that T-2 stimulates lipid peroxidation in a biological system due to an increased generation of hydroxyl radicals.\n\nFree radical-mediated lipid peroxidation induced by T-2 toxin in yeast (Kluyveromyces marxianus)", "token_count": 501, "char_count": 1818, "word_count": 258, "semantic_coherence": 1, "information_density": 0.593, "quality_score": 0.7965, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:57.093618", "source": { "split": "train_shard_00001", "doc_id": 4545 }, "chunk_id": "train_shard_00001_4545_0", "global_id": 12090 }, { "text": "

Purpose

Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. We conducted this study to determine unique gut microbial associated with allergic disease in children by shotgun gene sequencing.

Methods

We collected fecal samples from children with allergic asthma (n = 23) and allergic rhinitis (n = 18), and healthy control (n = 19). The gut microbiota of specimens was analyzed by high-throughput metagenomic shotgun gene sequencing.

Results

The intestinal microbiota of children with allergic asthma and allergic rhinitis was characterized by increased microbial richness and diversity. Simpson and Shannon were significantly elevated in children with allergic asthma. Principal coordinates analysis (PCoA) showed that the gut microbial communities cluster patterns of children with asthma or rhinitis were significantly different from those of healthy controls. However, no significant difference was found between asthma group and rhinitis group At the phylum level, higher relative abundance of Firmicutes was found in the allergic rhinitis group and allergic asthma group, while the level of Bacteroidetes was significantly lower. At the genus level, Corynebacterium, Streptococcus, Dorea, Actinomyces, Bifidobacterium, Blautia, and Rothia were significantly enriched in the allergic asthma group. Finally, a random forest classifier model selected 16 general signatures to discriminate the allergic asthma group from the healthy control group.

Conclusion

In conclusion, children in the allergic rhinitis group and allergic asthma group had altered gut microbiomes in comparison with the healthy control group. Compared to healthy children, the gut microbiome in children with allergic diseases has higher pro-inflammatory potential and increased production of pro-inflammatory molecules.\n\nAlterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing.", "token_count": 504, "char_count": 2056, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5, "quality_score": 0.75, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:57.750038", "source": { "split": "train_shard_00001", "doc_id": 4546 }, "chunk_id": "train_shard_00001_4546_0", "global_id": 12091 }, { "text": "Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world.\n\nPopulation genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections.", "token_count": 512, "char_count": 2048, "word_count": 266, "semantic_coherence": 1, "information_density": 0.594, "quality_score": 0.797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:58.424673", "source": { "split": "train_shard_00001", "doc_id": 4547 }, "chunk_id": "train_shard_00001_4547_0", "global_id": 12092 }, { "text": "A KfPDI gene high-expression cassette was constructed and cloned into different type of vectors. Some transformants with multi-copy number of integrated KfPDI gene was obtained by introducing the expression vectors into yeast Kluyveromyces fragilis. By the examination of protein disulfide isomerase activity, the result showed that the copy number of the KfPDI gene in the yeast transformants was closely related to the level of PDI activities. The K. fragilis strains for high expression of KfPDI gene can be used as genetic engineering host to enhance the secretion efficiency of foreign proteins.\n\nConstruction of Kluyveromyces fragilis strains for high expression of KfPDI gene", "token_count": 157, "char_count": 682, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:58.890791", "source": { "split": "train_shard_00001", "doc_id": 4548 }, "chunk_id": "train_shard_00001_4548_0", "global_id": 12093 }, { "text": "Long-chain flavodoxins, ubiquitous electron shuttles containing flavin mononucleotide (FMN) as prosthetic group, play an important protective role against reactive oxygen species (ROS) in various microorganisms. Pseudomonas aeruginosa is an opportunistic pathogen which frequently has to face ROS toxicity in the environment as well as within the host. We identified a single ORF, hereafter referred to as fldP (for fl avo d oxin from P . aeruginosa), displaying the highest similarity in length, sequence identity and predicted secondary structure with typical long-chain flavodoxins. The gene was cloned and expressed in Escherichia coli. The recombinant product (FldP) could bind FMN and exhibited flavodoxin activity in vitro. Expression of fldP in P. aeruginosa was induced by oxidative stress conditions through an OxyR-independent mechanism, and an fldP-null mutant accumulated higher intracellular ROS levels and exhibited decreased tolerance to H2O2 toxicity compared to wild-type siblings. The mutant phenotype could be complemented by expression of a cyanobacterial flavodoxin. Overexpression of FldP in a mutT-deficient P. aeruginosa strain decreased H2O2-induced cell death and the hypermutability caused by DNA oxidative damage. FldP contributed to the survival of P. aeruginosa within cultured mammalian macrophages and in infected Drosophila melanogaster, which led in turn to accelerated death of the flies. Interestingly, the fldP gene is present in some but not all P. aeruginosa strains, constituting a component of the P. aeruginosa accessory genome. It is located in a genomic island as part of a self-regulated polycistronic operon containing a suite of stress-associated genes. The collected results indicate that the fldP gene encodes a long-chain flavodoxin, which protects the cell from oxidative stress, thereby expanding the capabilities of P. aeruginosa to thrive in hostile environments.\n\nA long-chain flavodoxin protects Pseudomonas aeruginosa from oxidative stress and host bacterial clearance.", "token_count": 512, "char_count": 2027, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8084, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:52:59.533364", "source": { "split": "train_shard_00001", "doc_id": 4549 }, "chunk_id": "train_shard_00001_4549_0", "global_id": 12094 }, { "text": "We have isolated a Lactobacillus plantarum strain (MiLAB 393) from grass silage that produces broad-spectrum antifungal compounds, active against food- and feed-borne filamentous fungi and yeasts in a dual-culture agar plate assay. Fusarium sporotrichioides and Aspergillus fumigatus were the most sensitive among the molds, and Kluyveromyces marxianus was the most sensitive yeast species. No inhibitory activity could be detected against the mold Penicillium roqueforti or the yeast Zygosaccharomyces bailii. An isolation procedure, employing a microtiter well spore germination bioassay, was devised to isolate active compounds from culture filtrate. Cell-free supernatant was fractionated on a C(18) SPE column, and the 95% aqueous acetonitrile fraction was further separated on a preparative HPLC C(18) column. Fractions active in the bioassay were then fractionated on a porous graphitic carbon column. The structures of the antifungal compounds cyclo(L-Phe-L-Pro), cyclo(L-Phe-trans-4-OH-L-Pro) and 3-phenyllactic acid (L/D isomer ratio, 9:1), were determined by nuclear magnetic resonance spectroscopy, mass spectrometry, and gas chromatography. MIC values against A. fumigatus and P. roqueforti were 20 mg ml(-1) for cyclo(L-Phe-L-Pro) and 7.5 mg ml(-1) for phenyllactic acid. Combinations of the antifungal compounds revealed weak synergistic effects. The production of the antifungal cyclic dipeptides cyclo(L-Phe-L-Pro) and cyclo(L-Phe-trans-4-OH-L-Pro) by lactic acid bacteria is reported here for the first time.", "token_count": 472, "char_count": 1526, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6912, "quality_score": 0.8456, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:00.225025", "source": { "split": "train_shard_00001", "doc_id": 4550 }, "chunk_id": "train_shard_00001_4550_0", "global_id": 12095 }, { "text": "Lactobacillus plantarum MiLAB 393 produces the antifungal cyclic dipeptides cyclo(L-Phe-L-Pro) and cyclo(L-Phe-trans-4-OH-L-Pro) and 3-phenyllactic acid.", "token_count": 69, "char_count": 153, "word_count": 15, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:00.627181", "source": { "split": "train_shard_00001", "doc_id": 4550 }, "chunk_id": "train_shard_00001_4550_1", "global_id": 12096 }, { "text": "

Background

Corynebacterium pseudotuberculosis is a Gram-positive facultative intracellular pathogen and the etiologic agent of illnesses like caseous lymphadenitis in small ruminants, mastitis in dairy cattle, ulcerative lymphangitis in equines, and oedematous skin disease in buffalos. With the growing advance in high-throughput technologies, genomic studies have been carried out to explore the molecular basis of its virulence and pathogenicity. However, data large-scale functional genomics studies are necessary to complement genomics data and better understating the molecular basis of a given organism. Here we summarize, MS-based proteomics techniques and bioinformatics tools incorporated in genomic functional studies of C. pseudotuberculosis to discover the different patterns of protein modulation under distinct environmental conditions, and antigenic and drugs targets.

Methodology

In this study we performed an extensive search in Web of Science of original and relevant articles related to methods, strategy, technology, approaches, and bioinformatics tools focused on the functional study of the genome of C. pseudotuberculosis at the protein level.

Results

Here, we highlight the use of proteomics for understating several aspects of the physiology and pathogenesis of C. pseudotuberculosis at the protein level. The implementation and use of protocols, strategies, and proteomics approach to characterize the different subcellular fractions of the proteome of this pathogen. In addition, we have discussed the immunoproteomics, immunoinformatics and genetic tools employed to identify targets for immunoassays, drugs, and vaccines against C. pseudotuberculosis infection.

Conclusion

In this review, we showed that the combination of proteomics and bioinformatics studies is a suitable strategy to elucidate the functional aspects of the C. pseudotuberculosis genome. Together, all information generated from these proteomics studies allowed expanding our knowledge about factors related to the pathophysiology of this pathogen.", "token_count": 516, "char_count": 2118, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5746, "quality_score": 0.7873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:01.656622", "source": { "split": "train_shard_00001", "doc_id": 4551 }, "chunk_id": "train_shard_00001_4551_0", "global_id": 12097 }, { "text": "A journey through the Corynebacterium pseudotuberculosis proteome promotes insights into its functional genome.", "token_count": 32, "char_count": 118, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:02.016783", "source": { "split": "train_shard_00001", "doc_id": 4551 }, "chunk_id": "train_shard_00001_4551_1", "global_id": 12098 }, { "text": "

Aim

Nontuberculous mycobacterial (NTM) infection such as endophthalmitis, dacryocystitis, and canaliculitis are pervasive across the globe and are currently managed by antibiotics. However, the recent cases of Mycobacteroides developing drug resistance reported along with the improper practice of medicine intrigued us to explore its genomic and proteomic canvas at a global scale and develop a chimeric vaccine against Mycobacteroides.

Main methods

We carried out a vivid genomic study on five recently sequenced strains of Mycobacteroides and explored their Pan-core genome/proteome in three different phases. The promiscuous antigenic proteins were identified via a subtractive proteomics approach that qualified for virulence causation, resistance and essentiality factors for this notorious bacterium. An integrated pipeline was developed for the identification of B-Cell, MHC (Major histocompatibility complex) class I and II epitopes.

Key findings

Phase I identified the shreds of evidence of reductive evolution and propensity of the Pan-genome of Mycobacteroides getting closed soon. Phase II and Phase III produced 8 vaccine constructs. Our final vaccine construct, V6 qualified for all tests such as absence for allergenicity, presence of antigenicity, etc. V6 contains β-defensin as an adjuvant, linkers, Lysosomal-associated membrane protein 1 (LAMP1) signal peptide, and PADRE (Pan HLA-DR epitopes) amino acid sequence. Besides, V6 also interacts with a maximum number of MHC molecules and the TLR4/MD2 (Toll-like receptor 4/Myeloid differentiation factor 2) complex confirmed by docking and molecular dynamics simulation studies.

Significance

The knowledge harnessed from the current study can help improve the current treatment regimens or in an event of an outbreak and propel further related studies.\n\nToward a chimeric vaccine against multiple isolates of Mycobacteroides - An integrative approach.", "token_count": 503, "char_count": 1947, "word_count": 260, "semantic_coherence": 1, "information_density": 0.7231, "quality_score": 0.8615, "entities": { "genes": [ "LAMP1", "TLR4", "MD2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:02.673173", "source": { "split": "train_shard_00001", "doc_id": 4552 }, "chunk_id": "train_shard_00001_4552_0", "global_id": 12099 }, { "text": "

Objectives

Here we used whole genome sequencing (WGS) to understand strain diversity and potential for patient-to-patient transmission of Staphylococcus aureus among children with cystic fibrosis (CF) in Queensland, Australia.

Methods

S. aureus isolates (n = 401) collected between January 2018 and April 2019 from 184 patients with CF (n = 318 isolates) and 76 patients without CF (n = 83 isolates) were subjected to WGS and subsequent multilocus sequence typing (MLST), and a phylogeny was constructed from core genome single nucleotide polymorphism (SNP) analysis. The subsequent data was compared with available patient information.

Results

WGS revealed that patients with CF were essentially colonised by the same genotypes as those seen in patients without CF. Sequence types (ST) for our patients with CF were predominantly ST5 (20.1%), ST30 (7.3%), ST15 (6.3%) and ST8 (5.3%). Two Australian clones, ST93 and ST239, typically seen in skin infections and health-care settings, respectively, were notably absent from our patients with CF. Based on a SNP distance threshold of 14 SNPs, 20 cluster types involving 50/260 patients were evident; of these, 6 clusters contained only patients found to be siblings or otherwise living in the same household. Epidemiological relationships could not be determined for a remaining 14 cluster types involving 38 patients, comprising 2-7 (median 2) patients each. Multiple S. aureus genotypes were observed in 19/73 CF patients who provided more than one sample.

Conclusion

These results show that WGS is a useful tool for surveillance of S. aureus strains in children with CF and that the strains in our CF cohort were largely consistent with those circulating in patients without CF. Overall, this confirms previous findings and indicates that S", "token_count": 492, "char_count": 1820, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [ "ST239", "ST30", "ST5", "ST8", "ST15", "ST93" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:04.044025", "source": { "split": "train_shard_00001", "doc_id": 4553 }, "chunk_id": "train_shard_00001_4553_0", "global_id": 12100 }, { "text": "aureus acquisition in children with CF is similar to that of other patient groups, with limited evidence of potential patient-to-patient transmission within this patient group.\n\nLimited evidence of patient-to-patient transmission of Staphylococcus aureus strains between children with cystic fibrosis, Queensland, Australia.", "token_count": 71, "char_count": 324, "word_count": 41, "semantic_coherence": 1, "information_density": 0.7073, "quality_score": 0.8537, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:04.413751", "source": { "split": "train_shard_00001", "doc_id": 4553 }, "chunk_id": "train_shard_00001_4553_1", "global_id": 12101 }, { "text": "Aim: To compare the genome sequences among clinical and American-Type Culture Collection Ureaplasma strains and to reveal the potential molecular mechanisms of multiple banded antigen (MBA) variation. Materials & methods: Two strains of Ureaplasma urealyticum 132 and 315 and one strain of Ureaplasma parvum 106 isolated from infertile males were sequenced using Illumina and Nanopore technologies. Comparative genomic analysis was performed of the three strains and two American-Type Culture Collection strains. Results & conclusion: The Ureaplasma species shared a core genome. Strains 132 and 315 shared a distant relationship with previously sequenced Ureaplasma spp. The MBA locus is more informative for studying MBA mutations than is the mba gene alone. The mechanisms of MBA variation are more flexible and complex than previously reported. The variation in MBA is not limited to the mba gene but occurs in other genes within the MBA locus.\n\nComparative genomics of three clinical Ureaplasma species: analysis of their core genomes and multiple-banded antigen locus.", "token_count": 330, "char_count": 1151, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:04.985052", "source": { "split": "train_shard_00001", "doc_id": 4554 }, "chunk_id": "train_shard_00001_4554_0", "global_id": 12102 }, { "text": "Bloodstream infections (BSIs) are a major cause of morbidity and mortality in acute myeloid leukemia (AML) patients undergoing induction chemotherapy. Staphylococcus epidermidis, typically a skin commensal, is increasingly recognized as a pathogen in these vulnerable individuals. This study investigated whether genomic differences exist between infectious and gastrointestinal colonizing S. epidermidis isolates from AML patients and how these compare to colonizing and infectious isolates from other patient groups and biogeographic sites. We analyzed 114 isolates-44 from AML patients (23 infections, 21 GI colonizers) and 70 from public datasets (34 infections, 36 colonizers). Stool samples underwent 16S rRNA sequencing and culture to identify colonization, while bloodstream isolates were sequenced and compared. Genomic profiling using Roary, Scoary, Phyre2, and InterProScan revealed that infectious and GI-colonizing AML isolates were phylogenetically close but genomically distinct. Infectious isolates from AML patients were significantly enriched for resistance genes (e.g., mecA, mecR1, mecI, ANT(4')-Ib) and the biofilm-associated gene icaA. AML infectious isolates harbored more resistance genes and mobile elements than non-AML strains but lacked widespread classical virulence factors. These results suggest that S. epidermidis pathogenicity in immunocompromised hosts is driven by genomic adaptability and antibiotic tolerance rather than traditional virulence mechanisms.\n\n<i>Staphylococcus epidermidis</i> in Acute Myeloid Leukemia: A Comparative Genomic Study Against Non-AML Isolates.", "token_count": 473, "char_count": 1676, "word_count": 206, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:05.628427", "source": { "split": "train_shard_00001", "doc_id": 4555 }, "chunk_id": "train_shard_00001_4555_0", "global_id": 12103 }, { "text": "Human campylobacteriosis, caused by Campylobacter jejuni and C. coli, remains a leading cause of bacterial gastroenteritis in many countries, but the epidemiology of campylobacteriosis outbreaks remains poorly defined, largely due to limitations in the resolution and comparability of isolate characterization methods. Whole-genome sequencing (WGS) data enable the improvement of sequence-based typing approaches, such as multilocus sequence typing (MLST), by substantially increasing the number of loci examined. A core genome MLST (cgMLST) scheme defines a comprehensive set of those loci present in most members of a bacterial group, balancing very high resolution with comparability across the diversity of the group. Here we propose a set of 1,343 loci as a human campylobacteriosis cgMLST scheme (v1.0), the allelic profiles of which can be assigned to core genome sequence types. The 1,343 loci chosen were a subset of the 1,643 loci identified in the reannotation of the genome sequence of C. jejuni isolate NCTC 11168, chosen as being present in >95% of draft genomes of 2,472 representative United Kingdom campylobacteriosis isolates, comprising 2,207 (89.3%) C. jejuni isolates and 265 (10.7%) C. coli isolates. Validation of the cgMLST scheme was undertaken with 1,478 further high-quality draft genomes, containing 150 or fewer contiguous sequences, from disease isolate collections: 99.5% of these isolates contained ≥95% of the 1,343 cgMLST loci. In addition to the rapid and effective high-resolution analysis of large numbers of diverse isolates, the cgMLST scheme enabled the efficient identification of very closely related isolates from a well-defined single-source campylobacteriosis outbreak.", "token_count": 488, "char_count": 1749, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6032, "quality_score": 0.8016, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:06.276501", "source": { "split": "train_shard_00001", "doc_id": 4556 }, "chunk_id": "train_shard_00001_4556_0", "global_id": 12104 }, { "text": "Core Genome Multilocus Sequence Typing Scheme for Stable, Comparative Analyses of Campylobacter jejuni and C. coli Human Disease Isolates.", "token_count": 40, "char_count": 138, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:06.638158", "source": { "split": "train_shard_00001", "doc_id": 4556 }, "chunk_id": "train_shard_00001_4556_1", "global_id": 12105 }, { "text": "In this study, 250 vaginal samples from patients with vulvovaginal candidosis were inoculated onto two chromogenic media, Albicans ID(2) and Biggy agar, as well as onto Sabouraud chloramphenicol agar, yielding a total of 63 yeast (25.2 %) on all three media. These strains were identified as Candida glabrata in 20 (31.8 %) samples, Candida albicans in 15 samples (23.8 %), Candida tropicalis in 10 samples (15.9 %), Candida krusei in five samples (7.9 %), Candida kefyr in five samples (7.9 %), Candida dubliniensis in four samples (6.3 %), Candida parapsilosis in two samples (3.2 %) and Candida guilliermondii in two samples (3.2 %). Mixed fungal cultures and bacterial growth or filamentous fungi were not detected on any of the selected media. The sensitivity and specificity of the Albicans ID(2) and Biggy agar with regard to the identification of C. albicans were 80.0 and 64.6 %, and 86.7 and 56.3 %, respectively. This study showed these two chromogenic media to be as effective as Sabouraud chloramphenicol agar with respect to fungal detection. However, neither Albicans ID(2) nor Biggy agar was sufficient for reliable differentiation of yeasts to the species level.\n\nEvaluation of Albicans ID2 and Biggy agar for the isolation and direct identification of vaginal yeast isolates.", "token_count": 384, "char_count": 1293, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5437, "quality_score": 0.7718, "entities": { "genes": [ "ID2" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:07.256900", "source": { "split": "train_shard_00001", "doc_id": 4557 }, "chunk_id": "train_shard_00001_4557_0", "global_id": 12106 }, { "text": "Abstract

Background

Pediatric oncology and hematopoietic stem cell transplant patients (POTP) are at increased risk for Clostridioides difficile infection (CDI) and recurrence. It is unknown whether recurrent CDI is related to the same C. difficile strain as the initial CDI. We describe genomic relatedness of C. difficile strains in patients with multiple CDI using whole-genome sequencing (WGS).

Methods

This was a retrospective cohort study of CDI in POTP in 2016. CDI cases were identified by electronic medical record search for positive C. difficile toxin PCR tests. Patients with multiple CDI episodes were identified. CDI episodes were classified as incident, duplicate or recurrent using National Healthcare Safety Network (NHSN) definitions. Retrieved residual stool specimens were cultured anaerobically, toxin-producing C. difficile isolates were determined using a cell culture cytotoxicity assay with neutralization and WGS was performed followed by core genome MLST (cgMLST). Variability of the isolates was summarized by strain type (ST), and a minimum spanning tree was constructed, defining genomically related isolates as those with <7 allele difference.

Results

Eighteen patients had 51 positive C. difficile samples. CDI were classified as incident in 31 (61%) episodes, recurrent in 18 (36%), and duplicate in 2 (3%). Isolates from 47 (92%) samples were sequenced, identifying 14 different strain types (ST) in 41 (87%) isolates. Of the 31 incident CDI, 13 (42%) episodes occurred 8 weeks or more after the initial incident CDI. Among those 13 incident CDI, 7 (54%) had prior CDI due to a related isolate. Of the 18 recurrent CDIs, 10 (55%) were due to an isolate related to the previous incident CDI and 5 (28%) were due to an isolate unrelated to the incident CDI", "token_count": 509, "char_count": 1815, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:07.916052", "source": { "split": "train_shard_00001", "doc_id": 4558 }, "chunk_id": "train_shard_00001_4558_0", "global_id": 12107 }, { "text": "The relatedness of the remaining 3 recurrent episodes could not be evaluated because no isolate was available for sequence analysis.

Conclusion

CDI classification of incident vs. recurrent infection using NHSN definition might be not applicable in POTP. WGS showed that more than half of CDI episodes classified as incident were actually a recurrence of a previous C. difficile strain. Similarly, some CDI episodes classified as recurrent were actually re-infection with a different stain.

Disclosures

Randall Hayden, MD, Abbott Molecular: Advisory Board; Quidel: Advisory Board; Roche Diagnostics: Advisory Board\n\n2400. Are Multiple Clostridioides difficile Infections in Pediatric Oncology Patients Related to Recurrence of the Same Isolate or Re-infections with Different isolates?", "token_count": 200, "char_count": 802, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:08.381708", "source": { "split": "train_shard_00001", "doc_id": 4558 }, "chunk_id": "train_shard_00001_4558_1", "global_id": 12108 }, { "text": "

Background

Hypervirulent Klebsiella pneumoniae lacking classical virulence factors is uncommon, and the virulence mechanisms of this organism are not understood.

Methods

Following a retrospective study of carbapenem-resistant K. pneumoniae based on core genome multilocus sequence typing (cgMLST), isolates that caused high mortality were investigated with a genome-wide association study (GWAS), proteome analysis and an animal model.

Results

The sublineage of sequence type 11 (ST11) K. pneumoniae , which belongs to complex type 3176 (CT3176) and K-locus 47 (KL47), was highlighted due to the high mortality of infected patients. GWAS analysis showed that ampR was associated with the CT3176 isolates. In a mouse model, the mortality of ampR -carrying isolates was comparable to that of the typical hypervirulent isolate GM2. Even during the first 24 hours of infection, the bacterial load and pathological changes of the ampR -carrying isolates in the lungs were more severe than those of GM2. The ampR complement mutant was able to enhance the virulence of the KL47 isolate but not the virulence of KL1. Proteome analysis showed that the expression of WcaJ in the ampR + isolates was significantly higher than that in the ampR − isolates, and this result was also confirmed by transcription tests and capsule staining. It is suggested that the enhancement of the initial stage of capsule synthesis may be the cause of the high virulence of these non-hypermucoviscous ST11 carbapenem-resistant K. pneumoniae isolates.

Conclusions

Non-hypermucoviscous ST11 hypervirulent carbapenem-resistant K. pneumoniae warrants continued surveillance and investigation.", "token_count": 470, "char_count": 1695, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5656, "quality_score": 0.7828, "entities": { "genes": [ "KL1", "KL47", "ST11", "GM2", "CT3176" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:09.023411", "source": { "split": "train_shard_00001", "doc_id": 4559 }, "chunk_id": "train_shard_00001_4559_0", "global_id": 12109 }, { "text": "A Novel Non-hypermucoviscous ST11 Hypervirulent Carbapenem-resistantKlebsiella pneumoniaeLacking Classical Virulence Factors", "token_count": 51, "char_count": 131, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:09.385531", "source": { "split": "train_shard_00001", "doc_id": 4559 }, "chunk_id": "train_shard_00001_4559_1", "global_id": 12110 }, { "text": "In synchronized continuous cultures of Saccharomyces cerevisiae CBS 8066, the production of the extracellular invertase (EC 3.2.1.26) showed a cyclic behavior that coincided with the budding cycle. The invertase activity increased during bud development and ceased at bud maturation and cell scission. The cyclic changes in invertase production resulted in cyclic changes in amounts of invertase localized in the cell wall. However, the amount of enzyme invertase present in the culture liquid remained constant throughout the budding cycle. Also, in asynchronous continuous cultures of S. cerevisiae, the production and localization of invertase showed significant fluctuation. The overall invertase production in an asynchronous culture was two to three times higher than in synchronous cultures. This could be due to more-severe invertase-repressive conditions in a synchronous chemostat culture. Both the intracellular glucose-6-phosphate concentration and residual glucose concentration were significantly higher in synchronous chemostat cultures than in asynchronous chemostat cultures. In the asynchronous and synchronous continuous cultures of S. cerevisiae, about 40% of the invertase was released into the culture liquid; it has generally been believed that S. cerevisiae releases only about 5% of its invertase. In contrast to invertase production and localization in the chemostat cultures of S. cerevisiae, no significant changes in inulinase (EC 3.2.1.7) production and localization were observed in chemostat cultures of Kluyveromyces maxianus CBS 6556. In cultures of K. marxianus about 50% of the inulinase was present in the culture liquid.\n\nProduction and localization of beta-fructosidase in asynchronous and synchronous chemostat cultures of yeasts.", "token_count": 436, "char_count": 1770, "word_count": 246, "semantic_coherence": 1, "information_density": 0.4593, "quality_score": 0.7297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:10.015523", "source": { "split": "train_shard_00001", "doc_id": 4560 }, "chunk_id": "train_shard_00001_4560_0", "global_id": 12111 }, { "text": "The inhibition of growth by octanoic or decanoic acids, two subproducts of ethanolic fermentation, was evaluated in Saccharomyces cerevisiae and Kluyveromyces marxianus in association with ethanol, the main product of fermentation. In both strains, octanoic and decanoic acids, at concentrations up to 16 and 8 mg/liter, respectively, decreased the maximum specific growth rate and the biomass yield at 30 degrees C as an exponential function of the fatty acid concentration and increased the duration of growth latency. These toxic effects increased with a decrease in pH in the range of 5.4 to 3.0, indicating that the undissociated form is the toxic molecule. Decanoic acid was more toxic than octanoic acid. The concentrations of octanoic and decanoic acids were determined during the ethanolic fermentation (30 degrees C) of two laboratory media (mineral and complex) by S. cerevisiae and of Jerusalem artichoke juice by K. marxianus. Based on the concentrations detected (0.7 to 23 mg/liter) and the kinetics of growth inhibition, the presence of octanoic and decanoic acids cannot be ignored in the evaluation of the overall inhibition of ethanolic fermentation.\n\nInhibition of Yeast Growth by Octanoic and Decanoic Acids Produced during Ethanolic Fermentation.", "token_count": 335, "char_count": 1268, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5573, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:10.588742", "source": { "split": "train_shard_00001", "doc_id": 4561 }, "chunk_id": "train_shard_00001_4561_0", "global_id": 12112 }, { "text": "The thermotolerant methylotrophic yeast Hansenula polymorpha is able to ferment xylose to ethanol. To improve characteristics of xylose fermentation, the recombinant strain Delta xyl1 Delta xyl2-ADelta xyl2-B, with deletions of genes encoding first enzymes of xylose utilization (NAD(P)H-dependent xylose reductase and NAD-dependent xylitol dehydrogenases, respectively), was constructed and used as a recipient for co-overexpression of the Escherichia coli xylA gene coding for xylose isomerase and endogenous XYL3 gene coding for xylulokinase. The expression of both genes was driven by the H. polymorpha glyceraldehyde-3-phosphate dehydrogenase promoter. Xylose isomerase activities of obtained transformants amounted to approximately 80% of that of the bacterial host strain. Xylulokinase activities of the transformants increased twofold when compared with the parental strain. The recombinant strains displayed improved ethanol production during the fermentation of xylose.\n\nOverexpression of bacterial xylose isomerase and yeast host xylulokinase improves xylose alcoholic fermentation in the thermotolerant yeast Hansenula polymorpha.", "token_count": 323, "char_count": 1142, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [ "XYL3" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:11.177349", "source": { "split": "train_shard_00001", "doc_id": 4562 }, "chunk_id": "train_shard_00001_4562_0", "global_id": 12113 }, { "text": "

Background

The genus Saccharothrix is a representative of the family Pseudonocardiaceae, known to include producer strains of a wide variety of potent antibiotics. Saccharothrix espanaensis produces both saccharomicins A and B of the promising new class of heptadecaglycoside antibiotics, active against both bacteria and yeast.

Results

To better assess its capabilities, the complete genome sequence of S. espanaensis was established. With a size of 9,360,653 bp, coding for 8,501 genes, it stands alongside other Pseudonocardiaceae with large genomes. Besides a predicted core genome of 810 genes shared in the family, S. espanaensis has a large number of accessory genes: 2,967 singletons when compared to the family, of which 1,292 have no clear orthologs in the RefSeq database. The genome analysis revealed the presence of 26 biosynthetic gene clusters potentially encoding secondary metabolites. Among them, the cluster coding for the saccharomicins could be identified.

Conclusion

S. espanaensis is the first completely sequenced species of the genus Saccharothrix. The genome discloses the cluster responsible for the biosynthesis of the saccharomicins, the largest oligosaccharide antibiotic currently identified. Moreover, the genome revealed 25 additional putative secondary metabolite gene clusters further suggesting the strain's potential for natural product synthesis.\n\nComplete genome sequence of Saccharothrix espanaensis DSM 44229(T) and comparison to the other completely sequenced Pseudonocardiaceae.", "token_count": 404, "char_count": 1543, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:11.824098", "source": { "split": "train_shard_00001", "doc_id": 4563 }, "chunk_id": "train_shard_00001_4563_0", "global_id": 12114 }, { "text": "A bacterial and viral genome catalogue from Atlantic salmon highlights diverse gut microbiome compositions at pre- and post-smolt life stages", "token_count": 32, "char_count": 141, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:12.232675", "source": { "split": "train_shard_00001", "doc_id": 4564 }, "chunk_id": "train_shard_00001_4564_0", "global_id": 12115 }, { "text": "Despite their therapeutic benefits, antibiotics exert collateral damage on the microbiome and promote antimicrobial resistance. However, the mechanisms governing microbiome recovery from antibiotics are poorly understood. Treatment of Mycobacterium tuberculosis, the world's most common infection, represents the longest antimicrobial exposure in humans. Here, we investigate gut microbiome dynamics over 20 months of multidrug-resistant tuberculosis (TB) and 6 months of drug-sensitive TB treatment in humans. We find that gut microbiome dynamics and TB clearance are shared predictive cofactors of the resolution of TB-driven inflammation. The initial severe taxonomic and functional microbiome disruption, pathobiont domination, and enhancement of antibiotic resistance that initially accompanied long-term antibiotics were countered by later recovery of commensals. This resilience was driven by the competing evolution of antimicrobial resistance mutations in pathobionts and commensals, with commensal strains with resistance mutations reestablishing dominance. Fecal-microbiota transplantation of the antibiotic-resistant commensal microbiome in mice recapitulated resistance to further antibiotic disruption. These findings demonstrate that antimicrobial resistance mutations in commensals can have paradoxically beneficial effects by promoting microbiome resilience to antimicrobials and identify microbiome dynamics as a predictor of disease resolution in antibiotic therapy of a chronic infection.\n\nCommensal antimicrobial resistance mediates microbiome resilience to antibiotic disruption.", "token_count": 381, "char_count": 1608, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6103, "quality_score": 0.8051, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:12.822855", "source": { "split": "train_shard_00001", "doc_id": 4565 }, "chunk_id": "train_shard_00001_4565_0", "global_id": 12116 }, { "text": "Bacteria of the genus Flavobacterium are recovered from a large variety of environments. Among the described species, Flavobacterium psychrophilum and Flavobacterium columnare cause considerable losses in fish farms. Alongside these well-known fish-pathogenic species, isolates belonging to the same genus recovered from diseased or apparently healthy wild, feral, and farmed fish have been suspected to be pathogenic. Here, we report the identification and genomic characterization of a Flavobacterium collinsii isolate (TRV642) retrieved from rainbow trout spleen. A phylogenetic tree of the genus built by aligning the core genome of 195 Flavobacterium species revealed that F. collinsii stands within a cluster of species associated with diseased fish, the closest one being F. tructae, which was recently confirmed as pathogenic. We evaluated the pathogenicity of F. collinsii TRV642 as well as of Flavobacterium bernardetii F-372T, another recently described species reported as a possible emerging pathogen. Following intramuscular injection challenges in rainbow trout, no clinical signs or mortalities were observed with F. bernardetii. F. collinsii showed very low virulence but was isolated from the internal organs of survivors, indicating that the bacterium is able to survive inside the host and may provoke disease in fish under compromised conditions such as stress and/or wounds. Our results suggest that members of a phylogenetic cluster of fish-associated Flavobacterium species may be opportunistic fish pathogens causing disease under specific circumstances. IMPORTANCE Aquaculture has expanded significantly worldwide in the last decades and accounts for half of human fish consumption. However, infectious fish diseases are a major bottleneck for its sustainable development, and an increasing number of bacterial species from diseased fish raise a great concern. The current study revealed phylogenetic associations with ecological niches among the Flavobacterium species", "token_count": 511, "char_count": 2069, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6416, "quality_score": 0.8208, "entities": { "genes": [ "TRV642" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:13.475623", "source": { "split": "train_shard_00001", "doc_id": 4566 }, "chunk_id": "train_shard_00001_4566_0", "global_id": 12117 }, { "text": "We also focused on Flavobacterium collinsii, which belongs to a group of putative pathogenic species. The genome contents revealed a versatile metabolic repertoire suggesting the use of diverse nutrient sources, a characteristic of saprophytic or commensal bacteria. In a rainbow trout experimental challenge, the bacterium survived inside the host, likely escaping clearance by the immune system but without provoking massive mortality, suggesting opportunistic pathogenic behavior. This study highlights the importance of experimentally evaluating the pathogenicity of the numerous bacterial species retrieved from diseased fish.\n\nInvestigation of the Genus Flavobacterium as a Reservoir for Fish-Pathogenic Bacterial Species: the Case of Flavobacterium collinsii.", "token_count": 181, "char_count": 773, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7723, "quality_score": 0.8861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:13.922156", "source": { "split": "train_shard_00001", "doc_id": 4566 }, "chunk_id": "train_shard_00001_4566_1", "global_id": 12118 }, { "text": "

Background

Acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the Acidithiobacillales. As such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. In this study, we explore the genomic diversity of A. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome.

Principal findings

Comparative sequence analysis of A. caldus ATCC 51756 and SM-1 indicate that, despite sharing a conserved and highly syntenic genomic core, both strains have unique gene complements encompassing nearly 20% of their respective genomes. The differential gene complement of each strain is distributed between the chromosomal compartment, one megaplasmid and a variable number of smaller plasmids, and is directly associated to a diverse pool of mobile genetic elements (MGE). These include integrative conjugative and mobilizable elements, genomic islands and insertion sequences. Some of the accessory functions associated to these MGEs have been linked previously to the flexible gene pool in microorganisms inhabiting completely different econiches. Yet, others had not been unambiguously mapped to the flexible gene pool prior to this report and clearly reflect strain-specific adaption to local environmental conditions.

Significance

For many years, and because of DNA instability at low pH and recurrent failure to genetically transform acidophilic bacteria, gene transfer in acidic environments was considered negligible. Findings presented herein imply that a more or less conserved pool of actively excising MGEs occurs in the A. caldus population and point to a greater frequency of gene exchange in this econiche than previously recognized. Also, the data suggest that these elements endow the species with capacities to withstand the diverse abiotic and biotic stresses of natural environments, in particular those associated with its extreme econiche.\n\nArchitecture and gene repertoire of the flexible genome of the extreme acidophile Acidithiobacillus caldus.", "token_count": 502, "char_count": 2174, "word_count": 300, "semantic_coherence": 1, "information_density": 0.6467, "quality_score": 0.8233, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:14.579322", "source": { "split": "train_shard_00001", "doc_id": 4567 }, "chunk_id": "train_shard_00001_4567_0", "global_id": 12119 }, { "text": "Defining phenotypic and associated genotypic variation among Bdellovibrio may further our understanding of how this genus attacks and kills different Gram-negative bacteria. We isolated Bdellovibrio sp. NC01 from soil. Analysis of 16S rRNA gene sequences and average amino acid identity showed that NC01 belongs to a different species than the type species bacteriovorus. By clustering amino acid sequences from completely sequenced Bdellovibrio and comparing the resulting orthologue groups to a previously published analysis, we defined a 'core genome' of 778 protein-coding genes and identified four protein-coding genes that appeared to be missing only in NC01. To determine how horizontal gene transfer (HGT) may have impacted NC01 genome evolution, we performed genome-wide comparisons of Bdellovibrio nucleotide sequences, which indicated that eight NC01 genomic regions were likely acquired by HGT. To investigate how genome variation may impact predation, we compared protein-coding gene content between NC01 and the B. bacteriovorus type strain HD100, focusing on genes implicated as important in successful killing of prey. Of these, NC01 is missing ten genes that may play roles in lytic activity during predation. Compared to HD100, NC01 kills fewer tested prey strains and kills Escherichia coli ML35 less efficiently. NC01 causes a smaller log reduction in ML35, after which the prey population recovers and the NC01 population decreases. In addition, NC01 forms turbid plaques on lawns of E. coli ML35, in contrast to clear plaques formed by HD100. Linking phenotypic variation in interactions between Bdellovibrio and Gram-negative bacteria with underlying Bdellovibrio genome variation is valuable for understanding the ecological significance of predatory bacteria and evaluating their effectiveness in clinical applications.", "token_count": 502, "char_count": 1914, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [ "HD100", "NC01", "ML35" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:15.235716", "source": { "split": "train_shard_00001", "doc_id": 4568 }, "chunk_id": "train_shard_00001_4568_0", "global_id": 12120 }, { "text": "Variation in genome content and predatory phenotypes between Bdellovibrio sp. NC01 isolated from soil and B. bacteriovorus type strain HD100.", "token_count": 53, "char_count": 155, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [ "HD100", "NC01" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:15.594889", "source": { "split": "train_shard_00001", "doc_id": 4568 }, "chunk_id": "train_shard_00001_4568_1", "global_id": 12121 }, { "text": "The dead-end filtration characteristics of the dimorphic yeast Kluyveromyces marxianus var. marxianus (formerly fragilis) NRRLy2415 were investigated for a range of mean cell morphologies, ranging from predominantly yeast-like to predominantly filamentous. Semiautomated image analysis was used to measure the mean cell specific surface area, Sv, and the mean ratio of cell length to equivalent cylindrical diameter, Ldm, in each broth. The method of Ju and Ho (Biotechnol. Bioeng. 1988, 32, 95-99) was used to show that for broths with Ldm values between 1.72 and 10.03, the voidage of cell pellets formed by centrifugation increased with increasing Ldm. In the pressure range 30-180 kPa, the specific filter cake resistance, alpha, was found to be related to pressure, DeltaP, through the equation alpha = alpha0(1 + kcDeltaP). The dependence of alpha0/Sv2 on Ldm was found to be qualitatively consistent with the pellet voidage data and the Carman-Kozeny equation. Considerably better agreement with the experimental data was obtained when the Kozeny constant, K, was treated as variable and related to Ldm through the equation K = 4.83 + 7.08 log10 Ldm. The cake compressibility constant, kc, was found to increase with increasing Ldm, a phenomenon consistent with the wide range of voidages that can be displayed by beds of long cylinders.\n\nEffect of cell morphology on dead-end filtration of the dimorphic yeast Kluyveromyces marxianus var. marxianus NRRLy2415.", "token_count": 411, "char_count": 1467, "word_count": 224, "semantic_coherence": 1, "information_density": 0.5804, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:16.219054", "source": { "split": "train_shard_00001", "doc_id": 4569 }, "chunk_id": "train_shard_00001_4569_0", "global_id": 12122 }, { "text": "

Background

Gastric cancer is one of the global health concerns. A series of studies on the stomach have confirmed the role of the microbiome in shaping gastrointestinal diseases. Delineation of microbiome signatures to distinguish chronic gastritis from gastric cancer will provide a non-invasive preventative and treatment strategy. In this study, we performed whole metagenome shotgun sequencing of fecal samples to enhance the detection of rare bacterial species and increase genome sequence coverage. Additionally, we employed multiple bioinformatics approaches to investigate the potential targets of the microbiome as an indicator of differentiating gastric cancer from chronic gastritis.

Results

A total of 65 patients were enrolled, comprising 33 individuals with chronic gastritis and 32 with gastric cancer. Within each group, the chronic gastritis group was sub-grouped into intestinal metaplasia (n = 15) and non-intestinal metaplasia (n = 18); the gastric cancer group, early stage (stages 1 and 2, n = 13) and late stage (stages 3 and 4, n = 19) cancer. No significant differences in alpha and beta diversities were detected among the patient groups. However, in a two-group univariate comparison, higher Fusobacteria abundance was identified in phylum; Fusobacteria presented higher abundance in gastric cancer (LDA scored 4.27, q = 0.041 in LEfSe). Age and sex-adjusted MaAsLin and Random Forest variable of importance (VIMP) analysis in species provided meaningful features; Bacteria_caccae was the most contributing species toward gastric cancer and late-stage cancer (beta:2.43, se:0.891, p:0.008, VIMP score:2.543)", "token_count": 470, "char_count": 1649, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:16.866316", "source": { "split": "train_shard_00001", "doc_id": 4570 }, "chunk_id": "train_shard_00001_4570_0", "global_id": 12123 }, { "text": "In contrast, Bifidobacterium_longum significantly contributed to chronic gastritis (beta:-1.8, se:0.699, p:0.009, VIMP score:1.988). Age, sex, and BMI-adjusted MasAsLin on metabolic pathway analysis showed that GLCMANNANAUT-PWY degradation was higher in gastric cancer and one of the contributing species was Fusobacterium_varium.

Conclusion

Microbiomes belonging to the pathogenic phylum Fusobacteria and species Bacteroides_caccae and Streptococcus_anginosus can be significant targets for monitoring the progression of gastric cancer. Whereas Bifidobacterium_longum and Lachnospiraceae_bacterium_5_1_63FAA might be protection biomarkers against gastric cancer.\n\nMicrobiome signatures associated with clinical stages of gastric Cancer: whole metagenome shotgun sequencing study.", "token_count": 245, "char_count": 787, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7907, "quality_score": 0.8953, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:17.346010", "source": { "split": "train_shard_00001", "doc_id": 4570 }, "chunk_id": "train_shard_00001_4570_1", "global_id": 12124 }, { "text": "This article examines the potential of Jerusalem artichoke as a source for ethanol and single-cell protein SCP. In addition, experimental results are presented on batch fermentation kinetics employing two strains of Kluyveromyces marxianus and one strain of Saccharomyces rosei grown on the extract derived from the tubers of Jerusalem artichoke. Of the three cultures examined, Kluyveromyces marxianus UCD (FST) 55-82 was found to be the best producer of ethanol grown in a simple medium at 35 degrees C. The ethanol production was found to be growth-associated having a mu(max) = 0.41. h(-1) and the ethanol and biomass yields were determined to be Y(p/s) = 0.45 (88% of the theoretical) and Y(x/s) = 0.04 with 92% of the original sugars utilized. On the basis of carbohydrate yields of Jerusalem artichoke reported in the literature and these batch kinetic studies with K. maxxianus, the calculated ethanol yields were found to range from 1400 kg ethanol acre (-1) yr(-1)to a maximum of 2700 kg ethanol acre (-1) yr(-1). The SCP yields for K. marxianus were calculated to range between 130 to 250 kg dry wt cell acre (-1) yr(-1). The potential for developing an integrated process to produce ethanol and SCP is also discussed.\n\nEthanol production from Jerusalem artichoke tubers (Helianthus tuberosus) using Kluyveromyces marxianus and Saccharomyces rosei.", "token_count": 406, "char_count": 1359, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5581, "quality_score": 0.7791, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:17.966902", "source": { "split": "train_shard_00001", "doc_id": 4571 }, "chunk_id": "train_shard_00001_4571_0", "global_id": 12125 }, { "text": "

Objectives

Little is known about IMP-producing Enterobacterales (IMP-Ent) in Europe. We analyzed at genomic and phenotypic level IMP-Ent isolates circulating in Spain in a 9-year period.

Materials and methods

IMP-Ent isolates submitted to our reference laboratory were included. Antibiotic susceptibility was performed using microdilution method (EUCAST), and IMP-carbapenemase activity was measured with carbapenemase inhibitors, the β-CARBA method, the modified Hodge test (MHT), and the modified carbapenemase inhibition method (mCIM). All isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.

Results

Fifty IMP-Ent isolates, collected from 19 hospitals in 13 Spanish provinces, were detected: Klebsiella pneumoniae (IMP-Kpn) (24; 48%), Enterobacter roggenkampii (13; 26%), Enterobacter hormaechei (8, 16%), Klebsiella oxytoca (two; 4%), Enterobacter asburiae (one, 2%), Serratia marcescens (one; 2%) and Escherichia coli (one; 2%). All isolates were positive by the MHT and β-CARBA tests; 48 (96%) were mCIM positive; 12 (24%) and 26 (52%) displayed positive inhibition with dipicolinic (meropenem) and EDTA (ertapenem), respectively", "token_count": 465, "char_count": 1326, "word_count": 158, "semantic_coherence": 1, "information_density": 0.7722, "quality_score": 0.8861, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:18.610930", "source": { "split": "train_shard_00001", "doc_id": 4572 }, "chunk_id": "train_shard_00001_4572_0", "global_id": 12126 }, { "text": "Five IMP-carbapenemase types were identified: IMP-8 (22; 44%), IMP-22 (17; 34%), IMP-13 (7; 14%), IMP-28 (two; 4%), and IMP-15 (two; 4%), predominating IMP-8 in K. pneumoniae and IMP-22 in E. roggenkampii. IMP-28 was exclusively identified in K. oxytoca and IMP-15 in E. hormaechei. Predominant STs were ST405 (29.2%), ST15 (25%) and ST464 (20.8%) in IMP-Kpn; ST96 (100%) in E. roggenkampii and ST182 (62.5%) in E. hormachei. Colistin and amikacin were the most active non-carbapenem antibiotics against IMP-Ent.

Conclusion

IMP-Ent isolates remain infrequent in Spain, although in recent years have been circulating causing nosocomial outbreaks, being IMP-8-producing K. pneumoniae and IMP-22-producing E. roggenkampii the most frequently detected in this study. Inhibition with EDTA or dipicolinic acid presented false negative results in some IMP-producing strains. Active microbiological and molecular surveillance is essential for a better comprehension and control of IMP-Ent dissemination.\n\nPhenotypic and molecular characterization of IMP-producing Enterobacterales in Spain: Predominance of IMP-8 in Klebsiella pneumoniae and IMP-22 in Enterobacter roggenkampii.", "token_count": 461, "char_count": 1247, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6815, "quality_score": 0.8408, "entities": { "genes": [ "ST96", "ST405", "ST464", "ST15", "ST182" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:19.253179", "source": { "split": "train_shard_00001", "doc_id": 4572 }, "chunk_id": "train_shard_00001_4572_1", "global_id": 12127 }, { "text": "The potential probiotic benefits of Lactobacillus mucosae have received increasing attention. To investigate the genetic diversity of L. mucosae, comparative genomic analyses of 93 strains isolated from different niches (human and animal gut, human vagina, etc.) and eight strains of published genomes were conducted. The results showed that the core genome of L. mucosae mainly encoded translation and transcription, amino acid biosynthesis, sugar metabolism, and defense function while the pan-genomic curve tended to be close. The genetic diversity of L. mucosae mainly reflected in carbohydrate metabolism and immune/competitive-related factors, such as exopolysaccharide (EPS), enterolysin A, and clustered regularly interspaced short palindromic repeats (CRISPR)-Cas. It was worth noting that this research firstly predicted the complete EPS operon shared among L. mucosae. Additionally, the type IIIA CRISPR-Cas system was discovered in L. mucosae for the first time. This work provided new ideas for the study of this species.\n\nComparative Genomics Analysis of Lactobacillus mucosae from Different Niches.", "token_count": 326, "char_count": 1162, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7161, "quality_score": 0.8581, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:19.824214", "source": { "split": "train_shard_00001", "doc_id": 4573 }, "chunk_id": "train_shard_00001_4573_0", "global_id": 12128 }, { "text": "In the family Enterobacteriaceae, plasmids have been classified according to 27 incompatibility (Inc) or replicon types that are based on the inability of different plasmids with the same replication mechanism to coexist in the same cell. Certain replicon types such as IncA/C are associated with multidrug resistance (MDR). We developed a microarray that contains 286 unique 70-mer oligonucleotide probes based on sequences from five IncA/C plasmids: pYR1 (Yersinia ruckeri), pPIP1202 (Yersinia pestis), pP99-018 (Photobacterium damselae), pSN254 (Salmonella enterica serovar Newport), and pP91278 (Photobacterium damselae). DNA from 59 Salmonella enterica isolates was hybridized to the microarray and analyzed for the presence or absence of genes. These isolates represented 17 serovars from 14 different animal hosts and from different geographical regions in the United States. Qualitative cluster analysis was performed using CLUSTER 3.0 to group microarray hybridization results. We found that IncA/C plasmids occurred in two lineages distinguished by a major insertion-deletion (indel) region that contains genes encoding mostly hypothetical proteins. The most variable genes were represented by transposon-associated genes as well as four antimicrobial resistance genes (aphA, merP, merA, and aadA). Sixteen mercury resistance genes were identified and highly conserved, suggesting that mercury ion-related exposure is a stronger pressure than anticipated. We used these data to construct a core IncA/C genome and an accessory genome. The results of our studies suggest that the transfer of antimicrobial resistance determinants by transfer of IncA/C plasmids is somewhat less common than exchange within the plasmids orchestrated by transposable elements, such as transposons, integrating and conjugative elements (ICEs), and insertion sequence common regions (ISCRs), and thus pose less opportunity for exchange of antimicrobial resistance.", "token_count": 502, "char_count": 1951, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6357, "quality_score": 0.8178, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:20.476007", "source": { "split": "train_shard_00001", "doc_id": 4574 }, "chunk_id": "train_shard_00001_4574_0", "global_id": 12129 }, { "text": "Microarray-based analysis of IncA/C plasmid-associated genes from multidrug-resistant Salmonella enterica.", "token_count": 30, "char_count": 106, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:20.831424", "source": { "split": "train_shard_00001", "doc_id": 4574 }, "chunk_id": "train_shard_00001_4574_1", "global_id": 12130 }, { "text": "

Background

Recent reports have established the emergence and dissemination of extensively drug resistant (XDR) H58 Salmonella Typhi clone in Pakistan. In India where typhoid fever is endemic, only sporadic cases of ceftriaxone resistant S. Typhi are reported. This study aimed at elucidating the phylogenetic evolutionary framework of ceftriaxone resistant S. Typhi isolates from India to predict their potential dissemination.

Methods

Five ceftriaxone resistant S. Typhi isolates from three tertiary care hospitals in India were sequenced on an Ion Torrent Personal Genome Machine (PGM). A core genome single-nucleotide-polymorphism (SNP) based phylogeny of the isolates in comparison to the global collection of MDR and XDR S. Typhi isolates was built. Two of five isolates were additionally sequenced using Oxford Nanopore MinION to completely characterize the plasmid and understand its transmission dynamics within Enterobacteriaceae.

Results

Comparative genomic analysis and detailed plasmid characterization indicate that while in Pakistan (4.3.1 lineage I) the XDR trait is associated with blaCTX-M-15 gene on IncY plasmid, in India (4.3.1 lineage II), the ceftriaxone resistance is due to short term persistence of resistance plasmids such as IncX3 (blaSHV-12) or IncN (blaTEM-1B + blaDHA-1).

Conclusion

Considering the selection pressure exerted by the extensive use of ceftriaxone in India, there are potential risks for the occurrence of plasmid transmission events in the predominant H58 lineages. Therefore, continuous monitoring of S. Typhi lineages carrying plasmid-mediated cephalosporin resistant genes is vital not just for India but also globally.", "token_count": 494, "char_count": 1740, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:21.478312", "source": { "split": "train_shard_00001", "doc_id": 4575 }, "chunk_id": "train_shard_00001_4575_0", "global_id": 12131 }, { "text": "Salmonella Typhi acquires diverse plasmids from other Enterobacteriaceae to develop cephalosporin resistance.", "token_count": 28, "char_count": 109, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:21.829554", "source": { "split": "train_shard_00001", "doc_id": 4575 }, "chunk_id": "train_shard_00001_4575_1", "global_id": 12132 }, { "text": "'Filth flies' facilitate the dispersal of pathogens between animals and humans. The objective was to study the intestinal colonization with antimicrobial resistant and enteropathogenic bacteria in 'filth flies' from Nigeria. Flies from Southern Nigeria were screened for extended-spectrum β-lactamase producing Enterobacterales (ESBL-E), Staphylococcus aureus, Salmonella sp., Shigella sp., Campylobacter sp. and Yersinia enterocolitica by culture. ESBL-E were tested for blaSHV, blaCTX-M and blaTEM; S. aureus was screened for enterotoxins. Spa typing and multilocus sequence typing (MLST) was done for S. aureus and MLST for Escherichia coli. Of 2,000 flies, 400 were randomly collected for species identification. The most common species were Musca domestica (44.8%, 179/400), Chrysomya putoria (21.6%, 85/400) and Musca sorbens (18.8%, 75/400). Flies were colonized with S. aureus (13.8%, 275/2,000) and ESBL-E (0.8%, 16/2,000). No other enteropathogenic bacteria were detected. The enterotoxin sei was most common (26%, 70/275) in S. aureus, followed by sea (12%, n = 32/275). Four S. aureus isolates were methicillin resistant (mecA positive, t674 and t5305, ST15). The blaCTX-M (n = 16) was the most prevalent ESBL subtype, followed by blaTEM (n = 8). 'Filth flies' can carry antimicrobial resistant bacteria in Nigeria. Enterotoxin-positive S", "token_count": 519, "char_count": 1405, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8168, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:22.462609", "source": { "split": "train_shard_00001", "doc_id": 4576 }, "chunk_id": "train_shard_00001_4576_0", "global_id": 12133 }, { "text": "aureus might be the main reason for food poisoning by 'filth flies' in the study area.\n\nAntimicrobial resistant and enteropathogenic bacteria in 'filth flies': a cross-sectional study from Nigeria.", "token_count": 53, "char_count": 197, "word_count": 29, "semantic_coherence": 1, "information_density": 0.8621, "quality_score": 0.931, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:22.867192", "source": { "split": "train_shard_00001", "doc_id": 4576 }, "chunk_id": "train_shard_00001_4576_1", "global_id": 12134 }, { "text": "Aim: Genetic characterization of Pandoraea strains recovered from cystic fibrosis patients. Materials & methods: The whole-genome sequence of 12 Pandoraea strains was determined using Illumina technology. The position of the strains within the genus Pandoraea was analyzed using selected partial gene sequences, core genome multi-locus sequence typing and average nucleotide identity analysis. Furthermore, the sequences were annotated. Results: The results show that some strains previously identified as Pandoraea pnomenusa, Pandoraea sputorum, Pandoraea oxalativorans and Pandoraea pulmonicola belong to novel species. The strains did not harbor acquired antibiotic resistance genes but encoded an OXA-type ß-lactamase. Conclusion: The taxonomy of the genus Pandoraea needs to be revised.\n\nWhole-genome analysis of Pandoraea species strains from cystic fibrosis patients.", "token_count": 298, "char_count": 965, "word_count": 115, "semantic_coherence": 1, "information_density": 0.6957, "quality_score": 0.8478, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:23.467601", "source": { "split": "train_shard_00001", "doc_id": 4577 }, "chunk_id": "train_shard_00001_4577_0", "global_id": 12135 }, { "text": "Two Bifidobacterium strains, i.e., 2176BT and 2177BT, were isolated from Golden-Headed Lion Tamarin (Leontopithecus chrysomelas) and Goeldi's monkey (Callimico goeldii). Isolates were shown to be Gram-positive, non-motile, non-sporulating, facultative anaerobic and d-fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2176BT and 2177BT exhibit close phylogenetic relatedness to Bifidobacterium felsineum DSM 103139T and Bifidobacterium bifidum LMG 11041T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium cebidarum sp. nov. (2176BT=LMG 31469T=CCUG 73785T) and Bifidobacterium leontopitheci sp. nov", "token_count": 492, "char_count": 1184, "word_count": 125, "semantic_coherence": 1, "information_density": 0.752, "quality_score": 0.876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:24.148593", "source": { "split": "train_shard_00001", "doc_id": 4578 }, "chunk_id": "train_shard_00001_4578_0", "global_id": 12136 }, { "text": "(2177BT=LMG 31471T=CCUG 73786T are proposed as novel Bifidobacterium species.\n\nCharacterization of the phylogenetic diversity of two novel species belonging to the genus Bifidobacterium: Bifidobacterium cebidarum sp. nov. and Bifidobacterium leontopitheci sp. nov.", "token_count": 137, "char_count": 325, "word_count": 32, "semantic_coherence": 1, "information_density": 0.8125, "quality_score": 0.9062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:24.615290", "source": { "split": "train_shard_00001", "doc_id": 4578 }, "chunk_id": "train_shard_00001_4578_1", "global_id": 12137 }, { "text": "Pathogenic Leptospira, the causative agents of leptospirosis, comprise >200 serotypes (called serovars). Most have a restricted reservoir-host range, and some, e.g., serovar Copenhageni, are cosmopolitan and of public health importance owing to their propensity to produce severe, fatal disease in humans. Available serotyping approaches-such as multilocus sequence typing, core genome sequence typing, pulsed-field gel electrophoresis, and the cross-agglutination absorption test-are tedious and expensive, and require isolation of the organisms in culture media-a protracted and incredibly inefficient process-precluding their use in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. Here, we have developed a simple yet specific real-time qPCR assay-targeting a Leptospira-unique gene encoding a putative polysaccharide flippase-that provides intraspecies, serotype-defining (i.e., epidemiologically useful) information, and improves upon the sensitivity of preferred lipL32-based qPCR-based diagnostic tests. The assay, dubbed RAgI (\"rage one\"), is rapid and affordable, and reliably and specifically detects group I pathogenic Leptospira in culture, serum, and urine, with no detectable off-target amplification-even of the genetically related but low virulence group II pathogenic (formerly \"intermediate\") or nonpathogenic Leptospira. It retained 100% diagnostic specificity when tested against difficult sample types, including field-collected dog urine samples and environmental samples containing varied and complex microbial species-consortia. This assay holds considerable promise in the clinical setting, and for routine epidemiological and environmental surveillance studies", "token_count": 502, "char_count": 1888, "word_count": 225, "semantic_coherence": 1, "information_density": 0.7733, "quality_score": 0.8867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:25.276454", "source": { "split": "train_shard_00001", "doc_id": 4579 }, "chunk_id": "train_shard_00001_4579_0", "global_id": 12138 }, { "text": "IMPORTANCE Leptospirosis is caused by a diverse group of pathogenic spirochetes comprising over 200 different serotypes. Some are widely reported and of public health importance owing to their propensity to produce severe, fatal disease in humans. Apart from their tedium and expense, current serotyping approaches require isolation of the organisms in culture media-a protracted and incredibly inefficient process-rendering them useless clinically and limiting their utilization in prospective studies or outbreak investigations. The unavailability of culture-independent assays capable of distinguishing Leptospira serotypes remains a crucial gap in the field. The 11108 qPCR-assay overcomes this barrier to progress via direct taxonomic and serotype classification of Leptospira from urine and serum samples, and hence, is the first qPCR-based prognostic test for human leptospirosis.\n\nCulture-Independent Detection and Identification of Leptospira Serovars.", "token_count": 254, "char_count": 989, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7638, "quality_score": 0.8819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:25.757402", "source": { "split": "train_shard_00001", "doc_id": 4579 }, "chunk_id": "train_shard_00001_4579_1", "global_id": 12139 }, { "text": "Oligosaccharides extracted from cell walls of Kluyveromyces marxianus grown on whey.", "token_count": 25, "char_count": 84, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:26.118002", "source": { "split": "train_shard_00001", "doc_id": 4580 }, "chunk_id": "train_shard_00001_4580_0", "global_id": 12140 }, { "text": "The increase in infections with multidrug-resistant and virulent Klebsiella pneumoniae (K. pneumoniae) strains poses a serious threat to public health. However, environmental reservoirs and routes of transmission for Klebsiella spp. that cause infections in humans and in livestock animals are not well understood. In this study, we aimed to analyze the distribution of antibiotic resistance genes and important virulence determinants (ybt, clb, iro, iuc, rmpA/A2) among 94 Klebsiella spp. isolates from different animal and food sources isolated between 2013 and 2017 in Germany. Antibiotic susceptibility testing was performed, and the genomes were sequenced by Illumina and Nanopore technology. Genetic relationships were assessed by conducting core genome multilocus sequence typing (cgMLST). Kleborate was used to predict resistance and virulence genes; Kaptive was used to derive the capsule types. The results revealed that 72 isolates (76.6%) belonged to the K. pneumoniae sensu lato complex. Within this complex, 44 known sequence types (STs), 18 new STs, and 38 capsule types were identified. Extended-spectrum beta-lactamase (ESBL) genes were detected in 16 isolates (17.0%) and colistin resistance in one (1.1%) K. pneumoniae isolate. Virulence genes were found in 22 K. pneumoniae isolates. Overall, nine (9.6%) and 18 (19.1%) isolates possessed the genes ybt and iuc, respectively. Notably, aerobactin (iuc lineage 3) was only detected in K", "token_count": 512, "char_count": 1576, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:26.749176", "source": { "split": "train_shard_00001", "doc_id": 4581 }, "chunk_id": "train_shard_00001_4581_0", "global_id": 12141 }, { "text": "pneumoniae isolates from domestic pigs and wild boars. This study provides a snapshot of the genetic diversity of Klebsiella spp. in animals and food products in Germany. The siderophore aerobactin was found to be more prevalent in K. pneumoniae strains isolated from pigs than other sources. Further investigations are needed to evaluate if pigs constitute a reservoir for iuc lineage 3.\n\nGenome-Based Analysis of Klebsiella spp. Isolates from Animals and Food Products in Germany, 2013-2017.", "token_count": 163, "char_count": 525, "word_count": 75, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:27.195119", "source": { "split": "train_shard_00001", "doc_id": 4581 }, "chunk_id": "train_shard_00001_4581_1", "global_id": 12142 }, { "text": "BackgroundTwo epidemiologically-unrelated clusters of Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae were detected among several healthcare facilities (HCF) in Finland by routine surveillance using whole genome sequencing (WGS).AimThe objective was to investigate transmission chains to stop further spread of the responsible strain.MethodsIn this observational retrospective study, cases were defined as patients with K. pneumoniae KPC-3 sequence type (ST)512 strain detected in Finland from August 2013 to May 2018. Environmental specimens were obtained from surfaces, sinks and toilets in affected wards. WGS was performed on K. pneumoniae cultures using Illumina MiSeq platform and data were analysed using Ridom SeqShere software K. pneumoniae core genome multilocus sequence typing (cgMLST) scheme. Epidemiological information of the cases was provided by HCFs.ResultsWe identified 20 cases in six HCFs: cluster 1 included 18 cases in five HCFs and cluster 2 two cases in one HCF. In cluster 1, a link with a foreign country was unclear, 6/18 cases without overlapping stay had occupied the same room in one of the five HCFs within > 3 years. In cluster 2, the index case was transferred from abroad, both cases occupied the same room 8 months apart. A strain identical to that of the two cases in cgMLST was isolated from the toilet of the room, suggesting a clonal origin.ConclusionsThe clusters were mostly related to case transfer between facilities and likely involved environmental transmission. We show that CPE surveillance using WGS and collaboration between hospitals are crucial to identify clusters and trace transmission chains.\n\nTracing local and regional clusters of carbapenemase-producing Klebsiella pneumoniae ST512 with whole genome sequencing, Finland, 2013 to 2018.", "token_count": 507, "char_count": 1853, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [ "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:27.822245", "source": { "split": "train_shard_00001", "doc_id": 4582 }, "chunk_id": "train_shard_00001_4582_0", "global_id": 12143 }, { "text": "We have previously studied carbapenem non-susceptible Pseudomonas aeruginosa (CNPA) strains from intensive care units (ICUs) in a referral hospital in Jakarta, Indonesia (Pelegrin et al., 2019). We documented that CNPA transmissions and acquisitions among patients were variable over time and that these were not significantly reduced by a set of infection control measures. Three high risk international CNPA clones (sequence type (ST)235, ST823, ST357) dominated, and carbapenem resistance was due to carbapenemase-encoding genes and mutations in the porin OprD. Pelegrin et al. (2019) reported core genome analysis of these strains. We present a more refined and detailed whole genome-based analysis of major clones represented in the same dataset. As per our knowledge, this is the first study reporting Single Nucleotide Polymorphisms (wgSNP) analysis of Pseudomonas strains. With whole genome-based Multi Locus Sequence Typing (wgMLST) of the 3 CNPA clones (ST235, ST357 and ST823), three to eleven subgroups with up to 200 allelic variants were observed for each of the CNPA clones. Furthermore, we analyzed these CNPA clone clusters for the presence of wgSNP to redefine CNPA transmission events during hospitalization. A maximum number 35350 SNPs (including non-informative wgSNPs) and 398 SNPs (ST-specific_informative-wgSNPs) were found in ST235, 34,570 SNPs (including non-informative wgSNPs) and 111 SNPs (ST-specific_informative-wgSNPs) in ST357 and 26,443 SNPs (including non-informative SNPs) and 61 SNPs (ST-specific_informative-wgSNPs) in ST823. ST-specific_Informative-wgSNPs were commonly noticed in sensor-response regulator genes", "token_count": 515, "char_count": 1665, "word_count": 227, "semantic_coherence": 1, "information_density": 0.674, "quality_score": 0.837, "entities": { "genes": [ "ST823", "ST357", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:28.461186", "source": { "split": "train_shard_00001", "doc_id": 4583 }, "chunk_id": "train_shard_00001_4583_0", "global_id": 12144 }, { "text": "However, the majority of non-informative wgSNPs was found in conserved hypothetical proteins or in uncharacterized proteins. Of note, antibiotic resistance and virulence genes segregated according to the wgSNP analyses. A total of 8 transmission chains for ST235 strains followed by 9 and 4 possible transmission chains for ST357 and ST823 were traceable on the basis of pairwise distances of informative-wgSNPs (0 to 4 SNPs) among the strains. The present study demonstrates the value of detailed whole genome sequence analysis for highly refined epidemiological analysis of P. aeruginosa.\n\nWhole Genome Multi-Locus Sequence Typing and Genomic Single Nucleotide Polymorphism Analysis for Epidemiological Typing of Pseudomonas aeruginosa From Indonesian Intensive Care Units.", "token_count": 215, "char_count": 789, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7248, "quality_score": 0.8624, "entities": { "genes": [ "ST357", "ST823", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:28.932340", "source": { "split": "train_shard_00001", "doc_id": 4583 }, "chunk_id": "train_shard_00001_4583_1", "global_id": 12145 }, { "text": "

Background

The human gut microbiome harbors a collection of bacterial antimicrobial resistance genes (ARGs) known as the resistome. The factors associated with establishment of the resistome in early life are not well understood. We investigated the early-life exposures and taxonomic signatures associated with resistome development over the first year of life in a large, prospective cohort in the United States. Shotgun metagenomic sequencing was used to profile both microbial composition and ARGs in stool samples collected at 6 weeks and 1 year of age from infants enrolled in the New Hampshire Birth Cohort Study. Negative binomial regression and statistical modeling were used to examine infant factors such as sex, delivery mode, feeding method, gestational age, antibiotic exposure, and infant gut microbiome composition in relation to the diversity and relative abundance of ARGs.

Results

Metagenomic sequencing was performed on paired samples from 195 full term (at least 37 weeks' gestation) and 15 late preterm (33-36 weeks' gestation) infants. 6-week samples compared to 1-year samples had 4.37 times (95% CI: 3.54-5.39) the rate of harboring ARGs. The majority of ARGs that were at a greater relative abundance at 6 weeks (chi-squared p < 0.01) worked through the mechanism of antibiotic efflux. The overall relative abundance of the resistome was strongly correlated with Proteobacteria (Spearman correlation = 78.9%) and specifically Escherichia coli (62.2%) relative abundance in the gut microbiome. Among infant characteristics, delivery mode was most strongly associated with the diversity and relative abundance of ARGs", "token_count": 452, "char_count": 1656, "word_count": 240, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:29.579362", "source": { "split": "train_shard_00001", "doc_id": 4584 }, "chunk_id": "train_shard_00001_4584_0", "global_id": 12146 }, { "text": "Infants born via cesarean delivery had a trend towards a higher risk of harboring unique ARGs [relative risk = 1.12 (95% CI: 0.97-1.29)] as well as having an increased risk for overall ARG relative abundance [relative risk = 1.43 (95% CI: 1.12-1.84)] at 1 year compared to infants born vaginally.

Conclusions

Our findings suggest that the developing infant gut resistome may be alterable by early-life exposures. Establishing the extent to which infant characteristics and early-life exposures impact the resistome can ultimately lead to interventions that decrease the transmission of ARGs and thus the risk of antibiotic resistant infections.\n\nThe infant gut resistome is associated with E. coli and early-life exposures.", "token_count": 214, "char_count": 730, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:30.043020", "source": { "split": "train_shard_00001", "doc_id": 4584 }, "chunk_id": "train_shard_00001_4584_1", "global_id": 12147 }, { "text": "Escherichia coli sequence type 131 (ST131) has emerged rapidly to become the most prevalent extraintestinal pathogenic E. coli clones in circulation today. Previous investigations appeared to exonerate retail meat as a source of human exposure to ST131; however, these studies focused mainly on extensively multidrug-resistant ST131 strains, which typically carry allele 30 of the fimH type 1 fimbrial adhesin gene (ST131-H30). To estimate the frequency of extraintestinal human infections arising from foodborne ST131 strains without bias toward particular sublineages or phenotypes, we conducted a 1-year prospective study of E. coli from meat products and clinical cultures in Flagstaff, Arizona. We characterized all isolates by multilocus sequence typing, fimH typing, and core genome phylogenetic analyses, and we screened isolates for avian-associated ColV plasmids as an indication of poultry adaptation. E. coli was isolated from 79.8% of the 2,452 meat samples and 72.4% of the 1,735 culture-positive clinical samples. Twenty-seven meat isolates were ST131 and belonged almost exclusively (n = 25) to the ST131-H22 lineage. All but 1 of the 25 H22 meat isolates were from poultry products, and all but 2 carried poultry-associated ColV plasmids. Of the 1,188 contemporaneous human clinical E. coli isolates, 24 were ST131-H22, one-quarter of which occurred in the same high-resolution phylogenetic clades as the ST131-H22 meat isolates and carried ColV plasmids", "token_count": 506, "char_count": 1555, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6326, "quality_score": 0.8163, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:30.701846", "source": { "split": "train_shard_00001", "doc_id": 4585 }, "chunk_id": "train_shard_00001_4585_0", "global_id": 12148 }, { "text": "Molecular clock analysis of an international ST131-H22 genome collection suggested that ColV plasmids have been acquired at least six times since the 1940s and that poultry-to-human transmission is not limited to the United States.IMPORTANCEE. coli ST131 is an important extraintestinal pathogen that can colonize the gastrointestinal tracts of humans and food animals. Here, we combined detection of accessory traits associated with avian adaptation (ColV plasmids) with high-resolution phylogenetics to quantify the portion of human infections caused by ST131 strains of food animal origin. Our results suggest that one ST131 sublineage-ST131-H22-has become established in poultry populations around the world and that meat may serve as a vehicle for human exposure and infection. ST131-H22 is just one of many E. coli lineages that may be transmitted from food animals to humans. Additional studies that combine detection of host-associated accessory elements with phylogenetics may allow us to quantify the total fraction of human extraintestinal infections attributable to food animal E. coli strains.\n\nEscherichia coli ST131-H22 as a Foodborne Uropathogen.", "token_count": 346, "char_count": 1218, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6747, "quality_score": 0.8373, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:31.276067", "source": { "split": "train_shard_00001", "doc_id": 4585 }, "chunk_id": "train_shard_00001_4585_1", "global_id": 12149 }, { "text": "Formation of ethyl acetate and isoamyl acetate by seven wine yeast strains in a model grape juice was examined during fermentation. The amounts in which the two esters are produced during fermentation were found to depend on the particular yeast strain, its specific production rate and its rate of survival in the wine. Kloeckera apiculata exhibited the highest ability for acetate formation. Hansenula subpelliculosa, Kluyveromyces marxianus, Torulaspora delbrueckii and Saccharomyces cerevisiae produced intermediate levels and Pichia membranaefaciens and Candida guilliermondii very low levels of the two esters measured in this study.\n\nFormation of ethyl acetate and isoamyl acetate by various species of wine yeasts", "token_count": 189, "char_count": 721, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:31.724990", "source": { "split": "train_shard_00001", "doc_id": 4586 }, "chunk_id": "train_shard_00001_4586_0", "global_id": 12150 }, { "text": "Salmonella enterica subsp. enterica serotype Enteritidis (SE) is recognized as a major cause of human salmonellosis worldwide, and most human salmonellosis is due to the consumption of contaminated poultry meats and poultry byproducts. Whole-genome sequencing (data were obtained from 96 SE isolates from poultry sources, including an integrated broiler supply chain, farms, slaughterhouses, chicken transporting trucks, and retail chicken meats in South Korea during 2010-2017. Antimicrobial resistance and virulence genes were investigated using WGS data, and the phylogenetic relationship of the isolates was analyzed using single-nucleotide polymorphism (SNP) typing and core genome multilocus sequence typing (cgMLST). All isolates carried aminoglycoside resistance genes, aac\n(6')-\nIaa, and 56 isolates carried multiple antimicrobial resistance genes. The most frequent virulence gene profile, pef-fim-sop-inv.-org-sip-spa-sif-fli-flg-hil-ssa-sse-prg-pag-spv, was found in 90 isolates. The SNP analysis provided a higher resolution than the cgMLST analysis, but the cgMLST analysis was highly congruent with the SNP analysis. The phylogenetic results suggested the presence of resident SE within the facility of processing plants, environments of slaughterhouses, and the integrated broiler supply chain, and the phylogenetically related isolates were found in retail meats. In addition, the SE isolates from different origins showed close genetic relationships indicating that these strains may have originated from a common source. This study could be valuable reference data for future traceback investigations in South Korea.\n\nWhole-Genome Sequencing Analysis of Salmonella\nEnterica Serotype Enteritidis Isolated from Poultry Sources in South Korea, 2010-2017.", "token_count": 513, "char_count": 1826, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6368, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:32.350553", "source": { "split": "train_shard_00001", "doc_id": 4587 }, "chunk_id": "train_shard_00001_4587_0", "global_id": 12151 }, { "text": "The intracellular enzyme beta-D-galactosidase provides interesting applications in the dairy industry, which are able to solve problems related to product processing, or can alleviate lactose intolerance in some populations. In order to obtain a technical enzyme, yeast cells of Kluyveromyces marxianus CDB 002 were disrupted by high pressure homogenization and an innovative chromatographic technique was tested for the recovery of beta-D-galactosidase. A STREAMLINE 25 column, containing 65 ml STREAMLINE-DEAE was equilibrated with 50 mM potassium phosphate buffer pH 7.5 at an upward flow of 250 cmh-1. 100-200 ml cell homogenate were applied onto the expanded gel. After unbound proteins and cellular debris were washed out, the bed was allowed to sediment and beta-D-galactosidase was eluted with a downward flow of 0.2 M NaCl in the same buffer. A 6-fold purification factor was achieved with 63% activity recovery, while removing cell debris at a single step, thus avoiding a centrifugation step. Concentration and volume of the applied sample affected purification and gel performance. The results presented show STREAMLINE-DEAE chromatography to be an interesting method for the production of beta-D-galactosidase as a technical enzyme, since it can also be applied on a large scale without much modification.\n\nOne step partial purification of beta-D-galactosidase from Kluyveromyces marxianus CDB 002 using STREAMLINE-DEAE.", "token_count": 389, "char_count": 1433, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6875, "quality_score": 0.8438, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:32.974902", "source": { "split": "train_shard_00001", "doc_id": 4588 }, "chunk_id": "train_shard_00001_4588_0", "global_id": 12152 }, { "text": "Bacterial pathogens impose a heavy health burden worldwide. In the new era of high-throughput sequencing and online bioinformatics, real-time genome typing of infecting agents, and in particular those with potential severe clinical outcomes, holds promise for guiding clinical care to limit the detrimental effects of infections and to prevent potential local or global outbreaks. Here, we sequenced and compared 85 isolates of Streptococcus suis, a zoonotic human and swine pathogen, wherein we analyzed 32 recognized serotypes and 75 sequence types representing the diversity of the species and the human clinical isolates with high public health significance. We found that 1,077 of the 2,469 genes are shared by all isolates. Excluding 201 common but mobile genes, 876 genes were defined as the minimum core genome (MCG) of the species. Of 190,894 single-nucleotide polymorphisms (SNPs) identified, 58,501 were located in the MCG genes and were referred to as MCG SNPs. A population structure analysis of these MCG SNPs classified the 85 isolates into seven MCG groups, of which MCG group 1 includes all isolates from human infections and outbreaks. Our MCG typing system for S. suis provided a clear separation of groups containing human-associated isolates from those containing animal-associated isolates. It also separated the group containing outbreak isolates, including those causing life-threatening streptococcal toxic shock-like syndrome, from sporadic or less severe meningitis or bacteremia-only isolates. The typing system facilitates the application of genome data to the fields of clinical medicine and epidemiology and to the surveillance of S. suis. The MCG groups may also be used as the taxonomical units of S. suis to define bacterial subpopulations with the potential to cause severe clinical infections and large-scale outbreaks.\n\nMinimum core genome sequence typing of bacterial pathogens: a unified approach for clinical and public health microbiology.", "token_count": 481, "char_count": 1980, "word_count": 293, "semantic_coherence": 1, "information_density": 0.57, "quality_score": 0.785, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:33.622233", "source": { "split": "train_shard_00001", "doc_id": 4589 }, "chunk_id": "train_shard_00001_4589_0", "global_id": 12153 }, { "text": "Kluyveromyces marxianus UCD (FST) 55-82 cells were immobilized in Na alginate beads and used in a packed-bed bioreactor system for the continuous production of ethanol from the extract of Jerusalem artichoke tubers. Volumetric ethanol productivities of 104 and 80 g ethanol/ L/h were obtained at 80 and 92% sugar utilization, respectively. The maximum volumetric ethanol productivity of the immobilized cell bioreactor system was found to be 15 times higher than that of an ordinary-stirred-tank (CST) bioreactor using cells of K. marxianus. The immobilized cell bioreactor system was operated continuously at a constant dilution rate of 0.66 h(-1) for 12 days resulting in only an 8% loss of the original immobilized cell activity, which corresponds to an estimated half-life of ca. 72 days. The maximum specific ethanol productivity and maximum specific sugar uptake rate of the immobilized cells were found to be 0.55 g ethanol/g/biomass/h and 1.21 g sugars/g biomass/h, respectively.\n\nContinuous ethanol production from Jerusalem artichoke tubers. II. Use of immobilized cells of Kluyveromyces marxianus.", "token_count": 324, "char_count": 1108, "word_count": 165, "semantic_coherence": 1, "information_density": 0.5515, "quality_score": 0.7758, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:34.192255", "source": { "split": "train_shard_00001", "doc_id": 4590 }, "chunk_id": "train_shard_00001_4590_0", "global_id": 12154 }, { "text": "A comparative taxonomic study of Spiribacter and Halopeptonella species was carried out using a phylogenomic approach based on comparison of the core genome, orthologous average nucleotide identity (OrthoANIu), Genome-to-Genome Distance Calculator (GGDC) and average amino acid identity (AAI). Phylogenomic analysis based on 976 core translated gene sequences obtained from their genomes showed that Spiribacter aquaticus SP30T, S. curvatus UAH-SP71T, S. roseus SSL50T, S. salinus M19-40T and Halopeptonella vilamensis DSM 21056T formed a robust cluster, clearly separated from the remaining species of closely related taxa. AAI between H. vilamensis DSM 21056T and the species of the genus Spiribacter was ≥73.1 %, confirming that all these species belong to the same single genus. On the other hand, S. roseus SSL50T and S. aquaticus SP30T showed percentages of OrthoANIu and digital DNA-DNA hybridization of 98.4 % and 85.3 %, respectively, while these values among those strains and the type strains of the other species of Spiribacter and H. vilamensis DSM 21056T were ≤80.8 and 67.8 %, respectively. Overall, these data show that S. roseus SSL50T and S", "token_count": 500, "char_count": 1369, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [ "SP71", "SSL50", "SP30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:34.871294", "source": { "split": "train_shard_00001", "doc_id": 4591 }, "chunk_id": "train_shard_00001_4591_0", "global_id": 12155 }, { "text": "aquaticus SP30T constitute a single species and thus that S. aquaticus SP30T should be considered as a later, heterotypic synonym of S. roseus SSL50T based on the rules for priority of names. We propose an emended description of S. roseus, including the features of S. aquaticus. We also propose the reclassification of H. vilamensis as Spiribacter vilamensis comb. nov.\n\nSpiribacter aquaticus Leon et al. 2017 is a later heterotypic synonym of Spiribacter roseus Leon et al. 2016. Reclassification of Halopeptonella vilamensis Menes et al. 2016 as Spiribacter vilamensis comb. nov.", "token_count": 273, "char_count": 710, "word_count": 90, "semantic_coherence": 1, "information_density": 0.5889, "quality_score": 0.7944, "entities": { "genes": [ "SSL50", "SP30" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:35.435770", "source": { "split": "train_shard_00001", "doc_id": 4591 }, "chunk_id": "train_shard_00001_4591_1", "global_id": 12156 }, { "text": "The screening and selection of lactose-fermenting yeasts among 97 collection yeast strains belonging to different taxonomic groups has been conducted to obtain ethanol from whey. The strains (n=18) (1 strain of K. lactis. 16 strains of K. marxianus and 1 strain of C. kefyr) fermented lactose at 48 degrees C and 15 selected strains rapidly consumed lactose within 24-48 h of cultivation. The presence of 6% of ethanol in the medium resulted in a considerable growth inhibition (more than 80%) of the selected strains.\n\n[Selection of thermophilic lactose-fermenting yeast strains].", "token_count": 174, "char_count": 581, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7111, "quality_score": 0.8556, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:35.900116", "source": { "split": "train_shard_00001", "doc_id": 4592 }, "chunk_id": "train_shard_00001_4592_0", "global_id": 12157 }, { "text": "Fourteen yeast strains were screened for production of 2-phenylethanol from L-phenylalanine with molasses as carbon source. Up to 1 g 2-phenylethanol l-1 was obtained. Using oleyl alcohol as a second phase for in situ product removal to enhance the production of 2-phenylethanol increased the yield to about 3 g 2-phenylethanol l-1 at 35 degrees C. The most productive strains were Kluyveromyces marxianus CBS 600 and CBS 397.\n\nScreening of yeasts for the production of the aroma compound 2-phenylethanol in a molasses-based medium.", "token_count": 169, "char_count": 532, "word_count": 82, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:36.387573", "source": { "split": "train_shard_00001", "doc_id": 4593 }, "chunk_id": "train_shard_00001_4593_0", "global_id": 12158 }, { "text": "

Objectives

We evaluated the in vitro activity of posaconazole against nine Candida species using minimum fungicidal concentration (MFC) measurements and time-kill methods.

Methods

MFCs of posaconazole were determined for 209 clinical isolates (32 Candida albicans, 30 Candida glabrata, 21 Candida tropicalis, 29 Candida krusei, 28 Candida parapsilosis sensu stricto, 50 Candida inconspicua, 13 Candida kefyr, 3 Candida lusitaniae and 3 Candida guilliermondii) and 7 ATCC Candida strains. The following strains were tested in time-kill studies: 3 strains each of C. glabrata, C. kefyr, C. guilliermondii and C. lusitaniae; 2 C. tropicalis; 4 C. albicans; 4 C. inconspicua; 9 C. krusei; 12 C. parapsilosis; and 7 ATCC strains.

Results

Posaconazole was fungicidal in both MFC and time-kill experiments (at 2 mg/L within 48 h in time-kill assays) against each C. krusei, C. inconspicua and C. lusitaniae strain and was fungistatic against each C. albicans, C. glabrata, C. tropicalis and C. guilliermondii strain. For the C. parapsilosis strains, posaconazole MFCs were ConclusionsMFC values were good predictors of the fungistatic or fungicidal activity of posaconazole, as determined by time-kill curves, for all tested species except C. parapsilosis", "token_count": 513, "char_count": 1473, "word_count": 209, "semantic_coherence": 1, "information_density": 0.512, "quality_score": 0.756, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:37.037140", "source": { "split": "train_shard_00001", "doc_id": 4594 }, "chunk_id": "train_shard_00001_4594_0", "global_id": 12159 }, { "text": "Our results highlight the fungicidal action of posaconazole against a number of clinically relevant Candida species.\n\nCorrelation of posaconazole minimum fungicidal concentration and time kill test against nine Candida species.", "token_count": 50, "char_count": 227, "word_count": 30, "semantic_coherence": 1, "information_density": 0.7667, "quality_score": 0.8833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:37.401397", "source": { "split": "train_shard_00001", "doc_id": 4594 }, "chunk_id": "train_shard_00001_4594_1", "global_id": 12160 }, { "text": "From a phlegmon in a dog an aerobic and facultatively anaerobic, indole-, oxidase- and catalase-negative, non-motile bacterium was isolated in 2019 in Germany that stained Gram-negative and showed a pleomorphic, rod-shaped, non-spore-forming appearance. Based on the results of 16S rRNA gene sequence analyses, strain IHIT1603-19T was assigned to the genus Streptobacillus with sequence similarities of 98.6, 98.0, 97.9, 97.1 and 94.4 % to the type strains of Streptobacillus felis, Streptobacillus notomytis, Streptobacillus ratti, Streptobacillus moniliformis and Streptobacillus hongkongensis, respectively. Strain IHIT1603-19T could also clearly be differentiated from other Streptobacillus species by rpoB, groEL and recA gene, nucleotide and amino acid sequence analyses as well as by core genome phylogeny. Regarding DNA-DNA relatedness, strain IHIT1603-19T demonstrated an average nucleotide identity of 83.00 and 82.28 % compared to S. felis 131000547T and S. moniliformis DSM 12112T, respectively", "token_count": 455, "char_count": 1145, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7111, "quality_score": 0.8556, "entities": { "genes": [ "IHIT1603" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:38.043443", "source": { "split": "train_shard_00001", "doc_id": 4595 }, "chunk_id": "train_shard_00001_4595_0", "global_id": 12161 }, { "text": "Chemotaxonomic and physiological data of strain IHIT1603-19T were in congruence with other closely related members of the family Leptotrichiaceae, represented by highly similar enzyme profiles and fatty acid patterns. MALDI-TOF MS analysis also proved suitable in unequivocally discriminating strain IHIT1603-19T from all currently described taxa of the genus Streptobacillus. On the basis of these data, we propose the novel species Streptobacillus canis sp. nov. with the type strain IHIT1603-19T (=DSM 110501T=CCUG 74118T=CIP 111795T). The G+C content of the DNA of the type strain is 26.6 mol%, genome size is 1.60 Mbp.\n\nStreptobacillus canis sp. nov. isolated from a dog.", "token_count": 289, "char_count": 770, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [ "IHIT1603" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:38.599215", "source": { "split": "train_shard_00001", "doc_id": 4595 }, "chunk_id": "train_shard_00001_4595_1", "global_id": 12162 }, { "text": "The ST313 sequence type of Salmonella enterica serovar Typhimurium causes invasive non-typhoidal salmonellosis amongst immunocompromised people in sub-Saharan Africa (sSA). Previously, two distinct phylogenetic lineages of ST313 have been described which have rarely been found outside sSA. Following the introduction of routine whole genome sequencing of Salmonella enterica by Public Health England in 2014, we have discovered that 2.7% (79/2888) of S. Typhimurium from patients in England and Wales are ST313. Of these isolates, 59/72 originated from stool and 13/72 were from extra-intestinal sites. The isolation of ST313 from extra-intestinal sites was significantly associated with travel to Africa (OR 12 [95% CI: 3,53]). Phylogenetic analysis revealed previously unsampled diversity of ST313, and distinguished UK-linked isolates causing gastroenteritis from African-associated isolates causing invasive disease. Bayesian evolutionary investigation suggested that the two African lineages diverged from their most recent common ancestors independently, circa 1796 and 1903. The majority of genome degradation of African ST313 lineage 2 is conserved in the UK ST313 lineages and only 10/44 pseudogenes were lineage 2-specific. The African lineages carried a characteristic prophage and antibiotic resistance gene repertoire, suggesting a strong selection pressure for these horizontally-acquired genetic elements in the sSA setting. We identified an ST313 isolate associated with travel to Kenya that carried a chromosomally-located bla CTX-M-15 , demonstrating the continual evolution of this sequence type in Africa in response to selection pressure exerted by antibiotic usage. The S. Typhimurium ST313 sequence type has been primarily associated with invasive disease in Africa. Here, we highlight the power of routine whole-genome-sequencing by public health agencies to make epidemiologically-significant deductions that would be missed by conventional microbiological methods", "token_count": 511, "char_count": 1990, "word_count": 269, "semantic_coherence": 1, "information_density": 0.6245, "quality_score": 0.8123, "entities": { "genes": [ "ST313" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:39.260714", "source": { "split": "train_shard_00001", "doc_id": 4596 }, "chunk_id": "train_shard_00001_4596_0", "global_id": 12163 }, { "text": "The discovery of ST313 isolates responsible for gastroenteritis in the UK reveals new diversity in this important sequence type. We speculate that the niche specialization of sub-Saharan African ST313 lineages is driven in part by the acquisition of accessory genome elements.\n\nSalmonella enterica serovar Typhimurium ST313 responsible for gastroenteritis in the UK are genetically distinct from isolates causing bloodstream infections in Africa", "token_count": 112, "char_count": 452, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7258, "quality_score": 0.8629, "entities": { "genes": [ "ST313" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:39.641656", "source": { "split": "train_shard_00001", "doc_id": 4596 }, "chunk_id": "train_shard_00001_4596_1", "global_id": 12164 }, { "text": "Escherichia coli is a commensal inhabitant of the mammalian gut microbiota, frequently associated with various gastrointestinal diseases. There is increasing interest in comprehending the variety of bacteriophages (phages) that target this bacterium, as such insights could pave the way for their potential use in therapeutic applications. Here, we report the isolation and characterization of four newly identified E. coli infecting tailed phages (W70, A7-1, A5-4, and A73) that were found to constitute a novel genus, Septuagintavirus, within the subfamily Vequintavirinae. Genomes of these phages ranged from 137 kbp to 145 kbp, with a GC content of 41 mol%. They possess a maximum nucleotide similarity of 30% with phages of the closest phylogenetic genus, Certrevirus, while displaying limited homology to other genera of the Vequintavirinae family. Host range analysis showed that these phages have limited activity against a panel of E. coli strains, infecting 6 out of 16 tested isolates, regardless of their phylotype. Electrospray ionization-tandem mass spectrometry (ESI-MS/MS) was performed on the virion of phage W70, allowing the identification of 28 structural proteins, 19 of which were shared with phages of other genera of Vequintavirinae family. The greatest diversity was identified with proteins forming tail fiber structures, likely indicating the adaptation of virions of each phage genus of this subfamily for the recognition of their target receptor on host cells", "token_count": 432, "char_count": 1544, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6727, "quality_score": 0.8364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:40.281628", "source": { "split": "train_shard_00001", "doc_id": 4597 }, "chunk_id": "train_shard_00001_4597_0", "global_id": 12165 }, { "text": "The findings of this study provide greater insights into the phages of the subfamily Vequintavirinae, contributing to the pool of knowledge currently known about these phages.

Importance

Escherichia coli is a well-known bacterium that inhabits diverse ecological niches, including the mammalian gut microbiota. Certain strains are associated with gastrointestinal diseases, and there is a growing interest in using bacteriophages, viruses that infect bacteria, to combat bacterial infections. Here, we describe the isolation and characterization of four novel E. coli bacteriophages that constitute a new genus, Septuagintavirus, within the subfamily Vequintavirinae. We conducted mass spectrometry on virions of a representative phage of this novel clade and compared it to other phages within the subfamily. Our analysis shows that virion structure is highly conserved among all phages, except for proteins related to tail fiber structures implicated in the host range. These findings provide greater insights into the phages of the subfamily Vequintavirinae, contributing to the existing pool of knowledge about these phages.\n\nIsolation and characterization of Septuagintavirus; a novel clade of Escherichia coli phages within the subfamily Vequintavirinae.", "token_count": 348, "char_count": 1330, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:40.853469", "source": { "split": "train_shard_00001", "doc_id": 4597 }, "chunk_id": "train_shard_00001_4597_1", "global_id": 12166 }, { "text": "

Background

Bacteria belonging to the genus Novosphingobium are known to be metabolically versatile and occupy different ecological niches. In the absence of genomic data and/or analysis, knowledge of the bacteria that belong to this genus is currently limited to biochemical characteristics. In this study, we analyzed the whole genome sequencing data of six bacteria in the Novosphingobium genus and provide evidence to show the presence of genes that are associated with salt tolerance, cell-cell signaling and aromatic compound biodegradation phenotypes. Additionally, we show the taxonomic relationship between the sequenced bacteria based on phylogenomic analysis, average amino acid identity (AAI) and genomic signatures.

Results

The taxonomic clustering of Novosphingobium strains is generally influenced by their isolation source. AAI and genomic signature provide strong support the classification of Novosphingobium sp. PP1Y as Novosphingobium pentaromaticivorans PP1Y. The identification and subsequent functional annotation of the unique core genome in the marine Novosphingobium bacteria show that ectoine synthesis may be the main contributing factor in salt water adaptation. Genes coding for the synthesis and receptor of the cell-cell signaling molecules, of the N-acyl-homoserine lactones (AHL) class are identified. Notably, a solo luxR homolog was found in strain PP1Y that may have been recently acquired via horizontal gene transfer as evident by the presence of multiple mobile elements upstream of the gene. Additionally, phylogenetic tree analysis and sequence comparison with functionally validated aromatic ring hydroxylating dioxygenases (ARDO) revealed the presence of several ARDOs (oxygenase) in Novosphingobium bacteria with the majority of them belonging to the Groups II and III of the enzyme.

Conclusions

The combination of prior knowledge on the distinctive phenotypes of Novosphingobium strains and meta-analysis of their whole genomes enables the identification of several genes that are relevant in industrial applications and bioremediation", "token_count": 482, "char_count": 2102, "word_count": 284, "semantic_coherence": 1, "information_density": 0.581, "quality_score": 0.7905, "entities": { "genes": [ "PP1Y" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:41.501328", "source": { "split": "train_shard_00001", "doc_id": 4598 }, "chunk_id": "train_shard_00001_4598_0", "global_id": 12167 }, { "text": "The results from such targeted but comprehensive comparative genomics analysis have the potential to contribute to the understanding of adaptation, cell-cell communication and bioremediation properties of bacteria belonging to the genus Novosphingobium.\n\nComparative genomic analysis of six bacteria belonging to the genus Novosphingobium: insights into marine adaptation, cell-cell signaling and bioremediation.", "token_count": 81, "char_count": 412, "word_count": 51, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:41.870109", "source": { "split": "train_shard_00001", "doc_id": 4598 }, "chunk_id": "train_shard_00001_4598_1", "global_id": 12168 }, { "text": "The species Lactobacillus reuteri has diversified into host-specific lineages, implying a long-term association with different vertebrates. Strains from rodent lineages show specific adaptations to mice, but the processes underlying the evolution of L. reuteri in other hosts remain unknown. We administered three standardized inocula composed of strains from different host-confined lineages to mice, pigs, chickens, and humans. The ecological performance of each strain in the gastrointestinal tract of each host was determined by typing random colonies recovered from fecal samples collected over five consecutive days postadministration. Results revealed that rodent strains were predominant in mice, confirming previous findings of host adaptation. In chickens, poultry strains of the lineage VI (poultry VI) and human isolates from the same lineage (human VI) were recovered at the highest and second highest rates, respectively. Interestingly, human VI strains were virtually undetected in human feces. These findings, together with ancestral state reconstructions, indicate poultry VI and human VI strains share an evolutionary history with chickens. Genomic analysis revealed that poultry VI strains possess a large and variable accessory genome, whereas human VI strains display low genetic diversity and possess genes encoding antibiotic resistance and capsular polysaccharide synthesis, which might have allowed temporal colonization of humans. Experiments in pigs and humans did not provide evidence of host adaptation of L. reuteri to these hosts. Overall, our findings demonstrate host adaptation of L. reuteri to rodents and chickens, supporting a joint evolution of this bacterial species with several vertebrate hosts, although questions remain about its natural history in humans and pigs.IMPORTANCE Gut microbes are often hypothesized to have coevolved with their vertebrate hosts. However, the evidence is sparse and the evolutionary mechanisms have not been identified. We developed and applied an experimental approach to determine host adaptation of L. reuteri to different hosts. Our findings confirmed adaptation to rodents and provided evidence of adaptation to poultry, suggesting that L. reuteri evolved via natural selection in different hosts", "token_count": 523, "char_count": 2322, "word_count": 320, "semantic_coherence": 1, "information_density": 0.575, "quality_score": 0.7875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:42.503611", "source": { "split": "train_shard_00001", "doc_id": 4599 }, "chunk_id": "train_shard_00001_4599_0", "global_id": 12169 }, { "text": "By complementing phylogenetic analyses with experimental evidence, this study provides novel information about the mechanisms driving host-microbe coevolution with vertebrates and serve as a basis to inform the application of L. reuteri as a probiotic for different host species.\n\nExperimental Evaluation of Host Adaptation of Lactobacillus reuteri to Different Vertebrate Species.", "token_count": 97, "char_count": 388, "word_count": 51, "semantic_coherence": 1, "information_density": 0.7843, "quality_score": 0.8922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:42.885768", "source": { "split": "train_shard_00001", "doc_id": 4599 }, "chunk_id": "train_shard_00001_4599_1", "global_id": 12170 }, { "text": "Bacterial regulatory RNAs have been extensively studied for over a decade, and are progressively being integrated into the complex genetic regulatory network. Transcriptomic arrays, recent deep-sequencing data and bioinformatics suggest that bacterial genomes produce hundreds of regulatory RNAs. However, while some have been authenticated, the existence of the others varies according to strains and growth conditions, and their detection fluctuates with the methodologies used for data acquisition and interpretation. For example, several small RNA (sRNA) candidates are now known to be parts of UTR transcripts. Accurate annotation of regulatory RNAs is a complex task essential for molecular and functional studies. We defined bona fide sRNAs as those that (i) likely act in trans and (ii) are not expressed from the opposite strand of a coding gene. Using published data and our own RNA-seq data, we reviewed hundreds of Staphylococcus aureus putative regulatory RNAs using the DETR'PROK computational pipeline and visual inspection of expression data, addressing the question of which transcriptional signals correspond to sRNAs. We conclude that the model strain HG003, a NCTC8325 derivative commonly used for S. aureus genetic regulation studies, has only about 50 bona fide sRNAs, indicating that these RNAs are less numerous than commonly stated. Among them, about half are associated to the S. aureus sp. core genome and a quarter are possibly expressed in other Staphylococci. We hypothesize on their features and regulation using bioinformatic approaches.\n\nAssessment of Bona Fide sRNAs in Staphylococcus aureus.", "token_count": 436, "char_count": 1689, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6527, "quality_score": 0.8264, "entities": { "genes": [ "NCTC8325", "HG003" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:43.515989", "source": { "split": "train_shard_00001", "doc_id": 4600 }, "chunk_id": "train_shard_00001_4600_0", "global_id": 12171 }, { "text": "Salmonella enterica subspecies enterica serovar Gallinarum biovar Pullorum (S Pullorum) is the etiological agent of pullorum disease, causing white diarrhea with high mortality in chickens. There are many unsolved issues surrounding the epidemiology of S Pullorum, including its origin and transmission history as well as the discordance between its phenotypic heterogeneity and genetic monomorphism. In this paper, we report the results of whole-genome sequencing of a panel of 97 S Pullorum strains isolated between 1962 and 2014 from four countries across three continents. We utilized 6,795 core genome single nucleotide polymorphisms (SNPs) to reconstruct a phylogenetic tree within a spatiotemporal Bayesian framework, estimating that the most recent common ancestor of S Pullorum emerged in ∼914 CE (95% confidence interval [95%CI], 565 to 1273 CE). The extant S Pullorum strains can be divided into four distinct lineages, each of which is significantly associated with geographical distribution. The intercontinental transmissions of lineages III and IV can be traced to the mid-19th century and are probably related to the \"Hen Fever\" prevalent at that time. Further genomic analysis indicated that the loss or pseudogenization of functional genes involved in metabolism and virulence in S Pullorum has been ongoing since before and after divergence from the ancestor. In contrast, multiple prophages and plasmids have been acquired by S Pullorum, and these have endowed it with new characteristics, especially the multidrug resistance conferred by two large plasmids in lineage I", "token_count": 443, "char_count": 1653, "word_count": 235, "semantic_coherence": 1, "information_density": 0.7106, "quality_score": 0.8553, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:44.502542", "source": { "split": "train_shard_00001", "doc_id": 4601 }, "chunk_id": "train_shard_00001_4601_0", "global_id": 12172 }, { "text": "The results of this study provide insight into the evolution of S Pullorum and prove the efficiency of whole-genome sequencing in epidemiological surveillance of pullorum disease.IMPORTANCE Pullorum disease, an acute poultry septicemia caused by Salmonella Gallinarum biovar Pullorum, is fatal for young chickens and is a heavy burden on poultry industry. The pathogen is rare in most developed countries but still extremely difficult to eliminate in China. Efficient epidemiological surveillance necessitates clarifying the origin of the isolates from different regions and their phylogenic relationships. Genomic epidemiological analysis of 97 S Pullorum strains was carried out to reconstruct the phylogeny and transmission history of S Pullorum. Further analysis demonstrated that functional gene loss and acquisition occurred simultaneously throughout the evolution of S Pullorum, both of which reflected adaptation to the changing environment. The result of our study will be helpful in surveillance and prevention of pullorum disease.\n\nLoss and Gain in the Evolution of the Salmonella enterica Serovar Gallinarum Biovar Pullorum Genome.", "token_count": 282, "char_count": 1192, "word_count": 161, "semantic_coherence": 1, "information_density": 0.646, "quality_score": 0.823, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:45.058524", "source": { "split": "train_shard_00001", "doc_id": 4601 }, "chunk_id": "train_shard_00001_4601_1", "global_id": 12173 }, { "text": "

Objectives

To investigate the prevalence and transmission of mcr-3 among Salmonella enterica serotype Typhimurium and 1,4,[5],12:i:-.

Methods

A total of 4724 clinical Salmonella isolates were screened for the presence of mcr-3 in China during 2014-19. The clonal relationship of the mcr-3-positive isolates and their plasmid contents and complete sequence were also characterized based on WGS data from the Illumina and MinION platforms.

Results

We identified 10 mcr-3-positive isolates, and all were MDR, mostly resistant to colistin, cefotaxime, ciprofloxacin, doxycycline and florfenicol. mcr-3 was co-present with blaCTX-M-55-qnrS1 on hybrid ST3-IncC-FII conjugatable plasmids (n = 6) and an ST3-IncC non-conjugatable plasmid (n = 1) and embedded into a pCHL5009T-like IncFII plasmid on the Salmonella chromosome (n = 3). Four distinctive genetic contexts surrounded mcr-3 and all but one were closely related to each other and to the corresponding region of IncFII plasmid pCHL5009T. IS15DI was most likely the vehicle for integration of mcr-3-carrying IncFII plasmids into ST3-IncC plasmids and the chromosome and for shaping the MDR regions. In addition, a phylogenetic tree based on the core genome revealed a unique Salmonella lineage (≤665 SNPs) that contained these 10 mcr-3-positive isolates and another 38 (33 from patients) mcr-3-positive Salmonella from five countries", "token_count": 478, "char_count": 1405, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6237, "quality_score": 0.8119, "entities": { "genes": [ "ST3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:45.700788", "source": { "split": "train_shard_00001", "doc_id": 4602 }, "chunk_id": "train_shard_00001_4602_0", "global_id": 12174 }, { "text": "In particular, most of the 51 mcr-3-positive isolates belonged to ST34 and harboured diverse antibiotic resistance genes (ARGs), including mcr-3-blaCTX-M-55-qnrS1, and possessed similar ARG profiles.

Conclusions

Our findings revealed global clonal spread of MDR ST34 Salmonella from clinical isolates co-harbouring mcr-3 with blaCTX-M-55 and qnrS1 and a flexibility of mcr-3 co-transmittance with other ARGs mediated by mobile genetic elements.\n\nGlobal clonal spread of mcr-3-carrying MDR ST34 Salmonella enterica serotype Typhimurium and monophasic 1,4,[5],12:i:- variants from clinical isolates.", "token_count": 198, "char_count": 604, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7467, "quality_score": 0.8733, "entities": { "genes": [ "ST34" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:46.147939", "source": { "split": "train_shard_00001", "doc_id": 4602 }, "chunk_id": "train_shard_00001_4602_1", "global_id": 12175 }, { "text": "The purpose of the study was to investigate the molecular characteristics and genetic relatedness of the first reported cases of vancomycin-resistant enterococci (VRE) from the Tripoli Medical Center, Libya. In total, 43 VRE isolates were obtained from various clinical sites throughout the years 2013-2014, including 40 vanA-type and 2 vanB-type vancomycin-resistant Enterococcus faecium isolates and 1 vanC1-type Enterococcus gallinarum. Of the 42 E. faecium, 19 isolates were subjected to whole genome sequencing. Core genome multilocus sequence typing (cgMLST) analysis revealed three sequence clusters (SCs) of clonally related isolates, which were linked to different hospital wards. The first two VRE isolates, isolated early 2013 from patients in the medical intensive care unit, were grouped in SC1 (MLST [ST] 78, vanB) and differed in only 3 of 1423 cgMLST alleles. The SC2 (n = 16, special care baby unit, neonatal intensive care unit, pediatric surgery ward, and oncology ward) and SC3 (n = 1, antenatal ward) were all ST80 vanA-VRE, but the single SC3 isolate differed in 233 alleles compared with SC2. Within SC2, isolates differed in 1-23 alleles. Comparison with a larger database of E. faecium strains indicated that all isolates clustered within the previously defined hospital clade A1. A combination of Resfinder and mlplasmid analysis identified the presence of resistance genes on different plasmid predicted genetic elements among different SCs. In conclusion, this study documents the first isolates causing outbreaks with VRE in the Libyan health care system", "token_count": 508, "char_count": 1660, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "SC1", "SC3", "ST80", "SC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:46.803444", "source": { "split": "train_shard_00001", "doc_id": 4603 }, "chunk_id": "train_shard_00001_4603_0", "global_id": 12176 }, { "text": "Further surveillance efforts using molecular typing methods to monitor spread of multidrug-resistant bacteria in the Libyan health care system are urgently needed.\n\nWhole Genome Sequence Analysis of the First Vancomycin-Resistant Enterococcus faecium Isolates from a Libyan Hospital in Tripoli.", "token_count": 75, "char_count": 301, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8974, "quality_score": 0.9487, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:47.202353", "source": { "split": "train_shard_00001", "doc_id": 4603 }, "chunk_id": "train_shard_00001_4603_1", "global_id": 12177 }, { "text": "Bifidobacterium species are well recognized as probiotics and colonized in various parts of the human body. Here, we report the draft genome sequences of Bifidobacterium animalis isolated from two healthy Japanese volunteers, one of which was sampled twice before and after a 10-year interval. A core genome phylogeny analysis indicated that the strains isolated from the same volunteer were closely related. This paper is the first report of multiple draft genome sequences of B. animalis independently isolated from the same individual and provides insight into the probiotic potential of a member of this species.\n\nDraft Genome Sequences of Bifidobacterium animalis Consecutively Isolated from Healthy Japanese Individuals.", "token_count": 184, "char_count": 754, "word_count": 106, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:47.671873", "source": { "split": "train_shard_00001", "doc_id": 4604 }, "chunk_id": "train_shard_00001_4604_0", "global_id": 12178 }, { "text": "In this study, we characterized 84 Listeria monocytogenes (Lm) strains having an atypical IVb-v1 profile and isolated in a meat producing plant of Central Italy. They were assigned to the new MLST type ST2801 (CC218). The new ST was widespread in the food-producing environment where it was able to persist for over a year even after cleaning and sanitation. Cluster analysis identified three main clusters genetically close to each other (0-22 allelic differences and 0-28 SNPs) from two different cgMLST types, suggesting a common source. The coexistence of closely related clusters over time could be the result of a different evolution path starting from a common ancestor first introduced in the plant and/or the consequence of the repetitive reintroduction of closely related clones probably by raw materials. All the strains presented several determinants for heavy metals resistance, stress response, biofilm production, and multidrug efflux pumps with no significant differences among the clusters. A total of 53 strains carried pLI100 and the j1776 plasmids, while in one strain, the pLM33 was found in addition to pLI100. Only the strains carrying plasmids presented cadA and cadC for cadmium resistance and the mco gene encoding a multicopper oxidase and gerN for an additional Na+/H+-K+ antiporter. All the strains presented a virulence profile including a full-length inlA gene and the additional LIPI-3. The isolation of a new ST with a large pattern of stress-adaptation genes and able to persist is an important contribution to deepening the current knowledge on the uncommon IVb-v1 and in general on the genomic diversity of Lm.\n\nAtypical Serogroup IVb-v1 of Listeria monocytogenes Assigned to New ST2801, Widely Spread and Persistent in the Environment of a Pork-Meat Producing Plant of Central Italy.", "token_count": 508, "char_count": 1869, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6064, "quality_score": 0.8032, "entities": { "genes": [ "CC218", "ST2801" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:48.338159", "source": { "split": "train_shard_00001", "doc_id": 4605 }, "chunk_id": "train_shard_00001_4605_0", "global_id": 12179 }, { "text": "Citrus huanglongbing (HLB), caused by phloem-limited 'Candidatus Liberibacter' bacteria, is a destructive disease threatening the worldwide citrus industry. The mechanisms of pathogenesis are poorly understood and no efficient strategy is available to control HLB. Here, we used a comparative genomics screen to identify candidate microbe-associated molecular patterns (MAMPs) from 'Ca. Liberibacter' spp. We identified the core genome from multiple 'Ca. Liberibacter' pathogens, and searched for core genes with signatures of positive selection. We hypothesized that genes encoding putative MAMPs would evolve to reduce recognition by the plant immune system, while retaining their essential functions. To efficiently screen candidate MAMP peptides, we established a high-throughput microtiter plate-based screening assay, particularly for citrus, that measured reactive oxygen species (ROS) production, which is a common immune response in plants. We found that two peptides could elicit ROS production in Arabidopsis and Nicotiana benthamiana. One of these peptides elicited ROS production and defense gene expression in HLB-tolerant citrus genotypes, and induced MAMP-triggered immunity against the bacterial pathogen Pseudomonas syringae. Our findings identify MAMPs that boost immunity in citrus and could help prevent or reduce HLB infection.\n\nComparative Genomics Screen Identifies Microbe-Associated Molecular Patterns from 'Candidatus Liberibacter' spp. That Elicit Immune Responses in Plants.", "token_count": 396, "char_count": 1552, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:48.985523", "source": { "split": "train_shard_00001", "doc_id": 4606 }, "chunk_id": "train_shard_00001_4606_0", "global_id": 12180 }, { "text": "Clostridioides difficile is a common cause of nosocomial diarrhoea. Toxins TcdA and TcdB are considered to be the main virulence factors and are encoded by the PaLoc region, while the binary toxin encoded in the CdtLoc region also contributes to pathogenicity. Variant toxinotypes reflect the genetic diversity of a key toxin-encoding 19 kb genetic element (the PaLoc). Here, we present analysis of a comprehensive collection of all known major C. difficile toxinotypes to address the evolutionary relationships of the toxin gene variants, the mechanisms underlying the origin and development of variability in toxin genes and the PaLoc, and the relationship between structure and function in TcdB variants. The structure of both toxin genes is modular, composed of interspersed blocks of sequences corresponding to functional domains and having different evolutionary histories, as shown by the distribution of mutations along the toxin genes and by incongruences of domain phylogenies compared to overall C. difficile cluster organization. In TcdB protein, four mutation patterns could be differentiated, which correlated very well with the type of TcdB cytopathic effect (CPE) on cultured cells. Mapping these mutations to the three-dimensional structure of the TcdB showed that the majority of the variation occurs in surface residues and that point mutation at residue 449 in alpha helix 16 differentiated strains with different types of CPE. In contrast to the PaLoc, phylogenetic trees of the CdtLoc were more consistent with the core genome phylogenies, but there were clues that CdtLoc can also be exchanged between strains.\n\nComparative genomics of Clostridioides difficile toxinotypes identifies module-based toxin gene evolution.", "token_count": 450, "char_count": 1769, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8023, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:49.623012", "source": { "split": "train_shard_00001", "doc_id": 4607 }, "chunk_id": "train_shard_00001_4607_0", "global_id": 12181 }, { "text": "Idiomarinaceae is a family of Gram-stain negative, mesophilic euryhalophiles. To provide a robust framework for the evolutionary and taxonomic relationships of bacteria of this family, we compared herein the genomes of 36 type strains and 43 non-type strains using 16S rRNA gene sequences, core genome based 78 single-copy orthologous proteins, digital DNA-DNA hybridization and average nucleotide identity (ANI) estimation. The 79 bacteria of this family were consistently divided into taxon I, taxon II, and taxon III corresponding to the three genera Idiomarina, Pseudidiomarina, and Aliidiomarina, which contained 13 putative new genospecies in addition to 35 well-defined species represented by each type strain. Furthermore, genetic diversity of this family was evident at the genus- and species levels, and exceeded that which is defined currently by the named species. In view of multiple genotypic characteristics clearly distinct from the other two genera, we propose reinstating the genus Pseudidiomarina as a monophyletic taxon. Taken together, this is the first genome-based study of the taxonomy and diversity of bacteria within the family Idiomarinaceae, and will contribute to further insights into microbial evolution and adaptation to saline environments.\n\nGenome-Based Analysis Reveals the Taxonomy and Diversity of the Family Idiomarinaceae.", "token_count": 366, "char_count": 1403, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6804, "quality_score": 0.8402, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:50.203584", "source": { "split": "train_shard_00001", "doc_id": 4608 }, "chunk_id": "train_shard_00001_4608_0", "global_id": 12182 }, { "text": "

Introduction

S-adenosylmethionine (SAM), a key molecule in plant biology, plays an essential role in stress response and growth regulation. Despite its importance, the SAM synthetase (SAMS) gene family in sunflowers (Helianthus annuus L.) remains poorly understood.

Methods

In this study, the SAMS genes were identified from the sunflower genome. Subsequently, the protein properties, gene structure, chromosomal location, cis-acting elements, collinearity, and phylogeny of the SAMS gene family were analyzed by bioinformatic methods. Finally, the expression patterns of SAMS genes in different tissues, under different hormonal treatment and abiotic stress were analyzed based on transcriptome data and qRT-PCR.

Results

This study identified 58 SAMS genes across nine cultivated sunflower species, which were phylogenetically classified into seven distinct subgroups. Physicochemical properties and gene structure analysis showed that the SAMS genes are tightly conserved between cultivars. Collinearity analysis revealed segmental duplications as the primary driver of gene family expansion. The codon usage bias analysis suggested that natural selection substantially shapes the codon usage patterns of sunflower SAMS genes, with a bias for G/C-ending high-frequency codons, particularly encoding glycine, leucine, and arginine. Analysis of the cis-regulatory elements in promoter regions, implied their potential roles in stress responsiveness. Differential expression patterns for HanSAMS genes were observed in different tissues as well as under hormone treatment or abiotic stress conditions by analyzing RNA-seq data from previous studies and qRT-PCR data in our current study. The majority of genes demonstrated a robust response to BRA and IAA treatments in leaf tissues, with no significant expression change observed in roots, suggesting the response of HanSAMS genes to hormones is tissue-specific", "token_count": 497, "char_count": 1982, "word_count": 257, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:50.856126", "source": { "split": "train_shard_00001", "doc_id": 4609 }, "chunk_id": "train_shard_00001_4609_0", "global_id": 12183 }, { "text": "Expression analyses under abiotic stresses demonstrated diverse expression profiles of HanSAMS genes, with HanSAMS5 showing significant upregulation in response to both drought and salt stresses.

Discussion

This comprehensive genomic and expression analysis provides valuable insights into the SAMS gene family in sunflowers, laying a robust foundation for future functional studies and applications in crop improvement for stress resilience.\n\nPan-genome wide identification and analysis of the SAMS gene family in sunflowers (Helianthus annuus L.) revealed their intraspecies diversity and potential roles in abiotic stress tolerance.", "token_count": 172, "char_count": 677, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7683, "quality_score": 0.8841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:51.303328", "source": { "split": "train_shard_00001", "doc_id": 4609 }, "chunk_id": "train_shard_00001_4609_1", "global_id": 12184 }, { "text": "

Objectives

Ralstonia pickettii has been increasingly recognised as an emerging opportunistic pathogen in hospital settings in recent years, especially in patients with prolonged hospital stay. Clinical manifestations associated with R. pickettii infection range from mild infections to severe invasive life-threatening infections. Here we report the genome sequence of a clinical R. pickettii strain (PSLESD1) carrying two novel blaOXA allelic variants in China.

Methods

Whole-genome sequencing of strain PSLESD1 was performed using an Illumina NovaSeq 6000 platform. Antimicrobial resistance genes were identified using the BacWGSTdb server. The phylogenetic relationship betweenR. pickettii PSLESD1 and a total of 17 R. pickettii strains deposited in the NCBI GenBank database was analysed using NJ (neighbour joining)/UPGMA (unweighted pair-group method with arithmetic mean) phylogeny (MAFFT v.7) based on core genome single nucleotide polymorphism (SNP) data.

Results

The draft genome sequence of R. pickettii strain PSLESD1 consists of 25 contigs comprising 5 267 333 bp. Three antimicrobial resistance genes were identified in the genome, including blaOXA-898, blaOXA-899 and sul2. Strain PSLESD1 was resistant to aminoglycosides and carbapenems including meropenem. Phylogenetic analysis showed that all strains retrieved from the NCBI GenBank database were epidemiologically unrelated. The closest relative of strain PSLESD1 was H2Cu2, which differed by 2908 SNPs.

Conclusion

In summary, we report the first genome sequence of a clinicalR", "token_count": 472, "char_count": 1609, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6634, "quality_score": 0.8317, "entities": { "genes": [ "PSLESD1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:51.943352", "source": { "split": "train_shard_00001", "doc_id": 4610 }, "chunk_id": "train_shard_00001_4610_0", "global_id": 12185 }, { "text": "pickettii strain harbouring two novel class D β-lactamase genes (blaOXA-898 and blaOXA-899) recovered from a bloodstream infection in China. These data may help to understand the genomic features and antimicrobial resistance mechanisms of this bacterial pathogen.\n\nGenotypic and phylogenetic characterisation of a clinical Ralstonia pickettii strain carrying two novel OXA allelic variants, blaOXA-898 and blaOXA-899, isolated from a bloodstream infection in China.", "token_count": 161, "char_count": 509, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7581, "quality_score": 0.879, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:52.381081", "source": { "split": "train_shard_00001", "doc_id": 4610 }, "chunk_id": "train_shard_00001_4610_1", "global_id": 12186 }, { "text": "The activities of xylitol dehydrogenase and xylose reductase in the yeasts Candida shehatae, C. didensiae, C. intermediae, C. tropicalis, Kluyveromyces marxianus, Pichia stipitis, P. guillermondii, Pachysolen tannophilus, and Torulopsis molishiama were studied at different oxygen transfer rates (OTRs) to the fermentation medium (0, 5, and 140 mmol O2/(1 h)). The activities of these enzymes were maximum in the yeasts P. stipitis and C. shehatae. The xylitol dehydrogenase of all the yeasts was NAD-dependent, irrespective of the intensity of aeration. The xylose reductase of the yeasts C. didensiae, C. intermediae, C. tropicalis, Kl. marxianus, P. guillermondii, and T. molishiama was NADPH-dependent, whereas the xylose reductase of P. stipitis, C. shehatae, and Pa. tannophilus was specific for both NADPH and NADH. The effect of OTR on the activities of the different forms of xylitol dehydrogenase and xylose reductase in the xylose-assimilating yeasts is discussed.\n\n[Activity of the key enzymes in xylose-assimilating yeasts at different rates of oxygen transfer to the fermentation medium].", "token_count": 358, "char_count": 1102, "word_count": 160, "semantic_coherence": 1, "information_density": 0.4688, "quality_score": 0.7344, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:52.948796", "source": { "split": "train_shard_00001", "doc_id": 4611 }, "chunk_id": "train_shard_00001_4611_0", "global_id": 12187 }, { "text": "Polyphosphate synthesis was studied in phosphate-starved cells of Saccharomyces cerevisiae and Kluyveromyces marxianus. Incubation of these yeasts for a short time with phosphate and either glucose or ethanol resulted in the formation of polyphosphate with a short chain length. With increasing incubation times, polyphosphates with longer chain lengths were formed. Polyphosphates were synthesized faster during incubation with glucose than with ethanol. Antimycin did not affect the glucose-induced polyphosphate synthesis in either yeast. Using ethanol as an energy source, antimycin A treatment blocked both polyphosphate synthesis and accumulation of orthophosphate in the yeast S. cerevisiae. However, in K. marxianus, polyphosphate synthesis and orthophosphate accumulation proceeded normally in antimycin-treated cells, suggesting that endogenous reserves were used as energy source. This was confirmed in experiments, conducted in the absence of an exogenous energy source.\n\nPolyphosphate synthesis in yeast.", "token_count": 261, "char_count": 1017, "word_count": 135, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:53.497492", "source": { "split": "train_shard_00001", "doc_id": 4612 }, "chunk_id": "train_shard_00001_4612_0", "global_id": 12188 }, { "text": "Acinetobacter baumannii is a nosocomial pathogen that poses a serious threat due to the rise of incidence of multidrug resistant (MDR) strains. During the COVID-19 pandemic, MDR A.baumannii clones have caused several outbreaks worldwide. Here we describe a detailed investigation of an MDR A. baumannii outbreak that occurred at Fondazione IRCCS Policlinico San Matteo (Pavia, Italy). A total of 96 A. baumannii strains, isolated between January and July 2020 from 41 inpatients (both SARS-CoV-2 positive and negative) in different wards, were characterized by phenotypic and genomic analyses combining Illumina and Nanopore sequencing. Antibiotic susceptibility testing revealed that all isolates were resistant to carbapenems and the sequence analysis attributed this to the carbapenemase gene bla OXA-23 . Screening of virulence factors unveiled that all strains carried determinants for biofilm formation, while plasmid analysis revealed the presence of two plasmids, one of which was a ⍰100kbp long and encoded a phage sequence. A core genome-based phylogeny was inferred to integrate outbreak strain genomes with background genomes from public databases and from the local surveillance program. All strains belonged to the globally disseminated ST2 clone and were mainly divided into two clades. Isolates from the outbreak clustered with surveillance isolates from 2019, suggesting that the outbreak was caused by two strains that were already circulating in the hospital before the start of the pandemic. The intensive spread of A. baumannii in the hospital was enhanced by the extreme emergency situation of the first COVID-19 pandemic wave that resulted in minor attention to infection prevention and control practices.

Importance

The COVID-19 pandemic, especially during the first wave, posed a great challenge to the hospital management and generally promoted nosocomial pathogen dissemination. Multidrug resistant (MDR) A. baumannii can easily spread and persist for a long time on surfaces, causing outbreaks in healthcare settings", "token_count": 504, "char_count": 2053, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.807, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:54.152545", "source": { "split": "train_shard_00001", "doc_id": 4613 }, "chunk_id": "train_shard_00001_4613_0", "global_id": 12189 }, { "text": "Infection prevention and control practices, epidemiological surveillance and microbiological screening are fundamental in order to control such outbreaks. Here, we sequenced the genomes of 96 isolates from an outbreak of MDR A. baumannii strains using both short- and long-read technology in order to reconstruct the outbreak events in fine detail. The sequence data demonstrated that two endemic clones of MDR A. baumannii were the source of this large hospital outbreak during the first COVID-19 pandemic wave, confirming the effect of COVID-19 emergency disrupting the protection provided by the use of the standard prevention procedures.\n\nThe COVID-19 pandemic sparked off a large-scale outbreak of carbapenem-resistantAcinetobacter baumanniifrom the endemic strains of an Italian hospital", "token_count": 184, "char_count": 800, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6607, "quality_score": 0.8304, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:54.599014", "source": { "split": "train_shard_00001", "doc_id": 4613 }, "chunk_id": "train_shard_00001_4613_1", "global_id": 12190 }, { "text": "Addition of benzoate to the medium reservoir of glucose-limited chemostat cultures of Saccharomyces cerevisiae CBS 8066 growing at a dilution rate (D) of 0.10 h-1 resulted in a decrease in the biomass yield, and an increase in the specific oxygen uptake rate (qO2) from 2.5 to as high as 19.5 mmol g-1 h-1. Above a critical concentration, the presence of benzoate led to alcoholic fermentation and a reduction in qO2 to 13 mmol g-1 h-1. The stimulatory effect of benzoate on respiration was dependent on the dilution rate: at high dilution rates respiration was not enhanced by benzoate. Cells could only gradually adapt to growth in the presence of benzoate: a pulse of benzoate given directly to the culture resulted in wash-out. As the presence of benzoate in cultures growing at low dilution rates resulted in large changes in the catabolic glucose flux, it was of interest to study the effect of benzoate on the residual glucose concentration in the fermenter as well as on the level of some selected enzymes. At D = 0.10 h-1, the residual glucose concentration increased proportionally with increasing benzoate concentration. This suggests that modulation of the glucose flux mainly occurs via a change in the extracellular glucose concentration rather than by synthesis of an additional amount of carriers. Also various intracellular enzyme levels were not positively correlated with the rate of respiration. A notable exception was citrate synthase: its level increased with increasing respiration rate. Growth of S. cerevisiae in ethanol-limited cultures in the presence of benzoate also led to very high qO2 levels of 19-21 mmol g-1 h-1. During growth on glucose as well as on ethanol, the presence of benzoate coincided with an increase in the mitochondrial volume up to one quarter of the total cellular volume", "token_count": 477, "char_count": 1822, "word_count": 295, "semantic_coherence": 1, "information_density": 0.4949, "quality_score": 0.7475, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [ "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:55.240360", "source": { "split": "train_shard_00001", "doc_id": 4614 }, "chunk_id": "train_shard_00001_4614_0", "global_id": 12191 }, { "text": "Also with the Crabtree-negative yeasts Candida utilis, Kluyveromyces marxianus and Hansenula polymorpha, growth in the presence of benzoate resulted in an increase in qO2 and, at high concentrations of benzoate, in aerobic fermentation. In contrast to S. cerevisiae, the highest qO2 of these yeasts when growing at D = 0.10 h-1 in the presence of benzoate was equal to, or lower than the qO2 attainable at mu(max) without benzoate. Enzyme activities that were repressed by glucose in S. cerevisiae also declined in K. marxianus when the glucose flux was increased by the presence of benzoate.(ABSTRACT TRUNCATED AT 400 WORDS)\n\nEffect of benzoic acid on metabolic fluxes in yeasts: a continuous-culture study on the regulation of respiration and alcoholic fermentation.", "token_count": 227, "char_count": 768, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6639, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation", "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:55.713547", "source": { "split": "train_shard_00001", "doc_id": 4614 }, "chunk_id": "train_shard_00001_4614_1", "global_id": 12192 }, { "text": "Type VI secretion systems (T6SS), recently described in hypervirulent K. pneumoniae (hvKp) strains, are involved in bacterial warfare but their role in classical clinical strains (cKp) has been little investigated. In silico analysis indicated the presence of T6SS clusters (from zero to four), irrespective of the strains origin or virulence, with a high prevalence in the K. pneumoniae species (98%). In the strain CH1157, two T6SS-apparented pathogenicity islands were detected, T6SS-1 and -2, harboring a phospholipase-encoding gene (tle1) and a potential new effector-encoding gene named tke (Type VI Klebsiella effector). Tle1 expression in Escherichia coli periplasm affected cell membrane permeability. T6SS-1 isogenic mutants colonized the highest gastrointestinal tract of mice less efficiently than their parental strain, at long term. Comparative analysis of faecal 16S sequences indicated that T6SS-1 impaired the microbiota richness and its resilience capacity. Oscillospiraceae family members could be specific competitors for the long-term gut establishment of K. pneumoniae.\n\nRole of Klebsiella pneumoniae Type VI secretion system (T6SS) in long-term gastrointestinal colonization.", "token_count": 331, "char_count": 1198, "word_count": 164, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "CH1157" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:56.283518", "source": { "split": "train_shard_00001", "doc_id": 4615 }, "chunk_id": "train_shard_00001_4615_0", "global_id": 12193 }, { "text": "

Objectives

The resistance rate of Klebsiella pneumoniae to commonly used antibiotics has been increasing rapidly, causing serious concern among clinicians and microbiologists. Resistance to carbapenems in K. pneumoniae is increasing dramatically in Chinese hospitals. Here we report the genome sequence of an NDM-1 and KPC-2 co-producing K. pneumoniae (CRKP380) isolated from a bloodstream infection in Hangzhou, China.

Methods

The whole genome sequence of strain CRKP380 was determined using an Illumina NovaSeq 6000 platform. Antimicrobial resistance genes (ARGs) were identified using the BacWGSTdb server. The phylogenetic relationship between strain CRKP380 and other K. pneumoniae strains isolated from Hangzhou currently deposited in the NCBI GenBank database was analysed using a core genome-based single nucleotide polymorphism strategy.

Results

Klebsiella pneumoniae CRKP380 was resistant to all antibiotics tested except tigecycline and colistin. The genome sequence of K. pneumoniae CRKP380 consisted of 75 contigs comprising 5 590 460 bp. According to the Pasteur multilocus sequence typing (MLST) scheme, CRKP380 belongs to ST11. Eight ARGs were identified in CRKP380, including two carbapenemase genes (blaKPC-2 and blaNDM-1). Ten phylogenetically-related K. pneumoniae strains from Hangzhou were identified with identical ARGs and the same capsular serotype KL105, but none of these strains carried the blaNDM gene.

Conclusion

Here we report the genome sequence of a K. pneumoniae ST11 clinical strain co-carrying blaNDM-1 and blaKPC-2 from Hangzhou, China", "token_count": 523, "char_count": 1656, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6209, "quality_score": 0.8104, "entities": { "genes": [ "KL105", "ST11", "CRKP380" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:56.936284", "source": { "split": "train_shard_00001", "doc_id": 4616 }, "chunk_id": "train_shard_00001_4616_0", "global_id": 12194 }, { "text": "The genome sequence of CRKP380 can be used as a reference sequence for future comparative genomic analysis, including the acquisition and mobilisation of carbapenem resistance genes.\n\nUnravelling the genome sequence of NDM-1 and KPC-2 co-producing Klebsiella pneumoniae ST11 isolated from a bloodstream infection.", "token_count": 81, "char_count": 313, "word_count": 43, "semantic_coherence": 1, "information_density": 0.7907, "quality_score": 0.8953, "entities": { "genes": [ "ST11", "CRKP380" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:57.307073", "source": { "split": "train_shard_00001", "doc_id": 4616 }, "chunk_id": "train_shard_00001_4616_1", "global_id": 12195 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) consists of a group of diverse strains differing greatly in genetic make-up and pathogenicity potential. Here, we investigated production of Shiga toxins (Stxs) in a bovine isolate carrying multiple Shiga toxin genes (stxs) after exposure to several antibiotics commonly used in food animals. Strain RM10809-C3 was co-isolated with a STEC O145:H28 strain from cattle feces near a leafy greens-growing region in California. The genome of RM10809-C3 is composed of a 5,128,479-bp chromosome and a 122,641-bp plasmid, encoding 5108 coding sequences. Strain RM10809-C3 belongs to serotype O22:H8 and is clustered together with two STEC O168:H8 food isolates using either multilocus sequence type or core genome-based phylogenetic analysis. Six intact prophages were identified in the genome of RM10809-C3, among which prophage 4 contained two sets of stx2d; whereas prophage 9 carried one set of stx1a. Increased production of Stx1 was detected in RM10809-C3 after exposure to mitomycin C and enrofloxacin, but not in cells exposed to tetracycline. In contrast, Stx2 remained undetectable in cells treated with any of the antibiotics examined. Comparison of Stx-converting prophages in strain RM10809-C3 with those in strain EDL933 revealed altered stx2 promoters in RM10809-C3, including deletion of the late promoter PR' and the mutations in qut, the binding site of antitermination protein Q", "token_count": 517, "char_count": 1518, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6777, "quality_score": 0.8389, "entities": { "genes": [ "EDL933", "RM10809" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:53:57.940558", "source": { "split": "train_shard_00001", "doc_id": 4617 }, "chunk_id": "train_shard_00001_4617_0", "global_id": 12196 }, { "text": "In contrast, both PR' and qut within the promoter of stx1 in RM10809-C3 were identical to the corresponding one in EDL933. Further, the protein Q encoded by Stx1-prophage in RM10809-C3 exhibited >94% identity with either of the two EDL933 protein Q; whereas both protein Q encoded by Stx2-prophage in RM10809-C3 were distantly related to any of the EDL933 protein Q. Natural silence of Stx2 production in strain RM10809-C3 emphasizes that not only the stx coding regions but also their regulatory factors are important in STEC risk assessment.\n\nGenomic Insight into Natural Inactivation of Shiga Toxin 2 Production in an Environmental Escherichia coli Strain Producing Shiga Toxin 1.", "token_count": 246, "char_count": 729, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [ "EDL933", "RM10809" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:58.430548", "source": { "split": "train_shard_00001", "doc_id": 4617 }, "chunk_id": "train_shard_00001_4617_1", "global_id": 12197 }, { "text": "Toxin-antitoxin systems are genetic elements that are widespread in prokaryotes. Although molecular mode of action of many of these toxins has been identified, their biological functions are mostly unknown. We investigated the functional integration of the TisB/IstR toxin-antitoxin system in the Escherichia coli SOS genotoxic stress response network. We showed that the tisB gene is induced in cells exposed to high doses of the genotoxic antibiotic trimethoprim. However, we also found that TisB contributes to trimethoprim-induced lethality. This is a consequence of the TisB-induced drop in the proton motive force (PMF), which results in blocking the thymine import and therefore the functioning of the pyrimidine salvage pathway. Conversely, a TisB-induced PMF drop protects cells by preventing the import of some other toxic compounds, like the aminoglycoside antibiotic gentamicin and colicin M, in the SOS-induced cells. Colicins are cytotoxic molecules produced by Enterobacterales when they are exposed to strong genotoxic stresses in order to compete with other microbiota members. We indeed found that TisB contributes to E. coli's fitness during mouse gut colonization. Based on the results obtained here, we propose that the primary biological role of the TisB toxin is to increase the probability of survival and maintenance in the mammalian gut of their bacterial hosts when they have to simultaneously deal with massive DNA damages and a fierce chemical warfare with other microbiota members. IMPORTANCE The contribution of toxin-antitoxin systems to the persistence of bacteria to antibiotics has been intensively studied. This is also the case with the E. coli TisB/IstR toxin-antitoxin system, but the contribution of TisB to the persistence to antibiotics turned out to be not as straightforward as anticipated. In this study, we show that TisB can decrease, but also increase, cytotoxicity of different antibiotics", "token_count": 505, "char_count": 1966, "word_count": 289, "semantic_coherence": 1, "information_density": 0.5675, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:59.102930", "source": { "split": "train_shard_00001", "doc_id": 4618 }, "chunk_id": "train_shard_00001_4618_0", "global_id": 12198 }, { "text": "This inconsistency has a common origin, i.e., TisB-induced collapse of the PMF, which impacts the import and the action of different antibiotics. By taking into account the natural habitat of TisB bacterial hosts, the facts that this toxin-antitoxin system is integrated into the genotoxic stress response regulon SOS and that both SOS regulon and TisB are required for E. coli to colonize the host intestine, and the phenotypic consequences of the collapse of the PMF, we propose that TisB protects its hosts from cytotoxic molecules produced by competing intestinal bacteria.\n\nTisB Protein Protects Escherichia coli Cells Suffering Massive DNA Damage from Environmental Toxic Compounds.", "token_count": 182, "char_count": 688, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7019, "quality_score": 0.851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:53:59.566628", "source": { "split": "train_shard_00001", "doc_id": 4618 }, "chunk_id": "train_shard_00001_4618_1", "global_id": 12199 }, { "text": "Samples of Coffea arabica were collected during the different stages of the fermentation from two production sites in Tanzania. The yeasts community was identified by genotyping using ITS-PCR and sequence analysis of the D1/D2 domain of the 26S rRNA gene. For confirmation, denaturating gradient gel electrophoresis (DGGE) of PCR-amplified 26S rRNA gene was performed to detect yeast directly from coffee samples without cultivation. Yeast counts were in the range 4.0 x 10(4) - 5.0 x 10(7) CFU/g with an increase during fermentation. Three yeasts species were dominant. The predominant yeast found during fermentation and drying was Pichia kluyveri. Pichia anomala was found in high numbers during drying of coffee beans. Hanseniaspora uvarum was the predominant yeast during fermentation but decreased during drying. Kluyveromyces marxianus, Candida pseudointermedia, Issatchenkia orientalis, Pichia ohmeri and Torulaspora delbrueckii occurred in concentrations of 10(3) CFU/g or below in coffee samples. Saccharomyces cerevisiae and Candida xestobii were not isolated by cultivation, but by the DGGE technique. A good agreement was found between the sequence analysis of the D1/D2 domain of the 26S rRNA gene and sequencing of the DGGE bands.\n\nYeast involved in fermentation of Coffea arabica in East Africa determined by genotyping and by direct denaturating gradient gel electrophoresis.", "token_count": 391, "char_count": 1392, "word_count": 203, "semantic_coherence": 1, "information_density": 0.5665, "quality_score": 0.7833, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:00.857442", "source": { "split": "train_shard_00001", "doc_id": 4619 }, "chunk_id": "train_shard_00001_4619_0", "global_id": 12200 }, { "text": "

Background

The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group.

Results

Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance.

Conclusion

We propose that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data.\n\nUnraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria.", "token_count": 473, "char_count": 1920, "word_count": 255, "semantic_coherence": 1, "information_density": 0.698, "quality_score": 0.849, "entities": { "genes": [ "WH5701", "RS9917" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:01.502392", "source": { "split": "train_shard_00001", "doc_id": 4620 }, "chunk_id": "train_shard_00001_4620_0", "global_id": 12201 }, { "text": "The Solanaceae family, which includes economically important crops such as tomatoes, potatoes and peppers, has experienced a rapid expansion in genomic data due to advancements in sequencing technologies. However, existing databases are limited by incomplete species representation, a lack of comprehensive comparative genomic tools and the absence of systematic pan-genomic analyses. To address these gaps, we developed the Solanaceae Information Resource (SoIR, https://soir.bio2db.com), a comprehensive genomics database for the Solanaceae family. SoIR integrates genomic data from 81 species and transcriptomic data from 41 species, encompassing a total of 3 908 408 gene annotations derived from Gene Ontology, nonredundant protein, Pfam, Swiss-Prot and TrEMBL databases. The resource also includes 3 437 115 CRISPR guide sequences, 212 395 transcription factors and 19 086 genes associated with methylation modification. In addition to species-specific analyses, SoIR provides extensive bioinformatics tools for investigating gene family evolution, phylogenetic relationships and karyotype reconstruction across 25 fully sequenced genomes. With advanced tools such as Blast, Synteny and Sequence Alignment, the platform provides users with interactive and intuitive visualizations for conducting cross-species comparative genomics. As the first comprehensive pan-genomic resource for the entire Solanaceae family, SoIR facilitates in-depth cross-species analysis, supporting global research initiatives in plant evolution, functional genomics and crop improvement.\n\nSoIR: a comprehensive Solanaceae information resource for comparative and functional genomic study.", "token_count": 384, "char_count": 1671, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:02.117720", "source": { "split": "train_shard_00001", "doc_id": 4621 }, "chunk_id": "train_shard_00001_4621_0", "global_id": 12202 }, { "text": "Campylobacter jejuni is commonly isolated on selective media following incubation at 37 °C or 42 °C, but the impact of these temperatures on genome variation remains unclear. Previously, Campylobacter selective enrichments from the feces of steers before and after ceftiofur treatment were plated on selective agar media and incubated at either 37 °C or 42 °C. Here, we analyzed the whole genome sequence of C. jejuni strains of the same multilocus sequence typing (MLST)-based sequence type (ST) and isolated from the same sample upon incubation at both temperatures. Four such strain pairs (one ST8221 and three ST8567) were analyzed using core genome and whole genome MLST (cgMLST, wgMLST). Among the 1970 wgMLST loci, 7-25 varied within each pair. In all but one of the pairs more (1.7-8.5 fold) new alleles were found at 42 °C. Most frameshift, nonsense, or start-loss mutations were also found at 42 °C. Variable loci CAMP0575, CAMP0912, and CAMP0913 in both STs may regularly respond to different temperatures. Furthermore, frameshifts in four variable loci in ST8567 occurred at multiple time points, suggesting a persistent impact of temperature. These findings suggest that the temperature of isolation may impact the sequence of several loci in C. jejuni from cattle.\n\nGenomic Analysis Reveals That Isolation Temperature on Selective Media Introduces Genetic Variation in Campylobacter jejuni from Bovine Feces.", "token_count": 429, "char_count": 1464, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [ "CAMP0913", "CAMP0912", "CAMP0575", "ST8567", "ST8221" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:02.745067", "source": { "split": "train_shard_00001", "doc_id": 4622 }, "chunk_id": "train_shard_00001_4622_0", "global_id": 12203 }, { "text": "

Aim

In order to improve the surveillance of invasive pneumococcal disease (IPD), the National Reference Laboratory (NRL) for Streptococcal Infections implemented whole genome sequencing (WGS) of Streptococcus pneumoniae. This article reports the first WGS data on S. pneumoniae isolates in the Czech Republic.

Material and methods

Thirty-five isolates of S. pneumoniae from IPD recovered in 2017-2019 were selected for WGS. These were serotypes 4, 8, 9V, 19A, and 22F, which were determined by the Quellung reaction in combination with endpoint multiplex PCR (mPCR). Multilocus sequence typing (MLST) is routinely used for more detailed analysis termed sequence typing. The selected isolates were analysed by WGS on the Illumina MiSeq platform. The sequences obtained were processed using the Velvet de novo Assembler software. The assembled genomes were uploaded into the PubMLST database, using the BIGSdb platform, and then scanned automatically and molecularly characterized. The isolates were compared at three resolution levels: seven MLST genes, 53 ribosomal genes (rMLST), and 1420 genes (all loci). The all loci scheme covers MLST genes, ribosomal genes, and core genome MLST genes (cgMLST). These are all currently defined genes of S. pneumoniae available in the PubMLST database. Distance matrices based on the number and variability of all loci analysed were generated automatically using the Genome Comparator tool. Phylogenetic networks were created and edited with the SplitsTree4 package, using the NeighborNet algorithm. The final graphics were edited with the Inkscape software.

Results

Based on an overall view of the phylogenetic networks, it can be concluded that the genetic lines within each of S. pneumoniae serotypes 4, 8, 9V, 19A, and 22F are highly unrelated, to the same extent as if the isolates were of different serotypes. S", "token_count": 510, "char_count": 1877, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6277, "quality_score": 0.8139, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:03.402199", "source": { "split": "train_shard_00001", "doc_id": 4623 }, "chunk_id": "train_shard_00001_4623_0", "global_id": 12204 }, { "text": "pneumoniae isolates of the same serotype, whether or not of the same sequence type, can be described, based on the results, as a non-homogeneous group with a number of unrelated genetic clusters that share genes assigning them to a specific serotype. WGS has also shown its discriminatory power, allowing the assignment of isolates of the same serotype and sequence type to different genetic clusters.

Conclusion

Of the methods used so far in the Czech Republic, WGS allows the most detailed characterization of S. pneumoniae isolates. It is highly desirable to integrate it in the molecular surveillance of IPD in the Czech Republic, similarly to other countries in Europe and in the world.\n\nImplementation and use of whole genome sequencing (WGS) in the surveillance of invasive pneumococcal disease, Czech Republic, 2017-2019.", "token_count": 202, "char_count": 836, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:03.861889", "source": { "split": "train_shard_00001", "doc_id": 4623 }, "chunk_id": "train_shard_00001_4623_1", "global_id": 12205 }, { "text": "In Europe, very few studies are available regarding the diversity of Listeria monocytogenes (L. monocytogenes) clonal complexes (CCs) and sequence types (ST) in poultry and on the related typing of isolates using whole genome sequencing (WGS). In this study, we used a WGS approach to type 122 L. monocytogenes strains isolated from chicken neck skin samples collected in two different slaughterhouses of an integrated Italian poultry company. The studied strains were classified into five CCs: CC1-ST1 (21.3%), CC6-ST6 (22.9%), CC9-ST9 (44.2%), CC121-ST121 (10.6%) and CC193-ST193 (0.8%). CC1 and CC6 strains presented a virulence gene profile composed of 60 virulence genes and including the Listeria Pathogenicity Island 3, aut_IVb, gltA and gltB. According to cgMLST and SNPs analysis, long-term persistent clusters belonging to CC1 and CC6 were found in one of the two slaughterhouses. The reasons mediating the persistence of these CCs (up to 20 months) remain to be elucidated, and may involve the presence and the expression of stress response and environmental adaptation genes including heavy metals resistance genes (cadAC, arsBC, CsoR-copA-copZ), multidrug efflux pumps (mrpABCEF, EmrB, mepA, bmrA, bmr3, norm), cold-shock tolerance (cspD) and biofilm-formation determinants (lmo0673, lmo2504, luxS, recO). These findings indicated a serious risk of poultry finished products contamination with hypervirulent L. monocytogenes clones and raised concern for the consumer health", "token_count": 501, "char_count": 1557, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7523, "quality_score": 0.8762, "entities": { "genes": [ "ST6", "ST193", "CC121", "CC193", "CC9", "ST1", "CC6", "CC1", "ST121", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:04.522681", "source": { "split": "train_shard_00001", "doc_id": 4624 }, "chunk_id": "train_shard_00001_4624_0", "global_id": 12206 }, { "text": "In addition to the AMR genes norB, mprF, lin and fosX, ubiquitous in L. monocytogenes strains, we also identified parC for quinolones, msrA for macrolides and tetA for tetracyclines. Although the phenotypical expression of these AMR genes was not tested, none of them is known to confer resistance to the primary antibiotics used to treat listeriosis The obtained results increase the data on the L. monocytogenes clones circulating in Italy and in particular in the poultry chain.\n\nThe Slaughterhouse as Hotspot of CC1 and CC6 Listeria monocytogenes Strains with Hypervirulent Profiles in an Integrated Poultry Chain of Italy.", "token_count": 222, "char_count": 683, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7041, "quality_score": 0.852, "entities": { "genes": [ "CC1", "CC6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:04.994589", "source": { "split": "train_shard_00001", "doc_id": 4624 }, "chunk_id": "train_shard_00001_4624_1", "global_id": 12207 }, { "text": "The effect of fortification of concentrated whey with 0.5% inorganic nitrogen viz. NH4Cl, (NH4)2SO4, NaNO3 and urea, organic nitrogen viz. tryptone, tryptose, peptone and yeast extract and 0.1% metal ions viz. K2HPO4, MgSO4 and FeSO4, on growth stimulation of Kluyveromyces marxianus subsp. marxianus NRRL Y-665, NRRL Y-1195, NRRL Y-2415 and Kluyveromyces marxianus subsp. lactis NRRL Y-1193 were studied. Supplementation with 0.5% (NH4)2SO4, peptone, yeast extract or 0.1% K2HPO4 individually increased the biomass production by 8-20%, 17-25%, 13-14% and 14-17%, respectively. Addition of 0.5% each of (NH4)2SO4, peptone, yeast extract and 0.1% K2HPO4 together is recommended to increase the biomass production by 81-98% for commercial production of single cell protein.\n\nEffect of fortification of concentrated whey on growth of Kluyveromyces sp.", "token_count": 326, "char_count": 848, "word_count": 120, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [ "NH4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:05.560689", "source": { "split": "train_shard_00001", "doc_id": 4625 }, "chunk_id": "train_shard_00001_4625_0", "global_id": 12208 }, { "text": "Healthcare-associated outbreaks of vancomycin-resistant Enterococcus faecium (VREfm) are a worldwide problem with increasing prevalence. The genomic plasticity of this hospital-adapted pathogen contributes to its efficient spread despite infection control measures. Here, we aimed to identify the genomic and phenotypic determinants of health care-associated transmission of VREfm. We assessed the VREfm transmission networks at the tertiary-care University Hospital of Zurich (USZ) between October 2014 and February 2018 and investigated microevolutionary dynamics of this pathogen. We performed whole-genome sequencing for the 69 VREfm isolates collected during this time frame and assessed the population structure and variability of the vancomycin resistance transposon. Phylogenomic analysis allowed us to reconstruct transmission networks and to unveil external or wider transmission networks undetectable by routine surveillance. Notably, it unveiled a persistent clone, sampled 31 times over a 29-month period. Exploring the evolutionary dynamics of this clone and characterizing the phenotypic consequences revealed the spread of a variant with decreased daptomycin susceptibility and the acquired ability to utilize N-acetyl-galactosamine (GalNAc), one of the primary constituents of the human gut mucins. This nutrient utilization advantage was conferred by a novel plasmid, termed pELF_USZ, which exhibited a linear topology. This plasmid, which was harbored by two distinct clones, was transferable by conjugation. Overall, this work highlights the potential of combining epidemiological, functional genomic, and evolutionary perspectives to unveil adaptation strategies of VREfm. IMPORTANCE Sequencing microbial pathogens causing outbreaks has become a common practice to characterize transmission networks. In addition to the signal provided by vertical evolution, bacterial genomes harbor mobile genetic elements shared horizontally between clones", "token_count": 462, "char_count": 1977, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6797, "quality_score": 0.8398, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:06.206213", "source": { "split": "train_shard_00001", "doc_id": 4626 }, "chunk_id": "train_shard_00001_4626_0", "global_id": 12209 }, { "text": "While macroevolutionary studies have revealed an important role of plasmids and genes encoding carbohydrate utilization systems in the adaptation of Enterococcus faecium to the hospital environment, mechanisms of dissemination and the specific function of many of these genetic determinants remain to be elucidated. Here, we characterize a plasmid providing a nutrient utilization advantage and show evidence for its clonal and horizontal spread at a local scale. Further studies integrating epidemiological, functional genomics, and evolutionary perspectives will be critical to identify changes shaping the success of this pathogen.\n\nGenomic Surveillance of Vancomycin-Resistant Enterococcus faecium Reveals Spread of a Linear Plasmid Conferring a Nutrient Utilization Advantage.", "token_count": 174, "char_count": 781, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7212, "quality_score": 0.8606, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:06.647911", "source": { "split": "train_shard_00001", "doc_id": 4626 }, "chunk_id": "train_shard_00001_4626_1", "global_id": 12210 }, { "text": "The entire publicly available set of 37 genome sequences from the bacterial order Chlamydiales has been subjected to comparative analysis in order to reveal the salient features of this pangenome and its evolutionary history. Over 2,000 protein families are detected across multiple species, with a distribution consistent to other studied pangenomes. Of these, there are 180 protein families with multiple members, 312 families with exactly 37 members corresponding to core genes, 428 families with peripheral genes with varying taxonomic distribution and finally 1,125 smaller families. The fact that, even for smaller genomes of Chlamydiales, core genes represent over a quarter of the average protein complement, signifies a certain degree of structural stability, given the wide range of phylogenetic relationships within the group. In addition, the propagation of a corpus of manually curated annotations within the discovered core families reveals key functional properties, reflecting a coherent repertoire of cellular capabilities for Chlamydiales. We further investigate over 2,000 genes without homologs in the pangenome and discover two new protein sequence domains. Our results, supported by the genome-based phylogeny for this group, are fully consistent with previous analyses and current knowledge, and point to future research directions towards a better understanding of the structural and functional properties of Chlamydiales.\n\nThe chlamydiales pangenome revisited: structural stability and functional coherence.", "token_count": 332, "char_count": 1532, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6326, "quality_score": 0.8163, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:07.216826", "source": { "split": "train_shard_00001", "doc_id": 4627 }, "chunk_id": "train_shard_00001_4627_0", "global_id": 12211 }, { "text": "Transport of methyl beta-D-thiogalactoside and p-nitrophenyl beta-D-galactoside is shown to proceed through the H+-lactose symporter of Kluyveromyces marxianus. Uptake of these compounds is strongly reduced under anaerobic conditions or aerobically in the presence of antimycin. It is shown that antimycin treatment affects p-nitrophenyl beta-D-galactoside uptake in a similar way as it affects the cellular amount of ATP, suggesting regulation of p-nitrophenyl beta-D-galactoside transport by ATP. Also, manipulation of cellular ATP by antimycin treatment followed by glucose incubation, or by aerobic incubation of cells with 2-deoxy-D-glucose, showed a similar dependence of galactoside uptake on the ATP level. Transport of the lipophilic cation tetraphenylphosphonium is affected by ATP variations in a similar way as galactoside influx. It is concluded that ATP regulates H+-galactoside symport by its influence on charge translocation. It is discussed that a membrane ATPase probably plays a central role in the control of the activity of H+-sugar symport.\n\nThe role of ATP in the control of H+-galactoside symport in the yeast Kluyveromyces marxianus.", "token_count": 335, "char_count": 1159, "word_count": 164, "semantic_coherence": 1, "information_density": 0.5366, "quality_score": 0.7683, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:07.789440", "source": { "split": "train_shard_00001", "doc_id": 4628 }, "chunk_id": "train_shard_00001_4628_0", "global_id": 12212 }, { "text": "Genomic islands (GIs) are discrete gene clusters encoding for a variety of functions including antibiotic and heavy metal resistance, some of which are tightly associated to lineages of the core genome phylogenetic tree. We have investigated the functions of two distinct integrase genes in the mobilization of two metal resistant GIs, G08 and G62, of Acinetobacter baumannii. Real-time PCR demonstrated integrase-dependent GI excision, utilizing isopropyl β-d-1-thiogalactopyranoside IPTG-inducible integrase genes in plasmid-based mini-GIs in Escherichia coli. In A. baumannii, integrase-dependent excision of the original chromosomal GIs could be observed after mitomycin C induction. In both E. coli plasmids and A. baumannii chromosome, the rate of excision and circularization was found to be dependent on the expression level of the integrases. Susceptibility testing in A. baumannii strain ATCC 17978, A424, and their respective ΔG62 and ΔG08 mutants confirmed the contribution of the GI-encoded efflux transporters to heavy metal decreased susceptibility. In summary, the data evidenced the functionality of two integrases in the excision and circularization of the two Acinetobacter heavy-metal resistance GIs, G08 and G62, in E. coli, as well as when chromosomally located in their natural host. These recombination events occur at different frequencies resulting in genome plasticity and may participate in the spread of resistance determinants in A. baumannii.\n\nIntegrase-Controlled Excision of Metal-Resistance Genomic Islands in Acinetobacter baumannii.", "token_count": 473, "char_count": 1638, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.8119, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:08.425473", "source": { "split": "train_shard_00001", "doc_id": 4629 }, "chunk_id": "train_shard_00001_4629_0", "global_id": 12213 }, { "text": "Acinetobacter baumannii is listed by the World Health Organization as an emerging bacterial priority pathogen, the prevalence and multidrug resistance of which have been increasing. This functional genomics study aimed to understand the drug-resistance mechanisms of an extensively drug-resistant (XDR) A. baumannii strain (IRMCBCU95U) isolated from a transtracheal aspirate sample from a female patient with end-stage renal disease in Saudi Arabia. The whole genome of IRMCBCU95U (4.3 Mbp) was sequenced using Oxford Nanopore long-read sequencing to identify and compare the antibiotic-resistance profile and genomic features of A. baumannii IRMCBCU95U. The antibiogram of A. baumannii IRMCBCU95U revealed resistance to multiple antibiotics, including cefepime, ceftazidime, ciprofloxacin, imipenem, meropenem and piperacillin/tazobactam. A comparative genomic analysis between IRMCBCU95U and A. baumannii K09-14 and ATCC 19606 identified significant genetic heterogeneity and mosaicism among the strains. This analysis also demonstrated the hybrid nature of the genome of IRMCBCU95U and indicates that horizontal gene transfer may have occurred between these strains. The IRMCBCU95U genome has a diverse range of genes associated with antimicrobial resistance and mobile genetic elements (ISAba1 and IS26) associated with the spread of multidrug resistance. The presence of virulence-associated genes that are linked to iron acquisition, motility and transcriptional regulation confirmed that IRMCBCU95U is a priority human pathogen. The plasmid fragment IncFIB(pNDM-Mar) observed in the strain is homologous to the plasmid in Klebsiella pneumoniae (439 bp; similarity: 99.09%), which supports its antimicrobial resistance", "token_count": 511, "char_count": 1766, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [ "IS26", "IRMCBCU95U" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:09.078776", "source": { "split": "train_shard_00001", "doc_id": 4630 }, "chunk_id": "train_shard_00001_4630_0", "global_id": 12214 }, { "text": "From these observations, it can be concluded that the clinical A. baumannii IRMCBCU95U isolate is an emerging extensively drug-resistant human pathogen with a novel combination of resistance genes and a plasmid fragment. The complex resistome of IRMCBCU95U highlights the urgent need for genomic surveillance in hospital settings in Saudi Arabia to fight against the spread of extensively drug-resistant A. baumannii.\n\nHybrid Genome and Clinical Impact of Emerging Extensively Drug-Resistant Priority Bacterial Pathogen <i>Acinetobacter baumannii</i> in Saudi Arabia.", "token_count": 161, "char_count": 593, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7403, "quality_score": 0.8701, "entities": { "genes": [ "IRMCBCU95U" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:09.512504", "source": { "split": "train_shard_00001", "doc_id": 4630 }, "chunk_id": "train_shard_00001_4630_1", "global_id": 12215 }, { "text": "Six Helicobacter-like isolates were recovered from 15 gastric mucosa samples of red foxes (Vulpes vulpes) shot by hunters in the surroundings of Ljubljana, Slovenia. Gram-negative, tightly coiled, intensely motile, 7-15 µm long and ≤1 µm wide bacteria grew on the biphasic blood agar plates. By using a genus-specific polymerase chain reaction (PCR), all isolates were confirmed as Helicobacter sp. and subsequently subjected to whole-genome sequencing (WGS). Five isolates showed a genome-wide average nucleotide identity (ANI) value of <95 % to the previously described Helicobacter species and one isolate was classified as Helicobacter felis. In the five unidentified isolates, the 16S rRNA gene sequence similarity to the type strains of all Helicobacter species ranged from 98.6 to 98.9 %. Their taxonomic status was established using a polyphasic taxonomic approach comprising the core genome-based phylogeny, morphological and phenotypic characteristics, including an analysis of matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) mass spectra. Phylogeny revealed the existence of three novel and well-supported clusters, with Helicobacter bizzozeronii and Helicobacter baculiformis being the most closely related species. The isolates also differed from the previously described species in their MALDI-TOF profiles and some biochemical characteristics. In conclusion, the data presented herein indicate that the obtained isolates, excluding H. felis isolate, represent three novel Helicobacter species, for which the names Helicobacter labacensis sp. nov., Helicobacter mehlei sp", "token_count": 507, "char_count": 1692, "word_count": 218, "semantic_coherence": 1, "information_density": 0.7156, "quality_score": 0.8578, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:10.140082", "source": { "split": "train_shard_00001", "doc_id": 4631 }, "chunk_id": "train_shard_00001_4631_0", "global_id": 12216 }, { "text": "nov., and Helicobacter vulpis sp. nov. are proposed, with isolates L9T (=DSM 108823T=CRBIP 111719T), L15T (=DSM 108730T=CCUG 72910T) and L2T (=DSM 108727T=CCUG 72909T) as type strains, respectively.\n\nHelicobacter labacensis sp. nov., Helicobacter mehlei sp. nov., and Helicobacter vulpis sp. nov., isolated from gastric mucosa of red foxes (Vulpes vulpes).", "token_count": 243, "char_count": 490, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:10.620472", "source": { "split": "train_shard_00001", "doc_id": 4631 }, "chunk_id": "train_shard_00001_4631_1", "global_id": 12217 }, { "text": "Frankia sp. NRRL B-16219 was directly isolated from a soil sample obtained from the rhizosphere of Ceanothus jepsonii growing in the USA. Its host plant range includes members of Elaeagnaceae species. Phylogenetically, strain NRRL B-16219 is closely related to \"Frankia discariae\" with a 16S rRNA gene similarity of 99.78%. Because of the lack of genetic tools for Frankia, our understanding of the bacterial signals involved during the plant infection process and the development of actinorhizal root nodules is very limited. Since the first three Frankia genomes were sequenced, additional genome sequences covering more diverse strains have helped provide insight into the depth of the pangenome and attempts to identify bacterial signaling molecules like the rhizobial canonical nod genes. The genome sequence of Frankia sp. strain NRRL B-16219 was generated and assembled into 289 contigs containing 8,032,739 bp with 71.7% GC content. Annotation of the genome identified 6211 protein-coding genes, 561 pseudogenes, 1758 hypothetical proteins and 53 RNA genes including 4 rRNA genes. The NRRL B-16219 draft genome contained genes homologous to the rhizobial common nodulation genes clustered in two areas. The first cluster contains nodACIJH genes whereas the second has nodAB and nodH genes in the upstream region. Phylogenetic analysis shows that Frankia nod genes are more deeply rooted than their sister groups from rhizobia", "token_count": 469, "char_count": 1517, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6977, "quality_score": 0.8488, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:11.303083", "source": { "split": "train_shard_00001", "doc_id": 4632 }, "chunk_id": "train_shard_00001_4632_0", "global_id": 12218 }, { "text": "PCR-sequencing suggested the widespread occurrence of highly homologous nodA and nodB genes in microsymbionts of field collected Ceanothus americanus.\n\nPermanent draft genome sequence of Frankia sp. NRRL B-16219 reveals the presence of canonical nod genes, which are highly homologous to those detected in Candidatus Frankia Dg1 genome.", "token_count": 128, "char_count": 378, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8511, "quality_score": 0.9255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:11.728830", "source": { "split": "train_shard_00001", "doc_id": 4632 }, "chunk_id": "train_shard_00001_4632_1", "global_id": 12219 }, { "text": "

Objectives

The aim of the study was to molecularly characterize third-generation cephalosporin-resistant Klebsiella pneumoniae isolated from bloodstream infections in Denmark in 2018 using whole-genome sequencing (WGS) data, and to compare these isolates to the most common clones detected in 2006 and 2008.

Methods

Sixty-two extended-spectrum beta-lactamase (ESBL)/AmpC-producing K. pneumoniae isolates from Danish blood cultures from 2018 were analysed using WGS to obtain multilocus sequence typing (MLST), core genome MLST (cgMLST), resistance profile and phylogeny. These were compared to the most common ESBL K. pneumoniae clones detected in 2006 and 2008.

Results

The most common ESBL clone was ST15 CTX-M-15, the DHA-1 enzyme was the most common in AmpC isolates, and the OXA-48-like group was the most common carbapenemase. Thirty-nine different sequence types (STs) were found, with the most frequent being ST14, ST15 and ST37, accounting for 24% of the isolates. The isolates were subdivided into 55 complex types (CTs) of which 49 were singletons, with the most frequent being ST14-CT2080. Two of the CTX-M-15-producing isolates from 2018 belonged to the ST15-CT105/CT3078 clone, which was first detected in 2006.

Conclusions

The ESBL/AmpC K. pneumoniae isolates detected in Danish blood cultures belonged to many different types. No dominant clones were circulating in Danish hospitals, but the ST15-CT105/CT3078 CTX-M-15 K. pneumoniae clone was seen 13 years after its first detection.", "token_count": 505, "char_count": 1528, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5476, "quality_score": 0.7738, "entities": { "genes": [ "CT3078", "CT105", "ST37", "ST14", "ST15", "CT2080" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:12.427375", "source": { "split": "train_shard_00001", "doc_id": 4633 }, "chunk_id": "train_shard_00001_4633_0", "global_id": 12220 }, { "text": "Molecular characterization of Danish ESBL/AmpC-producing Klebsiella pneumoniae from bloodstream infections, 2018.", "token_count": 37, "char_count": 113, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:12.803260", "source": { "split": "train_shard_00001", "doc_id": 4633 }, "chunk_id": "train_shard_00001_4633_1", "global_id": 12221 }, { "text": "The Continuous fermentation of Jerusalem artichoke juice to ethanol by free cells of Kluyveromyces marxianus UCD (FST) 55-82 has been studied in a continuous-stirred-tank bioreactor at 35 degrees C and pH 4.6. A maximum yield of 90% of the theoretical was obtained at a dilution rate of 0.05 h(-1). About 95% of the sugars were utilized at dilution rates lower than 0.15 h(-1). Volumetric ethanol productivity and volumetric biomass productivity reached maximum values of 7 g ETOH/L/h and 0.6 g dry wt/L/h, respectively, at a dilution rate of 0.2 h(-1). The maintenance energy coefficient for K. marxianus culture was found to be 0.46 g sugar/g biomass/h/ Oscillatory behavior was following a change in dilution rate from a previous steady state and from batch to continuous culture. Values of specific ethanol production rate and specific sugar uptake were found to increase almost linearly with the increase of the dilution rate. The maximum specific ethanol production rate and maximum specific sugar uptake rate were found to be 2.6 g ethanol/g/ cell/h and 7.9 sugars/g cell/h, respectively. Washout occurred at a dilution rate of 0.41 h(-1).\n\nContinuous ethanol production from Jerusalem artichoke tubers. I. Use of free cells of Kluyveromyces marxianus.", "token_count": 372, "char_count": 1259, "word_count": 198, "semantic_coherence": 1, "information_density": 0.5404, "quality_score": 0.7702, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:13.389642", "source": { "split": "train_shard_00001", "doc_id": 4634 }, "chunk_id": "train_shard_00001_4634_0", "global_id": 12222 }, { "text": "Vibrio sp. strain 2521-89 is an environmental isolate from lake water in New Mexico, USA. Average nucleotide identity, in silico DNA-DNA hybridization, and core genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis suggest that this may be a potentially novel species that is closely related to Vibrio cholerae.\n\nComplete Genome Sequence of Vibrio sp. Strain 2521-89, a Close Relative of Vibrio cholerae Isolated from Lake Water in New Mexico, USA.", "token_count": 169, "char_count": 501, "word_count": 68, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:13.836224", "source": { "split": "train_shard_00001", "doc_id": 4635 }, "chunk_id": "train_shard_00001_4635_0", "global_id": 12223 }, { "text": "A total of 34 Corynebacterium sp. strains were isolated from caseous lymph node abscesses of wild boar and roe deer in different regions of Germany. They showed slow growth on Columbia sheep blood agar and sparse growth on Hoyle's tellurite agar. Cellular fatty acid analysis allocated them in the C. diphtheriae group of genus Corynebacterium. MALDI-TOF MS using specific database extensions and rpoB sequencing resulted in classification as C. ulcerans. Their quinone system is similar to C. ulcerans, with major menaquinone MK-8(H2). Their complex polar lipid profile includes major lipids phosphatidylinositol, phosphatidylinositol-mannoside, diphosphatidylglycerol, but also unidentified glycolipids, distinguishing them clearly from C. ulcerans. They ferment glucose, ribose and maltose (like C. ulcerans), but do not utilise d-xylose, mannitol, lactose, sucrose and glycogen (like C. pseudotuberculosis). They showed activity of catalase, urease and phospholipase D, but variable results for alkaline phosphatase and alpha-glucosidase. All were non-toxigenic, tox gene bearing and susceptible to clindamycin, penicillin and erythromycin. In 16SrRNA gene and RpoB protein phylogenies the strains formed distinct brancheswith C", "token_count": 429, "char_count": 1305, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7679, "quality_score": 0.8839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:14.473385", "source": { "split": "train_shard_00001", "doc_id": 4636 }, "chunk_id": "train_shard_00001_4636_0", "global_id": 12224 }, { "text": "ulcerans as nearest relative.Whole genome sequencing revealed the unique sequence type 578, a distinctbranch in pangenomic core genome MLST, average nucleotide identities <91%, enhancedgenome sizes (2.55 Mbp) and G/C content (54.4 mol%) compared to related species.These results suggest that the strains represent a novel species, for which wepropose the name Corynebactriumsilvaticum sp. nov., based on their first isolation from forest-dwellinggame animals. The type strain isKL0182T (= CVUAS 4292T = DSM 109166T = LMG 31313T= CIP 111 672T).\n\nCorynebacterium silvaticum sp. nov., a unique group of NTTB corynebacteria in wild boar and roe deer.", "token_count": 260, "char_count": 719, "word_count": 93, "semantic_coherence": 1, "information_density": 0.8602, "quality_score": 0.9301, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:15.016728", "source": { "split": "train_shard_00001", "doc_id": 4636 }, "chunk_id": "train_shard_00001_4636_1", "global_id": 12225 }, { "text": "The kinetic model of the hydrolysis of lactose with a beta-galactosidase from Kluyveromyces fragilis immobilized on a commercial silica-alumina (KA-3, from Südchemie) has been determined. A wide experimental range of the main variables has been employed: temperature, concentrations of substrate, and products and concentration of enzyme. The runs were performed in a complex buffer with the salt composition of milk. The effect of pH and temperature on the stability and the activity of the enzyme have been studied. The optimum pH for the enzyme activity was, approximately, seven. The immobilized enzyme was more stable than the free one at acidic pH, but more instable at basic pH. The maximum temperature used for the hydrolysis runs performed to select the kinetic model was 40 degrees C, so inactivation of the enzyme during the kinetic runs has been avoided. Agitation, concentration of enzyme in the solid and particle size were selected to ensure that the overall rate was that of the chemical reaction. Eleven kinetic models were proposed to fit experimental data, from first order to more complex ones, such as those taking into account inhibition by one of the compounds involved in the hydrolysis reaction. Applying statistical and physical criteria, a Michaelis-Menten model with a competitive inhibition by galactose has been selected. The model is able to fit the experimental data correctly in the wide experimental range studied. Finally, the model obtained is compared to the one selected in a previous work for the hydrolysis of lactose with the free enzyme.\n\nKinetic modeling of lactose hydrolysis with an immobilized beta-galactosidase from Kluyveromyces fragilis.", "token_count": 396, "char_count": 1687, "word_count": 262, "semantic_coherence": 1, "information_density": 0.4924, "quality_score": 0.7462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:15.634951", "source": { "split": "train_shard_00001", "doc_id": 4637 }, "chunk_id": "train_shard_00001_4637_0", "global_id": 12226 }, { "text": "The characterization of the PYL/RCAR ABA receptors in a great deal of plant species has dramatically advanced the study of ABA functions involved in key physiological processes. However, the genes in this family are still unclear in Lycium (Goji) plants, one of the well-known economically, medicinally, and ecologically valuable fruit crops. In the present work, 12 homologs of Arabidopsis PYL/RCAR ABA receptors were first identified and characterized from Lycium (L.) barbarum (LbPYLs). The quantitative real-time PCR (qRT-PCR) analysis showed that these genes had clear tissue-specific expression patterns, and most of them were transcribed in the root with the largest amount. Among the three subfamilies, while the Group I and Group III members were down-regulated by extraneous ABA, the Group II members were up-regulated. At 42 °C, most transcripts showed a rapid and violent up-regulation response to higher temperature, especially members of Group II. One of the genes in the Group II members, LbPYL10, was further functionally validated by virus-induced gene silencing (VIGS) technology. LbPYL10 positively regulates heat stress tolerance in L. barbarum by alleviating chlorophyll degradation, thus maintaining chlorophyll stability. Integrating the endogenous ABA level increase following heat stress, it may be concluded that LbPYL-mediated ABA signaling plays a vital role in the thermotolerance of L. barbarum plants. Our results highlight the strong potential of LbPYL genes in breeding genetically modified L. barbarum crops that acclimate to climate change.", "token_count": 461, "char_count": 1645, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6769, "quality_score": 0.8384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:16.275278", "source": { "split": "train_shard_00001", "doc_id": 4638 }, "chunk_id": "train_shard_00001_4638_0", "global_id": 12227 }, { "text": "Genome-Wide Identification of PYL/RCAR ABA Receptors and Functional Analysis of LbPYL10 in Heat Tolerance in Goji (Lycium barbarum).", "token_count": 59, "char_count": 146, "word_count": 18, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:16.637795", "source": { "split": "train_shard_00001", "doc_id": 4638 }, "chunk_id": "train_shard_00001_4638_1", "global_id": 12228 }, { "text": "The role of the microbiome in health and disease is attracting great attention, yet we still know little about some of the most prevalent microorganisms inside our bodies. Several years ago, Human Microbiome Project (HMP) researchers generated a list of \"most wanted\" taxa: bacteria both prevalent among healthy volunteers and distantly related to any sequenced organisms. Unfortunately, the challenge of assembling high-quality genomes from a tangle of metagenomic reads has slowed progress in learning about these uncultured bacteria. Here, we describe how recent advances in sequencing and analysis allowed us to assemble \"most wanted\" genomes from metagenomic data collected from four stool samples. Using a combination of both de novo and guided assembly methods, we assembled and binned over 100 genomes from an initial data set of over 1,300 Gbp. One of these genome bins, which met HMP's criteria for a \"most wanted\" taxa, contained three essentially complete genomes belonging to a previously uncultivated species. This species is most closely related to Eubacterium desmolans and the clostridial cluster IV/Clostridium leptum subgroup species Butyricicoccus pullicaecorum (71-76% average nucleotide identity). Gene function analysis indicates that the species is an obligate anaerobe, forms spores, and produces the anti-inflammatory short-chain fatty acids acetate and butyrate. It also appears to take up metabolically costly molecules such as cobalamin, methionine, and branch-chained amino acids from the environment, and to lack virulence genes. Thus, the evidence is consistent with a secondary degrader that occupies a host-dependent, nutrient-scavenging niche within the gut; its ability to produce butyrate, which is thought to play an anti-inflammatory role, makes it intriguing for the study of diseases such as colon cancer and inflammatory bowel disease. In conclusion, we have assembled essentially complete genomes from stool metagenomic data, yielding valuable information about uncultured organisms' metabolic and ecologic niches, factors that may be required to successfully culture these bacteria, and their role in maintaining health and causing disease.", "token_count": 512, "char_count": 2184, "word_count": 314, "semantic_coherence": 1, "information_density": 0.6688, "quality_score": 0.8344, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:17.268746", "source": { "split": "train_shard_00001", "doc_id": 4639 }, "chunk_id": "train_shard_00001_4639_0", "global_id": 12229 }, { "text": "Capturing One of the Human Gut Microbiome's Most Wanted: Reconstructing the Genome of a Novel Butyrate-Producing, Clostridial Scavenger from Metagenomic Sequence Data.", "token_count": 49, "char_count": 167, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:17.635732", "source": { "split": "train_shard_00001", "doc_id": 4639 }, "chunk_id": "train_shard_00001_4639_1", "global_id": 12230 }, { "text": "Abstract

Background

Sequence type 131 (EC-ST131) is a prevalent cause of extraintestinal Escherichia coli infection, including in neonates, and accounts for a majority of multidrug-resistant strains. Rare reports of neonatal unit outbreaks have emerged, with one linking the source to freshly expressed breast milk (BM) sharing. We report on premature twin girls whose infection was linked to their mother’s contaminated frozen BM.

Methods

Blood culture isolates were from twin girls born at 24–1/7 weeks’ gestation who developed severe sepsis caused by ampicillin- and gentamicin-resistant E. coli on days 11 (Baby A; died) and 8 (Baby B; survived) of life; both neonates had sterile blood cultures at birth, and received orogastric feeds using frozen BM provided by their mother. Five remaining frozen BM samples predating onset of sepsis were thawed and cultured; E. coli resistant to ampicillin and gentamicin was recovered from 1 collected on day 5 of life. DNA was extracted from cultured isolates using the Zymo Research Quick-DNA™ Fungal/Bacterial Miniprep kit, sequencing libraries prepared (Nextera® XT PE), and sequencing (Illumina MiSeq® with V2 2 X 250 bp chemistry) completed for the 2 blood and 1 BM isolates. Multilocus Sequence Typing (MLST) and core genome MLST (cgMLST) analyses were performed using SeqSphere+, version 5.1.0 (Ridom, Munster, DE) software, with 2513 alleles analyzed for cgMLST.

Results

The 2 blood and 1 BM isolates were typed as ST131 by MLST and were indistinguishable by cgMLST. Of the 2513 alleles queried, only 263 (10.5%) differed from the ST131 strain SCB34 (figure)", "token_count": 502, "char_count": 1637, "word_count": 248, "semantic_coherence": 1, "information_density": 0.7016, "quality_score": 0.8508, "entities": { "genes": [ "SCB34", "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:18.297006", "source": { "split": "train_shard_00001", "doc_id": 4640 }, "chunk_id": "train_shard_00001_4640_0", "global_id": 12231 }, { "text": "Thus, our EC-ST131 cluster isolates belong to the same clonal complex as, but are genetically divergent from, SCB34. In addition to the E. coli described above isolated from a BM sample, all 5 frozen BM samples grew multiple morphotypes of coagulase-negative staphylococci. The mother had acute chorioamnionitis and was treated with intravenous ampicillin, gentamicin, and metronidazole for 48 hours immediately after delivery.

Conclusion

Despite frozen BM’s persistent antibacterial activity, it is a potential source of multidrug-resistant bacteria for neonates, as evidenced by this report of EC-ST131 neonatal sepsis in premature twins.

Disclosures

Robin Patel, MD, ASM and IDSA: Other Financial or Material Support, Travel reimbursement, editor’s stipends; CD Diagnostics, Merck, Hutchison Biofilm Medical Solutions, Accelerate Diagnostics, ContraFect, TenNor Therapeutics Limited, Shionogi: Grant/Research Support; Curetis, Specific Technologies, NextGen Diagnostics, PathoQuest, Qvella: Consultant; NBME, Up-to-Date, the Infectious Diseases Board Review Course: Honorarium recipient, Other Financial or Material Support; Patent on Bordetella pertussis/parapertussis PCR issued, a patent on a device/method for sonication with royalties paid by Samsung to Mayo Clinic, and a patent on an anti-biofilm substance issued: Other Financial or Material Support, Patents.\n\n1517. Multidrug-Resistant Escherichia coli ST131 Late-Onset Neonatal Sepsis in Premature Twins Linked to Contaminated Maternal Frozen Breast Milk", "token_count": 443, "char_count": 1535, "word_count": 199, "semantic_coherence": 1, "information_density": 0.7688, "quality_score": 0.8844, "entities": { "genes": [ "SCB34", "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:18.924816", "source": { "split": "train_shard_00001", "doc_id": 4640 }, "chunk_id": "train_shard_00001_4640_1", "global_id": 12232 }, { "text": "Abstract

Background

Azithromycin is a recommended oral agent for treating nontyphoidal Salmonella (NTS), when antibiotics are indicated. Azithromycin nonsusceptibility among NTS is <1% in the United States. CDC, FSIS, and state health departments investigated an outbreak of azithromycin-nonsusceptible Salmonella serotype Newport infections to determine sources.

Methods

We classified isolates as the outbreak strain if they were within 11 alleles by core genome multilocus sequence typing. We defined a case as infection with the outbreak strain during June 2018–February 2019. After stratifying by gender and ethnicity, we compared food exposures ≤7 days before illness onset with those reported by healthy persons in the Foodborne Diseases Active Surveillance Network population survey (2006–2007). We used broth microdilution to determine antimicrobial susceptibility.

Results

We identified 218 case patients from 31 states; 49 of 176 (28%) were hospitalized and 2 died. Overall, 65% (121/187) were Hispanic, and 41% (70/169) visited Mexico in the 7 days before illness onset. Among travelers to Mexico, 71% (23/32) reported eating Mexican-style soft cheese; 16/23 (70%) recalled obtaining the cheese in Mexico. Among nontravelers, the proportion who ate Mexican-style soft cheese (30%, 18/60) was similar to that reported by healthy persons, whereas the proportion who consumed beef (91%, 60/66) was higher than reported by healthy persons (P = 0.04). The outbreak strain was detected in a sample of soft cheese obtained in Mexico, and in a cecal sample from a steer and a beef sample that was collected at FSIS-regulated establishments in the United States", "token_count": 478, "char_count": 1690, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6694, "quality_score": 0.8347, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:19.567314", "source": { "split": "train_shard_00001", "doc_id": 4641 }, "chunk_id": "train_shard_00001_4641_0", "global_id": 12233 }, { "text": "Isolates were resistant to ampicillin and trimethoprim–sulfamethoxazole, nonsusceptible to azithromycin, and showed decreased susceptibility to ciprofloxacin.

Conclusion

This is the first documented outbreak of azithromycin-nonsusceptible Salmonella infections in the United States. Two food vehicles—soft cheese obtained in Mexico, and beef obtained in the United States—were epidemiologically and genetically associated with this outbreak. Further investigation is warranted to determine the routes of entry, prevalence, and spread of azithromycin-nonsusceptible Salmonella in US and Mexican cattle.

Disclosures

All Authors: No reported Disclosures.\n\n81. Azithromycin-Nonsusceptible Salmonella Newport Infections Associated with Mexican-style Soft Cheese and Beef—the United States, 2018–2019", "token_count": 229, "char_count": 812, "word_count": 94, "semantic_coherence": 1, "information_density": 0.6809, "quality_score": 0.8404, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:20.032051", "source": { "split": "train_shard_00001", "doc_id": 4641 }, "chunk_id": "train_shard_00001_4641_1", "global_id": 12234 }, { "text": "Whole-genome sequencing has been skewed toward bacterial pathogens as a consequence of the prioritization of medical and veterinary diseases. However, it is becoming clear that in order to accurately measure genetic variation within and between pathogenic groups, multiple isolates, as well as commensal species, must be sequenced. This study examined the pangenomic content of Escherichia coli. Six distinct E. coli pathovars can be distinguished using molecular or phenotypic markers, but only two of the six pathovars have been subjected to any genome sequencing previously. Thus, this report provides a seminal description of the genomic contents and unique features of three unsequenced pathovars, enterotoxigenic E. coli, enteropathogenic E. coli, and enteroaggregative E. coli. We also determined the first genome sequence of a human commensal E. coli isolate, E. coli HS, which will undoubtedly provide a new baseline from which workers can examine the evolution of pathogenic E. coli. Comparison of 17 E. coli genomes, 8 of which are new, resulted in identification of approximately 2,200 genes conserved in all isolates. We were also able to identify genes that were isolate and pathovar specific. Fewer pathovar-specific genes were identified than anticipated, suggesting that each isolate may have independently developed virulence capabilities. Pangenome calculations indicate that E. coli genomic diversity represents an open pangenome model containing a reservoir of more than 13,000 genes, many of which may be uncharacterized but important virulence factors. This comparative study of the species E. coli, while descriptive, should provide the basis for future functional work on this important group of pathogens.\n\nThe pangenome structure of Escherichia coli: comparative genomic analysis of E. coli commensal and pathogenic isolates.", "token_count": 444, "char_count": 1852, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6259, "quality_score": 0.813, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:20.666291", "source": { "split": "train_shard_00001", "doc_id": 4642 }, "chunk_id": "train_shard_00001_4642_0", "global_id": 12235 }, { "text": "Chinese cabbage, Brassica rapa L. subsp. pekinensis is a crucial and extensively consumed vegetable in the world, especially Eastern Asia. The market demand for this leafy vegetable increases year by year, resulting in multiple challenges for agricultural researchers worldwide. Multi-omic approaches and the integration of functional genomics helps us understand the relationships between Chinese cabbage genomes and phenotypes under specific physiological and environmental conditions. However, challenges exist in integrating multi-omics for the functional analysis of genes and for developing potential traits for Chinese cabbage improvement. However, the panomics platform allows for the integration of complex omics, enhancing our understanding of molecular regulator networks in Chinese cabbage agricultural traits. In addition, the agronomic features of Chinese cabbage are significantly impacted by the environment. The expression of these agricultural features is tightly regulated by a combination of signals from both the internal regulatory network and the external growth environment. To comprehend the molecular process of these characteristics, it is necessary to have a prior understanding of molecular breeding for the objective of enhancing quality. While the use of various approaches in Chinese cabbage is still in its early stages, recent research has shown that it has the potential to uncover new regulators both rapidly and effectively, leading to updated regulatory networks. In addition, the utilization of the efficient transformation technique in conjunction with gene editing using CRISPR/Cas9 will result in a reduction in time requirements and facilitate a more precise understanding of the role of the regulators. Numerous studies about Chinese cabbage have been conducted in the past two decades, but a comprehensive review about its genome still limited. This review provides a concise summary of the latest discoveries in genomic research related to Brassica and explores the potential future developments for this species.\n\nExploiting Brassica rapa L. subsp. pekinensis Genome Research.", "token_count": 425, "char_count": 2151, "word_count": 300, "semantic_coherence": 1, "information_density": 0.58, "quality_score": 0.79, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:21.297500", "source": { "split": "train_shard_00001", "doc_id": 4643 }, "chunk_id": "train_shard_00001_4643_0", "global_id": 12236 }, { "text": "Adverse environmental conditions, such as acid stress, induce bacteria to employ several strategies to overcome these stressors. These strategies include forming biofilms and activating specific molecular pathways, such as the general stress response (GSR). The genome of Priestia megaterium strain G18 was sequenced using the Illumina NextSeq 500 system, resulting in a de novo assembly of 80 scaffolds. The scaffolded genome comprises 5,367,956 bp with a GC content of 37.89%, and was compared to related strains using the MiGA web server, revealing high similarity to P. megaterium NBRC 15308 and P. aryabhattai B8W22 with ANI scores of 95.4%. Phylogenetic and ribosomal multilocus sequence typing (rMLST) analyses, based on the 16S rRNA and ribosomal protein-encoding alleles, confirmed close relationships within the P. megaterium species. Functional annotation identified 5,484 protein-coding genes, with 72.31% classified into 22 COG categories, highlighting roles in amino acid transport, transcription, carbohydrate metabolism, and ribosomal structure. An in-depth genome analysis of P. megaterium G18 revealed several key genes associated with acid tolerance. Targeted inactivation of the ydaG gene from SigB regulon, a general stress response gene, significantly reduced growth under acidic conditions compared to the wild type. qRT-PCR analysis showed increased ydaG expression in acidic conditions, further supporting its role in acid stress response. Microscopic analysis revealed no morphological differences between wild-type and mutant cells, suggesting that ydaG is not involved in maintaining cellular morphology but in facilitating acid tolerance through stress protein production. This research contributes to understanding the molecular mechanisms underlying acid tolerance in soil bacteria, P", "token_count": 509, "char_count": 1881, "word_count": 251, "semantic_coherence": 1, "information_density": 0.7052, "quality_score": 0.8526, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:21.951799", "source": { "split": "train_shard_00001", "doc_id": 4644 }, "chunk_id": "train_shard_00001_4644_0", "global_id": 12237 }, { "text": "megaterium, shedding light on potential applications in agriculture and industry.\n\nGenomic analysis of acid tolerance genes and deciphering the function of ydaG gene in mitigating acid tolerance in Priestia megaterium.", "token_count": 64, "char_count": 236, "word_count": 30, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:22.316789", "source": { "split": "train_shard_00001", "doc_id": 4644 }, "chunk_id": "train_shard_00001_4644_1", "global_id": 12238 }, { "text": "

Aims

To isolate and characterize biosurfactants produced by a thermotolerant yeast isolated in Thailand.

Materials and results

Yeast strains isolated from plant material in Thailand were first screened for the ability to produce lipase and biosurfactant. A strain Y12, identified as Candida ishiwadae by physiological tests, survived at 45 degrees C and produced relatively large amounts of biosurfactants. From the culture filtrate of this strain, two glycolipid biosurfactants, a and b, were purified by solvent fractionation, silica gel and ODS column chromatographies. Compounds a and b were determined to be monoacylglycerols; 1-linoleylglycerol and 1-oleylglycerol, respectively. Both compounds exhibited higher surfactant activities tested by the drop collapse test than several artificial surfactants such as sodium dodecyl sulphate.

Conclusions

Glycolipid biosurfactants produced by a thermotolerant yeast, C. ishiwadae were characterized to be monoacylglycerols which exhibited high surfactant activities.

Significance and impact of the study

A thermotolerant yeast strain, C. ishiwadae, could be a potential candidate for producing monoacylglycerols which are useful in industrial applications.\n\nMonoacylglycerols: glycolipid biosurfactants produced by a thermotolerant yeast, Candida ishiwadae.", "token_count": 380, "char_count": 1335, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6545, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:22.952149", "source": { "split": "train_shard_00001", "doc_id": 4645 }, "chunk_id": "train_shard_00001_4645_0", "global_id": 12239 }, { "text": "Separation of inulinase from Kluyveromyces marxianus using reversed micellar extraction.", "token_count": 25, "char_count": 88, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:23.332676", "source": { "split": "train_shard_00001", "doc_id": 4646 }, "chunk_id": "train_shard_00001_4646_0", "global_id": 12240 }, { "text": "Host-microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host-microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.\n\nMicrobial-enrichment method enables high-throughput metagenomic characterization from host-rich samples.", "token_count": 397, "char_count": 1643, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:23.983452", "source": { "split": "train_shard_00001", "doc_id": 4647 }, "chunk_id": "train_shard_00001_4647_0", "global_id": 12241 }, { "text": "Isolates of Helicobacter pylori can be classified phylogeographically. High genetic diversity and rapid microevolution are a hallmark of H. pylori genomes, a phenomenon that is proposed to play a functional role in persistence and colonization of diverse human populations. To provide further genomic evidence in the lineage of H. pylori and to further characterize diverse strains of this pathogen in different human populations, we report the finished genome sequence of Sahul64, an H. pylori strain isolated from an indigenous Australian. Our analysis identified genes that were highly divergent compared to the 38 publically available genomes, which include genes involved in the biosynthesis and modification of lipopolysaccharide, putative prophage genes, restriction modification components, and hypothetical genes. Furthermore, the virulence-associated vacA locus is a pseudogene and the cag pathogenicity island (cagPAI) is not present. However, the genome does contain a gene cluster associated with pathogenicity, including dupA. Our analysis found that with the addition of Sahul64 to the 38 genomes, the core genome content of H. pylori is reduced by approximately 14% (∼170 genes) and the pan-genome has expanded from 2,070 to 2,238 genes. We have identified three putative horizontally acquired regions, including one that is likely to have been acquired from the closely related Helicobacter cetorum prior to speciation. Our results suggest that Sahul64, with the absence of cagPAI, highly divergent cell envelope proteins, and a predicted nontransportable VacA protein, could be more highly adapted to ancient indigenous Australian people but with lower virulence potential compared to other sequenced and cagPAI-positive H. pylori strains.\n\nComparative analysis of the full genome of Helicobacter pylori isolate Sahul64 identifies genes of high divergence.", "token_count": 456, "char_count": 1874, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5948, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:24.666188", "source": { "split": "train_shard_00001", "doc_id": 4648 }, "chunk_id": "train_shard_00001_4648_0", "global_id": 12242 }, { "text": "The optimum pH and temperature for the enzyme lactase isolated from the yeast kluyveromyces fragilis was found to be in the range of 6.5-7.0 and 37deg C, respectively. Incubating enzyme at 50deg C for 15 min, the residue activity was measured as 84.02%. The enzyme shows stability in pH range of 5.8-7.3. The lactase has Km value of 1.16 mmol/L and 5.63 mmol/L for ONPG and lactose respectively. Metal ions such as Mn~(2+), Mg~(2+), Na~(+), K~(+) and low concentration of Ca~(2+) have an activating effect on enzyme activity.\n\nProperties of an inducible lactase isolated from the yeast Kluyveromyces fragilis", "token_count": 214, "char_count": 608, "word_count": 99, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8232, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:25.149802", "source": { "split": "train_shard_00001", "doc_id": 4649 }, "chunk_id": "train_shard_00001_4649_0", "global_id": 12243 }, { "text": "Every year salmonellosis is responsible for $2.3 billion in costs to the U.S. food industry, with nearly 6% of the reported cases associated with pork and/or pork products. Several studies have demonstrated the role of pigs as Salmonella reservoirs. Furthermore, this pathogen has been identified as a potential biological hazard in many livestock feeds. The overall objective of this research was to characterize Salmonella enterica isolates in selected U.S. swine feed mills by whole-genome sequencing (WGS) and evaluate isolates in association with the season and feed production stages. Salmonella isolates were collected from 11 facilities during a previous study. Samples were analyzed for Salmonella prevalence following the U.S. Department of Agriculture guidelines and confirmed by PCR. WGS was carried out on either the MiSeq or NextSeq sequencer. De novo genome assemblies were obtained with the Shovill pipeline, version 0.9. ResFinder and SPIFinder were used to identify antibiotic resistance genes and pathogenicity islands. Finally, their phylogenetic relationship and diversity were determined by core genome multilocus sequence typing. Overall, our analysis showed the presence of S. enterica in the feed mill environment. Isolates belonged to 16 different serotypes. Salmonella Agona, Salmonella Mbandaka, Salmonella Senfenberg, and Salmonella Scharzengrund were the most frequently found, and 18 single-nucleotide polymorphism clusters were identified. In silico analysis showed that 40% of the strains carried at least one antimicrobial resistance gene. All isolates in this study could be considered of public health concern and pathogenic potential. Our findings underscore the potential role of the feed mill environment as the pathogen entry route into the human food value chain.", "token_count": 482, "char_count": 1881, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6769, "quality_score": 0.8385, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:25.795097", "source": { "split": "train_shard_00001", "doc_id": 4650 }, "chunk_id": "train_shard_00001_4650_0", "global_id": 12244 }, { "text": "Characterization of Salmonella enterica Isolates from Selected U.S. Swine Feed Mills by Whole-Genome Sequencing.", "token_count": 39, "char_count": 119, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:26.154053", "source": { "split": "train_shard_00001", "doc_id": 4650 }, "chunk_id": "train_shard_00001_4650_1", "global_id": 12245 }, { "text": "Antimicrobials have become a mainstay of healthcare in the past century due to their activity against pathogens. More recently, it has become clear that they can also affect health via their impact on the microbiota and inflammation. This may explain some of their clinical benefits despite global increases in antimicrobial resistance (AMR) and reduced antimicrobial effectiveness. We showed in a randomized controlled trial of stopping versus continuing cotrimoxazole prophylaxis among HIV-positive Zimbabwean children taking antiretroviral therapy (ART), that continuation of cotrimoxazole persistently suppressed gut-resident viridans group streptococcal species (VGS) that were associated with intestinal inflammation. In this addendum, we provide a broader overview of how antibiotics can shape the microbiota and use high read-depth whole metagenome sequencing data from our published study to investigate whether (i) the impact of cotrimoxazole on gut VGS and (ii) VGS associated inflammation, is attributable to strain-level variability. We focus on S. salivarius, the VGS species that was most prevalent in the cohort and for which there was sufficient genome coverage to differentiate strains. We demonstrate that suppression of S. salivarius by cotrimoxazole is not strain specific, nor did stool concentration of the pro-inflammatory mediator myeloperoxidase vary by S. salivarius strain. We also show that gut-resident S. salivarius strains present in this study population are distinct from common oral strains. This is the first analysis of how cotrimoxazole prophylaxis used according to international treatment guidelines for children living with HIV influences the gut microbiome at the strain-level. We also provide a detailed review of the literature on the mechanisms by which suppression of VGS may act synergistically with cotrimoxazole's anti-inflammatory effects to reduce gut inflammation. A greater understanding of the sub-clinical effects of antibiotics offers new insights into their responsible clinical use.", "token_count": 496, "char_count": 2068, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6237, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:27.173731", "source": { "split": "train_shard_00001", "doc_id": 4651 }, "chunk_id": "train_shard_00001_4651_0", "global_id": 12246 }, { "text": "Strain-level analysis of gut-resident pro-inflammatory viridans group Streptococci suppressed by long-term cotrimoxazole prophylaxis among HIV-positive children in Zimbabwe.", "token_count": 52, "char_count": 173, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:27.529136", "source": { "split": "train_shard_00001", "doc_id": 4651 }, "chunk_id": "train_shard_00001_4651_1", "global_id": 12247 }, { "text": "Vibrio parahaemolyticus is an important human foodborne pathogen whose transmission is associated with the consumption of contaminated seafood, with a growing number of infections reported over recent years worldwide. A multilocus sequence typing (MLST) database for V. parahaemolyticus was created in 2008, and a large number of clones have been identified, causing severe outbreaks worldwide (sequence type 3 [ST3]), recurrent outbreaks in certain regions (e.g., ST36), or spreading to other regions where they are nonendemic (e.g., ST88 or ST189). The current MLST scheme uses sequences of 7 genes to generate an ST, which results in a powerful tool for inferring the population structure of this pathogen, although with limited resolution, especially compared to pulsed-field gel electrophoresis (PFGE). The application of whole-genome sequencing (WGS) has become routine for trace back investigations, with core genome MLST (cgMLST) analysis as one of the most straightforward ways to explore complex genomic data in an epidemiological context. Therefore, there is a need to generate a new, portable, standardized, and more advanced system that provides higher resolution and discriminatory power among V. parahaemolyticus strains using WGS data. We sequenced 92 V. parahaemolyticus genomes and used the genome of strain RIMD 2210633 as a reference (with a total of 4,832 genes) to determine which genes were suitable for establishing a V. parahaemolyticus cgMLST scheme. This analysis resulted in the identification of 2,254 suitable core genes for use in the cgMLST scheme. To evaluate the performance of this scheme, we performed a cgMLST analysis of 92 newly sequenced genomes, plus an additional 142 strains with genomes available at NCBI. cgMLST analysis was able to distinguish related and unrelated strains, including those with the same ST, clearly showing its enhanced resolution over conventional MLST analysis. It also distinguished outbreak-related from non-outbreak-related strains within the same ST", "token_count": 517, "char_count": 2054, "word_count": 297, "semantic_coherence": 1, "information_density": 0.6566, "quality_score": 0.8283, "entities": { "genes": [ "ST36", "ST3", "ST189", "ST88" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:54:28.167954", "source": { "split": "train_shard_00001", "doc_id": 4652 }, "chunk_id": "train_shard_00001_4652_0", "global_id": 12248 }, { "text": "The sequences obtained from this work were deposited and are available in the public database (http://pubmlst.org/vparahaemolyticus). The application of this cgMLST scheme to the characterization of V. parahaemolyticus strains provided by different laboratories from around the world will reveal the global picture of the epidemiology, spread, and evolution of this pathogen and will become a powerful tool for outbreak investigations, allowing for the unambiguous comparison of strains with global coverage.\n\nDefining a Core Genome Multilocus Sequence Typing Scheme for the Global Epidemiology of Vibrio parahaemolyticus.", "token_count": 152, "char_count": 629, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6941, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:28.604442", "source": { "split": "train_shard_00001", "doc_id": 4652 }, "chunk_id": "train_shard_00001_4652_1", "global_id": 12249 }, { "text": "Heat stress significantly impacts global rice production, highlighting the critical need to understand the genetic basis of heat resistance in rice. U2AF (U2 snRNP auxiliary factor) is an essential splicing complex with critical roles in recognizing the 3'-splice site of precursor messenger RNAs (pre-mRNAs). The U2AF small subunit (U2AF35) can bind to the 3'-AG intron border and promote U2 snRNP binding to the branch-point sequences of introns through interaction with the U2AF large subunit (U2AF65). However, the functions of U2AF35 in plants are poorly understood. In this study, we discovered that the OsU2AF35a gene was vigorously induced by heat stress and could positively regulate rice thermotolerance during both the seedling and reproductive growth stages. OsU2AF35a interacts with OsU2AF65a within the nucleus, and both of them can form condensates through liquid-liquid phase separation (LLPS) following heat stress. The intrinsically disordered regions (IDR) are accountable for their LLPS. OsU2AF35a condensation is indispensable for thermotolerance. RNA-seq analysis disclosed that, subsequent to heat treatment, the expression levels of several genes associated with water deficiency and oxidative stress in osu2af35a-1 were markedly lower than those in ZH11. In accordance with this, OsU2AF35a is capable of positively regulating the oxidative stress resistance of rice. The pre-mRNAs of a considerable number of genes in the osu2af35a-1 mutant exhibited defective splicing, among which was the OsHSA32 gene. Knocking out OsHSA32 significantly reduced the thermotolerance of rice, while overexpressing OsHSA32 could partially rescue the heat sensitivity of osu2af35a-1. Together, our findings uncovered the essential role of OsU2AF35a in rice heat stress response through protein separation and regulating alternative pre-mRNA splicing.", "token_count": 492, "char_count": 1857, "word_count": 261, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [ "ZH11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:29.259119", "source": { "split": "train_shard_00001", "doc_id": 4653 }, "chunk_id": "train_shard_00001_4653_0", "global_id": 12250 }, { "text": "The splicing auxiliary factor OsU2AF35a enhances thermotolerance via protein separation and promoting proper splicing of OsHSA32 pre-mRNA in rice.", "token_count": 43, "char_count": 146, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:29.614168", "source": { "split": "train_shard_00001", "doc_id": 4653 }, "chunk_id": "train_shard_00001_4653_1", "global_id": 12251 }, { "text": "Bifidobacteria are common gut commensals with purported health-promoting effects. This has encouraged scientific research into bifidobacteria, though recalcitrance to genetic manipulation and scarcity of molecular tools has hampered our knowledge on the precise molecular determinants of their health-promoting attributes and gut adaptation. To overcome this problem and facilitate functional genomic analyses in bifidobacteria, we created a large Tn5 transposon mutant library of the commensal Bifidobacterium breve UCC2003 that was further characterized by means of a Transposon Directed Insertion Sequencing (TraDIS) approach. Statistical analysis of transposon insertion distribution revealed a set of 453 genes that are essential for or markedly contribute to growth of this strain under laboratory conditions. These essential genes encode functions involved in the so-called bifid-shunt, most enzymes related to nucleotide biosynthesis and a range of housekeeping functions. Comparison to the Bifidobacterium and B. breve core genomes highlights a high degree of conservation of essential genes at the species and genus level, while comparison to essential gene datasets from other gut bacteria identified essential genes that appear specific to bifidobacteria. This work establishes a useful molecular tool for scientific discovery of bifidobacteria and identifies targets for further studies aimed at characterizing essential functions not previously examined in bifidobacteria.\n\nThe essential genomic landscape of the commensal Bifidobacterium breve UCC2003.", "token_count": 353, "char_count": 1567, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.819, "entities": { "genes": [ "UCC2003" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:30.191889", "source": { "split": "train_shard_00001", "doc_id": 4654 }, "chunk_id": "train_shard_00001_4654_0", "global_id": 12252 }, { "text": "

Objectives

Mycoplasma hominis is one of the smallest free-living opportunistic human pathogens responsible for a diverse range of infections. However, knowledge regarding the genetic and pathogenic mechanisms of M. hominis is still very limited. This study aimed to investigate the genomic features of a multidrug-resistant M. hominis isolate recovered from a synovial fluid sample in China.

Methods

Antimicrobial susceptibility of M. hominis MH-1 was determined by broth microdilution. Genomic DNA was extracted and was sequenced using an Illumina HiSeq X Ten platform. De novo genome assembly was performed using SPAdes, and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). Core genome single nucleotide polymorphism (cgSNP) analysis between M. hominis MH-1 and all 25 M. hominis strains retrieved from the NCBI GenBank database was performed using BacWGSTdb server.

Results

Antimicrobial susceptibility testing showed that M. hominis MH-1 was resistant to macrolides and fluoroquinolones. The genome size was calculated as 720 262 bp, with 608 protein-coding sequences and a G + C content of 26.8%. Several antimicrobial resistance genes, virulence genes, genomic islands and insertion sequences were identified in the genome. Phylogenetic analysis showed that the strains retrieved from NCBI as well as M. hominis MH-1 were not epidemiologically related. The closest relative of M. hominis MH-1 was recovered from the USA, which differed by 5898 SNPs.

Conclusion

This study reports the first genome sequence of a multidrug-resistant M. hominis isolate in China. These data may help to understand the genomic features and antimicrobial resistance mechanisms of this pathogen.", "token_count": 484, "char_count": 1751, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5796, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:30.838079", "source": { "split": "train_shard_00001", "doc_id": 4655 }, "chunk_id": "train_shard_00001_4655_0", "global_id": 12253 }, { "text": "Genomic characterisation of a multidrug-resistant Mycoplasma hominis isolate recovered from a synovial fluid sample in China.", "token_count": 31, "char_count": 125, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:31.192850", "source": { "split": "train_shard_00001", "doc_id": 4655 }, "chunk_id": "train_shard_00001_4655_1", "global_id": 12254 }, { "text": "Non-aureus staphylococci (NAS) are most commonly isolated from subclinical mastitis. Different NAS species may, however, have diverse effects on the inflammatory response in the udder. We determined the genome sequences of 20 staphylococcal isolates from clinical or subclinical bovine mastitis, belonging to the NAS species Staphylococcus agnetis, S. chromogenes, and S. simulans, and focused on the putative virulence factor genes present in the genomes. For comparison we used our previously published genome sequences of four S. aureus isolates from bovine mastitis. The pan-genome and core genomes of the non-aureus isolates were characterized. After that, putative virulence factor orthologues were searched in silico. We compared the presence of putative virulence factors in the NAS species and S. aureus and evaluated the potential association between bacterial genotype and type of mastitis (clinical vs. subclinical). The NAS isolates had much less virulence gene orthologues than the S. aureus isolates. One third of the virulence genes were detected only in S. aureus. About 100 virulence genes were present in all S. aureus isolates, compared to about 40 to 50 in each NAS isolate. S. simulans differed the most. Several of the virulence genes detected among NAS were harbored only by S. simulans, but it also lacked a number of genes present both in S. agnetis and S. chromogenes. The type of mastitis was not associated with any specific virulence gene profile. It seems that the virulence gene profiles or cumulative number of different virulence genes are not directly associated with the type of mastitis (clinical or subclinical), indicating that host derived factors such as the immune status play a pivotal role in the manifestation of mastitis.", "token_count": 519, "char_count": 1851, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5294, "quality_score": 0.7647, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:54:31.822807", "source": { "split": "train_shard_00001", "doc_id": 4656 }, "chunk_id": "train_shard_00001_4656_0", "global_id": 12255 }, { "text": "Comparative genome analysis of 24 bovine-associated Staphylococcus isolates with special focus on the putative virulence genes.", "token_count": 41, "char_count": 134, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:32.190746", "source": { "split": "train_shard_00001", "doc_id": 4656 }, "chunk_id": "train_shard_00001_4656_1", "global_id": 12256 }, { "text": "Multilocus sequence typing (MLST) provides allele-based characterization of bacterial pathogens in a standardized framework. However, classical MLST schemes for Bordetella pertussis, the causative agent of whooping cough, seldom reveal diversity among the small number of gene targets and thereby fail to delineate population structure. To improve the discriminatory power of allele-based molecular typing of B. pertussis, we have developed a whole-genome MLST (wgMLST) scheme from 225 reference-quality genome assemblies. Iterative refinement and allele curation resulted in a scheme of 3,506 coding sequences and covering 81.4% of the B. pertussis genome. This wgMLST scheme was further evaluated with data from a convenience sample of 2,389 B. pertussis isolates sequenced on Illumina instruments, including isolates from known outbreaks and epidemics previously characterized by existing molecular assays, as well as replicates collected from individual patients. wgMLST demonstrated concordance with whole-genome single nucleotide polymorphism (SNP) profiles, accurately resolved outbreak and sporadic cases in a retrospective comparison, and clustered replicate isolates collected from individual patients during diagnostic confirmation. Additionally, a reanalysis of isolates from two statewide epidemics using wgMLST reconstructed the population structures of circulating strains with increased resolution, revealing new clusters of related cases. Comparison with an existing core genome (cgMLST) scheme highlights the stable gene content of this bacterium and forms the initial foundation for necessary standardization. These results demonstrate the utility of wgMLST for improving B. pertussis characterization and genomic surveillance during the current pertussis disease resurgence.\n\nGenomic Surveillance and Improved Molecular Typing of Bordetella pertussis Using wgMLST.", "token_count": 457, "char_count": 1919, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:32.824360", "source": { "split": "train_shard_00001", "doc_id": 4657 }, "chunk_id": "train_shard_00001_4657_0", "global_id": 12257 }, { "text": "Clostridioides difficile sequence type 2 (ST2) has been increasingly recognized as one of the major genotypes in China, while the genomic characteristics and biological phenotypes of Chinese ST2 strains remain to be determined. We used whole-genome sequencing and phylogenetic analysis to investigate the genomic features of 182 ST2 strains, isolated between 2011 and 2017. PCR ribotyping (RT) was performed, and antibiotic resistance, toxin concentration, and sporulation capacity were measured. The core genome Maximum-likelihood phylogenetic analysis showed that ST2 strains were distinctly segregated into two genetically diverse lineages [L1 (67.0% from Northern America) and L2], while L2 further divided into two sub-lineages, SL2a and SL2b (73.5% from China). The 36 virulence-related genes were widely distributed in ST2 genomes, but in which only 11 antibiotic resistance-associated genes were dispersedly found. Among the 25 SL2b sequenced isolates, RT014 (40.0%, n = 10) and RT020 (28.0%, n = 7) were two main genotypes with no significant difference on antibiotic resistance (χ2 = 0.024-2.667, P > 0.05). A non-synonymous amino acid substitution was found in tcdB (Y1975D) which was specific to SL2b", "token_count": 399, "char_count": 1258, "word_count": 177, "semantic_coherence": 1, "information_density": 0.7345, "quality_score": 0.8672, "entities": { "genes": [ "ST2", "RT014", "RT020" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:33.449581", "source": { "split": "train_shard_00001", "doc_id": 4658 }, "chunk_id": "train_shard_00001_4658_0", "global_id": 12258 }, { "text": "Although there was no significant difference in sporulation capacity between the two lineages, the average toxin B concentration (5.11 ± 3.20 ng/μL) in SL2b was significantly lower in comparison to those in L1 (10.49 ± 15.82 ng/μL) and SL2a (13.92 ± 2.39 ng/μL) (χ2 = 12.30, P < 0.05). This study described the genomic characteristics of C. difficile ST2, with many virulence loci and few antibiotic resistance elements. The Chinese ST2 strains with the mutation in codon 1975 of the tcdB gene clustering in SL2b circulating in China express low toxin B, which may be associated with mild or moderate C. difficile infection.\n\nComparative Whole Genome Sequence Analysis and Biological Features of Clostridioides difficile Sequence Type 2‡.", "token_count": 272, "char_count": 795, "word_count": 117, "semantic_coherence": 1, "information_density": 0.7607, "quality_score": 0.8803, "entities": { "genes": [ "ST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:34.000420", "source": { "split": "train_shard_00001", "doc_id": 4658 }, "chunk_id": "train_shard_00001_4658_1", "global_id": 12259 }, { "text": "

Unlabelled

The term \"auto-brewery syndrome\" has been frequently used to describe patients who show features of alcohol intoxication because of abnormal yeast proliferation after ingesting carbohydrate-rich meals. We present a case of a 3-y-old girl with short bowel syndrome (SBS) who demonstrated signs of alcohol intoxication on repeated occasions. A blood test indicated an ethanol concentration of 15 mmol/l, and cultures from gastric fluid and faeces showed the presence of Candida kefyr. An association was found between the introduction of a carbohydrate-rich fruit drink and the occurrence of symptoms.

Conclusion

The possibility of endogenous ethanol fermentation should be considered in patients with SBS and the diagnosis of auto-brewery syndrome added to the differential diagnosis list for D-lactic acidosis. Management includes both antifungal treatment and special diet modification.\n\nEndogenous ethanol fermentation in a child with short bowel syndrome.", "token_count": 241, "char_count": 984, "word_count": 134, "semantic_coherence": 1, "information_density": 0.709, "quality_score": 0.8545, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:34.486641", "source": { "split": "train_shard_00001", "doc_id": 4659 }, "chunk_id": "train_shard_00001_4659_0", "global_id": 12260 }, { "text": "A yeast strain secreting endopolygalacturonase was used in this work to study the possibility of continuous production of this enzyme. It is a feasible and interesting alternative to fungal batch production essentially due to the specificity of the type of pectinase excreted by Kluyveromyces marxianus CCT 3172, to the lower broth viscosity and to the easier downstream operations. In order to increase the reactors' productivity, a cellulosic carrier obtained from barley spent grains was tested as an immobilization support. Two types of reactors were studied for pectinase production using glucose as a carbon and energy source--a continuous stirred tank reactor (CSTR) and a packed bed reactor (PBR) with recycled flow. The highest value for pectinase volumetric productivity (P(V)=0.98 U ml(-1) h(-1)) was achieved in the PBR for D=0.40 h(-1), a glucose concentration on the inlet of S(in)=20 g l(-1), and a biomass load in the support of X(i)=0.225 g g(-1). The results demonstrate the attractiveness of the packed bed system for pectinase production.\n\nContinuous production of pectinase by immobilized yeast cells on spent grains.", "token_count": 309, "char_count": 1138, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:35.087320", "source": { "split": "train_shard_00001", "doc_id": 4660 }, "chunk_id": "train_shard_00001_4660_0", "global_id": 12261 }, { "text": "The field of microbiome research has developed rapidly over the past decades and has become a topic of major interest to basic, preclinical, and clinical research, the pharmaceutical industry as well as the general public. The microbiome is a complex and diverse ecosystem and defined as the collection of all host-associated microorganisms and their genes. It is acquired through vertical transmission and environmental exposure and includes microbes of all kingdoms: bacteria, archaea, prokaryotic and eukaryotic viruses, fungi, protozoa, and the meiofauna. These microorganisms co-evolved with their respective hosts over millions of years, thereby establishing a mutually beneficial, symbiotic relationship on all epithelial barriers. Thus, the microbiome plays a pivotal role in virtually every aspect of mammalian physiology, particularly in the development, homeostasis, and function of the immune system. Consequently, the combination of the host genome and the microbial genome, together referred to as the metagenome, largely drives the mammalian phenotype. So far, the majority of studies have unilaterally focused on the gastrointestinal bacterial microbiota. However, recent work illustrating the impact of viruses, fungi, and protozoa on host immunity urges us towards a holistic view of the mammalian microbiome and the appreciation for its non-bacterial kingdoms. In addition, the importance of microbiota on epithelial barriers other than the gut as well as their systemic effects via microbially-derived biologically active compounds is increasingly recognized. Here, we want to provide a brief but comprehensive overview of the most important findings and the current knowledge on how microbes of all kingdoms and microbial niches shape local and systemic immunity in health and disease.\n\nThe Mammalian Metaorganism: A Holistic View on How Microbes of All Kingdoms and Niches Shape Local and Systemic Immunity.", "token_count": 443, "char_count": 1936, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5971, "quality_score": 0.7986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:35.742304", "source": { "split": "train_shard_00001", "doc_id": 4661 }, "chunk_id": "train_shard_00001_4661_0", "global_id": 12262 }, { "text": "Isolation and genetic analysis of ethanol-sensitive mutants of thermotolerant Kluyveromyces marxianus.", "token_count": 29, "char_count": 102, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:36.125291", "source": { "split": "train_shard_00001", "doc_id": 4662 }, "chunk_id": "train_shard_00001_4662_0", "global_id": 12263 }, { "text": "IntroductionWater supply and air-conditioner cooling towers (ACCT) are potential sources of Legionella pneumophila infection in people. During outbreaks, traditional typing methods cannot sufficiently segregate L. pneumophila strains to reliably trace back transmissions to these artificial water systems. Moreover, because multiple L. pneumophila strains may be present within these systems, methods to adequately distinguish strains are needed. Whole genome sequencing (WGS) and core genome multilocus sequence typing (cgMLST), with their higher resolution are helpful in this respect. In summer 2017, the health administration of the city of Basel detected an increase of L. pneumophila infections compared with previous months, signalling an outbreak.AimWe aimed to identify L. pneumophila strains populating suspected environmental sources of the outbreak, and to assess the relations between these strains and clinical outbreak strains.MethodsAn epidemiological and WGS-based microbiological investigation was performed, involving isolates from the local water supply and two ACCTs (n = 60), clinical outbreak and non-outbreak related isolates from 2017 (n = 8) and historic isolates from 2003-2016 (n = 26).ResultsIn both ACCTs, multiple strains were found. Phylogenetic analysis of the ACCT isolates showed a diversity of a few hundred allelic differences in cgMLST. Furthermore, two isolates from one ACCT showed no allelic differences to three clinical isolates from 2017. Five clinical isolates collected in the Basel area in the last decade were also identical in cgMLST to recent isolates from the two ACCTs.ConclusionCurrent outbreak-related and historic isolates were linked to ACCTs, which form a complex environmental habitat where strains are conserved over years.\n\nAir-conditioner cooling towers as complex reservoirs and continuous source of Legionella pneumophila infection evidenced by a genomic analysis study in 2017, Switzerland.", "token_count": 511, "char_count": 1996, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:36.796183", "source": { "split": "train_shard_00001", "doc_id": 4663 }, "chunk_id": "train_shard_00001_4663_0", "global_id": 12264 }, { "text": "A semiautomatic image analysis method has been developed to characterize the morphology of the dimorphic yeast Kluyveromyces marxianus var. marxianus (formerly fragilis) NRRLy2415 undergoing alcoholic fermentation of cheese whey permeate. The method is capable of separating cells into six defined categories, varying from simple ovoid yeast cells to branched mycelial cells. A sample size of 300 cells was found to be sufficient to obtain a statistically significant categorization. The processing time for a sample was found to be approximately 90 min. In addition to qualitative characterization, the method permits the measurement of geometric properties such as the width, length, and volume of individual cells or clusters of cells. When the cells analyzed by the automatic method were categorized on a manual basis, the error level in the automatic routine was found to be less than 3%.\n\nMorphological characterization of the dimorphic yeast Kluyveromyces marxianus var. marxianus NRRLy2415 by semi-automated image analysis.", "token_count": 249, "char_count": 1031, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6291, "quality_score": 0.8146, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:37.293651", "source": { "split": "train_shard_00001", "doc_id": 4664 }, "chunk_id": "train_shard_00001_4664_0", "global_id": 12265 }, { "text": "

Introduction

Reproductive health in mares is pivotal for the sustainability of the equine industry, yet vaginal microbiota dysbiosis remains an underrecognized contributor to infections such as endometritis and bacterial vaginosis. While Lactobacillus spp. dominate healthy vaginal ecosystems in humans and livestock, their role in equine reproductive health, particularly in resilient breeds like Mongolian mares, is poorly understood. This study aimed to isolate and characterize a novel Lactobacillus strain from the vaginal microbiota of healthy Mongolian mares and evaluate its probiotic potential for mitigating equine reproductive disorders.

Methods

A polyphasic approach integrating phenotypic, biochemical, and 16S rRNA gene sequencing was employed to isolate and identify a novel Lactobacillus salivarius strain (Y20) from the vaginal microbiota of healthy Mongolian mares. The probiotic potential of Y20 was assessed through in vitro assays, including tolerance to low pH (pH 2.5) and bile salts (0.3%), antagonistic activity against equine pathogens (Staphylococcus aureus, Escherichia coli, Pseudomonas aeruginosa), and antioxidant capacity (DPPH radical scavenging assay). Whole-genome sequencing (1.74 Mb, 33.01% GC content) was performed to analyze genes related to carbohydrate metabolism, adhesion factors, bacteriocin biosynthesis, and stress response pathways", "token_count": 439, "char_count": 1443, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7207, "quality_score": 0.8603, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:37.923660", "source": { "split": "train_shard_00001", "doc_id": 4665 }, "chunk_id": "train_shard_00001_4665_0", "global_id": 12266 }, { "text": "Comparative genomics was used to explore phylogenetic relationships and genomic adaptations for vaginal colonization.

Results

Lactobacillus salivarius Y20 demonstrated robust tolerance to low pH and bile salts, potent antagonistic activity against key equine pathogens, and significant antioxidant capacity (82.4% DPPH radical scavenging). Genomic analysis revealed genes encoding carbohydrate metabolism, adhesion factors, bacteriocin biosynthesis (including a novel putative bacteriocin cluster), and stress response pathways. Comparative genomics confirmed Y20's close phylogenetic relationship with horse-derived Lactobacillus salivarius strains and identified unique genomic adaptations for vaginal colonization.

Discussion

These findings identify Lactobacillus salivarius Y20 as a promising candidate probiotic for mitigating equine reproductive disorders. Its multifaceted probiotic properties, including pathogen inhibition, antioxidant activity, and genomic adaptations for vaginal colonization, suggest potential applications in sustainable equine health management. This study advances microbiome-based strategies as viable alternatives to antibiotics, offering new avenues for improving reproductive health in mares.\n\nIsolation, identification and comparative genomic analysis of <i>Lactobacillus salivarius</i> from Mongolian horse vagina.", "token_count": 365, "char_count": 1399, "word_count": 151, "semantic_coherence": 1, "information_density": 0.7417, "quality_score": 0.8709, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:38.502682", "source": { "split": "train_shard_00001", "doc_id": 4665 }, "chunk_id": "train_shard_00001_4665_1", "global_id": 12267 }, { "text": "Production of an alcoholic beverage by fermentation of whey permeate with Kluyveromyces fragilis. II. Aroma composition.", "token_count": 33, "char_count": 120, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:38.864561", "source": { "split": "train_shard_00001", "doc_id": 4666 }, "chunk_id": "train_shard_00001_4666_0", "global_id": 12268 }, { "text": "Many antibiotic resistant uropathogenic Escherichia coli (UPEC) strains belong to clones defined by their multilocus sequence type (ST), with ST131 being the most dominant. Although we have a good understanding of resistance development to fluoroquinolones and third-generation cephalosporins by ST131, our understanding of the virulence repertoire that has contributed to its global dissemination is limited. Here we show that the genes encoding Afa/Dr fimbriae, a group of adhesins strongly associated with UPEC that cause gestational pyelonephritis and recurrent cystitis, are found in approximately one third of all ST131 strains. Sequence comparison of the AfaE adhesin protein revealed a unique allelic variant carried by 82.9% of afa-positive ST131 strains. We identify the afa regulatory region as a hotspot for the integration of insertion sequence (IS) elements, all but one of which alter afa transcription. Close investigation demonstrated that the integration of an IS1 element in the afa regulatory region leads to increased expression of Afa/Dr fimbriae, promoting enhanced adhesion to kidney epithelial cells and suggesting a mechanism for altered virulence. Finally, we provide evidence for a more widespread impact of IS1 on ST131 genome evolution, suggesting that IS dynamics contribute to strain level microevolution that impacts ST131 fitness. IMPORTANCE E. coli ST131 is the most common antibiotic resistant UPEC clone associated with human urinary tract and bloodstream infections. Understanding the features of ST131 that have driven its global dissemination remains a critical priority if we are to counter its increasing antibiotic resistance. Here, we utilized a large collection of ST131 isolates to investigate the prevalence, regulation, and function of Afa/Dr fimbriae, a well-characterized UPEC colonization and virulence factor", "token_count": 491, "char_count": 1909, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6142, "quality_score": 0.8071, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:39.507958", "source": { "split": "train_shard_00001", "doc_id": 4667 }, "chunk_id": "train_shard_00001_4667_0", "global_id": 12269 }, { "text": "We show that the afa genes are found frequently in ST131 and demonstrate how the integration of IS elements in the afa regulatory region modulates Afa expression, presenting an example of altered virulence capacity. We also exploit a curated set of ST131 genomes to map the integration of the antibiotic resistance-associated IS1 element in the ST131 pangenome, providing evidence for its widespread impact on ST131 genome evolution.\n\nDifferential Afa/Dr Fimbriae Expression in the Multidrug-Resistant Escherichia coli ST131 Clone.", "token_count": 155, "char_count": 552, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7564, "quality_score": 0.8782, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:39.945640", "source": { "split": "train_shard_00001", "doc_id": 4667 }, "chunk_id": "train_shard_00001_4667_1", "global_id": 12270 }, { "text": "In recent decades, Neisseria gonorrhoeae has developed resistance to several antimicrobial classes. Molecular epidemiology approaches are useful for detecting emerging, often resistant, gonococcal clones. In this study, 67 N. gonorrhoeae isolates from different anatomic sites, collected over 8 years in Italy, were analyzed by whole genome sequencing (WGS). WGS was performed using the Illumina NextSeq 500 platform. Phylogenetic analysis was based on core single nucleotide polymorphism (SNP) and core genome multilocus sequence typing (cgMLST). N. gonorrhoeae multi-antigen sequence typing (NG-MAST), MLST, and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR) were carried out in silico using WGS data. Antimicrobial susceptibility against a four-drug panel was evaluated using a gradient diffusion method. Overall, gonococci clustered in accordance with NG-MAST, MLST, NG-STAR, and antimicrobials susceptibility profiles, but not with the site of isolation, HIV status, and patient sexual orientation. Phylogenetic analysis identified nine clades: two of them were the predominant and including gonococci of G1407 and G2400 genogroups.\n\nGenomic Characterization of Gonococci from Different Anatomic Sites, Italy, 2007-2014.", "token_count": 384, "char_count": 1283, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7108, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:40.555329", "source": { "split": "train_shard_00001", "doc_id": 4668 }, "chunk_id": "train_shard_00001_4668_0", "global_id": 12271 }, { "text": "In view of the growing incidence and the high mortality of invasive aspergillosis and candidiasis, adequate diagnostic techniques permitting timely onset of treatment are of paramount importance. More than 90 % of all invasive fungal infections in immunocompromised individuals can be attributed to Candida and Aspergillus species. To date, standardized techniques permitting rapid, sensitive and, no less importantly, economic screening for the clinically most relevant fungi are lacking. In the present report, a real-time quantitative PCR assay, developed for the detection of the most common pathogenic Candida and Aspergillus species, is described. The single-reaction PCR assay targets a judiciously selected region of the 28S subunit of the fungal rDNA gene. The unique design of the universal primer/probe system, including a pan-Aspergillus and pan-Candida (Pan-AC) hydrolysis probe, facilitates the detection of numerous Aspergillus species (e.g. Aspergillus fumigatus, Aspergillus flavus, Aspergillus niger, Aspergillus terreus, Aspergillus versicolor and Aspergillus nidulans) and Candida species (e.g. Candida albicans, Candida glabrata, Candida krusei, Candida tropicalis, Candida parapsilosis, Candida kefyr, Candida guilliermondii, Candida lusitaniae and Candida dubliniensis). The assay permits highly reproducible detection of 10 fg fungal DNA, which corresponds to a fraction of a fungal genome, and facilitates accurate quantification of fungal load across a range of at least five logs. Upon standardization of the technique using cultured fungal strains, the applicability in the clinical setting was assessed by investigating a series of clinical specimens from patients with documented fungal infections (n=17). The Pan-AC assay provides an attractive and economic approach to the screening and monitoring of invasive aspergillosis and candidiasis, which is readily applicable to routine clinical diagnosis.", "token_count": 498, "char_count": 1931, "word_count": 263, "semantic_coherence": 1, "information_density": 0.597, "quality_score": 0.7985, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:41.214132", "source": { "split": "train_shard_00001", "doc_id": 4669 }, "chunk_id": "train_shard_00001_4669_0", "global_id": 12272 }, { "text": "The Pan-AC assay: a single-reaction real-time PCR test for quantitative detection of a broad range of Aspergillus and Candida species.", "token_count": 37, "char_count": 134, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:41.570608", "source": { "split": "train_shard_00001", "doc_id": 4669 }, "chunk_id": "train_shard_00001_4669_1", "global_id": 12273 }, { "text": "In the present study, 100 L. monocytogenes isolates of serogroup IIa from food and food production environments in Poland were characterized towards the presence of virulence, resistance, and stress response genes using whole-genome sequencing (WGS). The strains were also molecularly typed and compared with multi-locus sequence typing (MLST) and core genome MLST analyses. The present isolates were grouped into 6 sublineages (SLs), with the most prevalent SL155 (33 isolates), SL121 (32 isolates), and SL8 (28 isolates) and classified into six clonal complexes, with the most prevalent CC155 (33 strains), CC121 (32 isolates), and CC8 (28 strains). Furthermore, the strains were grouped to eight sequence types, with the most prevalent ST155 (33 strains), ST121 (30 isolates), and ST8 (28; strains) followed by 60 cgMLST types (CTs). WGS data showed the presence of several virulence genes or putative molecular markers playing a role in pathogenesis of listeriosis and involved in survival of L. monocytogenes in adverse environmental conditions. Some of the present strains were molecularly closely related to L. monocytogenes previously isolated in Poland. The results of the study showed that food and food production environments may be a source of L. monocytogenes of serogroup IIa with pathogenic potential.\n\nGenetic Diversity and Relationships of Listeria monocytogenes Serogroup IIa Isolated in Poland.", "token_count": 414, "char_count": 1449, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [ "ST121", "CC8", "CC121", "ST155", "SL121", "ST8", "SL155", "CC155", "SL8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:42.181373", "source": { "split": "train_shard_00001", "doc_id": 4670 }, "chunk_id": "train_shard_00001_4670_0", "global_id": 12274 }, { "text": "A strain of the yeast Kluyveromyces fragilis was screened for its ability to utilize a range of synthetic and natural organophosphonate compounds as the sole source of phosphorus, nitrogen or carbon. Only 4-aminobutylphosphonate was utilized as sole nitrogen source with protein yields increasing proportionally with substrate concentrations up to 10 mM. No 4-aminobutylphosphonate metabolizing enzyme activity was detectable in cell-free extracts prepared from K. fragilis pregrown on 2.5 mM 4-aminobutylphosphonate. None of the organophosphonates tested served as a source of carbon or phosphorus for K. fragilis.\n\nThe utilization of 4-aminobutylphosphonate as sole nitrogen source by a strain of Kluyveromyces fragilis.", "token_count": 200, "char_count": 722, "word_count": 100, "semantic_coherence": 1, "information_density": 0.65, "quality_score": 0.825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:42.628527", "source": { "split": "train_shard_00001", "doc_id": 4671 }, "chunk_id": "train_shard_00001_4671_0", "global_id": 12275 }, { "text": "

Objectives

Data on fungal infections occurring in Germany are rare to date. The aim of the present study was to survey the epidemiological situation in Germany, to provide data on the susceptibility of the fungal isolates to antifungals.

Methods

Five hundred and sixty-one Candida isolates were collected from primarily sterile sites of patients from July 2004 to August 2005 with the aid of a nationwide established laboratory network, MykolabNet-D. The MICs of amphotericin B, flucytosine, fluconazole, itraconazole, voriconazole and caspofungin were determined using the microdilution reference procedure M27-A2 of the CLSI.

Results

Candida albicans was the most frequently isolated species (58.5%), followed by Candida glabrata (19.1%), Candida parapsilosis (8.0%) and Candida tropicalis (7.5%). In contrast, the isolation rate of Candida krusei (1.4%) was low. Candida kefyr appeared as a new pathogen in this profile. Amphotericin B revealed excellent activity, with only three resistant isolates (0.5%). A total of 25 isolates (4.5%) showed resistance against flucytosine. All 25 isolates were identified as C. tropicalis indicating a peculiarity within German isolates. The resistance rate of all tested isolates to fluconazole and to itraconazole was 3.7% and 17.6%, respectively. According to the provisional breakpoints, two isolates (0.4%) were tested as resistant to voriconazole. Caspofungin was active against the majority of isolates where an intrinsic resistance is unknown.

Conclusions

This latest German survey of isolates from patients with fungaemia demonstrates a favourable situation with respect to antifungal susceptibilities for the antifungal substances tested.", "token_count": 480, "char_count": 1717, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6164, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:43.273325", "source": { "split": "train_shard_00001", "doc_id": 4672 }, "chunk_id": "train_shard_00001_4672_0", "global_id": 12276 }, { "text": "Epidemiology and antifungal susceptibilities of Candida spp. to six antifungal agents: results from a surveillance study on fungaemia in Germany from July 2004 to August 2005.", "token_count": 52, "char_count": 175, "word_count": 26, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:43.633057", "source": { "split": "train_shard_00001", "doc_id": 4672 }, "chunk_id": "train_shard_00001_4672_1", "global_id": 12277 }, { "text": "Serotype 4821 (ST-4821) clonal complex (cc4821) Neisseria meningitidis strains are divided into two groups (groups I and II) according to the core genome-based phylogenetic analysis. Group I contains the greater number of invasive disease isolates. However, the differences in pathogenicity between the two groups are unclear. In this study, the pathogenicity of cc4821 isolates (n = 28) belonging to group I and group II (each containing eight invasive isolates and six isolates from healthy carriers) was investigated, including adhesion, invasion, and induction of interleukin-6 (IL-6) and interleukin-8 (IL-8) release from host cells (Hep2 and A549). The invasive isolates had higher adhesion and invasion capabilities than the carried isolates in both groups. The carried cc4821 isolates in group I had stronger invasion capability than those in group II. Invasive isolates induced more IL-6 and IL-8 secretion than carried isolates in both groups. The carried cc4821 isolates stimulated higher levels of IL-8 in group I than in group II. The isolates were defined as hyperadherent and hypoadherent groups according to their adhesion ability and as hyperinvasive and hypoinvasive groups based on their invasion ability. The hyperadherent and hyperinvasive isolates mediated more IL-6 and IL-8 release than the hypoadherent and hypoinvasive isolates. There was no difference in the level of cytokine release when cc4821 isolates lost their adhesion and invasion capability after lysis. The results revealed that differences in pathogenicity existed between the two groups and that the differences were mainly determined by differences in adhesion and invasion capabilities.\n\nComparison of Pathogenicity of Invasive and Carried Meningococcal Isolates of ST-4821 Complex in China.", "token_count": 470, "char_count": 1796, "word_count": 260, "semantic_coherence": 1, "information_density": 0.4769, "quality_score": 0.7385, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:44.277177", "source": { "split": "train_shard_00001", "doc_id": 4673 }, "chunk_id": "train_shard_00001_4673_0", "global_id": 12278 }, { "text": "Hosting millions of microorganisms, the digestive tract is the primary and most important part of bacterial colonization. On one side, in cases of opportunistic invasion, the abundant bacterial population inside intestinal tissues may face potential health problems such as inflammation and infections. Therefore, the immune system has evolved to sustain the host-microbiota symbiotic relationship. On the other hand, to maintain host immune homeostasis, the intestinal microflora often exerts an immunoregulatory function that cannot be ignored. A field of great interest is the association of either microbiota or probiotics with the immune system concerning clinical uses. This microbial community regulates some of the host's metabolic and physiological functions and drives early-life immune system maturation, contributing to their homeostasis throughout life. Changes in gut microbiota can occur through modification in function, composition (dysbiosis), or microbiota-host interplays. Studies on animals and humans show that probiotics can have a pivotal effect on the modulation of immune and inflammatory mechanisms; however, the precise mechanisms have not yet been well defined. Diet, age, BMI (body mass index), medications, and stress may confound the benefits of probiotic intake. In addition to host gut functions (permeability and physiology), all these agents have profound implications for the gut microbiome composition. The use of probiotics could improve the gut microbial population, increase mucus-secretion, and prevent the destruction of tight junction proteins by decreasing the number of lipopolysaccharides (LPSs). When LPS binds endothelial cells to toll-like receptors (TLR 2, 4), dendritic cells and macrophage cells are activated, and inflammatory markers are increased. Furthermore, a decrease in gut dysbiosis and intestinal leakage after probiotic therapy may minimize the development of inflammatory biomarkers and blunt unnecessary activation of the immune system. In turn, probiotics improve the differentiation of T-cells against Th2 and development of Th2 cytokines such as IL-4 and IL-10", "token_count": 502, "char_count": 2129, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6577, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:44.931851", "source": { "split": "train_shard_00001", "doc_id": 4674 }, "chunk_id": "train_shard_00001_4674_0", "global_id": 12279 }, { "text": "The present narrative review explores the interactions between gut microflora/probiotics and the immune system starting from the general perspective of a biological plausibility to get to the in vitro and in vivo demonstrations of a probiotic-based approach up to the possible uses for novel therapeutic strategies.\n\nAnti-Inflammatory and Immunomodulatory Effects of Probiotics in Gut Inflammation: A Door to the Body.", "token_count": 116, "char_count": 432, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7167, "quality_score": 0.8583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:45.316322", "source": { "split": "train_shard_00001", "doc_id": 4674 }, "chunk_id": "train_shard_00001_4674_1", "global_id": 12280 }, { "text": "Bacillus subtilis and its sister species B. amyloliquefaciens comprise an evolutionary compact but physiologically versatile group of bacteria that includes strains isolated from diverse habitats. Many of these strains are used as plant growth-promoting rhizobacteria (PGPR) in agriculture and a plant-specialized subspecies of B. amyloliquefaciens-B. amyloliquefaciens subsp. plantarum, has recently been recognized, here we used 31 whole genomes [including two newly sequenced PGPR strains: B. amyloliquefaciens NJN-6 isolated from Musa sp. (banana) and B. subtilis HJ5 from Gossypium sp. (cotton)] to perform comparative analysis and investigate the genomic characteristics and evolution traits of both species in different niches. Phylogenomic analysis indicated that strains isolated from plant-associated (PA) habitats could be distinguished from those from non-plant-associated (nPA) niches in both species. The core genomes of PA strains are more abundant in genes relevant to intermediary metabolism and secondary metabolites biosynthesis as compared with those of nPA strains, and they also possess additional specific genes involved in utilization of plant-derived substrates and synthesis of antibiotics. A further gene gain/loss analysis indicated that only a few of these specific genes (18/192 for B. amyloliquefaciens and 53/688 for B. subtilis) were acquired by PA strains at the initial divergence event, but most were obtained successively by different subgroups of PA stains during the evolutional process. This study demonstrated the genomic differences between PA and nPA B. amyloliquefaciens and B. subtilis from different niches and the involved evolutional traits, and has implications for screening of PGPR strains in agricultural production.", "token_count": 513, "char_count": 1852, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6122, "quality_score": 0.8061, "entities": { "genes": [ "HJ5" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:54:45.953838", "source": { "split": "train_shard_00001", "doc_id": 4675 }, "chunk_id": "train_shard_00001_4675_0", "global_id": 12281 }, { "text": "Comparative Genomic Analysis of Bacillus amyloliquefaciens and Bacillus subtilis Reveals Evolutional Traits for Adaptation to Plant-Associated Habitats.", "token_count": 58, "char_count": 166, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:46.322941", "source": { "split": "train_shard_00001", "doc_id": 4675 }, "chunk_id": "train_shard_00001_4675_1", "global_id": 12282 }, { "text": "In August 2017, an increased incidence of Salmonella Bareilly was detected in the Czech Republic. An investigation was conducted with Slovakia to confirm the outbreak and identify the source. Probable outbreak cases were defined as cases with laboratory-confirmed S. Bareilly reported in either of the national surveillance systems, and/or the Czech and Slovak National Reference Laboratory databases from July 2017. Confirmed cases had the pulsed-field gel electrophoresis (PFGE) outbreak pulsotype or up to 5 alleles difference from outbreak cluster members by core genome multilocus sequence typing (cgMLST). PFGE and whole genome sequencing were used for isolate comparison. The same trawling questionnaire was used in both countries. By the end of October 2018, 325 cases were identified. Among 88 human S. Bareilly isolates analysed by PFGE, 82 (93%) shared an identical pulsotype; cgMLST of 17 S. Bareilly human isolates showed 1-2 allele difference. The trawling questionnaire excluded consumption of unusual or imported foods. In September 2018, an isolate closely related to the outbreak isolates was identified in a powdered egg product. A spray dryer was recognised as the contamination source and the production plant was closed. Using molecular typing methods, we detected a diffuse cross-border outbreak caused by S. Bareilly.\n\nA cross-border outbreak of Salmonella Bareilly cases confirmed by whole genome sequencing, Czech Republic and Slovakia, 2017 to 2018.", "token_count": 400, "char_count": 1518, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:46.946628", "source": { "split": "train_shard_00001", "doc_id": 4676 }, "chunk_id": "train_shard_00001_4676_0", "global_id": 12283 }, { "text": "

Background

Sugarcane distilleries use molasses for ethanol production and generate large volume of effluent containing high biological oxygen demand (BOD) and chemical oxygen demand (COD) along with melanoidin pigment. Melanoidin is a recalcitrant compound that causes several toxic effects on living system, therefore, may be treated before disposal. The aim of this study was to isolate a potential thermotolerant melanoidin decolorizing yeast from natural resources, and optimized different physico-chemical and nutritional parameters.

Results

Total 24 yeasts were isolated from the soil samples of near by distillery site, in which isolate Y-9 showed maximum decolorization and identified as Candida tropicalis by Microbial Type Culture Collection (MTCC) Chandigarh, India. The decolorization yield was expressed as the decrease in the absorbance at 475 nm against initial absorbance at the same wavelength. Uninoculated medium served as control. Yeast showed maximum decolorization (75%) at 45°C using 0.2%, glucose; 0.2%, peptone; 0.05%, MgSO4; 0.01%, KH₂PO₄; pH-5.5 within 24 h of incubation under static condition. Decolorizing ability of yeast was also confirmed by high performance liquid chromatography (HPLC) analysis.

Conclusion

The yeast strain efficiently decolorized melanoidin pigment of distillery effluent at higher temperature than the other earlier reported strains of yeast, therefore, this strain could also be used at industrial level for melanoidin decolorization as it tolerated a wide range of temperature and pH with very small amount of carbon and nitrogen sources.\n\nDecolorization of a recalcitrant organic compound (Melanoidin) by a novel thermotolerant yeast, Candida tropicalis RG-9.", "token_count": 474, "char_count": 1738, "word_count": 236, "semantic_coherence": 1, "information_density": 0.678, "quality_score": 0.839, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:47.606435", "source": { "split": "train_shard_00001", "doc_id": 4677 }, "chunk_id": "train_shard_00001_4677_0", "global_id": 12284 }, { "text": "Although the human gut microbiome plays a prominent role in xenobiotic transformation, most of the genes and enzymes responsible for this metabolism are unknown. Recently, we linked the two-gene 'cardiac glycoside reductase' (cgr) operon encoded by the gut Actinobacterium Eggerthella lenta to inactivation of the cardiac medication and plant natural product digoxin. Here, we compared the genomes of 25 E. lenta strains and close relatives, revealing an expanded 8-gene cgr-associated gene cluster present in all digoxin metabolizers and absent in non-metabolizers. Using heterologous expression and in vitro biochemical characterization, we discovered that a single flavin- and [4Fe-4S] cluster-dependent reductase, Cgr2, is sufficient for digoxin inactivation. Unexpectedly, Cgr2 displayed strict specificity for digoxin and other cardenolides. Quantification of cgr2 in gut microbiomes revealed that this gene is widespread and conserved in the human population. Together, these results demonstrate that human-associated gut bacteria maintain specialized enzymes that protect against ingested plant toxins.\n\nDiscovery and characterization of a prevalent human gut bacterial enzyme sufficient for the inactivation of a family of plant toxins.", "token_count": 337, "char_count": 1280, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:48.204083", "source": { "split": "train_shard_00001", "doc_id": 4678 }, "chunk_id": "train_shard_00001_4678_0", "global_id": 12285 }, { "text": "Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.\n\nExtending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.", "token_count": 305, "char_count": 1259, "word_count": 168, "semantic_coherence": 1, "information_density": 0.7381, "quality_score": 0.869, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:48.817458", "source": { "split": "train_shard_00001", "doc_id": 4679 }, "chunk_id": "train_shard_00001_4679_0", "global_id": 12286 }, { "text": "

Background

S. enterica subsp. houtenae has been rarely documented, and very limited genomic information is available. This report describes a rare case of primary extraintestinal salmonellosis in a young roe deer, associated with Salmonella enterica subsp. houtenae. Methods: A traditional cultural-based analysis was carried out from the contents of a neck abscess; biochemical identification and PCR assay were performed to isolate and identify the pathogen. Through whole-genome sequencing (WGS), multilocus sequence typing (MLST), core genome MLST (cgMLST), and the Salmonella pathogenicity islands (SPIs) survey, resistome and virulome genes were investigated to gain insight into the virulence and antimicrobial resistance of S. houtenae.

Results

Biochemical identification and PCR confirmed the presence of Salmonella spp. in the swelling. The WGS analysis identified Salmonella enterica subspecies houtenae serovar 43:z4,z23:- and ST 958. The virulence study predicted a multidrug resistance pattern with resistance shown against aminoglycosides, tetracycline, beta-lactamase, fluoroquinolones, fosfomycin, nitroimidazole, aminocoumarin, and peptide. Fifty-three antibiotic-resistant genes were identified. No plasmids were detected.

Conclusion

This study demonstrates the importance of continuous surveillance of pathogenic salmonellae. Biomolecular analyses combined with epidemiological data can provide important information about poorly described Salmonella strains and can help to improve animal welfare.\n\nSalmonella enterica Subsp. houtenae Associated with an Abscess in Young Roe Deer (Capreolus capreolus).", "token_count": 509, "char_count": 1727, "word_count": 201, "semantic_coherence": 1, "information_density": 0.7065, "quality_score": 0.8532, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:49.479789", "source": { "split": "train_shard_00001", "doc_id": 4680 }, "chunk_id": "train_shard_00001_4680_0", "global_id": 12287 }, { "text": "The T4-related bacteriophages are a group of bacterial viruses that share morphological similarities and genetic homologies with the well-studied Escherichia coli phage T4, but that diverge from T4 and each other by a number of genetically determined characteristics including the bacterial hosts they infect, the sizes of their linear double-stranded (ds) DNA genomes and the predicted compositions of their proteomes. The genomes of about 40 of these phages have been sequenced and annotated over the last several years and are compared here in the context of the factors that have determined their diversity and the diversity of other microbial genomes in evolution. The genomes of the T4 relatives analyzed so far range in size between ~160,000 and ~250,000 base pairs (bp) and are mosaics of one another, consisting of clusters of homology between them that are interspersed with segments that vary considerably in genetic composition between the different phage lineages. Based on the known biological and biochemical properties of phage T4 and the proteins encoded by the T4 genome, the T4 relatives reviewed here are predicted to share a genetic core, or \"Core Genome\" that determines the structural design of their dsDNA chromosomes, their distinctive morphology and the process of their assembly into infectious agents (phage morphogenesis). The Core Genome appears to be the most ancient genetic component of this phage group and constitutes a mere 12-15% of the total protein encoding potential of the typical T4-related phage genome. The high degree of genetic heterogeneity that exists outside of this shared core suggests that horizontal DNA transfer involving many genetic sources has played a major role in diversification of the T4-related phages and their spread to a wide spectrum of bacterial species domains in evolution. We discuss some of the factors and pathways that might have shaped the evolution of these phages and point out several parallels between their diversity and the diversity generally observed within all groups of interrelated dsDNA microbial genomes in nature.\n\nGenomes of the T4-related bacteriophages as windows on microbial genome evolution.", "token_count": 486, "char_count": 2186, "word_count": 336, "semantic_coherence": 1, "information_density": 0.5357, "quality_score": 0.7679, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:50.135164", "source": { "split": "train_shard_00001", "doc_id": 4681 }, "chunk_id": "train_shard_00001_4681_0", "global_id": 12288 }, { "text": "Growing interest in probiotics has spurred research into their health benefits for hosts. This study aimed to evaluate the probiotic properties, especially antibacterial activities and the safety of two Weissella confusa strains, W1 and W2, isolated from Khao-Mahk by describing their phenotypes and genotypes through phenotypic assays and whole genome sequencing. In vitro experiments demonstrated that both strains exhibited robust survival under gastric and intestinal conditions, such as in the presence of low pH, bile salt, pepsin, and pancreatin, indicating their favorable gut colonization traits. Additionally, both strains showed auto-aggregation and strong adherence to Caco2 cells, with adhesion rates of 86.86 ± 1.94% for W1 and 94.74 ± 2.29% for W2. These high adherence rates may be attributed to the significant exopolysaccharide (EPS) production observed in both strains. Moreover, they exerted remarkable antimicrobial activities against Stenotrophomonas maltophilia, Salmonella enterica serotype Typhi, Vibrio cholerae, and Acinetobacter baumannii, along with an absence of hemolytic activities and antibiotic resistance, underscoring their safety for probiotic application. Genomic analysis corroborated these findings, revealing genes related to probiotic traits, including EPS clusters, stress responses, adaptive immunity, and antimicrobial activity. Importantly, no transferable antibiotic-resistance genes or virulence genes were detected. This comprehensive characterization supports the candidacy of W1 and W2 as probiotics, offering substantial potential for promoting health and combating bacterial infections.\n\nExploring Weissella confusa W1 and W2 Strains Isolated from Khao-Mahk as Probiotic Candidates: From Phenotypic Traits to Genomic Insights.", "token_count": 491, "char_count": 1821, "word_count": 234, "semantic_coherence": 1, "information_density": 0.7051, "quality_score": 0.8526, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:50.783526", "source": { "split": "train_shard_00001", "doc_id": 4682 }, "chunk_id": "train_shard_00001_4682_0", "global_id": 12289 }, { "text": "The Klebsiella pneumoniae complex comprises several closely related entities, which are ubiquitous in the natural environment, including in plants, animals, and humans. K. pneumoniae is the major species within this complex. K. pneumoniae strains are opportunistic pathogens and a common cause of healthcare-associated infections. K. pneumoniae can colonize the human gastrointestinal tract, which may become a reservoir for infection. The aim of this study was to investigate the fecal K. pneumoniae carriage in six healthy individuals during a 1 year period. Stool samples were obtained once a week. Using direct and pre-enriched cultures streaked on ampicillin-supplemented agar plates, up to eight individual colonies per positive sample were selected for further characterization. Whole genome sequencing (WGS) was performed for strain characterization. Sequence type (ST), core genome complex type (CT), K and O serotypes, virulence traits, antibiotic resistance profiles, and plasmids were extracted from WGS data. In total, 80 K. pneumoniae isolates were obtained from 48 positive cultures of 278 stool samples from five of the six test subjects. The samples of the five colonized volunteers yielded at most two, three, four (two persons), and five different strains, respectively. These 80 K. pneumoniae isolates belonged to 60 STs, including nine new STs; they were of 70 CTs, yielded 48 K serotypes, 11 O serotypes, and 39 wzc and 51 wzi alleles. Four of the five subjects harbored serotypes K20 and K47, as well as STs ST37, ST101, ST1265, and ST20, which had previously been linked to high-risk K. pneumoniae clones. In total, 25 genes conferring antibiotic resistance and 42 virulence genes were detected among all 80 isolates", "token_count": 532, "char_count": 1810, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [ "ST20", "ST37", "ST1265", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:54:51.441237", "source": { "split": "train_shard_00001", "doc_id": 4683 }, "chunk_id": "train_shard_00001_4683_0", "global_id": 12290 }, { "text": "Plasmids of 15 different types were found among 65 of the isolates. Fecal carriage of individual strains was of short duration: 70 strains were found on a single sampling day only, and 5 strains were isolated in samples collected over two consecutive weeks. Two of the five colonized individuals-working colleagues having meals together-shared identical K. pneumoniae types four times during the study period. Our findings point toward the potential role of food as a reservoir for K. pneumoniae in humans.\n\nFecal Klebsiella pneumoniae Carriage Is Intermittent and of High Clonal Diversity.", "token_count": 162, "char_count": 611, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7363, "quality_score": 0.8681, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:51.879786", "source": { "split": "train_shard_00001", "doc_id": 4683 }, "chunk_id": "train_shard_00001_4683_1", "global_id": 12291 }, { "text": "The emergence of NDM-producing Escherichia coli has considerably threatened human and animal health worldwide. This study describes for the first time in Egypt, the draft genome sequences of emerging NDM-5-producing E. coli from humans and dogs, and investigates genetic relatedness between isolates from both sources. Two E. coli from human urine and seven from environmental clinical samples of dogs exhibited resistance to carbapenems and harbouring blaNDM were subjected to Illumina Miseq whole-genome sequencing (WGS). Assembly and analysis of the reads were performed to identify resistance genes, multilocus sequence types (MLST), plasmid replicon types (Inc) and insertion sequences (IS) of the blaNDM region; core genome MLST (cgMLST) analysis was also performed. Two different NDM alleles were identified; blaNDM-5 in E. coli HR119 from the urine of a healthy person and environmental samples of dogs, and blaNDM-1 in E. coli HR135 from a human patient's urine. Multiple mobilizable resistance genes to different antimicrobial classes were identified except the colistin resistance gene, mcr. E. coli isolates from humans and dogs were assigned to different sequence types (STs). Using cgMLST, dog isolates clustered together with only 1-2 allellic differences; however, human E. coli showed 1,978 different allelles compared with dog isolates. Plasmidfinder results indicated the presence of an IncX3 replicon in blaNDM-5 -producing E. coli; however, blaNDM-1 was linked to IncCoIKP3. Notably, the NDM region (3 Kb) in all isolates from humans and dogs was highly similar with variable flanking sequences that represented different IS elements. This study reports the first emergence of NDM-5-producing E. coli from dogs in Egypt that shared some genetic features with human isolates and could be considered potential public health threats.", "token_count": 507, "char_count": 1917, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5699, "quality_score": 0.7849, "entities": { "genes": [ "HR135", "HR119" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:52.512394", "source": { "split": "train_shard_00001", "doc_id": 4684 }, "chunk_id": "train_shard_00001_4684_0", "global_id": 12292 }, { "text": "Circulation of emerging NDM-5-producing Escherichia coli among humans and dogs in Egypt.", "token_count": 26, "char_count": 88, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:52.875337", "source": { "split": "train_shard_00001", "doc_id": 4684 }, "chunk_id": "train_shard_00001_4684_1", "global_id": 12293 }, { "text": "Bioinformatic analysis of whole genome sequence (WGS) data is emerging as a tool to provide powerful insights for clinical microbiology. We used WGS data to investigate the genetic diversity of clinical isolates of the bacterial pathogen Elizabethkingia anophelis to query the existence of a single-strain outbreak in Ontario, Canada. The Public Health Ontario Laboratory (PHOL) provides reference identification of clinical isolates of bacteria for Ontario and prior to 2016 had not identified E. anophelis . In the wake of the Wisconsin outbreak of 2015-2016 for which a source was never elucidated, the identification of E. anophelis from clinical specimens from five Ontario patients gave reason to question the presence of an outbreak. Genomic comparisons based on core genome multi-locus sequence typing conclusively refuted the existence of an outbreak, since the 5 Ontario isolates were genetically dissimilar, representing at least 3 distinct sub-lineages scattered among a set of 39 previously characterized isolates. Further interrogation of the genomic data revealed multiple antimicrobial resistance genes. Retrospective reidentification via rpoB sequence analysis of 22 clinical isolates of Elizabethkingia spp. collected by PHOL from 2010 to 2018 demonstrated that E. anophelis was isolated from clinical specimens as early as 2010. The uptick in E. anophelis in Ontario was not due to an outbreak or increased incidence of the pathogen, but rather enhanced laboratory identification techniques and improved sequence databases. This study demonstrates the usefulness of WGS analysis as a public health tool to quickly rule out the existence of clonally related case clusters of bacterial pathogens indicative of single-strain outbreaks.\n\nApplication of whole genome sequencing to query a potential outbreak of Elizabethkingia anophelis in Ontario, Canada.", "token_count": 484, "char_count": 1926, "word_count": 271, "semantic_coherence": 1, "information_density": 0.572, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:53.519481", "source": { "split": "train_shard_00001", "doc_id": 4685 }, "chunk_id": "train_shard_00001_4685_0", "global_id": 12294 }, { "text": "Continuous ethanol production by thermotolerant Kluyveromyces marxianus IMB3 immobilized on mineral Kissiris at 45 degrees C", "token_count": 37, "char_count": 124, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:53.879026", "source": { "split": "train_shard_00001", "doc_id": 4686 }, "chunk_id": "train_shard_00001_4686_0", "global_id": 12295 }, { "text": "

Background

People living with human immunodeficiency virus (PLHIV) are exposed to chronic immune dysregulation, even when virus replication is suppressed by antiretroviral therapy (ART). Given the emerging role of the gut microbiome in immunity, we hypothesized that the gut microbiome may be related to the cytokine production capacity of PLHIV.

Methods

To test this hypothesis, we collected metagenomic data from 143 ART-treated PLHIV and assessed the ex vivo production capacity of eight different cytokines [interleukin-1β (IL-1β), IL-6, IL-1Ra, IL-10, IL-17, IL-22, tumor necrosis factor, and interferon-γ] in response to different stimuli. We also characterized CD4+ T-cell counts, HIV reservoir, and other clinical parameters.

Results

Compared with 190 age- and sex-matched controls and a second independent control cohort, PLHIV showed microbial dysbiosis that was correlated with viral reservoir levels (CD4+ T-cell-associated HIV-1 DNA), cytokine production capacity, and sexual behavior. Notably, we identified two genetically different P. copri strains that were enriched in either PLHIV or healthy controls. The control-related strain showed a stronger negative association with cytokine production capacity than the PLHIV-related strain, particularly for Pam3Cys-incuded IL-6 and IL-10 production. The control-related strain is also positively associated with CD4+ T-cell level.

Conclusions

Our findings suggest that modulating the gut microbiome may be a strategy to modulate immune response in PLHIV.\n\nGut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV.", "token_count": 484, "char_count": 1696, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [ "CD4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:54.521414", "source": { "split": "train_shard_00001", "doc_id": 4687 }, "chunk_id": "train_shard_00001_4687_0", "global_id": 12296 }, { "text": "Gastrointestinal (GI) diseases, which include gastrointestinal reflux disease, gastric ulceration, inflammatory bowel disease, and other functional GI disorders, have become prevalent in a large part of the world population. Metabolic syndrome (MS) is cluster of disorders including obesity, hyperglycemia, hyperlipidemia, and hypertension, and is associated with high rate of morbidity and mortality. Gut dysbiosis is one of the contributing factors to the pathogenesis of both GI disorder and MS, and restoration of normal flora can provide a potential protective approach in both these conditions. Bioactive dietary components are known to play a significant role in the maintenance of health and wellness, as they have the potential to modify risk factors for a large number of serious disorders. Different classes of functional dietary components, such as dietary fibers, probiotics, prebiotics, polyunsaturated fatty acids, polyphenols, and spices, possess positive impacts on human health and can be useful as alternative treatments for GI disorders and metabolic dysregulation, as they can modify the risk factors associated with these pathologies. Their regular intake in sufficient amounts also aids in the restoration of normal intestinal flora, resulting in positive regulation of insulin signaling, metabolic pathways and immune responses, and reduction of low-grade chronic inflammation. This review is designed to focus on the health benefits of bioactive dietary components, with the aim of preventing the development or halting the progression of GI disorders and MS through an improvement of the most important risk factors including gut dysbiosis.\n\nGastrointestinal Disorders and Metabolic Syndrome: Dysbiosis as a Key Link and Common Bioactive Dietary Components Useful for their Treatment.", "token_count": 409, "char_count": 1810, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5753, "quality_score": 0.7876, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:55.150030", "source": { "split": "train_shard_00001", "doc_id": 4688 }, "chunk_id": "train_shard_00001_4688_0", "global_id": 12297 }, { "text": "

Background

The prevalence of ampicillin- and/or vancomycin-resistant Enterococcus faecium (AREf and VREf) has increased in hospitalized patients in the Netherlands.

Objectives

To quantify the prevalence, risk factors and co-carriage of AREf and VREf in humans, cats and dogs in the Dutch population.

Methods

From 2014 to 2015, ∼2000 inhabitants of the Netherlands each month were randomly invited to complete a questionnaire and provide a faecal sample. Subjects owning pets were also asked to submit one dog or cat sample. Faecal samples were screened for AREf and VREf. The genetic relatedness of isolates was determined using core genome MLST. Logistic regression analysis was used to determine risk factors.

Results

Of 25 365 subjects, 4721 (18.6%) completed the questionnaire and 1992 (42.2%) human, 277 dog and 118 cat samples were submitted. AREf was detected in 29 human (1.5%), 71 dog (25.6%) and 6 cat (5.1%) samples. VREf (vanA) was detected in one human and one dog. AREf/VREf co-carriage was not detected in 388 paired samples. The use of antibiotics (OR 4.2, 95% CI 1.7-11.2) and proton pump inhibitors (OR 2.7, 95% CI 1.1-6.3) were risk factors for AREf carriage in humans. In dogs, these were the use of antibiotics (OR 2.3, 95% CI 1.1-4.6) and eating raw meat (OR 3.2, 95% CI 1.4-6.6)", "token_count": 466, "char_count": 1330, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:55.790509", "source": { "split": "train_shard_00001", "doc_id": 4689 }, "chunk_id": "train_shard_00001_4689_0", "global_id": 12298 }, { "text": "Core genome MLST-based phylogenetic linkage indicated clonal relatedness for a minority of human (16.7%) and pet AREf isolates (23.8%) in three clusters.

Conclusions

Intestinal carriage with AREf or VREf is rare in the Dutch general population. Although AREf carriage is high in dogs, phylogenetic linkage between human and pet AREf isolates was limited.\n\nIntestinal carriage of ampicillin- and vancomycin-resistant Enterococcus faecium in humans, dogs and cats in the Netherlands.", "token_count": 139, "char_count": 488, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7015, "quality_score": 0.8507, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:56.219326", "source": { "split": "train_shard_00001", "doc_id": 4689 }, "chunk_id": "train_shard_00001_4689_1", "global_id": 12299 }, { "text": "The comparison of microbial genomes found in either freshwater or marine habitats indicated that in some cases ( Synechococcus and Ca . Pelagibacter) there were notable differences in the global isoelectric point (pI) of proteins. We have analysed global metagenomic proteomes and have added more prokaryotes to extend the pI comparison. Without exception, in a set that included archaea and multiple bacterial phyla, the proteome pI distribution varied, with more acidic values in marine and neutral/basic in freshwater microbes. Four pairs of highly related prokaryotes of marine and freshwater origin revealed marked differences manifested mostly in the residues located at the protein surface. This study has also shown that the magnitude of the change depended on protein location (secreted > cytoplasmic > transmembrane) and affected proteins encoded at both core and flexible genome. Our results point to a very extensive variation taking place in microbes when they move from marine (salt-rich) to freshwater habitats. These adaptations would require long evolutionary times to produce changes involving many genes in the core genome. They also point to significant differences in the physiology, probably at the level of membrane functioning, bioenergetics, intracellular ion concentration and pH (or all of them).\n\nMarine-freshwater prokaryotic transitions require extensive changes in the proteome", "token_count": 312, "char_count": 1408, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:57.446327", "source": { "split": "train_shard_00001", "doc_id": 4690 }, "chunk_id": "train_shard_00001_4690_0", "global_id": 12300 }, { "text": "Pseudomonas aeruginosa is a common opportunistic bacterial pathogen that causes a variety of infections in humans. Populations of P. aeruginosa are dominated by common clones that can be isolated from diverse clinical and environmental sources. To determine whether specific clones are associated with corneal infection, we used a portable genotyping microarray system to analyze a set of 63 P. aeruginosa isolates from patients with corneal ulcers (keratitis). We then used population analysis to compare the keratitis isolates to a wider collection of P. aeruginosa from various nonocular sources. We identified various markers in a subpopulation of P. aeruginosa associated with keratitis that were in strong disequilibrium with the wider P. aeruginosa population, including oriC, exoU, katN, unmodified flagellin, and the carriage of common genomic islands. The genome sequencing of a keratitis isolate (39016; representing the dominant serotype O11), which was associated with a prolonged clinical healing time, revealed several genomic islands and prophages within the accessory genome. The PCR amplification screening of all 63 keratitis isolates, however, provided little evidence for the shared carriage of specific prophages or genomic islands between serotypes. P. aeruginosa twitching motility, due to type IV pili, is implicated in corneal virulence. We demonstrated that 46% of the O11 keratitis isolates, including 39016, carry a distinctive pilA, encoding the pilin of type IV pili. Thus, the keratitis isolates were associated with specific characteristics, indicating that a subpopulation of P. aeruginosa is adapted to cause corneal infection.\n\nGenetic characterization indicates that a specific subpopulation of Pseudomonas aeruginosa is associated with keratitis infections.", "token_count": 432, "char_count": 1795, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5451, "quality_score": 0.7725, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:58.078527", "source": { "split": "train_shard_00001", "doc_id": 4691 }, "chunk_id": "train_shard_00001_4691_0", "global_id": 12301 }, { "text": "

Objectives

Klebsiella pneumoniae has emerged worldwide as a major cause of severe infections owing to the rising prevalence of multidrug-resistant strains in clinical settings. This study aimed to investigate the genomic features of pandrug-resistant K. pneumoniae strain KP2 with high colistin and tigecycline resistance isolated from a patient in China.

Methods

The antimicrobial susceptibility of K. pneumoniae KP2 was determined by microdilution broth assay. Whole genomic DNA was extracted and was sequenced using an Illumina HiSeq X10 platform. De novo genome assembly was performed using Unicycler, and the draft genome was annotated using the NCBI Prokaryotic Genome Annotation Pipeline (PGAP). The sequence type (ST), capsular type, antimicrobial resistance and virulence-related genes were identified from the genome sequence. Core genome multilocus sequence typing (cgMLST) analysis was performed by BacWGSTdb server.

Results

Klebsiella pneumoniae KP2 was resistant to all antimicrobial agents tested, including colistin and tigecycline. The genome size was calculated as 5 729 339bp, with 5772 protein-coding sequences and a G+C content of 57.0%. The isolate was assigned to ST11 with capsular serotype KL64. Several antimicrobial resistance genes and virulence genes as well as genomic islands and multiple insertion sequences were identified in the genome sequence. The closest relative of K. pneumoniae KP2 was another isolate from Hangzhou that differed by only 45 cgMLST loci.

Conclusion

The genome sequence data presented in this study can serve as an important reference sequence for further understanding of the antimicrobial resistance mechanisms and virulence potential of this bacterial species.", "token_count": 475, "char_count": 1747, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [ "KP2", "KL64", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:58.723644", "source": { "split": "train_shard_00001", "doc_id": 4692 }, "chunk_id": "train_shard_00001_4692_0", "global_id": 12302 }, { "text": "Unravelling the genome sequence of a pandrug-resistant Klebsiella pneumoniae isolate with sequence type 11 and capsular serotype KL64 from China.", "token_count": 42, "char_count": 145, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [ "KL64" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:59.110619", "source": { "split": "train_shard_00001", "doc_id": 4692 }, "chunk_id": "train_shard_00001_4692_1", "global_id": 12303 }, { "text": "The species Brassica rapa includes several important vegetable crops. The draft reference genome of B. rapa ssp. pekinensis was completed in 2011, and it has since been updated twice. The pangenome with structural variations of 18 B. rapa accessions was published in 2021. Although extensive genomic analysis has been conducted on B. rapa, a comprehensive genome annotation including gene structure, alternative splicing (AS) events, and non-coding genes is still lacking. Therefore, we used the Pacific Biosciences (PacBio) single-molecular long-read technology to improve gene models and produced the annotated genome version 3.5. In total, we obtained 753,041 full-length non-chimeric (FLNC) reads and collapsed these into 92,810 non-redundant consensus isoforms, capturing 48% of the genes annotated in the B. rapa reference genome annotation v3.1. Based on the isoform data, we identified 830 novel protein-coding genes that were missed in previous genome annotations, defined the untranslated regions (UTRs) of 20,340 annotated genes and corrected 886 wrongly spliced genes. We also identified 28,564 AS events and 1,480 long non-coding RNAs (lncRNAs). We produced a relatively complete and high-quality reference transcriptome for B. rapa that can facilitate further functional genomic research.\n\nImproved Reference Genome Annotation of Brassica rapa by Pacific Biosciences RNA Sequencing.", "token_count": 435, "char_count": 1452, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6768, "quality_score": 0.8384, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:54:59.755358", "source": { "split": "train_shard_00001", "doc_id": 4693 }, "chunk_id": "train_shard_00001_4693_0", "global_id": 12304 }, { "text": "The purpose of this work was to evaluate biochemical and serological methods to characterize and identify Candida species from the oral cavity. The strains used were five Candida species previously identified: C. albicans, C. guilliermondii, C. parapsilosis, C. krusei, C. tropicalis, and Kluyveromyces marxianus, as a negative control. The analyses were conducted through the SDS-PAGE associated with statistical analysis using software, chromogenic medium, and CHROMagar Candida (CA), as a differential medium for the isolation and presumptive identification of clinically important yeasts and an enzyme-linked immunoabsorbent assay (ELISA), using antisera produced against antigens from two C. albicans strains. This method enabled the screening of the three Candida species: C. albicans, C. tropicalis, and C. krusei, with 100% of specificity. The ELISA using purified immunoglobulin G showed a high level of cross-reaction against protein extracts of Candida species. The SDS-PAGE method allowed the clustering of species-specific isolates using the Simple Matching coefficient, S(SM) = 1.0. The protein profile analysis by SDS-PAGE increases what is known about the taxonomic relationships among oral yeasts. This methodology showed good reproducibility and allows collection of useful information for numerical analysis on information relevant to clinical application, and epidemiological and systematical studies.\n\nEvaluation of biochemical and serological methods to identify and clustering yeast cells of oral Candida species by CHROMagar test, SDS-PAGE and ELISA.", "token_count": 389, "char_count": 1574, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6037, "quality_score": 0.8018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:00.405621", "source": { "split": "train_shard_00001", "doc_id": 4694 }, "chunk_id": "train_shard_00001_4694_0", "global_id": 12305 }, { "text": "

Background

The extreme conditions of thermal springs constitute a unique aquatic habitat characterized by low nutrient contents and the absence of human impacts on the microbial community composition. Thus, these springs may host phylogenetically novel microorganisms with potential use in biotechnology. With this hypothesis in mind, we examined the microbial composition of four thermal springs of the world-renowned spa town of Karlovy Vary (Carlsbad), Czechia, which differ in their temperature and chemical composition.

Results

Microbial profiling using 16S rRNA gene sequencing revealed the presence of phylogenetically novel taxa at various taxonomic levels, spanning from genera to phyla. Many sequences belonged to novel classes within the phyla Hydrothermae, Altiarchaeota, Verrucomicrobia, and TA06. Cultivation-based methods employing oligotrophic media resulted in the isolation of 44 unique bacterial isolates. These include strains that withstand concentrations of up to 12% NaClw/v in cultivation media or survive a temperature of 100 °C, as well as hitherto uncultured bacterial species belonging to the genera Thermomonas, Paenibacillus, and Cellulomonas. These isolates harbored stress response genes that allow them to thrive in the extreme environment of thermal springs.

Conclusions

Our study is the first to analyze the overall microbial community composition of the renowned Karlovy Vary thermal springs. We provide insight into yet another level of uniqueness of these springs. In addition to their unique health benefits and cultural significance, we demonstrate that these springs harbor phylogenetically distinct microorganisms with unusual life strategies. Our findings open up avenues for future research with the promise of a deeper understanding of the metabolic potential of these microorganisms.\n\nProkaryotes of renowned Karlovy Vary (Carlsbad) thermal springs: phylogenetic and cultivation analysis.", "token_count": 492, "char_count": 1967, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6426, "quality_score": 0.8213, "entities": { "genes": [ "TA06" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:01.083276", "source": { "split": "train_shard_00001", "doc_id": 4695 }, "chunk_id": "train_shard_00001_4695_0", "global_id": 12306 }, { "text": "EnteroBase is an integrated software environment which supports the identification of global population structures within several bacterial genera that include pathogens. Here we provide an overview on how EnteroBase works, what it can do, and its future prospects. EnteroBase has currently assembled more than 300,000 genomes from Illumina short reads from Salmonella, Escherichia, Yersinia, Clostridiodes, Helicobacter, Vibrio , and Moraxella , and genotyped those assemblies by core genome Multilocus Sequence Typing (cgMLST). Hierarchical clustering of cgMLST sequence types allows mapping, a new bacterial strain to predefined population structures at multiple levels of resolution within a few hours after uploading its short reads. Case study 1 illustrates this process for local transmissions of Salmonella enterica serovar Agama between neighboring social groups of badgers and humans. EnteroBase also supports SNP calls from both genomic assemblies and after extraction from metagenomic sequences, as illustrated by case study 2 which summarizes the microevolution of Yersinia pestis over the last 5,000 years of pandemic plague. EnteroBase can also provide a global overview of the genomic diversity within an entire genus, as illustrated by case study 3 which presents a novel, global overview of the population structure of all of the species, subspecies and clades within Escherichia .\n\nThe user’s guide to comparative genomics with EnteroBase, including case studies on transmissions of micro-clades ofSalmonella, the phylogeny of ancient and modernYersinia pestisgenomes, and the core genomic diversity of allEscherichia", "token_count": 411, "char_count": 1657, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6595, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:01.703997", "source": { "split": "train_shard_00001", "doc_id": 4696 }, "chunk_id": "train_shard_00001_4696_0", "global_id": 12307 }, { "text": "

Background

Salmonellosis is one of the most common foodborne diseases worldwide. Although human infection by non-typhoidal Salmonella (NTS) enterica subspecies enterica is associated primarily with a self-limiting diarrhoeal illness, invasive bacterial infections (such as septicaemia, bacteraemia and meningitis) were also reported. Human outbreaks of NTS were reported in several countries all over the world including developing as well as high-income countries. Conventional laboratory methods such as pulsed field gel electrophoresis (PFGE) do not display adequate discrimination and have their limitations in epidemiological surveillance. It is therefore very crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological characterisation and outbreak investigation.

Methods

Here, we used different whole genome sequence (WGS)-based subtyping methods for retrospective investigation of two different outbreaks of Salmonella Typhimurium and Salmonella Dublin that occurred in 2013 in UK and Ireland respectively.

Results

Single nucleotide polymorphism (SNP)-based cluster analysis of Salmonella Typhimurium genomes revealed well supported clades, that were concordant with epidemiologically defined outbreak and confirmed the source of outbreak is due to consumption of contaminated mayonnaise. SNP-analyses of Salmonella Dublin genomes confirmed the outbreak however the source of infection could not be determined", "token_count": 375, "char_count": 1520, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:02.294428", "source": { "split": "train_shard_00001", "doc_id": 4697 }, "chunk_id": "train_shard_00001_4697_0", "global_id": 12308 }, { "text": "The core genome multilocus sequence typing (cgMLST) was discriminatory and separated the outbreak strains of Salmonella Dublin from the non-outbreak strains that were concordant with the epidemiological data however cgMLST could neither discriminate between the outbreak and non-outbreak strains of Salmonella Typhimurium nor confirm that contaminated mayonnaise is the source of infection, On the other hand, other WGS-based subtyping methods including multilocus sequence typing (MLST), ribosomal MLST (rMLST), whole genome MLST (wgMLST), clustered regularly interspaced short palindromic repeats (CRISPRs), prophage sequence profiling, antibiotic resistance profile and plasmid typing methods were less discriminatory and could not confirm the source of the outbreak.

Conclusions

Foodborne salmonellosis is an important concern for public health therefore, it is crucial to use accurate, reliable and highly discriminative subtyping methods for epidemiological surveillance and outbreak investigation. In this study, we showed that SNP-based analyses do not only have the ability to confirm the occurrence of the outbreak but also to provide definitive evidence of the source of the outbreak in real-time.\n\nEvaluation of WGS-subtyping methods for epidemiological surveillance of foodborne salmonellosis.", "token_count": 324, "char_count": 1327, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:02.856479", "source": { "split": "train_shard_00001", "doc_id": 4697 }, "chunk_id": "train_shard_00001_4697_1", "global_id": 12309 }, { "text": "A comparative taxonomic study of Halorubrum distributum, Halorubrum terrestre, Halorubrum arcis and Halorubrum litoreum was carried out using different approaches, 16S rRNA gene sequence analysis, multilocus sequence analysis (MLSA), phylogenomic analysis based on the comparison of the core genome, orthologous average nucleotide identity (OrthoANI), Genome-to-Genome Distance Calculator (GGDC), synteny plots and polar lipid profile (PLP). The MLSA study, using the five concatenated housekeeping genes atpB, EF-2, glnA, ppsA and rpoB', and the phylogenomic analysis based on 1347 core translated gene sequences obtained from their genomes showed that Halorubrum distributum JCM 9100T, Halorubrum terrestre JCM 10247T, Halorubrum arcis JCM 13916T and Halorubrum litoreum JCM 13561T formed a robust cluster, clearly separated from the rest of species of the genus Halorubrum. The OrthoANI and digital DDH values, calculated by the GGDC, showed percentages among Hrr. distributum JCM 9100T, Hrr. terrestre JCM 10247T, Hrr. arcis JCM 13916T and Hrr", "token_count": 474, "char_count": 1246, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:03.509354", "source": { "split": "train_shard_00001", "doc_id": 4698 }, "chunk_id": "train_shard_00001_4698_0", "global_id": 12310 }, { "text": "litoreum JCM 13561T that ranged from 98.1 to 97.5 %, and 84.0 to 78.0 %, respectively, while these values among those strains and the type strains of their most related species of Halorubrum were equal or lower than 90.8 and 41.2 %, respectively. Moreover, degree of synteny across the four genomes was very high, especially between the genomes of Halorubrum litoreum JCM 13561T and Halorubrum arcis JCM 13916T. In addition, the PLP is quite similar among the four strains studied, showing a common pattern typical of the neutrophilic species of the genus Halorubrum. Overall, these data show that Hrr. distributum, Hrr. terrestre, Hrr. arcis and Hrr. litoreum constitute a single species. Thus, the latter three should be considered as later, heterotypic synonyms of Hrr. distributum based on the rules for priority of names. We propose an emended description of Hrr. distributum, including the features of Hrr. terrestre, Hrr. arcis and Hrr. litoreum.", "token_count": 376, "char_count": 1081, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:04.088870", "source": { "split": "train_shard_00001", "doc_id": 4698 }, "chunk_id": "train_shard_00001_4698_1", "global_id": 12311 }, { "text": "Genome-based analyses reveal a synonymy among Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996, Halorubrum terrestre Ventosa et al. 2004, Halorubrum arcis Xu et al. 2007 and Halorubrum litoreum Cui et al. 2007. Emended description of Halorubrum distributum Zvyagintseva and Tarasov 1989; Oren and Ventosa 1996.", "token_count": 180, "char_count": 393, "word_count": 48, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:04.531057", "source": { "split": "train_shard_00001", "doc_id": 4698 }, "chunk_id": "train_shard_00001_4698_2", "global_id": 12312 }, { "text": "The Fifth International Symposium on Fungal Stress (ISFUS) brought together in Brazil many of the leaders in the field of fungal stress responses, from fourteen countries, for four days of outstanding science ranging from basic research to studies with agricultural, medical, industrial, and environmental significance. In addition to the excellent oral and poster presentations, the Symposium organisers ensured that all participants had ample opportunity to engage, socialise, and network to exchange ideas and share research. The conference was enhanced by the world-class venue near Iguazu Falls, probably the greatest natural phenomenon in South America.\n\nCelebrating the fifth edition of the International Symposium on Fungal Stress - ISFUS, a decade after its 2014 debut.", "token_count": 164, "char_count": 778, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7257, "quality_score": 0.8628, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:04.970354", "source": { "split": "train_shard_00001", "doc_id": 4699 }, "chunk_id": "train_shard_00001_4699_0", "global_id": 12313 }, { "text": "

Background

Listeria monocytogenes is an important food-borne pathogen and model organism for host-pathogen interaction, thus representing an invaluable target considering research on the forces governing the evolution of such microbes. The diversity of this species has not been exhaustively explored yet, as previous efforts have focused on analyses of serotypes primarily implicated in human listeriosis. We conducted complete genome sequencing of 11 strains employing 454 GS FLX technology, thereby achieving full coverage of all serotypes including the first complete strains of serotypes 1/2b, 3c, 3b, 4c, 4d, and 4e. These were comparatively analyzed in conjunction with publicly available data and assessed for pathogenicity in the Galleria mellonella insect model.

Results

The species pan-genome of L. monocytogenes is highly stable but open, suggesting an ability to adapt to new niches by generating or including new genetic information. The majority of gene-scale differences represented by the accessory genome resulted from nine hyper variable hotspots, a similar number of different prophages, three transposons (Tn916, Tn554, IS3-like), and two mobilizable islands. Only a subset of strains showed CRISPR/Cas bacteriophage resistance systems of different subtypes, suggesting a supplementary function in maintenance of chromosomal stability. Multiple phylogenetic branches of the genus Listeria imply long common histories of strains of each lineage as revealed by a SNP-based core genome tree highlighting the impact of small mutations for the evolution of species L. monocytogenes. Frequent loss or truncation of genes described to be vital for virulence or pathogenicity was confirmed as a recurring pattern, especially for strains belonging to lineages III and II. New candidate genes implicated in virulence function were predicted based on functional domains and phylogenetic distribution", "token_count": 459, "char_count": 1924, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6903, "quality_score": 0.8451, "entities": { "genes": [ "IS3" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:05.615801", "source": { "split": "train_shard_00001", "doc_id": 4700 }, "chunk_id": "train_shard_00001_4700_0", "global_id": 12314 }, { "text": "A comparative analysis of small regulatory RNA candidates supports observations of a differential distribution of trans-encoded RNA, hinting at a diverse range of adaptations and regulatory impact.

Conclusions

This study determined commonly occurring hyper variable hotspots and mobile elements as primary effectors of quantitative gene-scale evolution of species L. monocytogenes, while gene decay and SNPs seem to represent major factors influencing long-term evolution. The discovery of common and disparately distributed genes considering lineages, serogroups, serotypes and strains of species L. monocytogenes will assist in diagnostic, phylogenetic and functional research, supported by the comparative genomic GECO-LisDB analysis server (http://bioinfo.mikrobio.med.uni-giessen.de/geco2lisdb).\n\nReassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome.", "token_count": 226, "char_count": 972, "word_count": 117, "semantic_coherence": 1, "information_density": 0.735, "quality_score": 0.8675, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:06.084354", "source": { "split": "train_shard_00001", "doc_id": 4700 }, "chunk_id": "train_shard_00001_4700_1", "global_id": 12315 }, { "text": "Eukaryotes are habitats for bacterial organisms where the host colonization and dispersal among individual hosts have consequences for the bacterial ecology and evolution. Vertical symbiont transmission leads to geographic isolation of the microbial population and consequently to genetic isolation of microbiotas from individual hosts. In contrast, the extent of geographic and genetic isolation of horizontally transmitted microbiota is poorly characterized. Here we show that chemosynthetic symbionts of individual Bathymodiolus brooksi mussels constitute genetically isolated populations. The reconstruction of core genome-wide strain sequences from high-resolution metagenomes revealed distinct phylogenetic clades. Nucleotide diversity and strain composition vary along the mussel lifespan and individual hosts show a high degree of genetic isolation. Our results suggest that the uptake of environmental bacteria is a restricted process in B. brooksi , where self-infection of the gill tissue results in serial founder effects during symbiont evolution. We conclude that bacterial colonization dynamics over the host life-cycle is thus an important determinant of population structure and genome evolution of horizontally transmitted symbionts.\n\nHorizontally transmitted symbiont populations in deep-sea mussels are genetically isolated", "token_count": 288, "char_count": 1343, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6229, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:07.012963", "source": { "split": "train_shard_00001", "doc_id": 4701 }, "chunk_id": "train_shard_00001_4701_0", "global_id": 12316 }, { "text": "During the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing Klebsiella pneumoniae (CP-Kpn) from COVID-19 ICU patients and compare them to pre-pandemic populations of CP-Kpn. We analyzed 84 CP-Kpn isolates obtained during the pandemic and 74 CP-Kpn isolates obtained during the pre-pandemic period (2019) by whole genome sequencing, core genome multilocus sequence typing, plasmid reconstruction, and antibiotic susceptibility tests. More CP-Kpn COVID-19 isolates produced OXA-48 (60/84, 71.4%) and VIM-1 (18/84, 21.4%) than KPC (8/84, 9.5%). Fewer pre-pandemic CP-Kpn isolates produced VIM-1 (7/74, 9.5%). Cefiderocol (97.3-100%) and plazomicin (97.5-100%) had the highest antibiotic activity against pandemic and pre-pandemic isolates. Sequence type 307 (ST307) was the most widely distributed ST in both groups. VIM-1-producing isolates belonging to ST307, ST17, ST321 and ST485, (STs infrequently associated to VIM-1) were detected during the COVID-19 period", "token_count": 392, "char_count": 1179, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "ST17", "ST485", "ST321", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:07.630532", "source": { "split": "train_shard_00001", "doc_id": 4702 }, "chunk_id": "train_shard_00001_4702_0", "global_id": 12317 }, { "text": "Class 1 integron Int1-blaVIM-1-aac(6')-1b-dfrB1-aadAI-catB2-qacEΔ1/sul1, found on an IncL plasmid of approximately 70,000 bp, carried blaVIM-1 in ST307, ST17, ST485, and ST321 isolates. Thus, CP-Kpn populations from pandemic and pre-pandemic periods have similarities. However, VIM-1 isolates associated with atypical STs increased during the pandemic, which warrants additional monitoring and surveillance.\n\nCarbapenemase-Producing Klebsiella pneumoniae in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types.", "token_count": 277, "char_count": 673, "word_count": 66, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [ "ST17", "ST485", "ST321", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:08.181565", "source": { "split": "train_shard_00001", "doc_id": 4702 }, "chunk_id": "train_shard_00001_4702_1", "global_id": 12318 }, { "text": "We describe a case of cavitary pneumonia due to Candida dubliniensis along with fungemia due to Candida kefyr in a leukemic patient. This is the first case of C. dubliniensis isolated in our laboratory. The identification was performed by phenotypic and molecular methods such as thermotolerance test, carbohydrate fermentation and polymerase chain reaction.\n\nCould Candida dubliniensis be involved in lung fungus balls?", "token_count": 107, "char_count": 420, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7903, "quality_score": 0.8952, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:08.562955", "source": { "split": "train_shard_00001", "doc_id": 4703 }, "chunk_id": "train_shard_00001_4703_0", "global_id": 12319 }, { "text": "Until the 20th century fungal infections were rather easy cured, and the need of new antifungal drugs was low. However, low choice of antifungal preparations, their toxicity, limited spectrum of action, and ability to produce resistant strains show the need of new effective medicines for systemic fungal diseases in nowadays. Our goal of research was to synthesize new antimicrobial compounds containing three or more pharmacophores in one molecule. The initial 5-substituted-2-methylmercaptothiazolidin-4-ones were subjected to S-demethylation to yield 2-amino-substituted thiazolidinones. Ethacridine, nitrofuran aldehydes and nitrobenzene aldehyde as pharmacophoric amino or aldehyde group having compounds have been used. Antimicrobial (antifungal) activity of the new compounds was screened in vitro in these bacterial cultures: Staphylococcus aureus ATCC 25923, Escherichia coli ATCC 25922, Bacillus subtilis ATCC 6633, Klebsiella pneumoniae ATCC 33499 and fungal cultures: Candida albicans ATCC 60193, Candida glabrata, Candida krusei, Candida kefyr ATCC 8614, Candida tropicalis ATCC 8302, Candida parapsilosis. Results showed that the new compounds were significantly more effective as antimicrobial agents than initial preparation ethacridine. Ethacridine derivatives were not only effective against numerous gram-positive and some gram-negative bacteria, but the spectrum of action has been discovered against fungi. Minimal fungistatic concentration varies in the range 10.0-750 microg/mL and antibacterial concentration is in the range 62.5-1000 microg/mL. Compound 2a having nitrofuryl substituent in the fifth position of tiazolidine cycle was the most active of synthesized ethacridine compounds", "token_count": 512, "char_count": 1712, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:09.194265", "source": { "split": "train_shard_00001", "doc_id": 4704 }, "chunk_id": "train_shard_00001_4704_0", "global_id": 12320 }, { "text": "The obtained results gave the opportunity to separate the perspective group of potential antiinfective compounds.\n\nNew ethacridine derivatives as the potential antifungal and antibacterial preparations.", "token_count": 43, "char_count": 202, "word_count": 25, "semantic_coherence": 1, "information_density": 0.84, "quality_score": 0.92, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:09.556124", "source": { "split": "train_shard_00001", "doc_id": 4704 }, "chunk_id": "train_shard_00001_4704_1", "global_id": 12321 }, { "text": "Hypervirulent Klebsiella pneumoniae (hvKp) is a novel pathotype that has been rarely described in Europe. This study characterizes a hvKp isolate that caused a community-acquired infection. The hypermucoviscous Klebsiella pneumoniae (K. pneumoniae) strain 18-0005 was obtained from a German patient with tonsillopharyngitis in 2017. Antibiotic susceptibility testing was performed and the genome was sequenced by Illumina and Nanopore technology. Whole genome data were analyzed by conducting core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP) analysis. Virulence genes were predicted by applying Kleborate. Phenotypic and whole genome analyses revealed a high similarity of the study isolate 18-0005 to the recently reported antibiotic-susceptible hvKp isolate SB5881 from France and the \"ancestral\" strain Kp52.145; both were assigned to the ST66-K2 lineage. Comparative genomic analysis of the three plasmids showed that the 18-0005 plasmid II differs from SB5881 plasmid II by an additional 3 kb integrated fragment of plasmid I. Our findings demonstrate the genetic flexibility of hvKp and the occurrence of a strain of the clonal group CG66-K2 in Germany. Hence, it emphasizes the need to improve clinical awareness and infection monitoring of hvKp.\n\nHypervirulent Klebsiella pneumoniae of Lineage ST66-K2 Caused Tonsillopharyngitis in a German Patient.", "token_count": 436, "char_count": 1425, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": { "genes": [ "CG66", "SB5881", "ST66" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:10.188625", "source": { "split": "train_shard_00001", "doc_id": 4705 }, "chunk_id": "train_shard_00001_4705_0", "global_id": 12322 }, { "text": "The occurrence of yeasts in dairy products is significant because they can cause spoilage, effect desirable biochemical changes and they may adversely affect public health. While fermentative and spoilage activities of yeasts at elevated temperatures are well known in many food and beverage commodities, little attention has been given to the specific occurrence and significance of yeasts in dairy products at these temperatures. Since yeasts play a substantial role in the spoilage of commercial fruit yoghurts, especially when cold storage practices are neglected, the deterioration of yoghurt samples obtained from the manufacturers were evaluated at different temperatures for a period of 30 days during this study. Total yeast were enumerated, isolated and identified from the yoghurt samples. The highest number of yeast populations, up to 10(5) and 10(6) cfu/g, was found when yoghurts were exposed to elevated temperatures in the range of 25 degrees C, while lower yeast counts (10(3) and 10(4) cfu/g) were obtained from samples kept refrigerated at a temperature of 5 degrees C. Based on the results obtained, the interaction between the yeasts and lactic acid bacteria resulted in a decline in pH values and the stabilization of viable lactic acid bacterial loads. The most prevalent yeast species isolated, included strains of Kluyveromyces marxianus, Saccharomyces cerevisiae, Saccharomyces exiguus andYarrowia lipolytica.\n\nTemperature abuse initiating yeast growth in yoghurt", "token_count": 359, "char_count": 1490, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:10.770780", "source": { "split": "train_shard_00001", "doc_id": 4706 }, "chunk_id": "train_shard_00001_4706_0", "global_id": 12323 }, { "text": "Use of culture medium for distinguishing bacteria and yeast comprises detecting beta-galactosidase, glucuronidase and glucosidase activity/alpha-glucose metabolism by substrate, differentiating micro-organisms by marker. Use of culture medium for distinguishing bacteria and yeast comprises detecting beta-galactosidase, glucuronidase and glucosidase activity/alpha-glucose metabolism by substrate, differentiating micro-organisms by marker. The yeast are Candida albicans , Candida tropicalis, Candida lusitaniae, Candida kefyr , Candida glabrata, Candida krusei,which is resistant to amphotericin B and another group of yeast is non-resistant to amphotericin B or fluconazole. Alternatively, the yeast comprises Candida albicans , Candida tropicalis, Candida glabrata, Candida krusei which is resistant to fluconazole. The antifungal is amphotericin B, fluconazole. The antibiotic is ceftazidime, cloxacilline , combination of ceftriaxone and clavulanic acid, cefpodoxime and Aztreonam. The alpha methyl glucoside metabolism, hexosaminidase enzymatic activity, beta glucosidase activity, beta glucuronidase or beta galactosidase activity, phosphatase activity, tryptophanase/desaminase activity are detected using the culture medium in the presence of an indicator. The bacterias are Enterococcus faecalis, Enterococcus faecium, Enterococcus casseliflavus, Enterococcus gallinarum, Staphylococcus aureus, which is resistant to vancomycin and another group of micro-organism are non-resistant to vancomycin.\n\nMedium for the specific detection of resistant organisms", "token_count": 464, "char_count": 1566, "word_count": 187, "semantic_coherence": 1, "information_density": 0.4652, "quality_score": 0.7326, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:11.440547", "source": { "split": "train_shard_00001", "doc_id": 4707 }, "chunk_id": "train_shard_00001_4707_0", "global_id": 12324 }, { "text": "Bordetella avium (BA) is a respiratory pathogen of particular importance for turkeys. Specific adherence and damage to the respiratory epithelia are crucial steps of the pathogenesis, but knowledge about the mechanisms and the variety of virulence in field strains is limited. We analysed 17 BA field strains regarding their in vitro virulence-associated properties in tracheal organ cultures (TOC) of turkey embryos, and their genetic diversity. The TOC adherence assay indicated that BA field strains differ considerably in their ability to adhere to the tracheal mucosa, while the TOC ciliostasis assay illustrated a high degree of diversity in ciliostatic effects. These two virulence-associated properties were associated with each other in the investigated strains. Three of the investigated strains displayed significantly (P > 0.05) lower in vitro virulence in comparison to other strains. Genetic diversity of BA strains was analysed by core genome multilocus sequence typing (cgMLST). We applied a cgMLST scheme comprising 2667 targets of the reference genome (77.3% of complete genome, BA strain 197N). The results showed a broad genetic diversity in BA field strains but did not demonstrate a correlation between sequence type and virulence-associated properties. The cgMLST analysis revealed that strains with less marked virulence-associated properties had a variety of mutations in the putative filamentous haemagglutinin gene. Likewise, amino acid sequence alignment indicated variations in the protein. The results from our study showed that both adherence and ciliostasis assay can be used for virulence characterization of BA. Variations in the filamentous haemagglutinin protein may be responsible for reduced virulence of BA field strains.\n\nIn vitro characterization and genetic diversity of Bordetella avium field strains.", "token_count": 486, "char_count": 1886, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5414, "quality_score": 0.7707, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:12.111551", "source": { "split": "train_shard_00001", "doc_id": 4708 }, "chunk_id": "train_shard_00001_4708_0", "global_id": 12325 }, { "text": "Infections by multidrug-resistant Gram-negative bacteria are increasingly common, prompting the renewed interest in the use of colistin. Colistin specifically targets Gram-negative bacteria by interacting with the anionic lipid A moieties of lipopolysaccharides, leading to membrane destabilization and cell death. Here, we aimed to uncover the mechanisms of colistin resistance in nine colistin-resistant Escherichia coli strains and one E. albertii strain. These were the only colistin-resistant strains out of 1140 bloodstream Escherichia isolates collected in a tertiary hospital over a ten-year period (2006 - 2015). Core genome phylogenetic analysis showed that each patient was colonised by a unique strain, suggesting that colistin resistance was acquired independently in each strain. All colistin-resistant strains had lipid A that was modified with phosphoethanolamine. In addition, two E. coli strains had hepta-acylated lipid A species, containing an additional palmitate compared to the canonical hexa-acylated E. coli lipid A. One E. coli strain carried the mobile colistin resistance (mcr) gene mcr-1.1 on an IncX4-type plasmid. Through construction of chromosomal transgene integration mutants, we experimentally determined that mutations in basRS , encoding a two-component signal transduction system, contributed to colistin resistance in four strains. We confirmed these observations by reversing the mutations in basRS to the sequences found in reference strains, resulting in loss of colistin resistance. While the mcr -genes have become a widely studied mechanism of colistin resistance in E. coli , sequence variation in basRS is another, potentially more prevalent but relatively underexplored, cause of colistin resistance in this important nosocomial pathogen.

Importance

Multidrug resistance among Gram-negative bacteria has led to the use of colistin as a last-resort drug. The cationic colistin kills Gram-negative bacteria through electrostatic interaction with the anionic lipid A moiety of lipopolysaccharides", "token_count": 513, "char_count": 2051, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:12.814376", "source": { "split": "train_shard_00001", "doc_id": 4709 }, "chunk_id": "train_shard_00001_4709_0", "global_id": 12326 }, { "text": "Due to increased use in clinical and agricultural settings, colistin resistance has recently started to emerge. In this study, we used a combination of whole genome sequence analysis and experimental validation to characterise the mechanisms through which E. coli strains from bloodstream infections can develop colistin resistance. We found no evidence of direct transfer of colistin-resistant isolates between patients. The lipid A of all isolates was modified by the addition of phosphoethanolamine. In four isolates, colistin resistance was experimentally verified to be caused by mutations in the basRS genes, encoding a two-component regulatory system. Our data show that chromosomal mutations are an important cause of colistin resistance among clinical E. coli isolates.\n\nNon-clonal emergence of colistin resistance associated with mutations in the BasRS two-component system in Escherichia coli bloodstream isolates", "token_count": 207, "char_count": 931, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6846, "quality_score": 0.8423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:13.291235", "source": { "split": "train_shard_00001", "doc_id": 4709 }, "chunk_id": "train_shard_00001_4709_1", "global_id": 12327 }, { "text": "Cryptosporidium parvum is a significant pathogen causing gastrointestinal infections in humans and animals. It is spread through ingesting contaminated food and water. Despite its global health significance, generating a C. parvum genome sequence has been challenging for many reasons including cloning and challenging subtelomeric regions. A new, gapless, hybrid, telomere-to-telomere genome assembly was created for C. parvum IOWA II, here termed CpBGF. It reveals 8 chromosomes, a genome size of 9,259,183 bp, and resolves complex subtelomeric regions. To facilitate ease of use and consistency with the literature, the chromosomes have been oriented, and genes in this annotation have been given similar gene IDs as those used in the 2004, C. parvum IOWA II reference genome sequence. The new annotation utilized considerable RNA expression evidence including single-molecule Iso-Seq data; thus, untranslated regions, long noncoding RNAs, and antisense RNAs are annotated. The CpBGF genome assembly serves as a valuable resource for understanding the biology, pathogenesis, and transmission of C. parvum, and it facilitates the development of diagnostics, drugs, and vaccines against cryptosporidiosis.\n\nNew T2T assembly of Cryptosporidium parvum IOWA II annotated with Legacy-Compatible Gene identifiers.", "token_count": 350, "char_count": 1309, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:13.864818", "source": { "split": "train_shard_00001", "doc_id": 4710 }, "chunk_id": "train_shard_00001_4710_0", "global_id": 12328 }, { "text": "Hybrid Shiga toxin-producing Escherichia coli (STEC) and uropathogenic E. coli (UPEC) strains of multilocus sequence type 141 (ST141) cause both urinary tract infections and diarrhea in humans and are phylogenetically positioned between STEC and UPEC strains. We used comparative genomic analysis of 85 temporally and spatially diverse ST141 E. coli strains, including 14 STEC/UPEC hybrids, collected in Germany (n = 13) and the United States (n = 1) to reconstruct their molecular evolution. Whole-genome sequencing data showed that 89% of the ST141 E. coli strains either were STEC/UPEC hybrids or contained a mixture of virulence genes from other pathotypes. Core genome analysis and ancestral reconstruction revealed that the ST141 E. coli strains clustered into two lineages that evolved from a common ancestor in the mid-19th century. The STEC/UPEC hybrid emerged ∼100 years ago by acquiring an stx prophage, which integrated into previously unknown insertion site between rcsB and rcsD, followed by the insertion of a pathogenicity island (PAI) similar to PAI II of UPEC strain 536 (PAI II536-like). The two variants of PAI II536-like were associated with tRNA genes leuX and pheU, respectively. Finally, microevolution within PAI II536-like and acquisition of the enterohemorrhagic E. coli plasmid were observed. Our data suggest that intestinal pathogenic E", "token_count": 521, "char_count": 1493, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6878, "quality_score": 0.8439, "entities": { "genes": [ "ST141" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:14.522494", "source": { "split": "train_shard_00001", "doc_id": 4711 }, "chunk_id": "train_shard_00001_4711_0", "global_id": 12329 }, { "text": "coli (IPEC)/extraintestinal pathogenic E. coli (ExPEC) hybrids are widespread and that selection pressure within the ST141 E. coli population led to the emergence of the STEC/UPEC hybrid as a clinically important subgroup. We hypothesize that ST141 E. coli strains serve as a melting pot for pathogroup conversion between IPEC and ExPEC, contrasting the classical theory of pathogen emergence from nonpathogens and corroborating our recent phenomenon of heteropathogenicity among pathogenic E. coli strains.\n\nOrigin and Evolution of Hybrid Shiga Toxin-Producing and Uropathogenic Escherichia coli Strains of Sequence Type 141.", "token_count": 207, "char_count": 658, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [ "ST141" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:14.984411", "source": { "split": "train_shard_00001", "doc_id": 4711 }, "chunk_id": "train_shard_00001_4711_1", "global_id": 12330 }, { "text": "We report here a sensitive and specific polymerase chain reaction (PCR) detection assay for the pathogenic Candida yeast based on the novel LYS1 [encoding saccharopine dehydrogenase (SDH)] and LYS5 [encoding phosphopantetheinyl transferase (PPTase)] gene sequences of the fungal unique lysine biosynthetic pathway. Both LYS1 and LYS5 DNA-specific PCR primers SG1, SG2 and SG3, SG4, respectively, amplified predicted 483 and 648-bp fragments from Candida albicans genomic DNA but not from other selected fungal, bacterial, or human DNA. The 18S rDNA control primers exhibited positive amplifications in all PCR assays. The LYS1-and LYS5-specific primers strongly amplified C. albicans and Candida tropicalis target sequences; however, the LYS1 primers also weakly amplified fragments from Candida kefyr and Candida lusitaniae DNA. Both sets of primers amplified target sequences from less than 10 pg of serially diluted C. albicans DNA, and the LYS1 specific primers also detected DNA isolated from serially diluted 50 C. albicans cells. The PCR primers reported here are sufficiently sensitive and specific for the potential early detection of Candida infections with no possibility of false positive results from cross-contamination with bacterial or human DNA.\n\nNovel lysine biosynthetic gene sequences (LYS1 and LYS5) used as PCR targets for the detection of the pathogenic Candida yeast.", "token_count": 391, "char_count": 1391, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5792, "quality_score": 0.7896, "entities": { "genes": [ "SG2", "SG1", "LYS1", "SG4", "SG3", "LYS5" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:15.599235", "source": { "split": "train_shard_00001", "doc_id": 4712 }, "chunk_id": "train_shard_00001_4712_0", "global_id": 12331 }, { "text": "Colonization of the infant gut is an important developmental process characterized by high carriage of antimicrobial resistance genes (ARGs) and high abundances of pathobionts. The horizontal transfer of ARGs to pathogenic bacteria represents a major public health concern. However, there is still a paucity of longitudinal studies surveilling ARGs in healthy infant guts at high temporal resolution. Furthermore, we do not yet have a clear view of how temporal variation in ARG carriage relates to the dynamics of specific bacterial populations, as well as community virulence potential. Here, we performed deep shotgun metagenomic sequencing of monthly fecal samples from a cohort of 12 infants, covering the first year of life to interrogate the infant gut microbiome for ARG content. We further relate ARG dynamics to the dynamics of taxa, virulence potential, as well as the potential for ARG mobilization. We identify a core resistome dominated by efflux systems typically associated with Enterobacteriaceae. Overall ARG carriage declined over the first year of life and showed strong contemporaneous correlation with the population dynamics of Proteobacteria. Furthermore, the majority of ARGs could be further mapped to metagenome-assembled genomes (MAGs) classified to this phylum. We were able to assign a large number of ARGs to E. coli by correlating the temporal dynamics of individual genes with species dynamics, and we show that the temporal dynamics of ARGs and virulence factors are highly correlated, suggesting close taxonomic associations between these two gene classes. Finally, we identify ARGs linked with various categories of mobile genetic elements, demonstrating preferential linkage among mobility categories and resistance to different drug classes. While individual variation in ARG carriage is substantial during infancy there is a clear reduction over the first year of life. With few exceptions, ARG abundances closely track the dynamics of pathobionts and community virulence potential. These findings emphasize the potential for development of resistant pathogens in the developing infant gut, and the importance of effective surveillance in order to detect such events.\n\nAntibiotic resistance gene dynamics in the commensal infant gut microbiome over the first year of life.", "token_count": 485, "char_count": 2311, "word_count": 341, "semantic_coherence": 1, "information_density": 0.5572, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:16.247770", "source": { "split": "train_shard_00001", "doc_id": 4713 }, "chunk_id": "train_shard_00001_4713_0", "global_id": 12332 }, { "text": "The emergence of Sin Nombre orthohantavirus, an etiological agent of hantavirus cardiopulmonary syndrome, exacerbates the situation and imposes a heavy financial burden on healthcare organizations. Multidrug-resistant forms of the disease are prevalent, and there is currently no licensed commercial vaccine. Due to the numerous limitations of experimental vaccines, vaccines against various bacterial and viral diseases have developed via computational vaccine design. Several subtractive proteomics, immunoinformatics, docking, and simulation approaches were used in this study to develop a multi-epitope-based vaccine against Sin Nombre orthohantavirus. One possible antigenic protein-the glycoprotein precursor of surface glycoproteins (accession number >AAC42202.1)-was selected as a candidate for B cell-derived T cell epitopes mapping the detailed analysis of the core genome. Among the predicted epitopes, four epitopes (QVDWTKKSST, GLAASPPHL, SSYSYRRKLV, and MESGWSDTA), which were probably antigenic, nonallergenic, nontoxic, and water soluble, were used in the multi-epitope vaccine's construction. The shortlisted epitopes have the potency to cover 99.78% of the world's population, 97.93% of the Chinese population, and 97.36% of the Indian population. The epitopes were connected through AAY linkers and joined with >50S ribosomal adjuvant to enhance their efficacy. The vaccine comprises 182 amino acids with a molecular weight of 19.03770 kDa and an instability index of 26.52, indicating that the protein is stable. A molecular docking study revealed that the vaccine has a good binding affinity with TLR-4 and TLR-8, which is vital for inducing the immune system. Top-1 docked complexes of vaccine- TLR-4 and TLR-8 with the lowest binding energy of -12.52 kc/mol and -5.42 kc/mol, respectively, were considered for molecular dynamic simulation analysis", "token_count": 512, "char_count": 1877, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6783, "quality_score": 0.8391, "entities": { "genes": [ "AAC42202" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:16.899587", "source": { "split": "train_shard_00001", "doc_id": 4714 }, "chunk_id": "train_shard_00001_4714_0", "global_id": 12333 }, { "text": "Furthermore, we predicted that the docked complexes are properly stable throughout simulation time in both normal mode and AMBER-based simulation analysis. The MMGBSA analysis calculated -122.17 and -125.4 net binding energies for the TLR-8- and TLR4-vaccine complexes, respectively, while the MMPBSA analysis estimated -115.63 and -118.19 for the TLR-8- and TLR4-vaccine complex, respectively, confirming that the binding stability with receptors is stable, which is important for inducing a strong response. However, the current work is computation-based, so experimental validation is highly recommended.\n\nIntegrativesubtractive proteomics, immunoinformatics, docking, and simulation approaches reveal candidate vaccine against Sin Nombre orthohantavirus.", "token_count": 189, "char_count": 758, "word_count": 96, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "TLR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:17.340938", "source": { "split": "train_shard_00001", "doc_id": 4714 }, "chunk_id": "train_shard_00001_4714_1", "global_id": 12334 }, { "text": "

Background

The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.

Results

The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.

Conclusions

Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.\n\nResistome expansion in disease-associated human gut microbiomes.", "token_count": 369, "char_count": 1690, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6055, "quality_score": 0.8028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:17.914577", "source": { "split": "train_shard_00001", "doc_id": 4715 }, "chunk_id": "train_shard_00001_4715_0", "global_id": 12335 }, { "text": "Horizontal gene transfer (HGT) is known to promote the spread of genes in bacterial communities, which is of primary importance to human health when these genes provide resistance to antibiotics. Among the main HGT mechanisms, natural transformation stands out as being widespread and encoded by the bacterial core genome. From an evolutionary perspective, transformation is often viewed as a mean to generate genetic diversity and mixing within bacterial populations. However, another recent paradigm proposes that its main evolutionary function would be to cure bacterial genomes from their parasitic mobile genetic elements (MGEs). Here, we propose to combine these two seemingly opposing points of view because MGEs, although costly for bacterial cells, can carry functions that are point-in-time beneficial to bacteria under stressful conditions (e.g. antibiotic resistance genes under antibiotic exposure). Using computational modeling, we show that, in stochastic environments (unpredictable stress exposure), an intermediate transformation rate maximizes bacterial fitness by allowing the reversible integration of MGEs carrying resistance genes but costly for the replication of host cells. By ensuring such reversible genetic diversification (acquisition then removal of MGEs), transformation would be a key mechanism for stabilizing the bacterial genome in the long term, which would explain its striking conservation.\n\nBacterial transformation buffers environmental fluctuations through the reversible integration of mobile genetic elements", "token_count": 300, "char_count": 1552, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6745, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:18.489499", "source": { "split": "train_shard_00001", "doc_id": 4716 }, "chunk_id": "train_shard_00001_4716_0", "global_id": 12336 }, { "text": "Methods and compositions for the production of ethanol from lignocellulosic starting materials are provided herein. Embodiments of the invention provide methods of manipulating the carbon flux of a host cell transformed with plasmids of the invention. Plasmids of the invention may include nucleotides that encode pyruvate decarboxylase. In one embodiment, a strain of the thermotolerant yeast Hansenula polymorpha that has been transformed with plasmids and polynucleotides of the invention is provided.\n\nINCREASED ETHANOL PRODUCTION FROM XYLOSE", "token_count": 137, "char_count": 546, "word_count": 76, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:18.916542", "source": { "split": "train_shard_00001", "doc_id": 4717 }, "chunk_id": "train_shard_00001_4717_0", "global_id": 12337 }, { "text": "Selenium tolerance of yeasts widely varies: the growth of some yeasts can be inhibited by a selenium concentration as low as 10(-4) M, whereas others can grow in the presence of 10(-1) M selenium. Homogeneous yeast taxa are characterized by a certain level of selenium tolerance, and heterogeneous taxa show a variable level of tolerance to selenium. In general, ascomycetous yeasts are more tolerant to selenium than basidiomycetous yeasts. Among the ascomycetous yeasts, the genera Dekkera and Schizosaccharomyces exhibited the lowest and the species Candida maltosa, Hanseniaspora valbyensis, Kluyveromyces marxianus, and Yarrowia lipolytica the highest tolerance to selenium. Among the basidiomycetous yeasts, the genera Bullera, Cryptococcus, and Holtermannia showed the lowest and the species Cryptococcus curvatus, Cr. humicola, and Trichosporon spp. the highest tolerance to selenium. The selenium tolerance of yeasts depends on the composition of the growth medium, in particular, on the presence of sulfate, sulfur-containing amino acids, and glutamine in the medium.\n\n[Selenium tolerance of yeasts].", "token_count": 313, "char_count": 1110, "word_count": 158, "semantic_coherence": 1, "information_density": 0.5506, "quality_score": 0.7753, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:19.473444", "source": { "split": "train_shard_00001", "doc_id": 4718 }, "chunk_id": "train_shard_00001_4718_0", "global_id": 12338 }, { "text": "A new cytosine deaminase gene and protein from Candida kefyr are provided. This protein has increased ability to convert the 5-fluorocytosine prodrug to its toxic form when compared against the E. coli enzyme.\n\nAbstract

Background The Hafnia genus is an opportunistic pathogen that has been implicated in both nosocomial and community-acquired infections. Although Hafnia is fairly often isolated from clinical material, its taxonomy has remained an unsolved riddle, and the involvement and importance of Hafnia in human disease is also uncertain. Here, we used comparative genomic analysis to define the taxonomy of Hafnia, identify species-specific genes that may be the result of ecological and pathogenic specialization, and reveal virulence-related genetic profiles that may contribute to pathogenesis. Results One complete genome sequence and 19 draft genome sequences for Hafnia strains were generated and combined with 27 publicly available genomes. We provided high-resolution typing methods by constructing phylogeny and population structure based on single-copy core genes in combination with whole genome average nucleotide identity to identify two distant Hafnia species (alvei and paralvei) and one mislabeled strain. The open pan-genome and the presence of numerous mobile genetic elements reveal that Hafnia has undergone massive gene rearrangements. Presence of species-specific core genomes associated with metabolism and transport suggests the putative niche differentiation between alvei and paralvei. We also identified possession of diverse virulence-related profiles in both Hafnia species., including the macromolecular secretion system, virulence, and antimicrobial resistance. In the macromolecular system, T1SS, Flagellum 1, Tad pilus and T6SS-1 were conserved in Hafnia, whereas T4SS, T5SS, and other T6SSs exhibited the evolution of diversity. The virulence factors in Hafnia are related to adherence, toxin, iron uptake, stress adaptation, and efflux pump. The identified resistance genes are associated with beta-lactamases and tetracycline. These virulence-related profiles identified at the genomic level provide insights into Hafnia pathogenesis and the differentiation between alvei and paralvei", "token_count": 483, "char_count": 2038, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:20.947812", "source": { "split": "train_shard_00001", "doc_id": 4721 }, "chunk_id": "train_shard_00001_4721_0", "global_id": 12341 }, { "text": "Conclusions Our research using core genome phylogeny and comparative genomics analysis of a larger collection of strains provides a comprehensive view of the taxonomy and species-specific traits between Hafnia species. Deciphering the genome of Hafnia strains possessing a reservoir of macromolecular secretion systems, virulence factors, and resistance genes related to pathogenicity may provide insights into addressing its numerous infections and devising strategies to combat the pathogen.

\n\nComparative genomic analysis of the Hafnia genus reveals an explicit evolutionary relationship between the species alvei and paralvei and provides insights into pathogenicity", "token_count": 142, "char_count": 673, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:21.388107", "source": { "split": "train_shard_00001", "doc_id": 4721 }, "chunk_id": "train_shard_00001_4721_1", "global_id": 12342 }, { "text": "Abstract

Background

The incidence of Clostridioides difficile infection (CDI) has been rising among children, both in the community and hospital setting. The genomic variability and molecular epidemiology of CDI in children, especially with cancer are poorly understood. We aim to evaluate the molecular epidemiology and relatedness of C. difficile isolates among inpatient and outpatient pediatric oncology and stem cell transplant patients (POTP) using whole-genome sequencing (WGS).

Methods

This was a retrospective cohort study of CDI in POTP in 2016. CDI cases were identified by electronic medical record search for positive C. difficile toxin PCR tests. Retrieved residual stool specimens were cultured anaerobically using pre-reduced CCMB-TAL broth (Anaerobe Systems, Inc.), toxin-producing C. difficile isolates were determined using a cell culture cytotoxicity assay with neutralization (TechLab, Inc.), and WGS was performed, followed by core genome MLST (cgMLST). Variability of the isolates was summarized by strain type (ST), and a minimum spanning tree was constructed, defining clusters of genomically related isolates as those with < 7 alleles difference. Plausible epidemiologic links among the closely related strains such as receiving care on the same inpatient unit on the same day or on the same unit but on different days within 8 weeks before CDI were evaluated to identify potential transmission events.

Results

Among 141 CDI episodes in 89 patients; 103 stool samples were cultured, and 101 (98%) isolates were sequenced identifying 23 different strain types in 81 (80%) isolates. 34 (38%) patients had multiple episodes of CDI. 16 clusters of related isolates were identified (figure), 10 (62%) of which involved only multiple specimens from the same patient. For the 6 clusters involving multiple patients, epidemiologic investigation revealed only 2 (33%) potential transmission events.

Conclusion

WGS identified a highly diverse group of C", "token_count": 521, "char_count": 2005, "word_count": 288, "semantic_coherence": 1, "information_density": 0.6424, "quality_score": 0.8212, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:22.017719", "source": { "split": "train_shard_00001", "doc_id": 4722 }, "chunk_id": "train_shard_00001_4722_0", "global_id": 12343 }, { "text": "difficile isolates among POTP with CDI. Although WGS identified clusters of closely related isolates in multiple patients, epidemiologic investigation of shared inpatient exposures identified potential transmission in only two clusters. C. difficile transmission was uncommon.

Disclosures

Randall Hayden, MD, Abbott Molecular: Advisory Board; Quidel: Advisory Board; Roche Diagnostics: Advisory Board.\n\n2368. Molecular Epidemiology of Clostridioides difficile Infections in Pediatric Oncology and Transplant Patients", "token_count": 136, "char_count": 525, "word_count": 63, "semantic_coherence": 1, "information_density": 0.8095, "quality_score": 0.9048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:22.448232", "source": { "split": "train_shard_00001", "doc_id": 4722 }, "chunk_id": "train_shard_00001_4722_1", "global_id": 12344 }, { "text": "The reduction of BOD and production of biomass from acid whey by Kluyveromyces marxianus.", "token_count": 26, "char_count": 89, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:22.806920", "source": { "split": "train_shard_00001", "doc_id": 4723 }, "chunk_id": "train_shard_00001_4723_0", "global_id": 12345 }, { "text": "Abstract

Background

In 2018, an outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB) containing a rare β-lactamase (OXA-72) was detected at Research Medical Center, a 511 bed community hospital in Kansas City, MO. We describe a coordinated effort among hospital infection control personnel and public health to control the outbreak.

Methods

We defined a case as isolation of OXA-72-producing CRAB from any clinical culture collected from a hospitalized patient during 2018. We assessed infection control practices, including adherence to transmission-based precautions and hand hygiene, environmental cleaning and patient transfers. After patients with CRAB were discharged, terminal cleaning was performed using bleach and environmental cultures were collected; rooms were closed to new patients until CRAB was not isolated. Whole-genome sequencing and bioinformatics analyses were performed.

Results

From January through October, CRAB was isolated from clinical cultures among 20 patients; 6 OXA-72-positive cases were identified during June and July. We found practices for cleaning and disinfection of shared medical equipment were not clearly delineated among nursing and environmental services staff and we ensured responsibilities were well defined. W restricted all patients with CRAB to certain medical units in order to limit the spread. In total, 248 environmental cultures were collected; 151 (61%) from inside patient rooms and 97 (39%) from shared medical equipment or surfaces outside patient rooms. Overall, Acintobacter baumannii was isolated from 39 (16%) environmental cultures (21 from inside rooms and 18 from outside rooms); 5 isolates were confirmed to contain OXA-72. Using WGS, we compared 6 clinical and 5 environmental OXA-72 CRAB isolates; all were determined to be genetically related (0–6 single nucleotide polymorphisms, 88.4% core genome) (figure). No additional cases were identified after these interventions.

Conclusion

We identified widespread CRAB environmental contamination, illustrating the challenges of eradicating CRAB from the hospital environment", "token_count": 519, "char_count": 2138, "word_count": 292, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:23.484673", "source": { "split": "train_shard_00001", "doc_id": 4724 }, "chunk_id": "train_shard_00001_4724_0", "global_id": 12346 }, { "text": "We developed a comprehensive approach focusing on infection control, environmental cleaning and culturing, and patient movement to stop the outbreak.

Disclosures

All authors: No reported disclosures.\n\n2458. A comprehensive approach to ending an outbreak of rare OXA-72 producing carbapenem-resistant Acinetobacter baumannii at a Community Hospital, Kansas City, MO, 2018", "token_count": 97, "char_count": 379, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8776, "quality_score": 0.9388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:23.883939", "source": { "split": "train_shard_00001", "doc_id": 4724 }, "chunk_id": "train_shard_00001_4724_1", "global_id": 12347 }, { "text": "Abstract

Background

SOT recipients are an ideal population in which to study the impact of new antibiotics, since they are particularly dependent upon drug activity to clear infections. In 3/15, FDA approved CAZ-AVI, the first new anti-CRE agent to arrive in the clinic. Our objective was to determine whether CAZ-AVI improves short- and long-term outcomes of CRE-infected SOT recipients.

Methods

We performed a retrospective study of SOT recipients infected with CRE since 2012, who were treated with CAZ-AVI or salvage agents for ≥ 3 days.

Results

35 CRE-infected SOT recipients (14 liver, 11 lung, 6 kidney, 3 intestine, 1 heart) with bacteremia (20), pneumonia (11), intra-abdominal abscess (3) and soft-tissue infection/osteomyelitis (1) were enrolled. 16 and 19 patients (pts) were treated with CAZ-AVI and salvage agents, respectively. Types of infection or SOT, APACHE II and McCabe scores did not differ significantly between patients treated with CAZ-AVI or salvage agents. 30- and 90-d mortality rates were significantly lower among SOT recipients treated with CAZ-AVI (0% and 6%, respectively) compared with salvage agents (26% and 37%; P = 0.049 and 0.047). Among patients who survived 90 days, recurrent CRE infections were diagnosed in 53% and 17% of those treated with CAZ-AVI and a salvage regimen, respectively (P = 0.10). Median time from end of therapy for the 1st CRE infection to recurrent infection was 116 days (max 1,242) and 361 days (max 799) for CAZ-AVI and salvage regimens, respectively", "token_count": 488, "char_count": 1543, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:24.573905", "source": { "split": "train_shard_00001", "doc_id": 4725 }, "chunk_id": "train_shard_00001_4725_0", "global_id": 12348 }, { "text": "Survival and recurrence-free survival were greater for treatment with CAZ-AVI and salvage agents, respectively, as measured by Kaplan–Meier (Figures). CAZ-AVI resistance developed in 37% (n = 3) of patients with recurrent infections. Recurrent isolates were genetically indistinguishable from parent isolates by core genome SNP phylogeny (< 15 SNP).

Conclusion

CAZ-AVI significantly reduced short-term mortality among SOT recipients with CRE infections compared with salvage regimens, but was limited by recurrent infections and emergence of resistance. The same strains caused recurrent and initial infections, suggesting that CAZ-AVI did not eliminate CRE from GI sites that serve as sources of recurrence. Optimizing outcomes in SOT recipients with CRE infections will require new agents like CAZ-AVI, and strategies to eliminate long-term colonization.

Disclosures

All authors: No reported disclosures.\n\n2667. Does Ceftazidime–Avibactam (CAZ-AVI) Improve Short- and Long-Term Outcomes Among Solid-Organ Transplant (SOT) Recipients with Carbapenem-Resistant Enterobacteriaceae (CRE) Infections?", "token_count": 313, "char_count": 1115, "word_count": 143, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:25.170402", "source": { "split": "train_shard_00001", "doc_id": 4725 }, "chunk_id": "train_shard_00001_4725_1", "global_id": 12349 }, { "text": "This study aimed to investigate in vitro the probiotic potential of three yeasts strains (BB06, OBT05, and MT07) isolated from agro-food natural sources. Screening was performed, including several functional, technological, and safety aspects of the yeast strains, in comparison to a reference Saccharomyces boulardii, to identify the ones with suitable probiotic attributes in aquaculture. The yeast strains were identified by 5.8S rDNA-ITS region sequencing as Metschnikowia pulcherrima OBT05, Saccharomyces cerevisiae BB06, and Torulaspora delbrueckii MT07. All yeast strains were tolerant to different temperatures, sodium chloride concentrations, and wide pH ranges. S. cerevisiae BB06 showed a strong and broad antagonistic activity. Moreover, the S. cerevisiae strain exhibited a high auto-aggregation ability (92.08 ± 1.49%) and good surface hydrophobicity to hexane as a solvent (53.43%). All of the yeast strains have excellent antioxidant properties (>55%). The high survival rate in the gastrointestinal tract (GIT) can promote yeast isolates as probiotics. All yeast strains presented a resistance pattern to the antibacterial antibiotics. Non-hemolytic activity was detected. Furthermore, freeze-drying with cryoprotective agents maintained a high survival rate of yeast strains, in the range of 74.95−97.85%. According to the results obtained, the S. cerevisiae BB06 strain was found to have valuable probiotic traits.\n\nIn Vitro Assessment of Yeasts Strains with Probiotic Attributes for Aquaculture Use.", "token_count": 429, "char_count": 1526, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [ "BB06", "MT07", "OBT05" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:25.797492", "source": { "split": "train_shard_00001", "doc_id": 4726 }, "chunk_id": "train_shard_00001_4726_0", "global_id": 12350 }, { "text": "

Background

Microarray comparative genomic hybridization (aCGH) evaluates the distribution of genes of sequenced bacterial strains among unsequenced strains of the same or related species. As genomic sequences from multiple strains of the same species become available, multistrain microarrays are designed, containing spots for every unique gene in all sequenced strains. To perform two-color aCGH experiments with multistrain microarrays, the choice of control sample can be the genomic DNA of one strain or a mixture of all the strains used in the array design. This important problem has no universally accepted solution.

Results

We performed a comparative study of the two control sample options with a Streptococcus pneumoniae microarray designed with three fully sequenced strains. We separately hybridized two of these strains (R6 and G54) as test samples using the third strain alone (TIGR4) or a mixture of the three strains as control. We show that for both types of control it is advantageous to analyze spots in separate sets according to their expected control channel signal (5-15% AUC increase). Following this analysis, the use of a mix control leads to higher accuracies (5% increase). This enhanced performance is due to gains in sensitivity (21% increase, p = 0.001) that compensate minor losses in specificity (5% decrease, p = 0.014).

Conclusion

The use of a single strain control increases the error rate in genes that are part of the accessory genome, where more variation across unsequenced strains is expected, further justifying the use of the mix control.\n\nOptimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays.", "token_count": 405, "char_count": 1708, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5968, "quality_score": 0.7984, "entities": { "genes": [ "TIGR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:26.421762", "source": { "split": "train_shard_00001", "doc_id": 4727 }, "chunk_id": "train_shard_00001_4727_0", "global_id": 12351 }, { "text": "Long-term inserted and surgically implanted catheters can be colonised by Candida spp. Candida biofilms in vitro are often resistant to antifungal agents. The aim of this study was to investigate the in vitro activity of micafungin (MFG) against six Candida spp. biofilms on polystyrene (PS) and central venous catheter (CVC) sections. Safranin staining and differential interference contrast microscopy were used to demonstrate biofilm production. MFG activity was determined by the reduction in metabolic activity (%RMA) by tetrazolium reduction assay on both substrates. In vitro, Candida albicans, Candida parapsilosis, Candida glabrata, Candida tropicalis, Candida dubliniensis and Candida kefyr produced mature biofilms on PS and CVC sections. MFG was active against C. kefyr (0.5 microg/mL) and C. glabrata (<0.5 microg/mL) on PS. However, MFG displayed resistance (>16 microg/mL) against C. albicans, C. dubliniensis,C. tropicalis and C. parapsilosis. On CVC disks, MFG was active against C. glabrata (1 microg/mL) as well as C. parapsilosis and C. albicans (<0.5 microg/mL). MFG was resistant (>16 microg/mL) against C. dubliniensis, C. tropicalis and C. kefyr. MFG was active in vitro against all six Candida spp. on both substrates. However, MFG could not reduce the metabolic activity completely even at the highest concentration.\n\nIn vitro effects of micafungin against Candida biofilms on polystyrene and central venous catheter sections.", "token_count": 448, "char_count": 1452, "word_count": 211, "semantic_coherence": 1, "information_density": 0.4976, "quality_score": 0.7488, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:27.058263", "source": { "split": "train_shard_00001", "doc_id": 4728 }, "chunk_id": "train_shard_00001_4728_0", "global_id": 12352 }, { "text": "

Background

The increasing number of infections caused by Escherichia coli resistant to clinically important antibiotics is a global concern for human and animal health. High overall levels of extended-spectrum beta-lactamase (ESBL)-producing and ciprofloxacin-resistant (ciproR) Escherichia coli in livestock are reported in Belgium. This cross-sectional study aimed to genotypically characterize and trace ESBL-and ciproR-E. coli of Belgian food-producing animals.

Methods

A total of 798 fecal samples were collected in a stratified-random sampling design from Belgian broilers and sows. Consequently, 77 ESBL-E. coli and 84 ciproR-E. coli were sequenced using Illumina MiSeq. Minimum inhibitory concentration (MIC) for fluoroquinolones and cephalosporins were determined. Molecular in silico typing, resistance and virulence gene determination, and plasmid identification was performed. Scaffolds harboring ESBL or plasmid-mediated quinolone resistance (PMQR) genes were analyzed to detect mobile genetic elements (MGEs) and plasmid origins. Core genome allelic distances were used to determine genetic relationships among isolates.

Results

A variety of E. coli sequence types (ST) (n = 63), resistance genes and virulence profiles was detected. ST10 was the most frequently encountered ST (8.1%, n = 13). The pandemic multidrug-resistant clone ST131 was not detected. Most farms harbored more than one ESBL type, with bla CTX-M-1 (41.6% of ESBL-E", "token_count": 500, "char_count": 1555, "word_count": 193, "semantic_coherence": 1, "information_density": 0.7565, "quality_score": 0.8782, "entities": { "genes": [ "ST131", "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:27.717294", "source": { "split": "train_shard_00001", "doc_id": 4729 }, "chunk_id": "train_shard_00001_4729_0", "global_id": 12353 }, { "text": "coli) being the most prevalent and bla CTX M-15 (n = 3) being the least prevalent. PMQR genes (15.5%, n = 13) played a limited role in the occurrence of ciproR-E. coli. More importantly, sequential acquisition of mutations in quinolone resistance-determining regions (QRDR) of gyrA and parC led to increasing MICs for fluoroquinolones. GyrA S83L, D87N and ParC S80I mutations were strongly associated with high-level fluoroquinolone resistance. Genetically related isolates identified within the farms or among different farms highlight transmission of resistant E. coli or the presence of a common reservoir. IncI1-I(alpha) replicon type plasmids carried different ESBL genes (bla CTX-M-1, bla CTX-M-32 and bla TEM-52C). In addition, the detection of plasmid replicons with associated insertion sequence (IS) elements and ESBL/PMQR genes in different farms and among several STs (e.g., IncI1-I(alpha)/IncX3) underline that plasmid transmission could be another important contributor to transmission of resistance in these farms.

Conclusion

Our findings reveal a multifaceted narrative of transmission pathways. These findings could be relevant in understanding and battling the problem of antibiotic resistance in farms.\n\nGenetic characterization of ESBL-producing and ciprofloxacin-resistant Escherichia coli from Belgian broilers and pigs.", "token_count": 480, "char_count": 1474, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6902, "quality_score": 0.8451, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:28.363388", "source": { "split": "train_shard_00001", "doc_id": 4729 }, "chunk_id": "train_shard_00001_4729_1", "global_id": 12354 }, { "text": "Pathogenicity islands and plasmids bear genes for pathogenesis of various Escherichia coli pathotypes. Although there is a basic understanding of the contribution of these virulence factors to disease, less is known about variation in regulatory networks in determining disease phenotypes. Here, we dissected a regulatory network directed by the conserved iron homeostasis regulator, ferric uptake regulator (Fur), in uropathogenic E. coli (UPEC) strain CFT073. Comparing anaerobic genome-scale Fur DNA binding with Fur-dependent transcript expression and protein levels of the uropathogen to that of commensal E. coli K-12 strain MG1655 showed that the Fur regulon of the core genome is conserved but also includes genes within the pathogenicity/genetic islands. Unexpectedly, regulons indicative of amino acid limitation and the general stress response were also indirectly activated in the uropathogen fur mutant, suggesting that induction of the Fur regulon increases amino acid demand. Using RpoS levels as a proxy, addition of amino acids mitigated the stress. In addition, iron chelation increased RpoS to the same levels as in the fur mutant. The increased amino acid demand of the fur mutant or iron chelated cells was exacerbated by aerobic conditions, which could be partly explained by the O2-dependent synthesis of the siderophore aerobactin, encoded by an operon within a pathogenicity island. Taken together, these data suggest that in the iron-poor environment of the urinary tract, amino acid availability could play a role in the proliferation of this uropathogen, particularly if there is sufficient O2 to produce aerobactin.IMPORTANCE Host iron restriction is a common mechanism for limiting the growth of pathogens. We compared the regulatory network controlled by Fur in uropathogenic E. coli (UPEC) to that of nonpathogenic E", "token_count": 513, "char_count": 1929, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [ "CFT073", "MG1655" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:29.032411", "source": { "split": "train_shard_00001", "doc_id": 4730 }, "chunk_id": "train_shard_00001_4730_0", "global_id": 12355 }, { "text": "coli K-12 to uncover strategies that pathogenic bacteria use to overcome iron limitation. Although iron homeostasis functions were regulated by Fur in the uropathogen as expected, a surprising finding was the activation of the stringent and general stress responses in the uropathogen fur mutant, which was rescued by amino acid addition. This coordinated global response could be important in controlling growth and survival under nutrient-limiting conditions and during transitions from the nutrient-rich environment of the lower gastrointestinal (GI) tract to the more restrictive environment of the urinary tract. The coupling of the response of iron limitation to increased demand for amino acids could be a critical attribute that sets UPEC apart from other E. coli pathotypes.\n\nTailoring a Global Iron Regulon to a Uropathogen.", "token_count": 199, "char_count": 852, "word_count": 124, "semantic_coherence": 1, "information_density": 0.6855, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:29.479551", "source": { "split": "train_shard_00001", "doc_id": 4730 }, "chunk_id": "train_shard_00001_4730_1", "global_id": 12356 }, { "text": "The production of cellulases on minimal medium in the edible mushroom Agaricus bisporus is regulated by the carbon source: induced by cellulose and repressed by glucose. In order to isolate cellulose-growth specific sequences, a cDNA library from A. bisporus using suppression subtractive hybridization (SSH) was constructed. Northern blot analysis indicated that a high level of enrichment was achieved; 183 clones were isolated. A preliminary screen with cellulose-specific genes of A. bisporus (cel1, cel2, cel3 and cel4) using Southern hybridization resulted in 28 clones to be cel3, and 5 clones were cel2. The remaining 144 clones were sequenced. Partial sequences of the following genes were found: a beta-glucosidase homologue of the blvk gene of Kluyveromyces marxianus; a cellulase homologue of an endoglucanase (avicellase III) of Aspergillus aculeatus, four different xylanases homologue of the xyn genes of different fungi, and one hexose transporter homologue to the hxtA gene of Aspergillus parasiticus. The apparent full-length of two hydrophobins homologue to the abh3 gene of A. bisporus and one histone homologue to the h2a gene of Aspergillus niger were also found. The remaining sequences did not have homology to any known genes.\n\nEfficient isolation of genes differentially expressed on cellulose by suppression subtractive hybridization in Agaricus bisporus.", "token_count": 381, "char_count": 1382, "word_count": 203, "semantic_coherence": 1, "information_density": 0.5961, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:30.052636", "source": { "split": "train_shard_00001", "doc_id": 4731 }, "chunk_id": "train_shard_00001_4731_0", "global_id": 12357 }, { "text": "Dental caries, the most common chronic infectious disease worldwide, has a complex etiology involving the interplay of microbial and host factors that are not completely understood. In this study, the oral microbiome and 38 host cytokines and chemokines were analyzed across 23 children with caries and 24 children with healthy dentition. De novo assembly of metagenomic sequencing obtained 527 metagenome-assembled genomes (MAGs), representing 150 bacterial species. Forty-two of these species had no genomes in public repositories, thereby representing novel taxa. These new genomes greatly expanded the known pangenomes of many oral clades, including the enigmatic Saccharibacteria clades G3 and G6, which had distinct functional repertoires compared to other oral Saccharibacteria. Saccharibacteria are understood to be obligate epibionts, which are dependent on host bacteria. These data suggest that the various Saccharibacteria clades may rely on their hosts for highly distinct metabolic requirements, which would have significant evolutionary and ecological implications. Across the study group, Rothia, Neisseria, and Haemophilus spp. were associated with good dental health, whereas Prevotella spp., Streptococcus mutans, and Human herpesvirus 4 (Epstein-Barr virus [EBV]) were more prevalent in children with caries. Finally, 10 of the host immunological markers were significantly elevated in the caries group, and co-occurrence analysis provided an atlas of potential relationships between microbes and host immunological molecules. Overall, this study illustrated the oral microbiome at an unprecedented resolution and contributed several leads for further study that will increase the understanding of caries pathogenesis and guide therapeutic development.\n\nDeep metagenomics examines the oral microbiome during dental caries, revealing novel taxa and co-occurrences with host molecules.", "token_count": 486, "char_count": 1945, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6718, "quality_score": 0.8359, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:30.697549", "source": { "split": "train_shard_00001", "doc_id": 4732 }, "chunk_id": "train_shard_00001_4732_0", "global_id": 12358 }, { "text": "Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria. We report pan-genomic analysis of eleven species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D and likely is caused by the pressure from the host immune system. This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to changing host environment.\n\nChlamydiapan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction", "token_count": 261, "char_count": 1228, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:31.257089", "source": { "split": "train_shard_00001", "doc_id": 4733 }, "chunk_id": "train_shard_00001_4733_0", "global_id": 12359 }, { "text": "Hypercholesterolemia is a major risk factor for cardiovascular diseases (CVDs). Chemotherapeutic agents for CVDs exhibit several side effects. Specific probiotics with hypocholesterolemic effects can be safe and effective alternatives to chemotherapeutics. Here, we have analyzed and compared the genome of a novel rhizospheric Enterococcus faecium LR13 cholesterol-assimilating probiotic with other probiotic/pathogenic E. faecium strains to discern genetic factors underlying probiotic efficacy and cholesterol-assimilation. Genomic analyses of E. faecium probiotic strains revealed that LR13 and WEFA23 (cholesterol-assimilating probiotics) harbored 21 unique proteins absent in non-cholesterol-assimilating probiotics. Of these, 14 proteins could directly help in cholesterol-assimilation by producing short chain fatty acids, lipid (sterol) transport and membrane stabilization, and bile salt hydrolase activity. This suggests that cholesterol-assimilation is an intrinsic, strain-specific trait exhibited by probiotics with a specific genetic constitution. Moreover, the unique proteins identified in this study can serve as biomarkers for discerning/characterizing cholesterol-assimilating probiotics as novel biotherapeutics against CVDs.\n\nComprehensive genomic analysis of hypocholesterolemic probiotic Enterococcus faecium LR13 reveals unique proteins involved in cholesterol-assimilation.", "token_count": 400, "char_count": 1427, "word_count": 164, "semantic_coherence": 1, "information_density": 0.689, "quality_score": 0.8445, "entities": { "genes": [ "WEFA23", "LR13" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:31.874216", "source": { "split": "train_shard_00001", "doc_id": 4734 }, "chunk_id": "train_shard_00001_4734_0", "global_id": 12360 }, { "text": "Men who have sex with men (MSM), regardless of HIV infection status, have an intestinal microbiome that is compositionally distinct from men who have sex with women (MSW) and women. We recently showed HIV-negative MSM have elevated levels of intestinal CD4+ T cells expressing CCR5, a critical co-receptor for HIV. Whether elevated expression of CCR5 is driven by the altered gut microbiome composition in MSM has not been explored. Here we used in vitro stimulation of gut Lamina Propria Mononuclear Cells (LPMCs) with whole intact microbial cells isolated from stool to demonstrate that fecal bacterial communities (FBCs) from HIV-positive/negative MSM induced higher frequencies of CCR5+ CD4+ T cells compared to FBCs from HIV-negative MSW and women. To identify potential microbial drivers, we related the frequency of CCR5+ CD4+ T cells to the abundance of individual microbial taxa in rectal biopsy of HIV-positive/negative MSM and controls, and Holdemanella biformis was strongly associated with increased frequency of CCR5+ CD4+ T cells. We used in vitro stimulation of gut LPMCs with the type strain of H. biformis, a second strain of H.biformis and an isolate of the closely related Holdemanella porci , cultured from either a HIV-positive or a HIV-negative MSM stool. H. porci elevated the frequency of both CCR5+ CD4+ T cells and the ratio of TNF-α/IL-10 Genomic comparisons of the 3 Holdemanella isolates revealed unique cell wall and capsular components, which may be responsible for their differences in immunogenicity", "token_count": 496, "char_count": 1688, "word_count": 238, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [ "CCR5", "CD4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:32.523189", "source": { "split": "train_shard_00001", "doc_id": 4735 }, "chunk_id": "train_shard_00001_4735_0", "global_id": 12361 }, { "text": "These findings describe a novel mechanism potentially linking intestinal dysbiosis in MSM to HIV transmission and mucosal pathogenesis.\n\nIntestinal microbial communities and Holdemanella isolated from HIV+/- men who have sex with men increase frequencies of lamina propria CCR5+ CD4+ T cells.", "token_count": 93, "char_count": 321, "word_count": 41, "semantic_coherence": 1, "information_density": 0.9268, "quality_score": 0.9634, "entities": { "genes": [ "CCR5", "CD4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:32.899788", "source": { "split": "train_shard_00001", "doc_id": 4735 }, "chunk_id": "train_shard_00001_4735_1", "global_id": 12362 }, { "text": "Macroautophagy (hereafter referred to as autophagy) is a highly conserved catabolic eukaryotic pathway that is critical for stress responses and homeostasis. Atg18, one of the core proteins involved in autophagy, belongs to the PROPPIN family and is composed of seven WD40 repeats. Together with Atg2, Atg18 participates in the elongation of phagophores and the recycling of Atg9 in yeast. Despite extensive studies on the PROPPIN family, the structure of Atg18 from Saccharomyces cerevisiae has not been determined. Here, we report the structure of ScAtg18 at a resolution of 2.8 Å. Based on bioinformatics and structural analysis, we found that the 7AB loop of ScAtg18 is extended in Atg18, in comparison to other members of the PROPPIN family. Genetic analysis revealed that the 7AB loop of ScAtg18 is required for autophagy. Biochemical and biophysical experiments indicated that the 7AB loop of ScAtg18 is critical for interaction with ScAtg2 and the recruitment of ScAtg2 to the autophagy-initiating site. Collectively, our results show that the 7AB loop of ScAtg18 is a new binding site for Atg2 and is of functional importance to autophagy.\n\nThe crystal structure of Atg18 reveals a new binding site for Atg2 in Saccharomyces cerevisiae.", "token_count": 351, "char_count": 1245, "word_count": 195, "semantic_coherence": 1, "information_density": 0.5436, "quality_score": 0.7718, "entities": { "genes": [ "WD40" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:33.476453", "source": { "split": "train_shard_00001", "doc_id": 4736 }, "chunk_id": "train_shard_00001_4736_0", "global_id": 12363 }, { "text": "UDP-galactose 4-epimerase from yeast (Kluyveromyces fragilis) is a homodimer of total molecular mass 150 kDa having possibly one mole of NAD/dimer acting as a cofactor. The molecule could be dissociated and denatured by 8 M urea at pH 7.0 and could be functionally reconstituted after dilution with buffer having extraneous NAD. The unfolded and refolded equilibrium intermediates of the enzyme between 0-8 M urea have been characterized in terms of catalytic activity, NADH like characteristic coenzyme fluorescence, interaction with extrinsic fluorescence probe 1-anilino 8-naphthelene sulphonic acid (ANS), far UV circular dichroism spectra, fluorescence emission spectra of aromatic residues and subunit dissociation. While denaturation monitored by parameters associated with active site region e.g. inactivation and coenzyme fluorescence, were found to be cooperative having delta G between -8.8 to -4.4 kcals/mole, the overall denaturation process in terms of secondary and tertiary structure was however continuous without having a transition point. At 3 M urea a stable dimeric apoenzyme was formed having 65% of native secondary structure which was dissociated to monomer at 6 M urea with 12% of the said structure. The unfolding and refolding pathways involved identical structures except near the final stage of refolding where catalytic activity reappeared.\n\nUDP-galactose 4-epimerase from Kluyveromyces fragilis: equilibrium unfolding studies.", "token_count": 393, "char_count": 1457, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6942, "quality_score": 0.8471, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:34.090838", "source": { "split": "train_shard_00001", "doc_id": 4737 }, "chunk_id": "train_shard_00001_4737_0", "global_id": 12364 }, { "text": "Sporadic Alzheimer's disease (AD) is the most common neurodegenerative disorder with cognitive dysfunction. Remarkably, alteration in the gut microbiome and resultant insulin resistance has been shown to be connected to metabolic syndrome, the crucial risk factor for AD, and also to be implicated in AD pathogenesis. Thus, this study, we assessed the efficiency of probiotics fermentation technology (PFT), a kefir product, in enhancing insulin signaling via modulation of gut microbiota to halt the development of AD. We also compared its effectiveness to that of pioglitazone, an insulin sensitizer that has been confirmed to substantially treat AD. AD was induced in mice by a single injection of intracerebroventricular streptozotocin (STZ; 3 mg/kg). PFT (100, 200, 400 mg/kg) and pioglitazone (30 mg/kg) were administered orally for 3 weeks. Behavioral tests were conducted to assess cognitive function, and hippocampal levels of acetylcholine (Ach) and β-amyloid (Aβ1-42) protein were assessed along with histological examination. Moreover, the expression of the insulin receptor, insulin degrading enzyme (IDE), and the phosphorylated forms of phosphoinositide 3-kinase (PI3K), protein kinase B (Akt), glycogen synthase kinase-3β (GSK-3β), mammalian target of rapamycin (mTOR), and tau were detected. Furthermore, oxidative stress and inflammatory biomarkers were estimated. Treatment with PFT reversed STZ-induced neurodegeneration and cognitive impairment, enhanced hippocampal Ach levels, and reduced Aβ1-42 levels after restoration of IDE activity", "token_count": 459, "char_count": 1581, "word_count": 216, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [ "PI3K" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:34.736224", "source": { "split": "train_shard_00001", "doc_id": 4738 }, "chunk_id": "train_shard_00001_4738_0", "global_id": 12365 }, { "text": "PFT also improved insulin signaling, as evidenced by upregulation of insulin receptor expression and activation of PI3K/Akt signaling with subsequent suppression of GSK-3β and mTOR signaling, which result in the downregulation of hyperphosphorylated tau. Moreover, PFT significantly diminished oxidative stress and inflammation induced by STZ. These potential effects were parallel to those produced by pioglitazone. Therefore, PFT targets multiple mechanisms incorporated in the pathogenesis of AD and hence might be a beneficial therapy for AD.\n\nEnhancement of Insulin/PI3K/Akt Signaling Pathway and Modulation of Gut Microbiome by Probiotics Fermentation Technology, a Kefir Grain Product, in Sporadic Alzheimer's Disease Model in Mice.", "token_count": 192, "char_count": 739, "word_count": 100, "semantic_coherence": 1, "information_density": 0.77, "quality_score": 0.885, "entities": { "genes": [ "PI3K" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:35.183887", "source": { "split": "train_shard_00001", "doc_id": 4738 }, "chunk_id": "train_shard_00001_4738_1", "global_id": 12366 }, { "text": "Enterococcus faecium is a gut commensal of many mammals but is also recognized as a major nosocomial human pathogen, as it is listed on the WHO global priority list of multi-drug resistant organisms. Previous research has suggested that nosocomial strains have multiple zoonotic origins and are only distantly related to those involved in human commensal colonization. Here we present the first comprehensive population-wide joint genomic analysis of hospital, commensal and animal isolates using both short- and long-read sequencing techniques. This enabled us to investigate the population plasmidome, core genome variation and genome architecture in detail, using a combination of machine learning, population genomics and genome-wide co-evolution analysis. We observed a high level of genome plasticity with large-scale inversions and heterogeneous chromosome sizes, collectively painting a high-resolution picture of the adaptive landscape of E. faecium, and identified plasmids as the main indicator for host-specificity. Given the increasing availability of long-read sequencing technologies, our approach could be widely applied to other human and animal pathogen populations to unravel fine-scale mechanisms of their evolution.\n\nGenomes of a major nosocomial pathogenEnterococcus faeciumare shaped by adaptive evolution of the chromosome and plasmidome", "token_count": 304, "char_count": 1368, "word_count": 187, "semantic_coherence": 1, "information_density": 0.7112, "quality_score": 0.8556, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:35.772479", "source": { "split": "train_shard_00001", "doc_id": 4739 }, "chunk_id": "train_shard_00001_4739_0", "global_id": 12367 }, { "text": "Bromate is a byproduct of the ozone disinfection of drinking water. It is a genotoxic carcinogen and causes renal cell tumors in rats. Physicochemical removal of bromate is very difficult, making microbial reduction of bromate to bromide a promising approach to eliminate bromate from water. Rhodococcus sp. Br-6, isolated from soil, can efficiently reduce bromate by using acetate as an electron donor. We determined the draft genome sequence of Rhodococcus sp. Br-6 for the potential practical application of the bromate-reducing bacterium. Core genome phylogeny suggests that the Br-6 strain is most closely related to R. equi. The Br-6 genome contains genes encoding multiple isoforms of diaphorase, previously found to be involved in Br-6-mediated bromate reduction. The genes identified in the present study could be effective targets for experimental studies of microbial bromate reduction in the future.\n\nGenomic Analysis of Rhodococcus sp. Br-6, a Bromate Reducing Bacterium Isolated From Soil in Chiba, Japan.", "token_count": 293, "char_count": 1047, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6447, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:36.351074", "source": { "split": "train_shard_00001", "doc_id": 4740 }, "chunk_id": "train_shard_00001_4740_0", "global_id": 12368 }, { "text": "Abstract

Background

Multidrug-resistant Enterococci are a major cause of nosocomial infections, yet our understanding of how resistance emerges during antibiotic treatment remains incomplete. We performed whole- and complete-genome sequencing of all paired isolates from 11 Enterococcus faecium and 10 Enterococcus faecalis cases that acquired resistance during hospitalization at Mount Sinai Hospital. Comparative and phylogenetic genomic analyses identified novel mechanisms of resistance and heteroresistance.

Methods

2.5 years of electronic health records were analyzed to identify cases of bacteremia that acquired resistance to at least 1 of the 8 antibiotics. Core genome phylogenetic analyses of paired susceptible and resistant isolates was performed to confirm persistent single clone infections. Long read sequencing data, with Illumina error correction, were used to assemble and align complete genomes. Population analysis profile (PAP) assays were performed to assess the prevalence of heteroresistance.

Results

Among the 102 persistent enterococcal bacteremia cases, 57 isolates from 21 cases (20.6%) cases experienced a gain in resistance. Phylogenetic analyses confirmed that 80% of cases had single clone blood infections, with maximum of 138 days separating paired isolates. Known genetic determinants were responsible for emerging linezolid (LIN), vancomycin (VAN), and gentamicin synergy resistance in almost all cases. In 2 instances, emerging daptomycin (DAP) resistance was not accounted for by known resistance determinants. Notably, PAP assays revealed that LIN-, VAN-, and DAP-resistant subclones were present in only a subset of bacteria in clinical isolates. Longitudinal pairwise analyses of complete genomes revealed novel candidate SNPs for DAP resistance, both located in genes involving cell wall metabolism and maintenance, as well as multiplasmid recombination events that led to VAN heteroresistance.

Conclusion

Our study demonstrates the high prevalence of emerging antibiotic resistance during treatment", "token_count": 505, "char_count": 2078, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6462, "quality_score": 0.8231, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:37.052182", "source": { "split": "train_shard_00001", "doc_id": 4741 }, "chunk_id": "train_shard_00001_4741_0", "global_id": 12369 }, { "text": "We find previously unreported single and structural genomic events that contribute rapid adaptation to antibiotic treatment.

Disclosures

All authors: No reported disclosures.\n\n2561. Using Whole Genome Sequencing to Assess the Emergence of Antibiotic Resistance During Treatment of Enterococcus faecium and Enterococcus faecalis Bacteremia at Mount Sinai Hospital", "token_count": 98, "char_count": 371, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8936, "quality_score": 0.9468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:37.443048", "source": { "split": "train_shard_00001", "doc_id": 4741 }, "chunk_id": "train_shard_00001_4741_1", "global_id": 12370 }, { "text": "Evidence suggests many marine bacteria are cosmopolitan, with widespread but sparse strains poised to seed abundant populations under conducive growth conditions. However, studies supporting this \"microbial seed bank\" hypothesis have analyzed taxonomic marker genes rather than whole genomes/metagenomes, leaving open the possibility that disparate ocean regions harbor endemic gene content. The Red Sea is isolated geographically from the rest of the ocean and has a combination of high irradiance, high temperature, and high salinity that is unique among the oceans; we therefore asked whether it harbors endemic gene content. We sequenced and assembled single-cell genomes of 21 SAR11 (subclades Ia, Ib, Id, and II) and 5 Prochlorococcus (ecotype HLII) samples from the Red Sea and combined them with globally sourced reference genomes to cluster genes into ortholog groups (OGs). Ordination of OG composition could distinguish clades, including phylogenetically cryptic Prochlorococcus ecotypes LLII and LLIII. Compared with reference genomes, 1% of Prochlorococcus and 17% of SAR11 OGs were unique to the Red Sea genomes (RS-OGs). Most (83%) RS-OGs had no annotated function, but 65% of RS-OGs were expressed in diel Red Sea metatranscriptomes, suggesting they are functional. Searching Tara Oceans metagenomes, RS-OGs were as likely to be found as non-RS-OGs; nevertheless, Red Sea and other warm samples could be distinguished from cooler samples using the relative abundances of OGs. The results suggest that the prevalence of OGs in these surface ocean bacteria is largely cosmopolitan, with differences in population metagenomes manifested by differences in relative abundance rather than complete presence/absence of OGs.IMPORTANCE Studies have shown that as we sequence seawater from a selected environment deeper and deeper, we approach finding every bacterial taxon known for the ocean as a whole", "token_count": 500, "char_count": 1945, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6487, "quality_score": 0.8244, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:38.104726", "source": { "split": "train_shard_00001", "doc_id": 4742 }, "chunk_id": "train_shard_00001_4742_0", "global_id": 12371 }, { "text": "However, such studies have focused on taxonomic marker genes rather than on whole genomes, raising the possibility that the lack of endemism results from the method of investigation. We took a geographically isolated water body, the Red Sea, and sequenced single cells from it. We compared those single-cell genomes to available genomes from around the ocean and to ocean-spanning metagenomes. We showed that gene ortholog groups found in Red Sea genomes but not in other genomes are nevertheless common across global ocean metagenomes. These results suggest that Baas Becking's hypothesis \"everything is everywhere, but the environment selects\" also applies to gene ortholog groups. This widely dispersed functional diversity may give oceanic microbial communities the functional capacity to respond rapidly to changing conditions.\n\nRed Sea SAR11 and Prochlorococcus Single-Cell Genomes Reflect Globally Distributed Pangenomes.", "token_count": 205, "char_count": 935, "word_count": 133, "semantic_coherence": 1, "information_density": 0.7293, "quality_score": 0.8647, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:38.567771", "source": { "split": "train_shard_00001", "doc_id": 4742 }, "chunk_id": "train_shard_00001_4742_1", "global_id": 12372 }, { "text": "

Objectives

To determine the molecular characteristics of a sequence type 338 community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) strain and the relationship among MRSA strains from various lineages and areas.

Methods

Whole-genome sequencing, genomic comparison, antimicrobial susceptibility testing, and hemolysis analysis were performed to identify the resistance determinants and virulence factors of strain ZY05 and the relationships among CC59 clones.

Results

MRSA strain ZY05 was resistant to tetracycline, erythromycin, and clindamycin, and the resistance genes erm(B) and tet(K) were detected in the genome. ZY05 harbors the genomic islands νSaα, νSaβ, νSaγ, and ΦSa2, the pathogenicity island νSa1, and virulence factors such as Panton-Valentine leukocidin, phenol-soluble modulins, alpha-hemolysin, enterotoxin B, enterotoxin K, and enterotoxin Q, which are the same as those present in ST59 strains. In addition, the virulence potential of ST338 did not differ from that of ST59. This strain contains the staphylococcal cassette chromosome mec (SCCmec) type VT, a distinct SCCmec type previously reported from Taiwan. The results of core genome multilocus sequence typing (cgMLST) analysis showed that the gene distances between ST59 and ST338 were close among CC59 isolates, while strains from Taiwan were identical to isolates from the Chinese mainland with respect to these two sequence types.

Conclusions

The ST338 strain ZY05, which has a close genetic relationship to ST59 strains, is multidrug-resistant and highly virulent. Strains of two identical lineages, ST59 and ST338, from Taiwan and the Chinese mainland may have the same genetic background.", "token_count": 508, "char_count": 1728, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6087, "quality_score": 0.8043, "entities": { "genes": [ "ZY05", "ST59", "ST338", "CC59" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:39.227063", "source": { "split": "train_shard_00001", "doc_id": 4743 }, "chunk_id": "train_shard_00001_4743_0", "global_id": 12373 }, { "text": "Characterization of a community-acquired methicillin-resistant sequence type 338 Staphylococcus aureus strain containing a staphylococcal cassette chromosome mec type VT.", "token_count": 57, "char_count": 181, "word_count": 19, "semantic_coherence": 1, "information_density": 0.8947, "quality_score": 0.9474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:39.587407", "source": { "split": "train_shard_00001", "doc_id": 4743 }, "chunk_id": "train_shard_00001_4743_1", "global_id": 12374 }, { "text": "

Introduction

Streptococcus pneumoniae is a human pathobiont that asymptomatically colonizes the upper respiratory tract but can cause severe diseases such as pneumonia, sepsis, and meningitis, as well as non-invasive infections like otitis media and sinusitis. It thrives in the nutrient-limited environment of the nasopharynx and has evolved mechanisms to manage host-induced stress and regulate protein levels accordingly.

Methods

To investigate the molecular biology of S. pneumoniae under in vitro and infection-relevant conditions, a suitable cultivation medium is essential for reproducible experiments. We, therefore optimized a chemically defined minimal medium that mimics the nutrient-limited conditions of the human nasopharynx. This medium was used to cultivate clinical isolates and other streptococcal species for proteomic analysis.

Result

The optimized medium enhanced growth and shortened the lag phase of S. pneumoniae and related species. Using this medium, we analyzed the global proteome of the pneumococcal colonizing strain EF3030 during its transition from early to late logarithmic growth phase. Distinct changes in protein abundance were observed in functional categories such as metabolism, amino acid synthesis, natural competence, RNA and cell wall synthesis, protein degradation, and stress responses. Notably, proteins involved in DNA uptake and processing-such as choline-binding protein CbpD, competence factors ComGA and ComEA, and ssDNA-binding proteins Dpr and DprA-were more abundant in the late log phase.

Discussion

These findings highlight dynamic proteomic changes associated with pneumococcal adaptation to nutrient-limited conditions and provide insights into the biology of strain EF3030 during colonization. The optimized medium offers a reproducible platform for studying pneumococcal physiology and pathogenesis under defined conditions.", "token_count": 477, "char_count": 1934, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [ "EF3030" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:40.235255", "source": { "split": "train_shard_00001", "doc_id": 4744 }, "chunk_id": "train_shard_00001_4744_0", "global_id": 12375 }, { "text": "The global proteome of <i>Streptococcus pneumoniae</i> EF3030 under nutrient-defined <i>in vitro</i> conditions.", "token_count": 59, "char_count": 136, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "EF3030" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:40.591623", "source": { "split": "train_shard_00001", "doc_id": 4744 }, "chunk_id": "train_shard_00001_4744_1", "global_id": 12376 }, { "text": "

Background

Enterococcus faecalis is widely studied as a common gut commensal and a nosocomial pathogen. In fact, Enterococcus faecalis is ubiquitous in nature, and it has been isolated from various niches, including the gastrointestinal tract, faeces, blood, urine, water, and fermented foods (such as dairy products). In order to elucidate the role of habitat in shaping the genome of Enterococcus faecalis, we performed a comparative genomic analysis of 78 strains of various origins.

Results

Although no correlation was found between the strain isolation habitat and the phylogeny of Enterococcus faecalis from our whole genome-based phylogenetic analysis, our results revealed some environment-associated features in the analysed Enterococcus faecalis genomes. Significant differences were found in the genome size and the number of predicted open reading frames (ORFs) between strains originated from different environments. In general, strains from water sources had the smallest genome size and the least number of predicted ORFs. We also identified 293 environment-specific genes, some of which might link to the adaptive strategies for survival in particular environments. In addition, the number of antibiotic resistance genes was significantly different between strains isolated from dairy products, water, and blood. Strains isolated from blood had the largest number of antibiotic resistance genes.

Conclusion

These findings improve our understanding of the role of habitat in shaping the genomes of Enterococcus faecalis.\n\nComparative genomic analysis of Enterococcus faecalis: insights into their environmental adaptations.", "token_count": 394, "char_count": 1660, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5733, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:41.209595", "source": { "split": "train_shard_00001", "doc_id": 4745 }, "chunk_id": "train_shard_00001_4745_0", "global_id": 12377 }, { "text": "

Background

Bordetella bronchiseptica (B. bronchiseptica), as an opportunistic pathogen, can cause respiratory diseases in a variety of animals, including humans. In additional to being involved in porcine atrophic rhinitis through coinfection with Pasteurella multocida, B. bronchiseptica is associated with porcine respiratory disease complex (PRDC). While there are genomic data available from different host species, little is known about B. bronchiseptica isolates from pig lungs, especially from lungs characterized as having PRDC.

Results

A total of five B. bronchiseptica isolates were identified from pig lungs characterized as PRDC. The draft genomes of these strains were generated. In comparison with the other reported genomes, these five isolates showed the similar general characteristic including G+C content, rRNAs/tRNA, and clusters of orthologous groups of proteins (COGs). Phylogenetic analysis of all B. Bronchiseptica isolates of different species available at GenBank based on core genome multilocus sequence typing (cgMLST) classified them into two genogroups. All five isolates from this study, with the other isolates from pigs, were placed into a subclade of genogroup I consisting of only mammalian isolates. By contrast, genogroup II contained the isolates from an avian species (turkey) and some mammals (human and dog). Moreover, genome annotation revealed the presence of antibiotic resistance genes and virulence genes among these five genomes, consistent with the similarity and variety in genomic traits. Finally, comparative analysis of insertion sequence (IS) and prophages in five genomes further showed the similarity and variety in genomic characteristic.

Conclusions

This is the first study to provide comparative genomics of B. bronchiseptica strains from pig lungs characterized as having PRDC. Importantly, the findings presented in this study reveal novel genomic characteristic of B. bronchiseptica, which should provide insightful information on genome evolution.", "token_count": 486, "char_count": 2031, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5797, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:41.854063", "source": { "split": "train_shard_00001", "doc_id": 4746 }, "chunk_id": "train_shard_00001_4746_0", "global_id": 12378 }, { "text": "Comparative genomic analysis of Bordetella bronchiseptica isolates from the lungs of pigs with porcine respiratory disease complex (PRDC).", "token_count": 36, "char_count": 138, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:42.214696", "source": { "split": "train_shard_00001", "doc_id": 4746 }, "chunk_id": "train_shard_00001_4746_1", "global_id": 12379 }, { "text": "

Objective/background

Mycobacterium africanum (MAF) remains an important TB causing pathogen in West Africa; however, little is known about its population structure and actual diversity which may have implications for diagnostics and vaccines. We carried out comparative genomics analysis of candidate Mycobacterium tuberculosis (MTB) and MAF using whole genome sequencing.

Methods

Clinical MTB complex strains (n=187) comprising L4 (n=22), L5 (n=126), and L6 (n=39) isolated over 8years from Ghana were whole genome sequenced. The reads were mapped onto a reference genome for phylogenetic and functional genomics analysis. A maximum likelihood tree with 100 bootstraps was constructed from the single nucleotide polymorphisms (SNPs) found using RAxML and clustered with hierBAPS. A total of 147 (18 L4, 36 L6, and 93 L5) of the genomes were de novo assembled and annotated for comparative pangenome analysis using Roary.

Results

The population structure of MAF revealed at least five clusters of L5 as compared to three for L6. We also identified a group of three multi-drug-resistants (MDRs) within a single cluster of L5 strains from Southern Ghana isolated in 2013. Among the global collection of MTB complex, there were four Ghana-specific L5 clusters of which one (L5.1.1) had traits of clonal expansion. From the 5947pan genes extracted from the collection, 3215 (54.1%) were core to all the 147 genomes whereas 719 (12.1%) were found in single genomes. Most of the variable genes were PE-PGRS/PPE (1,281) duplicates of other genes (431). The genome degradation was more pronounced in Lineages 4 and 6 as compared to Lineage 5. We identified the absence of some unique genes among specific lineages and/or clades with possible clinical implications", "token_count": 515, "char_count": 1777, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:42.846410", "source": { "split": "train_shard_00001", "doc_id": 4747 }, "chunk_id": "train_shard_00001_4747_0", "global_id": 12380 }, { "text": "For example, mpt64 and mlaD encoding respectively an immunogenic protein and a mammalian cell entry protein were missing from all L6 genomes. In addition, all L5 strains had an amino acid substitution I43N within the mpt64 gene. Analysis of SNPs within some genes encoding proteins for substrate metabolism, ion transport and secretory systems showed higher proportion of SNPs among L6 compared to L5 and L4. We also identified a number of lineage/sublineage specific SNPs and indels that may be utilized in rapid PCR based genotyping of MTB complex.

Conclusion

This work emphasizes on the possibility that the mpt64-based rapid diagnostic kit would not be effective in MAF endemic settings. More mutations in ESAT-6 secretory system of MAF compared to MTB sensu stricto can affect efficacy of ESAT-6-based vaccines in the future.\n\nThe First population structure and comparative genomics analysis of Mycobacterium africanum strains from Ghana reveals higher diversity of Lineage 5.", "token_count": 254, "char_count": 988, "word_count": 149, "semantic_coherence": 1, "information_density": 0.7047, "quality_score": 0.8523, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:43.344136", "source": { "split": "train_shard_00001", "doc_id": 4747 }, "chunk_id": "train_shard_00001_4747_1", "global_id": 12381 }, { "text": "The genera Proteus and Cosenzaea are closely related members of the family Morganellaceae. The genus Cosenzaea consists of the species Cosenzaea myxofaciens originally separated from the genus Proteus by rpoB gene analysis. Due to the high similarity of the 16S rRNA genes between species of both genera, the taxonomic status is here re-evaluated by a genome-based approach. Based on a core genome phylogeny and genome relatedness indices, it is shown that the taxonomy and nomenclature given for the basonym Proteus myxofaciens is more appropriate. Therefore, we propose to use this name in preference. Furthermore, the species status of Proteus terrae and Proteus cibarius was reassessed. Both species are related at subspecies level by digital DNA-DNA hybridization (dDDH) analysis. Additionally, average amino acid identity (AAI) and average nucleotide identity (ANI) do not support a separate species status, and therefore it is proposed to classify P. cibarius as a subspecies of P. terrae. Consequently, both species are being renamed Proteus terrae subsp. cibarius subsp. nov. and Proteus terrae subsp. terrae subsp. nov., respectively. The genome relatedness indices revealed a close relationship of the Proteus genomospecies 5 with P. terrae subsp. terrae. Thus, it has been assigned to the same subspecies.", "token_count": 446, "char_count": 1450, "word_count": 198, "semantic_coherence": 1, "information_density": 0.6162, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:43.970028", "source": { "split": "train_shard_00001", "doc_id": 4748 }, "chunk_id": "train_shard_00001_4748_0", "global_id": 12382 }, { "text": "Genome-based phylogeny of the genera Proteus and Cosenzaea and description of Proteus terrae subsp. terrae subsp. nov. and Proteus terrae subsp. cibarius subsp. nov.", "token_count": 88, "char_count": 207, "word_count": 24, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:44.347222", "source": { "split": "train_shard_00001", "doc_id": 4748 }, "chunk_id": "train_shard_00001_4748_1", "global_id": 12383 }, { "text": "

Background

The predominant model for bacterial pandemics is the emergence of a virulent variant that diversifies as it spreads in human populations. We investigated a 40-year meningococcal disease pandemic caused by the hyper-invasive ET-5/ST-32 complex.

Methods

A global collection of Neisseria meningitidis isolates dating from 1969 to 2008 was whole genome sequenced (WGS) and analysed using a gene-by-gene approach at http://pubmlst.org/neisseria.

Findings

Analysis of WGS data identified a 'Lineage 5 pan genome' of 1940 genes, 1752 (92%) of which were present in all isolates (Lineage 5 'core genome'). Genetic diversity, which was mostly generated by horizontal gene transfer, was unevenly distributed in the genome; however, genealogical analysis of diverse and conserved core genes, accessory genes, and antigen encoding genes, robustly identified a star phylogeny with a number of sub-lineages. Most European and American isolates belonged to one of two closely related sub-lineages, which had diversified before the identification of the pandemic in the 1970s. A third, genetically more diverse sub-lineage, was associated with Asian isolates. Several isolates had acquired DNA from the related gonococcus.

Interpretation

These data were inconsistent with a single point of origin followed by pandemic spread, rather suggesting that the sub-lineages had diversified and spread by asymptomatic transmission, with multiple distinct strains causing localised hyperendemic outbreaks.\n\nGenomic Analysis of the Evolution and Global Spread of Hyper-invasive Meningococcal Lineage 5.", "token_count": 437, "char_count": 1622, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6744, "quality_score": 0.8372, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:44.976859", "source": { "split": "train_shard_00001", "doc_id": 4749 }, "chunk_id": "train_shard_00001_4749_0", "global_id": 12384 }, { "text": "

Background

Carbapenem-resistant Enterobacterales (CRE) are highly concerning MDR pathogens. Horizontal transfer of broad-host-range IncN plasmids may contribute to the dissemination of the Klebsiella pneumoniae carbapenemase (KPC), spreading carbapenem resistance among unrelated bacteria. However, the population structure and genetic diversity of IncN plasmids has not been fully elucidated.

Objectives

We reconstructed blaKPC-harbouring IncN plasmid genomes to characterize shared gene content, structural variability, and putative horizontal transfer within and across patients and diverse bacterial clones.

Methods

We performed short- and long-read sequencing and hybrid assembly on 45 CRE isolates with blaKPC-harbouring IncN plasmids. Eight serial isolates from two patients were included to assess intra-patient plasmid dynamics. Comparative genomic analysis was performed to assess structural and sequence similarity across plasmids. Within IncN sublineages defined by plasmid MLST and kmer-based clustering, phylogenetic analysis was used to identify closely related plasmids.

Results

Comparative analysis of IncN plasmid genomes revealed substantial heterogeneity including large rearrangements in serial patient plasmids and differences in structure and content across plasmid clusters. Within plasmid sublineages, core genome content and resistance gene regions were largely conserved. Closely related plasmids (≤1 SNP) were found in highly diverse isolates, including ten pST6 plasmids found in eight bacterial clones from three different species.

Conclusions

Genomic analysis of blaKPC-harbouring IncN plasmids revealed the presence of several distinct sublineages as well as substantial host diversity within plasmid clusters suggestive of frequent mobilization. This study reveals complex plasmid dynamics within a single plasmid family, highlighting the challenge of tracking plasmid-mediated transmission of blaKPC in clinical settings.", "token_count": 485, "char_count": 1991, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6208, "quality_score": 0.8104, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:45.622163", "source": { "split": "train_shard_00001", "doc_id": 4750 }, "chunk_id": "train_shard_00001_4750_0", "global_id": 12385 }, { "text": "Population structure of blaKPC-harbouring IncN plasmids at a New York City medical centre and evidence for multi-species horizontal transmission.", "token_count": 34, "char_count": 145, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:45.976420", "source": { "split": "train_shard_00001", "doc_id": 4750 }, "chunk_id": "train_shard_00001_4750_1", "global_id": 12386 }, { "text": "Acute hepatopancreatic necrosis disease (AHPND) is an emerging penaeid shrimp disease caused by Vibrio parahaemolyticus. Although V. parahaemolyticus has been isolated and sequenced from several Asia countries, the epidemiological links among the AHPND outbreaks in different locations remain unclear. In this study, we sequenced the genomes of nine strains isolated in China between 2014 and 2016 from four sampling sites in three provinces. Analysis of single nucleotide polymorphisms (SNPs) among the nine isolates yielded an average of 35,519 SNPs per isolate, ranging from 35,001 SNPs to 35,889 SNPs relative to the reference genome FDA_R31. To capture the genetic diversity of V. parahaemolyticus in Asia and Mexico, 93 published genomes were included in the analysis. Phylogenetic analysis divided the 102 isolates into 5 clades from I to V, with the majority belonging to Clade I and Clade II. There were at least 12 independent AHPND related clones. The results indicated that the clones recovered from AHPND affected shrimps in Asia were genomically distinct in various locations and there are no epidemiological links between Asian and Mexico outbreaks. Core genome analysis of pVA-1-like plasmid sequences from V. parahaemolyticus revealed that the AHPND-associated plasmids were also genetically diverse. Homology analysis of the publicly available microbial genomes showed that the conjugative transfer gene clusters of the plasmids in AHPND-causing strains were found in 27 V. parahaemolyticus strains and several other Vibrio sp. from 10 countries including five strains isolated prior to the first identification of AHPND outbreak, indicating that the backbone of AHPND- associated plasmid was widely distributed around the globe", "token_count": 491, "char_count": 1788, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6187, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:47.011362", "source": { "split": "train_shard_00001", "doc_id": 4751 }, "chunk_id": "train_shard_00001_4751_0", "global_id": 12387 }, { "text": "In conclusion, at least 11 origins of AHPND outbreaks were identified; as AHPND-causing plasmid is widely distributed globally, prevention strategies for AHPND need to focus on microbial management in the aquaculture system and establishing ecological friendly aquaculture practices instead of detection of plasmid alone. However, more strains from other Asia countries as well as Mexico need to be included for whole genome sequencing (WGS) for reconstruction of the global transmission and the spread patterns of AHPND.\n\nDelineating the Origins of Vibrio parahaemolyticus Isolated from Outbreaks of Acute Hepatopancreatic Necrosis Disease in Asia by the Use of Whole Genome Sequencing.", "token_count": 176, "char_count": 694, "word_count": 99, "semantic_coherence": 1, "information_density": 0.7071, "quality_score": 0.8535, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:47.483102", "source": { "split": "train_shard_00001", "doc_id": 4751 }, "chunk_id": "train_shard_00001_4751_1", "global_id": 12388 }, { "text": "Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition but also an overabundance of genomic virulence factors that have functional consequence on host immune evasion. IMPORTANCE Older adults suffer more frequent and worse outcomes from sepsis, a critical illness secondary to infection. The reasons underlying this unique susceptibility are incompletely understood. Prior work in this area has focused on how the immune response changes with age. The current study, however, focuses instead on alterations in the community of bacteria that humans live with within their gut (i.e., the gut microbiome). The central concept of this paper is that the bacteria in our gut evolve along with the host and \"age,\" making them more efficient at causing sepsis.\n\nAging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity.", "token_count": 353, "char_count": 1600, "word_count": 232, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:48.084757", "source": { "split": "train_shard_00001", "doc_id": 4752 }, "chunk_id": "train_shard_00001_4752_0", "global_id": 12389 }, { "text": "Capsules allow bacteria to colonize novel environments, to withstand numerous stresses, and to resist antibiotics. Yet, even though genetic exchanges with other cells should be adaptive under such circumstances, it has been suggested that capsules lower the rates of homologous recombination and horizontal gene transfer. We analysed over one hundred pan-genomes and thousands of bacterial genomes for the evidence of an association between genetic exchanges (or lack thereof) and the presence of a capsule system. We found that bacteria encoding capsules have larger pan-genomes, higher rates of horizontal gene transfer, and higher rates of homologous recombination in their core genomes. Accordingly, genomes encoding capsules have more plasmids, conjugative elements, transposases, prophages, and integrons. Furthermore, capsular loci are frequent in plasmids, and can be found in prophages. These results are valid for Bacteria, independently of their ability to be naturally transformable. Since we have shown previously that capsules are commonly present in nosocomial pathogens, we analysed their co-occurrence with antibiotic resistance genes. Genomes encoding capsules have more antibiotic resistance genes, especially those encoding efflux pumps, and they constitute the majority of the most worrisome nosocomial bacteria. We conclude that bacteria with capsule systems are more genetically diverse and have fast-evolving gene repertoires, which may further contribute to their success in colonizing novel niches such as humans under antibiotic therapy.\n\nGenetic exchanges are more frequent in bacteria encoding capsules.", "token_count": 353, "char_count": 1632, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5947, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:48.679713", "source": { "split": "train_shard_00001", "doc_id": 4753 }, "chunk_id": "train_shard_00001_4753_0", "global_id": 12390 }, { "text": "Carbapenemase-producing (CP) Pseudomonas aeruginosa is rare compared with mutation-driven carbapenem-resistance, but this situation may be changing. A collection of CP P. aeruginosa isolates was characterized in this study. In 2016, 232 unduplicated carbapenem-resistant P. aeruginosa isolates, of which 71 (30.6%) carried carbapenemase genes, were submitted to the Spanish antibiotic reference laboratory and were further analysed by whole-genome sequencing (WGS). Of the 71 CP P. aeruginosa, 39 (54.9%) carried blaVIM-2, 14 (19.7%) blaVIM-1, 8 (11.3%) blaIMP-8, 6 (8.5%) blaVIM-20, 2 (2.8%) blaVIM-2 plus blaKPC-2, one (1.4%) blaIMP-13 and one (1.4%) blaVIM-1 plus blaIMP-18. Four sequence types (ST175, ST244, ST815 and ST155) encompassed 83.1% of the 71 CP P. aeruginosa; ST175 was detected in hospitals from seven provinces. Using core genome multilocus sequence typing (cgMLST), four clusters were detected: Cluster 1 included nine ST815/VIM-2 isolates; Cluster 2 included five ST175/VIM-2 isolates; Cluster 3 included seven ST244 isolates (five VIM-2 and two VIM-2 plus KPC-2); and Cluster 4 included 11 ST175 isolates (seven VIM-2 and four IMP-8)", "token_count": 480, "char_count": 1253, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7134, "quality_score": 0.8567, "entities": { "genes": [ "ST815", "ST244", "ST155", "ST175" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:49.362536", "source": { "split": "train_shard_00001", "doc_id": 4754 }, "chunk_id": "train_shard_00001_4754_0", "global_id": 12391 }, { "text": "The average number of acquired resistance genes was significantly higher in the blaVIM-1-carying isolates (7.1 ± 0.94) than in the blaVIM-2-carrying isolates (4.5 ± 0.20). CP P. aeruginosa isolates are spreading in Spain, mainly due to the dissemination of high-risk clones such as ST175 and ST244 producing VIM and IMP carbapenemases. Emergence of CP P. aeruginosa is a cause of clinical and epidemiological concern.\n\nCarbapenemase-producing Pseudomonas aeruginosa in Spain: interregional dissemination of the high-risk clones ST175 and ST244 carrying blaVIM-2, blaVIM-1, blaIMP-8, blaVIM-20 and blaKPC-2.", "token_count": 248, "char_count": 683, "word_count": 85, "semantic_coherence": 1, "information_density": 0.6824, "quality_score": 0.8412, "entities": { "genes": [ "ST244", "ST175" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:49.845601", "source": { "split": "train_shard_00001", "doc_id": 4754 }, "chunk_id": "train_shard_00001_4754_1", "global_id": 12392 }, { "text": "More than 1200 isolates of lactic acid bacteria isolated from different environments were screened for antifungal activity in a dual-culture agar plate assay. Approximately 10% of the isolates showed inhibitory activity and 4% showed strong activity against the indicator mould Aspergillus fumigatus. The antifungal spectra for 37 isolates with strong activity and five isolates with low or no activity were determined. Several of the strains showed strong inhibitory activity against the moulds A. fumigatus, Aspergillus nidulans, Penicillium commune and Fusarium sporotrichioides, and also against the yeast Rhodotorula mucilaginosa. Penicillium roqueforti and the yeasts Pichia anomala and Kluyveromyces marxianus were not inhibited. Several isolates showed reduced antifungal activity after storage and handling. The majority of the fungal inhibitory isolates were identified by 16S rDNA sequencing as Lactobacillus coryniformis. Lactobacillus plantarum and Pediococcus pentosaceus were also frequently identified among the active isolates. The degree of fungal inhibition was not only related to production of lactic or acetic acid. In addition, antifungal cyclic dipeptides were identified after HPLC separation and several other active fractions were found suggesting a highly complex nature of the antifungal activity.\n\nBroad and complex antifungal activity among environmental isolates of lactic acid bacteria.", "token_count": 361, "char_count": 1419, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5773, "quality_score": 0.7887, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:50.441783", "source": { "split": "train_shard_00001", "doc_id": 4755 }, "chunk_id": "train_shard_00001_4755_0", "global_id": 12393 }, { "text": "

Background

Vancomycin-resistant Enterococcus faecium (VREfm) are an emerging threat worldwide. In Germany, a VRE-belt with higher VREfm prevalences transversing its central east-west axis and including the state of Hesse was previously described. Recently, we detected a predominant VREfm clone in hospitals throughout the Rhine-Main metropolitan area of Hesse.

Aim

Here we expanded our study on VREfm to a regional neurological acute hospital outside of the metropolitan area with patient referrals from throughout Hesse and the neighboring federal state of Rhineland-Palatinate.

Material/methods

VREfm isolates obtained between 2016-2018 from a regional neurological acute hospital with intensive care and early rehabilitation units were investigated (n=55). Patient data was collected and analyzed together with whole-genome sequencing data to investigate antibiotic resistance and virulence determinants of the VREfm. The population structure of VREfm was investigated using the Core genome-based multilocus sequence typing (cgMLST).

Findings

The average age of the patients was 67.1 years. For 96% of the patients, a previous hospital stay was reported. 64% of the patients were treated with antibiotics. All VREfm harbored the vanB vancomycin resistance gene. The multilocus sequence types (STs) detected changed abruptly from four different STs in 2016 to a predominant ST in 2017 and 2018 (ST117). Most of the ST117 isolates were members of the cgMLST type CT71.

Conclusion

The results indicate a sudden shift of the VREfm population structure from a semi-heterogeneous population to a pre-dominant clone within an interval of two years. Further investigations are warranted to understand the epidemiology and emergence of this clone.", "token_count": 483, "char_count": 1792, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6042, "quality_score": 0.8021, "entities": { "genes": [ "ST117", "CT71" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:51.084535", "source": { "split": "train_shard_00001", "doc_id": 4756 }, "chunk_id": "train_shard_00001_4756_0", "global_id": 12394 }, { "text": "Changing epidemiology of vancomycin-resistant Enterococcus faecium: Results of a genome-based study at a regional neurological acute hospital with intensive care and early rehabilitation treatment.", "token_count": 54, "char_count": 204, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:51.473226", "source": { "split": "train_shard_00001", "doc_id": 4756 }, "chunk_id": "train_shard_00001_4756_1", "global_id": 12395 }, { "text": "

Background

Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is an important zoonotic agent worldwide. The aim of this work was to compare genetically 117 S. Typhimurium isolated from different sources over 30 years in Brazil using different genomics strategies.

Results

The majority of the 117 S. Typhimurium strains studied were grouped into a single cluster (≅ 90%) by the core genome multilocus sequence typing and (≅ 77%) by single copy marker genes. The phylogenetic analysis based on single nucleotide polymorphism (SNP) grouped most strains from humans into a single cluster (≅ 93%), while the strains isolated from food and swine were alocated into three clusters. The different orthologous protein clusters found for some S. Typhimurium isolated from humans and food are involved in metabolic and regulatory processes. For 26 isolates from swine the sequence types (ST) 19 and ST1921 were the most prevalent ones, and the ST14, ST64, ST516 and ST639 were also detected. Previous results typed the 91 S. Typhimurium isolates from humans and foods as ST19, ST313, ST1921, ST3343 and ST1649. The main prophages detected were: Gifsy-2 in 79 (67.5%) and Gifsy-1 in 63 (54%) strains. All of the S. Typhimurium isolates contained the acrA, acrB, macA, macB, mdtK, emrA, emrB, emrR and tolC efflux pump genes.

Conclusions

The phylogenetic trees grouped the majority of the S. Typhimurium isolates from humans into a single cluster suggesting that there is one prevalent subtype in Brazil. Regarding strains isolated from food and swine, the SNPs' results suggested the circulation of more than one subtype over 30 years in this country", "token_count": 526, "char_count": 1682, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5859, "quality_score": 0.793, "entities": { "genes": [ "ST1921", "ST64", "ST639", "ST3343", "ST1649", "ST19", "ST516", "ST313", "ST14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:52.107796", "source": { "split": "train_shard_00001", "doc_id": 4757 }, "chunk_id": "train_shard_00001_4757_0", "global_id": 12396 }, { "text": "The orthologous protein clusters analysis revealed unique genes in the strains studied mainly related to bacterial metabolism. S. Typhimurium strains from swine showed greater diversity of STs and prophages in comparison to strains isolated from humans and foods. The pathogenic potential of S. Typhimurium strains was corroborated by the presence of exclusive prophages of this serovar involved in its virulence. The high number of resistance genes related to efflux pumps is worrying and may lead to therapeutic failures when clinical treatment is needed.\n\nInsights about the epidemiology of Salmonella Typhimurium isolates from different sources in Brazil using comparative genomics.", "token_count": 157, "char_count": 686, "word_count": 99, "semantic_coherence": 1, "information_density": 0.697, "quality_score": 0.8485, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:52.555270", "source": { "split": "train_shard_00001", "doc_id": 4757 }, "chunk_id": "train_shard_00001_4757_1", "global_id": 12397 }, { "text": "Abstract

Background: Shigella spp. and entero-invasive Escherichia coli (EIEC) can cause mild diarrhea to dysentery. In the Netherlands, although shigellosis is a notifiable disease, there is no laboratory surveillance for Shigella spp. and EIEC in place. Consequently, the population structure for circulating Shigella spp. and EIEC isolates is not known. This study describes the phenotypic and serological characteristics, the phenotypic and genetic antimicrobial resistance profiles, the virulence gene profiles, the classic multi-locus sequence types (MSLT) and core genome MLST (cgMLST) types, and the epidemiology of Shigella spp. and EIEC isolates collected during a cross-sectional study in the Netherlands in 2016 and 2017.

Results:

S. sonnei, S. flexneri and EIEC were predominantly detected in the Netherlands. A substantial part of the characterized isolates was resistant to antimicrobials advised for treatment, i.e., 73% was phenotypically resistant to co-trimoxazol and 19% to ciprofloxacin. Antimicrobial resistance was particularly observed in isolates from male patients who had sex with men or from patients that had travelled to Asia. Furthermore, isolates related to international clusters were also circulating in the Netherlands. Travel-related isolates formed clusters with isolates from patients without travel history, indicating their emergence into the Dutch population.

Conclusions:

In conclusion, laboratory surveillance using whole genome sequencing for genetic characterization of isolates complements the current epidemiological surveillance, as the latter is not sufficient to detect all (inter)national clusters, emphasizing the importance of multifactorial public health approaches.

\n\nThe importance of a multifactorial approach for (inter)national surveillance of Shigella spp. and entero-invasive Escherichia coli", "token_count": 480, "char_count": 1893, "word_count": 247, "semantic_coherence": 1, "information_density": 0.583, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:53.194606", "source": { "split": "train_shard_00001", "doc_id": 4758 }, "chunk_id": "train_shard_00001_4758_0", "global_id": 12398 }, { "text": "

Background

The Oxford Nanopore Technologies MinION(TM) is a mobile DNA sequencer that can produce long read sequences with a short turn-around time. Here we report the first demonstration of single contig genome assembly using Oxford Nanopore native barcoding when applied to a multiplexed library of 12 samples and combined with existing Illumina short read data. This paves the way for the closure of multiple bacterial genomes from a single MinION(TM) sequencing run, given the availability of existing short read data. The strain we used, MHO_001, represents the important community-acquired methicillin-resistant Staphylococcus aureus lineage USA300.

Findings

Using a hybrid assembly of existing short read and barcoded long read sequences from multiplexed data, we completed a genome of the S. aureus USA300 strain MHO_001. The long read data represented only ∼5% to 10% of an average MinION(TM) run (∼7x genomic coverage), but, using standard tools, this was sufficient to complete the circular chromosome of S. aureus strain MHO_001 (2.86 Mb) and two complete plasmids (27 Kb and 3 Kb). Minor differences were noted when compared to USA300 reference genome, USA300_FPR3757, including the translocation, loss, and gain of mobile genetic elements.

Conclusion

Here we demonstrate that MinION(TM) reads, multiplexed using native barcoding, can be used in combination with short read data to fully complete a bacterial genome. The ability to complete multiple genomes, for which short read data is already available, from a single MinION(TM) run is set to impact our understanding of accessory genome content, plasmid diversity, and genome rearrangements.\n\nThe use of Oxford Nanopore native barcoding for complete genome assembly.", "token_count": 468, "char_count": 1755, "word_count": 254, "semantic_coherence": 1, "information_density": 0.5669, "quality_score": 0.7835, "entities": { "genes": [ "USA300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:53.839412", "source": { "split": "train_shard_00001", "doc_id": 4759 }, "chunk_id": "train_shard_00001_4759_0", "global_id": 12399 }, { "text": "

Background

In bacteria, pan-genomes are the result of the evolutionary “tug of war” between selection and horizontal gene transfer (HGT). High rates of HGT increase the genetic pool and the effective population size, resulting in open pan-genomes. In contrast, selective pressures can lead to local adaptation by purging the variation introduced by HGT, resulting in closed pan-genomes and clonal lineages. In this study, we explored both hypotheses elucidating the pan-genome of Vibrionaceae isolates after a perturbation event in the endangered oasis of Cuatro Ciénegas Basin (CCB), Mexico, and looking for signals of adaptation to the environments in their genomes.

Results

We obtained 42 genomes of Vibrionaceae distributed in six lineages, two of them did not showed any close reference strain in databases. Five of the lineages showed closed pan-genomes and were associated to either water or sediment environment; their high effective population size ( N e ) estimates suggest that these lineages are not from a recent origin. The only clade with an open pan-genome was found in both environments and was formed by ten genetic groups with low N e , suggesting a recent origin. The recombination and mutation estimators (r/m) ranged from 0.0052 to 2.7249, which are similar to oceanic Vibrionaceae estimations; however, we identified 367 gene families with signals of positive selection, most of them found in the core genome; suggesting that despite recombination, natural selection moves the Vibrionaceae CCB lineages to local adaptation purging the genomes and keeping closed pan-genome patterns. Moreover, we identify 598 SNPs associated with an unstructured environment; some of the genes under this SNPs were related to sodium transport.

Conclusions

Different lines of evidence suggest that the sampled Vibrionaceae, are part of the rare biosphere usually living under famine conditions. Two of these lineages were reported by the first time. Most Vibrionaceae lineages of CCB are adapted to their microhabitats rather than to the sampled environments. This pattern of adaptation agrees with the association of closed pan-genomes and local adaptation.", "token_count": 520, "char_count": 2190, "word_count": 328, "semantic_coherence": 1, "information_density": 0.5671, "quality_score": 0.7835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:55:55.262349", "source": { "split": "train_shard_00001", "doc_id": 4760 }, "chunk_id": "train_shard_00001_4760_0", "global_id": 12400 }, { "text": "Population genomics of Vibrionaceae isolated from an endangered oasis reveals local adaptation after an environmental perturbation", "token_count": 25, "char_count": 130, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:55.621173", "source": { "split": "train_shard_00001", "doc_id": 4760 }, "chunk_id": "train_shard_00001_4760_1", "global_id": 12401 }, { "text": "Streptococcus suis is one of the important emerging zoonotic pathogens. Serotype 2 is most prevalent in patients worldwide. In the present study, we first isolated one S. suis serotype 7 strain GX69 from the blood culture of a patient with septicemia complicated with pneumonia in China. In order to deepen the understanding of S. suis serotype 7 population characteristics, we investigated the phylogenetic structure, genomic features, and virulence of S. suis serotype 7 population, including 35 strains and 79 genomes. Significant diversities were revealed in S. suis serotype 7 population, which were clustered into 22 sequence types (STs), five minimum core genome (MCG) groups, and six lineages. Lineages 1, 3a, and 6 were mainly constituted by genomes from Asia. Genomes of Lineages 2, 3b, and 5a were mainly from Northern America. Most of genomes from Europe (41/48) were clustered into Lineage 5b. In addition to strain GX69, 13 of 21 S. suis serotype 7 representative strains were classified as virulent strains using the C57BL/6 mouse model. Virulence-associated genes preferentially present in highly pathogenic S. suis serotype 2 strains were not suitable as virulence indicators for S. suis serotype 7 strains. Integrative mobilizable elements were widespread and may play a critical role in disseminating antibiotic resistance genes of S. suis serotype 7 strains. Our study confirmed S. suis serotype 7 is a non-negligible pathotype and deepened the understanding of the population structure of S. suis serotype 7, which provided valuable information for the improved surveillance of this serotype.", "token_count": 496, "char_count": 1690, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5668, "quality_score": 0.7834, "entities": { "genes": [ "GX69" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:56.274938", "source": { "split": "train_shard_00001", "doc_id": 4761 }, "chunk_id": "train_shard_00001_4761_0", "global_id": 12402 }, { "text": "Genomic and pathogenic investigations of Streptococcus suis serotype 7 population derived from a human patient and pigs.", "token_count": 37, "char_count": 127, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:56.633840", "source": { "split": "train_shard_00001", "doc_id": 4761 }, "chunk_id": "train_shard_00001_4761_1", "global_id": 12403 }, { "text": "A cybernetic model for microbial growth on mixed substrates, was used to simulate the anaerobic fermentation of cheese whey and multiple sugars in semisynthetic media by Kluyveromyces marxianus CBS 397. The model simulations quite successfully predicted the observed behavior in batch and during transients in continuous operation, in single-substrate systems as well as in media involving multiple substrates, and in semisynthetic and reconstituted cheese whey solutions. The results of simulations and their comparison with the experimental data are presented.\n\nA mathematical model of ethanol fermentation from cheese whey : II. Simulation and comparison with experimental data.", "token_count": 149, "char_count": 681, "word_count": 96, "semantic_coherence": 1, "information_density": 0.6562, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:57.071781", "source": { "split": "train_shard_00001", "doc_id": 4762 }, "chunk_id": "train_shard_00001_4762_0", "global_id": 12404 }, { "text": "A 10 kb of primary DNA clone containing the Kluyveromyces fragilis protein disulfide isomerase gene (KfPDI) was mapped and shortened into a 4 kb of subclone, followed by the complete gene DNA sequencing and analyzing. The results show that: (1) the KfPDI protein is consisted of 520 amino acid residues; (2) the homologous identity between KfPDI and the KlPDI from K. lactis is 78% at amino acid level; (3) Although the homology between KfPDI and other known PDI genes is not perfect but two highly conserved activity domains of protein disulfide isomerase can be found among all of them.\n\nStructure analysis on protein disulfide isomerase gene of Kluyveromyces fragilis", "token_count": 187, "char_count": 670, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6789, "quality_score": 0.8394, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:57.514139", "source": { "split": "train_shard_00001", "doc_id": 4763 }, "chunk_id": "train_shard_00001_4763_0", "global_id": 12405 }, { "text": "2,6-Bis(benzimidazol-2-yl)pyridine (L) ligand and complexes [M(L)Cl(2)] and [Fe(L)(2)](ClO(4))(2) (M=Zn, Cd, Hg) have been synthesized. The geometries of the [M(L)Cl(2)] complexes were derived from theoretical calculation in DGauss/DFT level (DZVP basis set) on CACHE. The central M(II) ion is penta-coordinated and surrounded by N(3)Cl(2) environment, adopting a distorted trigonal bipyramidal geometry. The ligand is tridentate, via three nitrogen atoms to metal centre and two chloride ions lie on each side of the distorted benzimidazole ring. In the [Fe(L)(2)](ClO(4))(2) complex, the central Fe(II) ion is surrounded by two (3N) units, adopting a octahedral geometry. The elemental analysis, molecular conductivity, FT-Raman, FT-IR (mid-, far-IR), (1)H, and (13)C NMR were reported. The antimicrobial activities of the free ligand, its hydrochloride salt, and the complexes were evaluated using the disk diffusion method in dimethyl sulfoxide (DMSO) as well as the minimal inhibitory concentration (MIC) dilution method, against 10 bacteria and the results compared with that for gentamycin. Antifungal activities were reported for Candida albicans, Kluyveromyces fragilis, Rhodotorula rubra, Debaryomyces hansenii, Hanseniaspora guilliermondii, and the results were referenced against nystatin, ketaconazole, and clotrimazole antifungal agents. In most cases, the compounds tested showed broad-spectrum (Gram positive and Gram negative bacteria) activities that were either more effective than or as potent as the references. The binding of two most biologically effective compounds of zinc and mercury to calf thymus DNA has also been investigated by absorption spectra.", "token_count": 502, "char_count": 1678, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6812, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:58.161546", "source": { "split": "train_shard_00001", "doc_id": 4764 }, "chunk_id": "train_shard_00001_4764_0", "global_id": 12406 }, { "text": "Synthesis, characterization and antimicrobial activity of Fe(II), Zn(II), Cd(II) and Hg(II) complexes with 2,6-bis(benzimidazol-2-yl) pyridine ligand.", "token_count": 61, "char_count": 150, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:58.522276", "source": { "split": "train_shard_00001", "doc_id": 4764 }, "chunk_id": "train_shard_00001_4764_1", "global_id": 12407 }, { "text": "The genus Lactobacillus includes a diverse group of bacteria consisting of many species that are associated with fermentations of plants, meat or milk. In addition, various lactobacilli are natural inhabitants of the intestinal tract of humans and other animals. Finally, several Lactobacillus strains are marketed as probiotics as their consumption can confer a health benefit to host. Presently, 154 Lactobacillus species are known and a growing fraction of these are subject to draft genome sequencing. However, complete genome sequences are needed to provide a platform for detailed genomic comparisons. Therefore, we selected a total of 20 genomes of various Lactobacillus strains for which complete genomic sequences have been reported. These genomes had sizes varying from 1.8 to 3.3 Mb and other characteristic features, such as G+C content that ranged from 33% to 51%. The Lactobacillus pan genome was found to consist of approximately 14 000 protein-encoding genes while all 20 genomes shared a total of 383 sets of orthologous genes that defined the Lactobacillus core genome (LCG). Based on advanced phylogeny of the proteins encoded by this LCG, we grouped the 20 strains into three main groups and defined core group genes present in all genomes of a single group, signature group genes shared in all genomes of one group but absent in all other Lactobacillus genomes, and Group-specific ORFans present in core group genes of one group and absent in all other complete genomes. The latter are of specific value in defining the different groups of genomes. The study provides a platform for present individual comparisons as well as future analysis of new Lactobacillus genomes.\n\nComparative genomics of Lactobacillus.", "token_count": 428, "char_count": 1731, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5593, "quality_score": 0.7796, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:59.145703", "source": { "split": "train_shard_00001", "doc_id": 4765 }, "chunk_id": "train_shard_00001_4765_0", "global_id": 12408 }, { "text": "DISPOSAL METHOD OF FOOD WASTES USING THE MIXTURE OF BACILLUS SMITHI AND THERMOTOLERANT YEAST", "token_count": 38, "char_count": 92, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:55:59.530907", "source": { "split": "train_shard_00001", "doc_id": 4766 }, "chunk_id": "train_shard_00001_4766_0", "global_id": 12409 }, { "text": "Polymyxins are used as treatments of last resort for Gram-negative bacterial infections. Their increased use has led to concerns about emerging polymyxin resistance (PR). Phenotypic polymyxin susceptibility testing is resource intensive and difficult to perform accurately. The complex polygenic nature of PR and our incomplete understanding of its genetic basis make it difficult to predict PR using detection of resistance determinants. We therefore applied machine learning (ML) to whole-genome sequencing data from >600 Klebsiella pneumoniae clonal group 258 (CG258) genomes to predict phenotypic PR. Using a reference-based representation of genomic data with ML outperformed a rule-based approach that detected variants in known PR genes (area under receiver-operator curve [AUROC], 0.894 versus 0.791, P = 0.006). We noted modest increases in performance by using a bacterial genome-wide association study to filter relevant genomic features and by integrating clinical data in the form of prior polymyxin exposure. Conversely, reference-free representation of genomic data as k-mers was associated with decreased performance (AUROC, 0.692 versus 0.894, P = 0.015). When ML models were interpreted to extract genomic features, six of seven known PR genes were correctly identified by models without prior programming and several genes involved in stress responses and maintenance of the cell membrane were identified as potential novel determinants of PR. These findings are a proof of concept that whole-genome sequencing data can accurately predict PR in K. pneumoniae CG258 and may be applicable to other forms of complex antimicrobial resistance.IMPORTANCE Polymyxins are last-resort antibiotics used to treat highly resistant Gram-negative bacteria. There are increasing reports of polymyxin resistance emerging, raising concerns of a postantibiotic era. Polymyxin resistance is therefore a significant public health threat, but current phenotypic methods for detection are difficult and time-consuming to perform", "token_count": 516, "char_count": 2060, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [ "CG258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:56:00.187791", "source": { "split": "train_shard_00001", "doc_id": 4767 }, "chunk_id": "train_shard_00001_4767_0", "global_id": 12410 }, { "text": "There have been increasing efforts to use whole-genome sequencing for detection of antibiotic resistance, but this has been difficult to apply to polymyxin resistance because of its complex polygenic nature. The significance of our research is that we successfully applied machine learning methods to predict polymyxin resistance in Klebsiella pneumoniae clonal group 258, a common health care-associated and multidrug-resistant pathogen. Our findings highlight that machine learning can be successfully applied even in complex forms of antibiotic resistance and represent a significant contribution to the literature that could be used to predict resistance in other bacteria and to other antibiotics.\n\nPredicting Phenotypic Polymyxin Resistance in Klebsiella pneumoniae through Machine Learning Analysis of Genomic Data.", "token_count": 185, "char_count": 829, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6637, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:00.653491", "source": { "split": "train_shard_00001", "doc_id": 4767 }, "chunk_id": "train_shard_00001_4767_1", "global_id": 12411 }, { "text": "

Background

Clostridium botulinum is a diverse group of bacteria characterized by the production of botulinum neurotoxin. Botulinum neurotoxins are classified into serotypes (BoNT/A-G), which are produced by six species/Groups of Clostridia, but the genetic background of the bacteria remains poorly understood. The purpose of this study was to use comparative genomics to provide insights into the genetic diversity and evolutionary history of bacteria that produce the potent botulinum neurotoxin.

Results

Comparative genomic analyses of over 170 Clostridia genomes, including our draft genome assemblies for 59 newly sequenced Clostridia strains from six continents and publicly available genomic data, provided in-depth insights into the diversity and distribution of BoNT-producing bacteria. These newly sequenced strains included Group I and II strains that express BoNT/A,/B,/E, or/F as well as bivalent strains. BoNT-producing Clostridia and closely related Clostridia species were delineated with a variety of methods including 16S rRNA gene, concatenated marker genes, core genome and concatenated multi-locus sequencing typing (MLST) gene phylogenies that related whole genome sequenced strains to publicly available strains and sequence types. These analyses illustrated the phylogenetic diversity in each Group and the diversity of genomic backgrounds that express the same toxin type or subtype. Comparisons of the botulinum neurotoxin genes did not identify novel toxin types or variants.

Conclusions

This study represents one of the most comprehensive analyses of whole genome sequence data for Group I and II BoNT-producing strains. Read data and draft genome assemblies generated for 59 isolates will be a resource to the research community. Core genome phylogenies proved to be a powerful tool for differentiating BoNT-producing strains and can provide a framework for the study of these bacteria", "token_count": 475, "char_count": 1936, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5506, "quality_score": 0.7753, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:01.341961", "source": { "split": "train_shard_00001", "doc_id": 4768 }, "chunk_id": "train_shard_00001_4768_0", "global_id": 12412 }, { "text": "Comparative genomic analyses of Clostridia species illustrate the diversity of botulinum-neurotoxin-producing strains and the plasticity of the genomic backgrounds in which bont genes are found.\n\nComparative genomic analyses reveal broad diversity in botulinum-toxin-producing Clostridia.", "token_count": 76, "char_count": 288, "word_count": 34, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:01.722049", "source": { "split": "train_shard_00001", "doc_id": 4768 }, "chunk_id": "train_shard_00001_4768_1", "global_id": 12413 }, { "text": "Production of an alcoholic beverage by fermentation of whey permeate with Kluyveromyces fragilis. I. Primary metabolism", "token_count": 32, "char_count": 119, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:02.085227", "source": { "split": "train_shard_00001", "doc_id": 4769 }, "chunk_id": "train_shard_00001_4769_0", "global_id": 12414 }, { "text": "The bacterial wilt pathogen, first known as Bacillus solanacearum, has undergone numerous taxonomic changes since its first description in 1896. The history and significance of this pathogen is covered in this review with an emphasis on the advances in technology that were used to support each reclassification that finally led to the current separation of Ralstonia solanacearum into three genomic species. Frequent name changes occurred as methodology transitioned from phenotypic, biochemical, and molecular studies, to genomics and functional genomics. The diversity, wide host range, and geographical distribution of the bacterial wilt pathogen resulted in its division into three species as genomic analyses elucidated phylogenetic relationships among strains. Current advances in phylogenetics and functional genomics now open new avenues for research into epidemiology and control of the devastating bacterial wilt disease.\n\nTaxonomy and Phylogenetic Research on Ralstonia solanacearum Species Complex: A Complex Pathogen with Extraordinary Economic Consequences.", "token_count": 247, "char_count": 1072, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6644, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:02.571712", "source": { "split": "train_shard_00001", "doc_id": 4770 }, "chunk_id": "train_shard_00001_4770_0", "global_id": 12415 }, { "text": "A novel irregularly shaped and slightly curved rod bacterial strain, GLDI4/2T, showing activity of fructose 6-phosphate phosphoketolase was isolated from a faecal sample of an adult gelada baboon (Theropithecus gelada). Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing fusA, gyrB and xfp genes) and the core genome revealed that GLDI4/2T exhibited phylogenetic relatedness to Alloscardovia omnicolens DSM 21503T and to Alloscardovia macacae DSM 24762T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain A. omnicolens DSM 21503T (96.0 %). Activities of α- and β-gluco(galacto)sidases were detected in strain GLDI4/2T, which is characteristic for almost all members of the family Bifidobacteriaceae. Compared to other Alloscardovia species its DNA G+C content (43.8 mol%) was very low. Phylogenetic studies and the evaluation of phenotypic characteristics, including the results of biochemical, physiological and chemotaxonomic analyses, confirmed the novel species status for strain GLDI4/2T, for which the name Alloscardoviatheropitheci sp. nov. is proposed. The type strain is GLDI4/2T (=DSM 106019T=JCM 32430T).", "token_count": 519, "char_count": 1424, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6901, "quality_score": 0.845, "entities": { "genes": [ "GLDI4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:56:03.228827", "source": { "split": "train_shard_00001", "doc_id": 4771 }, "chunk_id": "train_shard_00001_4771_0", "global_id": 12416 }, { "text": "Alloscardovia theropitheci sp. nov., isolated from the faeces of gelada baboon, the 'bleeding heart' monkey (Theropithecus gelada).", "token_count": 57, "char_count": 145, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:03.589004", "source": { "split": "train_shard_00001", "doc_id": 4771 }, "chunk_id": "train_shard_00001_4771_1", "global_id": 12417 }, { "text": "Pseudomonas aeruginosa is one of the most common pathogens related to healthcare-associated infections. The Brazilian isolate, named CCBH4851, is a multidrug-resistant clone belonging to the sequence type 277. The antimicrobial resistance mechanisms of the CCBH4851 strain are associated with the presence of bla SPM-1 gene, encoding a metallo-beta-lactamase, in addition to other exogenously acquired genes. Whole-genome sequencing studies focusing on emerging pathogens are essential to identify physiological key aspects that may lead to the exposure of new targets for therapy. This study was designed to characterize the genome of Pseudomonas aeruginosa CCBH4851 through the detection of genomic features and genome comparison with other Pseudomonas aeruginosa strains. The CCBH4851 closed genome showed features that were consistent with data reported for the specie. However, comparative genomics revealed the absence of genes important for pathogenesis. On the other hand, CCBH4851 genome contained acquired genomic islands that carry additional virulence and antimicrobial resistance-related genes. The presence of single nucleotide polymorphisms in the core genome, mainly those located in resistance-associated genes, suggests that these mutations could influence the multidrug-resistant behavior of CCBH4851. Overall, the characterization of Pseudomonas aeruginosa CCBH4851 complete genome revealed several features that could directly impact the profile of virulence and antibiotic resistance of this pathogen in infectious outbreaks.\n\nComparative genome analysis of a multidrug-resistant Pseudomonas aeruginosa sequence type 277 clone that harbours two copies of the blaSPM-1 gene and multiple single nucleotide polymorphisms in other resistance-associated genes", "token_count": 457, "char_count": 1801, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5787, "quality_score": 0.7894, "entities": { "genes": [ "CCBH4851" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:04.229773", "source": { "split": "train_shard_00001", "doc_id": 4772 }, "chunk_id": "train_shard_00001_4772_0", "global_id": 12418 }, { "text": "The poor survival of probiotic bacteria added to yoghurts is mainly attributed to the low pH of the product environment. Since yeasts have the ability to metabolize organic acids, resulting in a decrease in acidity, the inclusion of yeasts as part of the normal microflora, in association with probiotic bacteria has been suggested with the intention to assure better survival of the probiotic organisms in bio-yoghurt. Furthermore, a commensalistic association between yeasts and lactic acid bacteria exists. In order to understand the potential impact of yeast on probiotic bacteria, it was firstly important to assess the ability of yeast isolates to grow and survive in yoghurt. Accordingly, four dairy-associated yeasts, Debaryomyces hansenii, Kluyveromyces marxianus, Yarrowia lipolytica and Issatchenkia orientalis, associated commonly with yoghurt were isolated and inoculated subsequently into yoghurt and related dairy products during processing. The survival and growth of the yeasts were monitored over a 4-week storage period, the normal time accepted as the shelf-life of yoghurts. pH, sugar utilization and the production of organic acids were determined on a regular basis during the shelf-life to evaluate the possible contribution of the yeasts towards the products. The yeast species were able to survive in bio-yoghurt reaching maximum counts exceeding 10(7) cfu g(-1). Despite the inability of some species to utilize lactose, the yeast species utilized available organic acids, galactose and glucose derived from bacterial metabolism of the milk lactose, as well as possible free fatty acids or free amino acids present in the dairy products. Excessive gas and ethanol production initiated by some yeast species proved, however, to be major constraints.\n\nSurvival of dairy-associated yeasts in yoghurt and yoghurt-related products", "token_count": 449, "char_count": 1852, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5699, "quality_score": 0.7849, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:04.866155", "source": { "split": "train_shard_00001", "doc_id": 4773 }, "chunk_id": "train_shard_00001_4773_0", "global_id": 12419 }, { "text": "

Background

Reptile-associated Salmonella bacteria are a major, but often neglected cause of both gastrointestinal and bloodstream infection in humans globally. The diversity of Salmonella enterica has not yet been determined in venomous snakes, however other ectothermic animals have been reported to carry a broad range of Salmonella bacteria. We investigated the prevalence and diversity of Salmonella in a collection of venomous snakes and non-venomous reptiles.

Methodology/principle findings

We used a combination of selective enrichment techniques to establish a unique dataset of reptilian isolates to study Salmonella enterica species-level evolution and ecology and used whole-genome sequencing to investigate the relatedness of phylogenetic groups. We observed that 91% of venomous snakes carried Salmonella, and found that a diverse range of serovars (n = 58) were carried by reptiles. The Salmonella serovars belonged to four of the six Salmonella enterica subspecies: diarizonae, enterica, houtanae and salamae. Subspecies enterica isolates were distributed among two distinct phylogenetic clusters, previously described as clade A (52%) and clade B (48%). We identified metabolic differences between S. diarizonae, S. enterica clade A and clade B involving growth on lactose, tartaric acid, dulcitol, myo-inositol and allantoin.

Significance

We present the first whole genome-based comparative study of the Salmonella bacteria that colonise venomous and non-venomous reptiles and shed new light on Salmonella evolution. Venomous snakes examined in this study carried a broad range of Salmonella, including serovars which have been associated with disease in humans such as S. Enteritidis. The findings raise the possibility that venomous snakes could be a reservoir for Salmonella serovars associated with human salmonellosis.\n\nThe diversity, evolution and ecology of Salmonella in venomous snakes.", "token_count": 503, "char_count": 1934, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5627, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:05.516212", "source": { "split": "train_shard_00001", "doc_id": 4774 }, "chunk_id": "train_shard_00001_4774_0", "global_id": 12420 }, { "text": "Many bacterial species, such as the alphaproteobacterium Sinorhizobium meliloti, are characterized by open pangenomes and contain multipartite genomes consisting of a chromosome and other large-sized replicons, such as chromids, megaplasmids, and plasmids. The evolutionary forces in both functional and structural aspects that shape the pangenome of species with multipartite genomes are still poorly understood. Therefore, we sequenced the genomes of 10 new S. meliloti strains, analyzed with four publicly available additional genomic sequences. Results indicated that the three main replicons present in these strains (a chromosome, a chromid, and a megaplasmid) partly show replicon-specific behaviors related to strain differentiation. In particular, the pSymB chromid was shown to be a hot spot for positively selected genes, and, unexpectedly, genes resident in the pSymB chromid were also found to be more widespread in distant taxa than those located in the other replicons. Moreover, through the exploitation of a DNA proximity network, a series of conserved “DNA backbones” were found to shape the evolution of the genome structure, with the rest of the genome experiencing rearrangements. The presented data allow depicting a scenario where the pSymB chromid has a distinctive role in intraspecies differentiation and in evolution through positive selection, whereas the pSymA megaplasmid mostly contributes to structural fluidity and to the emergence of new functions, indicating a specific evolutionary role for each replicon in the pangenome evolution.\n\nReplicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti", "token_count": 389, "char_count": 1651, "word_count": 234, "semantic_coherence": 1, "information_density": 0.641, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:06.135087", "source": { "split": "train_shard_00001", "doc_id": 4775 }, "chunk_id": "train_shard_00001_4775_0", "global_id": 12421 }, { "text": "A strain of Vibrio parahaemolyticus that emerged in 1995 caused the first known pandemic involving this species. This strain comprises clonal autochthonous ocean-dwelling bacteria whose evolution has occurred in the ocean environment. The low sequence diversity in this population enabled the discovery of information on its origin and evolution that has been hidden in bacterial clones that have evolved over a long period. Multilocus sequencing and microarray analysis, together with phylogenetic analysis, of pandemic and pre-pandemic isolates has suggested that the founder clone was an O3:K6 non-pathogenic strain that initially acquired a toxRS/new region and subsequently acquired at least seven novel genomic islands. Sequencing and comparison of whole genomes later confirmed these early observations, and it confirmed that most of the genetic changes occurred via gene conversion involving horizontally transmitted DNA. The highly clonal population rapidly diversified, especially in terms of antigenicity, and 27 serotypes have already been reported. Comparisons of the core genomes derived from the founder clone indicate that there are only a few hundred single-nucleotide variations between isolates. However, when the whole genome is considered (the core plus non-core genome and from any clonal frame), the amount of DNA with a different clonal frame can reach up to 4.2% and the number of single-nucleotide variations can reach several hundred thousand. Altogether, these and previous observations based on multilocus sequence typing, microarray analysis, and whole-genome sequencing indicate the large contribution made by DNA with different clonal genealogy to genome diversification. The evidence also indicates that horizontal gene transfer (HGT) caused the emergence of new pathogens. Furthermore, the extent of HGT seems to depend on the vicissitudes of the life of each bacterium, as exemplified by differences in thousands of base pairs acquired by HGT among almost identical genetic isolates.\n\nInsight Into the Origin and Evolution of the Vibrio parahaemolyticus Pandemic Strain.", "token_count": 469, "char_count": 2126, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5974, "quality_score": 0.7987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:06.778612", "source": { "split": "train_shard_00001", "doc_id": 4776 }, "chunk_id": "train_shard_00001_4776_0", "global_id": 12422 }, { "text": "

Background

Campylobacter fetus (C. fetus) can cause disease in both humans and animals. C. fetus has been divided into three subspecies: C. fetus subsp. fetus (Cff), C. fetus subsp. venerealis (Cfv) and C. fetus subsp. testudinum (Cft). Subspecies identification of mammal-associated C. fetus strains is crucial in the control of Bovine Genital Campylobacteriosis (BGC), a syndrome associated with Cfv. The prescribed methods for subspecies identification of the Cff and Cfv isolates are: tolerance to 1 % glycine and H2S production.

Results

In this study, we observed the deletion of a putative cysteine transporter in the Cfv strains, which are not able to produce H2S from L-cysteine. Phylogenetic reconstruction of the core genome single nucleotide polymorphisms (SNPs) within Cff and Cfv strains divided these strains into five different clades and showed that the Cfv clade and a Cff clade evolved from a single Cff ancestor.

Conclusions

Multiple C. fetus clades were observed, which were not consistent with the biochemical differentiation of the strains. This suggests the need for a closer evaluation of the current C. fetus subspecies differentiation, considering that the phenotypic differentiation is still applied in BGC control programs.\n\nWhole genome sequence analysis indicates recent diversification of mammal-associated Campylobacter fetus and implicates a genetic factor associated with H2S production.", "token_count": 400, "char_count": 1443, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:07.398656", "source": { "split": "train_shard_00001", "doc_id": 4777 }, "chunk_id": "train_shard_00001_4777_0", "global_id": 12423 }, { "text": "

Objectives

The objective of this study was to determine the population structure of Escherichia coli ST73 isolated from human bacteraemia and urinary tract infections.

Methods

The genomes of 22 E. coli ST73 isolates were sequenced using the Illumina HiSeq platform. High-resolution SNP typing was used to create a phylogenetic tree. Comparative genomics were also performed using a pangenome approach. In silico and S1-PFGE plasmid profiling was conducted, and isolates were checked for their ability to survive exposure to human serum.

Results

E. coli ST73 isolates circulating in clinically unrelated episodes show a high degree of diversity at a whole-genome level, but exhibit conservation in gene content, particularly in virulence-associated gene carriage. The isolates also contain a highly diverse plasmid pool that confers MDR via carriage of CTX-M genes.

Conclusions

Our data show that a rise in incidence of MDR E. coli ST73 clinical isolates is not due to a circulating outbreak strain as in E. coli ST131. Rather the ST73 circulating strains are distantly related and carry a diverse set of resistance plasmids. This suggests that the evolutionary events behind emergence of drug-resistant E. coli differ between lineages.\n\nIncrease in bacteraemia cases in the East Midlands region of the UK due to MDR Escherichia coli ST73: high levels of genomic and plasmid diversity in causative isolates.", "token_count": 384, "char_count": 1435, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6172, "quality_score": 0.8086, "entities": { "genes": [ "ST131", "ST73" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:08.010848", "source": { "split": "train_shard_00001", "doc_id": 4778 }, "chunk_id": "train_shard_00001_4778_0", "global_id": 12424 }, { "text": "Clostridium difficile, recently renamed Clostridioides difficile, is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping (n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange.", "token_count": 503, "char_count": 1892, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8068, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:08.662208", "source": { "split": "train_shard_00001", "doc_id": 4779 }, "chunk_id": "train_shard_00001_4779_0", "global_id": 12425 }, { "text": "Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile.", "token_count": 36, "char_count": 120, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:09.015575", "source": { "split": "train_shard_00001", "doc_id": 4779 }, "chunk_id": "train_shard_00001_4779_1", "global_id": 12426 }, { "text": "A recent preliminary study from our group found that extended-spectrum cephalosporin-resistance determinants can be detected in the majority of composite fecal samples collected from Alberta feedlot cattle. Most notably, blaCTX-M genes were detected in 46.5% of samples. Further isolate characterization identified blaCTX-M-15 and blaCTX-M-27, which are widespread in bacteria from humans. We hypothesized that Escherichia coli of human and beef cattle origins share the same pool of blaCTX-M genes. In this study, we aimed to assess and compare the genomic profiles of a larger collection of blaCTX-M-positive E. coli recovered from fecal composite samples from Canadian beef feedlot cattle and human wastewater through whole-genome sequencing. The variants blaCTX-M-55, blaCTX-M-32, blaCTX-M-27, blaCTX-M-15, and blaCTX-M-14 were found in both urban wastewater and cattle fecal isolates. Core genome multilocus sequence typing showed little similarity between the fecal and wastewater isolates. Thus, if the dissemination of genes between urban wastewater and feedlot cattle occurs, it does not appear to be related to the expansion of specific clonal lineages. Further investigations are warranted to assemble and compare plasmids carrying these genes to better understand the modalities and directionality of transfer.\n\nPresence and Diversity of Extended-Spectrum Cephalosporin Resistance Among Escherichia coli from Urban Wastewater and Feedlot Cattle in Alberta, Canada.", "token_count": 501, "char_count": 1677, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:09.662413", "source": { "split": "train_shard_00001", "doc_id": 4780 }, "chunk_id": "train_shard_00001_4780_0", "global_id": 12427 }, { "text": "

Background

Essential genes are absolutely required for the survival of an organism. The identification of essential genes, besides being one of the most fundamental questions in biology, is also of interest for the emerging science of synthetic biology and for the development of novel antimicrobials. New antimicrobial therapies are desperately needed to treat multidrug-resistant pathogens, such as members of the Burkholderia cepacia complex.

Methodology/principal findings

We hypothesize that essential genes may be highly conserved within a group of evolutionary closely related organisms. Using a bioinformatics approach we determined that the core genome of the order Burkholderiales consists of 649 genes. All but two of these identified genes were located on chromosome 1 of Burkholderia cenocepacia. Although many of the 649 core genes of Burkholderiales have been shown to be essential in other bacteria, we were also able to identify a number of novel essential genes present mainly, or exclusively, within this order. The essentiality of some of the core genes, including the known essential genes infB, gyrB, ubiB, and valS, as well as the so far uncharacterized genes BCAL1882, BCAL2769, BCAL3142 and BCAL3369 has been confirmed experimentally in B. cenocepacia.

Conclusions/significance

We report on the identification of essential genes using a novel bioinformatics strategy and provide bioinformatics and experimental evidence that the large majority of the identified genes are indeed essential. The essential genes identified here may represent valuable targets for the development of novel antimicrobials and their detailed study may shed new light on the functions required to support life.\n\nHigh confidence prediction of essential genes in Burkholderia cenocepacia.", "token_count": 426, "char_count": 1810, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5765, "quality_score": 0.7882, "entities": { "genes": [ "BCAL3142", "BCAL3369", "BCAL1882", "BCAL2769" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:10.295833", "source": { "split": "train_shard_00001", "doc_id": 4781 }, "chunk_id": "train_shard_00001_4781_0", "global_id": 12428 }, { "text": "Staphylococcus aureus ST291 has been reported as a homologue recombinant double locus variant of the livestock associated S. aureus ST398. However, whole genome sequencing show that ST291 is a unique genetic lineage with highly variable content within its accessory genome compared to both human and livestock associated genome sequenced CC398s.\n\nGenome analysis of Staphylococcus aureus ST291, a double locus variant of ST398, reveals a distinct genetic lineage.", "token_count": 131, "char_count": 463, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7313, "quality_score": 0.8657, "entities": { "genes": [ "ST398", "ST291" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:10.723521", "source": { "split": "train_shard_00001", "doc_id": 4782 }, "chunk_id": "train_shard_00001_4782_0", "global_id": 12429 }, { "text": "Using whole-genome sequence (WGS) data from the GenomeTrakr network, a globally distributed network of laboratories sequencing foodborne pathogens, we present a new phylogeny of Salmonella enterica comprising 445 isolates from 266 distinct serovars and originating from 52 countries. This phylogeny includes two previously unidentified S. enterica subsp. enterica clades. Serovar Typhi is shown to be nested within clade A. Our findings are supported by both phylogenetic support, based on a core genome alignment, and Bayesian approaches, based on single-nucleotide polymorphisms. Serovar assignments were refined by in silico analysis using SeqSero. More than 10% of serovars were either polyphyletic or paraphyletic. We found variable genetic content in these isolates relating to gene mobilization and virulence factors which have different distributions within clades. Gifsy-1- and Gifsy-2-like phages appear more prevalent in clade A; other viruses are more evenly distributed. Our analyses reveal IncFII is the predominant plasmid replicon in S. enterica Few core or clade-defining virulence genes are observed, and their distributions appear probabilistic in nature. Together, these patterns demonstrate that genetic exchange within S. enterica is more extensive and frequent than previously realized, which significantly alters how we view the genetic structure of the bacterial species.IMPORTANCE Rapid improvements in nucleotide sequencing access and affordability have led to a drastic increase in availability of genetic information. This information will improve the accuracy of molecular descriptions, including serovars, within S. enterica Although the concept of serovars continues to be useful, it may have more significant limitations than previously understood. Furthermore, the discrete absence or presence of specific genes can be an unstable indicator of phylogenetic identity. Whole-genome sequencing provides more rigorous tools for assessing the distributions of these genes", "token_count": 504, "char_count": 2056, "word_count": 276, "semantic_coherence": 1, "information_density": 0.6486, "quality_score": 0.8243, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:11.396873", "source": { "split": "train_shard_00001", "doc_id": 4783 }, "chunk_id": "train_shard_00001_4783_0", "global_id": 12430 }, { "text": "Our phylogenetic and genetic content analyses reveal how active genetic elements are dynamically distributed within a species, allowing us to better understand genetic reservoirs and underlying bacterial evolution.\n\nSalmonella enterica Phylogeny Based on Whole-Genome Sequencing Reveals Two New Clades and Novel Patterns of Horizontally Acquired Genetic Elements.", "token_count": 82, "char_count": 363, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8936, "quality_score": 0.9468, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:11.803350", "source": { "split": "train_shard_00001", "doc_id": 4783 }, "chunk_id": "train_shard_00001_4783_1", "global_id": 12431 }, { "text": "The geographic and phylogenetic scale of ecologically relevant microbial diversity is still poorly understood. Using a model mutualism, fungus-growing ants and their defensive bacterial associate Pseudonocardia , we analyzed genetic diversity and biosynthetic potential in 46 strains isolated from ant colonies in a 20km transect near Barro Colorado Island in Panama. Despite an average pairwise core genome similarity of greater than 99%, population genomic analysis revealed several distinct bacterial populations matching ant host geographic distribution. We identified both genetic diversity signatures and divergent genes distinct to each lineage. We also identify natural product biosynthesis clusters specific to isolation locations. These geographic patterns were observable despite the populations living in close proximity to each other and provides evidence of ongoing genetic exchange. Our results add to the growing body of literature suggesting that variation in traits of interest can be found at extremely fine phylogenetic scales.\n\nBiogeography and Microscale Diversity Shape the Biosynthetic Potential of Fungus-growing Ant-associated Pseudonocardia", "token_count": 257, "char_count": 1174, "word_count": 157, "semantic_coherence": 1, "information_density": 0.7452, "quality_score": 0.8726, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:12.389603", "source": { "split": "train_shard_00001", "doc_id": 4784 }, "chunk_id": "train_shard_00001_4784_0", "global_id": 12432 }, { "text": "Bacteria commonly produce narrow spectrum bacteriocins as a means of inhibiting closely related species competing for similar resources in an environment. The increasing availability of genomic data means that it is becoming easier to identify bacteriocins encoded within genomes. Often, however, the presence of bacteriocin genes in a strain does not always translate into biological antimicrobial activity. For example, when analysing the Lactobacillus pangenome we identified strains encoding ten pediocin-like bacteriocin structural genes which failed to display inhibitory activity. Nine of these bacteriocins were novel whilst one was identified as the previously characterized bacteriocin \"penocin A.\" The composition of these bacteriocin operons varied between strains, often with key components missing which are required for bacteriocin production, such as dedicated bacteriocin transporters and accessory proteins. In an effort to functionally express these bacteriocins, the structural genes for the ten pediocin homologs were cloned alongside the dedicated pediocin PA-1 transporter in both Escherichia coli and Lactobacillus paracasei heterologous hosts. Each bacteriocin was cloned with its native leader sequence and as a fusion protein with the pediocin PA-1 leader sequence. Several of these bacteriocins displayed a broader spectrum of inhibition than the original pediocin PA-1. We show how potentially valuable bacteriocins can easily be \"reincarnated\" from in silico data and produced in vitro despite often lacking the necessary accompanying machinery. Moreover, the study demonstrates how genomic datasets such as the Lactobacilus pangenome harbor a potential \"arsenal\" of antimicrobial activity with the possibility of being activated when expressed in more genetically amenable hosts.\n\nReincarnation of Bacteriocins From the Lactobacillus Pangenomic Graveyard.", "token_count": 458, "char_count": 1935, "word_count": 257, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:13.051854", "source": { "split": "train_shard_00001", "doc_id": 4785 }, "chunk_id": "train_shard_00001_4785_0", "global_id": 12433 }, { "text": "The possibility of using waste Chinese cabbage (Brassica campestris) as a substrate for microbial biomass production was investigated. The juice from waste Chinese cabbage contains relatively high amounts of reducing sugars suitable for yeast culture. The cell mass and protein content of four species of yeast, Candida utilis, Pichia stipitis, Kluyveromyces marxianus, and Saccharomyces cerevisiae, were determined when cultured in juice extracted from cabbage waste. Compared to YM broth containing the same level of sugar, all the strains except C. utilis showed higher total protein production in cabbage juice medium (CJM).\n\nUse of waste Chinese cabbage as a substrate for yeast biomass production.", "token_count": 166, "char_count": 703, "word_count": 103, "semantic_coherence": 1, "information_density": 0.699, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:13.551595", "source": { "split": "train_shard_00001", "doc_id": 4786 }, "chunk_id": "train_shard_00001_4786_0", "global_id": 12434 }, { "text": "Hybridization between distantly related organisms can facilitate rapid adaptation to novel environments, but is potentially constrained by epistatic fitness interactions among cell components. The zoonotic pathogens Campylobacter coli and C. jejuni differ from each other by around 15% at the nucleotide level, corresponding to an average of nearly 40 amino acids per protein-coding gene. Using whole genome sequencing, we show that a single C. coli lineage, which has successfully colonized an agricultural niche, has been progressively accumulating C. jejuni DNA. Members of this lineage belong to two groups, the ST-828 and ST-1150 clonal complexes. The ST-1150 complex is less frequently isolated and has undergone a substantially greater amount of introgression leading to replacement of up to 23% of the C. coli core genome as well as import of novel DNA. By contrast, the more commonly isolated ST-828 complex bacteria have 10-11% introgressed DNA, and C. jejuni and nonagricultural C. coli lineages each have <2%. Thus, the C. coli that colonize agriculture, and consequently cause most human disease, have hybrid origin, but this cross-species exchange has so far not had a substantial impact on the gene pools of either C. jejuni or nonagricultural C. coli. These findings also indicate remarkable interchangeability of basic cellular machinery after a prolonged period of independent evolution.\n\nProgressive genome-wide introgression in agricultural Campylobacter coli.", "token_count": 359, "char_count": 1480, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6881, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:14.125245", "source": { "split": "train_shard_00001", "doc_id": 4787 }, "chunk_id": "train_shard_00001_4787_0", "global_id": 12435 }, { "text": "Bile salt hydrolase (BSH; EC 3.5.1.24) is the microbial enzyme that catalyzes the conversion of primary bile acids (BAs) into secondary ones, promoting microbial adaptation and modulating several host's biological functions. Probiotics with BSH activity are supposed to survive harsh intestinal conditions and exert a cholesterol-lowering effect. Here, Lacticaseibacillus rhamnosus strains (VB4 and VB1), isolated from the vaginal ecosystem, were submitted to a genomic survey, in vitro BSH activity, and BAs tolerance assay to unravel their probiotic potential as BAs modulators. The draft genomes of Lcb. rhamnosus VB4 and VB1 strains comprised 2769 and 2704 CDSs, respectively. Gene annotation revealed numerous strain-specific genes involved in metabolism and transport, as well as in DNA recombination. Each strain harbors a single bsh gene, encoding a C-N amide hydrolase, which conserved the essential residues required in the BSH core site. According to the results, compared to VB1, the VB4 strain tolerated better BAs stress and was more active in deconjugating BAs. However, BAs stress increased the bsh gene transcription in the VB1 strain but not in the VB4 strain, suggesting a partially nonlinear relationship between BSH activity and gene expression. In conclusion, despite the complexity of the BSH transcriptional system, the results support the VB4 strain as a promising BAs-deconjugating probiotic candidate.\n\nGenome Mining and Characterization of Two Novel <i>Lacticaseibacillus rhamnosus</i> Probiotic Candidates with Bile Salt Hydrolase Activity.", "token_count": 457, "char_count": 1609, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8356, "entities": { "genes": [ "VB1", "VB4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:14.758865", "source": { "split": "train_shard_00001", "doc_id": 4788 }, "chunk_id": "train_shard_00001_4788_0", "global_id": 12436 }, { "text": "Ochrobactrum is a ubiquitous Gram-negative microorganism, mostly found in the environment, which can cause opportunistic infections in humans. It is almost uniformly resistant to penicillins and cephalosporins through an AmpC-like β-lactamase enzyme class (OCH). We studied 130 assembled genomes, of which 5 were animal-derived isolates recovered in Israel, and 125 publicly available genomes. Our analysis focused on antimicrobial resistance (AMR) genes, virulence genes, and whole-genome phylogeny. We found that 76% of Ochrobactrum genomes harbored a blaOCH β-lactamase gene variant, while 7% harbored another AmpC-like gene. No virulence genes other than lipopolysaccharide-associated genes were found. Core genome multilocus sequence typing clustered most samples to known species, but neither geographical clustering nor isolation source clustering were evident. When analyzing the distribution of different blaOCH variants as well as of the blaOCH-deficient samples, a clear phylogenomic clustering was apparent for specific species. The current analysis of the largest collection to date of Ochrobactrum genomes sheds light on the resistome, virulome, phylogeny, and species classification of this increasingly reported human pathogen. Our findings also suggest that Ochrobactrum deserves further characterization to underpin its evolution, taxonomy, and antimicrobial resistance.\n\nGenomic Characterization of Antimicrobial Resistance, Virulence, and Phylogeny of the Genus Ochrobactrum.", "token_count": 457, "char_count": 1584, "word_count": 196, "semantic_coherence": 1, "information_density": 0.7296, "quality_score": 0.8648, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:15.400184", "source": { "split": "train_shard_00001", "doc_id": 4789 }, "chunk_id": "train_shard_00001_4789_0", "global_id": 12437 }, { "text": "The cybernetic approach to modeling of microbial kinetics in a mixed-substrate environment has been used in this work for the fermentative production of ethanol from cheese whey. In this system, the cells grow on multiple substrates and generate metabolic energy during product formation. This article deals with the development of a mathematical model in which the concept of cell maintenance was modified in light of the specific nature of product formation. Continuous culture data for anaerobic production of ethanol by Kluyveromyces marxianus CBS 397 on glucose and lactose were used to estimate the kinetic parameters for subsequent use in predicting the behavior of microbial growth and product formation in new situations.\n\nA mathematical model of ethanol fermentation from cheese whey : I: Model development and parameter estimation.", "token_count": 183, "char_count": 842, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:15.843795", "source": { "split": "train_shard_00001", "doc_id": 4790 }, "chunk_id": "train_shard_00001_4790_0", "global_id": 12438 }, { "text": "

Background

In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used the complete genome sequence of two MDR hvKp isolates belonging to ST23 to characterize the phylogenetic background and plasmid diversity.

Methods

Two hvKp isolates from patients with bacteremia were sequenced using Ion Torrent PGM and Oxford Nanopore MinION platforms and assembled by hybrid genome assembly approach. Comparative genomics approaches were used to investigate the population structure, evolution, virulence, and antimicrobial resistance of MDR hvKp strains.

Results

The study isolates exhibited typical features of hvKp phenotypes associated with ST23. The convergence of multidrug resistance and hypervirulence were attributed by the presence of multiple plasmids including a 216 kb virulence plasmid and MDR plasmids belonging to IncA/C2, IncFIB, IncX3, and ColKP3 groups. The insertion of catA1 gene into virulence plasmid was observed along with genetic factors such as aerobactin, salmochelin, and rmpA2 that confer hvKp's hypervirulent phenotype. The core genome single nucleotide polymorphism (SNP) phylogenetic analyses of the isolates showed the evolution of ST23 hvKp was predominantly driven by ICEKp acquisitions.

Conclusion

To the best of our knowledge, this is the first report of MDR hvKp isolates of ST23 with insertion of catA1 gene into the virulence plasmid which presents the possibility of hotspot integration sites on the plasmids to aid acquisition of AMR genes. ST23 is no longer confined to susceptible strains of hvKp", "token_count": 500, "char_count": 1730, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [ "ST23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:16.497110", "source": { "split": "train_shard_00001", "doc_id": 4791 }, "chunk_id": "train_shard_00001_4791_0", "global_id": 12439 }, { "text": "Our findings emphasize the need for more studies on recombinant events, plasmid transmission dynamics and evolutionary process involving hvKp.\n\nEmergence of Multidrug Resistant Hypervirulent ST23 Klebsiella pneumoniae: Multidrug Resistant Plasmid Acquisition Drives Evolution.", "token_count": 81, "char_count": 283, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [ "ST23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:16.865275", "source": { "split": "train_shard_00001", "doc_id": 4791 }, "chunk_id": "train_shard_00001_4791_1", "global_id": 12440 }, { "text": "

Objectives

MDR bacteria have become a prevailing health threat worldwide. We here aimed to use optical DNA mapping (ODM) as a rapid method to trace nosocomial spread of bacterial clones and gene elements. We believe that this method has the potential to be a tool of pivotal importance for MDR control.

Methods

Twenty-four Escherichia coli samples of ST410 from three different wards were collected at an Ethiopian hospital and their plasmids were analysed by ODM. Plasmids were specifically digested with Cas9 targeting the antibiotic resistance genes, stained by competitive binding and confined in nanochannels for imaging. The resulting intensity profiles (barcodes) for each plasmid were compared to identify potential clonal spread of resistant bacteria.

Results

ODM demonstrated that a large fraction of the patients carried bacteria with a plasmid of the same origin, carrying the ESBL gene blaCTX-M-15, suggesting clonal spread. The results correlate perfectly with core genome (cg)MLST data, where bacteria with the same plasmid also had very similar cgMLST profiles.

Conclusions

ODM is a rapid discriminatory method for identifying plasmids and antibiotic resistance genes. Long-range deletions/insertions, which are challenging for short-read next-generation sequencing, can be easily identified and used to trace bacterial clonal spread. We propose that plasmid typing can be a useful tool to identify clonal spread of MDR bacteria. Furthermore, the simplicity of the method enables possible future application in low- and middle-income countries.\n\nOptical maps of plasmids as a proxy for clonal spread of MDR bacteria: a case study of an outbreak in a rural Ethiopian hospital.", "token_count": 415, "char_count": 1720, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8082, "entities": { "genes": [ "ST410" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:17.492068", "source": { "split": "train_shard_00001", "doc_id": 4792 }, "chunk_id": "train_shard_00001_4792_0", "global_id": 12441 }, { "text": "Ethanol production from cellulose at 45 degrees using a batch-fed system containing alginate-immobilized Kluyveromyces marxianus IMB3", "token_count": 38, "char_count": 133, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "IMB3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:17.858690", "source": { "split": "train_shard_00001", "doc_id": 4793 }, "chunk_id": "train_shard_00001_4793_0", "global_id": 12442 }, { "text": "Abstract

Background

The majority of bacterial BSIs are believed to stem from a single, clonal organism. We hypothesized that most CRK BSIs are caused by genetically diverse, clonal strains that exhibit different phenotypes.

Methods

Blood cultures (BCs) that were positive for CRK from each of 10 patients (patients) were streaked onto agar plates, and 100 individual colonies were chosen for Illumina whole-genome sequencing. Strains from 3 patients were tested for in vitro phenotypes and virulence in mice.

Results

Patients had BSIs due to ST258 K. pneumoniae (Kp; 6), non-ST258 Kp (3), and K. michiganensis (Km; 1). 5 patients were infected with strains that differed by core genome single nucleotide polymorphism phylogeny (2–5 unique genotypes/patient) [figure]. 6 patients were infected with strains that differed by gene or plasmid content, and/or gene deletions [table]. Differences in individual patients encompassed antibiotic resistance and putative virulence genes (including mixtures of blaKPC+ and blaKPC– strains, and various capsular (CPS) and porin mutant strains). In total, BSIs in 8 of 10 patients were caused by a genotypically diverse population. In each of 3 patients, genotypically diverse ST258 Kp strains demonstrated significant differences in antibiotic susceptibility, CPS content, mucoviscosity, adherence, resistance to serum killing, and mortality rates and tissue burdens during BSIs of mice. ST258 strains from a pt with and without a KPC-bearing IncFIA plasmid differed in β-lactam susceptibility, but were equally virulent. Progressive loss of CPS in ST258 strains from another patient enhanced serum killing and adherence, and attenuated virulence", "token_count": 489, "char_count": 1711, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.798, "entities": { "genes": [ "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:18.510550", "source": { "split": "train_shard_00001", "doc_id": 4794 }, "chunk_id": "train_shard_00001_4794_0", "global_id": 12443 }, { "text": "Using PCR markers to test 96 colonies per positive BC bottle, we demonstrated that strains selected by the clinical micro lab accounted for 2% to 98% of a population in different patients.

Conclusion

CRK causing BSIs in most patients demonstrated remarkable genotypic diversity, which impacted antibiotic susceptibility, virulence and other phenotypes. Differences were not recognized during hospitalization since clinical labs select single, morphologically distinct colonies for evaluation. Studies are needed to understand the clinical implications of our findings, diversity during other BSIs, and whether clinical lab practices need revision.

Disclosures

All authors: No reported disclosures.\n\n246. Carbapenem-resistant Klebsiella (CRK) Bloodstream Infections (BSIs) Are Caused by Bacterial Populations That Are Genotypically and Phenotypically Diverse", "token_count": 214, "char_count": 875, "word_count": 113, "semantic_coherence": 1, "information_density": 0.823, "quality_score": 0.9115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:18.968140", "source": { "split": "train_shard_00001", "doc_id": 4794 }, "chunk_id": "train_shard_00001_4794_1", "global_id": 12444 }, { "text": "An outbreak of Shiga toxin-producing Escherichia coli (STEC) O157:H7 occurred on the Isle of Wight between August and October 2017. Of the seven cases linked to the outbreak, five were identified through the statutory notification process and two were identified through national surveillance of whole genome sequencing data. Enhanced surveillance questionnaires established a common link to a farm, and link to the likely food vehicle, raw drinking milk (RDM). Microbiological investigations, including PCR, identified the presence of STEC O157:H7 in samples of RDM. Analysis of core genome single nucleotide polymorphism (SNP) data of STEC O157:H7 from human stool specimens, animal faecal samples and RDM demonstrated a one SNP difference between isolates, and therefore close genetic relatedness. Control measures that were put in place included suspension of sales and recall of RDM, as well as restrictions on public access to parts of the farm. Successful integration of traditional epidemiological surveillance and advanced laboratory methods for the detection and characterisation of STEC O157:H7 from human, animal and environmental samples enabled prompt identification of the outbreak vehicle and provided evidence to support the outbreak control team's decision-making, leading to implementation of effective control measures in a timely manner.\n\nOutbreak of Shiga toxin-producing Escherichia coli O157:H7 linked to raw drinking milk resolved by rapid application of advanced pathogen characterisation methods, England, August to October 2017.", "token_count": 369, "char_count": 1570, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6063, "quality_score": 0.8032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:19.550785", "source": { "split": "train_shard_00001", "doc_id": 4795 }, "chunk_id": "train_shard_00001_4795_0", "global_id": 12445 }, { "text": "Cronobacter spp. are opportunistic pathogens of the Enterobacteriaceae family. The organism causes infections in all age groups, but the most serious cases occur in outbreaks related to neonates with meningitis and necrotizing enterocolitis. The objective was to determine the in silico and in vitro putative virulence factors of six Cronobacter sakazakii strains isolated from powdered milk (PM) in the Czech Republic. Strains were identified by MALDI-TOF MS and whole-genome sequencing (WGS). Virulence and resistance genes were detected with the Ridom SeqSphere+ software task template and the Comprehensive Antibiotic Resistance Database (CARD) platform. Adherence and invasion ability were performed using the mouse neuroblastoma (N1E-115 ATCCCRL-2263) cell line. The CRISPR-Cas system was searched with CRISPRCasFinder. Core genome MLST identified four different sequence types (ST1, ST145, ST245, and ST297) in six isolates. Strains 13755-1B and 1847 were able to adhere in 2.2 and 3.2 × 106 CFU/mL, while 0.00073% invasion frequency was detected only in strain 1847. Both strains 13755-1B and 1847 were positive for three (50.0%) and four virulence genes, respectively. The cpa gene was not detected. Twenty-eight genes were detected by WGS and grouped as flagellar or outer membrane proteins, chemotaxis, hemolysins, and invasion, plasminogen activator, colonization, transcriptional regulator, and survival in macrophages", "token_count": 455, "char_count": 1470, "word_count": 202, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [ "ST145", "ST245", "ST1", "ST297" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:20.188369", "source": { "split": "train_shard_00001", "doc_id": 4796 }, "chunk_id": "train_shard_00001_4796_0", "global_id": 12446 }, { "text": "The colistin-resistance-encoding mcr-9.1 and cephalothin-resis-encoding blaCSA genes and IncFII(pECLA) and IncFIB(pCTU3) plasmids were detected. All strains exhibited CRISPR matrices and four of them two type I-E and I-F matrices. Combined molecular methodologies improve Cronobacter spp. decision-making for health authorities to protect the population.\n\nMolecular Characterization of Cronobacter sakazakii Strains Isolated from Powdered Milk.", "token_count": 163, "char_count": 483, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8491, "quality_score": 0.9245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:20.630441", "source": { "split": "train_shard_00001", "doc_id": 4796 }, "chunk_id": "train_shard_00001_4796_1", "global_id": 12447 }, { "text": "After 20h fermentation of medium containing 5% (w/v) dehydrated whey, at 30 degrees C, pH 4.5, yeast cells were harvested, diluted in 0.1M KH2PO4, and autolyzed at different pHs (6.5-7.5) and temperatures (45-55 degrees C). Phosphodiesterase (0.2-1.0% w/v, 65 degrees C, pH 6.5, 6h) and adenyl deaminase (0.5-1.0% w/v, 60 degrees C, pH 5.5, 4h) were added to the autolysates. After heat treatment (100 degrees C, 15 min), samples were analyzed by RP-HPLC and LC/MS. Production of 5'-ribonucleotides was maximized at 50 degrees C, pH 6.5. Yields of 5'-AMP (800 micrograms/g of biomass) and 5'-GMP (2000 micrograms/g) increased considerably after addition of 1.0% phosphodiesterase. 5'-IMP increased only after addition of 1.0% adenyl deaminase.\n\nEnzymatic production of ribonucleotides from autolysates of Kluyveromyces marxianus grown on whey", "token_count": 345, "char_count": 842, "word_count": 125, "semantic_coherence": 1, "information_density": 0.712, "quality_score": 0.856, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:21.205518", "source": { "split": "train_shard_00001", "doc_id": 4797 }, "chunk_id": "train_shard_00001_4797_0", "global_id": 12448 }, { "text": "Klebsiella pneumoniae is one of the leading causes of nosocomial infections. Carbapenem-resistant K. pneumoniae are on the rise globally. The biofilm forming ability of K. pneumoniae further complicates patient management. There is still a knowledge gap on the association of biofilm formation with patient outcome and carbapenem susceptibility, which is investigated in present study. K. pneumoniae isolates from patients admitted in critical care units with catheters and ventilators were included. K. pneumoniae (n = 72) were subjected to 96-well plate biofilm formation assay followed by MBEC assay for subset of strong biofilm formers. Whole genome sequencing and a core genome phylogenetic analysis in comparison with global isolates were performed. Phenotypic analyses showed a positive correlation between biofilm formation and carbapenem resistance. Planktonic cells observed to be susceptible in vitro exhibited higher MICs in biofilm structure, hence MICs cannot be extrapolated for treatment. The biofilm forming ability had a significant association with morbidity/mortality. Infections by stronger biofilm forming pathogens significantly (p < 0.05) resulted in fewer \"average days alive\" for the patient (3.33 days) in comparison to those negative for biofilms (11.33 days). Phylogenetic analysis including global isolates revealed clear association of sequence types with genes for biofilm formation and carbapenem resistance. Known hypervirulent clone-ST23 with wcaG, magA, rmpA, rmpA2, and wzc with lack of mutation for hyper-capsulation might be poor biofilm formers. ST15, ST16, ST307, and ST258 (reported global high-risk clones) were wcaJ negative indicating the high potential of biofilm forming capacity", "token_count": 521, "char_count": 1824, "word_count": 242, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [ "ST23", "ST307", "ST16", "ST15", "ST258" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:56:21.899767", "source": { "split": "train_shard_00001", "doc_id": 4798 }, "chunk_id": "train_shard_00001_4798_0", "global_id": 12449 }, { "text": "Genes wabG and treC for CPS, bcsA and pgaC for adhesins, luxS for quorum sensing were common in all clades in addition to genes for aerobactin (iutA), allantoin (allS), type I and III fimbriae (fimA, fimH, and mrkD) and pili (pilQ and ecpA). This study is the first of its kind to compare genetic features of antimicrobial resistance with a spectrum covering most of the genetic factors for K. pneumoniae biofilm. These results highlight the importance of biofilm screening to effectively manage nosocomial infections by K. pneumoniae. Further, data obtained on epidemiology and associations of biofilm and resistance genetic factors will serve to enhance our understanding on biofilm mechanisms in K. pneumoniae.\n\nThe Influence of Biofilms on Carbapenem Susceptibility and Patient Outcome in Device Associated <i>K. pneumoniae</i> Infections: Insights Into Phenotype vs Genome-Wide Analysis and Correlation.", "token_count": 344, "char_count": 1025, "word_count": 136, "semantic_coherence": 1, "information_density": 0.7132, "quality_score": 0.8566, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:22.477318", "source": { "split": "train_shard_00001", "doc_id": 4798 }, "chunk_id": "train_shard_00001_4798_1", "global_id": 12450 }, { "text": "BackgroundCampylobacter is one of the most frequent causes of bacterial gastroenteritis. Campylobacter outbreaks are rarely reported, which could be a reflection of a surveillance without routine molecular typing. We have previously shown that numerous small outbreak-like clusters can be detected when whole genome sequencing (WGS) data of clinical Campylobacter isolates was applied.AimTyping-based surveillance of Campylobacter infections was initiated in 2019 to enable detection of large clusters of clinical isolates and to match them to concurrent retail chicken isolates in order to react on ongoing outbreaks.MethodsWe performed WGS continuously on isolates from cases (n = 701) and chicken meat (n = 164) throughout 2019. Core genome multilocus sequence typing was used to detect clusters of clinical isolates and match them to isolates from chicken meat.ResultsSeventy-two clusters were detected, 58 small clusters (2-4 cases) and 14 large clusters (5-91 cases). One third of the clinical isolates matched isolates from chicken meat. One large cluster persisted throughout the whole year and represented 12% of all studied Campylobacter cases. This cluster type was detected in several chicken samples and was traced back to one slaughterhouse, where interventions were implemented to control the outbreak.ConclusionOur WGS-based surveillance has contributed to an improved understanding of the dynamics of the occurrence of Campylobacter strains in chicken meat and the correlation to clusters of human cases.\n\nWhole genome sequencing data used for surveillance of Campylobacter infections: detection of a large continuous outbreak, Denmark, 2019.", "token_count": 423, "char_count": 1708, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5574, "quality_score": 0.7787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:23.101433", "source": { "split": "train_shard_00001", "doc_id": 4799 }, "chunk_id": "train_shard_00001_4799_0", "global_id": 12451 }, { "text": "

Objectives

The aim of this study was to investigate the occurrence of the newly described transferable colistin resistance gene mcr-9 in extended-spectrum β-lactamase (ESBL)-producing clinical Enterobacteriaceae isolates from horses in Sweden.

Methods

A total of 56 whole-genome sequenced ESBL-producing Enterobacteriaceae isolates from horses were subjected to in silico detection of antimicrobial resistance genes and identification of plasmid replicons types. The colistin minimum inhibitory concentration (MIC) for mcr-positive isolates was determined by broth microdilution. Relatedness between Enterobacteriaceae carrying mcr genes was determined by multilocus sequence typing (MLST) and core genome MLST.

Results

Thirty ESBL-producing Enterobacteriaceae isolates from horses were positive for the colistin resistance gene mcr-9. These isolates included Enterobacter cloacae, Escherichia coli, Klebsiella oxytoca and Citrobacter freundii and belonged to diverse MLST sequence types within each species. Two of the mcr-9-containing isolates originated from the same horse. All mcr-9-positive isolates had colistin MICs below or equal to the EUCAST epidemiological cut-off value of 2 mg/L and were negative for the two potential regulatory genes qseB-like and qseC-like for mcr-9. Except for one isolate carrying only blaTEM-1B, all of the isolates carried blaSHV-12 and blaTEM-1B, and were all considered multidrug-resistant as they harboured genes encoding resistance to aminoglycosides, chloramphenicol, fosfomycin, macrolides, quinolones, sulfonamides, trimethoprim and tetracyclines", "token_count": 479, "char_count": 1668, "word_count": 200, "semantic_coherence": 1, "information_density": 0.64, "quality_score": 0.82, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:23.760614", "source": { "split": "train_shard_00001", "doc_id": 4800 }, "chunk_id": "train_shard_00001_4800_0", "global_id": 12452 }, { "text": "Plasmid replicon types IncHI2 and IncHI2A were detected in all mcr-9-positive isolates.

Conclusion

The occurrence of mcr-9 was common among clinical ESBL-producing Enterobacteriaceae isolates from horses in Sweden and was linked to the ESBL-encoding gene blaSHV-12 and plasmid replicon types IncHI2 and IncHI2A.\n\nA link between the newly described colistin resistance gene mcr-9 and clinical Enterobacteriaceae isolates carrying blaSHV-12 from horses in Sweden.", "token_count": 151, "char_count": 490, "word_count": 61, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.8361, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:24.219743", "source": { "split": "train_shard_00001", "doc_id": 4800 }, "chunk_id": "train_shard_00001_4800_1", "global_id": 12453 }, { "text": "The influence of pH control and aeration (20% dissolved oxygen) on nisin production in a supplemented cheese whey permeate was examined during batch fermentation with Lactococcus lactis subsp. lactis A.T.C.C. 7962. A maximum nisin activity of 5280 i.u./ml of medium was observed in the raw extract of nisin after 9 h of fermentation with a constant pH at 4.9. However, the fermentation was continued until 24 h, when a decrease in the nisin activity was observed. The pH control did not influence the nisin production and aeration of the culture medium increased cell growth (biomass) but not nisin activity. The yeast Kluyveromyces marxianus, used as an alternative method to control pH, has not been efficient.\n\nNisin production from Lactococcus lactis A.T.C.C. 7962 using supplemented whey permeate.", "token_count": 241, "char_count": 802, "word_count": 126, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:25.171481", "source": { "split": "train_shard_00001", "doc_id": 4801 }, "chunk_id": "train_shard_00001_4801_0", "global_id": 12454 }, { "text": "

Background

The genomic diversity of different species within the genus Lactococcus and the relationships between genomic differentiation and environmental factors remain unclear. In this study, type isolates of ten Lactococcus species/subspecies were sequenced to assess their genomic characteristics, metabolic diversity, and phylogenetic relationships.

Results

The total genome sizes varied between 1.99 (Lactococcus plantarum) and 2.46 megabases (Mb; L. lactis subsp. lactis), and the G + C content ranged from 34.81 (L. lactis subsp. hordniae) to 39.67% (L. raffinolactis) with an average value of 37.02%. Analysis of genome dynamics indicated that the genus Lactococcus has an open pan-genome, while the core genome size decreased with sequential addition at the genus and species group levels. A phylogenetic dendrogram based on the concatenated amino acid sequences of 643 core genes was largely consistent with the phylogenetic tree obtained by 16S ribosomal RNA (rRNA) genes, but it provided a more robust phylogenetic resolution than the 16S rRNA gene-based analysis.

Conclusions

Comparative genomics indicated that species in the genus Lactococcus had high degrees of diversity in genome size, gene content, and carbohydrate metabolism. This may be important for the specific adaptations that allow different Lactococcus species to survive in different environments. These results provide a quantitative basis for understanding the genomic and metabolic diversity within the genus Lactococcus, laying the foundation for future studies on taxonomy and functional genomics.\n\nGenome-level comparisons provide insight into the phylogeny and metabolic diversity of species within the genus Lactococcus.", "token_count": 465, "char_count": 1730, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6383, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:25.838059", "source": { "split": "train_shard_00001", "doc_id": 4802 }, "chunk_id": "train_shard_00001_4802_0", "global_id": 12455 }, { "text": "

ABSTRACT

Gene-by-gene approaches are becoming increasingly popular in bacterial genomic epidemiology and outbreak detection. However, there is a lack of open-source scalable software for schema definition and allele calling for these methodologies. The chewBBACA suite was designed to assist users in the creation and evaluation of novel whole-genome or core-genome gene-by-gene typing schemas and subsequent allele calling in bacterial strains of interest. The software can run in a laptop or in high performance clusters making it useful for both small laboratories and large reference centers. ChewBBACA is available at https://github.com/B-UMMI/chewBBACA or as a docker image at https://hub.docker.com/r/ummidock/chewbbaca/ .

DATA SUMMARY

Assembled genomes used for the tutorial were downloaded from NCBI in August 2016 by selecting those submitted as Streptococcus agalactiae taxon or sub-taxa. All the assemblies have been deposited as a zip file in FigShare ( https://figshare.com/s/9cbe1d422805db54cd52 ), where a file with the original ftp link for each NCBI directory is also available. Code for the chewBBACA suite is available at https://github.com/B-UMMI/chewBBACA while the tutorial example is found at https://github.com/B-UMMI/chewBBACA_tutorial . I/We confirm all supporting data, code and protocols have been provided within the article or through supplementary data files. ⊠

IMPACT STATEMENT

The chewBBACA software offers a computational solution for the creation, evaluation and use of whole genome (wg) and core genome (cg) multilocus sequence typing (MLST) schemas. It allows researchers to develop wg/cgMLST schemes for any bacterial species from a set of genomes of interest. The alleles identified by chewBBACA correspond to potential coding sequences, possibly offering insights into the correspondence between the genetic variability identified and phenotypic variability", "token_count": 511, "char_count": 1925, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6475, "quality_score": 0.8238, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:26.494316", "source": { "split": "train_shard_00001", "doc_id": 4803 }, "chunk_id": "train_shard_00001_4803_0", "global_id": 12456 }, { "text": "The software performs allele calling in a matter of seconds to minutes per strain in a laptop but is easily scalable for the analysis of large datasets of hundreds of thousands of strains using multiprocessing options. The chewBBACA software thus provides an efficient and freely available open source solution for gene-by-gene methods. Moreover, the ability to perform these tasks locally is desirable when the submission of raw data to a central repository or web services is hindered by data protection policies or ethical or legal concerns.\n\nchewBBACA: A complete suite for gene-by-gene schema creation and strain identification", "token_count": 130, "char_count": 632, "word_count": 97, "semantic_coherence": 1, "information_density": 0.732, "quality_score": 0.866, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:26.912301", "source": { "split": "train_shard_00001", "doc_id": 4803 }, "chunk_id": "train_shard_00001_4803_1", "global_id": 12457 }, { "text": "Hemagglutinating properties of culture liquid and cells of 142 yeast strains of species Saccharomyces cerevisiae, Kluyveromyces marxianus, K. dobzhanskii, K. lactis var. lactis and K. lactis var. drosophilarum, isolated from various sources have been studied. A capacity of yeast (44% of the studied strains) to synthesize both lectins bound to a cell and extracellular lectins has been established; the latter have been found in yeast for the first time.\n\n[Search for lectin producers among some yeast species].", "token_count": 145, "char_count": 512, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7013, "quality_score": 0.8506, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:27.345191", "source": { "split": "train_shard_00001", "doc_id": 4804 }, "chunk_id": "train_shard_00001_4804_0", "global_id": 12458 }, { "text": "

Introduction

Pseudomonas aeruginosa (P. aeruginosa) represents a paradigm for studies on antibiotic resistance. Nevertheless, despite the considerable number of genome sequences that have been released in recent years, there is still a paucity of knowledge regarding the genomic determinants of the typical phenotypic traits associated with pulmonary infection.

Methods

The genomes of 40 strains of P. aeruginosa were sequenced over an 8-year period (2007-2014), isolated from the sputum of a single patient with cystic fibrosis in Trentino, Italy. The same isolates were characterised for a panel of 14 phenotypes, including biofilm formation, antibiotic resistance, secretion of siderophores and virulence factors. The phylogenetic coherence of the measured phenotypes was determined in relation to the tree based on single-nucleotide polymorphisms (SNPs). Subsequently, the semantic framework for comparative functional genomics (SAPP) was employed to investigate the depletion or enrichment of specific protein functional domains within the population in relation to the observed phenotypes.

Results

The majority of our findings regarding phenotypic adaptation over time were consistent with the population structure and followed the evolutionary pathways described in the literature. However, an exact relationship between the presence of genes and specific phenotypes could not be established. The SAPP approach enabled the identification of 189 protein domains that were significantly enriched in antibiotic-resistant strains, as well as 87 domains associated with other phenotypic adaptations. In some cases, the domains were commonly associated with antibiotic resistances, for example, outer membrane efflux pumps and porins. However, we also detected a number of domains with unknown function.

Discussion

Our findings provide a foundation for a more comprehensive understanding of the phenotypic adaptations occurring during microevolution in lung environments and facilitate the identification of new targets for the design of novel antimicrobial agents.", "token_count": 492, "char_count": 2109, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6462, "quality_score": 0.8231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:27.995437", "source": { "split": "train_shard_00001", "doc_id": 4805 }, "chunk_id": "train_shard_00001_4805_0", "global_id": 12459 }, { "text": "Protein functional domain analysis enhances genotype-phenotype associations in comparative genomic studies of <i>Pseudomonas aeruginosa</i>.", "token_count": 43, "char_count": 152, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:28.358883", "source": { "split": "train_shard_00001", "doc_id": 4805 }, "chunk_id": "train_shard_00001_4805_1", "global_id": 12460 }, { "text": "The unusual case of an oesophagitis caused by Candida kefyr in a patient with squamous cell carcinoma of the oropharynx is reported. The further implementation of C. kefyr in the production of milk products is discussed.\n\nOesophagitis caused by Candida kefyr.", "token_count": 69, "char_count": 259, "word_count": 41, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:28.725661", "source": { "split": "train_shard_00001", "doc_id": 4806 }, "chunk_id": "train_shard_00001_4806_0", "global_id": 12461 }, { "text": "An emergent clone of Haemophilus influenzae biogroup aegyptius (Hae) is responsible for outbreaks of Brazilian purpuric fever (BPF). First recorded in Brazil in 1984, the so-called BPF clone of Hae caused a fulminant disease that started with conjunctivitis but developed into septicemic shock; mortality rates were as high as 70%. To identify virulence determinants, we conducted a pan-genomic analysis. Sequencing of the genomes of the BPF clone strain F3031 and a noninvasive conjunctivitis strain, F3047, and comparison of these sequences with 5 other complete H. influenzae genomes showed that >77% of the F3031 genome is shared among all H. influenzae strains. Delineation of the Hae accessory genome enabled characterization of 163 predicted protein-coding genes; identified differences in established autotransporter adhesins; and revealed a suite of novel adhesins unique to Hae, including novel trimeric autotransporter adhesins and 4 new fimbrial operons. These novel adhesins might play a critical role in host-pathogen interactions.\n\nLineage-specific virulence determinants of Haemophilus influenzae biogroup aegyptius.", "token_count": 310, "char_count": 1132, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6855, "quality_score": 0.8428, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:29.307620", "source": { "split": "train_shard_00001", "doc_id": 4807 }, "chunk_id": "train_shard_00001_4807_0", "global_id": 12462 }, { "text": "The production of pectolytic enzyme in the genus Kluyveromyces was investigated. The production of the enzymewas dependent on the strain, and some strains belonging to K. fragilis, K. marxianus, and K. wickerhamii produced this enzyme among 11 species (29 strains) of the genus Kluyveromyces. K. fragilis IFO 0288 produced at least four endo-polygalacturonases which have different molecular weights. The dominant endo-polygalacturonase in the culture filtrate of the strain was purified and isolated as crystals. The purified enzyme was homogeneous based on analysis by polyacrylamide gel electrophoresis and ultracentrifugation. The enzyme was a glycoprotein having an isoelectric point around pH 5.6. The sedimentation coefficient (S20, w) was 3.77S, and the molecular weight was around 33, 000. The enzyme contained aspartic acid (asparagine), serine, threonine, and glycine at relatively high levels. The enzyme showed the highest activity around pH 5.0 and was stable at pH 5.0 up to 30°C. With the enzyme, and activity which releases highly polymerized pectin from various protopectins (protopectinase activity) was found.\n\nPurification, crystallization and some properties of endopolygalacturonase from Kluyveromyces fragilis.", "token_count": 365, "char_count": 1238, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6379, "quality_score": 0.819, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:29.884363", "source": { "split": "train_shard_00001", "doc_id": 4808 }, "chunk_id": "train_shard_00001_4808_0", "global_id": 12463 }, { "text": "Kluyveromyces marxianus had a higher specific activity of diacetyl reductase (EC 1.1.1.5) than all other organisms previously reported. The enzyme was NADH-dependent and irreversibly catalysed the conversion of diacetyl to acetoin with an optimum pH of 7.0. It was stable at 40°C but lost 50% of its activity at 50°C in 30 min. The K m and V max values for diacetyl were 1.8 mM and 0.053 mM/min, respectively.\n\nKluyveromyces marxianus: a potential source of diacetyl reductase.", "token_count": 169, "char_count": 477, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7922, "quality_score": 0.8961, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:30.333129", "source": { "split": "train_shard_00001", "doc_id": 4809 }, "chunk_id": "train_shard_00001_4809_0", "global_id": 12464 }, { "text": "

Background

Xanthomonas translucens pathovars differ in their individual host ranges among Poaceae. As the causal agent of bacterial wilt in Italian ryegrass (Lolium multiflorum Lam.), X. translucens pv. graminis (Xtg) is one of the most important bacterial pathogens in temperate grassland regions. The genomes of six Xtg strains from Switzerland, Norway, and New Zealand were sequenced in order to gain insight into conserved genomic traits from organisms covering a wide geographical range. Subsequent comparative analysis with previously published genome data of seven non-graminis X. translucens strains including the pathovars arrhenatheri, poae, phlei, cerealis, undulosa, and translucens was conducted to identify candidate genes linked to the host adaptation of Xtg to Italian ryegrass.

Results

Phylogenetic analysis revealed a tight clustering of Xtg strains, which were found to share a large core genome. Conserved genomic traits included a non-canonical type III secretion system (T3SS) and a type IV pilus (T4P), which both revealed distinct primary structures of the pilins when compared to the non-graminis X. translucens strains. Xtg-specific traits that had no homologues in the other X. translucens strains were further found to comprise several hypothetical proteins, a TonB-dependent receptor, transporters, and effector proteins as well as toxin-antitoxin systems and DNA methyltransferases. While a nearly complete flagellar gene cluster was identified in one of the sequenced Xtg strains, phenotypic analysis pointed to swimming-deficiency as a common trait of the pathovar graminis.

Conclusion

Our study suggests that host adaptation of X. translucens pv. graminis may be conferred by a combination of pathovar-specific effector proteins, regulatory mechanisms, and adapted nutrient acquisition", "token_count": 466, "char_count": 1840, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6389, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:30.970610", "source": { "split": "train_shard_00001", "doc_id": 4810 }, "chunk_id": "train_shard_00001_4810_0", "global_id": 12465 }, { "text": "Sequence deviations of pathogen-associated molecular patterns (PAMPs), as observed for the pilins of the T4P and T3SS, are moreover likely to impede perception by the plant defense machinery and thus facilitate successful host colonization of Italian ryegrass.\n\nComparative genomics of host adaptive traits in Xanthomonas translucens pv. graminis.", "token_count": 86, "char_count": 347, "word_count": 48, "semantic_coherence": 1, "information_density": 0.8542, "quality_score": 0.9271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:31.347458", "source": { "split": "train_shard_00001", "doc_id": 4810 }, "chunk_id": "train_shard_00001_4810_1", "global_id": 12466 }, { "text": "Encapsulated microbes have been used for decades to produce commodities ranging from methyl ketone to beer. Encapsulated cells undergo limited replication, which enables them to more efficiently convert substrate to product than planktonic cells and which contributes to their stress resistance. To determine how encapsulated yeast supports long-term, repeated fed-batch ethanologenic fermentation, and whether different matrices influence that process, fermentation and indicators of matrix durability and cell viability were monitored in high-dextrose, fed-batch culture over 7 weeks. At most timepoints, ethanol yield (g/g) in encapsulated cultures exceeded that in planktonic cultures. And frequently, ethanol yield differed among the four matrices tested: sodium alginate crosslinked with Ca2+ and chitosan, sodium alginate crosslinked with Ca2+ , Protanal alginate crosslinked with Ca2+ and chitosan, Protanal alginate crosslinked with Ca2+ , with the last of these consistently demonstrating the highest values. Young's modulus and viscosity were higher for matrices crosslinked with chitosan over the first week; thereafter values for both parameters declined and were indistinguishable among treatments. Encapsulated cells exhibited greater heat shock tolerance at 50°C than planktonic cells in either stationary or exponential phase, with similar thermotolerance observed across all four matrix types. Altogether, these data demonstrate the feasibility of re-using encapsulated yeast to convert dextrose to ethanol over at least 7 weeks.\n\nMatrices (re)loaded: Durability, viability, and fermentative capacity of yeast encapsulated in beads of different composition during long-term fed-batch culture.", "token_count": 430, "char_count": 1754, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:31.973962", "source": { "split": "train_shard_00001", "doc_id": 4811 }, "chunk_id": "train_shard_00001_4811_0", "global_id": 12467 }, { "text": "Vertical transmission of maternal microbes is a major route for establishing the gut microbiome in newborns. The impact of perinatal antibiotics on vertical transmission of microbes and antimicrobial resistance is not well understood. Using a metagenomic approach, we analyzed the fecal samples from mothers and vaginally delivered infants from a control group (10 pairs) and a treatment group (10 pairs) receiving perinatal antibiotics. Antibiotic-usage had a significant impact on the main source of inoculum in the gut microbiome of newborns. The control group had significantly more species transmitted from mothers to infants (P = .03) than the antibiotic-treated group. Approximately 72% of the gut microbial population of infants at 3-7 days after birth in the control group was transmitted from their mothers, versus only 25% in the antibiotic-treated group. In conclusion, perinatal antibiotics markedly disturbed vertical transmission and changed the source of gut colonization towards horizontal transfer from the environment to the infants.\n\nVertical Transmission of Gut Microbiome and Antimicrobial Resistance Genes in Infants Exposed to Antibiotics at Birth.", "token_count": 279, "char_count": 1172, "word_count": 169, "semantic_coherence": 1, "information_density": 0.5325, "quality_score": 0.7663, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:32.527007", "source": { "split": "train_shard_00001", "doc_id": 4812 }, "chunk_id": "train_shard_00001_4812_0", "global_id": 12468 }, { "text": "

Background

The global dissemination of colistin resistance encoded by mcr-1 has been attributed to extensive use of colistin in livestock, threatening colistin efficacy in medicine. The emergence of mcr-1 in common pathogens, such as Escherichia coli , is of particular concern. Therefore, China banned the use of colistin in animal feed from May 1 ST 2017. We investigated subsequent changes in mcr-1 prevalence, and the genomic epidemiology of mcr-1 -positive Escherichia coli (MCRPEC).

Methods

Sampling was conducted pre- (October-December 2016) and post-colistin ban (October-December, 2017 and 2018, respectively). 3675 non-duplicate pig fecal samples were collected from 14 provinces (66 farms) in China to determine intervention-related changes in mcr-1 prevalence. 15193 samples were collected from pigs, healthy human volunteers, colonized and infected hospital inpatients, food and the environment in Guangzhou, to characterize source-specific mcr-1 prevalence and the wider ecological impact of the ban. From these samples, 688 MCRPEC were analyzed with whole genome sequencing (WGS), plasmid conjugation and S1-PFGE/Southern blots to characterize associated genomic changes.

Findings

After the ban, mcr-1 prevalence decreased significantly in national pig farms, from 45·0% (308/684 samples) in 2016, to 19·4% (274/1416) in 2018 (p<0·0001). This trend was mirrored in samples from most sources in Guangzhou (overall 19·2% [959/5003 samples] in 2016; 5·3% [238/4489] in 2018; p<0·0001)", "token_count": 507, "char_count": 1523, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:33.186551", "source": { "split": "train_shard_00001", "doc_id": 4813 }, "chunk_id": "train_shard_00001_4813_0", "global_id": 12469 }, { "text": "The population structure of MCRPEC was diverse (23 sequence clusters [SCs]); ST10 clonal complex isolates were predominant (247/688 [36%]). MCRPEC causing infection in hospitalized inpatients were genetically more distinct and appeared less affected by the ban. mcr-1 was predominantly found on plasmids (632/688 [92%]). Common mcr-1 plasmid types included IncX4, IncI2 and IncHI2 (502/656 [76.5%]); significant increases in IncI2-associated mcr-1 and a distinct lineage of mcr-1 -associated IncHI2 were observed post-ban. Changes in the frequency of mcr-1 -associated flanking sequences (IS Apl1 -negative MCRPEC), 63 core genome SNPs and 30 accessory genes were also significantly different after the ban, consistent with rapid genetic adaptation in response to changing selection pressures.

Interpretation

A rapid, ecosystem-wide, decline in mcr-1 was observed after banning the use of colistin in animal feed, with associated genetic changes in MCRPEC. Genomic surveillance is key to assessing and monitoring stewardship interventions.

Funding

National Natural Science Foundation of China\n\nDynamics ofmcr-1prevalence andmcr-1-positiveEscherichia coliafter the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing based molecular epidemiological study", "token_count": 395, "char_count": 1365, "word_count": 179, "semantic_coherence": 1, "information_density": 0.7318, "quality_score": 0.8659, "entities": { "genes": [ "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:33.805954", "source": { "split": "train_shard_00001", "doc_id": 4813 }, "chunk_id": "train_shard_00001_4813_1", "global_id": 12470 }, { "text": "

Background

In many prokaryotic genera a clustered phylogeny is observed, akin to the occurrence of species in sexually reproducing organisms. For some taxa, homologous recombination has been invoked as the underlying mechanism providing genomic cohesion among conspecific individuals. Whether this mechanism is applicable to prokaryotes in freshwaters with low habitat connectivity - i.e. elevated geographic barriers to gene flow - is unclear. To investigate further we studied genomic trends within the globally abundant PnecC cluster (genus Polynucleobacter, Betaproteobacteria) and analyzed homologous recombination within the affiliated species P. asymbioticus.

Results

Comparisons among 20 PnecC genomes revealed a clearly discontinuous distribution of nucleotide sequence similarities. Among the nine conspecific individuals (P. asymbioticus) all average nucleotide identity (ANI) values were greater than 97%, whereas all other comparisons exhibited ANI values lower than 85%. The reconstruction of recombination and mutation events for the P. asymbioticus core genomes yielded an r/m ratio of 7.4, which is clearly above estimated thresholds for recombination to act as a cohesive force. Hotspots of recombination were found to be located in the flanking regions of genomic islands. Even between geographically separated habitats a high flux of recombination was evident. While a biogeographic population structure was suggested from MLST data targeting rather conserved loci, such a structure was barely visible when whole genome data was considered. However, both MLST and whole genome data showed evidence of differentiation between two lineages of P. asymbioticus. The ratios of non-synonymous to synonymous substitution rates as well as growth rates in transplantation experiments suggested that this divergence was not selectively neutral.

Conclusions

The high extent of homologous recombination among P. asymbioticus bacteria can act as a cohesive force that effectively counteracts genetic divergence. At least on a regional scale, homologous recombination can act across geographically separated ecosystems and therefore plays an important role in the evolution and consistency of bacterial freshwater species", "token_count": 527, "char_count": 2249, "word_count": 303, "semantic_coherence": 1, "information_density": 0.6502, "quality_score": 0.8251, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:56:34.474066", "source": { "split": "train_shard_00001", "doc_id": 4814 }, "chunk_id": "train_shard_00001_4814_0", "global_id": 12471 }, { "text": "A species model akin to the biological species concept may be applicable for P. asymbioticus. Nonetheless, two genetically distinct lineages have emerged and further research may clarify if their divergence has been initiated by reinforced geographical barriers or has been evolving in sympatry.\n\nGenomic divergence and cohesion in a species of pelagic freshwater bacteria.", "token_count": 83, "char_count": 373, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:34.846164", "source": { "split": "train_shard_00001", "doc_id": 4814 }, "chunk_id": "train_shard_00001_4814_1", "global_id": 12472 }, { "text": "

Background

Plants have evolved alongside microbes, enabling plants to better cope with abiotic and biotic stress. Interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants exhibit a \"home field advantage\" by preferentially recruiting microbes unique to their native environments, likely through mutual recognition and selective recruitment mechanisms.

Results

Using gene- and genome-centric approaches, we assess the functional potential of root-associated microbes and profile their host metabolites to uncover the metabolic outputs potentially regulating host‒microbe interactions in Andropogon gerardii. We find that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine is highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses.

Conclusions

This study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance their ability to thrive in stressful environments. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture when coping with climate change.\n\nInteraction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance.", "token_count": 433, "char_count": 2098, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:35.481157", "source": { "split": "train_shard_00001", "doc_id": 4815 }, "chunk_id": "train_shard_00001_4815_0", "global_id": 12473 }, { "text": "Bacillus thuringiensis (B. thuringiensis) is a soil-dwelling Gram-positive bacterium and its plasmid-encoded toxins (Cry) are commonly used as biological alternatives to pesticides. In a pangenomic study, we sequenced seven B. thuringiensis isolates in both high coverage and base-quality using the next-generation sequencing platform. The B. thuringiensis pangenome was extrapolated to have 4196 core genes and an asymptotic value of 558 unique genes when a new genome is added. Compared to the pangenomes of its closely related species of the same genus, B. thuringiensis pangenome shows an open characteristic, similar to B. cereus but not to B. anthracis; the latter has a closed pangenome. We also found extensive divergence among the seven B. thuringiensis genome assemblies, which harbor ample repeats and single nucleotide polymorphisms (SNPs). The identities among orthologous genes are greater than 84.5% and the hotspots for the genome variations were discovered in genomic regions of 2.3-2.8Mb and 5.0-5.6Mb. We concluded that high-coverage sequence assemblies from multiple strains, before all the gaps are closed, are very useful for pangenomic studies.\n\nA pangenomic study of Bacillus thuringiensis.", "token_count": 334, "char_count": 1214, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:36.098324", "source": { "split": "train_shard_00001", "doc_id": 4816 }, "chunk_id": "train_shard_00001_4816_0", "global_id": 12474 }, { "text": "Mitochondria are critical for brain development and homeostasis. Therefore, pathogenic variation in the mitochondrial or nuclear genome which disrupts mitochondrial function frequently results in developmental disorders and neurodegeneration at the organismal level. Large-scale application of genome-wide technologies to individuals with mitochondrial diseases has dramatically accelerated identification of mitochondrial disease-gene associations in humans. Multi-omic and high-throughput studies involving transcriptomics, proteomics, metabolomics, and saturation genome editing are providing deeper insights into the functional consequence of mitochondrial genomic variation. Integration of deep phenotypic and genomic data through allelic series continues to uncover novel mitochondrial functions and permit mitochondrial gene function dissection on an unprecedented scale. Finally, mitochondrial disease-gene associations illuminate disease mechanisms and thereby direct therapeutic strategies involving small molecules and RNA-DNA therapeutics. This review summarizes progress in functional genomics and small molecule therapeutics in mitochondrial neurodevelopmental disorders.\n\nFunctional genomics and small molecules in mitochondrial neurodevelopmental disorders.", "token_count": 267, "char_count": 1273, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6944, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:36.700543", "source": { "split": "train_shard_00001", "doc_id": 4817 }, "chunk_id": "train_shard_00001_4817_0", "global_id": 12475 }, { "text": "Background: Inflammatory bowel disease (IBD) represents multifactorial chronic inflammatory conditions in the gastrointestinal tract and includes Crohn's disease (CD) and ulcerative colitis (UC). Despite similarities in pathobiology and disease symptoms, UC and CD represent distinct diseases and exhibit diverse therapeutic responses. While studies have now confirmed that IBD is associated with dramatic changes in the gut microbiota, specific changes in the gut microbiome and associated metabolic effects on the host due to CD and UC are less well-understood. Methods: To address this knowledge gap, we performed an extensive unbiased meta-analysis of the gut microbiome data from five different IBD patient cohorts from five different countries using QIIME2, DIAMOND, and STAMP bioinformatics platforms. In-silico profiling of the metabolic pathways and community metabolic modeling were carried out to identify disease-specific association of the metabolic fluxes and signaling pathways. Results: Our results demonstrated a highly conserved gut microbiota community between healthy individuals and IBD patients at higher phylogenetic levels. However, at or below the order level in the taxonomic rank, we found significant disease-specific alterations. Similarly, we identified differential enrichment of the metabolic pathways in CD and UC, which included enriched pathways related to amino acid and glycan biosynthesis and metabolism, in addition to other metabolic pathways. Conclusions: In conclusion, this study highlights the prospects of harnessing the gut microbiota to improve understanding of the etiology of CD and UC and to develop novel prognostic, and therapeutic approaches.\n\nGut Microbiota and Metabolic Specificity in Ulcerative Colitis and Crohn's Disease.", "token_count": 440, "char_count": 1815, "word_count": 246, "semantic_coherence": 1, "information_density": 0.626, "quality_score": 0.813, "entities": { "genes": [ "QIIME2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:37.353906", "source": { "split": "train_shard_00001", "doc_id": 4818 }, "chunk_id": "train_shard_00001_4818_0", "global_id": 12476 }, { "text": "Mycobacteria have a distinct secretion system, termed type VII (T7SS), which is encoded by paralogous chromosomal loci (ESX) and associated with pathogenesis, conjugation, and metal homeostasis. Evolution of paralogous gene families is of interest because duplication is an important mechanism by which novel genes evolve, but there are potential conflicts between adaptive forces that stabilize duplications and those that enable evolution of new functions. Our objective was to delineate the adaptive forces underlying diversification of T7SS. Plasmid-borne ESX were described recently, and we found evidence that the initial duplication and divergence of ESX systems occurred on plasmids and was driven by selection for advantageous mutations. Plasmid conjugation has been linked to T7SS and type IV secretion systems (T4SS) in mycobacteria, and we discovered that T7SS and T4SS genes evolved in concert on the plasmids. We hypothesize that differentiation of plasmid ESX helps to prevent conjugation among cells harboring incompatible plasmids. Plasmid ESX appear to have been repurposed following migration to the chromosome, and there is evidence of positive selection driving further differentiation of chromosomal ESX. We hypothesize that ESX loci were initially stabilized on the chromosome by mediating their own transfer. These results emphasize the diverse adaptive paths underlying evolution of novelty, which in this case involved plasmid duplications, selection for advantageous mutations in the mobile and core genomes, migration of the loci between plasmids and chromosomes, and lateral transfer among chromosomes. We discuss further implications for the choice of model organism to study ESX functions in Mycobacterium tuberculosis.\n\nEvolutionary Thrift: Mycobacteria Repurpose Plasmid Diversity during Adaptation of Type VII Secretion Systems.", "token_count": 436, "char_count": 1862, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5878, "quality_score": 0.7939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:38.012897", "source": { "split": "train_shard_00001", "doc_id": 4819 }, "chunk_id": "train_shard_00001_4819_0", "global_id": 12477 }, { "text": "During the period 2006–2011, Pseudomonas syringae pv. syringae caused a bacterial inflorescence rot (BIR) epidemic in an Australian cool climate viticultural region. Molecular multilocus sequence typing of ‘housekeeping’ genes (MLST), biochemical testing and analysis of molecular variance (AMOVA) were used to characterize the genotypes and phenotypes of P. syringae pv. syringae grapevine isolates. Comparison of the MLST data with exemplars of phylogroups available at PAMDB demonstrated that the BIR isolates formed a new clade within P. syringae pv. syringae phylogroup 2 (PG02): putatively designated PG02f. Analysis of the MLST and phenotypic data by AMOVA demonstrated some genetic differences between the BIR isolates and the general vineyard P. syringae pv. syringae population. Isolates positive for syringopeptin, syringomycin and tyrosinase, tobacco leaf hypersensitivity reaction (HR), ampicillin resistance and grapevine leaf pathogenicity were genetically distinct from those negative for these factors. This study has shown that, generally, the core genome of P. syringae pv. syringae is only weakly associated with the virulence‐associated traits. As the new phylogroup PG02f consists of the epidemic BIR isolates and nonpathogenic grapevine isolates, these genetically similar isolates differ greatly in pathogenicity and most of the other tested phenotypic traits. However, within the PG02f group, tobacco leaf HR and presence of sylC (the gene for phytotoxin syringolin A) are associated with the BIR and bacterial leaf spot (BLS) isolates, and negative for the nonpathogens, indicating that these two virulence factors may be associated with vineyard pathogenicity within the new Australian phylogroup.\n\nPseudomonas syringae pv. syringae from cool climate Australian grapevine vineyards: new phylogroup PG02f associated with bacterial inflorescence rot", "token_count": 508, "char_count": 1874, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5538, "quality_score": 0.7769, "entities": { "genes": [ "PG02" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:38.670462", "source": { "split": "train_shard_00001", "doc_id": 4820 }, "chunk_id": "train_shard_00001_4820_0", "global_id": 12478 }, { "text": "Kombucha is a sour beverage reported to have potential health effects prepared from the fermentation of black tea and sugar with a \"tea fungus\", a symbiotic culture of acetic acid bacteria and yeasts. Although black tea is the preferred substrate for Kombucha fermentation, other beverages have also been tested as substrates with fair results. Cheese whey is a by-product with a good amount of fermentable lactose that has been used before in the production of beverages, so the objective of this study was to test three types of whey (fresh sweet, fresh acid and reconstituted sweet) in the elaboration of a fermented beverage using a kombucha culture as inoculum. The isolation and identification of bacteria and yeasts from the fermented tea and wheys was done along with the study of the rates of change in sugar consumption, acid production and pH decrease. Several species of acetic acid bacteria (Acetobacter aceti subsp. aceti, Gluconobacter oxydans subsp. industrius, subsp. oxydans and Gluconoacetobacter xylinus) were isolated from the different kombuchas along with the yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, and Brettanomyces bruxelensis. The main metabolic products in the fermented wheys included ethanol, lactic and acetic acids. A good growth was obtained in both sweet wheys in which a pH of 3.3 and a total acid content (mainly lactic and acetic acids) of 0.07 mol/l was reached after 96 h. The sweet whey fermented beverages contained a relatively low lactose concentration (< 12 g/l). The final ethanol content was low (5 g/l) in all the fermented wheys. The whey products were strongly sour and salty non sparkling beverages.\n\nManufacture of a beverage from cheese whey using a \"tea fungus\" fermentation.", "token_count": 475, "char_count": 1746, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5455, "quality_score": 0.7727, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:39.314908", "source": { "split": "train_shard_00001", "doc_id": 4821 }, "chunk_id": "train_shard_00001_4821_0", "global_id": 12479 }, { "text": "Here we describe a new species of the genus Streptococcus that was isolated from a dairy cow with mastitis in New Zealand. Strain NZ1587T was Gram-positive, coccus-shaped and arranged as chains, catalase and coagulase negative, γ-haemolytic and negative for Lancefield carbohydrates (A-D, F and G). The 16S rRNA sequence did not match sequences in the NCBI 16S rRNA or GreenGenes databases. Taxonomic classification of strain NZ1587T was investigated using 16S rRNA and core genome phylogeny, genome-wide average nucleotide identity (ANI) and predicted DNA-DNA hybridisation (DDH) analyses. Phylogeny based on 16S rRNA was unable to resolve the taxonomic position of strain NZ1587T, however NZ1587T shared 99.4 % identity at the 16S rRNA level with a distinct branch of S. pseudoporcinus. Importantly, core genome phylogeny demonstrated that NZ1587T grouped amongst the 'pyogenic' streptococcal species and formed a distinct branch supported by a 100 % bootstrap value. In addition, average nucleotide identity and inferred DNA-DNA hybridisation analyses showed that NZ1587T represents a novel species. Biochemical profiling using the rapid ID 32 strep identification test enabled differentiation of strain NZ1587T from closely related streptococcal species. In conclusion, strain NZ1587T can be classified as a novel species, and we propose a novel taxon named Streptococcus bovimastitidis sp. nov.; the type strain is NZ1587T", "token_count": 485, "char_count": 1526, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [ "NZ1587" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:39.962094", "source": { "split": "train_shard_00001", "doc_id": 4822 }, "chunk_id": "train_shard_00001_4822_0", "global_id": 12480 }, { "text": "NZ1587T has been deposited in the Culture Collection University of Gothenburg (CCUG 69277T) and the Belgian Co-ordinated Collections of Micro-organisms/LMG (LMG 29747).\n\nStreptococcus bovimastitidis sp. nov., isolated from a dairy cow with mastitis.", "token_count": 98, "char_count": 271, "word_count": 33, "semantic_coherence": 1, "information_density": 0.9394, "quality_score": 0.9697, "entities": { "genes": [ "NZ1587" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:40.341627", "source": { "split": "train_shard_00001", "doc_id": 4822 }, "chunk_id": "train_shard_00001_4822_1", "global_id": 12481 }, { "text": "Two fragments containing both an autonomous replicating sequence (ARS) and a centromere have been isolated and sequenced from the yeast Kluyveromyces marxianus. The ARS and centromeric core sequences are only 500 bp apart, but ARS activity could be separated from the centromeric sequences. Centromeric sequences are organized in a similar way to those of budding yeasts: two well-conserved elements: CDEI (5' TCACGTG 3') and CDEIII (5' TNTTCCGAAAGTWAAA 3'), are separated by a 165 bp AT-rich (+/- 90%) CDEII element whose length is twice that of Saccharomyces cerevisiae CDEII but almost identical to that of K. lactis. The ARS-core consensus sequence (5' TTTATTGTT 3') is also similar to that of K. lactis. Both ARS and centromeric elements function in this strain, albeit inefficiently, but not in S. cerevisiae. A third ARS-containing fragment with a different organization has been isolated and sequenced.\n\nKluyveromyces marxianus small DNA fragments contain both autonomous replicative and centromeric elements that also function in Kluyveromyces lactis.", "token_count": 310, "char_count": 1060, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6203, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:40.918177", "source": { "split": "train_shard_00001", "doc_id": 4823 }, "chunk_id": "train_shard_00001_4823_0", "global_id": 12482 }, { "text": "During a study on the prevalence and diversity of members of the genus Campylobacter in a shellfish-harvesting area and its catchment in Brittany, France, six urease-positive isolates of members of the genus Campylobacter were recovered from surface water samples, as well as three isolates from stools of humans displaying enteric infection in the same period. These strains were initially identified as members of the Campylobacter lari group by MALDI-TOF mass spectrometry and placed into a distinct group in the genus Campylobacter, following atpA gene sequence analysis based on whole-genome sequencing data. This taxonomic position was confirmed by phylogenetic analysis of the 16S rRNA, rpoB and hsp60 (groEL) loci, and an analysis of the core genome that provided an improved phylogenetic resolution. The average nucleotide identity between the representative strain CA656T (CCUG 73571T=CIP 111675T) and the type strain of the most closely related species Campylobacter ornithocola WBE38T was 88.5 %. The strains were found to be microaerobic and anaerobic, motile, non-spore-forming, Gram-stain-negative, spiral-shaped bacteria that exhibit catalase, oxidase and urease activities but not nitrate reduction. This study demonstrates clearly that the nine isolates represent a novel species within the C. lari group, for which the name Campylobacter armoricus is proposed. Here, we present phenotypic and morphological features of the nine strains and the description of their genome sequences", "token_count": 479, "char_count": 1621, "word_count": 217, "semantic_coherence": 1, "information_density": 0.659, "quality_score": 0.8295, "entities": { "genes": [ "WBE38", "CA656" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:41.562468", "source": { "split": "train_shard_00001", "doc_id": 4824 }, "chunk_id": "train_shard_00001_4824_0", "global_id": 12483 }, { "text": "The proposed type strain CA656T has a 1.589 Mbp chromosome with a DNA G+C content of 28.5 mol% and encodes 1588 predicted coding sequences, 38 tRNAs, and 3 rRNA operons.\n\nCampylobacter armoricus sp. nov., a novel member of the Campylobacter lari group isolated from surface water and stools from humans with enteric infection.", "token_count": 127, "char_count": 351, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8302, "quality_score": 0.9151, "entities": { "genes": [ "CA656" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:41.950050", "source": { "split": "train_shard_00001", "doc_id": 4824 }, "chunk_id": "train_shard_00001_4824_1", "global_id": 12484 }, { "text": "Colistin- and carbapenem-resistant Acinetobacter baumannii is a serious multidrug resistant (MDR) bacterium in clinical settings. Discovery of new antibacterial drugs against MDR is facing multiple challenges in drug development. Combination of known antibiotics with a robust adjuvant might be an alternative effective strategy for MDR treatment. In the study herein, we report an antibiotic adjuvant activity of a natural compound panduratin A from fingerroot (Boesenbergia rotunda) as a potent adjuvant to colistin. The present study investigated the antibiotic adjuvant effect of panduratin A against 10 colistin- and carbapenem-resistant A. baumannii. Antibacterial activities were tested by broth microdilution method. Biofilm assay was used to determine the efficacy of panduratin A in biofilm formation inhibition on two representative strains Aci46 and Aci44. Genomic and transcriptomic analyses of colistin- and carbapenem-resistant A. baumannii strains were used to identify potential resistance and tolerance mechanism in the bacteria. Panduratin A-colistin combination showed an increased effect on antibacterial in the A. baumannii. However, panduratin A did not improve the antibacterial activity of imipenem. In addition, panduratin A improves anti-biofilm activity of colistin against Aci44 and Aci46, the colistin- and carbapenem-resistant A. baumannii. Panduratin A markedly enhances bactericidal and anti-biofilm activity of colistin against colistin- resistant A. baumannii. Based on genome comparisons, single nucleotide polymorphism (SNP) patterns in six genes encoding biofilm and lipid A biosynthesis were shared in Aci44 and Aci46. In Aci44, we identified a partial sequence of pmrB encoding a polymyxin resistant component PmrB, whereas a full length of pmrB was observed in Aci46", "token_count": 487, "char_count": 1807, "word_count": 250, "semantic_coherence": 1, "information_density": 0.556, "quality_score": 0.778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:42.601551", "source": { "split": "train_shard_00001", "doc_id": 4825 }, "chunk_id": "train_shard_00001_4825_0", "global_id": 12485 }, { "text": "RNA-seq analyses of Aci44 revealed that panduratin A-colistin combination induced expression of ribosomal proteins and oxidative stress response proteins, whereas iron transporter and MFS-type transporter systems were suppressed. Panduratin A-colistin combination could promote intracellular reactive oxygen species (ROS) accumulation could lead to the cidal effect on colistin-resistant A. baumannii. Combination of panduratin A and colistin showed a significant increase in colistin efficacy against colistin- resistant A. baumannii in comparison of colistin alone. Genomic comparison between Aci44 and Aci46 showed mutations and SNPs that might affect different phenotypes. Additionally, based on RNA-Seq, panduratin A-colistin combination could lead to ROS production and accumulation. These findings confirmed the potency of panduratin as colistin adjuvant against multidrug resistant A. baumannii.\n\nEnhancing effect of natural adjuvant, panduratin A, on antibacterial activity of colistin against multidrug-resistant Acinetobacter baumannii.", "token_count": 272, "char_count": 1047, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6439, "quality_score": 0.822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:43.145660", "source": { "split": "train_shard_00001", "doc_id": 4825 }, "chunk_id": "train_shard_00001_4825_1", "global_id": 12486 }, { "text": "An oligonucleotide microarray based on the arrayed-primer extension (APEX) technique has been developed to simultaneously identify pathogenic fungi frequently isolated from invasive and superficial infections. Species-specific oligonucleotide probes complementary to the internal transcribed spacer 1 and 2 (ITS1 and ITS2) region were designed for 24 species belonging to 10 genera, including Candida species (Candida albicans, Candida dubliniensis, Candida famata, Candida glabrata, Candida tropicalis, Candida kefyr, Candida krusei, Candida guilliermondii, Candida lusitaniae, Candida metapsilosis, Candida orthopsilosis, Candida parapsilosis, and Candida pulcherrima), Cryptococcus neoformans, Aspergillus species (Aspergillus fumigatus and Aspergillus terreus), Trichophyton species (Trichophyton rubrum and Trichophyton tonsurans), Trichosporon cutaneum, Epidermophyton floccosum, Fusarium solani, Microsporum canis, Penicillium marneffei, and Saccharomyces cerevisiae. The microarray was tested for its specificity with a panel of reference and blinded clinical isolates. The APEX technique was proven to be highly discriminative, leading to unequivocal identification of each species, including the highly related ones C. parapsilosis, C. orthopsilosis, and C. metapsilosis. Because of the satisfactory basic performance traits obtained, such as reproducibility, specificity, and unambiguous interpretation of the results, this new system represents a reliable method of potential use in clinical laboratories for parallel one-shot detection and identification of the most common pathogenic fungi.\n\nDNA microarray based on arrayed-primer extension technique for identification of pathogenic fungi responsible for invasive and superficial mycoses.", "token_count": 474, "char_count": 1753, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6542, "quality_score": 0.8271, "entities": { "genes": [ "ITS2", "ITS1" ], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:43.798007", "source": { "split": "train_shard_00001", "doc_id": 4826 }, "chunk_id": "train_shard_00001_4826_0", "global_id": 12487 }, { "text": "

Background

Typhoid fever usually manifests as an acute disease. However, asymptomatic carriage with Salmonella Typhi may occur. This study investigated a family setting of severe typhoid fever in Switzerland months after return from Bangladesh.

Method

Standard microbiological procedures were performed. Testing for S. Typhi IgM antibodies was done using a novel immunochromographic lateral flow assay. Whole genome sequencing (WGS) followed by comparative core genome multilocus sequence typing (cgMLST) was performed on the S. Typhi isolates.

Results

Four months after returning from a visit to Bangladesh sibling 1 (9 months) was diagnosed with a S. Typhi meningitis and sibling 3 (8 years) was identified as asymptomatic S. Typhi carrier. Sibling 2 (2 years) was retrospectively diagnosed with typhoid fever by IgM serology at the time point of admission to the hospital. Parents were asymptomatic and culture-negative. WGS analysis of family S. Typhi isolates showed clonality and strongest homology with S. Typhi strains occurring in Bangladesh. The S. Typhi strain showed resistance against fluoroquinolones. A 4-week course of ceftriaxone resulted in full recovery of sibling 1. S. Typhi was eradicated from sibling 3 following azithromycin treatment for 14 days.

Conclusion

S. Typhi, acquired from a visit to Bangladesh, was most likely transmitted within the family from one brother as asymptomatic shedder to his 9-month-old brother who manifested S. Typhi meningitis as a very rare and life-threatening presentation of typhoid fever. S. Typhi infection should be considered even in case of uncommon manifestations and irrespective of the interval between disease presentation and travel to an endemic area.\n\nSiblings with typhoid fever: An investigation of intrafamilial transmission, clonality, and antibiotic susceptibility.", "token_count": 481, "char_count": 1867, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6192, "quality_score": 0.8096, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:44.448319", "source": { "split": "train_shard_00001", "doc_id": 4827 }, "chunk_id": "train_shard_00001_4827_0", "global_id": 12488 }, { "text": "High pressure homogenization of yeast cells followed by incubation at 50 degrees C for the dissociation of ribonucleic acid-protein complexes resulted in a high denaturation degree of isolated proteins. Proteins in intact cells exhibited an ample endothermic peak with peak temperatures (Tp) at 66.66 and 63.67 degrees C for S. cerevisiae and K. fragilis, respectively. No differences were found with respect to the associated enthalpy changes for both studied species. The isolation of proteins from its biomass shifts Tp to values around 50 degrees C. Impurities such as nucleic acid, polysaccharides and other intracellular components seem to play a protective role upon denaturation. Isolated proteins showed solubilities lower than 40% but exhibited water retention properties and wettability from 3.5 to 7.0 ml of water/g of protein.\n\nThermal behavior and hydration properties of yeast proteins from Saccharomyces cerevisiae and Kluyveromyces fragilis", "token_count": 251, "char_count": 957, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7214, "quality_score": 0.8607, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:44.937669", "source": { "split": "train_shard_00001", "doc_id": 4828 }, "chunk_id": "train_shard_00001_4828_0", "global_id": 12489 }, { "text": "It was shown that for the first two hours of inulinase fermentation, the effect of the pulse electromagnetic field was 94Hz, 14mT, keep time t_(k) 1300 mus, stop time t_(s) 8700 mus, and the up and down time was 200mus in rectangle electromagnetic wave. After fermentation, the amount of inulinase activity was raised by 23%. The pulse electromagnetic field evidently enhanced the biosynthesis of inulinase as induced by inulin. The enhancement was obtained by the occurrence of pulse electromagnetic field at that time. In addition, the amount of mRNA was efficiently increased. The total of inulinase amounted to 136% of the control. It indicates that pulsed electromagnetic field promotes not only the expression but also the transcription of the inulinase gene.\n\nThe effect of pulse electromagnetic field on the cell growth and inulinase biosynthesis of Kluyveromyces fragilis", "token_count": 234, "char_count": 880, "word_count": 137, "semantic_coherence": 1, "information_density": 0.5401, "quality_score": 0.7701, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:45.408295", "source": { "split": "train_shard_00001", "doc_id": 4829 }, "chunk_id": "train_shard_00001_4829_0", "global_id": 12490 }, { "text": "Advances in genome sequencing technologies have rapidly expanded the number of bacterial genome sequences available for study, permitting the emergence of the discipline of population genomics. Bioinformatics platforms were used to exploit this resource by the provision of data in an easily accessible and uniform format. The de novo assembly, combined with gene-by-gene annotation, generated high quality draft genomes in which the majority of protein-encoding genes were present with high accuracy. The approach catalogued diversity efficiently and was a practical approach to interpreting whole genome sequence data for a large bacterial population. The hyperinvasive meningococcal Lineage 3 core and accessory genome was described and mobile genetic elements and undescribed proteins were found to be influencing the shape of the lineages evolution and population structure. Commensal carriage of the meningococcus was examined using temporally paired isolates. Long-term carriage was found and the comparison of the genomes pairs found a highly conserved set of core genes. The methods used generated novel insights into the biology of the meningococcus and improved our understanding of the whole population structure, ... (continues)\n\nMeningococcal genome dynamics : an allele based, population approach to define lineage structure", "token_count": 275, "char_count": 1339, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6263, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:45.963258", "source": { "split": "train_shard_00001", "doc_id": 4830 }, "chunk_id": "train_shard_00001_4830_0", "global_id": 12491 }, { "text": "

Background

Highly parallel, 'second generation' sequencing technologies have rapidly expanded the number of bacterial whole genome sequences available for study, permitting the emergence of the discipline of population genomics. Most of these data are publically available as unassembled short-read sequence files that require extensive processing before they can be used for analysis. The provision of data in a uniform format, which can be easily assessed for quality, linked to provenance and phenotype and used for analysis, is therefore necessary.

Results

The performance of de novo short-read assembly followed by automatic annotation using the pubMLST.org Neisseria database was assessed and evaluated for 108 diverse, representative, and well-characterised Neisseria meningitidis isolates. High-quality sequences were obtained for >99% of known meningococcal genes among the de novo assembled genomes and four resequenced genomes and less than 1% of reassembled genes had sequence discrepancies or misassembled sequences. A core genome of 1600 loci, present in at least 95% of the population, was determined using the Genome Comparator tool. Genealogical relationships compatible with, but at a higher resolution than, those identified by multilocus sequence typing were obtained with core genome comparisons and ribosomal protein gene analysis which revealed a genomic structure for a number of previously described phenotypes. This unified system for cataloguing Neisseria genetic variation in the genome was implemented and used for multiple analyses and the data are publically available in the PubMLST Neisseria database.

Conclusions

The de novo assembly, combined with automated gene-by-gene annotation, generates high quality draft genomes in which the majority of protein-encoding genes are present with high accuracy. The approach catalogues diversity efficiently, permits analyses of a single genome or multiple genome comparisons, and is a practical approach to interpreting WGS data for large bacterial population samples. The method generates novel insights into the biology of the meningococcus and improves our understanding of the whole population structure, not just disease causing lineages.", "token_count": 492, "char_count": 2239, "word_count": 307, "semantic_coherence": 1, "information_density": 0.6124, "quality_score": 0.8062, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:46.612594", "source": { "split": "train_shard_00001", "doc_id": 4831 }, "chunk_id": "train_shard_00001_4831_0", "global_id": 12492 }, { "text": "A gene-by-gene population genomics platform: de novo assembly, annotation and genealogical analysis of 108 representative Neisseria meningitidis genomes.", "token_count": 43, "char_count": 153, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:46.973555", "source": { "split": "train_shard_00001", "doc_id": 4831 }, "chunk_id": "train_shard_00001_4831_1", "global_id": 12493 }, { "text": "In the twenty first century, the changing epidemiology of inflammatory bowel disease (IBD) globally with increasing disease incidence across many countries relates to the altered gut microbiota, due to a combinatorial effect of environmental factors, human immune responses and genetics. IBD is a gastrointestinal disease associated with a gut microbial dysbiosis, including an expansion of facultative anaerobic bacteria of the family Enterobacteriaceae. Advances in high-throughput sequencing enable us to entangle the gut microbiota in human health and IBD beyond the gut bacterial microbiota, expanding insights into the mycobiota, virobiota and helminthes. Caudovirales (viruses) and Basidiomycota, Ascomycota, and Candida albicans (fungi) are revealed to be increased in IBD. The deconvolution of the gut microbiota in IBD lays the basis for unveiling the roles of these various gut microbiota components in IBD pathogenesis and being conductive to instructing on future IBD diagnosis and therapeutics. Here we comprehensively elucidate the alterations in the gut microbiota in IBD, discuss the effect of diets in the gut microbiota in relation to IBD, and illustrate the potential of manipulation of gut microbiota for IBD therapeutics. The therapeutic strategy of antibiotics, prebiotics, probiotics and fecal microbiota transplantation will benefit the effective application of precision microbiome manipulation in IBD.\n\nThe Gut Microbiota in the Pathogenesis and Therapeutics of Inflammatory Bowel Disease.", "token_count": 401, "char_count": 1537, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5681, "quality_score": 0.784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:47.591445", "source": { "split": "train_shard_00001", "doc_id": 4832 }, "chunk_id": "train_shard_00001_4832_0", "global_id": 12494 }, { "text": "Pregnant women are more susceptible to both vaginal colonization and infection by yeast. Our objectives were to determine the prevalence in pregnant women of yeasts isolated from vaginal exudates and their susceptibility to current antifungal drugs. A total of 493 patients was studied between December 1998 and February 2000. The prevalence of Candida spp. was 28% (Candida albicans 90.4%; Candida glabrata 6.3%; Candida parapsilosis 1.1%, Candida kefyr 1.1 %; unidentified species 1.1 %). The diffusion test in Shadomy agar was employed to determine the susceptibility to fluconazole, ketoconazole, itraconazole and nistatine. All C. albicans, C. kefyr and C. parapsilosis isolates were susceptible in vitro to the antifungal agents tested, while 1 in 6 C. glabrata isolates showed resistance to azole drugs; all strains were susceptible to nistatine. In pregnant women, C. albicans was the yeast most frequently isolated from vaginal exudates; it continues to be highly susceptible to antifungal drugs. Azole resistance was detected only among C. glabrata isolates. Identification to the species level is recommended, specially in cases of treatment failure and recurrent or chronic infection.\n\n[Prevalence of vaginal candidiasis in pregnant women. Identification of yeasts and susceptibility to antifungal agents].", "token_count": 363, "char_count": 1318, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:48.207316", "source": { "split": "train_shard_00001", "doc_id": 4833 }, "chunk_id": "train_shard_00001_4833_0", "global_id": 12495 }, { "text": "BackgroundCarbapenem-resistant Enterobacteriaceae pose a serious threat to public health worldwide, and the role of companion animals as a reservoir is still unclear.AimsThis 4-month prospective observational study evaluated carriage of carbapenem-resistant Enterobacteriaceae at admission and after hospitalisation in a large referral hospital for companion animals in Switzerland.MethodsRectal swabs of dogs and cats expected to be hospitalised for at least 48 h were taken from May to August 2018 and analysed for the presence of carbapenem-resistant Enterobacteriaceae using selective agar plates. Resistant isolates were further characterised analysing whole genome sequences for resistance gene and plasmid identification, and ad hoc core genome multilocus sequence typing.ResultsThis study revealed nosocomial acquisition of Escherichia coli harbouring the carbapenemase gene bla OXA-181, the pAmpC cephalosporinase gene bla CMY-42 as well as quinolone resistance associated with qnrS1 and mutations in the topoisomerases II (GyrA) and IV (ParC). The bla OXA-181 and qnrS1 genes were identified on a 51 kb IncX3 plasmid and bla CMY-42 on a 47 kb IncI1 plasmid. All isolates belonged to sequence type ST410 and were genetically highly related. This E. coli clone was detected in 17 of 100 dogs and four of 34 cats after hospitalisation (21.6%), only one of the tested animals having tested positive at admission (0.75%). Two positive animals were still carriers 4 months after hospital discharge, but were negative after 6 months.ConclusionsCompanion animals may acquire carbapenemase-producing E", "token_count": 512, "char_count": 1705, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6388, "quality_score": 0.8194, "entities": { "genes": [ "ST410" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:48.882396", "source": { "split": "train_shard_00001", "doc_id": 4834 }, "chunk_id": "train_shard_00001_4834_0", "global_id": 12496 }, { "text": "coli during hospitalisation, posing the risk of further dissemination to the animal and human population and to the environment.\n\nShedding of OXA-181 carbapenemase-producing Escherichia coli from companion animals after hospitalisation in Switzerland: an outbreak in 2018.", "token_count": 81, "char_count": 283, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8056, "quality_score": 0.9028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:49.277988", "source": { "split": "train_shard_00001", "doc_id": 4834 }, "chunk_id": "train_shard_00001_4834_1", "global_id": 12497 }, { "text": "Whether to commit limited cellular resources toward growth and proliferation, or toward survival and stress responses, is an essential determination made by Target of Rapamycin Complex 1 (TORC1) for a eukaryotic cell in response to favorable or adverse conditions. Loss of TORC1 function is lethal. The TORC1 inhibitor rapamycin that targets the highly conserved Tor kinase domain kills fungal pathogens like Candida albicans, but is also severely toxic to human cells. The least conserved region of fungal and human Tor kinases are the N-terminal HEAT domains. We examined the role of the 8 most N-terminal HEAT repeats of C. albicans Tor1. We compared nutritional- and stress responses of cells that express a message for N-terminally truncated Tor1 from repressible tetO, with cells expressing wild type TOR1 from tetO or from the native promoter. Some but not all stress responses were significantly impaired by loss of Tor1 N-terminal HEAT repeats, including those to oxidative-, cell wall-, and heat stress; in contrast, plasma membrane stress and antifungal agents that disrupt plasma membrane function were tolerated by cells lacking this Tor1 region. Translation was inappropriately upregulated during oxidative stress in cells lacking N-terminal Tor1 HEAT repeats despite simultaneously elevated Gcn2 activity, while activation of the oxidative stress response MAP kinase Hog1 was weak. Conversely, these cells were unable to take advantage of favorable nutritional conditions by accelerating their growth. Consuming oxygen more slowly than cells containing wild type TOR1 alleles during growth in glucose, cells lacking N-terminal Tor1 HEAT repeats additionally were incapable of utilizing non-fermentable carbon sources. They were also hypersensitive to inhibitors of specific complexes within the respiratory electron transport chain, suggesting that inefficient ATP generation and a resulting dearth of nucleotide sugar building blocks for cell wall polysaccharides causes cell wall integrity defects in these mutants", "token_count": 466, "char_count": 2031, "word_count": 296, "semantic_coherence": 1, "information_density": 0.6182, "quality_score": 0.8091, "entities": { "genes": [ "TORC1", "TOR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:49.966548", "source": { "split": "train_shard_00001", "doc_id": 4835 }, "chunk_id": "train_shard_00001_4835_0", "global_id": 12498 }, { "text": "Genome-wide expression analysis of cells lacking N-terminal HEAT repeats showed dysregulation of carbon metabolism, cell wall biosynthetic enzymes, translational machinery biosynthesis, oxidative stress responses, and hyphal- as well as white-opaque cell type-associated genes. Targeting fungal-specific Tor1 N-terminal HEAT repeats with small molecules might selectively abrogate fungal viability, especially when during infection multiple stresses are imposed by the host immune system.\n\nStress- and metabolic responses of Candida albicans require Tor1 kinase N-terminal HEAT repeats.", "token_count": 148, "char_count": 586, "word_count": 73, "semantic_coherence": 1, "information_density": 0.8493, "quality_score": 0.9247, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:50.403707", "source": { "split": "train_shard_00001", "doc_id": 4835 }, "chunk_id": "train_shard_00001_4835_1", "global_id": 12499 }, { "text": "IBS is a prevalent functional gastrointestinal disorder, in which the microbiota has been demonstrated to play a role. An increasing number of studies have suggested how probiotics may alleviate IBS symptoms and several mechanisms of action have been proposed.   In the present study we characterized the intestinal microbiota of 19 subjects suffering from diagnosed IBS using a fully validated High Taxonomic Fingerprint Microbiota Array (HTF-Microbi.Array). We demonstrated that the IBS microbiota is different from that of healthy individuals due to an unbalance in a number of commensal species, with an increase in relative abundance of lactobacilli, B. cereus and B. clausii, bifidobacteria, Clostridium cluster IX and E. rectale, and a decrease in abundance of Bacteroides/Prevotella group and Veillonella genus. Additionally, we demonstrated that some bacterial groups of the human intestinal microbiota, recently defined as pathobionts, are increased in concentration in the IBS microbiota. Furthermore, we aimed at investigating if the daily administration of a novel probiotic yogurt containing B. animalis subsp lactis Bb12 and K. marxianus B0399, recently demonstrated to have beneficial effects in the management of IBS symptoms, could impact on the biostructure of IBS microbiota, modulating its composition to counteract putative dysbiosis found in IBS subjects. Notably, we demonstrated that the beneficial effects associated to the probiotic preparation are not related to significant modifications in the composition of the human intestinal microbiota.\n\nIBS-associated phylogenetic unbalances of the intestinal microbiota are not reverted by probiotic supplementation.", "token_count": 406, "char_count": 1693, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:51.677319", "source": { "split": "train_shard_00001", "doc_id": 4836 }, "chunk_id": "train_shard_00001_4836_0", "global_id": 12500 }, { "text": "

Unlabelled

Most Escherichia coli strains are nonpathogenic. However, for clinical diagnosis and food safety analysis, current identification methods for pathogenic E. coli either are time-consuming and/or provide limited information. Here, we utilized a custom DNA microarray with informative genetic features extracted from 368 sequence sets for rapid and high-throughput pathogen identification. The FDA Escherichia coli Identification (FDA-ECID) platform contains three sets of molecularly informative features that together stratify strain identification and relatedness. First, 53 known flagellin alleles, 103 alleles of wzx and wzy, and 5 alleles of wzm provide molecular serotyping utility. Second, 41,932 probe sets representing the pan-genome of E. coli provide strain-level gene content information. Third, approximately 125,000 single nucleotide polymorphisms (SNPs) of available whole-genome sequences (WGS) were distilled to 9,984 SNPs capable of recapitulating the E. coli phylogeny. We analyzed 103 diverse E. coli strains with available WGS data, including those associated with past foodborne illnesses, to determine robustness and accuracy. The array was able to accurately identify the molecular O and H serotypes, potentially correcting serological failures and providing better resolution for H-nontypeable/nonmotile phenotypes. In addition, molecular risk assessment was possible with key virulence marker identifications. Epidemiologically, each strain had a unique comparative genomic fingerprint that was extended to an additional 507 food and clinical isolates. Finally, a 99.7% phylogenetic concordance was established between microarray analysis and WGS using SNP-level data for advanced genome typing. Our study demonstrates FDA-ECID as a powerful tool for epidemiology and molecular risk assessment with the capacity to profile the global landscape and diversity of E. coli

Importance

This study describes a robust, state-of-the-art platform developed from available whole-genome sequences of E. coli and Shigella spp. by distilling useful signatures for epidemiology and molecular risk assessment into one assay", "token_count": 529, "char_count": 2157, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:56:52.342994", "source": { "split": "train_shard_00001", "doc_id": 4837 }, "chunk_id": "train_shard_00001_4837_0", "global_id": 12501 }, { "text": "The FDA-ECID microarray contains features that enable comprehensive molecular serotyping and virulence profiling along with genome-scale genotyping and SNP analysis. Hence, it is a molecular toolbox that stratifies strain identification and pathogenic potential in the contexts of epidemiology and phylogeny. We applied this tool to strains from food, environmental, and clinical sources, resulting in significantly greater phylogenetic and strain-specific resolution than previously reported for available typing methods.\n\nFDA Escherichia coli Identification (FDA-ECID) Microarray: a Pangenome Molecular Toolbox for Serotyping, Virulence Profiling, Molecular Epidemiology, and Phylogeny.", "token_count": 168, "char_count": 688, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7882, "quality_score": 0.8941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:52.784262", "source": { "split": "train_shard_00001", "doc_id": 4837 }, "chunk_id": "train_shard_00001_4837_1", "global_id": 12502 }, { "text": "

Aims

In this work the microflora present in kefir, a fermented milk product, was studied together with the effect of kefir administration on different groups of indigenous bacteria of mouse bowel.

Methods and results

Kefir microflora was composed of lactic acid bacteria, acetic acid bacteria and yeasts. Yeast population was composed of Saccharomyces cerevisiae, S. unisporus, Candida kefir, Kluyveromyces marxianus and K. lactis. The streptococci levels in kefir treated mice increased by 10-fold and the levels of sulfite-reducing clostridia decreased by 100-fold. The number of lactic acid bacteria increased significantly.

Conclusions

The administration of kefir significantly increased the lactic acid bacteria counts in the mucosa of the bowel. Ingestion of kefir specifically lowered microbial populations of Enterobacteriaceae and clostridia.

Significance and impact of the study

This is the first long-term study about the effects of the kefir administration on the intestinal microflora of mice.\n\nDietary influence of kefir on microbial activities in the mouse bowel.", "token_count": 308, "char_count": 1107, "word_count": 148, "semantic_coherence": 1, "information_density": 0.5608, "quality_score": 0.7804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:53.354179", "source": { "split": "train_shard_00001", "doc_id": 4838 }, "chunk_id": "train_shard_00001_4838_0", "global_id": 12503 }, { "text": "Neisseria meningitidis is a Gram-negative human commensal pathogen, with extensive phenotypic plasticity afforded by phase-variable (PV) gene expression. Phase variation is a stochastic switch in gene expression from an ON to an OFF state, mediated by localized hypermutation of simple sequence repeats (SSRs). Circulating N. meningitidis clones vary in propensity to cause disease, with some clonal complexes (ccs) classified as hypervirulent and others as carriage-associated. We examined the PV gene repertoires, or phasome, of these lineages in order to determine whether phase variation contributes to disease propensity. We analysed 3328 genomes representative of nine circulating meningococcal ccs with PhasomeIt, a tool that identifies PV genes by the presence of SSRs and homologous gene clusters. The presence, absence and functions of all identified PV gene clusters were confirmed by annotation or blast searches within the Neisseria PubMLST database. While no significant differences were detected in the number of PV genes or the core, conserved phasome content between hypervirulent and carriage lineages, individual ccs exhibited major variations in PV gene numbers. Phylogenetic clusters produced by phasome or core genome analyses were similar, indicating co-evolution of PV genes with the core genome. While conservation of PV clusters is high, with 76 % present in all meningococcal isolates, maintenance of an SSR is variable, ranging from conserved in all isolates to present only in a single cc, indicating differing evolutionary trajectories for each lineage. Diverse functional groups of PV genes were present across the meningococcal lineages; however, the majority directly or indirectly influence bacterial surface antigens and could impact on future vaccine development. Finally, we observe that meningococci have open pan phasomes, indicating ongoing evolution of PV gene content and a significant potential for adaptive changes in this clinically relevant genus.\n\nMeningococcal core and accessory phasomes vary by clonal complex.", "token_count": 507, "char_count": 2088, "word_count": 296, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:54.011144", "source": { "split": "train_shard_00001", "doc_id": 4839 }, "chunk_id": "train_shard_00001_4839_0", "global_id": 12504 }, { "text": "The human microbiota is a diverse microbial ecosystem associated with many beneficial physiological functions as well as numerous disease etiologies. Dominated by bacteria, the microbiota also includes commensal populations of fungi, viruses, archaea, and protists. Unlike bacterial microbiota, which was extensively studied in the past two decades, these non-bacterial microorganisms, their functional roles, and their interaction with one another or with host immune system have not been as widely explored. This review covers the recent findings on the non-bacterial communities of the human gastrointestinal microbiota and their involvement in health and disease, with particular focus on the pathophysiology of inflammatory bowel disease.\n\nGut Microbiota beyond Bacteria-Mycobiome, Virome, Archaeome, and Eukaryotic Parasites in IBD.", "token_count": 196, "char_count": 838, "word_count": 113, "semantic_coherence": 1, "information_density": 0.7611, "quality_score": 0.8805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:54.481282", "source": { "split": "train_shard_00001", "doc_id": 4840 }, "chunk_id": "train_shard_00001_4840_0", "global_id": 12505 }, { "text": "Due to the continuous increase of human candidiasis and the great diversity of yeasts of the Candida genera, it is indispensable to identify this yeast as early as possible. Early identification enables an early diagnostic and patient-adapted anti-fungal therapy, thus reducing morbidity and mortality related to these infections. In view of this, we have in this study investigated microcolonies using a method based on Fourier transform-infrared microspectroscopy (FTIRM) for a rapid and early identification of the most frequent Candida species encountered in human pathology. FTIR spectroscopy is a whole-cell \"fingerprinting\" method by which microorganisms can be identified. By exploiting the huge discriminating capacity of this technique, we identified 6 species (Candida albicans, Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei, and Candida kefyr) from a collection of 57 clinical strains of Candida, isolated from hospitalised patients. Data obtained on 10- to 18-h-old microcolonies were compared to cultures of 24 h. Our results clearly show the efficiency and the robustness of FTIR (micro)spectroscopy in identifying species with a classification rate of 100% for both microcolonies and 24-h cultures. FTIR microspectroscopy is thus a promising clinical approach, because compared to conventional and molecular techniques, it is time and money saving, has great identification and discriminating potentials, and is amenable to an automated high-throughput routine system.\n\nRapid identification of Candida species by FT-IR microspectroscopy.", "token_count": 386, "char_count": 1582, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:55.097784", "source": { "split": "train_shard_00001", "doc_id": 4841 }, "chunk_id": "train_shard_00001_4841_0", "global_id": 12506 }, { "text": "The Cation Diffusion Facilitator (CDF) family, also named Metal Tolerance Protein (MTP), is one of the gene families involved in heavy metal transport in plants. However, a comprehensive study of MTPs in Brassica napus has not been reported yet. In the present study, we identified 33 BnMTP genes from the rapeseed genome using bioinformatic analyses. Subsequently, we analyzed the phylogenetic relationship, gene structure, chromosome distribution, conserved domains, and motifs of the BnMTP gene family. The 33 BnMTPs were phylogenetically divided into three major clusters (Zn-CDFs, Fe/Zn-CDFs, and Mn-CDFs) and seven groups (group 1, 5, 6, 7, 8, 9, and 12). The structural characteristics of the BnMTP members were similar in the same group, but different among groups. Evolutionary analysis indicated that the BnMTP gene family mainly expanded through whole-genome duplication (WGD) and segmental duplication events. Moreover, the prediction of cis-acting elements and microRNA target sites suggested that BnMTPs might be involved in plant growth, development, and stress responses. In addition, we found the expression of 24 BnMTPs in rapeseed leaves or roots could respond to heavy metal ion treatments. These results provided an important basis for clarifying the biological functions of BnMTPs, especially in heavy metal detoxification, and will be helpful in the phytoremediation of heavy metal pollution in soil.\n\nGenome-Wide Identification and Expressional Profiling of the Metal Tolerance Protein Gene Family in Brassica napus.", "token_count": 480, "char_count": 1631, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6933, "quality_score": 0.8467, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:55.741644", "source": { "split": "train_shard_00001", "doc_id": 4842 }, "chunk_id": "train_shard_00001_4842_0", "global_id": 12507 }, { "text": "

Background

Bifidobacteria are commonly found as part of the microbiota of the gastrointestinal tract (GIT) of a broad range of hosts, where their presence is positively correlated with the host's health status. In this study, we assessed the genomes of thirteen representatives of Bifidobacterium breve, which is not only a frequently encountered component of the (adult and infant) human gut microbiota, but can also be isolated from human milk and vagina.

Results

In silico analysis of genome sequences from thirteen B. breve strains isolated from different environments (infant and adult faeces, human milk, human vagina) shows that the genetic variability of this species principally consists of hypothetical genes and mobile elements, but, interestingly, also genes correlated with the adaptation to host environment and gut colonization. These latter genes specify the biosynthetic machinery for sortase-dependent pili and exopolysaccharide production, as well as genes that provide protection against invasion of foreign DNA (i.e. CRISPR loci and restriction/modification systems), and genes that encode enzymes responsible for carbohydrate fermentation. Gene-trait matching analysis showed clear correlations between known metabolic capabilities and characterized genes, and it also allowed the identification of a gene cluster involved in the utilization of the alcohol-sugar sorbitol.

Conclusions

Genome analysis of thirteen representatives of the B. breve species revealed that the deduced pan-genome exhibits an essentially close trend. For this reason our analyses suggest that this number of B. breve representatives is sufficient to fully describe the pan-genome of this species. Comparative genomics also facilitated the genetic explanation for differential carbon source utilization phenotypes previously observed in different strains of B. breve.\n\nComparative genomics of the Bifidobacterium breve taxon.", "token_count": 440, "char_count": 1944, "word_count": 263, "semantic_coherence": 1, "information_density": 0.6236, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:56.382090", "source": { "split": "train_shard_00001", "doc_id": 4843 }, "chunk_id": "train_shard_00001_4843_0", "global_id": 12508 }, { "text": "Kefir grains consist of complex symbiotic mixtures of bacteria and yeasts, and are reported to impart numerous health-boosting properties to milk and water kefir beverages. The objective of this work was to investigate the microbial communities in kefir grains, and explore the possibility of deriving useful probiotic strains from them. A total of 158 microbial strains, representing six fungal and 17 bacterial species, were isolated from milk and water kefir grains collected from a Singapore-based homebrewer. Based on 16S rRNA sequencing, isolated genera included Lactobacillus, Liquorilactobacillus, Lacticaseibacillus, Lentilactobacillus, Leuconostoc, Lactococcus, Acetobacter, Gluconobacter, Oenococcus, Clostridium, Zymomonas, Saccharomyces, Kluyveromyces, Pichia, Lachancea, Candida, and Brettanomyces. To characterize these isolates, a funnel approach, involving numerous phenotypic and genomic screening assays, was applied to identify kefir-derived microbial strains with the highest probiotic potential. Particular focus was placed on examining the pathogen inhibitory properties of kefir isolates toward enteric pathogens which pose a considerable global health burden. Enteric pathogens tested include species of Bacillus, Salmonella, Vibrio, Clostridium, Klebsiella, Escherichia, and Staphylococcus", "token_count": 495, "char_count": 1483, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7152, "quality_score": 0.8576, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:57.034937", "source": { "split": "train_shard_00001", "doc_id": 4844 }, "chunk_id": "train_shard_00001_4844_0", "global_id": 12509 }, { "text": "Well diffusion assays were conducted to determine the propensity of kefir isolates to inhibit growth of enteric pathogens, and a competitive adhesion/exclusion assay was used to determine the ability of kefir isolates to out-compete or exclude attachment of enteric pathogens to Caco-2 cells. Seven bacterial strains of Lentilactobacillus hilgardii, Lacticaseibacillus paracasei, Liquorilactobacillus satsumensis, Lactobacillus helveticus, and Lentilactobacillus kefiri, were ultimately identified as potential probiotics, and combined to form a \"kefir probiotics blend.\" Desirable probiotic characteristics, including good survival in acid and bile environments, bile salt hydrolase activity, antioxidant activity, non-cytotoxicity and high adhesion to Caco-2 cells, and a lack of virulence or antimicrobial resistance genes. In addition, vitamin and γ-aminobutyric acid (GABA) synthesis genes, were identified in these kefir isolates. Overall, probiotic candidates derived in this study are well-characterized strains with a good safety profile which can serve as novel agents to combat enteric diseases. These kefir-derived probiotics also add diversity to the existing repertoire of probiotic strains, and may provide consumers with alternative product formats to attain the health benefits of kefir.\n\nPotential Probiotic Strains From Milk and Water Kefir Grains in Singapore-Use for Defense Against Enteric Bacterial Pathogens.", "token_count": 403, "char_count": 1467, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6684, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:57.657049", "source": { "split": "train_shard_00001", "doc_id": 4844 }, "chunk_id": "train_shard_00001_4844_1", "global_id": 12510 }, { "text": "

Background

Routine sequencing of MRSA could bring about significant improvements to outbreak detection and investigation. Sequencing is commonly performed using DNA extracted from a pure culture, but overcoming the delay associated with this step could reduce the time to infection control interventions.

Objectives

To develop and evaluate rapid sequencing of MRSA using primary clinical cultures.

Methods

Patients with samples submitted to the clinical laboratory at the Cambridge University Hospitals NHS Foundation Trust from which MRSA was isolated were identified, the routine laboratory culture plates obtained and DNA extraction and sequencing performed.

Results

An evaluation of routine MRSA cultures from 30 patients demonstrated that direct sequencing from bacterial colonies picked from four different culture media was feasible. The 30 clinical MRSA isolates were sequenced on the day of plate retrieval over five runs and passed quality control metrics for sequencing depth and coverage. The maximum contamination detected using Kraken was 1.09% fragments, which were identified as Prevotella dentalis. The most common contaminants were other staphylococcal species (25 isolate sequences) and Burkholderia dolosa (11 isolate sequences). Core genome pairwise SNP analysis to identify clusters based on isolates that were ≤50 SNPs different was used to triage cases for further investigation. This identified three clusters, but more detailed genomic and epidemiological evaluation excluded an acute outbreak.

Conclusions

Rapid sequencing of MRSA from clinical culture plates is feasible and reduces the delay associated with purity culture prior to DNA extraction.\n\nRapid sequencing of MRSA direct from clinical plates in a routine microbiology laboratory.", "token_count": 390, "char_count": 1804, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:58.275429", "source": { "split": "train_shard_00001", "doc_id": 4845 }, "chunk_id": "train_shard_00001_4845_0", "global_id": 12511 }, { "text": "To develop a novel yeast diet, production of Kluyveromyces fragilis has been carried out in aerobic continuous culture. With a 2.5% fructose medium, the maximum biomass productivity of the chemostat was 4.81 g l(-1) per h. At low dilution rates (D < 0.17 h(-1)) aerobic ethanol synthesis was almost not found and the maximum biomass yield was found to be 0.42 g dry biomass g(-1) fructose with 5.5 x 10(9) viable yeasts per ml. The protein content of the yeast biomass was 50-55% at all dilution rates studied. Fermentation parameters of Ks, Dc, m, and Yx/s(G) were estimated by the Monod equation and found to be 0.1 g l(-1), 0.79 h(-1), 0.2 g fructose consumed per g dry biomass h(-1) and 0.24 g dry biomass per g fructose, respectively. From the data, the specific productivity of biomass was estimated to be 0.74 h(-1).\n\nA continuous fermentation of Kluyveromyces fragilis for the production of a highly nutritious protein diet", "token_count": 303, "char_count": 931, "word_count": 158, "semantic_coherence": 1, "information_density": 0.5886, "quality_score": 0.7943, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:58.835040", "source": { "split": "train_shard_00001", "doc_id": 4846 }, "chunk_id": "train_shard_00001_4846_0", "global_id": 12512 }, { "text": "The opportunistic pathogen Aspergillus fumigatus is found on all continents and thrives in soil and agricultural environments. Its ability to readily adapt to novel environments and to produce billions of spores led to the spread of azole-resistant A. fumigatus across the globe, posing a threat to many immunocompromised patients, including critically ill patients with severe influenza or COVID-19. In our study, we sought to compare the adaptational response to azoles from A. fumigatus isolates that differ in azole susceptibility and genetic background. To gain more insight into how short-term adaptation to stressful azole compounds is managed through gene expression, we conducted an RNA-sequencing study on the response of A. fumigatus to itraconazole and the newest clinically approved azole, isavuconazole. We observed many similarities in ergosterol biosynthesis up-regulation across isolates, with the exception of the pan-azole-resistant isolate, which showed very little differential regulation in comparison to other isolates. Additionally, we found differential regulation of membrane efflux transporters, secondary metabolites, iron metabolism, and various stress response and cell signaling mechanisms.\n\nThe Transcriptome Response to Azole Compounds in Aspergillus fumigatus Shows Differential Gene Expression across Pathways Essential for Azole Resistance and Cell Survival.", "token_count": 355, "char_count": 1429, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6632, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:56:59.404864", "source": { "split": "train_shard_00001", "doc_id": 4847 }, "chunk_id": "train_shard_00001_4847_0", "global_id": 12513 }, { "text": "This study examined the phylogenetic structure of serotype a Haemophilus influenzae (Hia) isolates recovered from patients in Canada. Hia isolates from 490 separate patients and an American Type Culture Collection (ATCC) strain were analyzed by multilocus sequence typing (MLST), with 18 different sequence types (STs) identified. Most (85.7%) Hia patient isolates were typed as ST-23 and another 12.7% belonged to 14 different STs with 6, 5, or 4 MLST gene loci related to ST-23 (ST-23 complex). Core genome single-nucleotide variation phylogeny (SNVPhyl) on whole genome sequence (WGS) data of 121 Hia patient isolates representing all identified STs and the ATCC strain revealed 2 phylogenetic populations, with all the ST-23 complex isolates within 1 population. The other phylogenetic population contained only the ATCC strain and 3 patient isolates. Concatenated hitABC sequences retrieved from WGS data and analyzed by MEGA (Molecular Evolutionary Genetic Analysis) alignment confirmed the phylogeny obtained by SNVPhyl. The sodC gene was found only in isolates in the minor phylogenetic population. The 2 phylogenetic populations of the Canadian Hia isolates are similar to the 2 clonal divisions described for serotype b H. influenzae. Combining MLST, core SNVPhyl, and hitABC gene sequence alignment showed that most (99.4%) Canadian Hia patient isolates belonged to 1 major phylogenetic population.\n\nWhole genome sequencing to study the phylogenetic structure of serotype a Haemophilus influenzae recovered from patients in Canada.", "token_count": 457, "char_count": 1584, "word_count": 225, "semantic_coherence": 1, "information_density": 0.5733, "quality_score": 0.7867, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:00.042104", "source": { "split": "train_shard_00001", "doc_id": 4848 }, "chunk_id": "train_shard_00001_4848_0", "global_id": 12514 }, { "text": "

Background

Whole genome sequencing (WGS) is useful for determining clusters of human cases, investigating outbreaks, and defining the population genetics of bacteria. It also provides information about other aspects of bacterial biology, including classical typing results, virulence, and adaptive strategies of the organism. Cell culture invasion and protein expression patterns of four related multilocus sequence type 21 (ST21) C. jejuni isolates from a significant Canadian water-borne outbreak were previously associated with the presence of a CJIE1 prophage. Whole genome sequencing was used to examine the genetic diversity among these isolates and confirm that previous observations could be attributed to differential prophage carriage. Moreover, we sought to determine the presence of genome sequences that could be used as surrogate markers to delineate outbreak-associated isolates.

Results

Differential carriage of the CJIE1 prophage was identified as the major genetic difference among the four outbreak isolates. High quality single-nucleotide variant (hqSNV) and core genome multilocus sequence typing (cgMLST) clustered these isolates within expanded datasets consisting of additional C. jejuni strains. The number and location of homopolymeric tract regions was identical in all four outbreak isolates but differed from all other C. jejuni examined. Comparative genomics and PCR amplification enabled the identification of large chromosomal inversions of approximately 93 kb and 388 kb within the outbreak isolates associated with transducer-like proteins containing long nucleotide repeat sequences. The 93-kb inversion was characteristic of the outbreak-associated isolates, and the gene content of this inverted region displayed high synteny with the reference strain.

Conclusions

The four outbreak isolates were clonally derived and differed mainly in the presence of the CJIE1 prophage, validating earlier findings linking the prophage to phenotypic differences in virulence assays and protein expression. The identification of large, genetically syntenous chromosomal inversions in the genomes of outbreak-associated isolates provided a unique method for discriminating outbreak isolates from the background population. Transducer-like proteins appear to be associated with the chromosomal inversions", "token_count": 525, "char_count": 2346, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5922, "quality_score": 0.7961, "entities": { "genes": [ "ST21", "CJIE1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:00.721111", "source": { "split": "train_shard_00001", "doc_id": 4849 }, "chunk_id": "train_shard_00001_4849_0", "global_id": 12515 }, { "text": "CgMLST and hqSNV analysis also effectively delineated the outbreak isolates within the larger C. jejuni population structure.\n\nGenomic insights from whole genome sequencing of four clonal outbreak Campylobacter jejuni assessed within the global C. jejuni population.", "token_count": 62, "char_count": 266, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8056, "quality_score": 0.9028, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:01.094584", "source": { "split": "train_shard_00001", "doc_id": 4849 }, "chunk_id": "train_shard_00001_4849_1", "global_id": 12516 }, { "text": "The human pathogen Acinetobacter baumannii has emerged as a frequent cause of hospital-acquired infections, but infection of animals has rarely been observed. Here we analyzed an outbreak of epidemic pneumonia killing hundreds of sheep on a farm in Pakistan and identified A. baumannii as the infecting agent. A pure culture of strain AbPK1 isolated from lungs of sick animals was inoculated into healthy sheep, which subsequently developed similar disease symptoms. Bacteria re-isolated from the infected animals were shown to be identical to the inoculum, fulfilling Koch's postulates. Comparison of the AbPK1 genome against 2283 A. baumannii genomes from the NCBI database revealed that AbPK1 carries genes for unusual surface structures, including a unique composition of iron acquisition genes, genes for O-antigen synthesis and sialic acid-specific acetylases of cell-surface carbohydrates that could enable immune evasion. Several of these unusual and otherwise rarely present genes were also identified in genomes of phylogenetically unrelated A. baumannii isolates from combat-wounded US military from Afghanistan indicating a common gene pool in this geographical region. Based on core genome MLST this virulent isolate represents a newly emerging lineage of Global Clone 2, suggesting a human source for this disease outbreak. The observed epidemic, direct transmission from sheep to sheep, which is highly unusual for A. baumannii, has important consequences for human and animal health. First, direct animal-to-animal transmission facilitates fast spread of pathogen and disease in the flock. Second, it may establish a stable ecological niche and subsequent spread in a new host. And third, it constitutes a serious risk of transmission of this hyper-virulent clone from sheep back to humans, which may result in emergence of contagious disease amongst humans.\n\nVirulent Epidemic Pneumonia in Sheep Caused by the Human Pathogen Acinetobacter baumannii.", "token_count": 482, "char_count": 2008, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6202, "quality_score": 0.8101, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:01.795443", "source": { "split": "train_shard_00001", "doc_id": 4850 }, "chunk_id": "train_shard_00001_4850_0", "global_id": 12517 }, { "text": "Urinary tract infections (UTIs) are highly recurrent and frequently caused by Uropathogenic Escherichia coli (UPEC) strains that can be found in patient intestines. Seeding of the urinary tract from this intestinal reservoir likely contributes to UTI recurrence (rUTI) rates. Thus, understanding the factors that promote UPEC intestinal colonization is of critical importance to designing therapeutics to reduce rUTI incidence. Although E. coli is found in high abundance in large intestine mucus, little is known about how it is able to maintain residence in this continuously secreted hydrogel. We discovered that the FimH adhesin of type 1 pili (T1P) bound throughout the secreted mucus layers of the colon and to epithelial cells in mouse and human samples. Disruption of T1P led to reduced association with colon mucus. Notably, this mutant up-regulated flagellar production and infiltrated the protective inner mucus layer of the colon. This could explain how UPEC resists being washed off by the continuously secreted mucus layers of the colon.\n\nMechanisms of uropathogenic <i>E. coli</i> mucosal association in the gastrointestinal tract.", "token_count": 317, "char_count": 1172, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6784, "quality_score": 0.8392, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:02.825455", "source": { "split": "train_shard_00001", "doc_id": 4851 }, "chunk_id": "train_shard_00001_4851_0", "global_id": 12518 }, { "text": "Kluyveromyces fragilis cells fermented for 36h were treated with mild ultrasonic waves (20kHz,10W) for 24h. The results showed that the amount of inulinase secreted from Kluyveromyces fragilis was increased one time more than that of the cells untreated by ultrasonic waves, and the optimum pH and temperature for inulinase production were 6.5-7.0 and 32℃ respectively. Micoscopic observation and determination of nucleic acids in the broth revealed that the yeast cells were not broken during growth under ultrasonic waves.\n\nProduction of inulinase with Kluyveromyces fragilis under mild ultrasound waves", "token_count": 165, "char_count": 605, "word_count": 88, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:03.269276", "source": { "split": "train_shard_00001", "doc_id": 4852 }, "chunk_id": "train_shard_00001_4852_0", "global_id": 12519 }, { "text": "The growth inhibitory effects of combinations of T-2 toxin and verrucarin A on the yeast Kluyveromyces marxianus was studied. A combination index value was derived to indicate the type of interaction that existed between the binary mixture of these two toxins at various ratios and the target yeast cells. The type of interaction was dependent on the ratio of the toxins used to attain a particular level of growth inhibition. Further, the least change in the type and intensity of interaction or the maximally quiescent ratio (MQR) was found to be unique to the growth medium. In a rich medium, the MQR was 1.0 microgram/ml T-2 toxin:0.75 microgram/ml verrucarin A, where the two toxins had a very stable synergistic interaction over a 2 or 3 log value concentration range. Decreasing the nutrients changed the MQR to 1.0 micrograms/ml T-2 toxin:0.38 microgram/ml verrucarin A. Halving the concentration of the cells in the assay changed the MQR to 1.0 microgram/ml T-2 toxin:6.0 micrograms/ml verrucarin A. We have previously shown that the hierarchy of trichothecene toxicity in yeast bioassay is verrucarin A > roridin A > T-2 toxin > diacetoxyscirpenol > HT-2 toxin. The MQR of these toxins in combination with T-2 toxin follows the same order. This study shows an exception to the above order in that verrucarin A and roridin A exchange places.\n\nEffect of T-2 toxin and verrucarin A in combination on Kluyveromyces marxianus.", "token_count": 420, "char_count": 1431, "word_count": 234, "semantic_coherence": 1, "information_density": 0.4915, "quality_score": 0.7457, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:03.901990", "source": { "split": "train_shard_00001", "doc_id": 4853 }, "chunk_id": "train_shard_00001_4853_0", "global_id": 12520 }, { "text": "

Background

Streptococcus suis is a zoonotic pathogen that causes infections in young piglets. S. suis is a heterogeneous species. Thirty-three different capsular serotypes have been described, that differ in virulence between as well as within serotypes.

Results

In this study, the correlation between gene content, serotype, phenotype and virulence among 55 S. suis strains was studied using Comparative Genome Hybridization (CGH). Clustering of CGH data divided S. suis isolates into two clusters, A and B. Cluster A isolates could be discriminated from cluster B isolates based on the protein expression of extracellular factor (EF). Cluster A contained serotype 1 and 2 isolates that were correlated with virulence. Cluster B mainly contained serotype 7 and 9 isolates. Genetic similarity was observed between serotype 7 and serotype 2 isolates that do not express muramidase released protein (MRP) and EF (MRP⁻EF⁻), suggesting these isolates originated from a common founder. Profiles of 25 putative virulence-associated genes of S. suis were determined among the 55 isolates. Presence of all 25 genes was shown for cluster A isolates, whereas cluster B isolates lacked one or more putative virulence genes. Divergence of S. suis isolates was further studied based on the presence of 39 regions of difference. Conservation of genes was evaluated by the definition of a core genome that contained 78% of all ORFs in P1/7.

Conclusions

In conclusion, we show that CGH is a valuable method to study distribution of genes or gene clusters among isolates in detail, yielding information on genetic similarity, and virulence traits of S. suis isolates.\n\nGenetic diversity of Streptococcus suis isolates as determined by comparative genome hybridization.", "token_count": 470, "char_count": 1773, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5573, "quality_score": 0.7786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:04.546166", "source": { "split": "train_shard_00001", "doc_id": 4854 }, "chunk_id": "train_shard_00001_4854_0", "global_id": 12521 }, { "text": "In this study, the prevalence and intensity of Candida species were evaluated in 300 healthy Turkish children aged between 0 and 12 years. The candidal carriage in 26 children who were fed only with breast milk and 38 children who were fed with both breast milk and bottle milk or other fluids was also examined. Oral samples cultured for fungal growth and Candida species were identified using germ tube test, chlamydospore formation test and API 20C AUX system. The results demonstrated that the prevalence of oral candidal carriage in 300 healthy children was 26.3%. Candida albicans was the most frequently isolated yeast (84.8% of the isolates). The other yeasts were identified as Candida parapsilosis, Candida krusei, Candida kefyr, Candida famata, and Candida tropicalis. It was also observed that the frequency of carriage varied as a function of age. The prevalence of carriage in children who were fed with both breast milk and bottle milk or other fluids was 18.5%, while in children fed only with breast milk was 0%. This finding supports previously reported observations that there may be intrinsic differences in oral carriage of Candida species between different ages and populations and type of dietary intake may affect frequency of carriage.\n\nPrevalence of Candida species in Turkish children: relationship between dietary intake and carriage.", "token_count": 312, "char_count": 1362, "word_count": 215, "semantic_coherence": 1, "information_density": 0.4884, "quality_score": 0.7442, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:05.104169", "source": { "split": "train_shard_00001", "doc_id": 4855 }, "chunk_id": "train_shard_00001_4855_0", "global_id": 12522 }, { "text": "Corynebacterium diphtheriae is the etiological agent of diphtheria, a disease caused by the presence of the diphtheria toxin. However, an increasing number of records report non-toxigenic C. diphtheriae infections. Here, a C. diphtheriae strain was recovered from a patient with a past history of bronchiectasis who developed a severe tracheo-bronchitis with multiple whitish lesions of the distal trachea and the mainstem bronchi. Whole-genome sequencing (WGS), performed in parallel with PCR targeting the toxin gene and the Elek test, provided clinically relevant results in a short turnaround time, showing that the isolate was non-toxigenic. A comparative genomic analysis of the new strain (CHUV2995) with 56 other publicly available genomes of C. diphtheriae revealed that the strains CHUV2995, CCUG 5865 and CMCNS703 share a lower average nucleotide identity (ANI) (95.24 to 95.39%) with the C. diphtheriae NCTC 11397T reference genome than all other C. diphtheriae genomes (>98.15%). Core genome phylogeny confirmed the presence of two monophyletic clades. Based on these findings, we propose here two new C. diphtheriae subspecies to replace the lineage denomination used in previous multilocus sequence typing studies: C. diphtheriae subsp. lausannense subsp. nov. (instead of lineage-2), regrouping strains CHUV2995, CCUG 5865, and CMCNS703, and C. diphtheriae subsp. diphtheriae subsp. nov, regrouping all other C", "token_count": 522, "char_count": 1517, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6553, "quality_score": 0.8277, "entities": { "genes": [ "CMCNS703", "CHUV2995" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:05.761558", "source": { "split": "train_shard_00001", "doc_id": 4856 }, "chunk_id": "train_shard_00001_4856_0", "global_id": 12523 }, { "text": "diphtheriae in the dataset (instead of lineage-1). Interestingly, members of subspecies lausannense displayed a larger genome size than subspecies diphtheriae and were enriched in COG categories related to transport and metabolism of lipids (I) and inorganic ion (P). Conversely, they lacked all genes involved in the synthesis of pili (SpaA-type, SpaD-type and SpaH-type), molybdenum cofactor and of the nitrate reductase. Finally, the CHUV2995 genome is particularly enriched in mobility genes and harbors several prophages. The genome encodes a type II-C CRISPR-Cas locus with 2 spacers that lacks csn2 or cas4, which could hamper the acquisition of new spacers and render strain CHUV2995 more susceptible to bacteriophage infections and gene acquisition through various mechanisms of horizontal gene transfer.\n\nDistinct Genomic Features Characterize Two Clades of Corynebacterium diphtheriae: Proposal of Corynebacterium diphtheriae Subsp. diphtheriae Subsp. nov. and Corynebacterium diphtheriae Subsp. lausannense Subsp. nov.", "token_count": 360, "char_count": 1097, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6809, "quality_score": 0.8404, "entities": { "genes": [ "CHUV2995" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:06.338374", "source": { "split": "train_shard_00001", "doc_id": 4856 }, "chunk_id": "train_shard_00001_4856_1", "global_id": 12524 }, { "text": "NetF-producing type A Clostridium perfringens, a pathotype of C. perfringens, causes necrotizing enteritis in neonatal foals and necrotizing and hemorrhagic enteritis in dogs. Recent core genome multilocus sequence typing study revealed that netF+ C. perfringens strains belong to two distinct clonal populations (clonal complexes I and II). There are no reports on susceptibility to antimicrobial drugs of isolates from this pathotype. The susceptibility to 13 different antimicrobial drugs of 49 netF+ strains recovered from foals or dogs with necrotizing enteritis in Canada, the United States, and Switzerland was assessed using a commercial microdilution panel designed for anaerobic human pathogens. All isolates were highly susceptible to 12 antimicrobial agents, including all beta-lactams tested, such as penicillin G and ampicillin, as well as clindamycin, chloramphenicol, and metronidazole. The isolates consistently presented a reduced susceptibility or resistance to tetracycline, which was associated with previously described tetracycline resistance genes. Clonal complex I isolates (n = 41) possessed the tetA408(P) gene, whereas clonal complex II isolates (n = 8) possessed the tetA(P)-tetB(P) genes and were more likely to be fully resistant.\n\nAntimicrobial Susceptibility and Clonal Relationship of Tetracycline Resistance Genes in netF-Positive Clostridium perfringens.", "token_count": 464, "char_count": 1496, "word_count": 189, "semantic_coherence": 1, "information_density": 0.6508, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:06.978608", "source": { "split": "train_shard_00001", "doc_id": 4857 }, "chunk_id": "train_shard_00001_4857_0", "global_id": 12525 }, { "text": "Listeria monocytogenes is the causative agent of listeriosis, which is an uncommon but severe infection associated with high mortality rates in humans especially in high-risk groups. This bacterium survives a variety of stress conditions (e.g., high osmolality, low pH), which allows it to colonize different niches especially niches found in food processing environments. Additionally, a considerable heterogeneity in pathogenic potential has been observed in different strains. In this study, 38 isolates of L. monocytogenes collected in Chile from clinical samples (n = 22) and non-clinical samples (n = 16) were analyzed using whole genome sequencing (WGS) to determine their genomic diversity. A core genome Single Nucleotide Polymorphism (SNP) tree using 55 additional L. monocytogenes accessions classified the Chilean isolates in lineages I (n = 25) and II (n = 13). In silico, Multi-locus sequence typing (MLST) differentiated the isolates into 13 sequence types (ST) in which the most common were ST1 (15 isolates) and ST9 (6 isolates) and represented 55% of the isolates. Genomic elements associated with virulence (i.e., LIPI-1, LIPI-3, inlA, inlB, inlC, inlG, inlH, inlD, inlE, inlK, inlF, and inlJ) and stress survival (i.e., stress survival islet 1 and stress survival islet 2) were unevenly distributed among clinical and non-clinical isolates. In addition, one novel inlA premature stop codon (PMSC) was detected. Comparative analysis of L", "token_count": 519, "char_count": 1585, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6927, "quality_score": 0.8463, "entities": { "genes": [ "ST1", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:07.632931", "source": { "split": "train_shard_00001", "doc_id": 4858 }, "chunk_id": "train_shard_00001_4858_0", "global_id": 12526 }, { "text": "monocytogenes circulating in Chile revealed the presence of globally distributed sequence types along with differences among the isolates analyzed at a genomic level specifically associated with virulence and stress survival.\n\nGenomic Diversity of Listeria monocytogenes Isolated from Clinical and Non-Clinical Samples in Chile.", "token_count": 83, "char_count": 339, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:08.006414", "source": { "split": "train_shard_00001", "doc_id": 4858 }, "chunk_id": "train_shard_00001_4858_1", "global_id": 12527 }, { "text": "We present the pan-genome tree as a tool for visualizing similarities and differences between closely related microbial genomes within a species or genus. Distance between genomes is computed as a weighted relative Manhattan distance based on gene family presence/absence. The weights can be chosen with emphasis on groups of gene families conserved to various degrees inside the pan-genome. The software is available for free as an R-package.\n\nStandard operating procedure for computing pangenome trees.", "token_count": 103, "char_count": 504, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7973, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:08.384201", "source": { "split": "train_shard_00001", "doc_id": 4859 }, "chunk_id": "train_shard_00001_4859_0", "global_id": 12528 }, { "text": "Since the late 1990s, changes in the epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) were recognized with the emergence of community-associated MRSA (CA-MRSA). CA-MRSA belonging to clonal complex 152 (CC152), carrying the small staphylococcal cassette chromosome mec (SCCmec) type V and encoding the Panton-Valentine leukocidin (PVL), has been observed in Europe. The aim of this study was to investigate its origin, evolution, and dissemination. Whole-genome sequencing was performed on a global collection of 149 CC152 isolates spanning 20 years (93 methicillin-susceptible S. aureus [MSSA] and 56 MRSA isolates). Core genome phylogeny, Bayesian inference, in silico resistance analyses, and genomic characterization were applied. Phylogenetic analysis revealed two major distinct clades, one dominated by MSSA and the other populated only by MRSA. The MSSA isolates were predominately from sub-Saharan Africa, whereas MRSA was almost exclusively from Europe. The European MRSA isolates all harbored an SCCmec type V (5C2&5) element, whereas other SCCmec elements were sporadically detected in MRSA from the otherwise MSSA-dominated clade, including SCCmec types IV (2B), V (5C2), and XIII (9A). In total, 93% of the studied CC152 isolates were PVL positive. Bayesian coalescent inference suggests an emergence of the European CC152-MRSA in the 1990s, while the CC152 lineage dates back to the 1970s", "token_count": 483, "char_count": 1476, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [ "CC152" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:09.040638", "source": { "split": "train_shard_00001", "doc_id": 4860 }, "chunk_id": "train_shard_00001_4860_0", "global_id": 12529 }, { "text": "The CA-MRSA CC152 clone mimics the European CC80 CA-MRSA lineage by its emergence from a PVL-positive MSSA ancestor from North Africa or Europe. The CC152 lineage has acquired SCCmec several times, but acquisition of SCCmec type V (5C2&5) seems associated with expansion of MRSA CC152 in Europe.IMPORTANCE Understanding the evolution of CA-MRSA is important in light of the increasing importance of this reservoir in the dissemination of MRSA. Here, we highlight the story of the CA-MRSA CC152 lineage using whole-genome sequencing on an international collection of CC152. We show that the evolution of this lineage is novel and that antibiotic usage may have the potential to select for the phage-encoded Panton-Valentine leukocidin. The diversity of the strains correlated highly to geography, with higher level of resistance observed among the European MRSA isolates. The mobility of the SCCmec element is mandatory for the emergence of novel MRSA lineages, and we show here distinct acquisitions, one of which is linked to the successful clone found throughout Europe today.\n\nEvolution and Population Dynamics of Clonal Complex 152 Community-Associated Methicillin-Resistant Staphylococcus aureus.", "token_count": 337, "char_count": 1236, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6236, "quality_score": 0.8118, "entities": { "genes": [ "CC152", "CC80" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:09.607290", "source": { "split": "train_shard_00001", "doc_id": 4860 }, "chunk_id": "train_shard_00001_4860_1", "global_id": 12530 }, { "text": "Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients' exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.\n\nMicrobiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus.", "token_count": 368, "char_count": 1540, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:10.190186", "source": { "split": "train_shard_00001", "doc_id": 4861 }, "chunk_id": "train_shard_00001_4861_0", "global_id": 12531 }, { "text": "Abstract

Infant gut microbiome assembly influences childhood growth and development. However, current understanding is based almost exclusively on infants from highly industrialised, high-income countries. Here, we present a high-resolution map of gut microbiome assembly in 596 infants from six non-industrialised countries across sub-Saharan Africa and South Asia. Microbiome assembly followed a unified trajectory comprising three distinct stages, characterised by the ordered acquisition and loss of bacterial species and functions. Progression through these stages is governed by breastfeeding and the timing of weaning, revealing an ancestral pattern of microbiome succession conserved across diverse non-industrialised populations. Core microbiome functions are rapidly established by a defined consortium of pioneer species, followed by age-dependent expansions in functional capacity, including pathways implicated in metabolism, immune regulation, and neurodevelopment. Comparison with infant microbiomes from highly industrialised populations reveals that key bacteria underpinning the ancestral assembly trajectory—Bifidobacterium, Lactobacillus and Prevotella—are depleted with industrialisation. Our microbiome assembly map provides a reference for optimising infant microbiome development and supporting child growth through rational design of next-generation infant probiotics, and highlights commensal microbes that should be prioritised for preservation amid global lifestyle transitions.

\n\nAncestral trajectory of infant gut microbiome assembly in non-industrialised populations", "token_count": 353, "char_count": 1653, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6891, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:10.772346", "source": { "split": "train_shard_00001", "doc_id": 4862 }, "chunk_id": "train_shard_00001_4862_0", "global_id": 12532 }, { "text": "Roseburia species are important denizens of the human gut microbiome that ferment complex polysaccharides to butyrate as a terminal fermentation product, which influences human physiology and serves as an energy source for colonocytes. Previous comparative genomics analyses of the genus Roseburia have examined polysaccharide degradation genes. Here, we characterize the core and pangenomes of the genus Roseburia with respect to central carbon and energy metabolism, as well as biosynthesis of amino acids and B vitamins using orthology-based methods, uncovering significant differences among species in their biosynthetic capacities. Variation in gene content among Roseburia species and strains was most significant for cofactor biosynthesis. Unlike all other species of Roseburia that we analysed, Roseburia inulinivorans strains lacked biosynthetic genes for riboflavin or pantothenate but possessed folate biosynthesis genes. Differences in gene content for B vitamin synthesis were matched with differences in putative salvage and synthesis strategies among species. For example, we observed extended biotin salvage capabilities in R. intestinalis strains, which further suggest that B vitamin acquisition strategies may impact fitness in the gut ecosystem. As differences in the functional potential to synthesize components of biomass (e.g. amino acids, vitamins) can drive interspecies interactions, variation in auxotrophies of the Roseburia spp. genomes may influence in vivo gut ecology. This study serves to advance our understanding of the potential metabolic interactions that influence the ecology of Roseburia spp. and, ultimately, may provide a basis for rational strategies to manipulate the abundances of these species.\n\nComparative genomics of the genus Roseburia reveals divergent biosynthetic pathways that may influence colonic competition among species.", "token_count": 509, "char_count": 1957, "word_count": 258, "semantic_coherence": 1, "information_density": 0.593, "quality_score": 0.7965, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:11.426795", "source": { "split": "train_shard_00001", "doc_id": 4863 }, "chunk_id": "train_shard_00001_4863_0", "global_id": 12533 }, { "text": "IntroductionDuring summer 2016, Norway observed an increase in Salmonella enterica subsp. enterica serovar Chester cases among travellers to Greece.AimOur aim was to investigate genetic relatedness of S. Chester for surveillance and outbreak detection by core genome multilocus sequence typing (cgMLST) and compare the results to genome mapping.MethodsWe included S. Chester isolates from 51 cases of salmonellosis between 2000 and 2016. Paired-end sequencing (2 × 250 bp) was performed on Illumina MiSeq. Genetic relatedness by cgMLST for Salmonella enterica subsp. enterica, including 3,002 genes and seven housekeeping genes, was compared by reference genome mapping with CSI Phylogeny version 1.4 and conventional MLST.ResultsConfirmed travel history was available for 80% of included cases, to Europe (n = 13), Asia (n = 12) and Africa (n = 16). Isolates were distributed into four phylogenetic clusters corresponding to geographical regions. Sequence type (ST) ST411 and a single-locus variant ST5260 (n = 17) were primarily acquired in southern Europe, ST1954 (n = 15) in Africa, ST343 (n = 11) and ST2063 (n = 8) primarily in Asia. Part of the European cluster was further divided into a Greek (n = 10) and a Cypriot (n = 4) cluster", "token_count": 458, "char_count": 1289, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6771, "quality_score": 0.8385, "entities": { "genes": [ "ST1954", "ST411", "ST343", "ST2063", "ST5260" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:12.071482", "source": { "split": "train_shard_00001", "doc_id": 4864 }, "chunk_id": "train_shard_00001_4864_0", "global_id": 12534 }, { "text": "All isolates in the African cluster displayed resistance to ≥ 1 class of antimicrobials, while resistance was rare in the other clusters.ConclusionWhole genome sequencing of S. Chester in Norway showed four geographically distinct clusters, with a possible outbreak occurring during summer 2016 related to Greece. We recommend public health institutes to implement cgMLST-based real-time Salmonella enterica surveillance for early and accurate detection of future outbreaks and further development of cluster cut-offs.\n\nWhole genome sequencing of Salmonella Chester reveals geographically distinct clusters, Norway, 2000 to 2016.", "token_count": 173, "char_count": 657, "word_count": 85, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:12.538666", "source": { "split": "train_shard_00001", "doc_id": 4864 }, "chunk_id": "train_shard_00001_4864_1", "global_id": 12535 }, { "text": "Dietary carbohydrates impact the composition of the human gut microbiota. However, the relationship between carbohydrate availability for individual bacteria and their growth in the intestinal environment remains unclear. Here, we show that the availability of long-chain xylans (LCX), one of the most abundant dietary fibres in the human diet, promotes the growth of Bifidobacterium pseudocatenulatum in the adult human gut. Genomic and phenotypic analyses revealed that the availability of LCX-derived oligosaccharides is a fundamental feature of B. pseudocatenulatum, and that some but not all strains possessing the endo-1,4-β-xylanase (BpXyn10A) gene grow on LCX by cleaving the xylose backbone. The BpXyn10A gene, likely acquired by horizontal transfer, was incorporated into the gene cluster for LCX-derived oligosaccharide utilisation. Co-culturing with xylanolytic Bacteroides spp. demonstrated that LCX-utilising strains are more competitive than LCX non-utilising strains even when LCX-derived oligosaccharides were supplied. In LCX-rich dietary interventions in adult humans, levels of endogenous B. pseudocatenulatum increased only when BpXyn10A was detected, indicating that LCX availability is a fitness determinant in the human gut. Our findings highlight the enhanced intestinal adaptability of bifidobacteria via polysaccharide utilisation, and provide a cornerstone for systematic manipulation of the intestinal microbiota through dietary intervention using key enzymes that degrade polysaccharide as biomarkers.\n\nXylan utilisation promotes adaptation of Bifidobacterium pseudocatenulatum to the human gastrointestinal tract.", "token_count": 439, "char_count": 1644, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:13.181820", "source": { "split": "train_shard_00001", "doc_id": 4865 }, "chunk_id": "train_shard_00001_4865_0", "global_id": 12536 }, { "text": "

Purpose

Klebsiella pneumoniae producing extended-spectrum β-lactamases (ESBLs) causes nosocomial infections worldwide. The present study aimed to determine the molecular subtyping characteristics and antibiotic resistance mechanisms of ESBL-producing K. pneumoniae strains collected during an outbreak. Moreover, we attempted to reveal the fine transmission route of the strains within this outbreak using whole-genome sequencing (WGS).

Methods

Collecting cases and strain information were carried out. Outbreak-related strains were identified using pulsed-field gel electrophoresis (PFGE). The antibiotic susceptibility, drug-resistant genes, and molecular subtype characteristics of ESBL-producing K. pneumoniae were analyzed. The fine transmission route of the strains within this outbreak was revealed using WGS and minimum core genome (MCG) sequence typing.

Results

In mid-January, 2015, five cases of neonatal pneumonia caused by ESBL-producing K. pneumoniae were observed in the neonatal intensive care unit (NICU) of the Affiliated Hospital of Chifeng University, China. Eight ESBL-producing K. pneumoniae were isolated from these five cases, and two additional strains from another two cases were identified using PFGE. All ten isolates harbored bla CTX-M-15, bla TEM-1, bla SHV-108, and bla OXA-1 genes, and belonged to the sequence type 471 (ST471) clone. A putative transmission map was constructed via comprehensive consideration of genomic and epidemiological information. WGS identified the initial case and the \"superspreader\"", "token_count": 486, "char_count": 1671, "word_count": 200, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "ST471" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:13.881299", "source": { "split": "train_shard_00001", "doc_id": 4866 }, "chunk_id": "train_shard_00001_4866_0", "global_id": 12537 }, { "text": "The genomic epidemiological investigation revealed that the outbreak was caused by the introduction of the bacteria one month before the first case appeared.

Conclusion

As far as we know, this is the first report to describe the characteristics of an ST471 ESBL-producing K. pneumoniae outbreak. The data showed that epidemiological inferences could be greatly improved by interpretation in the context of WGS and that K. pneumoniae strains isolated from the same outbreak contain sufficient genomic differences to refine epidemiological linkages on the basis of genetic lineage. These findings suggested that integration of genomic and epidemiological data can help us to have a clearer understanding of when and how outbreaks occur, so as to better control nosocomial transmission.\n\nGenomic Epidemiology of an Outbreak of Klebsiella pneumoniae ST471 Producing Extended-Spectrum β-Lactamases in a Neonatal Intensive Care Unit.", "token_count": 236, "char_count": 955, "word_count": 133, "semantic_coherence": 1, "information_density": 0.6692, "quality_score": 0.8346, "entities": { "genes": [ "ST471" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:14.381360", "source": { "split": "train_shard_00001", "doc_id": 4866 }, "chunk_id": "train_shard_00001_4866_1", "global_id": 12538 }, { "text": "Oligo-2-hydroxy-1-naphthaldehyde (OHNA) was synthesized by oxidative polycondensation using H2O2 (35%, aqueous solution), air O2 and NaOCl (34%, aqueous solution) by Kaya and Senol and the products were characterized by spectral techniques. Antimicrobial activities of the first and second fractions of OHNA were tested against Corynobacterium xerosis CCM 2824, Proteus vulgaris ATCC 6897, Staphylococcus epidermidis NRRL B-4877, S. aureus ATCC 6538, Enterobacter aerogenes ATCC 13048, Salmonella thyphimurium CCM 5445, Pseudomonas aeroginosa ATCC 27853, Escherichia coli ATCC 11230, E. coli ATCC 23998, Bacillus cereus ATCC 7064, B. cereus ATCC 99, B. subtilis ATCC 6633, Yersinia spp., Neisseria canis, Rhodotorula rubra, Kluyveromyces fragilis NRRL 2415, Saccharomyces cerevisiae ATCC 9763, S. ovarum, Debaryomyces hensenii, Hansenula anamola, Candida albicans, C. utilis, Aspergillus niger, A. fumigates, A. versicolor, A. flavus, A. parasiticus, Penicillium granulatum, P. chrysogenum, and P. herque. OHNA demonstrated antimicrobial activity against various bacteria and yeast, but did not affect filamentous fungi.\n\nDetermination of the antimicrobial properties of oligo-2-hydroxy-1-naphthaldehyde.", "token_count": 476, "char_count": 1204, "word_count": 155, "semantic_coherence": 1, "information_density": 0.7613, "quality_score": 0.8806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:15.019887", "source": { "split": "train_shard_00001", "doc_id": 4867 }, "chunk_id": "train_shard_00001_4867_0", "global_id": 12539 }, { "text": "This study aimed to investigate the impact of the food matrix (orange juice and yogurt) on the effects of the spore-forming probiotic microorganism Bacillus coagulans GBI-30 6086 in health parameters and gastrointestinal tract (gut) bacterial diversity in Wistar male rats. Rats (n = 48) were randomly distributed into six groups. The groups were the Control (which received sterile distilled water), Juice (which received orange juice), Yogurt (which received yogurt), Probiotic Bacillus (which received B. coagulans GBI-30 6086 in distilled water), Probiotic Juice (which received orange juice with B. coagulans GBI-30 6086), and Probiotic Yogurt (which received yogurt with B. coagulans GBI-30 6086). Each animal belonging to the different groups was treated for 21 days. The daily administration of probiotic juice or probiotic yogurt did not affect the rats' food or body weight. Rats fed with Probiotic Yogurt showed lower glucose and triglycerides levels (p < 0.05) in comparison to the control group (p < 0.05), while no changes in these parameters were observed in the rats fed with Probiotic Juice. Rats fed with Probiotic Yogurt showed a higher gut bacterial diversity than the control group (p < 0.05), and higher abundance (p < 0.05) of Vibrionales, Enterobacteriales, Burkholderiales, Erysipelotrichales, and Bifidobacteriales compared to all other groups", "token_count": 498, "char_count": 1481, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5291, "quality_score": 0.7646, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:15.675012", "source": { "split": "train_shard_00001", "doc_id": 4868 }, "chunk_id": "train_shard_00001_4868_0", "global_id": 12540 }, { "text": "No changes were observed in the expression levels of antioxidant enzymes or heat shock protein 70 of rats fed with probiotic yogurt or probiotic juice. Results reveal that the consumption of yogurt containing B. coagulans GBI-30 6086 decreases triglycerides and glucose levels and positively impacts the gut bacterial ecology in healthy rats. These animal model findings indicate that the matrix also impacts the functionality of foods carrying spore-forming probiotics. Besides, this research indicates that yogurt is also a suitable food carrier of Bacillus coagulans GBI-30 6086.\n\nOrange Juice and Yogurt Carrying Probiotic Bacillus coagulans GBI-30 6086: Impact of Intake on Wistar Male Rats Health Parameters and Gut Bacterial Diversity.", "token_count": 227, "char_count": 763, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:16.149481", "source": { "split": "train_shard_00001", "doc_id": 4868 }, "chunk_id": "train_shard_00001_4868_1", "global_id": 12541 }, { "text": "Public health agencies are increasingly relying on genomics during Legionnaires’ disease investigations. However, the causative bacterium ( Legionella pneumophila ) has an unusual population structure with extreme temporal and spatial genome sequence conservation. Furthermore, Legionnaires’ disease outbreaks can be caused by multiple L. pneumophila genotypes in a single source. These factors can confound cluster identification using standard phylogenomic methods. Here, we show that a statistical learning approach based on L. pneumophila core genome single nucleotide polymorphism (SNP) comparisons eliminates ambiguity for defining outbreak clusters and accurately predicts exposure sources for clinical cases. We illustrate the performance of our method by genome comparisons of 234 L. pneumophila isolates obtained from patients and cooling towers in Melbourne, Australia between 1994 and 2014. This collection included one of the largest reported Legionnaires’ disease outbreaks, involving 125 cases at an aquarium. Using only sequence data from L. pneumophila cooling tower isolates and including all core genome variation, we built a multivariate model using discriminant analysis of principal components (DAPC) to find cooling tower-specific genomic signatures, and then used it to predict the origin of clinical isolates. Model assignments were 93% congruent with epidemiological data, including the aquarium Legionnaires’ outbreak and three other unrelated outbreak investigations. We applied the same approach to a recently described investigation of Legionnaires’ disease within a UK hospital and observed model predictive ability of 86%. We have developed a promising means to breach L. pneumophila genetic diversity extremes and provide objective source attribution data for outbreak investigations.\n\nA supervised statistical learning approach for accurateLegionella pneumophilasource attribution during outbreaks", "token_count": 420, "char_count": 1938, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6628, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:16.773868", "source": { "split": "train_shard_00001", "doc_id": 4869 }, "chunk_id": "train_shard_00001_4869_0", "global_id": 12542 }, { "text": "The aim of this study was to examine the feeding value of different yeasts as a substitute for soya bean meal, the main protein source in diets of weaned piglets. Tested two yeasts were already available on the market, Saccharomyces cerevisiae and Kluyveromyces lactis (beer and milk yeast), which replaced 40% of the soya bean meal in the diets. Furthermore, a yeast (Kluyveromyces fragilis) grown on whey, a side-product of cheese production, was used in increasing concentrations in the diets, so that increasing amounts of the soya bean meal (20%, 40% and 60%) could be replaced. As proved in these experiments, a replacement of 60% of the soya protein with whey yeast protein had positive effects on the performances (daily weight gain) and on the N-metabolism and did not have negative effects on the health or the faeces consistency. The whey yeast stands out because of its high protein quality (N-digestibility and N-retention). Furthermore, the replacement of soya bean meal with highly digestible yeasts is welcomed under the aspect of animal health, because of the reduction of anti-nutritive soya components (stachyose, glycinin) in diets of weaned piglets. The controlled production conditions of the yeasts result in a high feed safety; in addition, the yeast as an end-of-pipe-product is a resource conserving and valuable feed. A main stimulus for the use of yeasts, however, in a food production controlled by economic standpoints, is their price and the costs of other competing feeds.\n\nYeast (different sources and levels) as protein source in diets of reared piglets: effects on protein digestibility and N-metabolism.", "token_count": 408, "char_count": 1639, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:17.396821", "source": { "split": "train_shard_00001", "doc_id": 4870 }, "chunk_id": "train_shard_00001_4870_0", "global_id": 12543 }, { "text": "Microbial bioconversion studies conducted on the diterpene psiadin have revealed that it was metabolized by Aspergillus niger (NRRL 2295) to give 2alpha-hydroxydeoxopsiadin, Cunninghamella blakesleeana (ATCC 8688a) to give 11beta-hydroxypsiadin, and Cylindrocephalum aureum (ATCC 12720), Gongronella butleri (ATCC 22822), Kloeckera africana (ATCC 20111), and Kluyveromyces marxianus var. lactis (ATCC 2628) to yield 7alpha-hydroxypsiadin. Their structures have been established on the basis of spectral data. The structure and relative stereochemistry of 7alpha-hydroxypsiadin was confirmed by single-crystal X-ray analysis.\n\nMicrobial hydroxylation and reduction of the diterpene psiadin.", "token_count": 251, "char_count": 689, "word_count": 84, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:17.884297", "source": { "split": "train_shard_00001", "doc_id": 4871 }, "chunk_id": "train_shard_00001_4871_0", "global_id": 12544 }, { "text": "A diverse, stable community of microbes in the human gut is strongly tied to health. The factors that regulate microbial community structure and dynamics are ill-defined. In this study, we discover mediterrocin, a bacteriocin produced by the core member of the human gut microbiota, Mediterraneibacter gnavus (previously Ruminococcus gnavus). Following a screen for antimicrobial production by clinical isolates of M. gnavus, mediterrocin was isolated by bioactivity-guided fractionation from strain RJX1121, identified by mass spectrometry, and confirmed by gene disruption. Mediterrocin, an 89 amino acid secreted protein, is a broad-spectrum bacteriocin. Annotation of the mediterrocin biosynthetic gene cluster revealed a wide distribution among Bacillota (previously Firmicutes), including the M. gnavus type strain ATCC249149. The type strain of M. gnavus also produces mediterrocin, but in lower titers than RJX1121 under our culture conditions. Mediterrocin is inhibitory to multiple M. gnavus strains, but with varying sensitivity, with isolates from patients with inflammatory bowel disease displaying the greatest susceptibility. Beyond M. gnavus, mediterrocin demonstrated inhibitory activity against other Lachnospiraceae and the gram-negative pathogen Morganella morganii. Further characterization of mediterrocin may clarify how this core member of the healthy microbiome interacts with other community members and how the relative abundance of M. gnavus changes in microbiome dysbiosis associated with several diseases.

Importance

Mediterraneibacter gnavus is a core member of the gut microbiome and implicated in several diseases. Direct competition between M. gnavus and other members of the microbiome may contribute to the shift from a diverse, structured community to dysbiosis observed in disease", "token_count": 516, "char_count": 1902, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5772, "quality_score": 0.7886, "entities": { "genes": [ "ATCC249149", "RJX1121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:18.545156", "source": { "split": "train_shard_00001", "doc_id": 4872 }, "chunk_id": "train_shard_00001_4872_0", "global_id": 12545 }, { "text": "Identifying molecular mechanisms of microbial competition will aid future studies of these disease-relevant bacteria and clarify how community structure is maintained. We report the discovery of mediterrocin, a bacteriocin present in many species in the orders Lachnospirales and Eubacteriales, but clade-specific within M. gnavus. Mediterrocin, produced by health-associated strains of M. gnavus, inhibits the growth of disease-associated M. gnavus strains and a broad spectrum of gut commensal bacteria and pathogens.\n\nA core human gut microbe, <i>Mediterraneibacter gnavus</i>, produces a broad-spectrum bacteriocin mediterrocin.", "token_count": 189, "char_count": 665, "word_count": 82, "semantic_coherence": 1, "information_density": 0.7439, "quality_score": 0.872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:18.987013", "source": { "split": "train_shard_00001", "doc_id": 4872 }, "chunk_id": "train_shard_00001_4872_1", "global_id": 12546 }, { "text": "Abatement of greenhouse gas emitted from ruminants and promotion of biogas energy from animal effluent were comprehensively examined in each anaerobic fermentation reactor and animal experiments. Moreover, the energy conversion efficiency of biomass energy to power generation were evaluated with a gas engine generator or proton exchange membrane fuel cell (PEMFC). To mitigate safety rumen methanogenesis with nutritional manipulation the suppressing effects of some strains of lactic acid bacteria and yeast, bacteriocin, β1-4 galactooligosaccharide, plant extracts (Yucca schidigera and Quillaja saponarea), L-cysteine and/or nitrate on rumen methane emission were compared with antibiotics. For in vitro trials, cumulative methane production was evaluated using the continuous fermented gas qualification system inoculated with the strained rumen fluid from rumen fistulated Holstein cows. For in vivo, four sequential ventilated head cages equipped with a fully automated gas analyzing system were used to examine the manipulating effects of β1-4 galactooligosaccharide, lactic acid bacteria (Leuconostoc mesenteroides subsp. mesenteroides), yeast (Trichosporon serticeum), nisin and Yucca schidigera and/or nitrate on rumen methanogenesis. Furthermore, biogas energy recycled from animal effluent was evaluated with anaerobic bioreactors. Utilization of recycled energy as fuel for a co-generator and fuel cell was tested in the thermophilic biogas plant system. From the results of in vitro and in vivo trials, nitrate was shown to be a strong methane suppressor, although nitrate per se is hazardous. L-cysteine could remove this risk. β1-4 galactooligosaccharide, Candida kefyr, nisin, Yucca schidigera and Quillaja saponarea are thought to possibly control methanogenesis in the rumen. It is possible to simulate the available energy recycled through animal effluent from feed energy resources by making total energy balance sheets of the process from feed energy to recycled energy.", "token_count": 517, "char_count": 2009, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5797, "quality_score": 0.7899, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:19.619997", "source": { "split": "train_shard_00001", "doc_id": 4873 }, "chunk_id": "train_shard_00001_4873_0", "global_id": 12547 }, { "text": "Mitigation of methane emission and energy recycling in animal agricultural systems.", "token_count": 15, "char_count": 83, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:19.969131", "source": { "split": "train_shard_00001", "doc_id": 4873 }, "chunk_id": "train_shard_00001_4873_1", "global_id": 12548 }, { "text": "

Background

Helicobacter pullorum commonly colonized in the gastrointestinal tract of poultry and caused gastroenteritis. This bacterium could be transmitted to humans through contaminated food and caused colitis and hepatitis. Currently, the genetic characteristics of the H. pullorum were not recognized enough. In this study, the genomes of 23 H. pullorum strains from different counties were comparatively analyzed. Among them, H. pullorum 2013BJHL was the first isolated and reported in China.

Results

The genomes of the studied strains were estimated to vary from 1.55 to 2.03 Mb, with a GC content of ~ 34%. 4064 pan genes and 1267 core genes were obtained from the core-pan genome analysis using the Roary pipeline. Core genome SNPs (cg-SNPs) were obtained using Snippy4 software. Two groups were identified with the phylogenetic analysis based on the cg-SNPs. Some adhesion-related, immune regulation, motility-related, antiphagocytosis-related, toxin-related and quorum sensing related genes were identified as virulence factors. APH(3')-IIIa, APH(2'')-If, and AAC(6')-Ie-APH(2'')-Ia were identified as antibiotic resistance genes among the H. pullorum genomes. cat, SAT-4 and tetO genes were only identified in 2013BJHL, and tet(C) was identified in MIT98-5489. MIC determination revealed that the 2013BJHL showed acquired resistance to ciprofloxacin, nalidixic acid, tetracycline, gentamicin, streptomycin and erythromycin, only sensitive to ampicillin. The antibiotic resistance genetic determinants on the 2013BJHL genome correlate well with observed antimicrobial susceptibility patterns", "token_count": 486, "char_count": 1616, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6186, "quality_score": 0.8093, "entities": { "genes": [ "MIT98" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:20.624146", "source": { "split": "train_shard_00001", "doc_id": 4874 }, "chunk_id": "train_shard_00001_4874_0", "global_id": 12549 }, { "text": "Two types of VI secretion system (T6SS) were identified in 52.2% (12/23) the studied strains.

Conclusion

In this study, we obtained the genetic characteristics of H. pullorum from different sources in the world. The comprehensive genetic characteristics of H. pullorum were first described. H. pullorum showed highly genetic diversity and two sub-types of T6SSs were first identified in H. pullorum. 2013BJHL was found to be multidrug resistant as it was resistant to at least three different antibiotic classes.\n\nComparative genomics of Helicobacter pullorum from different countries.", "token_count": 152, "char_count": 592, "word_count": 84, "semantic_coherence": 1, "information_density": 0.6548, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:21.059050", "source": { "split": "train_shard_00001", "doc_id": 4874 }, "chunk_id": "train_shard_00001_4874_1", "global_id": 12550 }, { "text": "Two thermotolerant, ethanol-producing yeast cultures: THFY-4 and THFY-16 were isolated from 381 nature samples. THFY-4 can grow on 30% glucose plate at 51℃, while THFY-16 can grow on the same medium at 45℃. After preliminary identification, THFY-4 was identified as Kluyceromyces sp. and THFY-16 belongs to Saccharomyces genus. The ethanol fermentation experiment shows that THFY-4 can only produce 4.88% (v/v) ethanol from 20% glucose after 60 hours, while THFY-16 can produce 11.44% ethanol under the same condition. When using saccharified Canna edulis Ker wort as fermentation medium, 9.43% (v/v) ethanol were produced from 16.1% glucose, which is 91.0% of the theoretical yield.\n\nPreliminary stud on isolation, identification and ethanol fermentation of thermotolerant yeast", "token_count": 266, "char_count": 779, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6726, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:21.610678", "source": { "split": "train_shard_00001", "doc_id": 4875 }, "chunk_id": "train_shard_00001_4875_0", "global_id": 12551 }, { "text": "Evaluation of Kluyveromyces marxianus as baker's yeast.", "token_count": 20, "char_count": 55, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:21.965581", "source": { "split": "train_shard_00001", "doc_id": 4876 }, "chunk_id": "train_shard_00001_4876_0", "global_id": 12552 }, { "text": "Several studies have reported the presence of pre-existing humoral or cell-mediated cross-reactivity to SARS-CoV-2 peptides in healthy individuals unexposed to SARS-CoV-2. In particular, the current literature suggests that this pre-existing cross-reactivity could, in part, derive from prior exposure to ‘common cold’ endemic human coronaviruses (HCoVs). In this study, we characterised the sequence homology of SARS-CoV-2-derived T-cell epitopes reported in the literature across the entire diversity of the Coronaviridae family. Slightly over half (54.8%) of the tested epitopes did not have noticeable homology to any of the human endemic coronaviruses (HKU1, OC43, NL63 and 229E), suggesting prior exposure to these viruses cannot explain the full cross-reactive profiles observed in healthy unexposed individuals. Further, we find that the proportion of cross-reactive SARS-CoV-2 epitopes with noticeable sequence homology is extremely well predicted by the phylogenetic distance to SARS-CoV-2 ( R 2 = 96.6%). None of the coronaviruses sequenced to date showed a statistically significant excess of T-cell epitope homology relative to the proportion of expected random matches given the sequence similarity of their core genome to SARS-CoV-2. Taken together, our results suggest that the repertoire of cross-reactive epitopes reported in healthy adults cannot be primarily explained by prior exposure to any coronavirus known to date, or any related yet-uncharacterised coronavirus.\n\nPre-existing T cell-mediated cross-reactivity to SARS-CoV-2 cannot solely be explained by prior exposure to endemic human coronaviruses", "token_count": 422, "char_count": 1625, "word_count": 224, "semantic_coherence": 1, "information_density": 0.567, "quality_score": 0.7835, "entities": { "genes": [ "HKU1", "OC43", "NL63" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:22.591896", "source": { "split": "train_shard_00001", "doc_id": 4877 }, "chunk_id": "train_shard_00001_4877_0", "global_id": 12553 }, { "text": "The guts of animals and humans harbor diverse microbial communities that are regularly exposed to bacteria originating from food, water, and their surroundings. Species such as Escherichia coli are adept at colonizing multiple hosts, along with surviving in the environment. By encoding pathogenic traits and transmissible forms of antimicrobial resistance (AMR), E. coli can also pose a zoonotic risk. Our understanding of the factors that govern host residency is limited. Here, we used a chicken cecal fermentation model to study survival and the AMR transfer potential of 17 host-associated extended-spectrum β-lactamase (ESBL)-producing E. coli isolates. Vessels containing chicken cecal contents were stabilized for 4 days before the addition of a cocktail comprising ESBL-producing E. coli obtained from human, cattle, pig, and chicken hosts. Consecutive sampling showed that pig and cattle-associated isolates persisted in most vessels, although the recovery of all isolates declined over time. Increasing the inoculum dose or adding ceftiofur helped to stabilize populations of ESBL E. coli within the vessels, although this did not result in outgrowth of resistant populations in all vessels. Sequencing revealed that most new ESBL-producing E. coli recovered during the study acquired a blaCTX-M-1 plasmid from a single ESBL E. coli included in the cocktail that lacked host-specific traits (generalist). Our data highlight that isolate-specific differences in the E. coli genome composition likely explain the persistence of specific clones and efficiency of plasmid transfer, both of which could impact the spread of AMR in complex communities.IMPORTANCEThere are few insights into how host-associated Escherichia coli behave within the gut environment of other hosts. E. coli isolates that are immigrants to the gastrointestinal system of humans and animals have the potential to transfer their resistance to other native bacteria", "token_count": 519, "char_count": 2032, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6219, "quality_score": 0.811, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:23.256333", "source": { "split": "train_shard_00001", "doc_id": 4878 }, "chunk_id": "train_shard_00001_4878_0", "global_id": 12554 }, { "text": "A better understanding of this process is needed to assess how the gastrointestinal environment could serve as a reservoir and a melting pot of new, multidrug-resistant E. coli isolates.\n\nEvidence of ESBL plasmid transfer and selective persistence of multiple host-associated <i>Escherichia coli</i> isolates in a chicken cecal fermentation model.", "token_count": 107, "char_count": 366, "word_count": 49, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:23.640665", "source": { "split": "train_shard_00001", "doc_id": 4878 }, "chunk_id": "train_shard_00001_4878_1", "global_id": 12555 }, { "text": "

Unlabelled

A pangenome is the total of genes present in strains of the same species. Pangenome microarrays allow determining the genomic content of bacterial strains more accurately than conventional comparative genome hybridization microarrays. PanCGHweb is the first tool that effectively calls genotype based on pangenome microarray data.

Availability

PanCGHweb, the web tool is accessible from: http://bamics2.cmbi.ru.nl/websoftware/pancgh/.\n\nPanCGHweb: a web tool for genotype calling in pangenome CGH data.", "token_count": 149, "char_count": 527, "word_count": 64, "semantic_coherence": 1, "information_density": 0.7344, "quality_score": 0.8672, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:24.075083", "source": { "split": "train_shard_00001", "doc_id": 4879 }, "chunk_id": "train_shard_00001_4879_0", "global_id": 12556 }, { "text": "The gut microbiome becomes shaped in the first days of life and continues to increase its diversity during the first months. Links between the configuration of the infant gut microbiome and infant health are being shown, but a comprehensive strain-level assessment of microbes vertically transmitted from mother to infant is still missing. We collected fecal and breast milk samples from multiple mother-infant pairs during the first year of life and applied shotgun metagenomic sequencing followed by computational strain-level profiling. We observed that several specific strains, including those of Bifidobacterium bifidum, Coprococcus comes, and Ruminococcus bromii, were present in samples from the same mother-infant pair, while being clearly distinct from those carried by other pairs, which is indicative of vertical transmission. We further applied metatranscriptomics to study the in vivo gene expression of vertically transmitted microbes and found that transmitted strains of Bacteroides and Bifidobacterium species were transcriptionally active in the guts of both adult and infant. By combining longitudinal microbiome sampling and newly developed computational tools for strain-level microbiome analysis, we demonstrated that it is possible to track the vertical transmission of microbial strains from mother to infants and to characterize their transcriptional activity. Our work provides the foundation for larger-scale surveys to identify the routes of vertical microbial transmission and its influence on postinfancy microbiome development. IMPORTANCE Early infant exposure is important in the acquisition and ultimate development of a healthy infant microbiome. There is increasing support for the idea that the maternal microbial reservoir is a key route of microbial transmission, and yet much is inferred from the observation of shared species in mother and infant. The presence of common species, per se, does not necessarily equate to vertical transmission, as species exhibit considerable strain heterogeneity. It is therefore imperative to assess whether shared microbes belong to the same genetic variant (i.e., strain) to support the hypothesis of vertical transmission. Here we demonstrate the potential of shotgun metagenomics and strain-level profiling to identify vertical transmission events", "token_count": 511, "char_count": 2381, "word_count": 328, "semantic_coherence": 1, "information_density": 0.5671, "quality_score": 0.7835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:24.742565", "source": { "split": "train_shard_00001", "doc_id": 4880 }, "chunk_id": "train_shard_00001_4880_0", "global_id": 12557 }, { "text": "Combining these data with metatranscriptomics, we show that it is possible not only to identify and track the fate of microbes in the early infant microbiome but also to investigate the actively transcribing members of the community. These approaches will ultimately provide important insights into the acquisition, development, and community dynamics of the infant microbiome.\n\nStudying Vertical Microbiome Transmission from Mothers to Infants by Strain-Level Metagenomic Profiling.", "token_count": 102, "char_count": 483, "word_count": 67, "semantic_coherence": 1, "information_density": 0.806, "quality_score": 0.903, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:25.144914", "source": { "split": "train_shard_00001", "doc_id": 4880 }, "chunk_id": "train_shard_00001_4880_1", "global_id": 12558 }, { "text": "The increased consumer awareness of the health promoting effects of functional foods and nutraceuticals is the driving force of the functional food and nutraceutical market. Bioactive peptides are known for their high tissue affinity, specificity and efficiency in promoting health. For this reason, the search for food-derived bioactive peptides has increased exponentially. Over the years, many potential bioactive peptides from food have been documented; yet, obstacles such as the need to establish optimal conditions for industrial scale production and the absence of well-designed clinical trials to provide robust evidence for proving health claims continue to exist. Other important factors such as the possibility of allergenicity, cytotoxicity and the stability of the peptides during gastrointestinal digestion would need to be addressed. This review discusses our current knowledge on the health effects of food-derived bioactive peptides, their processing methods and challenges in their development.\n\nBioactive Peptides.", "token_count": 209, "char_count": 1034, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6458, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:25.643324", "source": { "split": "train_shard_00001", "doc_id": 4881 }, "chunk_id": "train_shard_00001_4881_0", "global_id": 12559 }, { "text": "

Background

Pseudomonas aeruginosa is a major bacterial pathogen responsible for hospital-acquired infections. Although its epidemiology is considered as non-clonal, certain international high-risk multidrug-resistant clones have been recognized.

Aim

From the first report of an intra-hospital outbreak due to an SHV2a-producing P. aeruginosa strain, to describe the emergence of a new ST235-specific lineage harbouring this rare extended-spectrum β-lactamase (ESBL).

Methods

Between May and October 2018, four patients hospitalized in the cardiovascular intensive care unit of a French teaching hospital were infected by a multidrug-resistant P. aeruginosa isolate. Serotype and antimicrobial susceptibility were tested; multi-locus sequence type (MLST), core genome MLST, and resistome were determined through whole genome sequencing. A phylogenetic analysis based on single nucleotide polymorphism was performed using available ST235 genomes.

Findings

The four strains were susceptible to colistin, ciprofloxacin, ceftazidime-avibactam, and ceftolozane-tazobactam. blaSHV2a was identified in each genome of this ST235-O11 serotype cluster that showed an identical cgMLST profile (0-2 out of 4162 different alleles). The phylogenic analysis of 162 ST235 genomes showed that only four other strains harboured a blaSHV2a, originating from France and USA, clustering together although being different from the outbreak strains.

Conclusions

Among the ST235 P. aeruginosa strains, a sub-lineage sharing a common genetic background and harbouring the blaSHV2a ESBL seems to emerge from different locations, yielding secondary local outbreaks.", "token_count": 507, "char_count": 1706, "word_count": 206, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8544, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:26.321902", "source": { "split": "train_shard_00001", "doc_id": 4882 }, "chunk_id": "train_shard_00001_4882_0", "global_id": 12560 }, { "text": "Local outbreak of extended-spectrum β-lactamase SHV2a-producing Pseudomonas aeruginosa reveals the emergence of a new specific sub-lineage of the international ST235 high-risk clone.", "token_count": 54, "char_count": 182, "word_count": 22, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [ "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:26.687425", "source": { "split": "train_shard_00001", "doc_id": 4882 }, "chunk_id": "train_shard_00001_4882_1", "global_id": 12561 }, { "text": "We have determined the nucleotide sequence of a 2360-basepair (bp) region of the Kluyveromyces marxianus genome containing the structural gene for the enzyme pyruvate decarboxylase (PDC). Comparison of the deduced amino-acid sequence of this gene to that of the Saccharomyces cerevisiae PDC genes reveals extensive homology including a motif common to thiamin diphosphate-dependent enzymes.\n\nThe isolation and nucleotide sequence of the pyruvate decarboxylase gene from Kluyveromyces marxianus.", "token_count": 142, "char_count": 494, "word_count": 67, "semantic_coherence": 1, "information_density": 0.6716, "quality_score": 0.8358, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:27.116783", "source": { "split": "train_shard_00001", "doc_id": 4883 }, "chunk_id": "train_shard_00001_4883_0", "global_id": 12562 }, { "text": "Chemical and microbiological composition of four Argentinean kefir grains from different sources as well as characteristics of the corresponding fermented milk were studied. Kefir grains CIDCA AGK1, AGK2 and AGK4 did not show significant differences in their chemical and microbiological composition. In contrast, protein and yeast content of AGK3 was higher than in the other grains. Although grain microflora comprised lactobacilli, lactococcus, acetic acid bacteria and yeast, we found an important difference regarding species. Lactococcus lactis subsp. lactis, Lactobacillus kefir, Lactobacillus plantarum, Acetobacter and Saccharomyces were present in all types of kefir grain. While Leuconostoc mesenteroides was only isolated from grains CIDCA AGK1 and Lactococcus lactis subsp. lactis biovar diacetylactis, Lactobacillus parakefir and Kluyveromyces marxianus were only isolated from CIDCA AGK2 grains. All grains produced acid products with pH between 3.5 and 4.0. The apparent viscosity of AGK1 fermented milk was greater than the product obtained with AGK4. All fermented milks had inhibitory power towards Escherichia coli but AGK1 and AGK2 supernatants were able to halt the bacterial growth for at least 25 h. Grain weight increment in AGK1, AGK2 and AGK3 during growth in milk did not show significant differences. Despite their fermenting activity, AGK4 grains did not increase their weight.\n\nChemical and microbiological characterisation of kefir grains.", "token_count": 410, "char_count": 1471, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [ "AGK2", "AGK4", "AGK3", "AGK1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:27.735828", "source": { "split": "train_shard_00001", "doc_id": 4884 }, "chunk_id": "train_shard_00001_4884_0", "global_id": 12563 }, { "text": "

Background

Bacterial genomes are mosaic structures composed of genes present in every strain of the same species (core genome), and genes present in some but not all strains of a species (accessory genome). The aim of this study was to compare the genetic diversity of core and accessory genes of a Salmonella enterica subspecies enterica serovar Typhimurium (Typhimurium) population isolated from food-animal and human sources in four regions of Mexico. Multilocus sequence typing (MLST) and macrorestriction fingerprints by pulsed-field gel electrophoresis (PFGE) were used to address the core genetic variation, and genes involved in pathogenesis and antibiotic resistance were selected to evaluate the accessory genome.

Results

We found a low genetic diversity for both housekeeping and accessory genes. Sequence type 19 (ST19) was supported as the founder genotype of STs 213, 302 and 429. We found a temporal pattern in which the derived ST213 is replacing the founder ST19 in the four geographic regions analyzed and a geographic trend in the number of resistance determinants. The distribution of the accessory genes was not random among chromosomal genotypes. We detected strong associations among the different accessory genes and the multilocus chromosomal genotypes (STs). First, the Salmonella virulence plasmid (pSTV) was found mostly in ST19 isolates. Second, the plasmid-borne betalactamase cmy-2 was found only in ST213 isolates. Third, the most abundant integron, IP-1 (dfrA12, orfF and aadA2), was found only in ST213 isolates. Fourth, the Salmonella genomic island (SGI1) was found mainly in a subgroup of ST19 isolates carrying pSTV", "token_count": 444, "char_count": 1668, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [ "SGI1", "ST19", "ST213" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:28.375114", "source": { "split": "train_shard_00001", "doc_id": 4885 }, "chunk_id": "train_shard_00001_4885_0", "global_id": 12564 }, { "text": "The mapping of accessory genes and multilocus genotypes on the dendrogram derived from macrorestiction fingerprints allowed the establishment of genetic subgroups within the population.

Conclusion

Despite the low levels of genetic diversity of core and accessory genes, the non-random distribution of the accessory genes across chromosomal backgrounds allowed us to discover genetic subgroups within the population. This study provides information about the importance of the accessory genome in generating genetic variability within a bacterial population.\n\nAssociation of virulence plasmid and antibiotic resistance determinants with chromosomal multilocus genotypes in Mexican Salmonella enterica serovar Typhimurium strains.", "token_count": 160, "char_count": 735, "word_count": 92, "semantic_coherence": 1, "information_density": 0.6413, "quality_score": 0.8207, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:28.816509", "source": { "split": "train_shard_00001", "doc_id": 4885 }, "chunk_id": "train_shard_00001_4885_1", "global_id": 12565 }, { "text": "

Background

Although pediatric Clostridium difficile infections (CDIs) are increasing, C. difficile transmission patterns among children are poorly understood.

Methods

We performed whole genome sequencing (WGS) on C. difficile isolates collected from children diagnosed with CDI between December 2012 and December 2013 at a single academic medical center. Genome sequences of isolates from CDIs diagnosed ≥8 weeks after study initiation were compared to all study isolate genome sequences. Among patients with isogenic isolates (≤2-3 core genome single nucleotide variants [SNVs] identified by pairwise SNV analyses), common inpatient and/or outpatient healthcare exposures were investigated.

Results

Among 131 CDIs in 107 children, WGS identified 104 genetically distinct isolates. Of 84 incident CDIs occurring ≥8 weeks after study initiation, only 10 (11.9%) were caused by a strain isogenic to another cohort CDI isolate (putative transmission events). Proportions of each CDI class putatively associated with transmission were hospital-onset healthcare facility-associated (HCFA), 2/16 (12.5%); community-onset HCFA, 1/17 (5.9%); indeterminate, 1/11 (9.1%); community-associated (CA), 5/40 (12.5%); and recurrent, 1/21 (4.8%). Transmission events among CA and HCFA CDIs were similarly infrequent (5/40 [12.5%] vs 3/33 [9.1%]; P = .64). Shared healthcare facility exposures were only identified among 7/10 putative transmission events. Potential community transmission (same postal code) was not identified.

Conclusions

WGS identified a highly diverse group of C. difficile isolates among children with CDI, including those with HCFA CDI. Clostridium difficile transmission among symptomatic children was very uncommon", "token_count": 509, "char_count": 1750, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6786, "quality_score": 0.8393, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:29.449880", "source": { "split": "train_shard_00001", "doc_id": 4886 }, "chunk_id": "train_shard_00001_4886_0", "global_id": 12566 }, { "text": "Among putatively transmitted cases, investigation of shared healthcare exposures often did not identify a potential transmission source.\n\nClostridium difficile Whole Genome Sequencing Reveals Limited Transmission Among Symptomatic Children: A Single-Center Analysis.", "token_count": 56, "char_count": 266, "word_count": 31, "semantic_coherence": 1, "information_density": 0.9032, "quality_score": 0.9516, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:29.822300", "source": { "split": "train_shard_00001", "doc_id": 4886 }, "chunk_id": "train_shard_00001_4886_1", "global_id": 12567 }, { "text": "Polyclonal antibodies were raised against the purified ribosomal proteins L1 and L2, the 5S rRNA binding protein L3, all from Saccharomyces cerevisiae, and against L1 and L2 from Schizosaccharomyces pombe (numbering according to Otaka and Osawa 1981; Otaka et al. 1983, respectively). For clarity prefixes Sc and Sp have been added to the numbering of proteins derived from S. cerevisiae and S. pombe, respectively. Ribosomal proteins from these yeasts and from Kluyveromyces marxianus, Rhodotorula glutinis, the slime mold Dictyostelium discoideum and the protozoan Tetrahymena thermophila were checked for antigenic cross-reactivity by the immunoblot technique. Anti-ScL1 bound to the largest ribosomal proteins of all organisms but not with equal strength. A fast migrating protein band from R. glutinis was also reactive. Anti-ScL2 reacted strongly with L2 or analogous proteins derived exclusively from the yeasts. Anti-ScL3 cross-reacted only with one protein band from K. marxianus, whereas anti-SpL1 cross-reacted with L1 or its analogues from the other organisms, but also with proteins of lower molecular weight. In S. cerevisiae, these proteins are located exclusively on the small ribosomal subunit. L2 or analogous ribosomal proteins of all organisms were recognized by anti-SpL2 but additionally the ribosomal protein YL28 of S. cerevisiae and fast migrating proteins of T. thermophila exhibited anti-SpL2 binding.\n\nImmunological homologies between ribosomal proteins amongst lower eukaryotes.", "token_count": 429, "char_count": 1507, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5814, "quality_score": 0.7907, "entities": { "genes": [ "YL28" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:30.453768", "source": { "split": "train_shard_00001", "doc_id": 4887 }, "chunk_id": "train_shard_00001_4887_0", "global_id": 12568 }, { "text": "Pseudomonas aeruginosa is a ubiquitous environmental microorganism that is also a common cause of nosocomial infections that vary in severity from chronic wound infections to pneumonia, bloodstream infections and sepsis. Its ability to survive in many different environments and persistently colonize human tissue is linked to its presence within biofilms that form on indwelling device surfaces such as plastics and stainless steel. Biofilm promotes bacterial adhesion and survival on surfaces, reduces susceptibility to desiccation, and the actions of antibiotics and disinfectants. Recent genome sequencing studies demonstrate that P. aeruginosa is a highly diverse species with a very large pan-genome consistent with its adaptability to differing environments. However, most MDR infections are caused by a small number of “high-risk” clones or lineages that recently emerged and spread globally. In our 2017 study of the resistome of P. aeruginosa we confirmed the power of genome-wide association (GWAS) techniques to explore the genetic basis of several antibiotic resistance phenotypes and discovered 46 novel putative resistance polymorphisms. In this study we sought to examine genetic associations within a subset of these isolates with simple biofilm phenotypes. We examined the genetic basis for biofilm production on polystyrene at room temperature (22°C) and body temperature (37°C) within a total of 280 isolates. 69% of isolates ( n =193) produced more biofilm mass at 22°C, whilst those producing more biofilm at 37°C had reduced optical density 540 variation. We found statistically significant associations with IpxO and other genes associated with arsenic resistance to be significantly associated with this trait. IpxO which encodes a lipid A hydroxylase and arsenic reduction genes have previously been found to be associated with biofilm production in this species. We analyzed 260 ST111 and ST235 genomes and found considerable genetic variation between isolates in their content of genes previously found associated with biofilm production. This is indicative of a highly variable and flexible population within these clades with frequent emergence of successful sub-lineages", "token_count": 504, "char_count": 2201, "word_count": 320, "semantic_coherence": 1, "information_density": 0.6188, "quality_score": 0.8094, "entities": { "genes": [ "ST111", "ST235" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:31.113561", "source": { "split": "train_shard_00001", "doc_id": 4888 }, "chunk_id": "train_shard_00001_4888_0", "global_id": 12569 }, { "text": "Analysis of 48 of these isolates’ ability to form biofilm on stainless steel surfaces showed that a ‘good’ biofilm-forming phenotype had significant intra-clone variation, independent of core genome phylogeny with pan-genome analysis, suggesting a possible association and involvement of components of the type IV secretion system. However, GWAS and pan-GWAS analyses yielded weaker statistical significance. This study confirms GWAS and pan-GWAS trait associations can be performed for biofilm phenotype and produce data in agreement with each other. This panel of 280 study isolates, matched to genomic data has potential for the investigation of other phenotypes in P. aeruginosa perhaps as part of a growing database / collection. A representative, curated, genome sequenced collection should increase in usefulness as it grows offering increasing statistical power.

Importance

P. aeruginosa is a major cause of multiply antibiotic infections worldwide but it is also found in many hospital and natural environments, especially aquatic ones. In this study we examined genetic polymorphism associated with biofilm production at room temperature and at body temperature, the biofilm associated gene repertoire of two major MDR clones and also genetic polymorphisms associated with biofilm production on stainless steel. Using these genome-wide and pan-genome wide association methods we identified / confirmed potential key genes involved in biofilm production and survival of P. aeruginosa . The study demonstrates the potential usefulness of large, genome sequenced isolate collections such as ours, to better understand the genetics underlying phenotypic diversity in this species.\n\nBiofilm Associated Genotypes of Multidrug-Resistant Pseudomonas aeruginosa", "token_count": 394, "char_count": 1778, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6437, "quality_score": 0.8219, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:31.728085", "source": { "split": "train_shard_00001", "doc_id": 4888 }, "chunk_id": "train_shard_00001_4888_1", "global_id": 12570 }, { "text": "The survival and growth of Escherichia coli 3339 and Salmonella enteritidis 949575 isolated from human clinical samples, in milk fermented with lactic acid bacteria (LAB) and yeast strains previously isolated from Zimbabwean naturally fermented milk (NFM) was studied. The LAB starter cultures used were Lactococcus lactis subsp. lactis biovar. diacetylactis C1 alone (C1) or in combination with Candida kefyr 23 (C1/23), L. lactis subsp. lactis Lc261 alone (LC261) or in combination with C. kefyr 23 (Lc261/23). The growth of the same pathogens in milk fermented with a commercial DL culture (CH-N 22) and spontaneously fermented raw milk was also monitored. The C1 and C1/23 cultures significantly (P<0.05) inhibited the growth of both pathogens. When inoculated at the beginning of the fermentation, both E. coli 3339 and S. enteritidis 949575 counts were significantly (P<0.05) reduced by about two log cycles in C1 and C1/23 cultured milk. However, in naturally fermented milk and the DL cultured milk, both E. coli 3339 and S. enteritidis 949575 grew and reached high populations of about 9 and 8.8 log cfu ml(-1), respectively, after 18 h. When E. coli 3339 was inoculated into previously fermented milk, the viable counts were significantly (P<0.05) reduced in the presence of C1 and C1/23 from 7 log cfu ml(-1) to 3 log cfu ml(-1) after 48 h. S. enteritidis 949575 could not be recovered from these cultures after 48 h. The addition of the yeast did not enhance or diminish the inhibitory capacity of the LAB cultures", "token_count": 504, "char_count": 1526, "word_count": 247, "semantic_coherence": 1, "information_density": 0.498, "quality_score": 0.749, "entities": { "genes": [ "LC261" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:32.383266", "source": { "split": "train_shard_00001", "doc_id": 4889 }, "chunk_id": "train_shard_00001_4889_0", "global_id": 12571 }, { "text": "The pathogens survived in high numbers when inoculated into pre-fermented NFM and the commercial DL- (CH-N 22) cultured milk. The C1 strain, therefore, offered the best protection against the pathogens. Its inhibitory effect was mainly related to fast acid production.\n\nAntimicrobial properties of lactic acid bacteria and yeast-LAB cultures isolated from traditional fermented milk against pathogenic Escherichia coli and Salmonella enteritidis strains.", "token_count": 114, "char_count": 454, "word_count": 62, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:32.761738", "source": { "split": "train_shard_00001", "doc_id": 4889 }, "chunk_id": "train_shard_00001_4889_1", "global_id": 12572 }, { "text": "Salmonellosis is an endemic human infection, associated with both sporadic cases and outbreaks throughout Colombia. Typhimurium is the most common Colombian serovar of Salmonella enterica , responsible for 32.5% of the Salmonella infections. Whole genome sequencing (WGS) is being used increasingly in Europe and the USA to study the epidemiology of Salmonella , but there has not yet been a WGS-based analysis of Salmonella associated with bloodstream infection in Colombia. Here, we analysed 209 genome sequences of Colombian S . Typhimurium and monophasic S . 4,[5],12:i:-isolates from Colombia from 1999 to 2017. We used a core genome-based maximum likelihood tree to define seven distinct clusters which were predominantly Sequence Type (ST) 19 isolates. We also identified the first ST313 and monophasic ST34 isolates to be reported in Colombia. The history of each cluster was reconstructed with a Bayesian tree to reveal a timeline of evolution. Cluster 7 was closely related to European multidrug-resistant (MDR) DT104. Cluster 4 became the dominant variant of Salmonella in 2016, and resistance to nalidixic acid was associated with a plasmid-encoded qnrB19 gene. Our findings suggest multiple transfers of S . Typhimurium between Europe and Colombia.

Author summary

The large-scale genome sequencing of Salmonella Typhimurium and monophasic Salmonella 4,[5],12:i:-involved bloodstream isolates from Colombia. The two serovars were responsible for about 1/3 of Salmonella infections in Colombia in the past 20 years. To identify the population structure we used Whole Genome Sequencing, performed in silico sequence typing, obtained phylogenetic trees, inferred the evolutionary history, detected the plasmids and prophages, and associated the antibiotic resistance (AMR) genotype with phenotype. Different clusters showed temporal replacement", "token_count": 493, "char_count": 1862, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6015, "quality_score": 0.8008, "entities": { "genes": [ "ST34", "DT104", "ST313" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:33.421354", "source": { "split": "train_shard_00001", "doc_id": 4890 }, "chunk_id": "train_shard_00001_4890_0", "global_id": 12573 }, { "text": "The Colombian sequence type 313 was distinct from African lineages due to the absence of a key virulence-related gene, bstA . One of the Colombian clusters is likely to belong to the global epidemic of DT104, according to the evolutionary history and the AMR profile. The most common cluster in recent years was resistant to nalidixic acid and carried a plasmid-mediated antibiotic resistant gene qnrB19 . Our findings will inform the ongoing efforts to combat Salmonellosis by Colombian public health departments.\n\nGenomic and phylogenetic analysis ofSalmonellaTyphimurium and its monophasic variants responsible for invasive endemic infections in Colombia", "token_count": 168, "char_count": 664, "word_count": 97, "semantic_coherence": 1, "information_density": 0.7526, "quality_score": 0.8763, "entities": { "genes": [ "DT104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:33.861556", "source": { "split": "train_shard_00001", "doc_id": 4890 }, "chunk_id": "train_shard_00001_4890_1", "global_id": 12574 }, { "text": "The genus Lactobacillus comprises 261 species (at March 2020) that are extremely diverse at phenotypic, ecological and genotypic levels. This study evaluated the taxonomy of Lactobacillaceae and Leuconostocaceae on the basis of whole genome sequences. Parameters that were evaluated included core genome phylogeny, (conserved) pairwise average amino acid identity, clade-specific signature genes, physiological criteria and the ecology of the organisms", "token_count": 135, "char_count": 473, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8167, "quality_score": 0.9083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:34.290318", "source": { "split": "train_shard_00001", "doc_id": 4891 }, "chunk_id": "train_shard_00001_4891_0", "global_id": 12575 }, { "text": "Based on this polyphasic approach, we propose reclassification of the genus Lactobacillus into 25 genera including the emended genus Lactobacillus, which includes host-adapted organisms that have been referred to as the Lactobacillus delbrueckii group, Paralactobacillus and 23 novel genera for which the names Holzapfelia, Amylolactobacillus, Bombilactobacillus, Companilactobacillus, Lapidilactobacillus, Agrilactobacillus, Schleiferilactobacillus, Loigolactobacilus, Lacticaseibacillus, Latilactobacillus, Dellaglioa, Liquorilactobacillus, Ligilactobacillus, Lactiplantibacillus, Furfurilactobacillus, Paucilactobacillus, Limosilactobacillus, Fructilactobacillus, Acetilactobacillus, Apilactobacillus, Levilactobacillus, Secundilactobacillus and Lentilactobacillus are proposed. We also propose to emend the description of the family Lactobacillaceae to include all genera that were previously included in families Lactobacillaceae and Leuconostocaceae", "token_count": 491, "char_count": 1165, "word_count": 93, "semantic_coherence": 1, "information_density": 0.8065, "quality_score": 0.9032, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:34.931044", "source": { "split": "train_shard_00001", "doc_id": 4891 }, "chunk_id": "train_shard_00001_4891_1", "global_id": 12576 }, { "text": "The generic term 'lactobacilli' will remain useful to designate all organisms that were classified as Lactobacillaceae until 2020. This reclassification reflects the phylogenetic position of the micro-organisms, and groups lactobacilli into robust clades with shared ecological and metabolic properties, as exemplified for the emended genus Lactobacillus encompassing species adapted to vertebrates (such as Lactobacillus delbrueckii, Lactobacillus iners, Lactobacillus crispatus, Lactobacillus jensensii, Lactobacillus johnsonii and Lactobacillus acidophilus) or invertebrates (such as Lactobacillus apis and Lactobacillus bombicola).\n\nA taxonomic note on the genus Lactobacillus: Description of 23 novel genera, emended description of the genus Lactobacillus Beijerinck 1901, and union of Lactobacillaceae and Leuconostocaceae.", "token_count": 340, "char_count": 927, "word_count": 101, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:35.501526", "source": { "split": "train_shard_00001", "doc_id": 4891 }, "chunk_id": "train_shard_00001_4891_2", "global_id": 12577 }, { "text": "A mathematical model describing the kinetics of continuous production of single cell protein from cheese whey using Kluyveromyces fragilis was developed from the basic principles of mass balance. The model takes into account the substrate utilization for growth and maintenance and the effect of substrate concentration and cell death rate on the net cell growth and substrate utilization during the fermentation process. A lactose concentration below 1.91 g/L limited growth of yeast cells whereas a lactose concentration above 75 g/L inhibited the growth of the yeast. The model was tested using experimental data obtained from a continuous system operated at various retention times (12, 18 and 24 h), mixing speeds (200, 400 and 600 rpm) and air flow rates (1 and 3 vvm). The model was capable of predicting the effluent cell and substrate concentrations with R2 ranging from 0.95 to 0.99. The viable cell mass and lactose consumption ranged from 1.3 to 34.3 g/L and from 74.31% to 99.02%, respectively. A cell yield of 0.74 g cell/g lactose (close to the stoichiometric value of 0.79 g cell/g lactose) was achieved at the 12 h retention time-3 vvm air flow rate-600 rpm mixing speed combination. The total biomass output (viable and dead cells) at this combination was 37 g/L.\n\nKinetic modelling of continuous submerged fermentation of cheese whey for single cell protein production.", "token_count": 376, "char_count": 1388, "word_count": 223, "semantic_coherence": 1, "information_density": 0.583, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:36.089171", "source": { "split": "train_shard_00001", "doc_id": 4892 }, "chunk_id": "train_shard_00001_4892_0", "global_id": 12578 }, { "text": "Klebsiella pneumoniae is a Gram-negative opportunistic pathogenic bacterium that occasionally inhabits the human gastrointestinal tracts. Gut-colonized K. pneumoniae may then metastasize to other organs and tissues, thus causing severe infections. In this study, we identified three cpxA mutations in K. pneumoniae that experimentally evolved to show reduced adhesive ability. CpxA is a sensor histidine kinase that rendered reduced surface adhesion and gut colonization ability in K. pneumoniae. Interestingly, one experimentally gained CpxA mutant (L168del) also commonly occurs in nature. K. pneumoniae containing CpxA variants showed different colonization potentials through altered type 3 fimbriae expression. Lastly, we demonstrated that CpxA contributes to amino acid sensing, thus regulating the colonization of K. pneumoniae both on solid surfaces and in mouse intestines. The polymorphism of CpxA may help to broaden the environmental adaptation of the bacterium. These findings together reveal a Cpx-mediated regulation to diversify intestinal colonization in K. pneumoniae.\n\nCpx-mediated amino acid sensing diversifies gastrointestinal colonization of <i>Klebsiella pneumoniae</i>.", "token_count": 365, "char_count": 1262, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6752, "quality_score": 0.8376, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:36.690759", "source": { "split": "train_shard_00001", "doc_id": 4893 }, "chunk_id": "train_shard_00001_4893_0", "global_id": 12579 }, { "text": "How do organisms with compact genomes maintain evolutionary adaptability? Mamiellales, marine picoeukaryotes including Ostreococcus tauri , the smallest known free-living eukaryote, achieve ecological success despite severe genomic constraints. Using chromosome conformation capture (Hi-C) to investigate three-dimensional genome organisation in O. tauri , we reveal that two outlier chromosomes with low-GC regions are spatially insulated from the core genome, forming compartments akin to topologically associated domains. These compartments exhibit hypomethylation, altered nucleosome dynamics, and enrichment in transposable elements, introns, and highly expressed genes. They harbour polyketide synthase genes undergoing active structural diversification, with species-specific metabolite profiles including putative polyketides. This genomic architecture enables evolutionary experimentation while protecting essential functions, a strategy we demonstrate is convergently evolved in the distantly related picoeukaryote Pelagomonas . Our findings reveal that spatial compartmentalisation of adaptive processes represents a fundamental mechanism for maintaining evolutionary flexibility under genomic streamlining.\n\nInsulated Outlier Chromosomes Enable Metabolic Innovation in Minimal Eukaryotic Algae", "token_count": 285, "char_count": 1305, "word_count": 152, "semantic_coherence": 1, "information_density": 0.8421, "quality_score": 0.9211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:37.289660", "source": { "split": "train_shard_00001", "doc_id": 4894 }, "chunk_id": "train_shard_00001_4894_0", "global_id": 12580 }, { "text": "

Background

Current approaches in tracking Clostridioides difficile infection (CDI) and individualizing patient management are incompletely defined.

Methods

We recruited 468 subjects with CDI at Mayo Clinic Rochester between May and December 2016 and performed whole-genome sequencing (WGS) on C. difficile isolates from 397. WGS was also performed on isolates from a subset of the subjects at the time of a recurrence of infection. The sequence data were analyzed by determining core genome multilocus sequence type (cgMLST), with isolates grouped by allelic differences and the predicted ribotype.

Results

There were no correlations between C. difficile isolates based either on cgMLST or ribotype groupings and CDI outcome. An epidemiologic assessment of hospitalized subjects harboring C. difficile isolates with ≤2 allelic differences, based on standard infection prevention and control assessment, revealed no evidence of person-to-person transmission. Interestingly, community-acquired CDI subjects in 40% of groups with ≤2 allelic differences resided within the same zip code. Among 18 subjects clinically classified as having recurrent CDI, WGS revealed 14 with initial and subsequent isolates differing by ≤2 allelic differences, suggesting a relapse of infection with the same initial strain, and 4 with isolates differing by >50 allelic differences, suggesting reinfection. Among the 5 subjects classified as having a reinfection based on the timing of recurrence, 3 had isolates with ≤2 allelic differences between them, suggesting a relapse, and 2 had isolates differing by >50 allelic differences, suggesting reinfection.

Conclusions

Our findings point to potential transmission of C. difficile in the community. WGS better differentiates relapse from reinfection than do definitions based on the timing of recurrence.\n\nClostridioides difficile Whole-genome Sequencing Differentiates Relapse With the Same Strain From Reinfection With a New Strain.", "token_count": 490, "char_count": 1991, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5167, "quality_score": 0.7584, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:37.977761", "source": { "split": "train_shard_00001", "doc_id": 4895 }, "chunk_id": "train_shard_00001_4895_0", "global_id": 12581 }, { "text": "

Background

Genetic variation in the ribosomal DNA (rDNA) internal transcribed spacer (ITS) region has been studied among fungi. However, the numbers of ITS sequence polymorphisms in the various Candida species and their associations with sources of invasive fungal infections remain poorly investigated. Here, we characterized the intraspecific and interspecific ITS diversity of Candida spp. strains collected from patients with bloodstream or oroesophageal candidiasis.

Methods

We selected cultures of representative medically important species of Candida as well as some rare and emerging pathogens. Identification was performed by micromorphology and by biochemical testing using an ID32C system, as well as by the sequencing of rDNA ITS. The presence of intraspecific ITS polymorphisms was characterized based on haplotype networks, and interspecific diversity was characterized based on Bayesian phylogenetic analysis.

Results

Among 300 Candida strains, we identified 76 C. albicans, 14 C. dubliniensis, 40 C. tropicalis, 47 C. glabrata, 34 C. parapsilosis (sensu stricto), 31 C. orthopsilosis, 3 C. metapsilosis, 21 Meyerozyma guilliermondii (C. guilliermondii), 12 Pichia kudriavzevii (C. krusei), 6 Clavispora lusitaniae (C. lusitaniae), 3 C. intermedia, 6 Wickerhamomyces anomalus (C. pelliculosa), and 2 C. haemulonii strains, and 1 C. duobushaemulonii, 1 Kluyveromyces marxianus (C. kefyr), 1 Meyerozyma caribbica (C. fermentati), 1 Pichia norvegensis (C. norvegensis), and 1 Lodderomyces elongisporus strain. Out of a total of seven isolates with inconsistent ID32C profiles, ITS sequencing identified one C. lusitaniae strain, three C", "token_count": 532, "char_count": 1670, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6592, "quality_score": 0.8296, "entities": { "genes": [ "ID32C" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:38.635562", "source": { "split": "train_shard_00001", "doc_id": 4896 }, "chunk_id": "train_shard_00001_4896_0", "global_id": 12582 }, { "text": "intermedia strains, two C. haemulonii strains and one C. duobushaemulonii strain. Analysis of ITS variability revealed a greater number of haplotypes among C. albicans, C. tropicalis, C. glabrata and C. lusitaniae, which are predominantly related to endogenous sources of acquisition. Bayesian analysis confirmed the major phylogenetic relationships among the isolates and the molecular identification of the different Candida spp.

Conclusions

Molecular studies based on ITS sequencing are necessary to identify closely related and emerging species. Polymorphism analysis of the ITS rDNA region demonstrated its utility as a genetic marker for species identification and phylogenetic relationships as well as for drawing inferences concerning the natural history of hematogenous infections caused by medically important and emerging Candida species.\n\nGenetic diversity of medically important and emerging Candida species causing invasive infection.", "token_count": 220, "char_count": 955, "word_count": 126, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:39.097460", "source": { "split": "train_shard_00001", "doc_id": 4896 }, "chunk_id": "train_shard_00001_4896_1", "global_id": 12583 }, { "text": "Cassava pulp, a solid by-product from starch processing, is a promising and underused biomass that can be converted to biofuels and other value-added bio-products. In this study, an alternative cassava pulp saccharification process, which utilizes the multi-activity enzyme from Aspergillus niger BCC17849 and obviates the need for a pre-gelatinization step, was developed. The crude multi-enzyme composed of non-starch polysaccharide hydrolyzing enzyme activities, including cellulase, pectinase and hemicellulase act cooperatively to release the trapped starch granules from the fibrous cell wall structure for subsequent saccharification by raw starch degrading activity. A high yield of fermentable sugars, equivalent to 716 mg glucose and 67 mg xylose/g of cassava pulp, was obtained after 48 h incubation at 40 degrees C and pH 5 using the multi-enzyme, which was greater than the yield obtained from the optimized combinations of the corresponding commercial enzymes. The multi-enzyme saccharification reaction can be performed simultaneously with the ethanol fermentation process using a thermotolerant yeast Candida tropicalis BCC7755. The combined process produced 14.3 g/l ethanol from 4% (w/v) cassava pulp after 30 h of fermentation. The productivity rate of 0.48 g/l/h is equivalent to 93.7% of the theoretical yield based on total starch and cellulose, or 85.4% based on total fermentable sugars. The non-thermal enzymatic saccharification process described is more energy efficient and yields more fermentable sugar than the conventional enzymatic process. Furthermore, the process is applicable for production of various bio-products of economic importance.\n\nSimultaneous non-thermal saccharification of cassava pulp by multi-enzyme activity and ethanol fermentation by Candida tropicalis.", "token_count": 477, "char_count": 1806, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6135, "quality_score": 0.8068, "entities": { "genes": [ "BCC7755", "BCC17849" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:39.738166", "source": { "split": "train_shard_00001", "doc_id": 4897 }, "chunk_id": "train_shard_00001_4897_0", "global_id": 12584 }, { "text": "Hemorrhagic pneumonia (HP) is a rare but highly lethal disease, mainly of dogs and cats, caused by hemolytic Escherichia coli strains that contain cnf1 (encoding cytotoxic necrotizing factor 1). After encountering fatal HP in two dogs, we used contemporary molecular methods, including multilocus sequence typing and whole-genome sequencing, to compare the corresponding case isolates with published HP clinical isolates and newly obtained fecal E. coli isolates from 20 humans and animals in the index HP case household. We also compared the aggregated HP clinical isolates, which represented 13 discrete strains, by pulsotype with a large, private pulsotype library of diverse-source E. coli. The HP clinical isolates represented a narrow range of phylogenetic group B2 lineages (mainly sequence types 12 and 127), O types (mainly O4 and O6), and H types (mainly H5 and H31), but diverse fimH alleles (type-1 fimbriae adhesin). Their extensive, highly conserved virulence genotypes, which qualified as extraintestinal pathogenic E. coli (ExPEC), encoded diverse adhesins, toxins, iron uptake systems, and protectins. Household surveillance identified multiple HP-like fecal strains, plus abundant between-host strain sharing, including of the household's index HP strain. The pulsotype library search identified, for five HP clinical strains, same-pulsotype human and animal fecal and clinical (predominantly urine) isolates, from diverse locales and time periods. Thus, E. coli strains that cause HP derive from a narrow range of ExPEC lineages within phylogroup B2, contain multiple virulence genes other than cnf1, are shared extensively between hosts, and likely function in nature mainly as intestinal colonizers and uropathogens. IMPORTANCE This study clarifies the clonal background and extensive virulence genotypes of the E", "token_count": 484, "char_count": 1862, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:40.393242", "source": { "split": "train_shard_00001", "doc_id": 4898 }, "chunk_id": "train_shard_00001_4898_0", "global_id": 12585 }, { "text": "coli strains that cause hemorrhagic pneumonia in domestic animals (mainly dogs and cats), shows that such strains circulate among animals and humans, identifies a substantial intestinal colonization component to their lifestyle, and extends their known clinical manifestations to include bacteremia and urinary tract infection. The findings place these strains better into context vis-à-vis current understandings of E. coli phylogeny, ecology, and pathogenesis; identify questions for future research; and may prove relevant for surveillance and prevention efforts.\n\nMolecular Characteristics, Ecology, and Zoonotic Potential of Escherichia coli Strains That Cause Hemorrhagic Pneumonia in Animals.", "token_count": 161, "char_count": 699, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:40.831264", "source": { "split": "train_shard_00001", "doc_id": 4898 }, "chunk_id": "train_shard_00001_4898_1", "global_id": 12586 }, { "text": "We report a direct polymerase chain reaction/sequence (d-PCRS)-based method for the rapid identification of clinically significant fungi from 5 different types of commercial broth enrichment media inoculated with clinical specimens. Media including BacT/ALERT FA (BioMérieux, Marcy l'Etoile, France) (n = 87), BACTEC Plus Aerobic/F (Becton Dickinson, Microbiology Systems, Sparks, MD) (n = 16), BACTEC Peds Plus/F (Becton Dickinson) (n = 15), BACTEC Lytic/10 Anaerobic/F (Becton Dickinson) (n = 11) bottles, and BBL MGIT (Becton Dickinson) (n = 11) were inoculated with specimens from 138 patients. A universal DNA extraction method was used combining a novel pretreatment step to remove PCR inhibitors with a column-based DNA extraction kit. Target sequences in the noncoding internal transcribed spacer regions of the rRNA gene were amplified by PCR and sequenced using a rapid (24 h) automated capillary electrophoresis system. Using sequence alignment software, fungi were identified by sequence similarity with sequences derived from isolates identified by upper-level reference laboratories or isolates defined as ex-type strains. We identified Candida albicans (n = 14), Candida parapsilosis (n = 8), Candida glabrata (n = 7), Candida krusei (n = 2), Scedosporium prolificans (n = 4), and 1 each of Candida orthopsilosis, Candida dubliniensis, Candida kefyr, Candida tropicalis, Candida guilliermondii, Saccharomyces cerevisiae, Cryptococcus neoformans, Aspergillus fumigatus, Histoplasma capsulatum, and Malassezia pachydermatis by d-PCRS analysis. All d-PCRS identifications from positive broths were in agreement with the final species identification of the isolates grown from subculture", "token_count": 510, "char_count": 1698, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:41.473964", "source": { "split": "train_shard_00001", "doc_id": 4899 }, "chunk_id": "train_shard_00001_4899_0", "global_id": 12587 }, { "text": "Earlier identification of fungi using d-PCRS may facilitate prompt and more appropriate antifungal therapy.\n\nRapid identification of fungal pathogens in BacT/ALERT, BACTEC, and BBL MGIT media using polymerase chain reaction and DNA sequencing of the internal transcribed spacer regions.", "token_count": 73, "char_count": 286, "word_count": 39, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:41.847484", "source": { "split": "train_shard_00001", "doc_id": 4899 }, "chunk_id": "train_shard_00001_4899_1", "global_id": 12588 }, { "text": "

Background

River water has been implicated as a source of non-typhoidal Salmonella (NTS) serovars in Mexico.

Objective

To dissect the molecular pathogenesis and defense strategies of seven NTS strains isolated from river water in Mexico.

Methods

The genome of Salmonella serovars Give, Pomona, Kedougou, Stanley, Oranienburg, Sandiego, and Muenchen were sequenced using the whole-genome shotgun methodology in the Illumina Miseq platform. The genoma annotation and evolutionary analyses were conducted in the RAST and FigTree servers, respectively. The MLST was performed using the SRST2 tool and the comparisons between strains were clustered and visualized using the Gview server. Experimental virulence assay was included to evaluate the pathogenic potential of strains.

Results

We report seven high-quality draft genomes, ranging from ~ 4.61 to ~ 5.12 Mb, with a median G + C value, coding DNA sequence, and protein values of 52.1%, 4697 bp, and 4,589 bp, respectively. The NTS serovars presented with an open pan-genome, offering novel genetic content. Each NTS serovar had an indistinguishable virulotype with a core genome (352 virulence genes) closely associated with Salmonella pathogenicity; 13 genes were characterized as serotype specific, which could explain differences in pathogenicity. All strains maintained highly conserved genetic content regarding the Salmonella pathogenicity islands (1-5) (86.9-100%), fimbriae (84.6%), and hypermutation (100%) genes. Adherence and invasion capacity were confirmed among NTS strains in Caco-2 cells.

Conclusion

Our results demonstrated the arsenal of virulence and defense molecular factors harbored on NTS serovars and highlight that environmental NTS strains are waterborne pathogens worthy of attention.", "token_count": 507, "char_count": 1798, "word_count": 240, "semantic_coherence": 1, "information_density": 0.6833, "quality_score": 0.8417, "entities": { "genes": [ "SRST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:42.479282", "source": { "split": "train_shard_00001", "doc_id": 4900 }, "chunk_id": "train_shard_00001_4900_0", "global_id": 12589 }, { "text": "Pathogenic potential of non-typhoidal Salmonella serovars isolated from aquatic environments in Mexico.", "token_count": 25, "char_count": 103, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:42.838251", "source": { "split": "train_shard_00001", "doc_id": 4900 }, "chunk_id": "train_shard_00001_4900_1", "global_id": 12590 }, { "text": "The oral microbiota is intimately linked to human health and various disease states. With the advent of the Human Microbiome Project, our comprehension of the oral microbiota has substantially improved. This microbial community is not only associated with a range of oral diseases, such as dental caries and periodontal diseases, but also with numerous digestive disorders, as demonstrated by recent clinical studies. Specific bacteria residing in the oral cavity, such as Porphyromonas gingivalis, Fusobacterium species and Streptococcus species, have been shown to translocate to the gastrointestinal tract, thereby establishing a potential connection between the oral and gut microbiota. The transfer and ectopic colonization of oral microbiota within the gastrointestinal tract may contribute to both the onset and exacerbation of gastrointestinal diseases. Following the principles of dysregulation characteristics, mechanism research and innovative treatment, this paper systematically reviews the association between the oral microbiota and various digestive system diseases. This paper explores how specific oral microbiota drive digestive system diseases mechanisms and evaluates treatments including probiotics, prebiotics, fecal microbiota transplantation, and targeted antimicrobial therapies. By clarifying the oral-gut microbiota-disease link, it highlights oral microbiota monitoring as a promising tool for early detection, diagnosis, and therapy.\n\nThe role of oral microbiota in digestive system diseases: current advances and perspectives.", "token_count": 350, "char_count": 1578, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6262, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:43.764976", "source": { "split": "train_shard_00001", "doc_id": 4901 }, "chunk_id": "train_shard_00001_4901_0", "global_id": 12591 }, { "text": "Streptococcus mutans is a primary cariogenic pathogen involved in dental biofilm formation, a major virulence factor in the development of dental caries. In S. mutans, the competence-stimulating peptide (CSP), encoded by comC, plays a critical role in environmental stress response, growth regulation, and virulence expression. In this study, we performed transcriptome analysis to investigate the role of SMU.1147, a unique core gene in S. mutans, in biological pathways related to transport, defense responses, and environmental sensing. The deletion of SMU.1147 led to the upregulation of genes involved in carbohydrate uptake and metabolism, particularly phosphotransferase system (PTS) transporters, thereby enhancing the sugar transport capacity. However, despite increased sugar uptake, the mutant strain did not show significant changes in growth rate or ATP production and displayed slightly reduced organic acid production. Additionally, the mutant exhibited significantly reduced cell viability after an 8-h incubation compared to the parental strain. Notably, genes associated with CSP-dependent signal transduction and stress defense, such as comX, comR, htrA, scnRK, and ciaRH, were downregulated in the mutant strain. Furthermore, stress-related genes, including spxA2, clpP, and clpX, were significantly downregulated, suggesting compromised protein quality control and oxidative stress responses. Our findings suggest that SMU.1147 plays a critical role in regulating peptide-mediated signaling, metabolic coordination, and environmental adaptation in S. mutans, positioning it as a key integrator of the metabolic and stress response networks that are essential for pathogenicity and survival.

Importance

Understanding the regulatory mechanisms that govern virulence and environmental adaptation in Streptococcus mutans is essential for developing strategies to mitigate dental caries", "token_count": 523, "char_count": 2007, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:57:44.417442", "source": { "split": "train_shard_00001", "doc_id": 4902 }, "chunk_id": "train_shard_00001_4902_0", "global_id": 12592 }, { "text": "This study reveals the critical role of the SMU.1147 gene in S. mutans in metabolic regulation, stress response, and cell viability. Our results demonstrate how the deletion of this gene affects sugar uptake and organic acid production, leading to imbalances in carbon metabolism and reduced long-term survival. These findings provide valuable insights into the ability of S. mutans to adapt to stressed conditions and highlight the role of SMU.1147 in modulating biofilm formation and virulence, contributing to our understanding of regulatory pathways in dental pathogens.\n\nDeciphering the role of SMU.1147 in peptide-mediated signaling and competence in <i>Streptococcus mutans</i>.", "token_count": 190, "char_count": 711, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6633, "quality_score": 0.8316, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:44.859308", "source": { "split": "train_shard_00001", "doc_id": 4902 }, "chunk_id": "train_shard_00001_4902_1", "global_id": 12593 }, { "text": "Alcoholic fermentation of cheese whey permeate was investigated using a recombinant flocculating Saccharomyces cerevisiae, expressing the LAC4 (coding for beta-galactosidase) and LAC12 (coding for lactose permease) genes of Kluyveromyces marxianus enabling for lactose metabolization. Data on yeast fermentation and growth on cheese whey permeate from a Portuguese dairy industry is presented. For cheese whey permeate having a lactose concentration of 50 gL(-1), total lactose consumption was observed with a conversion yield of ethanol close to the expected theoretical value. Using a continuously operating 5.5-L bioreactor, ethanol productivity near 10 g L(-1) h(-1) (corresponding to 0.45 h(-1) dilution rate) was obtained, which raises new perspectives for the economic feasibility of whey alcoholic fermentation. The use of 2-times concentrated cheese whey permeate, corresponding to 100 gL(-1) of lactose concentration, was also considered allowing for obtaining a fermentation product with 5% (w/v) alcohol.\n\nAlcohol production from cheese whey permeate using genetically modified flocculent yeast cells.", "token_count": 307, "char_count": 1113, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6513, "quality_score": 0.8257, "entities": { "genes": [ "LAC12", "LAC4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:45.434713", "source": { "split": "train_shard_00001", "doc_id": 4903 }, "chunk_id": "train_shard_00001_4903_0", "global_id": 12594 }, { "text": "Oenococcus oeni is responsible for the malolactic fermentation of wines. Genomic diversity has been recently established in the species and extensive attention is now being given to the genomic bases of strain-specific differences. We explored the role of insertion sequences (IS), which are considered as driving forces for novel genotypic and phenotypic variants in prokaryotes. The present study focuses on members of the IS30 family, which are widespread among lactic acid bacteria. An in silico analysis of the three available genomes of O. oeni in combination with the use of an inverse PCR strategy targeting conserved IS30-related sequences indicated the presence of seven IS30 copies in the pangenome of O. oeni. A primer designed to anneal to the conserved 3' end of the IS30 element was paired with each of the seven primers selected to bind to unique sequences upstream of each of the seven mobile elements identified. The study presents an overview of the abundance, and the genomic environment of IS30 elements in the O. oeni pangenome and shows that the two existing genetic sub-populations previously described in the species through multilocus sequence typing analysis (MLST) differ in their IS30 content. Possible IS30 impacts on bacterial adaptation are discussed.\n\nIS30 elements are mediators of genetic diversity in Oenococcus oeni.", "token_count": 309, "char_count": 1353, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5857, "quality_score": 0.7929, "entities": { "genes": [ "IS30" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:46.005120", "source": { "split": "train_shard_00001", "doc_id": 4904 }, "chunk_id": "train_shard_00001_4904_0", "global_id": 12595 }, { "text": "Enterococcus faecalis is a commensal bacterium of the gastrointestinal tract but also a major nosocomial pathogen. This bacterium uses regulators like BglG/SacY family of transcriptional antiterminators to adapt its metabolism during host colonization. In this report, we investigated the role of the BglG/SacY family antiterminator NagY in the regulation of the nagY-nagE operon in presence of N-acetylglucosamine, with nagE encoding a transporter of this carbohydrate, as well as the expression of the virulence factor HylA. We showed that this last protein is involved in biofilm formation and glycosaminoglycans degradation that are important features in bacterial infection, confirmed in the Galleria mellonella model. In order to elucidate the evolution of these actors, we performed phylogenomic analyses on E. faecalis and Enterococcaceae genomes, identified orthologous sequences of NagY, NagE, and HylA, and we report their taxonomic distribution. The study of the conservation of the upstream region of nagY and hylA genes showed that the molecular mechanism of NagY regulation involves ribonucleic antiterminator sequence overlapping a rho-independent terminator, suggesting a regulation conforming to the canonical model of BglG/SacY family antiterminators. In the perspective of opportunism understanding, we offer new insights into the mechanism of host sensing thanks to the NagY antiterminator and its targets expression.\n\nThe NagY regulator: A member of the BglG/SacY antiterminator family conserved in Enterococcus faecalis and involved in virulence.", "token_count": 463, "char_count": 1639, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5909, "quality_score": 0.7955, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:46.651336", "source": { "split": "train_shard_00001", "doc_id": 4905 }, "chunk_id": "train_shard_00001_4905_0", "global_id": 12596 }, { "text": "Countries of the Mediterranean area are characterized by production of artisanal cheeses, obtained from goat, sheep, cow and buffalo raw milk. The numbers and species of yeasts in the different cheeses are variable, but some species are more frequently detected than others. Kluyveromyces marxianus, K. lactis with their anamorph, Candida kefir, Debaryomyces hansenii and C. famata, C. colliculosa and C. catenulata are dominant species in several cheeses. However, Saccharomyces cerevisiae is often detected in pasta filata cheeses, such as Water Buffalo Mozzarella (WBM) or Cacio Cavallo Podolico. Recently, a comprehensive study of yeasts isolated from Mozzarella cheese produced in Basilicata (Southern Italy) has been carried out. The study has focused on lactose and/or galactose fermenting species (Kluyveromyces and Saccharomyces) to evaluate their role on the functional and sensory properties of the product. End products in milk were evaluated and the biodiversity in terms of production of sulphur dioxide, higher alcohols, ethyl acetate, and acetaldehyde was studied. In particular, S. cerevisiae strains from Water Buffalo Mozzarella cheese, compared to strains isolated from different habitats, such as wine, exhibited considerable difference in the production of some volatile compounds. The diversity observed could be related to the particular microhabitat of S. cerevisiae occurring in whey cheese of water buffalo milk.\n\nYeasts from Water Buffalo Mozzarella, a traditional cheese of the Mediterranean area.", "token_count": 383, "char_count": 1526, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6256, "quality_score": 0.8128, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:47.237698", "source": { "split": "train_shard_00001", "doc_id": 4906 }, "chunk_id": "train_shard_00001_4906_0", "global_id": 12597 }, { "text": "ABSTRACT Aggregatibacter actinomycetemcomitans is a Gram-negative periodontitis-associated bacterium that expresses a toxin that selectively affects leukocytes. Leukotoxin is encoded by an operon belonging to the core genome of this bacterial species. Variations in the expression of the leukotoxin have been reported, and a specific clonal type (JP2) of this bacterium with enhanced leukotoxin expression has been identified. Experimental studies have shown that leukotoxin, besides to kill leukocytes, also activates a substantial pro-inflammatory response in these cells. Characterization of clinical isolates from individuals with different geographic origin, age and periodontal status linked carriership of highly leukotoxic A. actinomycetemcomitans to disease. These highly virulent bacteria are of serotype b and have several common phenotypic and genetic features. Based on a great genetic diversity, A. actinomycetemcomitans can be distributed into a high number of different genotypes with various virulence capacities. It can be concluded that carriership of highly leukotoxic bacteria is associated with a significantly increased risk for initiation of aggressive forms of periodontitis.\n\nThe role of Aggregatibacter actinomycetemcomitans and its leukotoxin in periodontitis", "token_count": 317, "char_count": 1287, "word_count": 171, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "JP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:47.809964", "source": { "split": "train_shard_00001", "doc_id": 4907 }, "chunk_id": "train_shard_00001_4907_0", "global_id": 12598 }, { "text": "

Introduction

The ST-4821 complex (cc4821) is a leading cause of serogroup C and serogroup B invasive meningococcal disease in China where diverse strains in two phylogenetic groups (groups 1 and 2) have acquired fluoroquinolone resistance. cc4821 was recently prevalent among carriage isolates in men who have sex with men in New York City (USA). Genome-level population studies have thus far been limited to Chinese isolates. The aim of the present study was to build upon these with an extended panel of international cc4821 isolates.

Methods

Genomes of isolates from Asia (1972 to 2017), Europe (2011 to 2018), North America (2007), and South America (2014) were sequenced or obtained from the PubMLST Neisseria database. Core genome comparisons were performed in PubMLST.

Results

Four lineages were identified. Western isolates formed a distinct, mainly serogroup B sublineage with alleles associated with fluoroquinolone susceptibility (MIC <0.03 mg/L) and reduced penicillin susceptibility (MIC 0.094 to 1 mg/L). A third of these were from anogenital sites in men who have sex with men and had unique denitrification gene alleles. Generally 4CMenB vaccine strain coverage was reliant on strain-specific NHBA peptides.

Discussion

The previously identified cc4821 group 2 was resolved into three separate lineages. Clustering of western isolates was surprising given the overall diversity of cc4821. Possible association of this cluster with the anogenital niche is worthy of monitoring given concerns surrounding antibiotic resistance and potential subcapsular vaccine escape.\n\nGenomic analysis of the meningococcal ST-4821 complex-Western clade, potential sexual transmission and predicted antibiotic susceptibility and vaccine coverage.", "token_count": 478, "char_count": 1772, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6749, "quality_score": 0.8374, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:48.476724", "source": { "split": "train_shard_00001", "doc_id": 4908 }, "chunk_id": "train_shard_00001_4908_0", "global_id": 12599 }, { "text": "The addition of Ca (as CaCl(2)) in optimal concentrations (0.75 to 2.0 mM) to a fermentation medium with a trace contaminating concentration of Ca (0.025 mM) led to the rapid production of higher concentrations of ethanol by Saccharomyces cerevisiae, Saccharomyces bayanus, and Kluyveromyces marxianus. The positive effect of calcium supplementation (0.75 mM) on alcoholic fermentation by S. bayanus was explained by the increase in its ethanol tolerance. The ethanol inhibition of growth and fermentation followed the equation mu(xi) = mu(oi) [1 - (X/X(mi))], where mu(oi) and mu(xi) are, respectively, the specific growth (i = g) and fermentation (i = f) rates in the absence or presence of a concentration (X) of added ethanol, and X(mi) is the maximal concentration of ethanol which allows growth or fermentation. The toxic power is given by n(i). In Ca - supplemented medium (0.75 mM), n(g) = 0.42 for growth and n(f) = 0.43 for fermentation compared with 0.52 and 0.55, respectively, in unsupplemented medium; for both media, X(mg) = 10% (vol/vol) and X(mf) = 13% (vol/vol). For lethal concentrations of ethanol, the specific death rates were minimal for cells that were grown and incubated with ethanol in medium with an optimal concentration of Ca, maximal for cells grown and incubated with ethanol in unsupplemented medium, and intermediate for cells grown in unsupplemented medium and incubated with ethanol in calcium-supplemented medium. The effect of Ca on the acidification curve of energized cells in the presence of ethanol was found to be closely associated with its protective effect on growth, fermentation, and viability.\n\nInfluence of Calcium Ion on Ethanol Tolerance of Saccharomyces bayanus and Alcoholic Fermentation by Yeasts.", "token_count": 509, "char_count": 1752, "word_count": 272, "semantic_coherence": 1, "information_density": 0.4743, "quality_score": 0.7371, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:49.873354", "source": { "split": "train_shard_00001", "doc_id": 4909 }, "chunk_id": "train_shard_00001_4909_0", "global_id": 12600 }, { "text": "Our study aimed to elucidate the plant growth-promoting characteristics and the structure and composition of Sphingomonas sp. LK11 genome using the single molecule real-time (SMRT) sequencing technology of Pacific Biosciences. The results revealed that LK11 produces different types of gibberellins (GAs) in pure culture and significantly improves soybean plant growth by influencing endogenous GAs compared with non-inoculated control plants. Detailed genomic analyses revealed that the Sphingomonas sp. LK11 genome consists of a circular chromosome (3.78 Mbp; 66.2% G+C content) and two circular plasmids (122,975 bps and 34,160 bps; 63 and 65% G+C content, respectively). Annotation showed that the LK11 genome consists of 3656 protein-coding genes, 59 tRNAs, and 4 complete rRNA operons. Functional analyses predicted that LK11 encodes genes for phosphate solubilization and nitrate/nitrite ammonification, which are beneficial for promoting plant growth. Genes for production of catalases, superoxide dismutase, and peroxidases that confer resistance to oxidative stress in plants were also identified in LK11. Moreover, genes for trehalose and glycine betaine biosynthesis were also found in LK11 genome. Similarly, Sphingomonas spp. analysis revealed an open pan-genome and a total of 8507 genes were identified in the Sphingomonas spp. pan-genome and about 1356 orthologous genes were found to comprise the core genome. However, the number of genomes analyzed was not enough to describe complete gene sets. Our findings indicated that the genetic makeup of Sphingomonas sp. LK11 can be utilized as an eco-friendly bioresource for cleaning contaminated sites and promoting growth of plants confronted with environmental perturbations.", "token_count": 507, "char_count": 1776, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [ "LK11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:50.526815", "source": { "split": "train_shard_00001", "doc_id": 4910 }, "chunk_id": "train_shard_00001_4910_0", "global_id": 12601 }, { "text": "Complete genome sequencing and analysis of endophytic Sphingomonas sp. LK11 and its potential in plant growth.", "token_count": 36, "char_count": 117, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [ "LK11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:50.890916", "source": { "split": "train_shard_00001", "doc_id": 4910 }, "chunk_id": "train_shard_00001_4910_1", "global_id": 12602 }, { "text": "A strain of a Gram-positive, strictly aerobic, motile, rod-shaped, endospore forming bacterium was originally isolated from rhizospheric soil of a pepper plant when screening and bioprospecting for plant beneficial microorganisms. Phylogenetic analysis of the 16S rRNA gene sequences indicated that this strain, PB300T, is closely related to Lysinibacillus macroides DMS 54T (99.6%) and Lysinibacillus xylanilyticus DSM 23493T (99.4%). In phenotypic characterisation, the novel strain was found to grow between 15 and 40 °C and tolerate up to 10% (w/v) NaCl. Furthermore, the strain was found to grow in media with pH 5 to 10 (optimal growth at pH 7.0). The predominant cellular fatty acids were observed to be iso-C15 : 0 (56.6 %), anteiso-C15 : 0 (14.6%), C16 :1ω7C alcohol (9.3%) and C16 : 0 (7.1%). The cell wall peptidoglycan contains lysine-aspartic acid, as in its close relatives. A draft genome was completed and the DNA G + C content was determined to be 37.5% (mol content). A phylogenomic analysis of the core genome of the new strain and 5 closely related type strains of the genus Lysinibacillus revealed that this strain formed a distinct monophyletic clade with the nearest neighbour being Lysinibacillus boronitolerans. DNA-DNA relatedness studies using in silico DNA-DNA hybridizations (DDH) showed relationships for the new strain were below the species threshold of 70%", "token_count": 492, "char_count": 1466, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6713, "quality_score": 0.8356, "entities": { "genes": [ "PB300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:51.540052", "source": { "split": "train_shard_00001", "doc_id": 4911 }, "chunk_id": "train_shard_00001_4911_0", "global_id": 12603 }, { "text": "Based upon the consensus of phylogenetic and phenotypic analyses, we conclude that this strain represents a novel species within the genus Lysinibacillus, for which the name Lysinibacillus capsici sp. nov. is proposed, with type strain PB300T (= NRRL B-65515T, = CCUG 72241T).\n\nLysinibacillus capsici sp. nov, isolated from the rhizosphere of a pepper plant.", "token_count": 144, "char_count": 391, "word_count": 54, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [ "PB300" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:51.970638", "source": { "split": "train_shard_00001", "doc_id": 4911 }, "chunk_id": "train_shard_00001_4911_1", "global_id": 12604 }, { "text": "Bacterial toxin-antitoxin (TA) systems are widespread in chromosomes and plasmids of free-living microorganisms, but only a few have been identified in obligate intracellular species. We found seven putative type II TA modules in Waddlia chondrophila, a Chlamydia-related species that is able to infect a very broad series of eukaryotic hosts, ranging from protists to mammalian cells. The RNA levels of Waddlia TA systems are significantly upregulated by iron starvation and novobiocin, but they are not affected by antibiotics such as β-lactams and glycopeptides, which suggests different mechanisms underlying stress responses. Five of the identified TA modules, including HigBA1 and MazEF1, encoded on the Waddlia cryptic plasmid, proved to be functional when expressed in a heterologous host. TA systems have been associated with the maintenance of mobile genetic elements, bacterial defense against bacteriophages, and persistence upon exposure to adverse conditions. As their RNA levels are upregulated upon exposure to adverse conditions, Waddlia TA modules may be involved in survival to stress. Moreover, as Waddlia can infect a wide range of hosts including free-living amoebae, TA modules could also represent an innate immunity system to fight against bacteriophages and other microorganisms with which Waddlia has to share its replicative niche.IMPORTANCEThe response to adverse conditions, such as exposure to antibiotics, nutrient starvation and competition with other microorganisms, is essential for the survival of a bacterial population. TA systems are modules composed of two elements, a toxic protein and an antitoxin (protein or RNA) that counteracts the toxin. Although many aspects of TA biological functions still await to be elucidated, TAs have often been implicated in bacterial response to stress, including the response to nutrient starvation, antibiotic treatment and bacteriophage infection", "token_count": 497, "char_count": 1972, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:52.629701", "source": { "split": "train_shard_00001", "doc_id": 4912 }, "chunk_id": "train_shard_00001_4912_0", "global_id": 12605 }, { "text": "TAs are ubiquitous in free-living bacteria but rare in obligate intracellular species such as chlamydiae. We identified functional TA systems in Waddlia chondrophila, a chlamydial species with a strikingly broad host range compared to other chlamydiae. Our work contributes to understand how obligate intracellular bacteria react to adverse conditions that might arise from competition with other viruses/bacteria for the same replicative niche and would threaten their ability to replicate.\n\nThe Chlamydia-related Waddlia chondrophila encodes functional type II toxin-antitoxin systems.", "token_count": 169, "char_count": 608, "word_count": 79, "semantic_coherence": 1, "information_density": 0.7975, "quality_score": 0.8987, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:53.073453", "source": { "split": "train_shard_00001", "doc_id": 4912 }, "chunk_id": "train_shard_00001_4912_1", "global_id": 12606 }, { "text": "Volatile acyloins (alpha-hydroxy ketones) were obtained by condensing either aldehydes with pyruvate or 2-keto acids with acetaldehyde in a reaction catalyzed by yeast pyruvate decarboxylases (EC 4.1.1.1). Odor qualities and threshold values of 34 acyloins were evaluated, and 23 of them possessed distinct flavor properties. Sherry and soy sauce flavors were analyzed: 2-hydroxy-3-pentanone and 3-hydroxy-2-pentanone were identified in soy sauce for the first time; these and 2-hydroxy-5-methyl-3-hexanone and 3-hydroxy-1-phenyl-2-butanone were isolated from sherry for the first time. The biocatalytic efficiencies of crude pyruvate decarboxylase preparations from Zygosaccharomyces bisporus, Saccharomyces cerevisiae, Kluyveromyces lactis, and Kluyveromyces marxianus were compared. Product yields comparable to those of conversions with purified pyruvate decarboxylase demonstrated the suitability of crude enzyme extracts as cost-effective biocatalysts in acyloin formation. Conversion rates of >50% showed that the potential of this type of enzyme to catalyze the formation of aliphatic acyloins has been underestimated before.\n\nGeneration of odorous acyloins by yeast pyruvate decarboxylases and their occurrence in sherry and soy sauce.", "token_count": 387, "char_count": 1244, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:53.688835", "source": { "split": "train_shard_00001", "doc_id": 4913 }, "chunk_id": "train_shard_00001_4913_0", "global_id": 12607 }, { "text": "The prevalence of antimicrobial resistance (AMR) in bacterial pathogens resulting from the intensive usage of antibiotics and antibiotic compounds is acknowledged as a significant global concern that impacts both human and animal health. In this study, we sequenced and analyzed the genomes of two emergent onion-pathogenic species of Burkholderia, B. cenocepacia CCRMBC56 and B. orbicola CCRMBC23, focusing on genes that are potentially associated with their high level of antibiotic and copper resistance. We also identified genes contributing to the copper resistance of B. cenocepacia CCRMBC56 through high-throughput analysis of mutated genes in random transposon mutant populations that were differentially enriched in a copper-containing medium. The results indicated that genes involved in DNA integration, recombination, and cation transport are important for the survival of B. cenocepacia CCRMBC56 in copper-stressed conditions. Furthermore, the fitness effect analysis identified additional genes crucial for copper resistance, which are involved in functions associated with the oxidative stress response, the ABC transporter complex, and the cell outer membrane. In the same analysis, genes related to penicillin binding, the TCA cycle, and FAD binding were found to hinder bacterial adaptation to copper toxicity. This study provides potential targets for reducing the copper resistance of B. cenocepacia and other copper-resistant bacterial pathogens.\n\nCharacterization of the Antibiotic and Copper Resistance of Emergent Species of Onion-Pathogenic <i>Burkholderia</i> Through Genome Sequence Analysis and High-Throughput Sequencing of Differentially Enriched Random Transposon Mutants.", "token_count": 453, "char_count": 1778, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5852, "quality_score": 0.7926, "entities": { "genes": [ "CCRMBC23", "CCRMBC56" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:54.331403", "source": { "split": "train_shard_00001", "doc_id": 4914 }, "chunk_id": "train_shard_00001_4914_0", "global_id": 12608 }, { "text": "New results are presented on the equilibria and kinetics of the ion exchange onto CM-Sephadex of polygalacturonase (pectinase) produced by the fermentation of Kluyveromyces marxianus. It is found that the equilibrium behavior follows the form of the Langmuir isotherm; the equilibrium is strongly affected by pH. High partitioning onto the ion-exchange matrix, with good retention of enzyme activity, is achieved in the pH range 3.5-5.0, and this can be qualitatively explained in terms of simple models for protein adsorption by ion exchange. The kinetics of ion exchange is modeled by assuming that the transfer resistances can be lumped into a single coefficient, and the results show that this gives a reasonable description of the adsorption kinetics. Under optimum conditions protein adsorption is enhanced by electrostatic effects and is extremely fast, and it is suggested that in these circumstances external mass transfer resistance is significant. At pH values close to the isoelectric point, electrostatic interactions are weak and intraparticle diffusion is rate-limiting: pore-blocking by adsorbed proteins appears to be important under these conditions. The results also provide the basis for an efficient single-step purification scheme.\n\nAdsorption of Kluyveromyces marxianus pectinase on CM-Sephadex gels.", "token_count": 310, "char_count": 1323, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6094, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:54.903415", "source": { "split": "train_shard_00001", "doc_id": 4915 }, "chunk_id": "train_shard_00001_4915_0", "global_id": 12609 }, { "text": "Traditional fermented foods and beverages play an important role in a range of human diets, and several experimental studies have shown their potential positive effects on human health. Studies from different continents have revealed strong associations between the microorganisms present in certain fermented foods (e.g., agave fructans, kefir, yeats, kombucha, chungkookjang, cheeses and vegetables, among others) and weight maintenance, reductions in the risk of cardiovascular disease, antidiabetic and constipation benefits, improvement of glucose and lipids levels, stimulation of the immunological system, anticarcinogenic effects and, most importantly, reduced mortality. Accordingly, the aim of this review is to corroborate information reported in experimental studies that comprised interventions involving the consumption of traditional fermented foods or beverages and their association with human health. This work focuses on studies that used fermented food from 2014 to the present. In conclusion, traditional fermented foods or beverages could be important in the promotion of human health. Further studies are needed to understand the mechanisms involved in inflammatory, immune, chronic and gastrointestinal diseases and the roles of fermented traditional foods and beverages in terms of preventing or managing those diseases.\n\nTraditional Fermented Foods and Beverages from around the World and Their Health Benefits.", "token_count": 313, "char_count": 1437, "word_count": 196, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:55.460348", "source": { "split": "train_shard_00001", "doc_id": 4916 }, "chunk_id": "train_shard_00001_4916_0", "global_id": 12610 }, { "text": "The marine Roseobacter group encompasses numerous species which occupy a large variety of ecological niches. However, members of the genus Phaeobacter are specifically adapted to a surface-associated lifestyle and have so far been found nearly exclusively in disjunct, man-made environments including shellfish and fish aquacultures, as well as harbors. Therefore, the possible natural habitats, dispersal and evolution of Phaeobacter spp. have largely remained obscure. Applying a high-throughput cultivation strategy along a longitudinal Pacific transect, the present study revealed for the first time a widespread natural occurrence of Phaeobacter in the marine pelagial. These bacteria were found to be specifically associated to mesoplankton where they constitute a small but detectable proportion of the bacterial community. The 16S rRNA gene sequences of 18 isolated strains were identical to that of Phaeobacter gallaeciensis DSM26640T but sequences of internal transcribed spacer and selected genomes revealed that the strains form a distinct clade within P. gallaeciensis. The genomes of the Pacific and the aquaculture strains were highly conserved and had a fraction of the core genome of 89.6%, 80 synteny breakpoints, and differed 2.2% in their nucleotide sequences. Diversification likely occurred through neutral mutations. However, the Pacific strains exclusively contained two active Type I restriction modification systems which is commensurate with a reduced acquisition of mobile elements in the Pacific clade. The Pacific clade of P. gallaeciensis also acquired a second, homolog phosphonate transport system compared to all other P. gallaeciensis. Our data indicate that a previously unknown, distinct clade of P. gallaeciensis acquired a limited number of clade-specific genes that were relevant for its association with mesozooplankton and for colonization of the marine pelagial", "token_count": 498, "char_count": 1978, "word_count": 270, "semantic_coherence": 1, "information_density": 0.637, "quality_score": 0.8185, "entities": { "genes": [ "DSM26640" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:56.118053", "source": { "split": "train_shard_00001", "doc_id": 4917 }, "chunk_id": "train_shard_00001_4917_0", "global_id": 12611 }, { "text": "The divergence of the Pacific clade most likely was driven by the adaptation to this novel ecological niche rather than by geographic isolation.\n\nAdaptation of Surface-Associated Bacteria to the Open Ocean: A Genomically Distinct Subpopulation of Phaeobacter gallaeciensis Colonizes Pacific Mesozooplankton.", "token_count": 85, "char_count": 314, "word_count": 41, "semantic_coherence": 1, "information_density": 0.7805, "quality_score": 0.8902, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:56.489657", "source": { "split": "train_shard_00001", "doc_id": 4917 }, "chunk_id": "train_shard_00001_4917_1", "global_id": 12612 }, { "text": "Staphylococcus capitis is a frequent cause of Late-Onset Sepsis (LOS) in neonates admitted to Neonatal Intensive Care Units (NICU). The NRCS-A clone of S. capitis has been isolated from NICUs globally although the reasons for the global success of this clone are not understood. We analysed a collection of S. capitis colonising babies admitted to two NICUs, one in the UK and one in Germany as well as corresponding pathological clinical isolates. Genome analysis identified 3 groups; non-NRCS-A isolates, NRCS-A isolates, and a group of ‘proto NRCS-A’ - isolates closely related to NRCS-A but not associated with neonatal infection. All bloodstream isolates belonged to the NRCS-A group and were indistinguishable from strains carried on the skin or in the gut. NRCS-A isolates showed increased tolerance to chlorhexidine and antibiotics relative to the other S. capitis as well as enhanced ability to grow at higher pH values. Analysis of 138 pangenomes of the clades identified characteristic nsr and tarJ genes in the NRCS-A and proto groups with a CRISPR-cas system only seen in NRCS-A isolates which also showed enrichment of genes for metal acquisition and transport. We found evidence for transmission of S. capitis NRCS-A within NICU, with related isolates shared between babies and multiple acquisitions by some babies. Our data show NRCS-A strains commonly colonise uninfected babies in NICU representing a potential reservoir for potential infection. This work provides more evidence that adaptation to survive in the gut and on skin facilitates spread of NRCS-A, and that metal acquisition and tolerance may be important to the biology of NRCS-A. Understanding how NRCS-A survives in NICUs can help develop infection control procedures against this clone.\n\nCharacterisation of neonatalStaphylococcus capitisNRCS-A isolates compared with non NRCS-AStaphylococcus capitisfrom neonates and adults", "token_count": 502, "char_count": 1921, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:57.150054", "source": { "split": "train_shard_00001", "doc_id": 4918 }, "chunk_id": "train_shard_00001_4918_0", "global_id": 12613 }, { "text": "

Background

The nosocomial pathogen Enterococcus faecium can survive for prolonged periods of time on surfaces in the absence of nutrients. This trait is thought to contribute to the ability of E. faecium to spread among patients in hospitals. There is currently a lack of data on the mechanisms that are responsible for the ability of E. faecium to survive in the absence of nutrients.

Results

We performed a high-throughput transposon mutant library screening (Tn-seq) to identify genes that have a role in long-term survival during incubation in phosphate-buffered saline (PBS) at 20 °C. A total of 24 genes were identified by Tn-seq to contribute to survival in PBS, with functions associated with the general stress response, DNA repair, metabolism, and membrane homeostasis. The gene which was quantitatively most important for survival in PBS was usp (locus tag: EfmE745_02439), which is predicted to encode a 17.4 kDa universal stress protein. After generating a targeted deletion mutant in usp, we were able to confirm that usp significantly contributes to survival in PBS and this defect was restored by in trans complementation. The usp gene is present in 99% of a set of 1644 E. faecium genomes that collectively span the diversity of the species.

Conclusions

We postulate that usp is a key determinant for the remarkable environmental robustness of E. faecium. Further mechanistic studies into usp and other genes identified in this study may shed further light on the mechanisms by which E. faecium can survive in the absence of nutrients for prolonged periods of time.\n\nConditionally essential genes for survival during starvation in Enterococcus faecium E745.", "token_count": 440, "char_count": 1696, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5462, "quality_score": 0.7731, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:57.782062", "source": { "split": "train_shard_00001", "doc_id": 4919 }, "chunk_id": "train_shard_00001_4919_0", "global_id": 12614 }, { "text": "Temperature effects on all kinetic and inactivation parameters have been determined for chitin immobilized lactase from Kluyveromyces marxianus var. marxianus, and proper temperature functions have been validated. Maximum reaction rate, Michaelis constant referred to lactose, inhibition constant for galactose and inactivation rates increased with temperature. Enzyme inactivation was adequately modelled by a two-stage series mechanism. The effect of galactose and lactose on enzyme inactivation was determined in terms of modulation factors that were positive for galactose and negative for lactose over the whole range of temperature studied. Modulation factors were mild functions of temperature in the first stage and strong functions in the second stage of CIL inactivation where galactose positive modulation factors increase with temperature and lactose negative modulation factors decrease with temperature. Temperature explicit functions for all kinetic and inactivation parameters were incorporated into a scheme to optimize the temperature of operation for a sequential batch reactor with chitin-immobilized lactase, based on an annual cost objective function for reactor operation. Software for temperature optimization was developed creating a friendly interface with user that allows the introduction of variations in all parameters and operational criteria to perform sensitivity analysis.\n\nTemperature optimization for reactor operation with chitin-immobilized lactase under modulated inactivation.", "token_count": 311, "char_count": 1516, "word_count": 201, "semantic_coherence": 1, "information_density": 0.5323, "quality_score": 0.7662, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:58.354228", "source": { "split": "train_shard_00001", "doc_id": 4920 }, "chunk_id": "train_shard_00001_4920_0", "global_id": 12615 }, { "text": "

ABSTRACT

The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania, and continued local transmission. To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo District on the coastal mainland from 2016-2018. Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias , suggests ongoing low level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes. Our data support importation as a main source of genetic diversity and contribution to the parasite population on Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission. These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive for malaria reemergence due to susceptible hosts and competent vectors.\n\nStrong isolation by distance and evidence of population microstructure reflect ongoingPlasmodium falciparumtransmission in Zanzibar", "token_count": 432, "char_count": 1950, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6264, "quality_score": 0.8132, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:58.979745", "source": { "split": "train_shard_00001", "doc_id": 4921 }, "chunk_id": "train_shard_00001_4921_0", "global_id": 12616 }, { "text": "At present, the most used methods for Klebsiella pneumoniae subtyping are multilocus sequence typing (MLST) and pulsed-field gel electrophoresis (PFGE). However, the discriminatory power of MLST could not meet the need for distinguishing outbreak and non-outbreak isolates and the PFGE is time-consuming and labor-intensive. A core genome multilocus sequence typing (cgMLST) scheme for whole-genome sequence-based typing of K. pneumoniae was developed for solving the disadvantages of these traditional molecular subtyping methods. Firstly, we used the complete genome of K. pneumoniae strain HKUOPLC as the reference genome and 907 genomes of K. pneumoniae download from NCBI database as original genome dataset to determine cgMLST target genes. A total of 1,143 genes were retained as cgMLST target genes. Secondly, we used 26 K. pneumoniae strains from a nosocomial infection outbreak to evaluate the cgMLST scheme. cgMLST enabled clustering of outbreak strains with <10 alleles difference and unambiguous separation from unrelated outgroup strains. Moreover, cgMLST revealed that there may be several sub-clones of epidemic ST11 clone. In conclusion, the novel cgMLST scheme not only showed higher discriminatory power compared with PFGE and MLST in outbreak investigations but also showed ability to reveal more population structure characteristics than MLST.\n\nDefining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Klebsiella pneumoniae.", "token_count": 425, "char_count": 1544, "word_count": 212, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [ "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:57:59.601383", "source": { "split": "train_shard_00001", "doc_id": 4922 }, "chunk_id": "train_shard_00001_4922_0", "global_id": 12617 }, { "text": "Infectious diarrhoeal diseases remain a substantial health burden in young children in low- and middle-income countries. The disease and its variable treatment options significantly alter the gut microbiome, which may affect clinical outcomes and overall gut health. Antibiotics are often prescribed, but their impact on the gut microbiome during recovery is unclear. Here, we used 16S rRNA sequencing to investigate changes in the gut microbiota in Vietnamese children with acute watery diarrhoea, and highlight the impact of antibiotic treatment on these changes. Our analyses identified that, regardless of treatment, recovery was characterised by reductions in Streptococcus and Rothia species and expansion of Bacteroides/Phocaeicola, Lachnospiraceae and Ruminococcacae taxa. Antibiotic treatment significantly delayed the temporal increases in alpha- and beta-diversity within patients, resulting in distinctive patterns of taxonomic change. These changes included a pronounced, transient overabundance of Enterococcus species and depletion of Bifidobacterium pseudocatenulatum. Our findings demonstrate that antibiotic treatment slows gut microbiota recovery in children following watery diarrhoea.\n\nThe impact of antibiotics on the gut microbiota of children recovering from watery diarrhoea.", "token_count": 336, "char_count": 1342, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8246, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:00.195170", "source": { "split": "train_shard_00001", "doc_id": 4923 }, "chunk_id": "train_shard_00001_4923_0", "global_id": 12618 }, { "text": "Coliforms are usually used as a measure of hygiene status in the processing and packaging of dairy products. However, their limited chances of survival have placed a question mark over this role in acid products. Some authors propose Enterococcus as a group for hygienic condition inspections in process lines of fermented dairy products. The aims of this work were, first to evaluate the viability of enterococcus and non-lactic acid microflora (coliforms, Pseudomonas, Staphylococcus aureus and yeasts) in whole set sweetened yoghurt during refrigerated storage and; second, to evaluate the occurrence of bacterial contaminants in industrial process lines of whole set sweetened yoghurt through a critical control points plan (CCP). Test strains were inoculated at a level of 5.5 log orders. Enterococcus remained viable for 21 days and was still detectable after up to 49 days of cold storage. The viability of Pseudomonas was very poor (D-values lower than 0.69 days). Klebsiella spp., Escherichia coli and Citrobacter spp. showed D-values of 1.61, 1.85 and 2.56 days, respectively; while two S. aureus strains showed D-values of 0.61 and 1.56 days. Kluyveromyces marxianus var. lactis strains tested in this study remained viable for at least 42 days. The in vitro assays performed during this study demonstrated that enterococci could remain viable for a longer period than coliforms. However, from analysis of the industrial reality it became evident that in whole set yoghurt lines, coliforms are the most frequent contaminants. In addition they can remain viable during the fermentation step and, in some cases, during cold storage of the product. Finally; coliform detection is cheaper and faster than enterococci counts. It can thus be concluded that enterococci have little value as hygiene indicators in the industrial processes of yoghurt. Consequently, coliforms are a suitable hygiene indicator as long as they are determined in the first days after manufacture.", "token_count": 506, "char_count": 1978, "word_count": 304, "semantic_coherence": 1, "information_density": 0.5954, "quality_score": 0.7977, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:00.872231", "source": { "split": "train_shard_00001", "doc_id": 4924 }, "chunk_id": "train_shard_00001_4924_0", "global_id": 12619 }, { "text": "Enterococci vs non-lactic acid microflora as hygiene indicators for sweetened yoghurt", "token_count": 26, "char_count": 85, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:01.257326", "source": { "split": "train_shard_00001", "doc_id": 4924 }, "chunk_id": "train_shard_00001_4924_1", "global_id": 12620 }, { "text": "Gestational diabetes mellitus (GDM) is a metabolic complication that manifests as hyperglycemia during the later stages of pregnancy. In high resource settings, careful management of GDM limits risk to the pregnancy, and hyperglycemia typically resolves after birth. At the same time, previous studies have revealed that the gut microbiome of infants born to mothers who experienced GDM exhibit reduced diversity and reduction in the abundance of several key taxa, including Lactobacillus. What is not known is what the functional consequences of these changes might be. In this case control study, we applied 16S rRNA sequence surveys and metatranscriptomics to profile the gut microbiome of 30 twelve-month-old infants - 16 from mothers with GDM, 14 from mothers without - to examine the impact of GDM during pregnancy. Relative to the mode of delivery and sex of the infant, maternal GDM status had a limited impact on the structure and function of the developing microbiome. While GDM samples were associated with a decrease in alpha diversity, we observed no effect on beta diversity and no differentially abundant taxa. Further, while the mode of delivery and sex of infant affected the expression of multiple bacterial pathways, much of the impact of GDM status on the function of the infant microbiome appears to be lost by twelve months of age. These data may indicate that, while mode of delivery appears to impact function and diversity for longer than anticipated, GDM may not have persistent effects on the function nor composition of the infant gut microbiome.\n\nThe impact of gestational diabetes on functional capacity of the infant gut microbiome is modest and transient.", "token_count": 374, "char_count": 1694, "word_count": 268, "semantic_coherence": 1, "information_density": 0.5522, "quality_score": 0.7761, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:01.878778", "source": { "split": "train_shard_00001", "doc_id": 4925 }, "chunk_id": "train_shard_00001_4925_0", "global_id": 12621 }, { "text": "In the present work the sensitivity of yeast strains of Kluyveromyces marxianus, Pichia anomala, Candida utilis, Schizosaccharomyces pombe and Saccharomyces cerevisiae, to the fungicides cymoxanil, penconazol, and dichlofluanid, was evaluated. Dichlofluanid induced the most negative effects, whereas penconazol in general was not very toxic. Overall, our results show that the parameters IC50 for specific respiration rates of C. utilis and S. cerevisiae and C(D) for cell viability of S. cerevisiae can be applied to quantify the toxicity level of the above compounds in yeast. Hence, could be explored as an alternative or at least as a complementary test in toxicity studies and, therefore, its potential for inclusion in a tier testing toxicity test battery merits further research.\n\nYeasts as a model for assessing the toxicity of the fungicides Penconazol, Cymoxanil and Dichlofluanid.", "token_count": 243, "char_count": 892, "word_count": 132, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [ "IC50" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:02.386960", "source": { "split": "train_shard_00001", "doc_id": 4926 }, "chunk_id": "train_shard_00001_4926_0", "global_id": 12622 }, { "text": "An upshift of the growth temperature from 26 to 40 degrees C in the presence of calcium leads to the aggregation of Kluyveromyces marxianus cells and to the formation of flocs. Analysis of cell wall proteins, either by sodium dodecyl sulphate-polyacrylamide gel electrophoresis of extractable mannoproteins or by immunolocalization, revealed an accumulation of a protein with Mr 37 kDa(p37), upon flocculation. Immunological studies confirmed the homology of this protein with the glycolytic enzyme glyceraldehyde-3-phosphate dehydrogenase (GAPDH). When mRNA isolated from cells growing at 40 degrees C was translated in vitro, a 35 kDa newly labelled protein was synthesized and immunoprecipitation assays showed that this protein is recognized by p37-antiserum, suggesting that the 35 kDa polypeptide might be an unglycosylated precursor for of p37. The results indicated that the presence of this cell wall mannoprotein closely related to GAPDH is dependent on the growth temperature, suggesting its role as adhesin.\n\nFlocculation of Kluyveromyces marxianus is induced by a temperature upshift.", "token_count": 310, "char_count": 1097, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6415, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:02.952738", "source": { "split": "train_shard_00001", "doc_id": 4927 }, "chunk_id": "train_shard_00001_4927_0", "global_id": 12623 }, { "text": "Lactobacillus reuteri is a catalase-negative, Gram-positive, non-motile, obligately heterofermentative bacterial species that has been used as a model to describe the ecology and evolution of vertebrate gut symbionts. However, the genetic features and evolutionary strategies of L. reuteri from the gastrointestinal tract of herbivores remain unknown. Therefore, 16 L. reuteri strains isolated from goat, sheep, cow, and horse in Inner Mongolia, China were sequenced in this study. A comparative genomic approach was used to assess genetic diversity and gain insight into the distinguishing features related to the different hosts based on 21 published genomic sequences. Genome size, G + C content, and average nucleotide identity values of the L. reuteri strains from different hosts indicated that the strains have broad genetic diversity. The pan-genome of 37 L. reuteri strains contained 8,680 gene families, and the core genome contained 726 gene families. A total of 92,270 nucleotide mutation sites were discovered among 37 L. reuteri strains, and all core genes displayed a Ka/Ks ratio much lower than 1, suggesting strong purifying selective pressure (negative selection). A highly robust maximum likelihood tree based on the core genes shown in the herbivore isolates were divided into three clades; clades A and B contained most of the herbivore isolates and were more closely related to human isolates and vastly distinct from clade C. Some functional genes may be attributable to host-specific of the herbivore, omnivore, and sourdough groups. Moreover, the numbers of genes encoding cell surface proteins and active carbohydrate enzymes were host-specific. This study provides new insight into the adaptation of L. reuteri to the intestinal habitat of herbivores, suggesting that the genomic diversity of L", "token_count": 515, "char_count": 1909, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6154, "quality_score": 0.8077, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:03.612270", "source": { "split": "train_shard_00001", "doc_id": 4928 }, "chunk_id": "train_shard_00001_4928_0", "global_id": 12624 }, { "text": "reuteri from different ecological origins is closely associated with their living environment.\n\nComparative Genomics of the Herbivore Gut Symbiont Lactobacillus reuteri Reveals Genetic Diversity and Lifestyle Adaptation.", "token_count": 69, "char_count": 231, "word_count": 27, "semantic_coherence": 1, "information_density": 0.963, "quality_score": 0.9815, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:03.979508", "source": { "split": "train_shard_00001", "doc_id": 4928 }, "chunk_id": "train_shard_00001_4928_1", "global_id": 12625 }, { "text": "Improvement of xylose fermentation is of great importance to the fuel ethanol industry. The nonconventional thermotolerant yeast Hansenula polymorpha naturally ferments xylose to ethanol at high temperatures (48-50 degrees C). Introduction of a mutation that impairs ethanol reutilization in H. polymorpha led to an increase in ethanol yield from xylose. The native and heterologous (Kluyveromyces lactis) PDC1 genes coding for pyruvate decarboxylase were expressed at high levels in H. polymorpha under the control of the strong constitutive promoter of the glyceraldehyde-3-phosphate dehydrogenase gene (GAPDH). This resulted in increased pyruvate decarboxylase activity and improved ethanol production from xylose. The introduction of multiple copies of the H. polymorpha PDC1 gene driven by the strong constitutive promoter led to a 20-fold increase in pyruvate decarboxylase activity and up to a threefold elevation of ethanol production.\n\nOverexpression of pyruvate decarboxylase in the yeast Hansenula polymorpha results in increased ethanol yield in high-temperature fermentation of xylose.", "token_count": 308, "char_count": 1098, "word_count": 151, "semantic_coherence": 1, "information_density": 0.5298, "quality_score": 0.7649, "entities": { "genes": [ "PDC1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:04.549292", "source": { "split": "train_shard_00001", "doc_id": 4929 }, "chunk_id": "train_shard_00001_4929_0", "global_id": 12626 }, { "text": "Many insect species have established long-term symbiotic relationships with intracellular bacteria. Symbiosis with bacteria has provided insects with novel ecological capabilities, which have allowed them colonize previously unexplored niches. Despite its importance to the understanding of the emergence of biological complexity, the evolution of symbiotic relationships remains hitherto a mystery in evolutionary biology. In this study, we contribute to the investigation of the evolutionary leaps enabled by mutualistic symbioses by sequencing the genome of Blattabacterium cuenoti, primary endosymbiont of the omnivorous cockroach Blatta orientalis, and one of the most ancient symbiotic associations. We perform comparative analyses between the Blattabacterium cuenoti genome and that of previously sequenced endosymbionts, namely those from the omnivorous hosts the Blattella germanica (Blattelidae) and Periplaneta americana (Blattidae), and the endosymbionts harbored by two wood-feeding hosts, the subsocial cockroach Cryptocercus punctulatus (Cryptocercidae) and the termite Mastotermes darwiniensis (Termitidae). Our study shows a remarkable evolutionary stasis of this symbiotic system throughout the evolutionary history of cockroaches and the deepest branching termite M. darwiniensis, in terms of not only chromosome architecture but also gene content, as revealed by the striking conservation of the Blattabacterium core genome. Importantly, the architecture of central metabolic network inferred from the endosymbiont genomes was established very early in Blattabacterium evolutionary history and could be an outcome of the essential role played by this endosymbiont in the host's nitrogen economy.\n\nComparative genomics of Blattabacterium cuenoti: the frozen legacy of an ancient endosymbiont genome.", "token_count": 440, "char_count": 1818, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6345, "quality_score": 0.8172, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:05.181186", "source": { "split": "train_shard_00001", "doc_id": 4930 }, "chunk_id": "train_shard_00001_4930_0", "global_id": 12627 }, { "text": "

Background

The gut microbiome is a potentially modifiable risk factor for Alzheimer's disease (AD); however, understanding of its composition and function regarding AD pathology is limited.

Methods

Shallow-shotgun metagenomics was used to analyze the fecal microbiome of participants in the Wisconsin Microbiome in Alzheimer's Risk Study, leveraging clinical data and cerebrospinal fluid (CSF) biomarkers. Differential abundance and ordinary least squares regression analyses were performed to find differentially abundant gut microbiome features and their associations with CSF biomarkers of AD and related pathologies.

Results

Gut microbiome composition and function differed between individuals with and without AD dementia. The compositional difference was replicated in an independent cohort. Differentially abundant gut microbiome features were associated with CSF biomarkers of AD and related pathologies.

Discussion

These findings enhance our understanding of alterations in gut microbial composition and function in AD, and suggest that gut microbes and their pathways are linked to AD pathology.

Highlights

Gut microbiome composition and function differ between people with Alzheimer's disease (AD) dementia and cognitively unimpaired (CU) individuals. Co-occurring gut microbes show differential abundance across AD-related groups (AD vs CU, amyloid status+ vs amyloid status-, and apolipoprotein E (APOE) ε4 status+ vs APOE ε4 status-). Gut microbiome composition also differs between people with AD dementia and CU individuals in a larger validation cohort. Differentially abundant gut microbiome composition and function between AD and CU groups are correlated with cerebrospinal fluid biomarkers for AD and related pathologies.\n\nGut microbiome compositional and functional features associate with Alzheimer's disease pathology.", "token_count": 464, "char_count": 1878, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5168, "quality_score": 0.7584, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:05.822425", "source": { "split": "train_shard_00001", "doc_id": 4931 }, "chunk_id": "train_shard_00001_4931_0", "global_id": 12628 }, { "text": "A chemically synthesized short-chain peptide composed of six leucine and eight lysine (6K8L) residues was demonstrated to be biocidal against several foodborne organisms including Escherichia coli O157:H7, Listeria monocytogenes, Pseudomonas fluorescens, and Kluyveromyces marxianus suspended in phosphate buffer at concentrations of 5 to 50 microg/ml. All strains were reduced by 3 log10 CFU/ml within 10 min at peptide concentrations of <10 microg/ml. The peptide reduced by 3 log10 CFU/ml E. coli O157:H7 counts in apple juice and was active over the pH range of 3.5 to 7. Peptide concentrations of 100 microg/ml inhibited the aerobic and anaerobic microorganisms present in meat exudate liquid. However, the peptide was not effective against E. coli O157:H7 in skim milk at concentrations up to 100 microg/ml.\n\nAntimicrobial activity of a 14-residue synthetic peptide against foodborne microorganisms.", "token_count": 296, "char_count": 905, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6591, "quality_score": 0.8295, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:06.389560", "source": { "split": "train_shard_00001", "doc_id": 4932 }, "chunk_id": "train_shard_00001_4932_0", "global_id": 12629 }, { "text": "

Background

The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) has emerged as a serious public health problem worldwide, and the data on the fecal carriage of CRE strains in hospitalized children remain limited. This study aimed to investigate the molecular characteristics of intestinal colonization of CRE in hospitalized children in Shandong, China.

Methods

A retrospective study was conducted from August to November 2023. Antimicrobial susceptibility testing was performed by the broth microdilution method. Carbapenemase genes, drug resistance genes, and plasmid replicon types were detected using multiplex real-time PCR and whole-genome sequencing. Multilocus sequence typing (MLST) was used to determine the genetic relationships between strains.

Results

A total of 20 CRE isolates were identified from 432 fecal samples, with a fecal carriage rate of 4.6%. The CRE isolates predominantly consisted of Escherichia coli (E. coli, n = 13) and Klebsiella strains (n = 6). CRE isolates showed a high resistance rate of 90-100% to seven β-lactam antibiotics. Resistance rates for other antibiotics such as trimethoprim-sulfamethoxazole, tetracycline, azithromycin, ciprofloxacin, chloramphenicol, nalidixic acid, and streptomycin were 90, 85, 85, 80, 75, 75, and 75%, respectively. CRE isolates showed low resistance to amikacin (20%), and none of the isolates were resistant to tigecycline. Additionally, the multidrug resistance rate of CRE isolates was 95%", "token_count": 497, "char_count": 1546, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:07.046556", "source": { "split": "train_shard_00001", "doc_id": 4933 }, "chunk_id": "train_shard_00001_4933_0", "global_id": 12630 }, { "text": "All CRE strains carried sulfonamide antibiotic and β-lactamase resistance genes, of which the most common β-lactamase resistance genes were bla NDM-1 (n = 9), bla NDM-5 (n = 7) and bla OXA-1 (n = 7). Resistance genes to tetracycline and macrolide antibiotics were also widespread among the strains. The study found that IncFIB and IncFII series plasmids were present in 84 and 42% of the CRE strains, respectively. Additionally, Col, IncFIA, IncC, IncHI2, and IncX series plasmids were also detected. MLST analysis revealed diverse sequence types (STs) among CRE isolates, with ST167 being a common ST among E. coli isolates.

Conclusion

This study revealed bla NDM E. coli were the dominant isolates in fecal samples of hospitalized children in Shandong Province, with a broad multidrug resistance to antibiotics, emphasizing that infection control measures need to be taken to limit the spread of these strains.\n\nFecal carriage and molecular characterization of carbapenem-resistant <i>Enterobacteriaceae</i> from hospitalized children in a tertiary hospital of Shandong, China.", "token_count": 419, "char_count": 1212, "word_count": 160, "semantic_coherence": 1, "information_density": 0.6438, "quality_score": 0.8219, "entities": { "genes": [ "ST167" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:07.668905", "source": { "split": "train_shard_00001", "doc_id": 4933 }, "chunk_id": "train_shard_00001_4933_1", "global_id": 12631 }, { "text": "Sulfonamides are synthetic chemotherapeutic agents that work as competitive inhibitors of the di-hydro-pteroate synthase (DHPS) enzyme, encoded by the folP gene. Resistance to sulfonamides is widespread in the clinical setting and predominantly mediated by plasmid- and integron-borne sul1-3 genes encoding mutant DHPS enzymes that do not bind sulfonamides. In spite of their clinical importance, the genetic origin of sul1-3 genes remains unknown. Here we analyze sul genes and their genetic neighborhoods to uncover sul signature elements that enable the elucidation of their genetic origin. We identify a protein sequence Sul motif associated with sul-encoded proteins, as well as consistent association of a phosphoglucosamine mutase gene (glmM) with the sul2 gene. We identify chromosomal folP genes bearing these genetic markers in two bacterial families: the Rhodobiaceae and the Leptospiraceae. Bayesian phylogenetic inference of FolP/Sul and GlmM protein sequences clearly establishes that sul1-2 and sul3 genes originated as a mobilization of folP genes present in, respectively, the Rhodobiaceae and the Leptospiraceae, and indicate that the Rhodobiaceae folP gene was transferred from the Leptospiraceae. Analysis of %GC content in folP/sul gene sequences supports the phylogenetic inference results and indicates that the emergence of the Sul motif in chromosomally encoded FolP proteins is ancient and considerably predates the clinical introduction of sulfonamides", "token_count": 490, "char_count": 1619, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:08.321424", "source": { "split": "train_shard_00001", "doc_id": 4934 }, "chunk_id": "train_shard_00001_4934_0", "global_id": 12632 }, { "text": "In vitro assays reveal that both the Rhodobiaceae and the Leptospiraceae, but not other related chromosomally encoded FolP proteins confer resistance in a sulfonamide-sensitive Escherichia coli background, indicating that the Sul motif is associated with sulfonamide resistance. Given the absence of any known natural sulfonamides targeting DHPS, these results provide a novel perspective on the emergence of resistance to synthetic chemotherapeutic agents, whereby preexisting resistant variants in the vast bacterial pangenome may be rapidly selected for and disseminated upon the clinical introduction of novel chemotherapeuticals.\n\nOrigin of the Mobile Di-Hydro-Pteroate Synthase Gene Determining Sulfonamide Resistance in Clinical Isolates.", "token_count": 204, "char_count": 773, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7959, "quality_score": 0.898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:08.787443", "source": { "split": "train_shard_00001", "doc_id": 4934 }, "chunk_id": "train_shard_00001_4934_1", "global_id": 12633 }, { "text": "Escherichia coli is a leading contributor to infectious diarrhea and child mortality worldwide, but it remains unknown how alterations in the gut microbiome vary for distinct E. coli pathotype infections and whether these signatures can be used for diagnostic purposes. Further, the majority of enteric diarrheal infections are not diagnosed with respect to their etiological agent(s) due to technical challenges. To address these issues, we devised a novel approach that combined traditional, isolate-based and molecular-biology techniques with metagenomics analysis of stool samples and epidemiological data. Application of this pipeline to children enrolled in a case-control study of diarrhea in Ecuador showed that, in about half of the cases where an E. coli pathotype was detected by culture and PCR, E. coli was likely not the causative agent based on the metagenome-derived low relative abundance, the level of clonality, and/or the virulence gene content. Our results also showed that diffuse adherent E. coli (DAEC), a pathotype that is generally underrepresented in previous studies of diarrhea and thus, thought not to be highly virulent, caused several small-scale diarrheal outbreaks across a rural to urban gradient in Ecuador. DAEC infections were uniquely accompanied by coelution of large amounts of human DNA and conferred significant shifts in the gut microbiome composition relative to controls or infections caused by other E. coli pathotypes. Our study shows that diarrheal infections can be efficiently diagnosed for their etiological agent and categorized based on their effects on the gut microbiome using metagenomic tools, which opens new possibilities for diagnostics and treatment.IMPORTANCEE. coli infectious diarrhea is an important contributor to child mortality worldwide. However, diagnosing and thus treating E. coli infections remain challenging due to technical and other reasons associated with the limitations of the traditional culture-based techniques and the requirement to apply Koch's postulates", "token_count": 503, "char_count": 2104, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5946, "quality_score": 0.7973, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:09.440940", "source": { "split": "train_shard_00001", "doc_id": 4935 }, "chunk_id": "train_shard_00001_4935_0", "global_id": 12634 }, { "text": "In this study, we integrated traditional microbiology techniques with metagenomics and epidemiological data in order to identify cases of diarrhea where E. coli was most likely the causative disease agent and evaluate specific signatures in the disease-state gut microbiome that distinguish between diffuse adherent, enterotoxigenic, and enteropathogenic E. coli pathotypes. Therefore, our methodology and results should be highly relevant for diagnosing and treating diarrheal infections and have important applications in public health.\n\nMetagenomic Signatures of Gut Infections Caused by Different Escherichia coli Pathotypes.", "token_count": 161, "char_count": 650, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7952, "quality_score": 0.8976, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:09.879549", "source": { "split": "train_shard_00001", "doc_id": 4935 }, "chunk_id": "train_shard_00001_4935_1", "global_id": 12635 }, { "text": "The genome characterization of the Lactiplantibacillus plantarum strain UTNGt2, isolated from wild copoazu or white cacao (Theobroma grandiflorum), is described. A total of 31 contigs is assembled with a total length of 3,264,448 bases, with all contigs matching the core genome of different groups in the database. The genome size is 3,540,752 bases with GC content of 44.53% and the genome repeat sequences constitute around 457,386 bases of the assembly. The UTNGt2 matches the Lactiplantibacillus plantarum genome with 99% identity. The genome contains 3115 genes, 3052 protein-coding genes, assigned with the EggNOG database. On the basis of the results, 745 proteins are classified with an unknown function, from which 128 proteins have no match in the BLASTN database. It also contains 57 tRNAs, 5 copies of 5S rRNA, and 1 copy of tmRNA. Based on gene prediction and annotation results, 9.4% of proteins are involved in carbohydrate transport and metabolism and 8.46% in transcription, 2.36% are responsible for defense mechanisms, 0.5% are responsible for the biosynthesis of secondary metabolites, transport, and catabolism, while 25.11% have an unknown function. The genome revealed the presence of genes involved in riboflavin and folate production, the presence of CRISPR/Cas genes, phage sequences, the absence of acquired antibiotics resistance genes, virulence, and pathogenic factors, suggesting that UTNGt2 is a safe strain. Its highly antimicrobial capacity is related to the presence of two bacteriocin clusters (class IIc) of the sactipeptide class (contig 4) and plantaricin E class (contig 22), as detected by the BAGEL 4 webserver", "token_count": 509, "char_count": 1674, "word_count": 250, "semantic_coherence": 1, "information_density": 0.62, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:10.511559", "source": { "split": "train_shard_00001", "doc_id": 4936 }, "chunk_id": "train_shard_00001_4936_0", "global_id": 12636 }, { "text": "Several RiPP-like peptides (non-bactericidal ribosomally produced and post-translationally modified peptides), polyketides (PKs), and terpenes were predicted. Whole-genome sequencing analysis revealed that the UTNGt2 strain has diverse bacteriocins with a high inhibitory capacity, thus it is a bacteriocinogenic strain. Considering the safety profile, UTNGt2 is a nonpathogenic, nonvirulent strain with valuable biotechnological traits and can be further exploited for its probiotic and antimicrobial potential in the food industry or as a potential producer strain of antimicrobial peptides as an alternative to conventional antibiotics.\n\nGenome Characterization of Lactiplantibacillus plantarum Strain UTNGt2 Originated from Theobroma grandiflorum (White Cacao) of Ecuadorian Amazon: Antimicrobial Peptides from Safety to Potential Applications.", "token_count": 238, "char_count": 862, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7429, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:10.982939", "source": { "split": "train_shard_00001", "doc_id": 4936 }, "chunk_id": "train_shard_00001_4936_1", "global_id": 12637 }, { "text": "The beta-galactosidase from the Antarctic gram-negative bacterium Pseudoalteromonas haloplanktis TAE 79 was purified to homogeneity. The nucleotide sequence and the NH(2)-terminal amino acid sequence of the purified enzyme indicate that the beta-galactosidase subunit is composed of 1,038 amino acids with a calculated M(r) of 118,068. This beta-galactosidase shares structural properties with Escherichia coli beta-galactosidase (comparable subunit mass, 51% amino sequence identity, conservation of amino acid residues involved in catalysis, similar optimal pH value, and requirement for divalent metal ions) but is characterized by a higher catalytic efficiency on synthetic and natural substrates and by a shift of apparent optimum activity toward low temperatures and lower thermal stability. The enzyme also differs by a higher pI (7.8) and by specific thermodynamic activation parameters. P. haloplanktis beta-galactosidase was expressed in E. coli, and the recombinant enzyme displays properties identical to those of the wild-type enzyme. Heat-induced unfolding monitored by intrinsic fluorescence spectroscopy showed lower melting point values for both P. haloplanktis wild-type and recombinant beta-galactosidase compared to the mesophilic enzyme. Assays of lactose hydrolysis in milk demonstrate that P. haloplanktis beta-galactosidase can outperform the current commercial beta-galactosidase from Kluyveromyces marxianus var. lactis, suggesting that the cold-adapted beta-galactosidase could be used to hydrolyze lactose in dairy products processed in refrigerated plants.\n\nCold-adapted beta-galactosidase from the Antarctic psychrophile Pseudoalteromonas haloplanktis.", "token_count": 471, "char_count": 1682, "word_count": 216, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:11.627764", "source": { "split": "train_shard_00001", "doc_id": 4937 }, "chunk_id": "train_shard_00001_4937_0", "global_id": 12638 }, { "text": "Pathogens continuously adapt to changing host environments where variation in their virulence and antigenicity is critical to their long-term evolutionary success. The emergence of novel variants is accelerated in microbial mutator strains (mutators) deficient in DNA repair genes, most often from mismatch repair and oxidised-guanine repair systems (MMR and OG respectively). Bacterial MMR/OG mutants are abundant in clinical samples and show increased adaptive potential in experimental infection models, yet the role of mutators in the epidemiology and evolution of infectious disease is not well understood. Here we investigated the role of mutation rate dynamics in the evolution of a broad host range pathogen, Streptococcus iniae , using a set of 80 strains isolated globally over 40 years. We have resolved phylogenetic relationships using non-recombinant core genome variants, measured in vivo mutation rates by fluctuation analysis, identified variation in major MMR/OG genes and their regulatory regions, and phenotyped the major traits determining virulence in streptococci. We found that both mutation rate and MMR/OG genotype are remarkably conserved within phylogenetic clades but significantly differ between major phylogenetic lineages. Further, variation in MMR/OG loci correlates with occurrence of atypical virulence-associated phenotypes, infection in atypical hosts (mammals), and atypical tissue of a vaccinated primary hosts (barramundi bone). These findings suggest that mutators are likely to facilitate adaptations preceding major diversification events, and may promote emergence of variation permitting colonisation of a novel host tissue, novel host taxa (host jumps), and immune-escape in the vaccinated host.\n\nEvolutionary epidemiology ofStreptococcus iniae: linking mutation rate dynamics with adaptation to novel immunological landscapes", "token_count": 439, "char_count": 1878, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6392, "quality_score": 0.8196, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:12.261276", "source": { "split": "train_shard_00001", "doc_id": 4938 }, "chunk_id": "train_shard_00001_4938_0", "global_id": 12639 }, { "text": "

Background

Eukaryotes display remarkable genome plasticity, which can include supernumerary chromosomes that differ markedly from the core chromosomes. Despite the widespread occurrence of supernumerary chromosomes in fungi, their origin, relation to the core genome and the reason for their divergent characteristics are still largely unknown. The complexity of genome assembly due to the presence of repetitive DNA partially accounts for this.

Results

Here we use single-molecule real-time (SMRT) sequencing to assemble the genome of a prominent fungal wheat pathogen, Fusarium poae, including at least one supernumerary chromosome. The core genome contains limited transposable elements (TEs) and no gene duplications, while the supernumerary genome holds up to 25 % TEs and multiple gene duplications. The core genome shows all hallmarks of repeat-induced point mutation (RIP), a defense mechanism against TEs, specific for fungi. The absence of RIP on the supernumerary genome accounts for the differences between the two (sub)genomes, and results in a functional crosstalk between them. The supernumerary genome is a reservoir for TEs that migrate to the core genome, and even large blocks of supernumerary sequence (>200 kb) have recently translocated to the core. Vice versa, the supernumerary genome acts as a refuge for genes that are duplicated from the core genome.

Conclusions

For the first time, a mechanism was determined that explains the differences that exist between the core and supernumerary genome in fungi. Different biology rather than origin was shown to be responsible. A \"living apart together\" crosstalk exists between the core and supernumerary genome, accelerating chromosomal and organismal evolution.\n\nLiving apart together: crosstalk between the core and supernumerary genomes in a fungal plant pathogen.", "token_count": 451, "char_count": 1859, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5817, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:12.934751", "source": { "split": "train_shard_00001", "doc_id": 4939 }, "chunk_id": "train_shard_00001_4939_0", "global_id": 12640 }, { "text": "Dissolved oxygen concentration-controlled feeding of substrate into Kluyveromyces fragilis culture.", "token_count": 22, "char_count": 99, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:13.312039", "source": { "split": "train_shard_00001", "doc_id": 4940 }, "chunk_id": "train_shard_00001_4940_0", "global_id": 12641 }, { "text": "

Background

Transplant recipients are at high risk for infections. However, donor-recipient transmission of multidrug-resistant organisms (MDROs) remains mostly unaddressed in the protocols of pre-transplant infection and colonization screening. Vancomycin-resistant enterococci (VRE) are MDROs that colonize the gastrointestinal tract and are associated with a significant burden of disease. Besides the high mortality of invasive VRE infections, chronic colonization leads to costly isolation measures in the hospital setting. Whereas most post-transplantation VRE infections are endogenous and thus preceded by colonization of the recipient, conclusive evidence of VRE transmission via allograft in the context of intestinal transplantation is lacking.

Case presentation

We describe a donor-derived VRE infection after intestinal transplantation including small bowel and right hemicolon. The recipient, a 54-year old male with history of mesenteric ischemia and small bowel perforation due to generalized atherosclerosis and chronic stenosis of the celiac trunk and the superior mesenteric artery, developed an intra-abdominal infection and bloodstream infection after transplantation. VRE isolates recovered from the patient as well as from the allograft prior to transplantation were analyzed via whole genome sequencing. Isolates showed to be genetically identical, thus confirming the transmission from donor to recipient.

Conclusions

This case underlines the relevance of donor-recipient VRE transmission and invasive infection in the context of intestinal transplantation, highlighting the need for preoperative MDRO screening that facilitates the prompt and effective treatment of possible infections as well as the timely establishment of contact precautions to prevent further spread.\n\nDonor-derived vancomycin-resistant enterococci transmission and bloodstream infection after intestinal transplantation.", "token_count": 458, "char_count": 1939, "word_count": 242, "semantic_coherence": 1, "information_density": 0.5785, "quality_score": 0.7893, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:13.991757", "source": { "split": "train_shard_00001", "doc_id": 4941 }, "chunk_id": "train_shard_00001_4941_0", "global_id": 12642 }, { "text": "A selective and differential solid medium for the specific detection of some common yeasts frequently causing spoilage in intermediate moisture foods is described. The principle of the method is based on the detection of two enzymes, beta-glucosidase and beta-galactosidase, using the chromogenic substrates salmon-Gluc and X-Gal. Over 140 yeasts and bacteria were tested, and Debaryomyces hansenii and Kluyveromyces marxianus strains produced salmon and dark blue colonies, respectively, thus permitting their clear discrimination from other yeasts common in intermediate moisture foods. The medium was very satisfactory when intermediate moisture foods were tested.\n\nA chromogenic medium for the detection of yeasts with beta-galactosidase and beta-glucosidase activities from intermediate moisture foods.", "token_count": 185, "char_count": 807, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6296, "quality_score": 0.8148, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:14.465103", "source": { "split": "train_shard_00001", "doc_id": 4942 }, "chunk_id": "train_shard_00001_4942_0", "global_id": 12643 }, { "text": "The aim of this paper was to evaluate the suitability of Siran, a highly porous mineral carrier, to immobilization of Kluyveromyces fragilis--directly lactose-fermenting yeast. The ethanol concentration in the post-fermentation mash was 4.7-5.8% v/v and was less advantageous than in previous experiments with calcium alginate (on average 6.04% v/v in 9 sequential fermentations). The introduction of another yeast strain to the experiment--S. cerevisiae--enhanced the efficiency of the lactose mash fermentation. The ethanol concentration in the mash in sequential series of the process increased on average to 6.14% v/v.\n\nThe characteristics of fermentation abilities of K. fragilis immobilized on Siran.", "token_count": 193, "char_count": 706, "word_count": 99, "semantic_coherence": 1, "information_density": 0.6465, "quality_score": 0.8232, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:14.915844", "source": { "split": "train_shard_00001", "doc_id": 4943 }, "chunk_id": "train_shard_00001_4943_0", "global_id": 12644 }, { "text": "In February 2023, 52 cases of gastrointestinal illness were reported in customers of Takeaway A, South Wales. Shigella flexneri serotype 2a was the causative organism. An outbreak investigation was conducted to determine the extent and vehicle of the outbreak.Following descriptive summary and environmental investigations, a case-control study was completed. Participants completed a telephone questionnaire on food, travel, and environmental exposures. A multivariable logistic regression model was built, including exposures with p-values < 0.2 and interactions identified on stratified analysis. Staff faecal samples were screened for Shigella sp.Thirty-one cases and 29 controls were included in the study. Eighty-seven per cent of cases and 76% of controls ate from Takeaway A on 10 February 2023. Coleslaw was the main factor associated with illness (aOR: 200, 95% CI: 12-3220) and an interaction with cabbage was identified (aOR: 886, 95% CI: 26-30034). Shigella sp. were not detected in any staff samples.Coleslaw was the most likely vehicle. Though the contamination route is unknown, a food handler is the most likely source. This large outbreak differs from recent European outbreaks, which primarily have been associated with sexual transmission. Although uncommon in the UK, S. flexneri should be considered as a cause of foodborne outbreaks.\n\nLarge <i>Shigella flexneri</i> outbreak linked to a takeaway, South Wales: a case-control study.", "token_count": 415, "char_count": 1501, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6635, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:15.531818", "source": { "split": "train_shard_00001", "doc_id": 4944 }, "chunk_id": "train_shard_00001_4944_0", "global_id": 12645 }, { "text": "Despite the importance of horizontal gene transfer for rapid bacterial evolution, reliable assignment of mobile genetic elements to their microbial hosts in natural communities such as the human gut microbiota is lacking. We used high-throughput chromosomal conformation capture coupled with probabilistic modelling of experimental noise to resolve 88 strain-level metagenome-assembled genomes of distal gut bacteria from two participants, including 12,251 accessory elements. Comparisons of two samples collected 10 years apart for each of the participants revealed extensive in situ exchange of accessory elements as well as evidence of adaptive evolution in core genomes. Accessory elements were predominantly promiscuous and prevalent in the distal gut metagenomes of 218 adult individuals. This research provides a foundation and approach for studying microbial evolution in natural environments.\n\nTracking microbial evolution in the human gut using Hi-C reveals extensive horizontal gene transfer, persistence and adaptation.", "token_count": 210, "char_count": 1031, "word_count": 140, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:16.002209", "source": { "split": "train_shard_00001", "doc_id": 4945 }, "chunk_id": "train_shard_00001_4945_0", "global_id": 12646 }, { "text": "

Background

Nitrogen fixing bacteria isolated from hot arid areas in Asia, Africa and America but from diverse leguminous plants have been recently identified as belonging to a possible new species of Ensifer (Sinorhizobium). In this study, 6 strains belonging to this new clade were compared with Ensifer species at the genome-wide level. Their capacities to utilize various carbon sources and to establish a symbiotic interaction with several leguminous plants were examined.

Results

Draft genomes of selected strains isolated from Morocco (Merzouga desert), Mexico (Baja California) as well as from India (Thar desert) were produced. Genome based species delineation tools demonstrated that they belong to a new species of Ensifer. Comparison of its core genome with those of E. meliloti, E. medicae and E. fredii enabled the identification of a species conserved gene set. Predicted functions of associated proteins and pathway reconstruction revealed notably the presence of transport systems for octopine/nopaline and inositol phosphates. Phenotypic characterization of this new desert rhizobium species showed that it was capable to utilize malonate, to grow at 48 °C or under high pH while NaCl tolerance levels were comparable to other Ensifer species. Analysis of accessory genomes and plasmid profiling demonstrated the presence of large plasmids that varied in size from strain to strain. As symbiotic functions were found in the accessory genomes, the differences in symbiotic interactions between strains may be well related to the difference in plasmid content that could explain the different legumes with which they can develop the symbiosis.

Conclusions

The genomic analysis performed here confirms that the selected rhizobial strains isolated from desert regions in three continents belong to a new species. As until now only recovered from such harsh environment, we propose to name it Ensifer aridi. The presented genomic data offers a good basis to explore adaptations and functionalities that enable them to adapt to alkalinity, low water potential, salt and high temperature stresses", "token_count": 489, "char_count": 2128, "word_count": 311, "semantic_coherence": 1, "information_density": 0.6174, "quality_score": 0.8087, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:16.653154", "source": { "split": "train_shard_00001", "doc_id": 4946 }, "chunk_id": "train_shard_00001_4946_0", "global_id": 12647 }, { "text": "Finally, given the original phylogeographic distribution and the different hosts with which it can develop a beneficial symbiotic interaction, Ensifer aridi may provide new biotechnological opportunities for degraded land restoration initiatives in the future.\n\nGenomic characterization of Ensifer aridi, a proposed new species of nitrogen-fixing rhizobium recovered from Asian, African and American deserts.", "token_count": 87, "char_count": 408, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8679, "quality_score": 0.934, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:17.029020", "source": { "split": "train_shard_00001", "doc_id": 4946 }, "chunk_id": "train_shard_00001_4946_1", "global_id": 12648 }, { "text": "The insect-parasitic nematode, Steinernema feltiae Filipjev strain 42, was reared in liquid culture along with its bacterial symbiont, Xenorhabdus nematophilus Thomas &Poinar. First-stage juveniles developed into reproducing adults in a maintenance salts medium containing resuspended Xenorhabdus cells and the yeast Kluyveromyces marxianus (Hansen) van der Walt or cholesterol. Cultures with media depths greater than 4 mm required aeration. Nematode populations increased as bacterial density increased. An optimal culture system was obtained when the bacteria and nematodes developed in a semidefined medium containing tryptic soy, yeast extract, and cholesterol and were incubated on a rotary shaker at 25 +/- 1 C. Under these conditions, up to 86% of the final population were infective juveniles.\n\nLiquid Culture of the Entomogenous Nematode Steinernema feltiae with Its Bacterial Symbiont.", "token_count": 249, "char_count": 896, "word_count": 125, "semantic_coherence": 1, "information_density": 0.76, "quality_score": 0.88, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:17.517343", "source": { "split": "train_shard_00001", "doc_id": 4947 }, "chunk_id": "train_shard_00001_4947_0", "global_id": 12649 }, { "text": "Urinary tract infections (UTIs) are among the most common causes of infections worldwide and can be caused by numerous uropathogens. Enterococci are Gram-positive, facultative anaerobic commensal organisms of the gastrointestinal tract that are known uropathogens. Enterococcus spp. has become a leading cause of healthcare associated infections, ranging from endocarditis to UTIs. In recent years, there has been an increase in multidrug resistance due to antibiotic misuse, especially in enterococci. Additionally, infections due to enterococci pose a unique challenge due to their ability to survive in extreme environments, intrinsic antimicrobial resistance, and genomic malleability. Overall, this review aims to highlight the pathogenicity, epidemiology, and treatment recommendations (according to the most recent guidelines) of enterococci.\n\nEnterococcal Urinary Tract Infections: A Review of the Pathogenicity, Epidemiology, and Treatment.", "token_count": 245, "char_count": 963, "word_count": 125, "semantic_coherence": 1, "information_density": 0.688, "quality_score": 0.844, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:17.999653", "source": { "split": "train_shard_00001", "doc_id": 4948 }, "chunk_id": "train_shard_00001_4948_0", "global_id": 12650 }, { "text": "Aeromonas salmonicida is a global distributed Gram-negative teleost pathogen, affecting mainly salmonids in fresh and marine environments. A. salmonicida strains are classified as typical or atypical depending on their origin of isolation and phenotype. Five subspecies have been described, where A. salmonicida subsp. salmonicida is the only typical subspecies, and the subsp. achromogenes, masoucida, smithia, and pectinolytica are considered atypical. Genomic differences between A. salmonicida subsp. salmonicida isolates and their relationship with the current classification have not been explored. Here, we sequenced and compared the complete closed genomes of four virulent strains to elucidate their molecular diversity and pathogenic evolution using the more accurate genomic information so far. Phenotypes, biochemical, and enzymatic profiles were determined. PacBio and MiSeq sequencing platforms were utilized for genome sequencing. Comparative genomics showed that atypical strains belong to the subsp. salmonicida, with 99.55% ± 0.25% identity with each other, and are closely related to typical strains. The typical strain A. salmonicida J223 is closely related to typical strains, with 99.17% identity with the A. salmonicida A449. Genomic differences between atypical and typical strains are strictly related to insertion sequences (ISs) activity. The absence and presence of genes encoding for virulence factors, transcriptional regulators, and non-coding RNAs are the most significant differences between typical and atypical strains that affect their phenotypes. Plasmidome plays an important role in A. salmonicida virulence and genome plasticity", "token_count": 507, "char_count": 1790, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6222, "quality_score": 0.8111, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:18.653581", "source": { "split": "train_shard_00001", "doc_id": 4949 }, "chunk_id": "train_shard_00001_4949_0", "global_id": 12651 }, { "text": "Here, we determined that typical strains harbor a larger number of plasmids and virulence-related genes that contribute to its acute virulence. In contrast, atypical strains harbor a single, large plasmid and a smaller number of virulence genes, reflected by their less acute virulence and chronic infection. The relationship between phenotype and A. salmonicida subspecies' taxonomy is not evident. Comparative genomic analysis based on completed genomes revealed that the subspecies classification is more of a reflection of the ecological niche occupied by bacteria than their divergences at the genomic level except for their accessory genome.\n\nComparative Genomics of Typical and Atypical Aeromonas salmonicida Complete Genomes Revealed New Insights into Pathogenesis Evolution.", "token_count": 195, "char_count": 797, "word_count": 110, "semantic_coherence": 1, "information_density": 0.7091, "quality_score": 0.8545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:19.102649", "source": { "split": "train_shard_00001", "doc_id": 4949 }, "chunk_id": "train_shard_00001_4949_1", "global_id": 12652 }, { "text": "Background:Salmonella Typhimurium is a major zoonotic pathogen, in which type 1 fimbriae play a crucial role in intestinal colonization and immune modulation. This study aimed to improve the protective immunity of a previously developed growth-deficient strain-a double auxotroph for D-glutamate and D-alanine-by engineering the inducible expression of type 1 fimbriae. Methods: PtetA-driven expression of the fim operon was achieved by λ-Red mutagenesis. fimA expression was quantified by qRT-PCR, and fimbriation visualized by transmission electron microscopy. Adhesive properties were evaluated through FimH sequence analysis, yeast agglutination, mannose-binding/inhibition assays, and HT-29 cell adherence. BALB/c mice were immunized orogastrically with IRTA ΔΔΔ or IRTA ΔΔΔ PtetA::fim. Safety and immunogenicity were assessed by clinical monitoring, bacterial load, fecal shedding, ELISA tests, and adhesion/blocking assays using fecal extracts. Protection was evaluated after challenging with wild-type and heterologous strains. Results: IRTA ΔΔΔ PtetA::fim showed robust fimA expression, dense fimbrial coverage, a marked mannose-sensitive adhesive phenotype and enhanced HT-29 attachment. Fimbrial overexpression did not alter intestinal colonization or translocation to mesenteric lymph nodes (mLNs). Immunization elicited a mixed IgG1/IgG2a, significantly increased IgA and IgG against type 1 fimbriae-expressing Salmonella, and enhanced the ability of fecal extracts to inhibit the adherence of wild-type strains", "token_count": 515, "char_count": 1648, "word_count": 196, "semantic_coherence": 1, "information_density": 0.7245, "quality_score": 0.8622, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:19.769965", "source": { "split": "train_shard_00001", "doc_id": 4950 }, "chunk_id": "train_shard_00001_4950_0", "global_id": 12653 }, { "text": "Upon challenge (IRTA wild-type/20220258), IRTA ΔΔΔ PtetA::fim reduced infection burden in the cecum (-1.46/1.47-log), large intestine (-1.35/2.17-log), mLNs (-1.32/0.98-log) and systemic organs more effectively than IRTA ΔΔΔ. Conclusions: Inducible expression of type 1 fimbriae enhances mucosal immunity and protection, supporting their inclusion in next-generation Salmonella vaccines. Future work should assess cross-protection and optimize FimH-mediated targeting for mucosal delivery.\n\nEngineering and Evaluation of a Live-Attenuated Vaccine Candidate with Enhanced Type 1 Fimbriae Expression to Optimize Protection Against <i>Salmonella</i> Typhimurium.", "token_count": 251, "char_count": 710, "word_count": 78, "semantic_coherence": 1, "information_density": 0.8462, "quality_score": 0.9231, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:20.262018", "source": { "split": "train_shard_00001", "doc_id": 4950 }, "chunk_id": "train_shard_00001_4950_1", "global_id": 12654 }, { "text": "Selected endophytic fungi have been report to be inulin degraders to produce fructose or other oligosaccharides. In this study, the Aspergillus sp. producing inulinase were isolated from selected plant species at Serdang area in Malaysia. Fungal isolates were screened solely based on inulin degrading enzymes production and two isolates named Asf1 and Onf1 were selected as the best inulinase enzyme producers. Genomic DNA of these two isolates were extracted and amplified by polymerase chain reaction (PCR). A 1,341 bp DNA fragment containing inulinase gene was successfully amplified from Asf1 fungal isolate and was named as inu2 gene in this study. Based on the morphological characteristics, rDNA and neighbour-joining phylogenetic analysis, Asf1 fungal isolate could display closely-related to the genus of Aspergillus. The complete sequence designated Asf1 Inu2 gene was successfully obtained via rapid-amplification of cDNA ends-polymerase chain reaction (RACE-PCR). A 2.3 kb DNA fragment encoding endoinulinase, inu2, from Asf1 fungal isolate includes an open reading frame of 1,552 bp with calculated molecular weight of 55,954.1 Da and signal peptide sequence of 23 amino acids. The deduced amino acid sequence of the Asf1 inu2 displayed 97, 96, 69 and 22% identities to that of A. ficuum inu2, A. niger inuB, P. purpurogenum and K. marxianus, respectively. Phylogenetic analysis showed that fungal endo- and exo-inulinases have indepently evolved with the respective hydrolytic activities toward terminal and internal β-(2 → 1)-fructofuranosidic linkages in inulin.\n\nMolecular cloning and sequence analysis of an inulinase gene from an Aspergillus sp", "token_count": 486, "char_count": 1673, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6189, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:21.277304", "source": { "split": "train_shard_00001", "doc_id": 4951 }, "chunk_id": "train_shard_00001_4951_0", "global_id": 12655 }, { "text": "A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.\n\nDetailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach.", "token_count": 324, "char_count": 1315, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [ "ISRCTN53023014" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:21.848553", "source": { "split": "train_shard_00001", "doc_id": 4952 }, "chunk_id": "train_shard_00001_4952_0", "global_id": 12656 }, { "text": "

Objectives

Staphylococcus haemolyticus is an emerging cause of nosocomial infections, primarily affecting immunocompromised patients. A comparative genomic analysis was performed on clinical S. haemolyticus isolates to investigate their genetic relationship and explore the coding sequences with respect to antimicrobial resistance determinants and putative hospital adaptation.

Methods

Whole-genome sequencing was performed on 134 isolates of S. haemolyticus from geographically diverse origins (Belgium, 2; Germany, 10; Japan, 13; Norway, 54; Spain, 2; Switzerland, 43; UK, 9; USA, 1). Each genome was individually assembled. Protein coding sequences (CDSs) were predicted and homologous genes were categorized into three types: Type I, core genes, homologues present in all strains; Type II, unique core genes, homologues shared by only a subgroup of strains; and Type III, unique genes, strain-specific CDSs. The phylogenetic relationship between the isolates was built from variable sites in the form of single nucleotide polymorphisms (SNPs) in the core genome and used to construct a maximum likelihood phylogeny.

Results

SNPs in the genome core regions divided the isolates into one major group of 126 isolates and one minor group of isolates with highly diverse genomes. The major group was further subdivided into seven clades (A-G), of which four (A-D) encompassed isolates only from Europe. Antimicrobial multiresistance was observed in 77.7% of the collection. High levels of homologous recombination were detected in genes involved in adherence, staphylococcal host adaptation and bacterial cell communication.

Conclusions

The presence of several successful and highly resistant clones underlines the adaptive potential of this opportunistic pathogen.\n\nWhole-genome sequencing reveals clonal expansion of multiresistant Staphylococcus haemolyticus in European hospitals.", "token_count": 498, "char_count": 1913, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:22.500035", "source": { "split": "train_shard_00001", "doc_id": 4953 }, "chunk_id": "train_shard_00001_4953_0", "global_id": 12657 }, { "text": "

Background

The genetic diversity in Australian populations of Xanthomonas species associated with bacterial leaf spot in tomato, capsicum and chilli were compared to worldwide bacterial populations. The aim of this study was to confirm the identities of these Australian Xanthomonas species and classify them in comparison to overseas isolates. Analysis of whole genome sequence allows for the investigation of bacterial population structure, pathogenicity and gene exchange, resulting in better management strategies and biosecurity.

Results

Phylogenetic analysis of the core genome alignments and SNP data grouped strains in distinct clades. Patterns observed in average nucleotide identity, pan genome structure, effector and carbohydrate active enzyme profiles reflected the whole genome phylogeny and highlight taxonomic issues in X. perforans and X. euvesicatoria. Circular sequences with similarity to previously characterised plasmids were identified, and plasmids of similar sizes were isolated. Potential false positive and false negative plasmid assemblies were discussed. Effector patterns that may influence virulence on host plant species were analysed in pathogenic and non-pathogenic xanthomonads.

Conclusions

The phylogeny presented here confirmed X. vesicatoria, X. arboricola, X. euvesicatoria and X. perforans and a clade of an uncharacterised Xanthomonas species shown to be genetically distinct from all other strains of this study. The taxonomic status of X. perforans and X. euvesicatoria as one species is discussed in relation to whole genome phylogeny and phenotypic traits. The patterns evident in enzyme and plasmid profiles indicate worldwide exchange of genetic material with the potential to introduce new virulence elements into local bacterial populations.\n\nGenomic sequence analysis reveals diversity of Australian Xanthomonas species associated with bacterial leaf spot of tomato, capsicum and chilli.", "token_count": 452, "char_count": 1959, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:23.152866", "source": { "split": "train_shard_00001", "doc_id": 4954 }, "chunk_id": "train_shard_00001_4954_0", "global_id": 12658 }, { "text": "The rapid dissemination of carbapenemase-producing Enterobacterales (CPE) is a major public health concern. The role that the aquatic environment plays in this dissemination is underexplored. This study aimed to examine seawater as a reservoir for CPE. Seawater sampling took place at a bathing site throughout the 2017 bathing season. Each 30 L sample (n = 6) was filtered using the CapE filtration system. Wastewater samples (200 mL) (pre-treatment (n = 3) and post-treatment (n = 3)) were obtained from a nearby secondary wastewater treatment plant, during the same time period. All samples were examined for CPE. Whole genome sequencing of confirmed CPE was carried out using Illumina sequencing. Isolate genomes were hosted in corresponding BIGSdb databases and analyses were performed using multiple web-based tools. CPE was detected in 2/6 seawater samples. It was not detected in any wastewater samples. OXA-48-like-producing ST131 Escherichia coli (Ec_BM707) was isolated from a seawater sample collected in May 2017 and OXA-48-like-producing ST101 Klebsiella pneumoniae (Kp_BM758) was isolated from a seawater sample collected in August 2017. The genomes of the environmental isolates were compared to a collection of previously described Irish clinical OXA-48-like-producing Enterobacterales (n = 105). Ec_BM707 and Kp_BM758 harboured blaOXA-48 on similar mobile genetic elements to those identified in the clinical collection (pOXA-48 fragment in Ec_BM707 and IncL(pOXA-48) plasmid in Kp_BM758). Genetic similarities were observed between Ec_BM707 and several of the clinical ST131 E", "token_count": 510, "char_count": 1606, "word_count": 230, "semantic_coherence": 1, "information_density": 0.6261, "quality_score": 0.813, "entities": { "genes": [ "ST131", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:23.811384", "source": { "split": "train_shard_00001", "doc_id": 4955 }, "chunk_id": "train_shard_00001_4955_0", "global_id": 12659 }, { "text": "coli, with allele matches at up to 98.2% of 2513 core genome multilocus sequence type (cgMLST) loci. In contrast, Kp_BM758 and the 34 clinical K. pneumoniae were genetically distant. The source of the CPE at this site was not identified. The detection of OXA-48-like-producing ST131 E. coli and OXA-48-like-producing ST101 K. pneumoniae in Irish recreational water is a concern. The potential for contamination of the aquatic environment to contribute to dissemination of CPE in Europe warrants further study.\n\nDetection of OXA-48-like-producing Enterobacterales in Irish recreational water.", "token_count": 187, "char_count": 591, "word_count": 86, "semantic_coherence": 1, "information_density": 0.7093, "quality_score": 0.8547, "entities": { "genes": [ "ST131", "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:24.260267", "source": { "split": "train_shard_00001", "doc_id": 4955 }, "chunk_id": "train_shard_00001_4955_1", "global_id": 12660 }, { "text": "

Background

Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles.

Methods

We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision.

Results

The isolate's genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences.

Conclusions

This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X.", "token_count": 493, "char_count": 1767, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6266, "quality_score": 0.8133, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:24.930202", "source": { "split": "train_shard_00001", "doc_id": 4956 }, "chunk_id": "train_shard_00001_4956_0", "global_id": 12661 }, { "text": "In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes.", "token_count": 25, "char_count": 86, "word_count": 13, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:25.319328", "source": { "split": "train_shard_00001", "doc_id": 4956 }, "chunk_id": "train_shard_00001_4956_1", "global_id": 12662 }, { "text": "In November 2019, an outbreak of Shiga toxin-producing Escherichia coli O157:H7 was detected in South Yorkshire, England. Initial investigations established consumption of milk from a local dairy as a common exposure. A sample of pasteurised milk tested the next day failed the phosphatase test, indicating contamination of the pasteurised milk by unpasteurised (raw) milk. The dairy owner agreed to immediately cease production and initiate a recall. Inspection of the pasteuriser revealed a damaged seal on the flow divert valve. Ultimately, there were 21 confirmed cases linked to the outbreak, of which 11 (52%) were female, and 12/21 (57%) were either <15 or >65 years of age. Twelve (57%) patients were treated in hospital, and three cases developed haemolytic uraemic syndrome. Although the outbreak strain was not detected in the milk samples, it was detected in faecal samples from the cattle on the farm. Outbreaks of gastrointestinal disease caused by milk pasteurisation failures are rare in the UK. However, such outbreaks are a major public health concern as, unlike unpasteurised milk, pasteurised milk is marketed as 'safe to drink' and sold to a larger, and more dispersed, population. The rapid, co-ordinated multi-agency investigation initiated in response to this outbreak undoubtedly prevented further cases.\n\nOutbreak of STEC O157:H7 linked to a milk pasteurisation failure at a dairy farm in England, 2019.", "token_count": 373, "char_count": 1436, "word_count": 219, "semantic_coherence": 1, "information_density": 0.653, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:25.935040", "source": { "split": "train_shard_00001", "doc_id": 4957 }, "chunk_id": "train_shard_00001_4957_0", "global_id": 12663 }, { "text": "Abstract

Background: The COVID-19 pandemic in 2020 exerted immense pressure on health care systems worldwide, causing substantial resources to be diverted to respond to the pandemic. These changes raise the concern about the potential for reduction in adherence to long-established measures in the prevention of healthcare-associated infections (HAI). Enterococcus species account for most of human enterococcal HAI and multidrug-resistant infections and have become a major threat to modern public health. We examine the rise in the number of vancomycin resistant E. faecium blood stream and urinary tract infections in a COVID-19 department during an epidemiologic outbreak investigation to detect and eliminate nosocomial clusters of the bacteria. Methods: Strain identification was performed by classical isolation and biochemical and cultivation methods. Antibiotic testing results were interpreted according to European committee on antimicrobial susceptibility testing (EUCAST) guidelines. Six isolated samples underwent whole genome sequencing (WGS) during the outbreak investigation. Isolate relatedness was determined using core genome multilocus sequence typing.Results: WGS revealed two genotypically distinct VRE clusters, one of which had genetically closely related patient and environmental isolates. The cluster was terminated by enhanced infection control strategies.Conclusions: This study provides the first description of an outbreak caused by vanA-ST17 E. faecium strains among COVID-19 patients in central Europe, and the first description of an outbreak caused by vanB-ST117 and vanA-ST17 E. faecium strains in Slovakia. This study can help raise awareness about the need for strict adherence to infection control measures and the implementation of rational antimicrobial stewardship as a routine part of COVID-19 management.

", "token_count": 467, "char_count": 1992, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6773, "quality_score": 0.8386, "entities": { "genes": [ "ST17", "ST117" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:26.582615", "source": { "split": "train_shard_00001", "doc_id": 4958 }, "chunk_id": "train_shard_00001_4958_0", "global_id": 12664 }, { "text": "First Report of Nosocomial Outbreak of Vancomycin-Resistant Enterococcus Faecium Infection Among COVID-19 Patients Hospitalized in a Non-Intensive Care Unit Ward in Central Europe", "token_count": 47, "char_count": 179, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:26.944370", "source": { "split": "train_shard_00001", "doc_id": 4958 }, "chunk_id": "train_shard_00001_4958_1", "global_id": 12665 }, { "text": "Gut microbial community composition varies from one person to another. Potentially, this means the ecological interactions experienced by individual strains or species also vary among microbiomes of different people. However, testing this directly in human microbiomes and identifying ecological drivers involved is challenging. Here, we use replicated anaerobic microcosms to quantify variability of population growth for a key commensal species among microbiome samples from different individuals, and to identify underlying intra- and interspecific interactions. In a reciprocal transplant experiment, both absolute and relative growth performance of different Escherichia coli strains varied among gut microbiome samples from healthy individuals. This was partly explained by intraspecific competition: ecological success of individual E. coli strains was associated with displacement of resident conspecifics. However, the determinants of E. coli growth varied among samples. In one microbiome sample with a distinctive taxonomic composition, culture acidification by resident microbes impaired growth of all E. coli strains. We identified a strain of Clostridium butyricum contributing to this effect, and showed that transferring it into other microbiomes predictably altered pH, fermentation product profiles (butyrate accumulation and acetate/lactate depletion) and population growth of other species including E. coli , thereby reshaping overall taxonomic composition. Our results suggest natural inter-individual gut microbiome variation translates to variable ecological interactions with incoming bacteria, but these dynamics can be manipulated by a generalizable interspecies interaction.

Significance statement

Gut-microbiome variation among healthy individuals is widely documented, yet its impact on the success of incoming bacterial strains and its implications for microbiome-targeted interventions remain unclear. Here, we test this experimentally by cultivating stool samples from healthy individuals and transplanting strains across samples. We reveal a functional relationship between microbiome variation and growth performance of individual strains. This underscores the challenge of predicting colonization outcomes. Yet, we identify a taxon contributing to the distinct functional profile of one of the samples, and show that its transplantion into other microbiome samples reproducibly alters key properties, including pH and population growth of other bacteria, revealing a common ecological control point", "token_count": 518, "char_count": 2544, "word_count": 332, "semantic_coherence": 1, "information_density": 0.5753, "quality_score": 0.7877, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:27.581671", "source": { "split": "train_shard_00001", "doc_id": 4959 }, "chunk_id": "train_shard_00001_4959_0", "global_id": 12666 }, { "text": "These findings advance our ability to explain and manipulate human gut-microbiome variation.\n\nInterspecies interaction controls Escherichia coli growth in human gut microbiome samples", "token_count": 48, "char_count": 190, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:27.945018", "source": { "split": "train_shard_00001", "doc_id": 4959 }, "chunk_id": "train_shard_00001_4959_1", "global_id": 12667 }, { "text": "

Background

Lactococcus lactis is among the most widely studied lactic acid bacterial species due to its long history of safe use and economic importance to the dairy industry, where it is exploited as a starter culture in cheese production.

Results

In the current study, we report on the complete sequencing of 16 L. lactis subsp. lactis and L. lactis subsp. cremoris genomes. The chromosomal features of these 16 L. lactis strains in conjunction with 14 completely sequenced, publicly available lactococcal chromosomes were assessed with particular emphasis on discerning the L. lactis subspecies division, evolution and niche adaptation. The deduced pan-genome of L. lactis was found to be closed, indicating that the representative data sets employed for this analysis are sufficient to fully describe the genetic diversity of the taxon.

Conclusions

Niche adaptation appears to play a significant role in governing the genetic content of each L. lactis subspecies, while (differential) genome decay and redundancy in the dairy niche is also highlighted.\n\nComparative and functional genomics of the Lactococcus lactis taxon; insights into evolution and niche adaptation.", "token_count": 305, "char_count": 1194, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6725, "quality_score": 0.8363, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:28.514940", "source": { "split": "train_shard_00001", "doc_id": 4960 }, "chunk_id": "train_shard_00001_4960_0", "global_id": 12668 }, { "text": "The beta-galactosidase activity of Kluyveromyces fragilis cells immobilized in a kappa carrageenan gel was studied in a bioreactor functioning under isothermal and non-isothermal conditions. We observed an increase in enzyme activity which was found to be proportional to the intensity of the temperature gradient applied across the biocatalytic membrane, as well as to the average temperature of the bioreactor. The efficiency of such a non-isothermal bioreactor was calculated with respect to the yield of a bioreactor working under comparable isothermal conditions and was evaluated in terms of reduction of processing times in industrial applications. The possibility that enzyme activity in living cells is affected by non-isothermal conditions naturally existing owing to metabolic heat production is also discussed.\n\nIncrease in beta-galactosidase activity in a non-isothermal bioreactor utilizing immobilized cells of Kluyveromyces fragilis: fundamentals and applications.", "token_count": 219, "char_count": 980, "word_count": 134, "semantic_coherence": 1, "information_density": 0.5672, "quality_score": 0.7836, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:28.978074", "source": { "split": "train_shard_00001", "doc_id": 4961 }, "chunk_id": "train_shard_00001_4961_0", "global_id": 12669 }, { "text": "Inflammatory bowel disease (IBD) is a chronic immune-mediated disease that affects the gastrointestinal tract. It is argued that environment, microbiome, and immune-mediated factors interact in a genetically susceptible host to trigger IBD. Recently, there has been increased interest in the development, progression, and treatment of IBD because of our understanding of the microbiome. Researchers have proved that some factors can alter the microbiome and the pathogenesis of IBD. As a result, there has been increasing interest in the application of probiotics, prebiotics, antibiotics, fecal microbiota transplantation, and gene manipulation in treating IBD because of the possible curative effect of microbiome-modulating interventions. In this review, we summarize the findings from human and animal studies and discuss the effect of the gut microbiome in treating patients with IBD.\n\nGut microbiota and inflammatory bowel disease: The current status and perspectives.", "token_count": 225, "char_count": 974, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6204, "quality_score": 0.8102, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:29.444756", "source": { "split": "train_shard_00001", "doc_id": 4962 }, "chunk_id": "train_shard_00001_4962_0", "global_id": 12670 }, { "text": "

Background

Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease.

Methods

We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment.

Results

A phylogenetic tree based on single nucleotide polymorphisms (SNPs) in the core genome of the 180 isolates demonstrated several distinct clones. This was highly concordant with the population structure inferred by Bayesian methods, which contained four main BAPS (Bayesian Analysis of Population Structure) groups. The majority of isolates from each patient resided in a single group, but all four patients also carried minority populations in stool from multiple phylogenetic groups. Bloodstream isolates from each case belonged to a single BAPS group, which differed in all four patients. Analysis of 87 isolates (56 from blood) belonging to a single BAPS group that were cultured from the same patient over 54 days identified 30 SNPs in the core genome (nine intergenic, 13 non-synonymous, eight synonymous), and 250 accessory genes that were variably present. Comparison of these genetic variants in blood isolates versus those from stool or environment did not identify any variants associated with bloodstream infection. The substitution rate for these isolates was estimated to be 128 (95% confidence interval 79.82 181.77) mutations per genome per year, more than ten times higher than previous estimates for E. faecium. Within-patient variation in vancomycin resistance associated with vanA was common and could be explained by plasmid loss, or less often by transposon loss.

Conclusions

These findings demonstrate the diversity of E. faecium carriage by individual patients and significant within-host diversity of E. faecium, but do not provide evidence for adaptive genetic variation associated with invasion.", "token_count": 520, "char_count": 2131, "word_count": 299, "semantic_coherence": 1, "information_density": 0.6187, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:30.097559", "source": { "split": "train_shard_00001", "doc_id": 4963 }, "chunk_id": "train_shard_00001_4963_0", "global_id": 12671 }, { "text": "Within-host evolution of Enterococcus faecium during longitudinal carriage and transition to bloodstream infection in immunocompromised patients.", "token_count": 30, "char_count": 145, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:30.451188", "source": { "split": "train_shard_00001", "doc_id": 4963 }, "chunk_id": "train_shard_00001_4963_1", "global_id": 12672 }, { "text": "Industrial fermentation processes strive for high robustness to ensure optimal and consistent performance. Medium components, fermentation products, and physical perturbations may cause stress and lower performance. Cellular stress elicits a range of responses, whose extracellular manifestations have been extensively studied; whereas intracellular aspects remain poorly known due to lack of tools for real-time monitoring. Genetically encoded biosensors have emerged as promising tools and have been used to improve microbial productivity and tolerance toward industrially relevant stresses. Here, fluorescent biosensors able to sense the yeast intracellular environment (pH, ATP levels, oxidative stress, glycolytic flux, and ribosome production) were implemented into a versatile and easy-to-use toolbox. Marker-free and efficient genome integration at a conserved site on chromosome X of Saccharomyces cerevisiae strains and a commercial Saccharomyces boulardii strain was developed. Moreover, multiple biosensors were used to simultaneously monitor different intracellular parameters in a single cell. Even when combined together, the biosensors did not significantly affect key physiological parameters, such as specific growth rate and product yields. Activation and response of each biosensor and their interconnection were assessed using an advanced micro-cultivation system. Finally, the toolbox was used to screen cell behavior in a synthetic lignocellulosic hydrolysate that mimicked harsh industrial substrates, revealing differences in the oxidative stress response between laboratory (CEN.PK113-7D) and industrial (Ethanol Red) S. cerevisiae strains. In summary, the toolbox will allow both the exploration of yeast diversity and physiological responses in natural and complex industrial conditions, as well as the possibility to monitor production processes.\n\nReal-Time Monitoring of the Yeast Intracellular State During Bioprocesses With a Toolbox of Biosensors.", "token_count": 437, "char_count": 1980, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "PK113" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:31.080349", "source": { "split": "train_shard_00001", "doc_id": 4964 }, "chunk_id": "train_shard_00001_4964_0", "global_id": 12673 }, { "text": "

Background

Burkholderia cepacia complex (Bcc) is a group of serious pathogens in cystic fibrosis patients and causes life threatening infections in immunocompromised patients. Species within the Bcc are widely distributed within the environment, can survive in the presence of disinfectants and antiseptics, and are inherently multidrug resistant (MDR).

Methods

Dhaka Medical College Hospital (DMCH) patients with a B. cepacia positive blood culture between 20 October 2016 to 23rd September 2017 were considered as outbreak cases. Blood stream infections (BSIs) were detected using BacT/ALERT 3D at DMCH. B. cepacia was isolated on chromogenic UTI media followed by MALDI-TOF. Minimum inhibitory concentration (MIC) of clinically relevant antibiotics was determined by agar dilution. Whole genome sequencing was performed on an Illumina MiSeq platform. Patients' demographic and clinical data were collected. Patients' clinical history and genomic data of the outbreak strains were merged to investigate possible outbreaks. Ninety-one B. cepacia genomes were downloaded from 'Burkholderia Genome Database' and the genomic background of the global strains were compared with our outbreak strains.

Results

Among 236 BSIs, 6.35% (15/236) were B. cepacia. Outbreak cases were confined to the burn critical care unit and, to a lesser extent, the paediatrics department. There was a continuum of overlapping cases at DMCH between 23 October 2016 to 30 August 2017. Core genome SNPs showed that the outbreak strains were confined to a single clade, corresponded to a common clone (ST1578). The strains were shown to be MDR and associated with a mortality of 31% excluding discharge against medical advice. MIC profiles of the strains suggested that antibiotics deployed as empirical therapy were invariably inappropriate. The genetic background of the outbreak strains was very similar; however, a few variations were found regarding the presence of virulence genes", "token_count": 525, "char_count": 1981, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6383, "quality_score": 0.8191, "entities": { "genes": [ "ST1578" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:31.739521", "source": { "split": "train_shard_00001", "doc_id": 4965 }, "chunk_id": "train_shard_00001_4965_0", "global_id": 12674 }, { "text": "Compared to global strains from the Burkholderia Genome Database, the Bangladeshi strains were genetically distinct.

Conclusions

Environmental surveillance is required to investigate the aetiology and mode of transmission of the B. cepacia outbreak. Systematic management of nosocomial outbreaks, particularly in resource limited regions, will mitigate transmission and will improve patients' outcomes.\n\nMolecular and epidemiological analysis of a Burkholderia cepacia sepsis outbreak from a tertiary care hospital in Bangladesh.", "token_count": 124, "char_count": 536, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7424, "quality_score": 0.8712, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:32.123941", "source": { "split": "train_shard_00001", "doc_id": 4965 }, "chunk_id": "train_shard_00001_4965_1", "global_id": 12675 }, { "text": "UDP-galactose 4-epimerase from yeast Kluyveromyces fragilis is a dimeric molecule of 75 kDa per subunit with one molecule of cofactor NAD per dimer. It undergoes unfolding and complete dissociation in presence of 8 M urea at pH 7.0 by 10 min. It can be functionally reconstituted almost quantitatively in 2 h by dilution with 20 mM sodium phosphate buffer, pH 7 containing 1 mM extraneous NAD under a second order kinetics [Bhattacharyya, D. (1993) Biochemistry 32, 9726-9734]. Denaturation between 10-60 min inversely affects both the rate and maximum recovery of activity upon refolding. Aggregation of this protein has not been observed under these conditions. The time dependent reaction at the unfolded state is independent of pH between 5.4-10.4 but strongly dependent on temperature of denaturation between 0-20 degrees C. Unfolding at 0 degrees C divides the protein largely into two populations-34% of fast folding species following an apparent first order kinetics and 59% of slow folding species following a second order kinetics of reactivation. A very fast folding species of low abundance 3.5-7.5% depending on temperature of denaturation has been identified, which gets active status within the dead time of mixing. Interaction with the active site directed fluorescence probe 1-anilino 8-naphthalene sulfonic acid (1-ANS) and estimation of bound NAD suggest that the catalytic region of this enzyme is not formed in the long term denatured samples. The whole process of reactivation is catalysed by peptidyl prolyl cis-trans isomerase and thus suggests that one or more proline residues stereochemically control the rate limiting step of reactivation.\n\nMultiple unfolded states of UDP-galactose 4-epimerase from yeast Kluyveromyces fragilis. Involvement of proline cis-trans isomerization in reactivation.", "token_count": 513, "char_count": 1821, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:32.757833", "source": { "split": "train_shard_00001", "doc_id": 4966 }, "chunk_id": "train_shard_00001_4966_0", "global_id": 12676 }, { "text": "

Background

As the cost of sequencing has declined, clinical diagnostics based on next generation sequencing (NGS) have become reality. Diagnostics based on sequencing will require rapid and precise mapping against redundant databases because some of the most important determinants, such as antimicrobial resistance and core genome multilocus sequence typing (MLST) alleles, are highly similar to one another. In order to facilitate this, a novel mapping method, KMA (k-mer alignment), was designed. KMA is able to map raw reads directly against redundant databases, it also scales well for large redundant databases. KMA uses k-mer seeding to speed up mapping and the Needleman-Wunsch algorithm to accurately align extensions from k-mer seeds. Multi-mapping reads are resolved using a novel sorting scheme (ConClave scheme), ensuring an accurate selection of templates.

Results

The functionality of KMA was compared with SRST2, MGmapper, BWA-MEM, Bowtie2, Minimap2 and Salmon, using both simulated data and a dataset of Escherichia coli mapped against resistance genes and core genome MLST alleles. KMA outperforms current methods with respect to both accuracy and speed, while using a comparable amount of memory.

Conclusion

With KMA, it was possible map raw reads directly against redundant databases with high accuracy, speed and memory efficiency.\n\nRapid and precise alignment of raw reads against redundant databases with KMA.", "token_count": 351, "char_count": 1454, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6585, "quality_score": 0.8293, "entities": { "genes": [ "SRST2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:33.342624", "source": { "split": "train_shard_00001", "doc_id": 4967 }, "chunk_id": "train_shard_00001_4967_0", "global_id": 12677 }, { "text": "Foods and drinks with high solute concentration (fruit juices and concentrates, marzipan, salted and dry-cured meats, olives and cheeses), and foods containing preservatives (wine, beverages and sauces) were selected in order to characterise the contaminant yeast flora by rapid typing techniques. These included the testing of several types of molecular methods (e.g. RFLP, DNA-fingerprinting, PCR-based techniques), analysis of long-chain fatty acids and of isoenzymes. The PCR-based detection methods enabled a faster detection of emerging specific spoilers at earlier stages of processing. Fatty acid characterisation allowed the assessment of the most frequent types of contamination yeasts and supplied the information for the definition of relevant zymological indicators. A selected group of strains was used for further studies of mechanisms underlying the resistance/tolerance of yeasts towards preservatives (weak acids) and other stress factors (temperature, high sugar and salt concentrations). This study enabled the acquisition of data on the basic biology of yeasts used in the development of differential and selective media for Zygosaccharomyces bailii, Yarrowia lipolytica, Kluyveromyces marxianus and Dekkera sp.\n\nSpoilage yeasts in foods and beverages: characterisation and ecology for improved diagnosis and control", "token_count": 310, "char_count": 1337, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.8361, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:33.916424", "source": { "split": "train_shard_00001", "doc_id": 4968 }, "chunk_id": "train_shard_00001_4968_0", "global_id": 12678 }, { "text": "Fungal infections have increased dramatically in recent years and candidemia is a major risk factor for morbidity and mortality in intensive care units (ICUs). Candidemia has been considered to be a nosocomial infection that is strongly associated with neutropenia, recent surgery or presence of intravascular lines, and previous colonization is an independent risk factor. We evaluated the in vitro efficacy of fluconazole and amphotericin B against yeasts isolated from various clinical specimens of colonized or infected patients treated in the ICUs of the Institute of Cardiology, Istanbul University. A total of 1397 ICU patients were treated at the Institute of Cardiology between January 2000 and December 2002. A total of 117 yeasts isolated from 97 patients were included in this study. These ICU patients were hospitalized for a mean of 29 days. All yeasts were identified by conventional methods and using the API (20C AUX, ID 32C) system (Bio Meriéux, France). Susceptibility to fluconazole and amphotericin B was evaluated using the E-test (AB Biodisk, Solna, Sweden). The most commonly isolated yeast was Candida albicans (72.6%), followed by Candida tropicalis (16.2%), Candida kefyr, Candida krusei, Candida parapsilosis, Trichosporon mucoides and Geotrichum spp. Fluconazole and amphotericin B MIC90 values were 0.75 microg/ml; 0.19 microg/ml and 1 microg/ml; 0.38 microg/ml for C. albicans and C. tropicalis, respectively. All Geotrichum spp. were found to be susceptible-dose dependent (SDD) (MIC=16-32 microg/ml) to fluconazole. Two C. albicans, two C. tropicalis, one C. krusei and one Geotrichum spp. had a MIC value of > or = 0.38 microg/ml for amphotericin B", "token_count": 508, "char_count": 1682, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6102, "quality_score": 0.8051, "entities": { "genes": [ "MIC90" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:34.567692", "source": { "split": "train_shard_00001", "doc_id": 4969 }, "chunk_id": "train_shard_00001_4969_0", "global_id": 12679 }, { "text": "The rate of colonization was 3.36% (47/1397). Only 10 (0.71%) patients out of a total of 1397 developed candidemia during the period of the investigation. Of these, 7 (70%) were caused by non-albicans Candida spp.\n\nIn vitro susceptibility of yeasts isolated from patients in intensive care units to fluconazole and amphotericin B during a 3-year period.", "token_count": 113, "char_count": 353, "word_count": 56, "semantic_coherence": 1, "information_density": 0.8036, "quality_score": 0.9018, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:34.950277", "source": { "split": "train_shard_00001", "doc_id": 4969 }, "chunk_id": "train_shard_00001_4969_1", "global_id": 12680 }, { "text": "An enrichment and isolation program for new ethanol-producing thermotolerant yeasts as well as a screening program of some known thermotolerant strains resulted in the selection of several strains capable of growth at 40-43 degrees C. Among these strains four grew and fermented sugar cane molasses at 43 degrees C under batch conditions with sugar-conversion efficiencies >94% and ethanol concentrations 6.8-8.0% (w/v). The two best-performing strains, a Saccharomyces cerevisiae F111 and a Kluyveromyces marxianus WR12 were used in eight 87.5 m(3) fermentation runs (four using each strain) for industrial ethanol production in an Egyptian distillery using sugar cane molasses. Mean ethanol production was 7.7% and 7.4% (w/v), respectively, with an added advantage of cooling elimination during fermentation and higher ethanol yields compared to the distillery's S. cerevisiae SIIC (ATCC 24855) strain in use. The isolate S. cerevisiae F111 was subsequently adopted by the distillery for regular production with significant economical gains and water conservation.\n\nIsolation of thermotolerant ethanologenic yeasts and use of selected strains in industrial scale fermentation in an Egyptian distillery.", "token_count": 329, "char_count": 1204, "word_count": 171, "semantic_coherence": 1, "information_density": 0.655, "quality_score": 0.8275, "entities": { "genes": [ "WR12" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:35.514773", "source": { "split": "train_shard_00001", "doc_id": 4970 }, "chunk_id": "train_shard_00001_4970_0", "global_id": 12681 }, { "text": "DNA gyrase is an essential type II topoisomerase that is composed of two subunits, GyrA and GyrB, and has an A2 B2 structure. Although the A and B subunits are required in equal proportions to form DNA gyrase, the gyrA and gyrB genes that encode them in Salmonella (and in many other bacteria) are at separate locations on the chromosome, are under separate transcriptional control, and are present in different copy numbers in rapidly growing bacteria. In wild-type Salmonella, gyrA is near the chromosome's replication terminus, while gyrB is near the origin. We generated a synthetic gyrBA operon at the oriC-proximal location of gyrB to test the significance of the gyrase gene position for Salmonella physiology. Although the strain producing gyrase from an operon had a modest alteration to its DNA supercoiling set points, most housekeeping functions were unaffected. However, its SPI-2 virulence genes were expressed at a reduced level and its survival was reduced in macrophage. Our data reveal that the horizontally acquired SPI-2 genes have a greater sensitivity to disturbance of DNA topology than the core genome and we discuss its significance in the context of Salmonella genome evolution and the gyrA and gyrB gene arrangements found in other bacteria.\n\nConsequences of producing DNA gyrase from a synthetic gyrBA operon in Salmonella enterica serovar Typhimurium.", "token_count": 352, "char_count": 1402, "word_count": 217, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:36.079751", "source": { "split": "train_shard_00001", "doc_id": 4971 }, "chunk_id": "train_shard_00001_4971_0", "global_id": 12682 }, { "text": "

Importance

As deficiencies in tRNA modifications have been linked to human diseases such as cancer and diabetes, much research has focused on the modifications' impacts on translational regulation in eukaryotes. However, the significance of tRNA modifications in bacterial physiology remains largely unexplored. In this paper, we demonstrate that the m7G tRNA methyltransferase TrmB is crucial for a top-priority pathogen, Acinetobacter baumannii, to respond to stressors encountered during infection, including oxidative stress, low pH, and iron deprivation. We show that loss of TrmB dramatically attenuates a murine pulmonary infection. Given the current efforts to use another tRNA methyltransferase, TrmD, as an antimicrobial therapeutic target, we propose that TrmB, and other tRNA methyltransferases, may also be viable options for drug development to combat multidrug-resistant A. baumannii.\n\nThe tRNA methyltransferase TrmB is critical for Acinetobacter baumannii stress responses and pulmonary infection.", "token_count": 282, "char_count": 1054, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7299, "quality_score": 0.865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:36.670657", "source": { "split": "train_shard_00001", "doc_id": 4972 }, "chunk_id": "train_shard_00001_4972_0", "global_id": 12683 }, { "text": "The genus Idiomarina consists of halophilic and/or haloalkaliphilic organisms. We compared the complete genomes of seven strains of the genus Idiomarina to investigate its adaptation to saline environment. A total of 1,313 core genes related to salinity tolerance, stress response, antibiotic resistance genes, virulence factors, and drug targets were found. Comparative genomics revealed various genes involved in halo adaptations of these organisms, including transporters and influx or efflux systems for elements such as Fe, Cu, Zn, Pb, and Cd. In agreement with their isolation sources (such as hydrothermal vents and marine sediments) and environments abundant in heavy metals, various resistance proteins and transporters associated with metal tolerance were also identified. These included copper resistance proteins, zinc uptake transcriptional repressor Zur, MerC domain-containing protein, Cd(II)/Pb(II)-responsive transcriptional regulator, Co/Zn/Cd efflux system protein, and mercuric transporter. Interestingly, we observed that the carbohydrate metabolism pathways were incomplete in all the strains and transporters used for absorption of small sugars were also not found in them. Also, the presence of higher proportion of genes involved in protein metabolism than carbohydrate metabolism indicates that proteinaceous substrates act as the major food substrates for these bacterial strains than carbohydrates. Genomic islands were detected in some species, highlighting the role of horizontal gene transfer for acquisition in novel genes. Genomic rearrangements in terms of partially palindromic regions were detected in all strains. To our knowledge, this is the first comprehensive comparative genomics study among the genus Idiomarina revealing unique genomic features within bacterial species inhabiting different ecological niches.

Supplementary information

The online version contains supplementary material available at 10.1007/s13205-023-03887-3.", "token_count": 489, "char_count": 1999, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6834, "quality_score": 0.8417, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:37.347634", "source": { "split": "train_shard_00001", "doc_id": 4973 }, "chunk_id": "train_shard_00001_4973_0", "global_id": 12684 }, { "text": "Comparative genomics of seven genomes of genus Idiomarina reveals important halo adaptations and genes for stress response.", "token_count": 32, "char_count": 130, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:37.717418", "source": { "split": "train_shard_00001", "doc_id": 4973 }, "chunk_id": "train_shard_00001_4973_1", "global_id": 12685 }, { "text": "Bench-scale batch bioreactors were used to study the effectiveness of cheese whey fermentation for single-cell protein production using the yeast Kluyveromyces fragilis in reducing the pollution potential of whey as measured by solids, chemical oxygen demand (COD) and nitrogenous compounds concentrations. The four principal phases (lag, exponential, stationary and death) encountered in the history of a microbial culture grown under batch conditions were clearly recognized in the growth, temperature and dissolved oxygen curves. The lactose concentration and soluble COD displayed three distinct phases corresponding to the lag, exponential and stationary phases of the yeast growth. The minimum dissolved oxygen and maximum temperature observed in this study (at an air flow of 3 VVM, a mixing speed of 400 rpm and an ambient temperature) were 2.49 mg/L and 31.6 degrees C, respectively. About 99% of lactose (90.6% of soluble COD) was utilized after 28 h. The total COD continued to decline due to cell death resulting in a reduction of 42.98%. The total nitrogen concentration remained unchanged while the organic nitrogen increased during the exponential phase and then declined during the death phase. The ash content remained unchanged while a substantial reduction (56%) of the volatile solids was observed. These results indicated that sufficient oxygen for yeast growth was present in the medium and no cooling system was needed for this type of fermenter under similar experimental conditions. Recovering the yeast biomass with ultrafiltration reduced the total COD by 98% of its initial value in the raw whey.\n\nSubmerged yeast fermentation of acid cheese whey for protein production and pollution potential reduction.", "token_count": 395, "char_count": 1732, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6054, "quality_score": 0.8027, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:38.373297", "source": { "split": "train_shard_00001", "doc_id": 4974 }, "chunk_id": "train_shard_00001_4974_0", "global_id": 12686 }, { "text": "Illnesses caused by Shiga toxin-producing Escherichia coli (STECs) can be life threatening, such as hemolytic uremic syndrome (HUS). The STECs most frequently identified by USDA’s Microbiological Data Program (MDP) carried toxin gene subtypes stx1a and/or stx2a . Here we describe the genome sequences of 331 STECs isolated from foods regulated by the FDA 2010-2017, determining their genomic identity, serotype, sequence type, virulence potential, and prevalence of antimicrobial resistance. Isolates were selected from the MDP archive, routine food testing by field labs (ORA), food testing by a contract company, and our laboratory (ORS). Only 276 (83%) were confirmed as STECs by in silico analysis. Foods from which STECs were recovered included cilantro (6%), spinach (25%), lettuce (11%), and flour (9%). Phylogenetic analysis using core genome MLST revealed these STEC genomes were highly variable, with some clustering associated with ST types and serotypes. We detected 95 different sequence types (ST); several ST were previously associated with HUS: ST21 and ST29 (O26:H11), ST11 (O157:H7), ST33 (O91:H14), ST17 (O103:H2), and ST16 (O111:H-). in silico virulome analyses showed ~ 51% of these strains were potentially pathogenic [besides stx gene they also carried eae (25%) or 26% subA (26%)]. Virulence gene prevalence was also determined: stx 1 only (19%) -variants a and c; stx 2 only (66%) – variants a, b, c, d, e, and g; and stx 1/ sxt 2 (15%). Our data form a new WGS database that can be used to support food safety investigations and monitor the recurrence/emergence of E. coli in foods", "token_count": 512, "char_count": 1608, "word_count": 251, "semantic_coherence": 1, "information_density": 0.7291, "quality_score": 0.8645, "entities": { "genes": [ "ST29", "ST17", "ST21", "ST16", "ST33", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:39.047287", "source": { "split": "train_shard_00001", "doc_id": 4975 }, "chunk_id": "train_shard_00001_4975_0", "global_id": 12687 }, { "text": "

Importance

Shiga toxin-producing Escherichia coli (STECs) are associated with foodborne outbreaks worldwide; however, surveillance has not previously included genomic analyses for phylogenetics, prevalence, or potential virulence. We constructed the first genomic database of isolates from FDA-regulated foods to help monitor the emergence of new pathogenic STECs. Although only ~30 STECs were isolated per year, 50% of these carried markers associated with pathogenesis either a combination of eae plus stx , or subA plus stx . Moreover, those strains also carried virulence genes associated with severe illnesses. Here we showed that WGS enabled comparisons across isolates to establish phylogeny, help in identification of antibiotic resistance by monitoring the presence of antimicrobial resistance genes, and determined the presence of known virulence genes that have been linked with illnesses. Future food safety investigations will benefit from improved source tracking and risk assessments made possible by these analyses and new WGS database.\n\nVirulence gene profiles and phylogeny of Shiga toxin-positiveEscherichia colistrains isolated from FDA regulated foods during 2010-2017", "token_count": 299, "char_count": 1205, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7317, "quality_score": 0.8659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:39.611577", "source": { "split": "train_shard_00001", "doc_id": 4975 }, "chunk_id": "train_shard_00001_4975_1", "global_id": 12688 }, { "text": "As one of the promising next-generation probiotics (NGPs), Akkermansia muciniphila, a well-known mucin-degrading bacterium, has been proven to be closely related to the metabolic diseases of its human host. However, the role of A. muciniphila in the host's intestinal health remains ambiguous. Here, we comprehensively summarize and discuss the characteristics, the distribution, and the colonization of A. muciniphila in the human gastrointestinal tract (GIT). We propose that the application of A. muciniphila as a biomarker for longevity, for diagnostics and prognostics of intestinal diseases, or for intestinal health should be cautiously considered. Precise dietary regulation can mediate the treatment of intestinal diseases by altering the abundance of A. muciniphila. Although the beneficial role of A. muciniphila and its component in intestinal inflammation has been discovered, in gnotobiotic mice with specific gut microbiota, certain genotype, and colorectal cancer, or in animal models infected with a specific pathogen, A. muciniphila may be related to the occurrence and development of intestinal diseases. Genomic analysis, emphasizing the strain-level phylogenetic differences of A. muciniphila, indicates that a clear description and discussion of each strain is critical before its practical application. Our review provides much needed insight for the precise application of A. muciniphila.\n\nRational consideration of Akkermansia muciniphila targeting intestinal health: advantages and challenges.", "token_count": 377, "char_count": 1519, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5885, "quality_score": 0.7943, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:40.199287", "source": { "split": "train_shard_00001", "doc_id": 4976 }, "chunk_id": "train_shard_00001_4976_0", "global_id": 12689 }, { "text": "Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet's multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual's endogenous Bifidobacterium community", "token_count": 501, "char_count": 1840, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5844, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:40.853054", "source": { "split": "train_shard_00001", "doc_id": 4977 }, "chunk_id": "train_shard_00001_4977_0", "global_id": 12690 }, { "text": "Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.\n\nExploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy.", "token_count": 70, "char_count": 328, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:41.225652", "source": { "split": "train_shard_00001", "doc_id": 4977 }, "chunk_id": "train_shard_00001_4977_1", "global_id": 12691 }, { "text": "Clostridioides difficile is a ubiquitous, diarrheagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the C. difficile multilocus sequence typing (MLST) scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat un-related infections, which creates conditions ideal for C. difficile colonization and proliferation. In this study, we analyzed 27 isolates from a healthcare network in northern Arizona, USA, and 1,352 public ST1 genomes to place locally-sampled isolates into a global context. Core genome, single nucleotide polymorphism (SNP) analysis demonstrated that at least 6 separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates following two of these introductions, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally, we compared all high-quality C. difficile genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other C. difficile genomes; analyses of other toxigenic C. difficile sequence types demonstrates that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with C. difficile infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical C. difficile isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of C", "token_count": 524, "char_count": 2288, "word_count": 326, "semantic_coherence": 1, "information_density": 0.5982, "quality_score": 0.7991, "entities": { "genes": [ "ST1", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:41.860168", "source": { "split": "train_shard_00001", "doc_id": 4978 }, "chunk_id": "train_shard_00001_4978_0", "global_id": 12692 }, { "text": "difficile and for assessing the performance of infection prevention and control strategies.\n\nA global to local genomics analysis ofClostridioides difficileST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network", "token_count": 59, "char_count": 251, "word_count": 30, "semantic_coherence": 1, "information_density": 0.9333, "quality_score": 0.9667, "entities": { "genes": [ "ST1", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:42.232259", "source": { "split": "train_shard_00001", "doc_id": 4978 }, "chunk_id": "train_shard_00001_4978_1", "global_id": 12693 }, { "text": "Colonization of the gastrointestinal tract (GIT) generally precedes infection with antibiotic-resistant Enterococcus faecium We used a mouse GIT colonization model to test differences in the colonization levels by strains from different E. faecium lineages: clade B, part of the healthy human microbiota; subclade A1, associated with infections; and subclade A2, primarily associated with animals. After mono-inoculation, there was no significant difference in colonization (measured as the geometric mean number of colony-forming units per gram) by the E. faecium clades at any time point (P > .05). However, in competition assays, with 6 of the 7 pairs, clade B strains outcompeted clade A strains in their ability to persist in the GIT; this difference was significant in some pairs by day 2 and in all pairs by day 14 (P < .0008-.0283). This observation may explain the predominance of clade B in the community and why antibiotic-resistant hospital-associated E. faecium are often replaced by clade B strains once patients leave the hospital.\n\nGastrointestinal Tract Colonization Dynamics by Different Enterococcus faecium Clades.", "token_count": 298, "char_count": 1134, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:42.788712", "source": { "split": "train_shard_00001", "doc_id": 4979 }, "chunk_id": "train_shard_00001_4979_0", "global_id": 12694 }, { "text": "Cells of the wild-type yeast strain Zygosaccharomyces bisporus CBS 702 form alpha-hydroxy ketones from aromatic amino acid precursors during fermentation. Pyruvate decarboxylase (PDC, E.C. 4.1.1.1), the key enzyme of this biotransformation catalysing the non-oxidative decarboxylation of pyruvate and other 2-oxo-acids, was purified and characterised. The active enzyme is homotetrameric (alpha4) with a molecular mass of about 244 kDa. Activation of PDC by its substrate pyruvate results in a sigmoidal dependence of the reaction rate from substrate concentration (apparent Km value 1.73 mM; Hill coefficient 2.10). A cDNA library was screened using a PCR-based procedure, and a 1856 bp cDNA of PDC was identified and sequenced. The cDNA encodes a polypeptide of 563 amino acid residues (monomeric unit). Sequence alignments demonstrate high homologies (> 80%) to PDC genes from Saccharomyces cerevisiae, Kluyveromyces lactis and Kluyveromyces marxianus.\n\nPurification, characterisation and cDNA sequencing of pyruvate decarboxylase from Zygosaccharomyces bisporus.", "token_count": 350, "char_count": 1066, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7055, "quality_score": 0.8527, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:43.367091", "source": { "split": "train_shard_00001", "doc_id": 4980 }, "chunk_id": "train_shard_00001_4980_0", "global_id": 12695 }, { "text": "Members of the genus Bifidobacterium, of which the majority have been isolated as gut commensals, are Gram-positive, non-motile, saccharolytic, non-sporulating, anaerobic bacteria. Many bifidobacterial strains are considered probiotic and therefore are thought to bestow health benefits upon their host. Bifidobacteria are highly abundant among the gut microbiota of healthy, full term, breast-fed infants, yet the relative average abundance of bifidobacteria tends to decrease as the human host ages. Because of the inverse correlation between bifidobacterial abundance/prevalence and health, there has been an increasing interest in maintaining, increasing or restoring bifidobacterial populations in the infant, adult and elderly gut. In order to colonize and persist in the gastrointestinal environment, bifidobacteria must be able to metabolise complex dietary and/or host-derived carbohydrates, and be resistant to various environmental challenges of the gut. This is not only important for the autochthonous bifidobacterial species colonising the gut, but also for allochthonous bifidobacteria provided as probiotic supplements in functional foods. For example, Bifidobacterium longum subsp. longum is a taxon associated with the metabolism of plant-derived poly/oligosaccharides in the adult diet, being capable of metabolising hemicellulose and various pectin-associated glycans. Many of these plant glycans are believed to stimulate the metabolism and growth of specific bifidobacterial species and are for this reason classified as prebiotics. In this review, bifidobacterial carbohydrate metabolism, with a focus on plant poly-/oligosaccharide degradation and uptake, as well as its associated regulation, will be discussed.\n\nPlant Glycan Metabolism by Bifidobacteria.", "token_count": 477, "char_count": 1801, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6498, "quality_score": 0.8249, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:44.005052", "source": { "split": "train_shard_00001", "doc_id": 4981 }, "chunk_id": "train_shard_00001_4981_0", "global_id": 12696 }, { "text": "

Background

Although serotype O157:H7 is the predominant enterohemorrhagic Escherichia coli (EHEC), outbreaks of non-O157 EHEC that cause severe foodborne illness, including hemolytic uremic syndrome have increased worldwide. In fact, non-O157 serotypes are now estimated to cause over half of all the Shiga toxin-producing Escherichia coli (STEC) cases, and outbreaks of non-O157 EHEC infections are frequently associated with serotypes O26, O45, O103, O111, O121, and O145. Currently, there are no complete genomes for O145 in public databases.

Results

We determined the complete genome sequences of two O145 strains (EcO145), one linked to a US lettuce-associated outbreak (RM13514) and one to a Belgium ice-cream-associated outbreak (RM13516). Both strains contain one chromosome and two large plasmids, with genome sizes of 5,737,294 bp for RM13514 and 5,559,008 bp for RM13516. Comparative analysis of the two EcO145 genomes revealed a large core (5,173 genes) and a considerable amount of strain-specific genes. Additionally, the two EcO145 genomes display distinct chromosomal architecture, virulence gene profile, phylogenetic origin of Stx2a prophage, and methylation profile (methylome). Comparative analysis of EcO145 genomes to other completely sequenced STEC and other E. coli and Shigella genomes revealed that, unlike any other known non-O157 EHEC strain, EcO145 ascended from a common lineage with EcO157/EcO55. This evolutionary relationship was further supported by the pangenome analysis of the 10 EHEC str ains", "token_count": 503, "char_count": 1545, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6542, "quality_score": 0.8271, "entities": { "genes": [ "RM13516", "RM13514" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:44.655524", "source": { "split": "train_shard_00001", "doc_id": 4982 }, "chunk_id": "train_shard_00001_4982_0", "global_id": 12697 }, { "text": "Of the 4,192 EHEC core genes, EcO145 shares more genes with EcO157 than with the any other non-O157 EHEC strains.

Conclusions

Our data provide evidence that EcO145 and EcO157 evolved from a common lineage, but ultimately each serotype evolves via a lineage-independent nature to EHEC by acquisition of the core set of EHEC virulence factors, including the genes encoding Shiga toxin and the large virulence plasmid. The large variation between the two EcO145 genomes suggests a distinctive evolutionary path between the two outbreak strains. The distinct methylome between the two EcO145 strains is likely due to the presence of a BsuBI/PstI methyltransferase gene cassette in the Stx2a prophage of the strain RM13514, suggesting a role of horizontal gene transfer-mediated epigenetic alteration in the evolution of individual EHEC strains.\n\nComparative genomics of enterohemorrhagic Escherichia coli O145:H28 demonstrates a common evolutionary lineage with Escherichia coli O157:H7.", "token_count": 294, "char_count": 990, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6338, "quality_score": 0.8169, "entities": { "genes": [ "RM13514" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:45.216446", "source": { "split": "train_shard_00001", "doc_id": 4982 }, "chunk_id": "train_shard_00001_4982_1", "global_id": 12698 }, { "text": "The transgalactosilating ability of beta-galactosidase preparations obtained from Kluyveromyces fragilis, Penicillium canescens, and Escherichia coli was investigated. In samples of hydrolysates of 20% lactose solutions without or with a 2% addition of glucose, the galactose or fructose obtained with the use of the investigated preparations and the content of saccharides was determined with the HPLC method. Under experimental conditions, the highest quantity (56.0-64.1%) of galactooligosaccharides was synthesised by beta-galactosidase obtained from E. coli, while the lowest number (11.25-25.2%) was obtained by beta-galactosidase obtained from P. canescens. Beta-galactosidase from E. coli also synthesised considerable amounts of lactulose.\n\nA comparative study on galactoologosaccharide synthesis by selected beta-galactosidase preparations.", "token_count": 242, "char_count": 850, "word_count": 106, "semantic_coherence": 1, "information_density": 0.6321, "quality_score": 0.816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:45.695385", "source": { "split": "train_shard_00001", "doc_id": 4983 }, "chunk_id": "train_shard_00001_4983_0", "global_id": 12699 }, { "text": "Cell wall inulinase (EC 3.2.1.7) was purified from Kluyveromyces marxianus var. marxianus (formerly K. fragilis) and its N-terminal 33-amino acid sequence was established. PCR amplification of cDNA with 2 sets of degenerate primers yielded a genomic probe which was then used to screen a genomic library established in the YEp351 yeast shuttle vector. One of the selected recombinant plasmids allowed an invertase-negative Saccharomyces cerevisiae mutant to grow on inulin. It was shown to contain an inulinase gene (INU 1) encoding a 555-amino acid precursor protein with a typical N-terminal signal peptide. The sequence of inulinase displays a high similarity (67%) to S. cerevisiae invertase, suggesting a common evolutionary origin for yeast beta-fructosidases with different substrate preferences.\n\nCloning and sequencing of the inulinase gene of Kluyveromyces marxianus var. marxianus ATCC 12424.", "token_count": 269, "char_count": 903, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7077, "quality_score": 0.8538, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:46.954571", "source": { "split": "train_shard_00001", "doc_id": 4984 }, "chunk_id": "train_shard_00001_4984_0", "global_id": 12700 }, { "text": "Mycobacterium tuberculosis is the leading cause of death from an infectious disease worldwide. An understanding of tuberculosis transmission dynamics in outbreak settings is vital for its control. The advent of affordable whole genome sequencing (WGS) has provided scope for superior resolution of tuberculosis outbreaks, compared to previous methods. However, the challenge lies in standardising the vast quantities of resulting data in a structured manner which lends itself to easy comparison of isolates. Gene-by-gene Multi-Locus Sequence Typing (MLST) methods of analysing WGS data, as opposed to Single Nucleotide Polymorphism (SNP) mapping, have shown promise in providing a uniform platform for outbreak resolution. WGS was performed on clinical isolates from three M. tuberculosis outbreaks in South West Wales. Molecular typing by MIRU-VNTR and epidemiological investigation had resulted in conflicting conclusions. Outbreak analysis and phylogenetic typing of all isolates was carried out using the WGS gene-by-gene MLST analysis method of core genome MLST (cgMLST) and traditional WGS SNP mapping. Where DNA quality was unsatisfactory, an ancient DNA library preparation was used successfully. Provean and BEAST software ... (continues)\n\nUse of whole genome sequencing in understanding transmission dynamics of tuberculosis", "token_count": 302, "char_count": 1335, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:47.520960", "source": { "split": "train_shard_00001", "doc_id": 4985 }, "chunk_id": "train_shard_00001_4985_0", "global_id": 12701 }, { "text": "The genus Trichoderma is among the best studied groups of filamentous fungi, largely because of its high relevance in applications from agriculture to enzyme biosynthesis to biofuel production. However, the physiological competences of these fungi, that led to these beneficial applications are intriguing also from a scientific and ecological point of view. This review therefore summarizes recent developments in studies of fungal genomes, updates on previously started genome annotation efforts and novel discoveries as well as efforts towards bioprospecting for enzymes and bioactive compounds such as cellulases, enzymes degrading xenobiotics and metabolites with potential pharmaceutical value. Thereby insights are provided into genomes, mitochondrial genomes and genomes of mycoviruses of Trichoderma strains relevant for enzyme production, biocontrol and mycoremediation. In several cases, production of bioactive compounds could be associated with responsible genes or clusters and bioremediation capabilities could be supported or predicted using genome information. Insights into evolution of the genus Trichoderma revealed large scale horizontal gene transfer, predominantly of CAZyme genes, but also secondary metabolite clusters. Investigation of sexual development showed that Trichoderma species are competent of repeat induced point mutation (RIP) and in some cases, segmental aneuploidy was observed. Some random mutants finally gave away their crucial mutations like T. reesei QM9978 and QM9136 and the fertility defect of QM6a was traced back to its gene defect. The Trichoderma core genome was narrowed down to 7000 genes and gene clustering was investigated in the genomes of multiple species. Finally, recent developments in application of CRISPR/Cas9 in Trichoderma, cloning and expression strategies for the workhorse T. reesei as well as the use genome mining tools for bioprospecting Trichoderma are highlighted", "token_count": 500, "char_count": 2002, "word_count": 270, "semantic_coherence": 1, "information_density": 0.637, "quality_score": 0.8185, "entities": { "genes": [ "QM9978", "QM9136" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:48.173829", "source": { "split": "train_shard_00001", "doc_id": 4986 }, "chunk_id": "train_shard_00001_4986_0", "global_id": 12702 }, { "text": "The intriguing new findings on evolution, genomics and physiology highlight emerging trends and illustrate worthwhile perspectives in diverse fields of research with Trichoderma.\n\n<i>Trichoderma</i> - genomes and genomics as treasure troves for research towards biology, biotechnology and agriculture.", "token_count": 84, "char_count": 320, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8684, "quality_score": 0.9342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:48.558482", "source": { "split": "train_shard_00001", "doc_id": 4986 }, "chunk_id": "train_shard_00001_4986_1", "global_id": 12703 }, { "text": "The budding yeast Saccharomyces cerevisiae is certainly the prime industrial microorganism and is related to many biotechnological applications including food fermentations, biofuel production, green chemistry, and drug production. A noteworthy characteristic of this species is the existence of subgroups well adapted to specific processes with some individuals showing optimal technological traits. In the last 20 years, many studies have established a link between quantitative traits and single-nucleotide polymorphisms found in hundreds of genes. These natural variations constitute a pool of QTNs (quantitative trait nucleotides) that modulate yeast traits of economic interest for industry. By selecting a subset of genes functionally validated, a total of 284 QTNs were inventoried. Their distribution across pan and core genome and their frequency within the 1,011 Saccharomyces cerevisiae genomes were analyzed. We found that 150 of the 284 QTNs have a frequency lower than 5%, meaning that these variants would be undetectable by genome-wide association studies (GWAS). This analysis also suggests that most of the functional variants are private to a subpopulation, possibly due to their adaptive role to specific industrial environment. In this review, we provide a literature survey of their phenotypic impact and discuss the opportunities and the limits of their use for industrial strain selection.\n\nQuantitative Trait Nucleotides Impacting the Technological Performances of Industrial Saccharomyces cerevisiae Strains.", "token_count": 364, "char_count": 1556, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:49.170393", "source": { "split": "train_shard_00001", "doc_id": 4987 }, "chunk_id": "train_shard_00001_4987_0", "global_id": 12704 }, { "text": "A total of 500 combs of adult chickens from two different locations in Germany (Hessen and Schleswig-Holstein) were clinically and mycologically examined. The chickens came from three battery cages (n = 79), one voliere system (n=32), six flocks maintained on deep litter (n = 69) and 12 flocks kept on free outdoor range (n=320). Twenty-two of the 500 chicken combs (4.4%) were found to have clinical signs: only non-specific lesions neither typical of mycosis nor of avian pox such as desquamation with crust formation, yellow to brown or black dyschromic changes, alopecia in the surrounding area and moist inflammation. Only seven of the 22 clinically altered combs showed a positive mycological result; the non-pathogenic and geophilic Trichophyton terrestre in one case and non-pathogenic yeast in six cases. The following fungi were seen in the different housing systems: 13 dermatophytes (2.6% of 500 samples): 12 x T. terrestre, 1 x Trichophyton mentagrophytes, 11 isolates of Chrysosporium georgiae (2.2% of 500 samples) and 149 isolates of yeasts (29.8%): Malassezia sympodialis: n = 52, Kloeckera apiculata: n = 33, Trichosporon capitatum (syn. Geotrichum capitatum): n = 23, Trichosporon cutaneum/Trichosporon mucoides: n = 12, Trichosporon inkin (syn", "token_count": 418, "char_count": 1264, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6943, "quality_score": 0.8472, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:49.813332", "source": { "split": "train_shard_00001", "doc_id": 4988 }, "chunk_id": "train_shard_00001_4988_0", "global_id": 12705 }, { "text": "Sarcinosporon inkin): n = 8 and Candida spp.: n = 21, including pathogenic or possibly pathogenic species: Candida albicans: n = 3, Candida famata: n = 4, Candida guilliermondii: n = 3, Candida lipolytica: n = 3, Candida dattila: n = 2 and one isolate each of Candida glabrata, Candida parapsilosis, Candida aaseri, Candida catenulata sive brumpti, Candida fructus and Candida kefyr sive pseudotropicalis. There is no stringent correlation between the clinical symptoms diagnosed on the chicken combs and the species of yeasts isolated. The causative agent of favus in chickens, Trichophyton gallinae, and the saprophytic yeast in pigeons, Cr. neoformans were not isolated. The most frequently isolated yeasts M. sympodialis and Kloeckera apiculata are suggested to be classified as members of the resident flora of the chicken comb.\n\nMycological examinations on the fungal flora of the chicken comb.", "token_count": 272, "char_count": 900, "word_count": 139, "semantic_coherence": 1, "information_density": 0.6115, "quality_score": 0.8058, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:50.412317", "source": { "split": "train_shard_00001", "doc_id": 4988 }, "chunk_id": "train_shard_00001_4988_1", "global_id": 12706 }, { "text": "Two unusual catalase-negative, Gram-stain-positive, Vagococcus-like isolates that were referred to the CDC Streptococcus Laboratory for identification are described. Strain SS1994T was isolated from ground beef and strain SS1995T was isolated from a human foot wound. Comparative 16S rRNA gene sequence analysis of isolates SS1994T and SS1995T against Vagococcus type strain sequences supported their inclusion in the genus Vagococcus. Strain SS1994T showed high sequence similarity (>97.0 %) to the two most recently proposed species, Vagococcus martis (99.2 %) and Vagococcus teuberi (99.0 %) followed by Vagococcus penaei (98.8 %), strain SS1995T (98.6 %), Vagococcus carniphilus (98.0 %), Vagococcus acidifermentans (98.0 %) and Vagococcus fluvialis (97.9 %). The 16S rRNA gene sequence of strain SS1995T was most similar to V. penaei (99.1 %), followed by SS1994T (98.6 %), V. martis (98.4 %), V. teuberi (98.1 %), V. acidifermentans (97.8 %), and both V. carniphilus and V. fluvialis (97.5 %)", "token_count": 424, "char_count": 1086, "word_count": 147, "semantic_coherence": 1, "information_density": 0.551, "quality_score": 0.7755, "entities": { "genes": [ "SS1995", "SS1994" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:51.045249", "source": { "split": "train_shard_00001", "doc_id": 4989 }, "chunk_id": "train_shard_00001_4989_0", "global_id": 12707 }, { "text": "A polyphasic taxonomic study using conventional biochemical and the rapid ID 32 STREP system, MALDI-TOF MS, cell fatty acid analysis, pairwise sequence comparisons of the 16S rRNA, rpoA, rpoB, pheS and groL genes, and comparative core and whole genome sequence analyses revealed that strains SS1994T and SS1995T were two novel Vagococcus species. The novel taxonomic status of the two isolates was confirmed with core genome phylogeny, average nucleotide identity <84 % and in silico DNA-DNA hybridization <28 % to any other Vagococcus species. The names Vagococcusbubulae SS1994T=(CCUG 70831T=LMG 30164T) and Vagococcusvulneris SS1995T=(CCUG 70832T=LMG 30165T) are proposed.\n\nVagococcus bubulae sp. nov., isolated from ground beef, and Vagococcus vulneris sp. nov., isolated from a human foot wound.", "token_count": 331, "char_count": 888, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7565, "quality_score": 0.8783, "entities": { "genes": [ "SS1995", "SS1994" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:51.612393", "source": { "split": "train_shard_00001", "doc_id": 4989 }, "chunk_id": "train_shard_00001_4989_1", "global_id": 12708 }, { "text": "

Background

Ampicillin-resistant Enterococcus faecium (ARE) has emerged as a nosocomial pathogen. Here, we quantified ARE carriage in different community sources and determined genetic relatedness with hospital ARE.

Methods and results

ARE was recovered from rectal swabs of 24 of 79 (30%) dogs, 11 of 85 (13%) cats and 0 of 42 horses and from 3 of 40 (8%) faecal samples of non-hospitalized humans receiving amoxicillin. Multi-locus Sequence Typing revealed 21 sequence types (STs), including 5 STs frequently associated with hospital-acquired infections. Genes previously found to be enriched in hospital ARE, such as IS16, orf903, orf905, orf907, were highly prevalent in community ARE (≥79%), while genes with a proposed role in pathogenesis, such as esp, hyl and ecbA, were found rarely (≤5%) in community isolates. Comparative genome analysis of 2 representative dog isolates revealed that the dog strain of ST192 was evolutionarily closely linked to two previously sequenced hospital ARE, but had, based on gene content, more genes in common with the other, evolutionarily more distantly related, dog strain (ST266).

Conclusion

ARE were detected in dogs, cats and sporadically in healthy humans, with evolutionary linkage to hospital ARE. Yet, their accessory genome has diversified, probably as a result of niche adaptation.\n\nHospital and community ampicillin-resistant Enterococcus faecium are evolutionarily closely linked but have diversified through niche adaptation.", "token_count": 411, "char_count": 1500, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6635, "quality_score": 0.8318, "entities": { "genes": [ "IS16", "ST266", "ST192" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:52.235776", "source": { "split": "train_shard_00001", "doc_id": 4990 }, "chunk_id": "train_shard_00001_4990_0", "global_id": 12709 }, { "text": "Shiga toxin (Stx)-producing Escherichia coli (STEC) causes serious gastrointestinal illness, including hemorrhagic colitis and hemolytic uremic syndrome. Two types of Stxs (Stx1 and Stx2) are known and both are encoded by bacteriophages (Stx phages), but the production of Stx2 is known to be a major risk factor for severe STEC infections. The production of Stx2, but not Stx1, is tightly coupled with the induction of Stx phages, and Stx2 production levels vary between STEC strains even within the same serotype. Here, we analyzed the genomic diversity of all Stx phages in 71 strains representing the entire O145:H28 lineage, one of the often highly pathogenic STECs, and the relationship between the variations in Stx phage genomes and the levels of Stx2 production by host strains. Our analysis reveals highly dynamic natures of Stx phages in O145:H28, including the independent acquisition of similar Stx phages by different sublineages, the recent transfer of Stx phage between different sublineages, and the frequent gain and loss of Stx phages in some sublineages. We also show the association of the Stx2 phage types with the Stx2 production levels of host strains: strains carrying short-tailed Stx2 phages exhibited significantly higher Stx2 production levels than those carrying long-tailed Stx2 phages. Detailed analyses of the Stx2 phage genomes revealed that both of short- and long-tailed phages exhibited sequence diversification and they were divided into two groups, respectively, based on the sequence similarity of the phage early region encoding genes responsible for phage induction, short-tailed phages contained early regions clearly different in genetic organization from those in long-tailed phages. Therefore, the variations in the early regions between short-and long-tailed Stx2 phages appeared to be linked to a striking difference in Stx2 production levels in their host strains", "token_count": 479, "char_count": 1919, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5331, "quality_score": 0.7666, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:52.891406", "source": { "split": "train_shard_00001", "doc_id": 4991 }, "chunk_id": "train_shard_00001_4991_0", "global_id": 12710 }, { "text": "These results broaden our understanding of the diversification and dynamism of Stx phages in O145:H28 and the association of Stx2 phage types with the Stx2 production level in this STEC lineage.\n\nDiversity of Shiga toxin transducing phages in Escherichia coli O145:H28 and the different Shiga toxin 2 production levels associated with short- or long-tailed phages.", "token_count": 113, "char_count": 371, "word_count": 55, "semantic_coherence": 1, "information_density": 0.6909, "quality_score": 0.8455, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:53.272356", "source": { "split": "train_shard_00001", "doc_id": 4991 }, "chunk_id": "train_shard_00001_4991_1", "global_id": 12711 }, { "text": "The detection of borderline oxacillin-resistant Staphylococcus aureus (BORSA) represents a challenge to both, veterinary and human laboratories. Between 2015 and 2017, 19 equine S. aureus with elevated minimal inhibitory concentrations for oxacillin were detected in routine diagnostics. The aim of this study was to characterize these isolates to identify factors possibly associated with the BORSA phenotype. All S. aureus were subjected to antimicrobial susceptibility testing and whole genome sequencing (WGS). A quantifiable β-lactamase activity assay was performed for a representative subset of 13 isolates. The WGS data analysis of the 19 BORSA isolates identified two different genomic lineages, sequence type (ST) 1 and ST1660. The core genome multilocus sequence typing (cgMLST) revealed a close relatedness of all isolates belonging to either ST1 or ST1660. The WGS analysis identified the resistance genes aadD, dfrG, tet(L), and/or blaZ and aacA-aphD. Phenotypic resistance to penicillins, aminoglycosides, tetracyclines, fluoroquinolones and sulfamethoxazole/trimethoprim was observed in the respective isolates. For the penicillin-binding proteins 1-4, amino acid substitutions were predicted using WGS data. Since neither transglycosylase nor transpeptidase domains were affected, these alterations might not explain the BORSA phenotype. Moreover, β-lactamase activity was found to be associated with an inducible blaZ gene. The lineage-specific differences regarding the expression profiles were noted.\n\nMolecular Characterization of Equine Staphylococcus aureus Isolates Exhibiting Reduced Oxacillin Susceptibility.", "token_count": 506, "char_count": 1704, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6651, "quality_score": 0.8326, "entities": { "genes": [ "ST1660", "ST1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:53.899951", "source": { "split": "train_shard_00001", "doc_id": 4992 }, "chunk_id": "train_shard_00001_4992_0", "global_id": 12712 }, { "text": "The occurrence of killer wine yeasts in Comahue Region (Patagonia, Argentina) was studied. Wild wine yeasts were isolated from spontaneously fermenting Merlot and Malbec type musts. Out of 135 isolates analyzed 37% were sensitive to some well characterized killer toxins as K1-K10 and did not show killer activity (sensitive phenotype, S), 21% showed neutral phenotype (N) and 42% demonstrated killer activity (killer phenotype, K). All but two killer strains, identified as Candida pulcherrima and Kluyveromyces marxianus, were Saccharomyces cerevisiae. Additionally, all killer strains were sensitive to some killer reference strains, showing a killer-sensitive phenotype (KS); neither Saccharomyces or non-Saccharomyces wild yeasts were phenotype killer-resistant (KR). The incidence of the killer character varied with respect to fermentation stage and grape variety, increasing throughout fermentation (13-55% to 36-90%). Irrespective of grape must type, the neutral and sensitive yeasts were ever predominant at initial stages of fermentation. All but six neutral strains, identified as Saccharomyces cerevisiae, were Kloeckera apiculata.\n\nKiller behaviour in wild wine yeasts associated with Merlot and Malbec type musts spontaneously fermented from northwestern Patagonia (Argentina).", "token_count": 338, "char_count": 1292, "word_count": 175, "semantic_coherence": 1, "information_density": 0.6229, "quality_score": 0.8114, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:54.480161", "source": { "split": "train_shard_00001", "doc_id": 4993 }, "chunk_id": "train_shard_00001_4993_0", "global_id": 12713 }, { "text": "The occurrence of yeasts on ripe fruits and frozen pulps of pitanga (Eugenia uniflora L), mangaba (Hancornia speciosa Gom.), umbu (Spondias tuberosa Avr. Cam.), and acerola (Malpighia glaba L) was verified. The incidence of proteolytic, pectinolytic, and mycocinogenic yeasts on these communities was also determined. A total of 480 colonies was isolated and grouped in 405 different strains. These corresponded to 42 ascomycetous and 28 basidiomycetous species. Candida sorbosivorans, Pseudozyma antarctica, C. spandovensis-like, C. spandovensis, Kloeckera apis, C. parapsilosis, Rhodotorula graminis, Kluyveromyces marxianus, Cryptococcus laurentii, Metchnikowia sp (isolated only from pitanga ripe fruits), Issatchenkia occidentalis and C. krusei (isolated only from mangaba frozen pulps), were the most frequent species. The yeast communities from pitanga ripe fruits exhibited the highest frequency of species, followed by communities from acerola ripe fruits and mangaba frozen pulps. Yeast communities from frozen pulp and ripe fruits of umbu had the lowest number of species. Except the yeasts from pitanga, yeast communities from frozen pulp exhibited higher number of yeasts than ripe fruit communities. Mycocinogenic yeasts were found in all of the substrates studied except in communities from umbu ripe fruits and pitanga frozen pulps. Most of the yeasts found to produce mycocins were basidiomycetes and included P. antarctica, Cryptococcus albidus, C. bhutanensis-like, R. graminis and R. mucilaginosa-like from pitanga ripe fruits as well as black yeasts from pitanga and acerola ripe fruits. The umbu frozen pulps community had the highest frequency of proteolytic species. Yeasts able to hydrolyse casein at pH 5.0 represented 38.5% of the species isolated", "token_count": 531, "char_count": 1774, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5138, "quality_score": 0.7569, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:58:55.134696", "source": { "split": "train_shard_00001", "doc_id": 4994 }, "chunk_id": "train_shard_00001_4994_0", "global_id": 12714 }, { "text": "Thirty-seven percent of yeast isolates were able to hydrolyse casein at pH 7.0. Pectinolytic yeasts were found in all of the communities studied, excepted for those of umbu frozen pulps. The highest frequency of pectinolytic activity was found in mangaba frozen pulp communities. Around 30% of all isolates produced pectinases. The ability to split arbutin was observed in all communities ranging from 8% in yeasts from pitanga frozen pulps to 40.6% in acerola ripe fruit communities. Among 432 species tested, 125 were active for beta-glucosidase production, and Kloeckera apis, P. antarctica, C. sorbosivorans, and C. spandovensis-like were the most active species.\n\nYeasts associated with fresh and frozen pulps of Brazilian tropical fruits.", "token_count": 215, "char_count": 744, "word_count": 112, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:55.596028", "source": { "split": "train_shard_00001", "doc_id": 4994 }, "chunk_id": "train_shard_00001_4994_1", "global_id": 12715 }, { "text": "Non-typhoidal Salmonella infections represent a substantial burden of illness in humans, and the increasing prevalence of antimicrobial resistance among these infections is a growing concern. Using a combination of Salmonella isolate short-read whole-genome sequence data from select human cases, raccoons, livestock and environmental sources, and an epidemiological framework, our objective was to determine if there was evidence for potential transmission of Salmonella and associated antimicrobial resistance determinants between these different sources in the Grand River watershed in Ontario, Canada. Logistic regression models were used to assess the potential associations between source type and the presence of select resistance genes and plasmid incompatibility types. A total of 608 isolates were obtained from the following sources: humans (n = 58), raccoons (n = 92), livestock (n = 329), and environmental samples (n = 129). Resistance genes of public health importance, including bla CMY-2, were identified in humans, livestock, and environmental sources, but not in raccoons. Most resistance genes analyzed were significantly more likely to be identified in livestock and/or human isolates than in raccoon isolates. Based on a 3,002-loci core genome multi-locus sequence typing (cgMLST) scheme, human Salmonella isolates were often more similar to isolates from livestock and environmental sources, than with those from raccoons. Rare instances of serovars S. Heidelberg and S. Enteritidis in raccoons likely represent incidental infections and highlight possible acquisition and dissemination of predominantly poultry-associated Salmonella by raccoons within these ecosystems. Raccoon-predominant serovars were either not identified among human isolates (S. Agona, S", "token_count": 501, "char_count": 1892, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5918, "quality_score": 0.7959, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:56.252655", "source": { "split": "train_shard_00001", "doc_id": 4995 }, "chunk_id": "train_shard_00001_4995_0", "global_id": 12716 }, { "text": "Thompson) or differed by more than 350 cgMLST loci (S. Newport). Collectively, our findings suggest that the rural population of raccoons on swine farms in the Grand River watershed are unlikely to be major contributors to antimicrobial resistant human Salmonella cases in this region.\n\nRural Raccoons (Procyon lotor) Not Likely to Be a Major Driver of Antimicrobial Resistant Human Salmonella Cases in Southern Ontario, Canada: A One Health Epidemiological Assessment Using Whole-Genome Sequence Data.", "token_count": 155, "char_count": 530, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7838, "quality_score": 0.8919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:56.691104", "source": { "split": "train_shard_00001", "doc_id": 4995 }, "chunk_id": "train_shard_00001_4995_1", "global_id": 12717 }, { "text": "Escherichia coli is one of the most well-adapted and pathogenically versatile bacterial organisms. It causes a variety of human infections, including gastrointestinal illnesses and extraintestinal infections. It is also part of the intestinal commensal flora of humans and other mammals. Groups of E. coli that cause diarrhea are often described as intestinal pathogenic E. coli (IPEC), while those that cause infections outside of the gut are called extraintestinal pathogenic E. coli (ExPEC). IPEC can cause a variety of diarrheal illnesses as well as extraintestinal syndromes such as hemolytic-uremic syndrome. ExPEC cause urinary tract infections, bloodstream infection, sepsis, and neonatal meningitis. IPEC and ExPEC have thus come to be referred to as pathogenic variants of E. coli or pathovars. While IPEC can be distinguished from commensal E. coli based on their characteristic virulence factors responsible for their associated clinical manifestations, ExPEC cannot be so easily distinguished. IPEC most likely have reservoirs outside of the human intestine but it is unclear if ExPEC represent nothing more than commensal E. coli that breach a sterile barrier to cause extraintestinal infections. This question has become more complicated by the advent of whole genome sequencing (WGS) that has raised a new question about the taxonomic characterization of E. coli based on traditional clinical microbiologic and phylogenetic methods. This review discusses how molecular epidemiologic approaches have been used to address these questions, and how answers to these questions may contribute to our better understanding of the epidemiology of infections caused by E. coli. *This article is part of a curated collection.\n\nDistinguishing Pathovars from Nonpathovars: Escherichia coli.", "token_count": 501, "char_count": 1856, "word_count": 261, "semantic_coherence": 1, "information_density": 0.5939, "quality_score": 0.7969, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:57.341200", "source": { "split": "train_shard_00001", "doc_id": 4996 }, "chunk_id": "train_shard_00001_4996_0", "global_id": 12718 }, { "text": "The Fusobacterium genus comprises Gram-negative, obligate anaerobic bacteria that typically reside in the periodontium of the oral cavity, gastrointestinal tract, and female genital tract. The association of Fusobacterial spp. with colorectal tumours is widely accepted, with further evidence that this pathogen may also be implicated in the development of other malignancies. Fusobacterial spp. influence malignant cell behaviours and the tumour microenvironment in various ways, which can be related to the multiple surface adhesins expressed. These adhesins include Fap2 (fibroblast-activated protein 2), CpbF (CEACAM binding protein of Fusobacteria), FadA (Fusobacterium adhesin A) and FomA (Fusobacterial outer membrane protein A). This review outlines the influence of Fusobacteria in promoting cancer initiation and progression, impacts of therapeutic outcomes and discusses potential therapeutic interventions where appropriate.\n\nThe emerging role of Fusobacteria in carcinogenesis.", "token_count": 253, "char_count": 990, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7364, "quality_score": 0.8682, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:57.833260", "source": { "split": "train_shard_00001", "doc_id": 4997 }, "chunk_id": "train_shard_00001_4997_0", "global_id": 12719 }, { "text": "Lacticaseibacillus rhamnosus is a generalist that can adapt to different ecological niches, serving as a valuable source of probiotics. The genome of L. rhamnosus X253 contains one chromosome and no plasmids, with a size of 2.99 Mb. Both single-copy orthologous gene-based phylogenetic analysis and average nucleotide identity indicated that dairy-derived L. rhamnosus X253 was most closely related to the human-intestine-derived strain L. rhamnosus LOCK908, rather than other dairy strains. The adaptation of L. rhamnosus X253 and the human-intestine-derived strain L. rhamnosus GG to different ecological niches was explained by structural variation analysis and COG annotation. Hemolytic assays, API ZYM assays, and antimicrobial susceptibility tests were performed to validate risk-related sequences such as virulence factors, toxin-encoding genes, and antibiotic-resistance genes in the genomes of L. rhamnosus X253 and GG. The results showed that L. rhamnosus GG was able to use L-fucose, had a higher tolerance to bile salt, and adhered better to CaCo-2 cells. In contrast, L. rhamnosus X253 was capable of utilizing D-lactose, withstood larger quantities of hydrogen peroxide, and possessed excellent antioxidant properties. This study confirmed the safety and probiotic properties of L. rhamnosus X253 via complete genome and phenotype analysis, suggesting its potential as a probiotic.\n\nAssessing the Safety and Probiotic Characteristics of Lacticaseibacillus rhamnosus X253 via Complete Genome and Phenotype Analysis.", "token_count": 499, "char_count": 1605, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8037, "entities": { "genes": [ "LOCK908" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:58.482493", "source": { "split": "train_shard_00001", "doc_id": 4998 }, "chunk_id": "train_shard_00001_4998_0", "global_id": 12720 }, { "text": "Staphylococcus aureus and methicillin resistant Staphylococcus aureus (MRSA) are important pathogens of humans and livestock, including dairy cows. In livestock it represents a concern for public health as it may act as a reservoir that can infect humans and provide a source of transferrable resistance genes. The divergent mecA gene, mecC, was first identified in dairy cows in the UK, and has since been detected in many species in continental Europe. However, limited data exists on the epidemiological characteristics or the transmission dynamics of bovine mecC MRSA in the UK. S. aureus Mobile Genetic Elements (MGEs) often encode virulence and antimicrobial resistance genes that can contribute to the pathogenicity of the strain. Acquisition or loss of MGEs and variations within the core genome are reported to play an important role in S. aureus host adaptation although the mechanisms underlying S. aureus host specificity are not fully understood. This study was undertaken to determine the antimicrobial resistance and bovine associated virulence features of S. aureus isolated from bovine milk. The first two chapters of this thesis comprise of an introduction and a description of the methods used. Chapter 3 describes ... (continues)\n\nA genomic analysis of methicillin resistant Staphylococcus aureus from bovine milk and the discovery of a novel streptococcus species", "token_count": 338, "char_count": 1384, "word_count": 210, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:59.059345", "source": { "split": "train_shard_00001", "doc_id": 4999 }, "chunk_id": "train_shard_00001_4999_0", "global_id": 12721 }, { "text": "Aeromonas salmonicida is a Gram-negative bacterium, known as a fish pathogen since its discovery. Although the species was initially considered psychrophilic, a mesophilic subspecies (pectinolytica) and many other mesophilic strains still not attributed to subspecies have been described in the last two decades. These mesophilic strains were sampled from various sources, including humans, and some of them are known to be pathogenic. In this study, we describe a strain, JF2480, which was isolated from the spleen, and also found the kidney and liver of a dead pied avocet (Recurvirostra avosetta), a type of migratory bird inhabiting aquatic environments. A core genome phylogenomic analysis suggests that JF2480 is taxonomically distant from other known A. salmonicida subspecies. The genome sequence confirms that the strain possesses key virulence genes that are present in the typical A. salmonicida psychrophilic subspecies, with the exception of the genes encoding the type three secretion system (T3SS). Bacterial virulence assays conducted on the surrogate host Dictyostelium discoideum amoeba confirmed that the strain is virulent despite the lack of T3SS. Bacterial growth curves showed that strain JF2480 grow well at 40 °C, the body temperature of the pied avocet, and even faster at 41 °C, compared to other mesophilic strains. Discovery of this strain further demonstrates the extent of the phylogenomic tree of this species. This study also suggests that A. salmonicida can infect a wider array of hosts than previously suspected and that we need to rethink the way we perceive A. salmonicida's natural environment.", "token_count": 474, "char_count": 1701, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": { "genes": [ "JF2480" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:58:59.724459", "source": { "split": "train_shard_00002", "doc_id": 0 }, "chunk_id": "train_shard_00002_0_0", "global_id": 12722 }, { "text": "A Mesophilic Aeromonas salmonicida Strain Isolated from an Unsuspected Host, the Migratory Bird Pied Avocet.", "token_count": 43, "char_count": 115, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:00.078918", "source": { "split": "train_shard_00002", "doc_id": 0 }, "chunk_id": "train_shard_00002_0_1", "global_id": 12723 }, { "text": "

Background

Oral mucositis is a serious and debilitating side effect of conditioning regimens for hematopoietic stem cell transplant (HSCT). Through HSCT, the homeostasis in the oral cavity is disrupted. The contribution of the oral microflora to mucositis remains to be clarified. The aim of our study was to investigate the relationship between yeasts, bacteria associated with periodontitis, and oral ulcerations in HSCT recipients.

Methods

This prospective observational study included 49 adult HSCT recipients. Twice weekly, oral ulcerations were scored, and oral rinsing samples were obtained. Samples were evaluated for the total bacterial load; the Gram-negative bacteria: Aggregatibacter actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, Parvimonas micra, Fusobacterium nucleatum, Tannerella forsythia, and Treponema denticola; and the yeasts: Candida albicans, Candida glabrata, Candida kefyr, Candida krusei, Candida parapsilosis, and Candida tropicalis using real-time polymerase chain reaction with specific primers and probes. Explanatory variables for oral ulcerations were calculated using the multilevel generalized estimated equations (GEE) technique.

Results

None of the samples was positive for A. actinomycetemcomitans, while F. nucleatum was found most often (66 % of samples). C. albicans was the most isolated yeast (88 % of samples), whereas C. parapsilosis was found in only 8 % of the samples. Multivariate GEE analyses identified P. gingivalis, P. micra, T. denticola, F. nucleatum, C. glabrata, and C. kefyr as significant explanatory variables of oral ulcerations.

Conclusions

Our data indicate that P. gingivalis in particular, but also P. micra, T. denticola, F. nucleatum, C. glabrata, and C", "token_count": 517, "char_count": 1774, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:59:01.124349", "source": { "split": "train_shard_00002", "doc_id": 1 }, "chunk_id": "train_shard_00002_1_0", "global_id": 12724 }, { "text": "kefyr may play a role in ulcerative oral mucositis in patients undergoing HSCT.\n\nOral bacteria and yeasts in relationship to oral ulcerations in hematopoietic stem cell transplant recipients.", "token_count": 53, "char_count": 191, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8214, "quality_score": 0.9107, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:01.498764", "source": { "split": "train_shard_00002", "doc_id": 1 }, "chunk_id": "train_shard_00002_1_1", "global_id": 12725 }, { "text": "Different surveillance studies (2005-2015) in northwest Spain revealed the presence of eae-positive isolates of Escherichia coli O153:H10 in meat for human consumption, poultry farm, wildlife and human diarrheagenic samples. The aim of this study was to explore the genetic and genomic relatedness between human and animal/meat isolates, as well as the mechanism of its persistence. We also wanted to know whether it was a geographically restricted lineage, or whether it was also reported elsewhere. Conventional typing showed that 32 isolates were O153:H10-A-ST10 fimH54, fimAvMT78, traT and eae-beta1. Amongst these, 21 were CTX-M-32 or SHV-12 producers. The PFGE XbaI-macrorestriction comparison showed high similarity (>85%). The plasmidome analysis revealed a stable combination of IncF (F2:A-:B-), IncI1 (STunknown) and IncX1 plasmid types, together with non-conjugative Col-like plasmids. The core genome investigation based on the cgMLST scheme from EnteroBase proved close relatedness between isolates of human and animal origin. Our results demonstrate that a hybrid MDR aEPEC/ExPEC of the clonal group O153:H10-A-ST10 (CH11-54) is circulating in our region within different hosts, including wildlife. It seems implicated in human diarrhea via meat transmission, and in the spreading of ESBL genes (mainly of CTX-M-32 type). We found genomic evidence of a related hybrid aEPEC/ExPEC in at least one other country.", "token_count": 465, "char_count": 1484, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6961, "quality_score": 0.848, "entities": { "genes": [ "MT78", "ST10", "CH11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:02.185407", "source": { "split": "train_shard_00002", "doc_id": 2 }, "chunk_id": "train_shard_00002_2_0", "global_id": 12726 }, { "text": "Genomic Characterization of Escherichia coli Isolates Belonging to a New Hybrid aEPEC/ExPEC Pathotype O153:H10-A-ST10 eae-beta1 Occurred in Meat, Poultry, Wildlife and Human Diarrheagenic Samples.", "token_count": 87, "char_count": 210, "word_count": 24, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:02.607352", "source": { "split": "train_shard_00002", "doc_id": 2 }, "chunk_id": "train_shard_00002_2_1", "global_id": 12727 }, { "text": "Corynebacterium glutamicum is an excellent platform for the production of amino acids, and is widely used in the fermentation industry. Most industrial strains are traditionally obtained by repeated processes of random mutation and selection, but the genotype of these strains is often unclear owing to the absence of genomic information. As such, it is difficult to improve the growth and amino acid production of these strains via metabolic engineering. In this study, we generated a complete genome map of an industrial L-valine-producing strain, C. glutamicum XV. In order to establish the relationship between genotypes and physiological characteristics, a comparative genomic analysis was performed to explore the core genome, structural variations, and gene mutations referring to an industrial L-leucine-producing strain, C. glutamicum CP, and the widely used C. glutamicum ATCC 13032. The results indicate that a 36,349 bp repeat sequence in the CP genome contained an additional copy each of lrp and brnFE genes, which benefited the export of L-leucine. However, in XV, the kgd and panB genes were disrupted by nucleotide insertion, which increase the availability of precursors to synthesize L-valine. Moreover, the specific amino acid substitutions in key enzymes increased their activities. Additionally, a novel strategy is proposed to remodel central carbon metabolism and reduce pyruvate consumption without having a negative impact on cell growth by introducing the CP-derived mutant H+/citrate symporter. These results further our understanding regarding the metabolic networks in these strains and help to elucidate the influence of different genotypes on these processes.\n\nComparative Genomic and Genetic Functional Analysis of Industrial L-Leucine- and L-Valine-Producing Corynebacterium glutamicum Strains.", "token_count": 495, "char_count": 1902, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:03.261807", "source": { "split": "train_shard_00002", "doc_id": 3 }, "chunk_id": "train_shard_00002_3_0", "global_id": 12728 }, { "text": "

Background

Chlamydia are ancient intracellular pathogens with reduced, though strikingly conserved genome. Despite their parasitic lifestyle and isolated intracellular environment, these bacteria managed to avoid accumulation of deleterious mutations leading to subsequent genome degradation characteristic for many parasitic bacteria.

Results

We report pan-genomic analysis of sixteen species from genus Chlamydia including identification and functional annotation of orthologous genes, and characterization of gene gains, losses, and rearrangements. We demonstrate the overall genome stability of these bacteria as indicated by a large fraction of common genes with conserved genomic locations. On the other hand, extreme evolvability is confined to several paralogous gene families such as polymorphic membrane proteins and phospholipase D, and likely is caused by the pressure from the host immune system.

Conclusions

This combination of a large, conserved core genome and a small, evolvable periphery likely reflect the balance between the selective pressure towards genome reduction and the need to adapt to escape from the host immunity.\n\nChlamydia pan-genomic analysis reveals balance between host adaptation and selective pressure to genome reduction.", "token_count": 287, "char_count": 1282, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:03.814087", "source": { "split": "train_shard_00002", "doc_id": 4 }, "chunk_id": "train_shard_00002_4_0", "global_id": 12729 }, { "text": "Alcohol fermentation of lactose was investigated using a recombinant flocculating Saccharomyces cerevisiae, expressing the LAC4 (coding for beta-galactosidase) and LAC12 (coding for lactose permease) genes of Kluyveromyces marxianus. Data on yeast fermentation and growth on a medium containing lactose as the sole carbon source are presented. In the range of studied lactose concentrations, total lactose consumption was observed with a conversion yield of ethanol close to the expected theoretical value. For the continuously operating bioreactor, an ethanol productivity of 11 g L(-1) h(-1) (corresponding to a feed lactose concentration of 50 g L(-1) and a dilution rate of 0.55 h(-1)) was obtained, which is 7 times larger than the continuous conventional systems. The system stability was confirmed by keeping it in operation for 6 months.\n\nContinuous ethanol fermentation of lactose by a recombinant flocculating Saccharomyces cerevisiae strain.", "token_count": 258, "char_count": 952, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [ "LAC12", "LAC4" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:04.359712", "source": { "split": "train_shard_00002", "doc_id": 5 }, "chunk_id": "train_shard_00002_5_0", "global_id": 12730 }, { "text": "

Background

Africa has the highest incidence of gonorrhea in the world. However, little is known about gonococcal populations in this continent or mechanisms of antimicrobial resistance (AMR).

Methods

Whole-genome sequence data were analyzed from 103 Neisseria gonorrhoeae isolates from 73 patients, mainly men who have sex with men, from coastal Kenya. We annotated loci, defined the core genome, defined mechanisms of AMR, and performed phylogenetic analysis. For patients with multiple episodes of gonorrhea, we determined whether infections occurred with related strains.

Results

We identified 3 clusters of isolates that are phylogenetically distinct from isolates found elsewhere. Plasmids were virtually ubiquitous: pTetM and pblaTEM were found in 97%, and 55% of isolates, respectively. This was associated with high doxycycline use for undiagnosed sexually transmitted infections. Twenty-three percent of multiple episodes of gonorrhea in the same individual were caused by a related strain, suggesting inadequate treatment or reinfection.

Conclusions

The prevalence of plasmid-mediated AMR in Kenyan gonococci contrasts with that in wealthy countries, where AMR is largely chromosomally mediated. Antimicrobials have a profound effect on the maintenance of lineages harboring plasmids. Doxycycline can select for tetracycline and penicillin resistance, through plasmid cooperation. Understanding the mechanisms of AMR in high-risk groups is required to inform treatment strategies.\n\nIdentification of Novel Neisseria gonorrhoeae Lineages Harboring Resistance Plasmids in Coastal Kenya.", "token_count": 430, "char_count": 1623, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6746, "quality_score": 0.8373, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:04.986230", "source": { "split": "train_shard_00002", "doc_id": 6 }, "chunk_id": "train_shard_00002_6_0", "global_id": 12731 }, { "text": "Lactic acid bacteria and yeasts, representing the prevailing microbiota associated with different foods generally consumed without any cooking, were identified and characterized in vitro for some functional properties, such as acid-bile tolerance and antigenotoxic activity. In particular, 22 Lactobacillus plantarum strains and 14 yeasts were studied. The gastro-intestinal tract tolerance of all the strains was determined by exposing washed cell suspensions at 37°C to a simulated gastric juice (pH 2.0), containing pepsin (0.3% w/v) and to a simulated small intestinal juice (pH 8.0), containing pancreatin (1 mg mL-1) and bile extract (0.5%), thus monitoring changes in total viable count. In general, following a strain-dependent behavior, all the tested strains persisted alive after combined acid-bile challenge. Moreover, many strains showed high in vitro inhibitory activity against a model genotoxin, 4-nitroquinoline-1-oxide (4-NQO), as determined by the short-term method, SOS-Chromotest. Interestingly, the supernatants from bacteria- or yeasts-genotoxin co-incubations exhibited a suppression on SOS-induction produced by 4-NQO on the tester strain Escherichia coli PQ37 (sfiA::lacZ) exceeding, in general, the value of 75%. The results highlight that food associated microorganisms may reach the gut in viable form and prevent genotoxin DNA damage in situ. Our experiments can contribute to elucidate the functional role of food-associated microorganisms general recognized as safe ingested with foods as a part of the diet.\n\nFood-Associated Lactobacillus plantarum and Yeasts Inhibit the Genotoxic Effect of 4-Nitroquinoline-1-Oxide.", "token_count": 505, "char_count": 1717, "word_count": 225, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [ "PQ37" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:05.638392", "source": { "split": "train_shard_00002", "doc_id": 7 }, "chunk_id": "train_shard_00002_7_0", "global_id": 12732 }, { "text": "Production of polygalacturonases from Kluyveromyces marxianus fermentation: preliminary process design and economics.", "token_count": 29, "char_count": 117, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:05.997212", "source": { "split": "train_shard_00002", "doc_id": 8 }, "chunk_id": "train_shard_00002_8_0", "global_id": 12733 }, { "text": "

Introduction

A second botulism outbreak due to Clostridium baratii occurred in France in August 2015 and included three patients who had their meal in a restaurant the same day. We report the characterization of C. baratii isolates including whole genome sequencing (WGS).

Methods

Four C. baratii isolates collected in August 2015 from the outbreak 2 were analysed for toxin production and typing as well as for genetic characterization. WGS was done using using the NEBNext Ultra DNA Library Prep kit for Illumina (New England Biolabs) and sequenced on MiSeq machine (Illumina) in paired-end reads of 250 bases. The phylogenetic tree was generated based on the UPGMA method with genetic distances computed by using the Kimura two-parameter model. Evolutionary analyses were conducted in Bionumerics (V.6.6 Applied Maths).

Results

Three C. baratii isolates for patient's stools and one isolate from meat produced botulinum neurotoxin (BoNT) type F and retained a bont/F7 gene in OrfX cluster. All isolates were identical according to the WGS. However, phylogeny of the core genome showed that the four C. baratii strains were distantly related to that of the previous C. baratii outbreak in France in 2014 and from the other C. baratii strains reported in databanks.

Discussion

The fact that the strains isolated from the patients and meat samples were genetically identical supports that the meat used for the Bolognese sauce was responsible for this second botulism outbreak in France. These isolates were unrelated to that from the first C. baratii outbreak in France in 2014 indicating a distinct source of contamination. WGS provided robust determination of genetic relatedness and information regarding BoNT typing and toxin gene locus genomic localization.\n\nCharacterization of Clostridium Baratii Type F Strains Responsible for an Outbreak of Botulism Linked to Beef Meat Consumption in France.", "token_count": 508, "char_count": 1931, "word_count": 286, "semantic_coherence": 1, "information_density": 0.5559, "quality_score": 0.778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:06.629449", "source": { "split": "train_shard_00002", "doc_id": 9 }, "chunk_id": "train_shard_00002_9_0", "global_id": 12734 }, { "text": "Thirty-three Yersinia strains previously characterized by the French Yersinia National Reference Laboratory (YNRL) and isolated from humans and animals were suspected to belong to six novel species by a recently described core genome multilocus sequence typing scheme. These strains and five additional strains from the YNRL were characterized using a polyphasic taxonomic approach including a phylogenetic analysis based on 500 core genes, determination of average nucleotide identity (ANI), determination of DNA G+C content and identification of phenotypic features. Phylogenetic analysis confirmed that the 38 studied strains formed six well-demarcated clades. ANI values between these clades and their closest relatives were <94.7 % and ANI values within each putative novel species were >97.5 %. Distinctive biochemical characteristics were identified in five out of the six novel species. All of these data demonstrated that the 38 strains belong to six novel species of the genus Yersinia: Yersinia artesiana sp. nov., type strain IP42281T (=CIP 111845T=DSM 110725T); Yersinia proxima sp. nov., type strain IP37424T (=CIP 111847T=DSM 110727T); Yersinia alsatica sp. nov., type strain IP38850T (=CIP 111848T=DSM 110726T); Yersinia vastinensis sp", "token_count": 464, "char_count": 1399, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6384, "quality_score": 0.8192, "entities": { "genes": [ "IP37424", "IP42281", "IP38850" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:07.284124", "source": { "split": "train_shard_00002", "doc_id": 10 }, "chunk_id": "train_shard_00002_10_0", "global_id": 12735 }, { "text": "nov., type strain IP38594T (=CIP 111844T=DSM 110738T); Yersinia thracica sp. nov., type strain IP34646T (=CIP 111842T=DSM 110736T); and Yersinia occitanica sp. nov., type strain IP35638T (=CIP 111843T=DSM 110739T).\n\nYersinia artesiana sp. nov., Yersinia proxima sp. nov., Yersinia alsatica sp. nov., Yersina vastinensis sp. nov., Yersinia thracica sp. nov. and Yersinia occitanica sp. nov., isolated from humans and animals.", "token_count": 297, "char_count": 579, "word_count": 58, "semantic_coherence": 1, "information_density": 0.4828, "quality_score": 0.7414, "entities": { "genes": [ "IP38594", "IP34646", "IP35638" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:07.838932", "source": { "split": "train_shard_00002", "doc_id": 10 }, "chunk_id": "train_shard_00002_10_1", "global_id": 12736 }, { "text": "Five Bifidobacterium strains, i.e. 2020BT, 2028BT, 2033BT, 2034BT and 2036BT, were isolated from European beaver (Castor fiber), Goeldi's marmoset (Callimicogoeldii), black-capped squirrel monkey (Saimiriboliviensissubsp. peruviensis) and Patagonian mara (Dolichotispatagonum). All of these isolates were shown to be Gram-positive, facultative anaerobic, d-fructose 6-phosphate phosphoketolase-positive, non-motile and non-sporulating", "token_count": 204, "char_count": 489, "word_count": 46, "semantic_coherence": 1, "information_density": 0.9348, "quality_score": 0.9674, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:08.304173", "source": { "split": "train_shard_00002", "doc_id": 11 }, "chunk_id": "train_shard_00002_11_0", "global_id": 12737 }, { "text": "Phylogenetic analyses based on 16S rRNA gene sequences, multilocus sequences (including hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that bifidobacterial strains 2020BT, 2028BT, 2033BT, 2034BT and 2036BT exhibit close phylogenetic relatedness to Bifidobacterium biavatii DSM 23969T, Bifidobacterium bifidum LMG 11041T, Bifidobacterium choerinum LMG 10510T, Bifidobacterium gallicum LMG 11596T, Bifidobacterium imperatoris LMG 30297T, Bifidobacterium italicum LMG 30187T and Bifidobacterium vansinderenii LMG 30126T, respectively. Further genotyping based on the genome sequence of the isolated strains combined with phenotypic analyses, clearly show that these strains are distinct from each of the type strains of the so far recognized Bifidobacterium species. Thus, Bifidobacterium castoris sp. nov. (2020BT=LMG 30937T=CCUG 72816T), Bifidobacterium callimiconis sp. nov. (2028BT=LMG 30938T=CCUG 72814T), Bifidobacterium samirii sp. nov", "token_count": 496, "char_count": 1159, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7107, "quality_score": 0.8554, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:08.947457", "source": { "split": "train_shard_00002", "doc_id": 11 }, "chunk_id": "train_shard_00002_11_1", "global_id": 12738 }, { "text": "(2033BT=LMG 30940T=CCUG 72817T), Bifidobacterium goeldii sp. nov. (2034BT=LMG 30939T=CCUG 72815T) and Bifidobacterium dolichotidis sp. nov. (2036BT=LMG 30941T=CCUG 72818T) are proposed as novel Bifidobacterium species.\n\nCharacterization of the phylogenetic diversity of five novel species belonging to the genus Bifidobacterium: Bifidobacterium castoris sp. nov., Bifidobacterium callimiconis sp. nov., Bifidobacterium goeldii sp. nov., Bifidobacterium samirii sp. nov. and Bifidobacterium dolichotidis sp. nov.", "token_count": 267, "char_count": 610, "word_count": 59, "semantic_coherence": 1, "information_density": 0.5932, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:09.496211", "source": { "split": "train_shard_00002", "doc_id": 11 }, "chunk_id": "train_shard_00002_11_2", "global_id": 12739 }, { "text": "A flocculent Saccharomyces cerevisiae strain with the ability to express both the LAC4 (coding for beta-galactosidase) and LAC12 (coding for lactose permease) genes of Kluyveromyces marxianus was constructed. This recombinant strain is not only able to grow on lactose, but it can also ferment this substrate. To our knowledge this is the first time that a recombinant S. cervisiae has been found to ferment lactose in a way comparable to that of the existing lactose-fermenting yeast strains. Moreover, the flocculating capacity of the strain used in this work gives the process several advantages. On the one hand, it allows for operation in a continuous mode at high cell concentration, thus increasing the system's overall productivity; on the other hand, the biomass concentration in the effluent is reduced, thus decreasing product separation/purification costs.\n\nConstruction of a flocculent Saccharomyces cerevisiae fermenting lactose.", "token_count": 245, "char_count": 943, "word_count": 140, "semantic_coherence": 1, "information_density": 0.6643, "quality_score": 0.8321, "entities": { "genes": [ "LAC12", "LAC4" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:09.981007", "source": { "split": "train_shard_00002", "doc_id": 12 }, "chunk_id": "train_shard_00002_12_0", "global_id": 12740 }, { "text": "

Background

Knowledge about how bacterial populations are structured is an important prerequisite for studying their ecology and evolutionary history and facilitates inquiry into host specificity, pathogenicity, geographic dispersal and molecular epidemiology. Erysipelothrix rhusiopathiae is an opportunistic pathogen that is currently reemerging in both the swine and poultry industries globally. This bacterium sporadically causes mortalities in captive marine mammals, and has recently been implicated in large-scale wildlife die-offs. However, despite its economic relevance and broad geographic and host distribution, including zoonotic potential, the global diversity, recombination rates, and population structure of this bacterium remain poorly characterized. In this study, we conducted a broad-scale genomic comparison of E. rhusiopathiae based on a diverse collection of isolates in order to address these knowledge gaps.

Results

Eighty-three E. rhusiopathiae isolates from a range of host species and geographic origins, isolated between 1958 and 2014, were sequenced and assembled using both reference-based mapping and de novo assembly. We found that a high proportion of the core genome (58 %) had undergone recombination. Therefore, we used three independent methods robust to the presence of recombination to define the population structure of this species: a phylogenetic tree based on a set of conserved protein sequences, in silico chromosome painting, and network analysis. All three methods were broadly concordant and supported the existence of three distinct clades within the species E. rhusiopathiae. Although we found some evidence of host and geographical clustering, each clade included isolates from diverse host species and from multiple continents.

Conclusions

Using whole genome sequence data, we confirm recent suggestions that E. rhusiopathiae is a weakly clonal species that has been shaped extensively by homologous recombination. Despite frequent recombination, we can reliably identify three distinct clades that do not clearly segregate by host species or geographic origin. Our results provide an essential baseline for future molecular epidemiological, ecological and evolutionary studies of E", "token_count": 514, "char_count": 2257, "word_count": 304, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:59:10.643959", "source": { "split": "train_shard_00002", "doc_id": 13 }, "chunk_id": "train_shard_00002_13_0", "global_id": 12741 }, { "text": "rhusiopathiae and facilitate comparisons to other recombinogenic, multi-host bacteria.\n\nGenomic analysis of the multi-host pathogen Erysipelothrix rhusiopathiae reveals extensive recombination as well as the existence of three generalist clades with wide geographic distribution.", "token_count": 69, "char_count": 279, "word_count": 33, "semantic_coherence": 1, "information_density": 0.8485, "quality_score": 0.9242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:11.006177", "source": { "split": "train_shard_00002", "doc_id": 13 }, "chunk_id": "train_shard_00002_13_1", "global_id": 12742 }, { "text": "Alternative process to produce oligosaccharides from Kluyveromyces fragilis.", "token_count": 20, "char_count": 76, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:11.366525", "source": { "split": "train_shard_00002", "doc_id": 14 }, "chunk_id": "train_shard_00002_14_0", "global_id": 12743 }, { "text": "In late December 2018, an outbreak of listeriosis occurred after a group of 32 individuals celebrated in a tavern in Styria, Austria; traditional Austrian food (e.g. meat, meat products and cheese) was served. After the celebration, 11 individuals developed gastrointestinal symptoms, including one case with severe sepsis. Cases had consumed mixed platters with several meat products and pâtés originating from a local production facility (company X). Human, food and environmental samples taken from the tavern and company X were tested for L. monocytogenes. Whole genome sequence-based typing detected a novel L. monocytogenes strain of serotype IVb, sequence type 4 and CT7652 in 15 samples; 12 human, two food and one environmental sample from company X with an allelic difference of 0 to 1. Active case finding identified two further cases who had not visited the tavern but tested positive for the outbreak strain. In total, 13 cases (seven females and six males; age range: 4-84 years) were identified. Liver pâté produced by company X was identified as the likely source of the outbreak. Control measures were implemented and since the end of December 2018, no more cases were detected.\n\nListeriosis outbreak likely due to contaminated liver pâté consumed in a tavern, Austria, December 2018.", "token_count": 335, "char_count": 1315, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "CT7652" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:11.940835", "source": { "split": "train_shard_00002", "doc_id": 15 }, "chunk_id": "train_shard_00002_15_0", "global_id": 12744 }, { "text": "Microbial and chemical transformation studies of the marine sesquiterpene phenols (S)-(+)-curcuphenol (1) and (S)-(+)-curcudiol (2), isolated from the Jamaican sponge Didiscus oxeata, were accomplished. Preparative-scale fermentation of 1 with Kluyveromyces marxianus var. lactis (ATCC 2628) has resulted in the isolation of six new metabolites: (S)-(+)-15-hydroxycurcuphenol (3), (S)-(+)-12-hydroxycurcuphenol (4), (S)-(+)-12,15-dihydroxycurcuphenol (5), (S)-(+)-15-hydroxycurcuphenol-12-al (6), (S)-(+)-12-carboxy-10,11-dihydrocurcuphenol (7), and (S)-(+)-12-hydroxy-10,11-dihydrocurcuphenol (8). Fourteen-days incubation of 1 with Aspergillus alliaceus (NRRL 315) afforded the new compounds (S)-(+)-10beta-hydroxycurcudiol (9), (S)-(+)-curcudiol-10-one (10), and (S)-(+)-4-[1-(2-hydroxy-4-methyl)phenyl)]pentanoic acid (11). Rhizopus arrhizus (ATCC 11145) and Rhodotorula glutinus (ATCC 15125) afforded (S)-curcuphenol-1alpha-D-glucopyranoside (12) and (S)-curcudiol-1alpha-D-glucopyranoside (13) when incubated for 6 and 8 days with 1 and 2, respectively. The absolute configuration of C(10) and C(11) of metabolites 7-9 was established by optical rotation computations", "token_count": 497, "char_count": 1173, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7934, "quality_score": 0.8967, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:12.592408", "source": { "split": "train_shard_00002", "doc_id": 16 }, "chunk_id": "train_shard_00002_16_0", "global_id": 12745 }, { "text": "Reaction of 1 with NaNO(2) and HCl afforded (S)-(+)-4-nitrocurcuphenol (14) and (S)-(+)-2-nitrocurcuphenol (15) in a 2:1 ratio. Acylation of 1 and 2 with isonicotinoyl chloride afforded the expected esters (S)-(+)-curcuphenol-1-O-isonicotinate (16) and (S)-(+)-curcudiol-1-O-isonicotinate (17), respectively. Curcuphenol (1) shows potent antimicrobial activity against Candida albicans, Cryptococcus neoformans, methicillin-resistant Staphylococcus aureus, and S. aureus with MIC and MFC/MBC ranges of 7.5-25 and 12.5-50 microg/mL, respectively. Compounds 1 and 3 also display in vitro antimalarial activity against Palsmodium falciparium (D6 clone) with MIC values of 3600 and 3800 ng/mL, respectively (selectivity index >1.3). Both compounds were also active against P. falciparium (W2 clone) with MIC values of 1800 (S.I. >2.6) and 2900 (S.I. >1.6) ng/mL, respectively. Compound 14 shows anti-hepatitis B virus activity with an EC(50) of 61 microg/mL.\n\nMicrobial and chemical transformation studies of the bioactive marine sesquiterpenes (S)-(+)-curcuphenol and -curcudiol isolated from a deep reef collection of the Jamaican sponge Didiscus oxeata.", "token_count": 435, "char_count": 1152, "word_count": 151, "semantic_coherence": 1, "information_density": 0.6954, "quality_score": 0.8477, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:13.234166", "source": { "split": "train_shard_00002", "doc_id": 16 }, "chunk_id": "train_shard_00002_16_1", "global_id": 12746 }, { "text": "

ABSTRACT

Keystone species are thought to play a critical role in determining the structure and function of microbial communities. As they are important candidates for microbiome-targeted interventions, the identification and characterization of keystones is a pressing research goal. Both empirical as well as computational approaches to identify keystones have been proposed, and in particular correlation network analysis is frequently utilized to interrogate sequencing-based microbiome data. Here, we apply an established method for identifying putative keystone taxa in correlation networks. We develop a robust workflow for network construction and systematically evaluate the effects of taxonomic resolution on network properties and the identification of keystone taxa. We are able to identify correlation network keystone species and genera, but could not detect taxa with high keystone potential at lower taxonomic resolution. Based on the correlation patterns observed, we hypothesize that the identified putative keystone taxa have a stabilizing effect that is exerted on correlated taxa. Correlation network analysis further revealed subcommunities present in the dataset that are remarkably similar to previously described patterns. The interrogation of available metatranscriptomes also revealed distinct transcriptional states present in all putative keystone taxa.

IMPORTANCE

The work presented here contributes to the understanding of correlation network keystone taxa and sheds light on their potential ecological significance. By employing a robust workflow based on bootstrapping and subsampling techniques, we identify putative keystone species at the genus and species level. This emphasizes the importance of considering taxonomic resolution when investigating correlations. The potential impact of keystones on community stability provides valuable insights for systematic microbiome manipulation. Furthermore, the observed clusters of co-occurring taxa align well with recent findings and emphasize the reproducibility and relevance of the identified patterns in microbial community composition. We are able to add a functional dimension to the analysis with the identification of distinct transcriptional states in putative keystone taxa, highlighting their functional versatility and adaptability.\n\nCharacteristics of putative keystones in the healthy adult human gut microbiome as determined by correlation network analysis", "token_count": 493, "char_count": 2470, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5229, "quality_score": 0.7615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:13.892625", "source": { "split": "train_shard_00002", "doc_id": 17 }, "chunk_id": "train_shard_00002_17_0", "global_id": 12747 }, { "text": "The drug acarbose is used to treat diabetes and, by inhibiting α-amylase in the small intestine, increases the amount of starch entering the lower digestive tract. This results in changes to the composition of the microbiota and their fermentation products. Acarbose also increases longevity in mice, an effect that has been correlated with increased production of the short-chain fatty acids propionate and butyrate. In experiments replicated across three study sites, two distantly related species in the bacterial family Muribaculaceae were dramatically more abundant in acarbose-treated mice, distinguishing these responders from other members of the family. Bacteria in the family Muribaculaceae are predicted to produce propionate as a fermentation end product and are abundant and diverse in the guts of mice, although few isolates are available. We reconstructed genomes from metagenomes (MAGs) for nine populations of Muribaculaceae to examine factors that distinguish species that respond positively to acarbose. We found two closely related MAGs (B1A and B1B) from one responsive species that both contain a polysaccharide utilization locus with a predicted extracellular α-amylase. These genomes also shared a periplasmic neopullulanase with another, distantly related MAG (B2) representative of the only other responsive species. This gene differentiated these three MAGs from MAGs representative of nonresponding species. Differential gene content in B1A and B1B may be associated with the inconsistent response of this species to acarbose across study sites. This work demonstrates the utility of culture-free genomics for inferring the ecological roles of gut bacteria, including their response to pharmaceutical perturbations. IMPORTANCE The drug acarbose is used to treat diabetes by preventing the breakdown of starch in the small intestine, resulting in dramatic changes in the abundance of some members of the gut microbiome and its fermentation products", "token_count": 482, "char_count": 2003, "word_count": 285, "semantic_coherence": 1, "information_density": 0.5649, "quality_score": 0.7825, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:14.594010", "source": { "split": "train_shard_00002", "doc_id": 18 }, "chunk_id": "train_shard_00002_18_0", "global_id": 12748 }, { "text": "In mice, several of the bacteria that respond most positively are classified in the family Muribaculaceae, members of which produce propionate as a primary fermentation product. Propionate has been associated with gut health and increased longevity in mice. We found that genomes of the most responsive Muribaculaceae showed signs of specialization for starch fermentation, presumably providing them a competitive advantage in the large intestine of animals consuming acarbose. Comparisons among genomes enhance existing models for the ecological niches occupied by members of this family. In addition, genes encoding one type of enzyme known to participate in starch breakdown were found in all three genomes from responding species but none of the other genomes.\n\nMuribaculaceae Genomes Assembled from Metagenomes Suggest Genetic Drivers of Differential Response to Acarbose Treatment in Mice.", "token_count": 219, "char_count": 916, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7287, "quality_score": 0.8643, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:15.059508", "source": { "split": "train_shard_00002", "doc_id": 18 }, "chunk_id": "train_shard_00002_18_1", "global_id": 12749 }, { "text": "This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.\n\nAn Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture.", "token_count": 318, "char_count": 1513, "word_count": 192, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:15.622826", "source": { "split": "train_shard_00002", "doc_id": 19 }, "chunk_id": "train_shard_00002_19_0", "global_id": 12750 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) is a significant cause of gastrointestinal infection and the haemolytic-uremic syndrome (HUS). STEC outbreaks are commonly associated with food but animal contact is increasingly being implicated in its transmission. We report an outbreak of STEC affecting young infants at a nursery in a rural community (three HUS cases, one definite case, one probable case, three possible cases and five carriers, based on the combination of clinical, epidemiological and laboratory data) identified using culture-based and molecular techniques. The investigation identified repeated animal contact (animal farming and petting) as a likely source of STEC introduction followed by horizontal transmission. Whole genome sequencing (WGS) was used for real-time investigation of the incident and revealed a unique strain of STEC O26:H11 carrying stx2a and intimin. Following a public health intervention, no additional cases have occurred. This is the first STEC outbreak reported from Israel. WGS proved as a useful tool for rapid laboratory characterization and typing of the outbreak strain and informed the public health response at an early stage of this unusual outbreak.\n\nReal-time genomic investigation underlying the public health response to a Shiga toxin-producing Escherichia coli O26:H11 outbreak in a nursery.", "token_count": 303, "char_count": 1352, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6495, "quality_score": 0.8247, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:16.193162", "source": { "split": "train_shard_00002", "doc_id": 20 }, "chunk_id": "train_shard_00002_20_0", "global_id": 12751 }, { "text": "Syphilis, which is caused by the sexually transmitted bacterium Treponema pallidum subsp. pallidum, has an estimated 6.3 million cases worldwide per annum. In the past ten years, the incidence of syphilis has increased by more than 150% in some high-income countries, but the evolution and epidemiology of the epidemic are poorly understood. To characterize the global population structure of T. pallidum, we assembled a geographically and temporally diverse collection of 726 genomes from 626 clinical and 100 laboratory samples collected in 23 countries. We applied phylogenetic analyses and clustering, and found that the global syphilis population comprises just two deeply branching lineages, Nichols and SS14. Both lineages are currently circulating in 12 of the 23 countries sampled. We subdivided T. p. pallidum into 17 distinct sublineages to provide further phylodynamic resolution. Importantly, two Nichols sublineages have expanded clonally across 9 countries contemporaneously with SS14. Moreover, pairwise genome analyses revealed examples of isolates collected within the last 20 years from 14 different countries that had genetically identical core genomes, which might indicate frequent exchange through international transmission. It is striking that most samples collected before 1983 are phylogenetically distinct from more recently isolated sublineages. Using Bayesian temporal analysis, we detected a population bottleneck occurring during the late 1990s, followed by rapid population expansion in the 2000s that was driven by the dominant T. pallidum sublineages circulating today. This expansion may be linked to changing epidemiology, immune evasion or fitness under antimicrobial selection pressure, since many of the contemporary syphilis lineages we have characterized are resistant to macrolides.\n\nGlobal phylogeny of Treponema pallidum lineages reveals recent expansion and spread of contemporary syphilis.", "token_count": 463, "char_count": 1936, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6778, "quality_score": 0.8389, "entities": { "genes": [ "SS14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:16.836726", "source": { "split": "train_shard_00002", "doc_id": 21 }, "chunk_id": "train_shard_00002_21_0", "global_id": 12752 }, { "text": "Klebsiella pneumoniae infections affect infants and the immunocompromised, and the recent emergence of hypervirulent and multi-drug resistant K. pneumoniae lineages is a critical healthcare concern. Hypervirulence in K. pneumoniae is mediated by several factors, including the overproduction of extracellular capsule. However, the full details of how K. pneumoniae capsule biosynthesis is achieved or regulated are not known. We have developed a robust and sensitive procedure to identify genes influencing capsule production, density-TraDISort, which combines density gradient centrifugation with transposon-insertion sequencing. We have used this method to explore capsule regulation in two clinically-relevant Klebsiella strains; K. pneumoniae NTUH-K2044 (capsule type K1), and K. pneumoniae ATCC43816 (capsule type K2). We identified multiple genes required for full capsule production in K. pneumoniae , as well as putative suppressors of capsule in NTUH-K2044, and have validated the results of our screen with targeted knockout mutants. Further investigation of several of the K. pneumoniae capsule regulators identified – ArgR, MprA/KvrB, SlyA/KvrA and the Sap ABC transporter – revealed effects on capsule amount and architecture, serum resistance and virulence. We show that capsule production in K. pneumoniae is at the centre of a complex regulatory network involving multiple global regulators and environmental cues, and that the majority of capsule regulatory genes are located in the core genome. Overall our findings expand our understanding of how capsule is regulated in this medically-important pathogen, and provide a technology that can be easily implemented to study capsule regulation in other bacterial species.

Importance

Capsule production is essential for K. pneumoniae to cause infections, but its regulation and mechanism of synthesis are not fully understood in this organism. We have developed and applied a new method for genome-wide identification of capsule regulators. Using this method, many genes that positively or negatively affect capsule production in K", "token_count": 510, "char_count": 2104, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5608, "quality_score": 0.7804, "entities": { "genes": [ "ATCC43816" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:17.499437", "source": { "split": "train_shard_00002", "doc_id": 22 }, "chunk_id": "train_shard_00002_22_0", "global_id": 12753 }, { "text": "pneumoniae were identified, and we use these data to propose an integrated model for capsule regulation in this species. Several of the genes and biological processes identified have not previously been linked to capsule synthesis. We also show that the methods presented here can be applied to other species of capsulated bacteria, providing the opportunity to explore and compare capsule regulatory networks in other bacterial strains and species.\n\nThe capsule regulatory network ofKlebsiella pneumoniaedefined by density-TraDISort", "token_count": 113, "char_count": 540, "word_count": 76, "semantic_coherence": 1, "information_density": 0.7632, "quality_score": 0.8816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:17.878207", "source": { "split": "train_shard_00002", "doc_id": 22 }, "chunk_id": "train_shard_00002_22_1", "global_id": 12754 }, { "text": "For several years, the Platelia Candida mannan antigen enzyme immunoassay (Candida EIA) has been commercially available as a diagnostic test for invasive candidosis. We evaluated the Candida EIA with patients with proven fungemia caused by yeasts from which at least one serum sample was available. Fifty-nine patients with 121 serum samples were included in the study. Sixty-one different yeast strains were isolated from positive blood-cultures. The Candida EIA was positive (n = 35) or borderline positive (n = 8) in 43 of 59 patients with fungemia, resulting in an overall sensitivity of 73%. For the different yeast species, the following sensitivities were calculated: Candida albicans 30 of 39 (77%), Candida glabrata 7 of 11 (64%), Candida parapsilosis 1 of 3, Candida tropicalis 2 of 2, Candida kefyr 2 of 2, Candida lipolytica 0 of 1, Candida lusitaniae 1 of 1, Candida krusei 1 borderline positive of 1, Saccharomyces cerevisiae 1 of 1. In six patients the antigen levels over time were evaluable. In three cases the antigen was positive 3-4 days before the day the blood culture was drawn, in one case on the same day, and in two cases 2 and 5 days afterwards. In conclusion, the Candida EIA was suitable for the detection of fungemia due to the major facultatively pathogenic yeast species. The test was positive in about half of the patients before blood cultures became positive. In these cases, it contributed to an early diagnosis of invasive candidiasis.\n\n[Performance of the Candida mannan antigen detection in patients with fungemia].", "token_count": 438, "char_count": 1554, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5613, "quality_score": 0.7806, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:18.509837", "source": { "split": "train_shard_00002", "doc_id": 23 }, "chunk_id": "train_shard_00002_23_0", "global_id": 12755 }, { "text": "Oral pseudomembranous candidiasis and mucositis were assessed in 39 patients receiving a total dose of 39-70 Gy radiotherapy for head and neck cancer. Mucositis was scored using the Radiation Therapy Oncology Group criteria, and oral candidiasis was diagnosed on the basis of clinical evaluation and quantitative laboratory findings. Radiation-induced mucositis was observed in 9/39 patients. Only 3/39 patients discontinued radiotherapy due to acute severe mucosal effects. Candidiasis (colony-forming units 35 to > or = 60/lesion) associated with mucositis was diagnosed in 30/39 patients: the most frequent aetiology of the infection was Candida albicans (n = 23), followed by Candida glabrata (n = 3), Candida krusei (n = 2), Candida tropicalis (n = 1) and Candida kefyr (n = 1). Patients with confirmed oral pseudomembranous candidiasis were treated with either fluconazole 200 mg/day or itraconazole 200 mg/day for 2 weeks. Clinical improvement and concomitant negative Candida cultures (mycologic cure) were the criteria determining a response to antifungal treatment. Etest revealed very low voriconazole MICs (0.004-0.125 microg/ml) for all isolates, and fluconazole resistance for eight C. albicans strains (MIC > 64 microg/ml) and for the C. krusei isolates (MIC > 32 microg/ml). The same strains showed itraconazole susceptibility dose dependence (MIC 0.5 microg/ml). Despite the itraconazole susceptible dose dependent MIC readings, all patients with oral pseudomembranous candidiasis caused by these strains responded to antifungal treatment with 200 mg/day itraconazole", "token_count": 477, "char_count": 1584, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5903, "quality_score": 0.7952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:19.156894", "source": { "split": "train_shard_00002", "doc_id": 24 }, "chunk_id": "train_shard_00002_24_0", "global_id": 12756 }, { "text": "Oral mycologic surveillance of patients undergoing radiotherapy for head and neck malignancies and susceptibility testing of isolates may be indicated in cases with mucositis-associated confirmed oral pseudomembranous candidiasis to ensure prompt administration of targeted antifungal treatment. On the basis of the low MIC values found, clinical evaluation of voriconazole is indicated for management of oral pseudomembranous candidiasis refractory to other azoles.\n\nOral Candida isolates in patients undergoing radiotherapy for head and neck cancer: prevalence, azole susceptibility profiles and response to antifungal treatment.", "token_count": 141, "char_count": 631, "word_count": 82, "semantic_coherence": 1, "information_density": 0.6463, "quality_score": 0.8232, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:19.582549", "source": { "split": "train_shard_00002", "doc_id": 24 }, "chunk_id": "train_shard_00002_24_1", "global_id": 12757 }, { "text": "Members of the genus Sneathia are fastidious bacteria that predominantly colonise the female genital tract and are significantly associated with reproductive disorders and genital and neonatal disease. From a taxonomical perspective, the genus only comprises the species Sneathia sanguinegens. Numerous reports on a second species, 'Sneathia amnii', have been published, but the name has never been validated. The same is the case for 'Leptotrichia amnionii', which was previously shown to belong to the same species as 'Sneathia amnii'. We studied strains DSM 16631T and DSM 16630, which have been identified and deposited as 'Leptotrichia amnionii' previously. At the time of isolation, these strains were found to be most closely related to, but clearly different from, Sneathia sanguinegens based on 16S rRNA gene sequence similarities. Both strains proved to be almost indistinguishable from 'Sneathia amnii' based on molecular, morphological and physiological traits. The 16S rRNA gene sequence analysis revealed that strain DSM 16631T was assigned to the genus Sneathia with a sequence similarity of 95.47 % to Sneathia sanguinegens CCUG 41628T, followed by type strains of Caviibacter abscessus (93.03 %), Oceanivirga salmonicida (92.68 %) and Oceanivirga miroungae (91.97 %) as the next closely related members of the Leptotrichiaceae", "token_count": 475, "char_count": 1474, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6294, "quality_score": 0.8147, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:20.224557", "source": { "split": "train_shard_00002", "doc_id": 25 }, "chunk_id": "train_shard_00002_25_0", "global_id": 12758 }, { "text": "The novel species was also clearly differentiated from other related taxa by core genome phylogeny, average nucleotide and amino acid identities, in silico DNA-DNA hybridization and MALDI-TOF MS. With respect to chemotaxonomic and physiological patterns, strains DSM 16631T and DSM 16630 were again highly similar to Sneathia sanguinegens. On the basis of these data, we propose the novel species Sneathia vaginalis sp. nov. with the type strain DSM 16631T (=CCUG 52977T=CCUG 52889AT) and a second strain DSM 16630 (=CCUG 52976=CCUG 52888) that were both isolated from bloodstream infections in women with puerperal fever in France. The G+C content of the DNA of the type strain is 28.4 mol% and the genome size is 1.28 Mbp. Based on the observed extremely high similarities of genotypic and phenotypic traits of the novel proposed species to those reported for 'Sneathia amnii', we recommend using this new name in all further publications on this taxon.\n\nSneathia vaginalis sp. nov. (Fusobacteriales, Leptotrichiaceae) as a replacement of the species 'Sneathia amnii' Harwich et al. 2012 and 'Leptotrichia amnionii' Shukla et al. 2002, and emended description of Sneathia Collins et al. 2001.", "token_count": 469, "char_count": 1322, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6595, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:20.861412", "source": { "split": "train_shard_00002", "doc_id": 25 }, "chunk_id": "train_shard_00002_25_1", "global_id": 12759 }, { "text": "

Background

Rhizobium leguminosarum is an alpha-proteobacterial N2-fixing symbiont of legumes that has been the subject of more than a thousand publications. Genes for the symbiotic interaction with plants are well studied, but the adaptations that allow survival and growth in the soil environment are poorly understood. We have sequenced the genome of R. leguminosarum biovar viciae strain 3841.

Results

The 7.75 Mb genome comprises a circular chromosome and six circular plasmids, with 61% G+C overall. All three rRNA operons and 52 tRNA genes are on the chromosome; essential protein-encoding genes are largely chromosomal, but most functional classes occur on plasmids as well. Of the 7,263 protein-encoding genes, 2,056 had orthologs in each of three related genomes (Agrobacterium tumefaciens, Sinorhizobium meliloti, and Mesorhizobium loti), and these genes were over-represented in the chromosome and had above average G+C. Most supported the rRNA-based phylogeny, confirming A. tumefaciens to be the closest among these relatives, but 347 genes were incompatible with this phylogeny; these were scattered throughout the genome but were over-represented on the plasmids. An unexpectedly large number of genes were shared by all three rhizobia but were missing from A. tumefaciens.

Conclusion

Overall, the genome can be considered to have two main components: a 'core', which is higher in G+C, is mostly chromosomal, is shared with related organisms, and has a consistent phylogeny; and an 'accessory' component, which is sporadic in distribution, lower in G+C, and located on the plasmids and chromosomal islands. The accessory genome has a different nucleotide composition from the core despite a long history of coexistence.", "token_count": 492, "char_count": 1756, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8024, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:21.509093", "source": { "split": "train_shard_00002", "doc_id": 26 }, "chunk_id": "train_shard_00002_26_0", "global_id": 12760 }, { "text": "The genome of Rhizobium leguminosarum has recognizable core and accessory components.", "token_count": 22, "char_count": 85, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:21.868740", "source": { "split": "train_shard_00002", "doc_id": 26 }, "chunk_id": "train_shard_00002_26_1", "global_id": 12761 }, { "text": "Sphingolipids serve as vital structural and signaling components of the cell membranes in both eukaryotes and prokaryotes. Within the gut microbiome, Bacteroides species have been identified as major producers of sphingolipids, and Bacteroides-produced sphingolipids have been shown to be modulators of host immune and metabolic functions. While Bacteroides species are a prominent feature of the gut microbiomes of populations living in industrialized countries, Prevotella copri, a member of the same phyla, albeit a different family, is the dominant feature across the remainder of the global population, although their sphingolipid-producing capabilities have not been as thoroughly investigated. To fill this gap, we examined the genomes of over 60 diverse isolates of P. copri and identified several key enzymes involved in sphingolipid synthesis in P. copri. Combining bioorthogonal labeling and liquid chromatography-mass spectrometry (LC-MS) based lipidomics, we functionally characterized the first step in P. copri de novo sphingolipid synthesis in addition to profiling the sphingolipidomes of P. copri strains, identifying key enzymes that may play roles in producing a diverse set of P. copri sphingolipids. Given the limited genetic engineering tools amenable for use in P. copri, our approach takes advantage of comparative genomics and phenotypic profiling to explore sphingolipid production in these understudied, yet highly prevalent, organisms.IMPORTANCESphingolipids are important signaling molecules for maintaining metabolic and immune homeostasis in the host. These lipids are also produced by gut commensals, most notably by Bacteroides species", "token_count": 468, "char_count": 1746, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6422, "quality_score": 0.8211, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:22.513657", "source": { "split": "train_shard_00002", "doc_id": 27 }, "chunk_id": "train_shard_00002_27_0", "global_id": 12762 }, { "text": "Despite the global prevalence of Prevotella copri in gut microbiomes of individuals, little is known about the types of sphingolipids they produce and whether they are similar in composition and structure to those produced by Bacteroides. Given the varied associations of P. copri with diverse sphingolipid-related health outcomes, such as rheumatoid arthritis and glucose intolerance, it is important to first characterize the specific sphingolipids produced by individual strains of P. copri and to identify the genes involved in their pathways of production. This characterization of P. copri-derived sphingolipids provides further insight into how bacterial sphingolipid production can serve as a mechanism for microbial modulation of host phenotypes.\n\nPrevotella copri variants among a single host diverge in sphingolipid production.", "token_count": 232, "char_count": 880, "word_count": 118, "semantic_coherence": 1, "information_density": 0.6949, "quality_score": 0.8475, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:22.989485", "source": { "split": "train_shard_00002", "doc_id": 27 }, "chunk_id": "train_shard_00002_27_1", "global_id": 12763 }, { "text": "

Background

Ensete glaucum (2n = 2x = 18) is a giant herbaceous monocotyledonous plant in the small Musaceae family along with banana (Musa). A high-quality reference genome sequence assembly of E. glaucum is a resource for functional and evolutionary studies of Ensete, Musaceae, and the Zingiberales.

Findings

Using Oxford Nanopore Technologies, chromosome conformation capture (Hi-C), Illumina and RNA survey sequence, supported by molecular cytogenetics, we report a high-quality 481.5 Mb genome assembly with 9 pseudo-chromosomes and 36,836 genes. A total of 55% of the genome is composed of repetitive sequences with predominantly LTR-retroelements (37%) and DNA transposons (7%). The single 5S ribosomal DNA locus had an exceptionally long monomer length of 1,056 bp, more than twice that of the monomers at multiple loci in Musa. A tandemly repeated satellite (1.1% of the genome, with no similar sequence in Musa) was present around all centromeres, together with a few copies of a long interspersed nuclear element (LINE) retroelement. The assembly enabled us to characterize in detail the chromosomal rearrangements occurring between E. glaucum and the x = 11 species of Musa. One E. glaucum chromosome has the same gene content as Musa acuminata, while others show multiple, complex, but clearly defined evolutionary rearrangements in the change between x= 9 and 11.

Conclusions

The advance towards a Musaceae pangenome including E. glaucum, tolerant of extreme environments, makes a complete set of gene alleles, copy number variation, and a reference for structural variation available for crop breeding and understanding environmental responses. The chromosome-scale genome assembly shows the nature of chromosomal fusion and translocation events during speciation, and features of rapid repetitive DNA change in terms of copy number, sequence, and genomic location, critical to understanding its role in diversity and evolution.", "token_count": 520, "char_count": 1965, "word_count": 283, "semantic_coherence": 1, "information_density": 0.6572, "quality_score": 0.8286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:59:23.657945", "source": { "split": "train_shard_00002", "doc_id": 28 }, "chunk_id": "train_shard_00002_28_0", "global_id": 12764 }, { "text": "A chromosome-level reference genome of Ensete glaucum gives insight into diversity and chromosomal and repetitive sequence evolution in the Musaceae.", "token_count": 35, "char_count": 149, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:24.020990", "source": { "split": "train_shard_00002", "doc_id": 28 }, "chunk_id": "train_shard_00002_28_1", "global_id": 12765 }, { "text": "In the last decades, there has been a growing interest from consumers in their food choices. Organic, natural, less processed, functional, and pre-probiotic products were preferred. Although, Saccharomyces cerevisiae var. boulardii is the most well-characterized probiotic yeast available on the market, improvement in probiotic function using other yeast species is an attractive future direction. In the present study, un-anthropized natural environments and spontaneous processed foods were exploited for wild yeast isolation with the goal of amplifying the knowledge of probiotic aptitudes of different yeast species. For this purpose, 179 yeast species were isolated, identified as belonging to twelve different genera, and characterized for the most important probiotic features. Findings showed interesting probiotic characteristics for some yeast strains belonging to Lachancea thermotolerans, Metschnikowia ziziphicola, Saccharomyces cerevisiae, and Torulaspora delbrueckii species, although these probiotic aptitudes were strictly strain-dependent. These yeast strains could be proposed for different probiotic applications, such as a valid alternative to, or in combination with, the probiotic yeast S. cerevisiae var. boulardii.\n\nPotential Probiotic Yeasts Sourced from Natural Environmental and Spontaneous Processed Foods.", "token_count": 356, "char_count": 1392, "word_count": 174, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:24.594137", "source": { "split": "train_shard_00002", "doc_id": 29 }, "chunk_id": "train_shard_00002_29_0", "global_id": 12766 }, { "text": "Antibiotic resistance in pathogens is extensively studied, and yet little is known about how antibiotic resistance genes of typical gut bacteria influence microbiome dynamics. Here, we leveraged genomes from metagenomes to investigate how genes of the premature infant gut resistome correspond to the ability of bacteria to survive under certain environmental and clinical conditions. We found that formula feeding impacts the resistome. Random forest models corroborated by statistical tests revealed that the gut resistome of formula-fed infants is enriched in class D beta-lactamase genes. Interestingly, Clostridium difficile strains harboring this gene are at higher abundance in formula-fed infants than C. difficile strains lacking this gene. Organisms with genes for major facilitator superfamily drug efflux pumps have higher replication rates under all conditions, even in the absence of antibiotic therapy. Using a machine learning approach, we identified genes that are predictive of an organism's direction of change in relative abundance after administration of vancomycin and cephalosporin antibiotics. The most accurate results were obtained by reducing annotated genomic data to five principal components classified by boosted decision trees. Among the genes involved in predicting whether an organism increased in relative abundance after treatment are those that encode subclass B2 beta-lactamases and transcriptional regulators of vancomycin resistance. This demonstrates that machine learning applied to genome-resolved metagenomics data can identify key genes for survival after antibiotics treatment and predict how organisms in the gut microbiome will respond to antibiotic administration. IMPORTANCE The process of reconstructing genomes from environmental sequence data (genome-resolved metagenomics) allows unique insight into microbial systems. We apply this technique to investigate how the antibiotic resistance genes of bacteria affect their ability to flourish in the gut under various conditions. Our analysis reveals that strain-level selection in formula-fed infants drives enrichment of beta-lactamase genes in the gut resistome. Using genomes from metagenomes, we built a machine learning model to predict how organisms in the gut microbial community respond to perturbation by antibiotics. This may eventually have clinical applications.", "token_count": 509, "char_count": 2396, "word_count": 326, "semantic_coherence": 1, "information_density": 0.5767, "quality_score": 0.7883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:25.273836", "source": { "split": "train_shard_00002", "doc_id": 30 }, "chunk_id": "train_shard_00002_30_0", "global_id": 12767 }, { "text": "Machine Learning Leveraging Genomes from Metagenomes Identifies Influential Antibiotic Resistance Genes in the Infant Gut Microbiome.", "token_count": 34, "char_count": 133, "word_count": 16, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:25.647245", "source": { "split": "train_shard_00002", "doc_id": 30 }, "chunk_id": "train_shard_00002_30_1", "global_id": 12768 }, { "text": "

Background

As an important nosocomial pathogen, Enterococcus faecium has received increasing attention in recent years. However, a large number of studies have focused on the hospital-associated isolates and ignored isolates originated from the natural environments.

Results

In this study, comparative genomic analysis was conducted on 161 isolates originated from human, animal, and naturally fermented dairy products. The results showed that the environment played an important role in shaping the genomes of Enterococcus faecium. The isolates from human had the largest average genome size, while the isolates from dairy products had the smallest average genome size and fewest antibiotic resistance genes. A phylogenetic tree was reconstructed based on the genomes of these isolates, which revealed new insights into the phylogenetic relationships among the dairy isolates and those from hospitals, communities, and animals. Furthermore, 202 environment-specific genes were identified, including 136 dairy-specific, 31 human blood-specific, and 35 human gastrointestinal-specific genes. Interestingly, five dairy-specific genes (namely lacF, lacA/B, lacD, lacG, and lacC) that constituted an integrated lactose metabolism pathway existed in almost all dairy isolates. The pathway conservation demonstrated an active role of the environment in shaping the genomes of Enterococcus faecium.

Conclusions

This study shows that the Enterococcus faecium species has great genomic plasticity and high versatility to occupy broad ecological roles, dwelling as non-harmful dairy and animal gut commensals as well as significant nosocomial pathogens that disseminate antibiotic resistance genes.\n\nComparative genomic analysis revealed great plasticity and environmental adaptation of the genomes of Enterococcus faecium.", "token_count": 441, "char_count": 1835, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6067, "quality_score": 0.8033, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:26.316178", "source": { "split": "train_shard_00002", "doc_id": 31 }, "chunk_id": "train_shard_00002_31_0", "global_id": 12769 }, { "text": "Lineages of hypervirulent Aeromonas hydrophila (vAh) are the cause of persistent outbreaks of motile Aeromonas septicemia in warm-water fishes worldwide. Over the last decade, this virulent lineage of A. hydrophila has resulted in annual losses of millions of tons of farmed carp and catfish in the People's Republic of China and the United States (US). Multiple lines of evidence indicate US catfish and Asian carp isolates of A. hydrophila affiliated with sequence type 251 (ST251) share a recent common ancestor. To address the genomic context for the putative intercontinental transfer and subsequent geographic spread of this pathogen, we conducted a core genome phylogenetic analysis on 61 Aeromonas spp. genomes, of which 40 were affiliated with A. hydrophila, with 26 identified as epidemic strains. Phylogenetic analyses indicate all ST251 strains form a coherent lineage affiliated with A. hydrophila. Within this lineage, conserved genetic loci unique to A. hydrophila were identified, with some genes present in consistently higher copy numbers than in non-epidemic A. hydrophila isolates. In addition, results from analyses of representative ST251 isolates support the conclusion that multiple lineages are present within US vAh isolated from Mississippi, whereas vAh isolated from Alabama appear clonal. This is the first report of genomic heterogeneity within US vAh isolates, with some Mississippi isolates showing closer affiliation with the Asian grass carp isolate ZC1 than other vAh isolated in the US. To evaluate the biological significance of the identified heterogeneity, comparative disease challenges were conducted with representatives of different vAh genotypes. These studies revealed that isolate ZC1 yielded significantly lower mortality in channel catfish, relative to Alabama and Mississippi vAh isolates. Like other Asian vAh isolates, the ZC1 lineage contains all core genes for a complete type VI secretion system (T6SS)", "token_count": 514, "char_count": 2019, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5889, "quality_score": 0.7944, "entities": { "genes": [ "ST251", "ZC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:59:26.979051", "source": { "split": "train_shard_00002", "doc_id": 32 }, "chunk_id": "train_shard_00002_32_0", "global_id": 12770 }, { "text": "In contrast, more virulent US isolates retain only remnants of the T6SS (clpB, hcp, vgrG, and vasH) which may have functional implications. Collectively, these results characterize a hypervirulent A. hydrophila pathotype that affects farmed fish on multiple continents.\n\nClassification of a Hypervirulent Aeromonas hydrophila Pathotype Responsible for Epidemic Outbreaks in Warm-Water Fishes.", "token_count": 128, "char_count": 420, "word_count": 52, "semantic_coherence": 1, "information_density": 0.8846, "quality_score": 0.9423, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:27.399198", "source": { "split": "train_shard_00002", "doc_id": 32 }, "chunk_id": "train_shard_00002_32_1", "global_id": 12771 }, { "text": "Bacterial adaptation to growth with toxic halogenated chemicals was explored in the context of methylotrophic metabolism of Methylobacterium extorquens, by comparing strains CM4 and DM4, which show robust growth with chloromethane and dichloromethane, respectively. Dehalogenation of chlorinated methanes initiates growth-supporting degradation, with intracellular release of protons and chloride ions in both cases. The core, variable and strain-specific genomes of strains CM4 and DM4 were defined by comparison with genomes of non-dechlorinating strains. In terms of gene content, adaptation toward dehalogenation appears limited, strains CM4 and DM4 sharing between 75 and 85% of their genome with other strains of M. extorquens. Transcript abundance in cultures of strain CM4 grown with chloromethane and of strain DM4 grown with dichloromethane was compared to growth with methanol as a reference C1 growth substrate. Previously identified strain-specific dehalogenase-encoding genes were the most transcribed with chlorinated methanes, alongside other genes encoded by genomic islands (GEIs) and plasmids involved in growth with chlorinated compounds as carbon and energy source. None of the 163 genes shared by strains CM4 and DM4 but not by other strains of M. extorquens showed higher transcript abundance in cells grown with chlorinated methanes. Among the several thousand genes of the M. extorquens core genome, 12 genes were only differentially abundant in either strain CM4 or strain DM4. Of these, 2 genes of known function were detected, for the membrane-bound proton translocating pyrophosphatase HppA and the housekeeping molecular chaperone protein DegP. This indicates that the adaptive response common to chloromethane and dichloromethane is limited at the transcriptional level, and involves aspects of the general stress response as well as of a dehalogenation-specific response to intracellular hydrochloric acid production", "token_count": 505, "char_count": 1987, "word_count": 275, "semantic_coherence": 1, "information_density": 0.5709, "quality_score": 0.7855, "entities": { "genes": [ "CM4", "DM4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:28.056178", "source": { "split": "train_shard_00002", "doc_id": 33 }, "chunk_id": "train_shard_00002_33_0", "global_id": 12772 }, { "text": "Core genes only differentially abundant in either strain CM4 or strain DM4 total 13 and 58 CDS, respectively. Taken together, the obtained results suggest different transcriptional responses of chloromethane- and dichloromethane-degrading M. extorquens strains to dehalogenative metabolism, and substrate- and pathway-specific modes of growth optimization with chlorinated methanes.\n\nGenomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in Methylobacterium.", "token_count": 141, "char_count": 514, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [ "CM4", "DM4" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:28.484714", "source": { "split": "train_shard_00002", "doc_id": 33 }, "chunk_id": "train_shard_00002_33_1", "global_id": 12773 }, { "text": "

Introduction

The majority of vancomycin-resistant Enterococcus faecium (VREfm) in Australia is of the vanB genotype. An outbreak of vanA VREfm emerged in our haematology/oncology unit between November 2014 and May 2015. The first case of daptomycin non-susceptible E. faecium (DNSEfm) detected was a patient with vanA VREfm bacteraemia who showed clinical failure of daptomycin therapy, prompting microbiologic testing confirming daptomycin non-susceptibility.

Objectives

To describe the patient profiles, antibiotic susceptibility and genetic relatedness of vanA VREfm isolates in the outbreak.

Methods

Chart review of vanA VREfm colonized and infected patients was undertaken to describe the demographics, clinical features and outcomes of therapy. Whole genome sequencing of vanA VREfm isolates involved in the outbreak was conducted to assess clonality.

Results

In total, 29 samples from 24 patients tested positive for vanA VREfm (21 screening swabs and 8 clinical isolates). Five isolates were DNSEfm (four patients colonized, one patient with bacteraemia), with only one patient exposed to daptomycin previously. In silico multi-locus sequence typing of the isolates identified 25/26 as ST203, and 1/26 as ST796. Comparative genomic analysis revealed limited core genome diversity amongst the ST203 isolates, consistent with an outbreak of a single clone of vanA VREfm.

Conclusions

Here we describe an outbreak of vanA VREfm in a haematology/oncology unit. Genomic analysis supports transmission of an ST203 vanA VRE clone within this unit. Daptomycin non-susceptibility in 5/24 patients left linezolid as the only treatment option. Daptomycin susceptibility cannot be assumed in vanA VREfm isolates and confirmatory testing is recommended.", "token_count": 497, "char_count": 1783, "word_count": 238, "semantic_coherence": 1, "information_density": 0.584, "quality_score": 0.792, "entities": { "genes": [ "ST796", "ST203" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:29.138975", "source": { "split": "train_shard_00002", "doc_id": 34 }, "chunk_id": "train_shard_00002_34_0", "global_id": 12774 }, { "text": "Utilizing genomic analyses to investigate the first outbreak of vanA vancomycin-resistant Enterococcus in Australia with emergence of daptomycin non-susceptibility.", "token_count": 42, "char_count": 164, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:29.499755", "source": { "split": "train_shard_00002", "doc_id": 34 }, "chunk_id": "train_shard_00002_34_1", "global_id": 12775 }, { "text": "Edible bananas result from interspecific hybridization between Musa acuminata and Musa balbisiana , as well as among subspecies in M. acuminata . Four particular M. acuminata subspecies have been proposed as the main contributors of edible bananas, all of which radiated in a short period of time in southeastern Asia. Clarifying the evolution of these lineages at a whole-genome scale is therefore an important step toward understanding the domestication and diversification of this crop. This study reports the de novo genome assembly and gene annotation of a representative genotype from three different subspecies of M. acuminata . These data are combined with the previously published genome of the fourth subspecies to investigate phylogenetic relationships and genome evolution. Analyses of shared and unique gene families reveal that the four subspecies are quite homogenous, with a core genome representing at least 50% of all genes and very few M. acuminata species-specific gene families. Multiple alignments indicate high sequence identity between homologous single copy-genes, supporting the close relationships of these lineages. Interestingly, phylogenomic analyses demonstrate high levels of gene tree discordance, due to both incomplete lineage sorting and introgression. This pattern suggests rapid radiation within Musa acuminata subspecies that occurred after the divergence with M. balbisiana . Introgression between M. a. ssp. malaccensis and M. a. ssp. burmannica was detected across a substantial portion of the genome, though multiple approaches to resolve the subspecies tree converged on the same topology. To support future evolutionary and functional analyses, we introduce the PanMusa database, which enables researchers to exploration of individual gene families and trees.\n\nThree new genome assemblies support a rapid radiation in Musa acuminata (wild banana)", "token_count": 426, "char_count": 1898, "word_count": 273, "semantic_coherence": 1, "information_density": 0.6117, "quality_score": 0.8059, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:30.123431", "source": { "split": "train_shard_00002", "doc_id": 35 }, "chunk_id": "train_shard_00002_35_0", "global_id": 12776 }, { "text": "

Background

The epidemic Clostridioides difficile ribotype 027 strain resulted from the dissemination of 2 separate fluoroquinolone-resistant lineages: FQR1 and FQR2. Both lineages were reported to originate in North America; however, confirmatory large-scale investigations of C difficile ribotype 027 epidemiology using whole genome sequencing has not been undertaken in the United States.

Methods

Whole genome sequencing and single-nucleotide polymorphism (SNP) analysis was performed on 76 clinical ribotype 027 isolates obtained from hospitalized patients in Texas with C difficile infection and compared with 32 previously sequenced worldwide strains. Maximum-likelihood phylogeny based on a set of core genome SNPs was used to construct phylogenetic trees investigating strain macro- and microevolution. Bayesian phylogenetic and phylogeographic analyses were used to incorporate temporal and geographic variables with the SNP strain analysis.

Results

Whole genome sequence analysis identified 2841 SNPs including 900 nonsynonymous mutations, 1404 synonymous substitutions, and 537 intergenic changes. Phylogenetic analysis separated the strains into 2 prominent groups, which grossly differed by 28 SNPs: the FQR1 and FQR2 lineages. Five isolates were identified as pre-epidemic strains. Phylogeny demonstrated unique clustering and resistance genes in Texas strains indicating that spatiotemporal bias has defined the microevolution of ribotype 027 genetics.

Conclusions

Clostridioides difficile ribotype 027 lineages emerged earlier than previously reported, coinciding with increased use of fluoroquinolones. Both FQR1 and FQR2 ribotype 027 epidemic lineages are present in Texas, but they have evolved geographically to represent region-specific public health threats.", "token_count": 509, "char_count": 1836, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6726, "quality_score": 0.8363, "entities": { "genes": [ "FQR2", "FQR1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:30.773495", "source": { "split": "train_shard_00002", "doc_id": 36 }, "chunk_id": "train_shard_00002_36_0", "global_id": 12777 }, { "text": "Epidemic Clostridioides difficile Ribotype 027 Lineages: Comparisons of Texas Versus Worldwide Strains.", "token_count": 38, "char_count": 110, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:31.130254", "source": { "split": "train_shard_00002", "doc_id": 36 }, "chunk_id": "train_shard_00002_36_1", "global_id": 12778 }, { "text": "

Background

There are several studies describing loss of genes through reductive evolution in microbes, but how selective forces are associated with genome expansion due to horizontal gene transfer (HGT) has not received similar attention. The aim of this study was therefore to examine how selective pressures influence genome expansion in 53 fully sequenced and assembled Escherichia coli strains. We also explored potential connections between genome expansion and the attainment of virulence factors. This was performed using estimations of several genomic parameters such as AT content, genomic drift (measured using relative entropy), genome size and estimated HGT size, which were subsequently compared to analogous parameters computed from the core genome consisting of 1729 genes common to the 53 E. coli strains. Moreover, we analyzed how selective pressures (quantified using relative entropy and dN/dS), acting on the E. coli core genome, influenced lineage and phylogroup formation.

Results

Hierarchical clustering of dS and dN estimations from the E. coli core genome resulted in phylogenetic trees with topologies in agreement with known E. coli taxonomy and phylogroups. High values of dS, compared to dN, indicate that the E. coli core genome has been subjected to substantial purifying selection over time; significantly more than the non-core part of the genome (p<0.001). This is further supported by a linear association between strain-wise dS and dN values (β = 26.94 ± 0.44, R2~0.98, p<0.001). The non-core part of the genome was also significantly more AT-rich (p<0.001) than the core genome and E. coli genome size correlated with estimated HGT size (p<0.001). In addition, genome size (p<0.001), AT content (p<0.001) as well as estimated HGT size (p<0.005) were all associated with the presence of virulence factors, suggesting that pathogenicity traits in E. coli are largely attained through HGT", "token_count": 512, "char_count": 1937, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5575, "quality_score": 0.7787, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:31.768485", "source": { "split": "train_shard_00002", "doc_id": 37 }, "chunk_id": "train_shard_00002_37_0", "global_id": 12779 }, { "text": "No associations were found between selective pressures operating on the E. coli core genome, as estimated using relative entropy, and genome size (p~0.98).

Conclusions

On a larger time frame, genome expansion in E. coli, which is significantly associated with the acquisition of virulence factors, appears to be independent of selective forces operating on the core genome.\n\nAn evolutionary analysis of genome expansion and pathogenicity in Escherichia coli.", "token_count": 115, "char_count": 465, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7846, "quality_score": 0.8923, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:32.156228", "source": { "split": "train_shard_00002", "doc_id": 37 }, "chunk_id": "train_shard_00002_37_1", "global_id": 12780 }, { "text": "The ever increasing problem of environmental pollution and protein scarcity led us to begin producing protein biomass from cheese whey, having selected for this aim, Kluyveromyces marxianus va. lactis strain, which represents the right relationship between its protein content (53.3% d.w.) and that of the RNA (4.63% d.w.). On the other hand, the distribution of its essential amino acids is balanced, although it shows a deficiency in methionine, its value being 1.5 g/16 gN. The purpose of this work was to assess the biological quality of this protein concentrate, so as to use it in animal feeding. Protein quality was determined by the NPU method (net protein utilization), according to Miller and Bender's technique. Three balanced diets were prepared (10% protein), the test sample with casein, and the rest with protein biomass, one of then supplemented with methionine (0.5 g/100 g food). Based on the results it can be concluded that the biomass analyzed has an adequate biological value (55.37%) for use in animal feeding, especially when methionine as added (60.23%).\n\n[Biological value of the unicellular protein of Kluyveromyces marxianus var. lactis].", "token_count": 300, "char_count": 1166, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6868, "quality_score": 0.8434, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:32.728550", "source": { "split": "train_shard_00002", "doc_id": 38 }, "chunk_id": "train_shard_00002_38_0", "global_id": 12781 }, { "text": "The treatment of infections due to colistin-resistant (Col-E) and carbapenemase-producing (CPE) Enterobacterales challenges clinicians both in human and veterinary medicine. Preventing zoonotic transmission of these multidrug-resistant bacteria is a Public Health priority. This study investigates the prevalence of Col-E and CPE on 81 pig farms in North-West Germany as well as among 138 directly exposed humans working on these farms. Between March 2018 and September 2020, 318 samples of porcine feces were taken using boot swabs. Farm workers provided a stool sample. Both a selective culture-based approach and a molecular detection of colistin (mcr-1 to mcr-5) and carbapenem resistance determinants (bla OXA-48/bla VIM/bla KPC/bla NDM) was used to screen all samples. Isolates from farm workers and farms were compared using core genome multilocus-sequence typing (cgMLST) and plasmid-typing. CPE were cultured neither from porcine feces nor from human stool samples. In one stool sample, bla OXA-48 was detected, but no respective CPE isolate was found. Col-E were found in 18/318 porcine (5.7%) samples from 10/81 (12.3%) farms and 2/138 (1.4%) farmers, respectively. All Col-E isolates were Escherichia coli harboring mcr-1. Both farm workers colonized with Col-E worked on farms where no Col-E were detected in porcine samples. In conclusion, CPE were absent on German pig farms. This supports findings of culture-based national monitoring systems and provides evidence that even when improving the diagnostic sensitivity by using molecular detection techniques in addition to culture, CPE are not prevalent", "token_count": 523, "char_count": 1736, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6525, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T06:59:33.393289", "source": { "split": "train_shard_00002", "doc_id": 39 }, "chunk_id": "train_shard_00002_39_0", "global_id": 12782 }, { "text": "Col-E were prevalent in porcine feces despite a recent decrease in colistin usage among German livestock and absence of colistin treatments on the sampled farms. Farmers carried Col-E, but zoonotic transmission was not confirmed.\n\nPrevalence and zoonotic transmission of colistin-resistant and carbapenemase-producing Enterobacterales on German pig farms.", "token_count": 90, "char_count": 355, "word_count": 47, "semantic_coherence": 1, "information_density": 0.7872, "quality_score": 0.8936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:33.768404", "source": { "split": "train_shard_00002", "doc_id": 39 }, "chunk_id": "train_shard_00002_39_1", "global_id": 12783 }, { "text": "

ABSTRACT

The Pelagibacterales order (SAR11) in Alphaproteobacteria dominates marine surface bacterioplankton communities, where it plays a key role in carbon and nutrient cycling. SAR11 phages, known as pelagiphages, are among the most abundant phages in the ocean. Four pelagiphages that infect Pelagibacter HTCC1062 have been reported. Here we report 11 new pelagiphages in the Podoviridae family. Comparative genomic analysis revealed that they are all closely related to previously reported pelagiphages HTVC011P and HTVC019P, in the HTVC019Pvirus genus. HTVC019Pvirus pelagiphages share a core genome of 15 genes, with a pan-genome of 234 genes. Phylogenomic analysis clustered these pelagiphages into three subgroups. Integrases were identified in all but one pelagiphage genomes. Evidence of site-specific integration was obtained by high-throughput sequencing and sequencing PCR amplicons containing predicted integration sites, demonstrating the capacity of these pelagiphages to propagate by both lytic and lysogenic infection. HTVC019P, HTVC021P, HTVC022P, HTVC201P and HTVC121P integrate into tRNA-Cys genes. HTVC011P, HTVC025P, HTVC105P, HTVC109P, HTVC119P and HTVC200P target tRNA-Leu genes, while HTVC120P integrates into the tRNA-Arg. Evidence of pelagiphage integration was also retrieved from Global Ocean Survey (GOS) database, suggesting the occurrence of pelagiphage integration in situ . The capacity of HTVC019Pvirus pelagiphages to integrate into host genomes suggests they could impact SAR11 populations by a variety of mechanisms, including mortality, genetic transduction, and prophage-induced viral immunity", "token_count": 494, "char_count": 1644, "word_count": 217, "semantic_coherence": 1, "information_density": 0.7005, "quality_score": 0.8502, "entities": { "genes": [ "HTCC1062", "HTVC019P", "HTVC021P", "HTVC022P", "HTVC121P", "HTVC119P", "SAR11", "HTVC105P", "HTVC011P", "HTVC200P" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:34.428415", "source": { "split": "train_shard_00002", "doc_id": 40 }, "chunk_id": "train_shard_00002_40_0", "global_id": 12784 }, { "text": "HTVC019Pvirus pelagiphages are a rare example of a lysogenic phage that can be implicated in ecological processes on broad scales, and thus have potential to become a useful model for investigating strategies of host infection and phage-dependent horizontal gene transfer.

IMPORTANCE

Pelagiphages are ecologically important because of their extraordinarily high census numbers, which makes them potentially significant agents in the viral shunt, a concept that links viral predation to the recycling of dissolved organic matter released from lysing plankton cells. Lysogenic Pelagiphages, such as the HTVC019Pvirus pelagiphages we investigate here, are also important because of their potential to contribute to the hypothesized processes such as the “Piggy-Back-the-Winner” and “King-of-the-Mountain”. The former explains nonlinearities in virus to host ratios by postulating increased lysogenization of successful host cells, while the latter postulates host-density dependent propagation of defensive alleles. Here we report multiple Pelagiphage isolates, and provided detailed evidence of their integration into SAR11 genomes. The development of this ecologically significant experimental system for studying phage-dependent processes is progress towards the validation of broad hypotheses about phage ecology with specific examples based on knowledge of mechanisms.\n\nPelagiphages in the Podoviridiae family integrate into host genomes", "token_count": 331, "char_count": 1455, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6771, "quality_score": 0.8385, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:35.000563", "source": { "split": "train_shard_00002", "doc_id": 40 }, "chunk_id": "train_shard_00002_40_1", "global_id": 12785 }, { "text": "Due to the limitations of classical methods for the detection of systemic fungal infections and the high mortality rates associated with these infections, it has become essential to develop a quick, sensitive and specific detection assay. By using the Idaho Technologies Light-Cycler system, a qualitative real-time PCR system has been developed for the detection of the leading causes of systemic infection within the genus Candida. The sensitivity of the assay was comparable to previously described PCR methods (1-5 c.f.u. ml(-1)) and, by the use of a single Candida probe, it was able to detect, but not differentiate between, seven species of Candida (Candida albicans, Candida dubliniensis, Candida glabrata, Candida kefyr, Candida krusei, Candida parapsilosis and Candida tropicalis). Single-round amplification on the Light-Cycler allowed rapid turn-around of clinical samples (within one working day) and it was shown to be more sensitive than classical procedures, exposing 39 possible systemic infections that were not detected by blood culture.\n\nDetection of seven Candida species using the Light-Cycler system.", "token_count": 267, "char_count": 1123, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:35.555510", "source": { "split": "train_shard_00002", "doc_id": 41 }, "chunk_id": "train_shard_00002_41_0", "global_id": 12786 }, { "text": "Listeria monocytogenes (L. monocytogenes) is a ubiquitous organism that can easily enter the food chain. Infection with L. monocytogenes can cause invasive listeriosis. Since 2014, in Austria, L. monocytogenes isolates from human and food/food-associated samples have been provided on a mandatory basis by food producers and laboratories to the National Reference Laboratory. Since 2017, isolates undergo routinely whole genome sequencing (WGS) and core genome Multilocus Sequence Typing (cgMLST) for cluster analyses. Aims of this study were to characterize isolates and clusters of 2017 by using WGS data and to assess the usefulness of this isolate-based surveillance for generating hypotheses on sources of invasive listeriosis in real-time. WGS data from 31 human and 1744 non-human isolates originating from 2017, were eligible for the study. A cgMLST-cluster was defined as two or more isolates differing by ≤10 alleles. We extracted the sequence types (STs) from the WGS data and analyzed the food subcategories meat, fish, vegetable and diary for associations with the ten most prevalent STs among food, through calculating prevalence ratios (PR) with 95% confidence intervals (CI). The three most frequent STs among the human isolates were ST1 (7/31; 22.6%), ST155 (4/31; 12.9%) and ST451 (3/31; 9.7%) and among the non-human isolates ST451 (614/1744; 35.2%), ST8 (173/1744, 10.0%) and ST9 (117/1744; 6.7%)", "token_count": 467, "char_count": 1444, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6635, "quality_score": 0.8318, "entities": { "genes": [ "ST155", "ST451", "ST8", "ST1", "ST9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:36.198259", "source": { "split": "train_shard_00002", "doc_id": 42 }, "chunk_id": "train_shard_00002_42_0", "global_id": 12787 }, { "text": "We found ST21 associated with vegetables (PR: 11.39, 95% CI: 8.32-15.59), ST121 and ST155 with fish (PR: 7.05, 95% CI: 4.88-10.17, PR: 3.29, 95% CI: 1.86-5.82), and ST511, ST7 and ST451 with dairy products (PR: 8.55, 95% CI: 6.65-10.99; PR: 5.05, 95% CI: 3.83-6.66, PR: 3.03, 95% CI: 2.02-4.55). We identified 132 cgMLST-clusters. Six clusters contained human isolates (ST155, ST1, ST101, ST177, ST37 and ST7) and for five of those cgMLST-based cluster analyses solely was able to hypothesize the source: an Austrian meat processing company, two Austrian cheese manufacturers and two vegetable processing companies, one based in Austria and the other in Belgium. Determining routinely STs in food isolates by WGS allows to associate STs with food products. Real-time WGS of L. monocytogenes isolates provided mandatorily, proved to be useful in promptly generating hypotheses on sources of invasive listeriosis.\n\nIsolate-Based Surveillance of Listeria monocytogenes by Whole Genome Sequencing in Austria.", "token_count": 401, "char_count": 1018, "word_count": 150, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [ "ST101", "ST177", "ST21", "ST155", "ST37", "ST7", "ST1", "ST511", "ST121", "ST451" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:36.829631", "source": { "split": "train_shard_00002", "doc_id": 42 }, "chunk_id": "train_shard_00002_42_1", "global_id": 12788 }, { "text": "Abstract

Background

The MRSA Chilean-Cordobes (ChC) clone belongs to the clonal complex 5 (CC5) and typically carries SCCmec I. The ChC clone predominated widely throughout several countries of Latin America (LA), but during the mid-2000s a CA-MRSA CC8 LA variant (USA300-LV) quickly replaced the ChC in Colombia and Ecuador. Most notably, this replacement was not observed in Peru or Chile. Here, we aimed to understand the phylogenomic relatedness of the CC5 ChC clone obtained from different countries of LA.

Methods

We sequenced and analyzed the genomes of 115 MRSA isolates obtained between 2011–2014 from bloodstream infections in 6 LA countries (Argentina, Brazil, Colombia, Chile, Peru, and Venezuela). All isolates were confirmed as ChC clone by pulsed-field gel electrophoresis (PFGE). We used core genome-based phylogenomic reconstructions and molecular clock analysis to infer the relationships and time of divergence between clades.

Results

Whole-genome-based multilocus sequence typing determined that 110/115 isolates belonged to ST5 and carried SCCmec I. The phylogenomic reconstruction showed ChC isolates clustered into 4 major clades distinctly segregated by country of origin (Figure 1). Interestingly, isolates recovered from Chile divided into 2 different clades that segregate according to the city of origin (Santiago [SCL] or Concepción [CON]), suggesting these clades evolved independently. Molecular clock analyses suggested all clades share a common ancestor with the divergence of the Chilean clades occurring earlier (Figure 2). Of note, analysis of heavy metal genes suggested the divergence between Chilean isolates was characterized by the loss of a mercury resistance gene cluster, which is present in an 88% of CON isolates, but only in 28% of SCL (Figure 2)", "token_count": 481, "char_count": 1820, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8258, "entities": { "genes": [ "USA300", "ST5", "CC5", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:37.510045", "source": { "split": "train_shard_00002", "doc_id": 43 }, "chunk_id": "train_shard_00002_43_0", "global_id": 12789 }, { "text": "

Conclusion

MRSA isolates belonging to the ChC clone from 6 LA countries clustered in 4 clades according to the geographical region of isolation. This segregation suggests divergent adaptations that may respond to different selective pressures. Heavy metal resistance could play a role in the ability of the MRSA ChC to disseminate in specific geographical locations.

Disclosures

All authors: No reported disclosures.\n\n556. Phylogenomic Epidemiology of Methicillin-Resistant Staphylococcus aureus (MRSA) Chilean-Cordobes Clone in Latin America", "token_count": 155, "char_count": 560, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7973, "quality_score": 0.8986, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:37.957603", "source": { "split": "train_shard_00002", "doc_id": 43 }, "chunk_id": "train_shard_00002_43_1", "global_id": 12790 }, { "text": "Flavobacterium spartansii strain T16T was isolated from a disease outbreak in hatchery-reared Chinook salmon (Oncorhynchus tshawytscha) fingerlings. To gain insight into its genomic content, structure and virulence pathogenesis factors, comparative genome analyses were performed using genomes from environmental and virulent Flavobacterium strains. F. spartansii shared low average nucleotide identity (ANI) to well-known fish-pathogenic flavobacteria (e.g., F. columnare, F. psychrophilum, and F. branchiophilum), indicating that it is a new and emerging fish pathogen. The genome in T16T had a length of 5,359,952 bp, a GC-content 35.7%, and 4,422 predicted protein-coding sequences. Flavobacterium core genome analysis showed that the number of shared genes decreased with the addition of input genomes and converged at 1182 genes. At least 8 genomic islands and 5 prophages were predicted in T16T. At least 133 virulence factors associated with virulence in pathogenic bacteria were highly conserved in F. spartansii T16T. Furthermore, genes linked to virulence in other bacterial species (e.g., those encoding for a type IX secretion system, collagenase and hemolysin) were found in the genome of F. spartansii T16T and were conserved in most of the analyzed pathogenic Flavobacterium. F. spartansii was resistant to ampicillin and penicillin, consistent with the presence of multiple genes encoding diverse lactamases and the penicillin-binding protein in the genome. To allow for future investigations into F", "token_count": 524, "char_count": 1651, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8116, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:59:38.642629", "source": { "split": "train_shard_00002", "doc_id": 44 }, "chunk_id": "train_shard_00002_44_0", "global_id": 12791 }, { "text": "spartansii virulence in vivo, a transposon-based random mutagenesis strategy was attempted in F. spartansii T16T using pHimarEm1. Four putative gliding motility deficient mutants were obtained and the insertion sites of pHimarEm1 in the genome of these mutants were characterized. In total, study results clarify some of the mechanisms by which emerging flavobacterial fish pathogens may cause disease and also provide direly needed tools to investigate their pathogenesis.\n\nThe Emerging Fish Pathogen Flavobacterium spartansii Isolated from Chinook Salmon: Comparative Genome Analysis and Molecular Manipulation.", "token_count": 184, "char_count": 649, "word_count": 83, "semantic_coherence": 1, "information_density": 0.8072, "quality_score": 0.9036, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:39.098333", "source": { "split": "train_shard_00002", "doc_id": 44 }, "chunk_id": "train_shard_00002_44_1", "global_id": 12792 }, { "text": "Telomerase is a ribonucleoprotein, the main function of which is to synthesize telomeres, i.e. repetitive sequences which are localized at the ends of eukaryotic chromosomes. Telomerase maintains the stability of the genome in eukaryotic cells by replicating chromosomal ends. The structural and functional investigation of the telomerase complex is significantly restricted due to difficulties connected with the isolation of its main catalytic subunit in recombinant form. Herein, we describe a method developed for the isolation of the recombinant telomerase reverse transcriptase from thermotolerant yeastHansenula polymorpha. A functional test performed for the isolated protein and the RNA/DNA duplex, simulating the interaction of telomerase RNA and telomere, reveals that the isolated catalytic subunit of telomerase possesses limited reverse transcriptase activity.\n\nHansenula Polymorpha TERT: 
A Telomerase Catalytic Subunit Isolated in Recombinant Form with Limited Reverse Transcriptase Activity.", "token_count": 252, "char_count": 1008, "word_count": 134, "semantic_coherence": 1, "information_density": 0.5821, "quality_score": 0.791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:39.585868", "source": { "split": "train_shard_00002", "doc_id": 45 }, "chunk_id": "train_shard_00002_45_0", "global_id": 12793 }, { "text": "Thermophilic environments represent an interesting niche. Among thermophiles, the genus Thermus is among the most studied genera. In this study, we have sequenced the genome of Thermus parvatiensis strain RL, a thermophile isolated from Himalayan hot water springs (temperature >96°C) using PacBio RSII SMRT technique. The small genome (2.01 Mbp) comprises a chromosome (1.87 Mbp) and a plasmid (143 Kbp), designated in this study as pTP143. Annotation revealed a high number of repair genes, a squeezed genome but containing highly plastic plasmid with transposases, integrases, mobile elements and hypothetical proteins (44%). We performed a comparative genomic study of the group Thermus with an aim of analysing the phylogenetic relatedness as well as niche specific attributes prevalent among the group. We compared the reference genome RL with 16 Thermus genomes to assess their phylogenetic relationships based on 16S rRNA gene sequences, average nucleotide identity (ANI), conserved marker genes (31 and 400), pan genome and tetranucleotide frequency. The core genome of the analyzed genomes contained 1,177 core genes and many singleton genes were detected in individual genomes, reflecting a conserved core but adaptive pan repertoire. We demonstrated the presence of metagenomic islands (chromosome:5, plasmid:5) by recruiting raw metagenomic data (from the same niche) against the genomic replicons of T. parvatiensis. We also dissected the CRISPR loci wide all genomes and found widespread presence of this system across Thermus genomes", "token_count": 452, "char_count": 1591, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6872, "quality_score": 0.8436, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:40.225253", "source": { "split": "train_shard_00002", "doc_id": 46 }, "chunk_id": "train_shard_00002_46_0", "global_id": 12794 }, { "text": "Additionally, we performed a comparative analysis of competence loci wide Thermus genomes and found evidence for recent horizontal acquisition of the locus and continued dispersal among members reflecting that natural competence is a beneficial survival trait among Thermus members and its acquisition depicts unending evolution in order to accomplish optimal fitness.\n\nComplete Genome Analysis of Thermus parvatiensis and Comparative Genomics of Thermus spp. Provide Insights into Genetic Variability and Evolution of Natural Competence as Strategic Survival Attributes.", "token_count": 143, "char_count": 599, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7273, "quality_score": 0.8636, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:40.653899", "source": { "split": "train_shard_00002", "doc_id": 46 }, "chunk_id": "train_shard_00002_46_1", "global_id": 12795 }, { "text": "The adaptation of bacterial lineages to local environmental conditions creates the potential for broader genotypic diversity within a species, which can enable a species to dominate across ecological gradients because of niche flexibility. The genus Polynucleobacter maintains both free-living and symbiotic ecotypes and maintains an apparently ubiquitous distribution in freshwater ecosystems. Subspecies-level resolution supplemented with metagenome-derived genotype analysis revealed that differential functional constraints, not geographic distance, produce and maintain strain-level genetic conservation in Polynucleobacter populations across three geographically proximal riverine environments. Genes associated with cofactor biosynthesis and one-carbon metabolism showed habitat specificity, and protein-coding genes of unknown function and membrane transport proteins were under positive selection across each habitat. Characterized by different median ratios of nonsynonymous to synonymous evolutionary changes (dN/dS ratios) and a limited but statistically significant negative correlation between the dN/dS ratio and codon usage bias between habitats, the free-living and core genotypes were observed to be evolving under strong purifying selection pressure. Highlighting the potential role of genetic adaptation to the local environment, the two-component system protein-coding genes were highly stable (dN/dS ratio, < 0.03). These results suggest that despite the impact of the habitat on genetic diversity, and hence niche partition, strong environmental selection pressure maintains a conserved core genome for Polynucleobacter populations. IMPORTANCE Understanding the biological factors influencing habitat-wide genetic endemism is important for explaining observed biogeographic patterns. Polynucleobacter is a genus of bacteria that seems to have found a way to colonize myriad freshwater ecosystems and by doing so has become one of the most abundant bacteria in these environments", "token_count": 477, "char_count": 2078, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6797, "quality_score": 0.8398, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:41.299229", "source": { "split": "train_shard_00002", "doc_id": 47 }, "chunk_id": "train_shard_00002_47_0", "global_id": 12796 }, { "text": "We sequenced metagenomes from locations across the Chicago River system and assembled Polynucleobacter genomes from different sites and compared how the nucleotide composition, gene codon usage, and the ratio of synonymous (codes for the same amino acid) to nonsynonymous (codes for a different amino acid) mutations varied across these population genomes at each site. The environmental pressures at each site drove purifying selection for functional traits that maintained a streamlined core genome across the Chicago River Polynucleobacter population while allowing for site-specific genomic adaptation. These adaptations enable Polynucleobacter to become dominant across different riverine environmental gradients.\n\nDifferential Functional Constraints Cause Strain-Level Endemism in Polynucleobacter Populations.", "token_count": 196, "char_count": 844, "word_count": 105, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:41.749320", "source": { "split": "train_shard_00002", "doc_id": 47 }, "chunk_id": "train_shard_00002_47_1", "global_id": 12797 }, { "text": "The [URE3] prion of Saccharomyces cerevisiae is a self-propagating inactive amyloid form of the Ure2 protein. Ure2p residues 1-65 constitute the prion domain, and the remaining C-terminal portion regulates nitrogen catabolism. We have examined the URE2 genes of wild-type isolates of S. cerevisiae and those of several pathogenic yeasts and a filamentous fungus. We find that the normal function of the S. cerevisiae Ure2p in nitrogen regulation is fully complemented by the Ure2p of Candida albicans, Candida glabrata, Candida kefyr, Candida maltosa, Saccharomyces bayanus, and Saccharomyces paradoxus, all of which have high homology in the C-terminal nitrogen regulation domain. However, there is considerable divergence of their N-terminal domains from that of Ure2p of S. cerevisiae. [URE3(Sc)] showed efficient transmission into S. cerevisiae ure2Delta cells if expressing a Ure2p of species within Saccharomyces. However, [URE3(Sc)] did not seed self-propagating inactivation of the Ure2p's from the other yeasts. When overexpressed as a fusion with green fluorescent protein, residues 5-47 of the S. cerevisiae prion domain are necessary for curing the [URE3] prion. Residues 11-39 are necessary for an inactivating interaction with the full-length Ure2p. A nearly identical region is highly conserved among many of the yeasts examined in this study, despite the wide divergence of sequences found in other parts of the N-terminal domains.\n\nConservation of a portion of the S. cerevisiae Ure2p prion domain that interacts with the full-length protein.", "token_count": 445, "char_count": 1559, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5502, "quality_score": 0.7751, "entities": { "genes": [ "URE3", "URE2" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:42.380323", "source": { "split": "train_shard_00002", "doc_id": 48 }, "chunk_id": "train_shard_00002_48_0", "global_id": 12798 }, { "text": "The yeast content in feta cheese from three different dairies was examined. Almost all samples contained yeasts in considerable numbers, 10(4)-10(6) cfu g-1. A specific narrow yeast flora was found for each dairy. Torulaspora delbrueckii was the dominating species in feta from Dairy A. This strong-fermenting species was found to cause swelling of the cans. Debaryomyces hansenii, Candida sake and Kluyveromyces marxianus were dominant in samples from Dairy B. Candida butyri and Debaromyces hansenii were found in Dairy C. Yarrowia lipolytica was present in low numbers in cheese samples from all three dairies. Geotrichum candidum was also commonly found although in low concentrations. Yeast occurrence was due to recontamination. Yeasts were found in high concentrations in production areas.\n\nYeast occurrence in Danish feta cheese", "token_count": 221, "char_count": 836, "word_count": 124, "semantic_coherence": 1, "information_density": 0.621, "quality_score": 0.8105, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:42.854596", "source": { "split": "train_shard_00002", "doc_id": 49 }, "chunk_id": "train_shard_00002_49_0", "global_id": 12799 }, { "text": "

Background

As the number of genome-wide association study (GWAS) and quantitative trait locus (QTL) mappings in rice continues to grow, so does the already long list of genomic loci associated with important agronomic traits. Typically, loci implicated by GWAS/QTL analysis contain tens to hundreds to thousands of single-nucleotide polmorphisms (SNPs)/genes, not all of which are causal and many of which are in noncoding regions. Unraveling the biological mechanisms that tie the GWAS regions and QTLs to the trait of interest is challenging, especially since it requires collating functional genomics information about the loci from multiple, disparate data sources.

Results

We present RicePilaf, a web app for post-GWAS/QTL analysis, that performs a slew of novel bioinformatics analyses to cross-reference GWAS results and QTL mappings with a host of publicly available rice databases. In particular, it integrates (i) pangenomic information from high-quality genome builds of multiple rice varieties, (ii) coexpression information from genome-scale coexpression networks, (iii) ontology and pathway information, (iv) regulatory information from rice transcription factor databases, (v) epigenomic information from multiple high-throughput epigenetic experiments, and (vi) text-mining information extracted from scientific abstracts linking genes and traits. We demonstrate the utility of RicePilaf by applying it to analyze GWAS peaks of preharvest sprouting and genes underlying yield-under-drought QTLs.

Conclusions

RicePilaf enables rice scientists and breeders to shed functional light on their GWAS regions and QTLs, and it provides them with a means to prioritize SNPs/genes for further experiments. The source code, a Docker image, and a demo version of RicePilaf are publicly available at https://github.com/bioinfodlsu/rice-pilaf.", "token_count": 473, "char_count": 1867, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:44.190439", "source": { "split": "train_shard_00002", "doc_id": 50 }, "chunk_id": "train_shard_00002_50_0", "global_id": 12800 }, { "text": "RicePilaf: a post-GWAS/QTL dashboard to integrate pangenomic, coexpression, regulatory, epigenomic, ontology, pathway, and text-mining information to provide functional insights into rice QTLs and GWAS loci.", "token_count": 59, "char_count": 207, "word_count": 25, "semantic_coherence": 1, "information_density": 0.92, "quality_score": 0.96, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:44.547120", "source": { "split": "train_shard_00002", "doc_id": 50 }, "chunk_id": "train_shard_00002_50_1", "global_id": 12801 }, { "text": "Elucidation of the mechanism of high temperature tolerance in yeasts is important for the molecular breeding of high temperature-tolerant yeasts that can be used in bioethanol production. We identified genes whose expression is correlated with the degree of thermotolerance in Saccharomyces cerevisiae by DNA microarray analysis. Gene expression profiles of three S. cerevisiae strains showing different levels of thermotolerance were compared, and we chose three of them as candidate genes. Among these genes, FMP21 was investigated as a thermotolerance-related gene in S. cerevisiae by comparing the growth at high temperature with the gene expression in eight strains. The expression ratio of FMP21 at 37°C was correlated with the doubling time ratio at a coefficient of determination of 0.787. The potential involvement of the Fmp21 in the thermotolerance of yeasts was evaluated. The FMP21 deletion variant showed a decreased respiratory growth rate and increased thermosensitivity. Furthermore, the overexpression of FMP21 improved thermotolerance in yeasts. In conclusion, the function of Fmp21 is important for thermotolerance in yeasts.\n\nIdentification of a gene, FMP21, whose expression levels are involved in thermotolerance in Saccharomyces cerevisiae.", "token_count": 302, "char_count": 1264, "word_count": 180, "semantic_coherence": 1, "information_density": 0.5278, "quality_score": 0.7639, "entities": { "genes": [ "FMP21" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:45.493045", "source": { "split": "train_shard_00002", "doc_id": 51 }, "chunk_id": "train_shard_00002_51_0", "global_id": 12802 }, { "text": "

Background

Orientia tsutsugamushi is a clinically important but neglected obligate intracellular bacterial pathogen of the Rickettsiaceae family that causes the potentially life-threatening human disease scrub typhus. In contrast to the genome reduction seen in many obligate intracellular bacteria, early genetic studies of Orientia have revealed one of the most repetitive bacterial genomes sequenced to date. The dramatic expansion of mobile elements has hampered efforts to generate complete genome sequences using short read sequencing methodologies, and consequently there have been few studies of the comparative genomics of this neglected species.

Results

We report new high-quality genomes of Orientia tsutsugamushi, generated using PacBio single molecule long read sequencing, for six strains: Karp, Kato, Gilliam, TA686, UT76 and UT176. In comparative genomics analyses of these strains together with existing reference genomes from Ikeda and Boryong strains, we identify a relatively small core genome of 657 genes, grouped into core gene ‘islands’ and separated by repeat regions, and use the core genes to infer the first whole-genome phylogeny of Orientia .

Conclusions

Complete assemblies of multiple Orientia genomes verify initial suggestions that these are remarkable organisms. They have large genomes with widespread amplification of repeat elements and massive chromosomal rearrangements between strains. At the gene level, Orientia has a relatively small set of universally conserved genes, similar to other obligate intracellular bacteria, and the relative expansion in genome size can be accounted for by gene duplication and repeat amplification. Our study demonstrates the utility of long read sequencing to investigate complex bacterial genomes and characterise genomic variation.\n\nLong-read whole genome sequencing and comparative analysis of six strains of the human pathogenOrientia tsutsugamushi", "token_count": 472, "char_count": 1961, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6231, "quality_score": 0.8116, "entities": { "genes": [ "UT176", "TA686", "UT76" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:46.138132", "source": { "split": "train_shard_00002", "doc_id": 52 }, "chunk_id": "train_shard_00002_52_0", "global_id": 12803 }, { "text": "

ABSTRACT

Incidences of infection and occurrence of Kocuria rhizophila in human gut are prominent but certainly no reports on the species ability to withstand human gastrointestinal dynamics. Kocuria rhizophila strain D2 isolated from healthy human gut was comprehensively characterized. The functional analysis revealed the ability to produce various gastric enzymes and sensitive to major clinical antibiotics. It also exhibited tolerance to acidic pH and bile salts. Strain D2 displayed bile-salt hydrolytic (BSH) activity, strong cell surface traits such as hydrophobicity, auto-aggregation capacity and adherence to human HT-29 cell line. Prominently, it showed no hemolytic activity and was susceptible to the human serum. Exploration of the genome led to the discovery of the genes for the above said properties and has ability to produce various essential amino acids and vitamins. Further, comparative genomics have identified core, accessory and unique genetic features. The core genome has given insights into the phylogeny while the accessory and unique genes has led to the identification of niche specific genes. Bacteriophage, virulence factors and biofilm formation genes were absent with this species. Housing CRISPR and antibiotic resistance gene was strain specific. The integrated approach of functional, genomic and comparative analysis denotes the niche specific adaption to gut dynamics of strain D2. Moreover the study has comprehensively characterized genome sequence of each strain to know the genetic difference and intern recognize the effects of on phenotype and functionality complexity. The evolutionary relationship among strains along and adaptation strategies has been included in this study.

Significance

Reports of Kocuria rhizophila isolation from various sources have been reported but the few disease outbreaks in humans and fishes have been prominent, but no supportive evidence about the survival ability of Kocuria spp. within human GIT. Here, we report the gut adaption potential of K. rhizophila strain D2 by functional and genomic analysis. Further; comparative genomics reveals this adaption to be strain specific (Gluten degradation). Genetic difference, evolutionary relationship and adaptation strategies have been including in this study.", "token_count": 503, "char_count": 2305, "word_count": 327, "semantic_coherence": 1, "information_density": 0.5719, "quality_score": 0.7859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:46.792320", "source": { "split": "train_shard_00002", "doc_id": 53 }, "chunk_id": "train_shard_00002_53_0", "global_id": 12804 }, { "text": "Functional and Comparative Genomics of Niche-Specific Adapted ActinomycetesKocuria rhizophilaStrain D2 Isolated from Healthy Human Gut", "token_count": 48, "char_count": 141, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:47.152550", "source": { "split": "train_shard_00002", "doc_id": 53 }, "chunk_id": "train_shard_00002_53_1", "global_id": 12805 }, { "text": "Candida was isolated in 205 of 1060 clinical specimens (19.33%) in our laboratary sent from the intensive care unit for mycological investigation between January 98-December 99. All isolated strains were identified to species level using the API Candida system (Bio-Meieux, France) as follows; Candida albicans (n:115, 56.09%), Candida tropicalis (n:23, 11.21%), Candida parapsilosis (n:21, 10.24%), Candida glabrata (n:12, 5.83%). Candida kefyr (n:9, 4.39%), Candida lusitaniae (n:7, 3.41%), Candida famata (n:6, 2.92%), Candida krusei (n:6, 2.92%), Candida guilliermondii (n:6, 2.92%). These stains were identified using congo-red-glucose-brain-heart-infusion agar and slime production was determined in Candida albicans 53.91% and 67.77% in other than Candida species. In the present study, E test (AB Biodisk, Solna, Sweeden) was used to test antifungal susceptibility. The resistance to amphotericin B was 19.51%, to fluconazole 27.31% and to flucytosine 20.00%.\n\nIdentification and antifungal susceptibility of Candida isolated from intensive care unit patients.", "token_count": 402, "char_count": 1068, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:47.765329", "source": { "split": "train_shard_00002", "doc_id": 54 }, "chunk_id": "train_shard_00002_54_0", "global_id": 12806 }, { "text": "

ABSTRACT

Enterococcus faecium though commensals in human gut, few strains provide beneficial effect to humans as probiotics, few are responsible for nosocomial infection and few as non-pathogens. Comparative genomics of E. faecium will help to reveal the genomic differences responsible for the said properties. In this study, we compared E. faecium strain 17OM39 with a marketed probiotic, non-pathogenic non-probiotic (NPNP) and pathogenic strains. The core genome analysis revealed, 17OM39 was closely related with marketed probiotic strain T110. Strain 17OM39 was found to be devoid of known vancomycin, tetracycline resistance genes and functional virulence genes. Moreover, 17OM39 is „less open‟ due to absence of frequently found transposable elements. Genes imparting beneficial functional properties were observed to be present in marketed probiotic T110 and 17OM39 strains. Additional, genes associated with colonization within gastrointestinal tract were detected across all the strains. Beyond shared genetic features; this study particularly identified genes that are responsible to impart probiotic, non-pathogenic and pathogenic features to the strains of E. faecium. The study also provides insights into the acquired and intrinsic drug resistance genes, which will be helpful for better understanding of the physiology of antibiotic resistance in E. faecium strains. In addition, we could identify genes contributing to the intrinsic ability of 17OM39 E. faecium isolate to be a potential probiotic. The study has comprehensively characterized genome sequence of each strain to find the genetic variation and understand effects of these on functionality, phenotypic complexity. Further the evolutionary relationship of species along with adaptation strategies have been including in this study.\n\nComparative Genome Analysis Reveals Important Genetic Factors Associated with Probiotic Property inEnterococcus faeciumstrains", "token_count": 476, "char_count": 1955, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5955, "quality_score": 0.7978, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:48.410447", "source": { "split": "train_shard_00002", "doc_id": 55 }, "chunk_id": "train_shard_00002_55_0", "global_id": 12807 }, { "text": "

Purpose

The aim of the study was to characterize clinical and environmental Staphylococcus pettenkoferi isolates with regard to genomic diversity and antibiotic susceptibility pattern. Repetitive-sequence-based PCR and core genome phylogenetic analysis of whole-genome sequencing (WGS) data verified the presence of distinct clades comprising closely related S. pettenkoferi isolates from different geographical locations and origins.

Methodology

Phylogenetic relationships between 25 S. pettenkoferi isolates collected from blood cultures and intra-operative air sampling were determined by repetitive-sequence-based PCR typing and analysis of ~157 000 SNPs identified in the core genome after WGS. Antibiotic susceptibility testing and tests for biofilm production (microtitre plate assay) were performed.

Results

Repetitive-sequence-based PCR as well as WGS data demonstrated the close relatedness of clinically significant blood culture isolates to probable contaminants, as well as to environmental isolates. Antibiotic-susceptibility testing demonstrated a low level of antimicrobial resistance. The mecA gene was present in two cefoxitin-resistant isolates. No isolates were found to produce biofilm.

Conclusion

Close genomic relatedness of S. pettenkoferi isolates from different geographical locations and origins were found within clades, but with substantial genomic difference between the two major clades. The ecological niche of S. pettenkoferi remains unconfirmed, but the presence of S. pettenkoferi in the air of the operating field favours the suggestion of a role in skin flora. Identification of S. pettenkoferi in clinical samples should, in a majority of cases, most likely be regarded as a probable contamination, and its role as a possible pathogen in immunocompromised hosts remains to be clarified.\n\nGenomic relatedness of Staphylococcus pettenkoferi isolates of different origins.", "token_count": 488, "char_count": 1936, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5462, "quality_score": 0.7731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:49.110046", "source": { "split": "train_shard_00002", "doc_id": 56 }, "chunk_id": "train_shard_00002_56_0", "global_id": 12808 }, { "text": "When grown in the appropriate medium, several yeast species produce pectinases able to degrade pectic substances. It is mainly exocellular endopolygalacturonases that break pectins or pectate down by hydrolysis of alpha-1,4-glycosidic linkages in a random way. Biochemical characterisation of these enzymes has shown that they have an optimal pH in the acidic region and an optimal temperature between 40 and 55 degrees C. Their production by yeasts is a constitutive feature and is repressed by the glucose concentration and aeration. Pectic substances and their hydrolysis products are used as carbon sources by a limited number of yeasts and hence these enzymes must be involved in the colonisation of different parts of plants, including fruits. The first yeast pectic enzyme (encoded by the PSE3 gene) was cloned from Tichosporon penicillatum. Recently, a polygalacturonase-encoding gene from Saccharomyces cerevisiae has been cloned and overexpressed in several strains and the gene for an extracellular endopolygalacturonase from Kluyveromyces marxianus has also been described. Taking all the results together, the idea is now emerging that this type of yeast enzyme could offer an alternative to fungal enzymes for industrial applications.\n\nProduction of pectic enzymes in yeasts.", "token_count": 331, "char_count": 1289, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6526, "quality_score": 0.8263, "entities": { "genes": [ "PSE3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:49.699084", "source": { "split": "train_shard_00002", "doc_id": 57 }, "chunk_id": "train_shard_00002_57_0", "global_id": 12809 }, { "text": "

Background

Because biotechnological uses of bacteriophage gene products as alternatives to conventional antibiotics will require a thorough understanding of their genomic context, we sequenced and analyzed the genomes of four closely related phages isolated from Clostridium perfringens, an important agricultural and human pathogen.

Results

Phage whole-genome tetra-nucleotide signatures and proteomic tree topologies correlated closely with host phylogeny. Comparisons of our phage genomes to 26 others revealed three shared COGs; of particular interest within this core genome was an endolysin (PF01520, an N-acetylmuramoyl-L-alanine amidase) and a holin (PF04531). Comparative analyses of the evolutionary history and genomic context of these common phage proteins revealed two important results: 1) strongly significant host-specific sequence variation within the endolysin, and 2) a protein domain architecture apparently unique to our phage genomes in which the endolysin is located upstream of its associated holin. Endolysin sequences from our phages were one of two very distinct genotypes distinguished by variability within the putative enzymatically-active domain. The shared or core genome was comprised of genes with multiple sequence types belonging to five pfam families, and genes belonging to 12 pfam families, including the holin genes, which were nearly identical.

Conclusions

Significant genomic diversity exists even among closely-related bacteriophages. Holins and endolysins represent conserved functions across divergent phage genomes and, as we demonstrate here, endolysins can have significant variability and host-specificity even among closely-related genomes. Endolysins in our phage genomes may be subject to different selective pressures than the rest of the genome. These findings may have important implications for potential biotechnological applications of phage gene products.\n\nComparative genomics of four closely related Clostridium perfringens bacteriophages reveals variable evolution among core genes with therapeutic potential.", "token_count": 494, "char_count": 2093, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [ "PF04531", "PF01520" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:50.386906", "source": { "split": "train_shard_00002", "doc_id": 58 }, "chunk_id": "train_shard_00002_58_0", "global_id": 12810 }, { "text": "Acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (CO2) to multicarbon compounds coupled to the oxidation of inorganic substrates, such as hydrogen (H2) or carbon monoxide (CO), via the Wood-Ljungdahl pathway. Owing to the metabolic capability of CO2 fixation, much attention has been focused on understanding the unique pathways associated with acetogens, particularly their metabolic coupling of CO2 fixation to energy conservation. Most known acetogens are phylogenetically and metabolically diverse bacteria present in 23 different bacterial genera. With the increased volume of available genome information, acetogenic bacterial genomes can be analyzed by comparative genome analysis. Even with the genetic diversity that exists among acetogens, the Wood-Ljungdahl pathway, a central metabolic pathway, and cofactor biosynthetic pathways are highly conserved for autotrophic growth. Additionally, comparative genome analysis revealed that most genes in the acetogen-specific core genome were associated with the Wood-Ljungdahl pathway. The conserved enzymes and those predicted as missing can provide insight into biological differences between acetogens and allow for the discovery of promising candidates for industrial applications.\n\nAnalysis of the Core Genome and Pan-Genome of Autotrophic Acetogenic Bacteria.", "token_count": 349, "char_count": 1391, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6556, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:50.979936", "source": { "split": "train_shard_00002", "doc_id": 59 }, "chunk_id": "train_shard_00002_59_0", "global_id": 12811 }, { "text": "Sources of yeast which may contaminate the curd during the manufacture of Cheddar cheese, were examined in a single cheese factory. A total of 77 yeast species present in the factory environment, manufacturing and ripening of Cheddar cheese were identified according to cellular long-chain fatty acid analysis and verified with conventional identification techniques. Product line samples were taken at critical control points in the manufacturing process and analysed after incubation at 25 degrees C for 96 h. The progression of yeast species during cheese-making and ripening was monitored after renneting and at subsequent 48-h intervals. Dominant species were Debaryomyces hansenii and Cryptococcus albidus, while Yarrowia lipolytica, Rhodotorula minuta, Torulaspora delbrueckii, Rhodotorula glutinis and Kluyveromyces marxianus were present at low numbers. The results obtained showed that yeasts were present in all cheese samples examined, at quantities ranging from 9 X 10(2) to 1(.)4 X 10(7) cfu g-1.\n\nThe isolation and identification of yeasts obtained during the manufacture and ripening of Cheddar cheese", "token_count": 281, "char_count": 1117, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8168, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:51.535690", "source": { "split": "train_shard_00002", "doc_id": 60 }, "chunk_id": "train_shard_00002_60_0", "global_id": 12812 }, { "text": "Our previous study has shown that dietary supplementation with Lactococcus lactis WFLU12 can enhance the growth of olive flounder and its resistance against streptococcal infection. The objective of the present study was to use comparative genomics tools to investigate genomic characteristics of strain WFLU12 and the presence of genes supporting its probiotic action using sequenced genomes of L. lactis strains. Dispensable and singleton genes of strain WFLU12 were found to be more enriched in genes associated with metabolism (e.g., energy production and conversion, and carbohydrate transport and metabolism) than pooled dispensable and singleton genes in other L. lactis strains, reflecting WFLU12 strain-specific ecosystem origin and its ability to metabolize different energy sources. Strain WFLU12 produced antimicrobial compounds that could inhibit several bacterial fish pathogens. It possessed the nisin gene cluster (nisZBTCIPRKFEG) and genes encoding lysozyme and colicin V. However, only three other strains (CV56, IO-1, and SO) harbor a complete nisin gene cluster. We also found that L. lactis WFLU12 possessed many other important functional genes involved in stress responses to the gastrointestinal tract environment, dietary energy extraction, and metabolism to support the probiotic action of this strain found in our previous study. This strongly indicates that not all L. lactis strains can be used as probiotics. This study highlights comparative genomics approaches as very useful and powerful tools to select probiotic candidates and predict their probiotic effects.\n\nGenome-Wide Comparison Reveals a Probiotic Strain Lactococcus Lactis WFLU12 Isolated from the Gastrointestinal Tract of Olive Flounder (Paralichthys Olivaceus) Harboring Genes Supporting Probiotic Action.", "token_count": 488, "char_count": 1835, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5913, "quality_score": 0.7956, "entities": { "genes": [ "WFLU12", "CV56" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:52.183339", "source": { "split": "train_shard_00002", "doc_id": 61 }, "chunk_id": "train_shard_00002_61_0", "global_id": 12813 }, { "text": "

Background

Klebsiella pneumoniae is a leading cause of extended-spectrum β-lactamase (ESBL)-producing hospital-associated infections, for which elderly patients are at increased risk.

Methods

We conducted a 1-year prospective cohort study, in which a third of patients admitted to 2 geriatric wards in a specialized hospital were recruited and screened for carriage of K. pneumoniae by microbiological culture. Clinical isolates were monitored via the hospital laboratory. Colonizing and clinical isolates were subjected to whole-genome sequencing and antimicrobial susceptibility testing.

Results

K. pneumoniae throat carriage prevalence was 4.1%, rectal carriage 10.8%, and ESBL carriage 1.7%, and the incidence of K. pneumoniae infection was 1.2%. The isolates were diverse, and most patients were colonized or infected with a unique phylogenetic lineage, with no evidence of transmission in the wards. ESBL strains carried blaCTX-M-15 and belonged to clones associated with hospital-acquired ESBL infections in other countries (sequence type [ST] 29, ST323, and ST340). One also carried the carbapenemase blaIMP-26. Genomic and epidemiological data provided evidence that ESBL strains were acquired in the referring hospital. Nanopore sequencing also identified strain-to-strain transmission of a blaCTX-M-15 FIBK/FIIK plasmid in the referring hospital.

Conclusions

The data suggest the major source of K. pneumoniae was the patient's own gut microbiome, but ESBL strains were acquired in the referring hospital. This highlights the importance of the wider hospital network to understanding K. pneumoniae risk and infection prevention. Rectal screening for ESBL organisms on admission to geriatric wards could help inform patient management and infection control in such facilities.", "token_count": 479, "char_count": 1815, "word_count": 240, "semantic_coherence": 1, "information_density": 0.5917, "quality_score": 0.7958, "entities": { "genes": [ "ST323", "ST340" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:52.830568", "source": { "split": "train_shard_00002", "doc_id": 62 }, "chunk_id": "train_shard_00002_62_0", "global_id": 12814 }, { "text": "Antimicrobial-Resistant Klebsiella pneumoniae Carriage and Infection in Specialized Geriatric Care Wards Linked to Acquisition in the Referring Hospital.", "token_count": 41, "char_count": 153, "word_count": 18, "semantic_coherence": 1, "information_density": 0.9444, "quality_score": 0.9722, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:53.192428", "source": { "split": "train_shard_00002", "doc_id": 62 }, "chunk_id": "train_shard_00002_62_1", "global_id": 12815 }, { "text": "

Background

The sinorhizobia are amongst the most well studied members of nitrogen-fixing root nodule bacteria and contribute substantial amounts of fixed nitrogen to the biosphere. While the alfalfa symbiont Sinorhizobium meliloti RM 1021 was one of the first rhizobial strains to be completely sequenced, little information is available about the genomes of this large and diverse species group.

Results

Here we report the draft assembly and annotation of 48 strains of Sinorhizobium comprising five genospecies. While S. meliloti and S. medicae are taxonomically related, they displayed different nodulation patterns on diverse Medicago host plants, and have differences in gene content, including those involved in conjugation and organic sulfur utilization. Genes involved in Nod factor and polysaccharide biosynthesis, denitrification and type III, IV, and VI secretion systems also vary within and between species. Symbiotic phenotyping and mutational analyses indicated that some type IV secretion genes are symbiosis-related and involved in nitrogen fixation efficiency. Moreover, there is a correlation between the presence of type IV secretion systems, heme biosynthesis and microaerobic denitrification genes, and symbiotic efficiency.

Conclusions

Our results suggest that each Sinorhizobium strain uses a slightly different strategy to obtain maximum compatibility with a host plant. This large genome data set provides useful information to better understand the functional features of five Sinorhizobium species, especially compatibility in legume-Sinorhizobium interactions. The diversity of genes present in the accessory genomes of members of this genus indicates that each bacterium has adopted slightly different strategies to interact with diverse plant genera and soil environments.\n\nComparative genomics of the core and accessory genomes of 48 Sinorhizobium strains comprising five genospecies.", "token_count": 459, "char_count": 1938, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6269, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:53.836247", "source": { "split": "train_shard_00002", "doc_id": 63 }, "chunk_id": "train_shard_00002_63_0", "global_id": 12816 }, { "text": "Members of the genus Bifidobacterium are dominant and symbiotic inhabitants of the mammalian gastrointestinal tract. Being vertically transmitted, bifidobacterial host colonization commences immediately after birth and leads to a phase of host infancy during which bifidobacteria are highly prevalent and abundant to then transit to a reduced, yet stable abundance phase during host adulthood. However, in order to reach and stably colonize their elective niche, i.e. the large intestine, bifidobacteria have to cope with a multitude of oxidative, osmotic and bile salt/acid stress challenges that occur along the gastrointestinal tract (GIT). Concurrently, bifidobacteria not only have to compete with the myriad of other gut commensals for nutrient acquisition, but they also require protection against bacterial viruses. In this context, Next-Generation Sequencing (NGS) techniques, allowing large-scale comparative and functional genome analyses have helped to identify the genetic strategies that bifidobacteria have developed in order to colonize, survive and adopt to the highly competitive mammalian gastrointestinal environment. The current review is aimed at providing a comprehensive overview concerning the molecular strategies on which bifidobacteria rely to stably and successfully colonize the mammalian gut.\n\nThe genus bifidobacterium: From genomics to functionality of an important component of the mammalian gut microbiota running title: Bifidobacterial adaptation to and interaction with the host.", "token_count": 358, "char_count": 1523, "word_count": 207, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:54.418709", "source": { "split": "train_shard_00002", "doc_id": 64 }, "chunk_id": "train_shard_00002_64_0", "global_id": 12817 }, { "text": "The genomic library of Kluyveromyces fragilis was constructed in E. coli TG1, and 5 beta-galactosidase gene (LAC4) clones have been obtained from the library by complementation of the Kluyveromyces lactis lac4-8 mutation. The studies on the structure and the function of the LAC4 gene revealed that (i) the gene can also complement E. coli lacZ mutation; (ii) the physical map of the K. fragilis LAC4 gene was very similar to that of K. lactis; (iii) the beta-galactosidase levels expressed by the clone strains were much higher than that expressed by the original strain; (iv) the variation of the beta-galactosidase level of different clone strains induced by lactose or galactose was related to the retained degree of the 5' flanking region of LAC4 gene, suggesting that there might be a lactose specific transcription activating element in the region.\n\nCloning and expression of Kluyveromyces fragilis LAC4 gene.", "token_count": 245, "char_count": 916, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [ "LAC4", "TG1" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:54.901891", "source": { "split": "train_shard_00002", "doc_id": 65 }, "chunk_id": "train_shard_00002_65_0", "global_id": 12818 }, { "text": "

Background

The influence of the gut microbiota on long-term immune checkpoint inhibitor (ICI) efficacy and immune-related adverse events (irAEs) is poorly understood, as are the underlying mechanisms.

Methods

We performed gut metagenome and metabolome sequencing of gut microbiotas from patients with lung cancer initially treated with anti-PD-1/PD-L1 therapy and explored the underlying mechanisms mediating long-term (median follow-up 1167 days) ICI responses and immune-related adverse events (irAEs). Results were validated in external, publicly-available datasets (Routy, Lee, and McCulloch cohorts).

Findings

The ICI benefit group was enriched for propionate (P = 0.01) and butyrate/isobutyrate (P = 0.12) compared with the resistance group, which was validated in the McCulloch cohort (propionate P < 0.001, butyrate/isobutyrate P = 0.002). The acetyl-CoA pathway (P = 0.02) in beneficial species mainly mediated butyrate production. Microbiota sequences from irAE patients aligned with antigenic epitopes found in autoimmune diseases. Microbiotas of responsive patients contained more lung cancer-related antigens (P = 0.07), which was validated in the Routy cohort (P = 0.02). Escherichia coli and SGB15342 of Faecalibacterium prausnitzii showed strain-level variations corresponding to clinical phenotypes", "token_count": 408, "char_count": 1337, "word_count": 172, "semantic_coherence": 1, "information_density": 0.686, "quality_score": 0.843, "entities": { "genes": [ "SGB15342" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:55.522398", "source": { "split": "train_shard_00002", "doc_id": 66 }, "chunk_id": "train_shard_00002_66_0", "global_id": 12819 }, { "text": "Metabolome validation reviewed more abundant acetic acid (P = 0.03), propionic acid (P = 0.09), and butyric acid (P = 0.02) in the benefit group than the resistance group, and patients with higher acetic, propionic, and butyric acid levels had a longer progression-free survival and lower risk of tumor progression after adjusting for histopathological subtype and stage (P < 0.05).

Interpretation

Long-term ICI survivors have coevolved a compact microbial community with high butyrate production, and molecular mimicry of autoimmune and tumor antigens by microbiota contribute to outcomes. These results not only characterize the gut microbiotas of patients who benefit long term from ICIs but pave the way for \"smart\" fecal microbiota transplantation. Registered in the Chinese Clinical Trial Registry (ChiCTR2000032088).

Funding

This work was supported by Beijing Natural Science Foundation (7232110), National High Level Hospital Clinical Research Funding (2022-PUMCH-A-072, 2023-PUMCH-C-054), CAMS Innovation Fund for Medical Sciences (CIFMS) (2022-I2M-C&T-B-010).\n\nGut microbiome metabolites, molecular mimicry, and species-level variation drive long-term efficacy and adverse event outcomes in lung cancer survivors.", "token_count": 378, "char_count": 1237, "word_count": 163, "semantic_coherence": 1, "information_density": 0.7669, "quality_score": 0.8834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:56.099791", "source": { "split": "train_shard_00002", "doc_id": 66 }, "chunk_id": "train_shard_00002_66_1", "global_id": 12820 }, { "text": "In the thermophilic biogas-producing microbial community, the genus Methanothermobacter was previously described to be frequently abundant. The aim of this study was to establish and analyze the genome sequence of the archaeal strain Methanothermobacter wolfeii SIV6 originating from a thermophilic industrial-scale biogas fermenter and compare it to related reference genomes. The circular chromosome has a size of 1,686,891 bases, featuring a GC content of 48.89%. Comparative analyses considering three completely sequenced Methanothermobacter strains revealed a core genome of 1494 coding sequences and 16 strain specific genes for M. wolfeii SIV6, which include glycosyltransferases and CRISPR/cas associated genes. Moreover, M. wolfeii SIV6 harbors all genes for the hydrogenotrophic methanogenesis pathway and genome-centered metatranscriptomics indicates the high metabolic activity of this strain, with 25.18% of all transcripts per million (TPM) belong to the hydrogenotrophic methanogenesis pathway and 18.02% of these TPM exclusively belonging to the mcr operon. This operon encodes the different subunits of the enzyme methyl-coenzyme M reductase (EC: 2.8.4.1), which catalyzes the final and rate-limiting step during methanogenesis. Finally, fragment recruitment of metagenomic reads from the thermophilic biogas fermenter on the SIV6 genome showed that the strain is abundant (1.2%) within the indigenous microbial community. Detailed analysis of the archaeal isolate M. wolfeii SIV6 indicates its role and function within the microbial community of the thermophilic biogas fermenter, towards a better understanding of the biogas production process and a microbial-based management of this complex process.", "token_count": 516, "char_count": 1777, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [ "SIV6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T06:59:56.753642", "source": { "split": "train_shard_00002", "doc_id": 67 }, "chunk_id": "train_shard_00002_67_0", "global_id": 12821 }, { "text": "Genome Analyses and Genome-Centered Metatranscriptomics of Methanothermobacter wolfeii Strain SIV6, Isolated from a Thermophilic Production-Scale Biogas Fermenter.", "token_count": 60, "char_count": 170, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "SIV6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:57.115097", "source": { "split": "train_shard_00002", "doc_id": 67 }, "chunk_id": "train_shard_00002_67_1", "global_id": 12822 }, { "text": "

Objectives

Numerous studies show increased prevalence of MDR bacteria amongst asylum seekers, but data on the molecular profiles of such strains are limited. We aimed to evaluate the molecular profiles of ESBL-producing Escherichia coli (ESBL-E. coli) strains isolated from asylum seekers and investigate their phylogenetic relatedness.

Methods

WGS data of ESBL-E. coli isolates from asylum seekers, retrieved from 1 January to 31 December 2016, were analysed to assess MLST STs, fim types, phylogroups and resistance genes. Fifty-two ESBL-E. coli isolates from the Dutch-German border region were used for genome comparison purposes as a control group.

Results

Among 112 ESBL-E. coli isolates from asylum seekers, originating mostly from Syria (n = 40) and Iraq (n = 15), the majority belonged to ST131 (21.4%) and ST10 (17.0%). The predominant gene for β-lactam resistance was blaCTX-M-15 (67.9%), followed by the often co-detected blaTEM-1B (39.3%). No mcr or carbapenemase genes were detected. The majority of the strains belonged to phylogroups B2 (38.4%) and A (32.1%), carrying fimH27 (25%) and fimH30 (19.6%). A core genome MLST minimum spanning tree did not reveal clusters containing strains from the asylum seekers and the control group. Five clusters were formed within the asylum seeker group, by strains isolated from people originating from different countries.

Conclusions

The most frequently isolated clones in this study were isolated on a regular basis within the Dutch population before the increase in the asylum seeker population. No mcr- or carbapenemase-producing clones were detected among the asylum seeker population", "token_count": 512, "char_count": 1672, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6092, "quality_score": 0.8046, "entities": { "genes": [ "ST131", "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:57.748322", "source": { "split": "train_shard_00002", "doc_id": 68 }, "chunk_id": "train_shard_00002_68_0", "global_id": 12823 }, { "text": "Minor clustering was observed amongst the asylum seeker strains.\n\nPredominance of CTX-M-15-producing ST131 strains among ESBL-producing Escherichia coli isolated from asylum seekers in the Netherlands.", "token_count": 65, "char_count": 201, "word_count": 25, "semantic_coherence": 1, "information_density": 0.92, "quality_score": 0.96, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:58.119594", "source": { "split": "train_shard_00002", "doc_id": 68 }, "chunk_id": "train_shard_00002_68_1", "global_id": 12824 }, { "text": "Shigellosis is an acute enteric infection caused mainly by the species Shigella flexneri and Shigella sonnei. Since surveillance of these pathogens indicated an increase in ciprofloxacin-resistant samples collected in Belgium between 2013 and 2018, a subset of 148 samples was analyzed with whole genome sequencing (WGS) to investigate their dispersion and underlying genomic features associated with ciprofloxacin resistance. A comparison between observed phenotypes and WGS-based resistance prediction to ciprofloxacin revealed perfect correspondence for all samples. Core genome multi-locus sequence typing and single nucleotide polymorphism-typing were used for phylogenomic investigation to characterize the spread of these infections within Belgium, supplemented with data from international reference collections to place the Belgian isolates within their global context. For S. flexneri, substantial diversity was observed with ciprofloxacin-resistant isolates assigned to several phylogenetic groups. Besides travel-related imports, several clusters of highly similar Belgian isolates could not be linked directly to international travel suggesting the presence of domestically circulating strains. For S. sonnei, Belgian isolates were all limited to lineage III, and could often be traced back to travel to countries in Asia and Africa, sometimes followed by domestic circulation. For both species, several clusters of isolates obtained exclusively from male patients were observed. Additionally, we illustrated the limitations of conventional serotyping of S. flexneri, which was impacted by serotype switching. This study contributes to a better understanding of the spread of shigellosis within Belgium and internationally, and highlights the added value of WGS for the surveillance of this pathogen.\n\nPhylogenomic Investigation of Increasing Fluoroquinolone Resistance among Belgian Cases of Shigellosis between 2013 and 2018 Indicates Both Travel-Related Imports and Domestic Circulation.", "token_count": 481, "char_count": 2038, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6128, "quality_score": 0.8064, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:58.768401", "source": { "split": "train_shard_00002", "doc_id": 69 }, "chunk_id": "train_shard_00002_69_0", "global_id": 12825 }, { "text": "Yeasts are present in indigenous African fermented milks in numbers up to log 8 cfu g(-1), together with a varied lactic acid bacteria (LAB) flora, and therefore potentially contribute to product characteristics. However, interaction between yeasts and LAB in these products has received little notice. In studies of indigenous fermented milk in Zimbabwe and Uganda, many samples contained more than one species of yeast, but Saccharomyces cerevisiae was most commonly isolated. Other frequent isolates were other species of Saccharomyces and several species of Candida. Most yeast isolates were lactose-negative but usually galactose-positive. Some strains assimilated lactate and citrate. The growth in milk of strains of yeasts and LAB, isolated from naturally soured milk in Zimbabwe, and their interaction when selected pairs of strains were grown together has been studied. Interactions were shown by the significantly different amounts of certain metabolites produced, such as acetaldehyde and malty aldehydes, when co-cultures were compared to pure cultures. Preliminary sensory acceptance tests did not show, however, that milks made from a co-culture with Candida kefyr and LAB were preferable to the pure LAB culture. Further work is still needed to elucidate the reactions that may be taking place in fermented milk between varying LAB and yeast populations. The potential for use as starter cultures depends on various aspects, including the final product being prepared. The role of other microorganisms in naturally fermented milk also needs to be studied.\n\nThe role of interaction between yeasts and lactic acid bacteria in African fermented milks: a review.", "token_count": 383, "char_count": 1674, "word_count": 250, "semantic_coherence": 1, "information_density": 0.616, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T06:59:59.358805", "source": { "split": "train_shard_00002", "doc_id": 70 }, "chunk_id": "train_shard_00002_70_0", "global_id": 12826 }, { "text": "

Background

Carriage rates of Staphylococcus aureus on affected skin in atopic dermatitis (AD) are approximately 70%. Increasing disease severity during flares and overall disease severity correlate with increased burden of S. aureus. Treatment in AD therefore often targets S. aureus with topical and systemic antimicrobials.

Objectives

To determine whether antimicrobial sensitivities and genetic determinants of resistance differed in S. aureus isolates from the skin of children with AD and healthy child nasal carriers.

Methods

In this case-control study, we compared S. aureus isolates from children with AD (n = 50) attending a hospital dermatology department against nasal carriage isolates from children without skin disease (n = 49) attending a hospital emergency department for noninfective conditions. Using whole genome sequencing we generated a phylogenetic framework for the isolates based on variation in the core genome, then compared antimicrobial resistance phenotypes and genotypes between disease groups.

Results

Staphylococcus aureus from cases and controls had on average similar numbers of phenotypic resistances per isolate. Case isolates differed in their resistance patterns, with fusidic acid resistance (FusR ) being significantly more frequent in AD (P = 0·009). The genetic basis of FusR also differentiated the populations, with chromosomal mutations in fusA predominating in AD (P = 0·049). Analysis revealed that FusR evolved multiple times and via multiple mechanism in the population. Carriage of plasmid-derived qac genes, which have been associated with reduced susceptibility to antiseptics, was eight times more frequent in AD (P = 0·016).

Conclusions

The results suggest that strong selective pressure drives the emergence and maintenance of specific resistances in AD.", "token_count": 485, "char_count": 1878, "word_count": 250, "semantic_coherence": 1, "information_density": 0.62, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:00.007420", "source": { "split": "train_shard_00002", "doc_id": 71 }, "chunk_id": "train_shard_00002_71_0", "global_id": 12827 }, { "text": "The widespread use of topical antimicrobials enriches for resistance in Staphylococcus aureus isolated from patients with atopic dermatitis.", "token_count": 37, "char_count": 140, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:00.373775", "source": { "split": "train_shard_00002", "doc_id": 71 }, "chunk_id": "train_shard_00002_71_1", "global_id": 12828 }, { "text": "Lysogens, bacteria with one or more viruses (prophages) integrated into their genomes, are abundant in the gut of animals. Prophages often influence bacterial traits; however, the influence of prophages on the gut microbiota-host immune axis in animals remains poorly understood. Here, we investigate the influence of the prophage SfPat on Shewanella fidelis 3313, a persistent member of the gut microbiome of the model marine tunicate, Ciona robusta. Establishment of a SfPat deletion mutant (ΔSfPat) reveals the influence of this prophage on bacterial physiology in vitro and during colonization of the Ciona gut. In vitro, deletion of SfPat reduces S. fidelis 3313 motility and swimming while increasing biofilm formation. To understand the in vivo impact of these prophage-induced changes in bacterial traits, we exposed metamorphic stage 4 Ciona juveniles to wildtype (WT) and ΔSfPat strains. During colonization, ΔSfPat localizes to overlapping and distinct areas of the gut compared to the WT strain. We examined the differential expression of various regulators of cyclic-di-GMP, a secondary signaling molecule that mediates biofilm formation and motility. The pdeB gene, which encodes a bacterial phosphodiesterase known to influence biofilm formation and motility by degrading cyclic-di-GMP, is upregulated in the WT strain but not in ΔSfPat when examined in vivo. Expression of the Ciona gut immune effector, VCBP-C, is enhanced during colonization by ΔSfPat compared to the WT strain; however, VCBP-C binding to the WT strain does not promote the excision of SfPat in an SOS-dependent pathway. Instead, VCBP-C binding significantly reduces the expression of a phage major capsid protein", "token_count": 489, "char_count": 1747, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5692, "quality_score": 0.7846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:01.049668", "source": { "split": "train_shard_00002", "doc_id": 72 }, "chunk_id": "train_shard_00002_72_0", "global_id": 12829 }, { "text": "Our findings suggest that SfPat influences host perception of this important colonizing commensal and highlights the significance of investigating tripartite dynamics between prophages, bacteria, and their animal hosts to better understand the gut microbiota-host immune axis.\n\nProphage regulation of <i>Shewanella fidelis</i> 3313 motility and biofilm formation with implications for gut colonization dynamics in <i>Ciona robusta</i>.", "token_count": 118, "char_count": 459, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8727, "quality_score": 0.9364, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:01.467505", "source": { "split": "train_shard_00002", "doc_id": 72 }, "chunk_id": "train_shard_00002_72_1", "global_id": 12830 }, { "text": "Results indicated that it was a typical strain of Saccharomyces sp. with thermostability, relatively high ethanol resistance and low pH tolerance. The optical temperature and initial pH for alcoholic fermentation from 25% (w/v) of cassava flour in the fermentation broth were 34deg C and 3.5, respectively. Under these conditions and with a low temperature cooking process, 10.67%(v/v) of the ethanol could be obtained in 48 h with a yield rate of 93.1% based on the theoretical value of the starch content from cassava. The strain appeared suitable for ethanol production from cassava flour in industry.\n\nBiological and fermentative properties of a thermotolerant yeast strain in alcohol production from cassava flour", "token_count": 186, "char_count": 718, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6455, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:01.948509", "source": { "split": "train_shard_00002", "doc_id": 73 }, "chunk_id": "train_shard_00002_73_0", "global_id": 12831 }, { "text": "Lactic acid-grown cells of a strain of Kluyveromyces marxianus transported D- and L-lactic acid by a saturable mechanism that was partially inducible and subject to glucose repression, with the following kinetic parameters at pH 5.4: Vmax = 1.00 (+/- 0.13) mmol h-1 per g dry weight and Ks = 0.42 (+/- 0.08) mM. Lactic acid transport was competitively inhibited by pyruvic, glycolic, acetic and bromoacetic acids. The latter, a non-metabolizable analogue, was transiently accumulated, the extent depending on the extracellular pH. The pH dependence of the Ks values for undissociated lactic acid and for the lactate anion indicated that the latter was the transported species. Lactate uptake was not accompanied by the simultaneous uptake of protons, potassium ions or sodium ions excluding symport mechanisms. Initial lactic acid uptake led to transient membrane hyperpolarization as measured with a fluorescent dye excluding also an electroneutral anion antiport mechanism. It was concluded that lactate anions use a monocarboxylate uniport and that the counter anion, possibly bicarbonate, uses a separate channel, the coupling being electrical and loose.\n\nTransport of lactic acid in Kluyveromyces marxianus: evidence for a monocarboxylate uniport.", "token_count": 364, "char_count": 1252, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.827, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:02.575322", "source": { "split": "train_shard_00002", "doc_id": 74 }, "chunk_id": "train_shard_00002_74_0", "global_id": 12832 }, { "text": "

Background:

Phylogenetic reconstruction is a necessary first step in many analyses which use whole genome sequence data from bacterial populations. There are many available methods to infer phylogenies, and these have various advantages and disadvantages, but few unbiased comparisons of the range of approaches have been made.

Methods:

We simulated data from a defined 'true tree' using a realistic evolutionary model. We  built phylogenies from this data using a range of methods, and compared reconstructed trees to the true tree using two measures, noting the computational time needed for different phylogenetic reconstructions. We also used real data from Streptococcus pneumoniae alignments to compare individual core gene trees to a core genome tree.

Results:

We found that, as expected, maximum likelihood trees from good quality alignments were the most accurate, but also the most computationally intensive. Using less accurate phylogenetic reconstruction methods, we were able to obtain results of comparable accuracy; we found that approximate results can rapidly be obtained using genetic distance based methods. In real data we found that highly conserved core genes, such as those involved in translation, gave an inaccurate tree topology, whereas genes involved in recombination events gave inaccurate branch lengths. We also show a tree-of-trees, relating the results of different phylogenetic reconstructions to each other.

Conclusions:

We recommend three approaches, depending on requirements for accuracy and computational time. For the most accurate tree, use of either RAxML or IQ-TREE with an alignment of variable sites produced by mapping to a reference genome is best. Quicker approaches that do not perform full maximum likelihood optimisation may be useful for many analyses requiring a phylogeny, as generating a high quality input alignment is likely to be the major limiting factor of accurate tree topology.  We have publicly released our simulated data and code to enable further comparisons.\n\nEvaluation of phylogenetic reconstruction methods using bacterial whole genomes: a simulation based study", "token_count": 479, "char_count": 2173, "word_count": 317, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:03.229458", "source": { "split": "train_shard_00002", "doc_id": 75 }, "chunk_id": "train_shard_00002_75_0", "global_id": 12833 }, { "text": "

Background

Helicobacter pylori, the human gastric pathogen, causes a variety of gastric diseases ranging from mild gastritis to gastric cancer. While the studies on H. pylori are dominated by those based on either East Asian or Western strains, information regarding H. pylori strains prevalent in the Middle East remains scarce. Therefore, we carried out whole-genome sequencing and comparative analysis of three H. pylori strains isolated from three native Arab, Kuwaiti patients.

Materials and methods

H. pylori strains were sequenced using Illumina platform. The sequence reads were filtered and draft genomes were assembled and annotated. Various pathogenicity-associated regions and phages present within the genomes were identified. Phylogenetic analysis was carried out to determine the genetic relatedness of Kuwaiti strains to various lineages of H. pylori. The core genome content and virulence-related genes were analyzed to assess the pathogenic potential.

Results

The three genomes clustered along with HpEurope strains in the phylogenetic tree comprising various H. pylori lineages. A total of 1187 genes spread among various functional classes were identified in the core genome analysis. The three genomes possessed a complete cagPAI and also retained most of the known outer membrane proteins as well as virulence-related genes. The cagA gene in all three strains consisted of an AB-C type EPIYA motif.

Conclusions

The comparative genomic analysis of Kuwaiti H. pylori strains revealed a European ancestry and a high pathogenic potential.\n\nWhat constitutes an Arabian Helicobacter pylori? Lessons from comparative genomics.", "token_count": 430, "char_count": 1670, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6147, "quality_score": 0.8074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:03.863632", "source": { "split": "train_shard_00002", "doc_id": 76 }, "chunk_id": "train_shard_00002_76_0", "global_id": 12834 }, { "text": "This work deals with the feasibility of achieving an extractive fermentation of 2-phenylethyl alcohol, the rose aroma, coupling fermentation with Kluyveromyces marxianus and supercritical carbon dioxide (SCCO2) extraction. The extractive process is, in this case, of special interest due to the strong yeast inhibition by 2-phenylethyl alcohol. First results confirmed that direct SCCO2 extraction is not possible, due to a drastic CO2 effect on cell viability. It is therefore necessary to perform cell separation prior to the extraction. Aroma extraction conditions from a synthetic mixture were then optimized, a pressure of 200 bar and a temperature in the range 35-45 degrees C being chosen. Under these conditions, the distribution coefficient Kd is 2 times higher than during the extraction using a conventional organic solvent, n-hexane. Using a simple model of aroma partition between aqueous and SCCO2 phases, the parameters of a continuous extraction from a synthetic broth were defined. The two substrates, glucose and phenylalanine, are not extracted whatever the conditions. As predicted by the model, more than 90% of 2-phenylethyl alcohol can be extracted, while the extraction of ethanol, the second main product, can be easily tuned with respect to operating conditions, as a function of its influence on the fermentation. Finally, the feasibility of the aroma recovery using two depressurization steps at the outflow of the extraction vessel was demonstrated; 97% of the extracted aroma was recovered, and a mass purity of 91% was achieved. Copyright 1999 John Wiley & Sons, Inc.\n\nExtractive fermentation of aroma with supercritical CO2", "token_count": 407, "char_count": 1655, "word_count": 251, "semantic_coherence": 1, "information_density": 0.6215, "quality_score": 0.8108, "entities": { "genes": [ "CO2", "SCCO2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:04.482146", "source": { "split": "train_shard_00002", "doc_id": 77 }, "chunk_id": "train_shard_00002_77_0", "global_id": 12835 }, { "text": "

Background

Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis . Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult.

Methods

This study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated.

Findings

Our results suggest that clusters based on Spoligotyping could encompass transmission events that occurred over 70 years prior to sampling while 24-loci-MIRU-VNTR often represented two or more decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events in timespans of up to 10 years e.g. for a 5 SNP/allele cut-off.

Interpretation

With the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.\n\nThe relationship between transmission time and clustering methods inMycobacterium tuberculosisepidemiology", "token_count": 493, "char_count": 1957, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6538, "quality_score": 0.8269, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:05.135077", "source": { "split": "train_shard_00002", "doc_id": 78 }, "chunk_id": "train_shard_00002_78_0", "global_id": 12836 }, { "text": "

Background

Molecular typing of methicillin-resistant Staphylococcus aureus (MRSA) has documented the diversity of the genetic background of strains associated with healthcare (HA-MRSA), community (CA-MRSA) and livestock (LA-MRSA). The accessory and core-variable genomes of those strains however remain largely unknown.

Objective

To compare the genetic background and accessory and core variable gene content of ST398 LA-MRSA strains with those of HA-and CA-MRSA strains from the same region.

Methods

Representative strains of HA- (n=21), CA- (n=13) and ST398 LA-MRSA (n=18) were selected from Belgian National Reference Laboratory collections. The accessory and core-variable genomes of these strains were characterized by a DNA-microarray composed of oligonucleotide probes targeting ~400 resistance, adhesion and virulence associated genes.

Results

ST398 strains displayed very homogenous hybridization profiles irrespective of their host origin. This ST398 genomic profile was moderately related to that of certain human HA- or CA-lineages but distinctively lacked several virulence- and colonization-associated genes implicated in carriage in humans, such as proteases and adhesins. No enterotoxin gene was found among ST398 strains. Differences were observed in the mobile resistance gene content of ST398 strains, including antibiotic resistance determinants.

Conclusion

LA-MRSA strains represent a homogenous lineage distinct from co-local HA- and CA-MRSA strains, especially in its accessory genome content characterized by a lack of human-associated virulence and adhesion determinants. The absence of detectable enterotoxin gene among ST398 LA-MRSA strains from a wide host range is reassuring regarding their foodborne pathogenic potential.", "token_count": 478, "char_count": 1788, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6161, "quality_score": 0.808, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:05.780957", "source": { "split": "train_shard_00002", "doc_id": 79 }, "chunk_id": "train_shard_00002_79_0", "global_id": 12837 }, { "text": "Diversity of accessory genome of human and livestock-associated ST398 methicillin resistant Staphylococcus aureus strains.", "token_count": 39, "char_count": 122, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:06.133911", "source": { "split": "train_shard_00002", "doc_id": 79 }, "chunk_id": "train_shard_00002_79_1", "global_id": 12838 }, { "text": "Karyotypes and isozyme profiles do not correlate in Kluyveromyces marxianus var. marxianus.", "token_count": 30, "char_count": 91, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:06.486795", "source": { "split": "train_shard_00002", "doc_id": 80 }, "chunk_id": "train_shard_00002_80_0", "global_id": 12839 }, { "text": "Determination of infraspecific relationship in kluyveromyces marxianus by riboprinting.", "token_count": 27, "char_count": 87, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:06.846847", "source": { "split": "train_shard_00002", "doc_id": 81 }, "chunk_id": "train_shard_00002_81_0", "global_id": 12840 }, { "text": "Cachaça (aguardente) is a rum-style spirit made from sugar cane juice by artisanal methods in Brazil. A study was made of the production, biochemistry and microbiology of the process in fifteen distilleries in Sul de Minas. Identification of 443 yeasts showed Saccharomyces cerevisiae to be the predominant yeast but Rhodotorula glutinis and Candida maltosa were predominant in three cases. Bacterial infection is a potential problem, particularly in older wooden vats, when the ratio of yeasts:bacteria can be 10:1 or less. A study of daily batch fermentations in one distillery over one season in which 739 yeasts were identified revealed that S. cerevisiae was the predominant yeast. Six other yeast species showed a daily succession: Kluyveromyces marxianus, Pichia heimii and Hanseniaspora uvarum were present only at the beginning, Pichia subpelliculosa and Debaryomyces hansenii were detected from mid to the end of fermentation, and Pichia methanolica appeared briefly after the cessation of fermentation. Despite a steady influx of yeasts from nature, the species population in the fermenter was stable for at least four months suggesting strong physiological and ecological pressure for its maintenance. Cell densities during the fermentation were: yeasts - 4 x 108/ml; lactic acid bacteria -4 x 10(5)/ml; and bacilli - 5 x 10(4)/ml. Some acetic acid bacteria and enterobacteriaceae appeared at the end. Sucrose was immediately hydrolysed to fructose and glucose. The main fermentation was complete after 12 hours but not all fructose was utilised when harvesting after 24 hours.\n\nMicrobiology and physiology of Cachaça (Aguardente) fermentations.", "token_count": 454, "char_count": 1657, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:07.483833", "source": { "split": "train_shard_00002", "doc_id": 82 }, "chunk_id": "train_shard_00002_82_0", "global_id": 12841 }, { "text": "Kluyveromyces fragilis was grown in liquid medium, pH 5.5, 28℃ and about 3 0 hours in shake flasks. The inoculum 4% was then transferred into fermentive medium. Production of inulinase in batch fermentation was examined. It was shown that the optimal pH and inulin concentration were 6.0-6.5 and 2%, respectively. The temperature was controlled, at 28℃ before 30 hours and then 32-34℃. After about 70 hours, the maximum yield of inulinase was obtained (240u/ml). In a fermentor with a capacity of 5-liter, its fermentation period was shortened.\n\nStudy on production conditions of inulinase", "token_count": 176, "char_count": 589, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6989, "quality_score": 0.8495, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:07.934141", "source": { "split": "train_shard_00002", "doc_id": 83 }, "chunk_id": "train_shard_00002_83_0", "global_id": 12842 }, { "text": "The plant growth promoting model bacterium FZB42T was proposed as the type strain of Bacillus amyloliquefaciens subsp. plantarum (Borriss et al., 2011), but has been recently recognized as being synonymous to Bacillus velezensis due to phylogenomic analysis (Dunlap C. et al., 2016). However, until now, majority of publications consider plant-associated close relatives of FZB42 still as \"B. amyloliquefaciens.\" Here, we reinvestigated the taxonomic status of FZB42 and related strains in its context to the free-living soil bacterium DSM7T, the type strain of B. amyloliquefaciens. We identified 66 bacterial genomes from the NCBI data bank with high similarity to DSM7T. Dendrograms based on complete rpoB nucleotide sequences and on core genome sequences, respectively, clustered into a clade consisting of three tightly linked branches: (1) B. amyloliquefaciens, (2) Bacillus siamensis, and (3) a conspecific group containing the type strains of B. velezensis, Bacillus methylotrophicus, and B. amyloliquefaciens subsp. plantarum. The three monophyletic clades shared a common mutation rate of 0.01 substitutions per nucleotide position, but were distantly related to Bacillus subtilis (0.1 substitutions per nucleotide position). The tight relatedness of the three clusters was corroborated by TETRA, dDDH, ANI, and AAI analysis of the core genomes, but dDDH and ANI values were found slightly below species level thresholds when B", "token_count": 507, "char_count": 1557, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6971, "quality_score": 0.8486, "entities": { "genes": [ "FZB42", "DSM7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:08.559028", "source": { "split": "train_shard_00002", "doc_id": 84 }, "chunk_id": "train_shard_00002_84_0", "global_id": 12843 }, { "text": "amyloliquefaciens DSM7T genome sequence was used as query sequence. Due to these results, we propose that the B. amyloliquefaciens clade should be considered as a taxonomic unit above of species level, designated here as \"operational group B. amyloliquefaciens\" consisting of the soil borne B. amyloliquefaciens, and plant associated B. siamensis and B. velezensis, whose members are closely related and allow identifying changes on the genomic level due to developing the plant-associated life-style.\n\nBacillus amyloliquefaciens, Bacillus velezensis, and Bacillus siamensis Form an \"Operational Group B. amyloliquefaciens\" within the B. subtilis Species Complex.", "token_count": 243, "char_count": 741, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "DSM7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:09.049034", "source": { "split": "train_shard_00002", "doc_id": 84 }, "chunk_id": "train_shard_00002_84_1", "global_id": 12844 }, { "text": "

Background

The global dissemination of colistin resistance encoded by mcr-1 has been attributed to extensive use of colistin in livestock, threatening colistin efficacy in medicine. The emergence of mcr-1 in common pathogens, such as Escherichia coli, is of particular concern. China banned the use of colistin in animal feed from May 1, 2017. We investigated subsequent changes in mcr-1 prevalence in animals, humans, food, and the environment, and the genomic epidemiology of mcr-1-positive E coli (MCRPEC).

Methods

Sampling was done before (October to December, 2016) and after (October to December, 2017, and 2018, respectively) the colistin ban. 3675 non-duplicate pig faecal samples were collected from 14 provinces (66 farms) in China to measure intervention-related changes in mcr-1 prevalence. 15 193 samples were collected from pigs, healthy human volunteers, patients colonised or infected with Enterobacteriaceae who were admitted to hospital, food and the environment in Guangzhou, to characterise source-specific mcr-1 prevalence and the wider ecological effect of the ban. From these samples, 688 MCRPEC were analysed with whole genome sequencing, plasmid conjugation, and S1 pulsed-field gel electrophoresis with Southern blots to characterise associated genomic changes.

Findings

After the ban, mcr-1 prevalence decreased significantly in national pig farms, from 308 (45%) of 684 samples in 2016 to 274 (19%) of 1416 samples in 2018 (p<0·0001). A similar decrease occurred in samples from most sources in Guangzhou (959 [19%] of 5003 samples in 2016; 238 [5%] of 4489 samples in 2018; p<0·0001)", "token_count": 515, "char_count": 1634, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:09.703274", "source": { "split": "train_shard_00002", "doc_id": 85 }, "chunk_id": "train_shard_00002_85_0", "global_id": 12845 }, { "text": "The population structure of MCRPEC was diverse (23 sequence clusters); sequence type 10 clonal complex isolates were predominant (247 [36%] of 688). MCRPEC causing infection in patients admitted to hospital were genetically more distinct and appeared less affected by the ban. mcr-1 was predominantly found on plasmids (632 [92%] of 688). Common mcr-1 plasmid types included IncX4, IncI2, and IncHI2 (502 [76%] of 656); significant increases in IncI2-associated mcr-1 and a distinct lineage of mcr-1-associated IncHI2 were observed post ban. Changes in the frequency of mcr-1-associated flanking sequences (ISApl1-negative MCRPEC), 63 core genome single nucleotide polymorphisms, and 30 accessory genes were also significantly different after the ban (Benjamini-Hochberg-adjusted p<0·05), consistent with rapid genetic adaptation in response to changing selection pressures.

Interpretation

A rapid, ecosystem-wide, decline in mcr-1 was observed after the use of colistin in animal feed was banned, with associated genetic changes in MCRPEC. Withdrawal of antimicrobials from animal feed should be an important One Health measure contributing to the wider control of antimicrobial resistance globally.

Funding

National Natural Science Foundation of China.\n\nDynamics of mcr-1 prevalence and mcr-1-positive Escherichia coli after the cessation of colistin use as a feed additive for animals in China: a prospective cross-sectional and whole genome sequencing-based molecular epidemiological study.", "token_count": 422, "char_count": 1508, "word_count": 202, "semantic_coherence": 1, "information_density": 0.6931, "quality_score": 0.8465, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:10.325125", "source": { "split": "train_shard_00002", "doc_id": 85 }, "chunk_id": "train_shard_00002_85_1", "global_id": 12846 }, { "text": "

Introduction

Candidiasis is usually a superficial infection of the moist areas of the body and is generally caused by Candida albicans. Visceral infections occur in diabetes, lymphomas and leukemias, malnutrition, avitaminosis and they are associated with antibiotic, corticosteroid and immunosuppressive therapy. Candida albicans was isolated from middle ear inflammation. The diagnosis is made on the basis of microscopic appearance of colonies and characteristic smell. Candidiasis is successfully treated with nystatin, imidazol derivatives (fluconazole, ketoconazole and intraconazole), amphotericin B, 5-fluorocystosine and 1% iodine solution.

Case description

This is a case report of a 46-year-old patient with a persistent nasal, sinus and ear infection of unknown origin. The patient first received antibiotic and steroid therapy and trepanation of the right maxillary sinus was performed. As the patient's condition aggravated with increase of temperature and bad laboratory findings, he was hospitalized. Radiography revealed a pathological process in both maxillary sinuses and both mastoids, so mastoidectomy and left maxillary sinus trepanation were performed. Histopathological examination of the right mastoid revealed a mould infection. The immunologic status pointed to hypogammaglobulinemia IgG. The following diseases were excluded: systemic diseases, blood diseases, Reiter's syndrome, AIDS, Hepatitis B, other viral diseases, toxoplasmosis, trichinellosis, borreliosis, typhus, paratyphus and exanthematous typhus. The diagnosis of candidiasis caused by Candida crusei and Candida kefyr was made on the basis of macroscopic and microscopic findings and biochemical identification. Ketoconazole was introduced (400 mg/per day) as well as high doses of vitamins and povidone-iodine locally", "token_count": 485, "char_count": 1825, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6387, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:10.978358", "source": { "split": "train_shard_00002", "doc_id": 86 }, "chunk_id": "train_shard_00002_86_0", "global_id": 12847 }, { "text": "After a period of remission the patient died due to myocarditis, sepsis, acute kidney failure associated with severe mucosal necrosis of the mouth, esophagus and throat. Differential diagnosis in fever of unknown origin must include the possibility of mycotic infection, whereas the therapy of mycotic diseases must include two antimycotics at the same time.

Discussion and conclusion

Candida albicans is often found in the oral cavity and skin as well as in intestines of 18% of healthy subjects. It is unknown why it causes clinical illness. Antibiotic therapy of bacterial infections enables candida colonization especially in immunosuppressed patients. In our patient two types were found: Candida krusei and Candida kefyr. It is of special importance to perform differential diagnosis in cases with fever of unknown origin in order to include the possibility of mycotic infections, whereas treatment of systemic fungal infections requires a team of physicians.\n\n[Mycotic disease of the mucous membranes of the head and neck].", "token_count": 249, "char_count": 1037, "word_count": 155, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:11.457710", "source": { "split": "train_shard_00002", "doc_id": 86 }, "chunk_id": "train_shard_00002_86_1", "global_id": 12848 }, { "text": "The spread of antibiotic resistance is driving interest in new approaches to control bacterial pathogens. This includes applying multiple antibiotics strategically, using bacteriophages against antibiotic-resistant bacteria, and combining both types of antibacterial agents. All these approaches rely on or are impacted by associations among resistance phenotypes (where bacteria resistant to one antibacterial agent are also relatively susceptible or resistant to others). Experiments with laboratory strains have shown strong associations between some resistance phenotypes, but we lack a quantitative understanding of associations among antibiotic and phage resistance phenotypes in natural and clinical populations. To address this, we measured resistance to various antibiotics and bacteriophages for 94 natural and clinical Escherichia coli isolates. We found several positive associations between resistance phenotypes across isolates. Associations were on average stronger for antibacterial agents of the same type (antibiotic-antibiotic or phage-phage) than different types (antibiotic-phage). Plasmid profiles and genetic knockouts suggested that such associations can result from both colocalization of resistance genes and pleiotropic effects of individual resistance mechanisms, including one case of antibiotic-phage cross-resistance. Antibiotic resistance was predicted by core genome phylogeny and plasmid profile, but phage resistance was predicted only by core genome phylogeny. Finally, we used observed associations to predict genes involved in a previously uncharacterized phage resistance mechanism, which we verified using experimental evolution. Our data suggest that susceptibility to phages and antibiotics are evolving largely independently, and unlike in experiments with lab strains, negative associations between antibiotic resistance phenotypes in nature are rare. This is relevant for treatment scenarios where bacteria encounter multiple antibacterial agents.IMPORTANCE Rising antibiotic resistance is making it harder to treat bacterial infections. Whether resistance to a given antibiotic spreads or declines is influenced by whether it is associated with altered susceptibility to other antibiotics or other stressors that bacteria encounter in nature, such as bacteriophages (viruses that infect bacteria)", "token_count": 480, "char_count": 2356, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5809, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:12.113966", "source": { "split": "train_shard_00002", "doc_id": 87 }, "chunk_id": "train_shard_00002_87_0", "global_id": 12849 }, { "text": "We used natural and clinical isolates of Escherichia coli, an abundant species and key pathogen, to characterize associations among resistance phenotypes to various antibiotics and bacteriophages. We found associations between some resistance phenotypes, and in contrast to past work with laboratory strains, they were exclusively positive. Analysis of bacterial genome sequences and horizontally transferred genetic elements (plasmids) helped to explain this, as well as our finding that there was no overall association between antibiotic resistance and bacteriophage resistance profiles across isolates. This improves our understanding of resistance evolution in nature, potentially informing new rational therapies that combine different antibacterials, including bacteriophages.\n\nAssociations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates.", "token_count": 198, "char_count": 911, "word_count": 115, "semantic_coherence": 1, "information_density": 0.7043, "quality_score": 0.8522, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:12.560991", "source": { "split": "train_shard_00002", "doc_id": 87 }, "chunk_id": "train_shard_00002_87_1", "global_id": 12850 }, { "text": "

Background

Cell drug resistance can be due to the presence of active efflux pumps (AEP). Identification of yeast cells with a resistance phenotype is important either from a clinical, agricultural or biotechnological point of view. Rapid and reliable methods to detect AEP can be therefore very useful.

Methods

Some yeast cells change their staining by calcein-AM, BCECF-AM, rhodamine 123 and DiOC(5), when pretreated with verapamil, CCCP or ATP depletion, or when pretreated with specific antimicrobial agents. This fact may be interpreted as an indication of the presence/absence of AEP. Six yeast species were tested with a flow cytometric method (FCM) and an epifluorescence microscopic method (EFM), and ten other species were evaluated only by EFM. The minimum inhibitory concentration (MIC) of penconazol, benomyl and cycloheximide for Saccharomyces cerevisiae and Kluyveromyces marxianus, were determined by growth inhibition on solid medium and were compared to the staining changes detected by FCM.

Results

The FCM and the EFM allowed the detection of AEP in all the yeast species tested. High MIC values for a drug were related with the presence of at least one AEP indicated by the cytometric data.

Conclusions

The FCM revealed to be a robust assay whereas the EFM can be used as a preliminary test. It is possible to identify resistance/sensitivity patterns in yeast cells through cytometric detection methods of different efflux pumping systems.\n\nRapid detection of efflux pumps and their relation with drug resistance in yeast cells.", "token_count": 415, "char_count": 1577, "word_count": 232, "semantic_coherence": 1, "information_density": 0.5948, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:13.221924", "source": { "split": "train_shard_00002", "doc_id": 88 }, "chunk_id": "train_shard_00002_88_0", "global_id": 12851 }, { "text": "Cereibacter sphaeroides strains S3W10 and SS15, isolated from shrimp ponds, exhibit potential probiotic benefits for aquaculture. In this study, the genomic features of S3W10 and SS15 were thoroughly characterized to evaluate their probiotic properties and safety for aquaculture use. The genomes of S3W10 and SS15 consist of 130 and 74 contigs, with sizes of 4.6 Mb and 4.4 Mb and GC contents of 69.2%. Average nucleotide identity (ANI), digital DNA-DNA hybridization (dDDH), and phylogenomic analyses confirmed that these strains belong to C. sphaeroides. Genome annotation predicted 4260 coding sequences (CDS) in S3W10 and 4086 CDS in SS15, including genes associated with stress tolerance, nutrient absorption, and antioxidant activity. Notably, genes related to vitamin B12 synthesis, digestive enzyme production, and carotenoid biosynthesis, which support shrimp health, were identified in both genomes. CAZyme analysis identified 116 and 115 carbohydrate-active enzymes in S3W10 and SS15, respectively, supporting adaptation to gastrointestinal environments and the host immune response. Pan-genome analysis across C. sphaeroides strains revealed 7918 gene clusters, highlighting the open pan-genome structure of this species and its high genetic diversity. Further bioinformatic analyses assessing mobile genetic elements, antibiotic-resistance genes, and virulence factors demonstrated the safety of both strains for aquaculture, as no plasmids or virulence genes were identified. The genomic insights in this study provide a deeper understanding of the strains' adaptability and functional potential, aligning with previous in vitro and in vivo studies and highlighting their potential for use in shrimp cultivation.", "token_count": 482, "char_count": 1748, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6611, "quality_score": 0.8305, "entities": { "genes": [ "SS15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:13.888793", "source": { "split": "train_shard_00002", "doc_id": 89 }, "chunk_id": "train_shard_00002_89_0", "global_id": 12852 }, { "text": "Genomic Characterization of Probiotic Purple Nonsulfur Bacteria Cereibacter sphaeroides Strains S3W10 and SS15: Implications for Enhanced Shrimp Aquaculture.", "token_count": 57, "char_count": 164, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "SS15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:14.269894", "source": { "split": "train_shard_00002", "doc_id": 89 }, "chunk_id": "train_shard_00002_89_1", "global_id": 12853 }, { "text": "Microcystis aeruginosa is a bloom-forming cyanobacterium found in eutrophic water bodies worldwide. M. aeruginosa blooms usually occur in freshwater; however, they have also been reported to occur in brackish water. Because M. aeruginosa often produces the cyanotoxin microcystin, they are a major concern to public health and environment. Despite this, the ecology, genomic basis, and evolutionary process underlying the M. aeruginosa bloom invasion from fresh to brackish water have been poorly investigated. Hence, in the present study, we have sequenced and characterized genomes of two newly discovered salt-tolerant M. aeruginosa strains obtained from Japanese brackish water lakes (Lakes Shinji and Tofutsu). Both genomes contain a set of genes for the synthesis of osmolyte sucrose (sppA, spsA, and susA), hitherto identified in only one strain (PCC 7806) of M. aeruginosa. Chemical and gene expression analyses confirmed sucrose accumulation induced by salt. A comprehensive genetic survey of >200 strains indicated that sucrose genes are extremely rare in M. aeruginosa. Most surprisingly, comparative genome analyses of the three strains indicated extremely low genetic diversity in the sucrose genes compared with other core genome genes, suggesting very recent acquisitions via horizontal transfer. Invasion of M. aeruginosa blooms into brackish water may be a recent event triggered by anthropogenic eutrophication of brackish water.\n\nAdaptation of the Freshwater Bloom-Forming Cyanobacterium Microcystis aeruginosa to Brackish Water Is Driven by Recent Horizontal Transfer of Sucrose Genes.", "token_count": 463, "char_count": 1682, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6096, "quality_score": 0.8048, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:14.946945", "source": { "split": "train_shard_00002", "doc_id": 90 }, "chunk_id": "train_shard_00002_90_0", "global_id": 12854 }, { "text": "Fusobacterium nucleatum is an anaerobic commensal of the oral cavity recently reported to be associated with cancers of the gastrointestinal tract and oral squamous cell carcinoma (OSCC). In this study, we investigate the impact on oral keratinocytes of infection with a genetically diverse set of strains of F. nucleatum subsp. polymorphum recovered from patients with oral dysplasia (n=6). We employed H357 oral keratinocytes derived from a stage 1 OSCC and H376 cells derived from a stage 3 OSCC. Adhesion phenotypes were strain specific, with 3/6 clinical isolates examined exhibiting higher adherence to the stage 3 H376 cell line. Conversely, intracellular invasion was greatest in the H357 cells and was associated with specific transcriptional responses including autophagy and keratinization. Infection of both H357 and H376 cell lines induced transcriptional and cytokine responses linked to cancer cell migration and angiogenesis. F. nucleatum infection induced greater levels of MMP9 secretion in the H376 cell line which was associated with enhanced motility and invasion phenotypes. Additionally, the degree of F. nucleatum induced invasive growth by H376 cells varied between different clinical isolates of F. nucleatum subsp. polymorphum. Blockage of CCL5 signalling using the inhibitor metCCL5 resulted in reduced keratinocyte invasion. F. nucleatum infection also induced expression of the pro-angiogenic chemokine MCP-1 and the angiogenic growth factor VEGF-A resulting in increased capillary-like tube formation in HUVEC cells, most significantly in H376 cells. Treatment of HUVEC cells with resveratrol, a VEGF-A signalling inhibitor, significantly attenuated F. nucleatum induced tube formation. Our data indicate that the outcomes of F", "token_count": 514, "char_count": 1824, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5794, "quality_score": 0.7897, "entities": { "genes": [ "CCL5", "MMP9" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:15.609272", "source": { "split": "train_shard_00002", "doc_id": 91 }, "chunk_id": "train_shard_00002_91_0", "global_id": 12855 }, { "text": "nucleatum-oral cell interactions can vary greatly depending on the bacterial genotype and the malignant phenotype of the host cell.\n\nFusobacterium nucleatum induces invasive growth and angiogenic responses in malignant oral keratinocytes that are cell line- and bacterial strain-specific.", "token_count": 80, "char_count": 299, "word_count": 38, "semantic_coherence": 1, "information_density": 0.8158, "quality_score": 0.9079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:15.974562", "source": { "split": "train_shard_00002", "doc_id": 91 }, "chunk_id": "train_shard_00002_91_1", "global_id": 12856 }, { "text": "The gene encoding beta-galactosidase was isolated by functional complementation of Escherichia coli from Bifidobacterium longum MB219, which exhibited the highest activity among ten Bifidobacterium strains tested of the species B. longum, B. breve, B. adolescentis, B. indicum, B. animalis and B. cuniculi. The nucleotide sequence of the 5.0-kb fragment conferring the positive beta-galactosidase phenotype to E. coli revealed the presence of a lacZ-type gene encoding a 1023-amino-acid protein that was preceded by a ribosome binding site. A sequence showing 72% identity with the proline tRNA of Bacillus subtilis and a gene probably encoding the DNA-3-methyladenine glycosydase I were located downstream from the lacZ gene, after a gap of 30-50 unsequenced base pairs. By primer-extension analysis, the transcription start site of the lacZ gene was mapped 65 nt upstream from the start codon, and it enabled identification of the -10 region of the putative promoter. The nucleotide sequence of lacZ and its deduced amino acid sequence were compared with those of beta-galactosidase genes and enzymes from other microorganisms. High similarity was demonstrated between the B. longum beta-galactosidase and its counterparts in Lactobacillus delbruckii subsp. bulgaricus, Streptococcus salivarius subsp. thermophilus, E. coli, Clostridium acetobutylicum, Leuconostoc lactis, Klebsiella pneumoniae and Kluyveromyces marxianus var. lactis, all belonging to the LacZ family. The B. longum MB219 lacZ gene was cloned in Bifidobacterium and its expression was observed in strains with otherwise low levels of endogenous activity. The expression increased by factors of 1.5-50 and enabled those strains that do not grow on lactose to use this sugar as sole carbon source.", "token_count": 503, "char_count": 1765, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7988, "entities": { "genes": [ "MB219" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:16.622261", "source": { "split": "train_shard_00002", "doc_id": 92 }, "chunk_id": "train_shard_00002_92_0", "global_id": 12857 }, { "text": "Nucleotide sequence, expression and transcriptional analysis of the Bifidobacterium longum MB 219 lacZ gene.", "token_count": 32, "char_count": 108, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:16.979275", "source": { "split": "train_shard_00002", "doc_id": 92 }, "chunk_id": "train_shard_00002_92_1", "global_id": 12858 }, { "text": "The antimicrobial resistance crisis has persisted despite broad attempts at intervention. It has been proposed that an important driver of resistance is selection imposed on bacterial populations that are not the intended target of antimicrobial therapy. But to date, there has been limited quantitative measure of the mean and variance of resistance following antibiotic exposure. Here we focus on the important nosocomial pathogen Enterococcus faecium in a hospital system where resistance to daptomycin is evolving despite standard interventions. We hypothesized that the intravenous use of daptomycin generates off-target selection for resistance in transmissible gastrointestinal (carriage) populations of E. faecium. We performed a cohort study in which the daptomycin resistance of E. faecium isolated from rectal swabs from daptomycin-exposed patients was compared to a control group of patients exposed to linezolid, a drug with similar indications. In the daptomycin-exposed group, daptomycin resistance of E. faecium from the off-target population was on average 50% higher than resistance in the control group (n = 428 clones from 22 patients). There was also greater phenotypic diversity in daptomycin resistance within daptomycin-exposed patients. In patients where multiple samples over time were available, a wide variability in temporal dynamics were observed, from long-term maintenance of resistance to rapid return to sensitivity after daptomycin treatment stopped. Sequencing of isolates from a subset of patients supports the argument that selection occurs within patients. Our results demonstrate that off-target gastrointestinal populations rapidly respond to intravenous antibiotic exposure. Focusing on the off-target evolutionary dynamics may offer novel avenues to slow the spread of antibiotic resistance.\n\nDaptomycin treatment impacts resistance in off-target populations of vancomycin-resistant Enterococcus faecium.", "token_count": 429, "char_count": 1947, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:17.605671", "source": { "split": "train_shard_00002", "doc_id": 93 }, "chunk_id": "train_shard_00002_93_0", "global_id": 12859 }, { "text": "Health-associated biofilms in the oral cavity are composed of a diverse group of microbial species that can foster an environment that is less favorable for the outgrowth of dental caries pathogens, like Streptococcus mutans A novel oral bacterium, designated Streptococcus A12, was previously isolated from supragingival dental plaque of a caries-free individual and was shown to interfere potently with the growth and virulence properties of S. mutans In this study, we applied functional genomics to begin to identify molecular mechanisms used by A12 to antagonize, and to resist the antagonistic factors of, S. mutans Using bioinformatics, genes that could encode factors that enhance the ability of A12 to compete with S. mutans were identified. Selected genes, designated potential competitive factors (pcf), were deleted. Certain mutant derivatives showed a reduced capacity to compete with S. mutans compared to that of the parental strain. The A12 pcfO mutant lost the ability to inhibit comX -inducing peptide (XIP) signaling by S. mutans, while mutants with changes in the pcfFEG locus were impaired in sensing of, and were more sensitive to, the lantibiotic nisin. Loss of PcfV, annotated as a colicin V biosynthetic protein, resulted in diminished antagonism of S. mutans Collectively, the data provide new insights into the complexities and variety of factors that affect biofilm ecology and virulence. Continued exploration of the genomic and physiological factors that distinguish commensals from truly beneficial members of the oral microbiota will lead to a better understanding of the microbiome and new approaches to promote oral health.IMPORTANCE Advances in defining the composition of health-associated biofilms have highlighted the important role of beneficial species in maintaining health", "token_count": 522, "char_count": 1926, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6185, "quality_score": 0.8093, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:18.274158", "source": { "split": "train_shard_00002", "doc_id": 94 }, "chunk_id": "train_shard_00002_94_0", "global_id": 12860 }, { "text": "Comparatively little, however, has been done to address the genomic and physiological bases underlying the probiotic mechanisms of beneficial commensals. In this study, we explored the ability of a novel oral bacterial isolate, Streptococcus A12, to compete with the dental pathogen Streptococcus mutans using various gene products with diverse functions. A12 displayed enhanced competitiveness by (i) disrupting intercellular communication pathways of S. mutans, (ii) sensing and resisting antimicrobial peptides, and (iii) producing factors involved in the production of a putative antimicrobial compound. Research on the probiotic mechanisms employed by Streptococcus A12 is providing essential insights into how beneficial bacteria may help maintain oral health, which will aid in the development of biomarkers and therapeutics that can improve the practice of clinical dentistry.\n\nNovel Probiotic Mechanisms of the Oral Bacterium Streptococcus sp. A12 as Explored with Functional Genomics.", "token_count": 269, "char_count": 1029, "word_count": 137, "semantic_coherence": 1, "information_density": 0.7226, "quality_score": 0.8613, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:18.822244", "source": { "split": "train_shard_00002", "doc_id": 94 }, "chunk_id": "train_shard_00002_94_1", "global_id": 12861 }, { "text": "

Background

Shiga toxin-producing Escherchia coli (STEC) O157:H7 is a zoonotic pathogen that causes numerous food and waterborne disease outbreaks. It is globally distributed, but its origin and the temporal sequence of its geographical spread are unknown.

Methods

We analyzed whole-genome sequencing data of 757 isolates from 4 continents, and performed a pan-genome analysis to identify the core genome and, from this, extracted single-nucleotide polymorphisms. A timed phylogeographic analysis was performed on a subset of the isolates to investigate its worldwide spread.

Results

The common ancestor of this set of isolates occurred around 1890 (1845-1925) and originated from the Netherlands. Phylogeographic analysis identified 34 major transmission events. The earliest were predominantly intercontinental, moving from Europe to Australia around 1937 (1909-1958), to the United States in 1941 (1921-1962), to Canada in 1960 (1943-1979), and from Australia to New Zealand in 1966 (1943-1982). This pre-dates the first reported human case of E. coli O157:H7, which was in 1975 from the United States.

Conclusions

Inter- and intra-continental transmission events have resulted in the current international distribution of E. coli O157:H7, and it is likely that these events were facilitated by animal movements (eg, Holstein Friesian cattle). These findings will inform policy on action that is crucial to reduce the further spread of E. coli O157:H7 and other (emerging) STEC strains globally.\n\nPhylogeographic Analysis Reveals Multiple International transmission Events Have Driven the Global Emergence of Escherichia coli O157:H7.", "token_count": 489, "char_count": 1665, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6372, "quality_score": 0.8186, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:19.473385", "source": { "split": "train_shard_00002", "doc_id": 95 }, "chunk_id": "train_shard_00002_95_0", "global_id": 12862 }, { "text": "Background: Diagnostic tools designed to target Burkholderia pseudomallei, the causative agent of melioidosis that was classified as a Tier 1 Select Agent by the U.S. Centers for Disease Control and Prevention, have typically suffered from false-positive and false-negative results because of a lack of understanding of the genomic diversity of B. pseudomallei and its genetic near neighbors. Objective: In this review, we discuss a strategy for using comparative genomics to guide the design of inclusivity and exclusivity panels for the validation of assays as defined by the Standard Method Performance Requirement (SMPR). Methods: Based upon a literature review, comparative genomic analyses, and hands-on experience with diagnostic development and testing, we describe important factors to consider when developing inclusivity and exclusivity panels for testing diagnostic and/or detection tools. Results: The genomic diversity of B. pseudomallei is substantial, with the genome characterized by horizontal gene transfer, including the acquisition of genomic islands from near-neighbor species. This genomic diversity, core genome reduction, and signal erosion can complicate molecular diagnostic tool development and validation. Conclusions: Accurate diagnostic and/or detection tools targeting B. pseudomallei, an important pathogen from a public health and biodefense perspective, are needed for many applications. Utilizing whole genome sequencing data and comparative genomic techniques can guide the development and validation of such tools. Amplicon sequencing assays and assay redundancy can provide improved assay performance. Highlights: When developing and validating diagnostic and/or detection tools targeting B. pseudomallei, it is important to consider genomic diversity, genome reduction, and signal erosion to reduce the effects of typical diagnostic errors.\n\nDeveloping Inclusivity and Exclusivity Panels for Testing Diagnostic and Detection Tools Targeting Burkholderia pseudomallei, the Causative Agent of Melioidosis.", "token_count": 501, "char_count": 2127, "word_count": 274, "semantic_coherence": 1, "information_density": 0.5328, "quality_score": 0.7664, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:20.122434", "source": { "split": "train_shard_00002", "doc_id": 96 }, "chunk_id": "train_shard_00002_96_0", "global_id": 12863 }, { "text": "Enterococcus faecium, a common inhabitant of the human gut, has emerged in the last 2 decades as an important multidrug-resistant nosocomial pathogen. Since the start of the 21st century, multilocus sequence typing (MLST) has been used to study the molecular epidemiology of E. faecium. However, due to the use of a small number of genes, the resolution of MLST is limited. Whole-genome sequencing (WGS) now allows for high-resolution tracing of outbreaks, but current WGS-based approaches lack standardization, rendering them less suitable for interlaboratory prospective surveillance. To overcome this limitation, we developed a core genome MLST (cgMLST) scheme for E. faecium. cgMLST transfers genome-wide single nucleotide polymorphism(SNP) diversity into a standardized and portable allele numbering system that is far less computationally intensive than SNP-based analysis of WGS data. The E. faecium cgMLST scheme was built using 40 genome sequences that represented the diversity of the species. The scheme consists of 1,423 cgMLST target genes. To test the performance of the scheme, we performed WGS analysis of 103 outbreak isolates from five different hospitals in the Netherlands, Denmark, and Germany. The cgMLST scheme performed well in distinguishing between epidemiologically related and unrelated isolates, even between those that had the same sequence type (ST), which denotes the higher discriminatory power of this cgMLST scheme over that of conventional MLST. We also show that in terms of resolution, the performance of the E. faecium cgMLST scheme is equivalent to that of an SNP-based approach. In conclusion, the cgMLST scheme developed in this study facilitates rapid, standardized, and high-resolution tracing of E. faecium outbreaks.\n\nCore Genome Multilocus Sequence Typing Scheme for High- Resolution Typing of Enterococcus faecium.", "token_count": 461, "char_count": 1863, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5882, "quality_score": 0.7941, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:20.761920", "source": { "split": "train_shard_00002", "doc_id": 97 }, "chunk_id": "train_shard_00002_97_0", "global_id": 12864 }, { "text": "Bovine respiratory disease is a common health problem in beef production. The primary bacterial agent involved, Mannheimia haemolytica, is a target for antimicrobial therapy and at risk for associated antimicrobial resistance development. The role of M. haemolytica in pathogenesis is linked to serotype with serotypes 1 (S1) and 6 (S6) isolated from pneumonic lesions and serotype 2 (S2) found in the upper respiratory tract of healthy animals. Here, we sequenced the genomes of 11 strains of M. haemolytica, representing all three serotypes and performed comparative genomics analysis to identify genetic features that may contribute to pathogenesis. Possible virulence associated genes were identified within 14 distinct prophage, including a periplasmic chaperone, a lipoprotein, peptidoglycan glycosyltransferase and a stress response protein. Prophage content ranged from 2-8 per genome, but was higher in S1 and S6 strains. A type I-C CRISPR-Cas system was identified in each strain with spacer diversity and organization conserved among serotypes. The majority of spacers occur in S1 and S6 strains and originate from phage suggesting that serotypes 1 and 6 may be more resistant to phage predation. However, two spacers complementary to the host chromosome targeting a UDP-N-acetylglucosamine 2-epimerase and a glycosyl transferases group 1 gene are present in S1 and S6 strains only indicating these serotypes may employ CRISPR-Cas to regulate gene expression to avoid host immune responses or enhance adhesion during infection. Integrative conjugative elements are present in nine of the eleven genomes. Three of these harbor extensive multi-drug resistance cassettes encoding resistance against the majority of drugs used to combat infection in beef cattle, including macrolides and tetracyclines used in human medicine. The findings here identify key features that are likely contributing to serotype related pathogenesis and specific targets for vaccine design intended to reduce the dependency on antibiotics to treat respiratory infection in cattle.", "token_count": 509, "char_count": 2065, "word_count": 300, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8183, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:21.417260", "source": { "split": "train_shard_00002", "doc_id": 98 }, "chunk_id": "train_shard_00002_98_0", "global_id": 12865 }, { "text": "Comparative Genomic Analysis of Mannheimia haemolytica from Bovine Sources.", "token_count": 21, "char_count": 75, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:21.768527", "source": { "split": "train_shard_00002", "doc_id": 98 }, "chunk_id": "train_shard_00002_98_1", "global_id": 12866 }, { "text": "Four different yeast species (Metschnikowia pulcherrima, Saccharomycopsis vini, Kluyveromyces marxianus, Cryptococcus albidus), isolated from surface of grapes, were evaluated for biocontrol potential against Penicillium glabrum. In order to investigate the influence of temperature, pH, water activity and yeast cell concentration on Penicillium glabrum inhibition, the individual effects and the interaction of these factors were analyzed by means of a Central Composite Design (CCD). All yeast species tested showed antagonistic effects which were more pronounced at high cell concentrations. The other variables affected the antagonistic effect differentially depending on the yeast species. Results of the experimental design showed that the selective success of a competitive microflora is under environmental control; moreover, when microbial cells are subjected to multiple factors, the effects and the reciprocal interactions of the individual variables cannot be independently evaluated.\n\nInfluence of temperature, pH and water activity on \"in vitro\" inhibition of Penicillium glabrum (Wehmer) Westling by yeasts.", "token_count": 253, "char_count": 1123, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6867, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:22.254563", "source": { "split": "train_shard_00002", "doc_id": 99 }, "chunk_id": "train_shard_00002_99_0", "global_id": 12867 }, { "text": "Cross talk occurs between the human gut and the lung through a gut-lung axis involving the gut microbiota. However, the signatures of the human gut microbiota after active Mycobacterium tuberculosis infection have not been fully understood. Here, we investigated changes in the gut microbiota in tuberculosis (TB) patients by shotgun sequencing the gut microbiomes of 31 healthy controls and 46 patients. We observed a dramatic changes in gut microbiota in tuberculosis patients as reflected by significant decreases in species number and microbial diversity. The gut microbiota of TB patients were mostly featured by the striking decrease of short-chain fatty acids (SCFAs)-producingbacteria as well as associated metabolic pathways. A classification model based on the abundance of three species, Haemophilus parainfluenzae, Roseburia inulinivorans, and Roseburia hominis, performed well for discriminating between healthy and diseased patients. Additionally, the healthy and diseased states can be distinguished by SNPs in the species of B. vulgatus. We present a comprehensive profile of changes in the microbiota in clinical TB patients. Our findings will shed light on the design of future diagnoses and treatments for M. tuberculosis infections.\n\nThe Gut Microbiome Signatures Discriminate Healthy From Pulmonary Tuberculosis Patients.", "token_count": 342, "char_count": 1377, "word_count": 191, "semantic_coherence": 1, "information_density": 0.5969, "quality_score": 0.7984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:22.827719", "source": { "split": "train_shard_00002", "doc_id": 100 }, "chunk_id": "train_shard_00002_100_0", "global_id": 12868 }, { "text": "A novel colorimetric microbial bioassay for toxicity has been developed; it shows particular sensitivity to trichothecene mycotoxins. The assay uses inhibition of expression of beta-galactosidase activity within the yeast Kluyveromyces marxianus as a sensitive toxicity indicator, cultures remaining yellow, rather than turning deep green-blue, in the presence of X-gal, a chromogenic substrate. The assay is conducted in standard microtitre plates, permitting small volumes (160 microl) and many replicates, and can be scored either automatically by a plate-reader, or by eye. Factors likely to affect the efficacy of the bioassay, including carbon source, solvents, inoculum cell density, and the use of membrane-modulating agents (MMAs), were assessed. Polymyxin B nonapeptide was the most effective toxicity-enhancing MMA tested, enabling the trichothecene mycotoxin, verrucarin A, to be detected at a concentration of about 1 ng/ml. The assay's reproducibility was examined using polymyxin B sulfate, a cheaper MMA, and another trichothecene mycotoxin, T2 toxin: reproducibility and sensitivity were better for the beta-galactosidase X-gal endpoint than for an alternative chromogenic toxicity indicator, the respiratory substrate 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl tetrazolium bromide (MTT).\n\nA novel colorimetric yeast bioassay for detecting trichothecene mycotoxins.", "token_count": 396, "char_count": 1381, "word_count": 182, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:23.808197", "source": { "split": "train_shard_00002", "doc_id": 101 }, "chunk_id": "train_shard_00002_101_0", "global_id": 12869 }, { "text": "Multidrug-resistant (MDR) Klebsiella pneumoniae is considered a major global concern by the World Health Organization. Evidence is growing on the importance of circulation of MDR bacterial populations between animals and humans. Horses have been shown to carry commensal isolates of this bacterial species and can act as human MDR bacteria reservoirs. In this study, we characterized an extended-spectrum β-lactamase (ESBL)-producing K. pneumoniae sequence type (ST) 348 isolate from a horse, an ST reported for the first time in an animal, using next-generation sequencing. We compared it with six other MDR K. pneumoniae ST348 human isolates previously identified in health-care facilities in Portugal using a core genome multi-locus sequence typing approach to evaluate a possible genetic link. The horse isolate was resistant to most of the antimicrobials tested, including 3rd generation cephalosporins, fluoroquinolones, and aminoglycosides, and presented several antimicrobial resistance genes, including bla ESBL. Twenty-one allele differences were found between the horse isolate and the most similar human isolate, suggesting a recent common ancestor. Other similarities were observed regarding the content on antimicrobial resistance genes, plasmid incompatibility groups, and capsular and somatic antigens. This study illustrates the relevance of the dissemination of MDR strains, and enhances that identification of these types of bacterial strains in both human and veterinary settings is of significant relevance in order to understand and implement combined control strategies for MDR bacteria in animals and humans.\n\nCommonality of Multidrug-Resistant Klebsiella pneumoniae ST348 Isolates in Horses and Humans in Portugal.", "token_count": 450, "char_count": 1785, "word_count": 242, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [ "ST348" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:24.470936", "source": { "split": "train_shard_00002", "doc_id": 102 }, "chunk_id": "train_shard_00002_102_0", "global_id": 12870 }, { "text": "Escherichia coli are major bacterial pathogens causing bovine mastitis, a disease of great economic impact on dairy production worldwide. This work aimed to study the virulence determinants of mammary pathogenic E. coli (MPEC). By whole-genome sequencing analysis of 40 MPEC and 22 environmental (\"dairy-farm\" E. coli [DFEC]) strains, we found that only the fec locus (fecIRABCDE) for ferric dicitrate uptake was present in the core genome of MPEC and that it was absent in DFEC genomes (P < 0.05). Expression of the FecA receptor in the outer membrane was shown to be citrate dependent by mass spectrometry. FecA was overexpressed when bacteria were grown in milk. Transcription of the fecA gene and of the inner membrane transport component fecB gene was upregulated in bacteria recovered from experimental intramammary infection. The presence of the fec system was shown to affect the ability of E. coli to grow in milk. While the rate of growth in milk of fec-positive (fec+) DFEC was similar to that of MPEC, it was significantly lower in DFEC lacking fec Furthermore, deletion of fec reduced the rate of growth in milk of MPEC strain P4, whereas fec-transformed non-mammary gland-pathogenic DFEC strain K71 gained the phenotype of the level of growth in milk observed in MPEC. The role of fec in E", "token_count": 468, "char_count": 1429, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6028, "quality_score": 0.8014, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:25.135823", "source": { "split": "train_shard_00002", "doc_id": 103 }, "chunk_id": "train_shard_00002_103_0", "global_id": 12871 }, { "text": "coli intramammary pathogenicity was investigated in vivo in cows, with results showing that an MPEC P4 mutant lacking fec lost its ability to induce mastitis, whereas the fec+ DFEC K71 mutant was able to trigger intramammary inflammation. For the first time, a single molecular locus was shown to be crucial in MPEC pathogenicity.IMPORTANCE Bovine mastitis is the major infectious disease in dairy cows and the leading cause of economic loss to the global dairy industry, directly contributing to the price of dairy products on supermarket shelves and the financial hardships suffered by dairy farmers. Mastitis is also the leading reason for the use of antibiotics in dairy farms. Good farm management practices in many countries have dramatically reduced the incidence of contagious mastitis; however, the problems associated with the incidence of environmental mastitis caused by bacteria such as Escherichia coli have proven intractable. E. coli bacteria cause acute mastitis, which affects the health and welfare of cows and in extreme cases may be fatal. Here we show for the first time that the pathogenicity of E. coli causing mastitis in cows is highly dependent on the fecIRABCDE ferric citrate uptake system that allows the bacterium to capture iron from citrate. The Fec system is highly expressed during infection in the bovine udder and is ubiquitous in and necessary for the E. coli bacteria that cause mammary infections in cattle. These results have far-reaching implications, raising the possibility that mastitis may be controllable by targeting this system.\n\nPostgenomics Characterization of an Essential Genetic Determinant of Mammary Pathogenic Escherichia coli.", "token_count": 466, "char_count": 1769, "word_count": 258, "semantic_coherence": 1, "information_density": 0.5969, "quality_score": 0.7984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:25.795481", "source": { "split": "train_shard_00002", "doc_id": 103 }, "chunk_id": "train_shard_00002_103_1", "global_id": 12872 }, { "text": "Streptococcus suis is an important zoonotic pathogen that can cause meningitis and sepsis in both pigs and humans. Infections in humans have been sporadic worldwide but two severe outbreaks occurred in China in recent years, while infections in pigs are a major problem in the swine industry. Some S. suis strains are more pathogenic than others with 2 sequence types (ST), ST1 and ST7, being well recognized as highly pathogenic. We analyzed 31 isolates from 23 serotypes and 25 STs by NimbleGen tiling microarray using the genome of a high pathogenicity (HP) ST1 strain, GZ1, as reference and a new algorithm to detect gene content difference. The number of genes absent in a strain ranged from 49 to 225 with a total of 632 genes absent in at least one strain, while 1346 genes were found to be invariably present in all strains as the core genome of S. suis, accounting for 68% of the GZ1 genome. The majority of genes are located in chromosomal blocks with two or more contiguous genes. Sixty two blocks are absent in two or more strains and defined as regions of difference (RDs), among which 26 are putative genomic islands (GIs). Clustering and statistical analyses revealed that 8 RDs including 6 putative GIs and 21 genes within these RDs are significantly associated with HP. Three RDs encode known virulence related factors including the extracellular factor, the capsular polysaccharide and a SrtF pilus. The strains were divided into 5 groups based on population genetic analysis of multilocus sequence typing data and the distribution of the RDs among the groups revealed gain and loss of RDs in different groups. Our study elucidated the gene content diversity of S. suis and identified genes that potentially promote HP.\n\nIdentification of genes and genomic islands correlated with high pathogenicity in Streptococcus suis using whole genome tiling microarrays.", "token_count": 482, "char_count": 1878, "word_count": 308, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [ "ST7", "ST1", "GZ1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:26.470225", "source": { "split": "train_shard_00002", "doc_id": 104 }, "chunk_id": "train_shard_00002_104_0", "global_id": 12873 }, { "text": "In the past three decades, dietary and lifestyle changes worldwide have resulted in a global increase in the prevalence of obesity in both adults and children. Known to be highly influenced by genetic, environmental and lifestyle factors, obesity is characterized by a low-grade chronic inflammation that contributes to the development of other metabolic diseases such as diabetes and cardiovascular disease. Recently, the gut microbiome has been added as a cause/contributor to the development of obesity. As differences in the microbiome between obese and normoweight individuals have been observed, we set out to determine whether infants harbor an obesogenic microbiome early on and whether the pre-pregnancy status of the mother (obese or normoweight) is correlated to their infant's microbiome composition. Using shotgun sequencing, we analyzed stool samples throughout the first year of life from infants born to obese (n = 23 participants, m = 104 samples) and normoweight (n = 23 participants, m = 99 samples) mothers. We found that the infants' microbiome diversity at taxonomic and functional levels was significantly influenced by time (ANOVA p < 0.001) but not by the mother's pre-pregnancy status. Overall, no deterministic succession of taxa or functions was observed", "token_count": 360, "char_count": 1317, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6546, "quality_score": 0.8273, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:27.098959", "source": { "split": "train_shard_00002", "doc_id": 105 }, "chunk_id": "train_shard_00002_105_0", "global_id": 12874 }, { "text": "However, infants born to obese mothers were found to have a significantly higher Bacillota/Bacteroidota ratio (p = 0.02) at six months, were significantly depleted from six months old of the well-established obesity biomarkers Akkermansia municiphila and Faecalibacterium prausnitzii (p < 0.01), and were at one week old, significantly enriched in pathways such as the UDP-N-acetyl-D-glucosamine biosynthesis II (p = 0.02) involved in leptin production, suggesting perhaps that there may exist some underlying mechanisms that dictate the development of an obesogenic microbiota early on.\n\nThe infants' gut microbiome: setting the stage for the early onset of obesity.", "token_count": 240, "char_count": 702, "word_count": 96, "semantic_coherence": 1, "information_density": 0.7708, "quality_score": 0.8854, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:27.567393", "source": { "split": "train_shard_00002", "doc_id": 105 }, "chunk_id": "train_shard_00002_105_1", "global_id": 12875 }, { "text": "Malate is a major contributor to the sourness of grape berries (Vitis spp.) and their products, such as wine. Excessive malate at maturity, commonly observed in wild Vitis grapes, is detrimental to grape and wine quality and complicates the introgression of valuable disease resistance and cold hardy genes through breeding. This study investigated an interspecific Vitis family that exhibited strong and stable variation in malate at ripeness for five years and tested the separate contribution of accumulation, degradation, and dilution to malate concentration in ripe fruit in the last year of study. Genotyping was performed using transferable rhAmpSeq haplotype markers, based on the Vitis collinear core genome. Three significant QTL for ripe fruit malate on chromosomes 1, 7, and 17, accounted for over two-fold and 6.9 g/L differences, and explained 40.6% of the phenotypic variation. QTL on chromosomes 7 and 17 were stable in all and in three out of five years, respectively. Variation in pre-veraison malate was the major contributor to variation in ripe fruit malate (39%), and based on two and five years of data, respectively, their associated QTL overlapped on chromosome 7, indicating a common genetic basis. However, use of transferable markers on a closely related Vitis family did not yield a common QTL across families. This suggests that diverse physiological mechanisms regulate the levels of this key metabolite in the Vitis genus, a conclusion supported by a review of over a dozen publications from the past decade, showing malate-associated genetic loci on all 19 chromosomes.\n\nStable QTL for malate levels in ripe fruit and their transferability across Vitis species.", "token_count": 456, "char_count": 1743, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5779, "quality_score": 0.789, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:28.207101", "source": { "split": "train_shard_00002", "doc_id": 106 }, "chunk_id": "train_shard_00002_106_0", "global_id": 12876 }, { "text": "

Purpose

Carbapenem-resistant Enterobacteriaceae (CRE) infection has become a concerning threat, especially in hospital settings; however, its phenotypic characterization, association with rectal colonization and subsequent bloodstream infections (BSI) remain to be clarified. This study aimed to investigate the incidence and risk factors of CRE infection in rectal CRE carriers and to understand the clonality of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains and their association with subsequent BSI in these patients.

Patients and methods

This was a prospectively designed cohort study. Hospitalized patients treated at our institution from April 2019 to October 2020 with intestinal CRE carriage were screened at admission and weekly thereafter until death or discharge from the hospital. Stool and blood samples were obtained for strain growth and mass spectrometry. The colonization and clinical infection isolates were analyzed by antimicrobial susceptibility testing to identify CRE. The clonality of the CRE strains and their corresponding clinical infection strains was studied by whole-genome sequencing to explore the mechanism of drug resistance and evaluate possible transmission. CRE-associated risk factors were analyzed in combination with epidemiological data.

Results

Of the 1203 patients, 85 were colonized by CRE and 21 developed CRE infection, of whom 13 developed CRE bloodstream infection (BSI). Ninety-one CRE strains were isolated from the rectal specimens of the 85 patients. Tracheotomy and chemotherapy in the past three months were independent risk factors for CRE infection in intestinal CRE carriers. ST11-KL64 (92.3%, 24/26) was the most dominant capsule and multilocus sequence typing (MLST) type among clonal CRKP isolates. Single-nucleotide polymorphism clustering showed homology of representative colonization and infection CRKP strain pairs (n=13) in the same patient. One group of leading clones was endemic in surgical intensive care units (ICUs)", "token_count": 513, "char_count": 2028, "word_count": 272, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "KL64", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:28.872589", "source": { "split": "train_shard_00002", "doc_id": 107 }, "chunk_id": "train_shard_00002_107_0", "global_id": 12877 }, { "text": "Twenty-four CRKP strains carried β-lactamase K. pneumonia carbapenemase 2, and 73.1% (19 strains) of CRKP carried mucoid phenotype regulator genes A2 and iucABCD.

Conclusion

In summary, intestinal CRE colonization was detectable at an elevated rate among hospitalized patients and prevalent in ICU patients, with potential rapid horizontal transmission, providing evidence that CRE BSI infection in hospitalized patients might be due to their colonized strains and indicates the correlation between intestinal colonization and BSI.\n\nBloodstream Infections in Patients with Rectal Colonization by Carbapenem-Resistant Enterobacteriaceae: A Prospective Cohort Study.", "token_count": 189, "char_count": 678, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:29.325587", "source": { "split": "train_shard_00002", "doc_id": 107 }, "chunk_id": "train_shard_00002_107_1", "global_id": 12878 }, { "text": "This review will consider the gut as a reservoir for antimicrobial resistance, colonization resistance, and how disruption of the microbiome can lead to colonization by pathogenic organisms. There is a focus on the gut as a reservoir for β-lactam and plasmid-mediated quinolone resistance. Finally, the role of functional metagenomics and long-read sequencing technologies to detect and understand antimicrobial resistance genes within the gut microbiome is discussed, along with the potential for future microbiome-directed methods to detect and prevent infection.\n\nThe Gut Microbiome as a Reservoir for Antimicrobial Resistance.", "token_count": 152, "char_count": 630, "word_count": 88, "semantic_coherence": 1, "information_density": 0.6023, "quality_score": 0.8011, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:29.766511", "source": { "split": "train_shard_00002", "doc_id": 108 }, "chunk_id": "train_shard_00002_108_0", "global_id": 12879 }, { "text": "

Purpose

To investigate whether a Mediterranean diet (MD) affected the plasma concentrations of endocannabinoids (ECs), N-acylethanolamines (NAEs) and their specific ratios in subjects with lifestyle risk factors for metabolic diseases. To identify the relationship between circulating levels of these compounds and gut microbiome, insulin resistance and systemic inflammation.

Methods

A parallel 8-week randomised controlled trial was performed involving 82 overweight and obese subjects aged (mean ± SEM) 43 ± 1.4 years with a BMI of 31.1 ± 0.5 kg/m2, habitual Western diet (CT) and sedentary lifestyle. Subjects were randomised to consume an MD tailored to their habitual energy and macronutrient intake (n = 43) or to maintain their habitual diet (n = 39). Endocannabinoids and endocannabinoid-like molecules, metabolic and inflammatory markers and gut microbiome were monitored over the study period.

Results

The MD intervention lowered plasma arachidonoylethanolamide (AEA, p = 0.02), increased plasma oleoylethanolamide/palmitoylethanolamide (OEA/PEA, p = 0.009) and OEA/AEA (p = 0.006) and increased faecal Akkermansia muciniphila (p = 0.026) independent of body weight changes. OEA/PEA positively correlated with abundance of key microbial players in diet-gut-health interplay and MD adherence", "token_count": 457, "char_count": 1334, "word_count": 176, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:30.405324", "source": { "split": "train_shard_00002", "doc_id": 109 }, "chunk_id": "train_shard_00002_109_0", "global_id": 12880 }, { "text": "Following an MD, individuals with low-plasma OEA/PEA at baseline decreased homeostatic model assessment of insulin resistance index (p = 0.01), while individuals with high-plasma OEA/PEA decreased serum high-sensitive C-reactive protein (p = 0.02).

Conclusions

We demonstrated that a switch from a CT to an isocaloric MD affects the endocannabinoid system and increases A. muciniphila abundance in the gut independently of body weight changes. Endocannabinoid tone and microbiome functionality at baseline drives an individualised response to an MD in ameliorating insulin sensitivity and inflammation. Clinical Trial Registry number and website NCT03071718; www.clinicaltrials.gov.\n\nMediterranean diet consumption affects the endocannabinoid system in overweight and obese subjects: possible links with gut microbiome, insulin resistance and inflammation.", "token_count": 241, "char_count": 863, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6909, "quality_score": 0.8455, "entities": { "genes": [ "NCT03071718" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:30.889770", "source": { "split": "train_shard_00002", "doc_id": 109 }, "chunk_id": "train_shard_00002_109_1", "global_id": 12881 }, { "text": "One of the most demanding challenges in infection control is the worldwide dissemination of multidrug-resistant (MDR) bacteria in clinical settings. Especially the increasing prevalence of carbapenemase producing Gram-negative pathogens poses an urgent threat to public health, as these enzymes confer resistance to almost all β-lactam antibiotics including carbapenems. In this study, we report a prolonged nosocomial outbreak of various NDM-1-producing Enterobacterales species due to clonal spread and cross-species exchange of plasmids and possibly transposons. Between July 2015 and September 2017, a total of 51 carbapenemase-positive isolates were collected from 38 patients and three environmental sources in a single German hospital. Combining molecular typing methods and whole genome sequencing, the metallo-β-lactamase gene bla NDM-1 was found to be present in 35 isolates of which seven additionally carried the carbapenemase gene bla KPC-2. Core genome MLST (cgMLST) revealed different clusters of closely related isolates of Escherichia coli, Klebsiella pneumoniae, Citrobacter freundii, Morganella morganii or Enterobacter cloacae indicating clonal spread. The detailed reconstruction of the plasmid sequences revealed that in all outbreak-associated isolates blaNDM-1 was located on similar composite transposons, which were also very similar to Tn125 previously described for Acinetobacter baumannii. In contrast to Tn125, these structures were flanked by IS26 elements, which could facilitate horizontal gene transfer. Moreover, the identical plasmid was found to be shared by E. coli and M. morganii isolates", "token_count": 511, "char_count": 1766, "word_count": 222, "semantic_coherence": 1, "information_density": 0.7297, "quality_score": 0.8649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:31.544882", "source": { "split": "train_shard_00002", "doc_id": 110 }, "chunk_id": "train_shard_00002_110_0", "global_id": 12882 }, { "text": "Our results highlight the importance of detailed genome-based analyses for complex nosocomial outbreaks, allowing the identification of causal genetic determinants and providing insights into potential mechanisms involved in the dissemination of antibiotic resistances between different bacterial species.\n\nIS26-Mediated Transfer of bla NDM-1 as the Main Route of Resistance Transmission During a Polyclonal, Multispecies Outbreak in a German Hospital.", "token_count": 115, "char_count": 477, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8448, "quality_score": 0.9224, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:31.930035", "source": { "split": "train_shard_00002", "doc_id": 110 }, "chunk_id": "train_shard_00002_110_1", "global_id": 12883 }, { "text": "

Background

The bacterial genus Mycobacterium is of great interest in the medical and biotechnological fields. Despite a flood of genome sequencing and functional genomics data, significant gaps in knowledge between genome and phenome seriously hinder efforts toward the treatment of mycobacterial diseases and practical biotechnological applications. In this study, we propose the use of systematic, comparative functional pan-genomic analysis to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon (PAH) metabolism in the genus Mycobacterium.

Results

Phylogenetic, phenotypic, and genomic information for 27 completely genome-sequenced mycobacteria was systematically integrated to reconstruct a mycobacterial phenotype network (MPN) with a pan-genomic concept at a network level. In the MPN, mycobacterial phenotypes show typical scale-free relationships. PAH degradation is an isolated phenotype with the lowest connection degree, consistent with phylogenetic and environmental isolation of PAH degraders. A series of functional pan-genomic analyses provide conserved and unique types of genomic evidence for strong epistatic and pleiotropic impacts on evolutionary trajectories of the PAH-degrading phenotype. Under strong natural selection, the detailed gene gain/loss patterns from horizontal gene transfer (HGT)/deletion events hypothesize a plausible evolutionary path, an epistasis-based birth and pleiotropy-dependent death, for PAH metabolism in the genus Mycobacterium. This study generated a practical mycobacterial compendium of phenotypic and genomic changes, focusing on the PAH-degrading phenotype, with a pan-genomic perspective of the evolutionary events and the environmental challenges.

Conclusions

Our findings suggest that when selection acts on PAH metabolism, only a small fraction of possible trajectories is likely to be observed, owing mainly to a combination of the ambiguous phenotypic effects of PAHs and the corresponding pleiotropy- and epistasis-dependent evolutionary adaptation", "token_count": 494, "char_count": 2086, "word_count": 263, "semantic_coherence": 1, "information_density": 0.616, "quality_score": 0.808, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:32.583359", "source": { "split": "train_shard_00002", "doc_id": 111 }, "chunk_id": "train_shard_00002_111_0", "global_id": 12884 }, { "text": "Evolutionary constraints on the selection of trajectories, like those seen in PAH-degrading phenotypes, are likely to apply to the evolution of other phenotypes in the genus Mycobacterium.\n\nComparative functional pan-genome analyses to build connections between genomic dynamics and phenotypic evolution in polycyclic aromatic hydrocarbon metabolism in the genus Mycobacterium.", "token_count": 91, "char_count": 377, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7551, "quality_score": 0.8776, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:32.963797", "source": { "split": "train_shard_00002", "doc_id": 111 }, "chunk_id": "train_shard_00002_111_1", "global_id": 12885 }, { "text": "

Background

The population structure of extraintestinal pathogenic Escherichia coli evolves over time, notably due to the emergence of antibiotic-resistant clones such as ESBL-producing Enterobacteriaceae (ESBL-E).

Objectives

To analyse by WGS the genetic diversity of a large number of ESBL-E isolated from urinary tract infections in children from paediatric centres across France between 2014 and 2017 and collected by the National Observatory of febrile urinary tract infection (FUTI) caused by ESBL-E.

Methods

A total of 40 905 Enterobacteriaceae-positive urine cultures were identified. ESBL-E were found in 1983 samples (4.85%). WGS was performed on 251 ESBL-E causing FUTI. STs, core genome MLST (cgMLST), serotype, fimH allele, ESBL genes and presence of papGII key virulence factor were determined.

Results

E. coli and Klebsiella pneumoniae were found in 86.9% (218/251) and 11.2% (28/251) of cases, respectively. Several STs predominate among E. coli such as ST131, ST38, ST69, ST73, ST95, ST405, ST12 and ST1193, while no ST emerged in K. pneumoniae. E. coli ST131, ST38 and ST1193 increased during the study period, with a heterogeneity in papGII prevalence (64.5%, 35% and 20% respectively). Most isolates harboured the CTX-M type (97%) with a predominance of blaCTX-M-15. blaCTX-M-27, an emerging variant in E. coli, is found in various STs", "token_count": 487, "char_count": 1383, "word_count": 195, "semantic_coherence": 1, "information_density": 0.7385, "quality_score": 0.8692, "entities": { "genes": [ "ST131", "ST405", "ST12", "ST73", "ST95", "ST1193", "ST69", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:33.611337", "source": { "split": "train_shard_00002", "doc_id": 112 }, "chunk_id": "train_shard_00002_112_0", "global_id": 12886 }, { "text": "cgMLST enabled discrimination of clusters within the main STs.

Conclusions

The predominance of ST131, and the emergence of other STs such as ST38 and ST1193 combined with ESBL genes deserves close epidemiological surveillance considering their high threat in infectious disease. cgMLST could be a discriminant complementary tool for the analyses.\n\nDiversity and trends in population structure of ESBL-producing Enterobacteriaceae in febrile urinary tract infections in children in France from 2014 to 2017.", "token_count": 137, "char_count": 513, "word_count": 70, "semantic_coherence": 1, "information_density": 0.8286, "quality_score": 0.9143, "entities": { "genes": [ "ST131", "ST38", "ST1193" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:34.043271", "source": { "split": "train_shard_00002", "doc_id": 112 }, "chunk_id": "train_shard_00002_112_1", "global_id": 12887 }, { "text": "Escherichia coli (E.coli) O157 that do not produce Shiga toxin and do not possess flagellar antigen H7 are of diverse H serotypes. In this study, the antibiotic resistance properties, genotype of a set of virulence associated genes and the phylogenetic background of E. coli O157:non-H7 groups were compared. Whole genome sequencing was performed on fourteen O157:non-H7 isolates collected in the STEC-ID-net study. The genomes were compared with E. coli O157 genomes and a typical Enteropathogenic E. coli (tEPEC) genome downloaded from NCBI. Twenty-six (86%) of the analyzed genomes had the intimin encoding gene eae but of different types mostly correlating with their H types, e.g., H16, H26, H39, and H45 carried intimin type ε, β, κ, and α, respectively. They belonged to several E. coli phylogenetic groups, i.e., to phylogenetic group A, B1, B2, and D. Seven (50%) of our collected O157:non-H7 isolates were resistant to two or more antibiotics. Several mobile genetic elements, such as plasmids, insertion elements, and pathogenicity islands, carrying a set of virulence and resistance genes were found in the E. coli O157:non-H7 isolates. Core genome phylogenetic analysis showed that O157:non-H7 isolates probably evolved from different phylogenetic lineages and were distantly related to the E. coli O157:H7 lineage. We hypothesize that independent acquisition of mobile genetic elements by isolates of different lineages have contributed to the different molecular features of the O157:non-H7 strains. Although distantly related to the STEC O157, E", "token_count": 518, "char_count": 1627, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6085, "quality_score": 0.8043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:34.676415", "source": { "split": "train_shard_00002", "doc_id": 113 }, "chunk_id": "train_shard_00002_113_0", "global_id": 12888 }, { "text": "coli O157:non-H7 isolates from multiple genetic background could be considered as pathogen of concern for their diverse virulence and antibiotic resistance properties.\n\nVirulence, Antimicrobial Resistance Properties and Phylogenetic Background of Non-H7 Enteropathogenic Escherichia coli O157.", "token_count": 90, "char_count": 304, "word_count": 35, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:35.060490", "source": { "split": "train_shard_00002", "doc_id": 113 }, "chunk_id": "train_shard_00002_113_1", "global_id": 12889 }, { "text": "

Background

Gene gain and loss frequently occurs in the cyanobacterium Prochlorococcus, a phototroph that numerically dominates tropical and subtropical open oceans. However, little is known about the stabilization of its core genome, which contains approximately 1250 genes, in the context of genome streamlining. Using Prochlorococcus MED4 as a model organism, we investigated the constraints on core genome stabilization using transcriptome profiling.

Results

RNA-Seq technique was used to obtain the transcriptome map of Prochlorococcus MED4, including operons, untranslated regions, non-coding RNAs, and novel genes. Genome-wide expression profiles revealed that three factors contribute to core genome stabilization. First, a negative correlation between gene expression levels and protein evolutionary rates was observed. Highly expressed genes were overrepresented in the core genome but not in the flexible genome. Gene necessity was determined as a second powerful constraint on genome evolution through functional enrichment analysis. Third, quick mRNA turnover may increase corresponding proteins' fidelity among genes that were abundantly expressed. Together, these factors influence core genome stabilization during MED4 genome evolution.

Conclusions

Gene expression, gene necessity, and mRNA turnover contribute to core genome maintenance during cyanobacterium Prochlorococcus genus evolution.\n\nThe transcriptome landscape of Prochlorococcus MED4 and the factors for stabilizing the core genome.", "token_count": 365, "char_count": 1531, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6528, "quality_score": 0.8264, "entities": { "genes": [ "MED4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:35.640536", "source": { "split": "train_shard_00002", "doc_id": 114 }, "chunk_id": "train_shard_00002_114_0", "global_id": 12890 }, { "text": "Heavy metal pollutions in the soils are increasingly threatening the global crop and food production. Using plant associated bacteria to remediate heavy metal contamination is a promising approach. We have isolated a cadmium (Cd) resistant Enterococcus faecium strain CX 2-6 from a heavy metal contaminated farmland. We have shown that: (i) CX 2-6 can tolerate cadmium (Cd) with a slower growth rate; (ii) The CX 2-6 complete genome is fully assembled using PacBio long reads; (iii) Differential expression analysis found 47% of CX 2-6 genes are significantly affected by Cd treatment and form three gene groups with distinct expression profiles; (iv) Differentially expressed genes (DEGs) form physically linked gene clusters in the CX 2-6 genome, and one of the gene clusters corresponds to a prophage that is unique to CX 2-6 and is strongly activated when Cd concentration is higher; (v) A majority of DEGs responding to Cd treatment are present in the core genome; and (vi) 55 noncoding RNA genes are identified and 49 of them are DEGs responding to cadmium stress. Our pan-genome analysis and comparative RNA-seq data analysis has significantly improved our understanding of the metabolic reprogramming of E. faecium CX 2-6 under Cd stress.\n\nCadmium stress triggers significant metabolic reprogramming in Enterococcus faecium CX 2-6.", "token_count": 374, "char_count": 1360, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5933, "quality_score": 0.7967, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:36.229829", "source": { "split": "train_shard_00002", "doc_id": 115 }, "chunk_id": "train_shard_00002_115_0", "global_id": 12891 }, { "text": "The nucleocytoplasmic large DNA viruses (NCLDVs, phylum Nucleocytoviricota) infect vertebrates, invertebrates, algae, amoebae, and other unicellular organisms across supergroups of eukaryotes and in various ecosystems. The expanding collection of their genome sequences has revolutionized our view of virus genome size and coding capacity. Phylogenetic trees based on a few core genes are commonly used as a model to understand their evolution. However, the tree topology can differ between analyses, and the vast majority of encoded genes might not share a common evolutionary history. To explore the whole-genome variation and evolution of NCLDVs, we dissected their gene contents using clustering, network, and comparative analyses. Our updated core-gene tree served as a framework to classify NCLDVs into families and intrafamilial lineages, but networks of individual genomes and family pangenomes showed patterns of gene sharing that contradict with the tree topology, in particular at higher taxonomic levels. Clustering of NCLDV genomes revealed variable granularity and degrees of gene sharing within each family, which cannot be inferred from the tree. At the level of NCLDV families, a correlation exists between gene content variation, but not core-gene sequence divergence, and host supergroup diversity. In addition, there is significantly higher gene sharing between divergent viruses that infect similar host types. The identified shared genes would be a useful resource for further functional analyses of NCLDV-host interactions. Overall this study provides a comprehensive view of gene repertoire variation in NCLDVs at different taxonomic levels, as well as a novel approach to studying the extremely diverse giant virus genomes.\n\nUnraveling gene content variation across eukaryotic giant viruses based on network analyses and host associations.", "token_count": 424, "char_count": 1864, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6579, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:36.857118", "source": { "split": "train_shard_00002", "doc_id": 116 }, "chunk_id": "train_shard_00002_116_0", "global_id": 12892 }, { "text": "

Background

The microbial communities populating human and natural environments have been extensively characterized with shotgun metagenomics, which provides an in-depth representation of the microbial diversity within a sample. Microbes thriving in urban environments may be crucially important for human health, but have received less attention than those of other environments. Ongoing efforts started to target urban microbiomes at a large scale, but the most recent computational methods to profile these metagenomes have never been applied in this context. It is thus currently unclear whether such methods, that have proven successful at distinguishing even closely related strains in human microbiomes, are also effective in urban settings for tasks such as cultivation-free pathogen detection and microbial surveillance. Here, we aimed at a) testing the currently available metagenomic profiling tools on urban metagenomics; b) characterizing the organisms in urban environment at the resolution of single strain and c) discussing the biological insights that can be inferred from such methods.

Results

We applied three complementary methods on the 1614 metagenomes of the CAMDA 2017 challenge. With MetaMLST we identified 121 known sequence-types from 15 species of clinical relevance. For instance, we identified several Acinetobacter strains that were close to the nosocomial opportunistic pathogen A. nosocomialis. With StrainPhlAn, a generalized version of the MetaMLST approach, we inferred the phylogenetic structure of Pseudomonas stutzeri strains and suggested that the strain-level heterogeneity in environmental samples is higher than in the human microbiome. Finally, we also probed the functional potential of the different strains with PanPhlAn. We further showed that SNV-based and pangenome-based profiling provide complementary information that can be combined to investigate the evolutionary trajectories of microbes and to identify specific genetic determinants of virulence and antibiotic resistances within closely related strains.

Conclusion

We show that strain-level methods developed primarily for the analysis of human microbiomes can be effective for city-associated microbiomes. In fact, (opportunistic) pathogens can be tracked and monitored across many hundreds of urban metagenomes", "token_count": 518, "char_count": 2341, "word_count": 315, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:37.544657", "source": { "split": "train_shard_00002", "doc_id": 117 }, "chunk_id": "train_shard_00002_117_0", "global_id": 12893 }, { "text": "However, while more effort is needed to profile strains of currently uncharacterized species, this work poses the basis for high-resolution analyses of microbiomes sampled in city and mass transportation environments.

Reviewers

This article was reviewed by Alexandra Bettina Graf, Daniel Huson and Trevor Cickovski.\n\nProfiling microbial strains in urban environments using metagenomic sequencing data.", "token_count": 98, "char_count": 408, "word_count": 52, "semantic_coherence": 1, "information_density": 0.9231, "quality_score": 0.9615, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:37.938420", "source": { "split": "train_shard_00002", "doc_id": 117 }, "chunk_id": "train_shard_00002_117_1", "global_id": 12894 }, { "text": "Cell walls, representing 26%-32% of the cell dry weight, were prepared from several strains of the yeasts Kloeckera apiculata, Debaryomyces hansenii, Zygosaccharomyces bailii, Kluyveromyces marxianus and Saccharomyces cerevisiae. Extraction of the walls with potassium hydroxide at 4 degrees C, followed by saturation of the alkali-soluble extract with ammonium sulphate gave fractions of mannoprotein, alkali-soluble glucan and alkali-insoluble glucan. Chitin was associated with the alkali-insoluble glucan. The proportions of the different fractions within the walls varied with the species and strain. Mannoprotein comprised between 25% and 34% of the walls, the content of alkali-insoluble glucan ranged from 15% to 48%, and the content of alkali-soluble glucan ranged from 10% to 48%. There was significant variation in the physical appearance of the alkali-soluble glucans and the relative viscosity of suspensions of these glucans. The yeasts could represent novel sources of polysaccharides with industrial and medical applications.\n\nComposition of the cell walls of several yeast species.", "token_count": 324, "char_count": 1098, "word_count": 153, "semantic_coherence": 1, "information_density": 0.5948, "quality_score": 0.7974, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:38.530978", "source": { "split": "train_shard_00002", "doc_id": 118 }, "chunk_id": "train_shard_00002_118_0", "global_id": 12895 }, { "text": "A substance which was dyed blue by 4p-(nitrobenzyl)pyridine, that evidenced for its trichotecene nature, has been isolated in the crystalline form from conidia Dendrodochium toxicum Pidopl. et Bilai--roridine H producer. Thin-layer chromatography of the substance in three different systems, the well-known macrocyclic trichotecenes being used as standards, permitted it to be identified with verrucarine A. The substances possessed high biological activity with respect to the indicator test-culture Candida kefyr 900. No other compounds of trichotecene nature were found. Possible role of verrucarine A is discussed.\n\n[Verrucarin A from conidia of Dendrodochium toxicum Pidopl. et Bilai].", "token_count": 195, "char_count": 690, "word_count": 95, "semantic_coherence": 1, "information_density": 0.7789, "quality_score": 0.8895, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:39.028282", "source": { "split": "train_shard_00002", "doc_id": 119 }, "chunk_id": "train_shard_00002_119_0", "global_id": 12896 }, { "text": "Scheffersomyces stipitis and the closely related yeast Candida shehatae assimilated the L-amino acids glutamate, aspartate and proline as both carbon and nitrogen sole sources. We also found this rarely investigated ability in ascomycetous species such as Candida glabrata, C. reukaufii, C. utilis, Debaryomyces hansenii, Kluyveromyces lactis, K. marxianus, Candida albicans, L. elongisporus, Meyerozyma guilliermondii, C. maltosa, Pichia capsulata and Yarrowia lipolytica and in basidiomycetous species such as Rhodotorula rubra and Trichosporon beigelii. Glutamate was a very efficient carbon source for Sc. stipitis, which enabled a high biomass yield/mole, although the growth rate was lower when compared to growth on glucose medium. The cells secreted waste ammonium during growth on glutamate alone. In Sc. stipitis cultures grown in glucose medium containing glutamate as the nitrogen source the biomass yield was maximal, and ethanol concentration and specific ethanol formation rate were significantly higher than in glucose medium containing ammonium as the nitrogen source. Mainly C-assimilation of glutamate but also N-assimilation in glucose-containing medium correlated with enhanced activity of the NAD-dependent glutamate dehydrogenase 2 (GDH2). A Δgdh2 disruptant was unable to utilize glutamate as either a carbon or a nitrogen source; moreover, this disruptant was also unable to utilize aspartate as a carbon source. The mutation was complemented by retransformation of the GDH2 ORF into the Δgdh2 strain. The results show that Gdh2p plays a dual role in Sc. stipitis as both C- and N-catabolic enzyme, which indicates its role as an interface between the carbon and nitrogen metabolism of this yeast.", "token_count": 482, "char_count": 1722, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [ "GDH2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:39.679228", "source": { "split": "train_shard_00002", "doc_id": 120 }, "chunk_id": "train_shard_00002_120_0", "global_id": 12897 }, { "text": "C- and N-catabolic utilization of tricarboxylic acid cycle-related amino acids by Scheffersomyces stipitis and other yeasts.", "token_count": 39, "char_count": 124, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:40.036224", "source": { "split": "train_shard_00002", "doc_id": 120 }, "chunk_id": "train_shard_00002_120_1", "global_id": 12898 }, { "text": "The marine environment is the largest ecological habitat on Earth, albeit one of the least explored, particularly in terms of its microbial inhabitants. The marine fish gut is host to a diverse microbial community from which diverse bioactive molecules can be sourced. Due to the unique environmental pressures these microbial communities experience, the bioactive molecules they produce often evolve unique adaptations that give them diverse structures and activities, differentiating them from terrestrial homologues. Of particular interest, due to their structural and functional diversity, are the ribosomally-synthesized antimicrobial peptides (bacteriocins). With increasing pressure from emerging antibiotic-resistant disease and industrial demand for novel therapeutics, the marine fish gut microbiome represents a relatively untapped resource of novel bacteriocins that could prove beneficial to human health and aquaculture. This review presents an overview of the marine fish gut microbiome and explores its potential as a source of bacteriocins for human health with considerations for applications and future research in this area.\n\nThe Marine Fish Gut Microbiome as a Source of Novel Bacteriocins.", "token_count": 251, "char_count": 1211, "word_count": 168, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:40.523322", "source": { "split": "train_shard_00002", "doc_id": 121 }, "chunk_id": "train_shard_00002_121_0", "global_id": 12899 }, { "text": "In this study, the yeast strains were isolated from grapes by serial dilution technique to determine their alcohol-, sugar- and thermotolerance. 34 wild type yeast strains were isolated and alcohol-, sugar- and thermotolerance of these strains were determined. The maximum alcohol tolerance was found to be 9% (v/v) in yeast strain which is named Y2. Thermotolerance behavior of 6 strains were investigated. The strains were treated with UV light with intervals of 20, 30, 40 and 50 seconds. Selected resistant colonies were investigated for alcohol tolerance. It was found that alcohol tolerance increased from 9% (v/v) to 12% (v/v) on Y2 strain.\n\nIsolation of alcohol tolerant, osmotolerant and thermotolerant yeast strains and improvement of their alcohol tolerance by UV mutagenesis.", "token_count": 206, "char_count": 787, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6083, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:41.783553", "source": { "split": "train_shard_00002", "doc_id": 122 }, "chunk_id": "train_shard_00002_122_0", "global_id": 12900 }, { "text": "In August 2017, a cluster of four persons infected with genetically related strains of Shiga toxin-producing Escherichia coli (STEC) O157:H7 was identified. These strains possessed the Shiga toxin (stx) subtype stx2a, a toxin type known to be associated with severe clinical outcome. One person died after developing haemolytic uraemic syndrome. Interviews with cases revealed that three of the cases had been exposed to dogs fed on a raw meat-based diet (RMBD), specifically tripe. In two cases, the tripe had been purchased from the same supplier. Sampling and microbiological screening of raw pet food was undertaken and indicated the presence of STEC in the products. STEC was isolated from one sample of raw tripe but was different from the strain causing illness in humans. Nevertheless, the detection of STEC in the tripe provided evidence that raw pet food was a potential source of human STEC infection during this outbreak. This adds to the evidence of raw pet food as a risk factor for zoonotic transmission of gastrointestinal pathogens, which is widely accepted for Salmonella, Listeria and Campylobacter spp. Feeding RMBD to companion animals has recently increased in popularity due to the belief that they provide health benefits to animals. Although still rare, an increase in STEC cases reporting exposure to RMBDs was detected in 2017. There has also been an increased frequency of raw pet food incidents in 2017, suggesting an increasing trend in potential risk to humans from raw pet food. Recommendations to reduce the risk of infection included improved awareness of risk and promotion of good hygiene practices among the public when handling raw pet food.\n\nA cluster of Shiga Toxin-producing Escherichia coli O157:H7 highlights raw pet food as an emerging potential source of infection in humans.", "token_count": 436, "char_count": 1827, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5764, "quality_score": 0.7882, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:42.423213", "source": { "split": "train_shard_00002", "doc_id": 123 }, "chunk_id": "train_shard_00002_123_0", "global_id": 12901 }, { "text": "Rhizobium etli is a Gram-negative soil-dwelling alphaproteobacterium that carries out symbiotic biological nitrogen fixation in close association with legume hosts. R. etli strains exhibit high sequence divergence and are geographically structured, with a potentially dramatic influence on the outcome of symbiosis. Here, we present the genome sequence of R. etli CNPAF512, a Brazilian isolate from bean nodules. We anticipate that the availability of genome sequences of R. etli strains from distinctly different areas will provide valuable new insights into the geographic mosaic of the R. etli pangenome and the evolutionary dynamics that shape it.\n\nGenome sequence of Rhizobium etli CNPAF512, a nitrogen-fixing symbiont isolated from bean root nodules in Brazil.", "token_count": 195, "char_count": 766, "word_count": 110, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [ "CNPAF512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:42.869739", "source": { "split": "train_shard_00002", "doc_id": 124 }, "chunk_id": "train_shard_00002_124_0", "global_id": 12902 }, { "text": "Human infections with Brucella melitensis are occasionally reported in Sweden, despite the fact that the national flocks of sheep and goats are officially free from brucellosis. The aim of our study was to analyze 103 isolates of B. melitensis collected from patients in Sweden between 1994 and 2016 and determine their putative geographic origin using whole genome sequencing (WGS)-based tools. The majority of the strains were assigned to East Mediterranean and African lineages. Both in silico Multiple Loci VNTR (Variable Number of Tandem Repeats) Analysis (MLVA) and core genome Multilocus Sequence Typing (cgMLST) analyses identified countries of the Middle East as the most probable source of origin of the majority of the strains. Isolates collected from patients with travel history to Iraq or Syria were often associated with genotypes from Turkey, as the cgMLST profiles from these countries clustered together. Sixty strains were located within a distance of 20 core genes to related genotypes from the publicly available database, and for eighteen isolates, the closest genotype was different by more than 50 loci. Our study showed that WGS based tools are effective in tracing back the geographic origin of infection of patients with unknown travel status, provided that public sequences from the location of the source are available.\n\nWhole Genome Sequencing for Tracing Geographical Origin of Imported Cases of Human Brucellosis in Sweden.", "token_count": 361, "char_count": 1490, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6323, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:43.461499", "source": { "split": "train_shard_00002", "doc_id": 125 }, "chunk_id": "train_shard_00002_125_0", "global_id": 12903 }, { "text": "

Background

Oenococcus oeni is the bacterial species that drives malolactic fermentation in most wines. Several studies have described a high intraspecific diversity regarding carbohydrate degradation abilities but the link between the phenotypes and the genes and metabolic pathways has been poorly described.

Results

A collection of 41 strains whose genomic sequences were available and representative of the species genomic diversity was analyzed for growth on 18 carbohydrates relevant in wine. The most frequently used substrates (more than 75% of the strains) were glucose, trehalose, ribose, cellobiose, mannose and melibiose. Fructose and L-arabinose were used by about half the strains studied, sucrose, maltose, xylose, galactose and raffinose were used by less than 25% of the strains and lactose, L-sorbose, L-rhamnose, sorbitol and mannitol were not used by any of the studied strains. To identify genes and pathways associated with carbohydrate catabolic abilities, gene-trait matching and a careful analysis of gene mutations and putative complementation phenomena were performed.

Conclusions

For most consumed sugars, we were able to propose putatively associated metabolic pathways. Most associated genes belong to the core genome. O. oeni appears as a highly specialized species, ideally suited to fermented fruit juice and more specifically to wine for a subgroup of strains.\n\nCarbohydrate metabolism in Oenococcus oeni: a genomic insight.", "token_count": 393, "char_count": 1479, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6634, "quality_score": 0.8317, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:44.076774", "source": { "split": "train_shard_00002", "doc_id": 126 }, "chunk_id": "train_shard_00002_126_0", "global_id": 12904 }, { "text": "

Background

Escherichia coli bovine mastitis is a disease of significant economic importance in the dairy industry. Molecular characterization of mastitis-associated E. coli (MAEC) did not result in the identification of common traits. Nevertheless, a mammary pathogenic E. coli (MPEC) pathotype has been proposed suggesting virulence traits that differentiate MAEC from commensal E. coli. The present study was designed to investigate the MPEC pathotype hypothesis by comparing the genomes of MAEC and commensal bovine E. coli.

Results

We sequenced the genomes of eight E. coli isolated from bovine mastitis cases and six fecal commensal isolates from udder-healthy cows. We analyzed the phylogenetic history of bovine E. coli genomes by supplementing this strain panel with eleven bovine-associated E. coli from public databases. The majority of the isolates originate from phylogroups A and B1, but neither MAEC nor commensal strains could be unambiguously distinguished by phylogenetic lineage. The gene content of both MAEC and commensal strains is highly diverse and dominated by their phylogenetic background. Although individual strains carry some typical E. coli virulence-associated genes, no traits important for pathogenicity could be specifically attributed to MAEC. Instead, both commensal strains and MAEC have very few gene families enriched in either pathotype. Only the aerobactin siderophore gene cluster was enriched in commensal E. coli within our strain panel.

Conclusions

This is the first characterization of a phylogenetically diverse strain panel including several MAEC and commensal isolates. With our comparative genomics approach we could not confirm previous studies that argue for a positive selection of specific traits enabling MAEC to elicit bovine mastitis. Instead, MAEC are facultative and opportunistic pathogens recruited from the highly diverse bovine gastrointestinal microbiota. Virulence-associated genes implicated in mastitis are a by-product of commensalism with the primary function to enhance fitness in the bovine gastrointestinal tract", "token_count": 528, "char_count": 2106, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5586, "quality_score": 0.7793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:44.737371", "source": { "split": "train_shard_00002", "doc_id": 127 }, "chunk_id": "train_shard_00002_127_0", "global_id": 12905 }, { "text": "Therefore, we put the definition of the MPEC pathotype into question and suggest to designate corresponding isolates as MAEC.\n\nNo evidence for a bovine mastitis Escherichia coli pathotype.", "token_count": 48, "char_count": 188, "word_count": 28, "semantic_coherence": 1, "information_density": 0.9643, "quality_score": 0.9821, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:45.095041", "source": { "split": "train_shard_00002", "doc_id": 127 }, "chunk_id": "train_shard_00002_127_1", "global_id": 12906 }, { "text": "Efficient fluorescence energy transfer from aromatic residues to the pyridine moiety of the bound coenzyme (NAD) of UDP-glucose 4-epimerase from Kluyveromyces fragilis had been reported earlier (Mukherji, S., and Bhaduri, A. (1992) J. Biol. Chem. 267, 11709-11713). We have employed N-bromosuccinimide (NBS) to identify tryptophan as the exclusive aromatic donor in the energy transfer. The characteristic UV absorption spectrum associated with Trp oxidation is observed during NBS modification of two of the four Trp residues of native epimerase along with concomitant inactivation of the enzyme. Excellent correlation between the observed inactivation and abolition of fluorescence energy transfer to coenzyme from Trp in epimerase upon treatment with NBS implicates the involvement of the same two tryptophans in both catalytic activity and fluorescence energy transfer. SDS-polyacrylamide gel electrophoresis and fluorescence data preclude gross structural/conformational changes in epimerase due to NBS oxidation. The susceptible tryptophans do not reside at the substrate binding site as substrates and UMP fail to protect against NBS modification. However, failure of sodium borohydride to reduce the bound NAD in the NBS-inactivated epimerase suggests that the reactive tryptophans are close to the coenzyme. Tryptophan fluorescence lifetime values of 1.9 and 3.9 ns for the native and 3.5 ns for the NBS-modified epimerase, complemented by a linear Stern-Volmer plot (effective Stern-Volmer constant = 2.85 M-1) of acrylamide quenching, suggest that the two key tryptophans are buried close to an intrinsic quencher, presumably NAD.\n\nTwo tryptophans at the active site of UDP-glucose 4-epimerase from Kluyveromyces fragilis.", "token_count": 494, "char_count": 1733, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:45.738235", "source": { "split": "train_shard_00002", "doc_id": 128 }, "chunk_id": "train_shard_00002_128_0", "global_id": 12907 }, { "text": "Salmonella enterica serovar Typhimurium (S. Tm) is a major cause of gastrointestinal diseases worldwide. To date, options for prevention or curative therapy remain limited. The gut microbiota plays a protective role against enteric diseases, particularly in preventing establishment and proliferation of S. Tm. While most research has focused on microbiota-mediated pathogen exclusion during the later, inflammation-dominated stages of infection, little is known about how microbiota members mitigate S. Tm early gut colonization. To address this gap, we conducted 24 h in vivo competitive experiments using S. Tm and different commensal E. coli strains. We observed a significant reduction in pathogen load, which was strain-specific and particularly evident with E. coli 8178. To investigate the underlying molecular mechanisms, we performed an in vivo screen using a rationally designed S. Tm library-which includes a wide range of carbohydrate utilization mutants-both in the absence and presence of E. coli strains. Our findings revealed that E. coli 8178-mediated S. Tm competition was driven by the exploitation of galactose during the early stage of infection. Identifying galactose as a key metabolite in pathogen exclusion by gut microbiota members enhances our mechanistic understanding of microbiota-mediated protection and opens new avenues for developing microbiota- and dietary-based strategies to better control intestinal infections.\n\nStrain-specific galactose utilization by commensal E. coli mitigates Salmonella establishment in the gut.", "token_count": 375, "char_count": 1557, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6468, "quality_score": 0.8234, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:46.321355", "source": { "split": "train_shard_00002", "doc_id": 129 }, "chunk_id": "train_shard_00002_129_0", "global_id": 12908 }, { "text": "MLST (multi-locus sequence typing) is a classic technique for genotyping bacteria, widely applied for pathogen outbreak surveillance. Traditionally, MLST is based on identifying sequence types from a small number of housekeeping genes. With the increasing availability of whole-genome sequencing (WGS) data, MLST methods have evolved toward larger typing schemes, based on a few hundred genes (core genome MLST, cgMLST) to a few thousand genes (whole genome MLST, wgMLST). Such large-scale MLST schemes have been shown to provide a finer resolution and are increasingly used in various contexts such as hospital outbreaks or foodborne pathogen outbreaks. This methodological shift raises new computational challenges, especially given the large size of the schemes involved. Very few available MLST callers are currently capable of dealing with large MLST schemes. We introduce MentaLiST, a new MLST caller, based on a k -mer voting algorithm and written in the Julia language, specifically designed and implemented to handle large typing schemes. We test it on real and simulated data to show that MentaLiST is faster than any other available MLST caller while providing the same or better accuracy, and is capable of dealing with MLST scheme with up to thousands of genes while requiring limited computational resources. MentaLiST source code and easy installation instructions using a Conda package are available at https://github.com/WGS-TB/MentaLiST .\n\nMentaLiST – A fast MLST caller for large MLST schemes", "token_count": 332, "char_count": 1511, "word_count": 226, "semantic_coherence": 1, "information_density": 0.6416, "quality_score": 0.8208, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:46.885282", "source": { "split": "train_shard_00002", "doc_id": 130 }, "chunk_id": "train_shard_00002_130_0", "global_id": 12909 }, { "text": "Xylose-assimilating yeasts with tolerance to both fermentation inhibitors (such as weak organic acids) and high temperature are required for cost-effective simultaneous saccharification and cofermentation (SSCF) of lignocellulosic materials. Here, we demonstrate the construction of a novel xylose-utilizing Saccharomyces cerevisiae strain with improved fermentation ability under heat and acid co-stress using the drug resistance marker-aided genome shuffling technique. The mutagenized genome pools derived from xylose-utilizing diploid yeasts with thermotolerance or acid tolerance were shuffled by sporulation and mating. The shuffled strains were then subjected to screening under co-stress conditions of heat and acids, and the hybrid strain Hyb-8 was isolated. The hybrid strain displayed enhanced xylose fermentation ability in comparison to both parental strains under co-stress conditions of heat and acids. Hyb-8 consumed 33.1 ± 0.6 g/L xylose and produced 11.1 ± 0.4 g/L ethanol after 72 h of fermentation at 38°C with 20 mM acetic acid and 15 mM formic acid. We also performed transcriptomic analysis of the hybrid strain and its parental strains to screen for key genes for multiple stress tolerances. We found that 13 genes, including 5 associated with cellular transition metal ion homeostasis, were significantly upregulated in Hyb-8 compared to levels in both parental strains under co-stress conditions. The hybrid strain Hyb-8 has strong potential for cost-effective SSCF of lignocellulosic materials. Moreover, the transcriptome data gathered in this study will be useful for understanding the mechanisms of multiple tolerance to high temperature and acids in yeast and facilitate the development of robust yeast strains for SSCF.", "token_count": 469, "char_count": 1758, "word_count": 250, "semantic_coherence": 1, "information_density": 0.596, "quality_score": 0.798, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:47.530110", "source": { "split": "train_shard_00002", "doc_id": 131 }, "chunk_id": "train_shard_00002_131_0", "global_id": 12910 }, { "text": "Improvement of Xylose Fermentation Ability under Heat and Acid Co-Stress in Saccharomyces cerevisiae Using Genome Shuffling Technique.", "token_count": 45, "char_count": 141, "word_count": 17, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:47.883962", "source": { "split": "train_shard_00002", "doc_id": 131 }, "chunk_id": "train_shard_00002_131_1", "global_id": 12911 }, { "text": "The gut environment and gut microbiome dysbiosis have been demonstrated to significantly influence a range of disorders in humans, including obesity, diabetes, rheumatoid arthritis, and multiple sclerosis (MS). MS is an autoimmune disease affecting the central nervous system (CNS). The etiology of MS is not clear, and it should involve both genetic and extrinsic factors. The extrinsic factors responsible for predisposition to MS remain elusive. Recent studies on MS and its animal model, experimental autoimmune encephalomyelitis (EAE), have found that gastrointestinal microbiota may play an important role in the pathogenesis of MS/EAE. Thus, gut microbiome adjustment may be a future direction of treatment in MS. In this review, we discuss the characteristics of the gut microbiota, the connection between the brain and the gut, and the changes in gut microbiota in MS/EAE, and we explore the possibility of applying microbiota therapies in patients with MS.\n\nGut Microbiota in Multiple Sclerosis and Experimental Autoimmune Encephalomyelitis: Current Applications and Future Perspectives.", "token_count": 263, "char_count": 1097, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6289, "quality_score": 0.8145, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:48.430103", "source": { "split": "train_shard_00002", "doc_id": 132 }, "chunk_id": "train_shard_00002_132_0", "global_id": 12912 }, { "text": "Candida albicans survives as a commensal fungus in the gastrointestinal tract, and that its excessive growth causes infections in immunosuppressed individuals is widely accepted. However, any mutualistic relationship that may exist between C. albicans and the host remains undetermined. Here, we showed that a long-term feeding of C. albicans does not cause any noticeable infections in the mouse model. Our 16S and 18S ribosomal DNA (rDNA) sequence analyses suggested that C. albicans colonizes in the gut and modulates microbiome dynamics, which in turn mitigates high-fat-diet-induced uncontrolled body weight gain and metabolic hormonal imbalances. Interestingly, adding C. albicans to a nonobesogenic diet stimulated the appetite-regulated hormones and helped the mice maintain a healthy body weight. In concert, our results suggest a mutualism between C. albicans and the host, contrary to the notion that C. albicans is always an adversary and indicating it can instead be a bona fide admirable companion of the host. Finally, we discuss its potential translational implication as a probiotic, especially in obese people or people dependent on high-fat calorie intakes to manage obesity associated complications. IMPORTANCE Candida albicans is mostly considered an opportunistic pathogen that causes fetal systemic infections. However, this study demonstrates that in its commensal state, it maintains a long-term mutualistic relationship with the host and regulates microbial dynamics in the gut and host physiology. Thus, we concluded that C. albicans is not always an adversary but rather can be a bona fide admirable companion of the host. More importantly, as several genomic knockout strains of C. albicans were shown to be avirulent, such candidate strains may be explored further as preferable probiotic isolates to control obesity.\n\nCommensal Fungus Candida albicans Maintains a Long-Term Mutualistic Relationship with the Host To Modulate Gut Microbiota and Metabolism.", "token_count": 495, "char_count": 1993, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5724, "quality_score": 0.7862, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:49.078708", "source": { "split": "train_shard_00002", "doc_id": 133 }, "chunk_id": "train_shard_00002_133_0", "global_id": 12913 }, { "text": "

Background

A. baumannii is a common nosocomial pathogen known for its high transmission potential. A high rate of carbapenem-susceptible Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB)-complex in clinical specimens led to the implementation of a pathogen-based surveillance on a 32-bed surgical intensive care unit (SICU) in a German tertiary care centre.

Methods

Between April 2017 and March 2018, ACB-complex isolates with an epidemiological link to the SICU were further assessed. Identification to the species level was carried out using a multiplex PCR targeting the gyrB gene, followed by RAPD, PFGE (ApaI) and whole genome sequencing (WGS, core genome MLST, SeqSphere+ software, Ridom). Additional infection prevention and control (IPC) measures were introduced as follows: epidemiological investigations, hand hygiene training, additional terminal cleaning and disinfection incl. UV-light, screening for carbapenem-susceptible A. baumannii and environmental sampling. Hospital-acquired infections were classified according to the CDC definitions.

Results

Fourty four patients were colonized/infected with one or two (different) carbapenem-susceptible ACB-complex isolates. Fourty three out of 48 isolates were classified as hospital-acquired (detection on or after 3rd day of admission). Nearly all isolates were identified as A. baumannii, only four as A. pittii. Twelve patients developed A. baumannii infections. Genotyping revealed two pulsotype clusters, which were confirmed to be cgMLST clonal cluster type 1770 (n = 8 patients) and type 1769 (n = 12 patients) by WGS", "token_count": 523, "char_count": 1677, "word_count": 213, "semantic_coherence": 1, "information_density": 0.7089, "quality_score": 0.8545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:49.761075", "source": { "split": "train_shard_00002", "doc_id": 134 }, "chunk_id": "train_shard_00002_134_0", "global_id": 12914 }, { "text": "All other isolates were distinct from each other. Nearly all transmission events of the two clonal clusters were confirmed by conventional epidemiology. Transmissions stopped after a period of several months. Environmental sampling revealed a relevant dissemination of A. baumannii, but only a few isolates corresponded to clinical strains. Introduction of the additional screening revealed a significantly earlier detection of carbapenem-susceptible A. baumannii during hospitalization.

Conclusions

A molecular and infection surveillance of ACB-complex based on identification to the species level, classic epidemiology and genotyping revealed simultaneously occurring independent transmission events and clusters of hospital-acquired A. baumannii. This underlines the importance of such an extensive surveillance methodology in IPC programmes also for carbapenem-susceptible A. baumannii.\n\nOne-year molecular surveillance of carbapenem-susceptible A. baumannii on a German intensive care unit: diversity or clonality.", "token_count": 256, "char_count": 1061, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:50.323398", "source": { "split": "train_shard_00002", "doc_id": 134 }, "chunk_id": "train_shard_00002_134_1", "global_id": 12915 }, { "text": "Listeria monocytogenes is one of the major foodborne pathogens. Isolates of PCR-serogroups IIb (n = 17) and IVb (n = 31) recovered from food (n = 33) and food processing environment (n = 15) in Poland were characterized using whole genome sequencing. Most isolates belonged to Multi-Locus Sequence Type (MLST) ST2 (31.3%) and ST5 (22.9%). Core genome MLST (cgMLST) analysis classified isolates into seven sublineages (SL) and 25 different cgMLST types (CT). Consistent with the MLST results, most sublineages were SL2 and SL5. Eleven isolates harbored aacA4 encoding resistance to aminoglycosides, three isolates harbored emrC (n = 3) and one brcABC (n = 1) encoding tolerance to benzalkonium chloride. Isolates belonging to SL5 CT2323 carried a so far unreported inlB allele with a deletion of 141 nucleotides encoding the β-repeat sheet and partially the GW1 domain of InlB. Comparison with publicly available genome sequences from L. monocytogenes isolated from human listeriosis cases in Poland from 2004 to 2013 revealed five common CTs, suggesting a possible epidemiological link with these strains. The present study contributes to characterize the diversity of L. monocytogenes in ready-to-eat (RTE) meat and meat processing environments in Poland and unravels previously unnoticed links with clinical cases in Europe.\n\nGenomic Characterization of Listeria monocytogenes Isolated From Ready-to-Eat Meat and Meat Processing Environments in Poland.", "token_count": 513, "char_count": 1552, "word_count": 216, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [ "ST2", "CT2323", "SL5", "ST5", "GW1", "SL2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:00:51.036295", "source": { "split": "train_shard_00002", "doc_id": 135 }, "chunk_id": "train_shard_00002_135_0", "global_id": 12916 }, { "text": "

Importance

Enterococcus faecalis causes life-threatening invasive hospital- and community-associated infections that are usually associated with multidrug resistance globally. Although E. faecalis infections cause opportunistic infections typically associated with antibiotic use, immunocompromised immune status, and other factors, they also possess an arsenal of virulence factors crucial for their pathogenicity. Despite this, the relative contribution of these virulence factors and other genetic changes to the pathogenicity of E. faecalis strains remain poorly understood. Here, we investigated whether specific genomic changes in the genome of E. faecalis isolates influence its pathogenicity-infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection and intestinal colonization. Our findings indicate that E. faecalis genetics partially influence the infection of hospitalized and nonhospitalized individuals and the propensity to cause extraintestinal infection, possibly due to gut-to-bloodstream translocation, highlighting the potential substantial role of host and environmental factors, including gut microbiota, on the opportunistic pathogenic lifestyle of this bacterium.\n\nThe population-level impact of Enterococcus faecalis genetics on intestinal colonization and extraintestinal infection.", "token_count": 331, "char_count": 1412, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6341, "quality_score": 0.8171, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:51.614066", "source": { "split": "train_shard_00002", "doc_id": 136 }, "chunk_id": "train_shard_00002_136_0", "global_id": 12917 }, { "text": "The yeasts present in Gouda cheese during processing were monitored in a single cheese factory during a 32 day ripening period. Despite the predominance of lactic acid bacteria during Gouda making, yeasts played a significant role in the ripening process in reaching counts as high as 10(5) cfu g(-1) at the later stages of ripening. The increase in the number of yeasts corresponded with the depletion in lactose content and the simultaneous stabilization of lactic acid bacteria numbers. The sources of yeast contamination which may lead to contamination of the curd were also determined. The brine and equipment surfaces were responsible for the highest yield of contaminating yeasts. A diverse variety of 23 yeast species representing 13 genera were present in the factory environment, during processing and ripening. Samples were taken at critical control points in the manufacturing process and analysed after incubation at 25 degrees C for 96 h. Although a broad spectrum of yeasts were found in Gouda cheese, Debaryomyces hansenii was the most abundant yeast isolated. Other species encountered were Saccharomyces cerevisiae and Yarrowia lipolytica, Kluyveromyces marxianus, Torulaspora delbrueckii, Rhodotorula glutinis, Cryptococcus albidus and Candida catenulata.\n\nYeast profile in Gouda cheese during processing and ripening.", "token_count": 331, "char_count": 1337, "word_count": 198, "semantic_coherence": 1, "information_density": 0.601, "quality_score": 0.8005, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:52.185549", "source": { "split": "train_shard_00002", "doc_id": 137 }, "chunk_id": "train_shard_00002_137_0", "global_id": 12918 }, { "text": "In this work, the effect of the addition of different concentrations of Tween-80 and three different zeolite-like products on enzymatic hydrolysis, ethanol fermentation, and simultaneous saccharification and fermentation (SSF) process has been investigated. The ability of these products to enhance the effectiveness of the SSF process to ethanol of steam-exploded poplar biomass using the thermotolerant strain Kluyveromyces marxianus EMS-26 has been tested. Tween-80 (0.4 g/L) increased enzymatic hydrolysis yield by 20% when compared to results obtained in hydrolysis in absence of the additive. Zeolite-like products (ZESEP-56 and ZECER-56) (2.5 g/L) improved rates of conversion and ethanol yields in the fermentation of liquid fraction recovered from steam-exploded poplar. The periods required for the completion of fermentation were approx 10 h in the presence of zeolite-like products and 24 h in the absence of additives. The probable mode of action is through lowered levels of inhibitory substances because of adsorption by the additive.\n\nEffect of surfactants and zeolites on simultaneous saccharification and fermentation of steam-exploded poplar biomass to ethanol.", "token_count": 311, "char_count": 1180, "word_count": 167, "semantic_coherence": 1, "information_density": 0.5569, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:52.759372", "source": { "split": "train_shard_00002", "doc_id": 138 }, "chunk_id": "train_shard_00002_138_0", "global_id": 12919 }, { "text": "Since the isolation of the first giant virus, the Mimivirus, by T.J. Rowbotham in a cooling tower in Bradford, UK, and after its characterisation by our group in 2003, we have continued to develop novel strategies to isolate additional strains. By first focusing on cooling towers using our original time-consuming procedure, we were able to isolate a new lineage of giant virus called Marseillevirus and a new Mimivirus strain called Mamavirus. In the following years, we have accumulated the world's largest unique collection of giant viruses by improving the use of antibiotic combinations to avoid bacterial contamination of amoeba, developing strategies of preliminary screening of samples by molecular methods, and using a high-throughput isolation method developed by our group. Based on the inoculation of nearly 7,000 samples, our collection currently contains 43 strains of Mimiviridae (14 in lineage A, 6 in lineage B, and 23 in lineage C) and 17 strains of Marseilleviridae isolated from various environments, including 3 of human origin. This study details the procedures used to build this collection and paves the way for the high-throughput isolation of new isolates to improve the record of giant virus distribution in the environment and the determination of their pangenome.\n\nA decade of improvements in Mimiviridae and Marseilleviridae isolation from amoeba.", "token_count": 328, "char_count": 1378, "word_count": 211, "semantic_coherence": 1, "information_density": 0.5829, "quality_score": 0.7915, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:53.333398", "source": { "split": "train_shard_00002", "doc_id": 139 }, "chunk_id": "train_shard_00002_139_0", "global_id": 12920 }, { "text": "A survey was made to detect the sensitivity of 12 yeast genera to T-2 toxin. Seventy-five yeasts isolated from various sources were tested for their susceptibility to T-2 toxin. The MIC of T-2 for these yeasts varied from 1.0 to greater than 8.0 micrograms/ml. Of the yeasts studied, Kluyveromyces fragilis showed the greatest sensitivity, which ranged between 0.5 and 2.5 micrograms of T-2 toxin per ml of culture medium. The roles of incubation temperature, size of the inoculum, and incubation time on the MICs were determined. The results suggest that in comparison with other yeasts, K. fragilis is very sensitive to T-2 toxin.\n\nSurvey of sensitivity of twelve yeast genera toward T-2 toxin.", "token_count": 200, "char_count": 696, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:53.793191", "source": { "split": "train_shard_00002", "doc_id": 140 }, "chunk_id": "train_shard_00002_140_0", "global_id": 12921 }, { "text": "Multidrug-resistant Enterobacterales, including carbapenemase producers, are currently spreading in health care facilities and the community. The Bichat Claude Bernard hospital in Paris faced a prolonged NDM-producing Enterobacterales (NDM-CPE) outbreak. Whole-genome sequencing (WGS) was performed on all isolated NDM-CPE to evaluate its benefits for outbreak surveillance and comprehension. All NDM-CPE isolates collected during the outbreak period (August 2016 to January 2018) were sequenced using the Illumina NextSeq platform. Gene content and core genomes were compared. Genomics results underwent epidemiological analysis which classified NDM-CPE cases as imported (positive sample during the 48 h after admission), hospital acquired, or uncertain. Over the epidemic period, 61 patients were colonized or infected with 81 distinct NDM-CPE isolates. Klebsiella pneumoniae was the most common species (n = 52, 64%), followed by Escherichia coli (13.5%) and other species (22.5%). In all, 43/52 (83%) K. pneumoniae isolates were clonal (≤18 single nucleotide polymorphisms [SNPs] except for three isolates) and belonged to ST307. The IncFIIK [K2:A-/B-] plasmid carrying blaNDM-1 present in all ST307 K. pneumoniae isolates was also detected in 18 other NDM-CPE isolates. Additionally, eight clonal ST144 Klebsiella oxytoca (≤18 SNPs) isolates lacking the epidemic plasmid were observed. The WGS analyses confirmed the acquired and imported cases except for two patients and resolved uncertain cases, which all turned out to be hospital acquisitions. WGS coupled with epidemiological analysis unraveled three epidemic phenomena: mainly the spread of a clonal ST307 K", "token_count": 503, "char_count": 1709, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [ "ST144", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:54.462658", "source": { "split": "train_shard_00002", "doc_id": 141 }, "chunk_id": "train_shard_00002_141_0", "global_id": 12922 }, { "text": "pneumoniae strain and its conjugative plasmid carrying blaNDM-1 but also the unexpected clonal spread of an ST144 K. oxytoca strain. IMPORTANCE Carbapenemase-producing Enterobacterales (CPE) can spread and cause outbreaks in health care facilities, resulting in increased lengths of stay and morbidity. Control of outbreaks requires epidemiological surveillance, usually based on microbiological screening and patient follow-up. These data are sometimes insufficient to identify the routes of dissemination. There is therefore a need for more accurate tools such as whole-genome sequencing (WGS), which allows comparison of isolates but also plasmids carrying resistance with a high definition. In this work, we retrospectively sequenced the genomes of all NDM-producing Enterobacterales isolated during a prolonged NDM outbreak in our hospital. We demonstrated the value of combining WGS with epidemiological data that unveiled the multiple mechanisms of dissemination involved in the outbreak and confirmed transmission cases. This work reinforces the potential of WGS in outbreak surveillance and suggests that it could improve outbreak control if used in real time by confirming transmission cases more rapidly.\n\nSimultaneous Hospital Outbreaks of New Delhi Metallo-β-Lactamase-Producing Enterobacterales Unraveled Using Whole-Genome Sequencing.", "token_count": 339, "char_count": 1395, "word_count": 181, "semantic_coherence": 1, "information_density": 0.7238, "quality_score": 0.8619, "entities": { "genes": [ "ST144" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:55.033827", "source": { "split": "train_shard_00002", "doc_id": 141 }, "chunk_id": "train_shard_00002_141_1", "global_id": 12923 }, { "text": "Permeation of oxygen through polystyrene packaging is a factor in the growth of yeasts in natural yoghurt. Diffusion of oxygen through the packaging material can permit the growth of non-fermentative yeasts in yoghurt stored at refrigeration temperatures. Yarrowia lipolytica, a non-fermentative yeasts which does not utilize lactose was isolated from yoghurt. The growth in natural yoghurt of Yarrowia lipolytica and the lactose-fermenting yeast Kluyveromyces marxianus was investigated. Both yeasts grew in yoghurt with reduced fat content. Storage of yoghurt in an anaerobic atmosphere eliminated growth of Yarrowia lipolytica but permitted fermentative growth of Kluyveromyces marxianus.\n\nGrowth of fermentative and non-fermentative yeasts in natural yoghurt, stored in polystyrene cartons.", "token_count": 218, "char_count": 794, "word_count": 108, "semantic_coherence": 1, "information_density": 0.5463, "quality_score": 0.7731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:55.497908", "source": { "split": "train_shard_00002", "doc_id": 142 }, "chunk_id": "train_shard_00002_142_0", "global_id": 12924 }, { "text": "The major global pathogen Clostridium difficile (recently renamed Clostridioides difficile) has large genetic diversity including multiple mobile genetic elements. In this study, whole genome sequencing of 86 strains from the poorly characterised clade 3, predominantly PCR ribotype (RT)023, of C. difficile revealed distinctive surface architecture characteristics and a large mobile genetic island. These strains have a unique sortase substrate phenotype compared with well-characterised strains of C. difficile, and loss of the phage protection protein CwpV. A large genetic insertion (023_CTnT) comprised of three smaller elements (023_CTn1-3) is present in 80/86 strains analysed in this study, with genes common among other bacterial strains in the gut microbiome. Novel cargo regions of 023_CTnT include genes encoding a sortase, putative sortase substrates, lantibiotic ABC transporters and a putative siderophore biosynthetic cluster. We demonstrate the excision of 023_CTnT and sub-elements 023_CTn2 and 023_CTn3 from the genome of RT023 reference strain CD305 and the transfer of 023_CTn3 to a non-toxigenic C. difficile strain, which may have implications for the use of non-toxigenic C. difficile strains as live attenuated vaccines. Finally, we show that the genes within the island are expressed in a regulated manner in C. difficile RT023 strains conferring a distinct \"niche adaptation\".\n\nClostridium difficile clade 3 (RT023) have a modified cell surface and contain a large transposable island with novel cargo.", "token_count": 426, "char_count": 1530, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6239, "quality_score": 0.8119, "entities": { "genes": [ "RT023", "CD305" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:56.127278", "source": { "split": "train_shard_00002", "doc_id": 143 }, "chunk_id": "train_shard_00002_143_0", "global_id": 12925 }, { "text": "Nontyphoidal salmonellae (NTS) are a leading cause of invasive disease in young children in sub-Saharan Africa. We used suppression subtractive hybridization (SSH) to identify 41 sequences within the accessory genome of an invasive strain of Salmonella Heidelberg from Malawi. PCR assays and database searches, used to determine the distribution of 14 SSH sequences among a panel of African and UK NTS isolates and published genomes, indicated that two were specific for S. Heidelberg. However, we found no evidence for major differences in the accessory genome content between African invasive and gastrointestinal isolates of S. Heidelberg. Six of the SSH sequences were within fimbrial operons. The tcf operon, associated with the host specificity of Salmonella Typhi, and the stk operon, reported previously in Salmonella Paratyphi, were both present in either all (tcf) or most (stk) isolates of S. Heidelberg, but had restricted distributions among the other serovars tested. Reverse transcription PCR analysis of seven SSH sequences indicated variable expression of the stk operon among isolates of S. Heidelberg. Three of the seven targeted genes were not expressed in a UK veterinary isolate of S. Heidelberg, suggesting that although genome content per se may not explain the different pathogenicity of the invasive isolates, it is possible that variations in gene expression may play a role.\n\nIdentification and distribution of accessory genome DNA sequences from an invasive African isolate of Salmonella Heidelberg.", "token_count": 363, "char_count": 1528, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5721, "quality_score": 0.786, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:56.709078", "source": { "split": "train_shard_00002", "doc_id": 144 }, "chunk_id": "train_shard_00002_144_0", "global_id": 12926 }, { "text": "

Background

Phage ZZ1, which efficiently infects pathogenic Acinetobacter baumannii strains, is the fifth completely sequenced T4-like Acinetobacter phage to date. To gain a better understanding of the genetic characteristics of ZZ1, bioinformatics and comparative genomic analyses of the T4 phages were performed.

Results

The 166,687-bp double-stranded DNA genome of ZZ1 has the lowest GC content (34.4%) of the sequenced T4-like Acinetobacter phages. A total of 256 protein-coding genes and 8 tRNA genes were predicted. Forty-three percent of the predicted ZZ1 proteins share up to 73% amino acid identity with T4 proteins, and the homologous genes generally retained the same order and transcriptional direction. Beyond the conserved structural and DNA replication modules, T4 and ZZ1 have diverged substantially by the acquisition and deletion of large blocks of unrelated genes, especially in the first halves of their genomes. In addition, ZZ1 and the four other T4-like Acinetobacter phage genomes (Acj9, Acj61, 133, and Ac42) share a well-organised and highly conserved core genome, particularly in the regions encoding DNA replication and virion structural proteins. Of the ZZ1 proteins, 70, 64, 61, and 56% share up to 86, 85, 81, and 83% amino acid identity with Acj9, Acj61, 133, and Ac42 proteins, respectively. ZZ1 has a different number and types of tRNAs than the other 4 Acinetobacter phages, although some of the ZZ1-encoded tRNAs share high sequence similarity with the tRNAs from these phages. Over half of ZZ1-encoded tRNAs (5 out of 8) are related to optimal codon usage for ZZ1 proteins", "token_count": 489, "char_count": 1623, "word_count": 245, "semantic_coherence": 1, "information_density": 0.5959, "quality_score": 0.798, "entities": { "genes": [ "ZZ1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:57.361830", "source": { "split": "train_shard_00002", "doc_id": 145 }, "chunk_id": "train_shard_00002_145_0", "global_id": 12927 }, { "text": "However, this correlation was not present in any of the other 4 Acinetobacter phages.

Conclusions

The comparative genomic analysis of these phages provided some new insights into the evolution and diversity of Acinetobacter phages, which might elucidate the evolutionary origin and host-specific adaptation of these phages.\n\nGenome organisation of the Acinetobacter lytic phage ZZ1 and comparison with other T4-like Acinetobacter phages.", "token_count": 112, "char_count": 444, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7458, "quality_score": 0.8729, "entities": { "genes": [ "ZZ1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:57.744173", "source": { "split": "train_shard_00002", "doc_id": 145 }, "chunk_id": "train_shard_00002_145_1", "global_id": 12928 }, { "text": "The current invention relates to the field of detection and identification of clinically important fungi. More particularly, the present invention relates to species specific probes originating from the Internal Transcribed Spacer (ITS) region of rDNA for the detection of fungal species such as Candida albicans, Candida parapsilosis, Candida tropicalis, Candida kefyr, Candida krusei, Candida glabrata, Candida dubliniensis, Aspergillus flavus, Aspergillus versicolor, Aspergillus nidulans, Aspergillus fumigatus, Cryptococcus neoformans and Pneumocystis carinii in clinical samples, and methods using said probes.\n\nNUCLEIC ACID PROBES AND METHODS FOR DETECTING CLINICALLY IMPORTANT FUNGAL PATHOGENS", "token_count": 206, "char_count": 701, "word_count": 89, "semantic_coherence": 1, "information_density": 0.6629, "quality_score": 0.8315, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:58.223924", "source": { "split": "train_shard_00002", "doc_id": 146 }, "chunk_id": "train_shard_00002_146_0", "global_id": 12929 }, { "text": "Exophiala spinifera, a capsule-producing black yeast, is overrepresented as agent of disseminated infection in humans with inherited dysfunction of the CARD9 gene. In a review of published caspase recruitment domain-containing protein 9 (CARD9) deficiency cases, black fungi were linked to mutations other than those prevalent in yeast and dermatophyte cases, and were found to respond to a larger panel of cytokines. Here, we sequenced and annotated the genomes of BMU 08022 from a patient with CARD9 deficiency and two environmental strains, BMU 00051 and BMU 00047. We performed genomic and transcriptomic analysis for these isolates including published black yeasts genomes, using a combination of long-read (PACBIO) and short-read (Illumina) sequencing technologies with a hybrid assembly strategy. We identified the virulence factors, fitness, and the major genetic and gene expression differences between the strains with RNAseq technology. Genome assembly reached sub-chromosome level with between 12,043 and 12,130 predicted genes. The number of indels identified in the clinical strain was higher than observed in environmental strains. We identify a relatively large core genome of 9,887 genes. Moreover, substantial syntenic rearrangements of scaffolds I and III in the CARD9-related isolate were detected. Seventeen gene clusters were involved in the production of secondary metabolites. PKS-cluster 17 was consistently found to be absent in the clinical strain. Comparative transcriptome analysis demonstrated that 16 single-copy genes were significantly differentially expressed upon incubation in brain-heart infusion broth vs. Sabouraud glucose broth. Most of the single-copy genes upregulated with Brain Heart Infusion (BHI) were transporters. There were 48 unique genes differentially expressed exclusively to the clinical strain in two different media, including genes from various metabolic processes and transcriptional regulation", "token_count": 491, "char_count": 1973, "word_count": 272, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "CARD9" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:58.875616", "source": { "split": "train_shard_00002", "doc_id": 147 }, "chunk_id": "train_shard_00002_147_0", "global_id": 12930 }, { "text": "Up-regulated genes in the clinical strain with Gene Ontology (GO) enrichment are mainly involved in transmembrane transport, biosynthetic process and metabolic process. This study has provided novel insights into understanding of strain-differences in intrinsic virulence of the species and indicated that intraspecific variability may be related to habitat choice. This indicates that strains of E. spinifera are differentially prone to cause infection in susceptible patient populations, and provides clues for future studies exploring the mechanisms of pathogenic and adaptive strategies of black yeasts in immunodeficient patients.\n\nComparative Analysis of Clinical and Environmental Strains of Exophiala spinifera by Long-Reads Sequencing and RNAseq Reveal Adaptive Strategies.", "token_count": 187, "char_count": 796, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7596, "quality_score": 0.8798, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:59.319832", "source": { "split": "train_shard_00002", "doc_id": 147 }, "chunk_id": "train_shard_00002_147_1", "global_id": 12931 }, { "text": "

Motivation

Pangenome arrays contain DNA oligomers targeting several sequenced reference genomes from the same species. In microbiology, these can be employed to investigate the often high genetic variability within a species by comparative genome hybridization (CGH). The biological interpretation of pangenome CGH data depends on the ability to compare strains at a functional level, particularly by comparing the presence or absence of orthologous genes. Due to the high genetic variability, available genotype-calling algorithms can not be applied to pangenome CGH data.

Results

We have developed the algorithm PanCGH that incorporates orthology information about genes to predict the presence or absence of orthologous genes in a query organism using CGH arrays that target the genomes of sequenced representatives of a group of microorganisms. PanCGH was tested and applied in the analysis of genetic diversity among 39 Lactococcus lactis strains from three different subspecies (lactis.cremoris, hordniae) and isolated from two different niches (dairy and plant). Clustering of these strains using the presence/absence data of gene orthologs revealed a clear separation between different subspecies and reflected the niche of the strains.\n\nPanCGH: a genotype-calling algorithm for pangenome CGH data.", "token_count": 313, "char_count": 1321, "word_count": 183, "semantic_coherence": 1, "information_density": 0.623, "quality_score": 0.8115, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:00:59.873556", "source": { "split": "train_shard_00002", "doc_id": 148 }, "chunk_id": "train_shard_00002_148_0", "global_id": 12932 }, { "text": "Biosensors for the determination of glucose, sucrose and lactose were based on a Clark-type oxygen electrode covered with a membrane containing microbial cells. The glucose-sensing membrane was prepared with intact cells of Gluconobacter oxydans immobilized in gelatin cross-linked with glutardialdehyde. The disaccharide-sensing membranes were prepared by co-immobilization of G. oxydans with cells of Saccharomyces cerevisiae containing invertase for sucrose determination and with permeabilized cells of Kluyveromyces marxianus containing beta-galactosidase for lactose determination. The strain of G. oxydans that we used was able to oxidize both anomers of glucose at the same rate; there was therefore no need for mutarotase co-immobilization in disaccharide-sensing membranes. The sensitivity of glucose sensor was 50 nA/mM, the range of the calibration curve was 0-0.8 mM, the response time was 2 min, and the response after 1 week of storage was 62% of the initial response. The parameters of the disaccharide sensors were similar: linear range of calibration curve up to 4 mM, response time 5 min. The activities of the sensors after 1 week of storage at ambient temperature were in the range 50-65% of the initial activity.\n\nMicrobial cell-based biosensor for sensing glucose, sucrose or lactose.", "token_count": 357, "char_count": 1307, "word_count": 192, "semantic_coherence": 1, "information_density": 0.5469, "quality_score": 0.7734, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:00.444766", "source": { "split": "train_shard_00002", "doc_id": 149 }, "chunk_id": "train_shard_00002_149_0", "global_id": 12933 }, { "text": "Metagenome shotgun sequence projects offer the potential for large scale biogeographic analysis of microbial species. In this project we developed a method for detecting 33 common subtypes of the pathogenic bacterium Staphylococcus aureus. We used a binomial mixture model implemented in the binstrain software and the coverage counts at > 100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of each subtype in metagenome samples. Using this pipeline we were able to obtain > 87% sensitivity and > 94% specificity when testing on low genome coverage samples of diverse S. aureus strains (0.025X). We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S. aureus at genome coverage > 0.025. In both projects, CC8 and CC30 were the most common S. aureus subtypes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are risk factors for S. aureus but there was limited power to find factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city. We argue that pathogen detection in metagenome samples requires the use of subtypes based on whole species population genomic analysis rather than using ad hoc collections of reference strains.\n\nThe single-species metagenome: subtypingStaphylococcus aureuscore genome sequences from shotgun metagenomic data", "token_count": 491, "char_count": 2069, "word_count": 312, "semantic_coherence": 1, "information_density": 0.6058, "quality_score": 0.8029, "entities": { "genes": [ "CC398", "CC30", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:01.096075", "source": { "split": "train_shard_00002", "doc_id": 150 }, "chunk_id": "train_shard_00002_150_0", "global_id": 12934 }, { "text": "Twelve lactose-assimilating strains of the yeast species Kluyveromyces marxianus and its varieties marxianus, lactis and bulgaricus were studied with respect to transport mechanisms for lactose, glucose and galactose, fermentation of these sugars and the occurrence of extracellular lactose hydrolysis. The strains fell into three groups. Group I (two strains): Fermentation of lactose, glucose and galactose, extracellular lactose hydrolysis, apparent facilitated diffusion of glucose and galactose; Group II (two strains): Lactose not fermented, glucose and galactose fermented and transported by an apparent proton symport, extracellular hydrolysis of lactose present (one strain) or questionable; Group III (eight strains): Lactose, glucose and galactose fermented, lactose transported by an apparent proton symport mechanism, extracellular hydrolysis of lactose and transport modes for glucose and galactose variable.\n\nModes of lactose uptake in the yeast species Kluyveromyces marxianus.", "token_count": 280, "char_count": 993, "word_count": 131, "semantic_coherence": 1, "information_density": 0.542, "quality_score": 0.771, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:02.123768", "source": { "split": "train_shard_00002", "doc_id": 151 }, "chunk_id": "train_shard_00002_151_0", "global_id": 12935 }, { "text": "A recently emerged plant disease, bacterial canker of kiwifruit (Actinidia deliciosa and A. chinensis), is caused by Pseudomonas syringae pv. actinidiae (PSA). The disease was first reported in China and Japan in the 1980s. A severe outbreak of PSA began in Italy in 2008 and has spread to other European countries. PSA was found in both New Zealand and Chile in 2010. To study the evolution of the pathogen and analyse the transmission of PSA between countries, genomes of strains from China and Japan (where the genus Actinidia is endemic), Italy, New Zealand and Chile were sequenced. The genomes of PSA strains are very similar. However, all strains from New Zealand share several single nucleotide polymorphisms (SNPs) that distinguish them from all other PSA strains. Similarly, all the PSA strains from the 2008 Italian outbreak form a distinct clonal group and those from Chile form a third group. In addition to the rare SNPs present in the core genomes, there is abundant genetic diversity in a genomic island that is part of the accessory genome. The island from several Chinese strains is almost identical to the island present in the New Zealand strains. The island from a different Chinese strain is identical to the island present in the strains from the recent Italian outbreak. The Chilean strains of PSA carry a third variant of this island. These genomic islands are integrative conjugative elements (ICEs). Sequencing of these ICEs provides evidence of three recent horizontal transmissions of ICE from other strains of Pseudomonas syringae to PSA. The analyses of the core genome SNPs and the ICEs, combined with disease history, all support the hypothesis of an independent Chinese origin for both the Italian and the New Zealand outbreaks and suggest the Chilean strains also originate from China.\n\nPseudomonas syringae pv. actinidiae from recent outbreaks of kiwifruit bacterial canker belong to different clones that originated in China.", "token_count": 476, "char_count": 1962, "word_count": 315, "semantic_coherence": 1, "information_density": 0.4825, "quality_score": 0.7413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:02.805247", "source": { "split": "train_shard_00002", "doc_id": 152 }, "chunk_id": "train_shard_00002_152_0", "global_id": 12936 }, { "text": "Background: Although thousands of clinical isolates of Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions. Methods: Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15 P. falciparum isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal var genes clusters.   Results: The nearly complete sequence of these 15 isolates has enabled us to define a highly conserved core genome, to delineate the boundaries of the subtelomeric regions, and to compare these across isolates. We found highly structured variable regions in the genome. Some exported gene families purportedly involved in release of merozoites show copy number variation. As an example of ongoing genome evolution, we found a novel CLAG gene in six isolates.  We also found a novel gene that was relatively enriched in the South East Asian isolates compared to those from Africa. Conclusions: These 15 manually curated new reference genome sequences with their nearly complete subtelomeric regions and fully assembled genes are an important new resource for the malaria research community. We report the overall conserved structure and pattern of important gene families and the more clearly defined subtelomeric regions.\n\nLong read assemblies of geographically dispersed <i>Plasmodium falciparum</i> isolates reveal highly structured subtelomeres.", "token_count": 447, "char_count": 1857, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5923, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:03.458364", "source": { "split": "train_shard_00002", "doc_id": 153 }, "chunk_id": "train_shard_00002_153_0", "global_id": 12937 }, { "text": "

Objectives

Recently a highly virulent Escherichia coli O80:H2 pathotype carrying Shiga toxin genes, the intimin subtype eaeξ, and genes associated with the extraintestinal pathogenic E. coli (ExPEC) pS88 plasmid was described in France. In this study we examine the relatedness of Belgian E. coli O80:H2 isolated from humans and diarrhoeic calves as well their similarities with the French pathotype.

Methods

Eighteen Belgian E. coli O80:H2 strains (nine human Shiga toxin-producing E. coli (STEC) (2008-2016), two bovine STEC (1987) and seven bovine atypical enteropathogenic E. coli (aEPEC) (2009-2015)) were characterized with conventional PCR, disc diffusion susceptibility testing and whole genome sequencing.

Results

Only nine sporadic human STEC O80:H2 cases have been detected in Belgium. All patients were female, just two of them suffered from haemolytic uremic syndrome. All studied strains had the eaeξ subtype, belonged to the multi-locus sequence type ST-301, and carried virulence genes associated with the type III secretion system and effectors not encoded by the locus of enterocyte effacement (LEE). Multiple genes of the pS88 plasmid were detected in all but two strains (one human and one calf STEC). The Shiga toxin subtypes stx1a (n = 3; one human, two calf), stx2a (n = 2) and stx2d (n = 6) were detected. All strains were multidrug resistant, two were extended-spectrum β-lactamase positive. Core genome MLST revealed that some human and calf E", "token_count": 475, "char_count": 1491, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6484, "quality_score": 0.8242, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:04.105197", "source": { "split": "train_shard_00002", "doc_id": 154 }, "chunk_id": "train_shard_00002_154_0", "global_id": 12938 }, { "text": "coli differed by only 22 loci.

Conclusions

The STEC/ExPEC O80:H2 pathotype was present in calves in Belgium as early as 1987, but human infections have been rare and mostly mild. The human STEC and bovine aEPEC cluster together and have the potential to be as virulent as the French isolates, as shown by their similar gene content.\n\nCharacteristics of Shiga toxin producing- and enteropathogenic Escherichia coli of the emerging serotype O80:H2 isolated from humans and diarrhoeic calves in Belgium.", "token_count": 150, "char_count": 507, "word_count": 77, "semantic_coherence": 1, "information_density": 0.7403, "quality_score": 0.8701, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:04.541163", "source": { "split": "train_shard_00002", "doc_id": 154 }, "chunk_id": "train_shard_00002_154_1", "global_id": 12939 }, { "text": "

Background

Members of the genus Paenibacillus are important plant growth-promoting rhizobacteria that can serve as bio-reactors. Paenibacillus polymyxa promotes the growth of a variety of economically important crops. Our lab recently completed the genome sequence of Paenibacillus polymyxa CR1. As of January 2014, four P. polymyxa genomes have been completely sequenced but no comparative genomic analyses have been reported.

Results

Here we report the comparative and genetic analyses of four sequenced P. polymyxa genomes, which revealed a significantly conserved core genome. Complex metabolic pathways and regulatory networks were highly conserved and allow P. polymyxa to rapidly respond to dynamic environmental cues. Genes responsible for phytohormone synthesis, phosphate solubilization, iron acquisition, transcriptional regulation, σ-factors, stress responses, transporters and biomass degradation were well conserved, indicating an intimate association with plant hosts and the rhizosphere niche. In addition, genes responsible for antimicrobial resistance and non-ribosomal peptide/polyketide synthesis are present in both the core and accessory genome of each strain. Comparative analyses also reveal variations in the accessory genome, including large plasmids present in strains M1 and SC2. Furthermore, a considerable number of strain-specific genes and genomic islands are irregularly distributed throughout each genome. Although a variety of plant-growth promoting traits are encoded by all strains, only P. polymyxa CR1 encodes the unique nitrogen fixation cluster found in other Paenibacillus sp.

Conclusions

Our study revealed that genomic loci relevant to host interaction and ecological fitness are highly conserved within the P. polymyxa genomes analysed, despite variations in the accessory genome. This work suggets that plant-growth promotion by P. polymyxa is mediated largely through phytohormone production, increased nutrient availability and bio-control mechanisms. This study provides an in-depth understanding of the genome architecture of this species, thus facilitating future genetic engineering and applications in agriculture, industry and medicine", "token_count": 525, "char_count": 2211, "word_count": 287, "semantic_coherence": 1, "information_density": 0.6307, "quality_score": 0.8153, "entities": { "genes": [ "CR1", "SC2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:01:05.176392", "source": { "split": "train_shard_00002", "doc_id": 155 }, "chunk_id": "train_shard_00002_155_0", "global_id": 12940 }, { "text": "Furthermore, this study highlights the current gap in our understanding of complex plant biomass metabolism in Gram-positive bacteria.\n\nComparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness.", "token_count": 73, "char_count": 332, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8372, "quality_score": 0.9186, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:05.551870", "source": { "split": "train_shard_00002", "doc_id": 155 }, "chunk_id": "train_shard_00002_155_1", "global_id": 12941 }, { "text": "

ABSTRACT

Pseudomonas syringae is a highly diverse bacterial species complex capable of causing a wide range of serious diseases on numerous agronomically important crop species. Here, we examine the evolutionary relationships of 391 agricultural and environmental strains from the P. syringae species complex using whole-genome sequencing and evolutionary genomic analyses. Our collection includes strains from 11 of the 13 previously described phylogroups isolated off of over 90 hosts. We describe the phylogenetic distribution of all orthologous gene families in the P. syringae pan-genome, reconstruct the phylogeny of P. syringae using a core genome alignment and a hierarchical clustering analysis of pan-genome content, predict ecologically and evolutionary relevant loci, and establish the forces of molecular evolution operating on each gene family. We find that the common ancestor of the species complex likely carried a Rhizobium-like type III secretion system (TTSS) and later acquired the canonical TTSS. The phylogenetic analysis also showed that the species complex is subdivided into primary and secondary phylogroups based on genetic diversity and rates of genetic exchange. The primary phylogroups, which largely consist of agricultural isolates, are no more divergent than a number of other bacterial species, while the secondary phylogroups, which largely consists of environmental isolates, have levels of diversity more in line with multiple distinct species within a genus. An analysis of rates of recombination within and between phylogroups revealed a higher rate of recombination within primary phylogroups than between primary and secondary phylogroups. We also found that “ecologically significant” virulence-associated loci and “evolutionary significant” loci under positive selection are over-represented among loci that undergo inter-phylogroup genetic exchange. These results indicate that while inter-phylogroup recombination occurs relatively rarely in the species complex, it is an important force of genetic cohesion, particularly among the strains in the primary phylogroups. This level of genetic cohesion and the shared plant-associated niche argues for considering the primary phylogroups as a true biological species.", "token_count": 501, "char_count": 2268, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5637, "quality_score": 0.7818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:06.206873", "source": { "split": "train_shard_00002", "doc_id": 156 }, "chunk_id": "train_shard_00002_156_0", "global_id": 12942 }, { "text": "Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in thePseudomonas syringaespecies complex", "token_count": 36, "char_count": 141, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:06.567724", "source": { "split": "train_shard_00002", "doc_id": 156 }, "chunk_id": "train_shard_00002_156_1", "global_id": 12943 }, { "text": "

Background

Clostridium difficile is a Gram-positive anaerobe and the leading cause of antibiotic-associated diarrhea worldwide. The emergence of ribotype 027 (RT027) strains is associated with increased incidence of infection and mortality. To further understand the relationship between C. difficile NCKUH-21, a RT027 strain isolated from a patient in Taiwan, and other RT027 strains, we performed whole-genome shotgun sequencing on NCKUH-21 and comparative genomic analyses.

Results

The genome size, G+C content, and gene number for the NCKUH-21 strain were determined to be similar to those for other C. difficile strains. The core genome phylogeny indicated that the five RT027 strains R20291, CD196, NCKUH-21, BI1, and 2007855 formed a clade. A pathogenicity locus, tcdR-tcdB-tcdE-orf-tcdA-tcdC, was conserved in the genome. A genomic region highly similar to the Clostridium phage [Formula: see text]CD38-2 was present in the NCKUH-21 strain but absent in the other RT027 strains and designated as the prophage [Formula: see text]NCKUH-21. The prophage [Formula: see text]NCKUH-21 genes were significantly higher in G+C content than the other genes in the NCKUH-21 genome, indicating that the prophage does not match the base composition of the host genome.

Conclusions

This is the first whole-genome analysis of a RT027 C. difficile strain isolated from Taiwan", "token_count": 511, "char_count": 1466, "word_count": 195, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7897, "entities": { "genes": [ "CD196", "CD38", "BI1", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:07.195019", "source": { "split": "train_shard_00002", "doc_id": 157 }, "chunk_id": "train_shard_00002_157_0", "global_id": 12944 }, { "text": "Due to the high identity with [Formula: see text]CD38-2, the prophage identified in the NCKUH-21 genome has the potential to regulate toxin production. These results provide important information for understanding the pathogenicity of RT027 C. difficile in Taiwan.\n\nComparative genomic analysis of Clostridium difficile ribotype 027 strains including the newly sequenced strain NCKUH-21 isolated from a patient in Taiwan.", "token_count": 125, "char_count": 435, "word_count": 59, "semantic_coherence": 1, "information_density": 0.7966, "quality_score": 0.8983, "entities": { "genes": [ "CD38", "RT027" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:07.587789", "source": { "split": "train_shard_00002", "doc_id": 157 }, "chunk_id": "train_shard_00002_157_1", "global_id": 12945 }, { "text": "Streptococcus suis is one of the most important bacterial pathogens in the porcine industry and also a zoonotic agent. Serotype 9 is becoming one of the most prevalent serotypes within the S. suis population in certain European countries. In the present study, serotype 9 strains isolated from a country where infection due to this serotype is endemic (Spain), were compared to those recovered from Canada, where this serotype is rarely isolated from diseased pigs. For comparison purposes, strains from Brazil and the only strain isolated from a human case, in Thailand, were also incorporated. Firstly, sequence types (STs) were obtained followed by detection of putative virulence factors. Phylogenetic trees were constructed using the non-recombinant single nucleotide polymorphisms from core genomes of tested strains. Most Spanish strains were either ST123 or ST125, whereas Canadian strains were highly heterogeneous. However, the distribution of putative virulence factors was similar in both groups of strains. The fact that ST16 strains harbored more putative virulence genes and shared greater similarity with the genome of human serotype 2 strains suggests that they present a higher zoonotic and virulence potential than those from Canada and Spain. More than 80% of the strains included in this study carried genes associated with resistance to tetracycline, lincosamides and macrolides. Serotype 9 strains may be nearly 400 years old and have evolved in parallel into 2 lineages. The rapid population expansion of dominant lineage 1 occurred within the last 40 years probably due to the rapid development of the porcine industry.\n\nGenomic comparisons of Streptococcus suis serotype 9 strains recovered from diseased pigs in Spain and Canada.", "token_count": 418, "char_count": 1756, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5789, "quality_score": 0.7895, "entities": { "genes": [ "ST125", "ST16", "ST123" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:08.217842", "source": { "split": "train_shard_00002", "doc_id": 158 }, "chunk_id": "train_shard_00002_158_0", "global_id": 12946 }, { "text": "Single step method of preparation of detergent-permeabilized Kluyveromyces fragilis for lactose hydrolysis", "token_count": 27, "char_count": 106, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:08.586674", "source": { "split": "train_shard_00002", "doc_id": 159 }, "chunk_id": "train_shard_00002_159_0", "global_id": 12947 }, { "text": "Correction for Chen et al., Minimum Core Genome Sequence Typing of Bacterial Pathogens: a Unified Approach for Clinical and Public Health Microbiology", "token_count": 38, "char_count": 150, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:08.946214", "source": { "split": "train_shard_00002", "doc_id": 160 }, "chunk_id": "train_shard_00002_160_0", "global_id": 12948 }, { "text": "

Background

Antimicrobial resistance (AMR) is among the gravest threats to human health and food security worldwide. The use of antimicrobials in livestock production can lead to emergence of AMR, which can have direct effects on humans through spread of zoonotic disease. Pigs pose a particular risk as they are a source of zoonotic diseases and receive more antimicrobials than most other livestock. Here we use a large-scale genomic approach to characterise AMR in Streptococcus suis, a commensal found in most pigs, but which can also cause serious disease in both pigs and humans.

Results

We obtained replicated measures of Minimum Inhibitory Concentration (MIC) for 16 antibiotics, across a panel of 678 isolates, from the major pig-producing regions of the world. For several drugs, there was no natural separation into 'resistant' and 'susceptible', highlighting the need to treat MIC as a quantitative trait. We found differences in MICs between countries, consistent with their patterns of antimicrobial usage. AMR levels were high even for drugs not used to treat S. suis, with many multidrug-resistant isolates. Similar levels of resistance were found in pigs and humans from regions associated with zoonotic transmission. We next used whole genome sequences for each isolate to identify 43 candidate resistance determinants, 22 of which were novel in S. suis. The presence of these determinants explained most of the variation in MIC. But there were also interesting complications, including epistatic interactions, where known resistance alleles had no effect in some genetic backgrounds. Beta-lactam resistance involved many core genome variants of small effect, appearing in a characteristic order.

Conclusions

We present a large dataset allowing the analysis of the multiple contributing factors to AMR in S. suis. The high levels of AMR in S. suis that we observe are reflected by antibiotic usage patterns but our results confirm the potential for genomic data to aid in the fight against AMR.", "token_count": 486, "char_count": 2033, "word_count": 306, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:09.599147", "source": { "split": "train_shard_00002", "doc_id": 161 }, "chunk_id": "train_shard_00002_161_0", "global_id": 12949 }, { "text": "Large-scale genomic analysis of antimicrobial resistance in the zoonotic pathogen Streptococcus suis.", "token_count": 28, "char_count": 101, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:09.952251", "source": { "split": "train_shard_00002", "doc_id": 161 }, "chunk_id": "train_shard_00002_161_1", "global_id": 12950 }, { "text": "Pseudomonas aeruginosa isolates have a highly conserved core genome representing up to 90% of the total genomic sequence with additional variable accessory genes, many of which are found in genomic islands or islets. The identification of the Liverpool Epidemic Strain (LES) in a children's cystic fibrosis (CF) unit in 1996 and its subsequent observation in several centers in the United Kingdom challenged the previous widespread assumption that CF patients acquire only unique strains of P. aeruginosa from the environment. To learn about the forces that shaped the development of this important epidemic strain, the genome of the earliest archived LES isolate, LESB58, was sequenced. The sequence revealed the presence of many large genomic islands, including five prophage clusters, one defective (pyocin) prophage cluster, and five non-phage islands. To determine the role of these clusters, an unbiased signature tagged mutagenesis study was performed, followed by selection in the chronic rat lung infection model. Forty-seven mutants were identified by sequencing, including mutants in several genes known to be involved in Pseudomonas infection. Furthermore, genes from four prophage clusters and one genomic island were identified and in direct competition studies with the parent isolate; four were demonstrated to strongly impact on competitiveness in the chronic rat lung infection model. This strongly indicates that enhanced in vivo competitiveness is a major driver for maintenance and diversifying selection of these genomic prophage genes.\n\nNewly introduced genomic prophage islands are critical determinants of in vivo competitiveness in the Liverpool Epidemic Strain of Pseudomonas aeruginosa.", "token_count": 376, "char_count": 1714, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6048, "quality_score": 0.8024, "entities": { "genes": [ "LESB58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:10.539983", "source": { "split": "train_shard_00002", "doc_id": 162 }, "chunk_id": "train_shard_00002_162_0", "global_id": 12951 }, { "text": "Certain environmental microorganisms can cause severe human infections, even in the absence of an obvious requirement for transition through an animal host for replication (\"accidental virulence\"). To understand this process, we compared eleven isolate genomes of Burkholderia pseudomallei (Bp), a tropical soil microbe and causative agent of the human and animal disease melioidosis. We found evidence for the existence of several new genes in the Bp reference genome, identifying 282 novel genes supported by at least two independent lines of supporting evidence (mRNA transcripts, database homologs, and presence of ribosomal binding sites) and 81 novel genes supported by all three lines. Within the Bp core genome, 211 genes exhibited significant levels of positive selection (4.5%), distributed across many cellular pathways including carbohydrate and secondary metabolism. Functional experiments revealed that certain positively selected genes might enhance mammalian virulence by interacting with host cellular pathways or utilizing host nutrients. Evolutionary modifications improving Bp environmental fitness may thus have indirectly facilitated the ability of Bp to colonize and survive in mammalian hosts. These findings improve our understanding of the pathogenesis of melioidosis, and establish Bp as a model system for studying the genetics of accidental virulence.\n\nA genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence.", "token_count": 328, "char_count": 1511, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:11.106301", "source": { "split": "train_shard_00002", "doc_id": 163 }, "chunk_id": "train_shard_00002_163_0", "global_id": 12952 }, { "text": "Listeria monocytogenes (Lm) can persist in food processing environments (FPEs), surviving environmental stresses and disinfectants. We described an intensive environmental monitoring plan performed in Central Italy and involving food producing plants (FPPs) and retail grocery stores (RSs). The aim of the study was to provide a snapshot of the Lm circulation in different FPEs during a severe listeriosis outbreak, using whole genome sequencing (WGS) to investigate the genetic diversity of the Lm isolated, evaluating their virulence and stress resistance profiles. A total of 1217 samples were collected in 86 FPEs with 12.0% of positive surfaces at FPPs level and 7.5% at RSs level; 133 Lm isolates were typed by multilocus sequencing typing (MLST) and core genome MLST (cgMLST). Clonal complex (CC) 121 (25.6%), CC9 (22.6%), CC1 (11.3%), CC3 (10.5%), CC191 (4.5%), CC7 (4.5%) and CC31 (3.8%) were the most frequent MLST clones. Among the 26 cgMLST clusters obtained, 5 of them persisted after sanitization and were re-isolated during the follow-up sampling. All the CC121 harboured the Tn6188_qac gene for tolerance to benzalkonium chloride and the stress survival islet SSI-2. The CC3, CC7, CC9, CC31 and CC191 carried the SSI-1. All the CC9 and CC121 strains presented a premature stop codon in the inlA gene. In addition to the Lm Pathogenicity Island 1 (LIPI-1), CC1, CC3 and CC191 harboured the LIPI-3", "token_count": 500, "char_count": 1474, "word_count": 220, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [ "CC121", "CC9", "CC3", "CC7", "CC191", "CC31", "CC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:11.762694", "source": { "split": "train_shard_00002", "doc_id": 164 }, "chunk_id": "train_shard_00002_164_0", "global_id": 12953 }, { "text": "The application of intensive environmental sampling plans for the detection and WGS analysis of Lm isolates could improve surveillance and early detection of outbreaks.\n\nIntensive Environmental Surveillance Plan for Listeria monocytogenes in Food Producing Plants and Retail Stores of Central Italy: Prevalence and Genetic Diversity.", "token_count": 85, "char_count": 347, "word_count": 45, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:12.133844", "source": { "split": "train_shard_00002", "doc_id": 164 }, "chunk_id": "train_shard_00002_164_1", "global_id": 12954 }, { "text": "

Background:

Although thousands of clinical isolates of Plasmodium falciparum are being sequenced and analysed by short read technology, the data do not resolve the highly variable subtelomeric regions of the genomes that contain polymorphic gene families involved in immune evasion and pathogenesis. There is also no current standard definition of the boundaries of these variable subtelomeric regions.

Methods:

Using long-read sequence data (Pacific Biosciences SMRT technology), we assembled and annotated the genomes of 15 P. falciparum isolates, ten of which are newly cultured clinical isolates. We performed comparative analysis of the entire genome with particular emphasis on the subtelomeric regions and the internal var genes clusters.  

Results:

The nearly complete sequence of these 15 isolates has enabled us to define a highly conserved core genome, to delineate the boundaries of the subtelomeric regions, and to compare these across isolates. We found highly structured variable regions in the genome. Some exported gene families purportedly involved in release of merozoites show copy number variation. As an example of ongoing genome evolution, we found a novel CLAG gene in six isolates.  We also found a novel gene that was relatively enriched in the South East Asian isolates compared to those from Africa.

Conclusions:

These 15 manually curated new reference genome sequences with their nearly complete subtelomeric regions and fully assembled genes are an important new resource for the malaria research community. We report the overall conserved structure and pattern of important gene families and the more clearly defined subtelomeric regions.\n\nLong read assemblies of geographically dispersed Plasmodium falciparum isolates reveal highly structured subtelomeres", "token_count": 426, "char_count": 1828, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5795, "quality_score": 0.7898, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:12.762763", "source": { "split": "train_shard_00002", "doc_id": 165 }, "chunk_id": "train_shard_00002_165_0", "global_id": 12955 }, { "text": "Numbers of listeriosis illnesses have been increasing in Germany and the European Union during the last decade. In addition, reports on the occurrence of antibiotic resistance in Listeria monocytogenes in clinical and environmental isolates are accumulating. The susceptibility towards 14 antibiotics was tested in a selection of clinical L. monocytogenes isolates to get a more precise picture of the development and manifestation of antibiotic resistance in the L. monocytogenes population. Based on the population structure determined by core genome multi locus sequence typing (cgMLST) 544 out of 1220 sequenced strains collected in Germany between 2009 and 2019 were selected to cover the phylogenetic diversity observed in the clinical L. monocytogenes population. All isolates tested were susceptible towards ampicillin, penicillin and co-trimoxazole - the most relevant antibiotics in the treatment of listeriosis. Resistance to daptomycin and ciprofloxacin was observed in 493 (91%) and in 71 (13%) of 544 isolates, respectively. While all tested strains showed resistance towards ceftriaxone, their resistance levels varied widely between 4 mg/L and >128 mg/L. An allelic variation of the penicillin binding protein gene pbpB3 was identified as the cause of this difference in ceftriaxone resistance levels. This study is the first population structure-guided analysis of antimicrobial resistance in recent clinical isolates and confirms the importance of penicillin binding protein B3 (PBP B3) for the high level of intrinsic cephalosporin resistance of L. monocytogenes on a population-wide scale.", "token_count": 452, "char_count": 1651, "word_count": 231, "semantic_coherence": 1, "information_density": 0.5844, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:13.423771", "source": { "split": "train_shard_00002", "doc_id": 166 }, "chunk_id": "train_shard_00002_166_0", "global_id": 12956 }, { "text": "Population structure-guided profiling of antibiotic resistance patterns in clinical Listeria monocytogenes isolates from Germany identifies pbpB3 alleles associated with low levels of cephalosporin resistance.", "token_count": 61, "char_count": 223, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9583, "quality_score": 0.9792, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:13.821202", "source": { "split": "train_shard_00002", "doc_id": 166 }, "chunk_id": "train_shard_00002_166_1", "global_id": 12957 }, { "text": "The yeast Kluyveromyces marxianus var. marxianus isolated from onion bulbs showing soft rot symptoms from commercial fields, a cull pile, and packinghouse was confirmed as a soft rot pathogen of onion bulbs by completing Koch’s postulates. Resultant soft rot symptoms were significantly (P = 0.05) more severe at 27 and 20 C than at 10 or 5 C. Decay was significantly (P = 0.05) less in bulbs injected with 1 ml of 90 and 1,000 yeast cells per milliliter than bulbs inoculated with 11,000 or more yeast cells per milliliter. This is the first report known to us of a true yeast being pathogenic to onion bulbs.\n\nA soft rot of onion caused by the yeast Kluyveromyces marxianus var. marxianus.", "token_count": 216, "char_count": 691, "word_count": 120, "semantic_coherence": 1, "information_density": 0.6167, "quality_score": 0.8083, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:14.315796", "source": { "split": "train_shard_00002", "doc_id": 167 }, "chunk_id": "train_shard_00002_167_0", "global_id": 12958 }, { "text": "

Background

The relative pathogenicity of eight medically important Candida species was investigated in a mouse model.

Materials and methods

Seventeen isolates were included; two isolates of Candida albicans, Candida glabrata, Candida tropicalis, Candida lusitaniae, Candida parapsilosis, Candida kefyr and Candida guilliermondii and three Candida krusei isolates. Mice in groups of three or four were inoculated with 10(5) and 10(7) CFU, respectively. On days 2 and 7 kidneys were removed, weighed and CFU/g kidney determined by the spot technique.

Results

Mortality was only observed in mice inoculated with C. albicans and C. tropicalis. Inoculated with 10(7) CFU C. tropicalis, C. glabrata, C. kefyr, C. lusitaniae, C. parapsilosis, C. krusei and C. guilliermondii the median log CFU/g kidney was significantly different: 6.0, 6.0, 6.4, 7.0, 3.7, < 2 and < 2 respectively (p < 0.0001). Eye infection and histological changes of kidneys were examined for C. albicans, C. tropicalis, C. glabrata and C. krusei-infected mice. Weight loss, kidney weight, inflammation and infection and number of eyes infected decreased with the pathogenicity of the four species.

Conclusion

The virulence was highly different, illustrated by a 7-log difference in CFU/g kidney, a span of 0-100% mortality and histological changes in kidneys ranging from discrete to serious. The species could be divided into three groups with decreasing virulence: 1) C. albicans and C. tropicalis, 2) C. glabrata, C. kefyr and C. lusitaniae and 3) C. parapsilosis, C. krusei and C. guilliermondii", "token_count": 522, "char_count": 1593, "word_count": 229, "semantic_coherence": 1, "information_density": 0.5109, "quality_score": 0.7555, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:01:15.007173", "source": { "split": "train_shard_00002", "doc_id": 168 }, "chunk_id": "train_shard_00002_168_0", "global_id": 12959 }, { "text": "To our knowledge this is the first study with a simultaneous comparison of all eight species in an immunocompetent animal model.\n\nIn vivo pathogenicity of eight medically relevant Candida species in an animal model.", "token_count": 48, "char_count": 215, "word_count": 34, "semantic_coherence": 1, "information_density": 0.7647, "quality_score": 0.8824, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:15.404602", "source": { "split": "train_shard_00002", "doc_id": 168 }, "chunk_id": "train_shard_00002_168_1", "global_id": 12960 }, { "text": "Glass beads-salting out procedure was used to isolated DNA from 8 pathogenic fungi, including Candida albicans, Candida kefyr, Candida krusei, Candida guilliermondii, Cryptococcus neoformans, Aspergillus fumigatus, Aspergillus flavus and Penicillium marneffei, and compared with conventional phenol-chloroform extraction method. The efficiency of this procedure was estimated by using PCR. For all the eight organisms, the rapid extraction procedure resulted in high yield and intact DNA.\n\nGlass beads-salting out procedure for extracting DNA from common pathogenic fungi", "token_count": 156, "char_count": 571, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7333, "quality_score": 0.8667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:15.849380", "source": { "split": "train_shard_00002", "doc_id": 169 }, "chunk_id": "train_shard_00002_169_0", "global_id": 12961 }, { "text": "A major contributor to the emergence of antibiotic resistance in Gram-positive bacterial pathogens is the expansion of acquired, inducible genetic elements. Although acquired, inducible antibiotic resistance is not new, the interest in its molecular basis has been accelerated by the widening distribution and often 'silent' spread of the elements responsible, the diagnostic challenges of such resistance and the mounting limitations of available agents to treat Gram-positive infections. Acquired, inducible antibiotic resistance elements belong to the accessory genome of a species and are horizontally acquired by transformation/recombination or through the transfer of mobile DNA elements. The two key, but mechanistically very different, induction mechanisms are: ribosome-sensed induction, characteristic of the macrolide-lincosamide-streptogramin B antibiotics and tetracycline resistance, leading to ribosomal modifications or efflux pump activation; and resistance by cell surface-associated sensing of β-lactams (e.g., oxacillin), glycopeptides (e.g., vancomycin) and the polypeptide bacitracin, leading to drug inactivation or resistance due to cell wall alterations.\n\nAcquired inducible antimicrobial resistance in Gram-positive bacteria.", "token_count": 298, "char_count": 1251, "word_count": 158, "semantic_coherence": 1, "information_density": 0.6329, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:16.412077", "source": { "split": "train_shard_00002", "doc_id": 170 }, "chunk_id": "train_shard_00002_170_0", "global_id": 12962 }, { "text": "BackgroundCarbapenemase-producing Escherichia coli are increasing worldwide. In recent years, an increase in OXA-244-producing E. coli isolates has been seen in the national surveillance of carbapenemase-producing organisms in Denmark.AimMolecular characterisation and epidemiological investigation of OXA-244-producing E. coli isolates from January 2016 to August 2019.MethodsFor the epidemiological investigation, data from the Danish National Patient Registry and the Danish register of civil registration were used together with data from phone interviews with patients. Isolates were characterised by analysing whole genome sequences for resistance genes, MLST and core genome MLST (cgMLST).ResultsIn total, 24 OXA-244-producing E. coli isolates were obtained from 23 patients. Among the 23 patients, 13 reported travelling before detection of the E. coli isolates, with seven having visited countries in Northern Africa. Fifteen isolates also carried an extended-spectrum beta-lactamase gene and one had a plasmid-encoded AmpC gene. The most common detected sequence type (ST) was ST38, followed by ST69, ST167, ST10, ST361 and ST3268. Three clonal clusters were detected by cgMLST, but none of these clusters seemed to reflect nosocomial transmission in Denmark.ConclusionImport of OXA-244 E. coli isolates from travelling abroad seems likely for the majority of cases. Community sources were also possible, as many of the patients had no history of hospitalisation and many of the E. coli isolates belonged to STs that are present in the community. It was not possible to point at a single country or a community source as risk factor for acquiring OXA-244-producing E. coli.", "token_count": 486, "char_count": 1739, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6276, "quality_score": 0.8138, "entities": { "genes": [ "ST167", "ST361", "ST10", "ST3268", "ST69", "ST38" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:17.058672", "source": { "split": "train_shard_00002", "doc_id": 171 }, "chunk_id": "train_shard_00002_171_0", "global_id": 12963 }, { "text": "Surveillance of OXA-244-producing Escherichia coli and epidemiologic investigation of cases, Denmark, January 2016 to August 2019.", "token_count": 52, "char_count": 137, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:17.419730", "source": { "split": "train_shard_00002", "doc_id": 171 }, "chunk_id": "train_shard_00002_171_1", "global_id": 12964 }, { "text": "Two-dimensional electrophoretic analysis of endopolygalacturonases produced by Kluyveromyces marxianus.", "token_count": 29, "char_count": 103, "word_count": 9, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:17.777486", "source": { "split": "train_shard_00002", "doc_id": 172 }, "chunk_id": "train_shard_00002_172_0", "global_id": 12965 }, { "text": "Rotavirus is one of the main pathogens that cause diarrhoea in young animals, and countless animals have died of rotavirus infection worldwide. Three strains of lactic acid bacteria isolated from Tibetan mushrooms were used to study the inhibition of rotavirus in vitro and in vivo. One part was to identify and study the biochemical and probiotic characteristics of three isolated lactic acid bacteria, and the other part was to evaluate the inhibitory effect on rotavirus via in vivo and in vitro experiments. The whole genome of the lactic acid bacteria with the best antiviral effect was sequenced, and the differences between them and the standard strains were analyzed by comparative genomic analysis, so as to provide a theoretical basis for exploring the antiviral effect of lactic acid bacteria.The three strains were identified as Pediococcus acidilactici, Lactobacillus casei and Lactobacillus paracasei. Pediococcus acidilactici showed good acid tolerance, bile salt tolerance, survival in artificial intestinal fluid, survival in gastric fluid and bacteriostasis. In in vitro experiments, pig intestinal epithelial cells cocultured with Pediococcus acidilactici exhibited reduced viral infection. In the in vivo experiment, the duodenum of mice fed Pediococcus acidilactici had extremely low numbers of virus particles. The total genome size was 2,026,809 bp, the total number of genes was 1988, and the total length of genes was 1,767,273 bp. The proportion of glycoside hydrolases and glycoside transferases in CAZy was 50.6 and 29.6%, respectively. The Metabolism function in KEEG had the highest number of Global and overview maps", "token_count": 493, "char_count": 1731, "word_count": 247, "semantic_coherence": 1, "information_density": 0.5628, "quality_score": 0.7814, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:18.427318", "source": { "split": "train_shard_00002", "doc_id": 173 }, "chunk_id": "train_shard_00002_173_0", "global_id": 12966 }, { "text": "Among the comparative genomes, Pediococcus acidilactici had the highest homology with GCF 000146325.1, and had a good collinearity with GCF 013127755.1, without numerous gene rearrangement events such as insertion, deletion, inversion and translocation. In conclusion, Pediococcus acidilactici was a good candidate strain for antiviral probiotics.\n\nAntiviral effects of Pediococcus acidilactici isolated from Tibetan mushroom and comparative genomic analysis.", "token_count": 147, "char_count": 473, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7931, "quality_score": 0.8966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:18.863563", "source": { "split": "train_shard_00002", "doc_id": 173 }, "chunk_id": "train_shard_00002_173_1", "global_id": 12967 }, { "text": "Human gut microbiome research focuses on populations living in high-income countries and to a lesser extent, non-urban agriculturalist and hunter-gatherer societies. The scarcity of research between these extremes limits our understanding of how the gut microbiota relates to health and disease in the majority of the world's population. Here, we evaluate gut microbiome composition in transitioning South African populations using short- and long-read sequencing. We analyze stool from adult females living in rural Bushbuckridge (n = 118) or urban Soweto (n = 51) and find that these microbiomes are taxonomically intermediate between those of individuals living in high-income countries and traditional communities. We demonstrate that reference collections are incomplete for characterizing microbiomes of individuals living outside high-income countries, yielding artificially low beta diversity measurements, and generate complete genomes of undescribed taxa, including Treponema, Lentisphaerae, and Succinatimonas. Our results suggest that the gut microbiome of South Africans does not conform to a simple \"western-nonwestern\" axis and contains undescribed microbial diversity.\n\nShort- and long-read metagenomics of urban and rural South African gut microbiomes reveal a transitional composition and undescribed taxa.", "token_count": 305, "char_count": 1324, "word_count": 178, "semantic_coherence": 1, "information_density": 0.6236, "quality_score": 0.8118, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:19.434903", "source": { "split": "train_shard_00002", "doc_id": 174 }, "chunk_id": "train_shard_00002_174_0", "global_id": 12968 }, { "text": "Hypersaline photosynthetic microbial mats are stratified microbial communities known for their taxonomic and metabolic diversity and strong light-driven day-night environmental gradients. In this study of the upper photosynthetic zone of hypersaline microbial mats of Elkhorn Slough, California (USA), we show how reference-based and reference-free methods can be used to meaningfully assess microbial ecology and genetic partitioning in these complex microbial systems. Mapping of metagenome reads to the dominant Cyanobacteria observed in the system, Coleofasciculus (Microcoleus) chthonoplastes , was used to examine strain variants within these metagenomes. Highly conserved gene subsystems indicate a core genome for the species, and a number of variant genes and subsystems suggest strain level differentiation, especially for carbohydrate utilization. Metagenome sequence coverage binning was used to assess ecosystem partitioning of remaining microbes. Functional gene annotation of these bins (primarily of Proteobacteria, Bacteroidetes, and Cyanobacteria ) recapitulated the known biogeochemical functions in microbial mats using a genetic basis, and also revealed evidence of novel functional diversity within the Gemmatimonadetes and Gammaproteobacteria . Combined, these two approaches show how genetic partitioning can inform biogeochemical partitioning of the metabolic diversity within microbial ecosystems.\n\nMetagenomics reveals niche partitioning within the phototrophic zone of a microbial mat", "token_count": 358, "char_count": 1512, "word_count": 196, "semantic_coherence": 1, "information_density": 0.602, "quality_score": 0.801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:20.014751", "source": { "split": "train_shard_00002", "doc_id": 175 }, "chunk_id": "train_shard_00002_175_0", "global_id": 12969 }, { "text": "Enterococci are Gram-positive bacteria that are found in plants, soil and as commensals of the gastrointestinal tract of humans, mammals, and insects. Despite their commensal nature, they have also become globally important nosocomial pathogens. Within the genus Enterococcus, Enterococcus faecium, and Enterococcus faecalis are clinically most relevant. In this review, we will discuss how E. faecium and E. faecalis have evolved to become a globally disseminated nosocomial pathogen. E. faecium has a defined sub-population that is associated with hospitalized patients and is rarely encountered in community settings. These hospital-associated clones are characterized by the acquisition of adaptive genetic elements, including genes involved in metabolism, biofilm formation, and antibiotic resistance. In contrast to E. faecium, clones of E. faecalis isolated from hospitalized patients, including strains causing clinical infections, are not exclusively found in hospitals but are also present in healthy individuals and animals. This observation suggests that the division between commensals and hospital-adapted lineages is less clear for E. faecalis than for E. faecium. In addition, genes that are reported to be associated with virulence of E. faecalis are often not unique to clinical isolates, but are also found in strains that originate from commensal niches. As a reflection of more ancient association of E. faecalis with different hosts, these determinants Thus, they may not represent genuine virulence genes but may act as host-adaptive functions that are useful in a variety of intestinal environments. The scope of the review is to summarize recent trends in the emergence of antibiotic resistance and explore recent developments in the molecular epidemiology, population structure and mechanisms of adaptation of E. faecium and E. faecalis.\n\nGlobal Emergence and Dissemination of Enterococci as Nosocomial Pathogens: Attack of the Clones?", "token_count": 451, "char_count": 1961, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5567, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:20.648815", "source": { "split": "train_shard_00002", "doc_id": 176 }, "chunk_id": "train_shard_00002_176_0", "global_id": 12970 }, { "text": "Necrotic enteritis (NE) is an economically important disease of poultry caused by certain Clostridium perfringens type A strains. NE pathogenesis involves the NetB toxin, which is encoded on a large conjugative plasmid within a 42-kb pathogenicity locus. Recent multilocus sequence type (MLST) studies have identified two predominant NE-associated clonal groups, suggesting that host genes are also involved in NE pathogenesis. We used microarray comparative genomic hybridization (CGH) to assess the gene content of 54 poultry isolates from birds that were healthy or that suffered from NE. A total of 400 genes were variably present among the poultry isolates and nine nonpoultry strains, many of which had putative functions related to nutrient uptake and metabolism and cell wall and capsule biosynthesis. The variable genes were organized into 142 genomic regions, 49 of which contained genes significantly associated with netB-positive isolates. These regions included three previously identified NE-associated loci as well as several apparent fitness-related loci, such as a carbohydrate ABC transporter, a ferric-iron siderophore uptake system, and an adhesion locus. Additional loci were related to plasmid maintenance. Cluster analysis of the CGH data grouped all of the netB-positive poultry isolates into two major groups, separated according to two prevalent clonal groups based on MLST analysis. This study identifies chromosomal loci associated with netB-positive poultry strains, suggesting that the chromosomal background can confer a selective advantage to NE-causing strains, possibly through mechanisms involving iron acquisition, carbohydrate metabolism, and plasmid maintenance.\n\nIdentification of accessory genome regions in poultry Clostridium perfringens isolates carrying the netB plasmid.", "token_count": 449, "char_count": 1815, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6587, "quality_score": 0.8294, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:21.287192", "source": { "split": "train_shard_00002", "doc_id": 177 }, "chunk_id": "train_shard_00002_177_0", "global_id": 12971 }, { "text": "

Aim

To test the potential of whole genome sequencing (WGS) for molecular surveillance of invasive meningococcal disease in the Czech Republic. To check the success of the new method in the identification of gene and protein variants and to compare the outcomes between WGS and conventional sequencing methods.

Material and methods

WGS was carried out in a set of 20 N. meningitidis isolates from invasive meningococcal disease cases in the Czech Republic in 2015. WGS was performed using the Illumina MiSeq platform. The WGS data were processed by the Velvet de novo Assembler software, and the resultant genome contigs were submitted to the Neisseria PubMLST web database containing allelic and genomic data on strains of the genus Neisseria. The genomes were analysed and compared using the BIGSdb Genome Comparator, which is part of the PubMLST database. WGS data were compared at several levels of resolution: MLST (Multi Locus Sequence Typing), rMLST (ribosomal MLST), cgMLST (core genome MLST), and \"all loci\", i.e. all genes of N. meningitidis defined in the PubMLST database by 6 November 2017 (3028 loci). The WGS method was used to characterise in detail the genes of antigens involved in vaccines against N. meningitidis B.

Results

The new WGS method provided detailed characteristics of N. meningitidis isolates, which improved the results obtained previously by conventional sequencing methods. High quality WGS data made it possible to identify novel alleles and novel sequence types that could not be recognized by conventional sequencing methods. The analysis of genetic diversity confirmed closer relatedness between isolates belonging to the same clonal complex. The most accurate information on genetic diversity of isolates was obtained by the comparison of WGS data at the cgMLST and \"all loci\" levels. Distant relatedness of three clonal complexes (cc32, cc35, and cc269) was found", "token_count": 489, "char_count": 1925, "word_count": 290, "semantic_coherence": 1, "information_density": 0.5655, "quality_score": 0.7828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:21.937780", "source": { "split": "train_shard_00002", "doc_id": 178 }, "chunk_id": "train_shard_00002_178_0", "global_id": 12972 }, { "text": "WGS data also provided more accurate information on the coverage of isolates by MenB vaccines in comparison with conventional sequencing data.

Conclusions

The WGS method showed a higher discrimination potential and allowed a more accurate determination of genetic characteristics of N. meningitidis. The integration of the WGS method in routine molecular surveillance of invasive meningococcal disease in the Czech Republic is desirable.\n\nSurveillance of invasive meningococcal disease based on whole genome sequencing (WGS), Czech Republic, 2015.", "token_count": 126, "char_count": 554, "word_count": 74, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:22.324814", "source": { "split": "train_shard_00002", "doc_id": 178 }, "chunk_id": "train_shard_00002_178_1", "global_id": 12973 }, { "text": "Killer plasmids pGKL1 and pGKL2 of double-stranded linear DNAs were transferred from Kluyveromyces lactis to strains of Kluyveromyces fragilis and Candida pseudotropicalis. The resultant killer strains produced 17-fold and 6-fold larger amounts of killer toxin than K. lactis did, respectively. The killer toxin produced by each species appeared to be a glycoprotein.\n\nTransfer of DNA killer plasmids from Kluyveromyces lactis to Kluyveromyces fragilis and Candida pseudotropicalis.", "token_count": 144, "char_count": 482, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:22.758301", "source": { "split": "train_shard_00002", "doc_id": 179 }, "chunk_id": "train_shard_00002_179_0", "global_id": 12974 }, { "text": "The flow of genes between different species represents a form of genetic variation whose implications have not been fully appreciated. Here I examine some key findings on the extent of horizontal gene transfer (HGT) revealed by comparative genome analysis and their theoretical implications. In theoretical terms, HGT affects ideas pertaining to the tree of life, the notion of a last universal common ancestor, and the biological unities, as well as the rules of taxonomic nomenclature. This review discusses the emergence of the eukaryotic cell and the occurrence of HGT among metazoan phyla involving both transposable elements and structural genes for normal housekeeping functions. I also discuss the bacterial pangenome, which provides an important case study on the permeability of species boundaries. An interesting observation about bdelloid rotifers and their reversion to asexual reproduction as it pertains to HGT is included.\n\nEvolutionary implications of horizontal gene transfer.", "token_count": 207, "char_count": 994, "word_count": 146, "semantic_coherence": 1, "information_density": 0.726, "quality_score": 0.863, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:23.229760", "source": { "split": "train_shard_00002", "doc_id": 180 }, "chunk_id": "train_shard_00002_180_0", "global_id": 12975 }, { "text": "Poultry is considered a major reservoir of human campylobacteriosis. It also been reported that not only poultry, but also wild birds, are capable of carrying C. jejuni, thus demonstrating to be a risk of spreading the bacteria in the environment. To gain insight into the population structure and investigate the antimicrobial resistance genotypes and phenotypes, we analyzed a collection of 135 C. jejuni from 15 species of wild birds in Italy. MLST revealed the presence of 41 sequence types (STs) and 13 clonal complexes (CCs). ST-179 complex and the generalist ST-45 complex were the most prevalent. Core genome MLST revealed that C. jejuni from ST-45 complex clustered according to the bird species, unlike the ST-179 complex which featured 3 different species in the same cluster. Overall we found a moderate prevalence of resistance to tetracycline (12.5%), ciprofloxacin and nalidixic acid (10%). The novel ST isolated from one pigeon showed resistance to all the antibiotics tested. The ST-179 complex (33.3%) was identified with significantly higher nalidixic acid resistance relative to other tested STs. Nine AMR genes (tet(O), cmeA, cmeB, cmeC, cmeR, aad, blaOXA-61, blaOXA-184 and erm(B)) and 23S rRNA and gyrA-associated point mutations were also described, indicating a concordance level between genotypic and phenotypic resistance of 23.3%, 23.4% and of 37.5% for streptomycin, tetracycline and quinolones/fluoroquinolones, respectively", "token_count": 517, "char_count": 1550, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:01:23.878033", "source": { "split": "train_shard_00002", "doc_id": 181 }, "chunk_id": "train_shard_00002_181_0", "global_id": 12976 }, { "text": "We recommend that particular attention should be given to wild birds as key sentinel animals for the ecosystem contamination surveillance.\n\nMolecular Characterization and Antimicrobial Susceptibility of C. jejuni Isolates from Italian Wild Bird Populations.", "token_count": 61, "char_count": 264, "word_count": 34, "semantic_coherence": 1, "information_density": 0.9706, "quality_score": 0.9853, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:24.244365", "source": { "split": "train_shard_00002", "doc_id": 181 }, "chunk_id": "train_shard_00002_181_1", "global_id": 12977 }, { "text": "The inconvenience of conventional yeast identification methods has resulted in the development of rapid, commercial systems, mainly for clinical yeast species. The Biolog system (Biolog Inc., Hayward, CA, USA) is a new semi-automated, computer-linked technology for rapid identification of clinical and non-clinical yeasts. The system is based around a microtitre tray and includes assimilation and oxidation tests. This paper evaluates the Biolog system for the identification of 21 species (72 strains) of yeasts of food and wine origin. Species correctly identified included Saccharomyces cerevisiae, Debaryomyces hansenii, Yarrowia lipolytica, Kluyveromyces marxianus, Kloeckera apiculata, Dekkera bruxellensis and Schizosaccharomyces pombe. Zygosaccharomyces bailii and Zygosaccharomyces rouxii were identified correctly 50% of the time and Pichia membranaefaciens 20% of the time.\n\nEvaluation of the Biolog system for the identification of food and beverage yeasts.", "token_count": 257, "char_count": 971, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6434, "quality_score": 0.8217, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:24.800767", "source": { "split": "train_shard_00002", "doc_id": 182 }, "chunk_id": "train_shard_00002_182_0", "global_id": 12978 }, { "text": "A single extra-intestinal pathogenic Escherichia coli (ExPEC) clone, named sequence type (ST) 131, is responsible for millions of global antimicrobial-resistant (AMR) infections annually. Population genetics indicate that ST131 consists of different clades (i.e. A, B, and C); however, clade C is the most dominant globally. A ST131 subclade, named C1-M27, is emerging in Japan and has been responsible for the recent increase in AMR ExPEC in that country. The sequential acquisition of several virulence and AMR genes associated with mobile genetic elements during the 1960s to 1980s primed clade C (and its subclades C1 and C2) for success in the 1990s to 2000s. IncF plasmids with F1:A2:B20 and F2:A1:B replicons have shaped the evolution of the C1 and C2 subclades. It is possible that ST131 is a host generalist with different accessory gene profiles. Compensatory mutations within the core genome of this clone have counterbalanced the fitness cost associated with IncF plasmids. ST131 clade C had dramatically changed the population structure of ExPEC, but it still remains unclear which features of this clade resulted in one of the most unprecedented AMR successes of the 2000s.\n\nEscherichia coli ST131: a multidrug-resistant clone primed for global domination", "token_count": 372, "char_count": 1269, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.8179, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:25.387746", "source": { "split": "train_shard_00002", "doc_id": 183 }, "chunk_id": "train_shard_00002_183_0", "global_id": 12979 }, { "text": "HNP was succesfully isolated and purified by Sephadex G100 and Bio-gel P10 gel filtration chromatography, and concentration-dependent candidcidal activity to Candida albicans M1012R, NIH A-207, Candida kefyr, Candida tropicalis, and Candida guilliermondii of HNP was demonstreated in vitro. After exposing to HNP the Candida spp. were examined by electron microscope, profound cell wall changes such as cell surface collapse and perforation were noted, the separation of cell membrane from cell wall and formation of vacuole were also observed.\n\nIn vitro antifungal activity of defensin from human neutrophils against some Candida spp.", "token_count": 173, "char_count": 635, "word_count": 91, "semantic_coherence": 1, "information_density": 0.6813, "quality_score": 0.8407, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:25.858885", "source": { "split": "train_shard_00002", "doc_id": 184 }, "chunk_id": "train_shard_00002_184_0", "global_id": 12980 }, { "text": "Lactobacillus paracasei is a member of the normal human and animal gut microbiota and is used extensively in the food industry in starter cultures for dairy products or as probiotics. With the development of low-cost, high-throughput sequencing techniques it has become feasible to sequence many different strains of one species and to determine its \"pan-genome\". We have sequenced the genomes of 34 different L. paracasei strains, and performed a comparative genomics analysis. We analysed genome synteny and content, focussing on the pan-genome, core genome and variable genome. Each genome was shown to contain around 2800-3100 protein-coding genes, and comparative analysis identified over 4200 ortholog groups that comprise the pan-genome of this species, of which about 1800 ortholog groups make up the conserved core. Several factors previously associated with host-microbe interactions such as pili, cell-envelope proteinase, hydrolases p40 and p75 or the capacity to produce short branched-chain fatty acids (bkd operon) are part of the L. paracasei core genome present in all analysed strains. The variome consists mainly of hypothetical proteins, phages, plasmids, transposon/conjugative elements, and known functions such as sugar metabolism, cell-surface proteins, transporters, CRISPR-associated proteins, and EPS biosynthesis proteins. An enormous variety and variability of sugar utilization gene cassettes were identified, with each strain harbouring between 25-53 cassettes, reflecting the high adaptability of L. paracasei to different niches. A phylogenomic tree was constructed based on total genome contents, and together with an analysis of horizontal gene transfer events we conclude that evolution of these L. paracasei strains is complex and not always related to niche adaptation. The results of this genome content comparison was used, together with high-throughput growth experiments on various carbohydrates, to perform gene-trait matching analysis, in order to link the distribution pattern of a specific phenotype to the presence/absence of specific sets of genes.", "token_count": 520, "char_count": 2096, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6577, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:01:26.513056", "source": { "split": "train_shard_00002", "doc_id": 185 }, "chunk_id": "train_shard_00002_185_0", "global_id": 12981 }, { "text": "Lactobacillus paracasei comparative genomics: towards species pan-genome definition and exploitation of diversity.", "token_count": 28, "char_count": 114, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:26.895013", "source": { "split": "train_shard_00002", "doc_id": 185 }, "chunk_id": "train_shard_00002_185_1", "global_id": 12982 }, { "text": "Objectives: The analysis of epidemiology, risk factors and outcome of infections in children with malignant bone tumors (MBT) undergoing chemotherapy. Methods: In this retrospective nationwide multicenter cross-sectional study, a total number of 126 children with MBT including 70 with Ewing sarcoma (ES) and 56 with osteosarcoma (OSA) were screened for infections over a period of 72 consecutive months. Results: The risk of infection was 7.15-fold higher in patients with ES as compared to the OSA group, especially concerning bacterial infections (4.1-fold increase risk). Bacterial infections occurred in 74.3% patients with ES and in 41.1% with OSA. The median time from diagnosis to first infection was 4.9 months. 33.0% of bacterial episodes were diagnosed as bloodstream (BSI), 31.1% as gastrointestinal tract, 30.1% as urinary tract infection. Infection-related mortality (IRM) from bacterial infection was 6% and 15% in ES and OSA patients, respectively. Cumulative incidence was 7.1% for invasive fungal disease and 6.3% for viral infections. The only significant risk factor for IRM was time to infection ≥5 months since the beginning of chemotherapy. All patients who have died from infection had BSI and were in neutropenia. Conclusions: Infections in the children with MBT in our study occurred with high frequency, especially in patients with ES. The most frequent were bacterial infections, while fungal and viral infections were episodic. Among the bacterial infections, bloodstream, urinary tract and gastrointestinal tract infections occurred with similar frequency. All deceased patients died due to BSI. Bacterial infection occurring ≥5 months since the beginning of chemotherapy was a risk factor for death.\n\nInfectious complications in children with malignant bone tumors: a multicenter nationwide study.", "token_count": 493, "char_count": 1856, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5356, "quality_score": 0.7678, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:27.575361", "source": { "split": "train_shard_00002", "doc_id": 186 }, "chunk_id": "train_shard_00002_186_0", "global_id": 12983 }, { "text": "The use of microorganisms in industry has enabled the (over)production of various compounds (e.g., primary and secondary metabolites, proteins and enzymes) that are relevant for the production of antibiotics, food, beverages, cosmetics, chemicals and biofuels, among others. Industrial strains are commonly obtained by conventional (non-GMO) strain improvement strategies and random screening and selection. However, recombinant DNA technology has made it possible to improve microbial strains by adding, deleting or modifying specific genes. Techniques such as genetic engineering and genome editing are contributing to the development of industrial production strains. Nevertheless, there is still significant room for further strain improvement. In this review, we will focus on classical and recent methods, tools and technologies used for the development of fungal production strains with the potential to be applied at an industrial scale. Additionally, the use of functional genomics, transcriptomics, proteomics and metabolomics together with the implementation of genetic manipulation techniques and expression tools will be discussed.\n\nStrategies for the Development of Industrial Fungal Producing Strains.", "token_count": 247, "char_count": 1216, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6707, "quality_score": 0.8354, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:28.066001", "source": { "split": "train_shard_00002", "doc_id": 187 }, "chunk_id": "train_shard_00002_187_0", "global_id": 12984 }, { "text": "Carbapenem-resistant Acinetobacter baumannii (A. baumannii, CRAb) is an emerging global threat for healthcare systems, particularly in Southeast Asia. Next-generation sequencing (NGS) technology was employed to map genes associated with antimicrobial resistance (AMR) and to identify multilocus sequence types (MLST). Eleven strains isolated from humans in Vietnam were sequenced, and their AMR genes and MLST were compared to published genomes of strains originating from Southeast Asia, i.e., Thailand (n = 49), Myanmar (n = 38), Malaysia (n = 11), Singapore (n = 4) and Taiwan (n = 1). Ten out of eleven Vietnamese strains were CRAb and were susceptible only to colistin. All strains harbored ant(3\")-IIa, armA, aph(6)-Id and aph(3\") genes conferring resistance to aminoglycosides, and blaOXA-51 variants and blaADC-25 conferring resistance to ß-lactams. More than half of the strains harbored genes that confer resistance to tetracyclines, sulfonamides and macrolides. The strains showed high diversity, where six were assigned to sequence type (ST)/2, and two were allocated to two new STs (ST/1411-1412). MLST analyses of 108 strains from Southeast Asia identified 19 sequence types (ST), and ST/2 was the most prevalent found in 62 strains", "token_count": 441, "char_count": 1337, "word_count": 184, "semantic_coherence": 1, "information_density": 0.6522, "quality_score": 0.8261, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:28.701883", "source": { "split": "train_shard_00002", "doc_id": 188 }, "chunk_id": "train_shard_00002_188_0", "global_id": 12985 }, { "text": "A broad range of AMR genes was identified mediating resistance to ß-lactams, including cephalosporins and carbapenems (e.g., blaOXA-51-like, blaOXA-23, blaADC-25, blaADC-73, blaTEM-1, blaNDM-1), aminoglycosides (e.g., ant(3\")-IIa, aph(3\")-Ib, aph(6)-Id, armA and aph(3')-Ia), phenicoles (e.g., catB8), tetracyclines (e.g., tet.B and tet.39), sulfonamides (e.g., sul.1 and sul.2), macrolides and lincosamide (e.g., mph.E, msr.E and abaF). MLST and core genome MLST (cgMLST) showed an extreme diversity among the strains. Several strains isolated from different countries clustered together by cgMLST; however, different clusters shared the same ST. Developing an action plan on AMR, increasing awareness and prohibiting the selling of antibiotics without prescription must be mandatory for this region. Such efforts are critical for enforcing targeted policies on the rational use of carbapenem compounds and controlling AMR dissemination and emergence in general.\n\nWGS-Based Analysis of Carbapenem-Resistant Acinetobacter baumannii in Vietnam and Molecular Characterization of Antimicrobial Determinants and MLST in Southeast Asia.", "token_count": 473, "char_count": 1264, "word_count": 146, "semantic_coherence": 1, "information_density": 0.7808, "quality_score": 0.8904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:29.338964", "source": { "split": "train_shard_00002", "doc_id": 188 }, "chunk_id": "train_shard_00002_188_1", "global_id": 12986 }, { "text": "Second-generation sequencing technologies are revolutionizing the study of metagenomes. Whole-genome shotgun sequencing of metagenomic DNA may become an attractive alternative to the current widely used ribosomal RNA gene studies. Large data sets of short sequence reads are mapped onto a custom microbial reference sequence. If a bacterial pangenome of completely sequenced genomes is taken as a reference, the output consists of the distribution of bacterial taxa in and bacterial gene contents of the metagenome. The relative abundance of functional categories and of individual pathways and fitness traits encoded by the metagenomic gene pool provides insight into habitat-specific features of the microbial community. Polymorphic sites in sequence reads may resolve the number and abundance of individual clonal complexes of dominant species in the polymicrobial community. These SNPs and de novo mutations may be exploited to trace the spatiotemporal spread of clones and the emergence of novel traits such as fitness or resistance determinants. In conclusion, massively parallel sequencing of metagenomic DNA allows deep insights into the composition and the genetic repertoire of polymicrobial communities.\n\nAdvances in computational analysis of metagenome sequences.", "token_count": 265, "char_count": 1275, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6389, "quality_score": 0.8194, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:29.890447", "source": { "split": "train_shard_00002", "doc_id": 189 }, "chunk_id": "train_shard_00002_189_0", "global_id": 12987 }, { "text": "Among 47 tested yeast strains, belonging to different genera, only two cultures of Kluyveromyces fragilis and Fabospora fragilis showed beta-galactosidase activity in shaken flasks. Three types of extraction were used to release the enzyme from K. fragilis cells: solvent and detergent extraction, freezing and thawing extraction, and mechanical disintegration prior to extraction, using Triton X-100. The results indicate that the highest yield could be obtained by mechanical disintegration of cells. Factors affecting the enzyme production were studied using fermentation media of different chemical composition. The medium containing lactose, salts and yeast extract with initial pH 7.0 was selected as the best for enzyme production. Monobasic ammonium phosphate (2.0 g/dm3) was found to be the best inorganic nitrogen source for enzyme production. The effect of phosphorus level was also studied.\n\nSelection of strain, culture conditions and extraction procedures for optimum production of beta-galactosidase from Kluyveromyces fragilis.", "token_count": 259, "char_count": 1043, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:30.442267", "source": { "split": "train_shard_00002", "doc_id": 190 }, "chunk_id": "train_shard_00002_190_0", "global_id": 12988 }, { "text": "Toxin A-negative, toxin B-positive Clostridioides difficile strains, which primarily include the ST81 and ST37 genotypes, are predominant in C. difficile infections leading to antibiotic-associated diarrhea in China. Recently, ST81 has been reported as the most prevalent genotype rather than ST37, although the genetic and functional characteristics of the two genotypes remain ambiguous. In this study, we conducted comprehensive comparative analysis of these two genotypes through complete genome sequencing and phenotypic profiling. The whole genome sequencing revealed that the ST81 and ST37 isolates were closely related genetically with similar gene compositions, and high rate of the core genome shared. The integrative and conjugative elements identified in ST81 were similar to those in ST37, albeit with more diverse and insertion regions. By characterizing the phenotypes related to colonization or survival in the host, we found that the ST81 isolates exhibited robust colonization ability and survival both in vitro and in vivo, enhanced spore production, and slightly increased motility, which may be attributable to the discrepancy in non-synonymous single-nucleotide polymorphisms in the relevant functional genes. Furthermore, the ST81 isolates displayed a significantly higher rate of resistance to fluoroquinolones compared with the ST37 isolates (94.12% vs. 62.5%) and mostly carried the amino acid substitution Asp426Val in GyrB. In summary, the results of our study indicate that ST81 isolates exhibit enhanced ability to transmit between hosts and survive in harsh environments, providing key genetic insights for further epidemiological investigations and surveillance of C. difficile infection.\n\nComplete Genome Sequencing and Comparative Phenotypic Analysis Reveal the Discrepancy Between Clostridioides difficile ST81 and ST37 Isolates.", "token_count": 483, "char_count": 1906, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6031, "quality_score": 0.8016, "entities": { "genes": [ "ST81", "ST37" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:31.088946", "source": { "split": "train_shard_00002", "doc_id": 191 }, "chunk_id": "train_shard_00002_191_0", "global_id": 12989 }, { "text": "Rice brown spot disease, caused by Bipolaris oryzae, is a significant fungal disease that poses a major threat to global rice production. Despite its widespread impact, genomic studies of B. oryzae remain limited, particularly those involving high-quality genomic data. In this study, we performed whole-genome sequencing of the B. oryzae strain RBD1, which was isolated from the demonstration field for upland rice cultivation in Haozhiba Village, Lancang County, Pu'er City, Yunnan Province, China, using a combination of second-generation Illumina sequencing and third-generation Single-Molecule Real-Time (SMRT) sequencing. The assembled genome was 37.5 Mb in size with a G + C content of 49.39%, containing 42 contigs with a contig N50 of 2.0 Mb. Genomic analysis identified genes related to carbon, nitrogen, and lipid metabolism, highlighting the strain's metabolic flexibility under diverse environmental conditions and host interactions. Additionally, we identified pathogenicity-related genes involved in MAPK signaling, G protein signaling, and oxidative stress responses. Under 1.2 M sorbitol-induced osmotic stress, we observed significant differences in growth responses between RBD1 and the rice blast fungus Magnaporthe oryzae H7. Transcriptomic analysis using Illumina sequencing revealed that RBD1 responds to osmotic stress by enhancing carbohydrate metabolism, fatty acid degradation, and amino acid synthesis, while H7 primarily relies on protein synthesis to enhance growth tolerance. This study provides a valuable foundation for understanding the pathogenic mechanisms of rice brown spot and future disease control strategies.\n\nGenome Sequencing and Comparative Transcriptomic Analysis of Rice Brown Spot Pathogen <i>Bipolaris oryzae</i> Adaptation to Osmotic Stress.", "token_count": 480, "char_count": 1831, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [ "RBD1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:31.735014", "source": { "split": "train_shard_00002", "doc_id": 192 }, "chunk_id": "train_shard_00002_192_0", "global_id": 12990 }, { "text": "Whole genome sequencing (WGS) enables high resolution typing of bacteria up to the single nucleotide polymorphism (SNP) level. WGS is used in clinical microbiology laboratories for infection control, molecular surveillance and outbreak analyses. Given the large palette of WGS reagents and bioinformatics tools, the Swiss clinical bacteriology community decided to conduct a ring trial (RT) to foster harmonization of NGS-based bacterial typing. The RT aimed at assessing methicillin-susceptible Staphylococcus aureus strain relatedness from WGS and epidemiological data. The RT was designed to disentangle the variability arising from differences in sample preparation, SNP calling and phylogenetic methods. Nine laboratories participated. The resulting phylogenetic tree and cluster identification were highly reproducible across the laboratories. Cluster interpretation was, however, more laboratory dependent, suggesting that an increased sharing of expertise across laboratories would contribute to further harmonization of practices. More detailed bioinformatic analyses unveiled that while similar clusters were found across laboratories, these were actually based on different sets of SNPs, differentially retained after sample preparation and SNP calling procedures. Despite this, the observed number of SNP differences between pairs of strains, an important criterion to determine strain relatedness given epidemiological information, was similar across pipelines for closely related strains when restricting SNP calls to a common core genome defined by S. aureus cgMLST schema. The lessons learned from this pilot study will serve the implementation of larger-scale RT, as a mean to have regular external quality assessments for laboratories performing WGS analyses in a clinical setting.\n\nNGS-Based S. aureus Typing and Outbreak Analysis in Clinical Microbiology Laboratories: Lessons Learned From a Swiss-Wide Proficiency Test.", "token_count": 442, "char_count": 1961, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:32.370176", "source": { "split": "train_shard_00002", "doc_id": 193 }, "chunk_id": "train_shard_00002_193_0", "global_id": 12991 }, { "text": "Coryneform bacteria and yeasts of 21 brick cheeses from six German dairies, produced by using undefined ripening cultures, were identified. Arthrobacter nicotianae, Brevibacterium linens, Corynebacterium ammoniagenes, Corynebacterium variabilis and Rhodococcus fascians were found in significant numbers. Out of 148 coryneform isolates 36 could not be identified at the species level. With the exception of a large rennet cheese, the coryneform microflora of rennet and acid cured cheeses were similar, but the cheeses had clearly different yeast populations. Debaryomyces hansenii and Galactomyces geotrichum prevailed in rennet cheeses while Kluyveromyces marxianus and Pichia membranaefaciens were the main species found in acid cured cheese. The dominance of Yarrowia lipolytica probably indicates an improper yeast population, resulting in poor cheese quality. Some of the species identified are potential candidates for designing a defined ripening culture for rennet red smear cheese.\n\nIdentification of yeasts and coryneform bacteria from the surface microflora of brick cheeses.", "token_count": 284, "char_count": 1087, "word_count": 149, "semantic_coherence": 1, "information_density": 0.6577, "quality_score": 0.8289, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:32.925065", "source": { "split": "train_shard_00002", "doc_id": 194 }, "chunk_id": "train_shard_00002_194_0", "global_id": 12992 }, { "text": "Bacterial genomes are composed of core and accessory genomes. The first is composed of housekeeping and essential genes, while the second is highly enriched in mobile genetic elements, including transposable elements (TEs). Insertion sequences (ISs), the smallest TEs, have an important role in genome evolution, and contribute to bacterial genome plasticity and adaptability. ISs can spread in a genome, presenting different locations in nearly related strains, and producing phenotypic variations. Few tools are available which can identify differentially located ISs (DLISs) on assembled genomes. Here, we introduce ISCompare, a new program to profile IS mobilization events in related bacterial strains using complete or draft genome assemblies. ISCompare was validated using artificial genomes with simulated random IS insertions and real sequences, achieving the same or better results than other available tools, with the advantage that ISCompare can analyze multiple ISs at the same time and outputs a list of candidate DLISs. ISCompare provides an easy and straightforward approach to look for differentially located ISs on bacterial genomes.\n\nEasy identification of insertion sequence mobilization events in related bacterial strains with ISCompare.", "token_count": 263, "char_count": 1259, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6536, "quality_score": 0.8268, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:33.482098", "source": { "split": "train_shard_00002", "doc_id": 195 }, "chunk_id": "train_shard_00002_195_0", "global_id": 12993 }, { "text": "Neisseria meningitidis is a leading cause of bacterial meningitis and sepsis worldwide and an occasional cause of meningococcal urethritis. When isolates are unavailable for surveillance or outbreak investigations, molecular characterization of pathogens needs to be performed directly from clinical specimens, such as cerebrospinal fluid (CSF), blood, or urine. However, genome sequencing of specimens is challenging because of low bacterial and high human DNA abundances. We developed selective whole-genome amplification (SWGA), an isothermal multiple-displacement amplification-based method, to efficiently enrich, sequence, and de novo assemble N. meningitidis DNA from clinical specimens with low bacterial loads. SWGA was validated with 12 CSF specimens from invasive meningococcal disease cases and 12 urine specimens from meningococcal urethritis cases. SWGA increased the mean proportion of N. meningitidis reads by 2 to 3 orders of magnitude, enabling identification of at least 90% of the 1,605 N. meningitidis core genome loci for 50% of the specimens. The validated method was used to investigate two meningitis outbreaks recently reported in Togo and Burkina Faso. Twenty-seven specimens with low bacterial loads were processed by SWGA before sequencing, and 12 of 27 were successfully assembled to obtain the full molecular typing and vaccine antigen profile of the N. meningitidis pathogen, thus enabling thorough characterization of outbreaks. This method is particularly important for enhancing molecular surveillance in regions with low culture rates. SWGA produces enough reads for phylogenetic and allelic analysis at a low cost. More importantly, the procedure can be extended to enrich other important human bacterial pathogens.\n\nFull Molecular Typing of Neisseria meningitidis Directly from Clinical Specimens for Outbreak Investigation.", "token_count": 498, "char_count": 1904, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6077, "quality_score": 0.8038, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:34.136128", "source": { "split": "train_shard_00002", "doc_id": 196 }, "chunk_id": "train_shard_00002_196_0", "global_id": 12994 }, { "text": "Continuous ethanol production by a flocculating strain of Kluyveromyces marxianus: bioreactor performance.", "token_count": 29, "char_count": 106, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:34.505315", "source": { "split": "train_shard_00002", "doc_id": 197 }, "chunk_id": "train_shard_00002_197_0", "global_id": 12995 }, { "text": "The thermotolerant yeast Ogataea parapolymorpha (formerly Hansenula polymorpha) is an industrially relevant production host that exhibits a fully respiratory sugar metabolism in aerobic batch cultures. NADH-derived electrons can enter its mitochondrial respiratory chain either via a proton-translocating complex I NADH-dehydrogenase or via three putative alternative NADH dehydrogenases. This respiratory entry point affects the amount of ATP produced per NADH/O2 consumed and therefore impacts the maximum yield of biomass and/or cellular products from a given amount of substrate. To investigate the physiological importance of complex I, a wild-type O. parapolymorpha strain and a congenic complex I-deficient mutant were grown on glucose in aerobic batch, chemostat, and retentostat cultures in bioreactors. In batch cultures, the two strains exhibited a fully respiratory metabolism and showed the same growth rates and biomass yields, indicating that, under these conditions, the contribution of NADH oxidation via complex I was negligible. Both strains also exhibited a respiratory metabolism in glucose-limited chemostat cultures, but the complex I-deficient mutant showed considerably reduced biomass yields on substrate and oxygen, consistent with a lower efficiency of respiratory energy coupling. In glucose-limited retentostat cultures at specific growth rates down to ∼0.001 h-1, both O. parapolymorpha strains showed high viability. Maintenance energy requirements at these extremely low growth rates were approximately 3-fold lower than estimated from faster-growing chemostat cultures, indicating a stringent-response-like behavior", "token_count": 443, "char_count": 1699, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:35.134123", "source": { "split": "train_shard_00002", "doc_id": 198 }, "chunk_id": "train_shard_00002_198_0", "global_id": 12996 }, { "text": "Quantitative transcriptome and proteome analyses indicated condition-dependent expression patterns of complex I subunits and of alternative NADH dehydrogenases that were consistent with physiological observations.IMPORTANCE Since popular microbial cell factories have typically not been selected for efficient respiratory energy coupling, their ATP yields from sugar catabolism are often suboptimal. In aerobic industrial processes, suboptimal energy coupling results in reduced product yields on sugar, increased process costs for oxygen transfer, and volumetric productivity limitations due to limitations in gas transfer and cooling. This study provides insights into the contribution of mechanisms of respiratory energy coupling in the yeast cell factory Ogataea parapolymorpha under different growth conditions and provides a basis for rational improvement of energy coupling in yeast cell factories. Analysis of energy metabolism of O. parapolymorpha at extremely low specific growth rates indicated that this yeast reduces its energy requirements for cellular maintenance under extreme energy limitation. Exploration of the mechanisms for this increased energetic efficiency may contribute to an optimization of the performance of industrial processes with slow-growing eukaryotic cell factories.\n\nContribution of Complex I NADH Dehydrogenase to Respiratory Energy Coupling in Glucose-Grown Cultures of Ogataea parapolymorpha.", "token_count": 312, "char_count": 1461, "word_count": 187, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:35.694176", "source": { "split": "train_shard_00002", "doc_id": 198 }, "chunk_id": "train_shard_00002_198_1", "global_id": 12997 }, { "text": "The RapID Yeast Plus System (Innovative Diagnostic Systems, Norcross, Ga.) is a qualitative micromethod that uses conventional and chromogenic substrates for the identification of medically important yeasts. The ability of the RapID Yeast Plus system to accurately identify 304 clinical yeast isolates within 5 h was evaluated. The RapID Yeast Plus method correctly identified 286 (94.1%) of strains to the species level without the need for additional tests. A further 12 strains (3.9%) were classified as correct to the genus level or to a low-probability identification with two or more possibilities. In these latter cases, additional tests were required to delineate the correct identification. Organisms in the latter group comprised Candida parapsilosis (n = 1), Candida tropicalis (n = 1), Candida ciferrii (n = 1), Candida guilliermondii (n = 2), Candida humicola (n = 1), Candida kefyr (n = 1), Cryptococcus neoformans (n = 1), and Rhodotorula rubra (n = 4). Six strains (2.0%) were misidentified or did not yield codes in the manufacturer's database. These included one Candida utilis (identified as Candida famata/Candida guilliermondii), one Trichosporon beigelii (identified as Cryptococcus neoformans), one Candida diddensiae (identified as Candida albicans), one Candida membranaefaciens (identified as Candida parapsilosis), one Candida norvegensis (identified as Candida zeylanoides), and one Candida catenulata (no code) isolate; the last four strains are not included in the firm's current database. The RapID Yeast Plus system yielded excellent results and may be recommended for use in the routine laboratory for accurate same-day identification of clinically significant yeasts.\n\nAbility of RapID Yeast Plus System to identify 304 clinically significant yeasts within 5 hours.", "token_count": 484, "char_count": 1799, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5285, "quality_score": 0.7643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:36.353274", "source": { "split": "train_shard_00002", "doc_id": 199 }, "chunk_id": "train_shard_00002_199_0", "global_id": 12998 }, { "text": "Kluyveromyces-like intergeneric hybrids of thermotolerant Kluyveromyces marxianus and non-thermotolerant Saccharomyces cerevisiae, produced in a previous study by protoplasmic fusion, have been characterized. On molasses, these strains produced ethanol in excess of 6% (v/v) both at 30 and 45 degrees C as against 3% and 4.2% (v/v) by the former parent at 30 and 45 degrees C, respectively. In hybrids, the increase in ethanol production appeared to be a sequel to increased activities of alcohol dehydrogenase and pyruvate kinase, derived probably from S. cerevisiae parent. Hybrid ADH-isozyme pattern on polyacrylamide gel corroborated the presence of S. cerevisiae ADH in the tested hybrids. Regression analyses indicated a positive correlation between ethanol production and ADH or PK or both (r approximately 0.76-0.84).\n\nPhysiological and biochemical characterization of intergeneric hybrids of thermotolerant and non-thermotolerant yeasts.", "token_count": 278, "char_count": 946, "word_count": 131, "semantic_coherence": 1, "information_density": 0.6794, "quality_score": 0.8397, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:36.911325", "source": { "split": "train_shard_00002", "doc_id": 200 }, "chunk_id": "train_shard_00002_200_0", "global_id": 12999 }, { "text": "Saccharomyces cerevisiae cells, Kluyveromyces marxianus cells, inulase, glucose oxidase, chloroplasts, and mitochondria were immobilized in calcium alginate gels. Ethanol production from glucose solutions by an immobilized preparation of S. cerevisiae was deomonstrated over a total of twenty-three days, and the half-life of such a preparation was shown to be about ten days. Immobilized K. marxianus, inulase, and glucose oxidase preparations were used to demonstrate the porosity and retraining properties of calcium alginate gels. Calcium alginate-immobilized chloroplasts were shown to perform the Hill reaction. Some experiments with immobilized mitochondria are reported.\n\nThe immobilization of microbial cells, subcellular organelles, and enzymes in calcium alginate gels.", "token_count": 215, "char_count": 780, "word_count": 103, "semantic_coherence": 1, "information_density": 0.6408, "quality_score": 0.8204, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:38.686520", "source": { "split": "train_shard_00002", "doc_id": 201 }, "chunk_id": "train_shard_00002_201_0", "global_id": 13000 }, { "text": "Antimicrobial resistance (AMR) in Mycoplasma bovis has been previously associated with topoisomerase and ribosomal gene mutations rather than specific resistance-conferring genes. Using whole genome sequencing (WGS) to identify potential new AMR mechanisms for M. bovis, it was found that a 2019 clinical isolate with high MIC (2019-043682) for fluoroquinolones, macrolides, lincosamides, pleuromutilins and tetracyclines had a new core genome multilocus sequencing (cgMLST) type (ST10-like) and 91% sequence similarity to the published genome of M. bovis PG45. Closely related to PG45, a 1982 isolate (1982-M6152) shared the same cgMLST type (ST17), 97.2% sequence similarity and low MIC results. Known and potential AMR- associated genetic events were identified through multiple sequence alignment of the three genomes. Isolate 2019-043682 had 507 genes with non-synonymous mutations (NSMs) and 67 genes disrupted. Isolate 1982-M6152 had 81 NSMs and 20 disruptions. Using functional roles and known mechanisms of antimicrobials, a 55 gene subset was assessed for AMR potential. Seventeen were previously identified from other bacteria as sites of AMR mutation, 38 shared similar functions to them, and 11 contained gene-disrupting mutations. This study indicated that M. bovis may obtain high AMR characteristics by mutating or disrupting other functional genes, in addition to topoisomerases and ribosomal genes.\n\nIdentification of Antimicrobial Resistance-Associated Genes through Whole Genome Sequencing of Mycoplasma bovis Isolates with Different Antimicrobial Resistances.", "token_count": 501, "char_count": 1615, "word_count": 217, "semantic_coherence": 1, "information_density": 0.6406, "quality_score": 0.8203, "entities": { "genes": [ "ST17", "ST10", "PG45" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:39.379452", "source": { "split": "train_shard_00002", "doc_id": 202 }, "chunk_id": "train_shard_00002_202_0", "global_id": 13001 }, { "text": "High-risk ESBL-producing Enterobacteriaceae (ESBL-E) have been described in wild birds and rodents worldwide. Rats are of special interest not only due to their indicator role for environmental pollution with multi-resistant bacteria but also as possible infection source. Data on the presence of high-risk ESBL-E in urban wildlife from Africa remain scarce, however. Twenty-nine animals from three different rat (Rattus) species were captured in the city of Conakry (Guinea, West Africa) in 2015. Rectal swabs were analyzed for ESBL-E using selective media. Species typing and phenotypic antimicrobial resistance analysis to broad-spectrum beta-lactams and other classes of antimicrobials was performed for Enterobacteriaceae-like isolates using the VITEK®2 system (BioMérieux, Germany). Confirmed ESBL-producing E. coli and K. pneumoniae were whole-genome sequenced and resistance genes, phylogenetic background and genes related to bacterial fitness and virulence were analyzed. In total, six of twenty-nine rats (20%) carried ESBL-E (K. pneumoniae and E. coli). All ESBL-producers were multi-drug resistant with blaCTX-M-15 as the dominating ESBL-type. Interestingly, ESBL-associated clonal lineages E. coli ST38 and K. pneumoniae ST307 were found. The ESBL-plasmid in K. pneumoniae ST307 revealed high sequence similarities to pKPN3-307_TypeC, a >200 kbp IncFII plasmid originating from a human clinical ST307 isolate. This was in contrast to the core genome: the rat isolate was distantly related to the human clinical ST307 isolate (27 SNPs/Mbp)", "token_count": 505, "char_count": 1626, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6806, "quality_score": 0.8403, "entities": { "genes": [ "ST38", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:40.039818", "source": { "split": "train_shard_00002", "doc_id": 203 }, "chunk_id": "train_shard_00002_203_0", "global_id": 13002 }, { "text": "In addition, we identified π-fimbrial, capsule 2, and glycogen synthesis clusters in the rodent ST307 isolate, whose involvement in the adaptation to survival outside the host and in human urinary tracts has been suggested. Our results demonstrate the presence of clinically relevant, ESBL-producing K. pneumoniae ST307 and E. coli ST38 clonal lineages in an urban West African rat population. The human community is likely the initial source of ESBL-E however, rats might function as infection source and transmission hub, accelerated by frequent interactions at a human-wildlife interface.\n\nClinically Relevant ESBL-Producing K. pneumoniae ST307 and E. coli ST38 in an Urban West African Rat Population.", "token_count": 205, "char_count": 733, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [ "ST38", "ST307" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:40.497681", "source": { "split": "train_shard_00002", "doc_id": 203 }, "chunk_id": "train_shard_00002_203_1", "global_id": 13003 }, { "text": "A novel Bifidobacterium strain, Tam10BT, i.e. LMG 30126T, was isolated from emperor tamarin (Saguinus imperator). Cells were Gram-positive, non-motile, non-sporulating, non-haemolytic, facultative anaerobic and fructose 6-phosphate phosphoketolase-positive. Phylogenetic analyses based on 16S rRNA genes as well as multilocus sequences (representing hsp60, rpoB, dnaJ, dnaG and clpC genes) and the core genome revealed that Bifidobacterium Tam10BT exhibited close phylogenetic relatedness to Bifidobacterium tissieri DSM 100201T. Comparative analysis of 16S rRNA gene sequences confirmed the phylogenetic results showing the highest gene sequence identity with strain B. tissieri DSM 100201T (96.5 %). Furthermore, genotyping based on the genome sequence of Tam 10B, in combination with phenotypic analyses, clearly showed that strain Tam10BT is distinct from each of the type strains of the so far recognized Bifidobacterium species. The type strain Tam10BT (=LMG 30126T=CCUG 70655T) represents a novel species, for which the name Bifidobacteriumvansinderenii sp. nov is proposed.\n\nBifidobacterium vansinderenii sp. nov., isolated from faeces of emperor tamarin (Saguinus imperator).", "token_count": 447, "char_count": 1283, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6923, "quality_score": 0.8462, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:41.122992", "source": { "split": "train_shard_00002", "doc_id": 204 }, "chunk_id": "train_shard_00002_204_0", "global_id": 13004 }, { "text": "The emergence of antimicrobial resistance (AMR) is a principal global health crisis projected to cause 10 million deaths annually worldwide by 2050. While the Gram-negative bacteria Escherichia coli is commonly found as a commensal microbe in the human gut, some strains are dangerously pathogenic, contributing to the highest AMR-associated mortality. Strains of E. coli that can translocate from the gastrointestinal tract to distal sites, called extraintestinal E. coli (ExPEC), are particularly problematic and predominantly afflict women, the elderly, and immunocompromised populations. Despite nearly 40 years of clinical trials, there is still no vaccine against ExPEC. One reason for this is the remarkable diversity in the ExPEC pangenome across pathotypes, clades, and strains, with hundreds of genes associated with pathogenesis including toxins, adhesins, and nutrient acquisition systems. Further, ExPEC is intimately associated with human mucosal surfaces and has evolved creative strategies to avoid the immune system. This review summarizes previous and ongoing preclinical and clinical ExPEC vaccine research efforts to help identify key gaps in knowledge and remaining challenges.\n\nVaccines against extraintestinal pathogenic <i>Escherichia coli</i> (ExPEC): progress and challenges.", "token_count": 342, "char_count": 1334, "word_count": 178, "semantic_coherence": 1, "information_density": 0.736, "quality_score": 0.868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:41.696963", "source": { "split": "train_shard_00002", "doc_id": 205 }, "chunk_id": "train_shard_00002_205_0", "global_id": 13005 }, { "text": "

Study objective

Our understanding of the molecular dynamics driving the community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) epidemic at the whole genome level is limited. We sought to assess the use of whole genome sequencing (WGS) to evaluate the genomic diversity and genotypic prediction of antimicrobial resistance of CA-MRSA isolates from patients in South Texas.

Design

Comparative whole genome sequencing.

Isolates

Thirteen clinical CA-MRSA isolates recovered from patients presenting with skin and soft tissue infections to nine primary care clinics in the South Texas Ambulatory Research Network between 2010 and 2013.

Measurements and main results

Comparative WGS was performed on the 13 MRSA sequence type 8 clinical isolates. We compared the resistome of genes encoding for antibiotic resistance with a phenotypically derived antibiogram using standard antimicrobial susceptibility testing. The strains differed by an average of 72 single nucleotide polymorphisms (SNPs) per isolate in the core genome compared with FPR3757 (USA300, reference strain). There were a total of 623 unique SNPs in the core genome (range 47-88 SNPs per isolate). We identified 19 nonsynonymous SNPs in genes encoding proven or putative S. aureus virulence determinants in the core genome. There was complete concordance between genotypic evidence for antimicrobial resistance and the phenotypically derived antibiogram.

Conclusion

Overall, although these CA-MRSA isolates were similar on the level of clonal type, clinical syndrome, and geographic area, the strains were diverse at the genome level. Furthermore, our findings provide important proof-of-concept information for using WGS as a potential front-end screening tool for antimicrobial resistance predictions.", "token_count": 472, "char_count": 1817, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [ "USA300", "FPR3757" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:42.340996", "source": { "split": "train_shard_00002", "doc_id": 206 }, "chunk_id": "train_shard_00002_206_0", "global_id": 13006 }, { "text": "Comparative whole genome sequencing of community-associated methicillin-resistant Staphylococcus aureus sequence type 8 from primary care clinics in a Texas community.", "token_count": 42, "char_count": 167, "word_count": 20, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:42.696829", "source": { "split": "train_shard_00002", "doc_id": 206 }, "chunk_id": "train_shard_00002_206_1", "global_id": 13007 }, { "text": "The bacterial genus Bradyrhizobium is biologically important within soils, with different representatives found to perform a range of functions including nitrogen fixation through symbioses, photosynthesis and denitrification. The Highfield experiment at Rothamsted provides an opportunity to study the impact of plants on microbial communities as it has three long-term contrasting regimes; permanent grassland, arable and bare fallow (devoid of plants). The bare fallow plots have a significant reduction in soil carbon and microbial biomass. Bradyrhizobium has been shown by metagenomic studies on soil to be one of the most abundant and active groups including in bare fallow soil indicating that some phenotypes are adapted to survive in the absence of plants. A culture collection was created with isolates obtained from contrasting soil types from Highfield in addition to woodland soil, gorse (Ulex europeaus) and broom (Cytisus scoparius) root nodules. The collection’s phylogeny has been explored by sequencing housekeeping genes to determine whether soil treatment affects the core genome. One grassland and one bare fallow isolate had their genome sequenced and differences have been assessed to establish their ... (continues)\n\nThe microbiology of lean and obese soil", "token_count": 286, "char_count": 1280, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6828, "quality_score": 0.8414, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:43.257785", "source": { "split": "train_shard_00002", "doc_id": 207 }, "chunk_id": "train_shard_00002_207_0", "global_id": 13008 }, { "text": "

Objectives

Colonization and infection with third-generation cephalosporin-resistant Escherichia coli (3GCR-EC) are frequent in haematological and oncological patients. In this high-risk setting, German guidelines recommend single-room contact precautions (SCP) for patients with 3GCR-EC that are non-susceptible to fluoroquinolones (F3GCR-EC). However, this recommendation is controversial, as evidence is limited.

Methods

We performed a prospective, multicentre cohort study at four haematology and oncology departments assessing the impact of SCP on hospital-acquired colonization or bloodstream infection (BSI) with F3GCR-EC. Two sites performed SCP for F3GCR-EC patients including single rooms, gloves and gowns (SCP sites), and two did not (NCP sites). Active screening for 3GCR-EC was performed and isolates were characterized with molecular typing methods including whole genome sequencing and core genome multiple locus sequence typing to assess patient-to-patient transmission. Potential confounders were assessed by competing-risk regression analysis.

Results

Within 12 months, 1386 patients at NCP sites and 1582 patients at SCP sites were included. Hospital-acquisition of F3GCR-EC was observed in 22/1386 (1.59%) and 16/1582 (1.01%) patients, respectively (p 0.191). There were 3/1386 (0.22%) patients with BSI caused by F3GCR-EC at NCP sites and 4/1582 (0.25%) at SCP sites (p 1.000). Patient-to-patient transmission occurred in three cases at NCP and SCP sites each (p 1.000)", "token_count": 461, "char_count": 1512, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6821, "quality_score": 0.841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:43.902306", "source": { "split": "train_shard_00002", "doc_id": 208 }, "chunk_id": "train_shard_00002_208_0", "global_id": 13009 }, { "text": "The number of patients needed to screen in order to prevent one patient-to-patient transmission of F3GCR-EC was determined to be 3729.

Conclusions

Use of SCP had no significant impact on hospital-acquisition or patient-to-patient transmission of F3GCR-EC in this high-risk setting.\n\nImpact of single-room contact precautions on hospital-acquisition and transmission of multidrug-resistant Escherichia coli: a prospective multicentre cohort study in haematological and oncological wards.", "token_count": 137, "char_count": 493, "word_count": 61, "semantic_coherence": 1, "information_density": 0.7213, "quality_score": 0.8607, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:44.329849", "source": { "split": "train_shard_00002", "doc_id": 208 }, "chunk_id": "train_shard_00002_208_1", "global_id": 13010 }, { "text": "Since the description of the genus Arcobacter in 1991, a total of 27 species have been described, although some species have shown 16S rRNA similarities below 95%, which is the cut-off that usually separates species that belong to different genera. The objective of the present study was to reassess the taxonomy of the genus Arcobacter using information derived from the core genome (286 genes), a Multilocus Sequence Analysis (MLSA) with 13 housekeeping genes, as well as different genomic indexes like Average Nucleotide Identity (ANI), in silico DNA-DNA hybridization (isDDH), Average Amino-acid Identity (AAI), Percentage of Conserved Proteins (POCPs), and Relative Synonymous Codon Usage (RSCU). The study included a total of 39 strains that represent all the 27 species included in the genus Arcobacter together with 13 strains that are potentially new species, and the analysis of 57 genomes. The different phylogenetic analyses showed that the Arcobacter species grouped into four clusters. In addition, A. lekithochrous and the candidatus species 'A. aquaticus' appeared, as did A. nitrofigilis, the type species of the genus, in separate branches. Furthermore, the genomic indices ANI and isDDH not only confirmed that all the species were well-defined, but also the coherence of the clusters. The AAI and POCP values showed intra-cluster ranges above the respective cut-off values of 60% and 50% described for species belonging to the same genus. Phenotypic analysis showed that certain test combinations could allow the differentiation of the four clusters and the three orphan species established by the phylogenetic and genomic analyses. The origin of the strains showed that each of the clusters embraced species recovered from a common or related environment", "token_count": 497, "char_count": 1845, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:44.982643", "source": { "split": "train_shard_00002", "doc_id": 209 }, "chunk_id": "train_shard_00002_209_0", "global_id": 13011 }, { "text": "The results obtained enable the division of the current genus Arcobacter in at least seven different genera, for which the names Arcobacter, Aliiarcobacter gen. nov., Pseudoarcobacter gen. nov., Haloarcobacter gen. nov., Malacobacter gen. nov., Poseidonibacter gen. nov., and Candidate 'Arcomarinus' gen. nov. are proposed.\n\nRevisiting the Taxonomy of the Genus Arcobacter: Getting Order From the Chaos.", "token_count": 163, "char_count": 466, "word_count": 56, "semantic_coherence": 1, "information_density": 0.6964, "quality_score": 0.8482, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:45.422141", "source": { "split": "train_shard_00002", "doc_id": 209 }, "chunk_id": "train_shard_00002_209_1", "global_id": 13012 }, { "text": "

Background

The 13-valent pneumococcal conjugate vaccine (PCV-13) was introduced in the United States in 2010. Using a large pediatric carriage sample collected from shortly after the introduction of PCV-7 to several years after the introduction of PCV-13, we investigate alterations in the composition of the pneumococcal population following the introduction of PCV-13, evaluating the extent to which the post-vaccination non-vaccine type (NVT) population mirrors that from prior to vaccine introduction and the effect of PCV-13 on vaccine type lineages.

Methods and Findings

Draft genome assemblies from 736 newly sequenced and 616 previously published pneumococcal carriages isolates from children in Massachusetts between 2001 and 2014 were analyzed. Isolates were classified into one of 22 sequence clusters (SCs) on the basis of their core genome sequence. We calculated the SC diversity for each sampling period as the probability that any two randomly drawn isolates from that period belong to different SCs. The sampling period immediately after the introduction of PCV-13 (2011) was found to have higher diversity than preceding (2007) or subsequent (2014) sampling periods (Simpson’s D 2007: 0.915 95% CI [0.901, 0.929]; 2011: 0.935 [0.927, 0.942]; 2014: 0.912 [0.901, 0.923]). Amongst NVT isolates, we found the distribution of SCs in 2011 to be significantly different from that in 2007 or 2014 (Fisher’s Exact Test p=0.018, 0.0078), but did not find a difference comparing 2007 to 2014 (Fisher’s Exact Test p=0.24), indicating greater similarity between samples separated by a longer time period than between samples from closer time periods", "token_count": 513, "char_count": 1673, "word_count": 247, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8138, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:01:46.059260", "source": { "split": "train_shard_00002", "doc_id": 210 }, "chunk_id": "train_shard_00002_210_0", "global_id": 13013 }, { "text": "We also found changes in the accessory gene content of the NVT population between 2007 and 2011 to have been reduced by 2014. Amongst the new serotypes targeted by PCV-13, four were present in our sample. The proportion of our sample composed of PCV-13-only vaccine serotypes 19A, 6C, and 7F decreased between 2007 and 2014, but no such reduction was seen for serotype 3. We did, however, observe differences in the genetic composition of the pre- and post-PCV-13 serotype 3 population. Our isolates were collected during discrete sampling periods from a small geographic area, which may limit the generalizability our findings.

Conclusion

Pneumococcal diversity increased immediately following the introduction of PCV-13, but subsequently returned to pre-vaccination levels. This is reflected in the distribution of NVT lineages, and, to a lesser extent, their accessory gene frequencies. As such, there may be a period during which the population is particularly disrupted by vaccination before returning to a more stable distribution. The persistence and shifting genetic composition of serotype 3 is a concern and warrants further investigation.\n\nPopulation genomics of pneumococcal carriage in Massachusetts children following PCV-13 introduction", "token_count": 309, "char_count": 1260, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6595, "quality_score": 0.8297, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:46.629350", "source": { "split": "train_shard_00002", "doc_id": 210 }, "chunk_id": "train_shard_00002_210_1", "global_id": 13014 }, { "text": "

ABSTRACT

Background

The persistent decrease in cost and difficulty of whole genome sequencing of microbial organisms has led to a dramatic increase in the number of species and strains characterized from a wide variety of environments. Microbial genome sequencing can now be conducted by small laboratories and as part of undergraduate curriculum. While sequencing is routine in microbiology, assembly, annotation and downstream analyses still require computational resources and expertise, often necessitating familiarity with programming languages. To address this problem, we have created a light-weight, user-friendly tool for the assembly and annotation of microbial sequencing projects.

Results

The Prokaryotic Assembly and Annotation Tool, Peasant, automates the processes of read quality control, genome assembly, and annotation for microbial sequencing projects. High-quality assemblies and annotations can be generated by Peasant without the need of programming expertise or high-performance computing resources. Furthermore, statistics are calculated so that users can evaluate their sequencing project. To illustrate the computational speed and accuracy of Peasant, the SRA records of 322 Illumina platform whole genome sequencing assays for Bacillus species were retrieved from NCBI, assembled and annotated on a single desktop computer. From the assemblies and annotations produced, a comprehensive analysis of the diversity of over 200 high-quality samples was conducted, looking at both the 16S rRNA phylogenetic marker as well as the Bacillus core genome.

Conclusions

Peasant provides an intuitive solution for high-quality whole genome sequence assembly and annotation for users with limited programing experience and/or computational resources. The analysis of the Bacillus whole genome sequencing projects exemplifies the utility of this tool. Furthermore, the study conducted here provides insight into the diversity of the species, the largest such comparison conducted to date.\n\nExploring the Diversity ofBacilluswhole genome sequencing projects using Peasant, the Prokaryotic Assembly and Annotation Tool", "token_count": 488, "char_count": 2171, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5704, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:47.279450", "source": { "split": "train_shard_00002", "doc_id": 211 }, "chunk_id": "train_shard_00002_211_0", "global_id": 13015 }, { "text": "Campylobacter concisus is an emerging enteric pathogen that is associated with several gastrointestinal diseases, such as inflammatory bowel disease (IBD), which includes Crohn's disease (CD) and ulcerative colitis (UC). Currently, only three complete C. concisus genomes are available and more complete C. concisus genomes are needed in order to better understand the genomic features and pathogenicity of this emerging pathogen. DNA extracted from 22 C. concisus strains were subjected to Oxford Nanopore genome sequencing. Complete genome assembly was performed using Nanopore genome data in combination with previously reported short-read Illumina data. Genome features of complete C. concisus genomes were analysed using bioinformatic tools. The enteric disease associations of C. concisus plasmids were examined using 239 C. concisus strains and confirmed using PCRs. Proteomic analysis was used to examine T6SS secreted proteins. We successfully obtained 13 complete C. concisus genomes in this study. Analysis of 16 complete C. concisus genomes (3 from public databases) identified multiple novel plasmids. pSma1 plasmid was found to be associated with severe UC. Sec-SRP, Tat and T6SS were found to be the main secretion systems in C. concisus and proteomic data showed a functional T6SS despite the lack of ClpV. T4SS was found in 25% of complete C. concisus genomes. This study also found that GS2 strains had larger genomes and higher GC content than GS1 strains and more often had plasmids. In conclusion, this study provides fundamental genomic data for understanding C. concisus plasmids, genomospecies features, evolution, secretion systems and pathogenicity.", "token_count": 505, "char_count": 1773, "word_count": 246, "semantic_coherence": 1, "information_density": 0.5813, "quality_score": 0.7907, "entities": { "genes": [ "GS1", "GS2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:47.928266", "source": { "split": "train_shard_00002", "doc_id": 212 }, "chunk_id": "train_shard_00002_212_0", "global_id": 13016 }, { "text": "Analysis of complete Campylobacter concisus genomes identifies genomospecies features, secretion systems and novel plasmids and their association with severe ulcerative colitis.", "token_count": 45, "char_count": 184, "word_count": 21, "semantic_coherence": 1, "information_density": 0.9524, "quality_score": 0.9762, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:48.284699", "source": { "split": "train_shard_00002", "doc_id": 212 }, "chunk_id": "train_shard_00002_212_1", "global_id": 13017 }, { "text": "Verticillium dahliae is a widespread soilborne fungus that causes Verticillium wilt on numerous economically important plant species. In tomato, until now, three races have been characterized based on the response of differential cultivars to V. dahliae, but the genetic basis of race divergence in V. dahliae remains undetermined. To investigate the genetic basis of race divergence, we sequenced the genomes of two race 2 strains and four race 3 strains for comparative analyses with two known race 1 genomes. The genetic basis of race divergence was described by the pathogenicity-related genes among the three races, orthologue analyses, and genomic structural variations. Global comparative genomics showed that chromosomal rearrangements are not the only source of race divergence and that race 3 should be split into two genotypes based on orthologue clustering. Lineage-specific regions (LSRs), frequently observed between genomes of the three races, encode several predicted secreted proteins that potentially function as suppressors of immunity triggered by known effectors. These likely contribute to the virulence of the three races. Two genes in particular that can act as markers for race 2 and race 3 (VdR2e and VdR3e, respectively) contribute to virulence on tomato, and the latter acts as an avirulence factor of race 3. We elucidated the genetic basis of race divergence through global comparative genomics and identified secreted proteins in LSRs that could potentially play critical roles in the differential virulence among the races in V. dahliae. IMPORTANCE Deciphering the gene-for-gene relationships during host-pathogen interactions is the basis of modern plant resistance breeding. In the Verticillium dahliae-tomato pathosystem, two races (races 1 and 2) and their corresponding avirulence (Avr) genes have been identified, but strains that lack these two Avr genes exist in nature. In this system, race 3 has been described, but the corresponding Avr gene has not been identified", "token_count": 511, "char_count": 2050, "word_count": 300, "semantic_coherence": 1, "information_density": 0.5267, "quality_score": 0.7633, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:48.915900", "source": { "split": "train_shard_00002", "doc_id": 213 }, "chunk_id": "train_shard_00002_213_0", "global_id": 13018 }, { "text": "We de novo-sequenced genomes of six strains and identified secreted proteins within the lineage-specific regions (LSRs) distributed among the genomes of the three races that could potentially function as manipulators of host immunity. One of the LSR genes, VdR3e, was confirmed as the Avr gene for race 3. The results indicate that differences in transcriptional regulation may contribute to race differentiation. This is the first study to describe these differences and elucidate roles of secreted proteins in LSRs that play roles in race differentiation.\n\nFunctional Genomics and Comparative Lineage-Specific Region Analyses Reveal Novel Insights into Race Divergence in Verticillium dahliae.", "token_count": 185, "char_count": 716, "word_count": 100, "semantic_coherence": 1, "information_density": 0.71, "quality_score": 0.855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:49.368572", "source": { "split": "train_shard_00002", "doc_id": 213 }, "chunk_id": "train_shard_00002_213_1", "global_id": 13019 }, { "text": "Several individuals reported gastrointestinal symptoms following meals consumed in late January 2021 at a restaurant in western Finland. We conducted a retrospective cohort study and defined a case as a person who ate at the lunch restaurant between 27 and 29 January 2021 and had stomach pain, vomiting or diarrhoea and/or a laboratory-confirmed Salmonella Typhimurium infection within 2 weeks after the exposure. We collected faecal and food samples for microbiological analysis. Salmonella isolates were characterised in detail using whole genome sequencing (WGS) and cluster analysis by core genome multilocus sequence typing (cgMLST). Altogether, 393 meals were sold and 101 people (who ate 142 meals) participated in the cohort study. There were 49 cases; 23 were laboratory-confirmed infections with a multidrug-resistant S. Typhimurium. The S. Typhimurium isolates from cases and frozen tomato cubes used uncooked in salads were closely related and clustered together in cgMLST comparison. These salads were consumed by 76% of the cases. Based on the cgMLST clustering, they were the suggested source of the outbreak. Statistical association was not significant between eating the salads and being a case. Following the outbreak investigation, the producer decided to recommend cooking of their frozen tomato products before consumption.\n\nSalmonella Typhimurium outbreak associated with frozen tomato cubes at a restaurant in western Finland, January to February 2021.", "token_count": 391, "char_count": 1511, "word_count": 215, "semantic_coherence": 1, "information_density": 0.6558, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:50.007890", "source": { "split": "train_shard_00002", "doc_id": 214 }, "chunk_id": "train_shard_00002_214_0", "global_id": 13020 }, { "text": "Kefir is obtained by milk fermentation with a complex microbial population included in a matrix of polysaccharide and proteins. Several health-promoting activities has been attributed to kefir consumption. The aim of this study was to select microorganisms from kefir able to down-regulate intestinal epithelial innate response and further characterize this activity. Caco-2 cells stably transfected with a human CCL20 promoter luciferase reporter were used to screen a collection of 24 yeast and 23 bacterial strains isolated from kefir. The Toll-like receptor 5 agonist, flagellin was used to activate the reporter cells, while pre-incubation with the selected strains was tested to identify strains with the capacity to inhibit cell activation. In this system, 21 yeast strains from the genera Saccharomyces, Kluyveromyces and Issatchenkia inhibited almost 100% of the flagellin-dependent activation, whereas only some lactobacilli strains showed a partial effect. K. marxianus CIDCA 8154 was selected for further characterization. Inhibitory activity was confirmed at transcriptional level on Caco-2/TC-7 and HT-29 cells upon flagellin stimulation. A similar effect was observed using other pro-inflammatory stimulation such as IL-1beta and TNF-alpha. Pre-incubation with yeasts induced a down-regulation of NF-kappaB signalling in epithelial cells in vitro, as well as expression of other pro-inflammatory chemokines such as CXCL8 and CXCL2. Furthermore, modulation of CCL20 mRNA expression upon flagellin stimulation was evidenced in vivo, in a mouse ligated intestinal loop model. Results indicate kefir contains microorganisms able to abolish the intestinal epithelial inflammatory response that could explain some of the properties attributed to this fermented milk.\n\nDown-regulation of intestinal epithelial innate response by probiotic yeasts isolated from kefir.", "token_count": 495, "char_count": 1874, "word_count": 260, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [ "CCL20", "CXCL2", "CXCL8" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:50.684464", "source": { "split": "train_shard_00002", "doc_id": 215 }, "chunk_id": "train_shard_00002_215_0", "global_id": 13021 }, { "text": "Metataxonomic 16S rDNA based studies are a commonplace and useful tool in the research of the microbiome, but they do not provide the full investigative power of metagenomics and metatranscriptomics for revealing the functional potential of microbial communities. However, the use of metagenomic and metatranscriptomic technologies is hindered by high costs and skills barrier necessary to generate and interpret the data. To address this, a tool for Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was developed for inferring the functional potential of an observed microbiome profile, based on 16S data. This allows functional inferences to be made from metataxonomic 16S rDNA studies with little extra work or cost, but its accuracy relies on the availability of completely sequenced genomes of representative organisms from the community being investigated. The rumen microbiome is an example of a community traditionally underrepresented in genome and sequence databases, but recent efforts by projects such as the Global Rumen Census and Hungate 1000 have resulted in a wide sampling of 16S rDNA profiles and almost 500 fully sequenced microbial genomes from this environment. Using this information, we have developed \"CowPI,\" a focused version of the PICRUSt tool provided for use by the wider scientific community in the study of the rumen microbiome. We evaluated the accuracy of CowPI and PICRUSt using two 16S datasets from the rumen microbiome: one generated from rDNA and the other from rRNA where corresponding metagenomic and metatranscriptomic data was also available. We show that the functional profiles predicted by CowPI better match estimates for both the meta-genomic and transcriptomic datasets than PICRUSt, and capture the higher degree of genetic variation and larger pangenomes of rumen organisms. Nonetheless, whilst being closer in terms of predictive power for the rumen microbiome, there were differences when compared to both the metagenomic and metatranscriptome data and so we recommend, where possible, functional inferences from 16S data should not replace metagenomic and metatranscriptomic approaches", "token_count": 501, "char_count": 2182, "word_count": 321, "semantic_coherence": 1, "information_density": 0.5514, "quality_score": 0.7757, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:51.390952", "source": { "split": "train_shard_00002", "doc_id": 216 }, "chunk_id": "train_shard_00002_216_0", "global_id": 13022 }, { "text": "The tool can be accessed at http://www.cowpi.org and is provided to the wider scientific community for use in the study of the rumen microbiome.\n\nCowPI: A Rumen Microbiome Focussed Version of the PICRUSt Functional Inference Software.", "token_count": 65, "char_count": 234, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:51.759847", "source": { "split": "train_shard_00002", "doc_id": 216 }, "chunk_id": "train_shard_00002_216_1", "global_id": 13023 }, { "text": "

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is the most common healthcare-associated multidrug-resistant organism. Despite the interconnectedness between acute care hospitals (ACHs) and intermediate- and long-term care facilities (ILTCFs), the transmission dynamics of MRSA between healthcare settings is not well understood.

Methods

We conducted a cross-sectional study in a network comprising an ACH and 5 closely affiliated ILTCFs in Singapore. A total of 1700 inpatients were screened for MRSA over a 6-week period in 2014. MRSA isolates underwent whole-genome sequencing, with a pairwise single-nucleotide polymorphism (Hamming distance) cutoff of 60 core genome single-nucleotide polymorphisms used to define recent transmission clusters (clades) for the 3 major clones.

Results

MRSA prevalence was significantly higher in intermediate-term (29.9%) and long-term (20.4%) care facilities than in the ACH (11.8%) (P < .001). The predominant clones were sequence type [ST] 22 (n = 183; 47.8%), ST45 (n = 129; 33.7%), and ST239 (n = 26; 6.8%), with greater diversity of STs in ILTCFs relative to the ACH. A large proportion of the clades in ST22 (14 of 21 clades; 67%) and ST45 (7 of 13; 54%) included inpatients from the ACH and ILTCFs. The most frequent source of the interfacility transmissions was the ACH (n = 28 transmission events; 36.4%).

Conclusions

MRSA transmission dynamics between the ACH and ILTCFs were complex. The greater diversity of STs in ILTCFs suggests that the ecosystem in such settings might be more conducive for intrafacility transmission events", "token_count": 512, "char_count": 1621, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6332, "quality_score": 0.8166, "entities": { "genes": [ "ST45", "ST22", "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:52.394040", "source": { "split": "train_shard_00002", "doc_id": 217 }, "chunk_id": "train_shard_00002_217_0", "global_id": 13024 }, { "text": "ST22 and ST45 have successfully established themselves in ILTCFs. The importance of interconnected infection prevention and control measures and strategies cannot be overemphasized.\n\nMRSA Transmission Dynamics Among Interconnected Acute, Intermediate-Term, and Long-Term Healthcare Facilities in Singapore.", "token_count": 66, "char_count": 306, "word_count": 36, "semantic_coherence": 1, "information_density": 0.8611, "quality_score": 0.9306, "entities": { "genes": [ "ST45", "ST22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:52.765752", "source": { "split": "train_shard_00002", "doc_id": 217 }, "chunk_id": "train_shard_00002_217_1", "global_id": 13025 }, { "text": "

Background

Aeromonads make up a group of Gram-negative bacteria that includes human and fish pathogens. The Aeromonas salmonicida species has the peculiarity of including five known subspecies. However, few studies of the genomes of A. salmonicida subspecies have been reported to date.

Results

We sequenced the genomes of additional A. salmonicida isolates, including three from India, using next-generation sequencing in order to gain a better understanding of the genomic and phylogenetic links between A. salmonicida subspecies. Their relative phylogenetic positions were confirmed by a core genome phylogeny based on 1645 gene sequences. The Indian isolates, which formed a sub-group together with A. salmonicida subsp. pectinolytica, were able to grow at either at 18 °C and 37 °C, unlike the A. salmonicida psychrophilic isolates that did not grow at 37 °C. Amino acid frequencies, GC content, tRNA composition, loss and gain of genes during evolution, pseudogenes as well as genes under positive selection and the mobilome were studied to explain this intraspecies dichotomy.

Conclusion

Insertion sequences appeared to be an important driving force that locked the psychrophilic strains into their particular lifestyle in order to conserve their genomic integrity. This observation, based on comparative genomics, is in agreement with previous results showing that insertion sequence mobility induced by heat in A. salmonicida subspecies causes genomic plasticity, resulting in a deleterious effect on the virulence of the bacterium. We provide a proof-of-concept that selfish DNAs play a major role in the evolution of bacterial species by modeling genomes.\n\nIncreasing genomic diversity and evidence of constrained lifestyle evolution due to insertion sequences in Aeromonas salmonicida.", "token_count": 460, "char_count": 1819, "word_count": 257, "semantic_coherence": 1, "information_density": 0.6381, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:53.412203", "source": { "split": "train_shard_00002", "doc_id": 218 }, "chunk_id": "train_shard_00002_218_0", "global_id": 13026 }, { "text": "Using phylogenomic and gene compositional analyses, five highly conserved gene families have been detected in the core genome of the phylogenetically coherent genus Acidithiobacillus of the class Acidithiobacillia. These core gene families are absent in the closest extant genus Thermithiobacillus tepidarius that subtends the Acidithiobacillus genus and roots the deepest in this class. The predicted proteins encoded by these core gene families are not detected by a BLAST search in the NCBI non-redundant database of more than 90 million proteins using a relaxed cut-off of 1.0e-5. None of the five families has a clear functional prediction. However, bioinformatic scrutiny, using pI prediction, motif/domain searches, cellular location predictions, genomic context analyses, and chromosome topology studies together with previously published transcriptomic and proteomic data, suggests that some may have functions associated with membrane remodeling during cell division perhaps in response to pH stress. Despite the high level of amino acid sequence conservation within each family, there is sufficient nucleotide variation of the respective genes to permit the use of the DNA sequences to distinguish different species of Acidithiobacillus, making them useful additions to the armamentarium of tools for phylogenetic analysis. Since the protein families are unique to the Acidithiobacillus genus, they can also be leveraged as probes to detect the genus in environmental metagenomes and metatranscriptomes, including industrial biomining operations, and acid mine drainage (AMD).\n\nBioinformatic Analyses of Unique (Orphan) Core Genes of the Genus Acidithiobacillus: Functional Inferences and Use As Molecular Probes for Genomic and Metagenomic/Transcriptomic Interrogation.", "token_count": 474, "char_count": 1841, "word_count": 246, "semantic_coherence": 1, "information_density": 0.6504, "quality_score": 0.8252, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:54.054114", "source": { "split": "train_shard_00002", "doc_id": 219 }, "chunk_id": "train_shard_00002_219_0", "global_id": 13027 }, { "text": "Bioactive peptides are found in foods and dietary supplements and are responsible for health benefits with applications in human and animal medicine. The health benefits include antihypertensive, antimicrobial, antithrombotic, immunomodulatory, opioid, antioxidant, anti-allergic and anti-inflammatory functions. Bioactive peptides can be obtained by microbial action, mainly by the gastrointestinal microbiota from proteins present in food, originating from either vegetable or animal matter or by the action of different gastrointestinal proteases. Proteomics can play an important role in the identification of bioactive peptides. High-resolution mass spectrometry is the principal technique used to detect and identify different types of analytes present in complex mixtures, even when available at low concentrations. Moreover, proteomics may provide the characterization of epitopes to develop new food allergy vaccines and the use of immunomodulating peptides to induce oral tolerance toward offending food allergens or even to prevent allergic sensitization. In addition, food-derived bioactive peptides have been investigated for their anti-inflammatory properties to provide safer alternatives to nonsteroidal anti-inflammatory drugs (NSAIDs). All these bioactive peptides can be a potential source of novel drugs and ingredients in food and pharmaceuticals. The following review is focused on food-derived bioactive peptides with antiallergic and anti-inflammatory properties and summarizes the new insights into the use of proteomics for their identification and quantification.\n\nProteomics Characterization of Food-Derived Bioactive Peptides with Anti-Allergic and Anti-Inflammatory Properties.", "token_count": 395, "char_count": 1707, "word_count": 220, "semantic_coherence": 1, "information_density": 0.5864, "quality_score": 0.7932, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:54.673138", "source": { "split": "train_shard_00002", "doc_id": 220 }, "chunk_id": "train_shard_00002_220_0", "global_id": 13028 }, { "text": "The NaCl-induced autolysis of Kluyveromyces fragilis grown on lactose-based media was studied as a function of time (t) at different initial yeast concentrations (X(0)) and reaction temperatures (T) by carrying out a composite design experiment. By using the response surface methodology and canonical analysis, the experimental responses (viz. Kjeldhal, Y(KP), and Lowry, Y(LP), protein and total carbohydrates, Y(TC), solubilisation yields) were fined to the only statistically significant factors with mean percentage errors ranging from 1.7 to 7%. Whereas yeast protein solubilisation was essentially dependent upon temperature, hydrolysis of the total carbohydrates of cell walls was found to be controlled firstly by yeast concentration and secondly by temperature. The resulting empiric models were then used to determine the optimal values of X(0) (80-110 g/dm3) and T (51.5-54.5 degrees C) associated with Kjeldhal and Lowry protein recoveries greater than 88 and 51.5%, respectively, and with total carbohydrates solubilisation ranging from 50 to 55%. After establishing the validity of these data at the 95% confidence level, an optimal operating condition (X(0) = 100 g/dm3 and T = 54 degrees C) was further tested in the absence of NaCl. Since the observed values of Y(KP) and Y(LP) after an 8 h treatment were found to be insensitive to the presence of such a catalyst (at a probability level of 0.05), the latter operating condition might be further employed to produce no-salt autolysates with 54% crude protein and a chemical score of 45% as referred to the FAO/WHO standard (1973).\n\nEffect of temperature and yeast concentration on the autolysis of Kluyveromyces fragilis grown on lactose-based media", "token_count": 462, "char_count": 1718, "word_count": 261, "semantic_coherence": 1, "information_density": 0.6169, "quality_score": 0.8084, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:55.316591", "source": { "split": "train_shard_00002", "doc_id": 221 }, "chunk_id": "train_shard_00002_221_0", "global_id": 13029 }, { "text": "The investigation into the genome of the emerging pathogen reveals the genetic basis of the pathogen. In this study, Achromobacter xylosoxidans was used as an example for the genomic study of emerging pathogens. A. xylosoxidans is an emerging and opportunistic pathogen in patients with various underlying diseases, such as Cystic Fibrosis and cancers. In chapter 3, the objectives of the study were to compare and evaluate the approach for A. xylosoxidans identification. A wide range of methods, including phenotypic test, 16S rDNA gene sequencing, MALDI-TOF, RAPD and MLST, were utilised to demonstrate the species identification. MALDI-TOF was considered as the most appropriate method due to the least time consuming. The application of multiple approaches to identify A. xylosoxidans was suggested. In chapter 4, comprehensive genomic feature of A. xylosoxidans has not been elucidated. The objective of this study was to use comparative genomic tool to investigate genomic feature of A. xylosoxidans. The analysis revealed the opened pan-genome of the species. The core genome accounted for approximately 50% of the size of the genome. Furthermore, the analysis revealed recombination events in the core genome of the ... (continues)\n\nComparative genomic approaches to understanding Achromobacter xylosoxidans", "token_count": 327, "char_count": 1316, "word_count": 194, "semantic_coherence": 1, "information_density": 0.5567, "quality_score": 0.7784, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:55.884815", "source": { "split": "train_shard_00002", "doc_id": 222 }, "chunk_id": "train_shard_00002_222_0", "global_id": 13030 }, { "text": "Low genetic diversity of Epizootic haematopoietic necrosis virus (EHNV) was determined for the complete genome of 16 isolates spanning the natural range of hosts, geography and time since the first outbreaks of disease. Genomes ranged from 125,591-127,487 nucleotides with 97.47% pairwise identity and 106-109 genes. All isolates shared 101 core genes with 121 potential genes predicted within the pan-genome of this collection. There was high conservation within 90,181 nucleotides of the core genes with isolates separated by average genetic distance of 3.43 × 10-4 substitutions per site. Evolutionary analysis of the core genome strongly supported historical epidemiological evidence of iatrogenic spread of EHNV to naïve hosts and establishment of endemic status in discrete ecological niches. There was no evidence of structural genome reorganization, however, the complement of non-core genes and variation in repeat elements enabled fine scale molecular epidemiological investigation of this unpredictable pathogen of fish.\n\nMolecular epidemiology of Epizootic haematopoietic necrosis virus (EHNV).", "token_count": 299, "char_count": 1117, "word_count": 154, "semantic_coherence": 1, "information_density": 0.6753, "quality_score": 0.8377, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:56.450036", "source": { "split": "train_shard_00002", "doc_id": 223 }, "chunk_id": "train_shard_00002_223_0", "global_id": 13031 }, { "text": "Head blight caused by Fusarium graminearum threatens world-wide wheat production, resulting in both yield loss and mycotoxin contamination. We reconstructed the global F. graminearum gene regulatory network (GRN) from a large collection of transcriptomic data using Bayesian network inference, a machine-learning algorithm. This GRN reveals connectivity between key regulators and their target genes. Focusing on key regulators, this network contains eight distinct but interwoven modules. Enriched for unique functions, such as cell cycle, DNA replication, transcription, translation and stress responses, each module exhibits distinct expression profiles. Evolutionarily, the F. graminearum genome can be divided into core regions shared with closely related species and variable regions harboring genes that are unique to F. graminearum and perform species-specific functions. Interestingly, the inferred top regulators regulate genes that are significantly enriched from the same genomic regions (P < 0.05), revealing a compartmentalized network structure that may reflect network rewiring related to specific adaptation of this plant pathogen. This first-ever reconstructed filamentous fungal GRN primes our understanding of pathogenicity at the systems biology level and provides enticing prospects for novel disease control strategies involving the targeting of master regulators in pathogens. The program can be used to construct GRNs of other plant pathogens.\n\nCompartmentalized gene regulatory network of the pathogenic fungus Fusarium graminearum.", "token_count": 343, "char_count": 1558, "word_count": 209, "semantic_coherence": 1, "information_density": 0.7129, "quality_score": 0.8565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:57.023768", "source": { "split": "train_shard_00002", "doc_id": 224 }, "chunk_id": "train_shard_00002_224_0", "global_id": 13032 }, { "text": "Swine act as both maintenance and incidental hosts of pathogenic Leptospira spp. Here, a serological test was performed on 131,660 pig sera collected between 2002 and 2017 from 4715 farms in Northern Italy. A positivity rate of 13.05% was determined. Australis was the most frequently identified serogroup (77.29%), followed by Pomona (18.47%), Tarassovi (1.51%) and Icterohaemorrhagie (1.40%). Culture isolation and real-time Polymerase chain reaction (PCR) were carried out on 347 kidneys and 470 clinical samples, respectively. Overall, 133 strains were cultured successfully and 43 randomly chosen isolates were identified as serogroup Pomona. Multi-locus sequence typing (MLST) revealed that 41 isolates and 8 DNA extracted from biological samples belonged to sequence type 140. Using a multiple-locus, variable-number tandem repeat analysis, 43 samples produced identical profiles but, after 2014, three new Leptospira interrogans serogroup Pomona genotypes were observed. Interestingly, two isolates showed new MLST profiles and an unclassified identification by monoclonal antibodies. The 16S rRNA gene sequencing clustered them into L. kirschneri species and a core genome MLST analysis revealed an allelic identity of 96% compared with Mozdok strains. Genotyping allowed us to discriminate leptospires and to identify new emerging strains. The accurate identification of infective strains is required for formulating preventive methods and intervention strategies.\n\nSerological Survey and Molecular Typing Reveal New Leptospira Serogroup Pomona Strains among Pigs of Northern Italy.", "token_count": 458, "char_count": 1620, "word_count": 220, "semantic_coherence": 1, "information_density": 0.7364, "quality_score": 0.8682, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:57.675022", "source": { "split": "train_shard_00002", "doc_id": 225 }, "chunk_id": "train_shard_00002_225_0", "global_id": 13033 }, { "text": "Pistacia lentiscus L. has traditionally been employed as a diuretic and stimulant in the treatment of hypertension. Our interest centered on analyzing the chemical profile of the plant's leaves and its in vitro, in vivo, and in silico antioxidant, antimicrobial, anticoagulant, and antidiabetic effects in order to valorize this species and prepare new high-value products that can be used in the agro-food and pharmaceutical industries. When this species' essential oil was hydrodistilled and subjected to GC-MS analysis, the results showed that the principal components were germacrene D (17.54%), spathulenol (17.38%), bicyclogermacrene (12.52%), and terpinen-4-ol (9.95%). The extraction of phenolic compounds was carried out by decoction and Soxhlet. The determination of total polyphenols, flavonoids, and tannins of aqueous and organic extracts by spectrophotometric methods demonstrated the richness of this species in phenolic compounds. Chromatographic analysis by HPLC/UV-ESI-MS of the aqueous extract of P. lentiscus revealed the presence of 3,5-di-O-galloyl quinic acid, gallic acid, and 3,4,5-tri-O-galloyl quinic acid specific to this species. The study of antioxidant activity by three methods (DPPH, FRAP, and Total Antioxidant Capacity) revealed that P. lentiscus is a very promising source of natural antioxidants. The antimicrobial activity of the essential oil and aqueous extract (E0) was studied by microdilution on the microplate. The results revealed the effectiveness of the aqueous extract compared to the essential oil against Gram-negative bacteria (K. pneumoniae, A. baumannii, E. aerogenes, E", "token_count": 522, "char_count": 1693, "word_count": 228, "semantic_coherence": 1, "information_density": 0.614, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:01:58.334270", "source": { "split": "train_shard_00002", "doc_id": 226 }, "chunk_id": "train_shard_00002_226_0", "global_id": 13034 }, { "text": "cloacae, P. fluorescence, Salmonella sp., Shigella sp., and Y. enterolitica) and candidoses (C. krusei and C. albicans). The measurements of prothrombin time (PT) and activated partial thromboplastin time (aPTT) of the aqueous extract (E0) can significantly prolong these tests from concentrations of 2.875 and 5.750 mg/mL, respectively. The antihyperglycemic effect of the aqueous extract (E0) showed a strong in vitro inhibitory activity of α-amylase and α-glucosidase compared to acarbose. Thus, it significantly inhibited postprandial hyperglycemia in Wistar albino rats. The in-silico study of the major compounds of the essential oil and extract (E0) carried out using PASS, SwissADME, pkCSM, and molecular docking tools confirmed our in vitro and in vivo results. The studied compounds showed a strong ability to be absorbed by the gastrointestinal tract and to passively diffuse through the blood-brain barrier, a similarity to drugs, and water solubility. Molecular docking experiments deduced the probable mode of action of the identified compounds on their respective target proteins, such as NADPH oxidase, thrombin, α-amylase, and α-glucosidase. Furthermore, given the demonstrated antioxidant, antimicrobial, anticoagulant, and antidiabetic effects, we can affirm the richness of P. lentiscus in bioactive molecules and its use in traditional medicine as a source of preservative agent.\n\nAnalysis of the Chemical Composition and Evaluation of the Antioxidant, Antimicrobial, Anticoagulant, and Antidiabetic Properties of Pistacia lentiscus from Boulemane as a Natural Nutraceutical Preservative.", "token_count": 525, "char_count": 1702, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:01:58.986913", "source": { "split": "train_shard_00002", "doc_id": 226 }, "chunk_id": "train_shard_00002_226_1", "global_id": 13035 }, { "text": "The rapid expansion of Acinetobacter baumannii clinical isolates exhibiting resistance to carbapenems and most or all available antibiotics during the last decade is a worrying evolution. The apparent predominance of a few successful multidrug-resistant lineages worldwide underlines the importance of elucidating the mode of spread and the epidemiology of A. baumannii isolates in single hospitals, at a country-wide level and on a global scale. The evolutionary advantage of the dominant clonal lineages relies on the capability of the A. baumannii pangenome to incorporate resistance determinants. In particular, the simultaneous presence of divergent strains of the international clone II and their increasing prevalence in international hospitals further support the ongoing adaptation of this lineage to the hospital environment. Indeed, genomic and genetic studies have elucidated the role of mobile genetic elements in the transfer of antibiotic resistance genes and substantiate the rate of genetic alterations associated with acquisition in A. baumannii of various resistance genes, including OXA- and metallo-β-lactamase-type carbapenemase genes. The significance of single nucleotide polymorphisms and transposon mutagenesis in the evolution of A. baumannii has been also documented. Establishment of a network of reference laboratories in different countries would generate a more complete picture and a fuller understanding of the importance of high-risk A. baumannii clones in the international dissemination of antibiotic resistance.\n\nGlobal evolution of multidrug-resistant Acinetobacter baumannii clonal lineages.", "token_count": 357, "char_count": 1631, "word_count": 222, "semantic_coherence": 1, "information_density": 0.5856, "quality_score": 0.7928, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:01:59.571659", "source": { "split": "train_shard_00002", "doc_id": 227 }, "chunk_id": "train_shard_00002_227_0", "global_id": 13036 }, { "text": "

Aims

Genomic characterization of Harveyi clade vibrio strain Y6 causing 'Scale drop and Muscle Necrosis syndrome' (SDMN) isolated from barramundi (Lates calcarifer) in Vietnam.

Methods and results

A bacterial genome was sequenced using Illumina MiSeq platform. Multilocus sequence analysis confirmed that the bacterium belongs to Vibrio harveyi species. Further phylogenetic analysis inferred from core genome SNPs revealed a close relationship between our bacterium and the V. harveyi isolated from groupers in Taiwan and China. blastp results indicated that V. harveyi piscine strains carried numerous adhesin, secretion system, siderophore and toxin-related genes. Genome comparison between Y6 and 32 strains of V. harveyi from different origins showed that at least 17 potential virulence genes were present exclusively in the strain Y6. Many of these (six of 17 genes) were homologous to pyoverdine siderophore, a secreted high-affinity iron chelator, clusters originally found in Pseudomonas aeruginosa. Genome of V. harveyi Y6 was incorporated by a bacteriophage VHY6φ and replication protein of the phage was most similar to CTXφ described previously in Vibrio cholerae and Vibrio fischeri. However, the cholera toxin-encoding genes, namely ctxA and ctxB, were absent from VHY6φ, while the CTXφ-enterotoxin gene (zonula occludens toxin; zot) remained intact.

Conclusions

Several putative virulence genes and a phage carrying toxin gene were identified in the genomes of SDMN-associated V. harveyi Y6.

Significance and impact of the study

This study confers genomic information of the piscine pathogenic V. harveyi which recently caused widespread mortality. Such information is of importance to gain insight into bacterial molecular pathogenesis.", "token_count": 491, "char_count": 1783, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6584, "quality_score": 0.8292, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:00.220617", "source": { "split": "train_shard_00002", "doc_id": 228 }, "chunk_id": "train_shard_00002_228_0", "global_id": 13037 }, { "text": "Genome characterization of piscine 'Scale drop and Muscle Necrosis syndrome'-associated strain of Vibrio harveyi focusing on bacterial virulence determinants.", "token_count": 41, "char_count": 158, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:00.583102", "source": { "split": "train_shard_00002", "doc_id": 228 }, "chunk_id": "train_shard_00002_228_1", "global_id": 13038 }, { "text": "Outbreak strains of Acinetobacter baumannii are highly clonal, and cross-infection investigations can be difficult. We sought targets based on AbaR resistance islands and on other genes found in some, but not all, sequenced isolates of A. baumannii among a set of clinical isolates (n = 70) that included multiple representatives of a number of pulsed-field gel electrophoresis (PFGE)-defined types. These included representatives that varied in their profiles at two variable-number tandem repeat (VNTR) loci, which can provide discrimination within a PFGE cluster. Detection, or not, of each element sought provided some degree of discrimination among the set, with the presence or absence of genes coding for a phage terminase (ACICU_02185), a sialic acid synthase (ACICU_00080), a polysaccharide biosynthesis protein (AB57_0094), aphA1, bla(TEM), and integron-associated orfX (Kyoto Encyclopedia of Genes and Genomes [KEGG] no. K03830) proving the most helpful in discriminating between closely related isolates in our panel. The results support VNTR data in describing distinct populations of highly similar isolates. Such analysis, in combination with other typing methods, can inform epidemiological investigations and provide additional characterization of isolates. Most genotypes carrying bla(OXA-23-like) were PCR positive for a yeeA-bla(OXA-23) fragment found in an AbaR4-type island, suggesting that this is widespread.\n\nUse of the accessory genome for characterization and typing of Acinetobacter baumannii.", "token_count": 406, "char_count": 1521, "word_count": 211, "semantic_coherence": 1, "information_density": 0.7062, "quality_score": 0.8531, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:01.202916", "source": { "split": "train_shard_00002", "doc_id": 229 }, "chunk_id": "train_shard_00002_229_0", "global_id": 13039 }, { "text": "

Background

No updated data currently exist regarding Neisseria meningitidis carriage and genomic epidemiology among young Israeli adults.

Methods

Oropharyngeal swabs were collected from 1801 military recruits on the day of recruitment during 2019. Neisseria meningitidis was detected and identified by culture and quantitative polymerase chain reaction (qPCR). Confirmed isolates were serotyped by qPCR, and encapsulated strains underwent whole-genome sequencing. Risk factors for carriage were determined by analyzing focused questionnaires using uni- and multivariate models. Genomic typing was performed by means of core genome multilocus sequence typing.

Results

Carriage rates overall and of encapsulated strains were 20.1% and 6.7%, respectively. Genogroups B (49.2%) and Y (26.7%) were the most commonly encapsulated strains. Genogroups C, W, and X were scarce, and genogroup A was absent. The most notable clonal complexes (CCs) were CC23 (n = 30), CC32 (n = 16), and CC44/41 (n = 9). Carriage was significantly associated with smoking (odds ratio [OR], 1.82; 95% CI, 1.43-2.33) and boarding school attendance before recruitment (OR, 1.49; 95% CI, 1.14-1.96).

Conclusions

The prevalence of meningococcal carriage among young Israeli adults is high, compared with similar studies in other developed countries. This might be due to sociocultural characteristics including smoking and boarding school attendance during and after high school. The dominant genogroups and CCs found were compatible with those implicated in invasive disease in Israel.", "token_count": 486, "char_count": 1596, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7009, "quality_score": 0.8505, "entities": { "genes": [ "CC44", "CC32", "CC23" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:01.902141", "source": { "split": "train_shard_00002", "doc_id": 230 }, "chunk_id": "train_shard_00002_230_0", "global_id": 13040 }, { "text": "Prevalence and Characteristics of Carriage of Neisseria meningitidis Among Young Israeli Adults.", "token_count": 31, "char_count": 103, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:02.287874", "source": { "split": "train_shard_00002", "doc_id": 230 }, "chunk_id": "train_shard_00002_230_1", "global_id": 13041 }, { "text": "Microbroth dilution tests in vitro showed the same IC(50) values for itraconazole and hydroxy-itraconazole, within a mode +/- one dilution range of experimental error, for 90% of 1481 isolates of pathogenic fungi, representing 48 genera. Some 10-15% of Candida glabrata and Trichophyton mentagrophytes isolates were more susceptible to itraconazole than hydroxy-itraconazole. Replicate tests with bioassay marker strains of Candida kefyr and Candida albicans showed no susceptibility variations outside the mode +/- one dilution range. We conclude that few fungi differ substantially in their susceptibility to itraconazole and hydroxy-itraconazole.\n\nAntifungal activity of itraconazole compared with hydroxy-itraconazole in vitro.", "token_count": 213, "char_count": 731, "word_count": 97, "semantic_coherence": 1, "information_density": 0.701, "quality_score": 0.8505, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:02.774568", "source": { "split": "train_shard_00002", "doc_id": 231 }, "chunk_id": "train_shard_00002_231_0", "global_id": 13042 }, { "text": "Secretion signal peptides of inulinases derived from Kluyveromyces marxianus, which makes a heterologous protein produced in a yeast cell be secreted almost completely into the extracellular medium; nucleotide sequences encoding said secretion signal peptides; expression and secretion vectors comprising nucleotide sequences encoding said secretion signal peptides; recombinant yeast cells transformed with said expression and secretion vectors; and a process for producing heterologous proteins by culturing said recombinant yeast cells.\n\nSignal sequences for secretion of heterologous proteins from yeast", "token_count": 135, "char_count": 607, "word_count": 78, "semantic_coherence": 1, "information_density": 0.6026, "quality_score": 0.8013, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:03.227415", "source": { "split": "train_shard_00002", "doc_id": 232 }, "chunk_id": "train_shard_00002_232_0", "global_id": 13043 }, { "text": "The antifungal activity spectrum of Lactobacillus coryniformis subsp. coryniformis strain Si3 was investigated. The strain had strong inhibitory activity in dual-culture agar plate assays against the molds Aspergillus fumigatus, A. nidulans, Penicillium roqueforti, Mucor hiemalis, Talaromyces flavus, Fusarium poae, F. graminearum, F. culmorum, and F. sporotrichoides. A weaker activity was observed against the yeasts Debaryomyces hansenii, Kluyveromyces marxianus, and Saccharomyces cerevisiae. The yeasts Rhodotorula glutinis, Sporobolomyces roseus, and Pichia anomala were not inhibited. In liquid culture the antifungal activity paralleled growth, with maximum mold inhibition early in the stationary growth phase, but with a rapid decline in antifungal activity after 48 h. The addition of ethanol to the growth medium prevented the decline and gave an increased antifungal activity. The activity was stable during heat treatment and was retained even after autoclaving at 121 degrees C for 15 min. Maximum activity was observed at pH values of between 3. 0 and 4.5, but it decreased rapidly when pH was adjusted to a level between 4.5 and 6.0 and was lost at higher pH values. The antifungal activity was fully regained after readjustment of the pH to the initial value (pH 3.6). The activity was irreversibly lost after treatment with proteolytic enzymes (proteinase K, trypsin, and pepsin). The antifungal activity was partially purified using ion-exchange chromatography and (NH(4))(2)SO(4) precipitation, followed by gel filtration chromatography. The active compound(s) was estimated to have a molecular mass of approximately 3 kDa. This is the first report of the production of a proteinaceous antifungal compound(s) from L. coryniformis subsp. coryniformis.", "token_count": 508, "char_count": 1772, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6275, "quality_score": 0.8137, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:03.878130", "source": { "split": "train_shard_00002", "doc_id": 233 }, "chunk_id": "train_shard_00002_233_0", "global_id": 13044 }, { "text": "Lactobacillus coryniformis subsp. coryniformis strain Si3 produces a broad-spectrum proteinaceous antifungal compound.", "token_count": 37, "char_count": 118, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:04.246093", "source": { "split": "train_shard_00002", "doc_id": 233 }, "chunk_id": "train_shard_00002_233_1", "global_id": 13045 }, { "text": "Micafungin is an echinocandin antifungal agent that has recently been approved for the prevention of invasive fungal infection and the treatment of esophageal candidiasis. Prospective sentinel surveillance for the emergence of in vitro resistance to micafungin among invasive Candida sp. isolates is indicated. We determined the in vitro activity of micafungin against 2,656 invasive (bloodstream or sterile site) unique patient isolates of Candida spp. collected from 60 medical centers worldwide in 2004 and 2005. We performed antifungal susceptibility testing according to the Clinical and Laboratory Standards Institute (CLSI) M27-A2 method and used a 24-hour prominent inhibition endpoint for determination of the MIC. Caspofungin was tested in parallel against all isolates. Of 2,656 invasive Candida sp. isolates, species distribution was 55.6% Candida albicans, 14.4% Candida parapsilosis, 13.4% Candida glabrata, 10.1% Candida tropicalis, 2.4% Candida krusei, 1.7% Candida guilliermondii, 0.9% Candida lusitaniae, 0.6% Candida kefyr, and 0.9% other Candida species. Overall, micafungin was very active against Candida (MIC50/MIC at which 90% of the isolates tested are inhibited [MIC90], 0.015/1 microg/ml; 96% inhibited at a MIC of < or =1 microg/ml, 100% inhibited at a MIC of < or =2 microg/ml) and comparable to caspofungin (MIC50/MIC90, 0.03/0.25 mug/ml; 99% inhibited at a MIC of < or =2 microg/ml). Results by species, expressed as MIC50/MIC90 (micrograms per milliliter), were as follows: C", "token_count": 511, "char_count": 1507, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6376, "quality_score": 0.8188, "entities": { "genes": [ "MIC90", "MIC50" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:04.883294", "source": { "split": "train_shard_00002", "doc_id": 234 }, "chunk_id": "train_shard_00002_234_0", "global_id": 13046 }, { "text": "albicans, 0.015/0.03; C. glabrata, 0.015/0.015; C. tropicalis, 0.03/0.06; C. krusei, 0.06/0.12; C. kefyr, 0.06/0.06; C. parapsilosis, 1/2; C. guilliermondii, 0.5/1; C. lusitaniae, 0.12/0.25; other Candida spp., 0.25/1. Although the species distribution varied considerably among the different geographic regions, there was no difference in micafungin activity across the regions. Micafungin has excellent in vitro activity against invasive clinical isolates of Candida from centers worldwide.\n\nGlobal surveillance of in vitro activity of micafungin against Candida: a comparison with caspofungin by CLSI-recommended methods.", "token_count": 235, "char_count": 624, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7625, "quality_score": 0.8812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:05.356464", "source": { "split": "train_shard_00002", "doc_id": 234 }, "chunk_id": "train_shard_00002_234_1", "global_id": 13047 }, { "text": "The Deepwater Horizon oil spill is unparalleled among environmental hydrocarbon releases, because of the tremendous volume of oil, the additional contamination by dispersant, and the oceanic depth at which this release occurred. Here, we present data on general toxicity and mutagenicity of upper water column waters and, to a lesser degree, sediment porewater of the Northeastern Gulf of Mexico (NEGOM) and west Florida shelf (WFS) at the time of the Deepwater Horizon oil spill in 2010 and thereafter. During a research cruise in August 2010, analysis of water collected in the NEGOM indicated that samples of 3 of 14 (21%) stations were toxic to bacteria based on the Microtox assay, 4 of 13 (34%) were toxic to phytoplankton via the QwikLite assay, and 6 of 14 (43%) showed DNA damaging activity using the λ-Microscreen Prophage induction assay. The Microtox and Microscreen assays indicated that the degree of toxicity was correlated to total petroleum hydrocarbon concentration. Long-term monitoring of stations on the NEGOM and the WFS was undertaken by 8 and 6 cruises to these areas, respectively. Microtox toxicity was nearly totally absent by December 2010 in the Northeastern Gulf of Mexico (3 of 8 cruises with one positive station). In contrast, QwikLite toxicity assay yielded positives at each cruise, often at multiple stations or depths, indicating the greater sensitivity of the QwikLite assay to environmental factors. The Microscreen mutagenicity assays indicated that certain water column samples overlying the WFS were mutagenic at least 1.5 years after capping the Macondo well. Similarly, sediment porewater samples taken from 1000, 1200, and 1400 m from the slope off the WFS in June 2011 were also highly genotoxic. Our observations are consistent with a portion of the dispersed oil from the Macondo well area advecting to the southeast and upwelling onto the WFS, although other explanations exist", "token_count": 495, "char_count": 1926, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5875, "quality_score": 0.7937, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:06.013398", "source": { "split": "train_shard_00002", "doc_id": 235 }, "chunk_id": "train_shard_00002_235_0", "global_id": 13048 }, { "text": "Organisms in contact with these waters might experience DNA damage that could lead to mutation and heritable alterations to the community pangenome. Such mutagenic interactions might not become apparent in higher organisms for years.\n\nToxicity and mutagenicity of Gulf of Mexico waters during and after the deepwater horizon oil spill.", "token_count": 70, "char_count": 335, "word_count": 50, "semantic_coherence": 1, "information_density": 0.82, "quality_score": 0.91, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:06.380842", "source": { "split": "train_shard_00002", "doc_id": 235 }, "chunk_id": "train_shard_00002_235_1", "global_id": 13049 }, { "text": "Horizontal gene transfer (HGT) and gene loss are key processes in bacterial evolution. However, the role of gene gain and loss in the emergence and maintenance of ecologically differentiated bacterial populations remains an open question. Here, we use whole-genome sequence data to quantify gene gain and loss for 27 lineages of the plant-associated bacterium Pseudomonas syringae. We apply an extensive error-control procedure that accounts for errors in draft genome data and greatly improves the accuracy of patterns of gene occurrence among these genomes. We demonstrate a history of extensive genome fluctuation for this species and show that individual lineages could have acquired thousands of genes in the same period in which a 1% amino acid divergence accrues in the core genome. Elucidating the dynamics of genome fluctuation reveals the rapid turnover of gained genes, such that the majority of recently gained genes are quickly lost. Despite high observed rates of fluctuation, a phylogeny inferred from patterns of gene occurrence is similar to a phylogeny based on amino acid replacements within the core genome. Furthermore, the core genome phylogeny suggests that P. syringae should be considered a number of distinct species, with levels of divergence at least equivalent to those between recognized bacterial species. Gained genes are transferred from a variety of sources, reflecting the depth and diversity of the potential gene pool available via HGT. Overall, our results provide further insights into the evolutionary dynamics of genome fluctuation and implicate HGT as a major factor contributing to the diversification of P. syringae lineages.\n\nThe Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages", "token_count": 377, "char_count": 1754, "word_count": 267, "semantic_coherence": 1, "information_density": 0.588, "quality_score": 0.794, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:06.973062", "source": { "split": "train_shard_00002", "doc_id": 236 }, "chunk_id": "train_shard_00002_236_0", "global_id": 13050 }, { "text": "

Background

The thermotolerant methylotrophic yeast Hansenula polymorpha is capable of alcoholic fermentation of xylose at elevated temperatures (45 - 48 degrees C). Such property of this yeast defines it as a good candidate for the development of an efficient process for simultaneous saccharification and fermentation. However, to be economically viable, the main characteristics of xylose fermentation of H. polymorpha have to be improved.

Results

Site-specific mutagenesis of H. polymorpha XYL1 gene encoding xylose reductase was carried out to decrease affinity of this enzyme toward NADPH. The modified version of XYL1 gene under control of the strong constitutive HpGAP promoter was overexpressed on a Deltaxyl1 background. This resulted in significant increase in the KM for NADPH in the mutated xylose reductase (K341 --> R N343 --> D), while KM for NADH remained nearly unchanged. The recombinant H. polymorpha strain overexpressing the mutated enzyme together with native xylitol dehydrogenase and xylulokinase on Deltaxyl1 background was constructed. Xylose consumption, ethanol and xylitol production by the constructed strain were determined for high-temperature xylose fermentation at 48 degrees C. A significant increase in ethanol productivity (up to 7.3 times) was shown in this recombinant strain as compared with the wild type strain. Moreover, the xylitol production by the recombinant strain was reduced considerably to 0.9 mg x (L x h)-1 as compared to 4.2 mg x (L x h)-1 for the wild type strain.

Conclusion

Recombinant strains of H. polymorpha engineered for improved xylose utilization are described in the present work. These strains show a significant increase in ethanol productivity with simultaneous reduction in the production of xylitol during high-temperature xylose fermentation.", "token_count": 494, "char_count": 1835, "word_count": 262, "semantic_coherence": 1, "information_density": 0.542, "quality_score": 0.771, "entities": { "genes": [ "XYL1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:07.623095", "source": { "split": "train_shard_00002", "doc_id": 237 }, "chunk_id": "train_shard_00002_237_0", "global_id": 13051 }, { "text": "Engineering of xylose reductase and overexpression of xylitol dehydrogenase and xylulokinase improves xylose alcoholic fermentation in the thermotolerant yeast Hansenula polymorpha.", "token_count": 53, "char_count": 181, "word_count": 21, "semantic_coherence": 1, "information_density": 0.8571, "quality_score": 0.9286, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:07.984816", "source": { "split": "train_shard_00002", "doc_id": 237 }, "chunk_id": "train_shard_00002_237_1", "global_id": 13052 }, { "text": "The potential for genome-wide modeling of epistasis has recently surfaced given the possibility of sequencing densely sampled populations and the emerging families of statistical interaction models. Direct coupling analysis (DCA) has earlier been shown to yield valuable predictions for single protein structures, and has recently been extended to genome-wide analysis of bacteria, identifying novel interactions in the co-evolution between resistance, virulence and core genome elements. However, earlier computational DCA methods have not been scalable to enable model fitting simultaneously to 10 4 -10 5 polymorphisms, representing the amount of core genomic variation observed in analyses of many bacterial species. Here we introduce a novel inference method (SuperDCA) which employs a new scoring principle, efficient parallelization, optimization and filtering on phylogenetic information to achieve scalability for up to 10 5 polymorphisms. Using two large population samples of Streptococcus pneumoniae , we demonstrate the ability of SuperDCA to make additional significant biological findings about this major human pathogen. We also show that our method can uncover signals of selection that are not detectable by genome-wide association analysis, even though our analysis does not require phenotypic measurements. SuperDCA thus holds considerable potential in building understanding about numerous organisms at a systems biological level.

Author Summary

Recent work has demonstrated the emerging potential in statistical genome-wide modeling to uncover co-selection and epistatic interactions between polymorphisms in bacterial chromosomes from densely sampled population data. Here we develop the Potts model based approach further into a fully mature computational method which can be applied to most existing bacterial population genomic data sets in a straightforward manner. Our advances are relying on more efficient parameter scoring, highly optimized and parallelized open source C++ code, which does not rely on the computation-intensive polymorphism subsampling approximations used earlier. By analyzing the two largest available population samples of Streptococcus pneumoniae (the pneumococcus), we highlight several biological discoveries related to the survival of the pneumococcus and co-evolution of penicillin-binding loci, which were not uncovered by the earlier analyses. Our method holds considerable potential for building understanding about numerous organisms at a systems biological level.", "token_count": 515, "char_count": 2534, "word_count": 343, "semantic_coherence": 1, "information_density": 0.6093, "quality_score": 0.8047, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:02:08.616340", "source": { "split": "train_shard_00002", "doc_id": 238 }, "chunk_id": "train_shard_00002_238_0", "global_id": 13053 }, { "text": "SuperDCA for genome-wide epistasis analysis", "token_count": 12, "char_count": 43, "word_count": 5, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:08.970277", "source": { "split": "train_shard_00002", "doc_id": 238 }, "chunk_id": "train_shard_00002_238_1", "global_id": 13054 }, { "text": "Listeria monocytogenes is a high risk pathogen which can cause invasive diseases in humans. We previously reported that black-headed gulls from Dianchi Lake of Kunming carrying L. monocytogenes, while the characteristics of these isolates and the relationship with habitats of migratory gulls have not been explored. In this study, we investigated the prevalence and molecular characteristics of Listeria monocytogenes from black-headed gulls in Dianchi Lake, and phylogenetic analysis based on core genome SNPs was used to determine the genetic relationship of the strains from Dianchi Lake and other regions. Occurrence of L. monocytogenes in black-headed gull feces in 2016, 2017 and 2018 was 1.0%, 1.0% and 0.6% respectively. The predominant serotype of 28 isolates was 4b, while the predominant sequence types were ST145 and ST201. Based on their prevalence and genomic relationships, ST5 and ST87 were likely to be sourced locally while ST145 and ST201 were likely to be non-local. L. monocytogenes may travel along the bird migration route leading to transmission over a large geographical span carried by black-headed gull. Although the prevalence of L. monocytogenes was low, its carriage by the migratory black-headed gulls poses potential public health risks in regions where the migratory birds passage and reside.\n\nCarriage and potential long distance transmission of Listeria monocytogenes by migratory black-headed gulls in Dianchi Lake, Kunming.", "token_count": 427, "char_count": 1510, "word_count": 217, "semantic_coherence": 1, "information_density": 0.576, "quality_score": 0.788, "entities": { "genes": [ "ST145", "ST201", "ST87", "ST5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:09.595023", "source": { "split": "train_shard_00002", "doc_id": 239 }, "chunk_id": "train_shard_00002_239_0", "global_id": 13055 }, { "text": "Localization of the secretory heat-shock protein gp280 in the cell envelope of thermotolerant yeast Hansenula polymorpha.", "token_count": 35, "char_count": 121, "word_count": 16, "semantic_coherence": 1, "information_density": 0.875, "quality_score": 0.9375, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:09.956236", "source": { "split": "train_shard_00002", "doc_id": 240 }, "chunk_id": "train_shard_00002_240_0", "global_id": 13056 }, { "text": "Telomerase, a ribonucleoprotein, is responsible for the maintenance of eukaryotic genome integrity by replicating the ends of chromosomes. The core enzyme comprises the conserved protein TERT and an RNA subunit (TER) that, in contrast, displays large variations in size and structure. Here, we report the identification of the telomerase RNA from thermotolerant yeast Hansenula polymorpha (HpTER) and describe its structural features. We show further that the H. polymorpha telomerase reverse transcribes the template beyond the predicted boundary and adds a nontelomeric dT in vitro. Sequencing of the chromosomal ends revealed that this nucleotide is specifically present as a terminal nucleotide at the 3' end of telomeres. Mutational analysis of HpTER confirmed that the incorporation of dT functions to limit telomere length in this species.\n\nSpecific features of telomerase RNA from Hansenula polymorpha.", "token_count": 229, "char_count": 910, "word_count": 132, "semantic_coherence": 1, "information_density": 0.6894, "quality_score": 0.8447, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:10.427539", "source": { "split": "train_shard_00002", "doc_id": 241 }, "chunk_id": "train_shard_00002_241_0", "global_id": 13057 }, { "text": "UDP-galactose-4-epimerase from yeast Kluyveromyces fragilis is a dimeric molecule with one molecule of cofactor NAD per dimer. In presence of 8 M urea, the enzyme is inactivated with complete disorganization of its structure and dissociation of the subunits together with the cofactor. Dilution of the denaturant by sodium phosphate buffer (20 mM, pH 7.0) containing 1 mM NAD recovers the activity to the extent of 80-100%. At a monomer concentration of 0.8 microM, the reactivation follows second-order kinetics, k = 1.48 x 10(3) M-1 s-1, at 20 degrees C. The renatured enzyme resembles the native enzyme in terms of most of its physicochemical properties, e.g., circular dichroism spectrum, fluorescence spectrum, interaction with hydrophobic fluorophore 1-anilino-8-naphthalenesulfonic acid (ANS), hydrodynamic volume, Km for the substrate UDP-galactose, etc. The reactivation process has an energy of activation of 15.2 kcal/mol. The folding pathway could be divided into four major parts: in the first phase (within 10 min), the secondary and tertiary structures of the monomers are formed as found by circular dichroism and fluorescence spectroscopy; in the second phase (within 20 min), the folded monomers associate to form an inactive dimer as observed by size-exclusion HPLC; in the third phase, the NAD binding site is formed, which is possibly induced by the cofactor; and finally, NAD assembles over the cofactor binding site to yield an active holoenzyme (within 120 min). The third and fourth steps have been detected kinetically. They are slow and rate-limiting, depending upon the concentration of extraneous NAD.\n\nReversible folding of UDP-galactose-4-epimerase from yeast Kluyveromyces fragilis.", "token_count": 511, "char_count": 1714, "word_count": 255, "semantic_coherence": 1, "information_density": 0.651, "quality_score": 0.8255, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:11.085350", "source": { "split": "train_shard_00002", "doc_id": 242 }, "chunk_id": "train_shard_00002_242_0", "global_id": 13058 }, { "text": "Inflammatory bowel disease is a heterogeneous group of chronic disorders that result from the interaction of the intestinal immune system with the gut microbiome. Until recently, most investigative efforts and therapeutic breakthroughs were centered on understanding and manipulating the altered mucosal immune response that characterizes these diseases. However, more recent studies have highlighted the important role of environmental factors, and in particular the microbiota, in disease onset and disease exacerbation. Advances in genomic sequencing technology and bioinformatics have facilitated an explosion of investigative inquiries into the composition and function of the intestinal microbiome in health and disease and have advanced our understanding of the interplay between the gut microbiota and the host immune system. The gut microbiome is dynamic and changes with age and in response to diet, antibiotics and other environmental factors, and these alterations in the microbiome contribute to disease onset and exacerbation. Strategies to manipulate the microbiome through diet, probiotics, antibiotics or fecal microbiota transplantation may potentially be used therapeutically to influence modulate disease activity. This review will characterize the factors involved in the development of the intestinal microbiome and will describe the typical alterations in the microbiota that are characteristic of inflammatory bowel disease. Additionally, this manuscript will summarize the early but promising literature on the role of the gut microbiota in the pathogenesis of inflammatory bowel disease with implications for utilizing this data for diagnostic or therapeutic application in the clinical management of patients with these diseases.\n\nThe microbiota in inflammatory bowel disease: current and therapeutic insights.", "token_count": 374, "char_count": 1837, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5238, "quality_score": 0.7619, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:11.664919", "source": { "split": "train_shard_00002", "doc_id": 243 }, "chunk_id": "train_shard_00002_243_0", "global_id": 13059 }, { "text": "

Objectives

To analyse Klebsiella pneumoniae (KP) isolates from an outbreak of extended-spectrum β-lactamase (ESBL)-producing KP and Escherichia coli (EC) among infants admitted to neonatal intensive care units and to determine the duration of the intestinal colonization.

Methods

We performed a prospective cohort study of intestinal ESBL-KP/ESBL-EC colonized neonates after a 5-month outbreak in two neonatal intensive care units. Whole genome sequencing, multilocus sequence typing, core genome multilocus sequence typing, pulsed-field electrophoresis and PCR for blaCTX-M were performed on the first isolates. Stool cultures were performed every second month after discharge until 2 years after discharge and at 5 years of age. The last positive samples were analysed with pulsed-field gel electrophoresis and PCR for blaCTX-M. The intestinal relative dominance of ESBL-producing Enterobacteriaceae was determined.

Results

Thirteen of 17 patients colonized with ESBL-KP/ESBL-EC survived. Isolates from 16 of 17 patients were available for analysis and featured the same strain type of ESBL-KP: sequence type 101. The strain had capsule type K29 and harboured blaCTX-M-15. The virulence genes irp1, irp2, iutA, kfu and mrk were detected in all isolates. The median length of colonization was 12.5 months (range, 5-68 months). After 2 years, two of 13 patients were carriers of ESBL-KP and one of 13 of ESBL-EC. At 5 years of age, one neonate was colonized with ESBL-EC", "token_count": 480, "char_count": 1525, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6066, "quality_score": 0.8033, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:12.318212", "source": { "split": "train_shard_00002", "doc_id": 244 }, "chunk_id": "train_shard_00002_244_0", "global_id": 13060 }, { "text": "No infant experienced an ESBL-KP/EC-infection during follow-up.

Conclusions

Two years after discharge, almost one fourth of the study participants were ESBL/KP-EC carriers. ESBL-KP sequence type 101 persisted in two of 13 children for 23 to 26 months. One patient was colonized with ESBL-EC at age 5 years.\n\nNeonatal intestinal colonization with extended-spectrum β-lactamase-producing Enterobacteriaceae-a 5-year follow-up study.", "token_count": 144, "char_count": 437, "word_count": 55, "semantic_coherence": 1, "information_density": 0.9455, "quality_score": 0.9727, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:12.742581", "source": { "split": "train_shard_00002", "doc_id": 244 }, "chunk_id": "train_shard_00002_244_1", "global_id": 13061 }, { "text": "

Background

The presence of Bacillus in very diverse environments reflects the versatile metabolic capabilities of a widely distributed genus. Traditional phylogenetic analysis based on limited gene sampling is not adequate for resolving the genus evolutionary relationships. By distinguishing between core and pan-genome, we determined the evolutionary and functional relationships of known Bacillus.

Results

Our analysis is based upon twenty complete and draft Bacillus genomes, including a newly sequenced Bacillus isolate from an aquatic environment that we report for the first time here. Using a core genome, we were able to determine the phylogeny of known Bacilli, including aquatic strains whose position in the phylogenetic tree could not be unambiguously determined in the past. Using the pan-genome from the sequenced Bacillus, we identified functional differences, such as carbohydrate utilization and genes involved in signal transduction, which distinguished the taxonomic groups. We also assessed the genetic architecture of the defining traits of Bacillus, such as sporulation and competence, and showed that less than one third of the B. subtilis genes are conserved across other Bacilli. Most variation was shown to occur in genes that are needed to respond to environmental cues, suggesting that Bacilli have genetically specialized to allow for the occupation of diverse habitats and niches.

Conclusions

The aquatic Bacilli are defined here for the first time as a group through the phylogenetic analysis of 814 genes that comprise the core genome. Our data distinguished between genomic components, especially core vs. pan-genome to provide insight into phylogeny and function that would otherwise be difficult to achieve. A phylogeny may mask the diversity of functions, which we tried to uncover in our approach. The diversity of sporulation and competence genes across the Bacilli was unexpected based on previous studies of the B. subtilis model alone. The challenge of uncovering the novelties and variations among genes of the non-subtilis groups still remains. This task will be best accomplished by directing efforts toward understanding phylogenetic groups with similar ecological niches.", "token_count": 509, "char_count": 2240, "word_count": 321, "semantic_coherence": 1, "information_density": 0.5888, "quality_score": 0.7944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:13.373941", "source": { "split": "train_shard_00002", "doc_id": 245 }, "chunk_id": "train_shard_00002_245_0", "global_id": 13062 }, { "text": "Understanding the evolutionary relationships and major traits of Bacillus through comparative genomics.", "token_count": 20, "char_count": 103, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:13.737510", "source": { "split": "train_shard_00002", "doc_id": 245 }, "chunk_id": "train_shard_00002_245_1", "global_id": 13063 }, { "text": "Pseudomonas aeruginosa is a human opportunistic pathogen responsible for nosocomial infections, which is largely used as a model organism to study antibiotic resistance and pathogenesis. As other species of the genus, its wide metabolic versatility appears to be attractive to study biotechnological applications. However, its natural resistance to antibiotics and its capacity to produce a wide range of virulence factors argue against its biotechnological potential. By reducing the genome of the reference strain PAO1, we explored the development of four hypovirulent and hypersusceptible recombinant DNA hosts (rDNA hosts). Despite deleting up to 0.8% of the core genome, any of the developed strains presented alterations of fitness when cultured under standard laboratory conditions. Other features such as antibiotic susceptibility, cytotoxicity, in vivo pathogenesis, and expression of heterologous peptides were also explored to highlight the potential applications of these models. This work stands as the first stage of the development of a safe-platform strain of Pseudomonas aeruginosa that will be further optimized for biotechnological applications.\n\nTargeted Genome Reduction of Pseudomonas aeruginosa Strain PAO1 Led to the Development of Hypovirulent and Hypersusceptible rDNA Hosts.", "token_count": 324, "char_count": 1329, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6409, "quality_score": 0.8204, "entities": { "genes": [ "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:14.332595", "source": { "split": "train_shard_00002", "doc_id": 246 }, "chunk_id": "train_shard_00002_246_0", "global_id": 13064 }, { "text": "Helicobacter pylori, a member of Epsilonproteobacteria, is a Gram-negative microaerophilic bacterium that colonizes gastric mucosa of about 50% of the human population. Although most infections caused by H. pylori are asymptomatic, the microorganism is strongly associated with serious diseases of the upper gastrointestinal tract such as chronic gastritis, peptic ulcer, duodenal ulcer, and gastric cancer, and it is classified as a group I carcinogen. The prevalence of H. pylori infections varies worldwide. The H. pylori genotype, host gene polymorphisms, and environmental factors determine the type of induced disease. Currently, the most common therapy to treat H. pylori is the first line clarithromycin-based triple therapy or a quadruple therapy replacing clarithromycin with new antibiotics. Despite the enormous recent effort to introduce new therapeutic regimens to combat this pathogen, treatment for H. pylori still fails in more than 20% of patients, mainly due to the increased prevalence of antibiotic resistant strains. In this review we present recent progress aimed at designing new anti-H. pylori strategies to combat this pathogen. Some novel therapeutic regimens will potentially be used as an extra constituent of antibiotic therapy, and others may replace current antibiotic treatments. KEY POINTS: • Attempts to improve eradication rate of H. pylori infection. • Searching for new drug targets in anti-Helicobacter therapies.\n\nHelicobacter pylori treatment in the post-antibiotics era-searching for new drug targets.", "token_count": 388, "char_count": 1543, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6561, "quality_score": 0.8281, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:14.969813", "source": { "split": "train_shard_00002", "doc_id": 247 }, "chunk_id": "train_shard_00002_247_0", "global_id": 13065 }, { "text": "The black garden ant (Lasius niger) is a widely distributed species across Europe, North America, and North Africa, playing a pivotal role in ecological processes within its diverse habitats. However, the microbiome associated with L. niger remains poorly investigated. In the present study, we isolated a novel species, Paenarthrobacter lasiusi, from the soil of the L. niger anthill. The genome of P. lasiusi S21 was sequenced, annotated, and searched for groups of genes of physiological, medical, and biotechnological importance. Subsequently, a series of microbiological, physiological, and biochemical experiments were conducted to characterize P. lasiusi S21 with respect to its sugar metabolism, antibiotic resistance profile, lipidome, and capacity for atmospheric nitrogen fixation, among others. A notable feature of the P. lasiusi S21 genome is the presence of two prophages, which may have horizontally transferred host genes involved in stress responses. P. lasiusi S21 synthesizes a number of lipids, including mono- and digalactosyldiacylglycerol, as well as steroid compounds that are typically found in eukaryotic organisms rather than prokaryotes. P. lasiusi S21 exhibits resistance to penicillins, lincosamides, fusidins, and oxazolidinones, despite the absence of specific genes conferring resistance to these antibiotics. Genomic data and physiological tests indicate that P. lasiusi S21 is nonpathogenic to humans. The genome of P. lasiusi S21 contains multiple operons involved in heavy metal metabolism and organic compound inactivation. Consequently, P. lasiusi represents a novel species with an intriguing evolutionary history, manifesting in distinctive genomic, metabolomic, and physiological characteristics. This species may have potential applications in the bioaugmentation of contaminated soils.", "token_count": 527, "char_count": 1914, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:02:15.673134", "source": { "split": "train_shard_00002", "doc_id": 248 }, "chunk_id": "train_shard_00002_248_0", "global_id": 13066 }, { "text": "Unusual Genomic and Biochemical Features of <i>Paenarthrobacter lasiusi</i> sp. nov-A Novel Bacterial Species Isolated from <i>Lasius niger</i> Anthill Soil.", "token_count": 75, "char_count": 181, "word_count": 19, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:16.047814", "source": { "split": "train_shard_00002", "doc_id": 248 }, "chunk_id": "train_shard_00002_248_1", "global_id": 13067 }, { "text": "The present invention relates to secretion signal peptides of inulinase derived from Kluyveromyces marxianus, which cause a heterologous protein produced in a yeast cell to be secreted almost completely into the extracellular medium; nucleotide sequences encoding said secretion signal sequences; expression and secretion vectors comprising nucleotide sequences encoding said secretion signal peptides; recombinant yeast cells transformed with said expression and secretion vectors; and a process for producing heterologous proteins by culturing said recombinant yeast cells.\n\nSignal sequences for secretion of heterologous proteins from yeast", "token_count": 140, "char_count": 643, "word_count": 84, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:16.486732", "source": { "split": "train_shard_00002", "doc_id": 249 }, "chunk_id": "train_shard_00002_249_0", "global_id": 13068 }, { "text": "The methyl ester distribution of pectins was studied with a recently developed enzymatic method. Endopolygalacturonase of Kluyveromyces fragilis was used to degrade pectin and the composition of the degradation products was determined with high-performance anion-exchange chromatography at pH 5. Three characteristics indicative for the distribution of nonesterified galacturonic acid residues were obtained: the percentage of nonesterified galacturonic acid residues liberated of the total number of nonesterified galacturonic acid in the undigested polymer, the proportion of nonesterified mono-, di-, and trigalacturonic acid released, and the ratio of the sum of the peak areas of methyl ester containing oligomers divided by the sum of the peak areas of the nonesterified oligomers detected. From these characteristics and the degree of methyl esterification, the mean sequence similarity of the methyl ester distributions was calculated. Computational techniques commonly employed in the determination of the sequence similarity of DNA and proteins were used to discriminate the various types of distributions found and to construct a distance tree. In general, three types of methyl ester distributions could be discerned in pectin: random, high, and blockwise esterified. This report is the first to describe a parametric approach for the comparison of the substituent distribution in polymers. The importance of this novel approach in the study of the methyl ester distribution and the functional properties of pectin is discussed.\n\nNonesterified galacturonic acid sequence homology of pectins.", "token_count": 359, "char_count": 1603, "word_count": 227, "semantic_coherence": 1, "information_density": 0.4978, "quality_score": 0.7489, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:17.065094", "source": { "split": "train_shard_00002", "doc_id": 250 }, "chunk_id": "train_shard_00002_250_0", "global_id": 13069 }, { "text": "Silicon (Si) is gaining widespread attention due to its prophylactic activity to protect plants under stress conditions. Despite Si's abundance in the earth's crust, most soils do not have enough soluble Si for plants to absorb. In the present study, a silicate-solubilizing bacterium, Enterobacter sp. LR6, was isolated from the rhizospheric soil of rice and subsequently characterized through whole-genome sequencing. The size of the LR6 genome is 5.2 Mb with a GC content of 54.9% and 5182 protein-coding genes. In taxogenomic terms, it is similar to E. hormaechei subsp. xiangfangensis based on average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH). LR6 genomic data provided insight into potential genes involved in stress response, secondary metabolite production, and growth promotion. The LR6 genome contains two aquaporins, of which the aquaglyceroporin (GlpF) is responsible for the uptake of metalloids including arsenic (As) and antimony (Sb). The yeast survivability assay confirmed the metalloid transport activity of GlpF. As a biofertilizer, LR6 isolate has a great deal of tolerance to high temperatures (45 °C), salinity (7%), and acidic environments (pH 9). Most importantly, the present study provides an understanding of plant-growth-promoting activity of the silicate-solubilizing bacterium, its adaptation to various stresses, and its uptake of different metalloids including As, Ge, and Si.\n\nGenomic Landscape Highlights Molecular Mechanisms Involved in Silicate Solubilization, Stress Tolerance, and Potential Growth-Promoting Activity of Bacterium Enterobacter sp. LR6.", "token_count": 450, "char_count": 1637, "word_count": 228, "semantic_coherence": 1, "information_density": 0.6974, "quality_score": 0.8487, "entities": { "genes": [ "LR6" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:18.070501", "source": { "split": "train_shard_00002", "doc_id": 251 }, "chunk_id": "train_shard_00002_251_0", "global_id": 13070 }, { "text": "Recent studies have pointed to the existence of two subpopulations of Enterococcus faecium, one containing primarily commensal/community-associated (CA) strains and one that contains most clinical or hospital-associated (HA) strains, including those classified by multi-locus sequence typing (MLST) as belonging to the CC17 group. The HA subpopulation more frequently has IS16, pathogenicity island(s), and plasmids or genes associated with antibiotic resistance, colonization, and/or virulence. Supporting the two clades concept, we previously found a 3-10% difference between four genes from HA-clade strains vs. CA-clade strains, including 5% difference between pbp5-R of ampicillin-resistant, HA strains and pbp5-S of ampicillin-sensitive, CA strains. To further investigate the core genome of these subpopulations, we studied 100 genes from 21 E. faecium genome sequences; our analyses of concatenated sequences, SNPs, and individual genes all identified two distinct groups. With the concatenated sequence, HA-clade strains differed by 0-1% from one another while CA clade strains differed from each other by 0-1.1%, with 3.5-4.2% difference between the two clades. While many strains had a few genes that grouped in one clade with most of their genes in the other clade, one strain had 28% of its genes in the CA clade and 72% in the HA clade, consistent with the predicted role of recombination in the evolution of E. faecium. Using estimates for Escherichia coli, molecular clock calculations using sSNP analysis indicate that these two clades may have diverged ≥1 million years ago or, using the higher mutation rate for Bacillus anthracis, ∼300,000 years ago. These data confirm the existence of two clades of E. faecium and show that the differences between the HA and CA clades occur at the core genomic level and long preceded the modern antibiotic era.", "token_count": 494, "char_count": 1867, "word_count": 281, "semantic_coherence": 1, "information_density": 0.5872, "quality_score": 0.7936, "entities": { "genes": [ "IS16", "CC17" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:18.716763", "source": { "split": "train_shard_00002", "doc_id": 252 }, "chunk_id": "train_shard_00002_252_0", "global_id": 13071 }, { "text": "Genomic and SNP analyses demonstrate a distant separation of the hospital and community-associated clades of Enterococcus faecium.", "token_count": 30, "char_count": 130, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:19.071302", "source": { "split": "train_shard_00002", "doc_id": 252 }, "chunk_id": "train_shard_00002_252_1", "global_id": 13072 }, { "text": "Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different modes of evolution. Closely related strains can differ in the presence or absence of many genes, and the total number of distinct genes found in a set of related isolates – the pan-genome – is often many times larger than the genome of individual isolates. We have developed a pipeline that efficiently identifies orthologous gene clusters in the pan-genome. This pipeline is coupled to a powerful yet easy-to-use web-based visualization software for interactive exploration of the pan-genome. The visualization consists of connected components that allow rapid filtering and searching of genes and inspection of their evolutionary history. For each gene cluster, panX displays an alignment, a phylogenetic tree, maps mutations within that cluster to the branches of the tree and infers gain and loss of genes on the core-genome phylogeny. PanX is available at pangenome.de . Custom pan-genomes can be visualized either using a webserver or by serving panX locally as a browser-based application.\n\npanX: pan-genome analysis and exploration", "token_count": 255, "char_count": 1164, "word_count": 177, "semantic_coherence": 1, "information_density": 0.6723, "quality_score": 0.8362, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:19.559556", "source": { "split": "train_shard_00002", "doc_id": 253 }, "chunk_id": "train_shard_00002_253_0", "global_id": 13073 }, { "text": "The growth of yeasts, lactic acid bacteria, pseudomonads, and enterobacteria during the refrigerated storage of an Italian soft cheese (Stracchino) in various packaging conditions (under air, under vacuum, and in the presence of ethanol) was studied. Yeasts were found to play a significant role in cheese spoilage, producing unplesant flavors and odors and causing significant reductions in the shelf life of the paper-wrapped cheeses. Packaging under vacuum decreased the yeast growth rates and reduced the populations attained at the end of the exponential phase of growth, resulting in a shelf-life extension of the Stracchino cheese of over 28 days. A total of 129 yeasts isolates were identified according to conventional methods. The most frequently isolated yeasts were Candida colliculosa , Debaryomyces hansenii , and Candida famata . Other species encountered were Tolurospora delbrueckii , Kluyveromyces marxianus , and Saccharomyces cerevisiae.\n\nThe Behavior of Yeast Populations in Stracchino Cheese Packaged under Various Conditions.", "token_count": 256, "char_count": 1048, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:20.107303", "source": { "split": "train_shard_00002", "doc_id": 254 }, "chunk_id": "train_shard_00002_254_0", "global_id": 13074 }, { "text": "This study characterized cefoxitin-resistant and -susceptible Salmonella enterica serovar Heidelberg strains from humans, abattoir poultry, and retail poultry to assess the molecular relationships of isolates from these sources in Québec in 2012. Isolates were collected as part of the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). All isolates were subjected to antimicrobial susceptibility testing, PCR for CMY-2, pulsed-field gel electrophoresis (PFGE), and whole-genome sequencing (WGS). A total of 113 S Heidelberg isolates from humans (n = 51), abattoir poultry (n = 18), and retail poultry (n = 44) were studied. All cefoxitin-resistant isolates (n = 65) were also resistant to amoxicillin-clavulanic acid, ampicillin, ceftiofur, and ceftriaxone, and all contained the CMY-2 gene. PFGE analysis showed that 111/113 (98.2%) isolates clustered together with ≥90% similarity. Core genome analysis using WGS identified 13 small clusters of isolates with 0 to 4 single nucleotide variations (SNVs), consisting of cefoxitin-resistant and -susceptible human, abattoir poultry, and retail poultry isolates. CMY-2 plasmids from cefoxitin-resistant isolates all belonged to incompatibility group I1. Analysis of IncI1 plasmid sequences revealed high identity (95 to 99%) to a previously described plasmid (pCVM29188_101) found in Salmonella Kentucky", "token_count": 475, "char_count": 1429, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:20.757856", "source": { "split": "train_shard_00002", "doc_id": 255 }, "chunk_id": "train_shard_00002_255_0", "global_id": 13075 }, { "text": "When compared to pCVM29188_101, all sequenced cefoxitin-resistant isolates were found to carry 1 of 10 possible variant plasmids. Transmission of S Heidelberg may be occurring between human, abattoir poultry, and retail poultry sources, and transmission of a common CMY-2 plasmid may be occurring among S Heidelberg strains with variable genetic backgrounds.\n\nA Whole-Genome Sequencing Approach To Study Cefoxitin-Resistant Salmonella enterica Serovar Heidelberg Isolates from Various Sources.", "token_count": 154, "char_count": 507, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7727, "quality_score": 0.8864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:21.186176", "source": { "split": "train_shard_00002", "doc_id": 255 }, "chunk_id": "train_shard_00002_255_1", "global_id": 13076 }, { "text": "Pseudomonas aeruginosa infects patients with cystic fibrosis, burns, wounds and implants. Previously, our group showed that elevated Ca2+ positively regulates the production of several virulence factors in P. aeruginosa, such as biofilm formation, production of pyocyanin and secreted proteases. We have identified a Ca2+-regulated β-propeller putative phytase, CarP, which is required for Ca2+ tolerance, regulation of the intracellular Ca2+ levels, and plays a role in Ca2+ regulation of P. aeruginosa virulence. Here, we studied the conservation of carP sequence and its occurrence in diverse phylogenetic groups of bacteria. In silico analysis revealed that carP and its two paralogues PA2017 and PA0319 are primarily present in P. aeruginosa and belong to the core genome of the species. We identified 155 single nucleotide alterations within carP, 42 of which lead to missense mutations with only three that affected the predicted 3D structure of the protein. PCR analyses with carP-specific primers detected P. aeruginosa specifically in 70 clinical and environmental samples. Sequence comparison demonstrated that carP is overall highly conserved in P. aeruginosa isolated from diverse environments. Such evolutionary preservation of carP illustrates its importance for P. aeruginosa adaptations to diverse environments and demonstrates its potential as a biomarker.\n\ncarP, encoding a Ca2+-regulated putative phytase, is evolutionarily conserved in Pseudomonas aeruginosa and has potential as a biomarker.", "token_count": 508, "char_count": 1691, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6075, "quality_score": 0.8037, "entities": { "genes": [ "PA2017", "PA0319" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:21.811500", "source": { "split": "train_shard_00002", "doc_id": 256 }, "chunk_id": "train_shard_00002_256_0", "global_id": 13077 }, { "text": "The role of the accompanying microbiota in the presence of Listeria monocytogenes on meat processing surfaces is not yet understood, especially in industrial production conditions. In this study, 300 conveyor belt samples from the cutting room of a swine slaughterhouse were collected during production. The samples were subjected to the detection of L. monocytogenes. Recovered strains were characterized by serogrouping-PCR, InlA Sanger sequencing and for their ability to form biofilm. A selection of isolates was compared with core genome multi-locus sequence typing analysis (cgMLST). The sequencing of the V4 region of the 16S RNA gene of the microorganisms harvested from each sample was carried out in parallel using the Illumina MiSeq platform. Diversity analyses were performed and MaAsLin analysis was used to assess the link between L. monocytogenes detection and the surrounding bacteria. The 72 isolates collected showed a low genetic diversity and important persistence characteristics. L. monocytogenes isolates were not stochastically distributed on the surfaces: the isolates were detected on three out of six production lines, each associated with a specific meat cut: the half carcasses, the bostons and the picnics. MaAsLin biomarker analysis identified the taxa Veillonella (p ≤ 0.0397) as a bacterial determinant of the presence of L. monocytogenes on processing surfaces. The results of this study revealed a heterogenous contamination pattern of the processing surfaces by L. monocytogenes and targeted a bacterial indicator of the presence of the pathogen. These results could lead to a better risk assessment of the contamination of meat products.\n\nUse of an Ecosystem-Based Approach to Shed Light on the Heterogeneity of the Contamination Pattern of Listeria monocytogenes on Conveyor Belt Surfaces in a Swine Slaughterhouse in the Province of Quebec, Canada.", "token_count": 498, "char_count": 1950, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5429, "quality_score": 0.7714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:22.466170", "source": { "split": "train_shard_00002", "doc_id": 257 }, "chunk_id": "train_shard_00002_257_0", "global_id": 13078 }, { "text": "Bacillus sp. 7PJ-16, an endophytic bacterium isolated from a healthy mulberry stem and previously identified as Bacillus tequilensis 7PJ-16, exhibits strong antifungal activity and has the capacity to promote plant growth. This strain was studied for its effectiveness as a biocontrol agent to reduce mulberry fruit sclerotiniose in the field and as a growth-promoting agent for mulberry in the greenhouse. In field studies, the cell suspension and supernatant of strain 7PJ-16 exhibited biocontrol efficacy and the lowest disease incidence was reduced down to only 0.80%. In greenhouse experiments, the cell suspension (1.0 × 106 and 1.0 × 105 CFU/mL) and the cell-free supernatant (100-fold and 1000-fold dilution) stimulated mulberry seed germination and promoted mulberry seedling growth. In addition, to accurately identify the 7PJ-16 strain and further explore the mechanisms of its antifungal and growth-promoting properties, the complete genome of this strain was sequenced and annotated. The 7PJ-16 genome is comprised of two circular plasmids and a 4,209,045-bp circular chromosome, containing 4492 protein-coding genes and 116 RNA genes. This strain was ultimately designed as Bacillus subtilis based on core genome sequence analyses using a phylogenomic approach. In this genome, we identified a series of gene clusters that function in the synthesis of non-ribosomal peptides (surfactin, fengycin, bacillibactin, and bacilysin) as well as the ribosome-dependent synthesis of tasA and bacteriocins (subtilin, subtilosin A), which are responsible for the biosynthesis of numerous antimicrobial metabolites", "token_count": 489, "char_count": 1638, "word_count": 231, "semantic_coherence": 1, "information_density": 0.6061, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:23.120404", "source": { "split": "train_shard_00002", "doc_id": 258 }, "chunk_id": "train_shard_00002_258_0", "global_id": 13079 }, { "text": "Additionally, several genes with function that promote plant growth, such as indole-3-acetic acid biosynthesis, the production of volatile substances, and siderophores synthesis, were also identified. The information described in this study has established a good foundation for understanding the beneficial interactions between endophytes and host plants, and facilitates the further application of B. subtilis 7PJ-16 as an agricultural biofertilizer and biocontrol agent.\n\nGenomic and Functional Characterization of the Endophytic Bacillus subtilis 7PJ-16 Strain, a Potential Biocontrol Agent of Mulberry Fruit Sclerotiniose.", "token_count": 158, "char_count": 627, "word_count": 81, "semantic_coherence": 1, "information_density": 0.8025, "quality_score": 0.9012, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:23.564175", "source": { "split": "train_shard_00002", "doc_id": 258 }, "chunk_id": "train_shard_00002_258_1", "global_id": 13080 }, { "text": "

Objectives

Carbapenemase-producing Klebsiella pneumoniae pose an increasing risk for healthcare facilities worldwide. A continuous monitoring of ST distribution and its association with resistance and virulence genes is required for early detection of successful K. pneumoniae lineages. In this study, we used WGS to characterize MDR blaOXA-48-positive K. pneumoniae isolated from inpatients at the University Medical Center Göttingen, Germany, between March 2013 and August 2014.

Methods

Closed genomes for 16 isolates of carbapenemase-producing K. pneumoniae were generated by single molecule real-time technology using the PacBio RSII platform.

Results

Eight of the 16 isolates showed identical XbaI macrorestriction patterns and shared the same MLST, ST147. The eight ST147 isolates differed by only 1-25 SNPs of their core genome, indicating a clonal origin. Most of the eight ST147 isolates carried four plasmids with sizes of 246.8, 96.1, 63.6 and 61.0 kb and a novel linear plasmid prophage, named pKO2, of 54.6 kb. The blaOXA-48 gene was located on a 63.6 kb IncL plasmid and is part of composite transposon Tn1999.2. The ST147 isolates expressed the yersinabactin system as a major virulence factor. The comparative whole-genome analysis revealed several rearrangements of mobile genetic elements and losses of chromosomal and plasmidic regions in the ST147 isolates.

Conclusions

Single molecule real-time sequencing allowed monitoring of the genetic and epigenetic microevolution of MDR OXA-48-producing K. pneumoniae and revealed in addition to SNPs, complex rearrangements of genetic elements.", "token_count": 500, "char_count": 1635, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6682, "quality_score": 0.8341, "entities": { "genes": [ "ST147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:24.214770", "source": { "split": "train_shard_00002", "doc_id": 259 }, "chunk_id": "train_shard_00002_259_0", "global_id": 13081 }, { "text": "Monitoring microevolution of OXA-48-producing Klebsiella pneumoniae ST147 in a hospital setting by SMRT sequencing.", "token_count": 37, "char_count": 115, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [ "ST147" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:24.573045", "source": { "split": "train_shard_00002", "doc_id": 259 }, "chunk_id": "train_shard_00002_259_1", "global_id": 13082 }, { "text": "Pseudomonas aeruginosa is a Gram-negative opportunistic pathogen particularly associated with the inherited disease cystic fibrosis (CF). Pseudomonas aeruginosa is well known to have a large and adaptable genome that enables it to colonise a wide range of ecological niches. Here, we have used a comparative genomics approach to identify changes that occur during infection of the CF lung. We used the mucoid phenotype as an obvious marker of host adaptation and compared these genomes to analyse SNPs, indels and islands within near-isogenic pairs. To commence the correction of the natural bias towards clinical isolates in genomics studies and to widen our understanding of the genomic diversity of P. aeruginosa, we included four environmental isolates in our analysis. Our data suggest that genome plasticity plays an important role in chronic infection and that the strains sequenced in this study are representative of the two major phylogenetic groups as determined by core genome SNP analysis.\n\nDraft genomes of 12 host-adapted and environmental isolates of Pseudomonas aeruginosa and their positions in the core genome phylogeny.", "token_count": 260, "char_count": 1139, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:25.140690", "source": { "split": "train_shard_00002", "doc_id": 260 }, "chunk_id": "train_shard_00002_260_0", "global_id": 13083 }, { "text": "

Background

The incidence of invasive disease caused by encapsulated Haemophilus influenzae type f (Hif) has increased in the post-H. influenzae type b (Hib) vaccine era. We previously annotated the first complete Hif genome from a clinical isolate (KR494) that caused septic shock and necrotizing myositis. Here, the full genome of Hif KR494 was compared to sequenced reference strains Hib 10810, capsule type d (Hid) Rd Kw20, and finally nontypeable H. influenzae 3655. The goal was to identify possible genomic characteristics that may shed light upon the pathogenesis of Hif.

Results

The Hif KR494 genome exhibited large regions of synteny with other H. influenzae, but also distinct genome rearrangements. A predicted Hif core genome of 1390 genes was shared with the reference strains, and 6 unique genomic regions comprising half of the 191 unique coding sequences were revealed. The majority of these regions were inserted genetic fragments, most likely derived from the closely-related Haemophilus spp. including H. aegyptius, H. haemolyticus and H. parainfluenzae. Importantly, the KR494 genome possessed several putative virulence genes that were distinct from non-type f strains. These included the sap2 operon, aef3 fimbriae, and genes for kanamycin nucleotidyltranserase, iron-utilization proteins, and putative YadA-like trimeric autotransporters that may increase the bacterial virulence. Furthermore, Hif KR494 lacked a hisABCDEFGH operon for de novo histidine biosynthesis, hmg locus for lipooligosaccharide biosynthesis and biofilm formation, the Haemophilus antibiotic resistance island and a Haemophilus secondary molybdate transport system. We confirmed the histidine auxotrophy and kanamycin resistance in Hif by functional experiments", "token_count": 512, "char_count": 1772, "word_count": 245, "semantic_coherence": 1, "information_density": 0.649, "quality_score": 0.8245, "entities": { "genes": [ "KR494" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:25.800358", "source": { "split": "train_shard_00002", "doc_id": 261 }, "chunk_id": "train_shard_00002_261_0", "global_id": 13084 }, { "text": "Moreover, the pattern of unique or missing genes of Hif KR494 was similar in 20 Hif clinical isolates obtained from different years and geographical areas. A cross-species comparison revealed that the Hif genome shared more characteristics with H. aegyptius than Hid and NTHi.

Conclusions

The genomic comparative analyses facilitated identification of genotypic characteristics that may be related to the specific virulence of Hif. In relation to non-type f H. influenzae strains, the Hif genome contains differences in components involved in metabolism and survival that may contribute to its invasiveness.\n\nComparative genomic analysis reveals distinct genotypic features of the emerging pathogen Haemophilus influenzae type f.", "token_count": 177, "char_count": 736, "word_count": 102, "semantic_coherence": 1, "information_density": 0.7255, "quality_score": 0.8627, "entities": { "genes": [ "KR494" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:26.274989", "source": { "split": "train_shard_00002", "doc_id": 261 }, "chunk_id": "train_shard_00002_261_1", "global_id": 13085 }, { "text": "Enterococcus faecium is commonly isolated from the human gastrointestinal tract; however, important intraspecies variations exist with relevance for host health and well-being. Here, we describe the draft genome sequence of E. faecium PC4.1, a clade B strain isolated from human feces.\n\nDraft Genome Sequence of Enterococcus faecium PC4.1, a Clade B Strain Isolated from Human Feces.", "token_count": 108, "char_count": 383, "word_count": 56, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [ "PC4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:26.702073", "source": { "split": "train_shard_00002", "doc_id": 262 }, "chunk_id": "train_shard_00002_262_0", "global_id": 13086 }, { "text": "The presence of killer and proteolytic yeasts was studied among 944 isolates representing 105 species from tropical yeast communities. We found 13 killer toxin producing species, with Pichia kluyveri being the most frequent. Other killer yeast isolates were Candida apis, Candida bombicola, Candida fructus, Candida krusei, Candida sorbosa, Hanseniaspora uvarum, Issatchenkia occidentalis, Kloeckera apis, Kluyveromyces marxianus, Pichia membranaefaciens, Pichia ohmeri-like, and Sporobolomyces roseus. The communities from which killer yeasts were isolated had strains sensitive to them, and there were interspecific and intraspecific differences in the spectra of their killer activities. Pichia kluyveri had the broadest spectra of activity against sensitive isolates, and it apparently produced different toxins. The coexistence of sensitive and killer yeasts using the same substrate suggests that there is spatial separation in microhabitats or temporal separation in different stages of successions. Basidiomycetous yeasts were more frequently proteolytic than ascomycetous yeasts. Extracellular proteases could be important for the yeasts to have access to more nitrogen nutrients and obtain a better balance with available carbon sources.\n\nThe incidence of killer activity and extracellular proteases in tropical yeast communities.", "token_count": 335, "char_count": 1340, "word_count": 179, "semantic_coherence": 1, "information_density": 0.6313, "quality_score": 0.8156, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:27.306113", "source": { "split": "train_shard_00002", "doc_id": 263 }, "chunk_id": "train_shard_00002_263_0", "global_id": 13087 }, { "text": "

Background

Acinetobacter baumannii is a nosocomial pathogen of critical importance due to the increasing numbers of antibiotic-resistant isolates. Colonies can have a smooth or matt appearance, but also exhibit slimy, mucoid growth, with the latter being increasingly isolated in patients in recent years.

Methods

We isolated 60 A. baumannii strains from altogether 56 patients and found that all patients were infected by mucoid strains, with four patients having also matt phenotypes in addition to the mucoid ones. The morphology of the colonies and capsules was observed. The antibiotics susceptibilities were tested, and the biofilm formation ability was determined by crystal violet staining. The whole-genome sequencing (WGS) was performed on all the strains, and then the core genome multilocus sequence typing (cgMLST) and drug resistance gene analysis were performed. Finally, a part of isolates were selected to test virulence in a Galleria mellonella model.

Results

We observed much larger capsules in the mucoid strains compared to the matt isolates. But the mucoid phenotype did not correlate with the amount of biofilm produced by the strain. Almost all mucus-type A. baumannii were multi-drug resistant isolates, containing various antibiotic resistance genes. The main ST types of mucoid-type A.baumannii were ST191 and ST195, of which ST191 isolates were more virulence, while ST195 isolates were weaker.

Conclusion

The mucoid A. baumannii had resistance to most antibiotics and some strains had high virulence, which should be paid attention in clinical.", "token_count": 452, "char_count": 1644, "word_count": 227, "semantic_coherence": 1, "information_density": 0.6123, "quality_score": 0.8062, "entities": { "genes": [ "ST195", "ST191" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:27.986310", "source": { "split": "train_shard_00002", "doc_id": 264 }, "chunk_id": "train_shard_00002_264_0", "global_id": 13088 }, { "text": "Capsule Thickness, Not Biofilm Formation, Gives Rise to Mucoid Acinetobacter baumannii Phenotypes That are More Prevalent in Long-Term Infections: A Study of Clinical Isolates from a Hospital in China.", "token_count": 66, "char_count": 208, "word_count": 29, "semantic_coherence": 1, "information_density": 0.931, "quality_score": 0.9655, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:28.353207", "source": { "split": "train_shard_00002", "doc_id": 264 }, "chunk_id": "train_shard_00002_264_1", "global_id": 13089 }, { "text": "Partial sequences of 25 S ribosomal DNA for nine Candida yeast and one Kluyveromyces yeast strains were cloned and determined. We compared them with two published 25 S rDNA sequences of Saccharomyces cerevisiae and Candida albicans. An evolutionary tree of the twelve species was inferred from about 370 sites of 5^ end of 25 S ribosomal DNA using the methods of neighbor-joining and bootstrap. The molecular data indicate a very close affinity between Candida kefyr CBS834 and Kluyveromyces cicerisporus CBS4857.\n\nAnalysis of phylogenetic relationships among twelve yeast species", "token_count": 161, "char_count": 580, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7045, "quality_score": 0.8523, "entities": { "genes": [ "CBS834", "CBS4857" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:28.800737", "source": { "split": "train_shard_00002", "doc_id": 265 }, "chunk_id": "train_shard_00002_265_0", "global_id": 13090 }, { "text": "All five novel, thermotolerant, alcohol-producing Kluyveromyces marxianus yeast strains, capable of growth at 52°C, grew aerobically on lactose (growth rates of 0.43 to 0.5 h(-1)), whey permeate (0.38 to 0.43 h(-1)), cellobiose (0.18 to 0.3 h(-1)) and xylose (0.18 to 0.26 h(-1)). They also grew anaerobically at 40 (0.18 to 0.19 h(-1)) and 45°C (0.09 to 0.14 h(-1)). All fermented glucose to ethanol and tolerated ethanol at ≤95 g l(-1) at 45°C. Their potential for industrial alcohol production, possibly in combination with the dairy and wood-related industries, is discussed.\n\nCharacterization and potential industrial applications of five novel, thermotolerant, fermentative, yeast strains.", "token_count": 251, "char_count": 695, "word_count": 101, "semantic_coherence": 1, "information_density": 0.703, "quality_score": 0.8515, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:29.288292", "source": { "split": "train_shard_00002", "doc_id": 266 }, "chunk_id": "train_shard_00002_266_0", "global_id": 13091 }, { "text": "The lectin-mediated agglutination kinetics of Candida albicans, Candida tropicalis, Candida glabrata, Candida krusei, Candida kefyr, and Candida parapsilosis strains isolated from immunocompromised patients was investigated. The rate of the lectin-induced cell agglutination depends on the physiological state of the yeast cell population. Therefore, the Candida strains have to be cultivated and investigated under identical conditions. Lentil lectin (prepared from Lens culinaris), castor lectin, and concanavalin A were used. Different yeast species showed different agglutination behaviour. Furthermore, the lectin-mediated rate of agglutination is a strain-specific property which makes it possible to distinguish between different yeast strains of the same species. It is concluded that the lectin-mediated agglutination kinetics allows reproducible differentiation of yeast strains of the same species.\n\nDifferentiation of Candida strains by lectin-mediated agglutination kinetics.", "token_count": 247, "char_count": 988, "word_count": 125, "semantic_coherence": 1, "information_density": 0.576, "quality_score": 0.788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:29.773171", "source": { "split": "train_shard_00002", "doc_id": 267 }, "chunk_id": "train_shard_00002_267_0", "global_id": 13092 }, { "text": "Many plant pathogens subvert host immunity by injecting compositionally diverse but functionally similar repertoires of cytoplasmic effector proteins. The bacterial pathogen Pseudomonas syringae is a model for exploring the functional structure of such repertoires. The pangenome of P. syringae encodes 57 families of effectors injected by the type III secretion system. Distribution of effector genes among phylogenetically diverse strains reveals a small set of core effectors targeting antimicrobial vesicle trafficking and a much larger set of variable effectors targeting kinase-based recognition processes. Complete disassembly of the 28-effector repertoire of a model strain and reassembly of a minimal functional repertoire reveals the importance of simultaneously attacking both processes. These observations, coupled with growing knowledge of effector targets in plants, support a model for coevolving molecular dialogs between effector repertoires and plant immune systems that emphasizes mutually-driven expansion of the components governing recognition.\n\nPseudomonas syringae type III effector repertoires: last words in endless arguments.", "token_count": 255, "char_count": 1152, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6711, "quality_score": 0.8355, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:30.259893", "source": { "split": "train_shard_00002", "doc_id": 268 }, "chunk_id": "train_shard_00002_268_0", "global_id": 13093 }, { "text": "

ABSTRACT

The dissemination of carbapenem resistance in Escherichia coli has major implications for the management of common human infections. bla KPC , encoding a transmissible carbapenemase (KPC), has historically largely been associated with Klebsiella pneumoniae, a predominant plasmid (pKpQIL), and a specific transposable element (Tn 4401, ~10kb). Here we characterize the genetic features of the emergence of bla KPC in global E. coli, 2008-2013, using both long-and short-read whole genome sequencing. Amongst 43/45 successfully sequenced bla KPC - E. coli strains, we identified high strain (n=21 sequence types, 18% of annotated genes in the core genome); plasmid (≥9 replicon types); and bla KPC -associated, mobile genetic element (MGE) diversity (50% not within complete Tn 4401 elements). We also found evidence of interspecies, regional and international plasmid spread. In several cases bla KPC was found on high copy number, small Col-like plasmids, previously associated with horizontal transmission of resistance genes in the absence of antimicrobial selection pressures. E. coli is a common human pathogen, but also a commensal in a multiple environmental and animal reservoirs, and easily transmissible. The association of bla KPC with a range of MGEs previously linked to the successful spread of widely endemic resistance mechanisms (e.g. bla T EM , bla CTX-M ) suggests that it is likely to become similarly prevalent.\n\nGenomic epidemiology of globalKlebsiella pneumoniaecarbapenemase (KPC)-producingEscherichia coli", "token_count": 447, "char_count": 1562, "word_count": 222, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:30.896158", "source": { "split": "train_shard_00002", "doc_id": 269 }, "chunk_id": "train_shard_00002_269_0", "global_id": 13094 }, { "text": "This thesis concerns the influence of several metal cations on the growth and fermentative metabolism of industrial strains of yeast. Experiments were conducted in laboratory growth media (both synthetic and complex) and industrial fermentation media (molasses and malt wort) in order to investigate influences of K+, Mg2+, Ca2+ and Zn2+ on ethanol production by several strains of the yeast species, Saccharomyces cerevisiae and Kluyveromyces marxianus and Schizosaccharomyces pombe. Mg2+ supplementation studies in the media revealed positive effects on cell growth and ethanol production o f all yeasts studied. Although differences existed between yeast species with regard to fermentation, the yeast Saccharomyces cerevisiae, distillers strain DCL'M', was found to be the highest ethanol producer in all media studied. Defined media experiments were designed which mimicked high, intermediate and low K+, Ca2+ and Mg2+ levels reported in sugarcane molasses and Ca2+, Mg2+ and Zn2+ in malt wort in order to investigate their interactive effects on alcoholic fermentation. ... (continues)\n\nRole of metal ions in fermentative metabolism of yeast", "token_count": 380, "char_count": 1296, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6084, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:31.488471", "source": { "split": "train_shard_00002", "doc_id": 270 }, "chunk_id": "train_shard_00002_270_0", "global_id": 13095 }, { "text": "Bacteria belonging to the Pseudomonas genus are highly successful colonizers of the plant rhizosphere. The ability of different Pseudomonas species to live either commensal lifestyles or to act as agents of plant-growth promotion or disease is reflected in a large, highly flexible accessory genome. Nevertheless, adaptation to the plant environment involves a commonality of phenotypic outputs such as changes to motility, coupled with synthesis of nutrient uptake systems, stress-response molecules and adherence factors including exopolysaccharides. Cyclic-di-GMP (cdG) is a highly important second messenger involved in the integration of environmental signals with appropriate adaptive responses and is known to play a central role in mediating effective rhizosphere colonization. In this study, we examined the transcription of multiple, reportedly plant-upregulated cdG metabolism genes during colonization of the wheat rhizosphere by the plant-growth-promoting strain P. fluorescens SBW25. While transcription of the tested genes generally increased in the rhizosphere environment, we additionally observed a tightly orchestrated response to environmental cues, with a distinct transcriptional pattern seen for each gene throughout the colonization process. Extensive phenotypical analysis of deletion and overexpression strains was then conducted and used to propose cellular functions for individual cdG signaling genes. Finally, in-depth genetic analysis of an important rhizosphere colonization regulator revealed a link between cdG control of growth, motility and stress response, and the carbon sources available in the rhizosphere.\n\nDifferential Regulation of Genes for Cyclic-di-GMP Metabolism Orchestrates Adaptive Changes During Rhizosphere Colonization by Pseudomonas fluorescens.", "token_count": 423, "char_count": 1827, "word_count": 237, "semantic_coherence": 1, "information_density": 0.654, "quality_score": 0.827, "entities": { "genes": [ "SBW25" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:32.116198", "source": { "split": "train_shard_00002", "doc_id": 271 }, "chunk_id": "train_shard_00002_271_0", "global_id": 13096 }, { "text": "The aim of this research is to quantify the effect of temperature and enzyme origin on the enzymatic synthesis of oligosaccharides. Quantification of these effects is important because temperature and enzyme origin are important process parameters. A kinetic model was used to describe the concentrations in time. The kinetic parameters were determined by using data obtained in batch experiments at various temperatures (20, 30, 40, and 50 degrees C) and by using beta-galactosidases from Bacillus circulans, Aspergillus oryzae, Kluyveromyces lactis, and Kluyveromyces fragilis. The effect of temperature on the kinetic parameters could be described with the Arrhenius equation, except for the inhibition parameter. Slightly higher oligosaccharide yields were found at higher temperatures. However, the influence of the initial lactose concentration was much larger. The higher yield at higher temperatures is an additional advantage when operating at high initial lactose concentrations and consequently elevated temperatures. Clear differences between the beta-galactosidases were found concerning amount, size, and type of oligosaccharides produced. The beta-galactosidase from B. circulans produced the most abundant amount, the most different, and largest-sized oligosaccharides. The beta-galactosidases from Kluyveromyces spp. produced mainly trisaccharides. The kinetic parameters for the different enzymes were determined and differences were discussed.\n\nEffect of temperature and enzyme origin on the enzymatic synthesis of oligosaccharides.", "token_count": 367, "char_count": 1551, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5577, "quality_score": 0.7788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:32.699713", "source": { "split": "train_shard_00002", "doc_id": 272 }, "chunk_id": "train_shard_00002_272_0", "global_id": 13097 }, { "text": "The last three pieces of research associated with the late Anthony H. Rose, Professor of Microbiology at the University of Bath, are reviewed. The second messenger cyclic AMP was shown to vary up to 70-fold in concentration during the growth of batch cultures of Saccharomyces cerevisiae with different media. It seems to have a role in transducing information on actual levels of extracellular residual carbon source as well as entry into stationary phase. Another second messenger pathway, involving hydrolysis of phosphatidylinositol bisphosphate, was shown not to be glucose-stimulated as previously thought. Inositol trisphosphate kinase activity was detected but both the existence of the complete pathway and its role were unclear. The yeast Kluyveromyces marxianus isolated from cocoa fermentations was shown to produce abundant and almost pure endo-polygalacturonase in a constitutive manner. Some strains of Saccharomyces cerevisiae also secrete this pectinolytic enzyme. All three projects relate to the central role of membranes in regulating transport of either sensory information or molecules in and out of cells, a key focus of his research for thirty years.\n\nThe ins and outs of the yeast plasma membrane", "token_count": 293, "char_count": 1221, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6995, "quality_score": 0.8497, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:33.263452", "source": { "split": "train_shard_00002", "doc_id": 273 }, "chunk_id": "train_shard_00002_273_0", "global_id": 13098 }, { "text": "Invasive candidiasis has become a major cause of morbidity and mortality in immunocompromised hosts. Here we describe a fast and reliable DNA extraction and PCR amplification method in combination with a slot blot hybridization assay. A genus-specific probe was designed that allowed to detect DNA from a broad range of Candida species and 3 other yeasts. In addition, species-specific oligonucleotides for emerging Candida and other yeast species allowed to identify DNA extracted from Candida lusitaniae, Candida humicola, Candida kefyr, Candida inconspicua, Candida solani, Malassezia furfur and Trichosporon cutaneum. A sensitivity of at least 10(1) CFU, corresponding to 100 fg of fungal DNA, was documented for all species-specific probes and the common Candida probe. In addition, the 18S rRNA genes of 7 yeast species (C. humicola, C. kefyr, C. solani, C. inconspicua, C. norvegensis, C. utilis and M. furfur) were completely sequenced. The sequencing primers described bind to highly conserved primer binding sites. Therefore, these primers would allow rapid cycle sequence of additional ribosomal genes throughout the whole kingdom of fungi.\n\nIdentification of rare Candida species and other yeasts by polymerase chain reaction and slot blot hybridization.", "token_count": 330, "char_count": 1266, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6559, "quality_score": 0.828, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:33.831004", "source": { "split": "train_shard_00002", "doc_id": 274 }, "chunk_id": "train_shard_00002_274_0", "global_id": 13099 }, { "text": "Escherichia coli is a highly diverse group of pathogens ranging from commensal of the intestinal tract, through to intestinal pathogen, and extraintestinal pathogen. Here, we present data on the population diversity of E. coli, using Bayesian analysis to identify 13 distinct clusters within the population from multilocus sequence typing data, which map onto a whole-genome-derived phylogeny based on 62 genome sequences. Bayesian analysis of recombination within the core genome identified reduction in detectable core genome recombination as one moves from the commensals, through the intestinal pathogens down to the multidrug-resistant extraintestinal pathogenic clone E. coli ST131. Our data show that the emergence of a multidrug-resistant, extraintestinal pathogenic lineage of E. coli is marked by substantial reduction in detectable core genome recombination, resulting in a lineage which is phylogenetically distinct and sexually isolated in terms of core genome recombination.\n\nThe Evolutionary Path to Extraintestinal Pathogenic, Drug-Resistant Escherichia coli Is Marked by Drastic Reduction in Detectable Recombination within the Core Genome", "token_count": 290, "char_count": 1156, "word_count": 159, "semantic_coherence": 1, "information_density": 0.5472, "quality_score": 0.7736, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:35.251982", "source": { "split": "train_shard_00002", "doc_id": 275 }, "chunk_id": "train_shard_00002_275_0", "global_id": 13100 }, { "text": "

Background

Gut microbiota play a key role in host health, with certain Bifidobacterium strains critical for immune development. The healthy gut of breastfed infants is dominated by these pioneer microbes, especially the strains that feed on human milk oligosaccharides.

Objective

This is a scoping review of gut microbiome research from Zimbabwe. It focuses on distribution and dynamic changes of bifidobacteria, and milk components that promote growth of microbes in infants, together with the distribution of associated gut microbes in adults.

Design

Online databases were searched for publications from 2000 to 2023.

Results and analysis

Fourteen publications on microbiota of infants and adults were included in this scoping review. Most were cross-sectional, while three were clinical trials/cohort protocols. Publications focused on pediatrics (78.5%), pregnant women (14.3%), and men (7.2%). Zimbabwe has a high burden of HIV; hence 35.7% of study populations were delineated by HIV status. The laboratory methods used included shotgun metagenomics (62%) or 16S rRNA gene amplicon sequencing. Almost 85% of the studies focused on total microbiome profiles and rarely reported the distribution of different Bifidobacterium species and variants. None of the papers studied human breast milk composition. There were reports of reduced abundance of beneficial genera in pregnant women, children, and adolescents living with HIV. Additionally, gut microbiota was reported to be poorly predictive of child growth and vaccine response, though this was not conclusive.

Conclusion

There are few studies that characterize the gut microbiome by Zimbabwe-based researchers. However, studies on strain level diversity of Bifidobacterium and other key microbes, and their role in health during and beyond infancy, lag behind in Zimbabwe and other low- and middle-income countries", "token_count": 496, "char_count": 1929, "word_count": 262, "semantic_coherence": 1, "information_density": 0.6298, "quality_score": 0.8149, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:35.903523", "source": { "split": "train_shard_00002", "doc_id": 276 }, "chunk_id": "train_shard_00002_276_0", "global_id": 13101 }, { "text": "Such cohorts are needed to inform future mechanistic studies and downstream translational work such as next-generation probiotics and prebiotics.\n\nA Scoping Review of Gut Microbiome and <i>Bifidobacterium</i> Research in Zimbabwe: Implications for Future Studies.", "token_count": 79, "char_count": 275, "word_count": 34, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:36.279506", "source": { "split": "train_shard_00002", "doc_id": 276 }, "chunk_id": "train_shard_00002_276_1", "global_id": 13102 }, { "text": "Abstract

Background

Escherichia coli sequence type 131 (ST131), associated with CTX-M-15-type extended-spectrum β-lactamases (ESBLs), predominates globally among multidrug-resistant (MDR) E. coli. Among MDR E. coli ST131 isolates from North Carolina and other US regions, we explored genetic associations of the H30Rx and H30R1 subclones with IncF-type plasmid variants.

Methods

Sequence data from 144 clinical E. coli isolates, including 39 MDR ST131 isolates from our 7 NC community hospitals and previous 104 ST131 isolates from other US regions, were analyzed and compared. Specific genes were sought using a bioinformatic pipeline at the Center for Genomic Epidemiology and BLAST. Evolutionary analyses were performed using MEGA7. Plasmid incompatibility groups and its STs were identified using PlasmidFinder and pMLST. Comparisons of the completed sequences of 2 ST131 reference plasmids with 144 ST131 draft genome assemblies were performed using CGView Comparison Tool, and circular comparison maps were generated. Among 31 blaCTX-M-containing contigs, blaCTX-M gene insertion sites were examined.

Results

In the core genome phylogeny, the H30R1 and H30Rx clades were placed within a larger H30R clade (Figure 1). pMLST revealed association of IncF[F2:A1:B-] plasmids (mostly blaCTX-M-15-positive) with H30Rx, and IncF[F1:A2:B20] plasmids (all blaCTX-M-15-negative) with H30R1. The ST131-associated IncF[F2:A1:B-] plasmids from NC generally resembled those from other US regions (Figure 2)", "token_count": 495, "char_count": 1525, "word_count": 205, "semantic_coherence": 1, "information_density": 0.6634, "quality_score": 0.8317, "entities": { "genes": [ "ST131", "MEGA7" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:36.926488", "source": { "split": "train_shard_00002", "doc_id": 277 }, "chunk_id": "train_shard_00002_277_0", "global_id": 13103 }, { "text": "However, in contrast to the others, some of the NC plasmids lacked regions previously described as gisland
1 h and/or the gColla-region, h in addition to gisland 2 h (Figure 3). Among the 31 NC ST131 isolates producing CTX-M (26 H30Rx and 5 H30R1 isolates), blaCTX-M-15 was inserted at the same chromosomal site in 3 H30Rx isolates, at different chromosomal sites in 3 H30Rx isolates, and on IncF plasmids in 1 H30Rx and 1 H30R1 isolates, suggesting that the blaCTX-M-containing gene cassette has moved around among and/or within these strains.

Conclusion

Our genomic and plasmid analysis of community hospital-source ST131 isolates demonstrated fixation and ongoing evolution of specific plasmids within the separate but closely related H30Rx and H30R1 sublineages.

Disclosures

J. R. Johnson, Crucell/Janssen: Consultant, Consulting fee Merck: Grant Investigator, Grant recipient Tetraphase: Grant Investigator, Research grant Actavis/Allergan: Grant Investigator, Grant recipient\n\nComparative Phylogenomic Analysis of Escherichia coli ST131 Isolates and IncF-type Plasmids from North Carolina Community Hospitals and Other Regions of the United States", "token_count": 360, "char_count": 1171, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8152, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:37.498694", "source": { "split": "train_shard_00002", "doc_id": 277 }, "chunk_id": "train_shard_00002_277_1", "global_id": 13104 }, { "text": "

Background

In recent years, the idea of a highly immunogenic protein-based vaccine to combat Streptococcus pneumoniae and its severe invasive infectious diseases has gained considerable interest. However, the target proteins to be included in a vaccine formulation have to accomplish several genetic and immunological characteristics, (such as conservation, distribution, immunogenicity and protective effect), in order to ensure its suitability and effectiveness. This study aimed to get comprehensive insights into the genomic organization, population distribution and genetic conservation of all pneumococcal surface-exposed proteins, genetic regulators and other virulence factors, whose important function and role in pathogenesis has been demonstrated or hypothesized.

Results

After retrieving the complete set of DNA and protein sequences reported in the databases GenBank, KEGG, VFDB, P2CS and Uniprot for pneumococcal strains whose genomes have been fully sequenced and annotated, a comprehensive bioinformatic analysis and systematic comparison has been performed for each virulence factor, stand-alone regulator and two-component regulatory system (TCS) encoded in the pan-genome of S. pneumoniae. A total of 25 S. pneumoniae strains, representing different pneumococcal phylogenetic lineages and serotypes, were considered. A set of 92 different genes and proteins were identified, classified and studied to construct a pan-genomic variability map (variome) for S. pneumoniae. Both, pneumococcal virulence factors and regulatory genes, were well-distributed in the pneumococcal genome and exhibited a conserved feature of genome organization, where replication and transcription are co-oriented. The analysis of the population distribution for each gene and protein showed that 49 of them are part of the core genome in pneumococci, while 43 belong to the accessory-genome. Estimating the genetic variability revealed that pneumolysin, enolase and Usp45 (SP_2216 in S. p", "token_count": 479, "char_count": 1997, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6217, "quality_score": 0.8109, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:38.189281", "source": { "split": "train_shard_00002", "doc_id": 278 }, "chunk_id": "train_shard_00002_278_0", "global_id": 13105 }, { "text": "TIGR4) are the pneumococcal virulence factors with the highest conservation, while TCS08, TCS05, and TCS02 represent the most conserved pneumococcal genetic regulators.

Conclusions

The results identified well-distributed and highly conserved pneumococcal virulence factors as well as regulators, representing promising candidates for a new generation of serotype-independent protein-based vaccine(s) to combat pneumococcal infections.\n\nThe variome of pneumococcal virulence factors and regulators.", "token_count": 136, "char_count": 504, "word_count": 58, "semantic_coherence": 1, "information_density": 0.7241, "quality_score": 0.8621, "entities": { "genes": [ "TCS08", "TCS02", "TIGR4", "TCS05" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:38.631918", "source": { "split": "train_shard_00002", "doc_id": 278 }, "chunk_id": "train_shard_00002_278_1", "global_id": 13106 }, { "text": "Autophagy is a highly regulated bulk degradation process that plays a key role in the maintenance of cellular homeostasis. During autophagy, a double membrane-bound compartment termed the autophagosome is formed through de novo nucleation and assembly of membrane sources to engulf unwanted cytoplasmic components and targets them to the lysosome or vacuole for degradation. Central to this process are the autophagy-related (ATG) proteins, which play a critical role in plant fitness, immunity, and environmental stress response. Over the past few years, cryo-electron microscopy (cryo-EM) and single-particle analysis has matured into a powerful and versatile technique for the structural determination of protein complexes at high resolution and has contributed greatly to our current understanding of the molecular mechanisms underlying autophagosome biogenesis. Here we describe the plant-specific ATG proteins and summarize recent structural and mechanistic studies on the protein machinery involved in autophagy initiation with an emphasis on those by single-particle analysis.\n\nStructural Biology and Electron Microscopy of the Autophagy Molecular Machinery.", "token_count": 263, "char_count": 1166, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7188, "quality_score": 0.8594, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:39.189806", "source": { "split": "train_shard_00002", "doc_id": 279 }, "chunk_id": "train_shard_00002_279_0", "global_id": 13107 }, { "text": "In Kluyveromyces marxianus grown on a glucose-containing synthetic medium four different sugar transporters have been identified. In cells, harvested during the exponential phase, only the constitutive glucose/fructose carrier, probed with 6-deoxy-D-glucose or sorbose, appeared to be active. In cells from the stationary phase three proton symporters can be active, recognizing 6-deoxyglucose (a glucose/galactose carrier), sorbose (a fructose carrier) and galactosides (lactose carrier), respectively. These symporters appeared to be sensitive to catabolite inactivation. This process is induced by incubating cells in the presence of glucose, fructose or mannose. Catabolite inactivation was not influenced by the inhibitor of protein synthesis, anisomycin. Derepression of the proton/sorbose and the proton/galactoside symporters proceeded readily when cells were incubated in a medium without glucose. Activation of the proton/galactose symporter needed, in addition, the presence of specific molecules (inducers) in the medium. The activation of each of these active transport systems was inhibited by anisomycin, showing the involvement of protein synthesis.\n\nRegulation of sugar transport systems of Kluyveromyces marxianus: the role of carbohydrates and their catabolism.", "token_count": 336, "char_count": 1280, "word_count": 169, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8314, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:39.796364", "source": { "split": "train_shard_00002", "doc_id": 280 }, "chunk_id": "train_shard_00002_280_0", "global_id": 13108 }, { "text": "Abstract

Background

A large outbreak with different clones of vancomycin-resistant enterococci (VRE) affected the Bern University Hospital group for several months. The aim of this study was to describe the extent of the outbreak, using whole-genome sequencing (WGS).

Methods

Triggered by two cases of VRE bloodstream infections on our hemato-oncology ward, an outbreak investigation was started. Microbiological diagnosis of VRE was obtained by culture and PCR. Epidemiological links were assessed by meticulous chart review and supplemented with WGS analyses. Multiple infection control measures were implemented to avoid further transmissions.

Results

Between December 2017 and April 2018, 2,877 screening samples were obtained from 1,200 patients. Three out of six hospitals within the Bern University Hospital group were affected. Eighty-three patients (6.9%) were colonized with VR Enterococcus faecium. Of those, 76 (91.6%) had a strain carrying vanB, with 70 (84%) isolates virtually identical (separated by up to two alleles) by cgMLST and identified as MLST type ST796 (figure). The remaining seven patients (8.4%) were colonized with vanA carrying strains from five different STs. Five patients (7%) developed an invasive infection with VRE ST796. Temporo-spatial links were found in most patients carrying the outbreak strain. In order to control the outbreak, extensive infection control measures were implemented. By April 2018 the outbreak was contained with these specific measures.

Conclusion

This VRE outbreak was characterized by a rapid intra- and inter-institutional spread of the emergent clone ST796. This clone was recently described in Australia and New Zealand but never before in Europe.1,2 A multi-faceted infection control led to the containment of the outbreak. References 1. Mahony AA, et al. Vancomycin-resistant Enterococcus faecium sequence type 796—rapid international dissemination of a new epidemic clone. Antimicrob Resist Infect Control. 2018:7:44. 2", "token_count": 529, "char_count": 2025, "word_count": 284, "semantic_coherence": 1, "information_density": 0.6444, "quality_score": 0.8222, "entities": { "genes": [ "ST796" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:02:40.459221", "source": { "split": "train_shard_00002", "doc_id": 281 }, "chunk_id": "train_shard_00002_281_0", "global_id": 13109 }, { "text": "Leong KWC, et al. Emergence of vancomycin-resistant Enterococcus faecium at an Australian Hospital: a whole genome sequencing analysis. Sci Rep. 2018:8(1):6274. 3. de Been M, et al. Core genome multilocus sequence typing scheme for high- resolution typing of Enterococcus faecium. J Clin Microbiol. 2015:53(12):3788–97.

Disclosures

All authors: No reported disclosures.\n\n1255. First Outbreak Due to Vancomycin-Resistant Enterococcus Epidemic Clone ST796 in Europe", "token_count": 170, "char_count": 472, "word_count": 62, "semantic_coherence": 1, "information_density": 0.871, "quality_score": 0.9355, "entities": { "genes": [ "ST796" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:40.900140", "source": { "split": "train_shard_00002", "doc_id": 281 }, "chunk_id": "train_shard_00002_281_1", "global_id": 13110 }, { "text": "The commercialization of a probiotic microorganism requires genetic and phenotypic consistency across production lots. However, the large-scale industrial production of probiotic microbial biomasses over years poses a risk of genetic drift, potentially affecting the probiotic's ability to confer health benefits. This study assessed the stability of Lacticaseibacillus paracasei DG (DSM 34154), a commercial probiotic. Seven isolates from different commercial lots over 10 years, one 8-year-old laboratory subculture, one isolate from human feces, and the DG strain deposited at DSMZ were analyzed. Shotgun and PacBio sequencing were combined to obtain the complete genome of the 10 isolates. Comparative analysis showed that the seven commercial isolates had identical genomes, differing from the DSMZ isolate by one synonymous transition and one non-synonymous transversion. The laboratory subculture strain had two additional mutations. Phenotypic analyses, including antibiotic resistance, carbohydrate fermentation profile, survival to simulated gastrointestinal transit, immunomodulatory capacity, and radical scavenging ability, found no significant differences among isolates. Overall, this study demonstrates the substantial equivalence of L. paracasei DG over 10 years of industrial production, indicating that the current industrial practices help prevent genome alterations that could compromise probiotic performance. Similar studies should be part of continuous monitoring and quality control measures for the probiotic products on the market.IMPORTANCEThe genetic and functional stability of probiotic strains during years of industrial production is essential but has not been clearly demonstrated for many strains. This study shows that careful industrial practices can maintain the genetic integrity and functionality of probiotics. Using advanced genome sequencing and detailed laboratory tests, we confirmed that the probiotic Lacticaseibacillus paracasei DG (DSM 34154) has remained stable over a decade of production, consistently delivering its health-promoting properties. These findings support the quality and reliability of probiotic products, fostering consumer trust and highlighting the importance of continuous monitoring in probiotic manufacturing to sustain quality assurance.", "token_count": 517, "char_count": 2331, "word_count": 301, "semantic_coherence": 1, "information_density": 0.6213, "quality_score": 0.8106, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:02:41.533634", "source": { "split": "train_shard_00002", "doc_id": 282 }, "chunk_id": "train_shard_00002_282_0", "global_id": 13111 }, { "text": "Genetic and phenotypic stability of <i>Lacticaseibacillus paracasei</i> DG (DSM 34154) over 10 years of industrial production.", "token_count": 55, "char_count": 138, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:41.902149", "source": { "split": "train_shard_00002", "doc_id": 282 }, "chunk_id": "train_shard_00002_282_1", "global_id": 13112 }, { "text": "The growth of several yeast species in milk containing added sodium chloride (0-15%, w/v) at 25 degrees C and 10 degrees C was examined in conjunction with yeast metabolism of milk constituents. Depending on conditions, all yeasts grew to maximum populations of 10(7)-10(8) cfu/ml. Kluyveromyces marxianus gave strong utilisation of lactose and weak metabolism of citrate, protein and fat with the production of ethanol, glycerol, lactic acid and propionic acid. As measured by the production of free amino acids and free fatty acids, Candida lipolytica and Candida catenulata gave strong proteolytic and lipolytic reactions, the specificities of which appeared to be influenced by temperature and the presence of NaCl. These species also metabolised organic acids. Although giving strong growth responses, Debaryomyces hansenii and Saccharomyces cerevisiae did not metabolise lactose and gave only very weak lipolytic and proteolytic reactions. Citrate was metabolised by D. hansenii but not by S. cerevisiae. Both species produced small amounts of ethanol, glycerol and lactic acid.\n\nGrowth of yeasts in milk and associated changes to milk composition.", "token_count": 310, "char_count": 1154, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6257, "quality_score": 0.8129, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:42.485136", "source": { "split": "train_shard_00002", "doc_id": 283 }, "chunk_id": "train_shard_00002_283_0", "global_id": 13113 }, { "text": "Campylobacter is the major bacterial agent of human gastroenteritis worldwide and represents a crucial global public health burden. Species differentiation of C. jejuni and C. coli and phylogenetic analysis is challenged by inter-species horizontal gene transfer. Routine real-time PCR on more than 4000 C. jejuni and C. coli field strains identified isolates with ambiguous PCR results for species differentiation, in particular, from the isolation source eggs. K-mer analysis of whole genome sequencing data indicated the presence of C. coli hybrid strains with huge amounts of C. jejuni introgression. Recombination events were distributed over the whole chromosome. MLST typing was impaired, since C. jejuni sequences were also found in six of the seven housekeeping genes. cgMLST suggested that the strains were phylogenetically unrelated. Intriguingly, the strains shared a stress response set of C. jejuni variant genes, with proposed roles in oxidative, osmotic and general stress defence, chromosome maintenance and repair, membrane transport, cell wall and capsular biosynthesis and chemotaxis. The results have practical impact on routine typing and on the understanding of the functional adaption to harsh environments, enabling successful spreading and persistence of Campylobacter.\n\nWhole genome sequencing reveals extended natural transformation in Campylobacter impacting diagnostics and the pathogens adaptive potential.", "token_count": 328, "char_count": 1437, "word_count": 200, "semantic_coherence": 1, "information_density": 0.665, "quality_score": 0.8325, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:43.052451", "source": { "split": "train_shard_00002", "doc_id": 284 }, "chunk_id": "train_shard_00002_284_0", "global_id": 13114 }, { "text": "Long-read metagenomic sequencing is a powerful approach for cataloging the microbial diversity present in complex microbiomes, including the human gut microbiome. We performed a deep-sequencing experiment using PacBio HiFi reads to obtain metagenome-assembled genomes (MAGs) from a pooled human gut microbiome. We performed long-read metagenome assembly using two methods (hifiasm-meta, metMDBG), used improved bioinformatic and proximity ligation binning strategies to cluster contigs and identify MAGs, and developed a novel framework to compare and consolidate MAGs (pb-MAG-mirror). We found proximity ligation binning yielded more MAGs than bioinformatic binning, but our novel comparison framework resulted in higher MAG yields than either binning strategy individually. In total, from 255 Gbp of total HiFi data we produced 595 total MAGs (including 175 high-quality MAGs) using hifiasm-meta, and 547 total MAGs (including 277 high-quality MAGs) with metaMDBG. Hifiasm-meta assembled almost twice as many strain-level MAGs as metaMDBG (246 vs. 156), but both assembly methods produced up to five strains for a species. Approximately 85% of the MAGs were assigned to known species, but we recovered >35 high-quality MAGs that represent uncultured diversity. Based on strict similarity scores, we found 125 MAGs were unequivocally shared across the assembly methods at the strain level, representing ~22% of the total MAGs recovered per method. Finally, we detected more total viral sequences in the metaMDBG assembly versus the hifiasm-meta assembly (~6,700 vs. ~4,500). Overall, we find the use of HiFi sequencing, improved metagenome assembly methods, and complementary binning strategies is highly effective for rapidly cataloging microbial genomes in complex microbiomes.\n\nHighly accurate metagenome-assembled genomes from human gut microbiota using long-read assembly, binning, and consolidation methods", "token_count": 497, "char_count": 1913, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:43.699687", "source": { "split": "train_shard_00002", "doc_id": 285 }, "chunk_id": "train_shard_00002_285_0", "global_id": 13115 }, { "text": "Staphylococcus argenteus (S. argenteus) is a newly identified Staphylococcus species that has been misidentified as Staphylococcus aureus (S. aureus) and is clinically relevant. We identified 25 S. argenteus genomes in our collection of whole genome sequenced S. aureus. These genomes were compared to publicly available genomes and a phylogeny revealed seven clusters corresponding to seven clonal complexes. The genome of S. argenteus was found to be different from the genome of S. aureus and a core genome analysis showed that ~33% of the total gene pool was shared between the two species, at 90% homology level. An assessment of mobile elements shows flow of SCCmec cassettes, plasmids, phages, and pathogenicity islands, between S. argenteus and S. aureus. This dataset emphasizes that S. argenteus and S. aureus are two separate species that share genetic material.\n\nWhole Genome Sequencing of Danish Staphylococcus argenteus Reveals a Genetically Diverse Collection with Clear Separation from Staphylococcus aureus.", "token_count": 370, "char_count": 1136, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6184, "quality_score": 0.8092, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:44.278501", "source": { "split": "train_shard_00002", "doc_id": 286 }, "chunk_id": "train_shard_00002_286_0", "global_id": 13116 }, { "text": "

Background

Vancomycin-resistant Enterococcus faecium (VRE) is a leading cause of hospital-acquired infections. New, presumably better-adapted strains of VRE appear unpredictably; it is uncertain how they spread despite improved infection control. We aimed to investigate the relatedness of a novel sequence type (ST) of vanB E. faecium - ST796 - very near its time of origin from hospitals in three Australian states and New Zealand.

Methods

Following near-simultaneous outbreaks of ST796 in multiple institutions, we gathered then tested colonization and bloodstream infection isolates' antimicrobial resistance (AMR) phenotypes, and phylogenomic relationships using whole genome sequencing (WGS). Patient meta-data was explored to trace the spread of ST796.

Results

A novel clone of vanB E. faecium (ST796) was first detected at one Australian hospital in late 2011, then in two New Zealand hospitals linked by inter-hospital transfers from separate Melbourne hospitals. ST796 also appeared in hospitals in South Australia and New South Wales and was responsible for at least one major colonization outbreak in a Neonatal Intensive Care Unit without identifiable links between centers. No exceptional AMR was detected in the isolates. While WGS analysis showed very limited diversity at the core genome, consistent with recent emergence of the clone, clustering by institution was observed.

Conclusions

Evolution of new E. faecium clones, followed by recognized or unrecognized movement of colonized individuals then rapid intra-institutional cross-transmission best explain the multi-center, multistate and international outbreak we observed.\n\nVancomycin-resistant Enterococcus faecium sequence type 796 - rapid international dissemination of a new epidemic clone.", "token_count": 472, "char_count": 1831, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6778, "quality_score": 0.8389, "entities": { "genes": [ "ST796" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:44.922537", "source": { "split": "train_shard_00002", "doc_id": 287 }, "chunk_id": "train_shard_00002_287_0", "global_id": 13117 }, { "text": "The Staphylococcus intermedius group consists of three closely related coagulase-positive bacterial species including S. intermedius, Staphylococcus pseudintermedius, and Staphylococcus delphini. S. pseudintermedius is a major skin pathogen of dogs, which occasionally causes severe zoonotic infections of humans. S. delphini has been isolated from an array of different animals including horses, mink, and pigeons, whereas S. intermedius has been isolated only from pigeons to date. Here we provide a detailed analysis of the S. pseudintermedius whole genome sequence in comparison to high quality draft S. intermedius and S. delphini genomes, and to other sequenced staphylococcal species. The core genome of the SIG was highly conserved with average nucleotide identity (ANI) between the three species of 93.61%, which is very close to the threshold of species delineation (95% ANI), highlighting the close-relatedness of the SIG species. However, considerable variation was identified in the content of mobile genetic elements, cell wall-associated proteins, and iron and sugar transporters, reflecting the distinct ecological niches inhabited. Of note, S. pseudintermedius ED99 contained a clustered regularly interspaced short palindromic repeat locus of the Nmeni subtype and S. intermedius contained both Nmeni and Mtube subtypes. In contrast to S. intermedius and S. delphini and most other staphylococci examined to date, S. pseudintermedius contained at least nine predicted reverse transcriptase Group II introns. Furthermore, S. pseudintermedius ED99 encoded several transposons which were largely responsible for its multi-resistant phenotype. Overall, the study highlights extensive differences in accessory genome content between closely related staphylococcal species inhabiting distinct host niches, providing new avenues for research into pathogenesis and bacterial host-adaptation.\n\nComparative genomics of the Staphylococcus intermedius group of animal pathogens.", "token_count": 484, "char_count": 1984, "word_count": 268, "semantic_coherence": 1, "information_density": 0.6157, "quality_score": 0.8078, "entities": { "genes": [ "ED99" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:45.574369", "source": { "split": "train_shard_00002", "doc_id": 288 }, "chunk_id": "train_shard_00002_288_0", "global_id": 13118 }, { "text": "Glucose transport in the yeast Kluyveromyces marxianus proceeds by two functionally and presumably structurally distinct transporters depending on the carbon source of the culture medium. In lactose-grown cells, glucose was taken up through a high-affinity H+-sugar symporter (Km = 0.09 mM), whereas a low-affinity transporter (Km = 3.5 mM) was utilized in glucose-grown cells. The two transporters exhibited different substrate specificities. Galactose was demonstrated to be a selective substrate of the H+-glucose symporter (Km = 0.14 mM) and did not significantly enter glucose-grown cells. Fructose was a preferential substrate of the low-affinity carrier (Km = 3.5 mM), but it entered lactose-grown cells through a high-affinity H+-fructose symporter distinct from the H+-glucose one. Other putative substrates of the two glucose transporters were identified by competition experiments. 2-Deoxyglucose recognized both carriers with a similar affinity, while the non-phosphorylatable analogues 6-deoxyglucose, 3-O-methylglucose and D-fucose exhibited a 10-30 fold preference for the high-affinity transporter.\n\nCharacterization of low- and high-affinity glucose transports in the yeast Kluyveromyces marxianus.", "token_count": 356, "char_count": 1215, "word_count": 162, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:46.156485", "source": { "split": "train_shard_00002", "doc_id": 289 }, "chunk_id": "train_shard_00002_289_0", "global_id": 13119 }, { "text": "

Background

Bacterial whole-genome sequencing (WGS) has the potential to identify reservoirs of multidrug-resistant organisms and transmission of these pathogens across healthcare networks. We used WGS to define transmission of vancomycin-resistant enterococci (VRE) within a long-term care facility (LTCF), and between this and an acute hospital in the United Kingdom (UK).

Methods

A longitudinal prospective observational study of faecal VRE carriage was conducted in a LTCF in Cambridge, UK. Stool samples were collected at recruitment, and then repeatedly until the end of the study period, discharge or death. Selective culture media were used to isolate VRE, which were subsequently sequenced and analysed. We also analysed the genomes of 45 Enterococcus faecium bloodstream isolates collected at Cambridge University Hospitals NHS Foundation Trust (CUH).

Results

Forty-five residents were recruited during a 6-month period in 2014, and 693 stools were collected at a frequency of at least 1 week apart. Fifty-one stool samples from 3/45 participants (7 %) were positive for vancomycin-resistant E. faecium. Two residents carried multiple VRE lineages, and one carried a single VRE lineage. Genome analyses based on single nucleotide polymorphisms (SNPs) in the core genome indicated that VRE carried by each of the three residents were unrelated. Participants had extensive contact with the local healthcare network. We found that VRE genomes from LTCF residents and hospital-associated bloodstream infection were interspersed throughout the phylogenetic tree, with several instances of closely related VRE strains from the two settings.

Conclusions

A proportion of LTCF residents are long-term carriers of VRE. Evidence for genetic relatedness between these and VRE associated with bloodstream infection in a nearby acute NHS Trust indicate a shared bacterial population.\n\nWhole-genome sequencing reveals transmission of vancomycin-resistant Enterococcus faecium in a healthcare network.", "token_count": 509, "char_count": 2023, "word_count": 275, "semantic_coherence": 1, "information_density": 0.6145, "quality_score": 0.8073, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:46.810089", "source": { "split": "train_shard_00002", "doc_id": 290 }, "chunk_id": "train_shard_00002_290_0", "global_id": 13120 }, { "text": "We investigated the occurrence and diversity of yeasts and filamentous fungi in bryndza an artisanal Slovak soft spreadable cheese prepared from raw sheep milk or from a mixture of sheep and cow milk. Samples collected during four months of the summer production period from two locations (northern and southern parts of central Slovakia) contained 10(5)-10(7) (cfu) yeasts and about 10(2) (cfu) of mold per gram of wet weight. Further characterization by conventional taxonomy and sequence comparison of D1/D2 region from 26S rRNA gene revealed Mucor circinelloides v. Tieghem as the predominant filamentous fungus. A novel Geotrichum sp. together with Kluyveromyces (K. lactis/K. marxianus) was identified as the most abundant yeast species. Occasionally other yeasts, such as Candida inconspicua, Candida silvae, Pichia fermentans and Trichosporon domesticum were found. Conventional taxonomy readily identified isolates to the genus level, but DNA sequence comparison was capable of discriminating them at the species level.\n\nThe diversity of eukaryotic microbiota in the traditional Slovak sheep cheese--bryndza.", "token_count": 294, "char_count": 1117, "word_count": 160, "semantic_coherence": 1, "information_density": 0.7375, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:47.366122", "source": { "split": "train_shard_00002", "doc_id": 291 }, "chunk_id": "train_shard_00002_291_0", "global_id": 13121 }, { "text": "Here we report the genome sequence of Acinetobacter venetianus VE-C3, a strain isolated from the Venice Lagoon and known to be able to degrade n-alkanes. Post sequencing analyses revealed that this strain is relatively distantly related to the other Acinetobacter strains completely sequenced so far as shown by phylogenetic analysis and pangenome analysis (1285 genes shared with all the other Acinetobacter genomes sequenced so far). A. venetianus VE-C3 possesses a wide range of determinants whose molecular functions are probably related to the survival in a strongly impacted ecological niche. Among them, genes probably involved in the metabolism of long-chain n-alkanes and in the resistance to toxic metals (e.g. arsenic, cadmium, cobalt and zinc) were found. Genes belonging to these processes were found both on the chromosome and on plasmids. Also, our analysis documented one of the possible genetic bases underlying the strategy adopted by A. venetianus VE-C3 for the adhesion to oil fuel droplets, which could account for the differences existing in this process with other A. venetianus strains. Finally, the presence of a number of DNA mobilization-related genes (i.e. transposases, integrases, resolvases) strongly suggests an important role played by horizontal gene transfer in shaping the genome of A. venetianus VE-C3 and in its adaptation to its special ecological niche.\n\nThe genome sequence of the hydrocarbon-degrading Acinetobacter venetianus VE-C3.", "token_count": 376, "char_count": 1475, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6301, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:47.946918", "source": { "split": "train_shard_00002", "doc_id": 292 }, "chunk_id": "train_shard_00002_292_0", "global_id": 13122 }, { "text": "The optimum production of K6 type yeast killer protein by Kluyveromyces fragilis NCYC 587 occurred at pH 4.0-4.4 and at 22-24 degrees C in a killer-zone assay test. The K6 killer protein was concentrated by acetone precipitation of the culture supernatant and purified by native polyacrylamide rod gel electrophoresis. The protein migrated as a single band on discontinuous gradient SDS polyacrylamide gel electrophoresis and had a molecular weight of 42,313. The isoelectric point of the K6 type protein was determined at pH 5.97 by high voltage vertical polyacrylamide gel electrofocusing. Western blot analysis revealed that the K6 killer toxin was a nonglycosylated protein.\n\nIsolation and characterization of the K6 type yeast killer protein.", "token_count": 209, "char_count": 747, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6195, "quality_score": 0.8097, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:48.410064", "source": { "split": "train_shard_00002", "doc_id": 293 }, "chunk_id": "train_shard_00002_293_0", "global_id": 13123 }, { "text": "Abstract

Background

Recent work indicates that comprehensive genomic sequencing can be a highly effective tool in defining the transmission of microbial pathogens. We have studied the utility of the routine use of genomic sequencing for infection control surveillance in an academic medical center.

Methods

The genomes of inpatient and emergency department isolates of Staphylococcus aureus, Pseudomonas aeruginosa, Klebsiella pneumoniae, and Enterococcus faecium were sequenced. Within each species, single-nucleotide polymorphisms (SNP) were identified in the core genome for all isolates using alignment-based methods. The number of SNP differences between isolate pairs was determined and used, in combination with the patient’s electronic medical records to identify potential transmission events.

Results

Between September 2016 and March 2017, 388 S. aureus, 66 P. aeruginosa, 48 K. pneumoniae, and 29 E. faecium isolates were sequenced from 373 patients. There was variation in the distribution of SNP differences between intrapatient isolates for the four pathogens; with the least variability for E. faecium and greatest for P. aeruginosa. The majority of the bacterial isolates from separate patients appeared to be genetically unique exhibiting marked SNP differences from other isolates. There were 19 sets of isolates where the SNP variation between interpatient isolates was either comparable to that of intrapatient variation (12) and suggestive of recent transmission events, or with SNP variation somewhat greater than the intrapatient SNP variation (7) suggesting relative relatedness. Only one of the highly related sets had been previously identified by standard infection control surveillance. Likely transmissions appeared to have occurred both in the inpatient and outpatient settings, and the transmission routes were not always apparent.

Conclusion

The routine use of genomic sequencing analysis identified previously unrecognized likely transmission events within the institution’s patient population that are of relevance to infection control surveillance. This capacity should significantly enhance our understanding of the epidemiology of hospital acquired infections, and assist in developing and implementing new prevention strategies.

Disclosures

R", "token_count": 531, "char_count": 2325, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5924, "quality_score": 0.7962, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:02:49.067300", "source": { "split": "train_shard_00002", "doc_id": 294 }, "chunk_id": "train_shard_00002_294_0", "global_id": 13124 }, { "text": "T. Ellison III, Philips Healthcare: Consultant and Grant Investigator, Consulting fee and Research grant; A. Hoss, Philips: Employee, Salary; J. Mathew, Philips Healthcare: Investigator, Research grant; J. Halperin, Philips Healthcare: Employee and Shareholder, Salary; B. Gross, Philips: Employee and Shareholder, Salary; D. V. Ward, Philips Healthcare: Consultant, Investigator and Research Contractor, Consulting fee, Research support and Salary\n\nUtility of Routine Genomic Sequencing for Infection Control Surveillance", "token_count": 139, "char_count": 522, "word_count": 66, "semantic_coherence": 1, "information_density": 0.6515, "quality_score": 0.8258, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:49.490323", "source": { "split": "train_shard_00002", "doc_id": 294 }, "chunk_id": "train_shard_00002_294_1", "global_id": 13125 }, { "text": "A method was developed that enabled the study of non-esterified galacturonic acid sequences (so-called blocks) in pectin. Endopolygalacturonase of Kluyveromyces fragilis was used to extensively degrade pectin, and the composition of the galacturonic acid molecules produced was determined with high-performance anion-exchange chromatography at pH 5. With this technique, the amount of non-esterified mono-, di-, and trigalacturonic acid released was determined. In addition, the relative amounts of methyl-esterified oligomers--up to 10 galacturonic acid residues could be observed. By comparing the percentages of non-esterified mono-, di-, and trigalacturonic acids released, pectins with large enzyme-degradable blocks could be distinguished from pectins with small enzyme-degradable blocks. High percentages of mono- and digalacturonic acid were found for pectins containing small non-esterified blocks. The total area of all peaks corresponding to methyl-esterified oligomers was found to be indicative for the distribution of these blocks. The higher the ratio of the methyl- to non-esterified peak areas, the more closely associated blocks are present. Randomly esterified pectins, with degrees of methyl esterification of 50 and higher, contained smaller, more clustered blocks than commercial extracted pectins of comparable degrees of esterification. The approach developed enables a very detailed study of the methyl-ester distribution of pectin to be carried out and is a very important addition in the study of the functional behavior of this complex polymer.\n\nCharacterization of non-esterified galacturonic acid sequences in pectin with endopolygalacturonase.", "token_count": 409, "char_count": 1674, "word_count": 227, "semantic_coherence": 1, "information_density": 0.5595, "quality_score": 0.7797, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:50.123445", "source": { "split": "train_shard_00002", "doc_id": 295 }, "chunk_id": "train_shard_00002_295_0", "global_id": 13126 }, { "text": "Yeast populations greater than 10(6) cfu/g were found in approximately 54% and 36%, respectively in surface samples of retail Camembert (85 samples) and Blue-veined (45 samples) cheeses. The most predominant species isolated were Debaryomyces hansenii, Candida catenulata, C. lipolytica, C. kefyr, C. intermedia, Saccharomyces cerevisiae, Cryptococcus albidus and Kluyveromyces marxianus. The salt concentration of the surface samples of the cheeses varied between 2.5-5.5% (w/w) (Camembert) and 7.5-8.3 (Blue-veined), depending upon brand, and influenced the yeast ecology, especially the presence of S. cerevisiae. Yeasts grew to populations of 10(6)-10(8) cfu/g when cheeses were stored at either 25 degrees C or 10 degrees C. These populations decreased on continued storage at 25 degrees C, but such decreases were not so evident on storage at 10 degrees C. The properties of yeasts influencing their occurrence and growth in cheese were: fermentation/assimilation of lactose; production of extracellular lipolytic and proteolytic enzymes, utilisation of lactic and citric acids; and growth at 10 degrees C.\n\nThe occurrence and growth of yeasts in Camembert and blue-veined cheeses.", "token_count": 357, "char_count": 1187, "word_count": 170, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:50.743639", "source": { "split": "train_shard_00002", "doc_id": 296 }, "chunk_id": "train_shard_00002_296_0", "global_id": 13127 }, { "text": "We identified putative long terminal repeat- (LTR) retrotransposon sequences among the 50,000 random sequence tags (RSTs) obtained by the Génolevures project from genomic libraries of 13 Hemiascomycetes species. In most cases additional sequencing enabled us to assemble the whole sequences of these retrotransposons. These approaches identified 17 distinct families, 10 of which are defined by full-length elements. We also identified five families of solo LTRs that were not associated with retrotransposons. Ty1-like retrotransposons were found in four of five species that are phylogenetically related to Saccharomyces cerevisiae (S. uvarum, S. exiguus, S. servazzii, and S. kluyveri but not Zygosaccharomyces rouxii), and in two of three Kluyveromyces species (K. lactis and K. marxianus but not K. thermotolerans). Only multiply crippled elements could be identified in the K. lactis and S. servazzii strains analyzed, and only solo LTRs could be identified in S. uvarum. Ty4-like elements were only detected in S. uvarum, indicating that these elements appeared recently before speciation of the Saccharomyces sensu stricto species. Ty5-like elements were detected in S. exiguus, Pichia angusta, and Debaryomyces hansenii. A retrotransposon homologous with Tca2 from Candida albicans, an element absent from S. cerevisiae, was detected in the closely related species D. hansenii. A complete Ty3/gypsy element was present in S. exiguus, whereas only partial, often degenerate, sequences resembling this element were found in S. servazzii, Z. rouxii, S. kluyveri, C. tropicalis, and Yarrowica lipolytica. P. farinosa (syn. P. sorbitophila) is currently the only yeast species in which no LTR retrotransposons or remnants have been found", "token_count": 482, "char_count": 1741, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5992, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:51.419963", "source": { "split": "train_shard_00002", "doc_id": 297 }, "chunk_id": "train_shard_00002_297_0", "global_id": 13128 }, { "text": "Thorough analysis of protein sequences, structural characteristics of the elements, and phylogenetic relationships deduced from these data allowed us to propose a classification for the Ty1/copia elements of hemiascomycetous yeasts and a model of LTR-retrotransposon evolution in yeasts.\n\nGenomic evolution of the long terminal repeat retrotransposons in hemiascomycetous yeasts.", "token_count": 89, "char_count": 379, "word_count": 49, "semantic_coherence": 1, "information_density": 0.7551, "quality_score": 0.8776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:51.843590", "source": { "split": "train_shard_00002", "doc_id": 297 }, "chunk_id": "train_shard_00002_297_1", "global_id": 13129 }, { "text": "The majority of bacterial genomes have high coding efficiencies, but there are some genomes of intracellular bacteria that have low gene density. The genome of the endosymbiont Sodalis glossinidius contains almost 50% pseudogenes containing mutations that putatively silence them at the genomic level. We have applied multiple ‘omic strategies, combining: Illumina and Pacific Biosciences Single-Molecule Real Time DNA-sequencing and annotation; stranded RNA-sequencing; and proteome analysis to better understand the transcriptional and translational landscape of Sodalis pseudogenes, and potential mechanisms for their control. Between 53% and 74% of the Sodalis transcriptome remains active in cell-free culture. Mean sense transcription from Coding Domain Sequences (CDS) is four-times greater than that from pseudogenes. Comparative genomic analysis of six Illumina-sequenced Sodalis isolates from different host Glossina species shows pseudogenes make up ~40% of the 2,729 genes in the core genome, suggesting that they are stable and/or Sodalis is a recent introduction across the Glossina genus as a facultative symbiont. These data further shed light on the importance of transcriptional and translational control in deciphering host-microbe interactions. The combination of genomics, transcriptomics and proteomics give a multidimensional perspective for studying prokaryotic genomes with a view to elucidating evolutionary adaptation to novel environmental niches.

Importance

Bacterial genes are generally 1Kb in length, organized efficiently (i.e. with few gaps between genes or operons), and few open reading frames (ORFs) lack any predicted function. Intracellular bacteria have been removed from extracellular selection pressures acting on pathways of declining importance to fitness and thus, these bacteria tend to delete redundant genes in favour of smaller functional repertoires", "token_count": 455, "char_count": 1907, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6938, "quality_score": 0.8469, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:52.494754", "source": { "split": "train_shard_00002", "doc_id": 298 }, "chunk_id": "train_shard_00002_298_0", "global_id": 13130 }, { "text": "In the genomes of endosymbionts with a recent evolutionary relationship with their host, however, this process of genome reduction is not complete; Genes and pathways may be at an intermediate stage, undergoing mutation linked to reduced selection and small population numbers being vertically transmitted from mother to offspring in their hosts, resulting in an increase in abundance of pseudogenes and reduced coding capacities. A greater knowledge of the genomic architecture of persistent pseudogenes, with respect to their DNA structure, mRNA transcription and even putative translation to protein products, will lead to a better understanding of the evolutionary trajectory of endosymbiont genomes, many of which have important roles in arthropod ecology.\n\nLarge scale and significant expression from pseudogenes in Sodalis glossinidius - a facultative bacterial endosymbiont", "token_count": 197, "char_count": 888, "word_count": 125, "semantic_coherence": 1, "information_density": 0.72, "quality_score": 0.86, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:52.945330", "source": { "split": "train_shard_00002", "doc_id": 298 }, "chunk_id": "train_shard_00002_298_1", "global_id": 13131 }, { "text": "A genomic library from the yeast Pichia anomala has been constructed and employed to clone the gene encoding the sucrose-hydrolysing enzyme invertase by complementation of a sucrose non-fermenting mutant of Saccharomyces cerevisiae. The cloned gene, INV1, was sequenced and found to encode a polypeptide of 550 amino acids which contained a 22 amino-acid signal sequence and ten potential glycosylation sites. The amino-acid sequence shows significant identity with other yeast invertases and also with Kluyveromyces marxianus inulinase, a yeast beta-fructofuranosidase which has a different substrate specificity. The nucleotide sequences of the 5' and 3' non-coding regions were found to contain several consensus motifs probably involved in the initiation and termination of gene transcription.\n\nCloning and sequence analysis of the invertase gene INV 1 from the yeast Pichia anomala.", "token_count": 236, "char_count": 887, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6693, "quality_score": 0.8346, "entities": { "genes": [ "INV1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:53.419010", "source": { "split": "train_shard_00002", "doc_id": 299 }, "chunk_id": "train_shard_00002_299_0", "global_id": 13132 }, { "text": "We describe the development and application of a Pooled Suppression Subtractive Hybridization (PSSH) method to describe differences between the genomic content of a pool of clinical Staphylococcus aureus isolates and a sequenced reference strain. In comparative bacterial genomics, Suppression Subtractive Hybridization (SSH) is normally utilized to compare genomic features or expression profiles of one strain versus another, which limits its ability to analyze communities of isolates. However, a PSSH approach theoretically enables the user to characterize the entirety of gene content unique to a related group of isolates in a single reaction. These unique fragments may then be linked to individual isolates through standard PCR. This method was applied to examine the genomic diversity found in pools of S.aureus isolates associated with complicated bacteremia infections leading to endocarditis and osteomyelitis. Across four pools of 10 isolates each, four hundred and twenty seven fragments not found in or significantly divergent from the S. aureus NCTC 8325 reference genome were detected. These fragments could be linked to individual strains within its pool by PCR. This is the first use of PSSH to examine the S. aureus pangenome. We propose that PSSH is a powerful tool for researchers interested in rapidly comparing the genomic content of multiple unstudied isolates.\n\nDevelopment of pooled suppression subtractive hybridization to analyze the pangenome of Staphylococcus aureus.", "token_count": 341, "char_count": 1498, "word_count": 219, "semantic_coherence": 1, "information_density": 0.5845, "quality_score": 0.7922, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:53.995065", "source": { "split": "train_shard_00002", "doc_id": 300 }, "chunk_id": "train_shard_00002_300_0", "global_id": 13133 }, { "text": "Ethanol production from 200 g lactose/l by Kluyveromyces fragilis immobilized in calcium alginate was 63 g/l whereas with co-immobilized K. fragilis and Zymomonas mobilis 72 g ethanol/l was attained. With free cells of K. fragilis, only 52 g ethanol/l was obtained. The beads were relatively stable without significant reduction in activity for about six batches of fermentation.\n\nHigh ethanol productivity from lactose by immobilized cells of Kluyveromyces fragilis and Zymomonas mobilis.", "token_count": 144, "char_count": 489, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7183, "quality_score": 0.8592, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:54.784430", "source": { "split": "train_shard_00002", "doc_id": 301 }, "chunk_id": "train_shard_00002_301_0", "global_id": 13134 }, { "text": "Listeria monocytogenes (Lm) is a major human foodborne pathogen. Numerous Lm outbreaks have been reported worldwide and associated with a high case fatality rate, reinforcing the need for strongly coordinated surveillance and outbreak control. We developed a universally applicable genome-wide strain genotyping approach and investigated the population diversity of Lm using 1,696 isolates from diverse sources and geographical locations. We define, with unprecedented precision, the population structure of Lm, demonstrate the occurrence of international circulation of strains and reveal the extent of heterogeneity in virulence and stress resistance genomic features among clinical and food isolates. Using historical isolates, we show that the evolutionary rate of Lm from lineage I and lineage II is low (∼2.5 × 10-7 substitutions per site per year, as inferred from the core genome) and that major sublineages (corresponding to so-called 'epidemic clones') are estimated to be at least 50-150 years old. This work demonstrates the urgent need to monitor Lm strains at the global level and provides the unified approach needed for global harmonization of Lm genome-based typing and population biology.\n\nWhole genome-based population biology and epidemiological surveillance of Listeria monocytogenes.", "token_count": 320, "char_count": 1316, "word_count": 186, "semantic_coherence": 1, "information_density": 0.6882, "quality_score": 0.8441, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:55.350277", "source": { "split": "train_shard_00002", "doc_id": 302 }, "chunk_id": "train_shard_00002_302_0", "global_id": 13135 }, { "text": "Flavobacterium psychrophilum, the etiological agent of rainbow trout fry syndrome and bacterial cold-water disease in salmonid fish, is currently one of the main bacterial pathogens hampering the productivity of salmonid farming worldwide. In this study, the genomic diversity of the F. psychrophilum species is analyzed using a set of 41 genomes, including 30 newly sequenced isolates. These were selected on the basis of available MLST data with the two-fold objective of maximizing the coverage of the species diversity and of allowing a focus on the main clonal complex (CC-ST10) infecting farmed rainbow trout (Oncorhynchus mykiss) worldwide. The results reveal a bacterial species harboring a limited genomic diversity both in terms of nucleotide diversity, with ~0.3% nucleotide divergence inside CDSs in pairwise genome comparisons, and in terms of gene repertoire, with the core genome accounting for ~80% of the genes in each genome. The pan-genome seems nevertheless \"open\" according to the scaling exponent of a power-law fitted on the rate of new gene discovery when genomes are added one-by-one. Recombination is a key component of the evolutionary process of the species as seen in the high level of apparent homoplasy in the core genome. Using a Hidden Markov Model to delineate recombination tracts in pairs of closely related genomes, the average recombination tract length was estimated to ~4.0 Kbp and the typical ratio of the contributions of recombination and mutations to nucleotide-level differentiation (r/m) was estimated to ~13. Within CC-ST10, evolutionary distances computed on non-recombined regions and comparisons between 22 isolates sampled up to 27 years apart suggest a most recent common ancestor in the second half of the nineteenth century in North America with subsequent diversification and transmission of this clonal complex coinciding with the worldwide expansion of rainbow trout farming. With the goal to promote the development of tools for the genetic manipulation of F. psychrophilum, a particular attention was also paid to plasmids", "token_count": 517, "char_count": 2109, "word_count": 315, "semantic_coherence": 1, "information_density": 0.5905, "quality_score": 0.7952, "entities": { "genes": [ "ST10" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:02:56.012619", "source": { "split": "train_shard_00002", "doc_id": 303 }, "chunk_id": "train_shard_00002_303_0", "global_id": 13136 }, { "text": "Their extraction and sequencing to completion revealed plasmid diversity that remained hidden to classical plasmid profiling due to size similarities.\n\nGenomic Diversity and Evolution of the Fish Pathogen Flavobacterium psychrophilum.", "token_count": 60, "char_count": 241, "word_count": 30, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:56.374139", "source": { "split": "train_shard_00002", "doc_id": 303 }, "chunk_id": "train_shard_00002_303_1", "global_id": 13137 }, { "text": "

Aim

A comprehensive safety assessment of potential probiotic strains was essential for their application in the food industry. This article systematically evaluated the probiotic characteristics, whole-genome sequence analysis and safety of Lacticaseibacillus paracasei LC86 and Lacticaseibacillus casei LC89.

Methods

Firstly, the two strains of lactic acid bacteria selected were identified. Secondly, whole-genome sequencing was performed on LC86 and LC89, and their antibiotic resistance, pathogenicity, and virulence genes were analyzed. We tested various properties of the two strains, included tolerance, cell adhesion, hemolytic activity, catalase activity, gelatin hydrolysis, arginine hydrolysis ability, bile salt hydrolysis capacity, mucin degradation, bioamine, D-/L-lactic acid production and antibiotic susceptibility, to confirm the safety of LC86 and LC89 both in vitro and in vivo. Additionally, we studied the acute toxicity of LC86 and LC89 in mice through a 14-day oral gavage experiment.

Results

The two strains selected were identified as Lacticaseibacillus paracasei and Lacticaseibacillus casei. The genomes of both LC86 and LC89 were devoid of virulence, antibiotic resistance and pathogenicity genes. LC86 and LC89 exhibited good tolerance to temperature, artificial gastric fluid and artificial intestinal fluid; they were non-hemolytic, their catalase activity, gelatin hydrolysis, arginine hydrolysis and bile salt hydrolysis were all negative. They exhibited the capability to break down proteins and demonstrated sensitivity to a range of antibiotics", "token_count": 469, "char_count": 1645, "word_count": 207, "semantic_coherence": 1, "information_density": 0.5942, "quality_score": 0.7971, "entities": { "genes": [ "LC86", "LC89" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:57.023958", "source": { "split": "train_shard_00002", "doc_id": 304 }, "chunk_id": "train_shard_00002_304_0", "global_id": 13138 }, { "text": "The oral LD50 for both LC86 and LC89 in mice was >2 × 1010 CFU/kg.

Conclusion

The experimental results above demonstrated the probiotic characteristics and safety of LC86 and LC89, indicating their potential as candidates for probiotics for human and animal applications.\n\nGenome sequence and evaluation of safety and probiotic potential of Lacticaseibacillus paracasei LC86 and Lacticaseibacillus casei LC89.", "token_count": 150, "char_count": 452, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7018, "quality_score": 0.8509, "entities": { "genes": [ "LC86", "LC89" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:57.458923", "source": { "split": "train_shard_00002", "doc_id": 304 }, "chunk_id": "train_shard_00002_304_1", "global_id": 13139 }, { "text": "

Background

The Gram-positive bacterium Enterococcus faecium is a commensal of the human gastrointestinal tract and a frequent cause of bloodstream infections in hospitalized patients. The mechanisms by which E. faecium can survive and grow in blood during an infection have not yet been characterized. Here, we identify genes that contribute to growth of E. faecium in human serum through transcriptome profiling (RNA-seq) and a high-throughput transposon mutant library sequencing approach (Tn-seq).

Results

We first sequenced the genome of E. faecium E745, a vancomycin-resistant clinical isolate, using a combination of short- and long read sequencing, revealing a 2,765,010 nt chromosome and 6 plasmids, with sizes ranging between 9.3 kbp and 223.7 kbp. We then compared the transcriptome of E. faecium E745 during exponential growth in rich medium and in human serum by RNA-seq. This analysis revealed that 27.8% of genes on the E. faecium E745 genome were differentially expressed in these two conditions. A gene cluster with a role in purine biosynthesis was among the most upregulated genes in E. faecium E745 upon growth in serum. The E. faecium E745 transposon mutant library was then used to identify genes that were specifically required for growth of E. faecium in serum. Genes involved in de novo nucleotide biosynthesis (including pyrK_2, pyrF, purD, purH) and a gene encoding a phosphotransferase system subunit (manY_2) were thus identified to be contributing to E. faecium growth in human serum. Transposon mutants in pyrK_2, pyrF, purD, purH and manY_2 were isolated from the library and their impaired growth in human serum was confirmed. In addition, the pyrK_2 and manY_2 mutants were tested for their virulence in an intravenous zebrafish infection model and exhibited significantly attenuated virulence compared to E", "token_count": 529, "char_count": 1855, "word_count": 279, "semantic_coherence": 1, "information_density": 0.552, "quality_score": 0.776, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:02:58.090702", "source": { "split": "train_shard_00002", "doc_id": 305 }, "chunk_id": "train_shard_00002_305_0", "global_id": 13140 }, { "text": "faecium E745.

Conclusions

Genes involved in carbohydrate metabolism and nucleotide biosynthesis of E. faecium are essential for growth in human serum and contribute to the pathogenesis of this organism. These genes may serve as targets for the development of novel anti-infectives for the treatment of E. faecium bloodstream infections.\n\nRNA-seq and Tn-seq reveal fitness determinants of vancomycin-resistant Enterococcus faecium during growth in human serum.", "token_count": 132, "char_count": 466, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7097, "quality_score": 0.8548, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:58.511375", "source": { "split": "train_shard_00002", "doc_id": 305 }, "chunk_id": "train_shard_00002_305_1", "global_id": 13141 }, { "text": "The management of infectious diseases has become more critical due to the development of novel pathogenic strains with enhanced resistance. Prevotella melaninogenica, a gram-negative bacterium, was found to be involved in various infections of the respiratory tract, aerodigestive tract, and gastrointestinal tract. The need to explore novel drug and vaccine targets against this pathogen was triggered by the emergence of antimicrobial resistance against reported antibiotics to combat P. melaninogenica infections. The study involves core genes acquired from 14 complete P. melaninogenica strain genome sequences, where promiscuous drug and vaccine candidates were explored by state-of-the-art subtractive proteomics and reverse vaccinology approaches. A stringent bioinformatics analysis enlisted 18 targets as novel, essential, and non-homologous to humans and having druggability potential. Moreover, the extracellular and outer membrane proteins were subjected to antigenicity, allergenicity, and physicochemical analysis for the identification of the candidate proteins to design multi-epitope vaccines. Two candidate proteins (ADK95685.1 and ADK97014.1) were selected as the best target for the designing of a vaccine construct. Lead B- and T-cell overlapped epitopes were joined to generate potential chimeric vaccine constructs in combination with adjuvants and linkers. Finally, a prioritized vaccine construct was found to have stable interactions with the human immune cell receptors as confirmed by molecular docking and MD simulation studies. The vaccine construct was found to have cloning and expression ability in the bacterial cloning system. Immune simulation ensured the elicitation of significant immune responses against the designed vaccine. In conclusion, our study reported novel drug and vaccine targets and designed a multi-epitope vaccine against the P. melaninogenica infection. Further experimental validation will help open new avenues in the treatment of this multi-drug-resistant pathogen.\n\nProteome level analysis of drug-resistant Prevotella melaninogenica for the identification of novel therapeutic candidates.", "token_count": 511, "char_count": 2183, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7997, "entities": { "genes": [ "ADK95685", "ADK97014" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:59.139470", "source": { "split": "train_shard_00002", "doc_id": 306 }, "chunk_id": "train_shard_00002_306_0", "global_id": 13142 }, { "text": "

Background

Isolates of methicillin-resistant Staphylococcus aureus (MRSA) belonging to a single lineage are often indistinguishable by means of current typing techniques. Whole-genome sequencing may provide improved resolution to define transmission pathways and characterize outbreaks.

Methods

We investigated a putative MRSA outbreak in a neonatal intensive care unit. By using rapid high-throughput sequencing technology with a clinically relevant turnaround time, we retrospectively sequenced the DNA from seven isolates associated with the outbreak and another seven MRSA isolates associated with carriage of MRSA or bacteremia in the same hospital.

Results

We constructed a phylogenetic tree by comparing single-nucleotide polymorphisms (SNPs) in the core genome to a reference genome (an epidemic MRSA clone, EMRSA-15 [sequence type 22]). This revealed a distinct cluster of outbreak isolates and clear separation between these and the nonoutbreak isolates. A previously missed transmission event was detected between two patients with bacteremia who were not part of the outbreak. We created an artificial \"resistome\" of antibiotic-resistance genes and demonstrated concordance between it and the results of phenotypic susceptibility testing; we also created a \"toxome\" consisting of toxin genes. One outbreak isolate had a hypermutator phenotype with a higher number of SNPs than the other outbreak isolates, highlighting the difficulty of imposing a simple threshold for the number of SNPs between isolates to decide whether they are part of a recent transmission chain.

Conclusions

Whole-genome sequencing can provide clinically relevant data within a time frame that can influence patient care. The need for automated data interpretation and the provision of clinically meaningful reports represent hurdles to clinical implementation. (Funded by the U.K. Clinical Research Collaboration Translational Infection Research Initiative and others.).\n\nRapid whole-genome sequencing for investigation of a neonatal MRSA outbreak.", "token_count": 480, "char_count": 2063, "word_count": 274, "semantic_coherence": 1, "information_density": 0.6241, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:02:59.787957", "source": { "split": "train_shard_00002", "doc_id": 307 }, "chunk_id": "train_shard_00002_307_0", "global_id": 13143 }, { "text": "

Objectives

Carbapenemase-producing Klebsiella pneumoniae (CP-Kp) is a major cause of infections in transplanted patients and has been associated with high mortality rates in this group. There is a lack of information about the Brazilian structure population of CP-Kp isolated from transplanted patients. By whole-genome sequencing (WGS), we analyzed phylogeny, resistome, virulome of CP-Kp isolates, and the structure of plasmids encoding bla KPC- 2 and bla NDM- 1 genes.

Methods

One K. pneumoniae isolated from each selected transplanted patient colonized or infected by CP-Kp over a 16-month period in a hospital complex in Porto Alegre (Brazil) was submitted for WGS. The total number of strains sequenced was 80. The hospital complex in Porto Alegre comprised seven different hospitals. High-resolution SNP typing, core genome multilocus sequence typing (cgMLST), resistance and virulence genes inference, and plasmid reconstruction were performed in 80 CP-Kp.

Results

The mortality rate of CP-Kp colonized or infected transplanted inpatients was 21.3% (17/80). Four CP-Kp epidemic clones were described: ST11/KPC-2, ST16/KPC-2, and ST15/NDM-1, all responsible for interhospital outbreaks; and ST437/KPC-2 affecting a single hospital. The average number of acquired resistance and virulence genes was 9 (range = 2-14) and 27 (range = 6-36), respectively. Two plasmids carrying the bla KPC - 2 were constructed and belonged to IncN and IncM types", "token_count": 511, "char_count": 1583, "word_count": 206, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.835, "entities": { "genes": [ "ST15", "ST16", "ST11", "ST437" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:00.446071", "source": { "split": "train_shard_00002", "doc_id": 308 }, "chunk_id": "train_shard_00002_308_0", "global_id": 13144 }, { "text": "Additionally, an IncFIB plasmid carrying the bla NDM- 1 was described.

Conclusion

We detected intrahospital and interhospital spread of mobile structures and international K. pneumoniae clones as ST11, ST16, and ST15 among transplanted patients, which carry a significant range of acquired resistance and virulence genes and keep spreading across the world.\n\nCarbapenemase-Producing Klebsiella pneumoniae From Transplanted Patients in Brazil: Phylogeny, Resistome, Virulome and Mobile Genetic Elements Harboring bla KPC- 2 or bla NDM- 1.", "token_count": 224, "char_count": 652, "word_count": 72, "semantic_coherence": 1, "information_density": 0.8333, "quality_score": 0.9167, "entities": { "genes": [ "ST15", "ST16", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:00.907865", "source": { "split": "train_shard_00002", "doc_id": 308 }, "chunk_id": "train_shard_00002_308_1", "global_id": 13145 }, { "text": "Klebsiella pneumoniae is a Gram-negative pathogen responsible for community-acquired and nosocomial infections. The strains of this species belong to the opportunistic group, which is comprised of the multidrug-resistant strains, or the hypervirulent group, depending on their accessory genome, which determines bacterial pathogenicity and the host immune response. The aim of this survey is to present an overview of the murine models mimicking K. pneumoniae infectious processes (i.e., gastrointestinal colonization, urinary, pulmonary, and systemic infections), and the bacterial functions deployed to colonize and disseminate into the host. These in vivo approaches are pivotal to develop new therapeutics to limit K. pneumoniae infections via a modulation of the immune responses and/or microbiota.\n\nFrom Klebsiella pneumoniae Colonization to Dissemination: An Overview of Studies Implementing Murine Models.", "token_count": 252, "char_count": 941, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:01.403360", "source": { "split": "train_shard_00002", "doc_id": 309 }, "chunk_id": "train_shard_00002_309_0", "global_id": 13146 }, { "text": "The effect of temperature and pH on the kinetics of ethanol production by free and calcium alginate immobilized cells of Kluyveromyces marxianus grown on Jerusalem artichoke extract was investigated. With the free cells, the ethanol and biomass yields were relatively constant over the temperature range 25-35 degrees C, but dropped sharply beyond 35 degrees C. Other kinetic parameters, specific growth rate, specific ethanol production rate, and specific total sugar uptake rate were maximum at 35 degrees C. However, with the immobilized cells, ethanol yield remained almost constant in the temperature range 25-45 degrees C, and the specific ethanol production rate and specific total sugar uptake rate attained their maximum values at 40 degrees C. For the pH range between 3 and 7, the free-cell optimum for growth and product formation was found to be ca. pH 5. At this pH, the specific growth rate was 0.35 h(-1) and specific ethanol production rate was 2.83 g/g/h. At values higher or lower than pH 5, a sharp decrease in specific ethanol production rate as well as specific growth rate was observed. In comparison, the immobilized cells showed a broad optimum pH profile. The best ethanol production rates were observed between pH 4 and 6.\n\nThe effect of temperature and pH on ethanol production by free and immobilized cells of Kluyveromyces marxianus grown on Jerusalem artichoke extract.", "token_count": 355, "char_count": 1400, "word_count": 224, "semantic_coherence": 1, "information_density": 0.4643, "quality_score": 0.7321, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:01.986492", "source": { "split": "train_shard_00002", "doc_id": 310 }, "chunk_id": "train_shard_00002_310_0", "global_id": 13147 }, { "text": "In this paper, the influence of aeration rate on the alcoholic batch fermentation of whey by Kluyveromyces fragilis NRRL Y-2415 was investigated. Assays in 1.5-L fermentor using concentrated whey permeate containing 100 g/L of lactose were carried out at different oxygen supply rate (KLaC*) from 0 to 82 mmol/Lh. Optimum response was obtained at 14 mmol/Lh: ethanol production rate reached was 3.4 g/Lh yielding 0.46 g of product per gram of initial lactose. An increase of KLaC* from 0 to 14 mmol/Lh improved the ethanol production: maximum specific ethanol production rate (qpm) increased 3.3 times from 0.3 to 1.0 g/gh. For higher aeration levels, ethanol production diminished and biomass formation was stimulated. The declination of qpm and the increase of microns at higher aeration level lead to conclude the importance of a controlled oxygen supply in order to obtain the required balance between yeast biosynthetic needs and ethanol production.\n\nEffect of aeration rate on the alcoholic fermentation of whey by Kluyveromyces fragilis.", "token_count": 299, "char_count": 1044, "word_count": 162, "semantic_coherence": 1, "information_density": 0.642, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:02.571373", "source": { "split": "train_shard_00002", "doc_id": 311 }, "chunk_id": "train_shard_00002_311_0", "global_id": 13148 }, { "text": "Plant pathogenic phytoplasmas can infect hundreds of plant species and lead to enormous economic loss. To understand the interactions between phytoplasmas and their hosts, genome sequencing plays an important role. To date, ten phytoplasma genomes from five phylogenetic groups have been released. A comparative genomics analysis showed 170 common conserved genes existing in these ten genomes. Genes involved in translation, ribosomal structure and biogenesis (75 genes) are the largest proportion. Interestingly, the predicted secreted proteins were not found in our core set, suggesting that these genes were diverse. In addition, a highly stringent strategy was taken to mine the group‐specific genes among the five groups. Although the largest part was the hypothetical proteins, some putative secreted proteins (potential effectors) were identified. TENGU was selected to be one of the 16SrI group‐specific genes. This may partly account for the diverse pathogenicity in different 16Sr groups. In addition, our results revealed that Amp and Imp had great potentials of being group specific. Above all, based on the conserved genes, our results provide new insights for the phytoplasma genome assembly, identification and functional genomics.\n\nIdentification of a Conserved Core Genome with Group‐Specific Genes from Comparative Genomics of Ten Different Candidatus Phytoplasma Strains", "token_count": 319, "char_count": 1390, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6633, "quality_score": 0.8317, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:03.147833", "source": { "split": "train_shard_00002", "doc_id": 312 }, "chunk_id": "train_shard_00002_312_0", "global_id": 13149 }, { "text": "

Background

The prevalence of clinical multidrug-resistant (MDR) Pseudomonas aeruginosa has been increasing rapidly worldwide over the years and responsible for a wide range of acute and chronic infections with high mortalities. Although hundreds of complete genomes of clinical P. aeruginosa isolates have been sequenced, only a few complete genomes of mucoid strains are available, limiting a comprehensive understanding of this important group of opportunistic pathogens. Herein, the complete genome of a clinically isolated mucoid strain P. aeruginosa JNQH-PA57 was sequenced and assembled using Illumina and Oxford nanopore sequencing technologies. Genomic features, phylogenetic relationships, and comparative genomics of this pathogen were comprehensively analyzed using various bioinformatics tools. A series of phenotypic and molecular-genetic tests were conducted to investigate the mechanisms of carbapenem resistance in this strain.

Results

Several genomic features of MDR P. aeruginosa JNQH-PA57 were identified based on the whole-genome sequencing. We found that the accessory genome of JNQH-PA57 including several prophages, genomic islands, as well as a PAPI-1 family integrative and conjugative element (ICE), mainly contributed to the larger genome of this strain (6,747,067 bp) compared to other popular P. aeruginosa strains (with an average genome size of 6,445,223 bp) listed in Pseudomonas Genome Database. Colony morphology analysis and biofilm crystal staining assay respectively demonstrated an enhanced alginate production and a thicker biofilm formation capability of JNQH-PA57. A deleted mutation at nt 424 presented in mucA gene, resulted in the upregulated expression of a sigma-factor AlgU and a GDP mannose dehydrogenase AlgD, which might explain the mucoid phenotype of this strain", "token_count": 476, "char_count": 1829, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6627, "quality_score": 0.8313, "entities": { "genes": [ "PA57" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:03.825875", "source": { "split": "train_shard_00002", "doc_id": 313 }, "chunk_id": "train_shard_00002_313_0", "global_id": 13150 }, { "text": "As for the carbapenem resistance mechanisms, our results revealed that the interplay between impaired OprD porin, chromosomal β-lactamase OXA-488 expression, MexAB-OprM and MexXY-OprM efflux pumps overexpression, synergistically with the alginates-overproducing protective biofilm, conferred the high carbapenem resistance to P. aeruginosa JNQH-PA57.

Conclusion

Based on the genome analysis, we could demonstrate that the upregulated expression of algU and algD, which due to the truncation variant of MucA, might account for the mucoid phenotype of JNQH-PA57. Moreover, the resistance to carbapenem in P. aeruginosa JNQH-PA57 is multifactorial. The dataset presented in this study provided an essential genetic basis for the comprehensive cognition of the physiology, pathogenicity, and carbapenem resistance mechanisms of this clinical mucoid strain.\n\nComparative genome analysis of multidrug-resistant Pseudomonas aeruginosa JNQH-PA57, a clinically isolated mucoid strain with comprehensive carbapenem resistance mechanisms.", "token_count": 288, "char_count": 1034, "word_count": 129, "semantic_coherence": 1, "information_density": 0.6822, "quality_score": 0.8411, "entities": { "genes": [ "PA57" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:04.418110", "source": { "split": "train_shard_00002", "doc_id": 313 }, "chunk_id": "train_shard_00002_313_1", "global_id": 13151 }, { "text": "Phenotype switching from a wild type (WT) to a slow-growing subpopulation, referred to as small colony variants (SCVs), supports an infectious lifestyle of Staphylococcus epidermidis, the leading cause of medical device-related infections. Specific mechanisms underlying formation of SCVs and involved in the shaping of their pathogenic potential are of particular interest for stable strains as they have been only rarely cultured from clinical specimens. As the SCV phenotype stability implies the existence of genetic changes, the whole genome sequence of a stable, hemin-dependent S. epidermidis SCV strain (named 49SCV) involved in a late prosthetic joint infection was analyzed. The strain was isolated in a monoculture without a corresponding WT clone, therefore, its genome was compared against five reference S. epidermidis strains (ATCC12228, ATCC14990, NBRC113846, O47, and RP62A), both at the level of the genome structure and coding sequences. According to the Multilocus Sequence Typing analysis, the 49SCV strain represented the sequence type 2 (ST2) regarded as the most prominent infection-causing lineage with a worldwide dissemination. Genomic features unique to 49SCV included the absence of the Staphylococcal Cassette Chromosome (SCC), ~12 kb deletion with the loss of genes involved in the arginine deiminase pathway, and frameshift-generating mutations within the poly(A) and poly(T) homopolymeric tracts. Indels were identified in loci associated with adherence, metabolism, stress response, virulence, and cell wall synthesis. Of note, deletion in the poly(A) of the hemA gene has been considered a possible trigger factor for the phenotype transition and hemin auxotrophy in the strain. To our knowledge, the study represents the first genomic characterization of a clinical, stable and hemin-dependent S. epidermidis SCV strain", "token_count": 507, "char_count": 1890, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6466, "quality_score": 0.8233, "entities": { "genes": [ "ST2", "ATCC12228", "ATCC14990", "NBRC113846", "RP62A" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:05.072775", "source": { "split": "train_shard_00002", "doc_id": 314 }, "chunk_id": "train_shard_00002_314_0", "global_id": 13152 }, { "text": "We propose that previously unreported indels in the homopolymeric tracts can constitute a background of the SCV phenotype due to a resulting truncation of the corresponding proteins and their possible biological dysfunction. Streamline of genetic content evidenced by the loss of the SCC and a large genomic deletion can represent a possible strategy associated both with the SCV phenotype and its adaptation to chronicity.\n\nThe first genomic characterization of a stable, hemin-dependent small colony variant strain of Staphylococcus epidermidis isolated from a prosthetic-joint infection.", "token_count": 135, "char_count": 597, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:05.499606", "source": { "split": "train_shard_00002", "doc_id": 314 }, "chunk_id": "train_shard_00002_314_1", "global_id": 13153 }, { "text": "UDPglucose 4-epimerase from Kluyveromyces fragilis was completely inactivated by diethylpyrocarbonate following pseudo-first order reaction kinetics. The pH profile of diethylpyrocarbonate inhibition and reversal of inhibition by hydroxylamine suggested specific modification of histidyl residues. Statistical analysis of the residual enzyme activity and the extent of modification indicated modification of 1 essential histidine residue to be responsible for loss in catalytic activity of yeast epimerase. No major structural change in the quarternary structure was observed in the modified enzyme as shown by the identical elution pattern on a calibrated Sephacryl 200 column and association of coenzyme NAD to the apoenzyme. Failure of the substrates to afford any protection against diethylpyrocarbonate inactivation indicated the absence of the essential histidyl residue at the substrate binding region of the active site. Unlike the case of native enzyme, sodium borohydride failed to reduce the pyridine moiety of the coenzyme in the diethylpyrocarbonate-modified enzyme. This indicated the presence of the essential histidyl residue in close proximity to the coenzyme binding region of the active site. The abolition of energy transfer phenomenon between the tryptophan and coenzyme fluorophore on complete inactivation by diethylpyrocarbonate without any loss of protein or coenzyme fluorescence are also added evidences in this direction.\n\nAn essential histidine residue for the activity of UDPglucose 4-epimerase from Kluyveromyces fragilis.", "token_count": 388, "char_count": 1553, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5634, "quality_score": 0.7817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:06.118119", "source": { "split": "train_shard_00002", "doc_id": 315 }, "chunk_id": "train_shard_00002_315_0", "global_id": 13154 }, { "text": "Lactiplantibacillus pentosus 9D3, a prominent gamma-aminobutyric acid (GABA)-producing bacteria isolated from Thai pickled weed was characterized for its safety and probiotic properties via whole-genome analysis and in vitro testing. The whole-genome sequence of L. pentosus 9D3 was determined using a hybrid-sequencing approach, combining PacBio and Illumina technologies. A 3.81-Mbp genome of L. pentosus 9D3 consisting of one 3.65-Mbp chromosome and six plasmids (1.9-71.9 Kbp) was identified with an estimated GC content of 46.09% and 3,456 predicted genes. The strain was confirmed to be Lactiplantibacillus pentosus according to the high average nucleotide identity value of >95% and digital DNA-DNA hybridization scores of >70% to the L. pentosus type strain. Comparative genome analysis with other L. pentosus strains showed that the GABA-producing capability was specific to the strain 9D3. Genes related to GABA biosynthesis and transport were identified on a plasmid, pLPE-70K, indicating the acquired nature of this property. The safety of L. pentosus 9D3 was demonstrated through the lack of genes related to the production of toxins, biogenic amines, and antimicrobial drugs. Although the strain exhibited resistance to ampicillin and chloramphenicol, none of the antimicrobial resistance (AMR) genes were associated with mobile elements, i.e., plasmids and prophages. Therefore, the strain is considered to have low risk of transferring the AMR genes to other, potentially pathogenic bacteria. In addition, L", "token_count": 486, "char_count": 1589, "word_count": 218, "semantic_coherence": 1, "information_density": 0.633, "quality_score": 0.8165, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:06.771896", "source": { "split": "train_shard_00002", "doc_id": 316 }, "chunk_id": "train_shard_00002_316_0", "global_id": 13155 }, { "text": "pentosus 9D3 showed good survivability in the gastrointestinal tract environment and was able to adhere to the intestinal cell in vitro. Therefore, L. pentosus 9D3 is concluded to be safe, with the potential to be used as a probiotic, exerting its health benefit through GABA production in the food system. The GABA-producing capability of the strain in vivo is the subject of further investigation.\n\nWhole-genome sequence analysis for evaluating the safety and probiotic potential of Lactiplantibacillus pentosus 9D3, a gamma-aminobutyric acid (GABA)-producing strain isolated from Thai pickled weed.", "token_count": 189, "char_count": 633, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7386, "quality_score": 0.8693, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:07.211393", "source": { "split": "train_shard_00002", "doc_id": 316 }, "chunk_id": "train_shard_00002_316_1", "global_id": 13156 }, { "text": "The predominant microorganisms in the Sudanese traditional fermented dairy product Rob from cows' milk were isolated and identified by using morphological, physiological and molecular typing techniques. From seven production sites in Khartoum, samples of Rob used as inocula for fermentation were analysed by the determination of the cfu mL(-1) on MRS, M17, potato dextrose agar and plate count agar. Samples of inocula from two production sites were used for Rob fermentation in the laboratory followed by similar microbiological analysis. The results obtained showed that the Rob inocula contained lactococci and lactobacilli in the range of 10(7)-10(8) and yeasts in the range of 10(6)-10(7) cfu mL(-1). During the course of the two laboratory fermentations, the lactococci and lactobacilli increased to 10(8) cfu mL(-1), the yeasts to 10(7) cfu mL(-1) and the aerobic mesophilic counts decreased to 10(5) cfu mL(-1). The pH of the inocula ranged between 3.4 and 3.6 and the pH of Rob produced in the laboratory was 4.2-4.5. Using the internal transcribed spacer-polymerase chain reaction (PCR) technique, 189 representative strains of lactic acid bacteria and 109 representative isolates of yeasts were divided into nine and two groups, respectively, according to the size of the PCR product formed. Representative members of all groups were identified by the API 50 CH and the ID 32 API kits for lactic acid bacteria and yeasts, respectively. Confirmation of identification of lactic acid bacteria species was achieved by sequencing the 16S rRNA gene. The predominant lactic acid bacteria in Rob fermentation were found to be Lactobacillus fermentum, Lactobacillus acidophilus, Lactococcus lactis, and Streptococcus salivarius. The predominant yeasts were found to be Saccharomyces cerevisiae and Candida kefyr.", "token_count": 516, "char_count": 1816, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5257, "quality_score": 0.7629, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:03:07.841244", "source": { "split": "train_shard_00002", "doc_id": 317 }, "chunk_id": "train_shard_00002_317_0", "global_id": 13157 }, { "text": "Characterisation of the dominant microbiota of Sudanese fermented milk Rob", "token_count": 17, "char_count": 74, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:08.196263", "source": { "split": "train_shard_00002", "doc_id": 317 }, "chunk_id": "train_shard_00002_317_1", "global_id": 13158 }, { "text": "Lactobacillus crispatus is a common inhabitant of both healthy poultry gut and human vaginal tract, and the absence of this species has been associated with a higher risk of developing infectious diseases. In this study, we analyzed 105 L. crispatus genomes isolated from a variety of ecological niches, including the human vaginal tract, human gut, chicken gut and turkey gut, to shed light on the genetic and functional features that drive evolution and adaptation of this important species. We performed in silico analyses to identify the pan and core genomes of L. crispatus, and to reveal the genomic differences and similarities associated with their origins of isolation. Our results demonstrated that, although a significant portion of the genomic content is conserved, human and poultry L. crispatus isolates evolved to encompass different genomic features (e.g. carbohydrate usage, CRISPR-Cas immune systems, prophage occurrence) in order to thrive in different environmental niches. We also observed that chicken and turkey L. crispatus isolates can be differentiated based on their genomic information, suggesting significant differences may exist between these two poultry gut niches. These results provide insights into host and niche-specific adaptation patterns in species of human and animal importance.\n\nHost and body site-specific adaptation of Lactobacillus crispatus genomes.", "token_count": 349, "char_count": 1445, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5931, "quality_score": 0.7966, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:08.767179", "source": { "split": "train_shard_00002", "doc_id": 318 }, "chunk_id": "train_shard_00002_318_0", "global_id": 13159 }, { "text": "Several methods are available to probe cellular responses to external stresses at the whole genome level. RNAseq can be used to measure changes in expression of all genes following exposure to stress, but gives no information about the contribution of these genes to an organism's ability to survive the stress. The relative contribution of each non-essential gene in the genome to the fitness of the organism under stress can be obtained using methods that use sequencing to estimate the frequencies of members of a dense transposon library grown under different conditions, for example by transposon-directed insertion sequencing (TraDIS). These two methods thus probe different aspects of the underlying biology of the organism. We were interested to determine the extent to which the data from these two methods converge on related genes and pathways. To do this, we looked at a combination of biologically meaningful stresses. The human gut contains different organic short-chain fatty acids (SCFAs) produced by fermentation of carbon compounds, and Escherichia coli is exposed to these in its passage through the gut. Their effect is likely to depend on both the ambient pH and the level of oxygen present. We, therefore, generated RNAseq and TraDIS data on a uropathogenic E. coli strain grown at either pH 7 or pH 5.5 in the presence or absence of three SCFAs (acetic, propionic and butyric), either aerobically or anaerobically. Our analysis identifies both known and novel pathways as being likely to be important under these conditions. There is no simple correlation between gene expression and fitness, but we found a significant overlap in KEGG pathways that are predicted to be enriched following analysis of the data from the two methods, and the majority of these showed a fitness signature that would be predicted from the gene expression data, assuming expression to be adaptive. Genes which are not in the E. coli core genome were found to be particularly likely to show a positive correlation between level of expression and contribution to fitness.", "token_count": 462, "char_count": 2091, "word_count": 331, "semantic_coherence": 1, "information_density": 0.5468, "quality_score": 0.7734, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:09.405832", "source": { "split": "train_shard_00002", "doc_id": 319 }, "chunk_id": "train_shard_00002_319_0", "global_id": 13160 }, { "text": "Mapping the Transcriptional and Fitness Landscapes of a Pathogenic E. coli Strain: The Effects of Organic Acid Stress under Aerobic and Anaerobic Conditions.", "token_count": 53, "char_count": 164, "word_count": 23, "semantic_coherence": 1, "information_density": 0.8696, "quality_score": 0.9348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:09.764082", "source": { "split": "train_shard_00002", "doc_id": 319 }, "chunk_id": "train_shard_00002_319_1", "global_id": 13161 }, { "text": "The fundamental unit of biological diversity is the species. However, a remarkable extent of intraspecies diversity in bacteria was discovered by genome sequencing, and it reveals the need to develop clear criteria to group strains within a species. Two main types of analyses used to quantify intraspecies variation at the genome level are the average nucleotide identity (ANI), which detects the DNA conservation of the core genome, and the DNA content, which calculates the proportion of DNA shared by two genomes. Both estimates are based on BLAST alignments for the definition of DNA sequences common to the genome pair. Interestingly, however, results using these methods on intraspecies pairs are not well correlated. This prompted us to develop a genomic-distance index taking into account both criteria of diversity, which are based on DNA maximal unique matches (MUM) shared by two genomes. The values, called MUMi, for MUM index, correlate better with the ANI than with the DNA content. Moreover, the MUMi groups strains in a way that is congruent with routinely used multilocus sequence-typing trees, as well as with ANI-based trees. We used the MUMi to determine the relatedness of all available genome pairs at the species and genus levels. Our analysis reveals a certain consistency in the current notion of bacterial species, in that the bulk of intraspecies and intragenus values are clearly separable. It also confirms that some species are much more diverse than most. As the MUMi is fast to calculate, it offers the possibility of measuring genome distances on the whole database of available genomes.\n\nA genomic distance based on MUM indicates discontinuity between most bacterial species and genera.", "token_count": 380, "char_count": 1721, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5735, "quality_score": 0.7868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:10.349048", "source": { "split": "train_shard_00002", "doc_id": 320 }, "chunk_id": "train_shard_00002_320_0", "global_id": 13162 }, { "text": "Paenibacillus polymyxa is a multifaceted bacterium with widespread applications in agriculture, environmental management, medicine, and industry. In agricultural settings, it plays a crucial role in soil enhancement, plant growth promotion, and natural pathogen control, reducing the need for chemical interventions. Additionally, P. polymyxa exhibits promising potential in medical applications by aiding in infection prevention and supporting gastrointestinal health. In the realm of environmental management, this bacterium contributes to pollution remediation through biodegradation processes. Industrially, P. polymyxa is involved in producing enzymes, biofertilizers, bioplastics, and platform chemicals, offering sustainable alternatives that underscore its importance in driving sustainability initiatives. Despite these valuable attributes, widespread utilization of bioresources derived from naturally occurring P. polymyxa has been hampered by limited genetic manipulation capabilities and tools. In this comprehensive analysis, we aimed to provide a thorough understanding of P. polymyxa's characteristics, genetic resources, and metabolic capabilities, while highlighting its potential as a versatile platform for protein expression, metabolic engineering, and synthetic biology. We delved into the diverse sustainable applications of P. polymyxa in these domains, emphasizing its benefits, challenges, and future outlook in advancing sustainable practices. Furthermore, we underscore the critical need for continued research and development of advanced engineering techniques and genetic editing technologies tailored specifically for this bacterium.\n\nAdvancing sustainable practices with <i>Paenibacillus polymyxa</i>: From soil health to medical applications and molecular engineering.", "token_count": 398, "char_count": 1855, "word_count": 220, "semantic_coherence": 1, "information_density": 0.6636, "quality_score": 0.8318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:10.966663", "source": { "split": "train_shard_00002", "doc_id": 321 }, "chunk_id": "train_shard_00002_321_0", "global_id": 13163 }, { "text": "Pseudomonas aeruginosa is a common nosocomial pathogen and a major cause of morbidity and mortality in hospitalized patients. Multiple reports highlight that P. aeruginosa gastrointestinal colonization may precede systemic infections by this pathogen. Gaining a deeper insight into the dynamics of P. aeruginosa gastrointestinal carriage is an essential step in managing gastrointestinal colonization and could contribute to preventing bacterial transmission and progression to systemic infection. Here, we present a clinically relevant mouse model relying on parenteral vancomycin pretreatment and a single orogastric gavage of a controlled dose of P. aeruginosa. Robust carriage was observed with multiple clinical isolates, and carriage persisted for up to 60 days. Histological and microbiological examination of mice indicated that this model indeed represented carriage and not infection. We then used a barcoded P. aeruginosa library along with the sequence tag-based analysis of microbial populations (STAMPR) analytic pipeline to quantify bacterial population dynamics and bottlenecks during the establishment of the gastrointestinal carriage. Analysis indicated that most of the P. aeruginosa population was rapidly eliminated in the stomach, but the few bacteria that moved to the small intestine and the cecum expanded rapidly. Hence, the stomach constitutes a significant barrier against gastrointestinal carriage of P. aeruginosa, which may have clinical implications for hospitalized patients.

Importance

While Pseudomonas aeruginosa is rarely part of the normal human microbiome, carriage of the bacterium is quite frequent in hospitalized patients and residents of long-term care facilities. P. aeruginosa carriage is a precursor to infection. Options for treating infections caused by difficult-to-treat P. aeruginosa strains are dwindling, underscoring the urgency to better understand and impede pre-infection stages, such as colonization. Here, we use vancomycin-treated mice to model antibiotic-treated patients who become colonized with P", "token_count": 527, "char_count": 2141, "word_count": 280, "semantic_coherence": 1, "information_density": 0.5964, "quality_score": 0.7982, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:03:11.628858", "source": { "split": "train_shard_00002", "doc_id": 322 }, "chunk_id": "train_shard_00002_322_0", "global_id": 13164 }, { "text": "aeruginosa in their gastrointestinal tracts. We identify the stomach as a major barrier to the establishment of gastrointestinal carriage. These findings suggest that efforts to prevent gastrointestinal colonization should focus not only on judicious use of antibiotics but also on investigation into how the stomach eliminates orally ingested P. aeruginosa.\n\n<i>Pseudomonas aeruginosa</i> population dynamics in a vancomycin-induced murine model of gastrointestinal carriage.", "token_count": 131, "char_count": 499, "word_count": 62, "semantic_coherence": 1, "information_density": 0.7903, "quality_score": 0.8952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:12.049859", "source": { "split": "train_shard_00002", "doc_id": 322 }, "chunk_id": "train_shard_00002_322_1", "global_id": 13165 }, { "text": "UDPglucose 4-epimerase from Kluyveromyces fragilis was earlier shown to have two conformationally vicinal thiols at the active site. Upon treatment with diamide, these thiols form a disulfide linkage across the subunits that results in coordinated loss of catalytic activity and coenzyme fluorescence (Ray, M., and Bhaduri, A. (1980) J. Biol. Chem. 255, 10777-10786). Employing a number of thiol-specific reagents, we now suggest discriminatory and nonidentical roles for these two thiols. Kinetic and statistical analysis of 5,5'-dithiobis-(2-nitrobenzoic acid) and N-ethylmaleimide modification reaction of epimerase show that only one thiol is essential for activity. Consecutive modification experiments clearly show that the same active thiol is modified in both cases. However, significant differences are observed when the reactivity of these reagents is monitored in terms of coenzyme fluorescence. Treatment with N-ethylmaleimide leads to a form of inactive enzyme that fully retains its fluorescent properties whereas modification with 5,5'-dithiobis-(2-nitrobenzoic acid), on the other hand, results in the loss of both activity and fluorescence. The closely spaced nonessential second thiol, which is not modified by N-ethylmaleimide is therefore involved in generating and maintaining the coenzyme fluorescence. Modification studies with a series of spin-labeled maleimide shows that only 3-(maleimidomethyl)proxyl causes partial quenching of coenzyme fluorescence. This suggests that the active thiol is situated at a distance of 4.5 A approximately from the coenzyme fluorophore.\n\nDistinct functional roles of two active site thiols in UDPglucose 4-epimerase from Kluyveromyces fragilis.", "token_count": 481, "char_count": 1702, "word_count": 232, "semantic_coherence": 1, "information_density": 0.6078, "quality_score": 0.8039, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:12.694381", "source": { "split": "train_shard_00002", "doc_id": 323 }, "chunk_id": "train_shard_00002_323_0", "global_id": 13166 }, { "text": "Variable number tandem repeat (VNTR) analysis at nine loci of isolates of Pseudomonas aeruginosa submitted to the national reference laboratory from UK hospitals, from over 2000 patients, between June 2010 and June 2012 revealed four widely found types that collectively were received from approximately a fifth of patients, including from those with cystic fibrosis. These types were also prevalent among related submissions from the clinical environment and were received from up to 54 (out of 143) hospitals. Multi-locus sequence typing and blaOXA-50-like sequencing confirmed the clonal relationship within each cluster, and representatives from multiple centres clustered within about 70 % by pulsed-field gel electrophoresis. Illumina sequencing of 12 isolates of cluster A of VNTR profile 8, 3, 4, 5, 2, 3, 5, 2, x (where the repeat number at the last, most discriminatory locus is variable) revealed a large number of variably present targets in the accessory genome and seven of these were sought by PCR among a larger set of isolates. Representatives from patients within a single centre mostly had distinct accessory gene profiles, suggesting that these patients acquired the strain independently, while those with clear epidemiological links shared the same profile. Profiles also varied between representatives from different centres. Epidemiological investigations of widely found types such as these require the use of finer-typing methods, which increasingly will be informed by next generation sequencing.\n\nClusters of genetically similar isolates of Pseudomonas aeruginosa from multiple hospitals in the UK.", "token_count": 382, "char_count": 1625, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6527, "quality_score": 0.8264, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:13.271475", "source": { "split": "train_shard_00002", "doc_id": 324 }, "chunk_id": "train_shard_00002_324_0", "global_id": 13167 }, { "text": "Frequency of appearance of C. kefyr strains, their diagnosis, susceptibility to drugs and importance in pathogenesis of reproductive tract mycoses were investigated. The investigated material consisted of 2717 strains, and there were 67 strains of C. kefyr isolated from vaginal mucous membrane. C. kefyr strains constituted 2.5% of total number of 2717 isolated strains and 8.2% within fungi other than C. albicans species. Vaginal mycosis caused by C. kefyr occurs in presence of Lactobacillus sp. and correct values of pH in vaginal contents, however changing leukocyte number was observed. Clinical symptoms and complaints regarding reproductive tract were present in 47.8% of patients with C. kefyr infections. Investigating susceptibility to antimycotic drugs, regardless of appointed method, low susceptibility of C. kefyr strains to amphotericin B was noted (79% resistant strains). Strain of C. kefyr were sensitive to all remaining drugs.\n\n[The role of Candida kefyr (C. pseudotropicalis) in reproductive tract infections].", "token_count": 283, "char_count": 1033, "word_count": 150, "semantic_coherence": 1, "information_density": 0.62, "quality_score": 0.81, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:13.832792", "source": { "split": "train_shard_00002", "doc_id": 325 }, "chunk_id": "train_shard_00002_325_0", "global_id": 13168 }, { "text": "Methicillin-resistant Staphylococcus pseudintermedius (MRSP) is an important opportunistic pathogenic bacterium of dogs that also occasionally colonize and infect humans. However, whether MRSP can adapt to human hosts is not clear and whole genome sequences of MRSP from humans are still limited. Genomic comparative analyses of 3 couples of isolates from dogs (n = 3) and humans (n = 3) belonging to ST45, ST112, and ST181, the dominant clones in Thailand were conducted to determine the degree of similarities between human and animal MRSP of a same ST. Among eight prophages, three prophages associated with the leucocidins genes (lukF/S-I), φVB88-Pro1, φVB16-Pro1 and φAP20-Pro1, were distributed in the human MRSPs, while their remnants, φAH18-Pro1, were located in the dog MRSPs. A novel composite pathogenicity island, named SpPI-181, containing two integrase genes was identified in the ST181 isolates. The distribution of the integrase genes of the eight prophages and SpPI-181 was also analysed by PCR in 77 additional MRSP isolates belonging to different STs. The PCR screen revealed diversity in prophage carriage, especially in ST45 isolates. Prophage φAK9-Pro1 was only observed in ST112 isolates from dogs and SpPI-181 was found associated with ST181 clonal lineage. Among the 3 couple of isolates, ST45 strains showed the highest number of single nucleotide polymorphisms (SNP) in their core genomes (3,612 SNPs). The genomic diversity of ST45 isolates suggested a high level of adaptation that may lead to different host colonization of successful clones. This finding provided data on the genomic differences of MRSP associated with colonization and adaption to different hosts.\n\nGenomic insights into methicillin-resistant Staphylococcus pseudintermedius isolates from dogs and humans of the same sequence types reveals diversity in prophages and pathogenicity islands.", "token_count": 509, "char_count": 1888, "word_count": 278, "semantic_coherence": 1, "information_density": 0.5791, "quality_score": 0.7896, "entities": { "genes": [ "ST45", "ST112", "ST181" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:14.519400", "source": { "split": "train_shard_00002", "doc_id": 326 }, "chunk_id": "train_shard_00002_326_0", "global_id": 13169 }, { "text": "We have isolated a cDNA from the protozoan parasite Leishmania major (Lm) that encodes a protein homologous to the Saccharomyces cerevisiae and Kluyveromyces marxianus silent information regulator 2 (SIR2) proteins. The deduced Lm SIR2-related protein (termed LmSIR2rp) consists of 381 amino acids that share 40.5% identity with yeast SIR2, increasing to 60% when substitutions are included. Moreover, the LmSIR2rp aa sequence contains a single potential zinc-binding domain with a CysXaa2CysXaa20CysXaa2Cys motif, and its C-terminal part is rich in Ser (16 Ser residues over 40 aa) which constitute potential sites for phosphorylation. The characterization of a novel Lm gene product which shows considerable similarity to a yeast mating-type regulatory protein provides a new tool to investigate the parasite differentiation control mechanisms and gene expression regulation.\n\nA Leishmania major protein with extensive homology to silent information regulator 2 of Saccharomyces cerevisiae.", "token_count": 275, "char_count": 992, "word_count": 139, "semantic_coherence": 1, "information_density": 0.7122, "quality_score": 0.8561, "entities": { "genes": [ "SIR2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:15.099405", "source": { "split": "train_shard_00002", "doc_id": 327 }, "chunk_id": "train_shard_00002_327_0", "global_id": 13170 }, { "text": "Simulation of process conditions of continuous ethanol fermentation of whey permeate using alginate entrapped Kluyveromyces marxianus NCYC 179 cells in a packed-bed reactor system.", "token_count": 50, "char_count": 180, "word_count": 24, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:15.479352", "source": { "split": "train_shard_00002", "doc_id": 328 }, "chunk_id": "train_shard_00002_328_0", "global_id": 13171 }, { "text": "Clostridium perfringens is an extremely versatile pathogen of humans and livestock, causing wound infections like gas gangrene (clostridial myonecrosis), enteritis/enterocolitis (including one of the most common human food-borne illnesses), and enterotoxemia (where toxins produced in the intestine are absorbed and damage distant organs such as the brain). The virulence of this Gram-positive, spore-forming, anaerobe is largely attributable to its copious toxin production; the diverse actions and roles in infection of these toxins are now becoming established. Most C. perfringens toxin genes are encoded on conjugative plasmids, including the pCW3-like and the recently discovered pCP13-like plasmid families. Production of C. perfringens toxins is highly regulated via processes involving two-component regulatory systems, quorum sensing and/or sporulation-related alternative sigma factors. Non-toxin factors, such as degradative enzymes like sialidases, are also now being implicated in the pathogenicity of this bacterium. These factors can promote toxin action in vitro and, perhaps in vivo, and also enhance C. perfringens intestinal colonization, e.g. NanI sialidase increases C. perfringens adherence to intestinal tissue and generates nutrients for its growth, at least in vitro. The possible virulence contributions of many other factors, such as adhesins, the capsule and biofilms, largely await future study.\n\nPathogenicity and virulence of Clostridium perfringens.", "token_count": 431, "char_count": 1545, "word_count": 200, "semantic_coherence": 1, "information_density": 0.685, "quality_score": 0.8425, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:16.154737", "source": { "split": "train_shard_00002", "doc_id": 329 }, "chunk_id": "train_shard_00002_329_0", "global_id": 13172 }, { "text": "The INU genes of Kluyveromyces marxianus encode inulinases which are readily secreted from Saccharomyces cerevisiae into the culture medium. To evaluate the utility of the INU signal peptides for the secretion of heterologous proteins from S. cerevisiae, a variety of expression and secretion vectors were constructed with GAL10 promoter and GAL7 terminator. The coding sequence for human lipocortin-1 (LC1) was inserted in-frame with the INU signal sequences, and then the secretion efficiency and localization of LC1 were investigated in more detail and compared with those when being expressed by the vector with the MFalpha1 leader peptide. The vector systems with INU signal peptides secreted ca. 95% of the total LC1 expressed into the extracellular medium, while the MFalpha1 leader peptide-containing vector resulted in very low secretion efficiency below 10%. In addition, recombinant human interleukin-2 (IL-2) was expressed and secreted with the vector systems with INU signal peptide, and a majority fraction of the human IL-2 expressed was found to be secreted into the extracellular medium as observed in LC1 expression. (c) 1995 John Wiley & Sons, Inc.\n\nHighly efficient secretion of heterologous proteins from Saccharomyces cerevisiae using inulinase signal peptides.", "token_count": 332, "char_count": 1283, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5632, "quality_score": 0.7816, "entities": { "genes": [ "LC1", "GAL10", "GAL7" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:16.733356", "source": { "split": "train_shard_00002", "doc_id": 330 }, "chunk_id": "train_shard_00002_330_0", "global_id": 13173 }, { "text": "Most bacterial and archaeal genomes contain many genes with little or no similarity to other genes, a property that impedes identification of gene origins. By comparing the codon usage of genes shared among strains (primarily vertically inherited genes) and genes unique to one strain (primarily recently horizontally acquired genes), we found that the plurality of unique genes in Escherichia coli and Salmonella enterica are much more similar to each other than are their vertically inherited genes. We conclude that E. coli and S. enterica derive these unique genes from a common source, a supraspecies phylogenetic group that includes the organisms themselves. The phylogenetic range of the sharing appears to include other (but not all) members of the Enterobacteriaceae. We found evidence of similar gene sharing in other bacterial and archaeal taxa. Thus, we conclude that frequent gene exchange, particularly that of genetic novelties, extends well beyond accepted species boundaries.\n\nSimilarity of genes horizontally acquired by Escherichia coli and Salmonella enterica is evidence of a supraspecies pangenome.", "token_count": 252, "char_count": 1120, "word_count": 166, "semantic_coherence": 1, "information_density": 0.5904, "quality_score": 0.7952, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:17.222532", "source": { "split": "train_shard_00002", "doc_id": 331 }, "chunk_id": "train_shard_00002_331_0", "global_id": 13174 }, { "text": "Candidiasis is a frequent human infection caused mainly by Candida albicans. However, other species are emerging as important pathogens, as Candida glabrata, Candida parapsilosis, Candida tropicalis, Candida krusei or Candida guilliermondii. Rapid identification of clinical isolates could facilitate diagnosis and treatment. Candida ID (bioMerieux, Spain) is a new medium for the isolation and presumptive identification of yeasts: C. albicans grows as blue colonies, and C. tropicalis, C. guilliermondii, Candida kefyr and Candida lusitaniae as pink ones. The utility of Candida ID was evaluated with more than 700 clinical isolates and type culture collection strains from different genera including Candida, Cryptococcus, Saccharomyces, and Rhodotorula. Presumptive identification was confirmed by germ tube test, microscopic morphology and chlamydoconidia production on corn meal agar and carbohydrate assimilation on API-ATB ID 32C or Vitek (bioMerieux). Growth on Candida ID was rapid (18-24 h) for most of the yeast strains tested. Sensitivity and specificity of identification of C. albicans was significantly high (>98%), since a very low number of isolates were found to be false negative or false positive. A better result was obtained for species growing as pink colonies (>99.5%). Detection of different species of medical important yeasts was easy with Candida ID, as perfectly distinct colors and textures of colonies were observed on this medium. Candida ID allowed the discrimination between C. glabrata (creamy and smooth) and C. krusei (rough and white) colonies. Other species showed different colony textures and colours, white being the predominant colour. Candida ID was very useful for the presumptive identification C. albicans isolates.\n\n[Evaluation of a new chromogenic medium (Candida ID) for the isolation and presumptive identification of Candida albicans and other medically important yeasts].", "token_count": 484, "char_count": 1925, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5652, "quality_score": 0.7826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:17.878324", "source": { "split": "train_shard_00002", "doc_id": 332 }, "chunk_id": "train_shard_00002_332_0", "global_id": 13175 }, { "text": "Nine yeast and four lactic acid bacterial strains, previously isolated from Zimbabwean traditionally fermented milk, were inoculated into ultra-high temperature treated (UHT) milk in both single and yeast-lactic acid bacteria co-culture. The lactic acid bacteria (LAB) strains consisted of Lactococcus lactis subsp. lactis biovar. diacetylactis C1, L. lactis subsp. lactis Lc39, L. lactis subsp. lactis Lc261 and Lactobacillus paracasei subsp. paracasei Lb11. The yeast strains used were Candida kefyr 23, C. lipolytica 57, C. lusitaniae 63, C. lusitaniae 68, C. tropicalis 78, Saccharomyces cerevisiae 71, S. dairenensis 32, C. colliculosa 41 and Dekkera bruxellensis 43. After 48-h fermentation at 25 degrees C, the samples were analysed for pH, viable yeast and bacterial counts, organic acids, volatile organic compounds (VOC) and carbon dioxide. The Lactococcus strains reduced the pH from about 6.6 to between 4.0 and 4.2, while Lb. paracasei subsp. paracasei Lb11 reduced the pH to about 5.4. Most of the yeasts, however, did not affect the final pH of the milk except for C. kefyr 23, which reduced the pH from 6.6 to 5.8. All the Lactococcus strains grew two log cycles during the 48-h fermentation period, while Lb. paracasei subsp. paracasei Lb11 grew about one log cycle. S. cerevisiae 71, C. colliculosa 41 and D. bruxellensis 43 showed poor growth in the milk in both single and co-culture. The other species of yeast grew about two log cycles. Candida colliculosa 41, S. dairenensis 32 and D", "token_count": 537, "char_count": 1506, "word_count": 238, "semantic_coherence": 1, "information_density": 0.5504, "quality_score": 0.7752, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:03:18.537695", "source": { "split": "train_shard_00002", "doc_id": 333 }, "chunk_id": "train_shard_00002_333_0", "global_id": 13176 }, { "text": "bruxellensis 43 showed reduced viability when in co-culture with Lb. paracasei subsp. paracasei Lb11. The samples in which C. kefyr 23 was used were distinct and characterised by large amounts of acetaldehyde, carbon dioxide and ethanol. However, in the samples where S. dairenensis, C. colliculosa, D. bruxellensis, C. lusitaniae, C. tropicalis, C. lipolytica and S. cerevisiae were used in co-culture, the final pH and metabolite content were mainly determined by the correspondin\n\nThe growth and interaction of yeasts and lactic acid bacteria isolated from Zimbabwean naturally fermented milk in UHT milk.", "token_count": 184, "char_count": 608, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7253, "quality_score": 0.8626, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:18.984749", "source": { "split": "train_shard_00002", "doc_id": 333 }, "chunk_id": "train_shard_00002_333_1", "global_id": 13177 }, { "text": "Gut microbiota are the microbial organisms that play a pivotal role in intestinal health and during disease conditions. Keeping in view the characteristic functions of gut microbiota, in this study, Lactobacillus reuteri TPC32 (L. reuteri TPC32) was isolated and identified, and its whole genome was analyzed by the Illumina MiSeq sequencing platform. The results revealed that L. reuteri TPC32 had high resistance against acid and bile salts with fine in vitro antibacterial ability. Accordingly, a genome sequence of L. reuteri TPC32 has a total length of 2,214,495 base pairs with a guanine-cytosine content of 38.81%. Based on metabolic annotation, out of 2,212 protein-encoding genes, 118 and 101 were annotated to carbohydrate metabolism and metabolism of cofactors and vitamins, respectively. Similarly, drug-resistance and virulence genes were annotated using the comprehensive antibiotic research database (CARD) and the virulence factor database (VFDB), in which vatE and tetW drug-resistance genes were annotated in L. reuteri TPC32, while virulence genes are not annotated. The early prevention of L. reuteri TPC32 reduced the Salmonella typhimurium (S. Typhimurium) infection in mice. The results show that L. reuteri TPC32 could improve the serum IgM, decrease the intestinal cytokine secretion to relieve intestinal cytokine storm, reinforce the intestinal biochemical barrier function by elevating the sIgA expression, and strengthen the intestinal physical barrier function. Simultaneously, based on the 16S rRNA analysis, the L", "token_count": 513, "char_count": 1625, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6278, "quality_score": 0.8139, "entities": { "genes": [ "TPC32" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:03:19.615516", "source": { "split": "train_shard_00002", "doc_id": 334 }, "chunk_id": "train_shard_00002_334_0", "global_id": 13178 }, { "text": "reuteri TPC32 results affect the recovery of intestinal microbiota from disease conditions and promote the multiplication of beneficial bacteria. These results provide new insights into the biological functions and therapeutic potential of L. reuteri TPC32 for treating intestinal inflammation.\n\nThe Whole-Genome Sequencing and Probiotic Profiling of Lactobacillus reuteri Strain TPC32 Isolated from Tibetan Pig.", "token_count": 120, "char_count": 430, "word_count": 54, "semantic_coherence": 1, "information_density": 0.7222, "quality_score": 0.8611, "entities": { "genes": [ "TPC32" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:20.004098", "source": { "split": "train_shard_00002", "doc_id": 334 }, "chunk_id": "train_shard_00002_334_1", "global_id": 13179 }, { "text": "Carbapenem-resistant Enterobacteriaceae (CRE) represent one of the most urgent threats to human health posed by antibiotic resistant bacteria. Enterobacter hormaechei and other members of the Enterobacter cloacae complex are the most commonly encountered Enterobacter spp. within clinical settings, responsible for numerous outbreaks and ultimately poorer patient outcomes. Here we applied three complementary whole genome sequencing (WGS) technologies to characterise a hospital cluster of bla IMP-4 carbapenemase-producing E. hormaechei . In response to a suspected CRE outbreak in 2015 within an Intensive Care Unit (ICU)/Burns Unit in a Brisbane tertiary referral hospital we used Illumina sequencing to determine that all outbreak isolates were sequence type (ST)90 and near-identical at the core genome level. Comparison to publicly available data unequivocally linked all 10 isolates to a 2013 isolate from the same ward, confirming the hospital environment as the most likely original source of infection in the 2015 cases. No clonal relationship was found to IMP-4-producing isolates identified from other local hospitals. However, using Pacific Biosciences long-read sequencing we were able to resolve the complete context of the bla IMP-4 gene, which was found to be on a large IncHI2 plasmid carried by all IMP-4-producing isolates. Continued surveillance of the hospital environment was carried out using Oxford Nanopore long-read sequencing, which was able to rapidly resolve the true relationship of subsequent isolates to the initial outbreak. Shotgun metagenomic sequencing of environmental samples also found evidence of ST90 E. hormaechei and the IncHI2 plasmid within the hospital plumbing. Overall, our strategic application of three WGS technologies provided an in-depth analysis of the outbreak, including the transmission dynamics of a carbapenemase-producing E. hormaechei cluster, identification of possible hospital reservoirs and the full context of bla IMP-4 on a multidrug resistant IncHI2 plasmid that appears to be widely distributed in Australia.", "token_count": 489, "char_count": 2079, "word_count": 295, "semantic_coherence": 1, "information_density": 0.5932, "quality_score": 0.7966, "entities": { "genes": [ "ST90" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:20.651823", "source": { "split": "train_shard_00002", "doc_id": 335 }, "chunk_id": "train_shard_00002_335_0", "global_id": 13180 }, { "text": "Integrating multiple genomic technologies to investigate an outbreak of carbapenemase-producingEnterobacter hormaechei", "token_count": 32, "char_count": 125, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:21.013178", "source": { "split": "train_shard_00002", "doc_id": 335 }, "chunk_id": "train_shard_00002_335_1", "global_id": 13181 }, { "text": "Two Gram-stain-negative, facultative anaerobic, motile, rod-shaped strains, S-B4-1UT and JOB-63a, forming small whitish transparent colonies on marine agar, were isolated from a sponge of the genus Haliclona. The strains shared 99.7% 16S rRNA gene sequence identity and a DNA-DNA hybridization value of 100%, but were differentiated by genomic fingerprinting using rep-PCRs. 16S rRNA gene sequence phylogeny placed the strains as a sister branch to the monophyletic genus Endozoicomonas (Oceanospirillales; Gammaproteobacteria) with 92.3-94.3% 16S rRNA gene sequence similarity to Endozoicomonas spp., 91.9 and 92.1% to Candidatus Endonucleobacter bathymodiolin, and 91.9 to 92.1% to the type strains of Kistimonas spp. Core genome based phylogeny of strain S-B4-1UT confirmed the phylogenetic placement. Major fatty acids were summed feature 3 (C16:1 ω7c/C16:1 ω6c) and 8 (C18:1 ω7c/C18:1 ω6c) followed by C10:0 3-OH, C16:0, and C18:0. The G+C content was 50.1-51.4mol%", "token_count": 438, "char_count": 1069, "word_count": 136, "semantic_coherence": 1, "information_density": 0.7059, "quality_score": 0.8529, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:21.642487", "source": { "split": "train_shard_00002", "doc_id": 336 }, "chunk_id": "train_shard_00002_336_0", "global_id": 13182 }, { "text": "The peptidoglycan diamino acid of strain S-B4-1UT was meso-diaminopimelic acid, the predominant polyamine spermidine, the major respiratory quinone ubiquinone Q-9; phosphatidylethanolamine, phosphatidylglycerol and phosphatidylserine were major polar lipids. Based on the clear phylogenetic distinction, the genus Parendozoicomonas gen. nov. is proposed, with Parendozoicomonas haliclonae sp. nov. as type species and strain S-B4-1UT (=CCM 8713T=DSM 103671T=LMG 29769T) as type strain and JOB-63a as a second strain of the species. Based on the 16S rRNA gene sequence phylogeny of the Oceanospirillales within the Gammaproteobacteria, the Endozoicomonaceae fam. nov. is proposed including the genera Endozoicomonas, Parendozoicomonas, and Kistimonas as well as the Candidatus genus Endonucleobacter.\n\nParendozoicomonas haliclonae gen. nov. sp. nov. isolated from a marine sponge of the genus Haliclona and description of the family Endozoicomonadaceae fam. nov. comprising the genera Endozoicomonas, Parendozoicomonas, and Kistimonas.", "token_count": 390, "char_count": 1089, "word_count": 132, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7992, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:22.258747", "source": { "split": "train_shard_00002", "doc_id": 336 }, "chunk_id": "train_shard_00002_336_1", "global_id": 13183 }, { "text": "Colorectal cancer (CRC) is a severe gastrointestinal cancer and a leading cause of cancer-related deaths in Ghana. The potential role of gut Enterobacteriaceae in the increasing incidence of CRC in Ghana is yet to be thoroughly investigated. In this study, Enterobacteriaceae from CRC patients and healthy control participants were analyzed by whole genome sequencing to identify genomic features that are associated with CRC. Socio-demographic data showed a significant association between age and alcohol consumption and CRC. Escherichia coli was the most abundant Enterobacteriaceae isolated from the study participants and they were predominantly intestinal commensals. Escherichia coli isolates belonging to phylogroup D encoded the highest number of virulence genes. The agn43 and int genes were widespread in Escherichia coli isolates from the CRC patients. Multilocus sequence types of potentially pathogenic Escherichia coli from the CRC patients also encoded genes involved in aggregation, adherence and biofilm formation. The ampC2 and ampH antimicrobial resistance genes were also widespread in the genome of the Escherichia coli isolates. This study highlights the virulence tendencies of Escherichia coli from CRC patients and their ability to transfer virulence determinants to other Enterobacteriaceae residing in the gut.\n\nGenomic analysis of Enterobacteriaceae from colorectal cancer patients at a tertiary hospital in Ghana: a case-control study.", "token_count": 346, "char_count": 1465, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5631, "quality_score": 0.7816, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:22.826902", "source": { "split": "train_shard_00002", "doc_id": 337 }, "chunk_id": "train_shard_00002_337_0", "global_id": 13184 }, { "text": "Partial sequences of 25 S ribosomal DNA for nine Candida yeast and one Kluyveromyces yeast strains were cloned and determined. We compared them with two published 25 S rDNA sequences of Saccharomyces cerevisiae and Candida albicans. An evolutionary tree of the twelve species was inferred from about 370 sites of 5' end of 25 S ribosomal DNA using the methods of neighbor-joining and bootstrap. The molecular data indicate a very close affinity between Candida kefyr CBS834 and Kluyveromyces cicerisporus CBS4857.\n\nAnalysis of Phylogenetic Relationships Among Twelve Yeast Species.", "token_count": 166, "char_count": 581, "word_count": 88, "semantic_coherence": 1, "information_density": 0.7159, "quality_score": 0.858, "entities": { "genes": [ "CBS834", "CBS4857" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:23.270512", "source": { "split": "train_shard_00002", "doc_id": 338 }, "chunk_id": "train_shard_00002_338_0", "global_id": 13185 }, { "text": "Typical enteropathogenic Escherichia coli (tEPEC) is a leading cause of diarrhea and associated death in children worldwide. Atypical EPEC (aEPEC) lacks the plasmid encoding bundle-forming pili and is considered less virulent, but the molecular mechanism of virulence is poorly understood. We recently identified kittens as a host for aEPEC where intestinal epithelial colonization was associated with diarrheal disease and death. The purposes of this study were to (i) determine the genomic similarity between kitten aEPEC and human aEPEC isolates and (ii) identify genotypic or phenotypic traits associated with virulence in kitten aEPEC. We observed no differences between kitten and human aEPEC in core genome content or gene cluster sequence identities, and no distinguishing genomic content was observed between aEPEC isolates from kittens with nonclinical colonization (NC) versus those with lethal infection (LI). Variation in adherence patterns and ability to aggregate actin in cultured cells mirrored descriptions of human aEPEC. The aEPEC isolated from kittens with LI were significantly more motile than isolates from kittens with NC. Kittens may serve as a reservoir for aEPEC that is indistinguishable from human aEPEC isolates and may provide a needed comparative animal model for the study of aEPEC pathogenesis. Motility seems to be an important factor in pathogenesis of LI associated with aEPEC in kittens.\n\nComparative Genomics of Atypical Enteropathogenic Escherichia coli from Kittens and Children Identifies Bacterial Factors Associated with Virulence in Kittens.", "token_count": 419, "char_count": 1594, "word_count": 230, "semantic_coherence": 1, "information_density": 0.5783, "quality_score": 0.7891, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:23.892698", "source": { "split": "train_shard_00002", "doc_id": 339 }, "chunk_id": "train_shard_00002_339_0", "global_id": 13186 }, { "text": "This study examines the microbiological and epidemiological characteristics of toxigenic and nontoxigenic Corynebacterium isolates submitted to the national reference laboratory in Spain, between 2014 and 2019, in order to describe the current situation and improve our knowledge regarding these emerging pathogens. Epidemiological information was extracted from the Spanish Surveillance System. Microbiological and molecular characterization was carried out using phenotypic methods, multilocus sequence typing (MLST), whole-genome sequencing (WGS), and core genome MLST (cgMLST). Thirty-nine isolates were analyzed. Twenty-one isolates were identified as Corynebacterium diphtheriae (6 toxigenic), 14 as C. belfantii, 4 as C. ulcerans (3 toxigenic), and 1 as C. rouxii One C. diphtheriae isolate was identified as nontoxigenic tox gene bearing (NTTB). Ages of patients ranged from 1 to 89 years, with 10% (3/30) of nontoxigenic and 22% (2/9) of toxigenic isolates collected from children less than 15 years. Twenty-five of the patients were males (17/30 in nontoxigenic; 8/9 in toxigenic). MLST identified 28 sequence types (STs), of which 7 were described for the first time in Spain. WGS analysis showed that 10 isolates, including 3 toxigenic isolates, harbored a variety of antibiotic resistance genes in addition to the high prevalence of penicillin resistance phenotypically demonstrated. Phylogenetic analysis revealed one cluster of isolates from family members. Risk information was available for toxigenic isolates (9/39); 3 patients reported recent travels to countries of endemicity and 3 had contact with cats/dogs. One unvaccinated child with respiratory diphtheria had a fatal outcome", "token_count": 522, "char_count": 1750, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:03:24.547570", "source": { "split": "train_shard_00002", "doc_id": 340 }, "chunk_id": "train_shard_00002_340_0", "global_id": 13187 }, { "text": "Including nontoxigenic Corynebacterium infections in disease surveillance and using WGS could further improve current surveillance.\n\nMolecular and Epidemiological Characterization of Toxigenic and Nontoxigenic Corynebacterium diphtheriae, Corynebacterium belfantii, Corynebacterium rouxii, and Corynebacterium ulcerans Isolates Identified in Spain from 2014 to 2019.", "token_count": 120, "char_count": 373, "word_count": 40, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:24.929892", "source": { "split": "train_shard_00002", "doc_id": 340 }, "chunk_id": "train_shard_00002_340_1", "global_id": 13188 }, { "text": "A brief outline of the current taxonomic status of the genus Kluyveromyces is presented. Noteworthy are the transfer of several former Kluyveromyces species to other genera, the retention of the name Kluyveromyces for K. lactis, K. marxianus, and four related species, and some recent attempts to clarify the variety status of strains assigned to K. lactis.\n\nCurrent status of Kluyveromyces systematics.", "token_count": 107, "char_count": 403, "word_count": 61, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:25.314192", "source": { "split": "train_shard_00002", "doc_id": 341 }, "chunk_id": "train_shard_00002_341_0", "global_id": 13189 }, { "text": "Vibrio cholerae is a natural inhabitant of aquatic ecosystems. Some strains of V. cholerae can colonize the human host and cause cholera, a profuse watery diarrhea. The major pathogenicity factors and virulence regulators of V. cholerae are either encoded in mobile genetic elements acquired in the environment (e.g. pathogenicity islands or lysogenic phages) or in the core genome. Several lines of evidence indicate that the emergence of numerous virulence traits of V. cholerae occurred in its natural environment due to biotic and abiotic pressures. Here, we discuss the connection between the human host and the potential ecological role of these virulent traits. Unraveling these connections will help us understand the emergence of this organism and other facultative bacterial pathogens.\n\nEnvironmental role of pathogenic traits in Vibrio cholerae.", "token_count": 240, "char_count": 891, "word_count": 127, "semantic_coherence": 1, "information_density": 0.6693, "quality_score": 0.8346, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:25.804312", "source": { "split": "train_shard_00002", "doc_id": 342 }, "chunk_id": "train_shard_00002_342_0", "global_id": 13190 }, { "text": "

Objectives

Here we report on a long-term outbreak from 2009 to 2012 with an XDR Pseudomonas aeruginosa on two wards at a university hospital in southern Germany.

Methods

Whole-genome sequencing was performed on the outbreak isolates and a core genome was constructed for molecular epidemiological analysis. We applied a time-place-sequence algorithm to improve estimation of transmission probabilities.

Results

By using conventional infection control methods we identified 49 P. aeruginosa strains, including eight environmental isolates that belonged to ST308 (by MLST) and carried the metallo-β-lactamase IMP-8. Phylogenetic analysis on the basis of a non-recombinant core genome that contained 22 outbreak-specific SNPs revealed a pattern of four dominant clades with a strong phylogeographic structure and allowed us to determine the potential temporal origin of the outbreak to July 2008, 1 year before the index case was diagnosed. Superspreaders at the root of clades exhibited a high number of probable and predicted transmissions, indicating their exceptional position in the outbreak.

Conclusions

Our results suggest that the initial expansion of dominant sublineages was driven by a few superspreaders, while environmental contamination seemed to sustain the outbreak for a long period despite regular environmental control measures.\n\nAnalysis of a long-term outbreak of XDR Pseudomonas aeruginosa: a molecular epidemiological study.", "token_count": 353, "char_count": 1473, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6497, "quality_score": 0.8249, "entities": { "genes": [ "ST308" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:26.385117", "source": { "split": "train_shard_00002", "doc_id": 343 }, "chunk_id": "train_shard_00002_343_0", "global_id": 13191 }, { "text": "Biocontrol (BC) formulations prepared from plant-growth-promoting bacteria are increasingly applied in sustainable agriculture. Especially inoculants prepared from endospore-forming Bacillus strains have been proven as efficient and environmental-friendly alternative to chemical pesticides due to their long shelf life, which is comparable with that of agrochemicals. However, these formulations of the first generation are sometimes hampered in their action and do not fulfill in each case the expectations of the appliers. In this review we use the well-known plant-associated Bacillus amyloliquefaciens type strain FZB42 as example for the successful application of different techniques offered today by comparative, evolutionary and functional genomics, site-directed mutagenesis and strain construction including marker removal, for paving the way for preparing a novel generation of BC agents.\n\nNovel Routes for Improving Biocontrol Activity of Bacillus Based Bioinoculants.", "token_count": 216, "char_count": 981, "word_count": 129, "semantic_coherence": 1, "information_density": 0.7519, "quality_score": 0.876, "entities": { "genes": [ "FZB42" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:26.901928", "source": { "split": "train_shard_00002", "doc_id": 344 }, "chunk_id": "train_shard_00002_344_0", "global_id": 13192 }, { "text": "The authors analysed 10 years of experience of fungaemia at a Regional Italian Hospital, the Azienda Ospedaliera (A.O.) 'Ospedali Riuniti di Bergamo', Bergamo, Italy, from 1988 to 1997. One hundred and sixty-eight cases were observed, with a global incidence corresponding to 3.43/10,000 in-patients. Median age was 38.5 years and mean age was 38.9 years (range: 0-94 years). Female:male ratio was 1:1.75. Fungaemia occurred 25.7 days (mean value) after admission to the hospital. Aetiology was: 134 Candida spp. (70%), 11 Cryptococcus neoformans (6.5%), seven Torulopsis inconspicua (4.1%), three Trichosporon beigelii (1.8%), one Hansenula anomala (0.6%); three Fusarium verticillioides (1.8%), three Geotrichum candidum (1.8%) and one Histoplasma capsulatum (0.6%). Total mortality was 50.6%, and particularly related to Candida kefyr and Candida krusei, to Cr. neoformans and Fusarium spp.\n\nFungaemia survey: a 10-year experience in Bergamo, Italy.", "token_count": 352, "char_count": 952, "word_count": 134, "semantic_coherence": 1, "information_density": 0.7463, "quality_score": 0.8731, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:27.510128", "source": { "split": "train_shard_00002", "doc_id": 345 }, "chunk_id": "train_shard_00002_345_0", "global_id": 13193 }, { "text": "A thermotolerant yeast strain was constructed by protoplast fusion betweenSaccharomyces cerevisiae and respiratory defective Kluyveromyces sp. inactivated with iodoacetate. The fusant AY_(006) has a high ethanol yield (up to8.7%), using glucose as substrate at 45℃. Reversion inhibition of high density in protoplast was extensively decreased by deleting mitochondrion and adding chloromycetin. Meanwhile, colony morphology, isozymic feature and hightemperature fermentation were studied.\n\nConstruction of the thermotolerant yeasts by protoplast fusion between Kluyveromyces and Saccharomyces", "token_count": 168, "char_count": 592, "word_count": 73, "semantic_coherence": 1, "information_density": 0.7945, "quality_score": 0.8973, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:27.971887", "source": { "split": "train_shard_00002", "doc_id": 346 }, "chunk_id": "train_shard_00002_346_0", "global_id": 13194 }, { "text": "A yeast (Kluyveromyces marxianus) bioassay was used to establish the relative toxicity of 16 trichothecenes and some of their interactions. Removal of an isovaleryl group, one or two acetyl groups, or two acetyl plus an isovaleryl groups from T-2 toxin (T2) to form diacetoxyscirpenol, HT-2 toxin (HT2), T2-triol and T-2 tetraol (T2-4ol) decreased toxicity 7, 36, 276 and 558-fold, respectively. A combination of T2 and HT2, T2 and T2-4ol, deoxynivalenol (DON) and nivalenol (NIV), or DON and T2 exhibited synergistic (T2 and HT2 or DON and NIV) or antagonistic (DON and T2) responses.\n\nStructure-activity relationships and interactions among trichothecene mycotoxins as assessed by yeast bioassay.", "token_count": 251, "char_count": 698, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [ "HT2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:28.501466", "source": { "split": "train_shard_00002", "doc_id": 347 }, "chunk_id": "train_shard_00002_347_0", "global_id": 13195 }, { "text": "A broth microdilution method and an agar dilution method were used for testing fluconazole, itraconazole, ketoconazole, flucytosine and amphotericin B against 98 clinical isolates belonging to seven species of Candida. The approximate rank order of fluconazole MICs was Candida lusitaniae approximately Candida kefyr < Candida famata approximately Candida guilliermondii < Candida pelliculosa approximately C. lipolytica approximately Candida inconspicua. Candida lypolitica and C. pelliculosa were the species least susceptible to itraconazole and ketoconazole. Flucytosine MICs revealed the highest prevalence of resistant strains among C. lipolytica and C. lusitaniae. All isolates were susceptible to amphotericin B.\n\nIn-vitro activity of five antifungal agents against uncommon clinical isolates of Candida spp.", "token_count": 234, "char_count": 816, "word_count": 107, "semantic_coherence": 1, "information_density": 0.6262, "quality_score": 0.8131, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:28.971629", "source": { "split": "train_shard_00002", "doc_id": 348 }, "chunk_id": "train_shard_00002_348_0", "global_id": 13196 }, { "text": "

Background

More than 94 serotypes of Streptococcus pneumoniae have been described to date, however the majority of disease is caused by approximately 20 serotypes. Some pneumococci do not react with commercially available antisera used for serotyping and are thus regarded as non-serotypeable (NT). These pneumococci are commonly isolated during carriage studies and very rarely cause invasive disease. Colonization may occur with more than one serotype however disease with more than one serotype is rarely detected. Thus there are limited data describing cases of pneumococcal disease caused by more than one isolate.

Results

In two cases of invasive pneumococcal disease in South Africa, a non-serotypeable and a serotypeable isolate were co-detected during routine serotyping. A serotype 1 and 18C isolate were each co-detected with a non-serotypeable isolate in 2009 (case A) and 2010 (case B), from cerebrospinal fluid and blood, respectively. Both patients were 10-14 years old. For case A, the serotypeable isolate could not be obtained due to low representation in the mixed culture. Using electron microscopy we confirmed lack of capsule for the non-serotypeable isolates. Comparison of the case A non-serotypeable isolate with a serotype 1 genome revealed only the presence of the rhamnose biosynthesis genes (rmlA, B, C and D) in the capsular locus, all other capsular genes were absent. Nonetheless it had a multilocus sequence type (ST) associated with serotype 1 (ST217 and ribosomal ST3462) and its core genome clustered with other ST217 isolates. The case B non-serotypeable isolate had all serotype 18C capsular genes except for variation in the wchA and wze genes, compared to the 18C isolate", "token_count": 471, "char_count": 1726, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5869, "quality_score": 0.7934, "entities": { "genes": [ "ST3462", "ST217" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:29.614227", "source": { "split": "train_shard_00002", "doc_id": 349 }, "chunk_id": "train_shard_00002_349_0", "global_id": 13197 }, { "text": "Both case B isolates were ST9817 and their core genomes were identical.

Conclusions

The ability of pneumococci to alter capsule production is a potential vaccine escape mechanism and therefore non-serotypeable pneumococci should be monitored as such organisms may increase under vaccine pressure.\n\nTwo cases of serotypeable and non-serotypeable variants of Streptococcus pneumoniae detected simultaneously during invasive disease.", "token_count": 108, "char_count": 437, "word_count": 55, "semantic_coherence": 1, "information_density": 0.8545, "quality_score": 0.9273, "entities": { "genes": [ "ST9817" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:29.990941", "source": { "split": "train_shard_00002", "doc_id": 349 }, "chunk_id": "train_shard_00002_349_1", "global_id": 13198 }, { "text": "

Background

Legionella pneumophila is an intracellular pathogen of environmental protozoa. When humans inhale contaminated aerosols this bacterium may cause a severe pneumonia called Legionnaires' disease. Despite the abundance of dozens of Legionella species in aquatic reservoirs, the vast majority of human disease is caused by a single serogroup (Sg) of a single species, namely L. pneumophila Sg1. To get further insights into genome dynamics and evolution of Sg1 strains, we sequenced strains Lorraine and HL 0604 1035 (Sg1) and compared them to the available sequences of Sg1 strains Paris, Lens, Corby and Philadelphia, resulting in a comprehensive multigenome analysis.

Results

We show that L. pneumophila Sg1 has a highly conserved and syntenic core genome that comprises the many eukaryotic like proteins and a conserved repertoire of over 200 Dot/Icm type IV secreted substrates. However, recombination events and horizontal gene transfer are frequent. In particular the analyses of the distribution of nucleotide polymorphisms suggests that large chromosomal fragments of over 200 kbs are exchanged between L. pneumophila strains and contribute to the genome dynamics in the natural population. The many secretion systems present might be implicated in exchange of these fragments by conjugal transfer. Plasmids also play a role in genome diversification and are exchanged among strains and circulate between different Legionella species.

Conclusion

Horizontal gene transfer among bacteria and from eukaryotes to L. pneumophila as well as recombination between strains allows different clones to evolve into predominant disease clones and others to replace them subsequently within relatively short periods of time.\n\nExtensive recombination events and horizontal gene transfer shaped the Legionella pneumophila genomes.", "token_count": 458, "char_count": 1853, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8081, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:30.630283", "source": { "split": "train_shard_00002", "doc_id": 350 }, "chunk_id": "train_shard_00002_350_0", "global_id": 13199 }, { "text": "Photodynamic treatment of Kluyveromyces marxianus with chloroaluminum-phthalocyanine resulted in loss of clonogenicity. Several parameters were studied to identify targets that could be related to loss of colony-forming capacity. Inhibition of various plasma membrane-bound processes was observed, such as substrate transport and plasma membrane ATPase activity. Moreover, K+ loss from the cells was observed. Photodynamic treatment also reduced the activity of various enzymes involved in energy metabolism, thereby decreasing the cellular ATP level. It will be discussed however that none of these processes is likely to be related directly to loss of clonogenicity. Treatment with phthalocyanine and light resulted in a strong inhibition of the incorporation of 14C-phenylalanine in trichloracetic acid-precipitable material. The induction of the beta-galactoside utilization system was also strongly inhibited. The latter two processes did not recover during incubation, subsequent to photodynamic treatment. It is concluded that photodynamically induced inhibition of protein synthesis is a critical factor contributing to the loss of clonogenicity.\n\nThe effect of photodynamic treatment of yeast with the sensitizer chloroaluminum phthalocyanine on various cellular parameters.", "token_count": 295, "char_count": 1283, "word_count": 171, "semantic_coherence": 1, "information_density": 0.6082, "quality_score": 0.8041, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:32.050641", "source": { "split": "train_shard_00002", "doc_id": 351 }, "chunk_id": "train_shard_00002_351_0", "global_id": 13200 }, { "text": "Milk-derived bioactive peptides have been identified as potential ingredients of health-promoting functional foods. These bioactive peptides are targeted at diet-related chronic diseases especially the non-communicable diseases viz., obesity, cardiovascular diseases and diabetes. Peptides derived from the milk of cow, goat, sheep, buffalo and camel exert multifunctional properties, including anti-microbial, immune modulatory, anti-oxidant, inhibitory effect on enzymes, anti-thrombotic, and antagonistic activities against various toxic agents. Majority of those regulate immunological, gastrointestinal, hormonal and neurological responses, thereby playing a vital role in the prevention of cancer, osteoporosis, hypertension and other disorders as discussed in this review. For the commercial production of such novel bioactive peptides large scale technologies based on membrane separation and ion exchange chromatography methods have been developed. Separation and identification of those peptides and their pharmacodynamic parameters are necessary to transfer their potent functional properties into food applications. The present review summarizes the preliminary classes of bioactive milk-derived peptides along with their physiological functions, general characteristics and potential applications in health-care.\n\nMilk derived bioactive peptides and their impact on human health - A review.", "token_count": 302, "char_count": 1403, "word_count": 175, "semantic_coherence": 1, "information_density": 0.7029, "quality_score": 0.8514, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:32.611354", "source": { "split": "train_shard_00002", "doc_id": 352 }, "chunk_id": "train_shard_00002_352_0", "global_id": 13201 }, { "text": "Marine picocyanobacteria of the genera Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms on Earth, an ecological success thought to be linked to the differential partitioning of distinct ecotypes into specific ecological niches. However, the underlying processes that governed the diversification of these microorganisms and the appearance of niche-related phenotypic traits are just starting to be elucidated. Here, by comparing 81 genomes, including 34 new Synechococcus, we explored the evolutionary processes that shaped the genomic diversity of picocyanobacteria. Time-calibration of a core-protein tree showed that gene gain/loss occurred at an unexpectedly low rate between the different lineages, with for instance 5.6 genes gained per million years (My) for the major Synechococcus lineage (sub-cluster 5.1), among which only 0.71/My have been fixed in the long term. Gene content comparisons revealed a number of candidates involved in nutrient adaptation, a large proportion of which are located in genomic islands shared between either closely or more distantly related strains, as identified using an original network construction approach. Interestingly, strains representative of the different ecotypes co-occurring in phosphorus-depleted waters (Synechococcus clades III, WPC1, and sub-cluster 5.3) were shown to display different adaptation strategies to this limitation. In contrast, we found few genes potentially involved in adaptation to temperature when comparing cold and warm thermotypes. Indeed, comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation. Altogether, this study not only deciphers the respective roles of gene gains/losses and sequence variation but also uncovers numerous gene candidates likely involved in niche partitioning of two key members of the marine phytoplankton.", "token_count": 498, "char_count": 2117, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8474, "entities": { "genes": [ "WPC1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:33.261587", "source": { "split": "train_shard_00002", "doc_id": 353 }, "chunk_id": "train_shard_00002_353_0", "global_id": 13202 }, { "text": "Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria.", "token_count": 31, "char_count": 123, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:33.621867", "source": { "split": "train_shard_00002", "doc_id": 353 }, "chunk_id": "train_shard_00002_353_1", "global_id": 13203 }, { "text": "Avian pathogenic Escherichia coli (APEC) causes respiratory and systemic disease in poultry. Sequencing of a multilocus sequence type 95 (ST95) serogroup O1 strain previously indicated that APEC resembles E. coli causing extraintestinal human diseases. We sequenced the genomes of two strains of another dominant APEC lineage (ST23 serogroup O78 strains χ7122 and IMT2125) and compared them to each other and to the reannotated APEC O1 sequence. For comparison, we also sequenced a human enterotoxigenic E. coli (ETEC) strain of the same ST23 serogroup O78 lineage. Phylogenetic analysis indicated that the APEC O78 strains were more closely related to human ST23 ETEC than to APEC O1, indicating that separation of pathotypes on the basis of their extraintestinal or diarrheagenic nature is not supported by their phylogeny. The accessory genome of APEC ST23 strains exhibited limited conservation of APEC O1 genomic islands and a distinct repertoire of virulence-associated loci. In light of this diversity, we surveyed the phenotype of 2,185 signature-tagged transposon mutants of χ7122 following intra-air sac inoculation of turkeys. This procedure identified novel APEC ST23 genes that play strain- and tissue-specific roles during infection. For example, genes mediating group 4 capsule synthesis were required for the virulence of χ7122 and were conserved in IMT2125 but absent from APEC O1. Our data reveal the genetic diversity of E. coli strains adapted to cause the same avian disease and indicate that the core genome of the ST23 lineage serves as a chassis for the evolution of E. coli strains adapted to cause avian or human disease via acquisition of distinct virulence genes.", "token_count": 474, "char_count": 1691, "word_count": 260, "semantic_coherence": 1, "information_density": 0.5731, "quality_score": 0.7865, "entities": { "genes": [ "ST95", "ST23", "IMT2125" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:34.263299", "source": { "split": "train_shard_00002", "doc_id": 354 }, "chunk_id": "train_shard_00002_354_0", "global_id": 13204 }, { "text": "Sequencing and functional annotation of avian pathogenic Escherichia coli serogroup O78 strains reveal the evolution of E. coli lineages pathogenic for poultry via distinct mechanisms.", "token_count": 48, "char_count": 184, "word_count": 25, "semantic_coherence": 1, "information_density": 0.88, "quality_score": 0.94, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:34.624387", "source": { "split": "train_shard_00002", "doc_id": 354 }, "chunk_id": "train_shard_00002_354_1", "global_id": 13205 }, { "text": "Reasons for the rising clinical impact of the bacterium Enterococcus faecium include the species’ rapid acquisition of adaptive genetic elements. Here, we focused on the impact of recombination on the evolution of E. faecium. We used the recently developed BratNextGen algorithm to detect recombinant regions in the core genome of 34 E. faecium strains, including three newly sequenced clinical strains. Recombination was found to have a significant impact on the E. faecium genome: of the original 1.2 million positions in the core genome, 0.5 million were predicted to have been affected by recombination in at least one strain. Importantly, strains in one of the two major E. faecium clades (clade B), which contains most of the E. faecium human gut commensals, formed the most important reservoir for donating foreign DNA to the second major E. faecium clade (clade A), which contains most of the clinical isolates. Also, several genomic regions were found to mainly recombine in specific hospital-associated E. faecium strains. One of these regions (the epa-like locus) likely encodes the biosynthesis of cell wall polysaccharides. These findings suggest a crucial role for recombination in the emergence of E. faecium as a successful hospital-associated pathogen.\n\nRecent Recombination Events in the Core Genome Are Associated with Adaptive Evolution in Enterococcus faecium", "token_count": 343, "char_count": 1380, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5619, "quality_score": 0.781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:35.198834", "source": { "split": "train_shard_00002", "doc_id": 355 }, "chunk_id": "train_shard_00002_355_0", "global_id": 13206 }, { "text": "An investigation of the pectinolytic enzyme system of Kluyveromyces marxianus", "token_count": 24, "char_count": 77, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:35.561676", "source": { "split": "train_shard_00002", "doc_id": 356 }, "chunk_id": "train_shard_00002_356_0", "global_id": 13207 }, { "text": "PCR/RFLP of the NTS2 (IGS2) of rDNA was applied to differentiate two closely related yeast species, Kluyveromyces lactis var. lactis (referred to as K. lactis) and K. marxianus. Using specific primers, the NTS2 region was amplified from DNA of both K. lactis and K. marxianus type and collection strains. AluI restriction of amplified fragments generated patterns characteristic for each species. The NTS2 region from K. lactis var. drosophilarum and related species K. aestuarii, K. africanus, K. dobzhanskii, and K. wickerhamii could also be amplified with the same primers, but AluI patterns generated were clearly different. PCR/RFLP of the NTS2 appears thus to be a convenient method for rapid identification of K. lactis and K. marxianus, frequently found in dairy products. This test was validated therefore on K. lactis and K. marxianus from natural habitats. We showed that all yeast strains collected from whey samples and scoring blue on X-gal glucose plates were either K. lactis or K. marxianus. For application purposes, we propose here an approach for quickly screening for K. lactis/marxianus and Saccharomyces cerevisiae in dairy products using X-gal coloured and lysine growth media.\n\nRapid differentiation of the closely related Kluyveromyces lactis var. lactis and K. marxianus strains isolated from dairy products using selective media and PCR/RFLP of the rDNA non transcribed spacer 2.", "token_count": 401, "char_count": 1407, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5535, "quality_score": 0.7767, "entities": { "genes": [ "IGS2", "NTS2" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:36.175637", "source": { "split": "train_shard_00002", "doc_id": 357 }, "chunk_id": "train_shard_00002_357_0", "global_id": 13208 }, { "text": "

Unlabelled

A methicillin-resistant Staphylococcus aureus (MRSA) clone known as ST398 has emerged as a major cause of acute infections in individuals who have close contact with livestock. More recently, the emergence of an animal-independent ST398 methicillin-sensitive S. aureus (MSSA) clone has been documented in several countries. However, the limited surveillance of MSSA has precluded an accurate assessment of the global spread of ST398 and its clinical relevance. Here we provide evidence that ST398 is a frequent source of MSSA infections in northern Manhattan and is readily transmitted between individuals in households. This contrasts with the limited transmissibility of livestock-associated ST398 (LA-ST398) MRSA strains between humans. Our whole-genome sequence analysis revealed that the chromosome of the human-associated ST398 MSSA clone is smaller than that of the LA-ST398 MRSA reference strain S0385, due mainly to fewer mobile genetic elements (MGEs). In contrast, human ST398 MSSA isolates harbored the prophage ϕ3 and the human-specific immune evasion cluster (IEC) genes chp and scn. While most of the core genome was conserved between the human ST398 MSSA clone and S0385, these strains differed substantially in their repertoire and composition of intact adhesion genes. These genetic changes were associated with significantly enhanced adhesion of human ST398 MSSA isolates to human skin keratinocytes and keratin. We propose that the human ST398 MSSA clone can spread independent of animal contact using an optimized repertoire of MGEs and adhesion molecules adapted to transmission among humans.

Importance

Staphylococcus aureus strains have generally been considered to be species specific. However, cross-species transfers of S. aureus clones, such as ST398 methicillin-resistant S. aureus (MRSA), from swine to humans have been reported", "token_count": 504, "char_count": 1884, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:36.835486", "source": { "split": "train_shard_00002", "doc_id": 358 }, "chunk_id": "train_shard_00002_358_0", "global_id": 13209 }, { "text": "Recently, we observed the emergence of ST398 methicillin-susceptible S. aureus (MSSA) as a colonizing strain of humans in northern Manhattan. Here we report that ST398 is a frequent cause of MSSA infections in this urban setting. The ST398 MSSA clone was readily transmitted within households, independent of animal contact. We discovered that human ST398 MSSA genomes were smaller than that of the LA-ST398 strain S0385 due to fewer mobile genetic elements. Human and LA-ST398 strains also differed in their composition of adhesion genes and their ability to bind to human skin keratinocytes, providing a potential mechanism of S. aureus host adaptation. Our findings illustrate the importance of implementing molecular surveillance of MSSA given the evidence for the rapid and clinically undetected spread of ST398 MSSA.\n\nIdentification of a highly transmissible animal-independent Staphylococcus aureus ST398 clone with distinct genomic and cell adhesion properties.", "token_count": 247, "char_count": 969, "word_count": 142, "semantic_coherence": 1, "information_density": 0.669, "quality_score": 0.8345, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:37.317161", "source": { "split": "train_shard_00002", "doc_id": 358 }, "chunk_id": "train_shard_00002_358_1", "global_id": 13210 }, { "text": "

ABSTRACT

Recombination is one of the most important mechanisms of prokaryotic species evolution but its exact roles are still in debate. Here we try to infer genome-wide recombination events within a species uti-lizing a dataset of 104 complete genomes of Escherichia coli from diverse origins, among which 45 from world-wide animal-hosts are in-house sequenced using SMRT (single-molecular real time) technology.Two major clades are identified based on evidences of ecological and physiological characteristics, as well as distinct genomic features implying scarce inter-clade genetic exchange. By comparing the synteny of identical fragments genome-widely searched for each genome pair, we achieve a fine-scale map of re-combination within the population. The recombination is rather extensive within clade, which is able to break linkages between genes but does not interrupt core genome framework and primary metabolic port-folios possibly due to natural selection for physiological compatibility and ecological fitness. Meanwhile,the recombination between clades declines drastically as the phylogenetic distance increases, generally 10-fold reduced than those of the intra-clade, which establishes genetic barrier between clades. These empirical data of recombination suggest its critical role in the early stage of speciation, where recombina-tion rate differs according to phylogentic distance. The extensive intra-clade recombination coheres sister strains into a quasi-sexual group and optimizes genes or alleles to streamline physiological activities,whereas shapely declined inter-clade recombination split the population into clades adaptive to divergent ecological niches.

Significance Statement

Roles of recombination in species evolution have been debated for decades due to difficulties in inferring recombination events during the early stage of speciation, especially when recombination is always complicated by frequent gene transfer events of bacterial genomes. Based on 104 high-quality complete E. coli genomes, we infer gene-centric dynamics of recombination in the formation of two E", "token_count": 493, "char_count": 2126, "word_count": 285, "semantic_coherence": 1, "information_density": 0.6526, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:37.976294", "source": { "split": "train_shard_00002", "doc_id": 359 }, "chunk_id": "train_shard_00002_359_0", "global_id": 13211 }, { "text": "coli clades or subpopulations, and recombination is found to be rather intensive in a within-clade fashion, which forces them to be quasi-sexual. The recombination events can be mapped among individual genomes in the context of genes and their variations; decreased between-clade and increased intra-claderecombination engender a genetic barrier that further encourages clade-specific secondary metabolic portfolios for better environmental adaptation. Recombination is thus a major force that accelerates bacterial evolution to fit ecological diversity.\n\nGene-centric intra- and inter-clade recombination in a context ofEsche-richia colisubpopulations", "token_count": 158, "char_count": 659, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7711, "quality_score": 0.8855, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:38.411722", "source": { "split": "train_shard_00002", "doc_id": 359 }, "chunk_id": "train_shard_00002_359_1", "global_id": 13212 }, { "text": "Carbapenem-resistant Enterobacteriaceae have been a global public health issue in recent years. Here, a carbapenem-resistant Kluyvera cryocrescens strain SCW13 was isolated from hospital sewage, and was then subjected to whole-genome sequencing (WGS). Based on WGS data, antimicrobial resistance genes were identified. Resistance plasmids were completely circularized and further bioinformatics analyses of plasmids were performed. A conjugation assay was performed to identify a self-transmissible plasmid mediating carbapenem resistance. A phylogenetic tree was constructed based on the core genome of publicly available Kluyvera strains. The isolate SCW13 exhibited resistance to cephalosporin and carbapenem. blaNDM-1 was found to be located on a ~53-kb self-transmissible IncX3 plasmid, which exhibited high similarity to the previously reported pNDM-HN380, which is an epidemic blaNDM-1-carrying IncX3 plasmid. Further, we found that SCW13 contained a chromosomal blaKLUC-2 gene, which was the probable origin of the plasmid-born blaKLUC-2 found in Enterobacter cloacae. Phylogenetic analysis showed that K. cryocrescens SCW13 exhibited a close relationship with K. cryocrescens NCTC10483. These findings highlight the further dissemination of blaNDM through clonal IncX3 plasmids related to pNDM-HN380 among uncommon Enterobacteriaceae strains, including Kluyvera in this case.", "token_count": 506, "char_count": 1530, "word_count": 181, "semantic_coherence": 1, "information_density": 0.6685, "quality_score": 0.8343, "entities": { "genes": [ "SCW13", "NCTC10483", "HN380" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:39.081218", "source": { "split": "train_shard_00002", "doc_id": 360 }, "chunk_id": "train_shard_00002_360_0", "global_id": 13213 }, { "text": "Characterization of a Carbapenem-Resistant Kluyvera Cryocrescens Isolate Carrying Blandm-1 from Hospital Sewage.", "token_count": 54, "char_count": 137, "word_count": 12, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:39.478295", "source": { "split": "train_shard_00002", "doc_id": 360 }, "chunk_id": "train_shard_00002_360_1", "global_id": 13214 }, { "text": "Genotype-fitness maps of evolution have been well characterized for biological components, such as RNA and proteins, but remain less clear for systems-level properties, such as those of metabolic and transcriptional regulatory networks. Here, we take multi-omics measurements of 6 different E. coli strains throughout adaptive laboratory evolution (ALE) to maximal growth fitness. The results show the following: (i) convergence in most overall phenotypic measures across all strains, with the notable exception of divergence in NADPH production mechanisms; (ii) conserved transcriptomic adaptations, describing increased expression of growth promoting genes but decreased expression of stress response and structural components; (iii) four groups of regulatory trade-offs underlying the adjustment of transcriptome composition; and (iv) correlates that link causal mutations to systems-level adaptations, including mutation-pathway flux correlates and mutation-transcriptome composition correlates. We thus show that fitness landscapes for ALE can be described with two layers of causation: one based on system-level properties (continuous variables) and the other based on mutations (discrete variables). IMPORTANCE Understanding the mechanisms of microbial adaptation will help combat the evolution of drug-resistant microbes and enable predictive genome design. Although experimental evolution allows us to identify the causal mutations underlying microbial adaptation, it remains unclear how causal mutations enable increased fitness and is often explained in terms of individual components (i.e., enzyme rate) as opposed to biological systems (i.e., pathways). Here, we find that causal mutations in E. coli are linked to systems-level changes in NADPH balance and expression of stress response genes. These systems-level adaptation patterns are conserved across diverse E. coli strains and thus identify cofactor balance and proteome reallocation as dominant constraints governing microbial adaptation.\n\nExperimental Evolution Reveals Unifying Systems-Level Adaptations but Diversity in Driving Genotypes.", "token_count": 447, "char_count": 2119, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:40.133920", "source": { "split": "train_shard_00002", "doc_id": 361 }, "chunk_id": "train_shard_00002_361_0", "global_id": 13215 }, { "text": "The use of a proper signal sequence is one of the major determinants for the efficient secretion of heterologous proteins from yeast. The signal sequence derived from inulinase (INU1A) of Kluyveromyces marxianus was evaluated in directing the secretion of a human glycoprotein, alpha 1-antitrypsin (alpha 1-AT), from Saccharomyces cerevisiae. A yeast expression vector for alpha 1-AT was constructed by placing the coding sequence of human alpha 1-AT fused with the INU1A signal sequence downstream of the GAL10 promoter. S. cerevisiae transformants harboring the expression vector secreted about 70% of the total alpha 1-AT synthesized into the culture media. The intracellularly retained form of alpha 1-AT was mostly unglycosylated, whereas the secreted protein had high mannose-type glycosylation. The fed-batch cultivation of the recombinant yeast achieved a high-cell density, leading to the secretion of biologically active alpha 1-AT up to 75 mg l-1. The secreted protein was purified and subjected to N-terminal sequencing, which confirmed that the secreted alpha 1-AT was processed correctly at the Kex2 cleavage site as expected from the sequence of INU1A signal peptide. The results suggest that the inulinase signal sequence is useful for the high-level secretion of relatively large glycoproteins, such as human alpha 1-AT, from S. cerevisiae.\n\nHigh-level secretion of human alpha 1-antitrypsin from Saccharomyces cerevisiae using inulinase signal sequence.", "token_count": 399, "char_count": 1471, "word_count": 214, "semantic_coherence": 1, "information_density": 0.5327, "quality_score": 0.7664, "entities": { "genes": [ "GAL10", "INU1A" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:40.782136", "source": { "split": "train_shard_00002", "doc_id": 362 }, "chunk_id": "train_shard_00002_362_0", "global_id": 13216 }, { "text": "Legionella pneumophila grows within membrane-bound vacuoles in phylogenetically diverse hosts. Intracellular growth requires the function of the Icm/Dot type-IVb secretion system, which translocates more than 300 proteins into host cells. A screen was performed to identify L. pneumophila proteins that stimulate mitogen-activated protein kinase (MAPK) activation, using Icm/Dot translocated proteins ectopically expressed in mammalian cells. In parallel, a second screen was performed to identify L. pneumophila proteins expressed in yeast that cause growth inhibition in MAPK pathway-stimulatory high-osmolarity medium. LegA7 was shared in both screens, a protein predicted to be a member of the bacterial cysteine protease family that has five carboxyl-terminal ankyrin repeats. Three conserved residues in the predicted catalytic triad of LegA7 were mutated. These mutations abolished the ability of LegA7 to inhibit yeast growth. To identify other residues important for LegA7 function, a generalizable selection strategy in yeast was devised to isolate mutants that have lost function and no longer cause growth inhibition on a high-osmolarity medium. Mutations were isolated in the two carboxyl-terminal ankyrin repeats, as well as an inter-domain region located between the cysteine protease domain and the ankyrin repeats. These mutations were predicted by AlphaFold modeling to localize to the face opposite from the catalytic site, arguing that they interfere with the positive regulation of the catalytic activity. Based on our data, we present a model in which LegA7 harbors a cysteine protease domain with an inter-domain and two carboxyl-terminal ankyrin repeat regions that modulate the function of the catalytic domain.

Importance

Legionella pneumophila grows in a membrane-bound compartment in macrophages during disease. Construction of the compartment requires a dedicated secretion system that translocates virulence proteins into host cells", "token_count": 516, "char_count": 1997, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5421, "quality_score": 0.7711, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:03:41.442991", "source": { "split": "train_shard_00002", "doc_id": 363 }, "chunk_id": "train_shard_00002_363_0", "global_id": 13217 }, { "text": "One of these proteins, LegA7, is shown to activate a stress response pathway in host cells called the mitogen-activated protein kinase (MAPK) pathway. The effects on the mammalian MAPK pathway were reconstructed in yeast, allowing the development of a strategy to identify the role of individual domains of LegA7. A domain similar to cysteine proteases is demonstrated to be critical for impinging on the MAPK pathway, and the catalytic activity of this domain is required for targeting this path. In addition, a conserved series of repeats, called ankyrin repeats, controls this activity. Data are provided that argue the interaction of the ankyrin repeats with unknown targets probably results in activation of the cysteine protease domain.\n\nGenetic evidence for a regulated cysteine protease catalytic triad in LegA7, a Legionella pneumophila protein that impinges on a stress response pathway.", "token_count": 226, "char_count": 904, "word_count": 137, "semantic_coherence": 1, "information_density": 0.6131, "quality_score": 0.8066, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:41.904562", "source": { "split": "train_shard_00002", "doc_id": 363 }, "chunk_id": "train_shard_00002_363_1", "global_id": 13218 }, { "text": "

Background

Shigella is a major diarrheal pathogen for which there is presently no vaccine. Whole genome sequencing provides the ability to predict and derive novel antigens for use as vaccines. Here, we aimed to identify novel immunogenic Shigella antigens that could serve as Shigella vaccine candidates, either alone, or when conjugated to Shigella O-antigen.

Methods

Using a reverse vaccinology approach, where genomic analysis informed the Shigella immunome via an antigen microarray, we aimed to identify novel immunogenic Shigella antigens. A core genome analysis of Shigella species, pathogenic and non-pathogenic Escherichia coli, led to the selection of 234 predicted immunogenic Shigella antigens. These antigens were expressed and probed with acute and convalescent serum from microbiologically confirmed Shigella infections.

Results

Several Shigella antigens displayed IgG and IgA seroconversion, with no difference in sero-reactivity across by sex or age. IgG sero-reactivity to key Shigella antigens was observed at birth, indicating transplacental antibody transfer. Six antigens (FepA, EmrK, FhuA, MdtA, NlpB, and CjrA) were identified in in vivo testing as capable of producing binding IgG and complement-mediated bactericidal antibody.

Conclusions

These findings provide six novel immunogenic Shigella proteins that could serve as candidate vaccine antigens, species-specific carrier proteins, or targeted adjuvants.\n\nThe identification of novel immunogenic antigens as potential Shigella vaccine components.", "token_count": 425, "char_count": 1555, "word_count": 201, "semantic_coherence": 1, "information_density": 0.6418, "quality_score": 0.8209, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:42.524836", "source": { "split": "train_shard_00002", "doc_id": 364 }, "chunk_id": "train_shard_00002_364_0", "global_id": 13219 }, { "text": "Fresh and cooked agave, Drosophila spp., processing equipment, agave molasses, agave extract, and fermenting must at a traditional tequila distillery (Herradura, Amatitan, Jalisco, México) were studied to gain insight on the origin of yeasts involved in a natural tequila fermentations. Five yeast communities were identified. (1) Fresh agave contained a diverse mycobiota dominated by Clavispora lusitaniae and an endemic species, Metschnikowia agaveae. (2) Drosophila spp. from around or inside the distillery yielded typical fruit yeasts, in particular Hanseniaspora spp., Pichia kluyveri, and Candida krusei. (3) Schizosaccharomyces pombe prevailed in molasses. (4) Cooked agave and extract had a considerable diversity of species, but included Saccharomyces cerevisiae. (5) Fermenting juice underwent a gradual reduction in yeast heterogeneity. Torulaspora delbrueckii, Kluyveromyces marxianus, and Hanseniaspora spp. progressively ceded the way to S. cerevisiae, Zygosaccharomyces bailii, Candida milleri, and Brettanomyces spp. With the exception of Pichia membranaefaciens, which was shared by all communities, little overlap existed. That separation was even more manifest when species were divided into distinguishable biotypes based on morphology or physiology. It is concluded that crushing equipment and must holding tanks are the main source of significant inoculum for the fermentation process. Drosophila species appear to serve as internal vectors. Proximity to fruit trees probably contributes to maintaining a substantial Drosophila community, but the yeasts found in the distillery exhibit very little similarity to those found in adjacent vegetation. Interactions involving killer toxins had no apparent direct effects on the yeast community structure.\n\nYeast communities in a natural tequila fermentation.", "token_count": 471, "char_count": 1827, "word_count": 248, "semantic_coherence": 1, "information_density": 0.6935, "quality_score": 0.8468, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:43.168000", "source": { "split": "train_shard_00002", "doc_id": 365 }, "chunk_id": "train_shard_00002_365_0", "global_id": 13220 }, { "text": "

Objectives

CARB-ES-19 is a comprehensive, multicenter, nationwide study integrating whole-genome sequencing (WGS) in the surveillance of carbapenemase-producing K. pneumoniae (CP-Kpn) and E. coli (CP-Eco) to determine their incidence, geographical distribution, phylogeny, and resistance mechanisms in Spain.

Methods

In total, 71 hospitals, representing all 50 Spanish provinces, collected the first 10 isolates per hospital (February to May 2019); CPE isolates were first identified according to EUCAST (meropenem MIC > 0.12 mg/L with immunochromatography, colorimetric tests, carbapenem inactivation, or carbapenem hydrolysis with MALDI-TOF). Prevalence and incidence were calculated according to population denominators. Antibiotic susceptibility testing was performed using the microdilution method (EUCAST). All 403 isolates collected were sequenced for high-resolution single-nucleotide polymorphism (SNP) typing, core genome multilocus sequence typing (cgMLST), and resistome analysis.

Results

In total, 377 (93.5%) CP-Kpn and 26 (6.5%) CP-Eco isolates were collected from 62 (87.3%) hospitals in 46 (92%) provinces. CP-Kpn was more prevalent in the blood (5.8%, 50/853) than in the urine (1.4%, 201/14,464). The cumulative incidence for both CP-Kpn and CP-Eco was 0.05 per 100 admitted patients", "token_count": 443, "char_count": 1338, "word_count": 166, "semantic_coherence": 1, "information_density": 0.7651, "quality_score": 0.8825, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:43.799015", "source": { "split": "train_shard_00002", "doc_id": 366 }, "chunk_id": "train_shard_00002_366_0", "global_id": 13221 }, { "text": "The main carbapenemase genes identified in CP-Kpn were bla OXA-48 (263/377), bla KPC-3 (62/377), bla VIM-1 (28/377), and bla NDM-1 (12/377). All isolates were susceptible to at least two antibiotics. Interregional dissemination of eight high-risk CP-Kpn clones was detected, mainly ST307/OXA-48 (16.4%), ST11/OXA-48 (16.4%), and ST512-ST258/KPC (13.8%). ST512/KPC and ST15/OXA-48 were the most frequent bacteremia-causative clones. The average number of acquired resistance genes was higher in CP-Kpn (7.9) than in CP-Eco (5.5).

Conclusion

This study serves as a first step toward WGS integration in the surveillance of carbapenemase-producing Enterobacterales in Spain. We detected important epidemiological changes, including increased CP-Kpn and CP-Eco prevalence and incidence compared to previous studies, wide interregional dissemination, and increased dissemination of high-risk clones, such as ST307/OXA-48 and ST512/KPC-3.\n\nCARB-ES-19 Multicenter Study of Carbapenemase-Producing Klebsiella pneumoniae and Escherichia coli From All Spanish Provinces Reveals Interregional Spread of High-Risk Clones Such as ST307/OXA-48 and ST512/KPC-3.", "token_count": 487, "char_count": 1238, "word_count": 145, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.831, "entities": { "genes": [ "ST307", "ST11", "ST15", "ST258", "ST512" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:44.440901", "source": { "split": "train_shard_00002", "doc_id": 366 }, "chunk_id": "train_shard_00002_366_1", "global_id": 13222 }, { "text": "

Background

Necrotizing enterocolitis (NEC) is a devastating gastrointestinal disease with high morbidity and mortality that predominantly affects preterm neonates during outbreaks. In a previous study, the present authors identified 15 Clostridium butyricum isolates from stool samples during a series of NEC cases involving four neonatal intensive care units. A clonal lineage of these strains was observed by in-silico multi-locus sequence typing.

Aim

To confirm the previous findings by sequencing a larger number of C. butyricum genomes and using other genotyping approaches.

Methods

The previously isolated 15 C. butyricum strains were characterized and compared with 17 other commensal and environmental C. butyricum strains using whole-genome sequencing (WGS). In addition, the clustering was analysed using multi-spacer sequence typing (MST).

Findings

The core genome of C. butyricum was composed of 1251 genes, and its pan-genome consisted of 12,628 genes with high variability between strains. It was possible to distinguish the clonal lineage of strains from a series of NEC cases, forming three clades with geographical clustering. The results obtained using WGS and MST approaches were congruent.

Conclusion

MST is a fast, cheap and effective genotyping method for investigating NEC outbreaks associated with C. butyricum.\n\nMulti-spacer typing as an effective method to distinguish the clonal lineage of Clostridium butyricum strains isolated from stool samples during a series of necrotizing enterocolitis cases.", "token_count": 424, "char_count": 1562, "word_count": 208, "semantic_coherence": 1, "information_density": 0.5962, "quality_score": 0.7981, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:45.070277", "source": { "split": "train_shard_00002", "doc_id": 367 }, "chunk_id": "train_shard_00002_367_0", "global_id": 13223 }, { "text": "

Background

Members of the genus Cronobacter are causes of rare but severe illness in neonates and preterm infants following the ingestion of contaminated infant formula. Seven species have been described and two of the species genomes were subsequently published. In this study, we performed comparative genomics on eight strains of Cronobacter, including six that we sequenced (representing six of the seven species) and two previously published, closed genomes.

Results

We identified and characterized the features associated with the core and pan genome of the genus Cronobacter in an attempt to understand the evolution of these bacteria and the genetic content of each species. We identified 84 genomic regions that are present in two or more Cronobacter genomes, along with 45 unique genomic regions. Many potentially horizontally transferred genes, such as lysogenic prophages, were also identified. Most notable among these were several type six secretion system gene clusters, transposons that carried tellurium, copper and/or silver resistance genes, and a novel integrative conjugative element.

Conclusions

Cronobacter have diverged into two clusters, one consisting of C. dublinensis and C. muytjensii (Cdub-Cmuy) and the other comprised of C. sakazakii, C. malonaticus, C. universalis, and C. turicensis, (Csak-Cmal-Cuni-Ctur) from the most recent common ancestral species. While several genetic determinants for plant-association and human virulence could be found in the core genome of Cronobacter, the four Cdub-Cmuy clade genomes contained several accessory genomic regions important for survival in a plant-associated environmental niche, while the Csak-Cmal-Cuni-Ctur clade genomes harbored numerous virulence-related genetic traits.\n\nPan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation.", "token_count": 481, "char_count": 1925, "word_count": 259, "semantic_coherence": 1, "information_density": 0.6564, "quality_score": 0.8282, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:45.718455", "source": { "split": "train_shard_00002", "doc_id": 368 }, "chunk_id": "train_shard_00002_368_0", "global_id": 13224 }, { "text": "

Background

Members of Comamonas testosteroni are environmental microorganisms that are usually found in polluted environment samples. They utilize steroids and aromatic compounds but rarely sugars, and show resistance to multiple heavy metals and multiple drugs. However, comprehensive genomic analysis among the C. testosteroni strains is lacked.

Results

To understand the genome bases of the features of C. testosteroni, we sequenced 10 strains of this species and analyzed them together with other related published genome sequences. The results revealed that: 1) the strains of C. testosteroni have genome sizes ranging from 5.1 to 6.0 Mb and G + C contents ranging from 61.1% to 61.8%. The pan-genome contained 10,165 gene families and the core genome contained 3,599 gene families. Heap's law analysis indicated that the pan-genome of C. testosteroni may be open (α = 0.639); 2) by analyzing 31 phenotypes of 11 available C. testosteroni strains, 99.4% of the genotypes (putative genes) were found to be correlated to the phenotypes, indicating a high correlation between phenotypes and genotypes; 3) gene clusters for nitrate reduction, steroids degradation and metal and multi-drug resistance were found and were highly conserved among all the genomes of this species; 4) the genome similarity of C. testosteroni may be related to the geographical distances.

Conclusions

This work provided an overview on the genomes of C. testosteroni and new genome resources that would accelerate the further investigations of this species. Importantly, this work focused on the analysis of potential genetic determinants for the typical characters and found high correlation between the phenotypes and their corresponding genotypes.\n\nHigh correlation between genotypes and phenotypes of environmental bacteria Comamonas testosteroni strains.", "token_count": 481, "char_count": 1858, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5811, "quality_score": 0.7906, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:46.370432", "source": { "split": "train_shard_00002", "doc_id": 369 }, "chunk_id": "train_shard_00002_369_0", "global_id": 13225 }, { "text": "

Background

Corynebacterium pseudotuberculosis biovar ovis is a facultative intracellular pathogen, and the etiological agent of caseous lymphadenitis in small ruminants. During the infection process, the bacterium is subjected to several stress conditions, including nitrosative stress, which is caused by nitric oxide (NO). In silico analysis of the genome of C. pseudotuberculosis ovis 1002 predicted several genes that could influence the resistance of this pathogen to nitrosative stress. Here, we applied high-throughput proteomics using high definition mass spectrometry to characterize the functional genome of C. pseudotuberculosis ovis 1002 in the presence of NO-donor Diethylenetriamine/nitric oxide adduct (DETA/NO), with the aim of identifying proteins involved in nitrosative stress resistance.

Results

We characterized 835 proteins, representing approximately 41% of the predicted proteome of C. pseudotuberculosis ovis 1002, following exposure to nitrosative stress. In total, 102 proteins were exclusive to the proteome of DETA/NO-induced cells, and a further 58 proteins were differentially regulated between the DETA/NO and control conditions. An interactomic analysis of the differential proteome of C. pseudotuberculosis in response to nitrosative stress was also performed. Our proteomic data set suggested the activation of both a general stress response and a specific nitrosative stress response, as well as changes in proteins involved in cellular metabolism, detoxification, transcriptional regulation, and DNA synthesis and repair.

Conclusions

Our proteomic analysis validated previously-determined in silico data for C. pseudotuberculosis ovis 1002. In addition, proteomic screening performed in the presence of NO enabled the identification of a set of factors that can influence the resistance and survival of C. pseudotuberculosis during exposure to nitrosative stress.", "token_count": 482, "char_count": 1922, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5516, "quality_score": 0.7758, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:47.017191", "source": { "split": "train_shard_00002", "doc_id": 370 }, "chunk_id": "train_shard_00002_370_0", "global_id": 13226 }, { "text": "Label-free proteomic analysis to confirm the predicted proteome of Corynebacterium pseudotuberculosis under nitrosative stress mediated by nitric oxide.", "token_count": 37, "char_count": 152, "word_count": 18, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:47.381237", "source": { "split": "train_shard_00002", "doc_id": 370 }, "chunk_id": "train_shard_00002_370_1", "global_id": 13227 }, { "text": "The new paradigm in genetics is more sequence analysis driven, but linkage studies are frequently adopted in parallel to pinpoint loci of interest within the vast torrent of sequence data. Linkage analysis alone can identify a single causative gene under the scope of a rare disease model for the relatively low cost of a genotyping array, and has the added advantage of reconstituting genotypes of individuals absent from the analysis via haplotype reconstruction. Here we present our comprehensive linkage analysis pipeline consisting of a collection of well-established tools and utilities (GRR, Merlin, Alohomora) to perform analysis under all penetrance models (dominant/recessive, autosomal/X-linked) as well as large complex consanguineous pedigrees. Pre-analysis filtering selects a subset of markers indicative of informative meioses, and qualitative tests are performed to check for gender, relationship, and Mendelian inheritance consistency. A reliable lineup of linkage analysis suites (Allegro, GeneHunter, Simwalk) compute LOD scores to produce fast multi-core genome-wide and chromosome-specific linkage plots complete with sub-banding overlays and peak validation. Limitations in pedigree creation and post-analysis ... (continues)\n\nHigh-throughput linkage analysis pipeline", "token_count": 297, "char_count": 1291, "word_count": 175, "semantic_coherence": 1, "information_density": 0.7257, "quality_score": 0.8629, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:47.942086", "source": { "split": "train_shard_00002", "doc_id": 371 }, "chunk_id": "train_shard_00002_371_0", "global_id": 13228 }, { "text": "Candida kefyr DSM 70106 was cultivated in a medium containing inulin as a carbon source. About 92% of the inulinase was recovered directly from the medium. Different concentration (C(f)) and enrichment (E(f)) factors were obtained, using the following methods: Cross-flow filtration (microfiltration and cell diafiltration were carried out using a rotary filter; enzyme ultrafiltration and diafiltration were performed using a cassette module): C(f) = 7.5 and E(f) = 2.2; liquid-liquid extraction of N-Benzyl-N-Dodecyl-N-bis[2-hydroxyethyl] ammonium chloride (BDBAC) reversed micelles: C(f) = 2.5 and E(f) = 2.7; and expanded-bed adsorption: C(f) = 2.8 and E(f) = 4.3.\n\nDownstream processing of inulinase. Comparison of different techniques.", "token_count": 250, "char_count": 741, "word_count": 103, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8544, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:48.435500", "source": { "split": "train_shard_00002", "doc_id": 372 }, "chunk_id": "train_shard_00002_372_0", "global_id": 13229 }, { "text": "

Background

Streptomyces are widespread bacteria that contribute to the terrestrial carbon cycle and produce the majority of clinically useful antibiotics. While interspecific genomic diversity has been investigated among Streptomyces, information is lacking on intraspecific genomic diversity. Streptomyces pratensis has high rates of homologous recombination but the impact of such gene exchange on genome evolution and the evolution of natural product gene clusters remains uncharacterized.

Results

We report draft genome sequences of four S. pratensis strains and compare to the complete genome of Streptomyces flavogriseus IAF-45-CD (=ATCC 33331), a strain recently reclassified to S. pratensis. Despite disparate geographic origins, the genomes are highly similar with 85.9% of genes present in the core genome and conservation of all natural product gene clusters. Natural products include a novel combination of carbapenem and beta-lactamase inhibitor gene clusters. While high intraspecies recombination rates abolish the phylogenetic signal across the genome, intraspecies recombination is suppressed in two genomic regions. The first region is centered on an insertion/deletion polymorphism and the second on a hybrid NRPS-PKS gene. Finally, two gene families accounted for over 25% of the divergent genes in the core genome. The first includes homologs of bldB (required for spore development and antibiotic production) while the second includes homologs of an uncharacterized protein with a helix-turn-helix motif (hpb). Genes from these families co-occur with fifteen pairs spread across the genome. These genes have evidence for co-evolution of co-localized pairs, supporting previous assertions that these genes may function akin to a toxin-antitoxin system.

Conclusions

S. pratensis genomes are highly similar with exceptional levels of recombination which erase phylogenetic signal among strains of the species. This species has a large core genome and variable terminal regions that are smaller than those found in interspecies comparisons", "token_count": 505, "char_count": 2079, "word_count": 283, "semantic_coherence": 1, "information_density": 0.5901, "quality_score": 0.7951, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:49.086339", "source": { "split": "train_shard_00002", "doc_id": 373 }, "chunk_id": "train_shard_00002_373_0", "global_id": 13230 }, { "text": "There is no geographic differentiation between these strains, but there is evidence for local linkage disequilibrium affecting two genomic regions. We have also shown further observational evidence that the DUF397-HTH (bldB and hpb) are a novel toxin-antitoxin pair.\n\nIntraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin.", "token_count": 106, "char_count": 432, "word_count": 58, "semantic_coherence": 1, "information_density": 0.8621, "quality_score": 0.931, "entities": { "genes": [ "DUF397" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:49.469195", "source": { "split": "train_shard_00002", "doc_id": 373 }, "chunk_id": "train_shard_00002_373_1", "global_id": 13231 }, { "text": "

Background

Many of the bacterial genomic studies exploring evolution processes of the host adaptation focus on the accessory genome describing how the gains and losses of genes can explain the colonization of new habitats. Consequently, we developed a new approach focusing on the coregenome in order to describe the host adaptation of Salmonella serovars.

Methods

In the present work, we propose bioinformatic tools allowing (i) robust phylogenetic inference based on SNPs and recombination events, (ii) identification of fixed SNPs and InDels distinguishing homoplastic and non-homoplastic coregenome variants, and (iii) gene-ontology enrichment analyses to describe metabolic processes involved in adaptation of Salmonella enterica subsp. enterica to mammalian- (S. Dublin), multi- (S. Enteritidis), and avian- (S. Pullorum and S. Gallinarum) hosts.

Results

The 'VARCall' workflow produced a robust phylogenetic inference confirming that the monophyletic clade S. Dublin diverged from the polyphyletic clade S. Enteritidis which includes the divergent clades S. Pullorum and S. Gallinarum (i). The scripts 'phyloFixedVar' and 'FixedVar' detected non-synonymous and non-homoplastic fixed variants supporting the phylogenetic reconstruction (ii). The scripts 'GetGOxML' and 'EveryGO' identified representative metabolic pathways related to host adaptation using the first gene-ontology enrichment analysis based on bacterial coregenome variants (iii).

Conclusions

We propose in the present manuscript a new coregenome approach coupling identification of fixed SNPs and InDels with regards to inferred phylogenetic clades, and gene-ontology enrichment analysis in order to describe the adaptation of Salmonella serovars Dublin (i.e. mammalian-hosts), Enteritidis (i.e. multi-hosts), Pullorum (i.e. avian-hosts) and Gallinarum (i.e. avian-hosts) at the coregenome scale", "token_count": 509, "char_count": 1897, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5353, "quality_score": 0.7676, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:50.100601", "source": { "split": "train_shard_00002", "doc_id": 374 }, "chunk_id": "train_shard_00002_374_0", "global_id": 13232 }, { "text": "All these polyvalent Bioinformatic tools can be applied on other bacterial genus without additional developments.\n\nFirst gene-ontology enrichment analysis based on bacterial coregenome variants: insights into adaptations of Salmonella serovars to mammalian- and avian-hosts.", "token_count": 66, "char_count": 274, "word_count": 34, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:50.476161", "source": { "split": "train_shard_00002", "doc_id": 374 }, "chunk_id": "train_shard_00002_374_1", "global_id": 13233 }, { "text": "Staphylococcus aureus is a persistent companion bacterial species in one-third of humankind. Reservoirs include the nasal and nasopharyngeal cavities, skin, and gastrointestinal (GI) tract. Despite earlier claims that colonization of individuals is caused by clonal organisms, next-generation sequencing (NGS) has revealed that resident type heterogeneity is not exceptional. Carriage, whether overt or hidden, is correlated with a risk of autoinfection. In a recent article in mBio, it was shown that, based on staphylococcal genome sequencing, low-level GI persistence may cause long-term nosocomial outbreaks [L. Senn et al., 7(1):e02039-15, 2016, doi:10.1128/mBio.02039-15]. Institutional endemicity with methicillin-resistant S. aureus (MRSA) sequence type 228 (ST228) is shown to originate not from high-level nasal carriage or poor compliance with infection control practice but from low-grade asymptomatic GI colonization. This shows the power of NGS in elucidating staphylococcal epidemiology and, even more important, demonstrates that (drug-resistant) microorganisms may possess stealthy means of persistence. Identifying these persistence mechanisms is key to successful infection control.\n\nHidden Staphylococcus aureus Carriage: Overrated or Underappreciated?", "token_count": 363, "char_count": 1272, "word_count": 164, "semantic_coherence": 1, "information_density": 0.7805, "quality_score": 0.8902, "entities": { "genes": [ "ST228" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:51.085382", "source": { "split": "train_shard_00002", "doc_id": 375 }, "chunk_id": "train_shard_00002_375_0", "global_id": 13234 }, { "text": "Whole genome sequencing (WGS) can be used for molecular typing and characterisation of Mycobacterium tuberculosis complex (MTBC) strains. We evaluated the systematic use of a WGS-based approach for MTBC surveillance involving all European Union/European Economic Area (EU/EEA) countries and highlight the challenges and lessons learnt to be considered for the future development of a WGS-based surveillance system.WGS and epidemiological data of patients with rifampicin-resistant (RR) and multidrug-resistant (MDR) tuberculosis (TB) were collected from EU/EEA countries between January 2017 and December 2019. WGS-based genetic relatedness analysis was performed using a standardised approach including both core genome multilocus sequence typing (cgMLST) and single nucleotide polymorphism (SNP)-based calculation of distances on all WGS data that fulfilled minimum quality criteria to ensure data comparability.A total of 2218 RR/MDR-MTBC isolates were collected from 25 countries. Among these, 56 cross-border clusters with increased likelihood of recent transmission (≤5 SNPs distance) comprising 316 RR/MDR-MTBC isolates were identified. The cross-border clusters included between two and 30 resistant isolates from two to six countries, demonstrating different RR/MDR-TB transmission patterns in Western and Eastern EU countries.This pilot study shows that a WGS-based surveillance system is not only feasible but can efficiently elucidate the dynamics of in-country and cross-border RR/MDR-TB transmission across EU/EEA countries. Lessons learnt from this study highlight that the establishment of an EU/EEA centralised WGS-based surveillance system for TB will require strengthening of national integrated systems performing prospective WGS surveillance and the development of clear procedures to facilitate international collaboration for the investigation of cross-border clusters.\n\nUse of a whole genome sequencing-based approach for Mycobacterium tuberculosis surveillance in Europe in 2017-2019: an ECDC pilot study.", "token_count": 498, "char_count": 2044, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6255, "quality_score": 0.8127, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:51.765862", "source": { "split": "train_shard_00002", "doc_id": 376 }, "chunk_id": "train_shard_00002_376_0", "global_id": 13235 }, { "text": "The plasmids in gut microbiomes have the potential to contribute to the microbiome community, as well as human health and physiology. Nevertheless, this niche remains poorly explored. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups from South America and Africa, which would represent a link between ancestral and modern human groups. Based on open metagenomic data, we characterized the set of plasmids, including their genes and functions, from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami, semi-isolated groups with a hunter, gather or subsistence lifestyle. Unique plasmid clusters and gene functions for each human group were identified. Moreover, a dozen plasmid clusters circulating in other niches worldwide are shared by these distinct groups. In addition, novel and unique plasmids harboring resistance (encompassing six antibiotic classes and multiple metals) and virulence (as type VI secretion systems) genes were identified. Functional analysis revealed pathways commonly associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza gut plasmids. These results demonstrate the richness of plasmids in semi-isolated human groups' gut microbiome, which represents an important source of information with biotechnological/pharmaceutical potential, but also on the spread of resistance/virulence genes to semi-isolated groups.\n\nA plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits.", "token_count": 371, "char_count": 1614, "word_count": 221, "semantic_coherence": 1, "information_density": 0.6335, "quality_score": 0.8167, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:52.391043", "source": { "split": "train_shard_00002", "doc_id": 377 }, "chunk_id": "train_shard_00002_377_0", "global_id": 13236 }, { "text": "Reasons for the rising clinical impact of the bacterium Enterococcus faecium include the species' rapid acquisition of adaptive genetic elements. Here, we focused on the impact of recombination on the evolution of E. faecium. We used the recently developed BratNextGen algorithm to detect recombinant regions in the core genome of 34 E. faecium strains, including three newly sequenced clinical strains. Recombination was found to have a significant impact on the E. faecium genome: of the original 1.2 million positions in the core genome, 0.5 million were predicted to have been affected by recombination in at least one strain. Importantly, strains in one of the two major E. faecium clades (clade B), which contains most of the E. faecium human gut commensals, formed the most important reservoir for donating foreign DNA to the second major E. faecium clade (clade A), which contains most of the clinical isolates. Also, several genomic regions were found to mainly recombine in specific hospital-associated E. faecium strains. One of these regions (the epa-like locus) likely encodes the biosynthesis of cell wall polysaccharides. These findings suggest a crucial role for recombination in the emergence of E. faecium as a successful hospital-associated pathogen.\n\nRecent recombination events in the core genome are associated with adaptive evolution in Enterococcus faecium.", "token_count": 341, "char_count": 1381, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5619, "quality_score": 0.781, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:53.010023", "source": { "split": "train_shard_00002", "doc_id": 378 }, "chunk_id": "train_shard_00002_378_0", "global_id": 13237 }, { "text": "Growth temperature affected both the membrane lipid composition and microsoma (Na+, K+)-ATPase activity of Candida kefyr. Higher growth, temperature (37 degrees C) increased the amount of total lipids, phospholipids and free sterol. Ratios of phosphatidylcholine to phosphatidylethanolamine as well saturated to unsaturated fatty acids increased with a rise in growth temperature. Km of the ATPase isolated from the yeast grown at 27 degrees C was minimum, suggesting that the membranes of C. kefyr grown at optimal growth temperature provide the most suitable environment for the activity of ATPase.\n\nTemperature induced changes in microsomal (Na+,K+)-ATPase and lipid composition of Candida kefyr.", "token_count": 185, "char_count": 699, "word_count": 100, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:53.461040", "source": { "split": "train_shard_00002", "doc_id": 379 }, "chunk_id": "train_shard_00002_379_0", "global_id": 13238 }, { "text": "

Background

Intestinal microbiota restoration can be achieved by complementing a subject's perturbed microbiota with that of a healthy donor. Recurrent Clostridioides difficile infection (rCDI) is one key application of such treatment. Another emerging application of interest is reducing antibiotic-resistant genes (ARGs) and organisms (AROs). In this study, we investigated fecal specimens from a multicenter, randomized, double-blind, placebo-controlled phase 2b study of microbiota-based investigational drug RBX2660. Patients were administered either placebo, 1 dose of RBX2660 and 1 placebo, or 2 doses of RBX2660 via enema and longitudinally tracked for changes in their microbiome and antibiotic resistome.

Results

All patients exhibited significant recovery of gut microbiome diversity and a decrease of ARG relative abundance during the first 7 days post-treatment. However, the microbiome and resistome shifts toward average configurations from unperturbed individuals were more significant and longer-lasting in RBX2660 recipients compared to placebo. We quantified microbiome and resistome modification by RBX2660 using a novel \"transplantation index\" metric. We identified taxonomic and metabolic features distinguishing the baseline microbiome of non-transplanted patients and taxa specifically enriched during the process of transplantation. We elucidated the correlation between resistome and taxonomic transplantations and post-treatment dynamics of patient-specific and RBX2660-specific ARGs. Whole genome sequencing of AROs cultured from RBX2660 product and patient samples indicate ARO eradication in patients via RBX2660 administration, but also, to a lesser extent, introduction of RBX2660-derived AROs.

Conclusions

Through shotgun metagenomic sequencing, we elucidated the effects of RBX2660 in the microbiome and resistome", "token_count": 506, "char_count": 1868, "word_count": 235, "semantic_coherence": 1, "information_density": 0.6681, "quality_score": 0.834, "entities": { "genes": [ "RBX2660" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:54.097901", "source": { "split": "train_shard_00002", "doc_id": 380 }, "chunk_id": "train_shard_00002_380_0", "global_id": 13239 }, { "text": "Antibiotic discontinuation alone resulted in significant recovery of gut microbial diversity and reduced ARG relative abundance, but RBX2660 administration more rapidly and completely changed the composition of patients' microbiome, resistome, and ARO colonization by transplanting RBX2660 microbiota into the recipients. Although ARGs and AROs were transmitted through RBX2660, the resistome post-RBX2660 more closely resembled that of the administered product-a proxy for the donor-than an antibiotic perturbed state.

Trial registration

ClinicalTrials.gov, NCT02299570 . Registered 19 November 2014 Video Abstract.\n\nImpact of investigational microbiota therapeutic RBX2660 on the gut microbiome and resistome revealed by a placebo-controlled clinical trial.", "token_count": 216, "char_count": 766, "word_count": 94, "semantic_coherence": 1, "information_density": 0.7872, "quality_score": 0.8936, "entities": { "genes": [ "RBX2660", "NCT02299570" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:54.565962", "source": { "split": "train_shard_00002", "doc_id": 380 }, "chunk_id": "train_shard_00002_380_1", "global_id": 13240 }, { "text": "Enterococci are gastrointestinal commensals whose hardiness allowed them to colonize very diverse environments, including soils, water, food, and feed. This ability to overcome adverse conditions makes enterococci problematic once they colonize hospital niches. Together with the malleability of their genomes, the capacity to acquire and disseminate determinants of antibiotic resistance has contributed to converting what was once just another opportunistic pathogen into a first-class clinical problem. This review discusses the dimension of the emergence of enterococcal resistance to key antimicrobial agents, the dissemination of this resistance, and its significance in terms of public health, with the aim of raising awareness of the need to devise and implement surveillance programs and more effective antibiotic stewardship.\n\nEnterococci, from Harmless Bacteria to a Pathogen.", "token_count": 192, "char_count": 887, "word_count": 121, "semantic_coherence": 1, "information_density": 0.7355, "quality_score": 0.8678, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:55.009588", "source": { "split": "train_shard_00002", "doc_id": 381 }, "chunk_id": "train_shard_00002_381_0", "global_id": 13241 }, { "text": "Antibiotic properties of substances of a phytotoxic complex from Botrytis cinerea have been studied for a number of phytopathogenic bacteria, phytopathogenic and toxigenic fungi as well as saprophytic yeast strains. High fungistatic activity of preparations of phytotoxic metabolites (PTM) has been stated for Dendrodochium toxicum, Myrothecium verrucaria, M. roridum, Aspergillus fumigatus, Penicillium urticae, agents of heavy human and cattle mycotoxicoses. The studied representatives of phytopathogenic fusaria differed significantly in sensitivity to PTM: all the strains studied of the species from section Discolor (Fusarium gibbosum 54,624 and 51,463, F. graminearum 108,269, F. sambucinum 54,968, F. culmorum 54,951) were actively inhibited by the PTM concentrations studied; F. sporotrichiella 52,290 proved to be insensitive to them; the strains studied of the species from sections Elegans (F. oxysporum 55,715, F. moniliforme 54,262) and Martiella (F. javanicum 54,075, F. solani 54,719) possessed different sensitivity to PTM. The overwhelming majority of the yeast strains proved to be resistant to the PTM concentrations studied, except for the strains of Trichosporon cutaneum. In this connection the fact of high sensitivity of one of the strains of Kluyveromyces marxianus var. marxianus to B. cinerea metabolites arouses great interest. The strains of studied phytopathogenic bacteria (Erwinia carotovora subsp. carotovora 8,982 and Clavibacter michiganense 13) were sensitive to higher concentrations of PTM.", "token_count": 502, "char_count": 1530, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6114, "quality_score": 0.8057, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:55.661771", "source": { "split": "train_shard_00002", "doc_id": 382 }, "chunk_id": "train_shard_00002_382_0", "global_id": 13242 }, { "text": "[The antibiotic properties of the phytotoxic metabolites of Botrytis cinerea Pers].", "token_count": 26, "char_count": 83, "word_count": 11, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:56.034033", "source": { "split": "train_shard_00002", "doc_id": 382 }, "chunk_id": "train_shard_00002_382_1", "global_id": 13243 }, { "text": "Plant-associated bacteria exhibit a number of different strategies and specific genes allow bacteria to communicate and metabolically interact with plant tissues. Among the genes found in the genomes of plant-associated bacteria, the gene encoding the enzyme 1-aminocyclopropane-1-carboxylate (ACC) deaminase (acdS) is one of the most diffused. This gene is supposed to be involved in the cleaving of plant-produced ACC, the precursor of the plant stress-hormone ethylene toning down the plant response to infection. However, few reports are present on the actual role in rhizobia, one of the most investigated groups of plant-associated bacteria. In particular, still unclear is the origin and the role of acdS in symbiotic competitiveness and on the selective benefit it may confer to plant symbiotic rhizobia. Here we present a phylogenetic and functional analysis of acdS orthologs in the rhizobium model-species Sinorhizobium meliloti. Results showed that acdS orthologs present in S. meliloti pangenome have polyphyletic origin and likely spread through horizontal gene transfer, mediated by mobile genetic elements. When acdS ortholog from AK83 strain was cloned and assayed in S. meliloti 1021 (lacking acdS), no modulation of plant ethylene levels was detected, as well as no increase in fitness for nodule occupancy was found in the acdS-derivative strain compared to the parental one. Surprisingly, AcdS was shown to confer the ability to utilize formamide and some dipeptides as sole nitrogen source. Finally, acdS was shown to be negatively regulated by a putative leucine-responsive regulator (LrpL) located upstream to acdS sequence (acdR)", "token_count": 507, "char_count": 1745, "word_count": 245, "semantic_coherence": 1, "information_density": 0.6163, "quality_score": 0.8082, "entities": { "genes": [ "AK83" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:56.669125", "source": { "split": "train_shard_00002", "doc_id": 383 }, "chunk_id": "train_shard_00002_383_0", "global_id": 13244 }, { "text": "acdS expression was induced by root exudates of both legumes and non-leguminous plants. We conclude that acdS in S. meliloti is not directly related to symbiotic interaction, but it could likely be involved in the rhizospheric colonization or in the endophytic behavior.\n\nRole and Regulation of ACC Deaminase Gene in Sinorhizobium meliloti: Is It a Symbiotic, Rhizospheric or Endophytic Gene?", "token_count": 134, "char_count": 420, "word_count": 60, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:57.101617", "source": { "split": "train_shard_00002", "doc_id": 383 }, "chunk_id": "train_shard_00002_383_1", "global_id": 13245 }, { "text": "Ginsenoside Rb1 exhibits a wide range of biological activities, and gut microbiota is considered the main metabolic site for Rb1. However, the impact of gut microbiota on the pharmacokinetics of Rb1 are still uncertain. In this study, we investigated the gut microbiome changes and the pharmacokinetics after a 30 d Rb1 intervention. Results reveal that the systemic exposure and metabolic clearance rate of Rb1 and Rd were substantially affected after orally supplementing Rb1 (60 mg/kg) to rats. Significant increase in the relative abundance of Bacteroides cellulosilyticus in gut microbiota and specific glycoside hydrolase (GH) families, such as GH2, GH92, and GH20 were observed based on microbiome and metagenomic analysis. Moreover, a robust association was identified between the pharmacokinetic parameters of Rb1 and the relative abundance of specific Bacteroides species, and glycoside hydrolase families. Our study demonstrates that Rb1 administration significantly affects the gut microbiome, revealing a complex relationship between B. cellulosilyticus, key GH families, and Rb1 pharmacokinetics.\n\nImpact of ginsenoside Rb1 on gut microbiome and associated changes in pharmacokinetics in rats.", "token_count": 371, "char_count": 1306, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [ "GH92", "GH2", "GH20" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:57.686116", "source": { "split": "train_shard_00002", "doc_id": 384 }, "chunk_id": "train_shard_00002_384_0", "global_id": 13246 }, { "text": "We obtained two novel draft genomes of type Zobellia strains with estimated genome sizes of 5.14 Mb for Z. amurskyensis KMM 3526Т and 5.16 Mb for Z. laminariae KMM 3676Т. Comparative genomic analysis has been carried out between obtained and known genomes of Zobellia representatives. The pan-genome of Zobellia genus is composed of 4853 orthologous clusters and the core genome was estimated at 2963 clusters. The genus CAZome was represented by 775 GHs classified into 62 families, 297 GTs of 16 families, 100 PLs of 13 families, 112 CEs of 13 families, 186 CBMs of 18 families and 42 AAs of six families. A closer inspection of the carbohydrate-active enzyme (CAZyme) genomic repertoires revealed members of new putative subfamilies of GH16 and GH117, which can be biotechnologically promising for production of oligosaccharides and rare monomers with different bioactivities. We analyzed AA3s, among them putative FAD-dependent glycoside oxidoreductases (FAD-GOs) being of particular interest as promising biocatalysts for glycoside deglycosylation in food and pharmaceutical industries.\n\nComparative Genomics and CAZyme Genome Repertoires of Marine Zobellia amurskyensis KMM 3526T and Zobellia laminariae KMM 3676T.", "token_count": 459, "char_count": 1313, "word_count": 180, "semantic_coherence": 1, "information_density": 0.6778, "quality_score": 0.8389, "entities": { "genes": [ "GH117", "GH16" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:58.325918", "source": { "split": "train_shard_00002", "doc_id": 385 }, "chunk_id": "train_shard_00002_385_0", "global_id": 13247 }, { "text": "The strictly aerobic yeasts Candida pinus, Cryptococcus albidus, Rhodotorula minuta, Rhodotorula mucilaginosa and Trichosporon beigelii possess mitochondrial NADH dehydrogenases with significant features of the NADH:ubiquinone oxidoreductase (complex I). These species show in all growth phases and under standard cultivation conditions, NADH dehydrogenases of approximately 700 kDa, which are sensitive to rotenone, a specific inhibitor of this complex. Identical results were obtained with the weakly fermenting C. pinus. The facultatively fermenting yeasts Saccharomyces cerevisiae and Kluyveromyces marxianus do not possess the 700 kDa-complex and are insensitive to rotenone. In S. cerevisiae, a rotenone-insensitive NADH dehydrogenase of about 500-600 kDa is detected only in stationary phase cells. As in Neurospora crassa, upon incubation of the obligately aerobic yeast R. mucilaginosa with chloramphenicol, an intermediate NADH dehydrogenase of approximately 350 kDa was formed, which was insensitive to rotenone.\n\nNADH: ubiquinone oxidoreductase in obligate aerobic yeasts.", "token_count": 331, "char_count": 1084, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:58.897177", "source": { "split": "train_shard_00002", "doc_id": 386 }, "chunk_id": "train_shard_00002_386_0", "global_id": 13248 }, { "text": "SAR11 is an ancient and diverse clade of heterotrophic bacteria that are abundant throughout the world's oceans, where they play a major role in the ocean carbon cycle. Correlations between the phylogenetic branching order and spatiotemporal patterns in cell distributions from planktonic ocean environments indicate that SAR11 has evolved into perhaps a dozen or more specialized ecotypes that span evolutionary distances equivalent to a bacterial order. We isolated and sequenced genomes from diverse SAR11 cultures that represent three major lineages and encompass the full breadth of the clade. The new data expand observations about genome evolution and gene content that previously had been restricted to the SAR11 Ia subclade, providing a much broader perspective on the clade's origins, evolution, and ecology. We found small genomes throughout the clade and a very high proportion of core genome genes (48 to 56%), indicating that small genome size is probably an ancestral characteristic. In their level of core genome conservation, the members of SAR11 are outliers, the most conserved free-living bacteria known. Shared features of the clade include low GC content, high gene synteny, a large hypervariable region bounded by rRNA genes, and low numbers of paralogs. Variation among the genomes included genes for phosphorus metabolism, glycolysis, and C1 metabolism, suggesting that adaptive specialization in nutrient resource utilization is important to niche partitioning and ecotype divergence within the clade. These data provide support for the conclusion that streamlining selection for efficient cell replication in the planktonic habitat has occurred throughout the evolution and diversification of this clade. IMPORTANCE The SAR11 clade is the most abundant group of marine microorganisms worldwide, making them key players in the global carbon cycle. Growing knowledge about their biochemistry and metabolism is leading to a more mechanistic understanding of organic carbon oxidation and sequestration in the oceans. The discovery of small genomes in SAR11 provided crucial support for the theory that streamlining selection can drive genome reduction in low-nutrient environments", "token_count": 490, "char_count": 2203, "word_count": 322, "semantic_coherence": 1, "information_density": 0.5963, "quality_score": 0.7981, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [ "glycolysis", "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:59.545369", "source": { "split": "train_shard_00002", "doc_id": 387 }, "chunk_id": "train_shard_00002_387_0", "global_id": 13249 }, { "text": "Study of isolates in culture revealed atypical organic nutrient requirements that can be attributed to genome reduction, such as conditional auxotrophy for glycine and its precursors, a requirement for reduced sulfur compounds, and evidence for widespread cycling of C1 compounds in marine environments. However, understanding the genetic variation and distribution of such pathways and characteristics like streamlining throughout the group has required the isolation and genome sequencing of diverse SAR11 representatives, an analysis of which we provide here.\n\nStreamlining and core genome conservation among highly divergent members of the SAR11 clade.", "token_count": 136, "char_count": 656, "word_count": 91, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [ "SAR11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:03:59.971936", "source": { "split": "train_shard_00002", "doc_id": 387 }, "chunk_id": "train_shard_00002_387_1", "global_id": 13250 }, { "text": "Continuous ethanol production from Jerusalem artichoke stalks using immobilized cells of Kluyveromyces marxianus.", "token_count": 29, "char_count": 113, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:00.332169", "source": { "split": "train_shard_00002", "doc_id": 388 }, "chunk_id": "train_shard_00002_388_0", "global_id": 13251 }, { "text": "The safety of food production as concerns Listeria is the key to the sanitary wellbeing of manufactured products. Molecular-genetic methods for the analysis of Listeria, including whole-genome sequencing, are effective in monitoring persistent contaminants and in the epidemic investigation of cases of foodborne infections. They have been adopted in the European Union, United States, and Canada. In Russia, multilocus and whole-genome sequencing has proven itself in the analysis of clinical food isolates and Listeria from the environment. The objective of the study was molecular-genetic characterization of Listeria detected in the industrial environment of meat processing. To characterize the Listeria isolates, microbiological methods were used according to GOST (State Standard) 32031-2012, as well as multilocus sequencing, including the analysis of seven housekeeping genes and four virulence genes, as well as whole-genome sequencing. In swabs that were positive for the presence of Listeria spp. taken at two meat-processing plants in Moscow, Listeria monocytogenes constituted 81% and L. welshimeri 19%. The predominant genotype (Sequence Type, ST) of L. monocytogenes was ST8. The variety was supplemented with ST321, ST121, and ST2330 (CC9 (Clonal Complex 9)). L. welshimeri, which prevailed in the second production, was represented by ST1050 and ST2331. The genomic characteristics of L. welshimeri isolates confirmed that they have high adaptive capabilities both as concerns production conditions (including resistance to disinfectants) and the metabolic peculiarities of the gastrointestinal tract of animals. L. monocytogenes CC9 and CC121 are also correlated with food production in other countries. However, L", "token_count": 507, "char_count": 1827, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6107, "quality_score": 0.8053, "entities": { "genes": [ "ST1050", "ST321", "CC121", "ST2331", "CC9", "ST2330", "ST8", "ST121" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:00.963799", "source": { "split": "train_shard_00002", "doc_id": 389 }, "chunk_id": "train_shard_00002_389_0", "global_id": 13252 }, { "text": "monocytogenes CC8 and CC321 can cause invasive listeriosis. The concordance in the internalin profile of the ST8 isolates from the industrial environment with the clinical isolates ST8 and ST2096 (CC8) is a cause for concern. The study showed the effectiveness of molecular-genetic methods in determining the diversity of Listeria detected in the production environment of meat processing, and laid the foundation for monitoring of persistent contaminants.\n\nGenetic Diversity of Listeria Detected in the Production Environment of Meat Processing.", "token_count": 141, "char_count": 564, "word_count": 78, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7949, "entities": { "genes": [ "ST2096", "CC321", "ST8", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:01.399558", "source": { "split": "train_shard_00002", "doc_id": 389 }, "chunk_id": "train_shard_00002_389_1", "global_id": 13253 }, { "text": "Elizabethkingia miricola is a Gram-negative non-fermenting rod emerging as a life-threatening human pathogen. The multidrug-resistant (MDR) carbapenemase-producing clinical isolate E. miricola EM_CHUV was recovered in the setting of severe nosocomial pneumonia. In this study, the genome of E. miricola EM_CHUV was sequenced and a functional analysis was performed, including a comparative genomic study with Elizabethkingia meningoseptica and Elizabethkingia anophelis. The resistome of EM_CHUV revealed the presence of a high number of resistance genes, including the presence of the blaGOB-13 and blaB-9 carbapenemase-encoding genes. Twelve mobility genes, with only two of them located in the proximity of resistance genes, and four potential genomic islands were identified in the genome of EM_CHUV, but no prophages or CRISPR sequences. Ten restriction-modification system (RMS) genes were also identified. In addition, we report the presence of a putative conjugative plasmid (pEM_CHUV) that does not encode any antibiotic resistance genes. Altogether, these findings point towards a limited number of DNA exchanges with other bacteria and suggest that multidrug resistance is an intrinsic trait of E. miricola owing to the presence of a high number of resistance genes within the bacterial core genome.\n\nGenome of the carbapenemase-producing clinical isolate Elizabethkingia miricola EM_CHUV and comparative genomics with Elizabethkingia meningoseptica and Elizabethkingia anophelis: evidence for intrinsic multidrug resistance trait of emerging pathogens.", "token_count": 402, "char_count": 1586, "word_count": 213, "semantic_coherence": 1, "information_density": 0.5587, "quality_score": 0.7793, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:02.024144", "source": { "split": "train_shard_00002", "doc_id": 390 }, "chunk_id": "train_shard_00002_390_0", "global_id": 13254 }, { "text": "

Background

Early antimicrobial chemotherapy can prevent or at least delay chronic cystic fibrosis (CF) airways infections with Pseudomonas aeruginosa.

Methods

During a 10-year study period P. aeruginosa was detected for the first time in 54 CF patients regularly seen at the CF centre Hannover. Amplicon sequencing of 34 loci of the P. aeruginosa core genome was performed in baseline and post-treatment isolates of the 15 CF patients who had remained P. aeruginosa - positive after the first round of antipseudomonal chemotherapy.

Results

Deep sequencing uncovered coexisting alternative nucleotides at in total 33 of 55,284 examined genome positions including six non-synonymous polymorphisms in the lasR gene, a key regulator of quorum sensing. After early treatment 42 of 50 novel nucleotide substitutions had emerged in exopolysaccharide biosynthesis, efflux pump and porin genes.

Conclusions

Early treatment selects pathoadaptive mutations in P. aeruginosa that are typical for chronic infections of CF lungs.\n\nMultilocus amplicon sequencing of Pseudomonas aeruginosa cystic fibrosis airways isolates collected prior to and after early antipseudomonal chemotherapy.", "token_count": 342, "char_count": 1200, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6604, "quality_score": 0.8302, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:02.595287", "source": { "split": "train_shard_00002", "doc_id": 391 }, "chunk_id": "train_shard_00002_391_0", "global_id": 13255 }, { "text": "Hypermutable Pseudomonas aeruginosa isolates (hypermutators) have been identified in patients with cystic fibrosis (CF) and are associated with reduced lung function. Hypermutators display a greatly increased mutation rate and an enhanced ability to become resistant to antibiotics during treatment. Their prevalence has been established among patients with CF, but it has not been determined for patients with CF in Australia. This study aimed to determine the prevalence of hypermutable P. aeruginosa isolates from adult patients with CF from a health care institution in Australia and to characterize the genetic diversity and antibiotic susceptibility of these isolates. A total of 59 P. aeruginosa clinical isolates from patients with CF were characterized. For all isolates, rifampin (RIF) mutation frequencies and susceptibility to a range of antibiotics were determined. Of the 59 isolates, 13 (22%) were hypermutable. Whole-genome sequences were determined for all hypermutable isolates. Core genome polymorphisms were used to assess genetic relatedness of the isolates, both to each other and to a sample of previously characterized P. aeruginosa strains. Phylogenetic analyses showed that the hypermutators were from divergent lineages and that hypermutator phenotype was mostly the result of mutations in mutL or, less commonly, in mutS Hypermutable isolates also contained a range of mutations that are likely associated with adaptation of P. aeruginosa to the CF lung environment. Multidrug resistance was more prevalent in hypermutable than nonhypermutable isolates (38% versus 22%). This study revealed that hypermutable P. aeruginosa strains are common among isolates from patients with CF in Australia and are implicated in the emergence of antibiotic resistance.\n\nCharacterization of Hypermutator Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis in Australia.", "token_count": 483, "char_count": 1952, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5148, "quality_score": 0.7574, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:03.273401", "source": { "split": "train_shard_00002", "doc_id": 392 }, "chunk_id": "train_shard_00002_392_0", "global_id": 13256 }, { "text": "Thirteen investigated strains of ascomycetous yeasts able to produce secretory heat-shock proteins (sHSPs) do not response equally to a high temperature by induction of the synthesis and secretion of these proteins. In this respect the above yeasts can be divided into three groups having a positive (I), a negative (II), and an indefinite reaction (III) to the heat shock. The thermotolerant yeast Hansenula polymorpha belongs to the first group. In this yeast heat shock induces the synthesis and secretion of sHSP gp280. This new representative differs from known sHSPs in molecular mass and subunit composition. In other respects (glycosylation, mainly extracellular localization, and the character of export into the culture medium) it displays similar properties.\n\nSecretory heat-shock protein of the thermotolerant yeast Hansenula polymorpha. Identification and comparative characteristics.", "token_count": 220, "char_count": 897, "word_count": 128, "semantic_coherence": 1, "information_density": 0.6953, "quality_score": 0.8477, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:03.753704", "source": { "split": "train_shard_00002", "doc_id": 393 }, "chunk_id": "train_shard_00002_393_0", "global_id": 13257 }, { "text": "Ersho is a clear, yellow liquid that accumulates on the surface of fermenting teff-flour batter and is collected to serve as an inoculum for the next fermentation. The pH of ersho samples was about 3.5 and titratable acidity ranged between 3.1% and 5.7%. The mean aerobic mesophilic counts from four households varied between 6.9×10(6) and 1.3×10(8) c.f.u./ml and the aerobic bacterial flora consisted of Bacillus spp. Mean yeast counts ranged between 5.2×10(5) and 1.8×10(6) c.f.u./ml and comprised, in order of abundance, Candida milleri, Rhodotorula mucilaginosa, Kluyveromyces marxianus, Pichia naganishii and Debaromyces hansenii. Candida milleri was the most dominant isolate in all samples. About 90% of the teff flour samples had aerobic mesophilic counts ≥10(5) c.f.u./g and Gram-positive bacteria constituted about 71% of the total isolates. About 80% of samples had Enterobacteriaceae counts of 10(4) c.f.u./g.\n\nMicrobial flora and some chemical properties of ersho, a starter for teff (Eragrostis tef) fermentation.", "token_count": 352, "char_count": 1027, "word_count": 150, "semantic_coherence": 1, "information_density": 0.66, "quality_score": 0.83, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:04.336256", "source": { "split": "train_shard_00002", "doc_id": 394 }, "chunk_id": "train_shard_00002_394_0", "global_id": 13258 }, { "text": "Members of the Planctomycetes clade share many unusual features for bacteria. Their cytoplasm contains membrane-bound compartments, they lack peptidoglycan and FtsZ, they divide by polar budding, and they are capable of endocytosis. Planctomycete genomes have remained enigmatic, generally being quite large (up to 9 Mb), and on average, 55% of their predicted proteins are of unknown function. Importantly, proteins related to the unusual traits of Planctomycetes remain largely unknown. Thus, we embarked on bioinformatic analyses of these genomes in an effort to predict proteins that are likely to be involved in compartmentalization, cell division, and signal transduction. We used three complementary strategies. First, we defined the Planctomycetes core genome and subtracted genes of well-studied model organisms. Second, we analyzed the gene content and synteny of morphogenesis and cell division genes and combined both methods using a \"guilt-by-association\" approach. Third, we identified signal transduction systems as well as sigma factors. These analyses provide a manageable list of candidate genes for future genetic studies and provide evidence for complex signaling in the Planctomycetes akin to that observed for bacteria with complex life-styles, such as Myxococcus xanthus.\n\nIdentification of proteins likely to be involved in morphogenesis, cell division, and signal transduction in Planctomycetes by comparative genomics.", "token_count": 343, "char_count": 1444, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6404, "quality_score": 0.8202, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:04.948536", "source": { "split": "train_shard_00002", "doc_id": 395 }, "chunk_id": "train_shard_00002_395_0", "global_id": 13259 }, { "text": "The global epidemic of multidrug-resistant Salmonella Typhimurium DT104 provides an important example, both in terms of the agent and its resistance, of a widely disseminated zoonotic pathogen. Here, with an unprecedented national collection of isolates collected contemporaneously from humans and animals and including a sample of internationally derived isolates, we have used whole-genome sequencing to dissect the phylogenetic associations of the bacterium and its antimicrobial resistance genes through the course of an epidemic. Contrary to current tenets supporting a single homogeneous epidemic, we demonstrate that the bacterium and its resistance genes were largely maintained within animal and human populations separately and that there was limited transmission, in either direction. We also show considerable variation in the resistance profiles, in contrast to the largely stable bacterial core genome, which emphasizes the critical importance of integrated genotypic data sets in understanding the ecology of bacterial zoonoses and antimicrobial resistance.\n\nDistinguishable epidemics of multidrug-resistant Salmonella Typhimurium DT104 in different hosts.", "token_count": 253, "char_count": 1171, "word_count": 157, "semantic_coherence": 1, "information_density": 0.6688, "quality_score": 0.8344, "entities": { "genes": [ "DT104" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:05.444605", "source": { "split": "train_shard_00002", "doc_id": 396 }, "chunk_id": "train_shard_00002_396_0", "global_id": 13260 }, { "text": "The species in family Planctomycetaceae are ideal groups for investigating the origin of eukaryotes. Their cells are divided by a lipidic intracytoplasmic membrane and they share a number of eukaryote-like molecular characteristics. However, their genomic structures, potential abilities, and evolutionary status are still unknown. In this study, we searched for common protein families and a core genome/pan genome based on 11 sequenced species in family Planctomycetaceae. Then, we constructed phylogenetic tree based on their 832 common protein families. We also annotated the 11 genomes using the Clusters of Orthologous Groups database. Moreover, we predicted and reconstructed their core/pan metabolic pathways using the KEGG (Kyoto Encyclopedia of Genes and Genomes) orthology system. Subsequently, we identified genomic islands (GIs) and structural variations (SVs) among the five complete genomes and we specifically investigated the integration of two Planctomycetaceae plasmids in all 11 genomes. The results indicate that Planctomycetaceae species share diverse genomic variations and unique genomic characteristics, as well as have huge potential for human applications.\n\nGenomic evolution of 11 type strains within family Planctomycetaceae.", "token_count": 298, "char_count": 1254, "word_count": 172, "semantic_coherence": 1, "information_density": 0.6453, "quality_score": 0.8227, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:06.007350", "source": { "split": "train_shard_00002", "doc_id": 397 }, "chunk_id": "train_shard_00002_397_0", "global_id": 13261 }, { "text": "The mammalian gut is densely inhabited by microorganisms that have coevolved with their host. Amongst these latter microorganisms, bifidobacteria represent a key model to study host-microbe interaction within the mammalian gut. Remarkably, bifidobacteria naturally occur in a range of ecological niches that are either directly or indirectly connected to the animal gastrointestinal tract. They constitute one of the dominant bacterial members of the intestinal microbiota and are among the first colonizers of the mammalian gut. Notably, the presence of bifidobacteria in the gut has been associated with several health-promoting activities. In this review, we aim to provide an overview of current knowledge on the genetic diversity and ecology of bifidobacteria. Furthermore, we will discuss how this important group of gut bacteria is able to colonize and survive in the mammalian gut, so as to facilitate host interactions.\n\nExploring the Ecology of Bifidobacteria and Their Genetic Adaptation to the Mammalian Gut.", "token_count": 244, "char_count": 1020, "word_count": 150, "semantic_coherence": 1, "information_density": 0.6533, "quality_score": 0.8267, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:06.495365", "source": { "split": "train_shard_00002", "doc_id": 398 }, "chunk_id": "train_shard_00002_398_0", "global_id": 13262 }, { "text": "Torulopsis cremoris growth in whey was described satisfactorily by Monod's model. The maximum specific growth rate of T. cremoris obtained in batch culture was approximately 26% higher than that estimated in continuous culture. This rate was higher than that reported for Kluyveromyces fragilis, which is the yeast used in large-scale processes for the biomass production from whey. In batch and continuous cultures, the yeast utilized some other carbon and energy source, different from lactose. In batch cultures, the overall growth yield coefficients exhibited a significant dependence on initial lactose concentration. The single-stage continuous culture is not a convenient system for T. cremoris. The results obtained in this work demonstrate that the kinetic parameters may vary significantly according to the culture type used, and this could have economic repercussions.\n\nDifferences in the growth kinetic behaviour of Torulopsis cremoris in batch and continuous cultures.", "token_count": 208, "char_count": 981, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8099, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:06.961119", "source": { "split": "train_shard_00002", "doc_id": 399 }, "chunk_id": "train_shard_00002_399_0", "global_id": 13263 }, { "text": "Plant−water relations mediated by aquaporins (AQPs) play vital roles in both key plant growth processes and responses to environmental challenges. As a well-known medicinal and edible plant, the harsh natural growth habitat endows Lycium plants with ideal materials for stress biology research. However, the details of their molecular switch for water transport remain unclear. In the present work, we first identified and characterized AQP family genes from Lycium (L.) barbarum at the genome scale and conducted systemic bioinformatics and expression analyses. The results showed that there were 38 Lycium barbarum AQPs (LbAQPs) in L. barbarum, which were classified into four subfamilies, including 17 LbPIP, 9 LbTIP, 10 LbNIP, and 2 LbXIP. Their encoded genes were unevenly distributed on all 12 chromosomes, except chromosome 10. Three of these genes encoded truncated proteins and three genes underwent clear gene duplication events. Cis-acting element analysis indicated that the expression of LbAQPs may be mainly regulated by biotic/abiotic stress, phytohormones and light. The qRT-PCR assay indicated that this family of genes presented a clear tissue-specific expression pattern, in which most of the genes had maximal transcript levels in roots, stems, and leaves, while there were relatively lower levels in flowers and fruits. Most of the LbAQP genes were downregulated during L. barbarum fruit ripening and presented a negative correlation with the fruit relative water content (RWC). Most of their transcripts presented a quick and sharp upregulation response to heat stress following exposure of the 2-month-old seedlings to a 42 °C temperature for 0, 1, 3, 12, or 24 h. Our results proposed that LbAQPs were involved in L. barbarum key development events and abiotic stress responses, which may lay a foundation for further studying the molecular mechanism of the water relationship of Lycium plants, especially in harsh environments.", "token_count": 482, "char_count": 1952, "word_count": 294, "semantic_coherence": 1, "information_density": 0.6497, "quality_score": 0.8248, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:07.605294", "source": { "split": "train_shard_00002", "doc_id": 400 }, "chunk_id": "train_shard_00002_400_0", "global_id": 13264 }, { "text": "Genome-Wide Identification and Expression Analysis of the Aquaporin Gene Family in Lycium barbarum during Fruit Ripening and Seedling Response to Heat Stress.", "token_count": 47, "char_count": 165, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9545, "quality_score": 0.9773, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:07.963613", "source": { "split": "train_shard_00002", "doc_id": 400 }, "chunk_id": "train_shard_00002_400_1", "global_id": 13265 }, { "text": "ESBL-producing Klebsiella pneumoniae (K. pneumoniae) represent an increasing problem both in human and veterinary medicine. As SHV-2 - encoding K. pneumoniae were recently detected in the broiler production we were interested in investigating a possible transmission along the broiler production chain and furthermore, in evaluating their possible impact on human health. Therefore, 41 ESBL-producing K. pneumoniae originating from a parent flock, from the hatcherys' environment during the hatching of that parent flocks' chickens, and from an associated fattening flock were investigated on an Illumina Miseq. Whole genome sequences were analyzed concerning their MLST-type, cgMLST-type, genotypic and phenotypic resistance, plasmid profiles and virulence genes. Irrespective of the origin of isolation all investigated isolates were multi-drug resistant, harbored the same ESBL-gene bla SHV-2, shared the same sequence type (ST3128) and displayed 100% similarity in core genome multilocus sequence typing (cgMLST). In addition, in silico plasmid typing found several Inc/Rep types associated with ESBL-plasmids. Summarizing, identical clones of SHV-2-producing K. pneumoniae were detected in different stages of the industrial broiler production in one out of seven investigated broiler chains. This proves the possibility of pseudo-vertical transmission of multi-resistant human pathogens from parent flocks to hatcheries and fattening flocks. Furthermore, the importance of cross-contamination along the production chain was shown. Although the ESBL-producing K. pneumoniae clone detected here in the broiler production has not been associated with clinical settings so far, our findings present a potential public health threat.\n\nESBL-Producing Klebsiella pneumoniae in the Broiler Production Chain and the First Description of ST3128.", "token_count": 505, "char_count": 1908, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6104, "quality_score": 0.8052, "entities": { "genes": [ "ST3128" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:08.997465", "source": { "split": "train_shard_00002", "doc_id": 401 }, "chunk_id": "train_shard_00002_401_0", "global_id": 13266 }, { "text": "A mixture of Kluyveromyces fragilis biomass and coagulated whey proteins was obtained by fermentation of whole whey. This product had a chemical composition similar to that of washed products reported in the literature with high-crude protein and low-ash contents. The product had a high content of sulphur-containing amino acids and tryptophan, which are usually limiting in yeast biomass. Lysine content was inexplicably lower than the expected value, being the limiting amino acid in this case. The chemical score of the protein was 91%. From the biomass-whey proteins product a protein isolate could be recovered with a yield of 80%. The protein content of the isolate was 75%, and the nucleic acids were reduced by 90.8%. The cell-wall debris were also considerably reduced.\n\nChemical composition of a mixture of single-cell protein obtained from Kluyveromyces fragilis and whey proteins.", "token_count": 223, "char_count": 893, "word_count": 137, "semantic_coherence": 1, "information_density": 0.5693, "quality_score": 0.7847, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:09.466575", "source": { "split": "train_shard_00002", "doc_id": 402 }, "chunk_id": "train_shard_00002_402_0", "global_id": 13267 }, { "text": "A novel Weissella cibaria strain UTNGt21O from the fruit of the Solanum quitoense (naranjilla) shrub produces a peptide that inhibits the growth of both Salmonella enterica subsp. enterica ATCC51741 and Escherichia coli ATCC25922 at different stages. A total of 31 contigs were assembled, with a total length of 1,924,087 bases, 20 contig hits match the core genome of different groups within Weissella, while for 11 contigs no match was found in the database. The GT content was 39.53% and the genome repeats sequences constitute around 186,760 bases of the assembly. The UTNGt21O matches the W. cibaria genome with 83% identity and no gaps (0). The sequencing data were deposited in the NCBI Database (BioProject accessions: PRJNA639289). The antibacterial activity and interaction mechanism of the peptide UTNGt21O on target bacteria were investigated by analyzing the growth, integrity, and morphology of the bacterial cells following treatment with different concentrations (1×, 1.5× and 2× MIC) of the peptide applied alone or in combination with chelating agent ethylenediaminetetraacetic acid (EDTA) at 20 mM. The results indicated a bacteriolytic effect at both early and late target growth at 3 h of incubation and total cell death at 6 h when EDTA was co-inoculated with the peptide. Based on BAGEL 4 (Bacteriocin Genome Mining Tool) a putative bacteriocin having 33.4% sequence similarity to enterolysin A was detected within the contig 12", "token_count": 474, "char_count": 1500, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6489, "quality_score": 0.8244, "entities": { "genes": [ "ATCC51741", "ATCC25922", "PRJNA639289" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:10.107607", "source": { "split": "train_shard_00002", "doc_id": 403 }, "chunk_id": "train_shard_00002_403_0", "global_id": 13268 }, { "text": "The interaction between the peptide UTNGt21O and the target strains caused permeability in a dose-, time- response manner, with Salmonella (3200 AU/mL) more susceptible than E. coli (6400 AU/mL). The results indicated that UTNGt21O may damage the integrity of the cell target, leading to release of cytoplasmic components followed by cell death. Differences in membrane shape changes in target cells treated with different doses of peptide were observed by transmission electronic microscopy (TEM). Spheroplasts with spherical shapes were detected in Salmonella while larger shaped spheroplasts with thicker and deformed membranes along with filamentous cells were observed in E. coli upon the treatment with the UTNGt21O peptide. These results indicate the promising potential of the putative bacteriocin released by the novel W. cibaria strain UTNGt21O to be further tested as a new antimicrobial substance.\n\nA Novel Weissella cibaria Strain UTNGt21O Isolated from Wild Solanum quitoense Fruit: Genome Sequence and Characterization of a Peptide with Highly Inhibitory Potential toward Gram-Negative Bacteria.", "token_count": 339, "char_count": 1159, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:10.671571", "source": { "split": "train_shard_00002", "doc_id": 403 }, "chunk_id": "train_shard_00002_403_1", "global_id": 13269 }, { "text": "Staphylococcus aureus continues to be a serious health problem worldwide due to its intrinsic nature of virulence, ability to cause a wide array of infection, and its capacity to develop resistance to a number of antibiotics. The S aureus genome has continually evolved through both mutation and acquisition of exogenous genes, leading to the emergence of antibiotic-resistant strains with the ability for clonal dissemination across nations and continents. Methicillin-resistant S aureus (MRSA) is one of the most commonly identified antibiotic-resistant pathogens in the hospital and community settings with substantial mortality and morbidity. This review examines the accessory genome of 8 sequenced S aureus strains regarding the variety of virulence factors and mechanisms of antibiotic resistance. The remarkable nature of this organism to acquire and disseminate an array of mobile genetic elements (MBEs) through horizontal gene transfer illustrates the mechanisms for evolution and its fitness level in the face of constant environmental challenges. The relative ease of transfer of genetic materials, especially antibiotic-resistant genes, across staphylococcal species indicates that there is a potential pandemic problem in the hospital and community environment.\n\nInsights on Virulence and Antibiotic Resistance: A Review of the Accessory Genome of Staphylococcus aureus.", "token_count": 309, "char_count": 1387, "word_count": 195, "semantic_coherence": 1, "information_density": 0.5897, "quality_score": 0.7949, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:11.246473", "source": { "split": "train_shard_00002", "doc_id": 404 }, "chunk_id": "train_shard_00002_404_0", "global_id": 13270 }, { "text": "Streptococcus mutans is widely recognized as one of the key etiological agents of human dental caries. Despite its role in this important disease, our present knowledge of gene content variability across the species and its relationship to adaptation is minimal. Estimates of its demographic history are not available. In this study, we generated genome sequences of 57 S. mutans isolates, as well as representative strains of the most closely related species to S. mutans (S. ratti, S. macaccae, and S. criceti), to identify the overall structure and potential adaptive features of the dispensable and core components of the genome. We also performed population genetic analyses on the core genome of the species aimed at understanding the demographic history, and impact of selection shaping its genetic variation. The maximum gene content divergence among strains was approximately 23%, with the majority of strains diverging by 5-15%. The core genome consisted of 1,490 genes and the pan-genome approximately 3,296. Maximum likelihood analysis of the synonymous site frequency spectrum (SFS) suggested that the S. mutans population started expanding exponentially approximately 10,000 years ago (95% confidence interval [CI]: 3,268-14,344 years ago), coincidental with the onset of human agriculture. Analysis of the replacement SFS indicated that a majority of these substitutions are under strong negative selection, and the remainder evolved neutrally. A set of 14 genes was identified as being under positive selection, most of which were involved in either sugar metabolism or acid tolerance. Analysis of the core genome suggested that among 73 genes present in all isolates of S. mutans but absent in other species of the mutans taxonomic group, the majority can be associated with metabolic processes that could have contributed to the successful adaptation of S. mutans to its new niche, the human mouth, and with the dietary changes that accompanied the origin of agriculture.\n\nEvolutionary and population genomics of the cavity causing bacteria Streptococcus mutans.", "token_count": 470, "char_count": 2080, "word_count": 314, "semantic_coherence": 1, "information_density": 0.5732, "quality_score": 0.7866, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:11.886248", "source": { "split": "train_shard_00002", "doc_id": 405 }, "chunk_id": "train_shard_00002_405_0", "global_id": 13271 }, { "text": "Understanding the population structure and genetic diversity of plant pathogens, as well as the effect of agricultural practices on pathogen evolution, are important for disease management. Developments in molecular methods have contributed to increasing the resolution for accurate pathogen identification but those based on analysis of DNA sequences can be less straightforward to use. To address this, we developed Gall-ID, a web-based platform that uses DNA sequence information from 16S rDNA, multilocus sequence analysis and whole genome sequences to group disease-associated bacteria to their taxonomic units. Gall-ID was developed with a particular focus on gall-forming bacteria belonging to Agrobacterium , Pseudomonas savastanoi , Pantoea agglomerans , and Rhodococcus . Members of these groups of bacteria cause growth deformation of plants, and some are capable of infecting many species of field, orchard, and nursery crops. Gall-ID also enables the use of high-throughput sequencing reads to search for evidence for homologs of characterized virulence genes, and provides downloadable software pipelines for automating multilocus sequence analysis, analyzing genome sequences for average nucleotide identity, and constructing core genome phylogenies. Lastly, additional databases were included in Gall-ID to help determine the identity of other plant pathogenic bacteria that may be in microbial communities associated with galls or causative agents in other diseased tissues of plants. The URL for Gall-ID is http://gall-id.cgrb.oregonstate.edu/.\n\nGall-ID: tools for genotyping gall-causing phytopathogenic bacteria", "token_count": 367, "char_count": 1631, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6906, "quality_score": 0.8453, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:12.472633", "source": { "split": "train_shard_00002", "doc_id": 406 }, "chunk_id": "train_shard_00002_406_0", "global_id": 13272 }, { "text": "The positively charged photosensitizer toluidine blue (TB) can induce loss of clonogenicity in Kluyveromyces marxianus. Previous studies have revealed that, as a consequence of the localization of this dye at the cell surface, photodynamic action results in extensive damage at the level of the plasma membrane. In this paper, a study is reported on the effect of photodynamic treatment with TB on intracellular enzymes. It is shown that treatment with TB and light resulted in the inhibition of alcohol dehydrogenase, cytochrome c oxidase, glyceraldehyde-3-phosphate dehydrogenase and hexokinase. Photodynamic treatment also lowered the ATP levels. The ATP levels could be partially restored in the presence of glucose but not with ethanol. Toluidine blue binding experiments revealed that photodynamic treatment caused a rapid increase in the amount of cell-associated dye. Moreover, it also appeared that this treatment decreased the binding of TB to the cell surface. It is concluded that TB enters the cell during the first minutes of illumination, whereafter intracellular enzymes are inactivated. The data indicate that photodynamic damage of intracellular sites contributes to the loss of viability.\n\nIntracellular damage in yeast cells caused by photodynamic treatment with toluidine blue.", "token_count": 320, "char_count": 1298, "word_count": 190, "semantic_coherence": 1, "information_density": 0.5737, "quality_score": 0.7868, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:13.046671", "source": { "split": "train_shard_00002", "doc_id": 407 }, "chunk_id": "train_shard_00002_407_0", "global_id": 13273 }, { "text": "

Background

Diarrhea is the second leading cause of death in children under 5 years of age. Enhanced understanding of causal pathways, pathogenesis, and sequelae of diarrhea is urgently needed. Although the gut microbiota is believed to play a role in susceptibility to diarrheal diseases, our understanding of this association remains incomplete. Infant rhesus macaques (Macaca mulatta) are susceptible to diarrhea making them an ideal model to address this question.

Results

The maturation of the infant rhesus macaque gut microbiome throughout the first 8 months of life occurs in a similar pattern as that described for human infants. Moreover, the microbiome of the captive reared infant rhesus macaque more closely resembles that of human infants in the developing world than in the western world. Importantly, prior to disease onset, the gut microbiome of infants that later develop diarrhea is enriched in pathways of immunomodulatory metabolite synthesis, while those of infants that remain asymptomatic are enriched in pathways for short-chain fatty acid production. We identify Prevotella strains that are more abundant at 1 month in infants that later develop diarrhea. At 8 months, the microbiomes of animals that experience diarrhea show increased abundance of Campylobacter and a reduction in Helicobacter macacae.

Conclusion

The composition of the microbial community could provide a phenotypic marker of an infant's susceptibility to diarrheal disease. Given the significant physiological and immunological similarities between human and nonhuman primates, these findings provide potential markers of susceptibility to diarrhea that could be modulated to improve infant health, especially in the developing world.\n\nMaturation of the infant rhesus macaque gut microbiome and its role in the development of diarrheal disease.", "token_count": 464, "char_count": 1861, "word_count": 264, "semantic_coherence": 1, "information_density": 0.5682, "quality_score": 0.7841, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:13.683986", "source": { "split": "train_shard_00002", "doc_id": 408 }, "chunk_id": "train_shard_00002_408_0", "global_id": 13274 }, { "text": "Studies on the flocculation characteristics of Kluyveromyces marxianus.", "token_count": 19, "char_count": 71, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:14.034866", "source": { "split": "train_shard_00002", "doc_id": 409 }, "chunk_id": "train_shard_00002_409_0", "global_id": 13275 }, { "text": "Porcine Escherichia coli ST131 isolates are scarcely documented. Here, whole genome sequencing and core genome (CG) and plasmidome analysis of seven isolates collected from diarrheic piglets and four from pork meat were performed. All of the 11 ST131 isolates belonged to serotype O25b:H4 and clade B and showed fimH22 allele or mutational derivatives. The 11 porcine isolates possessed virulence traits that classified the isolates as avian pathogenic, uropathogenic, and extraintestinal pathogenic E. coli-like (APEC-, UPEC-, and ExPEC-like) and constituted virotype D. The CG was performed for all porcine isolates in addition to 73 ST131 reference isolates from different origins. Within clade B, the CG showed nine subclusters, allowing us to describe five new subclades (B6, B6-like, B7, B8, and B9). There was an association between subclade B6, PST43, virotype D2, and food origin, whereas subclade B7 included PST9 isolates with virotype D5 from diarrheic piglets (p = 0.007). The distance between human and porcine isolates from subclades B6 and B7 had an average of 20 and 15 SNP/Mb, respectively. [F2:A-:B1]-IncF, ColE1-like, and IncX plasmids were the most prevalent. Besides, IncF plasmids harbored a ColV region frequent among APEC isolates. Antimicrobial resistance genes conferring resistance to penicillin, tetracycline, quinolones, and colistin were the most common", "token_count": 458, "char_count": 1412, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": { "genes": [ "ST131", "PST9", "PST43" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:14.667854", "source": { "split": "train_shard_00002", "doc_id": 410 }, "chunk_id": "train_shard_00002_410_0", "global_id": 13276 }, { "text": "The mcr-1.1 gene was detected in 5 of 11 porcine isolates, integrated into the chromosome of one isolate and into plasmids in the remainder isolates (two MOB H 11/IncHI2-ST4, one MOB P 3/IncX4, and one MOB F 12/IncF [F2:A-:B1] supposedly cointegrated with an IncHI2). The surrounding environments of the mcr-1 cassette showed variability. However, there were conserved structures within the same plasmid family. In conclusion, CG analysis defined five new subclades. The ST131 porcine isolates belonged to new subclades B6 and B7. Moreover, porcine and clinical human isolates were strongly related. The 11 porcine ST131 isolates harbored a wide variety of plasmids, virulence, and resistance genes. Furthermore, epidemic plasmids IncX4 and IncHI2 are responsible for the acquisition of mcr-1.1 gene. We hypothesize that the APEC-IncF plasmid acquired the mcr-1.1 gene via cointegrating an IncHI2 plasmid, which is worrying due to combination of virulence and resistance attributes in a single mobile genetic element.\n\nWhole Genome Sequencing and Characteristics of mcr-1-Harboring Plasmids of Porcine Escherichia coli Isolates Belonging to the High-Risk Clone O25b:H4-ST131 Clade B.", "token_count": 444, "char_count": 1312, "word_count": 173, "semantic_coherence": 1, "information_density": 0.6705, "quality_score": 0.8353, "entities": { "genes": [ "ST131", "ST4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:15.314430", "source": { "split": "train_shard_00002", "doc_id": 410 }, "chunk_id": "train_shard_00002_410_1", "global_id": 13277 }, { "text": "Corynebacterium pseudotuberculosis is a facultative intracellular pathogen and the causative agent of several infectious and contagious chronic diseases, including caseous lymphadenitis, ulcerative lymphangitis, mastitis, and edematous skin disease, in a broad spectrum of hosts. In addition, Corynebacterium pseudotuberculosis infections pose a rising worldwide economic problem in ruminants. The complete genome sequences of 15 C. pseudotuberculosis strains isolated from different hosts and countries were comparatively analyzed using a pan-genomic strategy. Phylogenomic, pan-genomic, core genomic, and singleton analyses revealed close relationships among pathogenic corynebacteria, the clonal-like behavior of C. pseudotuberculosis and slow increases in the sizes of pan-genomes. According to extrapolations based on the pan-genomes, core genomes and singletons, the C. pseudotuberculosis biovar ovis shows a more clonal-like behavior than the C. pseudotuberculosis biovar equi. Most of the variable genes of the biovar ovis strains were acquired in a block through horizontal gene transfer and are highly conserved, whereas the biovar equi strains contain great variability, both intra- and inter-biovar, in the 16 detected pathogenicity islands (PAIs). With respect to the gene content of the PAIs, the most interesting finding is the high similarity of the pilus genes in the biovar ovis strains compared with the great variability of these genes in the biovar equi strains. Concluding, the polymerization of complete pilus structures in biovar ovis could be responsible for a remarkable ability of these strains to spread throughout host tissues and penetrate cells to live intracellularly, in contrast with the biovar equi, which rarely attacks visceral organs. Intracellularly, the biovar ovis strains are expected to have less contact with other organisms than the biovar equi strains, thereby explaining the significant clonal-like behavior of the biovar ovis strains.", "token_count": 496, "char_count": 1982, "word_count": 276, "semantic_coherence": 1, "information_density": 0.5761, "quality_score": 0.788, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:15.975148", "source": { "split": "train_shard_00002", "doc_id": 411 }, "chunk_id": "train_shard_00002_411_0", "global_id": 13278 }, { "text": "The pan-genome of the animal pathogen Corynebacterium pseudotuberculosis reveals differences in genome plasticity between the biovar ovis and equi strains.", "token_count": 41, "char_count": 155, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:16.347926", "source": { "split": "train_shard_00002", "doc_id": 411 }, "chunk_id": "train_shard_00002_411_1", "global_id": 13279 }, { "text": "Escherichia coli K12 is a commensal bacteria and one of the best-studied model organisms. Salmonella enterica serovar Typhimurium, on the other hand, is a facultative intracellular pathogen. These two prokaryotic species can be considered related phylogenetically, and they share a large amount of their genetic material, which is commonly termed the \"core genome.\" Despite their shared core genome, both species display very different lifestyles, and it is unclear to what extent the core genome, apart from the species-specific genes, plays a role in this lifestyle divergence. In this study, we focus on the differences in expression domains for the orthologous genes in E. coli and S. Typhimurium. The iterative comparison of coexpression methodology was used on large expression compendia of both species to uncover the conservation and divergence of gene expression. We found that gene expression conservation occurs mostly independently from amino acid similarity. According to our estimates, at least more than one quarter of the orthologous genes has a different expression domain in E. coli than in S. Typhimurium. Genes involved with key cellular processes are most likely to have conserved their expression domains, whereas genes showing diverged expression are associated with metabolic processes that, although present in both species, are regulated differently. The expression domains of the shared \"core\" genome of E. coli and S. Typhimurium, consisting of highly conserved orthologs, have been tuned to help accommodate the differences in lifestyle and the pathogenic potential of Salmonella.\n\nExpression divergence between Escherichia coli and Salmonella enterica serovar Typhimurium reflects their lifestyles.", "token_count": 396, "char_count": 1728, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5913, "quality_score": 0.7956, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:16.998590", "source": { "split": "train_shard_00002", "doc_id": 412 }, "chunk_id": "train_shard_00002_412_0", "global_id": 13280 }, { "text": "

Background

Streptomycetes are filamentous soil-dwelling bacteria. They are best known as the producers of a great variety of natural products such as antibiotics, antifungals, antiparasitics, and anticancer agents and the decomposers of organic substances for carbon recycling. They are also model organisms for the studies of gene regulatory networks, morphological differentiation, and stress response. The availability of sets of genomes from closely related Streptomyces strains makes it possible to assess the mechanisms underlying genome plasticity and systems adaptation.

Results

We present the results of a comprehensive analysis of the genomes of five Streptomyces species with distinct phenotypes. These streptomycetes have a pan-genome comprised of 17,362 orthologous families which includes 3,096 components in the core genome, 5,066 components in the dispensable genome, and 9,200 components that are uniquely present in only one species. The core genome makes up about 33%-45% of each genome repertoire. It contains important genes for Streptomyces biology including those involved in gene regulation, secretion, secondary metabolism and morphological differentiation. Abundant duplicate genes have been identified, with 4%-11% of the whole genomes composed of lineage-specific expansions (LSEs), suggesting that frequent gene duplication or lateral gene transfer events play a role in shaping the genome diversification within this genus. Two patterns of expansion, single gene expansion and chromosome block expansion are observed, representing different scales of duplication.

Conclusions

Our results provide a catalog of genome components and their potential functional roles in gene regulatory networks and metabolic networks. The core genome components reveal the minimum requirement for streptomycetes to sustain a successful lifecycle in the soil environment, reflecting the effects of both genome evolution and environmental stress acting upon the expressed phenotypes. A better understanding of the LSE gene families will, on the other hand, bring a wealth of new insights into the mechanisms underlying strain-specific phenotypes, such as the production of novel antibiotics, pathogenesis, and adaptive response to environmental challenges.", "token_count": 513, "char_count": 2287, "word_count": 307, "semantic_coherence": 1, "information_density": 0.6189, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:04:17.662778", "source": { "split": "train_shard_00002", "doc_id": 413 }, "chunk_id": "train_shard_00002_413_0", "global_id": 13281 }, { "text": "Genome plasticity and systems evolution in Streptomyces.", "token_count": 13, "char_count": 56, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:17.999632", "source": { "split": "train_shard_00002", "doc_id": 413 }, "chunk_id": "train_shard_00002_413_1", "global_id": 13282 }, { "text": "Optimization studies for production of high fructose syrup from Jerusalem artichoke using calcium alginate immobilized cells of Kluyveromyces marxianus.", "token_count": 37, "char_count": 152, "word_count": 19, "semantic_coherence": 1, "information_density": 0.9474, "quality_score": 0.9737, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:18.359470", "source": { "split": "train_shard_00002", "doc_id": 414 }, "chunk_id": "train_shard_00002_414_0", "global_id": 13283 }, { "text": "

Objective

To evaluate the in vitro activity of antiseptics and detergents against Candida.

Design

One strain each of Candida albicans, Candida tropicalis, Candida lusitaniae, Candida parapsilosis, Candida kefyr, Candida glabrata, and an American Type Culture Collection strain of Escherichia coli (control) were studied. Clinical isolates were obtained from patients in a bone marrow unit of a large tertiary hospital. Antiseptic and disinfectant agents studied were used in the hospital where isolates were identified for cleaning of inanimate surfaces or hand washing. In vitro susceptibility was determined using a broth macrodilution method with exposure times to antiseptic or disinfectant agent of 15 seconds to 4 minutes and concentrations of agents that ranged from undiluted to 1:10,000 dilution.

Setting

A 900-bed teaching hospital.

Results

Of disinfectants tested, Vestal and Sparquat inhibited growth of all species at dilutions of < or = 1:100 at all contact times for all species. Clorox showed inhibition of growth at 1:100 dilution after 30 seconds of contact time for all isolates. Of antiseptics studied, Hibiclens inhibited growth of all species except C tropicalis at dilutions of < or = 1:100 at all contact times and for C tropicalis after 60 seconds. Clinidine inhibited growth of all species at dilutions of < or = 1:100 at all contact times for all species with the exception of Cglabrata and C tropicalis, which grew at the undiluted concentration. Ultradex failed to demonstrate killing of any species for any dilutions tested.

Conclusions

The results of this study show varying degrees of in vitro inhibition of growth by a variety of antiseptics and disinfectants against clinical isolates of Candida species from hospitalized patients.", "token_count": 493, "char_count": 1801, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5153, "quality_score": 0.7576, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:19.005317", "source": { "split": "train_shard_00002", "doc_id": 415 }, "chunk_id": "train_shard_00002_415_0", "global_id": 13284 }, { "text": "Comparative in vitro activity of antiseptics and disinfectants versus clinical isolates of Candida species.", "token_count": 25, "char_count": 107, "word_count": 14, "semantic_coherence": 1, "information_density": 0.9286, "quality_score": 0.9643, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:19.361958", "source": { "split": "train_shard_00002", "doc_id": 415 }, "chunk_id": "train_shard_00002_415_1", "global_id": 13285 }, { "text": "Streptococcus mitis is the closest relative of the major human pathogen S. pneumoniae. The 2,15 Mb sequence of the Streptococcus mitis B6 chromosome, an unusually high-level beta-lactam resistant and multiple antibiotic resistant strain, has now been determined to encode 2100 genes. The accessory genome is estimated to represent over 40%, including 75 mostly novel transposases and IS, the prophage phiB6 and another seven phage related regions. Tetracycline resistance mediated by Tn5801, and an unusual and large gene cluster containing three aminoglycoside resistance determinants have not been described in other Streptococcus spp. Comparative genomic analyses including hybridization experiments on a S. mitis B6 specific microarray reveal that individual S. mitis strains are almost as distantly related to the B6 strain as S. pneumoniae. Both species share a core of over 900 genes. Most proteins described as pneumococcal virulence factors are present in S. mitis B6, but the three choline binding proteins PcpA, PspA and PspC, and three gene clusters containing the hyaluronidase gene, ply and lytA, and the capsular genes are absent in S. mitis B6 and other S. mitis as well and confirm their importance for the pathogenetic potential of S. pneumoniae. Despite the close relatedness between the two species, the S. mitis B6 genome reveals a striking X-alignment when compared with S. pneumoniae.\n\nThe genome of Streptococcus mitis B6--what is a commensal?", "token_count": 399, "char_count": 1467, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6143, "quality_score": 0.8072, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:19.973572", "source": { "split": "train_shard_00002", "doc_id": 416 }, "chunk_id": "train_shard_00002_416_0", "global_id": 13286 }, { "text": "Background. Ruminants are successful herbivorous mammals, in part due to their specialized forestomachs, the rumen complex, which facilitates the conversion of feed to soluble nutrients by micro-organisms. Is the rumen complex a modified stomach expressing new epithelial (cornification) and metabolic programs, or a specialised stratified epithelium that has acquired new metabolic activities, potentially similar to those of the colon. How has the presence of the rumen affected other sections of the gastrointestinal tract (GIT) of ruminants compared to non-ruminants. Methods. Transcriptome data from 11 tissues covering the sheep GIT, two stratified epithelial and two control tissues, was analysed using principal components to cluster tissues based on gene expression profile similarity. Expression profiles of genes along the sheep GIT were used to generate a network to identify genes enriched for expression in different compartments of the GIT. The data from sheep was compared to similar data sets from two non-ruminants, pigs (closely related) and humans (more distantly related). Results. The rumen transcriptome clustered with the skin and tonsil, but not the GIT transcriptomes, driven by genes from the epidermal differentiation complex, and genes encoding stratified epithelium keratins and innate immunity proteins. By analysing all of the gene expression profiles across tissues together 16 major clusters were identified. The strongest of these, and consistent with the high turnover rate of the GIT, showed a marked enrichment of cell cycle process genes (P = 1.4 E-46), across the whole GIT, relative to liver and muscle, with highest expression in the caecum followed by colon and rumen. The expression patterns of several membrane transporters (chloride, zinc, nucleosides, amino acids, fatty acids, cholesterol and bile acids) along the GIT was very similar in sheep, pig and humans. In contrast, short chain fatty acid uptake and metabolism appeared to be different between the species and different between the rumen and colon in sheep", "token_count": 493, "char_count": 2063, "word_count": 307, "semantic_coherence": 1, "information_density": 0.5928, "quality_score": 0.7964, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:20.623206", "source": { "split": "train_shard_00002", "doc_id": 417 }, "chunk_id": "train_shard_00002_417_0", "global_id": 13287 }, { "text": "The importance of nitrogen and iodine recycling in sheep was highlighted by the highly preferential expression of SLC14A1-urea (rumen), RHBG-ammonia (intestines) and SLC5A5-iodine (abomasum). The gene encoding a poorly characterized member of the maltase-glucoamylase family (MGAM2), predicted to play a role in the degradation of starch or glycogen, was highly expressed in the small and large intestines. Discussion. The rumen appears to be a specialised stratified cornified epithelium, probably derived from the oesophagus, which has gained some liver-like and other specialized metabolic functions, but probably not by expression of pre-existing colon metabolic programs. Changes in gene transcription downstream of the rumen also appear have occurred as a consequence of the evolution of the rumen and its effect on nutrient composition flowing down the GIT.\n\nEpithelial, metabolic and innate immunity transcriptomic signatures differentiating the rumen from other sheep and mammalian gastrointestinal tract tissues.", "token_count": 259, "char_count": 1022, "word_count": 142, "semantic_coherence": 1, "information_density": 0.6761, "quality_score": 0.838, "entities": { "genes": [ "MGAM2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:21.161878", "source": { "split": "train_shard_00002", "doc_id": 417 }, "chunk_id": "train_shard_00002_417_1", "global_id": 13288 }, { "text": "

Background

Staphylococcus aureus is commonly carried asymptomatically in the human anterior nares and occasionally enters the bloodstream to cause invasive disease. Much of the global diversity of S. aureus remains uncharacterised, and is not clear how disease propensity varies between strains, and between host populations.

Methodology

We compared 147 isolates recovered from five kindergartens in Chengdu, China, with 51 isolates contemporaneously recovered from cases of pediatric infection from the main hospital serving this community. The samples were characterised by MLST, the presence/absence of PVL, and antibiotic resistance profiling.

Principal findings

Genotype frequencies within individual kindergartens differ, but the sample recovered from cases of disease shows a general enrichment of certain MLST genotypes and PVL positive isolates. Genotypes under-represented in the disease sample tend to correspond to a single sequence cluster, and this cluster is more common in China than in other parts of the world.

Conclusions/significance

Virulence propensity likely reflects a synergy between variation in the core genome (MLST) and accessory genome (PVL). By combining evidence form biogeography and virulence we demonstrate the existence of a \"native\" clade in West China which has lowered virulence, possibility due to acquired host immunity.\n\nBiogeography and virulence of Staphylococcus aureus.", "token_count": 350, "char_count": 1444, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6684, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:21.740214", "source": { "split": "train_shard_00002", "doc_id": 418 }, "chunk_id": "train_shard_00002_418_0", "global_id": 13289 }, { "text": "

Unlabelled

Background

The genus Mycobacterium comprises different species, among them the most contagious and infectious bacteria. The members of the complex Mycobacterium tuberculosis are the most virulent microorganisms that have killed human and other mammals since millennia. Additionally, with the many different mycobacterial sequences available, there is a crucial need for the visualization and the simplification of their data. In this present study, we aim to highlight a comparative genome, proteome and phylogeny analysis between twenty-one mycobacterial (Tuberculosis and non tuberculosis) strains using a set of computational and bioinformatics tools (Pan and Core genome plotting, BLAST matrix and phylogeny analysis).

Results

Considerably the result of pan and core genome Plotting demonstrated that less than 1250 Mycobacterium gene families are conserved across all species, and a total set of about 20,000 gene families within the Mycobacterium pan-genome of twenty one mycobacterial genomes.Viewing the BLAST matrix a high similarity was found among the species of the complex Mycobacterium tuberculosis and less conservation is found with other slow growing pathogenic mycobacteria.Phylogeny analysis based on both protein conservation, as well as rRNA clearly resolve known relationships between slow growing mycobacteria.

Conclusion

Mycobacteria include important pathogenic species for human and animals and the Mycobacterium tuberculosis complex is the most cause of death of the humankind. The comparative genome analysis could provide a new insight for better controlling and preventing these diseases.\n\nComputational genomics-proteomics and Phylogeny analysis of twenty one mycobacterial genomes (Tuberculosis & non Tuberculosis strains).", "token_count": 450, "char_count": 1796, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5872, "quality_score": 0.7936, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:22.377495", "source": { "split": "train_shard_00002", "doc_id": 419 }, "chunk_id": "train_shard_00002_419_0", "global_id": 13290 }, { "text": "

Background

The timing of and risk factors for intestinal colonization with multidrug-resistant Enterobacteriaceae (MDRE) are still poorly understood in areas with high MDRE carriage. We determined the prevalence, timing, and risk factors associated with MDRE intestinal colonization among infants in southern Sri Lanka.

Methods

Women and their newborn children were enrolled within 48 h after delivery in southern Sri Lanka. Rectal swabs were collected from women and infants at enrollment and 4-6 weeks later. Enterobacteriaceae were isolated and identified as MDRE (positive for extended-spectrum β-lactamases or carbapenem resistant) using standard microbiologic procedures. We used exact methods (Fisher's exact and Kruskal-Wallis tests) and multivariable logistic regression to identify sociodemographic and clinical features associated with MDRE intestinal colonization. Whole-genome sequencing was performed on selected MDRE isolates to identify phylogroups and antibiotic resistance-encoding genes were identified with NCBI's AMRfinder tool.

Results

Overall, 199 post-partum women and 199 infants were enrolled; 148/199 (74.4%) women and 151/199 (75.9%) infants were reassessed later in the community. Twenty-four/199 (12.1%) women and 3/199 (1.5%) infants displayed intestinal colonization with MDRE at enrollment, while 26/148 (17.6%) women and 24/151 (15.9%) infants displayed intestinal colonization with MDRE at the reassessment", "token_count": 421, "char_count": 1463, "word_count": 185, "semantic_coherence": 1, "information_density": 0.6378, "quality_score": 0.8189, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:23.001890", "source": { "split": "train_shard_00002", "doc_id": 420 }, "chunk_id": "train_shard_00002_420_0", "global_id": 13291 }, { "text": "While there were no risk factors associated with infant colonization at enrollment, multivariable analysis indicated that risk factors for infant colonization at reassessment included mother colonized at enrollment (aOR = 3.62) or reassessment (aOR = 4.44), delivery by Cesarean section (aOR = 2.91), and low birth weight (aOR = 5.39). Of the 20 MDRE isolates from infants that were sequenced, multilocus sequence typing revealed that 6/20 (30%) were clustered on the same branch as MDRE isolates found in the respective mothers. All sequenced isolates for mothers (47) and infants (20) had at least one ESBL-producing gene. Genes encoding fosfomycin resistance were found in 33/47 (70%) of mothers' isolates and 16/20 (80%) of infants' isolates and genes encoding resistance to colistin were found in one (2%) mother's isolate.

Conclusions

Our results suggest that a substantial proportion of infants undergo MDRE intestinal colonization within 6 weeks of birth, potentially due to postnatal rather than intranatal transmission.\n\nColonization with multidrug-resistant Enterobacteriaceae among infants: an observational study in southern Sri Lanka.", "token_count": 339, "char_count": 1155, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6848, "quality_score": 0.8424, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:23.561078", "source": { "split": "train_shard_00002", "doc_id": 420 }, "chunk_id": "train_shard_00002_420_1", "global_id": 13292 }, { "text": "

ABSTRACT

Next-generation sequencing is increasingly being used to examine closely related organisms. However, while genome-wide single nucleotide polymorphisms (SNPs) provide an excellent resource for phylogenetic reconstruction, to date evolutionary analyses have been performed using different ad hoc methods that are not often widely applicable across different projects. To facilitate the construction of robust phylogenies, we have developed a method for genome-wide identification/characterization of SNPs from sequencing reads and genome assemblies. Our phylogenetic and molecular evolutionary (PhaME) analysis software is unique in its ability to take reads and draft/complete genome(s) as input, derive core genome alignments, identify SNPs, construct phylogenies and perform evolutionary analyses. Several examples using genomes and read datasets for bacterial, eukaryotic and viral linages demonstrate the broad and robust functionality of PhaME. Furthermore, the ability to incorporate raw metagenomic reads from clinical samples with suspected infectious agents shows promise for the rapid phylogenetic characterization of pathogens within complex samples.\n\nFrom raw reads to trees: Whole genome SNP phylogenetics across the tree of life", "token_count": 280, "char_count": 1259, "word_count": 165, "semantic_coherence": 1, "information_density": 0.7394, "quality_score": 0.8697, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:24.109901", "source": { "split": "train_shard_00002", "doc_id": 421 }, "chunk_id": "train_shard_00002_421_0", "global_id": 13293 }, { "text": "

Background

Mycoplasma hominis is an opportunistic human pathogen, associated with clinically diverse disease. Currently, there is no standardised method for typing M. hominis, which would aid in understanding pathogen epidemiology and transmission. Due to availability and costs of whole genome sequencing and the challenges in obtaining adequate M. hominis DNA, the use of whole genome sequence analysis to provide clinical guidance is unpractical for this bacterial species as well as other fastidious organisms.

Results

This study identified pan-genome set of 700 genes found to be present in four published reference genomes. A subset of 417 genes was identified to be core genome for 18 isolates and 1 reference. Leave-one-out analysis of the core genes highlighted set of 48 genes that are required to recapture the original phylogenetic relationships observed using whole genome SNP analysis. Three 7-locus MLST schemas with high diversity index (97%) and low dN/dS ratios (0.1, 0.13, and 0.11) were derived that could be used to confer good discrimination between strains and could be of practical use in future studies direct on clinical specimens.

Conclusions

The genes proposed in this study could be utilised to design a cost-effective and rapid PCR-based MLST assay that could be applied directly to clinical isolates, without prior isolation. This study includes additional genomic analysis revealing high levels of genetic heterogeneity among this species. This provides a novel and evidence based approach for the development of MLST schema that accurately represent genomic phylogeny for use in epidemiology and transmission studies.\n\nGenomic determination of minimum multi-locus sequence typing schemas to represent the genomic phylogeny of Mycoplasma hominis.", "token_count": 421, "char_count": 1800, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6279, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:24.729770", "source": { "split": "train_shard_00002", "doc_id": 422 }, "chunk_id": "train_shard_00002_422_0", "global_id": 13294 }, { "text": "

ABSTRACT

Recurring epidemics of kiwifruit ( Actinidia spp.) bleeding canker disease are caused by Pseudomonas syringae pv. actinidiae ( Psa ), whose emergence coincided with domestication of its host. The most recent pandemic has had a deleterious effect on kiwifruit production worldwide. In order to strengthen understanding of population structure, phylogeography and evolutionary dynamics of Psa , we sampled 746 Pseudomonas isolates from cultivated and wild kiwifruit across six provinces in China, of which 87 were Psa . Of 234 Pseudomonas isolated from wild Actinidia spp. none were identified as Psa . Genome sequencing of fifty isolates and the inclusion of an additional thirty from previous studies show that China is the origin of the recently emerged pandemic lineage. However China harbours only a fraction of global Psa diversity, with greatest diversity found in Korea and Japan. Distinct transmission events were responsible for introduction of the pandemic lineage of Psa into New Zealand, Chile and Europe. Two independent transmission events occurred between China and Korea, and two Japanese isolates from 2014 cluster with New Zealand Psa . Despite high similarity at the level of the core genome and negligible impact of within-lineage recombination, there has been substantial gene gain and loss even within the single clade from which the global pandemic arose.

SIGNIFICANCE STATEMENT

Bleeding canker disease of kiwifruit caused by Pseudomonas syringae pv. actinidiae ( Psa ) has come to prominence in the last three decades. Emergence has coincided with domestication of the host plant and provides a rare opportunity to understand ecological and genetic factors affecting the evolutionary origins of Psa . Here, based on genomic analysis of an extensive set of strains sampled from China and augmented by isolates from a global sample, we show, contrary to earlier predictions, that China is not the native home of the pathogen, but is nonetheless the source of the recent global pandemic. Our data identify specific transmission events, substantial genetic diversity and point to non-agricultural plants in either Japan or Korea as home to the source population.", "token_count": 517, "char_count": 2208, "word_count": 337, "semantic_coherence": 1, "information_density": 0.5757, "quality_score": 0.7878, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:04:25.389443", "source": { "split": "train_shard_00002", "doc_id": 423 }, "chunk_id": "train_shard_00002_423_0", "global_id": 13295 }, { "text": "Origin and Evolution of a Pandemic Lineage of the Kiwifruit PathogenPseudomonas syringaepv.actinidiae", "token_count": 43, "char_count": 115, "word_count": 12, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:25.746896", "source": { "split": "train_shard_00002", "doc_id": 423 }, "chunk_id": "train_shard_00002_423_1", "global_id": 13296 }, { "text": "Pasteurella multocida is a Gram-negative commensal bacterium which resides in the upper respiratory tract of mammals and birds. The organism is responsible for a variety of economically important diseases in a wide range of domestic animal species. It causes fowl cholera of poultry, haemorrhagic septicaemia of cattle and water buffalo, atrophic rhinitis of pigs, and pneumonia of cattle, sheep and pigs. In the present study, P. multocida isolates were selected based on an established framework of evolutionary relationships among 123 isolates of P. multocida based on the concatenated partial sequences (3990 bp) of seven housekeeping enzyme genes (Davies et al., unpublished; http://pubmlst.org/pmultocida_multihost). The isolates were recovered from different host species (cattle, sheep, pigs and poultry) and were associated with different diseases. The isolates represented various capsular serotypes, outer membrane protein (OMP)-types, 16S rRNA types, and sequence types. Phylogenetic trees based on the concatenated partial sequences (3990 bp) of the seven housekeeping enzyme genes, complete sequences (22,371 bp) of fifteen housekeeping enzyme genes and the core genome were almost identical in their topographies. ... (continues)\n\nMolecular evolution of outer membrane proteins and characterization of temperate bacteriophages of Pasteurella multocida strains from different host species", "token_count": 364, "char_count": 1402, "word_count": 193, "semantic_coherence": 1, "information_density": 0.6321, "quality_score": 0.8161, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:26.331152", "source": { "split": "train_shard_00002", "doc_id": 424 }, "chunk_id": "train_shard_00002_424_0", "global_id": 13297 }, { "text": "Although noroviruses are the causative agents of most non-bacterial foodborne disease outbreaks, effective antivirals are currently unavailable. Certain probiotic strains have been reported as active antivirals for norovirus infections, but their mechanisms have not been fully elucidated. Herein, we examined the antiviral potential of 122 lactic acid bacteria isolates against murine norovirus (MNV), a human norovirus surrogate. A centenarian gut-derived strain, Limosilactobacillus fermentum PV22, exhibited the strongest MNV antagonism and reduced the viral titer by 2.23 ± 0.38 (log-value) in 5 min with stable activity at 25°C (P < 0.01). Genome mining revealed that its antiviral activity can be attributed to the synthesis of γ-aminobutyric acid, and this finding was experimentally verified. Furthermore, we demonstrated the safety of the isolate and its high intestinal colonization ability. In conclusion, we discovered a centenarian gut-derived L. fermentum strain with strong anti-norovirus activity and identified its antiviral metabolite. Our results will offer new solutions for the prevention and treatment of food-related norovirus infections.\n\nDetermination of Antiviral Mechanism of Centenarian Gut-Derived Limosilactobacillus fermentum Against Norovirus.", "token_count": 361, "char_count": 1304, "word_count": 171, "semantic_coherence": 1, "information_density": 0.731, "quality_score": 0.8655, "entities": { "genes": [ "PV22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:26.919301", "source": { "split": "train_shard_00002", "doc_id": 425 }, "chunk_id": "train_shard_00002_425_0", "global_id": 13298 }, { "text": "A whey protein hydrolysate was prepared by incubation of reconstituted whey or a whey protein concentrate with Alcalase 0.6L. The proteolytic degradation of alpha-lactalbumin and beta-lactoglobulin initially resulted in 6-kDa and, later, 2.5-kDa degradation products, quickly followed by the appearance of multiple peptides of 1 kDa or smaller. The hydrolysate showed a steady increase in solubility and a biphasic change in foaming characteristics with decreasing peptide size. At the highest degree of hydrolysis achieved (22%), the majority of the peptides were smaller than 1 kDa and could be efficiently assimilated by the yeast Kluyveromyces marxianus growing in a defined medium.\n\nPreparation and characterization of whey protein hydrolysates: applications in industrial whey bioconversion processes.", "token_count": 215, "char_count": 807, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6637, "quality_score": 0.8319, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:27.401376", "source": { "split": "train_shard_00002", "doc_id": 426 }, "chunk_id": "train_shard_00002_426_0", "global_id": 13299 }, { "text": "Extreme arid environments harbor diverse yet underexplored microorganisms with unique ecological adaptations and significant biotechnological potential. Here, we characterized a novel actinobacterium, strain SYSU D00978T, isolated from desert soil in the Gurbantunggut Desert, Xinjiang, China. The strain was Gram-stain-positive, aerobic, curved-rod-shaped, non-motile, catalase-positive, and oxidase-negative. Phylogenetic analysis based on the 16S rRNA gene placed it within the family Microbacteriaceae, showing highest similarity to Schumannella soli 10F1D-1T (97.3 % sequence identity) and Schumannella luteola KHIAT (97.2 %), while phylogenomic analyses consistently supported its distinction from known genera. The genome of SYSU D00978T was 2.98 Mb with a G + C content of 70.8 %. Comparative genomic analysis showed that its average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values against the closest related taxa were below the species delineation thresholds (ANI: 95-96 %; dDDH: 70 %). The strain exhibited psychrotolerance and pectin-degrading activity, indicating ecological adaptation to cold periods and involvement in organic matter turnover in desert soils. Functional annotation identified genes linked to oxidative and osmotic stress responses, carbon starvation, cold and heat shock, DNA repair, and ribosome hibernation, reflecting resilience to extreme conditions. Additionally, biosynthetic gene clusters for terpene, type III polyketide synthase, and beta-lactone suggested potential for novel bioactive compounds. Phenotypic and chemotaxonomic traits further supported its taxonomic novelty", "token_count": 496, "char_count": 1706, "word_count": 212, "semantic_coherence": 1, "information_density": 0.8019, "quality_score": 0.9009, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:28.879671", "source": { "split": "train_shard_00002", "doc_id": 427 }, "chunk_id": "train_shard_00002_427_0", "global_id": 13300 }, { "text": "Based on polyphasic evidence, strain SYSU D00978T (= CGMCC 1.18633T = MCCC 1K04997T = KCTC 49492T) represents a novel species of a new genus within the family Microbacteriaceae, for which the name Desertivibrio insolitus gen. nov., sp. nov. is proposed. This study expands our understanding of microbial diversity and ecological adaptations in extreme desert environments and provides a valuable resource for future biotechnological exploration.\n\nPolyphasic taxonomy and genome mining of <i>Desertivibrio insolitus</i> gen. nov., sp. nov., a novel psychrotolerant pectin-degrading actinobacterium isolated from desert soil.", "token_count": 231, "char_count": 693, "word_count": 85, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:29.350731", "source": { "split": "train_shard_00002", "doc_id": 427 }, "chunk_id": "train_shard_00002_427_1", "global_id": 13301 }, { "text": "DNA methylation is widespread among prokaryotes, and most DNA methylation reactions are catalyzed by adenine DNA methyltransferases, which are part of restriction-modification (R-M) systems. R-M systems are known for their role in the defense against foreign DNA; however, DNA methyltransferases also play functional roles in gene regulation. In this study, we used single-molecule real-time (SMRT) sequencing to uncover the genome-wide DNA methylation pattern in the opportunistic pathogen Pseudomonas aeruginosa PAO1. We identified a conserved sequence motif targeted by an adenine methyltransferase of a type I R-M system and quantified the presence of N6-methyladenine using liquid chromatography-tandem mass spectrometry (LC-MS/MS). Changes in the PAO1 methylation status were dependent on growth conditions and affected P. aeruginosa pathogenicity in a Galleria mellonella infection model. Furthermore, we found that methylated motifs in promoter regions led to shifts in sense and antisense gene expression, emphasizing the role of enzymatic DNA methylation as an epigenetic control of phenotypic traits in P. aeruginosa Since the DNA methylation enzymes are not encoded in the core genome, our findings illustrate how the acquisition of accessory genes can shape the global P. aeruginosa transcriptome and thus may facilitate adaptation to new and challenging habitats.IMPORTANCE With the introduction of advanced technologies, epigenetic regulation by DNA methyltransferases in bacteria has become a subject of intense studies. Here we identified an adenosine DNA methyltransferase in the opportunistic pathogen Pseudomonas aeruginosa PAO1, which is responsible for DNA methylation of a conserved sequence motif. The methylation level of all target sequences throughout the PAO1 genome was approximated to be in the range of 65 to 85% and was dependent on growth conditions", "token_count": 496, "char_count": 1942, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6105, "quality_score": 0.8052, "entities": { "genes": [ "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:30.001492", "source": { "split": "train_shard_00002", "doc_id": 428 }, "chunk_id": "train_shard_00002_428_0", "global_id": 13302 }, { "text": "Inactivation of the methyltransferase revealed an attenuated-virulence phenotype in the Galleria mellonella infection model. Furthermore, differential expression of more than 90 genes was detected, including the small regulatory RNA prrF1, which contributes to a global iron-sparing response via the repression of a set of gene targets. Our finding of a methylation-dependent repression of the antisense transcript of the prrF1 small regulatory RNA significantly expands our understanding of the regulatory mechanisms underlying active DNA methylation in bacteria.\n\nIdentification of a Pseudomonas aeruginosa PAO1 DNA Methyltransferase, Its Targets, and Physiological Roles.", "token_count": 182, "char_count": 702, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7191, "quality_score": 0.8596, "entities": { "genes": [ "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:30.446549", "source": { "split": "train_shard_00002", "doc_id": 428 }, "chunk_id": "train_shard_00002_428_1", "global_id": 13303 }, { "text": "Although there are increasing reports on the prevalence of Listeria monocytogenes in wild species, this is the first case of listeriosis in sea turtle. An adult female Caretta caretta was rescued after being stranded alive along the coast of the Abruzzo region (Italy) in summer 2021. The turtle died in 6 days due to respiratory failure. The necropsy showed widespread organ lesions, such as yellow foci of necrosis in many organs, gastrointestinal erosions, pericarditis, and granulomatous pneumonia. Microbiological and histological analyses were performed on several organs. Listeria monocytogenes was isolated from multiple organs, indicating a case of septicaemic listeriosis, and the genome was sequenced and characterized. All the colonies analysed belonged to the same strain serogroup IVb, ST388, and CC388.\n\nFirst Report of Septicaemic Listeriosis in a Loggerhead Sea Turtle (Caretta caretta) Stranded along the Adriatic Coast: Strain Detection and Sequencing.", "token_count": 288, "char_count": 999, "word_count": 141, "semantic_coherence": 1, "information_density": 0.7092, "quality_score": 0.8546, "entities": { "genes": [ "ST388", "CC388" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:31.003222", "source": { "split": "train_shard_00002", "doc_id": 429 }, "chunk_id": "train_shard_00002_429_0", "global_id": 13304 }, { "text": "In order to compare natural abundance isotopic properties of lactose with those of other carbohydrates such as glucose, fructose, sucrose and starch, the accessibility to ethanol obtained by fermentation, as a common probe, has been investigated. Only strictly reproducible isotopic fractionation will ensure that the fermentation products are always representative of their lactose precursor. An analytical strategy has therefore been designed that avoids discriminating isotope effects in the fermentation of pure lactose or whey permeates by Kluyveromyces fragilis. Appropriate experimental conditions ensure nearly full consumption of lactose and a high yield of conversion into ethanol. A lactose concentration of the order of magnitude of that found in whey permeates (50 g l-1) is convenient and an inoculum grown for 24 h is selected. Whereas sodium ions exert an inhibitory effect, added peptones optimize the fermentation process without introducing isotopic perturbations. The overall carbon isotope parameter of ethanol, delta 13C, is measured by isotope ratio mass spectrometry with a reproducibility of 0.2 per thousand and the site-specific natural isotope ratios of the methyl, (D/H)I, and methylene, (D/H)II, sites of ethanol are obtained with a reproducibility of about 1.5 ppm. These parameters provide useful criteria for comparing various starting materials such as lactoses (alpha or beta) from different commercial producers, milk powders, ordinary or skimmed milks and lactoserum. The methyl parameter, (D/H)I, mainly reflects the deuterium content of the lactose precursor, which is itself expected to provide information on the feeding of the animal and on the metabolism. The methylene isotope ratio is connected to that of the fermentation medium and may be influenced by isotopic fractionation introduced in the exchangeable sites of lactose by the extraction process.\n\nIsotopic characterization of the bioconversion of lactose into ethanol", "token_count": 484, "char_count": 1969, "word_count": 285, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:31.648351", "source": { "split": "train_shard_00002", "doc_id": 430 }, "chunk_id": "train_shard_00002_430_0", "global_id": 13305 }, { "text": "PCR primers were developed for the specific detection of Clavispora lusitaniae, Debaryomyces hansenii var hansenii, Geotrichum candidum, Kluyveromyces lactis and K. marxianus and Yarrowia lipolytica, yeast species commonly found on the surface of smear cheese. Forty eight representative strains frequently found in smear cheeses or taxonomically related to the target yeasts were used as templates, to validate the designed primers. The specific and selective detection of these yeasts was effective in situ, in Livarot smear, without yeast isolation and culture and was comparable with data obtained with a conventional method. The primers described here have thus potential for PCR studies applied to cheese. It should also be possible to use some of these primers with other substrates.\n\nDevelopment of primers for detecting dominant yeasts in smear-ripened cheeses.", "token_count": 210, "char_count": 870, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7008, "quality_score": 0.8504, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:32.117693", "source": { "split": "train_shard_00002", "doc_id": 431 }, "chunk_id": "train_shard_00002_431_0", "global_id": 13306 }, { "text": "A chromophorics and fluorescent analog of uridine 5'-monophosphate (UMP), a known competitive inhibitor of UDPglucose 4-epimerase was synthesised. This analog, namely 2',3'-O-(2,4,6-trinitrocyclohexadienylidene) uridine 5'-monophosphate, was found to be a powerful reversible inhibitor of UDPglucose 4-epimerase indicating its interaction with the substrate binding site of the enzyme. The extreme sensitivity of the fluorescence emission spectrum of this analog to solvent polarity makes it an excellent probe for the study of the environment at the active site of the enzyme. We report here the effective use of this UMP analog to demonstrate that the hydroxyl groups of the ribose moiety of UMP and presumably the substrates (UDPgalactose and UDPglucose) do not reside in a hydrophobic milieu.\n\nMicroenvironment at the substrate binding subsite of the active site of UDPglucose 4-epimerase from Kluyveromyces fragilis using a fluorescent analog of UMP.", "token_count": 272, "char_count": 955, "word_count": 136, "semantic_coherence": 1, "information_density": 0.5956, "quality_score": 0.7978, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:32.669317", "source": { "split": "train_shard_00002", "doc_id": 432 }, "chunk_id": "train_shard_00002_432_0", "global_id": 13307 }, { "text": "

Background

Staphylococcus argenteus and S. schweitzeri, were recently proposed as novel species within S. aureus complex (SAC). S. argenteus has been reported in many countries and can threaten human health. S. schweitzeri has not been associated with human infections, but has been isolated from non-human primates. Questions regarding the evolution of pathogenicity of these two species will remain elusive until an exploratory evolutionary framework is established.

Results

We present genomic comparison analysis among members of SAC based on a pan-genome definition, which included 15 S. argenteus genomes (five newly sequenced), six S. schweitzeri genomes and 30 divergent S. aureus genomes. The three species had divergent core genomes and rare interspecific recombination was observed among the core genes. However, some subtypes of staphylococcal cassette chromosome mec (SCCmec) elements and prophages were present in different species. Of 111 tested virulence genes of S. aureus, 85 and 86 homologous genes were found in S. argenteus and S. schweitzeri, respectively. There was no difference in virulence gene content among the three species, but the sequence of most core virulence genes was divergent. Analysis of the agr locus and the genes in the capsular polysaccharides biosynthetic operon revealed that they both diverged before the speciation of SAC members. Furthermore, the widespread geographic distribution of S. argenteus, sequence type 2250, showed ambiguous biogeographical structure among geographically isolated populations, demonstrating an international spread of this pathogen.

Conclusions

S. argenteus has spread among several countries, and invasive infections and persistent carriage may be not limited to currently reported regions. S. argenteus probably had undergone a recent host adaption and can cause human infections with a similar pathogenic potential.\n\nPreliminary comparative genomics revealed pathogenic potential and international spread of Staphylococcus argenteus.", "token_count": 500, "char_count": 2033, "word_count": 277, "semantic_coherence": 1, "information_density": 0.6318, "quality_score": 0.8159, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:33.330628", "source": { "split": "train_shard_00002", "doc_id": 433 }, "chunk_id": "train_shard_00002_433_0", "global_id": 13308 }, { "text": "Following an outbreak of Salmonella Typhimurium in Wales in July 2021 associated with sheep meat and offal, further genetically related cases were detected across the UK. Cases were UK residents with laboratory-confirmed Salmonella Typhimurium in the same 5-single-nucleotide polymorphism (SNP) single-linkage cluster with specimen date between 01/08/2021-2031/12/2022. We described cases using routine (UK) and enhanced (Wales only) surveillance data. Exposures in cases in Wales were compared with non-Typhimurium Salmonella case-controls. Environmental Health Practitioners and the Food Standards Agency investigated supply chains of food premises reported by ≥2 cases. Animal, carcass, and environmental samples taken for diagnostic or monitoring purposes for gastrointestinal pathogens were included in microbiological investigations. We identified 142 cases: 75% in England, 23% in Wales and 3% in Scotland. Median age was 32 years, and 59% were male. Direct contact with sheep was associated with becoming a case (aOR: 14, 95%CI: 1.4-145) but reported by few (6/32 cases). No single food item, premises, or supplier linked all cases. Multi-agency collaboration enabled the identification of isolates in the same 5-SNP single-linkage cluster from a sheep carcass at an English abattoir and in ruminant, wildlife, poultry, and environmental samples, suggesting multiple vehicles and pathways of infection.\n\nA genetically related cluster of Salmonella Typhimurium cases in humans associated with ruminant livestock and related food chains, United Kingdom, August 2021-December 2022.", "token_count": 456, "char_count": 1614, "word_count": 219, "semantic_coherence": 1, "information_density": 0.6621, "quality_score": 0.8311, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:33.964119", "source": { "split": "train_shard_00002", "doc_id": 434 }, "chunk_id": "train_shard_00002_434_0", "global_id": 13309 }, { "text": "The gut microbiome, linked significantly to host diseases, offers potential for disease diagnosis through machine learning (ML) pipelines. These pipelines, crucial in modeling diseases using high-dimensional microbiome data, involve selecting profile modalities, data preprocessing techniques, and classification algorithms, each impacting the model accuracy and generalizability. Despite whole metagenome shotgun sequencing (WMS) gaining popularity for human gut microbiome profiling, a consensus on the optimal methods for ML pipelines in disease diagnosis using WMS data remains elusive. Addressing this gap, we comprehensively evaluated ML methods for diagnosing Crohn's disease and colorectal cancer, using 2,553 fecal WMS samples from 21 case-control studies. Our study uncovered crucial insights: gut-specific, species-level taxonomic features proved to be the most effective for profiling; batch correction was not consistently beneficial for model performance; compositional data transformations markedly improved the models; and while nonlinear ensemble classification algorithms typically offered superior performance, linear models with proper regularization were found to be more effective for diseases that are linearly separable based on microbiome data. An optimal ML pipeline, integrating the most effective methods, was validated for generalizability using holdout data. This research offers practical guidelines for constructing reliable disease diagnostic ML models with fecal WMS data.\n\nComprehensive assessment of machine learning methods for diagnosing gastrointestinal diseases through whole metagenome sequencing data.", "token_count": 322, "char_count": 1643, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6857, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:34.532249", "source": { "split": "train_shard_00002", "doc_id": 435 }, "chunk_id": "train_shard_00002_435_0", "global_id": 13310 }, { "text": "Acinetobacter baumannii has rapidly emerged as a major cause of gram-negative hospital infections worldwide. A. baumannii encodes for the transport protein AceI, which confers resistance to chlorhexidine, a widely used antiseptic. AceI is also the prototype for the recently discovered proteobacterial antimicrobial compound efflux (PACE) family of transport proteins that confer resistance to a range of antibiotics and antiseptics in many gram-negative bacteria, including pathogens. The gene encoding AceI is conserved in the core genome of A. baumannii, suggesting that it has an important primordial function. This is incongruous with the sole characterized substrate of AceI, chlorhexidine, an entirely synthetic biocide produced only during the last century. Here we investigated a potential primordial function of AceI and other members of the PACE family in the transport of naturally occurring polyamines. Polyamines are abundant in living cells, where they have physiologically important functions and play multifaceted roles in bacterial infection. Gene expression studies revealed that the aceI gene is induced in A. baumannii by the short-chain diamines cadaverine and putrescine. Membrane transport experiments conducted in whole cells of A. baumannii and Escherichia coli and also in proteoliposomes showed that AceI mediates the efflux of these short-chain diamines when energized by an electrochemical gradient. Assays conducted using 8 additional diverse PACE family proteins identified 3 that also catalyze cadaverine transport. Taken together, these results demonstrate that short-chain diamines are common substrates for the PACE family of transport proteins, adding to their broad significance as a novel family of efflux pumps.\n\nShort-chain diamines are the physiological substrates of PACE family efflux pumps.", "token_count": 474, "char_count": 1884, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7954, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:35.173241", "source": { "split": "train_shard_00002", "doc_id": 436 }, "chunk_id": "train_shard_00002_436_0", "global_id": 13311 }, { "text": "

Background

Soil salinization is a worldwide problem that is intensifying because of the effects of climate change. An effective method for the reclamation of salt-affected soils involves initiating plant succession using fast growing, nitrogen fixing actinorhizal trees such as the Casuarina. The salt tolerance of Casuarina is enhanced by the nitrogen-fixing symbiosis that they form with the actinobacterium Frankia. Identification and molecular characterization of salt-tolerant Casuarina species and associated Frankia is imperative for the successful utilization of Casuarina trees in saline soil reclamation efforts. In this study, salt-tolerant and salt-sensitive Casuarina associated Frankia strains were identified and comparative genomics, transcriptome profiling, and proteomics were employed to elucidate the molecular mechanisms of salt and osmotic stress tolerance.

Results

Salt-tolerant Frankia strains (CcI6 and Allo2) that could withstand up to 1000 mM NaCl and a salt-sensitive Frankia strain (CcI3) which could withstand only up to 475 mM NaCl were identified. The remaining isolates had intermediate levels of salt tolerance with MIC values ranging from 650 mM to 750 mM. Comparative genomic analysis showed that all of the Frankia isolates from Casuarina belonged to the same species (Frankia casuarinae). Pangenome analysis revealed a high abundance of singletons among all Casuarina isolates. The two salt-tolerant strains contained 153 shared single copy genes (most of which code for hypothetical proteins) that were not found in the salt-sensitive(CcI3) and moderately salt-tolerant (CeD) strains. RNA-seq analysis of one of the two salt-tolerant strains (Frankia sp. strain CcI6) revealed hundreds of genes differentially expressed under salt and/or osmotic stress. Among the 153 genes, 7 and 7 were responsive to salt and osmotic stress, respectively", "token_count": 503, "char_count": 1893, "word_count": 263, "semantic_coherence": 1, "information_density": 0.5817, "quality_score": 0.7909, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:35.829874", "source": { "split": "train_shard_00002", "doc_id": 437 }, "chunk_id": "train_shard_00002_437_0", "global_id": 13312 }, { "text": "Proteomic profiling confirmed the transcriptome results and identified 19 and 8 salt and/or osmotic stress-responsive proteins in the salt-tolerant (CcI6) and the salt-sensitive (CcI3) strains, respectively.

Conclusion

Genetic differences between salt-tolerant and salt-sensitive Frankia strains isolated from Casuarina were identified. Transcriptome and proteome profiling of a salt-tolerant strain was used to determine molecular differences correlated with differential salt-tolerance and several candidate genes were identified. Mechanisms involving transcriptional and translational regulation, cell envelop remodeling, and previously uncharacterized proteins appear to be important for salt tolerance. Physiological and mutational analyses will further shed light on the molecular mechanism of salt tolerance in Casuarina associated Frankia isolates.\n\nGenomic, transcriptomic, and proteomic approaches towards understanding the molecular mechanisms of salt tolerance in Frankia strains isolated from Casuarina trees.", "token_count": 229, "char_count": 1029, "word_count": 122, "semantic_coherence": 1, "information_density": 0.6557, "quality_score": 0.8279, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:36.306989", "source": { "split": "train_shard_00002", "doc_id": 437 }, "chunk_id": "train_shard_00002_437_1", "global_id": 13313 }, { "text": "

Background

High-temperature fermentation is desirable for the industrial production of ethanol, which requires thermotolerant yeast strains. However, yeast thermotolerance is a complicated quantitative trait. The understanding of genetic basis behind high-temperature fermentation performance is still limited. Quantitative trait locus (QTL) mapping by pooled-segregant whole genome sequencing has been proved to be a powerful and reliable approach to identify the loci, genes and single nucleotide polymorphism (SNP) variants linked to quantitative traits of yeast.

Results

One superior thermotolerant industrial strain and one inferior thermosensitive natural strain with distinct high-temperature fermentation performances were screened from 124 Saccharomyces cerevisiae strains as parent strains for crossing and segregant isolation. Based on QTL mapping by pooled-segregant whole genome sequencing as well as the subsequent reciprocal hemizygosity analysis (RHA) and allele replacement analysis, we identified and validated total eight causative genes in four QTLs that linked to high-temperature fermentation of yeast. Interestingly, loss of heterozygosity in five of the eight causative genes including RXT2, ECM24, CSC1, IRA2 and AVO1 exhibited positive effects on high-temperature fermentation. Principal component analysis (PCA) of high-temperature fermentation data from all the RHA and allele replacement strains of those eight genes distinguished three superior parent alleles including VPS34, VID24 and DAP1 to be greatly beneficial to high-temperature fermentation in contrast to their inferior parent alleles", "token_count": 441, "char_count": 1702, "word_count": 210, "semantic_coherence": 1, "information_density": 0.6333, "quality_score": 0.8167, "entities": { "genes": [ "VPS34", "CSC1", "RXT2", "VID24", "DAP1", "ECM24", "AVO1", "IRA2" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:36.943902", "source": { "split": "train_shard_00002", "doc_id": 438 }, "chunk_id": "train_shard_00002_438_0", "global_id": 13314 }, { "text": "Strikingly, physiological impacts of the superior parent alleles of VPS34, VID24 and DAP1 converged on cell membrane by increasing trehalose accumulation or reducing membrane fluidity.

Conclusions

This work revealed eight novel causative genes and SNP variants closely associated with high-temperature fermentation performance. Among these genes, VPS34 and DAP1 would be good targets for improving high-temperature fermentation of the industrial yeast. It also showed that loss of heterozygosity of causative genes could contribute to the improvement of high-temperature fermentation capacities. Our findings would provide guides to develop more robust and thermotolerant strains for the industrial production of ethanol.\n\nQTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast.", "token_count": 222, "char_count": 879, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7156, "quality_score": 0.8578, "entities": { "genes": [ "VPS34", "VID24", "DAP1" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:37.414700", "source": { "split": "train_shard_00002", "doc_id": 438 }, "chunk_id": "train_shard_00002_438_1", "global_id": 13315 }, { "text": "In the past decade, molecular surveys of viral diversity have revealed that viruses are the most diverse and abundant biological entities on Earth. In culture, however, most viral isolates that infect microbes are represented by a few variants isolated on type strains, limiting our ability to study how natural variation affects virus-host interactions in the laboratory. We screened a set of 137 hot spring samples for viruses that infect a geographically diverse panel of the hyperthemophilic crenarchaeon Sulfolobus islandicus. We isolated and characterized eight SIRVs (Sulfolobus islandicus rod-shaped viruses) from two different regions within Yellowstone National Park (USA). Comparative genomics revealed that all SIRV sequenced isolates share 30 core genes that represent 50-60% of the genome. The core genome phylogeny, as well as the distribution of variable genes (shared by some but not all SIRVs) and the signatures of host-virus interactions recorded on the CRISPR (clustered regularly interspaced short palindromic repeats) repeat-spacer arrays of S. islandicus hosts, identify different SIRV lineages, each associated with a different geographic location. Moreover, our studies reveal that SIRV core genes do not appear to be under diversifying selection and thus we predict that the abundant and diverse variable genes govern the coevolutionary arms race between SIRVs and their hosts.\n\nDifferentiation and Structure in Sulfolobus islandicus Rod-Shaped Virus Populations.", "token_count": 366, "char_count": 1511, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6776, "quality_score": 0.8388, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:37.988738", "source": { "split": "train_shard_00002", "doc_id": 439 }, "chunk_id": "train_shard_00002_439_0", "global_id": 13316 }, { "text": "In bacterial populations, subtle expressional differences may promote ecological specialization through the formation of distinct ecotypes. In a barrier-free habitat, this process most likely precedes population divergence and may predict speciation events. To examine this, we used four sequenced strains of the bacterium Shewanella baltica, OS155, OS185, OS195, and OS223, as models to assess transcriptional variation and ecotype formation within a prokaryotic population. All strains were isolated from different depths throughout a water column of the Baltic Sea, occupying different ecological niches characterized by various abiotic parameters. Although the genome sequences are nearly 100% conserved, when grown in the laboratory under standardized conditions, all strains exhibited different growth rates, suggesting significant expressional variation. Using the Ecotype Simulation algorithm, all strains were considered to be discrete ecotypes when compared to 32 other S. baltica strains isolated from the same water column, suggesting ecological divergence. Next, we employed custom microarray slides containing oligonucleotide probes representing the core genome of OS155, OS185, OS195, and OS223 to detect natural transcriptional variation among strains grown under identical conditions. Significant transcriptional variation was noticed among all four strains. Differentially expressed gene profiles seemed to coincide with the metabolic signatures of the environment at the original isolation depth. Transcriptional pattern variations such as the ones highlighted here may be used as indicators of short-term evolution emerging from the formation of bacterial ecotypes. IMPORTANCE Eukaryotic studies have shown considerable transcriptional variation among individuals from the same population. It has been suggested that natural variation in eukaryotic gene expression may have significant evolutionary consequences and may explain large-scale phenotypic divergence of closely related species, such as humans and chimpanzees (M.-C. King and A. C. Wilson, Science 188:107-116, 1975, http://dx.doi.org/10.1126/science.1090005; M. F. Oleksiak, G. A. Churchill, and D. L", "token_count": 526, "char_count": 2203, "word_count": 289, "semantic_coherence": 1, "information_density": 0.6505, "quality_score": 0.8253, "entities": { "genes": [ "OS155", "OS185", "OS223", "OS195" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:04:38.642720", "source": { "split": "train_shard_00002", "doc_id": 440 }, "chunk_id": "train_shard_00002_440_0", "global_id": 13317 }, { "text": "Crawford, Nat Genet 32:261-266, 2002, http://dx.doi.org/10.1038/ng983). However, natural variation in gene expression is much less well understood in prokaryotic organisms. In this study, we used four sequenced strains of the marine bacterium Shewanella baltica to better understand the natural transcriptional divergence of a stratified prokaryotic population. We found substantial low-magnitude expressional variation among the four S. baltica strains cultivated under identical laboratory conditions. Collectively, our results indicate that transcriptional variation is an important factor for ecological speciation.\n\nShewanella baltica Ecotypes Have Wide Transcriptional Variation under the Same Growth Conditions.", "token_count": 202, "char_count": 739, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7528, "quality_score": 0.8764, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:39.117261", "source": { "split": "train_shard_00002", "doc_id": 440 }, "chunk_id": "train_shard_00002_440_1", "global_id": 13318 }, { "text": "

Background

Lactic acid bacteria (LAB) are a group of gram-positive, lactic acid producing Firmicutes. They have been extensively used in food fermentations, including the production of various dairy products. The proteolytic system of LAB converts proteins to peptides and then to amino acids, which is essential for bacterial growth and also contributes significantly to flavor compounds as end-products. Recent developments in high-throughput genome sequencing and comparative genomics hybridization arrays provide us with opportunities to explore the diversity of the proteolytic system in various LAB strains.

Results

We performed a genome-wide comparative genomics analysis of proteolytic system components, including cell-wall bound proteinase, peptide transporters and peptidases, in 22 sequenced LAB strains. The peptidase families PepP/PepQ/PepM, PepD and PepI/PepR/PepL are described as examples of our in silico approach to refine the distinction of subfamilies with different enzymatic activities. Comparison of protein 3D structures of proline peptidases PepI/PepR/PepL and esterase A allowed identification of a conserved core structure, which was then used to improve phylogenetic analysis and functional annotation within this protein superfamily.The diversity of proteolytic system components in 39 Lactococcus lactis strains was explored using pangenome comparative genome hybridization analysis. Variations were observed in the proteinase PrtP and its maturation protein PrtM, in one of the Opp transport systems and in several peptidases between strains from different Lactococcus subspecies or from different origin.

Conclusions

The improved functional annotation of the proteolytic system components provides an excellent framework for future experimental validations of predicted enzymatic activities. The genome sequence data can be coupled to other \"omics\" data e.g. transcriptomics and metabolomics for prediction of proteolytic and flavor-forming potential of LAB strains. Such an integrated approach can be used to tune the strain selection process in food fermentations.", "token_count": 516, "char_count": 2121, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6129, "quality_score": 0.8065, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:04:39.796208", "source": { "split": "train_shard_00002", "doc_id": 441 }, "chunk_id": "train_shard_00002_441_0", "global_id": 13319 }, { "text": "The proteolytic system of lactic acid bacteria revisited: a genomic comparison.", "token_count": 20, "char_count": 79, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:40.155091", "source": { "split": "train_shard_00002", "doc_id": 441 }, "chunk_id": "train_shard_00002_441_1", "global_id": 13320 }, { "text": "In common with other bacterial taxa, members of the genus Neisseria are classified using a range of phenotypic and biochemical approaches, which are not entirely satisfactory in assigning isolates to species groups. Recently, there has been increasing interest in using nucleotide sequences for bacterial typing and taxonomy, but to date, no broadly accepted alternative to conventional methods is available. Here, the taxonomic relationships of 55 representative members of the genus Neisseria have been analysed using whole-genome sequence data. As genetic material belonging to the accessory genome is widely shared among different taxa but not present in all isolates, this analysis indexed nucleotide sequence variation within sets of genes, specifically protein-coding genes that were present and directly comparable in all isolates. Variation in these genes identified seven species groups, which were robust to the choice of genes and phylogenetic clustering methods used. The groupings were largely, but not completely, congruent with current species designations, with some minor changes in nomenclature and the reassignment of a few isolates necessary. In particular, these data showed that isolates classified as Neisseria polysaccharea are polyphyletic and probably include more than one taxonomically distinct organism. The seven groups could be reliably and rapidly generated with sequence variation within the 53 ribosomal protein subunit (rps) genes, further demonstrating that ribosomal multilocus sequence typing (rMLST) is a practicable and powerful means of characterizing bacteria at all levels, from domain to strain.\n\nA genomic approach to bacterial taxonomy: an examination and proposed reclassification of species within the genus Neisseria.", "token_count": 379, "char_count": 1767, "word_count": 250, "semantic_coherence": 1, "information_density": 0.628, "quality_score": 0.814, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:40.785951", "source": { "split": "train_shard_00002", "doc_id": 442 }, "chunk_id": "train_shard_00002_442_0", "global_id": 13321 }, { "text": "

Background

Plant aquaporins are critical genetic players performing multiple biological functions, especially climate resilience and water-use efficiency. Their genomic diversity across genus Oryza is yet to be explored.

Results

This study identified 369 aquaporin-encoding genes from 11 cultivated and wild rice species and further categorized these into four major subfamilies, among which small basic intrinsic proteins are speculated to be ancestral to all land plant aquaporins. Evolutionarily conserved motifs in peptides of aquaporins participate in transmembrane transport of materials and their relatively complex gene structures provide an evolutionary playground for regulation of genome structure and transcription. Duplication and evolution analyses revealed higher genetic conservation among Oryza aquaporins and strong purifying selections are assisting in conserving the climate resilience associated functions. Promoter analysis highlighted enrichment of gene upstream regions with cis-acting regulatory elements involved in diverse biological processes, whereas miRNA target site prediction analysis unveiled substantial involvement of osa-miR2102-3p, osa-miR2927 and osa-miR5075 in post-transcriptional regulation of gene expression patterns. Moreover, expression patterns of japonica aquaporins were significantly perturbed in response to different treatment levels of six phytohormones and four abiotic stresses, suggesting their multifarious roles in plants survival under stressed environments. Furthermore, superior haplotypes of seven conserved orthologous aquaporins for higher thousand-grain weight are reported from a gold mine of 3,010 sequenced rice pangenomes.

Conclusions

This study unveils the complete genomic atlas of aquaporins across genus Oryza and provides a comprehensive genetic resource for genomics-assisted development of climate-resilient rice cultivars.\n\nGenomic diversity of aquaporins across genus Oryza provides a rich genetic resource for development of climate resilient rice cultivars.", "token_count": 461, "char_count": 2059, "word_count": 253, "semantic_coherence": 1, "information_density": 0.668, "quality_score": 0.834, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:41.431305", "source": { "split": "train_shard_00002", "doc_id": 443 }, "chunk_id": "train_shard_00002_443_0", "global_id": 13322 }, { "text": "

Background

Since 2009, the incidence of meningococcal serogroup W disease has increased rapidly in the UK because of a single strain (the so-called original UK strain) belonging to the hypervirulent sequence type-11 clonal complex (cc11), with a variant outbreak strain (the so-called 2013 strain) emerging in 2013. Subsequently, the Netherlands has had an increase in the incidence of meningococcal serogroup W disease. We assessed the temporal and phylogenetic associations between the serogroup W outbreaks in the Netherlands and England, and the historical serogroup C outbreaks in both countries.

Methods

For this observational cohort study, we used national surveillance data for meningococcal serogroup W and serogroup C disease in the Netherlands and England for the epidemiological years (July to June) 1992-93 to 2015-16. We also did whole genome sequencing and core genome multilocus sequence typing (1546 loci) on serogroup W disease isolates from both countries for surveillance years 2008-09 to 2015-16. We used Poisson regression to compare the annual relative increase in the incidence of serogroup W and serogroup C between both countries.

Findings

In the Netherlands, the incidence of meningococcal serogroup W disease increased substantially in 2015-16 compared with 2014-15, with an incidence rate ratio of 5·2 (95% CI 2·0-13·5) and 11% case fatality. In England, the incidence increased substantially in 2012-13 compared with 2011-12, with an incidence rate ratio of 1·8 (1·2-2·8)", "token_count": 453, "char_count": 1523, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5046, "quality_score": 0.7523, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:42.077727", "source": { "split": "train_shard_00002", "doc_id": 444 }, "chunk_id": "train_shard_00002_444_0", "global_id": 13323 }, { "text": "The relative increase in the Netherlands from 2014-15 to 2015-16 was 418% (95% CI 99-1248), which was significantly higher than the annual relative increase of 79% (61-99) per year in England from 2011-12 to 2014-15 (p=0·03). Cases due to meningococcal serogroup W cc11 (MenW:cc11) emerged in 2012-13 in the Netherlands. Of 29 MenW:cc11 cases found up to 2015-16, 26 (90%) were caused by the 2013 strain. For both the current serogroup W outbreak and the historical serogroup C outbreak, the increase in incidence started several years later in the Netherlands than in England, the rate of increase was higher in the Netherlands, and age distributions were similar in both countries.

Interpretation

Given the historical similarities of meningococcal serogroup W with meningococcal serogroup C emergence, the rapid expansion of the MenW:cc11 2013 strain in the Netherlands, its high case fatality, and the availability of a safe and effective vaccine, urgent consideration is needed for public health interventions in the Netherlands and other affected countries to prevent further serogroup W cases and deaths.

Funding

National Institute for Public Health and the Environment (Netherlands), Academic Medical Center (Netherlands), and Public Health England.\n\nTemporal associations between national outbreaks of meningococcal serogroup W and C disease in the Netherlands and England: an observational cohort study.", "token_count": 405, "char_count": 1426, "word_count": 206, "semantic_coherence": 1, "information_density": 0.5583, "quality_score": 0.7791, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:42.695848", "source": { "split": "train_shard_00002", "doc_id": 444 }, "chunk_id": "train_shard_00002_444_1", "global_id": 13324 }, { "text": "FIELD: food, agricultural and biotechnological industries. ^ SUBSTANCE: invention relates to manufacturing edible biologically active semifinished foodstuffs based on microorganisms. Method for preparing edible biologically active semifinished product involves milling the wetted edible carbohydrate vegetable substrate, among them, nutrient or agricultural waste. Then the milled mass is subjected for spontaneous fermentation under aerobic conditions due to the own microflora of substrate to be used. Then separate colonies are separated from the fermented substrate. The pure culture of thermotolerant yeast or yeast-like fungi is isolated from colonies that are taken among the following group of genus: Pichia, Candida, Rhodotorula, Metchnikovia that grow at temperature 30-37 C actively. For the further solid-phase fermentation cultures with cells size (1.5-4.0) x (3.0-10.0) mcm are selected and inoculated their on carbohydrate nutrient medium with neutral reaction that is applied on solid carrier providing the humidity index 30-75%. Solid-phase culturing is carried out under aerobic conditions at temperature 30-37 C for 12-48 h up to accumulation of 2-6 billion cells/g of wet culture. Then the grown culture is inactivated to obtain the end product. Invention provides preparing the universal edible biologically active semifinished product with prebiotic properties for different biological objects being both humans and animals. The prepared semifinished product promotes to the complex regulation of different functions in human and animal body also. ^ EFFECT: improved preparing method, valuable biological and medicinal properties of product. ^ 12 cl, 11 tbl, 11 ex\n\nMETHOD FOR PREPARING EDIBLE BIOLOGICALLY ACTIVE SEMIFINISHED PRODUCT AND EDIBLE BIOLOGICAL ACTIVE SEMIFINISHED PRODUCT PREPARED BY THIS METHOD", "token_count": 470, "char_count": 1830, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6078, "quality_score": 0.8039, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:43.341959", "source": { "split": "train_shard_00002", "doc_id": 445 }, "chunk_id": "train_shard_00002_445_0", "global_id": 13325 }, { "text": "Rhizobia are soil bacteria able to form symbioses with legumes and fix atmospheric nitrogen, converting it into a form that can be assimilated by the plant. The biological nitrogen fixation is a possible strategy to reduce the environmental pollution caused by the use of chemical N-fertilizers in agricultural fields. Successful colonization of the host root by free-living rhizobia requires that these bacteria are able to deal with adverse conditions in the soil, in addition to stresses that may occur in their endosymbiotic life inside the root nodules. Stress response genes, such as otsAB, groEL, clpB, rpoH play an important role in tolerance of free-living rhizobia to different environmental conditions and some of these genes have been shown to be involved in the symbiosis. This review will focus on stress response genes that have been reported to improve the symbiotic performance of rhizobia with their host plants. For example, chickpea plants inoculated with a Mesorhizobium strain modified with extra copies of the groEL gene showed a symbiotic effectiveness approximately 1.5 fold higher than plants inoculated with the wild-type strain. Despite these promising results, more studies are required to obtain highly efficient and tolerant rhizobia strains, suitable for different edaphoclimatic conditions, to be used as field inoculants.\n\nCan stress response genes be used to improve the symbiotic performance of rhizobia?", "token_count": 363, "char_count": 1482, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:43.921432", "source": { "split": "train_shard_00002", "doc_id": 446 }, "chunk_id": "train_shard_00002_446_0", "global_id": 13326 }, { "text": "We investigated the correlation between in vitro susceptibility to fluconazole and clinical response in severely ill patients with oropharyngeal candidiasis treated with fluconazole. The study included 48 adult patients, of whom 23 were neutropenic (absolute neutrophil count, < 500/mm3). Forty-eight isolates (20 Candida albicans, 12 Candida krusei, 10 Candida kefyr, 3 Torulopsis glabrata, and 3 Candida tropicalis) were tested for susceptibility to fluconazole with use of the macrodilution method of the National Committee for Clinical Laboratory Standards. A strain was considered to be susceptible to fluconazole if the MIC was < or = 8 micrograms/mL and resistant if the value was > or = 64 micrograms/mL. All but one of the resistant strains were C. krusei isolates. Species of causative Candida, persistent neutropenia, and susceptibility to fluconazole were significant predictors of clinical response by univariate analysis. Logistic regression analysis indicated that the only significant factor was the species of Candida isolates, validating the recently recommended MIC breakpoint and the correlation between clinical outcome and in vitro antifungal susceptibility.\n\nCorrelation of in vitro fluconazole susceptibility with clinical outcome for severely ill patients with oropharyngeal candidiasis.", "token_count": 340, "char_count": 1312, "word_count": 184, "semantic_coherence": 1, "information_density": 0.587, "quality_score": 0.7935, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:44.494611", "source": { "split": "train_shard_00002", "doc_id": 447 }, "chunk_id": "train_shard_00002_447_0", "global_id": 13327 }, { "text": "Candida albicans, Saccharomyces cerevisiae and their cell wall components, zymosan and glucan, have been shown to stimulate interleukin-8 (IL-8/CXCL-8) production by intestinal epithelial cell-like Caco-2 cells pre-cultured with 10 mM butyric acid. We examined in this study whether these yeasts also altered the production of other cytokines and cyclooxygenases (COXs) by Caco-2 cells. Culturing Caco-2 cells with 10 mM butyric acid and 15% FBS for 4 days enhanced the basal levels of mRNA encoding IL-6, IL-8, IL-18, monocyte chemoattractant protein (MCP)-1, stem cell factor, transforming growth factor (TGF)-beta1, TGF-beta3, tumor necrosis factor (TNF)-alpha, COX-1, and COX-2, but not of granulocyte-macrophage colony-stimulating factor (GM-CSF) and TGF-beta2. The inclusion of live S. cerevisiae or C. albicans further enhanced the production of IL-8, but not of the other cytokines and COXs. The non-pathogenic yeasts, C. kefyr, C. utilis, C. versatilis, Kluyveromyces lactis, K. marxianus, Schizosaccharomyces pombe and Zygosaccharomyces rouxii, used for the production of fermented foods and probiotics, and the opportunistic pathogens, C. glabrata, C. krusei, C. parapsilosis and C. tropicalis, isolated from human tissue samples also enhanced IL-8 secretion by Caco-2 cells.\n\nCytokine responses of intestinal epithelial-like Caco-2 cells to non-pathogenic and opportunistic pathogenic yeasts in the presence of butyric acid.", "token_count": 478, "char_count": 1436, "word_count": 199, "semantic_coherence": 1, "information_density": 0.6432, "quality_score": 0.8216, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:45.133783", "source": { "split": "train_shard_00002", "doc_id": 448 }, "chunk_id": "train_shard_00002_448_0", "global_id": 13328 }, { "text": "The disease caused by Shiga toxin-producing Escherichia coli (STEC) remains a significant public health challenge globally, but the incidence of human STEC infections in Australia remains relatively low. This study examined the virulence characteristics and diversity of STEC isolates in the state of New South Wales between December 2017 and May 2020. Utilisation of both whole and core genome multi-locus sequence typing (MLST) allowed for the inference of genomic diversity and detection of isolates that were likely to be epidemiologically linked. The most common STEC serotype and stx subtype detected in this study were O157:H7 and stx 1a, respectively. A genomic scan of other virulence factors present in STEC suggested interplay between iron uptake system and virulence factors that mediate either iron release or countermeasures against host defence that could result in a reduction of stx 1a expression. This reduced expression of the dominant stx genotype could contribute to the reduced incidence of STEC-related illness in Australia. Genomic surveillance of STEC becomes an important part of public health response and ongoing interrogation of virulence factors in STEC offers additional insights for the public health risk assessment.\n\nAdded Value of Genomic Surveillance of Virulence Factors in Shiga Toxin-Producing Escherichia coli in New South Wales, Australia.", "token_count": 363, "char_count": 1444, "word_count": 204, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:45.709249", "source": { "split": "train_shard_00002", "doc_id": 449 }, "chunk_id": "train_shard_00002_449_0", "global_id": 13329 }, { "text": "Hypervirulent atypical El Tor biotype Vibrio cholerae O1 isolates harbour mutations in the DNA-binding domain of the nucleoid-associated protein H-NS and the receiver domain of the response regulator VieA. Here, we provide two examples in which inactivation of H-NS in El Tor biotype vibrios unmasks hidden regulatory connections. First, deletion of the helix-turn-helix domain of VieA in an hns mutant background diminished biofilm formation and exopolysaccharide gene expression, a function that phenotypically opposes its phosphodiesterase activity. Second, deletion of vieA in an hns mutant diminished the expression of σE, a virulence determinant that mediates the envelope stress response. hns mutants were highly sensitive to envelope stressors compared to wild-type. However, deletion of vieA in the hns mutant restored or exceeded wild-type resistance. These findings suggest an evolutionary path for the emergence of hypervirulent strains starting from nucleotide sequence diversification affecting the interaction of H-NS with DNA.\n\nDeletion of gene encoding the nucleoid-associated protein H-NS unmasks hidden regulatory connections in El Tor biotype Vibrio cholerae.", "token_count": 296, "char_count": 1190, "word_count": 164, "semantic_coherence": 1, "information_density": 0.6159, "quality_score": 0.8079, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:46.264555", "source": { "split": "train_shard_00002", "doc_id": 450 }, "chunk_id": "train_shard_00002_450_0", "global_id": 13330 }, { "text": "

Background

Methicillin-resistant Staphylococcus aureus (MRSA) is a major cause of hospital-associated infection, but there is growing awareness of the emergence of multidrug-resistant lineages in community settings around the world. One such lineage is ST772-MRSA-V, which has disseminated globally and is increasingly prevalent in India. Here, we present the complete genome sequence of DAR4145, a strain of the ST772-MRSA-V lineage from India, and investigate its genomic characteristics in regards to antibiotic resistance and virulence factors.

Results

Sequencing using single-molecule real-time technology resulted in the assembly of a single continuous chromosomal sequence, which was error-corrected, annotated and compared to nine draft genome assemblies of ST772-MRSA-V from Australia, Malaysia and India. We discovered numerous and redundant resistance genes associated with mobile genetic elements (MGEs) and known core genome mutations that explain the highly antibiotic resistant phenotype of DAR4145. Staphylococcal toxins and superantigens, including the leukotoxin Panton-Valentinin Leukocidin, were predominantly associated with genomic islands and the phage φ-IND772PVL. Some of these mobile resistance and virulence factors were variably present in other strains of the ST772-MRSA-V lineage.

Conclusions

The genomic characteristics presented here emphasize the contribution of MGEs to the emergence of multidrug-resistant and highly virulent strains of community-associated MRSA. Antibiotic resistance was further augmented by chromosomal mutations and redundancy of resistance genes. The complete genome of DAR4145 provides a valuable resource for future investigations into the global dissemination and phylogeography of ST772-MRSA-V.\n\nSingle-molecule sequencing reveals the molecular basis of multidrug-resistance in ST772 methicillin-resistant Staphylococcus aureus.", "token_count": 512, "char_count": 1911, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6229, "quality_score": 0.8114, "entities": { "genes": [ "DAR4145", "ST772" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:47.290331", "source": { "split": "train_shard_00002", "doc_id": 451 }, "chunk_id": "train_shard_00002_451_0", "global_id": 13331 }, { "text": "Magnaporthe oryzae and Ustilaginoidea virens are two filamentous fungal pathogens that threaten rice production worldwide. Genetic tools that permit fast gene deletion and silencing are of great interest for functional genomics of fungal pathogens. As a revolutionary genome editing tool, clustered regularly interspaced palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) enable many innovative applications. Here, we developed a CRISPR interference (CRISPRi) toolkit using nuclease activity dead Cas9 (dCas9) to silence genes of interest in M. oryzae and U. virens. We optimized the components of CRISPRi vectors, including transcriptional repression domains, dCas9 promoters, and guide RNA (gRNA) promoters. The CRISPRi tool was tested using nine gRNAs to target the promoters of MoATG3, MoATG7, and UvPal1. The results indicated that a single gRNA could direct the dCas9-fused transcriptional repression domain to efficiently silence the target gene in M. oryzae and U. virens. In both fungi, the target genes were repressed >100-fold, and desired phenotypes were observed in CRISPRi strains. Importantly, we showed that multiple genes could be easily silenced using polycistronic tRNA-gRNA in CRISPRi. Furthermore, gRNAs that bind different promoter regions displayed variable repression levels of target genes, highlighting the importance of gRNA design for CRISPRi efficiency. Together, this study provides an efficient and robust CRISPRi tool for targeted gene silencing in M. oryzae and U. virens. Owing to its simplicity and multiplexity, CRISPRi will be a useful tool for gene function discovery in fungal pathogens. IMPORTANCE Many devastating plant diseases are caused by fungal pathogens that evolve rapidly to adapt to host resistance and environmental changes", "token_count": 504, "char_count": 1840, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:47.947483", "source": { "split": "train_shard_00002", "doc_id": 452 }, "chunk_id": "train_shard_00002_452_0", "global_id": 13332 }, { "text": "Therefore, genetic tools that enable fast gene function discovery are needed to study the pathogenicity and stress adaptation of fungal pathogens. In this study, we adopted the CRISPR/Cas9 system to silence genes in Magnaporthe oryzae and Ustilaginoidea virens, which are two dominant fungal pathogens that threaten rice production worldwide. We present a versatile and robust CRISPRi toolkit that represses target gene expression >100-fold using a single gRNA. We also demonstrated that CRISPRi could simultaneously silence multiple genes using the tRNA-gRNA strategy. The CRISPRi technologies described in this study would accelerate the functional genomics of fungal pathogens.\n\nCRISPR/dCas9-Mediated Gene Silencing in Two Plant Fungal Pathogens.", "token_count": 190, "char_count": 749, "word_count": 104, "semantic_coherence": 1, "information_density": 0.6827, "quality_score": 0.8413, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:48.399952", "source": { "split": "train_shard_00002", "doc_id": 452 }, "chunk_id": "train_shard_00002_452_1", "global_id": 13333 }, { "text": "Clinical isolates of Pseudomonas aeruginosa from patients with cystic fibrosis (CF) are known to differ from those associated with non-CF hosts by colony morphology, drug susceptibility patterns, and genomic hypermutability. Pseudomonas aeruginosa isolates from CF patients have long been recognized for their overall reduced rate of antimicrobial susceptibility, but their intraclonal MIC heterogeneity has long been overlooked. Using two distinct cohorts of clinical strains (n = 224 from 56 CF patients, n = 130 from 68 non-CF patients) isolated in 2013, we demonstrated profound Etest MIC heterogeneity in CF P. aeruginosa isolates in comparison to non-CF P. aeruginosa isolates. On the basis of whole-genome sequencing of 19 CF P. aeruginosa isolates from 9 patients with heterogeneous MICs, the core genome phylogenetic tree confirmed the within-patient CF P. aeruginosa clonal lineage along with considerable coding sequence variability. No extrachromosomal DNA elements or previously characterized antibiotic resistance mutations could account for the wide divergence in antimicrobial MICs between P. aeruginosa coisolates, though many heterogeneous mutations in efflux and porin genes and their regulators were present. A unique OprD sequence was conserved among the majority of isolates of CF P. aeruginosa analyzed, suggesting a pseudomonal response to selective pressure that is common to the isolates. Genomic sequence data also suggested that CF pseudomonal hypermutability was not entirely due to mutations in mutL, mutS, and uvr. We conclude that the net effect of hundreds of adaptive mutations, both shared between clonally related isolate pairs and unshared, accounts for their highly heterogeneous MIC variances", "token_count": 498, "char_count": 1822, "word_count": 249, "semantic_coherence": 1, "information_density": 0.6386, "quality_score": 0.8193, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:49.054287", "source": { "split": "train_shard_00002", "doc_id": 453 }, "chunk_id": "train_shard_00002_453_0", "global_id": 13334 }, { "text": "We hypothesize that this heterogeneity is indicative of the pseudomonal syntrophic-like lifestyle under conditions of being \"locked\" inside a host focal airway environment for prolonged periods. IMPORTANCE Patients with cystic fibrosis endure \"chronic focal infections\" with a variety of microorganisms. One microorganism, Pseudomonas aeruginosa, adapts to the host and develops resistance to a wide range of antimicrobials. Interestingly, as the infection progresses, multiple isogenic strains of P. aeruginosa emerge and coexist within the airways of these patients. Despite a common parental origin, the multiple strains of P. aeruginosa develop vastly different susceptibility patterns to actively used antimicrobial agents-a phenomenon we define as \"heterogeneous MICs.\" By sequencing pairs of P. aeruginosa isolates displaying heterogeneous MICs, we observed widespread isogenic gene lesions in drug transporters, DNA mismatch repair machinery, and many other structural or cellular functions. Coupled with the heterogeneous MICs, these genetic lesions demonstrated a symbiotic response to host selection and suggested evolution of a multicellular syntrophic bacterial lifestyle. Current laboratory standard interpretive criteria do not address the emergence of heterogeneous growth and susceptibilities in vitro with treatment implications.\n\nHeterogeneous Antimicrobial Susceptibility Characteristics in Pseudomonas aeruginosa Isolates from Cystic Fibrosis Patients.", "token_count": 381, "char_count": 1522, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6947, "quality_score": 0.8474, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:49.634539", "source": { "split": "train_shard_00002", "doc_id": 453 }, "chunk_id": "train_shard_00002_453_1", "global_id": 13335 }, { "text": "The role of Blastocystis in intestinal health is an open controversy, and little is known about the potential effect of this microorganism in autoinflammatory diseases such as spondyloarthritis (SpA). Here, we analyzed the gut microbiome of 36 SpA patients and 13 control individuals and demonstrated that the richness, diversity, and taxonomic composition between these two groups are different. We also showed that colonization by Blastocystis in control individuals increases the richness and diversity of the intestinal microbiome, whereas in SpA patients, it does not seem to have any impact. This may reflect a potential role of Blastocystis in sculpting the gut microbiome architecture in control individuals, whereas in subjects with SpA, the modulation of the microbiome may be governed by disease-dependent factors that cannot be overcome by Blastocystis. Regarding taxonomic characterization, SpA patients colonized by Blastocystis showed significant increases in the phylum Pseudomonadota, class Gammaproteobacteria, family Succinivibrionaceae, and genus Succinivibrio. Simultaneously, there were significant increases in the class Bacilli, order Lactobacillales, families Lactobacillaceae and Clostridiaceae, and genera Lactobacillus and Clostridium in non-colonized SpA patients. On the other hand, PICRUSt analysis in Blastocystis-positive SpA patients showed elevations in pathways that may enhance antioxidant capacities and alleviate intestinal inflammation, while Blastocystis-negative SpA patients showed significant changes in pathways that promote cell division/proliferation and can lead to larger changes in the gut microbiome. Our analyses lead us to believe that these changes in the gut microbiome of SpA patients may trigger protective mechanisms as an initial response to inflammation in an attempt to restore balance in the intestinal environment.\n\nDifferential gut microbiome in spondyloarthritis patients associated to Blastocystis colonization.", "token_count": 481, "char_count": 1977, "word_count": 266, "semantic_coherence": 1, "information_density": 0.5602, "quality_score": 0.7801, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:50.286228", "source": { "split": "train_shard_00002", "doc_id": 454 }, "chunk_id": "train_shard_00002_454_0", "global_id": 13336 }, { "text": "The composition of the gut microbiome was previously found to be associated with clinical responses to dyslipidemia, but there is limited consensus on the dynamic change of the gut microbiota during pregnancy and the specific microbiome characteristics linked to dyslipidemia in pregnant women. We collected fecal samples from 513 pregnant women at multiple time points during pregnancy in a prospective cohort. Taxonomic composition and functional annotations were determined by 16S rRNA amplicon sequencing and shotgun metagenomic sequencing. The predictive potential of gut microbiota on the risk of dyslipidemia was determined. The gut microbiome underwent dynamic changes during pregnancy, with significantly lower alpha diversity observed in dyslipidemic patients compared to their healthy counterparts. Several genera, including Bacteroides, Paraprevotella, Alistipes, Christensenellaceae R7 group, Clostridia UCG-014, and UCG-002 were negatively associated with lipid profiles and dyslipidemia. Further metagenomic analysis recognized a common set of pathways involved in gastrointestinal inflammation, where disease-specific microbes played an important role. Machine learning analysis confirmed the link between the microbiome and its progression to dyslipidemia, with a micro-averaged AUC of 0.824 (95% CI: 0.782-0.855) combined with blood biochemical data. Overall, the human gut microbiome, including Alistipes and Bacteroides, was associated with the lipid profile and maternal dyslipidemia during pregnancy by perturbing inflammatory functional pathways. Gut microbiota combined with blood biochemical data at the mid-pregnancy stage could predict the risk of dyslipidemia in late pregnancy. Therefore, the gut microbiota may represent a potential noninvasive diagnostic and therapeutic strategy for preventing dyslipidemia in pregnancy.\n\nEcological change of the gut microbiota during pregnancy and progression to dyslipidemia.", "token_count": 479, "char_count": 1943, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6016, "quality_score": 0.8008, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:50.931142", "source": { "split": "train_shard_00002", "doc_id": 455 }, "chunk_id": "train_shard_00002_455_0", "global_id": 13337 }, { "text": "

Background

The Zanzibar archipelago of Tanzania has become a low-transmission area for Plasmodium falciparum. Despite being considered an area of pre-elimination for years, achieving elimination has been difficult, likely due to a combination of imported infections from mainland Tanzania and continued local transmission.

Methods

To shed light on these sources of transmission, we applied highly multiplexed genotyping utilizing molecular inversion probes to characterize the genetic relatedness of 282 P. falciparum isolates collected across Zanzibar and in Bagamoyo district on the coastal mainland from 2016 to 2018.

Results

Overall, parasite populations on the coastal mainland and Zanzibar archipelago remain highly related. However, parasite isolates from Zanzibar exhibit population microstructure due to the rapid decay of parasite relatedness over very short distances. This, along with highly related pairs within shehias, suggests ongoing low-level local transmission. We also identified highly related parasites across shehias that reflect human mobility on the main island of Unguja and identified a cluster of highly related parasites, suggestive of an outbreak, in the Micheweni district on Pemba island. Parasites in asymptomatic infections demonstrated higher complexity of infection than those in symptomatic infections, but have similar core genomes.

Conclusions

Our data support importation as a main source of genetic diversity and contribution to the parasite population in Zanzibar, but they also show local outbreak clusters where targeted interventions are essential to block local transmission", "token_count": 403, "char_count": 1677, "word_count": 218, "semantic_coherence": 1, "information_density": 0.6514, "quality_score": 0.8257, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:51.596781", "source": { "split": "train_shard_00002", "doc_id": 456 }, "chunk_id": "train_shard_00002_456_0", "global_id": 13338 }, { "text": "These results highlight the need for preventive measures against imported malaria and enhanced control measures in areas that remain receptive to malaria reemergence due to susceptible hosts and competent vectors.

Funding

This research was funded by the National Institutes of Health, grants R01AI121558, R01AI137395, R01AI155730, F30AI143172, and K24AI134990. Funding was also contributed from the Swedish Research Council, Erling-Persson Family Foundation, and the Yang Fund. RV acknowledges funding from the MRC Centre for Global Infectious Disease Analysis (reference MR/R015600/1), jointly funded by the UK Medical Research Council (MRC) and the UK Foreign, Commonwealth & Development Office (FCDO), under the MRC/FCDO Concordat agreement and is also part of the EDCTP2 program supported by the European Union. RV also acknowledges funding by Community Jameel.\n\nStrong isolation by distance and evidence of population microstructure reflect ongoing Plasmodium falciparum transmission in Zanzibar.", "token_count": 280, "char_count": 1015, "word_count": 135, "semantic_coherence": 1, "information_density": 0.7185, "quality_score": 0.8593, "entities": { "genes": [ "EDCTP2" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:52.167591", "source": { "split": "train_shard_00002", "doc_id": 456 }, "chunk_id": "train_shard_00002_456_1", "global_id": 13339 }, { "text": "Antibiotic-induced gut dysbiosis (AID) is a frequent and serious side effect of antibiotic use and mitigating this dysbiosis is a critical therapeutic target. We propose that the host diet can modulate the chemical environment of the gut resulting in changes to the structure and function of the microbiome during antibiotic treatment. Gut dysbiosis is typically characterized by increases in aerobic respiratory bacterial metabolism, redox potential, and abundance of Proteobacteria. In this study, we explore dietary fiber supplements as potential modulators of the chemical environment in the gut to reduce this pattern of dysbiosis. Using defined-diets and whole-genome sequencing of female murine microbiomes during diet modulation and antibiotic treatment, we find that fiber prebiotics significantly reduced the impact of antibiotic treatment on microbiome composition and function. We observe reduced abundance of aerobic bacteria as well as metabolic pathways associated with oxidative metabolism. These metatranscriptomic results are corroborated by chemical measurements of eH and pH suggesting that fiber dampens the dysbiotic effects of antibiotics. This work indicates that fiber may act as a potential therapeutic for AID by modulating bacterial metabolism in the gut to prevent an increase in redox potential and protect commensal microbes during antibiotic treatment.\n\nFiber supplementation protects from antibiotic-induced gut microbiome dysbiosis by modulating gut redox potential.", "token_count": 344, "char_count": 1500, "word_count": 209, "semantic_coherence": 1, "information_density": 0.5694, "quality_score": 0.7847, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:52.777274", "source": { "split": "train_shard_00002", "doc_id": 457 }, "chunk_id": "train_shard_00002_457_0", "global_id": 13340 }, { "text": "We obtained the complete genome sequence of the psychrotolerant extremophile Pseudomonas sp. MPC6, a natural Polyhydroxyalkanoates (PHAs) producing bacterium able to rapidly grow at low temperatures. Genomic and phenotypic analyses allowed us to situate this isolate inside the Pseudomonas fluorescens phylogroup of pseudomonads as well as to reveal its metabolic versatility and plasticity. The isolate possesses the gene machinery for metabolizing a variety of toxic aromatic compounds such as toluene, phenol, chloroaromatics, and TNT. In addition, it can use both C6- and C5-carbon sugars like xylose and arabinose as carbon substrates, an uncommon feature for bacteria of this genus. Furthermore, Pseudomonas sp. MPC6 exhibits a high-copy number of genes encoding for enzymes involved in oxidative and cold-stress response that allows it to cope with high concentrations of heavy metals (As, Cd, Cu) and low temperatures, a finding that was further validated experimentally. We then assessed the growth performance of MPC6 on glycerol using a temperature range from 0 to 45°C, the latter temperature corresponding to the limit at which this Antarctic isolate was no longer able to propagate. On the other hand, the MPC6 genome comprised considerably less virulence and drug resistance factors as compared to pathogenic Pseudomonas strains, thus supporting its safety. Unexpectedly, we found five PHA synthases within the genome of MPC6, one of which clustered separately from the other four. This PHA synthase shared only 40% sequence identity at the amino acid level against the only PHA polymerase described for Pseudomonas (63-1 strain) able to produce copolymers of short- and medium-chain length PHAs. Batch cultures for PHA synthesis in Pseudomonas sp", "token_count": 490, "char_count": 1804, "word_count": 264, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "MPC6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:53.442483", "source": { "split": "train_shard_00002", "doc_id": 458 }, "chunk_id": "train_shard_00002_458_0", "global_id": 13341 }, { "text": "MPC6 using sugars, decanoate, ethylene glycol, and organic acids as carbon substrates result in biopolymers with different monomer compositions. This indicates that the PHA synthases play a critical role in defining not only the final chemical structure of the biosynthesized PHA, but also the employed biosynthetic pathways. Based on the results obtained, we conclude that Pseudomonas sp. MPC6 can be exploited as a bioremediator and biopolymer factory, as well as a model strain to unveil molecular mechanisms behind adaptation to cold and extreme environments.\n\nIn-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential.", "token_count": 207, "char_count": 767, "word_count": 105, "semantic_coherence": 1, "information_density": 0.781, "quality_score": 0.8905, "entities": { "genes": [ "MPC6" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:53.896864", "source": { "split": "train_shard_00002", "doc_id": 458 }, "chunk_id": "train_shard_00002_458_1", "global_id": 13342 }, { "text": "The in-vitro susceptibilities of 120 clinical isolates of yeasts to liposomal nystatin were compared with those to amphotericin B lipid complex (ABLC), liposomal amphotericin B (LAB), amphotericin B cholesteryl sulphate (ABCD), amphotericin B desoxycholate, nystatin, fluconazole and itraconazole. Yeast isolates examined included strains of Candida albicans, Candida parapsilosis, Candida glabrata, Candida krusei, Candida guilliermondii, Candida tropicalis, Candida kefyr, Candida viswanathii, Candida famata, Candida rugosa, Rhodotorula rubra, Trichosporon spp., Cryptococcus laurentii and Cryptococcus neoformans. The mean MICs for all strains examined were: liposomal nystatin 0.96 mg/L; nystatin 0.54 mg/L; ABLC 0.65 mg/L; LAB 1.07 mg/L; ABCD 0.75 mg/L; amphotericin B 0.43 mg/L; fluconazole 5.53 mg/L; and itraconazole 0.33 mg/L. No significant differences were seen between the activity of liposomal nystatin and the polyene drugs or itraconazole, but liposomal nystatin was more active than fluconazole. MICs were lower than the reported blood concentrations following therapeutic doses of this drug, indicating the potential for a therapeutic use of liposomal nystatin in humans. These results indicate good activity in vitro against medically important yeasts, which compares favourably with the activities of other currently available antifungal drugs. Liposomal nystatin may have a role in the treatment of disseminated and systemic mycoses.", "token_count": 468, "char_count": 1454, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:54.536773", "source": { "split": "train_shard_00002", "doc_id": 459 }, "chunk_id": "train_shard_00002_459_0", "global_id": 13343 }, { "text": "In-vitro antifungal activity of liposomal nystatin in comparison with nystatin, amphotericin B cholesteryl sulphate, liposomal amphotericin B, amphotericin B lipid complex, amphotericin B desoxycholate, fluconazole and itraconazole.", "token_count": 82, "char_count": 232, "word_count": 27, "semantic_coherence": 1, "information_density": 0.7778, "quality_score": 0.8889, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:54.899867", "source": { "split": "train_shard_00002", "doc_id": 459 }, "chunk_id": "train_shard_00002_459_1", "global_id": 13344 }, { "text": "

Introduction

Cardiac surgery-associated acute kidney injury (CSA-AKI) is a common hospital-acquired AKI that carries a grave disease burden. Recently, gut-kidney crosstalk has greatly changed our understanding of the pathogenesis of kidney diseases. However, the relationship between gut microbial dysbiosis and CSA-AKI remains unclear. The purpose of this study was to investigate the possible contributions of gut microbiota alterations in CSA-AKI patients.

Methods

Patients undergoing cardiac surgery were enrolled and divided into acute kidney injury (AKI) and Non_AKI groups. Faecal samples were collected before the operation. Shotgun metagenomic sequencing was performed to identify the taxonomic composition of the intestinal microbiome. All groups were statistically compared with alpha- and beta-diversity analysis, and linear discriminant analysis effect size (LEfSe) analysis was performed.

Results

A total of 70 individuals comprising 35 AKI and 35 Non_AKI were enrolled in the study. There was no significant difference between the AKI and Non_AKI groups with respect to the alpha-and beta-diversity of the Shannon index, Simpson or Chao1 index values except with respect to functional pathways (p < 0.05). However, the relative abundance of top 10 gut microbiota in CSA-AKI was different from the Non_AKI group. Interestingly, both LEfSe and multivariate analysis confirmed that the species Escherichia coli, Rothia mucilaginosa, and Clostridium innocuum were associated with CSA-AKI", "token_count": 430, "char_count": 1548, "word_count": 204, "semantic_coherence": 1, "information_density": 0.6569, "quality_score": 0.8284, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:55.524310", "source": { "split": "train_shard_00002", "doc_id": 460 }, "chunk_id": "train_shard_00002_460_0", "global_id": 13345 }, { "text": "Moreover, correlation heat map indicated that altered pathways and disrupted function could be attributed to disturbances of gut microbiota involving Escherichia coli.

Conclusion

Dysbiosis of the intestinal microbiota in preoperative stool affects susceptibility to CSA-AKI, indicating the crucial role of key microbial players in the development of CSA-AKI. This work provides valuable knowledge for further study of the contribution of gut microbiota in CSA-AKI.\n\nEvaluation of the contribution of gut microbiome dysbiosis to cardiac surgery-associated acute kidney injury by comparative metagenome analysis.", "token_count": 157, "char_count": 624, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7375, "quality_score": 0.8688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:55.959096", "source": { "split": "train_shard_00002", "doc_id": 460 }, "chunk_id": "train_shard_00002_460_1", "global_id": 13346 }, { "text": "A way of viewing the genetic information in all organisms on Earth as constituents of the Pangenome is proposed. According to this concept, the Pangenome is the common (collective) genetic system of all living organisms, the organic molecules and their complexes (DNA- and RNA-containing viruses, plasmids, transposons, insertion sequences) involved in the storage and transmission processes of genetic information. Pangenomic stability and variability are discussed. This concept alerts to the inherent fluidity and transmissibility of DNA among organisms of all types, including horizontal gene transfer between closely related and formally unrelated macro- and microorganisms. The roles of death and of all known food chains as universal ways of gene distribution among different organisms are discussed. The contribution of bacteria and viruses in maintaining the circulation of genes within the Pangenome is presented. This concept implies that newly emerging genes are not bound to disappear together with the death of an organism or the extinction of a species and microorganisms are the main pool of genes. Some negative aspects of the intervention of molecular genetics, biotechnology, and ecology, including the spread of transgenic plants and animals, are summarized. It is shown that this concept may be used in medicine for the prognosis of an epidemic situation, particularly newly spreading pathogens, and for the development of new methods for the prophylaxis and early diagnosis of oncologic diseases. This concept can also help to find promising approaches to the discovery of drugs with novel principles of action.\n\nThe pangenome concept: a unifying view of genetic information.", "token_count": 348, "char_count": 1697, "word_count": 253, "semantic_coherence": 1, "information_density": 0.5929, "quality_score": 0.7964, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:56.540056", "source": { "split": "train_shard_00002", "doc_id": 461 }, "chunk_id": "train_shard_00002_461_0", "global_id": 13347 }, { "text": "A Saccharomyces-cerevisiae-based simultaneous saccharification and fermentation (SSF) of lignocellulosic biomass is limited to an operating temperature of about 37 degrees C, and even a small increase in temperature can have a deleterious effect. This points to a need for a more thermotolerant yeast. To this end, S. cerevisiae D5A and a thermotolerant yeast, Candida acidothermophilum, were tested at 37 degrees C, 40 degrees C, and 42 degrees C using dilute-acid-pretreated poplar as substrate. At 40 degrees C, C. acidothermophilum produced 80% of the theoretical ethanol yield, which was higher than the yield from S. cerevisiae D5A at either 37 degrees C or 40 degrees C. At 42 degrees C, C. acidothermophilum showed a slight drop in performance. On the basis of preliminary estimates, SSF with C. acidothermophilum at 40 degrees C can reduce cellulase costs by about 16%. Proportionately greater savings can be realized at higher temperatures if such a high-temperature SSF is feasible. This demonstrates the advantage of using thermophilic or thermotolerant yeasts.\n\nEvaluation of Candida acidothermophilum in ethanol production from lignocellulosic biomass.", "token_count": 338, "char_count": 1166, "word_count": 174, "semantic_coherence": 1, "information_density": 0.5805, "quality_score": 0.7902, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:57.114087", "source": { "split": "train_shard_00002", "doc_id": 462 }, "chunk_id": "train_shard_00002_462_0", "global_id": 13348 }, { "text": "The prevalence of vaginal yeast species has been studied in 140 women (41 pregnant, 66 infertile and 33 healthy controls) attending a gynaecological private clinic in Amman, Jordan. Yeast species were isolated from pregnant (68.2%), infertile (51.5%) and healthy control (48.4%) women. Patients manifesting one, two or three symptoms of vulvovaginitis were 22.1%, 26.8% or 24.2% respectively. Asymptomatic cases and cases with more than three symptoms were 22.4% and 4.5% respectively. Candida albicans was the dominant species (in 51.3% of the patients) followed by C. glabrata (17.9%). The percentage occurrence as well as the pattern of Candida species differed among the different groups of patients. Candida kefyr was found to be significantly higher in the infertile women. In vitro sensitivity tests using amphotericin B, nystatin, miconazole nitrate and chlorhexidine were carried out; amphotericin B was the most effective and miconazole nitrate the least.\n\nPrevalence and susceptibility of vaginal yeast isolates in Jordan.", "token_count": 295, "char_count": 1033, "word_count": 152, "semantic_coherence": 1, "information_density": 0.6645, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:57.666781", "source": { "split": "train_shard_00002", "doc_id": 463 }, "chunk_id": "train_shard_00002_463_0", "global_id": 13349 }, { "text": "The nonpathogenic yeast Saccharomyces boulardii (Sb) has beneficial effects on the human intestine, and thus has been prescribed as probiotics for the treatment of diarrhea and gastrointestinal diseases. This is the only commercialized yeast with the purpose of being used as human medicine. Currently, little is known about their multiple mechanisms of actions. The S. boulardii yeast strain is isolated and identified by using the BIOLOGTM microarray identification system and morphologically. To understand its functional roles, the present study investigates the ability of this yeast to tolerate different concentrations of bile salt up to 2.5%, cell hydrophobicity, antioxidants, autoaggregation activity, and simulated gastrointestinal digestion. The effect of temperatures (up to 50°C), pH (up to 8.0), and salinity (at best 7%) was also monitored on the growth and survival of the yeast cell. The physicochemical analyses revealed that S. boulardii could survive in stomach conditions at pH 2.5, temperature 37°C, and 2% bile salt. Antibiotic susceptibility of S. boulardii was carried out using commercial antibiotic discs. The antimicrobial activity of the isolated S. boulardii against bacterial pathogens related to diarrhea diseases was in-vitro determined by the Well Diffusion method. The biosafety assay findings also claimed S. boulardii could be a potential probiotic. The experimental findings suggest that the isolated S. boulardii possesses excellent probiotic capacities as a biotherapeutic agent for antidiarrheal and gastrointestinal disorders.\n\nIdentification and Growth Characterization of a Novel Strain of Saccharomyces boulardii Isolated From Soya Paste.", "token_count": 496, "char_count": 1758, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6176, "quality_score": 0.8088, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "bile", "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:58.324423", "source": { "split": "train_shard_00002", "doc_id": 464 }, "chunk_id": "train_shard_00002_464_0", "global_id": 13350 }, { "text": "Yersinia pestis, the causative agent of plague, is best known for historical pandemics, but still actively causes disease in many parts of the world. Y. pestis is a recently derived clone of the pathogenic species Yersinia pseudotuberculosis, but is more associated with human infection. Numerous studies have documented genomic changes since the two species differentiated, although all of these studies used a relatively small sample set for defining these differences. In this study, we compared the complete genomic content between a diverse set of Y. pestis and Y. pseudotuberculosis genomes, and identified unique loci that could serve as diagnostic markers or for better understanding the evolution and pathogenesis of each group. Comparative genomics analyses also identified subtle variations in gene content between individual monophyletic clades within these species, based on a core genome single nucleotide polymorphism phylogeny that would have been undetected in a less comprehensive genome dataset. We also screened loci that were identified in other published studies as unique to either species and generally found a non-uniform distribution, suggesting that the assignment of these unique genes to either species should be re-evaluated in the context of current sequencing efforts. Overall, this study provides a high-resolution view into the genomic differences between Y. pestis and Y. pseudotuberculosis, demonstrating fine-scale differentiation and unique gene composition in both species.\n\nRedefining the differences in gene content between Yersinia pestis and Yersinia pseudotuberculosis using large-scale comparative genomics.", "token_count": 408, "char_count": 1715, "word_count": 234, "semantic_coherence": 1, "information_density": 0.6197, "quality_score": 0.8098, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:58.944036", "source": { "split": "train_shard_00002", "doc_id": 465 }, "chunk_id": "train_shard_00002_465_0", "global_id": 13351 }, { "text": "Phages promise to be important and unprecedented bioresources for use as tools. Rapid identification of new phages is pivotal for phage resource collection. However, current methods for their characterization are usually laborious and complex. Conserved gene sharing by the same phage group can be exploited to expedite this process. In this study, mycobacteriophages were used as a model phage group to test this approach. First, we obtained the core genome of mycobacteriophages, which was divided into six groups based on homology. Second, we found that one kind of gene belonging to group A (TM4 gene 23-like) was conserved among all mycobacteriophages, and the primers targeting such genes were designed to interrogate the diversity of mycobacteriophages. The obtained data indicate that the conserved genes present in groups of closely-related phages could be used to simplify and streamline new phage identification.\n\nFast detection of mycobacteriophages through conserved genes", "token_count": 230, "char_count": 985, "word_count": 146, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8253, "entities": { "genes": [ "TM4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:04:59.423496", "source": { "split": "train_shard_00002", "doc_id": 466 }, "chunk_id": "train_shard_00002_466_0", "global_id": 13352 }, { "text": "In this study we developed a genome-based method for detecting Staphylococcus aureus subtypes from metagenome shotgun sequence data. We used a binomial mixture model and the coverage counts at >100,000 known S. aureus SNP (single nucleotide polymorphism) sites derived from prior comparative genomic analysis to estimate the proportion of 40 subtypes in metagenome samples. We were able to obtain >87% sensitivity and >94% specificity at 0.025X coverage for S. aureus. We found that 321 and 149 metagenome samples from the Human Microbiome Project and metaSUB analysis of the New York City subway, respectively, contained S. aureus at genome coverage >0.025. In both projects, CC8 and CC30 were the most common S. aureus clonal complexes encountered. We found evidence that the subtype composition at different body sites of the same individual were more similar than random sampling and more limited evidence that certain body sites were enriched for particular subtypes. One surprising finding was the apparent high frequency of CC398, a lineage often associated with livestock, in samples from the tongue dorsum. Epidemiologic analysis of the HMP subject population suggested that high BMI (body mass index) and health insurance are possibly associated with S. aureus carriage but there was limited power to identify factors linked to carriage of even the most common subtype. In the NYC subway data, we found a small signal of geographic distance affecting subtype clustering but other unknown factors influence taxonomic distribution of the species around the city.\n\nThe single-species metagenome: subtyping Staphylococcus aureus core genome sequences from shotgun metagenomic data.", "token_count": 451, "char_count": 1736, "word_count": 254, "semantic_coherence": 1, "information_density": 0.622, "quality_score": 0.811, "entities": { "genes": [ "CC398", "CC30", "CC8" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:00.059341", "source": { "split": "train_shard_00002", "doc_id": 467 }, "chunk_id": "train_shard_00002_467_0", "global_id": 13353 }, { "text": "

Background

Helicobacter pylori is well known for its relationship with the occurrence of several severe gastric diseases. The mechanisms of pathogenesis triggered by H. pylori are less well known. In this study, we report the genome sequence and genomic characterizations of H. pylori strain HLJ039 that was isolated from a patient with gastric cancer in the Chinese province of Heilongjiang, where there is a high incidence of gastric cancer. To investigate potential genomic features that may be involved in pathogenesis of carcinoma, the genome was compared to three previously sequenced genomes in this area.

Result

We obtained 42 contigs with a total length of 1,611,192 bp and predicted 1,687 coding sequences. Compared to strains isolated from gastritis and ulcers in this area, 10 different regions were identified as being unique for HLJ039; they mainly encoded type II restriction-modification enzyme, type II m6A methylase, DNA-cytosine methyltransferase, DNA methylase, and hypothetical proteins. A unique 547-bp fragment sharing 93% identity with a hypothetical protein of Helicobacter cinaedi ATCC BAA-847 was not present in any other previous H. pylori strains. Phylogenetic analysis based on core genome single nucleotide polymorphisms shows that HLJ039 is defined as hspEAsia subgroup, which belongs to the hpEastAsia group.

Conclusion

DNA methylations, variations of the genomic regions involved in restriction and modification systems, are the \"hot\" regions that may be related to the mechanism of H. pylori-induced gastric cancer. The genome sequence will provide useful information for the deep mining of potential mechanisms related to East Asian gastric cancer.\n\nGenomic characterization of a Helicobacter pylori isolate from a patient with gastric cancer in China.", "token_count": 483, "char_count": 1810, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5985, "quality_score": 0.7992, "entities": { "genes": [ "HLJ039" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:00.705346", "source": { "split": "train_shard_00002", "doc_id": 468 }, "chunk_id": "train_shard_00002_468_0", "global_id": 13354 }, { "text": "The Brazilian Purpuric Fever (BPF) clone of Haemophilus influenzae biogroup Aegyptius (Hae) emerged in São Paulo in 1984, causing epidemic outbreaks of a life-threatening childhood infection characterised by shock and purpura fulminans. Strains of Hae have long been known to cause highly contagious and purulent conjunctivitis, but never previously implicated in invasive disease. Laboratory studies have revealed phenotypic and genetic differences between the BPF clone and other Hae strains, but failed to identify virulence factors responsible for the unusual virulence of this clone. This thesis describes the exhaustive annotation of the whole genome sequences of the invasive BPF clone isolate F3031 and non-invasive Hae conjunctivitis isolate F3047, inferring gene function through sequence homologies, and identifying insertions, deletions, pseudogenes and regulatory sites that may underlie phenotypic variation between these strains. Pan-genomic comparison of F3031 and F3047 to 5 other complete H. influenzae genomes allowed delineation of the 'Hae accessory genome', revealing a suite of novel adhesins not previously described for H. influenzae, presumably reflecting the conjunctival niche to which Hae has specialised. ... (continues)\n\nThe complete genome and functional analysis of the Brazilian Purpuric Fever clone of Haemophilus influenzae biogroup Aegyptius", "token_count": 349, "char_count": 1378, "word_count": 190, "semantic_coherence": 1, "information_density": 0.6684, "quality_score": 0.8342, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:01.293152", "source": { "split": "train_shard_00002", "doc_id": 469 }, "chunk_id": "train_shard_00002_469_0", "global_id": 13355 }, { "text": "

Objective

Mass drug administration (MDA) with azithromycin for trachoma elimination reduces nasopharyngeal carriage of Streptococcus pneumoniae in the short term. We evaluated S. pneumoniae carried in the nasopharynx before and after a round of azithromycin MDA to determine whether MDA was associated with changes in pneumococcal population structure and resistance.

Methods

We analysed 514 pneumococcal whole genomes randomly selected from nasopharyngeal samples collected in two Gambian villages that received three annual rounds of MDA for trachoma elimination. The 514 samples represented 293 participants, of which 75% were children aged 0-9 years, isolated during three cross-sectional surveys (CSSs) conducted before the third round of MDA (CSS-1) and at 1 (CSS-2) and 6 (CSS-3) months after MDA. Bayesian Analysis of Population Structure (BAPS) was used to cluster related isolates by capturing variation in the core genome. Serotype and multilocus sequence type were inferred from the genotype. Antimicrobial resistance determinants were identified from assemblies, including known macrolide resistance genes.

Results

Twenty-seven BAPS clusters were assigned. These consisted of 81 sequence types (STs). Two BAPS clusters not observed in CSS-1 (n = 109) or CSS-2 (n = 69), increased in frequency in CSS-3 (n = 126); BAPS20 (8.73%, p 0.016) and BAPS22 (7.14%, p 0.032) but were not associated with antimicrobial resistance", "token_count": 430, "char_count": 1453, "word_count": 203, "semantic_coherence": 1, "information_density": 0.6847, "quality_score": 0.8424, "entities": { "genes": [ "BAPS22", "BAPS20" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:01.922928", "source": { "split": "train_shard_00002", "doc_id": 470 }, "chunk_id": "train_shard_00002_470_0", "global_id": 13356 }, { "text": "Macrolide resistance within BAPS17 increased after treatment (CSS-1 n = 0/6, CSS-2/3 n = 5/5, p 0.002) and was carried on a mobile transposable element that also conferred resistance to tetracycline.

Discussion

Limited changes in pneumococcal population structure were observed after the third round of MDA, suggesting treatment had little effect on the circulating lineages. An increase in macrolide resistance within one BAPS highlights the need for antimicrobial resistance surveillance in treated villages.\n\nMass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx.", "token_count": 175, "char_count": 663, "word_count": 89, "semantic_coherence": 1, "information_density": 0.7528, "quality_score": 0.8764, "entities": { "genes": [ "BAPS17" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:02.374476", "source": { "split": "train_shard_00002", "doc_id": 470 }, "chunk_id": "train_shard_00002_470_1", "global_id": 13357 }, { "text": "Novel antifungal antibiotic, ergokonin C has the chemical name C-13-carboxy-3-O(2'-amino-2'-methylpropionylcarboxy) steriol and is of formula (I). USE/ADVANTAGE - (I) is an ergokonin-type antifungal and antibiotic cpd. In tests (I) has a minimal growth inhibiting effect of 0.3, 0.05 and 10 microg (I)/diffusion zone for candida befir, Kluyveromyces marxianus and Bacillus subtilis respectively. (I) are also intermediate in the prepn. of steroid cpds.\n\nNew 13-carboxy-sterol cpd. ergokonin C - useful as antibiotic and antifungal agent, and as intermediate for steroid synthesis", "token_count": 213, "char_count": 585, "word_count": 80, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:02.840173", "source": { "split": "train_shard_00002", "doc_id": 471 }, "chunk_id": "train_shard_00002_471_0", "global_id": 13358 }, { "text": "Bifidobacterium is a diverse genus of anaerobic, saccharolytic bacteria that colonize many animals, notably humans and other mammals. The presence of these bacteria in the gastrointestinal tract represents a potential coevolution between the gut microbiome and its mammalian host mediated by diet. To study the relationship between bifidobacterial gut symbionts and host nutrition, we analyzed the genome of two bifidobacteria strains isolated from the feces of a common marmoset (Callithrix jacchus), a primate species studied for its ability to subsist on host-indigestible carbohydrates. Whole genome sequencing identified these isolates as unique strains of Bifidobacterium callitrichos. All three strains, including these isolates and the previously described type strain, contain genes that may enable utilization of marmoset dietary substrates. These include genes predicted to contribute to galactose, arabinose, and trehalose metabolic pathways. In addition, significant genomic differences between strains suggest that bifidobacteria possess distinct roles in carbohydrate metabolism within the same host. Thus, bifidobacteria utilize dietary components specific to their host, both humans and non-human primates alike. Comparative genomics suggests conservation of possible coevolutionary relationships within the primate clade.\n\nThe comparative genomics of Bifidobacterium callitrichos reflects dietary carbohydrate utilization within the common marmoset gut.", "token_count": 356, "char_count": 1471, "word_count": 192, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:03.455502", "source": { "split": "train_shard_00002", "doc_id": 472 }, "chunk_id": "train_shard_00002_472_0", "global_id": 13359 }, { "text": "Salmonella enterica serovar Goldcoast infection was rare in Taiwan; it was not detected in routine surveillance from 2004 to 2013. This serovar was first identified in 2014, but the frequency of infection remained low until 2017. From 2014 to 2016, all but one isolate was pan-susceptible. S Goldcoast infections abruptly increased in 2018, and all isolates were multidrug-resistant (MDR). All MDR isolates harbored an IncHI2 plasmid, and the majority carried 14 antimicrobial resistance genes, aac(3)-IId, aadA22, aph(3')-Ia, aph(6)-Id, blaTEM-1B, blaCTX-M-55, lnu(F), floR, qnrS13, arr-2, sul2, sul3, tet(A), and dfrA14. S Goldcoast strains recovered in Taiwan and 96 of 99 strains from Germany, the Netherlands, the United Kingdom, and the United States belonged to sequence type 358 (ST358). Whole-genome single-nucleotide polymorphism and core genome multilocus sequence type analyses revealed that all strains of the ST358 clone shared a high degree of genetic relatedness. The present study highlighted that a dramatic increase in S Goldcoast infections followed the emergence of MDR strains and indicated that a genetically closely related S Goldcoast ST358 clone may have widespread significance internationally.", "token_count": 485, "char_count": 1369, "word_count": 176, "semantic_coherence": 1, "information_density": 0.6818, "quality_score": 0.8409, "entities": { "genes": [ "ST358" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:04.132374", "source": { "split": "train_shard_00002", "doc_id": 473 }, "chunk_id": "train_shard_00002_473_0", "global_id": 13360 }, { "text": "Emergence of Multidrug-Resistant Salmonella enterica Serovar Goldcoast Strains in Taiwan and International Spread of the ST358 Clone.", "token_count": 37, "char_count": 133, "word_count": 17, "semantic_coherence": 1, "information_density": 0.9412, "quality_score": 0.9706, "entities": { "genes": [ "ST358" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:04.522056", "source": { "split": "train_shard_00002", "doc_id": 473 }, "chunk_id": "train_shard_00002_473_1", "global_id": 13361 }, { "text": "Modern genomic and bioinformatic approaches have been applied to interrogate the V. cholerae genome, the role of genomic elements in cholera disease, and the origin, relatedness, and dissemination of epidemic strains. A universal attribute of choleragenic strains includes a repertoire of pathogenicity islands and virulence genes, namely the CTXϕ prophage and Toxin Co-regulated Pilus (TCP) in addition to other virulent genetic elements including those referred to as Seventh Pandemic Islands. During the last decade, the advent of Next Generation Sequencing (NGS) has provided highly resolved and often complete genomic sequences of epidemic isolates in addition to both clinical and environmental strains isolated from geographically unconnected regions. Genomic comparisons of these strains, as was completed during and following the Haitian outbreak in 2010, reveals that most epidemic strains appear closely related, regardless of region of origin. Non-O1 clinical or environmental strains may also possess some virulence islands, but phylogenic analysis of the core genome suggests they are more diverse and distantly related than those isolated during epidemics. Like Haiti, genomic studies that examine both the Vibrio core and pan-genome in addition to Single Nucleotide Polymorphisms (SNPs) conclude that a number of epidemics are caused by strains that closely resemble those in Asia, and often appear to originate there and then spread globally. The accumulation of SNPs in the epidemic strains over time can then be applied to better understand the evolution of the V. cholerae genome as an etiological agent.\n\nGenomic science in understanding cholera outbreaks and evolution of Vibrio cholerae as a human pathogen.", "token_count": 403, "char_count": 1730, "word_count": 254, "semantic_coherence": 1, "information_density": 0.6142, "quality_score": 0.8071, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:05.184506", "source": { "split": "train_shard_00002", "doc_id": 474 }, "chunk_id": "train_shard_00002_474_0", "global_id": 13362 }, { "text": "

Background

Crohn's disease (CD) is a chronic non-specific inflammatory bowel disease. Current CD therapeutics cannot fundamentally change the natural course of CD. Therefore, it is of great significance to find new treatment strategies for CD. Preclinical and clinical studies have shown that mesenchymal stromal cells (MSCs) are a promising therapeutic approach. However, the mechanism by which MSCs alleviate CD and how MSCs affect gut microbes are still unclear and need further elucidation.

Methods

We used 2,4,6-trinitrobenzenesulfonic acid (TNBS) to induce experimental colitis in mice and analysed the microbiota in faecal samples from the control group, the TNBS group and the TNBS + MSC group with faecal 16S rDNA sequencing. Subsequent analyses of alpha and beta diversity were all performed based on the rarified data. PICRUStII analysis was performed on the 16S rRNA gene sequences to infer the gut microbiome functions.

Results

MSC Treatment improved TNBS-induced colitis by increasing survival rates and relieving symptoms. A distinct bacterial signature was found in the TNBS group that differed from the TNBS + MSC group and controls. MSCs prevented gut microbiota dysbiosis, including increasing α-diversity and the amount of Bacteroidetes Firmicutes and Tenericutes at the phylum level and decreasing the amount of Proteobacteria at the phylum level. MSCs alleviated the increased activities of sulphur and riboflavin metabolism", "token_count": 415, "char_count": 1468, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6683, "quality_score": 0.8341, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:05.822897", "source": { "split": "train_shard_00002", "doc_id": 475 }, "chunk_id": "train_shard_00002_475_0", "global_id": 13363 }, { "text": "Meanwhile some metabolic pathways such as biosynthesis of amino acids lysine biosynthesis sphingolipid metabolism and secondary bile acid biosynthesis were decreased in the TNBS group compared with the control group and the TNBS + MSC group CONCLUSIONS: Overall, our findings preliminarily confirmed that colitis in mice is closely related to microbial and metabolic dysbiosis. MSC treatment could modulate the dysregulated metabolism pathways in mice with colitis, restoring the abnormal microbiota function to that of the normal control group. This study provides insight into specific intestinal microbiota and metabolism pathways linked with MSC treatment, suggesting a new approach to the treatment of CD.\n\nHuman umbilical cord-derived mesenchymal stem cells ameliorate experimental colitis by normalizing the gut microbiota.", "token_count": 219, "char_count": 830, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6897, "quality_score": 0.8448, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:06.291019", "source": { "split": "train_shard_00002", "doc_id": 475 }, "chunk_id": "train_shard_00002_475_1", "global_id": 13364 }, { "text": "The yeast, Kluyveromyces fragilis was permeabilized to a number of low-molecular-weight substrates using digitonin. The activities of intracellular yeast enzymes, viz., alcohol dehydrogenase (ADH), beta-galactosidase, glucose-6-phosphate dehydrogenase, aspartase, and hexokinase were found to be much higher in the permeabilized cells than the untreated cells. The optimum conditions for permeabilization with reference to ADH were 0.1% digitonin at 37 degrees C for 15 min. The ADH activity in permeabilized cells was several-fold higher than that in cell free extracts prepared by either physical or chemical methods.\n\nIn situ assay of intracellular enzymes of yeast (Kluyveromyces fragilis) by digitonin permeabilization of cell membrane.", "token_count": 216, "char_count": 741, "word_count": 101, "semantic_coherence": 1, "information_density": 0.7129, "quality_score": 0.8564, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:06.764201", "source": { "split": "train_shard_00002", "doc_id": 476 }, "chunk_id": "train_shard_00002_476_0", "global_id": 13365 }, { "text": "

Background

Recently, a new livestock-associated methicillin-resistant Staphylococcus aureus (MRSA) Sequence Type 398 (ST398) isolate has emerged worldwide. Although there have been reports of invasive disease in humans, MRSA ST398 colonization is much more common in livestock and demonstrates especially high prevalence rates in pigs and calves. The aim of this study was to compare the genome sequence of an ST398 MRSA isolate with other S. aureus genomes in order to identify genetic traits that may explain the success of this particular lineage. Therefore, we determined the whole genome sequence of S0385, an MRSA ST398 isolate from a human case of endocarditis.

Results

The entire genome sequence of S0385 demonstrated considerable accessory genome content differences relative to other S. aureus genomes. Several mobile genetic elements that confer antibiotic resistance were identified, including a novel composite of an type V (5C2&5) Staphylococcal Chromosome Cassette mec (SCCmec) with distinct joining (J) regions. The presence of multiple integrative conjugative elements combined with the absence of a type I restriction and modification system on one of the two nuSa islands, could enhance horizontal gene transfer in this strain. The ST398 MRSA isolate carries a unique pathogenicity island which encodes homologues of two excreted virulence factors; staphylococcal complement inhibitor (SCIN) and von Willebrand factor-binding protein (vWbp). However, several virulence factors such as enterotoxins and phage encoded toxins, including Panton-Valentine leukocidin (PVL), were not identified in this isolate.

Conclusions

Until now MRSA ST398 isolates did not cause frequent invasive disease in humans, which may be due to the absence of several common virulence factors. However, the proposed enhanced ability of these isolates to acquire mobile elements may lead to the rapid acquisition of determinants which contribute to virulence in human infections.", "token_count": 502, "char_count": 1993, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6344, "quality_score": 0.8172, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:07.415283", "source": { "split": "train_shard_00002", "doc_id": 477 }, "chunk_id": "train_shard_00002_477_0", "global_id": 13366 }, { "text": "Whole genome analysis of a livestock-associated methicillin-resistant Staphylococcus aureus ST398 isolate from a case of human endocarditis.", "token_count": 45, "char_count": 140, "word_count": 17, "semantic_coherence": 1, "information_density": 0.8824, "quality_score": 0.9412, "entities": { "genes": [ "ST398" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:07.779115", "source": { "split": "train_shard_00002", "doc_id": 477 }, "chunk_id": "train_shard_00002_477_1", "global_id": 13367 }, { "text": "

Background

RNA post-transcriptional modification is an exciting field of research that has evidenced this editing process as a sophisticated epigenetic mechanism to fine tune the ribosome function and to control gene expression. Although tRNA modifications seem to be more relevant for the ribosome function and cell physiology as a whole, some rRNA modifications have also been seen to play pivotal roles, essentially those located in central ribosome regions. RNA methylation at nucleobases and ribose moieties of nucleotides appear to frequently modulate its chemistry and structure. RNA methyltransferases comprise a superfamily of highly specialized enzymes that accomplish a wide variety of modifications. These enzymes exhibit a poor degree of sequence similarity in spite of using a common reaction cofactor and modifying the same substrate type.

Results

Relationships and lineages of RNA methyltransferases have been extensively discussed, but no consensus has been reached. To shed light on this topic, we performed amino acid and codon-based sequence analyses to determine phylogenetic relationships and molecular evolution. We found that most Class I RNA MTases are evolutionarily related to protein and cofactor/vitamin biosynthesis methyltransferases. Additionally, we found that at least nine lineages explain the diversity of RNA MTases. We evidenced that RNA methyltransferases have high content of polar and positively charged amino acid, which coincides with the electrochemistry of their substrates.

Conclusions

After studying almost 12,000 bacterial genomes and 2,000 patho-pangenomes, we revealed that molecular evolution of Class I methyltransferases matches the different rates of synonymous and non-synonymous substitutions along the coding region. Consequently, evolution on Class I methyltransferases selects against amino acid changes affecting the structure conformation.\n\nEvolutionary and sequence-based relationships in bacterial AdoMet-dependent non-coding RNA methyltransferases.", "token_count": 464, "char_count": 2034, "word_count": 268, "semantic_coherence": 1, "information_density": 0.653, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:08.418891", "source": { "split": "train_shard_00002", "doc_id": 478 }, "chunk_id": "train_shard_00002_478_0", "global_id": 13368 }, { "text": "Nucleic acid probes and primers are described for detecting fungi that cause disease in humans and animals, as well as spoilage of food and beverages. These probes can detect rRNA, rDNA or polymerase chain reaction products from a majority of fungi in clinical, environmental or food samples", "token_count": 70, "char_count": 291, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:08.794105", "source": { "split": "train_shard_00002", "doc_id": 479 }, "chunk_id": "train_shard_00002_479_0", "global_id": 13369 }, { "text": "Nucleic acid hybridization assay probes specific for Acremonium sp., Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus terreus, Aspergillus unguis, Aspergillus ustus, Beauveria sp., Bipolaris sp., Blastoschizomyces sp., Blastomyces dermatitidis, Candida albicans, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida lusitaniae, Candida parapsilosis, Candida tropicalis, Chrysosporium sp., Cladosporium sp., Coccidioides immitis,Cryptococcus neoformans var gattii serotype B, Cryptococcus neoformans serotype A, Cryptococcus laurentii, Cryptococcus terreus, Curvularia sp., Fusarium sp., Filobasidium capsuligenum, Filobasidiella (Cryptococcus) neoformans var bacillispora serotype C, Filobasidiella (Cryptococcus) neoformans var neoformans serotype D, Filobasidium uniguttulatum, Geotrichum sp., Histoplasma capsulatum, Malbranchea sp., Mucor sp., Paecilomyces sp., Penicillium species, Pseudallescheria boydii, Rhizopus sp., Sporothrix schenkii, Scopulariopsis brevicaulis, Scopulariopsis brumpti, Saccharomyces cerevisiae, and Trichosporon beigelii are also described.\n\nExtraction of DNA by boiling cells in an alkaline phenol/guanidine thiocyanate solution", "token_count": 487, "char_count": 1300, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6765, "quality_score": 0.8382, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:09.433548", "source": { "split": "train_shard_00002", "doc_id": 479 }, "chunk_id": "train_shard_00002_479_1", "global_id": 13370 }, { "text": "The Sensititre Yeast One method (AccuMed International Ltd, East Grinstead, UK) is a microplate-based procedure that incorporates an oxidation-reduction indicator, Alamar Blue, for the in-vitro testing of five antifungal agents (amphotericin B, fluconazole, itraconazole, ketoconazole and flucytosine). We compared this colorimetric method with a standard broth microdilution test, performed according to US National Committee for Clinical Laboratory Standards document M27-A guidelines, for determining the in-vitro susceptibilities of 180 isolates of Candida spp. (50 Candida albicans, 50 Candida glabrata, ten Candida kefyr, 20 Candida krusei, ten Candida lusitaniae, 20 Candida parapsilosis and 20 Candida tropicalis) and 20 isolates of Cryptococcus neoformans. The overall agreement between the results of the two methods (colorimetric MICs within +/- two log2 dilutions of standard MICs) were 99% for amphotericin B, 96.5% for flucytosine, 93% for itraconazole, 91.5% for fluconazole and 85.5% for ketoconazole. The overall levels of agreement between the two methods were > or = 94% for six of the eight species tested, the exceptions being C. neoformans and C. tropicalis where the overall agreement was 89% and 80% respectively. The poorest agreement between the results for individual agents was seen with C. tropicalis and the three azole agents (60-75% of colorimetric MICs within +/- two log2 dilutions of standard MICs), and C. neoformans for ketoconazole (50%). The Yeast One method appears to be a suitable alternative procedure for routine antifungal susceptibility testing of Candida spp. and C. neoformans.", "token_count": 492, "char_count": 1625, "word_count": 235, "semantic_coherence": 1, "information_density": 0.5617, "quality_score": 0.7809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:10.080608", "source": { "split": "train_shard_00002", "doc_id": 480 }, "chunk_id": "train_shard_00002_480_0", "global_id": 13371 }, { "text": "Comparison of a new commercial colorimetric microdilution method with a standard method for in-vitro susceptibility testing of Candida spp. and Cryptococcus neoformans.", "token_count": 44, "char_count": 168, "word_count": 22, "semantic_coherence": 1, "information_density": 0.8636, "quality_score": 0.9318, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:10.442611", "source": { "split": "train_shard_00002", "doc_id": 480 }, "chunk_id": "train_shard_00002_480_1", "global_id": 13372 }, { "text": "The complete nucleotide sequence of the beta-glucosidase gene of Kluyveromyces fragilis has been determined. This sequence contains an open reading frame of 2535 base pairs encoding a protein of 845 amino acids. Analysis of the transcription products revealed only one transcript of about 3 kb identical in both Kluyveromyces fragilis and in the expression host Saccharomyces cerevisiae. The protein molecular weight of 93,811 Kd deduced from the sequence is consistent with the 90,000 Kd determined by SDS polyacrylamide gel electrophoresis with the purified protein. Mapping of the starts of transcription shows that two starting points are used in the natural host Kluyveromyces fragilis. A comparison of the amino acid sequence with that of other beta-glucosidases revealed three regions of homology. One of these regions contains an amino acid sequence very similar to a peptide isolated from the active site of beta-glucosidase A3 from Aspergillus wentii and could be implicated in the catalytic mechanism of these glucolytic enzymes.\n\nSequence and transcription of the beta-glucosidase gene of Kluyveromyces fragilis cloned in Saccharomyces cerevisiae.", "token_count": 300, "char_count": 1159, "word_count": 171, "semantic_coherence": 1, "information_density": 0.5848, "quality_score": 0.7924, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:11.003848", "source": { "split": "train_shard_00002", "doc_id": 481 }, "chunk_id": "train_shard_00002_481_0", "global_id": 13373 }, { "text": "One fifth to one quarter of the human population is asymptomatically, naturally and persistently colonised by Staphylococcus aureus. Observational human studies indicate that although the whole population is intermittently exposed, some individuals lose S. aureus rapidly. Others become persistent carriers, as assessed by nasal cultures, with many individuals colonised for decades. Current animal models of S. aureus colonisation are expensive and normally require antibiotics. Importantly, these animal models have not yet contributed to our poor understanding of the dichotomy in human colonisation status. Here, we identify a single strain of S. aureus found to be persistently colonising the gastrointestinal tract of BALB/c mice. Phylogenetic analyses suggest it diverged from a human ST15 lineage in the recent past. We show that murine carriage of this organism occurs in the bowel and nares, is acquired early in life, and can persist for months. Importantly, we observe the development of persistent and non-persistent gastrointestinal carriage states in genetically identical mice. We developed a needle- and antibiotic-free model in which we readily induced S. aureus colonisation of the gastrointestinal tract experimentally by environmental exposure. Using our experimental model, impact of adaptive immunity on S. aureus colonisation could be assessed. Vaccine efficacy to eliminate colonisation could also be investigated using this model.\n\nDevelopment of persistent gastrointestinal S. aureus carriage in mice.", "token_count": 350, "char_count": 1528, "word_count": 216, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [ "ST15" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:11.576286", "source": { "split": "train_shard_00002", "doc_id": 482 }, "chunk_id": "train_shard_00002_482_0", "global_id": 13374 }, { "text": "Genome sequencing of Fusarium oxysporum revealed that pathogenic forms of this fungus harbour supernumerary chromosomes with a wide variety of genes, many of which likely encode traits required for pathogenicity or niche specialization. Specific transcription factor gene families are expanded on these chromosomes including the EBR1 family (Enhanced Branching). The significance of the EBR1 family expansion on supernumerary chromosomes and whether EBR1 paralogues are functional is currently unknown. EBR1 is found as a single copy in F.graminearum and other fungi but as multiple paralogues in pathogenic F.oxysporum strains. These paralogues exhibit sequence and copy number variation among different host-specific strains and even between more closely related strains. Relative expression of the EBR1 paralogues depends on growth conditions and on the presence of the single EBR1 gene in the core genome. Deletion of EBR1 in the core genome in different F.oxysporum strains resulted in impaired growth, reduced pathogenicity and slightly reduced biocontrol capacities. To identify genes regulated by EBR1, the transcriptomes of wild-type and Δebr1 strains were compared for both F.oxysporum and F.graminearum. These studies showed that in both species, EBR1 regulates genes involved in general metabolism as well as virulence.\n\nEBR1 genomic expansion and its role in virulence of Fusarium species.", "token_count": 346, "char_count": 1402, "word_count": 201, "semantic_coherence": 1, "information_density": 0.607, "quality_score": 0.8035, "entities": { "genes": [ "EBR1" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:12.152732", "source": { "split": "train_shard_00002", "doc_id": 483 }, "chunk_id": "train_shard_00002_483_0", "global_id": 13375 }, { "text": "Saccharomyces cerevisiae strains having a broad range of substrate utilization, rapid substrate consumption, and conversion to ethanol, as well as good tolerance to inhibitory conditions are ideal for cost-competitive ethanol production from lignocellulose. A major drawback to directly design S. cerevisiae tolerance to inhibitory conditions of lignocellulosic ethanol production processes is the lack of knowledge about basic aspects of its cellular signaling network in response to stress. Here, we highlight the inhibitory conditions found in ethanol production processes, the targeted cellular functions, the key contributions of integrated -omics analysis to reveal cellular stress responses according to these inhibitors, and current status on design-based engineering of tolerant and efficient S. cerevisiae strains for ethanol production from lignocellulose.\n\nModifying Yeast Tolerance to Inhibitory Conditions of Ethanol Production Processes.", "token_count": 210, "char_count": 952, "word_count": 126, "semantic_coherence": 1, "information_density": 0.627, "quality_score": 0.8135, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:12.617884", "source": { "split": "train_shard_00002", "doc_id": 484 }, "chunk_id": "train_shard_00002_484_0", "global_id": 13376 }, { "text": "

Background

Collimonas is a genus belonging to the class of Betaproteobacteria and consists mostly of soil bacteria with the ability to exploit living fungi as food source (mycophagy). Collimonas strains differ in a range of activities, including swimming motility, quorum sensing, extracellular protease activity, siderophore production, and antimicrobial activities.

Results

In order to reveal ecological traits possibly related to Collimonas lifestyle and secondary metabolites production, we performed a comparative genomics analysis based on whole-genome sequencing of six strains representing 3 recognized species. The analysis revealed that the core genome represents 43.1 to 52.7% of the genomes of the six individual strains. These include genes coding for extracellular enzymes (chitinase, peptidase, phospholipase), iron acquisition and type II secretion systems. In the variable genome, differences were found in genes coding for secondary metabolites (e.g. tripropeptin A and volatile terpenes), several unknown orphan polyketide synthase-nonribosomal peptide synthetase (PKS-NRPS), nonribosomal peptide synthetase (NRPS) gene clusters, a new lipopeptide and type III and type VI secretion systems. Potential roles of the latter genes in the interaction with other organisms were investigated. Mutation of a gene involved in tripropeptin A biosynthesis strongly reduced the antibacterial activity against Staphylococcus aureus, while disruption of a gene involved in the biosynthesis of the new lipopeptide had a large effect on the antifungal/oomycetal activities.

Conclusions

Overall our results indicated that Collimonas genomes harbour many genes encoding for novel enzymes and secondary metabolites (including terpenes) important for interactions with other organisms and revealed genomic plasticity, which reflect the behaviour, antimicrobial activity and lifestylesof Collimonas spp.\n\nExploring the genomic traits of fungus-feeding bacterial genus Collimonas.", "token_count": 514, "char_count": 2000, "word_count": 258, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:13.286739", "source": { "split": "train_shard_00002", "doc_id": 485 }, "chunk_id": "train_shard_00002_485_0", "global_id": 13377 }, { "text": "Antibiotic-induced gut microbiome dysbiosis (AID) is known to be influenced by host dietary composition. However, how and when diet modulates gut dysbiosis remains poorly characterized. Thus, here, we utilize a multi-omics approach to characterize how a diet supplemented with oats, a rich source of microbiota-accessible carbohydrates, or dextrose impacts amoxicillin-induced changes to gut microbiome structure and transcriptional activity. We demonstrate that oat administration during amoxicillin challenge provides greater protection from AID than the always oats or recovery oats diet groups. In particular, the group in which oats were provided at the time of antibiotic exposure induced the greatest protection against AID while the other oat diets saw greater effects after amoxicillin challenge. The oat diets likewise reduced amoxicillin-driven elimination of Firmicutes compared to the dextrose diet. Functionally, gut communities fed dextrose were carbohydrate starved and favored respiratory metabolism and consequent metabolic stress management while oat-fed communities shifted their transcriptomic profile and emphasized antibiotic stress management. The metabolic trends were exemplified when assessing transcriptional activity of the following two common gut commensal bacteria: Akkermansia muciniphila and Bacteroides thetaiotaomicron. These findings demonstrate that while host diet is important in shaping how antibiotics effect the gut microbiome composition and function, diet timing may play an even greater role in dietary intervention-based therapeutics. IMPORTANCE We utilize a multi-omics approach to demonstrate that diets supplemented with oats, a rich source of microbiota-accessible carbohydrates, are able to confer protection against antibiotic-induced dysbiosis (AID). Our findings affirm that not only is host diet important in shaping antibiotics effects on gut microbiome composition and function but also that the timing of these diets may play an even greater role in managing AID. This work provides a nuanced perspective on dietary intervention against AID and may be informative on preventing AID during routine antibiotic treatment.", "token_count": 508, "char_count": 2191, "word_count": 296, "semantic_coherence": 1, "information_density": 0.5541, "quality_score": 0.777, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:13.947209", "source": { "split": "train_shard_00002", "doc_id": 486 }, "chunk_id": "train_shard_00002_486_0", "global_id": 13378 }, { "text": "Short-Term Dietary Intervention with Whole Oats Protects from Antibiotic-Induced Dysbiosis.", "token_count": 29, "char_count": 91, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:14.301763", "source": { "split": "train_shard_00002", "doc_id": 486 }, "chunk_id": "train_shard_00002_486_1", "global_id": 13379 }, { "text": "Six bacterial genera containing species commonly used as probiotics for human consumption or starter cultures for food fermentation were compared and contrasted, based on publicly available complete genome sequences. The analysis included 19 Bifidobacterium genomes, 21 Lactobacillus genomes, 4 Lactococcus and 3 Leuconostoc genomes, as well as a selection of Enterococcus (11) and Streptococcus (23) genomes. The latter two genera included genomes from probiotic or commensal as well as pathogenic organisms to investigate if their non-pathogenic members shared more genes with the other probiotic genomes than their pathogenic members. The pan- and core genome of each genus was defined. Pairwise BLASTP genome comparison was performed within and between genera. It turned out that pathogenic Streptococcus and Enterococcus shared more gene families than did the non-pathogenic genomes. In silico multilocus sequence typing was carried out for all genomes per genus, and the variable gene content of genomes was compared within the genera. Informative BLAST Atlases were constructed to visualize genomic variation within genera. The clusters of orthologous groups (COG) classes of all genes in the pan- and core genome of each genus were compared. In addition, it was investigated whether pathogenic genomes contain different COG classes compared to the probiotic or fermentative organisms, again comparing their pan- and core genomes. The obtained results were compared with published data from the literature. This study illustrates how over 80 genomes can be broadly compared using simple bioinformatic tools, leading to both confirmation of known information as well as novel observations.\n\nComparative genomics of Bifidobacterium, Lactobacillus and related probiotic genera.", "token_count": 424, "char_count": 1781, "word_count": 256, "semantic_coherence": 1, "information_density": 0.5977, "quality_score": 0.7988, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:14.933327", "source": { "split": "train_shard_00002", "doc_id": 487 }, "chunk_id": "train_shard_00002_487_0", "global_id": 13380 }, { "text": "The problem of antibiotic resistance among pathogenic bacteria has reached a crisis level. The treatment options against infections caused by multiple drug-resistant bacteria are shrinking gradually. The current pace of the discovery of new antibacterial entities is lagging behind the rate of development of new resistance. Efflux pumps play a central role in making a bacterium resistant to multiple antibiotics due to their ability to expel a wide range of structurally diverse compounds. Besides providing an escape from antibacterial compounds, efflux pumps are also involved in bacterial stress response, virulence, biofilm formation, and altering host physiology. Efflux pumps are unique yet challenging targets for the discovery of novel efflux pump inhibitors (EPIs). EPIs could help rejuvenate our currently dried pipeline of antibacterial drug discovery. The current article highlights the recent developments in the field of efflux pumps, challenges faced during the development of EPIs and potential approaches for their development. Additionally, this review highlights the utility of resources such as natural products and machine learning to expand our EPIs arsenal using these latest technologies.\n\nRole of bacterial efflux pumps in antibiotic resistance, virulence, and strategies to discover novel efflux pump inhibitors.", "token_count": 278, "char_count": 1340, "word_count": 191, "semantic_coherence": 1, "information_density": 0.6597, "quality_score": 0.8298, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:15.497489", "source": { "split": "train_shard_00002", "doc_id": 488 }, "chunk_id": "train_shard_00002_488_0", "global_id": 13381 }, { "text": "Campylobacter is the leading cause of bacterial gastroenteritis worldwide and an emerging and neglected pathogen in South America. This zoonotic pathogen colonizes the gastrointestinal tract of a wide range of mammals and birds, with poultry as the most important reservoir for human infections. Apart from its high morbidity rates, the emergence of resistant strains is of global concern. The aims of this work were to determine genetic diversity, presence of antimicrobial resistance determinants and virulence potential of Campylobacter spp. isolated from patients with acute gastrointestinal disease at 'Clinica Alemana', Santiago de Chile. The study considered the isolation of Campylobacter spp., from stool samples during a 20-month period (January 2020 to September 2021). We sequenced (NextSeq, Illumina) and performed an in-depth analysis of the genome sequences of 88 Campylobacter jejuni and 2 Campylobacter coli strains isolated from clinical samples in Chile. We identified a high genetic diversity among C. jejuni strains and the emergence of prevalent clonal complexes, which were not identified in our previous reports. While ~40% of strains harbored a mutation in the gyrA gene associated with fluoroquinolone resistance, no macrolide-resistance determinants were detected. Interestingly, gene clusters encoding virulence factors such as the T6SS or genes associated with long-term sequelae such as Guillain-Barré syndrome showed lineage-relatedness. In addition, our analysis revealed a high degree of variability regarding the presence of fT3SS and T6SS effector proteins in comparison to type strains 81-176, F38011, and NCTC 11168 and 488. Our study provides important insights into the molecular epidemiology of this emerging foodborne pathogen", "token_count": 479, "char_count": 1809, "word_count": 252, "semantic_coherence": 1, "information_density": 0.631, "quality_score": 0.8155, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:16.174273", "source": { "split": "train_shard_00002", "doc_id": 489 }, "chunk_id": "train_shard_00002_489_0", "global_id": 13382 }, { "text": "In addition, the differences observed regarding the repertoire of fT3SS and T6SS effector proteins could have an impact on the pathogenic potential and transmissibility of these Latin American isolates, posing another challenge in characterizing the infection dynamics of this emergent and neglected bacterial pathogen.\n\nWhole-genome sequencing reveals changes in genomic diversity and distinctive repertoires of T3SS and T6SS effector candidates in Chilean clinical Campylobacter strains.", "token_count": 116, "char_count": 496, "word_count": 65, "semantic_coherence": 1, "information_density": 0.7692, "quality_score": 0.8846, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:16.567324", "source": { "split": "train_shard_00002", "doc_id": 489 }, "chunk_id": "train_shard_00002_489_1", "global_id": 13383 }, { "text": "

Background

The bacterial plant pathogenic Ralstonia species belong to the beta-proteobacteria class and are soil-borne pathogens causing vascular bacterial wilt disease, affecting a wide range of plant hosts. These bacteria form a heterogeneous group considered as a \"species complex\" gathering three newly defined species. Like many other Gram negative plant pathogens, Ralstonia pathogenicity relies on a type III secretion system, enabling bacteria to secrete/inject a large repertoire of type III effectors into their plant host cells. Type III-secreted effectors (T3Es) are thought to participate in generating a favorable environment for the pathogen (countering plant immunity and modifying the host metabolism and physiology).

Methods

Expert genome annotation, followed by specific type III-dependent secretion, allowed us to improve our Hidden-Markov-Model and Blast profiles for the prediction of type III effectors.

Results

We curated the T3E repertoires of 12 plant pathogenic Ralstonia strains, representing a total of 12 strains spread over the different groups of the species complex. This generated a pangenome repertoire of 102 T3E genes and 16 hypothetical T3E genes. Using this database, we scanned for the presence of T3Es in the 155 available genomes representing 140 distinct plant pathogenic Ralstonia strains isolated from different host plants in different areas of the globe. All this information is presented in a searchable database. A presence/absence analysis, modulated by a strain sequence/gene annotation quality score, enabled us to redefine core and accessory T3E repertoires.\n\nPangenomic type III effector database of the plant pathogenic Ralstonia spp.", "token_count": 460, "char_count": 1746, "word_count": 237, "semantic_coherence": 1, "information_density": 0.6414, "quality_score": 0.8207, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:17.257405", "source": { "split": "train_shard_00002", "doc_id": 490 }, "chunk_id": "train_shard_00002_490_0", "global_id": 13384 }, { "text": "

Background

Enterococcus faecalis is a multifaceted microorganism known to act as a beneficial intestinal commensal bacterium. It is also a dreaded nosocomial pathogen causing life-threatening infections in hospitalised patients. Isolates of a distinct MLST type ST40 represent the most frequent strain type of this species, distributed worldwide and originating from various sources (animal, human, environmental) and different conditions (colonisation/infection). Since enterococci are known to be highly recombinogenic we determined to analyse the microevolution and niche adaptation of this highly distributed clonal type.

Results

We compared a set of 42 ST40 isolates by assessing key molecular determinants, performing whole genome sequencing (WGS) and a number of phenotypic assays including resistance profiling, formation of biofilm and utilisation of carbon sources. We generated the first circular closed reference genome of an E. faecalis isolate D32 of animal origin and compared it with the genomes of other reference strains. D32 was used as a template for detailed WGS comparisons of high-quality draft genomes of 14 ST40 isolates. Genomic and phylogenetic analyses suggest a high level of similarity regarding the core genome, also demonstrated by similar carbon utilisation patterns. Distribution of known and putative virulence-associated genes did not differentiate between ST40 strains from a commensal and clinical background or an animal or human source. Further analyses of mobile genetic elements (MGE) revealed genomic diversity owed to: (1) a modularly structured pathogenicity island; (2) a site-specifically integrated and previously unknown genomic island of 138 kb in two strains putatively involved in exopolysaccharide synthesis; and (3) isolate-specific plasmid and phage patterns. Moreover, we used different cell-biological and animal experiments to compare the isolate D32 with a closely related ST40 endocarditis isolate whose draft genome sequence was also generated", "token_count": 479, "char_count": 2019, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6547, "quality_score": 0.8273, "entities": { "genes": [ "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:17.912095", "source": { "split": "train_shard_00002", "doc_id": 491 }, "chunk_id": "train_shard_00002_491_0", "global_id": 13385 }, { "text": "D32 generally showed a greater capacity of adherence to human cell lines and an increased pathogenic potential in various animal models in combination with an even faster growth in vivo (not in vitro).

Conclusion

Molecular, genomic and phenotypic analysis of representative isolates of a major clone of E. faecalis MLST ST40 revealed new insights into the microbiology of a commensal bacterium which can turn into a conditional pathogen.\n\nComprehensive molecular, genomic and phenotypic analysis of a major clone of Enterococcus faecalis MLST ST40.", "token_count": 143, "char_count": 555, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7037, "quality_score": 0.8519, "entities": { "genes": [ "ST40" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:18.343707", "source": { "split": "train_shard_00002", "doc_id": 491 }, "chunk_id": "train_shard_00002_491_1", "global_id": 13386 }, { "text": "Klebsiella pneumoniae and related species are frequent causes of nosocomial infections and outbreaks. Therefore, quick and reliable strain typing is crucial for the detection of transmission routes in the hospital. The aim of this study was to evaluate Fourier transform infrared spectroscopy (FTIR) and matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) as rapid methods for typing clinical Klebsiella isolates in comparison to whole-genome sequencing (WGS), which was considered the gold standard for typing and identification. Here, 68 clinical Klebsiella strains were analyzed by WGS, FTIR, and MALDI-TOF MS. FTIR showed high discriminatory power in comparison to the WGS reference, whereas MALDI-TOF MS exhibited a low ability to type the isolates. MALDI-TOF mass spectra were further analyzed for peaks that showed high specificity for different Klebsiella species. Phylogenetic analysis revealed that the Klebsiella isolates comprised three different species: K. pneumoniae, K. variicola, and K. quasipneumoniae Genome analysis showed that MALDI-TOF MS can be used to distinguish K. pneumoniae from K. variicola due to shifts of certain mass peaks. The peaks were tentatively identified as three ribosomal proteins (S15p, L28p, L31p) and one stress response protein (YjbJ), which exhibit amino acid differences between the two species. Overall, FTIR has high discriminatory power to recognize the clonal relationship of isolates, thus representing a valuable tool for rapid outbreak analysis and for the detection of transmission events due to fast turnaround times and low costs per sample. Furthermore, specific amino acid substitutions allow the discrimination of K. pneumoniae and K. variicola by MALDI-TOF MS.", "token_count": 513, "char_count": 1846, "word_count": 253, "semantic_coherence": 1, "information_density": 0.6126, "quality_score": 0.8063, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:18.975421", "source": { "split": "train_shard_00002", "doc_id": 492 }, "chunk_id": "train_shard_00002_492_0", "global_id": 13387 }, { "text": "Typing and Species Identification of Clinical Klebsiella Isolates by Fourier Transform Infrared Spectroscopy and Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry.", "token_count": 51, "char_count": 190, "word_count": 22, "semantic_coherence": 1, "information_density": 0.9091, "quality_score": 0.9545, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:19.346850", "source": { "split": "train_shard_00002", "doc_id": 492 }, "chunk_id": "train_shard_00002_492_1", "global_id": 13388 }, { "text": "Staphylococcus aureus causes disease in humans and a wide array of animals. Of note, S. aureus mastitis of ruminants, including cows, sheep, and goats, results in major economic losses worldwide. Extensive variation in genome content exists among S. aureus pathogenic clones. However, the genomic variation among S. aureus strains infecting different animal species has not been well examined. To investigate variation in the genome content of human and ruminant S. aureus, we carried out whole-genome PCR scanning (WGPS), comparative genomic hybridizations (CGH), and the directed DNA sequence analysis of strains of human, bovine, ovine, and caprine origin. Extensive variation in genome content was discovered, including host- and ruminant-specific genetic loci. Ovine and caprine strains were genetically allied, whereas bovine strains were heterogeneous in gene content. As expected, mobile genetic elements such as pathogenicity islands and bacteriophages contributed to the variation in genome content between strains. However, differences specific for ruminant strains were restricted to regions of the conserved core genome, which contained allelic variation in genes encoding proteins of known and unknown function. Many of these proteins are predicted to be exported and could play a role in host-pathogen interactions. The genomic regions of difference identified by the whole-genome approaches adopted in the current study represent excellent targets for studies of the molecular basis of S. aureus host adaptation.\n\nGenome-wide analysis of ruminant Staphylococcus aureus reveals diversification of the core genome.", "token_count": 376, "char_count": 1628, "word_count": 231, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:19.935475", "source": { "split": "train_shard_00002", "doc_id": 493 }, "chunk_id": "train_shard_00002_493_0", "global_id": 13389 }, { "text": "Shiga toxin-producing Escherichia coli (STEC) can cause severe gastrointestinal disease and colonization among food handlers. In Japan, STEC infection is a notifiable disease, and food handlers are required to undergo routine stool examination for STEC. However, the molecular epidemiology of STEC is not entirely known. We investigated the genomic characteristics of STEC from patients and asymptomatic food handlers in Miyagi Prefecture, Japan. Whole-genome sequencing (WGS) was performed on 65 STEC isolates obtained from 38 patients and 27 food handlers by public health surveillance in Miyagi Prefecture between April 2016 and March 2017. Isolates of O157:H7 ST11 and O26:H11 ST21 were predominant (n = 19, 29%, respectively). Non-O157 isolates accounted for 69% (n = 45) of all isolates. Among 48 isolates with serotypes found in the patients (serotype O157:H7 and 5 non-O157 serotypes, O26:H11, O103:H2, O103:H8, O121:H19 and O145:H28), adhesion genes eae, tir, and espB, and type III secretion system genes espA, espJ, nleA, nleB, and nleC were detected in 41 to 47 isolates (85-98%), whereas isolates with other serotypes found only in food handlers were negative for all of these genes. Non-O157 isolates were especially prevalent among patients younger than 5 years old. Shiga-toxin gene stx1a, adhesion gene efa1, secretion system genes espF and cif, and fimbrial gene lpfA were significantly more frequent among non-O157 isolates from patients than among O157 isolates from patients. The most prevalent resistance genes among our STEC isolates were aminoglycoside resistance genes, followed by sulfamethoxazole/trimethoprim resistance genes", "token_count": 520, "char_count": 1653, "word_count": 242, "semantic_coherence": 1, "information_density": 0.624, "quality_score": 0.812, "entities": { "genes": [ "ST21", "ST11" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:20.590338", "source": { "split": "train_shard_00002", "doc_id": 494 }, "chunk_id": "train_shard_00002_494_0", "global_id": 13390 }, { "text": "WGS revealed that 20 isolates were divided into 9 indistinguishable core genomes (<5 SNPs), demonstrating clonal expansion of these STEC strains in our region, including an O26:H11 strain with stx1a+stx2a. Non-O157 STEC with multiple virulence genes were prevalent among both patients and food handlers in our region of Japan, highlighting the importance of monitoring the genomic characteristics of STEC.\n\nGenomic analysis of Shiga toxin-producing Escherichia coli from patients and asymptomatic food handlers in Japan.", "token_count": 141, "char_count": 520, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7838, "quality_score": 0.8919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:21.015726", "source": { "split": "train_shard_00002", "doc_id": 494 }, "chunk_id": "train_shard_00002_494_1", "global_id": 13391 }, { "text": "Photodynamic treatment of yeast with the sensitizer Toluidine blue results in loss of cell viability. In previous investigations it was suggested that plasma membrane damage might be responsible for the loss of colony forming capacity. In this context the influence of photodynamic treatment on transmembrane transport systems was studied. It appeared that the uptake of the sugars glucose, lactose and galactose, the amino acids arginine, phenylalanine, glycine and aspartic acid and of the inorganic compound phosphate was inhibited by photodynamic treatment. The different elements of the energy providing system necessary for active transport, viz. the plasma membrane ATPase and the protonmotive force, were not significantly affected by Toluidine blue and light, indicating that inhibition of transport is not caused by a reduction of the membrane potential or the transmembrane pH gradient. These observations suggest that the transport carriers themselves were damaged by treatment with Toluidine blue and light. This could be confirmed in experiments, in which the lactose and galactose transport proteins of treated and untreated cells were reconstituted in plasma membrane vesicles. It appeared that the carriers, obtained from photodynamically treated Kluyveromyces marxianus cell, had lost their transport capacity.\n\nInhibition of transport systems in yeast by photodynamic treatment with toluidine blue.", "token_count": 316, "char_count": 1417, "word_count": 202, "semantic_coherence": 1, "information_density": 0.5644, "quality_score": 0.7822, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:21.573135", "source": { "split": "train_shard_00002", "doc_id": 495 }, "chunk_id": "train_shard_00002_495_0", "global_id": 13392 }, { "text": "

Background

Tracking recent transmission is a vital part of controlling widespread pathogens such as Mycobacterium tuberculosis. Multiple methods with specific performance characteristics exist for detecting recent transmission chains, usually by clustering strains based on genotype similarities. With such a large variety of methods available, informed selection of an appropriate approach for determining transmissions within a given setting/time period is difficult.

Methods

This study combines whole genome sequence (WGS) data derived from 324 isolates collected 2005-2010 in Kinshasa, Democratic Republic of Congo (DRC), a high endemic setting, with phylodynamics to unveil the timing of transmission events posited by a variety of standard genotyping methods. Clustering data based on Spoligotyping, 24-loci MIRU-VNTR typing, WGS based SNP (Single Nucleotide Polymorphism) and core genome multi locus sequence typing (cgMLST) typing were evaluated.

Findings

Our results suggest that clusters based on Spoligotyping could encompass transmission events that occurred almost 200 years prior to sampling while 24-loci-MIRU-VNTR often represented three decades of transmission. Instead, WGS based genotyping applying low SNP or cgMLST allele thresholds allows for determination of recent transmission events, e.g. in timespans of up to 10 years for a 5 SNP/allele cut-off.

Interpretation

With the rapid uptake of WGS methods in surveillance and outbreak tracking, the findings obtained in this study can guide the selection of appropriate clustering methods for uncovering relevant transmission chains within a given time-period. For high resolution cluster analyses, WGS-SNP and cgMLST based analyses have similar clustering/timing characteristics even for data obtained from a high incidence setting.\n\nThe relationship between transmission time and clustering methods in Mycobacterium tuberculosis epidemiology.", "token_count": 492, "char_count": 1943, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6508, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:22.227137", "source": { "split": "train_shard_00002", "doc_id": 496 }, "chunk_id": "train_shard_00002_496_0", "global_id": 13393 }, { "text": "Alcohol production from whey permeate by immobilized and free cells of Kluyveromyces marxianus NCYC 179.", "token_count": 34, "char_count": 104, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:22.589129", "source": { "split": "train_shard_00002", "doc_id": 497 }, "chunk_id": "train_shard_00002_497_0", "global_id": 13394 }, { "text": "

Background

Shigatoxigenic Escherichia coli (STEC) and enterotoxigenic E. coli (ETEC) cause serious foodborne infections in humans. These two pathogroups are defined based on the pathogroup-associated virulence genes: stx encoding Shiga toxin (Stx) for STEC and elt encoding heat-labile and/or est encoding heat-stable enterotoxin (ST) for ETEC. The study investigated the genomics of STEC/ETEC hybrid strains to determine their phylogenetic position among E. coli and to define the virulence genes they harbor.

Methods

The whole genomes of three STEC/ETEC strains possessing both stx and est genes were sequenced using PacBio RS sequencer. Two of the strains were isolated from the patients, one with hemolytic uremic syndrome, and one with diarrhea. The third strain was of bovine origin. Core genome analysis of the shared chromosomal genes and comparison with E. coli and Shigella spp. reference genomes was performed to determine the phylogenetic position of the STEC/ETEC strains. In addition, a set of virulence genes and ETEC colonization factors were extracted from the genomes. The production of Stx and ST were studied.

Results

The human STEC/ETEC strains clustered with strains representing ETEC, STEC, enteroaggregative E. coli, and commensal and laboratory-adapted E. coli. However, the bovine STEC/ETEC strain formed a remote cluster with two STECs of bovine origin. All three STEC/ETEC strains harbored several other virulence genes, apart from stx and est, and lacked ETEC colonization factors. Two STEC/ETEC strains produced both toxins and one strain Stx only.

Conclusions

This study shows that pathogroup-associated virulence genes of different E. coli can co-exist in strains originating from different phylogenetic lineages. The possibility of virulence genes to be associated with several E", "token_count": 520, "char_count": 1841, "word_count": 259, "semantic_coherence": 1, "information_density": 0.5483, "quality_score": 0.7741, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:23.225577", "source": { "split": "train_shard_00002", "doc_id": 498 }, "chunk_id": "train_shard_00002_498_0", "global_id": 13395 }, { "text": "coli pathogroups should be taken into account in strain typing and in epidemiological surveillance. Development of novel hybrid E. coli strains may cause a new public health risk, which challenges the traditional diagnostics of E. coli infections.\n\nComparative Genomics and Characterization of Hybrid Shigatoxigenic and Enterotoxigenic Escherichia coli (STEC/ETEC) Strains.", "token_count": 94, "char_count": 373, "word_count": 50, "semantic_coherence": 1, "information_density": 0.8, "quality_score": 0.9, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:23.614992", "source": { "split": "train_shard_00002", "doc_id": 498 }, "chunk_id": "train_shard_00002_498_1", "global_id": 13396 }, { "text": "

Background

Helicobacter pylori, a bacterium associated with severe gastrointestinal diseases and malignancies, poses a significant challenge because of its increasing antibiotic resistance rates. This study aimed to identify potential drug targets and inhibitors against H. pylori using a structure-based virtual screening (SBVS) approach.

Methods

Core-proteome analysis of 132 H. pylori genomes was performed using the EDGAR database. Essential genes were identified and human and gut microbiota homolog proteins were excluded. The DAH7PS protein involved in the shikimate pathway was selected for the structure-based virtual screening (SBVS) approach. The tertiary structure of the protein was predicted through homology modeling (based on PDB ID: 5UXM). Molecular docking was performed to identify potential inhibitors of DAH7PS among StreptomeDB compounds using the AutoDock Vina tool. Molecular dynamics (MD) simulations assessed the stability of DAH7PS-ligand complexes. The complexes were further evaluated in terms of their binding affinity, Lipinski's Rule of Five, and ADMET properties.

Results

A total of 54 novel drug targets with desirable properties were identified. DAH7PS was selected for further investigation, and virtual screening of StreptomeDB compounds yielded 36 high-affinity binding of the ligands. Two small molecules, 6,8-Dihydroxyisocoumarin-3-carboxylic acid and Epicatechin, also showed favorable RO5 and ADMET properties. MD simulations confirmed the stability and reliability of DAH7PS-ligand complexes, indicating their potential as inhibitors.

Conclusion

This study identified 54 novel drug targets against H. pylori. The DAH7PS protein as a promising drug target was evaluated using a computer-aided drug design. 6,8-Dihydroxyisocoumarin-3-carboxylic acid and Epicatechin demonstrated desirable properties and stable interactions, highlighting their potential to inhibit DAH7PS as an essential protein", "token_count": 520, "char_count": 1993, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5823, "quality_score": 0.7912, "entities": { "genes": [ "RO5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:24.248464", "source": { "split": "train_shard_00002", "doc_id": 499 }, "chunk_id": "train_shard_00002_499_0", "global_id": 13397 }, { "text": "Undoubtedly, more experimental validations are needed to advance these findings into practical therapies for treating drug-resistant H. pylori.\n\nIdentification of novel drug targets for Helicobacter pylori: structure-based virtual screening of potential inhibitors against DAH7PS protein involved in the shikimate pathway.", "token_count": 80, "char_count": 336, "word_count": 40, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:24.622760", "source": { "split": "train_shard_00002", "doc_id": 499 }, "chunk_id": "train_shard_00002_499_1", "global_id": 13398 }, { "text": "Non-typhoidal Salmonella enterica is an important gastrointestinal pathogen causing a considerable burden of disease. Resistance to third generation cephalosporins poses a serious threat for treatment of severe infections. In this study occurrence, phylogenetic relationship, and mechanisms of third generation cephalosporin resistance were investigated for clinical non-typhoidal S. enterica isolates in Germany. From 2017 to 2019, we detected 168 unique clinical S. enterica isolates with phenotypic resistance to third generation cephalosporins in a nation-wide surveillance. Compared to previous years, we observed a significant (P=0.0002) and consistent increase in resistant isolates from 0.41 % in 2005 to 1.71 % in 2019. In total, 34 different serovars were identified, most often S. Infantis (n=41; 24.4 %), S. Typhimurium (n=27; 16.1 %), S. Kentucky (n=21; 12.5 %), and S. Derby (n=17; 10.1 %). Whole genome analyses revealed extended-spectrum β-lactamase (ESBL) genes as main cause for third generation cephalosporin resistance, and most prevalent were blaCTX-M-1 (n=55), blaCTX-M-14 (n=25), and blaCTX-M-65 (n=23)", "token_count": 483, "char_count": 1284, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6859, "quality_score": 0.8429, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:25.271607", "source": { "split": "train_shard_00002", "doc_id": 500 }, "chunk_id": "train_shard_00002_500_0", "global_id": 13399 }, { "text": "There was no strict correlation between serovar, phylogenetic lineage, and ESBL type but some serovar/ESBL gene combinations were detected frequently, such as blaCTX-M-1 and blaCTX-M-65 in S. Infantis or blaCTX-M-14b in S. Kentucky. The ESBL genes were mainly located on plasmids, including IncI, IncA/C variants, emerging pESI variants, and a novel blaCTX-M-1harbouring plasmid. We conclude that third generation cephalosporin resistance is on the rise among clinical S. enterica isolates in Germany, and occurrence in various S. enterica serovars is most probably due to multiple acquisition events of plasmids.\n\nThird generation cephalosporin resistance in clinical non-typhoidal Salmonella enterica in Germany and emergence of blaCTX-M-harbouring pESI plasmids.", "token_count": 304, "char_count": 890, "word_count": 105, "semantic_coherence": 1, "information_density": 0.7429, "quality_score": 0.8714, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:25.831259", "source": { "split": "train_shard_00002", "doc_id": 500 }, "chunk_id": "train_shard_00002_500_1", "global_id": 13400 }, { "text": "Candida Kefyr cells and their spheroplasts grown in media enriched with choline, N,N'-dimethylethanolamine (DMEA) or ethanolamine (EA) showed decreased concanavalin A (Con A) and ph to hemagglutinin (PHA) mediated agglutination while supplementation with N-monomethylethanolamine (MMEA) increased PHA-mediated agglutination. In all cases, the amount of phospholipid was increased and, consequently, a decrease in the free sterol; phospholipid ratio was observed except in the case of MMEA where this ratio remained almost unchanged. In the cells grown in media enriched with choline. DMEA or MMEA, but not in the EA-supplemented medium, the phosphatidylcholine to phosphatidylethanolamine ratio was increased. Saturation of fatty acids as well as their chain length decreased, which could lead to increased membrane fluidity. No breakpoint in Arrhenius plots of Mg2+ -ATPase of the choline-supplmented cells was observed. Cells grown in media enriched with EA and MMEA did not show any sharp break in Arrhenius plots of Mg2+ -ATPase.\n\nLipid composition and lectin-mediated agglutination of Candida kefyr cells grown in media enriched with choline or its analogues.", "token_count": 342, "char_count": 1164, "word_count": 167, "semantic_coherence": 1, "information_density": 0.6108, "quality_score": 0.8054, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:26.772856", "source": { "split": "train_shard_00002", "doc_id": 501 }, "chunk_id": "train_shard_00002_501_0", "global_id": 13401 }, { "text": "In vitro susceptibilities were determined for a total of 159 clinical isolates and 12 reference strains of yeasts belonging to different Candida species including 94 Candida albicans strains, and further genera such as Cryptococcus, Trichosporon, Geotrichum and Saccharomyces. Minimum inhibitory concentration (MIC) values for fluconazole and itraconazole were assessed using a microdilution technique with the semisynthetic high resolution (HR) medium supplemented with glucose and asparagine but without sodium hydrogen carbonate (pH 7.0), according to a proposal of the working group 'Clinical Mycology' of the German Speaking Mycological Society. Fluconazole MIC values for C. albicans were between 0.125 and > or = 128 micrograms ml-1. Thus, the median of 1 microgram ml-1 showed that the overall fluconazole susceptibility was good. As expected, Candida krusei (seven strains) exhibited diminished in vitro susceptibility with MIC values for fluconazole of 8 to 128 micrograms ml-1 with a median of 64 micrograms ml-1. Some Candida kefyr strains seemed to be less susceptible against fluconazole which was indicated by a MIC90 of 64 micrograms ml-1. Surprisingly, no Candida glabrata isolate exhibited a MIC value greater than 16 micrograms ml-1. Other Candida species, Trichosporon cutaneum, Geotrichum candidum and Saccharomyces cerevisiae showed low MICs to fluconazole. In vitro susceptibility testing of itraconazole revealed that all Candida species except C. albicans, but also Trichosporon cutaneum, Geotrichum candidum, and Saccharomyces cerevisiae exhibited acceptable low MIC values against itraconazole (0.03-2 micrograms ml-1). Their MIC90 values for itraconazole were in the close range between 0.125 and 2 micrograms ml-1", "token_count": 514, "char_count": 1742, "word_count": 247, "semantic_coherence": 1, "information_density": 0.583, "quality_score": 0.7915, "entities": { "genes": [ "MIC90" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:27.434850", "source": { "split": "train_shard_00002", "doc_id": 502 }, "chunk_id": "train_shard_00002_502_0", "global_id": 13402 }, { "text": "MIC values between 0.125 and 2 micrograms ml-1 were obtained, even for C. krusei strains. On the other hand, the range of C. albicans MICs was between 0.0125 and > or = 16 micrograms ml-1 with MIC50 and MIC90 values of 0.125 and > or = 16 micrograms ml-1, respectively, indicating that a considerable number of yeast strains have high MICs. The comparative evaluation of different experimental conditions revealed that there exists a marked influence both of inoculum size and incubation time on the results of susceptibility testing. Therefore, for routine usage 10(2) CFU ml-1 and 18-24 h incubation time for this microdilution method with HR medium are recommended.\n\nIn vitro susceptibility of yeasts for fluconazole and itraconazole. Evaluation of a microdilution test.", "token_count": 228, "char_count": 773, "word_count": 123, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [ "MIC90", "MIC50" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:27.925220", "source": { "split": "train_shard_00002", "doc_id": 502 }, "chunk_id": "train_shard_00002_502_1", "global_id": 13403 }, { "text": "

Summary

Prophages account for a substantial part of most bacterial genomes, but the impacts on hosts remain poorly understood. Here, we combined computational and laboratory experiments to explore the abundance, distribution, and activity of prophage elements in Bacillus subtilis . NCBI database genome sequences and isolates from 1 cm 3 riverbank soil samples were analyzed to provide insights at global and local geographical scales, respectively. Most prophages in wild B. subtilis isolates were related to mobile genetic elements previously identified in laboratory strains. Some large groups of prophages were closely related to completely uncharacterized yet functional Bacillus phages, or completely unknown. As certain prophage groups were unique to local isolates, we explored factors influencing prophages within a single genome. Phylogenetic relatedness was a slightly better predictor of host prophage repertoire than geographical origin. We show that cryptic phages can play a major role in acquisition and/or maintenance of other prophage elements both via strong antagonism or by co-dependence. Laboratory experiments showed that most predicted prophages may be cryptic, since they failed to induce under DNA-damaging stress conditions. Interestingly, the magnitude of stress responses remained proportional to the total number of prophage elements predicted, suggesting their importance in host physiology. This study highlights the diversity, integration patterns, and co-occurrence of prophages in B. subtilis and their potential impact on host evolution and physiology. Understanding these dynamics provides insight into bacterial genome evolution and prophage-host interactions, laying the groundwork for future experimental studies on the roles of phages in the ecology and evolution of this bacterial species.\n\nEcology of prophage-like elements inBacillus subtilisat global and local geographical scale", "token_count": 419, "char_count": 1941, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6429, "quality_score": 0.8214, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:28.574616", "source": { "split": "train_shard_00002", "doc_id": 503 }, "chunk_id": "train_shard_00002_503_0", "global_id": 13404 }, { "text": "Calmodulin (CaM) and calmodulin-like (CML) proteins are Ca2+ relays and play diverse and multiple roles in plant growth, development and stress responses. However, CaM/CML gene family has not been identified in barley (Hordeum vulgare). In the present study, 5 HvCaMs and 80 HvCMLs were identified through a genome-wide analysis. All HvCaM proteins possessed 4 EF-hand motifs, whereas HvCMLs contained 1 to 4 EF-hand motifs. HvCaM2, HvCaM3 and HvCaM5 coded the same polypeptide although they differed in nucleotide sequence, which was identical to the polypeptides coded by OsCaM1-1, OsCaM1-2 and OsCaM1-3. HvCaMs/CMLs were unevenly distributed over barley 7 chromosomes, and could be phylogenetically classified into 8 groups. HvCaMs/CMLs differed in gene structure, cis-acting elements and tissue expression patterns. Segmental and tandem duplication were observed among HvCaMs/CMLs during evolution. HvCML16, HvCML18, HvCML50 and HvCML78 were dispensable genes and the others were core genes in barley pan-genome. In addition, 14 HvCaM/CML genes were selected to examine their responses to salt, osmotic and low potassium stresses by qRT-PCR, and their expression were stress-and time-dependent", "token_count": 507, "char_count": 1341, "word_count": 170, "semantic_coherence": 1, "information_density": 0.7235, "quality_score": 0.8618, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:29.275847", "source": { "split": "train_shard_00002", "doc_id": 504 }, "chunk_id": "train_shard_00002_504_0", "global_id": 13405 }, { "text": "These results facilitate our understanding and further functional identification of HvCaMs/CMLs.\n\nCalmodulin and calmodulin-like gene family in barley: Identification, characterization and expression analyses.", "token_count": 64, "char_count": 230, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:29.686036", "source": { "split": "train_shard_00002", "doc_id": 504 }, "chunk_id": "train_shard_00002_504_1", "global_id": 13406 }, { "text": "Probiotic bacteria offer a number of potential health benefits when administered in sufficient amounts that in part include reducing the number of harmful organisms in the intestine, producing antimicrobial substances and stimulating the body's immune response. However, precisely elucidating the probiotic effect of a specific bacterium has been challenging due to the complexity of the gut's microbial ecosystem and a lack of definitive means for its characterization. This review provides an overview of widely used and recently described probiotics, their impact on the human's gut microflora as a preventative treatment of disease, human/animal models being used to help show efficacy, and discusses the potential use of probiotics in gastrointestinal diseases associated with antibiotic administration.\n\nProbiotic-based strategies for therapeutic and prophylactic use against multiple gastrointestinal diseases.", "token_count": 196, "char_count": 917, "word_count": 125, "semantic_coherence": 1, "information_density": 0.744, "quality_score": 0.872, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:30.135754", "source": { "split": "train_shard_00002", "doc_id": 505 }, "chunk_id": "train_shard_00002_505_0", "global_id": 13407 }, { "text": "Mitochondrial DNA from the yeast Kluyveromyces marxianus var. lactis (K.lactis) is a circular molecule of 39 kilobase-pairs. A genetic and physical map was constructed. We found that this genome contained a large number of guanine-cytosine (GC)-rich sequence clusters, many of which are characterized by the presence of SacII restriction sites (CCGCGG). The primary sequence of the GC clusters often showed a palindromic structure. These GC clusters were present in several varieties of K.marxianus, but not in others. The presence of these clusters is a major feature that distinguishes K.lactis strains from those of K.marxianus var. marxianus (including K.fragilis).\n\nMitochondrial DNA of the yeast Kluyveromyces: guanine-cytosine rich sequence clusters.", "token_count": 205, "char_count": 757, "word_count": 108, "semantic_coherence": 1, "information_density": 0.6852, "quality_score": 0.8426, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:30.596315", "source": { "split": "train_shard_00002", "doc_id": 506 }, "chunk_id": "train_shard_00002_506_0", "global_id": 13408 }, { "text": "Peritonitis is the major disease problem of laying hens in commercial table egg and parent stock operations. Despite its importance, the etiology and pathogenesis of this disease have not been completely clarified. Although avian pathogenic Escherichia coli (APEC) isolates have been incriminated as the causative agent of laying hen peritonitis, Gallibacterium anatis are frequently isolated from peritonitis lesions. Despite recent studies suggesting a role for G. anatis in the pathogenesis of peritonitis, little is known about the organism's virulence mechanisms, genomic composition and population dynamics. Here, we compared the genome sequences of three G. anatis isolates in an effort to understand its virulence mechanisms and identify novel antigenic traits. A multilocus sequence typing method was also established for G. anatis and used to characterize the genotypic relatedness of 71 isolates from commercial laying hens in Iowa and 18 international reference isolates. Genomic comparisons suggest that G. anatis is a highly diverse bacterial species, with some strains possessing previously described and potential virulence factors, but with a core genome containing several antigenic candidates. Multilocus sequence typing effectively distinguished 82 sequence types and several clonal complexes of G. anatis, and some clones seemed to predominate among G. anatis populations from commercial layers in Iowa. Biofilm formation and resistance to antimicrobial agents was also observed in several clades. Overall, the genomic diversity of G. anatis suggests that multiple lineages exist with differing pathogenic potential towards birds.\n\nGenome analysis and phylogenetic relatedness of Gallibacterium anatis strains from poultry.", "token_count": 390, "char_count": 1744, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:31.213532", "source": { "split": "train_shard_00002", "doc_id": 507 }, "chunk_id": "train_shard_00002_507_0", "global_id": 13409 }, { "text": "

Background

Microbial taxonomy remains a conservative discipline, relying on phenotypic information derived from growth in pure culture and techniques that are time-consuming and difficult to standardize, particularly when compared to the ease of modern high-throughput genome sequencing. Here, drawing on the genus Acinetobacter as a test case, we examine whether bacterial taxonomy could abandon phenotypic approaches and DNA-DNA hybridization and, instead, rely exclusively on analyses of genome sequence data.

Results

In pursuit of this goal, we generated a set of thirteen new draft genome sequences, representing ten species, combined them with other publically available genome sequences and analyzed these 38 strains belonging to the genus. We found that analyses based on 16S rRNA gene sequences were not capable of delineating accepted species. However, a core genome phylogenetic tree proved consistent with the currently accepted taxonomy of the genus, while also identifying three misclassifications of strains in collections or databases. Among rapid distance-based methods, we found average-nucleotide identity (ANI) analyses delivered results consistent with traditional and phylogenetic classifications, whereas gene content based approaches appear to be too strongly influenced by the effects of horizontal gene transfer to agree with previously accepted species.

Conclusion

We believe a combination of core genome phylogenetic analysis and ANI provides an appropriate method for bacterial species delineation, whereby bacterial species are defined as monophyletic groups of isolates with genomes that exhibit at least 95% pair-wise ANI. The proposed method is backwards compatible; it provides a scalable and uniform approach that works for both culturable and non-culturable species; is faster and cheaper than traditional taxonomic methods; is easily replicable and transferable among research institutions; and lastly, falls in line with Darwin's vision of classification becoming, as far as is possible, genealogical.\n\nDefining bacterial species in the genomic era: insights from the genus Acinetobacter.", "token_count": 470, "char_count": 2148, "word_count": 291, "semantic_coherence": 1, "information_density": 0.6701, "quality_score": 0.8351, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:31.863587", "source": { "split": "train_shard_00002", "doc_id": 508 }, "chunk_id": "train_shard_00002_508_0", "global_id": 13410 }, { "text": "The exchange of genetic material among bacterial strains and species is recognized as an important factor determining their evolutionary, population genetic, and epidemiological features. We present a detailed analysis of nonvertical inheritance in Legionella pneumophila, a human pathogen and facultative intracellular parasite of amoebas. We have analyzed the exchange of L. pneumophila genetic material with other bacteria at three different levels: population genetics, population genomics, and phylogenomics. At the population genetics level, we have analyzed 89 clinical and environmental isolates after sequencing six coding loci and three intergenic regions for a total of 3,923 bp. In the population genomics analysis, we have studied the roles of recombination and mutation in the common portion of the genome sequence of four L. pneumophila strains. In the phylogenomic analysis, we have studied the phylogenetic origin of 1,700 genes in the L. pneumophila pangenome. For this, we have considered 12 possible phylogenetic alternatives, derived from a reference tree obtained from 104 genes from 41 species, which have been tested under a rigorous statistical framework. The results obtained agree in assigning an important role to nonvertical inheritance in shaping the composition of the L. pneumophila genome and of the genetic variation in its populations. We have found a negative correlation between phylogenetic distance and likelihood of horizontal gene transfer. Phylogenetic proximity and increased chances resulting from sharing the ecological niche provided by the amoeba host have likely had a major influence on the rate of gene exchange in Legionella.\n\nQuantifying nonvertical inheritance in the evolution of Legionella pneumophila.", "token_count": 399, "char_count": 1757, "word_count": 253, "semantic_coherence": 1, "information_density": 0.585, "quality_score": 0.7925, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:32.480184", "source": { "split": "train_shard_00002", "doc_id": 509 }, "chunk_id": "train_shard_00002_509_0", "global_id": 13411 }, { "text": "The utilization of the intracellular and extracellular sources of carbon and energy during the mitotic cycle of yeasts Saccharomyces cerevisiae, Kluyveromyces marxianus, Candida boidinii, Candida tropicalis has been studied. Increase in the consumption rate of carbon and energy sources and in the exogenous respiration rate at G1- and G2-phases of the mitotic cycle is shown. The rate of the endogenous respiration of the cells at these phases decreased. The hypothesis has been proposed that during the mitotic cycle of the yeast cell the regular alternation of exotrophy (the utilization of the extracellular carbon and energy sources by a cell) and endotrophy (the process of the utilization of the intracellular carbon and energy sources by a cell) occurs. It is possible to reveal the exotrophic cells by the cytological method which is based on the calculation of dead cells after incubation of the yeast suspension in amyl alcohol solution. This method has revealed that exotrophic and endotrophic processes do not predominate one over another but alternate at the mitotic cycle. Exotrophy and endotrophy are phase-specific processes. The G1- and G2-phases are exotrophic processes, phases S and M are endotrophic ones.\n\nAlternation of exo- and endotrophy during the mitotic cycle of the yeast cells.", "token_count": 333, "char_count": 1308, "word_count": 202, "semantic_coherence": 1, "information_density": 0.4653, "quality_score": 0.7327, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:33.052086", "source": { "split": "train_shard_00002", "doc_id": 510 }, "chunk_id": "train_shard_00002_510_0", "global_id": 13412 }, { "text": "Although genome data from unicellular marine eukaryotes is sparse, sequences from several supergroups have initiated an era of genome-enabled research aimed at understanding gene function, evolution, and adaptation in non-traditional model protists. Trends in genomic content within and between different lineages are emerging, including phylogenetically anomalous patterns, sometimes resulting from horizontal gene transfer. Some such genes have nutrient uptake and metabolism roles suggesting that bacterial and eukaryotic microbes have similar cellular-mineral-environmental constraints. Many 'accessory genome' components are of unknown function, but low gene copy numbers combined with small genomes make protists ideal for systems biology. Cultured and uncultured protists are providing insights to ecology, ancestral features and the role of cooption in development of complex traits. Various protists harbor features important in sexuality and multicellularity once believed to have originated in metazoans or other multicellular taxa.\n\nThe voyage of the microbial eukaryote.", "token_count": 238, "char_count": 1083, "word_count": 142, "semantic_coherence": 1, "information_density": 0.7887, "quality_score": 0.8944, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:33.525793", "source": { "split": "train_shard_00002", "doc_id": 511 }, "chunk_id": "train_shard_00002_511_0", "global_id": 13413 }, { "text": "Salmonella enterica sv. Typhimurium modulates the expression of factors essential for virulence, contributing to its survival against the surge of copper (Cu) in the Salmonella-containing vacuole. This bactericidal host innate immune component primarily targets the bacterial envelope, where most cuproproteins are localized. While in most enteric species periplasmic Cu homeostasis is maintained by the CusR/CusS-controlled CusCFBA efflux system encoded in the cus locus, we noticed that these genes were lost from the Salmonella-core genome. At the same time, Salmonella acquired cueP, coding for a periplasmic Cu chaperone. As cus, cueP was shown to be essential for bacterial survival in a copper-rich environment under anaerobiosis, suggesting that it can functionally substitute the CusCFBA system. In the present study, the whole Escherichia coli cus locus was reintroduced to the chromosome of the Salmonella wild-type or the ΔcueP strain. While the integrated cus locus did not affect Cu resistance under aerobic conditions, it increases Cu tolerance under anaerobiosis, irrespective of the presence or absence of cueP. In contrast to the Cus system, CueP expression is higher at high copper concentrations and persisted over time, suggesting separate functions. Finally, we observed that, regardless of the presence or absence of cus, a mutant deleted of cueP shows a deficiency in replication inside macrophages compared to the wild-type strain. Our results demonstrate that CueP and CusCFBA exert redundant functions for metal resistance, but not for intracellular survival, and therefore for the virulence of this pathogen.", "token_count": 496, "char_count": 1741, "word_count": 239, "semantic_coherence": 1, "information_density": 0.6402, "quality_score": 0.8201, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:34.173826", "source": { "split": "train_shard_00002", "doc_id": 512 }, "chunk_id": "train_shard_00002_512_0", "global_id": 13414 }, { "text": "Evolution of Copper Homeostasis and Virulence in Salmonella.", "token_count": 22, "char_count": 67, "word_count": 8, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:34.529207", "source": { "split": "train_shard_00002", "doc_id": 512 }, "chunk_id": "train_shard_00002_512_1", "global_id": 13415 }, { "text": "Most known virulence determinants of Pseudomonas aeruginosa are remarkably conserved in this bacterium's core genome, yet individual strains differ significantly in virulence. One explanation for this discrepancy is that pathogenicity islands, regions of DNA found in some strains but not in others, contribute to the overall virulence of P. aeruginosa. Here we employed a strategy in which the virulence of a panel of P. aeruginosa isolates was tested in mouse and plant models of disease, and a highly virulent isolate, PSE9, was chosen for comparison by subtractive hybridization to a less virulent strain, PAO1. The resulting subtractive hybridization sequences were used as tags to identify genomic islands found in PSE9 but absent in PAO1. One 99-kb island, designated P. aeruginosa genomic island 5 (PAGI-5), was a hybrid of the known P. aeruginosa island PAPI-1 and novel sequences. Whereas the PAPI-1-like sequences were found in most tested isolates, the novel sequences were found only in the most virulent isolates. Deletional analysis confirmed that some of these novel sequences contributed to the highly virulent phenotype of PSE9. These results indicate that targeting highly virulent strains of P. aeruginosa may be a useful strategy for identifying pathogenicity islands and novel virulence determinants.\n\nHybrid pathogenicity island PAGI-5 contributes to the highly virulent phenotype of a Pseudomonas aeruginosa isolate in mammals.", "token_count": 353, "char_count": 1451, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5278, "quality_score": 0.7639, "entities": { "genes": [ "PSE9", "PAO1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:35.099977", "source": { "split": "train_shard_00002", "doc_id": 513 }, "chunk_id": "train_shard_00002_513_0", "global_id": 13416 }, { "text": "A total of 436 milk samples from non-infected and 80 from infected quarters were investigated: 24.5% of the samples collected from non-infected and 55% of those collected from infected quarters were positive. Normal milk yielded not less than 16 different species and among them many potentially pathogenic yeast species such as C. parapsilosis, C. guilliermondii, C. tropicalis, C. glabrata and T. asahii, all five able to grow at 40 degrees C. In contrast, the yeasts isolated from infected quarters were from 3 species: C. kefyr, C. catenulata and C. lambica, which were also among the yeasts species recovered from normal milk. Among the three species, only one i.e. Candida kefyr is able to grow above 40 degrees C and from there can be considered as potentially pathogenic, even if bacterial association is necessary to cause mastitis.\n\nIsolation of yeasts from bovine milk in Belgium.", "token_count": 238, "char_count": 891, "word_count": 144, "semantic_coherence": 1, "information_density": 0.6181, "quality_score": 0.809, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:35.571848", "source": { "split": "train_shard_00002", "doc_id": 514 }, "chunk_id": "train_shard_00002_514_0", "global_id": 13417 }, { "text": "The relationship between the promoter length of the Kluyveromyces fragilis beta-glucosidase gene and the level of its expression in Saccharomyces cerevisiae was studied by gene fusion between deleted promoter fragments of various lengths and the promoterless beta-galactosidase gene of Escherichia coli. The removal of a region from position -425 to -232 led to a tenfold increase in the expression of the gene. The same results were obtained for the reconstructed beta-glucosidase gene with the same promoter length. It is likely that the deletion of this part of the promoter removes negative regulatory elements which are functional in Saccharomyces cerevisiae. This increase in activity is the main event which may explain the high increase in gene expression (60-fold) previously observed for an upstream deletion obtained during subcloning experiments of the beta-glucosidase gene. It is also shown that the expression of the gene greatly depends upon the nature of the recipient strain, the growth phase of the cell and that of the vector carrying it.\n\nThe promoter of the beta-glucosidase gene from Kluyveromyces fragilis contains sequences that act as upstream repressing sequences in Saccharomyces cerevisiae.", "token_count": 286, "char_count": 1219, "word_count": 183, "semantic_coherence": 1, "information_density": 0.5301, "quality_score": 0.765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:36.138949", "source": { "split": "train_shard_00002", "doc_id": 515 }, "chunk_id": "train_shard_00002_515_0", "global_id": 13418 }, { "text": "The major staphylococcal autolysin Atl is an important player in cell separation and daughter cell formation. In this study, we investigated the amino acid sequences of Atl proteins derived from 15 staphylococcal and 1 macrococcal species representatives. The overall organization of the bifunctional precursor protein consisting of the signal peptide, a propeptide (PP), the amidase (AM), six repeat sequences (R(1) to R(6)), and the glucosaminidase (GL) was highly conserved in all of the species. The most-conserved domains were the enzyme domains AM and GL; the least-conserved regions were the PP and R regions. An Atl-based phylogenetic tree for the various species representatives correlated well with the corresponding 16S rRNA-based tree and also perfectly matched the phylogenetic trees based on core genome analysis. The phylogenetic distance analysis of 18 AtlA proteins of various Staphylococcus aureus strains and 15 AtlE proteins of S. epidermidis revealed that both species representatives formed a relatively homogeneous cluster. Two S. epidermidis strains, M23864:W1 and VCU116, were identified by Atl typing that clustered far more distantly and belonged to either S. caprae and S. capitis or a new subspecies. Here we show that Atl typing is a useful tool for staphylococcal genus and species typing by using either the highly conserved AM domain or the less-conserved PP domain.\n\nPhylogeny of the staphylococcal major autolysin and its use in genus and species typing.", "token_count": 393, "char_count": 1489, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6044, "quality_score": 0.8022, "entities": { "genes": [ "VCU116" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:36.754482", "source": { "split": "train_shard_00002", "doc_id": 516 }, "chunk_id": "train_shard_00002_516_0", "global_id": 13419 }, { "text": "Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes. By analyzing the core genome of mycoplasmas, we finally revealed the conserved essential genes set for mycoplasma survival. Further analysis showed that the core genome set has many characteristics in common with experimentally identified essential genes. Several key genes, which are related to DNA replication and repair and can be disrupted in transposon mutagenesis studies, may be critical for bacteria survival especially over long period natural selection. Phylogenomic reconstructions based on 3,355 homologous groups allowed robust estimation of phylogenetic relatedness among mycoplasma strains. To obtain deeper insight into the relative roles of molecular evolution in pathogen adaptation to their hosts, we also analyzed the positive selection pressures on particular sites and lineages. There appears to be an approximate correlation between the divergence of species and the level of positive selection detected in corresponding lineages.\n\nComparative genomics of Mycoplasma: analysis of conserved essential genes and diversity of the pan-genome.", "token_count": 290, "char_count": 1407, "word_count": 197, "semantic_coherence": 1, "information_density": 0.6802, "quality_score": 0.8401, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:37.320243", "source": { "split": "train_shard_00002", "doc_id": 517 }, "chunk_id": "train_shard_00002_517_0", "global_id": 13420 }, { "text": "

Objectives

To describe a spatio-temporal cluster of invasive meningococcal disease (IMD) due to serogroup C meningococci, occurred in a restricted area of Tuscany between January and October 2015, and the results of whole genome sequencing (WGS).

Methods

Surveillance activities and public health measures were implemented in the Region. Bacterial isolates from IMD cases were characterized by the National Reference Laboratory of the Istituto Superiore di Sanità (ISS), and WGS was performed on available strains. The kSNP software was used to identify core genome SNPs.

Results

Overall, 28 IMD cases due to meningococcus C were identified up to 31st October, 2015. Of them, 26 were due to meningococcus C:P1.5-1,10-8: F3-6:ST-11 (cc11) and 2 to C:P1.5-1,10-8: F3-6:ST-2780 (cc11). WGS of 13 meningococci isolated during the outbreak occurred in Tuscany in 2015 showed higher similarity when compared with those of 47 C: P1.5-1,10-8: F3-6:ST-11 (cc11) invasive strains from sporadic cases previously detected in Italy.

Conclusions

A highly aggressive meningococcal C strain was involved in the cluster of severe IMD occurred in Tuscany, a Region with high vaccine coverage among children. Whether this was due to low herd immunity related to the short duration of vaccine protection needs further investigation.\n\nGenome-based study of a spatio-temporal cluster of invasive meningococcal disease due to Neisseria meningitidis serogroup C, clonal complex 11.", "token_count": 469, "char_count": 1486, "word_count": 208, "semantic_coherence": 1, "information_density": 0.6394, "quality_score": 0.8197, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:37.967225", "source": { "split": "train_shard_00002", "doc_id": 518 }, "chunk_id": "train_shard_00002_518_0", "global_id": 13421 }, { "text": "Nucleic acid probes and primers are described for detecting fungi that cause disease in humans and animals, as well as spoilage of food and beverages. These probes can detect rRNA, rDNA or polymerase chain reaction products from a majority of fungi in clinical, environmental or food samples", "token_count": 70, "char_count": 291, "word_count": 47, "semantic_coherence": 1, "information_density": 0.8085, "quality_score": 0.9043, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:38.345568", "source": { "split": "train_shard_00002", "doc_id": 519 }, "chunk_id": "train_shard_00002_519_0", "global_id": 13422 }, { "text": "Nucleic acid hybridization assay probes specific for Acremonium sp., Aspergillus clavatus, Aspergillus flavus, Aspergillus fumigatus, Aspergillus glaucus, Aspergillus nidulans, Aspergillus niger, Aspergillus ochraceus, Aspergillus terreus, Aspergillus unguis, Aspergillus ustus, Beauveria sp., Bipolaris sp., Blastoschizomyces sp., Blastomyces dermatitidis, Candida albicans, Candida glabrata, Candida guilliermondii, Candida kefyr, Candida krusei, Candida lusitaniae, Candida parapsilosis, Candida tropicalis, Chrysosporium sp., Cladosporium sp., Coccidioides immitis,Cryptococcus neoformans var gattii serotype B, Cryptococcus neoformans serotype A, Cryptococcus laurentii, Cryptococcus terreus, Curvularia sp., Fusarium sp., Filobasidium capsuligenum, Filobasidiella (Cryptococcus) neoformans var bacillispora serotype C, Filobasidiella (Cryptococcus) neoformans var neoformans serotype D, Filobasidium uniguttulatum, Geotrichum sp., Histoplasma capsulatum, Malbranchea sp., Mucor sp., Paecilomyces sp., Paracoccidioides brasiliensis, Penicillium species, Pneumocystis carinii, Pseudallescheria boydii, Rhizopus sp., Sporothrix schenkii, Scopulariopsis brevicaulis, Scopulariopsis brumpti, Saccharomyces cerevisiae, and Trichosporon beigelii are also described.\n\nNucleic acid probes for the detection and identification of fungi", "token_count": 495, "char_count": 1331, "word_count": 138, "semantic_coherence": 1, "information_density": 0.6449, "quality_score": 0.8225, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "gut", "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:38.994610", "source": { "split": "train_shard_00002", "doc_id": 519 }, "chunk_id": "train_shard_00002_519_1", "global_id": 13423 }, { "text": "

Background

Previous studies exploring sequence variation in the model legume, Medicago truncatula, relied on mapping short reads to a single reference. However, read-mapping approaches are inadequate to examine large, diverse gene families or to probe variation in repeat-rich or highly divergent genome regions. De novo sequencing and assembly of M. truncatula genomes enables near-comprehensive discovery of structural variants (SVs), analysis of rapidly evolving gene families, and ultimately, construction of a pan-genome.

Results

Genome-wide synteny based on 15 de novo M. truncatula assemblies effectively detected different types of SVs indicating that as much as 22% of the genome is involved in large structural changes, altogether affecting 28% of gene models. A total of 63 million base pairs (Mbp) of novel sequence was discovered, expanding the reference genome space for Medicago by 16%. Pan-genome analysis revealed that 42% (180 Mbp) of genomic sequences is missing in one or more accession, while examination of de novo annotated genes identified 67% (50,700) of all ortholog groups as dispensable - estimates comparable to recent studies in rice, maize and soybean. Rapidly evolving gene families typically associated with biotic interactions and stress response were found to be enriched in the accession-specific gene pool. The nucleotide-binding site leucine-rich repeat (NBS-LRR) family, in particular, harbors the highest level of nucleotide diversity, large effect single nucleotide change, protein diversity, and presence/absence variation. However, the leucine-rich repeat (LRR) and heat shock gene families are disproportionately affected by large effect single nucleotide changes and even higher levels of copy number variation.

Conclusions

Analysis of multiple M. truncatula genomes illustrates the value of de novo assemblies to discover and describe structural variation, something that is often under-estimated when using read-mapping approaches. Comparisons among the de novo assemblies also indicate that different large gene families differ in the architecture of their structural variation.", "token_count": 511, "char_count": 2148, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6305, "quality_score": 0.8153, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:39.654132", "source": { "split": "train_shard_00002", "doc_id": 520 }, "chunk_id": "train_shard_00002_520_0", "global_id": 13424 }, { "text": "Exploring structural variation and gene family architecture with De Novo assemblies of 15 Medicago genomes.", "token_count": 24, "char_count": 107, "word_count": 15, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:40.067019", "source": { "split": "train_shard_00002", "doc_id": 520 }, "chunk_id": "train_shard_00002_520_1", "global_id": 13425 }, { "text": "

Background

In the present study, we sequenced the complete genomes of three novel bacteriophages v_B-Bak1, v_B-Bak6, v_B-Bak10 previously isolated from historical anthrax burial sites in the South Caucasus country of Georgia. We report here major trends in the molecular evolution of these phages, which we designate as \"Basilisk-Like-Phages\" (BLPs), and illustrate patterns in their evolution, genomic plasticity and core genome architecture.

Results

Comparative whole genome sequence analysis revealed a close evolutionary relationship between our phages and two unclassified Bacillus cereus group phages, phage Basilisk, a broad host range phage (Grose JH et al., J Vir. 2014;88(20):11846-11860) and phage PBC4, a highly host-restricted phage and close relative of Basilisk (Na H. et al. FEMS Microbiol. letters. 2016;363(12)). Genome comparisons of phages v_B-Bak1, v_B-Bak6, and v_B-Bak10 revealed significant similarity in sequence, gene content, and synteny with both Basilisk and PBC4. Transmission electron microscopy (TEM) confirmed the three phages belong to the Siphoviridae family. In contrast to the broad host range of phage Basilisk and the single-strain specificity of PBC4, our three phages displayed host specificity for Bacillus anthracis. Bacillus species including Bacillus cereus, Bacillus subtilis, Bacillus anthracoides, and Bacillus megaterium were refractory to infection.

Conclusions

Data reported here provide further insight into the shared genomic architecture, host range specificity, and molecular evolution of these rare B. cereus group phages. To date, the three phages represent the only known close relatives of the Basilisk and PBC4 phages and their shared genetic attributes and unique host specificity for B. anthracis provides additional insight into candidate host range determinants.", "token_count": 522, "char_count": 1848, "word_count": 249, "semantic_coherence": 1, "information_density": 0.5984, "quality_score": 0.7992, "entities": { "genes": [ "PBC4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:40.727448", "source": { "split": "train_shard_00002", "doc_id": 521 }, "chunk_id": "train_shard_00002_521_0", "global_id": 13426 }, { "text": "Genomic characterization of three novel Basilisk-like phages infecting Bacillus anthracis.", "token_count": 24, "char_count": 90, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:41.105876", "source": { "split": "train_shard_00002", "doc_id": 521 }, "chunk_id": "train_shard_00002_521_1", "global_id": 13427 }, { "text": "Municipal wastewater includes human waste that contains both commensal and pathogenic enteric microorganisms, and this collective community microbiome can be monitored for community diseases. In a previous study, we assessed the salmonellosis disease burden using municipal wastewater from Honolulu, Hawaii, which was monitored over a 54-week period. During that time, a strain of Salmonella enterica serovar Paratyphi B variant L(+) tartrate(+) (also known as Salmonella enterica serovar Paratyphi B variant Java) was identified; this strain was detected simultaneously with a clinically reported outbreak, and pulsed-field gel electrophoresis patterns were identical for clinical and municipal wastewater isolates. Months after the outbreak subsided, the same pulsotype was detected as the dominant pulsotype in municipal wastewater samples, with no corresponding clinical cases reported. Using genomic characterization (including core single-nucleotide polymorphism alignment, core genome multilocus sequence typing, and screening for virulence and antibiotic resistance genes), all S Java municipal wastewater isolates were determined to be clonal, indicating a resurgence of the original outbreak strain. This demonstrates the feasibility and utility of municipal wastewater surveillance for determining enteric disease outbreaks that may be missed by traditional clinical surveillance methods.IMPORTANCE Underdetection of microbial infectious disease outbreaks in human communities carries enormous health costs and is an ongoing problem in public health monitoring (which relies almost exclusively on data from health clinics). Surveillance of municipal wastewater for community-level monitoring of infectious disease burdens has the potential to fill this information gap, due to its easy access to the mixed community microbiome. In the present study, the genomes of 21 S Java isolates (collected from municipal wastewater in Honolulu) were analyzed; results showed that the same Salmonella strain that caused a known salmonellosis clinical outbreak in spring 2010 remerged as the most dominant strain in municipal wastewater in spring 2011, indicating a new outbreak that was not detected by health clinics", "token_count": 503, "char_count": 2258, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5743, "quality_score": 0.7871, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:41.803775", "source": { "split": "train_shard_00002", "doc_id": 522 }, "chunk_id": "train_shard_00002_522_0", "global_id": 13428 }, { "text": "Our results show that wastewater monitoring holds great promise to inform the field of public health regarding outbreak status within communities.\n\nClinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates.", "token_count": 63, "char_count": 286, "word_count": 35, "semantic_coherence": 1, "information_density": 0.9143, "quality_score": 0.9571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:42.166412", "source": { "split": "train_shard_00002", "doc_id": 522 }, "chunk_id": "train_shard_00002_522_1", "global_id": 13429 }, { "text": "Two isolates of a Gram-stain-positive, strictly aerobic, motile, rod-shaped, endospore-forming bacterium were identified during a survey of the Bacillus diversity of the Agriculture Research Service Culture Collection. These strains were originally isolated from soil and have a phenotype of producing a dark pigment on tryptic soy agar. Phylogenetic analysis of the 16S rRNA gene indicated that these strains were related most closely to Bacillus subtilis subsp. inaquosorum (99.7% similarity) and Bacillus axarquiensis (99.7 %). In phenotypic characterization, the novel strains were found to grow between 17 and 50 _C and can tolerate up to 9% (w/v) NaCl. Furthermore, the strains grew in media of pH 5.5–10 (optimal growth at pH 7.0–8.0). The predominant cellular fatty acids were anteiso-C15 : 0 (34.8 %) and iso-C15 : 0 (21.9 %). The cell-wall peptidoglycan contained meso-diaminopimelic acid. A draft genome of both strains was completed. The DNA G+C content was 43.8 mol%. A phylogenomic analysis on the core genome of these two new strains and all members of the Bacillus subtilis group revealed these two strains formed a distinct monophyletic clade with the nearest neighbour Bacillus amyloliquefaciens. DNA–DNA relatedness studies using in silico DNA–DNA hybridizations showed the two strains were conspecific (93.8 %), while values with all other species (<31.5 %) were well below the species threshold of 70 %. Based on the consensus of phylogenetic and phenotypic analyses, these strains are considered to represent a novel species within the genus Bacillus, for which the name Bacillus nakamurai sp. nov. is proposed, with type strain NRRL B-41091T (=CCUG 68786T).", "token_count": 516, "char_count": 1680, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6523, "quality_score": 0.8262, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:42.803150", "source": { "split": "train_shard_00002", "doc_id": 523 }, "chunk_id": "train_shard_00002_523_0", "global_id": 13430 }, { "text": "Bacillus nakamurai sp. nov., a black-pigment-producing strain", "token_count": 23, "char_count": 61, "word_count": 7, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:43.163015", "source": { "split": "train_shard_00002", "doc_id": 523 }, "chunk_id": "train_shard_00002_523_1", "global_id": 13431 }, { "text": "

Background:

Nontyphoidal Salmonella (NTS) is a globally important bacterial pathogen, typically associated with foodborne gastrointestinal infection. Some NTS serovars can also colonise normally sterile sites in humans to cause invasive NTS (iNTS) disease. One understudied Salmonella enterica serovar which is responsible for a significant number of cases of iNTS disease is Panama. Despite global dissemination, numerous outbreaks, and a reported association with iNTS disease, S. enterica serovar Panama (S. Panama) has not been investigated in detail. Methods Using combined epidemiological and whole genome sequencing data we analysed 836 S. Panama genomes derived from historical collections, national surveillance datasets, and publicly available data. The collection represents all inhabited continents and includes isolates collected between 1931 and 2019. Maximum likelihood and Bayesian phylodynamic approaches were used to determine population structure & evolutionary history, and to infer geo-temporal dissemination. A combination of different bioinformatic approaches utilising short-read and long-read data were used to characterise geographic and clade-specific trends in antimicrobial resistance (AMR), and genetic markers for invasiveness. Findings We identified the presence of multiple geographically linked S. Panama clades, and regional trends in antimicrobial resistance profiles. Most isolates were pan-susceptible to antibiotics and belonged to clades circulating in the United States of America, Latin America, and the Caribbean. Multidrug resistant (MDR) isolates in our collection belonged to two phylogenetic clades circulating in Europe and Asia/Oceania, which exhibited the highest invasiveness indices based on the conservation of 196 extra-intestinal predictor genes. Interpretation This first large-scale phylogenetic analysis of S. Panama revealed important information about population structure, AMR, global ecology, and genetic markers of invasiveness of the identified genomic subtypes. Our findings provide an important baseline for understanding S. Panama infection in the future. The presence of MDR clades with an elevated invasiveness index should be monitored by ongoing surveillance as such clades may pose an increased public health risk.", "token_count": 525, "char_count": 2296, "word_count": 306, "semantic_coherence": 1, "information_density": 0.6699, "quality_score": 0.835, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:43.806705", "source": { "split": "train_shard_00002", "doc_id": 524 }, "chunk_id": "train_shard_00002_524_0", "global_id": 13432 }, { "text": "Global diversity and evolution of Salmonella Panama, an understudied serovar causing gastrointestinal and invasive disease worldwide: a genomic epidemiology study", "token_count": 37, "char_count": 162, "word_count": 20, "semantic_coherence": 1, "information_density": 0.95, "quality_score": 0.975, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:44.167435", "source": { "split": "train_shard_00002", "doc_id": 524 }, "chunk_id": "train_shard_00002_524_1", "global_id": 13433 }, { "text": "Non-alcoholic fatty liver disease (NAFLD) is an emerging global health problem and a potential risk factor for metabolic diseases. The bidirectional interactions between liver and gut made dysbiotic gut microbiome one of the key risk factors for NAFLD. In this study, we reported an increased abundance of Collinsella aerofaciens in the gut of obese and NASH patients living in India. We isolated C. aerofaciens from the fecal samples of biopsy-proven NASH patients and observed that their genome is enriched with carbohydrate metabolism, fatty acid biosynthesis, and pro-inflammatory functions and have the potency to increase ethanol level in blood. An animal study indicated that mice supplemented with C. aerofaciens had increased levels of circulatory ethanol, high levels of hepatic hydroxyproline, triglyceride, and inflammation in the liver. The present findings indicate that perturbation in the gut microbiome composition is a key risk factor for NAFLD.\n\n<i>Collinsella aerofaciens</i> linked with increased ethanol production and liver inflammation contribute to the pathophysiology of NAFLD.", "token_count": 309, "char_count": 1136, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6101, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:44.736788", "source": { "split": "train_shard_00002", "doc_id": 525 }, "chunk_id": "train_shard_00002_525_0", "global_id": 13434 }, { "text": "Saccharomyces cerevisiae TYKF2 was obtained by cloning in S. cerevisiae the gene coding for beta-glucosidase in Kluyveromyces fragilis Y610 (ATCC 12424). The beta-glucosidases of both organisms were purified and their biochemical characteristics were determined. The two beta-glucosidases had the same enzymatic properties as those previously described in the literature. The strain S. cerevisiae TYKF2 is able to produce enhanced amounts of enzyme.\n\nComparison of the properties of the purified beta-glucosidase from the transformed strain of Saccharomyces cerevisiae TYKF2 with that of the donor strain Kluyveromyces fragilis Y610.", "token_count": 185, "char_count": 633, "word_count": 87, "semantic_coherence": 1, "information_density": 0.6322, "quality_score": 0.8161, "entities": { "genes": [ "TYKF2" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:45.187189", "source": { "split": "train_shard_00002", "doc_id": 526 }, "chunk_id": "train_shard_00002_526_0", "global_id": 13435 }, { "text": "Propionibacterium acnes is a Gram-positive bacterium that is intimately associated with humans. The nature and consequences of this symbiosis are poorly understood; it might comprise both mutualistic and parasitic properties. Recent advances in distinguishing phylotypes of P. acnes have revealed that certain type I lineages are predominantly associated with acne vulgaris. Genome analyses revealed a highly conserved core genome and the existence of island-like genomic regions and possible mobile genetic elements as part of the flexible gene pool. The analysis of clustered regularly interspaced short palindromic repeats (CRISPR), found exclusively in type II P. acnes, recently revealed the presence of CRISPR spacers that derived from mobile genetic elements. These elements are present in a subset of P. acnes type I lineages. Their significance for type-specific host-interacting properties and their contribution to pathogenicity is currently under investigation.\n\nThe flexible gene pool of Propionibacterium acnes.", "token_count": 224, "char_count": 1025, "word_count": 143, "semantic_coherence": 1, "information_density": 0.6853, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:45.654903", "source": { "split": "train_shard_00002", "doc_id": 527 }, "chunk_id": "train_shard_00002_527_0", "global_id": 13436 }, { "text": "The ability to capture genetic variation with unprecedented resolution improves our understanding of bacterial populations and their ability to cause disease. The goal of the pathogenomics era is to define genetic diversity that results in disease. Despite the economic losses caused by vector-borne bacteria in the Order Rickettsiales, little is known about the genetic variants responsible for observed phenotypes. The tick-transmitted rickettsial pathogen Anaplasma marginale infects cattle in tropical and subtropical regions worldwide, including Australia. Genomic analysis of North American A. marginale strains reveals a closed core genome defined by high levels of Single Nucleotide Polymorphisms (SNPs). Here we report the first genome sequences and comparative analysis for Australian strains that differ in virulence and transmissibility. A list of genetic differences that segregate with phenotype was evaluated for the ability to distinguish the attenuated strain from virulent field strains. Phylogenetic analyses of the Australian strains revealed a marked evolutionary distance from all previously sequenced strains. SNP analysis showed a strikingly reduced genetic diversity between these strains, with the smallest number of SNPs detected between any two A. marginale strains. The low diversity between these phenotypically distinct bacteria presents a unique opportunity to identify the genetic determinants of virulence and transmission.\n\nGenetic Diversity of Tick-Borne Rickettsial Pathogens; Insights Gained from Distant Strains.", "token_count": 344, "char_count": 1572, "word_count": 211, "semantic_coherence": 1, "information_density": 0.6398, "quality_score": 0.8199, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:46.233996", "source": { "split": "train_shard_00002", "doc_id": 528 }, "chunk_id": "train_shard_00002_528_0", "global_id": 13437 }, { "text": "Carbapenem-resistant Acinetobacter baumannii (CRAB) is a persistent nosocomial pathogen that poses a significant threat to global public health. A three-month cross-sectional observational study was conducted in a 28-bed ICU in Hangzhou, China. The same ICU was sampled for the same duration and with a similar methodology in 2019, 20 months prior to the outset of this study. Following COVID-19-associated delays, a series of IPC measures targeting patients, staff and the ICU environment were implemented for 8 months prior to and throughout this study. A total of 5,341 samples were collected from the ICU environment (n = 4450) and patients (n = 891). A. baumannii isolates were obtained from 9·5% of these samples (n = 505). Most A. baumannii isolated in this ICU were CRAB (419/518; 80·9%). Fewer CRAB were isolated here (407 from 363 sampling occasions) than in 2019 (502 from 336 sampling occasions). However, MIC 50 /MIC 90 values for imipenem increased from 32/64 mg/L in the 2019 study to 64/128 mg/L here. This was accompanied by the proportion of global clone 2 (GC2) isolates falling from 99·5% in 2019 to 50·8% (213/419) in 2021. The phylogenetic diversity of GC2 increased, apparently driven by regular introductions of distinct clusters in association with patients. The remaining CRAB (40·2%; 206/419) were a highly clonal population of ST164, which appears to have persisted in the ICU since an introduction in mid-2020. We found clusters of GC2 and ST164 isolates with identical core genomes in different room or bed unit environments, and in multiple patients, indicative of transmission in the ICU", "token_count": 501, "char_count": 1619, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6047, "quality_score": 0.8023, "entities": { "genes": [ "GC2", "ST164" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:46.893983", "source": { "split": "train_shard_00002", "doc_id": 529 }, "chunk_id": "train_shard_00002_529_0", "global_id": 13438 }, { "text": "Changes to IPC procedures in this ICU were associated with a reduction in the total prevalence of CRAB, and in the number of CRAB isolated from clinical specimens. At the phenotypic level, the CRAB population exhibited increased resistance to carbapenems, and this may be the result of increased antibiotic prescribing over the COVID-19 period. The increased diversity of this CRAB population appears to have been the result of repeated introductions to the ICU with patients, which have continued despite interventions.\n\nChanges to an intensive care unitAcinetobacter baumanniipopulation following COVID-19 disruptions and targeted infection prevention interventions", "token_count": 152, "char_count": 674, "word_count": 95, "semantic_coherence": 1, "information_density": 0.6526, "quality_score": 0.8263, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:47.338431", "source": { "split": "train_shard_00002", "doc_id": 529 }, "chunk_id": "train_shard_00002_529_1", "global_id": 13439 }, { "text": "A respiratory-deficient, mutant of Kluyveromyces fragilis was isolated using a ethidium bromide mutagenesis. It was characterized by a loss of cytochromes a + a3 and by an improvement of its inulinase activity. Under anaerobic conditions this mutant was always better than the wild strain for ethanol production especially from Jerusalem artichoke extracts containing large amounts of high polyfructosans (\"early\" extracts).\n\nIsolation of a respiratory-deficient Kluyveromyces fragilis mutant for the production of ethanol from Jerusalem artichoke.", "token_count": 140, "char_count": 548, "word_count": 75, "semantic_coherence": 1, "information_density": 0.7067, "quality_score": 0.8533, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:47.768277", "source": { "split": "train_shard_00002", "doc_id": 530 }, "chunk_id": "train_shard_00002_530_0", "global_id": 13440 }, { "text": "The Périgord black truffle (Tuber melanosporum Vittad.), considered a gastronomic delicacy worldwide, is an ectomycorrhizal filamentous fungus that is ecologically important in Mediterranean French, Italian and Spanish woodlands. In this study, we developed a novel resource of single nucleotide polymorphisms (SNPs) for T. melanosporum using Illumina high‐throughput resequencing. The genome from six T. melanosporum geographical accessions was sequenced to a depth of approximately 20×. These geographical accessions were selected from different populations within the northern and southern regions of the geographical species distribution. Approximately 80% of the reads for each of the six resequenced geographical accessions mapped against the reference T. melanosporum genome assembly, estimating the core genome size of this organism to be approximately 110 Mbp. A total of 442 326 SNPs corresponding to 3540 SNPs/Mbps were identified as being included in all seven genomes. The SNPs occurred more frequently in repeated sequences (85%), although 4501 SNPs were also identified in the coding regions of 2587 genes. Using the ratio of nonsynonymous mutations per nonsynonymous site (pN) to synonymous mutations per synonymous site (pS) and Tajima's D index scanning the whole genome, we were able to identify genomic regions and genes potentially subjected to positive or purifying selection. The SNPs identified represent a valuable resource for future population genetics and genomics studies.\n\nA survey of genome‐wide single nucleotide polymorphisms through genome resequencing in the Périgord black truffle (Tuber melanosporum Vittad.)", "token_count": 413, "char_count": 1645, "word_count": 231, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:48.398146", "source": { "split": "train_shard_00002", "doc_id": 531 }, "chunk_id": "train_shard_00002_531_0", "global_id": 13441 }, { "text": "The shape of the distribution of evolutionary distances between orthologous genes in pairs of closely related genomes is universal throughout the entire range of cellular life forms. The near invariance of this distribution across billions of years of evolution can be accounted for by the Universal Pace Maker (UPM) model of genome evolution that yields a significantly better fit to the phylogenetic data than the Molecular Clock (MC) model. Unlike the MC, the UPM model does not assume constant gene-specific evolutionary rates but rather postulates that, in each evolving lineage, the evolutionary rates of all genes change (approximately) in unison although the pacemakers of different lineages are not necessarily synchronized. Here, we dissect the nearly constant evolutionary rate distribution by comparing the genome-wide relative rates of evolution of individual genes in pairs or triplets of closely related genomes from diverse bacterial and archaeal taxa. We show that, although the gene-specific relative rate is an important feature of genome evolution that explains more than half of the variance of the evolutionary distances, the ranges of relative rate variability are extremely broad even for universal genes. Because of this high variance, the gene-specific rate is a poor predictor of the conservation rank for any gene in any particular lineage.\n\nStability along with Extreme Variability in Core Genome Evolution", "token_count": 295, "char_count": 1435, "word_count": 216, "semantic_coherence": 1, "information_density": 0.5926, "quality_score": 0.7963, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:48.958817", "source": { "split": "train_shard_00002", "doc_id": 532 }, "chunk_id": "train_shard_00002_532_0", "global_id": 13442 }, { "text": "Photodynamic treatment of Kluyveromyces marxianus with the sensitizer Toluidine blue leads to the loss of colony forming capacity. In this paper, the influence of this treatment on the barrier properties of the plasma membrane has been studied. Photodynamic treatment with the dye Toluidine blue resulted in efflux of potassium ions and E260-absorbing material. Moreover, cells became stainable with erythrosine. It is concluded that the permeability change induced by photodynamic treatment proceeds in an all-or-none fashion. Treatment of this yeast strain, with the dye and light, also induced a diminution of the cell volume. This process is most likely not coupled to the cellular potassium content, but rather to the integrity of the vacuole. These data suggest that the vacuole has an important function in the maintenance of cell volume. Finally, it was observed that the loss of cell viability was not induced by the all-or-none loss of barrier properties.\n\nPhotodynamic treatment of yeast cells with the dye toluidine blue: all-or-none loss of plasma membrane barrier properties.", "token_count": 259, "char_count": 1089, "word_count": 166, "semantic_coherence": 1, "information_density": 0.512, "quality_score": 0.756, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:49.509585", "source": { "split": "train_shard_00002", "doc_id": 533 }, "chunk_id": "train_shard_00002_533_0", "global_id": 13443 }, { "text": "Supplementation of the growth medium with erosterol, cholesterol and lanosterol enriched the Candida kefyr cells, presumably cell membranes with sterols. Sterol enriched C. kefyr cells showed a decrease in percentage of PHA and Con-A mediated agglutination. Sterol supplementation also increased the sterol: phospholipid ratio and in such cells unsaturated fatty acids predominated over saturated ones. The overall effect of these changes resulted in rigidifying the cell membranes as indicated by shift of break in Arrhenius plots of Mg2+ ATPase. This showed that lectin mediated agglutination of yeast cells may be affected by its membrane fluidity.\n\nLectin mediated agglutination of Candida kefyr cells and their spheroplasts grown in sterol enriched growth medium and its correlation with lipid composition.", "token_count": 206, "char_count": 811, "word_count": 117, "semantic_coherence": 1, "information_density": 0.641, "quality_score": 0.8205, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:49.973198", "source": { "split": "train_shard_00002", "doc_id": 534 }, "chunk_id": "train_shard_00002_534_0", "global_id": 13444 }, { "text": "Emiliania huxleyi, a key player in the global carbon cycle is one of the best studied coccolithophores with respect to biogeochemical cycles, climatology, and host-virus interactions. Strains of E. huxleyi show phenotypic plasticity regarding growth behaviour, light-response, calcification, acidification, and virus susceptibility. This phenomenon is likely a consequence of genomic differences, or transcriptomic responses, to environmental conditions or threats such as viral infections. We used an E. huxleyi genome microarray based on the sequenced strain CCMP1516 (reference strain) to perform comparative genomic hybridizations (CGH) of 16 E. huxleyi strains of different geographic origin. We investigated the genomic diversity and plasticity and focused on the identification of genes related to virus susceptibility and coccolith production (calcification). Among the tested 31940 gene models a core genome of 14628 genes was identified by hybridization among 16 E. huxleyi strains. 224 probes were characterized as specific for the reference strain CCMP1516. Compared to the sequenced E. huxleyi strain CCMP1516 variation in gene content of up to 30 percent among strains was observed. Comparison of core and non-core transcripts sets in terms of annotated functions reveals a broad, almost equal functional coverage over all KOG-categories of both transcript sets within the whole annotated genome. Within the variable (non-core) genome we identified genes associated with virus susceptibility and calcification. Genes associated with virus susceptibility include a Bax inhibitor-1 protein, three LRR receptor-like protein kinases, and mitogen-activated protein kinase. Our list of transcripts associated with coccolith production will stimulate further research, e.g. by genetic manipulation. In particular, the V-type proton ATPase 16 kDa proteolipid subunit is proposed to be a plausible target gene for further calcification studies.\n\nGenome variations associated with viral susceptibility and calcification in Emiliania huxleyi.", "token_count": 498, "char_count": 2045, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6121, "quality_score": 0.806, "entities": { "genes": [ "CCMP1516" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:50.626601", "source": { "split": "train_shard_00002", "doc_id": 535 }, "chunk_id": "train_shard_00002_535_0", "global_id": 13445 }, { "text": "A total of 365 yeasts were isolated from the brines of soft, semihard and hard cheeses from different manufacturers. Identification was based on 131 characteristics, primarily employing a method with microtitration plates. Most brines exhibited a characteristic yeast flora. The predominant strains proved to be mainly Debaryomyces hansenii and Candida versatilis. In a few brines Trichosporon beigelii, C. rugosa, C. intermedia, Kluyveromyces marxianus, Saccharomyces sp. and C. tenuis/polymorpha were predominant. Also of importance were C. tropicalis, C. parapsilosis, C. zeylanoides, Issatchenkia orientalis and Geotrichum klebahnii. Not all strains could be clearly identified. Lists of characters are provided for subdividing D. hansenii and T. beigelii. The specificity of the yeast flora of brines is assumed to contribute to the sensory variety of cheeses.\n\nThe yeasts of cheese brines.", "token_count": 251, "char_count": 895, "word_count": 127, "semantic_coherence": 1, "information_density": 0.7087, "quality_score": 0.8543, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:51.116047", "source": { "split": "train_shard_00002", "doc_id": 536 }, "chunk_id": "train_shard_00002_536_0", "global_id": 13446 }, { "text": "In order to study the potential use of supercritical CO2 extraction for the recovery of products from yeast cell cultures, the effects of CO2 on different yeast strains over a range of pressures and temperatures have been examined. Viability was shown to be dependent on temperature and dissolved CO2 concentration, and can be described by a sigmoidal (S-shaped) curve. Cell death was mainly due to an 'anaesthesia effect' rather than cell rupture. Important differences in sensitivity were observed for the strains studied, with the following order of resistance: Kluyveromyces fragilis > Saccharomyces cerevisiae > Candida utilis.\n\nThe influence of pressure and temperature of compressed CO2 on the survival of yeast cells.", "token_count": 165, "char_count": 725, "word_count": 111, "semantic_coherence": 1, "information_density": 0.6757, "quality_score": 0.8378, "entities": { "genes": [ "CO2" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:51.557425", "source": { "split": "train_shard_00002", "doc_id": 537 }, "chunk_id": "train_shard_00002_537_0", "global_id": 13447 }, { "text": "Prepn. of a whey-based prod. (A) comprises fermenting whey with a mixt. contg.\\-1 each of:(a) a Lactobacillus (La) of the species hilgardii, casei, cellobiosus, brevis, acidophilus, kefir and delbrueckii;(b) a Streptococcus (St) of the species lactis, cremoris and diacetylactis;(c) a Leuconostoc (Le) of the species mesenteroides and kefir, and(d) a yeast of the species Saccharomyces delbrueckii, S. cerevisiae, S. unisporus, S. globosus, S. carlbergensis, Kluyveromyces fragilis, K. bulgaricus, K. lactis, Torula holmii, Candida tenuis and C. kefir. Also claimed are:(1) the prod. (A) as above;(2) a drinkable cosmetic compsn. which contains (A), and(3) a cosmetic compsn. for external use which contains (A).", "token_count": 271, "char_count": 713, "word_count": 102, "semantic_coherence": 1, "information_density": 0.6863, "quality_score": 0.8431, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:52.137846", "source": { "split": "train_shard_00002", "doc_id": 538 }, "chunk_id": "train_shard_00002_538_0", "global_id": 13448 }, { "text": "Cerato-platanins (CPs) form a family of fungal small secreted cysteine-rich proteins (SSCPs) and are of particular interest not only because of their surface activity but also their abundant secretion by fungi. We performed an evolutionary analysis of 283 CPs from 157 fungal genomes with the focus on the environmental opportunistic plant-beneficial and mycoparasitic fungus Trichoderma Our results revealed a long evolutionary history of CPs in Dikarya fungi that have undergone several events of lateral gene transfer and gene duplication. Three genes were maintained in the core genome of Trichoderma, while some species have up to four CP-encoding genes. All Trichoderma CPs evolve under stabilizing natural selection pressure. The functional genomic analysis of CPs in Trichoderma guizhouense and Trichoderma harzianum revealed that only epl1 is active at all stages of development but that it plays a minor role in interactions with other fungi and bacteria. The deletion of this gene results in increased colonization of tomato roots by Trichoderma spp. Similarly, biochemical tests of EPL1 heterologously produced by Pichia pastoris support the claims described above. Based on the results obtained, we conclude that the function of CPs is probably linked to their surfactant properties and the ability to modify the hyphosphere of submerged mycelia and, thus, facilitate the nutritional versatility of fungi. The effector-like functions do not sufficiently describe the diversity and evolution of these proteins in fungi, as they are also maintained, duplicated, or laterally transferred in the genomes of nonherbivore fungi.IMPORTANCE Cerato-platanins (CPs) are surface-active small proteins abundantly secreted by filamentous fungi. Consequently, immune systems of plants and other organisms recognize CPs and activate defense mechanisms. Some CPs are toxic to plants and act as virulence factors in plant-pathogenic fungi", "token_count": 515, "char_count": 1997, "word_count": 281, "semantic_coherence": 1, "information_density": 0.6299, "quality_score": 0.8149, "entities": { "genes": [ "EPL1" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:52.824668", "source": { "split": "train_shard_00002", "doc_id": 539 }, "chunk_id": "train_shard_00002_539_0", "global_id": 13449 }, { "text": "Our analysis, however, demonstrates that the interactions with plants do not explain the origin and evolution of CPs in the fungal kingdom. We revealed a long evolutionary history of CPs with multiple cases of gene duplication and events of interfungal lateral gene transfers. In the mycoparasitic Trichoderma spp., CPs evolve under stabilizing natural selection and hamper the colonization of roots. We propose that the ability to modify the hydrophobicity of the fungal hyphosphere is a key to unlock the evolutionary and functional paradox of these proteins.\n\nThe Evolutionary and Functional Paradox of Cerato-platanins in Fungi.", "token_count": 157, "char_count": 639, "word_count": 95, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:53.278462", "source": { "split": "train_shard_00002", "doc_id": 539 }, "chunk_id": "train_shard_00002_539_1", "global_id": 13450 }, { "text": "

Background

Actinobacteria have adapted to contrasted ecological niches such as the soil, and among others to plants or animals as pathogens or symbionts. Mycobacterium genus contains mostly pathogens that cause a variety of mammalian diseases, among which the well-known leprosy and tuberculosis, it also has saprophytic relatives. Streptomyces genus is mostly a soil microbe known for its secondary metabolites, it contains also plant pathogens, animal pathogens and symbionts. Frankia, a nitrogen-fixing actinobacterium establishes a root symbiosis with dicotyledonous pionneer plants. Pathogens and symbionts live inside eukaryotic cells and tissues and interact with their cellular environment through secreted proteins and effectors transported through transmembrane systems; nevertheless they also need to avoid triggering host defense reactions. A comparative genome analysis of the secretomes of symbionts and pathogens allows a thorough investigation of selective pressures shaping their evolution. In the present study, the rates of silent mutations to non-silent mutations in secretory proteins were assessed in different strains of Frankia, Streptomyces and Mycobacterium, of which several genomes have recently become publicly available.

Results

It was found that secreted proteins as a whole have a stronger purifying evolutionary rate (non-synonymous to synonymous substitutions or Ka/Ks ratio) than the non-secretory proteins in most of the studied genomes. This difference becomes statistically significant in cases involving obligate symbionts and pathogens. Amongst the Frankia, secretomes of symbiotic strains were found to have undergone evolutionary trends different from those of the mainly saprophytic strains. Even within the secretory proteins, the signal peptide part has a higher Ka/Ks ratio than the mature part. Two contrasting trends were noticed amongst the Frankia genomes regarding the relation between selection strength (i.e. Ka/Ks ratio) and the codon adaptation index (CAI), a predictor of the expression rate, in all the genes belonging to the core genome as well as the core secretory protein genes", "token_count": 519, "char_count": 2153, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:05:53.957325", "source": { "split": "train_shard_00002", "doc_id": 540 }, "chunk_id": "train_shard_00002_540_0", "global_id": 13451 }, { "text": "The genomes of pathogenic Mycobacterium and Streptomyces also had reduced secretomes relative to saprophytes, as well as in general significant pairwise Ka/Ks ratios in their secretomes.

Conclusion

In marginally free-living facultative symbionts or pathogenic organisms under consideration, secretory protein genes as a whole evolve at a faster rate than the rest and this process may be an adaptive life-strategy to counter the host selection pressure. The higher evolutionary rate of signal peptide part compared to mature protein provides an indication that signal peptide parts may be under relaxed purifying selection, indicative of the signal peptides not being secreted into host cells. Codon usage analysis suggests that in actinobacterial strains under host selection pressure such as symbiotic Frankia, ACN, FD and the pathogenic Mycobacterium, codon usage bias was negatively correlated to the selective pressure exerted on the secretory protein genes.\n\nContrasted evolutionary constraints on secreted and non-secreted proteomes of selected Actinobacteria.", "token_count": 256, "char_count": 1074, "word_count": 148, "semantic_coherence": 1, "information_density": 0.6892, "quality_score": 0.8446, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:54.512258", "source": { "split": "train_shard_00002", "doc_id": 540 }, "chunk_id": "train_shard_00002_540_1", "global_id": 13452 }, { "text": "Alcoholic fermentation of Jerusalem artichoke juice, a natural complex medium, allowed the production of 13% (v/v) ethanol utilizing an inulin-fermenting strain of Kluyveromyces fragilis, strongly sensitive to ethanol. However, the fermentation of a simple medium with a similar concentration of fermentable sugars (235 g/L) as saccharose stopped prematurely when only 7% (v/v) ethanol had been produced. Differences in the two fermentation profiles were attributed to the significantly lower ethanol tolerance of K. fragilis IGC 2671 in the simple medium with 2% saccharose as compared with diluted J.a. juice with a similar sugar concentration, in fact, (1) in diluted J. a. juice, growth was possible up to 8% (v/v) added ethanol compared with 6% (v/v) in simple medium and (2) ethanol-induced inhibition of the specific growth and fermentation rate as well as ethanol-induced stimulation of the specific death rate were much more drastic in simple medium. Present results show that (1) the complex composition of the medium used for alcoholic fermentation plays a marked role in the ability of the yeast to tolerate and produce ethanol; (2) J. a. juice proved a very appropriate medium for a productive alcoholic fermentation, namely, in processes based on strains with a low ethanol resistance; and (3) to characterize and compare the ethanol tolerance of fermenting yeasts, the standardization of the medium composition must be taken in consideration.\n\nImprovements in ethanol tolerance of Kluyveromyces fragilis in jerusalem artichoke juice.", "token_count": 403, "char_count": 1548, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5513, "quality_score": 0.7756, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:55.124104", "source": { "split": "train_shard_00002", "doc_id": 541 }, "chunk_id": "train_shard_00002_541_0", "global_id": 13453 }, { "text": "Production of Exopolysaccharide pullulan from inulin by a mixed culture of Aureobasidium pullulans and Kluyveromyces fragilis.", "token_count": 37, "char_count": 126, "word_count": 16, "semantic_coherence": 1, "information_density": 0.9375, "quality_score": 0.9688, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:55.484129", "source": { "split": "train_shard_00002", "doc_id": 542 }, "chunk_id": "train_shard_00002_542_0", "global_id": 13454 }, { "text": "The notoriously multi-resistant Staphylococcus haemolyticus is an emerging pathogen causing serious infections in immunocompromised patients. Defining the population structure is important to detect outbreaks and spread of antimicrobial resistant clones. Currently, the standard typing technique is pulsed-field gel electrophoresis (PFGE). In this study we describe novel molecular typing schemes for S. haemolyticus using multi locus sequence typing (MLST) and multi locus variable number of tandem repeats (VNTR) analysis. Seven housekeeping genes (MLST) and five VNTR loci (MLVF) were selected for the novel typing schemes. A panel of 45 human and veterinary S. haemolyticus isolates was investigated. The collection had diverse PFGE patterns (38 PFGE types) and was sampled over a 20 year-period from eight countries. MLST resolved 17 sequence types (Simpsons index of diversity [SID]=0.877) and MLVF resolved 14 repeat types (SID=0.831). We found a low sequence diversity. Phylogenetic analysis clustered the isolates in three (MLST) and one (MLVF) clonal complexes, respectively. Taken together, neither the MLST nor the MLVF scheme was suitable to resolve the population structure of this S. haemolyticus collection. Future MLVF and MLST schemes will benefit from addition of more variable core genome sequences identified by comparing different fully sequenced S. haemolyticus genomes.\n\nCore genome conservation of Staphylococcus haemolyticus limits sequence based population structure analysis.", "token_count": 379, "char_count": 1503, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6555, "quality_score": 0.8278, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:56.058670", "source": { "split": "train_shard_00002", "doc_id": 543 }, "chunk_id": "train_shard_00002_543_0", "global_id": 13455 }, { "text": "Carbapenems represent the mainstay therapy for the treatment of serious P. aeruginosa infections. However, the emergence of carbapenem resistance has jeopardized the clinical use of this important class of compounds. The production of SPM-1 metallo-β-lactamase has been the most common mechanism of carbapenem resistance identified in P. aeruginosa isolated from Brazilian medical centers. Interestingly, a single SPM-1-producing P. aeruginosa clone belonging to the ST277 has been widely spread within the Brazilian territory. In the current study, we performed a next-generation sequencing of six SPM-1-producing P. aeruginosa ST277 isolates. The core genome contains 5899 coding genes relative to the reference strain P. aeruginosa PAO1. A total of 26 genomic islands were detected in these isolates. We identified remarkable elements inside these genomic islands, such as copies of the blaSPM-1 gene conferring resistance to carbapenems and a type I-C CRISPR-Cas system, which is involved in protection of the chromosome against foreign DNA. In addition, we identified single nucleotide polymorphisms causing amino acid changes in antimicrobial resistance and virulence-related genes. Together, these factors could contribute to the marked resistance and persistence of the SPM-1-producing P. aeruginosa ST277 clone. A comparison of the SPM-1-producing P. aeruginosa ST277 genomes showed that their core genome has a high level nucleotide similarity and synteny conservation. The variability observed was mainly due to acquisition of genomic islands carrying several antibiotic resistance genes.\n\nIntraclonal Genome Stability of the Metallo-β-lactamase SPM-1-producing Pseudomonas aeruginosa ST277, an Endemic Clone Disseminated in Brazilian Hospitals.", "token_count": 508, "char_count": 1830, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5934, "quality_score": 0.7967, "entities": { "genes": [ "PAO1", "ST277" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:56.711112", "source": { "split": "train_shard_00002", "doc_id": 544 }, "chunk_id": "train_shard_00002_544_0", "global_id": 13456 }, { "text": "The basic defect in cystic fibrosis (CF) predisposes to chronic bacterial airway infections, particularly with Pseudomonas aeruginosa. Airway infections with P. aeruginosa in individuals with CF are unique in that they chronically affect a host who is immunocompetent in terms of cellular and humoral responses but is immunocompromised by impaired airway clearance. The initially acquired P. aeruginosa clone typically persists for many years in the patients' airways and thereby diversifies by de novo point mutations and the composition of its accessory genome. Co-colonizations with 2 or more clones are preferentially observed during the first 3 years of colonization. Upper and lower airways are commonly colonized by the same clone suggesting that the sinuses are the reservoir and gateway for the colonization of the lower airways. Early antipseudomonal chemotherapy has an 80% chance to eradicate the P. aeruginosa clone. This regimen introduced in the late 1980s has shifted the median age of the onset of chronic airways colonization with P. aeruginosa from school age to early adulthood at the most successful CF centres. The measures to prevent and to treat the Pseudomonas infections in CF have been considerably improved during the last 20 years. Highly transmissible epidemic strains, however, that emerge within a clonal lineage remain a major, still unresolved health threat for the CF community.\n\nClonal epidemiology of Pseudomonas aeruginosa in cystic fibrosis.", "token_count": 359, "char_count": 1480, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6233, "quality_score": 0.8117, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:57.310638", "source": { "split": "train_shard_00002", "doc_id": 545 }, "chunk_id": "train_shard_00002_545_0", "global_id": 13457 }, { "text": "

Background

The dual concepts of pan and core genomes have been widely adopted as means to assess the distribution of gene families within microbial species and genera. The core genome is the set of genes shared by a group of organisms; the pan genome is the set of all genes seen in any of these organisms. A variety of methods have provided drastically different estimates of the sizes of pan and core genomes from sequenced representatives of the same groups of bacteria.

Results

We use a combination of mathematical, statistical and computational methods to show that current predictions of pan and core genome sizes may have no correspondence to true values. Pan and core genome size estimates are problematic because they depend on the estimation of the occurrence of rare genes and genomes, respectively, which are difficult to estimate precisely because they are rare. Instead, we introduce and evaluate a robust metric - genomic fluidity - to categorize the gene-level similarity among groups of sequenced isolates. Genomic fluidity is a measure of the dissimilarity of genomes evaluated at the gene level.

Conclusions

The genomic fluidity of a population can be estimated accurately given a small number of sequenced genomes. Further, the genomic fluidity of groups of organisms can be compared robustly despite variation in algorithms used to identify genes and their homologs. As such, we recommend that genomic fluidity be used in place of pan and core genome size estimates when assessing gene diversity within genomes of a species or a group of closely related organisms.\n\nGenomic fluidity: an integrative view of gene diversity within microbial populations.", "token_count": 364, "char_count": 1694, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5191, "quality_score": 0.7595, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:57.889162", "source": { "split": "train_shard_00002", "doc_id": 546 }, "chunk_id": "train_shard_00002_546_0", "global_id": 13458 }, { "text": "Lactobacillus reuteri is a natural inhabitant of selected animal and human gastrointestinal tract (GIT). Certain strains have the capacity to transform glycerol to 3-hydroxypropionaldehyde (3-HPA), further excreted to form reuterin, a potent antimicrobial system. Reuterin-producing strains may be applied as a natural antimicrobial in feed to prevent pathogen colonization of animals, such as in chicken, and replace added antimicrobials. To date, only seven L. reuteri strains isolated from chicken have been characterized which limits phylogenetic studies and host-microbes interactions characterization. This study aimed to isolate L. reuteri strains from chicken GIT and to characterize their reuterin production and antimicrobial resistance (AMR) profiles using phenotypic and genetic methods. Seventy strains were isolated from faces, crops and ceca of six chicken from poultry farms and samples from slaughterhouse. Twenty-five strains were selected for further characterization. Draft genomes were generated for the new 25 isolates and integrated into a phylogenetic tree of 40 strains from different hosts. Phylogenetic analysis based on gene content as well as on core genomes showed grouping of the selected 25 L. reuteri chicken isolates within the poultry/human lineage VI. Strains harboring pdu-cob-cbi-hem genes (23/25) produced between 156 mM ± 11 and 330 mM ± 14 3-HPA, from 600 mM of glycerol, in the conditions of the test. All 25 chicken strains were sensitive to cefotaxime (MIC between 0.016 and 1 μg/mL) and penicillin (MIC between 0.02 and 4 μg/mL)", "token_count": 486, "char_count": 1608, "word_count": 231, "semantic_coherence": 1, "information_density": 0.619, "quality_score": 0.8095, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:58.544941", "source": { "split": "train_shard_00002", "doc_id": 547 }, "chunk_id": "train_shard_00002_547_0", "global_id": 13459 }, { "text": "Akin to the reference strains DSM20016 and SD2112, the novel isolates were resistant to penicillin, possibly associated with identified point mutations in ponA, pbpX, pbpF and pbpB. All strains resistant to erythromycin (4/27) carried the ermB gene, and it was only present in chicken strains. All strains resistant to tetracycline (5/27) harbored tetW gene. This study confirms the evolutionary history of poultry/human lineage VI and identifies pdu-cob-cbi-hem as a frequent trait but not always present in this lineage. L. reuteri chicken strains producing high 3-HPA yield may have potential to prevent enteropathogen colonization of chicken.\n\nIsolation and Comparative Genomic Analysis of Reuterin-Producing Lactobacillus reuteri From the Chicken Gastrointestinal Tract.", "token_count": 278, "char_count": 838, "word_count": 109, "semantic_coherence": 1, "information_density": 0.7523, "quality_score": 0.8761, "entities": { "genes": [ "SD2112", "DSM20016" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:59.097416", "source": { "split": "train_shard_00002", "doc_id": 547 }, "chunk_id": "train_shard_00002_547_1", "global_id": 13460 }, { "text": "Xylella fastidiosa is a bacterial pathogen causing severe diseases and asymptomatic colonization in more than 600 plants worldwide. Copper (Cu) is a widely used antimicrobial treatment for various plant diseases, including those affecting X. fastidiosa hosts. Cu homeostasis among X. fastidiosa strains from different geographical locations and host species has not been characterized. Here, we assessed minimum inhibitory concentration (MIC) of Cu for 54 X. fastidiosa strains. We observed strain-level variation in MIC values within each subspecies. We hypothesized that these differences could be explained by sequence variation in Cu homeostasis genes. Phylogenies based on copA, copB, copL, and cutC were created using 74 genomes (including 43 strains used in vitro) of X. fastidiosa, showing that the phylogenetic clustering of Cu homeostasis associated with clustering was based on core genome phylogenies, rather than on pattern of MIC. No association was found among Cu MIC, subspecies classification, and host and location of isolation, probably due to uneven and limited group of strains whose genomes are available. Further analysis focused on a subgroup of isolates from Georgia's vineyards that shared similar Cu-related phenotypes. Further research is needed to better understand the distribution of Cu homeostasis for this pathogen.\n\nPhenotypic and Phylogenetic Characterization of Cu Homeostasis among Xylella fastidiosa Strains.", "token_count": 412, "char_count": 1516, "word_count": 207, "semantic_coherence": 1, "information_density": 0.6812, "quality_score": 0.8406, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:05:59.720193", "source": { "split": "train_shard_00002", "doc_id": 548 }, "chunk_id": "train_shard_00002_548_0", "global_id": 13461 }, { "text": "In the current work, we describe genome diversity and core genome sequences among representatives of three bifidobacterial species, i.e., Bifidobacterium adolescentis, Bifidobacterium catenulatum, and Bifidobacterium pseudocatenulatum, by employing a polyphasic approach involving analysis of 16S rRNA gene and 16S-23S internal transcribed spacer (ITS) sequences, pulsed-field gel electrophoresis (PFGE), and comparative genomic hybridization (CGH) assays.\n\nExploration of the genomic diversity and core genome of the Bifidobacterium adolescentis phylogenetic group by means of a polyphasic approach.", "token_count": 172, "char_count": 600, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7162, "quality_score": 0.8581, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:00.161237", "source": { "split": "train_shard_00002", "doc_id": 549 }, "chunk_id": "train_shard_00002_549_0", "global_id": 13462 }, { "text": "Ampicillin resistance has greatly contributed to the recent dramatic increase of a cluster of human adapted Enterococcus faecium lineages (ST17, ST18, and ST78) in hospital-based infections. Changes in the chromosomal pbp5 gene have been associated with different levels of ampicillin susceptibility, leading to protein variants (designated as PBP5 C-types to keep the nomenclature used in previous works) with diverse degrees of reduction in penicillin affinity. Our goal was to use a comparative genomics approach to evaluate the relationship between the diversity of PBP5 among E. faecium isolates of different phylogenomic groups as well as to assess the pbp5 transferability among isolates of disparate clonal lineages. The analyses of 78 selected E. faecium strains as well as published E. faecium genomes, suggested that the diversity of pbp5 mirrors the phylogenomic diversification of E. faecium. The presence of identical PBP5 C-types as well as similar pbp5 genetic environments in different E. faecium lineages and clones from quite different geographical and environmental origin was also documented and would indicate their horizontal gene transfer among E. faecium populations. This was supported by experimental assays showing transfer of large (≈180-280 kb) chromosomal genetic platforms containing pbp5 alleles, ponA (transglycosilase) and other metabolic and adaptive features, from E. faecium donor isolates to suitable E. faecium recipient strains. Mutation profile analysis of PBP5 from available genomes and strains from this study suggests that the spread of PBP5 C-types might have occurred even in the absence of a significant ampicillin resistance phenotype. In summary, genetic platforms containing pbp5 sequences were stably maintained in particular E", "token_count": 522, "char_count": 1895, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5759, "quality_score": 0.7879, "entities": { "genes": [ "ST17", "PBP5", "ST18", "ST78" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:06:00.792595", "source": { "split": "train_shard_00002", "doc_id": 550 }, "chunk_id": "train_shard_00002_550_0", "global_id": 13463 }, { "text": "faecium lineages, but were also able to be transferred among E. faecium clones of different origins, emphasizing the growing risk of further spread of ampicillin resistance in this nosocomial pathogen.\n\nCo-diversification of Enterococcus faecium Core Genomes and PBP5: Evidences of pbp5 Horizontal Transfer.", "token_count": 102, "char_count": 332, "word_count": 43, "semantic_coherence": 1, "information_density": 0.8605, "quality_score": 0.9302, "entities": { "genes": [ "PBP5" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:01.171266", "source": { "split": "train_shard_00002", "doc_id": 550 }, "chunk_id": "train_shard_00002_550_1", "global_id": 13464 }, { "text": "Pseudomonas aeruginosa is a primary cause of opportunistic infections. We have sequenced and annotated the genomes of two P. aeruginosa clinical isolates evidencing different antibiotic susceptibilities. Registered differences in the composition of their accessory genomes may provide clues on P. aeruginosa strategies to thrive in different environments like infection loci.\n\nDraft genome sequences of two Pseudomonas aeruginosa clinical isolates with different antibiotic susceptibilities.", "token_count": 111, "char_count": 491, "word_count": 63, "semantic_coherence": 1, "information_density": 0.7143, "quality_score": 0.8571, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:01.922005", "source": { "split": "train_shard_00002", "doc_id": 551 }, "chunk_id": "train_shard_00002_551_0", "global_id": 13465 }, { "text": "In yeasts, growth temperature is known to affect the membrane phospholipid content. The effect of temperature on the growth inhibition of Kluyveromyces marxianus and Saccharomyces cerevisiae by the trichothecene mycotoxins, T-2 toxin and roridin A, was investigated. Examination of EC50 values for T-2 toxin and roridin A showed that these toxins were least inhibitory to both yeasts at 30 and 25 degrees C, respectively. Increasing or decreasing growth temperature from these temperatures gradually increased the inhibitory effect of the trichothecene mycotoxins. Temperature may affect the toxicity of the trichothecenes to the yeasts by regulating the composition of yeast cell membranes.\n\nEffects of growth temperature on toxicity of T-2 toxin and roridin A to yeast.", "token_count": 210, "char_count": 771, "word_count": 114, "semantic_coherence": 1, "information_density": 0.5965, "quality_score": 0.7982, "entities": { "genes": [ "EC50" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:02.399932", "source": { "split": "train_shard_00002", "doc_id": 552 }, "chunk_id": "train_shard_00002_552_0", "global_id": 13466 }, { "text": "Characterization of an 'endopolygalacturonase' of the yeast Kluyveromyces marxianus.", "token_count": 28, "char_count": 84, "word_count": 9, "semantic_coherence": 1, "information_density": 0.8889, "quality_score": 0.9444, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:02.753876", "source": { "split": "train_shard_00002", "doc_id": 553 }, "chunk_id": "train_shard_00002_553_0", "global_id": 13467 }, { "text": "We previously identified an operon involved in an arginine deiminase (ADI) pathway (arc operon) on a CTX-M-producing plasmid from an O102-ST405 strain of Escherichia coli As the ADI pathway was shown to be involved in the virulence of various Gram-positive bacteria, we tested whether the ADI pathway could be involved in the epidemiological success of extended-spectrum-β-lactamase (ESBL)-producing E. coli strains. We studied two collections of human E. coli isolated in France (n = 493) and England (n = 1,509) and show that the prevalence of the arc operon (i) is higher in ESBL-producing strains (12.1%) than in nonproducers (2.5%), (ii) is higher in CTX-M-producing strains (16%) than in other ESBL producers (3.5%), and (iii) increased over time in ESBL-producing strains from 0% before 2000 to 43.3% in 2011 to 2012. The arc operon, found in strains from various phylogenetic backgrounds, is carried by IncF plasmids (85%) or chromosomes (15%) in regions framed by numerous insertion sequences, indicating multiple arrivals. Competition experiments showed that the arc operon enhances fitness of the strain in vitro in lysogeny broth with arginine. In vivo competition experiments showed that the arc operon is advantageous for the strain in a mouse model of urinary tract infection (UTI), whereas it is a burden in a mouse model of intestinal colonization", "token_count": 487, "char_count": 1448, "word_count": 213, "semantic_coherence": 1, "information_density": 0.6056, "quality_score": 0.8028, "entities": { "genes": [ "ST405" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:03.403355", "source": { "split": "train_shard_00002", "doc_id": 554 }, "chunk_id": "train_shard_00002_554_0", "global_id": 13468 }, { "text": "In summary, we have identified a trait linked to CTX-M-producing strains that is responsible for a trade-off between two main E. coli lifestyles, UTI and gut commensalism. This trait alone cannot explain the wide spread of ESBLs in E. coli but merits epidemiological surveillance.\n\nThe Arginine Deiminase Operon Is Responsible for a Fitness Trade-Off in Extended-Spectrum-β-Lactamase-Producing Strains of Escherichia coli.", "token_count": 135, "char_count": 436, "word_count": 60, "semantic_coherence": 1, "information_density": 0.7667, "quality_score": 0.8833, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:03.827254", "source": { "split": "train_shard_00002", "doc_id": 554 }, "chunk_id": "train_shard_00002_554_1", "global_id": 13469 }, { "text": "The effect of polyenic antibiotic amphotericin B on photodynamically induced cell damage was investigated using Kluyveromyces fragilis. The photosensitizers applied are known to act via cell membrane damage (rose bengal and toluidine blue) or via DNA modification causing genotoxic effects (8-methoxypsoralen). Methylene blue was shown to cause membrane damage comparable with the effect of rose bengal and toluidine blue. Under conditions of photodynamic damage a pronounced protective effect of the antibiotic was evident in increased cell survival with all of the photosensitizers tested. Mitochondrial activity indicated a tendency of the antibiotic to protect the cells. The protective role of amphotericin B is discussed in the light of possible implications for photodynamic therapy of microbial infections.\n\nProtective effect of amphotericin B against lethal photodynamic treatment in yeast.", "token_count": 214, "char_count": 899, "word_count": 126, "semantic_coherence": 1, "information_density": 0.6111, "quality_score": 0.8056, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:04.334139", "source": { "split": "train_shard_00002", "doc_id": 555 }, "chunk_id": "train_shard_00002_555_0", "global_id": 13470 }, { "text": "

Background

Bifidobacterium species, including Bifidobacterium pseudocatenulatum, are among the dominant microbial populations of the human gastrointestinal tract. They are also major components of many commercial probiotic products. Resident and transient bifidobacteria are thought to have several beneficial health effects. However, our knowledge of how these bacteria interact and communicate with host cells remains poor. This knowledge is essential for scientific support of their purported health benefits and their rational inclusion in functional foods.

Results

This work describes the draft genome sequence of Bifidobacterium pseudocatenulatum IPLA 36007, a strain isolated as dominant from the feces of a healthy human. Besides several properties of probiosis, IPLA 36007 exhibited the capability of releasing aglycones from soy isoflavone glycosides. The genome contains 1,851 predicted genes, including 54 genes for tRNAs and fie copies of unique 16S, 23S and 5S rRNA genes. As key attributes of the IPLA 36007 genome we can mention the presence of a lysogenic phage, a cluster encoding type IV fimbriae, and a locus encoding a clustered, regularly interspaced, short, palindromic repeat (CRISPR)-Cas system. Four open reading frames (orfs) encoding β-glucosidases belonging to the glycosyl hydrolase family 3, which may act on isoflavone glycosides, were encountered. Additionally, one gene was found to code for a glycosyl hydrolase of family 1 that might also have β-glucosidase activity.

Conclusion

The availability of the B. pseudocatenulatum IPLA 36007 genome should allow the enzyme system involved in the release of soy isoflavone aglycones from isoflavone glycosides, and the molecular mechanisms underlying the strain's probiotic properties, to be more easily understood.", "token_count": 497, "char_count": 1815, "word_count": 250, "semantic_coherence": 1, "information_density": 0.684, "quality_score": 0.842, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:05.002817", "source": { "split": "train_shard_00002", "doc_id": 556 }, "chunk_id": "train_shard_00002_556_0", "global_id": 13471 }, { "text": "The genome of Bifidobacterium pseudocatenulatum IPLA 36007, a human intestinal strain with isoflavone-activation activity.", "token_count": 42, "char_count": 122, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:05.383135", "source": { "split": "train_shard_00002", "doc_id": 556 }, "chunk_id": "train_shard_00002_556_1", "global_id": 13472 }, { "text": "

Background

The ST239 lineage is a globally disseminated, multiply drug-resistant hospital-associated methicillin-resistant Staphylococcus aureus (HA-MRSA). We performed whole-genome sequencing of representative HA-MRSA isolates of the ST239 lineage from bacteremic patients in hospitals in Hong Kong (HK) and Beijing (BJ) and compared them with three published complete genomes of ST239, namely T0131, TW20 and JKD6008. Orthologous gene group (OGG) analyses of the Hong Kong and Beijing cluster strains were also undertaken.

Results

Homology analysis, based on highest-percentage nucleotide identity, indicated that HK isolates were closely related to TW20, whereas BJ isolates were more closely related to T0131 from Tianjin. Phylogenetic analysis, incorporating a total of 30 isolates from different continents, revealed that strains from HK clustered with TW20 into the 'Asian clade', whereas BJ isolates and T0131 clustered closely with strains of the 'Turkish clade' from Eastern Europe. HK isolates contained the typical φSPβ-like prophage with the SasX gene similar to TW20. In contrast, BJ isolates contained a unique 15 kb PT1028-like prophage but lacked φSPβ-like and φSA1 prophages", "token_count": 365, "char_count": 1207, "word_count": 165, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [ "JKD6008", "TW20", "PT1028", "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:06.017844", "source": { "split": "train_shard_00002", "doc_id": 557 }, "chunk_id": "train_shard_00002_557_0", "global_id": 13473 }, { "text": "Besides distinct mobile genetic elements (MGE) in the two clusters, OGG analyses and whole-genome alignment of these clusters highlighted differences in genes located in the core genome, including the identification of single nucleotide deletions in several genes, resulting in frameshift mutations and the subsequent predicted truncation of encoded proteins involved in metabolism and antimicrobial resistance.

Conclusions

Comparative genomics, based on de novo assembly and deep sequencing of HK and BJ strains, revealed different origins of the ST239 lineage in northern and southern China and identified differences between the two clades at single nucleotide polymorphism (SNP), core gene and MGE levels. The results suggest that ST239 strains isolated in Hong Kong since the 1990s belong to the Asian clade, present mainly in southern Asia, whereas those that emerged in northern China were of a distinct origin, reflecting the complexity of dissemination and the dynamic evolution of this ST239 lineage.\n\nComparative genomics of methicillin-resistant Staphylococcus aureus ST239: distinct geographical variants in Beijing and Hong Kong.", "token_count": 268, "char_count": 1150, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6832, "quality_score": 0.8416, "entities": { "genes": [ "ST239" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:06.571850", "source": { "split": "train_shard_00002", "doc_id": 557 }, "chunk_id": "train_shard_00002_557_1", "global_id": 13474 }, { "text": "Under proper operating conditions, a low dead volume continuous filtration module operated on biological broths (yeast and bacteria suspensions in stirred reactors) still fulfills the flow-rate requirements of an analytical apparatus (for example HPLC or FIA) without membrane regeneration. The filtrate stream has been successfully connected to a bioreactor in order to perform the automated HPLC analysis of broth components. The monitoring of the carbon source (lactose), and minor products (glycerol, acetate and succinate) during a yeast culture (Kluyveromyces marxianus) is shown.\n\nAutomated HPLC monitoring of broth components on bioreactors.", "token_count": 157, "char_count": 649, "word_count": 90, "semantic_coherence": 1, "information_density": 0.7889, "quality_score": 0.8944, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:07.009473", "source": { "split": "train_shard_00002", "doc_id": 558 }, "chunk_id": "train_shard_00002_558_0", "global_id": 13475 }, { "text": "The interactive effect of the combinations of trichothecene mycotoxins often found in fungus infected plants, contaminated grain, and other biological systems is poorly understood. Growth inhibition of the yeast Kluyveromyces marxianus was used to measure the effects of HT-2 toxin, roridin A, and T-2 toxin as individual toxins or as binary mixtures. A value, the combination index, was derived which indicates the interactive effects of a binary mixture of toxins. The interaction is affected by the ratio of the individual toxins, and the percent inhibition of yeast growth. Generally the interaction of T-2 toxin and roridin A or T-2 toxin and HT-2 toxin changes from antagonistic when they cause a low percent inhibition of yeast growth to synergistic when they cause a high percent inhibition of yeast growth. Additionally, any two trichothecenes have a unique ratio, which we name the maximally quiescent ratio (or MQR), where there is the least change in the type and intensity of their interaction. The maximally quiescent ratio in this case has helped to define the nature of toxin interactions and could be used to provide insights into hormone, immune system, developmental, enzyme, and gene regulation, combined drug therapy, and the action of mixtures of natural or synthetic toxins, carcinogens, pesticides, and environmental pollutants.\n\nTrichothecene synergism, additivity, and antagonism: the significance of the maximally quiescent ratio.", "token_count": 360, "char_count": 1457, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5701, "quality_score": 0.7851, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:07.585275", "source": { "split": "train_shard_00002", "doc_id": 559 }, "chunk_id": "train_shard_00002_559_0", "global_id": 13476 }, { "text": "Probiotics represent a possible strategy for controlling intestinal infections in livestock. Members of the Weissella genus are increasingly being studied for health-related applications in animals and humans. Here we investigated the functional properties of two Weissella cibaria strains isolated from cows reared in Kuwait breeding facilities by combining phenotypic with genomic analyses. W. cibaria SP7 and SP19 exhibited good growth in vitro under acidic conditions and in the presence of bile salts compared to the reference probiotic Lacticaseibacillus (formerly Lactobacillus) rhamnosus GG. Both strains were able to adhere to Caco-2 and HT-29 cell lines, as well as to mucin. The cell-free supernatants of the two isolates exhibited inhibitory activity towards Escherichia coli ATCC 25,922 and Salmonella enterica UC3605, which was ultimately due to the low pH of supernatants. W. cibaria SP19 showed a co-aggregation ability similar to that of L. rhamnosus GG when incubated with S. enterica. Whole genome sequencing and analysis revealed that both strains harbored several genes involved in carbohydrate metabolism and general stress responses, indicating bacterial adaptation to the gastrointestinal environment. We also detected genes involved in the adhesion to host epithelial cells or extracellular matrix. No evidence of acquired antibiotic resistance or hemolytic activity was found in either strain. These findings shed light on the potential of W. cibaria for probiotic use in livestock and on the mechanisms underlying host-microbe interaction in the gut. W. cibaria` strain SP19 exhibited the best combination of in vitro probiotic properties and genetic markers, and is a promising candidate for further investigation.\n\nIntegrated Phenotypic-Genotypic Analysis of Candidate Probiotic Weissella Cibaria Strains Isolated from Dairy Cows in Kuwait.", "token_count": 476, "char_count": 1869, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6554, "quality_score": 0.8277, "entities": { "genes": [ "SP7", "UC3605", "SP19" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:08.235359", "source": { "split": "train_shard_00002", "doc_id": 560 }, "chunk_id": "train_shard_00002_560_0", "global_id": 13477 }, { "text": "Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.\n\nBifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools.", "token_count": 375, "char_count": 1558, "word_count": 214, "semantic_coherence": 1, "information_density": 0.6449, "quality_score": 0.8224, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:08.831392", "source": { "split": "train_shard_00002", "doc_id": 561 }, "chunk_id": "train_shard_00002_561_0", "global_id": 13478 }, { "text": "Genomic surveillance that combines bacterial sequencing and epidemiological information will become the gold standard for outbreak detection, but its clinical translation is hampered by the lack of automated interpretation tools. We performed a prospective pilot study to evaluate the analysis of methicillin-resistant Staphylococcus aureus (MRSA) genomes using the Next Gen Diagnostics (NGD) automated bioinformatics system. Seventeen unselected MRSA-positive patients were identified in a clinical microbiology laboratory in England over a period of 2 weeks in 2018, and 1 MRSA isolate per case was sequenced on the Illumina MiniSeq instrument. The NGD system automatically activated after sequencing and processed fastq folders to determine species, multilocus sequence type, the presence of a mec gene, antibiotic susceptibility predictions, and genetic relatedness based on mapping to a reference MRSA genome and detection of pairwise core genome single-nucleotide polymorphisms. The NGD system required 90 s per sample to automatically analyze data from each run, the results of which were automatically displayed. The same data were independently analyzed using a research-based approach. There was full concordance between the two analysis methods regarding species (S. aureus), detection of mecA, sequence type assignment, and detection of genetic determinants of resistance. Both analysis methods identified two MRSA clusters based on relatedness, one of which contained 3 cases that were involved in an outbreak linked to a clinic and ward associated with diabetic patient care. We conclude that, in this pilot study, the NGD system provided rapid and accurate data that could support infection control practices.\n\nPilot Evaluation of a Fully Automated Bioinformatics System for Analysis of Methicillin-Resistant Staphylococcus aureus Genomes and Detection of Outbreaks.", "token_count": 443, "char_count": 1909, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6491, "quality_score": 0.8245, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:09.469076", "source": { "split": "train_shard_00002", "doc_id": 562 }, "chunk_id": "train_shard_00002_562_0", "global_id": 13479 }, { "text": "Prepn. of a compsn. (A) based on lactoserum comprises fermentation of the lactoserum by a mixt. of microorganisms contg.:(a) a lactobacillus comprising Lactobacillus hilgardii, L. casei, L. cellobiosus, L. brevis, L. acidophilus, and/or L. kefir;(b) a streptococcus comprising Streptococcus lactis, S. cremoris, and/or S. diacetylactis;(c) a leuconostoc comprising Leuconostoc mesenteriodes and/or L. kefir, and(d) a yeast comprising Saccharomyces delbrueckii, S. cerevisiae, S. unisporous, S. Globosus and/or S. carlbergensis, Kluyveromyces fragilis, K. bulgaricus and/or K. lactis, Torula holmii, Candida tenuis and/or C. kefir. Also claimed are:(i) the compsn. (A) as above, and(ii) a drinkable cosmetic compsn. which contains (A).", "token_count": 288, "char_count": 734, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:10.029957", "source": { "split": "train_shard_00002", "doc_id": 563 }, "chunk_id": "train_shard_00002_563_0", "global_id": 13480 }, { "text": "The prevalence of age-related cognitive disorders/dementia is increasing, and effective prevention and treatment interventions are lacking due to an incomplete understanding of aging neuropathophysiology. Emerging evidence suggests that abnormalities in gut microbiome are linked with age-related cognitive decline and getting acceptance as one of the pillars of the Geroscience hypothesis. However, the potential clinical importance of gut microbiome abnormalities in predicting the risk of cognitive decline in older adults is unclear. Till now the majority of clinical studies were done using 16S rRNA sequencing which only accounts for analyzing bacterial abundance, while lacking an understanding of other crucial microbial kingdoms, such as viruses, fungi, archaea, and the functional profiling of the microbiome community. Utilizing data and samples of older adults with mild cognitive impairment (MCI; n = 23) and cognitively healthy controls (n = 25). Our whole-genome metagenomic sequencing revealed that the gut of older adults with MCI harbors a less diverse microbiome with a specific increase in total viruses and a decrease in bacterial abundance compared with controls. The virome, bacteriome, and microbial metabolic signatures were significantly distinct in subjects with MCI versus controls. Selected bacteriome signatures show high predictive potential of cognitive dysfunction than virome signatures while combining virome and metabolic signatures with bacteriome boosts the prediction power. Altogether, the results from our pilot study indicate that trans-kingdom microbiome signatures are significantly distinct in MCI gut compared with controls and may have utility for predicting the risk of developing cognitive decline and dementia- debilitating public health problems in older adults.\n\nUnique trans-kingdom microbiome structural and functional signatures predict cognitive decline in older adults.", "token_count": 420, "char_count": 1926, "word_count": 265, "semantic_coherence": 1, "information_density": 0.5623, "quality_score": 0.7811, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:10.651962", "source": { "split": "train_shard_00002", "doc_id": 564 }, "chunk_id": "train_shard_00002_564_0", "global_id": 13481 }, { "text": "Stenotrophomonas maltophilia is an environmental bacterium as well as an emerging opportunistic multidrug-resistant pathogen. They use the endogenous diffusible signal factor (DSF) quorum sensing (QS) system to coordinate population behavior and regulate virulence processes but can also respond to exogenous N-acyl-homoserine lactone (AHL) signals produced by neighboring bacteria. The effect of these QS signals on the global gene expression of this species remains, however, unknown. Whole-transcriptome sequencing analyses were performed for exponential cultures of S. maltophilia K279a treated with exogenous DSF or AHLs. Addition of DSF and AHLs signals resulted in changes in expression of at least 2-fold for 28 and 82 genes, respectively. Interestingly, 22 of these genes were found upregulated by both QS signals, 14 of which were shown to also be induced during the stationary phase. Gene functions regulated by all conditions included lipid and amino acid metabolism, stress response and signal transduction, nitrogen and iron metabolism, and adaptation to microoxic conditions. Among the common top upregulated QS core genes, a putative TetR-like regulator (locus tag SMLT2053) was selected for functional characterization. This regulator controls its own β-oxidation operon (Smlt2053-Smlt2051), and it is found to sense long-chain fatty acids (FAs), including the QS signal DSF. Gene knockout experiments reveal that operon Smlt2053-Smlt2051 is involved in biofilm formation. Overall, our findings provide clues on the effect that QS signals have in S. maltophilia QS-related phenotypes and the transition from the exponential to the stationary phase and bacterial fitness under high-density growth", "token_count": 472, "char_count": 1740, "word_count": 243, "semantic_coherence": 1, "information_density": 0.6996, "quality_score": 0.8498, "entities": { "genes": [ "SMLT2053" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:11.299220", "source": { "split": "train_shard_00002", "doc_id": 565 }, "chunk_id": "train_shard_00002_565_0", "global_id": 13482 }, { "text": "IMPORTANCE The quorum sensing system in Stenotrophomonas maltophilia, in addition to coordinating the bacterial population, controls virulence-associated phenotypes, such as biofilm formation, motility, protease production, and antibiotic resistance mechanisms. Biofilm formation is frequently associated with the persistence and chronic nature of nosocomial infections. In addition, biofilms exhibit high resistance to antibiotics, making treatment of these infections extremely difficult. The importance of studying the metabolic and regulatory systems controlled by quorum sensing autoinducers will make it possible to discover new targets to control pathogenicity mechanisms in S. maltophilia.\n\nA Stenotrophomonas maltophilia TetR-Like Transcriptional Regulator Involved in Fatty Acid Metabolism Is Controlled by Quorum Sensing Signals.", "token_count": 200, "char_count": 847, "word_count": 104, "semantic_coherence": 1, "information_density": 0.7596, "quality_score": 0.8798, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:11.745604", "source": { "split": "train_shard_00002", "doc_id": 565 }, "chunk_id": "train_shard_00002_565_1", "global_id": 13483 }, { "text": "Patients with hematological malignancies or undergoing hematopoietic stem cell transplantation are vulnerable to colonization and infection with multidrug-resistant organisms, including vancomycin-resistant Enterococcus faecium (VREfm). Over a 10-y period, we collected and sequenced the genomes of 110 VREfm isolates from gastrointestinal and blood cultures of 24 pediatric patients undergoing chemotherapy or hematopoietic stem cell transplantation for hematological malignancy at St. Jude Children's Research Hospital. We used patient-specific reference genomes to identify variants that arose over time in subsequent gastrointestinal and blood isolates from each patient and analyzed these variants for insight into how VREfm adapted during colonization and bloodstream infection within each patient. Variants were enriched in genes involved in carbohydrate metabolism, and phenotypic analysis identified associated differences in carbohydrate utilization among isolates. In particular, a Y585C mutation in the sorbitol operon transcriptional regulator gutR was associated with increased bacterial growth in the presence of sorbitol. We also found differences in biofilm-formation capability between isolates and observed that increased biofilm formation correlated with mutations in the putative E. faecium capsular polysaccharide (cps) biosynthetic locus, with different mutations arising independently in distinct genetic backgrounds. Isolates with cps mutations showed improved survival following exposure to lysozyme, suggesting a possible reason for the selection of capsule-lacking bacteria. Finally, we observed mutations conferring increased tolerance of linezolid and daptomycin in patients who were treated with these antibiotics. Overall, this study documents known and previously undescribed ways that VREfm evolve during intestinal colonization and subsequent bloodstream infection in immunocompromised pediatric patients.\n\nEvolution of vancomycin-resistant Enterococcus faecium during colonization and infection in immunocompromised pediatric patients.", "token_count": 514, "char_count": 2113, "word_count": 258, "semantic_coherence": 1, "information_density": 0.6124, "quality_score": 0.8062, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:06:12.406409", "source": { "split": "train_shard_00002", "doc_id": 566 }, "chunk_id": "train_shard_00002_566_0", "global_id": 13484 }, { "text": "

Background

Technological advances in high throughput genome sequencing are making whole genome sequencing (WGS) available as a routine tool for bacterial typing. Standardized procedures for identification of relevant genes and of variation are needed to enable comparison between studies and over time. The core genes--the genes that are conserved in all (or most) members of a genus or species--are potentially good candidates for investigating genomic variation in phylogeny and epidemiology.

Results

We identify a set of 2,882 core genes clusters based on 73 publicly available Salmonella enterica genomes and evaluate their value as typing targets, comparing whole genome typing and traditional methods such as 16S and MLST. A consensus tree based on variation of core genes gives much better resolution than 16S and MLST; the pan-genome family tree is similar to the consensus tree, but with higher confidence. The core genes can be divided into two categories: a few highly variable genes and a larger set of conserved core genes, with low variance. For the most variable core genes, the variance in amino acid sequences is higher than for the corresponding nucleotide sequences, suggesting that there is a positive selection towards mutations leading to amino acid changes.

Conclusions

Genomic variation within the core genome is useful for investigating molecular evolution and providing candidate genes for bacterial genome typing. Identification of genes with different degrees of variation is important especially in trend analysis.\n\nGenomic variation in Salmonella enterica core genes for epidemiological typing.", "token_count": 352, "char_count": 1646, "word_count": 237, "semantic_coherence": 1, "information_density": 0.5696, "quality_score": 0.7848, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:12.989113", "source": { "split": "train_shard_00002", "doc_id": 567 }, "chunk_id": "train_shard_00002_567_0", "global_id": 13485 }, { "text": "Riboregulation involving regulatory RNAs, RNA chaperones, and ribonucleases is fundamental for the rapid adaptation of gene expression to changing environmental conditions. The gene coding for the RNase YbeY belongs to the minimal prokaryotic genome set and has a profound impact on physiology in a wide range of bacteria. Here, we show that the Agrobacterium tumefaciensybeY gene is not essential. Deletion of the gene in the plant pathogen reduced growth, motility, and stress tolerance. Most interestingly, YbeY is crucial for A. tumefaciens-mediated T-DNA transfer and tumor formation. Comparative proteomics by using isobaric tags for relative and absolute quantitation (iTRAQ) revealed dysregulation of 59 proteins, many of which have previously been found to be dependent on the RNA chaperone Hfq. YbeY and Hfq have opposing effects on production of these proteins. Accumulation of a 16S rRNA precursor in the ybeY mutant suggests that A. tumefaciens YbeY is involved in rRNA processing. RNA coimmunoprecipitation-sequencing (RIP-Seq) showed binding of YbeY to the region immediately upstream of the 16S rRNA. Purified YbeY is an oligomer with RNase activity. It does not physically interact with Hfq and thus plays a partially overlapping but distinct role in the riboregulatory network of the plant pathogen.IMPORTANCE Although ybeY gene belongs to the universal bacterial core genome, its biological function is incompletely understood. Here, we show that YbeY is critical for fitness and host-microbe interaction in the plant pathogen Agrobacterium tumefaciens Consistent with the reported endoribonuclease activity of YbeY, A. tumefaciens YbeY acts as a RNase involved in maturation of 16S rRNA", "token_count": 503, "char_count": 1769, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6071, "quality_score": 0.8036, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:13.650162", "source": { "split": "train_shard_00002", "doc_id": 568 }, "chunk_id": "train_shard_00002_568_0", "global_id": 13486 }, { "text": "This report adds a worldwide plant pathogen and natural genetic engineer of plants to the growing list of bacteria that require the conserved YbeY protein for host-microbe interaction.\n\nThe RNase YbeY Is Vital for Ribosome Maturation, Stress Resistance, and Virulence of the Natural Genetic Engineer Agrobacterium tumefaciens.", "token_count": 87, "char_count": 333, "word_count": 47, "semantic_coherence": 1, "information_density": 0.766, "quality_score": 0.883, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:14.017126", "source": { "split": "train_shard_00002", "doc_id": 568 }, "chunk_id": "train_shard_00002_568_1", "global_id": 13487 }, { "text": "In all sexual organisms, adaptations exist that secure the safe reassortment of homologous alleles and prevent the intrusion of potentially hazardous alien DNA. Some bacteria engage in a simple form of sex known as transformation. In the human pathogen Neisseria meningitidis and in related bacterial species, transformation by exogenous DNA is regulated by the presence of a specific DNA Uptake Sequence (DUS), which is present in thousands of copies in the respective genomes. DUS affects transformation by limiting DNA uptake and recombination in favour of homologous DNA. The specific mechanisms of DUS-dependent genetic transformation have remained elusive. Bioinformatic analyses of family Neisseriaceae genomes reveal eight distinct variants of DUS. These variants are here termed DUS dialects, and their effect on interspecies commutation is demonstrated. Each of the DUS dialects is remarkably conserved within each species and is distributed consistent with a robust Neisseriaceae phylogeny based on core genome sequences. The impact of individual single nucleotide transversions in DUS on meningococcal transformation and on DNA binding and uptake is analysed. The results show that a DUS core 5'-CTG-3' is required for transformation and that transversions in this core reduce DNA uptake more than two orders of magnitude although the level of DNA binding remains less affected. Distinct DUS dialects are efficient barriers to interspecies recombination in N. meningitidis, N. elongata, Kingella denitrificans, and Eikenella corrodens, despite the presence of the core sequence. The degree of similarity between the DUS dialect of the recipient species and the donor DNA directly correlates with the level of transformation and DNA binding and uptake. Finally, DUS-dependent transformation is documented in the genera Eikenella and Kingella for the first time. The results presented here advance our understanding of the function and evolution of DUS and genetic transformation in bacteria, and define the phylogenetic relationships within the Neisseriaceae family.\n\nDialects of the DNA uptake sequence in Neisseriaceae.", "token_count": 483, "char_count": 2132, "word_count": 310, "semantic_coherence": 1, "information_density": 0.5323, "quality_score": 0.7661, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:14.666441", "source": { "split": "train_shard_00002", "doc_id": 569 }, "chunk_id": "train_shard_00002_569_0", "global_id": 13488 }, { "text": "A new chromogenic agar medium (Candida diagnostic agar [CDA]) for differentiation of Candida spp. is described. This medium is based on Sabouraud dextrose agar (Oxoid CM41) and contains (per liter) 40.0 g of glucose, 10.0 g of mycological peptone, and 15.0 g of agar along with a novel chromogenic glucosaminidase substrate, ammonium 4-(2-[4-(2-acetamido-2-deoxy-beta-D-glucopyranosyloxy)-3-methoxyphenyl]-vinyl)-1-(propan-3-yl-oate)-quinolium bromide (0.32 g liter(-1)). The glucosaminidase substrate in CDA was hydrolyzed by Candida albicans and Candida dubliniensis, yielding white colonies with deep-red spots on a yellow transparent background after 24 to 48 h of incubation at 37 degrees C. Colonies of Candida tropicalis and Candida kefyr were uniformly pink, and colonies of other Candida spp., including Candida glabrata and Candida parapsilosis, were white. CDA was evaluated by using 115 test strains of Candida spp. and other clinically important yeasts and was compared with two commercially available chromogenic agars (Candida ID agar [bioMerieux] and CHROMagar Candida [CHROMagar Company Ltd.]). On all three agars, colonies of C. albicans were not distinguished from colonies of C. dubliniensis. However, for the group containing C. albicans plus C. dubliniensis, both the sensitivity and the specificity of detection when CDA was used were 100%, compared with values of 97.6 and 100%, respectively, with CHROMagar Candida and 100 and 96.8%, respectively, with Candida ID agar. In addition, for the group containing C. tropicalis plus C", "token_count": 491, "char_count": 1553, "word_count": 221, "semantic_coherence": 1, "information_density": 0.5701, "quality_score": 0.7851, "entities": { "genes": [ "CM41" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:15.319336", "source": { "split": "train_shard_00002", "doc_id": 570 }, "chunk_id": "train_shard_00002_570_0", "global_id": 13489 }, { "text": "kefyr, the sensitivity and specificity of detection when CDA was used were also 100%, compared with 72.7 and 98.1%, respectively, with CHROMagar Candida. Candida ID agar did not differentiate C. tropicalis and C. kefyr strains but did differentiate members of a broader group (C. tropicalis, C. kefyr, Candida lusitaniae plus Candida guilliermondii); the sensitivity and specificity of detection for members of this group were 94.7 and 93.8%, respectively. In addition to the increased sensitivity and/or specificity of Candida detection when CDA was used, differentiation of colony types on CDA (red spotted, pink, or no color) was unambiguous and did not require precise assessment of colony color.\n\nNew chromogenic agar medium for the identification of Candida spp.", "token_count": 203, "char_count": 768, "word_count": 116, "semantic_coherence": 1, "information_density": 0.6207, "quality_score": 0.8103, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:15.778739", "source": { "split": "train_shard_00002", "doc_id": 570 }, "chunk_id": "train_shard_00002_570_1", "global_id": 13490 }, { "text": "The probiotic yeast Saccharomyces boulardii (Sb) is a promising chassis to deliver therapeutic proteins to the gut due to Sb's innate therapeutic properties, resistance to phage and antibiotics, and high protein secretion capacity. To maintain therapeutic efficacy in the context of challenges such as washout, low rates of diffusion, weak target binding, and/or high rates of proteolysis, it is desirable to engineer Sb strains with enhanced levels of protein secretion. In this work, we explored genetic modifications in both cis- (i.e. to the expression cassette of the secreted protein) and trans- (i.e. to the Sb genome) that enhance Sb's ability to secrete proteins, taking a Clostridioides difficile Toxin A neutralizing peptide (NPA) as our model therapeutic. First, by modulating the copy number of the NPA expression cassette, we found NPA concentrations in the supernatant could be varied by sixfold (76-458 mg/L) in microbioreactor fermentations. In the context of high NPA copy number, we found a previously-developed collection of native and synthetic secretion signals could further tune NPA secretion between 121 and 463 mg/L. Then, guided by prior knowledge of S. cerevisiae's secretion mechanisms, we generated a library of homozygous single gene deletion strains, the most productive of which achieved 2297 mg/L secretory production of NPA. We then expanded on this library by performing combinatorial gene deletions, supplemented by proteomics experiments. We ultimately constructed a quadruple protease-deficient Sb strain that produces 5045 mg/L secretory NPA, an improvement of > tenfold over wild-type Sb. Overall, this work systematically explores a broad collection of engineering strategies to improve protein secretion in Sb and highlights the ability of proteomics to highlight under-explored mediators of this process", "token_count": 480, "char_count": 1847, "word_count": 272, "semantic_coherence": 1, "information_density": 0.636, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:16.458752", "source": { "split": "train_shard_00002", "doc_id": 571 }, "chunk_id": "train_shard_00002_571_0", "global_id": 13491 }, { "text": "In doing so, we created a set of probiotic strains that are capable of delivering a wide range of protein titers and therefore furthers the ability of Sb to deliver therapeutics to the gut and other settings to which it is adapted.\n\nImproving therapeutic protein secretion in the probiotic yeast Saccharomyces boulardii using a multifactorial engineering approach.", "token_count": 87, "char_count": 364, "word_count": 57, "semantic_coherence": 1, "information_density": 0.7719, "quality_score": 0.886, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:16.858473", "source": { "split": "train_shard_00002", "doc_id": 571 }, "chunk_id": "train_shard_00002_571_1", "global_id": 13492 }, { "text": "A comparative genomics analysis revealed 702 genes present in the bacterial Gram-negative core gene set (92 species analyzed) and 959 genes in the Gram-positive core gene set (93 species analyzed). Mycoplasma genitalium, which has the smallest known genome (517 genes) of a non-symbiont, was used in a three-way reciprocal analysis with the Gram-negative core genes and the Gram-positive core genes, and 151 common bacterial core genes were found. Of these 151 core genes, 39 were putative genes encoding the 30S and 50S ribosomal subunits, whilst among recognized cell division genes, only one gene, the major ftsZ, was present. In addition, 86 reciprocal matches were identified between the 151 common bacterial genes and a previously determined 2,723 common eukaryotic core gene set. An analysis was also done to optimize the threshold bit score used to declare that genes were homologous, and a bit score cutoff of 40 was selected.\n\nComparative bacterial genomics: defining the minimal core genome.", "token_count": 266, "char_count": 1002, "word_count": 156, "semantic_coherence": 1, "information_density": 0.5833, "quality_score": 0.7917, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:17.421637", "source": { "split": "train_shard_00002", "doc_id": 572 }, "chunk_id": "train_shard_00002_572_0", "global_id": 13493 }, { "text": "

Background

Bread wheat is one of the most important crops for the human diet, but the increasing soil salinization is causing yield reductions worldwide. Improving salt stress tolerance in wheat requires the elucidation of the mechanistic basis of plant response to this abiotic stress factor. Although several studies have been performed to analyze wheat adaptation to salt stress, there are still some gaps to fully understand the molecular mechanisms from initial signal perception to the onset of responsive tolerance pathways. The main objective of this study is to exploit the dynamic salt stress transcriptome in underlying QTL regions to uncover candidate genes controlling salt stress tolerance in bread wheat. The massive analysis of 3'-ends sequencing protocol was used to analyze leave samples at osmotic and ionic phases. Afterward, stress-responsive genes overlapping QTL for salt stress-related traits in two mapping populations were identified.

Results

Among the over-represented salt-responsive gene categories, the early up-regulation of calcium-binding and cell wall synthesis genes found in the tolerant genotype are presumably strategies to cope with the salt-related osmotic stress. On the other hand, the down-regulation of photosynthesis-related and calcium-binding genes, and the increased oxidative stress response in the susceptible genotype are linked with the greater photosynthesis inhibition at the osmotic phase. The specific up-regulation of some ABC transporters and Na+/Ca2+ exchangers in the tolerant genotype at the ionic stage indicates their involvement in mechanisms of sodium exclusion and homeostasis. Moreover, genes related to protein synthesis and breakdown were identified at both stress phases. Based on the linkage disequilibrium blocks, salt-responsive genes within QTL intervals were identified as potential components operating in pathways leading to salt stress tolerance. Furthermore, this study conferred evidence of novel regions with transcription in bread wheat.

Conclusion

The dynamic transcriptome analysis allowed the comparison of osmotic and ionic phases of the salt stress response and gave insights into key molecular mechanisms involved in the salt stress adaptation of contrasting bread wheat genotypes", "token_count": 492, "char_count": 2312, "word_count": 316, "semantic_coherence": 1, "information_density": 0.5665, "quality_score": 0.7832, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:18.117047", "source": { "split": "train_shard_00002", "doc_id": 573 }, "chunk_id": "train_shard_00002_573_0", "global_id": 13494 }, { "text": "The leveraging of the highly contiguous chromosome-level reference genome sequence assembly facilitated the QTL dissection by targeting novel candidate genes for salt tolerance.\n\nTranscriptome profiling at osmotic and ionic phases of salt stress response in bread wheat uncovers trait-specific candidate genes.", "token_count": 67, "char_count": 310, "word_count": 41, "semantic_coherence": 1, "information_density": 0.878, "quality_score": 0.939, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "osmotic" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:18.483818", "source": { "split": "train_shard_00002", "doc_id": 573 }, "chunk_id": "train_shard_00002_573_1", "global_id": 13495 }, { "text": "Emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) strains that also exhibit resistance to tigecycline and colistin have become a major clinical concern, as these two agents are the last-resort antibiotics used for treatment of CRKP infections. A leukemia patient infected with CRKP was subjected to follow-up analysis of variation in phenotypic and genotypic characteristics of CRKP strains isolated from various specimens at different stages of treatment over a period of 3 years. Our data showed that (1) carbapenem treatment led to the emergence of CRKP in the gastrointestinal (GI) tract of the patient, which subsequently caused infections at other body sites as well as septicemia; (2) treatment with tigecycline led to the emergence of tigecycline-resistant CRKP, possibly through induction of the expression of a variant tet(A) gene located in a conjugative plasmid; (3) colistin treatment was effective in clearing CRKP from the bloodstream but led to the emergence of mcr-1-positive Enterobacteriaceae strains as well as colistin-resistant CRKP in the GI tract due to inactivation of the mgrB gene; and (4) tigecycline- and colistin-resistant CRKP could persist in the human GI tract for a prolonged period even without antibiotic selection pressure. In conclusion, clinical CRKP strains carrying a conjugative plasmid that harbors the blaKPC-2 and tet(A) variant genes readily evolve into tigecycline- and colistin-resistant CRKP upon treatment with these two antibiotics and persist in the human GI tract.\n\nEvolution of tigecycline- and colistin-resistant CRKP (carbapenem-resistant Klebsiella pneumoniae) in vivo and its persistence in the GI tract.", "token_count": 475, "char_count": 1686, "word_count": 244, "semantic_coherence": 1, "information_density": 0.5369, "quality_score": 0.7684, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:19.125041", "source": { "split": "train_shard_00002", "doc_id": 574 }, "chunk_id": "train_shard_00002_574_0", "global_id": 13496 }, { "text": "Population genomics of prokaryotes has been studied in depth in only a small number of primarily pathogenic bacteria, as genome sequences of isolates of diverse origin are lacking for most species. Here, we conducted a large-scale survey of population structure in prevalent human gut microbial species, sampled from their natural environment, with a culture-independent metagenomic approach. We examined the variation landscape of 71 species in 2,144 human fecal metagenomes and found that in 44 of these, accounting for 72% of the total assigned microbial abundance, single-nucleotide variation clearly indicates the existence of sub-populations (here termed subspecies). A single subspecies (per species) usually dominates within each host, as expected from ecological theory. At the global scale, geographic distributions of subspecies differ between phyla, with Firmicutes subspecies being significantly more geographically restricted. To investigate the functional significance of the delineated subspecies, we identified genes that consistently distinguish them in a manner that is independent of reference genomes. We further associated these subspecies-specific genes with properties of the microbial community and the host. For example, two of the three Eubacterium rectale subspecies consistently harbor an accessory pro-inflammatory flagellum operon that is associated with lower gut community diversity, higher host BMI, and higher blood fasting insulin levels. Using an additional 676 human oral samples, we further demonstrate the existence of niche specialized subspecies in the different parts of the oral cavity. Taken together, we provide evidence for subspecies in the majority of abundant gut prokaryotes, leading to a better functional and ecological understanding of the human gut microbiome in conjunction with its host.\n\nSubspecies in the global human gut microbiome.", "token_count": 421, "char_count": 1899, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6316, "quality_score": 0.8158, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:19.754054", "source": { "split": "train_shard_00002", "doc_id": 575 }, "chunk_id": "train_shard_00002_575_0", "global_id": 13497 }, { "text": "Pseudomonas aeruginosa is a ubiquitous Gram negative opportunistic pathogen which belongs to the gamma subclass of proteobacteria. P. aeruginosa genomes consist of a highly conserved core component making up ~90% of the total genome and a highly variable accessory genome that makes up the remaining ~10% of the organism's DNA blueprint.;The extent and nature of tRNA-integrated genomic islands in the available sequenced P. aeruginosa genomes and clinical isolates were defined by both in silico comparative genomics methods and in vitro approaches. These investigations demonstrated that certain tRNA sites seemed to be favoured for integration and that most strains exhibited divergent tRNA site island-occupation profiles.;The contribution of three P. aeruginosa genomic islands PAPI-1, PAPI-2 and the tRNAPro21 island in strain PA14 to fitness and virulence were evaluated. By creating 'en bloc' deletant mutants that lacked islands and testing the resulting phenotype of the mutants alongside the wild-type parent, three islands (PAPI-1, PAPI-2 and tRNAPro21 island) were demonstrated to be important to full virulence of strain PA14.;The dynamics of site-specific integration of the PAPI-1 island into both of its cognate ... (continues)\n\nGenomic mosaicism in the opportunistic pathogen Pseudomonas aeruginosa and its contribution to virulence", "token_count": 337, "char_count": 1350, "word_count": 193, "semantic_coherence": 1, "information_density": 0.5907, "quality_score": 0.7953, "entities": { "genes": [ "PA14" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:20.327698", "source": { "split": "train_shard_00002", "doc_id": 576 }, "chunk_id": "train_shard_00002_576_0", "global_id": 13498 }, { "text": "Staphylococcus aureus is an important opportunistic pathogen in humans and animals. In humans, there has been an increase in community-associated methicillin-resistant Staphylococcus aureus (MRSA) causing disease in healthy humans. The exact evolutionary origins and basis for its recent expansion are not yet clear. In livestock, S. aureus is an important cause of diseases of welfare and economic importance, including bovine mastitis. Molecular typing studies demonstrate that natural populations of S. aureus are highly clonal and largely adapted to a specific host, however there are some lineages that colonise multiple host species. In particular, clonal complex 97 (CC97) is a dominant bovine mastitis-associated lineage which has been isolated from other animal species, and more recently there are increasing reports of CC97 S. aureus from human infections worldwide. The basis for this wide host tropism is currently unknown. In order to investigate the evolutionary origins of S. aureus CC97, 43 strains were selected for whole genome sequencing, isolated from humans, cattle and pigs, from 18 different countries on 4 continents, ranging from 1956 to 2012. Phylogenetic analysis using high quality core genome single ... (continues)\n\nEvolutionary history of a clone of Staphylococcus aureus infecting multiple host-species", "token_count": 326, "char_count": 1335, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6649, "quality_score": 0.8325, "entities": { "genes": [ "CC97" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:20.900257", "source": { "split": "train_shard_00002", "doc_id": 577 }, "chunk_id": "train_shard_00002_577_0", "global_id": 13499 }, { "text": "Escherichia coli is a diverse bacterial species found largely as a harmless commensal in the gastrointestinal tract of warm-blooded mammals. However, an array of highly adapted E. coli pathotypes have evolved over time capable of causing a variety of niche specific diseases, both intestinally and extraintestinally. This ability to cause disease results from the adaptation of the core genome to the host and the acquisition of horizontally acquired virulence factors. Furthermore, these foreign virulence factors are integrated into the regulatory network of the cell allowing niche specific competitive advantages for the emerged pathogen. Enterohaemorrhagic E. coli O157:H7 is a dangerous pathogen capable of causing haemorrhagic colitis and the potentially fatal haemolytic uremic syndrome. This pathogen is a harmless coloniser of ruminants whereas humans are extremely susceptible with transmission via the faecal-oral route, commonly associated with contaminated food products. It is becoming apparent that the carriage of virulence factors is only one element to the adaptive nature of E. coli pathogens, with the specific response to niche specific signals governing when and where these virulence factors are utilised. ... (continues)\n\nA molecular and biochemical analysis of a novel D-serine sensory system in Escherichia coli O157:H7", "token_count": 318, "char_count": 1346, "word_count": 194, "semantic_coherence": 1, "information_density": 0.6443, "quality_score": 0.8222, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:22.216411", "source": { "split": "train_shard_00002", "doc_id": 578 }, "chunk_id": "train_shard_00002_578_0", "global_id": 13500 }, { "text": "The in-vitro antifungal activity of sertaconazole against 110 strains of Candida yeasts (50 Candida albicans, 15 Candida glabrata, 2 Candida guilliermodii, 8 Candida krusei, 1 Candida kefyr, 8 Candida parapsilosis and 26 Candida tropicalis) was assessed in comparison with bifonazole, ketoconazole, econazole and miconazole. The majority of the strains were clinical isolates; some reference strains were included. A commercial agar diffusion method (NeoSensitabs, Rosco, Taastrup, Denmark) in Shadomy's modified medium pH 7 was used. Using the manufacturer's criteria, 86.4% of the strains were classified as \"sensitive\" to sertaconazole. The only strain classified as \"resistant\" to sertaconazole was the control reference strain of C. albicans. The remaining strains were classified as \"moderately sensitive\". The sensitivity/resistance percentages for the other antifungals tested were 75.5/1.8 for ketoconazole, 71.8/2.7 for miconazole, 63.7/13.6 for econazole, and 59.1/5.5 for bifonazole. Sertaconazole showed a higher antifungal activity than that of the other antimycotics, tested in vitro which was statistically significant (P < 0.001), as well as a lower resistance rate than that of econazole, bifonazole and ketoconazole.\n\nIn-vitro antifungal activity of sertaconazole, bifonazole, ketoconazole, and miconazole against yeasts of the Candida genus.", "token_count": 442, "char_count": 1361, "word_count": 185, "semantic_coherence": 1, "information_density": 0.5838, "quality_score": 0.7919, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:22.847334", "source": { "split": "train_shard_00002", "doc_id": 579 }, "chunk_id": "train_shard_00002_579_0", "global_id": 13501 }, { "text": "A global rise in antimicrobial resistance among pathogenic bacteria has proved to be a major public health threat, with the rate of multidrug-resistant bacterial infections increasing over time. The gut microbiome has been studied as a reservoir of antibiotic resistance genes (ARGs) that can be transferred to bacterial pathogens via horizontal gene transfer (HGT) of conjugative plasmids and mobile genetic elements (the gut resistome). Advances in metagenomic sequencing have facilitated the identification of resistome modulators, including live microbial therapeutics such as probiotics and fecal microbiome transplantation that can either expand or reduce the abundances of ARG-carrying bacteria in the gut. While many different gut microbes encode for ARGs, they are not uniformly distributed across, or transmitted by, various members of the microbiome, and not all are of equal clinical relevance. Both experimental and theoretical approaches in microbial ecology have been applied to understand differing frequencies of ARG horizontal transfer between commensal microbes as well as between commensals and pathogens. In this commentary, we assess the evidence for the role of commensal gut microbes in encoding antimicrobial resistance genes, the degree to which they are shared both with other commensals and with pathogens, and the host and environmental factors that can impact resistome dynamics. We further discuss novel sequencing-based approaches for identifying ARGs and predicting future transfer events of clinically relevant ARGs from commensals to pathogens.\n\nGood microbes, bad genes? The dissemination of antimicrobial resistance in the human microbiome.", "token_count": 371, "char_count": 1677, "word_count": 238, "semantic_coherence": 1, "information_density": 0.6303, "quality_score": 0.8151, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:23.425616", "source": { "split": "train_shard_00002", "doc_id": 580 }, "chunk_id": "train_shard_00002_580_0", "global_id": 13502 }, { "text": "

Objectives

The first hospital outbreak of carbapenemase-producing Enterobacteriaceae in Slovenia occurred in 2014-2016. Whole genome sequencing was used to analyse the population of carbapenem-resistant Klebsiella pneumoniae collected in Slovenia in 2014-2017, including OXA-48 and/or NDM-1 producing strains from the outbreak.

Methods

A total of 32 K. pneumoniae isolates were analysed using short-read sequencing. Multi-locus sequence typing and core genome multi-locus sequence typing were used to infer genetic relatedness. Antimicrobial resistance markers, virulence factors, plasmid content and wzi types were determined. Long-read sequencing was used for six isolates for detailed analysis of plasmids and their possible transmission.

Results

Overall, we detected 10 different sequence types (STs), the most common being ST437 (40.6%). Isolates from the initial outbreak belonged to ST437 (12/16) and ST147 (4/16). A second outbreak of four ST15 isolates was discovered. A new ST (ST3390) and two new wzi types (wzi-556, wzi-559) were identified. blaOXA-48 was found in 17 (53.1%) isolates, blaNDM-1 in five (15.6%), and a combination of blaOXA-48/NDM-1 in seven (21.9%) isolates. Identical plasmids carrying blaOXA-48 were found in outbreak isolates sequenced with long-read sequencing technology.

Conclusions

Whole genome sequencing of Slovenian carbapenem-resistant K. pneumoniae isolates revealed multiple clusters of STs, two of which were involved in the first hospital outbreak of carbapenem producing K. pneumoniae in Slovenia. Transmission of the plasmid carrying blaOXA-48 between two STs was likely to have occurred", "token_count": 522, "char_count": 1662, "word_count": 218, "semantic_coherence": 1, "information_density": 0.5872, "quality_score": 0.7936, "entities": { "genes": [ "ST15", "ST147", "ST3390", "ST437" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:06:24.081436", "source": { "split": "train_shard_00002", "doc_id": 581 }, "chunk_id": "train_shard_00002_581_0", "global_id": 13503 }, { "text": "A previously unidentified second outbreak was also discovered, highlighting the importance of whole genome sequencing in detection and/or characterization of hospital outbreaks and surveillance of drug-resistant bacterial clones.\n\nWhole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates.", "token_count": 91, "char_count": 384, "word_count": 44, "semantic_coherence": 1, "information_density": 0.7955, "quality_score": 0.8977, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:24.454635", "source": { "split": "train_shard_00002", "doc_id": 581 }, "chunk_id": "train_shard_00002_581_1", "global_id": 13504 }, { "text": "In a previous paper (S. Kawai, S. Murao, M. Mochizuki, I. Shibuya, K. Yano, and M. Takagi, J. Bacteriol. 174:254-262, 1992), we showed that in each genome of several yeast species, there is one of two types of L41 gene, one for an L41 (Q-type) protein which confers cycloheximide (CYH) resistance or one for an L41 (P-type) protein which does not. These genes have been suggested to be responsible for the CYH response used in taxonomy. For example, Saccharomyces cerevisiae, which is CYH sensitive, has a P-type L41 gene, while Kluyveromyces fragilis and Candida maltosa, which are CYH resistant, have Q-type L41 genes. However, in contrast to K. fragilis, which is constitutively resistant to CYH, C. maltosa is inducibly resistant to CYH. Here, we show that C. maltosa has both types of the L41 gene in its genome and that expression of the Q-type L41 gene is induced by CYH while the P-type L41 gene is constitutively expressed.\n\nInducible expression of a gene encoding an L41 ribosomal protein responsible for the cycloheximide-resistant phenotype in the yeast Candida maltosa.", "token_count": 351, "char_count": 1082, "word_count": 178, "semantic_coherence": 1, "information_density": 0.573, "quality_score": 0.7865, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:25.037443", "source": { "split": "train_shard_00002", "doc_id": 582 }, "chunk_id": "train_shard_00002_582_0", "global_id": 13505 }, { "text": "Immobilization of beta-galactosidase from Kluyveromyces fragilis on ion exchange resin.", "token_count": 25, "char_count": 87, "word_count": 10, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:25.397538", "source": { "split": "train_shard_00002", "doc_id": 583 }, "chunk_id": "train_shard_00002_583_0", "global_id": 13506 }, { "text": "Escherichia coli is a major causative agent of environmental bovine mastitis and this disease causes significant economic losses for the dairy industry. There is still debate in the literature as to whether mammary pathogenic E. coli (MPEC) is indeed a unique E. coli pathotype, or whether this infection is merely an opportunistic infection caused by any E. coli isolate being displaced from the bovine gastrointestinal tract to the environment and, then, into the udder. In this study, we conducted a thorough genomic analysis of 113 novel MPEC isolates from clinical mastitis cases and 100 bovine commensal E. coli isolates. A phylogenomic analysis indicated that MPEC and commensal E. coli isolates formed clades based on common sequence types and O antigens, but did not cluster based on mammary pathogenicity. A comparative genomic analysis of MPEC and commensal isolates led to the identification of nine genes that were part of either the core or the soft-core MPEC genome, but were not found in any bovine commensal isolates. These apparent MPEC marker genes were genes involved with nutrient intake and metabolism [adeQ, adenine permease; nifJ, pyruvate-flavodoxin oxidoreductase; and yhjX, putative major facilitator superfamily (MFS)-type transporter], included fitness and virulence factors commonly seen in uropathogenic E. coli (pqqL, zinc metallopeptidase, and fdeC, intimin-like adhesin, respectively), and putative proteins [yfiE, uncharacterized helix-turn-helix-type transcriptional activator; ygjI, putative inner membrane transporter; and ygjJ, putative periplasmic protein]", "token_count": 518, "char_count": 1701, "word_count": 229, "semantic_coherence": 1, "information_density": 0.6419, "quality_score": 0.821, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:06:26.033674", "source": { "split": "train_shard_00002", "doc_id": 584 }, "chunk_id": "train_shard_00002_584_0", "global_id": 13507 }, { "text": "Further characterization of these highly conserved MPEC genes may be critical to understanding the pathobiology of MPEC.\n\nComparative genomic analysis of <i>Escherichia coli</i> isolates from cases of bovine clinical mastitis identifies nine specific pathotype marker genes.", "token_count": 75, "char_count": 286, "word_count": 36, "semantic_coherence": 1, "information_density": 0.9167, "quality_score": 0.9583, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:26.407720", "source": { "split": "train_shard_00002", "doc_id": 584 }, "chunk_id": "train_shard_00002_584_1", "global_id": 13508 }, { "text": "The gastrointestinal colonizer Enterococcus faecium is a leading cause of hospital-acquired infections. Multidrug-resistant (MDR) E. faecium isolates are particularly concerning for infection treatment. Previous comparative genomic studies revealed that subspecies referred to as clade A and clade B exist within E. faecium MDR E. faecium isolates belong to clade A, while clade B consists of drug-susceptible fecal commensal E. faecium isolates. Isolates from clade A are further grouped into two subclades, clades A1 and A2. In general, clade A1 isolates are hospital-epidemic isolates, whereas clade A2 isolates are isolates from animals and sporadic human infections. Such phylogenetic separation indicates that reduced gene exchange occurs between the clades. We hypothesize that endogenous barriers to gene exchange exist between E. faecium clades. Restriction-modification (R-M) systems are such barriers in other microbes. We utilized a bioinformatics analysis coupled with second-generation and third-generation deep-sequencing platforms to characterize the methylomes of two representative E. faecium strains, one from clade A1 and one from clade B. We identified a type I R-M system that is clade A1 specific, is active for DNA methylation, and significantly reduces the transformability of clade A1 E. faecium Based on our results, we conclude that R-M systems act as barriers to horizontal gene exchange in E. faecium and propose that R-M systems contribute to E. faecium subspecies separation.IMPORTANCEEnterococcus faecium is a leading cause of hospital-acquired infections around the world. Rising antibiotic resistance in certain E. faecium lineages leaves fewer treatment options", "token_count": 505, "char_count": 1788, "word_count": 240, "semantic_coherence": 1, "information_density": 0.55, "quality_score": 0.775, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:27.070476", "source": { "split": "train_shard_00002", "doc_id": 585 }, "chunk_id": "train_shard_00002_585_0", "global_id": 13509 }, { "text": "The overarching aim of this work was to determine whether restriction-modification (R-M) systems contribute to the structure of the E. faecium species, wherein hospital-epidemic and non-hospital-epidemic isolates have distinct evolutionary histories and highly resolved clade structures. R-M provides bacteria with a type of innate immunity to horizontal gene transfer (HGT). We identified a type I R-M system that is enriched in the hospital-epidemic clade and determined that it is active for DNA modification activity and significantly impacts HGT. Overall, this work is important because it provides a mechanism for the observed clade structure of E. faecium as well as a mechanism for facilitated gene exchange among hospital-epidemic E. faecium isolates.\n\nA Type I Restriction-Modification System Associated with Enterococcus faecium Subspecies Separation.", "token_count": 218, "char_count": 883, "word_count": 121, "semantic_coherence": 1, "information_density": 0.6364, "quality_score": 0.8182, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:27.548166", "source": { "split": "train_shard_00002", "doc_id": 585 }, "chunk_id": "train_shard_00002_585_1", "global_id": 13510 }, { "text": "This work is aimed at analyzing yeast strains, possibly used in animal feeding, obtained by batch cultivation from cheese whey as main carbohydrated substrate. For that purpose 10 yeast strains selected for its biomass production capacity were chemically analyzed. From the results, it can be observed that the chemical composition of the strains is quiet variable, showing in all cases high protein content, good solubility and enzymatic digestibility. In all of them, the RNA content is low, being this important if the biomass is utilized in human feeding. On the other hand, they have an adequate content of essential amino acids, although the sulphur amino acids content is deficient. Among the tested yeasts, Kluyveromyces marxianus var. lactis (No. 10) stands out for the good relationship it has between protein and RNA content, as well as for the detection of methionine among its essential amino acids.\n\n[Chemical composition of the cellular biomass of yeasts].", "token_count": 234, "char_count": 971, "word_count": 153, "semantic_coherence": 1, "information_density": 0.6797, "quality_score": 0.8399, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:28.010338", "source": { "split": "train_shard_00002", "doc_id": 586 }, "chunk_id": "train_shard_00002_586_0", "global_id": 13511 }, { "text": "

Background

Divergence of bacterial populations into distinct subpopulations is often the result of ecological isolation. While some studies have suggested the existence of Salmonella enterica subsp. enterica subclades, evidence for these subdivisions has been ambiguous. Here we used a comparative genomics approach to define the population structure of Salmonella enterica subsp. enterica, and identify clade-specific genes that may be the result of ecological specialization.

Results

Multi-locus sequence analysis (MLSA) and single nucleotide polymorphisms (SNPs) data for 16 newly sequenced and 30 publicly available genomes showed an unambiguous subdivision of S. enterica subsp. enterica into at least two subpopulations, which we refer to as clade A and clade B. Clade B strains contain several clade-specific genes or operons, including a β-glucuronidase operon, a S-fimbrial operon, and cell surface related genes, which strongly suggests niche specialization of this subpopulation. An additional set of 123 isolates was assigned to clades A and B by using qPCR assays targeting subpopulation-specific SNPs and genes of interest. Among 98 serovars examined, approximately 20% belonged to clade B. All clade B isolates contained two pathogenicity related genomic islands, SPI-18 and a cytolethal distending toxin islet; a combination of these two islands was previously thought to be exclusive to serovars Typhi and Paratyphi A. Presence of β-glucuronidase in clade B isolates specifically suggests an adaptation of this clade to the vertebrate gastrointestinal environment.

Conclusions

S. enterica subsp. enterica consists of at least two subpopulations that differ specifically in genes involved in host and tissue tropism, utilization of host specific carbon and nitrogen sources and are therefore likely to differ in ecology and transmission characteristics.\n\nGenome sequencing reveals diversification of virulence factor content and possible host adaptation in distinct subpopulations of Salmonella enterica.", "token_count": 501, "char_count": 2042, "word_count": 279, "semantic_coherence": 1, "information_density": 0.6165, "quality_score": 0.8082, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:28.688286", "source": { "split": "train_shard_00002", "doc_id": 587 }, "chunk_id": "train_shard_00002_587_0", "global_id": 13512 }, { "text": "

Background

Mucosal-associated Escherichia coli are commonly found in inflamed tissues during inflammatory bowel disease (IBD). These bacteria often possess an adherent and invasive phenotype but lack virulence-associated features of well-described intestinal E. coli pathogens, and are of diverse serology and phylotypes, making it difficult to correlate strain characteristics with exacerbations of disease.

Methods

The genome sequences of 14 phenotypically assigned adherent-invasive Escherichia coli (AIEC) isolates obtained from intestinal biopsies of patients with IBD were compared with the genome sequences of 37 other pathogenic and commensal E. coli available from public databases.

Results

Core genome-based phylogenetic analyses and genome-wide comparison of genetic content established the existence of a closely related cluster of AIEC strains with 3 distinct genetic insertions differentiating them from commensal E. coli. These strains are of the B2 phylotype have a variant type VI secretion system (T6SS-1), and are highly related to extraintestinal pathogenic E. coli, suggesting that these 2 clinically distinct pathovars have common virulence strategies. Four other mucosally adherent E. coli strains from patients with IBD were of diverse phylogenetic origins and lacked the 3 genetic features, suggesting that they are not related to the B2 AIEC cluster. Although AIEC are often considered as having a unique association with Crohn's disease, isolates from Crohn's disease and ulcerative colitis were genetically indistinguishable.

Conclusions

B2 AIEC thus represent a closely related cluster of IBD-associated E. coli strains that are distinct from normal commensal isolates, and which should be considered separately from the phenotypically similar but genetically distinct non-B2 AIEC strains when considering their association with intestinal pathogenesis.", "token_count": 493, "char_count": 1911, "word_count": 252, "semantic_coherence": 1, "information_density": 0.5714, "quality_score": 0.7857, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:29.372762", "source": { "split": "train_shard_00002", "doc_id": 588 }, "chunk_id": "train_shard_00002_588_0", "global_id": 13513 }, { "text": "Genome-based Definition of an Inflammatory Bowel Disease-associated Adherent-Invasive Escherichia coli Pathovar.", "token_count": 36, "char_count": 112, "word_count": 11, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:29.750006", "source": { "split": "train_shard_00002", "doc_id": 588 }, "chunk_id": "train_shard_00002_588_1", "global_id": 13514 }, { "text": "

Background

The food spoilage yeast species Zygosaccharomyces bailii exhibits an extraordinary capacity to tolerate weak acids, in particular acetic acid. In Saccharomyces cerevisiae, the transcription factor Haa1 (ScHaa1) is considered the main player in genomic expression reprogramming in response to acetic acid stress, but the role of its homologue in Z. bailii (ZbHaa1) is unknown.

Results

In this study it is demonstrated that ZbHaa1 is a ScHaa1 functional homologue by rescuing the acetic acid susceptibility phenotype of S. cerevisiae haa1Δ. The disruption of ZbHAA1 in Z. bailii IST302 and the expression of an extra ZbHAA1 copy confirmed ZbHAA1 as a determinant of acetic acid tolerance. ZbHaa1 was found to be required for acetic acid stress-induced transcriptional activation of Z. bailii genes homologous to ScHaa1-target genes. An evolutionary analysis of the Haa1 homologues identified in 28 Saccharomycetaceae species genome sequences, including Z bailii, was carried out using phylogenetic and gene neighbourhood approaches. Consistent with previous studies, this analysis revealed a group containing pre-whole genome duplication species Haa1/Cup2 single orthologues, including ZbHaa1, and two groups containing either Haa1 or Cup2 orthologues from post-whole genome duplication species. S. cerevisiae Cup2 (alias Ace1) is a transcription factor involved in response and tolerance to copper stress. Taken together, these observations led us to hypothesize and demonstrate that ZbHaa1 is also involved in copper-induced transcriptional regulation and copper tolerance.

Conclusions

The transcription factor ZbHaa1 is required for adaptive response and tolerance to both acetic acid and copper stresses. The subfunctionalization of the single ancestral Haa1/Cup2 orthologue that originated Haa1 and Cup2 paralogues after whole genome duplication is proposed.", "token_count": 507, "char_count": 1894, "word_count": 257, "semantic_coherence": 1, "information_density": 0.5837, "quality_score": 0.7918, "entities": { "genes": [ "IST302" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:30.420004", "source": { "split": "train_shard_00002", "doc_id": 589 }, "chunk_id": "train_shard_00002_589_0", "global_id": 13515 }, { "text": "The Zygosaccharomyces bailii transcription factor Haa1 is required for acetic acid and copper stress responses suggesting subfunctionalization of the ancestral bifunctional protein Haa1/Cup2.", "token_count": 48, "char_count": 191, "word_count": 23, "semantic_coherence": 1, "information_density": 0.9565, "quality_score": 0.9783, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "saccharomyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:30.781852", "source": { "split": "train_shard_00002", "doc_id": 589 }, "chunk_id": "train_shard_00002_589_1", "global_id": 13516 }, { "text": "

Background

The increasing resistance of Plasmodium, the malaria parasites, to multiple commonly used drugs has underscored the urgent need to develop effective antimalarial drugs and vaccines. The new direction of genomics-driven target discovery has become possible with the completion of parasite genome sequencing, which can lead us to a better understanding of how the parasites develop the genetic variability that is associated with their response to environmental challenges and other adaptive phenotypes.

Results

We present the results of a comprehensive analysis of the genomes of six Plasmodium species, including two species that infect humans, one that infects monkeys, and three that infect rodents. The core genome shared by all six species is composed of 3,351 genes, which make up about 22%-65% of the genome repertoire. These components play important roles in fundamental functions as well as in parasite-specific activities. We further investigated the distribution and features of genes that have been expanded in specific Plasmodium lineage(s). Abundant duplicate genes are present in the six species, with 5%-9% of the whole genomes composed lineage specific radiations. The majority of these gene families are hypothetical proteins with unknown functions; a few may have predicted roles such as antigenic variation.

Conclusions

The core genome components in the malaria parasites have functions ranging from fundamental biological processes to roles in the complex networks that sustain the parasite-specific lifestyles appropriate to different hosts. They represent the minimum requirement to maintain a successful life cycle that spans vertebrate hosts and mosquito vectors. Lineage specific expansions (LSEs) have given rise to abundant gene families in Plasmodium. Although the functions of most families remain unknown, these LSEs could reveal components in parasite networks that, by their enhanced genetic variability, can contribute to pathogenesis, virulence, responses to environmental challenges, or interesting phenotypes.\n\nCore genome components and lineage specific expansions in malaria parasites plasmodium.", "token_count": 470, "char_count": 2168, "word_count": 299, "semantic_coherence": 1, "information_density": 0.5853, "quality_score": 0.7926, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:31.428813", "source": { "split": "train_shard_00002", "doc_id": 590 }, "chunk_id": "train_shard_00002_590_0", "global_id": 13517 }, { "text": "In this work, the effects of salt and mechanical cell breaking on the overall activity of the endogenous enzymes of Kluyveromyces fragilis grown on whey-based media were studied at the optimal values of temperature (54 degrees C) and initial concentration of yeast and whey protein (100 g dm-3) previously selected. An unstructured kinetic model of first order was found to be capable of simulating quite satisfactorily the time course of residual suspended solids (Y) in the slurry, as well as Kjeldahl (KP) and Lowry (LP) protein and total carbohydrates (G) accumulation in the clear extract. The autolysis kinetic rate constant (ka), and yield factors for Kjeldahl and Lowry protein and reducing sugars on total solids hydrolysed were found to be insensitive to the salt level and preliminary mechanical disruption of cells. Nevertheless, maximum production of yeast-whey protein extracts was achieved when the endogenous enzymes of ground cells are induced by 5% w/v salt addition. Except for their respective salt contents, both autolysates exhibited no apparent difference in chemical composition.\n\nEffect of some physico-chemical treatments on the kinetics of autolysed-yeast extract production from whey", "token_count": 294, "char_count": 1211, "word_count": 183, "semantic_coherence": 1, "information_density": 0.6721, "quality_score": 0.8361, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:31.984516", "source": { "split": "train_shard_00002", "doc_id": 591 }, "chunk_id": "train_shard_00002_591_0", "global_id": 13518 }, { "text": "While the microbiota resident in the human gut is now known to provide a range of functions relevant to host health, many of the microbial members of the community have not yet been cultured or are represented by a limited number of isolates. We describe here the draft genome sequence of Turicibacter sanguinis PC909, isolated from a pooled healthy human fecal sample as part of the Australian Human Gut Microbiome Project.\n\nDraft genome sequence of Turicibacter sanguinis PC909, isolated from human feces.", "token_count": 121, "char_count": 507, "word_count": 82, "semantic_coherence": 1, "information_density": 0.6829, "quality_score": 0.8415, "entities": { "genes": [ "PC909" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:32.376006", "source": { "split": "train_shard_00002", "doc_id": 592 }, "chunk_id": "train_shard_00002_592_0", "global_id": 13519 }, { "text": "

Background

Genomic Islands (GIs) have key roles since they modulate the structure and size of bacterial genomes displaying a diverse set of laterally transferred genes. Despite their importance, GIs in marine bacterial genomes have not been explored systematically to uncover possible trends and to analyze their putative ecological significance.

Results

We carried out a comprehensive analysis of GIs in 70 selected marine bacterial genomes detected with IslandViewer to explore the distribution, patterns and functional gene content in these genomic regions. We detected 438 GIs containing a total of 8152 genes. GI number per genome was strongly and positively correlated with the total GI size. In 50% of the genomes analyzed the GIs accounted for approximately 3% of the genome length, with a maximum of 12%. Interestingly, we found transposases particularly enriched within Alphaproteobacteria GIs, and site-specific recombinases in Gammaproteobacteria GIs. We described specific Homologous Recombination GIs (HR-GIs) in several genera of marine Bacteroidetes and in Shewanella strains among others. In these HR-GIs, we recurrently found conserved genes such as the β-subunit of DNA-directed RNA polymerase, regulatory sigma factors, the elongation factor Tu and ribosomal protein genes typically associated with the core genome.

Conclusions

Our results indicate that horizontal gene transfer mediated by phages, plasmids and other mobile genetic elements, and HR by site-specific recombinases play important roles in the mobility of clusters of genes between taxa and within closely related genomes, modulating the flexible pool of the genome. Our findings suggest that GIs may increase bacterial fitness under environmental changing conditions by acquiring novel foreign genes and/or modifying gene transcription and/or transduction.\n\nPatterns and architecture of genomic islands in marine bacteria.", "token_count": 457, "char_count": 1929, "word_count": 266, "semantic_coherence": 1, "information_density": 0.6541, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:33.008126", "source": { "split": "train_shard_00002", "doc_id": 593 }, "chunk_id": "train_shard_00002_593_0", "global_id": 13520 }, { "text": "Since fluconazole achieves high urine concentrations, we assessed its usefulness in the treatment of urinary candidiasis. We studied 24 patients (8 male) aged 23 to 97 years old, that presented pyuria with a negative urine culture for bacteria and fungal colony counts in urine of 10(4) CFU/ml or more. Isolated strains were Candida albicans in 20 cases, Candida kefyr in one case, Candida glabrata in one case and Candida spp in two cases. All patients were treated with fluconazole in doses of 50 to 100 mg/day for 2 to 4 weeks. The fungus was eradicated in 21 patients (88%), the infection persisted in two (8.5%) and one had a relapse (4.2%). Two patients had transient elevations of transaminases, one had abdominal pain and one, a purpuric syndrome without thrombocytopenia in whom the drug was discontinued. It is concluded that fluconazole is efficacious and safe in the treatment of urinary candidiasis.\n\n[Fluconazole in treatment of urinary candidiasis. Experience with 24 patients].", "token_count": 293, "char_count": 993, "word_count": 160, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:33.569031", "source": { "split": "train_shard_00002", "doc_id": 594 }, "chunk_id": "train_shard_00002_594_0", "global_id": 13521 }, { "text": "Bacterial biofilms are involved in chronic infections and confer 10 to 1,000 times more resistance to antibiotics compared with planktonic growth, leading to complications and treatment failure. When transitioning from a planktonic lifestyle to biofilms, some Gram-positive bacteria are likely to modulate several cellular pathways, including central carbon metabolism, biosynthesis pathways, and production of secondary metabolites. These metabolic adaptations might play a crucial role in biofilm formation by Gram-positive pathogens such as Staphylococcus aureus and Enterococcus faecalis. Here, we performed a transcriptomic approach to identify cellular pathways that might be similarly regulated during biofilm formation in these bacteria. Different strains and biofilm-inducing media were used to identify a set of regulated genes that are common and independent of the environment or accessory genomes analyzed. Our approach highlighted that the de novo purine biosynthesis pathway was upregulated in biofilms of both species when using a tryptone soy broth-based medium but not so when a brain heart infusion-based medium was used. We did not identify other pathways commonly regulated between both pathogens. Gene deletions and usage of a drug targeting a key enzyme showed the importance of this pathway in biofilm formation of S. aureus. The importance of the de novo purine biosynthesis pathway might reflect an important need for purine during biofilm establishment, and thus could constitute a promising drug target. IMPORTANCE Biofilms are often involved in nosocomial infections and can cause serious chronic infections if not treated properly. Current anti-biofilm strategies rely on antibiotic usage, but they have a limited impact because of the biofilm intrinsic tolerance to drugs. Metabolism remodeling likely plays a central role during biofilm formation. Using comparative transcriptomics of different strains of Staphylococcus aureus and Enterococcus faecalis, we determined that almost all cellular adaptations are not shared between strains and species", "token_count": 491, "char_count": 2101, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6034, "quality_score": 0.8017, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:34.220291", "source": { "split": "train_shard_00002", "doc_id": 595 }, "chunk_id": "train_shard_00002_595_0", "global_id": 13522 }, { "text": "Interestingly, we observed that the de novo purine biosynthesis pathway was upregulated during biofilm formation by both species in a specific medium. The requirement for purine could constitute an interesting new anti-biofilm target with a wide spectrum that could also prevent resistance evolution. These results are also relevant to a better understanding of the physiology of biofilm formation.\n\nThe de novo Purine Biosynthesis Pathway Is the Only Commonly Regulated Cellular Pathway during Biofilm Formation in TSB-Based Medium in Staphylococcus aureus and Enterococcus faecalis.", "token_count": 150, "char_count": 598, "word_count": 83, "semantic_coherence": 1, "information_density": 0.7229, "quality_score": 0.8614, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:34.659300", "source": { "split": "train_shard_00002", "doc_id": 595 }, "chunk_id": "train_shard_00002_595_1", "global_id": 13523 }, { "text": "

Background

The genus Brachyspira currently encompasses seven valid species that colonize the intestines of mammals and birds. In a previous study a group of strongly haemolytic isolates from pigs and mallards was provisionally described as a new species within genus Brachyspira, \"B. suanatina\", and enteropathogenic properties were demonstrated in a porcine challenge model.

Methods

In the current study characterization of B. suanatina was performed on the basis of cell morphology, growth characteristics, enzyme profiles, DNA-DNA hybridization (DDH) and whole genome comparisons. The draft genome sequence of B. suanatina strain AN4859/03 was determined and compared with the available genomes of all valid species of Brachyspira.

Results

According to morphological traits, growth characteristics and enzymatic profiles, B. suanatina was similar to the type strain of B. hyodysenteriae, but using the recommended threshold value of 70% similarity by DDH it did not belong to any of the recognized Brachyspira species (range 16-64% similarity). This was further supported by average nucleotide identity values. Phylogenetic analysis performed using housekeeping genes and core genomes of all valid Brachyspira sp. and \"B. hampsonii\" revealed that B. suanatina and B. intermedia formed a clade distinct from B. hyodysenteriae. By comparing the genomes of the three closely related species B. intermedia, B. hyodysenteriae and B. suanatina similar profiles of general genomic features and distribution of genes in different functional categories were obtained. However, the genome size of B. hyodysenteriae was smallest among the species, suggesting the possibility of reductive evolution in the divergence of this species. A bacteriophage region and a putative plasmid sequence were also found in the genome of B. suanatina strain AN4859/03.

Conclusions

The results of our study suggest that despite being similar to B. hyodysenteriae phenotypically, B. suanatina should be regarded as a separate species based on its genetic characteristics", "token_count": 534, "char_count": 2072, "word_count": 288, "semantic_coherence": 1, "information_density": 0.5729, "quality_score": 0.7865, "entities": { "genes": [ "AN4859" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:06:35.296119", "source": { "split": "train_shard_00002", "doc_id": 596 }, "chunk_id": "train_shard_00002_596_0", "global_id": 13524 }, { "text": "Based on characteristics presented in this report we propose that strains AN4859/03, AN1681:1/04, AN2384/04 and Dk12570-2 from pigs in Sweden and Denmark, and strains AN3949:2/02 and AN1418:2/01 isolated from mallards in Sweden, represent a unique species within genus Brachyspira. For this new species we propose the name B. suanatina for which the type strain is AN4859/03T (=ATCC® BAA-2592™=DSM 100974T).\n\nBrachyspira suanatina sp. nov., an enteropathogenic intestinal spirochaete isolated from pigs and mallards: genomic and phenotypic characteristics.", "token_count": 201, "char_count": 556, "word_count": 76, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [ "AN1681", "AN4859", "AN3949", "AN1418", "AN2384" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:35.756362", "source": { "split": "train_shard_00002", "doc_id": 596 }, "chunk_id": "train_shard_00002_596_1", "global_id": 13525 }, { "text": "The malaria parasite Plasmodium falciparum has a great capacity for evolutionary adaptation to evade host immunity and develop drug resistance. Current understanding of parasite evolution is impeded by the fact that a large fraction of the genome is either highly repetitive or highly variable, and thus difficult to analyse using short read technologies. Here we describe a resource of deep sequencing data on parents and progeny from genetic crosses, which has enabled us to perform the first genome-wide, integrated analysis of SNP, INDEL and complex polymorphisms, using Mendelian error rates as an indicator of genotypic accuracy. These data reveal that INDELs are exceptionally abundant, being more common than SNPs and thus the dominant mode of polymorphism within the core genome. We use the high density of SNP and INDEL markers to analyse patterns of meiotic recombination, confirming a high rate of crossover events, and providing the first estimates for the rate of non-crossover events and the length of conversion tracts. We observe several instances of recombination that modify copy number variants associated with drug resistance, demonstrating a mechanism whereby fitness costs associated with resistance mutations could be compensated and greater phenotypic plasticity could be acquired. We describe a novel web application that allows these data to be explored in detail.\n\nGenome variation and meiotic recombination inPlasmodium falciparum: insights from deep sequencing of genetic crosses", "token_count": 336, "char_count": 1516, "word_count": 224, "semantic_coherence": 1, "information_density": 0.6696, "quality_score": 0.8348, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:36.328999", "source": { "split": "train_shard_00002", "doc_id": 597 }, "chunk_id": "train_shard_00002_597_0", "global_id": 13526 }, { "text": "The development and application of a partial composite S. aureus virulence-associated gene micro array is described. Epidemic, pandemic and sporadic lineages of healthcare associated(HA-) and community-associated (CA-) S. aureus were compared. The clonal population structure was supported but further evidence for large-scale recombination events was obtained. Phage structural genes linked with the CA phenotype were identified and in silico analysis revealed these to be correlated with phage serogroup. CA strains generally carried a PVL-associated phage either of the A or Fb serogroup, whilst the HA strains predominantly carried sero group B phage. It is proposed that carriage of PVL associated phage rather than the specific pvl genes is correlated with the CA phenotype. These findings further support the role of the accessory genome in shaping the epidemiology of S. aureus. The microarray was used to study gene expression in isogenic strains differing by a deletion in the agr locus. Microarray analysis revealed significant differences between the levels of expression of several genes of the normal and mutant strains. However, RNAIII levels in the non-mutant strain ... (continues)\n\nStaphylococcus aureus virulence gene studies : a comparative microarray based approach", "token_count": 329, "char_count": 1328, "word_count": 188, "semantic_coherence": 1, "information_density": 0.6543, "quality_score": 0.8271, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:36.897820", "source": { "split": "train_shard_00002", "doc_id": 598 }, "chunk_id": "train_shard_00002_598_0", "global_id": 13527 }, { "text": "

Background

Honey bee gut microbiota transmitted via social interactions are beneficial to the host health. Although the microbial community is relatively stable, individual variations and high strain-level diversity have been detected across honey bees. Although the bee gut microbiota structure is influenced by environmental factors, the heritability of the gut members and the contribution of the host genetics remains elusive. Considering bees within a colony are not readily genetically identical due to the polyandry of the queen, we hypothesize that the microbiota structure can be shaped by host genetics.

Results

We used shotgun metagenomics to simultaneously profile the microbiota and host genotypes of bees from hives of four different subspecies. Gut composition is more distant between genetically different bees at both phylotype- and \"sequence-discrete population\" levels. We then performed a successive passaging experiment within colonies of hybrid bees generated by artificial insemination, which revealed that the microbial composition dramatically shifts across batches of bees during the social transmission. Specifically, different strains from the phylotype of Snodgrassella alvi are preferentially selected by genetically varied hosts, and strains from different hosts show a remarkably biased distribution of single-nucleotide polymorphism in the Type IV pili loci. Genome-wide association analysis identified that the relative abundance of a cluster of Bifidobacterium strains is associated with the host glutamate receptor gene specifically expressed in the bee brain. Finally, mono-colonization of Bifidobacterium with a specific polysaccharide utilization locus impacts the alternative splicing of the gluR-B gene, which is associated with an increased GABA level in the brain.

Conclusions

Our results indicated that host genetics influence the bee gut composition and suggest a gut-brain connection implicated in the gut bacterial strain preference. Honey bees have been used extensively as a model organism for social behaviors, genetics, and the gut microbiome. Further identification of host genetic function as a shaping force of microbial structure will advance our understanding of the host-microbe interactions. Video abstract.", "token_count": 510, "char_count": 2287, "word_count": 310, "semantic_coherence": 1, "information_density": 0.6, "quality_score": 0.8, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:37.556696", "source": { "split": "train_shard_00002", "doc_id": 599 }, "chunk_id": "train_shard_00002_599_0", "global_id": 13528 }, { "text": "Honey bee genetics shape the strain-level structure of gut microbiota in social transmission.", "token_count": 21, "char_count": 93, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:37.903992", "source": { "split": "train_shard_00002", "doc_id": 599 }, "chunk_id": "train_shard_00002_599_1", "global_id": 13529 }, { "text": "Time-kill and postantifungal effect (PAFE) of amphotericin B, caspofungin, fluconazole, and voriconazole were determined against clinical isolates of Candida guilliermondii, Candida kefyr, and Candida lusitaniae. Azoles displayed fungistatic activity and no measurable PAFE, regardless of the concentration tested. Amphotericin B and caspofungin demonstrated concentration-dependent fungicidal activity, although amphotericin B only produced a significant dose-dependent PAFE against all isolates tested.\n\nIn vitro pharmacodynamic characteristics of amphotericin B, caspofungin, fluconazole, and voriconazole against bloodstream isolates of infrequent Candida species from patients with hematologic malignancies.", "token_count": 190, "char_count": 712, "word_count": 82, "semantic_coherence": 1, "information_density": 0.6951, "quality_score": 0.8476, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:38.349193", "source": { "split": "train_shard_00002", "doc_id": 600 }, "chunk_id": "train_shard_00002_600_0", "global_id": 13530 }, { "text": "The yeast Candida albicans coaggregates with a variety of streptococcal species, an interaction that may promote oral colonization by yeast cells. C. albicans and Candida tropicalis are the yeasts most frequently isolated from the human oral cavity and our data demonstrate that both these species bind to Streptococcus gordonii NCTC 7869 while two other Candida species (Candida krusei and Candida kefyr) do not. Adherence of C. albicans was greatest when the yeast had been grown at 30 degrees C to mid-exponential growth phase. For 21 strains of C. albicans there was a positive correlation between the ability to adhere to S. gordonii and adherence to experimental salivary pellicle. Whole saliva either stimulated or slightly inhibited adherence of C. albicans to S. gordonii depending on the streptococcal growth conditions. The results suggest that the major salivary adhesins and coaggregation adhesins of C. albicans are co-expressed.\n\nInteractions of Candida albicans with bacteria and salivary molecules in oral biofilms.", "token_count": 275, "char_count": 1032, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6346, "quality_score": 0.8173, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:39.272806", "source": { "split": "train_shard_00002", "doc_id": 601 }, "chunk_id": "train_shard_00002_601_0", "global_id": 13531 }, { "text": "

Background

In spite of its association with gastroenteritis and inflammatory bowel diseases, the isolation of Campylobacter concisus from both diseased and healthy individuals has led to controversy regarding its role as an intestinal pathogen. One proposed reason for this is the presence of high genetic diversity among the genomes of C. concisus strains.

Results

In this study the genomes of six C. concisus strains were sequenced, assembled and annotated including two strains isolated from Crohn's disease patients (UNSW2 and UNSW3), three from gastroenteritis patients (UNSW1, UNSWCS and ATCC 51562) and one from a healthy individual (ATCC 51561). The genomes of C. concisus BAA-1457 and UNSWCD, available from NCBI, were included in subsequent comparative genomic analyses. The Pan and Core genomes for the sequenced C. concisus strains consisted of 3254 and 1556 protein coding genes, respectively.

Conclusion

Genes were identified with specific conservation in C. concisus strains grouped by phenotypes such as invasiveness, adherence, motility and diseased states. Phylogenetic trees based on ribosomal RNA sequences and concatenated host-related pathways for the eight C. concisus strains were generated using the neighbor-joining method, of which the 16S rRNA gene and peptidoglycan biosynthesis grouped the C. concisus strains according to their pathogenic phenotypes. Furthermore, 25 non-synonymous amino acid changes with 14 affecting functional domains, were identified within proteins of conserved host-related pathways, which had possible associations with the pathogenic potential of C. concisus strains. Finally, the genomes of the eight C. concisus strains were compared to the nine available genomes of the well-established pathogen Campylobacter jejuni, which identified several important differences in the respiration pathways of these two species. Our findings indicate that C", "token_count": 502, "char_count": 1924, "word_count": 265, "semantic_coherence": 1, "information_density": 0.6038, "quality_score": 0.8019, "entities": { "genes": [ "UNSW3", "UNSW2", "UNSW1" ], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:39.926792", "source": { "split": "train_shard_00002", "doc_id": 602 }, "chunk_id": "train_shard_00002_602_0", "global_id": 13532 }, { "text": "concisus strains are genetically diverse, and suggest the genomes of this bacterium contain respiration pathways and modifications in the peptidoglycan layer that may play an important role in its virulence.\n\nComparative genomics of Campylobacter concisus isolates reveals genetic diversity and provides insights into disease association.", "token_count": 74, "char_count": 338, "word_count": 45, "semantic_coherence": 1, "information_density": 0.8667, "quality_score": 0.9333, "entities": { "genes": [], "proteins": [], "pathways": [ "respiration" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:40.295585", "source": { "split": "train_shard_00002", "doc_id": 602 }, "chunk_id": "train_shard_00002_602_1", "global_id": 13533 }, { "text": "

Objectives

This study aimed to explore the effects of an isocaloric Mediterranean diet (MD) intervention on metabolic health, gut microbiome and systemic metabolome in subjects with lifestyle risk factors for metabolic disease.

Design

Eighty-two healthy overweight and obese subjects with a habitually low intake of fruit and vegetables and a sedentary lifestyle participated in a parallel 8-week randomised controlled trial. Forty-three participants consumed an MD tailored to their habitual energy intakes (MedD), and 39 maintained their regular diets (ConD). Dietary adherence, metabolic parameters, gut microbiome and systemic metabolome were monitored over the study period.

Results

Increased MD adherence in the MedD group successfully reprogrammed subjects' intake of fibre and animal proteins. Compliance was confirmed by lowered levels of carnitine in plasma and urine. Significant reductions in plasma cholesterol (primary outcome) and faecal bile acids occurred in the MedD compared with the ConD group. Shotgun metagenomics showed gut microbiome changes that reflected individual MD adherence and increase in gene richness in participants who reduced systemic inflammation over the intervention. The MD intervention led to increased levels of the fibre-degrading Faecalibacterium prausnitzii and of genes for microbial carbohydrate degradation linked to butyrate metabolism. The dietary changes in the MedD group led to increased urinary urolithins, faecal bile acid degradation and insulin sensitivity that co-varied with specific microbial taxa.

Conclusion

Switching subjects to an MD while maintaining their energy intake reduced their blood cholesterol and caused multiple changes in their microbiome and metabolome that are relevant in future strategies for the improvement of metabolic health.\n\nMediterranean diet intervention in overweight and obese subjects lowers plasma cholesterol and causes changes in the gut microbiome and metabolome independently of energy intake.", "token_count": 497, "char_count": 2027, "word_count": 269, "semantic_coherence": 1, "information_density": 0.5465, "quality_score": 0.7732, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:40.966900", "source": { "split": "train_shard_00002", "doc_id": 603 }, "chunk_id": "train_shard_00002_603_0", "global_id": 13534 }, { "text": "Citrus canker, caused by Xanthomonas citri pv. citri, is a serious disease of citrus plants worldwide. Earlier phylogenetic studies using housekeeping genes revealed that X. citri pv. citri is related to many other pathovars, which can be collectively referred as Xanthomonas citri pathovars (XCPs). From the present study, we report the genome sequences of 18 XCPs and compared them with four XCPs available in the public domain. In a tree based on phylogenomic marker genes, all the XCPs form a monophyletic cluster, suggesting their origin from a common ancestor. Phylogenomic analysis using the type strain further established that all the XCPs belong to one species. Clonal analysis of the core genome revealed the presence of two major lineages within this monophyletic cluster consisting of some clonal variants. Incidentally, the majority of these XCPs were first noticed in India, corroborating their clonal relationship and their common origin. Comparative analysis revealed an open pan-genome and the role of interstrain genomic flux of these XCPs since their diversification from a common ancestor. Even though there are wide variations in type III gene effectomes, we identified three core effectors which can be valuable in resistance-breeding programs. Overall, genomic examination of ecological relatives allowed us to dissect the tremendous genomic potential of X. citri species to rapidly evolve into specialized strains infecting diverse crop plants.IMPORTANCE Host specialization is one of the characteristic features of highly evolved pathogens such as the Xanthomonas group of phytopathogenic bacteria. Since the hosts involve staple crops and economically important fruits such as citrus, detailed understanding of the diversity and evolution of such strains infecting diverse plants is important for quarantine purposes. In the present study, we carried out genomic investigation of members of a phylogenetically and ecologically defined group of Xanthomonas strains pathogenic to diverse plants, including citrus", "token_count": 497, "char_count": 2086, "word_count": 298, "semantic_coherence": 1, "information_density": 0.6141, "quality_score": 0.807, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:41.640254", "source": { "split": "train_shard_00002", "doc_id": 604 }, "chunk_id": "train_shard_00002_604_0", "global_id": 13535 }, { "text": "This group includes the oldest Xanthomonas pathovars and also recently emerged pathovars in a particular country where they are endemic. Our high-throughput genomic study has provided novel insights into the evolution of a unique lineage consisting of serious pathogens and their ecological relatives, suggesting the nature, scope, and pattern of rapid and recent diversification. Further, from the level of species to that of clonal variants, the study revealed interesting genomic patterns in diversification of a Xanthomonas lineage and perhaps will inspire careful study of the host range of the included pathovars.\n\nEcological and Evolutionary Insights into Xanthomonas citri Pathovar Diversity.", "token_count": 163, "char_count": 714, "word_count": 100, "semantic_coherence": 1, "information_density": 0.7, "quality_score": 0.85, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:42.113318", "source": { "split": "train_shard_00002", "doc_id": 604 }, "chunk_id": "train_shard_00002_604_1", "global_id": 13536 }, { "text": "Bacteria of the genus Salmonella comprise a large and evolutionary related population of zoonotic pathogens that can infect mammals, including humans and domestic animals, birds, reptiles and amphibians. Salmonella carries a plethora of virulence genes, including fimbrial adhesins, some of them known to participate in mammalian or avian host colonization. Each type of fimbria has its structural subunit and biogenesis genes encoded by one fimbrial gene cluster (FGC). The accumulation of new genomic information offered a timely opportunity to better evaluate the number and types of FGCs in the Salmonella pangenome, to test the use of current classifications based on phylogeny, and to infer potential correlations between FGC evolution in various Salmonella serovars and host niches. This study focused on the FGCs of the currently deciphered 90 genomes and 60 plasmids of Salmonella. The analysis highlighted a fimbriome consisting of 35 different FGCs, of which 16 were new, each strain carrying between 5 and 14 FGCs. The Salmonella fimbriome was extremely diverse with FGC representatives in 8 out of 9 previously categorized fimbrial clades and subclades. Phylogenetic analysis of Salmonella suggested macroevolutionary shifts detectable by extensive FGC deletion and acquisition. In addition, microevolutionary drifts were best depicted by the high level of allelic variation in predicted or known adhesins, such as the type 1 fimbrial adhesin FimH for which 67 different natural alleles were identified in S. enterica subsp. I. Together with strain-specific collections of FGCs, allelic variation among adhesins attested to the pathoadaptive evolution of Salmonella towards specific hosts and tissues, potentially modulating host range, strain virulence, disease progression, and transmission efficiency. Further understanding of how each Salmonella strain utilizes its panel of FGCs and specific adhesin alleles for survival and infection will support the development of new approaches for the control of Salmonellosis.\n\nDiversification of the Salmonella fimbriae: a model of macro- and microevolution.", "token_count": 509, "char_count": 2116, "word_count": 306, "semantic_coherence": 1, "information_density": 0.6307, "quality_score": 0.8154, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:42.756635", "source": { "split": "train_shard_00002", "doc_id": 605 }, "chunk_id": "train_shard_00002_605_0", "global_id": 13537 }, { "text": "We conducted a structural analysis of the antigenic cell wall mannoprotein (mannan) isolated from Candida kefyr (formerly Candida pseudotropicalis) IFO 0586. The result of two-dimensional homonuclear Hartmann-Hahn analysis of this mannan indicates that the molecule is constructed from alpha-1,2- and alpha-1,6-linked mannopyranose residues. Upon alkali treatment (beta-elimination reaction), this mannan released two alpha-1,2-linked mannooligosaccharides, biose and triose. The structure of the alkali-stable mannan (outer chain) moiety was investigated by acetolysis. The structures of the resultant oligosaccharides, biose and triose, from the outer chain moiety were found to be the same as those of the alkali-released ones. Further, the treatment of the parent mannan with an Arthrobacter GJM-1 exo-alpha-mannosidase gave a linear mannan consisting solely of alpha-1,6-linked mannopyranose residues. These results indicate that the mannan forms the long backbone of the alpha-1,6 linkage, with a large number of short alpha-1,2-linked oligomannosyl side chains forming a comblike structure. Moreover, we investigated the serological properties of this mannan by performing an inhibition assay of a slide agglutination reaction with mannooligosaccharides and polyclonal factor sera (Candida Check; Iatron). The result indicates that the factor 1 serum preferentially recognizes the alpha-1,2-linked oligomannosyl side chains in this mannan. On the other hand, the fact that the mannan does not contain an antigenic determinant(s) corresponding to factor 8 suggests that the epitope(s) of this factor resides in other molecules on the cell surface of this strain.\n\nStructure of cell wall mannan of Candida kefyr IFO 0586.", "token_count": 467, "char_count": 1726, "word_count": 239, "semantic_coherence": 1, "information_density": 0.5732, "quality_score": 0.7866, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:43.403383", "source": { "split": "train_shard_00002", "doc_id": 606 }, "chunk_id": "train_shard_00002_606_0", "global_id": 13538 }, { "text": "

Introduction

Microbial biofertilizers or biocontrol agents are potential sustainable approaches to overcome the limitations of conventional agricultural practice. However, the limited catalog of microbial candidates for diversified crops creates hurdles in successfully implementing sustainable agriculture for increasing global/local populations. The present study aimed to explore the wheat rhizosphere microbiota for microbial strains with a biofertilizer and biocontrol potential.

Methods

Using a microbial culturing-based approach, 12 unique microbial isolates were identified and screened for biofertilizer/biocontrol potential using genomics and physiological experimentations.

Results and discussion

Molecular, physiological, and phylogenetic characterization identified Stenotrophomonas maltophilia BCM as a potential microbial candidate for sustainable agriculture. Stenotrophomonas maltophilia BCM was identified as a coccus-shaped gram-negative microbe having optimal growth at 37°C in a partially alkaline environment (pH 8.0) with a proliferation time of ~67 minutes. The stress response physiology of Stenotrophomonas maltophilia BCM indicates its successful survival in dynamic environmental conditions. It significantly increased (P <0.05) the wheat seed germination percentage in the presence of phytopathogens and saline conditions. Genomic characterization decoded the presence of genes involved in plant growth promotion, nutrient assimilation, and antimicrobial activity. Experimental evidence also correlates with genomic insights to explain the potential of Stenotrophomonas maltophilia BCM as a potential biofertilizer and biocontrol agent. With these properties, Stenotrophomonas maltophilia BCM could sustainably promote wheat production to ensure food security for the increasing population, especially in native wheat-consuming areas.\n\nBiofertilizer and biocontrol properties of Stenotrophomonas maltophilia BCM emphasize its potential application for sustainable agriculture.", "token_count": 514, "char_count": 2069, "word_count": 236, "semantic_coherence": 1, "information_density": 0.6059, "quality_score": 0.803, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:06:44.053692", "source": { "split": "train_shard_00002", "doc_id": 607 }, "chunk_id": "train_shard_00002_607_0", "global_id": 13539 }, { "text": "

Objectives

We noted four cases of apparent in vivo emergence of teicoplanin resistance during failed therapy for initially teicoplanin-susceptible vanB vancomycin-resistant Enterococcus faecium (VREfm) infections in solid organ transplant recipients at our institution over a 12 month period. We investigated if in vivo emergence of resistance had occurred, if transplant-related vancomycin-resistant Enterococcus (VRE) infections had occurred and identified clinical predictors of resistance emergence.

Methods

Whole genome sequencing was performed on nine VREfm isolates for phylogenetic analysis and to identify determinants of teicoplanin resistance. Clinical treatment details were compared with other patients who received teicoplanin for confirmed vanB VRE infections but did not develop resistance during the same year at our institution.

Results

A high-resolution, core genome phylogeny was inferred for nine VREfm isolates and confirmed in vivo development of resistance during failed therapy in four cases. Four different non-synonymous single nucleotide polymorphisms (SNPs) were observed in the vanRS genes of teicoplanin-resistant strains compared with the index teicoplanin-susceptible strains, and these SNPs were predicted to confer teicoplanin resistance. VREfm within a cluster of early transplant-related infections were phylogenetically identical at the core genome level, indicating a common source donor. Focus eradication and absence of prosthetic material were characteristics of those patients treated successfully.

Conclusions

Clinicians should be cautious of resistance emerging during teicoplanin therapy for vanB VRE, particularly in immunosuppressed patients or where source control is difficult.\n\nGenomic analysis of teicoplanin resistance emerging during treatment of vanB vancomycin-resistant Enterococcus faecium infections in solid organ transplant recipients including donor-derived cases.", "token_count": 476, "char_count": 1955, "word_count": 241, "semantic_coherence": 1, "information_density": 0.5726, "quality_score": 0.7863, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:44.696300", "source": { "split": "train_shard_00002", "doc_id": 608 }, "chunk_id": "train_shard_00002_608_0", "global_id": 13540 }, { "text": "

Background

Comparative genomics can be an initial step in finding the genetic basis for phenotypic differences among bacterial strains and species. Bacteria belonging to the genus Providencia have been isolated from numerous and varied environments. We sequenced, annotated and compared draft genomes of P. rettgeri, P. sneebia, P. alcalifaciens, and P. burhodogranariea. These bacterial species that were all originally isolated as infections of wild Drosophila melanogaster and have been previously shown to vary in virulence to experimentally infected flies.

Results

We found that these Providencia species share a large core genome, but also possess distinct sets of genes that are unique to each isolate. We compared the genomes of these isolates to draft genomes of four Providencia isolated from the human gut and found that the core genome size does not substantially change upon inclusion of the human isolates. We found many adhesion related genes among those genes that were unique to each genome. We also found that each isolate has at least one type 3 secretion system (T3SS), a known virulence factor, though not all identified T3SS belong to the same family nor are they in syntenic genomic locations.

Conclusions

The Providencia species examined here are characterized by high degree of genomic similarity which will likely extend to other species and isolates within this genus. The presence of T3SS islands in all of the genomes reveal that their presence is not sufficient to indicate virulence towards D. melanogaster, since some of the T3SS-bearing isolates are known to cause little mortality. The variation in adhesion genes and the presence of T3SSs indicates that host cell adhesion is likely an important aspect of Providencia virulence.\n\nComparative genomics of bacteria in the genus Providencia isolated from wild Drosophila melanogaster.", "token_count": 449, "char_count": 1888, "word_count": 282, "semantic_coherence": 1, "information_density": 0.5674, "quality_score": 0.7837, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:45.335050", "source": { "split": "train_shard_00002", "doc_id": 609 }, "chunk_id": "train_shard_00002_609_0", "global_id": 13541 }, { "text": "The key genes required for Bacillus anthracis to cause anthrax have been acquired recently by horizontal gene transfer. To understand the genetic background for the evolution of B. anthracis virulence, we obtained high-redundancy genome sequences of 45 strains of the Bacillus cereus sensu lato (s.l.) species that were chosen for their genetic diversity within the species based on the existing multilocus sequence typing scheme. From the resulting data, we called more than 324,000 new genes representing more than 12,333 new gene families for this group. The core genome size for the B. cereus s.l. group was ∼1750 genes, with another 2150 genes found in almost every genome constituting the extended core. There was a paucity of genes specific and conserved in any clade. We found no evidence of recent large-scale gene loss in B. anthracis or for unusual accumulation of nonsynonymous DNA substitutions in the chromosome; however, several B. cereus genomes isolated from soil and not previously associated with human disease were degraded to various degrees. Although B. anthracis has undergone an ecological shift within the species, its chromosome does not appear to be exceptional on a macroscopic scale compared with close relatives.\n\nGenomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis.", "token_count": 333, "char_count": 1360, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6507, "quality_score": 0.8254, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:45.910236", "source": { "split": "train_shard_00002", "doc_id": 610 }, "chunk_id": "train_shard_00002_610_0", "global_id": 13542 }, { "text": "The gut microbiome is a major determinant of host health, yet it is only in the last 2 decades that the advent of next-generation sequencing has enabled it to be studied at a genomic level. Shotgun sequencing is beginning to provide insight into the prokaryotic as well as eukaryotic and viral components of the gut community, revealing not just their taxonomy, but also the functions encoded by their collective metagenome. This revolution in understanding is being driven by continued development of sequencing technologies and in consequence necessitates reciprocal development of computational approaches that can adapt to the evolving nature of sequence datasets. In this review, we provide an overview of current bioinformatic strategies for handling metagenomic sequence data and discuss their strengths and limitations. We then go on to discuss key technological developments that have the potential to once again revolutionise the way we are able to view and hence understand the microbiome.\n\nMetagenomics: a path to understanding the gut microbiome.", "token_count": 218, "char_count": 1059, "word_count": 161, "semantic_coherence": 1, "information_density": 0.6646, "quality_score": 0.8323, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:46.370392", "source": { "split": "train_shard_00002", "doc_id": 611 }, "chunk_id": "train_shard_00002_611_0", "global_id": 13543 }, { "text": "

Background

The phenylalanine ammonia-lyase (PAL) gene, a well-studied plant defense gene, is crucial for growth, development, and stress resistance. The PAL gene family has been studied in many plants. Citrus is among the most vital cash crops worldwide. However, the PAL gene family has not been comprehensively studied in most Citrus species, and the biological functions and specific underlying mechanisms are unclear.

Results

We identified 41 PAL genes from nine Citrus species and revealed different patterns of evolution among the PAL genes in different Citrus species. Gene duplication was found to be a vital mechanism for the expansion of the PAL gene family in citrus. In addition, there was a strong correlation between the ability of PAL genes to respond to stress and their evolutionary duration in citrus. PAL genes with shorter evolutionary times were involved in more multiple stress responses, and these PAL genes with broad-spectrum resistance were all single-copy genes. By further integrating the lignin and flavonoid synthesis pathways in citrus, we observed that PAL genes contribute to the synthesis of lignin and flavonoids, which enhance the physical defense and ROS scavenging ability of citrus plants, thereby helping them withstand stress.

Conclusions

This study provides a comprehensive framework of the PAL gene family in citrus, and we propose a hypothetical model for the stress resistance mechanism in citrus. This study provides a foundation for further investigations into the biological functions of PAL genes in the growth, development, and response to various stresses in citrus.\n\nComparative analysis of the PAL gene family in nine citruses provides new insights into the stress resistance mechanism of Citrus species.", "token_count": 395, "char_count": 1779, "word_count": 262, "semantic_coherence": 1, "information_density": 0.5038, "quality_score": 0.7519, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:46.987589", "source": { "split": "train_shard_00002", "doc_id": 612 }, "chunk_id": "train_shard_00002_612_0", "global_id": 13544 }, { "text": "The transcription of the majority of the ribosomal protein (rp) genes of Saccharomyces cerevisiae is activated by cis-acting elements, designated RPG boxes, which specifically bind the multifunctional protein RAP1 in vitro. To investigate to what extent this global system of transcription regulation has been conserved, we have isolated a number of rp genes of the related yeast species Kluyveromyces lactis and Kluyveromyces marxianus, whose counterparts in Saccharomyces are controlled by RAP1. The coding regions of these genes showed a sequence similarity of about 90% when compared to their Saccharomyces counterparts. In contrast, little or no sequence similarity was found between the upstream regions and the intervening sequences of Kluyveromyces and Saccharomyces homologs. However, the occurrence and the position of the introns is conserved. The sequence data also show that the physical linkage that exists in S. cerevisiae between the rp genes encoding RP59 (CRY1), S24 and L46 is conserved in Kluyveromyces. Northern analysis demonstrated that each of the isolated Kluyveromyces genes is transcriptionally active. By sequence comparison we identified a number of conserved sequences in the upstream region of each of the Kluyveromyces rp genes, which we designated the X, Z and RPGK boxes. The last one is highly similar, though not identical, to the S. cerevisiae RPG box. Functional analysis of the intergenic region between the genes encoding Kluyveromyces ribosomal proteins S24 and L46 showed that the RPGK box (+Z box) functions as a transcriptional activator, while the X box acts as a transcriptional repressor. Band-shift assays confirmed the existence of a RAP1-like protein in Kluyveromyces that binds to the RPGK box but not to the S. cerevisiae RPG box. In contrast, S. cerevisiae RAP1 did recognize the RPGK box.\n\nStructural and putative regulatory sequences of Kluyveromyces ribosomal protein genes.", "token_count": 491, "char_count": 1930, "word_count": 291, "semantic_coherence": 1, "information_density": 0.5017, "quality_score": 0.7509, "entities": { "genes": [ "RAP1", "CRY1", "RP59" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:47.634538", "source": { "split": "train_shard_00002", "doc_id": 613 }, "chunk_id": "train_shard_00002_613_0", "global_id": 13545 }, { "text": "

Background and objectives

Streptococcus pneumoniae, a major human pathogen, is closely related to the commensal species S. mitis and S. oralis. S. pneumoniae surface proteins are implicated in virulence and host interaction of this species, but many of them have recently been detected in S. mitis B6 in silico. We tested for the presence of such genes usinga set of eight S. mitis and eleven S. oralis strains from different geographic locations.

Materials and methods

An oligonucleotide microarray was designed based on the genomes of S. pneumoniae R6 and TIGR4 as well as S. mitis B6 to include 63 cell surface proteins. The S. pneumoniae genes encoding neuraminidases, hyaluronidase and pneumolysin were also included. In addition to comparative genomic hybridization experiments, homologues were identified in silico in the genome of S. oralis Uo5.

Results and conclusions

The results document that many S. pneumoniae related surface proteins are ubiquitously present among the Mitis group of streptococci. All 19 samples hybridized with the pavA probe representing a gene important for adherence and invasion of S. pneumoniae. Only eight genes were not recognized in any strain, including the S. pneumoniae PcpC gene as the only virulence gene of the S. pneumoniae core genome.The fact that only 12 out of 26 genes present in the S. oralis Uo5 genome could be detected by microarray analysis confirms the sequence variation of surface components.\n\nCell surface proteins in S. pneumoniae, S. mitis and S. oralis.", "token_count": 424, "char_count": 1539, "word_count": 234, "semantic_coherence": 1, "information_density": 0.5641, "quality_score": 0.7821, "entities": { "genes": [ "TIGR4" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:48.259089", "source": { "split": "train_shard_00002", "doc_id": 614 }, "chunk_id": "train_shard_00002_614_0", "global_id": 13546 }, { "text": "Salmonella enterica subspecies enterica is a highly diverse subspecies with more than 1500 serovars and the ability to distinguish serovars within this group is vital for surveillance. With the development of whole-genome sequencing technology, serovar prediction by traditional serotyping is being replaced by molecular serotyping. Existing in silico serovar prediction approaches utilize surface antigen encoding genes, core genome MLST and serovar-specific gene markers or DNA fragments for serotyping. However, these serovar-specific gene markers or DNA fragments only distinguished a small number of serovars. In this study, we compared 2258 Salmonella accessory genomes to identify 414 candidate serovar-specific or lineage-specific gene markers for 106 serovars which includes 24 polyphyletic serovars and the paraphyletic serovar Enteritidis. A combination of several lineage-specific gene markers can be used for the clear identification of the polyphyletic serovars and the paraphyletic serovar. We designed and evaluated an in silico serovar prediction approach by screening 1089 genomes representing 106 serovars against a set of 131 serovar-specific gene markers. The presence or absence of one or more serovar-specific gene markers was used to predict the serovar of an isolate from genomic data. We show that serovar-specific gene markers have comparable accuracy to other in silico serotyping methods with 84.8% of isolates assigned to the correct serovar with no false positives (FP) and false negatives (FN) and 10.5% of isolates assigned to a small subset of serovars containing the correct serovar with varied FP. Combined, 95.3% of genomes were correctly assigned to a serovar. This approach would be useful as diagnosis moves to culture-independent and metagenomic methods as well as providing a third alternative to confirm other genome-based analyses", "token_count": 508, "char_count": 1916, "word_count": 270, "semantic_coherence": 1, "information_density": 0.5556, "quality_score": 0.7778, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:48.915294", "source": { "split": "train_shard_00002", "doc_id": 615 }, "chunk_id": "train_shard_00002_615_0", "global_id": 13547 }, { "text": "The identification of a set of gene markers may also be useful in the development of more cost-effective molecular assays designed to detect specific gene markers of the all major serovars in a region. These assays would be useful in serotyping isolates where cultures are no longer obtained and traditional serotyping is therefore impossible.\n\nIn silico Identification of Serovar-Specific Genes for Salmonella Serotyping.", "token_count": 108, "char_count": 436, "word_count": 63, "semantic_coherence": 1, "information_density": 0.746, "quality_score": 0.873, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:49.296608", "source": { "split": "train_shard_00002", "doc_id": 615 }, "chunk_id": "train_shard_00002_615_1", "global_id": 13548 }, { "text": "Subgenome dominance has been reported in diverse allopolyploid species, where genes from one subgenome are preferentially retained and are more highly expressed than those from other subgenome(s). However, the molecular mechanisms responsible for subgenome dominance remain poorly understood. Here, we develop genome-wide map of accessible chromatin regions (ACRs) in cultivated strawberry (2n = 8x = 56, with A, B, C, D subgenomes). Each ACR is identified as an MNase hypersensitive site (MHS). We discover that the dominant subgenome A contains a greater number of total MHSs and MHS per gene than the submissive B/C/D subgenomes. Subgenome A suffers fewer losses of MHS-related DNA sequences and fewer MHS fragmentations caused by insertions of transposable elements. We also discover that genes and MHSs related to stress response have been preferentially retained in subgenome A. We conclude that preservation of genes and their cognate ACRs, especially those related to stress responses, play a major role in the establishment of subgenome dominance in octoploid strawberry.\n\nDynamics of accessible chromatin regions and subgenome dominance in octoploid strawberry.", "token_count": 293, "char_count": 1171, "word_count": 172, "semantic_coherence": 1, "information_density": 0.657, "quality_score": 0.8285, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:49.858287", "source": { "split": "train_shard_00002", "doc_id": 616 }, "chunk_id": "train_shard_00002_616_0", "global_id": 13549 }, { "text": "Bacteriophages have important roles in the ecology of the human gut microbiome but are under-represented in reference databases. To address this problem, we assembled the Metagenomic Gut Virus catalogue that comprises 189,680 viral genomes from 11,810 publicly available human stool metagenomes. Over 75% of genomes represent double-stranded DNA phages that infect members of the Bacteroidia and Clostridia classes. Based on sequence clustering we identified 54,118 candidate viral species, 92% of which were not found in existing databases. The Metagenomic Gut Virus catalogue improves detection of viruses in stool metagenomes and accounts for nearly 40% of CRISPR spacers found in human gut Bacteria and Archaea. We also produced a catalogue of 459,375 viral protein clusters to explore the functional potential of the gut virome. This revealed tens of thousands of diversity-generating retroelements, which use error-prone reverse transcription to mutate target genes and may be involved in the molecular arms race between phages and their bacterial hosts.\n\nMetagenomic compendium of 189,680 DNA viruses from the human gut microbiome.", "token_count": 298, "char_count": 1138, "word_count": 166, "semantic_coherence": 1, "information_density": 0.6506, "quality_score": 0.8253, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:50.417263", "source": { "split": "train_shard_00002", "doc_id": 617 }, "chunk_id": "train_shard_00002_617_0", "global_id": 13550 }, { "text": "The Rad51 protein from the methylotrophic yeast Pichia angusta (Rad51(Pa)) of the taxonomic complex Hansenula polymorpha is a homolog of the RecA-RadA-Rad51 protein superfamily, which promotes homologous recombination and recombination repair in prokaryotes and eukaryotes. We cloned the RAD51 gene from the cDNA library of the thermotolerant P. angusta strain BKM Y1397. Induction of this gene in a rad51-deficient Saccharomyces cerevisiae strain partially complemented the survival rate after ionizing radiation. Purified Rad51(Pa) protein exhibited properties typical of the superfamily, including the stoichiometry of binding to single-stranded DNA (ssDNA) (one protomer of Rad51(Pa) per 3 nucleotides) and DNA specificity for ssDNA-dependent ATP hydrolysis [poly(dC) > poly(dT) > phiX174 ssDNA > poly(dA) > double-stranded M13 DNA]. An inefficient ATPase and very low cooperativity for ATP interaction position Rad51(Pa) closer to Rad51 than to RecA. Judging by thermoinactivation, Rad51(Pa) alone was 20-fold more thermostable at 37 degrees C than its S. cerevisiae homolog (Rad51(Sc)). Moreover, it maintained ssDNA-dependent ATPase and DNA transferase activities up to 52 to 54 degrees C, whereas Rad51(Sc) was completely inactive at 47 degrees C. A quick nucleation and an efficient final-product formation in the strand exchange reaction promoted by Rad51(Pa) occurred only at temperatures above 42 degrees C. These reaction characteristics suggest that Rad51(Pa) is dependent on high temperatures for activity.\n\nRad51 protein from the thermotolerant yeast Pichia angusta as a typical but thermodependent member of the Rad51 family.", "token_count": 483, "char_count": 1642, "word_count": 231, "semantic_coherence": 1, "information_density": 0.645, "quality_score": 0.8225, "entities": { "genes": [ "RAD51" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:51.069156", "source": { "split": "train_shard_00002", "doc_id": 618 }, "chunk_id": "train_shard_00002_618_0", "global_id": 13551 }, { "text": "DNA from the yeast Kluyveromyces marxianus was studied for its heterogeneity and the multiplicity of rRNA cistrons. These cistrons banded at a slightly different density from the bulk DNA in preparative CsCl or Hg2+-Cs2SO4 equilibrium density gradients. The reassociation kinetics of the bulk DNA showed that the repetitive fraction represented a small amount of the total cellular DNA (10%) and that the single copy fraction had a complexity of 6.3 X 10(9) daltons. Approximately 2.2% of the DNA hybridized to 3H-labelled rRNA at saturation. On the basis of the above genome size, the multiplicity of the rRNA cistrons was calculated to be about 70 per haploid nucleus.\n\nRibosomal RNA genes in Kluyveromyces marxianus.", "token_count": 210, "char_count": 719, "word_count": 113, "semantic_coherence": 1, "information_density": 0.6549, "quality_score": 0.8274, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:51.532164", "source": { "split": "train_shard_00002", "doc_id": 619 }, "chunk_id": "train_shard_00002_619_0", "global_id": 13552 }, { "text": "Escherichia coli is a versatile bacterial species that includes both harmless commensal strains and pathogenic strains found in the gastrointestinal tract in humans and warm-blooded animals. The growing amount of DNA sequence information generated in the era of \"genomics\" has helped to increase our understanding of the factors and mechanisms involved in the diversification of this bacterial species. The pathogenic side of E. coli that is afforded through horizontal transfers of genes encoding virulence factors enables this bacterium to become a highly diverse and adapted pathogen that is responsible for intestinal or extraintestinal diseases in humans and animals. Many of the accessory genes acquired by horizontal transfers form syntenic blocks and are recognized as genomic islands (GIs). These genomic regions contribute to the rapid evolution, diversification and adaptation of E. coli variants because they are frequently subject to rearrangements, excision and transfer, as well as to further acquisition of additional DNA. Here, we review a subgroup of GIs from E. coli termed pathogenicity islands (PAIs), a concept defined in the late 1980s by Jörg Hacker and colleagues in Werner Goebel's group at the University of Würzburg, Würzburg, Germany. As with other GIs, the PAIs comprise large genomic regions that differ from the rest of the genome by their G + C content, by their typical insertion within transfer RNA genes, and by their harboring of direct repeats (at their ends), integrase determinants, or other mobility loci. The hallmark of PAIs is their contribution to the emergence of virulent bacteria and to the development of intestinal and extraintestinal diseases. This review summarizes the current knowledge on the structure and functional features of PAIs, on PAI-encoded E. coli pathogenicity factors and on the role of PAIs in host-pathogen interactions.\n\nPathogenicity Factors of Genomic Islands in Intestinal and Extraintestinal Escherichia coli.", "token_count": 495, "char_count": 2025, "word_count": 298, "semantic_coherence": 1, "information_density": 0.5705, "quality_score": 0.7852, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:52.192020", "source": { "split": "train_shard_00002", "doc_id": 620 }, "chunk_id": "train_shard_00002_620_0", "global_id": 13553 }, { "text": "In the present work, the occurrence of yeasts in different types of typical Sardinian ewe's cheeses (32 samples of pecorino, 32 of caciotta, 40 of feta, 56 of ricotta) was determined. For the strains isolated the following properties were studied: proteolytic and lipolytic activities, the ability to grow at different temperatures, different concentrations of salt, and to assimilate and/or ferment compounds like lactate, citrate, lactose, glucose, galactose, lactic acid. Of 160 samples analysed, 76.2% yielded growth of yeasts. Yeast counts showed a certain variability among the samples. The highest levels were observed in caciotta and feta cheeses. A total of 281 strains belonging to 16 genera and 25 species were identified. In general, Debaryomyces hansenii was the dominant species, representing 28.8% of the total isolates. Other frequently appearing species were Geotrichum candidum, Kluyveromyces lactis and K. marxianus. Other genera encountered were Pichia, Candida, Dekkera, Yarrowia and Rhodotorula. With regard to the biochemical and technological properties of the yeasts, only K. lactis, K. marxianus and Dek. anomala assimilated and fermented lactose, whereas the majority of the species assimilated lactic acid. The assimilation of citrate was a characteristic of D. hansenii, R. rubra and Y. lipolytica. On the whole, the yeasts were weakly proteolytic while lipolytic activity was present in several species. A high percentage of strains showed a certain tolerance to low temperatures while only some strains of D. hansenii and K. lactis were able to grow at a 10% NaCl concentration.\n\nYeasts associated with Sardinian ewe's dairy products.", "token_count": 466, "char_count": 1665, "word_count": 248, "semantic_coherence": 1, "information_density": 0.5968, "quality_score": 0.7984, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "acid", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:52.861846", "source": { "split": "train_shard_00002", "doc_id": 621 }, "chunk_id": "train_shard_00002_621_0", "global_id": 13554 }, { "text": "A one-year examination of mammary secretions (n = 2,896) from Danish cattle with clinical or subclinical mastitis revealed 45 strains of fungi and algae. The strains originated from 44 mammary secretions of 42 cows in 40 herds. The following species of fungi were identified: Candida catenulata (n = 2), Candida kefyr (n = 6), Candida krusei (n = 17), Candida rugosa (n = 6), Candida tropicalis (n = 3), Candida valida (n = 1), Geotrichum capitatum (n = 5). The algal species Prototheca zopfii was demonstrated in five samples.\n\nMycotic and algal bovine mastitis in Denmark.", "token_count": 196, "char_count": 574, "word_count": 96, "semantic_coherence": 1, "information_density": 0.625, "quality_score": 0.8125, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:53.345650", "source": { "split": "train_shard_00002", "doc_id": 622 }, "chunk_id": "train_shard_00002_622_0", "global_id": 13555 }, { "text": "Today, next-generation whole-genome sequencing (WGS) is increasingly used to determine the genetic relationships of bacteria on a nearly whole-genome level for infection control purposes and molecular surveillance. Here, we conducted a multicenter ring trial comprising five laboratories to determine the reproducibility and accuracy of WGS-based typing. The participating laboratories sequenced 20 blind-coded Staphylococcus aureus DNA samples using 250-bp paired-end chemistry for library preparation in a single sequencing run on an Illumina MiSeq sequencer. The run acceptance criteria were sequencing outputs >5.6 Gb and Q30 read quality scores of >75%. Subsequently, spa typing, multilocus sequence typing (MLST), ribosomal MLST, and core genome MLST (cgMLST) were performed by the participants. Moreover, discrepancies in cgMLST target sequences in comparisons with the included and also published sequence of the quality control strain ATCC 25923 were resolved using Sanger sequencing. All five laboratories fulfilled the run acceptance criteria in a single sequencing run without any repetition. Of the 400 total possible typing results, 394 of the reported spa types, sequence types (STs), ribosomal STs (rSTs), and cgMLST cluster types were correct and identical among all laboratories; only six typing results were missing. An analysis of cgMLST allelic profiles corroborated this high reproducibility; only 3 of 183,927 (0.0016%) cgMLST allele calls were wrong. Sanger sequencing confirmed all 12 discrepancies of the ring trial results in comparison with the published sequence of ATCC 25923. In summary, this ring trial demonstrated the high reproducibility and accuracy of current next-generation sequencing-based bacterial typing for molecular surveillance when done with nearly completely locked-down methods.\n\nHigh Interlaboratory Reproducibility and Accuracy of Next-Generation-Sequencing-Based Bacterial Genotyping in a Ring Trial.", "token_count": 492, "char_count": 1959, "word_count": 267, "semantic_coherence": 1, "information_density": 0.5993, "quality_score": 0.7996, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:54.033650", "source": { "split": "train_shard_00002", "doc_id": 623 }, "chunk_id": "train_shard_00002_623_0", "global_id": 13556 }, { "text": "The genus Nocardiopsis, a widespread group in phylum Actinobacteria, has received much attention owing to its ecological versatility, pathogenicity, and ability to produce a rich array of bioactive metabolites. Its high environmental adaptability might be attributable to its genome dynamics, which can be estimated through comparative genomic analysis targeting microorganisms with close phylogenetic relationships but different phenotypes. To shed light on speciation, gene content evolution, and environmental adaptation in these unique actinobacteria, we sequenced draft genomes for 16 representative species of the genus and compared them with that of the type species N. dassonvillei subsp. dassonvillei DSM 43111(T). The core genome of 1,993 orthologous and paralogous gene clusters was identified, and the pan-genomic reservoir was found not only to accommodate more than 22,000 genes, but also to be open. The top ten paralogous genes in terms of copy number could be referred to three functional categories: transcription regulators, transporters, and synthases related to bioactive metabolites. Based on phylogenomic reconstruction, we inferred past evolutionary events, such as gene gains and losses, and identified a list of clade-specific genes implicated in environmental adaptation. These results provided insights into the genetic causes of environmental adaptability in this cosmopolitan actinobacterial group and the contributions made by its inherent features, including genome dynamics and the constituents of core and accessory proteins.\n\nComparative genomic analysis of the genus Nocardiopsis provides new insights into its genetic mechanisms of environmental adaptability.", "token_count": 379, "char_count": 1696, "word_count": 233, "semantic_coherence": 1, "information_density": 0.6567, "quality_score": 0.8283, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:54.633122", "source": { "split": "train_shard_00002", "doc_id": 624 }, "chunk_id": "train_shard_00002_624_0", "global_id": 13557 }, { "text": "A novel denaturing high-performance liquid chromatography (DHPLC)-based technique allows rapid high-resolution analysis of PCR products. We used this technique for unequivocal molecular identification of seven Candida species. We show the application of this PCR/DHPLC approach for direct detection and identification of yeast species from blood cultures and for detection of Candida colonization in the gastrointestinal tract of allogeneic transplant patients.\n\nUse of denaturing high-performance liquid chromatography for rapid detection and identification of seven Candida species.", "token_count": 126, "char_count": 584, "word_count": 75, "semantic_coherence": 1, "information_density": 0.6133, "quality_score": 0.8067, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:55.017532", "source": { "split": "train_shard_00002", "doc_id": 625 }, "chunk_id": "train_shard_00002_625_0", "global_id": 13558 }, { "text": "Microgard, a commercially available fermented milk product containing antimicrobial metabolites, was a potent inhibitor for Gram-negative bacteria such as Pseudomonas, Salmonella, and Yersinia when 1% concentration was incorporated into agar media. Gram-positive Bacillus cereus, Staphylococcus aureus, and Listeria monocytogenes were insensitive to Microgard. Kluyveromyces marxianus, an unidentified black yeast, and Penicillium expansum were partially suppressed, whereas Aspergillus niger and a yogurt spoilage yeast were tolerant to 5% Microgard. Optimum activity of Microgard was at pH 5.3 and below; the concentration that gave complete inhibition depended upon the number of bacteria present as well as the genus tested. Blood agar base reversed the antagonistic activity of Microgard against Pseudomonas putida compared with plate count agar.\n\nAntimicrobial activity of Microgard against food spoilage and pathogenic microorganisms.", "token_count": 256, "char_count": 941, "word_count": 124, "semantic_coherence": 1, "information_density": 0.75, "quality_score": 0.875, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:55.568176", "source": { "split": "train_shard_00002", "doc_id": 626 }, "chunk_id": "train_shard_00002_626_0", "global_id": 13559 }, { "text": "

Background

Next-generation sequencing (NGS) is a powerful tool for understanding both patterns of descent over time and space (phylogeography) and the molecular processes underpinning genome divergence in pathogenic bacteria. Here, we describe a synthesis between these perspectives by employing a recently developed Bayesian approach, BRATNextGen, for detecting recombination on an expanded NGS dataset of the globally disseminated methicillin-resistant Staphylococcus aureus (MRSA) clone ST239.

Results

The data confirm strong geographical clustering at continental, national and city scales and demonstrate that the rate of recombination varies significantly between phylogeographic sub-groups representing independent introductions from Europe. These differences are most striking when mobile non-core genes are included, but remain apparent even when only considering the stable core genome. The monophyletic ST239 sub-group corresponding to isolates from South America shows heightened recombination, the sub-group predominantly from Asia shows an intermediate level, and a very low level of recombination is noted in a third sub-group representing a large collection from Turkey.

Conclusions

We show that the rapid global dissemination of a single pathogenic bacterial clone results in local variation in measured recombination rates. Possible explanatory variables include the size and time since emergence of each defined sub-population (as determined by the sampling frame), variation in transmission dynamics due to host movement, and changes in the bacterial genome affecting the propensity for recombination.\n\nPhylogeographic variation in recombination rates within a global clone of methicillin-resistant Staphylococcus aureus.", "token_count": 398, "char_count": 1763, "word_count": 225, "semantic_coherence": 1, "information_density": 0.6933, "quality_score": 0.8467, "entities": { "genes": [ "ST239" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:56.188467", "source": { "split": "train_shard_00002", "doc_id": 627 }, "chunk_id": "train_shard_00002_627_0", "global_id": 13560 }, { "text": "The genetic variability in bacterial species is much larger than in other kingdoms of life. The gene content between pairs of isolates can diverge by as much as 30% in species like Escherichia coli or Streptococcus pneumoniae. This unexpected finding led to the introduction of the concept of the pan-genome, the set of genes that can be found in a given bacterial species. The genome of any isolate is thus composed by a \"core genome\" shared by all strains and characteristic of the species, and a \"dispensable genome\" that accounts for many of the phenotypic differences between strains. The pan-genome is usually much larger than the genome of any single isolate and, given the ability of many bacteria to exchange genetic material with the environment, constitutes a reservoir that could enhance their ability to survive in a mutating environment. To understand the evolution of the pan-genome of an important pathogen and its interactions with the commensal microbial flora, we have analyzed the genomes of 44 strains of Streptococcus pneumoniae, one of the most important causes of microbial diseases in humans. Despite evidence of extensive homologous recombination, the S. pneumoniae phylogenetic tree reconstructed from polymorphisms in the core genome identified major groups of genetically related strains. With the exception of serotype 1, the tree correlated poorly with capsular serotype, geographical site of isolation and disease outcome. The distribution of dispensable genes was consistent with phylogeny, although horizontal gene transfer events attenuated this correlation in the case of ancient lineages. Homologous recombination, involving short stretches of DNA, was the dominant evolutionary process of the core genome of S. pneumoniae. Genetic exchange with related species sharing the same ecological niche was the main mechanism of evolution of S. pneumonia; and S. mitis was the main reservoir of genetic diversity of S. pneumoniae. The pan-genome of S. pneumoniae increased logarithmically with the number of strains and linearly with the variability of the sample, suggesting that acquired genes accumulate proportionately to the age of clones.", "token_count": 500, "char_count": 2174, "word_count": 330, "semantic_coherence": 1, "information_density": 0.5333, "quality_score": 0.7667, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:56.839783", "source": { "split": "train_shard_00002", "doc_id": 628 }, "chunk_id": "train_shard_00002_628_0", "global_id": 13561 }, { "text": "Population genetics and evolution of the pan-genome of Streptococcus pneumoniae.", "token_count": 23, "char_count": 80, "word_count": 10, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:57.189925", "source": { "split": "train_shard_00002", "doc_id": 628 }, "chunk_id": "train_shard_00002_628_1", "global_id": 13562 }, { "text": "Long considered to be a consequence of human antibiotics use by deduction, antibiotic resistance mechanisms appear to be in fact a much older phenomenon as antibiotic resistance genes have previously been detected from millions of year-old permafrost samples. As these specimens guarantee the viability of archaic bacteria, we herein propose to apply the culturomics approach to recover the bacterial content of a Siberian permafrost sample dated, using the in situ-produced cosmogenic nuclide chlorine36 (36Cl), at 2.7 million years to study the dynamics of bacterial evolution in an evolutionary perspective. As a result, we cultured and sequenced the genomes of 28 ancient bacterial species including one new species. To perform genome comparison between permafrost strains and modern isolates we selected 7 of these species (i.e., Achromobacter insolitus, Bacillus idriensis, Brevundimonas aurantiaca, Janibacter melonis, Kocuria rhizophila, Microbacterium hydrocarbonoxydans and Paracoccus yeei). We observed a high level of variability in genomic content with a percentage of shared genes in the core genomes ranging from 21.23% to 55.59%. In addition, the Single Nucleotide Polymorphism (SNP) comparison between permafrost and modern strains for the same species did not allow a dating of ancient strains based on genomic content. There were no significant differences in antibiotic resistance profiles between modern and ancient isolates of each species. Acquired resistance to antibiotics was phenotypically detected in all gram-negative bacterial species recovered from permafrost, with a significant number of genes coding for antibiotic resistance detected. Taken together, these findings confirm previously obtained data that antibiotic resistance predates humanity as most of antimicrobial agents are natural weapons used in inter-microbial conflicts within the biosphere.\n\nCulturing Ancient Bacteria Carrying Resistance Genes from Permafrost and Comparative Genomics with Modern Isolates.", "token_count": 504, "char_count": 2028, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6187, "quality_score": 0.8094, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:57.842065", "source": { "split": "train_shard_00002", "doc_id": 629 }, "chunk_id": "train_shard_00002_629_0", "global_id": 13563 }, { "text": "Staphylococcus aureus is a pathogen commonly found in nosocomial environments where infections can easily spread - especially given the reduced immune response of patients and large overlap between personnel in charge of their care. Although antibiotics are available to treat nosocomial infections, the increased occurrence of antibiotic resistance has rendered many treatments ineffective. Such is the case for methicillin resistant S. aureus (MRSA), which has continued to be a threat to public health since its emergence. For this reason, alternative treatment technologies utilizing antimicrobials such as bacteriocins, bacteriophages (phages) and phage endolysins are being developed. These antimicrobials provide an advantage over antibiotics in that many have narrow inhibition spectra, enabling treatments to be selected based on the target (pathogenic) bacterium while allowing for survival of commensal bacteria and thus avoiding collateral damage to the microbiome. Bacterial resistance to these treatments occurs less frequently than with antibiotics, particularly in circumstances where combinatory antimicrobial therapies are used. Phage therapy has been well established in Eastern Europe as an effective treatment against bacterial infections. While there are no Randomized Clinical Trials (RCTs) to our knowledge examining phage treatment of S. aureus infections that have completed all trial phases, numerous clinical trials are underway, and several commercial phage preparations are currently available to treat S. aureus infections. Bacteriocins have primarily been used in the food industry for bio-preservation applications. However, the idea of repurposing bacteriocins for human health is an attractive one considering their efficacy against many bacterial pathogens. There are concerns about the ability of bacteriocins to survive the gastrointestinal tract given their proteinaceous nature, however, this obstacle may be overcome by altering the administration route of the therapy through encapsulation, or by bioengineering protease-resistant variants. Obstacles such as enzymatic digestion are less of an issue for topical/local administration, for example, application to the surface of the skin", "token_count": 493, "char_count": 2255, "word_count": 305, "semantic_coherence": 1, "information_density": 0.6361, "quality_score": 0.818, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:58.501671", "source": { "split": "train_shard_00002", "doc_id": 630 }, "chunk_id": "train_shard_00002_630_0", "global_id": 13564 }, { "text": "Bacteriocins have also shown impressive synergistic effects when used in conjunction with other antimicrobials, including antibiotics, which may allow antibiotic-based therapies to be used more sparingly with less resistance development. This review provides an updated account of known bacteriocins, phages and phage endolysins which have demonstrated an impressive ability to kill S. aureus strains. In particular, examples of antimicrobials with the ability to target MRSA strains and their subsequent use in a clinical setting are outlined.\n\nEfficacy of Phage- and Bacteriocin-Based Therapies in Combatting Nosocomial MRSA Infections.", "token_count": 156, "char_count": 645, "word_count": 87, "semantic_coherence": 1, "information_density": 0.7816, "quality_score": 0.8908, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:58.936557", "source": { "split": "train_shard_00002", "doc_id": 630 }, "chunk_id": "train_shard_00002_630_1", "global_id": 13565 }, { "text": "The response of three amino acid biosynthetic enzymes, threonine dehydratase, tyrosine aminotransferase and saccharopine dehydrogenase, to conditions of histidine, tryptophan or lysine limitation was investigated in 15 yeast species. The activities of all these enzymes increased about two- to fourfold as a result of action of the general control of amino acid biosynthesis in Brettanomyces anomalus, Candida maltosa, Hansenula polymorpha, Rhodosporidium toruloides, Saccharomyces cerevisiae and Yarrowia lipolytica. No evidence for the existence of the general control was found in Candida brumptii, Candida utilis, Hansenula anomala, Hansenula henricii, Kluyveromyces marxianus, Pichia guilliermondii, Saccharomycopsis capsularis, Trichosporon adeninovorans and Trigonopsis variabilis.\n\nOccurrence of the general control of amino acid biosynthesis in yeasts.", "token_count": 264, "char_count": 861, "word_count": 109, "semantic_coherence": 1, "information_density": 0.6972, "quality_score": 0.8486, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:06:59.488103", "source": { "split": "train_shard_00002", "doc_id": 631 }, "chunk_id": "train_shard_00002_631_0", "global_id": 13566 }, { "text": "

Background

We applied comparative phylogenomics (whole genome comparisons of microbes using DNA microarrays combined with Bayesian-based phylogenies) to investigate S. pneumoniae isolates from West Africa, with the aim of providing insights into the pathogenicity and other features related to the biology of the organism. The strains investigated comprised a well defined collection of 58 invasive and carriage isolates that were sequenced typed and included eight different S. pneumoniae serotypes (1, 3, 5, 6A, 11, 14, 19 F and 23 F) of varying invasive disease potential.

Results

The core genome of the isolates was estimated to be 38% and was mainly represented by gene functional categories associated with housekeeping functions. Comparison of the gene content of invasive and carriage isolates identified at least eleven potential genes that may be important in virulence including surface proteins, transport proteins, transcription factors and hypothetical proteins. Thirteen accessory regions (ARs) were also identified and did not show any loci association with the eleven virulence genes. Intraclonal diversity (isolates of the same serotype and MLST but expressing different patterns of ARs) was observed among some clones including ST 1233 (serotype 5), ST 3404 (serotype 5) and ST 3321 (serotype 14). A constructed phylogenetic tree of the isolates showed a high level of heterogeneity consistent with the frequent S. pneumoniae recombination. Despite this, a homogeneous clustering of all the serotype 1 strains was observed.

Conclusions

Comparative phylogenomics of invasive and carriage S. pneumoniae isolates identified a number of putative virulence determinants that may be important in the progression of S. pneumoniae from the carriage phase to invasive disease. Virulence determinants that contribute to S. pneumoniae pathogenicity are likely to be distributed randomly throughout its genome rather than being clustered in dedicated loci or islands. Compared to other S", "token_count": 510, "char_count": 2016, "word_count": 286, "semantic_coherence": 1, "information_density": 0.6084, "quality_score": 0.8042, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:00.140447", "source": { "split": "train_shard_00002", "doc_id": 632 }, "chunk_id": "train_shard_00002_632_0", "global_id": 13567 }, { "text": "pneumoniae serotypes, serotype 1 appears most genetically uniform.\n\nComparative phylogenomics of Streptococcus pneumoniae isolated from invasive disease and nasopharyngeal carriage from West Africans.", "token_count": 57, "char_count": 200, "word_count": 23, "semantic_coherence": 1, "information_density": 0.913, "quality_score": 0.9565, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:00.499346", "source": { "split": "train_shard_00002", "doc_id": 632 }, "chunk_id": "train_shard_00002_632_1", "global_id": 13568 }, { "text": "

Background

Our previously published reports have described an effective biocontrol agent named Pseudomonas sp. M18 as its 16S rDNA sequence and several regulator genes share homologous sequences with those of P. aeruginosa, but there are several unusual phenotypic features. This study aims to explore its strain specific genomic features and gene expression patterns at different temperatures.

Results

The complete M18 genome is composed of a single chromosome of 6,327,754 base pairs containing 5684 open reading frames. Seven genomic islands, including two novel prophages and five specific non-phage islands were identified besides the conserved P. aeruginosa core genome. Each prophage contains a putative chitinase coding gene, and the prophage II contains a capB gene encoding a putative cold stress protein. The non-phage genomic islands contain genes responsible for pyoluteorin biosynthesis, environmental substance degradation and type I and III restriction-modification systems. Compared with other P. aeruginosa strains, the fewest number (3) of insertion sequences and the most number (3) of clustered regularly interspaced short palindromic repeats in M18 genome may contribute to the relative genome stability. Although the M18 genome is most closely related to that of P. aeruginosa strain LESB58, the strain M18 is more susceptible to several antimicrobial agents and easier to be erased in a mouse acute lung infection model than the strain LESB58. The whole M18 transcriptomic analysis indicated that 10.6% of the expressed genes are temperature-dependent, with 22 genes up-regulated at 28°C in three non-phage genomic islands and one prophage but none at 37°C.

Conclusions

The P. aeruginosa strain M18 has evolved its specific genomic structures and temperature dependent expression patterns to meet the requirement of its fitness and competitiveness under selective pressures imposed on the strain in rhizosphere niche.", "token_count": 494, "char_count": 1963, "word_count": 278, "semantic_coherence": 1, "information_density": 0.6403, "quality_score": 0.8201, "entities": { "genes": [ "LESB58" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:01.148863", "source": { "split": "train_shard_00002", "doc_id": 633 }, "chunk_id": "train_shard_00002_633_0", "global_id": 13569 }, { "text": "Genomic analysis and temperature-dependent transcriptome profiles of the rhizosphere originating strain Pseudomonas aeruginosa M18.", "token_count": 32, "char_count": 131, "word_count": 14, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:01.511670", "source": { "split": "train_shard_00002", "doc_id": 633 }, "chunk_id": "train_shard_00002_633_1", "global_id": 13570 }, { "text": "Clostridium perfringens is a gastrointestinal pathogen capable of causing disease in a variety of hosts. Necrotic enteritis in chickens is caused by C. perfringens strains that produce the pore-forming toxin NetB, the major virulence factor for this disease. Like many other C. perfringens toxins and antibiotic resistance genes, NetB is encoded on a conjugative plasmid. Conjugative transfer of the netB-containing plasmid pJIR3535 has been demonstrated in vitro with a netB-null mutant. This study has investigated the effect of plasmid transfer on disease pathogenesis, with two genetically distinct transconjugants constructed under in vitro conditions, within the intestinal tract of chickens. This study also demonstrates that plasmid transfer can occur naturally in the host gut environment without the need for antibiotic selective pressure to be applied. The demonstration of plasmid transfer within the chicken host may have implications for the progression and pathogenesis of C. perfringens-mediated disease. Such horizontal gene transfer events are likely to be common in the clostridia and may be a key factor in strain evolution, both within animals and in the wider environment.IMPORTANCEClostridium perfringens is a major gastrointestinal pathogen of poultry. C. perfringens strains that express the NetB pore-forming toxin, which is encoded on a conjugative plasmid, cause necrotic enteritis. This study demonstrated that the conjugative transfer of the netB-containing plasmid to two different nonpathogenic strains converted them into disease-causing strains with disease-causing capability similar to that of the donor strain", "token_count": 469, "char_count": 1730, "word_count": 233, "semantic_coherence": 1, "information_density": 0.5408, "quality_score": 0.7704, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:02.155165", "source": { "split": "train_shard_00002", "doc_id": 634 }, "chunk_id": "train_shard_00002_634_0", "global_id": 13571 }, { "text": "Plasmid transfer of netB and antibiotic resistance was also demonstrated to occur within the gastrointestinal tract of chickens, with approximately 14% of the isolates recovered comprising three distinct, in vivo-derived, transconjugant types. The demonstration of in vivo plasmid transfer indicates the potential importance of strain plasticity and the contribution of plasmids to strain virulence.\n\nConjugation-Mediated Horizontal Gene Transfer of Clostridium perfringens Plasmids in the Chicken Gastrointestinal Tract Results in the Formation of New Virulent Strains.", "token_count": 157, "char_count": 591, "word_count": 75, "semantic_coherence": 1, "information_density": 0.68, "quality_score": 0.84, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:02.591020", "source": { "split": "train_shard_00002", "doc_id": 634 }, "chunk_id": "train_shard_00002_634_1", "global_id": 13572 }, { "text": "Links between gut microbiota and autism spectrum disorder (ASD) have been explored in many studies using 16S rRNA gene amplicon and shotgun sequencing. Based on these links, microbiome therapies have been proposed to improve gastrointestinal (GI) and ASD symptoms in ASD individuals. Previously, our open-label microbiota transfer therapy (MTT) study provided insight into the changes in the gut microbial community of children with ASD after MTT and showed significant and long-term improvement in ASD and GI symptoms. Using samples from the same study, the objective of this work was to perform a deeper taxonomic and functional analysis applying shotgun metagenomic sequencing. Taxonomic analyses revealed that ASD Baseline had many bacteria at lower relative abundances, and their abundance increased after MTT. The relative abundance of fiber consuming and beneficial microbes including Prevotella (P. dentalis, P. enoeca, P. oris, P. meloninogenica), Bifidobacterium bifidum, and a sulfur reducer Desulfovibrio piger increased after MTT-10wks in children with ASD compared to Baseline (consistent at genus level with the previous 16S rRNA gene study). Metabolic pathway analysis at Baseline compared to typically developing (TD) children found an altered abundance of many functional genes but, after MTT, they became similar to TD or donors. Important functional genes that changed included: genes encoding enzymes involved in folate biosynthesis, sulfur metabolism and oxidative stress. These results show that MTT treatment not only changed the relative abundance of important genes involved in metabolic pathways, but also seemed to bring them to a similar level to the TD controls. However, at a two-year follow-up, the microbiota and microbial genes shifted into a new state, distinct from their levels at Baseline and distinct from the TD group. Our current findings suggest that microbes from MTT lead to initial improvement in the metabolic profile of children with ASD, and major additional changes at two years post-treatment", "token_count": 515, "char_count": 2091, "word_count": 303, "semantic_coherence": 1, "information_density": 0.5842, "quality_score": 0.7921, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:07:03.221957", "source": { "split": "train_shard_00002", "doc_id": 635 }, "chunk_id": "train_shard_00002_635_0", "global_id": 13573 }, { "text": "In the future, larger cohort studies, mechanistic in vitro experiments and metatranscriptomics studies are recommended to better understand the role of these specific microbes, functional gene expression, and metabolites relevant to ASD.\n\nShotgun Metagenomics Study Suggests Alteration in Sulfur Metabolism and Oxidative Stress in Children with Autism and Improvement after Microbiota Transfer Therapy.", "token_count": 95, "char_count": 402, "word_count": 53, "semantic_coherence": 1, "information_density": 0.8491, "quality_score": 0.9245, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:03.603178", "source": { "split": "train_shard_00002", "doc_id": 635 }, "chunk_id": "train_shard_00002_635_1", "global_id": 13574 }, { "text": "A single extra-intestinal pathogenic Escherichia coli (ExPEC) clone, named sequence type (ST) 131, is responsible for millions of global antimicrobial-resistant (AMR) infections annually. Population genetics indicate that ST131 consists of different clades (i.e. A, B, and C); however, clade C is the most dominant globally. A ST131 subclade, named C1-M27, is emerging in Japan and has been responsible for the recent increase in AMR ExPEC in that country. The sequential acquisition of several virulence and AMR genes associated with mobile genetic elements during the 1960s to 1980s primed clade C (and its subclades C1 and C2) for success in the 1990s to 2000s. IncF plasmids with F1:A2:B20 and F2:A1:B replicons have shaped the evolution of the C1 and C2 subclades. It is possible that ST131 is a host generalist with different accessory gene profiles. Compensatory mutations within the core genome of this clone have counterbalanced the fitness cost associated with IncF plasmids. ST131 clade C had dramatically changed the population structure of ExPEC, but it still remains unclear which features of this clade resulted in one of the most unprecedented AMR successes of the 2000s.\n\nEscherichia coli ST131: a multidrug-resistant clone primed for global domination.", "token_count": 385, "char_count": 1284, "word_count": 195, "semantic_coherence": 1, "information_density": 0.6359, "quality_score": 0.8179, "entities": { "genes": [ "ST131" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:04.225953", "source": { "split": "train_shard_00002", "doc_id": 636 }, "chunk_id": "train_shard_00002_636_0", "global_id": 13575 }, { "text": "The origins of crop diseases are linked to domestication of plants. Most crops were domesticated centuries--even millennia--ago, thus limiting opportunity to understand the concomitant emergence of disease. Kiwifruit (Actinidia spp.) is an exception: domestication began in the 1930s with outbreaks of canker disease caused by P. syringae pv. actinidiae (Psa) first recorded in the 1980s. Based on SNP analyses of two circularized and 34 draft genomes, we show that Psa is comprised of distinct clades exhibiting negligible within-clade diversity, consistent with disease arising by independent samplings from a source population. Three clades correspond to their geographical source of isolation; a fourth, encompassing the Psa-V lineage responsible for the 2008 outbreak, is now globally distributed. Psa has an overall clonal population structure, however, genomes carry a marked signature of within-pathovar recombination. SNP analysis of Psa-V reveals hundreds of polymorphisms; however, most reside within PPHGI-1-like conjugative elements whose evolution is unlinked to the core genome. Removal of SNPs due to recombination yields an uninformative (star-like) phylogeny consistent with diversification of Psa-V from a single clone within the last ten years. Growth assays provide evidence of cultivar specificity, with rapid systemic movement of Psa-V in Actinidia chinensis. Genomic comparisons show a dynamic genome with evidence of positive selection on type III effectors and other candidate virulence genes. Each clade has highly varied complements of accessory genes encoding effectors and toxins with evidence of gain and loss via multiple genetic routes. Genes with orthologs in vascular pathogens were found exclusively within Psa-V. Our analyses capture a pathogen in the early stages of emergence from a predicted source population associated with wild Actinidia species. In addition to candidate genes as targets for resistance breeding programs, our findings highlight the importance of the source population as a reservoir of new disease.", "token_count": 487, "char_count": 2059, "word_count": 295, "semantic_coherence": 1, "information_density": 0.6644, "quality_score": 0.8322, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:04.908668", "source": { "split": "train_shard_00002", "doc_id": 637 }, "chunk_id": "train_shard_00002_637_0", "global_id": 13576 }, { "text": "Genomic analysis of the Kiwifruit pathogen Pseudomonas syringae pv. actinidiae provides insight into the origins of an emergent plant disease.", "token_count": 39, "char_count": 142, "word_count": 20, "semantic_coherence": 1, "information_density": 0.9, "quality_score": 0.95, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:05.296169", "source": { "split": "train_shard_00002", "doc_id": 637 }, "chunk_id": "train_shard_00002_637_1", "global_id": 13577 }, { "text": "Three hundred yeasts isolated from tropical fruits were screened in relation to secretion of pectinases. Twenty-one isolates were able to produce polygalacturonase and among them seven isolates could secrete pectin lyase. None of the isolates was able to secrete pectin methylesterase. The pectinolytic yeasts identified belonged to six different genera. Kluyveromyces wickerhamii isolated from the fruit mangaba (Hancornia speciosa) secreted the highest amount of polygalacturonase, followed by K. marxianus and Stephanoascus smithiae. The yeast Debaryomyces hansenii produced the greatest decrease in viscosity while only 3% of the glycosidic linkages were hydrolysed, indicating that the enzyme secreted was an endo-polygalacturonase. The hydrolysis of pectin by polygalacturonase secreted by S. smithiae suggested an exo-splitting mechanism. The other yeast species studied showed low polygalacturonase activity.\n\nPectinolytic enzymes secreted by yeasts from tropical fruits.", "token_count": 269, "char_count": 979, "word_count": 130, "semantic_coherence": 1, "information_density": 0.6615, "quality_score": 0.8308, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:05.889106", "source": { "split": "train_shard_00002", "doc_id": 638 }, "chunk_id": "train_shard_00002_638_0", "global_id": 13578 }, { "text": "

Objectives

In group B Streptococcus (GBS), cross-resistance to lincosamides, streptogramin A and pleuromutilins (LSAP) is mediated by the acquisition of lsa genes. Here, we characterized the diversity, mobility and ecology of lsa genes in this species.

Methods

lsa variants were systematically identified by BLAST searches in the genomes of 531 GBS strains from different hosts and geographical origins. The associated phenotypes were determined by a microdilution MIC method. Acquisition of resistance genes was deduced from comparative genomics and phylogeny. Their mobility was tested by conjugation experiments.

Results

lsa(E) and three variants of lsa(C) were identified in GBS strains. Two lsa(C) variants had not been previously reported. All four variants conferred LSAP phenotypes. lsa(E) was located in a multiresistance gene cluster of a single human strain. This gene was transferred by a high-frequency recombination-type mechanism between GBS strains. Two lsa(C) variants are carried in six unrelated human strains by two similar elements specifically integrated in the oriT site of four different classes of integrative and conjugative elements (ICEs). Strikingly, the acquisition of the resistance gene always occurred by the integration of the element into a resident ICE. The third lsa(C) variant was located at the same site in the core genome of 11 genetically distant bovine strains and was likely propagated by horizontal transfer of the corresponding chromosomal region.

Conclusions

lsa genes in GBS show distinct host specificities and modes of transfer. In general, their dissemination is mediated by recombination rather than by the transfer of conjugative elements.\n\nHost specificity in the diversity and transfer of lsa resistance genes in group B Streptococcus.", "token_count": 459, "char_count": 1819, "word_count": 255, "semantic_coherence": 1, "information_density": 0.5608, "quality_score": 0.7804, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:06.558011", "source": { "split": "train_shard_00002", "doc_id": 639 }, "chunk_id": "train_shard_00002_639_0", "global_id": 13579 }, { "text": "Abstract

Shigella sonnei causes shigellosis, a severe gastrointestinal illness that is sexually transmissible among men who have sex with men (MSM). Multidrug resistance in S. sonnei is common and can include resistance to the World Health Organisation recommended treatment options, azithromycin, and ciprofloxacin. Recently, an MSM-associated outbreak of extended-spectrum β-lactamase producing, extensively drug resistant S. sonnei was reported in the United Kingdom. Here, we aimed to identify the genetic basis, natural history, and international dissemination of the outbreak strain. Our genomic epidemiological analyses of 3,304 isolates from the United Kingdom, Australia, Belgium, France, and the United States of America revealed an internationally connected outbreak with a common, low fitness-cost resistance plasmid, previously observed in travel associated sublineages of S. flexneri. Our results highlight the persistent threat of horizontally transmitted antimicrobial resistance and the value of continuing to work towards early and open international sharing of genomic surveillance data.

\n\nThe evolution and international spread of extensively drug resistant Shigella sonnei", "token_count": 309, "char_count": 1283, "word_count": 159, "semantic_coherence": 1, "information_density": 0.6918, "quality_score": 0.8459, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:07.133413", "source": { "split": "train_shard_00002", "doc_id": 640 }, "chunk_id": "train_shard_00002_640_0", "global_id": 13580 }, { "text": "In this paper we describe the transmission of a multi-drug resistant Klebsiella pneumoniae ST101 clone from hospital to wastewater and its persistence after chlorine treatment. Water samples from influents and effluents of the sewage tank of an infectious diseases hospital and clinical strains collected from the intra-hospital infections, during a period of 10 days prior to wastewater sampling were analyzed. Antibiotic resistant K. pneumoniae strains from wastewaters were recovered on selective media. Based on antibiotic susceptibility profiles and PCR analyses of antibiotic resistance (AR) genetic background, as well as whole-genome sequencing (Illumina MiSeq) and subsequent bioinformatic analyses, 11 ST101 K. pneumoniae strains isolated from hospital wastewater influent, wastewater effluent and clinical sector were identified as clonally related. The SNP and core genome analyses pointed out that five strains were found to be closely related (with ≤18 SNPs and identical cgMLST profile)", "token_count": 264, "char_count": 1022, "word_count": 141, "semantic_coherence": 1, "information_density": 0.6879, "quality_score": 0.844, "entities": { "genes": [ "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:07.686768", "source": { "split": "train_shard_00002", "doc_id": 641 }, "chunk_id": "train_shard_00002_641_0", "global_id": 13581 }, { "text": "The strains belonging to this clone harbored multiple acquired AR genes [bla CTX-M- 15, bla OXA- 48, bla OXA- 1, bla SHV- 106, bla TEM- 150, aac(3)-IIa, aac(6')-Ib-cr, oqxA10, oqxB17, fosA, catB3, dfrA14, tet(D)] and chromosomal mutations involved in AR (ΔmgrB, ΔompK35, amino acid substitutions in GyrA Ser83Tyr, Asp87Asn, ParC Ser80Tyr). Twenty-nine virulence genes involved in iron acquisition, biofilm and pili formation, adherence, and the type six secretion system - T6SS-III were identified. Our study proves the transmission of MDR K. pneumoniae from hospital to the hospital effluent and its persistence after the chlorine treatment, raising the risk of surface water contamination and further dissemination to different components of the trophic chain, including humans.\n\nMultidrug Resistant Klebsiella pneumoniae ST101 Clone Survival Chain From Inpatients to Hospital Effluent After Chlorine Treatment.", "token_count": 457, "char_count": 1142, "word_count": 130, "semantic_coherence": 1, "information_density": 0.7538, "quality_score": 0.8769, "entities": { "genes": [ "ST101" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:08.323341", "source": { "split": "train_shard_00002", "doc_id": 641 }, "chunk_id": "train_shard_00002_641_1", "global_id": 13582 }, { "text": "

Background

Meticillin-resistant Staphylococcus aureus (MRSA) bacteraemia cases have declined since 2003, and have mostly been due to two epidemic (E) strains, E15 (multi-locus sequence type clonal complex CC22) and E16 (CC30). By contrast, the incidence of meticillin-susceptible S. aureus (MSSA) bacteraemia has remained largely unchanged and our understanding of these isolates has remained poor.

Aim

To investigate the distribution and nucleotide sequence of heterogeneous regions between successful lineages using the 2009 British Society for Antimicrobial Chemotherapy (BSAC) Bacteraemia Resistance Surveillance Programme collection of S. aureus.

Methods

S. aureus isolates (N = 202) comprised of 103 MRSA and 99 MSSA isolates were analysed using fluorescent amplified fragment length polymorphism (FAFLP) to detect nucleotide variations due to lineage-specific sequence motifs as well as differences in the distribution of mobile genetic elements between lineages.

Findings

E15 and E16 MRSA strains comprised 79% and 6% of the collection in 2009 respectively. Six lineages, including CC22 and CC30, were associated with MRSA bacteraemia in the UK and Ireland. MSSA isolates were more diverse with 19 different lineages detected. FAFLP revealed lineage-specific sequence variations in loci encoding factors such as proteases or factors involved in haem biosynthesis, both of which may affect the success of major S. aureus lineages. Proteins encoded on certain mobile genetic elements or involved in cobalamin biosynthesis were found to be exclusive to CC8, CC22, or CC30.

Conclusion

Overall, the genetic diversity among regions of the core genome and mobile genetic elements may alter antimicrobial resistance and the production of virulence or fitness factors that may be linked to strain success.", "token_count": 515, "char_count": 1840, "word_count": 250, "semantic_coherence": 1, "information_density": 0.616, "quality_score": 0.808, "entities": { "genes": [ "CC8", "CC30", "CC22" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:07:08.981233", "source": { "split": "train_shard_00002", "doc_id": 642 }, "chunk_id": "train_shard_00002_642_0", "global_id": 13583 }, { "text": "Identification of genetic variation exclusive to specific lineages associated with Staphylococcus aureus bacteraemia.", "token_count": 27, "char_count": 117, "word_count": 13, "semantic_coherence": 1, "information_density": 1.0, "quality_score": 1.0, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:09.335107", "source": { "split": "train_shard_00002", "doc_id": 642 }, "chunk_id": "train_shard_00002_642_1", "global_id": 13584 }, { "text": "Lactobacilli occupy a unique position in human culture and scientific history. Like brewer's and baker's yeast, lactobacilli have been associated with food production and preservation for thousands of years. Lactobacillus species are used in mixed microbial cultures, such as the classical Lactobacillus bulgaricus/Streptococcus thermophilus inoculum for yogurt fermentation, or combinations of diverse lactobacilli/yeasts in kefir grains. The association of lactobacilli consumption with greater longevity and improved health formed the basis for developing lactobacilli as probiotics, whose market has exploded worldwide in the past 10 years. The decade that followed the determination of the first genome sequence of a food-associated species, Lactobacillus plantarum, saw the application to lactobacilli of a full range of functional genomics methods to identify the genes and gene products that govern their distinctive phenotypes and health associations. In this review, we will briefly remind the reader of the range of beneficial effects attributed to lactobacilli, and then explain the phylogenomic basis for the distribution of these traits across the genus. Recognizing the strain specificity of probiotic effects, we review studies of intraspecific genomic variation and their contributions to identifying probiotic traits. Finally we offer a perspective on classification of lactobacilli into new genera in a scheme that will make attributing probiotic properties to clades, taxa, and species more logical and more robust.\n\nThe Genomic Basis of Lactobacilli as Health-Promoting Organisms.", "token_count": 406, "char_count": 1629, "word_count": 223, "semantic_coherence": 1, "information_density": 0.6457, "quality_score": 0.8229, "entities": { "genes": [], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:09.954611", "source": { "split": "train_shard_00002", "doc_id": 643 }, "chunk_id": "train_shard_00002_643_0", "global_id": 13585 }, { "text": "

Background

The Gram negative anaerobic bacterium Porphyromonas gingivalis has long been recognized as a causative agent of periodontitis. Periodontitis is a chronic infectious disease of the tooth supporting tissues eventually leading to tooth-loss. Capsular polysaccharide (CPS) of P. gingivalis has been shown to be an important virulence determinant. Seven capsular serotypes have been described. Here, we used micro-array based comparative genomic hybridization analysis (CGH) to analyze a representative of each of the capsular serotypes and a non-encapsulated strain against the highly virulent and sequenced W83 strain. We defined absent calls using Arabidopsis thaliana negative control probes, with the aim to distinguish between aberrations due to mutations and gene gain/loss.

Results

Our analyses allowed us to call aberrant genes, absent genes and divergent regions in each of the test strains. A conserved core P. gingivalis genome was described, which consists of 80% of the analyzed genes from the sequenced W83 strain. The percentage of aberrant genes between the test strains and control strain W83 was 8.2% to 13.7%. Among the aberrant genes many CPS biosynthesis genes were found. Most other virulence related genes could be found in the conserved core genome. Comparing highly virulent strains with less virulent strains indicates that hmuS, a putative CobN/Mg chelatase involved in heme uptake, may be a more relevant virulence determinant than previously expected. Furthermore, the description of the 39 W83-specific genes could give more insight in why this strain is more virulent than others.

Conclusion

Analyses of the genetic content of the P. gingivalis capsular serotypes allowed the description of a P. gingivalis core genome. The high resolution data from three types of analysis of triplicate hybridization experiments may explain the higher divergence between P. gingivalis strains than previously recognized.\n\nThe core genome of the anaerobic oral pathogenic bacterium Porphyromonas gingivalis.", "token_count": 514, "char_count": 2051, "word_count": 292, "semantic_coherence": 1, "information_density": 0.5616, "quality_score": 0.7808, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:07:10.601735", "source": { "split": "train_shard_00002", "doc_id": 644 }, "chunk_id": "train_shard_00002_644_0", "global_id": 13586 }, { "text": "

Background

Ancient microbiota information represents an important resource to evaluate bacterial evolution and to explore the biological spread of infectious diseases in history. The soft tissue of frozen mummified humans, such as the Tyrolean Iceman, has been shown to contain bacterial DNA that is suitable for population profiling of the prehistoric bacteria that colonized such ancient human hosts.

Results

Here, we performed a microbial cataloging of the distal gut microbiota of the Tyrolean Iceman, which highlights a predominant abundance of Clostridium and Pseudomonas species. Furthermore, in silico analyses allowed the reconstruction of the genome sequences of five ancient bacterial genomes, including apparent pathogenic ancestor strains of Clostridium perfringens and Pseudomonas veronii species present in the gut of the Tyrolean Iceman.

Conclusions

Genomic analyses of the reconstructed C. perfringens chromosome clearly support the occurrence of a pathogenic profile consisting of virulence genes already existing in the ancient strain, thereby reinforcing the notion of a very early speciation of this taxon towards a pathogenic phenotype. In contrast, the evolutionary development of P. veronii appears to be characterized by the acquisition of antibiotic resistance genes in more recent times as well as an evolution towards an ecological niche outside of the (human) gastrointestinal tract.\n\nAncient bacteria of the Ötzi's microbiome: a genomic tale from the Copper Age.", "token_count": 357, "char_count": 1514, "word_count": 209, "semantic_coherence": 1, "information_density": 0.6268, "quality_score": 0.8134, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:11.176869", "source": { "split": "train_shard_00002", "doc_id": 645 }, "chunk_id": "train_shard_00002_645_0", "global_id": 13587 }, { "text": "Abstract

Antimicrobial resistance (AMR) poses a serious threat to the clinical management of typhoid fever. AMR in Salmonella Typhi (S. Typhi) is commonly associated with the H58 lineage, a lineage that arose comparatively recently before becoming globally disseminated. To better understand when and how H58 emerged and became dominant, we performed detailed phylogenetic analyses on contemporary genome sequences from S. Typhi isolated in the period spanning the emergence. Our dataset, which contains the earliest described H58 S. Typhi organism, indicates that ancestral H58 organisms were already multi-drug resistant (MDR). These organisms emerged spontaneously in India in 1987 and became radially distributed throughout South Asia and then globally in the ensuing years. These early organisms were associated with a single long branch, possessing mutations associated with increased bile tolerance, suggesting that the first H58 organism was generated during chronic carriage. The subsequent use of fluoroquinolones led to several independent mutations in gyrA. The ability of H58 to acquire and maintain AMR genes continues to pose a threat, as extensively drug-resistant (XDR; MDR plus resistance to ciprofloxacin and third generation cephalosporins) variants, have emerged recently in this lineage. Understanding where and how H58 S. Typhi originated and became successful is key to understand how AMR drives successful lineages of bacterial pathogens. Additionally, these data can inform optimal targeting of typhoid conjugate vaccines (TCVs) for reducing the potential for emergence and the impact of new drug-resistant variants. Emphasis should also be placed upon the prospective identification and treatment of chronic carriers to prevent the emergence of new drug resistant variants with the ability to spread efficiently.

\n\nThe origins of haplotype 58 (H58) Salmonella enterica serovar Typhi", "token_count": 503, "char_count": 2033, "word_count": 273, "semantic_coherence": 1, "information_density": 0.652, "quality_score": 0.826, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "bile", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:11.826254", "source": { "split": "train_shard_00002", "doc_id": 646 }, "chunk_id": "train_shard_00002_646_0", "global_id": 13588 }, { "text": "

Objective

Clostridium perfringens causes gastrointestinal diseases in both humans and domestic animals. Type A strains expressing the NetB toxin are the main cause of necrotic enteritis (NE) in chickens, which has remarkable impact on animal welfare and production economy in the international poultry industry. Three pathogenicity loci NELoc-1, -2 and -3 and a collagen adhesion gene cnaA have been found to be associated with NE in chickens, whereas the presence of these has not been investigated in diseased turkeys. The purpose was to investigate the virulence associated genome content and the genetic relationship among 30 C. perfringens isolates from both healthy and NE infected chickens and turkeys, applying whole-genome sequencing.

Results

NELoc-1, -3, netB and cnaA were significantly associated with NE isolates from chickens, whereas only NELoc-2 was commonly observed in both diseased turkeys and chickens. A putative collagen adhesion gene that encodes a von Willebrand Factor (vWF) domain was identified in all diseased turkeys and designated as cnaD. The phylogenetic analysis based on single nucleotide polymorphisms showed that the isolates generally were not closely related. These results indicate that virulence factors and pathogenicity loci associated with NE in chickens are not important to the same extent in diseased turkeys except for NELoc-2. A putative collagen adhesion gene which potentially could be of importance in regard to the NE pathogenesis in turkeys was identified and need to be further investigated. Thus, the pathogenesis of NE in turkeys appears to be different from that of broiler chickens.\n\nGenome analysis of Clostridium perfringens isolates from healthy and necrotic enteritis infected chickens and turkeys.", "token_count": 428, "char_count": 1775, "word_count": 258, "semantic_coherence": 1, "information_density": 0.531, "quality_score": 0.7655, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:12.449396", "source": { "split": "train_shard_00002", "doc_id": 647 }, "chunk_id": "train_shard_00002_647_0", "global_id": 13589 }, { "text": "The Gram-positive species Enterococcus faecium has long been thought of as a harmless commensal of the mammalian GI tract. In the last two decades, however, E. faecium has become an important cause of nosocomial bacteremias. These infections are often difficult to treat owing to the resistance of E. faecium to a large number of antibiotics. In this article, we review the recent transition of E. faecium from commensal to nosocomial pathogen. We focus on population biology-based studies, which suggest that several clonal populations of E. faecium are mostly responsible for causing infections. We also discuss the role of the accessory genome of E. faecium in contributing to the infectious phenotype and examine the role that surface proteins of E. faecium may have in colonization and infection.\n\nTransition of Enterococcus faecium from commensal organism to nosocomial pathogen.", "token_count": 216, "char_count": 885, "word_count": 136, "semantic_coherence": 1, "information_density": 0.6029, "quality_score": 0.8015, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:12.914120", "source": { "split": "train_shard_00002", "doc_id": 648 }, "chunk_id": "train_shard_00002_648_0", "global_id": 13590 }, { "text": "Classical molecular analyses of Mycobacterium bovis based on spoligotyping and Variable Number Tandem Repeat (MIRU-VNTR) brought the first insights into the epidemiology of animal tuberculosis (TB) in Portugal, showing high genotypic diversity of circulating strains that mostly cluster within the European 2 clonal complex. Previous surveillance provided valuable information on the prevalence and spatial occurrence of TB and highlighted prevalent genotypes in areas where livestock and wild ungulates are sympatric. However, links at the wildlife-livestock interfaces were established mainly via classical genotype associations. Here, we apply whole genome sequencing (WGS) to cattle, red deer and wild boar isolates to reconstruct the M. bovis population structure in a multi-host, multi-region disease system and to explore links at a fine genomic scale between M. bovis from wildlife hosts and cattle. Whole genome sequences of 44 representative M. bovis isolates, obtained between 2003 and 2015 from three TB hotspots, were compared through single nucleotide polymorphism (SNP) variant calling analyses. Consistent with previous results combining classical genotyping with Bayesian population admixture modelling, SNP-based phylogenies support the branching of this M. bovis population into five genetic clades, three with apparent geographic specificities, as well as the establishment of an SNP catalogue specific to each clade, which may be explored in the future as phylogenetic markers. The core genome alignment of SNPs was integrated within a spatiotemporal metadata framework to further structure this M. bovis population by host species and TB hotspots, providing a baseline for network analyses in different epidemiological and disease control contexts. WGS of M. bovis isolates from Portugal is reported for the first time in this pilot study, refining the spatiotemporal context of TB at the wildlife-livestock interface and providing further support to the key role of red deer and wild boar on disease maintenance", "token_count": 523, "char_count": 2083, "word_count": 293, "semantic_coherence": 1, "information_density": 0.6382, "quality_score": 0.8191, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:07:13.568066", "source": { "split": "train_shard_00002", "doc_id": 649 }, "chunk_id": "train_shard_00002_649_0", "global_id": 13591 }, { "text": "The SNP diversity observed within this dataset supports the natural circulation of M. bovis for a long time period, as well as multiple introduction events of the pathogen in this Iberian multi-host system.\n\nWhole Genome Sequencing Refines Knowledge on the Population Structure of Mycobacterium bovis from a Multi-Host Tuberculosis System.", "token_count": 94, "char_count": 353, "word_count": 50, "semantic_coherence": 1, "information_density": 0.78, "quality_score": 0.89, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:13.935363", "source": { "split": "train_shard_00002", "doc_id": 649 }, "chunk_id": "train_shard_00002_649_1", "global_id": 13592 }, { "text": "Recurrent C. difficile infection (rCDI) is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we use longitudinal stool samples collected from patients undergoing FMT to evaluate intra-individual changes in the microbiome, metabolome, and lipidome after successful FMTs relative to their baselines pre-FMT. We show changes in the abundance of many lipids, specifically a decrease in acylcarnitines post-FMT, and a shift from conjugated bile acids pre-FMT to deconjugated secondary bile acids post-FMT. These changes correlate with a decrease in Enterobacteriaceae, which encode carnitine metabolism genes, and an increase in Lachnospiraceae, which encode bile acid altering genes such as bile salt hydrolases (BSHs) and the bile acid-inducible (bai) operon, post-FMT. We also show changes in gut microbe-encoded amino acid biosynthesis genes, of which Enterobacteriaceae was the primary contributor to amino acids C. difficile is auxotrophic for. Liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT and generate hypotheses that require further experimental validation. This information is meant to help guide the development of new microbiota-focused therapeutics to treat rCDI.IMPORTANCERecurrent C. difficile infection is an urgent public health threat, for which the last resort and lifesaving treatment is a fecal microbiota transplant. However, the exact mechanisms that mediate a successful FMT are not well-understood. Here, we show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT", "token_count": 513, "char_count": 1961, "word_count": 273, "semantic_coherence": 1, "information_density": 0.5201, "quality_score": 0.7601, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "acid", "bile", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:07:14.565692", "source": { "split": "train_shard_00002", "doc_id": 650 }, "chunk_id": "train_shard_00002_650_0", "global_id": 13593 }, { "text": "These changes correlate with Enterobacteriaceae pre-FMT, which encodes carnitine metabolism genes, and Lachnospiraceae post-FMT, which encodes bile salt hydrolases and baiA genes. There was also a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here, we define the structural and functional changes associated with a successful FMT, which we hope will help aid in the development of new microbiota-focused therapeutics to treat rCDI.\n\nMetagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection.", "token_count": 174, "char_count": 643, "word_count": 84, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "acid", "bile" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:15.026566", "source": { "split": "train_shard_00002", "doc_id": 650 }, "chunk_id": "train_shard_00002_650_1", "global_id": 13594 }, { "text": "Protoplast fusion between Saccharomyces cerevisiae A001 and Kluyveromyces Y034 has been studied. A001 is a high alcohol yield yeast and can ferment maltose into ethanol, but can not grow at 45 degrees C. However, Y034 can grow above 45 degrees C but has a lower alcohol yield and can not ferment maltose. We obtained the fusants which were tested in several aspects such as cell morphology, physiological and biochemical feature, isozyme patterns analysis, alcohol fermentation at high temperature(45 degrees C) and so on. The fusant AY023 with the final ethanol concentration of 7.4% has been selected, which is thermotolerant yeast with the highest alcohol yield at 45 degrees C until now.\n\n[Construction of thermotolerant ethanol-producing yeast by protoplast fusion].", "token_count": 215, "char_count": 771, "word_count": 119, "semantic_coherence": 1, "information_density": 0.6471, "quality_score": 0.8235, "entities": { "genes": [ "AY023" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:15.862381", "source": { "split": "train_shard_00002", "doc_id": 651 }, "chunk_id": "train_shard_00002_651_0", "global_id": 13595 }, { "text": "The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities between children in low- and middle-income countries (LMICs) vs. high-income countries (HICs). Here, we describe and compare the microbiome profile of children aged under 48 months in two urban areas: Maputo, Mozambique and Atlanta, USA using shotgun metagenomics. The gut microbiome of American children showed distinct development, characterized by higher alpha diversity after infancy, compared to the same age group of African children, and the microbiomes clustered separately based on geographic location or age. The abundances of antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly higher in Maputo children, driven primarily by several primary and opportunistic pathogens. Most notably, about 50% of Maputo children under the age of two were positive for enterotoxigenic (ETEC) and typical enteropathogenic (EPEC) Escherichia coli diagnostic genes while none of the Atlanta age-matched children showed such a positive signal. In contrast, commensal species such as Phocaeicola vulgatus and Bacteroides caccae were more abundant in Atlanta, potentially reflecting diets rich in animal protein and susceptibility to inflammatory diseases. Overall, our results suggest that the different environments characterizing the two cities have significant, distinctive signatures on the microbiota of children and its development over time. Lack of safe water, sanitation, and hygiene (WASH) conditions and/or unsafe food sources may explain the higher enteric pathogen load among children in Maputo.\n\nHigher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling.", "token_count": 408, "char_count": 1800, "word_count": 252, "semantic_coherence": 1, "information_density": 0.6865, "quality_score": 0.8433, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:16.481711", "source": { "split": "train_shard_00002", "doc_id": 652 }, "chunk_id": "train_shard_00002_652_0", "global_id": 13596 }, { "text": "The growth of Bradyrhizobium japonicum E-109 using cheese whey as carbon source was studied. The cheese whey was previously hydrolyzed by acid or enzymatic treatment with purified beta galactosidase or a crude extract from Kluyveromyces fragilis. The results obtained demonstrated that the use of the modified enzymatic hydrolyzed whey as carbon source allowed the growth of B. japonicum E-109 reaching a concentration of approximately 10(10) viable cells/ml. These results are considered of industrial value because the poluent power whey is greatly reduced.\n\n[Use of cheese whey for growing the Bradyrhizobium japonicum E-109 strain].", "token_count": 163, "char_count": 636, "word_count": 93, "semantic_coherence": 1, "information_density": 0.6452, "quality_score": 0.8226, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces" ], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:16.955809", "source": { "split": "train_shard_00002", "doc_id": 653 }, "chunk_id": "train_shard_00002_653_0", "global_id": 13597 }, { "text": "The pan-genome of a taxonomic group consists of evolutionarily conserved core genes shared by all members and accessory genes that are present only in some members of the group. Group- and subgroup-specific core genes are thought to contribute to shared phenotypes such as virulence and niche specificity. In this study we analyzed 39 Salmonella enterica genomes (16 closed, 23 draft), a species that contains two human-specific serovars that cause typhoid fever, as well as a large number of zoonotic serovars that cause gastroenteritis in humans. Panseq 2.0 was used to define the pan-genome by adjusting the threshold at which group-specific \"core\" loci are defined. We found the pan-genome to be 9.03 Mbp in size, and that the core genome size decreased, while the number of SNPs/100 bp increased, as the number of strains used to define the core genome increased, suggesting substantial divergence among S. enterica subgroups. Subgroup-specific \"core\" genes, in contrast, had fewer SNPs/100 bp, likely reflecting their more recent acquisition. Phylogenetic trees were created from the concatenated and aligned pan-genome, the core genome, and multi-locus-sequence typing (MLST) loci. Branch support increased among the trees, and strains of the same serovar grouped closer together as the number of loci used to create the tree increased. Further, high levels of discrimination were achieved even amongst the most closely related strains of S. enterica Typhi, suggesting that the data generated by Panseq may also be of value in short-term epidemiological studies. Panseq provides an easy and fast way of performing pan-genomic analyses, which can include the identification of group-dominant as well as group-specific loci and is available as a web-server and a standalone version at http://lfz.corefacility.ca/panseq/.\n\nIdentification of Salmonella enterica species- and subgroup-specific genomic regions using Panseq 2.0.", "token_count": 477, "char_count": 1929, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5958, "quality_score": 0.7979, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:17.618475", "source": { "split": "train_shard_00002", "doc_id": 654 }, "chunk_id": "train_shard_00002_654_0", "global_id": 13598 }, { "text": "

Objectives

Many outer multidomain proteins play fundamental virulent roles in an allele-dependent manner. We aimed to investigate the influence of the outer SP1992 protein, here renamed DiiA (Dimorphic invasion-involved A), in pneumococcal disease.

Methods

The presence and type of diiA allele was screened by PCR in 560 clinical isolates. Isogenic mutants carrying progressive diiA deletions were constructed and checked in mouse models of infection. DiiA binding to human molecules was carried out by surface plasmon resonance.

Results

The diiA gene is exclusive of Streptococcus pneumoniae and included in the core genome. DiiA variants contain one or two imperfect repeats (R1 and R2), an unstructured region and a cell-wall anchor domain. Clonal complexes carrying both repeats were associated with invasive disease, while those carrying R2 preferentially caused non-invasive syndromes in patients with underlying risk factors. Mutants lacking both repeats were less efficient in nasopharyngeal colonization and dissemination from lungs. Moreover, the ΔdiiA defective strain suffered a severe impairment in bacterial proliferation in blood. Purified DiiA bound to collagen and lactoferrin with high affinity.

Conclusions

DiiA is a distinctive pneumococcal virulence factor contributing to colonization and long-term invasion in this pathogen.\n\nDiiA is a novel dimorphic cell wall protein of Streptococcus pneumoniae involved in invasive disease.", "token_count": 389, "char_count": 1479, "word_count": 197, "semantic_coherence": 1, "information_density": 0.7056, "quality_score": 0.8528, "entities": { "genes": [ "SP1992" ], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:18.282651", "source": { "split": "train_shard_00002", "doc_id": 655 }, "chunk_id": "train_shard_00002_655_0", "global_id": 13599 }, { "text": "We have compared genomes of Alteromonas macleodii \"deep ecotype\" isolates from two deep Mediterranean sites and two surface samples from the Aegean and the English Channel. A total of nine different genomes were analyzed. They belong to five clonal frames (CFs) that differ among them by approximately 30,000 single-nucleotide polymorphisms (SNPs) over their core genomes. Two of the CFs contain three strains each with nearly identical genomes (~100 SNPs over the core genome). One of the CFs had representatives that were isolated from samples taken more than 1,000 km away, 2,500 m deeper, and 5 years apart. These data mark the longest proven persistence of a CF in nature (outside of clinical settings). We have found evidence for frequent recombination events between or within CFs and even with the distantly related A. macleodii surface ecotype. The different CFs had different flexible genomic islands. They can be classified into two groups; one type is additive, that is, containing different numbers of gene cassettes, and is very variable in short time periods (they often varied even within a single CF). The other type was more stable and produced the complete replacement of a genomic fragment by another with different genes. Although this type was more conserved within each CF, we found examples of recombination among distantly related CFs including English Channel and Mediterranean isolates.\n\nGenomic diversity of \"deep ecotype\" Alteromonas macleodii isolates: evidence for Pan-Mediterranean clonal frames.", "token_count": 358, "char_count": 1528, "word_count": 235, "semantic_coherence": 1, "information_density": 0.634, "quality_score": 0.817, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:19.689273", "source": { "split": "train_shard_00002", "doc_id": 656 }, "chunk_id": "train_shard_00002_656_0", "global_id": 13600 }, { "text": "Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.\n\nGut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua.", "token_count": 416, "char_count": 1784, "word_count": 244, "semantic_coherence": 1, "information_density": 0.6148, "quality_score": 0.8074, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "gut", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:20.315190", "source": { "split": "train_shard_00002", "doc_id": 657 }, "chunk_id": "train_shard_00002_657_0", "global_id": 13601 }, { "text": "Enterohemorrhagic and enteropathogenic Escherichia coli are gastrointestinal pathogens that disrupt the intestinal microvilli to form attaching and effacing (A/E) lesions on infected cells and cause diarrhea. This pathomorphological trait is encoded within the pathogenicity island locus of enterocyte effacement (LEE). The LEE houses a type 3 secretion system (T3SS), which upon assembly bridges the bacterial cytosol to that of the host and enables the bacterium to traffic dozens of effectors into the host where they hijack regulatory and signal transduction pathways and contribute to bacterial colonization and disease. Owing to the importance of the LEE to EHEC and EPEC pathogenesis, much of the research on these pathogens has centered on its regulation. To date, over 40 proteinaceous factors have been identified that control the LEE at various hierarchical levels of gene expression. In contrast, RNA-based regulatory mechanisms that converge on the LEE have only just begun to be unraveled. In this minireview, we highlight major breakthroughs in small RNAs (sRNAs)-dependent regulation of the LEE, with an emphasis on their mechanisms of action and/or LEE-encoded targets.\n\nThe Tip of the Iceberg: On the Roles of Regulatory Small RNAs in the Virulence of Enterohemorrhagic and Enteropathogenic Escherichia coli.", "token_count": 353, "char_count": 1340, "word_count": 196, "semantic_coherence": 1, "information_density": 0.6531, "quality_score": 0.8265, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:20.894786", "source": { "split": "train_shard_00002", "doc_id": 658 }, "chunk_id": "train_shard_00002_658_0", "global_id": 13602 }, { "text": "About 2,500 papers dated 2014-2016 were recovered by searching the PubMed database for Streptomyces, which are the richest known source of antibiotics. This review integrates around 100 of these papers in sections dealing with evolution, ecology, pathogenicity, growth and development, stress responses and secondary metabolism, gene expression, and technical advances. Genomic approaches have greatly accelerated progress. For example, it has been definitively shown that interspecies recombination of conserved genes has occurred during evolution, in addition to exchanges of some of the tens of thousands of non-conserved accessory genes. The closeness of the association of Streptomyces with plants, fungi, and insects has become clear and is reflected in the importance of regulators of cellulose and chitin utilisation in overall Streptomyces biology. Interestingly, endogenous cellulose-like glycans are also proving important in hyphal growth and in the clumping that affects industrial fermentations. Nucleotide secondary messengers, including cyclic di-GMP, have been shown to provide key input into developmental processes such as germination and reproductive growth, while late morphological changes during sporulation involve control by phosphorylation. The discovery that nitric oxide is produced endogenously puts a new face on speculative models in which regulatory Wbl proteins (peculiar to actinobacteria) respond to nitric oxide produced in stressful physiological transitions. Some dramatic insights have come from a new model system for Streptomyces developmental biology, Streptomyces venezuelae, including molecular evidence of very close interplay in each of two pairs of regulatory proteins. An extra dimension has been added to the many complexities of the regulation of secondary metabolism by findings of regulatory crosstalk within and between pathways, and even between species, mediated by end products", "token_count": 466, "char_count": 1968, "word_count": 267, "semantic_coherence": 1, "information_density": 0.6854, "quality_score": 0.8427, "entities": { "genes": [], "proteins": [], "pathways": [ "metabolism", "fermentation" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:21.540851", "source": { "split": "train_shard_00002", "doc_id": 659 }, "chunk_id": "train_shard_00002_659_0", "global_id": 13603 }, { "text": "Among many outcomes from the application of chromosome immunoprecipitation sequencing (ChIP-seq) analysis and other methods based on \"next-generation sequencing\" has been the finding that 21% of Streptomyces mRNA species lack leader sequences and conventional ribosome binding sites. Further technical advances now emerging should lead to continued acceleration of knowledge, and more effective exploitation, of these astonishing and critically important organisms.\n\nRecent advances in understanding Streptomyces.", "token_count": 123, "char_count": 527, "word_count": 65, "semantic_coherence": 1, "information_density": 0.8769, "quality_score": 0.9385, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:21.919650", "source": { "split": "train_shard_00002", "doc_id": 659 }, "chunk_id": "train_shard_00002_659_1", "global_id": 13604 }, { "text": "N-Acyl lipids are important mediators of several biological processes including immune function and stress response. To enhance the detection of N-acyl lipids with untargeted mass spectrometry-based metabolomics, we created a reference spectral library retrieving N-acyl lipid patterns from 2,700 public datasets, identifying 851 N-acyl lipids that were detected 356,542 times. 777 are not documented in lipid structural databases, with 18% of these derived from short-chain fatty acids and found in the digestive tract and other organs. Their levels varied with diet and microbial colonization and in people living with diabetes. We used the library to link microbial N-acyl lipids, including histamine and polyamine conjugates, to HIV status and cognitive impairment. This resource will enhance the annotation of these compounds in future studies to further the understanding of their roles in health and disease and to highlight the value of large-scale untargeted metabolomics data for metabolite discovery.\n\nThe microbiome diversifies long- to short-chain fatty acid-derived N-acyl lipids.", "token_count": 267, "char_count": 1094, "word_count": 156, "semantic_coherence": 1, "information_density": 0.6731, "quality_score": 0.8365, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "acid" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:22.473857", "source": { "split": "train_shard_00002", "doc_id": 660 }, "chunk_id": "train_shard_00002_660_0", "global_id": 13605 }, { "text": "

Background

Immunoglobulin (Ig)A proteases of Haemophilus influenzae are highly specific endopeptidases that cleave the hinge region of human IgA1 and also mediate invasion and trafficking in human respiratory epithelial cells, facilitating persistence of H. influenzae. Little is known about the expression of IgA proteases in clinical settings of H. influenzae infection.

Methods

We identified and characterized IgA protease genes in H. influenzae and studied their expression and proteolytic specificity, in vitro and in vivo in 169 independent strains of H. influenzae collected longitudinally over 10 years from adults with chronic obstructive pulmonary disease.

Results

The H. influenzae pangenome has 2 alleles of IgA protease genes; all strains have igaA, and 40% of strains have igaB. Each allele has 2 variants with differing proteolytic specificities for human IgA1. A total of 88% of 169 strains express IgA protease activity. Expression of the 4 forms of IgA protease varies among strains. Based on the presence of IgA1 fragments in sputum samples, each of the different forms of IgA protease is selectively expressed in the human airways during infection.

Conclusions

Four variants of IgA proteases are variably expressed by H. influenzae during infection of the human airways.\n\nExpression of IgA Proteases by Haemophilus influenzae in the Respiratory Tract of Adults With Chronic Obstructive Pulmonary Disease.", "token_count": 415, "char_count": 1453, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5317, "quality_score": 0.7659, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:23.095480", "source": { "split": "train_shard_00002", "doc_id": 661 }, "chunk_id": "train_shard_00002_661_0", "global_id": 13606 }, { "text": "Defining bacterial species and understanding the relative cohesiveness of different components of their genomes remains a fundamental problem in microbiology. Bacterial species tend to be comprised of both a set of core and dispensable genes, with the sum of these two components forming the species pan-genome. The role of the core and dispensable genes in defining bacterial species and the question of whether pan-genomes are finite or infinite remain unclear. Here we demonstrate, through the analysis of 96 genome sequences derived from two closely related sympatric sister species of pathogenic bacteria (Campylobacter coli and C. jejuni), that their pan-genome is indeed finite and that there are unique and cohesive features to each of their genomes defining their genomic identity. The two species have a similar pan-genome size; however, C. coli has acquired a larger core genome and each species has evolved a number of species-specific core genes, possibly reflecting different adaptive strategies. Genome-wide assessment of the level of lateral gene transfer within and between the two sister species, as well as within the core and non-core genes, demonstrates a resistance to interspecies recombination in the core genome of the two species and therefore provides persuasive support for the core genome hypothesis for bacterial species.\n\nEvolutionary dynamics of complete Campylobacter pan-genomes and the bacterial species concept.", "token_count": 310, "char_count": 1447, "word_count": 215, "semantic_coherence": 1, "information_density": 0.5488, "quality_score": 0.7744, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:23.667799", "source": { "split": "train_shard_00002", "doc_id": 662 }, "chunk_id": "train_shard_00002_662_0", "global_id": 13607 }, { "text": "Soft rot of onion disks inoculated with the yeast Kluyveromyces marxianus var. marxianus increased significantly (P = 0.01) as temperature increased from 10 to 30 C. Rot was not evident in onion disks inoculated with the yeast and incubated for 12 days at 2 C. A temperature of 2 C or less during transit and storage of bulbs will reduce damage caused by the yeast. The amount of soft rot caused by seven isolates of K. m. var. marxianus from the Walla Walla Valley of southeastern Washington and northeastern Oregon did not vary significantly (P = 0.05) when tested on onion disks. A strain of the bacterium Erwinia carotovora subsp. carotovora from onion produced significantly (P = 0.01) more soft rot in onion than K. m. var. marxianus at 25 and 15 C, whereas K. m. var. marxianus produced significantly more soft rot in onion than a strain of E. c. subsp. carotovora from potato. Resistance to K. m. var. marxianus was not evident in 25 onion cultivars grown in the Pacific Northwest.\n\nYeast soft rot of onion in the Walla Walla Valley of Washington and Oregon.", "token_count": 317, "char_count": 1066, "word_count": 187, "semantic_coherence": 1, "information_density": 0.4652, "quality_score": 0.7326, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:24.222981", "source": { "split": "train_shard_00002", "doc_id": 663 }, "chunk_id": "train_shard_00002_663_0", "global_id": 13608 }, { "text": "Cellobiose, the last product in cellulose degradation, is converted into two molecules of glucose by a beta-glucosidase. S. cerevisiae does posses the structural gene for a beta-glucosidase, but it is very poorly expressed; we thus decided to isolate and characterize that of Kluyveromyces fragilis. We constructed in E. coli HB101 strain a genomic library of the Kluyveromyces fragilis Y610 strain (ATCC 12424), a yeast able to grow on cellobiose and which constitutively produces the beta-glucosidase. The structural gene for beta-glucosidase was identified by its expression in E. coli. The initial isolated cosmid KF1 contained an insert of 35 Kb and by successive subcloning the insert size was reduced to 3.5 Kb (KF4). This cloned beta-glucosidase gene introduced in S. cerevisiae by transformation is expressed at a level of about 500 times that of K. fragilis. We checked by Southern hybridization that the high expression level was not due to a rearrangement of K. fragilis DNA during the cloning experiments. Nevertheless to obtain yeast transformants able to grow on cellobiose a yeast strain whose permeability to sugar is increased must be used and this last point is discussed.\n\nCloning and expression of the structural gene for beta-glucosidase of Kluyveromyces fragilis in Escherichia coli and Saccharomyces cerevisiae.", "token_count": 364, "char_count": 1335, "word_count": 205, "semantic_coherence": 1, "information_density": 0.5707, "quality_score": 0.7854, "entities": { "genes": [ "KF1", "KF4", "HB101" ], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:24.804701", "source": { "split": "train_shard_00002", "doc_id": 664 }, "chunk_id": "train_shard_00002_664_0", "global_id": 13609 }, { "text": "Mycobacterium avium subsp. paratuberculosis (MAP) is the causative agent of Johne's disease, a chronic debilitating disease in ruminants. To control this disease, it is crucial to understand immune evasion and the mechanism of persistence by analyzing the early phase interplays of the intracellular pathogens and their hosts. In the present study, host-pathogen interactions at the transcriptomic level were investigated in an in vitro macrophage infection model. When differentiated human THP-1 cells were infected with MAP, the expression of various genes associated with stress responses and metabolism was altered in both host and MAP at 3 h post-infection. MAP upregulates stress-responsive global gene regulators, such as two-component systems and sigma factors, in response to oxidative and cell wall stress. Downstream genes involved in type VII secretion systems, cell wall synthesis (polyketide biosynthesis proteins), and iron uptake were changed in response to the intracellular environment of macrophages. On the host side, upregulation of inflammatory cytokine genes was observed along with pattern recognition receptor genes. Notably, alterations in gene sets involved in arginine metabolism were observed in both the host and MAP, along with significant downregulation of NOS2 expression. These observations suggest that the utilization of metabolites such as arginine by intracellular MAP might affect host NO production. Our dual RNA-seq data can provide novel insights by capturing the global transcriptome with higher resolution, especially in MAP, thus enabling a more systematic understanding of host-pathogen interactions.\n\nDelineating transcriptional crosstalk between Mycobacterium avium subsp. paratuberculosis and human THP-1 cells at the early stage of infection via dual RNA-seq analysis.", "token_count": 426, "char_count": 1818, "word_count": 255, "semantic_coherence": 1, "information_density": 0.6314, "quality_score": 0.8157, "entities": { "genes": [ "NOS2" ], "proteins": [], "pathways": [ "metabolism" ], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:25.431677", "source": { "split": "train_shard_00002", "doc_id": 665 }, "chunk_id": "train_shard_00002_665_0", "global_id": 13610 }, { "text": "Kluyveromyces fragilis immobilized in calcium alginate gel was compared to Saccharomyces cerevisiae coimmobilized with beta-galactosidase, for continuous ethanol production from whey permeate in packed-bed-type columns. Four different whey concentrations were studied, equivalent to 4.5, 10, 15, and 20% lactose, respectively. In all cases the coimmobilized preparation produced more ethanol than K. fragilis. The study went on for more than 5 weeks. K. fragilis showed a decline in activity after 20 days, while the coimmobilized preparation was stableduring the entrire investigation. Under experimental conditions theoretical yields of ethanol were obtained from 4.5 and 10% lactose substrates with the coimmobilized system. Using 15% lactose substrate, theoretical yields were only obtained when a galactose-adapted immobilized S. cerevisiae column was run in series with the coimmobilized column. Then a maximum of 71 g/L ethanol was produced with a productivity of 2.5 g/L h. The coimmobilized column alone gave a maximum ethanol concentration of 52 g/L with a productivity of 4.5 g/L h, whereas immobolized K. fragilis only produced 13 g/L ethanol with a productivity of 1.1 g/L h. It was not possible to obtain theoretical yields of ethanol from the highest substrate concentration.\n\nComparison between immobilized Kluyveromyces fragilis and Saccharomyces cerevisiae coimmobilized with beta-galactosidase, with respect to continuous ethanol production from concentrated whey permeate.", "token_count": 405, "char_count": 1492, "word_count": 210, "semantic_coherence": 1, "information_density": 0.5381, "quality_score": 0.769, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "kluyveromyces", "saccharomyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:26.049205", "source": { "split": "train_shard_00002", "doc_id": 666 }, "chunk_id": "train_shard_00002_666_0", "global_id": 13611 }, { "text": "Streptococcus oralis, a commensal species of the human oral cavity, belongs to the Mitis group of streptococci, which includes one of the major human pathogens as well, S. pneumoniae. We report here the first complete genome sequence of this species. S. oralis Uo5, a high-level penicillin- and multiple-antibiotic-resistant isolate from Hungary, is competent for genetic transformation under laboratory conditions. Comparative and functional genomics of Uo5 will be important in understanding the evolution of pathogenesis among Mitis streptococci and their potential to engage in interspecies gene transfer.\n\nGenome of Streptococcus oralis strain Uo5.", "token_count": 167, "char_count": 653, "word_count": 92, "semantic_coherence": 1, "information_density": 0.7717, "quality_score": 0.8859, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:26.489747", "source": { "split": "train_shard_00002", "doc_id": 667 }, "chunk_id": "train_shard_00002_667_0", "global_id": 13612 }, { "text": "The mechanisms by which different microbes colonize the healthy human gut versus other body sites, the gut in disease states, or other environments remain largely unknown. Identifying microbial genes influencing fitness in the gut could lead to new ways to engineer probiotics or disrupt pathogenesis. We approach this problem by measuring the statistical association between a species having a gene and the probability that the species is present in the gut microbiome. The challenge is that closely related species tend to be jointly present or absent in the microbiome and also share many genes, only a subset of which are involved in gut adaptation. We show that this phylogenetic correlation indeed leads to many false discoveries and propose phylogenetic linear regression as a powerful solution. To apply this method across the bacterial tree of life, where most species have not been experimentally phenotyped, we use metagenomes from hundreds of people to quantify each species' prevalence in and specificity for the gut microbiome. This analysis reveals thousands of genes potentially involved in adaptation to the gut across species, including many novel candidates as well as processes known to contribute to fitness of gut bacteria, such as acid tolerance in Bacteroidetes and sporulation in Firmicutes. We also find microbial genes associated with a preference for the gut over other body sites, which are significantly enriched for genes linked to fitness in an in vivo competition experiment. Finally, we identify gene families associated with higher prevalence in patients with Crohn's disease, including Proteobacterial genes involved in conjugation and fimbria regulation, processes previously linked to inflammation. These gene targets may represent new avenues for modulating host colonization and disease. Our strategy of combining metagenomics with phylogenetic modeling is general and can be used to identify genes associated with adaptation to any environment.\n\nPhylogeny-corrected identification of microbial gene families relevant to human gut colonization.", "token_count": 419, "char_count": 2084, "word_count": 309, "semantic_coherence": 1, "information_density": 0.5728, "quality_score": 0.7864, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "gut", "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:27.111195", "source": { "split": "train_shard_00002", "doc_id": 668 }, "chunk_id": "train_shard_00002_668_0", "global_id": 13613 }, { "text": "

Background

Efficient natural transformation in Neisseria requires the presence of short DNA uptake sequences (DUSs). Doubts remain whether DUSs propagate by pure selfish molecular drive or are selected for 'safe sex' among conspecifics.

Results

Six neisserial genomes were aligned to identify gene conversion fragments, DUS distribution, spacing, and conservation. We found a strong link between recombination and DUS: DUS spacing matches the size of conversion fragments; genomes with shorter conversion fragments have more DUSs and more conserved DUSs; and conversion fragments are enriched in DUSs. Many recent and singly occurring DUSs exhibit too high divergence with homologous sequences in other genomes to have arisen by point mutation, suggesting their appearance by recombination. DUSs are over-represented in the core genome, under-represented in regions under diversification, and absent in both recently acquired genes and recently lost core genes. This suggests that DUSs are implicated in genome stability rather than in generating adaptive variation. DUS elements are most frequent in the permissive locations of the core genome but are themselves highly conserved, undergoing mutation selection balance and/or molecular drive. Similar preliminary results were found for the functionally analogous uptake signal sequence in Pasteurellaceae.

Conclusion

As do many other pathogens, Neisseria and Pasteurellaceae have hyperdynamic genomes that generate deleterious mutations by intrachromosomal recombination and by transient hypermutation. The results presented here suggest that transformation in Neisseria and Pasteurellaceae allows them to counteract the deleterious effects of genome instability in the core genome. Thus, rather than promoting hypervariation, bacterial sex could be regenerative.\n\nThe impact of the neisserial DNA uptake sequences on genome evolution and stability.", "token_count": 447, "char_count": 1922, "word_count": 256, "semantic_coherence": 1, "information_density": 0.6367, "quality_score": 0.8184, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:27.752391", "source": { "split": "train_shard_00002", "doc_id": 669 }, "chunk_id": "train_shard_00002_669_0", "global_id": 13614 }, { "text": "The objective of this case-control study, conducted in a large Italian university hospital over a 12-month period, was to evaluate the risk factors associated with the emergence of azole resistant oral candidosis in 64 Human Immunodeficiency Virus (HIV) infected patients. A swab was obtained from each patient by brushing candidal lesions. Candida albicans was isolated in 41 patients (64%), Candida glabrata in ten (16%), Candida krusei in five (8%), Candida kefyr in two (3%), Candida tropicalis in two (3%), and Candida lipolytica and Candida guilliermondii in one case, respectively. Two patients suffered a double infection i.e. C. albicans+C. krusei and C. albicans+C. glabrata, respectively. Candida species were tested in vitro for their susceptibility to ketoconazole, fluconazole, itraconazole and amphotericin B. MICs of the four antifungal drugs were obtained for each yeast using a microdilution broth method developed in our laboratory. Twenty four (37%) of the isolated strains were resistant both to itraconazole and fluconazole, five (8%) to fluconazole alone, and two (3%) to ketoconazole alone, while none of the isolated strains was resistant to amphotericin B. Patients with oral candidosis caused by a strain resistant to one or more azole drug were compared to control patients with azole-susceptible oral candidosis. On univariate analysis, more than five episodes of oral candidosis in the last year (P = 0.01), previous use of azole therapy (P = 0.001), C2-3 category of HIV infection (P = 0.01) and low number of circulating CD4+ T-cells (P = 0.03) were significantly associated with an increased risk for the development of azole resistance. However, previous use of azole therapy was the only factor selected by a stepwise logistic regression analysis which was independently associated with the isolation of azole resistant strains (P = 0.003)", "token_count": 518, "char_count": 1874, "word_count": 287, "semantic_coherence": 1, "information_density": 0.5505, "quality_score": 0.7753, "entities": { "genes": [ "CD4" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:07:28.417306", "source": { "split": "train_shard_00002", "doc_id": 670 }, "chunk_id": "train_shard_00002_670_0", "global_id": 13615 }, { "text": "Our findings indicate that, in view of the potential risk for the emergence and selection of azole resistant strains of Candida in patients with AIDS, it is important to carefully choose the antifungal drug for the therapy of mild fungal infections after evaluation of the in-vitro susceptibility of the isolated strains.\n\nAnalysis of the risk factors associated with the emergence of azole resistant oral candidosis in the course of HIV infection.", "token_count": 98, "char_count": 448, "word_count": 71, "semantic_coherence": 1, "information_density": 0.662, "quality_score": 0.831, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:28.837730", "source": { "split": "train_shard_00002", "doc_id": 670 }, "chunk_id": "train_shard_00002_670_1", "global_id": 13616 }, { "text": "Background and Objective: Vibrio cholerae continues to emerge as a dangerous pathogen because of increasing resistance to a number of antibiotics. This paper provides a solution to emerging antibiotic resistance by introducing novel proteins as vaccine candidates against cholera. Materials and Methods: Vibrio cholerae genome versatility is a hurdle for developing a vaccine to combat diarrhoeal infection, so its core gene information was used to determine a potential vaccine candidate. Whole genome sequence data of more than 100 Vibrio cholerae strains were used simultaneously to get core genome information. The VacSol pipeline based on reverse vaccinology was selected to address the problem of safe, cheap, temperature-stable, and effective vaccine candidates which can be used for vaccine development against Vibrio cholerae. VacSol screens vaccine candidates using integrated, well-known, and robust algorithms/tools for proteome analysis. The proteomes of the pathogens were initially screened to predict homology using BLASTp. Proteomes that are non-homologous to humans are then subjected to a predictor for localization. Helicer predicts transmembrane helices for the protein. Proteins failing to comply with the set parameters were filtered at each step, and finally, 11 proteins were filtered as vaccine candidates. Results: This selected group of vaccine candidates consists of proteins from almost all structural parts of Vibrio cholerae. Their blast results show that this filtered group includes flagellin A protein, a protein from the Zn transporter system, a lipocarrier outer membrane protein, a peptidoglycan-associated protein, a DNA-binding protein, a chemotaxis protein, a tRNA Pseuriudine synthase A, and two selected proteins, which were beta lactamases. The last two uncharacterized proteins possess 100% similarity to V. albensis and Enterobacter, respectively. Tertiary structure and active site determination show a large number of pockets on each protein", "token_count": 510, "char_count": 2059, "word_count": 282, "semantic_coherence": 1, "information_density": 0.6099, "quality_score": 0.805, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:29.501889", "source": { "split": "train_shard_00002", "doc_id": 671 }, "chunk_id": "train_shard_00002_671_0", "global_id": 13617 }, { "text": "Conclusions: The most interesting finding of this study is that 10 proteins out of 11 filtered proteins are introduced as novel potential vaccine candidates. These novel vaccine candidates can result in the development of cost-effective and broad-spectrum vaccines which can be used in countries where cholera is a major contributor to diarrheal disease.\n\nPreliminary Work Towards Finding Proteins as Potential Vaccine Candidates for Vibrio cholerae Pakistani Isolates through Reverse Vaccinology.", "token_count": 128, "char_count": 511, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:29.943017", "source": { "split": "train_shard_00002", "doc_id": 671 }, "chunk_id": "train_shard_00002_671_1", "global_id": 13618 }, { "text": "Phospholipase C (PLC) enzymes are essential in regulating several important cellular functions in eukaryotes, including yeasts. In this study, PCR was used to identify a gene encoding PLC activity in Candida albicans, using oligonucleotide primers complementary to sequences encoding highly conserved amino acid regions within the X domains of previously characterized eukaryotic phospholipase C genes. The nucleotide sequence of the C. albicans gene, CAPLC1 (2997 bp), was determined from a recombinant clone containing C. albicans 132A genomic DNA; it encoded a polypeptide of 1099 amino acids with a predicted molecular mass of 124.6 kDa. The deduced amino acid sequence of this polypeptide (CAPLC1) exhibited many of the features common to previously characterized PLCs, including specific X and Y catalytic domains. The CAPLC1 protein also exhibited several unique features, including a novel stretch of 18-19 amino acid residues within the X domain and an unusually long N-terminus which did not contain a recognizable EF-hand Ca(2+)-binding domain. An overall amino acid homology of more than 27% with PLCs previously characterized from Saccharomyces cerevisiae and Schizosaccharomyces pombe suggested that the CAPLC1 protein is a delta-form of phosphoinositide-specific PLC (PI-PLC). PLC activity was detected in cell-free extracts of both yeast and hyphal forms of C. albicans 132A following 7 h and 24 h growth using the PLC-specific substrate p-nitrophenylphosphorylcholine (p-NPPC). In addition, CAPLC1 mRNA was detected by reverse transcriptase PCR in both yeast and hyphal forms of C. albicans 132A at the same time intervals. Expression of CAPLC1 activity was also detected in extracts of Escherichia coli DH5 alpha harbouring plasmids which contained portions of the CAPLC1 gene lacking sequences encoding part of the N-terminus", "token_count": 514, "char_count": 1844, "word_count": 271, "semantic_coherence": 1, "information_density": 0.5904, "quality_score": 0.7952, "entities": { "genes": [ "DH5", "CAPLC1" ], "proteins": [], "pathways": [], "organisms": [ "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:07:30.607492", "source": { "split": "train_shard_00002", "doc_id": 672 }, "chunk_id": "train_shard_00002_672_0", "global_id": 13619 }, { "text": "Southern hybridization and PCR analyses revealed that all C. albicans and Candida dubliniensis isolates examined possessed sequences homologous to CAPLC1. Sequences related to CAPLC1 were detected in some but not all isolates of Candida tropicalis, Candida glabrata and Candida parapsilosis tested, but not in the isolates of Candida krusei, Candida kefyr, Candida guillermondii and Candida lusitaniae examined. This paper reports the first description of the cloning and sequencing of a PLC gene from a pathogenic yeast species.\n\nGenetic characterization of a phospholipase C gene from Candida albicans: presence of homologous sequences in Candida species other than Candida albicans.", "token_count": 179, "char_count": 685, "word_count": 98, "semantic_coherence": 1, "information_density": 0.6327, "quality_score": 0.8163, "entities": { "genes": [ "CAPLC1" ], "proteins": [], "pathways": [], "organisms": [ "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:31.060686", "source": { "split": "train_shard_00002", "doc_id": 672 }, "chunk_id": "train_shard_00002_672_1", "global_id": 13620 }, { "text": "

Background

Public Health England (PHE) holds a collection of Shigella flexneri Type strains isolated between 1949 and 1972 representing 15 established serotypes and one provisional type, E1037. In this study, the genomes of all 16 PHE Type strains were sequenced using the Illumina HiSeq platform. The relationship between core genome phylogeny and serotype was examined.

Results

The most common target gene for the detection of Shigella species in clinical PCR assays, ipaH, was detected in all genomes. The type-specific target genes were correctly identified in each genome sequence. In contrast to the S. flexneri in serotype 5 strain described by Sun et al. (2012), the two PHE serotype 5 Type strains possessed an additional oac gene and were differentiated by the presence (serotype 5b) or absence (serotype 5a) of gtrX. The somatic antigen structure and phylogenetic relationship were broadly congruent for strains expressing serotype specific antigens III, IV and V, but not for those expressing I and II. The whole genome phylogenies of the 15 isolates sequenced showed that the serotype 6 Type Strain was phylogenetically distinct from the other S. flexneri serotypes sequenced. The provisional serotype E1037 fell within the serotype 4 clade, being most closely related to the Serotype 4a Type Strain.

Conclusions

The S. flexneri genome sequences were used to evaluate phylogenetic relationships between Type strains and validate genotypic and phenotypic assays. The analysis confirmed that the PHE S. flexneri Type strains are phenotypically and genotypically distinct. Novel variants will continue to be added to this archive.\n\nDraft genome sequences of the type strains of Shigella flexneri held at Public Health England: comparison of classical phenotypic and novel molecular assays with whole genome sequence.", "token_count": 496, "char_count": 1848, "word_count": 272, "semantic_coherence": 1, "information_density": 0.5809, "quality_score": 0.7904, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:31.708769", "source": { "split": "train_shard_00002", "doc_id": 673 }, "chunk_id": "train_shard_00002_673_0", "global_id": 13621 }, { "text": "Genome: ASM5205707v1\n\nASM5205707v1", "token_count": 27, "char_count": 34, "word_count": 3, "semantic_coherence": 1, "information_density": 0.6667, "quality_score": 0.8333, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:32.075392", "source": { "split": "train_shard_00002", "doc_id": 674 }, "chunk_id": "train_shard_00002_674_0", "global_id": 13622 }, { "text": "{\"uid\": \"29576111\", \"rsuid\": \"\", \"gbuid\": \"76762418\", \"assemblyaccession\": \"GCA_052057075.1\", \"lastmajorreleaseaccession\": \"GCA_052057075.1\", \"latestaccession\": \"\", \"chainid\": \"52057075\", \"assemblyname\": \"ASM5205707v1\", \"ucscname\": \"\", \"ensemblname\": \"\", \"taxid\": \"4911\", \"organism\": \"Kluyveromyces marxianus (budding yeasts & allies)\", \"speciestaxid\": \"4911\", \"speciesname\": \"Kluyveromyces marxianus\", \"assemblytype\": \"haploid\", \"assemblystatus\": \"Contig\", \"assemblystatussort\": 6, \"wgs\": \"JBPVIK01\", \"gb_bioprojects\": [{\"bioprojectaccn\": \"PRJNA1295373\", \"bioprojectid\": 1295373}], \"gb_projects\": [], \"rs_bioprojects\": [], \"rs_projects\": [], \"biosampleaccn\": \"SAMN50166912\", \"biosampleid\": \"50166912\", \"biosource\": {\"infraspecieslist\": 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"proteins": [], "pathways": [], "organisms": [], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:07:33.074965", "source": { "split": "train_shard_00002", "doc_id": 675 }, "chunk_id": "train_shard_00002_675_0", "global_id": 13624 }, { "text": "{\"uid\": \"26135151\", \"rsuid\": \"\", \"gbuid\": \"67942538\", \"assemblyaccession\": \"GCA_046562785.1\", \"lastmajorreleaseaccession\": \"GCA_046562785.1\", \"latestaccession\": \"\", \"chainid\": \"46562785\", \"assemblyname\": \"ASM4656278v1\", \"ucscname\": \"\", \"ensemblname\": \"\", \"taxid\": \"4911\", \"organism\": \"Kluyveromyces marxianus (budding yeasts & allies)\", \"speciestaxid\": \"4911\", \"speciesname\": \"Kluyveromyces marxianus\", \"assemblytype\": \"haploid\", \"assemblystatus\": \"Contig\", \"assemblystatussort\": 6, \"wgs\": \"JBJBSF01\", \"gb_bioprojects\": [{\"bioprojectaccn\": \"PRJNA957743\", \"bioprojectid\": 957743}], \"gb_projects\": [], \"rs_bioprojects\": [], \"rs_projects\": [], 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\"asmreleasedate_refseq\": \"1/01/01 00:00\", \"seqreleasedate\": \"2014/06/30 00:00\", \"asmupdatedate\": \"2022/12/12 00:00\", \"submissiondate\": \"2014/06/30 00:00\", \"lastupdatedate\": \"2022/12/12 00:00\", \"submitterorganization\": \"National Institute of Advanced Industrial Science and Technology\", \"refseq_category\": \"na\", \"anomalouslist\": [], \"exclfromrefseq\": [], \"propertylist\": [\"full-genome-representation\", \"latest\", \"latest_genbank\", \"wgs\"], \"fromtype\": \"\", \"synonym\": {\"genbank\": \"GCA_000747785.1\", \"refseq\": \"\", \"similarity\": \"\"}, \"contign50\": 1416405, \"scaffoldn50\": 1416405, \"annotrpturl\": \"\", \"ftppath_genbank\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/747/785/GCA_000747785.1_ASM74778v1\", \"ftppath_refseq\": \"\", \"ftppath_assembly_rpt\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/747/785/GCA_000747785.1_ASM74778v1/GCA_000747785.1_ASM74778v1_assembly_report.txt\", \"ftppath_stats_rpt\": \"ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/747/785/GCA_000747785.1_ASM74778v1/GCA_000747785.1_ASM74778v1_assembly_stats.txt\", \"ftppath_regions_rpt\": \"\", \"busco\": {\"refseqannotationrelease\": \"\", \"buscolineage\": \"\", \"buscover\": \"\", \"complete\": \"\", \"singlecopy\": \"\", \"duplicated\": \"\", \"fragmented\": \"\", \"missing\": \"\", \"totalcount\": \"\"}, \"sortorder\": \"5C6X91959985835940007477859800\", \"meta\": \" 0 0 36 4 1416405 0 0 36 0 0 36 4 1416405 11165408 11165408 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/747/785/GCA_000747785.1_ASM74778v1/GCA_000747785.1_ASM74778v1_assembly_report.txt ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/747/785/GCA_000747785.1_ASM74778v1 ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/747/785/GCA_000747785.1_ASM74778v1/GCA_000747785.1_ASM74778v1_assembly_stats.txt 1 Contig na National Institute of Advanced Industrial Science and Technology \"}", "token_count": 1820, "char_count": 4045, "word_count": 232, "semantic_coherence": 1, "information_density": 0.7026, "quality_score": 0.8513, "entities": { "genes": [ "SAMD00017758", "PRJDB2926", "BBIL01", "DMB1" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:08:10.307373", "source": { "split": "train_shard_00002", "doc_id": 711 }, "chunk_id": "train_shard_00002_711_1", "global_id": 13697 }, { "text": "Cellular responses to maladaptive environmental changes—stresses—allow for organismal adaptation to diverse and dynamic conditions. Across the tree of life, cells upregulate a highly conserved transcriptional program in response to so-called proteotoxic stresses such as heat shock. Correspondingly, in eukaryotes, these stresses induce the formation of biomolecular condensates, clusters of mRNA and protein which are referred to as stress granules under severe stress. However, major questions remain about this stress-induced response. How conserved is the condensation response relative to the transcriptional response? How does it vary across environmental niches, and to what extent does it correspond with the conserved transcriptional response? To answer these fundamental questions, we studied the growth, transcriptional, and condensation heat-induced stress responses in three fungal species adapted to thrive in different thermal environments: cryophilic S. kudriavzevii, mesophilic S. cerevisiae, and thermotolerant K. marxianus. Here we show that transcriptional heat shock responses track each species’ evolved temperature range of growth. Further, orthologous proteins—including poly(A)-binding protein, Pab1, a core marker of stress granules—form condensates in vivo at temperatures systematically tuned to the temperature at which the organisms activate the transcriptional heat shock response and slow their growth. In vitro, purified Pab1 from each species condenses autonomously at niche-specific temperatures. Homologous mutations in Pab1 cause similar shifts in relative condensation temperature across species, and crucially, mutations which suppress condensation in vitro also reduce fitness during heat stress. Our findings indicate that stress-induced protein condensation is adaptive, conserved, integrated with the growth and transcriptional responses, and tuned to features of the cellular and organismal environment to initiate at niche-specific levels.\n\nAn adaptive biomolecular condensation response is conserved across environmentally divergent species", "token_count": 463, "char_count": 2086, "word_count": 270, "semantic_coherence": 1, "information_density": 0.6074, "quality_score": 0.8037, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:10.955495", "source": { "split": "train_shard_00002", "doc_id": 712 }, "chunk_id": "train_shard_00002_712_0", "global_id": 13698 }, { "text": "{\"uid\": \"200234499\", \"accession\": \"GSE234499\", \"gds\": \"\", \"title\": \"An adaptive biomolecular condensation response is conserved across environmentally divergent species\", \"summary\": \"Cellular responses to maladaptive environmental changes\\u2014stresses\\u2014allow for organismal adaptation to diverse and dynamic conditions. Across the tree of life, cells upregulate a highly conserved transcriptional program in response to so-called proteotoxic stresses such as heat shock. Correspondingly, in eukaryotes, these stresses induce the formation of biomolecular condensates, clusters of mRNA and protein which are referred to as stress granules under severe stress. However, major questions remain about this stress-induced response. How conserved is the condensation response relative to the transcriptional response? How does it vary across environmental niches, and to what extent does it correspond with the conserved transcriptional response? To answer these fundamental questions, we studied the growth, transcriptional, and condensation heat-induced stress responses in three fungal species adapted to thrive in different thermal environments: cryophilic S. kudriavzevii, mesophilic S. cerevisiae, and thermotolerant K. marxianus. Here we show that transcriptional heat shock responses track each species\\u2019 evolved temperature range of growth. Further, orthologous proteins\\u2014including poly(A)-binding protein, Pab1, a core marker of stress granules\\u2014form condensates in vivo at temperatures systematically tuned to the temperature at which the organisms activate the transcriptional heat shock response and slow their growth. In vitro, purified Pab1 from each species condenses autonomously at niche-specific temperatures. Homologous mutations in Pab1 cause similar shifts in relative condensation temperature across species, and crucially, mutations which suppress condensation in vitro also reduce fitness during heat stress. Our findings indicate that stress-induced protein condensation is adaptive, conserved, integrated with the growth and transcriptional responses, and tuned to features of the cellular and organismal environment to initiate at niche-specific levels.\", \"gpl\": \"27812;29573;33472\", \"gse\": \"234499\", \"taxon\": \"Kluyveromyces marxianus; Saccharomyces cerevisiae; Saccharomyces kudriavzevii\", \"entrytype\": \"GSE\", \"gdstype\": \"Expression profiling by high throughput sequencing\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2023/07/31\", \"suppfile\": \"TSV\", \"samples\": [{\"accession\": \"GSM7469738\", \"title\": \"Kmarx_37C_BR2\"}, {\"accession\": \"GSM7469735\", \"title\": \"Scer_40C_BR1\"}, {\"accession\": \"GSM7469730\", \"title\": \"Skud_24C_BR2\"}, {\"accession\": \"GSM7469733\", \"title\": \"Scer_33C_BR1\"}, {\"accession\": \"GSM7469736\", \"title\": \"Scer_40C_BR2\"}, {\"accession\": \"GSM7469739\", \"title\": \"Kmarx_46C_BR1\"}, {\"accession\": \"GSM7469731\", \"title\": \"Skud_31C_BR1\"}, {\"accession\": \"GSM7469740\", \"title\": \"Kmarx_46C_BR2\"}, {\"accession\": \"GSM7469734\", \"title\": \"Scer_33C_BR2\"}, {\"accession\": \"GSM7469737\", \"title\": \"Kmarx_37C_BR1\"}, {\"accession\": \"GSM7469729\", \"title\": \"Skud_24C_BR1\"}, {\"accession\": \"GSM7469732\", \"title\": \"Skud_31C_BR2\"}], \"relations\": [], \"extrelations\": [], \"n_samples\": 12, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [\"38605014\"], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE234nnn/GSE234499/\", \"geo2r\": \"no\", \"bioproject\": \"PRJNA981544\"}", "token_count": 1160, "char_count": 3477, "word_count": 383, "semantic_coherence": 1, "information_density": 0.6423, "quality_score": 0.8211, "entities": { "genes": [ "GSE234499", "GSM7469732", "PRJNA981544", "GSM7469738", "GSM7469731", "GSM7469734", "GSM7469737", "GSM7469736", "GSM7469730", "GSM7469733" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "saccharomyces" ], "conditions": [ "ph", "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:08:11.612404", "source": { "split": "train_shard_00002", "doc_id": 712 }, "chunk_id": "train_shard_00002_712_1", "global_id": 13699 }, { "text": "Analysis of gene expression changes in S. cerevisiae and K. marxianus in response to oxygen-limitation\n\nEngineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth ssing sterol requirements enables anaerobic growth of the thermotolerant yeast Kluyveromyces marxianus", "token_count": 83, "char_count": 299, "word_count": 37, "semantic_coherence": 1, "information_density": 0.7297, "quality_score": 0.8649, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:12.792422", "source": { "split": "train_shard_00002", "doc_id": 713 }, "chunk_id": "train_shard_00002_713_0", "global_id": 13700 }, { "text": "{\"uid\": \"200164344\", \"accession\": \"GSE164344\", \"gds\": \"\", \"title\": \"Engineering the thermotolerant industrial yeast Kluyveromyces marxianus for anaerobic growth ssing sterol requirements enables anaerobic growth of the thermotolerant yeast Kluyveromyces marxianus\", \"summary\": \"Analysis of gene expression changes in S. cerevisiae and K. marxianus in response to oxygen-limitation\", \"gpl\": \"27812;29573\", \"gse\": \"164344\", \"taxon\": \"Kluyveromyces marxianus; Saccharomyces cerevisiae\", \"entrytype\": \"GSE\", \"gdstype\": \"Expression profiling by high throughput sequencing\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2021/01/06\", \"suppfile\": \"TXT\", \"samples\": [{\"accession\": \"GSM5007921\", \"title\": \"ELOX36-08L1\"}, {\"accession\": \"GSM5007915\", \"title\": \"ELOX24-10L1\"}, {\"accession\": \"GSM5007918\", \"title\": \"ELOX24-10R3\"}, {\"accession\": \"GSM5007924\", \"title\": \"ELOX38-08R1\"}, {\"accession\": \"GSM5007913\", \"title\": \"ELOX23-08L1\"}, {\"accession\": \"GSM5007916\", \"title\": \"ELOX24-10L3\"}, {\"accession\": \"GSM5007910\", \"title\": \"ELOX19-08R3\"}, {\"accession\": \"GSM5007922\", \"title\": \"ELOX36-08R1\"}, {\"accession\": \"GSM5007919\", \"title\": \"ELOX34-08L1\"}, {\"accession\": \"GSM5007911\", \"title\": \"ELOX19-09L2\"}, {\"accession\": \"GSM5007925\", \"title\": \"ELOX39-09R1\"}, {\"accession\": \"GSM5007914\", \"title\": \"ELOX23-08R1\"}, {\"accession\": \"GSM5007917\", \"title\": \"ELOX24-10R1\"}, {\"accession\": \"GSM5007923\", \"title\": \"ELOX38-08L1\"}, {\"accession\": \"GSM5007926\", \"title\": \"ELOX39-10L1\"}, {\"accession\": \"GSM5007912\", \"title\": \"ELOX19-09L3\"}, {\"accession\": \"GSM5007920\", \"title\": \"ELOX34-09L1\"}, {\"accession\": \"GSM5007909\", \"title\": \"ELOX19-08R2\"}], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRP293599\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP293/SRP293599/\"}], \"n_samples\": 18, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [\"34303845\"], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE164nnn/GSE164344/\", \"geo2r\": \"no\", \"bioproject\": \"PRJNA679749\"}", "token_count": 1013, "char_count": 2094, "word_count": 177, "semantic_coherence": 1, "information_density": 0.7062, "quality_score": 0.8531, "entities": { "genes": [ "SRP293", "ELOX39", "GSM5007924", "GSM5007914", "GSM5007918", "GSM5007922", "GSE164344", "GSM5007913", "GSM5007919", "GSM5007923" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:08:13.411857", "source": { "split": "train_shard_00002", "doc_id": 713 }, "chunk_id": "train_shard_00002_713_1", "global_id": 13701 }, { "text": "K.marxianus and S. cerevisiae differed by their consumption of some amino acids and the production of aroma compounds (especially higher alcohols). To complete this phenotypic observation, RNA sequencing experiment was performed. Two samples were realized: at 6h of fermentation corresponding to lag phase and at the time of half of the maximal population was reached (20h for S. cerevisiae and 36h for K. marxianus). Thanks to this analyse, we can understand what regulations explain the differences between these two strains.\n\nNext Generation Sequencing Facilitates Quantitative Analysis of two wine yeasts: Saccharomyces cerevisiae EC1118 and Kluyveromyces marxianus IWBT Y855", "token_count": 177, "char_count": 679, "word_count": 98, "semantic_coherence": 1, "information_density": 0.7551, "quality_score": 0.8776, "entities": { "genes": [ "EC1118" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:13.863720", "source": { "split": "train_shard_00002", "doc_id": 714 }, "chunk_id": "train_shard_00002_714_0", "global_id": 13702 }, { "text": "{\"uid\": \"200129483\", \"accession\": \"GSE129483\", \"gds\": \"\", \"title\": \"Next Generation Sequencing Facilitates Quantitative Analysis of two wine yeasts: Saccharomyces cerevisiae EC1118 and Kluyveromyces marxianus IWBT Y855\", \"summary\": \"K.marxianus and S. cerevisiae differed by their consumption of some amino acids and the production of aroma compounds (especially higher alcohols). To complete this phenotypic observation, RNA sequencing experiment was performed. Two samples were realized: at 6h of fermentation corresponding to lag phase and at the time of half of the maximal population was reached (20h for S. cerevisiae and 36h for K. marxianus). Thanks to this analyse, we can understand what regulations explain the differences between these two strains.\", \"gpl\": \"26472;17342\", \"gse\": \"129483\", \"taxon\": \"Saccharomyces cerevisiae; Kluyveromyces marxianus\", \"entrytype\": \"GSE\", \"gdstype\": \"Expression profiling by high throughput sequencing\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2019/08/09\", \"suppfile\": \"TAB\", \"samples\": [{\"accession\": \"GSM3713848\", \"title\": \"KMA36\"}, {\"accession\": \"GSM3714421\", \"title\": \"SCC6\"}, {\"accession\": \"GSM3713846\", \"title\": \"KMB6\"}, {\"accession\": \"GSM3714424\", \"title\": \"SCC20\"}, {\"accession\": \"GSM3713849\", \"title\": \"KMB36\"}, {\"accession\": \"GSM3714425\", \"title\": \"SCD20\"}, {\"accession\": \"GSM3714422\", \"title\": \"SCD6\"}, {\"accession\": \"GSM3713847\", \"title\": \"KMC6\"}, {\"accession\": \"GSM3713850\", \"title\": \"KMC36\"}, {\"accession\": \"GSM3714420\", \"title\": \"SCB6\"}, {\"accession\": \"GSM3713845\", \"title\": \"KMA6\"}, {\"accession\": \"GSM3714423\", \"title\": \"SCB20\"}], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRP191463\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP191/SRP191463/\"}], \"n_samples\": 12, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [\"31336027\"], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE129nnn/GSE129483/\", \"geo2r\": \"no\", \"bioproject\": \"PRJNA531495\"}", "token_count": 848, "char_count": 2078, "word_count": 214, "semantic_coherence": 1, "information_density": 0.7336, "quality_score": 0.8668, "entities": { "genes": [ "KMA36", "SCC6", "GSE129483", "KMB6", "SCC20", "GSM3714422", "SCB20", "SCD20", "SCB6", "GSM3713848" ], "proteins": [], "pathways": [ "fermentation" ], "organisms": [ "marxianus", "kluyveromyces", "yeast", "saccharomyces" ], "conditions": [ "acid", "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:08:14.489268", "source": { "split": "train_shard_00002", "doc_id": 714 }, "chunk_id": "train_shard_00002_714_1", "global_id": 13703 }, { "text": "This experiment was performed to measure differences in pathway-level evolution of cis-regulation between closely related Kluyveromyces species. Sequencing of mRNA as well as DNA was performed in hybrids of Kl. lactis with two other species, Kl. wickerhamii and Kl. marxianus. Cells were grown overnight for DNA sequencing and for 4-8h to an OD600=0.7-1.0 for mRNA sequencing. DNA and mRNA reads were mapped to hybrid genomes, multimapping reads discarded, and allele-specific expression ratio for each gene was calculated after first normalizing mRNA reads to the number of DNA reads for each gene in each species. We found that the ribosomal protein genes showed pathway-level allele-specific expression differences between species in both interspecies hybrids.\n\nAllele-specific mRNA expression experiment in lactis-wickerhamii and lactis-marxianus interespecies hybrids", "token_count": 229, "char_count": 872, "word_count": 122, "semantic_coherence": 1, "information_density": 0.5902, "quality_score": 0.7951, "entities": { "genes": [ "OD600" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:14.965041", "source": { "split": "train_shard_00002", "doc_id": 715 }, "chunk_id": "train_shard_00002_715_0", "global_id": 13704 }, { "text": "{\"uid\": \"200108389\", \"accession\": \"GSE108389\", \"gds\": \"\", \"title\": \"Allele-specific mRNA expression experiment in lactis-wickerhamii and lactis-marxianus interespecies hybrids\", \"summary\": \"This experiment was performed to measure differences in pathway-level evolution of cis-regulation between closely related Kluyveromyces species. Sequencing of mRNA as well as DNA was performed in hybrids of Kl. lactis with two other species, Kl. wickerhamii and Kl. marxianus. Cells were grown overnight for DNA sequencing and for 4-8h to an OD600=0.7-1.0 for mRNA sequencing. DNA and mRNA reads were mapped to hybrid genomes, multimapping reads discarded, and allele-specific expression ratio for each gene was calculated after first normalizing mRNA reads to the number of DNA reads for each gene in each species. We found that the ribosomal protein genes showed pathway-level allele-specific expression differences between species in both interspecies hybrids.\", \"gpl\": \"22716;24418;24419;24417;24420\", \"gse\": \"108389\", \"taxon\": \"Kluyveromyces lactis x Kluyveromyces wickerhamii; Kluyveromyces marxianus; Kluyveromyces wickerhamii; Kluyveromyces lactis x Kluyveromyces marxianus; Kluyveromyces lactis\", \"entrytype\": \"GSE\", \"gdstype\": \"Expression profiling by high throughput sequencing; Other\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2017/12/22\", \"suppfile\": \"TXT\", \"samples\": [{\"accession\": \"GSM2897278\", \"title\": \"Kl. marxianus parental gDNA\"}, {\"accession\": \"GSM2897298\", \"title\": \"lactis-wickerhamii mRNA isolate 7\"}, {\"accession\": \"GSM2897295\", \"title\": \"lactis-marxianus mRNA isolate 1\"}, {\"accession\": \"GSM2897289\", \"title\": \"lactis-wickerhamii mRNA isolate 1\"}, {\"accession\": \"GSM2897286\", \"title\": \"lactis-marxianus gDNA isolate 2\"}, {\"accession\": \"GSM2897290\", \"title\": \"lactis-wickerhamii mRNA isolate 2\"}, {\"accession\": \"GSM2897292\", \"title\": \"lactis-wickerhamii mRNA isolate 4\"}, {\"accession\": \"GSM2897296\", \"title\": \"lactis-marxianus mRNA isolate 2\"}, {\"accession\": \"GSM2897293\", \"title\": \"lactis-wickerhamii mRNA isolate 5\"}, {\"accession\": \"GSM2897287\", \"title\": \"lactis-marxianus gDNA isolate 3\"}, {\"accession\": \"GSM2897281\", \"title\": \"Kl. wickerhamii parental gDNA isolate 2\"}, {\"accession\": \"GSM2897284\", \"title\": \"lactis-wickerhamii gDNA isolate 2\"}, {\"accession\": \"GSM2897288\", \"title\": \"lactis-wickerhamii gDNA isolate 3\"}, {\"accession\": \"GSM2897291\", \"title\": \"lactis-wickerhamii mRNA isolate 3\"}, {\"accession\": \"GSM2897285\", \"title\": \"lactis-marxianus gDNA isolate 1\"}, {\"accession\": \"GSM2897282\", \"title\": \"Kl. wickerhamii parental gDNA isolate 3\"}, {\"accession\": \"GSM2897299\", \"title\": \"lactis-wickerhamii mRNA isolate 8\"}, {\"accession\": \"GSM2897279\", \"title\": \"Kl. wickerhamii parental gDNA isolate 1\"}, {\"accession\": \"GSM2897280\", \"title\": \"Kl. lactis parental gDNA isolate 2\"}, {\"accession\": \"GSM2897300\", \"title\": \"lactis-wickerhamii mRNA isolate 9\"}, {\"accession\": \"GSM2897283\", \"title\": \"lactis-wickerhamii gDNA isolate 1\"}, {\"accession\": \"GSM2897297\", \"title\": \"lactis-marxianus mRNA isolate 3\"}, {\"accession\": \"GSM2897277\", \"title\": \"Kl. lactis parental gDNA isolate 1\"}, {\"accession\": \"GSM2897294\", \"title\": \"lactis-wickerhamii mRNA isolate 6\"}], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRP127324\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP127/SRP127324/\"}], \"n_samples\": 24, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [\"30198843\"], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE108nnn/GSE108389/\", \"geo2r\": \"no\", \"bioproject\": \"PRJNA427120\"}", "token_count": 1526, "char_count": 3661, "word_count": 381, "semantic_coherence": 1, "information_density": 0.4672, "quality_score": 0.7336, "entities": { "genes": [ "GSM2897298", "GSM2897277", "GSM2897290", "GSM2897281", "PRJNA427120", "SRP127324", "GSM2897282", "GSM2897295", "GSE108389", "GSM2897296" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": false, "timestamp": "2025-11-01T07:08:15.616680", "source": { "split": "train_shard_00002", "doc_id": 715 }, "chunk_id": "train_shard_00002_715_1", "global_id": 13705 }, { "text": "To understand functional roles of ncRNAs during exponential growth phase, we captured transcriptome changes by conducting strand-specific RNA-seq.\n\nTranscriptional expression level during exponential growth phase in Kluyveromyces marxianus", "token_count": 55, "char_count": 239, "word_count": 28, "semantic_coherence": 1, "information_density": 0.8929, "quality_score": 0.9464, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:15.979488", "source": { "split": "train_shard_00002", "doc_id": 716 }, "chunk_id": "train_shard_00002_716_0", "global_id": 13706 }, { "text": "{\"uid\": \"200070111\", \"accession\": \"GSE70111\", \"gds\": \"\", \"title\": \"Transcriptional expression level during exponential growth phase in Kluyveromyces marxianus\", \"summary\": \"To understand functional roles of ncRNAs during exponential growth phase, we captured transcriptome changes by conducting strand-specific RNA-seq.\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSE\", \"gdstype\": \"Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2016/08/20\", \"suppfile\": \"GFF, TXT\", \"samples\": [{\"accession\": \"GSM1717189\", \"title\": \"RNA-seq LE rep1\"}, {\"accession\": \"GSM1717186\", \"title\": \"RNA-seq EE rep2\"}, {\"accession\": \"GSM1717190\", \"title\": \"RNA-seq LE rep2\"}, {\"accession\": \"GSM1717187\", \"title\": \"RNA-seq ME rep1\"}, {\"accession\": \"GSM1717188\", \"title\": \"RNA-seq ME rep2\"}, {\"accession\": \"GSM1717185\", \"title\": \"RNA-seq EE rep1\"}], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRP059737\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP059/SRP059737/\"}], \"n_samples\": 6, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [\"26923790\"], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE70nnn/GSE70111/\", \"geo2r\": \"no\", \"bioproject\": \"PRJNA287655\"}", "token_count": 606, "char_count": 1446, "word_count": 138, "semantic_coherence": 1, "information_density": 0.7174, "quality_score": 0.8587, "entities": { "genes": [ "SRP059737", "GSM1717190", "GSM1717186", "GSM1717188", "SRP059", "GSE70111", "PRJNA287655", "GSM1717185", "GSM1717187", "GSM1717189" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [ "ph" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:08:16.601409", "source": { "split": "train_shard_00002", "doc_id": 716 }, "chunk_id": "train_shard_00002_716_1", "global_id": 13707 }, { "text": "Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30°C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions.\n\nTSS-seq analysis of K. marxianus", "token_count": 136, "char_count": 600, "word_count": 81, "semantic_coherence": 1, "information_density": 0.7531, "quality_score": 0.8765, "entities": { "genes": [], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:17.044610", "source": { "split": "train_shard_00002", "doc_id": 717 }, "chunk_id": "train_shard_00002_717_0", "global_id": 13708 }, { "text": "{\"uid\": \"200066600\", \"accession\": \"GSE66600\", \"gds\": \"\", \"title\": \"TSS-seq analysis of K. marxianus\", \"summary\": \"Thermotolerant Kluyveromyces marxianus possesses intrinsic abilities to ferment and assimilate a wide variety of substrates including xylose and to efficiently produce proteins. The transcriptome analysis clarified distinctive metabolic pathways under three different growth conditions, static culture, high temperature and xylose medium, in comparison to the control condition of glucose medium under a shaking condition at 30\\u00b0C. Interestingly, the yeast appears to overcome the issue of reactive oxygen species, which tend to accumulate under all three conditions.\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSE\", \"gdstype\": \"Expression profiling by high throughput sequencing\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"XLSX\", \"samples\": [{\"accession\": \"GSM1626078\", \"title\": \"30D-\\u2462 (110624_EAS74_lane8)\"}, {\"accession\": \"GSM1626081\", \"title\": \"30X-\\u2462 (110614_EAS798_lane8)\"}, {\"accession\": \"GSM1626087\", \"title\": \"45D-\\u2462 (110614_EAS74_lane8)\"}, {\"accession\": \"GSM1626084\", \"title\": \"30DS-\\u2462 (110614_EAS798_lane2)\"}, {\"accession\": \"GSM1626076\", \"title\": \"30D-\\u2460 (110401_lane5)\"}, {\"accession\": \"GSM1626085\", \"title\": \"45D-\\u2460 (110401_lane8)\"}, {\"accession\": \"GSM1626082\", \"title\": \"30DS-\\u2460 (110401_lane7)\"}, {\"accession\": \"GSM1626079\", \"title\": \"30X-\\u2460 (110614_EAS798_lane6)\"}, {\"accession\": \"GSM1626077\", \"title\": \"30D-\\u2461 (110624_EAS74_lane7)\"}, {\"accession\": \"GSM1626086\", \"title\": \"45D-\\u2461 (110614_EAS74_lane7)\"}, {\"accession\": \"GSM1626083\", \"title\": \"30DS-\\u2461 (110614_EAS798_lane1)\"}, {\"accession\": \"GSM1626080\", \"title\": \"30X-\\u2461 (110614_EAS798_lane7)\"}], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRP055903\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByStudy/sra/SRP/SRP055/SRP055903/\"}], \"n_samples\": 12, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [\"25834639\"], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE66nnn/GSE66600/\", \"geo2r\": \"no\", \"bioproject\": \"PRJNA277420\"}", "token_count": 1042, "char_count": 2277, "word_count": 207, "semantic_coherence": 1, "information_density": 0.7488, "quality_score": 0.8744, "entities": { "genes": [ "GSM1626085", "SRP055", "GSM1626079", "GSM1626077", "GSM1626086", "PRJNA277420", "GSM1626080", "GSM1626078", "SRP055903", "GSM1626084" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "temperature" ] }, "biobert_ready": false, "timestamp": "2025-11-01T07:08:17.694838", "source": { "split": "train_shard_00002", "doc_id": 717 }, "chunk_id": "train_shard_00002_717_1", "global_id": 13709 }, { "text": "Illumina NovaSeq 6000 (Kluyveromyces marxianus)\n\n{\"uid\": \"100029573\", \"accession\": \"GPL29573\", \"gds\": \"\", \"title\": \"Illumina NovaSeq 6000 (Kluyveromyces marxianus)\", \"summary\": \"\", \"gpl\": \"29573\", \"gse\": \"164344;234499\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GPL\", \"gdstype\": \"\", \"ptechtype\": \"high-throughput sequencing\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2021/01/06\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [], \"n_samples\": 12, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL29nnn/GPL29573/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 308, "char_count": 705, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [ "GPL29573" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:18.281774", "source": { "split": "train_shard_00002", "doc_id": 718 }, "chunk_id": "train_shard_00002_718_0", "global_id": 13710 }, { "text": "Illumina HiSeq 2500 (Kluyveromyces marxianus)\n\n{\"uid\": \"100026472\", \"accession\": \"GPL26472\", \"gds\": \"\", \"title\": \"Illumina HiSeq 2500 (Kluyveromyces marxianus)\", \"summary\": \"\", \"gpl\": \"26472\", \"gse\": \"129483\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GPL\", \"gdstype\": \"\", \"ptechtype\": \"high-throughput sequencing\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2019/04/08\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [], \"n_samples\": 6, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL26nnn/GPL26472/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 300, "char_count": 693, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [ "GPL26472" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:18.882121", "source": { "split": "train_shard_00002", "doc_id": 719 }, "chunk_id": "train_shard_00002_719_0", "global_id": 13711 }, { "text": "Illumina HiSeq 4000 (Kluyveromyces marxianus)\n\n{\"uid\": \"100024417\", \"accession\": \"GPL24417\", \"gds\": \"\", \"title\": \"Illumina HiSeq 4000 (Kluyveromyces marxianus)\", \"summary\": \"\", \"gpl\": \"24417\", \"gse\": \"108389\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GPL\", \"gdstype\": \"\", \"ptechtype\": \"high-throughput sequencing\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2017/12/21\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [], \"n_samples\": 1, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL24nnn/GPL24417/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 300, "char_count": 693, "word_count": 69, "semantic_coherence": 1, "information_density": 0.7391, "quality_score": 0.8696, "entities": { "genes": [ "GPL24417" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:19.445613", "source": { "split": "train_shard_00002", "doc_id": 720 }, "chunk_id": "train_shard_00002_720_0", "global_id": 13712 }, { "text": "Illumina MiSeq (Kluyveromyces marxianus)\n\n{\"uid\": \"100020596\", \"accession\": \"GPL20596\", \"gds\": \"\", \"title\": \"Illumina MiSeq (Kluyveromyces marxianus)\", \"summary\": \"\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GPL\", \"gdstype\": \"\", \"ptechtype\": \"high-throughput sequencing\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/06/22\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [], \"n_samples\": 6, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL20nnn/GPL20596/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 289, "char_count": 682, "word_count": 67, "semantic_coherence": 1, "information_density": 0.7463, "quality_score": 0.8731, "entities": { "genes": [ "GPL20596" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:20.009041", "source": { "split": "train_shard_00002", "doc_id": 721 }, "chunk_id": "train_shard_00002_721_0", "global_id": 13713 }, { "text": "Illumina Genome Analyzer IIx (Kluyveromyces marxianus)\n\n{\"uid\": \"100019857\", \"accession\": \"GPL19857\", \"gds\": \"\", \"title\": \"Illumina Genome Analyzer IIx (Kluyveromyces marxianus)\", \"summary\": \"\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GPL\", \"gdstype\": \"\", \"ptechtype\": \"high-throughput sequencing\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/06\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [], \"n_samples\": 12, \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/platforms/GPL19nnn/GPL19857/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 300, "char_count": 711, "word_count": 71, "semantic_coherence": 1, "information_density": 0.7324, "quality_score": 0.8662, "entities": { "genes": [ "GPL19857" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:20.564669", "source": { "split": "train_shard_00002", "doc_id": 722 }, "chunk_id": "train_shard_00002_722_0", "global_id": 13714 }, { "text": "DMKU3-1042\n\nKmarx_46C_BR2\n\n{\"uid\": \"307469740\", \"accession\": \"GSM7469740\", \"gds\": \"\", \"title\": \"Kmarx_46C_BR2\", \"summary\": \"DMKU3-1042\", \"gpl\": \"29573\", \"gse\": \"234499\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2023/07/31\", \"suppfile\": \"TSV\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX20642061\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX206/SRX20642061/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM7469nnn/GSM7469740/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 391, "char_count": 796, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [ "SRX206", "GSM7469740", "SRX20642061", "DMKU3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:21.175879", "source": { "split": "train_shard_00002", "doc_id": 723 }, "chunk_id": "train_shard_00002_723_0", "global_id": 13715 }, { "text": "DMKU3-1042\n\nKmarx_46C_BR1\n\n{\"uid\": \"307469739\", \"accession\": \"GSM7469739\", \"gds\": \"\", \"title\": \"Kmarx_46C_BR1\", \"summary\": \"DMKU3-1042\", \"gpl\": \"29573\", \"gse\": \"234499\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2023/07/31\", \"suppfile\": \"TSV\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX20642060\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX206/SRX20642060/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM7469nnn/GSM7469739/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 391, "char_count": 796, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [ "SRX20642060", "SRX206", "GSM7469739", "DMKU3" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:21.783524", "source": { "split": "train_shard_00002", "doc_id": 724 }, "chunk_id": "train_shard_00002_724_0", "global_id": 13716 }, { "text": "DMKU3-1042\n\nKmarx_37C_BR2\n\n{\"uid\": \"307469738\", \"accession\": \"GSM7469738\", \"gds\": \"\", \"title\": \"Kmarx_37C_BR2\", \"summary\": \"DMKU3-1042\", \"gpl\": \"29573\", \"gse\": \"234499\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2023/07/31\", \"suppfile\": \"TSV\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX20642059\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX206/SRX20642059/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM7469nnn/GSM7469738/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 391, "char_count": 796, "word_count": 66, "semantic_coherence": 1, "information_density": 0.7879, "quality_score": 0.8939, "entities": { "genes": [ "SRX206", "SRX20642059", 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"global_id": 13726 }, { "text": "KM 36h rep3\n\nKMC36\n\n{\"uid\": \"303713850\", \"accession\": \"GSM3713850\", \"gds\": \"\", \"title\": \"KMC36\", \"summary\": \"KM 36h rep3\", \"gpl\": \"26472\", \"gse\": \"129483\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2019/08/09\", \"suppfile\": \"TAB\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX5654583\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX565/SRX5654583/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3713nnn/GSM3713850/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 375, "char_count": 780, "word_count": 70, 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\"summary\": \"KM 36h rep1\", \"gpl\": \"26472\", \"gse\": \"129483\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2019/08/09\", \"suppfile\": \"TAB\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX5654581\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX565/SRX5654581/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3713nnn/GSM3713848/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 375, "char_count": 780, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [ "GSM3713848", "KMA36", "SRX565", "SRX5654581" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:29.373710", "source": { "split": "train_shard_00002", "doc_id": 737 }, "chunk_id": "train_shard_00002_737_0", "global_id": 13729 }, { "text": "KM 6h rep3\n\nKMC6\n\n{\"uid\": \"303713847\", \"accession\": \"GSM3713847\", \"gds\": \"\", \"title\": \"KMC6\", \"summary\": \"KM 6h rep3\", \"gpl\": \"26472\", \"gse\": \"129483\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2019/08/09\", \"suppfile\": \"TAB\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX5654580\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX565/SRX5654580/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3713nnn/GSM3713847/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 371, "char_count": 776, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [ "SRX5654580", "GSM3713847", "SRX565", "KMC6" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:29.972221", "source": { "split": "train_shard_00002", "doc_id": 738 }, "chunk_id": "train_shard_00002_738_0", "global_id": 13730 }, { "text": "KM 6h rep2\n\nKMB6\n\n{\"uid\": \"303713846\", \"accession\": \"GSM3713846\", \"gds\": \"\", \"title\": \"KMB6\", \"summary\": \"KM 6h rep2\", \"gpl\": \"26472\", \"gse\": \"129483\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2019/08/09\", \"suppfile\": \"TAB\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX5654579\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX565/SRX5654579/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3713nnn/GSM3713846/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 371, "char_count": 776, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [ "SRX5654579", "GSM3713846", "KMB6", "SRX565" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:30.571489", "source": { "split": "train_shard_00002", "doc_id": 739 }, "chunk_id": "train_shard_00002_739_0", "global_id": 13731 }, { "text": "KM 6h rep1\n\nKMA6\n\n{\"uid\": \"303713845\", \"accession\": \"GSM3713845\", \"gds\": \"\", \"title\": \"KMA6\", \"summary\": \"KM 6h rep1\", \"gpl\": \"26472\", \"gse\": \"129483\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2019/08/09\", \"suppfile\": \"TAB\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX5654578\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX565/SRX5654578/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"ftp://ftp.ncbi.nlm.nih.gov/geo/samples/GSM3713nnn/GSM3713845/\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 371, "char_count": 776, "word_count": 70, "semantic_coherence": 1, "information_density": 0.7857, "quality_score": 0.8929, "entities": { "genes": [ "KMA6", "SRX5654578", "SRX565", "GSM3713845" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:31.181810", "source": { "split": "train_shard_00002", "doc_id": 740 }, "chunk_id": "train_shard_00002_740_0", "global_id": 13732 }, { "text": "yeast in stationary phase\n\nKl. marxianus parental gDNA\n\n{\"uid\": \"302897278\", \"accession\": \"GSM2897278\", \"gds\": \"\", \"title\": \"Kl. marxianus parental gDNA\", \"summary\": \"yeast in stationary phase\", \"gpl\": \"24417\", \"gse\": \"108389\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2017/12/22\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX3502487\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX350/SRX3502487/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 343, "char_count": 788, "word_count": 78, "semantic_coherence": 1, "information_density": 0.7436, "quality_score": 0.8718, "entities": { "genes": [ "GSM2897278", "SRX350", "SRX3502487" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces", "yeast" ], "conditions": [ "ph" ] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:31.748827", "source": { "split": "train_shard_00002", "doc_id": 741 }, "chunk_id": "train_shard_00002_741_0", "global_id": 13733 }, { "text": "Kluyveromyces marxianus_late exponential\n\nRNA-seq LE rep2\n\n{\"uid\": \"301717190\", \"accession\": \"GSM1717190\", \"gds\": \"\", \"title\": \"RNA-seq LE rep2\", \"summary\": \"Kluyveromyces marxianus_late exponential\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2016/08/20\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX1067725\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX106/SRX1067725/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 347, "char_count": 793, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [ "SRX1067725", "SRX106", "GSM1717190" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:32.330689", "source": { "split": "train_shard_00002", "doc_id": 742 }, "chunk_id": "train_shard_00002_742_0", "global_id": 13734 }, { "text": "Kluyveromyces marxianus_late exponential\n\nRNA-seq LE rep1\n\n{\"uid\": \"301717189\", \"accession\": \"GSM1717189\", \"gds\": \"\", \"title\": \"RNA-seq LE rep1\", \"summary\": \"Kluyveromyces marxianus_late exponential\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2016/08/20\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX1067724\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX106/SRX1067724/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 347, "char_count": 793, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [ "SRX106", "SRX1067724", "GSM1717189" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:32.897306", "source": { "split": "train_shard_00002", "doc_id": 743 }, "chunk_id": "train_shard_00002_743_0", "global_id": 13735 }, { "text": "Kluyveromyces marxianus_mid exponential\n\nRNA-seq ME rep2\n\n{\"uid\": \"301717188\", \"accession\": \"GSM1717188\", \"gds\": \"\", \"title\": \"RNA-seq ME rep2\", \"summary\": \"Kluyveromyces marxianus_mid exponential\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2016/08/20\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX1067723\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX106/SRX1067723/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 347, "char_count": 791, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [ "GSM1717188", "SRX1067723", "SRX106" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:33.476317", "source": { "split": "train_shard_00002", "doc_id": 744 }, "chunk_id": "train_shard_00002_744_0", "global_id": 13736 }, { "text": "Kluyveromyces marxianus_mid exponential\n\nRNA-seq ME rep1\n\n{\"uid\": \"301717187\", \"accession\": \"GSM1717187\", \"gds\": \"\", \"title\": \"RNA-seq ME rep1\", \"summary\": \"Kluyveromyces marxianus_mid exponential\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2016/08/20\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX1067722\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX106/SRX1067722/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 347, "char_count": 791, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [ "SRX1067722", "GSM1717187", "SRX106" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:34.043822", "source": { "split": "train_shard_00002", "doc_id": 745 }, "chunk_id": "train_shard_00002_745_0", "global_id": 13737 }, { "text": "Kluyveromyces marxianus_early exponential\n\nRNA-seq EE rep2\n\n{\"uid\": \"301717186\", \"accession\": \"GSM1717186\", \"gds\": \"\", \"title\": \"RNA-seq EE rep2\", \"summary\": \"Kluyveromyces marxianus_early exponential\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2016/08/20\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX1067721\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX106/SRX1067721/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 351, "char_count": 795, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [ "SRX1067721", "SRX106", "GSM1717186" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:34.619637", "source": { "split": "train_shard_00002", "doc_id": 746 }, "chunk_id": "train_shard_00002_746_0", "global_id": 13738 }, { "text": "Kluyveromyces marxianus_early exponential\n\nRNA-seq EE rep1\n\n{\"uid\": \"301717185\", \"accession\": \"GSM1717185\", \"gds\": \"\", \"title\": \"RNA-seq EE rep1\", \"summary\": \"Kluyveromyces marxianus_early exponential\", \"gpl\": \"20596\", \"gse\": \"70111\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2016/08/20\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX1067720\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX106/SRX1067720/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 351, "char_count": 795, "word_count": 74, "semantic_coherence": 1, "information_density": 0.7432, "quality_score": 0.8716, "entities": { "genes": [ "GSM1717185", "SRX1067720", "SRX106" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:35.187296", "source": { "split": "train_shard_00002", "doc_id": 747 }, "chunk_id": "train_shard_00002_747_0", "global_id": 13739 }, { "text": "TSS-seq K.marxianus 45D\n\n45D-③ (110614_EAS74_lane8)\n\n{\"uid\": \"301626087\", \"accession\": \"GSM1626087\", \"gds\": \"\", \"title\": \"45D-\\u2462 (110614_EAS74_lane8)\", \"summary\": \"TSS-seq K.marxianus 45D\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905365\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905365/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 379, "char_count": 784, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7639, "quality_score": 0.8819, "entities": { "genes": [ "SRX905", "GSM1626087", "SRX905365" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:35.768173", "source": { "split": "train_shard_00002", "doc_id": 748 }, "chunk_id": "train_shard_00002_748_0", "global_id": 13740 }, { "text": "TSS-seq K.marxianus 45D\n\n45D-② (110614_EAS74_lane7)\n\n{\"uid\": \"301626086\", \"accession\": \"GSM1626086\", \"gds\": \"\", \"title\": \"45D-\\u2461 (110614_EAS74_lane7)\", \"summary\": \"TSS-seq K.marxianus 45D\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905364\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905364/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 379, "char_count": 784, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7639, "quality_score": 0.8819, "entities": { "genes": [ "GSM1626086", "SRX905364", "SRX905" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:36.349210", "source": { "split": "train_shard_00002", "doc_id": 749 }, "chunk_id": "train_shard_00002_749_0", "global_id": 13741 }, { "text": "TSS-seq K.marxianus 45D\n\n45D-① (110401_lane8)\n\n{\"uid\": \"301626085\", \"accession\": \"GSM1626085\", \"gds\": \"\", \"title\": \"45D-\\u2460 (110401_lane8)\", \"summary\": \"TSS-seq K.marxianus 45D\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905363\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905363/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 369, "char_count": 772, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7639, "quality_score": 0.8819, "entities": { "genes": [ "SRX905363", "GSM1626085", "SRX905" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:36.929419", "source": { "split": "train_shard_00002", "doc_id": 750 }, "chunk_id": "train_shard_00002_750_0", "global_id": 13742 }, { "text": "TSS-seq K.marxianus 30DS\n\n30DS-③ (110614_EAS798_lane2)\n\n{\"uid\": \"301626084\", \"accession\": \"GSM1626084\", \"gds\": \"\", \"title\": \"30DS-\\u2462 (110614_EAS798_lane2)\", \"summary\": \"TSS-seq K.marxianus 30DS\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905362\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905362/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 381, "char_count": 790, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7639, "quality_score": 0.8819, "entities": { "genes": [ "SRX905", "SRX905362", "GSM1626084" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:37.874889", "source": { "split": "train_shard_00002", "doc_id": 751 }, "chunk_id": "train_shard_00002_751_0", "global_id": 13743 }, { "text": "TSS-seq K.marxianus 30DS\n\n30DS-② (110614_EAS798_lane1)\n\n{\"uid\": \"301626083\", \"accession\": \"GSM1626083\", \"gds\": \"\", \"title\": \"30DS-\\u2461 (110614_EAS798_lane1)\", \"summary\": \"TSS-seq K.marxianus 30DS\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905361\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905361/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", 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"train_shard_00002_753_0", "global_id": 13745 }, { "text": "TSS-seq K.marxianus 30X\n\n30X-③ (110614_EAS798_lane8)\n\n{\"uid\": \"301626081\", \"accession\": \"GSM1626081\", \"gds\": \"\", \"title\": \"30X-\\u2462 (110614_EAS798_lane8)\", \"summary\": \"TSS-seq K.marxianus 30X\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905359\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905359/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 381, 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\"accession\": \"GSM1626079\", \"gds\": \"\", \"title\": \"30X-\\u2460 (110614_EAS798_lane6)\", \"summary\": \"TSS-seq K.marxianus 30X\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905357\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905357/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 381, "char_count": 786, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7639, "quality_score": 0.8819, "entities": { "genes": [ "SRX905", "SRX905357", "GSM1626079" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:40.792553", "source": { "split": "train_shard_00002", "doc_id": 756 }, "chunk_id": "train_shard_00002_756_0", "global_id": 13748 }, { "text": "TSS-seq K.marxianus 30D\n\n30D-③ (110624_EAS74_lane8)\n\n{\"uid\": \"301626078\", \"accession\": \"GSM1626078\", \"gds\": \"\", \"title\": \"30D-\\u2462 (110624_EAS74_lane8)\", \"summary\": \"TSS-seq K.marxianus 30D\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905356\", \"targetftplink\": 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\"TSS-seq K.marxianus 30D\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905355\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905355/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", \"samplestaxa\": \"\", \"pubmedids\": [], \"projects\": [], \"ftplink\": \"\", \"geo2r\": \"\", \"bioproject\": \"\"}", "token_count": 379, "char_count": 784, "word_count": 72, "semantic_coherence": 1, "information_density": 0.7639, "quality_score": 0.8819, "entities": { "genes": [ "SRX905355", "SRX905", "GSM1626077" ], "proteins": [], "pathways": [], "organisms": [ "marxianus", "kluyveromyces" ], "conditions": [] }, "biobert_ready": true, "timestamp": "2025-11-01T07:08:42.013108", "source": { "split": "train_shard_00002", "doc_id": 758 }, "chunk_id": "train_shard_00002_758_0", "global_id": 13750 }, { "text": "TSS-seq K.marxianus 30D\n\n30D-① (110401_lane5)\n\n{\"uid\": \"301626076\", \"accession\": \"GSM1626076\", \"gds\": \"\", \"title\": \"30D-\\u2460 (110401_lane5)\", \"summary\": \"TSS-seq K.marxianus 30D\", \"gpl\": \"19857\", \"gse\": \"66600\", \"taxon\": \"Kluyveromyces marxianus\", \"entrytype\": \"GSM\", \"gdstype\": \"\", \"ptechtype\": \"\", \"valtype\": \"\", \"ssinfo\": \"\", \"subsetinfo\": \"\", \"pdat\": \"2015/03/07\", \"suppfile\": \"\", \"samples\": [], \"relations\": [], \"extrelations\": [{\"relationtype\": \"SRA\", \"targetobject\": \"SRX905354\", \"targetftplink\": \"ftp://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByExp/sra/SRX/SRX905/SRX905354/\"}], \"n_samples\": \"\", \"seriestitle\": \"\", \"platformtitle\": \"\", \"platformtaxa\": \"\", 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